Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 134 of 259
Found at i:43636575 original size:30 final size:30
Alignment explanation
Indices: 43636518--43636575 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
43636508 TTAAATTCTA
* *
43636518 AAAGATAAATACAAATAATTAATGATAATT
1 AAAGATAAATACAAATAAATAAAGATAATT
*
43636548 AAAGATAAATA-AGGATAAATAAAGATAA
1 AAAGATAAATACA-AATAAATAAAGATAA
43636576 AAGCTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.24
Consensus pattern (30 bp):
AAAGATAAATACAAATAAATAAAGATAATT
Found at i:43640031 original size:13 final size:13
Alignment explanation
Indices: 43640013--43640038 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43640003 ATTTTCCCAA
43640013 GTAAAGCTTGAAC
1 GTAAAGCTTGAAC
43640026 GTAAAGCTTGAAC
1 GTAAAGCTTGAAC
43640039 TTGGGACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
GTAAAGCTTGAAC
Found at i:43642931 original size:47 final size:45
Alignment explanation
Indices: 43642856--43642945 Score: 126
Period size: 47 Copynumber: 2.0 Consensus size: 45
43642846 TCGGCACGGA
* *
43642856 TACGTGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC
1 TACGTAAGAGCCAGTATAAGACCATGTCTGGGACATGGCATCGAC
* *
43642901 TTAGCGTAAGAGCCAGTATAAAACCATGTCTGGGACGTGGCATCG
1 -TA-CGTAAGAGCCAGTATAAGACCATGTCTGGGACATGGCATCG
43642946 GCATTATACC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 2 0.05
47 37 0.95
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (45 bp):
TACGTAAGAGCCAGTATAAGACCATGTCTGGGACATGGCATCGAC
Found at i:43645497 original size:283 final size:284
Alignment explanation
Indices: 43644989--43645557 Score: 1023
Period size: 283 Copynumber: 2.0 Consensus size: 284
43644979 TTCCTGGAAG
* *
43644989 AGTTCTGAAAGAAGTACATTAGCCAGAGGTTTATACACTAGAAAAGAAAAGAATTTTTAGAGCCG
1 AGTTCTGAAAGAAGTACATTAGCCAGAAGTTTATACACCAGAAAAGAAAAGAATTTTTAGAGCCG
* *
43645054 AAGCAAGGTCGTAGGACGGTGACTGAGTACGAGCGTGAGTTTGTGAGACTCAGTAAATATGTACG
66 AAGCAAGGTCGTAGGACGGTGACTGAGTACGAACGTGAGTTTGTGAGACTCAGCAAATATGTACG
43645119 GGAGTGCGTATCTACAAAATTCATTATGTACAAAAGGTTTGAAGATGGTTTGAACGAAGATATTC
131 GGAGTGCGTATCTACAAAATTCATTATGTACAAAAGGTTTGAAGATGGTTTGAACGAAGATATTC
43645184 ATCTATTAGTCGGCATCTTAGAGATAAGAGAATTTGTGGTGCTCGTGGAAAGAGCACGTAAGACC
196 ATCTATTAGTCGGCATCTTAGAGATAAGAGAATTTGTGGTGCTCGTGGAAAGAGCACGTAAGACC
43645249 AAGGAATTGGCCAAAGAGAAGAAA
261 AAGGAATTGGCCAAAGAGAAGAAA
* *
43645273 AGTTCTGAAAGAAGTACATTAGCCAGAAGTTTATAGACCAGAAAA-AAAATAATTTTTAGAGCCG
1 AGTTCTGAAAGAAGTACATTAGCCAGAAGTTTATACACCAGAAAAGAAAAGAATTTTTAGAGCCG
43645337 AAGCAAGGTCGTAGGACGGTGACTGAGTACGAACGTGAGTTTGTGAGACTCAGCAAATATGTACG
66 AAGCAAGGTCGTAGGACGGTGACTGAGTACGAACGTGAGTTTGTGAGACTCAGCAAATATGTACG
* *
43645402 GGAGTGCGTATTTACAAAATTCATTATGTACAAAAGGTTTGAAGATGGTTTGAATGAAGATATTC
131 GGAGTGCGTATCTACAAAATTCATTATGTACAAAAGGTTTGAAGATGGTTTGAACGAAGATATTC
* * * *
43645467 ATCTATTAGTTGGCATCTTGGAGATAAGAGAATTTGTGGTGCTTGTGGAAAGAGCATGTAAGACC
196 ATCTATTAGTCGGCATCTTAGAGATAAGAGAATTTGTGGTGCTCGTGGAAAGAGCACGTAAGACC
43645532 AAGGAATTGGCCAAAGAGAAGAAA
261 AAGGAATTGGCCAAAGAGAAGAAA
43645556 AG
1 AG
43645558 AGCTGACATT
Statistics
Matches: 273, Mismatches: 12, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
283 231 0.85
284 42 0.15
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.25
Consensus pattern (284 bp):
AGTTCTGAAAGAAGTACATTAGCCAGAAGTTTATACACCAGAAAAGAAAAGAATTTTTAGAGCCG
AAGCAAGGTCGTAGGACGGTGACTGAGTACGAACGTGAGTTTGTGAGACTCAGCAAATATGTACG
GGAGTGCGTATCTACAAAATTCATTATGTACAAAAGGTTTGAAGATGGTTTGAACGAAGATATTC
ATCTATTAGTCGGCATCTTAGAGATAAGAGAATTTGTGGTGCTCGTGGAAAGAGCACGTAAGACC
AAGGAATTGGCCAAAGAGAAGAAA
Found at i:43651600 original size:50 final size:49
Alignment explanation
Indices: 43651491--43651669 Score: 187
Period size: 47 Copynumber: 3.8 Consensus size: 49
43651481 CATCGACCTA
*
43651491 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACAT-G-GT--G
1 AGCCAATGTAAGACCATGTCTGGGACATGGCATCGGC-ACATAGCGTGAG
* * *
43651535 TGCCAATATAAGACCATGTCTAGGACATGGCATCGGCACGAATA-CGTGAG
1 AGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCAC--ATAGCGTGAG
* * *
43651585 AGTCAATGTAAGACCATGTCTGGGACATGGCAT-TG-ACTTAGCGTGAG
1 AGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCACATAGCGTGAG
* *
43651632 AGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCA
1 AGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCA
43651670 TTATACCCTA
Statistics
Matches: 110, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
44 10 0.09
45 15 0.14
46 10 0.09
47 38 0.35
48 5 0.05
49 2 0.02
50 30 0.27
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (49 bp):
AGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCACATAGCGTGAG
Found at i:43652847 original size:20 final size:21
Alignment explanation
Indices: 43652808--43652847 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
43652798 GTTATAAGGA
*
43652808 CCACATGGGCGTGTTGCCCTT
1 CCACATAGGCGTGTTGCCCTT
*
43652829 CCACATAGGTGTG-TGCCCT
1 CCACATAGGCGTGTTGCCCT
43652848 ATTTCAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.12, C:0.33, G:0.28, T:0.28
Consensus pattern (21 bp):
CCACATAGGCGTGTTGCCCTT
Found at i:43655834 original size:175 final size:175
Alignment explanation
Indices: 43655543--43655891 Score: 698
Period size: 175 Copynumber: 2.0 Consensus size: 175
43655533 GGGGACTTGC
43655543 ATGTCAAATTCCCCCCTAACTAGTAGTGGCCGGCCATGACAAGCATGGTAGACCAAGTGTGATGG
1 ATGTCAAATTCCCCCCTAACTAGTAGTGGCCGGCCATGACAAGCATGGTAGACCAAGTGTGATGG
43655608 GCAAGACATGTCATAGACATGTTGTGTTGGTGCATCATGGGTGGAAAAAAATAAAATAAGGAGCA
66 GCAAGACATGTCATAGACATGTTGTGTTGGTGCATCATGGGTGGAAAAAAATAAAATAAGGAGCA
43655673 TGGGCATAAAATAATGAAAGGGAATATGATGAAAACAAAAAAAAA
131 TGGGCATAAAATAATGAAAGGGAATATGATGAAAACAAAAAAAAA
43655718 ATGTCAAATTCCCCCCTAACTAGTAGTGGCCGGCCATGACAAGCATGGTAGACCAAGTGTGATGG
1 ATGTCAAATTCCCCCCTAACTAGTAGTGGCCGGCCATGACAAGCATGGTAGACCAAGTGTGATGG
43655783 GCAAGACATGTCATAGACATGTTGTGTTGGTGCATCATGGGTGGAAAAAAATAAAATAAGGAGCA
66 GCAAGACATGTCATAGACATGTTGTGTTGGTGCATCATGGGTGGAAAAAAATAAAATAAGGAGCA
43655848 TGGGCATAAAATAATGAAAGGGAATATGATGAAAACAAAAAAAA
131 TGGGCATAAAATAATGAAAGGGAATATGATGAAAACAAAAAAAA
43655892 GTGTGTAGTT
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 174 1.00
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (175 bp):
ATGTCAAATTCCCCCCTAACTAGTAGTGGCCGGCCATGACAAGCATGGTAGACCAAGTGTGATGG
GCAAGACATGTCATAGACATGTTGTGTTGGTGCATCATGGGTGGAAAAAAATAAAATAAGGAGCA
TGGGCATAAAATAATGAAAGGGAATATGATGAAAACAAAAAAAAA
Found at i:43664467 original size:40 final size:39
Alignment explanation
Indices: 43664383--43664567 Score: 169
Period size: 40 Copynumber: 4.6 Consensus size: 39
43664373 TTGAATGATG
* *
43664383 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCAAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGACA-T-ACTAAA
* *
43664423 TCCGGACTAAGATCCGAAGGCATTTGTGCGACATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGACATACTAAA
* **
43664463 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGACATACTAAA
* * **
43664502 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGACATACTA-AA
* *
43664543 -CCAGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
43664568 AATGAGTAGC
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 34 0.27
40 77 0.62
41 12 0.10
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGACATACTAAA
Found at i:43664519 original size:79 final size:81
Alignment explanation
Indices: 43664383--43664567 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
43664373 TTGAATGATG
*
43664383 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
43664447 TGTGCGACATACTA-A
66 TGTGCGACATACTATA
* * * **
43664462 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
**
43664524 ATTGTGCGAGTTACTATA
64 ATTGTGCGACATACTATA
* * *
43664542 ACCAGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
43664568 AATGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 33 0.37
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGACATACTATA
Found at i:43665968 original size:21 final size:21
Alignment explanation
Indices: 43665916--43665969 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
43665906 GTGTTACATG
* * * *
43665916 TAAGGGTTGAACGGAAGCTCA
1 TAAGGGTTAAACAGAAACCCA
* *
43665937 TAAGAGCTAAACAGAAACCCA
1 TAAGGGTTAAACAGAAACCCA
43665958 TAAGGGTTAAAC
1 TAAGGGTTAAAC
43665970 TGAAGCTCAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
TAAGGGTTAAACAGAAACCCA
Found at i:43665975 original size:42 final size:42
Alignment explanation
Indices: 43665916--43666022 Score: 133
Period size: 42 Copynumber: 2.5 Consensus size: 42
43665906 GTGTTACATG
* *
43665916 TAAGGGTTGAACGGAAGCTCATAAGAGCTAAACAGAAACCCA
1 TAAGGGTTAAACTGAAGCTCATAAGAGCTAAACAGAAACCCA
* * ** *
43665958 TAAGGGTTAAACTGAAGCTCAAAAGAGCTGAATTGAAACCTA
1 TAAGGGTTAAACTGAAGCTCATAAGAGCTAAACAGAAACCCA
* *
43666000 GAAGGGTTAAACTGAAACTCATA
1 TAAGGGTTAAACTGAAGCTCATA
43666023 TGAGTTAACT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (42 bp):
TAAGGGTTAAACTGAAGCTCATAAGAGCTAAACAGAAACCCA
Found at i:43666029 original size:21 final size:21
Alignment explanation
Indices: 43666005--43666051 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
43665995 ACCTAGAAGG
43666005 GTTAAACTGAAACTCAT-ATGA
1 GTTAAACTGAAACTCATGA-GA
*
43666026 GTT-AACTGAAGCTCATGAGA
1 GTTAAACTGAAACTCATGAGA
43666046 GTTAAA
1 GTTAAA
43666052 AGGAAAGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (21 bp):
GTTAAACTGAAACTCATGAGA
Found at i:43673278 original size:23 final size:21
Alignment explanation
Indices: 43673232--43673292 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 21
43673222 ATATGAGTCC
43673232 AAAAAATGAAATAAAAACAACT
1 AAAAAAT-AAATAAAAACAACT
43673254 AAAATAA-AAATAAAAGCACAACT
1 AAAA-AATAAATAAAA--ACAACT
43673277 AAAAAATAAATAAAAA
1 AAAAAATAAATAAAAA
