Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3329
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: 1261902
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 4 of 4
Found at i:1112807 original size:28 final size:28
Alignment explanation
Indices: 1112774--1112835 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
1112764 GTTCTAAATA
* * *
1112774 TAAAAATTTTAAAAAAGTATACAACTTAT
1 TAAAAGTTTT-AAAAAGTATAAAAATTAT
1112803 TAAAAGTTTTAAAAAGTATAAAAATTAT
1 TAAAAGTTTTAAAAAGTATAAAAATTAT
1112831 TAAAA
1 TAAAA
1112836 ACTATTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 21 0.70
29 9 0.30
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (28 bp):
TAAAAGTTTTAAAAAGTATAAAAATTAT
Found at i:1114310 original size:32 final size:31
Alignment explanation
Indices: 1114251--1114318 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
1114241 ATAGTAATGT
*
1114251 ATTTTTATAATTTTTAAAGAGTTAAATTA-A
1 ATTTTTATAATTTTTAAAGAGTCAAATTATA
**
1114281 ATTTTTATAATTTTTTTAGATGATCAAATTATA
1 ATTTTTATAATTTTTAAAGA-G-TCAAATTATA
1114314 ATTTT
1 ATTTT
1114319 ATCACTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 18 0.56
31 1 0.03
32 7 0.22
33 6 0.19
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.54
Consensus pattern (31 bp):
ATTTTTATAATTTTTAAAGAGTCAAATTATA
Found at i:1117599 original size:3 final size:3
Alignment explanation
Indices: 1117591--1117623 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1117581 AATTTGATTC
*
1117591 TGA TGA TGA AGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1117624 GAAGTCACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.30
Consensus pattern (3 bp):
TGA
Found at i:1119222 original size:16 final size:16
Alignment explanation
Indices: 1119203--1119235 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1119193 TATGTATTTA
1119203 TATATATATTTATGTT
1 TATATATATTTATGTT
1119219 TATATATATTTATGTT
1 TATATATATTTATGTT
1119235 T
1 T
1119236 TCTCTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TATATATATTTATGTT
Found at i:1131934 original size:21 final size:19
Alignment explanation
Indices: 1131888--1131934 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1131878 TCTATGTACT
* *
1131888 CTAAATAGGGGATAGAGTT
1 CTAAATAGGGGATAGAATA
1131907 CTAAATAGGGGATAGAATGA
1 CTAAATAGGGGATAGAAT-A
1131927 CATAAATA
1 C-TAAATA
1131935 TTAACTCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 1 0.04
21 6 0.25
ACGTcount: A:0.45, C:0.06, G:0.26, T:0.23
Consensus pattern (19 bp):
CTAAATAGGGGATAGAATA
Found at i:1132494 original size:16 final size:17
Alignment explanation
Indices: 1132455--1132495 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
1132445 AATAAATAAT
1132455 TAATAA-TATATTTAAA
1 TAATAATTATATTTAAA
1132471 -AATAAATTAT-TTTAAA
1 TAAT-AATTATATTTAAA
1132487 TAATAATTA
1 TAATAATTA
1132496 AAAATATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.14
16 13 0.59
17 6 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATAATTATATTTAAA
Found at i:1132525 original size:27 final size:29
Alignment explanation
Indices: 1132495--1132552 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
1132485 AATAATAATT
1132495 AAAAAT-ATCAAAACTAT-GTTTATATTA
1 AAAAATAATCAAAACTATAGTTTATATTA
* * *
1132522 AAAAATAATTAAAATTATATTTTATATTA
1 AAAAATAATCAAAACTATAGTTTATATTA
1132551 AA
1 AA
1132553 TTATAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 6 0.23
28 9 0.35
29 11 0.42
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (29 bp):
AAAAATAATCAAAACTATAGTTTATATTA
Found at i:1133301 original size:29 final size:30
Alignment explanation
Indices: 1133245--1133301 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
1133235 TTTAAAATAT
* * *
1133245 ATTTATTTTCACTATTTTTAAATATAAAAG
1 ATTTATTTTCACTATTATAAAAAATAAAAG
*
1133275 ATTTATTTTTA-TATTATAAAAAATAAA
1 ATTTATTTTCACTATTATAAAAAATAAA
1133302 TTTATTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 13 0.57
30 10 0.43
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (30 bp):
ATTTATTTTCACTATTATAAAAAATAAAAG
Found at i:1133709 original size:19 final size:20
Alignment explanation
Indices: 1133669--1133706 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1133659 ATTTTTTAAA
1133669 ATTTTAAAAAATAAAAAAAT
1 ATTTTAAAAAATAAAAAAAT
*
1133689 ATTTTAAAAATTAAAAAA
1 ATTTTAAAAAATAAAAAA
1133707 TATAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATTTTAAAAAATAAAAAAAT
Found at i:1134731 original size:23 final size:23
Alignment explanation
Indices: 1134680--1134725 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1134670 GTATGAGCAC
* *
1134680 CTGTAATATCCTGAAAATTACTA
1 CTGTAATACCCCGAAAATTACTA
1134703 CTGTAATACCCCGAAAATTACTA
1 CTGTAATACCCCGAAAATTACTA
1134726 TAGTAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (23 bp):
CTGTAATACCCCGAAAATTACTA
Found at i:1139716 original size:15 final size:16
Alignment explanation
Indices: 1139696--1139730 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1139686 TTCAAATTTA
*
1139696 TAAATACTCTCAAT-T
1 TAAATACTATCAATAT
1139711 TAAATACTATCAATAT
1 TAAATACTATCAATAT
1139727 TAAA
1 TAAA
1139731 ATTGATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATACTATCAATAT
Found at i:1141336 original size:40 final size:40
Alignment explanation
