Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 9 of 29
Found at i:1218416 original size:19 final size:19
Alignment explanation
Indices: 1218373--1218409 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1218363 ATGTATTTAT
*
1218373 ATTATTTTTATATTATATA
1 ATTATTTTTATATCATATA
1218392 ATTATTTTTATATCATAT
1 ATTATTTTTATATCATAT
1218410 TTATATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTATTTTTATATCATATA
Found at i:1218838 original size:2 final size:2
Alignment explanation
Indices: 1218831--1218863 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1218821 TTTATTTCAA
1218831 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 C
1218864 CGTCCGAAGA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1222274 original size:4 final size:4
Alignment explanation
Indices: 1222265--1222304 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
1222255 ACATGTGGTG
1222265 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1222305 AATCAAAACG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:1229183 original size:14 final size:15
Alignment explanation
Indices: 1229157--1229197 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1229147 TAAAGATAAA
1229157 AAAATTATAAATATT
1 AAAATTATAAATATT
1229172 AAAATT-TAAATA-T
1 AAAATTATAAATATT
*
1229185 AAATTTACTAAAT
1 AAAATTA-TAAAT
1229198 GTTACATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 6 0.26
14 6 0.26
15 11 0.48
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATTATAAATATT
Found at i:1230551 original size:12 final size:12
Alignment explanation
Indices: 1230534--1230560 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1230524 AATAATTTTT
1230534 TTTAAAAAAATA
1 TTTAAAAAAATA
1230546 TTTAAAAAAATA
1 TTTAAAAAAATA
1230558 TTT
1 TTT
1230561 TTTGAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TTTAAAAAAATA
Found at i:1230561 original size:27 final size:27
Alignment explanation
Indices: 1230521--1230593 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
1230511 CTAATCAACG
*
1230521 AAAAATAATTTTTTTTAAAAAAATATT-T
1 AAAAA-AATATTTTTTAAAAAAAT-TTAT
*
1230549 AAAAAAATATTTTTTGAAAAAATTTAT
1 AAAAAAATATTTTTTAAAAAAATTTAT
* * *
1230576 AATAATATAATTTTTAAA
1 AAAAAAATATTTTTTAAA
1230594 TTGAAATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 2 0.05
27 31 0.82
28 5 0.13
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (27 bp):
AAAAAAATATTTTTTAAAAAAATTTAT
Found at i:1230674 original size:14 final size:14
Alignment explanation
Indices: 1230634--1230720 Score: 60
Period size: 14 Copynumber: 6.4 Consensus size: 14
1230624 TATTATTAAA
*
1230634 AATATTTAATTTTT
1 AATATTAAATTTTT
1230648 AATATTAAA-----
1 AATATTAAATTTTT
*
1230657 AATATTAAATTATT
1 AATATTAAATTTTT
*
1230671 AATATAAAATAATTTT
1 AATATTAAAT--TTTT
1230687 AATATTATAATTTTT
1 AATATTA-AATTTTT
*
1230702 AATATTTACA-TTTT
1 AATA-TTAAATTTTT
1230716 AATAT
1 AATAT
1230721 GATTAAACAT
Statistics
Matches: 59, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
9 9 0.15
13 1 0.02
14 25 0.42
15 9 0.15
16 12 0.20
17 3 0.05
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (14 bp):
AATATTAAATTTTT
Found at i:1230692 original size:22 final size:23
Alignment explanation
Indices: 1230616--1230693 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
1230606 TTAATTTGAG
* *
1230616 TTAAATATTATTATTAAAAATAT
1 TTAATTATTAATATTAAAAATAT
*
1230639 TTAATTTTTAATATTAAAAATAT
1 TTAATTATTAATATTAAAAATAT
* *
1230662 TAAATTATTAATATAAAATAAT-T
1 TTAATTATTAATATTAAA-AATAT
1230685 TTAA-TATTA
1 TTAATTATTA
1230694 TAATTTTTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
22 5 0.11
23 39 0.83
24 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAATTATTAATATTAAAAATAT
Found at i:1231130 original size:26 final size:25
Alignment explanation
Indices: 1231077--1231134 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
1231067 TTAAGTATTT
***
1231077 AATATTAATATAATATTTAGTTTTA
1 AATATTAATATAATATTTAGTACAA
1231102 AATATTAATATAATATTTTAGTACAA
1 AATATTAATATAATA-TTTAGTACAA
1231128 AATATTA
1 AATATTA
1231135 TTATTAAAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 15 0.52
26 14 0.48
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (25 bp):
AATATTAATATAATATTTAGTACAA
Found at i:1231168 original size:6 final size:6
Alignment explanation
Indices: 1231157--1231197 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
1231147 TACTATTGGT
*
1231157 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA GTATT
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATT
1231198 GCTTTTTGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (6 bp):
ATATTA
Found at i:1231637 original size:16 final size:15
Alignment explanation
Indices: 1231618--1231677 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 15
1231608 TCAAAATTAT
*
1231618 TCGAATTCGAGAAAAC
1 TCGAACTCGA-AAAAC
*
1231634 TCGAACCCGAAAAAGC
1 TCGAACTCGAAAAA-C
1231650 TCGAACTCGAAAAAAC
1 TCGAACTCG-AAAAAC
* *
1231666 TTGAACCCGAAA
1 TCGAACTCGAAA
1231678 GAATTCGAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
15 7 0.19
16 25 0.68
17 5 0.14
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (15 bp):
TCGAACTCGAAAAAC
Found at i:1231686 original size:32 final size:31
Alignment explanation
Indices: 1231616--1231686 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 31
1231606 ATTCAAAATT
* *
1231616 ATTCGAATTCGAGAAAACTCGAACCCGAAAA
1 ATTCGAACTCGAAAAAACTCGAACCCGAAAA
* *
1231647 AGCTCGAACTCGAAAAAACTTGAACCCGAAAGA
1 A-TTCGAACTCGAAAAAACTCGAACCCGAAA-A
1231680 ATTCGAA
1 ATTCGAA
1231687 TCCGAAGGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
31 1 0.03
32 30 0.91
33 2 0.06
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (31 bp):
ATTCGAACTCGAAAAAACTCGAACCCGAAAA
Found at i:1231691 original size:16 final size:16
Alignment explanation
Indices: 1231668--1231707 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1231658 GAAAAAACTT
*
1231668 GAACCCGAAAGAATTC
1 GAACCCGAAAGAATCC
* *
1231684 GAATCCGAAGGAATCC
1 GAACCCGAAAGAATCC
1231700 GAACCCGA
1 GAACCCGA
1231708 GACCGACTCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.40, C:0.28, G:0.23, T:0.10
Consensus pattern (16 bp):
GAACCCGAAAGAATCC
Found at i:1232402 original size:8 final size:8
Alignment explanation
Indices: 1232391--1232428 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
1232381 GAAAAATACA
1232391 AAAAAAAC
1 AAAAAAAC
1232399 AAAAAAA-
1 AAAAAAAC
*
1232406 ATAAAAAC
1 AAAAAAAC
*
1232414 AAAAAAAT
1 AAAAAAAC
1232422 AAAAAAA
1 AAAAAAA
1232429 AGAGTGAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.89, C:0.05, G:0.00, T:0.05
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1232407 original size:20 final size:20
Alignment explanation
Indices: 1232382--1232426 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
1232372 GCTTATTTTG
1232382 AAAAATACAAAA-AAAACAAA-
1 AAAAATA-AAAACAAAA-AAAT
1232402 AAAAATAAAAACAAAAAAAT
1 AAAAATAAAAACAAAAAAAT
1232422 AAAAA
1 AAAAA
1232427 AAAGAGTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.87, C:0.07, G:0.00, T:0.07
Consensus pattern (20 bp):
AAAAATAAAAACAAAAAAAT
Found at i:1232416 original size:24 final size:24
Alignment explanation
Indices: 1232383--1232429 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1232373 CTTATTTTGA
1232383 AAAATACAAAAAAAACAAAAAAAAT
1 AAAATAC-AAAAAAACAAAAAAAAT
*
1232408 AAAA-ACAAAAAAATAAAAAAAA
1 AAAATACAAAAAAACAAAAAAAA
1232430 GAGTGAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.71
24 2 0.10
25 4 0.19
ACGTcount: A:0.87, C:0.06, G:0.00, T:0.06
Consensus pattern (24 bp):
AAAATACAAAAAAACAAAAAAAAT
Found at i:1232417 original size:14 final size:15
Alignment explanation
Indices: 1232393--1232426 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
1232383 AAAATACAAA
1232393 AAAAACAAAAAAAAT
1 AAAAACAAAAAAAAT
1232408 AAAAAC-AAAAAAAT
1 AAAAACAAAAAAAAT
1232422 AAAAA
1 AAAAA
1232427 AAAGAGTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.88, C:0.06, G:0.00, T:0.06
Consensus pattern (15 bp):
AAAAACAAAAAAAAT
Found at i:1232427 original size:15 final size:14
Alignment explanation
Indices: 1232390--1232427 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
1232380 TGAAAAATAC
1232390 AAAAAAAACAAAAA
1 AAAAAAAACAAAAA
1232404 AAATAAAAACAAAAA
1 AAA-AAAAACAAAAA
1232419 AATAAAAAA
1 AA-AAAAAA
1232428 AAGAGTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 18 0.82
16 1 0.05
ACGTcount: A:0.89, C:0.05, G:0.00, T:0.05
Consensus pattern (14 bp):
AAAAAAAACAAAAA
