Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008082.1 Hibiscus syriacus cultivar Beakdansim tig00110584_pilon, 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: 6025995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 28
Found at i:5792099 original size:19 final size:18
Alignment explanation
Indices: 5792062--5792106 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
5792052 ATACTTGAAT
*
5792062 AAATGC-AATGTGAATGC
1 AAATGCAAATGTAAATGC
5792079 AAATGCAAATGTAAGATGC
1 AAATGCAAATGTAA-ATGC
5792098 AAATGCAAA
1 AAATGCAAA
5792107 AGATATTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 6 0.24
18 6 0.24
19 13 0.52
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (18 bp):
AAATGCAAATGTAAATGC
Found at i:5794200 original size:13 final size:13
Alignment explanation
Indices: 5794182--5794207 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5794172 TATAACATAT
5794182 AATTTTTGAAAAC
1 AATTTTTGAAAAC
5794195 AATTTTTGAAAAC
1 AATTTTTGAAAAC
5794208 GTATATAATA
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:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
AATTTTTGAAAAC
Found at i:5794239 original size:38 final size:38
Alignment explanation
Indices: 5794088--5794344 Score: 329
Period size: 39 Copynumber: 6.7 Consensus size: 38
5794078 GAATATATAT
*
5794088 AACGCATATAATATATAGTTTTGAAAACATTTTTTTGAA
1 AACGTATATAATATATAGTTTTGAAAACA-TTTTTTGAA
* * *
5794127 AACGTACATAACATATAAGTTTTGAAAATATTTTTTGAA
1 AACGTATATAATATAT-AGTTTTGAAAACATTTTTTGAA
* * *
5794166 AACGTATATAACATATAATTTTTGAAAACAATTTTTGAA
1 AACGTATATAATATAT-AGTTTTGAAAACATTTTTTGAA
* *
5794205 AACGTATATAATACATACTTTTGAAAACATTTTTTGAA
1 AACGTATATAATATATAGTTTTGAAAACATTTTTTGAA
* ***
5794243 AACGTATATCATATATAAGTTTTG--ATTTTTTTTTGAA
1 AACGTATATAATATAT-AGTTTTGAAAACATTTTTTGAA
5794280 AACGTATATAATATATAGTTTTGAAAACATTTTTTGAA
1 AACGTATATAATATATAGTTTTGAAAACATTTTTTGAA
* *
5794318 AACATATATAATATATAGTTTTTAAAA
1 AACGTATATAATATATAGTTTTGAAAA
5794345 ATACCTTTGA
Statistics
Matches: 190, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
36 7 0.04
37 25 0.13
38 69 0.36
39 77 0.41
40 12 0.06
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (38 bp):
AACGTATATAATATATAGTTTTGAAAACATTTTTTGAA
Found at i:5794302 original size:75 final size:76
Alignment explanation
Indices: 5794088--5794339 Score: 321
Period size: 75 Copynumber: 3.3 Consensus size: 76
5794078 GAATATATAT
* * *
5794088 AACGCATATAATATAT-AGTTTTGAAAACATTTTTTTGAAAACGTACATAACATATAAGTTTTGA
1 AACGTATATAATATATAAGTTTTG-AAAC-TTTTTTTGAAAACGTATATAATATAT-AGTTTTGA
*
5794152 AAATATTTTTTGAA
63 AAACATTTTTTGAA
* * ** * *
5794166 AACGTATATAACATATAATTTTTGAAAACAATTTTTGAAAACGTATATAATACATACTTTTGAAA
1 AACGTATATAATATATAAGTTTTG-AAACTTTTTTTGAAAACGTATATAATATATAGTTTTGAAA
5794231 ACATTTTTTGAA
65 ACATTTTTTGAA
* **
5794243 AACGTATATCATATATAAGTTTTG-ATTTTTTTTTGAAAACGTATATAATATATAGTTTTGAAAA
1 AACGTATATAATATATAAGTTTTGAAACTTTTTTTGAAAACGTATATAATATATAGTTTTGAAAA
5794307 CATTTTTTGAA
66 CATTTTTTGAA
*
5794318 AACATATATAATATAT-AGTTTT
1 AACGTATATAATATATAAGTTTT
5794340 TAAAAATACC
Statistics
Matches: 152, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
74 6 0.04
75 59 0.39
77 41 0.27
78 35 0.23
79 11 0.07
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (76 bp):
AACGTATATAATATATAAGTTTTGAAACTTTTTTTGAAAACGTATATAATATATAGTTTTGAAAA
CATTTTTTGAA
Found at i:5794316 original size:13 final size:13
Alignment explanation
Indices: 5794298--5794322 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5794288 TAATATATAG
5794298 TTTTGAAAACATT
1 TTTTGAAAACATT
5794311 TTTTGAAAACAT
1 TTTTGAAAACAT
5794323 ATATAATATA
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTTTGAAAACATT
Found at i:5794354 original size:38 final size:39
Alignment explanation
Indices: 5794088--5794370 Score: 271
Period size: 38 Copynumber: 7.4 Consensus size: 39
5794078 GAATATATAT
* * *
5794088 AACGCATATAATATATAGTTTTGAAAACATTTTTTTGAA
1 AACGTATATAATATATAGTTTTTAAAACATATTTTTGAA
* * * *
5794127 AACGTACATAACATATAAGTTTTGAAAATAT-TTTTTGAA
1 AACGTATATAATATAT-AGTTTTTAAAACATATTTTTGAA
* *
5794166 AACGTATATAACATATAATTTTTGAAAACA-ATTTTTGAA
1 AACGTATATAATATATAGTTTTT-AAAACATATTTTTGAA
* * *
5794205 AACGTATATAATACATACTTTTGAAAACAT-TTTTTGAA
1 AACGTATATAATATATAGTTTTTAAAACATATTTTTGAA
* * ** *
5794243 AACGTATATCATATATAAG-TTTT--GATTTTTTTTTGAA
1 AACGTATATAATATAT-AGTTTTTAAAACATATTTTTGAA
*
5794280 AACGTATATAATATATAGTTTTGAAAACAT-TTTTTGAA
1 AACGTATATAATATATAGTTTTTAAAACATATTTTTGAA
* **
5794318 AACATATATAATATATAGTTTTTAAAA-ATACCTTTGAA
1 AACGTATATAATATATAGTTTTTAAAACATATTTTTGAA
*
5794356 AAC--ATATAATTTATA
1 AACGTATATAATATATA
5794371 ATTAAAAAAG
Statistics
Matches: 205, Mismatches: 29, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
36 15 0.07
37 28 0.14
38 78 0.38
39 71 0.35
40 13 0.06
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.41
Consensus pattern (39 bp):
AACGTATATAATATATAGTTTTTAAAACATATTTTTGAA
Found at i:5794386 original size:113 final size:113
Alignment explanation
Indices: 5794093--5794375 Score: 279
Period size: 113 Copynumber: 2.5 Consensus size: 113
5794083 TATATAACGC
* * ** * * * *
5794093 ATATAATATATAGTTTTGAAAACATTTTTTTGAAAACGTACATAACATATAAGTTTTGAA-AATA
1 ATATAATACATACTTTTGAAAACA-TCCTTTGAAAACG-ATATAATATATAAG--TT-AAGATTT
* *
5794157 TTTTTTGAAAACGTATATAACATATAATTTTTGAAAACAATTTTTGAAAACGT
61 TTTTTTGAAAACGTATATAACATATAAGTTTTGAAAACAATTTTTGAAAACAT
** * **
5794210 ATATAATACATACTTTTGAAAACATTTTTTGAAAACGTATATCATATATAAGTTTTGATTTTTTT
1 ATATAATACATACTTTTGAAAACATCCTTTGAAAACG-ATATAATATATAAGTTAAGATTTTTTT
* *
5794275 TTGAAAACGTATATAATATAT-AGTTTTGAAAACATTTTTTGAAAACAT
65 TTGAAAACGTATATAACATATAAGTTTTGAAAACAATTTTTGAAAACAT
* * * *
5794323 ATATAATATATAGTTTTTAAAA-ATACCTTTGAAAAC-ATATAATTTATAA-TTAA
1 ATATAATACATACTTTTGAAAACAT-CCTTTGAAAACGATATAATATATAAGTTAA
5794376 AAAAGATTTT
Statistics
Matches: 142, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
110 2 0.01
111 11 0.08
112 2 0.01
113 52 0.37
114 28 0.20
116 25 0.18
117 22 0.15
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (113 bp):
ATATAATACATACTTTTGAAAACATCCTTTGAAAACGATATAATATATAAGTTAAGATTTTTTTT
TGAAAACGTATATAACATATAAGTTTTGAAAACAATTTTTGAAAACAT
Found at i:5794434 original size:14 final size:16
Alignment explanation
Indices: 5794412--5794443 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5794402 AGAATACACA
5794412 TTTTATATTA-TATAG
