Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold5
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: 1536239
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.33
Warning! 124408 characters in sequence are not A, C, G, or T
File 11 of 14
Found at i:1229772 original size:21 final size:23
Alignment explanation
Indices: 1229732--1229773 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1229722 TATATTATAT
*
1229732 ATTTTTTAATTTAATATTTAATA
1 ATTTTTTAATTAAATATTTAATA
1229755 ATTTTTT-ATTAAAT-TTTAA
1 ATTTTTTAATTAAATATTTAA
1229774 AATATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATTTTTTAATTAAATATTTAATA
Found at i:1231050 original size:2 final size:2
Alignment explanation
Indices: 1231043--1231073 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1231033 CTTCAGTCTA
1231043 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 A
1231074 GTTCATATGA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1231131 original size:3 final size:3
Alignment explanation
Indices: 1231123--1231147 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1231113 AAAATGTTTA
1231123 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1231148 TATTATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1232294 original size:47 final size:42
Alignment explanation
Indices: 1232230--1232327 Score: 108
Period size: 47 Copynumber: 2.2 Consensus size: 42
1232220 TATTTAATAA
*
1232230 TTAAA-AAATATTTTTATTTAAATTTAATAATAAAATATATAAAT
1 TTAAATAATTATTTTTATTTAAA-TTAATAAT-AAATA-ATAAAT
** *
1232274 ATTAATATAATTATTTTTATTTTTATTAATTATAAATAATAAAT
1 -TTAA-ATAATTATTTTTATTTAAATTAATAATAAATAATAAAT
1232318 TTAAATAATT
1 TTAAATAATT
1232328 TAAATTAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
42 6 0.13
43 4 0.09
44 6 0.13
45 9 0.19
46 8 0.17
47 14 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (42 bp):
TTAAATAATTATTTTTATTTAAATTAATAATAAATAATAAAT
Found at i:1232322 original size:13 final size:13
Alignment explanation
Indices: 1232301--1232361 Score: 65
Period size: 13 Copynumber: 4.6 Consensus size: 13
1232291 TATTTTTATT
1232301 AATTATAAATAATA
1 AATT-TAAATAATA
1232315 AATTTAAATAATTTA
1 AATTTAAATAA--TA
1232330 AA-TTAAA-AATA
1 AATTTAAATAATA
1232341 AATTTAAATAA-A
1 AATTTAAATAATA
1232353 ATATTTAAA
1 A-ATTTAAA
1232362 ATTTTTTAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
11 4 0.10
12 7 0.17
13 18 0.43
14 9 0.21
15 4 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTTAAATAATA
Found at i:1232344 original size:17 final size:15
Alignment explanation
Indices: 1232320--1232361 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
1232310 TAATAAATTT
1232320 AAATAATTTAAATTAA
1 AAATAATTTAAA-TAA
1232336 AAATAAATTTAAAT-A
1 AAAT-AATTTAAATAA
1232351 AAAT-ATTTAAA
1 AAATAATTTAAA
1232362 ATTTTTTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.28
15 5 0.20
16 5 0.20
17 8 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATAATTTAAATAA
Found at i:1232730 original size:24 final size:23
Alignment explanation
Indices: 1232703--1232788 Score: 65
Period size: 24 Copynumber: 3.9 Consensus size: 23
1232693 TTAGATCTTT
*
1232703 TATATTATTTATTGTAAATATAAA
1 TATAATATTTATT-TAAATATAAA
* *
1232727 TATAATA-TAAATT--ATA-AAA
1 TATAATATTTATTTAAATATAAA
* *
1232746 TATATTAATT-TTTAAATATAAA
1 TATAATATTTATTTAAATATAAA
*
1232768 TATAATATATATTATAAATAT
1 TATAATATTTATT-TAAATAT
1232789 TATATTTAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
19 11 0.23
20 4 0.09
21 3 0.06
22 11 0.23
23 5 0.11
24 13 0.28
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (23 bp):
TATAATATTTATTTAAATATAAA
Found at i:1232744 original size:7 final size:6
Alignment explanation
Indices: 1232717--1232788 Score: 53
Period size: 6 Copynumber: 12.2 Consensus size: 6
1232707 TTATTTATTG
* * *
1232717 TAAATA TAAATA T-AATA TAAATTA TAAA-A TATAT- TAATTTT TAAATA
1 TAAATA TAAATA TAAATA TAAA-TA TAAATA TAAATA TAA-ATA TAAATA
*
1232764 TAAATA T-AATA TATATTA TAAATA T
1 TAAATA TAAATA TA-AATA TAAATA T
1232789 TATATTTAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
5 16 0.31
6 22 0.42
7 14 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATA
Found at i:1232764 original size:41 final size:45
Alignment explanation
Indices: 1232702--1232794 Score: 140
Period size: 41 Copynumber: 2.2 Consensus size: 45
1232692 TTTAGATCTT
*
1232702 TTATATTATTTATTGTAAATATAAATATAATATAAATTATAAA-A
1 TTATATTAATTATTGTAAATATAAATATAATATAAATTATAAATA
*
1232746 -TATATTAATT-TT-TAAATATAAATATAATATATATTATAAATA
1 TTATATTAATTATTGTAAATATAAATATAATATAAATTATAAATA
1232788 TTATATT
1 TTATATT
1232795 TAACATATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
41 27 0.60
42 3 0.07
43 15 0.33
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (45 bp):
TTATATTAATTATTGTAAATATAAATATAATATAAATTATAAATA
Found at i:1232850 original size:23 final size:26
Alignment explanation
Indices: 1232824--1232875 Score: 74
Period size: 23 Copynumber: 2.1 Consensus size: 26
1232814 TTATTTAGTA
1232824 TATTATTTTT-TAT-ATATTTAA-AT
1 TATTATTTTTATATCATATTTAAGAT
*
1232847 TATTATTTTTATTTCATATTTAAGAT
1 TATTATTTTTATATCATATTTAAGAT
1232873 TAT
1 TAT
1232876 AAAATGTAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 10 0.40
24 2 0.08
25 8 0.32
26 5 0.20
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (26 bp):
TATTATTTTTATATCATATTTAAGAT
Found at i:1233051 original size:16 final size:17
Alignment explanation
Indices: 1233012--1233051 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1233002 ATTCATGCAA
1233012 AAAATTT-TAATTAAAT
1 AAAATTTATAATTAAAT
1233028 AAAA-TTATAATT-AAT
1 AAAATTTATAATTAAAT
1233043 AAAATTTAT
1 AAAATTTAT
1233052 TTAAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATTTATAATTAAAT
Found at i:1233075 original size:23 final size:25
Alignment explanation
Indices: 1233027--1233085 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 25
1233017 TTTAATTAAA
*
1233027 TAAAATTATAATTAATAAAATTTATT
1 TAAAATTAT-ATTAATAAAATATATT
1233053 TAAAATTAT-TTAAT-AAATATATT
1 TAAAATTATATTAATAAAATATATT
*
1233076 TAAAGTTATA
1 TAAAATTATA
1233086 ATTTAATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 16 0.53
24 5 0.17
26 9 0.30
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
TAAAATTATATTAATAAAATATATT
Found at i:1235915 original size:2 final size:2
Alignment explanation
Indices: 1235904--1235932 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1235894 ATTATTTAGA
1235904 AT AT -T 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
1235933 TGAAAGCAGA
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:1236561 original size:21 final size:19
Alignment explanation
Indices: 1236515--1236563 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1236505 ATTAAGATTT
1236515 TTTATA-TATTTTTATTAA
1 TTTATATTATTTTTATTAA
*
1236533 TTTAATATTATTTTTATGTCA
1 TTT-ATATTATTTTTAT-TAA
1236554 TATTATATTA
1 T-TTATATTA
1236564 GTGTTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 3 0.12
19 3 0.12
20 9 0.35
21 9 0.35
22 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTATATTATTTTTATTAA
Found at i:1237914 original size:16 final size:17
Alignment explanation
Indices: 1237863--1237917 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
1237853 GTTAAATGTA
1237863 ATAAAA-ATTATTAATAT
1 ATAAAATATTATTAA-AT
1237880 ATTAAAAT-TTATATAAAT
1 A-TAAAATATTAT-TAAAT
1237898 ATAAAATATT-TTAAAT
1 ATAAAATATTATTAAAT
1237914 ATAA
1 ATAA
1237918 TTATATATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
16 9 0.26
17 8 0.24
18 14 0.41
19 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAAATATTATTAAAT
Found at i:1238221 original size:19 final size:19
Alignment explanation
Indices: 1238190--1238228 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1238180 TGAAAATTTA