43673293 AACAACGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
21 9 0.26
22 6 0.17
23 20 0.57
ACGTcount: A:0.75, C:0.08, G:0.03, T:0.13
Consensus pattern (21 bp):
AAAAAATAAATAAAAACAACT
Found at i:43673774 original size:8 final size:8
Alignment explanation
Indices: 43673763--43673787 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
43673753 TAAATTTTGG
43673763 AATAATAA
1 AATAATAA
43673771 AATAATAA
1 AATAATAA
43673779 AATAATAA
1 AATAATAA
43673787 A
1 A
43673788 GATGACAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAATAA
Found at i:43677168 original size:91 final size:91
Alignment explanation
Indices: 43676998--43677190 Score: 226
Period size: 91 Copynumber: 2.1 Consensus size: 91
43676988 TTAATTTCAG
** * **
43676998 GTACCATAATAATACACGGATTGATAGTTCAAGTACCACATTGAATATTGTCAAGGTATAAGTAC
1 GTACCA-AATAATACACAAATTGATAGTTCAAGTACCACATTAAATATTGTCAAAATATAAGTAC
*
43677063 CATATTGAACATTTTATAAAAATACAA
65 CATATTAAACATTTTATAAAAATACAA
* * * * *
43677090 GTACTAAATAATACACAAATTGATTGTTTAAGTACCACATTAAATATTTTTAAAATATAAAG-AC
1 GTACCAAATAATACACAAATTGATAGTTCAAGTACCACATTAAATATTGTCAAAATAT-AAGTAC
* * * *
43677154 TATATTAAAGATTTTATAAAATTACAG
65 CATATTAAACATTTTATAAAAATACAA
43677181 GTACCAAATA
1 GTACCAAATA
43677191 TTAAGAGAAA
Statistics
Matches: 84, Mismatches: 16, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
91 76 0.90
92 8 0.10
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (91 bp):
GTACCAAATAATACACAAATTGATAGTTCAAGTACCACATTAAATATTGTCAAAATATAAGTACC
ATATTAAACATTTTATAAAAATACAA
Found at i:43677525 original size:15 final size:15
Alignment explanation
Indices: 43677505--43677536 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43677495 ATTTTCTCGA
*
43677505 ATCGAGTTGAGTGAG
1 ATCGAGTCGAGTGAG
43677520 ATCGAGTCGAGTGAG
1 ATCGAGTCGAGTGAG
43677535 AT
1 AT
43677537 GAAATTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.09, G:0.38, T:0.25
Consensus pattern (15 bp):
ATCGAGTCGAGTGAG
Found at i:43678377 original size:21 final size:20
Alignment explanation
Indices: 43678353--43678440 Score: 55
Period size: 21 Copynumber: 4.6 Consensus size: 20
43678343 TTTAATTAAC
43678353 TTTTAAAAATTATAAAAATAT
1 TTTTAAAAATTATAAAAA-AT
**
43678374 TTTTTTAAA-T-T--AAAAT
1 TTTTAAAAATTATAAAAAAT
*
43678390 TATTAAAAATTATAAAAAAAT
1 TTTTAAAAATTAT-AAAAAAT
*
43678411 ATTTT-AAAATT-T-TAAAAT
1 -TTTTAAAAATTATAAAAAAT
*
43678429 TTTAAAAAATTA
1 TTTTAAAAATTA
43678441 ATTAAATGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 18
0.66 0.10 0.23
Matches are distributed among these distances:
16 8 0.16
17 7 0.14
18 12 0.24
19 1 0.02
20 2 0.04
21 18 0.35
22 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTTAAAAATTATAAAAAAT
Found at i:43678397 original size:37 final size:37
Alignment explanation
Indices: 43678353--43678436 Score: 116
Period size: 37 Copynumber: 2.2 Consensus size: 37
43678343 TTTAATTAAC
* * *
43678353 TTTTAAAAATTATAAAAATATTTTTTTAAA-TTAAAA
1 TTTTAAAAATTATAAAAAAATATTTTAAAATTTAAAA
43678389 TTATTAAAAATTATAAAAAAATATTTTAAAATTTTAAAA
1 TT-TTAAAAATTATAAAAAAATATTTTAAAA-TTTAAAA
43678428 TTTTAAAAA
1 TTTTAAAAA
43678437 ATTAATTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
36 2 0.05
37 25 0.60
38 7 0.17
39 8 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (37 bp):
TTTTAAAAATTATAAAAAAATATTTTAAAATTTAAAA
Found at i:43678422 original size:8 final size:8
Alignment explanation
Indices: 43678411--43678435 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
43678401 ATAAAAAAAT
43678411 ATTTTAAA
1 ATTTTAAA
43678419 ATTTTAAA
1 ATTTTAAA
43678427 ATTTTAAA
1 ATTTTAAA
43678435 A
1 A
43678436 AATTAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTTAAA
Found at i:43678728 original size:66 final size:66
Alignment explanation
Indices: 43678656--43678782 Score: 200
Period size: 66 Copynumber: 1.9 Consensus size: 66
43678646 TTTAATCTCT
* ** *
43678656 ATACTTAATTTCTAACGTAATTTGGTTCATTCATTTTATGCTGTTATTAATTAGTCCAAAAAGTA
1 ATACTTAATTTCTAACGTAATTTGGTTCATACATTTTATAATGTTATCAATTAGTCCAAAAAGTA
43678721 A
66 A
* *
43678722 ATACTTAATTTCTAATGTAATTTGGTTCATACATTTTGTAATGTTATCAATTAGTCCAAAA
1 ATACTTAATTTCTAACGTAATTTGGTTCATACATTTTATAATGTTATCAATTAGTCCAAAA
43678783 GTTATTATCA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (66 bp):
ATACTTAATTTCTAACGTAATTTGGTTCATACATTTTATAATGTTATCAATTAGTCCAAAAAGTA
A
Found at i:43696739 original size:18 final size:17
Alignment explanation
Indices: 43696718--43696759 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
43696708 AAAAATAGAT
43696718 TTATTTATATTTAATATA
1 TTATTTATATTTAA-ATA
43696736 TTATTT-TATTTAAATA
1 TTATTTATATTTAAATA
*
43696752 TAATTTAT
1 TTATTTAT
43696760 TATGTTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 8 0.36
17 8 0.36
18 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATTTATATTTAAATA
Found at i:43696743 original size:23 final size:24
Alignment explanation
Indices: 43696717--43696767 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
43696707 TAAAAATAGA
* *
43696717 TTTATTTATATTTAATATATTAT-
1 TTTATTTAAATATAATATATTATG
*
43696740 TTTATTTAAATATAATTTATTATG
1 TTTATTTAAATATAATATATTATG
43696764 TTTA
1 TTTA
43696768 AGTTTAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 20 0.83
24 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTATTTAAATATAATATATTATG
Found at i:43697181 original size:31 final size:31
Alignment explanation
Indices: 43697146--43697205 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
43697136 AGTCACTAAT
* * *
43697146 GTTTTAGATTATTTGTATTTTGGTCACTCCC
1 GTTTTAGATCATTTCTATTTTGATCACTCCC
*
43697177 GTTTTATATCATTTCTATTTTGATCACTC
1 GTTTTAGATCATTTCTATTTTGATCACTC
43697206 TTCGTTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.18, C:0.17, G:0.12, T:0.53
Consensus pattern (31 bp):
GTTTTAGATCATTTCTATTTTGATCACTCCC
Found at i:43699465 original size:42 final size:42
Alignment explanation
Indices: 43699418--43699502 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
43699408 TAATCCTTCA
43699418 AAAATTCTCATTCATTATTTCTAATCCTAAAGCAATTTTCTT
1 AAAATTCTCATTCATTATTTCTAATCCTAAAGCAATTTTCTT
43699460 AAAATTCTCATTCATTATTTCTAATCCTAAAGCAATTTTCTT
1 AAAATTCTCATTCATTATTTCTAATCCTAAAGCAATTTTCTT
43699502 A
1 A
43699503 CTTCATCACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.34, C:0.19, G:0.02, T:0.45
Consensus pattern (42 bp):
AAAATTCTCATTCATTATTTCTAATCCTAAAGCAATTTTCTT
Found at i:43701945 original size:26 final size:26
Alignment explanation
Indices: 43701914--43701970 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
43701904 CATTGAAGTC
**
43701914 AAACTCAAGTTTCAAATTGAAAAAAA
1 AAACTCAAGTACCAAATTGAAAAAAA
* *
43701940 AAACTCAAGTACCAAATTGAATATAA
1 AAACTCAAGTACCAAATTGAAAAAAA
43701966 AAACT
1 AAACT
43701971 ACACTTAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.56, C:0.14, G:0.07, T:0.23
Consensus pattern (26 bp):
AAACTCAAGTACCAAATTGAAAAAAA
Found at i:43703016 original size:21 final size:22
Alignment explanation
Indices: 43702986--43703030 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
43702976 ATCCATAAAT
*
43702986 AATTTCAAAAAATATAATAGTA
1 AATTTCAAAAAATATAACAGTA
*
43703008 AATTT-AAAATATATAACAGTA
1 AATTTCAAAAAATATAACAGTA
43703029 AA
1 AA
43703031 AAGATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (22 bp):
AATTTCAAAAAATATAACAGTA
Found at i:43715275 original size:11 final size:9
Alignment explanation
Indices: 43715239--43715358 Score: 50
Period size: 9 Copynumber: 12.8 Consensus size: 9
43715229 AAATATATAA
*
43715239 ATAAAATTT
1 ATAAAAATT
43715248 ATCAAAAATT
1 AT-AAAAATT
43715258 ATAAAAATT
1 ATAAAAATT
*
43715267 ATAGGAAAATG
1 ATA--AAAATT
*
43715278 ATAAAAA-A
1 ATAAAAATT
*
43715286 AGTATAAA--
1 A-TAAAAATT
**
43715294 ATAGTAATT
1 ATAAAAATT
43715303 ATTAAAAATT
1 A-TAAAAATT
* *
43715313 ATGGAAAAGT
1 AT-AAAAATT
*
43715323 ATAAATATT
1 ATAAAAATT
43715332 ATTTAAAAATT
1 A--TAAAAATT
43715343 ATAAAATATT
1 ATAAAA-ATT
43715353 -TAAAAA
1 ATAAAAA
43715359 AATGATATTT
Statistics
Matches: 86, Mismatches: 14, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
7 4 0.05
8 3 0.03
9 38 0.44
10 25 0.29
11 16 0.19
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.33
Consensus pattern (9 bp):
ATAAAAATT
Found at i:43715354 original size:18 final size:20
Alignment explanation
Indices: 43715317--43715358 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
43715307 AAAATTATGG
43715317 AAAAGTATAAATATTATTTA
1 AAAAGTATAAATATTATTTA
*
43715337 AAAATTATAAA-A-TATTTA
1 AAAAGTATAAATATTATTTA
43715355 AAAA
1 AAAA
43715359 AATGATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 1 0.05
20 10 0.48
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAGTATAAATATTATTTA
Found at i:43717882 original size:23 final size:23
Alignment explanation
Indices: 43717856--43717902 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
43717846 ATAGCCGGCT
43717856 TTTGAATCCACCATTGATAGGTA
1 TTTGAATCCACCATTGATAGGTA
43717879 TTTGAATCCACCATTGATAGGTA
1 TTTGAATCCACCATTGATAGGTA
43717902 T
1 T
43717903 CAACCAACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (23 bp):
TTTGAATCCACCATTGATAGGTA
Found at i:43718706 original size:11 final size:11
Alignment explanation
Indices: 43718667--43718705 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
43718657 CACAATAGTC
43718667 CTCTCACAATT
1 CTCTCACAATT
43718678 CTCTCACAATT
1 CTCTCACAATT
43718689 CTCTCA-AATTT
1 CTCTCACAA-TT
43718700 CTCTCA
1 CTCTCA
43718706 ATTTTTGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 2 0.07
11 25 0.93
ACGTcount: A:0.26, C:0.36, G:0.00, T:0.38
Consensus pattern (11 bp):
CTCTCACAATT
Found at i:43719897 original size:7 final size:7
Alignment explanation
Indices: 43719885--43719916 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
43719875 AGTCGTTTCA
