Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 59 of 66
Found at i:22226921 original size:22 final size:20
Alignment explanation
Indices: 22226876--22226924 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
22226866 TAGAGCCACC
* *
22226876 ATATATGAAAATGTTTTATA
1 ATATATGAAAATGATTCATA
22226896 ATATATGAAAATGATTCATA
1 ATATATGAAAATGATTCATA
22226916 ATATATGAA
1 ATATATGAA
22226925 GAATTGGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (20 bp):
ATATATGAAAATGATTCATA
Found at i:22244018 original size:2 final size:2
Alignment explanation
Indices: 22244011--22244046 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
22244001 ATTCTTTTTG
22244011 AT 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 AT
22244047 TTGAAAAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22253197 original size:4 final size:4
Alignment explanation
Indices: 22253190--22253218 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
22253180 TATATATATA
22253190 TACT TACT TACT TACT TACT TACT TACT T
1 TACT TACT TACT TACT TACT TACT TACT T
22253219 TGATATAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TACT
Found at i:22254432 original size:2 final size:2
Alignment explanation
Indices: 22254425--22254457 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
22254415 AAGCAGTTAA
*
22254425 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22254458 CAAGAAGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:22258153 original size:4 final size:4
Alignment explanation
Indices: 22258144--22258169 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
22258134 TCATAGAGTA
22258144 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
22258170 AAAAGCATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:22270625 original size:13 final size:14
Alignment explanation
Indices: 22270599--22270641 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
22270589 TTTGATAAAT
22270599 TTTTTTTTATTAAG
1 TTTTTTTTATTAAG
22270613 TTTTTTTTA-TAAG
1 TTTTTTTTATTAAG
22270626 TTATAATTTTTATTAA
1 TT-T--TTTTTATTAA
22270642 AATTATCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.24
14 10 0.40
16 6 0.24
17 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (14 bp):
TTTTTTTTATTAAG
Found at i:22287453 original size:27 final size:27
Alignment explanation
Indices: 22287419--22287489 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
22287409 ATTTTTCAAT
*
22287419 ATTAATAATTTATAATTGATTTAAAAC
1 ATTAATAATTTATAATTGATTAAAAAC
22287446 ATTAATAATTTATAATTGATTAAAAAC
1 ATTAATAATTTATAATTGATTAAAAAC
*
22287473 ATTAATAATTGATAATT
1 ATTAATAATTTATAATT
22287490 TAAATATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (27 bp):
ATTAATAATTTATAATTGATTAAAAAC
Found at i:22288062 original size:37 final size:37
Alignment explanation
Indices: 22288012--22288086 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
22288002 ACATGCCAAC
22288012 ACCTATACCTGAGAGTCTCATTTGGAGTTCCTTATAT
1 ACCTATACCTGAGAGTCTCATTTGGAGTTCCTTATAT
*
22288049 ACCTATACCTGAGAGTCTCGTTTGGAGTTCCTTATAT
1 ACCTATACCTGAGAGTCTCATTTGGAGTTCCTTATAT
22288086 A
1 A
22288087 TAGAATTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.37
Consensus pattern (37 bp):
ACCTATACCTGAGAGTCTCATTTGGAGTTCCTTATAT
Found at i:22292287 original size:22 final size:22
Alignment explanation
Indices: 22292262--22292311 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
22292252 TGCGTAACTG
*
22292262 ATTTTGAATATTACGTGACTAA
1 ATTTTGAACATTACGTGACTAA
* *
22292284 A-TTTGAGCATTACGTGACTGA
1 ATTTTGAACATTACGTGACTAA
*
22292305 TTTTTGA
1 ATTTTGA
22292312 TAAGGCATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (22 bp):
ATTTTGAACATTACGTGACTAA
Found at i:22292310 original size:43 final size:44
Alignment explanation
Indices: 22292216--22292311 Score: 108
Period size: 43 Copynumber: 2.2 Consensus size: 44
22292206 ATAGTTTTTG
* ** * *
22292216 TGATTTTTGAGAATTATGTGACTAGTTTTTAGGCATTGCGTAAC
1 TGATTTTTGAGAATTACGTGACTAAATTTGAGGCATTACGTAAC
*
22292260 TGA-TTTTGA-ATATTACGTGACTAAATTTGA-GCATTACGTGAC
1 TGATTTTTGAGA-ATTACGTGACTAAATTTGAGGCATTACGTAAC
22292302 TGATTTTTGA
1 TGATTTTTGA
22292312 TAAGGCATTG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
42 14 0.32
43 27 0.61
44 3 0.07
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.43
Consensus pattern (44 bp):
TGATTTTTGAGAATTACGTGACTAAATTTGAGGCATTACGTAAC
Found at i:22292326 original size:26 final size:25
Alignment explanation
Indices: 22292290--22292496 Score: 128
Period size: 26 Copynumber: 8.5 Consensus size: 25
22292280 CTAAATTTGA
*
22292290 GCATTACGTGACTGATTTTTGATAAG
1 GCATTGCGTGACT-ATTTTTGATAAG
* *
22292316 GCATTGCGTGACTAATTTATGATAAA
1 GCATTGCGTGACT-ATTTTTGATAAG
* * *
22292342 ACATTGCGTGACTA--GTTAAT-AG
1 GCATTGCGTGACTATTTTTGATAAG
22292364 GCATTGCGTGACTAGTTTTTGATAAG
1 GCATTGCGTGACTA-TTTTTGATAAG
** *
22292390 ATATTGCGTGACTAGTTTCTGATAAG
1 GCATTGCGTGACTA-TTTTTGATAAG
* * *
22292416 GTATTGCATGACTA--GTTGAT-AG
1 GCATTGCGTGACTATTTTTGATAAG
* * *
22292438 GCATTGCATGACT-TATTAG-TAAG
1 GCATTGCGTGACTATTTTTGATAAG
* * * *
22292461 GTATTGTGTGACTA-GTTAG-TAAG
1 GCATTGCGTGACTATTTTTGATAAG
*
22292484 GCATTGTGTGACT
1 GCATTGCGTGACT
22292497 TAGGTATTGC
Statistics
Matches: 146, Mismatches: 27, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
22 29 0.20
23 41 0.28
25 5 0.03
26 71 0.49
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.37
Consensus pattern (25 bp):
GCATTGCGTGACTATTTTTGATAAG
Found at i:22292370 original size:48 final size:48
Alignment explanation
Indices: 22292314--22292406 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
22292304 ATTTTTGATA
22292314 AGGCATTGCGTGACTAATTTATGATAAAACATTGCGTGACTAGTTAAT
1 AGGCATTGCGTGACTAATTTATGATAAAACATTGCGTGACTAGTTAAT
* * * *
22292362 AGGCATTGCGTGACTAGTTTTTGATAAGATATTGCGTGACTAGTT
1 AGGCATTGCGTGACTAATTTATGATAAAACATTGCGTGACTAGTT
22292407 TCTGATAAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (48 bp):
AGGCATTGCGTGACTAATTTATGATAAAACATTGCGTGACTAGTTAAT
Found at i:22292375 original size:74 final size:74
Alignment explanation
Indices: 22292290--22292450 Score: 207
Period size: 74 Copynumber: 2.2 Consensus size: 74
22292280 CTAAATTTGA
* * *
22292290 GCATTACGTGACT-GATTTTTGATAAGGCATTGCGTGACTAATTTATGATAAAACATTGCGTGAC
1 GCATTGCGTGACTAG-TTTTTGATAAGACATTGCGTGACTAATTTATGATAAAACATTGCATGAC
22292354 TAGTTAATAG
65 TAGTTAATAG
* * * ***
22292364 GCATTGCGTGACTAGTTTTTGATAAGATATTGCGTGACTAGTTTCTGATAAGGTATTGCATGACT
1 GCATTGCGTGACTAGTTTTTGATAAGACATTGCGTGACTAATTTATGATAAAACATTGCATGACT
*
22292429 AGTTGATAG
66 AGTTAATAG
*
22292438 GCATTGCATGACT
1 GCATTGCGTGACT
22292451 TATTAGTAAG
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
74 74 0.99
75 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (74 bp):
GCATTGCGTGACTAGTTTTTGATAAGACATTGCGTGACTAATTTATGATAAAACATTGCATGACT
AGTTAATAG
Found at i:22292555 original size:22 final size:22
Alignment explanation
Indices: 22292530--22292586 Score: 80
Period size: 21 Copynumber: 2.6 Consensus size: 22
22292520 ACGCAATATA
*
22292530 TAAAAACTAGTCACGTAATGTC
1 TAAAAACTAGTCACGTAATGAC
* *
22292552 T-AAAACCAATCACGTAATGAC
1 TAAAAACTAGTCACGTAATGAC
22292573 TAAAAACTAGTCAC
1 TAAAAACTAGTCAC
22292587 ACGATAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.23
Consensus pattern (22 bp):
TAAAAACTAGTCACGTAATGAC
Found at i:22293294 original size:19 final size:20
Alignment explanation
Indices: 22293260--22293297 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
22293250 AGTCATACTA
*
22293260 AAAATTGATCAAAAATAATT
1 AAAATTGATAAAAAATAATT
22293280 AAAATT-ATAAAAAATAAT
1 AAAATTGATAAAAAATAAT
22293298 ATTTTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAATTGATAAAAAATAATT
Found at i:22293941 original size:2 final size:2
Alignment explanation
Indices: 22293934--22293987 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
22293924 GAAATTTGCC
22293934 AT AT AT AT 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 AT AT AT AT
22293976 AT AT AT AT AT AT
1 AT AT AT AT AT AT
22293988 TCAATTGATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22315604 original size:21 final size:21
Alignment explanation
Indices: 22315580--22315635 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
22315570 TCCGGCCGCA
* * *
22315580 CCGATCACGACTCCAACGACC
1 CCGACCACAACTCCAACAACC
22315601 CCGACCACAACTCCAACAACC
1 CCGACCACAACTCCAACAACC
*
22315622 CCAACCACAACTCC
1 CCGACCACAACTCC
22315636 TGCAACATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.34, C:0.52, G:0.07, T:0.07