Indices: 1141290--1141365 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
1141280 TCAAAGAAAT
1141290 CGCCGCTAAGGCAGGCCTATTGCGGCGTTTGTTTTTCGAG
1 CGCCGCTAAGGCAGGCCTATTGCGGCGTTTGTTTTTCGAG
* * *
1141330 CGCCGCTAATGCAGGTCTATTGTGGCGTTTGTTTTT
1 CGCCGCTAAGGCAGGCCTATTGCGGCGTTTGTTTTT
1141366 TTGCGCTGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.12, C:0.22, G:0.30, T:0.36
Consensus pattern (40 bp):
CGCCGCTAAGGCAGGCCTATTGCGGCGTTTGTTTTTCGAG
Found at i:1142243 original size:24 final size:24
Alignment explanation
Indices: 1142210--1142266 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
1142200 AAACCTAATT
* * *
1142210 CTAATCAATGTCAAATATATTATG
1 CTAATAAATGTCAAACATATTATA
*
1142234 CTAATAAATGTTAAACATATTATA
1 CTAATAAATGTCAAACATATTATA
*
1142258 TTAATAAAT
1 CTAATAAAT
1142267 ACTAAATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (24 bp):
CTAATAAATGTCAAACATATTATA
Found at i:1142272 original size:24 final size:24
Alignment explanation
Indices: 1142226--1142272 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1142216 AATGTCAAAT
* **
1142226 ATATTATGCTAATAAATGTTAAAC
1 ATATTATACTAATAAATACTAAAC
*
1142250 ATATTATATTAATAAATACTAAA
1 ATATTATACTAATAAATACTAAA
1142273 TTTTCTAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.38
Consensus pattern (24 bp):
ATATTATACTAATAAATACTAAAC
Found at i:1145535 original size:31 final size:31
Alignment explanation
Indices: 1145499--1145564 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 31
1145489 AATTAATTAT
1145499 TTTTAAAATTTTTAAAAAATTCA-AA-AAAATA
1 TTTTAAAA-TTTTAAAAAATT-ATAAGAAAATA
1145530 TTTTAAAATTTTAAAAAATTATAAGAAAATA
1 TTTTAAAATTTTAAAAAATTATAAGAAAATA
1145561 TTTT
1 TTTT
1145565 TTAATATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 1 0.03
30 14 0.42
31 18 0.55
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (31 bp):
TTTTAAAATTTTAAAAAATTATAAGAAAATA
Found at i:1148002 original size:12 final size:12
Alignment explanation
Indices: 1147976--1148009 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1147966 CCACATATCA
*
1147976 ATTAA-TCCTTT
1 ATTAATTCCTTC
1147987 ATTAATTCCTTC
1 ATTAATTCCTTC
1147999 ATTAATTCCTT
1 ATTAATTCCTT
1148010 TGTTTAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTAATTCCTTC
Found at i:1151541 original size:30 final size:31
Alignment explanation
Indices: 1151474--1151543 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1151464 AGGCTTAGGA
* * *
1151474 AAAATTTTTAAAAAAATTGAGGAGTTCAATT
1 AAAATTTTCAAAAAAATTGAGGACTTCAATG
1151505 AAAATTTTCAAAAAAATTGAAGG-CTT-AATG
1 AAAATTTTCAAAAAAATTG-AGGACTTCAATG
*
1151535 AGAATTTTC
1 AAAATTTTC
1151544 CAAATTTGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 11 0.32
31 20 0.59
32 3 0.09
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (31 bp):
AAAATTTTCAAAAAAATTGAGGACTTCAATG
Found at i:1156370 original size:15 final size:15
Alignment explanation
Indices: 1156352--1156384 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1156342 TCCTTTTTGC
1156352 TTATTTTTA-TCTTTA
1 TTATTTTTACT-TTTA
1156367 TTATTTTTACTTTTA
1 TTATTTTTACTTTTA
1156382 TTA
1 TTA
1156385 CATTAGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTTTTACTTTTA
Found at i:1157995 original size:11 final size:10
Alignment explanation
Indices: 1157968--1158042 Score: 59
Period size: 9 Copynumber: 7.8 Consensus size: 10
1157958 ATTATTTTTT
*
1157968 AAAATTTTAA
1 AAAATATTAA
*
1157978 AACAT-TTAA
1 AAAATATTAA
*
1157987 AAAATATT-T
1 AAAATATTAA
* *
1157996 TAAACATTAA
1 AAAATATTAA
1158006 AAAA-ATTAA
1 AAAATATTAA
1158015 AAAA-ATTAA
1 AAAATATTAA
*
1158024 AAAATAATAA
1 AAAATATTAA
1158034 GAAAATATT
1 -AAAATATT
1158043 TTTTAATTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
9 32 0.62
10 13 0.25
11 7 0.13
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (10 bp):
AAAATATTAA
Found at i:1158000 original size:20 final size:21
Alignment explanation
Indices: 1157971--1158011 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
1157961 ATTTTTTAAA
*
1157971 ATTTTAAAACATTTAAAAAAT
1 ATTTTAAAACATTAAAAAAAT
1157992 ATTTT-AAACATTAAAAAAAT
1 ATTTTAAAACATTAAAAAAAT
1158012 TAAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
ATTTTAAAACATTAAAAAAAT
Found at i:1164322 original size:21 final size:21
Alignment explanation
Indices: 1164296--1164336 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1164286 AGACGAGCAA
* *
1164296 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1164317 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1164337 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1167542 original size:28 final size:28
Alignment explanation
Indices: 1167509--1167570 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1167499 GTTCTAAATA
* * *
1167509 TAAAAATTTAAAAAAAGTATACAACTTAT
1 TAAAAGTTT-AAAAAAGTATAAAAATTAT
*
1167538 TAAAAGTTTTAAAAAGTATAAAAATTAT
1 TAAAAGTTTAAAAAAGTATAAAAATTAT
1167566 TAAAA
1 TAAAA
1167571 ACTATTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 21 0.72
29 8 0.28
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.32
Consensus pattern (28 bp):
TAAAAGTTTAAAAAAGTATAAAAATTAT
Found at i:1169036 original size:32 final size:31
Alignment explanation
Indices: 1168977--1169044 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
1168967 ATAGTAATGT
*