43719885 TATTTAG
1 TATTTAG
43719892 TATTTAG
1 TATTTAG
*
43719899 TATTTAT
1 TATTTAG
43719906 TATTTAG
1 TATTTAG
43719913 TATT
1 TATT
43719917 ACGTATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.62
Consensus pattern (7 bp):
TATTTAG
Found at i:43720843 original size:21 final size:21
Alignment explanation
Indices: 43720819--43720876 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
43720809 CAACACCCAT
* *
43720819 AACCAGATCCCCTGCCAGAGG
1 AACCAAATCCCCTGCCAGAGC
*
43720840 AACCACAATCCCC-ACCAGAGC
1 AACCA-AATCCCCTGCCAGAGC
43720861 AACCACAA-CCCCTGCC
1 AACCA-AATCCCCTGCC
43720877 GAAAGCTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.13
21 21 0.68
22 6 0.19
ACGTcount: A:0.33, C:0.47, G:0.14, T:0.07
Consensus pattern (21 bp):
AACCAAATCCCCTGCCAGAGC
Found at i:43721407 original size:131 final size:132
Alignment explanation
Indices: 43720983--43721497 Score: 892
Period size: 131 Copynumber: 3.9 Consensus size: 132
43720973 TTGTAGAAAT
* * * *
43720983 TTTTTTATATAGTTTC-ATATAATAAAGTAAAAAATTCTTTTTAATATTTTAATTATACTTTACT
1 TTTTTTATATAGTTTCAAT-TAATAAAAT-AAAAGTTGTTTTTAATATTTTAATTGTACTTTACT
43721047 TTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTATTTTTATAT
64 TTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTATTTTTATAT
43721112 TTAA
129 TTAA
43721116 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
1 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
43721181 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTTATTATTTTTATATT
66 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATA-TTTTTTATTATTTTTATATT
43721246 TAA
130 TAA
*
43721249 TTTTTTATATAGTTTCAGTTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAC-TT
1 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
*
43721313 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGACAATATTTTTTATTATTTTTATATTT
66 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTATTTTTATATTT
43721378 AA
131 AA
43721380 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAC-TT
1 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
* * * *
43721444 TTTTTAATTTTAATACAATAAATGTTCTTTTAAATTAGTCAATAATTTTTATTA
66 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTA
43721498 AAATAAATGT
Statistics
Matches: 369, Mismatches: 11, Indels: 6
0.96 0.03 0.02
Matches are distributed among these distances:
131 136 0.37
132 123 0.33
133 108 0.29
134 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (132 bp):
TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTATTTTTATATTT
AA
Found at i:43721432 original size:264 final size:264
Alignment explanation
Indices: 43720983--43721497 Score: 901
Period size: 264 Copynumber: 2.0 Consensus size: 264
43720973 TTGTAGAAAT
*
43720983 TTTTTTATATAGTTTCATATAATAAAGTAAAAAATTCTTTTTAATATTTTAATTATACTTTACTT
1 TTTTTTATATAGTTTCATATAATAAAATAAAAAATTCTTTTTAATATTTTAATTATACTTTACTT
*
43721048 TTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTATTTTTATATT
66 TTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGACAATATTTTTTATTATTTTTATATT
43721113 TAATTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAC
131 TAATTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAC
* *
43721178 TTTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTTATTATTTTTAT
196 -TTTTTTTAATTTTAATAAAATAAATGTTCTTTTAAATTAGGCAATA-ATTTTTATTATTTTTAT
43721243 ATTTAA
259 ATTTAA
* * *
43721249 TTTTTTATATAGTTTCAGT-TAATAAAAT-AAAAGTTGTTTTTAATATTTTAATTGTACTTTAC-
1 TTTTTTATATAGTTTCA-TATAATAAAATAAAAAATTCTTTTTAATATTTTAATTATACTTTACT
43721311 TTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGACAATATTTTTTATTATTTTTATAT
65 TTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGACAATATTTTTTATTATTTTTATAT
43721376 TTAATTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTA
130 TTAATTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTA
* *
43721441 CTTTTTTTAATTTTAATACAATAAATGTTCTTTTAAATTAGTCAATAATTTTTATTA
195 CTTTTTTTAATTTTAATAAAATAAATGTTCTTTTAAATTAGGCAATAATTTTTATTA
43721498 AAATAAATGT
Statistics
Matches: 239, Mismatches: 9, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
262 9 0.04
263 43 0.18
264 130 0.54
265 31 0.13
266 25 0.10
267 1 0.00
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (264 bp):
TTTTTTATATAGTTTCATATAATAAAATAAAAAATTCTTTTTAATATTTTAATTATACTTTACTT
TTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGACAATATTTTTTATTATTTTTATATT
TAATTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAC
TTTTTTTAATTTTAATAAAATAAATGTTCTTTTAAATTAGGCAATAATTTTTATTATTTTTATAT
TTAA
Found at i:43721526 original size:39 final size:38
Alignment explanation
Indices: 43721451--43721535 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 38
43721441 CTTTTTTTAA
* * *
43721451 TTTTAATACAATAAATGTTCTTTTAAATTAGTCAATAAT
1 TTTTAATAAAATAAATGTTATTTTAAATTAGACAAT-AT
* *
43721490 TTTTATTAAAATAAATGTTATTTTGAA-TAGGACAATAT
1 TTTTAATAAAATAAATGTTATTTTAAATTA-GACAATAT
43721528 TTTTAATA
1 TTTTAATA
43721536 TTTTCAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
38 11 0.28
39 28 0.72
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (38 bp):
TTTTAATAAAATAAATGTTATTTTAAATTAGACAATAT
Found at i:43721537 original size:9 final size:9
Alignment explanation
Indices: 43721523--43721553 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
43721513 TGAATAGGAC
43721523 AATATTTTT
1 AATATTTTT
*
43721532 AATATTTTC
1 AATATTTTT
43721541 AATATTTTT
1 AATATTTTT
43721550 AATA
1 AATA
43721554 AAACATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTTTT
Found at i:43723687 original size:19 final size:20
Alignment explanation
Indices: 43723659--43723697 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
43723649 AAAAAACTTT
43723659 CAAAATATAAT-TTTGTTAAA
1 CAAAATATAATATTT-TTAAA
43723679 CAAAA-ATAATATTTTTAAA
1 CAAAATATAATATTTTTAAA
43723698 TAATAAGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (20 bp):
CAAAATATAATATTTTTAAA
Found at i:43724339 original size:21 final size:21
Alignment explanation
Indices: 43724315--43724354 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
43724305 CGCTCAAATT
43724315 TCTC-TCAATTTTTGTCAAAGC
1 TCTCTTCAATTTTTG-CAAAGC
*
43724336 TCTCTTTAATTTTTGCAAA
1 TCTCTTCAATTTTTGCAAA
43724355 ATAGCTCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (21 bp):
TCTCTTCAATTTTTGCAAAGC
Found at i:43725726 original size:265 final size:265
Alignment explanation
Indices: 43725241--43725768 Score: 887
Period size: 265 Copynumber: 2.0 Consensus size: 265
43725231 TTTTCACTTT
* *
43725241 TCATTTTTACATCATCGAGTGAACCACCCATATACATCCCCACTAATAATGAGGTAAAATTTATA
1 TCATTTTTACATCATCGAGTAAACCACCCATATACATCCCCACTAATAACGAGGTAAAATTTATA
**
43725306 TTAGATTTTACAATTATTATGTAGATTTAAAATATAATTGTATGCTAAAAAATTATTTAATTAGG
66 TTAGATTTTACAATTATTACATAGATTTAAAATATAATTGTATGCTAAAAAATTATTTAATTAGG
* *
43725371 TGAAACCATTCGGCGAGTTATGTTGGAATACCCATATCTCTTAAAGATATACGGCTTCTATTAGA
131 TGAAACCATTCGGCGAGTTATGTTGGAATACCCACATCTCTTAAAGATATACGACTTCTATTAGA
* * * *
43725436 CCAACGGTCGGAAGCACAGGTAAGTATTAAATAAAATATATATACATAATAAAATAGTCGTTTCA
196 CCAACGGTCGGAAACACAAGTAAGTACTAAATAAAATATATATACATAATAAAATAGTCCTTTCA
43725501 TATAG
261 TATAG
*
43725506 TCATTTTTACATCATCGAGTAAACCACCCATATACATTCCCACTAATAACGAGGTAAAATTTATA
1 TCATTTTTACATCATCGAGTAAACCACCCATATACATCCCCACTAATAACGAGGTAAAATTTATA
*
43725571 TTAGATTTTACAATTATTACATAGATTTCAAATATAATTGTATGCTAAAAAATTATTTAATTAGG
66 TTAGATTTTACAATTATTACATAGATTTAAAATATAATTGTATGCTAAAAAATTATTTAATTAGG
* * * *
43725636 TGGAACCATTCGGTGAGTTATGTTGTAATACCCACATCTCTTGAAGATATACGACTTCTATTATG
131 TGAAACCATTCGGCGAGTTATGTTGGAATACCCACATCTCTTAAAGATATACGACTTCTATTA-G
*
43725701 -CCAACGGTCGGAAACACAAGTAAGTACTAAATAAAATATATATACATAATAAAATAGTCCTTTG
195 ACCAACGGTCGGAAACACAAGTAAGTACTAAATAAAATATATATACATAATAAAATAGTCCTTTC
43725765 ATAT
260 ATAT
43725769 TTAGTATTTA
Statistics
Matches: 245, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
265 244 1.00
266 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.34
Consensus pattern (265 bp):
TCATTTTTACATCATCGAGTAAACCACCCATATACATCCCCACTAATAACGAGGTAAAATTTATA
TTAGATTTTACAATTATTACATAGATTTAAAATATAATTGTATGCTAAAAAATTATTTAATTAGG
TGAAACCATTCGGCGAGTTATGTTGGAATACCCACATCTCTTAAAGATATACGACTTCTATTAGA
CCAACGGTCGGAAACACAAGTAAGTACTAAATAAAATATATATACATAATAAAATAGTCCTTTCA
TATAG
Found at i:43726493 original size:18 final size:18
Alignment explanation
Indices: 43726470--43726507 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
43726460 TGCCAGTTGC
*
43726470 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
*
43726488 GTATCCTAACCCTTTTAT
1 GTATCCTAACCCTTATAT
43726506 GT
1 GT
43726508 TTTCTTTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:43726762 original size:21 final size:21
Alignment explanation
Indices: 43726738--43726788 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
43726728 ATTACCAGAT
* *
43726738 TCCCTGCCGGAGGAACCACAA
1 TCCCTGCCAGAGCAACCACAA
**
43726759 TCCCCACCAGAGCAACCACAA
1 TCCCTGCCAGAGCAACCACAA
*
43726780 CCCCTGCCA
1 TCCCTGCCA
43726789 AAAGCTGAAC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.47, G:0.16, T:0.08
Consensus pattern (21 bp):
TCCCTGCCAGAGCAACCACAA
Found at i:43727128 original size:132 final size:131
Alignment explanation
Indices: 43726894--43727405 Score: 857
Period size: 132 Copynumber: 3.9 Consensus size: 131
43726884 TTGTAGAAAT
* * *
43726894 TTTTTTATATAGTTTC-ATATAATAAAATAAAAATTATTTTTAATATTTTAATTATACTTTACTT
1 TTTTTTATATAGTTTCAAT-TAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTT
*
43726958 TTTTTAATTTTATTAAAATAAATGTTCTTTGAAATTAGGCAATATTTTTTATTATTTTTATATTT
65 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTATTTTTATATTT
43727023 AA
130 AA
43727025 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
1 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAC-TT
