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 184 of 204
Found at i:54421041 original size:48 final size:45
Alignment explanation
Indices: 54420989--54421086 Score: 117
Period size: 48 Copynumber: 2.1 Consensus size: 45
54420979 GGTCCGGCCC
54420989 AAATATAATAAATA-TATATTTTTATTTTATTTTTAATTTTTAATTTTA
1 AAATATAATAAATACTATA-TTTTATTTTA-TTTT-A-TTTTAATTTTA
** * *
54421037 AAATATTTTAAATACTTTATTTTATTTTATTTTATTTTATTTTTA
1 AAATATAATAAATACTATATTTTATTTTATTTTATTTTAATTTTA
54421082 AAATA
1 AAATA
54421087 ATTTTTTGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
45 15 0.33
46 1 0.02
47 4 0.09
48 22 0.49
49 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (45 bp):
AAATATAATAAATACTATATTTTATTTTATTTTATTTTAATTTTA
Found at i:54421062 original size:5 final size:5
Alignment explanation
Indices: 54421052--54421079 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
54421042 TTTTAAATAC
54421052 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
54421080 TAAAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:54421067 original size:24 final size:24
Alignment explanation
Indices: 54421008--54421070 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
54420998 AAATATATAT
* *
54421008 TTTTATTTTATTTTTAATTTTTAA
1 TTTTATTTTATTTTAAATCTTTAA
***
54421032 TTTTAAAATATTTTAAATACTTT-A
1 TTTTATTTTATTTTAAAT-CTTTAA
54421056 TTTTATTTTATTTTA
1 TTTTATTTTATTTTA
54421071 TTTTATTTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
24 27 0.90
25 3 0.10
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (24 bp):
TTTTATTTTATTTTAAATCTTTAA
Found at i:54424380 original size:23 final size:23
Alignment explanation
Indices: 54424354--54424402 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
54424344 GAGCAGAAAA
54424354 TCAGTAAAGAAACTAGTAAGAAC
1 TCAGTAAAGAAACTAGTAAGAAC
54424377 TCAGTAAAGAAACTAGTAAGAAC
1 TCAGTAAAGAAACTAGTAAGAAC
54424400 TCA
1 TCA
54424403 CATGATGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.18
Consensus pattern (23 bp):
TCAGTAAAGAAACTAGTAAGAAC
Found at i:54424382 original size:11 final size:13
Alignment explanation
Indices: 54424348--54424395 Score: 59
Period size: 12 Copynumber: 4.0 Consensus size: 13
54424338 AGGGTTGAGC
*
54424348 AGAAAATCAGTAA
1 AGAAACTCAGTAA
54424361 AGAAACT-AGT-A
1 AGAAACTCAGTAA
54424372 AG-AACTCAGTAA
1 AGAAACTCAGTAA
54424384 AGAAACT-AGTAA
1 AGAAACTCAGTAA
54424396 GAACTCACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 4 0.13
11 6 0.19
12 11 0.35
13 10 0.32
ACGTcount: A:0.56, C:0.10, G:0.17, T:0.17
Consensus pattern (13 bp):
AGAAACTCAGTAA
Found at i:54424386 original size:12 final size:12
Alignment explanation
Indices: 54424348--54424402 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 12
54424338 AGGGTTGAGC
*
54424348 AGAAAATCAGTAA
1 AGAAACTCAGT-A
54424361 AGAAACT-AGTA
1 AGAAACTCAGTA
54424372 AG-AACTCAGTAA
1 AGAAACTCAGT-A
54424384 AGAAACT-AGTA
1 AGAAACTCAGTA
54424395 AG-AACTCA
1 AGAAACTCA
54424403 CATGATGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
10 8 0.22
11 10 0.27
12 9 0.24
13 10 0.27
ACGTcount: A:0.55, C:0.13, G:0.16, T:0.16
Consensus pattern (12 bp):
AGAAACTCAGTA
Found at i:54424731 original size:24 final size:25
Alignment explanation
Indices: 54424699--54424746 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
54424689 CTTGGCAAAT
54424699 AGGGAAACCA-ATCTTAGAAGATTG
1 AGGGAAACCATATCTTAGAAGATTG
* * *
54424723 AGGGGAACCATGTCTTATAAGATT
1 AGGGAAACCATATCTTAGAAGATT
54424747 AGGTTTGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (25 bp):
AGGGAAACCATATCTTAGAAGATTG
Found at i:54437490 original size:3 final size:3
Alignment explanation
Indices: 54437482--54437507 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
54437472 TTCATAAATC
54437482 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
54437508 TCAGGCCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:54439810 original size:2 final size:2
Alignment explanation
Indices: 54439803--54439829 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
54439793 AATTAAAGTG
54439803 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
54439830 NNNNNNNNNN
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:54441661 original size:13 final size:13
Alignment explanation
Indices: 54441645--54441697 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
54441635 TTTAAACCAA
54441645 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
54441658 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
*
54441671 ACTTTTCAAAAAC
1 ACTTTTCAAAAGC
54441684 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
54441697 A
1 A
54441698 TCGCCAAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:54441663 original size:26 final size:26
Alignment explanation
Indices: 54441634--54441689 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
54441624 AACACTCAAA
*
54441634 TTTTAAACCA-AACTTTTCAAAAGCAC
1 TTTTAAA-CAGAACTTTTCAAAAACAC
** *
54441660 TTTTCCACAGCACTTTTCAAAAACAC
1 TTTTAAACAGAACTTTTCAAAAACAC
54441686 TTTT
1 TTTT
54441690 CAAAAGCATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (26 bp):
TTTTAAACAGAACTTTTCAAAAACAC
Found at i:54442494 original size:20 final size:20
Alignment explanation
Indices: 54442471--54442508 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
54442461 TAATAAAAAA
54442471 TATAAATTTATAATTTTTCT
1 TATAAATTTATAATTTTTCT
*
54442491 TATAATTTTATAATTTTT
1 TATAAATTTATAATTTTT
54442509 AAATTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TATAAATTTATAATTTTTCT
Found at i:54443615 original size:18 final size:18
Alignment explanation
Indices: 54443592--54443628 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
54443582 TGAGTTTTCG
54443592 AATTTGAATAACTCGAAT
1 AATTTGAATAACTCGAAT
*
54443610 AATTTGAATAATTCGAAT
1 AATTTGAATAACTCGAAT
54443628 A
1 A
54443629 TCAAACTATA
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:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (18 bp):
AATTTGAATAACTCGAAT
Found at i:54443966 original size:30 final size:31
Alignment explanation
Indices: 54443932--54443991 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
54443922 AAACCTTTTA
*
54443932 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
54443962 TTTTCCCCGAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
54443992 TCTCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.02, T:0.38
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:54451433 original size:13 final size:13
Alignment explanation
Indices: 54451401--54451425 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54451391 ATAAAATATC
54451401 TTTATAATTTGTA
1 TTTATAATTTGTA
54451414 TTTATAATTTGT
1 TTTATAATTTGT
54451426 TTATATAAAA
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:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (13 bp):
TTTATAATTTGTA
Found at i:54451597 original size:8 final size:8
Alignment explanation
Indices: 54451581--54451615 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
54451571 TGTTATTTAC
*
54451581 TAAAATGT
1 TAAATTGT
54451589 TAAATTGT
1 TAAATTGT
54451597 TAAATTGT
1 TAAATTGT
54451605 TAAATTGT
1 TAAATTGT
54451613 TAA
1 TAA
54451616 CACATAGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (8 bp):
TAAATTGT
Found at i:54453577 original size:23 final size:23
Alignment explanation
Indices: 54453549--54453642 Score: 97
Period size: 23 Copynumber: 4.3 Consensus size: 23
54453539 AGTGTATCCT
54453549 TTCATATTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
* * * * *
54453572 TTCATA---ATGTGT-GTAACTT
1 TTCATATTCAAGTCTCTTCACTC
* *
54453591 TTCATCTTCAAGTCTCTTCACTA
1 TTCATATTCAAGTCTCTTCACTC
54453614 TTCATATTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
54453637 TTCATA
1 TTCATA
54453643 ATTTTTCATA
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
19 9 0.17
20 4 0.07
22 4 0.07
23 37 0.69
ACGTcount: A:0.23, C:0.26, G:0.06, T:0.45
Consensus pattern (23 bp):
TTCATATTCAAGTCTCTTCACTC
Found at i:54458056 original size:23 final size:23
Alignment explanation
Indices: 54458028--54458121 Score: 97
Period size: 23 Copynumber: 4.3 Consensus size: 23
54458018 AGTGTATCCT
54458028 TTCATATTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
* * * * *
