Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 143 of 204
Found at i:43203963 original size:6 final size:6
Alignment explanation
Indices: 43203952--43203979 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
43203942 AGTGCATAAT
43203952 AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAA
43203980 CAAAGAAAGA
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:43206481 original size:60 final size:58
Alignment explanation
Indices: 43206355--43206483 Score: 163
Period size: 61 Copynumber: 2.1 Consensus size: 58
43206345 TTTGTTTCTA
43206355 TTTTTTTTTTCAAAAAAAATTTCAAGTAATAAAAAATAAAAATGATTTTTTTTGAAGTTT
1 TTTTTTTTTTCAAAAAAAATTTCAAGTAATAAAAAATAAAAATGATTTTTTTTGAAG--T
*
43206415 TCTTTTTTTTTTAAAAAAAATTT-AAGTAAT-AAAAATAAAAATGAATGTAATTTTTTTGAAGT
1 T-TTTTTTTTTCAAAAAAAATTTCAAGTAATAAAAAATAAAAATG-A--T--TTTTTTTGAAGT
43206477 TTTTTTT
1 TTTTTTT
43206484 CAAATTTTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 11
0.84 0.01 0.15
Matches are distributed among these distances:
59 13 0.21
60 9 0.15
61 26 0.42
62 3 0.05
64 11 0.18
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (58 bp):
TTTTTTTTTTCAAAAAAAATTTCAAGTAATAAAAAATAAAAATGATTTTTTTTGAAGT
Found at i:43210920 original size:14 final size:14
Alignment explanation
Indices: 43210903--43210965 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
43210893 TACAGAACTC
43210903 TAAATTTAATTCCG
1 TAAATTTAATTCCG
*
43210917 TAAA-TT--TTCCC
1 TAAATTTAATTCCG
* *
43210928 TGAAACATAAATTCCG
1 T-AAA-TTTAATTCCG
43210944 TAAATTTAATTCCG
1 TAAATTTAATTCCG
43210958 TAAATTTA
1 TAAATTTA
43210966 TCTCTCTATC
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
11 5 0.13
12 3 0.08
13 2 0.05
14 21 0.54
15 3 0.08
16 5 0.13
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (14 bp):
TAAATTTAATTCCG
Found at i:43211271 original size:30 final size:30
Alignment explanation
Indices: 43211236--43211293 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
43211226 CCTCGACTCT
*
43211236 AACTTTTTCAAAATTACAATTTTACCCCTA
1 AACTTTTGCAAAATTACAATTTTACCCCTA
* * *
43211266 AACTTTTGCATAATTACATTTTTGCCCC
1 AACTTTTGCAAAATTACAATTTTACCCC
43211294 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTGCAAAATTACAATTTTACCCCTA
Found at i:43212373 original size:10 final size:8
Alignment explanation
Indices: 43212362--43212391 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
43212352 TAAAATTTAA
43212362 AAAATATT
1 AAAATATT
43212370 AAAATATT
1 AAAATATT
43212378 AAAATATT
1 AAAATATT
43212386 AAAATA
1 AAAATA
43212392 AAAAATGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAATATT
Found at i:43212375 original size:24 final size:25
Alignment explanation
Indices: 43212339--43212389 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
43212329 CAAACAAACG
*
43212339 AAAAATTAGAATA-TAAAAT-TTAA
1 AAAAATTAAAATATTAAAATATTAA
43212362 AAAATATTAAAATATTAAAATATTAA
1 AAAA-ATTAAAATATTAAAATATTAA
43212388 AA
1 AA
43212390 TAAAAAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 8 0.33
25 6 0.25
26 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
AAAAATTAAAATATTAAAATATTAA
Found at i:43214274 original size:16 final size:16
Alignment explanation
Indices: 43214250--43214280 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43214240 AATTAACTAA
*
43214250 TTAACCTAAAAATTAT
1 TTAAACTAAAAATTAT
43214266 TTAAACTAAAAATTA
1 TTAAACTAAAAATTA
43214281 ACCAATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (16 bp):
TTAAACTAAAAATTAT
Found at i:43215260 original size:36 final size:36
Alignment explanation
Indices: 43215213--43215285 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
43215203 CCCACTTCCT
43215213 GGTATCGCGACATTACAGTCGTCATTCACCTTCTAA
1 GGTATCGCGACATTACAGTCGTCATTCACCTTCTAA
43215249 GGTATCGCGACATTACAGTCGTCATTCACCTTCTAA
1 GGTATCGCGACATTACAGTCGTCATTCACCTTCTAA
43215285 G
1 G
43215286 CCTGAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (36 bp):
GGTATCGCGACATTACAGTCGTCATTCACCTTCTAA
Found at i:43224019 original size:18 final size:20
Alignment explanation
Indices: 43223981--43224019 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43223971 AAGATGTAAG
*
43223981 TTGAACTTTAGAAATAGAAT
1 TTGAACCTTAGAAATAGAAT
43224001 TTGAACCTT-GAAA-AGAAT
1 TTGAACCTTAGAAATAGAAT
43224019 T
1 T
43224020 AGACATTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (20 bp):
TTGAACCTTAGAAATAGAAT
Found at i:43225365 original size:36 final size:37
Alignment explanation
Indices: 43225318--43225387 Score: 133
Period size: 36 Copynumber: 1.9 Consensus size: 37
43225308 AAACAGATAC
43225318 CCTGAGGTGCTTTTCATGTCA-TTATCGATCCAATAA
1 CCTGAGGTGCTTTTCATGTCATTTATCGATCCAATAA
43225354 CCTGAGGTGCTTTTCATGTCATTTATCGATCCAA
1 CCTGAGGTGCTTTTCATGTCATTTATCGATCCAA
43225388 CCCAGTCACT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 21 0.64
37 12 0.36
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (37 bp):
CCTGAGGTGCTTTTCATGTCATTTATCGATCCAATAA
Found at i:43241522 original size:12 final size:12
Alignment explanation
Indices: 43241505--43241537 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
43241495 CAGCTCGCCC
43241505 ATATTAATTTTT
1 ATATTAATTTTT
43241517 ATATT-ATTTTT
1 ATATTAATTTTT
43241528 ATA-TAATTTT
1 ATATTAATTTT
43241538 AAAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:43241562 original size:18 final size:18
Alignment explanation
Indices: 43241539--43241578 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
43241529 TATAATTTTA
*
43241539 AAAAATA-TATAATACATC
1 AAAAATACTA-AAAACATC
43241557 AAAAATACTAAAAACATC
1 AAAAATACTAAAAACATC
43241575 AAAA
1 AAAA
43241579 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATACTAAAAACATC
Found at i:43254053 original size:16 final size:16
Alignment explanation
Indices: 43254028--43254064 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
43254018 ATATATGAGG
* *
43254028 GATTTTAAAATAAATT
1 GATTTCAAAATAAATA
43254044 GATTTCAAAATAAATA
1 GATTTCAAAATAAATA
43254060 GATTT
1 GATTT
43254065 TAATTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (16 bp):
GATTTCAAAATAAATA
Found at i:43262599 original size:20 final size:21
Alignment explanation
Indices: 43262553--43262601 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
43262543 TGACTTAAAA
43262553 ATTAATTTCCAAAAATATCAT
1 ATTAATTTCCAAAAATATCAT
43262574 ATTAATTTCCAAAAATATCAT
1 ATTAATTTCCAAAAATATCAT
43262595 A-TAATTT
1 ATTAATTT
43262602 TAATTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAATTTCCAAAAATATCAT
Found at i:43263803 original size:15 final size:15
Alignment explanation
Indices: 43263779--43263810 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43263769 ATGCATACAA
*
43263779 AAATATAAAAGACAT
1 AAATACAAAAGACAT
43263794 AAATACAAAAGACAT
1 AAATACAAAAGACAT
43263809 AA
1 AA
43263811 TAGTGAAATG
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:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:43268126 original size:21 final size:22
Alignment explanation
Indices: 43268096--43268140 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
43268086 GAACAAATTG
43268096 TTGATTCTATTTCTTTCTTG-AT
1 TTGATTCTA-TTCTTTCTTGTAT
*
43268118 TTGA-TCTATTCTTTTTTGTAT
1 TTGATTCTATTCTTTCTTGTAT
43268139 TT
1 TT
43268141 CTTTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.13, C:0.11, G:0.09, T:0.67
Consensus pattern (22 bp):
TTGATTCTATTCTTTCTTGTAT
Found at i:43272279 original size:22 final size:22
Alignment explanation
Indices: 43272254--43272338 Score: 98
Period size: 22 Copynumber: 3.9 Consensus size: 22
43272244 CCTTAACATG
*
43272254 ACGTGAAACATGAGAGCTTAGT
1 ACGTTAAACATGAGAGCTTAGT
**
43272276 ACGTTAGCCATGAGAGCTTAGT
1 ACGTTAAACATGAGAGCTTAGT
** * *
43272298 ACGTTAGCCATGAGGGTTTAGT
1 ACGTTAAACATGAGAGCTTAGT
*
43272320 TCGTTAAACATGAGAGCTT
1 ACGTTAAACATGAGAGCTT
43272339 TGAAAACAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.28
Consensus pattern (22 bp):
ACGTTAAACATGAGAGCTTAGT
Found at i:43272488 original size:21 final size:21
Alignment explanation
Indices: 43272464--43272518 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
43272454 AAAGCTTAAG
43272464 TTTGGAAACTTAATTTGAAAA
1 TTTGGAAACTTAATTTGAAAA
*
43272485 TTTGAAAACTTAATTTGAAAA
1 TTTGGAAACTTAATTTGAAAA
43272506 TTTGGAAACTTAA
1 TTTGGAAACTTAA
43272519 AAATTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (21 bp):
TTTGGAAACTTAATTTGAAAA
Found at i:43272971 original size:17 final size:15
Alignment explanation
Indices: 43272930--43272965 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
43272920 TAAAATTATA
43272930 ATTTTTTTGTATTTC
1 ATTTTTTTGTATTTC
*
43272945 ATTTTTTTGTATTTT
1 ATTTTTTTGTATTTC
43272960 ATTTTT
1 ATTTTT
43272966 ATTTGTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.78
Consensus pattern (15 bp):
ATTTTTTTGTATTTC
Found at i:43273373 original size:7 final size:7
Alignment explanation
Indices: 43273363--43273516 Score: 64
Period size: 7 Copynumber: 21.7 Consensus size: 7
43273353 TCATAAAATA
43273363 TAAACCC
1 TAAACCC
43273370 TAAACCCC
1 TAAA-CCC
*
43273378 TAACCCC
1 TAAACCC
43273385 T-AA-CC
1 TAAACCC
43273390 TCAAACCCC
1 T-AAA-CCC
43273399 TAAACCC
1 TAAACCC
* *
43273406 -CAACTCA
1 TAAAC-CC
*
43273413 TAAACCA
1 TAAACCC
*
43273420 TAAACCA
1 TAAACCC
*
43273427 TAATCCC
1 TAAACCC
43273434 TAAACCC
1 TAAACCC
* *
43273441 ATAATCCA
1 -TAAACCC
* *
43273449 TAGACCT
1 TAAACCC
***
43273456 TAAATAG
1 TAAACCC
43273463 T-AACTCC
1 TAAAC-CC
*
43273470 TAAACCT
1 TAAACCC
43273477 TAAACCC
1 TAAACCC
**
43273484 TAAACTA
1 TAAACCC
*
43273491 TATACCC
1 TAAACCC
*
43273498 TAAATCC
1 TAAACCC
43273505 TAAACCC
1 TAAACCC
