Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007725.1 Hibiscus syriacus cultivar Beakdansim tig00109972_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: 3026330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 14
Found at i:2321169 original size:35 final size:35
Alignment explanation
Indices: 2321120--2321205 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
2321110 ATTGAAGTAT
** * *
2321120 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
2321155 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
2321190 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
2321206 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:2324527 original size:16 final size:16
Alignment explanation
Indices: 2324506--2324538 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2324496 TAATAAATAA
2324506 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2324522 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2324538 A
1 A
2324539 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2324633 original size:16 final size:16
Alignment explanation
Indices: 2324608--2324672 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
2324598 TAATAAATAA
*
2324608 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
2324624 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
2324640 ACGAACACAAATGAAC
1 ACGAACATAAACGAAC
2324656 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2324672 A
1 A
2324673 TAAACGTTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2324637 original size:10 final size:10
Alignment explanation
Indices: 2324604--2324678 Score: 54
Period size: 10 Copynumber: 7.7 Consensus size: 10
2324594 CATTTAATAA
*
2324604 ATAAACGAAT
1 ATAAACGAAC
2324614 ATAAACGAAC
1 ATAAACGAAC
2324624 ----ACGAAC
1 ATAAACGAAC
2324630 ATAAACGAAC
1 ATAAACGAAC
*
2324640 ACGAACAC-AA-
1 A-TAA-ACGAAC
2324650 ATGAACACGAAC
1 AT-AA-ACGAAC
2324662 ATAAACGAAC
1 ATAAACGAAC
2324672 ATAAACG
1 ATAAACG
2324679 TTGGAGATCC
Statistics
Matches: 53, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
6 6 0.11
10 35 0.66
11 8 0.15
12 4 0.08
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:2325795 original size:14 final size:14
Alignment explanation
Indices: 2325776--2325804 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2325766 GAACATAAGA
2325776 GAACATAACCGAAC
1 GAACATAACCGAAC
2325790 GAACATAACCGAAC
1 GAACATAACCGAAC
2325804 G
1 G
2325805 TTCACGAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.28, G:0.17, T:0.07
Consensus pattern (14 bp):
GAACATAACCGAAC
Found at i:2329619 original size:20 final size:20
Alignment explanation
Indices: 2329585--2329631 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2329575 GTCTTTAAAC
2329585 TTTTAAATATTTTATATTTA
1 TTTTAAATATTTTATATTTA
*
2329605 TTATTAAAT-TTTTATTTTTA
1 TT-TTAAATATTTTATATTTA
2329625 TTTTAAA
1 TTTTAAA
2329632 CCGGTCCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 5 0.20
20 14 0.56
21 6 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTAAATATTTTATATTTA
Found at i:2333800 original size:20 final size:20
Alignment explanation
Indices: 2333766--2333812 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2333756 GTCTTTAAAC
2333766 TTTTAAATATTTTATATTTA
1 TTTTAAATATTTTATATTTA
*
2333786 TTATTAAAT-TTTTATTTTTA
1 TT-TTAAATATTTTATATTTA
2333806 TTTTAAA
1 TTTTAAA
2333813 CCGGTCCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 5 0.20
20 14 0.56
21 6 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTAAATATTTTATATTTA
Found at i:2343690 original size:19 final size:17
Alignment explanation
Indices: 2343656--2343693 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
2343646 AATTCAAATC
2343656 AATATAATAATATATTA
1 AATATAATAATATATTA
2343673 AATATCAATAATTATATTA
1 AATAT-AATAA-TATATTA
2343692 AA
1 AA
2343694 GATTAAAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
AATATAATAATATATTA
Found at i:2348471 original size:17 final size:17
Alignment explanation
Indices: 2348451--2348491 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
2348441 GTTTAGGGTT
2348451 TTTTTTATAAAAAAATA
1 TTTTTTATAAAAAAATA
2348468 TTTTTTATAAAAAAATA
1 TTTTTTATAAAAAAATA
*
2348485 ATTTTTA
1 TTTTTTA
2348492 ATTATAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTTTTATAAAAAAATA
Found at i:2354705 original size:17 final size:17
Alignment explanation
Indices: 2354685--2354722 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
2354675 GTAATATTAT
2354685 ACAAATATATAATAAGG
1 ACAAATATATAATAAGG
2354702 ACAAATATATAATAAGG
1 ACAAATATATAATAAGG
2354719 ACAA
1 ACAA
2354723 TTTGGTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.61, C:0.08, G:0.11, T:0.21
Consensus pattern (17 bp):
ACAAATATATAATAAGG
Found at i:2354873 original size:20 final size:20
Alignment explanation
Indices: 2354837--2354874 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2354827 TTCTTATTTC
**
2354837 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
2354857 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
2354875 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:2357311 original size:31 final size:31
Alignment explanation
Indices: 2357273--2357392 Score: 172
Period size: 31 Copynumber: 3.9 Consensus size: 31
2357263 GAAGGACCTA
*
2357273 TCCATATGTTCCGAAGAACATAGGTAATCTG
1 TCCATATGTCCCGAAGAACATAGGTAATCTG
*
2357304 TCCATATGTCCAGAAGAACATAGGTAAAT-TG
1 TCCATATGTCCCGAAGAACATAGGT-AATCTG
*
2357335 TCCATATGTCCCGAA-AGACATAGGTAAACTG
