Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold132
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2458301
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 8 of 15
Found at i:1341464 original size:23 final size:22
Alignment explanation
Indices: 1341431--1341477 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1341421 TATTTAAATA
1341431 TAAATATA-AAAAT-ATAATTTT
1 TAAATATATAAAATAAT-ATTTT
1341452 TAAATATATAAAATAATATTTT
1 TAAATATATAAAATAATATTTT
1341474 TAAA
1 TAAA
1341478 AATTTAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 8 0.33
22 14 0.58
23 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATATATAAAATAATATTTT
Found at i:1341485 original size:22 final size:22
Alignment explanation
Indices: 1341432--1341506 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
1341422 ATTTAAATAT
1341432 AAATATAAAAATATAATTTTTAA
1 AAATAT-AAAATATAATTTTTAA
*
1341455 ATATATAAAATA-ATATTTTTAA
1 AAATATAAAATATA-ATTTTTAA
*
1341477 AAATTTAAACATAT--TTATATTAA
1 AAATATAAA-ATATAATT-T-TTAA
1341500 AAATATA
1 AAATATA
1341507 TTCGTATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
21 3 0.07
22 22 0.51
23 18 0.42
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATATAAAATATAATTTTTAA
Found at i:1342058 original size:30 final size:30
Alignment explanation
Indices: 1341979--1342060 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
1341969 TATCCGACAG
*
1341979 ATATATTT-AATTAT-ATATATATATATAT
1 ATATATTTGAATGATAATATATATATATAT
**
1342007 ATATATTTGAATGATTTTATATATATATAT
1 ATATATTTGAATGATAATATATATATATAT
*
1342037 ATATGTTTGAATG-TGAATATATAT
1 ATATATTTGAATGAT-AATATATAT
1342061 TATTTAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 8 0.17
29 6 0.13
30 32 0.70
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (30 bp):
ATATATTTGAATGATAATATATATATATAT
Found at i:1342060 original size:2 final size:2
Alignment explanation
Indices: 1341990--1342040 Score: 52
Period size: 2 Copynumber: 25.5 Consensus size: 2
1341980 TATATTTAAT
* *
1341990 TA TA TA TA TA TA TA TA TA TA TA TT TGA -A TGA T- TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T-A TA TA TA TA TA TA
1342032 TA TA TA TA T
1 TA TA TA TA T
1342041 GTTTGAATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
1 2 0.05
2 38 0.90
3 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1342348 original size:35 final size:37
Alignment explanation
Indices: 1342301--1342373 Score: 116
Period size: 35 Copynumber: 2.0 Consensus size: 37
1342291 TGATATTTTA
1342301 TAAATTTAATTTTAAATAATAATAA-TATAA-ATATT
1 TAAATTTAATTTTAAATAATAATAATTATAATATATT
1342336 TAAATATT-ATTTTAAATAATAATAATTATAATATATT
1 TAAAT-TTAATTTTAAATAATAATAATTATAATATATT
1342373 T
1 T
1342374 TTAAATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
35 22 0.63
36 7 0.20
37 6 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (37 bp):
TAAATTTAATTTTAAATAATAATAATTATAATATATT
Found at i:1342357 original size:27 final size:27
Alignment explanation
Indices: 1342327--1342394 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
1342317 TAATAATAAT
1342327 ATAAATATTTAAATAT-TATTTTAAATA
1 ATAAATATTTAAATATAT-TTTTAAATA
* *
1342354 AT-AATAATTATAATATATTTTTAAATT
1 ATAAATATTTA-AATATATTTTTAAATA
1342381 A-AAATAATTTAAAT
1 ATAAAT-ATTTAAAT
1342395 CTAAATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
26 7 0.21
27 22 0.65
28 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATAAATATTTAAATATATTTTTAAATA
Found at i:1342844 original size:25 final size:25
Alignment explanation
Indices: 1342814--1342879 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 25
1342804 AATTAAATTA
* *
1342814 ATTAAAATTTAATAAATTTTTAAAT
1 ATTAAAATTTAATAAAATTATAAAT
* *
1342839 ATTAAAATTTTAAAAAAATTATAATT
1 ATTAAAA-TTTAATAAAATTATAAAT
1342865 A-TAAAATTT-ATAAAA
1 ATTAAAATTTAATAAAA
1342880 AATCAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 5 0.14
24 3 0.09
25 12 0.34
26 15 0.43
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTAAAATTTAATAAAATTATAAAT
Found at i:1343178 original size:12 final size:12
Alignment explanation
Indices: 1343156--1343191 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1343146 AACACGATAT
1343156 TAAATATATAATA
1 TAAA-ATATAATA
*
1343169 TGAAATATAATA
1 TAAAATATAATA
1343181 TAAAATATAAT
1 TAAAATATAAT
1343192 TTATTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 18 0.86
13 3 0.14
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (12 bp):
TAAAATATAATA
Found at i:1343358 original size:17 final size:17
Alignment explanation
Indices: 1343325--1343358 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1343315 ACCCAAAATT
* *
1343325 AAAAATATTTTTTTTAA
1 AAAAATATTATTATTAA
1343342 AAAAATATTATTATTAA
1 AAAAATATTATTATTAA
1343359 GAGTTAAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAAATATTATTATTAA
Found at i:1344869 original size:24 final size:26
Alignment explanation
Indices: 1344841--1344901 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 26
1344831 GTGATTTGAA
*
1344841 TTTTAAATTTATTATAT-ATT-ATTT
1 TTTTAAATTTATAATATAATTAATTT
*
1344865 TTTTAAATTGATAATATGAATTAATTT
1 TTTTAAATTTATAATAT-AATTAATTT
*
1344892 ATTTAAATTT
1 TTTTAAATTT
1344902 TAAATTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 15 0.50
26 3 0.10
27 12 0.40
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (26 bp):
TTTTAAATTTATAATATAATTAATTT
Found at i:1345829 original size:2 final size:2
Alignment explanation
Indices: 1345822--1345856 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1345812 AATTCTCTTT
1345822 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1345857 CATCGTAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1346903 original size:12 final size:12
Alignment explanation
Indices: 1346886--1346914 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1346876 TACTTTATTT
1346886 AAAATAATAATA
1 AAAATAATAATA
1346898 AAAATAATAATA
1 AAAATAATAATA
1346910 AAAAT
1 AAAAT
1346915 TGGAAACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:1347542 original size:29 final size:29
Alignment explanation
Indices: 1347510--1347565 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
1347500 TTTATTTAAA
**
1347510 TATAAATTAAAATTTAATTACTTATTTGG
1 TATAAATTAAAATTTAAGGACTTATTTGG
*
1347539 TATAAATTTAAATTTAAGGACTTATTT
1 TATAAATTAAAATTTAAGGACTTATTT
1347566 TGAGAGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (29 bp):
TATAAATTAAAATTTAAGGACTTATTTGG
Found at i:1348384 original size:17 final size:19
Alignment explanation
Indices: 1348358--1348395 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1348348 AAAAATATAT
1348358 AAAATAATTTTTT-TTTAA
1 AAAATAATTTTTTATTTAA
1348376 AAAAT-ATTTTTTATTTAA
1 AAAATAATTTTTTATTTAA
1348394 AA
1 AA
1348396 TTTAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAAATAATTTTTTATTTAA
Found at i:1348430 original size:30 final size:30
Alignment explanation
Indices: 1348389--1348449 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
1348379 ATATTTTTTA
*
1348389 TTTAAAATTTAAAATAT-ATTAATATTTAAT
1 TTTAAAATTTAAAATATAAAT-ATATTTAAT
* *
1348419 TTTATAATTTAAATTATAAATATATTTAAT
1 TTTAAAATTTAAAATATAAATATATTTAAT
1348449 T
1 T
1348450 ATTTATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTAAAATTTAAAATATAAATATATTTAAT
Found at i:1348445 original size:25 final size:25
Alignment explanation
Indices: 1348417--1348465 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1348407 TTAATATTTA
*
1348417 ATTTTATAATTTAAATTATAAATAT
1 ATTTAATAATTTAAATTATAAATAT
* * *
1348442 ATTTAATTATTTATATTATTAATA
1 ATTTAATAATTTAAATTATAAATA
1348466 AAATTATCGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTTAATAATTTAAATTATAAATAT
Found at i:1348470 original size:37 final size:37
Alignment explanation
Indices: 1348390--1348472 Score: 93
Period size: 36 Copynumber: 2.3 Consensus size: 37
1348380 TATTTTTTAT
*
1348390 TTAAAATT-TAAAATATATTAATATTTAATTTTATAA
1 TTAAAATTATAAAATATATTAATATTTAATTATATAA
*
