Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold132
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: 2458301
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 2 of 15
Found at i:250037 original size:2 final size:2
Alignment explanation
Indices: 250025--250069 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
250015 TGAACCCAAA
* *
250025 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
250066 AT AT
1 AT AT
250070 TTGTAAGTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:256040 original size:24 final size:26
Alignment explanation
Indices: 255988--256036 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
255978 GGACTTTCTT
255988 TAAAAAATATATATATATTTTAAAAA
1 TAAAAAATATATATATATTTTAAAAA
256014 TAAAAAATAT-TAT-T-TTTTAAAAA
1 TAAAAAATATATATATATTTTAAAAA
256037 ATAATTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.39
24 1 0.04
25 3 0.13
26 10 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TAAAAAATATATATATATTTTAAAAA
Found at i:257757 original size:2 final size:2
Alignment explanation
Indices: 257750--257786 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
257740 CCGATTTTTC
*
257750 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
257787 CCATCGATCT
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:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:260208 original size:2 final size:2
Alignment explanation
Indices: 260201--260235 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
260191 TGCCCTCTAA
* *
260201 TC TC TC TC GC TC TC TC TC TC TC TC TC TC TT TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
260236 TTATTTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.46, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:260583 original size:17 final size:16
Alignment explanation
Indices: 260563--260607 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
260553 AAATAAAATT
*
260563 ATATAATATTATATTTA
1 ATATAATATTAT-TATA
260580 ATATAATATTATTATA
1 ATATAATATTATTATA
260596 A-ATAATA-TATTA
1 ATATAATATTATTA
260608 ATTAATCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
16 4 0.15
17 12 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATAATATTATTATA
Found at i:260601 original size:20 final size:19
Alignment explanation
Indices: 260558--260604 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
260548 ATAATAAATA
*
260558 AAATTATATAATATTATAT
1 AAATAATATAATATTATAT
*
260577 --TTAATATAATATTATTAT
1 AAATAATATAATATTA-TAT
260595 AAATAATATA
1 AAATAATATA
260605 TTAATTAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
17 12 0.55
18 3 0.14
20 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATAATATAATATTATAT
Found at i:261058 original size:5 final size:5
Alignment explanation
Indices: 261048--261146 Score: 56
Period size: 5 Copynumber: 21.2 Consensus size: 5
261038 AATAATTTTA
* * *
261048 AATAT AATAT -A-AT AATAT AATAA AAAAT AATTTAA AATAT AATAT AA-A-
1 AATAT AATAT AATAT AATAT AATAT AATAT AA--TAT AATAT AATAT AATAT
* *
261096 AATAT AAATAT AATAT AA-AT TAT-T AATAT AA-A- AAT-T TATAT AATAT
1 AATAT -AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
261142 -ATAT A
1 AATAT A
261147 CATCTTAAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 26
0.66 0.09 0.24
Matches are distributed among these distances:
3 6 0.08
4 17 0.24
5 40 0.56
6 5 0.07
7 3 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:261066 original size:13 final size:13
Alignment explanation
Indices: 261048--261126 Score: 73
Period size: 13 Copynumber: 6.5 Consensus size: 13
261038 AATAATTTTA
261048 AATATAATATAAT
1 AATATAATATAAT
261061 AATATAATA-AA-
1 AATATAATATAAT
*
261072 AA-ATAATTTAA-
1 AATATAATATAAT
*
261083 AATATAATATAAA
1 AATATAATATAAT
261096 AATATAA-AT-AT
1 AATATAATATAAT
*
261107 AATATAA-ATTATT
1 AATATAATA-TAAT
261120 AATATAA
1 AATATAA
261127 AAATTTATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
10 5 0.09
11 15 0.26
12 13 0.23
13 24 0.42
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATATAATATAAT
Found at i:262061 original size:15 final size:18
Alignment explanation
Indices: 262041--262080 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 18
262031 AAGCAACTTG
262041 TTAAATTTGA-TTTA-A-
1 TTAAATTTGAGTTTAGAT
262056 TTAAATTTGAGTTTAGAT
1 TTAAATTTGAGTTTAGAT
262074 TTAAATT
1 TTAAATT
262081 ATTTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.45
16 4 0.18
17 1 0.05
18 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (18 bp):
TTAAATTTGAGTTTAGAT
Found at i:262419 original size:15 final size:15
Alignment explanation
Indices: 262383--262431 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 15
262373 TAAAAATAAT
*
262383 TAAATTATTATTTTA
1 TAAATTAATATTTTA
262398 -AAA-TAATATTTTA
1 TAAATTAATATTTTA
262411 TAAATTAAT-TTTTA
1 TAAATTAATATTTTA
262425 TCAAATT
1 T-AAATT
262432 TAAAAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 9 0.30
14 12 0.40
15 9 0.30
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TAAATTAATATTTTA
Found at i:262706 original size:16 final size:15
Alignment explanation
Indices: 262685--262751 Score: 55
Period size: 16 Copynumber: 4.2 Consensus size: 15
262675 TTTATTATAA
262685 TTATATTTAAAATATT
1 TTATATTTAAAA-ATT
*
262701 TTATATTTTTATAAATT
1 TTATA--TTTAAAAATT
*
262718 TTAT-TTTATTAAATAT
1 TTATATTTA-AAAAT-T
*
262734 TTATATTTATAAATT
1 TTATATTTAAAAATT
262749 TTA
1 TTA
262752 AAAAATTAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
14 4 0.09
15 9 0.20
16 15 0.33
17 11 0.24
18 6 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATATTTAAAAATT
Found at i:262711 original size:33 final size:32
Alignment explanation
Indices: 262666--262748 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 32
262656 CATATTCGTT
262666 TATTT-TATTTTTATTATAATTATA-TTTA-AAA
1 TATTTATATTTTTA-TA-AATTATATTTTATAAA
*
262697 TATTTTATATTTTTATAAATTTTATTTTATTAAA
1 TA-TTTATATTTTTATAAATTATATTTTA-TAAA
262731 TATTTATA--TTTATAAATT
1 TATTTATATTTTTATAAATT
262749 TTAAAAAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
31 18 0.39
32 9 0.20
33 14 0.30
34 5 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (32 bp):
TATTTATATTTTTATAAATTATATTTTATAAA
Found at i:262720 original size:17 final size:17
Alignment explanation
Indices: 262698--262751 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 17
262688 TATTTAAAAT
262698 ATTTTATATTTTTATAA
1 ATTTTATATTTTTATAA
*
262715 ATTTTAT-TTTAT-TAA
1 ATTTTATATTTTTATAA
262730 ATATTTATA--TTTATAA
1 AT-TTTATATTTTTATAA
262746 ATTTTA
1 ATTTTA
262752 AAAAATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 11 0.34
16 14 0.44
17 7 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTTATATTTTTATAA
Found at i:262788 original size:18 final size:19
Alignment explanation
Indices: 262760--262797 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
262750 TAAAAAATTA
*
262760 ATATATTATATTATATTTTT
1 ATATAATATA-TATATTTTT
262780 ATATAATATATATATTTT
1 ATATAATATATATATTTT
262798 CGTGTCGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATAATATATATATTTTT
Found at i:264523 original size:2 final size:2
Alignment explanation
Indices: 264516--264545 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
264506 CAGAGAATAG
264516 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
264546 CTGTAAACAA
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):
AT
Found at i:266432 original size:69 final size:67
Alignment explanation
Indices: 266331--266469 Score: 179
