Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold170
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: 1632119
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.33
Warning! 57634 characters in sequence are not A, C, G, or T
File 8 of 11
Found at i:1169075 original size:2 final size:2
Alignment explanation
Indices: 1169068--1169102 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1169058 CAAATCAAGA
1169068 AT 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 A
1169103 ACACTCAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1169801 original size:16 final size:16
Alignment explanation
Indices: 1169780--1169838 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 16
1169770 ATATATATTT
1169780 TAAAATTTATTTAATA
1 TAAAATTTATTTAATA
*
1169796 TAAAA--TATTAATATA
1 TAAAATTTATTTA-ATA
*
1169811 TCAAAATTTATATAA-A
1 T-AAAATTTATTTAATA
*
1169827 TAAAATATATTT
1 TAAAATTTATTT
1169839 TAAATATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
14 5 0.15
15 13 0.38
16 11 0.32
17 1 0.03
18 4 0.12
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAATTTATTTAATA
Found at i:1171664 original size:23 final size:23
Alignment explanation
Indices: 1171638--1171686 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
1171628 TTTTTATTAA
1171638 TTATTTAATAT-AAAATT-TAATAT
1 TTATTT-ATATCAAAATTAT-ATAT
1171661 TTATTTATATCAAAATTATATAT
1 TTATTTATATCAAAATTATATAT
1171684 TTA
1 TTA
1171687 ATATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.17
23 19 0.79
24 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TTATTTATATCAAAATTATATAT
Found at i:1172292 original size:2 final size:2
Alignment explanation
Indices: 1172285--1172316 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1172275 TTATATGTAA
1172285 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
1172317 GAGTTTGATT
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:1173455 original size:15 final size:16
Alignment explanation
Indices: 1173417--1173455 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1173407 ATTTAAAAAA
1173417 TAATATTTAATAAATTT
1 TAAT-TTTAATAAATTT
*
1173434 TAATTTTAAT-ATTTT
1 TAATTTTAATAAATTT
1173449 TAATTTT
1 TAATTTT
1173456 TAAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.52
16 6 0.29
17 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TAATTTTAATAAATTT
Found at i:1173456 original size:16 final size:17
Alignment explanation
Indices: 1173417--1173463 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
1173407 ATTTAAAAAA
*
1173417 TAATATTTAATAAATTT
1 TAATTTTTAATAAATTT
*
1173434 TAA-TTTTAAT-ATTTT
1 TAATTTTTAATAAATTT
*
1173449 TAATTTTTAAAAAAT
1 TAATTTTTAATAAAT
1173464 AAAGATTAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
15 7 0.29
16 12 0.50
17 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TAATTTTTAATAAATTT
Found at i:1174130 original size:13 final size:13
Alignment explanation
Indices: 1174091--1174131 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1174081 AATTTTATAA
1174091 ATAAAAATATATT
1 ATAAAAATATATT
*
1174104 TTAAAAAT-TA-T
1 ATAAAAATATATT
*
1174115 ATAAAATTATATT
1 ATAAAAATATATT
1174128 ATAA
1 ATAA
1174132 TTTATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 7 0.30
12 4 0.17
13 12 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATAAAAATATATT
Found at i:1174501 original size:29 final size:28
Alignment explanation
Indices: 1174463--1174589 Score: 97
Period size: 29 Copynumber: 4.7 Consensus size: 28
1174453 AATTGGAGTT
1174463 AATATTTTATATATTTATATTATATTTA
1 AATATTTTATATATTTATATTATATTTA
* *
1174491 AATTATTTTATGTA-TTATAATTATTTTTA
1 AA-TATTTTATATATTTAT-ATTATATTTA
* * *
1174520 AA-ATATTATATATTTATA-TAAATTTT
1 AATATTTTATATATTTATATTATATTTA
* * *
1174546 AATATATTA-ATAATTTGTGTTATA--TA
1 AATATTTTATAT-ATTTATATTATATTTA
*
1174572 AAT-TTTAATATATTTATA
1 AATATTTTATATATTTATA
1174590 CATTTTTATT
Statistics
Matches: 77, Mismatches: 15, Indels: 17
0.71 0.14 0.16
Matches are distributed among these distances:
25 8 0.10
26 15 0.19
27 20 0.26
28 13 0.17
29 21 0.27
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (28 bp):
AATATTTTATATATTTATATTATATTTA
Found at i:1174550 original size:20 final size:20
Alignment explanation
Indices: 1174466--1174553 Score: 62
Period size: 18 Copynumber: 4.7 Consensus size: 20
1174456 TGGAGTTAAT
*
1174466 ATTTT-ATATATTTATATTAT
1 ATTTTAATATATTTATA-TAA
* **
1174486 ATTTAAAT-TATTT-TATGT
1 ATTTTAATATATTTATATAA
* *
1174504 ATTATAAT-TATTTTTA-AA
1 ATTTTAATATATTTATATAA
*
1174522 ATATT-ATATATTTATATAA
1 ATTTTAATATATTTATATAA
1174541 ATTTTAATATATT
1 ATTTTAATATATT
1174554 AATAATTTGT
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
17 2 0.04
18 23 0.43
19 10 0.19
20 16 0.30
21 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (20 bp):
ATTTTAATATATTTATATAA
Found at i:1174569 original size:32 final size:33
Alignment explanation
Indices: 1174533--1174594 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 33
1174523 TATTATATAT
1174533 TTATATAAATTTTAATATATTAATA-ATTTGTG
1 TTATATAAATTTTAATATATTAATACATTTGTG
*
1174565 TTATATAAATTTTAATATATTTATACATTT
1 TTATATAAATTTTAATATATTAATACATTT
1174595 TTATTTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (33 bp):
TTATATAAATTTTAATATATTAATACATTTGTG
Found at i:1174656 original size:24 final size:24
Alignment explanation
Indices: 1174603--1174659 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
1174593 TTTTATTTTT
* *
1174603 TATTATATTTTAATTATTTTTTAA
1 TATTATATTTTAATTATATATTAA
* *
1174627 TCTTATA-TTTATATTATATATTAG
1 TATTATATTTTA-ATTATATATTAA
1174651 TATTATATT
1 TATTATATT
1174660 CAAAACTACT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 4 0.15
24 21 0.81
25 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (24 bp):
TATTATATTTTAATTATATATTAA
Found at i:1174898 original size:19 final size:16
Alignment explanation
Indices: 1174857--1174888 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1174847 TTATATTTTA
*
1174857 TTATATTTAAAATATT
1 TTATATTTAAAAAATT
1174873 TTATATTTAAAAAATT
1 TTATATTTAAAAAATT
1174889 ATAATATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATATTTAAAAAATT
Found at i:1174961 original size:21 final size:21
Alignment explanation
Indices: 1174929--1174981 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
1174919 TTTTAAAATA
*
1174929 TATATTTATATAATATTAATAT
1 TATATTTTTATAATATT-ATAT
*
1174951 TAT-TTTTTATAATATTTTAT
1 TATATTTTTATAATATTATAT
1174971 TATATTTTTAT
1 TATATTTTTAT
1174982 TTTATAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 6 0.21
21 19 0.68
22 3 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATATTTTTATAATATTATAT
Found at i:1174965 original size:26 final size:26
Alignment explanation
Indices: 1174936--1174989 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
1174926 ATATATATTT
1174936 ATATAATATTAATATTATT-TTTTATA
1 ATATAATATT-ATATTATTATTTTATA
** *
1174962 ATATTTTATTATATTTTTATTTTATA
1 ATATAATATTATATTATTATTTTATA
1174988 AT
1 AT
1174990 TCTATCGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
ATATAATATTATATTATTATTTTATA
Found at i:1177323 original size:2 final size:2
Alignment explanation
Indices: 1177316--1177341 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1177306 GTTCTTTCTT
1177316 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
1177342 AATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1178975 original size:18 final size:17
Alignment explanation
Indices: 1178952--1178985 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1178942 AAGTTAAAAA
1178952 AATTAAATTGATTTAATT
1 AATTAAATT-ATTTAATT
1178970 AATTAAATTATTTAAT
1 AATTAAATTATTTAAT
1178986 AGATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
AATTAAATTATTTAATT
Found at i:1179150 original size:23 final size:20
Alignment explanation
