Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 8 of 202
Found at i:2647313 original size:30 final size:31
Alignment explanation
Indices: 2647277--2647336 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
2647267 AAACCTTTTA
*
2647277 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
2647307 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
2647337 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:2650297 original size:31 final size:31
Alignment explanation
Indices: 2650241--2650301 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
2650231 GTTAATAGTT
*
2650241 AGACTTAAATTTTGAAATTTAAAAAGTACAG
1 AGACTTAAATTTTGAAATTAAAAAAGTACAG
2650272 AGAC-TAAATTCTT-AAATTAAGAAAAGTACA
1 AGACTTAAATT-TTGAAATTAA-AAAAGTACA
2650302 TAGATTTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (31 bp):
AGACTTAAATTTTGAAATTAAAAAAGTACAG
Found at i:2652308 original size:21 final size:23
Alignment explanation
Indices: 2652263--2652312 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 23
2652253 AAAAAAGTTG
*
2652263 TTTTTATTTTTAAATTTTAATTA
1 TTTTTATTTTTAAATATTAATTA
*
2652286 TTTTTA-TTTTAAA-ATTGATTA
1 TTTTTATTTTTAAATATTAATTA
2652307 TTTTTA
1 TTTTTA
2652313 ACTCACATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 12 0.48
22 7 0.28
23 6 0.24
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TTTTTATTTTTAAATATTAATTA
Found at i:2656344 original size:6 final size:6
Alignment explanation
Indices: 2656333--2656361 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2656323 GTTGTAGTTT
2656333 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
2656362 TCCCTTCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:2658142 original size:18 final size:18
Alignment explanation
Indices: 2658119--2658154 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2658109 CAATTAAACC
2658119 ATTTGATTGATATATTTA
1 ATTTGATTGATATATTTA
* *
2658137 ATTTGATTTATTTATTTA
1 ATTTGATTGATATATTTA
2658155 TAAATAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (18 bp):
ATTTGATTGATATATTTA
Found at i:2658354 original size:20 final size:20
Alignment explanation
Indices: 2658329--2658368 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2658319 AATATTTTCA
2658329 GTAAATCATTTTCCAGAAAT
1 GTAAATCATTTTCCAGAAAT
*
2658349 GTAAATCATTTTCTAGAAAT
1 GTAAATCATTTTCCAGAAAT
2658369 CGTTTTCCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (20 bp):
GTAAATCATTTTCCAGAAAT
Found at i:2658369 original size:34 final size:33
Alignment explanation
Indices: 2658318--2658381 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
2658308 AAACACCAGA
2658318 AAATATTTTCAGTAAATCATTTTCCAGAAATGT
1 AAATATTTTCAGTAAATCATTTTCCAGAAATGT
* *
2658351 AAATCATTTTCTAG-AAATCGTTTTCCGGAAA
1 AAAT-ATTTTC-AGTAAATCATTTTCCAGAAA
2658382 ACATTTTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 4 0.15
34 21 0.78
35 2 0.07
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (33 bp):
AAATATTTTCAGTAAATCATTTTCCAGAAATGT
Found at i:2661119 original size:20 final size:20
Alignment explanation
Indices: 2661094--2661131 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2661084 ATTATAAAAA
2661094 TTAAAATATATATATTTTAC
1 TTAAAATATATATATTTTAC
* *
2661114 TTAAAATTTATTTATTTT
1 TTAAAATATATATATTTT
2661132 TTCTATGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TTAAAATATATATATTTTAC
Found at i:2662332 original size:83 final size:84
Alignment explanation
Indices: 2662190--2662356 Score: 282
Period size: 83 Copynumber: 2.0 Consensus size: 84
2662180 CCAAGTATAA
* *
2662190 GAAAGAAGAAGAGGGATAAGGGGGGGGGGAGAAAGACAAGTGGCATAGGTTTAGTGAAATTAGGT
1 GAAAGAAGAAGAGGGATAA--GGGGGAGGAGAAAGACAAGTGGCATAGATTTAGTGAAATTAGGT
*
2662255 AGCTGTTATCGTTAAAGTGGT
64 AGCTGTTATCATTAAAGTGGT
2662276 GAAAGAAGAAGAGGGATAA-GGGGAGGAGAAAGACAAGTGGCATAGATTTAGTGAAATTAGGTAG
1 GAAAGAAGAAGAGGGATAAGGGGGAGGAGAAAGACAAGTGGCATAGATTTAGTGAAATTAGGTAG
2662340 CTGTTATCATTAAAGTG
66 CTGTTATCATTAAAGTG
2662357 ATGATGTGAA
Statistics
Matches: 78, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
83 59 0.76
86 19 0.24
ACGTcount: A:0.38, C:0.05, G:0.37, T:0.21
Consensus pattern (84 bp):
GAAAGAAGAAGAGGGATAAGGGGGAGGAGAAAGACAAGTGGCATAGATTTAGTGAAATTAGGTAG
CTGTTATCATTAAAGTGGT
Found at i:2664184 original size:23 final size:23
Alignment explanation
Indices: 2664145--2664195 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
2664135 GGATATAATT
* *
2664145 GCAATGCATTTTGGCACTTTGAA
1 GCAATGCATCTTGGCACTTCGAA
*
2664168 GCAATGCACTCTT-GCACTTCGAT
1 GCAATGCA-TCTTGGCACTTCGAA
2664191 GCAAT
1 GCAAT
2664196 TAATTCAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (23 bp):
GCAATGCATCTTGGCACTTCGAA
Found at i:2669266 original size:6 final size:6
Alignment explanation
Indices: 2669245--2669284 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
2669235 ACCCTCTCTG
*
2669245 GAAGAC GAAGA- AAAGAC GAAGAC GAAGAC GAAGAC GAAGA
1 GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC GAAGAC GAAGA
2669285 GCCCTTTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.55, C:0.12, G:0.33, T:0.00
Consensus pattern (6 bp):
GAAGAC
Found at i:2677123 original size:4 final size:4
Alignment explanation
Indices: 2677114--2677177 Score: 56
Period size: 4 Copynumber: 15.0 Consensus size: 4
2677104 TATACATTTG
* * * *
2677114 TACA TACA TACA TACA TACA TCGCCA TGCACA TACA TGCA TGCA TGCA
1 TACA TACA TACA TACA TACA T--ACA T--ACA TACA TACA TACA TACA
2677162 TACA TACA TACA TACA
1 TACA TACA TACA TACA
2677178 CATACGTGCA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
4 46 0.88
6 6 0.12
ACGTcount: A:0.41, C:0.28, G:0.08, T:0.23
Consensus pattern (4 bp):
TACA
Found at i:2677174 original size:28 final size:27
Alignment explanation
Indices: 2677143--2677239 Score: 72
Period size: 28 Copynumber: 3.4 Consensus size: 27
2677133 ATCGCCATGC
2677143 ACATACATGCATGCATGCATACATACAT
1 ACATACAT-CATGCATGCATACATACAT
* * *
2677171 ACATACA-CATACGTGCATGCACATACAC
1 ACATACATCATGCATGCAT--ACATACAT
* * *
2677199 ACATACACATCACGCACGCATCCATACAT
1 ACAT--ACATCATGCATGCATACATACAT
2677228 A-ATACATGCATG
1 ACATACAT-CATG
2677240 AAATGGAAAG
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
26 13 0.25
27 3 0.06
28 20 0.38
29 7 0.13
30 3 0.06
31 7 0.13
ACGTcount: A:0.39, C:0.30, G:0.10, T:0.21
Consensus pattern (27 bp):
ACATACATCATGCATGCATACATACAT
Found at i:2677207 original size:14 final size:14
Alignment explanation
Indices: 2677163--2677208 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
2677153 ATGCATGCAT
2677163 ACATACATACATAC
1 ACATACATACATAC
* * *
2677177 ACATACGTGCATGC
1 ACATACATACATAC
*
2677191 ACATACACACATAC
1 ACATACATACATAC
2677205 ACAT
1 ACAT
2677209 CACGCACGCA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.43, C:0.30, G:0.07, T:0.20
Consensus pattern (14 bp):
ACATACATACATAC
Found at i:2687891 original size:30 final size:30
Alignment explanation
Indices: 2687855--2687912 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
2687845 TTTTTTTGTT
2687855 AAAGTGTCAAATTATCTGTCAAACTTCTCA
1 AAAGTGTCAAATTATCTGTCAAACTTCTCA
2687885 AAAGTGTCAAATTATCTGTCAAACTTCT
1 AAAGTGTCAAATTATCTGTCAAACTTCT
2687913 TGACTTTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.34
Consensus pattern (30 bp):
AAAGTGTCAAATTATCTGTCAAACTTCTCA
Found at i:2691512 original size:21 final size:22
Alignment explanation
Indices: 2691488--2691533 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
2691478 ACAATATATA
*
2691488 AAAAAAC-TTAAAATGAATAAT
1 AAAAAACATTAAAATAAATAAT
2691509 AAAAAACAGTTTAAAATAAATAAT
1 AAAAAACA--TTAAAATAAATAAT
2691533 A
1 A
2691534 TATAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
24 14 0.67
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (22 bp):
AAAAAACATTAAAATAAATAAT
Found at i:2691543 original size:89 final size:89
Alignment explanation
Indices: 2691450--2691626 Score: 193
Period size: 89 Copynumber: 2.0 Consensus size: 89
2691440 AGAACAATTC
2691450 AAAATAA-ATA-AGAAAAAGTTTCAAATAAACAAT-ATATAAAAAAACTTAAAATGAATAATA-A
1 AAAATAACATATA-AAAAA-TTTCAAA-AAACAATAATATAAAAAAACTTAAAA-G-ATAATATA
2691511 -AAAACAGTTTAAAATAAATAATATATAA
61 TAAAACAGTTTAAAATAAATAATATATAA
* *** * * * *
2691539 AAAATAACATATAAAACATTTTTTAAAACAATAATGTATAAAAATTTAAAAGATAATATATATAA
1 AAAATAACATATAAAAAATTTCAAAAAACAATAATATAAAAAAACTTAAAAGATAATATATAAAA
*
2691604 TAGTTTAAAATAAATAATATATA
66 CAGTTTAAAATAAATAATATATA
2691627 TATATATATA
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
87 6 0.08
88 9 0.12
89 51 0.69
90 7 0.09
91 1 0.01
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (89 bp):
AAAATAACATATAAAAAATTTCAAAAAACAATAATATAAAAAAACTTAAAAGATAATATATAAAA
CAGTTTAAAATAAATAATATATAA
Found at i:2691659 original size:26 final size:24
Alignment explanation
Indices: 2691632--2691711 Score: 79
Period size: 27 Copynumber: 3.1 Consensus size: 24
2691622 ATATATATAT
*
2691632 ATATATATAAAATTTAAATAAATA
1 ATATATAAAAAATTTAAATAAATA
* *
2691656 ATATGTAAAACAGTTTGAAATAAATA
1 ATATATAAAA-AATTT-AAATAAATA
*
2691682 ATATATGAAAGAAACTTAAAATAAATA
1 ATATAT-AAA-AAA-TTTAAATAAATA
2691709 ATA
1 ATA
2691712 AAAGAGTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
24 8 0.18
25 4 0.09
26 14 0.31
27 16 0.36
28 3 0.07
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (24 bp):
ATATATAAAAAATTTAAATAAATA
Found at i:2691664 original size:22 final size:26
Alignment explanation
Indices: 2691632--2691687 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
2691622 ATATATATAT
2691632 ATATATATAAA-A-TTT-AAATAAATA