1348426 TTTAAATTAT-AAATATATTTAATTATTTATATTAT-TAA
1 TTAAAATTATAAAATATA-TTAA-TATTTA-ATTATATAA
1348464 -TAAAATTAT
1 TTAAAATTAT
1348473 CGAATTTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
36 14 0.35
37 13 0.32
38 9 0.22
39 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
TTAAAATTATAAAATATATTAATATTTAATTATATAA
Found at i:1348931 original size:31 final size:30
Alignment explanation
Indices: 1348883--1348940 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
1348873 TTATGTAAAC
*
1348883 CAAAAAGAAATATTTTAAGATCTTAATTAGA
1 CAAAAAGAAATACTTTAAGAT-TTAATTAGA
1348914 CAAAAA-ATAATACTTTAAGATTTAATT
1 CAAAAAGA-AATACTTTAAGATTTAATT
1348941 TAATACAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (30 bp):
CAAAAAGAAATACTTTAAGATTTAATTAGA
Found at i:1355142 original size:2 final size:2
Alignment explanation
Indices: 1355131--1355175 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
1355121 ACCTTTTATG
*
1355131 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1355171 TA TA T
1 TA TA T
1355176 TGTTAAACAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1355321 original size:24 final size:25
Alignment explanation
Indices: 1355290--1355345 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 25
1355280 TATATTAATT
*
1355290 TAAA-TTTTTAATAAA-AAATTA-A
1 TAAATTTTTTTATAAATAAATTATA
*
1355312 TAAATTTTTTTTTAAATAAATTATA
1 TAAATTTTTTTATAAATAAATTATA
*
1355337 TATATTTTT
1 TAAATTTTT
1355346 AAATTTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.14
23 9 0.32
24 6 0.21
25 9 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TAAATTTTTTTATAAATAAATTATA
Found at i:1355674 original size:15 final size:15
Alignment explanation
Indices: 1355654--1355685 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1355644 AAATCTAACA
1355654 AAGAAGAGACGTAGG
1 AAGAAGAGACGTAGG
1355669 AAGAAGAGACGTAGG
1 AAGAAGAGACGTAGG
1355684 AA
1 AA
1355686 CAACAATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.38, T:0.06
Consensus pattern (15 bp):
AAGAAGAGACGTAGG
Found at i:1355755 original size:2 final size:2
Alignment explanation
Indices: 1355748--1355781 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1355738 AAGAAACTTC
1355748 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1355782 GTGAATTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1357894 original size:9 final size:10
Alignment explanation
Indices: 1357872--1357904 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1357862 TAATTAATAA
*
1357872 ATAAAATTTT
1 ATAAAATATT
1357882 ATAAAA-ATT
1 ATAAAATATT
1357891 ATAAAATATT
1 ATAAAATATT
1357901 ATAA
1 ATAA
1357905 TTTATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATAAAATATT
Found at i:1358990 original size:2 final size:2
Alignment explanation
Indices: 1358983--1359010 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1358973 TAAAATCATT
1358983 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
1359011 AGTATAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1360179 original size:11 final size:11
Alignment explanation
Indices: 1360163--1360190 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1360153 TTAATAAAAA
1360163 AATATCAACAT
1 AATATCAACAT
1360174 AATATCAACAT
1 AATATCAACAT
1360185 AATATC
1 AATATC
1360191 TTTTCGGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.29
Consensus pattern (11 bp):
AATATCAACAT
Found at i:1362178 original size:21 final size:20
Alignment explanation
Indices: 1362139--1362196 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 20
1362129 AATAAAAAAT
*
1362139 TATTTTTATATTAATATTTATA
1 TATTTTTATATT-A-ATTTAAA
1362161 TATTTTTATAATTAATTTAAA
1 TATTTTTAT-ATTAATTTAAA
1362182 TATTTTTATTATTAA
1 TATTTTTA-TATTAA
1362197 ATAATAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 19 0.58
22 11 0.33
23 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTTATATTAATTTAAA
Found at i:1362220 original size:10 final size:9
Alignment explanation
Indices: 1362205--1362250 Score: 65
Period size: 10 Copynumber: 4.8 Consensus size: 9
1362195 AAATAATAAT
1362205 TTAAATTGAA
1 TTAAATT-AA
1362215 TTAAATTAA
1 TTAAATTAA
1362224 TTGAAATTAA
1 TT-AAATTAA
1362234 TTTAAATTAA
1 -TTAAATTAA
1362244 TTAAATT
1 TTAAATT
1362251 TTTATCCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 11 0.32
10 21 0.62
11 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (9 bp):
TTAAATTAA
Found at i:1362221 original size:5 final size:5
Alignment explanation
Indices: 1362205--1362250 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
1362195 AAATAATAAT
* *
1362205 TTAAA TTGAA TTAAA TT-AA TTGAAA TTAAT TTAAA TT-AA TTAAA TT
1 TTAAA TTAAA TTAAA TTAAA TT-AAA TTAAA TTAAA TTAAA TTAAA TT
1362251 TTTATCCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
4 8 0.24
5 22 0.65
6 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (5 bp):
TTAAA
Found at i:1363468 original size:32 final size:32
Alignment explanation
Indices: 1363379--1363486 Score: 105
Period size: 32 Copynumber: 3.4 Consensus size: 32
1363369 TTGAATATCT
* *
1363379 TTTTTCTATGTTATGTACTGTTCAAATATCTTA
1 TTTTT-TATGTTATGTACTGTTCAAAGATGTTA
* * * * *
1363412 --TTTTATGTTCTATGCAGTCCAAAGATGTTA
1 TTTTTTATGTTATGTACTGTTCAAAGATGTTA
*
1363442 TTTTTTATGTTATGTACTGTTGAAAGATGTTA
1 TTTTTTATGTTATGTACTGTTCAAAGATGTTA
1363474 TCTTTTT-TGTTAT
1 T-TTTTTATGTTAT
1363487 TATAATATCC
Statistics
Matches: 59, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
30 20 0.34
31 3 0.05
32 31 0.53
33 5 0.08
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.54
Consensus pattern (32 bp):
TTTTTTATGTTATGTACTGTTCAAAGATGTTA
Found at i:1368241 original size:369 final size:368
Alignment explanation
Indices: 1367562--1368297 Score: 1350
Period size: 369 Copynumber: 2.0 Consensus size: 368
1367552 CACTGACCCG
1367562 TTGGTCAAGCACCAGATAAAAAACACCTCAAATTATATTTGCAAAATACTGAAACATTTCCATCC
1 TTGGTCAAGCACCAGATAAAAAACACCTCAAATTATATTTGCAAAATACTGAAACATTTCCATCC
*
1367627 CTCATATTATTTTCTACTTGCTTCTGCTCTTTTCTTTCCCTTGTTTTGTCAGTGCAGTAACATTT
66 CTCATATTATTTTCTACTTGCTTCTGCTCTTTTCTTTCCCTTGTCTTGTCAGTGCAGTAACATTT
*
1367692 TAAACACTTAACAAATATTCAGAAAATGAAATTAAAAAAAAAAATCCCTTTGGTTGCTGCTTTTG
131 TAAACACTTAACAAATATTCAGAAAATGAAATTAAAAAAAAAAAACCCTTTGGTTGCTGCTTTTG
1367757 CAGAAGTGTCTTCATTTACAAAAGAAGAATAAAAAATTCAAGTGTCATCGAATGTAGGTTCGTCC
196 CAGAAGTGTCTTCATTTACAAAAGAAGAATAAAAAATTCAAGTGTCATCGAATGTAGGTTCGTCC
* *
1367822 TAAAGACCAAAGTCCTGTATCCTTAACTGGTGTCTGAAAAAGAGGGGGGGGGGGGGAACAGCTGA
261 TAAAGACCAAAGTCCTGTATCCTTAACTGGCGTCTGAAAAAGAAGGGGGGGGGGGGAACAGCTGA
1367887 TGAATCTATTACTGAGGTAACAAAACAAAAATAACAATAATAT
326 TGAATCTATTACTGAGGTAACAAAACAAAAATAACAATAATAT
1367930 TTGGTCAAGCACCAGATAAAAAACACCTCAAATTATATTTGCAAAATACTGAAACATTTCCATCC
1 TTGGTCAAGCACCAGATAAAAAACACCTCAAATTATATTTGCAAAATACTGAAACATTTCCATCC
* *
1367995 CTCATATTATTTTCTACTTTCTTCTGTTC-TTTCTTTCCCTTGTCTTGTCAGTGCAGTAACATTT
66 CTCATATTATTTTCTACTTGCTTCTGCTCTTTTCTTTCCCTTGTCTTGTCAGTGCAGTAACATTT
*
1368059 TAAATACTT-ACAAATATTCAGAAAATGAAATTGAAAAAAAAAAAAAACCCTTTGGTTGCTGCTT
131 TAAACACTTAACAAATATTCAGAAAATGAAATT---AAAAAAAAAAAACCCTTTGGTTGCTGCTT
1368123 TTGCAGAAGTGTCTTCATTTACAAAAGAAGAATAAAAAATTCAAGTGTCATCGAATGTAGGTTCG
193 TTGCAGAAGTGTCTTCATTTACAAAAGAAGAATAAAAAATTCAAGTGTCATCGAATGTAGGTTCG
*
1368188 TCCTAAAGACCAGAGTCCTGTATCCTTAACTGGCGTCTGAAAAAGAAGGGGGGGGGGGGAACAGC
258 TCCTAAAGACCAAAGTCCTGTATCCTTAACTGGCGTCTGAAAAAGAAGGGGGGGGGGGGAACAGC
*
1368253 TGATGAATCTATTACTGAGGTAACAAAACAAAAGTAACAATAATA
323 TGATGAATCTATTACTGAGGTAACAAAACAAAAATAACAATAATA
1368298 ATAATTGTTG
Statistics
Matches: 356, Mismatches: 9, Indels: 5
0.96 0.02 0.01
Matches are distributed among these distances:
366 23 0.06
367 42 0.12
368 92 0.26
369 199 0.56
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (368 bp):
TTGGTCAAGCACCAGATAAAAAACACCTCAAATTATATTTGCAAAATACTGAAACATTTCCATCC
CTCATATTATTTTCTACTTGCTTCTGCTCTTTTCTTTCCCTTGTCTTGTCAGTGCAGTAACATTT
TAAACACTTAACAAATATTCAGAAAATGAAATTAAAAAAAAAAAACCCTTTGGTTGCTGCTTTTG
