Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, whole genome shotgun sequence
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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 5 of 130
Found at i:1216751 original size:21 final size:17
Alignment explanation
Indices: 1216706--1216756 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
1216696 TTTTTTTAAG
1216706 AATAATAAATAAAAATT
1 AATAATAAATAAAAATT
*
1216723 AATGAATATAATAAAAAAT
1 AAT-AATA-AATAAAAATT
1216742 -ATAAGT-AATAAAAAT
1 AATAA-TAAATAAAAAT
1216757 AAGAAGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 8 0.28
17 5 0.17
18 7 0.24
19 9 0.31
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (17 bp):
AATAATAAATAAAAATT
Found at i:1216941 original size:21 final size:23
Alignment explanation
Indices: 1216916--1216965 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
1216906 TTTTTTCTTC
*
1216916 AAAATTTTAAT-TAA-AATTAAT
1 AAAATTTTAATAAAATAATTAAT
1216937 AAAA--TTAATAAAATAATTAAT
1 AAAATTTTAATAAAATAATTAAT
1216958 AAAATTTT
1 AAAATTTT
1216966 TGAATGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 5 0.21
20 2 0.08
21 15 0.62
23 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAATTTTAATAAAATAATTAAT
Found at i:1217693 original size:3 final size:3
Alignment explanation
Indices: 1217685--1217733 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1217675 AAGGTTAAGG
1217685 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1217733 T
1 T
1217734 ATTGTAATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1219996 original size:69 final size:69
Alignment explanation
Indices: 1219875--1220011 Score: 177
Period size: 69 Copynumber: 2.0 Consensus size: 69
1219865 TTATTCTTTT
* * * * * * * *
1219875 ATAAACGTAATGTTTGTAAATTTTTTTAATCAAAGATTATGATTTTACTTTTATGAACTTAGTGA
1 ATAAACGTAATGATTATAAATTTTTTTAATAAAAAATCATGATTTTACTTTTATAAACATAATGA
1219940 TTGC
66 TTGC
*
1219944 ATAAACGTAATGATTAT-AATTTTTTTAATAAAAAATCATGTTTTTACTTTTTATAAACATAATG
1 ATAAACGTAATGATTATAAATTTTTTTAATAAAAAATCATGATTTTAC-TTTTATAAACATAATG
1220008 ATTG
65 ATTG
1220012 TAAAAGAATT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
68 26 0.45
69 32 0.55
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (69 bp):
ATAAACGTAATGATTATAAATTTTTTTAATAAAAAATCATGATTTTACTTTTATAAACATAATGA
TTGC
Found at i:1220140 original size:21 final size:22
Alignment explanation
Indices: 1220115--1220157 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1220105 CTATATCCAA
1220115 TAAAATATAGTCTTT-ACTTAT
1 TAAAATATAGTCTTTGACTTAT
*
1220136 TAAAATGTAGTCTTTGACTTAT
1 TAAAATATAGTCTTTGACTTAT
1220158 ATTTTTATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (22 bp):
TAAAATATAGTCTTTGACTTAT
Found at i:1221362 original size:7 final size:7
Alignment explanation
Indices: 1221350--1221382 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
1221340 CTAATGTTTA
1221350 AAAAAAG
1 AAAAAAG
1221357 AAAAAAG
1 AAAAAAG
1221364 AAAAAAG
1 AAAAAAG
*
1221371 AAAACAG
1 AAAAAAG
1221378 AAAAA
1 AAAAA
1221383 TTACTAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1221755 original size:30 final size:30
Alignment explanation
Indices: 1221698--1221757 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1221688 TAATTATGTA
** *
1221698 AAAATAAATATTTAAAGGCTCATTTAATTG
1 AAAATAAATATTTAAAAACTCAATTAATTG
*
1221728 AAAATAAATATTTAAAAATTCAATTAATTG
1 AAAATAAATATTTAAAAACTCAATTAATTG
1221758 CAATAAAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.37
Consensus pattern (30 bp):
AAAATAAATATTTAAAAACTCAATTAATTG
Found at i:1222511 original size:108 final size:108
Alignment explanation
Indices: 1222317--1222534 Score: 418
Period size: 108 Copynumber: 2.0 Consensus size: 108
1222307 ACGAACGTGA
1222317 TTGCAGTCGTTACACAAAACAAAAATCTGGGCTGCCTTGTTTACTTTGATATACAAAAACAATAA
1 TTGCAGTCGTTACACAAAACAAAAATCTGGGCTGCCTTGTTTACTTTGATATACAAAAACAATAA
*
1222382 GTTAATCATTGTTGGTTAATCTTAAACCAAACCCCCTTGATTT
66 GTTAATCATTGTTGGTTAATCTAAAACCAAACCCCCTTGATTT
*
1222425 TTGCTGTCGTTACACAAAACAAAAATCTGGGCTGCCTTGTTTACTTTGATATACAAAAACAATAA
1 TTGCAGTCGTTACACAAAACAAAAATCTGGGCTGCCTTGTTTACTTTGATATACAAAAACAATAA
1222490 GTTAATCATTGTTGGTTAATCTAAAACCAAACCCCCTTGATTT
66 GTTAATCATTGTTGGTTAATCTAAAACCAAACCCCCTTGATTT
1222533 TT
1 TT
1222535 ACAATTCCAT
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (108 bp):
TTGCAGTCGTTACACAAAACAAAAATCTGGGCTGCCTTGTTTACTTTGATATACAAAAACAATAA
GTTAATCATTGTTGGTTAATCTAAAACCAAACCCCCTTGATTT
Found at i:1223948 original size:22 final size:23
Alignment explanation
Indices: 1223923--1223973 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 23
1223913 TGTATTTGTG
*
1223923 TTTATTTGATAGTTA-AA-TTTTT
1 TTTATTTAATA-TTATAAGTTTTT
1223945 TTTATTTAATATTATAAGTTTTT
1 TTTATTTAATATTATAAGTTTTT
1223968 TGTTAT
1 T-TTAT
1223974 ATTTGTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 3 0.12
22 12 0.48
23 6 0.24
24 4 0.16
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (23 bp):
TTTATTTAATATTATAAGTTTTT
Found at i:1224209 original size:20 final size:21
Alignment explanation
Indices: 1224184--1224228 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1224174 ATCCATATCC
*
1224184 TTATATAT-AATAA-ATAGATT
1 TTATAT-TGAATAATATAAATT
1224204 TTATATTGAATAATATAAATT
1 TTATATTGAATAATATAAATT
1224225 TTAT
1 TTAT
1224229 TTTAAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.50
21 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
TTATATTGAATAATATAAATT
Found at i:1227272 original size:29 final size:29
Alignment explanation
Indices: 1227230--1227288 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1227220 TGTCAAATTT
1227230 GTATAACGCGTAATGGCTATACTTTCCAA
1 GTATAACGCGTAATGGCTATACTTTCCAA
* *
1227259 GTATAGCGCGTAATGGCTATACTTTTCAA
1 GTATAACGCGTAATGGCTATACTTTCCAA
1227288 G
1 G
1227289 AAAAATGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (29 bp):
GTATAACGCGTAATGGCTATACTTTCCAA
Found at i:1233845 original size:21 final size:20
Alignment explanation
Indices: 1233811--1233849 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1233801 TACACAAAAA
1233811 TAATAATAATAAAAATTAATC
1 TAATAATAA-AAAAATTAATC
*
1233832 TAATACTAAAAAAATTAA
1 TAATAATAAAAAAATTAA
1233850 CAATACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
TAATAATAAAAAAATTAATC
Found at i:1237675 original size:18 final size:19
Alignment explanation
Indices: 1237642--1237677 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1237632 AGAATTAACG
1237642 ATAGGAAAGCAGAACAAAC
1 ATAGGAAAGCAGAACAAAC
*
1237661 ATAGGCAAG-AGAACAAA
1 ATAGGAAAGCAGAACAAA
1237678 AATAAACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.14, G:0.22, T:0.06
Consensus pattern (19 bp):
ATAGGAAAGCAGAACAAAC
Found at i:1239448 original size:52 final size:50
Alignment explanation
Indices: 1239366--1239515 Score: 151
Period size: 52 Copynumber: 2.9 Consensus size: 50
1239356 AGAAGATTTG
* * *
1239366 TAAAAGAAA-AATTCTAAGAGAAAGATGATTCTTAATAGGGAAGTTTCACTT
1 TAAAAAAAAGAATTCTAAAAGAAAG-GGATTCTTAATAGGGAAGTTTCAC-T
* *
1239417 TAAAAAAAAGAATTCTAAAATGAAAGGGATTCTTAATAGGCAAGTTTGACT
1 TAAAAAAAAGAATTCTAAAA-GAAAGGGATTCTTAATAGGGAAGTTTCACT
** * *
1239468 TACACGAAAAGAATTTTAAGAAGAGAGGGATTCTTAAT-GGGCAAGTTT
1 TA-AAAAAAAGAATTCTAA-AAGAAAGGGATTCTTAATAGGG-AAGTTT
1239516 GTATGGTTAT
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
51 13 0.15
52 64 0.76
53 7 0.08
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (50 bp):
TAAAAAAAAGAATTCTAAAAGAAAGGGATTCTTAATAGGGAAGTTTCACT
Found at i:1243619 original size:21 final size:20
Alignment explanation
Indices: 1243593--1243636 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
1243583 TATAAATTTA
1243593 TTTTTAA-AATATGTATTAAAT
1 TTTTTAATAATATG-A-TAAAT
*
1243614 TTTTTAATAATTTGATAAAT
1 TTTTTAATAATATGATAAAT
1243634 TTT
1 TTT
1243637 AATTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 8 0.38
22 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
TTTTTAATAATATGATAAAT
Found at i:1243851 original size:26 final size:24
Alignment explanation
Indices: 1243814--1243861 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
1243804 ATAATCATGC
* *
1243814 AAAAAAATAATAATTATAGCATTA