Found at i:1235140 original size:16 final size:16
Alignment explanation
Indices: 1235096--1235142 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
1235086 CCCAAACTCG
*
1235096 AACGAACTCAAACCCA
1 AACGAACTCGAACCCA
*
1235112 AACGAGCTCGAACCCA
1 AACGAACTCGAACCCA
*
1235128 AACGAACTTGAACCC
1 AACGAACTCGAACCC
1235143 GAATGAATCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.43, C:0.36, G:0.13, T:0.09
Consensus pattern (16 bp):
AACGAACTCGAACCCA
Found at i:1235272 original size:23 final size:23
Alignment explanation
Indices: 1235246--1235295 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1235236 CATGCATATT
1235246 TTATGAAT-AAATTTATTTATAAA
1 TTAT-AATAAAATTTATTTATAAA
** *
1235269 TTATTTTAAAATTTATTTATAAT
1 TTATAATAAAATTTATTTATAAA
1235292 TTAT
1 TTAT
1235296 TTATTGTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTATAATAAAATTTATTTATAAA
Found at i:1235274 original size:11 final size:12
Alignment explanation
Indices: 1235252--1235299 Score: 66
Period size: 11 Copynumber: 4.2 Consensus size: 12
1235242 TATTTTATGA
1235252 ATAAATTTATTT
1 ATAAATTTATTT
1235264 ATAAA-TTATTT
1 ATAAATTTATTT
1235275 -TAAAATTTATTT
1 AT-AAATTTATTT
1235287 AT-AATTTATTT
1 ATAAATTTATTT
1235298 AT
1 AT
1235300 TGTTTAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
10 1 0.03
11 20 0.61
12 11 0.33
13 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATAAATTTATTT
Found at i:1235296 original size:23 final size:23
Alignment explanation
Indices: 1235254--1235297 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1235244 TTTTATGAAT
1235254 AAATTTATTTATAAATTATTTTA
1 AAATTTATTTATAAATTATTTTA
*
1235277 AAATTTATTTATAATTTATTT
1 AAATTTATTTATAAATTATTT
1235298 ATTGTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AAATTTATTTATAAATTATTTTA
Found at i:1235386 original size:40 final size:41
Alignment explanation
Indices: 1235310--1235396 Score: 99
Period size: 40 Copynumber: 2.1 Consensus size: 41
1235300 TGTTTAATTA
* *
1235310 TTATAATATAATCAATATTATTATTATTTATTTTATT-TAT
1 TTATAATATAATCAATAATATTATTATTTATATTATTCTAT
*
1235350 TTATAATATAATTAATAAATATT-TATATTT-TATTATTCTAT
1 TTATAATATAATCAAT-AATATTAT-TATTTATATTATTCTAT
*
1235391 ATATAA
1 TTATAA
1235397 AACTAACAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
40 22 0.55
41 18 0.45
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (41 bp):
TTATAATATAATCAATAATATTATTATTTATATTATTCTAT
Found at i:1235386 original size:45 final size:44
Alignment explanation
Indices: 1235282--1235386 Score: 101
Period size: 45 Copynumber: 2.4 Consensus size: 44
1235272 TTTTAAAATT
* * * *
1235282 TATTTATAATTTATT-TATTGTTTAATTATTATAATATAATCAA
1 TATTTATATTTTATTATTTTATTTAATTATTATAATATAATAAA
* *
1235325 TA-TTAT-TATTATTTATTTTATTTATTTATAATATAAT-TAATAAA
1 TATTTATATTTTA-TTATTTTATTTAATTAT--TATAATATAATAAA
1235369 TATTTATATTTTATTATT
1 TATTTATATTTTATTATT
1235387 CTATATATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
41 3 0.06
42 6 0.12
43 13 0.27
44 8 0.16
45 15 0.31
46 4 0.08
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (44 bp):
TATTTATATTTTATTATTTTATTTAATTATTATAATATAATAAA
Found at i:1235749 original size:11 final size:12
Alignment explanation
Indices: 1235707--1235773 Score: 61
Period size: 11 Copynumber: 5.8 Consensus size: 12
1235697 TTATACATTA
*
1235707 ATATCATATTTAT
1 ATATTATATTT-T
*
1235720 ATATT-TGATATT
1 ATATTAT-ATTTT
*
1235732 AAATTATATTTT
1 ATATTATATTTT
1235744 A-ATTAT-TTTT
1 ATATTATATTTT
1235754 ATATTATA-TTT
1 ATATTATATTTT
1235765 ATATTATAT
1 ATATTATAT
1235774 AATATCACCA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
10 5 0.11
11 21 0.47
12 11 0.24
13 8 0.18
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (12 bp):
ATATTATATTTT
Found at i:1235970 original size:20 final size:19
Alignment explanation
Indices: 1235924--1235971 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1235914 GTTTTAAAAT
1235924 TTAT-ATATTTTAAATAAA
1 TTATAATATTTTAAATAAA
*
1235942 TATAAAATATTTTAAATATAA
1 T-TATAATATTTTAAATA-AA
1235963 TTATAATAT
1 TTATAATAT
1235972 AATAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 1 0.04
19 2 0.08
20 19 0.76
21 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTATAATATTTTAAATAAA
Found at i:1236945 original size:2 final size:2
Alignment explanation
Indices: 1236938--1236971 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1236928 TTTATTTGTC
1236938 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
1236972 TCTGAACTGT
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:1243682 original size:8 final size:9
Alignment explanation
Indices: 1243652--1243689 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
1243642 TTTAAATATA
1243652 TTTATATTAT
1 TTTATATT-T
1243662 GTTTATATTT
1 -TTTATATTT
1243672 TTTAT-TTT
1 TTTATATTT
1243680 TTTATATTT
1 TTTATATTT
1243689 T
1 T
1243690 ATCTAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 8 0.31
9 9 0.35
10 1 0.04
11 8 0.31
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTATATTT
Found at i:1243689 original size:15 final size:18
Alignment explanation
Indices: 1243647--1243691 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 18
1243637 TTTTATTTAA
1243647 ATATATTTATATTATGTTT
1 ATATATTT-TATTATGTTT
*
1243666 ATATTTTTTATT-T-TTT
1 ATATATTTTATTATGTTT
1243682 -TATATTTTAT
1 ATATATTTTAT
1243692 CTAAAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 9 0.38
16 3 0.12
17 1 0.04
18 4 0.17
19 7 0.29
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
ATATATTTTATTATGTTT
Found at i:1249033 original size:22 final size:22
Alignment explanation
Indices: 1248990--1249057 Score: 55
Period size: 22 Copynumber: 2.9 Consensus size: 22
1248980 TAAAATTACT
* *
1248990 ATTTAATAATAAAAATTTTATTTGA
1 ATTTAATTATAAAAA---TATTTAA
1249015 ATTTAATTATAAAAATATTTAA
1 ATTTAATTATAAAAATATTTAA
* * *
1249037 ATATATTTAAAAACAATATTT
1 ATTTAATTATAAA-AATATTT
1249058 TTATAGCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 16 0.43
23 7 0.19
25 14 0.38
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (22 bp):
ATTTAATTATAAAAATATTTAA
Found at i:1249044 original size:26 final size:26
Alignment explanation
Indices: 1248989--1249046 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
1248979 TTAAAATTAC
**
1248989 TATTTAATAATAAAAATTTTATTTGA
1 TATTTAATAATAAAAATTTTAAATGA
*
1249015 -ATTTAATTATAAAAATATTTAAAT-A
1 TATTTAATAATAAAAAT-TTTAAATGA
1249040 TATTTAA
1 TATTTAA
1249047 AAACAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TATTTAATAATAAAAATTTTAAATGA
Found at i:1249241 original size:30 final size:31
Alignment explanation
Indices: 1249206--1249264 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1249196 TGTTATATTT
1249206 TTATCTATT-ACTTTTAAAAATTACATTTTA
1 TTATCTATTAACTTTTAAAAATTACATTTTA
* *
1249236 TTATCTTTTAACTTTTAAAAATTATATTT
1 TTATCTATTAACTTTTAAAAATTACATTT
1249265 AACATTCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (31 bp):
TTATCTATTAACTTTTAAAAATTACATTTTA
Found at i:1252567 original size:69 final size:69
Alignment explanation
Indices: 1252456--1252596 Score: 246
Period size: 69 Copynumber: 2.0 Consensus size: 69
1252446 CACCAAGTCC
*
1252456 ATGTGAAACGAACAAAAAACTAAGAGAAAGAGACTATCTATTTTCTATAACTGGAGACATAAATG
1 ATGTGAAACGAACAAAAAACTAAGAGAAAGAGACTATCTATTTTCTATAACTGGAAACATAAATG
1252521 TATT
66 TATT
* * *
1252525 ATGTGAAATGAACAAAAAACTAATAGAAAGAGACTATTTATTTTCTATAACTGGAAACATAAATG
1 ATGTGAAACGAACAAAAAACTAAGAGAAAGAGACTATCTATTTTCTATAACTGGAAACATAAATG
1252590 TATT
66 TATT
1252594 ATG
1 ATG
1252597 GTTAAAGTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (69 bp):
ATGTGAAACGAACAAAAAACTAAGAGAAAGAGACTATCTATTTTCTATAACTGGAAACATAAATG
TATT
Found at i:1257758 original size:2 final size:2
Alignment explanation
Indices: 1257746--1257786 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1257736 AACTTTTAAA
*
1257746 AT AT AT GT AT AT 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 AT AT AT AT AT AT A
1257787 AAAGAGTAAA
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:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1257913 original size:75 final size:75
Alignment explanation
Indices: 1257788--1257928 Score: 255
Period size: 75 Copynumber: 1.9 Consensus size: 75
1257778 ATATATATAA
*
1257788 AAGAGTAAAGTTTTAATCTATGCAATGAAGTAACAAAAAGCAAAAGGTTCAATTTTTAGGCCGAG
1 AAGAGTAAAGTTTTAATCTATGCAATGAAGTAACAAAAAGCAAAAAGTTCAATTTTTAGGCCGAG
1257853 TATTTATTGT
66 TATTTATTGT
* *
1257863 AAGAGTAAAGTTTTAATCTATGCAATGAAGTAACGAGAAGCAAAAAGTTCAATTTTTAGGCCGAG