1 TTTTATATTATTATAG
5794427 TTTT-TATTATTATAG
1 TTTTATATTATTATAG
5794442 TT
1 TT
5794444 ACATTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (16 bp):
TTTTATATTATTATAG
Found at i:5794470 original size:17 final size:17
Alignment explanation
Indices: 5794445--5794488 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
5794435 ATTATAGTTA
5794445 CATTATATTTATTTTATT
1 CATT-TATTTATTTTATT
*
5794463 CATTTATTTTGTTTTATT
1 CATTTA-TTTATTTTATT
5794481 C-TTTATTT
1 CATTTATTT
5794489 TTATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.12
17 6 0.25
18 15 0.62
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.70
Consensus pattern (17 bp):
CATTTATTTATTTTATT
Found at i:5794490 original size:18 final size:18
Alignment explanation
Indices: 5794456--5794489 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5794446 ATTATATTTA
5794456 TTTTATTCATTTATTTTG
1 TTTTATTCATTTATTTTG
5794474 TTTTATTC-TTTATTTT
1 TTTTATTCATTTATTTT
5794490 TATTATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (18 bp):
TTTTATTCATTTATTTTG
Found at i:5806104 original size:37 final size:37
Alignment explanation
Indices: 5805948--5806234 Score: 409
Period size: 37 Copynumber: 7.7 Consensus size: 37
5805938 ATATATAACG
*
5805948 TATATAATATATATTTTTGAAAACATTTTTTGAAAACA
1 TATATAATATATAGTTTTGAAAACA-TTTTTGAAAACA
* *
5805986 TATATAATGTATAAGTTTTGAAAACATTTTTTGAAAACT
1 TATATAATATAT-AGTTTTGAAAACA-TTTTTGAAAACA
* * *
5806025 TATATAATACATAGTTTTGAAAACATTTTTTGGAAACG
1 TATATAATATATAGTTTTGAAAACA-TTTTTGAAAACA
5806063 TATATAATATATAGTTTTGAAAACATTTTTGAAAACA
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAACA
* *
5806100 TATATAATATATAGTTTTGAAAATATTTTTTAAAA-A
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAACA
*
5806136 GTATATAATATATAGTTTTTAAAACATTTTTGAAAACA
1 -TATATAATATATAGTTTTGAAAACATTTTTGAAAACA
*
5806174 TATATAATATATAGTTTTTAAAACATTTTTGAAAAC-
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAACA
*
5806210 -GTATAATATATAGTTTTGAAAACAT
1 TATATAATATATAGTTTTGAAAACAT
5806235 ATATAATATA
Statistics
Matches: 229, Mismatches: 17, Indels: 9
0.90 0.07 0.04
Matches are distributed among these distances:
35 23 0.10
36 1 0.00
37 111 0.48
38 60 0.26
39 34 0.15
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (37 bp):
TATATAATATATAGTTTTGAAAACATTTTTGAAAACA
Found at i:5806230 original size:23 final size:24
Alignment explanation
Indices: 5806200--5806256 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
5806190 TTTAAAACAT
*
5806200 TTTTGAAAAC-GTATAATATATAG
1 TTTTGAAAACAATATAATATATAG
5806223 TTTTGAAAACATATATAATATATAG
1 TTTTGAAAACA-ATATAATATATAG
*
5806248 TTTTTAAAA
1 TTTTGAAAA
5806257 ATACTTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 10 0.33
25 20 0.67
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.42
Consensus pattern (24 bp):
TTTTGAAAACAATATAATATATAG
Found at i:5806231 original size:60 final size:60
Alignment explanation
Indices: 5806163--5806282 Score: 206
Period size: 60 Copynumber: 2.0 Consensus size: 60
5806153 TTTAAAACAT
*
5806163 TTTTGAAAACATATATAATATATAGTTTTTAAAACAT-TTTTGAAAACGTATAATATATAG
1 TTTTGAAAACATATATAATATATAGTTTTTAAAA-ATATTTTGAAAACATATAATATATAG
5806223 TTTTGAAAACATATATAATATATAGTTTTTAAAAATACTTTTGAAAACATATAATATATA
1 TTTTGAAAACATATATAATATATAGTTTTTAAAAATA-TTTTGAAAACATATAATATATA
5806283 ATTTAAAAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
59 2 0.04
60 34 0.60
61 21 0.37
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (60 bp):
TTTTGAAAACATATATAATATATAGTTTTTAAAAATATTTTGAAAACATATAATATATAG
Found at i:5806282 original size:36 final size:37
Alignment explanation
Indices: 5806223--5806313 Score: 107
Period size: 36 Copynumber: 2.5 Consensus size: 37
5806213 TAATATATAG
* *
5806223 TTTTGAAAACATATATAATATATAGTTTTTAAAAA-T-AC
1 TTTTGAAAAC--ATATAATATATA-ATTTAAAAAATTGAC
*
5806261 TTTTGAAAACATATAATATATAATTTAAAAAATTGAT
1 TTTTGAAAACATATAATATATAATTTAAAAAATTGAC
5806298 TTTTG-AAACATATAAT
1 TTTTGAAAACATATAAT
5806314 TTTTGAAAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
35 8 0.17
36 24 0.50
37 6 0.12
38 10 0.21
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (37 bp):
TTTTGAAAACATATAATATATAATTTAAAAAATTGAC
Found at i:5807458 original size:17 final size:17
Alignment explanation
Indices: 5807429--5807471 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
5807419 TCTTTTCTAA
5807429 TTATTTTAATATTCATTTT
1 TTATTTT-AT-TTCATTTT
*
5807448 ATTATTTTATTTTATTTT
1 -TTATTTTATTTCATTTT
5807466 TTATTT
1 TTATTT
5807472 AACTTTCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 6 0.27
18 7 0.32
19 2 0.09
20 7 0.32
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATTTTATTTCATTTT
Found at i:5807467 original size:12 final size:12
Alignment explanation
Indices: 5807429--5807471 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
5807419 TCTTTTCTAA
* *
5807429 TTATTTTAATAT
1 TTATTTTATTTT
*
5807441 TCATTTTATTATT
1 TTATTTTATT-TT
5807454 TTATTTTATTTT
1 TTATTTTATTTT
5807466 TTATTT
1 TTATTT
5807472 AACTTTCATG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:5808308 original size:45 final size:47
Alignment explanation
Indices: 5808246--5808353 Score: 125
Period size: 47 Copynumber: 2.3 Consensus size: 47
5808236 GCACCACTAC
*
5808246 TCTTCAGGGTAGTTCAAA-T-ATAA-AAAATGGAATATGC-TCTACTGA
1 TCTTCAGGGTAGGTCAAAGTCA-AACAAAATGGAATATGCTTC-ACTGA
* * * *
5808291 TCTTCAAGGTAGGTCAAAGTCAAACAAAATGGGATCTGCTTCACTGC
1 TCTTCAGGGTAGGTCAAAGTCAAACAAAATGGAATATGCTTCACTGA
5808338 TCTTCAGGGTAGGTCA
1 TCTTCAGGGTAGGTCA
5808354 GATCAAGATA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
45 16 0.30
46 3 0.06
47 32 0.60
48 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (47 bp):
TCTTCAGGGTAGGTCAAAGTCAAACAAAATGGAATATGCTTCACTGA
Found at i:5808537 original size:41 final size:41
Alignment explanation
Indices: 5808466--5808568 Score: 106
Period size: 41 Copynumber: 2.5 Consensus size: 41
5808456 GCTCCGCTGC
* *
5808466 CTTCAAGGTTGGTCAGATCCATATAGATTTGCTCCTC-TT-CT
1 CTTCAAGGTAGGTCAAATCCATATAGATTTGCT--TCGTTGCT
* *
5808507 CTTCAAGGTAGGTCAAATCTA-ATGGAATTTGCTTCGTTGCT
1 CTTCAAGGTAGGTCAAATCCATATAG-ATTTGCTTCGTTGCT
5808548 CTT-AAGGGTAGGTCAAATCCA
1 CTTCAA-GGTAGGTCAAATCCA
5808569 CTGTACATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
39 2 0.04
40 7 0.13
41 44 0.83
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (41 bp):
CTTCAAGGTAGGTCAAATCCATATAGATTTGCTTCGTTGCT