1 AAAAAAATAATAAATAAAGCATTA
1243838 AAAATAAATAAATAAATAAAGCAT
1 AAAA-AAAT-AATAAATAAAGCAT
1243862 CATTTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 4 0.20
26 12 0.60
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (24 bp):
AAAAAAATAATAAATAAAGCATTA
Found at i:1243900 original size:3 final size:3
Alignment explanation
Indices: 1243892--1243930 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1243882 CTTCATTCCT
1243892 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1243931 ATAAATAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1245068 original size:24 final size:24
Alignment explanation
Indices: 1245016--1245070 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1245006 GTTTCCTTTT
1245016 TTTTTTTTTCATGAAACTTTTAAC
1 TTTTTTTTTCATGAAACTTTTAAC
*
1245040 CTTTTTTTTCATGAAACTTTTGAA-
1 TTTTTTTTTCATGAAACTTTT-AAC
1245064 TTTTTTT
1 TTTTTTT
1245071 AACTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.22, C:0.11, G:0.05, T:0.62
Consensus pattern (24 bp):
TTTTTTTTTCATGAAACTTTTAAC
Found at i:1245881 original size:17 final size:18
Alignment explanation
Indices: 1245861--1245903 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
1245851 CTTTTTCCTC
1245861 TTTTTTTTC-TTTTTGCA
1 TTTTTTTTCATTTTTGCA
*
1245878 -TTTTTTTCATTTTTTCA
1 TTTTTTTTCATTTTTGCA
1245895 TTTTATTTT
1 TTTT-TTTT
1245904 TGCTTTGCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 8 0.36
17 7 0.32
18 3 0.14
19 4 0.18
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTTTTCATTTTTGCA
Found at i:1246220 original size:12 final size:12
Alignment explanation
Indices: 1246187--1246233 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
1246177 GCCCAATTAA
*
1246187 TTTCTTTTTTTT
1 TTTCTTCTTTTT
*
1246199 ATTTTTTCTTTTT
1 -TTTCTTCTTTTT
1246212 CTTTC-TCTTTTT
1 -TTTCTTCTTTTT
1246224 TTTCTTCTTT
1 TTTCTTCTTT
1246234 GCTTTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 4 0.14
12 12 0.41
13 13 0.45
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTCTTCTTTTT
Found at i:1246231 original size:18 final size:18
Alignment explanation
Indices: 1246200--1246244 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
1246190 CTTTTTTTTA
1246200 TTTTTTCTTT-TTCTTT-C
1 TTTTTT-TTTCTTCTTTGC
1246217 TCTTTTTTTTCTTCTTTGC
1 T-TTTTTTTTCTTCTTTGC
1246236 TTTTTTTTT
1 TTTTTTTTT
1246245 TTTTACACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.16
18 19 0.76
19 2 0.08
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (18 bp):
TTTTTTTTTCTTCTTTGC
Found at i:1249024 original size:12 final size:12
Alignment explanation
Indices: 1249009--1249033 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1248999 AATAACATTA
1249009 ATTCCTTAATTC
1 ATTCCTTAATTC
1249021 ATTCCTTAATTC
1 ATTCCTTAATTC
1249033 A
1 A
1249034 ATTAGAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTCCTTAATTC
Found at i:1250851 original size:2 final size:2
Alignment explanation
Indices: 1250844--1250890 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
1250834 TCCCAACTCA
* * *
1250844 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AT AT AC AC AT AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1250886 AC AC A
1 AC AC A
1250891 TAGATATAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.43, G:0.00, T:0.06
Consensus pattern (2 bp):
AC
Found at i:1251566 original size:29 final size:31
Alignment explanation
Indices: 1251520--1251577 Score: 77
Period size: 29 Copynumber: 1.9 Consensus size: 31
1251510 GCAATGTGAA
1251520 TTTATTAAATTAAAATAT-T-AAATAATATT
1 TTTATTAAATTAAAATATATAAAATAATATT
*
1251549 TTTATT-AATATAATATATATAAAATAATA
1 TTTATTAAAT-TAAAATATATAAAATAATA
1251578 AATAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 3 0.12
29 13 0.52
30 1 0.04
31 8 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
TTTATTAAATTAAAATATATAAAATAATATT
Found at i:1251800 original size:19 final size:19
Alignment explanation
Indices: 1251759--1251816 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1251749 ATATTTAATA
1251759 AAAATAATTAAATAAAAACATT
1 AAAATAATT-AA-AAAAA-ATT
1251781 AAAATAATTAAAAAAAATT
1 AAAATAATTAAAAAAAATT
***
1251800 ATGTTAATTAAAAAAAA
1 AAAATAATTAAAAAAAA
1251817 AGGGGGGCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 17 0.52
20 5 0.15
21 2 0.06
22 9 0.27
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATAATTAAAAAAAATT
Found at i:1252338 original size:22 final size:21
Alignment explanation
Indices: 1252313--1252353 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1252303 TCTTATATAT
*
1252313 ATTTAAAAATATGAAAATTTTA
1 ATTTAAAAATA-AAAAATTTTA
*
1252335 ATTTTAAAATAAAAAATTT
1 ATTTAAAAATAAAAAATTT
1252354 AATATCAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
ATTTAAAAATAAAAAATTTTA
Found at i:1254339 original size:21 final size:22
Alignment explanation
Indices: 1254305--1254347 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1254295 AAAAAATTAT
*
1254305 ATTATATATAAAACATTAAAAA
1 ATTATATATAAAACATGAAAAA
*
1254327 ATTATTTA-AAAACATGAAAAA
1 ATTATATATAAAACATGAAAAA
1254348 GGTTAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (22 bp):
ATTATATATAAAACATGAAAAA
Found at i:1254423 original size:15 final size:15
Alignment explanation
Indices: 1254403--1254435 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1254393 TTAATTTAAA
1254403 AATATAAA-AATTTAT
1 AATATAAATAA-TTAT
1254418 AATATAAATAATTAT
1 AATATAAATAATTAT
1254433 AAT
1 AAT
1254436 TTTAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATATAAATAATTAT
Found at i:1262104 original size:19 final size:22
Alignment explanation
Indices: 1262066--1262105 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
1262056 TTATAGTTAA
1262066 TATATTATTAGTATATAAATTT
1 TATATTATTAGTATATAAATTT
1262088 TATA-TATT-GTA-ATAAATT
1 TATATTATTAGTATATAAATT
1262106 AAATGATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 4 0.22
22 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (22 bp):
TATATTATTAGTATATAAATTT
Found at i:1263061 original size:46 final size:47
Alignment explanation
Indices: 1262999--1263087 Score: 162
Period size: 47 Copynumber: 1.9 Consensus size: 47
1262989 CAAAACTAAT
1262999 TAATTGAATTAATTT-AATATTTTTTAATAGTGTGAAGTAAGAAAAC
1 TAATTGAATTAATTTAAATATTTTTTAATAGTGTGAAGTAAGAAAAC
*
1263045 TAATTGAATTCATTTAAATATTTTTTAATAGTGTGAAGTAAGA
1 TAATTGAATTAATTTAAATATTTTTTAATAGTGTGAAGTAAGA
1263088 TTGATTTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
46 14 0.34
47 27 0.66
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.43
Consensus pattern (47 bp):
TAATTGAATTAATTTAAATATTTTTTAATAGTGTGAAGTAAGAAAAC
Found at i:1263121 original size:2 final size:2
Alignment explanation
Indices: 1263114--1263141 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1263104 TTTGAATCTC
1263114 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
1263142 GGATATTATT
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:1264788 original size:16 final size:16
Alignment explanation
Indices: 1264767--1264816 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
1264757 TCGAAGTTTA
1264767 CAACAATAAGAATATG
1 CAACAATAAGAATATG
* *
1264783 CAAC-A-AAG--TTTA
1 CAACAATAAGAATATG
1264795 CAACAATAAGAATATG
1 CAACAATAAGAATATG
1264811 CAACAA
1 CAACAA
1264817 AATTTACAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
12 6 0.23
13 1 0.04
14 6 0.23
15 1 0.04
16 12 0.46
ACGTcount: A:0.56, C:0.16, G:0.10, T:0.18
Consensus pattern (16 bp):
CAACAATAAGAATATG
Found at i:1264791 original size:28 final size:28
Alignment explanation
Indices: 1264729--1264828 Score: 129
Period size: 28 Copynumber: 3.7 Consensus size: 28
1264719 TAGCGGAGAC
1264729 TGCAACAAAGTTTACAAC---AAG-ATA
1 TGCAACAAAGTTTACAACAATAAGAATA
* *
1264753 TAGC-TCGAAGTTTACAACAATAAGAATA
1 T-GCAACAAAGTTTACAACAATAAGAATA
1264781 TGCAACAAAGTTTACAACAATAAGAATA
1 TGCAACAAAGTTTACAACAATAAGAATA
*
1264809 TGCAACAAAATTTACAACAA
1 TGCAACAAAGTTTACAACAA
1264829 AGTTTACAAC
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
24 13 0.20
25 2 0.03
27 5 0.08
28 45 0.69
ACGTcount: A:0.51, C:0.16, G:0.11, T:0.22
Consensus pattern (28 bp):