Indices: 1179117--1179170 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
1179107 AAATCAAATA
1179117 TATATTTTTTAATGAATTAAT
1 TATATTTTTTAAT-AATTAAT
*
1179138 TATATTATATTTAATATTTAAT
1 TATATT-T-TTTAATAATTAAT
1179160 T-TATTTTTTAA
1 TATATTTTTTAA
1179171 ACAAATCATC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.17
20 1 0.03
21 10 0.33
22 8 0.27
23 6 0.20
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TATATTTTTTAATAATTAAT
Found at i:1179996 original size:7 final size:7
Alignment explanation
Indices: 1179984--1180015 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
1179974 TAACTCGAAA
1179984 AAATTTT
1 AAATTTT
1179991 AAATTTT
1 AAATTTT
1179998 AAA-TTT
1 AAATTTT
1180004 AAA-TTT
1 AAATTTT
1180010 AAATTT
1 AAATTT
1180016 GATCTGGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
AAATTTT
Found at i:1180083 original size:19 final size:20
Alignment explanation
Indices: 1180061--1180101 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
1180051 TATAATAAAA
1180061 TATTTAAAAATTATAT-TTT
1 TATTTAAAAATTATATATTT
* *
1180080 TA-TTAATATTTATATATTT
1 TATTTAAAAATTATATATTT
1180099 TAT
1 TAT
1180102 AATTTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 3
0.78 0.09 0.13
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TATTTAAAAATTATATATTT
Found at i:1180239 original size:2 final size:2
Alignment explanation
Indices: 1180232--1180346 Score: 96
Period size: 2 Copynumber: 58.0 Consensus size: 2
1180222 TACAGTAGTG
* * *
1180232 TA TA TA TA TA TA TA TA -A TA CA GTA GTG TA CA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA -TA TA TA TA TA TA TA TA TA
* * * *
1180274 -A TA TA TA TA TA TA -A AA TA CA GTA GTG TA CA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA -TA TA TA TA TA TA TA TA TA
1180315 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
1180347 GGCGAGGGGG
Statistics
Matches: 93, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
1 5 0.05
2 82 0.88
3 6 0.06
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (2 bp):
TA
Found at i:1180259 original size:27 final size:26
Alignment explanation
Indices: 1180221--1180276 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 26
1180211 AGGTCTATGG
*
1180221 ATACAGTAGTGTATATATATATATATA
1 ATACAGTAGTGTACATATATA-ATATA
1180248 ATACAGTAGTGTACATATATAATATA
1 ATACAGTAGTGTACATATATAATATA
1180274 ATA
1 ATA
1180277 TATATATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (26 bp):
ATACAGTAGTGTACATATATAATATA
Found at i:1180292 original size:41 final size:42
Alignment explanation
Indices: 1180232--1180328 Score: 178
Period size: 41 Copynumber: 2.3 Consensus size: 42
1180222 TACAGTAGTG
*
1180232 TATATATATATATATAATACAGTAGTGTACATATATAATATA
1 TATATATATATATAAAATACAGTAGTGTACATATATAATATA
1180274 -ATATATATATATAAAATACAGTAGTGTACATATATAATATA
1 TATATATATATATAAAATACAGTAGTGTACATATATAATATA
1180315 TATATATATATATA
1 TATATATATATATA
1180329 TATATATATA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
41 40 0.75
42 13 0.25
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.40
Consensus pattern (42 bp):
TATATATATATATAAAATACAGTAGTGTACATATATAATATA
Found at i:1180306 original size:23 final size:23
Alignment explanation
Indices: 1180239--1180310 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
1180229 GTGTATATAT
*
1180239 ATATATATAATACAGTAGTGTAC
1 ATATATAAAATACAGTAGTGTAC
* *
1180262 ATATATAATATA-A-TA---TAT
1 ATATATAAAATACAGTAGTGTAC
1180280 ATATATAAAATACAGTAGTGTAC
1 ATATATAAAATACAGTAGTGTAC
1180303 ATATATAA
1 ATATATAA
1180311 TATATATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 2 0.05
21 2 0.05
22 1 0.03
23 20 0.51
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (23 bp):
ATATATAAAATACAGTAGTGTAC
Found at i:1181785 original size:43 final size:37
Alignment explanation
Indices: 1181695--1181786 Score: 89
Period size: 43 Copynumber: 2.4 Consensus size: 37
1181685 TTAGTGAAAT
**
1181695 AAAA-ATTTTTAATTTAAATTATTATTTATTTAATAA
1 AAAATATTTTTAATTTAAATTATTATAAATTTAATAA
1181731 AAAAT-TATTTTATATTTAAATTTAATTATAAAATTTAAATATA
1 AAAATAT-TTTTA-ATTTAAA-TT-ATTAT-AAATTT-AATA-A
1181774 AAAATATTTTTAA
1 AAAATATTTTTAA
1181787 ATATTTTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
36 5 0.11
37 5 0.11
38 7 0.16
39 2 0.04
40 5 0.11
41 4 0.09
42 5 0.11
43 11 0.24
44 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (37 bp):
AAAATATTTTTAATTTAAATTATTATAAATTTAATAA
Found at i:1181790 original size:10 final size:10
Alignment explanation
Indices: 1181775--1181799 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1181765 TTAAATATAA
1181775 AAATATTTTT
1 AAATATTTTT
1181785 AAATATTTTT
1 AAATATTTTT
1181795 AAATA
1 AAATA
1181800 ATAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
AAATATTTTT
Found at i:1181817 original size:29 final size:28
Alignment explanation
Indices: 1181764--1181818 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
1181754 AATTATAAAA
* *
1181764 TTTAAATATAAAAATATTTTTAAATATT
1 TTTAAATATAAAAATAATTTAAAATATT
1181792 TTTAAATA-ATAAAATAAATTTAAAATA
1 TTTAAATATA-AAAAT-AATTTAAAATA
1181819 AAAAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 1 0.04
28 13 0.57
29 9 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TTTAAATATAAAAATAATTTAAAATATT
Found at i:1181909 original size:21 final size:22
Alignment explanation
Indices: 1181883--1181923 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1181873 GCTTGACTAG
1181883 CCTAAC-TAATAAATAAACTTA
1 CCTAACATAATAAATAAACTTA
*
1181904 CCTAACATATTAAATAAACT
1 CCTAACATAATAAATAAACT
1181924 GACACAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (22 bp):
CCTAACATAATAAATAAACTTA
Found at i:1182110 original size:18 final size:17
Alignment explanation
Indices: 1182089--1182132 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1182079 ATATGAAATT
1182089 ATATATATAAAATATTAA
1 ATATATATAAAATA-TAA
**
1182107 ATATATAATATGATATAA
1 ATATAT-ATAAAATATAA
1182125 ATATATAT
1 ATATATAT
1182133 TTTAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 15 0.65
19 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
ATATATATAAAATATAA
Found at i:1182147 original size:36 final size:37
Alignment explanation
Indices: 1182063--1182155 Score: 93
Period size: 38 Copynumber: 2.5 Consensus size: 37
1182053 AGATTTTAAT
*
1182063 AATTTTAAATATAAT-TATATGAAATTATATATATAA
1 AATTTTATATATAATATATATGAAATTATATATATAA
* * *
1182099 AATATTAAATATATAATATGATAT-AAA-TATATATTTTA
1 AAT-TT-TATATATAATAT-ATATGAAATTATATATATAA
*
1182137 AATTTTATATATTATATAT
1 AATTTTATATATAATATAT
1182156 TATTAATGTA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
35 2 0.04
36 13 0.28
37 4 0.09
38 20 0.43
39 4 0.09
40 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (37 bp):
AATTTTATATATAATATATATGAAATTATATATATAA
Found at i:1182301 original size:17 final size:16
Alignment explanation
Indices: 1182279--1182336 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 16
1182269 AATACATAAA
1182279 TAAAAAAAAGTT-ATAT
1 TAAAAAAAA-TTAATAT
1182295 CTAAAAAATAATTAATAT
1 -TAAAAAA-AATTAATAT
1182313 T-AAAAAAATTAA-AT
1 TAAAAAAAATTAATAT
*
1182327 TAAATAAAAT
1 TAAAAAAAAT
1182337 GATTGAATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 3 0.08
15 13 0.35
16 5 0.14
17 10 0.27
18 6 0.16
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (16 bp):
TAAAAAAAATTAATAT
Found at i:1182312 original size:18 final size:16
Alignment explanation
Indices: 1182279--1182320 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
1182269 AATACATAAA
1182279 TAAAAAAAAGTTATAT
1 TAAAAAAAAGTTATAT
1182295 CTAAAAAATAA-TTAATAT
1 -TAAAAAA-AAGTT-ATAT
1182313 TAAAAAAA
1 TAAAAAAA
1182321 TTAAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 16 0.70
18 6 0.26
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (16 bp):
TAAAAAAAAGTTATAT