Consensus pattern (21 bp):
CCGACCACAACTCCAACAACC
Found at i:22318099 original size:2 final size:2
Alignment explanation
Indices: 22318094--22318124 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22318084 AATGACACAC
22318094 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
22318125 ATTACGCAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:22320314 original size:151 final size:151
Alignment explanation
Indices: 22320039--22320340 Score: 487
Period size: 151 Copynumber: 2.0 Consensus size: 151
22320029 TTTTCTTGGT
* *
22320039 AACAAAAATGGAGGTACAAATTTCAACAACTGAAACAGAGTCGCATCCTGAAACGGGAGATTCTT
1 AACAAAAATGGAAGTACAAATTTCAACAACTGAAACAGAGTCGCATCCTAAAACGGGAGATTCTT
* * *
22320104 TAGGTAAACATTTGATTAAACAGCTATTACTGGTGAGCTTACTCTTTCTTTTCTGTATATATATT
66 TAGGTAAACATATGATTAAACAGCTATTACTAGTGAACTTACTCTTTCTTTTCTGTATATATATT
22320169 GTTTAGCTTTGAAACTGTATG
131 GTTTAGCTTTGAAACTGTATG
* *
22320190 AACAAAAATGGAAGTACAAATTTCAACAACTGAAACAGAGTCGCATCCTAAAATGGGGGATTCTT
1 AACAAAAATGGAAGTACAAATTTCAACAACTGAAACAGAGTCGCATCCTAAAACGGGAGATTCTT
* * * * *
22320255 TAGGTTAACATATGATTAAACAGCTATTACTAGTGAACTTATTCTTTCTTTTCTTTATATTTCTT
66 TAGGTAAACATATGATTAAACAGCTATTACTAGTGAACTTACTCTTTCTTTTCTGTATATATATT
*
22320320 GTTTGGCTTTGAAACTGTATG
131 GTTTAGCTTTGAAACTGTATG
22320341 TTCTCGTTCT
Statistics
Matches: 138, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
151 138 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (151 bp):
AACAAAAATGGAAGTACAAATTTCAACAACTGAAACAGAGTCGCATCCTAAAACGGGAGATTCTT
TAGGTAAACATATGATTAAACAGCTATTACTAGTGAACTTACTCTTTCTTTTCTGTATATATATT
GTTTAGCTTTGAAACTGTATG
Found at i:22356052 original size:13 final size:14
Alignment explanation
Indices: 22356036--22356068 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
22356026 TAAATAACTT
22356036 ATTTATAAAAA-AA
1 ATTTATAAAAATAA
22356049 ATTTATAAAAATAA
1 ATTTATAAAAATAA
22356063 ATTTAT
1 ATTTAT
22356069 TAAACAGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATTTATAAAAATAA
Found at i:22363320 original size:3 final size:3
Alignment explanation
Indices: 22363312--22363358 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
22363302 TGTAGGAGGT
* *
22363312 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG GAT AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
22363359 ATGGCGGTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:22378344 original size:26 final size:24
Alignment explanation
Indices: 22378282--22378355 Score: 85
Period size: 26 Copynumber: 3.0 Consensus size: 24
22378272 AGAAGTGGAT
* *
22378282 AATAATTTTACCATCAAAATCTAAG
1 AATAATTTTACCACCAAAA-GTAAG
*
22378307 AATAAGTTTACCACCAAAAGTAGATG
1 AATAATTTTACCACCAAAAGTA-A-G
*
22378333 GATAATTTTACCACCAAAAGTAA
1 AATAATTTTACCACCAAAAGTAA
22378356 ATGAATACCC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
24 2 0.05
25 19 0.45
26 21 0.50
ACGTcount: A:0.47, C:0.16, G:0.09, T:0.27
Consensus pattern (24 bp):
AATAATTTTACCACCAAAAGTAAG
Found at i:22382700 original size:20 final size:20
Alignment explanation
Indices: 22382675--22382717 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
22382665 CACACTTCAA
22382675 TAAGATCTCTTTTCTCCCCC
1 TAAGATCTCTTTTCTCCCCC
*
22382695 TAAGATTTCTTTTCTCCCCC
1 TAAGATCTCTTTTCTCCCCC
22382715 TAA
1 TAA
22382718 ACACTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.35, G:0.05, T:0.42
Consensus pattern (20 bp):
TAAGATCTCTTTTCTCCCCC
Found at i:22382730 original size:21 final size:20
Alignment explanation
Indices: 22382682--22382728 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 20
22382672 CAATAAGATC
*
22382682 TCTTTTCTCCCCCTAAGATT
1 TCTTTTCTCCCCCTAACATT
22382702 TCTTTTCTCCCCCTAAACACTT
1 TCTTTTCTCCCCCT-AACA-TT
22382724 TCTTT
1 TCTTT
22382729 CTTCTCTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 14 0.58
21 3 0.12
22 7 0.29
ACGTcount: A:0.15, C:0.36, G:0.02, T:0.47
Consensus pattern (20 bp):
TCTTTTCTCCCCCTAACATT
Found at i:22384319 original size:18 final size:18
Alignment explanation
Indices: 22384281--22384328 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
22384271 ATTAAAAAGC
* **
22384281 TTTTAAAAAAAGTAACTT
1 TTTTAAAAAAAATAAAAT
22384299 TTTTAAAAAAAATAAAAT
1 TTTTAAAAAAAATAAAAT
*
22384317 TTTGAAAAAAAA
1 TTTTAAAAAAAA
22384329 AACTTAAGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (18 bp):
TTTTAAAAAAAATAAAAT
Found at i:22384451 original size:98 final size:96
Alignment explanation
Indices: 22384335--22384521 Score: 234
Period size: 98 Copynumber: 1.9 Consensus size: 96
22384325 AAAAAACTTA
* * *
22384335 AGGAAAAGCTCCTGTGAGGAACTTTTTCTT-TTCTTCTTTTAAAAATACAAGAGAATTTTTA-TT
1 AGGAAAAACTCATATGAGGAACTTTTTCTTCTTCTT-TTTT--AAATACAAGAGAATTTTTATTT
22384398 TTATTTAAAAATATCCTCATATGTTNAAGAATTTT
63 TTATTTAAAAATATCCTCATATGTT-AAGAATTTT
* * **
22384433 AGGAAAAACTCATATGAGGAGCTTTTTCTTCTTCTTTTTTTAATGTAAGAGAATTTTTATTTTTA
1 AGGAAAAACTCATATGAGGAACTTTTTCTTCTTCTTTTTTAAATACAAGAGAATTTTTATTTTTA
* * *
22384498 TTTTAAAATATTCTCATCTGTTAA
66 TTTAAAAATATCCTCATATGTTAA
22384522 AATAATTACA
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
96 18 0.23
97 24 0.31
98 30 0.39
99 5 0.06
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (96 bp):
AGGAAAAACTCATATGAGGAACTTTTTCTTCTTCTTTTTTAAATACAAGAGAATTTTTATTTTTA
TTTAAAAATATCCTCATATGTTAAGAATTTT
Found at i:22384598 original size:12 final size:12
Alignment explanation
Indices: 22384583--22384608 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
22384573 TCAAAATTAT
22384583 AACTTATAAAAA
1 AACTTATAAAAA
22384595 AACTTATAAAAA
1 AACTTATAAAAA
22384607 AA
1 AA
22384609 AATTTACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AACTTATAAAAA
Found at i:22402211 original size:26 final size:26
Alignment explanation
Indices: 22402171--22402234 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
22402161 GGACAAGAAA
*
22402171 CTATAGCCCATTCACACCCATTTCCT
1 CTATAGCCCACTCACACCCATTTCCT
*
22402197 CTATAGACCACTCACACCCATTTCCT
1 CTATAGCCCACTCACACCCATTTCCT
22402223 CTATAGCCCACT
1 CTATAGCCCACT
22402235 TTTATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.25, C:0.42, G:0.05, T:0.28
Consensus pattern (26 bp):
CTATAGCCCACTCACACCCATTTCCT
Found at i:22404185 original size:159 final size:158
Alignment explanation
Indices: 22403970--22404261 Score: 503
Period size: 159 Copynumber: 1.8 Consensus size: 158
22403960 ATGGGTAACC
* *
22403970 AAGGTGACAATTAGAACAATCGGTTTAAAATGTTTGATTGCTTGTGCTTTATACATTGTGATATT
1 AAGGTGACAATTAGAACAATCAGTTTAAAATGTTTGATTGCTTGTGCTGTATACATTGTGATATT
*
22404035 GTAGAGGTTACAATGAGGTTCTTTCCAATTTACGACTATTTGGTGTGCCTTGTCTATGGAGAAGA
66 CTAGAGGTTACAATGAGGTT-TTTCCAATTTACGACTATTTGGTGTGCCTTGTCTATGGAGAAGA
22404100 AAGTTCTGCCTCAGGGACATATATTCTTA
130 AAGTTCTGCCTCAGGGACATATATTCTTA
* *
22404129 AAGGTGACAATTAGAGCAATCAGTTTAAAATGTTTGATTGCTTGTGCTGTATACATTGTTATATT
1 AAGGTGACAATTAGAACAATCAGTTTAAAATGTTTGATTGCTTGTGCTGTATACATTGTGATATT
* * *
22404194 CTAGAGGTTACCATGAGGTTTTTCCAATTTATGACTATTTGGTTTGCCTTGTCTATGGAGAAGAA
66 CTAGAGGTTACAATGAGGTTTTTCCAATTTACGACTATTTGGTGTGCCTTGTCTATGGAGAAGAA
22404259 AGT
131 AGT
22404262 AATGTATCTC
Statistics
Matches: 125, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
158 46 0.37
159 79 0.63
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (158 bp):
AAGGTGACAATTAGAACAATCAGTTTAAAATGTTTGATTGCTTGTGCTGTATACATTGTGATATT
CTAGAGGTTACAATGAGGTTTTTCCAATTTACGACTATTTGGTGTGCCTTGTCTATGGAGAAGAA
AGTTCTGCCTCAGGGACATATATTCTTA
Found at i:22409619 original size:29 final size:29
Alignment explanation
Indices: 22409568--22409660 Score: 111
Period size: 29 Copynumber: 3.2 Consensus size: 29
22409558 TGCATTAAAA
* *
22409568 TGTAAC-ATAAT-TTTTTTGAATATAGTG
1 TGTAACAATAATATTTTTTCAATATAGCG
22409595 TGTAACAATAATATTTTTTCAATAT-GACG
1 TGTAACAATAATATTTTTTCAATATAG-CG
* *
22409624 TATAACAATAATATTTTTTACAATATAACG
1 TGTAACAATAATATTTTTT-CAATATAGCG
22409654 TGTAACA
1 TGTAACA
22409661 TGTTTTTATA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
27 6 0.11
28 6 0.11
29 30 0.54
30 14 0.25
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.42
Consensus pattern (29 bp):
TGTAACAATAATATTTTTTCAATATAGCG
Found at i:22409726 original size:25 final size:27
Alignment explanation
Indices: 22409691--22409740 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
22409681 AATAATAATA
* *
22409691 TTTTTCTTAA-CATGATGTGTAACAAC
1 TTTTTCTTAACCATGACGTATAACAAC
22409717 TTTTT-TTAACCATGACGTATAACA
1 TTTTTCTTAACCATGACGTATAACA
22409741 TGCTATTGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (27 bp):
TTTTTCTTAACCATGACGTATAACAAC