1238190 TTTATTTTATATTAATATT
1 TTTATTTTATATTAATATT
*
1238209 TTTATATTT-TATTTATATT
1 TTTAT-TTTATATTAATATT
1238228 T
1 T
1238229 AAAATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTATTTTATATTAATATT
Found at i:1238230 original size:26 final size:26
Alignment explanation
Indices: 1238190--1238249 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
1238180 TGAAAATTTA
* *
1238190 TTTATTT-TATATTAATATTTTTATAT
1 TTTATTTATATATTAA-AATATTATAT
1238216 TTTATTTATAT-TTAAAATATTATAT
1 TTTATTTATATATTAAAATATTATAT
1238241 TTT-TTTATA
1 TTTATTTATA
1238250 AATTTTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 6 0.19
25 11 0.35
26 11 0.35
27 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTATTTATATATTAAAATATTATAT
Found at i:1238308 original size:23 final size:24
Alignment explanation
Indices: 1238281--1238325 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1238271 TTTATATGTA
*
1238281 TTATATTATATTT-TAATTATTTT
1 TTATATTATATTTAAAATTATTTT
1238304 TTATATTATATTTAAAATTATT
1 TTATATTATATTTAAAATTATT
1238326 GAGGATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTATATTATATTTAAAATTATTTT
Found at i:1238968 original size:18 final size:16
Alignment explanation
Indices: 1238945--1238983 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
1238935 TTTTAATATT
1238945 TTAAAAAATATCAAAATA
1 TTAAAAAAT-TCAAAA-A
*
1238963 TTAAAAAATTTAAAAA
1 TTAAAAAATTCAAAAA
1238979 TTAAA
1 TTAAA
1238984 TTATTTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 5 0.25
18 9 0.45
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
TTAAAAAATTCAAAAA
Found at i:1240323 original size:23 final size:20
Alignment explanation
Indices: 1240295--1240346 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 20
1240285 AAAAATTTTA
1240295 AAAATTTATATTAATATTTAAAT
1 AAAATTTATATT--T-TTTAAAT
*
1240318 AAAATTTTTATTTTTTAAAT
1 AAAATTTATATTTTTTAAAT
1240338 AATAATTTA
1 AA-AATTTA
1240347 AATCGAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 9 0.35
21 6 0.23
23 11 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AAAATTTATATTTTTTAAAT
Found at i:1241014 original size:20 final size:20
Alignment explanation
Indices: 1240991--1241032 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1240981 AAAAAATAAA
1240991 TAATATAATCGAT-TAAGTAT
1 TAATATAATCGATATAA-TAT
* *
1241011 TAATTTAATTGATATAATAT
1 TAATATAATCGATATAATAT
1241031 TA
1 TA
1241033 TTAATAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (20 bp):
TAATATAATCGATATAATAT
Found at i:1246614 original size:15 final size:15
Alignment explanation
Indices: 1246571--1246615 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
1246561 AAGTATTTAG
1246571 TTTTTATATTATTAAA
1 TTTTT-TATTATTAAA
**
1246587 TTTAATATT-TTAAA
1 TTTTTTATTATTAAA
1246601 TTTTTTATTATTAAA
1 TTTTTTATTATTAAA
1246616 ATATTAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 12 0.50
15 9 0.38
16 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTTATTATTAAA
Found at i:1247304 original size:15 final size:15
Alignment explanation
Indices: 1247286--1247359 Score: 71
Period size: 15 Copynumber: 4.9 Consensus size: 15
1247276 AAAAATTATA
*
1247286 ATTAAATTTAATAAT
1 ATTAAATATAATAAT
*
1247301 ATTAAATATAATTAT
1 ATTAAATATAATAAT
1247316 A-TAAATATAATAAAT
1 ATTAAATATAAT-AAT
*
1247331 ATAAAATAATAA-AAT
1 ATTAAAT-ATAATAAT
* *
1247346 ATAAAATAAAATAA
1 ATTAAATATAATAA
1247360 ATACATATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
14 13 0.26
15 29 0.58
16 4 0.08
17 4 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTAAATATAATAAT
Found at i:1247396 original size:16 final size:15
Alignment explanation
Indices: 1247372--1247422 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 15
1247362 ACATATATTA
1247372 AAATTTTAATAATAT
1 AAATTTTAATAATAT
1247387 AAATTATTAAT-ATATT
1 AAATT-TTAATAATA-T
1247403 AAATTTTATATAAATAT
1 AAATTTTA-AT-AATAT
1247420 AAA
1 AAA
1247423 ATATTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 11 0.35
16 13 0.42
17 4 0.13
18 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATTTTAATAATAT
Found at i:1247401 original size:15 final size:16
Alignment explanation
Indices: 1247366--1247415 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
1247356 ATAAATACAT
1247366 ATATTAAAATTTTAATA
1 ATATT-AAATTTTAATA
1247383 ATA-TAAATTATTAAT-
1 ATATTAAATT-TTAATA
1247398 ATATTAAATTTTATATA
1 ATATTAAATTTTA-ATA
1247415 A
1 A
1247416 ATATAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 11 0.38
16 14 0.48
17 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTAAATTTTAATA
Found at i:1247405 original size:32 final size:33
Alignment explanation
Indices: 1247344--1247427 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 33
1247334 AAATAATAAA
*
1247344 ATATAAA-ATAAAATAAATACATATATTAAAATTTT
1 ATATAAATATAAAAT-ATTA-ATATATT-AAATTTT
*
1247379 A-AT-AATATAAATTATTAATATATTAAATTTT
1 ATATAAATATAAAATATTAATATATTAAATTTT
1247410 ATATAAATATAAAATATT
1 ATATAAATATAAAATATT
1247428 TTTAAAATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
31 8 0.19
32 9 0.21
33 17 0.40
34 8 0.19
35 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (33 bp):
ATATAAATATAAAATATTAATATATTAAATTTT
Found at i:1247426 original size:7 final size:8
Alignment explanation
Indices: 1247306--1247426 Score: 69
Period size: 7 Copynumber: 15.2 Consensus size: 8
1247296 ATAATATTAA
*
1247306 ATATAATT
1 ATATAAAT
1247314 ATATAAAT
1 ATATAAAT
1247322 ATAATAAAT
1 AT-ATAAAT
1247331 ATA-AAAT
1 ATATAAAT
1247338 A-ATAAA-
1 ATATAAAT
1247344 ATATAAA-
1 ATATAAAT
1247351 ATA-AAAT
1 ATATAAAT
* *
1247358 AAATACAT
1 ATATAAAT
1247366 ATATTAAA-
1 ATA-TAAAT
* *
1247374 ATTTTAAT
1 ATATAAAT
1247382 AATATAAAT
1 -ATATAAAT
*
1247391 -TATTAAT
1 ATATAAAT
1247398 ATATTAAATTTT
1 ATA-TAAA---T
1247410 ATATAAAT
1 ATATAAAT
1247418 ATA-AAAT
1 ATATAAAT
1247425 AT
1 AT
1247427 TTTTAAAATA
Statistics
Matches: 89, Mismatches: 11, Indels: 27
0.70 0.09 0.21
Matches are distributed among these distances:
6 5 0.06
7 33 0.37
8 23 0.26
9 20 0.22
11 4 0.04
12 4 0.04
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAAAT
Found at i:1247755 original size:28 final size:29
Alignment explanation
Indices: 1247714--1247797 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 29
1247704 ATATAAAATT
* *
1247714 TAATATATTAAAATTTATATT-TTTTTTA
1 TAATATATTAAAATATATATTATATTTTA
1247742 TAATATA-TATAAATATATATTATATTTTA
1 TAATATATTA-AAATATATATTATATTTTA
** * * *
1247771 TGTTATTTTTATAT-TATATTATATTTT
1 TAATATATTAAAATATATATTATATTTT
1247798 TTATATTATA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
27 2 0.04
28 30 0.65
29 13 0.28
30 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (29 bp):
TAATATATTAAAATATATATTATATTTTA
Found at i:1247765 original size:5 final size:5
Alignment explanation
Indices: 1247757--1247809 Score: 51
Period size: 5 Copynumber: 11.2 Consensus size: 5
1247747 TATATAAATA
* *
1247757 TATAT TATAT TTTAT GT-TAT T-T-T TATAT TATAT TATAT T-TTT TATAT
1 TATAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1247804 TATAT T
1 TATAT T
1247810 TATACGTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
3 2 0.05
4 6 0.15
5 32 0.78
6 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (5 bp):
TATAT
Found at i:1247782 original size:11 final size:12
Alignment explanation
Indices: 1247757--1247810 Score: 57
Period size: 11 Copynumber: 5.0 Consensus size: 12
1247747 TATATAAATA
1247757 TATATTATATTT
1 TATATTATATTT
*
1247769 TATGTTAT-TTT
1 TATATTATATTT
1247780 TATATTATA--T
1 TATATTATATTT
1247790 TATA-T-T-TTT
1 TATATTATATTT
1247799 TATATTATATTT
1 TATATTATATTT
1247811 ATACGTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
8 1 0.03
9 6 0.18
10 6 0.18
11 11 0.32
12 10 0.29