Period size: 69 Copynumber: 2.0 Consensus size: 67
266321 TTTTTACTAT
* * * * * *
266331 AAAAAAAATGAACGAGAGAACATGATAAAAAATTGCTCGATTTTTAAATATATTAATATGCTTTA
1 AAAAAAAATGAACGACAGAACAAGAGAAAAAATTACTCAATTTTTAAATATATTAATATACTTTA
266396 AA
66 AA
* * *
266398 AAAATAAAATGAATCGACAGAACAAGAGAAAAAATTATTCAATTTTTAAATGTATTAATATATTT
1 AAAA-AAAATGAA-CGACAGAACAAGAGAAAAAATTACTCAATTTTTAAATATATTAATATACTT
266463 TAAA
64 TAAA
266467 AAA
1 AAA
266470 TAATTATATA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
67 4 0.07
68 8 0.13
69 49 0.80
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.30
Consensus pattern (67 bp):
AAAAAAAATGAACGACAGAACAAGAGAAAAAATTACTCAATTTTTAAATATATTAATATACTTTA
AA
Found at i:266818 original size:20 final size:17
Alignment explanation
Indices: 266793--266832 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
266783 TAAATAAAAA
266793 ATTAATATAATATATTTTAT
1 ATTAATAT--TATA-TTTAT
266813 ATTAATATTATATTTAT
1 ATTAATATTATATTTAT
266830 ATT
1 ATT
266833 TAAAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 4 0.20
20 8 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTAATATTATATTTAT
Found at i:267707 original size:16 final size:15
Alignment explanation
Indices: 267686--267733 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 15
267676 ATTCAATAAA
267686 AAATAATTAAAATAT
1 AAATAATTAAAATAT
267701 AATATAATTTTAAAAATAT
1 AA-ATAA--TT-AAAATAT
267720 AAATATATTAAAAT
1 AAATA-ATTAAAAT
267734 TTATATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 2 0.07
16 9 0.32
17 2 0.07
18 5 0.18
19 10 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATAATTAAAATAT
Found at i:267726 original size:25 final size:26
Alignment explanation
Indices: 267695--267745 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
267685 AAAATAATTA
*
267695 AAATATAATATAATTT-TAAAAATAT
1 AAATATAATAAAATTTATAAAAATAT
* *
267720 AAATATATTAAAATTTATATAAATAT
1 AAATATAATAAAATTTATAAAAATAT
267746 TTAATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AAATATAATAAAATTTATAAAAATAT
Found at i:267745 original size:18 final size:18
Alignment explanation
Indices: 267686--267746 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
267676 ATTCAATAAA
267686 AAATAATTAAAATATA-AT
1 AAAT-ATTAAAATATATAT
*
267704 ATAATTTTAAAA-ATATA-
1 A-AATATTAAAATATATAT
*
267721 AATATATTAAAATTTATAT
1 AA-ATATTAAAATATATAT
267740 AAATATT
1 AAATATT
267747 TAATATTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
16 1 0.03
17 12 0.34
18 17 0.49
19 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATATTAAAATATATAT
Found at i:267747 original size:12 final size:12
Alignment explanation
Indices: 267716--267793 Score: 58
Period size: 11 Copynumber: 6.4 Consensus size: 12
267706 AATTTTAAAA
267716 ATATAAATA--T
1 ATATAAATATTT
267726 AT-TAAA-ATTT
1 ATATAAATATTT
267736 ATATAAATATTT
1 ATATAAATATTT
267748 AATATTTTAAATATAATT
1 -ATA---TAAATAT--TT
*
267766 ATATAAATAATT
1 ATATAAATATTT
267778 A-ATAAATATTT
1 ATATAAATATTT
267789 ATATA
1 ATATA
267794 TTTATATATC
Statistics
Matches: 55, Mismatches: 2, Indels: 20
0.71 0.03 0.26
Matches are distributed among these distances:
8 1 0.02
9 4 0.07
10 5 0.09
11 14 0.25
12 10 0.18
13 3 0.05
14 6 0.11
16 7 0.13
17 3 0.05
18 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
ATATAAATATTT
Found at i:267769 original size:42 final size:42
Alignment explanation
Indices: 267714--267796 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
267704 ATAATTTTAA
*
267714 AAATATAAATATATTAAA-ATTTATATAAATATTTA-ATATTTT
1 AAATATAAATATA-TAAATAATTA-ATAAATATTTATATATTTT
*
267756 AAATATAATTATATAAATAATTAATAAATATTTATATATTT
1 AAATATAAATATATAAATAATTAATAAATATTTATATATTT
267797 ATATATCACA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 15 0.41
42 22 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (42 bp):
AAATATAAATATATAAATAATTAATAAATATTTATATATTTT
Found at i:268666 original size:21 final size:21
Alignment explanation
Indices: 268636--268697 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
268626 ACATAAAATA
268636 TTAACATATAAAAATATTAAAC
1 TTAA-ATATAAAAATATTAAAC
* *
268658 TTAAATATAAATATA-TAAAT
1 TTAAATATAAAAATATTAAAC
268678 TATCAAAT-TAAAAA-ATTAAA
1 T-T-AAATATAAAAATATTAAA
268698 AATTTCTACG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 6 0.18
21 20 0.59
22 8 0.24
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (21 bp):
TTAAATATAAAAATATTAAAC
Found at i:275581 original size:2 final size:2
Alignment explanation
Indices: 275574--275601 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
275564 CAAGCATACT
275574 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
275602 CACACACACA
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:277622 original size:2 final size:2
Alignment explanation
Indices: 277615--277639 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
277605 TAGTAATAAG
277615 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
277640 GTTTTTCTAA
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:278022 original size:2 final size:2
Alignment explanation
Indices: 278015--278055 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
278005 TGGAAAACTA
* *
278015 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT TT 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
278056 AATGTTGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:279530 original size:30 final size:30
Alignment explanation
Indices: 279443--279517 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
279433 AACAAATATA
* * *
279443 TAACCTTTAATTTTTA-TTAAAATAAATCTT
1 TAACTTTTAATTTATACTT-AAATAAATCTC
279473 TAACTTTTAATTTATACTTAAATAAATCTC
1 TAACTTTTAATTTATACTTAAATAAATCTC
279503 TAACTTTTAATTTAT
1 TAACTTTTAATTTAT
279518 TTTTGAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 39 0.95
31 2 0.05
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.51
Consensus pattern (30 bp):
TAACTTTTAATTTATACTTAAATAAATCTC
Found at i:280923 original size:12 final size:12
Alignment explanation
Indices: 280906--280934 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
280896 CATGGAGATC
280906 ATATAACTATAT
1 ATATAACTATAT
280918 ATATAACTATAT
1 ATATAACTATAT
280930 ATATA
1 ATATA
280935 CACACACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATAACTATAT
Found at i:283764 original size:2 final size:2
Alignment explanation
Indices: 283752--283789 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
283742 GGAAAATAGA
*
283752 AT AT AT GT 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
283790 TTTTTTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:284521 original size:10 final size:10
Alignment explanation
Indices: 284506--284537 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
284496 ATATAATTAA
284506 AAATTAATAT
1 AAATTAATAT
284516 AAATTAATAT
1 AAATTAATAT
284526 AAA-T-ATAT
1 AAATTAATAT
284534 AAAT
1 AAAT
284538 AATTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 7 0.33
9 1 0.05
10 13 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAATTAATAT
Found at i:284556 original size:30 final size:30
Alignment explanation
Indices: 284520--284581 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
284510 TAATATAAAT
284520 TAATATAAATATATAAATA-ATTAAAATTTA
1 TAATATAAAT-TATAAATATATTAAAATTTA
* *
284550 TAATATAAATTATTAATATTTTAAAATTTA
1 TAATATAAATTATAAATATATTAAAATTTA
284580 TA
1 TA
284582 TAAATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
TAATATAAATTATAAATATATTAAAATTTA
Found at i:284594 original size:27 final size:28