Found at i:22409799 original size:81 final size:81
Alignment explanation
Indices: 22409678--22409939 Score: 235
Period size: 81 Copynumber: 3.2 Consensus size: 81
22409668 ATATATAGTA
* * ** *
22409678 TGTAATAATAATATTTTTCTT-AACATGATGTGTAACAACTTTTTTTAACCATGACGTATAACAT
1 TGTAACAATAATATTTTTTTTCAACATGGCGTGTAATAACTTTTTTTAACCATGACGTATAACAT
**
22409742 GCTATT-GCACATGGTG
66 G-TATTCGCACATGACG
* ** * *
22409758 TGTAACAATAATATTTTTTTTCAACATGGCGTGTAATAACTTTTTTTAATCATGGTGTGTAATAT
1 TGTAACAATAATATTTTTTTTCAACATGGCGTGTAATAACTTTTTTTAACCATGACGTATAACAT
* * *
22409823 GTTTTCGTATATGACG
66 GTATTCGCACATGACG
* * *
22409839 TGTAACAATAGTATTATTTTTTTTCAATATGGCGTATAATAACTTTTTTTAATCA--ACGTATAA
1 TGTAACAATA--A-TATTTTTTTTCAACATGGCGTGTAATAACTTTTTTTAACCATGACGTATAA
* * * * *
22409902 TATATTTTTGTACATGACG
63 CATGTATTCGCACATGACG
* *
22409921 TGTAATAATAATGTTTTTT
1 TGTAACAATAATATTTTTT
22409940 CAACATTGTG
Statistics
Matches: 152, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
79 7 0.05
80 23 0.15
81 52 0.34
82 30 0.20
83 1 0.01
84 39 0.26
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (81 bp):
TGTAACAATAATATTTTTTTTCAACATGGCGTGTAATAACTTTTTTTAACCATGACGTATAACAT
GTATTCGCACATGACG
Found at i:22409811 original size:26 final size:26
Alignment explanation
Indices: 22409772--22409821 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
22409762 ACAATAATAT
22409772 TTTTTTTCAACATGGCGTGTAATAAC
1 TTTTTTTCAACATGGCGTGTAATAAC
*
22409798 TTTTTTT-AATCATGGTGTGTAATA
1 TTTTTTTCAA-CATGGCGTGTAATA
22409822 TGTTTTCGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.48
Consensus pattern (26 bp):
TTTTTTTCAACATGGCGTGTAATAAC
Found at i:22409827 original size:26 final size:25
Alignment explanation
Indices: 22409766--22409827 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
22409756 TGTGTAACAA
22409766 TAATATTTTTTTTCAACATGGCGTG
1 TAATATTTTTTTTCAACATGGCGTG
* *
22409791 TAATAACTTTTTTT-AATCATGGTGTG
1 TAAT-ATTTTTTTTCAA-CATGGCGTG
*
22409817 TAATATGTTTT
1 TAATATTTTTT
22409828 CGTATATGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 11 0.35
26 20 0.65
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.52
Consensus pattern (25 bp):
TAATATTTTTTTTCAACATGGCGTG
Found at i:22411015 original size:10 final size:10
Alignment explanation
Indices: 22410998--22411038 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
22410988 ATTATTAAAA
22410998 TATATTTAAT
1 TATATTTAAT
*
22411008 TATTTTTAAT
1 TATATTTAAT
*
22411018 TATATTTAAC
1 TATATTTAAT
22411028 TATAATTTAAT
1 TAT-ATTTAAT
22411039 AAAAATATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 20 0.77
11 6 0.23
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (10 bp):
TATATTTAAT
Found at i:22411741 original size:79 final size:83
Alignment explanation
Indices: 22411598--22411767 Score: 188
Period size: 79 Copynumber: 2.1 Consensus size: 83
22411588 TTAACATAAT
* ** * **
22411598 GTGTAATAACAATATTTTTTTCTTCAACATGGTGTGTAACAGTTTTTTTTAATCATGGTATGTAA
1 GTGTAACAACAATATTTTTTTCTTCAACATGGTGTGTAACAACTTTTTTTAACCATGACATGTAA
*
22411663 CATGT-TTTCATACATGAC
66 CATATATTT-ATACATGAC
* *
22411681 GTGTAACAACAAT-TTTTTTT-TTCAATAT-G-GTGTAACAACTTTTTTTAACCATGACGTGTAA
1 GTGTAACAACAATATTTTTTTCTTCAACATGGTGTGTAACAACTTTTTTTAACCATGACATGTAA
* * *
22411742 TATATATTTGTATATGAC
66 CATATATTTATACATGAC
22411760 GTGTAACA
1 GTGTAACA
22411768 TCGTGTAATA
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
79 44 0.59
80 4 0.05
81 7 0.09
82 7 0.09
83 12 0.16
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.44
Consensus pattern (83 bp):
GTGTAACAACAATATTTTTTTCTTCAACATGGTGTGTAACAACTTTTTTTAACCATGACATGTAA
CATATATTTATACATGAC
Found at i:22418765 original size:20 final size:23
Alignment explanation
Indices: 22418737--22418781 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
22418727 ATTTCTATTT
*
22418737 AAACTTATAATAC-T-AAATATA
1 AAACTTATAACACGTAAAATATA
22418758 AAAC-TATAACACGTAAAATATA
1 AAACTTATAACACGTAAAATATA
22418780 AA
1 AA
22418782 TAGTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 5 0.24
22 9 0.43
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.27
Consensus pattern (23 bp):
AAACTTATAACACGTAAAATATA
Found at i:22420837 original size:2 final size:2
Alignment explanation
Indices: 22420830--22420901 Score: 114
Period size: 2 Copynumber: 37.0 Consensus size: 2
22420820 TGGAATATTT
22420830 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TNA T- TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
22420871 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22420902 AGATTAGATG
Statistics
Matches: 66, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.05
2 61 0.92
3 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22426952 original size:17 final size:17
Alignment explanation
Indices: 22426920--22426953 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
22426910 ATTAATATTT
*
22426920 TAATATTTTAACTATAA
1 TAATATTTAAACTATAA
*
22426937 TAATATTTAAATTATAA
1 TAATATTTAAACTATAA
22426954 ATAAAATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATTTAAACTATAA
Found at i:22426992 original size:43 final size:45
Alignment explanation
Indices: 22426919--22427007 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 45
22426909 AATTAATATT
**
22426919 TTAATATTTTAACTATAATAATATTTAAATTATAAA-T-AAAATA
1 TTAATATTTTAAAAATAATAATATTTAAATTATAAAGTGAAAATA
* *
22426962 TTAATATTTTAAAAATATTAAT-TTTAAAATTTTAAAGTGAAAATA
1 TTAATATTTTAAAAATAATAATATTT-AAATTATAAAGTGAAAATA
22427007 T
1 T
22427008 AAATTAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
42 3 0.08
43 28 0.72
44 1 0.03
45 7 0.18
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (45 bp):
TTAATATTTTAAAAATAATAATATTTAAATTATAAAGTGAAAATA
Found at i:22426996 original size:14 final size:15
Alignment explanation
Indices: 22426956--22426990 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 15
22426946 AATTATAAAT
22426956 AAAATATTAATATTTTA
1 AAAATATT-A-ATTTTA
22426973 AAAATATTAATTTTA
1 AAAATATTAATTTTA
22426988 AAA
1 AAA
22426991 TTTTAAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 1 0.06
17 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATATTAATTTTA
Found at i:22427364 original size:26 final size:25
Alignment explanation
Indices: 22427335--22427429 Score: 72
Period size: 26 Copynumber: 3.7 Consensus size: 25
22427325 ATTTCAATGA
22427335 TTAAATTGTAAATAAAATATTAATAT
1 TTAAATT-TAAATAAAATATTAATAT
*
22427361 TTAAA-TT--ATCAAAAAATTAATATT
1 TTAAATTTAAAT-AAAATATTAATA-T
*
22427385 TTAAA-TAAATGATAAAATATTAATAT
1 TTAAATTTAA--ATAAAATATTAATAT
* *
22427411 TTAAAAATAAAATAAAATA
1 TT-AAATTTAAATAAAATA
22427430 AAAAATAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
22 2 0.03
23 11 0.19
24 8 0.14
25 1 0.02
26 16 0.28
27 14 0.24
28 6 0.10
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (25 bp):
TTAAATTTAAATAAAATATTAATAT
Found at i:22427379 original size:23 final size:24
Alignment explanation
Indices: 22427343--22427415 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 24
22427333 GATTAAATTG
*
22427343 TAAAT-AAAATATTAATATTTAAA
1 TAAATCAAAAAATTAATATTTAAA
*
22427366 T-TATCAAAAAATTAATATTTTAAA
1 TAAATCAAAAAATTAATA-TTTAAA
*
22427390 TAAATGATAAAATATTAATATTTAAA
1 TAAATCA-AAAA-ATTAATATTTAAA
22427416 AATAAAATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
22 2 0.05
23 12 0.29
24 7 0.17
25 3 0.07
26 10 0.24
27 7 0.17
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (24 bp):
TAAATCAAAAAATTAATATTTAAA
Found at i:22427380 original size:42 final size:42
Alignment explanation
Indices: 22427262--22427539 Score: 122
Period size: 42 Copynumber: 6.3 Consensus size: 42
22427252 AAAAATTAAT
* * *
22427262 TAAAAGTATTAATATTTTAATCAT-AATTAAAGTT-AATTATAAA
1 TAAAA-TATTAATATTTAAATTATCAA--AAAATTAAATTATAAA
* ** *
22427305 TACAATATTAATATTTTAAAATT-TC-AATGATTAAATTGTAAA
1 TAAAATATTAATA-TTT-AAATTATCAAAAAATTAAATTATAAA
22427347 TAAAATATTAATATTTAAATTATCAAAAAATTAATATTTTAAATAAATGA
1 TAAAATATTAATATTTAAATTATCAAAAAATTAA-A--TT--AT-AA--A
* * * **
22427397 TAAAATATTAATATTTAAA-AATAAAATAAAATAAAAAATAAA
1 TAAAATATTAATATTTAAATTATCAAA-AAATTAAATTATAAA
* * * * **
22427439 TAATTATAATAATATTTAAATTAT-AAACAA-TATATTAATATTT
1 TAA-AATATTAATATTTAAATTATCAAAAAATTAAATT-ATA-AA
* * *
22427482 TATAATATTAATGA-TTAAATTATAAAAAAATTAATATCTAAAAA
1 TAAAATATTAAT-ATTTAAATTATCAAAAAATTAA-AT-TATAAA
*
22427526 TAAAATAATAATAT
1 TAAAATATTAATAT
22427540 AAATAATAAA
Statistics
Matches: 175, Mismatches: 35, Indels: 49
0.68 0.14 0.19
Matches are distributed among these distances:
40 5 0.03
41 11 0.06
42 60 0.34
43 36 0.21
44 19 0.11
45 8 0.05
46 1 0.01
47 1 0.01
48 2 0.01
49 6 0.03
50 26 0.15
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (42 bp):
TAAAATATTAATATTTAAATTATCAAAAAATTAAATTATAAA
Found at i:22427406 original size:27 final size:26
Alignment explanation
Indices: 22427346--22427429 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 26
22427336 TAAATTGTAA
22427346 ATAAAATATTAATA-TTTAAAT---T
1 ATAAAATATTAATATTTTAAATAAAT
*
22427368 ATCAAAAAATTAATATTTTAAATAAAT
1 AT-AAAATATTAATATTTTAAATAAAT
*
22427395 GATAAAATATTAATATTTAAAAATAAA-
1 -ATAAAATATTAATATTT-TAAATAAAT
22427422 ATAAAATA
1 ATAAAATA
22427430 AAAAATAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
22 2 0.04
23 11 0.21
24 7 0.13
26 8 0.15
27 15 0.29
28 9 0.17
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (26 bp):
ATAAAATATTAATATTTTAAATAAAT
Found at i:22427523 original size:23 final size:21
Alignment explanation
Indices: 22427488--22427550 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
22427478 ATTTTATAAT
*
22427488 ATTAATGATTAAATTATAAAAAA
1 ATTAAT-ATTAAA-AATAAAAAA
*
22427511 ATTAATATCTAAAAATAAAATA
1 ATTAATAT-TAAAAATAAAAAA
22427533 A-TAATA-TAAATAATAAAA
1 ATTAATATTAAA-AATAAAA
22427551 TATATTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
19 4 0.11
20 7 0.19
21 5 0.14
22 10 0.28
23 10 0.28
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
ATTAATATTAAAAATAAAAAA
Found at i:22427702 original size:16 final size:16
Alignment explanation
Indices: 22427678--22427710 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
22427668 TAAATAATAA
*
22427678 TTATTTTATTTTATTT
1 TTATCTTATTTTATTT
22427694 TTATCTTATTTTATTT
1 TTATCTTATTTTATTT
22427710 T
1 T
22427711 CATAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATCTTATTTTATTT
Found at i:22434320 original size:3 final size:3
Alignment explanation
Indices: 22434307--22434340 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
22434297 TATAATCCTT
22434307 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
22434341 ATTGTTGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:22435722 original size:32 final size:31
Alignment explanation
Indices: 22435668--22435731 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
22435658 TTAAATAGCA
** *
22435668 TTTGGCATGAGGTTAGTAAAAGCATCTTTCCT
1 TTTGGCATGAGGAAAGTAAAAGCA-CATTCCT
* *
22435700 TTTGGTATGAGGAAAGTGAAAGCACATTCCT
1 TTTGGCATGAGGAAAGTAAAAGCACATTCCT
22435731 T
1 T
22435732 ACAATATGCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.34
Consensus pattern (31 bp):
TTTGGCATGAGGAAAGTAAAAGCACATTCCT
Found at i:22436594 original size:23 final size:23
Alignment explanation
Indices: 22436568--22436613 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
22436558 ATACAATAAC
*
22436568 CTTATCCTAATACAATTAGGAAT
1 CTTATCCTAATACAATTAAGAAT
* *
22436591 CTTATTCTAATATAATTAAGAAT
1 CTTATCCTAATACAATTAAGAAT
22436614 TGTTATTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (23 bp):
CTTATCCTAATACAATTAAGAAT
Found at i:22439970 original size:23 final size:23
Alignment explanation
Indices: 22439944--22439989 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
22439934 ATACAATAAC
22439944 CTTATCCTAATACAATTAGGAAT
1 CTTATCCTAATACAATTAGGAAT
* *
22439967 CTTATTCTAATATAATTAGGAAT
1 CTTATCCTAATACAATTAGGAAT
22439990 TGTTATTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (23 bp):
CTTATCCTAATACAATTAGGAAT
Found at i:22440792 original size:28 final size:28
Alignment explanation
Indices: 22440761--22440830 Score: 68
Period size: 33 Copynumber: 2.3 Consensus size: 28
22440751 ATAGAAAATT
22440761 ATATTAAAAAATAAAAATAAAATATATA
1 ATATTAAAAAATAAAAATAAAATATATA
* *
22440789 ATATTATAATAGAAAATTAAAATAAAATATATG
1 ATA-T-T-A-A-AAAATAAAAATAAAATATATA
*
22440822 ACATTAAAA
1 ATATTAAAA
22440831 TTATATTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
28 5 0.15
29 2 0.06
30 2 0.06
31 2 0.06
32 2 0.06
33 21 0.62
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (28 bp):
ATATTAAAAAATAAAAATAAAATATATA
Found at i:22440795 original size:33 final size:33
Alignment explanation
Indices: 22440734--22440820 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
22440724 AATAGAAATT
* * *
22440734 AAAATAAAATATATAATATAGAAAATTATATTAA
1 AAAATAAAA-ATAAAATATATAAAATTATAATAA
* *
22440768 AAAATAAAAATAAAATATATAATATTATAATAG
1 AAAATAAAAATAAAATATATAAAATTATAATAA
*
22440801 AAAATTAAAATAAAATATAT
1 AAAATAAAAATAAAATATAT
22440821 GACATTAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 38 0.81
34 9 0.19
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (33 bp):
AAAATAAAAATAAAATATATAAAATTATAATAA
Found at i:22444250 original size:15 final size:17
Alignment explanation
Indices: 22444221--22444261 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
22444211 CTCAATTAAA
22444221 AAAATATTTATTTATTT
1 AAAATATTTATTTATTT
22444238 AAAAT-TTTA-TTATTT
1 AAAATATTTATTTATTT
22444253 AATAATATT
1 AA-AATATT
22444262 AATGAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.36
16 7 0.32
17 7 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAAATATTTATTTATTT
Found at i:22444363 original size:24 final size:24
Alignment explanation
Indices: 22444336--22444389 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
22444326 TCTATATATT
*
22444336 AATAATATTAAAATATTTTTAAAA
1 AATAATATTAAAATATTATTAAAA
*
22444360 AATAATATTTAAATATTATTAAAA
1 AATAATATTAAAATATTATTAAAA
22444384 AATAAT
1 AATAAT
22444390 TTATATATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AATAATATTAAAATATTATTAAAA
Found at i:22447534 original size:15 final size:17
Alignment explanation
Indices: 22447504--22447540 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
22447494 ATTTAAATAT
22447504 TATTATTTTTACTTAAA
1 TATTATTTTTACTTAAA
*
22447521 -ATTA-TTTTAGTTAAA
1 TATTATTTTTACTTAAA
22447536 TATTA
1 TATTA
22447541 ATATTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
TATTATTTTTACTTAAA
Found at i:22447575 original size:37 final size:36
Alignment explanation
Indices: 22447523--22447618 Score: 117
Period size: 36 Copynumber: 2.6 Consensus size: 36
22447513 TACTTAAAAT
*
22447523 TATTTTAGTTAAATATTAATATTT-TAAATTTTTTTA
1 TATTTTAATTAAATATTAATATTTATAAA-TTTTTTA
*
22447559 TATTTTAAATTAAATATTAAATAGTTTNTAAATTTTTTA
1 TATTTT-AATTAAATATT-AATA-TTTATAAATTTTTTA
22447598 TA--TTAATTAAATATTAATATT
1 TATTTTAATTAAATATTAATATT
22447619 CATCCAACTT
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
34 2 0.04
35 4 0.07
36 17 0.31
37 12 0.22
38 4 0.07
39 12 0.22
40 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (36 bp):
TATTTTAATTAAATATTAATATTTATAAATTTTTTA
Found at i:22447809 original size:13 final size:14
Alignment explanation
Indices: 22447791--22447819 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
22447781 CAAATATAAG
22447791 TTCT-AAAAATATT
1 TTCTAAAAAATATT
22447804 TTCTAAAAAATATT
1 TTCTAAAAAATATT
22447818 TT
1 TT
22447820 AGTCAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
TTCTAAAAAATATT
Found at i:22448742 original size:2 final size:2
Alignment explanation
Indices: 22448730--22448775 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
22448720 TCTTGAGGTT
22448730 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
22448771 TC TC T
1 TC TC T
22448776 TGTTGGCTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:22458933 original size:30 final size:26
Alignment explanation
Indices: 22458878--22458931 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
22458868 AAGCTCACTG
*
22458878 ATGACAAACCCCTAGCCGACTCATTC
1 ATGACAAAACCCTAGCCGACTCATTC
22458904 ATGACAAAACCCTAGCCGACTCATTC
1 ATGACAAAACCCTAGCCGACTCATTC
22458930 AT
1 AT
22458932 TCCAACATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.35, G:0.11, T:0.20
Consensus pattern (26 bp):
ATGACAAAACCCTAGCCGACTCATTC
Found at i:22470891 original size:2 final size:2
Alignment explanation
Indices: 22470884--22470920 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
22470874 CCTCTTCCTC
22470884 CT CT CT CT CT 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 CT CT CT CT CT C
22470921 CTATGCTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:22472625 original size:24 final size:23
Alignment explanation
Indices: 22472581--22472625 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
22472571 AAGAGTTTTT
22472581 TAATAATATTTTTATATTAAATA
1 TAATAATATTTTTATATTAAATA
22472604 TAATAA-ATTTTAATATATTAAA
1 TAATAATATTTT--TATATTAAA
22472626 AAATGTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 6 0.30