Found at i:1182843 original size:16 final size:16
Alignment explanation
Indices: 1182815--1182858 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 16
1182805 GGTTGATGTA
1182815 AAATT-TTTATAAATTT
1 AAATTATTT-TAAATTT
1182831 AAATTATTTTAAA-TT
1 AAATTATTTTAAATTT
1182846 --ATTATTTTAAATT
1 AAATTATTTTAAATT
1182859 AATTATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 11 0.42
14 1 0.04
15 2 0.08
16 9 0.35
17 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATTATTTTAAATTT
Found at i:1182849 original size:13 final size:14
Alignment explanation
Indices: 1182832--1182864 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
1182822 TATAAATTTA
1182832 AATTATTTTAAATT
1 AATTATTTTAAATT
1182846 -ATTATTTTAAATT
1 AATTATTTTAAATT
1182859 AATTAT
1 AATTAT
1182865 AAAAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATTATTTTAAATT
Found at i:1183512 original size:15 final size:15
Alignment explanation
Indices: 1183478--1183515 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1183468 ATATGTTATT
*
1183478 TATAATAATAATAATA
1 TATAAT-ATAATAAGA
1183494 -ATAATATAATAAGA
1 TATAATATAATAAGA
1183508 TATAATAT
1 TATAATAT
1183516 TTAAAACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (15 bp):
TATAATATAATAAGA
Found at i:1184472 original size:26 final size:24
Alignment explanation
Indices: 1184436--1184484 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
1184426 ATATAGTAGG
*
1184436 TGAATAATAAATAAATTTAAATTT
1 TGAATAATAAACAAATTTAAATTT
*
1184460 TGAATTAATTAAACAAATTTGAATT
1 TGAA-TAA-TAAACAAATTTAAATT
1184485 CATTTCTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 3 0.14
26 14 0.67
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (24 bp):
TGAATAATAAACAAATTTAAATTT
Found at i:1184939 original size:4 final size:4
Alignment explanation
Indices: 1184930--1184960 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1184920 TTCTAACAGT
1184930 TTTA TTTA TTTA TTTA TTTA TTTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1184961 CCAGCAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1185429 original size:6 final size:6
Alignment explanation
Indices: 1185410--1185448 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
1185400 ATATTAAAAT
*
1185410 TATTTA -ATTTA TATTCA TATTTA TATTTA TATTTA -ATTT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTT
1185449 TTTAAACTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
5 9 0.30
6 21 0.70
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (6 bp):
TATTTA
Found at i:1190099 original size:271 final size:271
Alignment explanation
Indices: 1189592--1190408 Score: 1535
Period size: 271 Copynumber: 3.0 Consensus size: 271
1189582 CCTTTCAAGG
* * *
1189592 CTCCAACAACAGCCTCAGCTATTAAAATAGCCACTCCTTCCTGAACAAGCGTACCAATGCTCCAT
1 CTCCAACAACAGCTTCAGCTA-T-AAATAGCCACTCCTTCCTTAAAAAGCGTACCAATGCTCCAT
* *
1189657 TCAGTGATCTCATTTGGAAACAAATGAAACACGGATATGTGCATTAAACAATTACCCTGCCTGAG
64 TCAATGATCTCATTTTGAAACAAATGAAACACGGATATGTGCATTAAACAATTACCCTGCCTGAG
* *
1189722 CCTCCATTGTACTAGCGCTGAGATGTGGAGTGACAGTAACCCTCTCATGCTGCACCAACTTGCTG
129 CCTCCGTTGTACTAGCGCTGAGATGTGGAGTGACAGCAACCCTCTCATGCTGCACCAACTTGCTG
*
1189787 TCCTGTTTTGGTGGCTCCTTGGAGAAAACATCAAGAGCAGCCTGAGCTACAATTCCAATATCCAA
194 TCCTGTTTTGGTGGCTACTTGGAGAAAACATCAAGAGCAGCCTGAGCTACAATTCCAATATCCAA
1189852 TACAAACACCTTT
259 TACAAACACCTTT
1189865 CTCCAACAACAGCTTCAGCTATAAATAGCCACTCCTTCCTTAAAAAGCGTACCAATGCTCCATTC
1 CTCCAACAACAGCTTCAGCTATAAATAGCCACTCCTTCCTTAAAAAGCGTACCAATGCTCCATTC
1189930 AATGATCTCATTTTGAAACAAATGAAACACGGATATGTGCATTAAACAATTACCCTGCCTGAGCC
66 AATGATCTCATTTTGAAACAAATGAAACACGGATATGTGCATTAAACAATTACCCTGCCTGAGCC
1189995 TCCGTTGTACTAGCGCTGAGATGTGGAGTGACAGCAACCCTCTCATGCTGCACCAACTTGCTGTC
131 TCCGTTGTACTAGCGCTGAGATGTGGAGTGACAGCAACCCTCTCATGCTGCACCAACTTGCTGTC
1190060 CTGTTTTGGTGGCTACTTGGAGAAAACATCAAGAGCAGCCTGAGCTACAATTCCAATATCCAATA
196 CTGTTTTGGTGGCTACTTGGAGAAAACATCAAGAGCAGCCTGAGCTACAATTCCAATATCCAATA
1190125 CAAACACCTTT
261 CAAACACCTTT
1190136 CTCCAACAACAGCTTCAGCTATAAATAGCCACTCCTTCCTTAAAAAGCGTACCAATGCTCCATTC
1 CTCCAACAACAGCTTCAGCTATAAATAGCCACTCCTTCCTTAAAAAGCGTACCAATGCTCCATTC
*
1190201 AATGATCTCATTTTGAAACAAATGAAACACGGATATGTGTATTAAACAATTACCCTGCCTGAGCC
66 AATGATCTCATTTTGAAACAAATGAAACACGGATATGTGCATTAAACAATTACCCTGCCTGAGCC
1190266 TCCGTTGTACTAGCGCTGAGATGTGGAGTGACAGCAACCCTCTCATGCTGCACCAACTTGCTGTC
131 TCCGTTGTACTAGCGCTGAGATGTGGAGTGACAGCAACCCTCTCATGCTGCACCAACTTGCTGTC
1190331 CTGTTTTGGTGGCTACTTGGAGAAAACATCAAGAGCAGCCTGAGCTACAATTCCAATATCCAATA
196 CTGTTTTGGTGGCTACTTGGAGAAAACATCAAGAGCAGCCTGAGCTACAATTCCAATATCCAATA
1190396 CAAACACCTTT
261 CAAACACCTTT
1190407 CT
1 CT
1190409 TCATCTTGGC
Statistics
Matches: 535, Mismatches: 9, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
271 514 0.96
272 1 0.00
273 20 0.04
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (271 bp):
CTCCAACAACAGCTTCAGCTATAAATAGCCACTCCTTCCTTAAAAAGCGTACCAATGCTCCATTC
AATGATCTCATTTTGAAACAAATGAAACACGGATATGTGCATTAAACAATTACCCTGCCTGAGCC
TCCGTTGTACTAGCGCTGAGATGTGGAGTGACAGCAACCCTCTCATGCTGCACCAACTTGCTGTC
CTGTTTTGGTGGCTACTTGGAGAAAACATCAAGAGCAGCCTGAGCTACAATTCCAATATCCAATA
CAAACACCTTT
Found at i:1191695 original size:33 final size:33
Alignment explanation
Indices: 1191657--1191740 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
1191647 ATTATGAAAA
1191657 ATAATATAAATATATTAATATT-TTAAAA-TTTAT
1 ATAATATAAA-ATATTAAT-TTATTAAAATTTTAT
1191690 ATAATATAAAATTATTAATTTATTAAAATTTTAT
1 ATAATATAAAA-TATTAATTTATTAAAATTTTAT
*
1191724 GTAAATATAAAAATATT
1 AT-AATAT-AAAATATT
1191741 TTAAATATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
32 3 0.07
33 23 0.51
34 6 0.13
35 9 0.20
36 4 0.09
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (33 bp):
ATAATATAAAATATTAATTTATTAAAATTTTAT
Found at i:1191760 original size:17 final size:17
Alignment explanation
Indices: 1191725--1191770 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1191715 AAATTTTATG
** *
1191725 TAAATATAAAAATATTT
1 TAAATATAATTATAATT
1191742 TAAATATAATTATAATT
1 TAAATATAATTATAATT
1191759 T-AATA-AATTATA
1 TAAATATAATTATA
1191771 TATAATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 7 0.27
16 4 0.15
17 15 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATATAATTATAATT
Found at i:1191776 original size:14 final size:16
Alignment explanation
Indices: 1191744--1191780 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1191734 AAATATTTTA
*
1191744 AATATAATTATAATTT
1 AATATAATTATAATAT
1191760 AATA-AATTAT-ATAT
1 AATATAATTATAATAT
1191774 AATATAA
1 AATATAA
1191781 ATTTACCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 7 0.37
15 8 0.42
16 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATAATTATAATAT
Found at i:1192458 original size:19 final size:19
Alignment explanation
Indices: 1192436--1192491 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 19
1192426 TTTTTATTTT
1192436 TTTATATTTTTTAAAAATA
1 TTTATATTTTTTAAAAATA
1192455 -TT-TA-TTTTT---AATA
1 TTTATATTTTTTAAAAATA
*
1192468 TTTATATTTTATAAAAATA
1 TTTATATTTTTTAAAAATA
1192487 CTTTA
1 -TTTA
1192492 ATATAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 13
0.67 0.02 0.30
Matches are distributed among these distances:
13 4 0.14
14 2 0.07
15 2 0.07
16 9 0.31
17 2 0.07
18 2 0.07
19 4 0.14
20 4 0.14
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATATTTTTTAAAAATA
Found at i:1193915 original size:52 final size:52
Alignment explanation
Indices: 1193858--1194002 Score: 141
Period size: 52 Copynumber: 2.7 Consensus size: 52
1193848 AAACAAACAG
*
1193858 ATAATAAATTTAAATATTTAATTTTATTATTTTAAAAAATAATATAAA-TCAT
1 ATAATAAATTTAAATATTTAATTTTATTA-TTTAAAAAATAATATAAATTCAA
* * * * *
1193910 ATAATAAA-TTAATATATTCAAATTTATTATCTATAAAATAATATAAATTTAA
1 ATAATAAATTTAA-ATATTTAATTTTATTATTTAAAAAATAATATAAATTCAA
*
1193962 ATAATAAAATTTTAAAAATTTATATTTGTATCTAATTTAAA