1 TCCATATGTCCCGAAGA-ACATAGGTAATCTG
*
2357366 TCCATATGTCCCGAAAAACATAGGTAA
1 TCCATATGTCCCGAAGAACATAGGTAA
2357393 CCCTTGACTC
Statistics
Matches: 81, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
30 3 0.04
31 74 0.91
32 4 0.05
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (31 bp):
TCCATATGTCCCGAAGAACATAGGTAATCTG
Found at i:2361284 original size:2 final size:2
Alignment explanation
Indices: 2361271--2361301 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
2361261 GTCTCTTCAC
2361271 AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
2361302 TAATTGCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2363092 original size:24 final size:24
Alignment explanation
Indices: 2363060--2363107 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
2363050 GAAATTTAGT
2363060 TGGAGTAAAACTCTCTCGAAATTC
1 TGGAGTAAAACTCTCTCGAAATTC
2363084 TGGAGTAAAACTCTCTCGAAATTC
1 TGGAGTAAAACTCTCTCGAAATTC
2363108 ATCTATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (24 bp):
TGGAGTAAAACTCTCTCGAAATTC
Found at i:2366566 original size:29 final size:28
Alignment explanation
Indices: 2366529--2366599 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
2366519 ATATCGATCA
* * * *
2366529 CCAAGCTTTTGAATGTTCTACCTTCATC
1 CCAAACTTTTAAATATTCTAACTTCATC
2366557 CCTAAACTTTTAAATATTCTAACTTCATC
1 CC-AAACTTTTAAATATTCTAACTTCATC
2366586 CCAAA-TTTTCAAAT
1 CCAAACTTTT-AAAT
2366600 GGTTTTGGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.11
28 9 0.24
29 24 0.65
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.39
Consensus pattern (28 bp):
CCAAACTTTTAAATATTCTAACTTCATC
Found at i:2368661 original size:15 final size:17
Alignment explanation
Indices: 2368630--2368661 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2368620 ATGTATTTTT
2368630 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
2368647 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
2368662 CAAAAAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:2369260 original size:15 final size:16
Alignment explanation
Indices: 2369240--2369282 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2369230 AATTTTAAAA
2369240 TAATAATATTAT-TTT
1 TAATAATATTATCTTT
*
2369255 TAATAAAATTATCTTT
1 TAATAATATTATCTTT
2369271 TAA-AATACTTAT
1 TAATAATA-TTAT
2369283 AATTTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATAATATTATCTTT
Found at i:2374101 original size:10 final size:10
Alignment explanation
Indices: 2374088--2374121 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
2374078 CGACCGAGGC
2374088 CATCCGAAAG
1 CATCCGAAAG
2374098 CATCCGAAAG
1 CATCCGAAAG
2374108 CATCC-AAGAG
1 CATCCGAA-AG
2374118 CATC
1 CATC
2374122 TGAGGCCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 2 0.09
10 21 0.91
ACGTcount: A:0.38, C:0.32, G:0.18, T:0.12
Consensus pattern (10 bp):
CATCCGAAAG
Found at i:2374177 original size:33 final size:33
Alignment explanation
Indices: 2374117--2374191 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
2374107 GCATCCAAGA
* *
2374117 GCATCTGAGGCCATCCGAACGAGCTATGCGAGG
1 GCATCCGAGGCCAACCGAACGAGCTATGCGAGG
* * * *
2374150 GCATCCGAGGGCAACCGAGCGATCTATGGGAGG
1 GCATCCGAGGCCAACCGAACGAGCTATGCGAGG
2374183 GCATCCGAG
1 GCATCCGAG
2374192 CGAGGGTAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.24, C:0.27, G:0.36, T:0.13
Consensus pattern (33 bp):
GCATCCGAGGCCAACCGAACGAGCTATGCGAGG
Found at i:2374269 original size:33 final size:33
Alignment explanation
Indices: 2374228--2374312 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
2374218 GCGACCTACC
*
2374228 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
*
2374261 CTCGCTCGGTTGTCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
* * *
2374294 CTCGTTCGGATGGCCTCGG
1 CTCGCTCGGTTGCCCTCGG
2374313 TCGGATGGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.08, C:0.36, G:0.28, T:0.27
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:2374287 original size:10 final size:10
Alignment explanation
Indices: 2374232--2374386 Score: 58
Period size: 10 Copynumber: 14.1 Consensus size: 10
2374222 CCTACCCTCG
*
2374232 CTCGGTTGCC
1 CTCGGATGCC
*
2374242 CTCGGATTCC
1 CTCGGATGCC
*
2374252 CTCGCATAGCTC
1 CTCGGAT-GC-C
* *
2374264 GCTCGGTTGTC
1 -CTCGGATGCC
2374275 CTCGGATGCC
1 CTCGGATGCC
*
2374285 CTCGCATAGCTC
1 CTCGGAT-GC-C
*
2374297 GTTCGGATGGCC
1 -CTCGGAT-GCC
*
2374309 TCGGTCGGATGGC
1 -C--TCGGATGCC
*
2374322 CTCGGATGCT
1 CTCGGATGCC
* *
2374332 CTCAGATGGC
1 CTCGGATGCC
*
2374342 CTCGGATGCT
1 CTCGGATGCC
*
2374352 TTCGGATGGCC
1 CTCGGAT-GCC
*
2374363 TCAGTCGGATGGC
1 -C--TCGGATGCC
2374376 CTCGGATGCC
1 CTCGGATGCC
2374386 C
1 C
2374387 AGCGTGTTGG
Statistics
Matches: 104, Mismatches: 29, Indels: 24
0.66 0.18 0.15
Matches are distributed among these distances:
10 64 0.62
11 6 0.06
12 6 0.06
13 16 0.15
14 12 0.12
ACGTcount: A:0.10, C:0.33, G:0.31, T:0.26
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:2374316 original size:14 final size:14
Alignment explanation
Indices: 2374294--2374326 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2374284 CCTCGCATAG
*
2374294 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
2374308 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
2374322 CTCGG
1 CTCGG
2374327 ATGCTCTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:2374341 original size:20 final size:20
Alignment explanation
Indices: 2374316--2374364 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