CAGAAGTGTCTTCATTTACAAAAGAAGAATAAAAAATTCAAGTGTCATCGAATGTAGGTTCGTCC
TAAAGACCAAAGTCCTGTATCCTTAACTGGCGTCTGAAAAAGAAGGGGGGGGGGGGAACAGCTGA
TGAATCTATTACTGAGGTAACAAAACAAAAATAACAATAATAT
Found at i:1377491 original size:17 final size:17
Alignment explanation
Indices: 1377450--1377492 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1377440 TATTATAATT
1377450 AAATTTATAATATATATA
1 AAATTTA-AATATATATA
*
1377468 AATTTTAAATATAT-TA
1 AAATTTAAATATATATA
1377484 ATAATTTAA
1 A-AATTTAA
1377493 TTTATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 3 0.14
17 13 0.59
18 6 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTTAAATATATATA
Found at i:1377522 original size:31 final size:30
Alignment explanation
Indices: 1377470--1377531 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
1377460 TATATATAAA
* *
1377470 TTTTAAATATATTAATAATTTA-ATTTATAT
1 TTTTAAATATATAAAAAATTTATA-TTATAT
*
1377500 TTTTTAATATATAAAAATATTTATATTATAT
1 TTTTAAATATATAAAAA-ATTTATATTATAT
1377531 T
1 T
1377532 AATATTTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 14 0.52
31 12 0.44
32 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TTTTAAATATATAAAAAATTTATATTATAT
Found at i:1377541 original size:19 final size:19
Alignment explanation
Indices: 1377496--1377549 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
1377486 AATTTAATTT
*
1377496 ATATTTTT-TAATATATAA
1 ATATTTTTATATTATATAA
* * *
1377514 AAATATTTATATTATATTA
1 ATATTTTTATATTATATAA
1377533 ATATTTTTATATTATAT
1 ATATTTTTATATTATAT
1377550 CATAATTGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
18 6 0.21
19 23 0.79
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTTTTATATTATATAA
Found at i:1378815 original size:16 final size:16
Alignment explanation
Indices: 1378794--1378859 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
1378784 TTATATTATA
1378794 TTTATATTTTA-AATAT
1 TTTATATTTTATAA-AT
1378810 TTTATATTTATATAAAT
1 TTTATATTT-TATAAAT
* *
1378827 TTTA-ATTTTTTTAAAA
1 TTTATA-TTTTATAAAT
*
1378843 TTTATATTATATAAAT
1 TTTATATTTTATAAAT
1378859 T
1 T
1378860 ATAAAAATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
16 27 0.66
17 12 0.29
18 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATATTTTATAAAT
Found at i:1379038 original size:15 final size:15
Alignment explanation
Indices: 1379018--1379058 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
1379008 GAAAGAAAGG
1379018 AAGAAAAAAAAGAAA
1 AAGAAAAAAAAGAAA
1379033 AAGAAAAAAAAGAAA
1 AAGAAAAAAAAGAAA
1379048 AAGAAAAAAAA
1 AAGAAAAAAAA
1379059 TTTTGTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAGAAA
Found at i:1380081 original size:27 final size:27
Alignment explanation
Indices: 1380043--1380105 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
1380033 TATTCCTGCC
*
1380043 AAGAAAGAAAGAAAAAAAGAAAG-AAAA
1 AAGAAAAAAAGAAAAAAA-AAAGAAAAA
*
1380070 AAGAAAAAAAGAAAAAGAAAAGAAAAA
1 AAGAAAAAAAGAAAAAAAAAAGAAAAA
1380097 AAGAAAAAA
1 AAGAAAAAA
1380106 TTATGTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 4 0.12
27 29 0.88
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (27 bp):
AAGAAAAAAAGAAAAAAAAAAGAAAAA
Found at i:1380103 original size:8 final size:8
Alignment explanation
Indices: 1380043--1380105 Score: 63
Period size: 8 Copynumber: 7.1 Consensus size: 8
1380033 TATTCCTGCC
*
1380043 AAGAAAGA
1 AAGAAAAA
1380051 AAGAAAAA
1 AAGAAAAA
1380059 AAGAAAGAAAA
1 AAG--A-AAAA
1380070 AAGAAAAA
1 AAGAAAAA
1380078 AAGAAAAAGAA
1 AAG--AAA-AA
1380089 AAGAAAAA
1 AAGAAAAA
1380097 AAGAAAAA
1 AAGAAAAA
1380105 A
1 A
1380106 TTATGTATTC
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
8 28 0.58
9 4 0.08
10 4 0.08
11 12 0.25
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:1380103 original size:19 final size:19
Alignment explanation
Indices: 1380046--1380104 Score: 95
Period size: 19 Copynumber: 3.2 Consensus size: 19
1380036 TCCTGCCAAG
1380046 AAAG-AAAGAAAAAAAGAA
1 AAAGAAAAGAAAAAAAGAA
1380064 AGAA-AAAAGAAAAAAAGAA
1 A-AAGAAAAGAAAAAAAGAA
1380083 AAAGAAAAGAAAAAAAGAA
1 AAAGAAAAGAAAAAAAGAA
1380102 AAA
1 AAA
1380105 ATTATGTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.08
19 35 0.92
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAGAAAAGAAAAAAAGAA
Found at i:1380937 original size:13 final size:13
Alignment explanation
Indices: 1380919--1380969 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 13
1380909 TCATAACAAT
1380919 TTTTATATAAATA
1 TTTTATATAAATA
1380932 TTTTATATTAATAATTCA
1 TTTTATA-T-A-AA-T-A
1380950 TTTTATATAAATA
1 TTTTATATAAATA
1380963 -TTTATAT
1 TTTTATAT
1380970 GTTTATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
12 7 0.21
13 8 0.24
14 2 0.06
15 3 0.09
16 3 0.09
17 2 0.06
18 8 0.24
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTATATAAATA
Found at i:1381016 original size:27 final size:23
Alignment explanation
Indices: 1380986--1381068 Score: 62
Period size: 23 Copynumber: 3.4 Consensus size: 23
1380976 ATATTTTATC
1380986 ATATTCATATTATTTTTGTATCATATT
1 ATATT-ATATTATTTTT-TA--ATATT
*
1381013 ATATTTTAATTA-TTTTTAATATT
1 ATATTAT-ATTATTTTTTAATATT
* *
1381036 ATATTTATATTATATCTTAAT-TT
1 ATA-TTATATTATTTTTTAATATT
*
1381059 ATTTTATATT
1 ATATTATATT
1381069 TTATATAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
22 7 0.15
23 16 0.33
24 9 0.19
25 2 0.04
26 5 0.10
27 9 0.19
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.63
Consensus pattern (23 bp):
ATATTATATTATTTTTTAATATT
Found at i:1381064 original size:34 final size:35
Alignment explanation
Indices: 1381008--1381074 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 35
1380998 TTTTTGTATC
*
1381008 ATATTATATTTTAATTATTTTTA-ATATTATATTT
1 ATATTATATCTTAATTATTTTTATATATTATATTT
*
1381042 ATATTATATCTTAATT-TATTTTATATTTTATAT
1 ATATTATATCTTAATTAT-TTTTATATATTATAT
1381075 AAATTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 1 0.03
34 20 0.69
35 8 0.28
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (35 bp):
ATATTATATCTTAATTATTTTTATATATTATATTT
Found at i:1381074 original size:24 final size:24
Alignment explanation
Indices: 1381008--1381068 Score: 76
Period size: 23 Copynumber: 2.7 Consensus size: 24
1380998 TTTTTGTATC
*
1381008 ATATTATATTT-TAATTAT-TTTTA
1 ATATTATATTTAT-ATTATATCTTA
1381031 ATATTATATTTATATTATATCTTA
1 ATATTATATTTATATTATATCTTA
1381055 AT-TTAT-TTTATATT
1 ATATTATATTTATATT
1381069 TTATATAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
22 8 0.23
23 20 0.57
24 7 0.20
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (24 bp):
ATATTATATTTATATTATATCTTA
Found at i:1381079 original size:22 final size:22
Alignment explanation
Indices: 1381034--1381088 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
1381024 ATTTTTAATA
* *
1381034 TTATATTTATATTATATCTTAAT
1 TTAT-TTTATATTATATATAAAT
*
1381057 TTATTTTATATTTTATATAAAT
1 TTATTTTATATTATATATAAAT
1381079 TT-TTTATATA
1 TTATTT-TATA
1381089 ATTAAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.11
22 21 0.75
23 4 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
TTATTTTATATTATATATAAAT
Found at i:1381085 original size:13 final size:13
Alignment explanation
Indices: 1381067--1381170 Score: 50
Period size: 16 Copynumber: 7.2 Consensus size: 13
1381057 TTATTTTATA
1381067 TTTTATATAAATT
1 TTTTATATAAATT
1381080 TTTTATAT-AATT
1 TTTTATATAAATT
*
1381092 AAATTTTAACTTTAAATT
1 ---TTTT-A-TATAAATT
1381110 TATTTAT-TAAATAT
1 T-TTTATATAAAT-T
*
1381124 TTTTAAATAAATT
1 TTTTATATAAATT
*
1381137 TTATTAATTATAATTT
1 TT-TT-A-TATAAATT
1381153 TATTTAATTATAAATT
1 T-TTT-A-TATAAATT
1381169 TT
1 TT
1381171 ATAAATATTA
Statistics
Matches: 73, Mismatches: 5, Indels: 24
0.72 0.05 0.24
Matches are distributed among these distances:
12 4 0.05
13 20 0.27
14 10 0.14
15 8 0.11
16 24 0.33
17 3 0.04
18 4 0.05
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTATATAAATT
Found at i:1381159 original size:16 final size:15
Alignment explanation
Indices: 1381080--1381172 Score: 72
Period size: 14 Copynumber: 6.4 Consensus size: 15