Found at i:5815537 original size:58 final size:58
Alignment explanation
Indices: 5815105--5815515 Score: 585
Period size: 58 Copynumber: 7.1 Consensus size: 58
5815095 GCATGTACAT
* *** *
5815105 AAATTCATCCACTTCGTATGAATTTCTTAAGTTTACACAT--AAA-GTGCATGTACAG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACGG
* * * * *
5815160 AAATTCATCCACTTATTATAAATTTCTTAAGTTTACATATAAAAATGTACACATACGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACGG
* *
5815218 AAATTCTTCCACTTAGTATGAATTGCTTAAGTTTACACATAAAAATGTGCCCATACGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACGG
* *
5815276 AAATTCATCCACTTAGTATAAATTTCTTAAGTTTGCACATAAAAATGTGCCCATACGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACGG
* * *
5815334 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTGCACTTAAAAATGTGCCCATATGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACGG
* * *
5815392 AAATTCATCCACTTAGTACGAATTTATTAAGTTTACACATAAAAATGTGCCCATATGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACGG
* * *
5815450 AAATTCATCCTCTTAGTATGAATTTCTTAAGTTTATACATAAAAATGTGCCAATACGG
1 AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACGG
*
5815508 AAAATCAT
1 AAATTCAT
5815516 AAACAAAATA
Statistics
Matches: 320, Mismatches: 33, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
55 36 0.11
57 3 0.01
58 281 0.88
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (58 bp):
AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAAATGTGCCCATACGG
Found at i:5815672 original size:45 final size:45
Alignment explanation
Indices: 5815608--5815755 Score: 206
Period size: 45 Copynumber: 3.3 Consensus size: 45
5815598 CTATGACTAC
*
5815608 CATTTCAACTATAGCATACTTTTTTATTGATAATGCACCCATATA
1 CATTTCAACTATAGCATACTTTTTTGTTGATAATGCACCCATATA
* * * * ** *
5815653 CATTTGAACTACAACATACTTTTATGTTGATAATGCAGTCATATG
1 CATTTCAACTATAGCATACTTTTTTGTTGATAATGCACCCATATA
* *
5815698 TATTTCAACTATAGCATACTTTTTTGTTGATAATGCACCCATATC
1 CATTTCAACTATAGCATACTTTTTTGTTGATAATGCACCCATATA
5815743 CATTTCAACTATA
1 CATTTCAACTATA
5815756 TGGGTGCATT
Statistics
Matches: 86, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 86 1.00
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (45 bp):
CATTTCAACTATAGCATACTTTTTTGTTGATAATGCACCCATATA
Found at i:5815967 original size:58 final size:57
Alignment explanation
Indices: 5815888--5816074 Score: 247
Period size: 58 Copynumber: 3.3 Consensus size: 57
5815878 TAATTTGTTT
*
5815888 ATGAATTTCCGT-TTGTGCACATTTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGT-CACA-TTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* *
5815946 ATGAATTTCCATATGGTCACATCTTTACGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGTCACAT-TTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * *
5816004 ATGAATTTCCGTATGGGCAC--TTTATGTGTAATCTTAA-AGAATTCATACTAAGAGG
1 ATGAATTTCCGTATGGTCACATTTTATGTGTAAACTTAAGA-AATTCATACTAAGTGG
*
5816059 ATGAATTTCTGTATGG
1 ATGAATTTCCGTATGG
5816075 GTACTTTATA
Statistics
Matches: 117, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
54 1 0.01
55 45 0.38
57 1 0.01
58 67 0.57
59 3 0.03
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (57 bp):
ATGAATTTCCGTATGGTCACATTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
Found at i:5816052 original size:55 final size:55
Alignment explanation
Indices: 5815888--5816127 Score: 250
Period size: 55 Copynumber: 4.3 Consensus size: 55
5815878 TAATTTGTTT
* *
5815888 ATGAATTTCCGTTTGTGCACATTTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGGGCAC---TTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* * *
5815946 ATGAATTTCCATATGGTCACATCTTTACGTGTAAACTTAAGAAATTCATACTAAGTGG
1 ATGAATTTCCGTATGG--GCA-CTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
* *
5816004 ATGAATTTCCGTATGGGCACTTTATGTGTAATCTTAA-AGAATTCATACTAAGAGG
1 ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGA-AATTCATACTAAGTGG
* * * * * * * *
5816059 ATGAATTTCTGTATGGGTACTTTATATGCAAAACTTGA-AAAGTCGTACTAAGTGT
1 ATGAATTTCCGTATGGGCACTTTATGTG-TAAACTTAAGAAATTCATACTAAGTGG
*
5816114 ATAAATTTCCGTAT
1 ATGAATTTCCGTAT
5816128 TGGTAGTGGT
Statistics
Matches: 155, Mismatches: 22, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
54 1 0.01
55 80 0.52
56 9 0.06
58 62 0.40
60 2 0.01
61 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (55 bp):
ATGAATTTCCGTATGGGCACTTTATGTGTAAACTTAAGAAATTCATACTAAGTGG
Found at i:5832436 original size:27 final size:28
Alignment explanation
Indices: 5832406--5832458 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
5832396 ATTGCCCTTG
5832406 AAGTGTAAAATGACC-AAAATACCTTTA
1 AAGTGTAAAATGACCTAAAATACCTTTA
* *
5832433 AAGTGTAAAATTACCTAAAGTACCTT
1 AAGTGTAAAATGACCTAAAATACCTT
5832459 CATGCCATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.28
Consensus pattern (28 bp):
AAGTGTAAAATGACCTAAAATACCTTTA
Found at i:5833677 original size:35 final size:35
Alignment explanation
Indices: 5833627--5833752 Score: 119
Period size: 35 Copynumber: 3.6 Consensus size: 35
5833617 TTTATCTCTA
*
5833627 ATCAAGTTGGTAATTCCATATATAGGTTCAACACCG
1 ATCAAGTTGGTAATTCCTTATATAGGTTCAAC-CCG
** * *
5833663 ATC-AGTTGGTAATTCCTTATGGCAGGTTCAGCTCG
1 ATCAAGTTGGTAATTCCTTAT-ATAGGTTCAACCCG
* * * *
5833698 GTCAAGTTGGTAATTCCTTATATATGTTCAAACCA
1 ATCAAGTTGGTAATTCCTTATATAGGTTCAACCCG
* **
5833733 ATCGAGCAGGTAATTCCTTA
1 ATCAAGTTGGTAATTCCTTA
5833753 CGGATCTAAA
Statistics
Matches: 71, Mismatches: 17, Indels: 5
0.76 0.18 0.05
Matches are distributed among these distances:
35 43 0.61
36 28 0.39
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (35 bp):
ATCAAGTTGGTAATTCCTTATATAGGTTCAACCCG
Found at i:5837870 original size:20 final size:20
Alignment explanation
Indices: 5837830--5837868 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
5837820 CATTGCAAGA
*
5837830 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
5837850 ATTTCATGGCCTCAACAAA
1 ATTT-ATGGCCTCAACAAA
5837869 GACCTTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:5843128 original size:21 final size:22
Alignment explanation
Indices: 5843092--5843133 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5843082 AGCACCAGTT
* *
5843092 CCTGCACAATCGACTC-CAATA
1 CCTGCACAACCCACTCTCAATA
5843113 CCTGCACAACCCACTCTCAAT
1 CCTGCACAACCCACTCTCAAT
5843134 GAAGAACAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.31, C:0.43, G:0.07, T:0.19
Consensus pattern (22 bp):
CCTGCACAACCCACTCTCAATA