1 ATATATA-AAACAGTTTGAAATAAATA
*
2691656 ATATGTAAAACAGTTTGAAATAAATA
1 ATATATAAAACAGTTTGAAATAAATA
2691682 ATATAT
1 ATATAT
2691688 GAAAGAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 3 0.11
24 7 0.26
25 3 0.11
26 14 0.52
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (26 bp):
ATATATAAAACAGTTTGAAATAAATA
Found at i:2692496 original size:12 final size:13
Alignment explanation
Indices: 2692479--2692507 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2692469 TTCGTATGTA
2692479 AAAAAATG-AAAT
1 AAAAAATGAAAAT
2692491 AAAAAATGAAAAT
1 AAAAAATGAAAAT
2692504 AAAA
1 AAAA
2692508 TCAAACTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAAAATGAAAAT
Found at i:2694554 original size:41 final size:39
Alignment explanation
Indices: 2694428--2694567 Score: 133
Period size: 40 Copynumber: 3.6 Consensus size: 39
2694418 ACAAACTAGT
* * * *
2694428 TTGATACCCAGTACCTCATCGGATAATTCGAAGTAATAA
1 TTGACACCCAGTGCCTCATCGAATAATCCGAAGTAATAA
* ** * *
2694467 GTTGACACTCAGTGTCC-CATCGGCTAAACTGAAGT-A-AA
1 -TTGACACCCAGTG-CCTCATCGAATAATCCGAAGTAATAA
2694505 TTGACACCCAGTGCCTCATCGAATTAATCCGAAGTAATAGA
1 TTGACACCCAGTGCCTCATCGAA-TAATCCGAAGTAATA-A
*
2694546 TTGACACCCAGTGTCTCATCGA
1 TTGACACCCAGTGCCTCATCGA
2694568 CTCAAAGACG
Statistics
Matches: 81, Mismatches: 13, Indels: 11
0.77 0.12 0.10
Matches are distributed among these distances:
36 2 0.02
37 17 0.21
38 11 0.14
39 2 0.02
40 25 0.31
41 24 0.30
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (39 bp):
TTGACACCCAGTGCCTCATCGAATAATCCGAAGTAATAA
Found at i:2695011 original size:22 final size:21
Alignment explanation
Indices: 2694986--2695060 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 21
2694976 AACCCTTAGC
*
2694986 TTTTCTTTCTCCTTTCCTTTTT
1 TTTTCTTTCT-CTTTCCTTTCT
* *
2695008 TTTTCTTTCTTTTTCCCTTCT
1 TTTTCTTTCTCTTTCCTTTCT
* *
2695029 ATTTCGTTTCACTTTCTCTTTCT
1 TTTTC-TTTCTCTTTC-CTTTCT
2695052 TTTTCTTTC
1 TTTTCTTTC
2695061 ATTTATTTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 12 0.28
22 22 0.51
23 9 0.21
ACGTcount: A:0.03, C:0.27, G:0.01, T:0.69
Consensus pattern (21 bp):
TTTTCTTTCTCTTTCCTTTCT
Found at i:2698319 original size:197 final size:197
Alignment explanation
Indices: 2697984--2698376 Score: 777
Period size: 197 Copynumber: 2.0 Consensus size: 197
2697974 GTTTACAAGT
2697984 TTGCTAGCTAAAATTTTAAAAAAAATTAACGACTGAAATAAAACTAAACCTTTCGAATAGTTTAT
1 TTGCTAGCTAAAATTTTAAAAAAAATTAACGACTGAAATAAAACTAAACCTTTCGAATAGTTTAT
2698049 TAACTTAAATAAAAGCTTTCAAATAGTATAGTAACCATTTTATTAATTTTTTAAAATTAAGTGAC
66 TAACTTAAATAAAAGCTTTCAAATAGTATAGTAACCATTTTATTAATTTTTTAAAATTAAGTGAC
2698114 TGAAATATAATTCTACTAATAATTTAATGACCTTTGGTGCAATTTTCCCTTAAAATAATTGAAGA
131 TGAAATATAATTCTACTAATAATTTAATGACCTTTGGTGCAATTTTCCCTTAAAATAATTGAAGA
2698179 AA
196 AA
*
2698181 TTGCTAGCTAAAATTTTTAAAAAAATTAACGACTGAAATAAAACTAAACCTTTCGAATAGTTTAT
1 TTGCTAGCTAAAATTTTAAAAAAAATTAACGACTGAAATAAAACTAAACCTTTCGAATAGTTTAT
2698246 TAACTTAAATAAAAGCTTTCAAATAGTATAGTAACCATTTTATTAATTTTTTAAAATTAAGTGAC
66 TAACTTAAATAAAAGCTTTCAAATAGTATAGTAACCATTTTATTAATTTTTTAAAATTAAGTGAC
2698311 TGAAATATAATTCTACTAATAATTTAATGACCTTTGGTGCAATTTTCCCTTAAAATAATTGAAGA
131 TGAAATATAATTCTACTAATAATTTAATGACCTTTGGTGCAATTTTCCCTTAAAATAATTGAAGA
2698376 A
196 A
2698377 CCCAAATGTA
Statistics
Matches: 195, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
197 195 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (197 bp):
TTGCTAGCTAAAATTTTAAAAAAAATTAACGACTGAAATAAAACTAAACCTTTCGAATAGTTTAT
TAACTTAAATAAAAGCTTTCAAATAGTATAGTAACCATTTTATTAATTTTTTAAAATTAAGTGAC
TGAAATATAATTCTACTAATAATTTAATGACCTTTGGTGCAATTTTCCCTTAAAATAATTGAAGA
AA
Found at i:2713639 original size:9 final size:9
Alignment explanation
Indices: 2713627--2713663 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
2713617 TTTATCAAAT
2713627 TATTAATTG
1 TATTAATTG
2713636 TATTAATTG
1 TATTAATTG
2713645 TATTAATTG
1 TATTAATTG
2713654 TATTAATTG
1 TATTAATTG
2713663 T
1 T
2713664 TGTAACAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:2720180 original size:16 final size:16
Alignment explanation
Indices: 2720159--2720190 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2720149 AAACAAAACG
2720159 TGAAAGGGAATGGGAA
1 TGAAAGGGAATGGGAA
2720175 TGAAAGGGAATGGGAA
1 TGAAAGGGAATGGGAA
2720191 AGAAGTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (16 bp):
TGAAAGGGAATGGGAA
Found at i:2723879 original size:140 final size:140
Alignment explanation
Indices: 2723627--2723911 Score: 471
Period size: 140 Copynumber: 2.0 Consensus size: 140
2723617 GAAGTCAAAG
* *
2723627 AAACTTATCTAAATTCATTTGTAAATGATAAATTTAAGTTTTGGACATCAGCCTTCCTTTAAAAT
1 AAACTTATCTAAATTCATTTGTAAATGATAAATTTAAGATTTGGACATCAACCTTCCTTTAAAAT
* *
2723692 TTTGAACACTCCTCGAAGTACAAACTCCAACATCCCTCATGTTCCGATAGCGTTCCTCCTCTAAA
66 TTCGAACACTCCTCGAAGTACAAACTCCAACATCCCTCATGTTCCGATAGCGTTCCTCCTCAAAA
2723757 GACTATCAAC
131 GACTATCAAC
* * *
2723767 AAACTTATCTAAATTCATTTGTAAATGATAAATTTAAGATTTGGACATCAACTTTTCTTTGAAAT
1 AAACTTATCTAAATTCATTTGTAAATGATAAATTTAAGATTTGGACATCAACCTTCCTTTAAAAT
* * * *
2723832 TTCGAACGCTTCTCGAAGTACAAACTCCGACATCCCTCATGTTCCGATAGTGTTCCTCCTCAAAA
66 TTCGAACACTCCTCGAAGTACAAACTCCAACATCCCTCATGTTCCGATAGCGTTCCTCCTCAAAA
2723897 GACTATCAAC
131 GACTATCAAC
2723907 AAACT
1 AAACT
2723912 GCATAATTAT
Statistics
Matches: 134, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
140 134 1.00
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (140 bp):
AAACTTATCTAAATTCATTTGTAAATGATAAATTTAAGATTTGGACATCAACCTTCCTTTAAAAT
TTCGAACACTCCTCGAAGTACAAACTCCAACATCCCTCATGTTCCGATAGCGTTCCTCCTCAAAA
GACTATCAAC
Found at i:2735684 original size:23 final size:23
Alignment explanation
Indices: 2735649--2735694 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2735639 GGCTAGCTTA
*
2735649 TTTTTTTATTTAATATTAAATAT
1 TTTTTTTATTTAAAATTAAATAT
*
2735672 TTTTATTTA-TTAAAATTATATAT
1 TTTT-TTTATTTAAAATTAAATAT
2735695 ATGCAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTTTTTATTTAAAATTAAATAT
Found at i:2750915 original size:26 final size:28
Alignment explanation
Indices: 2750869--2750931 Score: 94
Period size: 26 Copynumber: 2.3 Consensus size: 28
2750859 GAGATCATGG
2750869 AAGATGATCTCATAGGAGATGATCAACT
1 AAGATGATCTCATAGGAGATGATCAACT
*
2750897 AAGATGA-C-CATAGGAGATGATCAAGT
1 AAGATGATCTCATAGGAGATGATCAACT
*
2750923 GAGATGATC
1 AAGATGATC
2750932 CAGACGAGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 23 0.72
27 2 0.06
28 7 0.22
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (28 bp):
AAGATGATCTCATAGGAGATGATCAACT
Found at i:2750930 original size:13 final size:13
Alignment explanation
Indices: 2750884--2750931 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
2750874 GATCTCATAG
*
2750884 GAGATGATCAACT
1 GAGATGATCAAGT
* *
2750897 AAGATGACCATAG-
1 GAGATGATCA-AGT
2750910 GAGATGATCAAGT
1 GAGATGATCAAGT
2750923 GAGATGATC
1 GAGATGATC
2750932 CAGACGAGGC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
12 2 0.07
13 25 0.89
14 1 0.04
ACGTcount: A:0.40, C:0.12, G:0.27, T:0.21
Consensus pattern (13 bp):
GAGATGATCAAGT
Found at i:2753222 original size:64 final size:62
Alignment explanation
Indices: 2753078--2753329 Score: 396
Period size: 62 Copynumber: 4.0 Consensus size: 62
2753068 AATTTGGATT
* *
2753078 ATATTGTGGCACATTATACTTTTTAAGCCTAAAATGCAACTCCATTTCCTCAAAATTGGACC
1 ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACC
* *
2753140 CTATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACTCCATATTTCCTCAAAATTGGACC
1 ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAAC-CC-CATTTCCTCAAAATTGGACC
*
2753204 ATATTGTGGCACATTATACTTTTAAAGCCTAAATTGCAACCCCATTTCCTCAAAATTGGACC
1 ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACC
* * * * *
2753266 ATATTGTGGCACATTATGCTTTTGAAGTCTAAAATGCAACCCCATCTCCTCAAGATTGGACC
1 ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACC
2753328 AT
1 AT
2753330 GATGGCCTTG
Statistics
Matches: 175, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
62 115 0.66
63 3 0.02
64 57 0.33
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (62 bp):
ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACC
Found at i:2753224 original size:126 final size:124
Alignment explanation
Indices: 2753078--2753329 Score: 396
Period size: 126 Copynumber: 2.0 Consensus size: 124
2753068 AATTTGGATT
* * *
2753078 ATATTGTGGCACATTATACTTTTTAAGCCTAAAATGCAACTCCATTTCCTCAAAATTGGACCCTA
1 ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACCATA
* *
2753143 TTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACTCCATATTTCCTCAAAATTGGACC
66 TTGTGGCACATTATACTTTTAAAGCCTAAAATGCAAC-CC-CATCTCCTCAAAATTGGACC
*
2753204 ATATTGTGGCACATTATACTTTTAAAGCCTAAATTGCAACCCCATTTCCTCAAAATTGGACCATA
1 ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACCATA
* * * *
2753269 TTGTGGCACATTATGCTTTTGAAGTCTAAAATGCAACCCCATCTCCTCAAGATTGGACC
66 TTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATCTCCTCAAAATTGGACC
2753328 AT
1 AT
2753330 GATGGCCTTG
Statistics
Matches: 116, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
124 19 0.16
125 2 0.02
126 95 0.82
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (124 bp):
ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACCATA
TTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATCTCCTCAAAATTGGACC
Found at i:2753911 original size:6 final size:6
Alignment explanation
Indices: 2753900--2753928 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2753890 TATAATCTTA
2753900 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