24 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATAATATTTTTATATTAAATA
Found at i:22473891 original size:2 final size:2
Alignment explanation
Indices: 22473884--22473908 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22473874 ATAATCAATG
22473884 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 T
22473909 TGTTAATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22487086 original size:23 final size:21
Alignment explanation
Indices: 22487049--22487095 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
22487039 AATTTAAATA
**
22487049 AATTTATATTTTTAATCTTTT
1 AATTTATATTTTTAAAATTTT
22487070 AATTTATATTTTATTAAAATTTT
1 AATTTATA-TTT-TTAAAATTTT
22487093 AAT
1 AAT
22487096 AATTTAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 8 0.36
22 3 0.14
23 11 0.50
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
AATTTATATTTTTAAAATTTT
Found at i:22488236 original size:53 final size:53
Alignment explanation
Indices: 22488152--22488256 Score: 201
Period size: 53 Copynumber: 2.0 Consensus size: 53
22488142 AAATGAAGCA
22488152 ATAAGACAGTGCAGGTCACTTTCCAACGCCTTCTGGCAGGCTGAGGGGGACTC
1 ATAAGACAGTGCAGGTCACTTTCCAACGCCTTCTGGCAGGCTGAGGGGGACTC
*
22488205 ATAAGACAGTGCAGGTCACTTTCCAAGGCCTTCTGGCAGGCTGAGGGGGACT
1 ATAAGACAGTGCAGGTCACTTTCCAACGCCTTCTGGCAGGCTGAGGGGGACT
22488257 AGGTACATAG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.23, C:0.25, G:0.31, T:0.21
Consensus pattern (53 bp):
ATAAGACAGTGCAGGTCACTTTCCAACGCCTTCTGGCAGGCTGAGGGGGACTC
Found at i:22531444 original size:15 final size:15
Alignment explanation
Indices: 22531424--22531455 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
22531414 ATTTGAAGAG
22531424 ATTAAATATTCATTA
1 ATTAAATATTCATTA
22531439 ATTAAATATTCATTA
1 ATTAAATATTCATTA
22531454 AT
1 AT
22531456 AGCTTTAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTAAATATTCATTA
Found at i:22538900 original size:5 final size:5
Alignment explanation
Indices: 22538886--22538920 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
22538876 AGTACTGAAA
*
22538886 TTTTC CTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
22538921 AAGAGGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:22540040 original size:20 final size:20
Alignment explanation
Indices: 22540011--22540050 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
22540001 TAGAGGCTTT
22540011 GATCTCCATAATCTTCCTTG
1 GATCTCCATAATCTTCCTTG
*
22540031 GATCTTCATAATCTTCCTTG
1 GATCTCCATAATCTTCCTTG
22540051 CAAAGGCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.20, C:0.28, G:0.10, T:0.42
Consensus pattern (20 bp):
GATCTCCATAATCTTCCTTG
Found at i:22540250 original size:20 final size:20
Alignment explanation
Indices: 22540225--22540288 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
22540215 TCGTTTGGAA
22540225 GCTTTGATTTCTA-AGATCTT
1 GCTTTGATTTCTAGA-ATCTT
22540245 GCTTTGATTTCTAGAATCTT
1 GCTTTGATTTCTAGAATCTT
* * *
22540265 CCTTTGATTTCCATAATCTT
1 GCTTTGATTTCTAGAATCTT
22540285 -CTTT
1 GCTTT
22540289 CTAGAGGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
19 4 0.10
20 35 0.88
21 1 0.03
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.52
Consensus pattern (20 bp):
GCTTTGATTTCTAGAATCTT
Found at i:22540604 original size:118 final size:120
Alignment explanation
Indices: 22540401--22540623 Score: 288
Period size: 118 Copynumber: 1.9 Consensus size: 120
22540391 TCTTGATCCT
* * * *
22540401 TGACTTGGTCTTGAACTTTGTATTTTGATGAAGAATTTCCTCTGATTAATTTCTTCAATCTTCGA
1 TGACTTGGTCTTGAAC-GTGTATTTTAATGAAGAATTTCCTCTAATTAATTTATTCAATCTTCGA
* * * ** **
22540466 TTCAAGGGTTTTAATGACTTGGTCTTGAACTTCGTATTTTACTTTAAATGTCTCGA
65 TTCAAGGATCTCAACAACTTGGTCCAGAACTTCGTATTTTACTTTAAATGTCTCGA
* * *
22540522 TGACTTGGTCTTG-A-GTGTATTTTAATGAAGAATTTTCTTTAATTAATTTATTCAATCTTCGTT
1 TGACTTGGTCTTGAACGTGTATTTTAATGAAGAATTTCCTCTAATTAATTTATTCAATCTTCGAT
*
22540585 TCAAGGATCTCGACAACTTGGTCCAGAACTTCGTATTTT
66 TCAAGGATCTCAACAACTTGGTCCAGAACTTCGTATTTT
22540624 GATGAAAATT
Statistics
Matches: 87, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
118 73 0.84
120 1 0.01
121 13 0.15
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (120 bp):
TGACTTGGTCTTGAACGTGTATTTTAATGAAGAATTTCCTCTAATTAATTTATTCAATCTTCGAT
TCAAGGATCTCAACAACTTGGTCCAGAACTTCGTATTTTACTTTAAATGTCTCGA
Found at i:22540646 original size:79 final size:79
Alignment explanation
Indices: 22540538--22540704 Score: 219
Period size: 79 Copynumber: 2.1 Consensus size: 79
22540528 GGTCTTGAGT
* *
22540538 GTATTTTAATGAAGAATTTTCTTTAATTAATTTATTCAATCTTCGTTTCAAGGATCTCGACAACT
1 GTATTTTGATGAAGAATTTTCTTTAATTAATTTATTCAATCTTCATTTCAAGGATCTCGACAACT
22540603 TGGTCCAGAACTTC
66 TGGTCCAGAACTTC
* * * * *
22540617 GTATTTTGATGAA-AATTTTCCTTTGATTAATTTATTCAATCTTTATTTCAAGGGTCTTGATAAC
1 GTATTTTGATGAAGAATTTT-CTTTAATTAATTTATTCAATCTTCATTTCAAGGATCTCGACAAC
** *
22540681 TTGGTCTTGAATTTC
65 TTGGTCCAGAACTTC
*
22540696 ATATTTTGA
1 GTATTTTGA
22540705 CGAATAATAT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
78 6 0.08
79 70 0.92
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (79 bp):
GTATTTTGATGAAGAATTTTCTTTAATTAATTTATTCAATCTTCATTTCAAGGATCTCGACAACT
TGGTCCAGAACTTC
Found at i:22540724 original size:79 final size:77
Alignment explanation
Indices: 22540563--22540746 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 77
22540553 ATTTTCTTTA
* * *
22540563 ATTAATTTATTCAATCTTCGTTTCAAGGATCTCGACAACTTGGTCCAGAACTTCGTATTTTGATG
1 ATTAATTTATTCAATCTTCATTTCAAGGATCTCGACAACTTGGTCCAGAACTTCATATTTTGACG
22540628 AAAATTTTCCTTTG
66 AAAATTTTCC--TG
* * * * ** *
22540642 ATTAATTTATTCAATCTTTATTTCAAGGGTCTTGATAACTTGGTCTTGAATTTCATATTTTGACG
1 ATTAATTTATTCAATCTTCATTTCAAGGATCTCGACAACTTGGTCCAGAACTTCATATTTTGACG
22540707 AATAATATCTTCC-G
66 AA-AAT-T-TTCCTG
* * * *
22540721 ATTAATTTCTTTAATCTCCACTTCAA
1 ATTAATTTATTCAATCTTCATTTCAA
22540747 AGGAGTCTAT
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
79 79 0.91
80 3 0.03
81 1 0.01
82 4 0.05
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (77 bp):
ATTAATTTATTCAATCTTCATTTCAAGGATCTCGACAACTTGGTCCAGAACTTCATATTTTGACG
AAAATTTTCCTG
Found at i:22556048 original size:70 final size:68
Alignment explanation
Indices: 22555935--22556072 Score: 240
Period size: 70 Copynumber: 2.0 Consensus size: 68
22555925 TTTTCCCTTC
* *
22555935 AGTGCCTTCAACAGTCCTTGTTGCACTAGCAATGCGCGCATCTTAACACGCCACAGGCTGAAATC
1 AGTGCCTTCAACAGTCCTGGTTGCACTAGCAATGCGCGCATCTTAACACGCCACA-ACTGAAATC
22556000 GTTT
65 GTTT
22556004 NAGTGCCTTCAACAGTCCTGGTTGCACTAGCAATGCGCGCATCTTAACACGCCACAACTGAAATC
1 -AGTGCCTTCAACAGTCCTGGTTGCACTAGCAATGCGCGCATCTTAACACGCCACAACTGAAATC
22556069 GTTT
65 GTTT
22556073 CTTCCATTAA
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
69 12 0.18
70 54 0.82
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (68 bp):
AGTGCCTTCAACAGTCCTGGTTGCACTAGCAATGCGCGCATCTTAACACGCCACAACTGAAATCG
TTT
Found at i:22557149 original size:22 final size:22
Alignment explanation
Indices: 22557118--22557159 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
22557108 ATTACATATA
22557118 TTAAAAGTTGTCCCTAAATAAG
1 TTAAAAGTTGTCCCTAAATAAG
*
22557140 TTAAACGTTGTCCCTAAATA
1 TTAAAAGTTGTCCCTAAATA
22557160 GGATAATTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (22 bp):
TTAAAAGTTGTCCCTAAATAAG
Found at i:22604594 original size:18 final size:19
Alignment explanation
Indices: 22604558--22604600 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
22604548 TTCTCTCAAT
**
22604558 TTTTTTGTTTTGTTTATGA
1 TTTTTTGTTTTGTGGATGA
22604577 TTTTTT-TTTTGTGGATGA
1 TTTTTTGTTTTGTGGATGA
22604595 TGTTTT
1 T-TTTT
22604601 CTATGGATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.09, C:0.00, G:0.19, T:0.72
Consensus pattern (19 bp):
TTTTTTGTTTTGTGGATGA
Found at i:22616555 original size:12 final size:11
Alignment explanation
Indices: 22616531--22616626 Score: 60
Period size: 11 Copynumber: 9.0 Consensus size: 11
22616521 GGAATGAAAA
22616531 TATTTAAATAT
1 TATTTAAATAT
22616542 TATTT-AATA-
1 TATTTAAATAT
22616551 TA-TT-AATAT
1 TATTTAAATAT
* *
22616560 TATTTCACTA-
1 TATTTAAATAT
*
22616570 TA-ATAAATAT
1 TATTTAAATAT
**
22616580 TATAAAACATAT
1 TATTTAA-ATAT
*
22616592 TACTTAATATTAT
1 TATTTAA-A-TAT
22616605 TATTTAAATAT
1 TATTTAAATAT
*
22616616 TAATTAAATAT
1 TATTTAAATAT
22616627 AACNNNNNNN
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
8 6 0.09
9 8 0.12
10 10 0.15
11 24 0.36
12 10 0.15
13 9 0.13
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (11 bp):
TATTTAAATAT
Found at i:22616937 original size:22 final size:23
