Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 132 of 193
Found at i:41750573 original size:23 final size:23
Alignment explanation
Indices: 41750519--41750574 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
41750509 TCCATCCTTG
* * * *
41750519 CTGACTAGACCTTCTGGAAGCTG
1 CTGACTGGATCTTCTAGAAGCTA
* *
41750542 CTAATTGGATCTTCTAGAAGCTA
1 CTGACTGGATCTTCTAGAAGCTA
41750565 CTGACTGGAT
1 CTGACTGGAT
41750575 GCCACGTCAG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (23 bp):
CTGACTGGATCTTCTAGAAGCTA
Found at i:41756352 original size:17 final size:17
Alignment explanation
Indices: 41756330--41756363 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41756320 CTAAGAATTT
*
41756330 AAAGAAAGTAAATTTAA
1 AAAGAAACTAAATTTAA
*
41756347 AAAGAAACTCAATTTAA
1 AAAGAAACTAAATTTAA
41756364 GTATCAGCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.06, G:0.09, T:0.24
Consensus pattern (17 bp):
AAAGAAACTAAATTTAA
Found at i:41767016 original size:6 final size:6
Alignment explanation
Indices: 41767007--41767034 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
41766997 TGGGAAATAA
41767007 AGAGGC AGAGGC AGAGGC AGAGGC AGAG
1 AGAGGC AGAGGC AGAGGC AGAGGC AGAG
41767035 TCGGTTTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.50, T:0.00
Consensus pattern (6 bp):
AGAGGC
Found at i:41774606 original size:39 final size:38
Alignment explanation
Indices: 41774532--41774608 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
41774522 ATTTCATCTA
**
41774532 AAATTAATTAAATAATAGTATTTTTGAAAATTTAATTTT
1 AAATTAATTAAATAATA-TATTAGTGAAAATTTAATTTT
41774571 AAATTAATTAAATAAT-TATTAGTGAAAATAATTAATTT
1 AAATTAATTAAATAATATATTAGTGAAAAT--TTAATTT
41774609 GGGTTGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 11 0.32
39 23 0.68
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.45
Consensus pattern (38 bp):
AAATTAATTAAATAATATATTAGTGAAAATTTAATTTT
Found at i:41776816 original size:25 final size:25
Alignment explanation
Indices: 41776784--41776991 Score: 209
Period size: 25 Copynumber: 8.2 Consensus size: 25
41776774 ACAAGCCTAG
* *
41776784 ACAGAATATTGCTCATACGTGCCAA
1 ACAGAATATCGCTCATACGAGCCAA
*
41776809 ACAGAATATCGCTCAAACGAGCCAA
1 ACAGAATATCGCTCATACGAGCCAA
* *
41776834 ACAAAATATCGCTCATACGAGCCAG
1 ACAGAATATCGCTCATACGAGCCAA
* * *
41776859 ATAGAATATCGCTCATACGAGCTAG
1 ACAGAATATCGCTCATACGAGCCAA
* ** * *
41776884 ACAAAATATTACTCATACGAGCTAG
1 ACAGAATATCGCTCATACGAGCCAA
*
41776909 ACAGAATATCGCTCTTACGAGCCAGA
1 ACAGAATATCGCTCATACGAGCCA-A
* * * * *
41776935 ATCAAAATTTCACTCTTACGAGCCAG
1 A-CAGAATATCGCTCATACGAGCCAA
* *
41776961 ACAAAATATCGCTCTTACGAGCCAA
1 ACAGAATATCGCTCATACGAGCCAA
41776986 ACAGAA
1 ACAGAA
41776992 ATACGCTTTT
Statistics
Matches: 154, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
25 132 0.86
26 2 0.01
27 20 0.13
ACGTcount: A:0.39, C:0.25, G:0.15, T:0.20
Consensus pattern (25 bp):
ACAGAATATCGCTCATACGAGCCAA
Found at i:41776848 original size:50 final size:50
Alignment explanation
Indices: 41776788--41776998 Score: 244
Period size: 50 Copynumber: 4.2 Consensus size: 50
41776778 GCCTAGACAG
* * * *
41776788 AATATTGCTCATACGTGCCAAACAGAATATCGCTCAAACGAGCCAAACAA
1 AATATCGCTCATACGAGCCAGACAGAATATCGCTCATACGAGCCAAACAA
* * *
41776838 AATATCGCTCATACGAGCCAGATAGAATATCGCTCATACGAGCTAGACAA
1 AATATCGCTCATACGAGCCAGACAGAATATCGCTCATACGAGCCAAACAA
** * *
41776888 AATATTACTCATACGAGCTAGACAGAATATCGCTCTTACGAGCCAGAATCAA
1 AATATCGCTCATACGAGCCAGACAGAATATCGCTCATACGAGCCA-AA-CAA
* * * * *
41776940 AATTTCACTCTTACGAGCCAGACAAAATATCGCTCTTACGAGCCAAACAGA
1 AATATCGCTCATACGAGCCAGACAGAATATCGCTCATACGAGCCAAACA-A
41776991 AATA-CGCT
1 AATATCGCT
41776999 TTTATGAGCC
Statistics
Matches: 137, Mismatches: 21, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
50 87 0.64
51 7 0.05
52 43 0.31
ACGTcount: A:0.39, C:0.25, G:0.15, T:0.21
Consensus pattern (50 bp):
AATATCGCTCATACGAGCCAGACAGAATATCGCTCATACGAGCCAAACAA
Found at i:41776877 original size:75 final size:75
Alignment explanation
Indices: 41776777--41776998 Score: 239
Period size: 75 Copynumber: 2.9 Consensus size: 75
41776767 GGCTCTAACA
* * * * * *
41776777 AGCCTAGACAGAATATTGCTCATACGTGCCAAACAGAATATCGCTCAAACGAGCCAAACAAAATA
1 AGCC-AGATAGAATATCGCTCATACGAGCCAGACAAAATATCGCTCATACGAGCCAAACAAAATA
41776842 TCGCTCATACG
65 TCGCTCATACG
* ** * * *
41776853 AGCCAGATAGAATATCGCTCATACGAGCTAGACAAAATATTACTCATACGAGCTAGACAGAATAT
1 AGCCAGATAGAATATCGCTCATACGAGCCAGACAAAATATCGCTCATACGAGCCAAACAAAATAT
*
41776918 CGCTCTTACG
66 CGCTCATACG
* * * * *
41776928 AGCCAGAATCAAAATTTCACTCTTACGAGCCAGACAAAATATCGCTCTTACGAGCCAAACAGAAA
1 AGCCAG-AT-AGAATATCGCTCATACGAGCCAGACAAAATATCGCTCATACGAGCCAAACA-AAA
41776993 TA-CGCT
63 TATCGCT
41776999 TTTATGAGCC
Statistics
Matches: 119, Mismatches: 24, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
75 64 0.54
76 6 0.05
77 45 0.38
78 4 0.03
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (75 bp):
AGCCAGATAGAATATCGCTCATACGAGCCAGACAAAATATCGCTCATACGAGCCAAACAAAATAT
CGCTCATACG
Found at i:41776980 original size:77 final size:77
Alignment explanation
Indices: 41776795--41777020 Score: 260
Period size: 77 Copynumber: 3.0 Consensus size: 77
41776785 CAGAATATTG
* * * * * *
41776795 CTCATACGTGCCAAACAGAATATCGCTCAAACGAGCCAAACAAAATATCGCTCATACGAGCCAG-
1 CTCATACGAGCCAGACAAAATATCGCTCATACGAGCCAAACAGAATATCGCTCTTACGAGCCAGA
* *
41776859 AT-AGAATATCG
66 ATCAGAATTTCA
* ** * *
41776870 CTCATACGAGCTAGACAAAATATTACTCATACGAGCTAGACAGAATATCGCTCTTACGAGCCAGA
1 CTCATACGAGCCAGACAAAATATCGCTCATACGAGCCAAACAGAATATCGCTCTTACGAGCCAGA
*
41776935 ATCAAAATTTCA
66 ATCAGAATTTCA
* * * *
41776947 CTCTTACGAGCCAGACAAAATATCGCTCTTACGAGCCAAACAGAA-ATACGCTTTTATGAGCCAG
1 CTCATACGAGCCAGACAAAATATCGCTCATACGAGCCAAACAGAATAT-CGCTCTTACGAGCCAG
41777011 AATCAGAATT
65 AATCAGAATT
41777021 CCTTCGTCTT
Statistics
Matches: 124, Mismatches: 24, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
75 53 0.43
76 4 0.03
77 67 0.54
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.21
Consensus pattern (77 bp):
CTCATACGAGCCAGACAAAATATCGCTCATACGAGCCAAACAGAATATCGCTCTTACGAGCCAGA
ATCAGAATTTCA
Found at i:41777007 original size:25 final size:26
Alignment explanation
Indices: 41776784--41777018 Score: 182
Period size: 25 Copynumber: 9.2 Consensus size: 26
41776774 ACAAGCCTAG
* * *
41776784 ACAG-AATATTGCTCATACGTGCCAA
1 ACAGAAATATCGCTCTTACGAGCCAA
**
41776809 ACAG-AATATCGCTCAAACGAGCCAA
1 ACAGAAATATCGCTCTTACGAGCCAA
* *
41776834 ACA-AAATATCGCTCATACGAGCCAG
1 ACAGAAATATCGCTCTTACGAGCCAA
* * * *
41776859 ATAG-AATATCGCTCATACGAGCTAG
1 ACAGAAATATCGCTCTTACGAGCCAA
** * * *
41776884 ACA-AAATATTACTCATACGAGCTAG
1 ACAGAAATATCGCTCTTACGAGCCAA
41776909 ACAG-AATATCGCTCTTACGAGCCAGA
1 ACAGAAATATCGCTCTTACGAGCCA-A
* * *
41776935 ATCA-AAATTTCACTCTTACGAGCCAG
1 A-CAGAAATATCGCTCTTACGAGCCAA
41776961 ACA-AAATATCGCTCTTACGAGCCAA
1 ACAGAAATATCGCTCTTACGAGCCAA
* *
41776986 ACAGAAATA-CGCTTTTATGAGCCAGA
1 ACAGAAATATCGCTCTTACGAGCCA-A
41777012 ATCAGAA
1 A-CAGAA
41777019 TTCCTTCGTC
Statistics
Matches: 177, Mismatches: 23, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
25 143 0.81
26 9 0.05
27 25 0.14
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (26 bp):
ACAGAAATATCGCTCTTACGAGCCAA
Found at i:41779344 original size:43 final size:42
Alignment explanation
Indices: 41779288--41779434 Score: 154
Period size: 43 Copynumber: 3.5 Consensus size: 42
41779278 AGACACTTGA
* * *
41779288 TGTATAAAAGGAAGACTCATGTCTTGGATTGAGCATGAGAATT
1 TGTATTAAAGGAAGACTCATGTCTTGGAATGAGAATGAGAA-T
* * * * * * *
41779331 TGTATGAATGGAAGACTCGTGACTTGAAATGAGTATGAGGA-
1 TGTATTAAAGGAAGACTCATGTCTTGGAATGAGAATGAGAAT
* *
41779372 TATATTAAAGGAAGACTCATGTCTCGGAATGAGAATGAGAAT
1 TGTATTAAAGGAAGACTCATGTCTTGGAATGAGAATGAGAAT
41779414 ATGT-TTAAAGGAAGACTCATG
1 -TGTATTAAAGGAAGACTCATG
41779435 ACTCAAAAAT
Statistics
Matches: 84, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
41 32 0.38
42 17 0.20
43 35 0.42
ACGTcount: A:0.37, C:0.09, G:0.27, T:0.28
Consensus pattern (42 bp):
TGTATTAAAGGAAGACTCATGTCTTGGAATGAGAATGAGAAT
Found at i:41779403 original size:41 final size:41
Alignment explanation
Indices: 41779294--41779434 Score: 147
Period size: 41 Copynumber: 3.4 Consensus size: 41
41779284 TTGATGTATA
* * * *
41779294 AAAGGAAGACTCATGTCTTGGATTGAGCATGAGAATTTGTATG
1 AAAGGAAGACTCATGTCTTGGAATGAGAATGAGAA--TATATT
* * * * * *
41779337 AATGGAAGACTCGTGACTTGAAATGAGTATGAGGATATATT
1 AAAGGAAGACTCATGTCTTGGAATGAGAATGAGAATATATT
* *
41779378 AAAGGAAGACTCATGTCTCGGAATGAGAATGAGAATATGTTT
1 AAAGGAAGACTCATGTCTTGGAATGAGAATGAGAATAT-ATT
41779420 AAAGGAAGACTCATG
1 AAAGGAAGACTCATG
41779435 ACTCAAAAAT
Statistics
Matches: 80, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
41 35 0.44
42 17 0.21
43 28 0.35
ACGTcount: A:0.37, C:0.09, G:0.27, T:0.27
Consensus pattern (41 bp):
AAAGGAAGACTCATGTCTTGGAATGAGAATGAGAATATATT
Found at i:41779445 original size:84 final size:84
Alignment explanation
Indices: 41779294--41779447 Score: 211
Period size: 84 Copynumber: 1.8 Consensus size: 84
41779284 TTGATGTATA
* * * * * * **
41779294 AAAGGAAGACTCATGTCTTGGATTGAGCATGAGAATTTGTATGAATGGAAGACTCGTGACTTGAA
1 AAAGGAAGACTCATGTCTCGGAATGAGAATGAGAATATGTATGAAAGGAAGACTCATGACTAAAA
41779359 ATGAGTATGAGGATATATT
66 ATGAGTATGAGGATATATT
*
41779378 AAAGGAAGACTCATGTCTCGGAATGAGAATGAGAATATGT-TTAAAGGAAGACTCATGACTCAAA
1 AAAGGAAGACTCATGTCTCGGAATGAGAATGAGAATATGTATGAAAGGAAGACTCATGACT-AAA
41779442 AATGAG
65 AATGAG
41779448 CGTGAGATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
83 17 0.28
84 43 0.72
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (84 bp):
AAAGGAAGACTCATGTCTCGGAATGAGAATGAGAATATGTATGAAAGGAAGACTCATGACTAAAA
ATGAGTATGAGGATATATT
Found at i:41779482 original size:44 final size:41
Alignment explanation
Indices: 41779378--41779519 Score: 117
Period size: 42 Copynumber: 3.4 Consensus size: 41
41779368 AGGATATATT
* * * * * *
41779378 AAAGGAAGACTCATGTCTCGGAATGAGAATGAGAATATGTTT-
1 AAAGGAAGACTTATGACTC-AAAAGAGCATGAGATTA-GTTTA
* *
41779420 AAAGGAAGACTCATGACTCAAAAATGAGCGTGAGATTACGTTTA
1 AAAGGAAGACTTATGACTC-AAAA-GAGCATGAGATTA-GTTTA
*** *
41779464 AAAGGAAGACTTATGACTCGGTAGAGCATAAGATT-GTTTA
1 AAAGGAAGACTTATGACTCAAAAGAGCATGAGATTAGTTTA
41779504 AAAGGAAGACTTATGA
1 AAAGGAAGACTTATGA
41779520 ATCTATTAAG
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
40 21 0.25
42 30 0.36
43 15 0.18
44 18 0.21
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.25
Consensus pattern (41 bp):
AAAGGAAGACTTATGACTCAAAAGAGCATGAGATTAGTTTA
Found at i:41779532 original size:40 final size:40
Alignment explanation
Indices: 41779459--41779537 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
41779449 GTGAGATTAC
* *
41779459 GTTTAAAAGGAAGACTTATGACTCGGTAGAGCATAAGATT
1 GTTTAAAAGGAAGACTTATGAATCAGTAGAGCATAAGATT
*
41779499 GTTTAAAAGGAAGACTTATGAATCTATTA-AGCATAAGAT
1 GTTTAAAAGGAAGACTTATGAATC-AGTAGAGCATAAGAT
41779538 CATCTAAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 33 0.94
41 2 0.06
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.29
Consensus pattern (40 bp):
GTTTAAAAGGAAGACTTATGAATCAGTAGAGCATAAGATT
Found at i:41780218 original size:21 final size:21
Alignment explanation
Indices: 41780192--41780233 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
41780182 GTTTTTAGTA
41780192 TCGGTAGAAGC-ACGACTTGTT
1 TCGGTAGAAGCTAC-ACTTGTT
41780213 TCGGTAGAAGCTACACTTGTT
1 TCGGTAGAAGCTACACTTGTT
41780234 GATAATACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (21 bp):
TCGGTAGAAGCTACACTTGTT
Found at i:41787008 original size:24 final size:24
Alignment explanation
Indices: 41786980--41787030 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 24
41786970 AGGTTTTGTC
41786980 GTGGAAGAAAGTTCTGAGGTTCAG
1 GTGGAAGAAAGTTCTGAGGTTCAG
*
41787004 GT-G--GAAAGTTTTGAGGTTCAG
1 GTGGAAGAAAGTTCTGAGGTTCAG
41787025 GTGGAA
1 GTGGAA
41787031 AGGTAAGCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
21 19 0.83
22 1 0.04
23 1 0.04
24 2 0.09
ACGTcount: A:0.27, C:0.06, G:0.39, T:0.27
Consensus pattern (24 bp):
GTGGAAGAAAGTTCTGAGGTTCAG
Found at i:41787012 original size:21 final size:21
Alignment explanation
Indices: 41786986--41787032 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
41786976 TGTCGTGGAA
41786986 GAAAGTTCTGAGGTTCAGGTG
1 GAAAGTTCTGAGGTTCAGGTG
*
41787007 GAAAGTTTTGAGGTTCAGGTG
1 GAAAGTTCTGAGGTTCAGGTG
41787028 GAAAG
1 GAAAG
41787033 GTAAGCTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.06, G:0.38, T:0.28
Consensus pattern (21 bp):
GAAAGTTCTGAGGTTCAGGTG
Found at i:41789712 original size:31 final size:31
Alignment explanation
Indices: 41789677--41789735 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
41789667 TGAACTAATC
* *
41789677 GGTTCACAAATTGCTTCTGCATTAATAATTT
1 GGTTCACAAATTACTTCCGCATTAATAATTT
41789708 GGTTCACAAATTACTTCCGCATTAATAA
1 GGTTCACAAATTACTTCCGCATTAATAA
41789736 ATAATTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (31 bp):
GGTTCACAAATTACTTCCGCATTAATAATTT
Found at i:41790336 original size:5 final size:5
Alignment explanation
Indices: 41790312--41790393 Score: 137
Period size: 5 Copynumber: 16.2 Consensus size: 5
41790302 GAATTTAAAT
* *
41790312 ATATA ATTTT ATACTA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATA-TA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
41790363 ATATA ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA A
41790394 ATGTTTTAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
5 68 0.94
6 4 0.06
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:41790780 original size:19 final size:19
Alignment explanation
Indices: 41790756--41790793 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
41790746 ATTTTAGTTC
41790756 ATAGAAAAATCAATTCTCT
1 ATAGAAAAATCAATTCTCT
*
41790775 ATAGAAAAATCACTTCTCT
1 ATAGAAAAATCAATTCTCT
41790794 TTGATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (19 bp):
ATAGAAAAATCAATTCTCT
Found at i:41801882 original size:14 final size:14
Alignment explanation
Indices: 41801863--41801900 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
41801853 AGGGAACGGT
41801863 GGAGCAAATAGAGG
1 GGAGCAAATAGAGG
41801877 GGAGCAAATAGAGG
1 GGAGCAAATAGAGG
*
41801891 GGAACAAATA
1 GGAGCAAATA
41801901 ATGGTTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.08, G:0.37, T:0.08
Consensus pattern (14 bp):
GGAGCAAATAGAGG
Found at i:41804492 original size:163 final size:163
Alignment explanation
Indices: 41804222--41804731 Score: 846
Period size: 163 Copynumber: 3.1 Consensus size: 163
41804212 TTTTAATTGG
*
41804222 TTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGATGCTGCCACGTGTCACTTTTTGGTTTA
1 TTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