1168977 ATTTTTATAATTTTTAAAGAGTTAAATTA-A
1 ATTTTTATAATTTTTAAAGAGTCAAATTATA
**
1169007 ATTTTTATAATTTTTTTAGATGATCAAATTATA
1 ATTTTTATAATTTTTAAAGA-G-TCAAATTATA
1169040 ATTTT
1 ATTTT
1169045 ATCACTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 18 0.56
31 1 0.03
32 7 0.22
33 6 0.19
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.54
Consensus pattern (31 bp):
ATTTTTATAATTTTTAAAGAGTCAAATTATA
Found at i:1172262 original size:3 final size:3
Alignment explanation
Indices: 1172254--1172289 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
1172244 AATATGATTC
*
1172254 TGA TGA TGA AGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1172290 GAAGTCACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:1178094 original size:30 final size:29
Alignment explanation
Indices: 1178058--1178141 Score: 89
Period size: 30 Copynumber: 2.9 Consensus size: 29
1178048 CTTTTATATA
1178058 ATATTTTTAAAATATATTTATTTATTTTC
1 ATATTTTTAAAATATATTTATTTATTTTC
** *
1178087 ACTATTTTT-AAATATAAAATATTTATTTTT
1 A-TATTTTTAAAATAT-ATTTATTTATTTTC
* * *
1178117 ATATTATAAAAATAAATTTATTTAT
1 ATATTTTTAAAATATATTTATTTAT
1178142 AAATTAAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 20 0.45
30 24 0.55
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (29 bp):
ATATTTTTAAAATATATTTATTTATTTTC
Found at i:1178113 original size:21 final size:21
Alignment explanation
Indices: 1178089--1178152 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 21
1178079 TTATTTTCAC
1178089 TATTTTTAAATATAAAATATT
1 TATTTTTAAATATAAAATATT
*
1178110 TATTTTTATATTATAAAAATAAATT
1 TATTTTTA-AATAT-AAAAT--ATT
*
1178135 TATTTATAAAT-TAAAATA
1 TATTTTTAAATATAAAATA
1178153 AAGAATAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
20 1 0.03
21 8 0.22
22 9 0.25
23 6 0.17
24 2 0.06
25 10 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTTTTAAATATAAAATATT
Found at i:1178139 original size:29 final size:31
Alignment explanation
Indices: 1178066--1178141 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 31
1178056 TAATATTTTT
* *
1178066 AAAATATATTTATTTATTTTCACTATTTTTA
1 AAAATAAATTTATTTATTTTCACTATTTATA
* * *
1178097 AATATAAA-ATATTTATTTTTA-TA-TTATA
1 AAAATAAATTTATTTATTTTCACTATTTATA
1178125 AAAATAAATTTATTTAT
1 AAAATAAATTTATTTAT
1178142 AAATTAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 11 0.30
29 9 0.24
30 11 0.30
31 6 0.16
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (31 bp):
AAAATAAATTTATTTATTTTCACTATTTATA
Found at i:1179338 original size:13 final size:13
Alignment explanation
Indices: 1179317--1179367 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
1179307 AAATACATGT
*
1179317 ATATGTAAAATAA
1 ATATTTAAAATAA
*
1179330 ATATTTAAAA-AT
1 ATATTTAAAATAA
1179342 ATATTTAAAAATAAA
1 ATATTT-AAAAT-AA
1179357 ATATCTTAAAA
1 ATAT-TTAAAA
1179368 AAAAACCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 7 0.23
13 13 0.42
15 9 0.29
16 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:1179347 original size:12 final size:12
Alignment explanation
Indices: 1179316--1179354 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1179306 AAAATACATG
*
1179316 TATATGTAAAATA
1 TATATTTAAAA-A
*
1179329 AATATTTAAAAA
1 TATATTTAAAAA
1179341 TATATTTAAAAA
1 TATATTTAAAAA
1179353 TA
1 TA
1179355 AAATATCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (12 bp):
TATATTTAAAAA
Found at i:1179367 original size:16 final size:14
Alignment explanation
Indices: 1179323--1179368 Score: 60
Period size: 12 Copynumber: 3.3 Consensus size: 14
1179313 ATGTATATGT
1179323 AAAATAAATATTTA
1 AAAATAAATATTTA
1179337 AAAAT--ATATTTA
1 AAAATAAATATTTA
1179349 AAAATAAAATATCTTA
1 AAAAT-AAATAT-TTA
1179365 AAAA
1 AAAA
1179369 AAAACCAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 12 0.43
14 5 0.18
15 4 0.14
16 7 0.25
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATAAATATTTA
Found at i:1182620 original size:21 final size:21
Alignment explanation
Indices: 1182588--1182628 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1182578 AGGCTCGAGG
1182588 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
1182609 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
1182629 CCAATTGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:1186758 original size:12 final size:12
Alignment explanation
Indices: 1186732--1186765 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1186722 CCACATATCA
*
1186732 ATTAA-TCCTTT
1 ATTAATTCCTTC
1186743 ATTAATTCCTTC
1 ATTAATTCCTTC
1186755 ATTAATTCCTT
1 ATTAATTCCTT
1186766 TGTTTAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTAATTCCTTC
Found at i:1189720 original size:25 final size:26
Alignment explanation
Indices: 1189675--1189730 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
1189665 TATGTATGTG
* *
1189675 TAAAATAAATAATTAAGAAT-ATATT
1 TAAAATAAAAAATTAAGAATAATAAT
*
1189700 TAAAATAAAAAATTTTA-AATAATAAT
1 TAAAATAAAAAA-TTAAGAATAATAAT
1189726 TAAAA
1 TAAAA
1189731 ATATCAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (26 bp):
TAAAATAAAAAATTAAGAATAATAAT
Found at i:1194488 original size:216 final size:216
Alignment explanation
Indices: 1194113--1194555 Score: 764
Period size: 216 Copynumber: 2.1 Consensus size: 216
1194103 TGAGTGCCTG
1194113 CAACATCTCACCAGCCTCAAAAGATTAACAATAAGAGATTGCAAGGAGGTTGATTTAGAGGGCAT