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TATATTATATTT
Found at i:1247800 original size:30 final size:28
Alignment explanation
Indices: 1247728--1247813 Score: 84
Period size: 30 Copynumber: 3.0 Consensus size: 28
1247718 ATATTAAAAT
* * * *
1247728 TTATATT-TTTTTTATAATATATATAAA
1 TTATATTATATTTTATATTATATTTATA
* *
1247755 TATATATTATATTTTATGTTATTTTTATA
1 T-TATATTATATTTTATATTATATTTATA
1247784 TTATATTATATTTTTTATATTATATTTATA
1 TTATATTATA--TTTTATATTATATTTATA
1247814 CGTATAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
27 1 0.02
28 15 0.32
29 15 0.32
30 16 0.34
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (28 bp):
TTATATTATATTTTATATTATATTTATA
Found at i:1248104 original size:16 final size:16
Alignment explanation
Indices: 1248069--1248143 Score: 55
Period size: 18 Copynumber: 4.6 Consensus size: 16
1248059 AAAATATTTT
*
1248069 TATTAAAAT-T-TAAT
1 TATTAAAATATATAAA
1248083 TATTAAAATATATAAA
1 TATTAAAATATATAAA
* *
1248099 TATTAATAAAAAATAATA
1 TATTAA-AATATATAA-A
*
1248117 TTTTAATAATATAATAAA
1 TATTAA-AATAT-ATAAA
*
1248135 TAATAAAAT
1 TATTAAAAT
1248144 TGACTTTCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
14 9 0.19
15 1 0.02
16 9 0.19
17 10 0.21
18 15 0.31
19 4 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATTAAAATATATAAA
Found at i:1248847 original size:21 final size:20
Alignment explanation
Indices: 1248809--1248854 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
1248799 TGACACTATT
*
1248809 TTATATGAGAAAAAAATAA-
1 TTATATCAGAAAAAAATAAG
1248828 TTATATCACGAAATAAAATAAG
1 TTATATCA-GAAA-AAAATAAG
1248850 TTATA
1 TTATA
1248855 ATATGAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 4 0.17
21 7 0.30
22 5 0.22
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (20 bp):
TTATATCAGAAAAAAATAAG
Found at i:1248862 original size:22 final size:20
Alignment explanation
Indices: 1248810--1248863 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
1248800 GACACTATTT
1248810 TATATGAGAAAAAAATAATTA
1 TATATGA-AAAAAAATAATTA
* *
1248831 TATCACGAAATAAAATAAGTTA
1 TAT-ATGAAAAAAAATAA-TTA
1248853 TAATATGAAAA
1 T-ATATGAAAA
1248864 GTAATACACA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
21 12 0.46
22 12 0.46
23 2 0.08
ACGTcount: A:0.59, C:0.04, G:0.09, T:0.28
Consensus pattern (20 bp):
TATATGAAAAAAAATAATTA
Found at i:1248948 original size:19 final size:19
Alignment explanation
Indices: 1248866--1248954 Score: 67
Period size: 19 Copynumber: 4.7 Consensus size: 19
1248856 TATGAAAAGT
*
1248866 AATACACAAATATGATATG
1 AATATACAAATATGATATG
* ** *
1248885 AATATATAAATATTTTA-A
1 AATATACAAATATGATATG
*
1248903 AATATA-TAATAT-ATATG
1 AATATACAAATATGATATG
1248920 ATATGAATACAAATATGATATG
1 A-AT--ATACAAATATGATATG
*
1248942 AATATACGAATAT
1 AATATACAAATAT
1248955 TTCAAAATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
16 2 0.04
17 6 0.11
18 8 0.15
19 22 0.41
20 3 0.06
21 7 0.13
22 6 0.11
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (19 bp):
AATATACAAATATGATATG
Found at i:1252013 original size:7 final size:7
Alignment explanation
Indices: 1252003--1252027 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1251993 AATATTTAAT
1252003 AAATTTA
1 AAATTTA
1252010 AAATTTA
1 AAATTTA
1252017 AAATTTA
1 AAATTTA
1252024 AAAT
1 AAAT
1252028 ACGTAATTCT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:1252467 original size:19 final size:20
Alignment explanation
Indices: 1252443--1252482 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1252433 CAGCCAAATC
* *
1252443 ATTTAA-ATTTAAAAGATTT
1 ATTTAATATTAAAAAAATTT
1252462 ATTTAATATTAAAAAAATTT
1 ATTTAATATTAAAAAAATTT
1252482 A
1 A
1252483 AATAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
ATTTAATATTAAAAAAATTT
Found at i:1253154 original size:24 final size:24
Alignment explanation
Indices: 1253122--1253168 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1253112 CTCCAAATCC
1253122 AATTTCTTCCACCTCTCGAGATCA
1 AATTTCTTCCACCTCTCGAGATCA
1253146 AATTTCTTCCACCTCTCGAGATC
1 AATTTCTTCCACCTCTCGAGATC
1253169 GATCGATCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.34, G:0.09, T:0.34
Consensus pattern (24 bp):
AATTTCTTCCACCTCTCGAGATCA
Found at i:1253808 original size:14 final size:15
Alignment explanation
Indices: 1253779--1253811 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1253769 TATCATATAA
*
1253779 TAATTATATTTAAAT
1 TAATTATATATAAAT
1253794 TAATT-TATATAAAT
1 TAATTATATATAAAT
1253808 TAAT
1 TAAT
1253812 AATTAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTATATATAAAT
Found at i:1254268 original size:18 final size:19
Alignment explanation
Indices: 1254222--1254268 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1254212 TTATAGTCAC
1254222 AACATGATTAAATATAATT
1 AACATGATTAAATATAATT
**
1254241 AACAACATTAAA-ATAATT
1 AACATGATTAAATATAATT
*
1254259 AATATGATTA
1 AACATGATTA
1254269 TTAACTTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.34
Consensus pattern (19 bp):
AACATGATTAAATATAATT
Found at i:1254521 original size:19 final size:19
Alignment explanation
Indices: 1254484--1254522 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1254474 TTTGACTAGC
** *
1254484 ATAATTATATTTTTTTTTT
1 ATAATTATACATTTCTTTT
1254503 ATAATTATACATTTCTTTT
1 ATAATTATACATTTCTTTT
1254522 A
1 A
1254523 AAATAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (19 bp):
ATAATTATACATTTCTTTT
Found at i:1254646 original size:41 final size:41
Alignment explanation
Indices: 1254600--1254678 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
1254590 ATACAATTTC
*
1254600 TTATTTATGGTTAAAATAAAATATAAAATATAAAAATAAGT
1 TTATTTATAGTTAAAATAAAATATAAAATATAAAAATAAGT
* * * * * *
1254641 TTATTTTTATTTAAATTTAATTATAAAATATATAAATA
1 TTATTTATAGTTAAAATAAAATATAAAATATAAAAATA
1254679 TTAATATAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (41 bp):
TTATTTATAGTTAAAATAAAATATAAAATATAAAAATAAGT
Found at i:1254915 original size:16 final size:16
Alignment explanation
Indices: 1254870--1254913 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
1254860 AATATTCATA
*
1254870 TTATATTTATTTTATTT
1 TTATA-TTATTTTATAT
1254887 TTATATTATTTTATAT
1 TTATATTATTTTATAT
1254903 TTA-ATTATTTT
1 TTATATTATTTT
1254914 TACATATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 8 0.31
16 13 0.50
17 5 0.19
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATATTATTTTATAT
Found at i:1255374 original size:13 final size:15
Alignment explanation
Indices: 1255344--1255388 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
1255334 AGATGCAAAC
1255344 AATTATAAATATTAA
1 AATTATAAATATTAA
*
1255359 AATTA-AAATTTTAA
1 AATTATAAATATTAA
*
1255373 ATTTATTAAATATTAA
1 AATTA-TAAATATTAA
1255389 TTTTAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 12 0.48
15 5 0.20
16 8 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTATAAATATTAA
Found at i:1256294 original size:42 final size:42
Alignment explanation
Indices: 1256199--1256309 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
1256189 TTTAAGTGTG
* * * **
1256199 TTAATCGTGCCGTGTTTATATTTCAAAATCTGACATGATTAA
1 TTAATCGTGTCGTGTTTGTGTTTCAAAATCTGACACAATTAA
* *
1256241 TTAATCATGTCGTGTTTGTGTTTCAAAGTCTGACACAATTAA
1 TTAATCGTGTCGTGTTTGTGTTTCAAAATCTGACACAATTAA
* * * *
1256283 TTAATTGTGTCGTATTCGTGTATCAAA
1 TTAATCGTGTCGTGTTTGTGTTTCAAA
1256310 TAATCATATT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (42 bp):
TTAATCGTGTCGTGTTTGTGTTTCAAAATCTGACACAATTAA
Found at i:1256998 original size:56 final size:57
Alignment explanation
Indices: 1256931--1257043 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
1256921 ATGCTAAGAG
1256931 CAATTTTTGTTGCTGTGAA-TTGATGTTGGTTATGTCAAGTATCACATCCCAAATGT
1 CAATTTTTGTTGCTGTGAACTTGATGTTGGTTATGTCAAGTATCACATCCCAAATGT
* *
