Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 23 of 24
Found at i:3076251 original size:2 final size:2
Alignment explanation
Indices: 3076244--3076277 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3076234 CTTATCTTGA
3076244 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
3076278 GTACACATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3076555 original size:2 final size:2
Alignment explanation
Indices: 3076548--3076582 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3076538 TAAACTTAAT
3076548 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 T
3076583 GAATGAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3076749 original size:13 final size:12
Alignment explanation
Indices: 3076731--3076773 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
3076721 TTATTTTTTA
3076731 AATATTTATAGTT
1 AATATTTATA-TT
3076744 AATATTTATATT
1 AATATTTATATT
* *
3076756 AAATATATATTTT
1 -AATATTTATATT
3076769 AATAT
1 AATAT
3076774 GAATATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 7 0.26
13 20 0.74
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (12 bp):
AATATTTATATT
Found at i:3076903 original size:3 final size:3
Alignment explanation
Indices: 3076895--3076931 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3076885 AAGCTAAATT
3076895 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3076932 CAAAAATCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3077374 original size:50 final size:50
Alignment explanation
Indices: 3077299--3077498 Score: 262
Period size: 50 Copynumber: 4.0 Consensus size: 50
3077289 TGAGTTACTT
* *
3077299 ATAGTCAACAATTA-TGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGA
1 ATAGTCAACAATTACAGA-CACCTCTCTCGATTGTCAAAGGTTGGTGAAGA
* *
3077349 ATAGTCAATAATTACAGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGA
1 ATAGTCAACAATTACAGACACCTCTCTCGATTGTCAAAGGTTGGTGAAGA
* * * *
3077399 ATAGTCAACAATTAC-GACAATCTCTCTCGATTGTTAAAGGTTGATGAAAA
1 ATAGTCAACAATTACAGAC-ACCTCTCTCGATTGTCAAAGGTTGGTGAAGA
* *
3077449 ATAGTTAACAATTACA-ACCACCTCTCTTGATTGTCAAAGGTTGGTGAAGA
1 ATAGTCAACAATTACAGA-CACCTCTCTCGATTGTCAAAGGTTGGTGAAGA
3077499 TCACCAAATC
Statistics
Matches: 130, Mismatches: 16, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
49 2 0.02
50 126 0.97
51 2 0.02
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (50 bp):
ATAGTCAACAATTACAGACACCTCTCTCGATTGTCAAAGGTTGGTGAAGA
Found at i:3077472 original size:100 final size:100
Alignment explanation
Indices: 3077299--3077498 Score: 292
Period size: 100 Copynumber: 2.0 Consensus size: 100
3077289 TGAGTTACTT
* * * * * *
3077299 ATAGTCAACAATTATGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATAGTCAATAATTAC
1 ATAGTCAACAATTACGACAACCTCTCTCGATTGTCAAAGGTTGATGAAAAATAGTCAACAATTAC
**
3077364 AGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGA
66 AACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGA
* * *
3077399 ATAGTCAACAATTACGACAATCTCTCTCGATTGTTAAAGGTTGATGAAAAATAGTTAACAATTAC
1 ATAGTCAACAATTACGACAACCTCTCTCGATTGTCAAAGGTTGATGAAAAATAGTCAACAATTAC
*
3077464 AACCACCTCTCTTGATTGTCAAAGGTTGGTGAAGA
66 AACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGA
3077499 TCACCAAATC
Statistics
Matches: 88, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
100 88 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (100 bp):
ATAGTCAACAATTACGACAACCTCTCTCGATTGTCAAAGGTTGATGAAAAATAGTCAACAATTAC
AACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGA
Found at i:3078057 original size:33 final size:35
Alignment explanation
Indices: 3077996--3078076 Score: 132
Period size: 33 Copynumber: 2.4 Consensus size: 35
3077986 AAAAAATCAA
*
3077996 AAAAATTAA-AAATAATAATATTCAATATAATAAT
1 AAAAATCAAGAAATAATAATATTCAATATAATAAT
3078030 AAAAATCAAGAAATAA-AA-ATTCAATATAATAAT
1 AAAAATCAAGAAATAATAATATTCAATATAATAAT
3078063 AAAAATCAAGAAAT
1 AAAAATCAAGAAAT
3078077 TCAAAAAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 29 0.64
34 10 0.22
35 6 0.13
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (35 bp):
AAAAATCAAGAAATAATAATATTCAATATAATAAT
Found at i:3084985 original size:50 final size:50
Alignment explanation
Indices: 3084926--3085212 Score: 423
Period size: 50 Copynumber: 5.7 Consensus size: 50
3084916 AGTTACTTAG
* * *
3084926 AGTCAACAATTACGGTCACCTCTCTCTATTGTTAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
3084976 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
** *
3085026 AGTCAACAATTACGATCACTTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
3085076 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * *
3085126 AGTCAACAATTACGACCACCTCTCTCGATTGTCAAAAGTTGATGGAA-AATT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGT-GAAGAA-T
* * * * *
3085177 AATCAACAATTACGGTCAACTCTCTCTATTATCAAA
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAA
3085213 AATTGATAAA
Statistics
Matches: 217, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
50 183 0.84
51 34 0.16
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (50 bp):
AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
Found at i:3086566 original size:2 final size:2
Alignment explanation
Indices: 3086559--3086585 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3086549 TAGTGAATTA
3086559 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3086586 GTCTGAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3094370 original size:20 final size:20
Alignment explanation
Indices: 3094345--3094390 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3094335 AAGAATTGAA
*
3094345 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
3094365 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
3094385 GAGGGA
1 GAGGGA
3094391 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.52, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:3094508 original size:28 final size:27
Alignment explanation
Indices: 3094484--3094537 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
3094474 TGACAAATAT
3094484 AAAAGAAACTACCATTTTTTACAAACAC
1 AAAAGAAAC-ACCATTTTTTACAAACAC
* * *
3094512 AAAATAATCATCATTTTTTACAAACA
1 AAAAGAAACACCATTTTTTACAAACA
3094538 AATGGGTGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.30
Consensus pattern (27 bp):
AAAAGAAACACCATTTTTTACAAACAC
Found at i:3095002 original size:26 final size:25
Alignment explanation
Indices: 3094973--3095033 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
3094963 TTTATGTTAC
*
3094973 TTATATTTTTATTATTTTTTAAATAT
1 TTATATTTTTATT-TTTATTAAATAT
* *
3094999 TTATATTTAATATTTTTATTGAATAT
1 TTATATTT-TTATTTTTATTAAATAT
*
3095025 ATATATTTT
1 TTATATTTT
3095034 GATGTAACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (25 bp):
TTATATTTTTATTTTTATTAAATAT
Found at i:3095012 original size:13 final size:13
Alignment explanation
Indices: 3094994--3095032 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3094984 TTATTTTTTA
3094994 AATATTTATATTT
1 AATATTTATATTT
* *
3095007 AATATTTTTATTG
1 AATATTTATATTT
*
3095020 AATATATATATTT
1 AATATTTATATTT