43273512 TAAAC
1 TAAAC
43273517 TATAATAATA
Statistics
Matches: 107, Mismatches: 30, Indels: 20
0.68 0.19 0.13
Matches are distributed among these distances:
5 3 0.03
6 6 0.06
7 75 0.70
8 20 0.19
9 3 0.03
ACGTcount: A:0.42, C:0.36, G:0.01, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:43273692 original size:21 final size:20
Alignment explanation
Indices: 43273667--43273739 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
43273657 AAAACATAAA
43273667 CCCTAAACCCTAACCCTTAAC
1 CCCTAAACCCTAACCC-TAAC
* *
43273688 CCCTAACCCCTAAACCCCAAC
1 CCCTAAACCCT-AACCCTAAC
* * * *
43273709 CCATAAACCATAAACCATAAT
1 CCCTAAACCCT-AACCCTAAC
43273730 CCCTAAACCC
1 CCCTAAACCC
43273740 ATAATCCATA
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 36 0.88
22 5 0.12
ACGTcount: A:0.38, C:0.47, G:0.00, T:0.15
Consensus pattern (20 bp):
CCCTAAACCCTAACCCTAAC
Found at i:43273697 original size:7 final size:7
Alignment explanation
Indices: 43273667--43273710 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
43273657 AAAACATAAA
*
43273667 CCCTAAA
1 CCCTAAC
43273674 CCCTAAC
1 CCCTAAC
*
43273681 CCTTAAC
1 CCCTAAC
43273688 CCCTAAC
1 CCCTAAC
43273695 CCCTAAAC
1 CCCT-AAC
43273703 CCC-AAC
1 CCCTAAC
43273709 CC
1 CC
43273711 ATAAACCATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
6 5 0.15
7 22 0.67
8 6 0.18
ACGTcount: A:0.32, C:0.55, G:0.00, T:0.14
Consensus pattern (7 bp):
CCCTAAC
Found at i:43273715 original size:14 final size:13
Alignment explanation
Indices: 43273665--43273717 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 13
43273655 ATAAAACATA
*
43273665 AACCCTAAACCCT
1 AACCCTAAACCCC
*
43273678 AACCCTTAACCCC
1 AACCCTAAACCCC
43273691 TAACCCCTAAACCCC
1 -AA-CCCTAAACCCC
43273706 AACCCATAAACC
1 AACCC-TAAACC
43273718 ATAAACCATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 14 0.41
14 10 0.29
15 10 0.29
ACGTcount: A:0.38, C:0.49, G:0.00, T:0.13
Consensus pattern (13 bp):
AACCCTAAACCCC
Found at i:43273719 original size:7 final size:7
Alignment explanation
Indices: 43273709--43273820 Score: 59
Period size: 7 Copynumber: 15.9 Consensus size: 7
43273699 AAACCCCAAC
43273709 CCATAAA
1 CCATAAA
43273716 CCATAAA
1 CCATAAA
*
43273723 CCATAAT
1 CCATAAA
*
43273730 CCCTAAA
1 CCATAAA
*
43273737 CCCATAAT
1 -CCATAAA
43273745 CCATAAA
1 CCATAAA
* *
43273752 CCTTTAA
1 CCATAAA
43273759 --ATAGTAA
1 CCATA--AA
*
43273766 CTCCTAAA
1 C-CATAAA
*
43273774 CCTTAAA
1 CCATAAA
43273781 CC-TAAA
1 CCATAAA
* *
43273787 CTATATA
1 CCATAAA
*
43273794 CCCTAAA
1 CCATAAA
43273801 CCATAAA
1 CCATAAA
*
43273808 CCCTAAA
1 CCATAAA
*
43273815 CTATAA
1 CCATAA
43273821 TGATAATTAA
Statistics
Matches: 77, Mismatches: 21, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
5 1 0.01
6 5 0.06
7 61 0.79
8 8 0.10
10 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.23
Consensus pattern (7 bp):
CCATAAA
Found at i:43273726 original size:14 final size:14
Alignment explanation
Indices: 43273656--43273820 Score: 88
Period size: 14 Copynumber: 11.7 Consensus size: 14
43273646 CCTTGAATCA
*
43273656 TAAAACATAAACCC
1 TAAACCATAAACCC
*
43273670 TAAACCCT-AACCC
1 TAAACCATAAACCC
* * *
43273683 TTAACCCCTAACCCC
1 -TAAACCATAAACCC
**
43273698 TAAACC-CCAACCC
1 TAAACCATAAACCC
*
43273711 ATAAACCATAAACCA
1 -TAAACCATAAACCC
* *
43273726 TAATCCCTAAACCC
1 TAAACCATAAACCC
* *
43273740 ATAATCCATAAACCT
1 -TAAACCATAAACCC
*
43273755 TTAA--ATAGTAACTCC
1 TAAACCATA--AAC-CC
*
43273770 TAAACCTTAAA-CC
1 TAAACCATAAACCC
* *
43273783 TAAACTATATACCC
1 TAAACCATAAACCC
43273797 TAAACCATAAACCC
1 TAAACCATAAACCC
*
43273811 TAAACTATAA
1 TAAACCATAA
43273821 TGATAATTAA
Statistics
Matches: 113, Mismatches: 27, Indels: 22
0.70 0.17 0.14
Matches are distributed among these distances:
12 3 0.03
13 19 0.17
14 63 0.56
15 26 0.23
17 2 0.02
ACGTcount: A:0.45, C:0.34, G:0.01, T:0.21
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:43273761 original size:300 final size:299
Alignment explanation
Indices: 43273212--43273902 Score: 1127
Period size: 300 Copynumber: 2.3 Consensus size: 299
43273202 TTAAATAATT
*
43273212 TAAACTATAATGATAATTTTAATATATTAAAATTAATATTATCTCTTTTATAATTATATAAGAAA
1 TAAACTATAATGATAATTTTAATATATTAAAATTAATATTATCTCTTTTACAATTATATAAGAAA
*
43273277 TTATTTAATATATAAATTAAAAAACTCTAATTAATATAAACCGTAAACCCCTATCCCCTATCCCT
66 TTATTTAATATATAAATTAAAAAACTCTAATTAATATAAACCCTAAACCCCTATCCCCTATCCCT
* *
43273342 TAAACCTTGAATCATAAAATATAAACCCTAAACCCCTAACCCCTAACCTCAAACCCCTAAACCCC
131 TAAACCTTGAATCATAAAACATAAACCCTAAACCCCTAACCCCTAACCCCAAACCCCTAAACCCC
* *
43273407 AACTCATAAACCATAAACCATAATCCCTAAACCCATAATCCATAGACCTTAAATAGTAACTCCTA
196 AACCCATAAACCATAAACCATAATCCCTAAACCCATAATCCATAAACCTTAAATAGTAACTCCTA
43273472 AACCTTAAACCCTAAACTATATACCCTAAATCC-TAAACCC
261 AACCTTAAA-CCTAAACTATATACCCTAAA-CCATAAACCC
* * * *
43273512 TAAACTATAATAATAATTTTAATATATTAAAATTAATATTACCTTTTTTACAATTATATACGAAA
1 TAAACTATAATGATAATTTTAATATATTAAAATTAATATTATCTCTTTTACAATTATATAAGAAA
* * * *
43273577 TTATTCAATATATGAATTAAAAAA-TACTAATTAATGTAAACCCTAAACCTCTATCCCCTATCCC
66 TTATTTAATATATAAATTAAAAAACT-CTAATTAATATAAACCCTAAACCCCTATCCCCTATCCC
* *
43273641 TTAAACCTTGAATCATAAAACATAAACCCTAAA-CCCTAACCCTTAACCCCTAACCCCTAAACCC
130 TTAAACCTTGAATCATAAAACATAAACCCTAAACCCCTAACCCCTAACCCCAAACCCCTAAACCC
43273705 CAACCCATAAACCATAAACCATAATCCCTAAACCCATAATCCATAAACCTTTAAATAGTAACTCC
195 CAACCCATAAACCATAAACCATAATCCCTAAACCCATAATCCATAAACC-TTAAATAGTAACTCC
43273770 TAAACCTTAAACCTAAACTATATACCCTAAACCATAAACCC
259 TAAACCTTAAACCTAAACTATATACCCTAAACCATAAACCC
* * *
43273811 TAAACTATAATGATAATTAATTCAATATTTTAAAATTAATACTATCTCTTTTACGATTATATAAG
1 TAAACTATAATGATAATT--TT-AATATATTAAAATTAATATTATCTCTTTTACAATTATATAAG
43273876 AAATTATTTAATATATAAATTAAAAAA
63 AAATTATTTAATATATAAATTAAAAAA
43273903 ATCAGTTATG
Statistics
Matches: 360, Mismatches: 25, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
298 2 0.01
299 120 0.33
300 175 0.49
301 2 0.01
302 61 0.17
ACGTcount: A:0.44, C:0.23, G:0.02, T:0.30
Consensus pattern (299 bp):
TAAACTATAATGATAATTTTAATATATTAAAATTAATATTATCTCTTTTACAATTATATAAGAAA
TTATTTAATATATAAATTAAAAAACTCTAATTAATATAAACCCTAAACCCCTATCCCCTATCCCT
TAAACCTTGAATCATAAAACATAAACCCTAAACCCCTAACCCCTAACCCCAAACCCCTAAACCCC
AACCCATAAACCATAAACCATAATCCCTAAACCCATAATCCATAAACCTTAAATAGTAACTCCTA
AACCTTAAACCTAAACTATATACCCTAAACCATAAACCC
Found at i:43274295 original size:41 final size:40
Alignment explanation
Indices: 43274209--43274325 Score: 130
Period size: 40 Copynumber: 2.9 Consensus size: 40
43274199 TTTTGCAGCG
* * **
43274209 TTTTTAAAAAAGCGCCGCTAATAG-TCGACCTATAGCTGCA
1 TTTTTTAAAAAGCGCCGCTAAT-GCTCGATCTATAGCAACA
*
43274249 TTTTTTCAAAAAGCGCCGCTAATGCTCGATCTGTAGCAACGA
1 TTTTTT-AAAAAGCGCCGCTAATGCTCGATCTATAGCAAC-A
* *
43274291 -TTTTTAAAAAGTGCCTCTAATGCTCGATCTATAGC
1 TTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGC
43274326 GGCGTTTCTA
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
40 33 0.50
41 32 0.48
42 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (40 bp):
TTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCAACA
Found at i:43274641 original size:18 final size:18
Alignment explanation
Indices: 43274618--43274652 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
43274608 TAGCACCCAT
43274618 GTGATGCCCAAAATTGAA
1 GTGATGCCCAAAATTGAA
43274636 GTGATGCCCAAAATTGA
1 GTGATGCCCAAAATTGA
43274653 CACCCTGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (18 bp):
GTGATGCCCAAAATTGAA
Found at i:43275632 original size:7 final size:7
Alignment explanation
Indices: 43275620--43275653 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
43275610 AAGCAAGTTT
43275620 AGGGGTC
1 AGGGGTC
43275627 AGGGGTC
1 AGGGGTC
43275634 AGGGGTC
1 AGGGGTC
43275641 AGGGGTC
1 AGGGGTC
43275648 AGGGGT
1 AGGGGT
43275654 TTAAGGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.15, C:0.12, G:0.59, T:0.15
Consensus pattern (7 bp):
AGGGGTC
Found at i:43281361 original size:43 final size:43
Alignment explanation
Indices: 43281301--43281390 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
43281291 CTTTGAGTTC
* * *
43281301 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGAATTATATCTTTT
* *
43281343 ATTACCAAGATTTACTTGATTAAGAAAATGAATTGTATTTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGAATTATATCTTTT
43281386 ATTAC
1 ATTAC
43281391 ATTGCAATGT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.10
43 38 0.90
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.46
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGAATTATATCTTTT
Found at i:43282829 original size:36 final size:36
Alignment explanation
Indices: 43282784--43282855 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 36
43282774 ATTTTTCACT
* *
43282784 ATAATAAATAGAGATATATAAAT-ATATAAAAATTAA
1 ATAACAAATAGAGATATAAAAATAATAT-AAAATTAA
* **
43282820 ATAACAAATATATTTATAAAAATAATATAAAATTAA
1 ATAACAAATAGAGATATAAAAATAATATAAAATTAA
43282856 GATATTGCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 26 0.87
37 4 0.13
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (36 bp):
ATAACAAATAGAGATATAAAAATAATATAAAATTAA
Found at i:43284955 original size:23 final size:25
Alignment explanation
Indices: 43284905--43284955 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
43284895 ATTGCTTTAT
*
43284905 TATATATATGATATGTATGTGTATA
1 TATATATATGATATGTATGTGTAAA
43284930 TATATAATAT-ATAT-TATGT-TAAA
1 TATAT-ATATGATATGTATGTGTAAA
43284953 TAT
1 TAT
43284956 CAAGTTTACT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 6 0.25
24 5 0.21
25 9 0.38
26 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (25 bp):