2753929 GGGTGTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:2763550 original size:2 final size:2
Alignment explanation
Indices: 2763545--2763588 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2763535 CAGTGTGTGA
2763545 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2763587 AT
1 AT
2763589 TACAACAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2765745 original size:22 final size:20
Alignment explanation
Indices: 2765699--2765747 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
2765689 AGCTCTGTTA
*
2765699 CCAAAAATTGTATATAAGTT
1 CCAAAAATTGTATAGAAGTT
*
2765719 CCAAAAATTGTATGTAGAATTT
1 CCAAAAATTGTA--TAGAAGTT
2765741 CCAAAAA
1 CCAAAAA
2765748 GAAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.48
22 13 0.52
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
CCAAAAATTGTATAGAAGTT
Found at i:2768090 original size:31 final size:32
Alignment explanation
Indices: 2768047--2768112 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
2768037 TTAGGCTATT
* *
2768047 AAAAATTTTAATTAGA-CTTCTAAATTATTTG
1 AAAAATTCTAATTAGACCTTCAAAATTATTTG
*
2768078 AAAAATTCTAATTAGACCCTTCAAAATTTTTTG
1 AAAAATTCTAATTAGA-CCTTCAAAATTATTTG
2768111 AA
1 AA
2768113 TTCTCATTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 15 0.50
33 15 0.50
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.41
Consensus pattern (32 bp):
AAAAATTCTAATTAGACCTTCAAAATTATTTG
Found at i:2768122 original size:30 final size:30
Alignment explanation
Indices: 2768081--2768139 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
2768071 TTATTTGAAA
2768081 AATTCTAATTAGACCCTTCAAAATTTTTTG
1 AATTCTAATTAGACCCTTCAAAATTTTTTG
* **
2768111 AATTCTCATTAGATTCTTCAAAATTTTTT
1 AATTCTAATTAGACCCTTCAAAATTTTTT
2768140 TTTAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.05, T:0.47
Consensus pattern (30 bp):
AATTCTAATTAGACCCTTCAAAATTTTTTG
Found at i:2775313 original size:2 final size:2
Alignment explanation
Indices: 2775306--2775334 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2775296 CAAAGCAACG
2775306 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2775335 CTGTCATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2778019 original size:22 final size:22
Alignment explanation
Indices: 2777970--2778020 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
2777960 GTTAGTGAAT
2777970 AAAAATATATAAATATAAATAA
1 AAAAATATATAAATATAAATAA
* * *
2777992 ACAAATATTTATATATAAA-AA
1 AAAAATATATAAATATAAATAA
2778013 ATAAAATA
1 A-AAAATA
2778021 AATTGAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAATATATAAATATAAATAA
Found at i:2779011 original size:125 final size:125
Alignment explanation
Indices: 2778772--2779306 Score: 684
Period size: 125 Copynumber: 4.3 Consensus size: 125
2778762 ATTAATGCAG
* * * * *
2778772 TCGCGGCCACGTGAACGCGCTTTTGGTACAGTAGGTCCTGAA-AAATTTATTTCGAGTTGATGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAGAAA-TAATTTCGAGTTGACGTT
* * * * *
2778836 TCTGAGCAAATAGTATAAAAAACACTTCAAGCAGGGTGCTATATGCGAAGAATTTGTGAAA
65 TCTGAGCAAATAGTATAAAAATCGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAA
* * *
2778897 TCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGGAATAATTTCGAGTTGACGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCT-GAAGAAATAATTTCGAGTTGACGTT
* **
2778962 TCTAAGCAAATAGTAT-AAAATCGCTTC-TCCTAGGATGCTTTATGAGAAGAATTTGTGAAA
65 TCTGAGCAAATAGTATAAAAATCGCTTCAAGC-AGGATGCTTTATGAGAAGAATTTGTGAAA
* * * *
2779022 TCGCACCCACGTGGACGTGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACGTTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAGAAATAATTTCGAGTTGACGTTT
* * *
2779087 CTGAGCAAATAGTATAAAAAAGCGCTTCAAGCAGGATG-TTATTTGCGAAGAATTTGTGAAA
66 CTGAGCAAATAGTAT-AAAAATCGCTTCAAGCAGGATGCTT-TATGAGAAGAATTTGTGAAA
* * * * *
2779148 TCGCGGCCTCATGGACGCGCTTTTGCTACAATTGGTCCTGGAAGAAATAATTTCGAGTTGACGTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCT-GAAGAAATAATTTCGAGTTGACGTT
* * * **
2779213 TCTGAGCAAATAGTAT-AAAATTGCTTCTATCAGGATGCTTTATGAGGGGAATTTGTGAAA
65 TCTGAGCAAATAGTATAAAAATCGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAA
2779273 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
2779307 CATGTTTGGG
Statistics
Matches: 350, Mismatches: 51, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
124 38 0.11
125 168 0.48
126 102 0.29
127 42 0.12
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (125 bp):
TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAGAAATAATTTCGAGTTGACGTTT
CTGAGCAAATAGTATAAAAATCGCTTCAAGCAGGATGCTTTATGAGAAGAATTTGTGAAA
Found at i:2779223 original size:251 final size:250
Alignment explanation
Indices: 2778778--2779306 Score: 862
Period size: 251 Copynumber: 2.1 Consensus size: 250
2778768 GCAGTCGCGG
* * * *
2778778 CCACGTGAACGCGCTTTTGGTACAGTAGGTCCTGAAAAATTTATTTCGAGTTGATGTTTCTGAGC
1 CCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGC
* *
2778843 AAATAGTATAAAAAACACTTCAAGCAGGGTGCTATATGCGAAGAATTTGTGAAATCGCGCCCTCG
66 AAATAGTATAAAAAACACTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAATCGCGCCCTCA
* *
2778908 TGGACGCGCTTTTGCTACAGTTGGTCCTGGAAGGAATAATTTCGAGTTGACGTTTCTAAGCAAAT
131 TGGACGCGCTTTTGCTACAATTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTAAGCAAAT
*
2778973 AGTATAAAATCGCTTCT-CCTAGGATGCTTTATGAGAAGAATTTGTGAAATCGCAC
196 AGTATAAAATCGCTTCTATC-AGGATGCTTTATGAGAAGAATTTGTGAAATCGCAC
*
2779028 CCACGTGGACGTGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGC
1 CCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGC
* * * *
2779093 AAATAGTATAAAAAAGCGCTTCAAGCAGGATGTTATTTGCGAAGAATTTGTGAAATCGCGGCCTC
66 AAATAGTATAAAAAA-CACTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAATCGCGCCCTC
*
2779158 ATGGACGCGCTTTTGCTACAATTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAA
130 ATGGACGCGCTTTTGCTACAATTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTAAGCAAA
* ** *
2779223 TAGTATAAAATTGCTTCTATCAGGATGCTTTATGAGGGGAATTTGTGAAATCGCGC
195 TAGTATAAAATCGCTTCTATCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCAC
2779279 CCACGTGGACGCGCTTTTGCTACAGTAG
1 CCACGTGGACGCGCTTTTGCTACAGTAG
2779307 CATGTTTGGG
Statistics
Matches: 257, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
250 75 0.29
251 181 0.70
252 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (250 bp):
CCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGC
AAATAGTATAAAAAACACTTCAAGCAGGATGCTATATGCGAAGAATTTGTGAAATCGCGCCCTCA
TGGACGCGCTTTTGCTACAATTGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTAAGCAAAT
AGTATAAAATCGCTTCTATCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCAC
Found at i:2779878 original size:58 final size:59
Alignment explanation
Indices: 2779804--2779925 Score: 219
Period size: 59 Copynumber: 2.1 Consensus size: 59
2779794 GTAAAAAAGA
2779804 GGGGGGACTTTTG-TTTTTTTGAAATCGGTATACAAACCGATTGAAACCTTTGTAACGG
1 GGGGGGACTTTTGTTTTTTTTGAAATCGGTATACAAACCGATTGAAACCTTTGTAACGG
* *
2779862 GGGGGGACTTTTGTTTTTTTTTAAATCGGTATACAAACCGATTGAAACCTTTGTAATGG
1 GGGGGGACTTTTGTTTTTTTTGAAATCGGTATACAAACCGATTGAAACCTTTGTAACGG
2779921 GGGGG
1 GGGGG
2779926 TTTTATTTTC
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
58 13 0.21
59 48 0.79
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.35
Consensus pattern (59 bp):
GGGGGGACTTTTGTTTTTTTTGAAATCGGTATACAAACCGATTGAAACCTTTGTAACGG
Found at i:2780831 original size:24 final size:23
Alignment explanation
Indices: 2780800--2780844 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2780790 TATACATACC
* *
2780800 TTATTATATATCTTTATATCTTA
1 TTATTATATATATCTATATCTTA
2780823 TTATGTATATATATCTATATCT
1 TTAT-TATATATATCTATATCT
2780845 CTTCTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATTATATATATCTATATCTTA
Found at i:2780992 original size:20 final size:20
Alignment explanation
Indices: 2780967--2781004 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2780957 TTTATTTCAT
2780967 ATATATACATACATACATGC
1 ATATATACATACATACATGC
* *
2780987 ATATATATATATATACAT
1 ATATATACATACATACAT
2781005 TATAATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (20 bp):
ATATATACATACATACATGC
Found at i:2781142 original size:18 final size:18
Alignment explanation
Indices: 2781095--2781138 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2781085 CTTAAAGTGC
*
2781095 TTTAATTTTATTTGTTTA
1 TTTACTTTTATTTGTTTA
2781113 TTTACTTTTATTTGTTTA
1 TTTACTTTTATTTGTTTA
2781131 TTT-CTTTT
1 TTTACTTTT
2781139 TATTATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTACTTTTATTTGTTTA
Found at i:2787485 original size:22 final size:21
Alignment explanation
Indices: 2787417--2787488 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
2787407 TGCGAAATAT
*
2787417 GGTTTTTAAGGTTAGGGTTTGG
1 GGTTTTT-AGGTAAGGGTTTGG
* * *
2787439 GGTGTTTAGGTTAAGGTTTTAG
1 GGTTTTTAGG-TAAGGGTTTGG
*
2787461 GGTTTTTAGGCTAAGGGTGTGG
1 GGTTTTTAGG-TAAGGGTTTGG
2787483 GGTTTT
1 GGTTTT
2787489 AAAGTTAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 3 0.08
22 37 0.93
ACGTcount: A:0.14, C:0.01, G:0.40, T:0.44
Consensus pattern (21 bp):
GGTTTTTAGGTAAGGGTTTGG
Found at i:2788098 original size:18 final size:18
Alignment explanation
Indices: 2788066--2788105 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2788056 GACTCAGAAA
** *
2788066 AGGATACATGTAAGGGTT
1 AGGATACATAAAAGGGCT
2788084 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
2788102 AGGA
1 AGGA
2788106 AACGCACCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:2790050 original size:12 final size:11
Alignment explanation