1 AAGAGTAAAGTTTTAATCTATGCAATGAAGTAACAAAAAGCAAAAAGTTCAATTTTTAGGCCGAG
1257928 T
66 T
1257929 TTTTTTTTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 63 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (75 bp):
AAGAGTAAAGTTTTAATCTATGCAATGAAGTAACAAAAAGCAAAAAGTTCAATTTTTAGGCCGAG
TATTTATTGT
Found at i:1259118 original size:22 final size:22
Alignment explanation
Indices: 1259092--1259151 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 22
1259082 TTATATTTAA
1259092 TATATTATTTTTAATTAAAAAT
1 TATATTATTTTTAATTAAAAAT
* *
1259114 TATA-TATTTTTTA-TAAATAT
1 TATATTATTTTTAATTAAAAAT
1259134 TAT-TTATTGATTTAATTA
1 TATATTATT--TTTAATTA
1259152 GAGTTTAGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 13 0.42
21 8 0.26
22 8 0.26
23 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TATATTATTTTTAATTAAAAAT
Found at i:1259120 original size:33 final size:31
Alignment explanation
Indices: 1259054--1259122 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 31
1259044 TTTGCACAAT
*
1259054 TATTTAATTATTATTTTAAAAAATAATTTTA
1 TATTTAATTATTATTTTAAAAAATAATTATA
*
1259085 TATTTAATATATTATTTTTAATTAAA-AATTATA
1 TATTTAAT-TATTA-TTTTAA-AAAATAATTATA
1259118 TATTT
1 TATTT
1259123 TTTATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 8 0.24
32 5 0.15
33 17 0.52
34 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
TATTTAATTATTATTTTAAAAAATAATTATA
Found at i:1261663 original size:16 final size:17
Alignment explanation
Indices: 1261642--1261676 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1261632 AGTTCAAATT
*
1261642 AAAACTTG-CTATATCC
1 AAAACTTGACTAGATCC
1261658 AAAACTTGACTAGATCC
1 AAAACTTGACTAGATCC
1261675 AA
1 AA
1261677 TAGCTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (17 bp):
AAAACTTGACTAGATCC
Found at i:1267734 original size:27 final size:29
Alignment explanation
Indices: 1267689--1267744 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
1267679 ATATAAATAT
* *
1267689 TAAAAATATGTCAAGTTATTAAAATTTAA
1 TAAAAATATGTCAAATTATTAAAAATTAA
1267718 TAAAAATAT-T-AAATTATTAAAAATTAA
1 TAAAAATATGTCAAATTATTAAAAATTAA
1267745 ATTTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.60
28 1 0.04
29 9 0.36
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (29 bp):
TAAAAATATGTCAAATTATTAAAAATTAA
Found at i:1267755 original size:15 final size:16
Alignment explanation
Indices: 1267718--1267756 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
1267708 TAAAATTTAA
1267718 TAAAAATATTAAATTAT
1 TAAAAA-ATTAAATTAT
1267735 T-AAAAATTAAATT-T
1 TAAAAAATTAAATTAT
1267749 TAAAAAAT
1 TAAAAAAT
1267757 ATATTTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 2 0.10
15 14 0.67
16 4 0.19
17 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAAAATTAAATTAT
Found at i:1270455 original size:11 final size:11
Alignment explanation
Indices: 1270435--1270467 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1270425 AATTTGGTAA
1270435 TTTA-TATATT
1 TTTATTATATT
1270445 TTTATTATATT
1 TTTATTATATT
*
1270456 TTAATTATATT
1 TTTATTATATT
1270467 T
1 T
1270468 AAAATATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTATTATATT
Found at i:1271819 original size:14 final size:13
Alignment explanation
Indices: 1271800--1271837 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1271790 ACTCTTAATC
1271800 TAATTTTATATTT
1 TAATTTTATATTT
1271813 ATAATTTTA-ATTT
1 -TAATTTTATATTT
*
1271826 TAATTTTTTATT
1 TAATTTTATATT
1271838 ATTTTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 7 0.32
13 7 0.32
14 8 0.36
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TAATTTTATATTT
Found at i:1272065 original size:12 final size:12
Alignment explanation
Indices: 1272048--1272082 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1272038 ATTATAAATA
1272048 TAAATATTATTT
1 TAAATATTATTT
*
1272060 TTAATATTATTT
1 TAAATATTATTT
1272072 TAAATAATTAT
1 TAAAT-ATTAT
1272083 ATAAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TAAATATTATTT
Found at i:1272652 original size:25 final size:25
Alignment explanation
Indices: 1272603--1272662 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
1272593 TTATAAATAA
**
1272603 TTTTATTT-TAAATAAAATATTATT
1 TTTTATTTATAAATAAAATAAAATT
*
1272627 TTTTATTTATAAATAATATAAAATT
1 TTTTATTTATAAATAAAATAAAATT
*
1272652 TTATATATTAT
1 TTTTAT-TTAT
1272663 TAATTAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 8 0.27
25 18 0.60
26 4 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTTATTTATAAATAAAATAAAATT
Found at i:1273290 original size:14 final size:14
Alignment explanation
Indices: 1273266--1273315 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1273256 ATATAAATAT
1273266 AATAT-TTATATTA
1 AATATATTATATTA
*
1273279 AATATATTATATTT
1 AATATATTATATTA
* *
1273293 ATTATATTAAATTTA
1 AATATATTATA-TTA
1273308 AAT-TATTA
1 AATATATTA
1273316 AATCTCTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 5 0.17
14 21 0.70
15 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATATATTATATTA
Found at i:1274088 original size:20 final size:20
Alignment explanation
Indices: 1274065--1274104 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1274055 TAATTAAAAT
*
1274065 TTTATTTTTTAAAAATTTAA
1 TTTAATTTTTAAAAATTTAA
*
1274085 TTTAATTTTTAAAATTTTAA
1 TTTAATTTTTAAAAATTTAA
1274105 AAAGATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTAATTTTTAAAAATTTAA
Found at i:1275262 original size:91 final size:90
Alignment explanation
Indices: 1275158--1275339 Score: 301
Period size: 91 Copynumber: 2.0 Consensus size: 90
1275148 TAATAACTTA
* **
1275158 ACTCTTAAAATCTATTTATATAAATTTTCTGTAAAAACTAAATTTATCTATAAATTGAGCTACAT
1 ACTCTTAAAATCTATTTATATAAATTCTCTGTAAAAACTAAATTTATCTATAAATCAAGCTACAT
* *
1275223 GCACAACTCAGATAAGTTTAATATGC
66 ACACAACTC-GATAAGTTCAATATGC
*
1275249 ACTCTTAAAATCTATTTATATAAATTCTCTGTAAAAACTAAATTTATCTATAGATCAAGCTACAT
1 ACTCTTAAAATCTATTTATATAAATTCTCTGTAAAAACTAAATTTATCTATAAATCAAGCTACAT
1275314 ACACAACTCGATAAGTTCAATATGC
66 ACACAACTCGATAAGTTCAATATGC
1275339 A
1 A
1275340 TAAGCCAAGT
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
90 16 0.19
91 69 0.81
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (90 bp):
ACTCTTAAAATCTATTTATATAAATTCTCTGTAAAAACTAAATTTATCTATAAATCAAGCTACAT
ACACAACTCGATAAGTTCAATATGC
Found at i:1275461 original size:22 final size:22
Alignment explanation
Indices: 1275426--1275467 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1275416 TATTTTTATT
1275426 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
1275448 TAAATATTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
1275468 ATTTTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:1278551 original size:26 final size:26
Alignment explanation
Indices: 1278522--1278581 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
1278512 TAAAAGATTT
1278522 TTAATATTTATAAAAATTTAATTAAA
1 TTAATATTTATAAAAATTTAATTAAA
* *
1278548 TTAATAATTATATAAATTTAATTAAA
1 TTAATATTTATAAAAATTTAATTAAA
*
1278574 ATAATATT
1 TTAATATT
1278582 AAATAATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TTAATATTTATAAAAATTTAATTAAA
Found at i:1278631 original size:17 final size:18
Alignment explanation
Indices: 1278600--1278638 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1278590 ATTATTTATA
*
1278600 TAAATATTTTTTATAATT
1 TAAATATTTTATATAATT
1278618 TAAA-ATTTTATATAA-T
1 TAAATATTTTATATAATT
1278634 TAAAT
1 TAAAT
1278639 TTAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 5 0.26
17 10 0.53
18 4 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAAATATTTTATATAATT
Found at i:1278759 original size:21 final size:23
Alignment explanation
Indices: 1278702--1278760 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
1278692 AAACACAACA
1278702 TAAATATAATATGAAAAAATAAT
1 TAAATATAATATGAAAAAATAAT
1278725 TAAATATAATATGAAATAAA-AA-
1 TAAATATAATATGAAA-AAATAAT
*
1278747 T-AATATGATATGAA
1 TAAATATAATATGAA
1278761 TATATAAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.35
22 1 0.03
23 18 0.53
24 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.31
Consensus pattern (23 bp):
TAAATATAATATGAAAAAATAAT
Found at i:1279627 original size:21 final size:21
Alignment explanation
Indices: 1279598--1279640 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1279588 TATAATACTT
* *
1279598 TAAATAATAAAAATATATAAA
1 TAAAAAATAAAAACATATAAA
*
1279619 TAAAAAATATAAACATATAAA
1 TAAAAAATAAAAACATATAAA
1279640 T
1 T
1279641 TTTTTCTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAAAAATAAAAACATATAAA
Found at i:1282316 original size:12 final size:13