TGCAACAAAGTTTACAACAATAAGAATA
Found at i:1264800 original size:12 final size:12
Alignment explanation
Indices: 1264783--1264840 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 12
1264773 TAAGAATATG
1264783 CAACAAAGTTTA
1 CAACAAAGTTTA
* *
1264795 CAACAATAAGAATATG
1 CAAC-A-AAG--TTTA
*
1264811 CAACAAAATTTA
1 CAACAAAGTTTA
1264823 CAACAAAGTTTA
1 CAACAAAGTTTA
1264835 CAACAA
1 CAACAA
1264841 GAAAGTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
12 23 0.64
13 1 0.03
14 5 0.14
15 1 0.03
16 6 0.17
ACGTcount: A:0.55, C:0.17, G:0.07, T:0.21
Consensus pattern (12 bp):
CAACAAAGTTTA
Found at i:1276013 original size:96 final size:96
Alignment explanation
Indices: 1275849--1276037 Score: 333
Period size: 96 Copynumber: 2.0 Consensus size: 96
1275839 AAGTTGTGTG
*
1275849 TGAAACTTGATAAACATTAATTGACCAAGAAATCAATTAATGTTGTATGATTTAGTAAGTTGCCT
1 TGAAACTTGATAAACATTAATTGACCAAGAAATCAATTAATGTTGTATGATTTAGTAAGTTCCCT
1275914 TGCATTACTCTTCTTTGTTTAAATCTGAAAA
66 TGCATTACTCTTCTTTGTTTAAATCTGAAAA
* * *
1275945 TGAAACTTGGTATACCTTAATTGACCAAGAAATCAATTAATGTTGTATGATTTAGTAAGTTCCCT
1 TGAAACTTGATAAACATTAATTGACCAAGAAATCAATTAATGTTGTATGATTTAGTAAGTTCCCT
*
1276010 TGCATTACTGTTCTTTGTTTAAATCTGA
66 TGCATTACTCTTCTTTGTTTAAATCTGA
1276038 TATAAGGAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 88 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (96 bp):
TGAAACTTGATAAACATTAATTGACCAAGAAATCAATTAATGTTGTATGATTTAGTAAGTTCCCT
TGCATTACTCTTCTTTGTTTAAATCTGAAAA
Found at i:1299940 original size:28 final size:28
Alignment explanation
Indices: 1299898--1299956 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
1299888 TAGTCTTATG
*
1299898 CTCTTGTTTTCAATGGTTTAGCTTGTGA
1 CTCTTGTTTTAAATGGTTTAGCTTGTGA
1299926 CTCTTGTTTTAAATGGTTTAGCTTGTGA
1 CTCTTGTTTTAAATGGTTTAGCTTGTGA
1299954 CTC
1 CTC
1299957 GTAAACATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.49
Consensus pattern (28 bp):
CTCTTGTTTTAAATGGTTTAGCTTGTGA
Found at i:1317853 original size:25 final size:25
Alignment explanation
Indices: 1317802--1317853 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1317792 GTTTGGTGAG
* *
1317802 ATTTTATTTGAAAATCATTTATAAA
1 ATTTTATTTGAAAATAATGTATAAA
*
1317827 ATTTTATTTTGAAAA-AATGTATTAA
1 ATTTTA-TTTGAAAATAATGTATAAA
1317852 AT
1 AT
1317854 CTTTCAATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (25 bp):
ATTTTATTTGAAAATAATGTATAAA
Found at i:1318121 original size:21 final size:21
Alignment explanation
Indices: 1318095--1318135 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1318085 TATTATGCAA
1318095 ATAATAATATAATACCATGCC
1 ATAATAATATAATACCATGCC
* *
1318116 ATAATAATATGATAGCATGC
1 ATAATAATATAATACCATGC
1318136 AATTAATATA
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:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (21 bp):
ATAATAATATAATACCATGCC
Found at i:1318155 original size:21 final size:21
Alignment explanation
Indices: 1318131--1318184 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1318121 AATATGATAG
* *
1318131 CATGCAATTAATATAAACTAT
1 CATGCAATTAAGATAAAATAT
*
1318152 CATGTAATTAAGATAAAATAT
1 CATGCAATTAAGATAAAATAT
*
1318173 CATACAAATTAA
1 CATGC-AATTAA
1318185 CTAATAATCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 21 0.78
22 6 0.22
ACGTcount: A:0.52, C:0.11, G:0.06, T:0.31
Consensus pattern (21 bp):
CATGCAATTAAGATAAAATAT
Found at i:1318370 original size:18 final size:17
Alignment explanation
Indices: 1318349--1318383 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1318339 AATAGAGAAA
*
1318349 CAAAAAATAAAATAAAAC
1 CAAAAAA-AAAAAAAAAC
1318367 CAAAAAAAAAAAAAAAC
1 CAAAAAAAAAAAAAAAC
1318384 TTGCGATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.83, C:0.11, G:0.00, T:0.06
Consensus pattern (17 bp):
CAAAAAAAAAAAAAAAC
Found at i:1319391 original size:20 final size:20
Alignment explanation
Indices: 1319366--1319403 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1319356 ACAAGAATTT
1319366 AAAGTTTCGTAAA-GATTTTG
1 AAAGTTT-GTAAATGATTTTG
1319386 AAAGTTTGTAAATGATTT
1 AAAGTTTGTAAATGATTT
1319404 AAGATTCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (20 bp):
AAAGTTTGTAAATGATTTTG
Found at i:1319594 original size:35 final size:36
Alignment explanation
Indices: 1319521--1319594 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 36
1319511 TTCATAAGAA
* *
1319521 TTTTCAAGTTTCACAAATGTTCCAAATTCGCAAAGG
1 TTTTCAAGTTTCACAAAGGTTCCAAATTCACAAAGG
* * * *
1319557 TTTT-AAGTTTCACAGAGGTTCTAGATTCACAAGGG
1 TTTTCAAGTTTCACAAAGGTTCCAAATTCACAAAGG
1319592 TTT
1 TTT
1319595 CAAATTCGCA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 28 0.88
36 4 0.12
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (36 bp):
TTTTCAAGTTTCACAAAGGTTCCAAATTCACAAAGG
Found at i:1319601 original size:17 final size:17
Alignment explanation
Indices: 1319481--1319645 Score: 89
Period size: 17 Copynumber: 9.5 Consensus size: 17
1319471 TCAAGCTTTT
* *
1319481 CAAAGATTTTAAATTCA
1 CAAAGGTTTCAAATTCA
* *
1319498 TAAAGGTTTCAGATTCA
1 CAAAGGTTTCAAATTCA
* ** *
1319515 TAAGAATTTTCAAGTTTCA
1 CAA-AGGTTTCAA-ATTCA
* * *
1319534 CAAATGTTCCAAATTCG
1 CAAAGGTTTCAAATTCA
* *
1319551 CAAAGGTTTTAAGTTTCA
1 CAAAGGTTTCAA-ATTCA
* *
1319569 CAGAGG-TTCTAGATTCA
1 CAAAGGTTTC-AAATTCA
* *
1319586 CAAGGGTTTCAAATTCG
1 CAAAGGTTTCAAATTCA
* *
1319603 CAAAGATTTTAAATTTCA
1 CAAAGGTTTCAAA-TTCA
* *
1319621 TAGAGGTTTCAAATTCA
1 CAAAGGTTTCAAATTCA
1319638 CAAAGGTT
1 CAAAGGTT
1319646 CCAGATTTGC
Statistics
Matches: 105, Mismatches: 37, Indels: 12
0.68 0.24 0.08
Matches are distributed among these distances:
17 63 0.60
18 36 0.34
19 6 0.06
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (17 bp):
CAAAGGTTTCAAATTCA
Found at i:1319658 original size:17 final size:17
Alignment explanation
Indices: 1319624--1319709 Score: 55
Period size: 17 Copynumber: 5.0 Consensus size: 17
1319614 AATTTCATAG
* **
1319624 AGGTTTCAAATTCACAA
1 AGGTTCCAAATTTGCAA
*
1319641 AGGTTCCAGATTTGCAA
1 AGGTTCCAAATTTGCAA
** * *
1319658 ATATTCCAAAATTCGAAA
1 AGGTTCC-AAATTTGCAA
*
1319676 AGGTTTCAAATTTGCAA
1 AGGTTCCAAATTTGCAA
* * *
1319693 AAGTTTCAGATTTGCAA
1 AGGTTCCAAATTTGCAA
1319710 TAATTCAAAA
Statistics
Matches: 52, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
17 41 0.79
18 11 0.21
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (17 bp):
AGGTTCCAAATTTGCAA
Found at i:1319658 original size:52 final size:51
Alignment explanation
Indices: 1319530--1319687 Score: 156
Period size: 52 Copynumber: 3.0 Consensus size: 51
1319520 ATTTTCAAGT
* * * *
1319530 TTCACAAATGTTCCAAATTCGCAAAGGTTTTAAGTTTCACAGAGG-TTCTAGA
1 TTCACAAAGGTTCCAAATTCGCAAAGATTTTAAATTTCA-AGAGGTTTC-AAA
* *
1319582 TTCACAAGGGTTTCAAATTCGCAAAGATTTTAAATTTCATAGAGGTTTCAAA
1 TTCACAAAGGTTCCAAATTCGCAAAGATTTTAAATTTCA-AGAGGTTTCAAA
* * * ** * *
1319634 TTCACAAAGGTTCCAGATTTGCAAATATTCCAAAATTCGAAAAGGTTTCAAA
1 TTCACAAAGGTTCCAAATTCGCAAAGATTTTAAATTTC-AAGAGGTTTCAAA
1319686 TT
1 TT
1319688 TGCAAAAGTT
Statistics
Matches: 88, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
52 84 0.95
53 4 0.05
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (51 bp):
TTCACAAAGGTTCCAAATTCGCAAAGATTTTAAATTTCAAGAGGTTTCAAA
Found at i:1319760 original size:17 final size:17
Alignment explanation
Indices: 1319724--1319762 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1319714 TCAAAATCAG
**
1319724 AAGAATAGAAGATTTGC
1 AAGAATAGAAGATTCAC
*
1319741 AAGAATTGAAGATTCAC
1 AAGAATAGAAGATTCAC
1319758 AAGAA
1 AAGAA
1319763 ATACATTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.08, G:0.21, T:0.21
Consensus pattern (17 bp):
AAGAATAGAAGATTCAC
Found at i:1319813 original size:17 final size:17
Alignment explanation
Indices: 1319774--1319848 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 17
1319764 TACATTTTCA
1319774 TAAGAATTTCTAAATTCG
1 TAAGAATTTC-AAATTCG
* * *
1319792 CAAGAGTTTCAAATTCT
1 TAAGAATTTCAAATTCG
*
1319809 TAAGAATTTCAATTTCG
1 TAAGAATTTCAAATTCG
* **
1319826 TAAAAATTTCAGGTTCG
1 TAAGAATTTCAAATTCG
1319843 TAAGAA
1 TAAGAA
1319849 ATCAAATATT
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
17 38 0.83
18 8 0.17