TATATATATGATATGTATGTGTAAA
Found at i:43286871 original size:3 final size:3
Alignment explanation
Indices: 43286863--43286918 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
43286853 ACTAAACCTT
43286863 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43286911 TTA TTA TT
1 TTA TTA TT
43286919 GTACTTTAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43291417 original size:10 final size:10
Alignment explanation
Indices: 43291399--43291471 Score: 50
Period size: 10 Copynumber: 7.9 Consensus size: 10
43291389 ATATAAGAAT
*
43291399 AATTATATTG
1 AATTATATTA
*
43291409 AATTTTATTA
1 AATTATATTA
43291419 AATTATA-T-
1 AATTATATTA
* *
43291427 ATTTTTATTA
1 AATTATATTA
*
43291437 AATTATATTT
1 AATTATATTA
43291447 AA-TA-A-T-
1 AATTATATTA
*
43291453 AATTATTTTA
1 AATTATATTA
43291463 AATTATATT
1 AATTATATT
43291472 TTATAGTATT
Statistics
Matches: 47, Mismatches: 10, Indels: 12
0.68 0.14 0.17
Matches are distributed among these distances:
6 2 0.04
7 3 0.06
8 6 0.13
9 5 0.11
10 31 0.66
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (10 bp):
AATTATATTA
Found at i:43291445 original size:28 final size:27
Alignment explanation
Indices: 43291396--43291471 Score: 84
Period size: 28 Copynumber: 2.9 Consensus size: 27
43291386 ACAATATAAG
* *
43291396 AATAATTA-TATTGAATTTTATTAAAT
1 AATAATTATTATTAAATTATATTAAAT
* * *
43291422 TATATATTTTTATTAAATTATATTTAAT
1 AATA-ATTATTATTAAATTATATTAAAT
43291450 AATAATTATT-TTAAATTATATT
1 AATAATTATTATTAAATTATATT
43291472 TTATAGTATT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
26 15 0.37
27 8 0.20
28 18 0.44
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
AATAATTATTATTAAATTATATTAAAT
Found at i:43291550 original size:18 final size:18
Alignment explanation
Indices: 43291529--43291564 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
43291519 TAATACTAAG
43291529 AATTTTATTAAATTATAT
1 AATTTTATTAAATTATAT
43291547 AATTTTATTAAATTATAT
1 AATTTTATTAAATTATAT
43291565 TTAATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATTTTATTAAATTATAT
Found at i:43291756 original size:39 final size:43
Alignment explanation
Indices: 43291711--43291816 Score: 130
Period size: 39 Copynumber: 2.5 Consensus size: 43
43291701 TTTACTTATG
* *
43291711 CTATTACACCTCTATTCCATT-C-AACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCCTAACCAAACAAAAGAATTAC
43291751 C-ATTACGCCTCTATTCCATTCCATTTAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATTCCATTCC---TAACCAAACAAAAGAATTAC
*
43291796 CTATTACGCATCTATTCCATT
1 CTATTACGCCTCTATTCCATT
43291817 ACGCATCTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
39 18 0.32
40 2 0.04
44 14 0.25
45 4 0.07
46 18 0.32
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (43 bp):
CTATTACGCCTCTATTCCATTCCTAACCAAACAAAAGAATTAC
Found at i:43291791 original size:44 final size:46
Alignment explanation
Indices: 43291724--43291816 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 46
43291714 TTACACCTCT
* *
43291724 ATTCCATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCATCTATTCC
*
43291768 ATTCCATTTAACCAAACAAAAGAATTACCTATTACGCATCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCATCTATTCC
43291814 ATT
1 ATT
43291817 ACGCATCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 22 0.50
45 4 0.09
46 18 0.41
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCATCTATTCC
Found at i:43291819 original size:16 final size:16
Alignment explanation
Indices: 43291798--43291850 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
43291788 AGAATTACCT
43291798 ATTACGCATCTATTCC
1 ATTACGCATCTATTCC
43291814 ATTACGCATCTATTCC
1 ATTACGCATCTATTCC
*
43291830 ATTACGCCTCTATTCC
1 ATTACGCATCTATTCC
43291846 ATTAC
1 ATTAC
43291851 AGCGAACCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.25, C:0.32, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTACGCATCTATTCC
Found at i:43298521 original size:20 final size:21
Alignment explanation
Indices: 43298497--43298542 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
43298487 GAGCGAAACT
*
43298497 ACCCT-CGATGTTGCGACATA
1 ACCCTCCGATGTCGCGACATA
* *
43298517 GCCCTCCTATGTCGCGACATA
1 ACCCTCCGATGTCGCGACATA
43298538 ACCCT
1 ACCCT
43298543 TGCGCAGCCA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (21 bp):
ACCCTCCGATGTCGCGACATA
Found at i:43304494 original size:40 final size:40
Alignment explanation
Indices: 43304450--43304527 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
43304440 ACACAAAAAA
* *
43304450 TAGAGCATTAGCGGCGATTTAGCCA-AAGCGCCGCTAAAGG
1 TAGAGCATCAGCGGCG-TTTAGACAGAAGCGCCGCTAAAGG
*
43304490 TAGAGCATCAGCGGCGTTTATACAGAAGCGCCGCTAAA
1 TAGAGCATCAGCGGCGTTTAGACAGAAGCGCCGCTAAA
43304528 AATAGGAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 6 0.18
40 28 0.82
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (40 bp):
TAGAGCATCAGCGGCGTTTAGACAGAAGCGCCGCTAAAGG
Found at i:43304558 original size:39 final size:39
Alignment explanation
Indices: 43304445--43304560 Score: 99
Period size: 40 Copynumber: 2.9 Consensus size: 39
43304435 AAGCGACACA
* * * **
43304445 AAAAATAGAGCATTAGCGGCGATTTAGCCAAAGCGCCGCT
1 AAAAATAGAGAATCAACGGCG-TTTATACAAAGCGCCGCT
** * *
43304485 AAAGGTAGAGCATCAGCGGCGTTTATACAGAAGCGCCGCT
1 AAAAATAGAGAATCAACGGCGTTTATACA-AAGCGCCGCT
* *
43304525 AAAAATAG-GAATTAACGGCGTTTTATATAAAGCGCC
1 AAAAATAGAGAATCAACGGCG-TTTATACAAAGCGCC
43304561 ACAAAAAACC
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
39 22 0.35
40 41 0.65
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (39 bp):
AAAAATAGAGAATCAACGGCGTTTATACAAAGCGCCGCT
Found at i:43304668 original size:41 final size:41
Alignment explanation
Indices: 43304611--43304763 Score: 279
Period size: 41 Copynumber: 3.7 Consensus size: 41
43304601 TTTAAACATT
43304611 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTA
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTA
43304652 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTA
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTA
43304693 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTA
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTA
* *
43304734 TAGCGGCGTTTTCGTGTAAGCGCCGGCTAA
1 TAGCGGCGTTTTTGTCTAAGCGCC-GCTAA
43304764 NNNNNNNNNN
Statistics
Matches: 109, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
41 104 0.95
42 5 0.05
ACGTcount: A:0.15, C:0.24, G:0.30, T:0.31
Consensus pattern (41 bp):
TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTA
Found at i:43304923 original size:42 final size:42
Alignment explanation
Indices: 43304864--43305068 Score: 200
Period size: 42 Copynumber: 4.9 Consensus size: 42
43304854 NNNNNNNNNN
* *
43304864 CGAGTCTTTAGCGGCGTTTTCGTTTAAGCGCCGATAATGCTC
1 CGAGTCTTTAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTC
*
43304906 CGAGTCTTTAGTGGCGTTTTCGTCTAAGCGCCGCTAATGCTC
1 CGAGTCTTTAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTC
* * * * * *
43304948 TGGGTCTATAGCGGCGTTTTTGCCTATGCGCCGCTAATGCT-
1 CGAGTCTTTAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTC
* ** * * *
43304989 CGGGTCTTTAGCGGCGTTTTTATATATGCGCCGCTAATTCTC
1 CGAGTCTTTAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTC
* * * * *
43305031 C-TGTATTCAGCGGCGTTTGT-ATCTAAGCGCCGCGAATG
1 CGAGTCTTTAGCGGCGTTT-TCGTCTAAGCGCCGCTAATG
43305069 TATTAACCTT
Statistics
Matches: 138, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
41 63 0.46
42 75 0.54
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.34
Consensus pattern (42 bp):
CGAGTCTTTAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTC
Found at i:43305942 original size:16 final size:16
Alignment explanation
Indices: 43305921--43305951 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43305911 AGGGTTATGC
*
43305921 TTTAGGGGTTAGGGGA
1 TTTAGGGGTAAGGGGA
43305937 TTTAGGGGTAAGGGG
1 TTTAGGGGTAAGGGG
43305952 CTAGGGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.52, T:0.29
Consensus pattern (16 bp):
TTTAGGGGTAAGGGGA
Found at i:43307215 original size:25 final size:22
Alignment explanation
Indices: 43307161--43307217 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 22
43307151 CACGATTTCA
*
43307161 TTTCCCCAATTTCCCAACTTCT
1 TTTCCCCAATTTCCCAACTTAT
*
43307183 TTTCCCCCAATTTCCCCCAAGTTAT
1 TTT-CCCCAATTT--CCCAACTTAT
43307208 TCTTCCCCAA
1 T-TTCCCCAA
43307218 AGTATTTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 3 0.10
23 9 0.31
25 15 0.52
26 2 0.07
ACGTcount: A:0.19, C:0.42, G:0.02, T:0.37
Consensus pattern (22 bp):
TTTCCCCAATTTCCCAACTTAT
Found at i:43307229 original size:14 final size:15
Alignment explanation
Indices: 43307193--43307231 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
43307183 TTTCCCCCAA
*
43307193 TTTCCCCCAAGTTAT
1 TTTCCCCAAAGTTAT
43307208 TCTTCCCCAAAG-TAT
1 T-TTCCCCAAAGTTAT
43307223 TTTCCCCAA
1 TTTCCCCAA
43307232 TTTCCCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 5 0.23
16 9 0.41
ACGTcount: A:0.23, C:0.36, G:0.05, T:0.36
Consensus pattern (15 bp):
TTTCCCCAAAGTTAT
Found at i:43307366 original size:160 final size:160
Alignment explanation
Indices: 43307175--43307497 Score: 637
Period size: 160 Copynumber: 2.0 Consensus size: 160
43307165 CCCAATTTCC
43307175 CAACTTCTTTTCCCCCAATTTCCCCCAAGTTATTCTTCCCCAAAGTATTTTCCCCAATTTCCCAA
1 CAACTTCTTTTCCCCCAATTTCCCCCAAGTTATTCTTCCCCAAAGTATTTTCCCCAATTTCCCAA
43307240 TTGCTCAATCCCTTTCTGATAGCCGAACAACATTATTTTCTGGTATCGATGGACTTCCCCTTTCC
66 TTGCTCAATCCCTTTCTGATAGCCGAACAACATTATTTTCTGGTATCGATGGACTTCCCCTTTCC
*
43307305 CGTATTTTTTTGTGCATTTTGGGTTTGGAT
131 CGTATTTTTTTGTACATTTTGGGTTTGGAT