Alignment explanation
Indices: 1282299--1282327 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1282289 GTAAAAATCA
1282299 AAAATTAAAATT-
1 AAAATTAAAATTC
1282311 AAAATTAAAATTC
1 AAAATTAAAATTC
1282324 AAAA
1 AAAA
1282328 AAATAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAAATTC
Found at i:1283131 original size:36 final size:36
Alignment explanation
Indices: 1283070--1283139 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
1283060 CCAATATTGG
* ** *
1283070 CAGCGGCTTCCAGCAGCAGGGACGTTCAAAAAAATC
1 CAGCAGCTTCCAGCAGCAGCCACGTTAAAAAAAATC
*
1283106 CAGCAGCTTCCAGCAGCATCCACGTTAAAAAAAA
1 CAGCAGCTTCCAGCAGCAGCCACGTTAAAAAAAA
1283140 AAGCATAACG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.37, C:0.29, G:0.20, T:0.14
Consensus pattern (36 bp):
CAGCAGCTTCCAGCAGCAGCCACGTTAAAAAAAATC
Found at i:1283398 original size:240 final size:239
Alignment explanation
Indices: 1283127--1283605 Score: 904
Period size: 240 Copynumber: 2.0 Consensus size: 239
1283117 AGCAGCATCC
1283127 ACGTTAAAAAAAAAAGCATAACGGCAGCCTCCAATCCACGAACGATCCCGAACAGCTCAACAACC
1 ACGTTAAAAAAAAAAGCATAACGGCAGCCTCCAATCCACGAACGATCCCGAACAGCTCAACAACC
1283192 ACGAGCAGCCCCCCAACAGCTCATCCAACCTCCACGAGCTCTCAGCAGCTTGCAGTTCCAGCAGC
66 ACGAGCAGCCCCCCAACAGCTCATCCAACCTCCACGAGCTCTCAGCAGCTTGCAGTTCCAGCAGC
*
1283257 CAAAAGCAATGCCATCAGCAGCAACCAGTAGCATAGCAAGCAAGACAGCAGCTTCCACGAGCTCT
131 CAAAAGCAACGCCATCAGCAGCAACCAGTAGCATAGCAAGCAAGACAGCAGCTTCCACGAGCTCT
1283322 CAGCAGCTTGCAGTTCTAGCAGCCGAAAGCAACACCATCAGTAG
196 CAGCAGCTTGCAGTTCTAGCAGCCGAAAGCAACACCATCAGTAG
* * *
1283366 ACGTTAAAAAAAACAAGCATAACGGTAGCCTCCAATCCACGAACGATCCCGGACAGCTCAGCAAC
1 ACGTTAAAAAAAA-AAGCATAACGGCAGCCTCCAATCCACGAACGATCCCGAACAGCTCAACAAC
1283431 CACGAGCAGCCCCCCAACAGCTCATCCAACCTCCACGAGCTCTCAGCAGCTTGCAGTTCCAGCAG
65 CACGAGCAGCCCCCCAACAGCTCATCCAACCTCCACGAGCTCTCAGCAGCTTGCAGTTCCAGCAG
*
1283496 CCGAAAGCAACGCCATCAGCAGCAACCAGTAGCATAGCAAGCAAGACAGCAGCTTCCACGAGCTC
130 CCAAAAGCAACGCCATCAGCAGCAACCAGTAGCATAGCAAGCAAGACAGCAGCTTCCACGAGCTC
1283561 TCAGCAGCTTGCAGTTCTAGCAGCCGAAAGCAACACCATCAGTAG
195 TCAGCAGCTTGCAGTTCTAGCAGCCGAAAGCAACACCATCAGTAG
1283606 CAATAACAGC
Statistics
Matches: 234, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
239 13 0.06
240 221 0.94
ACGTcount: A:0.34, C:0.34, G:0.19, T:0.13
Consensus pattern (239 bp):
ACGTTAAAAAAAAAAGCATAACGGCAGCCTCCAATCCACGAACGATCCCGAACAGCTCAACAACC
ACGAGCAGCCCCCCAACAGCTCATCCAACCTCCACGAGCTCTCAGCAGCTTGCAGTTCCAGCAGC
CAAAAGCAACGCCATCAGCAGCAACCAGTAGCATAGCAAGCAAGACAGCAGCTTCCACGAGCTCT
CAGCAGCTTGCAGTTCTAGCAGCCGAAAGCAACACCATCAGTAG
Found at i:1289440 original size:22 final size:23
Alignment explanation
Indices: 1289396--1289440 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1289386 ATATTCATGA
* *
1289396 CATTCATTCATTATTTTCATAAT
1 CATTCATTCAGTATTTGCATAAT
*
1289419 CATTCA-TCAGTATTTGCTTAAT
1 CATTCATTCAGTATTTGCATAAT
1289441 TAATAAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (23 bp):
CATTCATTCAGTATTTGCATAAT
Found at i:1297687 original size:42 final size:42
Alignment explanation
Indices: 1297630--1298102 Score: 401
Period size: 42 Copynumber: 11.3 Consensus size: 42
1297620 CTTTTTTTTT
* * *
1297630 CCTTAGTCTGTCTGTCGGCTTTGACCTTGGAGACTTCTTTTC
1 CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTTTC
* *
1297672 CCTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTATC
1 CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTTTC
* * * *
1297715 CCTCAGTCTGCTTGTCGGCTTTGACCCTAGAGACTTTCCATT-
1 CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTTTC
* * *
1297757 CTTTAGTCTGCCTGTCGGTTTTGACCCTAGAGACTTTCC-TTC
1 CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTTTC
* ** * * **
1297799 CCTTAGTCTACCTGTTAGCTTCGTCCCTGGAGACAGCC--TC
1 CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTTTC
** * *
1297839 ATTTAAAATCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATC
1 CCTT--AGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTTTC
* * *
1297884 CCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCATT-
1 CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTTTC
* * * *
1297926 CTTTAGTCTGCCTATCAGCTTTGACCCTGGAGACTTTCTTTC
1 CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTTTC
* * * **
1297968 CCTTAGTCTACCTGTCGGC-TTCATCCCTAGAGAC-AGC---C
1 CCTTAGTCTGCCTGTCGGCTTTGA-CCCTGGAGACTTCCTTTC
* *
1298006 CCTTATGTTTGCCTATCGGCTTTGACCCTGGAGACTTTCCTTT-
1 CCTTA-GTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTTTC
* * * *
1298049 CCTTAGTCTACCTGTCGGCTTTGACTCTAGAGACTTTCTTTC
1 CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTTTC
*
1298091 CCTAAGTCTGCC
1 CCTTAGTCTGCC
1298103 CGTTGTTTAC
Statistics
Matches: 344, Mismatches: 70, Indels: 34
0.77 0.16 0.08
Matches are distributed among these distances:
38 6 0.02
39 20 0.06
40 7 0.02
41 20 0.06
42 205 0.60
43 83 0.24
45 3 0.01
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.37
Consensus pattern (42 bp):
CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTTTC
Found at i:1297909 original size:169 final size:166
Alignment explanation
Indices: 1297678--1298086 Score: 586
Period size: 169 Copynumber: 2.5 Consensus size: 166
1297668 TTTCCCTTAG
* *
1297678 TCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCTATCCCTCAGTCTGCTTGTCGGCTTTGACCCT
1 TCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCCTGTCGGCTTTGACCCT
* * *
1297743 AGAGACTTTCCATTCTTTAGTCTGCCTGTCGGTTTTGACCCTAGAGACTTTCCTTCCCTTAGTCT
66 AGAGACTTTCCATTCTTTAGTCTGCCTATCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCT
* * * *
1297808 ACCTGTTAGCTTCGTCCCTGGAGACAGCCTCATTTAAAA
131 ACCTGTCAGCTTCATCCCTAGAGACAGCC-C-CTT-AAA
*
1297847 TCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCCTGTCGGCTTTGACCTT
1 TCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCCTGTCGGCTTTGACCCT
* * *
1297912 GGAGACTTTCCATTCTTTAGTCTGCCTATCAGCTTTGACCCTGGAGACTTTCTTTCCCTTAGTCT
66 AGAGACTTTCCATTCTTTAGTCTGCCTATCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCT
* **
1297977 ACCTGTCGGCTTCATCCCTAGAGACAGCCCCTTATG
131 ACCTGTCAGCTTCATCCCTAGAGACAGCCCCTTAAA
* * * * * *
1298013 TTTGCCTATCGGCTTTGACCCTGGAGACTTTCCT-TTCCTTAGTCTACCTGTCGGCTTTGACTCT
1 TCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCCTGTCGGCTTTGACCCT
1298077 AGAGACTTTC
66 AGAGACTTTC
1298087 TTTCCCTAAG
Statistics
Matches: 216, Mismatches: 24, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
165 34 0.16
166 33 0.15
167 2 0.01
168 1 0.00
169 146 0.68
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.36
Consensus pattern (166 bp):
TCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCCTGTCGGCTTTGACCCT
AGAGACTTTCCATTCTTTAGTCTGCCTATCAGCTTTGACCCTAGAGACTTTCCTTCCCTTAGTCT
ACCTGTCAGCTTCATCCCTAGAGACAGCCCCTTAAA
Found at i:1297982 original size:127 final size:127
Alignment explanation
Indices: 1297630--1298102 Score: 464
Period size: 127 Copynumber: 3.8 Consensus size: 127
1297620 CTTTTTTTTT
* * * * *
1297630 CCTTAGTCTGTCTGTCGGCTTTGACCTTGGAGAC-TTCTTTTCCCTTAGTCTGCCTGTCGGCTTT
1 CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTTTCCCTTAGTCTACCTGTCAGCTTT
* * * * *
1297694 GACCTTGGAGACTTTCCTATCCCTCAGTCTGCTTGTCGGCTTTGACCCTAGAGACTTTCCATT
66 GACCCTGGAGACTTT-CTTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCATC
* * * * *
1297757 CTTTAGTCTGCCTGTCGGTTTTGACCCTAGAGACTTTCC-TTCCCTTAGTCTACCTGTTAGCTTC
1 CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTTTCCCTTAGTCTACCTGTCAGCTTT
* ** * ** * *
1297821 GTCCCTGGAGAC-AGC-CTCATTTAAAATCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATC
66 GACCCTGGAGACTTTCTTTCCCTT--AGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCC-ATC
* * * * * *
1297884 CCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCCATT-CTTTAGTCTGCCTATCAGCTTT
1 CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTTTCCCTTAGTCTACCTGTCAGCTTT
* * **
1297948 GACCCTGGAGACTTTCTTTCCCTTAGTCTACCTGTCGGC-TTCATCCCTAGAGAC--AGC--C
66 GACCCTGGAGACTTTCTTTCCCTTAGTCTGCCTGTCGGCTTTGA-CCCTAGAGACTTTCCATC
* * *
1298006 CCTTATGTTTGCCTATCGGCTTTGACCCTGGAGACTTTCCTTT-CCTTAGTCTACCTGTCGGCTT
1 CCTTA-GTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTTTCCCTTAGTCTACCTGTCAGCTT
* * *
1298070 TGACTCTAGAGACTTTCTTTCCCTAAGTCTGCC
65 TGACCCTGGAGACTTTCTTTCCCTTAGTCTGCC
1298103 CGTTGTTTAC
Statistics
Matches: 280, Mismatches: 57, Indels: 22
0.78 0.16 0.06
Matches are distributed among these distances:
122 5 0.02
123 79 0.28
124 3 0.01
125 2 0.01
126 35 0.12
127 146 0.52
128 6 0.02
129 4 0.01
ACGTcount: A:0.14, C:0.30, G:0.19, T:0.37
Consensus pattern (127 bp):
CCTTAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTTTCCCTTAGTCTACCTGTCAGCTTT
GACCCTGGAGACTTTCTTTCCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTCCATC
Found at i:1298405 original size:12 final size:13
Alignment explanation
Indices: 1298388--1298416 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1298378 GTAAAAATCA
1298388 AAAATTAAAATT-
1 AAAATTAAAATTC
1298400 AAAATTAAAATTC
1 AAAATTAAAATTC
1298413 AAAA
1 AAAA
1298417 AAAATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAAATTC
Found at i:1302868 original size:10 final size:10
Alignment explanation
Indices: 1302840--1302878 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
1302830 TATATATTCG
1302840 AAATATATTAA
1 AAATAT-TTAA
1302851 AAAT-TTTAA
1 AAATATTTAA
1302860 AAATATTTAA
1 AAATATTTAA
*
1302870 ATATATTTA
1 AAATATTTA
1302879 TATCAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 8 0.31
10 14 0.54
11 4 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AAATATTTAA
Found at i:1308904 original size:2 final size:2
Alignment explanation
Indices: 1308897--1308921 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1308887 GTATCTTTTC
1308897 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
1308922 GTTGTTATCA
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:1311809 original size:2 final size:2
Alignment explanation
Indices: 1311804--1311837 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1311794 ATCAAACCAA
*
1311804 AT AT AT AT AT AT AT TT 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
1311838 GGTTTGGTTT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1312080 original size:28 final size:30
Alignment explanation
Indices: 1312048--1312111 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
1312038 TCATATCATA
*
1312048 TTATTATCA-TTTTTAAAAAATTA-AATAT
1 TTATTATAATTTTTTAAAAAATTATAATAT
* *
1312076 TTATTA-AATTTTTTAATAAATTATTATAT
1 TTATTATAATTTTTTAAAAAATTATAATAT
1312105 TTATTAT
1 TTATTAT
1312112 TTAATTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 1 0.03
28 19 0.63
29 10 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (30 bp):
TTATTATAATTTTTTAAAAAATTATAATAT
Found at i:1312099 original size:20 final size:20
Alignment explanation
Indices: 1312076--1312121 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1312066 AATTAAATAT
*
1312076 TTATTAAATTTTTTAATAAA
1 TTATTAAATTTATTAATAAA
* * *
1312096 TTATTATATTTATTATTTAA
1 TTATTAAATTTATTAATAAA
1312116 TTATTA
1 TTATTA
1312122 TATCGATATA
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATTAAATTTATTAATAAA
Found at i:1315665 original size:22 final size:22
Alignment explanation
Indices: 1315615--1315665 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1315605 TATCAATTAA
*
1315615 AATATTAATAACTAATAATATT
1 AATATTAATAAATAATAATATT
* *
1315637 AAAATTATTAAATAATAATCA-T
1 AATATTAATAAATAATAAT-ATT
1315659 AATATTA
1 AATATTA
1315666 CATTATAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (22 bp):
AATATTAATAAATAATAATATT
Found at i:1315926 original size:8 final size:8
Alignment explanation
Indices: 1315913--1316078 Score: 70
Period size: 8 Copynumber: 19.6 Consensus size: 8
1315903 AAACTAAGCA
1315913 ATTTTTAT
1 ATTTTTAT
1315921 ATTTTTATT
1 ATTTTTA-T
*
1315930 ATATTTAT
1 ATTTTTAT
1315938 ATTATTT-T
1 ATT-TTTAT
*
1315946 A-TATTAT
1 ATTTTTAT
1315953 -TTTTATATT
1 ATTTT-TA-T
1315962 ATTTTTAT
1 ATTTTTAT
1315970 ATTTTTA-
1 ATTTTTAT
* *
1315977 ATATTAAT
1 ATTTTTAT
*
1315985 ATTTATTCAA
1 ATTT-TT-AT
1315995 ATTTTTAT
1 ATTTTTAT
* * *
1316003 ATATTAAA
1 ATTTTTAT
*
1316011 ATTATGATAT
1 ATT-T-TTAT
1316021 AATTTTTTAT
1 -A-TTTTTAT
*
1316031 ATATTTAT
1 ATTTTTAT
*
1316039 ATATTTAT
1 ATTTTTAT
1316047 ATTATATTAT
1 ATT-T-TTAT
*
1316057 ATTTTAATT
1 ATTTTTA-T
*
1316066 ATTTTTTT
1 ATTTTTAT
1316074 ATTTT
1 ATTTT
1316079 CATAATATAA
Statistics
Matches: 118, Mismatches: 23, Indels: 34
0.67 0.13 0.19
Matches are distributed among these distances:
6 2 0.02
7 9 0.08
8 57 0.48
9 26 0.22
10 20 0.17
11 2 0.02
12 2 0.02
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.66
Consensus pattern (8 bp):
ATTTTTAT
Found at i:1315933 original size:11 final size:10
Alignment explanation
Indices: 1315914--1315975 Score: 60
Period size: 10 Copynumber: 6.4 Consensus size: 10
1315904 AACTAAGCAA
1315914 TTTTTA-TA-
1 TTTTTATTAT
1315922 TTTTTATTAT
1 TTTTTATTAT
*
1315932 ATTTATATTAT
1 -TTTTTATTAT
*
1315943 TTTATATTAT
1 TTTTTATTAT
1315953 TTTTATATTA-
1 TTTT-TATTAT
1315963 TTTTTA-TAT
1 TTTTTATTAT
1315972 TTTT
1 TTTT
1315976 AATATTAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
8 8 0.17
9 8 0.17
10 17 0.36
11 14 0.30
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTTATTAT
Found at i:1315969 original size:27 final size:27
Alignment explanation
Indices: 1315915--1316070 Score: 90
Period size: 26 Copynumber: 6.1 Consensus size: 27
1315905 ACTAAGCAAT
1315915 TTTTATATTTTTATTATATTTATATTA
1 TTTTATATTTTTATTATATTTATATTA
1315942 TTTTATA---TTA-T-T-TTTATATTA
1 TTTTATATTTTTATTATATTTATATTA
*
1315963 TTTTTATATTTTTA--ATATTAATATT-
1 -TTTTATATTTTTATTATATTTATATTA
* * * *
1315988 TATTCAAATTTTTA-TATATTAAAATTA
1 T-TTTATATTTTTATTATATTTATATTA
**
1316015 TGATATAATTTTT-TATATATTTATA-TA
1 TTTTAT-ATTTTTAT-TATATTTATATTA
*
1316042 -TTTATA-TTATATTATATTT-TAATTA
1 TTTTATATTTTTATTATATTTAT-ATTA
1316067 TTTT
1 TTTT
1316071 TTTATTTTCA
Statistics
Matches: 100, Mismatches: 13, Indels: 33
0.68 0.09 0.23
Matches are distributed among these distances:
21 9 0.09
22 8 0.08
23 2 0.02
24 15 0.15
25 18 0.18
26 24 0.24
27 16 0.16
28 8 0.08
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.65
Consensus pattern (27 bp):
TTTTATATTTTTATTATATTTATATTA
Found at i:1315970 original size:38 final size:36
Alignment explanation
Indices: 1315914--1316075 Score: 137
Period size: 36 Copynumber: 4.4 Consensus size: 36
1315904 AACTAAGCAA
1315914 TTTTTATATTTTTATTATATTTATATTATTTTATATT
1 TTTTTATATTTTTA-TATATTTATATTATTTTATATT
* * * *
1315951 ATTTTTATATTATTTTTATATTTTTAATA-TTAATATT
1 -TTTTTATATT-TTTATATATTTATATTATTTTATATT
* * * * * ** *
1315988 TATTCAAATTTTTATATATTAAAATTATGATATAAT
1 TTTTTATATTTTTATATATTTATATTATTTTATATT
* *
1316024 TTTTTATATATTTATATATTTATATTATATTATATT
1 TTTTTATATTTTTATATATTTATATTATTTTATATT
* *
1316060 TTAATTATTTTTTTAT
1 TT-TTTATATTTTTAT
1316076 TTTCATAATA
Statistics
Matches: 93, Mismatches: 28, Indels: 7
0.73 0.22 0.05
Matches are distributed among these distances:
35 12 0.13
36 40 0.43
37 17 0.18
38 21 0.23
39 3 0.03
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (36 bp):
TTTTTATATTTTTATATATTTATATTATTTTATATT
Found at i:1315990 original size:32 final size:32
Alignment explanation
Indices: 1315917--1316069 Score: 108
Period size: 32 Copynumber: 4.9 Consensus size: 32
1315907 TAAGCAATTT
* *
1315917 TTATATTTTTATTATATTTATATTATTTTATA
1 TTATATTTATATTATATTTATATTATTTAATA
* *
1315949 TTATTTTTATATTATTTTTATATT-TTTAATA
1 TTATATTTATATTATATTTATATTATTTAATA
* * * *
1315980 TTAATATTTAT-TCAAATTTTTA-TATATTAAAA
1 TT-ATATTTATATTATATTTATATTAT-TTAATA
*
1316012 TTATGATATA-ATT-T-TTTATA-TATTTATATA
1 TTAT-ATTTATATTATATTTATATTATTTA-ATA
1316042 TT-TATATTATATTATATTT-TAATTATTT
1 TTATAT-TTATATTATATTTAT-ATTATTT
1316070 TTTTATTTTC
Statistics
Matches: 93, Mismatches: 16, Indels: 23
0.70 0.12 0.17
Matches are distributed among these distances:
28 2 0.02
29 6 0.06
30 16 0.17
31 20 0.22
32 44 0.47
33 5 0.05
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.64
Consensus pattern (32 bp):
TTATATTTATATTATATTTATATTATTTAATA
Found at i:1327103 original size:2 final size:2
Alignment explanation
Indices: 1327096--1327134 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1327086 TTATAGACTG
* *
1327096 AT AT AT AT AT AT AT AT AT GT 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 AT A
1327135 AAATTTTGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1327149 original size:21 final size:20
Alignment explanation
Indices: 1327123--1327175 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1327113 TGTATATATA
1327123 TATATATTTATAAAATTTTGT
1 TATATATTTATAAAATTTT-T
*
1327144 TATATATTT-GAAAATTTTT
1 TATATATTTATAAAATTTTT
* *
1327163 GATATATTAATAA
1 TATATATTTATAA
1327176 TTTTATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 8 0.30
20 10 0.37
21 9 0.33
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (20 bp):
TATATATTTATAAAATTTTT
Found at i:1327167 original size:19 final size:21
Alignment explanation
Indices: 1327124--1327170 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