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (17 bp):
TAAGAATTTCAAATTCG
Found at i:1319897 original size:81 final size:81
Alignment explanation
Indices: 1319810--1320043 Score: 290
Period size: 81 Copynumber: 2.9 Consensus size: 81
1319800 TCAAATTCTT
* * * **
1319810 AAGAATTTCAATTTCGTAAAAATTTCAGGTTCGTAAGAAATCAAATATTTGAATTTCAAATTTTC
1 AAGAATTTCAGTTTCGTAAGAATTTCAGGTTCATAAGAAATCAAATATTTGAATTTCAAATTCGC
*
1319875 AATAACTCA-AATAATC
66 AAGAACTCAGAATAA-C
* * * ** *
1319891 AAGAATTTTAGTTTGGCAAGAATTTCAGGTTCATAAGAAATCAAATATTCAAATTTCAGATTCGC
1 AAGAATTTCAGTTTCGTAAGAATTTCAGGTTCATAAGAAATCAAATATTTGAATTTCAAATTCGC
* *
1319956 AAGAACTCAGATTCAC
66 AAGAACTCAGAATAAC
* * * *
1319972 AAGAATTTCAGTTTCGTAAGAATTTCAGGTTTACAAGAAATCAAATATTTGAATTTCATATTCAC
1 AAGAATTTCAGTTTCGTAAGAATTTCAGGTTCATAAGAAATCAAATATTTGAATTTCAAATTCGC
1320037 AAGAACT
66 AAGAACT
1320044 TTAAATTCTA
Statistics
Matches: 129, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
81 126 0.98
82 3 0.02
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (81 bp):
AAGAATTTCAGTTTCGTAAGAATTTCAGGTTCATAAGAAATCAAATATTTGAATTTCAAATTCGC
AAGAACTCAGAATAAC
Found at i:1319967 original size:16 final size:16
Alignment explanation
Indices: 1319946--1319976 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1319936 TATTCAAATT
*
1319946 TCAGATTCGCAAGAAC
1 TCAGATTCACAAGAAC
1319962 TCAGATTCACAAGAA
1 TCAGATTCACAAGAA
1319977 TTTCAGTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (16 bp):
TCAGATTCACAAGAAC
Found at i:1320134 original size:17 final size:17
Alignment explanation
Indices: 1320105--1320165 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
1320095 TAAGTTTCGA
*
1320105 AAGAACTTCAGGTTCAT
1 AAGAACTTTAGGTTCAT
* *
1320122 AACAACTTTAGGTT-TT
1 AAGAACTTTAGGTTCAT
*
1320138 CAAGAATTTTAGGTTCAT
1 -AAGAACTTTAGGTTCAT
1320156 AAGAACTTTA
1 AAGAACTTTA
1320166 AATTAGCAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
16 1 0.03
17 33 0.94
18 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (17 bp):
AAGAACTTTAGGTTCAT
Found at i:1320250 original size:27 final size:27
Alignment explanation
Indices: 1320220--1320277 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
1320210 AAGTTTCAAA
* *
1320220 AATTCTTAAAAGATTT-AGGTTCATAAG
1 AATTCATAAAAG-TTTCAGATTCATAAG
* *
1320247 AATTCATAAGAGTTTCTGATTCATAAG
1 AATTCATAAAAGTTTCAGATTCATAAG
1320274 AATT
1 AATT
1320278 GGTAGAGTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38
Consensus pattern (27 bp):
AATTCATAAAAGTTTCAGATTCATAAG
Found at i:1320610 original size:21 final size:22
Alignment explanation
Indices: 1320595--1320666 Score: 74
Period size: 24 Copynumber: 3.2 Consensus size: 22
1320585 TATTCCTTCA
1320595 AAAAATTT-AAAAATTCACATC
1 AAAAATTTCAAAAATTCACATC
* *
1320616 CAAAATTTCAAAAATTCACATTTG
1 AAAAATTTCAAAAATTCACA--TC
* *
1320640 AAAAATTTTAGAAATTCACATC
1 AAAAATTTCAAAAATTCACATC
*
1320662 TAAAA
1 AAAAA
1320667 GTTAAAAGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
21 7 0.17
22 16 0.39
24 18 0.44
ACGTcount: A:0.53, C:0.14, G:0.03, T:0.31
Consensus pattern (22 bp):
AAAAATTTCAAAAATTCACATC
Found at i:1320628 original size:22 final size:21
Alignment explanation
Indices: 1320564--1320673 Score: 78
Period size: 22 Copynumber: 5.0 Consensus size: 21
1320554 GTTTTGGGGT
*
1320564 TTCACATCCAAAAGTTAAAGATA
1 TTCACATCCAAAATTTAAA-A-A
* *
1320587 TTC-CTTCAAAAAATTTAAAAA
1 TTCACATC-CAAAATTTAAAAA
1320608 TTCACATCCAAAATTTCAAAAA
1 TTCACATCCAAAATTT-AAAAA
** *
1320630 TTCACATTTGAAAAATTTTAGAAA
1 TTCACA--TCCAAAA-TTTAAAAA
* *
1320654 TTCACATCTAAAAGTTAAAA
1 TTCACATCCAAAATTTAAAA
1320674 GATTTTTATT
Statistics
Matches: 69, Mismatches: 12, Indels: 14
0.73 0.13 0.15
Matches are distributed among these distances:
21 16 0.23
22 23 0.33
23 12 0.17
24 15 0.22
25 3 0.04
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (21 bp):
TTCACATCCAAAATTTAAAAA
Found at i:1320670 original size:90 final size:88
Alignment explanation
Indices: 1320564--1320808 Score: 235
Period size: 91 Copynumber: 2.7 Consensus size: 88
1320554 GTTTTGGGGT
*
1320564 TTCACATCCAAAAGTTAAAGATATTCCTTCAAAAAATTTAAAAATTCACATCCAAAATTTCAAAA
1 TTCACATCCAAAAGTTAAAGATATTCCTTCAAAAAATTTAAAGATTCACATCCAAAATTTCAAAA
* * *
1320629 ATTCACATTTGAAAAATTTTAGAAA
66 ATTCA-AATTCAAAAA-ATTAGAAA
* * ** * *
1320654 TTCACATCTAAAAGTTAAAAGATTTTTATTCAAAAAATTTAAGGATTCA-ATTACAAAGATTTCA
1 TTCACATCCAAAAGTT-AAAGATATTCCTTCAAAAAATTTAAAGATTCACA-TCCAAA-ATTTCA
* *
1320718 AATATTTAAATTCAAAAAATTAGAAA
63 AAAATTCAAATTCAAAAAATTAGAAA
* * * * * *
1320744 TTCACATCCAAAGATTTCAA-ATATTCACATTCGAAATA-TTAGAGATTCACATCCAAAGTTTCA
1 TTCACATCCAAA-AGTTAAAGATATTC-C-TTCAAAAAATTTAAAGATTCACATCCAAAATTTCA
1320807 AA
63 AA
1320809 TGTATTTTTT
Statistics
Matches: 124, Mismatches: 24, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
89 11 0.09
90 50 0.40
91 51 0.41
92 12 0.10
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.32
Consensus pattern (88 bp):
TTCACATCCAAAAGTTAAAGATATTCCTTCAAAAAATTTAAAGATTCACATCCAAAATTTCAAAA
ATTCAAATTCAAAAAATTAGAAA
Found at i:1320690 original size:46 final size:45
Alignment explanation
Indices: 1320564--1320800 Score: 164
Period size: 45 Copynumber: 5.3 Consensus size: 45
1320554 GTTTTGGGGT
* *
1320564 TTCACATCCAAAAGTT-AAAGATATT-CCTTCAAAAAATTTAAAAA
1 TTCACATCCAAAAGTTAAAAGAT-TTACATTCAAAAAATTTAGAAA
* * * *
1320608 TTCACATCCAAAATTTCAAAA-ATTCACATTTGAAAAATTTTAGAAA
1 TTCACATCCAAAAGTT-AAAAGATTTACA-TTCAAAAAATTTAGAAA
* ** *
1320654 TTCACATCTAAAAGTTAAAAGATTTTTATTCAAAAAATTTA-AGGA
1 TTCACATCCAAAAGTTAAAAGATTTACATTCAAAAAATTTAGA-AA
* * * * *
1320699 TTCA-ATTACAAAGATTTCAAATATTTAAATTCAAAAAA-TTAGAAA
1 TTCACA-TCCAAA-AGTTAAAAGATTTACATTCAAAAAATTTAGAAA
* * * * * * *
1320744 TTCACATCCAAAGATTTCAAATATTCACATTCGAAATA-TTAGAGA
1 TTCACATCCAAA-AGTTAAAAGATTTACATTCAAAAAATTTAGAAA
1320789 TTCACATCCAAA
1 TTCACATCCAAA
1320801 GTTTCAAATG
Statistics
Matches: 155, Mismatches: 28, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
44 18 0.12
45 80 0.52
46 57 0.37
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (45 bp):
TTCACATCCAAAAGTTAAAAGATTTACATTCAAAAAATTTAGAAA
Found at i:1320755 original size:22 final size:22
Alignment explanation
Indices: 1320730--1320800 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
1320720 TATTTAAATT
1320730 CAAAAAATTAGAAATTCACATC
1 CAAAAAATTAGAAATTCACATC
* * *
1320752 CAAAGATTTCA-AATATTCACATT
1 CAAAAAATT-AGAA-ATTCACATC
* * *
1320775 CGAAATATTAGAGATTCACATC
1 CAAAAAATTAGAAATTCACATC
1320797 CAAA
1 CAAA
1320801 GTTTCAAATG
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
22 21 0.58
23 15 0.42
ACGTcount: A:0.48, C:0.18, G:0.07, T:0.27
Consensus pattern (22 bp):
CAAAAAATTAGAAATTCACATC
Found at i:1320756 original size:45 final size:45
Alignment explanation
Indices: 1320591--1320809 Score: 178
Period size: 45 Copynumber: 4.8 Consensus size: 45
1320581 AAGATATTCC
* * *
1320591 TTCAAAAAATTTAAAAATTCACATCCAAA-ATTTCAAAAATTCACAT
1 TTCAAAAAA-TTAGAAATTCACATCCAAAGATTTCAAATATTCA-AA
* * * * * * ***
1320637 TTGAAAAATTTTAGAAATTCACATCTAAA-AGTTAAAAGATTTTTA
1 TTCAAAAA-ATTAGAAATTCACATCCAAAGATTTCAAATATTCAAA
* * *
1320682 TTCAAAAAATTTA-AGGATTCA-ATTACAAAGATTTCAAATATTTAAA
1 TTCAAAAAA-TTAGA-AATTCACA-TCCAAAGATTTCAAATATTCAAA
*
1320728 TTCAAAAAATTAGAAATTCACATCCAAAGATTTCAAATATTCACA
1 TTCAAAAAATTAGAAATTCACATCCAAAGATTTCAAATATTCAAA
* * *
1320773 TTCGAAATATTAGAGATTCACATCCAAAG-TTTCAAAT
1 TTCAAAAAATTAGAAATTCACATCCAAAGATTTCAAAT
1320810 GTATTTTTTC
Statistics
Matches: 138, Mismatches: 28, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
44 10 0.07
45 73 0.53
46 55 0.40
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (45 bp):
TTCAAAAAATTAGAAATTCACATCCAAAGATTTCAAATATTCAAA
Found at i:1321056 original size:23 final size:23
Alignment explanation
Indices: 1321009--1321065 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
1320999 ATTCAATGAT
1321009 TCAAATGTCAAAATTTTGCTCCAA
1 TCAAATGTC-AAATTTTGCTCCAA
*
1321033 TCAAA-GTCAAATTTTGCATGCAA
1 TCAAATGTCAAATTTTGC-TCCAA
1321056 T-AAATGTCAA
1 TCAAATGTCAA
1321066 TGCAAATGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 12 0.40
23 13 0.43
24 5 0.17