43307335 CAACTTCTTTTCCCCCAATTTCCCCCAAGTTATTCTTCCCCAAAGTATTTTCCCCAATTTCCCAA
1 CAACTTCTTTTCCCCCAATTTCCCCCAAGTTATTCTTCCCCAAAGTATTTTCCCCAATTTCCCAA
43307400 TTGCTCAATCCCTTTCTGATAGCCGAACAACATTATTTTCTGGTATCGATGGACTTCCCCTTTCC
66 TTGCTCAATCCCTTTCTGATAGCCGAACAACATTATTTTCTGGTATCGATGGACTTCCCCTTTCC
43307465 CGTATTTTTTTGTACATTTTGGGTTTGGAT
131 CGTATTTTTTTGTACATTTTGGGTTTGGAT
43307495 CAA
1 CAA
43307498 TGGCAATTCA
Statistics
Matches: 162, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 162 1.00
ACGTcount: A:0.20, C:0.29, G:0.11, T:0.40
Consensus pattern (160 bp):
CAACTTCTTTTCCCCCAATTTCCCCCAAGTTATTCTTCCCCAAAGTATTTTCCCCAATTTCCCAA
TTGCTCAATCCCTTTCTGATAGCCGAACAACATTATTTTCTGGTATCGATGGACTTCCCCTTTCC
CGTATTTTTTTGTACATTTTGGGTTTGGAT
Found at i:43307389 original size:14 final size:15
Alignment explanation
Indices: 43307353--43307391 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
43307343 TTTCCCCCAA
*
43307353 TTTCCCCCAAGTTAT
1 TTTCCCCAAAGTTAT
43307368 TCTTCCCCAAAG-TAT
1 T-TTCCCCAAAGTTAT
43307383 TTTCCCCAA
1 TTTCCCCAA
43307392 TTTCCCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 5 0.23
16 9 0.41
ACGTcount: A:0.23, C:0.36, G:0.05, T:0.36
Consensus pattern (15 bp):
TTTCCCCAAAGTTAT
Found at i:43309300 original size:24 final size:24
Alignment explanation
Indices: 43309269--43309321 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
43309259 TAATTGTATA
43309269 ATATTTGTAACTAAAATTAATATT
1 ATATTTGTAACTAAAATTAATATT
*
43309293 ATATTTGTATCTAAAATTAATATT
1 ATATTTGTAACTAAAATTAATATT
43309317 ATATT
1 ATATT
43309322 ATAAAATACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
ATATTTGTAACTAAAATTAATATT
Found at i:43309472 original size:22 final size:22
Alignment explanation
Indices: 43309427--43309472 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
43309417 AACTTAATTA
*
43309427 ATTAATATTATACATAACTTAC
1 ATTAATATTATACATAACTGAC
43309449 ATTAATATTATACATAGA-TGAC
1 ATTAATATTATACATA-ACTGAC
43309471 AT
1 AT
43309473 AACTTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (22 bp):
ATTAATATTATACATAACTGAC
Found at i:43309473 original size:31 final size:31
Alignment explanation
Indices: 43309437--43309697 Score: 247
Period size: 31 Copynumber: 8.1 Consensus size: 31
43309427 ATTAATATTA
* *
43309437 TACATAACTTACATTAATATTATACATAGAT
1 TACATAACTTAAATTAATATTATACATAAAT
* *
43309468 GACATAACTTAATTAATTAATATTATACATAACT
1 TACATAACTT-A--AATTAATATTATACATAAAT
* * *
43309502 TACATAAATT-AATTACTTAATATACATAAAT
1 TACATAACTTAAATTA-ATATTATACATAAAT
* *
43309533 TACATAACTTACATTAATATGATACATAAAT
1 TACATAACTTAAATTAATATTATACATAAAT
* *
43309564 GACATAACTTAATTAATTAATATTATACATAACT
1 TACATAACTT-A--AATTAATATTATACATAAAT
* * *
43309598 TACATAAATT-AATTAGTTAATATACATAAAT
1 TACATAACTTAAATTA-ATATTATACATAAAT
* *
43309629 TACATAACTTACATTAATATGATACATAAAT
1 TACATAACTTAAATTAATATTATACATAAAT
* *
43309660 GACATAACTTAGTTAATTAATATTATACATAACT
1 TACATAACTTA---AATTAATATTATACATAAAT
43309694 TACA
1 TACA
43309698 ACTTACATAA
Statistics
Matches: 184, Mismatches: 33, Indels: 23
0.77 0.14 0.10
Matches are distributed among these distances:
30 10 0.05
31 94 0.51
32 10 0.05
34 70 0.38
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (31 bp):
TACATAACTTAAATTAATATTATACATAAAT
Found at i:43309475 original size:56 final size:56
Alignment explanation
Indices: 43309412--43309697 Score: 257
Period size: 56 Copynumber: 4.7 Consensus size: 56
43309402 TATTGTAAGG
*
43309412 GACATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAGAT
1 GACATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
43309468 GACATAACTTAATTAATTAATATTATACATAACTTACATAAATTAATTACTTAATATACATAAAT
1 GACATAACTTAATTAATTAATATTATACATAACTTAC----ATTAA-TA--T--TATACATAAAT
* * * * *
43309533 TACATAACTTACATTAATATGATACATAAATGACATAACTTAATTAATTAATATTATACATAACT
1 GACATAACTTA-ATTAAT-T-A-ATAT-TAT-ACATAACTT-A--CATTAATATTATACATAAAT
* * * *
43309598 TACATAAATTAATTAGTTAATATACATAAATTACATAACTTACATTAATATGATACATAAAT
1 GACATAACTTAATTAATTAATAT---T--A-TACATAACTTACATTAATATTATACATAAAT
*
43309660 GACATAACTTAGTTAATTAATATTATACATAACTTACA
1 GACATAACTTAATTAATTAATATTATACATAACTTACA
43309698 ACTTACATAA
Statistics
Matches: 190, Mismatches: 17, Indels: 46
0.75 0.07 0.18
Matches are distributed among these distances:
56 50 0.26
57 1 0.01
59 1 0.01
60 5 0.03
61 5 0.03
62 37 0.19
63 3 0.02
64 6 0.03
65 50 0.26
66 7 0.04
67 2 0.01
68 1 0.01
69 5 0.03
70 7 0.04
71 9 0.05
72 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (56 bp):
GACATAACTTAATTAATTAATATTATACATAACTTACATTAATATTATACATAAAT
Found at i:43309507 original size:9 final size:9
Alignment explanation
Indices: 43309493--43309817 Score: 72
Period size: 9 Copynumber: 37.7 Consensus size: 9
43309483 ATTAATATTA
43309493 TACATAACT
1 TACATAACT
*
43309502 TACATAAAT
1 TACATAACT
*
43309511 TA-ATTACT
1 TACATAACT
43309519 TA-AT-A--
1 TACATAACT
*
43309524 TACATAAAT
1 TACATAACT
43309533 TACATAACT
1 TACATAACT
*
43309542 TACATTAATAT
1 TACA-TAA-CT
*
43309553 GATACATAAAT
1 --TACATAACT
*
43309564 GACATAACT
1 TACATAACT
43309573 TA-ATTAA-T
1 TACA-TAACT
*
43309581 TA-AT-ATT
1 TACATAACT
43309588 ATACATAACT
1 -TACATAACT
*
43309598 TACATAAAT
1 TACATAACT
* *
43309607 TA-ATTAGT
1 TACATAACT
43309615 TA-AT-A--
1 TACATAACT
*
43309620 TACATAAAT
1 TACATAACT
43309629 TACATAACT
1 TACATAACT
*
43309638 TACATTAATAT
1 TACA-TAA-CT
*
43309649 GATACATAAAT
1 --TACATAACT
*
43309660 GACATAACT
1 TACATAACT
**
43309669 TAGTTAA-T
1 TACATAACT
*
43309677 TA-AT-ATT
1 TACATAACT
43309684 ATACATAACT
1 -TACATAACT
43309694 TAC--AACT
1 TACATAACT
43309701 TACATAACT
1 TACATAACT
**
43309710 TACATATTTT
1 TACATA-ACT
*
43309720 TA-ATTA-T
1 TACATAACT
* *
43309727 T-CGTAAAT
1 TACATAACT
43309735 TACATAACT
1 TACATAACT
* *
43309744 TACTTAATT
1 TACATAACT
*
43309753 TTCATAA--
1 TACATAACT
*
43309760 TAAATAACT
1 TACATAACT
*
43309769 TACATAAAT
1 TACATAACT
* *
43309778 AAC-T-TCT
1 TACATAACT
43309785 TACATAACT
1 TACATAACT
** *
43309794 TATGTGACT
1 TACATAACT
43309803 TACATAACT
1 TACATAACT
43309812 TACATA
1 TACATA
43309818 GCATAATTTT
Statistics
Matches: 233, Mismatches: 48, Indels: 70
0.66 0.14 0.20
Matches are distributed among these distances:
5 4 0.02
6 6 0.03
7 27 0.12
8 32 0.14
9 131 0.56
10 13 0.06
11 6 0.03
12 6 0.03
13 8 0.03
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (9 bp):
TACATAACT
Found at i:43309559 original size:22 final size:21
Alignment explanation
Indices: 43309483--43309561 Score: 60
Period size: 22 Copynumber: 3.8 Consensus size: 21
43309473 AACTTAATTA
43309483 ATTAATATTATACATAACTTAC
1 ATTAATA-TATACATAACTTAC
*
43309505 A-TAA-AT-TA-ATTACTTA-
1 ATTAATATATACATAACTTAC
*
43309521 ATATACATAAATTACATAACTTAC
1 AT-TA-ATATA-TACATAACTTAC
43309545 ATTAATATGATACATAA
1 ATTAATAT-ATACATAA
43309562 ATGACATAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 18
0.67 0.06 0.27
Matches are distributed among these distances:
16 1 0.02
17 7 0.16
18 4 0.09
19 2 0.05
20 2 0.05
21 3 0.07
22 13 0.30
23 10 0.23
24 2 0.05
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.38
Consensus pattern (21 bp):
ATTAATATATACATAACTTAC
Found at i:43309571 original size:96 final size:96
Alignment explanation
Indices: 43309437--43309697 Score: 486
Period size: 96 Copynumber: 2.7 Consensus size: 96
43309427 ATTAATATTA
* *
43309437 TACATAACTTACATTAATATTATACATAGATGACATAACTTAATTAATTAATATTATACATAACT
1 TACATAACTTACATTAATATGATACATAAATGACATAACTTAATTAATTAATATTATACATAACT
43309502 TACATAAATTAATTACTTAATATACATAAAT
66 TACATAAATTAATTACTTAATATACATAAAT
43309533 TACATAACTTACATTAATATGATACATAAATGACATAACTTAATTAATTAATATTATACATAACT
1 TACATAACTTACATTAATATGATACATAAATGACATAACTTAATTAATTAATATTATACATAACT
*
43309598 TACATAAATTAATTAGTTAATATACATAAAT
66 TACATAAATTAATTACTTAATATACATAAAT
*
43309629 TACATAACTTACATTAATATGATACATAAATGACATAACTTAGTTAATTAATATTATACATAACT
1 TACATAACTTACATTAATATGATACATAAATGACATAACTTAATTAATTAATATTATACATAACT
43309694 TACA
66 TACA
43309698 ACTTACATAA
Statistics
Matches: 161, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 161 1.00
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (96 bp):
TACATAACTTACATTAATATGATACATAAATGACATAACTTAATTAATTAATATTATACATAACT
TACATAAATTAATTACTTAATATACATAAAT
Found at i:43309772 original size:34 final size:34
Alignment explanation
Indices: 43309697--43309775 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
43309687 CATAACTTAC
* * ***
43309697 AACTTACATAACTTACATATTTTTAATTATTCGT
1 AACTTACATAACTTACATAATTTTAATAATAAAT
* * *
43309731 AAATTACATAACTTACTTAATTTTCATAATAAAT
1 AACTTACATAACTTACATAATTTTAATAATAAAT
43309765 AACTTACATAA
1 AACTTACATAA
43309776 ATAACTTCTT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.42
Consensus pattern (34 bp):
AACTTACATAACTTACATAATTTTAATAATAAAT
Found at i:43315366 original size:66 final size:65
Alignment explanation
Indices: 43315272--43315442 Score: 200
Period size: 66 Copynumber: 2.6 Consensus size: 65
43315262 GAGCAAATTA
* * * * *
43315272 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGATGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAACGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCA
43315336 G
65 G
*
43315337 CTACAACTTAAAGCAGATGCAGCAACGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCA
1 C-ACAACTTAAAGCAGATGCAGCAACGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCA
43315402 G
65 G
* * * * * *
43315403 CAGCAGCTTAGAGCAGATGCGGCAGCAAGAGAAGCAGAGG
1 CA-CAACTTAAAGCAGATGCAGCAACGAGAGAAGCTGAGG
43315443 CGACAGCGAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 85 0.93
67 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAACGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:43315483 original size:42 final size:42