Alignment explanation
Indices: 22616912--22616955 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
22616902 GTTTTTTTTT
*
22616912 ATTTTAATTAAAAA-ATTTTTAA
1 ATTTTAATAAAAAATATTTTTAA
22616934 ATTTTAATAAAAAATATTTTTA
1 ATTTTAATAAAAAATATTTTTA
22616956 TCATTTACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTTTAATAAAAAATATTTTTAA
Found at i:22616962 original size:23 final size:21
Alignment explanation
Indices: 22616907--22616962 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
22616897 TCATAGTTTT
*
22616907 TTTTTAT-TTTAATTAAAAAA
1 TTTTTATATTTAATAAAAAAA
*
22616927 TTTTTAAATTTTAATAAAAAATA
1 TTTTTATA-TTTAATAAAAAA-A
22616950 TTTTTATCATTTA
1 TTTTTAT-ATTTA
22616963 CCCATTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 6 0.21
22 11 0.38
23 11 0.38
24 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTTATATTTAATAAAAAAA
Found at i:22621470 original size:15 final size:17
Alignment explanation
Indices: 22621450--22621482 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
22621440 GTTTGACTTG
22621450 AGAGAAG-T-GGAGATA
1 AGAGAAGCTAGGAGATA
22621465 AGAGAAGCTAGGAGATA
1 AGAGAAGCTAGGAGATA
22621482 A
1 A
22621483 CACTAATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.48, C:0.03, G:0.36, T:0.12
Consensus pattern (17 bp):
AGAGAAGCTAGGAGATA
Found at i:22624212 original size:2 final size:2
Alignment explanation
Indices: 22624207--22624235 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22624197 AAAAAAATGA
22624207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22624236 AGATCTGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22626897 original size:18 final size:20
Alignment explanation
Indices: 22626874--22626911 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
22626864 ATTATCTCAT
22626874 CAACCAAAA-AAAAA-AAAA
1 CAACCAAAAGAAAAAGAAAA
22626892 CAACCAAAAGAAAAAGAAAA
1 CAACCAAAAGAAAAAGAAAA
22626912 TCTTTTACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 5 0.28
20 4 0.22
ACGTcount: A:0.79, C:0.16, G:0.05, T:0.00
Consensus pattern (20 bp):
CAACCAAAAGAAAAAGAAAA
Found at i:22630912 original size:116 final size:117
Alignment explanation
Indices: 22630747--22630980 Score: 416
Period size: 116 Copynumber: 2.0 Consensus size: 117
22630737 AGTTATATAA
*
22630747 ATTCAAAATATGAAATACCCTAATCTTATACACTCCGCACTAAGGAGGTCGAAAAATAAAAAATA
1 ATTCAAAATATGAAATACCCTAATCTTATACACTCCGCACTAAGGAGGTCAAAAAATAAAAAATA
22630812 TATTAAAAAATATAATATTT-AAATAAAATTTTAAATTATTTAAATATATTT
66 TATTAAAAAATATAATATTTAAAATAAAATTTTAAATTATTTAAATATATTT
* * * *
22630863 ATTCAAAATATGAGATACTCTAATCTTATACACTTCGCACTAAGGAGGTCAAAAAATAAAAGATA
1 ATTCAAAATATGAAATACCCTAATCTTATACACTCCGCACTAAGGAGGTCAAAAAATAAAAAATA
22630928 TATTAAAAAATATAATATTTAAAATAAAATTTTAAATTATTTAAATATATTT
66 TATTAAAAAATATAATATTTAAAATAAAATTTTAAATTATTTAAATATATTT
22630980 A
1 A
22630981 CATAATTTTT
Statistics
Matches: 112, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
116 80 0.71
117 32 0.29
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.34
Consensus pattern (117 bp):
ATTCAAAATATGAAATACCCTAATCTTATACACTCCGCACTAAGGAGGTCAAAAAATAAAAAATA
TATTAAAAAATATAATATTTAAAATAAAATTTTAAATTATTTAAATATATTT
Found at i:22631017 original size:27 final size:28
Alignment explanation
Indices: 22630973--22631025 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
22630963 ATTATTTAAA
*
22630973 TATATTTACATAATTTTTTAT-TTTTAT
1 TATATTTACATAAATTTTTATATTTTAT
22631000 TATATTTA-ATTAAATTTTTATATTTT
1 TATATTTACA-TAAATTTTTATATTTT
22631026 TATTTTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 1 0.04
27 18 0.78
28 4 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (28 bp):
TATATTTACATAAATTTTTATATTTTAT
Found at i:22631040 original size:26 final size:27
Alignment explanation
Indices: 22630950--22631040 Score: 71
Period size: 27 Copynumber: 3.3 Consensus size: 27
22630940 TAATATTTAA
* *
22630950 AATAAAATTTTAAATTATTTAAATATATTT
1 AATAAAATTTT-TA-TATTT-ATTATATTT
* *
22630980 ACAT-AATTTTTTATTTTTATTATATTT
1 A-ATAAAATTTTTATATTTATTATATTT
*
22631007 AATTAAATTTTTATATTT-TTAT-TTT
1 AATAAAATTTTTATATTTATTATATTT
22631032 GAATAAAAT
1 -AATAAAAT
22631041 AAACTCTTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
25 3 0.06
26 13 0.25
27 21 0.41
28 4 0.08
29 1 0.02
30 7 0.14
31 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (27 bp):
AATAAAATTTTTATATTTATTATATTT
Found at i:22631305 original size:28 final size:30
Alignment explanation
Indices: 22631248--22631314 Score: 91
Period size: 32 Copynumber: 2.2 Consensus size: 30
22631238 AATTATAACG
22631248 ATTTATTTGACTCAAAATAAAAAAATATAAAA
1 ATTTATTTGACTCAAAAT--AAAAATATAAAA
*
22631280 ATTTATTTGATTCAAAATAAAAATA-AAATA
1 ATTTATTTGACTCAAAATAAAAATATAAA-A
22631310 ATTTA
1 ATTTA
22631315 ATTAAAAGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 3 0.09
30 13 0.39
32 17 0.52
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (30 bp):
ATTTATTTGACTCAAAATAAAAATATAAAA
Found at i:22650603 original size:63 final size:63
Alignment explanation
Indices: 22650526--22650653 Score: 229
Period size: 63 Copynumber: 2.0 Consensus size: 63
22650516 ATTATGGTCG
**
22650526 TTTTACCTTTTTCAACTTGTGATATTCTTCCTTAGGTTGTCAATAGTCAAATGGGTTCTTGAT
1 TTTTACCTCCTTCAACTTGTGATATTCTTCCTTAGGTTGTCAATAGTCAAATGGGTTCTTGAT
*
22650589 TTTTACCTCCTTCAACTTGTGATATTCTTCCTTTGGTTGTCAATAGTCAAATGGGTTCTTGAT
1 TTTTACCTCCTTCAACTTGTGATATTCTTCCTTAGGTTGTCAATAGTCAAATGGGTTCTTGAT
22650652 TT
1 TT
22650654 GTTTGTTGCC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.20, C:0.17, G:0.16, T:0.48
Consensus pattern (63 bp):
TTTTACCTCCTTCAACTTGTGATATTCTTCCTTAGGTTGTCAATAGTCAAATGGGTTCTTGAT
Found at i:22652267 original size:16 final size:15
Alignment explanation
Indices: 22652242--22652272 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
22652232 TGAGAAAAAG
22652242 AATGGAAAAAGGAAA
1 AATGGAAAAAGGAAA
22652257 AATGTGAAAAAGGAAA
1 AATG-GAAAAAGGAAA
22652273 CAAGCTTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.10
Consensus pattern (15 bp):
AATGGAAAAAGGAAA
Found at i:22658602 original size:2 final size:2
Alignment explanation
Indices: 22658597--22658677 Score: 95
Period size: 2 Copynumber: 44.0 Consensus size: 2
22658587 CAAGAGGGGT
*
22658597 GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA -A GA -A GA -A NA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
22658635 -A G- GA G- GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
22658674 GA GA
1 GA GA
22658678 AATTGGATTT
Statistics
Matches: 70, Mismatches: 2, Indels: 14
0.81 0.02 0.16
Matches are distributed among these distances:
1 7 0.10
2 63 0.90
ACGTcount: A:0.53, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:22660629 original size:66 final size:66
Alignment explanation
Indices: 22660520--22660710 Score: 260
Period size: 66 Copynumber: 2.9 Consensus size: 66
22660510 TACGCTATGT
* * * *
22660520 TGTTACACGCCATGTACAAAAATATATGACAAGCAATGATTAGGTTTTTACAC-TCTATGGGTAG
1 TGTTACACGCCATGTACAAAAATATGTGACAAGCAATGGTTAGGTTGTTACACGTC-ATGAGTAG
22660584 GC
65 GC
* * *
22660586 TGTTACACGTCATGTATAAAAATATGTGACAAGCAATGGTTAGGTTGTTACACGTCATGATTAGG
1 TGTTACACGCCATGTACAAAAATATGTGACAAGCAATGGTTAGGTTGTTACACGTCATGAGTAGG
*
22660651 T
66 C
* *
22660652 TGTTACATGCCATGTACAAAAATATGTGACAAGTC-ATGGTTAGGTTGTTACACATCATG
1 TGTTACACGCCATGTACAAAAATATGTGACAAG-CAATGGTTAGGTTGTTACACGTCATG
22660711 TACAAAAACA
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
66 108 0.97
67 3 0.03
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (66 bp):
TGTTACACGCCATGTACAAAAATATGTGACAAGCAATGGTTAGGTTGTTACACGTCATGAGTAGG
C
Found at i:22660665 original size:21 final size:21
Alignment explanation
Indices: 22660625--22660665 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
22660615 CAAGCAATGG
*
22660625 TTAGGTTGTTACACGTCATGA
1 TTAGGTTGTTACACGCCATGA
*
22660646 TTAGGTTGTTACATGCCATG
1 TTAGGTTGTTACACGCCATG
22660666 TACAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (21 bp):
TTAGGTTGTTACACGCCATGA
Found at i:22660769 original size:90 final size:90
Alignment explanation
Indices: 22660641--22660841 Score: 278
Period size: 90 Copynumber: 2.2 Consensus size: 90
22660631 TGTTACACGT
* * * * * *
22660641 CATGATTAGGTTGTTACATGCCATGTACAAAAATATGTGACAAGTCATGGTTAGGTTGTTACACA
1 CATGATTAGGTTGTTACACGTCATATACAAAAACATGTGACAAATCATGGTTAGGTTATTACACA
*
22660706 TCATGTACAAAAACATGTGACAAGC
66 TCATGTACAAAAACATATGACAAGC
*
22660731 CATGATTAGGTTGTTACACGTCATATACAAAAACATGTGACAAATCATGGTTAGGTTATTACACG
1 CATGATTAGGTTGTTACACGTCATATACAAAAACATGTGACAAATCATGGTTAGGTTATTACACA