* *
43727090 TTTTTAATTTTATTAAAATAAGTGTTCTTTTAAATTAGGAAATATTTTTTATTATTTTTATATTT
65 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTATTTTTATATTT
43727155 AA
130 AA
* *
43727157 GTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAATTT
1 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTT-ACTT
*
43727222 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGACAATATTTTTTATTATTTTTATATTT
65 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTATTTTTATATTT
43727287 AA
130 AA
*
43727289 TTTTTTATATAG-TTCAATTAATATAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
1 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
* * * *
43727353 TTTTAATTTTAATACAATAAATGTTCTTTTAAATTAGTCAATAATTTTTATTA
66 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTA
43727406 AAATAAATGT
Statistics
Matches: 360, Mismatches: 18, Indels: 7
0.94 0.05 0.02
Matches are distributed among these distances:
130 53 0.15
131 102 0.28
132 204 0.57
133 1 0.00
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (131 bp):
TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTTATTATTTTTATATTTA
A
Found at i:43727337 original size:263 final size:262
Alignment explanation
Indices: 43726895--43727405 Score: 864
Period size: 263 Copynumber: 1.9 Consensus size: 262
43726885 TGTAGAAATT
43726895 TTTTTATATAGTTTCATATAATAAAATAAAAATTATTTTTAATATTTTAATTATACTTTACTTTT
1 TTTTTATATAGTTTCATATAATAAAATAAAAATTATTTTTAATATTTTAATTATACTTTACTTTT
*
43726960 TTTAATTTTATTAAAATAAATGTTCTTTGAAATTAGGCAATATTTTTTATTATTTTTATATTTAA
66 TTTAATTTTATTAAAATAAATGTTCTTTGAAATTAGACAATATTTTTTATTATTTTTATATTTAA
43727025 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
131 TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAC-TT
* * *
43727090 TTTTTAATTTTATTAAAATAAGTGTTCTTTTAAATTAGGAAATATTTTTTATTATTTTTATATTT
195 TTTTTAATTTTAATAAAATAAATGTTCTTTTAAATTAGGAAATAATTTTTATTATTTTTATATTT
43727155 AAG
260 AAG
* * * *
43727158 TTTTTATATAGTTTCA-ATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAATTT
1 TTTTTATATAGTTTCATA-TAATAAAATAAAAATTATTTTTAATATTTTAATTATACTTT-ACTT
*
43727222 TTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGACAATATTTTTTATTATTTTTATATTT
64 TTTTTAATTTTATTAAAATAAATGTTCTTTGAAATTAGACAATATTTTTTATTATTTTTATATTT
*
43727287 AATTTTTTATATAG-TTCAATTAATATAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACT
129 AATTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACT
* **
43727351 TTTTTTAATTTTAATACAATAAATGTTCTTTTAAATTAGTCAATAATTTTTATTA
194 TTTTTTAATTTTAATAAAATAAATGTTCTTTTAAATTAGGAAATAATTTTTATTA
43727406 AAATAAATGT
Statistics
Matches: 233, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
262 51 0.22
263 102 0.44
264 80 0.34
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.56
Consensus pattern (262 bp):
TTTTTATATAGTTTCATATAATAAAATAAAAATTATTTTTAATATTTTAATTATACTTTACTTTT
TTTAATTTTATTAAAATAAATGTTCTTTGAAATTAGACAATATTTTTTATTATTTTTATATTTAA
TTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTT
TTTTAATTTTAATAAAATAAATGTTCTTTTAAATTAGGAAATAATTTTTATTATTTTTATATTTA
AG
Found at i:43727434 original size:39 final size:38
Alignment explanation
Indices: 43727359--43727443 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 38
43727349 CTTTTTTTAA
* * *
43727359 TTTTAATACAATAAATGTTCTTTTAAATTAGTCAATAAT
1 TTTTAATAAAATAAATGTTATTTTAAATTAGACAAT-AT
* *
43727398 TTTTATTAAAATAAATGTTATTTTGAA-TACGACAATAT
1 TTTTAATAAAATAAATGTTATTTTAAATTA-GACAATAT
43727436 TTTTAATA
1 TTTTAATA
43727444 TTTTTAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
38 11 0.28
39 28 0.72
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (38 bp):
TTTTAATAAAATAAATGTTATTTTAAATTAGACAATAT
Found at i:43727445 original size:9 final size:9
Alignment explanation
Indices: 43727431--43727461 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
43727421 TGAATACGAC
43727431 AATATTTTT
1 AATATTTTT
43727440 AATATTTTT
1 AATATTTTT
43727449 AATATTTTT
1 AATATTTTT
43727458 AATA
1 AATA
43727462 AAACATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
AATATTTTT
Found at i:43731393 original size:20 final size:20
Alignment explanation
Indices: 43731368--43731422 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
43731358 ATAAATTTGA
*
43731368 AAAAAATAAAAAAATGATAT
1 AAAAAATAAAAAAATGACAT
* * *
43731388 AAAAAATCAAAATATTACAT
1 AAAAAATAAAAAAATGACAT
* *
43731408 AAAAATTGAAAAAAT
1 AAAAAATAAAAAAAT
43731423 ATAAATATAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.22
Consensus pattern (20 bp):
AAAAAATAAAAAAATGACAT
Found at i:43731420 original size:21 final size:21
Alignment explanation
Indices: 43731396--43731461 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
43731386 ATAAAAAATC
*
43731396 AAAATATTACATAAAAATTGA
1 AAAATATTAAATAAAAATTGA
* *
43731417 AAAA-ATATAAATATAAATTTAA
1 AAAATAT-TAAATA-AAAATTGA
*
43731439 AAAATATTATATAAAAATTGA
1 AAAATATTAAATAAAAATTGA
43731460 AA
1 AA
43731462 TTTTTTCATA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
20 2 0.06
21 17 0.47
22 15 0.42
23 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (21 bp):
AAAATATTAAATAAAAATTGA
Found at i:43731424 original size:22 final size:22
Alignment explanation
Indices: 43731396--43731461 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
43731386 ATAAAAAATC
*
43731396 AAAATATTACATAAAAATTGAA
1 AAAATATTAAATAAAAATTGAA
* *
43731418 AAAATA-TAAATATAAATTTAA
1 AAAATATTAAATAAAAATTGAA
*
43731439 AAAATATTATATAAAAATTGAA
1 AAAATATTAAATAAAAATTGAA
43731461 A
1 A
43731462 TTTTTTCATA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 18 0.49
22 19 0.51
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (22 bp):
AAAATATTAAATAAAAATTGAA
Found at i:43731560 original size:2 final size:2
Alignment explanation
Indices: 43731553--43731579 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43731543 AAACATCATA
43731553 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
43731580 AAGTTTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43731969 original size:32 final size:30
Alignment explanation
Indices: 43731899--43732064 Score: 132
Period size: 29 Copynumber: 5.6 Consensus size: 30
43731889 AATTTGACCA
*
43731899 TTTTTCAATTTTATATAATA-TTTT-GATT
1 TTTTTCAATTTTATATAATATTTTTAAATT
* *
43731927 TTTTTAAATTTATACATAAATATTTTTAAATT
1 TTTTTCAATTT-TATAT-AATATTTTTAAATT
43731959 TTTTTCAATTTTTATATAATATTTTT--ATT
1 TTTTTCAA-TTTTATATAATATTTTTAAATT
** *
43731988 TTTTAAAATTTTA-ATTATATATTATT-AA-T
1 TTTTTCAATTTTATA-TA-ATATTTTTAAATT
* * *
43732017 TTTTTAAATTTTTTA-AATTTTTTTAAATT
1 TTTTTCAATTTTATATAATATTTTTAAATT
43732046 TTTTTCAACTATTTATATA
1 TTTTTCAA-T-TTTATATA
43732065 TTTTATATGA
Statistics
Matches: 110, Mismatches: 14, Indels: 24
0.74 0.09 0.16
Matches are distributed among these distances:
27 7 0.06
28 20 0.18
29 40 0.36
30 7 0.06
31 18 0.16
32 15 0.14
33 3 0.03
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (30 bp):
TTTTTCAATTTTATATAATATTTTTAAATT
Found at i:43732010 original size:60 final size:59
Alignment explanation
Indices: 43731899--43732041 Score: 170
Period size: 61 Copynumber: 2.5 Consensus size: 59
43731889 AATTTGACCA
* * *
43731899 TTTTTCAA-TTTTATATAATATTTTGATTTTTTTAAATTTATACATAAATATTTTTAAATT
1 TTTTTCAATTTTTATATAATATTTTTATTTTTTAAAATTTATACATAAATATTATT-AA-T
*
43731959 TTTTTCAATTTTTATATAATATTTTTATTTTTTAAAATTT-TA-ATTATATATTATTAAT
1 TTTTTCAATTTTTATATAATATTTTTATTTTTTAAAATTTATACA-TAAATATTATTAAT
* *
43732017 TTTTTAAATTTTT-TA-AATTTTTTTA
1 TTTTTCAATTTTTATATAATATTTTTA
43732042 AATTTTTTTC
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
56 9 0.12
57 2 0.03
58 13 0.17
59 3 0.04
60 19 0.25
61 29 0.39
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (59 bp):
TTTTTCAATTTTTATATAATATTTTTATTTTTTAAAATTTATACATAAATATTATTAAT
Found at i:43732050 original size:10 final size:10
Alignment explanation
Indices: 43731924--43732050 Score: 84
Period size: 10 Copynumber: 12.8 Consensus size: 10
43731914 TAATATTTTG
43731924 ATTTTTTTAA
1 ATTTTTTTAA
**
43731934 ATTTATACATAA
1 ATTT-T-TTTAA
*
43731946 ATATTTTTAA
1 ATTTTTTTAA
*
43731956 ATTTTTTTCA
1 ATTTTTTTAA
*
43731966 ATTTTTATATA
1 ATTTTTTTA-A
*
43731977 ATATTTTT--
1 ATTTTTTTAA
*
43731985 ATTTTTTAAA
1 ATTTTTTTAA
* *
43731995 ATTTTAATTAT
1 ATTTT-TTTAA
* *
43732006 ATATTATT-A
1 ATTTTTTTAA
43732015 A-TTTTTTAA
1 ATTTTTTTAA
43732024 A-TTTTTTAA
1 ATTTTTTTAA
43732033 ATTTTTTTAA
1 ATTTTTTTAA
43732043 ATTTTTTT
1 ATTTTTTT
43732051 CAACTATTTA
Statistics
Matches: 89, Mismatches: 20, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
8 10 0.11
9 12 0.13
10 46 0.52
11 15 0.17
12 6 0.07
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTTTAA
Found at i:43732893 original size:22 final size:23
Alignment explanation
Indices: 43732866--43732910 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
43732856 TGATATCTAC
43732866 AAATCAAATC-TCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
*
43732888 AAATCATATCTTCTAAGATTACA
1 AAATCAAATCTTCTAAGATTACA
43732911 TATCATATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (23 bp):
AAATCAAATCTTCTAAGATTACA
Found at i:43732915 original size:22 final size:21
Alignment explanation
Indices: 43732863--43732926 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 21
43732853 AAATGATATC
*
43732863 TACAAATCAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
43732884 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
*
43732907 TACATATCATATC-C-AAGAT
1 TACAAATCATATCTCTAAGAT
43732926 T
1 T
43732927 GCATATCCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 6 0.15
20 1 0.03
21 3 0.08
22 18 0.46
23 11 0.28
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.33
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:43735010 original size:7 final size:7
Alignment explanation