*
41804287 TTTATGTATCTAGTCCTTGTCATTTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTGCT
66 TTTATGTATCTAGTCCCTGTCATTTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTGCT
*
41804352 TAATTACAAAATTGACCCAGGAATCTTTTGAGA
131 TAATTACAAAATTGACCCAAGAATCTTTTGAGA
*
41804385 TTTTTAAATTAGTCCTTTGACTGTTTGACTACACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
1 TTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
*
41804450 TTTATGTATCTAGTCCCTGTCATTTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTGCT
66 TTTATGTATCTAGTCCCTGTCATTTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTGCT
41804515 TAATTACAAAATTGACCCAAGAATCTTTTGAGA
131 TAATTACAAAATTGACCCAAGAATCTTTTGAGA
*
41804548 TTTTTAAATTAGTCCTTTAACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
1 TTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
* **
41804613 TTTATGTATCTAGTCCCTGTCA-TTTTTAATTTGTTTTAATTTAATCCTTAAATTAACTTTTATT
66 TTTATGTATCTAGTCCCTGTCATTTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTGCT
* *
41804677 TAATTATAAAATT-AGCCCAAGAAT-TTTTCAAGA
131 TAATTACAAAATTGA-CCCAAGAATCTTTT-GAGA
** * *
41804710 TTTACAAATTCGTTCTTTGACT
1 TTTTTAAATTAGTCCTTTGACT
41804732 TCTGGATGCC
Statistics
Matches: 327, Mismatches: 18, Indels: 5
0.93 0.05 0.01
Matches are distributed among these distances:
161 5 0.02
162 79 0.24
163 243 0.74
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.45
Consensus pattern (163 bp):
TTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
TTTATGTATCTAGTCCCTGTCATTTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTGCT
TAATTACAAAATTGACCCAAGAATCTTTTGAGA
Found at i:41804878 original size:30 final size:30
Alignment explanation
Indices: 41804834--41805053 Score: 133
Period size: 30 Copynumber: 7.4 Consensus size: 30
41804824 TAAAACTTCT
*
41804834 AAAATTCCATTTTTAACCCAGGTTTCACCA
1 AAAATTCCATTTTTAACCCAGATTTCACCA
* * * *
41804864 AAAATTGCCA-TTTTACCCCCGAACTT--CCT
1 AAAATT-CCATTTTTAACCCAG-ATTTCACCA
*
41804893 ATAATTCCATTTTTAACCCTAG-TTTCACCA
1 AAAATTCCATTTTTAACCC-AGATTTCACCA
* * *
41804923 AAAATTACCA-TTTTACCCCTAAAACTT--CC-
1 AAAATT-CCATTTTTAACCC--AGATTTCACCA
*
41804952 AAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTCCATTTTTAACCCAGATTTCACCA
* *
41804982 AAAATTACCA-TTTT-ACCCTCGAACTTC-CC-
1 AAAATT-CCATTTTTAACCC-AG-ATTTCACCA
*
41805011 AGAATTCCATTTTTAACCCCAG-TTTCACCA
1 AAAATTCCATTTTTAA-CCCAGATTTCACCA
41805041 AAAATTACCATTT
1 AAAATT-CCATTT
41805054 ACCCCTAAAC
Statistics
Matches: 144, Mismatches: 24, Indels: 43
0.68 0.11 0.20
Matches are distributed among these distances:
27 3 0.02
28 14 0.10
29 46 0.32
30 54 0.38
31 25 0.17
32 2 0.01
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCCAGATTTCACCA
Found at i:41805117 original size:117 final size:119
Alignment explanation
Indices: 41804802--41805171 Score: 473
Period size: 118 Copynumber: 3.1 Consensus size: 119
41804792 CCTAGATGGT
* * * * *
41804802 CCAAAAACTACCATTTTACCCTTAAAACTTCT-AAAATTCCATTTTTAACCCAGGTTTCACCAAA
1 CCAAAAATTACCATTTTACCCCTAAAACTTTTCAAAATTCCATTTTTAACCCCGATTTCACCAAA
* * * * *
41804866 AATTGCCATTTTACCCCCGAACTTCCTATAATTCCATTTTTAACCCTAGTTTCA
66 AATTACCATTTTACCCTCGAACTTCCCAAAATTCCATTTTTAACCCCAGTTTCA
*
41804920 CCAAAAATTACCATTTTACCCCTAAAAC-TTCCAAAATTCCATTTTTAACCCCGATTTCACCAAA
1 CCAAAAATTACCATTTTACCCCTAAAACTTTTCAAAATTCCATTTTTAACCCCGATTTCACCAAA
*
41804984 AATTACCATTTTACCCTCGAACTTCCCAGAATTCCATTTTTAACCCCAGTTTCA
66 AATTACCATTTTACCCTCGAACTTCCCAAAATTCCATTTTTAACCCCAGTTTCA
* * *
41805038 CCAAAAATTACCA-TTTACCCCT-AAACTTTTCAAAATTCTATTTTTAACCCCGATTTAACAAAA
1 CCAAAAATTACCATTTTACCCCTAAAACTTTTCAAAATTCCATTTTTAACCCCGATTTCACCAAA
* * * * * * *
41805101 AATTACTATTTTACCCTCAAATTTTCCAAAATTCTC-TTTTTGATCTC-GATTTCA
66 AATTACCATTTTACCCTCGAACTTCCCAAAATTC-CATTTTTAACCCCAG-TTTCA
*
41805155 TCAAAAATTACCATTTT
1 CCAAAAATTACCATTTT
41805172 GCCCTCGGAT
Statistics
Matches: 223, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
116 5 0.02
117 96 0.43
118 122 0.55
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.36
Consensus pattern (119 bp):
CCAAAAATTACCATTTTACCCCTAAAACTTTTCAAAATTCCATTTTTAACCCCGATTTCACCAAA
AATTACCATTTTACCCTCGAACTTCCCAAAATTCCATTTTTAACCCCAGTTTCA
Found at i:41805212 original size:59 final size:60
Alignment explanation
Indices: 41804802--41805199 Score: 392
Period size: 59 Copynumber: 6.8 Consensus size: 60
41804792 CCTAGATGGT
* * * * *
41804802 CCAAAAACTACCATTTTACCCTTAAAAC-TTCTAAAATTC-CATTTTTAACCCAGGTTTCA
1 CCAAAAATTACCATTTTACCC-TCAAACTTTCCAAAATTCTCATTTTTAACCCCGATTTCA
* * * * *
41804861 CCAAAAATTGCCATTTTACCCCCGAAC-TTCCTATAATTC-CATTTTTAA-CCCTAGTTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCC-AAAATTCTCATTTTTAACCCCGA-TTTCA
*
41804920 CCAAAAATTACCATTTTACCCCTAAAAC-TTCCAAAATTC-CATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTA-CCCTCAAACTTTCCAAAATTCTCATTTTTAACCCCGATTTCA
* * *
41804979 CCAAAAATTACCATTTTACCCTCGAACTTCCCAGAATTC-CATTTTTAACCCC-AGTTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCTCATTTTTAACCCCGA-TTTCA
* *
41805038 CCAAAAATTACCA-TTTACCC-CTAAACTTTTCAAAATTCT-ATTTTTAACCCCGATTTAA
1 CCAAAAATTACCATTTTACCCTC-AAACTTTCCAAAATTCTCATTTTTAACCCCGATTTCA
* * * * * *
41805096 CAAAAAATTACTATTTTACCCTCAAATTTTCCAAAATTCTC-TTTTTGATCTCGATTTCA
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCTCATTTTTAACCCCGATTTCA
* * ** * *
41805155 TCAAAAATTACCATTTTGCCCTCGGA-TATCCAAAAGTCTCATTTT
1 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCTCATTTT
41805200 CAACTCCAAT
Statistics
Matches: 285, Mismatches: 41, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
57 1 0.00
58 74 0.26
59 195 0.68
60 15 0.05
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (60 bp):
CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCTCATTTTTAACCCCGATTTCA
Found at i:41817258 original size:76 final size:77
Alignment explanation
Indices: 41817132--41817276 Score: 256
Period size: 76 Copynumber: 1.9 Consensus size: 77
41817122 TCACGCCAAC
* *
41817132 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC-TGAAATTGA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTTGAAATTGA
41817196 AGTAAGAGCAAG
66 AGTAAGAGCAAG
*
41817208 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTTGAAATTGA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTTGAAATTGA
41817273 AGTA
66 AGTA
41817277 GAGTTGGATA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
76 52 0.80
77 13 0.20
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (77 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTTGAAATTGA
AGTAAGAGCAAG
Found at i:41817347 original size:115 final size:115
Alignment explanation
Indices: 41817145--41817612 Score: 475
Period size: 115 Copynumber: 4.1 Consensus size: 115
41817135 ATTTCCTATC
* *
41817145 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
41817210 CATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
66 CATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
*
41817260 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
* * *
41817325 TATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTAT
66 CATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
* ** ** * *
41817375 CTC-CGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTATC-CACTTGAAATTGAAGTAA-AGCT
1 CTCTTGAAATTGAAGT-AGAGCTGGATAACAAGTCTTTATCTC-C--GAAATTGAAGTAAGAGCA
* ** * * * * ** *
41817434 GGATAACAAGTCTTTAT-CTC-CGAAATTGAAGTAAGAGC--AAGATCATTTC-CTAT
62 AGAT--CATTTC-CTATCCTCTTGAAATTGAAGTAA-AGCTGGATATCAAGTCTTTAT
* * * *
41817487 CCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAATAAGAGCAAGA
1 -CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGA
*
41817552 TCA-TTCCTATCCTCTTGAAATTGAAGT-----TGGATAGCAAGTCTTTAT
65 TCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
41817597 CTCTCTGAAATTGAAG
1 CTCT-TGAAATTGAAG
41817613 CAAGAGCAGG
Statistics
Matches: 287, Mismatches: 45, Indels: 47
0.76 0.12 0.12
Matches are distributed among these distances:
109 10 0.03
110 14 0.05
111 4 0.01
112 13 0.05
113 39 0.14
114 60 0.21
115 139 0.48
116 7 0.02
117 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (115 bp):
CTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
CATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTAT
Found at i:41817358 original size:76 final size:76
Alignment explanation
Indices: 41817260--41817620 Score: 572
Period size: 76 Copynumber: 4.8 Consensus size: 76
41817250 AAGTCTTTAT
*
41817260 CTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
*
41817325 TATTTCCTATC
66 CATTTCCTATC
41817336 CTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
41817401 CATTTCCTATC
66 CATTTCCTATC
* *
41817412 CACTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
41817477 CATTTCCTATC
66 CATTTCCTATC
* * * *
41817488 CTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAATAAGAGCAAGAT
1 CTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
41817553 CA-TTCCTATC
66 CATTTCCTATC
* *
41817563 CTCTTGAAATT---G--AAGTTGGATAGCAAGTCTTTATCTCTCTGAAATTGAAGCAAGAGCA
1 CTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTC-C-GAAATTGAAGTAAGAGCA
41817621 GGATGAAGCC
Statistics
Matches: 270, Mismatches: 13, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
70 23 0.09
72 17 0.06
75 19 0.07
76 211 0.78
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (76 bp):
CTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCCGAAATTGAAGTAAGAGCAAGAT
CATTTCCTATC
Found at i:41817916 original size:6 final size:6
Alignment explanation
Indices: 41817896--41817983 Score: 60
Period size: 6 Copynumber: 15.0 Consensus size: 6
41817886 TTTTTAAAAG
* ** *
41817896 TTTAAA -TTAAT TTTAAA TTTATT TTTAAA TTT--A TCTTAAA TTTCAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* *
41817942 TTTACTTA TTTAAA TTT-AT TTTAAA TTTAAA TTT-AA TTTAAA
1 TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
41817984 ATAATATTAA
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
4 2 0.03
5 15 0.24
6 38 0.61
7 2 0.03
8 5 0.08
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:41817938 original size:11 final size:11
Alignment explanation
Indices: 41817896--41817970 Score: 75
Period size: 11 Copynumber: 6.9 Consensus size: 11
41817886 TTTTTAAAAG
*
41817896 TTTAAATTAAT
1 TTTAAATTTAT
41817907 TTTAAATTTATT
1 TTTAAATTTA-T
41817919 TTTAAATTTAT
1 TTTAAATTTAT
* *
41817930 CTTAAATTTCAA
1 TTTAAATTT-AT
*
41817942 TTT--ACTTA-
1 TTTAAATTTAT
41817950 TTTAAATTTAT
1 TTTAAATTTAT
41817961 TTTAAATTTA
1 TTTAAATTTA
41817971 AATTTAATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
8 3 0.06
9 1 0.02
10 7 0.13
11 28 0.53
12 14 0.26
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:41817945 original size:17 final size:17
Alignment explanation
Indices: 41817919--41817976 Score: 77
Period size: 17 Copynumber: 3.6 Consensus size: 17
41817909 TAAATTTATT
41817919 TTTAAATTTATCTTAAA
1 TTTAAATTTATCTTAAA
*
41817936 TTTCAATTTA-CTT--A
1 TTTAAATTTATCTTAAA
*
41817950 TTTAAATTTATTTTAAA
1 TTTAAATTTATCTTAAA
41817967 TTTAAATTTA
1 TTTAAATTTA
41817977 ATTTAAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
14 10 0.29
15 2 0.06
16 3 0.09
17 20 0.57
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATCTTAAA
Found at i:41817954 original size:31 final size:29
Alignment explanation
Indices: 41817902--41817985 Score: 105
Period size: 31 Copynumber: 2.8 Consensus size: 29
41817892 AAAGTTTAAA
*
41817902 TTAATTTTAAATTTATTTTTAAATTTATC
1 TTAAATTTAAATTTATTTTTAAATTTATC
* *
41817931 TTAAATTTCAATTTACTTATTTAAATTTATT
1 TTAAATTTAAATTTA-TT-TTTAAATTTATC
* *
41817962 TTAAATTTAAATTTAATTTAAAAT
1 TTAAATTTAAATTTATTTTTAAAT
41817986 AATATTAAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 19 0.40
30 3 0.06
31 25 0.53
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (29 bp):
TTAAATTTAAATTTATTTTTAAATTTATC
Found at i:41817983 original size:11 final size:11
Alignment explanation
Indices: 41817896--41817982 Score: 60
Period size: 11 Copynumber: 8.0 Consensus size: 11
41817886 TTTTTAAAAG
41817896 TTTAAA-TTAA
1 TTTAAATTTAA
*
41817906 TTTTAAATTTATT
1 -TTTAAATTTA-A
41817919 TTTAAATTT-A
1 TTTAAATTTAA
41817929 TCTTAAATTTCAA
1 T-TTAAATTT-AA
*
41817942 TTT--ACTT-A
1 TTTAAATTTAA
*
41817950 TTTAAATTTAT
1 TTTAAATTTAA
41817961 TTTAAATTTAAA
1 TTTAAATTT-AA
41817973 TTT-AATTTAA
1 TTTAAATTTAA
41817983 AATAATATTA
Statistics
Matches: 61, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
8 4 0.07
10 9 0.15
11 28 0.46
12 18 0.30
13 2 0.03
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:41818746 original size:18 final size:16
Alignment explanation
Indices: 41818723--41818765 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
41818713 GGCATTAATG
*
41818723 ATAATATTAATAATAA
1 ATAATATTAACAATAA
*
41818739 GTATAATAGTAACAATAA
1 --ATAATATTAACAATAA
41818757 ATAATATTA
1 ATAATATTA
41818766 GTATTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
18 14 0.64
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (16 bp):
ATAATATTAACAATAA
Found at i:41819070 original size:16 final size:16
Alignment explanation
Indices: 41819049--41819079 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41819039 TTAAGTATTT
41819049 CCAGATCTGGATTTTC
1 CCAGATCTGGATTTTC
41819065 CCAGATCTGGATTTT
1 CCAGATCTGGATTTT
41819080 GTTTTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (16 bp):
CCAGATCTGGATTTTC
Found at i:41819103 original size:9 final size:9
Alignment explanation
Indices: 41819086--41819142 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
41819076 TTTTGTTTTC
41819086 AAAAAGAAG
1 AAAAAGAAG
*
41819095 AAAATGAAG
1 AAAAAGAAG
41819104 AAAAAGAA-
1 AAAAAGAAG
*
41819112 ATAAAGAA-
1 AAAAAGAAG
* *
41819120 TAAAAGATG
1 AAAAAGAAG
41819129 AAAAAGAAAG
1 AAAAAG-AAG
41819139 AAAA
1 AAAA
41819143 GAGAGAAGAG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
8 12 0.32
9 20 0.53
10 6 0.16
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:41819137 original size:25 final size:26
Alignment explanation
Indices: 41819088--41819137 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
41819078 TTGTTTTCAA
41819088 AAAGAAGAAAATGAAGAAAAAGAAAT
1 AAAGAAGAAAATGAAGAAAAAGAAAT
* *
41819114 AAAGAATAAAA-GATGAAAAAGAAA
1 AAAGAAGAAAATGAAGAAAAAGAAA
41819138 GAAAAGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (26 bp):
AAAGAAGAAAATGAAGAAAAAGAAAT
Found at i:41819143 original size:26 final size:26
Alignment explanation
Indices: 41819086--41819149 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
41819076 TTTTGTTTTC
41819086 AAAAAGAAGAAAATGAAGAAAAAGAA
1 AAAAAGAAGAAAATGAAGAAAAAGAA
* * *
41819112 ATAAAGAATAAAA-GATGAAAAAGAA
1 AAAAAGAAGAAAATGAAGAAAAAGAA
41819137 AGAAAAGAGAGAA