Alignment explanation
Indices: 284516--284601 Score: 97
Period size: 27 Copynumber: 3.1 Consensus size: 28
284506 AAATTAATAT
* *
284516 AAATTAATATAAATATATAAATA-ATTA
1 AAATTTATATAAATATATAAATATTTTA
*
284543 AAATTTATAATATAA-ATTATTAATATTTTA
1 AAATTTAT-ATA-AATA-TATAAATATTTTA
284573 AAATTTATATAAATATA-AAATATTTTA
1 AAATTTATATAAATATATAAATATTTTA
284600 AA
1 AA
284602 TGTGATTACT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
27 18 0.36
28 8 0.16
29 13 0.26
30 11 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
AAATTTATATAAATATATAAATATTTTA
Found at i:296780 original size:16 final size:14
Alignment explanation
Indices: 296759--296798 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 14
296749 ATTTTTAATG
296759 ATTTATTTAAAAATTA
1 ATTTATTTAAAAA--A
296775 ATTTATTTAAAAAA
1 ATTTATTTAAAAAA
296789 ATTTATTTAA
1 ATTTATTTAA
296799 TTTAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 11 0.46
16 13 0.54
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTATTTAAAAAA
Found at i:296789 original size:19 final size:19
Alignment explanation
Indices: 296767--296803 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
296757 TGATTTATTT
296767 AAAAATTAATTT-ATTTAA
1 AAAAATTAATTTAATTTAA
*
296785 AAAAATTTATTTAATTTAA
1 AAAAATTAATTTAATTTAA
296804 TATTTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAAATTAATTTAATTTAA
Found at i:297244 original size:23 final size:24
Alignment explanation
Indices: 297218--297278 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
297208 TTTTATTTAA
297218 TAAATTATTTAAAATTAAAT-ATT
1 TAAATTATTTAAAATTAAATAATT
* *
297241 TAAATTTATTT--TATTTAATAATT
1 TAAA-TTATTTAAAATTAAATAATT
297264 TAAATTA-TTAAAATT
1 TAAATTATTTAAAATT
297279 TTAAAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 2 0.06
22 9 0.29
23 14 0.45
24 6 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TAAATTATTTAAAATTAAATAATT
Found at i:297348 original size:33 final size:33
Alignment explanation
Indices: 297272--297350 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 33
297262 TTTAAATTAT
* *
297272 TAAAATTTTAA-AATAATTTTACCTTATTTAAA
1 TAAAATTTAAATAATAATTCTACCTTATTTAAA
**
297304 T-ATTTTATAAATAATAATTCT-CCTTTATTTAAA
1 TAAAATT-TAAATAATAATTCTACC-TTATTTAAA
297337 TAAAATTTAAATAA
1 TAAAATTTAAATAA
297351 CGTGTACGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
31 3 0.08
32 6 0.16
33 25 0.68
34 3 0.08
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (33 bp):
TAAAATTTAAATAATAATTCTACCTTATTTAAA
Found at i:301545 original size:20 final size:20
Alignment explanation
Indices: 301522--301559 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
301512 GATACCAAAA
301522 TTACATGTCA-GGTAGGAACG
1 TTACATG-CAGGGTAGGAACG
*
301542 TTACTTGCAGGGTAGGAA
1 TTACATGCAGGGTAGGAA
301560 AACTCATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26
Consensus pattern (20 bp):
TTACATGCAGGGTAGGAACG
Found at i:303601 original size:6 final size:6
Alignment explanation
Indices: 303590--303630 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
303580 AAAGAAATAG
* * *
303590 CATCAT CATCAT CACCAC CATCAC CATCAC CATCAC CATCA
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCA
303631 TCCTCTTCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.34, C:0.46, G:0.00, T:0.20
Consensus pattern (6 bp):
CATCAC
Found at i:305310 original size:27 final size:27
Alignment explanation
Indices: 305256--305383 Score: 95
Period size: 27 Copynumber: 4.6 Consensus size: 27
305246 AAATGATACG
*
305256 AATATAATATAAAAAATAAT-TAATATAT
1 AATATTATAT-AAAAATAATATAA-ATAT
305284 AATATTATATAAAAATAATATAAATAT
1 AATATTATATAAAAATAATATAAATAT
* * *
305311 AATATTA-ATAAATA-AATAT-ATTAA
1 AATATTATATAAAAATAATATAAATAT
305335 AAT-TTATATAAATATATAATATTTTAAATAT
1 AATATTATATAAA-A-ATAATA---TAAATAT
* *
305366 GATATAATAATAAAAATA
1 AATATTAT-ATAAAAATA
305384 TCAAAAATAA
Statistics
Matches: 80, Mismatches: 9, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
23 3 0.04
24 11 0.14
25 5 0.06
26 7 0.09
27 24 0.30
28 12 0.15
30 1 0.01
31 8 0.10
32 4 0.05
33 5 0.06
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (27 bp):
AATATTATATAAAAATAATATAAATAT
Found at i:305311 original size:50 final size:52
Alignment explanation
Indices: 305256--305356 Score: 129
Period size: 50 Copynumber: 2.0 Consensus size: 52
305246 AAATGATACG
* *
305256 AATATAATA-TAAAAAATAATTA-ATATATAATATTATATAAA-A-ATAATATA
1 AATATAATATTAAAAAATAAATATAT-TAAAAT-TTATATAAATATATAATATA
*
305306 AATATAATATTAATAAATAAATATATTAAAATTTATATAAATATATAATAT
1 AATATAATATTAAAAAATAAATATATTAAAATTTATATAAATATATAATAT
305357 TTTAAATATG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
50 18 0.41
51 17 0.39
52 9 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (52 bp):
AATATAATATTAAAAAATAAATATATTAAAATTTATATAAATATATAATATA
Found at i:305360 original size:20 final size:20
Alignment explanation
Indices: 305307--305364 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
305297 AATAATATAA
*
305307 ATATAATATTAATAAATAAAT
1 ATATAATATT-TTAAATAAAT
* *
305328 ATATTAA-AATTTATATAAAT
1 ATA-TAATATTTTAAATAAAT
305348 ATATAATATTTTAAATA
1 ATATAATATTTTAAATA
305365 TGATATAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
19 3 0.10
20 19 0.63
21 5 0.17
22 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATAATATTTTAAATAAAT
Found at i:306677 original size:19 final size:18
Alignment explanation
Indices: 306655--306720 Score: 66
Period size: 19 Copynumber: 3.7 Consensus size: 18
306645 ACTTTGTTAA
306655 ATATATTAAAAATTTATTT
1 ATATATTAAAAATTT-TTT
* *
306674 ATATATTATATA-TTTTT
1 ATATATTAAAAATTTTTT
306691 ATA-ATTAAAAATATTTTT
1 ATATATTAAAAAT-TTTTT
306709 A-ATATTTAAAAA
1 ATATA-TTAAAAA
306721 ATAATTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 6 0.15
17 7 0.18
18 9 0.23
19 17 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATATTAAAAATTTTTT
Found at i:308195 original size:21 final size:22
Alignment explanation
Indices: 308169--308221 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
308159 AATTTTTAAT
308169 ATTAAATATAATAATTAA-TTA
1 ATTAAATATAATAATTAATTTA
*
308190 ATTAAA-ATATATATTTAATTTA
1 ATTAAATATA-ATAATTAATTTA
308212 A-T-AATATAAT
1 ATTAAATATAAT
308222 TTTTAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 7 0.25
21 17 0.61
22 4 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTAAATATAATAATTAATTTA
Found at i:308214 original size:33 final size:33
Alignment explanation
Indices: 308167--308235 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
308157 ATAATTTTTA
308167 ATATTAAATATAATAAT-TAATTAATTAAAATAT
1 ATATTAAATATAATAATATAATT-ATTAAAATAT
* * * *
308200 ATATTTAATTTAATAATATAATTTTTAAATTAT
1 ATATTAAATATAATAATATAATTATTAAAATAT
308233 ATA
1 ATA
308236 ATTACAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
ATATTAAATATAATAATATAATTATTAAAATAT
Found at i:308312 original size:19 final size:18
Alignment explanation
Indices: 308276--308335 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 18
308266 AAAAGCAAAA
308276 TAATTTTT-ATTAATTTAAT
1 TAATTTTTAATT-A-TTAAT
* *
308295 TTATTTATTATTTATTAAAT
1 TAATTT-TTAATTATT-AAT
308315 TAATTTTTAATTATT-AT
1 TAATTTTTAATTATTAAT
308332 TAAT
1 TAAT
308336 ATTAATGTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 6 0.18
19 15 0.44
20 11 0.32
21 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TAATTTTTAATTATTAAT
Found at i:308315 original size:20 final size:19
Alignment explanation
Indices: 308276--308330 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