1 ATAAT-AAA-TTTAAATATTTA-ATTT-TAT-T-ATTTAAA
1194003 TGAATTAAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
51 20 0.27
52 29 0.40
53 3 0.04
54 5 0.07
55 7 0.10
56 3 0.04
57 1 0.01
58 5 0.07
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.45
Consensus pattern (52 bp):
ATAATAAATTTAAATATTTAATTTTATTATTTAAAAAATAATATAAATTCAA
Found at i:1193977 original size:15 final size:15
Alignment explanation
Indices: 1193945--1193973 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1193935 ATTATCTATA
1193945 AAATAATATAAATTT
1 AAATAATATAAATTT
1193960 AAATAATA-AAATTT
1 AAATAATATAAATTT
1193974 TAAAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATAATATAAATTT
Found at i:1194348 original size:24 final size:25
Alignment explanation
Indices: 1194244--1194349 Score: 84
Period size: 23 Copynumber: 4.4 Consensus size: 25
1194234 TTATTACCTT
*
1194244 TTATTAAATTTAAAAT-TAATATAT-
1 TTATT-AATTTAAAATATATTATATA
* *
1194268 TTA-TATATTT-TATTATATTATA-A
1 TTATTA-ATTTAAAATATATTATATA
*
1194291 TTA-T-ATTTAAAATATATTATATT
1 TTATTAATTTAAAATATATTATATA
*
1194314 TGTATTAATTTAAAAT-TTTTATATA
1 T-TATTAATTTAAAATATATTATATA
1194339 TTATTAATTTA
1 TTATTAATTTA
1194350 TATTATATAA
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
21 4 0.06
22 13 0.20
23 16 0.24
24 15 0.23
25 9 0.14
26 9 0.14
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (25 bp):
TTATTAATTTAAAATATATTATATA
Found at i:1194357 original size:20 final size:19
Alignment explanation
Indices: 1194332--1194398 Score: 56
Period size: 18 Copynumber: 3.7 Consensus size: 19
1194322 TTTAAAATTT
*
1194332 TTATATATTATTAATTTATA
1 TTATATATAATT-ATTTATA
1194352 TTATATA-AATT-TTGTATA
1 TTATATATAATTATT-TATA
*
1194370 TTATAT-T-TTTA-TTATA
1 TTATATATAATTATTTATA
1194386 TT-TATATAATTAT
1 TTATATATAATTAT
1194399 ATTTAATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 14
0.69 0.05 0.25
Matches are distributed among these distances:
15 3 0.08
16 7 0.18
17 8 0.21
18 10 0.26
19 3 0.08
20 7 0.18
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (19 bp):
TTATATATAATTATTTATA
Found at i:1194373 original size:31 final size:29
Alignment explanation
Indices: 1194267--1194415 Score: 94
Period size: 32 Copynumber: 5.0 Consensus size: 29
1194257 AATTAATATA
* *
1194267 TTTATATATTTTA-TTATATTATAATTATAT
1 TTTATATATTATATTTATATTAT-A-TAAAT
* * *
1194297 TTAAAATATATTATATTTGTATTAATTTAAAATT
1 TT--TATATATTATATTTATATT-ATAT-AAA-T
1194331 TTTATATATTATTAATTTATATTATATAAAT
1 TTTATATATTA-T-ATTTATATTATATAAAT
* *
1194362 TTTGTATATTATATTTTTATTATAT---T
1 TTTATATATTATATTTATATTATATAAAT
*
1194388 TATATA-ATTATATTTAATATTAT-TAAAT
1 TTTATATATTATATTT-ATATTATATAAAT
1194416 CTATTAATAT
Statistics
Matches: 94, Mismatches: 13, Indels: 26
0.71 0.10 0.20
Matches are distributed among these distances:
25 10 0.11
26 11 0.12
28 1 0.01
29 12 0.13
30 3 0.03
31 11 0.12
32 21 0.22
33 12 0.13
34 13 0.14
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (29 bp):
TTTATATATTATATTTATATTATATAAAT
Found at i:1194382 original size:11 final size:13
Alignment explanation
Indices: 1194263--1194410 Score: 76
Period size: 13 Copynumber: 11.2 Consensus size: 13
1194253 TTAAAATTAA
1194263 TATATTTATATAT
1 TATATTTATATAT
*
1194276 TTTATTATATTATAAT
1 TATATT-TA-TAT-AT
*
1194292 TATATTTA-A-AA
1 TATATTTATATAT
1194303 TATA-TTATAT-T
1 TATATTTATATAT
* * * *
1194314 TGTATTAATTTAA
1 TATATTTATATAT
* *
1194327 AATTTTTATATAT
1 TATATTTATATAT
1194340 TATTAATTTATATTAT
1 TA-T-ATTTATA-TAT
* *
1194356 ATAAATTTTGTATAT
1 -TATA-TTTATATAT
1194371 TATATTT-T-TAT
1 TATATTTATATAT
1194382 TATATTTATATAAT
1 TATATTTATAT-AT
1194396 TATATTTA-ATAT
1 TATATTTATATAT
1194408 TAT
1 TAT
1194411 TAAATCTATT
Statistics
Matches: 101, Mismatches: 19, Indels: 31
0.67 0.13 0.21
Matches are distributed among these distances:
10 3 0.03
11 19 0.19
12 11 0.11
13 20 0.20
14 16 0.16
15 15 0.15
16 15 0.15
17 2 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (13 bp):
TATATTTATATAT
Found at i:1194385 original size:16 final size:16
Alignment explanation
Indices: 1194262--1194392 Score: 60
Period size: 17 Copynumber: 8.2 Consensus size: 16
1194252 TTTAAAATTA
*
1194262 ATATATTTA-TATATT
1 ATATTTTTATTATATT
* *
1194277 TTA-TTATATTATAATT
1 ATATTTTTATTAT-ATT
** *
1194293 ATATTTAAAATATATT
1 ATATTTTTATTATATT
*
1194309 ATATTTGTATTA-ATTT
1 ATATTTTTATTATA-TT
*
1194325 AAAATTTTTA-TATATT
1 -ATATTTTTATTATATT
*
1194341 ATTAATTTATATTATA-T
1 A-T-ATTTTTATTATATT
* *
1194358 A-AATTTT-GTATATT
1 ATATTTTTATTATATT
1194372 ATATTTTTATTATATTT
1 ATATTTTTATTATA-TT
1194389 ATAT
1 ATAT
1194393 AATTATATTT
Statistics
Matches: 85, Mismatches: 18, Indels: 24
0.67 0.14 0.19
Matches are distributed among these distances:
13 4 0.05
14 9 0.11
15 12 0.14
16 27 0.32
17 29 0.34
18 4 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
ATATTTTTATTATATT
Found at i:1194571 original size:27 final size:27
Alignment explanation
Indices: 1194539--1194601 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
1194529 TTTATATGAC
1194539 ATAAATATAATAAAAATAAAAAATTAT
1 ATAAATATAATAAAAATAAAAAATTAT
* * * * *
1194566 ATAAATATTATATATATTAAAATTTAT
1 ATAAATATAATAAAAATAAAAAATTAT
1194593 AT-AATATAA
1 ATAAATATAA
1194602 ATATTTAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 6 0.20
27 24 0.80
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
ATAAATATAATAAAAATAAAAAATTAT
Found at i:1194586 original size:16 final size:15
Alignment explanation
Indices: 1194563--1194614 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
1194553 AATAAAAAAT
1194563 TATA-TAAATATTATA
1 TATATTAAATATT-TA
1194578 TATATTAAA-ATTTA
1 TATATTAAATATTTA
1194592 TATAATATAAATATTTAA
1 TAT-AT-TAAATATTT-A
1194610 TATAT
1 TATAT
1194615 CAAAAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 5 0.16
15 9 0.28
16 8 0.25
17 6 0.19
18 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATTAAATATTTA
Found at i:1194621 original size:18 final size:17
Alignment explanation
Indices: 1194600--1194646 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
1194590 TATATAATAT
*
1194600 AAATATTTAATATATCAA
1 AAATATTTAA-AAATCAA
*
1194618 AAAT-TTTAAAAATTAA
1 AAATATTTAAAAATCAA
1194634 AAATATATTAAAA
1 AAATAT-TTAAAA
1194647 TTATGATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 9 0.36
17 6 0.24
18 10 0.40
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATATTTAAAAATCAA
Found at i:1195051 original size:10 final size:11
Alignment explanation
Indices: 1195036--1195096 Score: 54
Period size: 12 Copynumber: 5.5 Consensus size: 11
1195026 ATTTAAAATA
1195036 TTTATA-TAAT
1 TTTATATTAAT
1195046 TTTATATTAAT
1 TTTATATTAAT
*
1195057 TTTATGTTAAAT
1 TTTATATT-AAT
* *
1195069 ATTATATTTA-
1 TTTATATTAAT
*
1195079 TTTAAATTAAAT
1 TTTATATT-AAT
1195091 TTTATA
1 TTTATA
1195097 ATTTATGTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
10 12 0.31
11 13 0.33
12 14 0.36
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (11 bp):
TTTATATTAAT
Found at i:1195072 original size:18 final size:17
Alignment explanation
Indices: 1195049--1195095 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1195039 ATATAATTTT
1195049 ATATTAATTTTATGTTAA
1 ATATTAATTTTAT-TTAA
1195067 ATATT-ATATTTATTTAA
1 ATATTAAT-TTTATTTAA
*
1195084 AT-TAAATTTTAT
1 ATATTAATTTTAT
1195096 AATTTATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 6 0.23
17 10 0.38
18 10 0.38
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
ATATTAATTTTATTTAA
Found at i:1195169 original size:18 final size:18
Alignment explanation
Indices: 1195146--1195184 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1195136 TTAATAATTA
1195146 ATAATTTGATATATATTT
1 ATAATTTGATATATATTT
*
1195164 ATAATTTGATGTATATTT
1 ATAATTTGATATATATTT
1195182 ATA
1 ATA
1195185 TCGTACGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (18 bp):