1 A-AAAAGA-AGAA
41819150 GAGACTTATC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 12 0.39
26 16 0.52
27 3 0.10
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.06
Consensus pattern (26 bp):
AAAAAGAAGAAAATGAAGAAAAAGAA
Found at i:41819843 original size:163 final size:163
Alignment explanation
Indices: 41819573--41820083 Score: 898
Period size: 163 Copynumber: 3.1 Consensus size: 163
41819563 TTTTAATTGG
*
41819573 TTTTTAAATTAGTCCTTTGATTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
1 TTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
41819638 TTTATGTATCTAGTCCCTGTCATTTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTGCT
66 TTTATGTATCTAGTCCCTGTCATTTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTGCT
*
41819703 TAATTACAAAATTGACCCAGGAATCTTTTGAGA
131 TAATTACAAAATTGACCCAAGAATCTTTTGAGA
41819736 TTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
1 TTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
*
41819801 TTTATGTATCTAGTCCCTGTCATTTTTTAATTTATTTTAATTTAATCCTCAAATCAACTTTTGCT
66 TTTATGTATCTAGTCCCTGTCATTTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTGCT
41819866 TAATTACAAAATTGACCCAAGAATCTTTTGAGA
131 TAATTACAAAATTGACCCAAGAATCTTTTGAGA
41819899 TTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
1 TTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
* **
41819964 TTTATGTATCTAGTCCCTGTCA-TTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTATT
66 TTTATGTATCTAGTCCCTGTCATTTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTGCT
* * *
41820028 TAATTACAAAATTGGCCCAAGAATTTTTTCAAGA
131 TAATTACAAAATTGACCCAAGAATCTTTT-GAGA
** *
41820062 TTTACAAATTCGTCCTTTGACT
1 TTTTTAAATTAGTCCTTTGACT
41820084 TCTAGATACC
Statistics
Matches: 334, Mismatches: 13, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
162 65 0.19
163 269 0.81
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.44
Consensus pattern (163 bp):
TTTTTAAATTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTA
TTTATGTATCTAGTCCCTGTCATTTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTTTGCT
TAATTACAAAATTGACCCAAGAATCTTTTGAGA
Found at i:41820230 original size:30 final size:29
Alignment explanation
Indices: 41820189--41820524 Score: 149
Period size: 30 Copynumber: 11.3 Consensus size: 29
41820179 AACTTCCAAC
41820189 ATTCCATTTTTAACCCCGATTTCACCAAAA
1 ATTCCA-TTTTAACCCCGATTTCACCAAAA
* * *
41820219 ATTGCCATTTTACCCCCGAACTT--CCTAAA
1 ATT-CCATTTTAACCCCG-ATTTCACCAAAA
*
41820248 ATTCCATTTTTAACCCCAATTTCACCAAAA
1 ATTCCA-TTTTAACCCCGATTTCACCAAAA
* *** ** *
41820278 ATTACCATTTT-ACCCCTAAAACTTCTAAA
1 ATT-CCATTTTAACCCCGATTTCACCAAAA
*
41820307 ATTCCATTTTTAACCTCGATTTCACCAAAA
1 ATTCCA-TTTTAACCCCGATTTCACCAAAA
** *
41820337 ATTACCATTTT-ACCTCTAAACTTC-CC-AAA
1 ATT-CCATTTTAACC-C-CGATTTCACCAAAA
** *
41820366 ATTCCATTTTTAACCCTTATTTCACTAAAA
1 ATTCCA-TTTTAACCCCGATTTCACCAAAA
*
41820396 ATTACCATTTT-ACCCCTAAACTTT--CC-AAA
1 ATT-CCATTTTAACCCC--GA-TTTCACCAAAA
* * *
41820425 ATTCCATTTTTAACCCTGATTTAACAAAAA
1 ATTCCA-TTTTAACCCCGATTTCACCAAAA
* *
41820455 ATTTCTATTTT-ACCCTCGAATTT-TCC-AAA
1 A-TTCCATTTTAACCC-CG-ATTTCACCAAAA
* * * *
41820484 ATTCTCTTTTTGATCCCGATTTCATCAAAA
1 ATTC-CATTTTAACCCCGATTTCACCAAAA
41820514 ATTACCATTTT
1 ATT-CCATTTT
41820525 GCCCCCGGAT
Statistics
Matches: 228, Mismatches: 46, Indels: 64
0.67 0.14 0.19
Matches are distributed among these distances:
27 3 0.01
28 27 0.12
29 80 0.35
30 86 0.38
31 29 0.13
32 3 0.01
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.38
Consensus pattern (29 bp):
ATTCCATTTTAACCCCGATTTCACCAAAA
Found at i:41820252 original size:59 final size:58
Alignment explanation
Indices: 41820154--41820565 Score: 450
Period size: 59 Copynumber: 7.0 Consensus size: 58
41820144 CCTGAATGGT
* *
41820154 CCAAAAATTACCATTTTACCCCTAAAACTTCCAACATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCC-CAAACTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
41820213 CCAAAAATTGCCATTTTACCCCCGAACTTCCTAAAATTCCATTTTTAACCCCAATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTCC-AAAATTCCATTTTTAACCCCGATTTCA
* * *
41820272 CCAAAAATTACCATTTTACCCCTAAAACTTCTAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCC-CAAACTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * **
41820331 CCAAAAATTACCATTTTACCTCTAAACTTCCCAAAATTCCATTTTTAACCCTTATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTT-CCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
41820390 CTAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTGATTTAA
1 CCAAAAATTACCATTTTACCCCCAAAC-TTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * ** * *
41820449 CAAAAAATTTCTATTTTACCCTCGAATTTTCCAAAATTCTC-TTTTTGATCCCGATTTCA
1 CCAAAAATTACCATTTTACCC-CCAAACTTCCAAAATTC-CATTTTTAACCCCGATTTCA
* * ** * * *
41820508 TCAAAAATTACCATTTTGCCCCCGGA-TATCCAAAAGTCTCATTTTCAACTCCGATTTC
1 CCAAAAATTACCATTTTACCCCCAAACT-TCCAAAATTC-CATTTTTAACCCCGATTTC
41820566 GTCGTTTCTT
Statistics
Matches: 300, Mismatches: 45, Indels: 16
0.83 0.12 0.04
Matches are distributed among these distances:
57 1 0.00
58 25 0.08
59 262 0.87
60 12 0.04
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCCAAACTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:41822338 original size:53 final size:53
Alignment explanation
Indices: 41822258--41822500 Score: 333
Period size: 53 Copynumber: 4.6 Consensus size: 53
41822248 TTCTCATTTA
* * * * *
41822258 ATACTCACGATGACACATAGTCATCGAACTTTTTAATCCGTAATAGGATTCAT
1 ATACTCACGATGACACAAAATCATCGGACCTGTTAATCCGTAATAGGATTCAT
* * * * * *
41822311 ATACTCACGATTACAAAAAATCATCGAACCTATTAATCTGTAATAGGATTCTT
1 ATACTCACGATGACACAAAATCATCGGACCTGTTAATCCGTAATAGGATTCAT
41822364 ATACTCACGATGACACAAAATCATCGGACCTGTTAATCCGTAATAGGATTCAT
1 ATACTCACGATGACACAAAATCATCGGACCTGTTAATCCGTAATAGGATTCAT
* * *
41822417 ATACTCATGATGACAGAAAATCATCGGACCTGTTAATCCATAATAGGATTCAT
1 ATACTCACGATGACACAAAATCATCGGACCTGTTAATCCGTAATAGGATTCAT
* * *
41822470 ATACACACAATGACATAAAATCATCGGACCT
1 ATACTCACGATGACACAAAATCATCGGACCT
41822501 TTTACATTTA
Statistics
Matches: 169, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 169 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (53 bp):
ATACTCACGATGACACAAAATCATCGGACCTGTTAATCCGTAATAGGATTCAT
Found at i:41824163 original size:21 final size:21
Alignment explanation
Indices: 41824139--41824178 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41824129 CACTAATATT
41824139 AACTATT-AATTCAATAATTAA
1 AACTATTCAATTCAA-AATTAA
*
41824160 AACTCTTCAATTCAAAATT
1 AACTATTCAATTCAAAATT
41824179 CCATATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (21 bp):
AACTATTCAATTCAAAATTAA
Found at i:41829242 original size:12 final size:12
Alignment explanation
Indices: 41829205--41829254 Score: 73
Period size: 12 Copynumber: 4.0 Consensus size: 12
41829195 GTTTTTTCTT
*
41829205 TTTTGTGTTTGTC
1 TTTTGTCTTTG-C
41829218 TTTTGTGCTTTGC
1 TTTTGT-CTTTGC
41829231 TTTTGTCTTTGC
1 TTTTGTCTTTGC
41829243 TTTTGTCTTTGC
1 TTTTGTCTTTGC
41829255 AGGTGATGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
12 18 0.51
13 13 0.37
14 4 0.11
ACGTcount: A:0.00, C:0.14, G:0.20, T:0.66
Consensus pattern (12 bp):
TTTTGTCTTTGC
Found at i:41829551 original size:6 final size:6
Alignment explanation
Indices: 41829540--41829574 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
41829530 AGGCTCCAAA
41829540 AATTAT AATTATT AATTAT AATTATT AATTAT AAT
1 AATTAT AATTA-T AATTAT AATTA-T AATTAT AAT
41829575 GATTTCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 15 0.56
7 12 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
AATTAT
Found at i:41829556 original size:13 final size:13
Alignment explanation
Indices: 41829540--41829574 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
41829530 AGGCTCCAAA
41829540 AATTATAATTATT
1 AATTATAATTATT
41829553 AATTATAATTATT
1 AATTATAATTATT
41829566 AATTATAAT
1 AATTATAAT
41829575 GATTTCATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AATTATAATTATT
Found at i:41829557 original size:7 final size:7
Alignment explanation
Indices: 41829540--41829571 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
41829530 AGGCTCCAAA
41829540 AATTA-T
1 AATTATT
41829546 AATTATT
1 AATTATT
41829553 AATTA-T
1 AATTATT
41829559 AATTATT
1 AATTATT
41829566 AATTAT
1 AATTAT
41829572 AATGATTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 11 0.46
7 13 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AATTATT
Found at i:41829788 original size:123 final size:122
Alignment explanation
Indices: 41829585--41829826 Score: 387
Period size: 123 Copynumber: 2.0 Consensus size: 122
41829575 GATTTCATTA
*
41829585 AATATTAAAACATTGAAGCTAATATCCTTCTGGAAAGGATATAATGTTTTAATAAACCTTCCATA
1 AATATTAAAACATGGAAGCTAATATCCTTCTGGAAAGGATATAATGTTTTAATAAACCTTCCATA
* * * *
41829650 TATTTCTTGAAAGGAATATTTCTATTTTCATATGAGATATTATATAAAAGGAAATAG
66 TATTTCTTGAAAGGAATATTTCCATTTTAATACGAGATATTAAATAAAAGGAAATAG
* * *
41829707 AATATTAGAAACATGGAAGTTAATATCCTTTTGGAAATGATATAATGTTTTAATAAACCTTCCAT
1 AATATTA-AAACATGGAAGCTAATATCCTTCTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
41829772 ATATTTCTCT-AAAGGAATATTTCCATTTTAATACGAGATATTAAATAAAAGGAAA
65 ATATTTCT-TGAAAGGAATATTTCCATTTTAATACGAGATATTAAATAAAAGGAAA
41829827 GATAGCATAA
Statistics
Matches: 110, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
122 7 0.06
123 102 0.93
124 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (122 bp):
AATATTAAAACATGGAAGCTAATATCCTTCTGGAAAGGATATAATGTTTTAATAAACCTTCCATA
TATTTCTTGAAAGGAATATTTCCATTTTAATACGAGATATTAAATAAAAGGAAATAG
Found at i:41836985 original size:11 final size:11
Alignment explanation
Indices: 41836969--41836993 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41836959 AATAGAGGAA
41836969 TTTAAATTATT
1 TTTAAATTATT
41836980 TTTAAATTATT
1 TTTAAATTATT
41836991 TTT
1 TTT
41836994 CCATATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTAAATTATT
Found at i:41838103 original size:43 final size:44
Alignment explanation
Indices: 41838036--41838160 Score: 198
Period size: 43 Copynumber: 2.9 Consensus size: 44
41838026 TTTGAAAGTT
*
41838036 GGAAAATTGTTTCCTTATTATTGAAAGTATGTGATTGATTGAGA
1 GGAACATTGTTTCCTTATTATTGAAAGTATGTGATTGATTGAGA
* * **
41838080 GTAACATTGTTT-CTTATTATTGAAATTATGTGATCAATTGAGA
1 GGAACATTGTTTCCTTATTATTGAAAGTATGTGATTGATTGAGA
41838123 GGAACATTGTTTCCTTATTATTGAAAGTATGTGATTGA
1 GGAACATTGTTTCCTTATTATTGAAAGTATGTGATTGA
41838161 CTAAGAGCAA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
43 39 0.55
44 32 0.45
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.42
Consensus pattern (44 bp):
GGAACATTGTTTCCTTATTATTGAAAGTATGTGATTGATTGAGA
Found at i:41842217 original size:2 final size:2
Alignment explanation
Indices: 41842208--41842236 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
41842198 TTATATACAC
41842208 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41842237 CAATCTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:41849195 original size:5 final size:5
Alignment explanation
Indices: 41849180--41849212 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
41849170 AACCTATTGT
41849180 TTTTA -TTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
41849213 TCGTCATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:41849259 original size:15 final size:15
Alignment explanation
Indices: 41849219--41849279 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 15
41849209 TTTTTCGTCA
41849219 TTAATTTATTTTGATTAT
1 TTAA-TTATTTT-ATT-T
41849237 TTATATTATTTTATTT
1 TTA-ATTATTTTATTT
41849253 TTAATTATTTTTATTT
1 TTAATTA-TTTTATTT
*
41849269 TT-GTTATTTTA
1 TTAATTATTTTA
41849280 GGTACGCGGA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 5 0.12
15 7 0.17
16 14 0.35
17 3 0.08
18 10 0.25
19 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (15 bp):
TTAATTATTTTATTT
Found at i:41849834 original size:16 final size:16
Alignment explanation
Indices: 41849813--41849845 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41849803 CGACAAAGAA
41849813 CCCACAATCGAACGTC
1 CCCACAATCGAACGTC
*
41849829 CCCACAATTGAACGTC
1 CCCACAATCGAACGTC
41849845 C
1 C
41849846 ATGATGAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.42, G:0.12, T:0.15
Consensus pattern (16 bp):
CCCACAATCGAACGTC
Found at i:41850642 original size:9 final size:9
Alignment explanation
Indices: 41850622--41850715 Score: 55
Period size: 9 Copynumber: 10.0 Consensus size: 9
41850612 TTTATTCCAT
41850622 GAAAAAATAA
1 GAAAAAA-AA
41850632 GAAAAAAAA
1 GAAAAAAAA
*
41850641 GAGAAAAAA
1 GAAAAAAAA
****
41850650 GAAAGGAGTTC
1 GAAA--AAAAA
41850661 GAATAAATAAA
1 GAA-AAA-AAA
*
41850672 -AAAAAGAA
1 GAAAAAAAA
41850680 GAAAAAAAA
1 GAAAAAAAA
*
41850689 GAGAAAAAA
1 GAAAAAAAA
* *
41850698 GGAGAAAAA
1 GAAAAAAAA
41850707 GAAAAAAAA
1 GAAAAAAAA
41850716 ACATGGTTGC
Statistics
Matches: 61, Mismatches: 18, Indels: 11
0.68 0.20 0.12
Matches are distributed among these distances:
8 2 0.03
9 44 0.72
10 10 0.16
11 4 0.07
12 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.05
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:41850686 original size:12 final size:11
Alignment explanation
Indices: 41850669--41850706 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
41850659 TCGAATAAAT
41850669 AAAAAAAAGAAG
1 AAAAAAAAG-AG
41850681 AAAAAAAAGAG
1 AAAAAAAAGAG
*
41850692 -AAAAAAGGAG
1 AAAAAAAAGAG
41850702 AAAAA
1 AAAAA
41850707 GAAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 9 0.38
11 6 0.25
12 9 0.38
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:41853316 original size:82 final size:78
Alignment explanation
Indices: 41853191--41853492 Score: 246
Period size: 82 Copynumber: 3.7 Consensus size: 78
41853181 TTAAATTGGA
* * ** *
41853191 AAAT-AATCTGTTTCGGGATTTATTTCTCGTCAGTTAACAGATTTTATTCTATTTGATTTTATTT
1 AAATAAATCTGTTTCGAGATTTA-TTCCCACCA-TTAACAGATTTTATTCTATTTGATTTTGTTT
41853255 ACAAAAATGAGAATAAGT
64 -CAAAAAT-A-AATAAGT
* * *
41853273 AAATAAATCTGTTTCGGGATTTATTCCCACCATTGAACAGATTTAATTTTATATTTGGATTTTGG
1 AAATAAATCTGTTTCGAGATTTATTCCCACCATT-AACAGATTT--TATTCTATTT-GATTTT-G
*
41853338 TTTCAAATAATAACTAAGT
61 TTTCAAA-AATAAATAAGT
* * * * *
41853357 AAATAAATCTATTTTGAGATTTATTCCCACCGTTTAATAGATTTTATTCAAGTTTGATTTTGTTT
1 AAATAAATCTGTTTCGAGATTTATTCCCACC-ATTAACAGATTTTATTCTA-TTTGATTTTGTTT
*
41853422 CCAAAATAAAATAAGTT
64 CAAAAAT-AAATAAG-T
* * * ** * * *
41853439 GACTAAATCTGTTTTGAGATTTATTCTCGTCTATTAACAGATTATATTTTATTT
1 AAATAAATCTGTTTCGAGATTTATTC-CCACCATTAACAGATTTTATTCTATTT
41853493 TTTATTTTAT
Statistics
Matches: 180, Mismatches: 28, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
80 3 0.02
81 18 0.10
82 67 0.37
83 23 0.13
84 50 0.28
85 13 0.07
86 6 0.03