* *
22660796 TTATGTACAAAAATATATGACAAGC
66 TCATGTACAAAAACATATGACAAGC
**
22660821 CAT-AGTTAAATTGTTACACGT
1 CATGA-TTAGGTTGTTACACGT
22660842 TATGGTTAGG
Statistics
Matches: 98, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
89 1 0.01
90 97 0.99
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (90 bp):
CATGATTAGGTTGTTACACGTCATATACAAAAACATGTGACAAATCATGGTTAGGTTATTACACA
TCATGTACAAAAACATATGACAAGC
Found at i:22660845 original size:45 final size:45
Alignment explanation
Indices: 22660641--22660841 Score: 249
Period size: 45 Copynumber: 4.5 Consensus size: 45
22660631 TGTTACACGT
* * * * *
22660641 CATGATTAGGTTGTTACATGCCATGTACAAAAATATGTGACAAGT
1 CATGGTTAGGTTGTTACACGTCATGTACAAAAACATGTGACAAGC
*
22660686 CATGGTTAGGTTGTTACACATCATGTACAAAAACATGTGACAAGC
1 CATGGTTAGGTTGTTACACGTCATGTACAAAAACATGTGACAAGC
* * **
22660731 CATGATTAGGTTGTTACACGTCATATACAAAAACATGTGACAAAT
1 CATGGTTAGGTTGTTACACGTCATGTACAAAAACATGTGACAAGC
* * * *
22660776 CATGGTTAGGTTATTACACGTTATGTACAAAAATATATGACAAGC
1 CATGGTTAGGTTGTTACACGTCATGTACAAAAACATGTGACAAGC
* **
22660821 CATAGTTAAATTGTTACACGT
1 CATGGTTAGGTTGTTACACGT
22660842 TATGGTTAGG
Statistics
Matches: 133, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 133 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (45 bp):
CATGGTTAGGTTGTTACACGTCATGTACAAAAACATGTGACAAGC
Found at i:22661032 original size:31 final size:31
Alignment explanation
Indices: 22660974--22661040 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
22660964 TGTTACACAC
* *
22660974 CATGTTGAAAAAAAATATTATTGTTACACGT
1 CATGTTGAAAAAAAATACTATTATTACACGT
*
22661005 CATGTTGAAAAAAAATACTGTTATTACACGT
1 CATGTTGAAAAAAAATACTATTATTACACGT
22661036 CATGT
1 CATGT
22661041 ACAAAAACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (31 bp):
CATGTTGAAAAAAAATACTATTATTACACGT
Found at i:22661096 original size:25 final size:26
Alignment explanation
Indices: 22661050--22661098 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
22661040 TACAAAAACA
**
22661050 TGTTACACGTTATGGTTAAAAAAAGT
1 TGTTACACGCCATGGTTAAAAAAAGT
*
22661076 TGTTACACGCCAT-GTTGAAAAAA
1 TGTTACACGCCATGGTTAAAAAAA
22661099 TATTGTTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (26 bp):
TGTTACACGCCATGGTTAAAAAAAGT
Found at i:22661096 original size:26 final size:28
Alignment explanation
Indices: 22660962--22661111 Score: 100
Period size: 31 Copynumber: 5.3 Consensus size: 28
22660952 TTGTGGTTAG
**
22660962 GTTGTTACACACCATGTTGAAAAAAAATATT
1 GTTGTTACACGTCATGTTG--AAAAAATA-T
*
22660993 ATTGTTACACGTCATGTTGAAAAAAAATACT
1 GTTGTTACACGTCATGTTG--AAAAAATA-T
* *
22661024 GTTATTACACGTCATG-T-ACAAAAACA-
1 GTTGTTACACGTCATGTTGA-AAAAATAT
*
22661050 --TGTTACACGTTATGGTT-AAAAAA-A-
1 GTTGTTACACGTCAT-GTTGAAAAAATAT
*
22661074 GTTGTTACACGCCATGTTGAAAAAATATT
1 GTTGTTACACGTCATGTTGAAAAAATA-T
22661103 GTTGTTACA
1 GTTGTTACA
22661112 TGACATATTC
Statistics
Matches: 99, Mismatches: 11, Indels: 20
0.76 0.08 0.15
Matches are distributed among these distances:
24 12 0.12
25 9 0.09
26 19 0.19
27 2 0.02
28 6 0.06
29 9 0.09
30 1 0.01
31 41 0.41
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (28 bp):
GTTGTTACACGTCATGTTGAAAAAATAT
Found at i:22661125 original size:29 final size:28
Alignment explanation
Indices: 22661074--22661130 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
22661064 GTTAAAAAAA
* * *
22661074 GTTGTTACACGCCATGTTGAAAAAATATT
1 GTTGTTACACGACATATT-CAAAAATATT
*
22661103 GTTGTTACATGACATATTCAAAAATATT
1 GTTGTTACACGACATATTCAAAAATATT
22661131 TTATTATACT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (28 bp):
GTTGTTACACGACATATTCAAAAATATT
Found at i:22675294 original size:3 final size:3
Alignment explanation
Indices: 22675280--22675315 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
22675270 GTTATCAGGC
*
22675280 GAT GAC GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
22675316 TGGCTTAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:22685566 original size:2 final size:2
Alignment explanation
Indices: 22685559--22685585 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
22685549 TTGGTAAATA
22685559 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
22685586 GCCACTACTG
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:22686551 original size:33 final size:33
Alignment explanation
Indices: 22686514--22686588 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
22686504 TCATATCAAG
* *
22686514 TTAATATGTCA-AGTCATCATCAATTATGATATA
1 TTAATATATCACA-TCATCATCAATTATAATATA
* *
22686547 TTAATATATCACATCTTTATCAATTATAATATA
1 TTAATATATCACATCATCATCAATTATAATATA
22686580 TTAATATAT
1 TTAATATAT
22686589 TATGTTTGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 36 0.97
34 1 0.03
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (33 bp):
TTAATATATCACATCATCATCAATTATAATATA
Found at i:22686680 original size:29 final size:28
Alignment explanation
Indices: 22686648--22686754 Score: 81
Period size: 29 Copynumber: 3.7 Consensus size: 28
22686638 TTATCATTAT
*
22686648 TATAAAAAATTATTTAACTCAAAATAAAA
1 TATAAAAAATTATTTAAAT-AAAATAAAA
* * * **
22686677 TATAATAATTTATCTAGTGTAAAATAAATA
1 TATAAAAAATTATTTA-AATAAAATAAA-A
* * *
22686707 TATAAAAATTTAATTAAATATAATAAAA
1 TATAAAAAATTATTTAAATAAAATAAAA
22686735 -ATAAAAAAATTTATTTAAAT
1 TAT-AAAAAA-TTATTTAAAT
22686755 TTTTAAAAAT
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
27 2 0.03
28 6 0.10
29 38 0.62
30 15 0.25
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (28 bp):
TATAAAAAATTATTTAAATAAAATAAAA
Found at i:22686761 original size:28 final size:29
Alignment explanation
Indices: 22686699--22686767 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
22686689 TCTAGTGTAA
* *
22686699 AATAAATATATAAAAATTTAATTAAATAT
1 AATAAAAATAAAAAAATTTAATTAAATAT
*
22686728 AATAAAAATAAAAAAATTTATTTAAAT-T
1 AATAAAAATAAAAAAATTTAATTAAATAT
**
22686756 TTTAAAAATAAA
1 AATAAAAATAAA
22686768 TTAAAGTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
28 11 0.31
29 24 0.69
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
AATAAAAATAAAAAAATTTAATTAAATAT
Found at i:22701597 original size:16 final size:16
Alignment explanation
Indices: 22701570--22701615 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
22701560 AATATTTTAA
22701570 TTTAAA-TATTAATAT
1 TTTAAATTATTAATAT
22701585 TTTAAATTATTAATAT
1 TTTAAATTATTAATAT
*
22701601 TTTAAATTATAAATA
1 TTTAAATTATTAATA
22701616 AAATATTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 6 0.21
16 23 0.79
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAATTATTAATAT
Found at i:22701644 original size:27 final size:28
Alignment explanation
Indices: 22701577--22701644 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
22701567 TAATTTAAAT
*
22701577 ATTAATATTTTAAATTATTAATATTTTAA
1 ATTAAT-TTTTAAAATATTAATATTTTAA
***
22701606 ATT-ATAAATAAAATATTAATATTTT-A
1 ATTAATTTTTAAAATATTAATATTTTAA
22701632 ATTAATTTTTAAA
1 ATTAATTTTTAAA
22701645 TTTAAAGTAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
26 4 0.13
27 22 0.71
28 2 0.06
29 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
ATTAATTTTTAAAATATTAATATTTTAA
Found at i:22702043 original size:22 final size:22
Alignment explanation
Indices: 22702011--22702089 Score: 86
Period size: 22 Copynumber: 3.4 Consensus size: 22
22702001 TTAAATTATA
*
22702011 AATAAAATATTAATATTTAAAT
1 AATAAATTATTAATATTTAAAT
*
22702033 GATAAATTATTAATATTATAAAT
1 AATAAATTATTAATATT-TAAAT
*
22702056 AAAATATAAATTATTAATATTTAAAA
1 ---A-ATAAATTATTAATATTTAAAT
22702082 AATAAATT
1 AATAAATT
22702090 GAAATAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
22 22 0.46
23 6 0.12
26 4 0.08
27 16 0.33
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (22 bp):
AATAAATTATTAATATTTAAAT
Found at i:22702066 original size:27 final size:27
Alignment explanation
Indices: 22702029--22702080 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
22702019 ATTAATATTT
22702029 AAATGATAAATTATTAATATTATAAATA
1 AAATGATAAATTATTAATATT-TAAATA
22702057 AAAT-ATAAATTATTAATATTTAAA
1 AAATGATAAATTATTAATATTTAAA
22702081 AAATAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 4 0.17
27 16 0.67
28 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
AAATGATAAATTATTAATATTTAAATA
Found at i:22702121 original size:118 final size:116
Alignment explanation
Indices: 22701912--22702127 Score: 339
Period size: 118 Copynumber: 1.8 Consensus size: 116
22701902 NNNNNNNNAC
*
22701912 TTAAATAATCAATTATTAATATT-T-AA-AAAATATAAATTATTAATATTTAAAAGATAAAATTA