308266 AAAAGCAAAA
* *
308276 TAATTTTTATTAATTTAAT
1 TAATTTTTATTTATTAAAT
*
308295 TTATTTATTATTTATTAAAT
1 TAATTT-TTATTTATTAAAT
*
308315 TAATTTTTAATTATTA
1 TAATTTTTATTTATTA
308331 TTAATATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TAATTTTTATTTATTAAAT
Found at i:308339 original size:23 final size:23
Alignment explanation
Indices: 308277--308373 Score: 83
Period size: 23 Copynumber: 4.2 Consensus size: 23
308267 AAAGCAAAAT
* *
308277 AATTTTTATTAAT-TTAATTTATT
1 AATTATTATTAATATTAATTT-TA
* *
308300 TATTATTTATTAA-ATTAATTTTT
1 AATTA-TTATTAATATTAATTTTA
*
308323 AATTATTATTAATATTAATGTTA
1 AATTATTATTAATATTAATTTTA
* *
308346 AATTA-AATAAATTATTAATTTTA
1 AATTATTATTAA-TATTAATTTTA
308369 AATTA
1 AATTA
308374 AATGTTATGA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
22 11 0.18
23 37 0.60
24 14 0.23
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (23 bp):
AATTATTATTAATATTAATTTTA
Found at i:309487 original size:24 final size:24
Alignment explanation
Indices: 309455--309544 Score: 67
Period size: 24 Copynumber: 3.7 Consensus size: 24
309445 TCGCCGGAAA
* *
309455 ATATTTAAAATATAATATATATAT
1 ATATATAAAATATAATATATTTAT
* * *
309479 ATATATAAATTAAAAAAT-TTTAT
1 ATATATAAAATATAATATATTTAT
* *
309502 ATAATATAAATTATAA-ATATTTTT
1 AT-ATATAAAATATAATATATTTAT
309526 AATATTATTAAAATATAAT
1 -ATA-TA-TAAAATATAAT
309545 TAAAAATATA
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
23 8 0.15
24 31 0.60
25 4 0.08
26 9 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATATATAAAATATAATATATTTAT
Found at i:309526 original size:26 final size:25
Alignment explanation
Indices: 309474--309524 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
309464 ATATAATATA
309474 TATATATATATAAATTA-AAAAATTT
1 TATATA-ATATAAATTATAAAAATTT
*
309499 TATATAATATAAATTATAAATATTT
1 TATATAATATAAATTATAAAAATTT
309524 T
1 T
309525 TAATATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TATATAATATAAATTATAAAAATTT
Found at i:309537 original size:26 final size:25
Alignment explanation
Indices: 309474--309543 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 25
309464 ATATAATATA
309474 TATATATATATAAATTA-AAAAATTT
1 TATAT-TATATAAATTATAAAAATTT
* *
309499 TATATAATATAAATTATAAATATTTT
1 TATATTATATAAATTATAAA-AATTT
*
309525 TAATATTAT-TAAAATATAA
1 T-ATATTATATAAATTATAA
309544 TTAAAAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
24 10 0.26
25 8 0.21
26 14 0.37
27 6 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TATATTATATAAATTATAAAAATTT
Found at i:310463 original size:2 final size:2
Alignment explanation
Indices: 310456--310481 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
310446 TCGATTTTTG
310456 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
310482 CACATATACA
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):
TA
Found at i:310895 original size:24 final size:23
Alignment explanation
Indices: 310840--310896 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
310830 TAAATCTAAT
310840 TTTTTATAATGTATAAATATATAA
1 TTTTTA-AATGTATAAATATATAA
* *
310864 ATTATAAATGTATTAAATATA-AA
1 TTTTTAAATGTA-TAAATATATAA
310887 CTTTTTAAAT
1 -TTTTTAAAT
310897 TGAAATGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (23 bp):
TTTTTAAATGTATAAATATATAA
Found at i:311667 original size:13 final size:13
Alignment explanation
Indices: 311649--311682 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
311639 ATTTATATTT
*
311649 TTAAATATTCATA
1 TTAAATATTAATA
311662 TTAAATATTAATA
1 TTAAATATTAATA
*
311675 TTTAATAT
1 TTAAATAT
311683 GTGTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAAATATTAATA
Found at i:312713 original size:13 final size:14
Alignment explanation
Indices: 312695--312735 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
312685 TTTTTAAAAT
312695 TAAAATTAATTT-A
1 TAAAATTAATTTAA
*
312708 TAAAATTATTTTAA
1 TAAAATTAATTTAA
312722 T-AAA-TAATTTAA
1 TAAAATTAATTTAA
312734 TA
1 TA
312736 TTTATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 8 0.33
13 14 0.58
14 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TAAAATTAATTTAA
Found at i:312933 original size:6 final size:7
Alignment explanation
Indices: 312915--312939 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
312905 TAACCACCCA
312915 ATTTTTT
1 ATTTTTT
312922 ATTTTTT
1 ATTTTTT
312929 ATTTTTT
1 ATTTTTT
312936 ATTT
1 ATTT
312940 AAAACTACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
ATTTTTT
Found at i:313775 original size:16 final size:16
Alignment explanation
Indices: 313716--313777 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 16
313706 AATTTAATAA
*
313716 AATTTAATATTTAATTT
1 AATTTAATATTT-ATAT
313733 AA-TTAAT-TTATATAAT
1 AATTTAATATT-TAT-AT
* *
313749 TATTTATTATTTATAT
1 AATTTAATATTTATAT
313765 AATTTAATATTTA
1 AATTTAATATTTA
313778 AATGTTAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
15 4 0.11
16 21 0.58
17 9 0.25
18 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTTAATATTTATAT
Found at i:313775 original size:19 final size:19
Alignment explanation
Indices: 313727--313775 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
313717 ATTTAATATT
*
313727 TAATTTAAT-TAATTTATA
1 TAATTTAATATTATTTATA
*
313745 TAA-TTATTTATTATTTATA
1 TAATTTA-ATATTATTTATA
313764 TAATTTAATATT
1 TAATTTAATATT
313776 TAAATGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 3 0.12
18 4 0.16
19 15 0.60
20 3 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TAATTTAATATTATTTATA
Found at i:317467 original size:2 final size:2
Alignment explanation
Indices: 317462--317490 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
317452 TCTGACTCGC
317462 AT AT AT AT -T 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
317491 GAATTTCAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:318529 original size:2 final size:2
Alignment explanation
Indices: 318522--318546 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
318512 TTCATTTTCT
318522 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
318547 TTTTTTTTAA
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:319156 original size:48 final size:48
Alignment explanation
Indices: 319084--319179 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
319074 CTTAAGTTAG
*
319084 CAAAGTTATGAATTGACATGGGGATGTTGAGAACATTTTATCTTATGA
1 CAAAGTTATGAATTGACATAGGGATGTTGAGAACATTTTATCTTATGA
319132 CAAAGTTATGAATTGACATAGGGATGTTGAGAACATTTTATCTTATGA
1 CAAAGTTATGAATTGACATAGGGATGTTGAGAACATTTTATCTTATGA
319180 TCATAATTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.35
Consensus pattern (48 bp):
CAAAGTTATGAATTGACATAGGGATGTTGAGAACATTTTATCTTATGA
Found at i:320936 original size:2 final size:2
Alignment explanation
Indices: 320929--320956 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
320919 TTTTGAGGGT
320929 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
320957 AAGTTTATTT
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:323628 original size:21 final size:21
Alignment explanation
Indices: 323581--323631 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
323571 ATTTAAAATG
*
323581 ATTTTAATTTAAATAATAAAA
1 ATTTAAATTTAAATAATAAAA
* * **
323602 AATTAAATTTAAATATTTTAA
1 ATTTAAATTTAAATAATAAAA
323623 ATTTAAATT
1 ATTTAAATT
323632 AATTTAAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTAAATTTAAATAATAAAA
Found at i:323639 original size:16 final size:15
Alignment explanation
Indices: 323585--323639 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
323575 AAAATGATTT
*