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (78 bp):
AAATAAATCTGTTTCGAGATTTATTCCCACCATTAACAGATTTTATTCTATTTGATTTTGTTTCA
AAAATAAATAAGT
Found at i:41853399 original size:84 final size:81
Alignment explanation
Indices: 41853226--41853464 Score: 234
Period size: 84 Copynumber: 2.9 Consensus size: 81
41853216 CTCGTCAGTT
* * * * * * *
41853226 AACAGATTTTATTCTA-TTTGATTTTATTTACAAAAATGAGAATAAGTAAATAAATCTGTTTCGG
1 AACAGATTTAATTCAAGTTTGATTTTGTTT-CCAAAAT-AAAATAAGTAAATAAATCTGTTTTGA
41853290 GATTTATTCCCACCATTG
64 GATTTATTCCCACCATTG
* *
41853308 AACAGATTTAATTTTATA-TTTGGATTTTGGTTT-C-AAATAATAACTAAGTAAATAAATCTATT
1 AACAGATTTAA-TTCA-AGTTT-GATTTT-GTTTCCAAAATAA-AA-TAAGTAAATAAATCTGTT
* *
41853370 TTGAGATTTATTCCCACCGTTT
60 TTGAGATTTATTCCCACCATTG
* * * *
41853392 AATAGATTTTATTCAAGTTTGATTTTGTTTCCAAAATAAAATAAGTTGACTAAATCTGTTTTGAG
1 AACAGATTTAATTCAAGTTTGATTTTGTTTCCAAAATAAAATAAG-TAAATAAATCTGTTTTGAG
41853457 ATTTATTC
65 ATTTATTC
41853465 TCGTCTATTA
Statistics
Matches: 130, Mismatches: 17, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
81 8 0.06
82 45 0.35
83 20 0.15
84 48 0.37
85 6 0.05
86 3 0.02
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (81 bp):
AACAGATTTAATTCAAGTTTGATTTTGTTTCCAAAATAAAATAAGTAAATAAATCTGTTTTGAGA
TTTATTCCCACCATTG
Found at i:41855693 original size:29 final size:29
Alignment explanation
Indices: 41855649--41855704 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
41855639 ACCATCCTGT
* *
41855649 AACCACTTGAAAATGTGGGGGTGTCTTAC
1 AACCACTTGAAAATGTGAGGGTATCTTAC
*
41855678 AACCACTTGAATATGTGAGGGTATCTT
1 AACCACTTGAAAATGTGAGGGTATCTT
41855705 GTTAAATGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (29 bp):
AACCACTTGAAAATGTGAGGGTATCTTAC
Found at i:41870179 original size:58 final size:57
Alignment explanation
Indices: 41870089--41870207 Score: 211
Period size: 58 Copynumber: 2.1 Consensus size: 57
41870079 TATCCTCTTG
41870089 TAATACAATAAAATATTTATTATATTTATGGTAGTGTTTTTTTAATATAAATACTTTT
1 TAATACAATAAAATATTTATTATATTTATGGTAGTG-TTTTTTAATATAAATACTTTT
* *
41870147 TAATACAATAAAATATTTATTATATTTGTGGTAGTGTTTTTTAATATAAATATTTTT
1 TAATACAATAAAATATTTATTATATTTATGGTAGTGTTTTTTAATATAAATACTTTT
41870204 TAAT
1 TAAT
41870208 GTGTTAGAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 24 0.41
58 35 0.59
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.52
Consensus pattern (57 bp):
TAATACAATAAAATATTTATTATATTTATGGTAGTGTTTTTTAATATAAATACTTTT
Found at i:41879227 original size:15 final size:15
Alignment explanation
Indices: 41879207--41879242 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
41879197 GGTTTTTTAA
41879207 ATAATTATAAAAATT
1 ATAATTATAAAAATT
**
41879222 ATAATTATAAATTTT
1 ATAATTATAAAAATT
41879237 ATAATT
1 ATAATT
41879243 TATTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAATTATAAAAATT
Found at i:41881435 original size:15 final size:15
Alignment explanation
Indices: 41881415--41881443 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41881405 ATAGTACTTA
41881415 GCCCTCATAATTCTG
1 GCCCTCATAATTCTG
41881430 GCCCTCATAATTCT
1 GCCCTCATAATTCT
41881444 AGCTGATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.34, G:0.10, T:0.34
Consensus pattern (15 bp):
GCCCTCATAATTCTG
Found at i:41882735 original size:44 final size:44
Alignment explanation
Indices: 41882672--41882762 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
41882662 ATTAAGCAAT
41882672 TCTATATAATAAGCAGCAACTTCATTGCCCACAATATTCCAAAA
1 TCTATATAATAAGCAGCAACTTCATTGCCCACAATATTCCAAAA
41882716 TCTATATAATAAGCAGCAACTTCATTGCCCACAATATTCCAAAA
1 TCTATATAATAAGCAGCAACTTCATTGCCCACAATATTCCAAAA
41882760 TCT
1 TCT
41882763 TTGGTAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.29
Consensus pattern (44 bp):
TCTATATAATAAGCAGCAACTTCATTGCCCACAATATTCCAAAA
Found at i:41885449 original size:11 final size:12
Alignment explanation
Indices: 41885427--41885455 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
41885417 AAAAAAAACG
41885427 AAAGACGTGTCA
1 AAAGACGTGTCA
41885439 AAAGA-GTGTCA
1 AAAGACGTGTCA
41885450 AAAGAC
1 AAAGAC
41885456 AAAGGTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.48, C:0.14, G:0.24, T:0.14
Consensus pattern (12 bp):
AAAGACGTGTCA
Found at i:41887192 original size:17 final size:17
Alignment explanation
Indices: 41887147--41887198 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
41887137 TTAAGTTGGG
41887147 TTTAAATTTG-TTTAAA
1 TTTAAATTTGCTTTAAA
41887163 TTT--A-TT-C-TTAAA
1 TTTAAATTTGCTTTAAA
41887175 TTTAAATTTGCTTTAAA
1 TTTAAATTTGCTTTAAA
41887192 TTTAAAT
1 TTTAAAT
41887199 ATAATTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
12 8 0.27
13 2 0.07
14 2 0.07
15 2 0.07
16 4 0.13
17 12 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTAAATTTGCTTTAAA
Found at i:41887457 original size:22 final size:23
Alignment explanation
Indices: 41887422--41887479 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 23
41887412 CCACTTGTAT
41887422 TGCTGTTGCCCACCAGCTTCAACC
1 TGCT-TTGCCCACCAGCTTCAACC
41887446 TG-TTCTGCCACCACCAGCTTCAACC
1 TGCTT-TG-C-CCACCAGCTTCAACC
41887471 TGCTTTGCC
1 TGCTTTGCC
41887480 ATCACCGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
22 1 0.03
23 4 0.13
24 4 0.13
25 19 0.63
26 2 0.07
ACGTcount: A:0.16, C:0.41, G:0.16, T:0.28
Consensus pattern (23 bp):
TGCTTTGCCCACCAGCTTCAACC
Found at i:41887461 original size:25 final size:25
Alignment explanation
Indices: 41887431--41887485 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
41887421 TTGCTGTTGC
41887431 CCACCAGCTTCAACCTG-TTCTGCCA
1 CCACCAGCTTCAACCTGCTT-TGCCA
41887456 CCACCAGCTTCAACCTGCTTTGCCA
1 CCACCAGCTTCAACCTGCTTTGCCA
*
41887481 TCACC
1 CCACC
41887486 GTCACTGCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 26 0.93
26 2 0.07
ACGTcount: A:0.20, C:0.45, G:0.11, T:0.24
Consensus pattern (25 bp):
CCACCAGCTTCAACCTGCTTTGCCA
Found at i:41889183 original size:59 final size:58
Alignment explanation
Indices: 41889085--41889345 Score: 197
Period size: 59 Copynumber: 4.4 Consensus size: 58
41889075 CCCTAAAGGT
* * * *
41889085 CCCTAAACTTCTCCAAAATTAAATTTTTGA-CCTCAAACTTTCCAAAAATTACATTTTTAC
1 CCCTGAACTTC-CTAAAATTCAATTTTTAACCCT-AAACTTTCCAAAAATTACA-TTTTAC
* * ***
41889145 CCTTGAACTTCCTAAAATTCAATTTTTAACCTTAAACTTTTTGAAAATTACATTTTTAC
1 CCCTGAACTTCCTAAAATTCAATTTTTAACCCTAAACTTTCCAAAAATTACA-TTTTAC
* * * * * ***
41889204 CCCTAAACTTTCTAAAATTCCATTTTTGACCCT-AATTTTTTTAAAATTACATTTTAC
1 CCCTGAACTTCCTAAAATTCAATTTTTAACCCTAAACTTTCCAAAAATTACATTTTAC
* * * * ** *
41889261 CCCCGAACTTTCAAAAATTCCA-TTTTAACCCTAATTTTTCCCAAAATTACCATTTTAC
1 CCCTGAACTTCCTAAAATTCAATTTTTAACCCTAAACTTTCCAAAAATTA-CATTTTAC
* *
41889319 CCCTAAACTT-TTAAAAATTTCAATTTT
1 CCCTGAACTTCCT-AAAA-TTCAATTTT
41889346 GATCCCGATT
Statistics
Matches: 165, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
56 9 0.05
57 37 0.22
58 36 0.22
59 69 0.42
60 14 0.08
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (58 bp):
CCCTGAACTTCCTAAAATTCAATTTTTAACCCTAAACTTTCCAAAAATTACATTTTAC
Found at i:41889236 original size:29 final size:28
Alignment explanation
Indices: 41889085--41889334 Score: 168
Period size: 29 Copynumber: 8.6 Consensus size: 28
41889075 CCCTAAAGGT
* *
41889085 CCCTAAACTTCTCCAAAATTAAATTTTTGA
1 CCCTAAACTT-TCTAAAATTACATTTTT-A
*
41889115 -CCTCAAACTTTCCAAAAATTACATTTTTA
1 CCCT-AAACTTT-CTAAAATTACATTTTTA
* *
41889144 CCCTTGAACTTCCTAAAATT-CAATTTTTAA
1 CCC-TAAACTTTCTAAAATTAC-ATTTTT-A
* *
41889174 CCTTAAACTTTTTGAAAATTACATTTTTA
1 CCCTAAACTTTCT-AAAATTACATTTTTA
*
41889203 CCCCTAAACTTTCTAAAATTCCATTTTTGA
1 -CCCTAAACTTTCTAAAATTACATTTTT-A
** *
41889233 CCCTAATTTTTTTAAAATTACA-TTTTA
1 CCCTAAACTTTCTAAAATTACATTTTTA
** * * *
41889260 CCCCCGAACTTTCAAAAATTCCATTTTAA
1 -CCCTAAACTTTCTAAAATTACATTTTTA
** *
41889289 CCCTAATTTTTCCCAAAATTACCA-TTTTA
1 CCCTAAACTTT-CTAAAATTA-CATTTTTA
41889318 CCCCTAAACTTT-TAAAA
1 -CCCTAAACTTTCTAAAA
41889335 ATTTCAATTT
Statistics
Matches: 171, Mismatches: 34, Indels: 32
0.72 0.14 0.14
Matches are distributed among these distances:
27 1 0.01
28 31 0.18
29 72 0.42
30 65 0.38
31 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (28 bp):
CCCTAAACTTTCTAAAATTACATTTTTA
Found at i:41889315 original size:58 final size:57
Alignment explanation
Indices: 41889123--41889403 Score: 227
Period size: 59 Copynumber: 4.8 Consensus size: 57
41889113 GACCTCAAAC
* * * *
41889123 TTTCCAAAAATTACATTTTTACCCTTGAACTTCCTAAAATTCAATTTTTAACCTTAAACTT
1 TTTCCAAAAATTACA-TTTTACCCCTGAACTTTCTAAAATTCCA-TTTTAACCCT-AA-TT
* * *
41889184 TTT--GAAAATTACATTTTTACCCCTAAACTTTCTAAAATTCCATTTTTGACCCTAATT
1 TTTCCAAAAATTACA-TTTTACCCCTGAACTTTCTAAAATTCCA-TTTTAACCCTAATT
** * *
41889241 TTT-TTAAAATTACATTTTACCCCCGAACTTTCAAAAATTCCATTTTAACCCTAATT
1 TTTCCAAAAATTACATTTTACCCCTGAACTTTCTAAAATTCCATTTTAACCCTAATT
* * * * *
41889297 TTTCCCAAAATTACCATTTTACCCCTAAACTTT-TAAAAATTTCAATTTTGATCCC-GA-T
1 TTTCCAAAAATTA-CATTTTACCCCTGAACTTTCT-AAAA-TTCCATTTT-AACCCTAATT
*
41889355 TTTCCAAAAAAATTACCATTTTA-CCCTCGAA-TGTCTAAAATTCCATTTT
1 TTTCC--AAAAATTA-CATTTTACCCCT-GAACTTTCTAAAATTCCATTTT
41889404 TAATCCCGAG
Statistics
Matches: 186, Mismatches: 24, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
56 16 0.09
57 37 0.20
58 46 0.25
59 62 0.33
60 22 0.12
61 3 0.02
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.41
Consensus pattern (57 bp):
TTTCCAAAAATTACATTTTACCCCTGAACTTTCTAAAATTCCATTTTAACCCTAATT
Found at i:41889394 original size:60 final size:60
Alignment explanation
Indices: 41889188--41889424 Score: 156
Period size: 57 Copynumber: 4.0 Consensus size: 60
41889178 AAACTTTTTG
* * * * ***
41889188 AAAATTA-CATTTTTACCCCTAAACTTTCTAAAATTCCATTTTTGA-CCCTAATTTT--TTT
1 AAAATTACCA-TTTTACCCCTAAAC-TTCTAAAATTCCAATTTTAATCCCGACTTTTCCAAA
** * * * *
41889246 AAAATTA-CATTTTACCCCCGAACTTTCAAAAATTCC-ATTTTAA-CCCTAATTTTTCC--C
1 AAAATTACCATTTTACCCCTAAAC-TTCTAAAATTCCAATTTTAATCCC-GACTTTTCCAAA
* * *
41889303 AAAATTACCATTTTACCCCTAAACTTTTAAAAATTTCAATTTTGATCCCGA-TTTTCCAAA
1 AAAATTACCATTTTACCCCTAAACTTCT-AAAATTCCAATTTTAATCCCGACTTTTCCAAA
* *
41889363 AAAATTACCATTTTA-CCCTCGAA-TGTCTAAAATTCCATTTTTAATCCCGAGCTTTTCCAAA
1 AAAATTACCATTTTACCCCT-AAACT-TCTAAAATTCCAATTTTAATCCCGA-CTTTTCCAAA
41889424 A
1 A
41889425 TTATAATTTT
Statistics
Matches: 145, Mismatches: 21, Indels: 23
0.77 0.11 0.12
Matches are distributed among these distances:
56 8 0.06
57 38 0.26
58 36 0.25
59 31 0.21
60 22 0.15
61 10 0.07
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (60 bp):
AAAATTACCATTTTACCCCTAAACTTCTAAAATTCCAATTTTAATCCCGACTTTTCCAAA
Found at i:41900646 original size:18 final size:18
Alignment explanation
Indices: 41900612--41900646 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41900602 CATCCAATAC
* *
41900612 TGTTCCTTTTAATTATTT
1 TGTTCCTTGTAAATATTT
41900630 TGTTCCTTGTAAATATT
1 TGTTCCTTGTAAATATT
41900647 CAGCATTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (18 bp):
TGTTCCTTGTAAATATTT
Found at i:41901183 original size:100 final size:99
Alignment explanation
Indices: 41901040--41901524 Score: 382
Period size: 100 Copynumber: 4.9 Consensus size: 99
41901030 CAGTACCATG
**
41901040 AGACATGAAGGGAAAGATCTAAGCCGCAACAACGGATCCAGTACCATAAAGATACAAAAGGGAAA
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCATAAAGATACAAAAGGGAAA
41901105 GGTTTAAGTCGCAACGACGAACCTAGTACCTCAA
66 GGTTTAAGTCGCAACGACGAACCTAGTACCTCAA
* *
41901139 A-AGCATGACGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGTAAAGATACAAAAGGGA
1 AGA-CATGAAGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCATAAAGATACAAAAGGGA
* * *
41901203 AAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAA
64 AAGGTTTAAGTCGCAACGACGAACCTAGTACCTCAA
* * * *
41901239 AGACATGAAGAGAAAGATCTAAGCCGTAACGGTGGATCCAGTACCATGAAG--ACATAAAGGGAA
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCATAAAGATACA-AAAGGGAA
* * * * ** * *
41901302 AGATCTAAGACCGCAATAGTGGATCC-AGTACCGCAA
65 AGGTTTAAG-TCGCAA-CGACGAACCTAGTACCTCAA
* ** * * * * * *
41901338 AGATACA-AAAGGGATGGGTTTAAGTCGCAATGGC-GAACCTTGTACC-TCAAAG--ACATAAAG
1 AG--ACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCC-AGTACCAT-AAAGATACA-AAAG
* * * * * * *
41901398 GGAAAGATCTAAGCCGCAATGGCGGATCC-AGTACCAT-GA
61 GGAAAGGTTTAAGTCGCAACGAC-GAACCTAGTACC-TCAA
* * * * * * *
41901437 AGACATAAAGGGAAGGTTCTAAGCCGCAACGGCGGATCCAATACCACAAAGACAC-AAAGGGAAG
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCATAAAGATACAAAAGGGAAA
* *
41901501 GGTTTAAGTCGCAATGGCGAACCT
66 GGTTTAAGTCGCAACGACGAACCT
41901525 TATACCTTAG
Statistics
Matches: 314, Mismatches: 54, Indels: 37
0.78 0.13 0.09
Matches are distributed among these distances:
97 10 0.03
98 70 0.22
99 88 0.28
100 142 0.45
101 4 0.01
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.15
Consensus pattern (99 bp):
AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCATAAAGATACAAAAGGGAAA
GGTTTAAGTCGCAACGACGAACCTAGTACCTCAA
Found at i:41901283 original size:49 final size:49
Alignment explanation
Indices: 41901040--41901519 Score: 334
Period size: 49 Copynumber: 9.7 Consensus size: 49
41901030 CAGTACCATG
* ***
41901040 AGACATGAAGGGAAAGATCTAAGCCGCAACAACGGATCCAGTACCAT-AA
1 AGACATAAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACC-TCAA
* * * * * *
41901089 AGATACA-AAAGGGAAAGGTTTAAGTCGCAACGAC-GAACCTAGTACCTCAA
1 AG--ACATAAAGGGAAAGATCTAAGCCGCAATGGCGGATCC-AGTACCTCAA
* * *
41901139 A-AGCATGACGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGT-AA
1 AGA-CATAAAGGGAAAGATCTAAG-CCGCAATGGCGGATCCAGTACC-TCAA
* * * * *
41901189 AGATACA-AAAGGGAAAGGTTTAAGTCGCAATGGC-GAACCTTGTACCTCAA
1 AG--ACATAAAGGGAAAGATCTAAGCCGCAATGGCGGATCC-AGTACCTCAA
* * * * * *
41901239 AGACATGAAGAGAAAGATCTAAGCCGTAACGGTGGATCCAGTACCAT-GA
1 AGACATAAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACC-TCAA
* * *
41901288 AGACATAAAGGGAAAGATCTAAGACCGCAATAGTGGATCCAGTACCGCAA
1 AGACATAAAGGGAAAGATCTAAG-CCGCAATGGCGGATCCAGTACCTCAA
** * * * * *
41901338 AGATACA-AAAGGGATGGGTTTAAGTCGCAATGGC-GAACCTTGTACCTCAA
1 AG--ACATAAAGGGAAAGATCTAAGCCGCAATGGCGGATCC-AGTACCTCAA
*
41901388 AGACATAAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCAT-GA
1 AGACATAAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACC-TCAA
* * * * *
41901437 AGACATAAAGGGAAGGTTCTAAGCCGCAACGGCGGATCCAATACCACAA
1 AGACATAAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCTCAA
* * * * *
41901486 AGACACAAAGGGAAGGGTTTAAGTCGCAATGGCG
1 AGACATAAAGGGAAAGATCTAAGCCGCAATGGCG
41901520 AACCTTATAC
Statistics
Matches: 337, Mismatches: 68, Indels: 52
0.74 0.15 0.11
Matches are distributed among these distances:
47 1 0.00
48 8 0.02
49 174 0.52
50 114 0.34
51 34 0.10
52 5 0.01
53 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.26, T:0.15