1381070 TATATAAATT
*
1381080 TTTTATATAATTAAA
1 TTTTATTTAATTAAA
**
1381095 TTTTAACT--TTAAA
1 TTTTATTTAATTAAA
1381108 -TTTATTT-ATTAAA
1 TTTTATTTAATTAAA
* *
1381121 TATT-TTTAAATAAA
1 TTTTATTTAATTAAA
1381135 TTTTA-TTAATTATAA
1 TTTTATTTAATTA-AA
1381150 TTTTATTTAATTATAAA
1 TTTTATTTAA-T-TAAA
1381167 TTTTAT
1 TTTTAT
1381173 AAATATTAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
12 5 0.08
13 13 0.21
14 16 0.26
15 13 0.21
16 4 0.06
17 9 0.15
18 2 0.03
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTATTTAATTAAA
Found at i:1381706 original size:19 final size:18
Alignment explanation
Indices: 1381673--1381709 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1381663 GAGTCAATTT
1381673 TTAATTATATATTATATA
1 TTAATTATATATTATATA
*
1381691 TTAATTCTATTATTATATA
1 TTAATTATA-TATTATATA
1381710 CATTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAATTATATATTATATA
Found at i:1381730 original size:23 final size:24
Alignment explanation
Indices: 1381668--1381733 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 24
1381658 GAATTGAGTC
*
1381668 AATTTTTAATTATATATTATATATT
1 AATTTTT-ATTATATAATATATATT
1381693 AATTCTATTATTATATACAT-TATA-T
1 AATT-T-TTATTATATA-ATATATATT
1381718 AATTTTTATTATATAA
1 AATTTTTATTATATAA
1381734 AAAATAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
22 1 0.03
23 10 0.27
24 1 0.03
25 9 0.24
26 13 0.35
27 3 0.08
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (24 bp):
AATTTTTATTATATAATATATATT
Found at i:1382674 original size:21 final size:22
Alignment explanation
Indices: 1382650--1382690 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1382640 AATTAAAATA
*
1382650 ATATTTTTAA-AATAAATTATT
1 ATATTTTAAATAATAAATTATT
1382671 ATATTTTAAATAATAAATTA
1 ATATTTTAAATAATAAATTA
1382691 AATTATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATATTTTAAATAATAAATTATT
Found at i:1382681 original size:19 final size:18
Alignment explanation
Indices: 1382627--1382683 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
1382617 TTATATTCAT
*
1382627 ATTATTATTTATTAATTAA
1 ATTATTATTT-TTAAATAA
* *
1382646 AATAATATTTTTAAAATAA
1 ATTATTATTTTT-AAATAA
1382665 ATTATTATATTTTAAATAA
1 ATTATTAT-TTTTAAATAA
1382684 TAAATTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
18 2 0.06
19 25 0.81
20 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTATTATTTTTAAATAA
Found at i:1383386 original size:13 final size:13
Alignment explanation
Indices: 1383363--1383412 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
1383353 ATTTAAATAT
1383363 TTATGTAATATAAA
1 TTAT-TAATATAAA
*
1383377 TTATTAATATAGA
1 TTATTAATATAAA
1383390 TT-TTAA-ATATAA
1 TTATTAATATA-AA
1383402 TTA-TAATATAA
1 TTATTAATATAA
1383413 TAAGATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
11 3 0.10
12 11 0.35
13 13 0.42
14 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (13 bp):
TTATTAATATAAA
Found at i:1383427 original size:29 final size:27
Alignment explanation
Indices: 1383361--1383428 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 27
1383351 ATATTTAAAT
*
1383361 ATTTATGTAATATAAATTATTAATATAG
1 ATTTATG-AATATAAATAATTAATATAG
*
1383389 ATTT-TAAATATAATTATAATATAATA-AG
1 ATTTATGAATATAA--ATAAT-TAATATAG
1383417 ATTTATGAATAT
1 ATTTATGAATAT
1383429 TATGCATTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 7 0.21
27 1 0.03
28 14 0.42
29 11 0.33
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (27 bp):
ATTTATGAATATAAATAATTAATATAG
Found at i:1383535 original size:5 final size:5
Alignment explanation
Indices: 1383524--1383584 Score: 70
Period size: 5 Copynumber: 12.2 Consensus size: 5
1383514 CCATTTGGAG
* * * *
1383524 AAAGC TAAGC TAAGC AAAGC AAAGC AAAGC TAAA-C CAAGC TAAGC AAAGC
1 AAAGC AAAGC AAAGC AAAGC AAAGC AAAGC -AAAGC AAAGC AAAGC AAAGC
1383574 AAAGC AAAGC A
1 AAAGC AAAGC A
1383585 GTGCAATGCT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
4 2 0.04
5 44 0.90
6 3 0.06
ACGTcount: A:0.54, C:0.21, G:0.18, T:0.07
Consensus pattern (5 bp):
AAAGC
Found at i:1383563 original size:25 final size:25
Alignment explanation
Indices: 1383524--1383578 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
1383514 CCATTTGGAG
* *
1383524 AAAGCTAAGCTAAGCAAAGCAAAGC
1 AAAGCTAAACCAAGCAAAGCAAAGC
*
1383549 AAAGCTAAACCAAGCTAAGCAAAGC
1 AAAGCTAAACCAAGCAAAGCAAAGC
1383574 AAAGC
1 AAAGC
1383579 AAAGCAGTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.53, C:0.22, G:0.18, T:0.07
Consensus pattern (25 bp):
AAAGCTAAACCAAGCAAAGCAAAGC
Found at i:1383690 original size:53 final size:53
Alignment explanation
Indices: 1383627--1383730 Score: 172
Period size: 53 Copynumber: 2.0 Consensus size: 53
1383617 TAGGAAGTGA
** *
1383627 TCGGCGGAATTTCTGGGCTGTTTTTGATGAATCATTACCAAGCTGGTTATTGT
1 TCGGCGGAATTTCTGGGCTGTTTTTGACAAATCATTACAAAGCTGGTTATTGT
*
1383680 TCGGCGGAATTTCTGGGCTGTTTTTGACAAATCATTTCAAAGCTGGTTATT
1 TCGGCGGAATTTCTGGGCTGTTTTTGACAAATCATTACAAAGCTGGTTATT
1383731 ATGATGCTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.39
Consensus pattern (53 bp):
TCGGCGGAATTTCTGGGCTGTTTTTGACAAATCATTACAAAGCTGGTTATTGT
Found at i:1384333 original size:24 final size:24
Alignment explanation
Indices: 1384306--1384352 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1384296 AAAAATTCAA
1384306 TCTCTTCGTGCTGAATCCTTCATG
1 TCTCTTCGTGCTGAATCCTTCATG
1384330 TCTCTTCGTGCTGAATCCTTCAT
1 TCTCTTCGTGCTGAATCCTTCAT
1384353 CGGGGCCAAA
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:0.13, C:0.30, G:0.15, T:0.43
Consensus pattern (24 bp):
TCTCTTCGTGCTGAATCCTTCATG
Found at i:1386116 original size:33 final size:32
Alignment explanation
Indices: 1386077--1386152 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
1386067 AAAAAATTTT
* *
1386077 TTATCTTTATTTTAACAGTATTAAAAATGAGTA
1 TTATCTTTAATTTAACAATATTAAAAATGA-TA
* *
1386110 TTATCTTTAATTTAATAATATTAAAGATGATA
1 TTATCTTTAATTTAACAATATTAAAAATGATA
*
1386142 TTTTTCTTTAA
1 -TTATCTTTAA
1386153 AATCTTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.05
33 35 0.95
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (32 bp):
TTATCTTTAATTTAACAATATTAAAAATGATA
Found at i:1386248 original size:22 final size:22
Alignment explanation
Indices: 1386201--1386248 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
1386191 AAATAATTTT
1386201 TTATTTTTTAAATTTTTAAAAA
1 TTATTTTTTAAATTTTTAAAAA
*
1386223 -TATTTTTT-TATCTTTTAAAAA
1 TTATTTTTTAAAT-TTTTAAAAA
1386244 TTATT
1 TTATT
1386249 ATCAATCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 2 0.09
21 17 0.74
22 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATTTTTTAAATTTTTAAAAA
Found at i:1386356 original size:350 final size:348
Alignment explanation
Indices: 1385727--1386423 Score: 900
Period size: 350 Copynumber: 2.0 Consensus size: 348
1385717 TAAAAAAAAA
* * * *
1385727 TTTATCTTAATTTTAGCAGTATTATAAATAAATATTATCCATAATTTAAATTATTAAGGATGATA
1 TTTATCTTAATTTTAACAGTATTAAAAATAAATATTATCCATAATTTAAAATATTAAAGATGATA
* *
1385792 TTCATCTCTAAAACTTTTCAAACACACAATTTTAGAAGATGATTATTAAAGATAATTTTTTATCT
66 TTCATCTCTAAAACTTTTCAAACACACAATTTTAAAAGATGATTATTAAAAATAATTTTTTATCT
* * *
1385857 TTTAAACTTTTAAAAATAATTTTTTATTTTAAAAATAATTATTAATCATTATTAATTTTTTTTAA
131 TTTAAACTTTTAAAAATAATTTTTTATTTTAAAAATAATTATCAATCATTATTAAGTTTCTTTAA
* * * * ** * **
1385922 ATATTTTTTTTTTATTTTTGTTATAACTTTAATTAAATCATTGCTTCAAACAAAACAAAAGTAGC
196 ATAGTTTTTGTTTATTTTTGCTATAACTTCAATTAAATCATCCCTTCAAACAAAAAAAAAAAAGC
* * *
1385987 AAAGCATAGAAGCTTTGATTTTACATACCTAGGAATCTTATTTTTTAAAAATATTCTATACCTAA
261 AAACCATAGAAGCTTTGATTTGACATACCTAAGAATCTTA-TTTTTAAAAATATTCTATACCTAA
1386052 TT-AGAAAATAAATTTAAAAAATTT
325 TTGA-AAAATAAATTTAAAAAATTT
* * * **
1386076 TTTATCTTTATTTTAACAGTATTAAAAATGAGTATTATCTTTAATTTAATAATATTAAAGATGAT
1 TTTATCTTAATTTTAACAGTATTAAAAATAAATATTATCCATAATTTAA-AATATTAAAGATGAT
** * * * *
1386141 ATTTTTCTTTAAAATCTTTT-AAATATATAATTTTAAAAGATGATTATTAAAAATAATTTTTTAT
65 ATTCATCTCTAAAA-CTTTTCAAACACACAATTTTAAAAGATGATTATTAAAAATAATTTTTTAT
* * * * *