323585 TAATTTAAATAATAAA
1 TAATTTAAAT-TTAAA
*
323601 -AAATTAAATTTAAA
1 TAATTTAAATTTAAA
*
323615 TATTTTAAATTTAAA
1 TAATTTAAATTTAAA
323630 TTAATTTAAA
1 -TAATTTAAA
323640 AATTTTATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 4 0.12
15 20 0.62
16 8 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATTTAAATTTAAA
Found at i:323657 original size:26 final size:26
Alignment explanation
Indices: 323601--323655 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
323591 AAATAATAAA
* *
323601 AAATTAAATTTAAATATTTTAAATTT
1 AAATTAAATTTAAAAATTTTAAAATT
323627 AAATT-AATTTAAAAATTTTATTAAATT
1 AAATTAAATTTAAAAATTTTA--AAATT
323654 AA
1 AA
323656 TTTTTTATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 14 0.56
26 5 0.20
27 6 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
AAATTAAATTTAAAAATTTTAAAATT
Found at i:326243 original size:14 final size:14
Alignment explanation
Indices: 326218--326253 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
326208 ACTTATTATT
326218 TATTTT-TTAAATA
1 TATTTTATTAAATA
326231 TATTTTATTAAATA
1 TATTTTATTAAATA
*
326245 TATATTATT
1 TATTTTATT
326254 TTATAAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTTTATTAAATA
Found at i:329290 original size:3 final size:3
Alignment explanation
Indices: 329282--329314 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
329272 TTTCATATTA
329282 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
329315 GAATTAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:351752 original size:29 final size:30
Alignment explanation
Indices: 351719--351786 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 30
351709 TTATTAAAAT
*
351719 TTATATATTATAT-AATAT-TTTAAATATAA
1 TTATA-ATTATATAAAAATATTTAAATATAA
351748 TTATAA-TATATAAAAATATTTAAATATAA
1 TTATAATTATATAAAAATATTTAAATATAA
351777 -TATAAATTAT
1 TTAT-AATTAT
351787 TATGTTTACC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 5 0.15
28 8 0.24
29 18 0.53
30 3 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TTATAATTATATAAAAATATTTAAATATAA
Found at i:360559 original size:16 final size:17
Alignment explanation
Indices: 360535--360567 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
360525 CTGTTATTTA
*
360535 TTCT-TTTTTTCTTGCC
1 TTCTCTTTTGTCTTGCC
360551 TTCTCTTTTGTCTTGCC
1 TTCTCTTTTGTCTTGCC
360568 ACCACTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.27, G:0.09, T:0.64
Consensus pattern (17 bp):
TTCTCTTTTGTCTTGCC
Found at i:362824 original size:66 final size:66
Alignment explanation
Indices: 362718--362850 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
362708 TCCGATCAGG
*
362718 ATCTCCAACAGGTATGCATCTTTTGTTGTTTGGTTTGAATGTTGTATAGTTAGTTCTTTTCCCTC
1 ATCTCCAACAGGTATGCATCTTTTGTTGCTTGGTTTGAATGTTGTATAGTTAGTTCTTTTCCCTC
362783 T
66 T
*
362784 ATCTCCAACAGGTATGCTTCTTTTGTTGCTTGGTTTGAATGTTGTATAGTTAGTTCTTTTCCCTC
1 ATCTCCAACAGGTATGCATCTTTTGTTGCTTGGTTTGAATGTTGTATAGTTAGTTCTTTTCCCTC
362849 T
66 T
362850 A
1 A
362851 GAGCATTGTA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.17, G:0.18, T:0.48
Consensus pattern (66 bp):
ATCTCCAACAGGTATGCATCTTTTGTTGCTTGGTTTGAATGTTGTATAGTTAGTTCTTTTCCCTC
T
Found at i:382010 original size:3 final size:3
Alignment explanation
Indices: 382002--382042 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
381992 GGCCCAAGAA
382002 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT GAA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
382043 TTTGATGCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.11
3 29 0.83
4 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:382660 original size:28 final size:27
Alignment explanation
Indices: 382591--382660 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 27
382581 ATTTTTTTAA
*
382591 TTATAATTATATTTAAAGTATTATAGAT
1 TTAT-ATTATTTTTAAAGTATTATAGAT
*
382619 TTATA-TATTTTTTAATA-TATTCATATAT
1 TTATATTA-TTTTTAA-AGTATT-ATAGAT
382647 TTATATTATTTTTA
1 TTATATTATTTTTA
382661 TATTATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
26 2 0.06
27 11 0.31
28 21 0.58
29 2 0.06
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (27 bp):
TTATATTATTTTTAAAGTATTATAGAT
Found at i:382662 original size:11 final size:11
Alignment explanation
Indices: 382646--382677 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
382636 TATTCATATA
382646 TTTATATTATT
1 TTTATATTATT
382657 TTTATATTATT
1 TTTATATTATT
382668 TTTATATTAT
1 TTTATATTAT
382678 ATGTTTTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTATATTATT
Found at i:383522 original size:14 final size:15
Alignment explanation
Indices: 383503--383537 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
383493 TGTAATTTTT
*
383503 ATTTATAATAAT-AA
1 ATTTATAAAAATAAA
383517 ATTTATAAAAATAAA
1 ATTTATAAAAATAAA
383532 ATTTAT
1 ATTTAT
383538 TTATTGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTTATAAAAATAAA
Found at i:383907 original size:20 final size:19
Alignment explanation
Indices: 383864--383908 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
383854 GTTTTCAAGA
*
383864 ATTAAATTTAATAATTTAT
1 ATTATATTTAATAATTTAT
*
383883 ATTATATTTATATATTTTAT
1 ATTATATTTA-ATAATTTAT
*
383903 TTTATA
1 ATTATA
383909 ATAATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATATTTAATAATTTAT
Found at i:383951 original size:30 final size:26
Alignment explanation
Indices: 383902--383958 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 26
383892 ATATATTTTA
383902 TTTTATAATAATTATATTTAAAATAT
1 TTTTATAATAATTATATTTAAAATAT
*
383928 TTTTATATATATATATATAATTTAATATAT
1 TTTTATA-ATA-AT-TAT-ATTTAAAATAT
383958 T
1 T
383959 AAATATTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 7 0.27
27 3 0.12
28 2 0.08
29 3 0.12
30 11 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTTATAATAATTATATTTAAAATAT
Found at i:383976 original size:18 final size:18
Alignment explanation
Indices: 383922--383977 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
383912 ATTATATTTA
383922 AAATATTTTTATATATATAT
1 AAATA-TTTTATATATAT-T
* *
383942 ATATAATTTA-ATATATT
1 AAATATTTTATATATATT
*
383959 AAATATTTTATATGTATT
1 AAATATTTTATATATATT
383977 A
1 A
383978 TATTTATCTG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 9 0.30
18 13 0.43
19 4 0.13
20 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
AAATATTTTATATATATT
Found at i:384513 original size:30 final size:28
Alignment explanation
Indices: 384463--384526 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 28
384453 AACTCAAAGG
* *
384463 ATAAACTAAACATTAATAATTTATTTAAA
1 ATAAATTAAAAATTAATAATTT-TTTAAA
*
384492 TATAAATTAAAAATTATTAATTTTTTAAA
1 -ATAAATTAAAAATTAATAATTTTTTAAA
384521 ATAAAT
1 ATAAAT
384527 ACAAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 6 0.19
29 6 0.19
30 19 0.61
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (28 bp):
ATAAATTAAAAATTAATAATTTTTTAAA
Found at i:384534 original size:30 final size:30
Alignment explanation
Indices: 384474--384533 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
384464 TAAACTAAAC
*
384474 ATTAATAATTTATTTAAATATAAATTAAAA
1 ATTAATAATTTATTTAAATATAAATAAAAA
*
384504 ATTATTAATTT-TTTAAA-ATAAATACAAAA
1 ATTAATAATTTATTTAAATATAAATA-AAAA
384533 A
1 A
384534 AATTTATGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 6 0.22
29 11 0.41
30 10 0.37
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (30 bp):
ATTAATAATTTATTTAAATATAAATAAAAA
Found at i:385537 original size:19 final size:18
Alignment explanation
Indices: 385490--385545 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