Indices: 2790004--2790042 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
2789994 AATATGAATA
2790004 TGAGA-GAAAT
1 TGAGAGGAAAT
2790014 TGAGAGGAAAT
1 TGAGAGGAAAT
2790025 TGAGAGGAAATT
1 TGAGAGGAAA-T
2790037 TGAGAG
1 TGAGAG
2790043 AAGATTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 5 0.19
11 15 0.56
12 7 0.26
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.21
Consensus pattern (11 bp):
TGAGAGGAAAT
Found at i:2791012 original size:30 final size:30
Alignment explanation
Indices: 2790978--2791036 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
2790968 TTAACAAGCA
2790978 AATGCCTTTAAAATAATAACAAAATTAACG
1 AATGCCTTTAAAATAATAACAAAATTAACG
*
2791008 AATGCCTTTAAATTAATAACAAAATTAAC
1 AATGCCTTTAAAATAATAACAAAATTAAC
2791037 AATAAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.29
Consensus pattern (30 bp):
AATGCCTTTAAAATAATAACAAAATTAACG
Found at i:2791093 original size:22 final size:22
Alignment explanation
Indices: 2791068--2791110 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2791058 TATCCAAACA
2791068 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* *
2791090 ATAATAACAAAATGGTAGCAA
1 ATAACAACAAAATAGTAGCAA
2791111 AATAGGGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.14, G:0.12, T:0.16
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:2791699 original size:14 final size:15
Alignment explanation
Indices: 2791680--2791709 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2791670 CAACCCAAAA
2791680 ATCAAACCC-ATTAC
1 ATCAAACCCAATTAC
2791694 ATCAAACCCAATTAC
1 ATCAAACCCAATTAC
2791709 A
1 A
2791710 GGCCCAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (15 bp):
ATCAAACCCAATTAC
Found at i:2792853 original size:23 final size:22
Alignment explanation
Indices: 2792826--2792933 Score: 83
Period size: 23 Copynumber: 4.5 Consensus size: 22
2792816 AATTTATCGA
2792826 ATATTATTATTTTAATTTTGCAT
1 ATATTATTATTTTAATTTT-CAT
*
2792849 GTATTATT-TTTCTAAGCTTTTCATGT
1 ATATTATTATTT-TAA--TTTTCA--T
* * *
2792875 ATTAATATTTTTTTAATTTATTAT
1 A-TATTATTATTTTAATTT-TCAT
*
2792899 ATATTATTATTTTAATTTCCAT
1 ATATTATTATTTTAATTTTCAT
2792921 ATATATATTATTT
1 ATAT-TATTATTT
2792934 CATATGTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
22 9 0.13
23 33 0.49
24 4 0.06
25 7 0.10
26 3 0.04
27 9 0.13
28 3 0.04
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.61
Consensus pattern (22 bp):
ATATTATTATTTTAATTTTCAT
Found at i:2798733 original size:6 final size:6
Alignment explanation
Indices: 2798722--2798754 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
2798712 TTAATAATAA
2798722 ATATAG ATATAG ATATAG ATATAG ATATAG ATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATA
2798755 GGCTAACAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (6 bp):
ATATAG
Found at i:2806778 original size:24 final size:26
Alignment explanation
Indices: 2806751--2806799 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
2806741 AGTTTAGACT
2806751 CATA-GCAAATT-AGTTACATATATA
1 CATATGCAAATTCAGTTACATATATA
* *
2806775 CATATGCAATTTCAGTTTCATATAT
1 CATATGCAAATTCAGTTACATATAT
2806800 GATACAGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 6 0.29
26 11 0.52
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (26 bp):
CATATGCAAATTCAGTTACATATATA
Found at i:2812127 original size:30 final size:30
Alignment explanation
Indices: 2812086--2812152 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
2812076 CACATGGCCA
* * * *
2812086 TGTGGCTCACACGGCTTGGACCCACACTCG
1 TGTGCCTCACACGGCTTAGACACACACCCG
*
2812116 TGTGCCTCACACGGCTTAGACACACGCCCG
1 TGTGCCTCACACGGCTTAGACACACACCCG
2812146 TGTGCCT
1 TGTGCCT
2812153 AGGCTTGTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.16, C:0.37, G:0.25, T:0.21
Consensus pattern (30 bp):
TGTGCCTCACACGGCTTAGACACACACCCG
Found at i:2817322 original size:36 final size:36
Alignment explanation
Indices: 2817282--2817394 Score: 95
Period size: 36 Copynumber: 3.1 Consensus size: 36
2817272 TGCCAATAGC
* *
2817282 ATGTTTTTGATTTGTTAAACTATATGTGCAATTAGT
1 ATGTTTTTGATCTGTTAAACTATATGTGCAACTAGT
* * * * * * * *
2817318 ATG-TTCTGATCCGTTTTATCTGA-ATATGCCAGTAGC
1 ATGTTTTTGATCTG-TTAAACT-ATATGTGCAACTAGT
*
2817354 ATGTTTTTTATCTGTTAAACTATATGTGCAACTAGT
1 ATGTTTTTGATCTGTTAAACTATATGTGCAACTAGT
2817390 ATGTT
1 ATGTT
2817395 CTAATTTGTT
Statistics
Matches: 55, Mismatches: 18, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
35 8 0.15
36 39 0.71
37 8 0.15
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.46
Consensus pattern (36 bp):
ATGTTTTTGATCTGTTAAACTATATGTGCAACTAGT
Found at i:2817390 original size:72 final size:72
Alignment explanation
Indices: 2817271--2817411 Score: 219
Period size: 72 Copynumber: 2.0 Consensus size: 72
2817261 ATGGTCGAAC
* * *
2817271 ATGCCAATAGCATGTTTTTGATTTGTTAAACTATATGTGCAATTAGTATGTTCTGATCCGTTTTA
1 ATGCCAATAGCATGTTTTTGATCTGTTAAACTATATGTGCAACTAGTATGTTCTAATCCGTTTTA
2817336 TCTGAAT
66 TCTGAAT
* * **
2817343 ATGCCAGTAGCATGTTTTTTATCTGTTAAACTATATGTGCAACTAGTATGTTCTAATTTGTTTTA
1 ATGCCAATAGCATGTTTTTGATCTGTTAAACTATATGTGCAACTAGTATGTTCTAATCCGTTTTA
2817408 TCTG
66 TCTG
2817412 TATAAGGGCA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (72 bp):
ATGCCAATAGCATGTTTTTGATCTGTTAAACTATATGTGCAACTAGTATGTTCTAATCCGTTTTA
TCTGAAT
Found at i:2818874 original size:22 final size:23
Alignment explanation
Indices: 2818844--2818886 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
2818834 AAACATATAT
2818844 ATATATATA-TATATATAATTTAG
1 ATATATATAGTAT-TATAATTTAG
2818867 ATAT-TATAGTATTATAATTT
1 ATATATATAGTATTATAATTT
2818887 TATCATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (23 bp):
ATATATATAGTATTATAATTTAG
Found at i:2823010 original size:27 final size:26
Alignment explanation
Indices: 2822954--2823011 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
2822944 GTTAACACTT
* *
2822954 AAAAACTAAAGAATTTAAAGTTCATC
1 AAAAACTAAAGAAATTAAAGTGCATC
* * *
2822980 AAAACACTAAATAAATTAATGTGCATG
1 AAAA-ACTAAAGAAATTAAAGTGCATC
2823007 AAAAA
1 AAAAA
2823012 TGTATGAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.57, C:0.10, G:0.09, T:0.24
Consensus pattern (26 bp):
AAAAACTAAAGAAATTAAAGTGCATC
Found at i:2824501 original size:20 final size:20
Alignment explanation
Indices: 2824465--2824502 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2824455 GTTTTTTGTT
**
2824465 TTTGTTGCGTTTTTTGTGCG
1 TTTGTTGCGTTCGTTGTGCG
2824485 TTTGTTGCGTTCGTTGTG
1 TTTGTTGCGTTCGTTGTG
2824503 TGTAGGGGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.11, G:0.32, T:0.58
Consensus pattern (20 bp):
TTTGTTGCGTTCGTTGTGCG
Found at i:2825356 original size:21 final size:21
Alignment explanation
Indices: 2825332--2825394 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
2825322 CTCAATTATG
* *
2825332 TTTGAGAAATTTAATTTTGAT
1 TTTGAGAAAATGAATTTTGAT
2825353 TTTGAGAAAATGAATTTTGAT
1 TTTGAGAAAATGAATTTTGAT
2825374 TTTGAGAAAATGAATTTTGAT
1 TTTGAGAAAATGAATTTTGAT
2825395 CAAGCAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (21 bp):
TTTGAGAAAATGAATTTTGAT
Found at i:2825956 original size:24 final size:21
Alignment explanation
Indices: 2825928--2825994 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
2825918 AATATTAAAT
2825928 TAAATTTAATATTTATATTGTAGA
1 TAAATTTAATATTTA-ATT-TA-A
2825952 TAAATATT-ATA-TTAATTTAA
1 TAAAT-TTAATATTTAATTTAA
* *
2825972 TAGATTTAATATTAAATTTAA
1 TAAATTTAATATTTAATTTAA
2825993 TA
1 TA
2825995 TAATACTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 2 0.05
20 8 0.21
21 12 0.32
22 3 0.08
23 3 0.08
24 8 0.21
25 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
TAAATTTAATATTTAATTTAA
Found at i:2825988 original size:61 final size:59
Alignment explanation
Indices: 2825831--2826030 Score: 181
Period size: 68 Copynumber: 3.2 Consensus size: 59
2825821 TCCAAAAATA
* * **
2825831 ATATTATTTTAATAAATTTAATATTAAATTTAATTTAATACTTATCTTCATAG-TATTTTATT
1 ATATTAATTTAATAGATTTAATATTAAATTTAATTTAATACTTAT-TT--TAGATA-AATATT
* *
2825893 A-ATTTAATATTAAAGTGAGTATCTTAATATTAAATTAAATTTAATATTTATATTGTAGATAAAT
1 ATA-TTAAT-TT-AA-T-AG-AT-TTAATATTAAATTTAATTTAATACTTAT-TT-TAGATAAAT
2825957 ATT
57 ATT
* * *
2825960 ATATTAATTTAATAGATTTAATATTAAATTTAATATAATACTTATCTTA-ATAAGTATT
1 ATATTAATTTAATAGATTTAATATTAAATTTAATTTAATACTTATTTTAGATAAATATT
2826018 ATATTAATTTAAT
1 ATATTAATTTAAT
2826031 TAGAGTGATT
Statistics
Matches: 116, Mismatches: 13, Indels: 22
0.77 0.09 0.15
Matches are distributed among these distances:
58 21 0.18
59 2 0.02
60 1 0.01
61 26 0.22
62 7 0.06
63 4 0.03
64 3 0.03
65 3 0.03
66 3 0.03
67 15 0.13
68 31 0.27
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (59 bp):
ATATTAATTTAATAGATTTAATATTAAATTTAATTTAATACTTATTTTAGATAAATATT
Found at i:2827754 original size:36 final size:36
Alignment explanation
Indices: 2827707--2827805 Score: 162
Period size: 36 Copynumber: 2.8 Consensus size: 36
2827697 GCTAAGCTAC
*
2827707 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAA
* *
2827743 CACTTATCACTTTTTCACTTGATCAGATAATTATAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAA
*
2827779 CACTTATCACTTTGTCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
2827806 AGTACTCAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.39
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAA
Found at i:2827754 original size:43 final size:42
Alignment explanation
Indices: 2827662--2827790 Score: 121
Period size: 36 Copynumber: 3.2 Consensus size: 42
2827652 CTTACGTATG
* *
2827662 ATCACTTATCATTTGTC-CCTGATCAGATAAGTGTAGCTAAGC-T