1386205 TTTTTAAATTTTTAAAAATATTTTTTTATCTTTTAAAAATTATTATCAATCATT-TTCAGTTTCT
129 CTTTTAAACTTTTAAAAATAATTTTTTA--TTTTAAAAATAATTATCAATCATTATTAAGTTTCT
*
1386269 TTAAAT-GTTTTTGTTTGTTTTTGCTATAACTTCAATTAAATCATCCCTTCAAA-AAAAAAAAAA
192 TTAAATAGTTTTTGTTTATTTTTGCTATAACTTCAATTAAATCATCCCTTCAAACAAAAAAAAAA
* * * *
1386332 AAGCCAACCAATTGAAGCTTTGATTTGACATACCTAAGAATTTTATTTTTAAAAGTATTCTATAC
257 AAGCAAACC-ATAGAAGCTTTGATTTGACATACCTAAGAATCTTATTTTTAAAAATATTCTATAC
* *
1386397 GTAGTTGAAAAATAAATTTAAAAAATT
321 CTAATTGAAAAATAAATTTAAAAAATT
1386424 AAATATATTT
Statistics
Matches: 298, Mismatches: 44, Indels: 12
0.84 0.12 0.03
Matches are distributed among these distances:
349 98 0.33
350 160 0.54
351 18 0.06
352 22 0.07
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.45
Consensus pattern (348 bp):
TTTATCTTAATTTTAACAGTATTAAAAATAAATATTATCCATAATTTAAAATATTAAAGATGATA
TTCATCTCTAAAACTTTTCAAACACACAATTTTAAAAGATGATTATTAAAAATAATTTTTTATCT
TTTAAACTTTTAAAAATAATTTTTTATTTTAAAAATAATTATCAATCATTATTAAGTTTCTTTAA
ATAGTTTTTGTTTATTTTTGCTATAACTTCAATTAAATCATCCCTTCAAACAAAAAAAAAAAAGC
AAACCATAGAAGCTTTGATTTGACATACCTAAGAATCTTATTTTTAAAAATATTCTATACCTAAT
TGAAAAATAAATTTAAAAAATTT
Found at i:1386441 original size:15 final size:16
Alignment explanation
Indices: 1386420--1386463 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
1386410 AAATTTAAAA
1386420 AATTAAATATATTTAT
1 AATTAAATATATTTAT
1386436 -ATTAAATATGTATTTAT
1 AATTAAATA--TATTTAT
1386453 AATTAAA-ATAT
1 AATTAAATATAT
1386464 AAATTAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
15 11 0.44
17 8 0.32
18 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
AATTAAATATATTTAT
Found at i:1386466 original size:54 final size:52
Alignment explanation
Indices: 1386404--1386512 Score: 148
Period size: 54 Copynumber: 2.1 Consensus size: 52
1386394 TACGTAGTTG
* *
1386404 AAAAATAAATTTAAAA-AATTAAATATATTTATATTAAATATGTATTTATAATT
1 AAAAATAAA-TTAAAAGAATTAAATATAATTATATTAAATATGTATATAT-ATT
* *
1386457 AAAATATAAATTAAAAGTATTAAATATAATTATATTATATATGTATATATATT
1 AAAA-ATAAATTAAAAGAATTAAATATAATTATATTAAATATGTATATATATT
1386510 AAA
1 AAA
1386513 CACGTATAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
53 16 0.32
54 34 0.68
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (52 bp):
AAAAATAAATTAAAAGAATTAAATATAATTATATTAAATATGTATATATATT
Found at i:1386972 original size:2 final size:2
Alignment explanation
Indices: 1386965--1387048 Score: 127
Period size: 2 Copynumber: 42.5 Consensus size: 2
1386955 TAATTCTGAG
* *
1386965 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT A- AT -T CT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
1387006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1387048 A
1 A
1387049 AACTCTAACC
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.03
2 73 0.96
3 1 0.01
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1387421 original size:2 final size:2
Alignment explanation
Indices: 1387414--1387444 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1387404 GCTGTGAACA
1387414 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
1387445 ATTGCAAATT
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:1388288 original size:2 final size:2
Alignment explanation
Indices: 1388275--1388305 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1388265 ATAATTATGC
*
1388275 AT AT AC 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
1388306 AACTTTATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1391127 original size:2 final size:2
Alignment explanation
Indices: 1391122--1391155 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1391112 AGCAATACCA
1391122 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1391156 TTTCAGATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1395853 original size:2 final size:2
Alignment explanation
Indices: 1395846--1395874 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1395836 GATTATAGGA
1395846 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 A
1395875 ATTAAAACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1396135 original size:15 final size:15
Alignment explanation
Indices: 1396117--1396178 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 15
1396107 AAATATTAAT
1396117 ATATATTTAATATAA
1 ATATATTTAATATAA
* *
1396132 ATATATTTAATTTTA
1 ATATATTTAATATAA
* *
1396147 ATATA-AT-ATATAT
1 ATATATTTAATATAA
* *
1396160 ATATATTAAAAATAA
1 ATATATTTAATATAA
1396175 ATAT
1 ATAT
1396179 CAAATAAAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
13 8 0.23
14 1 0.03
15 26 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATTTAATATAA
Found at i:1396546 original size:29 final size:29
Alignment explanation
Indices: 1396481--1396547 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
1396471 TAATCAACAT
*
1396481 AAATAAAATATAAAATATAATAATTAAATA
1 AAATTAAATATAAAATATAATAATT-AATA
1396511 AAA-TAAATATAAATAATATAA-AATT-ATA
1 AAATTAAATAT-AA-AATATAATAATTAATA
1396539 AAATTAAAT
1 AAATTAAAT
1396548 TAGGAATGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
28 6 0.18
29 11 0.33
30 9 0.27
31 7 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (29 bp):
AAATTAAATATAAAATATAATAATTAATA
Found at i:1396570 original size:2 final size:2
Alignment explanation
Indices: 1396563--1396588 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1396553 ATGAATCCTT
1396563 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
1396589 ATTTCGCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1400567 original size:2 final size:2
Alignment explanation
Indices: 1400560--1400593 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1400550 ATACTTTTTA
1400560 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1400594 TTGCTTTGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1400759 original size:18 final size:18
Alignment explanation
Indices: 1400736--1400780 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1400726 AATTTTAAAT
1400736 ATTTATATAATAATAATA
1 ATTTATATAATAATAATA
* * *
1400754 ATTTATATCATATTAATT
1 ATTTATATAATAATAATA
*
1400772 ATTTTTATA
1 ATTTATATA
1400781 TTTGATAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTATATAATAATAATA
Found at i:1404186 original size:14 final size:14
Alignment explanation
Indices: 1404167--1404207 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1404157 CTTGCATGGA
*
1404167 TTTTTTTTCTTTTT
1 TTTTTTTTCTTTTC
1404181 TTTTTTTTCTTTTC
1 TTTTTTTTCTTTTC
*
1404195 TTCTTTTTCTTTT
1 TTTTTTTTCTTTT
1404208 AATCTCCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTTCTTTTC
Found at i:1404195 original size:19 final size:20
Alignment explanation
Indices: 1404167--1404207 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1404157 CTTGCATGGA
1404167 TTTTTTTTCTT-TTTTT-TT
1 TTTTTTTTCTTCTTTTTCTT
1404185 TTTTCTTTTCTTCTTTTTCTT
1 TTTT-TTTTCTTCTTTTTCTT
1404206 TT
1 TT
1404208 AATCTCCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
20 5 0.25
21 4 0.20
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (20 bp):
TTTTTTTTCTTCTTTTTCTT
Found at i:1405556 original size:9 final size:9
Alignment explanation
Indices: 1405514--1405639 Score: 53
Period size: 9 Copynumber: 13.1 Consensus size: 9
1405504 AGTTTTGTTA
1405514 TAAAAA-AT
1 TAAAAATAT
1405522 TAGAAAA-AT
1 TA-AAAATAT
1405531 TAAAGAAATAAT
1 T-AA-AAAT-AT
*
1405543 GAAAAATAT
1 TAAAAATAT
*
1405552 TAAAAATTT
1 TAAAAATAT
*
1405561 TAAATAT-T
1 TAAAAATAT
*
1405569 TAATATTATTAT
1 TAA-A--AATAT
1405581 ATAAAAATAT
1 -TAAAAATAT
1405591 TATAAAA-AT
1 TA-AAAATAT
1405600 TAAAATATAT
1 TAAAA-ATAT
*
1405610 AAAAAATATAT
1 -TAAAA-ATAT
* *
1405621 TTAAAATAA
1 TAAAAATAT
1405630 TAAAAATAT
1 TAAAAATAT
1405639 T
1 T
1405640 TATTCAAAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 27
0.69 0.10 0.21
Matches are distributed among these distances:
8 9 0.10
9 42 0.46
10 21 0.23
11 12 0.13
12 4 0.04
13 3 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (9 bp):
TAAAAATAT