385480 AGTGTAATGT
385490 AAAAATATAA-TAAAATA
1 AAAAATATAATTAAAATA
*
385507 AAAATATTTAATTAAAATA
1 AAAA-ATATAATTAAAATA
*
385526 AAATAATATAATTAATATA
1 AAA-AATATAATTAAAATA
385545 A
1 A
385546 TTAATATATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 4 0.12
18 5 0.15
19 23 0.70
20 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAAATATAATTAAAATA
Found at i:385543 original size:9 final size:9
Alignment explanation
Indices: 385515--385553 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
385505 TAAAAATATT
*
385515 TAATTAAAA
1 TAATTAATA
*
385524 TAAAATAATA
1 T-AATTAATA
385534 TAATTAATA
1 TAATTAATA
385543 TAATTAATA
1 TAATTAATA
385552 TA
1 TA
385554 TCATATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
TAATTAATA
Found at i:385577 original size:13 final size:13
Alignment explanation
Indices: 385561--385587 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
385551 ATATCATATT
385561 TATATTTAAATAA
1 TATATTTAAATAA
385574 TATATTTAAATAA
1 TATATTTAAATAA
385587 T
1 T
385588 TAACATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATTTAAATAA
Found at i:385867 original size:30 final size:28
Alignment explanation
Indices: 385833--385964 Score: 74
Period size: 30 Copynumber: 4.6 Consensus size: 28
385823 TTAATAAAGC
*
385833 ATATTTATATTATATTTTTGTGATATAATT
1 ATATTTATATTATATTTTTAT-ATA-AATT
385863 ATATTTAAAATATTATATTTTTATATAAATT
1 ATATTT---ATATTATATTTTTATATAAATT
* ** *
385894 ATA-ATATATTAATAAATGATAATATAAATT
1 ATATTTATATT-AT--ATTTTTATATAAATT
* * *
385924 -TA-TTATATTAT-TTTATATTTAATTT
1 ATATTTATATTATATTTTTATATAAATT
* *
385949 ATGTTTTTATTATATT
1 ATATTTATATTATATT
385965 CTTACGTAAT
Statistics
Matches: 79, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
25 8 0.10
26 1 0.01
27 13 0.16
28 6 0.08
29 8 0.10
30 19 0.24
31 7 0.09
32 3 0.04
33 14 0.18
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (28 bp):
ATATTTATATTATATTTTTATATAAATT
Found at i:385900 original size:20 final size:19
Alignment explanation
Indices: 385877--385918 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
385867 TTAAAATATT
* *
385877 ATATTTTTATATAAATTATA
1 ATATTATTA-ATAAATGATA
385897 ATA-TATTAATAAATGATA
1 ATATTATTAATAAATGATA
385915 ATAT
1 ATAT
385919 AAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
18 12 0.63
19 4 0.21
20 3 0.16
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
ATATTATTAATAAATGATA
Found at i:392208 original size:22 final size:22
Alignment explanation
Indices: 392180--392224 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
392170 AAAATATTAC
*
392180 TCATTAAAATTATATTTGATAT
1 TCATTAAAATTATATTTAATAT
392202 TCATTAAAATTATATTTAATAT
1 TCATTAAAATTATATTTAATAT
392224 T
1 T
392225 TAAAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
TCATTAAAATTATATTTAATAT
Found at i:392957 original size:5 final size:5
Alignment explanation
Indices: 392949--392977 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
392939 GCCAACTTGG
392949 TGGGT TGGGT TGGGT TGGGT TGGG- TGGGT
1 TGGGT TGGGT TGGGT TGGGT TGGGT TGGGT
392978 ATATAGGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.00, G:0.62, T:0.38
Consensus pattern (5 bp):
TGGGT
Found at i:393151 original size:21 final size:19
Alignment explanation
Indices: 393136--393188 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
393126 GAATTATGTA
393136 ATATTTTAAAATAATTATT
1 ATATTTTAAAATAATTATT
*
393155 -TATATTTAATAT-ATTATT
1 ATAT-TTTAAAATAATTATT
393173 AT-TTTTAAAAATAATT
1 ATATTTT-AAAATAATT
393189 TAATTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 3 0.11
18 14 0.50
19 11 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTTTAAAATAATTATT
Found at i:393202 original size:35 final size:35
Alignment explanation
Indices: 393137--393203 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
393127 AATTATGTAA
*
393137 TATTTTAAAATAATTATTTATATTTAATATATTAT
1 TATTTTAAAATAATAATTTATATTTAATATATTAT
*
393172 TATTTTTAAA-AATAATTTA-ATTATATATATAT
1 TATTTTAAAATAATAATTTATATT-TA-ATATAT
393204 AAATATCACA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 3 0.11
34 10 0.36
35 15 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (35 bp):
TATTTTAAAATAATAATTTATATTTAATATATTAT
Found at i:395856 original size:22 final size:22
Alignment explanation
Indices: 395828--395869 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
395818 TCACTAGCAC
395828 CAACAACATC-ATCACCTTTCAG
1 CAACAAC-TCAATCACCTTTCAG
*
395850 CAACAACTCAATCATCTTTC
1 CAACAACTCAATCACCTTTC
395870 TACGGGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (22 bp):
CAACAACTCAATCACCTTTCAG
Found at i:397206 original size:6 final size:6
Alignment explanation
Indices: 397197--397242 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
397187 AATCAAAGGT
*
397197 GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG AAAAT- GAAAT
1 GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG GAAAT
397243 TTGTAATGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 4 0.11
6 34 0.89
ACGTcount: A:0.54, C:0.00, G:0.28, T:0.17
Consensus pattern (6 bp):
GAAATG
Found at i:397394 original size:15 final size:14
Alignment explanation
Indices: 397362--397409 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
397352 CAATAATAAC
*
397362 AATATAAAATTAAGA
1 AATATAAAA-TAAAA
397377 AATATAAAGATAAAA
1 AATATAAA-ATAAAA
*
397392 AATAAAAAAATAAAA
1 AAT-ATAAAATAAAA
397407 AAT
1 AAT
397410 TTATTCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 24 0.83
16 5 0.17
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (14 bp):
AATATAAAATAAAA
Found at i:397501 original size:13 final size:13
Alignment explanation
Indices: 397485--397573 Score: 56
Period size: 14 Copynumber: 6.5 Consensus size: 13
397475 AATATTAATA
397485 AATATAATTATAT
1 AATATAATTATAT
* *
397498 AATATTTATATATAA
1 AATA-TAAT-TATAT
397513 AATATAATTATA-
1 AATATAATTATAT
397525 AGATATAAATATATAT
1 A-ATAT-AAT-TATAT
** *
397541 TTTAAAATTTATAT
1 AATATAA-TTATAT
397555 AATATAAATTAT-T
1 AATAT-AATTATAT
397568 AATATA
1 AATATA
397574 TTAAATTTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
12 2 0.03
13 18 0.31
14 22 0.37
15 17 0.29
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (13 bp):
AATATAATTATAT
Found at i:397530 original size:28 final size:28
Alignment explanation
Indices: 397484--397605 Score: 83
Period size: 28 Copynumber: 4.4 Consensus size: 28
397474 AAATATTAAT
**
397484 AAATATAATTATATAATATTTATATATA
1 AAATATAATTATATAATATAAATATATA
397512 AAATATAATTATA-AGATATAAATATATA
1 AAATATAATTATATA-ATATAAATATATA
*** *
397540 TTTTAAAATTTATATAATATAAAT-TATTA
1 AAATATAA-TTATATAATATAAATATA-TA
* * *
397569 ATATATTAAATT-TAT-ATA-AAATATTTT
1 AAATA-T-AATTATATAATATAAATATATA
397596 AAATATAATT
1 AAATATAATT
397606 TTAATTTAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
25 4 0.05
26 1 0.01
27 10 0.13
28 34 0.45
29 21 0.28
30 3 0.04
31 2 0.03
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
AAATATAATTATATAATATAAATATATA
Found at i:397592 original size:18 final size:18
Alignment explanation
Indices: 397545--397593 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
397535 ATATATTTTA
397545 AAATTTATAT--AATA-T
1 AAATTTATATAAAATATT
*
397560 AAA-TTAT-TAATATATT
1 AAATTTATATAAAATATT
397576 AAATTTATATAAAATATT
1 AAATTTATATAAAATATT
397594 TTAAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
13 1 0.04
14 4 0.15
15 6 0.22
16 4 0.15
17 4 0.15
18 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATTTATATAAAATATT
Found at i:397612 original size:31 final size:32
Alignment explanation
Indices: 397530--397622 Score: 88
Period size: 31 Copynumber: 2.9 Consensus size: 32
397520 TTATAAGATA
*
397530 TAAATATATATTTTAAAATTTATATAATATAAATTAT
1 TAAATATA-ATTTT--AATTTATATAA-A-ATATTAT
*
397567 T-AATAT-A-TTAAATTTATATAAAATATT-T
1 TAAATATAATTTTAATTTATATAAAATATTAT
397595 TAAATATAATTTTAATTTA-ATAAAATAT
1 TAAATATAATTTTAATTTATATAAAATAT
397623 AAAATAATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
28 2 0.04
29 9 0.18
30 11 0.22
31 19 0.38
33 2 0.04
34 1 0.02
36 5 0.10
37 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
TAAATATAATTTTAATTTATATAAAATATTAT
Found at i:398160 original size:21 final size:22
Alignment explanation
Indices: 398085--398170 Score: 72
Period size: 20 Copynumber: 3.8 Consensus size: 22
398075 AGTTGGGGTG
398085 ATTTTAAATTTAATTTTTTATTTAA
1 ATTTTAAA--TAA-TTTTTATTTAA
* *
398110 ATCGTTTGAATAATTTTTAAATTAA
1 AT--TTTAAATAATTTTT-ATTTAA
398135 A-TTTAAATAA-TTTTATTTAA
1 ATTTTAAATAATTTTTATTTAA
398155 ATTTTAAAT--TTTTTAT
1 ATTTTAAATAATTTTTAT
398171 CAATTTAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
20 12 0.23
21 11 0.21
22 8 0.15
24 5 0.10
25 11 0.21
27 5 0.10
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTTTAAATAATTTTTATTTAA
Found at i:398672 original size:33 final size:33
Alignment explanation
Indices: 398634--398696 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
398624 TATGTATAAT
* *
398634 TAATTTGTTAATT-TATTTTATGATTTAATTCAA
1 TAATTTGTTAATTAAATTTAAT-ATTTAATTCAA
*
398667 TAATTTTTTAATTAAATTTAATATTTAATT
1 TAATTTGTTAATTAAATTTAATATTTAATT
398697 AAAAATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 20 0.77
34 6 0.23
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.59
Consensus pattern (33 bp):
TAATTTGTTAATTAAATTTAATATTTAATTCAA
Found at i:399145 original size:15 final size:16
Alignment explanation
Indices: 399121--399160 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
399111 AAAATAAAAA
399121 ATTA-ATTTATTA-AT
1 ATTATATTTATTATAT
399135 ATTATATTTA-TATAT
1 ATTATATTTATTATAT
*
399150 AATATATTTAT
1 ATTATATTTAT
399161 ATTTAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTATATTTATTATAT
Found at i:399161 original size:15 final size:15
Alignment explanation
Indices: 399137--399189 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
399127 TTATTAATAT
399137 TATATTTATATATAA
1 TATATTTATATATAA
*
399152 TATATTTATATTTAA
1 TATATTTATATATAA
*
399167 AATATTT-TA-ATAA
1 TATATTTATATATAA
399180 TA-ATTTATAT
1 TATATTTATAT
399190 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
12 4 0.12
13 6 0.19
14 2 0.06
15 20 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATTTATATATAA
Found at i:400445 original size:104 final size:102
Alignment explanation
Indices: 400242--400434 Score: 237
Period size: 104 Copynumber: 1.9 Consensus size: 102
400232 AATTCAACTA
* * *
400242 TTAATGCATGACTTTTATATTAAAAAATAAAATTTGATATATTTAAAACTTAATTCAATTTATGC
1 TTAATACATGACTTTTATATTAAAAAATAAAATTTGATAAATTAAAAACTTAATTCAATTTATGC
* * *
400307 ATACAAATACAGATTTAAAATTTGAATCTAATTTAATGT
66 ATACAAATAC--ATCTAAAATTTAAATCAAATTTAATGT
* * * *
400346 TTAATACATGA-TTTTATATTCAAAAATTAAAGTTTGATAAATTAAAAACTTAATTTAATTTATT
1 TTAATACATGACTTTTATATT-AAAAAATAAAATTTGATAAATTAAAAACTTAATTCAATTTATG
* *
400410 CATATAATTAC-TCTAAAATTTAAAT
65 CATACAAATACATCTAAAATTTAAAT
400435 TTCAATATTT
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
101 12 0.16
103 9 0.12
104 56 0.73
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (102 bp):
TTAATACATGACTTTTATATTAAAAAATAAAATTTGATAAATTAAAAACTTAATTCAATTTATGC
ATACAAATACATCTAAAATTTAAATCAAATTTAATGT
Found at i:400755 original size:27 final size:27
Alignment explanation
Indices: 400725--400776 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
400715 TATGTGATAT
*
400725 AAATATTATAC-TTTAATAAATATAAAA
1 AAATATT-TACATATAATAAATATAAAA
*
400752 AAATATTTACATATAATTAATATAA
1 AAATATTTACATATAATAAATATAA
400777 TATGTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (27 bp):
AAATATTTACATATAATAAATATAAAA
Found at i:401364 original size:30 final size:30
Alignment explanation
Indices: 401330--401398 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
401320 AATGTATAAT
* *
401330 TTATATTTAAATAAGTCTTTAACTTTCAAA
1 TTATATTTAAATAAATCCTTAACTTTCAAA
* *
401360 TTATATTTAAATAAATCCTTAACTTTTAAT
1 TTATATTTAAATAAATCCTTAACTTTCAAA
401390 TTATATTTA
1 TTATATTTA
401399 TACACCTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (30 bp):
TTATATTTAAATAAATCCTTAACTTTCAAA
Found at i:402253 original size:132 final size:133
Alignment explanation
Indices: 402015--402281 Score: 414
Period size: 132 Copynumber: 2.0 Consensus size: 133
402005 ATTAATTTGT
402015 GCAATAATTGTATGTATGGCATTTGATTAATACAATCAAAATTATAATAATAGTCAATCTCACTT
1 GCAATAATTGTATGTATGGCATTTGATTAATACAATCAAAATTATAATAATAGTCAATCTCACTT
402080 AATTTTTTAATAATCTTATACTTTAAAAATTACGTACAAATTCAACCAAC-AGTATGTAACATAT
66 AATTTTTTAATAATCTTATACTTTAAAAATTACGTACAAATTCAACCAACAAGTATGTAACATAT
402144 GTC
131 GTC
* * *
402147 GCAATAATTGTATGTATGGCATTTGATTAATACAGA-CAAAATTATAATAATAGTTAGTC-CTAT
1 GCAATAATTGTATGTATGGCATTTGATTAATACA-ATCAAAATTATAATAATAGTCAATCTC-AC
* * * *
402210 TTAATTTTTTAATAATCTTATGCTTTAAGAATTGCGTATAAATTCAACCAACATAAGTATGTAAC
64 TTAATTTTTTAATAATCTTATACTTTAAAAATTACGTACAAATTCAACCAAC--AAGTATGTAAC
402275 ATATGTC
127 ATATGTC
402282 CCACATACTT
Statistics
Matches: 123, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
131 1 0.01
132 104 0.85
133 1 0.01
135 17 0.14
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (133 bp):
GCAATAATTGTATGTATGGCATTTGATTAATACAATCAAAATTATAATAATAGTCAATCTCACTT
AATTTTTTAATAATCTTATACTTTAAAAATTACGTACAAATTCAACCAACAAGTATGTAACATAT
GTC
Found at i:403025 original size:11 final size:11
Alignment explanation
Indices: 403005--403038 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
402995 AATTGTCAAA
*
403005 TTTAATTTAAT
1 TTTAACTTAAT
403016 TTTAACTTAAT
1 TTTAACTTAAT
*
403027 TTTAACTCAAT
1 TTTAACTTAAT
403038 T
1 T
403039 AATTTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTAACTTAAT
Found at i:405393 original size:11 final size:11
Alignment explanation
Indices: 405377--405419 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
405367 ATTAATTATA
405377 ATAATATAAAT
1 ATAATATAAAT
405388 ATAATATAAAT
1 ATAATATAAAT
*
405399 AAAATAATTAAAAT
1 ATAAT-A-T-AAAT
405413 ATAATAT
1 ATAATAT
405420 TATATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 15 0.56
12 2 0.07
13 2 0.07
14 8 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:405412 original size:25 final size:25
Alignment explanation
Indices: 405362--405419 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
405352 GATAAATCTG
* *
405362 ATAATATTAATTATAATAATATAAAT
1 ATAATA-TAAATAAAATAATATAAAT
405388 ATAATATAAATAAAATAAT-TAAAAT
1 ATAATATAAATAAAATAATAT-AAAT
405413 ATAATAT
1 ATAATAT
405420 TATATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 1 0.03
25 22 0.76
26 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
ATAATATAAATAAAATAATATAAAT
Found at i:406361 original size:2 final size:2
Alignment explanation
Indices: 406356--406397 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
406346 AGTGATGACA
406356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
406398 TCCTTTTTTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:408380 original size:24 final size:26
Alignment explanation
Indices: 408353--408404 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
408343 TTTGTTTTAG