1 ATCACTTATCATTTGTCACTTGATCAGATAAGTATAGC--A-CTT
*
2827705 ACCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCACTT
1 ATCACTTATCA-TTTGTCACTTGATCAGATAAGTATAGCACTT
* *
2827748 ATCAC---T--TTT-TCACTTGATCAGATAATTATAACACTT
1 ATCACTTATCATTTGTCACTTGATCAGATAAGTATAGCACTT
2827784 ATCACTT
1 ATCACTT
2827791 TGTCTCTTGA
Statistics
Matches: 75, Mismatches: 6, Indels: 15
0.78 0.06 0.16
Matches are distributed among these distances:
36 30 0.40
37 3 0.04
40 1 0.01
42 1 0.01
43 16 0.21
44 6 0.08
45 18 0.24
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (42 bp):
ATCACTTATCATTTGTCACTTGATCAGATAAGTATAGCACTT
Found at i:2833390 original size:17 final size:18
Alignment explanation
Indices: 2833368--2833402 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2833358 ATTTGGGTCA
2833368 TGTGGG-CCACACGGGCG
1 TGTGGGCCCACACGGGCG
*
2833385 TGTGGGCCCACTCGGGCG
1 TGTGGGCCCACACGGGCG
2833403 AACATCATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.09, C:0.31, G:0.46, T:0.14
Consensus pattern (18 bp):
TGTGGGCCCACACGGGCG
Found at i:2834335 original size:18 final size:17
Alignment explanation
Indices: 2834313--2834356 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
2834303 TAAAAATACG
2834313 TTTTGAAATTGAATAATGA
1 TTTTGAAA-TGAATAAT-A
2834332 -TTTGTAAATGAATAATA
1 TTTTG-AAATGAATAATA
2834349 TTTTGAAA
1 TTTTGAAA
2834357 ACAAACGACA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.17
18 16 0.70
19 3 0.13
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (17 bp):
TTTTGAAATGAATAATA
Found at i:2836434 original size:2 final size:2
Alignment explanation
Indices: 2836422--2836452 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2836412 TTTAATGAAG
2836422 AT AT A- 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
2836453 CAGCATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2841128 original size:25 final size:25
Alignment explanation
Indices: 2841100--2841149 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2841090 CCTGCAAAGA
2841100 TAAAAATGAAAATAA-AATAA-AATAG
1 TAAAAAT--AAATAATAATAATAATAG
2841125 TAAAAATAAATAATAATAATAATAG
1 TAAAAATAAATAATAATAATAATAG
2841150 GAATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.26
24 5 0.22
25 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (25 bp):
TAAAAATAAATAATAATAATAATAG
Found at i:2848544 original size:8 final size:8
Alignment explanation
Indices: 2848531--2848560 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
2848521 CCAACTTAAT
2848531 TATTAAAA
1 TATTAAAA
2848539 TATTAAAA
1 TATTAAAA
2848547 TATTAAAA
1 TATTAAAA
2848555 TATTAA
1 TATTAA
2848561 TAAATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TATTAAAA
Found at i:2849002 original size:71 final size:71
Alignment explanation
Indices: 2848884--2849023 Score: 262
Period size: 72 Copynumber: 2.0 Consensus size: 71
2848874 ACCAACACCA
*
2848884 TGATAAAGAATTGTACTCATTTTTTATTTTTAATTTGATGTATTTTTTTGTGTTTAAATTTCGTT
1 TGATAAAGAATTGTACTCATTTTTTATTTCTAATTTGATGTATTTTTTTGTGTTTAAATTTCGTT
2848949 TTAATT
66 TTAATT
2848955 TGATAAAGAATTGTACTCATTTTTTTATTTCTAATTTGATGTATTTTTTTGTGTTTAAATTTCGT
1 TGATAAAGAATTGTACTCA-TTTTTTATTTCTAATTTGATGTATTTTTTTGTGTTTAAATTTCGT
2849020 TTTA
65 TTTA
2849024 CTTACAATTT
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
71 19 0.28
72 48 0.72
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.59
Consensus pattern (71 bp):
TGATAAAGAATTGTACTCATTTTTTATTTCTAATTTGATGTATTTTTTTGTGTTTAAATTTCGTT
TTAATT
Found at i:2849600 original size:22 final size:22
Alignment explanation
Indices: 2849575--2849616 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2849565 TTTAATATTG
*
2849575 TTAAATATGTAATTATTAATCC
1 TTAAATATATAATTATTAATCC
* *
2849597 TTAAATTTATAATTCTTAAT
1 TTAAATATATAATTATTAAT
2849617 TTTTTTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.50
Consensus pattern (22 bp):
TTAAATATATAATTATTAATCC
Found at i:2849814 original size:18 final size:18
Alignment explanation
Indices: 2849775--2849818 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
2849765 CATTGCTTCT
*
2849775 CAAAAGTACTTTTGAGAT
1 CAAAAGTACTTTTGAGAC
2849793 CAAAAGTACTTTTGA-AGC
1 CAAAAGTACTTTTGAGA-C
2849811 CAAAAGTA
1 CAAAAGTA
2849819 ATGTCAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (18 bp):
CAAAAGTACTTTTGAGAC
Found at i:2850221 original size:100 final size:100
Alignment explanation
Indices: 2850113--2850305 Score: 350
Period size: 100 Copynumber: 1.9 Consensus size: 100
2850103 CTTAAAAATA
*
2850113 TTTAAAATTTATATTTCATATATTAAAATATTAACAAAAAATTATAATAAATTGTGTTTTATATT
1 TTTAAAATTTATATTTCATATATTAAAATATTAACAAAAAATTATAATAAATTATGTTTTATATT
2850178 CTTACTAAGATATCATAAGATTAACTAACTTATTT
66 CTTACTAAGATATCATAAGATTAACTAACTTATTT
* *
2850213 TTTAAAATTTATATTTCATATATTAAAATATTAACAACAAATTATAATAAATTATTTTTTATATT
1 TTTAAAATTTATATTTCATATATTAAAATATTAACAAAAAATTATAATAAATTATGTTTTATATT
*
2850278 CTTACTAAGATATCATAATATTAACTAA
66 CTTACTAAGATATCATAAGATTAACTAA
2850306 TTTGAATATT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 89 1.00
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (100 bp):
TTTAAAATTTATATTTCATATATTAAAATATTAACAAAAAATTATAATAAATTATGTTTTATATT
CTTACTAAGATATCATAAGATTAACTAACTTATTT
Found at i:2850274 original size:50 final size:49
Alignment explanation
Indices: 2850120--2850277 Score: 119
Period size: 50 Copynumber: 3.2 Consensus size: 49
2850110 ATATTTAAAA
* *
2850120 TTTATATTTCATATATTAAAATATTAACAAAAAATTATAATAAATTGTGT
1 TTTATATTTCATATATTAAAATATTAACAACAAATTATAATAAATTAT-T
* * * * ** **
2850170 TTTATATTCTTACTAAGATATCATAAGATTAACTAACTTATT-TTTTAAA--A--
1 TTTATA-T-TT-C--ATATATTAAAATATTAAC-AACAAATTATAATAAATTATT
2850220 TTTATATTTCATATATTAAAATATTAACAACAAATTATAATAAATTATTT
1 TTTATATTTCATATATTAAAATATTAACAACAAATTATAATAAATTA-TT
2850270 TTTATATT
1 TTTATATT
2850278 CTTACTAAGA
Statistics
Matches: 78, Mismatches: 18, Indels: 24
0.65 0.15 0.20
Matches are distributed among these distances:
44 6 0.08
45 19 0.24
47 2 0.03
48 2 0.03
49 1 0.01
50 20 0.26
51 1 0.01
52 2 0.03
53 1 0.01
55 19 0.24
56 5 0.06
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (49 bp):
TTTATATTTCATATATTAAAATATTAACAACAAATTATAATAAATTATT
Found at i:2851662 original size:39 final size:39
Alignment explanation
Indices: 2851618--2851705 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 39
2851608 TAAACTTCTA
* * *
2851618 ATTTTTTTAATATTTTTAGAATAT-TTT-AAGATTGTTAAT
1 ATTTTTTTAATATTTTTACAAT-TCTTTAAAGATT-CTAAC
* *
2851657 ATTTTTATAATTTTTTTACAATTCTTTAAAGATTCTAAC
1 ATTTTTTTAATATTTTTACAATTCTTTAAAGATTCTAAC
2851696 ATTTTTTTAA
1 ATTTTTTTAA
2851706 AAAAAATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
38 1 0.02
39 34 0.83
40 6 0.15
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (39 bp):
ATTTTTTTAATATTTTTACAATTCTTTAAAGATTCTAAC
Found at i:2859269 original size:32 final size:32
Alignment explanation
Indices: 2859233--2859331 Score: 101
Period size: 32 Copynumber: 3.0 Consensus size: 32
2859223 TTTTCGAAAA
* *
2859233 TTTTTGAAAATTCTCATTAAACATTTAAATTT
1 TTTTTGAAAATTCTCATTAAACCTTCAAATTT
* * * *
2859265 TTTTTAAAAAGT-TCAGTTAGATGCCTTGAAATTT
1 TTTTTGAAAATTCTCA-TTA-A-ACCTTCAAATTT
*
2859299 TTTTTGTAAATTCTCATTAAACCTTCAAATTT
1 TTTTTGAAAATTCTCATTAAACCTTCAAATTT
2859331 T
1 T
2859332 CTGAAATTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
31 3 0.06
32 24 0.45
33 2 0.04
34 21 0.40
35 3 0.06
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.48
Consensus pattern (32 bp):
TTTTTGAAAATTCTCATTAAACCTTCAAATTT
Found at i:2878046 original size:13 final size:13
Alignment explanation
Indices: 2878028--2878053 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2878018 TATTTGGCAG
2878028 ATTTCATAAAAAT
1 ATTTCATAAAAAT
2878041 ATTTCATAAAAAT
1 ATTTCATAAAAAT
2878054 TGTTTTCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTTCATAAAAAT
Found at i:2883833 original size:30 final size:29
Alignment explanation
Indices: 2883754--2883842 Score: 83
Period size: 31 Copynumber: 3.0 Consensus size: 29
2883744 ATACTAAAAC
2883754 TATACATG-AACTATGATTTAATGTACAATTG
1 TATACATGAAACT-TGATTTAATG--CAATTG
* *
2883785 TATACAT-AAACTTTGATTTTATGCAATTT
1 TATACATGAAAC-TTGATTTAATGCAATTG
* *
2883814 TATACATGAAATCTTGATTTGATCCAATT
1 TATACATGAAA-CTTGATTTAATGCAATT
2883843 CTTGTAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
29 12 0.24
30 17 0.34
31 20 0.40
32 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (29 bp):
TATACATGAAACTTGATTTAATGCAATTG
Found at i:2885256 original size:14 final size:14
Alignment explanation
Indices: 2885237--2885298 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
2885227 ATAAAATATT
*
2885237 TTTATTTGAATTTA
1 TTTATTTAAATTTA
* *
2885251 TTTATTAAAAATTA
1 TTTATTTAAATTTA
*
2885265 TTAATTTAATATTTA
1 TTTATTTAA-ATTTA
*
2885280 TATATTT-AATTTAA
1 TTTATTTAAATTT-A
2885294 TTTAT
1 TTTAT
2885299 CTCAATCTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
13 4 0.11
14 24 0.65
15 9 0.24
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTTATTTAAATTTA
Found at i:2888185 original size:279 final size:279
Alignment explanation
Indices: 2887685--2888245 Score: 1077
Period size: 279 Copynumber: 2.0 Consensus size: 279
2887675 TATAAATAAT
2887685 ATAGATCCAAATATTTATAACCAAAATAAACTATTATCAAAATAGATTTGTATAAAACCTACATA
1 ATAGATCCAAATATTTATAACCAAAATAAACTATTATCAAAATAGATTTGTATAAAACCTACATA
*
2887750 TAATCGAACTTAAACTAGAATAAATCTTAGATAACTCATTAGAGGTGTTCATGAGTGTCAAGTAT
66 TAATCGAACTTAAACTAGAATAAATCTTAGATAACTCATTAGAGGTGTTCATGAGTGTCAAGTAA
*