ATAATTTGATATATATTT
Found at i:1196486 original size:2 final size:2
Alignment explanation
Indices: 1196479--1196514 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1196469 ACTTCACCGG
* *
1196479 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1196515 TCAATGGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1197618 original size:2 final size:2
Alignment explanation
Indices: 1197611--1197635 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1197601 AGAACCAGCC
1197611 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1197636 ATCGTCCTTT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1197879 original size:2 final size:2
Alignment explanation
Indices: 1197872--1197904 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1197862 AGGTCCAACT
1197872 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1197905 GGATCTCATC
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:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1202391 original size:19 final size:20
Alignment explanation
Indices: 1202369--1202411 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1202359 CAATGGGTTT
1202369 TTTTAA-AATAAATGTG-TAG
1 TTTTAAGAATAAATG-GATAG
*
1202388 TTTTAAGAATAGATGGATAG
1 TTTTAAGAATAAATGGATAG
1202408 TTTT
1 TTTT
1202412 TTTTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTTAAGAATAAATGGATAG
Found at i:1203146 original size:126 final size:126
Alignment explanation
Indices: 1203014--1203250 Score: 402
Period size: 126 Copynumber: 1.9 Consensus size: 126
1203004 GAGAAAGAAA
*
1203014 AGATAAAAATTTCTTTATAAAAATAAAATAATCGAGAGACTTTCTAAAGTTTAACCAGACAAGTT
1 AGATAAAAATTTCTTTATAAAAATAAAATAATCGAGAGACTTTCTAAAGTTTAACCAAACAAGTT
*
1203079 TAGAGGAGAGCCAATTCACGGGTAGAGTAAAGGCCACGTCACCATTTAAATATGAAATAAT
66 TAGAGGAGAGCCAATTCACGGGTAGAGTAAAGGACACGTCACCATTTAAATATGAAATAAT
*
1203140 AGATAAAAATTTCTTTATAAAAATAAAATAATCGAGGGACTTTCTAAAGTTTAACCAAACAAGTT
1 AGATAAAAATTTCTTTATAAAAATAAAATAATCGAGAGACTTTCTAAAGTTTAACCAAACAAGTT
* * * * *
1203205 TCGGGGAGAGCCACTTCGCGGGTAGGGTAAAGGACACGTCACCATT
66 TAGAGGAGAGCCAATTCACGGGTAGAGTAAAGGACACGTCACCATT
1203251 GAACTATGCT
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
126 103 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (126 bp):
AGATAAAAATTTCTTTATAAAAATAAAATAATCGAGAGACTTTCTAAAGTTTAACCAAACAAGTT
TAGAGGAGAGCCAATTCACGGGTAGAGTAAAGGACACGTCACCATTTAAATATGAAATAAT
Found at i:1203607 original size:17 final size:18
Alignment explanation
Indices: 1203585--1203633 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 18
1203575 CAACATGAGT
1203585 TATTTATTTAATTTA-AA
1 TATTTATTTAATTTATAA
1203602 TATTTATTTGATATTTATAA
1 TATTTATTT-A-ATTTATAA
*
1203622 TAATTTAATTAA
1 T-ATTTATTTAA
1203634 AAATATTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 9 0.33
18 1 0.04
19 6 0.22
20 4 0.15
21 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TATTTATTTAATTTATAA
Found at i:1207247 original size:15 final size:15
Alignment explanation
Indices: 1207223--1207275 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
1207213 ATAAAAAAAA
*
1207223 ATTAATATTAATATT
1 ATTAAAATTAATATT
1207238 ATTAAAATTAATATT
1 ATTAAAATTAATATT
* **
1207253 -TTAATATTTTTATT
1 ATTAAAATTAATATT
*
1207267 TTTAAAATT
1 ATTAAAATT
1207276 TTACTAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 11 0.34
15 21 0.66
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTAAAATTAATATT
Found at i:1216102 original size:2 final size:2
Alignment explanation
Indices: 1216097--1216127 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1216087 TTAGACACAC
1216097 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1216128 AGAAGATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1216423 original size:20 final size:20
Alignment explanation
Indices: 1216393--1216455 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
1216383 TTAATTAATT
1216393 TTAAA-TAATTTTTTATAAA
1 TTAAATTAATTTTTTATAAA
* *
1216412 TTAAATTAATTTGATTA-AAT
1 TTAAATTAATTT-TTTATAAA
* *
1216432 TTAAATTAATATTTAAT-AA
1 TTAAATTAATTTTTTATAAA
1216451 TTAAA
1 TTAAA
1216456 AAAATTTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 13 0.37
20 19 0.54
21 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TTAAATTAATTTTTTATAAA
Found at i:1216429 original size:39 final size:39
Alignment explanation
Indices: 1216380--1216473 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 39
1216370 TTATTTAATA
* * *
1216380 AATTTAATTAATTTTAAA-TAATTTTTTATAAATTAAATT
1 AATTTAATTAAATTTAAATTAATATTTAAT-AATTAAATT
* **
1216419 AATTTGATTAAATTTAAATTAATATTTAATAATTAAAAA
1 AATTTAATTAAATTTAAATTAATATTTAATAATTAAATT
*
1216458 AATTTTATTTAAATTT
1 AA-TTTAATTAAATTT
1216474 TATTATAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
39 25 0.56
40 20 0.44
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (39 bp):
AATTTAATTAAATTTAAATTAATATTTAATAATTAAATT
Found at i:1216492 original size:21 final size:21
Alignment explanation
Indices: 1216467--1216539 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
1216457 AAATTTTATT
1216467 TAAATTTTATTATAAAATATA
1 TAAATTTTATTATAAAATATA
* * *
1216488 TAAATATTAATATAAAATTTTA
1 TAAATTTTATTATAAAA-TATA
*
1216510 TAAATTTTGTTAAATATAAATA-A
1 TAAATTTTATT--ATA-AAATATA
1216533 TAAATTT
1 TAAATTT
1216540 AAGTAATATT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
21 15 0.37
22 11 0.27
23 8 0.20
24 4 0.10
25 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (21 bp):
TAAATTTTATTATAAAATATA
Found at i:1216536 original size:45 final size:43
Alignment explanation
Indices: 1216456--1216541 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 43
1216446 AATAATTAAA
1216456 AAAATTTTATTTAAATTTTATTATAAAATATATAAATATTAATAT
1 AAAATTTTA-TTAAATTTTATTATAAAATATATAAAT-TTAATAT
*
1216501 AAAATTTTA-TAAATTTTGTTAAATATAAATA-ATAAATTTAA
1 AAAATTTTATTAAATTTTATT--ATA-AAATATATAAATTTAA
1216542 GTAATATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
43 10 0.27
44 4 0.11
45 18 0.49
46 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (43 bp):
AAAATTTTATTAAATTTTATTATAAAATATATAAATTTAATAT
Found at i:1219010 original size:15 final size:15
Alignment explanation
Indices: 1218987--1219017 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1218977 TGATTGTGAT
1218987 TTATATATATATATA
1 TTATATATATATATA
*
1219002 TTATGTATATATATA
1 TTATATATATATATA
1219017 T
1 T
1219018 ATTTCAGGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATATATATATATA
Found at i:1219476 original size:26 final size:27
Alignment explanation
Indices: 1219435--1219505 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 27
1219425 TATATTTTTA
* * *
1219435 ATATGTATTTAAATAT-GAATATAAAT
1 ATATTTATTTAAATATAAAAAATAAAT
1219461 ATAATTT-TTTAAATATAAAAAATAAAT
1 AT-ATTTATTTAAATATAAAAAATAAAT
1219488 ATATTTATATTAAATATA
1 ATATTTAT-TTAAATATA
1219506 TTTATACTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
26 15 0.39
27 14 0.37
28 9 0.24
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (27 bp):
ATATTTATTTAAATATAAAAAATAAAT
Found at i:1219501 original size:15 final size:15
Alignment explanation
Indices: 1219483--1219511 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1219473 ATATAAAAAA
1219483 TAAATATATTTATAT
1 TAAATATATTTATAT
1219498 TAAATATATTTATA
1 TAAATATATTTATA
1219512 CTTGTCACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAAATATATTTATAT
Found at i:1220005 original size:13 final size:13
Alignment explanation
Indices: 1219987--1220033 Score: 76
Period size: 13 Copynumber: 3.5 Consensus size: 13
1219977 TTAAAATTAA
1219987 AGATTTTATTTAT
1 AGATTTTATTTAT
*
1220000 AGATTTTATTTAAC
1 AGATTTTATTT-AT
1220014 AGATTTTATTTAT
1 AGATTTTATTTAT
1220027 AGATTTT
1 AGATTTT
1220034 CTGAACAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 19 0.61
14 12 0.39