2374306 GCCTCGGTCG
2374316 GATGGCCTCGGATGCTCTCA
1 GATGGCCTCGGATGCTCTCA
* *
2374336 GATGGCCTCGGATGCTTTCG
1 GATGGCCTCGGATGCTCTCA
2374356 GATGGCCTC
1 GATGGCCTC
2374365 AGTCGGATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.12, C:0.29, G:0.33, T:0.27
Consensus pattern (20 bp):
GATGGCCTCGGATGCTCTCA
Found at i:2375277 original size:21 final size:21
Alignment explanation
Indices: 2375240--2375292 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
2375230 ATAATTATTT
* *
2375240 AAAAAATTAAATAAAAATACC
1 AAAAAATTTAATAAAAAAACC
* *
2375261 AAAAACATTTAATAAAAAATCA
1 AAAAA-ATTTAATAAAAAAACC
2375283 AAAAAATTTA
1 AAAAAATTTA
2375293 GGTTGAACCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAATTTAATAAAAAAACC
Found at i:2389488 original size:24 final size:23
Alignment explanation
Indices: 2389456--2389500 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2389446 TCAATTGTCA
* *
2389456 CATTATGGGTGGCAATTTGGTGG
1 CATTATGGGGGGCAAATTGGTGG
2389479 CATTAATGGGGGGCAAATTGGT
1 CATT-ATGGGGGGCAAATTGGT
2389501 CAAATTTGGC
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:0.22, C:0.09, G:0.38, T:0.31
Consensus pattern (23 bp):
CATTATGGGGGGCAAATTGGTGG
Found at i:2395139 original size:30 final size:30
Alignment explanation
Indices: 2395103--2395162 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
2395093 AGATTTTTTG
*
2395103 CATACATAGAGACTCGAACCCGAAACCTTA
1 CATACATAAAGACTCGAACCCGAAACCTTA
* *
2395133 CATACATAAATACTCGAATCCGAAACCTTA
1 CATACATAAAGACTCGAACCCGAAACCTTA
2395163 ATTGATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.20
Consensus pattern (30 bp):
CATACATAAAGACTCGAACCCGAAACCTTA
Found at i:2401092 original size:32 final size:31
Alignment explanation
Indices: 2401050--2401202 Score: 193
Period size: 32 Copynumber: 4.9 Consensus size: 31
2401040 AGTCGAGGGT
2401050 ATACCTATGTTCTACGGAACATATGGACAGA
1 ATACCTATGTTCTACGGAACATATGGACAGA
* * *
2401081 ATTACCTATGTTTTTC-GAGACATATGGACAGT
1 A-TACCTATGTTCTACGGA-ACATATGGACAGA
2401113 ATACCTATGTTCTACGGAACATATGGACAGA
1 ATACCTATGTTCTACGGAACATATGGACAGA
* * *
2401144 ATTACCTATGTTTTTC-GAGACATATGGACAGT
1 A-TACCTATGTTCTACGGA-ACATATGGACAGA
*
2401176 ATACCTATGTTCTAAGGAACATATGGA
1 ATACCTATGTTCTACGGAACATATGGA
2401203 TAGTTTACCT
Statistics
Matches: 104, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
31 50 0.48
32 54 0.52
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (31 bp):
ATACCTATGTTCTACGGAACATATGGACAGA
Found at i:2401121 original size:31 final size:31
Alignment explanation
Indices: 2401048--2401226 Score: 202
Period size: 31 Copynumber: 5.7 Consensus size: 31
2401038 AGAGTCGAGG
2401048 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * *
2401079 GAATTACCTATGTTTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTCTACGGA-ACATATGGACA
2401111 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * *
2401142 GAATTACCTATGTTTTTC-GAGACATATGGACA
1 GTA-TACCTATGTTCTACGGA-ACATATGGACA
* *
2401174 GTATACCTATGTTCTAAGGAACATATGGATA
1 GTATACCTATGTTCTACGGAACATATGGACA
* *
2401205 GTTTACCTAGGTTC-ATCGGAAC
1 GTATACCTATGTTCTA-CGGAAC
2401227 CTATATACAG
Statistics
Matches: 124, Mismatches: 17, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
30 1 0.01
31 69 0.56
32 54 0.44
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:2401126 original size:63 final size:63
Alignment explanation
Indices: 2401048--2401202 Score: 301
Period size: 63 Copynumber: 2.5 Consensus size: 63
2401038 AGAGTCGAGG
2401048 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTTTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTTTTTCGAGACATATGGACA
2401111 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTTTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTTTTTCGAGACATATGGACA
*
2401174 GTATACCTATGTTCTAAGGAACATATGGA
1 GTATACCTATGTTCTACGGAACATATGGA
2401203 TAGTTTACCT
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 91 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTTTTTCGAGACATATGGACA
Found at i:2406078 original size:80 final size:80
Alignment explanation
Indices: 2405979--2406142 Score: 328
Period size: 80 Copynumber: 2.0 Consensus size: 80
2405969 ACATACGGTC
2405979 AGAACATGTTCAGTTCACATACTAATGAAAAATACAAATCATGTCATTATTTAGTCATGTATGCA
1 AGAACATGTTCAGTTCACATACTAATGAAAAATACAAATCATGTCATTATTTAGTCATGTATGCA
2406044 CAATGAGTATAATGA
66 CAATGAGTATAATGA
2406059 AGAACATGTTCAGTTCACATACTAATGAAAAATACAAATCATGTCATTATTTAGTCATGTATGCA
1 AGAACATGTTCAGTTCACATACTAATGAAAAATACAAATCATGTCATTATTTAGTCATGTATGCA
2406124 CAATGAGTATAATGA
66 CAATGAGTATAATGA
2406139 AGAA
1 AGAA
2406143 ATGCACATGA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 84 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.30
Consensus pattern (80 bp):
AGAACATGTTCAGTTCACATACTAATGAAAAATACAAATCATGTCATTATTTAGTCATGTATGCA
CAATGAGTATAATGA
Found at i:2409822 original size:22 final size:23
Alignment explanation
Indices: 2409773--2409824 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
2409763 GTTGATTTTT
*
2409773 AAAAA-AATATATATATATATTT
1 AAAAATAATATATATATATATTA
* *
2409795 AAAAATAATATTTTTAT-TATTA
1 AAAAATAATATATATATATATTA
2409817 AAAAATAA
1 AAAAATAA
2409825 AAAAAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAAATAATATATATATATATTA
Found at i:2430850 original size:14 final size:14
Alignment explanation
Indices: 2430831--2430866 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
2430821 TAAATGTTAG
2430831 GAGCTGATACCGAA
1 GAGCTGATACCGAA