1 CAACATCTCACCAGCCTCAAAAGATTAACAATAAGAGATTGCAAGGAGGTTGATTTAGAGGGCAT
*
1194178 GCAATGGGAACCACTTAAGAATCTCTCTCATTTGAAGATTGATAATATTCCAAAGCTGGTGTCTC
66 GCAATGGGAACCACTTAAGAATCTCTCTCAATTGAAGATTGATAATATTCCAAAGCTGGTGTCTC
*
1194243 TCCCCATTTCTCTTCAACATCTTGTTCAATTGGAAACATTAAAAATTC-AGAACTGCAATCGATT
131 TCCCCATTTCTCTTCAACATCTTGTTCAATTGAAAACATTAAAAATTCGAGAA-TGCAATCGATT
*
1194307 GAGGTCACTGC-TTCCTGTGTTT
195 GAGGTCACT-CTTTCCTGTGTTC
*
1194329 GAACATCTCACCAGCCTCAAAAGATTAACAATAAGAGATTGCAAGGAGGTTGATTTAGAGGGCAT
1 CAACATCTCACCAGCCTCAAAAGATTAACAATAAGAGATTGCAAGGAGGTTGATTTAGAGGGCAT
*
1194394 GCAATGGGAACCCCTTAAGAATCTCTCTCAATTGAAGATTGATAATATTCCAAAGCTGGTGTCTC
66 GCAATGGGAACCACTTAAGAATCTCTCTCAATTGAAGATTGATAATATTCCAAAGCTGGTGTCTC
* * * * *
1194459 TCCTCATTTCTCTTCAACATCTTGTTCAATTGAAAACATTAGAAATTCGTGAATGCCATGGATTG
131 TCCCCATTTCTCTTCAACATCTTGTTCAATTGAAAACATTAAAAATTCGAGAATGCAATCGATTG
1194524 AGGTCACTCTTTCCTGTGTTC
196 AGGTCACTCTTTCCTGTGTTC
1194545 CAACATCTCAC
1 CAACATCTCAC
1194556 TTTCCTTGAA
Statistics
Matches: 214, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
215 1 0.00
216 210 0.98
217 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (216 bp):
CAACATCTCACCAGCCTCAAAAGATTAACAATAAGAGATTGCAAGGAGGTTGATTTAGAGGGCAT
GCAATGGGAACCACTTAAGAATCTCTCTCAATTGAAGATTGATAATATTCCAAAGCTGGTGTCTC
TCCCCATTTCTCTTCAACATCTTGTTCAATTGAAAACATTAAAAATTCGAGAATGCAATCGATTG
AGGTCACTCTTTCCTGTGTTC
Found at i:1199586 original size:2 final size:2
Alignment explanation
Indices: 1199574--1199607 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1199564 AACGATATTT
*
1199574 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1199608 GTTTAAACTA
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1200699 original size:49 final size:50
Alignment explanation
Indices: 1200635--1200874 Score: 211
Period size: 51 Copynumber: 4.8 Consensus size: 50
1200625 TCATTCGATA
* *
1200635 CACGTAGTAGTCTTCACATAGTACTACACACGTGATC-AGTTTTACAATT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAACT
**
1200684 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGCT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAACT
* ***
1200734 CACGTAGTAGCCTTCAC-TCAGTACTACACACGTGCTCAAAGCTTCTTGGTA--
1 CACGTAGTAGCCTTCACAT-AGTACTACACACGTGATC-AAG-TT-TTACAACT
* * * * * * **
1200785 CACATAGTAGCCTTCACTTAGTACTACACATGTGACCGTAG-TTTACCGAGA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTTTTA-CAACT
* * * *
1200836 CACGTGGTAGCATTCACACAGTACTACACACGTGCTCAA
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAA
1200875 AGCTTCTTGG
Statistics
Matches: 155, Mismatches: 27, Indels: 17
0.78 0.14 0.09
Matches are distributed among these distances:
48 2 0.01
49 39 0.25
50 44 0.28
51 65 0.42
52 3 0.02
53 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACAACT
Found at i:1200808 original size:51 final size:51
Alignment explanation
Indices: 1200688--1200913 Score: 223
Period size: 51 Copynumber: 4.5 Consensus size: 51
1200678 ACAATTCACG
* * *
1200688 TAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TT-TTACGGCT-CACG
1 TAGTAGCCTTCACTTAGTACTACACACGTGCTCAAAGCTTCTT--GG-TACACA
*
1200738 TAGTAGCCTTCACTCAGTACTACACACGTGCTCAAAGCTTCTTGGTACACA
1 TAGTAGCCTTCACTTAGTACTACACACGTGCTCAAAGCTTCTTGGTACACA
* ** * * *
1200789 TAGTAGCCTTCACTTAGTACTACACATGTGAC-CGTAGTTTAC-CGAG-ACACG
1 TAGTAGCCTTCACTTAGTACTACACACGTG-CTCAAAGCTT-CTTG-GTACACA
* * **
1200840 TGGTAGCATTCACACAGTACTACACACGTGCTCAAAGCTTCTTGGTACACA
1 TAGTAGCCTTCACTTAGTACTACACACGTGCTCAAAGCTTCTTGGTACACA
1200891 TAGTAGCCTTCACTTAGTACTAC
1 TAGTAGCCTTCACTTAGTACTAC
1200914 CCATGTGAAC
Statistics
Matches: 141, Mismatches: 25, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
50 34 0.24
51 100 0.71
52 5 0.04
53 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (51 bp):
TAGTAGCCTTCACTTAGTACTACACACGTGCTCAAAGCTTCTTGGTACACA
Found at i:1200863 original size:102 final size:100
Alignment explanation
Indices: 1200688--1200971 Score: 374
Period size: 102 Copynumber: 2.8 Consensus size: 100
1200678 ACAATTCACG
* * * * * *
1200688 TAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACG-GCTCACGTAGTAGCCTTCACT
1 TAGTAGCCTTCACTTAGTACTACACATGTGACCTAG-TTTACGAG-ACACGTAGTAGCCTTCACA
1200752 CAGTACTACACACGTGCTCAAAGCTTCTTGGTACACA
64 CAGTACTACACACGTGCTCAAAGCTTCTTGGTACACA
* *
1200789 TAGTAGCCTTCACTTAGTACTACACATGTGACCGTAGTTTACCGAGACACGTGGTAGCATTCACA
1 TAGTAGCCTTCACTTAGTACTACACATGTGACC-TAGTTTA-CGAGACACGTAGTAGCCTTCACA
1200854 CAGTACTACACACGTGCTCAAAGCTTCTTGGTACACA
64 CAGTACTACACACGTGCTCAAAGCTTCTTGGTACACA
* * * *
1200891 TAGTAGCCTTCACTTAGTACTACCCATGTGAACATTA-CTTATCGATACACGTAGTAGCCTTCAC
1 TAGTAGCCTTCACTTAGTACTACACATGTG-AC-CTAGTTTA-CGAGACACGTAGTAGCCTTCAC
*
1200955 ACAATACTACACACGTG
63 ACAGTACTACACACGTG
1200972 TTCATCGATA
Statistics
Matches: 162, Mismatches: 16, Indels: 9
0.87 0.09 0.05
Matches are distributed among these distances:
101 34 0.21
102 123 0.76
103 5 0.03
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (100 bp):
TAGTAGCCTTCACTTAGTACTACACATGTGACCTAGTTTACGAGACACGTAGTAGCCTTCACACA
GTACTACACACGTGCTCAAAGCTTCTTGGTACACA
Found at i:1200940 original size:51 final size:50
Alignment explanation
Indices: 1200629--1200954 Score: 180
Period size: 51 Copynumber: 6.5 Consensus size: 50
1200619 TTTTTATCAT