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (13 bp):
AGATTTTATTTAT
Found at i:1220005 original size:27 final size:27
Alignment explanation
Indices: 1219975--1220032 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
1219965 AGTAACATAA
1219975 ATTTAAAATTAA-AGATTTTATTTATAG
1 ATTT-AAATTAACAGATTTTATTTATAG
* *
1220002 ATTTTATTTAACAGATTTTATTTATAG
1 ATTTAAATTAACAGATTTTATTTATAG
1220029 ATTT
1 ATTT
1220033 TCTGAACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (27 bp):
ATTTAAATTAACAGATTTTATTTATAG
Found at i:1220033 original size:27 final size:26
Alignment explanation
Indices: 1219983--1220033 Score: 93
Period size: 27 Copynumber: 1.9 Consensus size: 26
1219973 AAATTTAAAA
1219983 TTAAAGATTTTATTTATAGATTTTAT
1 TTAAAGATTTTATTTATAGATTTTAT
1220009 TTAACAGATTTTATTTATAGATTTT
1 TTAA-AGATTTTATTTATAGATTTT
1220034 CTGAACAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (26 bp):
TTAAAGATTTTATTTATAGATTTTAT
Found at i:1226059 original size:16 final size:16
Alignment explanation
Indices: 1226040--1226075 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1226030 ATTTACATAT
1226040 TTATATTAT-TTTTAAA
1 TTATATTATATTTT-AA
1226056 TTATATTATATTTTAA
1 TTATATTATATTTTAA
1226072 TTAT
1 TTAT
1226076 TTTTTTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATATTATATTTTAA
Found at i:1226292 original size:32 final size:31
Alignment explanation
Indices: 1226254--1226324 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 31
1226244 GGAACTTTAT
*
1226254 TTTTATTTCAATAAAATATTATATTTTTATCA
1 TTTTATTTCAATAAAATATTA-AATTTTATCA
** * * *
1226286 TTTTATTTTGATAAATTTTTAAATTTTATTA
1 TTTTATTTCAATAAAATATTAAATTTTATCA
1226317 TTTTATTT
1 TTTTATTT
1226325 ATGTAAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 16 0.48
32 17 0.52
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (31 bp):
TTTTATTTCAATAAAATATTAAATTTTATCA
Found at i:1226320 original size:31 final size:32
Alignment explanation
Indices: 1226273--1226354 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
1226263 AATAAAATAT
* * *
1226273 TATATTTTTATCATTTTATTT-TGATAAATTTT
1 TATAATTTTATTATTTTATTTATG-TAAATTTA
1226305 TA-AATTTTATTATTTTATTTATGTAAATTTA
1 TATAATTTTATTATTTTATTTATGTAAATTTA
*
1226336 TATATTTTTATTATATTTA
1 TATAATTTTATTAT-TTTA
1226355 AATAAACTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
31 25 0.58
32 14 0.33
33 4 0.09
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (32 bp):
TATAATTTTATTATTTTATTTATGTAAATTTA
Found at i:1226331 original size:23 final size:26
Alignment explanation
Indices: 1226305--1226357 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
1226295 GATAAATTTT
1226305 TAAATTTTAT-TA-TTTTATT-TATG
1 TAAATTTTATATATTTTTATTATATG
*
1226328 TAAA-TTTATATATTTTTATTATATT
1 TAAATTTTATATATTTTTATTATATG
1226353 TAAAT
1 TAAAT
1226358 AAACTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.20
23 6 0.24
24 7 0.28
25 7 0.28
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TAAATTTTATATATTTTTATTATATG
Found at i:1226360 original size:29 final size:31
Alignment explanation
Indices: 1226296--1226360 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 31
1226286 TTTTATTTTG
* * *
1226296 ATAAATTTTTAAATTTTATTATTTTATTTAT
1 ATAAATTTATAAATTTTATTATTATATTTAA
* *
1226327 GTAAATTTATATA-TTT-TTATTATATTTAA
1 ATAAATTTATAAATTTTATTATTATATTTAA
1226356 ATAAA
1 ATAAA
1226361 CTATTAACTT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
29 15 0.54
30 3 0.11
31 10 0.36
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
ATAAATTTATAAATTTTATTATTATATTTAA
Found at i:1228011 original size:17 final size:18
Alignment explanation
Indices: 1227975--1228017 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1227965 TTTACTCCAA
1227975 TTTAAATATATTTAA-TTT
1 TTTAAA-ATATTTAATTTT
* *
1227993 TTTAAAATTTTTTATTTT
1 TTTAAAATATTTAATTTT
1228011 TTTAAAA
1 TTTAAAA
1228018 AATAAATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTAAAATATTTAATTTT
Found at i:1228412 original size:18 final size:18
Alignment explanation
Indices: 1228391--1228450 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
1228381 AAAAATAATT
*
1228391 AAATATAATATAATATAA
1 AAATATAATAAAATATAA
*
1228409 AAATATATTAAAATATATTA
1 AAATATAATAAAATATA--A
*
1228429 AAATTTATATAAAAATATAA
1 AAATATA-AT-AAAATATAA
1228449 AA
1 AA
1228451 TATTTTTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 15 0.44
20 10 0.29
21 1 0.03
22 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATATAATAAAATATAA
Found at i:1228470 original size:46 final size:44
Alignment explanation
Indices: 1228415--1228500 Score: 118
Period size: 46 Copynumber: 1.9 Consensus size: 44
1228405 ATAAAAATAT
* *
1228415 ATTAAAATATATTAAAATTTATATAAAAATATAAAATATTTTTTTA
1 ATTAAAATATAATAAAATATATAT-AAAATAT-AAATATTTTTTTA
* *
1228461 ATTATAATATAATAAAATATATATATAATATAAATATTTT
1 ATTAAAATATAATAAAATATATATAAAATATAAATATTTT
1228501 AATTACGAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 9 0.25
45 6 0.17
46 21 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (44 bp):
ATTAAAATATAATAAAATATATATAAAATATAAATATTTTTTTA
Found at i:1228496 original size:27 final size:27
Alignment explanation
Indices: 1228376--1228497 Score: 79
Period size: 27 Copynumber: 4.4 Consensus size: 27
1228366 GCATAGGAAA
* * *
1228376 AATAAAAAAATAATTAAATATA-ATAT
1 AATATAAATATAATAAAATATATATAT
* *
1228402 AATATAAAAATATATTAAAATATATTAAAATT
1 AATAT--AAATATAATAAAATATA-T-ATA-T
* * * * *
1228434 TATATAAAAAT-ATAAAATATTTTTTT
1 AATATAAATATAATAAAATATATATAT
1228460 AAT-TATAATATAATAAAATATATATAT
1 AATATA-AATATAATAAAATATATATAT
1228487 AATATAAATAT
1 AATATAAATAT
1228498 TTTAATTACG
Statistics
Matches: 70, Mismatches: 17, Indels: 17
0.67 0.16 0.16
Matches are distributed among these distances:
25 2 0.03
26 11 0.16
27 20 0.29
28 17 0.24
29 8 0.11
30 5 0.07
31 2 0.03
32 5 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
AATATAAATATAATAAAATATATATAT
Found at i:1229011 original size:3 final size:3
Alignment explanation
Indices: 1229003--1229038 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1228993 GAAAGAGATT
1229003 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1229039 ATTTCAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1229886 original size:16 final size:16
Alignment explanation
Indices: 1229851--1229905 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1229841 GATATATTCG
*
1229851 TATATTCATATTACATT
1 TATATT-ATATTATATT
*
1229868 TATATTATATTATAAT
1 TATATTATATTATATT
* * *
1229884 TATTTTTTATCATATT
1 TATATTATATTATATT
1229900 TATATT
1 TATATT
1229906 GTTTAATTAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 25 0.81
17 6 0.19
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (16 bp):
TATATTATATTATATT
Found at i:1230067 original size:34 final size:35
Alignment explanation
Indices: 1230040--1230102 Score: 89
Period size: 32 Copynumber: 1.9 Consensus size: 35
1230030 CATATCTCAT
*
1230040 AATTTATAT-AATAT-AAAT-TTTTAACATATTAA
1 AATTAATATAAATATAAAATATTTTAACATATTAA
1230072 AATTAATATAAATATAAAATATTTTAA-ATAT
1 AATTAATATAAATATAAAATATTTTAACATAT
1230103 AATTATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 8 0.30
33 5 0.19
34 8 0.30
35 6 0.22
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (35 bp):
AATTAATATAAATATAAAATATTTTAACATATTAA
Found at i:1230101 original size:16 final size:16
Alignment explanation
Indices: 1230049--1230104 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
1230039 TAATTTATAT
1230049 AATAT-AAAT-TTTTA
1 AATATAAAATATTTTA
* *
1230063 ACATATTAAAATTAATATA
1 A-ATA-TAAAA-TATTTTA
1230082 AATATAAAATATTTTA
1 AATATAAAATATTTTA
1230098 AATATAA
1 AATATAA
1230105 TTATAATATG
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 1 0.03
15 3 0.09
16 13 0.39
17 8 0.24
18 4 0.12
19 4 0.12