54458051 TTCATA---ATGTGT-GTAACTT
1 TTCATATTCAAGTCTCTTCACTC
* *
54458070 TTCATCTTCAAGTCTCTTCACTA
1 TTCATATTCAAGTCTCTTCACTC
54458093 TTCATATTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
54458116 TTCATA
1 TTCATA
54458122 ATTTTTCATA
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
19 9 0.17
20 4 0.07
22 4 0.07
23 37 0.69
ACGTcount: A:0.23, C:0.26, G:0.06, T:0.45
Consensus pattern (23 bp):
TTCATATTCAAGTCTCTTCACTC
Found at i:54461518 original size:43 final size:43
Alignment explanation
Indices: 54461443--54461524 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
54461433 GCGGCGTTTA
*
54461443 TACCAACAAACGCCGCTAAAGAACATGATCTTTAGCGGCACTT
1 TACCAACAAACGCCGCTAAAGAACAGGATCTTTAGCGGCACTT
* * *
54461486 TACCCACAAACGCCGCTAAAAGTAC-GGTTCTTTAGCGGC
1 TACCAACAAACGCCGCT-AAAGAACAGGATCTTTAGCGGC
54461525 GTTTATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 28 0.82
44 6 0.18
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (43 bp):
TACCAACAAACGCCGCTAAAGAACAGGATCTTTAGCGGCACTT
Found at i:54466264 original size:52 final size:52
Alignment explanation
Indices: 54466202--54466307 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
54466192 AACAATAAAG
54466202 TAGCGTCAGGATACAGATCCACCACATTTTAGCACCATTTGCAAAACTATCA
1 TAGCGTCAGGATACAGATCCACCACATTTTAGCACCATTTGCAAAACTATCA
54466254 TAGCGTCAGGATACAGATCCACCACATTTTAGCACCATTTGCAAAACTATCA
1 TAGCGTCAGGATACAGATCCACCACATTTTAGCACCATTTGCAAAACTATCA
54466306 TA
1 TA
54466308 AGTTTATATG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.25
Consensus pattern (52 bp):
TAGCGTCAGGATACAGATCCACCACATTTTAGCACCATTTGCAAAACTATCA
Found at i:54467403 original size:28 final size:28
Alignment explanation
Indices: 54467363--54467420 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
54467353 GACAAGAAGA
*
54467363 CATAGTTCAGACTAAGGAGAAAATATAT
1 CATAGTCCAGACTAAGGAGAAAATATAT
54467391 CATAGTCCAGACTAAGGAGAAAATATAT
1 CATAGTCCAGACTAAGGAGAAAATATAT
54467419 CA
1 CA
54467421 GCACTAAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (28 bp):
CATAGTCCAGACTAAGGAGAAAATATAT
Found at i:54471997 original size:28 final size:28
Alignment explanation
Indices: 54471922--54472000 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 28
54471912 TATGTTAAGA
*
54471922 ATATTTTAATTATGATTTGA-AAATTTT
1 ATATTTTAATTATGATTTAATAAATTTT
* * *
54471949 ATATTATAATATTTGAATTAATAAATTTAT
1 ATATTTTAAT-TATGATTTAATAAATTT-T
54471979 ATATTTTAATTAT-ATTTAATAA
1 ATATTTTAATTATGATTTAATAA
54472001 TTCATACAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
27 9 0.21
28 15 0.36
29 8 0.19
30 10 0.24
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (28 bp):
ATATTTTAATTATGATTTAATAAATTTT
Found at i:54486801 original size:26 final size:25
Alignment explanation
Indices: 54486761--54486810 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
54486751 TATTGGAGAA
*
54486761 AGTAATTTAGACTTTAGTCAATTAAG
1 AGTAAATTAGACTTTAGTC-ATTAAG
*
54486787 AGTAAATTAGGCTTTAGTCATTAA
1 AGTAAATTAGACTTTAGTCATTAA
54486811 TTATATCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (25 bp):
AGTAAATTAGACTTTAGTCATTAAG
Found at i:54487486 original size:2 final size:2
Alignment explanation
Indices: 54487474--54487508 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
54487464 ACTTTTTCTA
54487474 AT AT AT CAT 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
54487509 TCAGTACACA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54488249 original size:21 final size:21
Alignment explanation
Indices: 54488223--54488281 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
54488213 AAGTTAAAAA
54488223 AAGCTCGTAAGAGCTGAACAG
1 AAGCTCGTAAGAGCTGAACAG
* *
54488244 AAGCTCGTAAGAGCTTAATAG
1 AAGCTCGTAAGAGCTGAACAG
*
54488265 AAGCTCATAAGAGCTGA
1 AAGCTCGTAAGAGCTGA
54488282 TCCACCCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (21 bp):
AAGCTCGTAAGAGCTGAACAG
Found at i:54488277 original size:42 final size:39
Alignment explanation
Indices: 54488200--54488281 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 39
54488190 GTACATCGTT
*
54488200 AACAGAAGCTCGAAAGTTAAAAAAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGAAAGTTAAAAAAAGCTCATAAGAGCTG
* *
54488239 AACAGAAGCTCGTAAGAGCTTAATAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCG-AA-AG-TTAAAAAAAGCTCATAAGAGCTG
54488281 A
1 A
54488282 TCCACCCAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 12 0.32
40 2 0.05
41 2 0.05
42 21 0.57
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.17
Consensus pattern (39 bp):
AACAGAAGCTCGAAAGTTAAAAAAAGCTCATAAGAGCTG
Found at i:54490453 original size:12 final size:13
Alignment explanation
Indices: 54490436--54490475 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
54490426 TGCAAACATT
54490436 AAAAAGAAAA-AA
1 AAAAAGAAAAGAA
54490448 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
*
54490461 AGAAAGAAATAGAA
1 AAAAAGAAA-AGAA
54490475 A
1 A
54490476 GGGAGAAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 10 0.40
13 10 0.40
14 5 0.20
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Found at i:54490459 original size:17 final size:19
Alignment explanation
Indices: 54490437--54490475 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
54490427 GCAAACATTA
54490437 AAAAGAAA-AAA-AAAAAG
1 AAAAGAAAGAAAGAAAAAG
*
54490454 AAAAGAAAGAAAGAAATAG
1 AAAAGAAAGAAAGAAAAAG
54490473 AAA
1 AAA
54490476 GGGAGAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 3 0.16
19 8 0.42
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAAGAAAGAAAGAAAAAG
Found at i:54490482 original size:14 final size:13
Alignment explanation
Indices: 54490438--54490476 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
54490428 CAAACATTAA
*
54490438 AAAGAAAA-AAAA
1 AAAGAAAAGAAAG
54490450 AAAGAAAAGAAAG
1 AAAGAAAAGAAAG
54490463 AAAGAAATAGAAAG
1 AAAGAAA-AGAAAG
54490477 GGAGAAGCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 8 0.33
13 10 0.42
14 6 0.25
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (13 bp):
AAAGAAAAGAAAG
Found at i:54491623 original size:18 final size:18
Alignment explanation
Indices: 54491600--54491650 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
54491590 GAGAAGTCAA
*
54491600 AGATGAGAAATGAATTTG
1 AGATGAGAAATGAATATG
54491618 AGATGAGAAATGAAATATG
1 AGATGAGAAATG-AATATG
*
54491637 AAATGATGAAATGA
1 AGATGA-GAAATGA
54491651 GATGTGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 12 0.41
19 11 0.38
20 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.24
Consensus pattern (18 bp):
AGATGAGAAATGAATATG
Found at i:54493633 original size:6 final size:6
Alignment explanation
Indices: 54493622--54493655 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
54493612 TAGATCATAA
*
54493622 TTTTCT TTTTCT TTTTCT TTTTTT CTTTTCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTCT -TTTTCT TTT
54493656 ACAGGATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:54498822 original size:12 final size:12
Alignment explanation
Indices: 54498805--54498838 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
54498795 TTATTTTTCT
54498805 TTACTTTATTTA
1 TTACTTTATTTA
54498817 TTACTTTATTTTA
1 TTACTTTA-TTTA
54498830 TTA-TTTATT
1 TTACTTTATT
54498839 ACATATTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 12 0.57
13 7 0.33
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (12 bp):
TTACTTTATTTA
Found at i:54499875 original size:9 final size:9
Alignment explanation
Indices: 54499861--54499899 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
54499851 CCTAAAGCAT
54499861 AACAAAAAA
1 AACAAAAAA
54499870 AACAAAAAA
1 AACAAAAAA
54499879 AAGCAAAAAA
1 AA-CAAAAAA
54499889 AA-AAGAAAA
1 AACAA-AAAA
54499898 AA
1 AA
54499900 AATAATTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.07
9 17 0.61
10 9 0.32
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (9 bp):
AACAAAAAA
Found at i:54499879 original size:10 final size:10
Alignment explanation
Indices: 54499864--54499901 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
54499854 AAAGCATAAC
54499864 AAAAAAAACA
1 AAAAAAAACA
*
54499874 AAAAAAAGCA
1 AAAAAAAACA
54499884 AAAAAAAA-A
1 AAAAAAAACA
54499893 GAAAAAAAA
1 -AAAAAAAA
54499902 TAATTTGGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 1 0.04