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (23 bp):
TCAAATGTCAAATTTTGCTCCAA
Found at i:1325821 original size:21 final size:22
Alignment explanation
Indices: 1325797--1325846 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
1325787 GATATCAGGC
*
1325797 AATTAATATAAACTATCATAT-
1 AATTAATATAAAATATCATATA
*
1325818 AATTAAGATAAAATATCATATA
1 AATTAATATAAAATATCATATA
1325840 AATTAAT
1 AATTAAT
1325847 TAATAATCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (22 bp):
AATTAATATAAAATATCATATA
Found at i:1325920 original size:24 final size:25
Alignment explanation
Indices: 1325880--1325934 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
1325870 ACACAAACAA
* *
1325880 AATCATGCAAATTAATATATTA-AT
1 AATCATGCAAATTAATAAAATATAT
1325904 AATCATGC-AATTAAATAAAATATAT
1 AATCATGCAAATT-AATAAAATATAT
1325929 AATCAT
1 AATCAT
1325935 ATCAGGCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 4 0.15
24 15 0.56
25 8 0.30
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.35
Consensus pattern (25 bp):
AATCATGCAAATTAATAAAATATAT
Found at i:1332124 original size:4 final size:4
Alignment explanation
Indices: 1332115--1332140 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1332105 ATATATTCTC
1332115 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
1332141 TAGTAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1332500 original size:26 final size:26
Alignment explanation
Indices: 1332464--1332513 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1332454 TAGAATATAA
*
1332464 ATTTTTAATTTTAAGTATTAAAATTT
1 ATTTTTAATTTTAAGTATCAAAATTT
*
1332490 ATTTTTAATTTTAATTATCAAAAT
1 ATTTTTAATTTTAAGTATCAAAAT
1332514 CGAATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (26 bp):
ATTTTTAATTTTAAGTATCAAAATTT
Found at i:1339453 original size:2 final size:2
Alignment explanation
Indices: 1339446--1339478 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1339436 ACAAAAAGAA
1339446 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1339479 TCCCAGAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1341293 original size:15 final size:15
Alignment explanation
Indices: 1341273--1341304 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1341263 ATAATTTTTG
*
1341273 TTTTTATTTTTTATT
1 TTTTTATTTTTCATT
1341288 TTTTTATTTTTCATT
1 TTTTTATTTTTCATT
1341303 TT
1 TT
1341305 AGAAAATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTATTTTTCATT
Found at i:1341462 original size:24 final size:24
Alignment explanation
Indices: 1341438--1341493 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 24
1341428 AATAATTATT
1341438 TTTTAAATAT-TATATA-TTAAAA
1 TTTTAAATATATATATATTTAAAA
*
1341460 TTTTAATTATATATATATTTAAAAAA
1 TTTTAAATATATATATATTT--AAAA
1341486 TTTTAAAT
1 TTTTAAAT
1341494 TTCTCGAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 9 0.32
23 6 0.21
24 2 0.07
26 11 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTTAAATATATATATATTTAAAA
Found at i:1357771 original size:14 final size:16
Alignment explanation
Indices: 1357752--1357786 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
1357742 CAAAAAATAC
1357752 AATAAAA-TGAAA-GA
1 AATAAAATTGAAAGGA
1357766 AATAAAATTGAAAGGA
1 AATAAAATTGAAAGGA
1357782 AATAA
1 AATAA
1357787 GCTGAGAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.37
15 5 0.26
16 7 0.37
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (16 bp):
AATAAAATTGAAAGGA
Found at i:1359133 original size:13 final size:13
Alignment explanation
Indices: 1359115--1359139 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1359105 AATTTTCAGA
1359115 AACCAAAACCATC
1 AACCAAAACCATC
1359128 AACCAAAACCAT
1 AACCAAAACCAT
1359140 TAATCACTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.36, G:0.00, T:0.08
Consensus pattern (13 bp):
AACCAAAACCATC
Found at i:1359496 original size:19 final size:20
Alignment explanation
Indices: 1359468--1359507 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1359458 AAAACCCATA
*
1359468 AAAAATAGA-CTTGAGAGGG
1 AAAAACAGACCTTGAGAGGG
1359487 AAAAACAGACCTTGAGAGGG
1 AAAAACAGACCTTGAGAGGG
1359507 A
1 A
1359508 GGCTCATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.47, C:0.10, G:0.30, T:0.12
Consensus pattern (20 bp):
AAAAACAGACCTTGAGAGGG
Found at i:1360543 original size:24 final size:22
Alignment explanation
Indices: 1360491--1360543 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
1360481 TATAATTTAA
*
1360491 AATTTTAATAATTATTATATTT
1 AATTTTAATAATTATTATATAT
*
1360513 AAATTTAATAAAATTATTA-ATAT
1 AATTTTAAT--AATTATTATATAT
1360536 ATATTTTA
1 A-ATTTTA
1360544 TATTTTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 8 0.32
23 4 0.16
24 13 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTTTAATAATTATTATATAT
Found at i:1360811 original size:74 final size:72
Alignment explanation
Indices: 1360670--1360827 Score: 253
Period size: 74 Copynumber: 2.2 Consensus size: 72
1360660 ACTCGTATCT
*
1360670 CACTGAAATCCATGGCCTGGTTTGGTCCATATAAATCCAGGCGTCGGATAGAATCCAGACATAAA
1 CACTGAAATCCATGGCCTGGTTTGGTCCATATAAATCCAGGCGTCAGATAGAATCCAGACATAAA
1360735 ACTTGGA
66 ACTTGGA
* *
1360742 CACTGAAATCCATGGCCTGGTTTGGTCCATATATAAATCCATGTGTCAGATAGAATCCAGACATA
1 CACTGAAATCCATGGCCTGGTTTGGTCC--ATATAAATCCAGGCGTCAGATAGAATCCAGACATA
1360807 AAACTTGGA
64 AAACTTGGA
* *
1360816 CAGTGAAGTCCA
1 CACTGAAATCCA
1360828 AATTCAATTA
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
72 28 0.35
74 51 0.65
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.25
Consensus pattern (72 bp):
CACTGAAATCCATGGCCTGGTTTGGTCCATATAAATCCAGGCGTCAGATAGAATCCAGACATAAA
ACTTGGA
Found at i:1363037 original size:42 final size:42
Alignment explanation
Indices: 1362976--1363059 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
1362966 TTGATTAAGA
* * *
1362976 TAGAACCTCCAAGCGGTTGATCATGTTACTTCGTTAAAGCAT
1 TAGAACCTCCAAGCAGTTGATCATATTACTTCATTAAAGCAT
* *
1363018 TAGAACCTCCAAGTAGTTGATCATATTACTTCATTTAAGCAT
1 TAGAACCTCCAAGCAGTTGATCATATTACTTCATTAAAGCAT
1363060 GCTGACATGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (42 bp):
TAGAACCTCCAAGCAGTTGATCATATTACTTCATTAAAGCAT
Found at i:1367197 original size:39 final size:39
Alignment explanation
Indices: 1367134--1367208 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
1367124 ATATCTTCTT
*
1367134 TTTTCACCGCTAAACTCGATAACCCATTTGAATTTTTAC
1 TTTTCACCGCTAAACTCGAAAACCCATTTGAATTTTTAC
* * *
1367173 TTTTCACCTCTAAATTCGAAAACCCATTTGCATTTT
1 TTTTCACCGCTAAACTCGAAAACCCATTTGAATTTT
1367209 CCACTAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (39 bp):
TTTTCACCGCTAAACTCGAAAACCCATTTGAATTTTTAC
Found at i:1368853 original size:21 final size:20
Alignment explanation
Indices: 1368823--1368866 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1368813 TTTTATATAT
*
1368823 TATTTTAATAAAATTTTGATA
1 TATTTAAAT-AAATTTTGATA
* *
1368844 TATTTAAATAGATTTTTATA
1 TATTTAAATAAATTTTGATA
1368864 TAT
1 TAT
1368867 AACAATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TATTTAAATAAATTTTGATA
Found at i:1379534 original size:24 final size:23
Alignment explanation
Indices: 1379503--1379556 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
1379493 CTTTACTTTC
*
1379503 TTTTGATTAGCCTTTCTTGTGGA
1 TTTTGATTAGACTTTCTTGTGGA
1379526 TTTTAGATTAGACTTTCTTGTGGA
1 TTTT-GATTAGACTTTCTTGTGGA
*
1379550 TATTGAT
1 TTTTGAT
1379557 GATAACTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.19, C:0.09, G:0.20, T:0.52
Consensus pattern (23 bp):
TTTTGATTAGACTTTCTTGTGGA
Found at i:1394676 original size:11 final size:12
Alignment explanation
Indices: 1394629--1394677 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
1394619 TTGAAGTATT
1394629 TAAAAATATATA
1 TAAAAATATATA
*
1394641 TACAATAATA-AAA
1 TA-AA-AATATATA
1394654 TAAAAA-ATATA
1 TAAAAATATATA
1394665 TAAAAATA-ATA
1 TAAAAATATATA
1394676 TA
1 TA
1394678 GTGTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
10 1 0.03
11 15 0.48
12 5 0.16
13 6 0.19
14 4 0.13
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (12 bp):
TAAAAATATATA
Found at i:1403859 original size:9 final size:10
Alignment explanation
Indices: 1403846--1403895 Score: 52