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATAAAATATTTTA
Found at i:1230105 original size:27 final size:26
Alignment explanation
Indices: 1230045--1230120 Score: 64
Period size: 27 Copynumber: 2.7 Consensus size: 26
1230035 CTCATAATTT
* *
1230045 ATATAATATAAATTTTTAACATATTAAA
1 ATATAATATAAA--TATAAAATATTAAA
*
1230073 AT-TAATATAAATATAAAATATTTTAA
1 ATATAATATAAATATAAAATA-TTAAA
1230099 ATATAATTATAATATGATAAAA
1 ATATAA-TATAA-AT-ATAAAA
1230121 ATATAAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
25 7 0.17
26 6 0.15
27 12 0.30
28 7 0.17
29 2 0.05
30 6 0.15
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (26 bp):
ATATAATATAAATATAAAATATTAAA
Found at i:1230525 original size:34 final size:35
Alignment explanation
Indices: 1230486--1230564 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 35
1230476 TTATTAATTA
* *
1230486 TATATT-TATGTAAATTTTAATATATATT-TATATT
1 TATATTATATGTAAATTATAATA-AAATTATATATT
* *
1230520 TATATTATAT-TATATTATATTAAAATTATATATT
1 TATATTATATGTAAATTATAATAAAATTATATATT
1230554 TATATTATATG
1 TATATTATATG
1230565 ATTTTATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
33 4 0.11
34 31 0.82
35 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (35 bp):
TATATTATATGTAAATTATAATAAAATTATATATT
Found at i:1230529 original size:5 final size:5
Alignment explanation
Indices: 1230508--1230577 Score: 67
Period size: 5 Copynumber: 14.2 Consensus size: 5
1230498 AATTTTAATA
*
1230508 TATATT TATATT TATAT TATAT TATAT TATAT TAAAAT TATA- TAT-T
1 TATA-T TATA-T TATAT TATAT TATAT TATAT T-ATAT TATAT TATAT
*
1230554 TATAT TATAT GAT-T T-TAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT T
1230578 TAAAATTATT
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
3 1 0.02
4 9 0.16
5 31 0.56
6 14 0.25
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:1230533 original size:24 final size:23
Alignment explanation
Indices: 1230472--1230534 Score: 58
Period size: 24 Copynumber: 2.8 Consensus size: 23
1230462 TAGTTCGTAC
*
1230472 ATTTTTATTA-ATTATATA-TTT
1 ATTTATATTATATTATATATTTT
* * * *
1230493 ATGTAAATTTTAATATATATTTAT
1 ATTTATATTATATTATATATTT-T
1230517 ATTTATATTATATTATAT
1 ATTTATATTATATTATAT
1230535 TATATTAAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
21 6 0.20
22 7 0.23
23 2 0.07
24 15 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTTATATTATATTATATATTTT
Found at i:1230762 original size:16 final size:17
Alignment explanation
Indices: 1230737--1230772 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1230727 ACTTTTTTTT
1230737 AATTATTTTTAAATTTA
1 AATTATTTTTAAATTTA
*
1230754 AATTA-TTTTAATTTTA
1 AATTATTTTTAAATTTA
1230770 AAT
1 AAT
1230773 CCATTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AATTATTTTTAAATTTA
Found at i:1230869 original size:17 final size:18
Alignment explanation
Indices: 1230824--1230870 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
1230814 TTTATATTAA
1230824 TTAATTTATAATTATAATT
1 TTAATTTA-AATTATAATT
*
1230843 TT-TTTATAAATT-TAATT
1 TTAATT-TAAATTATAATT
1230860 TTAATTTAAAT
1 TTAATTTAAAT
1230871 AATCTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 12 0.50
18 8 0.33
19 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATTTAAATTATAATT
Found at i:1230904 original size:19 final size:18
Alignment explanation
Indices: 1230875--1230910 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1230865 TTAAATAATC
*
1230875 TAAATAAAATTTTAAATT
1 TAAATAAAATTATAAATT
1230893 TAAATCAAAATTATAAAT
1 TAAAT-AAAATTATAAAT
1230911 CCGACTGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAATAAAATTATAAATT
Found at i:1231535 original size:2 final size:2
Alignment explanation
Indices: 1231528--1231554 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1231518 AACTCTTTTG
1231528 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1231555 TTAACTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1231606 original size:21 final size:22
Alignment explanation
Indices: 1231582--1231635 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
1231572 GATTTATTGA
* *
1231582 TATTATTTTATATATTATA-AT
1 TATTATTTAATACATTATATAT
* *
1231603 TATTAATTAATGCATTATATAT
1 TATTATTTAATACATTATATAT
*
1231625 TATTATATAAT
1 TATTATTTAAT
1231636 TTTTAATAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTATTTAATACATTATATAT
Found at i:1231674 original size:19 final size:17
Alignment explanation
Indices: 1231652--1231696 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
1231642 TAAATTAATA
1231652 ATTTATTATATAATTTTAT
1 ATTTATTATAT-A-TTTAT
*
1231671 ATTTTTTATATATTTAT
1 ATTTATTATATATTTAT
1231688 ATTATATTA
1 ATT-TATTA
1231697 CATTTCAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 8 0.35
18 5 0.22
19 10 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTATTATATATTTAT
Found at i:1232162 original size:27 final size:27
Alignment explanation
Indices: 1232110--1232162 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
1232100 TCTTCAAAAT
* **
1232110 ATTATATTTATATATTTTTTTATTATA
1 ATTATATTTATATAATTTAATATTATA
1232137 ATTATATTTATATAAATTTAAT-TTAT
1 ATTATATTTATAT-AATTTAATATTAT
1232163 TAATAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
ATTATATTTATATAATTTAATATTATA
Found at i:1232398 original size:4 final size:4
Alignment explanation
Indices: 1232389--1232415 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1232379 ATCGAATATA
1232389 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1232416 AGAAAAGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1232996 original size:19 final size:19
Alignment explanation
Indices: 1232974--1233028 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
1232964 TCAGTATAAA
*
1232974 TTTATAAATTTATATTATT
1 TTTATAAATTTATATTATG
* * *
1232993 TTTATATATTAAAATTATG
1 TTTATAAATTTATATTATG
1233012 TTTA-AAATATTAT-TTAT
1 TTTATAAAT-TTATATTAT
1233029 ATAAATTTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTATAAATTTATATTATG
Found at i:1233061 original size:18 final size:16
Alignment explanation
Indices: 1233016--1233071 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 16
1233006 ATTATGTTTA
*
1233016 AAATATTAT-TTATAT
1 AAATTTTATATTATAT
1233031 AAATTTTA-A-TATAT
1 AAATTTTATATTATAT
1233045 AAATAATTTATATTATAT
1 AAAT--TTTATATTATAT
1233063 AAATTTTAT
1 AAATTTTAT
1233072 TATTTTATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
14 9 0.26
15 7 0.20
16 9 0.26
17 1 0.03
18 9 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AAATTTTATATTATAT
Found at i:1233072 original size:14 final size:14
Alignment explanation
Indices: 1233025--1233074 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 14
1233015 AAAATATTAT
1233025 TTATATAAATTTTAA
1 TTATATAAATTTT-A
*
1233040 TATATAAATAATTTATA
1 T-TATATA-AATTT-TA
1233057 TTATATAAATTTTA
1 TTATATAAATTTTA
1233071 TTAT
1 TTAT
1233075 TTTATTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 6 0.20
15 6 0.20
16 10 0.33
17 7 0.23
18 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATATAAATTTTA
Found at i:1233670 original size:11 final size:11
Alignment explanation
Indices: 1233656--1233698 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 11
1233646 TTTATTTAAA
1233656 TTATATTTATT
1 TTATATTTATT
1233667 TTATATTATATT
1 TTATATT-TATT
1233679 TTAATTATTTATT
1 TT-A-TATTTATT
1233692 TTATATT
1 TTATATT
1233699 ATATAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.38
12 7 0.24
13 7 0.24
14 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATATTTATT
Found at i:1233674 original size:16 final size:16
Alignment explanation
Indices: 1233633--1233679 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
1233623 TTTAAATAAG
*
1233633 TTTTGATATTTTATTTA
1 TTTT-ATATTATATTTA
*
1233650 -TTTAAATTATATTTA
1 TTTTATATTATATTTA
1233665 TTTTATATTATATTT
1 TTTTATATTATATTT
1233680 TAATTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 10 0.38