Found at i:1405627 original size:22 final size:22
Alignment explanation
Indices: 1405599--1405649 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1405589 ATTATAAAAA
1405599 TTAAAATATATAAAAA-ATATAT
1 TTAAAATA-ATAAAAATATATAT
*
1405621 TTAAAATAATAAAAATATTTAT
1 TTAAAATAATAAAAATATATAT
*
1405643 TCAAAAT
1 TTAAAAT
1405650 GTAGCTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TTAAAATAATAAAAATATATAT
Found at i:1406135 original size:38 final size:38
Alignment explanation
Indices: 1406093--1406187 Score: 100
Period size: 38 Copynumber: 2.4 Consensus size: 38
1406083 TTAATATATC
* * * *
1406093 ATTTAACTTTTATATTACACCTTAATTTATAATTTAAT
1 ATTTAAATTATATATTACACATTAATTTAAAATTTAAT
* *
1406131 ATTTAAATTATATATTATATATTAATTTAAAATTTAAT
1 ATTTAAATTATATATTACACATTAATTTAAAATTTAAT
*
1406169 AATATTAATATGATATATT
1 -AT-TTAA-ATTATATATT
1406188 TTTTATTATT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
38 32 0.68
39 2 0.04
40 4 0.09
41 9 0.19
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (38 bp):
ATTTAAATTATATATTACACATTAATTTAAAATTTAAT
Found at i:1406495 original size:11 final size:11
Alignment explanation
Indices: 1406479--1406538 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
1406469 GATAAAATTT
1406479 TATAATATAAA
1 TATAATATAAA
1406490 TATAATATAAAAA
1 TATAATAT--AAA
*
1406503 TTAAAATATAAA
1 -TATAATATAAA
1406515 TAT-ATA-AAA
1 TATAATATAAA
* *
1406524 TATATTAAAAA
1 TATAATATAAA
1406535 TATA
1 TATA
1406539 TAAATTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
9 6 0.15
10 5 0.12
11 17 0.41
12 3 0.07
13 3 0.07
14 7 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TATAATATAAA
Found at i:1406530 original size:25 final size:26
Alignment explanation
Indices: 1406470--1406538 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
1406460 TTTTTATACG
*
1406470 ATAAAAT-T-TTATAATATAAATATA
1 ATAAAATATATTAAAATATAAATATA
1406494 ATATAAA-A-ATTAAAATATAAATAT-
1 ATA-AAATATATTAAAATATAAATATA
1406518 ATAAAATATATTAAAAATATA
1 ATAAAATATATT-AAAATATA
1406539 TAAATTATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
23 3 0.08
24 7 0.18
25 20 0.53
26 8 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATAAAATATATTAAAATATAAATATA
Found at i:1406559 original size:18 final size:19
Alignment explanation
Indices: 1406483--1406559 Score: 62
Period size: 18 Copynumber: 4.3 Consensus size: 19
1406473 AAATTTTATA
1406483 ATATAAATATAATATAAA-A-
1 ATATAAATAT-AT-TAAATAT
1406502 AT-TAAA-ATA-TAAATAT
1 ATATAAATATATTAAATAT
*
1406518 ATA-AAATATATTAAAAAT
1 ATATAAATATATTAAATAT
1406536 ATATAAAT-TATT-AATAT
1 ATATAAATATATTAAATAT
1406553 ATCATAA
1 AT-ATAA
1406560 TTTTTATATA
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 4 0.08
15 1 0.02
16 6 0.12
17 11 0.22
18 21 0.43
19 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (19 bp):
ATATAAATATATTAAATAT
Found at i:1407493 original size:29 final size:30
Alignment explanation
Indices: 1407435--1407491 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
1407425 TCGAATCATT
**
1407435 ATTTAAATAATAAAAATATATTTTATTTAA
1 ATTTAAATAATAAAAATATATAATATTTAA
*
1407465 ATTT-AATTATAAAAATATATAAATATT
1 ATTTAAATAATAAAAATATAT-AATATT
1407492 AATATAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 15 0.65
30 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
ATTTAAATAATAAAAATATATAATATTTAA
Found at i:1411623 original size:2 final size:2
Alignment explanation
Indices: 1411616--1411655 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1411606 TGAATCTAAC
1411616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1411656 TAGATACACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1415587 original size:11 final size:11
Alignment explanation
Indices: 1415571--1415664 Score: 52
Period size: 11 Copynumber: 8.5 Consensus size: 11
1415561 ATAAAATTAA
1415571 ATAATATAAAT
1 ATAATATAAAT
* *
1415582 ATAATAAAAAA
1 ATAATATAAAT
1415593 ATAA-A-AAAT
1 ATAATATAAAT
* *
1415602 ACAATAAAAAAT
1 ATAAT-ATAAAT
*
1415614 AAAATATAAAT
1 ATAATATAAAT
*
1415625 ATTATATAAAAGT
1 ATAATAT-AAA-T
*
1415638 ATAAATATTAAT
1 AT-AATATAAAT
1415650 -TAA-AGTAAAT
1 ATAATA-TAAAT
1415660 ATAAT
1 ATAAT
1415665 TTTATTACAA
Statistics
Matches: 63, Mismatches: 11, Indels: 17
0.69 0.12 0.19
Matches are distributed among these distances:
9 7 0.11
10 7 0.11
11 28 0.44
12 12 0.19
13 5 0.08
14 4 0.06
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1415595 original size:19 final size:17
Alignment explanation
Indices: 1415568--1415622 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 17
1415558 ATAATAAAAT
*
1415568 TAAATAATATAAATATAA
1 TAAAAAATA-AAATATAA
*
1415586 TAAAAAAATAAAAAATACAA
1 T-AAAAAAT--AAAATATAA
1415606 TAAAAAATAAAATATAA
1 TAAAAAATAAAATATAA
1415623 ATATTATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
17 8 0.26
18 1 0.03
19 13 0.42
20 8 0.26
21 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAAAATAAAATATAA
Found at i:1415607 original size:20 final size:19
Alignment explanation
Indices: 1415578--1415617 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1415568 TAAATAATAT
*
1415578 AAATATAATAAAAAAATAAA
1 AAATACAAT-AAAAAATAAA
1415598 AAATACAATAAAAAATAAA
1 AAATACAATAAAAAATAAA
1415617 A
1 A
1415618 TATAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (19 bp):
AAATACAATAAAAAATAAA
Found at i:1415609 original size:12 final size:12
Alignment explanation
Indices: 1415560--1415619 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
1415550 TATTAGACAT
1415560 AATAAAATTAAATA
1 AATAAAA-TAAA-A
*
1415574 ATATAAATATAATA
1 A-ATAAA-ATAAAA
1415588 AA-AAAATAAAA
1 AATAAAATAAAA
*
1415599 AATACAATAAAA
1 AATAAAATAAAA
1415611 AATAAAATA
1 AATAAAATA
1415620 TAAATATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 7 0.18
12 19 0.49
13 1 0.03
14 3 0.08
15 8 0.21
16 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (12 bp):
AATAAAATAAAA
Found at i:1415642 original size:19 final size:18
Alignment explanation
Indices: 1415611--1415656 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1415601 TACAATAAAA
1415611 AATAAAA-TATAAATATT
1 AATAAAAGTATAAATATT
1415628 ATATAAAAGTATAAATATT
1 A-ATAAAAGTATAAATATT
*
1415647 AATTAAAGTA
1 AATAAAAGTA
1415657 AATATAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 1 0.04
18 14 0.54
19 11 0.42
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
AATAAAAGTATAAATATT
Found at i:1415654 original size:18 final size:19
Alignment explanation
Indices: 1415613--1415656 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1415603 CAATAAAAAA
*
1415613 TAAAATATAAATATTATAT
1 TAAAGTATAAATATTATAT
*
1415632 AAAAGTATAAATATTA-AT
1 TAAAGTATAAATATTATAT
1415650 TAAAGTA
1 TAAAGTA
1415657 AATATAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
TAAAGTATAAATATTATAT
Found at i:1416186 original size:11 final size:12
Alignment explanation
Indices: 1416168--1416210 Score: 61
Period size: 11 Copynumber: 3.6 Consensus size: 12
1416158 TAAATGTCTC
1416168 ATTAAATAAATT
1 ATTAAATAAATT
1416180 A-TAAATAAATT
1 ATTAAATAAATT
*
1416191 ATTAATTAAATT
1 ATTAAATAAATT
1416203 AATTAAAT
1 -ATTAAAT
1416211 TGATCAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 11 0.41
12 10 0.37
13 6 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTAAATAAATT
Found at i:1416775 original size:17 final size:17
Alignment explanation
Indices: 1416753--1416852 Score: 87
Period size: 17 Copynumber: 5.6 Consensus size: 17
1416743 ATTGATATTA
*
1416753 AATACAATATAAAAAAT
1 AATATAATATAAAAAAT
*
1416770 AATACAATCATAAAATATAT
1 AATATAAT-ATAAAA-A-AT
*
1416790 AAT-TAATGT-AAAAAT
1 AATATAATATAAAAAAT
* *
1416805 AATATAAAATATAAAAT
1 AATATAATATAAAAAAT
1416822 AATATAATAAATATAAAAAT
1 AATATAAT--ATA-AAAAAT
1416842 AATATAATATA
1 AATATAATATA
1416853 TTATTTTATC
Statistics
Matches: 68, Mismatches: 7, Indels: 15
0.76 0.08 0.17
Matches are distributed among these distances:
15 5 0.07
16 5 0.07
17 23 0.34
18 10 0.15
19 7 0.10
20 18 0.26
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (17 bp):