3095033 TGATGTAACA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:3095126 original size:3 final size:3
Alignment explanation
Indices: 3095118--3095149 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3095108 TAAATCAAAT
3095118 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3095150 GGAAACAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3096026 original size:21 final size:20
Alignment explanation
Indices: 3096002--3096040 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3095992 TATATATAAC
3096002 ATATTT-TTTGGAATAAAATTT
1 ATATTTATTT-GAA-AAAATTT
3096023 ATATTTATTTGAAAAAAT
1 ATATTTATTTGAAAAAAT
3096041 GAAGAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 9 0.53
22 3 0.18
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (20 bp):
ATATTTATTTGAAAAAATTT
Found at i:3096391 original size:30 final size:31
Alignment explanation
Indices: 3096355--3096448 Score: 102
Period size: 31 Copynumber: 3.0 Consensus size: 31
3096345 GAATGATAAA
**
3096355 AATTTTTAAAAAGTCATGGAT-AAT-AAATAT
1 AATTTTTAAAAA-TCATAAATAAATAAAATAT
*
3096385 AATTTTTAAAAATTATAAATAAATAAAATAT
1 AATTTTTAAAAATCATAAATAAATAAAATAT
* *
3096416 AACTTTTAAAAATTATAAATAAAAATAAAATAT
1 AATTTTTAAAAATCATAAAT--AAATAAAATAT
3096449 TAATAAAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
29 5 0.09
30 15 0.27
31 25 0.45
33 11 0.20
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (31 bp):
AATTTTTAAAAATCATAAATAAATAAAATAT
Found at i:3096417 original size:31 final size:32
Alignment explanation
Indices: 3096379--3096448 Score: 115
Period size: 31 Copynumber: 2.2 Consensus size: 32
3096369 CATGGATAAT
*
3096379 AAATATAATTTTTAAAAATTATAAAT-AAATA
1 AAATATAACTTTTAAAAATTATAAATAAAATA
3096410 AAATATAACTTTTAAAAATTATAAATAAAAATA
1 AAATATAACTTTTAAAAATTATAAAT-AAAATA
3096443 AAATAT
1 AAATAT
3096449 TAATAAAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 25 0.69
33 11 0.31
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (32 bp):
AAATATAACTTTTAAAAATTATAAATAAAATA
Found at i:3098266 original size:21 final size:19
Alignment explanation
Indices: 3098232--3098273 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 19
3098222 ATATTTTATT
3098232 ATTTTATAAATAATAATTAAA
1 ATTTTATAAATAAT--TTAAA
3098253 ATTTT-TAAATTAATTTAAA
1 ATTTTATAAA-TAATTTAAA
3098272 AT
1 AT
3098274 AAATTTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.35
20 4 0.20
21 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTTATAAATAATTTAAA
Found at i:3098621 original size:12 final size:12
Alignment explanation
Indices: 3098593--3098629 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3098583 ATAGATCTTA
*
3098593 TATTTTTAATA-
1 TATTTTTTATAT
3098604 TA-TTTTTATAT
1 TATTTTTTATAT
3098615 TATTTTTTATAT
1 TATTTTTTATAT
3098627 TAT
1 TAT
3098630 AATTATACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
10 7 0.30
11 4 0.17
12 12 0.52
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TATTTTTTATAT
Found at i:3101753 original size:2 final size:2
Alignment explanation
Indices: 3101746--3101779 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3101736 ATTGTTCTTC
3101746 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
3101780 TGATGTCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3102278 original size:3 final size:3
Alignment explanation
Indices: 3102270--3102304 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3102260 CATTATATCC
3102270 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3102305 TTCTTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3103971 original size:18 final size:19
Alignment explanation
Indices: 3103948--3103985 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3103938 AATTTGAATT
*
3103948 ATTTATTTAA-ATTTAAAA
1 ATTTATTTAATATATAAAA
3103966 ATTTATTTAATATATAAAA
1 ATTTATTTAATATATAAAA
3103985 A
1 A
3103986 AATTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTATTTAATATATAAAA
Found at i:3104432 original size:34 final size:34
Alignment explanation
Indices: 3104386--3104705 Score: 425
Period size: 34 Copynumber: 9.5 Consensus size: 34
3104376 GTAAAAACCA
*
3104386 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3104420 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
3104454 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
3104488 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3104522 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
3104556 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
3104590 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
3104623 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
3104657 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
3104690 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
3104706 TCTCCCACTT
Statistics
Matches: 252, Mismatches: 27, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
33 46 0.18
34 202 0.80
35 4 0.02
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:3104562 original size:102 final size:102
Alignment explanation
Indices: 3104386--3104705 Score: 556
Period size: 102 Copynumber: 3.2 Consensus size: 102
3104376 GTAAAAACCA
3104386 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
3104451 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
66 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
3104488 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
3104553 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
66 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
* * * *
3104590 CCATTTAATCAACAATGGTAAGCTACCAAATCT-CCATTTAGTCAACAATGGCAAACCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
* *
3104654 CACCCATTTAATCAACAATGGTAAACTACTAAA--TC
66 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
3104689 ACCATTTAATCAACAAT
1 -CCATTTAATCAACAAT
3104706 TCTCCCACTT
Statistics
Matches: 211, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
99 2 0.01
100 16 0.08
101 60 0.28
102 133 0.63
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.25
Consensus pattern (102 bp):
CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
CACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
Found at i:3108798 original size:19 final size:19
Alignment explanation
Indices: 3108771--3108833 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
3108761 TCACGTGTAC
* *
3108771 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
3108790 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
3108809 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
3108828 AGTACC
1 AGTACC
3108834 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:3109181 original size:34 final size:34
Alignment explanation
Indices: 3109135--3109452 Score: 403
Period size: 34 Copynumber: 9.4 Consensus size: 34
3109125 GTAAAAACCA
*
3109135 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3109169 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
3109203 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
3109237 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3109271 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* * * *