16 16 0.62
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
TTTTATATTATATTTA
Found at i:1233711 original size:20 final size:22
Alignment explanation
Indices: 1233662--1233708 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 22
1233652 TAAATTATAT
1233662 TTATTTTATATTATATTTTAATTA
1 TTATTTTATATTATA--TTAATTA
1233686 TTTATTTTATATTATA-TAATTA
1 -TTATTTTATATTATATTAATTA
1233708 T
1 T
1233709 ATTGTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 1 0.05
22 6 0.27
25 15 0.68
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATTTTATATTATATTAATTA
Found at i:1234411 original size:2 final size:2
Alignment explanation
Indices: 1234406--1234431 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1234396 AACCAGCTTG
1234406 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
1234432 TAACTAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1234568 original size:11 final size:12
Alignment explanation
Indices: 1234512--1234574 Score: 53
Period size: 11 Copynumber: 5.4 Consensus size: 12
1234502 AAAATTATGG
* *
1234512 TATTAAATTAAA
1 TATTATATTTAA
*
1234524 TA-TATATTT-T
1 TATTATATTTAA
1234534 TATTA-ATTTAA
1 TATTATATTTAA
1234545 TTTATTATATTTAA
1 --TATTATATTTAA
1234559 TATT-TATTTAA
1 TATTATATTTAA
1234570 TATTA
1 TATTA
1234575 AAATGATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
10 6 0.15
11 18 0.44
12 6 0.15
13 5 0.12
14 6 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATATTTAA
Found at i:1234896 original size:16 final size:17
Alignment explanation
Indices: 1234864--1234911 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1234854 AATAATATAA
1234864 TATATATTTATAA-ATTT
1 TATATATTTA-AATATTT
1234881 TATA-ATTTAAATATTT
1 TATATATTTAAATATTT
* *
1234897 AATATATTAAAATAT
1 TATATATTTAAATAT
1234912 ATAAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 2 0.07
16 12 0.44
17 13 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATTTAAATATTT
Found at i:1234911 original size:17 final size:17
Alignment explanation
Indices: 1234889--1234939 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
1234879 TTTATAATTT
*
1234889 AAATATTT-AATATATTA
1 AAATATTTAAAAATA-TA
*
1234906 AAATATATAAAAATATA
1 AAATATTTAAAAATATA
*
1234923 AAATATTT-TAAATATA
1 AAATATTTAAAAATATA
1234939 A
1 A
1234940 TTGTCATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 8 0.28
17 16 0.55
18 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATTTAAAAATATA
Found at i:1234921 original size:8 final size:9
Alignment explanation
Indices: 1234897--1234983 Score: 59
Period size: 9 Copynumber: 9.1 Consensus size: 9
1234887 TTAAATATTT
1234897 AATATATTAA
1 AATATA-TAA
1234907 AATATATAA
1 AATATATAA
1234916 AA-ATATAA
1 AATATATAA
* *
1234924 AATATTTTA
1 AATATATAA
**
1234933 AATATAATTGT
1 AATAT-A-TAA
*
1234944 CATATGATAA
1 AATAT-ATAA
*
1234954 AATATATTA
1 AATATATAA
1234963 AATATAATATA
1 AATAT-ATA-A
1234974 AATATATAA
1 AATATATAA
1234983 A
1 A
1234984 TAATTAAATT
Statistics
Matches: 60, Mismatches: 12, Indels: 11
0.72 0.14 0.13
Matches are distributed among these distances:
8 8 0.13
9 24 0.40
10 16 0.27
11 12 0.20
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (9 bp):
AATATATAA
Found at i:1234999 original size:28 final size:28
Alignment explanation
Indices: 1234953--1235010 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
1234943 TCATATGATA
* * *
1234953 AAATATATTAAATATAATATAAATATAT
1 AAATATATTAAATAGAATAAAAAAATAT
1234981 AAATA-ATTAAATTAGAATAAAAAAATAT
1 AAATATATTAAA-TAGAATAAAAAAATAT
1235009 AA
1 AA
1235011 GTGTATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (28 bp):
AAATATATTAAATAGAATAAAAAAATAT
Found at i:1236497 original size:15 final size:16
Alignment explanation
Indices: 1236472--1236502 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1236462 CTTTAATTTT
1236472 AATTTATATAATAAAA
1 AATTTATATAATAAAA
1236488 AATTTA-ATAATAAAA
1 AATTTATATAATAAAA
1236503 TTTATTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATTTATATAATAAAA
Found at i:1236748 original size:25 final size:26
Alignment explanation
Indices: 1236686--1236735 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1236676 TTTTAACTAT
* *
1236686 TAAATTATATAAAATATAAATATTAA
1 TAAAATATAAAAAATATAAATATTAA
1236712 TAAAATATAAAAAAT-TAAATATTA
1 TAAAATATAAAAAATATAAATATTA
1236736 TATATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
TAAAATATAAAAAATATAAATATTAA
Found at i:1236758 original size:32 final size:31
Alignment explanation
Indices: 1236694--1236763 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 31
1236684 ATTAAATTAT
1236694 ATAAAATATAAATATTAATAAAATATAAAAA
1 ATAAAATATAAATATTAATAAAATATAAAAA
* * *
1236725 ATTAAATATTATATATTAATAAAAT-TATTAAA
1 ATAAAATA-TAAATATTAATAAAATATA-AAAA
1236757 ATAAAAT
1 ATAAAAT
1236764 TTTTTATTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (31 bp):
ATAAAATATAAATATTAATAAAATATAAAAA
Found at i:1238296 original size:28 final size:28
Alignment explanation
Indices: 1238265--1238331 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
1238255 TATTATTATA
1238265 TTATAATTATATTTAAAAT-ATTTAATAT
1 TTAT-ATTATATTTAAAATAATTTAATAT
* * *
1238293 TTATATAAAATTTAAAATAATTTTATAT
1 TTATATTATATTTAAAATAATTTAATAT
1238321 TTATATTATAT
1 TTATATTATAT
1238332 ATATATATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 12 0.36
28 21 0.64
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTATATTATATTTAAAATAATTTAATAT
Found at i:1238340 original size:15 final size:15
Alignment explanation
Indices: 1238316--1238357 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1238306 AAAATAATTT
*
1238316 TATATTTATATTATA
1 TATATATATATTATA
*
1238331 TATATATATATTATC
1 TATATATATATTATA
1238346 T-TATATAATATT
1 TATATAT-ATATT
1238358 TTAATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATATATATTATA
Found at i:1238364 original size:21 final size:21
Alignment explanation
Indices: 1238340--1238379 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1238330 ATATATATAT
1238340 ATTATCTTATATAATATTTTA
1 ATTATCTTATATAATATTTTA
* * *
1238361 ATTATTTTTTATTATATTT
1 ATTATCTTATATAATATTT
1238380 ATAACGTGGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTATCTTATATAATATTTTA
Found at i:1239546 original size:25 final size:25
Alignment explanation
Indices: 1239512--1239565 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
1239502 GTATTTATAT
1239512 ATTACATTTTATAATTGTTAAAGGC
1 ATTACATTTTATAATTGTTAAAGGC
*
1239537 ATTACATTTTATAATTGTTAAAGGT
1 ATTACATTTTATAATTGTTAAAGGC
1239562 ATTA
1 ATTA
1239566 TTTATTAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (25 bp):
ATTACATTTTATAATTGTTAAAGGC
Found at i:1239675 original size:30 final size:29
Alignment explanation
Indices: 1239641--1239698 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
1239631 TATTTTTTTG
*
1239641 ATTTTAGTAAAAATAATATATTAAATATTA
1 ATTTTAGTAAAAATAATA-ATAAAATATTA
** *
1239671 ATTTTTTTAAAATTAATAATAAAATATT
1 ATTTTAGTAAAAATAATAATAAAATATT
1239699 CTTTAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
ATTTTAGTAAAAATAATAATAAAATATTA
Found at i:1243690 original size:16 final size:16
Alignment explanation
Indices: 1243669--1243699 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1243659 TGGGTTTCAA
*
1243669 TATTATTTTTAAATTT
1 TATTATTATTAAATTT
1243685 TATTATTATTAAATT
1 TATTATTATTAAATT
1243700 AATATTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTATTATTAAATTT
Found at i:1243715 original size:20 final size:19
Alignment explanation
Indices: 1243690--1243727 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1243680 AATTTTATTA
1243690 TTATTAAATTAATATTAATT
1 TTATTAAA-TAATATTAATT
*
1243710 TTATTAAATAATTTTAAT
1 TTATTAAATAATATTAAT
1243728 AAAAATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATTAAATAATATTAATT
Done.