1 TTAAAT-ATCAATTATTAATATTATAAATAAAATATAAATTATTAATATTTAAAAAAT-AAATTA
*
22701974 AATAAAAATAAATAATCATAATAAAATTTAAATTATAAATAAAATATTAATAT
64 AATAAAAATAAATAATCATAATAACATTTAAATTATAAATAAAATATTAATAT
*
22702027 TTAAATGATAAATTATTAATATTATAAATAAAATATAAATTATTAATATTTAAAAAATAAATTGA
1 TTAAAT-ATCAATTATTAATATTATAAATAAAATATAAATTATTAATATTTAAAAAATAAATT-A
22702092 AATAAAAATAAATAATCATAATAACATTTAATATTA
64 AATAAAAATAAATAATCATAATAACATTTAA-ATTA
22702128 ATGATTAAAG
Statistics
Matches: 92, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
115 21 0.23
116 1 0.01
117 7 0.08
118 59 0.64
119 4 0.04
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (116 bp):
TTAAATATCAATTATTAATATTATAAATAAAATATAAATTATTAATATTTAAAAAATAAATTAAA
TAAAAATAAATAATCATAATAACATTTAAATTATAAATAAAATATTAATAT
Found at i:22702150 original size:131 final size:129
Alignment explanation
Indices: 22702001--22702265 Score: 365
Period size: 131 Copynumber: 2.0 Consensus size: 129
22701991 ATAATAAAAT
*
22702001 TTAAATTATAAATAAAATATTAATATTTAAA-TGATAAATTATTAATA-TTATAAATAAAATATA
1 TTAAAGTATAAATAAAATATTAATATTTAAACT-ATAAATTATTAATATTTATAAATAAAATATA
*
22702064 AATTATTAATATTTAAAAAATAAATTGAA-ATAAAAATAAATAATCATAATAACATTTAATATTA
65 AATTATTAATATTT-AAAAATAAAAT-AATATAAAAATAAATAATCATAATAACATTTAA-ATT-
22702128 ATGA
126 ATGA
** * * * *
22702132 TTAAAGTATAAATAAAATATTAATATTTAAACTATCGATTTTTAATATTTTTAAATAAATTATAC
1 TTAAAGTATAAATAAAATATTAATATTTAAACTATAAATTATTAATATTTATAAATAAAATATAA
* *
22702197 ATTATTAATGTTTAAAAATAAAATAATTTAAAAATAAATAATCATAATAACATTTAAATTATGA
66 ATTATTAATATTTAAAAATAAAATAATATAAAAATAAATAATCATAATAACATTTAAATTATGA
*
22702261 ATAAA
1 TTAAA
22702266 ATATTAGTAT
Statistics
Matches: 120, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
129 8 0.07
130 5 0.04
131 80 0.67
132 27 0.22
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (129 bp):
TTAAAGTATAAATAAAATATTAATATTTAAACTATAAATTATTAATATTTATAAATAAAATATAA
ATTATTAATATTTAAAAATAAAATAATATAAAAATAAATAATCATAATAACATTTAAATTATGA
Found at i:22702235 original size:15 final size:16
Alignment explanation
Indices: 22702207--22702238 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
22702197 ATTATTAATG
22702207 TTTAAAAATAAAATAA
1 TTTAAAAATAAAATAA
22702223 TTTAAAAAT-AAATAA
1 TTTAAAAATAAAATAA
22702238 T
1 T
22702239 CATAATAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TTTAAAAATAAAATAA
Found at i:22704041 original size:3 final size:3
Alignment explanation
Indices: 22704033--22704057 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
22704023 CTATTTCTAC
22704033 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
22704058 GTTGTTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:22728191 original size:76 final size:76
Alignment explanation
Indices: 22728071--22728212 Score: 239
Period size: 76 Copynumber: 1.9 Consensus size: 76
22728061 ATAAACAACT
* *
22728071 TATATATATATACAAGGAGTTGTTTGGTGATTAGTTGCTCCACATGCCGATGGACTGCCTTGCGG
1 TATATATATATACAAGGAGTTGCTTGGTGATTAGTTGCTCCACATGCCAATGGACTGCCTTGCGG
22728136 CAAAATATATA
66 CAAAATATATA
* * *
22728147 TATATATATTTATAAGGAGTTGCTTGGTGATTAGTTGCTCCACATGCCAATGGACTGCTTTGCGG
1 TATATATATATACAAGGAGTTGCTTGGTGATTAGTTGCTCCACATGCCAATGGACTGCCTTGCGG
22728212 C
66 C
22728213 GATTTTGCGC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 61 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (76 bp):
TATATATATATACAAGGAGTTGCTTGGTGATTAGTTGCTCCACATGCCAATGGACTGCCTTGCGG
CAAAATATATA
Found at i:22733056 original size:22 final size:21
Alignment explanation
Indices: 22733007--22733056 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
22732997 TAATAAAAAA
22733007 AATTATTTCTAAAAAAAAATT
1 AATTATTTCTAAAAAAAAATT
* **
22733028 AATTTATTTCTTAATCAAAATT
1 AA-TTATTTCTAAAAAAAAATT
22733050 ATATTAT
1 A-ATTAT
22733057 ATATTGTCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 21 0.88
23 1 0.04
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTATTTCTAAAAAAAAATT
Found at i:22742796 original size:25 final size:25
Alignment explanation
Indices: 22742745--22742798 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
22742735 CTTTTTAAAC
* ** *
22742745 TAATGTTTATTTATTTTATAAATAT
1 TAATGTTAATTTATTGCATAAAGAT
*
22742770 TAATGTTAATTTATTGCATGAAGAT
1 TAATGTTAATTTATTGCATAAAGAT
22742795 TAAT
1 TAAT
22742799 ATTATTAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (25 bp):
TAATGTTAATTTATTGCATAAAGAT
Found at i:22749467 original size:2 final size:2
Alignment explanation
Indices: 22749460--22749509 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
22749450 TTGATGACTG
22749460 AT AT AT AT 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 AT AT AT AT
22749502 AT AT AT AT
1 AT AT AT AT
22749510 NNNNNNNNNN
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22769261 original size:80 final size:81
Alignment explanation
Indices: 22769128--22769288 Score: 261
Period size: 80 Copynumber: 2.0 Consensus size: 81
22769118 CTCCAGGCCA
* * * *
22769128 CTTAAAGAAAATTCCAGGCATATTATGCTATAAACGAGCAAGAATTCTTGCCTTCACT-TGTTAA
1 CTTAAAGAAAATTCCAAGCATATTATGCTACAAACGAGCAAGAATGCTTGCCTTCACTGGGTTAA
22769192 TGTCAAATAATTCAAT
66 TGTCAAATAATTCAAT
* *
22769208 CTTAAAGAAAATTTCAAGCATATTATGCTACAAACGAGCAAGAATGCTTGCCTTCACTGGGTTTA
1 CTTAAAGAAAATTCCAAGCATATTATGCTACAAACGAGCAAGAATGCTTGCCTTCACTGGGTTAA
22769273 TGTCAAATAATTCAAT
66 TGTCAAATAATTCAAT
22769289 ATTATTATTA
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
80 54 0.73
81 20 0.27
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (81 bp):
CTTAAAGAAAATTCCAAGCATATTATGCTACAAACGAGCAAGAATGCTTGCCTTCACTGGGTTAA
TGTCAAATAATTCAAT
Found at i:22798463 original size:16 final size:18
Alignment explanation
Indices: 22798442--22798475 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
22798432 ACTCTTATAC
22798442 TTTTATTG-A-ATTTTTA
1 TTTTATTGTAGATTTTTA
22798458 TTTTATTGTAGATTTTTA
1 TTTTATTGTAGATTTTTA
22798476 CAAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (18 bp):
TTTTATTGTAGATTTTTA
Found at i:22815238 original size:30 final size:30
Alignment explanation
Indices: 22815202--22815276 Score: 150
Period size: 30 Copynumber: 2.5 Consensus size: 30
22815192 AGGAGCAAAG
22815202 CGAAGAAGAAGAAGAGAGATAGGGTTAGGT
1 CGAAGAAGAAGAAGAGAGATAGGGTTAGGT
22815232 CGAAGAAGAAGAAGAGAGATAGGGTTAGGT
1 CGAAGAAGAAGAAGAGAGATAGGGTTAGGT
22815262 CGAAGAAGAAGAAGA
1 CGAAGAAGAAGAAGA
22815277 AGCAAATAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.47, C:0.04, G:0.39, T:0.11
Consensus pattern (30 bp):
CGAAGAAGAAGAAGAGAGATAGGGTTAGGT
Found at i:22826772 original size:24 final size:24
Alignment explanation
Indices: 22826745--22826791 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
22826735 TACACCACTC
22826745 TTTGTCAATTT-CTACATT-TGACCT
1 TTTG-CAATTTACT-CATTATGACCT
22826769 TTTGCAATTTACTCATTATGACC
1 TTTGCAATTTACTCATTATGACC
22826792 AAAAACAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (24 bp):
TTTGCAATTTACTCATTATGACCT
Found at i:22831583 original size:22 final size:22
Alignment explanation
Indices: 22831558--22831600 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
22831548 TTAAAATTTT
22831558 CAAATCTACTAATAAATGGCTC
1 CAAATCTACTAATAAATGGCTC
*
22831580 CAAATCTGCTAATAAATGGCT
1 CAAATCTACTAATAAATGGCT
22831601 TTTCCAAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (22 bp):
CAAATCTACTAATAAATGGCTC
Found at i:22837924 original size:21 final size:20
Alignment explanation
Indices: 22837886--22837924 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
22837876 ACAGAGAACA
* *
22837886 GAAAGAAGAAAGGTTGAGAC
1 GAAAGAAGAAAAGATGAGAC
22837906 GAAAGAAAGAAAAGATGAG
1 GAAAG-AAGAAAAGATGAG
22837925 CAAGTTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.56, C:0.03, G:0.33, T:0.08
Consensus pattern (20 bp):
GAAAGAAGAAAAGATGAGAC
Found at i:22839012 original size:80 final size:80
Alignment explanation
Indices: 22838879--22839040 Score: 324
Period size: 80 Copynumber: 2.0 Consensus size: 80
22838869 TTGTTTACCG
22838879 ACTAGTTGACATGTGTAGCATACATATGGTAACTGCAGGAATGAATGGCAGGGCAATTCTCCTTT
1 ACTAGTTGACATGTGTAGCATACATATGGTAACTGCAGGAATGAATGGCAGGGCAATTCTCCTTT
22838944 GGCAAAACAGAAGTC
66 GGCAAAACAGAAGTC
22838959 ACTAGTTGACATGTGTAGCATACATATGGTAACTGCAGGAATGAATGGCAGGGCAATTCTCCTTT
1 ACTAGTTGACATGTGTAGCATACATATGGTAACTGCAGGAATGAATGGCAGGGCAATTCTCCTTT
22839024 GGCAAAACAGAAGTC
66 GGCAAAACAGAAGTC
22839039 AC
1 AC
22839041 GTATGCCATG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (80 bp):
ACTAGTTGACATGTGTAGCATACATATGGTAACTGCAGGAATGAATGGCAGGGCAATTCTCCTTT
GGCAAAACAGAAGTC
Done.