2430845 GAGCTGATACCGAA
1 GAGCTGATACCGAA
2430859 GAGCTGAT
1 GAGCTGAT
2430867 TGGGTTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.31, T:0.17
Consensus pattern (14 bp):
GAGCTGATACCGAA
Found at i:2439404 original size:13 final size:13
Alignment explanation
Indices: 2439386--2439412 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2439376 AGTTAGGAGA
2439386 TAATTAGGTTAGT
1 TAATTAGGTTAGT
2439399 TAATTAGGTTAGT
1 TAATTAGGTTAGT
2439412 T
1 T
2439413 CTATCATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TAATTAGGTTAGT
Found at i:2441304 original size:31 final size:33
Alignment explanation
Indices: 2441268--2441341 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
2441258 TCGTTAGGAG
* * * *
2441268 TATTTTATCATAGTTTGAT-AA-ATTTTATTAT
1 TATTTTATAATAATTTAATAAAGATTTAATTAT
2441299 TATTTTATAATAATTTAATAAAGATTTAATTAT
1 TATTTTATAATAATTTAATAAAGATTTAATTAT
*
2441332 CATTTTATAA
1 TATTTTATAA
2441342 ATATTAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
31 16 0.44
32 2 0.06
33 18 0.50
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (33 bp):
TATTTTATAATAATTTAATAAAGATTTAATTAT
Found at i:2442262 original size:56 final size:55
Alignment explanation
Indices: 2442177--2442287 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 55
2442167 TTTACGATTC
2442177 TTTAAATTGATATGTTTATCTATCCAAACGACACTTACTCATGTTGCTTAATACA
1 TTTAAATTGATATGTTTATCTATCCAAACGACACTTACTCATGTTGCTTAATACA
2442232 TTTAAATTTGATATGTTTATCTATCCAAACGACACTTACTCATGTTGCTTAATACA
1 TTTAAA-TTGATATGTTTATCTATCCAAACGACACTTACTCATGTTGCTTAATACA
2442288 AATTACATCT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 6 0.11
56 49 0.89
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (55 bp):
TTTAAATTGATATGTTTATCTATCCAAACGACACTTACTCATGTTGCTTAATACA
Found at i:2442959 original size:15 final size:16
Alignment explanation
Indices: 2442929--2442963 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2442919 TAAAATACAA
2442929 ATAAAAATATCATTAT
1 ATAAAAATATCATTAT
*
2442945 ATAAAAATAT-TTTAT
1 ATAAAAATATCATTAT
2442960 ATAA
1 ATAA
2442964 CTCACTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAAAAATATCATTAT
Found at i:2443104 original size:33 final size:34
Alignment explanation
Indices: 2443036--2443106 Score: 117
Period size: 36 Copynumber: 2.1 Consensus size: 34
2443026 TTCAAATAAT
2443036 AAATTATTTTTTAAGGATGATAGTATTATATTATTA
1 AAATTATTTTTTAAGGATGATAG--TTATATTATTA
2443072 AAATTATTTTTTAAGGATGATAG-TATATTATTA
1 AAATTATTTTTTAAGGATGATAGTTATATTATTA
2443105 AA
1 AA
2443107 TAAATGTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
33 12 0.34
36 23 0.66
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (34 bp):
AAATTATTTTTTAAGGATGATAGTTATATTATTA
Found at i:2444053 original size:40 final size:42
Alignment explanation
Indices: 2443973--2444063 Score: 159
Period size: 40 Copynumber: 2.2 Consensus size: 42
2443963 CTGAAGTAAC
2443973 TTATCGTGAACGAATTGAAAATGTAAAAACCCTACTCGTCTT
1 TTATCGTGAACGAATTGAAAATGTAAAAACCCTACTCGTCTT
2444015 TTATCGTGAACGAATTG-AAATGT-AAAACCCTACTCGTCTT
1 TTATCGTGAACGAATTGAAAATGTAAAAACCCTACTCGTCTT
*
2444055 TTATGGTGA
1 TTATCGTGA
2444064 TTCCAAGCTC
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 25 0.52
41 6 0.12
42 17 0.35
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (42 bp):
TTATCGTGAACGAATTGAAAATGTAAAAACCCTACTCGTCTT
Found at i:2444893 original size:30 final size:30
Alignment explanation
Indices: 2444852--2444920 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
2444842 TGCCTCCGAT
2444852 TATATAT-ATATA-ATA-TTTTATTAATTA
1 TATATATAATATATATATTTTTATTAATTA
2444879 TATATATAATATATATATTTTTATTAATTA
1 TATATATAATATATATATTTTTATTAATTA
*
2444909 TATATAAAATAT
1 TATATATAATAT
2444921 TTTCGGGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
27 7 0.18
28 5 0.13
29 3 0.08
30 23 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
TATATATAATATATATATTTTTATTAATTA
Found at i:2444913 original size:23 final size:26
Alignment explanation
Indices: 2444850--2444923 Score: 77
Period size: 25 Copynumber: 2.9 Consensus size: 26
2444840 AATGCCTCCG
2444850 ATTATATATATATA-ATAT-TTTATTA
1 ATTATATATATATATATATATTT-TTA
2444875 ATTATATATATAATATATATATTTTT-
1 ATTATATATAT-ATATATATATTTTTA
*
2444901 ATTA-AT-TATATATAAAATATTTT
1 ATTATATATATATAT-ATATATTTT
2444924 CGGGTTTGGG
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
23 4 0.09
24 11 0.25
25 13 0.30
26 7 0.16
27 6 0.14
28 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTATATATATATATATATATTTTTA
Found at i:2449878 original size:20 final size:20
Alignment explanation
Indices: 2449853--2449910 Score: 100
Period size: 20 Copynumber: 2.9 Consensus size: 20
2449843 GTTTGGTTCA
2449853 GAGAATGTAAGATTACCAAT
1 GAGAATGTAAGATTACCAAT
2449873 GAGAATGTAAGATTACCAAT
1 GAGAATGTAAGATTACCAAT
2449893 G-GAAATGTAAGATTACCA
1 GAG-AATGTAAGATTACCA
2449911 GAGAATAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 1 0.03
20 36 0.97
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.24
Consensus pattern (20 bp):
GAGAATGTAAGATTACCAAT
Found at i:2450140 original size:36 final size:37
Alignment explanation
Indices: 2450068--2450141 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
2450058 GTTGGAAAAT
* *
2450068 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
2450105 ATTTATA-ATTTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATATA-TTTTCTTTAAAAAATTGAAAATCATAAA
2450141 A
1 A
2450142 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 7 0.22