10 24 0.96
ACGTcount: A:0.89, C:0.05, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:54499888 original size:12 final size:11
Alignment explanation
Indices: 54499864--54499901 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
54499854 AAAGCATAAC
*
54499864 AAAAAAA-ACA
1 AAAAAAAGAAA
54499874 AAAAAAAGCAAA
1 AAAAAAAG-AAA
54499886 AAAAAAAGAAA
1 AAAAAAAGAAA
54499897 AAAAA
1 AAAAA
54499902 TAATTTGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 7 0.28
11 8 0.32
12 10 0.40
ACGTcount: A:0.89, C:0.05, G:0.05, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:54499891 original size:24 final size:23
Alignment explanation
Indices: 54499854--54499901 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
54499844 GTATATTCCT
* *
54499854 AAAGCATAACAAAAAAAACAAAAA
1 AAAGCA-AAAAAAAAAAAAAAAAA
*
54499878 AAAGCAAAAAAAAAAGAAAAAAA
1 AAAGCAAAAAAAAAAAAAAAAAA
54499901 A
1 A
54499902 TAATTTGGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.83, C:0.08, G:0.06, T:0.02
Consensus pattern (23 bp):
AAAGCAAAAAAAAAAAAAAAAAA
Found at i:54504405 original size:64 final size:64
Alignment explanation
Indices: 54504331--54504460 Score: 242
Period size: 64 Copynumber: 2.0 Consensus size: 64
54504321 CAATCCGTTC
54504331 TCCTTTAATCCTCAACATTTATTGGGGTAGGATTGTATGAGACAGTAACGTTACGTAAATTGTA
1 TCCTTTAATCCTCAACATTTATTGGGGTAGGATTGTATGAGACAGTAACGTTACGTAAATTGTA
* *
54504395 TCCTTTAATCCTCAACATTTATTGGGGTAGGATTGTATGAGACAGTAACGTTACGTCATTTGTA
1 TCCTTTAATCCTCAACATTTATTGGGGTAGGATTGTATGAGACAGTAACGTTACGTAAATTGTA
54504459 TC
1 TC
54504461 ATTTTTCTAA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (64 bp):
TCCTTTAATCCTCAACATTTATTGGGGTAGGATTGTATGAGACAGTAACGTTACGTAAATTGTA
Found at i:54506796 original size:34 final size:34
Alignment explanation
Indices: 54506754--54506824 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
54506744 ACTTAACATT
54506754 TTTTAGGGGGTTTTGTAATATAAATAACTTCATA
1 TTTTAGGGGGTTTTGTAATATAAATAACTTCATA
54506788 TTTTAGGGGGTTTTGTAATATAAATAACTTCATA
1 TTTTAGGGGGTTTTGTAATATAAATAACTTCATA
54506822 TTT
1 TTT
54506825 ATGTAATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (34 bp):
TTTTAGGGGGTTTTGTAATATAAATAACTTCATA
Found at i:54507329 original size:27 final size:27
Alignment explanation
Indices: 54507265--54507349 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
54507255 GTTGTGGGCC
54507265 CCACCATTGGCGTCTCTCAACAT-GGCA
1 CCACCATTGGCGTCTCTCAA-ATAGGCA
* * * *
54507292 CAACTAGTGGCGTCTCTCAAATAGGCT
1 CCACCATTGGCGTCTCTCAAATAGGCA
* * * *
54507319 CCACCATTGGCGCCTCTGAGATAGGCG
1 CCACCATTGGCGTCTCTCAAATAGGCA
54507346 CCAC
1 CCAC
54507350 TACTCTTGTA
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
26 2 0.04
27 44 0.96
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
CCACCATTGGCGTCTCTCAAATAGGCA
Found at i:54507474 original size:51 final size:51
Alignment explanation
Indices: 54507417--54507526 Score: 193
Period size: 51 Copynumber: 2.2 Consensus size: 51
54507407 TTATTAAAAG
54507417 AAAAAAATTAATATAAAAAATTCATTGGCGCCTATCAGATAGGCGCCATTA
1 AAAAAAATTAATATAAAAAATTCATTGGCGCCTATCAGATAGGCGCCATTA
* * *
54507468 AAAAAAATTAATATAAAATATTCATTGGCGCCTTTCAGATAGGCTCCATTA
1 AAAAAAATTAATATAAAAAATTCATTGGCGCCTATCAGATAGGCGCCATTA
54507519 AAAAAAAT
1 AAAAAAAT
54507527 ATCATTTCTG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (51 bp):
AAAAAAATTAATATAAAAAATTCATTGGCGCCTATCAGATAGGCGCCATTA
Found at i:54511388 original size:32 final size:30
Alignment explanation
Indices: 54511311--54511388 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 30
54511301 TTTACAAAAT
*
54511311 AGTCACTAAATTATTCAAAAAATTTTATTTA
1 AGTCACT-AACTATTCAAAAAATTTTATTTA
* **
54511342 AGTCATTGAACTATTCAAAAGTTTTTTATTTA
1 AGTCACT-AACTATTCAAAA-AATTTTATTTA
54511374 AGTCACTAAGCTATT
1 AGTCACTAA-CTATT
54511389 AAATTTAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
31 19 0.49
32 20 0.51
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (30 bp):
AGTCACTAACTATTCAAAAAATTTTATTTA
Found at i:54512007 original size:16 final size:17
Alignment explanation
Indices: 54511984--54512028 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
54511974 AATGCTTCAA
* *
54511984 TCTCTCCTTTCCCTTTC
1 TCTCTCCTTCCCCTCTC
54512001 T-TCTCCTTCCCCTCTC
1 TCTCTCCTTCCCCTCTC
*
54512017 TCTCTCCCTCCC
1 TCTCTCCTTCCC
54512029 TTCCATAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (17 bp):
TCTCTCCTTCCCCTCTC
Found at i:54516037 original size:11 final size:10
Alignment explanation
Indices: 54516010--54516042 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
54516000 TATTCGAATT
54516010 TAATTT-AAA
1 TAATTTAAAA
54516019 TAATTTAAAA
1 TAATTTAAAA
54516029 TATATTTAAAA
1 TA-ATTTAAAA
54516040 TAA
1 TAA
54516043 AAAAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.27
10 6 0.27
11 10 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TAATTTAAAA
Found at i:54517661 original size:3 final size:3
Alignment explanation
Indices: 54517606--54517646 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
54517596 CTTTGCATAT
* *
54517606 TTA TTA TTA TTA TCA TTA TTA TT- TTA TTT TTA TT- TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
54517647 CATCCTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:54517768 original size:25 final size:25
Alignment explanation
Indices: 54517735--54517783 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
54517725 TTTTTGAGTT
* *
54517735 ATCATTGTCATTCTCATTATTATTC
1 ATCAATGTCATTATCATTATTATTC
54517760 ATCAATGTCATTATCATTATTATT
1 ATCAATGTCATTATCATTATTATT
54517784 ATAGCTGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (25 bp):
ATCAATGTCATTATCATTATTATTC
Found at i:54517862 original size:16 final size:17
Alignment explanation
Indices: 54517826--54517872 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
54517816 CCATCGCTAC
*
54517826 TATTATTTTATTTCT--
1 TATTATTTTATTTGTAA
54517841 TATTA-TTTATTTGTAA
1 TATTATTTTATTTGTAA
54517857 TATTATTTTATTTGTA
1 TATTATTTTATTTGTA
54517873 CTCATATAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 8 0.29
15 5 0.18
16 5 0.18
17 10 0.36
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (17 bp):
TATTATTTTATTTGTAA
Found at i:54519400 original size:19 final size:20
Alignment explanation
Indices: 54519356--54519401 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
54519346 ACAAGTAAAT
*
54519356 TTAATAATTAATAATTTTAA
1 TTAATATTTAATAATTTTAA
**
54519376 AAAATATTTAATAA-TTTAA
1 TTAATATTTAATAATTTTAA
54519395 TTAATAT
1 TTAATAT
54519402 AGTTTTAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAATATTTAATAATTTTAA
Found at i:54519979 original size:73 final size:73
Alignment explanation
Indices: 54519855--54520000 Score: 256
Period size: 73 Copynumber: 2.0 Consensus size: 73
54519845 AGGGCTTTTC
*
54519855 TTGATGGCGGCAAGATGTAATCGCATATGAGTTTTTGTGAGAGTTTCATGGTAACTATGTAGAGA
1 TTGAGGGCGGCAAGATGTAATCGCATATGAGTTTTTGTGAGAGTTTCATGGTAACTATGTAGAGA
54519920 ATTTTGTT
66 ATTTTGTT
* * *
54519928 TTGAGGGCGGCAAGATTTAGTCTCATATGAGTTTTTGTGAGAGTTTCATGGTAACTATGTAGAGA
1 TTGAGGGCGGCAAGATGTAATCGCATATGAGTTTTTGTGAGAGTTTCATGGTAACTATGTAGAGA
54519993 ATTTTGTT
66 ATTTTGTT
54520001 CCCGAGCTAG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.39
Consensus pattern (73 bp):
TTGAGGGCGGCAAGATGTAATCGCATATGAGTTTTTGTGAGAGTTTCATGGTAACTATGTAGAGA
ATTTTGTT
Found at i:54523201 original size:22 final size:21
Alignment explanation
Indices: 54523175--54523219 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
54523165 CTTTTGAAGT
54523175 AATTAA-TATAAATTATTTATAA
1 AATTAATTATAAA-TATTT-TAA
*
54523197 AATTAATTATACATATTTTAA
1 AATTAATTATAAATATTTTAA
54523218 AA
1 AA
54523220 AACTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 11 0.52
23 5 0.24
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTAATTATAAATATTTTAA
Found at i:54531742 original size:21 final size:21
Alignment explanation
Indices: 54531718--54531770 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
54531708 CCAAATTGGA
*
54531718 AAAAGTTAACATTTATTTTTT
1 AAAAGTTAACATTTATTGTTT
*
54531739 AAAA-TATATCATTTATTGTTT
1 AAAAGT-TAACATTTATTGTTT
54531760 AATAGAGTTAA
1 AA-A-AGTTAA
54531771 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