Indices: 43734998--43735022 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
43734988 ATTGATGTGC
43734998 TATTATT
1 TATTATT
43735005 TATTATT
1 TATTATT
43735012 TATTATT
1 TATTATT
43735019 TATT
1 TATT
43735023 TTTGTTGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTATT
Found at i:43736575 original size:22 final size:23
Alignment explanation
Indices: 43736548--43736592 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
43736538 GGATATCTAC
*
43736548 AAATCAAATC-TCTAAGATTACA
1 AAATCAAATCTTCTAAAATTACA
*
43736570 AAATCATATCTTCTAAAATTACA
1 AAATCAAATCTTCTAAAATTACA
43736593 TATCATATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (23 bp):
AAATCAAATCTTCTAAAATTACA
Found at i:43736597 original size:22 final size:21
Alignment explanation
Indices: 43736545--43736601 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
43736535 AAAGGATATC
* *
43736545 TACAAATCAAATCTCTAAGAT
1 TACAAATCATATCTCTAAAAT
43736566 TACAAAATCATATCTTCTAAAAT
1 TAC-AAATCATATC-TCTAAAAT
*
43736589 TACATATCATATC
1 TACAAATCATATC
43736602 CAAGATTGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (21 bp):
TACAAATCATATCTCTAAAAT
Found at i:43737677 original size:16 final size:16
Alignment explanation
Indices: 43737644--43737685 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
43737634 AAAGAAAAAC
* *
43737644 AAGAGAA-GCAGAATA
1 AAGAGAAGGAAGAAGA
*
43737659 AAGAGAGGGAAGAAGA
1 AAGAGAAGGAAGAAGA
43737675 AAGAGAAGGAA
1 AAGAGAAGGAA
43737686 AAAAATAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.60, C:0.02, G:0.36, T:0.02
Consensus pattern (16 bp):
AAGAGAAGGAAGAAGA
Found at i:43738469 original size:9 final size:9
Alignment explanation
Indices: 43738455--43738493 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
43738445 TATTGCCATG
43738455 TTATTTTTA
1 TTATTTTTA
*
43738464 TTATTTTAA
1 TTATTTTTA
43738473 TATATATTTTA
1 T-TAT-TTTTA
43738484 TTATTTTTA
1 TTATTTTTA
43738493 T
1 T
43738494 GTAAGTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 15 0.58
10 6 0.23
11 5 0.19
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTATTTTTA
Found at i:43742270 original size:18 final size:19
Alignment explanation
Indices: 43742249--43742290 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
43742239 GATATATAGG
43742249 CAGAGCCT-GAGCCAGAGC
1 CAGAGCCTAGAGCCAGAGC
*
43742267 CAGAG-CTAGAGCCCGAGC
1 CAGAGCCTAGAGCCAGAGC
*
43742285 CCGAGC
1 CAGAGC
43742291 TGTCGCATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.26, C:0.36, G:0.33, T:0.05
Consensus pattern (19 bp):
CAGAGCCTAGAGCCAGAGC
Found at i:43742867 original size:14 final size:14
Alignment explanation
Indices: 43742848--43742876 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43742838 TGGAACAAAC
43742848 TTTGTAATATAAAT
1 TTTGTAATATAAAT
43742862 TTTGTAATATAAAT
1 TTTGTAATATAAAT
43742876 T
1 T
43742877 AAATACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTGTAATATAAAT
Found at i:43742897 original size:62 final size:62
Alignment explanation
Indices: 43742819--43743048 Score: 397
Period size: 62 Copynumber: 3.7 Consensus size: 62
43742809 ATTAATTGCA
* * *
43742819 ACATTACAACACTAAAACTTGGAACAAACTTTGTAATATAAATTTTGTAATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
* *
43742881 ACATTACAATATTAAAAATTGGAATAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
*
43742943 ACATTGCAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
*
43743005 ACATTACAACATTAAAAATTGGAACAAAGTTTGTAATATAAATT
1 ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATT
43743049 AGGTACATCG
Statistics
Matches: 158, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 158 1.00
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.36
Consensus pattern (62 bp):
ACATTACAACATTAAAAATTGGAACAAACTTTGTAATATAAATTTTGTTATATAAATTAAAT
Found at i:43742927 original size:14 final size:14
Alignment explanation
Indices: 43742904--43742938 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
43742894 AAAAATTGGA
*
43742904 ATAAACTTTGTAAT
1 ATAAATTTTGTAAT
*
43742918 ATAAATTTTGTTAT
1 ATAAATTTTGTAAT
43742932 ATAAATT
1 ATAAATT
43742939 AAATACATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (14 bp):
ATAAATTTTGTAAT
Found at i:43747258 original size:72 final size:71
Alignment explanation
Indices: 43747141--43747288 Score: 228
Period size: 72 Copynumber: 2.1 Consensus size: 71
43747131 TGGACTATTA
* *
43747141 TTAGTTTTGGTGGTTTCAGTTTAATCATGAATTATGACTAATTTTGGAGTTTGGTTTGTC-GATT
1 TTAGTTTTGCTGGTTTCAGTTTAATCATGAATTATGACTAATTTTGGAGTTTGGTTTATCAG-TT
43747205 TTAGGTT
65 TTAGGTT
*
43747212 GTTAGTTTTGCTGGTTTC-GATTTAATCATGAATTATGACTGATTTTGGAGTTTGGTTTATCAGT
1 -TTAGTTTTGCTGGTTTCAG-TTTAATCATGAATTATGACTAATTTTGGAGTTTGGTTTATCAGT
43747276 TTTAGGTT
64 TTTAGGTT
43747284 TTAGT
1 TTAGT
43747289 GATCTCGGGT
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
71 6 0.08
72 64 0.90
73 1 0.01
ACGTcount: A:0.20, C:0.06, G:0.24, T:0.51
Consensus pattern (71 bp):
TTAGTTTTGCTGGTTTCAGTTTAATCATGAATTATGACTAATTTTGGAGTTTGGTTTATCAGTTT
TAGGTT
Found at i:43747800 original size:13 final size:13
Alignment explanation
Indices: 43747761--43747805 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
43747751 TCAAGCATGA
*
43747761 TATTTCTGTATCTA
1 TATTT-TGTATCTG
* *
43747775 TATATTGTTTCTG
1 TATTTTGTATCTG
43747788 TATTTTGTATCTG
1 TATTTTGTATCTG
43747801 TATTT
1 TATTT
43747806 GGGGTGGAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 22 0.85
14 4 0.15
ACGTcount: A:0.18, C:0.09, G:0.11, T:0.62
Consensus pattern (13 bp):
TATTTTGTATCTG
Found at i:43751050 original size:10 final size:10
Alignment explanation
Indices: 43751034--43751119 Score: 60
Period size: 9 Copynumber: 9.0 Consensus size: 10
43751024 AAATTAGAAA
43751034 ATTATAAAAT
1 ATTATAAAAT
*
43751044 CTTAT-AAAT
1 ATTATAAAAT
43751053 ATTATAAAA-
1 ATTATAAAAT
*
43751062 ATTCTAATAA-
1 ATTATAA-AAT
43751072 ATTATAAAA-
1 ATTATAAAAT
*
43751081 AATATAAAAT
1 ATTATAAAAT
*
43751091 -TAATAAAACTT
1 ATTATAAAA--T
43751102 ATT-TAAAAT
1 ATTATAAAAT
43751111 ATT-TAAAAT
1 ATTATAAAAT
43751120 TAGGAAAAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
9 40 0.65
10 15 0.24
11 6 0.10
12 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (10 bp):
ATTATAAAAT
Found at i:43751057 original size:9 final size:9
Alignment explanation
Indices: 43750992--43751103 Score: 75
Period size: 9 Copynumber: 12.1 Consensus size: 9
43750982 TAAGAAATAT
*
43750992 TAAATATTA
1 TAAAAATTA
*
43751001 CAAAAATTGA
1 TAAAAATT-A
43751011 TACAAAATTA
1 TA-AAAATTA
**
43751021 TTTAAATTA
1 TAAAAATTA
*
43751030 -GAAAATTA
1 TAAAAATTA
*
43751038 TAAAATCTTA
1 TAAAA-ATTA
*
43751048 TAAATATTA
1 TAAAAATTA
*
43751057 TAAAAATTC
1 TAAAAATTA
43751066 TAATAAATTA
1 TAA-AAATTA
*
43751076 TAAAAAATA
1 TAAAAATTA
43751085 T-AAAATTAA
1 TAAAAATT-A
*
43751094 TAAAACTTA
1 TAAAAATTA
43751103 T
1 T
43751104 TTAAAATATT
Statistics
Matches: 79, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
8 11 0.14
9 38 0.48
10 24 0.30
11 6 0.08
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (9 bp):
TAAAAATTA
Found at i:43751062 original size:28 final size:26
Alignment explanation
Indices: 43751031--43751121 Score: 74
Period size: 28 Copynumber: 3.3 Consensus size: 26
43751021 TTTAAATTAG
* *
43751031 AAAATTATAAAATCTTATAAATATTAT
1 AAAATTATAAAA-CTTATAAAAAATAT
* *
43751058 AAAAATTCTAATAAATTATAAAAAATAT
1 -AAAATTATAA-AACTTATAAAAAATAT
* *
43751086 AAAATTAATAAAACTTATTTAAAATATTT
1 AAAATT-ATAAAACTTA--TAAAAAATAT
43751115 AAAATTA
1 AAAATTA
43751122 GGAAAAACAT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
27 11 0.22
28 24 0.47
29 16 0.31
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (26 bp):
AAAATTATAAAACTTATAAAAAATAT
Found at i:43751075 original size:19 final size:19
Alignment explanation
Indices: 43751031--43751098 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
43751021 TTTAAATTAG
*
43751031 AAAATTAT-AAAATCTTAT
1 AAAATTATAAAAATCTAAT
43751049 AAATATTATAAAAATTCTAAT
1 AAA-ATTATAAAAA-TCTAAT
*
43751070 -AAATTATAAAAA-AT-AT
1 AAAATTATAAAAATCTAAT
43751086 AAAATTAATAAAA
1 AAAATT-ATAAAA
43751099 CTTATTTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
16 2 0.05
17 6 0.14
18 9 0.21
19 15 0.35
20 6 0.14
21 5 0.12
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTATAAAAATCTAAT
Found at i:43751118 original size:29 final size:29
Alignment explanation
Indices: 43751076--43751185 Score: 86
Period size: 29 Copynumber: 3.8 Consensus size: 29
43751066 TAATAAATTA
* * *
43751076 TAAAAAATATAAAATTAATAAAACTTATT
1 TAAAATATTTAAAATTAATAAAACATATT
43751105 TAAAATATTTAAAATTAGGA-AAAACAT-TT
1 TAAAATATTTAAAATTA--ATAAAACATATT
** *
43751134 TGGAAT-TCTTAAAAATAATAAAA-ATATT
1 TAAAATAT-TTAAAATTAATAAAACATATT
*
43751162 TAAAATA-TTAAAATTCATATAAAC
1 TAAAATATTTAAAATTAATA-AAAC
43751186 TTACAAAAAT
Statistics
Matches: 63, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
27 13 0.21
28 14 0.22
29 29 0.46
30 6 0.10
31 1 0.02
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.35
Consensus pattern (29 bp):
TAAAATATTTAAAATTAATAAAACATATT
Found at i:43759530 original size:21 final size:20
Alignment explanation
Indices: 43759493--43759534 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
43759483 TACTCAAGGA
*
43759493 AAGCCGATTGATCCATCTAAG
1 AAGCCGATTCATCCATC-AAG
43759514 AAGCCGAATTCAT-CATCAAG
1 AAGCCG-ATTCATCCATCAAG
43759534 A
1 A
43759535 CTGAAGATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
AAGCCGATTCATCCATCAAG
Found at i:43763498 original size:46 final size:45
Alignment explanation
Indices: 43763351--43763565 Score: 134
Period size: 46 Copynumber: 4.6 Consensus size: 45
43763341 TGTGAGCTAC
* * * * *
43763351 TGTAAGACATGTCTGAGACATGCATGGGCC-ACATTATGA-GAGCCAG
1 TGTAAGACATGTCTGGGACATGCATCGGCCTAC--GA-GACGTGTCAG
* * * * * *