Alignment explanation
Indices: 43315424--43315525 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
43315414 AGCAGATGCG
* * *
43315424 GCAGCAAGAGAAGCAGAGGCGACAGCGAGAGAAGAATAGGCT
1 GCAGCAAGGGAAGCAGAGGCGAAAGCGAGAGAAGAAGAGGCT
* * *
43315466 GCAGCAAGGGAAGCAGAGGCTAAAGCGAGGGAAGCAGAGGCT
1 GCAGCAAGGGAAGCAGAGGCGAAAGCGAGAGAAGAAGAGGCT
* *
43315508 ACAGCGAGGGAAGCAGAG
1 GCAGCAAGGGAAGCAGAG
43315526 CAGCGTCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.38, C:0.17, G:0.41, T:0.04
Consensus pattern (42 bp):
GCAGCAAGGGAAGCAGAGGCGAAAGCGAGAGAAGAAGAGGCT
Found at i:43315486 original size:21 final size:21
Alignment explanation
Indices: 43315414--43315525 Score: 109
Period size: 21 Copynumber: 5.3 Consensus size: 21
43315404 AGCAGCTTAG
* * * *
43315414 AGCAGATGCGGCAGCAAGAGA
1 AGCAGAGGCTGCAGCGAGGGA
*
43315435 AGCAGAGGC-GACAGCGAGAGA
1 AGCAGAGGCTG-CAGCGAGGGA
* * *
43315456 AGAATAGGCTGCAGCAAGGGA
1 AGCAGAGGCTGCAGCGAGGGA
**
43315477 AGCAGAGGCTAAAGCGAGGGA
1 AGCAGAGGCTGCAGCGAGGGA
*
43315498 AGCAGAGGCTACAGCGAGGGA
1 AGCAGAGGCTGCAGCGAGGGA
43315519 AGCAGAG
1 AGCAGAG
43315526 CAGCGTCAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
20 1 0.01
21 75 0.97
22 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.41, T:0.04
Consensus pattern (21 bp):
AGCAGAGGCTGCAGCGAGGGA
Found at i:43315879 original size:43 final size:42
Alignment explanation
Indices: 43315831--43316036 Score: 220
Period size: 43 Copynumber: 4.7 Consensus size: 42
43315821 ATCTGCCAAA
*
43315831 TTTAGCGGCGTTTTTGGTAAAAGCGCCGCTATAGATTAGGGTC
1 TTTAGCGGCGTTTTTGG-AAAAGCGCCGCTATAGATCAGGGTC
** *
43315874 TTTAGCGGCGTTTTTGCGCGAAGCGCCGCTATATAGA-CAAAGGGTA
1 TTTAGCGGCGTTTTTG-GAAAAGCGCCGC--TATAGATC--AGGGTC
* *
43315920 TTTAGCGGCGTTTTCTGGATAAGCACCGCTATAGATCAGGGTC
1 TTTAGCGGCGTTTT-TGGAAAAGCGCCGCTATAGATCAGGGTC
* *
43315963 TATT-GCGGCATTTTCTGGATAAGCGCCGCTATAGATCAGGGTC
1 T-TTAGCGGCGTTTT-TGGAAAAGCGCCGCTATAGATCAGGGTC
43316006 TATT-GCGGCGTTTTTGGGAAAAGCGCCGCTA
1 T-TTAGCGGCGTTTTT-GGAAAAGCGCCGCTA
43316037 AAGGCCATGT
Statistics
Matches: 142, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
42 1 0.01
43 95 0.67
44 9 0.06
45 7 0.05
46 28 0.20
47 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTGGAAAAGCGCCGCTATAGATCAGGGTC
Found at i:43315987 original size:89 final size:89
Alignment explanation
Indices: 43315830--43316036 Score: 232
Period size: 89 Copynumber: 2.4 Consensus size: 89
43315820 AATCTGCCAA
* * * *
43315830 ATTTAGCGGCGTTTTTGGTAAAAGCGCCGCTATAGATTAGGGTCTTTAGCGGCGTTTTTGCGCGA
1 ATTTAGCGGCGTTTTTGGTAAAAGCACCGCTATAGATCAGGGTCTTTAGCGGCATTTTTGCGAGA
43315895 AGCGCCGCTATATAGACAAAGGGT
66 AGCGCCGCTATATAGACAAAGGGT
*
43315919 ATTTAGCGGCGTTTTCTGG-ATAAGCACCGCTATAGATCAGGGTCTATT-GCGGCATTTTCTG-G
1 ATTTAGCGGCGTTTT-TGGTAAAAGCACCGCTATAGATCAGGGTCT-TTAGCGGCATTTT-TGCG
*
43315981 ATAAGCGCCGC--TATAGATC--AGGGT
63 AGAAGCGCCGCTATATAGA-CAAAGGGT
* * *
43316005 CTATT-GCGGCGTTTTTGGGAAAAGCGCCGCTA
1 AT-TTAGCGGCGTTTTTGGTAAAAGCACCGCTA
43316037 AAGGCCATGT
Statistics
Matches: 103, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
85 3 0.03
86 27 0.26
87 8 0.08
88 1 0.01
89 57 0.55
90 7 0.07
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (89 bp):
ATTTAGCGGCGTTTTTGGTAAAAGCACCGCTATAGATCAGGGTCTTTAGCGGCATTTTTGCGAGA
AGCGCCGCTATATAGACAAAGGGT
Found at i:43316103 original size:43 final size:43
Alignment explanation
Indices: 43316024--43316168 Score: 179
Period size: 43 Copynumber: 3.3 Consensus size: 43
43316014 CGTTTTTGGG
* * *
43316024 AAAAGCGCCGCTAAAGGCCATGTATCTATAGCGGCGCTTATATA
1 AAAAACGCCGCTAAAGACCCTG-ATCTATAGCGGCGCTTATATA
43316068 AAAAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTT-TCA-A
1 AAAAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTAT-ATA
* * *
43316110 CAAAAACGCCGCTAAAGACACC-AATCTATAGCGGCGGTTATATT
1 -AAAAACGCCGCTAAAGAC-CCTGATCTATAGCGGCGCTTATATA
43316154 AAAAACGCCGCTAAA
1 AAAAACGCCGCTAAA
43316169 ACTCTTAGTC
Statistics
Matches: 90, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
42 2 0.02
43 66 0.73
44 22 0.24
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTATATA
Found at i:43316332 original size:22 final size:22
Alignment explanation
Indices: 43316304--43316346 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
43316294 TTGCGGCACT
*
43316304 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
*
43316326 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
43316347 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:43318545 original size:12 final size:12
Alignment explanation
Indices: 43318530--43318557 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
43318520 AAATGATCAC
43318530 AAAAAACATAAA
1 AAAAAACATAAA
43318542 AAAAAACATAAA
1 AAAAAACATAAA
43318554 AAAA
1 AAAA
43318558 TGGGATAAAA
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:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAAAACATAAA
Found at i:43321837 original size:5 final size:5
Alignment explanation
Indices: 43321827--43321857 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
43321817 TGAGCATTCG
*
43321827 ATCGA ATCGA ATCGA CTCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
43321858 AATTTTCGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:43322605 original size:7 final size:7
Alignment explanation
Indices: 43322593--43322618 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43322583 TTGGGGTAGA
43322593 TGGGAGG
1 TGGGAGG
43322600 TGGGAGG
1 TGGGAGG
43322607 TGGGAGG
1 TGGGAGG
43322614 TGGGA
1 TGGGA
43322619 TGAGAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.69, T:0.15
Consensus pattern (7 bp):
TGGGAGG
Found at i:43322654 original size:31 final size:30
Alignment explanation
Indices: 43322619--43322678 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
43322609 GGAGGTGGGA
*
43322619 TGAGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGAG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
43322650 TGAGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGAGAGAGAATAAAAATTTTAGGGGAAAA
43322679 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.20
Consensus pattern (30 bp):
TGAGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:43322915 original size:18 final size:18
Alignment explanation
Indices: 43322892--43322928 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
43322882 TATAGTTTGA
43322892 TATTTGAATTATTCGAAT
1 TATTTGAATTATTCGAAT
*
43322910 TATTTGAGTTATTCGAAT
1 TATTTGAATTATTCGAAT
43322928 T
1 T
43322929 CGAAAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (18 bp):
TATTTGAATTATTCGAAT
Found at i:43323285 original size:16 final size:16
Alignment explanation
Indices: 43323264--43323294 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
43323254 CTTCCAAAAC
43323264 CAAAATGTTGTAGGCT
1 CAAAATGTTGTAGGCT
43323280 CAAAATGTTGTAGGC
1 CAAAATGTTGTAGGC
43323295 AAAATACCTT
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:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (16 bp):
CAAAATGTTGTAGGCT
Found at i:43323299 original size:14 final size:15
Alignment explanation
Indices: 43323263--43323299 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
43323253 TCTTCCAAAA
43323263 CCAAAATGTTGTAGG
1 CCAAAATGTTGTAGG
43323278 CTCAAAATGTTGTAGG
1 C-CAAAATGTTGTAGG
43323294 -CAAAAT
1 CCAAAAT
43323300 ACCTTACACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 1 0.05
16 14 0.67
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (15 bp):
CCAAAATGTTGTAGG
Found at i:43323721 original size:20 final size:21
Alignment explanation
Indices: 43323692--43323731 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
43323682 AAAATAACGA
*
43323692 TGACTTATTCATGT-TTCCTG
1 TGACTAATTCATGTGTTCCTG
*
43323712 TGACTAATTCTTGTGTTCCT
1 TGACTAATTCATGTGTTCCT
43323732 AAATGGTCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.15, C:0.20, G:0.15, T:0.50
Consensus pattern (21 bp):
TGACTAATTCATGTGTTCCTG
Found at i:43329702 original size:4 final size:4
Alignment explanation
Indices: 43329693--43329765 Score: 146
Period size: 4 Copynumber: 18.2 Consensus size: 4
43329683 TTCATAGTTA
43329693 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
43329741 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
43329766 GATTTAATTA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 69 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:43332020 original size:33 final size:35
Alignment explanation
Indices: 43331968--43332040 Score: 114
Period size: 34 Copynumber: 2.1 Consensus size: 35
43331958 ATTGATAAAA
*
43331968 AAAAATTTGGAAACTTCAGGTAC-TAAACTGATAT
1 AAAAATTTGAAAACTTCAGGTACTTAAACTGATAT
*
43332002 AAAAA-TTGAAAACTTCAGGTACTTAAATTGATAT
1 AAAAATTTGAAAACTTCAGGTACTTAAACTGATAT
43332036 AAAAA
1 AAAAA
43332041 GTTCTCTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 16 0.44
34 20 0.56
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (35 bp):
AAAAATTTGAAAACTTCAGGTACTTAAACTGATAT
Found at i:43332262 original size:90 final size:84
Alignment explanation
Indices: 43332159--43332384 Score: 283
Period size: 90 Copynumber: 2.6 Consensus size: 84
43332149 CTTCAAAGTA
* * **
43332159 TTTTTTTGCACTCAATTAGGTACTTGAACTTTCAAAAGGCATAAAAAAGGTCCTCAAACTTTTTA
1 TTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATAAAAAAGACCCTCAAACTTTTT-
43332224 AAAAAAAAAGCAATTAAGCCCTTAC
65 -AAAAAAAAGCAATTAAG-CC---C
* * * *
43332249 TTTTTTTGCACTCAATTGGGTGCTTGAACTTTCAAAATACATAAAAAAAACCCTCAAACTTTTTC
1 TTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATAAAAAAGACCCTCAAACTTTTTA
*