2887815 GACTCCTATTTTCAGTCAAATTTGAAAAATAATCTTTTAGTTAAACTCTATTTATTTATTTCAGT
131 GACTCCTATTTTCAGTCAAATTTGAAAAATAATCTTTTAATTAAACTCTATTTATTTATTTCAGT
*
2887880 CAAACACTGATTAGTTTAGATTATTTTATTATTATTTGACATATGAATTTAGCCTATAAATAGGC
196 CAAACACAGATTAGTTTAGATTATTTTATTATTATTTGACATATGAATTTAGCCTATAAATAGGC
2887945 TCTTTTATAACCTTAGAAA
261 TCTTTTATAACCTTAGAAA
2887964 ATAGATCCAAATATTTATAACCAAAATAAACTATTATCAAAATAGATTTGTATAAAACCTACATA
1 ATAGATCCAAATATTTATAACCAAAATAAACTATTATCAAAATAGATTTGTATAAAACCTACATA
*
2888029 TAATCGAACTTAAACTAGAATAAATCTTAGATAACTCATTAGAGGTGTTCATGAGTGTTAAGTAA
66 TAATCGAACTTAAACTAGAATAAATCTTAGATAACTCATTAGAGGTGTTCATGAGTGTCAAGTAA
*
2888094 GACTCCTATTTTCAGTCAAATTTGAAAAATAATCTTTTAATTAAACTCTGTTTATTTATTTCAGT
131 GACTCCTATTTTCAGTCAAATTTGAAAAATAATCTTTTAATTAAACTCTATTTATTTATTTCAGT
2888159 CAAACACAGATTAGTTTAGATTATTTTATTATTATTTGACATATGAATTTAGCCTATAAATAGGC
196 CAAACACAGATTAGTTTAGATTATTTTATTATTATTTGACATATGAATTTAGCCTATAAATAGGC
2888224 TCTTTTATAACCTTAGAAA
261 TCTTTTATAACCTTAGAAA
2888243 ATA
1 ATA
2888246 CACCCATTAG
Statistics
Matches: 277, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
279 277 1.00
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.38
Consensus pattern (279 bp):
ATAGATCCAAATATTTATAACCAAAATAAACTATTATCAAAATAGATTTGTATAAAACCTACATA
TAATCGAACTTAAACTAGAATAAATCTTAGATAACTCATTAGAGGTGTTCATGAGTGTCAAGTAA
GACTCCTATTTTCAGTCAAATTTGAAAAATAATCTTTTAATTAAACTCTATTTATTTATTTCAGT
CAAACACAGATTAGTTTAGATTATTTTATTATTATTTGACATATGAATTTAGCCTATAAATAGGC
TCTTTTATAACCTTAGAAA
Found at i:2889130 original size:20 final size:19
Alignment explanation
Indices: 2889106--2889150 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
2889096 AATAAATTTT
2889106 ATTTTTTAATTTTAAAATA
1 ATTTTTTAATTTTAAAATA
*
2889125 ATTTTTTATTTTTAAAATAA
1 ATTTTTTAATTTTAAAAT-A
2889145 ATTTTT
1 ATTTTT
2889151 GGTGTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTTTAATTTTAAAATA
Found at i:2889158 original size:20 final size:19
Alignment explanation
Indices: 2889116--2889158 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
2889106 ATTTTTTAAT
* *
2889116 TTTAAAATAATTTTTTATT
1 TTTAAAATAATTTTTGATG
*
2889135 TTTAAAATAAATTTTTGGTG
1 TTTAAAAT-AATTTTTGATG
2889155 TTTA
1 TTTA
2889159 TTAAAAAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (19 bp):
TTTAAAATAATTTTTGATG
Found at i:2897102 original size:17 final size:17
Alignment explanation
Indices: 2897080--2897122 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
2897070 AAACAATTAA
*
2897080 TATTAATTGCTTAAATG
1 TATTAATTACTTAAATG
2897097 TATTAATTACTTAAATG
1 TATTAATTACTTAAATG
2897114 TATTAATTA
1 TATTAATTA
2897123 TTGACATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.49
Consensus pattern (17 bp):
TATTAATTACTTAAATG
Found at i:2903863 original size:12 final size:13
Alignment explanation
Indices: 2903840--2903869 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2903830 AAACTGATGC
2903840 TTTACTATAAAAT
1 TTTACTATAAAAT
2903853 TTTAC-ATAAAAT
1 TTTACTATAAAAT
2903865 TTTAC
1 TTTAC
2903870 GAGCATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (13 bp):
TTTACTATAAAAT
Found at i:2903973 original size:67 final size:67
Alignment explanation
Indices: 2903865--2903994 Score: 181
Period size: 66 Copynumber: 1.9 Consensus size: 67
2903855 TACATAAAAT
* ** * **
2903865 TTTACGAGCATTTTGTCTCAGTAACTTAGCCTGCTGCCAACCTGA-ACTGATGCTTAGCTATATA
1 TTTACAAGCATTTTGTAACAGTAACCTAGCCTGCTGCCAACCTGAGACCCATGCTTAGCTATATA
2903929 AA
66 AA
*
2903931 TTTACAAGCATTTTGTAACAGTAGCCTATGCCTGCTGCCAACCTGAGACCCATGCTTAGCTATA
1 TTTACAAGCATTTTGTAACAGTAACCTA-GCCTGCTGCCAACCTGAGACCCATGCTTAGCTATA
2903995 AAAAATTTGC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 23 0.42
67 17 0.31
68 15 0.27
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (67 bp):
TTTACAAGCATTTTGTAACAGTAACCTAGCCTGCTGCCAACCTGAGACCCATGCTTAGCTATATA
AA
Found at i:2910208 original size:216 final size:215
Alignment explanation
Indices: 2909693--2910763 Score: 1413
Period size: 216 Copynumber: 5.0 Consensus size: 215
2909683 CTTGGTTAAT
* * *
2909693 GAGTTGTAATGGCTAAAGATACTAACAATGTCACGCTAGCATGCAGAGAGATTATT-GCCAA-TT
1 GAGTTGTAATGGCTAAAGATATTAACAATGTCACGCTAGCTTGCAGAAAGATT-TTCGCCAACTT
* * * * *
2909756 AAGAATTCAAGCTAGGATTATTTTCATTCGAGGAACCCTTCTTTTGATGAACAAACAAGGATCAA
65 GAGAATTCAAGCTAGGATTATTCTCATTCGACGAACCCTTCTTTTGATGAACAAACAGGGATCGA
* ** *
2909821 CTCATGCAAAAGGAGGTCAACATTTAAGCAACATTTGTTGCTTGGTAGACATCTTTTTTAGC-AA
130 CTCATGCAAAAGGAAGTCAACATTTAAGCAACATTCATTGCTTGGTAGACATC-TTTTTAGCTAG
* *
2909885 CCAAAATT-CTAACTTGTCAAG
194 CCATAATTCCTTACTTGTCAAG
* * *
2909906 GACTTGTAATGGCTAAAGATATTAACAATGTCATGCTAGCTTGCAGAAAGATTATCGCCAACTTG
1 GAGTTGTAATGGCTAAAGATATTAACAATGTCACGCTAGCTTGCAGAAAGATTTTCGCCAACTTG
* * * * * * *
2909971 AGAATTCAAGCTAGAATTATTCTCATTTGAGGAACCCTTCTTTTGATGCACAAAGAGGGATTGAT
66 AGAATTCAAGCTAGGATTATTCTCATTCGACGAACCCTTCTTTTGATGAACAAACAGGGATCGAC
* * *
2910036 TCATACAAAAGGACGTCAACAATTAAGCAACATTCATTGCTTGGTAGACATCTTTTTCAGCTAGC
131 TCATGCAAAAGGAAGTCAACATTTAAGCAACATTCATTGCTTGGTAGACATCTTTTT-AGCTAGC
*
2910101 CATAATTCTTTACTTGTCAAG
195 CATAATTCCTTACTTGTCAAG
** *
2910122 GAGTTGTAATGGCTAAAGATATTAACAATGTCACGCTAGCTTATAGAAATATTTTCGCCAACTTG
1 GAGTTGTAATGGCTAAAGATATTAACAATGTCACGCTAGCTTGCAGAAAGATTTTCGCCAACTTG
* * * * * * *
2910187 AGAATTCAAGTTAAGATTATTCTCATTCGACGAACCCTTGTTTTAATGAAAAAACAAGGACCGAC
66 AGAATTCAAGCTAGGATTATTCTCATTCGACGAACCCTTCTTTTGATGAACAAACAGGGATCGAC
* * * *
2910252 TAATGCCAAATGAAGTCAACATTTAAGCAACA-TCAATTGCTTGGTAGACATCTTTTTTAGTTAG
131 TCATGCAAAAGGAAGTCAACATTTAAGCAACATTC-ATTGCTTGGTAGACATC-TTTTTAGCTAG
2910316 CCATAATTCCTTACTTGTCAAG
194 CCATAATTCCTTACTTGTCAAG
* * * *
2910338 GAGTTGCAATGGCTAAAGATATTAACGATGTCACGCTAGCTTGTAGAAAGATTATCGCCAACTTG
1 GAGTTGTAATGGCTAAAGATATTAACAATGTCACGCTAGCTTGCAGAAAGATTTTCGCCAACTTG
* * *
2910403 AGAATTCGAGCTAGGATTATTCTCATTCGACAAATCCTTCTTTTGATGAACAAACAGGGATCGAC
66 AGAATTCAAGCTAGGATTATTCTCATTCGACGAACCCTTCTTTTGATGAACAAACAGGGATCGAC
*
2910468 TCATGCAAAAGGAAGTCAACATTTAAGCAACA-TCTGTTGCTTGGTAGACCCAT-TTTTTAGCTA
131 TCATGCAAAAGGAAGTCAACATTTAAGCAACATTC-ATTGCTTGGTAGA--CATCTTTTTAGCTA
*
2910531 GCCATAATTCCTCACTTGTCAAG
193 GCCATAATTCCTTACTTGTCAAG
* *
2910554 GAGTTGTAATGGCTAAAGATATTAACAATGTCATGCTAGCTTGCAGAAAGATTATT-GCTAACTT
1 GAGTTGTAATGGCTAAAGATATTAACAATGTCACGCTAGCTTGCAGAAAGATT-TTCGCCAACTT
* * * * * *
2910618 GAGAGTTCAAGCTAGGATTATTCTTATTCGACAAACCCTTCTTTTGATGCACAAATAGGGAT-TA
65 GAGAATTCAAGCTAGGATTATTCTCATTCGACGAACCCTTCTTTTGATGAACAAACAGGGATCGA
* * * *
2910682 GCTCATGTAAAAGGAAGTCAACAATTAAGCAACATCCATTGCTTGGTAGACATCATTTTAGCTAG
130 -CTCATGCAAAAGGAAGTCAACATTTAAGCAACATTCATTGCTTGGTAGACATCTTTTTAGCTAG
*
2910747 CCATAATTCCTCACTTG
194 CCATAATTCCTTACTTG
2910764 GTGTTTTTAT
Statistics
Matches: 752, Mismatches: 93, Indels: 24
0.87 0.11 0.03
Matches are distributed among these distances:
212 1 0.00
213 58 0.08
214 111 0.15
215 38 0.05
216 534 0.71
217 7 0.01
218 3 0.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (215 bp):
GAGTTGTAATGGCTAAAGATATTAACAATGTCACGCTAGCTTGCAGAAAGATTTTCGCCAACTTG
AGAATTCAAGCTAGGATTATTCTCATTCGACGAACCCTTCTTTTGATGAACAAACAGGGATCGAC
TCATGCAAAAGGAAGTCAACATTTAAGCAACATTCATTGCTTGGTAGACATCTTTTTAGCTAGCC
ATAATTCCTTACTTGTCAAG
Found at i:2914340 original size:43 final size:43
Alignment explanation
Indices: 2914292--2914380 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
2914282 CAATTCTATT
2914292 GATACTTAGATCACACAAGGCAGAAATCATGACAGTGTGAGAC
1 GATACTTAGATCACACAAGGCAGAAATCATGACAGTGTGAGAC
2914335 GATACTTAGATCACACAAGGCAGAAATCATGACAGTGTGAGAC
1 GATACTTAGATCACACAAGGCAGAAATCATGACAGTGTGAGAC
2914378 GAT
1 GAT
2914381 TCACCTTGTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (43 bp):
GATACTTAGATCACACAAGGCAGAAATCATGACAGTGTGAGAC
Found at i:2918835 original size:138 final size:145
Alignment explanation
Indices: 2918600--2919071 Score: 513
Period size: 138 Copynumber: 3.2 Consensus size: 145
2918590 TTTAGTGTGT
* *
2918600 TTTTTATTGAAAGTAATAAAATTC-AGAAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTTT
1 TTTTTATTGAAAGTAATAAAATCCGAG-AAAAAATACGAATAAAGGGCCGAAATAAGAG--TTTT
* *
2918664 TTTAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGT-C-AAATAA-TAAAA
63 TTTAATTTATTTAAAAAATACACTAAATTAATACATTTCAAACATAATGTACAAAATAAGTAAAA
* *
2918726 T-T-AGAAAAT-AGTATA
128 TATAAAAAAATAAATATA
* * *
2918741 -TTTT-TT-AAAGTAATAAACTCTGGGGAAAAAATACGAATAAAGGGCCGAAATAAGAGTTTTTT
1 TTTTTATTGAAAGTAATAAAATC-CGAGAAAAAATACGAATAAAGGGCCGAAATAAGAGTTTTTT
2918803 TAAATTTATTTAAAAAATACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAA
65 T-AATTTATTTAAAAAATACACTAAATTAATACATTTCAAACATAATGTAC-AAAATAA-GTAAA
2918868 ATAATAAAAAAATAAAAAAATATA
127 AT-ATAAAAAAAT----AAATATA
* * *
2918892 TTTTTATTGAAAGTAATAAAATCCGAGAAAAAATACGAATAAATGACCGAAATAAG-GGTTTTTT
1 TTTTTATTGAAAGTAATAAAATCCGAGAAAAAATACGAATAAAGGGCCGAAATAAGAGTTTTTTT
* *
2918956 AATTTATTT-AAAAATACATTAAATTAATACATTTCAAACTTAATGTACTAAAATAATGTAAAAT
66 AATTTATTTAAAAAATACACTAAATTAATACATTTCAAACATAATGTAC-AAAATAA-GTAAAAT
*
2919020 A-AAAAAATAGAAAATGATA
129 ATAAAAAA-A-TAAAT-ATA
* * * *
2919039 TATTTT-TTAAAAATAATAAAATTCAAGAAAAAA
1 T-TTTTATTGAAAGTAATAAAATCCGAGAAAAAA
2919072 ACATTAAAAA
Statistics
Matches: 286, Mismatches: 22, Indels: 40
0.82 0.06 0.11
Matches are distributed among these distances:
137 7 0.02
138 57 0.20
139 33 0.12
140 5 0.02
141 6 0.02
143 6 0.02
145 1 0.00
146 10 0.03
147 27 0.09
148 10 0.03
149 2 0.01
150 53 0.19
151 14 0.05
152 11 0.04
153 31 0.11
154 13 0.05
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.31