1256987 CAATTTTTGTTGCTGTGAACTTGATGTTGGTTATGTCATGTATCACATGCCAAATGT
1 CAATTTTTGTTGCTGTGAACTTGATGTTGGTTATGTCAAGTATCACATCCCAAATGT
1257044 ATATGTGAGT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
56 19 0.35
57 35 0.65
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (57 bp):
CAATTTTTGTTGCTGTGAACTTGATGTTGGTTATGTCAAGTATCACATCCCAAATGT
Found at i:1258496 original size:12 final size:12
Alignment explanation
Indices: 1258481--1258505 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1258471 CTGGTTGTTT
1258481 TAGCTGTTGGAG
1 TAGCTGTTGGAG
1258493 TAGCTGTTGGAG
1 TAGCTGTTGGAG
1258505 T
1 T
1258506 TTACATCCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.40, T:0.36
Consensus pattern (12 bp):
TAGCTGTTGGAG
Found at i:1259657 original size:27 final size:27
Alignment explanation
Indices: 1259619--1259674 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
1259609 AAGAAGATAA
1259619 TATCAATCATATT-TCCATACTCATGTC
1 TATCAATCATATTCT-CATACTCATGTC
1259646 TATCAATCATATTCTCATACTCATGTC
1 TATCAATCATATTCTCATACTCATGTC
1259673 TA
1 TA
1259675 GATATATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.41
Consensus pattern (27 bp):
TATCAATCATATTCTCATACTCATGTC
Found at i:1265842 original size:24 final size:24
Alignment explanation
Indices: 1265815--1265892 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 24
1265805 GTTTGATGTT
1265815 AAATATTTATTTAATATAAATTAA
1 AAATATTTATTTAATATAAATTAA
*
1265839 AAATTAAATTTTATTAAAATATAAATT-A
1 AAA-T--A-TTTATT-TAATATAAATTAA
* *
1265867 ATA-ATTTATTTAAATACAAATTAA
1 AAATATTTATTT-AATATAAATTAA
1265891 AA
1 AA
1265893 GTTAAAATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
23 15 0.36
24 6 0.14
25 1 0.02
27 1 0.02
28 9 0.21
29 10 0.24
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATATTTATTTAATATAAATTAA
Found at i:1265845 original size:29 final size:29
Alignment explanation
Indices: 1265813--1265872 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
1265803 AAGTTTGATG
*
1265813 TTAAATATTTATT-TAATATAAATTAAAAA
1 TTAAAT-TTTATTAAAATATAAATTAAAAA
*
1265842 TTAAATTTTATTAAAATATAAATTAATAA
1 TTAAATTTTATTAAAATATAAATTAAAAA
1265871 TT
1 TT
1265873 TATTTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TTAAATTTTATTAAAATATAAATTAAAAA
Found at i:1265858 original size:23 final size:22
Alignment explanation
Indices: 1265831--1265892 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
1265821 TTATTTAATA
* *
1265831 TAAATTAAAAATTAAATTTTAT
1 TAAAATAAAAATTAAAATTTAT
*
1265853 TAAAATATAAATTAATAATTTAT
1 TAAAATAAAAATTAA-AATTTAT
* *
1265876 TTAAATACAAATTAAAA
1 TAAAATAAAAATTAAAA
1265893 GTTAAAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAATAAAAATTAAAATTTAT
Found at i:1265887 original size:29 final size:29
Alignment explanation
Indices: 1265827--1265904 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
1265817 ATATTTATTT
* *
1265827 AATATAAATTAAAAATTAAATTTTATTAA
1 AATATAAATTAAAAATTAAATTTAAATAA
* *
1265856 AATATAAATTAATAATT-TATTTAAATACA
1 AATATAAATTAAAAATTAAATTTAAATA-A
1265885 AAT-TAAAAGTT-AAAATTAAA
1 AATAT-AAA-TTAAAAATTAAA
1265905 AGTTATTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
28 8 0.21
29 28 0.72
30 3 0.08
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (29 bp):
AATATAAATTAAAAATTAAATTTAAATAA
Found at i:1265900 original size:13 final size:13
Alignment explanation
Indices: 1265884--1265909 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1265874 ATTTAAATAC
1265884 AAATTAAAAGTTA
1 AAATTAAAAGTTA
1265897 AAATTAAAAGTTA
1 AAATTAAAAGTTA
1265910 TTTAAGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
AAATTAAAAGTTA
Found at i:1268548 original size:40 final size:39
Alignment explanation
Indices: 1268471--1268548 Score: 88
Period size: 40 Copynumber: 1.9 Consensus size: 39
1268461 ATATATTTAA
* *
1268471 ATATAAATATTAAAAAATAAACTTATGATTTTTTTAAAAT
1 ATATAAAAATTAAAAAATAAAC-TATGATTTTATTAAAAT
1268511 ATATAAAAAATTAAAAAATTAAA-TAT-ATTTATATTAAA
1 ATAT-AAAAATTAAAAAA-TAAACTATGATTT-TATTAAA
1268549 TACATACTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
39 4 0.12
40 13 0.39
41 12 0.36
42 4 0.12
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (39 bp):
ATATAAAAATTAAAAAATAAACTATGATTTTATTAAAAT
Found at i:1274005 original size:2 final size:2
Alignment explanation
Indices: 1273998--1274034 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1273988 GATTTTCAAA
*
1273998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1274035 AATAAAATAA
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:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1274430 original size:11 final size:11
Alignment explanation
Indices: 1274414--1274454 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
1274404 TTTCATATTT
1274414 TTTTTTCTTTC
1 TTTTTTCTTTC
1274425 TTTTTTCTTCATC
1 TTTTTTCTT--TC
*
1274438 TTCTTTCTTTC
1 TTTTTTCTTTC
1274449 TTTTTT
1 TTTTTT
1274455 ACCTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:1274468 original size:24 final size:22
Alignment explanation
Indices: 1274414--1274468 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
1274404 TTTCATATTT
**
1274414 TTTTTTCTTTCTTTTTTCTTCA
1 TTTTTTCTTTCTTTTTTCTAAA
1274436 TCTTCTTTCTTTCTTTTTTACCTAAA
1 T-TT-TTTCTTTCTTTTTT--CTAAA
1274462 TTTTTTC
1 TTTTTTC
1274469 AACCCATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
23 2 0.07
24 18 0.67
25 2 0.07
26 4 0.15
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTCTTTCTTTTTTCTAAA
Found at i:1274836 original size:24 final size:23
Alignment explanation
Indices: 1274809--1274855 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1274799 CCACTCAATC
1274809 GGAAAACCCACTTTGGTTTTTTTT
1 GGAAAACCC-CTTTGGTTTTTTTT
* **
1274833 GGAAAGCCCCTTTTTTTTTTTTT
1 GGAAAACCCCTTTGGTTTTTTTT
1274856 TCGATCCCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.51
Consensus pattern (23 bp):
GGAAAACCCCTTTGGTTTTTTTT
Found at i:1275809 original size:31 final size:32
Alignment explanation
Indices: 1275688--1275809 Score: 156
Period size: 32 Copynumber: 3.8 Consensus size: 32
1275678 AAAATGGTGA
* ** **
1275688 TTTGAAAAGGGTTGCCACTAACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1275720 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1275752 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
1275784 TTTGGAATGGG-TGCCACAGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
1275810 GATTTAAAAG
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
31 13 0.16
32 67 0.84
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:1275826 original size:27 final size:27
Alignment explanation
Indices: 1275792--1276365 Score: 950
Period size: 27 Copynumber: 21.0 Consensus size: 27
1275782 GCTTTGGAAT
* *
1275792 GGGTGCCACAGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1275819 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1275846 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1275873 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1275900 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1275928 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1275955 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
* *
1275983 GGATGCCACGGAGCTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1276010 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
1276038 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1276065 GGGGGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1276092 GGGATGCCACGGAGTTGTGGACTTAAAA
1 GGG-TGCCACGGAGTTGTGGACTTAAAA
*
1276120 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1276147 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1276174 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1276201 GGGGGCCACGGAGTTGTGGACTTAAAAA
1 GGGTGCCACGGAGTTGTGGACTT-AAAA