Period size: 9 Copynumber: 5.2 Consensus size: 10
1403836 TTAACTAAGT
1403846 TATATATATAA
1 TATATA-ATAA
* *
1403857 TATTTATTAA
1 TATATAATAA
1403867 -ATATAATAA
1 TATATAATAA
1403876 TA-ATAATAA
1 TATATAATAA
1403885 TA-ATAATAA
1 TATATAATAA
1403894 TA
1 TA
1403896 AGAAGAAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 25 0.74
10 4 0.12
11 5 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TATATAATAA
Found at i:1403877 original size:3 final size:3
Alignment explanation
Indices: 1403869--1403896 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1403859 TTTATTAAAT
1403869 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1403897 GAAGAAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1403901 original size:3 final size:3
Alignment explanation
Indices: 1403895--1403920 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1403885 TAATAATAAT
1403895 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
1403921 ACTAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1406603 original size:87 final size:87
Alignment explanation
Indices: 1406443--1406603 Score: 207
Period size: 87 Copynumber: 1.9 Consensus size: 87
1406433 AGGAAATAAA
* * * *
1406443 CAATGAAAAGCTTAAGAACATAGATGGAACAGTGAAGAAAATAGAGTTGCCTGAAAATTGTTTAT
1 CAATGAAAAGCTCAAGAACATAGATAGAACAGTGAAGAAAATAGAGGTGCCTGAAAATCGTTTAT
* *
1406508 GCGGAGCTATTTATTTTGGGGG
66 CCGAAGCTATTTATTTTGGGGG
* * * **
1406530 CAATGAAGAGCTCAAGAATATAGATAGAACAGTGAGGAAAATAGAGGTGCCTGAGTATCGTTTA-
1 CAATGAAAAGCTCAAGAACATAGATAGAACAGTGAAGAAAATAGAGGTGCCTGAAAATCGTTTAT
1406594 CCTGAAGCTA
66 CC-GAAGCTA
1406604 AATATATCTG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
86 1 0.02
87 61 0.98
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (87 bp):
CAATGAAAAGCTCAAGAACATAGATAGAACAGTGAAGAAAATAGAGGTGCCTGAAAATCGTTTAT
CCGAAGCTATTTATTTTGGGGG
Found at i:1406673 original size:102 final size:102
Alignment explanation
Indices: 1406533--1406926 Score: 547
Period size: 102 Copynumber: 3.9 Consensus size: 102
1406523 TTGGGGGCAA
* * * *
1406533 TGAAGAGCTCAAGAATATAGATAGAACAGTGAGGAAAATAGAGGTGCCTGAGTATCGTTTACCTG
1 TGAAGAGCTCAAGAACATAGATGGAACAGTGAGGAAAATAGAGGTGCCTGAGGATTGTTTACCTG
* *
1406598 AAGCTAAATATATCTGGGGC-AGCGAGGGGATCGACAT
66 AAGCTAAATATTTCTGGGGCAAG-GAGGAGATCGACAT
* * *
1406635 TGAAGAGTTCAAGAACATAGATGGAACAGTGAGTAAAATAGAGATGCCTGAGGATTGTTTACCTG
1 TGAAGAGCTCAAGAACATAGATGGAACAGTGAGGAAAATAGAGGTGCCTGAGGATTGTTTACCTG
*
1406700 AAGCTCAATATTTCTGGGGCAAGGAGGAGATCGACAT
66 AAGCTAAATATTTCTGGGGCAAGGAGGAGATCGACAT
* * * *
1406737 TGAAGAGTTCAAGAACATAGATGGAACAGTGAGTAAAATAGAGGTGCCAGAGGATTGTTTACGTG
1 TGAAGAGCTCAAGAACATAGATGGAACAGTGAGGAAAATAGAGGTGCCTGAGGATTGTTTACCTG
* ** *
1406802 AAGCTAAATATTTTTGGGGCAAGGAGGAGATAAACAA
66 AAGCTAAATATTTCTGGGGCAAGGAGGAGATCGACAT
* * * * **
1406839 CGAAGAGCTCAAGAACATAGATGGAACAGTGAGGAAAAAAAAGGTGCTTGAGGATTGTTTATGTG
1 TGAAGAGCTCAAGAACATAGATGGAACAGTGAGGAAAATAGAGGTGCCTGAGGATTGTTTACCTG
*
1406904 AAGCTAAATATTTTTGGGGCAAG
66 AAGCTAAATATTTCTGGGGCAAG
1406927 CCTCTTAGCA
Statistics
Matches: 265, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
102 263 0.99
103 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.23
Consensus pattern (102 bp):
TGAAGAGCTCAAGAACATAGATGGAACAGTGAGGAAAATAGAGGTGCCTGAGGATTGTTTACCTG
AAGCTAAATATTTCTGGGGCAAGGAGGAGATCGACAT
Found at i:1410307 original size:6 final size:6
Alignment explanation
Indices: 1410296--1410320 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1410286 TAAGCAATAT
1410296 GATGGC GATGGC GATGGC GATGGC G
1 GATGGC GATGGC GATGGC GATGGC G
1410321 GAGAGATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.52, T:0.16
Consensus pattern (6 bp):
GATGGC
Found at i:1414466 original size:16 final size:16
Alignment explanation
Indices: 1414445--1414478 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1414435 CCAAAATATA
1414445 ATTTTTCTTCCCTAGC
1 ATTTTTCTTCCCTAGC
1414461 ATTTTTCTTCCCTAGC
1 ATTTTTCTTCCCTAGC
1414477 AT
1 AT
1414479 AAATTGTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.15, C:0.29, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTTTTCTTCCCTAGC
Found at i:1417483 original size:21 final size:21
Alignment explanation
Indices: 1417442--1417483 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1417432 ATCAACAATT
* *
1417442 CTAAACAAAAAATTTACAAAA
1 CTAAACAAAAAATTAAAAAAA
1417463 CTAAA-AAATAAATTAAAAAAA
1 CTAAACAAA-AAATTAAAAAAA
1417484 GTCAGTAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (21 bp):
CTAAACAAAAAATTAAAAAAA
Found at i:1429046 original size:17 final size:18
Alignment explanation
Indices: 1429021--1429054 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1429011 AAAAAAAAGT
*
1429021 TAAAGATTGTT-CATATA
1 TAAAAATTGTTACATATA
1429038 TAAAAATTGTTACATAT
1 TAAAAATTGTTACATAT
1429055 CTTGGCGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (18 bp):
TAAAAATTGTTACATATA
Found at i:1429482 original size:30 final size:30
Alignment explanation
Indices: 1429439--1429543 Score: 120
Period size: 30 Copynumber: 3.5 Consensus size: 30
1429429 TATTACATTA
* * * *
1429439 AAATATATCTTTAACCTTTACTTTGCATCC
1 AAATAAATTTTTAACCTTTAATTTGTATCC
* *
1429469 AAATAAATTTTTAACCTTTAATTTATATTC
1 AAATAAATTTTTAACCTTTAATTTGTATCC
* **
1429499 AAATAAATTTTTAACTTTTAATTTGTATGT
1 AAATAAATTTTTAACCTTTAATTTGTATCC
*
1429529 AAATAAACTTTTAAC
1 AAATAAATTTTTAAC
1429544 ATAAATTAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (30 bp):
AAATAAATTTTTAACCTTTAATTTGTATCC
Found at i:1429616 original size:25 final size:26
Alignment explanation
Indices: 1429588--1429639 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1429578 TTTGATACAA
1429588 ATAAAA-AATGAAGA-CTTATTTAAAT
1 ATAAAAGAAT-AAGAGCTTATTTAAAT
*
1429613 ATAAAAGTATAAGAGCTTATTTAAAT
1 ATAAAAGAATAAGAGCTTATTTAAAT
1429639 A
1 A
1429640 ATATGATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.33
Consensus pattern (26 bp):
ATAAAAGAATAAGAGCTTATTTAAAT
Found at i:1430786 original size:18 final size:20
Alignment explanation
Indices: 1430750--1430789 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
1430740 TCGAATTAAA
*
1430750 TTATATATTTTTATTAATTT
1 TTATATATTTTTATAAATTT
1430770 TTATATA-TTTTA-AAATTT
1 TTATATATTTTTATAAATTT
1430788 TT
1 TT
1430790 TTAAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 5 0.26
20 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATATATTTTTATAAATTT
Found at i:1430951 original size:25 final size:24
Alignment explanation
Indices: 1430893--1430953 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
1430883 AAAATTGATT
* *
1430893 AATTAAATCAATTTAATAAATTTA
1 AATTAAATTAATTTAATAAAATTA
1430917 AATTTAAATTAATTTCAA-AAAATTA
1 AA-TTAAATTAATTT-AATAAAATTA
1430942 AATTCAAATTAA
1 AATT-AAATTAA
1430954 GAGTATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 4 0.12
25 26 0.81
26 2 0.06
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (24 bp):
AATTAAATTAATTTAATAAAATTA
Found at i:1431673 original size:159 final size:159
Alignment explanation
Indices: 1431374--1431690 Score: 419
Period size: 159 Copynumber: 2.0 Consensus size: 159
1431364 TTTTTTATTT
*
1431374 TTATAATTAACACTATCAGAATAAATTAAGAATTTCATATTTTATAAATCATGTAATTATTGATA
1 TTATAATTAACACTATCAGAATAAATTAAGAATTTAATATTTTATAAATCATGTAATTATTGATA
* * * **
1431439 AAAATTTAAGGTAATATTATTCTTTCTTTTTTTTCAGTTAAGTGGTAATTTAATGTAAAAAATTA
66 AAAATTAAAGCTAATATTACTCTTTCTTTTTTTTCAGACAAGTGGTAATTTAATGTAAAAAATTA
* *
1431504 TGGTAATTTGTGGTTGATTTTGTATTATA
131 TGATAATTTGTGATTGATTTTGTATTATA
* * * *
1431533 TTATAATTAA-ATTTATCAGCATAAATTAA-AAGTTTAATA-TTTATTAGATCATGTTATTATTG
1 TTATAATTAACA-CTATCAGAATAAATTAAGAA-TTTAATATTTTA-TAAATCATGTAATTATTG
*
1431595 ATAAAAAATTAAAGCT-ATATTACTCTTTTTTTTTTTTCA-ACAAGTGGTAATTTAATGTAAAAA
63 AT-AAAAATTAAAGCTAATATTACTCTTTCTTTTTTTTCAGACAAGTGGTAATTTAATGT-AAAA
* *
1431658 AATTGTGATACTTTGTGATTGATTTTGTATTAT
126 AATTATGATAATTTGTGATTGATTTTGTATTAT
1431691 GATAAGGTGT
Statistics
Matches: 138, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
158 24 0.17
159 103 0.75
160 11 0.08
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.47
Consensus pattern (159 bp):