20 1 0.04
21 19 0.76
22 1 0.04
23 3 0.12
24 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.47
Consensus pattern (21 bp):
AAAAGTTAACATTTATTGTTT
Found at i:54535609 original size:21 final size:21
Alignment explanation
Indices: 54535585--54535624 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
54535575 TATTTATTGT
54535585 TTAAAAAAATCATTTTTTTGC
1 TTAAAAAAATCATTTTTTTGC
* * *
54535606 TTAACAAAGTTATTTTTTT
1 TTAAAAAAATCATTTTTTT
54535625 TAAAGATGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (21 bp):
TTAAAAAAATCATTTTTTTGC
Found at i:54541194 original size:14 final size:15
Alignment explanation
Indices: 54541169--54541197 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
54541159 ATATTCAATT
54541169 ATTATCTCTATTAAA
1 ATTATCTCTATTAAA
54541184 ATTAT-TCTATTAAA
1 ATTATCTCTATTAAA
54541198 TTTACTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATCTCTATTAAA
Found at i:54543578 original size:20 final size:20
Alignment explanation
Indices: 54543537--54543583 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
54543527 AAATTACAAA
*
54543537 AAAAAATCAAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
*
54543557 AAAAATTCAAAAT-GTTTATT
1 AAAAATTCAAAATAATTT-TT
54543577 AAAAATT
1 AAAAATT
54543584 TCCAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTT
Found at i:54543581 original size:21 final size:21
Alignment explanation
Indices: 54543536--54543591 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
54543526 AAAATTACAA
*
54543536 AAAAAAATCAAAATAATTTTT
1 AAAAAATTCAAAATAATTTTT
*
54543557 -AAAAATTCAAAAT-GTTTATT
1 AAAAAATTCAAAATAATTT-TT
*
54543577 AAAAATTTCCAAAAT
1 AAAAAATT-CAAAAT
54543592 TTAGATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 3 0.10
20 14 0.48
21 6 0.21
22 6 0.21
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (21 bp):
AAAAAATTCAAAATAATTTTT
Found at i:54543825 original size:22 final size:22
Alignment explanation
Indices: 54543783--54543827 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
54543773 TATAATAAGA
**
54543783 TTTTAATTTAACATGTTTAATT
1 TTTTAATTTAACATGAATAATT
54543805 TTTTAATTTAAC-TCGAATAATT
1 TTTTAATTTAACAT-GAATAATT
54543827 T
1 T
54543828 CACTCGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTTAATTTAACATGAATAATT
Found at i:54549111 original size:18 final size:17
Alignment explanation
Indices: 54549061--54549107 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
54549051 TGTAAATACT
54549061 AAAATA-ATT-AAAATA
1 AAAATATATTAAAAATA
54549076 AAAAT-T-TTAATAAATA
1 AAAATATATTAA-AAATA
54549092 AAAATATATTAAAAAT
1 AAAATATATTAAAAAT
54549108 TAAATTAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.07
15 6 0.22
16 10 0.37
17 5 0.19
18 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATATATTAAAAATA
Found at i:54550497 original size:2 final size:2
Alignment explanation
Indices: 54550490--54550515 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54550480 TCCAACTAAC
54550490 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
54550516 AGAGAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:54550520 original size:2 final size:2
Alignment explanation
Indices: 54550515--54550557 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
54550505 GTGTGTGTGT
54550515 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
54550557 G
1 G
54550558 GTAGGAGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:54561766 original size:16 final size:17
Alignment explanation
Indices: 54561736--54561767 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
54561726 AATCAATTGA
54561736 AAATTAATATTTTTAAT
1 AAATTAATATTTTTAAT
54561753 AAATTAAT-TTTTTAA
1 AAATTAATATTTTTAA
54561768 ACACGTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATTAATATTTTTAAT
Found at i:54567097 original size:20 final size:20
Alignment explanation
Indices: 54567074--54567114 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
54567064 ATTATTACTG
*
54567074 AATTACTGAATCTCTTACAA
1 AATTACTAAATCTCTTACAA
* *
54567094 AATTATTAAATTTCTTACAA
1 AATTACTAAATCTCTTACAA
54567114 A
1 A
54567115 TTTGTAATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (20 bp):
AATTACTAAATCTCTTACAA
Found at i:54567233 original size:19 final size:19
Alignment explanation
Indices: 54567206--54567266 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
54567196 AATATTATTG
54567206 GAATC-CTTACAAATTACT
1 GAATCACTTACAAATTACT
* * *
54567224 GCA-CATCTTAAAAATTATT
1 GAATCA-CTTACAAATTACT
54567243 GAATCACTTACAAAATTACT
1 GAATCACTTAC-AAATTACT
54567263 GAAT
1 GAAT
54567267 TTCTTTCAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
17 1 0.03
18 2 0.06
19 17 0.52
20 13 0.39
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (19 bp):
GAATCACTTACAAATTACT
Found at i:54567259 original size:20 final size:20
Alignment explanation
Indices: 54567206--54567282 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
54567196 AATATTATTG
54567206 GAATC-CTTAC-AAATTACT
1 GAATCACTTACAAAATTACT
* *
54567224 GCA-CATCTTA-AAAATTATT
1 GAATCA-CTTACAAAATTACT
54567243 GAATCACTTACAAAATTACT
1 GAATCACTTACAAAATTACT
** *
54567263 GAATTTCTTTCAAAATTACT
1 GAATCACTTACAAAATTACT
54567283 AATGTTTACC
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
17 1 0.02
18 2 0.04
19 17 0.36
20 27 0.57
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.36
Consensus pattern (20 bp):
GAATCACTTACAAAATTACT
Found at i:54567329 original size:76 final size:77
Alignment explanation
Indices: 54567235--54567418 Score: 246
Period size: 76 Copynumber: 2.4 Consensus size: 77
54567225 CACATCTTAA
* ** *
54567235 AAATTATTGAATCACTTACAAAATTACTGAATTTCTT-TCAAAATTACTAATGTTTACCTAGTTT
1 AAATTATTGAATCTCTTACAAAATTACTGAATTTCTTAT-AAAATTACTAATACTTACCTAATTT
*
54567299 GTTATAACATTGT
65 CTTATAACATTGT
** *
54567312 AAATT-TTGAATCTCTTACAAAATTTTTGAATTTCTTATAAAATTACTAATACTTACTTAATTTC
1 AAATTATTGAATCTCTTACAAAATTACTGAATTTCTTATAAAATTACTAATACTTACCTAATTTC
**
54567376 TTATAATTTTGT
66 TTATAACATTGT
*
54567388 AAATTATTGAATCTCTTACCAAATTACTGAA
1 AAATTATTGAATCTCTTACAAAATTACTGAA
54567419 AAATTTACAT
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
76 64 0.70
77 28 0.30
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (77 bp):
AAATTATTGAATCTCTTACAAAATTACTGAATTTCTTATAAAATTACTAATACTTACCTAATTTC
TTATAACATTGT
Found at i:54567338 original size:20 final size:20
Alignment explanation
Indices: 54567315--54567355 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
54567305 ACATTGTAAA
54567315 TTTTGAATCTCTTACAAAAT
1 TTTTGAATCTCTTACAAAAT
* *
54567335 TTTTGAATTTCTTATAAAAT
1 TTTTGAATCTCTTACAAAAT
54567355 T
1 T
54567356 ACTAATACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (20 bp):
TTTTGAATCTCTTACAAAAT
Found at i:54568522 original size:17 final size:17
Alignment explanation
Indices: 54568485--54568532 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
54568475 GAATTTAGAA
*
54568485 GAATTTT-TGAATTAGT
1 GAATTTTGTGATTTAGT
*
54568501 GAATTTTGTGATTTATT
1 GAATTTTGTGATTTAGT
54568518 GAATTTTGTGATTTA
1 GAATTTTGTGATTTA
54568533 AAAAGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (17 bp):
GAATTTTGTGATTTAGT
Found at i:54569827 original size:46 final size:46
Alignment explanation
Indices: 54569759--54569943 Score: 259
Period size: 46 Copynumber: 4.0 Consensus size: 46
54569749 CATGGCAAAG
*
54569759 TGTGAAAAGTAGGTATGATATTTCGAT-AAGGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGATGAA-GAAAACCATACTGAGT
*
54569805 TGTGAAAAGTAGGTATGGTATTTCGATAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGATGAAGAAAACCATACTGAGT
* *
54569851 TGTGAAAAGTAGGTATGGTGTTTC-AGTGAAGAAAGCCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCGA-TGAAGAAAACCATACTGAGT
* * *
54569897 TGGGAAAAGTAGGTATGGTATTCCCG-TGAAGAAAACCATACCGAGT
1 TGTGAAAAGTAGGTATGGTATT-TCGATGAAGAAAACCATACTGAGT
54569943 T
1 T
54569944 ATAGCAATGT
Statistics
Matches: 126, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
45 1 0.01
46 122 0.97
47 3 0.02
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.27
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCGATGAAGAAAACCATACTGAGT
Found at i:54574788 original size:46 final size:46
Alignment explanation
Indices: 54574732--54574916 Score: 275