Consensus pattern (49 bp):
AGACATAAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCTCAA
Found at i:41901326 original size:149 final size:149
Alignment explanation
Indices: 41901148--41901531 Score: 601
Period size: 149 Copynumber: 2.6 Consensus size: 149
41901138 AAAGCATGAC
* *
41901148 GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGTAAAGATACAAAAGGGAAAGGTTTAAG
1 GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAGGGTTTAAG
* * *
41901213 TCGCAATGGCGAACCTTGTACCTCAAAGACATGAAGAGAAAGATCTAAGCCGTAACGGTGGATCC
66 TCGCAATGGCGAACCTTGTACCTCAAAGACATAAAGAGAAAGATCTAAGCCGCAACGGCGGATCC
41901278 AGTACCATGAAGACATAAA
131 AGTACCATGAAGACATAAA
** * *
41901297 GGGAAAGATCTAAGACCGCAATAGTGGATCCAGTACCGCAAAGATACAAAAGGGATGGGTTTAAG
1 GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAGGGTTTAAG
* *
41901362 TCGCAATGGCGAACCTTGTACCTCAAAGACATAAAGGGAAAGATCTAAGCCGCAATGGCGGATCC
66 TCGCAATGGCGAACCTTGTACCTCAAAGACATAAAGAGAAAGATCTAAGCCGCAACGGCGGATCC
41901427 AGTACCATGAAGACATAAA
131 AGTACCATGAAGACATAAA
* * * * *
41901446 GGGAAGGTTCTAAG-CCGCAACGGCGGATCCAATACCACAAAGACAC-AAAGGGAAGGGTTTAAG
1 GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAGGGTTTAAG
*
41901509 TCGCAATGGCGAACCTTATACCT
66 TCGCAATGGCGAACCTTGTACCT
41901532 TAGAAGCAGA
Statistics
Matches: 214, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
147 38 0.18
148 26 0.12
149 150 0.70
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (149 bp):
GGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAGGGTTTAAG
TCGCAATGGCGAACCTTGTACCTCAAAGACATAAAGAGAAAGATCTAAGCCGCAACGGCGGATCC
AGTACCATGAAGACATAAA
Found at i:41902029 original size:6 final size:6
Alignment explanation
Indices: 41902007--41902089 Score: 57
Period size: 6 Copynumber: 13.8 Consensus size: 6
41901997 TTTAAATTGG
* **
41902007 TTTAAA TTT-AT TCTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTATTTT
1 TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA--AA
**
41902056 TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
41902090 TTAAATGTGA
Statistics
Matches: 59, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
4 2 0.03
5 7 0.12
6 42 0.71
7 4 0.07
8 4 0.07
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:41902040 original size:17 final size:18
Alignment explanation
Indices: 41902007--41902088 Score: 105
Period size: 17 Copynumber: 4.6 Consensus size: 18
41901997 TTTAAATTGG
41902007 TTTAAATTTATTCTTAAA
1 TTTAAATTTATTCTTAAA
41902025 TTTAAATTTA-TCTTAAA
1 TTTAAATTTATTCTTAAA
*
41902042 TTTAAATTTATTTTTTTAAA
1 TTTAAATTTA--TTCTTAAA
**
41902062 TTTAAATTTGCT-TTAAA
1 TTTAAATTTATTCTTAAA
41902079 TTTAAATTTA
1 TTTAAATTTA
41902089 ATTAAATGTG
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
17 31 0.54
18 11 0.19
20 15 0.26
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (18 bp):
TTTAAATTTATTCTTAAA
Found at i:41902068 original size:37 final size:35
Alignment explanation
Indices: 41902007--41902088 Score: 112
Period size: 37 Copynumber: 2.3 Consensus size: 35
41901997 TTTAAATTGG
*
41902007 TTTAAATTTATTCTTAAATTTAAATTT-ATCTTAAA
1 TTTAAATTTATTCTTAAATTTAAATTTGCT-TTAAA
*
41902042 TTTAAATTTATTTTTTTAAATTTAAATTTGCTTTAAA
1 TTTAAATTTA--TTCTTAAATTTAAATTTGCTTTAAA
41902079 TTTAAATTTA
1 TTTAAATTTA
41902089 ATTAAATGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
35 10 0.24
37 31 0.74
38 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (35 bp):
TTTAAATTTATTCTTAAATTTAAATTTGCTTTAAA
Found at i:41904017 original size:29 final size:28
Alignment explanation
Indices: 41903974--41904289 Score: 230
Period size: 29 Copynumber: 10.9 Consensus size: 28
41903964 GAAGGTCCCC
* *
41903974 AAACTTCTCCAAAATTATATTTTTGACCAT
1 AAACTT-TCCAAAATTACATTTTT-ACCCT
*
41904004 AAACTTTTCAAAATTACATTTTTATCCCT
1 AAACTTTCCAAAATTACATTTTTA-CCCT
* * *
41904033 GAACTTTCCAAAATTATA-TTTTACCCC
1 AAACTTTCCAAAATTACATTTTTACCCT
** *
41904060 AAACATTTTAAAAATTACATTTTTACCCC
1 AAAC-TTTCCAAAATTACATTTTTACCCT
* *
41904089 AAACTTTCCAAAATTCCACTTTTGACCCT
1 AAACTTTCCAAAATTACA-TTTTTACCCT
* *
41904118 AAACTTTCCAAAAACTATATTTTTACCCTT
1 AAACTTTCC-AAAATTACATTTTTACCC-T
*
41904148 AAACTTTTCAAAATTACATTTTTACCCCT
1 AAACTTTCCAAAATTACATTTTTA-CCCT
*
41904177 AAAC-TTCCAAAAATTCCATTTTTAACCTCT
1 AAACTTTCC-AAAATTACATTTTT-ACC-CT
**
41904207 -ATTTTTCCAAAAATTATC-TTTTTCACCCT
1 AAACTTTCC-AAAATTA-CATTTTT-ACCCT
* **
41904236 CAAAC-TTCTACAAATTATGTTTTTACCCTT
1 -AAACTTTCCA-AAATTACATTTTTACCC-T
* *
41904266 GAAC-TTCCAAAAATTCCATTTTTA
1 AAACTTTCC-AAAATTACATTTTTA
41904290 TCCTCGATTT
Statistics
Matches: 230, Mismatches: 38, Indels: 37
0.75 0.12 0.12
Matches are distributed among these distances:
27 6 0.03
28 31 0.13
29 129 0.56
30 62 0.27
31 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.02, T:0.40
Consensus pattern (28 bp):
AAACTTTCCAAAATTACATTTTTACCCT
Found at i:41904271 original size:89 final size:89
Alignment explanation
Indices: 41903973--41904338 Score: 303
Period size: 89 Copynumber: 4.2 Consensus size: 89
41903963 CGAAGGTCCC
* * * * * *
41903973 CAAACTTCTCCAAAATTATATTTTTGA-CCATAAACTTTTC-AAAATTACATTTTTATCC-CTGA
1 CAAACTTCTACAAAATTACATTTTT-ACCCCTAAAC-TTCCAAAAATTCCATTTTTAACCTC-GA
** *
41904035 ACTTTCC-AAAATTAT-ATTTTACCC-
63 TTTTTCCAAAAATTATCTTTTTACCCT
* * * *
41904059 CAAACATTTTA-AAAATTACATTTTTACCCC-AAACTTTCC-AAAATTCCACTTTTGACC-CTAA
1 CAAAC-TTCTACAAAATTACATTTTTACCCCTAAAC-TTCCAAAAATTCCATTTTTAACCTC-GA
** * *
41904120 ACTTTCCAAAAACTATATTTTTACCCT
63 TTTTTCCAAAAATTATCTTTTTACCCT
* * *
41904147 TAAACTT-TTCAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCTCTATTT
1 CAAACTTCTACAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCTCGATTT
41904211 TTCCAAAAATTATCTTTTTCACCCT
66 TTCCAAAAATTATCTTTTT-ACCCT
** * * *
41904236 CAAACTTCTAC-AAATTATGTTTTTACCCTTGAACTTCCAAAAATTCCATTTTTATCCTCGATTT
1 CAAACTTCTACAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCTCGATTT
* * *
41904300 TTCTC-AAAATTACCATTTTACCCC
66 TTC-CAAAAATTATCTTTTTACCCT
41904324 CAAACTTC-A-AAAATT
1 CAAACTTCTACAAAATT
41904339 CCAATTTTGA
Statistics
Matches: 235, Mismatches: 32, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
85 33 0.14
86 28 0.12
87 42 0.18
88 55 0.23
89 74 0.31
90 3 0.01
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.40
Consensus pattern (89 bp):
CAAACTTCTACAAAATTACATTTTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCTCGATTT
TTCCAAAAATTATCTTTTTACCCT
Found at i:41904397 original size:60 final size:60
Alignment explanation
Indices: 41904267--41904426 Score: 170
Period size: 60 Copynumber: 2.7 Consensus size: 60
41904257 TTTACCCTTG
* * * *
41904267 AACTTCCAAAAATTCCATTTT-TATCCTCGATTTTTCTC--AAAATTACCATTTTACCCCCA
1 AACTT-CAAAAATTCCATTTTGAACCCT-GAATTTTCCCAAAAAATTACCATTTTACCCCCA
*
41904326 AACTTCAAAAATTCCAATTTTGAA-CCTG-ATTTTCCCCAAAAAATTACCATTTTACCCCCG
1 AACTTCAAAAATTCC-ATTTTGAACCCTGAATTTT-CCCAAAAAATTACCATTTTACCCCCA
* *
41904386 AA-TGTCTAAAATTCCATTTTTAACCCTGAATTTTCCCAAAA
1 AACT-TCAAAAATTCCATTTTGAACCCTGAATTTTCCCAAAA
41904427 TTATCATTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 15
0.81 0.06 0.14
Matches are distributed among these distances:
57 4 0.05
58 13 0.15
59 21 0.24
60 44 0.51
61 5 0.06
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.36
Consensus pattern (60 bp):
AACTTCAAAAATTCCATTTTGAACCCTGAATTTTCCCAAAAAATTACCATTTTACCCCCA
Found at i:41906296 original size:36 final size:37
Alignment explanation
Indices: 41906256--41906325 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 37
41906246 TTTTCAACAT
*
41906256 TTATTTTTTCAATTTATC-AATATTGTTTGGTTTTTG
1 TTATTTTTTCAATTTATCAAATATTGTTTAGTTTTTG
*
41906292 TTATTTTTTCAGTTTATCAAATATTGTTTAGTTT
1 TTATTTTTTCAATTTATCAAATATTGTTTAGTTT
41906326 CGAGTATGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 17 0.55
37 14 0.45
ACGTcount: A:0.21, C:0.06, G:0.10, T:0.63
Consensus pattern (37 bp):
TTATTTTTTCAATTTATCAAATATTGTTTAGTTTTTG
Found at i:41908239 original size:30 final size:29
Alignment explanation
Indices: 41908183--41908743 Score: 480
Period size: 30 Copynumber: 18.9 Consensus size: 29
41908173 CTTAAAAGGT
* * * *
41908183 CCCTTAACTTTTCAAAAATCATATTTTCAT
1 CCCTAAACTTTTCAAAAATTACATTTT-AA
*
41908213 TCCTAAACTTTTCAAAAATTACATTTTAA
1 CCCTAAACTTTTCAAAAATTACATTTTAA
* *
41908242 CCCCAAACTTCTCAAAAATTACATTTTAA
1 CCCTAAACTTTTCAAAAATTACATTTTAA
* *
41908271 CCCCTCAAACTTTCCAAAAATTACATTTTGAC
1 -CCCT-AAACTTTTCAAAAATTACATTTT-AA
** *
41908303 CCCTAAACTTTAAAAAAATTACATTTTGA
1 CCCTAAACTTTTCAAAAATTACATTTTAA
*
41908332 CCTCTAAAC-TTCCTAAAAATTACA-TTTAA
1 CC-CTAAACTTTTC-AAAAATTACATTTTAA
* *
41908361 CCCCAAACTTCTCAAAAATTACATTTTAA
1 CCCTAAACTTTTCAAAAATTACATTTTAA
*
41908390 CCCCTAAACTTCTCAAAAATTACATTTTAA
1 -CCCTAAACTTTTCAAAAATTACATTTTAA
*
41908420 CCCCTAAACTTTCCAAAAATTACATTTTAA
1 -CCCTAAACTTTTCAAAAATTACATTTTAA
* *
41908450 CCCTTAAAC-TTTCTAAAATTACATTTTGA
1 CCC-TAAACTTTTCAAAAATTACATTTTAA
* * *
41908479 CCCATAAACTTCAT-AAAAATTATATTTTGA
1 CCC-TAAACTT-TTCAAAAATTACATTTTAA
*
41908509 CCCTTAAACTTCAT-AAAAATTACATTTTAA
1 CCC-TAAACTT-TTCAAAAATTACATTTTAA
*
41908539 CCCTTTAAACTTTGCAAAAATTACATTTTAA
1 CCC--TAAACTTTTCAAAAATTACATTTTAA
* * * *
41908570 CCTTAAACTTTTCTAAAATTGCATTTTTGA
1 CCCTAAACTTTTCAAAAATTACA-TTTTAA
*
41908600 --CT-AACTTCAT-AAAAATTACATTTTAA
1 CCCTAAACTT-TTCAAAAATTACATTTTAA
*
41908626 CCCTTTAAACTTTGCAAAAATTACATTTTAA
1 CCC--TAAACTTTTCAAAAATTACATTTTAA
* * *
41908657 CCCTAAACTTTTCTAAAATTGCATTTTTGA
1 CCCTAAACTTTTCAAAAATTACA-TTTTAA
* *
41908687 CTCCCAAACTTCCTT--AAAATTACATTTTGA
1 C-CCTAAACTT--TTCAAAAATTACATTTTAA
** *
41908717 CCC-AAACTCATCCAAAATTACCATTTT
1 CCCTAAACTTTTCAAAAATTA-CATTTT
41908744 GCCCCCGAAC
Statistics
Matches: 446, Mismatches: 57, Indels: 57
0.80 0.10 0.10
Matches are distributed among these distances:
26 6 0.01
27 13 0.03
28 30 0.07
29 114 0.26
30 188 0.42
31 92 0.21
32 1 0.00
33 2 0.00
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.37
Consensus pattern (29 bp):
CCCTAAACTTTTCAAAAATTACATTTTAA
Found at i:41908438 original size:119 final size:118
Alignment explanation
Indices: 41908227--41908743 Score: 553
Period size: 119 Copynumber: 4.4 Consensus size: 118
41908217 AAACTTTTCA
41908227 AAAATTACATTTTAACCCCAAACTTC-TCAAAAATTACATTTTAACCCCTCAAACTTTCCAAAAA
1 AAAATTACATTTTAACCCCAAACTTCATCAAAAATTACATTTTAACCCCT-AAACTTTCCAAAAA
* * *
41908291 TTACATTTTGACCCCTAAACTTTAAAAAAATTACATTTTGACCTCTAAACTTCCT
65 TTACATTTTAACCCCTAAACTTT-CAAAAATTACATTTTAACCTCTAAACTTCCT
41908346 AAAAATTACA-TTTAACCCCAAACTTC-TCAAAAATTACATTTTAACCCCTAAAC-TTCTCAAAA
1 -AAAATTACATTTTAACCCCAAACTTCATCAAAAATTACATTTTAACCCCTAAACTTTC-CAAAA
*
41908408 ATTACATTTTAACCCCTAAACTTTCCAAAAATTACATTTTAACC-CTTAAACTTTCT
64 ATTACATTTTAACCCCTAAACTTT-CAAAAATTACATTTTAACCTC-TAAACTTCCT
* * * * * *
41908464 AAAATTACATTTTGACCCATAAACTTCAT-AAAAATTATATTTTGACCCTTAAAC-TTCATAAAA
1 AAAATTACATTTTAACCC-CAAACTTCATCAAAAATTACATTTTAACCCCTAAACTTTC-CAAAA
* *
41908527 ATTACATTTTAACCCTTTAAACTTTGCAAAAATTACATTTTAACCT-TAAACTTTTCT
64 ATTACATTTTAACCC-CTAAACTTT-CAAAAATTACATTTTAACCTCTAAAC-TTCCT
* * * * *
41908584 AAAATTGCATTTTTGA---CTAACTTCAT-AAAAATTACATTTTAACCCTTTAAACTTTGCAAAA
1 AAAATTACA-TTTTAACCCCAAACTTCATCAAAAATTACATTTTAACCC-CTAAACTTTCCAAAA
* * * *
41908645 ATTACATTTTAA-CCCTAAACTTTTCTAAAATTGCATTTTTGA-CTCCCAAACTTCCTT
64 ATTACATTTTAACCCCTAAAC-TTTCAAAAATTACA-TTTTAACCT-CTAAACTTCC-T
* *
41908702 AAAATTACATTTTGA-CCCAAAC-TCATCCAAAATTACCATTTT
1 AAAATTACATTTTAACCCCAAACTTCATCAAAAATTA-CATTTT
41908744 GCCCCCGAAC
Statistics
Matches: 347, Mismatches: 30, Indels: 40
0.83 0.07 0.10
Matches are distributed among these distances:
116 16 0.05
117 57 0.16
118 104 0.30
119 108 0.31
120 56 0.16
121 6 0.02
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.36
Consensus pattern (118 bp):
AAAATTACATTTTAACCCCAAACTTCATCAAAAATTACATTTTAACCCCTAAACTTTCCAAAAAT
TACATTTTAACCCCTAAACTTTCAAAAATTACATTTTAACCTCTAAACTTCCT
Found at i:41908771 original size:118 final size:116
Alignment explanation
Indices: 41908227--41908772 Score: 556
Period size: 118 Copynumber: 4.6 Consensus size: 116
41908217 AAACTTTTCA
*
41908227 AAAATTACATTTTAACCCCAAACTTC-TCAAAAATTACATTTTAACCCCTCAAACTTTCCAAAAA
1 AAAATTACATTTTGA-CCCAAACTTCATCAAAAATTACATTTTAACCCCT-AAAC-TTCCAAAAA
* * * *
41908291 TTACATTTTGACCCCTAAACTTTAAAAAAATTACATTTTGACCTCTAAACTTCCTA
63 TTACATTTT-AACCCTAAACTTTACAAAAATTACATTTTAACC-CTAAACTTCCTT
*
41908347 AAAATTACA-TTTAACCCCAAACTTC-TCAAAAATTACATTTTAACCCCTAAACTTCTCAAAAAT
1 AAAATTACATTTTGA-CCCAAACTTCATCAAAAATTACATTTTAACCCCTAAACTTC-CAAAAAT
* *
41908410 TACATTTTAACCCCTAAACTTTCCAAAAATTACATTTTAACCCTTAAACTTTC-T
64 TACATTTTAA-CCCTAAACTTTACAAAAATTACATTTTAACCC-TAAACTTCCTT
* * * *
41908464 AAAATTACATTTTGACCCATAAACTTCAT-AAAAATTATATTTTGACCCTTAAACTTCATAAAAA
1 AAAATTACATTTTGACCC--AAACTTCATCAAAAATTACATTTTAACCCCTAAACTTC-CAAAAA
* * *
41908528 TTACATTTTAACCCTTTAAACTTTGCAAAAATTACATTTTAACCTTAAACTT-TTCT
63 TTACATTTTAACCC--TAAACTTTACAAAAATTACATTTTAACCCTAAACTTCCT-T
* * * *
41908584 AAAATTGCATTTTTGA--CTAACTTCAT-AAAAATTACATTTTAACCCTTTAAACTTTGCAAAAA
1 AAAATTACA-TTTTGACCCAAACTTCATCAAAAATTACATTTTAACCC-CTAAAC-TTCCAAAAA
* * * * *
41908646 TTACATTTTAACCCTAAACTTTTCTAAAATTGCATTTTTGACTCCCAAACTTCCTT
63 TTACATTTTAACCCTAAACTTTACAAAAATTACA-TTTTAAC-CCTAAACTTCCTT
* * ** *
41908702 AAAATTACATTTTGACCCAAAC-TCATCCAAAATTACCATTTT-GCCCCCGAACATCCAAAAATT
1 AAAATTACATTTTGACCCAAACTTCATCAAAAATTA-CATTTTAACCCCTAAACTTCCAAAAATT
41908765 ACCATTTT
65 A-CATTTT
41908773 GCCCCCAAAT
Statistics
Matches: 367, Mismatches: 37, Indels: 46
0.82 0.08 0.10
Matches are distributed among these distances:
116 17 0.05
117 64 0.17
118 116 0.32
119 112 0.31
120 52 0.14
121 6 0.02
ACGTcount: A:0.39, C:0.23, G:0.02, T:0.36
Consensus pattern (116 bp):
AAAATTACATTTTGACCCAAACTTCATCAAAAATTACATTTTAACCCCTAAACTTCCAAAAATTA
CATTTTAACCCTAAACTTTACAAAAATTACATTTTAACCCTAAACTTCCTT
Found at i:41910236 original size:17 final size:18
Alignment explanation
Indices: 41910214--41910255 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
41910204 CTTCATATTA
* *
41910214 ATTTTTATAAA-AATTTT
1 ATTTTTATAAATAAATAT
*
41910231 ATTTTTTTAAATAAATAT
1 ATTTTTATAAATAAATAT
41910249 ATTTTTA
1 ATTTTTA
41910256 AATTTTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTATAAATAAATAT
Found at i:41910449 original size:7 final size:7
Alignment explanation
Indices: 41910432--41910463 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
41910422 AAATTAACAA
41910432 AAAAATAT
1 AAAAAT-T
41910440 AAAAATT
1 AAAAATT
41910447 AAAAATT
1 AAAAATT
41910454 AAAAATT
1 AAAAATT
41910461 AAA
1 AAA
41910464 TTTAACATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (7 bp):
AAAAATT
Found at i:41911596 original size:27 final size:25
Alignment explanation
Indices: 41911549--41911603 Score: 58