*
1276229 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1276256 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
** *
1276283 GAATGCCACGGAGTTGTGGACTTGAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1276310 GGGTGCCACGAAGTTGGGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1276337 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
1276365 G
1 G
1276366 AAAATGTGAA
Statistics
Matches: 511, Mismatches: 30, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
27 377 0.74
28 134 0.26
ACGTcount: A:0.28, C:0.15, G:0.36, T:0.22
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:1276008 original size:82 final size:81
Alignment explanation
Indices: 1275792--1276365 Score: 950
Period size: 82 Copynumber: 7.0 Consensus size: 81
1275782 GCTTTGGAAT
* * *
1275792 GGGTGCCACAGAGTTGTGGATTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1275857 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
*
1275873 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGCCACA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACG
1275938 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
* *
1275955 GGGATGCCACGGAGTTGTGGACTTAAAAGGATGCCACGGAGCTGTGGACTTAAAAGGGATGCCAC
1 GGG-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCAC
1276020 GGAGTTGTGGACTTAAAA
64 GGAGTTGTGGACTTAAAA
*
1276038 GGGTGCCACGGAGTTGTGGACTTAAAAGGGGGCCACGGAGTTGTGGACTTAAAAGGGATGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGG-TGCCACG
1276103 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
*
1276120 GGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1276185 AGTTGTGGACTTAAAA
66 AGTTGTGGACTTAAAA
* * *
1276201 GGGGGCCACGGAGTTGTGGACTTAAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACA
1 GGGTGCCACGGAGTTGTGGACTT-AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1276266 GAGTTGTGGACTTAAAA
65 GAGTTGTGGACTTAAAA
** * * *
1276283 GAATGCCACGGAGTTGTGGACTTGAAAGGGTGCCACGAAGTTGGGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1276348 AGTTGTGGACTTTAAAA
66 AGTTGTGGAC-TTAAAA
1276365 G
1 G
1276366 AAAATGTGAA
Statistics
Matches: 464, Mismatches: 24, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
81 137 0.30
82 258 0.56
83 69 0.15
ACGTcount: A:0.28, C:0.15, G:0.36, T:0.22
Consensus pattern (81 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAA
Found at i:1276396 original size:46 final size:46
Alignment explanation
Indices: 1276329--1276417 Score: 169
Period size: 46 Copynumber: 1.9 Consensus size: 46
1276319 GAAGTTGGGG
*
1276329 ACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAAAATGTGA
1 ACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAAAATGTGA
1276375 ACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAAAATG
1 ACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAAAATG
1276418 CCACTGAGTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.38, C:0.11, G:0.27, T:0.24
Consensus pattern (46 bp):
ACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGAAAATGTGA
Found at i:1276421 original size:30 final size:31
Alignment explanation
Indices: 1276385--1276442 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
1276375 ACTTAAAAGG
*
1276385 ATGCCACGGAGTTGTGGACTTT-AAAAGAAA
1 ATGCCACGGAGTCGTGGACTTTGAAAAGAAA
*
1276415 ATGCCACTGAGTCGTGGACTTTGAAAAG
1 ATGCCACGGAGTCGTGGACTTTGAAAAG
1276443 GTCACAGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.24
Consensus pattern (31 bp):
ATGCCACGGAGTCGTGGACTTTGAAAAGAAA
Found at i:1283842 original size:2 final size:2
Alignment explanation
Indices: 1283835--1283869 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1283825 GATTTTCAAA
*
1283835 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1283870 AATAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1284266 original size:11 final size:11
Alignment explanation
Indices: 1284250--1284290 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
1284240 TTTCATATTT
1284250 TTTTTTCTTTC
1 TTTTTTCTTTC
1284261 TTTTTTCTTCATC
1 TTTTTTCTT--TC
*
1284274 TTCTTTCTTTC
1 TTTTTTCTTTC
1284285 TTTTTT
1 TTTTTT
1284291 ACCTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:1284304 original size:24 final size:22
Alignment explanation
Indices: 1284250--1284304 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
1284240 TTTCATATTT
**
1284250 TTTTTTCTTTCTTTTTTCTTCA
1 TTTTTTCTTTCTTTTTTCTAAA
1284272 TCTTCTTTCTTTCTTTTTTACCTAAA
1 T-TT-TTTCTTTCTTTTTT--CTAAA
1284298 TTTTTTC
1 TTTTTTC
1284305 AACCCATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
23 2 0.07
24 18 0.67
25 2 0.07
26 4 0.15
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTCTTTCTTTTTTCTAAA
Found at i:1284672 original size:24 final size:23
Alignment explanation
Indices: 1284645--1284691 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1284635 CCACTCAATC
1284645 GGAAAACCCACTTTGGTTTTTTTT
1 GGAAAACCC-CTTTGGTTTTTTTT
* **
1284669 GGAAAGCCCCTTTTTTTTTTTTT
1 GGAAAACCCCTTTGGTTTTTTTT
1284692 TCGATCCCCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.17, C:0.17, G:0.15, T:0.51
Consensus pattern (23 bp):
GGAAAACCCCTTTGGTTTTTTTT
Found at i:1286917 original size:67 final size:66
Alignment explanation
Indices: 1286807--1286942 Score: 236
Period size: 67 Copynumber: 2.0 Consensus size: 66
1286797 GCAGATGGAG
* *
1286807 ATCAAGCTCATTGGGACCGAAATTTAATTCTATCATACACGACCAAAGTTAACAGTACTTCTAGG
1 ATCAAGCTCATTGGGACCGAAATTTAATTCTATCATACACGACC-AAGGTAACACTACTTCTAGG
1286872 CT
65 CT
*
1286874 ATCAAGCTCATTGGGACCGAAATTTAATTCTATCATACCCGACCAAGGTAACACTACTTCTAGGC
1 ATCAAGCTCATTGGGACCGAAATTTAATTCTATCATACACGACCAAGGTAACACTACTTCTAGGC
1286939 T
66 T
1286940 ATC
1 ATC
1286943 TTTCTTGGAC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
66 23 0.35
67 43 0.65
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (66 bp):
ATCAAGCTCATTGGGACCGAAATTTAATTCTATCATACACGACCAAGGTAACACTACTTCTAGGC
T
Found at i:1288554 original size:17 final size:18
Alignment explanation
Indices: 1288532--1288565 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1288522 CAAATAAAAA
1288532 AAATTAA-ACAAAAGAAT
1 AAATTAATACAAAAGAAT
*
1288549 AAATTAATTCAAAAGAA
1 AAATTAATACAAAAGAA
1288566 AATACTACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (18 bp):
AAATTAATACAAAAGAAT
Found at i:1289027 original size:2 final size:2
Alignment explanation
Indices: 1289020--1289056 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1289010 AAGAATAATA
1289020 AG AG AG 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 AG AG AG A
1289057 TTAAAACAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1290339 original size:11 final size:10
Alignment explanation
Indices: 1290310--1290348 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1290300 TTAAAAATTT
*
1290310 AATTATAAAA
1 AATTATATAA
1290320 AATTATATAA
1 AATTATATAA
1290330 AATTATTATAA
1 AATTA-TATAA
*
1290341 AATAATAT
1 AATTATAT
1290349 TTTCATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AATTATATAA
Found at i:1290392 original size:13 final size:13
Alignment explanation
Indices: 1290374--1290398 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1290364 TATAATAATA
1290374 TAAATTTTTAAAT
1 TAAATTTTTAAAT
1290387 TAAATTTTTAAA
1 TAAATTTTTAAA
1290399 AATTTTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAATTTTTAAAT
Found at i:1290778 original size:11 final size:11
Alignment explanation
Indices: 1290764--1290828 Score: 82
Period size: 11 Copynumber: 6.1 Consensus size: 11
1290754 TGATATATTT
1290764 TTATATTTATA
1 TTATATTTATA
*
1290775 TTATATTTATG
1 TTATATTTATA
*
1290786 TTATTTTTATA
1 TTATATTTATA
1290797 TTATATTT-TAA
1 TTATATTTAT-A
1290808 TTAT-TTT-TA
1 TTATATTTATA
1290817 TTATATTTATA
1 TTATATTTATA
1290828 T
1 T