37 25 0.78
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:2450913 original size:14 final size:14
Alignment explanation
Indices: 2450896--2450945 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2450886 TAAACGAACA
*
2450896 TAAACGAACGGATG
1 TAAACGAACGAATG
*
2450910 TAAACGAAC-ACA-A
1 TAAACGAACGA-ATG
*
2450923 TAAACGAAAGAATG
1 TAAACGAACGAATG
2450937 TAAACGAAC
1 TAAACGAAC
2450946 ACAAATGAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
13 9 0.32
14 19 0.68
ACGTcount: A:0.54, C:0.16, G:0.18, T:0.12
Consensus pattern (14 bp):
TAAACGAACGAATG
Found at i:2450937 original size:27 final size:28
Alignment explanation
Indices: 2450895--2450958 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 28
2450885 ATAAACGAAC
* *
2450895 ATAAACGAACGGATGTAAACGAACAC-A
1 ATAAACGAAAGAATGTAAACGAACACAA
2450922 ATAAACGAAAGAATGTAAACGAACACAA
1 ATAAACGAAAGAATGTAAACGAACACAA
*
2450950 ATGAACGAA
1 ATAAACGAA
2450959 CATAAACCAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 24 0.73
28 9 0.27
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.11
Consensus pattern (28 bp):
ATAAACGAAAGAATGTAAACGAACACAA
Found at i:2451202 original size:20 final size:20
Alignment explanation
Indices: 2451177--2451416 Score: 161
Period size: 20 Copynumber: 11.8 Consensus size: 20
2451167 AAAAACCAAC
2451177 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
* **
2451197 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTTAG
**
2451217 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
**
2451237 AAAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TTAG
* ***
2451258 AAGAATCGCAATGCGAGGCA-
1 AA-AATCGCAACGCGATTTAG
* *
2451278 AAGAATCGCAATGCGATCTTCG
1 AA-AATCGCAACGCGAT-TTAG
*
2451300 AAGAATCGCAACGCGATTGAG
1 AA-AATCGCAACGCGATTTAG
2451321 AAAATCGCAACGCGATTTCA-
1 AAAATCGCAACGCGATTT-AG
* *
2451341 ATAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
2451361 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-TAG
* *
2451381 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
2451401 -AAATCGCAATGCGATT
1 AAAATCGCAACGCGATT
2451417 CCAAGAATCG
Statistics
Matches: 178, Mismatches: 29, Indels: 27
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.01
19 16 0.09
20 121 0.68
21 11 0.06
22 29 0.16
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:2451285 original size:42 final size:41
Alignment explanation
Indices: 2451235--2451429 Score: 258
Period size: 40 Copynumber: 4.8 Consensus size: 41
2451225 AACGGTCAAA
* *
2451235 AGAAAATCGCAACGCGATCTTCCAAGAATCGCAATGCGA-GG
1 AGAAAATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTG
* *
2451276 CA-AAGAATCGCAATGCGATCTTCGAAGAATCGCAACGCGATTG
1 -AGAA-AATCGCAACGCGAT-TTCCAAGAATCGCAACGCGATTG
*
2451319 AGAAAATCGCAACGCGATTT-CAATAATCGCAACGCGATTG
1 AGAAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTG
2451359 AGAAAATCGCAACGCGA-TTCCAAGAATCGCAACGCGATTG
1 AGAAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTG
*
2451399 AG-AAATCGCAATGCGA-TTCCAAGAATCGCAA
1 AGAAAATCGCAACGCGATTTCCAAGAATCGCAA
2451430 AACGGCAAAA
Statistics
Matches: 140, Mismatches: 9, Indels: 11
0.88 0.06 0.07
Matches are distributed among these distances:
39 30 0.21
40 56 0.40
41 4 0.03
42 47 0.34
43 3 0.02
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (41 bp):
AGAAAATCGCAACGCGATTTCCAAGAATCGCAACGCGATTG
Found at i:2451427 original size:20 final size:20
Alignment explanation
Indices: 2451239--2451429 Score: 165
Period size: 20 Copynumber: 9.4 Consensus size: 20
2451229 GTCAAAAGAA
2451239 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
* ** *
2451261 AATCGCAATGCGAGGCAAAG
1 AATCGCAACGCGATTCCAAG
* *
2451281 AATCGCAATGCGATCTTCGAAG
1 AATCGCAACGCGA--TTCCAAG
* *
2451303 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
* *
2451323 AATCGCAACGCGATTTCAAT
1 AATCGCAACGCGATTCCAAG
* *
2451343 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
2451363 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
*
2451383 AATCGCAACGCGATT--GAG
1 AATCGCAACGCGATTCCAAG
*
2451401 AAATCGCAATGCGATTCCAAG
1 -AATCGCAACGCGATTCCAAG
2451422 AATCGCAA
1 AATCGCAA
2451430 AACGGCAAAA
Statistics
Matches: 142, Mismatches: 18, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
18 2 0.01
19 17 0.12
20 91 0.64
21 4 0.03
22 28 0.20
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGATTCCAAG
Found at i:2451548 original size:6 final size:6
Alignment explanation
Indices: 2451537--2451658 Score: 209
Period size: 6 Copynumber: 21.2 Consensus size: 6
2451527 GACACGTATT
2451537 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A-CAC-
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2451583 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2451631 -CCAC- -CCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
2451659 GAAGGCGGCG
Statistics
Matches: 112, Mismatches: 0, Indels: 8
0.93 0.00 0.07
Matches are distributed among these distances:
4 5 0.04
5 10 0.09
6 97 0.87
ACGTcount: A:0.34, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2452400 original size:6 final size:6
Alignment explanation
Indices: 2452391--2452427 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
2452381 CGCCGCCGTC
2452391 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
2452428 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:2452487 original size:20 final size:20
Alignment explanation
Indices: 2452462--2452541 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