Consensus pattern (145 bp):
TTTTTATTGAAAGTAATAAAATCCGAGAAAAAATACGAATAAAGGGCCGAAATAAGAGTTTTTTT
AATTTATTTAAAAAATACACTAAATTAATACATTTCAAACATAATGTACAAAATAAGTAAAATAT
AAAAAAATAAATATA
Found at i:2919006 original size:150 final size:150
Alignment explanation
Indices: 2918707--2919071 Score: 495
Period size: 150 Copynumber: 2.4 Consensus size: 150
2918697 CATTTCAAAC
* * * * * *
2918707 ATAATGTCAAATAATAAAATTAGAAAATAGTATATTTTTTAAAGTAATAAACTCTGGGGAAAAAA
1 ATAATGTAAAATAATAAAAATAGAAAATAATATATTTTTTAAAGTAATAAAATC-CGAGAAAAAA
* *
2918772 TACGAATAAAGGGCCGAAATAAGAGTTTTTTTAAATTTATTTAAAAAATACACTAAATTAATACA
65 TACGAATAAAGGACCGAAATAAGAGGTTTTTTAAATTTATTTAAAAAATACACTAAATTAATACA
2918837 TTTCAAACATAATGTACTAAA
130 TTTCAAACATAATGTACTAAA
* * *
2918858 ATAATGTAAAATAATAAAAAAATAAAAAAATATATTTTTATTGAAAGTAATAAAATCCGAGAAAA
1 ATAATGTAAAATAATAAAAATAGAAAATAATATA-TTTT-TT-AAAGTAATAAAATCCGAGAAAA
* *
2918923 AATACGAATAAATGACCGAAATAAG-GGTTTTTT-AATTTATTT-AAAAATACATTAAATTAATA
63 AATACGAATAAAGGACCGAAATAAGAGGTTTTTTAAATTTATTTAAAAAATACACTAAATTAATA
*
2918985 CATTTCAAACTTAATGTACTAAA
128 CATTTCAAACATAATGTACTAAA
* * * *
2919008 ATAATGTAAAATAA-AAAAATAGAAAATGATATATTTTTTAAAAATAATAAAATTCAAGAAAAAA
1 ATAATGTAAAATAATAAAAATAGAAAATAATATATTTTTT-AAAGTAATAAAATCCGAGAAAAAA
2919072 ACATTAAAAA
Statistics
Matches: 189, Mismatches: 22, Indels: 10
0.86 0.10 0.05
Matches are distributed among these distances:
147 23 0.12
148 4 0.02
149 15 0.08
150 55 0.29
151 37 0.20
152 11 0.06
153 31 0.16
154 13 0.07
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (150 bp):
ATAATGTAAAATAATAAAAATAGAAAATAATATATTTTTTAAAGTAATAAAATCCGAGAAAAAAT
ACGAATAAAGGACCGAAATAAGAGGTTTTTTAAATTTATTTAAAAAATACACTAAATTAATACAT
TTCAAACATAATGTACTAAA
Found at i:2919784 original size:16 final size:16
Alignment explanation
Indices: 2919763--2919793 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2919753 AATAAAACAT
2919763 TTAATTATAATTTTTA
1 TTAATTATAATTTTTA
*
2919779 TTAATTTTAATTTTT
1 TTAATTATAATTTTT
2919794 GAAAAATAAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTAATTATAATTTTTA
Found at i:2919814 original size:15 final size:15
Alignment explanation
Indices: 2919795--2919824 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
2919785 TTAATTTTTG
2919795 AAAAATAAATTACTTT
1 AAAAA-AAATTACTTT
2919811 AAAAAAAATTACTT
1 AAAAAAAATTACTT
2919825 AGCGGTCTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAAAAATTACTTT
Found at i:2924720 original size:23 final size:24
Alignment explanation
Indices: 2924668--2924722 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
2924658 TTTGATGGGT
* *
2924668 AAAATTAATAATAGTATAGTATTG
1 AAAAATAATAATAGTATAGTAGTG
*
2924692 AAAAATAATAATAGTA-ATTAGTG
1 AAAAATAATAATAGTATAGTAGTG
2924715 AAAAATAA
1 AAAAATAA
2924723 GATTTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (24 bp):
AAAAATAATAATAGTATAGTAGTG
Found at i:2926944 original size:61 final size:60
Alignment explanation
Indices: 2926814--2926967 Score: 177
Period size: 61 Copynumber: 2.5 Consensus size: 60
2926804 TCAAATGGTT
* * * *
2926814 GACTAATAAAATTAGTCTTCAATGTTTATAAAATTTGTCATTTTAATTTTAATTTTAAAA
1 GACTAATAAATTTAGTCTTCAATATTTATAAAATTTGTCATTTTAATTCTAATTCTAAAA
* * *
2926874 AATTTAATAAATTTAGTCTTCAATATTTATAAAAGTTT-TCATTTTAGTTCTAATTCTAAAA
1 GA-CTAATAAATTTAGTCTTCAATATTTATAAAA-TTTGTCATTTTAATTCTAATTCTAAAA
* *
2926935 GACTCAATAAATTT-GATCCTCAACATTTATAAA
1 GACT-AATAAATTTAG-TCTTCAATATTTATAAA
2926968 TTCTATCAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
60 3 0.04
61 73 0.92
62 3 0.04
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (60 bp):
GACTAATAAATTTAGTCTTCAATATTTATAAAATTTGTCATTTTAATTCTAATTCTAAAA
Found at i:2929227 original size:15 final size:15
Alignment explanation
Indices: 2929207--2929235 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2929197 AAAATAATAA
2929207 TAATATTTTTATTTT
1 TAATATTTTTATTTT
2929222 TAATATTTTTATTT
1 TAATATTTTTATTT
2929236 CAAAAATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TAATATTTTTATTTT
Found at i:2931943 original size:2 final size:2
Alignment explanation
Indices: 2931936--2931964 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2931926 AACCATAAGA
2931936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2931965 ATTATAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2933610 original size:20 final size:22
Alignment explanation
Indices: 2933585--2933624 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2933575 ACAAAAAATT
2933585 TGCTA-TT-CTTGTTGTTTTAA
1 TGCTATTTCCTTGTTGTTTTAA
2933605 TGCTATTTCCTTGTTGTTTT
1 TGCTATTTCCTTGTTGTTTT
2933625 CTCTTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.10, C:0.12, G:0.15, T:0.62
Consensus pattern (22 bp):
TGCTATTTCCTTGTTGTTTTAA
Found at i:2938321 original size:20 final size:20
Alignment explanation
Indices: 2938296--2938387 Score: 75
Period size: 19 Copynumber: 4.8 Consensus size: 20
2938286 AAAGTTATAG
*
2938296 AATTATAAAATTTTATTAAA
1 AATTATAAAATTATATTAAA
*
2938316 AATTATAAAAATATA-TAAA
1 AATTATAAAATTATATTAAA
* * *
2938335 AATCATAAAA-AATATAAAA
1 AATTATAAAATTATATTAAA
* * *
2938354 AATTGTAAAATTTTA-TAAT
1 AATTATAAAATTATATTAAA
*
2938373 AA-TAAAAAATTATAT
1 AATTATAAAATTATAT
2938388 AATGCATCAA
Statistics
Matches: 55, Mismatches: 14, Indels: 7
0.72 0.18 0.09
Matches are distributed among these distances:
18 12 0.22
19 28 0.51
20 15 0.27
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (20 bp):
AATTATAAAATTATATTAAA
Found at i:2938326 original size:9 final size:9
Alignment explanation
Indices: 2938259--2938386 Score: 77
Period size: 10 Copynumber: 14.1 Consensus size: 9
2938249 TGACATGAGG
*
2938259 AAAAAATAT
1 AAAAATTAT
2938268 AAAAA--AT
1 AAAAATTAT
*
2938275 AAAAATCAAT
1 AAAAAT-TAT
*
2938285 AAAAGTTAT
1 AAAAATTAT
*
2938294 -AGAATTAT
1 AAAAATTAT
*
2938302 AAAATTTTATT
1 AAAA-ATTA-T
2938313 AAAAATTAT
1 AAAAATTAT
2938322 AAAAATATAT
1 AAAAAT-TAT
*
2938332 AAAAATCAT
1 AAAAATTAT
*
2938341 AAAAAATAT
1 AAAAATTAT
*
2938350 AAAAAATTGT
1 -AAAAATTAT
*
2938360 AAAATTTTAT
1 AAAA-ATTAT
*
2938370 AATAA-TA-
1 AAAAATTAT
2938377 AAAAATTAT
1 AAAAATTAT
2938386 A
1 A
2938387 TAATGCATCA
Statistics
Matches: 91, Mismatches: 17, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
7 11 0.12
8 10 0.11
9 30 0.33
10 35 0.38
11 5 0.05
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:2938343 original size:28 final size:27
Alignment explanation
Indices: 2938259--2938363 Score: 81
Period size: 28 Copynumber: 3.8 Consensus size: 27
2938249 TGACATGAGG
*
2938259 AAAAAATATAAAAA--ATAAAAATCAAT
1 AAAAATTATAAAAATTATAAAAATC-AT
* * * *
2938285 AAAAGTTAT-AGAATTATAAAATTTTATT
1 AAAAATTATAAAAATTATAAAA-ATCA-T
2938313 AAAAATTATAAAAATATATAAAAATCAT
1 AAAAATTATAAAAAT-TATAAAAATCAT
* *
2938341 AAAAAATATAAAAAATTGTAAAA
1 AAAAATTAT-AAAAATTATAAAA
2938364 TTTTATAATA
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
25 3 0.05
26 7 0.11
27 7 0.11
28 25 0.41
29 12 0.20
30 7 0.11
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.29
Consensus pattern (27 bp):
AAAAATTATAAAAATTATAAAAATCAT
Found at i:2938388 original size:38 final size:40
Alignment explanation
Indices: 2938302--2938389 Score: 94
Period size: 38 Copynumber: 2.3 Consensus size: 40
2938292 ATAGAATTAT
* *
2938302 AAAATTTTATTAAAAATTATAAAAATATATAAAAATCATA
1 AAAATTATATAAAAAATTATAAAAATATATAAAAATCATA
* * * *
2938342 AAAA--ATATAAAAAATTGTAAAATTTTATAATAAT-A-A
1 AAAATTATATAAAAAATTATAAAAATATATAAAAATCATA
2938378 AAAATTATATAA
1 AAAATTATATAA
2938390 TGCATCAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
36 5 0.12
37 1 0.03
38 30 0.75
40 4 0.10
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (40 bp):
AAAATTATATAAAAAATTATAAAAATATATAAAAATCATA
Found at i:2938584 original size:21 final size:20
Alignment explanation
Indices: 2938560--2938635 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 20
2938550 TTGGTACGAT
2938560 AATTTTTATAATTTTTTTAC
1 AATTTTTATAATTTTTTTAC
*
2938580 AAATTTTAT-ATTTTTTTAC
1 AATTTTTATAATTTTTTTAC
*
2938599 AATTCTTTATAATTTTCTTAC
1 AATT-TTTATAATTTTTTTAC
* *
2938620 GATTTTATAAAATTTT
1 AATTTT-TATAATTTT
2938636 ATATTTTTTC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
19 13 0.27
20 15 0.31
21 20 0.42
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.61
Consensus pattern (20 bp):
AATTTTTATAATTTTTTTAC
Found at i:2938594 original size:19 final size:20
Alignment explanation
Indices: 2938563--2938629 Score: 84
Period size: 19 Copynumber: 3.4 Consensus size: 20
2938553 GTACGATAAT
2938563 TTTTATAATTTTTTTACAAA
1 TTTTATAATTTTTTTACAAA
*
2938583 TTTTAT-ATTTTTTTACAAT
1 TTTTATAATTTTTTTACAAA
* *
2938602 TCTTTATAATTTTCTTAC-GA
1 T-TTTATAATTTTTTTACAAA
2938622 TTTTATAA
1 TTTTATAA
2938630 AATTTTATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 20 0.49
20 12 0.29
21 9 0.22
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.61
Consensus pattern (20 bp):
TTTTATAATTTTTTTACAAA
Found at i:2938611 original size:49 final size:50
Alignment explanation
Indices: 2938558--2938676 Score: 124
Period size: 49 Copynumber: 2.4 Consensus size: 50
2938548 TTTTGGTACG
*
2938558 ATAATTTTTATAATTTTTTTACAAATTTTATATTTTTT-TACAATTCTTT
1 ATAATTTTTATAATTTTTTTACAAATTTTATATTTTTTCTACAATTCTAT
* * *
2938607 ATAATTTTCT-TACGA-TTTTATA-AAATTTTATATTTTTTCTATATTTCTAT
1 ATAATTTT-TATA--ATTTTTTTACAAATTTTATATTTTTTCTACAATTCTAT
*
2938657 AT-A-TTTTATATTTTTTTTAC
1 ATAATTTTTATAATTTTTTTAC
2938677 GATTTTTACA
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
47 7 0.12
48 5 0.09
49 27 0.47
50 17 0.30