Period size: 27 Copynumber: 2.1 Consensus size: 25
41911539 TTTTACTTTG
* *
41911549 TTTTCTTCTTTATTTTGCTTTGTTTCT
1 TTTTCTTCTTTATCTTCCTTT-TTT-T
41911576 TTTTCTTCTTCT-TCTTCCTTTTTTT
1 TTTTCTTCTT-TATCTTCCTTTTTTT
41911601 TTT
1 TTT
41911604 CTCTATTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 4 0.16
26 3 0.12
27 17 0.68
28 1 0.04
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.76
Consensus pattern (25 bp):
TTTTCTTCTTTATCTTCCTTTTTTT
Found at i:41915487 original size:6 final size:6
Alignment explanation
Indices: 41915466--41915526 Score: 54
Period size: 6 Copynumber: 10.0 Consensus size: 6
41915456 TTAAATTGAT
** *
41915466 TTTAAA TTTATT TTTAAA TTTAAA TTTATCTAT TTTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA---AA TTTAAA TTTAAA TTTAAA
41915516 -TTAAA TTTAAA
1 TTTAAA TTTAAA
41915527 ATTATATTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
4 2 0.05
5 4 0.09
6 33 0.75
9 5 0.11
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:41915501 original size:33 final size:35
Alignment explanation
Indices: 41915464--41915531 Score: 95
Period size: 37 Copynumber: 1.9 Consensus size: 35
41915454 GTTTAAATTG
*
41915464 ATTTTAAATTT-ATTT-TTAAATTTAAATTTATCT
1 ATTTTAAATTTAATTTATTAAATTTAAAATTATCT
41915497 ATTTTAAATTTAAATTTAATTAAATTTAAAATTAT
1 ATTTTAAATTT-AATTT-ATTAAATTTAAAATTAT
41915532 ATTAAACTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 11 0.37
35 4 0.13
37 15 0.50
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (35 bp):
ATTTTAAATTTAATTTATTAAATTTAAAATTATCT
Found at i:41915503 original size:21 final size:18
Alignment explanation
Indices: 41915466--41915531 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 18
41915456 TTAAATTGAT
41915466 TTTAAATTTATTTTTAAA
1 TTTAAATTTATTTTTAAA
41915484 TTTAAATTTATCTATTTTAAA
1 TTTAAATTTA--T-TTTTAAA
*
41915505 TTTAAATTTA--ATTAAA
1 TTTAAATTTATTTTTAAA
*
41915521 TTTAAAATTAT
1 TTTAAATTTAT
41915532 ATTAAACTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
16 14 0.33
18 10 0.24
20 1 0.02
21 17 0.40
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAATTTATTTTTAAA
Found at i:41915521 original size:16 final size:17
Alignment explanation
Indices: 41915500--41915542 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
41915490 TTTATCTATT
*
41915500 TTAAATTTAAATTTA-A
1 TTAAATTTAAAATTATA
41915516 TTAAATTTAAAATTATA
1 TTAAATTTAAAATTATA
*
41915533 TTAAACTTAA
1 TTAAATTTAA
41915543 TTAAATGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAATTTAAAATTATA
Found at i:41916344 original size:20 final size:20
Alignment explanation
Indices: 41916319--41916360 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
41916309 TAAAAACGGT
41916319 AATAATAATAAATATTAATA
1 AATAATAATAAATATTAATA
* * *
41916339 AATAATATTAATTTTTAATA
1 AATAATAATAAATATTAATA
41916359 AA
1 AA
41916361 AAAGAAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAATAATAAATATTAATA
Found at i:41917474 original size:30 final size:29
Alignment explanation
Indices: 41917430--41917700 Score: 193
Period size: 29 Copynumber: 9.3 Consensus size: 29
41917420 AAAAATCACA
41917430 TTACCCCTAAACTTCCAAAAATTCTATTT
1 TTACCCCTAAACTTCCAAAAATTCTATTT
*
41917459 TTACCCCCAAAACTTCCAAAAATTCCT-TTT
1 TTA-CCCCTAAACTTCCAAAAATT-CTATTT
*
41917489 TTA-CCCTCGAACTTCCAAAAATTTCT-TTT
1 TTACCCCT-AAACTTCCAAAAA-TTCTATTT
* * * *
41917518 TTACCCTTGAACTTCTAAAAATTCCATTT
1 TTACCCCTAAACTTCCAAAAATTCTATTT
* *
41917547 TTGACCCCGAAACTCCCAAAAATTAC-A-TT
1 TT-ACCCCTAAACTTCCAAAAATT-CTATTT
*
41917576 TTACCCCTGAACTTCCAAAAATT-TCATTT
1 TTACCCCTAAACTTCCAAAAATTCT-ATTT
* *
41917605 TTGA--CCTGAACTTCAAAAAATTAC-ATTT
1 TT-ACCCCTAAACTTCCAAAAATT-CTATTT
* * *
41917633 TTACCCCCGAAA-TTCTAAAAATTCCATTT
1 TTA-CCCCTAAACTTCCAAAAATTCTATTT
* * * * **
41917662 TTGACCTCGAAACTTCTAAAAATTATCGTT
1 TT-ACCCCTAAACTTCCAAAAATTCTATTT
41917692 TTACCCCTA
1 TTACCCCTA
41917701 GATGTCTAAA
Statistics
Matches: 197, Mismatches: 25, Indels: 40
0.75 0.10 0.15
Matches are distributed among these distances:
27 1 0.01
28 49 0.25
29 76 0.39
30 68 0.35
31 3 0.02
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (29 bp):
TTACCCCTAAACTTCCAAAAATTCTATTT
Found at i:41917479 original size:29 final size:28
Alignment explanation
Indices: 41917430--41917685 Score: 160
Period size: 30 Copynumber: 8.8 Consensus size: 28
41917420 AAAAATCACA
*
41917430 TTACCCCTAAACTTCCAAAAATTCTATTT
1 TTACCCCCAAACTTCCAAAAATTCT-TTT
41917459 TTACCCCCAAAACTTCCAAAAATTCCTTTT
1 TTACCCCC-AAACTTCCAAAAATT-CTTTT
* *
41917489 TTACCCTCGAACTTCCAAAAATTTCTTTT
1 TTACCCCCAAACTTCCAAAAA-TTCTTTT
*** *
41917518 TTACCCTTGAACTTCTAAAAATTCCATTTT
1 TTACCCCCAAACTTCCAAAAATT-C-TTTT
* * * *
41917548 TGACCCCGAAACTCCCAAAAATTAC-ATT
1 TTACCCCCAAACTTCCAAAAATT-CTTTT
**
41917576 TTACCCCTGAACTTCCAAAAATTTCATTTT
1 TTACCCCCAAACTTCCAAAAA-TTC-TTTT
* ** * *
41917606 TGA--CCTGAACTTCAAAAAATTACATTT
1 TTACCCCCAAACTTCCAAAAATT-CTTTT
*
41917633 TTACCCCCGAAA-TTCTAAAAATTCCATTTT
1 TTACCCCC-AAACTTCCAAAAATT-C-TTTT
* * * *
41917663 TGACCTCGAAACTTCTAAAAATT
1 TTACCCCCAAACTTCCAAAAATT
41917686 ATCGTTTTAC
Statistics
Matches: 183, Mismatches: 30, Indels: 27
0.76 0.12 0.11
Matches are distributed among these distances:
27 7 0.04
28 38 0.21
29 62 0.34
30 74 0.40
31 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.36
Consensus pattern (28 bp):
TTACCCCCAAACTTCCAAAAATTCTTTT
Found at i:41917548 original size:58 final size:59
Alignment explanation
Indices: 41917438--41917699 Score: 286
Period size: 59 Copynumber: 4.5 Consensus size: 59
41917428 CATTACCCCT
** *
41917438 AAACTTCCAAAAATT-CTATTTTTACCCCCAAAACTTCCAAAAATTCC-TTTTTTACCCTCG
1 AAACTTCCAAAAATTACT-TTTTTA-CCCCTGAACTTCCAAAAATTCCATTTTTGA-CCTCG
* * * *
41917498 -AACTTCCAAAAATTTCTTTTTTACCCTTGAACTTCTAAAAATTCCATTTTTGACCCCG
1 AAACTTCCAAAAATTACTTTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCTCG
* * *
41917556 AAACTCCCAAAAATTAC-ATTTTACCCCTGAACTTCCAAAAATTTCATTTTTGACCT-G
1 AAACTTCCAAAAATTACTTTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCTCG
* * * * *
41917613 -AACTTCAAAAAATTACATTTTTACCCCCGAAATTCTAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTACTTTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCTCG
* *
41917671 AAACTTCTAAAAATTA-TCGTTTTACCCCT
1 AAACTTCCAAAAATTACT-TTTTTACCCCT
41917700 AGATGTCTAA
Statistics
Matches: 171, Mismatches: 24, Indels: 15
0.81 0.11 0.07
Matches are distributed among these distances:
56 14 0.08
57 35 0.20
58 57 0.33
59 63 0.37
60 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (59 bp):
AAACTTCCAAAAATTACTTTTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCTCG
Found at i:41917721 original size:115 final size:115
Alignment explanation
Indices: 41917432--41917699 Score: 315
Period size: 115 Copynumber: 2.3 Consensus size: 115
41917422 AAATCACATT
* * ** * *
41917432 ACCCCTAAACTTCCAAAAATT-CTATTTTTACCCCCAAAACTTCCAAAAAT-TCCTTTTTTACCC
1 ACCCCGAAACTCCCAAAAATTAC-A-TTTTA-CCCCTGAACTTCCAAAAATGTCATTTTTGA-CC
* * * ** *
41917495 TCGAACTTCCAAAAATTTCTTTTTTACCCTTGAACTTCTAAAAATTCCATTTTTG
62 T-GAACTTCAAAAAATTACATTTTTACCCCCGAAATTCTAAAAATTCCATTTTTG
*
41917550 ACCCCGAAACTCCCAAAAATTACATTTTACCCCTGAACTTCCAAAAATTTCATTTTTGACCTGAA
1 ACCCCGAAACTCCCAAAAATTACATTTTACCCCTGAACTTCCAAAAATGTCATTTTTGACCTGAA
41917615 CTTCAAAAAATTACATTTTTACCCCCGAAATTCTAAAAATTCCATTTTTG
66 CTTCAAAAAATTACATTTTTACCCCCGAAATTCTAAAAATTCCATTTTTG
* * * *
41917665 ACCTCGAAACTTCTAAAAATTATCGTTTTACCCCT
1 ACCCCGAAACTCCCAAAAATTA-CATTTTACCCCT
41917700 AGATGTCTAA
Statistics
Matches: 131, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
115 66 0.50
116 31 0.24
117 13 0.10
118 20 0.15
119 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.35
Consensus pattern (115 bp):
ACCCCGAAACTCCCAAAAATTACATTTTACCCCTGAACTTCCAAAAATGTCATTTTTGACCTGAA
CTTCAAAAAATTACATTTTTACCCCCGAAATTCTAAAAATTCCATTTTTG
Found at i:41922139 original size:8 final size:8
Alignment explanation
Indices: 41922126--41922156 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
41922116 TGTATTGGTT
41922126 AAAAAAAC
1 AAAAAAAC
41922134 AAAAAAAC
1 AAAAAAAC
41922142 AAAAAAAC
1 AAAAAAAC
41922150 AAAAAAA
1 AAAAAAA
41922157 GATGAGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:41924416 original size:49 final size:49
Alignment explanation
Indices: 41924339--41924434 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 49
41924329 TCAGAGACAT
* * *
41924339 GAAGGGAAAGATCTAAGCCGCGACGACAGACCCAGTACTACGAAGATAG
1 GAAGAGAAAGATCTAAGCCACGACGACAGACCCAGTACCACGAAGATAG
* * *
41924388 GAAGAGAAAGATCTAAGCCACGATGACAGATCTAGTACCACGAAGAT
1 GAAGAGAAAGATCTAAGCCACGACGACAGACCCAGTACCACGAAGAT
41924435 TTGAAGGTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.41, C:0.21, G:0.26, T:0.12
Consensus pattern (49 bp):
GAAGAGAAAGATCTAAGCCACGACGACAGACCCAGTACCACGAAGATAG
Found at i:41925343 original size:207 final size:207
Alignment explanation
Indices: 41924810--41926653 Score: 2896
Period size: 207 Copynumber: 8.9 Consensus size: 207
41924800 CCAACTTAGG
* * * * * *
41924810 GCTCGATGTGAGCAAATCTTCGAA-CTCCAACTTCCTGATAAGATATTGAGAAGCAGGTTGAAGC
1 GCTCGATGAGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
* * *
41924874 AATAAAATAGTTAGCTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCATCCTGATGAGAT
66 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
** * *
41924939 ACAGAGAAGCGGATTGAAACAAACGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACGA
131 ACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
41925004 AATCAAACCCAC
196 AATCAAACCCAC
* * * * *
41925016 GTTCAATGCGAGCAAATCTTGGAA-CCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
1 GCTCGATGAGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
*
41925080 AATAAAATGATTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
66 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
* * * *
41925145 AGAGAGAAACGGATTGAAACAAGTGATACGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCA
131 ACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
41925210 AATCAAACCCAC
196 AATCAAACCCAC
* * * *
41925222 GCTCGATGTGAGCAAATCTTCAAACCCCCAGCTTCCTAATGAGATACTGAGAAGCAAGTCGAAGC
1 GCTCGATGAGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
* * *
41925287 AATAAAATGGTTAGCTTCCTGATGAGATATTGAGAAGGGGACCAAATTCATCTTCCTGATGAGAT
66 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
* * *
41925352 ACAGAGAAGCAGATTGAAACAAGTGATGCGATTATCTTCCTGATGAGATACTGAGAAGAAGACCA
131 ACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
*
41925417 AATCAAACCCAT
196 AATCAAACCCAC
* *
41925429 GCTCGATGAGAGCAAATCTTCGAACCCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCGAAGC
1 GCTCGATGAGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
*
41925494 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGATCAAATTCGTCTTCCTGATGAGAT
66 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
* *** *
41925559 ACAGAGAAGCAGATTGAAACAAGTGATATAGTCATCTTCCTGATGAGATACTGAGAAGAAGAACA
131 ACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
*
41925624 AATTAAACCCAC
196 AATCAAACCCAC
* * * *
41925636 GCTCGATGAGAGCAAATTTTCGAA-CCCTAACTTCCTGATGAGATACTGAGAAGCAGGTTGAAGC
1 GCTCGATGAGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
* *
41925700 ----AAATAGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
66 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
* * ** *
41925761 ACAGTGAAGCAGATTGAAACAAGTGATGCGGTCATCTTTTTGATGAGATACTGAAAAGAAGACCA
131 ACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
41925826 AATTC-AACCCAC
196 AA-TCAAACCCAC
* *
41925838 GCTCGATGTGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGC
1 GCTCGATGAGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
*
41925903 AATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
66 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
* *
41925968 ACAGAGAAGCAGATTGAAATAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
131 ACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
*
41926033 AATCAAACCCAT
196 AATCAAACCCAC
*
41926045 GCTCGATGAGAGCAAATCTTCGAACCCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGC
1 GCTCGATGAGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
*
41926110 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGATCAAATTCGTCTTCCTGATGAGAT
66 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
*
41926175 ACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCA
131 ACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
41926240 AATCAAACCCAC
196 AATCAAACCCAC
*
41926252 GCTCGATGTGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
1 GCTCGATGAGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
*
41926317 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGATCAAATTCGTCTTCCTGATGAGAT
66 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
*
41926382 ACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCA
131 ACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
41926447 AATCAAACCCAC
196 AATCAAACCCAC
* * * * * *
41926459 ACTCGATGAGAGCAAATTTTCGAA-CCCGAACTTCCTGATGAGATACTAAGAAGGAGGTCGAAGC
1 GCTCGATGAGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
* * * * *
41926523 AATAAAATAGTTAGCTTCCTAATGAGATACTGAGAAGTGAACTAAATTTGTCTTCCTGATGAGAT
66 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
* * *
41926588 ATAGAGAAGCGGATTGAAACAAGTAATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCA
131 ACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
41926653 A
196 A
41926654 GCCAATGAAA
Statistics
Matches: 1513, Mismatches: 117, Indels: 16
0.92 0.07 0.01
Matches are distributed among these distances:
202 146 0.10
203 39 0.03
206 399 0.26
207 929 0.61
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (207 bp):
GCTCGATGAGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
ACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
AATCAAACCCAC
Found at i:41925626 original size:86 final size:85
Alignment explanation
Indices: 41925460--41925627 Score: 212
Period size: 86 Copynumber: 2.0 Consensus size: 85
41925450 GAACCCCCAA
* * * *
41925460 CTTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACT
1 CTTCCTGATGAGATACTAAGAAGCAGATCGAAACAATAAAATAGTCAGCTTCCTGATGAGATACT
** *
41925525 GAGAAGTGGATCAAATTCGT
66 GAGAAGAAGAACAAATTCGT
* * * *
41925545 CTTCCTGATGAGATAC-AGAGAAGCAGATTGAAACAAGTGATATAGTCATCTTCCTGATGAGATA
1 CTTCCTGATGAGATACTA-AGAAGCAGATCGAAACAA-TAAAATAGTCAGCTTCCTGATGAGATA
41925609 CTGAGAAGAAGAACAAATT
64 CTGAGAAGAAGAACAAATT
41925628 AAACCCACGC
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
84 1 0.01
85 31 0.44
86 38 0.54
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (85 bp):
CTTCCTGATGAGATACTAAGAAGCAGATCGAAACAATAAAATAGTCAGCTTCCTGATGAGATACT