3109305 CCATTTAATCAACAATGGTAAGCTATCAAATTTT
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
3109339 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
3109372 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
3109406 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
3109439 CCATTTAATCAACA
1 CCATTTAATCAACA
3109453 GTAACATAAT
Statistics
Matches: 247, Mismatches: 30, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
33 44 0.18
34 199 0.81
35 4 0.02
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:3109311 original size:102 final size:102
Alignment explanation
Indices: 3109135--3109452 Score: 534
Period size: 102 Copynumber: 3.1 Consensus size: 102
3109125 GTAAAAACCA
3109135 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
3109200 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
66 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
3109237 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
* *
3109302 CACCCATTTAATCAACAATGGTAAGCTATCAAATTTT
66 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
* * * *
3109339 CCATTTAATCAACAATGGTAAGCTACCAAATCT-CCATTTAGTCAACAATGGCAAACCACCAAAT
1 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
* *
3109403 CACCCATTTAATCAACAATGGTAAACTACTAAA--TC
66 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
3109438 ACCATTTAATCAACA
1 -CCATTTAATCAACA
3109453 GTAACATAAT
Statistics
Matches: 205, Mismatches: 10, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
99 1 0.00
100 14 0.07
101 59 0.29
102 131 0.64
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (102 bp):
CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
CACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
Found at i:3109937 original size:24 final size:24
Alignment explanation
Indices: 3109921--3109969 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
3109911 TTAATTATAT
* *
3109921 AATATTATTTTTATTTATATATAA
1 AATATAATTTATATTTATATATAA
3109945 AATATAATTTATATTT-TATA-AA
1 AATATAATTTATATTTATATATAA
3109967 AAT
1 AAT
3109970 TAAATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 4 0.17
24 14 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
AATATAATTTATATTTATATATAA
Found at i:3109978 original size:29 final size:29
Alignment explanation
Indices: 3109911--3109984 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
3109901 AATCTCTTTT
* ** *
3109911 TTAATTATATAATATTATTTTTATTTATA
1 TTAAATATATAATATTATTTTTATAAAAA
3109940 TATAAA-ATATAAT-TTATATTTTATAAAAA
1 T-TAAATATATAATATTAT-TTTTATAAAAA
3109969 TTAAATATATAATATT
1 TTAAATATATAATATT
3109985 GTAATGAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
28 8 0.22
29 24 0.65
30 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TTAAATATATAATATTATTTTTATAAAAA
Found at i:3109979 original size:22 final size:24
Alignment explanation
Indices: 3109932--3109979 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
3109922 ATATTATTTT
*
3109932 TATTTATATATAAAATATAATTTA
1 TATTTATATATAAAATATAATATA
3109956 TATTT-TATA-AAAAT-TAAATATA
1 TATTTATATATAAAATAT-AATATA
3109978 TA
1 TA
3109980 ATATTGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 1 0.05
22 12 0.55
23 4 0.18
24 5 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TATTTATATATAAAATATAATATA
Found at i:3110997 original size:27 final size:26
Alignment explanation
Indices: 3110936--3110998 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
3110926 CATATAAAAC
3110936 AATAATTA-AAATATAAATATATTAA
1 AATAATTATAAATATAAATATATTAA
* *
3110961 AAT-TTATATAAATATATAATATTTTAA
1 AATAAT-TATAAATATA-AATATATTAA
3110988 AATAATTATAA
1 AATAATTATAA
3110999 GGTGTGAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 1 0.03
25 5 0.16
26 7 0.23
27 17 0.55
28 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AATAATTATAAATATAAATATATTAA
Found at i:3115626 original size:6 final size:6
Alignment explanation
Indices: 3115615--3115640 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3115605 ATACACTGAC
3115615 AGGCCA AGGCCA AGGCCA AGGCCA AG
1 AGGCCA AGGCCA AGGCCA AGGCCA AG
3115641 CCACTCTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.31, G:0.35, T:0.00
Consensus pattern (6 bp):
AGGCCA
Found at i:3116186 original size:17 final size:17
Alignment explanation
Indices: 3116164--3116199 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3116154 TAACTCGTAT
3116164 AAATTGATAATCGATTG
1 AAATTGATAATCGATTG
3116181 AAATTGATAATCGATTG
1 AAATTGATAATCGATTG
3116198 AA
1 AA
3116200 CCAACTGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (17 bp):
AAATTGATAATCGATTG
Found at i:3117054 original size:2 final size:2
Alignment explanation
Indices: 3117049--3117080 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3117039 AAAAAAAAAA
3117049 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
3117081 TTGAGATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3120078 original size:2 final size:2
Alignment explanation
Indices: 3120071--3120112 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3120061 CTTTTATTTT
3120071 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3120112 T
1 T
3120113 TGTAATTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3120953 original size:3 final size:3
Alignment explanation
Indices: 3120945--3120978 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3120935 ATTAGAATCA
*
3120945 ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3120979 ATAATAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:3121387 original size:15 final size:15
Alignment explanation
Indices: 3121357--3121390 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3121347 ATTATTGATG
**
3121357 TATTAAATAATTATT
1 TATTAAATAAAAATT
3121372 TATTAAATAAAAATT
1 TATTAAATAAAAATT
3121387 TATT
1 TATT
3121391 TATCAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAAATAAAAATT
Found at i:3130652 original size:2 final size:2
Alignment explanation
Indices: 3130640--3130680 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3130630 AATACAATGT
*
3130640 TA TA TA CA 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 TA T
3130681 TCTATTTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3132043 original size:26 final size:25
Alignment explanation
Indices: 3132014--3132062 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
3132004 TTTTATATTT
* * *
3132014 AAATTCAAATATAAATATCGAAAAAA
1 AAATACAAAAATAAAAAT-GAAAAAA
3132040 AAATACAAAAATAAAAATGAAAA
1 AAATACAAAAATAAAAATGAAAA
3132063 TCTAAGTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 5 0.25
26 15 0.75
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.18
Consensus pattern (25 bp):
AAATACAAAAATAAAAATGAAAAAA
Found at i:3132577 original size:5 final size:5
Alignment explanation
Indices: 3132567--3132594 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3132557 GTTGAGTTTC
3132567 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
3132595 GAGGCAGAAA
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:3149367 original size:28 final size:28