* * * * *
1200629 TCGATACACGTAGTAGTCTTCACATAGTACTACACACGTG--ATCAG-TTT
1 TCGATACACATAGTAGCCTTCACTTAGTACTACACATGTGACAT-AGCTTA
* * * * * *
1200677 TACAATTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCA-AG-TTT
1 T-CGATACACATAGTAGCCTTCACTTAGTACTACACATGTGA-CATAGCTTA
* * * * * * *
1200727 TACGGCT-CACGTAGTAGCCTTCACTCAGTACTACACACGTGCTCAAAGCTTC
1 T-C-GATACACATAGTAGCCTTCACTTAGTACTACACATGTG-ACATAGCTTA
* * * *
1200779 TTGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCGTAGTTTA
1 TCGATACACATAGTAGCCTTCACTTAGTACTACACATGTGA-CATAGCTTA
* * * * * ** * * * *
1200830 CCGAGACACGTGGTAGCATTCACACAGTACTACACACGTGCTCAAAGCTTC
1 TCGATACACATAGTAGCCTTCACTTAGTACTACACATGTG-ACATAGCTTA
* * *
1200881 TTGGTACACATAGTAGCCTTCACTTAGTACTACCCATGTGAACATTA-CTTA
1 TCGATACACATAGTAGCCTTCACTTAGTACTACACATGTG-ACA-TAGCTTA
*
1200932 TCGATACACGTAGTAGCCTTCAC
1 TCGATACACATAGTAGCCTTCAC
1200955 ACAATACTAC
Statistics
Matches: 214, Mismatches: 52, Indels: 21
0.75 0.18 0.07
Matches are distributed among these distances:
48 1 0.00
49 36 0.17
50 44 0.21
51 128 0.60
52 5 0.02
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (50 bp):
TCGATACACATAGTAGCCTTCACTTAGTACTACACATGTGACATAGCTTA
Found at i:1200950 original size:153 final size:149
Alignment explanation
Indices: 1200629--1200971 Score: 361
Period size: 153 Copynumber: 2.3 Consensus size: 149
1200619 TTTTTATCAT
* * **
1200629 TCGATACACGTAGTAGTCTTCACATAGTACTACACACGTGATCAGTTTTACAATTCACGTAGTAG
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAGTTTTACAAGACACGTAGTAG
* * *
1200694 CCTTCACATAGTACTACACACGTGATCAAGTTTTACGGCTCACGTAGTAGCCTTCACTCAGTACT
66 CATTCACACAGTACTACACACGTGATCAAGTTTTA-GGCTCACATAGTAGCCTTCACTCAGTACT
** *
1200759 ACACACGTGCTCAAAGCTTC
130 ACACACGTGAACAAAGCTTA
* * * * * * *
1200779 TTGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACC-GTAGTTTACCGAGACACGTGG
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAGT--TTTA-CAAGACACGTAG
* *
1200843 TAGCATTCACACAGTACTACACACGTGCTCAAAGCTTCTT-GG-TACACATAGTAGCCTTCACTT
63 TAGCATTCACACAGTACTACACACGTGATC-AAG-TT-TTAGGCT-CACATAGTAGCCTTCACTC
* * *
1200906 AGTACTACCCATGTGAACATTA-CTTA
124 AGTACTACACACGTGAACA-AAGCTTA
* *
1200932 TCGATACACGTAGTAGCCTTCACACAATACTACACACGTG
1 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTG
1200972 TTCATCGATA
Statistics
Matches: 156, Mismatches: 29, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
149 2 0.01
150 36 0.23
151 4 0.03
152 36 0.23
153 73 0.47
154 3 0.02
155 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (149 bp):
TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAGTTTTACAAGACACGTAGTAG
CATTCACACAGTACTACACACGTGATCAAGTTTTAGGCTCACATAGTAGCCTTCACTCAGTACTA
CACACGTGAACAAAGCTTA
Found at i:1202446 original size:21 final size:23
Alignment explanation
Indices: 1202399--1202448 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1202389 TCTTTTATAG
* * *
1202399 ATTTTTATATTATATATATATTA
1 ATTTATATATTATATATAAAATA
1202422 ATTTATATATTATA-ATAAAATA
1 ATTTATATATTATATATAAAATA
*
1202444 TTTTA
1 ATTTA
1202449 AATAATAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTATATATTATATATAAAATA
Found at i:1202489 original size:27 final size:28
Alignment explanation
Indices: 1202456--1202515 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1202446 TTAAATAATA
1202456 ATTAAAAAT-ATCAAAACTAT-GTTTAT
1 ATTAAAAATAATCAAAACTATAGTTTAT
* * *
1202482 ATTAAAAATAATTAAAATTATATTTTAT
1 ATTAAAAATAATCAAAACTATAGTTTAT
1202510 ATTAAA
1 ATTAAA
1202516 TTATAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 9 0.31
27 9 0.31
28 11 0.38
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (28 bp):
ATTAAAAATAATCAAAACTATAGTTTAT
Found at i:1204275 original size:29 final size:30
Alignment explanation
Indices: 1204219--1204275 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
1204209 TTTAAAATAT
* * *
1204219 ATTTATTTTCACTATTTTTAAATATAAAAG
1 ATTTATTTTCACTATTATAAAAAATAAAAG
*
1204249 ATTTATTTTTA-TATTATAAAAAATAAA
1 ATTTATTTTCACTATTATAAAAAATAAA
1204276 TTTATTTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 13 0.57
30 10 0.43
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (30 bp):
ATTTATTTTCACTATTATAAAAAATAAAAG
Found at i:1204283 original size:24 final size:28
Alignment explanation
Indices: 1204256--1204313 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
1204246 AAGATTTATT
1204256 TTTAT-ATT-ATAAAAAATA-AATTT-A
1 TTTATAATTAATAAAAAATAGAATTTGA
1204280 TTTATAAATTAAATAAAAAATAGAATTTGA
1 TTTAT-AATT-AATAAAAAATAGAATTTGA
1204310 TTTA
1 TTTA
1204314 GTTTCGGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 5 0.18
26 3 0.11
28 10 0.36
29 5 0.18
30 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (28 bp):
TTTATAATTAATAAAAAATAGAATTTGA
Found at i:1204290 original size:26 final size:28
Alignment explanation
Indices: 1204249--1204313 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 28
1204239 AATATAAAAG
* *
1204249 ATTTATTTTTATATT-ATAAAAAATA-A
1 ATTTATTTATAAATTAATAAAAAATAGA
1204275 ATTTATTTATAAATTAAATAAAAAATAGA
1 ATTTATTTATAAATT-AATAAAAAATAGA
1204304 ATTTGATTTA
1 ATTT-ATTTA
1204314 GTTTCGGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 13 0.39
28 10 0.30
29 5 0.15
30 5 0.15
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (28 bp):