2452452 GCGGATACTA
2452462 TCTTTTTAGCATTGCGATTT
1 TCTTTTTAGCATTGCGATTT
* *
2452482 TCTTTTCAACATTGCGATTT
1 TCTTTTTAGCATTGCGATTT
*** * *
2452502 TCTAAATCGCGTTGCGATTT
1 TCTTTTTAGCATTGCGATTT
* *
2452522 T-TGTTTCGCATTGCGATTT
1 TCTTTTTAGCATTGCGATTT
2452541 T
1 T
2452542 GTTGGTCATT
Statistics
Matches: 47, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 15 0.32
20 32 0.68
ACGTcount: A:0.16, C:0.17, G:0.16, T:0.50
Consensus pattern (20 bp):
TCTTTTTAGCATTGCGATTT
Found at i:2452693 original size:14 final size:14
Alignment explanation
Indices: 2452674--2452730 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
2452664 ATATTGGGTA
2452674 AACATAAATGAACG
1 AACATAAATGAACG
2452688 AAC----AT-AACG
1 AACATAAATGAACG
* * *
2452697 AACAGAAGTAAACG
1 AACATAAATGAACG
2452711 AACATAAATGAACG
1 AACATAAATGAACG
2452725 AACATA
1 AACATA
2452731 TTATCGAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
9 7 0.21
10 2 0.06
13 1 0.03
14 24 0.71
ACGTcount: A:0.58, C:0.16, G:0.14, T:0.12
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:2454461 original size:23 final size:23
Alignment explanation
Indices: 2454417--2454461 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2454407 GACGACCATT
*
2454417 GAAGGGGGAAAGTTGGGAAGGGA
1 GAAGGGGGAAAGTCGGGAAGGGA
*
2454440 GAAGGAGGGAAA-TCGGGTAGGG
1 GAAGG-GGGAAAGTCGGGAAGGG
2454462 GCGCAGCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.33, C:0.02, G:0.56, T:0.09
Consensus pattern (23 bp):
GAAGGGGGAAAGTCGGGAAGGGA
Found at i:2455403 original size:190 final size:190
Alignment explanation
Indices: 2455080--2455459 Score: 719
Period size: 190 Copynumber: 2.0 Consensus size: 190
2455070 GGTAAAAAAT
2455080 TACCAGAAACATTATTATTTCTTCCGGTTTGTTATTATTGGGCGCTTTATAGGGTTTGTAAAACG
1 TACCAGAAACATTATTATTTCTTCCGGTTTGTTATTATTGGGCGCTTTATAGGGTTTGTAAAACG
2455145 CTACCTAAAACATTATTTTTTCTACCGATTTTGTTATTATTGGGCATTTTACCGAAATGTTTAAA
66 CTACCTAAAACATTATTTTTTCTACCGATTTTGTTATTATTGGGCATTTTACCGAAATGTTTAAA
2455210 ACATTAATGTTTAGGTA-TTTTTACCGGAAATATTAAAAAAATAATAACAAAACCGATAAC
131 ACATTAATGTTTAGGTATTTTTTACCGGAAATATTAAAAAAATAATAAC-AAACCGATAAC
*
2455270 TACCAGAAACATTATTATTTCTTCCGGTTTGTTATTATTGGGCGCTTTATCGGGTTTGTAAAACG
1 TACCAGAAACATTATTATTTCTTCCGGTTTGTTATTATTGGGCGCTTTATAGGGTTTGTAAAACG
2455335 -TACCTAAAACATTATTTTTTCTACCGATTTTGTTATTATTGGGCATTTTACCGTAAATGTTTAA
66 CTACCTAAAACATTATTTTTTCTACCGATTTTGTTATTATTGGGCATTTTACCG-AAATGTTTAA
2455399 AACATTAATGTTTAGGTATTTTTTACCGGAAATATTAAAAAAATAATAACAAACCGATAAC
130 AACATTAATGTTTAGGTATTTTTTACCGGAAATATTAAAAAAATAATAACAAACCGATAAC
2455460 ACATTTCCTT
Statistics
Matches: 187, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
189 53 0.28
190 103 0.55
191 31 0.17
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (190 bp):
TACCAGAAACATTATTATTTCTTCCGGTTTGTTATTATTGGGCGCTTTATAGGGTTTGTAAAACG
CTACCTAAAACATTATTTTTTCTACCGATTTTGTTATTATTGGGCATTTTACCGAAATGTTTAAA
ACATTAATGTTTAGGTATTTTTTACCGGAAATATTAAAAAAATAATAACAAACCGATAAC
Found at i:2456543 original size:17 final size:18
Alignment explanation
Indices: 2456516--2456550 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
2456506 CCTTTCTCCT
2456516 CTAACTGTGTTCATAGAA
1 CTAACTGTGTTCATAGAA
2456534 CTAA-TGTGTTCATAGAA
1 CTAACTGTGTTCATAGAA
2456551 AAAGCTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
CTAACTGTGTTCATAGAA
Found at i:2457812 original size:29 final size:30
Alignment explanation
Indices: 2457765--2457836 Score: 110
Period size: 29 Copynumber: 2.4 Consensus size: 30
2457755 AAAATATATT
* *
2457765 TTTATCTCTTTAAATTTTTATAAGTTTAAA
1 TTTATCTCTTTAAAATTTTATAAATTTAAA
2457795 TTTAT-TCTTTAAAATTTTATAAATTTAAA
1 TTTATCTCTTTAAAATTTTATAAATTTAAA
*
2457824 TTTATCCCTTTAA
1 TTTATCTCTTTAA
2457837 TATAAAATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 27 0.71
30 11 0.29
ACGTcount: A:0.35, C:0.08, G:0.01, T:0.56
Consensus pattern (30 bp):
TTTATCTCTTTAAAATTTTATAAATTTAAA
Found at i:2459052 original size:2 final size:2
Alignment explanation
Indices: 2459045--2459076 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2459035 AATAGACCAC
2459045 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
2459077 GAGTTATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2459199 original size:22 final size:22
Alignment explanation
Indices: 2459155--2459197 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
2459145 TTAAAATATA
2459155 TAACTCATAAATAAATATTTTT
1 TAACTCATAAATAAATATTTTT
*
2459177 TAACTCA-CAAT-AATATTTTT
1 TAACTCATAAATAAATATTTTT
2459197 T
1 T
2459198 TTCTTTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 3 0.15
22 7 0.35
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.47
Consensus pattern (22 bp):
TAACTCATAAATAAATATTTTT
Found at i:2459353 original size:7 final size:7
Alignment explanation
Indices: 2459333--2459370 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
2459323 TGGTATTATG
2459333 TTTAGGA
1 TTTAGGA
2459340 TTTTAGGA
1 -TTTAGGA
*
2459348 TTTAGGG
1 TTTAGGA
2459355 TTTAGGA
1 TTTAGGA
2459362 TTTAGGA
1 TTTAGGA
2459369 TT
1 TT
2459371 AAAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
7 21 0.75
8 7 0.25
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (7 bp):
TTTAGGA
Found at i:2463336 original size:15 final size:15
Alignment explanation
Indices: 2463316--2463344 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2463306 CTGAATATAA
2463316 TGGATAATTTTAAAT
1 TGGATAATTTTAAAT
2463331 TGGATAATTTTAAA
1 TGGATAATTTTAAA