Alignment explanation
Indices: 3149327--3149383 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3149317 TGGCATCCTT
3149327 ACCTTCCACATACGGAAAGCTTAAAAAA
1 ACCTTCCACATACGGAAAGCTTAAAAAA
3149355 ACCTTCCACATACGGAAAGCTTAAAAAA
1 ACCTTCCACATACGGAAAGCTTAAAAAA
3149383 A
1 A
3149384 TTGAATGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.25, G:0.11, T:0.18
Consensus pattern (28 bp):
ACCTTCCACATACGGAAAGCTTAAAAAA
Found at i:3151589 original size:26 final size:27
Alignment explanation
Indices: 3151513--3151591 Score: 67
Period size: 26 Copynumber: 3.0 Consensus size: 27
3151503 TTTTATTGAA
* *
3151513 TTAAATTAAAATAAAAA-ATTTATAAT-T
1 TTAAATT--AATAAAAATATATATATTAT
* *
3151540 TTAAATTAATATAAAT-TAAAATATTAT
1 TTAAATTAATAAAAATAT-ATATATTAT
3151567 TTAAA-TAATAAAAATATATATATTA
1 TTAAATTAATAAAAATATATATATTA
3151592 AATTTAATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
25 8 0.19
26 20 0.48
27 14 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
TTAAATTAATAAAAATATATATATTAT
Found at i:3156799 original size:6 final size:6
Alignment explanation
Indices: 3156788--3156812 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3156778 GCTTGTCTGG
3156788 CCCTTT CCCTTT CCCTTT CCCTTT C
1 CCCTTT CCCTTT CCCTTT CCCTTT C
3156813 TCTCTCCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CCCTTT
Found at i:3160467 original size:24 final size:25
Alignment explanation
Indices: 3160438--3160488 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
3160428 TTTAAGCAAA
*
3160438 AAATATAAAGAATAATAATAA-AAT
1 AAATATAAAGAAGAATAATAATAAT
*
3160462 AAATATAGAGAAGAATAATAATAAT
1 AAATATAAAGAAGAATAATAATAAT
3160487 AA
1 AA
3160489 TAATAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.24
Consensus pattern (25 bp):
AAATATAAAGAAGAATAATAATAAT
Found at i:3161444 original size:3 final size:3
Alignment explanation
Indices: 3161438--3161472 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3161428 CTTCTTGTTG
*
3161438 TTA TTA TTA TTA TTA TTA TTA TTC TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3161473 TTGATAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3162723 original size:5 final size:5
Alignment explanation
Indices: 3162715--3162745 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
3162705 TTTAAATAAA
3162715 AAATT AAATT AAATT AAATT AAATT AAATT A
1 AAATT AAATT AAATT AAATT AAATT AAATT A
3162746 CAACATAAAA
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):
AAATT
Found at i:3164533 original size:17 final size:18
Alignment explanation
Indices: 3164511--3164557 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
3164501 ATAATAAAAA
3164511 AATTAAATTTTA-TTAAT
1 AATTAAATTTTATTTAAT
*
3164528 AATTAAA-TATATTTAAT
1 AATTAAATTTTATTTAAT
*
3164545 ATTTAAAATTTTA
1 AATT-AAATTTTA
3164558 AAAATATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 3 0.12
17 15 0.62
18 3 0.12
19 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTAAATTTTATTTAAT
Found at i:3165917 original size:4 final size:4
Alignment explanation
Indices: 3165908--3165932 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3165898 TTTTAATCAG
3165908 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
3165933 GTTTGCACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:3166424 original size:20 final size:20
Alignment explanation
Indices: 3166374--3166428 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
3166364 TATACGAATT
3166374 AATAATATAATATAAACATAA
1 AATAATATAATA-AAACATAA
* *
3166395 TAT-ATTTAATAAAA-ATAAA
1 AATAATATAATAAAACAT-AA
3166414 AATAATATAATAAAA
1 AATAATATAATAAAA
3166429 TTGGTGCAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 2 0.07
19 7 0.25
20 17 0.61
21 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
AATAATATAATAAAACATAA
Found at i:3168022 original size:2 final size:2
Alignment explanation
Indices: 3168017--3168054 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3168007 ATGTGTGTGC
3168017 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
3168055 GCCCGTGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3177090 original size:31 final size:32
Alignment explanation
Indices: 3177055--3177120 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
3177045 TAATAATTAT
3177055 AATAATAATTTT-TACT-AATTATAAAATTTAA
1 AATAA-AATTTTATACTAAATTATAAAATTTAA
* *
3177086 AATAAAATTTTATAGTAAATTTTAAAATTTAA
1 AATAAAATTTTATACTAAATTATAAAATTTAA
3177118 AAT
1 AAT
3177121 TTTAATCACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 6 0.19
31 8 0.26
32 17 0.55
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (32 bp):
AATAAAATTTTATACTAAATTATAAAATTTAA
Found at i:3177858 original size:22 final size:26
Alignment explanation
Indices: 3177833--3177886 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 26
3177823 TTTATGTTTC
3177833 GAATTTTTT-GGTTTT-TT-ATG-TA
1 GAATTTTTTGGGTTTTGTTAATGATA
3177855 GAATTTTTTTGGGTTTTGTTAATGATA
1 GAA-TTTTTTGGGTTTTGTTAATGATA
3177882 GAATT
1 GAATT
3177887 AGGTCAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 3 0.11
23 6 0.22
24 6 0.22
25 2 0.07
26 5 0.19
27 5 0.19
ACGTcount: A:0.22, C:0.00, G:0.20, T:0.57
Consensus pattern (26 bp):
GAATTTTTTGGGTTTTGTTAATGATA
Found at i:3177863 original size:24 final size:27
Alignment explanation
Indices: 3177836--3177886 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3177826 ATGTTTCGAA
3177836 TTTTTT-GGTTTT-TT-ATG-TAGAAT
1 TTTTTTGGGTTTTGTTAATGATAGAAT
3177859 TTTTTTGGGTTTTGTTAATGATAGAAT
1 TTTTTTGGGTTTTGTTAATGATAGAAT
3177886 T
1 T
3177887 AGGTCAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 6 0.25
24 6 0.25
25 2 0.08
26 3 0.12
27 7 0.29
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.61
Consensus pattern (27 bp):
TTTTTTGGGTTTTGTTAATGATAGAAT
Found at i:3178461 original size:15 final size:15
Alignment explanation
Indices: 3178441--3178473 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3178431 ATGGGAACTC
3178441 TGGAATGTACGGTGG
1 TGGAATGTACGGTGG
*
3178456 TGGAATGTATGGTGG
1 TGGAATGTACGGTGG
3178471 TGG
1 TGG
3178474 TCTTGGTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.03, G:0.48, T:0.30
Consensus pattern (15 bp):
TGGAATGTACGGTGG
Found at i:3180366 original size:82 final size:82
Alignment explanation
Indices: 3180236--3180390 Score: 220
Period size: 82 Copynumber: 1.9 Consensus size: 82
3180226 TCGGATTAAA
* * * *
3180236 TATTTGTTTAAGATTTATTCAATATTTACGAAAATTTGTATAAAAATATTAAGTTCGAAAAATAA
1 TATTTGTTTAAGATTTACTCAATATTTACGAAAATTTATATAAAAATATTAAATTCAAAAAATAA
3180301 ATTTAGATGAATTAAGT
66 ATTTAGATGAATTAAGT
* *** * *
3180318 TATTTGTTTAAGATTTGCTCAATATTTGTTAAATTTTATATAAAAATATTAAATTTAAAAAATAA
1 TATTTGTTTAAGATTTACTCAATATTTACGAAAATTTATATAAAAATATTAAATTCAAAAAATAA
3180383 ATTTAGAT
66 ATTTAGAT
3180391 AAAAAAAATA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
82 63 1.00
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (82 bp):
TATTTGTTTAAGATTTACTCAATATTTACGAAAATTTATATAAAAATATTAAATTCAAAAAATAA
ATTTAGATGAATTAAGT
Found at i:3181067 original size:15 final size:15
Alignment explanation