Found at i:5850404 original size:21 final size:19
Alignment explanation
Indices: 5850376--5850416 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
5850366 CATTGTAGGA
5850376 ATTTATGGCCTCGAAAAAAG
1 ATTTATGGCCTC-AAAAAAG
*
5850396 ATTTCATGGCCTCAACAAAG
1 ATTT-ATGGCCTCAAAAAAG
5850416 A
1 A
5850417 CCTTGATGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (19 bp):
ATTTATGGCCTCAAAAAAG
Found at i:5869537 original size:13 final size:13
Alignment explanation
Indices: 5869521--5869562 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
5869511 TATGATGCGT
5869521 ATTTATGACACGC
1 ATTTATGACACGC
*
5869534 ATTTATGACGCGC
1 ATTTATGACACGC
*
5869547 ATTTATGACACTC
1 ATTTATGACACGC
5869560 ATT
1 ATT
5869563 GCGCGTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:5869540 original size:26 final size:26
Alignment explanation
Indices: 5869511--5869562 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
5869501 GTCATAAATC
* *
5869511 TATGATGCGTATTTATGACACGCATT
1 TATGACGCGCATTTATGACACGCATT
*
5869537 TATGACGCGCATTTATGACACTCATT
1 TATGACGCGCATTTATGACACGCATT
5869563 GCGCGTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (26 bp):
TATGACGCGCATTTATGACACGCATT
Found at i:5869726 original size:2 final size:2
Alignment explanation
Indices: 5869719--5869751 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5869709 TTTCATAAAT
5869719 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5869752 GATTGGCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5871198 original size:30 final size:30
Alignment explanation
Indices: 5871162--5871221 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
5871152 GATCCATTAG
5871162 ACAAATTTACTAGGTGGATGTAGGTATCAA
1 ACAAATTTACTAGGTGGATGTAGGTATCAA
5871192 ACAAATTTACTAGGTGGATGTAGGTATCAA
1 ACAAATTTACTAGGTGGATGTAGGTATCAA
5871222 GAGCAAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (30 bp):
ACAAATTTACTAGGTGGATGTAGGTATCAA
Found at i:5875517 original size:21 final size:21
Alignment explanation
Indices: 5875491--5875531 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
5875481 AGTATGTCCA
5875491 GGGGGGTATCGATTCCCCCTG
1 GGGGGGTATCGATTCCCCCTG
5875512 GGGGGGTATCGATTCCCCCT
1 GGGGGGTATCGATTCCCCCT
5875532 AAAAGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.10, C:0.29, G:0.37, T:0.24
Consensus pattern (21 bp):
GGGGGGTATCGATTCCCCCTG
Found at i:5880041 original size:42 final size:42
Alignment explanation
Indices: 5879994--5880083 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
5879984 TAGTAAGCCC
* *
5879994 TCCGAGCATGATGCTTAAATCCTTCGAGTCATCTGTCAGGCT
1 TCCGAGCATGATGATAAAATCCTTCGAGTCATCTGTCAGGCT
* * * *
5880036 TCCGAGCATGATGATAAAATCCTTTGGGTTATCTGTCAGTCT
1 TCCGAGCATGATGATAAAATCCTTCGAGTCATCTGTCAGGCT
5880078 TCCGAG
1 TCCGAG
5880084 AAAGTCGATA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.32
Consensus pattern (42 bp):
TCCGAGCATGATGATAAAATCCTTCGAGTCATCTGTCAGGCT
Found at i:5880162 original size:37 final size:37
Alignment explanation
Indices: 5880107--5880366 Score: 373
Period size: 37 Copynumber: 7.0 Consensus size: 37
5880097 CCTATGGGCC
*
5880107 ATCTATAAGCCTTCACGGAAGAGTAGTAAAGCAAATCA
1 ATCT-TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCA
5880145 ATCTTAAGCCTTCACGGAAGAGT-GTGAAGCAAATCA
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCA
* * *
5880181 ATCTTAAGGCGTCACGGAAGAGTAATGAAGCAAATCA
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCA
* * * *
5880218 ATTTTAAGCCTTCACAGATGAGTAGTAAAGCAAATCA
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCA
* *
5880255 ATCTTAAGCCTTAACGAAAGAGTAGTTG-AGCAAATCA
1 ATCTTAAGCCTTCACGGAAGAGTAG-TGAAGCAAATCA
5880292 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATC-
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCA
*
5880328 ATCTATAAGCCTTCACAGAAGAGTAGTGAAGCAAATCA
1 ATCT-TAAGCCTTCACGGAAGAGTAGTGAAGCAAATCA
5880366 A
1 A
5880367 ATCAAGTCTT
Statistics
Matches: 197, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
36 39 0.20
37 152 0.77
38 6 0.03
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (37 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCA
Found at i:5880501 original size:81 final size:81
Alignment explanation
Indices: 5880364--5880535 Score: 245
Period size: 81 Copynumber: 2.1 Consensus size: 81
5880354 TGAAGCAAAT
* *
5880364 CAAATCAAGTCTTATCTCCCTGAATGAATAGTGGAGCAGACACATAATCCAGAATTGATCTGTCT
1 CAAATCAAGTCTTATCTCCCTGAATGAATAGTGGAGCAGACACACAATCCAAAATTGATCTGTCT
*
5880429 ACGCGAAAAAGAGGCA
66 ACCCGAAAAAGAGGCA
* * * * ** *
5880445 CAAATCGAGTCTTATCTCCCTTAATGAATAGTGGAGCATACACGCCTTTCAAAATTGATCTGTCT
1 CAAATCAAGTCTTATCTCCCTGAATGAATAGTGGAGCAGACACACAATCCAAAATTGATCTGTCT
*
5880510 ACCCGAAAGAGAGGCA
66 ACCCGAAAAAGAGGCA
5880526 CAAATCAAGT
1 CAAATCAAGT
5880536 ATGATTTCCC
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (81 bp):
CAAATCAAGTCTTATCTCCCTGAATGAATAGTGGAGCAGACACACAATCCAAAATTGATCTGTCT
ACCCGAAAAAGAGGCA
Found at i:5881517 original size:21 final size:20
Alignment explanation
Indices: 5881487--5881526 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5881477 AAAACAGAGA
*
5881487 AAAAATGGAAAGAAAAAAAGG
1 AAAAAGGGAAA-AAAAAAAGG
*
5881508 AAAAAGGGAAAAAAGAAAG
1 AAAAAGGGAAAAAAAAAAG
5881527 ATTCTTACCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (20 bp):
AAAAAGGGAAAAAAAAAAGG
Found at i:5884941 original size:79 final size:77
Alignment explanation
Indices: 5884844--5885002 Score: 273
Period size: 79 Copynumber: 2.0 Consensus size: 77
5884834 ACAACGCGTC
5884844 AAATCATAGAGAAAAATGGGAACAATAACCAACACAAAACTCATACAAAATAAAAATTAATCCTA
1 AAATCATAGAGAAAAATGGGAACAATAACCAACACAAAACTCATACAAAATAAAAATTAATCCTA
5884909 AAAAGACGAAGA
66 AAAAGACGAAGA
* * *
5884921 AAATCATAGAGAGAAAAATGGGGATAATAGCCAACACAAAACTCATACAAAATAAAAATTAATCC
1 AAATCAT--AGAGAAAAATGGGAACAATAACCAACACAAAACTCATACAAAATAAAAATTAATCC
5884986 TAAAAAGACGAAGA
64 TAAAAAGACGAAGA
5885000 AAA
1 AAA
5885003 ATAAAATCTT
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
77 7 0.09
79 70 0.91
ACGTcount: A:0.59, C:0.14, G:0.12, T:0.14
Consensus pattern (77 bp):
AAATCATAGAGAAAAATGGGAACAATAACCAACACAAAACTCATACAAAATAAAAATTAATCCTA
AAAAGACGAAGA
Found at i:5891428 original size:56 final size:56
Alignment explanation
Indices: 5891338--5891508 Score: 225
Period size: 57 Copynumber: 3.0 Consensus size: 56
5891328 GTTGAAGGAA
*
5891338 GAATACTTGCAGGTTCCTCGGCTTTGTGCTGAGGGCCTTACTATTCGTGATGGGGTT