2463345 AATTAAAAGA
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:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (15 bp):
TGGATAATTTTAAAT
Found at i:2485887 original size:31 final size:32
Alignment explanation
Indices: 2485826--2485897 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 32
2485816 CAAAACCGTG
* *
2485826 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCCAAGAACACATCTCAGGGCCGCA
* *
2485858 GGGCCTACCCGAGAATA-ATCTCAGGGCCGCA
1 GGGCCTACCCAAGAACACATCTCAGGGCCGCA
*
2485889 GAGCCTACC
1 GGGCCTACC
2485898 TAGAGTCACA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 21 0.60
32 14 0.40
ACGTcount: A:0.26, C:0.33, G:0.26, T:0.14
Consensus pattern (32 bp):
GGGCCTACCCAAGAACACATCTCAGGGCCGCA
Found at i:2486726 original size:9 final size:9
Alignment explanation
Indices: 2486714--2486784 Score: 61
Period size: 9 Copynumber: 7.4 Consensus size: 9
2486704 ACGGTCGGGT
*
2486714 CGGTCAGAC
1 CGGTCAAAC
2486723 CGGTCAAAC
1 CGGTCAAAC
* *
2486732 CGATTCAGAC
1 CG-GTCAAAC
2486742 CGGTCAAAC
1 CGGTCAAAC
*
2486751 CGGTTCGAAC
1 CGG-TCAAAC
*
2486761 CGGTTGAAAAC
1 CGG-T-CAAAC
2486772 CGGTCAAAC
1 CGGTCAAAC
2486781 CGGT
1 CGGT
2486785 TTCCAGCAGC
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
9 26 0.52
10 18 0.36
11 6 0.12
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.15
Consensus pattern (9 bp):
CGGTCAAAC
Found at i:2486783 original size:20 final size:21
Alignment explanation
Indices: 2486747--2486785 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2486737 CAGACCGGTC
*
2486747 AAACCGGTTCGAACCGGTTGA
1 AAACCGGTTCAAACCGGTTGA
2486768 AAACCGG-TCAAACCGGTT
1 AAACCGGTTCAAACCGGTT
2486786 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTTCAAACCGGTTGA
Found at i:2492947 original size:32 final size:31
Alignment explanation
Indices: 2492909--2492993 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
2492899 ATAGATTTCG
* *
2492909 GGGCCGTGGGGCCTACCTAAGAACACATCTTA
1 GGGCCGTAGGGCCTACCTAAGAACA-ATCTCA
** *
2492941 GGGCCGTAGGGCCTACCCGAGAATAATCTCA
1 GGGCCGTAGGGCCTACCTAAGAACAATCTCA
* *
2492972 GGGCCGCAGAGCCTACCTAAGA
1 GGGCCGTAGGGCCTACCTAAGA
2492994 GTCACATTAG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 23 0.52
32 21 0.48
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.15
Consensus pattern (31 bp):
GGGCCGTAGGGCCTACCTAAGAACAATCTCA
Found at i:2492976 original size:63 final size:63
Alignment explanation
Indices: 2492870--2492993 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
2492860 CCCTAAGGGA
* * ** *
2492870 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
2492933 ACATCTTAGGGCC-GTAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
2492994 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:2493877 original size:7 final size:7
Alignment explanation
Indices: 2493865--2493902 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
2493855 GTCAAAGAAA
2493865 GTCAACG
1 GTCAACG
2493872 GTCAACG
1 GTCAACG
*
2493879 GTCAACA
1 GTCAACG
2493886 GTCAACG
1 GTCAACG
2493893 GTCAACG
1 GTCAACG
2493900 GTC
1 GTC
2493903 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:2493909 original size:5 final size:5
Alignment explanation
Indices: 2493899--2493956 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
2493889 AACGGTCAAC
* * *
2493899 GGTCG GGTCG GGTCG GGCCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
2493948 GGTCG GGTC
1 GGTCG GGTC
2493957 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 36 0.84
7 7 0.16
ACGTcount: A:0.07, C:0.24, G:0.52, T:0.17
Consensus pattern (5 bp):
GGTCG
Found at i:2493923 original size:22 final size:22
Alignment explanation
Indices: 2493895--2493956 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
2493885 AGTCAACGGT
2493895 CAACGGTCGGGTCGGGTCGGGC
1 CAACGGTCGGGTCGGGTCGGGC
*
2493917 CAACGGTCGGGTCGGGTCGGGT
1 CAACGGTCGGGTCGGGTCGGGC
2493939 CAACGGTCGGGTCGGGTC
1 CAACGGTCGGGTCGGGTC
2493957 AGACCGGTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.10, C:0.26, G:0.48, T:0.16
Consensus pattern (22 bp):
CAACGGTCGGGTCGGGTCGGGC
Found at i:2493971 original size:9 final size:9
Alignment explanation
Indices: 2493953--2494022 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
2493943 GGTCGGGTCG
*
2493953 GGTCAGACC
1 GGTCAAACC
2493962 GGTCAAACC
1 GGTCAAACC
* *
2493971 GATTCAGACC
1 G-GTCAAACC
2493981 GGTCAAACC
1 GGTCAAACC
*
2493990 GGTTCGAACC
1 GG-TCAAACC
*
2494000 GGTTGAAAACC
1 GG-T-CAAACC
*
2494011 GGTCGAACC
1 GGTCAAACC
2494020 GGT
1 GGT
2494023 TTCCAGCAGC
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
9 24 0.50
10 18 0.38
11 6 0.12
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2494000 original size:19 final size:19
Alignment explanation
Indices: 2493959--2494022 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
2493949 GTCGGGTCAG
*
2493959 ACCGGTCAAACCGATTC-A
1 ACCGGTCAAACCGGTTCGA
2493977 GACCGGTCAAACCGGTTCGA
1 -ACCGGTCAAACCGGTTCGA
*
2493997 ACCGGTTGAAAACCGG-TCGA
1 ACCGG-T-CAAACCGGTTCGA
2494017 ACCGGT
1 ACCGGT
2494023 TTCCAGCAGC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
19 22 0.55
20 11 0.28
21 7 0.17
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:2494018 original size:20 final size:21
Alignment explanation
Indices: 2493985--2494023 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2493975 CAGACCGGTC
2493985 AAACCGGTTCGAACCGGTTGA
1 AAACCGGTTCGAACCGGTTGA
2494006 AAACCGG-TCGAACCGGTT
1 AAACCGGTTCGAACCGGTT