43763397 TGTAAGACCATGTTTGGGACATGGGATCGACAT-TGAGACGAGTGCTAG
1 TGTAAGA-CATGTCTGGGACAT-GCATCGGCCTACGAGACGTGT-C-AG
*
43763445 TGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGTAAGTCAT
1 TGTAAGACATGTCTGGGACATGCATCGGCCTACGAGACGT--GTCAG
** * * *
43763491 TGTAAGACATGTCCAGAACATGCATC-GACTACGAGATGTGTCAG
1 TGTAAGACATGTCTGGGACATGCATCGGCCTACGAGACGTGTCAG
*
43763535 TGTAAGACCATGTCTGAGACATGGCATCGGC
1 TGTAAGA-CATGTCTGGGACAT-GCATCGGC
43763566 ACAGATATGC
Statistics
Matches: 130, Mismatches: 27, Indels: 23
0.72 0.15 0.13
Matches are distributed among these distances:
44 11 0.08
45 15 0.12
46 60 0.46
47 28 0.22
48 16 0.12
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (45 bp):
TGTAAGACATGTCTGGGACATGCATCGGCCTACGAGACGTGTCAG
Found at i:43766699 original size:21 final size:20
Alignment explanation
Indices: 43766685--43766743 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
43766675 TTTTTATGGA
*
43766685 TTTTTATAGAATTTTAATATG
1 TTTTTATAAAATTTT-ATATG
43766706 TTTTTATAAAATTTTAAATATG
1 TTTTTATAAAATTTT--ATATG
*
43766728 -TTTTAT-TAATTTTATA
1 TTTTTATAAAATTTTATA
43766744 ATTTATTAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 3 0.09
20 6 0.17
21 20 0.57
22 6 0.17
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTTATAAAATTTTATATG
Found at i:43766725 original size:22 final size:21
Alignment explanation
Indices: 43766685--43766731 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
43766675 TTTTTATGGA
*
43766685 TTTTTATAGAATTTTAATATG
1 TTTTTATAAAATTTTAATATG
43766706 TTTTTATAAAATTTTAAATATG
1 TTTTTATAAAATTTT-AATATG
43766728 TTTT
1 TTTT
43766732 ATTAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (21 bp):
TTTTTATAAAATTTTAATATG
Found at i:43766776 original size:9 final size:9
Alignment explanation
Indices: 43766728--43766778 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
43766718 TTTAAATATG
43766728 TTTTATTAA-
1 TTTTA-TAAT
43766737 TTTTATAAT
1 TTTTATAAT
* *
43766746 TTATTAGATT
1 TT-TTATAAT
43766756 TTTTAT-AT
1 TTTTATAAT
43766764 TTTTATAAT
1 TTTTATAAT
43766773 TTTTAT
1 TTTTAT
43766779 GAGTCCATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 10 0.29
9 18 0.51
10 7 0.20
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (9 bp):
TTTTATAAT
Found at i:43766846 original size:17 final size:18
Alignment explanation
Indices: 43766825--43766866 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
43766815 AATTTAAATA
*
43766825 ATTTTT-TATATTTTAT-
1 ATTTTTATAAATTTTATG
43766841 ATTTTTATAAATTTTATG
1 ATTTTTATAAATTTTATG
43766859 ATTTTTAT
1 ATTTTTAT
43766867 TCATTATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.26
17 9 0.39
18 8 0.35
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
ATTTTTATAAATTTTATG
Found at i:43766881 original size:26 final size:26
Alignment explanation
Indices: 43766822--43766890 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 26
43766812 AATAATTTAA
*
43766822 ATAATTTTTTAT-ATTTTATATTTTT
1 ATAATTTTTTATGATTTTATATTATT
*
43766847 ATAA-ATTTTATGATTTT-TATTCATT
1 ATAATTTTTTATGATTTTATATT-ATT
*
43766872 ATAATTTTTTCTGATTTTA
1 ATAATTTTTTATGATTTTA
43766891 GTTTTTTATG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 10 0.28
25 15 0.42
26 11 0.31
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (26 bp):
ATAATTTTTTATGATTTTATATTATT
Found at i:43766899 original size:26 final size:25
Alignment explanation
Indices: 43766822--43766908 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 25
43766812 AATAATTTAA
43766822 ATAATTTTTTAT-ATTTTATATTTTT
1 ATAATTTTTTATGATTTTAT-TTTTT
* **
43766847 ATAA-ATTTTATGATTTTTATTCATT
1 ATAATTTTTTATGA-TTTTATTTTTT
*
43766872 ATAATTTTTTCTGATTTTAGTTTTTT
1 ATAATTTTTTATGATTTTA-TTTTTT
* *
43766898 ATGATCTTTTA
1 ATAATTTTTTA
43766909 ATCATTTTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
24 6 0.12
25 17 0.35
26 25 0.52
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (25 bp):
ATAATTTTTTATGATTTTATTTTTT
Found at i:43787171 original size:259 final size:258
Alignment explanation
Indices: 43786712--43787229 Score: 833
Period size: 259 Copynumber: 2.0 Consensus size: 258
43786702 TTCCATATTG
* * *
43786712 TTAATTAAACCTTGAATTAGGGATCTAATTGCTAACACTTCTAAATTGATTTAATTTTACCTCTC
1 TTAATTAAACCTTGAATTAGGGATCTAATTACTAACACTCCTAAATTAATTTAATTTTACCTCTC
* * *
43786777 GGTCTCAAATTTACCAAATTAGACAAATTGGCCCAATTTACCTCTCGATCTCACTGGCTAATCTG
66 GGTCTCAAATTTACCAAATTAGACAAATTAGCCCAATTTACCTCTCGATCTCACAGCCTAATCTG
* * * * *
43786842 GGACAAATGAGTTGGTGCCCAATAAGATTACCTCTTGATCTCACTTCTCTTGATTTTCCCTTAGG
131 GGACAAATGAATTGGTGCCCAATAAGATTACATCTCGATCTCACTTATCTTGATTTTCCCTTAAG
*
43786907 GTTGTCAATCTTAAGTTTTTAAGTCTATTTGATTTAATCCTTCTACCAAAGACTAACTAAACA
196 GTTGTCAATCTTAAGTTTTTAAGTCTATTCGATTTAATCCTTCTACCAAAGACTAACTAAACA
43786970 TTAATTAAACCTTGAATTAGGGATCTAAATTACTAACACTCCTAAATTAATTTAATTTTACCTCT
1 TTAATTAAACCTTGAATTAGGGATCT-AATTACTAACACTCCTAAATTAATTTAATTTTACCTCT
* * * *
43787035 TGGTCAT-AACTTTACCAAATTAGACAAATTAGTCCAATTTATCTCTCGATCTCACAGCCTAA-C
65 CGGTC-TCAAATTTACCAAATTAGACAAATTAGCCCAATTTACCTCTCGATCTCACAGCCTAATC
43787098 TTGGGACAAATGAATTGGTGCCCAATAAGATTACATCTCGATCTCACTTATCTTGATTTTCCCTT
129 -TGGGACAAATGAATTGGTGCCCAATAAGATTACATCTCGATCTCACTTATCTTGATTTTCCCTT
* *
43787163 AAGGTTGTCAATTTTAAGTTTTTAAGTCTATTCGATTTAATCCTTCTACCAAAGGCTAACTAAAC
193 AAGGTTGTCAATCTTAAGTTTTTAAGTCTATTCGATTTAATCCTTCTACCAAAGACTAACTAAAC
43787228 A
258 A
43787229 T
1 T
43787230 CACTTCCATT
Statistics
Matches: 239, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
258 27 0.11
259 211 0.88
260 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (258 bp):
TTAATTAAACCTTGAATTAGGGATCTAATTACTAACACTCCTAAATTAATTTAATTTTACCTCTC
GGTCTCAAATTTACCAAATTAGACAAATTAGCCCAATTTACCTCTCGATCTCACAGCCTAATCTG
GGACAAATGAATTGGTGCCCAATAAGATTACATCTCGATCTCACTTATCTTGATTTTCCCTTAAG
GTTGTCAATCTTAAGTTTTTAAGTCTATTCGATTTAATCCTTCTACCAAAGACTAACTAAACA
Found at i:43792291 original size:47 final size:47
Alignment explanation
Indices: 43792225--43792556 Score: 540
Period size: 47 Copynumber: 7.1 Consensus size: 47
43792215 GAAATGATAG
43792225 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
43792272 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
43792319 TAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATGTGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
43792366 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTAA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
43792413 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
43792460 TAAGGCCTAATGGCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * * *
43792506 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGCATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
43792553 TAAG
1 TAAG
43792557 TCCCGAAGGG
Statistics
Matches: 267, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
46 40 0.15
47 227 0.85
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:43792731 original size:37 final size:37
Alignment explanation
Indices: 43792675--43792753 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
43792665 CCGAGCTCTA
* *
43792675 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
43792712 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
43792749 AAGAC
1 AAGAC
43792754 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:43794595 original size:20 final size:20
Alignment explanation
Indices: 43794570--43794621 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
43794560 CGAAGCGCAG
43794570 GAATCCACAAATTGTTGACT
1 GAATCCACAAATTGTTGACT
* * **
43794590 GAATCCACAGAGTGTTGGTT
1 GAATCCACAAATTGTTGACT
43794610 GAATCCACAAAT
1 GAATCCACAAAT
43794622 CAGATTCCCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (20 bp):
GAATCCACAAATTGTTGACT
Found at i:43811611 original size:57 final size:53
Alignment explanation
Indices: 43811548--43811655 Score: 182
Period size: 53 Copynumber: 2.1 Consensus size: 53
43811538 TATTGTATCA
* *
43811548 TATCATTTC-TTTCTTTCTTTCTTTGTGAATTTAGTTTCTATTATAAATAGGC
1 TATCATATCATTTCTTTCTTTCTTTGTGAATTTAGTTTCTACTATAAATAGGC
*
43811600 TATCATATCATTTCTTTCTTTCTTTGTGTATTTAGTTTCTACTATAAATAGGC
1 TATCATATCATTTCTTTCTTTCTTTGTGAATTTAGTTTCTACTATAAATAGGC
43811653 TAT
1 TAT
43811656 GTAACCCAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
52 8 0.15
53 44 0.85
ACGTcount: A:0.22, C:0.14, G:0.09, T:0.55
Consensus pattern (53 bp):
TATCATATCATTTCTTTCTTTCTTTGTGAATTTAGTTTCTACTATAAATAGGC
Found at i:43815248 original size:34 final size:33
Alignment explanation
Indices: 43815210--43815275 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 33
43815200 ATTCTTACGC
43815210 TATATACATCTCCAATTTCCCTCTTTTTAATATT
1 TATATACATCTCCAATTTCCCT-TTTTTAATATT
* * * * *
43815244 TATATTCCTTTCTAATTTCTCTTTTTTAATAT
1 TATATACATCTCCAATTTCCCTTTTTTAATAT
43815276 CCTTATTCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 10 0.37
34 17 0.63
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (33 bp):
TATATACATCTCCAATTTCCCTTTTTTAATATT
Found at i:43815283 original size:33 final size:34
Alignment explanation
Indices: 43815223--43815286 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
43815213 ATACATCTCC
*
43815223 AATTTCCCTCTTTTTAATATTTATATTCCTTTCT
1 AATTTCCCTCTTTTTAATATCTATATTCCTTTCT
*
43815257 AATTTCTCT-TTTTTAATATCCT-TATTCCTT
1 AATTTCCCTCTTTTTAATAT-CTATATTCCTT
43815287 ATATTACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.59
Consensus pattern (34 bp):
AATTTCCCTCTTTTTAATATCTATATTCCTTTCT
Found at i:43820920 original size:73 final size:73
Alignment explanation
Indices: 43820800--43820939 Score: 235
Period size: 73 Copynumber: 1.9 Consensus size: 73
43820790 CTTTAGATCT
* *
43820800 TATGCATGTTTTGAGTTTTATATAGGAATGGATGCGATATTATATATTTGTTATATAATTGTTTT
1 TATGCATGTTTTGAGTTATATATAGGAATGGATGCGATATTAGATATTTGTTATATAATTGTTTT