ATTTATTTATAAATTAATAAAAAATAGA
Found at i:1204533 original size:2 final size:2
Alignment explanation
Indices: 1204526--1204560 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1204516 GAGATCGAAA
1204526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1204561 ACAATAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1204881 original size:11 final size:11
Alignment explanation
Indices: 1204865--1204898 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
1204855 AATATTTTTT
1204865 AAAATTTTAAA
1 AAAATTTTAAA
1204876 AAAA-TTTAAA
1 AAAATTTTAAA
1204886 AAATATTTTAAA
1 AAA-ATTTTAAA
1204898 A
1 A
1204899 TTTATAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.43
11 5 0.24
12 7 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAATTTTAAA
Found at i:1204895 original size:30 final size:31
Alignment explanation
Indices: 1204852--1204911 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
1204842 ACATAAGCAA
* *
1204852 TAAAATATTTTTTAAAATTT-TAAAAAAATT
1 TAAAAAATATTTTAAAATTTATAAAAAAATT
*
1204882 TAAAAAATATTTTAAAATTTATAAGAAAAT
1 TAAAAAATATTTTAAAATTTATAAAAAAAT
1204912 ATTTTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (31 bp):
TAAAAAATATTTTAAAATTTATAAAAAAATT
Found at i:1220249 original size:21 final size:20
Alignment explanation
Indices: 1220197--1220238 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
1220187 TTAACTCTGT
*
1220197 TAATATTAATTCTGTTACAA
1 TAATGTTAATTCTGTTACAA
1220217 TAAATGTTAATTCTGTTACAA
1 T-AATGTTAATTCTGTTACAA
1220238 T
1 T
1220239 TTGATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (20 bp):
TAATGTTAATTCTGTTACAA
Found at i:1220730 original size:10 final size:10
Alignment explanation
Indices: 1220715--1220758 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
1220705 TGTGGTTGTA
*
1220715 TTATATGTAT
1 TTATATATAT
1220725 TTATATATAT
1 TTATATATAT
* * *
1220735 ATATTTATGT
1 TTATATATAT
1220745 TTATATATAT
1 TTATATATAT
1220755 TTAT
1 TTAT
1220759 GTTTTCTCTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (10 bp):
TTATATATAT
Found at i:1220749 original size:16 final size:16
Alignment explanation
Indices: 1220730--1220762 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1220720 TGTATTTATA
1220730 TATATATATTTATGTT
1 TATATATATTTATGTT
1220746 TATATATATTTATGTT
1 TATATATATTTATGTT
1220762 T
1 T
1220763 TCTCTTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (16 bp):
TATATATATTTATGTT
Found at i:1222189 original size:12 final size:12
Alignment explanation
Indices: 1222167--1222200 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1222157 CCACATATCA
1222167 ATTAA-TCCTTC
1 ATTAATTCCTTC
1222178 ATTAATTCCTTC
1 ATTAATTCCTTC
1222190 ATTAATTCCTT
1 ATTAATTCCTT
1222201 TGTTTAAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 5 0.23
12 17 0.77
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTAATTCCTTC
Found at i:1225962 original size:21 final size:21
Alignment explanation
Indices: 1225937--1225977 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1225927 TAACTCTGTT
1225937 AATGTTAATTCTGTTACAATA
1 AATGTTAATTCTGTTACAATA
1225958 AATGTTAATTCTGTTACAAT
1 AATGTTAATTCTGTTACAAT
1225978 TTGATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.44
Consensus pattern (21 bp):
AATGTTAATTCTGTTACAATA
Found at i:1226244 original size:3 final size:3
Alignment explanation
Indices: 1226236--1226260 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1226226 GCCCAGAGCA
1226236 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
1226261 TCTTATCAAA
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:1227748 original size:22 final size:21
Alignment explanation
Indices: 1227702--1227748 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
1227692 TATTTTCACT
* **
1227702 ATTTTTAAATATAAAAGATTT
1 ATTTTTAAATATAAAAAATAA
1227723 ATTTTTAAATTATAAAAAATAA
1 ATTTTTAAA-TATAAAAAATAA
1227745 ATTT
1 ATTT
1227749 ATTTATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTTTTAAATATAAAAAATAA
Found at i:1228348 original size:21 final size:21
Alignment explanation
Indices: 1228316--1228355 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1228306 CATTTTTTAA
1228316 ATTTTAAAAAATTCAAAAAAAT
1 ATTTTAAAAAATT-AAAAAAAT
1228338 ATTTT-AAAAATTAAAAAA
1 ATTTTAAAAAATTAAAAAA
1228356 TTTATAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTTTAAAAAATTAAAAAAAT
Found at i:1228349 original size:31 final size:31
Alignment explanation
Indices: 1228310--1228373 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
1228300 ATTACTCATT
**
1228310 TTTTAAATTTTAAAAAATTCA-AA-AAAATA
1 TTTTAAAAATTAAAAAATTCATAAGAAAATA
*
1228339 TTTTAAAAATTAAAAAATTTATAAGAAAATA
1 TTTTAAAAATTAAAAAATTCATAAGAAAATA
1228370 TTTT
1 TTTT
1228374 TTAATATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 18 0.60
30 2 0.07
31 10 0.33
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (31 bp):
TTTTAAAAATTAAAAAATTCATAAGAAAATA
Found at i:1234631 original size:26 final size:26
Alignment explanation
Indices: 1234595--1234646 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1234585 GATACCATCT
1234595 TCAGCATGCTTCATCAGATTGACAAA
1 TCAGCATGCTTCATCAGATTGACAAA
1234621 TCAGCATGCTTCATCAGATTGACAAA
1 TCAGCATGCTTCATCAGATTGACAAA
1234647 CTTTTTCGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (26 bp):