TTATAATTAACACTATCAGAATAAATTAAGAATTTAATATTTTATAAATCATGTAATTATTGATA
AAAATTAAAGCTAATATTACTCTTTCTTTTTTTTCAGACAAGTGGTAATTTAATGTAAAAAATTA
TGATAATTTGTGATTGATTTTGTATTATA
Found at i:1439545 original size:18 final size:18
Alignment explanation
Indices: 1439522--1439565 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1439512 TGCTGTTATG
1439522 ATATTTAGCCTTAATGTA
1 ATATTTAGCCTTAATGTA
*
1439540 ATATTTGGCCTTAATGTA
1 ATATTTAGCCTTAATGTA
1439558 ATTATTTA
1 A-TATTTA
1439566 TTATTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (18 bp):
ATATTTAGCCTTAATGTA
Found at i:1449692 original size:21 final size:23
Alignment explanation
Indices: 1449650--1449706 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
1449640 AATAATTATT
*
1449650 ATATATAAAAATCTATATAAAT-
1 ATATATAAAAATTTATATAAATA
*
1449672 TTAT-TAAAAATTTAT-TAAAATA
1 ATATATAAAAATTTATAT-AAATA
1449694 ATATATAAAAATT
1 ATATATAAAAATT
1449707 AAAATTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.03
21 14 0.48
22 6 0.21
23 8 0.28
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
ATATATAAAAATTTATATAAATA
Found at i:1455609 original size:13 final size:13
Alignment explanation
Indices: 1455578--1455602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1455568 GGAACTGTCT
1455578 CTTTCTTTTTCCC
1 CTTTCTTTTTCCC
1455591 CTTTCTTTTTCC
1 CTTTCTTTTTCC
1455603 TTTTTCTCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (13 bp):
CTTTCTTTTTCCC
Found at i:1462927 original size:32 final size:32
Alignment explanation
Indices: 1462884--1462946 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1462874 ATGGATGTTA
*
1462884 TAATATTTGAATTATATGAATTCTAAACTATG
1 TAATATCTGAATTATATGAATTCTAAACTATG
1462916 TAATATCTGAATTATATGAATTCTAAACTAT
1 TAATATCTGAATTATATGAATTCTAAACTAT
1462947 ATTTAACTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (32 bp):
TAATATCTGAATTATATGAATTCTAAACTATG
Found at i:1465759 original size:29 final size:29
Alignment explanation
Indices: 1465696--1465759 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
1465686 AAATATTACT
* *
1465696 AATATATGATAATTGGAAAATAAAATTAA
1 AATAAATGATAATTGGAAAATAAAAGTAA
* *
1465725 TATAAATGA-AATTGGAAAAGTAACAGTAA
1 AATAAATGATAATTGGAAAA-TAAAAGTAA
1465754 AATAAA
1 AATAAA
1465760 AAGGAAAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
28 10 0.34
29 19 0.66
ACGTcount: A:0.59, C:0.02, G:0.12, T:0.27
Consensus pattern (29 bp):
AATAAATGATAATTGGAAAATAAAAGTAA
Found at i:1469901 original size:196 final size:196
Alignment explanation
Indices: 1469562--1469954 Score: 653
Period size: 196 Copynumber: 2.0 Consensus size: 196
1469552 AATTCCAGCA
* * *
1469562 AGCATGGTGAGCTATGACAACCACACCAGCAATTAAAGCATGATTAATGACAAAGAAGCAGAAGT
1 AGCATGGTGAACTATGACAACCACACAAGCAATTAAAACATGATTAATGACAAAGAAGCAGAAGT
* *
1469627 GACGAAAGTGTAGATCGTGAGCAGCATCCATATGACATCTGTTTATGAAATAAGAAGAAAGTCGA
66 GACGAAAGTGTAGATCGTAAGCAGCATCCATATGACATCTGTTTATGAAATAAAAAGAAAGTCGA
1469692 CAGGAAATGCTCTATTGCAACTTCAAATAATTAAAGTCAATTTGTAAAGTTGAAAGATTGGGTAG
131 CAGGAAATGCTCTATTGCAACTTCAAATAATTAAAGTCAATTTGTAAAGTTGAAAGATTGGGTAG
1469757 C
196 C
1469758 AGCATGGTGAACTATGACAACCACACAAGCAATTAAAACATGATTAATGACAAAGAAGCAGAAGT
1 AGCATGGTGAACTATGACAACCACACAAGCAATTAAAACATGATTAATGACAAAGAAGCAGAAGT
* * * *
1469823 GATGAAAGT-TAAGATCGTAAGCAGCATCCATATGACGTCTGTTTATGGAATAAAAAGAAAGTTG
66 GACGAAAGTGT-AGATCGTAAGCAGCATCCATATGACATCTGTTTATGAAATAAAAAGAAAGTCG
* * * *
1469887 ACAGGAAGTGCTCTATTTCAACTTTAAATAATTCAAGTCAATTTGTAAAGTTGAAAGATTGGGTA
130 ACAGGAAATGCTCTATTGCAACTTCAAATAATTAAAGTCAATTTGTAAAGTTGAAAGATTGGGTA
1469952 GC
195 GC
1469954 A
1 A
1469955 ATTTGTAGAA
Statistics
Matches: 183, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
195 1 0.01
196 182 0.99
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.24
Consensus pattern (196 bp):
AGCATGGTGAACTATGACAACCACACAAGCAATTAAAACATGATTAATGACAAAGAAGCAGAAGT
GACGAAAGTGTAGATCGTAAGCAGCATCCATATGACATCTGTTTATGAAATAAAAAGAAAGTCGA
CAGGAAATGCTCTATTGCAACTTCAAATAATTAAAGTCAATTTGTAAAGTTGAAAGATTGGGTAG
C
Found at i:1478159 original size:1 final size:1
Alignment explanation
Indices: 1478153--1478179 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1478143 TCTCCATTAC
1478153 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1478180 CCTCTGCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1478421 original size:22 final size:22
Alignment explanation
Indices: 1478396--1478449 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1478386 TTGATTTTCG
*
1478396 GATAATATATAAAATATATATT
1 GATAATATATAAAATATAAATT
* *
1478418 GATAACATATCAAATATAAATT
1 GATAATATATAAAATATAAATT
1478440 -ATAAT-TATAA
1 GATAATATATAA
1478450 CAAATTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 4 0.15
21 4 0.15
22 19 0.70
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (22 bp):
GATAATATATAAAATATAAATT
Found at i:1478727 original size:21 final size:22
Alignment explanation
Indices: 1478695--1478736 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1478685 AGCTTTAATT
*
1478695 TTAATTGATTTA-ATATTAAAA
1 TTAATTGATTTATAAATTAAAA
1478716 TTAATTTG-TTTATAAATTAAA
1 TTAA-TTGATTTATAAATTAAA
1478737 GTTTTCAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
TTAATTGATTTATAAATTAAAA
Found at i:1479872 original size:46 final size:47
Alignment explanation
Indices: 1479821--1479931 Score: 116
Period size: 46 Copynumber: 2.4 Consensus size: 47
1479811 ATTTTATAAG
* *
1479821 ATTATTTTTTATGAACAAATGTAATTTTTAATCAATGA-AAAACATT
1 ATTATTCTTTATGAACAAATGTAATATTTAATCAATGATAAAACATT
** * * * * *
1479867 ATTATTCTCGATTAATAATTGTAATATTTCATCAATGATTAAACATT
1 ATTATTCTTTATGAACAAATGTAATATTTAATCAATGATAAAACATT
* *
1479914 ATTATTGTTTGTGAACAA
1 ATTATTCTTTATGAACAA
1479932 TTGAAAATTT
Statistics
Matches: 49, Mismatches: 15, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
46 30 0.61
47 19 0.39
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (47 bp):
ATTATTCTTTATGAACAAATGTAATATTTAATCAATGATAAAACATT
Found at i:1479934 original size:47 final size:46
Alignment explanation
Indices: 1479821--1479966 Score: 118
Period size: 47 Copynumber: 3.1 Consensus size: 46
1479811 ATTTTATAAG
* * * * *
1479821 ATTATTTTTTATGAACAAATGTAATTTTTAATCAATGA-AAAACATT
1 ATTA-TTTTTGTGAACAATTGTAATATTTCATCAATGATTAAACATT
* * * *
1479867 ATTATTCTCGATTAATAATTGTAATATTTCATCAATGATTAAACATT
1 ATTATTTTTG-TGAACAATTGTAATATTTCATCAATGATTAAACATT
* *
1479914 ATTATTGTTTGTGAACAATTG-AAAATTTTCATTC-ATTATTAAACATT
1 ATTATT-TTTGTGAACAATTGTAATA-TTTCA-TCAATGATTAAACATT
*
1479961 ACTATT
1 ATTATT
1479967 ATTGGAGAAC
Statistics
Matches: 79, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
45 3 0.04
46 29 0.37
47 43 0.54
48 4 0.05
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (46 bp):
ATTATTTTTGTGAACAATTGTAATATTTCATCAATGATTAAACATT
Found at i:1482733 original size:31 final size:31
Alignment explanation
Indices: 1482698--1482766 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
1482688 TATATTTTAT
*
1482698 ATTTTTATGTTAACATAT-AT-TATAATATATA
1 ATTTTTATG-TAAAATATGATATA-AATATATA
1482729 ATTTTTATGTAAAATATGATATAAATATATA
1 ATTTTTATGTAAAATATGATATAAATATATA
*
1482760 AATTTTA
1 ATTTTTA
1482767 ATATTTTACA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 7 0.21
31 25 0.74
32 2 0.06
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (31 bp):
ATTTTTATGTAAAATATGATATAAATATATA
Found at i:1487157 original size:2 final size:2
Alignment explanation
Indices: 1487150--1487183 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1487140 TTCTAGTTAA
1487150 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
1487184 GTGGCTGTCA
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:1488810 original size:18 final size:19
Alignment explanation
Indices: 1488769--1488810 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1488759 ATTAATAAAA
**
1488769 AAATTTTAAGAGAAATTTT
1 AAATTTTAAGAGAAATAAT
*
1488788 CAATTTTAAGA-AAATAAT
1 AAATTTTAAGAGAAATAAT
1488806 AAATT
1 AAATT
1488811 AAATATTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (19 bp):
AAATTTTAAGAGAAATAAT
Found at i:1490524 original size:2 final size:2
Alignment explanation