1290829 CGTATAATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
9 5 0.11
10 8 0.17
11 34 0.72
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (11 bp):
TTATATTTATA
Found at i:1291107 original size:13 final size:13
Alignment explanation
Indices: 1291085--1291114 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1291075 AAAAAAGAGT
1291085 ATAT-GCATTTAA
1 ATATGGCATTTAA
1291097 ATATGGCATTTAA
1 ATATGGCATTTAA
1291110 ATATG
1 ATATG
1291115 TCAATTTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (13 bp):
ATATGGCATTTAA
Found at i:1291231 original size:32 final size:34
Alignment explanation
Indices: 1291165--1291241 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 34
1291155 TAATCCTGTT
*
1291165 TTAA-ATATTATATATTTATATAAATTTTAGTATA
1 TTAATATATT-TATATTTATATAAATTTGAGTATA
1291199 TTAATA-ATTTATA-TTATATAAAATTTGA-TATA
1 TTAATATATTTATATTTATAT-AAATTTGAGTATA
*
1291231 TTTATATATTT
1 TTAATATATTT
1291242 TTATCAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
32 15 0.39
33 15 0.39
34 7 0.18
35 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (34 bp):
TTAATATATTTATATTTATATAAATTTGAGTATA
Found at i:1291823 original size:21 final size:21
Alignment explanation
Indices: 1291777--1291843 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 21
1291767 AAGTATGATA
* *
1291777 AAAAATATATTTAT-TAATTT
1 AAAAATTTATTTATAAAATTT
**
1291797 TTAAATTTATTTATAAAATTT
1 AAAAATTTATTTATAAAATTT
1291818 AAAAATTTTATTATATATAAATTT
1 AAAAA-TTTATT-TATA-AAATTT
1291842 AA
1 AA
1291844 TCCGTATTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 11 0.30
21 8 0.22
22 6 0.16
23 4 0.11
24 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAAAATTTATTTATAAAATTT
Found at i:1292337 original size:23 final size:22
Alignment explanation
Indices: 1292298--1292359 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 22
1292288 AACATATATA
1292298 TATATATATATATAAATGATCATTTT
1 TATATAT-TATA-AAAT--TCATTTT
*
1292324 TA-ATATTATAAAATTTATTTT
1 TATATATTATAAAATTCATTTT
1292345 TATATATTAATAAAA
1 TATATATT-ATAAAA
1292360 AATTTTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 8 0.24
22 5 0.15
23 10 0.30
24 4 0.12
25 4 0.12
26 2 0.06
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
TATATATTATAAAATTCATTTT
Found at i:1292364 original size:21 final size:20
Alignment explanation
Indices: 1292319--1292376 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
1292309 ATAAATGATC
*
1292319 ATTTTTAATATTATAAAATTT
1 ATTTTTAATATTATAAAA-TA
1292340 ATTTTTATATATTAATAAAA-A
1 ATTTTTA-ATATT-ATAAAATA
*
1292361 A-TTTTAATTTTATAAA
1 ATTTTTAATATTATAAA
1292377 TGATATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
18 5 0.15
19 4 0.12
20 5 0.15
21 8 0.24
22 5 0.15
23 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTTTAATATTATAAAATA
Found at i:1292791 original size:33 final size:32
Alignment explanation
Indices: 1292747--1292829 Score: 82
Period size: 33 Copynumber: 2.6 Consensus size: 32
1292737 GATATAATTT
*
1292747 ATTTATA--TTTAAATTTAAATAA-AAAATTAA
1 ATTTATACTTTTAAATTT-AATAATAAAATAAA
*
1292777 ATCTTTTACTTTTAAAATTTAATAATAAAATAAA
1 AT-TTATACTTTT-AAATTTAATAATAAAATAAA
*
1292811 ATTTATATTTTTATAATTT
1 ATTTATACTTTTA-AATTT
1292830 TTAATATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
30 2 0.05
31 4 0.09
32 1 0.02
33 21 0.49
34 15 0.35
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (32 bp):
ATTTATACTTTTAAATTTAATAATAAAATAAA
Found at i:1292796 original size:34 final size:33
Alignment explanation
Indices: 1292757--1292829 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
1292747 ATTTATATTT
* *
1292757 AAATTTAAATAA-AAAATTAAATCTTTTACTTTTA
1 AAATTT-AATAATAAAATAAAAT-TTATACTTTTA
*
1292791 AAATTTAATAATAAAATAAAATTTATATTTTTA
1 AAATTTAATAATAAAATAAAATTTATACTTTTA
*
1292824 TAATTT
1 AAATTT
1292830 TTAATATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 19 0.56
34 15 0.44
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (33 bp):
AAATTTAATAATAAAATAAAATTTATACTTTTA
Found at i:1293876 original size:31 final size:32
Alignment explanation
Indices: 1293822--1293881 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
1293812 ATACAAATGT
* *
1293822 TTTTTCCATTTCCTTTCTCCTCACTTTCTTTC
1 TTTTTCCATTCCCTTTATCCTCACTTTCTTTC
*
1293854 TTTTTCC-TTCCCTTTATTCTCACTTTCT
1 TTTTTCCATTCCCTTTATCCTCACTTTCT
1293882 CTGTCACCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.60
Consensus pattern (32 bp):
TTTTTCCATTCCCTTTATCCTCACTTTCTTTC
Found at i:1295719 original size:22 final size:22
Alignment explanation
Indices: 1295694--1295737 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1295684 TATATATATA
1295694 TTTTATATAAGTCATAGATTTT
1 TTTTATATAAGTCATAGATTTT
* * *
1295716 TTTTATTTATGTTATAGATTTT
1 TTTTATATAAGTCATAGATTTT
1295738 GAAAACGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTTATATAAGTCATAGATTTT
Found at i:1296256 original size:19 final size:20
Alignment explanation
Indices: 1296220--1296261 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
1296210 TGATTTGATT
*
1296220 TAATATAAATTATTATTTAAA
1 TAATAAAAATTA-TATTTAAA
*
1296241 TAATAAAAATTA-ATTTTAA
1 TAATAAAAATTATATTTAAA
1296260 TA
1 TA
1296262 TTATTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.42
21 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATAAAAATTATATTTAAA
Found at i:1296270 original size:31 final size:31
Alignment explanation
Indices: 1296230--1296300 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
1296220 TAATATAAAT
*
1296230 TATTA-TTTAAATAATAAAAATTAA-TTTTAA
1 TATTATTTTAAATAAT-AAAATAAATTTTTAA
1296260 TATTATTTTAAATAATAAAATAAATTTTTAA
1 TATTATTTTAAATAATAAAATAAATTTTTAA
1296291 TATT-TTTTAA
1 TATTATTTTAA
1296301 TCAAATTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
30 18 0.47
31 20 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TATTATTTTAAATAATAAAATAAATTTTTAA
Found at i:1296294 original size:28 final size:30
Alignment explanation
Indices: 1296235--1296296 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1296225 TAAATTATTA
* *
1296235 TTTAAATAATAAAAATTAATTTTAATATTAT
1 TTTAAATAATAAAAATAAATTTT-ATAATAT
1296266 TTTAAATAAT-AAAATAAATTTT-TAATAT
1 TTTAAATAATAAAAATAAATTTTATAATAT
1296294 TTT
1 TTT
1296297 TTAATCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 8 0.28
30 11 0.38
31 10 0.34
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TTTAAATAATAAAAATAAATTTTATAATAT
Found at i:1296637 original size:22 final size:22
Alignment explanation
Indices: 1296572--1296637 Score: 53
Period size: 23 Copynumber: 2.9 Consensus size: 22
1296562 TATTTATAAA
*
1296572 TTTAATTTAAATTTAAGTTAT-TT
1 TTTAA-TTAAATATAA-TTATATT
* * * *
1296595 TTTAAATAATTAAAAAATATATT
1 TTTAATTAAAT-ATAATTATATT
1296618 TTTAATTAAATATAATTATA
1 TTTAATTAAATATAATTATA
1296638 AATATTATTA
Statistics
Matches: 32, Mismatches: 9, Indels: 5
0.70 0.20 0.11
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTAATTAAATATAATTATATT
Found at i:1296680 original size:23 final size:22
Alignment explanation
Indices: 1296623--1296697 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
1296613 ATATTTTTAA
1296623 TTAAATATAATTATAAATATTAT
1 TTAAATATAATT-TAAATATTAT
* * *
1296646 TAAAAAATTAATTTTAATATTATT
1 TTAAATA-TAATTTAAATATTA-T
* *
1296670 TTAAATATAATTTAATTA-AAT
1 TTAAATATAATTTAAATATTAT
1296691 TTAAATA
1 TTAAATA
1296698 AAAAATTTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
21 8 0.19
22 1 0.02
23 22 0.52
24 11 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAAATATAATTTAAATATTAT
Found at i:1296683 original size:11 final size:11
Alignment explanation
Indices: 1296623--1296697 Score: 62
Period size: 12 Copynumber: 6.6 Consensus size: 11
1296613 ATATTTTTAA
1296623 TTAAATATAAT
1 TTAAATATAAT
*
1296634 TATAAATATTAT
1 T-TAAATATAAT
* *
1296646 TAAAAAATTAAT