GAGAAGAAGAACAAATTCGT
Found at i:41926013 original size:616 final size:617
Alignment explanation
Indices: 41924810--41926653 Score: 2960
Period size: 616 Copynumber: 3.0 Consensus size: 617
41924800 CCAACTTAGG
* * * * *
41924810 GCTCGATGTGAGCAAATCTTCGAA-CTCCAACTTCCTGATAAGATATTGAGAAGCAGGTTGAAGC
1 GCTCGATGAGAGCAAATCTTCGAACCCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
* * * *
41924874 AATAAAATAGTTAGCTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCATCCTGATGAGAT
66 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGATCAAATTCGTCTTCCTGATGAGAT
**
41924939 ACAGAGAAGCGGATTGAAACAAACGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAG-ACG
131 ACAGAGAAGCGGATTGAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGAAC-
* * * *
41925003 AAATCAAACCCACGTTCAATGCGAGCAAATCTTGGAACCCTAGCTTCCTGATGAGATACTGAGAA
195 AAATCAAACCCACGCTCGATGAGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAA
*
41925068 GCAGGTCGAAGCAATAAAATGATTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCT
260 GCAGGTCGAAGCAA-AATA-G-TTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCT
* * *
41925133 TCCTGATGAGATAGAGAGAAACGGATTGAAACAAGTGATACGGTCATCTTCTTGATGAGATACTG
322 TCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCTTGATGAGATACTG
* *
41925198 AGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCAAACCCCCAGCTTCCTAATG
387 AGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCCAGCTTCCTGATG
* * *
41925263 AGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATATTGAGAAGGGGA
452 AGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGA
* * *
41925328 CCAAATTCATCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTGATGCGATTATCTTCCT
517 CCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTGATGCGGTCATCTTCCT
41925393 GATGAGATACTGAGAAGAAGACCAAATCAAACCCAT
582 GATGAGATACTGAGAAGAAGACCAAATCAAACCCAT
*
41925429 GCTCGATGAGAGCAAATCTTCGAACCCCCAACTTCCTGATGAGATACTAAGAAGCAGGTCGAAGC
1 GCTCGATGAGAGCAAATCTTCGAACCCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
41925494 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGATCAAATTCGTCTTCCTGATGAGAT
66 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGATCAAATTCGTCTTCCTGATGAGAT
* **
41925559 ACAGAGAAGCAGATTGAAACAAGTGATATAGTCATCTTCCTGATGAGATACTGAGAAGAAGAACA
131 ACAGAGAAGCGGATTGAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGAACA
* * *
41925624 AATTAAACCCACGCTCGATGAGAGCAAATTTTCGAACCCTAACTTCCTGATGAGATACTGAGAAG
196 AATCAAACCCACGCTCGATGAGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAG
* *
41925689 CAGGTTGAAGC-AAATAGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCT
261 CAGGTCGAAGCAAAATAGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCT
* * * *
41925753 GATGAGATACAGTGAAGCAGATTGAAACAAGTGATGCGGTCATCTTTTTGATGAGATACTGAAAA
326 GATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCTTGATGAGATACTGAGAA
41925818 GAAGACCAAATTC-AACCCACGCTCGATGTGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGA
391 GAAGACCAAA-TCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGA
* *
41925882 TACTGAGAAGCAGGTTGAAGCAATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCA
455 TACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCA
*
41925947 AATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAATAAGTGATGCGGTCATCTTCCTGAT
520 AATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTGATGCGGTCATCTTCCTGAT
41926012 GAGATACTGAGAAGAAGACCAAATCAAACCCAT
585 GAGATACTGAGAAGAAGACCAAATCAAACCCAT
* *
41926045 GCTCGATGAGAGCAAATCTTCGAACCCCCAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAGC
1 GCTCGATGAGAGCAAATCTTCGAACCCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
41926110 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGATCAAATTCGTCTTCCTGATGAGAT
66 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGATCAAATTCGTCTTCCTGATGAGAT
* * *
41926175 ACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATATTGAGAAGAAGACCA
131 ACAGAGAAGCGGATTGAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGAACA
* *
41926240 AATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGATACTGAGAA
196 AATCAAACCCACGCTCGATGAGAGCAAATCTTCGAA-CCCTAGCTTCCTGATGAGATACTGAGAA
* *
41926305 GCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGATCAAATTCGTCT
260 GCAGGTCGAAGC---AAAATAGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCT
41926370 TCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCTTGATGAGATACTG
322 TCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCTTGATGAGATACTG
* * * * *
41926435 AGAAGAAGACCAAATCAAACCCACACTCGATGAGAGCAAATTTTCGAA-CCCGAACTTCCTGATG
387 AGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCCAGCTTCCTGATG
* * * * *
41926499 AGATACTAAGAAGGAGGTCGAAGCAATAAAATAGTTAGCTTCCTAATGAGATACTGAGAAGTGAA
452 AGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGA
* * * * *
41926564 CTAAATTTGTCTTCCTGATGAGATATAGAGAAGCGGATTGAAACAAGTAATGCGGTCATCTTCCT
517 CCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTGATGCGGTCATCTTCCT
*
41926629 GATGAGATACTGAGAAGAAGGCCAA
582 GATGAGATACTGAGAAGAAGACCAA
41926654 GCCAATGAAA
Statistics
Matches: 1132, Mismatches: 84, Indels: 17
0.92 0.07 0.01
Matches are distributed among these distances:
616 536 0.47
617 40 0.04
618 3 0.00
619 24 0.02
620 378 0.33
621 151 0.13
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (617 bp):
GCTCGATGAGAGCAAATCTTCGAACCCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGATCAAATTCGTCTTCCTGATGAGAT
ACAGAGAAGCGGATTGAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGAACA
AATCAAACCCACGCTCGATGAGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGATACTGAGAAG
CAGGTCGAAGCAAAATAGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCT
GATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCTTGATGAGATACTGAGAA
GAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGAT
ACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAA
ATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTGATGCGGTCATCTTCCTGATG
AGATACTGAGAAGAAGACCAAATCAAACCCAT
Found at i:41926466 original size:823 final size:822
Alignment explanation
Indices: 41924811--41926653 Score: 2997
Period size: 823 Copynumber: 2.2 Consensus size: 822
41924801 CAACTTAGGG
* * * *
41924811 CTCGATGTGAGCAAATCTTCGAACTCCAACTTCCTGATAAGATATTGAGAAGCAGGTTGAAGCAA
1 CTCGATGAGAGCAAATTTTCGAAC-CCAACTTCCTGATGAGATACTGAGAAGCAGGTTGAAGC--
* *
41924876 TAAAATAGTTAGCTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCATCCTGATGAGATAC
63 -AAAATAGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
** * *
41924941 AGAGAAGCGGATTGAAACAAACGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACGAAA
127 AGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
* * *
41925006 TCAAACCCACGTTCAATGCGAGCAAATCTTGGAACCCTAGCTTCCTGATGAGATACTGAGAAGCA
192 TCAAACCCACGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA
41925071 GGTCGAAGCAATAAAATGATTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCC
257 GGTCGAAGCAATAAAATGATTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCC
* * *
41925136 TGATGAGATAGAGAGAAACGGATTGAAACAAGTGATACGGTCATCTTCTTGATGAGATACTGAGA
322 TGATGAGATACAGAGAAACAGATTGAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGA
*
41925201 AGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCAAACCCCCAGCTTCCTAATGAGA
387 AGAAGACCAAATCAAACCCACGCTCGATGAGAGCAAATCTTCAAACCCCCAGCTTCCTAATGAGA
*
41925266 TACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATATTGAGAAGGGGACCA
452 TACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGGGGACCA
*
41925331 AATTCATCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTGATGCGATTATCTTCCTGAT
517 AATTCATCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTGATGCGATCATCTTCCTGAT
*
41925396 GAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGATGAGAGCAAATCTTCGAACCCCCAAC
582 GAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGAGAGCAAATCTTCGAACCCCCAAC
41925461 TTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTG
647 TTCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTG
*
41925526 AGAAGTGGATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTGATATAGT
712 AGAAGTGGATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTGATACAGT
* *
41925591 CATCTTCCTGATGAGATACTGAGAAGAAGAACAAATTAAACCCACG
777 CATCTTCCTGATGAGATACTGAGAAGAAGAACAAATCAAACCCACA
41925637 CTCGATGAGAGCAAATTTTCGAACCCTAACTTCCTGATGAGATACTGAGAAGCAGGTTGAAGC-A
1 CTCGATGAGAGCAAATTTTCGAACCC-AACTTCCTGATGAGATACTGAGAAGCAGGTTGAAGCAA
* *
41925701 AATAGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGT
65 AATAGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGA
* ** *
41925766 GAAGCAGATTGAAACAAGTGATGCGGTCATCTTTTTGATGAGATACTGAAAAGAAGACCAAATTC
130 GAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA-TC
* *
41925831 -AACCCACGCTCGATGTGAGCAAATCTTCGAACCCCCAGCTTCCTGATGAGATACTGAGAAGCAG
194 AAACCCACGCTCAATGCGAGCAAATCTTCGAA-CCCCAGCTTCCTGATGAGATACTGAGAAGCAG
* * *
41925895 GTTGAAGCAATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCT
258 GTCGAAGCAATAAAATGATTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCT
* * *
41925960 GATGAGATACAGAGAAGCAGATTGAAATAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAA
323 GATGAGATACAGAGAAACAGATTGAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAA
* *
41926025 GAAGACCAAATCAAACCCATGCTCGATGAGAGCAAATCTTCGAACCCCCAGCTTCCTAATGAGAT
388 GAAGACCAAATCAAACCCACGCTCGATGAGAGCAAATCTTCAAACCCCCAGCTTCCTAATGAGAT
* * *
41926090 ACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGATCAA
453 ACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGGGGACCAA
* * *
41926155 ATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATG
518 ATTCATCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTGATGCGATCATCTTCCTGATG
* * *
41926220 AGATATTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCCAGCT
583 AGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGAGAGCAAATCTTCGAACCCCCAACT
*
41926285 TCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGA
648 TCCTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGA
* * *
41926350 GAAGTGGATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTC
713 GAAGTGGATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTGATACAGTC
* *
41926415 ATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACA
778 ATCTTCCTGATGAGATACTGAGAAGAAGAACAAATCAAACCCACA
* * *
41926460 CTCGATGAGAGCAAATTTTCGAACCCGAACTTCCTGATGAGATACTAAGAAGGAGGTCGAAGCAA
1 CTCGATGAGAGCAAATTTTCGAACCC-AACTTCCTGATGAGATACTGAGAAGCAGGTTGAAGC--
* * * * *
41926525 TAAAATAGTTAGCTTCCTAATGAGATACTGAGAAGTGAACTAAATTTGTCTTCCTGATGAGATAT
63 -AAAATAGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAC
* *
41926590 AGAGAAGCGGATTGAAACAAGTAATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGGCCAA
127 AGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
41926654 GCCAATGAAA
Statistics
Matches: 939, Mismatches: 71, Indels: 13
0.92 0.07 0.01
Matches are distributed among these distances:
822 143 0.15
823 624 0.66
825 2 0.00
826 56 0.06
827 114 0.12
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (822 bp):
CTCGATGAGAGCAAATTTTCGAACCCAACTTCCTGATGAGATACTGAGAAGCAGGTTGAAGCAAA
ATAGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAG
AAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
ACCCACGCTCAATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTC
GAAGCAATAAAATGATTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGAT
GAGATACAGAGAAACAGATTGAAACAAGTGATACGGTCATCTTCCTGATGAGATACTGAGAAGAA
GACCAAATCAAACCCACGCTCGATGAGAGCAAATCTTCAAACCCCCAGCTTCCTAATGAGATACT
GAGAAGCAAGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGGGGACCAAATT
CATCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTGATGCGATCATCTTCCTGATGAGA
TACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGAGAGCAAATCTTCGAACCCCCAACTTCC
TGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAA
GTGGATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAGTGATACAGTCATC
TTCCTGATGAGATACTGAGAAGAAGAACAAATCAAACCCACA
Found at i:41927030 original size:12 final size:12
Alignment explanation
Indices: 41927005--41927037 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41926995 TTAATTGAGG
41927005 TTTAAA-TTAGT
1 TTTAAATTTAGT
*
41927016 TTTAAATTTATT
1 TTTAAATTTAGT
41927028 TTTAAATTTA
1 TTTAAATTTA
41927038 AATTTATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (12 bp):
TTTAAATTTAGT
Found at i:41927037 original size:6 final size:6
Alignment explanation
Indices: 41927016--41927093 Score: 56
Period size: 6 Copynumber: 13.0 Consensus size: 6
41927006 TTAAATTAGT
** * *
41927016 TTTAAA TTTATT TTTAAA TTTAAA TTT--A TCTTGAA TTTAAA TTTATCTAT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA---AA
41927066 TTTAAA TTTAAA TTT-AA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
41927094 ATTGTATTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
4 4 0.07
5 6 0.11
6 40 0.70
7 2 0.04
9 5 0.09
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:41927054 original size:17 final size:16
Alignment explanation
Indices: 41927016--41927075 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 16
41927006 TTAAATTAGT
*
41927016 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-TCTT-AA
41927034 TTTAAATTTATCTTGAA
1 TTTAAATTTATCTT-AA
*
41927051 TTTAAATTTATC-TAT
1 TTTAAATTTATCTTAA
41927066 TTTAAATTTA
1 TTTAAATTTA
41927076 AATTTAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
15 11 0.28
16 1 0.03
17 17 0.44
18 10 0.26
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (16 bp):
TTTAAATTTATCTTAA
Found at i:41927102 original size:17 final size:17
Alignment explanation
Indices: 41927067--41927109 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
41927057 TTTATCTATT
41927067 TTAAATTT-AAATTTAA
1 TTAAATTTAAAATTTAA
41927083 TTAAATTTAAAATTGT-A
1 TTAAATTTAAAATT-TAA
*
41927100 TTAAACTTAA
1 TTAAATTTAA
41927110 TTAAATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 8 0.33
17 15 0.62
18 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
TTAAATTTAAAATTTAA
Found at i:41928987 original size:29 final size:28
Alignment explanation
Indices: 41928937--41929169 Score: 211
Period size: 29 Copynumber: 8.0 Consensus size: 28
41928927 GGAGGTCCCT
* *
41928937 AAACTGTCAAAAAATTACATTTTTACTGCC
1 AAACT-TCCAAAAATTACATTTTTAC-CCC
* *
41928967 GAACTTCCAAAAATTCCATTTTTGACCCC
1 AAACTTCCAAAAATTACATTTTT-ACCCC
*
41928996 GAAACTTCCAAAAATCACATTTTTACCCTC
1 -AAACTTCCAAAAATTACATTTTTACCC-C
41929026 AAAC-TCTCAAAAATTACA-TTTTACCCCC
1 AAACTTC-CAAAAATTACATTTTTA-CCCC
* *
41929054 AAACTTTCAAAAATTCCATTTTTGACCCC
1 AAACTTCCAAAAATTACATTTTT-ACCCC
* *
41929083 AAAACTTCAAAAAATTACATTTTTACCATC