Indices: 1490517--1490551 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1490507 CCATGAATAG
1490517 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1490552 ATACACATAC
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1497183 original size:2 final size:2
Alignment explanation
Indices: 1497176--1497207 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1497166 GGTACGATTC
1497176 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1497208 AAACACCCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1510421 original size:32 final size:32
Alignment explanation
Indices: 1510378--1510438 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1510368 ATGTTAGTAC
*
1510378 TTTTTAATTTTTAAAATTCAT-TTTATTATTA
1 TTTTTAATTTTTAAAATACATATTTATTATTA
*
1510409 TTTTTATATTTTTAACATACATATTTATTA
1 TTTTTA-ATTTTTAAAATACATATTTATTA
1510439 AAAACTATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 6 0.23
32 13 0.50
33 7 0.27
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (32 bp):
TTTTTAATTTTTAAAATACATATTTATTATTA
Found at i:1511520 original size:8 final size:10
Alignment explanation
Indices: 1511477--1511521 Score: 63
Period size: 10 Copynumber: 4.2 Consensus size: 10
1511467 TTCATAATTT
1511477 TATTTTAATA
1 TATTTTAATA
1511487 TAAAATTTTAATA
1 T---ATTTTAATA
1511500 TATTTTAATA
1 TATTTTAATA
1511510 TATTTTAATA
1 TATTTTAATA
1511520 TA
1 TA
1511522 AATTTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
10 22 0.69
13 10 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TATTTTAATA
Found at i:1511535 original size:20 final size:20
Alignment explanation
Indices: 1511491--1511536 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1511481 TTAATATAAA
*
1511491 ATTTTAATATATTTTAATAT
1 ATTTTAATATAATTTAATAT
*
1511511 ATTTTAATATAAATTTATTAT
1 ATTTTAATAT-AATTTAATAT
1511532 -TTTTA
1 ATTTTA
1511537 TTTTATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTAATATAATTTAATAT
Found at i:1512810 original size:16 final size:16
Alignment explanation
Indices: 1512759--1512817 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
1512749 AATTTTTAAT
*
1512759 ATAAAATATTATAAATA
1 ATAAAATATTA-ATATA
* *
1512776 TATAAAA-ATAAATAAA
1 -ATAAAATATTAATATA
1512792 ATAAAATATTAATATA
1 ATAAAATATTAATATA
*
1512808 ATAAATTATT
1 ATAAAATATT
1512818 TCATTAAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 6 0.18
16 19 0.56
17 3 0.09
18 6 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAAAATATTAATATA
Found at i:1515065 original size:14 final size:14
Alignment explanation
Indices: 1515037--1515087 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1515027 ATTAAATTTA
1515037 AATATAAT-TTATTT
1 AATATAATATT-TTT
1515051 AATATAATATTTTT
1 AATATAATATTTTT
* *
1515065 ATTA-AAAATTTTT
1 AATATAATATTTTT
1515078 AACTATAATA
1 AA-TATAATA
1515088 ATAATAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 9 0.30
14 16 0.53
15 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
AATATAATATTTTT
Found at i:1515623 original size:21 final size:20
Alignment explanation
Indices: 1515593--1515632 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1515583 AATATTTGGA
*
1515593 GTTATAAAAAGTTAAAATTTG
1 GTTATAAAAA-ATAAAATTTG
*
1515614 GTTATTAAAAATAAAATTT
1 GTTATAAAAAATAAAATTT
1515633 CAGCTTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (20 bp):
GTTATAAAAAATAAAATTTG
Found at i:1519190 original size:18 final size:18
Alignment explanation
Indices: 1519164--1519206 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1519154 ATTTTAATTA
* *
1519164 TTTAATTTAAAATTTATT
1 TTTATTTTAAAATTTATC
1519182 TTTATTTTAAAATTTATC
1 TTTATTTTAAAATTTATC
1519200 TTTATTT
1 TTTATTT
1519207 GTTAATAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATTTTAAAATTTATC
Found at i:1522173 original size:45 final size:44
Alignment explanation
Indices: 1522109--1522240 Score: 194
Period size: 45 Copynumber: 3.0 Consensus size: 44
1522099 TTTTCAATCA
* * *
1522109 TTAGAACTTCTGGTTCTATGA-GATAGGGTAGACCAACAGGTGCC
1 TTAGAACTACTGGTGCTATGATG-TAGGGTAGACCAACAGGTACC
*
1522153 TTAGAACCTACTGGTGCTATGATGTAGGATAGACCAACAGGTACC
1 TTAGAA-CTACTGGTGCTATGATGTAGGGTAGACCAACAGGTACC
1522198 TTAGAATCTACTGGTGCTATGATGTAGGGTAGACCAACAGGTA
1 TTAGAA-CTACTGGTGCTATGATGTAGGGTAGACCAACAGGTA
1522241 TGATTGATCT
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
44 6 0.08
45 73 0.91
46 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (44 bp):
TTAGAACTACTGGTGCTATGATGTAGGGTAGACCAACAGGTACC
Found at i:1525635 original size:68 final size:67
Alignment explanation
Indices: 1525514--1525640 Score: 166
Period size: 68 Copynumber: 1.9 Consensus size: 67
1525504 CATCTCCTAA
*
1525514 TGGTCTTCTTGCTCAGGTCTAATTTTCCTCTTGCATTATTCAAAAATTGCTTTTTTGATTGGTTA
1 TGGTATTCTTGCTCAGGTCTAATTTTCCTCTTGCATTATTCAAAAATTGC-TTTTTGATTGGTTA
1525579 CAT
65 CAT
* * * * * *
1525582 TGGTATTCTTGCTGATGTCTAATTTTCCTCTTTTCATTCTTC-ACAATTTCTTTTTGATT
1 TGGTATTCTTGCTCAGGTCTAATTTTCCTC-TTGCATTATTCAAAAATTGCTTTTTGATT
1525641 TGTAACCCAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
67 9 0.18
68 33 0.65
69 9 0.18
ACGTcount: A:0.17, C:0.18, G:0.13, T:0.52
Consensus pattern (67 bp):
TGGTATTCTTGCTCAGGTCTAATTTTCCTCTTGCATTATTCAAAAATTGCTTTTTGATTGGTTAC
AT
Found at i:1542947 original size:43 final size:43
Alignment explanation
Indices: 1542885--1542966 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
1542875 CATAAATACG
* * *
1542885 ATTTCTGTTTAACTTTTTGATATTGGGTAGTCTTTATATTTAT
1 ATTTCTGTTCAACTTTTTGATACTGGGTAGCCTTTATATTTAT
*
1542928 ATTTCTGTTCAA-TTGTTTGATACTGGTTAGCCTTTATAT
1 ATTTCTGTTCAACTT-TTTGATACTGGGTAGCCTTTATAT
1542967 CCATATTTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 2 0.06
43 32 0.94
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.55
Consensus pattern (43 bp):
ATTTCTGTTCAACTTTTTGATACTGGGTAGCCTTTATATTTAT
Found at i:1558249 original size:12 final size:12
Alignment explanation
Indices: 1558232--1558256 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1558222 AACTATCACA
1558232 AACCTAACTAGT
1 AACCTAACTAGT
1558244 AACCTAACTAGT
1 AACCTAACTAGT
1558256 A
1 A
1558257 GTTGGTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (12 bp):
AACCTAACTAGT
Found at i:1561460 original size:18 final size:18
Alignment explanation
Indices: 1561437--1561471 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1561427 CAGAAAGCAA
1561437 TGGAATATGGA-AATTTCC
1 TGGAAT-TGGAGAATTTCC
1561455 TGGAATTGGAGAATTTC
1 TGGAATTGGAGAATTTC
1561472 AGTGCTATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (18 bp):
TGGAATTGGAGAATTTCC
Found at i:1565960 original size:22 final size:22
Alignment explanation
Indices: 1565935--1565987 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
1565925 TTGAATTATT
1565935 ATTAATTTACAACTAAGTCATC
1 ATTAATTTACAACTAAGTCATC
* * * * *
1565957 ATTACTTTGCTATTAAGTTATC
1 ATTAATTTACAACTAAGTCATC
1565979 ACTTAATTT
1 A-TTAATTT
1565988 TATTAAATTA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.34, C:0.15, G:0.06, T:0.45
Consensus pattern (22 bp):
ATTAATTTACAACTAAGTCATC
Found at i:1565993 original size:21 final size:19
Alignment explanation
Indices: 1565967--1566011 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
1565957 ATTACTTTGC
*
1565967 TATTAAGTTATCACTTAATTT
1 TATTAAATTATCA-TTAA-TT
1565988 TATTAAATTATCATTAATT
1 TATTAAATTATCATTAATT
1566007 TATTA
1 TATTA
1566012 CTGTATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.30
20 4 0.17
21 12 0.52
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (19 bp):
TATTAAATTATCATTAATT
Found at i:1566151 original size:44 final size:44
Alignment explanation
Indices: 1566094--1566185 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 44
1566084 TACAATTATC
* * * * * *
1566094 TTATCAATTATTTACTACTA-AATTATTATTTATTTATTATTAAG
1 TTATCAATAATTTAATA-TACAATTATTATTGATTAAATATAAAG
*
1566138 TTATCCATAATTTAATATACAATTATTATTGATTAAATATAAAG
1 TTATCAATAATTTAATATACAATTATTATTGATTAAATATAAAG
1566182 TTAT
1 TTAT
1566186 TGTTGATGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 2 0.05
44 38 0.95
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (44 bp):
TTATCAATAATTTAATATACAATTATTATTGATTAAATATAAAG
Done.