1 GAATACTTGCAGGTTCCTC-GCTTTGTGCTGAGGGCCTTACTGTTCGTGATGGGGTT
** * * * *
5891395 GAATACTTGCAGGTAACTCGCTTTGTACTGAGGGCCTTATTGTTTGTGACGGGGTT
1 GAATACTTGCAGGTTCCTCGCTTTGTGCTGAGGGCCTTACTGTTCGTGATGGGGTT
* * * *
5891451 GAATACTTGCAGGTTCCTTGGCTTTGTGCTCAGGGTCTTACTGTTCATGATGGGGTT
1 GAATACTTGCAGGTTCC-TCGCTTTGTGCTGAGGGCCTTACTGTTCGTGATGGGGTT
5891508 G
1 G
5891509 TATGGTTCAG
Statistics
Matches: 96, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
56 47 0.49
57 49 0.51
ACGTcount: A:0.15, C:0.18, G:0.31, T:0.36
Consensus pattern (56 bp):
GAATACTTGCAGGTTCCTCGCTTTGTGCTGAGGGCCTTACTGTTCGTGATGGGGTT
Found at i:5896062 original size:24 final size:25
Alignment explanation
Indices: 5896003--5896070 Score: 97
Period size: 24 Copynumber: 2.8 Consensus size: 25
5895993 TATGATACCT
5896003 GACCTGGATTCTGATCT-A-ATATA
1 GACCTGGATTCTGATCTGATATATA
* *
5896026 GACATGGATTCTGATATGATATATA
1 GACCTGGATTCTGATCTGATATATA
5896051 -ACCTGGATTCTGATCTGATA
1 GACCTGGATTCTGATCTGATA
5896071 CTTGACCTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
23 15 0.38
24 19 0.49
25 5 0.13
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (25 bp):
GACCTGGATTCTGATCTGATATATA
Found at i:5896078 original size:24 final size:23
Alignment explanation
Indices: 5896002--5896078 Score: 91
Period size: 24 Copynumber: 3.3 Consensus size: 23
5895992 TTATGATACC
*
5896002 TGACCTGGATTCTGATCTAATAT
1 TGACCTGGATTCTGATCTGATAT
* * *
5896025 AGACATGGATTCTGATATGATAT
1 TGACCTGGATTCTGATCTGATAT
*
5896048 ATAACCTGGATTCTGATCTGATACT
1 -TGACCTGGATTCTGATCTGATA-T
5896073 TGACCT
1 TGACCT
5896079 AAATTATGTT
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
23 19 0.44
24 23 0.53
25 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (23 bp):
TGACCTGGATTCTGATCTGATAT
Found at i:5897837 original size:17 final size:18
Alignment explanation
Indices: 5897806--5897839 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5897796 TGGGAACTAA
5897806 TAATAAATGTAAGAAAGT
1 TAATAAATGTAAGAAAGT
*
5897824 TAAT-AATGTTAGAAAG
1 TAATAAATGTAAGAAAG
5897840 AAGATTGTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (18 bp):
TAATAAATGTAAGAAAGT
Found at i:5914593 original size:27 final size:27
Alignment explanation
Indices: 5914555--5914611 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
5914545 GCCATCCTCC
5914555 TTAGTCCAACAGTTGAATAATACATAT
1 TTAGTCCAACAGTTGAATAATACATAT
5914582 TTAGTCCAACAGTTGAATAATACATAT
1 TTAGTCCAACAGTTGAATAATACATAT
5914609 TTA
1 TTA
5914612 CTTGTTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (27 bp):
TTAGTCCAACAGTTGAATAATACATAT
Found at i:5920791 original size:450 final size:450
Alignment explanation
Indices: 5919948--5921234 Score: 1998
Period size: 450 Copynumber: 2.9 Consensus size: 450
5919938 AAAAAGTTGT
* * *
5919948 TATATTAGCTATAGGGACATATGTTTTATCTTTG-CCTATAAGACTTGATTTAAATTTAGAGAAT
1 TATATTAGCTATAGGGACATATGTTTTATTTTTGAAC-ATTAGACTTGATTTAAATTTAGAGAAT
**
5920012 TTATATTTTGTGCCTATTTTAACTAAAAACATTATTTCTTTTTCTTGTTTGGACAAGATTGGTTT
65 TGCTATTTTGTGCCTATTTTAACTAAAAACATTATTTCTTTTTCTTGTTTGGACAAGATTGGTTT
* * * *
5920077 TGAGATAATTATAAAGAATAATTGTTG-ATTTTTTATCTTGATAGTGTTTTCTATGGATTGACAC
130 TGAGATAATTATAAAGAATAATTGTTGTTTTTTTTATCTCGATAGTGTTTTATATGGATCGACAC
* *
5920141 AATTAGTTAATGGTCTTTTTATTTTGGATCAAGATAATACCATTTATAATATAAATACAAGAAGA
195 AATTAGTTAATGGTCTTTATATTTTGGATCAAGATAATACCATTTATAACATAAATACAAGAAGA
* *
5920206 TAAAAAACAAATGACTCAAATCAAACTTATCTTTAGCACTGTTGTTCATACCATATATATGAGAA
260 TAAAAAACAAATGACTCAAATCAAACTTATCTTTAGCATTGTTGTTCAGACCATATATATGAGAA
* * *
5920271 AAGCATATCAAAGCTCTATAAAGATGGATCCCTA-AGTTCATTTATTTTCAAACAATTTGATGTC
325 AAACATATCAAAGCTCTATAAAGATGGATCCTTAGA-TTCATTTATTTTCAAACAATTTGATGTA
* * *
5920335 TGTGAATCATGCTTGTCGGAAAAAATGACTAAGGCTCCTTATATTCCA-TAAACTATTTTGAC
389 TGTGAATCATGCTTGTCAGAAAAAATGACTAAAGCTCCTTATA-TCCACTAAACAATTTTGAC
* * *
5920397 TATATTAACTATAGGGACATATTTTTTATTTTTGAACATTGGACTTGATTTAAATTTAGAGAATT
1 TATATTAGCTATAGGGACATATGTTTTATTTTTGAACATTAGACTTGATTTAAATTTAGAGAATT
5920462 GCTATTTTGTGCCTATTTTAACTAAAAACATTATTTCTTTTTCTTGTTTGGACAAGATTGGTTTT
66 GCTATTTTGTGCCTATTTTAACTAAAAACATTATTTCTTTTTCTTGTTTGGACAAGATTGGTTTT
* *
5920527 GAGATAATTATAAAGAATAATTGATGTTTTTTTTATCTCGATAGTGTTTTTTATGGATCGACACA
131 GAGATAATTATAAAGAATAATTGTTGTTTTTTTTATCTCGATAGTGTTTTATATGGATCGACACA
*
5920592 ATTAGTTAATGGTCTTTGTATTTTGGATCAAGATAATACCATTTATAACATAAATACAAGAAGAT
196 ATTAGTTAATGGTCTTTATATTTTGGATCAAGATAATACCATTTATAACATAAATACAAGAAGAT
* *
5920657 AAAAAATAAATGACTCAAATCAAACTTATCTTTAGCATTGTTGTTCAGACCATGTATATGAGAAA
261 AAAAAACAAATGACTCAAATCAAACTTATCTTTAGCATTGTTGTTCAGACCATATATATGAGAAA
* *
5920722 AACATATCAAAGCTCTATAAAGATGGATCCTTAGATTCACTTATTTTCGAACAATTTGATGTATG
326 AACATATCAAAGCTCTATAAAGATGGATCCTTAGATTCATTTATTTTCAAACAATTTGATGTATG
* * ** *
5920787 TGAATCATGCTTGTTAGAAAAAATGACTAAAGCTCCTTGTATGGACTCAACAATTTTGAC
391 TGAATCATGCTTGTCAGAAAAAATGACTAAAGCTCCTTATATCCACTAAACAATTTTGAC
*
5920847 TATATTAGCTATAGGGACATATGTTTTATTTTTGAACATTAGACTTGATTTAAATTTAGAGAACT
1 TATATTAGCTATAGGGACATATGTTTTATTTTTGAACATTAGACTTGATTTAAATTTAGAGAATT
* * * * * *
5920912 GCTATTTTTTGCCTATTTTGACTAAAAATATTGTTTATTTTTCTTGTTTGGACATGATTGGTTTT
66 GCTATTTTGTGCCTATTTTAACTAAAAACATTATTTCTTTTTCTTGTTTGGACAAGATTGGTTTT
* * *
5920977 GAGATAATTATAAAGAATTATTGTTGTTTCTTTTATCTCGATAGTGTTTTATATGGATCAACACA
131 GAGATAATTATAAAGAATAATTGTTGTTTTTTTTATCTCGATAGTGTTTTATATGGATCGACACA
* * *
5921042 ATTAGTTAATGGTATTTATATCTTGGATCAAGAAAATACCATTTATAACATAAATACAAGAAGAT
196 ATTAGTTAATGGTCTTTATATTTTGGATCAAGATAATACCATTTATAACATAAATACAAGAAGAT
* * *
5921107 GATAAACAAATGACTCAAATCAAACTTATCTTTAGCTTTGTTGTTCAGACCATATA-AGTGAGAA
261 AAAAAACAAATGACTCAAATCAAACTTATCTTTAGCATTGTTGTTCAGACCATATATA-TGAGAA
* * *
5921171 ACACATATCAAAG-T-TAT--AGATGGATTCTTAGATTCATTTGTTTTCAAACAATTTGATGTAT
325 AAACATATCAAAGCTCTATAAAGATGGATCCTTAGATTCATTTATTTTCAAACAATTTGATGTAT
5921232 GTG
390 GTG
5921235 GGCAATGAAT
Statistics
Matches: 772, Mismatches: 61, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
446 43 0.06
448 3 0.00
449 149 0.19
450 576 0.75
451 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (450 bp):
TATATTAGCTATAGGGACATATGTTTTATTTTTGAACATTAGACTTGATTTAAATTTAGAGAATT
GCTATTTTGTGCCTATTTTAACTAAAAACATTATTTCTTTTTCTTGTTTGGACAAGATTGGTTTT
GAGATAATTATAAAGAATAATTGTTGTTTTTTTTATCTCGATAGTGTTTTATATGGATCGACACA
ATTAGTTAATGGTCTTTATATTTTGGATCAAGATAATACCATTTATAACATAAATACAAGAAGAT