43820865 TTGCATCC
66 TTGCATCC
* * *
43820873 TATGCATGTTTTGAGTTATATATGGGAGTGGATGTGATATTAGATATTTGTTATATAATTGTTTT
1 TATGCATGTTTTGAGTTATATATAGGAATGGATGCGATATTAGATATTTGTTATATAATTGTTTT
43820938 TT
66 TT
43820940 ACCGAGGTTG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.26, C:0.04, G:0.20, T:0.50
Consensus pattern (73 bp):
TATGCATGTTTTGAGTTATATATAGGAATGGATGCGATATTAGATATTTGTTATATAATTGTTTT
TTGCATCC
Found at i:43824150 original size:17 final size:18
Alignment explanation
Indices: 43824123--43824156 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
43824113 CCCTTATCCT
43824123 CTAAGGGGAAACAAAAAA
1 CTAAGGGGAAACAAAAAA
*
43824141 CTAA-GGGAAAGAAAAA
1 CTAAGGGGAAACAAAAA
43824157 CCCGACTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.09, G:0.24, T:0.06
Consensus pattern (18 bp):
CTAAGGGGAAACAAAAAA
Found at i:43828532 original size:12 final size:12
Alignment explanation
Indices: 43828515--43828542 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
43828505 GTTGTGGATG
43828515 GTGCTTAGGCTT
1 GTGCTTAGGCTT
43828527 GTGCTTAGGCTT
1 GTGCTTAGGCTT
43828539 GTGC
1 GTGC
43828543 CAAGCTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.18, G:0.36, T:0.39
Consensus pattern (12 bp):
GTGCTTAGGCTT
Found at i:43831232 original size:15 final size:16
Alignment explanation
Indices: 43831203--43831234 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
43831193 AGTTTATGCT
43831203 AAGTAAATGAAATGGA
1 AAGTAAATGAAATGGA
43831219 AAGTAAAT-AAATGGA
1 AAGTAAATGAAATGGA
43831234 A
1 A
43831235 TGCTAAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (16 bp):
AAGTAAATGAAATGGA
Found at i:43831252 original size:20 final size:20
Alignment explanation
Indices: 43831202--43831253 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
43831192 AAGTTTATGC
* *
43831202 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGGAATGCAAAG
* *
43831222 TAAATAAATGGAATGCTAAG
1 TAAGTAAATGGAATGCAAAG
43831242 TAAGTAAATGGA
1 TAAGTAAATGGA
43831254 GTGGTTCATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.52, C:0.02, G:0.23, T:0.23
Consensus pattern (20 bp):
TAAGTAAATGGAATGCAAAG
Found at i:43833836 original size:5 final size:5
Alignment explanation
Indices: 43833826--43833852 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
43833816 ATAGTTTAAT
43833826 ATTTA ATTTA ATTTA ATTTA ATTTA AT
1 ATTTA ATTTA ATTTA ATTTA ATTTA AT
43833853 ACTTATCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTTA
Found at i:43836029 original size:37 final size:37
Alignment explanation
Indices: 43835979--43836051 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
43835969 AATGATATCC
43835979 TCTCATTAGCATTGTGTGGATTGATAAATATGGAACT
1 TCTCATTAGCATTGTGTGGATTGATAAATATGGAACT
43836016 TCTCATTAGCATTGTGTGGATTGATAAATATGGAAC
1 TCTCATTAGCATTGTGTGGATTGATAAATATGGAAC
43836052 GTGGCCACAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (37 bp):
TCTCATTAGCATTGTGTGGATTGATAAATATGGAACT
Found at i:43837121 original size:37 final size:37
Alignment explanation
Indices: 43837070--43837177 Score: 102
Period size: 37 Copynumber: 2.9 Consensus size: 37
43837060 ATTCCAAAAA
*
43837070 TAATA-TTATTTTAATAGTTTAATATTAAATTTAAT-T
1 TAATACTTATCTTAATAGTTTAATATT-AATTTAATAT
*
43837106 TAATACTTATCTTAATAGTATT-TTATTAATTTAATAT
1 TAATACTTATCTTAATAGT-TTAATATTAATTTAATAT
*
43837143 TAA-AGCGATTATCTTAATA-TTAAAT-TTAATTTAAT
1 TAATA-C--TTATCTTAATAGTTTAATATTAATTTAAT
43837178 GTTTATATTG
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
36 14 0.23
37 32 0.52
38 4 0.07
39 11 0.18
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.52
Consensus pattern (37 bp):
TAATACTTATCTTAATAGTTTAATATTAATTTAATAT
Found at i:43837429 original size:11 final size:11
Alignment explanation
Indices: 43837415--43837439 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43837405 AATTTCTAGA
43837415 GATACTTTTCT
1 GATACTTTTCT
43837426 GATACTTTTCT
1 GATACTTTTCT
43837437 GAT
1 GAT
43837440 TTATAACTTG
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:0.20, C:0.16, G:0.12, T:0.52
Consensus pattern (11 bp):
GATACTTTTCT
Found at i:43839964 original size:56 final size:53
Alignment explanation
Indices: 43839835--43839967 Score: 126
Period size: 56 Copynumber: 2.4 Consensus size: 53
43839825 AAAAACCATA
* * *
43839835 AAAATATAA-AAATAATAAAAAATATGAATGTTATTAAATATTAAAAGATATG
1 AAAATATAATAAATTATAAAAAATATGAATGTTATTAAATATTAAAAAATATC
* * * *
43839887 AAAATTTATATGAACTTATAAATACTATGAAATGTTA-TAAATATTATAAAAATATAAC
1 AAAATATA-AT-AAATTATAAAAAATATG-AATGTTATTAAATATTA-AAAAATAT--C
*
43839945 AAAATCTAATAAATTATAAAAAA
1 AAAATATAATAAATTATAAAAAA
43839968 ATTATAAATT
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
52 7 0.11
53 1 0.02
55 22 0.35
56 24 0.38
57 2 0.03
58 7 0.11
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.32
Consensus pattern (53 bp):
AAAATATAATAAATTATAAAAAATATGAATGTTATTAAATATTAAAAAATATC
Found at i:43839968 original size:20 final size:18
Alignment explanation
Indices: 43839929--43839977 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
43839919 TGTTATAAAT
* *
43839929 ATTATAAAAATATAACAAA
1 ATTAT-AAATTATAAAAAA
43839948 ATCTAATAAATTATAAAAAA
1 AT-T-ATAAATTATAAAAAA
43839968 ATTATAAATT
1 ATTATAAATT
43839978 TAATATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 7 0.27
19 3 0.12
20 14 0.54
21 2 0.08
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
ATTATAAATTATAAAAAA
Found at i:43840038 original size:9 final size:9
Alignment explanation
Indices: 43840026--43840079 Score: 63
Period size: 9 Copynumber: 5.8 Consensus size: 9
43840016 ATAAAAACAC
*
43840026 ATAAAAAGT
1 ATAAAAATT
43840035 ATAAAAATT
1 ATAAAAATT
*
43840044 ATTAAAATT
1 ATAAAAATT
*
43840053 GATATAAACTT
1 -ATA-AAAATT
43840064 ATAAAAATT
1 ATAAAAATT
43840073 ATAAAAA
1 ATAAAAA
43840080 CAATCATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
9 28 0.74
10 5 0.13
11 5 0.13
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:43840080 original size:19 final size:19
Alignment explanation
Indices: 43840014--43840080 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
43840004 TATTAAATTT
**
43840014 TTATAAAAACACATAAAAA
1 TTATAAAAACTTATAAAAA
* *
43840033 GTATAAAAA-TTATTAAAA
1 TTATAAAAACTTATAAAAA
*
43840051 TTGATATAAACTTATAAAAA
1 TT-ATAAAAACTTATAAAAA
43840071 TTATAAAAAC
1 TTATAAAAAC
43840081 AATCATAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
18 7 0.18
19 21 0.55
20 10 0.26
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (19 bp):
TTATAAAAACTTATAAAAA
Found at i:43840088 original size:29 final size:29
Alignment explanation
Indices: 43840017--43840089 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
43840007 TAAATTTTTA
**
43840017 TAAAAACACATA-AAAAGTATAAAAATTAT
1 TAAAAACA-ATATAAACTTATAAAAATTAT
***
43840046 TAAAATTGATATAAACTTATAAAAATTA-
1 TAAAAACAATATAAACTTATAAAAATTAT
43840074 TAAAAACAATCATAAA
1 TAAAAACAAT-ATAAA
43840090 AACTTGAGCT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
28 10 0.29
29 24 0.71
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.27
Consensus pattern (29 bp):
TAAAAACAATATAAACTTATAAAAATTAT
Found at i:43840484 original size:9 final size:9
Alignment explanation
Indices: 43840468--43840656 Score: 78
Period size: 10 Copynumber: 20.0 Consensus size: 9
43840458 CAATCCATTT
43840468 TAATTTTTA
1 TAATTTTTA
*
43840477 TGATTTTTTA
1 T-AATTTTTA
43840487 TAATTTTTA
1 TAATTTTTA
*
43840496 TAAGTTTATA
1 TAA-TTTTTA
*
43840506 TCAATTTTAA
1 T-AATTTTTA
*
43840516 T-ATTTTAA
1 TAATTTTTA
43840524 T-ATTTTTA
1 TAATTTTTA
*
43840532 TAATATTTAA
1 TAAT-TTTTA
* *
43840542 GAATTTTAA
1 TAATTTTTA
43840551 TACATTTTTTA
1 TA-A-TTTTTA
* **
43840562 AAATTTGAAA
1 TAATTT-TTA
*
43840572 TAAGTTTTA
1 TAATTTTTA
43840581 TTAA-TTTTA
1 -TAATTTTTA
*
43840590 TAAGCTTTTA
1 TAA-TTTTTA
*
43840600 AAATTTTTA
1 TAATTTTTA
*
43840609 TAATTTTAA
1 TAATTTTTA
* *
43840618 CAAGTTTATA
1 TAA-TTTTTA
*
43840628 TGAATTTTAA
1 T-AATTTTTA
*
43840638 TATTTTTTAA
1 TAATTTTT-A
*
43840648 TATTTTTTA
1 TAATTTTTA
43840657 ATATTTAGTT
Statistics
Matches: 137, Mismatches: 29, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
8 18 0.13
9 48 0.35
10 61 0.45
11 10 0.07
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (9 bp):
TAATTTTTA
Found at i:43840522 original size:19 final size:19
Alignment explanation
Indices: 43840468--43840646 Score: 90
Period size: 19 Copynumber: 9.5 Consensus size: 19
43840458 CAATCCATTT
* *
43840468 TAATTTTTATGATTTTTTA
1 TAATTTTTATAATTTTATA
*
43840487 TAATTTTTATAAGTTTATA
1 TAATTTTTATAATTTTATA
*
43840506 TCAATTTTAAT-ATTTTA-A
1 T-AATTTTTATAATTTTATA
43840524 T-ATTTTTATAATATTTA-A
1 TAATTTTTATAAT-TTTATA
* * *
43840542 GAATTTTAATACATTTTTTA
1 TAATTTTTATA-ATTTTATA
* **
43840562 AAATTTGAAATAAGTTTTAT-
1 TAATTT-TTATAA-TTTTATA
43840582 TAA-TTTTATAAGCTTTTA-A
1 TAATTTTTATAA--TTTTATA
43840601 -AATTTTTATAATTTTA-A
1 TAATTTTTATAATTTTATA
* *
43840618 CAAGTTTATATGAATTTTA-A
1 TAA-TTTTTAT-AATTTTATA
*
43840638 TATTTTTTA
1 TAATTTTTA
43840647 ATATTTTTTA
Statistics
Matches: 126, Mismatches: 20, Indels: 28
0.72 0.11 0.16
Matches are distributed among these distances:
16 7 0.06
17 8 0.06
18 15 0.12
19 59 0.47
20 28 0.22
21 9 0.07
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.56
Consensus pattern (19 bp):
TAATTTTTATAATTTTATA
Found at i:43840558 original size:45 final size:44
Alignment explanation
Indices: 43840463--43840558 Score: 99
Period size: 45 Copynumber: 2.1 Consensus size: 44
43840453 CTAATCAATC
* *
43840463 CATTTTAATTTTTATGATTTTTTATAATTTTTATAAGTTTATAT
1 CATTTTAATTTTTATGATTTTTTATAATTTTAAGAAGTTTATAT
*
43840507 CAATTTTAATATTTTA--ATATTTTTATAATATTTAAGAATTTTA-AT
1 C-ATTTTAAT-TTTTATGAT-TTTTTATAAT-TTTAAGAAGTTTATAT
43840552 ACATTTT
1 -CATTTT
43840559 TTAAAATTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