43332314 AAAAATAGCAATTAAGCCC
66 AAAAAAAGCAATTAAGCCC
* *
43332333 TTTTTTTGCAATCAATTGGGTACTTGAA-TTGTCAAAATGCATCAAAAAGACC
1 TTTTTTTGCACTCAATTGGGTACTTGAACTT-TCAAAATGCATAAAAAAGACC
43332385 TTAGATTGTT
Statistics
Matches: 121, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
83 2 0.02
84 45 0.37
87 2 0.02
88 15 0.12
90 57 0.47
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (84 bp):
TTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATAAAAAAGACCCTCAAACTTTTTA
AAAAAAAGCAATTAAGCCC
Found at i:43338944 original size:13 final size:13
Alignment explanation
Indices: 43338926--43338950 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43338916 AGTTCTTCAT
43338926 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
43338939 TGCTTTTGAGAA
1 TGCTTTTGAGAA
43338951 ATTTGAGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:43339723 original size:60 final size:60
Alignment explanation
Indices: 43339650--43339771 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
43339640 CCTTAGATTA
43339650 AATGTTTGAGAATATAAAACAAAATACTTAGAATTATAAAAGCAAACATAGTTTCAATTG
1 AATGTTTGAGAATATAAAACAAAATACTTAGAATTATAAAAGCAAACATAGTTTCAATTG
43339710 AATGTTTGAGAATATAAAACAAAATACTTAGAATTATAAAAGCAAACATAGTTTCAATTG
1 AATGTTTGAGAATATAAAACAAAATACTTAGAATTATAAAAGCAAACATAGTTTCAATTG
43339770 AA
1 AA
43339772 CAGTTTAGTG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (60 bp):
AATGTTTGAGAATATAAAACAAAATACTTAGAATTATAAAAGCAAACATAGTTTCAATTG
Found at i:43342883 original size:9 final size:9
Alignment explanation
Indices: 43342871--43343000 Score: 63
Period size: 9 Copynumber: 13.9 Consensus size: 9
43342861 AGTATGTCTA
43342871 TTATGTATG
1 TTATGTATG
*
43342880 TTATGTATA
1 TTATGTATG
*
43342889 TTA-CTAT-
1 TTATGTATG
43342896 TTATGTATG
1 TTATGTATG
*
43342905 TTACGTA-G
1 TTATGTATG
43342913 TATAT-TATTG
1 T-TATGTA-TG
43342923 TTTATGTATG
1 -TTATGTATG
*
43342933 TTATGTATA
1 TTATGTATG
43342942 TTACTGTTTAT-
1 TTA-TG--TATG
43342953 TTCATGTATG
1 TT-ATGTATG
* *
43342963 TTATGTTTA
1 TTATGTATG
*
43342972 TTATTGTTTATA
1 TTA-TG--TATG
43342984 TTATGTATG
1 TTATGTATG
*
43342993 TCATGTAT
1 TTATGTAT
43343001 ATTACAATTT
Statistics
Matches: 95, Mismatches: 11, Indels: 30
0.70 0.08 0.22
Matches are distributed among these distances:
7 3 0.03
8 10 0.11
9 51 0.54
10 12 0.13
11 9 0.09
12 10 0.11
ACGTcount: A:0.25, C:0.04, G:0.15, T:0.57
Consensus pattern (9 bp):
TTATGTATG
Found at i:43342926 original size:28 final size:25
Alignment explanation
Indices: 43342871--43342952 Score: 119
Period size: 25 Copynumber: 3.2 Consensus size: 25
43342861 AGTATGTCTA
*
43342871 TTATGTATGTTATGTATATTACTAT
1 TTATGTATGTTATGTATATTACTGT
*
43342896 TTATGTATGTTACGTAGTATATTATTGT
1 TTATGTATGTTA--T-GTATATTACTGT
43342924 TTATGTATGTTATGTATATTACTGT
1 TTATGTATGTTATGTATATTACTGT
43342949 TTAT
1 TTAT
43342953 TTCATGTATG
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
25 27 0.53
26 1 0.02
27 1 0.02
28 22 0.43
ACGTcount: A:0.26, C:0.04, G:0.15, T:0.56
Consensus pattern (25 bp):
TTATGTATGTTATGTATATTACTGT
Found at i:43342959 original size:21 final size:20
Alignment explanation
Indices: 43342935--43343004 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
43342925 TATGTATGTT
43342935 ATGTATATTACTGTTTATTTC
1 ATGTATATTA-TGTTTATTTC
* *
43342956 ATGTATGTTATGTTTATTATT
1 ATGTATATTATGTTTATT-TC
* * *
43342977 GTTTATATTATG--TATGTC
1 ATGTATATTATGTTTATTTC
43342995 ATGTATATTA
1 ATGTATATTA
43343005 CAATTTACAT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
18 9 0.23
19 3 0.08
20 8 0.21
21 19 0.49
ACGTcount: A:0.26, C:0.04, G:0.13, T:0.57
Consensus pattern (20 bp):
ATGTATATTATGTTTATTTC
Found at i:43342962 original size:30 final size:29
Alignment explanation
Indices: 43342871--43343080 Score: 200
Period size: 30 Copynumber: 7.2 Consensus size: 29
43342861 AGTATGTCTA
43342871 TTATGTATGTTATGTATATTAC----TAT
1 TTATGTATGTTATGTATATTACTGTTTAT
* *
43342896 TTATGTATGTTACGTAGTA-TA-T-TATTGT
1 TTATGTATGTTATGTA-TATTACTGT-TTAT
43342924 TTATGTATGTTATGTATATTACTGTTTAT
1 TTATGTATGTTATGTATATTACTGTTTAT
* *
43342953 TTCATGTATGTTATGTTTATTATTGTTTAT
1 TT-ATGTATGTTATGTATATTACTGTTTAT
* ** *
43342983 ATTATGTATGTCATGTATATTACAATTTACA
1 -TTATGTATGTTATGTATATTACTGTTTA-T
* **
43343014 TTATGTATGTTCTGTATATTGTTGTTTAT
1 TTATGTATGTTATGTATATTACTGTTTAT
*
43343043 ATTATTTATGTTATGTATATTACTGTTTAT
1 -TTATGTATGTTATGTATATTACTGTTTAT
43343073 ATTATGTA
1 -TTATGTA
43343081 CCTGATTTTA
Statistics
Matches: 149, Mismatches: 24, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
25 17 0.11
26 2 0.01
27 2 0.01
28 19 0.13
29 6 0.04
30 101 0.68
31 2 0.01
ACGTcount: A:0.26, C:0.04, G:0.13, T:0.57
Consensus pattern (29 bp):
TTATGTATGTTATGTATATTACTGTTTAT
Found at i:43342964 original size:15 final size:15
Alignment explanation
Indices: 43342924--43343080 Score: 50
Period size: 15 Copynumber: 10.5 Consensus size: 15
43342914 ATATTATTGT
*
43342924 TTATGTATG-TTATG
1 TTATGTATGTTTATA
43342938 TATAT-TACTGTTTAT-
1 T-TATGTA-TGTTTATA
*
43342953 TTCATGTATG-TTATGT
1 TT-ATGTATGTTTAT-A
43342969 TTAT-TATTGTTTATA
1 TTATGTA-TGTTTATA
43342984 TTATGTATGTCATGTATA
1 TTATGTATGT--T-TATA
* * *
43343002 TTA--CA-ATTTACA
1 TTATGTATGTTTATA
*
43343014 TTATGTATGTTCTGTA
1 TTATGTATGTT-TATA
43343030 -TATTGT-TGTTTATA
1 TTA-TGTATGTTTATA
* *
43343044 TTATTTATG-TTATG
1 TTATGTATGTTTATA
43343058 TATAT-TACTGTTTATA
1 T-TATGTA-TGTTTATA
43343074 TTATGTA
1 TTATGTA
43343081 CCTGATTTTA
Statistics
Matches: 107, Mismatches: 12, Indels: 46
0.65 0.07 0.28
Matches are distributed among these distances:
12 6 0.06
13 1 0.01
14 23 0.21
15 42 0.39
16 27 0.25
17 1 0.01
18 7 0.07
ACGTcount: A:0.25, C:0.04, G:0.13, T:0.57
Consensus pattern (15 bp):
TTATGTATGTTTATA
Found at i:43343002 original size:60 final size:59
Alignment explanation
Indices: 43342869--43343080 Score: 240
Period size: 60 Copynumber: 3.6 Consensus size: 59
43342859 TTAGTATGTC
* * *
43342869 TATTATGTATGTTATGTATATTAC----TATTTATGTATGTTACGTAGTA-TATT-ATTG
1 TATTATGTATGTTATGTATATTACTGTTTATTTATGTATGTTATGTA-TATTATTGTTTA
*
43342923 T-TTATGTATGTTATGTATATTACTGTTTATTTCATGTATGTTATGTTTATTATTGTTTA
1 TATTATGTATGTTATGTATATTACTGTTTATTT-ATGTATGTTATGTATATTATTGTTTA
* ** * * *
43342982 TATTATGTATGTCATGTATATTACAATTTACATTATGTATGTTCTGTATATTGTTGTTTA
1 TATTATGTATGTTATGTATATTACTGTTTA-TTTATGTATGTTATGTATATTATTGTTTA
*
43343042 TATTATTTATGTTATGTATATTACTGTTTATATTATGTA
1 TATTATGTATGTTATGTATATTACTGTTTAT-TTATGTA
43343081 CCTGATTTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
53 22 0.17
54 1 0.01
57 7 0.05
58 16 0.12
59 3 0.02
60 81 0.61
61 2 0.02
ACGTcount: A:0.26, C:0.04, G:0.13, T:0.57
Consensus pattern (59 bp):
TATTATGTATGTTATGTATATTACTGTTTATTTATGTATGTTATGTATATTATTGTTTA
Found at i:43347076 original size:27 final size:27
Alignment explanation
Indices: 43347018--43347211 Score: 234
Period size: 27 Copynumber: 7.3 Consensus size: 27
43347008 TATAACAGTT
*
43347018 ATTTTACCCTATGGGGGTATTTTCGATC
1 ATTTTACCCTATGGGGGTA-TTTCGGTC
* *
43347046 ATTTTACCCTATAGGAGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * * *
43347073 ATTTTGCCCTGTGGGGGTATTTCGATG
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
43347100 ATTTTACCCTATGGGGGTATTTCGATC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
43347127 ATTTTACCTTAT-GGGG---TTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
*
43347150 ATTTTACCCTATGGGAGTATTTCGGTC
1 ATTTTACCCTATGGGGGTATTTCGGTC
* * *
43347177 ATTTTACCCTATGGGTGTATTTTGGTT
1 ATTTTACCCTATGGGGGTATTTCGGTC
43347204 ATTTTACC
1 ATTTTACC
43347212 TATTTTGGGG
Statistics
Matches: 143, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
23 17 0.12
24 3 0.02
26 4 0.03
27 102 0.71
28 17 0.12
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (27 bp):
ATTTTACCCTATGGGGGTATTTCGGTC
Found at i:43347181 original size:77 final size:80
Alignment explanation
Indices: 43347018--43347212 Score: 252
Period size: 77 Copynumber: 2.5 Consensus size: 80
43347008 TATAACAGTT
* * *
43347018 ATTTTACCCTATGGGGGTATTTTCGATCATTTTACCCTATAGGAGTATTTCGGTCATTTTGCCCT
1 ATTTTACCCTATGGGGGTA-TTTCGATCATTTTACCTTATAGGAG-AGTTCGGTCATTTTACCCT
* * *
43347083 GTGGGGGTATTTCGATG
64 ATGGGAGTATTTCGATC
43347100 ATTTTACCCTATGGGGGTATTTCGATCATTTTACCTTAT-GG-G-GTTCGGTCATTTTACCCTAT
1 ATTTTACCCTATGGGGGTATTTCGATCATTTTACCTTATAGGAGAGTTCGGTCATTTTACCCTAT
*
43347162 GGGAGTATTTCGGTC
66 GGGAGTATTTCGATC
* * * *
43347177 ATTTTACCCTATGGGTGTATTTTGGTTATTTTACCT
1 ATTTTACCCTATGGGGGTATTTCGATCATTTTACCT
43347213 ATTTTGGGGT
Statistics
Matches: 102, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
77 61 0.60
79 1 0.01
80 2 0.02
81 19 0.19
82 19 0.19
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.44
Consensus pattern (80 bp):
ATTTTACCCTATGGGGGTATTTCGATCATTTTACCTTATAGGAGAGTTCGGTCATTTTACCCTAT
GGGAGTATTTCGATC
Found at i:43349533 original size:9 final size:9
Alignment explanation
Indices: 43349519--43349737 Score: 69
Period size: 9 Copynumber: 23.7 Consensus size: 9
43349509 ATATTATTAG
43349519 TATGTATAT
1 TATGTATAT
*
43349528 TATGTATGT
1 TATGTATAT
43349537 TATGTATAT
1 TATGTATAT
*
43349546 T-TCTAT-T
1 TATGTATAT
* *
43349553 TATGCATGT
1 TATGTATAT
43349562 TATGTA-AT
1 TATGTATAT
*
43349570 ATAT-TATTGCT
1 -TATGTA-T-AT
*
43349581 TATGTATGT
1 TATGTATAT
43349590 TATGTATAT
1 TATGTATAT
*
43349599 TAATTTTTATAT
1 T-A--TGTATAT
* *
43349611 AATGTATGT
1 TATGTATAT
*
43349620 TATGTTTAT
1 TATGTATAT
*
43349629 TATTGTTTGTAT
1 TA-TG--TATAT
* *
43349641 TATATATGT
1 TATGTATAT
*
43349650 TATGTTTAT
1 TATGTATAT
*
43349659 TACAATTTATAT
1 T---ATGTATAT
*
43349671 TATGTATGT
1 TATGTATAT
43349680 TATGTATA-