TCAGCATGCTTCATCAGATTGACAAA
Found at i:1248189 original size:9 final size:9
Alignment explanation
Indices: 1248175--1248204 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1248165 GTTTCTCTTT
1248175 GCAGGTGGA
1 GCAGGTGGA
1248184 GCAGGTGGA
1 GCAGGTGGA
1248193 GCAGGT-GA
1 GCAGGTGGA
1248201 GCAG
1 GCAG
1248205 CGATGGGACG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.29
9 15 0.71
ACGTcount: A:0.23, C:0.13, G:0.53, T:0.10
Consensus pattern (9 bp):
GCAGGTGGA
Found at i:1248776 original size:46 final size:44
Alignment explanation
Indices: 1248636--1249012 Score: 271
Period size: 44 Copynumber: 8.7 Consensus size: 44
1248626 TTTTAACCCA
* *
1248636 CTCCACTGTAACTTCAGGGAGATAGGAT-AG-TGTCTTCGATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATCTGAT-TCTTCGATCTG
* * * * *
1248679 CTCCGCTGTAA-TCTCGGGGAGATAAGATCT-CTGGCTTCAATCTG
1 CTCCACTGTAACT-TCAGGGAGATAAGATCTGAT-TCTTCGATCTG
* * *
1248723 CTCCACTGTAACTTCAGGGGGATAAGATCTGCAATTCTTCGGTCTA
1 CTCCACTGTAACTTCAGGGAGATAAGATCTG--ATTCTTCGATCTG
* * * * *
1248769 CTCCACTGTAACCTCAGAGAGATAAGACCTGA---TGCGATCTA
1 CTCCACTGTAACTTCAGGGAGATAAGATCTGATTCTTCGATCTG
* * * * *
1248810 CTCTACTGTAACTTCAGAGAGATAAGATCCTTTATT-TT-AATCCG
1 CTCCACTGTAACTTCAGGGAGATAAGAT-C-TGATTCTTCGATCTG
*
1248854 CTCCACTGTAACTTCAGGGAGATAGGAT-T-ATATCTTCGATCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATCTGAT-TCTTCGATCTG
* * * *
1248897 CTCCGCTGTAACCTCAGGGAGACAAGATCTGCGATTCTTCGGTCTG
1 CTCCACTGTAACTTCAGGGAGATAAGATCT--GATTCTTCGATCTG
* * * *
1248943 TTCCACTGTAA-TCTCAGGGAGATAAGACCTGA-T-GT-GATCTT
1 CTCCACTGTAACT-TCAGGGAGATAAGATCTGATTCTTCGATCTG
* *
1248984 CTCTACTGTAACTTCAGAGAGATAAGATC
1 CTCCACTGTAACTTCAGGGAGATAAGATC
1249013 CTTTAATCCG
Statistics
Matches: 264, Mismatches: 50, Indels: 42
0.74 0.14 0.12
Matches are distributed among these distances:
40 2 0.01
41 61 0.23
42 6 0.02
43 54 0.20
44 68 0.26
45 2 0.01
46 68 0.26
47 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (44 bp):
CTCCACTGTAACTTCAGGGAGATAAGATCTGATTCTTCGATCTG
Found at i:1248818 original size:87 final size:87
Alignment explanation
Indices: 1248636--1249012 Score: 302
Period size: 87 Copynumber: 4.3 Consensus size: 87
1248626 TTTTAACCCA
* * * * * * *
1248636 CTCCACTGTAACTTCAGGGAGATAGGA--T--AGTGTCTTCGATCTGCTCCGCTGTAATCTCGGG
1 CTCCACTGTAACTTCAGAGAGATAAGATCTGCAAT-TCTTCGGTCTGCTCCACTGTAACCTCAGG
* * *
1248697 GAGATAAGATCTCTGGCTTCAATCTG
65 GAGATAAGA-C-CT-GATGCGATCTG
* * * *
1248723 CTCCACTGTAACTTCAGGGGGATAAGATCTGCAATTCTTCGGTCTACTCCACTGTAACCTCAGAG
1 CTCCACTGTAACTTCAGAGAGATAAGATCTGCAATTCTTCGGTCTGCTCCACTGTAACCTCAGGG
*
1248788 AGATAAGACCTGATGCGATCTA
66 AGATAAGACCTGATGCGATCTG
* ** ** * *
1248810 CTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATT-TT-AATCCGCTCCACTGTAACTTCAGG
1 CTCCACTGTAACTTCAGAGAGATAAGAT-CTGCAATTCTTCGGTCTGCTCCACTGTAACCTCAGG
* * * *
1248872 GAGATAGGA-TTATATCTTCGATCTG
65 GAGATAAGACCT-GA--TGCGATCTG
* * * * * * *
1248897 CTCCGCTGTAACCTCAGGGAGACAAGATCTGCGATTCTTCGGTCTGTTCCACTGTAATCTCAGGG
1 CTCCACTGTAACTTCAGAGAGATAAGATCTGCAATTCTTCGGTCTGCTCCACTGTAACCTCAGGG
* *
1248962 AGATAAGACCTGATGTGATCTT
66 AGATAAGACCTGATGCGATCTG
*
1248984 CTCTACTGTAACTTCAGAGAGATAAGATC
1 CTCCACTGTAACTTCAGAGAGATAAGATC
1249013 CTTTAATCCG
Statistics
Matches: 225, Mismatches: 53, Indels: 24
0.75 0.18 0.08
Matches are distributed among these distances:
84 1 0.00
85 27 0.12
86 4 0.02
87 123 0.55
88 6 0.03
89 29 0.13
90 33 0.15
91 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (87 bp):
CTCCACTGTAACTTCAGAGAGATAAGATCTGCAATTCTTCGGTCTGCTCCACTGTAACCTCAGGG
AGATAAGACCTGATGCGATCTG
Found at i:1248900 original size:174 final size:170
Alignment explanation
Indices: 1248678--1249068 Score: 509
Period size: 174 Copynumber: 2.3 Consensus size: 170
1248668 TCTTCGATCT
* ** * ** * *
1248678 GCTCCGCTGTAATCTCGGGGAGATAAGATCT-CTGGCTTCAATCTGCTCCACTGTAACTTCAGGG
1 GCTCCACTGTAATCTCAAGGAGATAGGAT-TACTATCTTCGATCTGCTCCACTGTAACCTCAGGG
* *
1248742 GGATAAGATCTGCAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGAT
65 AGACAAGATCTGCAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGAT
1248807 CTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCC
130 CTACTCTACTGTAACTTCAGAGAGATAAGATCC-----TTTAATCC
* *
1248853 GCTCCACTGTAA-CTTCAGGGAGATAGGATTA-TATCTTCGATCTGCTCCGCTGTAACCTCAGGG
1 GCTCCACTGTAATC-TCAAGGAGATAGGATTACTATCTTCGATCTGCTCCACTGTAACCTCAGGG
* ** * * *
1248916 AGACAAGATCTGCGATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGTGAT
65 AGACAAGATCTGCAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGAT
*
1248981 CTTCTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
130 CTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
* *
1249022 GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCT
1 GCTCCACTGTAATCTCAAGGAGATAGGATTACTATCTTCGATCTGCT
1249069 TCGCTGTTAA
Statistics
Matches: 192, Mismatches: 20, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
169 35 0.18
170 15 0.08
174 118 0.61
175 24 0.12
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (170 bp):
GCTCCACTGTAATCTCAAGGAGATAGGATTACTATCTTCGATCTGCTCCACTGTAACCTCAGGGA
GACAAGATCTGCAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGATC
TACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCC
Found at i:1249006 original size:41 final size:41