1327114 GTATATATAT
* *
1327124 ATATATTTATAAAATTTTGTT
1 ATATATTTAGAAAATTTTGTG
1327145 ATATATTT-GAAAATTTT-TG
1 ATATATTTAGAAAATTTTGTG
1327164 ATATATT
1 ATATATT
1327171 AATAATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.33
20 8 0.33
21 8 0.33
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.55
Consensus pattern (21 bp):
ATATATTTAGAAAATTTTGTG
Found at i:1329865 original size:42 final size:42
Alignment explanation
Indices: 1329818--1329929 Score: 188
Period size: 44 Copynumber: 2.6 Consensus size: 42
1329808 CATTAATTTT
1329818 GCATAAGTGCATGTACACAGACAAAATTAACAACAAGCAAAA
1 GCATAAGTGCATGTACACAGACAAAATTAACAACAAGCAAAA
1329860 GCATAAGTGCATGTACACATAGACAAAATTAACAACAAGCAAAA
1 GCATAAGTGCATGTACAC--AGACAAAATTAACAACAAGCAAAA
* *
1329904 GCATAAATGCATGTACACAGAGAAAA
1 GCATAAGTGCATGTACACAGACAAAA
1329930 AACAATAGTT
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
42 25 0.38
44 41 0.62
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.15
Consensus pattern (42 bp):
GCATAAGTGCATGTACACAGACAAAATTAACAACAAGCAAAA
Found at i:1335244 original size:14 final size:14
Alignment explanation
Indices: 1335227--1335291 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
1335217 ATTTTTTATT
1335227 AATAAATATTTAAA
1 AATAAATATTTAAA
*
1335241 AATATATATTTAAA
1 AATAAATATTTAAA
* * * *
1335255 TATATATATATATA
1 AATAAATATTTAAA
*
1335269 TATAAAT-TTTAAA
1 AATAAATATTTAAA
1335282 AATTAAATAT
1 AA-TAAATAT
1335292 GTTATCTCAA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
13 5 0.12
14 35 0.85
15 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATAAATATTTAAA
Found at i:1335257 original size:10 final size:10
Alignment explanation
Indices: 1335228--1335275 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
1335218 TTTTTTATTA
*
1335228 ATAAATATTT
1 ATAAATATAT
*
1335238 AAAAATATAT
1 ATAAATATAT
1335248 ATTTAAATATAT
1 A--TAAATATAT
*
1335260 ATATATATAT
1 ATAAATATAT
1335270 ATAAAT
1 ATAAAT
1335276 TTTAAAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 22 0.71
12 9 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
ATAAATATAT
Found at i:1335729 original size:35 final size:34
Alignment explanation
Indices: 1335653--1335726 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 34
1335643 TATTTTTAAA
* * *
1335653 TTAAATATTAATATAAAATAATATTTTAATATTT
1 TTAAATAATAATATAAAATAATAATTTAATAATT
1335687 TTAAATAATAAT-TAAAATATATAAATTTAATCAATT
1 TTAAATAATAATATAAAATA-AT-AATTTAAT-AATT
1335723 TTAA
1 TTAA
1335727 TAAAAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 7 0.21
34 13 0.38
35 7 0.21
36 7 0.21
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (34 bp):
TTAAATAATAATATAAAATAATAATTTAATAATT
Found at i:1335930 original size:2 final size:2
Alignment explanation
Indices: 1335923--1335964 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1335913 GAATAGAAGG
1335923 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1335965 GGGTTCATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1336465 original size:22 final size:22
Alignment explanation
Indices: 1336439--1336514 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
1336429 ATTACATAAA
*
1336439 TTTTATTAAAATATAAAAATAT
1 TTTTATTAAAATTTAAAAATAT
* **
1336461 TTTTA-TATTAATTTTTAAATAT
1 TTTTATTA-AAATTTAAAAATAT
*
1336483 TTATATT-AAATTTAAATAATTAT
1 TTTTATTAAAATTTAAA-AA-TAT
1336506 TTTTATTAA
1 TTTTATTAA
1336515 TTAAATAATA
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
21 8 0.20
22 21 0.52
23 10 0.25
24 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTATTAAAATTTAAAAATAT
Found at i:1336498 original size:19 final size:20
Alignment explanation
Indices: 1336462--1336505 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1336452 TAAAAATATT
*
1336462 TTTATATTAATTTTTAAATA
1 TTTATATTAATATTTAAATA
1336482 TTTATATTAA-ATTTAAATA
1 TTTATATTAATATTTAAATA
*
1336501 ATTAT
1 TTTAT
1336506 TTTTATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTATATTAATATTTAAATA
Found at i:1336520 original size:21 final size:23
Alignment explanation
Indices: 1336480--1336529 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
1336470 AATTTTTAAA
1336480 TATTTATATTAAATTTAAATAAT
1 TATTTATATTAAATTTAAATAAT
*
1336503 TATTTTTATT-AA-TTAAATAAT
1 TATTTATATTAAATTTAAATAAT
*
1336524 AATTTA
1 TATTTA
1336530 AATCCTATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 13 0.54
22 2 0.08
23 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTTATATTAAATTTAAATAAT
Found at i:1336834 original size:15 final size:16
Alignment explanation
Indices: 1336814--1336844 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1336804 ATTAATATAT
1336814 ATTTTTT-ATTTTTAA
1 ATTTTTTAATTTTTAA
1336829 ATTTTTTAATTTTTAA
1 ATTTTTTAATTTTTAA
1336845 TATTATGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTTAATTTTTAA
Found at i:1336908 original size:16 final size:16
Alignment explanation
Indices: 1336871--1336909 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1336861 AAAATTAATT
* *
1336871 TTTAAATTAATTTAAA
1 TTTAATTTAATCTAAA
1336887 TTTAATTTAATCTAAA
1 TTTAATTTAATCTAAA
1336903 TTTAATT
1 TTTAATT
1336910 ATAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTAATTTAATCTAAA
Found at i:1341424 original size:27 final size:25
Alignment explanation
Indices: 1341394--1341456 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 25
1341384 TAAAGATATT
1341394 TAATTAAAATGTAT-TTATATATATAAA
1 TAATTAAAAT-TATATT-TATAT-TAAA
1341421 TAATTAAAAATTATATTTATATTAAA
1 TAATT-AAAATTATATTTATATTAAA
1341447 TAA-TAAAATT
1 TAATTAAAATT
1341457 TAAAATTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
24 6 0.18
25 1 0.03
26 7 0.21
27 13 0.38
28 7 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
TAATTAAAATTATATTTATATTAAA
Found at i:1341465 original size:25 final size:26
Alignment explanation
Indices: 1341411--1341468 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
1341401 AATGTATTTA
* *
1341411 TATATATAAATAATTAAAAATTATATT
1 TATAT-TAAATAATTAAAAATTAAAAT
*
1341438 TATATTAAATAA-TAAAATTTAAAAT
1 TATATTAAATAATTAAAAATTAAAAT
1341463 TATATT
1 TATATT
1341469 TATGTTGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 16 0.57
26 7 0.25
27 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TATATTAAATAATTAAAAATTAAAAT
Found at i:1341465 original size:31 final size:31
Alignment explanation
Indices: 1341397--1341605 Score: 150
Period size: 31 Copynumber: 6.7 Consensus size: 31
1341387 AGATATTTAA
* * *
1341397 TTAAAA-TGTATTTATA-TATATAA-ATAAT
1 TTAAAATTATATTTATATTAAATAATAAAAT
*
1341425 TAAAAATTATATTTATATTAAATAATAAAAT
1 TTAAAATTATATTTATATTAAATAATAAAAT
*
1341456 TTAAAATTATATTTATGTTGAATACTAATAAAA-
1 TTAAAATTATATTTATATT-AA-A-TAATAAAAT
** *
1341489 --ATGATTAAATTTATATTAAATAATAATTAA-
1 TTAAAATTATATTTATATTAAATAATAA--AAT
* *
1341519 TT-AAATTATA--TATATTAAAAAATAAATT
1 TTAAAATTATATTTATATTAAATAATAAAAT
1341547 ATTAAAATTATATTTATATTAAATAATAAAAATAT
1 -TTAAAATTATATTTATATTAAATAAT--AAA-AT
*
1341582 ATTAAAAATTATAATTATATTAAA
1 -TT-AAAATTATATTTATATTAAA
1341606 ATATTATTTA
Statistics
Matches: 144, Mismatches: 18, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
27 1 0.01
28 11 0.08
29 26 0.18
30 18 0.12
31 39 0.27
32 14 0.10
33 1 0.01
34 11 0.08
35 4 0.03
36 19 0.13
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (31 bp):
TTAAAATTATATTTATATTAAATAATAAAAT
Found at i:1341497 original size:37 final size:32
Alignment explanation
Indices: 1341418--1341605 Score: 160
Period size: 31 Copynumber: 5.8 Consensus size: 32
1341408 TTATATATAT
1341418 AAATAATTAAAAATTATATTTATATTAAATAATA
1 AAAT-ATT-AAAATTATATTTATATTAAATAATA
*
1341452 AAAT-TTAAAATTATATTTATGTTGAATACTAATA
1 AAATATTAAAATTATATTTATATT-AA-A-TAATA
* *
1341486 AAA-A-T--GATTAAATTTATATTAAATAAT-
1 AAATATTAAAATTATATTTATATTAAATAATA
* *
1341513 AATTAATT-AAATTATA--TATATTAAAAAATA
1 AAAT-ATTAAAATTATATTTATATTAAATAATA
*
1341543 AATTATTAAAATTATATTTATATTAAATAATAAA
1 AAATATTAAAATTATATTTATATTAAATAAT--A
*
1341577 AATATATTAAAAATTATAATTATATTAAA
1 AA-ATATT-AAAATTATATTTATATTAAA
1341606 ATATTATTTA
Statistics
Matches: 127, Mismatches: 11, Indels: 30
0.76 0.07 0.18
Matches are distributed among these distances:
27 2 0.02
28 4 0.03
29 17 0.13
30 15 0.12
31 33 0.26
32 16 0.13
33 2 0.02
34 15 0.12
35 4 0.03
36 19 0.15
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (32 bp):
AAATATTAAAATTATATTTATATTAAATAATA
Found at i:1341502 original size:91 final size:87
Alignment explanation
Indices: 1341406--1341639 Score: 243
Period size: 91 Copynumber: 2.6 Consensus size: 87