Indices: 3181047--3181076 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3181037 TACGTATGAA
3181047 GCACTGATTTATTTG
1 GCACTGATTTATTTG
3181062 GCACTGATTTATTTG
1 GCACTGATTTATTTG
3181077 CTCAATACGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (15 bp):
GCACTGATTTATTTG
Found at i:3184224 original size:11 final size:11
Alignment explanation
Indices: 3184208--3184249 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
3184198 TTATTAATTT
3184208 AATATAAAATA
1 AATATAAAATA
3184219 AATATAAAATA
1 AATATAAAATA
*
3184230 TAAT-TAATAATT
1 -AATATAA-AATA
3184242 AATATAAA
1 AATATAAA
3184250 TATATTTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATATAAAATA
Found at i:3190039 original size:17 final size:17
Alignment explanation
Indices: 3190019--3190052 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3190009 ATATTATTTA
* *
3190019 ATATTTTATATATATAT
1 ATATATTATACATATAT
3190036 ATATATTATACATATAT
1 ATATATTATACATATAT
3190053 TAAAAAAGAA
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:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATTATACATATAT
Found at i:3190794 original size:16 final size:17
Alignment explanation
Indices: 3190762--3190794 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3190752 ATAAATATTA
3190762 TTTAATAAAATTTAATT
1 TTTAATAAAATTTAATT
*
3190779 TTTATTAAAA-TTAATT
1 TTTAATAAAATTTAATT
3190795 AAAAATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATAAAATTTAATT
Found at i:3190815 original size:17 final size:18
Alignment explanation
Indices: 3190785--3190819 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
3190775 AATTTTTATT
3190785 AAAATTAATTAAAAATTAA
1 AAAATTAA-TAAAAATTAA
3190804 AAAATTAA-AAAAATTA
1 AAAATTAATAAAAATTA
3190820 GTTATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATTAATAAAAATTAA
Found at i:3191107 original size:21 final size:19
Alignment explanation
Indices: 3191082--3191120 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
3191072 ATAATTTTAA
3191082 AATTAATATAATATAAAAATT
1 AATTAA-ATAA-ATAAAAATT
*
3191103 AATTAAATTAATAAAAAT
1 AATTAAATAAATAAAAAT
3191121 AAATATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTAAATAAATAAAAATT
Found at i:3191141 original size:16 final size:17
Alignment explanation
Indices: 3191120--3191167 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
3191110 TTAATAAAAA
*
3191120 TAAATATTTTAAATT-T
1 TAAATATTATAAATTAT
*
3191136 TAAATAATATAAATTAT
1 TAAATATTATAAATTAT
3191153 TAATATATTA-AAATT
1 TAA-ATATTATAAATT
3191168 TATATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 13 0.48
17 9 0.33
18 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAATATTATAAATTAT
Found at i:3191163 original size:25 final size:25
Alignment explanation
Indices: 3191083--3191164 Score: 62
Period size: 25 Copynumber: 3.2 Consensus size: 25
3191073 TAATTTTAAA
* *
3191083 ATTAATATAATATAAA-AATTAATTAA
1 ATTAA-ATAATATAAATTATTAA-TAT
* *
3191109 ATT-AATAAAAATAAATATTTTAA-AT
1 ATTAAAT-AATATAAAT-TATTAATAT
*
3191134 TTTAAATAATATAAATTATTAATAT
1 ATTAAATAATATAAATTATTAATAT
3191159 ATTAAA
1 ATTAAA
3191165 ATTTATATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
24 7 0.16
25 26 0.60
26 6 0.14
27 4 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
ATTAAATAATATAAATTATTAATAT
Found at i:3193877 original size:2 final size:2
Alignment explanation
Indices: 3193870--3193895 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3193860 TGAACGAGCC
3193870 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
3193896 GTTTAGACCA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3195777 original size:2 final size:2
Alignment explanation
Indices: 3195770--3195796 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3195760 AAAGAGAAGT
3195770 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 T
3195797 GTATGTATGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3195801 original size:4 final size:4
Alignment explanation
Indices: 3195794--3195826 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
3195784 TATATATATA
*
3195794 TATG TATG TATG TATG CATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG T
3195827 CATCAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.24, C:0.03, G:0.24, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:3198885 original size:2 final size:2
Alignment explanation
Indices: 3198878--3198918 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3198868 GTAGGAAGAT
*
3198878 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AA AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
3198919 GATATGGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3199560 original size:2 final size:2
Alignment explanation
Indices: 3199553--3199581 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3199543 TCAATCAGAA
3199553 TC 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 TC T
3199582 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3199586 original size:2 final size:2
Alignment explanation
Indices: 3199581--3199613 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3199571 TCTCTCTCTC
3199581 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
3199614 TTTAAATTAT
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:3200686 original size:21 final size:21
Alignment explanation
Indices: 3200656--3200720 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
3200646 AATTTTTTTG
*
3200656 ATTAATTTAATTATAATTATA
1 ATTAAATTAATTATAATTATA
* *
3200677 ATTAAATTAATTA-AATAATT
1 ATTAAATTAATTATAATTATA
*
3200697 ATTTAATTATATT-TAAATTATA
1 ATTAAATTA-ATTAT-AATTATA
3200719 AT
1 AT
3200721 ATTTTTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
20 13 0.37
21 15 0.43
22 7 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTAAATTAATTATAATTATA
Found at i:3208783 original size:2 final size:2
Alignment explanation
Indices: 3208776--3208804 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3208766 GTGTAAAAAG
3208776 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
3208805 GACCCCAAAC
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3208900 original size:2 final size:2
Alignment explanation
Indices: 3208893--3208923 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3208883 TTTGCAATTT
3208893 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 T
3208924 GCAATTAATG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3209150 original size:25 final size:25
Alignment explanation
Indices: 3209116--3209170 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
3209106 ATGATCGAAA
*
3209116 TGAATTGAATTGGTAAAAATTGAGT
1 TGAATTGAATCGGTAAAAATTGAGT
3209141 TGAATTGAATCGGTAAAAATTGAGT
1 TGAATTGAATCGGTAAAAATTGAGT
3209166 TGAAT
1 TGAAT
3209171 ATTACTGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.35
Consensus pattern (25 bp):
TGAATTGAATCGGTAAAAATTGAGT
Found at i:3210102 original size:19 final size:19
Alignment explanation
Indices: 3210080--3210116 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3210070 TATTACTAAT
*
3210080 TTATCTGATAATTATTTTA