Period size: 46 Copynumber: 4.0 Consensus size: 46
54574722 ACATTGTTAT
* * *
54574732 AACTCGGTATGGTTTTCTTCA-CGGGAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTATC-GAAATACCATACCTACTTTTCAC
* * *
54574778 AACTCAGTATGGCTTTCTTTA-CTGAAACACCATACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTTATC-GAAATACCATACCTACTTTTCAC
54574824 AACTCAGTATGGTTTTCTTTATCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTATCGAAATACCATACCTACTTTTCAC
*
54574870 AACTCAGTATGGTTTTCCTTATCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTATCGAAATACCATACCTACTTTTCAC
54574916 A
1 A
54574917 CTTTGCCATG
Statistics
Matches: 127, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
46 126 0.99
47 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.37
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTATCGAAATACCATACCTACTTTTCAC
Found at i:54577282 original size:30 final size:30
Alignment explanation
Indices: 54577211--54577282 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
54577201 AGGGAGAAGG
* * *
54577211 ATGGAAAATGGCAGCTCCGTTAAGTTTGTA
1 ATGGAAAATGGTAGCTCCGCTAAGTTTATA
* * *
54577241 ACGGAAAATGGTAGCTCTGCTACGTTTATA
1 ATGGAAAATGGTAGCTCCGCTAAGTTTATA
54577271 ATGGAAAATGGT
1 ATGGAAAATGGT
54577283 TAGTGGTGAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (30 bp):
ATGGAAAATGGTAGCTCCGCTAAGTTTATA
Found at i:54579071 original size:36 final size:36
Alignment explanation
Indices: 54579024--54579296 Score: 285
Period size: 36 Copynumber: 7.0 Consensus size: 36
54579014 GCTAAGCTAC
* *
54579024 CACTTATCACTTTGTCACCTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
54579060 CACTTATCACTTTTTCACTTGATCAGATAAGTATAA
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
54579096 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--AG
*
54579138 CTACCACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 ----CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
54579178 CACTTATCACTTTTTCACTTGATCAGGTAAGTGTAGCTAAAG
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--AG
* *
54579220 CTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
* *
54579260 CACTTATCACTTTTTCACTTGATCACATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
54579296 C
1 C
54579297 TAAAGCTACC
Statistics
Matches: 205, Mismatches: 12, Indels: 40
0.80 0.05 0.16
Matches are distributed among these distances:
36 126 0.61
38 6 0.03
40 6 0.03
42 5 0.02
44 5 0.02
46 57 0.28
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:54579147 original size:46 final size:46
Alignment explanation
Indices: 54579096--54579332 Score: 280
Period size: 46 Copynumber: 5.6 Consensus size: 46
54579086 ATAAGTATAA
*
54579096 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
54579142 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
54579178 CACTTATCACTTTTTCACTTGATCAGGTAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
54579224 CACTTATCACTTTGTCACTTGATCAGATAA--GT-G-T--AG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
54579260 CACTTATCACTTTTTCACTTGATCACATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
54579306 CACTTATCACTTTGTCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
54579333 AGTACTCAAA
Statistics
Matches: 161, Mismatches: 10, Indels: 40
0.76 0.05 0.19
Matches are distributed among these distances:
36 56 0.35
38 5 0.03
39 1 0.01
40 6 0.04
42 6 0.04
43 1 0.01
44 5 0.03
46 81 0.50
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:54579152 original size:82 final size:82
Alignment explanation
Indices: 54579060--54579332 Score: 492
Period size: 82 Copynumber: 3.3 Consensus size: 82
54579050 ATAAGTATAG
* *
54579060 CACTTATCACTTTTTCACTTGATCAGATAAGTATAACACTTATCACTTTTTCACTTGATCAGATA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATA
54579125 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
*
54579142 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGGTA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATA
54579207 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
* *
54579224 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCACATA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATA
54579289 AGTGTAGCTAAAGCTAC
66 AGTGTAGCTAAAGCTAC
*
54579306 CACTTATCACTTTGTCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
54579333 AGTACTCAAA
Statistics
Matches: 184, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 184 1.00
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (82 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATA
AGTGTAGCTAAAGCTAC
Found at i:54579153 original size:118 final size:122
Alignment explanation
Indices: 54578981--54579260 Score: 412
Period size: 118 Copynumber: 2.3 Consensus size: 122
54578971 TACGTATGAT
* *
54578981 CACTTATCA-TTTGTC-CCTAATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACCT
54579044 GATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAA-GTA-T-A-A-
66 GATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGGTACTAACAC
* *
54579096 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACC
*
54579161 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGGTAAGTGTAGCTAAAGCTAC
65 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAG-GTA-CT-AA-C-AC
54579224 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
54579261 ACTTATCACT
Statistics
Matches: 146, Mismatches: 6, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
115 9 0.06
116 5 0.03
117 19 0.13
118 71 0.49
120 3 0.02
122 1 0.01
124 1 0.01
127 1 0.01
128 36 0.25
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (122 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACCT
GATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGGTACTAACAC
Found at i:54579264 original size:118 final size:113
Alignment explanation
Indices: 54578981--54579296 Score: 340
Period size: 118 Copynumber: 2.7 Consensus size: 113
54578971 TACGTATGAT
* * *
54578981 CACTTATCA-TTTGTC-CCTAATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTGTCACCT
1 CACTTATCACTTTGTCACTTGATCAGATAAG-GTAGCTAAG---CCACTTATCACTTTGTCACTT
54579044 GATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAA
62 GATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAA
*
54579096 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAG-GTAGCT-AAG---CCACTTATCACTTTGTCACT
*
54579161 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGGTAAGTGTAGCTAAAGCTA
61 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--A---A
*
54579223 CCACTTATCACTTTGTCACTTGATCAGATAA-GT-G-T-AG-CACTTATCACTTTTTCACTTGAT
1 -CACTTATCACTTTGTCACTTGATCAGATAAGGTAGCTAAGCCACTTATCACTTTGTCACTTGAT
* *
54579283 CACATAAGTGTAGC
65 CAGATAAGTATAGC
54579297 TAAAGCTACC
Statistics
Matches: 179, Mismatches: 9, Indels: 23
0.85 0.04 0.11
Matches are distributed among these distances:
115 9 0.05
116 5 0.03
117 19 0.11
118 105 0.59
120 3 0.02
122 3 0.02
124 2 0.01
125 1 0.01
126 2 0.01
127 1 0.01
128 29 0.16
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (113 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGGTAGCTAAGCCACTTATCACTTTGTCACTTGATC
AGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAA
Found at i:54583930 original size:19 final size:20
Alignment explanation
Indices: 54583893--54583931 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
54583883 TAAATCACAT
*
54583893 TAGAGTTAAAAGTTGAATTA
1 TAGAGTTAAAAGTTAAATTA
*
54583913 TAGA-TTAAAATTTAAATTA
1 TAGAGTTAAAAGTTAAATTA
54583932 AAGGCTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.38
Consensus pattern (20 bp):
TAGAGTTAAAAGTTAAATTA
Found at i:54584871 original size:2 final size:2
Alignment explanation
Indices: 54584864--54584910 Score: 76
Period size: 2 Copynumber: 22.5 Consensus size: 2
54584854 ATTGAAATGA
54584864 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T AT
54584908 AT A
1 AT A
54584911 GTANNNNNNN
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 39 0.89
3 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:54587629 original size:22 final size:23
Alignment explanation
Indices: 54587604--54587648 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
54587594 GTTTATTTTC
54587604 TTAATTTAT-TAAATAATATATT
1 TTAATTTATATAAATAATATATT
* *
54587626 TTAATTTATATAATTCATATATT
1 TTAATTTATATAAATAATATATT