AATATAATATAAAAAAT
Found at i:1416809 original size:20 final size:19
Alignment explanation
Indices: 1416781--1416850 Score: 92
Period size: 20 Copynumber: 3.7 Consensus size: 19
1416771 ATACAATCAT
*
1416781 AAAAT-ATATAATTAATGTA
1 AAAATAATATAA-TAATATA
1416800 AAAATAATATAA-AATAT-
1 AAAATAATATAATAATATA
1416817 AAAATAATATAATAAATATA
1 AAAATAATATAAT-AATATA
1416837 AAAATAATATAATA
1 AAAATAATATAATA
1416851 TATTATTTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
17 12 0.26
18 4 0.09
19 11 0.24
20 19 0.41
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (19 bp):
AAAATAATATAATAATATA
Found at i:1416839 original size:37 final size:36
Alignment explanation
Indices: 1416753--1416853 Score: 116
Period size: 37 Copynumber: 2.8 Consensus size: 36
1416743 ATTGATATTA
*
1416753 AATACAATAT-AAAA-AATAATACAATCATAAAATATAT
1 AATA-AATATAAAAATAAT-ATAAAAT-ATAAAATATAT
* *
1416790 AATTAATGTAAAAATAATATAAAATATAAAATAATAT
1 AATAAATATAAAAATAATATAAAATATAAAAT-ATAT
*
1416827 AATAAATATAAAAATAATATAATATAT
1 AATAAATATAAAAATAATATAAAATAT
1416854 TATTTTATCT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
36 11 0.20
37 41 0.75
38 3 0.05
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (36 bp):
AATAAATATAAAAATAATATAAAATATAAAATATAT
Found at i:1419929 original size:3 final size:3
Alignment explanation
Indices: 1419921--1419949 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1419911 TTTATTAGTC
1419921 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1419950 TTATTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1421828 original size:17 final size:17
Alignment explanation
Indices: 1421808--1421851 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1421798 ATCTAACTGA
*
1421808 TTTTTTCTTTTTTATTT
1 TTTTTTCATTTTTATTT
* *
1421825 TTTTATAATTTTTATTT
1 TTTTTTCATTTTTATTT
*
1421842 ATTTTTCATT
1 TTTTTTCATT
1421852 GATTTTAAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTCATTTTTATTT
Found at i:1422192 original size:2 final size:2
Alignment explanation
Indices: 1422185--1422214 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1422175 TTTGCTTACA
1422185 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1422215 ACGGTCCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1422568 original size:18 final size:19
Alignment explanation
Indices: 1422535--1422574 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1422525 AAATAAACTC
*
1422535 AAAAAATTATATTAAAATT
1 AAAAAATTATAATAAAATT
*
1422554 AAAAAATT-TAATAAATTT
1 AAAAAATTATAATAAAATT
1422572 AAA
1 AAA
1422575 TTTTAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAAATTATAATAAAATT
Found at i:1423549 original size:29 final size:30
Alignment explanation
Indices: 1423499--1423566 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
1423489 AATATTTAAA
* * *
1423499 TAAGATTGATAAAACACTTTTA-ATGTGTT
1 TAAGATTAACAAAACACTTTTATATATGTT
*
1423528 TAAGATTAACAAAACA-TATTTATTTATGTT
1 TAAGATTAACAAAACACT-TTTATATATGTT
1423558 TAAGATTAA
1 TAAGATTAA
1423567 AAAGATAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 1 0.03
29 18 0.55
30 14 0.42
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (30 bp):
TAAGATTAACAAAACACTTTTATATATGTT
Found at i:1423579 original size:30 final size:30
Alignment explanation
Indices: 1423524--1423581 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1423514 ACTTTTAATG
*
1423524 TGTTTAAGATTAACAAAACATATTTATTTA
1 TGTTTAAGATTAACAAAACAAATTTATTTA
*
1423554 TGTTTAAGATTAA-AAAGATAAATTTATT
1 TGTTTAAGATTAACAAA-ACAAATTTATT
1423582 CGTATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (30 bp):
TGTTTAAGATTAACAAAACAAATTTATTTA
Found at i:1424580 original size:28 final size:27
Alignment explanation
Indices: 1424548--1424611 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
1424538 TGAATTAACC
*
1424548 AAATTAATCTTTAAA-ATATTTAAAATAT
1 AAATTAAAC-TTAAACATATTT-AAATAT
*
1424576 AAATTTAAACTTAAACTTATTTAAATAT
1 AAA-TTAAACTTAAACATATTTAAATAT
1424604 AAATTAAA
1 AAATTAAA
1424612 AGCTCATCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 5 0.16
28 17 0.53
29 10 0.31
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (27 bp):
AAATTAAACTTAAACATATTTAAATAT
Found at i:1424672 original size:29 final size:31
Alignment explanation
Indices: 1424628--1424686 Score: 95
Period size: 29 Copynumber: 1.9 Consensus size: 31
1424618 TCTAAATCTA
1424628 AACAAAACTTCCAATTAAAACA-AAAAAAAGC
1 AACAAAAC-TCCAATTAAAACAGAAAAAAAGC
1424659 AACAAAA-TCCAATTAAAACAGAAAAAAA
1 AACAAAACTCCAATTAAAACAGAAAAAAA
1424687 AGATATAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 13 0.48
30 7 0.26
31 7 0.26
ACGTcount: A:0.68, C:0.17, G:0.03, T:0.12
Consensus pattern (31 bp):
AACAAAACTCCAATTAAAACAGAAAAAAAGC
Found at i:1425838 original size:12 final size:13
Alignment explanation
Indices: 1425813--1425850 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
1425803 ATAAAAAATA
1425813 ATATATTATTTAT
1 ATATATTATTTAT
1425826 ATATATT-TTTAT
1 ATATATTATTTAT
*
1425838 AAATATTAATTTA
1 ATATATT-ATTTA
1425851 ACCAATATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 11 0.50
13 7 0.32
14 4 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATATATTATTTAT
Found at i:1426863 original size:35 final size:35
Alignment explanation
Indices: 1426797--1426863 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
1426787 AAATTAAAAT
* * * *
1426797 AAATAAATATTTTATTTTAAATTTAATAATATTAA
1 AAATAAAAATTTTATTTGAAACTTAAAAATATTAA
1426832 AAATAAAAATTATTA-TTGAAACTTAAAAATAT
1 AAATAAAAATT-TTATTTGAAACTTAAAAATAT
1426864 AATTTAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 24 0.89
36 3 0.11
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (35 bp):
AAATAAAAATTTTATTTGAAACTTAAAAATATTAA
Found at i:1427438 original size:25 final size:25
Alignment explanation
Indices: 1427410--1427514 Score: 65
Period size: 25 Copynumber: 4.1 Consensus size: 25
1427400 TTACTGTATT
1427410 TAAATTTAAATATAATTGTTAAATA
1 TAAATTTAAATATAATTGTTAAATA
* * * * * *
1427435 TAAATATATATTTAATTTTTAATTTT
1 TAAATTTAAATATAATTGTTAA-ATA
*
1427461 TAAA-TT--ATATAAAT-TTAAATA
1 TAAATTTAAATATAATTGTTAAATA
1427482 TAAATATTAAATATATATTTGATATAAATA
1 TAAAT-TTAAATATA-A-TTG-T-TAAATA
1427512 TAA
1 TAA
1427515 TTAATTTTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 15
0.68 0.14 0.18
Matches are distributed among these distances:
21 5 0.09
22 4 0.07
23 8 0.14
25 24 0.41
26 6 0.10
27 1 0.02
29 1 0.02
30 9 0.16
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
TAAATTTAAATATAATTGTTAAATA
Found at i:1427493 original size:13 final size:12
Alignment explanation
Indices: 1427410--1427510 Score: 57
Period size: 13 Copynumber: 8.4 Consensus size: 12
1427400 TTACTGTATT
1427410 TAAATTTAAATA
1 TAAATTTAAATA
*
1427422 TAATTGTTAAATA
1 TAAAT-TTAAATA
* * *
1427435 TAAATATATATT
1 TAAATTTAAATA
* * *
1427447 TAATTTTTAATTTT
1 TAA-ATTTAA-ATA
1427461 TAAA-TT--ATA
1 TAAATTTAAATA
1427470 TAAATTTAAATA
1 TAAATTTAAATA
1427482 TAAATATTAAATA
1 TAAAT-TTAAATA
* *
1427495 TATATTT-GATA
1 TAAATTTAAATA
1427506 TAAAT
1 TAAAT
1427511 ATAATTAATT
Statistics
Matches: 67, Mismatches: 15, Indels: 15
0.69 0.15 0.15
Matches are distributed among these distances:
9 5 0.07
10 2 0.03
11 7 0.10
12 23 0.34
13 25 0.37
14 5 0.07
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
TAAATTTAAATA
Found at i:1431334 original size:20 final size:20
Alignment explanation
Indices: 1431309--1431392 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 20
1431299 ACTAAATCAA
*
1431309 TTTATTAAATATAAATATTT
1 TTTATTAAATATAAATAATT
* *
1431329 TTTATTACAT-TAATTAATT
1 TTTATTAAATATAAATAATT
*
1431348 TATTTTTAAATAT--ATAATT
1 T-TTATTAAATATAAATAATT
1431367 TTTATTAACA-ATAAAATAATT
1 TTTATTAA-ATAT-AAATAATT
1431388 TTTAT
1 TTTAT
1431393 ATATTATTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
18 8 0.16
19 15 0.29
20 16 0.31
21 12 0.24
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTATTAAATATAAATAATT
Found at i:1431387 original size:40 final size:40
Alignment explanation
Indices: 1431308--1431388 Score: 94
Period size: 40 Copynumber: 2.0 Consensus size: 40
1431298 TACTAAATCA
* * *
1431308 ATTTATTAAATATAAATATTTTTTATTACATTAATTAATTT
1 ATTTATTAAATAT-AATAATTTTTATTACATAAAATAATTT
1431349 ATTT-TTAAATAT-ATAATTTTTATTAACAATAAAATAATTT
1 ATTTATTAAATATAATAATTTTTATT-AC-ATAAAATAATTT
1431389 TTATATATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
38 11 0.31
39 2 0.06
40 18 0.51
41 4 0.11
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (40 bp):
ATTTATTAAATATAATAATTTTTATTACATAAAATAATTT
Found at i:1431908 original size:3 final size:3
Alignment explanation
Indices: 1431894--1431928 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1431884 ATTTGCTTCT
*
1431894 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1431929 TGTACTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:1432496 original size:2 final size:2
Alignment explanation
Indices: 1432485--1432515 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1432475 TATTTTGTGT
1432485 TA TA -A 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
1432516 AACACATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1432682 original size:2 final size:2
Alignment explanation
Indices: 1432669--1432700 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1432659 ATTTTTCTAC
*
1432669 AT AT AC 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
1432701 GAGTCACATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1432907 original size:12 final size:13
Alignment explanation
Indices: 1432890--1432918 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1432880 TGTTGATAAA
1432890 TAAATTT-AAATT
1 TAAATTTAAAATT
1432902 TAAATTTAAAATT
1 TAAATTTAAAATT
1432915 TAAA
1 TAAA
1432919 AATTTTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAATTTAAAATT
Found at i:1435007 original size:20 final size:20
Alignment explanation
Indices: 1434979--1435019 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1434969 CATTTGATTC
* *
1434979 AAAACTTTATTTTATTATTT
1 AAAACTTTATATTAATATTT
*
1434999 AAAATTTTATATTAATATTT
1 AAAACTTTATATTAATATTT
1435019 A
1 A
1435020 TATATTTTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
AAAACTTTATATTAATATTT
Found at i:1435390 original size:24 final size:24
Alignment explanation
Indices: 1435357--1435403 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1435347 TAAACTTAAA
* *
1435357 TCTATTTAAACCTAAATTAAAAAC
1 TCTATCTAAACCTAAACTAAAAAC
*
1435381 TCTATCTAAACTTAAACTAAAAA
1 TCTATCTAAACCTAAACTAAAAA
1435404 ACTAATTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
TCTATCTAAACCTAAACTAAAAAC
Found at i:1436563 original size:2 final size:2
Alignment explanation
Indices: 1436556--1436589 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1436546 TTTTAGATTC
*
1436556 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1436590 TTAGTTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1441345 original size:5 final size:5
Alignment explanation
Indices: 1441335--1441436 Score: 74
Period size: 5 Copynumber: 21.2 Consensus size: 5
1441325 AAACACAATG
*
1441335 AATAT AATAT ATTTAAT AATAT AA-AT AATAT -A-AT AATAT AATA- AATAT
1 AATAT AATAT A-AT-AT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* * * * *
1441383 AAAAT AATAT AATA- AATAT TATAT GAT-T TATTT AAATAT AAT-T AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT
1441431 AATAT A
1 AATAT A
1441437 TTTAAAATTT
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
3 2 0.03
4 21 0.27
5 47 0.60
6 5 0.06
7 3 0.04
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (5 bp):
AATAT
Found at i:1441357 original size:17 final size:17
Alignment explanation
Indices: 1441335--1441401 Score: 73
Period size: 17 Copynumber: 3.8 Consensus size: 17
1441325 AAACACAATG
*
1441335 AATATAATATATTTAAT
1 AATATAATATATATAAT
1441352 AATATAA-ATAATATAAT
1 AATATAATAT-ATATAAT
*
1441369 AATATAATAAATATAAAAT
1 AATATAAT--ATATATAAT
*
1441388 AATATAATAAATAT
1 AATATAATATATAT
1441402 TATATGATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
16 2 0.05
17 24 0.57
19 14 0.33
20 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATATAATATATATAAT
Found at i:1441390 original size:19 final size:19
Alignment explanation
Indices: 1441355--1441401 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
1441345 ATTTAATAAT
*
1441355 ATAAATAATATAATAATATA
1 ATAAAT-ATAAAATAATATA
1441375 ATAAATATAAAATAATATA
1 ATAAATATAAAATAATATA
1441394 ATAAATAT
1 ATAAATAT
1441402 TATATGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 20 0.77
20 6 0.23
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAATATAAAATAATATA
Found at i:1441455 original size:25 final size:25
Alignment explanation
Indices: 1441398--1441478 Score: 71
Period size: 24 Copynumber: 3.3 Consensus size: 25
1441388 AATATAATAA
* *
1441398 ATATTATATGATTTATTT-AAA-TAT
1 ATATTATAT-ATATATTTAAAATTTT
1441422 A-ATTAATATAATATATTTAAAATTTT
1 ATATT-ATAT-ATATATTTAAAATTTT
* *
1441448 -TATTATATTTATATTTATAATTTT
1 ATATTATATATATATTTAAAATTTT
1441472 ATATTAT
1 ATATTAT
1441479 CAATAATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
23 3 0.06
24 26 0.55
25 13 0.28
26 5 0.11
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (25 bp):
ATATTATATATATATTTAAAATTTT
Found at i:1445590 original size:89 final size:89
Alignment explanation
Indices: 1445463--1445629 Score: 282
Period size: 89 Copynumber: 1.9 Consensus size: 89
1445453 GATGAACATC
* *
1445463 AAGCTGATAGTAGAAATGCAAAGAAAACTGAGAAAGAGATGGAAGCAGACCTATAAAAATGGCAC
1 AAGCTGATAGTAGAAATGCAAAGAAAACAGAGAAAGAGATGGAAGCAGACCTAT-AAAATGGCAA
1445528 AAAAAATCTGAAAATCAAGAAAATG
65 AAAAAATCTGAAAATCAAGAAAATG
* *
1445553 AAGCTGATCGTAGAAAT-CAAAGAAAACAGAGAAAGAGATGGAAGCAGACCTGTAAAATGGCAAA
1 AAGCTGATAGTAGAAATGCAAAGAAAACAGAGAAAGAGATGGAAGCAGACCTATAAAATGGCAAA
1445617 AAAAATCTGAAAA
66 AAAAATCTGAAAA
1445630 AAATTTGGAC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
88 23 0.32
89 34 0.47
90 16 0.22
ACGTcount: A:0.53, C:0.11, G:0.22, T:0.14
Consensus pattern (89 bp):
AAGCTGATAGTAGAAATGCAAAGAAAACAGAGAAAGAGATGGAAGCAGACCTATAAAATGGCAAA
AAAAATCTGAAAATCAAGAAAATG
Found at i:1448695 original size:2 final size:2
Alignment explanation
Indices: 1448688--1448715 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1448678 ATATGTCCAG
1448688 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
1448716 TCGGGCATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1450750 original size:28 final size:28
Alignment explanation
Indices: 1450703--1450766 Score: 80
Period size: 27 Copynumber: 2.3 Consensus size: 28
1450693 ATTTTTATTT
*
1450703 ATTTATATTTAAATAATTTTTAG-TT-AA
1 ATTT-TATTTAAAAAATTTTTAGATTCAA
1450730 ATTTTATTTCAAAAAATTTTTAGATTCAA
1 ATTTTATTT-AAAAAATTTTTAGATTCAA
1450759 A-TTTATTT
1 ATTTTATTT
1450767 TTTTGTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 5 0.15
27 16 0.48
28 9 0.27
29 3 0.09
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (28 bp):
ATTTTATTTAAAAAATTTTTAGATTCAA
Found at i:1450988 original size:22 final size:21
Alignment explanation
Indices: 1450949--1450989 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1450939 ATATTAAATA
1450949 TAAAAATTTTAAAATAATAAT
1 TAAAAATTTTAAAATAATAAT
* *
1450970 TAAATAATTTTTAATTAATA
1 TAAA-AATTTTAAAATAATA
1450990 TTACGTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAAATTTTAAAATAATAAT
Found at i:1451414 original size:2 final size:2
Alignment explanation
Indices: 1451340--1451399 Score: 56
Period size: 2 Copynumber: 30.5 Consensus size: 2
1451330 TTATGTAGGA
*
1451340 AT AT AT AT AT AT AT AT AT A- AT AT -T AT GT GAGT AT A- ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -A-T AT AT A-T AT
1451380 -T AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
1451400 CTATTTAGGA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
1 4 0.08
2 42 0.86
3 2 0.04
4 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Done.