* *
408353 TTCT-ATTTTCTTTTTCT-TTTTTTT
1 TTCTAATTTTCTTGTGCTGTTTTTTT
*
408377 TTCTAATTTTGTTGTGCTGTTTTTTT
1 TTCTAATTTTCTTGTGCTGTTTTTTT
408403 TT
1 TT
408405 ATTCCTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 4 0.17
25 10 0.43
26 9 0.39
ACGTcount: A:0.06, C:0.10, G:0.08, T:0.77
Consensus pattern (26 bp):
TTCTAATTTTCTTGTGCTGTTTTTTT
Found at i:412779 original size:20 final size:21
Alignment explanation
Indices: 412744--412790 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
412734 TTTTTTTTCG
* *
412744 GATGAATGTAGGGAAGTAATT
1 GATGAATATAGGGAAGGAATT
412765 GATGAATAT-GGGAAGGAATT
1 GATGAATATAGGGAAGGAATT
*
412785 GGTGAA
1 GATGAA
412791 GTTATGTGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.36, T:0.26
Consensus pattern (21 bp):
GATGAATATAGGGAAGGAATT
Found at i:415235 original size:21 final size:22
Alignment explanation
Indices: 415206--415273 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
415196 TTTAAAAATA
*
415206 TTAAAATTTTTAT-TTTTTATT
1 TTAAAATTTATATATTTTTATT
* *
415227 TTAATATTTATATATTTTTATAA
1 TTAAAATTTATATATTTTTAT-T
*
415250 TT-AAATTTAAATAATTTTTTATT
1 TTAAAATTTATAT-A-TTTTTATT
415273 T
1 T
415274 AAGTAATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 11 0.30
22 15 0.41
23 4 0.11
24 7 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTAAAATTTATATATTTTTATT
Found at i:415268 original size:24 final size:23
Alignment explanation
Indices: 415216--415275 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
415206 TTAAAATTTT
* *
415216 TATTTTTTATTTTAATATTTATA
1 TATTTTTTATATTAATATTTAAA
415239 TA-TTTTTATAATTAA-ATTTAAA
1 TATTTTTTAT-ATTAATATTTAAA
415261 TAATTTTTTAT-TTAA
1 T-ATTTTTTATATTAA
415276 GTAATTAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 18 0.56
23 7 0.22
24 7 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTTTTTATATTAATATTTAAA
Found at i:415275 original size:22 final size:22
Alignment explanation
Indices: 415216--415275 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
415206 TTAAAATTTT
*
415216 TATTTTTTATTTTAATATTTATA
1 TATTTTTTA-TTTAATATTTAAA
*
415239 TATTTTTATAATTAA-ATTTAAA
1 TATTTTT-TATTTAATATTTAAA
415261 TAATTTTTTATTTAA
1 T-ATTTTTTATTTAA
415276 GTAATTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 13 0.41
23 17 0.53
24 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTTTTTATTTAATATTTAAA
Found at i:419674 original size:155 final size:155
Alignment explanation
Indices: 419387--419697 Score: 541
Period size: 155 Copynumber: 2.0 Consensus size: 155
419377 CAGATTGAGG
*
419387 ATAAAAACATCAGACAAAAAGGAGAAAGTAGTCTCTACTTAAAGGATTCATGAGATTGAAGATAG
1 ATAAAAACATCAGACAAAAAGGAGAAAGTAGTCTCTACCTAAAGGATTCATGAGATTGAAGATAG
*
419452 AAGGTATTAATCTCCAGATTCCCATCTTACAATCCATAAACAAAGGAATGGCTGACTCCAGATTG
66 AAGGTATTAATCTCCAGATTCCCATCTTACAATCCATAAACAAAGGAATGGCTGACTCCAGAATG
* *
419517 AAGTAAAGAAAATTGGTAAAAGGTA
131 AAGTAAAGAAAAATGGCAAAAGGTA
*
419542 ATAAAAACATCAGATAAAAAGGAGAAAGTAGTCTCTACCTAAAGGATTCATGAGATTGAAGATAG
1 ATAAAAACATCAGACAAAAAGGAGAAAGTAGTCTCTACCTAAAGGATTCATGAGATTGAAGATAG
* * * *
419607 AAGGTTTTAGTCTCCAGATTCCCATCTTACGATCCATAAACAAAGGAGTGGCTGACTCCAGAATG
66 AAGGTATTAATCTCCAGATTCCCATCTTACAATCCATAAACAAAGGAATGGCTGACTCCAGAATG
419672 AAGTAAAGAAAAATGGCAAAAGGTA
131 AAGTAAAGAAAAATGGCAAAAGGTA
419697 A
1 A
419698 GAGTAAGGTC
Statistics
Matches: 147, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
155 147 1.00
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (155 bp):
ATAAAAACATCAGACAAAAAGGAGAAAGTAGTCTCTACCTAAAGGATTCATGAGATTGAAGATAG
AAGGTATTAATCTCCAGATTCCCATCTTACAATCCATAAACAAAGGAATGGCTGACTCCAGAATG
AAGTAAAGAAAAATGGCAAAAGGTA
Found at i:426206 original size:2 final size:2
Alignment explanation
Indices: 426199--426231 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
426189 AATCCTTCAA
426199 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 A
426232 ACTTTGAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:427927 original size:19 final size:19
Alignment explanation
Indices: 427878--427932 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
427868 AATGTTATGA
*
427878 TTATTATTTATAATTATAATTT
1 TTATTATTT-TAA-TA-AATAT
427900 TTA-TATTTTAATAAATAT
1 TTATTATTTTAATAAATAT
427918 TTATTATTTTAATAA
1 TTATTATTTTAATAA
427933 CTATAAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 7 0.23
19 13 0.42
20 3 0.10
21 5 0.16
22 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATTATTTTAATAAATAT
Found at i:428072 original size:16 final size:17
Alignment explanation
Indices: 428051--428086 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
428041 ATATTTAATC
428051 ATAATTTT-TATAAAAA
1 ATAATTTTGTATAAAAA
*
428067 ATAATTTTGTGTAAAAA
1 ATAATTTTGTATAAAAA
428084 ATA
1 ATA
428087 GAAAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
ATAATTTTGTATAAAAA
Found at i:428276 original size:12 final size:12
Alignment explanation
Indices: 428242--428304 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
428232 TTGATCCAAT
*
428242 TTTATTAAATTA
1 TTTATTAATTTA
* **
428254 TATATCGATTTA
1 TTTATTAATTTA
428266 TTTATTAATTTA
1 TTTATTAATTTA
* *
428278 TTTATTTACTTTG
1 TTTA-TTAATTTA
*
428291 TTTATTATTTTA
1 TTTATTAATTTA
428303 TT
1 TT
428305 CATAGTTGAT
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
12 29 0.74
13 10 0.26
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (12 bp):
TTTATTAATTTA
Found at i:429499 original size:15 final size:16
Alignment explanation
Indices: 429470--429500 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
429460 TTTATATTTA
429470 ATTATAAATAATAAAT
1 ATTATAAATAATAAAT
429486 ATTATAAA-AATAAAT
1 ATTATAAATAATAAAT
429501 TTTAATATTT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTATAAATAATAAAT
Found at i:430056 original size:29 final size:31
Alignment explanation
Indices: 429991--430056 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 31
429981 ATTCATAAAT
* *
429991 TAAAATAAATTTAATTAAATTTATTTATAAA
1 TAAAATAAATTTAATTAAATTTATATAGAAA
* * *
430022 TTAAAT-AATTT-ATTCAATTTATATAGACA
1 TAAAATAAATTTAATTAAATTTATATAGAAA
430051 TAAAAT
1 TAAAAT
430057 TTAATTAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
29 19 0.66
30 5 0.17
31 5 0.17
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (31 bp):
TAAAATAAATTTAATTAAATTTATATAGAAA
Found at i:431522 original size:18 final size:18
Alignment explanation
Indices: 431481--431529 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
431471 TAATTATATT
431481 ATAAAAATAATTAAAATAAA
1 ATAAAAAT-A-TAAAATAAA
* *
431501 ATAAAAATATAACATAAG
1 ATAAAAATATAAAATAAA
431519 ATAAAAATATA
1 ATAAAAATATA
431530 TTAATATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 18 0.67
19 1 0.04
20 8 0.30
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (18 bp):
ATAAAAATATAAAATAAA
Found at i:431991 original size:26 final size:26
Alignment explanation
Indices: 431961--432050 Score: 84
Period size: 26 Copynumber: 3.5 Consensus size: 26
431951 TTTAAAATTT
431961 ATTTAAATTTTAATAAATATTTTATA
1 ATTTAAATTTTAATAAATATTTTATA
431987 ATTTAAATTAGATTAATTAAAT-TTTTATA
1 ATTTAAATT---TTAA-TAAATATTTTATA
432016 ATTT---TTTTAATAAAAATATTTT-T-
1 ATTTAAATTTTAAT--AAATATTTTATA
432039 ATTTAAATTTTA
1 ATTTAAATTTTA
432051 TTATAAAATT
Statistics
Matches: 54, Mismatches: 0, Indels: 20
0.73 0.00 0.27
Matches are distributed among these distances:
22 1 0.02
23 8 0.15
24 5 0.09
25 4 0.07
26 16 0.30
29 15 0.28
30 5 0.09
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
ATTTAAATTTTAATAAATATTTTATA
Done.