54587649 ATTCGAATAC
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:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAATTTATATAAATAATATATT
Found at i:54587719 original size:17 final size:17
Alignment explanation
Indices: 54587699--54587743 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
54587689 CAATTTAAAT
*
54587699 TATAAAATATAATTTAA
1 TATAAAATATAATATAA
54587716 TAT-AAATATAAATATAA
1 TATAAAATAT-AATATAA
*
54587733 TAAAAAATATA
1 TATAAAATATA
54587744 TTATTTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 6 0.25
17 12 0.50
18 6 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TATAAAATATAATATAA
Found at i:54589173 original size:19 final size:20
Alignment explanation
Indices: 54589135--54589173 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
54589125 AACTCTTTTT
54589135 TTTTTCCTTGAATTTTCAGGA
1 TTTTTCCTTGAA-TTTCAGGA
*
54589156 TTTTTCTTTGAA-TTCAGG
1 TTTTTCCTTGAATTTCAGG
54589174 TTACTGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.18, C:0.13, G:0.15, T:0.54
Consensus pattern (20 bp):
TTTTTCCTTGAATTTCAGGA
Found at i:54599446 original size:19 final size:21
Alignment explanation
Indices: 54599398--54599444 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
54599388 CCTATTTTAC
54599398 TTTTATATCAACCACTTTCTCCA
1 TTTT-TAT-AACCACTTTCTCCA
*
54599421 TTTTTATAACCA-TTTCTCTA
1 TTTTTATAACCACTTTCTCCA
54599441 TTTT
1 TTTT
54599445 ATTTCATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 11 0.48
21 5 0.22
22 3 0.13
23 4 0.17
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTTATAACCACTTTCTCCA
Found at i:54602820 original size:29 final size:29
Alignment explanation
Indices: 54602777--54602834 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
54602767 TATTTAGATA
54602777 ATTTTATTTTCCAAATCAACCATATCTCT
1 ATTTTATTTTCCAAATCAACCATATCTCT
* *
54602806 ATTTTATTTTTCAAATCAACCATTTCTCT
1 ATTTTATTTTCCAAATCAACCATATCTCT
54602835 TCTTTCTCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.48
Consensus pattern (29 bp):
ATTTTATTTTCCAAATCAACCATATCTCT
Found at i:54605385 original size:180 final size:174
Alignment explanation
Indices: 54605085--54605428 Score: 458
Period size: 180 Copynumber: 1.9 Consensus size: 174
54605075 TGCATCTAAT
* * *
54605085 AATCCAAAGACAAATTAAGGATACAAGTAGGCACTAGTAAGCAAATACAATCAATGACTAATCAG
1 AATCCAAAGACAAATCAAGGATACAAGTAGACACTAGTAAGCAAATACAATAAATGACTAATCAG
*
54605150 CAATACCAAGGATCATTCTATAATGAATAATCATATAGTCAAGTCACTACTTGAATTGAATGACA
66 CAATACCAAGGATCATTCTATAATGAATAATCATATAATCAAGTCACTACTTGAATTGAATGA-A
* * * *
54605215 TCTACCAACATTAAGGGTCAGCATACCAACGAAAAGGAGAAAAAA
130 TCTACCAACATTAAGGATCAACATACAAAAGAAAAGGAGAAAAAA
* **
54605260 AATCCAAA-ATCAAATCAAGGATACAAGTAGACACTAGTAAGTAAACTTGATATAAATGACGACT
1 AATCCAAAGA-CAAATCAAGGATACAAGTAGACACTAGTAAGCAAA-TACA-ATAAAT---GACT
** * *
54605324 AATCAGCAATGTCAAGGATCGTTCTA-AGATGAATAATCATATAATCAAGTCACTTCTTGAATTG
60 AATCAGCAATACCAAGGATCATTCTATA-ATGAATAATCATATAATCAAGTCACTACTTGAATTG
*
54605388 AATGAATCTCCCAACATTAAGGATCAACATACAAAAGAAAA
124 AATGAATCTACCAACATTAAGGATCAACATACAAAAGAAAA
54605429 TCCAAAAGCA
Statistics
Matches: 146, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
174 1 0.01
175 40 0.27
176 2 0.01
177 5 0.03
179 32 0.22
180 66 0.45
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (174 bp):
AATCCAAAGACAAATCAAGGATACAAGTAGACACTAGTAAGCAAATACAATAAATGACTAATCAG
CAATACCAAGGATCATTCTATAATGAATAATCATATAATCAAGTCACTACTTGAATTGAATGAAT
CTACCAACATTAAGGATCAACATACAAAAGAAAAGGAGAAAAAA
Found at i:54610133 original size:20 final size:20
Alignment explanation
Indices: 54610108--54610149 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
54610098 AGGAACGAAG
54610108 AAAATGAAAAACAAAAGTAA
1 AAAATGAAAAACAAAAGTAA
54610128 AAAATGAAAAACAAAAGTAA
1 AAAATGAAAAACAAAAGTAA
54610148 AA
1 AA
54610150 GAACTAAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.76, C:0.05, G:0.10, T:0.10
Consensus pattern (20 bp):
AAAATGAAAAACAAAAGTAA
Found at i:54612194 original size:88 final size:87
Alignment explanation
Indices: 54612026--54612251 Score: 292
Period size: 88 Copynumber: 2.6 Consensus size: 87
54612016 TTTAAGGGTG
* * * ** * *
54612026 CAAAAAGTCTTCAAACTTTTTCAAAAAAAGCAATTAAGCCTTTGTTTTTTTTTTTACACTCATTT
1 CAAAAAGCCCTCAAACCTTTTCAAAAAAAGCAATTAAGCC---CCTATTTTTTTTACACTCAATT
54612091 GGGTACTTAAACTTTCAAAATACAT
63 GGGTACTTAAACTTTCAAAATACAT
* *
54612116 CAAAAAGGCCCTCAAGCCTTTTCAAAAAAAGCAATTAAGCCCCTATTTTTTTTGCACTCAATTGG
1 CAAAAA-GCCCTCAAACCTTTTCAAAAAAAGCAATTAAGCCCCTATTTTTTTTACACTCAATTGG
* *
54612181 GTACTTGAACTTTCAAAATGCAT
65 GTACTTAAACTTTCAAAATACAT
* *
54612204 CAAAAAGCCCTCAAACTTTTTC-AAAAAAGCAATTAAGCCCCTGTTTTT
1 CAAAAAGCCCTCAAACCTTTTCAAAAAAAGCAATTAAGCCCCTATTTTT
54612252 ATTAAAAATT
Statistics
Matches: 121, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
86 25 0.21
87 14 0.12
88 46 0.38
90 6 0.05
91 30 0.25
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (87 bp):
CAAAAAGCCCTCAAACCTTTTCAAAAAAAGCAATTAAGCCCCTATTTTTTTTACACTCAATTGGG
TACTTAAACTTTCAAAATACAT
Found at i:54612332 original size:20 final size:20
Alignment explanation
Indices: 54612299--54612357 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
54612289 TATAGGCTAT
*
54612299 AAATATTATTAAATTTTAATAA
1 AAATATTA-AAAATTTTAA-AA
*
54612321 AAATA-TAAAAATCTT-AAA
1 AAATATTAAAAATTTTAAAA
54612339 AAATATTAAAATATTTTAA
1 AAATATTAAAA-ATTTTAA
54612358 CATTTTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 7 0.23
19 6 0.19
20 10 0.32
21 3 0.10
22 5 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATATTAAAAATTTTAAAA
Found at i:54612419 original size:25 final size:25
Alignment explanation
Indices: 54612374--54612422 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
54612364 ATAAAGATCG
*
54612374 TAAAAAATTATAATATATATAAATA
1 TAAAAAATTAAAATATATATAAATA
*
54612399 TAAAAAATATAAAAT-TTTATAAAT
1 TAAAAAAT-TAAAATATATATAAAT
54612423 TTGTAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAAAAATTAAAATATATATAAATA
Found at i:54612838 original size:31 final size:31
Alignment explanation
Indices: 54612774--54612838 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
54612764 TTCAAAATTC
* ** *
54612774 AAAAAGTATAGTGATTAAAAAGGACCAATTT
1 AAAAAGTATAGTGACTAAAAACAACCAACTT
* *
54612805 AAAAAGTATAGTGACTAAAAACAATCACCTT
1 AAAAAGTATAGTGACTAAAAACAACCAACTT
54612836 AAA
1 AAA
54612839 TTATAGAGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.54, C:0.11, G:0.12, T:0.23
Consensus pattern (31 bp):
AAAAAGTATAGTGACTAAAAACAACCAACTT
Found at i:54615926 original size:21 final size:20
Alignment explanation
Indices: 54615872--54615929 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 20
54615862 TAGACCCAAT
54615872 GTGAGCAGGAGAGTCAAC-A
1 GTGAGCAGGAGAGTCAACAA
* * * *
54615891 -TTAGGATGAGGGTCAACAA
1 GTGAGCAGGAGAGTCAACAA
54615910 CGTGAGCAGGAGAGTCAACA
1 -GTGAGCAGGAGAGTCAACA
54615930 TTGAGATGAG
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
18 13 0.46
19 1 0.04
21 14 0.50
ACGTcount: A:0.36, C:0.16, G:0.34, T:0.14
Consensus pattern (20 bp):
GTGAGCAGGAGAGTCAACAA
Found at i:54615940 original size:18 final size:18
Alignment explanation
Indices: 54615880--54615946 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
54615870 ATGTGAGCAG
54615880 GAGAGTCAACATT-AGGAT
1 GAGAGTCAACATTGA-GAT
* * *
54615898 GAGGGTCAACAACGTGAGCAG
1 GAGAGTCAAC-A-TTGAG-AT
54615919 GAGAGTCAACATTGAGAT
1 GAGAGTCAACATTGAGAT
*
54615937 GAGAATCAAC
1 GAGAGTCAAC
54615947 TATCGGTAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 19 0.50
19 5 0.13
20 3 0.08
21 11 0.29
ACGTcount: A:0.39, C:0.15, G:0.30, T:0.16
Consensus pattern (18 bp):
GAGAGTCAACATTGAGAT
Found at i:54615946 original size:39 final size:39
Alignment explanation
Indices: 54615872--54615946 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
54615862 TAGACCCAAT
**
54615872 GTGAGCAGGAGAGTCAACATTAGGATGAGGGTCAACAAC
1 GTGAGCAGGAGAGTCAACATTAGGATGAGAATCAACAAC
54615911 GTGAGCAGGAGAGTCAACATT-GAGATGAGAATCAAC
1 GTGAGCAGGAGAGTCAACATTAG-GATGAGAATCAAC
54615947 TATCGGTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 32 0.97
ACGTcount: A:0.37, C:0.15, G:0.32, T:0.16
Consensus pattern (39 bp):
GTGAGCAGGAGAGTCAACATTAGGATGAGAATCAACAAC