AAAAAACAAATGACTCAAATCAAACTTATCTTTAGCATTGTTGTTCAGACCATATATATGAGAAA
AACATATCAAAGCTCTATAAAGATGGATCCTTAGATTCATTTATTTTCAAACAATTTGATGTATG
TGAATCATGCTTGTCAGAAAAAATGACTAAAGCTCCTTATATCCACTAAACAATTTTGAC
Found at i:5929446 original size:21 final size:22
Alignment explanation
Indices: 5929422--5929476 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
5929412 ACCCTTTCTA
5929422 TGTATCGATACA-CCTTAAATG
1 TGTATCGATACATCCTTAAATG
* *
5929443 TGTACCGATACATTCCTTGAATG
1 TGTATCGATACA-TCCTTAAATG
*
5929466 TGTATCAATAC
1 TGTATCGATAC
5929477 CCCTCACGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 11 0.39
23 17 0.61
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (22 bp):
TGTATCGATACATCCTTAAATG
Found at i:5931720 original size:13 final size:13
Alignment explanation
Indices: 5931699--5931733 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
5931689 CGGTAATTTT
*
5931699 TTTTCAAAATTGA
1 TTTTCAAAAATGA
5931712 -TTTCAAAAATGA
1 TTTTCAAAAATGA
5931724 TTTTCAAAAA
1 TTTTCAAAAA
5931734 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:5934794 original size:39 final size:39
Alignment explanation
Indices: 5934751--5934827 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
5934741 TGCTAATAAA
* * *
5934751 ATAAAATACTACTAATTAATCATAATCATAATATAACTC
1 ATAAAATACTAATAATCAACCATAATCATAATATAACTC
* * *
5934790 ATAAAATACTAATTATCAGCCCTAATCATAATATAACT
1 ATAAAATACTAATAATCAACCATAATCATAATATAACT
5934828 TACACTCCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.32
Consensus pattern (39 bp):
ATAAAATACTAATAATCAACCATAATCATAATATAACTC
Found at i:5939168 original size:21 final size:21
Alignment explanation
Indices: 5939144--5939193 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
5939134 AAAACTAGAA
5939144 GTATCGGTACTCCACTATAGG-
1 GTATCGGTACTCCACTAT-GGC
5939165 GTATCGGTACTCCACTATGGC
1 GTATCGGTACTCCACTATGGC
5939186 GTATCGGT
1 GTATCGGT
5939194 GCTACCTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (21 bp):
GTATCGGTACTCCACTATGGC
Found at i:5951485 original size:138 final size:138
Alignment explanation
Indices: 5951232--5951495 Score: 325
Period size: 138 Copynumber: 1.9 Consensus size: 138
5951222 CATACTTCGT
* * *
5951232 GTATGAAAGTTATCGATCGATTTTAATTAATGCATAATGGTGCATTTTCGTATCAGTACTATGTG
1 GTATAAAAGTTATCGATCGATTTTAATTAAAGCATAACGGTGCATTTTCGTATCAGTACTATGTG
** * * *
5951297 TACATTTTTCACTAGATGAGCAAAAATGGTATTCATAATGAGTTTATGAATTACCATTTCGATAT
66 TACATTTGGCACTAGATGAGCAAAAATGGAATTAATAATAAGTTTATGAATTACCATTTCGATAT
5951362 AAAATATA
131 AAAATATA
* * ** *
5951370 GTATAAAAGTTATTGATTGATTTTGTTTAAAGCATAACGTTGCATTTTCGTATCAGTACTATGTG
1 GTATAAAAGTTATCGATCGATTTTAATTAAAGCATAACGGTGCATTTTCGTATCAGTACTATGTG
* *** * *
5951435 TAC-TTTCGGCACTATG-TGTGCATCCATGGAATTAATAATAAGTTTTTGAATTTCCATTTCG
66 TACATTT-GGCACTA-GATGAGCAAAAATGGAATTAATAATAAGTTTATGAATTACCATTTCG
5951496 GCACTTCGGT
Statistics
Matches: 105, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
137 3 0.03
138 101 0.96
139 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (138 bp):
GTATAAAAGTTATCGATCGATTTTAATTAAAGCATAACGGTGCATTTTCGTATCAGTACTATGTG
TACATTTGGCACTAGATGAGCAAAAATGGAATTAATAATAAGTTTATGAATTACCATTTCGATAT
AAAATATA
Found at i:5952755 original size:6 final size:6
Alignment explanation
Indices: 5952746--5952843 Score: 52
Period size: 6 Copynumber: 17.5 Consensus size: 6
5952736 TACTAATAAT
* * * *
5952746 TAATCA TAATCG TAAT-A TAACTCA TAA-AA TACTAA TAAT-- TAATCA
1 TAATCA TAATCA TAATCA TAA-TCA TAATCA TAATCA TAATCA TAATCA
* * *
5952791 TAATCA TAAT-A TAACTCA TAA-AA TAATAA TAAT-- TAATCC TAATCA
1 TAATCA TAATCA TAA-TCA TAATCA TAATCA TAATCA TAATCA TAATCA
5952836 TAAT-A TAA
1 TAATCA TAA
5952844 CTCTCAATCA
Statistics
Matches: 75, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
4 8 0.11
5 18 0.24
6 41 0.55
7 8 0.11
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (6 bp):
TAATCA
Found at i:5952773 original size:39 final size:39
Alignment explanation
Indices: 5952730--5952846 Score: 207
Period size: 39 Copynumber: 3.0 Consensus size: 39
5952720 TACTAATAAA
*
5952730 ATAAAATACTAATAATTAATCATAATCGTAATATAACTC
1 ATAAAATACTAATAATTAATCATAATCATAATATAACTC
5952769 ATAAAATACTAATAATTAATCATAATCATAATATAACTC
1 ATAAAATACTAATAATTAATCATAATCATAATATAACTC
* *
5952808 ATAAAATAATAATAATTAATCCTAATCATAATATAACTC
1 ATAAAATACTAATAATTAATCATAATCATAATATAACTC
5952847 TCAATCATTA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.33
Consensus pattern (39 bp):
ATAAAATACTAATAATTAATCATAATCATAATATAACTC
Found at i:5953630 original size:58 final size:58
Alignment explanation
Indices: 5953560--5953676 Score: 225
Period size: 58 Copynumber: 2.0 Consensus size: 58
5953550 CTCGTCCAAT
*
5953560 TCCAAGTTAAGGTATAATATGTATTATCAATTCAAATTTCTGGACAATTTTAGACTTA
1 TCCAAGTTAAGGTATAATATGTATTATAAATTCAAATTTCTGGACAATTTTAGACTTA
5953618 TCCAAGTTAAGGTATAATATGTATTATAAATTCAAATTTCTGGACAATTTTAGACTTA
1 TCCAAGTTAAGGTATAATATGTATTATAAATTCAAATTTCTGGACAATTTTAGACTTA
5953676 T
1 T
5953677 ATAAACATCT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (58 bp):
TCCAAGTTAAGGTATAATATGTATTATAAATTCAAATTTCTGGACAATTTTAGACTTA
Found at i:5953852 original size:21 final size:21
Alignment explanation
Indices: 5953828--5953867 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5953818 TTGGGATCGA
* *
5953828 AGAAATGGATTGATCCTTTTT
1 AGAAAGGGATCGATCCTTTTT
*
5953849 AGAAAGGGATCGGTCCTTT
1 AGAAAGGGATCGATCCTTT
5953868 CCCCTAAGGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (21 bp):
AGAAAGGGATCGATCCTTTTT
Found at i:5969894 original size:27 final size:27
Alignment explanation
Indices: 5969853--5969916 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
5969843 ATTTAAGAAA
5969853 ATGAGTTTTTGAGTGATATGATGATAT
1 ATGAGTTTTTGAGTGATATGATGATAT
* *
5969880 ATGAGTTTTTTAGTGATATGATTATAT
1 ATGAGTTTTTGAGTGATATGATGATAT
5969907 ATGAGTTTTT
1 ATGAGTTTTT
5969917 ATTGAGGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (27 bp):
ATGAGTTTTTGAGTGATATGATGATAT
Found at i:5981426 original size:96 final size:95
Alignment explanation
Indices: 5981269--5981492 Score: 259
Period size: 96 Copynumber: 2.3 Consensus size: 95
5981259 TACCGACAAG
* * * *
5981269 GTAGTATCGATACAATGGTAAGGGTATCAATACCAAGAAATATCGAATCTAATTTTGGTATCGAT
1 GTAGTATCGATACCATGGTAAGGGTATCAATACCAAGAAACATCGAACCTAATTTGGGTATCGAT
* * **
5981334 ACCATAAGGGGATATTGGTACCATAGTATA
66 ACAAGAAGGGGATATCAGTACCATAGTATA
* *** **