1 TTATATGATAATTATTTTA
*
3210099 TTATATTATAATTATTTT
1 TTATATGATAATTATTTT
3210117 TAAAATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTATATGATAATTATTTTA
Found at i:3210139 original size:27 final size:31
Alignment explanation
Indices: 3210092--3210153 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 31
3210082 ATCTGATAAT
3210092 TATTTTATTATATTATAATTATTTTTAAA-A
1 TATTTTATTATATTATAATTATTTTTAAATA
3210122 TATTTTATT-T-TTAT-ATTATTTTTAAATA
1 TATTTTATTATATTATAATTATTTTTAAATA
3210150 TATT
1 TATT
3210154 AATAATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 12 0.39
28 9 0.29
29 1 0.03
30 9 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (31 bp):
TATTTTATTATATTATAATTATTTTTAAATA
Found at i:3210141 original size:16 final size:16
Alignment explanation
Indices: 3210099--3210143 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3210089 AATTATTTTA
*
3210099 TTATATTATAATTATTT
1 TTATATTAT-TTTATTT
* *
3210116 TTAAAATATTTTATTT
1 TTATATTATTTTATTT
3210132 TTATATTATTTT
1 TTATATTATTTT
3210144 TAAATATATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATATTATTTTATTT
Found at i:3210162 original size:28 final size:28
Alignment explanation
Indices: 3210100--3210163 Score: 71
Period size: 27 Copynumber: 2.3 Consensus size: 28
3210090 ATTATTTTAT
*
3210100 TATA-TTATAATTATTTTTAAAATATTT
1 TATATTTATAATTATTTTTAAAATATTA
*
3210127 TATTTTTAT-ATTATTTTTAAATATATTA
1 TATATTTATAATTATTTTTAAA-ATATTA
3210155 -ATAATTTAT
1 TAT-ATTTAT
3210164 GTAATAAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 17 0.55
28 14 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
TATATTTATAATTATTTTTAAAATATTA
Found at i:3213033 original size:20 final size:19
Alignment explanation
Indices: 3212983--3213033 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
3212973 GTAATTTTAT
* *
3212983 TTTATTTTATTTTTATAAT
1 TTTATTTAATTTTTATAAA
*
3213002 TTTAATTAAATTTTTATATAA
1 TTT-ATTTAATTTTTATA-AA
3213023 TTTATTTAATT
1 TTTATTTAATT
3213034 AAGTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 3 0.12
20 19 0.73
21 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATTTAATTTTTATAAA
Found at i:3213560 original size:2 final size:2
Alignment explanation
Indices: 3213553--3213579 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3213543 GATTAATTTT
3213553 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 T
3213580 GAAATAAACA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3214246 original size:17 final size:17
Alignment explanation
Indices: 3214215--3214248 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3214205 TATTATAATT
**
3214215 TAAATTTAATTAATTAA
1 TAAATTTAAAAAATTAA
3214232 TAAATTTAAAAAATTAA
1 TAAATTTAAAAAATTAA
3214249 ATTAAATTTT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAAAAATTAA
Found at i:3214651 original size:15 final size:15
Alignment explanation
Indices: 3214631--3214668 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
3214621 TTTTAATAAC
3214631 TTTATATATATTATA
1 TTTATATATATTATA
3214646 TTTATATA-ATTATA
1 TTTATATATATTATA
3214660 TTTA-ATATA
1 TTTATATATA
3214669 GTCAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 11 0.50
15 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTATATATATTATA
Found at i:3214658 original size:23 final size:24
Alignment explanation
Indices: 3214599--3214660 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
3214589 ATATTTTTAA
*
3214599 AATATACTTACATAATATTATATTTT
1 AATA-ACTTATAT-ATATTATATTTT
3214625 AATAACTTTATATATATTATA-TTT
1 AATAAC-TTATATATATTATATTTT
3214649 ATATAA-TTATAT
1 A-ATAACTTATAT
3214661 TTAATATAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
23 6 0.18
24 4 0.12
25 14 0.42
26 9 0.27
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (24 bp):
AATAACTTATATATATTATATTTT
Found at i:3214900 original size:21 final size:20
Alignment explanation
Indices: 3214868--3214907 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3214858 AATTTAAAAA
*
3214868 TTTATATATTTATTTTATAT
1 TTTATATATTTATATTATAT
*
3214888 TTTATTATTTTTATATTATA
1 TTTA-TATATTTATATTATA
3214908 ATAATGTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTATATATTTATATTATAT
Found at i:3216278 original size:15 final size:16
Alignment explanation
Indices: 3216248--3216283 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
3216238 AAGTAATAAT
3216248 TTAAATATATATTATA
1 TTAAATATATATTATA
3216264 TTAAATATA-ATTATA
1 TTAAATATATATTATA
3216279 TTAAA
1 TTAAA
3216284 AAAACAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATATATATTATA
Found at i:3216977 original size:17 final size:17
Alignment explanation
Indices: 3216955--3217008 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
3216945 AAATAGATAA
3216955 TAAATAAATTTAAATTT
1 TAAATAAATTTAAATTT
*
3216972 TAAAT-AA-TTAAATAAAT
1 TAAATAAATTTAAAT--TT
3216989 TAAATAAATTTAAATTT
1 TAAATAAATTTAAATTT
3217006 TAA
1 TAA
3217009 TAATTCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 6 0.19
16 2 0.06
17 15 0.48
18 2 0.06
19 6 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATAAATTTAAATTT
Found at i:3216991 original size:9 final size:9
Alignment explanation
Indices: 3216971--3217003 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3216961 AATTTAAATT
3216971 TTAAAT-AA
1 TTAAATAAA
3216979 TTAAATAAA
1 TTAAATAAA
3216988 TTAAATAAA
1 TTAAATAAA
3216997 TTTAAAT
1 -TTAAAT
3217004 TTTAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 6 0.26
9 11 0.48
10 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TTAAATAAA
Found at i:3216996 original size:21 final size:21
Alignment explanation
Indices: 3216944--3216997 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 21
3216934 ATTAAAACAA
*
3216944 TAAATAGATAATAAATAAATT
1 TAAATAAATAATAAATAAATT
3216965 TAAATTTTAAATAATTAAATAAA-T
1 TAAA---TAAATAA-TAAATAAATT
3216989 TAAATAAAT
1 TAAATAAAT
3216998 TTAAATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
21 9 0.32
24 11 0.39
25 8 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAATAAATAATAAATAAATT
Found at i:3216998 original size:34 final size:32
Alignment explanation
Indices: 3216955--3217022 Score: 109
Period size: 34 Copynumber: 2.1 Consensus size: 32
3216945 AAATAGATAA
3216955 TAAATAAATTTAAATTTTAAATAATTAAATAAAT
1 TAAATAAATTTAAATTTT-AATAATTAAA-AAAT
*
3216989 TAAATAAATTTAAATTTTAATAATTCAAAAAT
1 TAAATAAATTTAAATTTTAATAATTAAAAAAT
3217021 TA
1 TA
3217023 TAATTATTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
32 6 0.18
33 9 0.27
34 18 0.55
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (32 bp):
TAAATAAATTTAAATTTTAATAATTAAAAAAT
Found at i:3218081 original size:16 final size:16
Alignment explanation
Indices: 3218060--3218100 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
3218050 ATATTACAGT
3218060 TATTTAATTTATAAAA
1 TATTTAATTTATAAAA
*
3218076 TATTTATTTTATAAAA
1 TATTTAATTTATAAAA
*
3218092 TAATTAATT
1 TATTTAATT
3218101 ATATTTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATTTAATTTATAAAA
Found at i:3218308 original size:16 final size:15
Alignment explanation