Found at i:54618542 original size:10 final size:10
Alignment explanation
Indices: 54618527--54618554 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
54618517 ACCATAACAG
54618527 CTAACTGATA
1 CTAACTGATA
54618537 CTAACTGATA
1 CTAACTGATA
54618547 CTAACTGA
1 CTAACTGA
54618555 CTAACTGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (10 bp):
CTAACTGATA
Found at i:54618627 original size:10 final size:10
Alignment explanation
Indices: 54618612--54618639 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
54618602 TTATGCTGCT
54618612 GTTTTGTTTA
1 GTTTTGTTTA
54618622 GTTTTGTTTA
1 GTTTTGTTTA
54618632 GTTTTGTT
1 GTTTTGTT
54618640 ACTTCAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.07, C:0.00, G:0.21, T:0.71
Consensus pattern (10 bp):
GTTTTGTTTA
Found at i:54621126 original size:15 final size:15
Alignment explanation
Indices: 54621106--54621156 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
54621096 ACAAAAAGAT
54621106 AATGTAAGTGACTAA
1 AATGTAAGTGACTAA
* * *
54621121 AATGTAA--CATTTTA
1 AATGTAAGTGA-CTAA
54621135 AATGTAAGTGACTAA
1 AATGTAAGTGACTAA
54621150 AATGTAA
1 AATGTAA
54621157 TTTGAAGTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 1 0.04
14 9 0.33
15 16 0.59
16 1 0.04
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (15 bp):
AATGTAAGTGACTAA
Found at i:54625388 original size:20 final size:20
Alignment explanation
Indices: 54625363--54625403 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
54625353 ATTTTCCATT
54625363 TCCTCGAAGGGCAGCTAAAG
1 TCCTCGAAGGGCAGCTAAAG
54625383 TCCTCGAAGGGCAGCTAAAG
1 TCCTCGAAGGGCAGCTAAAG
54625403 T
1 T
54625404 GGTCTCTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.17
Consensus pattern (20 bp):
TCCTCGAAGGGCAGCTAAAG
Found at i:54639056 original size:20 final size:19
Alignment explanation
Indices: 54639024--54639061 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
54639014 AAATTGTTTA
54639024 AAATATAAAAAATTAAAAAT
1 AAATATAAAAAA-TAAAAAT
54639044 AAATA-AAAGAAATAAAAA
1 AAATATAAA-AAATAAAAA
54639062 GGAATTGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (19 bp):
AAATATAAAAAATAAAAAT
Found at i:54642302 original size:2 final size:2
Alignment explanation
Indices: 54642295--54642327 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54642285 TATGTTTTTC
54642295 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54642328 CCTATATCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54642852 original size:20 final size:20
Alignment explanation
Indices: 54642824--54642862 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
54642814 CTCTTTTAGC
54642824 TTTCATCTTCT-TTTTCATCT
1 TTTCATCTT-TGTTTTCATCT
*
54642844 TTTCTTCTTTGTTTTCATC
1 TTTCATCTTTGTTTTCATC
54642863 CCCAATAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTCATCTTTGTTTTCATCT
Found at i:54648356 original size:31 final size:31
Alignment explanation
Indices: 54648277--54648357 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
54648267 AACTATGAAA
54648277 ATTTTTAATTTTATCACT-ATCGTTTTAGATC
1 ATTTTT-ATTTTATCACTCATCGTTTTAGATC
* *
54648308 ATTTCTATTTTGGTCACTCATC-TTTTAGATC
1 ATTTTTATTTT-ATCACTCATCGTTTTAGATC
*
54648339 GTTTTTATTTTATTCACTC
1 ATTTTTATTTTA-TCACTC
54648358 TTCATTAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
30 5 0.12
31 34 0.81
32 3 0.07
ACGTcount: A:0.21, C:0.16, G:0.07, T:0.56
Consensus pattern (31 bp):
ATTTTTATTTTATCACTCATCGTTTTAGATC
Found at i:54649483 original size:31 final size:31
Alignment explanation
Indices: 54649447--54649513 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
54649437 ATTTAACGGA
* *
54649447 GAGTGACCAAAATAGAAACAATCTAAAGTGT
1 GAGTGACCAAAATAGAAACAATATAAAATGT
*
54649478 GAGTGACCAAAATAGAAATAATATAAAATGT
1 GAGTGACCAAAATAGAAACAATATAAAATGT
*
54649509 AAGTG
1 GAGTG
54649514 GCTAAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.51, C:0.09, G:0.19, T:0.21
Consensus pattern (31 bp):
GAGTGACCAAAATAGAAACAATATAAAATGT
Found at i:54652603 original size:2 final size:2
Alignment explanation
Indices: 54652596--54652628 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
54652586 TGCTTATTCT
54652596 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54652629 GATGTAGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54657745 original size:26 final size:24
Alignment explanation
Indices: 54657694--54657748 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
54657684 AATTTTAAAG
* *
54657694 TATTTTTAAAATACTTTTTATTTT
1 TATTTTTAAAATACTTTTGATGTT
54657718 TATTTTTAAAATACAATTTTGATGTT
1 TATTTTTAAAATAC--TTTTGATGTT
54657744 TATTT
1 TATTT
54657749 AAAAAAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 14 0.52
26 13 0.48
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (24 bp):
TATTTTTAAAATACTTTTGATGTT
Found at i:54658046 original size:28 final size:27
Alignment explanation
Indices: 54658015--54658068 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
54658005 GCGCGGTATT
54658015 GATT-AATAATATATAACAACTAAAAAGG
1 GATTGAATAA-ATATAACAAC-AAAAAGG
* *
54658043 GATTGCATAAATGTAACAACAAAAAG
1 GATTGAATAAATATAACAACAAAAAG
54658069 AAAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 6 0.26
28 13 0.57
29 4 0.17
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (27 bp):
GATTGAATAAATATAACAACAAAAAGG
Found at i:54658819 original size:33 final size:33
Alignment explanation
Indices: 54658782--54658853 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
54658772 AAATAAAATT
*
54658782 TAAAATTCTTTTATTATCAAATAAATTTCTTAA
1 TAAAATTCTTTTATTATCAAATAAAATTCTTAA
54658815 TAAAATTCTTTTATTATCAAATAAAATTCTTAA
1 TAAAATTCTTTTATTATCAAATAAAATTCTTAA
54658848 TGAAAA
1 T-AAAA
54658854 AATAAAACAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 33 0.89
34 4 0.11
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.44
Consensus pattern (33 bp):
TAAAATTCTTTTATTATCAAATAAAATTCTTAA
Found at i:54661892 original size:15 final size:15
Alignment explanation
Indices: 54661872--54661904 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
54661862 ATACCCACAA
54661872 CTAATGTTCAATATT
1 CTAATGTTCAATATT
54661887 CTAATGTTCAATATT
1 CTAATGTTCAATATT
54661902 CTA
1 CTA
54661905 TAATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.45
Consensus pattern (15 bp):
CTAATGTTCAATATT
Found at i:54661914 original size:2 final size:2
Alignment explanation
Indices: 54661903--54661938 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
54661893 TTCAATATTC
54661903 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54661939 TAGATTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54671203 original size:5 final size:5
Alignment explanation
Indices: 54671195--54671225 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
54671185 TATTTAGTTT
54671195 ATATA ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA A
54671226 AACATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:54673419 original size:2 final size:2
Alignment explanation
Indices: 54673412--54673439 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54673402 GATTTACTAA
54673412 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
54673440 CCACAACAAT
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:54673719 original size:26 final size:27
Alignment explanation
Indices: 54673664--54673721 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
54673654 AATAACTTGT
* * * *
54673664 TAGAA-GGGTTGATTAATTGGAAAGCA
1 TAGAATGGGTTAATCAATTAGAAAACA
54673690 TAGAATGGGTTAATCAATTAGAAAAC-
1 TAGAATGGGTTAATCAATTAGAAAACA
54673716 TAGAAT
1 TAGAAT
54673722 TTATAAAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.43, C:0.05, G:0.24, T:0.28
Consensus pattern (27 bp):
TAGAATGGGTTAATCAATTAGAAAACA
Found at i:54678263 original size:31 final size:31
Alignment explanation
Indices: 54678204--54678263 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
54678194 TTATCTCTAT
* **
54678204 CGTTTTAGATCATTTCTATTTTGGTCACTTA
1 CGTTTTAGAGCATTTCTATTTTACTCACTTA
*
54678235 CGTTTTAGAGCATTTTTATTTTACTCACT
1 CGTTTTAGAGCATTTCTATTTTACTCACT
54678264 CTTCATTAAA
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:0.20, C:0.17, G:0.12, T:0.52
Consensus pattern (31 bp):
CGTTTTAGAGCATTTCTATTTTACTCACTTA
Found at i:54684606 original size:23 final size:23