1 TATGTATAT
*
43349688 T-TGT-TGT
1 TATGTATAT
43349695 T-T-TATAT
1 TATGTATAT
* *
43349702 TATTTATGT
1 TATGTATAT
43349711 TATGTATAT
1 TATGTATAT
43349720 TACTGTTTATAT
1 TA-TG--TATAT
43349732 TATGTA
1 TATGTA
43349738 CCTGACTTTA
Statistics
Matches: 153, Mismatches: 34, Indels: 46
0.66 0.15 0.20
Matches are distributed among these distances:
6 2 0.01
7 10 0.07
8 12 0.08
9 87 0.57
10 9 0.06
11 7 0.05
12 26 0.17
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.58
Consensus pattern (9 bp):
TATGTATAT
Found at i:43349608 original size:25 final size:25
Alignment explanation
Indices: 43349527--43349608 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
43349517 AGTATGTATA
* *
43349527 TTATGTATGTTATGTATATTTCTAT
1 TTATGTATGTTATGTATATTTATTT
* *
43349552 TTATGCATGTTATGTAATATATTATTGC
1 TTATGTATGTTATGT-ATAT-TTATT-T
*
43349580 TTATGTATGTTATGTATATTAATTT
1 TTATGTATGTTATGTATATTTATTT
43349605 TTAT
1 TTAT
43349609 ATAATGTATG
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
25 18 0.38
26 8 0.17
27 7 0.15
28 14 0.30
ACGTcount: A:0.27, C:0.04, G:0.12, T:0.57
Consensus pattern (25 bp):
TTATGTATGTTATGTATATTTATTT
Found at i:43349618 original size:30 final size:30
Alignment explanation
Indices: 43349523--43349737 Score: 180
Period size: 30 Copynumber: 7.4 Consensus size: 30
43349513 TATTAGTATG
*
43349523 TATATTATGTATGTTATG--TA-T-ATTTC
1 TATATTATGTATGTTATGTATATTAATTTT
* *
43349549 TAT-TTATGCATGTTATGTA-A-TATATTAT
1 TATATTATGTATGTTATGTATATTA-ATTTT
**
43349577 T-GCTTATGTATGTTATGTATATTAATTTT
1 TATATTATGTATGTTATGTATATTAATTTT
* *
43349606 TATATAATGTATGTTATGTTTATT-ATTGTT
1 TATATTATGTATGTTATGTATATTAATT-TT
* * * *
43349636 TGTATTATATATGTTATGTTTATTACA-ATT
1 TATATTATGTATGTTATGTATATTA-ATTTT
**
43349666 TATATTATGTATGTTATGTATATTGTTGTTT
1 TATATTATGTATGTTATGTATATTAAT-TTT
* * *
43349697 TATATTATTTATGTTATGTATATTACTGTT
1 TATATTATGTATGTTATGTATATTAATTTT
43349727 TATATTATGTA
1 TATATTATGTA
43349738 CCTGACTTTA
Statistics
Matches: 151, Mismatches: 25, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
25 13 0.09
26 5 0.03
28 19 0.13
29 9 0.06
30 78 0.52
31 26 0.17
32 1 0.01
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.58
Consensus pattern (30 bp):
TATATTATGTATGTTATGTATATTAATTTT
Found at i:43349660 original size:60 final size:61
Alignment explanation
Indices: 43349580--43349737 Score: 203
Period size: 60 Copynumber: 2.6 Consensus size: 61
43349570 ATATTATTGC
* * * * *
43349580 TTATGTATGTTATGTATATTAATTTTTATATAATGTATGTTATGTTTATTATTG-TTTGTA
1 TTATATATGTTATGTATATTAATATTTATATTATGTATGTTATGTATATTATTGTTTTATA
* *
43349640 TTATATATGTTATGTTTATTACA-ATTTATATTATGTATGTTATGTATATTGTTGTTTTATA
1 TTATATATGTTATGTATATTA-ATATTTATATTATGTATGTTATGTATATTATTGTTTTATA
* * *
43349701 TTATTTATGTTATGTATATTACTGTTTATATTATGTA
1 TTATATATGTTATGTATATTAATATTTATATTATGTA
43349738 CCTGACTTTA
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
60 46 0.55
61 38 0.45
ACGTcount: A:0.27, C:0.01, G:0.12, T:0.59
Consensus pattern (61 bp):
TTATATATGTTATGTATATTAATATTTATATTATGTATGTTATGTATATTATTGTTTTATA
Found at i:43350120 original size:17 final size:17
Alignment explanation
Indices: 43350098--43350131 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
43350088 AACACACTTG
43350098 ATGTTATTGATGATACC
1 ATGTTATTGATGATACC
43350115 ATGTTATTGATGATACC
1 ATGTTATTGATGATACC
43350132 TCCCAGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (17 bp):
ATGTTATTGATGATACC
Found at i:43350204 original size:26 final size:26
Alignment explanation
Indices: 43350168--43350242 Score: 141
Period size: 26 Copynumber: 2.9 Consensus size: 26
43350158 TACAATAGAA
43350168 AATTTGATGGTTCTATTTTGTTGGAT
1 AATTTGATGGTTCTATTTTGTTGGAT
43350194 AATTTGATGGTTCTATTTTGTTGGAT
1 AATTTGATGGTTCTATTTTGTTGGAT
*
43350220 AATTTGATGGTTCTACTTTGTTG
1 AATTTGATGGTTCTATTTTGTTG
43350243 ATCTCAACCT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.19, C:0.05, G:0.23, T:0.53
Consensus pattern (26 bp):
AATTTGATGGTTCTATTTTGTTGGAT
Found at i:43352379 original size:69 final size:69
Alignment explanation
Indices: 43352251--43352395 Score: 220
Period size: 69 Copynumber: 2.1 Consensus size: 69
43352241 AATGTTTACA
* * *
43352251 CATTCTATCAATTTAATCCTAAATATAAAAAGTTTAACAAACTTAGTGCTCAATGTTTACAAAAT
1 CATTTTATCAATTTAATCCTAAATATAAAAAGTTCAACAAACTTAGAGCTCAATGTTTACAAAAT
43352316 TTGT
66 TTGT
* * *
43352320 CATTTTATCAATTTAATCCTAAATATAAAAAAGTTCAACAAATTTAGAGCTC-ATTTTTACAATA
1 CATTTTATCAATTTAATCCTAAATAT-AAAAAGTTCAACAAACTTAGAGCTCAATGTTTACAAAA
43352384 TTTGT
65 TTTGT
43352389 CATTTTA
1 CATTTTA
43352396 GTTCAAATTC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
69 47 0.68
70 22 0.32
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.40
Consensus pattern (69 bp):
CATTTTATCAATTTAATCCTAAATATAAAAAGTTCAACAAACTTAGAGCTCAATGTTTACAAAAT
TTGT
Found at i:43353675 original size:61 final size:61
Alignment explanation
Indices: 43353564--43353697 Score: 175
Period size: 61 Copynumber: 2.2 Consensus size: 61
43353554 AATGTTGAGG
* *
43353564 ACTAAATTTATTGAATTTTTATAATTTAAACTAAAATGATAAATTTTGTAAACATTA-A-A
1 ACTAAATTTGTTGAATTTTTATAATTTAAACTAAAATGATAAATTATGTAAACATTAGAGA
* * *
43353623 GCTAAATTTGTTGAACTTTTT-TATATTTAAGATTAAATTGATAAATTATGTAAACATTAGAGA
1 ACTAAATTTGTTGAA-TTTTTATA-ATTTAA-ACTAAAATGATAAATTATGTAAACATTAGAGA
43353686 ACTAAATTTGTT
1 ACTAAATTTGTT
43353698 ATTAGACTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
59 15 0.23
60 11 0.17
61 25 0.39
62 1 0.02
63 12 0.19
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (61 bp):
ACTAAATTTGTTGAATTTTTATAATTTAAACTAAAATGATAAATTATGTAAACATTAGAGA
Found at i:43371210 original size:21 final size:22
Alignment explanation
Indices: 43371181--43371227 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
43371171 CAGAAGGAGT
* *
43371181 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
43371203 GAGT-GTACTCCACAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
43371224 GAGT
1 GAGT
43371228 TTGAGCAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCACAGCAGGTG
Found at i:43374263 original size:17 final size:15
Alignment explanation
Indices: 43374224--43374268 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
43374214 ACAAATAATT
43374224 TTAAAAATATATAAA
1 TTAAAAATATATAAA
*
43374239 TTAAAAATATTTAAAA
1 TTAAAAATATAT-AAA
43374255 TTAAAAA-ATATAAA
1 TTAAAAATATATAAA
43374269 AAGTTCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 3 0.11
15 14 0.52
16 10 0.37
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TTAAAAATATATAAA
Found at i:43374269 original size:15 final size:15
Alignment explanation
Indices: 43374226--43374269 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
43374216 AAATAATTTT
43374226 AAAAATATATAAATTA
1 AAAAATATA-AAATTA
*
43374242 AAAATATTTAAAATTA
1 AAAA-ATATAAAATTA
43374258 AAAAATATAAAA
1 AAAAATATAAAA
43374270 AGTTCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 14 0.56
17 4 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAATATAAAATTA
Found at i:43374442 original size:30 final size:30
Alignment explanation
Indices: 43374387--43374443 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
43374377 ACAATTTAAC
*
43374387 TTTTTTTAAAAGGTTAATGGTCAAATTCGA
1 TTTTTTTAAAAGGTTAATGGCCAAATTCGA
43374417 TTTTTTTAAAAGGTTAA-GCGCCAAATT
1 TTTTTTTAAAAGGTTAATG-GCCAAATT
43374444 TAATATTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (30 bp):
TTTTTTTAAAAGGTTAATGGCCAAATTCGA
Found at i:43381683 original size:34 final size:35
Alignment explanation
Indices: 43381623--43381690 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 35
43381613 CAAACACTAG
*
43381623 AAAATATTTTCCAGTAAATCATTTTACAGAAAATT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAATT
* * *
43381658 AAAACATTTTCCCG-AAATTATTTTACGGAAAAT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAT
43381691 ATTTTACTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.35
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAATT
Found at i:43385574 original size:2 final size:2
Alignment explanation
Indices: 43385567--43385600 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
43385557 TAGATCATGC
43385567 AT AT AT AT AT 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 AT AT
43385601 TTCACATGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43387159 original size:20 final size:22
Alignment explanation
Indices: 43387134--43387183 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
43387124 TGTACCAATT
*
43387134 TTCAAACAAATTAAAGT-A-CA
1 TTCAAACAAAATAAAGTCATCA
* *
43387154 TTCAAATAAAATAAATTCATCA
1 TTCAAACAAAATAAAGTCATCA
43387176 TTCAAACA
1 TTCAAACA
43387184 TATATATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 14 0.58
21 1 0.04
22 9 0.38
ACGTcount: A:0.54, C:0.16, G:0.02, T:0.28
Consensus pattern (22 bp):
TTCAAACAAAATAAAGTCATCA
Found at i:43390332 original size:22 final size:22
Alignment explanation
Indices: 43390301--43390362 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
43390291 AAAAAAGTTT
*
43390301 CTATTTTTTTCCTGTTTTCTTG
1 CTATTTTTTTACTGTTTTCTTG
* *
43390323 CTTTTTTTTTACTGTTTTGTTG
1 CTATTTTTTTACTGTTTTCTTG
* *
43390345 CTATTTTCTTATTGTTTT
1 CTATTTTTTTACTGTTTT
43390363 TTTTATTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.06, C:0.13, G:0.10, T:0.71
Consensus pattern (22 bp):
CTATTTTTTTACTGTTTTCTTG
Found at i:43390539 original size:21 final size:22
Alignment explanation
Indices: 43390515--43390565 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
43390505 ATATATATAT
43390515 ATTTTT-AAAAAA-TTATTTTTA
1 ATTTTTGAAAAAATTTA-TTTTA
*