Alignment explanation
Indices: 1248718--1249010 Score: 167
Period size: 46 Copynumber: 6.8 Consensus size: 41
1248708 TCTGGCTTCA
* * *
1248718 ATCTGCTCCACTGTAACTTCAGGGGGATAAGATCTGCAATTCTTCG
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGACCTG--A-T-TT-G
* * * **
1248764 GTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGCG
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGACCTGATTTG
* * * *
1248805 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGA-CC-TGA-TTTG
* * * * *
1248849 ATCCGCTCCACTGTAACTTCAGGGAGATAGGA-TTATATCTTCG
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGACCT-GAT-TT-G
* * * * *
1248892 ATCTGCTCCGCTGTAACCTCAGGGAGACAAGATCTGCGATTCTTCG
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGACCT--GA-T-TT-G
* * * *
1248938 GTCTGTTCCACTGTAA-TCTCAGGGAGATAAGACCTGATGTG
1 ATCTGCTCCACTGTAACT-TCAGAGAGATAAGACCTGATTTG
* *
1248979 ATCTTCTCTACTGTAACTTCAGAGAGATAAGA
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGA
1249011 TCCTTTAATC
Statistics
Matches: 194, Mismatches: 42, Indels: 27
0.74 0.16 0.10
Matches are distributed among these distances:
41 58 0.30
42 8 0.04
43 31 0.16
44 32 0.16
45 1 0.01
46 64 0.33
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (41 bp):
ATCTGCTCCACTGTAACTTCAGAGAGATAAGACCTGATTTG
Found at i:1249220 original size:44 final size:44
Alignment explanation
Indices: 1249172--1249412 Score: 185
Period size: 44 Copynumber: 5.5 Consensus size: 44
1249162 TAATGTAGGA
*
1249172 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAAAG
1 AGGCAAGATCTTTTGTCTTCGACCAGCTCCATCACAACCGAAAG
* * * * ** *
1249216 AGGCAAGGT-TTGTGTCTTCGATCTGCTTCGC-TGTCAA-TGCAGAA-
1 AGGCAAGATCTTTTGTCTTCGACCAGC-TC-CATCACAACCG-A-AAG
1249260 AGGCAAGATCTTTTGTCTTCGACCAGCTCCATCACAACCGAAAG
1 AGGCAAGATCTTTTGTCTTCGACCAGCTCCATCACAACCGAAAG
* * * * ** *
1249304 AGGCAAGGT-TTGTGTCTTCGATCTGCTTCGC-TGTCAA-TGCAGAA-
1 AGGCAAGATCTTTTGTCTTCGACCAGC-TC-CATCACAACCG-A-AAG
*
1249348 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAAAG
1 AGGCAAGATCTTTTGTCTTCGACCAGCTCCATCACAACCGAAAG
* *
1249392 AGGCAAGGT-TTGTGTCTTCGA
1 AGGCAAGATCTTTTGTCTTCGA
1249413 TCTGCTTCGC
Statistics
Matches: 148, Mismatches: 33, Indels: 33
0.69 0.15 0.15
Matches are distributed among these distances:
43 45 0.30
44 68 0.46
45 35 0.24
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (44 bp):
AGGCAAGATCTTTTGTCTTCGACCAGCTCCATCACAACCGAAAG
Found at i:1249263 original size:88 final size:88
Alignment explanation
Indices: 1249056--1249448 Score: 589
Period size: 88 Copynumber: 4.5 Consensus size: 88
1249046 AGGATTACTA
* * ** * * *
1249056 TCTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTACT-TCTTTAACTAGCTCCA-CTG
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATC-A
* * *
1249119 CAATCG-ATGGGTGCAAGGCTTTGT-
65 CAACCGAAAGAG-GCAAGG-TTTGTG
* *
1249143 T-TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCAC
1249207 AACCGAAAGAGGCAAGGTTTGTG
66 AACCGAAAGAGGCAAGGTTTGTG
* *
1249230 TCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTTTTGTCTTCGACCAGCTCCATCAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCAC
1249295 AACCGAAAGAGGCAAGGTTTGTG
66 AACCGAAAGAGGCAAGGTTTGTG
*
1249318 TCTTCGATCTGCTTCGCTGTCAATGCAGAAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCAC
1249383 AACCGAAAGAGGCAAGGTTTGTG
66 AACCGAAAGAGGCAAGGTTTGTG
1249406 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTT
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTT
1249449 AACTTCATTG
Statistics
Matches: 285, Mismatches: 16, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
86 43 0.15
87 27 0.09
88 215 0.75
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (88 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCAC
AACCGAAAGAGGCAAGGTTTGTG
Found at i:1249440 original size:44 final size:44
Alignment explanation
Indices: 1249216--1249442 Score: 169
Period size: 44 Copynumber: 5.2 Consensus size: 44
1249206 CAACCGAAAG
*
1249216 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAA
1 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
* * * * ** * * *
1249260 AGGCAAGATCTTTTGTCTTCGACCAGC-TC-CATCACAACCGAAAG-
1 AGGCAAGGT-TTGTGTCTTCGATCTGCTTCGC-TGTCAA-TGCAGGA
*
1249304 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAA
1 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
* * * * * ** * * *
1249348 AGGCAAGATCTTTTGTCTTCAACCAGC-TC-CATCACAACCGAAAG-
1 AGGCAAGGT-TTGTGTCTTCGATCTGCTTCGC-TGTCAA-TGCAGGA
1249392 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
1 AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
1249436 AGGCAAG
1 AGGCAAG
1249443 ATCTTTAACT
Statistics
Matches: 130, Mismatches: 41, Indels: 24
0.67 0.21 0.12
Matches are distributed among these distances:
43 34 0.26
44 63 0.48
45 33 0.25
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (44 bp):
AGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
Found at i:1251607 original size:7 final size:8
Alignment explanation
Indices: 1251582--1251611 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
1251572 CTATTTTGAC
1251582 TTTGATTTT
1 TTTGA-TTT
1251591 TTTGATTT
1 TTTGATTT
1251599 TTTGATTT
1 TTTGATTT
1251607 TTTGA
1 TTTGA
1251612 ATTCATGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (8 bp):
TTTGATTT
Done.