1341396 ATTAAAATGT
1341406 ATTTATATATATAAATAATTAAAAATTATATTTATATTAAATAATAAAATTTAAAATTATATTTA
1 ATTTATAT-TATAAATAATTAAAAATTATATTTATATTAAA-AATAAAATTTAAAATTATATTTA
*
1341471 TGTTGAATACTAATAAAAAT-GATTAA
64 TATT-AA-A-TAATAAAAATAGATTAA
* *
1341497 ATTTATATTAAATAATAATTAATTAAATTATA--TATATTAAAAAATAAATTATTAAAATTATAT
1 ATTTATATTATA-AATAATTAA--AAATTATATTTATATT-AAAAATAAAAT-TTAAAATTATAT
*
1341560 TTATATTAAATAATAAAAATATATTAA
61 TTATATTAAATAATAAAAATAGATTAA
*
1341587 A---A-ATTATAATTATATT-AAAA-TATTATTTATATTAAAAATAAAATTTTAAAATT
1 ATTTATATTATAAATA-ATTAAAAATTA-TATTTATATTAAAAATAAAA-TTTAAAATT
1341640 TTAAAAACGG
Statistics
Matches: 125, Mismatches: 7, Indels: 29
0.78 0.04 0.18
Matches are distributed among these distances:
82 2 0.02
83 5 0.04
84 17 0.14
85 11 0.09
86 8 0.06
87 1 0.01
89 10 0.08
90 10 0.08
91 32 0.26
92 21 0.17
93 8 0.06
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (87 bp):
ATTTATATTATAAATAATTAAAAATTATATTTATATTAAAAATAAAATTTAAAATTATATTTATA
TTAAATAATAAAAATAGATTAA
Found at i:1341523 original size:15 final size:16
Alignment explanation
Indices: 1341499--1341627 Score: 88
Period size: 16 Copynumber: 8.0 Consensus size: 16
1341489 ATGATTAAAT
1341499 TTATATTAAATAATAA
1 TTATATTAAATAATAA
*
1341515 TTA-ATTAAATTAT-A
1 TTATATTAAATAATAA
*
1341529 -TATATTAAAAAATAAA
1 TTATATTAAATAAT-AA
* * *
1341545 TTAT-TAAAATTATAT
1 TTATATTAAATAATAA
1341560 TTATATTAAATAATAAAA
1 TTATATTAAATAAT--AA
* *
1341578 ATATATTAAAAATTATAA
1 TTATATT--AAATAATAA
* *
1341596 TTATATTAAAATATTAT
1 TTATATT-AAATAATAA
1341613 TTATATTAAA-AATAA
1 TTATATTAAATAATAA
1341628 AATTTTAAAA
Statistics
Matches: 86, Mismatches: 18, Indels: 19
0.70 0.15 0.15
Matches are distributed among these distances:
13 2 0.02
14 9 0.10
15 17 0.20
16 20 0.23
17 17 0.20
18 15 0.17
20 6 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTATATTAAATAATAA
Found at i:1341523 original size:26 final size:26
Alignment explanation
Indices: 1341487--1341560 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 26
1341477 ATACTAATAA
* *
1341487 AAATGATTAAATTTATATTAAATAAT
1 AAATTATTAAATTTATATTAAAAAAT
1341513 -AATTAATTAAATTATATATATTAAAAAAT
1 AAATT-ATTAAA-T-T-TATATTAAAAAAT
*
1341542 AAATTATTAAAATTATATT
1 AAATTATTAAATTTATATT
1341561 TATATTAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
25 3 0.08
26 12 0.30
27 2 0.05
28 1 0.03
29 18 0.45
30 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (26 bp):
AAATTATTAAATTTATATTAAAAAAT
Found at i:1341618 original size:53 final size:49
Alignment explanation
Indices: 1341528--1341629 Score: 143
Period size: 53 Copynumber: 2.0 Consensus size: 49
1341518 ATTAAATTAT
1341528 ATATATTAAAAAATAAATTATTAAAATTATATTTATATTAAATAATAAAA
1 ATATATTAAAAAATAAATTATTAAAATTATATTTATATTAAA-AATAAAA
*
1341578 ATATATTAAAAATTATAATTATATTAAAA-TATTATTTATATTAAAAATAAAA
1 ATATATTAAAAA--ATAAAT-TATTAAAATTA-TATTTATATTAAAAATAAAA
1341630 TTTTAAAATT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
50 12 0.26
52 14 0.30
53 21 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (49 bp):
ATATATTAAAAAATAAATTATTAAAATTATATTTATATTAAAAATAAAA
Found at i:1341624 original size:18 final size:17
Alignment explanation
Indices: 1341499--1341631 Score: 102
Period size: 18 Copynumber: 8.1 Consensus size: 17
1341489 ATGATTAAAT
*
1341499 TTATATTAAATA-ATAA
1 TTATATTAAAAATATAA
*
1341515 TTA-ATT-AAATTAT-A
1 TTATATTAAAAATATAA
1341529 -TATATTAAAAA-ATAA
1 TTATATTAAAAATATAA
* * *
1341544 AT-TATTAAAATTATAT
1 TTATATTAAAAATATAA
*
1341560 TTATATTAAATAATAAAA
1 TTATATTAAA-AATATAA
*
1341578 ATATATTAAAAATTATAA
1 TTATATTAAAAA-TATAA
*
1341596 TTATATT-AAAATATTAT
1 TTATATTAAAAATA-TAA
*
1341613 TTATATTAAAAATAAAA
1 TTATATTAAAAATATAA
1341630 TT
1 TT
1341632 TTAAAATTTT
Statistics
Matches: 91, Mismatches: 15, Indels: 21
0.72 0.12 0.17
Matches are distributed among these distances:
13 2 0.02
14 8 0.09
15 17 0.19
16 10 0.11
17 25 0.27
18 29 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTATATTAAAAATATAA
Found at i:1341846 original size:9 final size:9
Alignment explanation
Indices: 1341832--1341875 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
1341822 TTAAATAAAA
1341832 ATTAAATTT
1 ATTAAATTT
1341841 ATTAAATTT
1 ATTAAATTT
* *
1341850 ATTTAATTA
1 ATTAAATTT
*
1341859 ATTTAATTT
1 ATTAAATTT
1341868 ATTTAAAT
1 A-TTAAAT
1341876 AGATTTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
9 25 0.83
10 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
ATTAAATTT
Found at i:1341866 original size:18 final size:18
Alignment explanation
Indices: 1341845--1341900 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
1341835 AAATTTATTA
1341845 AATTTATTTAATTAATTT
1 AATTTATTTAATTAATTT
*
1341863 AATTTATTTAAATAGATTTT
1 AATTTATTTAATTA-A-TTT
*
1341883 AATTT-TTATATTTAATTT
1 AATTTATT-TAATTAATTT
1341901 CAAATAAGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 16 0.50
19 4 0.12
20 12 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
AATTTATTTAATTAATTT
Found at i:1341900 original size:29 final size:30
Alignment explanation
Indices: 1341851--1341911 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 30
1341841 ATTAAATTTA
1341851 TTTAATTAATTTAATTTATTT-AAAT-AGAT
1 TTTAATT-ATTTAATTTATTTCAAATAAGAT
1341880 TTTAATT-TTTATATTTAATTTCAAATAAGAT
1 TTTAATTATTTA-ATTT-ATTTCAAATAAGAT
1341911 T
1 T
1341912 ATTTAAACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
27 4 0.14
28 4 0.14
29 11 0.39
30 4 0.14
31 5 0.18
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (30 bp):
TTTAATTATTTAATTTATTTCAAATAAGAT
Found at i:1342683 original size:12 final size:12
Alignment explanation
Indices: 1342666--1342690 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1342656 TTGCGGTGCT
1342666 ACGTTAGAGGTG
1 ACGTTAGAGGTG
1342678 ACGTTAGAGGTG
1 ACGTTAGAGGTG
1342690 A
1 A
1342691 AAAGATCGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.40, T:0.24
Consensus pattern (12 bp):
ACGTTAGAGGTG
Found at i:1343659 original size:14 final size:15
Alignment explanation
Indices: 1343634--1343662 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1343624 AAATTAATTT
1343634 AAATTAAATTTTAAA
1 AAATTAAATTTTAAA
1343649 AAATT-AATTTTAAA
1 AAATTAAATTTTAAA
1343663 TTAAATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTAAATTTTAAA
Found at i:1348476 original size:2 final size:2
Alignment explanation
Indices: 1348469--1348500 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1348459 CTATATCAAA
1348469 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
1348501 TTATTAAGTT
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:1349038 original size:24 final size:25
Alignment explanation
Indices: 1348989--1349039 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 25
1348979 TTTGAAAAGC
1348989 ATATATATTTTAATATAGATATAAAA
1 ATATATATTTTAATATA-ATATAAAA
* *
1349015 ATATATTTTTTAA-CT-ATATAAAA
1 ATATATATTTTAATATAATATAAAA
1349038 AT
1 AT
1349040 TTTAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 10 0.43
25 1 0.04
26 12 0.52
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
ATATATATTTTAATATAATATAAAA
Found at i:1351178 original size:2 final size:2
Alignment explanation
Indices: 1351171--1351204 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1351161 TTATTTATGT
1351171 TA TA 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 TA TA
1351205 AATAAGTTAA
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):
TA
Found at i:1352333 original size:23 final size:23
Alignment explanation
Indices: 1352307--1352356 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1352297 TATTAAGTTT
**
1352307 TTAAATTTTTTTA-AAATTTTTAA
1 TTAAATTACTTTATAAATTTTT-A
1352330 TTAAATTACTTTATAAATTTTTA
1 TTAAATTACTTTATAAATTTTTA
1352353 TTAA
1 TTAA
1352357 TAATAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TTAAATTACTTTATAAATTTTTA
Found at i:1352889 original size:22 final size:23
Alignment explanation
Indices: 1352859--1352929 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 23
1352849 TATTAAATTT
* *
1352859 ATATGATAATAAGATAAAATAAA
1 ATATTATAATAAAATAAAATAAA
** *
1352882 AT-TTATAATATTATAAAATATA
1 ATATTATAATAAAATAAAATAAA
1352904 ATATTAT-ATAAAATATAAA-AAA
1 ATATTATAATAAAATA-AAATAAA
1352926 ATAT
1 ATAT
1352930 ATTTAATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
22 30 0.77
23 9 0.23
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (23 bp):
ATATTATAATAAAATAAAATAAA
Found at i:1352897 original size:27 final size:27
Alignment explanation