43390536 ATTTGTTGAAAATATTTATTTTA
1 ATTT-TTGAAAAAATTTATTTTA
43390559 ATGTTTT
1 AT-TTTT
43390566 TAGTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 4 0.16
22 2 0.08
23 14 0.56
24 5 0.20
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (22 bp):
ATTTTTGAAAAAATTTATTTTA
Found at i:43390590 original size:16 final size:18
Alignment explanation
Indices: 43390554--43390593 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
43390544 AAAATATTTA
*
43390554 TTTTAATGTTTTTAGTAT
1 TTTTAATGTTATTAGTAT
43390572 TTTTAAT-TTATTA-TAT
1 TTTTAATGTTATTAGTAT
43390588 TTTTAA
1 TTTTAA
43390594 AAAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.43
17 5 0.24
18 7 0.33
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTAATGTTATTAGTAT
Found at i:43392123 original size:28 final size:27
Alignment explanation
Indices: 43392075--43392127 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
43392065 GTTAATGATT
43392075 TTTATTAAATTTTTTGAAAATTTTAGA
1 TTTATTAAATTTTTTGAAAATTTTAGA
*
43392102 TTTATTTAATATTTTT-ATAAATTTTA
1 TTTATTAAAT-TTTTTGA-AAATTTTA
43392128 ATAATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (27 bp):
TTTATTAAATTTTTTGAAAATTTTAGA
Found at i:43392144 original size:19 final size:21
Alignment explanation
Indices: 43392108--43392147 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
43392098 TAGATTTATT
43392108 TAATATTTTTATAAATTTTAA
1 TAATATTTTTATAAATTTTAA
43392129 TAATA-TTTTA-AAATTTTAA
1 TAATATTTTTATAAATTTTAA
43392148 AAAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
20 5 0.26
21 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATATTTTTATAAATTTTAA
Found at i:43400142 original size:16 final size:16
Alignment explanation
Indices: 43400123--43400169 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
43400113 AATATATACC
43400123 ATATTTAATATAAATA
1 ATATTTAATATAAATA
*
43400139 ATATTTAAGATAAATA
1 ATATTTAATATAAATA
43400155 ATATTT--TATAAATA
1 ATATTTAATATAAATA
43400169 A
1 A
43400170 AAGAGATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 8 0.28
16 21 0.72
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
ATATTTAATATAAATA
Found at i:43402520 original size:27 final size:29
Alignment explanation
Indices: 43402476--43402538 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
43402466 TGAATTTTTG
* *
43402476 GTGAAATTGAGTAATTA-GGGA-TAAATT
1 GTGAAATTGAATAATTAGGGGACTAAAAT
**
43402503 GTGAAATTGAATTTTTAGGGGACTAAAAT
1 GTGAAATTGAATAATTAGGGGACTAAAAT
43402532 GTGAAAT
1 GTGAAAT
43402539 AAATGAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 14 0.47
28 4 0.13
29 12 0.40
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33
Consensus pattern (29 bp):
GTGAAATTGAATAATTAGGGGACTAAAAT
Found at i:43403057 original size:17 final size:19
Alignment explanation
Indices: 43403023--43403059 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
43403013 TTAGTTAAAG
43403023 TATAAATGGTATATAATTA
1 TATAAATGGTATATAATTA
43403042 TATAAAT-GTATA-AATTA
1 TATAAATGGTATATAATTA
43403059 T
1 T
43403060 TGGATTAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 5 0.28
19 7 0.39
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (19 bp):
TATAAATGGTATATAATTA
Found at i:43403602 original size:2 final size:2
Alignment explanation
Indices: 43403560--43403589 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43403550 ATAAGCATTG
43403560 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43403590 AATGGAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43404209 original size:35 final size:36
Alignment explanation
Indices: 43404147--43404235 Score: 94
Period size: 35 Copynumber: 2.5 Consensus size: 36
43404137 ATACACTTAT
* * *
43404147 TATAACTAAATGTATATATGTATTTATCACCTGCA-
1 TATATCTAAATGCATATATGTACTTATCACCTGCAC
* * *
43404182 TATATCTAAATGCATATATGTGCTTATCGCTTGCAC
1 TATATCTAAATGCATATATGTACTTATCACCTGCAC
43404218 T-TCATC-AAATGCATATAT
1 TAT-ATCTAAATGCATATAT
43404236 ATTATTCAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
35 42 0.91
36 4 0.09
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (36 bp):
TATATCTAAATGCATATATGTACTTATCACCTGCAC
Found at i:43404577 original size:41 final size:41
Alignment explanation
Indices: 43404525--43404834 Score: 476
Period size: 41 Copynumber: 7.6 Consensus size: 41
43404515 TTAAATAGAT
* * * *
43404525 TCACTGGCACTTAGCTTGTTAGGCTTAAAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* * * *
43404566 TCACCGACACTTAGCCTGCTAGGCTTATAGCCTAATTTAGT
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
43404607 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
* *
43404648 TCACCAGCACTTAGCCTGCTAGGCTTATAGCCTGATTTAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
*
43404689 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGT
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
*
43404730 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGT
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
** *
43404771 TCACCGGCACTTAGCCTGCTAGGCTTATAATCTGATTTAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
*
43404812 TCACCGGTACTTAGCCTGCTAGG
1 TCACCGGCACTTAGCCTGCTAGG
43404835 TTTTAAAACT
Statistics
Matches: 247, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 247 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
Found at i:43405800 original size:2 final size:2
Alignment explanation
Indices: 43405795--43405822 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43405785 TTATATAAGC
43405795 AT AT 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
43405823 TCGAACACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43406662 original size:26 final size:26
Alignment explanation
Indices: 43406633--43406683 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
43406623 TCTTTTAATA
* *
43406633 TATTTTAA-CTTTATAATATAATATAT
1 TATTATAACCTTTAT-ACATAATATAT
43406659 TATTATAACCTTTATACATAATATA
1 TATTATAACCTTTATACATAATATA
43406684 AAAACTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (26 bp):
TATTATAACCTTTATACATAATATAT
Found at i:43414259 original size:30 final size:29
Alignment explanation
Indices: 43414221--43414277 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
43414211 TATTCTTGCA
43414221 TTTAGAATTTAGTCT-TTATATTTTTCATT
1 TTTAGAATTTAGT-TATTATATTTTTCATT
*
43414250 TTTAGGAATTTAGTTATTTTATTTTTCA
1 TTTA-GAATTTAGTTATTATATTTTTCA
43414278 AATCTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.61
Consensus pattern (29 bp):
TTTAGAATTTAGTTATTATATTTTTCATT
Found at i:43418478 original size:13 final size:13
Alignment explanation
Indices: 43418460--43418502 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
43418450 AACAAATAGG
43418460 ATAATTAATATTT
1 ATAATTAATATTT
43418473 ATAATTAATATGTCT
1 ATAATTAATAT-T-T
43418488 ATAA--AATATTT
1 ATAATTAATATTT
43418499 ATAA
1 ATAA
43418503 ACATATAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 5 0.18
12 1 0.04
13 16 0.57
14 1 0.04
15 5 0.18
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (13 bp):
ATAATTAATATTT
Found at i:43419053 original size:6 final size:6
Alignment explanation
Indices: 43419042--43419097 Score: 60
Period size: 6 Copynumber: 9.2 Consensus size: 6
43419032 TGTTGTTGAT
* * *
43419042 AATGGG AATGGG AATGGG AAATGGG AATGGG TAT-TG CATGGG AATGGG
1 AATGGG AATGGG AATGGG -AATGGG AATGGG AATGGG AATGGG AATGGG
43419090 AAATGGG A
1 -AATGGG A
43419098 GGAGGGCACG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
5 3 0.07
6 27 0.64
7 12 0.29
ACGTcount: A:0.34, C:0.02, G:0.45, T:0.20
Consensus pattern (6 bp):
AATGGG
Found at i:43419066 original size:13 final size:13
Alignment explanation
Indices: 43419042--43419097 Score: 60
Period size: 13 Copynumber: 4.1 Consensus size: 13
43419032 TGTTGTTGAT
43419042 AATGGG-AATGGG
1 AATGGGAAATGGG
43419054 AATGGGAAATGGG
1 AATGGGAAATGGG
*
43419067 AATGGGTATTGCATGGG
1 AATGGG-A---AATGGG
43419084 AATGGGAAATGGG
1 AATGGGAAATGGG
43419097 A
1 A
43419098 GGAGGGCACG
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
12 6 0.16
13 18 0.49
14 1 0.03
16 1 0.03
17 11 0.30
ACGTcount: A:0.34, C:0.02, G:0.45, T:0.20
Consensus pattern (13 bp):
AATGGGAAATGGG
Found at i:43419150 original size:6 final size:6
Alignment explanation
Indices: 43419134--43419174 Score: 64
Period size: 6 Copynumber: 6.5 Consensus size: 6
43419124 GATGGAAGAG
43419134 GGGAGAT GGGAAT GGGAAAT GGGAAT GGGAAT GGGAAT GGG
1 GGGA-AT GGGAAT GGG-AAT GGGAAT GGGAAT GGGAAT GGG
43419175 TATTGCATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 23 0.70
7 10 0.30
ACGTcount: A:0.32, C:0.00, G:0.54, T:0.15
Consensus pattern (6 bp):
GGGAAT
Found at i:43419155 original size:13 final size:13
Alignment explanation
Indices: 43419134--43419174 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
43419124 GATGGAAGAG
*
43419134 GGGAGATGGGAAT
1 GGGAAATGGGAAT
43419147 GGGAAATGGGAAT
1 GGGAAATGGGAAT
43419160 GGG-AATGGGAAT
1 GGGAAATGGGAAT
43419172 GGG
1 GGG
43419175 TATTGCATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 12 0.44
13 15 0.56
ACGTcount: A:0.32, C:0.00, G:0.54, T:0.15
Consensus pattern (13 bp):
GGGAAATGGGAAT
Found at i:43419163 original size:19 final size:19
Alignment explanation
Indices: 43419134--43419174 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
43419124 GATGGAAGAG
43419134 GGGAGATGGGAATGGGAAAT
1 GGGAGATGGGAATGGG-AAT
43419154 GGGA-ATGGGAATGGGAAT
1 GGGAGATGGGAATGGGAAT
43419172 GGG
1 GGG
43419175 TATTGCATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.29
19 11 0.52
20 4 0.19
ACGTcount: A:0.32, C:0.00, G:0.54, T:0.15
Consensus pattern (19 bp):
GGGAGATGGGAATGGGAAT
Done.