Indices: 3218283--3218317 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
3218273 TTTTTTTAAA
3218283 ATAATTTATTCTATT
1 ATAATTTATTCTATT
*
3218298 ATAATTTTATTTTATT
1 ATAA-TTTATTCTATT
3218314 ATAA
1 ATAA
3218318 AAAATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
ATAATTTATTCTATT
Found at i:3224322 original size:2 final size:2
Alignment explanation
Indices: 3224277--3224310 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3224267 TAATATTCAG
3224277 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
3224311 TTGCTCATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3229247 original size:9 final size:9
Alignment explanation
Indices: 3229235--3229330 Score: 76
Period size: 9 Copynumber: 10.7 Consensus size: 9
3229225 TCATTATAAT
3229235 AAATATATA
1 AAATATATA
3229244 AAATATA-A
1 AAATATATA
3229252 AAATACTATAAA
1 AAATA-TAT--A
3229264 AAATATATA
1 AAATATATA
*
3229273 AAATA-ACA
1 AAATATATA
3229281 TAAA-A-ATA
1 -AAATATATA
* *
3229289 ATATAAATA
1 AAATATATA
3229298 AAATATATA
1 AAATATATA
*
3229307 ATATATATA
1 AAATATATA
3229316 AACATAT-TA
1 AA-ATATATA
3229325 AAATAT
1 AAATAT
3229331 TTATAACATA
Statistics
Matches: 72, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
7 2 0.03
8 16 0.22
9 41 0.57
10 4 0.06
11 3 0.04
12 6 0.08
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (9 bp):
AAATATATA
Found at i:3229261 original size:11 final size:11
Alignment explanation
Indices: 3229247--3229295 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
3229237 ATATATAAAA
3229247 TATAAAAATAC
1 TATAAAAATAC
3229258 TATAAAAA-A-
1 TATAAAAATAC
3229267 TATATAAAATAAC
1 TATA-AAAAT-AC
*
3229280 -ATAAAAATAA
1 TATAAAAATAC
3229290 TATAAA
1 TATAAA
3229296 TAAAATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
9 4 0.12
10 6 0.19
11 18 0.56
12 4 0.12
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (11 bp):
TATAAAAATAC
Found at i:3229329 original size:20 final size:19
Alignment explanation
Indices: 3229237--3229336 Score: 77
Period size: 20 Copynumber: 5.4 Consensus size: 19
3229227 ATTATAATAA
*
3229237 ATATATAAAATATAAAAAT
1 ATATATAAAATATTAAAAT
*
3229256 ACTATAAAAAATATATAAAAT
1 A-TATATAAAATAT-TAAAAT
*
3229277 A-ACATAAAA-A-T--AAT
1 ATATATAAAATATTAAAAT
* *
3229291 ATAAATAAAATA-TATAAT
1 ATATATAAAATATTAAAAT
3229309 ATATATAAACATATTAAAAT
1 ATATATAAA-ATATTAAAAT
*
3229329 ATTTATAA
1 ATATATAA
3229337 CATAAATTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
14 4 0.06
15 7 0.11
16 3 0.05
18 12 0.18
19 10 0.15
20 23 0.35
21 6 0.09
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
ATATATAAAATATTAAAAT
Found at i:3231445 original size:9 final size:9
Alignment explanation
Indices: 3231433--3231462 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3231423 TTTAAATATA
3231433 TAAAAAAAT
1 TAAAAAAAT
3231442 TAAAAAAAT
1 TAAAAAAAT
3231451 T-AAAAAAT
1 TAAAAAAAT
3231459 TAAA
1 TAAA
3231463 TATATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:3232846 original size:2 final size:2
Alignment explanation
Indices: 3232839--3232872 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3232829 CCAATTTAGA
3232839 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3232873 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3238262 original size:12 final size:13
Alignment explanation
Indices: 3238230--3238261 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3238220 TGTGTGGGTA
3238230 AAAAAAATAATTT
1 AAAAAAATAATTT
*
3238243 AAAAAAATATTTT
1 AAAAAAATAATTT
3238256 AAAAAA
1 AAAAAA
3238262 TGAATAGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAAAATAATTT
Found at i:3238635 original size:9 final size:9
Alignment explanation
Indices: 3238623--3238647 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3238613 AAAAATTATA
3238623 AAATTAATT
1 AAATTAATT
3238632 AAATTAATT
1 AAATTAATT
3238641 AAATTAA
1 AAATTAA
3238648 ATCTGATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAATTAATT
Found at i:3245814 original size:38 final size:38
Alignment explanation
Indices: 3245772--3245848 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
3245762 AGGCATTCCC
3245772 AGATTTTCACTGTTACAGTATGTATTGGCATGAAACAA
1 AGATTTTCACTGTTACAGTATGTATTGGCATGAAACAA
3245810 AGATTTTCACTGTTACAGTATGTATTGGCATGAAACAA
1 AGATTTTCACTGTTACAGTATGTATTGGCATGAAACAA
3245848 A
1 A
3245849 ACTATCTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (38 bp):
AGATTTTCACTGTTACAGTATGTATTGGCATGAAACAA
Found at i:3247261 original size:2 final size:2
Alignment explanation
Indices: 3247256--3247283 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3247246 AAAAATCCAC
3247256 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
3247284 TACCTAGGGG
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:3247364 original size:2 final size:2
Alignment explanation
Indices: 3247357--3247393 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3247347 TTTAAAAAGA
*
3247357 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3247394 GCAGCTGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3249865 original size:2 final size:2
Alignment explanation
Indices: 3249858--3249885 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3249848 GGTAAGCATG
3249858 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
3249886 GGAATTTACT
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:3259709 original size:26 final size:26
Alignment explanation
Indices: 3259663--3259721 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
3259653 TATTATTTTA
3259663 TTATAATTATATTTAAAATATTATATAT
1 TTAT-ATTATATTTAAAATATTA-ATAT
*
3259691 TTATATTA-ATTTAATATATTAATAT
1 TTATATTATATTTAAAATATTAATAT
3259716 TT-TATT
1 TTATATT
3259722 TTTATAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 4 0.13
25 6 0.20
26 12 0.40
27 4 0.13
28 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTATATTATATTTAAAATATTAATAT
Found at i:3259942 original size:2 final size:2
Alignment explanation
Indices: 3259935--3259964 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3259925 TCGGTGAACG
3259935 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3259965 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3259969 original size:2 final size:2
Alignment explanation
Indices: 3259964--3259992 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3259954 ATATATATAT
3259964 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 A
3259993 AATCAAATAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3260331 original size:11 final size:11
Alignment explanation
Indices: 3260312--3260400 Score: 64
Period size: 11 Copynumber: 8.5 Consensus size: 11
3260302 AAATAAGATT
*
3260312 ATATGATATAA
1 ATATAATATAA
3260323 ATATAATATAA
1 ATATAATATAA
3260334 A-ATAAT-TAAA
1 ATATAATAT-AA
*
3260344 ATATAATAAAAA
1 ATATAAT-ATAA
* *
3260356 ATATAATGT-G
1 ATATAATATAA
*
3260366 ATAT-AT-GAA
1 ATATAATATAA
*
3260375 A-GTAATATAA
1 ATATAATATAA
3260385 ATATAATATAA
1 ATATAATATAA
3260396 ATATA
1 ATATA
3260401 TAAATATATC
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
8 1 0.02
9 6 0.10
10 15 0.25