Indices: 1352853--1352906 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1352843 GGTAAATATT
*
1352853 AAATTTATATGATAATAAGATAAAATA
1 AAATTTATATGATAATAAAATAAAATA
* *
1352880 AAATTTATAAT-ATTATAAAATATAATA
1 AAATTTAT-ATGATAATAAAATAAAATA
1352907 TTATATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
AAATTTATATGATAATAAAATAAAATA
Found at i:1352905 original size:15 final size:17
Alignment explanation
Indices: 1352885--1352921 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1352875 AAATAAAATT
1352885 TATAATA-T-TATAAAA
1 TATAATATTATATAAAA
1352900 TATAATATTATATAAAA
1 TATAATATTATATAAAA
1352917 TATAA
1 TATAA
1352922 AAAAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.35
16 1 0.05
17 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAATATTATATAAAA
Found at i:1353422 original size:21 final size:20
Alignment explanation
Indices: 1353380--1353446 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
1353370 AAGTTTAAAA
*
1353380 TTTTT-AAATTAAATTTAAT
1 TTTTTAAAAATAAATTTAAT
*
1353399 TTTTTAAAAATAAATTTAGT
1 TTTTTAAAAATAAATTTAAT
*
1353419 TTTTATAAAAATAATTTTTAAAT
1 TTTT-TAAAAATAA-ATTT-AAT
1353442 TTTTT
1 TTTTT
1353447 TATCGAATAC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 5 0.12
20 16 0.40
21 9 0.22
22 4 0.10
23 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (20 bp):
TTTTTAAAAATAAATTTAAT
Found at i:1353515 original size:20 final size:20
Alignment explanation
Indices: 1353490--1353540 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1353480 AAATATATAT
1353490 TTTATAAAAATTAATTTTTA
1 TTTATAAAAATTAATTTTTA
1353510 TTTATAAAAATTAATTTTTA
1 TTTATAAAAATTAATTTTTA
* *
1353530 ATCATAAAAAT
1 TTTATAAAAAT
1353541 ATATAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTATAAAAATTAATTTTTA
Found at i:1353567 original size:22 final size:22
Alignment explanation
Indices: 1353536--1353586 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1353526 TTTAATCATA
* *
1353536 AAAATATATAATATTAATATGAT
1 AAAAT-TATAATATAAATATAAT
1353559 AAAATTATAATATAAATATAAT
1 AAAATTATAATATAAATATAAT
*
1353581 ATAATT
1 AAAATT
1353587 TATTAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
AAAATTATAATATAAATATAAT
Found at i:1353580 original size:11 final size:11
Alignment explanation
Indices: 1353541--1353584 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
1353531 TCATAAAAAT
*
1353541 ATATAATATTA
1 ATATAATATAA
*
1353552 ATATGATA-AA
1 ATATAATATAA
1353562 ATTATAATATAA
1 A-TATAATATAA
1353574 ATATAATATAA
1 ATATAATATAA
1353585 TTTATTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 2 0.07
11 23 0.82
12 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1357468 original size:17 final size:16
Alignment explanation
Indices: 1357433--1357494 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 16
1357423 AATGTTATAA
*
1357433 TTATATTTA-AAATATT
1 TTATATTTATATA-ATT
1357449 TTATATTTATATCAATT
1 TTATATTTATAT-AATT
1357466 TTAATATGTTA-ATAA-T
1 TT-ATAT-TTATATAATT
1357482 TTATA-TTATATAA
1 TTATATTTATATAA
1357495 AATTTAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 3 0.08
14 4 0.10
15 3 0.08
16 12 0.30
17 8 0.20
18 7 0.17
19 3 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
TTATATTTATATAATT
Found at i:1358475 original size:21 final size:21
Alignment explanation
Indices: 1358451--1358491 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1358441 ATAAATTATT
*
1358451 TTAATTTTAAAATAA-ATAAAA
1 TTAATTAT-AAATAATATAAAA
1358472 TTAATTATAAATAATATAAA
1 TTAATTATAAATAATATAAA
1358492 TATCAACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TTAATTATAAATAATATAAAA
Found at i:1358739 original size:16 final size:16
Alignment explanation
Indices: 1358704--1358746 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1358694 TTTTAATATC
*
1358704 AAATATCAAAATAATTA
1 AAATAT-AAAATAATAA
*
1358721 AAATATAATATAATAA
1 AAATATAAAATAATAA
1358737 AAATATAAAA
1 AAATATAAAA
1358747 ATATTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATATAAAATAATAA
Found at i:1358767 original size:22 final size:21
Alignment explanation
Indices: 1358739--1358780 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1358729 TATAATAAAA
1358739 ATATAAAAATATTAAATTTATG
1 ATATAAAAATA-TAAATTTATG
**
1358761 ATATAAATTTATAAATTTAT
1 ATATAAAAATATAAATTTAT
1358781 AAAATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
ATATAAAAATATAAATTTATG
Found at i:1358775 original size:8 final size:8
Alignment explanation
Indices: 1358762--1358792 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1358752 AAATTTATGA
1358762 TATAAATT
1 TATAAATT
1358770 TATAAATT
1 TATAAATT
1358778 TATAAAATT
1 TAT-AAATT
1358787 TATAAA
1 TATAAA
1358793 AATATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
TATAAATT
Found at i:1358787 original size:9 final size:9
Alignment explanation
Indices: 1358765--1358793 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1358755 TTTATGATAT
1358765 AAATTTAT-
1 AAATTTATA
1358773 AAATTTATA
1 AAATTTATA
1358782 AAATTTATA
1 AAATTTATA
1358791 AAA
1 AAA
1358794 ATATATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AAATTTATA
Found at i:1361101 original size:22 final size:22
Alignment explanation
Indices: 1361066--1361121 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1361056 ACATAAACAC
*
1361066 AACATAA-ATAAAAAAAATTAA-
1 AACATAATATAAAAAAAA-CAAG
*
1361087 AACATAATATAAAAATAACAAG
1 AACATAATATAAAAAAAACAAG
1361109 AACATAATATAAA
1 AACATAATATAAA
1361122 TATCCGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 9 0.29
22 22 0.71
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.20
Consensus pattern (22 bp):
AACATAATATAAAAAAAACAAG
Found at i:1361326 original size:19 final size:18
Alignment explanation
Indices: 1361274--1361326 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
1361264 ATGAATATAC
*
1361274 AAATATAAAAAATATTTAT
1 AAATATTAAAAA-ATTTAT
*
1361293 AAATATTATATAAATTTAT
1 AAATATTA-AAAAATTTAT
*
1361312 AATATTTTAAAAAAT
1 AA-ATATTAAAAAAT
1361327 AAAAATTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 20 0.71
20 8 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATTAAAAAATTTAT
Found at i:1361341 original size:13 final size:13
Alignment explanation
Indices: 1361323--1361351 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1361313 ATATTTTAAA
1361323 AAATAAAAATTAT
1 AAATAAAAATTAT
1361336 AAATAAAAATTAT
1 AAATAAAAATTAT
1361349 AAA
1 AAA
1361352 CACTCAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAAAAATTAT
Found at i:1361393 original size:199 final size:199
Alignment explanation
Indices: 1361188--1361591 Score: 634
Period size: 200 Copynumber: 2.0 Consensus size: 199
1361178 AAACTTTTAA
**
1361188 TACTTTAAATATA-AAAAAATAACATAAATATGACATTAAAAATTAATTAAAAAATAATACAAAA
1 TACTTTAAATATATAAAAAATAACATAAATAAAACATTAAAAATTAATTAAAAAATAATACAAAA
*
1361252 AATAAATATAACATGAATATACAAATATAAAAAATATTTATAAATATTATATAAATTTATAATAT
66 AATAAATATAACATGAATATACAAATATAAAAAATATTTATAAATAGTATATAAATTTATAATAT
* * *
1361317 TTTAAAAAATAAAAATTATAAATAAAAATTATAAACACTC-AAATTATTCTT-TCTCTCATTTCC
131 TTTAAAAAATAAAAAATACAAATAAAAATCATAAACAC-CAAAATT-TT-TTGTCTCTCATTTCC
1361380 TCTCTTT
193 TCTCTTT
*
1361387 TACTTTAAATATATAAAAAATAACATAAATAAAACATTAAAAATTAATTAAAACATAATACAAAA
1 TACTTTAAATATATAAAAAATAACATAAATAAAACATTAAAAATTAATTAAAAAATAATACAAAA
*
1361452 AGTAAATATAACATGAATATACAAATATAAAAAATATTTATAAATAGTATATAAATTTATAATAT
66 AATAAATATAACATGAATATACAAATATAAAAAATATTTATAAATAGTATATAAATTTATAATAT
* * * * *
1361517 TTTAAATAATAAAAAATACATATAAAAATCATAAATACCAAAATTTTTTGTCTCTCCTTTCCTTT
131 TTTAAAAAATAAAAAATACAAATAAAAATCATAAACACCAAAATTTTTTGTCTCTCATTTCCTCT
1361582 CTTT
196 CTTT
*
1361586 TTCTTT
1 TACTTT
1361592 CTTTTCTTTG
Statistics
Matches: 188, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
198 2 0.01
199 38 0.20
200 148 0.79
ACGTcount: A:0.53, C:0.09, G:0.01, T:0.36
Consensus pattern (199 bp):
TACTTTAAATATATAAAAAATAACATAAATAAAACATTAAAAATTAATTAAAAAATAATACAAAA
AATAAATATAACATGAATATACAAATATAAAAAATATTTATAAATAGTATATAAATTTATAATAT
TTTAAAAAATAAAAAATACAAATAAAAATCATAAACACCAAAATTTTTTGTCTCTCATTTCCTCT
CTTT
Found at i:1361451 original size:23 final size:24
Alignment explanation
Indices: 1361425--1361470 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
1361415 ATAAAACATT
* *
1361425 AAAAATTAATTAAAACAT-AATAC
1 AAAAAGTAAATAAAACATGAATAC
*
1361448 AAAAAGTAAATATAACATGAATA
1 AAAAAGTAAATAAAACATGAATA
1361471 TACAAATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.65, C:0.07, G:0.04, T:0.24
Consensus pattern (24 bp):
AAAAAGTAAATAAAACATGAATAC
Done.