1 TTAAATA-TAAT
* *
1296658 TTTAATATTATT
1 TTAAATA-TAAT
1296670 TTAAATATAAT
1 TTAAATATAAT
*
1296681 TTAATTA-AAT
1 TTAAATATAAT
1296691 TTAAATA
1 TTAAATA
1296698 AAAAATTTTA
Statistics
Matches: 50, Mismatches: 12, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
10 9 0.18
11 14 0.28
12 27 0.54
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAAATATAAT
Found at i:1296837 original size:20 final size:21
Alignment explanation
Indices: 1296807--1296847 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1296797 ATATTATATT
**
1296807 AATATATTTTATTATATTTTA
1 AATATATTTTAAAATATTTTA
1296828 AATATA-TTTAAAATATTTTA
1 AATATATTTTAAAATATTTTA
1296848 TATTATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AATATATTTTAAAATATTTTA
Found at i:1296863 original size:20 final size:21
Alignment explanation
Indices: 1296819--1296864 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1296809 TATATTTTAT
*
1296819 TATATTTTAAATATATTTAAA
1 TATATTTTAAATATATATAAA
*
1296840 -ATATTTTATAT-TATATAAA
1 TATATTTTAAATATATATAAA
1296859 TATATT
1 TATATT
1296865 AATAATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATATTTTAAATATATATAAA
Found at i:1297310 original size:23 final size:23
Alignment explanation
Indices: 1297284--1297327 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1297274 ATATAAATGT
*
1297284 TAAATATAAATATATTTTTTATA
1 TAAAAATAAATATATTTTTTATA
**
1297307 TAAAAATATTTATATTTTTTA
1 TAAAAATAAATATATTTTTTA
1297328 AAATTTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TAAAAATAAATATATTTTTTATA
Found at i:1297886 original size:11 final size:12
Alignment explanation
Indices: 1297870--1297911 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
1297860 AAAAAATTAA
1297870 AATTATTA-AAC
1 AATTATTATAAC
1297881 AATTATTATAA-
1 AATTATTATAAC
*
1297892 AATTA-TATTAC
1 AATTATTATAAC
1297903 AATTATTAT
1 AATTATTAT
1297912 TTAAATTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 4 0.15
11 18 0.67
12 5 0.19
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (12 bp):
AATTATTATAAC
Found at i:1297892 original size:22 final size:22
Alignment explanation
Indices: 1297867--1297911 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1297857 AATAAAAAAT
1297867 TAAAATTAT-TAAACAATTATTA
1 TAAAATTATAT-AACAATTATTA
*
1297889 TAAAATTATATTACAATTATTA
1 TAAAATTATATAACAATTATTA
1297911 T
1 T
1297912 TTAAATTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAAATTATATAACAATTATTA
Found at i:1298237 original size:16 final size:16
Alignment explanation
Indices: 1298200--1298243 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
1298190 AATTAAATTC
1298200 AATTATAAA-ATTTTT
1 AATTATAAATATTTTT
*
1298215 ATTTTATAAATATTTTT
1 A-ATTATAAATATTTTT
1298232 AATTATTAAATA
1 AATTA-TAAATA
1298244 ATATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 1 0.04
16 10 0.42
17 13 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTATAAATATTTTT
Found at i:1298248 original size:20 final size:20
Alignment explanation
Indices: 1298223--1298261 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1298213 TTATTTTATA
* *
1298223 AATATTTTTAATTATTAAAT
1 AATATTTTAAATTAATAAAT
1298243 AATATTTTAAATTAATAAA
1 AATATTTTAAATTAATAAA
1298262 GTGTAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATTTTAAATTAATAAAT
Found at i:1298792 original size:2 final size:2
Alignment explanation
Indices: 1298785--1298822 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1298775 CCCATGTTTC
*
1298785 AT AT AT AT AT AT AT AT AT AT AT AT A- AA AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1298823 CATGAAATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1299541 original size:2 final size:2
Alignment explanation
Indices: 1299536--1299573 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1299526 ATTTCACGTG
1299536 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1299574 TGTCCATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1301814 original size:23 final size:22
Alignment explanation
Indices: 1301769--1301810 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1301759 TATTTTTATT
1301769 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
1301791 TAAATATTAATT-TAAAAATA
1 TAAAT-TTAATTATAAAAATA
1301811 ATATTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:1301823 original size:23 final size:23
Alignment explanation
Indices: 1301769--1301824 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
1301759 TATTTTTATT
1301769 TAAA-TTTAATTATAAAAATATA
1 TAAATTTTAATTATAAAAATATA
*
1301791 TAAATATTAATT-TAAAAATAATA
1 TAAATTTTAATTATAAAAAT-ATA
* *
1301814 TTATTTTTAAT
1 TAAATTTTAAT
1301825 AATTTAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAAATTTTAATTATAAAAATATA
Found at i:1301981 original size:17 final size:18
Alignment explanation
Indices: 1301951--1301991 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1301941 ATTAATATTA
*
1301951 AACAC-AACACTAAATAC
1 AACACAAACACTAAACAC
*
1301968 AATACAAACA-TAAACAC
1 AACACAAACACTAAACAC
1301985 AACACAA
1 AACACAA
1301992 GTTACTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.63, C:0.27, G:0.00, T:0.10
Consensus pattern (18 bp):
AACACAAACACTAAACAC
Found at i:1304889 original size:18 final size:17
Alignment explanation
Indices: 1304839--1304892 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
1304829 ATCAAATTAA
*
1304839 TTTATTTAAAAAAATAT
1 TTTATTTAAAAAAATTT
*
1304856 TTTA-ATAAAATTAAATTT
1 TTTATTTAAAA--AAATTT
1304874 TTTATTTATAAAAAATTT
1 TTTATTTA-AAAAAATTT
1304892 T
1 T
1304893 ATTAATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
16 5 0.17
17 4 0.13
18 16 0.53
19 2 0.07
20 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTATTTAAAAAAATTT
Found at i:1304913 original size:35 final size:35
Alignment explanation
Indices: 1304838--1304913 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
1304828 CATCAAATTA
* *
1304838 ATTTATTTAAAAAAATATTTTAATAAAATTAAATT
1 ATTTATTTAAAAAAATATTTTAATAAAATAAAAAT
* * *
1304873 TTTTATTTATAAAAA-ATTTTATTAATAATAAAAAT
1 ATTTATTTAAAAAAATATTTTAATAA-AATAAAAAT
1304908 ATTTAT
1 ATTTAT
1304914 AATGACAATC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 9 0.26
35 25 0.74
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (35 bp):
ATTTATTTAAAAAAATATTTTAATAAAATAAAAAT
Found at i:1304937 original size:22 final size:24
Alignment explanation
Indices: 1304901--1304945 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1304891 TTATTAATAA
*
1304901 TAAAAATATTTATAAT-GACAATC
1 TAAAAATATTAATAATCGACAATC
1304924 TAAAAATA-TAATAATCGACAAT
1 TAAAAATATTAATAATCGACAAT
1304946 AATTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (24 bp):
TAAAAATATTAATAATCGACAATC
Found at i:1305736 original size:22 final size:22
Alignment explanation
Indices: 1305693--1305767 Score: 96
Period size: 22 Copynumber: 3.3 Consensus size: 22
1305683 TTAAGTGATA
*
1305693 AACTTGATTGACTTAAATCCGATT
1 AACTTGATT-A-TTAAACCCGATT
1305717 AACTTGATTATTAAACCCGATT
1 AACTTGATTATTAAACCCGATT
* * *
1305739 AACTTGAGTATTAAACTCAATT
1 AACTTGATTATTAAACCCGATT
1305761 AACTTGA
1 AACTTGA
1305768 ACTAGAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
22 37 0.79
23 1 0.02
24 9 0.19
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (22 bp):
AACTTGATTATTAAACCCGATT
Found at i:1309264 original size:17 final size:17
Alignment explanation
Indices: 1309242--1309296 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
1309232 CACAAAATAA
*
1309242 TAAATGAAAATTATAAT
1 TAAATGAAAATTAAAAT
1309259 TAAATGTCAAAAATTAAAAT
1 TAAATG---AAAATTAAAAT
* *
1309279 CAAATAAAAATTAAAAT
1 TAAATGAAAATTAAAAT
1309296 T
1 T
1309297 CAAGTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
17 17 0.55
20 14 0.45
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (17 bp):