11 29 0.48
12 9 0.15
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.34
Consensus pattern (11 bp):
ATATAATATAA
Found at i:3260401 original size:19 final size:19
Alignment explanation
Indices: 3260317--3260408 Score: 73
Period size: 21 Copynumber: 4.6 Consensus size: 19
3260307 AGATTATATG
3260317 ATATAAATATAATATAAA-
1 ATATAAATATAATATAAAT
*
3260335 ATAATTAAAATATAATA-AAAA
1 AT-A-T-AAATATAATATAAAT
*
3260356 ATAT-AATGTGATATATGAAAGT
1 ATATAAATAT-A-ATAT-AAA-T
3260378 AATATAAATATAATATAAAT
1 -ATATAAATATAATATAAAT
3260398 ATATAAATATA
1 ATATAAATATA
3260409 TCAAATTTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 21
0.71 0.04 0.25
Matches are distributed among these distances:
17 4 0.07
18 3 0.05
19 16 0.27
20 6 0.10
21 18 0.30
22 4 0.07
23 5 0.08
24 4 0.07
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (19 bp):
ATATAAATATAATATAAAT
Found at i:3260457 original size:31 final size:31
Alignment explanation
Indices: 3260385--3260461 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 31
3260375 AGTAATATAA
3260385 ATATAATATAAATATATAAATATATCAAATTT
1 ATATAA-ATAAATATATAAATATATCAAATTT
* * *
3260417 ATGTAAAATAAAT-TATTAATATATTAATATTT
1 ATAT-AAATAAATATATAAATATATCAA-ATTT
3260449 ATATAAATAAATA
1 ATATAAATAAATA
3260462 ATATTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
31 20 0.53
32 16 0.42
33 2 0.05
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (31 bp):
ATATAAATAAATATATAAATATATCAAATTT
Found at i:3261929 original size:14 final size:14
Alignment explanation
Indices: 3261910--3261936 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3261900 TACGATGTAT
3261910 ATTTAATTTTTTTA
1 ATTTAATTTTTTTA
3261924 ATTTAATTTTTTT
1 ATTTAATTTTTTT
3261937 TCTTTTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
ATTTAATTTTTTTA
Found at i:3264021 original size:5 final size:5
Alignment explanation
Indices: 3264013--3264042 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3264003 GTTCGATGAG
*
3264013 AATAG AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA
3264043 TTATATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:3264875 original size:2 final size:2
Alignment explanation
Indices: 3264868--3264895 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3264858 CAAGTCTGAG
3264868 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3264896 AAACTTATTC
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):
TA
Found at i:3265208 original size:20 final size:21
Alignment explanation
Indices: 3265146--3265226 Score: 82
Period size: 20 Copynumber: 4.1 Consensus size: 21
3265136 TGAAGGCTTA
*
3265146 TTTTATTATTTAAATTATAA-
1 TTTTATTATTTAAATAATAAT
** * *
3265166 -TAAAATATTTAAAT-ATTAT
1 TTTTATTATTTAAATAATAAT
3265185 TTTT-TTATTTAAATAATAAT
1 TTTTATTATTTAAATAATAAT
3265205 TTTTATTA-TTAAATAATAAT
1 TTTTATTATTTAAATAATAAT
3265225 TT
1 TT
3265227 ATATAAAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
18 3 0.06
19 20 0.41
20 23 0.47
21 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATTATTTAAATAATAAT
Found at i:3265235 original size:17 final size:19
Alignment explanation
Indices: 3265187--3265235 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
3265177 AATATTATTT
3265187 TTTTATT-T-AAATAATAA
1 TTTTATTATAAAATAATAA
*
3265204 TTTTTATTATTAAATAATAA
1 -TTTTATTATAAAATAATAA
3265224 -TTTA-TATAAAAT
1 TTTTATTATAAAAT
3265236 TAAATTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.25
18 11 0.39
19 1 0.04
20 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTATTATAAAATAATAA
Found at i:3271497 original size:21 final size:20
Alignment explanation
Indices: 3271457--3271498 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3271447 TAAATAACAC
*
3271457 TTTTTGAAAAATATTTTATA
1 TTTTTGAAAAATATTATATA
*
3271477 TTTTTTAAAAATATATATATA
1 TTTTTGAAAAATAT-TATATA
3271498 T
1 T
3271499 AAATTTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTTTGAAAAATATTATATA
Found at i:3274146 original size:16 final size:16
Alignment explanation
Indices: 3274103--3274148 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
3274093 ATAAGATATC
3274103 AATT-TTTTTAA-AAA
1 AATTATTTTTAACAAA
3274117 AATTATTTTT--CAAA
1 AATTATTTTTAACAAA
*
3274131 ATTTATTTTTAACAAA
1 AATTATTTTTAACAAA
3274147 AA
1 AA
3274149 CTAACCAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 16 0.62
15 5 0.19
16 5 0.19
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (16 bp):
AATTATTTTTAACAAA
Found at i:3282338 original size:2 final size:2
Alignment explanation
Indices: 3282333--3282366 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3282323 ATAGTTGGCT
*
3282333 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3282367 GAGAGAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3283720 original size:11 final size:11
Alignment explanation
Indices: 3283704--3283801 Score: 99
Period size: 11 Copynumber: 8.6 Consensus size: 11
3283694 ACTAAGTTAC
*
3283704 ATATTTATTTT
1 ATATTTATATT
3283715 ATATTTATATT
1 ATATTTATATT
*
3283726 ATTTTTTATATT
1 A-TATTTATATT
3283738 ATATTTATATT
1 ATATTTATATT
3283749 ATATTTTTATATT
1 ATA--TTTATATT
*
3283762 ATTTTTA-ATAT
1 ATATTTATAT-T
* *
3283773 ATTTTTATTTT
1 ATATTTATATT
*
3283784 ATAGTTATATT
1 ATATTTATATT
3283795 ATATTTA
1 ATATTTA
3283802 AAATTATAGT
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
10 2 0.03
11 50 0.68
12 11 0.15
13 10 0.14
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (11 bp):
ATATTTATATT
Found at i:3283773 original size:22 final size:24
Alignment explanation
Indices: 3283707--3283800 Score: 113
Period size: 23 Copynumber: 4.0 Consensus size: 24
3283697 AAGTTACATA
* *
3283707 TTTATTTTATATTTATATTAT-TT
1 TTTATATTATATTTATAATATATT
*
3283730 TTTATATTATATTTATATTATATT
1 TTTATATTATATTTATAATATATT
3283754 TTTATATTAT-TTT-TAATATATT
1 TTTATATTATATTTATAATATATT
* * *
3283776 TTTATTTTATAGTTATATTATATT
1 TTTATATTATATTTATAATATATT
3283800 T
1 T
3283801 AAAATTATAG
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
22 17 0.27
23 25 0.40
24 21 0.33
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (24 bp):
TTTATATTATATTTATAATATATT
Found at i:3283792 original size:33 final size:34
Alignment explanation
Indices: 3283707--3283802 Score: 122
Period size: 33 Copynumber: 2.8 Consensus size: 34
3283697 AAGTTACATA
3283707 TTTATTTTATATTTATATTATTTTTTATATTATATT
1 TTTATTTTATATTTATATTA-TTTTTA-ATTATATT
* * *
3283743 TATATTATATTTTTATATTATTTTTAA-TATATT
1 TTTATTTTATATTTATATTATTTTTAATTATATT
* *
3283776 TTTATTTTATAGTTATATTATATTTAA
1 TTTATTTTATATTTATATTATTTTTAA
3283803 AATTATAGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
33 28 0.54
34 1 0.02
35 6 0.12
36 17 0.33
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (34 bp):
TTTATTTTATATTTATATTATTTTTAATTATATT
Found at i:3286394 original size:2 final size:2
Alignment explanation
Indices: 3286387--3286413 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3286377 TGATCAAGGG
3286387 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 T
3286414 GTAATGTATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.