5981364 GTAGTATCGATACCATGGTAAGAGGTATCAATACCAGGCTGCATTTAACCTAATTTGGGTATCGA
1 GTAGTATCGATACCATGGTAAG-GGTATCAATACCAAGAAACATCGAACCTAATTTGGGTATCGA
* * *
5981429 TACAAGGAGGGGGTATCAGTACCATAGTGTA
65 TACAAGAAGGGGATATCAGTACCATAGTATA
* * *
5981460 GTAATATCTATACCATGGTAAGGGTATCGATAC
1 GTAGTATCGATACCATGGTAAGGGTATCAATAC
5981493 TATAAAGCCA
Statistics
Matches: 108, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
95 31 0.29
96 77 0.71
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (95 bp):
GTAGTATCGATACCATGGTAAGGGTATCAATACCAAGAAACATCGAACCTAATTTGGGTATCGAT
ACAAGAAGGGGATATCAGTACCATAGTATA
Found at i:5981878 original size:54 final size:54
Alignment explanation
Indices: 5981818--5982153 Score: 352
Period size: 54 Copynumber: 6.2 Consensus size: 54
5981808 CCAAATAGGA
* * *
5981818 ACTAAGTGTGCATTTCATAGAATTCATCCTATGTGGATGAATAACCGTTTTGAT
1 ACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGAC
* * ** *
5981872 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCGCCTCGGC
1 ACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGAC
* * ** *
5981926 ACTAAGTGTTCATTTCACAGAATTCATCCTATATGGATGAATAATTGTTTCGTC
1 ACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGAC
* *
5981980 ACTAATTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCATTTC-ACC
1 ACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGA-C
* **** * * *
5982034 ATTAAGTGTGCAAAAGAC-GAAATTCATCCTATATGGATGATTAACCGTTTCGGC
1 ACTAAGTGTGCATTTCACAG-AATTCATCCTATGTGGATGAATAACCGTTTCGAC
*** * * ** *
5982088 ACTAAGTGTGCAAAACACAAAATTCATCATATGTGGATGAATAACTATTTCGGC
1 ACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGAC
*
5982142 ACTGAGTGTGCA
1 ACTAAGTGTGCA
5982154 AAACATGGAA
Statistics
Matches: 237, Mismatches: 41, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
53 1 0.00
54 236 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (54 bp):
ACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGAC
Found at i:5982091 original size:162 final size:162
Alignment explanation
Indices: 5981818--5982153 Score: 413
Period size: 162 Copynumber: 2.1 Consensus size: 162
5981808 CCAAATAGGA
* * * *
5981818 ACTAAGTGTGCATTTCATAGAATTCATCCTATGTGGATGAATAACCGTTTTGATACTAAGTGTGC
1 ACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGATTTCACACTAAGTGTGC
*** * * * * *** *
5981883 ATTTCACGGAATTCATCCTATGTGGATGAATAATCGCCTCGGCACTAAGTGTTCATTTCACAGAA
66 AAAACACGAAATTCATCCTATATGGATGAATAACCGCCTCGGCACTAAGTGTGCAAAACACAAAA
*
5981948 TTCATCCTATATGGATGAATAATTGTTTCGTC
131 TTCATCATATATGGATGAATAATTGTTTCGTC
* *
5981980 ACTAATTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACC-ATTTCACCATTAAGTGTG
1 ACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGATTTCA-CACTAAGTGTG
* * **
5982044 CAAAAGACGAAATTCATCCTATATGGATGATTAACCGTTTCGGCACTAAGTGTGCAAAACACAAA
65 CAAAACACGAAATTCATCCTATATGGATGAATAACCGCCTCGGCACTAAGTGTGCAAAACACAAA
* * * *
5982109 ATTCATCATATGTGGATGAATAACTATTTCGGC
130 ATTCATCATATATGGATGAATAATTGTTTCGTC
*
5982142 ACTGAGTGTGCA
1 ACTAAGTGTGCA
5982154 AAACATGGAA
Statistics
Matches: 145, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
161 4 0.03
162 141 0.97
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (162 bp):
ACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGATTTCACACTAAGTGTGC
AAAACACGAAATTCATCCTATATGGATGAATAACCGCCTCGGCACTAAGTGTGCAAAACACAAAA
TTCATCATATATGGATGAATAATTGTTTCGTC
Found at i:5984765 original size:16 final size:17
Alignment explanation
Indices: 5984744--5984777 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5984734 TAAATTCATA
*
5984744 TTGTTTTCGGTTC-GGG
1 TTGTTTTCCGTTCAGGG
5984760 TTGTTTTCCGTTCAGGG
1 TTGTTTTCCGTTCAGGG
5984777 T
1 T
5984778 GATTAGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.03, C:0.15, G:0.32, T:0.50
Consensus pattern (17 bp):
TTGTTTTCCGTTCAGGG
Found at i:5986994 original size:3 final size:3
Alignment explanation
Indices: 5986986--5987072 Score: 63
Period size: 3 Copynumber: 28.0 Consensus size: 3
5986976 CATGTATACT
*
5986986 TAA TAA TAA TACA TAA TAAA TAA TAA TAA TAA TTAA TAA TAAA TAA GAA
1 TAA TAA TAA TA-A TAA T-AA TAA TAA TAA TAA -TAA TAA T-AA TAA TAA
* * *
5987035 -AA TAAA TGA TAA -GA TAA -AA TAA GTGA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
5987073 AATTATGAGT
Statistics
Matches: 68, Mismatches: 7, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
2 5 0.07
3 46 0.68
4 17 0.25
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:5987002 original size:13 final size:12
Alignment explanation
Indices: 5986986--5987072 Score: 63
Period size: 13 Copynumber: 7.0 Consensus size: 12
5986976 CATGTATACT
5986986 TAATAATAATACA
1 TAATAATAATA-A
5986999 TAATAAATAATAA
1 TAAT-AATAATAA
5987012 TAATAATTAATAA
1 TAATAA-TAATAA
*
5987025 TAAATAAGAA-AA
1 T-AATAATAATAA
* *
5987037 TAAATGATAA-GA
1 T-AATAATAATAA
*
5987049 TAA-AATAAGTGA
1 TAATAATAA-TAA
5987061 TAATAATAATAA
1 TAATAATAATAA
5987073 AATTATGAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
10 4 0.06
11 2 0.03
12 21 0.34
13 23 0.37
14 12 0.19
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (12 bp):
TAATAATAATAA
Found at i:5987003 original size:10 final size:9
Alignment explanation
Indices: 5986986--5987072 Score: 63
Period size: 10 Copynumber: 9.3 Consensus size: 9
5986976 CATGTATACT
5986986 TAATAATAA
1 TAATAATAA
5986995 TACATAATAAA
1 TA-ATAAT-AA
5987006 TAATAATAA
1 TAATAATAA
5987015 TAATTAATAA
1 TAA-TAATAA
*
5987025 TAAATAAGAA
1 T-AATAATAA
*
5987035 -AATAAATGA
1 TAAT-AATAA
*
5987044 TAA-GATAA
1 TAATAATAA
*
5987052 -AATAAGTGA
1 TAATAA-TAA
5987061 TAATAATAA
1 TAATAATAA
5987070 TAA
1 TAA
5987073 AATTATGAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
7 2 0.03
8 7 0.11
9 17 0.28
10 29 0.48
11 6 0.10
ACGTcount: A:0.64, C:0.01, G:0.06, T:0.29
Consensus pattern (9 bp):
TAATAATAA
Found at i:5987016 original size:23 final size:23
Alignment explanation
Indices: 5986986--5987073 Score: 76
Period size: 23 Copynumber: 3.9 Consensus size: 23
5986976 CATGTATACT
5986986 TAATAATAA-TACATAATAAATAA
1 TAATAATAATTA-ATAATAAATAA
5987009 TAATAATAATTAATAATAAATAA
1 TAATAATAATTAATAATAAATAA
* * * *
5987032 GAA-AATAAATGATAAGATAA-AA
1 TAATAATAATTAATAATA-AATAA
*
5987054 TAAGTGATAA-TAATAATAAA
1 TAA-TAATAATTAATAATAAA
5987074 ATTATGAGTA
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
22 17 0.32
23 30 0.57
24 6 0.11
ACGTcount: A:0.65, C:0.01, G:0.06, T:0.28
Consensus pattern (23 bp):