51 1 0.02
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (50 bp):
ATAATTTTTATAATTTTTTTACAAATTTTATATTTTTTCTACAATTCTAT
Found at i:2938641 original size:28 final size:28
Alignment explanation
Indices: 2938604--2938682 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 28
2938594 TTTACAATTC
2938604 TTTATAATTTTCTTACGATTTTATA-AAAT
1 TTTAT-ATTTT-TTACGATTTTATATAAAT
* * *
2938633 TTTATATTTTTT-CTATATTTCTATATAT
1 TTTATATTTTTTACGAT-TTTATATAAAT
2938661 TTTATATTTTTTTTACGATTTT
1 TTTATA--TTTTTTACGATTTT
2938683 TACAAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
26 3 0.07
27 7 0.17
28 14 0.34
29 5 0.12
30 9 0.22
31 3 0.07
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.65
Consensus pattern (28 bp):
TTTATATTTTTTACGATTTTATATAAAT
Found at i:2938644 original size:19 final size:20
Alignment explanation
Indices: 2938621--2938666 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
2938611 TTTTCTTACG
2938621 ATTTTATAAAATTT-TATAT
1 ATTTTATAAAATTTCTATAT
* * *
2938640 TTTTTCT-ATATTTCTATAT
1 ATTTTATAAAATTTCTATAT
2938659 ATTTTATA
1 ATTTTATA
2938667 TTTTTTTTAC
Statistics
Matches: 20, Mismatches: 5, Indels: 3
0.71 0.18 0.11
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTATAAAATTTCTATAT
Found at i:2938661 original size:10 final size:9
Alignment explanation
Indices: 2938621--2938671 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
2938611 TTTTCTTACG
*
2938621 ATTTTATAAA
1 ATTTTAT-AT
2938631 ATTTTATAT
1 ATTTTATAT
* *
2938640 TTTTTCTAT
1 ATTTTATAT
2938649 ATTTCTATAT
1 ATTT-TATAT
2938659 ATTTTATAT
1 ATTTTATAT
2938668 -TTTT
1 ATTTT
2938672 TTTACGATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
8 4 0.11
9 16 0.46
10 15 0.43
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (9 bp):
ATTTTATAT
Found at i:2938777 original size:10 final size:9
Alignment explanation
Indices: 2938696--2938776 Score: 78
Period size: 9 Copynumber: 8.9 Consensus size: 9
2938686 AAAAAAATTC
2938696 TAATTTTTA
1 TAATTTTTA
2938705 -ATATTTTTA
1 TA-ATTTTTA
* *
2938714 TTAAAATTTAA
1 -T-AATTTTTA
2938725 TAATTTTTA
1 TAATTTTTA
2938734 TAATTTTTA
1 TAATTTTTA
*
2938743 TAACTTTTA
1 TAATTTTTA
2938752 TTAATTTTTA
1 -TAATTTTTA
2938762 T--TTTTTA
1 TAATTTTTA
2938769 TAATTTTT
1 TAATTTTT
2938777 TGTCACATGT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
7 7 0.12
8 1 0.02
9 36 0.61
10 9 0.15
11 5 0.08
12 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (9 bp):
TAATTTTTA
Found at i:2957350 original size:21 final size:22
Alignment explanation
Indices: 2957308--2957356 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 22
2957298 AGCGGAAACT
2957308 AAAATATAAATTTTTTGAATGTA
1 AAAATATAAATTTTTT-AATGTA
2957331 AAAATAT-AATTTTATT-ATGTA
1 AAAATATAAATTTT-TTAATGTA
*
2957352 TAAAT
1 AAAAT
2957357 TTATGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 9 0.38
22 6 0.25
23 9 0.38
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (22 bp):
AAAATATAAATTTTTTAATGTA
Found at i:2970572 original size:15 final size:16
Alignment explanation
Indices: 2970546--2970580 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2970536 GGATTAATTG
2970546 TATATATTAATTAAAT
1 TATATATTAATTAAAT
*
2970562 TATAT-TTAATTATAT
1 TATATATTAATTAAAT
2970577 TATA
1 TATA
2970581 ATTTTTATAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATATTAATTAAAT
Found at i:2971626 original size:23 final size:22
Alignment explanation
Indices: 2971592--2971635 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
2971582 AAATCAAATA
* *
2971592 TAAAAATAAAAAATAAAAGAAC
1 TAAAAAGAAAAAAGAAAAGAAC
*
2971614 TAAAAAGATAAAAGGAAAAGAA
1 TAAAAAGA-AAAAAGAAAAGAA
2971636 AAAAGAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.75, C:0.02, G:0.11, T:0.11
Consensus pattern (22 bp):
TAAAAAGAAAAAAGAAAAGAAC
Found at i:2983586 original size:18 final size:18
Alignment explanation
Indices: 2983563--2983597 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2983553 ATAAGTTGAG
*
2983563 GGCGTCACCCACTGAACT
1 GGCGTCAACCACTGAACT
2983581 GGCGTCAACCACTGAAC
1 GGCGTCAACCACTGAAC
2983598 AAATACCTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.23, T:0.14
Consensus pattern (18 bp):
GGCGTCAACCACTGAACT
Found at i:2991246 original size:23 final size:23
Alignment explanation
Indices: 2991220--2991266 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2991210 ATGTTATAAT
2991220 TTTTTTTTATTTACCAAAATATA
1 TTTTTTTTATTTACCAAAATATA
2991243 TTTTTTTTATTTACCAAAATATA
1 TTTTTTTTATTTACCAAAATATA
2991266 T
1 T
2991267 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTTTTTATTTACCAAAATATA
Found at i:2991339 original size:27 final size:27
Alignment explanation
Indices: 2991309--2991392 Score: 123
Period size: 27 Copynumber: 3.1 Consensus size: 27
2991299 CCTTGGTCAC
** *
2991309 GCCAATGGGATTGGCGGCACCAAAGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
*
2991336 GCCAAAGCCATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
*
2991363 GCCAATACCATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
2991390 GCC
1 GCC
2991393 GTATTGATTG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.25, C:0.29, G:0.31, T:0.15
Consensus pattern (27 bp):
GCCAATGCCATTGGCGGCACCAATGGT
Found at i:2991408 original size:27 final size:27
Alignment explanation
Indices: 2991318--2991392 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
2991308 CGCCAATGGG
*
2991318 ATTGGCGGCACCAAAGGTGCCAA-AGCC
1 ATTGGCGGCACCAATGGTGCCAATA-CC
2991345 ATTGGCGGCACCAATGGTGCCAATACC
1 ATTGGCGGCACCAATGGTGCCAATACC
2991372 ATTGGCGGCACCAATGGTGCC
1 ATTGGCGGCACCAATGGTGCC
2991393 GTATTGATTG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 45 0.98
28 1 0.02
ACGTcount: A:0.25, C:0.29, G:0.29, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATACC
Found at i:2991508 original size:11 final size:11
Alignment explanation
Indices: 2991492--2991521 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2991482 GTTGCTGCGG
2991492 AAAAGAAGAGA
1 AAAAGAAGAGA
*
2991503 AAAAGAGGAGA
1 AAAAGAAGAGA
2991514 AAAAGAAG
1 AAAAGAAG
2991522 CTATTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:2991582 original size:19 final size:21
Alignment explanation
Indices: 2991544--2991582 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
2991534 AATAATTGAT
*
2991544 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
2991565 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
2991583 TTGTTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:2991655 original size:3 final size:3
Alignment explanation
Indices: 2991649--2991683 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2991639 ATTATTATTA
2991649 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
2991684 AGTATTAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:2992495 original size:18 final size:18
Alignment explanation
Indices: 2992472--2992509 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2992462 GGTTGGTGGT
2992472 GAAGAAGAAGGTGCTGGC
1 GAAGAAGAAGGTGCTGGC
*
2992490 GAAGAAGAAGGTGGTGGC
1 GAAGAAGAAGGTGCTGGC
2992508 GA
1 GA
2992510 TCATTGGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.08, G:0.47, T:0.11
Consensus pattern (18 bp):
GAAGAAGAAGGTGCTGGC
Found at i:2996220 original size:27 final size:27
Alignment explanation
Indices: 2996180--2996418 Score: 76
Period size: 27 Copynumber: 9.3 Consensus size: 27
2996170 AAAAATACCT
*
2996180 TTTCTTTTTTTTTTTCCTTC-CTTC-CC
1 TTTCTTTTTCTTTTT-CTTCTCTTCTCC
* *
2996206 TCTTCTTCTTCTTTTTTTTCTCTTCTCC
1 T-TTCTTTTTCTTTTTCTTCTCTTCTCC
2996234 TTTCTTTTTC--TTTCTT-TCTT-T-C
1 TTTCTTTTTCTTTTTCTTCTCTTCTCC
*
2996256 TTTC-TTTT-TTCTTC-TC-CTT-TCC
1 TTTCTTTTTCTTTTTCTTCTCTTCTCC
* *
2996278 TTTTCTTCTTCTTTCTTTCTT-TCTT-T-T
1 -TTTCTTTTTC-TT-TTTCTTCTCTTCTCC
* * * *
2996305 TTTCTGTTCTCCTTTCCTTTTCTT-TCC
1 TTTCT-TTTTCTTTTTCTTCTCTTCTCC
*
2996332 -TTCTTTTTC--TTTCTT-TCCTCTCC
1 TTTCTTTTTCTTTTTCTTCTCTTCTCC
*
2996355 TTTCTTTTT-TCTGTTC-TC-CTT-TCC
1 TTTCTTTTTCT-TTTTCTTCTCTTCTCC
*
2996379 TTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCC
1 -TTTCTTT--TTCTTTTTC-TTC--TCTTCTCC
2996412 TTTCTTT
1 TTTCTTT
2996419 CTTTCTTTCT
Statistics
Matches: 159, Mismatches: 21, Indels: 60
0.66 0.09 0.25
Matches are distributed among these distances:
21 9 0.06
22 12 0.08
23 13 0.08
24 18 0.11
25 24 0.15
26 24 0.15
27 36 0.23
28 9 0.06
29 2 0.01
32 9 0.06
33 3 0.02
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (27 bp):
TTTCTTTTTCTTTTTCTTCTCTTCTCC
Found at i:2996240 original size:4 final size:4
Alignment explanation
Indices: 2996240--2996435 Score: 133
Period size: 4 Copynumber: 48.0 Consensus size: 4
2996230 CTCCTTTCTT
2996240 TTTC TTTC TTTC TTTC TTTC TTT- TTTC TTCTCC TTTCC TTT- TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C TTTC T-TTC
* * *
2996286 -TTC TTTC TTTC TTTC TTTT TTTC TGTTC -TCC TTTCC TTTTC TTTC CTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC TTTC TTTC
* *
2996335 -TT- TTTC TTTC TTTCC TCTCC TTTC TTT- TTTC TGTTC -TCC TTTCC
1 TTTC TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC T-TTC TTTC TTT-C
* *
2996379 TTTTC TTTC CTTC -TT- TTTC TTTC TTTCC TCTCC TTTC TTTC TTTC TTTC
1 -TTTC TTTC TTTC TTTC TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC
2996428 TTTC TTTC
1 TTTC TTTC
2996436 CCCCTCCTTC
Statistics
Matches: 157, Mismatches: 12, Indels: 46
0.73 0.06 0.21
Matches are distributed among these distances:
3 22 0.14
4 99 0.63
5 25 0.16
6 11 0.07
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (4 bp):
TTTC
Done.