TAAATGAAAATTAAAAT
Found at i:1310841 original size:81 final size:81
Alignment explanation
Indices: 1310706--1310868 Score: 290
Period size: 81 Copynumber: 2.0 Consensus size: 81
1310696 GTCGATTTAT
*
1310706 GTTTTAATTGCATTTATTCCTTCATGAACCAAAAATGTACGTTTTAACAGAACTCTCGGCAAGGG
1 GTTTTAATTGCATTTATTCCTTCATGAACCAAAAATGTACGTTTTAACAGAACTCTCGGAAAGGG
*
1310771 GAGAGAGAGAGGGAGA
66 GAGAGAGAGAGAGAGA
*
1310787 GTTTTAATTGCATTTATTCCTTCATGAACCAAAAATGTATGTTTTAACAGAACTCTCGGAAAGGG
1 GTTTTAATTGCATTTATTCCTTCATGAACCAAAAATGTACGTTTTAACAGAACTCTCGGAAAGGG
*
1310852 GGGAGAGAGAGAGAGA
66 GAGAGAGAGAGAGAGA
1310868 G
1 G
1310869 AGTACCCAAT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (81 bp):
GTTTTAATTGCATTTATTCCTTCATGAACCAAAAATGTACGTTTTAACAGAACTCTCGGAAAGGG
GAGAGAGAGAGAGAGA
Found at i:1314048 original size:23 final size:19
Alignment explanation
Indices: 1314006--1314044 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1313996 GAGTACAGCC
1314006 AGCAAGCATTTAACCAAAA
1 AGCAAGCATTTAACCAAAA
1314025 AGCAAGCATTTAACCAAAA
1 AGCAAGCATTTAACCAAAA
1314044 A
1 A
1314045 AAAAAACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.21, G:0.10, T:0.15
Consensus pattern (19 bp):
AGCAAGCATTTAACCAAAA
Found at i:1318747 original size:20 final size:18
Alignment explanation
Indices: 1318715--1318774 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 18
1318705 AATAGTGATT
1318715 TTTTATATAAAAAAATTTA
1 TTTTAT-TAAAAAAATTTA
*
1318734 TTTATAATTAAAAACATTTAAA
1 TTT-T-ATTAAAAAAATTT--A
*
1318756 TTTTATAAAAAAAATTTA
1 TTTTATTAAAAAAATTTA
1318774 T
1 T
1318775 AAAATAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
18 2 0.06
19 3 0.09
20 22 0.65
21 3 0.09
22 4 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTTATTAAAAAAATTTA
Found at i:1319343 original size:21 final size:21
Alignment explanation
Indices: 1319305--1319344 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1319295 AATTAAAAAA
*
1319305 TATTAATTAAAATTATTTAAT
1 TATTAATTAAAATAATTTAAT
1319326 TATTAATTTAAAA-AATTTA
1 TATTAA-TTAAAATAATTTA
1319345 TATATAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTAATTAAAATAATTTAAT
Found at i:1320472 original size:18 final size:18
Alignment explanation
Indices: 1320449--1320486 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1320439 ACAACTATAT
1320449 AAAAAAAGTAAAAAATAAA
1 AAAAAAAG-AAAAAATAAA
*
1320468 AAAAAAAGAACAAATAAA
1 AAAAAAAGAAAAAATAAA
1320486 A
1 A
1320487 TAAAGAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.84, C:0.03, G:0.05, T:0.08
Consensus pattern (18 bp):
AAAAAAAGAAAAAATAAA
Found at i:1320983 original size:14 final size:14
Alignment explanation
Indices: 1320945--1320986 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1320935 AAATTTAAAA
1320945 ATAAATA-TTTAAT
1 ATAAATATTTTAAT
*
1320958 ATAAATATATTTTGAT
1 AT-AA-ATATTTTAAT
1320974 ATAAATATTTTAA
1 ATAAATATTTTAA
1320987 AAAATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 2 0.08
14 10 0.42
15 5 0.21
16 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATAAATATTTTAAT
Found at i:1325278 original size:18 final size:18
Alignment explanation
Indices: 1325244--1325278 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1325234 TATATTATTT
*
1325244 TTATATTTATTAAATATA
1 TTATATTTATGAAATATA
*
1325262 TTATATTTATGACATAT
1 TTATATTTATGAAATAT
1325279 TTTTACAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TTATATTTATGAAATATA
Found at i:1326927 original size:20 final size:19
Alignment explanation
Indices: 1326904--1326990 Score: 54
Period size: 20 Copynumber: 4.4 Consensus size: 19
1326894 TTTATACATT
1326904 TATTTTATTATTTAAAATAA
1 TATTTTATTATTT-AAATAA
* *
1326924 TA--TTA-AATTTATATTAA
1 TATTTTATTATTTA-AATAA
1326941 TATTTATAATTAAATTTAAATAA
1 TATTT-T-ATT--ATTTAAATAA
*
1326964 AATTTTTATTATTTAAATAA
1 TA-TTTTATTATTTAAATAA
*
1326984 TAATTTA
1 TATTTTA
1326991 AATTAAATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 19
0.66 0.09 0.25
Matches are distributed among these distances:
16 1 0.02
17 10 0.20
18 3 0.06
19 5 0.10
20 14 0.27
21 1 0.02
22 3 0.06
23 6 0.12
24 8 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTTATTATTTAAATAA
Found at i:1326934 original size:29 final size:30
Alignment explanation
Indices: 1326901--1326994 Score: 86
Period size: 32 Copynumber: 3.1 Consensus size: 30
1326891 TAATTTATAC
1326901 ATTTATTTTATTATTTAAAATAATA-TTAA
1 ATTTATTTTATTATTTAAAATAATATTTAA
* * *
1326930 ATTTATATTAATATTTATAATTAA-ATTTAA
1 ATTTATTTTATTATTTA-AAATAATATTTAA
**
1326960 ATAAAATTTTTATTATTT-AAATAATAATTTAA
1 AT-TTA-TTTTATTATTTAAAATAAT-ATTTAA
1326992 ATT
1 ATT
1326995 AAATTAAATC
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
29 16 0.32
30 16 0.32
31 1 0.02
32 17 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
ATTTATTTTATTATTTAAAATAATATTTAA
Found at i:1326945 original size:12 final size:11
Alignment explanation
Indices: 1326923--1326974 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
1326913 ATTTAAAATA
1326923 ATATTAAATTT
1 ATATTAAATTT
1326934 ATATTAATATTT
1 ATATTAA-ATTT
1326946 ATAATTAAATTT
1 AT-ATTAAATTT
* *
1326958 AAATAAAATTT
1 ATATTAAATTT
*
1326969 TTATTA
1 ATATTA
1326975 TTTAAATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
11 18 0.53
12 11 0.32
13 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATTAAATTT
Found at i:1327119 original size:4 final size:4
Alignment explanation
Indices: 1327112--1327136 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1327102 GGGAGGGAAT
1327112 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
1327137 AATTATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1354927 original size:5 final size:5
Alignment explanation
Indices: 1354917--1354977 Score: 52
Period size: 5 Copynumber: 11.6 Consensus size: 5
1354907 TCGTAATTAT
* *
1354917 TTAAA TTAAA TTTTAAA TTTTAAA TTAAT TTAAT TTAAA TTAAA -TAAA
1 TTAAA TTAAA --TTAAA --TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
*
1354965 TTAAT TTAAA TTA
1 TTAAA TTAAA TTA
1354978 TAAAAAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
4 4 0.08
5 33 0.67
7 12 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (5 bp):
TTAAA
Found at i:1354949 original size:24 final size:25
Alignment explanation
Indices: 1354917--1354981 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 25
1354907 TCGTAATTAT
* *
1354917 TTAAATTAAATTTTAAATT-TTAAA
1 TTAATTTAAATTTTAAATTAATAAA
*
1354941 TTAATTTAAT--TTAAATTAAATAAA
1 TTAATTTAAATTTTAAATT-AATAAA
*
1354965 TTAATTTAAATTATAAA
1 TTAATTTAAATTTTAAA
1354982 AAATATGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
22 7 0.22
24 21 0.66
26 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TTAATTTAAATTTTAAATTAATAAA
Found at i:1354970 original size:19 final size:20
Alignment explanation
Indices: 1354917--1354977 Score: 70
Period size: 19 Copynumber: 2.9 Consensus size: 20
1354907 TCGTAATTAT
1354917 TTAAATTAAATTTTAAATTTTAAA
1 TTAAATT-AA-TTTAAA--TTAAA
*
1354941 TTAATTTAATTTAAATTAAA
1 TTAAATTAATTTAAATTAAA
1354961 -TAAATTAATTTAAATTA
1 TTAAATTAATTTAAATTA
1354978 TAAAAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 16 0.46
20 5 0.14
22 6 0.17
23 2 0.06
24 6 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAAATTAATTTAAATTAAA
Found at i:1354985 original size:24 final size:23
Alignment explanation
Indices: 1354937--1354986 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
1354927 TTTTAAATTT
1354937 TAAATTAATTTAATTTAAATTAAA
1 TAAATTAATTTAATTTAAA-TAAA
1354961 TAAATTAATTTAAATTATAAA-AAA
1 TAAATTAATTT-AATT-TAAATAAA
1354985 TA
1 TA
1354987 TGTTTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 16 0.67
25 4 0.17
26 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAATTAATTTAATTTAAATAAA
Done.