Alignment explanation
Indices: 54684578--54684696 Score: 139
Period size: 23 Copynumber: 5.2 Consensus size: 23
54684568 GTTATTGATT
* *
54684578 AGTGGTAACTTCGGCTACATTTC
1 AGTGGTAGCTTCGGCTACATATC
* * *
54684601 AATGGTAGCTACAGCTACATATC
1 AGTGGTAGCTTCGGCTACATATC
* *
54684624 AGTGGTAGCTTCGGCTACATTTT
1 AGTGGTAGCTTCGGCTACATATC
* * *
54684647 AGTGGTATCTACGTCTACATATC
1 AGTGGTAGCTTCGGCTACATATC
*
54684670 AGTGGTAGCTTCGGCTACATATT
1 AGTGGTAGCTTCGGCTACATATC
54684693 AGTG
1 AGTG
54684697 TGACACTTAT
Statistics
Matches: 77, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 77 1.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (23 bp):
AGTGGTAGCTTCGGCTACATATC
Found at i:54684645 original size:46 final size:46
Alignment explanation
Indices: 54684578--54684689 Score: 172
Period size: 46 Copynumber: 2.4 Consensus size: 46
54684568 GTTATTGATT
*
54684578 AGTGGTAACTTCGGCTACATTTCAATGGTAGCTACAG-CTACATATC
1 AGTGGTAGCTTCGGCTACATTTCAATGGTAGCTAC-GTCTACATATC
* * *
54684624 AGTGGTAGCTTCGGCTACATTTTAGTGGTATCTACGTCTACATATC
1 AGTGGTAGCTTCGGCTACATTTCAATGGTAGCTACGTCTACATATC
54684670 AGTGGTAGCTTCGGCTACAT
1 AGTGGTAGCTTCGGCTACAT
54684690 ATTAGTGTGA
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 1 0.02
46 60 0.98
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (46 bp):
AGTGGTAGCTTCGGCTACATTTCAATGGTAGCTACGTCTACATATC
Found at i:54685712 original size:31 final size:30
Alignment explanation
Indices: 54685677--54685744 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
54685667 ATTTAAAGGA
* *
54685677 GAGTGATCAAAATAGAAACAATCTAAAGTGT
1 GAGTGACCAAAATAGAAACAATATAAA-TGT
*
54685708 GAGTGACCAAAATAGAAATAATATAAATGT
1 GAGTGACCAAAATAGAAACAATATAAATGT
*
54685738 AAGTGAC
1 GAGTGAC
54685745 TAAATTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
30 9 0.27
31 24 0.73
ACGTcount: A:0.50, C:0.09, G:0.19, T:0.22
Consensus pattern (30 bp):
GAGTGACCAAAATAGAAACAATATAAATGT
Found at i:54685757 original size:30 final size:31
Alignment explanation
Indices: 54685678--54685757 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
54685668 TTTAAAGGAG
* * * * *
54685678 AGTGATCAAAATAGAAACAATCTAAAGTGTG
1 AGTGACCAAAATAAAAATAATATAAAGTGTA
*
54685709 AGTGACCAAAATAGAAATAATATAAA-TGTA
1 AGTGACCAAAATAAAAATAATATAAAGTGTA
* *
54685739 AGTGACTAAATTAAAAATA
1 AGTGACCAAAATAAAAATA
54685758 TTCATAGTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 19 0.45
31 23 0.55
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24
Consensus pattern (31 bp):
AGTGACCAAAATAAAAATAATATAAAGTGTA
Found at i:54693581 original size:149 final size:148
Alignment explanation
Indices: 54693330--54693631 Score: 471
Period size: 149 Copynumber: 2.0 Consensus size: 148
54693320 AAAAAAGAGA
* * * * *
54693330 ATAAAAGAAACATGAAATTATACCTGTCAATTTGTTATAGCTAAGATAAAGTGATTGGAGAGATG
1 ATAAAAGAAACATGAAATTATACCTGTAAATGTATTATAGCTAAGAGAAAGTGATTGGAGAGAAG
54693395 TCAAGTTCCCAATAACAAGAGGAATTTCACCTAAAACATATAATTAAATCAATAACTTTTATTTT
66 TCAAGTTCCCAATAACAAGAGGAATTTCACCTAAAACATATAATTAAATCAATAACTTTTA-TTT
54693460 ATTTACTTAAAAAGATTGC
130 ATTTACTTAAAAAGATTGC
* * * *
54693479 ATAAACGAAACATGAAATTGTACCTGTAAATGTATTATTG-TAAAGAGAAAGTGTTTGGAGAGAA
1 ATAAAAGAAACATGAAATTATACCTGTAAATGTATTATAGCT-AAGAGAAAGTGATTGGAGAGAA
* * *
54693543 GTCAAGTTTCCAATAACAAGAGGAATTTCACCTGAAACATATAATTAAATCAGTAACTTTTATTT
65 GTCAAGTTCCCAATAACAAGAGGAATTTCACCTAAAACATATAATTAAATCAATAACTTTTATTT
54693608 ATTTACTTAAAAAGATTGC
130 ATTTACTTAAAAAGATTGC
54693627 ATAAA
1 ATAAA
54693632 TTTAAAAACA
Statistics
Matches: 140, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
148 28 0.20
149 112 0.80
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (148 bp):
ATAAAAGAAACATGAAATTATACCTGTAAATGTATTATAGCTAAGAGAAAGTGATTGGAGAGAAG
TCAAGTTCCCAATAACAAGAGGAATTTCACCTAAAACATATAATTAAATCAATAACTTTTATTTA
TTTACTTAAAAAGATTGC
Found at i:54694839 original size:2 final size:2
Alignment explanation
Indices: 54694832--54694870 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
54694822 TTGAGGCTTT
54694832 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54694871 GCAGAGTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54696130 original size:149 final size:149
Alignment explanation
Indices: 54695860--54696162 Score: 561
Period size: 149 Copynumber: 2.0 Consensus size: 149
54695850 AAAAAGGAGA
* *
54695860 ATAAACGAAACATGAAATTGTACCTGTAAATTTATTATTGTCAAGACCAAGTGATTGGAGAGAAG
1 ATAAACGAAACATGAAATTGTACCTGTAAATTTATTATTGTAAAGACAAAGTGATTGGAGAGAAG
54695925 TCAAGTTTCCAATAACAAGAGGAATTTCACCTGAAACATATAATTAAATCAATAACTTTTATTTT
66 TCAAGTTTCCAATAACAAGAGGAATTTCACCTGAAACATATAATTAAATCAATAACTTTTATTTT
54695990 ATTTACTTAAAAAGATTGC
131 ATTTACTTAAAAAGATTGC
* *
54696009 ATAAACGAAACATGAAATTGTACCTGTAAATTTATTATTGTAAAGATAAAGTGTTTGGAGAGAAG
1 ATAAACGAAACATGAAATTGTACCTGTAAATTTATTATTGTAAAGACAAAGTGATTGGAGAGAAG
*
54696074 TCAAGTTTCCAATAACAAGAGGAATTTCACCTGAAACATATAATTAAATCAGTAACTTTTATTTT
66 TCAAGTTTCCAATAACAAGAGGAATTTCACCTGAAACATATAATTAAATCAATAACTTTTATTTT
54696139 ATTTACTTAAAAAGATTGC
131 ATTTACTTAAAAAGATTGC
54696158 ATAAA
1 ATAAA
54696163 TTTAAAAACA
Statistics
Matches: 149, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.33
Consensus pattern (149 bp):
ATAAACGAAACATGAAATTGTACCTGTAAATTTATTATTGTAAAGACAAAGTGATTGGAGAGAAG
TCAAGTTTCCAATAACAAGAGGAATTTCACCTGAAACATATAATTAAATCAATAACTTTTATTTT
ATTTACTTAAAAAGATTGC
Found at i:54697387 original size:16 final size:16
Alignment explanation
Indices: 54697366--54697396 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54697356 GGCAGTTATT
54697366 TTTATTTTTATATTTG
1 TTTATTTTTATATTTG
*
54697382 TTTATTTTTTTATTT
1 TTTATTTTTATATTT
54697397 TAAAAAAATA
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:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTATTTTTATATTTG
Found at i:54706388 original size:33 final size:33
Alignment explanation
Indices: 54706347--54706453 Score: 130
Period size: 31 Copynumber: 3.2 Consensus size: 33
54706337 AAAAAGGGAA
54706347 ATATAATATATATATATATAAATATACATGTTT
1 ATATAATATATATATATATAAATATACATGTTT
54706380 ATATAATATATATATATATAAAATATACATG-TT
1 ATATAATATATATATATAT-AAATATACATGTTT
* * * *
54706413 -T-TAATATATATAAAAATAATATATATATGTAT
1 ATATAATATATATATATATAA-ATATACATGTTT
54706445 ATATGAATA
1 ATAT-AATA
54706454 GGTATATAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
30 2 0.03
31 22 0.34
32 2 0.03
33 22 0.34
34 12 0.19
35 4 0.06
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (33 bp):
ATATAATATATATATATATAAATATACATGTTT
Found at i:54706461 original size:2 final size:2
Alignment explanation
Indices: 54706347--54706448 Score: 63
Period size: 2 Copynumber: 54.0 Consensus size: 2
54706337 AAAAAGGGAA
* * * *
54706347 AT AT A- AT AT AT AT AT AT AT AA AT AT AC AT GT TT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
54706387 AT AT AT AT AT AT A- AA AT AT AC AT GT -T TT A- AT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
54706426 AA AT A- AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
54706449 GAATAGGTAT
Statistics
Matches: 78, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
1 6 0.08
2 72 0.92
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:54706520 original size:18 final size:18
Alignment explanation
Indices: 54706493--54706527 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54706483 ATAAGAGAAA
* *
54706493 TAACAGTAATATTAATAC
1 TAACAATAATAGTAATAC
54706511 TAACAATAATAGTAATA
1 TAACAATAATAGTAATA
54706528 ATAATAACCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (18 bp):
TAACAATAATAGTAATAC
Found at i:54706529 original size:3 final size:3
Alignment explanation
Indices: 54706499--54706595 Score: 97
Period size: 3 Copynumber: 32.0 Consensus size: 3
54706489 GAAATAACAG
* * * * **
54706499 TAA TAT TAA TAC TAA CAA TAA TAG TAA TAA TAA TAA CCA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
54706547 TAA TAG TAA -AC TAA TAA TAA TAA TAA TAA TAA TAA TAA CTAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -T-AA TAA
54706593 TAA
1 TAA
54706596 AATTGCGAAA
Statistics
Matches: 75, Mismatches: 16, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
2 1 0.01
3 70 0.93
4 2 0.03
5 2 0.03
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Done.