44 3 0.07
45 25 0.57
46 16 0.36
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (44 bp):
CATTTTAATTTTTATGATTTTTTATAATTTTAAGAAGTTTATAT
Found at i:43840647 original size:10 final size:10
Alignment explanation
Indices: 43840632--43840662 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
43840622 TTTATATGAA
43840632 TTTTAATATT
1 TTTTAATATT
43840642 TTTTAATATT
1 TTTTAATATT
43840652 TTTTAATATT
1 TTTTAATATT
43840662 T
1 T
43840663 AGTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTAATATT
Found at i:43844252 original size:18 final size:17
Alignment explanation
Indices: 43844229--43844263 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
43844219 AAATAGATTT
43844229 TTAATTAAATAAATTTAA
1 TTAATTAAA-AAATTTAA
43844247 TTAATTAAAAAATTTAA
1 TTAATTAAAAAATTTAA
43844264 ACCTTAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTAAAAAATTTAA
Found at i:43849055 original size:11 final size:11
Alignment explanation
Indices: 43849039--43849069 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
43849029 AAGTATGGGT
43849039 AGGTATGGGAA
1 AGGTATGGGAA
*
43849050 AGGTATGGGCA
1 AGGTATGGGAA
43849061 AGGTATGGG
1 AGGTATGGG
43849070 GTATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:43853142 original size:18 final size:18
Alignment explanation
Indices: 43853119--43853209 Score: 128
Period size: 18 Copynumber: 5.1 Consensus size: 18
43853109 CAATCCCAAC
* *
43853119 TACTGTATACGTGAACAA
1 TACTGTATACGTGAATAG
43853137 TACTGTATACGTGAATAG
1 TACTGTATACGTGAATAG
* *
43853155 TGCTGTATACGTAAATAG
1 TACTGTATACGTGAATAG
43853173 TACTGTATACGTGAATAG
1 TACTGTATACGTGAATAG
* *
43853191 TGCCGTATACGTGAATAG
1 TACTGTATACGTGAATAG
43853209 T
1 T
43853210 GCCGTAAACG
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (18 bp):
TACTGTATACGTGAATAG
Found at i:43853177 original size:36 final size:36
Alignment explanation
Indices: 43853121--43853209 Score: 142
Period size: 36 Copynumber: 2.5 Consensus size: 36
43853111 ATCCCAACTA
* *
43853121 CTGTATACGTGAACAATACTGTATACGTGAATAGTG
1 CTGTATACGTGAATAGTACTGTATACGTGAATAGTG
*
43853157 CTGTATACGTAAATAGTACTGTATACGTGAATAGTG
1 CTGTATACGTGAATAGTACTGTATACGTGAATAGTG
*
43853193 CCGTATACGTGAATAGT
1 CTGTATACGTGAATAGT
43853210 GCCGTAAACG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.31
Consensus pattern (36 bp):
CTGTATACGTGAATAGTACTGTATACGTGAATAGTG
Found at i:43853775 original size:11 final size:11
Alignment explanation
Indices: 43853759--43853789 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
43853749 AAGTATGGGT
43853759 AGGTATGGGAA
1 AGGTATGGGAA
*
43853770 AGGTATGGGCA
1 AGGTATGGGAA
43853781 AGGTATGGG
1 AGGTATGGG
43853790 GTATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:43860185 original size:20 final size:22
Alignment explanation
Indices: 43860147--43860189 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
43860137 TTAATTAATA
43860147 TTTTAAAATTTTAAAAAATTAT
1 TTTTAAAATTTTAAAAAATTAT
43860169 TTTTAAAA-TTT-AAAAATTAT
1 TTTTAAAATTTTAAAAAATTAT
43860189 T
1 T
43860190 AAAATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.48
21 3 0.14
22 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAATTTTAAAAAATTAT
Found at i:43860193 original size:29 final size:29
Alignment explanation
Indices: 43860161--43860258 Score: 106
Period size: 29 Copynumber: 3.2 Consensus size: 29
43860151 AAAATTTTAA
43860161 AAAATTATTTTTAAAATTTAAAAATTATT
1 AAAATTATTTTTAAAATTTAAAAATTATT
** * *
43860190 AAAATTATTTAAAAAATATAAAAGTTATT
1 AAAATTATTTTTAAAATTTAAAAATTATT
**
43860219 AAAAAAATTTTTAAAAATTTTAAAAATTAATT
1 AAAATTATTTTT-AAAA-TTTAAAAATT-ATT
43860251 AAATATTA
1 AAA-ATTA
43860259 ACATGTCATC
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
29 33 0.62
30 4 0.08
31 8 0.15
32 6 0.11
33 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (29 bp):
AAAATTATTTTTAAAATTTAAAAATTATT
Found at i:43860199 original size:20 final size:20
Alignment explanation
Indices: 43860176--43860258 Score: 80
Period size: 20 Copynumber: 4.0 Consensus size: 20
43860166 TATTTTTAAA
43860176 ATTTAAAAATTATTAAAATT
1 ATTTAAAAATTATTAAAATT
*
43860196 ATTTAAAAAATA-TAAAAGTT
1 ATTTAAAAATTATTAAAA-TT
* * *
43860216 ATTAAAAAAATTTTTAAAAAT
1 ATT-TAAAAATTATTAAAATT
43860237 -TTTAAAAATTAATTAAATATT
1 ATTTAAAAATT-ATTAAA-ATT
43860258 A
1 A
43860259 ACATGTCATC
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
19 12 0.24
20 23 0.47
21 9 0.18
22 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (20 bp):
ATTTAAAAATTATTAAAATT
Found at i:43860239 original size:9 final size:9
Alignment explanation
Indices: 43860167--43860246 Score: 54
Period size: 9 Copynumber: 8.3 Consensus size: 9
43860157 TTAAAAAATT
*
43860167 ATTTTTAAA
1 ATTTTAAAA
43860176 A-TTTAAAA
1 ATTTTAAAA
43860184 ATTATTAAAA
1 ATT-TTAAAA
*
43860194 TTATTTAAAA
1 AT-TTTAAAA
* *
43860204 AATATAAAA
1 ATTTTAAAA
*
43860213 GTTATTAAAAAA
1 ATT-TT--AAAA
43860225 ATTTTTAAAA
1 A-TTTTAAAA
43860235 ATTTTAAAA
1 ATTTTAAAA
43860244 ATT
1 ATT
43860247 AATTAAATAT
Statistics
Matches: 55, Mismatches: 9, Indels: 14
0.71 0.12 0.18
Matches are distributed among these distances:
8 7 0.13
9 20 0.36
10 19 0.35
11 1 0.02
12 6 0.11
13 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:43862223 original size:17 final size:17
Alignment explanation
Indices: 43862201--43862234 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43862191 CCTGGGACAT
*
43862201 GTGGCAGCATAGCAAAC
1 GTGGCAGCACAGCAAAC
43862218 GTGGCAGCACAGCAAAC
1 GTGGCAGCACAGCAAAC
43862235 CTCCTGGTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.26, G:0.29, T:0.09
Consensus pattern (17 bp):
GTGGCAGCACAGCAAAC
Found at i:43862816 original size:9 final size:9
Alignment explanation
Indices: 43862794--43862850 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
43862784 AAACTTATTT
43862794 TTAAAATT-
1 TTAAAATTA
*
43862802 TAAAAATTA
1 TTAAAATTA
43862811 TTAAAATTA
1 TTAAAATTA
*
43862820 TTTAAAAAGTA
1 -TT-AAAATTA
*
43862831 TAAAAATTA
1 TTAAAATTA
*
43862840 TTTAAATTA
1 TTAAAATTA
43862849 TT
1 TT
43862851 TTTAAAAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
8 7 0.18
9 23 0.59
10 3 0.08
11 6 0.15
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (9 bp):
TTAAAATTA
Found at i:43862820 original size:29 final size:29
Alignment explanation
Indices: 43862782--43862862 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
43862772 TTCAAAAAAA
43862782 TAAAACTTATTTTTAAAATTTAAAAATTAT
1 TAAAA-TTATTTTTAAAATTTAAAAATTAT
* *
43862812 TAAAATTA-TTTAAAAAGTATAAAAATTAT
1 TAAAATTATTTTTAAAA-TTTAAAAATTAT
* *
43862841 TTAAATTATTTTTAAAAATTAA
1 TAAAATTATTTTTAAAATTTAA
43862863 TTAAATGTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 7 0.16
29 24 0.56
30 12 0.28
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (29 bp):
TAAAATTATTTTTAAAATTTAAAAATTAT
Found at i:43862822 original size:20 final size:20
Alignment explanation
Indices: 43862799--43862845 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
43862789 TATTTTTAAA
* *
43862799 ATTTAAAAATTATTAAAATT
1 ATTTAAAAAGTATAAAAATT
43862819 ATTTAAAAAGTATAAAAATT
1 ATTTAAAAAGTATAAAAATT
43862839 ATTTAAA
1 ATTTAAA
43862846 TTATTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
ATTTAAAAAGTATAAAAATT
Found at i:43863088 original size:17 final size:18
Alignment explanation
Indices: 43863066--43863099 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43863056 ATACTTATAA
43863066 TTTAAAT-TCTAATTATT
1 TTTAAATATCTAATTATT
*
43863083 TTTAAATATGTAATTAT
1 TTTAAATATCTAATTAT
43863100 CACAAACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTAAATATCTAATTATT
Found at i:43868362 original size:1 final size:1
Alignment explanation
Indices: 43868356--43868380 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
43868346 ATGATTTGCC
43868356 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
43868381 GGTGCCTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:43872851 original size:18 final size:18
Alignment explanation
Indices: 43872830--43872888 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
43872820 ATAAAAATAA
*
43872830 TTATATTAATAATATATG
1 TTATATTAATATTATATG
* *
43872848 TTATAATAATTTTATATG
1 TTATATTAATATTATATG
43872866 -TATA-T-ATATTATAT-
1 TTATATTAATATTATATG
43872880 TTATATTAA
1 TTATATTAA
43872889 ACCATTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
15 12 0.35
16 2 0.06
17 5 0.15
18 15 0.44
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TTATATTAATATTATATG
Found at i:43873041 original size:146 final size:147
Alignment explanation
Indices: 43872850--43873147 Score: 535
Period size: 146 Copynumber: 2.0 Consensus size: 147
43872840 AATATATGTT
43872850 ATAATAATTTTATATGTATATATATTATATTTATATTAAACCATTAATTTAATAACAATTAAAAT
1 ATAATAATTTTATATG-ATATATATTATATTTATATTAAACCATTAATTTAATAACAATTAAAAT
* * *
43872915 TATTATTCAAAATTTAAAATAAAACTTACCTAAATAAGCAACCCAATCCAAACTATAAAATTTTA
65 TATTATTCAAAACTTAAAATAAAACTTACCAAAATAAGCAACCCAATCCAAACTATAAAATTCTA
43872980 AAAATTATATTTAATACA
130 AAAATTATATTTAATACA
*
43872998 ATAATAATTTTATATG-TATATATTATATTTATATTAAACCATTAATTTAATAACAATTAAACTT
1 ATAATAATTTTATATGATATATATTATATTTATATTAAACCATTAATTTAATAACAATTAAAATT
*
43873062 ATTATTCAAAACTTAAAATAAAACTTACCAAAATAAGTAACCCAATCCAAACTATAAAATTCTAA
66 ATTATTCAAAACTTAAAATAAAACTTACCAAAATAAGCAACCCAATCCAAACTATAAAATTCTAA
43873127 AAATTATATTTAATACA
131 AAATTATATTTAATACA
43873144 ATAA
1 ATAA
43873148 AACATTTATT
Statistics
Matches: 145, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
146 129 0.89
148 16 0.11
ACGTcount: A:0.50, C:0.11, G:0.01, T:0.38
Consensus pattern (147 bp):
ATAATAATTTTATATGATATATATTATATTTATATTAAACCATTAATTTAATAACAATTAAAATT
ATTATTCAAAACTTAAAATAAAACTTACCAAAATAAGCAACCCAATCCAAACTATAAAATTCTAA
AAATTATATTTAATACA
Done.