1 -AAACTTCCAAAAATTACATTTTTACC-CC
* * *
41929113 AAAATTCTAAAAATTACATTTTTAACCCTG
1 AAACTTCCAAAAATTACATTTTT-ACCC-C
*
41929143 AAACTTGCAAAAATTACCA-TTTTACCC
1 AAACTTCCAAAAATTA-CATTTTTACCC
41929170 TCGGTTGTCC
Statistics
Matches: 169, Mismatches: 21, Indels: 27
0.78 0.10 0.12
Matches are distributed among these distances:
28 22 0.13
29 76 0.45
30 69 0.41
31 2 0.01
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.32
Consensus pattern (28 bp):
AAACTTCCAAAAATTACATTTTTACCCC
Found at i:41929002 original size:30 final size:29
Alignment explanation
Indices: 41928937--41929169 Score: 217
Period size: 30 Copynumber: 7.9 Consensus size: 29
41928927 GGAGGTCCCT
* *
41928937 AAACTGTCAAAAAATTACATTTTTACTGCCG
1 AAACT-TCCAAAAATTACATTTTTAC-CCCG
*
41928968 -AACTTCCAAAAATTCCATTTTTGACCCCG
1 AAACTTCCAAAAATTACATTTTT-ACCCCG
*
41928997 AAACTTCCAAAAATCACATTTTTACCCTC-
1 AAACTTCCAAAAATTACATTTTTACCC-CG
*
41929026 AAAC-TCTCAAAAATTACA-TTTTACCCCC
1 AAACTTC-CAAAAATTACATTTTTACCCCG
* * *
41929054 AAACTTTCAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTACATTTTT-ACCCCG
* *
41929084 AAACTTCAAAAAATTACATTTTTACCATC-
1 AAACTTCCAAAAATTACATTTTTACC-CCG
* * *
41929113 AAAATTCTAAAAATTACATTTTTAACCCTG
1 AAACTTCCAAAAATTACATTTTT-ACCCCG
*
41929143 AAACTTGCAAAAATTACCA-TTTTACCC
1 AAACTTCCAAAAATTA-CATTTTTACCC
41929170 TCGGTTGTCC
Statistics
Matches: 170, Mismatches: 20, Indels: 26
0.79 0.09 0.12
Matches are distributed among these distances:
27 1 0.01
28 24 0.14
29 70 0.41
30 73 0.43
31 2 0.01
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTTACCCCG
Found at i:41929166 original size:59 final size:56
Alignment explanation
Indices: 41928937--41929169 Score: 206
Period size: 59 Copynumber: 4.0 Consensus size: 56
41928927 GGAGGTCCCT
* *
41928937 AAACTGTCAAAAAATTACATTTTTACTGCC-G-AACTTCCAAAAATTCCATTTTTGACCCC
1 AAACT-TCTAAAAATTACATTTTTAC--CCTGAAACTT-CAAAAATTACATTTTT-ACCCC
* * *
41928996 GAAACTTCCAAAAATCACATTTTTACCCTCAAACTCTCAAAAATTACA-TTTTACCCCC
1 -AAACTTCTAAAAATTACATTTTTACCCTGAAACT-TCAAAAATTACATTTTTA-CCCC
* ** *
41929054 AAACTT-TCAAAAATTCCATTTTTGACCCCAAAACTTCAAAAAATTACATTTTTACCATC
1 AAACTTCT-AAAAATTACATTTTT-ACCCTGAAACTTC-AAAAATTACATTTTTACC-CC
*
41929113 AAAATTCTAAAAATTACATTTTTAACCCTGAAACTTGCAAAAATTACCA-TTTTACCC
1 AAACTTCTAAAAATTACATTTTT-ACCCTGAAACTT-CAAAAATTA-CATTTTTACCC
41929170 TCGGTTGTCC
Statistics
Matches: 145, Mismatches: 16, Indels: 26
0.78 0.09 0.14
Matches are distributed among these distances:
57 24 0.17
58 29 0.20
59 82 0.57
60 10 0.07
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.32
Consensus pattern (56 bp):
AAACTTCTAAAAATTACATTTTTACCCTGAAACTTCAAAAATTACATTTTTACCCC
Found at i:41931482 original size:25 final size:25
Alignment explanation
Indices: 41931423--41931482 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 25
41931413 GTCCAAAATA
41931423 AATCT-CAAAAAAAAATCCACCATG
1 AATCTACAAAAAAAAATCCACCATG
* *
41931447 AATCTAC-AAAAAAACTCCACCGTG
1 AATCTACAAAAAAAAATCCACCATG
*
41931471 AATTTACAAAAA
1 AATCTACAAAAA
41931483 TTAACATTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 26 0.84
25 5 0.16
ACGTcount: A:0.53, C:0.23, G:0.05, T:0.18
Consensus pattern (25 bp):
AATCTACAAAAAAAAATCCACCATG
Found at i:41931916 original size:24 final size:24
Alignment explanation
Indices: 41931889--41931940 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
41931879 TAAATCTCAA
41931889 AAAAAAAATCAACCATGAATCTAC
1 AAAAAAAATCAACCATGAATCTAC
* * * *
41931913 AAAAAAACTCTACCGTGAATTTAC
1 AAAAAAAATCAACCATGAATCTAC
41931937 AAAA
1 AAAA
41931941 TTAACATTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.19, G:0.06, T:0.19
Consensus pattern (24 bp):
AAAAAAAATCAACCATGAATCTAC
Found at i:41931943 original size:458 final size:458
Alignment explanation
Indices: 41931279--41932204 Score: 1683
Period size: 458 Copynumber: 2.0 Consensus size: 458
41931269 TCTGATTATG
* *
41931279 AATGAGATATGTTGAATGACATATTTGATCATGCTTGCTCAAAAATTACTCCTTTTACCACATGC
1 AATGA-ATATGTGGAATGACATATTTGATCATGCTTGCTCAAAAACTACTCCTTTTACCACATGC
*
41931344 GCTCAAATCTAATAGGGCTGTCAAGATATTAGTCGCCTCAATCCTCCCATTTTCACTTTCACCTC
65 GCTCAAATCTAATAGGGCTATCAAGATATTAGTCGCCTCAATCCTCCCATTTTCACTTTCACCTC
* *
41931409 CAAAGTCCAAAATAAATCTCAAAAAAAAATCCACCATGAATCTACAAAAAAACTCCACCGTGAAT
130 CAAAATCCAAAATAAATCTCAAAAAAAAATCAACCATGAATCTACAAAAAAACTCCACCGTGAAT
*
41931474 TTACAAAAATTAACATTGCCACGAGAAATTTTCAATCATGCCCATTCATCCTTAAATATTTATGT
195 TTACAAAAATTAACATTGCCACGAGAAATTTTCAATCATGCCCATTCATCCATAAATATTTATGT
41931539 ACTCTTAATTTATTTTCAATTTACTTGTGTAAAATGATTTCATTGCAACTTTATATTAATTGAAA
260 ACTCTTAATTTATTTTCAATTTACTTGTGTAAAATGATTTCATTGCAACTTTATATTAATTGAAA
*
41931604 TATGATACTTGACAAATTTATTCAAAGTGTGACATAATTATCACTAATTTACTTAGTAAGAACAT
325 TATGATACTTGACAAATTTATTCAAAGTGTGACATAATTATCACTAATTTACTTAGTAAGAAAAT
41931669 GACATAATTATCACTAAAAATATAGCTTACAATTATATTGATACACTATAAATATTTATCAATTT
390 GACATAATTATCACTAAAAATATAGCTTACAATTATATTGATACACTATAAATATTTATCAATTT
41931734 TCAT
455 TCAT
41931738 AATGAATATGTGGAATGACATATTTGATCATGCTTGCTCAAAAACTACTCCTTTTACCACATGCG
1 AATGAATATGTGGAATGACATATTTGATCATGCTTGCTCAAAAACTACTCCTTTTACCACATGCG
* * *
41931803 CTTAAATCTAATGGGGCTATCAAGATATTAGTCGCCTCAATCCTCCCATTTTCATTTTCACCTCC
66 CTCAAATCTAATAGGGCTATCAAGATATTAGTCGCCTCAATCCTCCCATTTTCACTTTCACCTCC
* *
41931868 AAAATCCAAAGTAAATCTCAAAAAAAAAATCAACCATGAATCTACAAAAAAACTCTACCGTGAAT
131 AAAATCCAAAATAAATCTC-AAAAAAAAATCAACCATGAATCTACAAAAAAACTCCACCGTGAAT
*
41931933 TTAC-AAAATTAACATTGCTACGAGAAATTTTCAATCATGCCCATTCATCCATAAATATTTATGT
195 TTACAAAAATTAACATTGCCACGAGAAATTTTCAATCATGCCCATTCATCCATAAATATTTATGT
41931997 ACTCTTAATTTATTTTCAATTTACTTGTGTAAAATGATTTCATTGCAACTTTATATTAATTGAAA
260 ACTCTTAATTTATTTTCAATTTACTTGTGTAAAATGATTTCATTGCAACTTTATATTAATTGAAA
*
41932062 TATGATACTTGACAAATTTATTCAGAGTGTGACATAATTATCACTAATTTACTTAGTAAGAAAAT
325 TATGATACTTGACAAATTTATTCAAAGTGTGACATAATTATCACTAATTTACTTAGTAAGAAAAT
*
41932127 GACATAATTATCAGTAAAAATATAGCTTACAATTATATTGATACACTATAAATATTTATCAATTT
390 GACATAATTATCACTAAAAATATAGCTTACAATTATATTGATACACTATAAATATTTATCAATTT
41932192 TCAT
455 TCAT
*
41932196 AATGGATAT
1 AATGAATAT
41932205 TTTTGAAAAT
Statistics
Matches: 450, Mismatches: 16, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
458 398 0.88
459 52 0.12
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (458 bp):
AATGAATATGTGGAATGACATATTTGATCATGCTTGCTCAAAAACTACTCCTTTTACCACATGCG
CTCAAATCTAATAGGGCTATCAAGATATTAGTCGCCTCAATCCTCCCATTTTCACTTTCACCTCC
AAAATCCAAAATAAATCTCAAAAAAAAATCAACCATGAATCTACAAAAAAACTCCACCGTGAATT
TACAAAAATTAACATTGCCACGAGAAATTTTCAATCATGCCCATTCATCCATAAATATTTATGTA
CTCTTAATTTATTTTCAATTTACTTGTGTAAAATGATTTCATTGCAACTTTATATTAATTGAAAT
ATGATACTTGACAAATTTATTCAAAGTGTGACATAATTATCACTAATTTACTTAGTAAGAAAATG
ACATAATTATCACTAAAAATATAGCTTACAATTATATTGATACACTATAAATATTTATCAATTTT
CAT
Found at i:41934965 original size:24 final size:23
Alignment explanation
Indices: 41934938--41934990 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
41934928 ACAAAATGAT
41934938 ATGGAAAACTTAATGATATCTTTA
1 ATGGAAAACTTAATGATATC-TTA
* ** *
41934962 ATGGAAGACTTGGTGATTTCTTA
1 ATGGAAAACTTAATGATATCTTA
41934985 ATGGAA
1 ATGGAA
41934991 GAGCATACGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (23 bp):
ATGGAAAACTTAATGATATCTTA
Found at i:41945262 original size:18 final size:18
Alignment explanation
Indices: 41945236--41945289 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 18
41945226 ATGCGTTGCA
* *
41945236 TTTAGTTGTCATTACATT
1 TTTAATTGTCACTACATT
*
41945254 TTTAATTGTCACTGCA-T
1 TTTAATTGTCACTACATT
* *
41945271 TTTAATTGTTAGTACATT
1 TTTAATTGTCACTACATT
41945289 T
1 T
41945290 GCATTGTAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTAATTGTCACTACATT
Found at i:41945288 original size:17 final size:17
Alignment explanation
Indices: 41945236--41945289 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
41945226 ATGCGTTGCA
* *
41945236 TTTAGTTGTCATTACATT
1 TTTAATTGTCACTACA-T
*
41945254 TTTAATTGTCACTGCAT
1 TTTAATTGTCACTACAT
* *
41945271 TTTAATTGTTAGTACAT
1 TTTAATTGTCACTACAT
41945288 TT
1 TT
41945290 GCATTGTAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.54
Consensus pattern (17 bp):
TTTAATTGTCACTACAT
Found at i:41946411 original size:43 final size:44
Alignment explanation
Indices: 41946361--41946500 Score: 198
Period size: 43 Copynumber: 3.3 Consensus size: 44
41946351 TAATGCGAAA
** * *
41946361 AAGCGCCGCTAAAGAG-CATGGCCTTTAGCGGCGCTTTTTTCGC
1 AAGCGCCGCTAAAGAGCCATGTTCTTTAGCGGCGCTTTTTCCAC
*
41946404 AAGCGCCGCTAAA-AGCCATGTTCTTTAGCGACGC-TTTTCCAC
1 AAGCGCCGCTAAAGAGCCATGTTCTTTAGCGGCGCTTTTTCCAC
*
41946446 AAGCGCCGCTAAAG-GCCATGTTCTTTAGCGGCGCTTTCTCCAC
1 AAGCGCCGCTAAAGAGCCATGTTCTTTAGCGGCGCTTTTTCCAC
41946489 AAGCGCCGCTAA
1 AAGCGCCGCTAA
41946501 TATAACAGAT
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
42 40 0.46
43 47 0.54
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.24
Consensus pattern (44 bp):
AAGCGCCGCTAAAGAGCCATGTTCTTTAGCGGCGCTTTTTCCAC
Found at i:41946928 original size:66 final size:66
Alignment explanation
Indices: 41946814--41946967 Score: 218
Period size: 66 Copynumber: 2.3 Consensus size: 66
41946804 GCTTGCCTCG
* * * * *
41946814 CTGCTGCCTCCACTTTAAGTTGTAGGTGGAGTTCTTCATATTTGTTTTGAGACTCTGCTTCTCTC
1 CTGCAGCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTGTTTTGAGACTCTACTTCTCTC
41946879 A
66 A
* * * *
41946880 CTGCAGCCTCCTCTTTAAGTTTTAGATTGAGTTCATCATATTTTTTTTGAGCCTCTACTTCTCTC
1 CTGCAGCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTGTTTTGAGACTCTACTTCTCTC
*
41946945 G
66 A
41946946 CTGCAGCCTCCTCTTTAAGTTG
1 CTGCAGCCTCCTCTTTAAGTTG
41946968 AGTAATTTGC
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 77 1.00
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.43
Consensus pattern (66 bp):
CTGCAGCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTGTTTTGAGACTCTACTTCTCTC
A
Found at i:41952903 original size:69 final size:69
Alignment explanation
Indices: 41952801--41953536 Score: 300
Period size: 69 Copynumber: 10.8 Consensus size: 69
41952791 TAAACTAAAT
*
41952801 AATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATA
1 AATTAAATATTTGGATTG-TTTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATA
41952866 TTTTG
65 TTTTG
* *
41952871 AATTAAATATTTGGATTGTTTTAATAATTAAATATTTAATTAAATGT-ATTCAAATAA-TAACAT
1 AATTAAATATTTGGATTGTTTTAATAATTAAATATTAAATTAAATATAATT-AAATAATTAA-AT
*
41952934 ATTTTT
64 ATTTTG
*
41952940 AATTAAATATTTCGG-TTG--TT--T--TT--A-A-T-AATTAAATATAATTAAGTAATTAAATA
1 AATTAAATATTT-GGATTGTTTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATA
41952993 TTTTG
65 TTTTG
* * * * *
41952998 AATTAAGTATTTGGGTTGTTTTAATAAATAACCAATTATTAAACT-AA-ATAATTAAATATTTGA
1 AATTAAATATTTGGATTGTTTTAAT-AATTA--AA-TATTAAATTAAATATAATTAAATAATT-A
* * *
41953061 ATTGTTTTTAAT
61 AAT-ATTTT--G
** *** * * * * *
41953073 AATTAAATA-TTAAATT-AAAT-ATAATTAAATAATTAAA-T-ATTTTGAATTAAATATTTGGAT
1 AATTAAATATTTGGATTGTTTTAATAATTAAAT-ATTAAATTAAATAT-AATTAAATAATT-AAA
* *
41953133 TGTTTTAAT
63 TATTTT--G
* * *
41953142 AATTAAATATTT-AATTAAATGTATTTAAATAA-TAACATATTTTTAATTAAATATTTCGGTTGT
1 AATTAAATATTTGGA-T---TGT-TTT-AATAATTAA-ATA--TTAAATTAAATA-------T-A
* * * **
41953205 TTTTAATAATGGTTCAAT-TAAAT-
49 ATTAAATAA---TTAAATAT-TTTG
* * * *
41953228 ATTTAAATATTTGGATTGTTTTTAATTATTAAATATTTAATTAAATATAATTAAGTAATTAAATA
1 AATTAAATATTTGGATTG-TTTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATA
41953293 TTTTG
65 TTTTG
* * * * *
41953298 AATTAAGTATTTGGGTTGTTTT--TAA-TAAATAACT-AATT-ATTA-AACTAAATAATTAAATA
1 AATTAAATATTTGGATTGTTTTAATAATTAAAT-ATTAAATTAAATATAATTAAATAATTAAATA
41953357 -TTTG
65 TTTTG
41953361 AATT---------G--T-TTTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATA-
1 AATTAAATATTTGGATTGTTTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATAT
41953413 TTTG
66 TTTG
* * *
41953417 AATTAAATATTTGGATTGTTTTAATAATTAAATATTTAATTAAATGTATTTAAATAA-TAACATA
1 AATTAAATATTTGGATTGTTTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAA-ATA
*
41953481 TTTTT
65 TTTTG
41953486 AATTAAATATTTCGG-TTGTTTT--TAA-TAAATAATT-AATTAAATAT--TTAAATA
1 AATTAAATATTT-GGATTGTTTTAATAATTAAAT-ATTAAATTAAATATAATTAAATA
41953537 TTTGGATTGT
Statistics
Matches: 518, Mismatches: 67, Indels: 168
0.69 0.09 0.22
Matches are distributed among these distances:
51 4 0.01
52 1 0.00
53 5 0.01
54 10 0.02
55 3 0.01
56 24 0.05
57 2 0.00
58 35 0.07
59 7 0.01
60 3 0.01
61 1 0.00
62 1 0.00
63 10 0.02
64 22 0.04
65 6 0.01
66 23 0.04
67 16 0.03
68 48 0.09
69 115 0.22
70 56 0.11
71 17 0.03
72 14 0.03
73 10 0.02
74 4 0.01
75 9 0.02
76 4 0.01
77 6 0.01
78 4 0.01
79 1 0.00
80 14 0.03
82 7 0.01
83 8 0.02
84 1 0.00
86 12 0.02
87 9 0.02
88 1 0.00
89 3 0.01
90 2 0.00
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (69 bp):
AATTAAATATTTGGATTGTTTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATAT
TTTG
Found at i:41953089 original size:119 final size:119
Alignment explanation
Indices: 41952719--41953143 Score: 532
Period size: 119 Copynumber: 3.5 Consensus size: 119
41952709 TATTTTTAAT
* * *
41952719 AATTAAATATAATTAAGTAATTAAATATTTTGAATTAAGTATTTGGGTTGTTTTTAATAAATAAC
1 AATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGATTG-TTTTAATAAATAAC
41952784 TAATTATTAAACTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTA
65 TAATTATTAAACTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTA
* *
41952839 AATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGATTGTTTTAATAATTAAAT
1 AATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGATTGTTTTAATAAATAACT
* * * * *** ** ** *
41952904 ATTTAATTAAATGTATTCAAATAA-TAACATATTTTTAATTAAATATTTCGGTTGTT-TTTAAT-
66 AATT-ATT-AA---ACT-AAATAATTAA-ATA-TTTGAATT--GT-TTTTAATAATTAAATATTA
* * * *
41952966 AATTAAATATAATTAAGTAATTAAATATTTTGAATTAAGTATTTGGGTTGTTTTAATAAATAACC
1 AATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGATTGTTTTAATAAATAACT
41953031 AATTATTAAACTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTA
66 AATTATTAAACTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTA
41953085 AATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGATTGTTTTAATAA
1 AATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGATTGTTTTAATAA
41953144 TTAAATATTT
Statistics
Matches: 253, Mismatches: 38, Indels: 29
0.79 0.12 0.09
Matches are distributed among these distances:
117 6 0.02
118 4 0.02
119 72 0.28
120 57 0.23
121 11 0.04
122 5 0.02
124 5 0.02
125 11 0.04
126 10 0.04
127 62 0.25
128 4 0.02
129 6 0.02
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (119 bp):
AATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGATTGTTTTAATAAATAACT
AATTATTAAACTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTA
Done.