TAATAATAATTAATAATAAATAA
Found at i:5987953 original size:142 final size:144
Alignment explanation
Indices: 5987695--5987982 Score: 562
Period size: 142 Copynumber: 2.0 Consensus size: 144
5987685 ATTTTTAAGA
5987695 AAAAATCAAATTTATAAAGTAAATATCGAATTCATTACAGAATCAAATATACGAATAAATAATTT
1 AAAAATCAAATTTATAAAGTAAATATCGAATTCATTACAGAATCAAATATACGAATAAATAATTT
5987760 TAAATATTATATTTATATGTTTTATTACTCAATGTATATTATTTTTGAAATTTAATTCAATGAAA
66 TAAATATTATATTTATATGTTTTATTACTCAATGTATATTATTTTTGAAATTTAATTCAATGAAA
5987825 CAAAGTTAATCGGT
131 CAAAGTTAATCGGT
5987839 AAAAATCAAATTTATAAAGTAAATATCGAATTCATTACAGAATC-AATATACGAAT-AATAATTT
1 AAAAATCAAATTTATAAAGTAAATATCGAATTCATTACAGAATCAAATATACGAATAAATAATTT
5987902 TAAATATTATATTTATATGTTTTATTACTCAATGTATATTATTTTTGAAATTTAATTCAATGAAA
66 TAAATATTATATTTATATGTTTTATTACTCAATGTATATTATTTTTGAAATTTAATTCAATGAAA
5987967 CAAAGTTAATCGGT
131 CAAAGTTAATCGGT
5987981 AA
1 AA
5987983 GATTTTTTTT
Statistics
Matches: 144, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
142 89 0.62
143 11 0.08
144 44 0.31
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (144 bp):
AAAAATCAAATTTATAAAGTAAATATCGAATTCATTACAGAATCAAATATACGAATAAATAATTT
TAAATATTATATTTATATGTTTTATTACTCAATGTATATTATTTTTGAAATTTAATTCAATGAAA
CAAAGTTAATCGGT
Found at i:5988307 original size:16 final size:17
Alignment explanation
Indices: 5988286--5988320 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5988276 CTAAGATCGT
5988286 TTTCTC-ATTCCTTATA
1 TTTCTCTATTCCTTATA
*
5988302 TTTCTCTTTTCCTTATA
1 TTTCTCTATTCCTTATA
5988319 TT
1 TT
5988321 ACATACTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTCTCTATTCCTTATA
Found at i:5992677 original size:8 final size:8
Alignment explanation
Indices: 5992664--5992701 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
5992654 AGACGAGAAC
5992664 CAAGGAAA
1 CAAGGAAA
5992672 CAAGGAAA
1 CAAGGAAA
5992680 CAAGGAAA
1 CAAGGAAA
*
5992688 CAAGGAAG
1 CAAGGAAA
5992696 CAAGGA
1 CAAGGA
5992702 TTGTGAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.58, C:0.13, G:0.29, T:0.00
Consensus pattern (8 bp):
CAAGGAAA
Found at i:6009441 original size:29 final size:29
Alignment explanation
Indices: 6009408--6009467 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
6009398 ATTCATTTAC
*
6009408 ATCAAAGAAAGGCATCATTGGCGCAAATG
1 ATCAAAGAAAGGCATCATTGGCGAAAATG
* * *
6009437 ATCAAAGTAAGGCATCGTTGGTGAAAATG
1 ATCAAAGAAAGGCATCATTGGCGAAAATG
6009466 AT
1 AT
6009468 ATGAATGCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (29 bp):
ATCAAAGAAAGGCATCATTGGCGAAAATG
Found at i:6009690 original size:27 final size:27
Alignment explanation
Indices: 6009660--6009716 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
6009650 TTTAGTTAGA
* * * *
6009660 TTTATTGTTTCAAATTATTTATGATGT
1 TTTAATGTTTCAAAGTAATTATGATAT
*
6009687 TTTAATGTTTTAAAGTAATTATGATAT
1 TTTAATGTTTCAAAGTAATTATGATAT
6009714 TTT
1 TTT
6009717 GTGCTTTATC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.58
Consensus pattern (27 bp):
TTTAATGTTTCAAAGTAATTATGATAT
Found at i:6013448 original size:19 final size:20
Alignment explanation
Indices: 6013418--6013468 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
6013408 CGTCCAAGAG
* *
6013418 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
*
6013437 CGTGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
6013457 CATGTATTTTCA
1 CATGTATTTTCA
6013469 AAGGGGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:6017153 original size:2 final size:2
Alignment explanation
Indices: 6017146--6017199 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
6017136 TAAAAACATA
6017146 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
6017188 AT AT AT AT AT AT
1 AT AT AT AT AT AT
6017200 TATTCATTCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6019769 original size:15 final size:16
Alignment explanation
Indices: 6019743--6019773 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
6019733 AGTTACCGTT
6019743 TTCCATTGAAAATATC
1 TTCCATTGAAAATATC
6019759 TTCCA-TGAAAATATC
1 TTCCATTGAAAATATC
6019774 CCATAGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (16 bp):
TTCCATTGAAAATATC
Found at i:6020795 original size:45 final size:44
Alignment explanation
Indices: 6020742--6020898 Score: 226
Period size: 45 Copynumber: 3.5 Consensus size: 44
6020732 CCATTTATTA
* *
6020742 ACCATAAGCTCGTAATCTTATTTTACCAAAATACTTACCATTTGT
1 ACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTT-T
6020787 ACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAT
1 ACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTT-T
* * *
6020832 CCCATAAGCTCGTAAGCTTATTTTACCTATATACTTTCCATTATT
1 ACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATT-TT
*
6020877 -CCATAAGCTTGTAAGCTTATTT
1 ACCATAAGCTCGTAAGCTTATTT
6020899 GCATGCTTAC
Statistics
Matches: 104, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
44 21 0.20
45 82 0.79
46 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (44 bp):
ACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTT
Found at i:6020896 original size:44 final size:44
Alignment explanation
Indices: 6020721--6020898 Score: 225
Period size: 45 Copynumber: 4.0 Consensus size: 44
6020711 ATTTGCATCT
* *
6020721 CCAATAT-TTTACCATTTATTAACCATAAGCTCGTAATCTTATTTTA
1 CCAATATACTTACCA-TTATT--CCATAAGCTCGTAAGCTTATTTTA
*
6020767 CCAAAATACTTACCATT-TGTACCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTAT-T-CCATAAGCTCGTAAGCTTATTTTA
*
6020812 CCAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTA
* * *
6020857 CCTATATACTTTCCATTATTCCATAAGCTTGTAAGCTTATTT
1 CCAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTT
6020899 GCATGCTTAC
Statistics
Matches: 119, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
44 25 0.21
45 76 0.64
46 11 0.09
47 7 0.06
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (44 bp):
CCAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTA
Found at i:6021029 original size:40 final size:40
Alignment explanation
Indices: 6020980--6021063 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
6020970 ATAGGAGTCA
* * * *
6020980 AATATTGCACCGAAGTGCTGAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
* *
6021020 AATAATGCACCGTAGTGCTGAGGTCGGGATTTACCCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
6021060 AATA
1 AATA
6021064 CACCGTAGTG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAGGTCGAGATTTACCCACCT
Done.