2494024 TCCAGCAGCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (21 bp):
AAACCGGTTCGAACCGGTTGA
Found at i:2495216 original size:19 final size:19
Alignment explanation
Indices: 2495192--2495229 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2495182 AACTCCTTTA
2495192 CAAAAAGGATAAAAAGAAG
1 CAAAAAGGATAAAAAGAAG
2495211 CAAAAAGGATAAAAAGAAG
1 CAAAAAGGATAAAAAGAAG
2495230 TAAACAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.68, C:0.05, G:0.21, T:0.05
Consensus pattern (19 bp):
CAAAAAGGATAAAAAGAAG
Found at i:2495602 original size:18 final size:18
Alignment explanation
Indices: 2495579--2495613 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2495569 TATACGAAAT
*
2495579 AGTATCGGTACCATTTTG
1 AGTATCGATACCATTTTG
2495597 AGTATCGATACCATTTT
1 AGTATCGATACCATTTT
2495614 TACATTCTGG
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:0.17, G:0.17, T:0.40
Consensus pattern (18 bp):
AGTATCGATACCATTTTG
Found at i:2496982 original size:41 final size:43
Alignment explanation
Indices: 2496880--2496984 Score: 115
Period size: 41 Copynumber: 2.5 Consensus size: 43
2496870 AAGTAATTTA
* * ** *
2496880 ATTTTTTATTTTTATAATCGAGGTCCTTAATTTTTATAATTAT
1 ATTTTTTATATTTATAATTGAGGTCCTTAATTTTTATAACCAC
* * * *
2496923 ACTTTTTATCTTTATAATTGAGGTTC-TAATTTTT-TAACCCC
1 ATTTTTTATATTTATAATTGAGGTCCTTAATTTTTATAACCAC
2496964 ATTTTTTATATTTATAATTGA
1 ATTTTTTATATTTATAATTGA
2496985 TAATCCTAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 22 0.42
42 8 0.15
43 22 0.42
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.56
Consensus pattern (43 bp):
ATTTTTTATATTTATAATTGAGGTCCTTAATTTTTATAACCAC
Found at i:2497010 original size:42 final size:41
Alignment explanation
Indices: 2496880--2497140 Score: 148
Period size: 42 Copynumber: 6.2 Consensus size: 41
2496870 AAGTAATTTA
* *
2496880 ATTTTTTATTTTTATAATCGAGGTCCTTAATTTTTATAATTAT
1 ATTTTTTATATTTATAATTGAGGTCC-TAATTTTT-TAATTAT
* * * ****
2496923 ACTTTTTATCTTTATAATTGAGGTTCTAATTTTTTAACCCC
1 ATTTTTTATATTTATAATTGAGGTCCTAATTTTTTAATTAT
** *
2496964 ATTTTTTATATTTATAATTGATAATCCTAATTTTTCAATTAT
1 ATTTTTTATATTTATAATTGA-GGTCCTAATTTTTTAATTAT
** * * * * *
2497006 ATTTTGCACATTTATAATTAAGTTCTTAAATTTTTTCATCT-T
1 ATTTTTTATATTTATAATTGAGGTCCT-AATTTTTTAAT-TAT
* * ** * * *
2497048 ACTTTCTACCTTTATAATTGAAGCCTCTAATTTTTTAAATTTT
1 ATTTTTTATATTTATAATTGAGGTC-CTAATTTTTT-AATTAT
** * * *
2497091 ATTTTTTAGCTTTACAATTGAGG-CCTTAATTTTTTCAGTAT
1 ATTTTTTATATTTATAATTGAGGTCC-TAATTTTTTAATTAT
2497132 CATTTTTTA
1 -ATTTTTTA
2497141 CTTATATAAT
Statistics
Matches: 165, Mismatches: 45, Indels: 17
0.73 0.20 0.07
Matches are distributed among these distances:
41 29 0.18
42 91 0.55
43 45 0.27
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.54
Consensus pattern (41 bp):
ATTTTTTATATTTATAATTGAGGTCCTAATTTTTTAATTAT
Found at i:2497083 original size:43 final size:42
Alignment explanation
Indices: 2497034--2497125 Score: 105
Period size: 43 Copynumber: 2.2 Consensus size: 42
2497024 TAAGTTCTTA
* *
2497034 AATTTTTT-CATCTTACTTTCTACCTTTATAATTGAAGCCTCT
1 AATTTTTTAAATCTTACTTTCTACCTTTACAATTGAAGCCT-T
* * * * *
2497076 AATTTTTTAAATTTTATTTTTTAGCTTTACAATTGAGGCCTT
1 AATTTTTTAAATCTTACTTTCTACCTTTACAATTGAAGCCTT
2497118 AATTTTTT
1 AATTTTTT
2497126 CAGTATCATT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 17 0.40
43 25 0.60
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (42 bp):
AATTTTTTAAATCTTACTTTCTACCTTTACAATTGAAGCCTT
Found at i:2499373 original size:64 final size:64
Alignment explanation
Indices: 2499290--2499417 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
2499280 AAATACTTTG
* *
2499290 AAACGGTACATTAAAACACTTTGATACTAATACCGGAACAAAAATTATATAACCATTCATATGA
1 AAACAGTACATTAAAACACTTTGATACTAATACCAGAACAAAAATTATATAACCATTCATATGA
*
2499354 AAACAGTACATTAACACACTTTGATACTAATACCAGAACAAAAATTATATAACCATTCATATGA
1 AAACAGTACATTAAAACACTTTGATACTAATACCAGAACAAAAATTATATAACCATTCATATGA
2499418 TATTTATCAC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.27
Consensus pattern (64 bp):
AAACAGTACATTAAAACACTTTGATACTAATACCAGAACAAAAATTATATAACCATTCATATGA
Found at i:2499521 original size:34 final size:34
Alignment explanation
Indices: 2499438--2499524 Score: 147
Period size: 34 Copynumber: 2.6 Consensus size: 34
2499428 ATATACGGAC
* *
2499438 GTAGAAATTTTTGTTAGGGGTGTAAATTTGAGAA
1 GTAGAAATTTTTGTTTGGGGTGTAAACTTGAGAA
*
2499472 GTAGAAAATTTTGTTTGGGGTGTAAACTTGAGAA
1 GTAGAAATTTTTGTTTGGGGTGTAAACTTGAGAA
2499506 GTAGAAATTTTTGTTTGGG
1 GTAGAAATTTTTGTTTGGG
2499525 TGGGAACTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.30, C:0.01, G:0.30, T:0.39
Consensus pattern (34 bp):
GTAGAAATTTTTGTTTGGGGTGTAAACTTGAGAA
Found at i:2507720 original size:3 final size:3
Alignment explanation
Indices: 2507712--2507763 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
2507702 TATATTTATT
*
2507712 TAA TAA TAA TAA T-A TATA TAG TAA T-A TAAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA T-AA TAA TAA TAA TAA TAA
2507756 TAA TAA TA
1 TAA TAA TA
2507764 GAATGAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
2 6 0.14
3 31 0.74
4 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:2507738 original size:12 final size:11
Alignment explanation
Indices: 2507714--2507760 Score: 67
Period size: 12 Copynumber: 4.1 Consensus size: 11
2507704 TATTTATTTA
2507714 ATAATAATAAT
1 ATAATAATAAT
*
2507725 ATATATAGTAAT
1 ATA-ATAATAAT
2507737 ATAAATAATAAT
1 AT-AATAATAAT
2507749 ATAATAATAAT
1 ATAATAATAAT
2507760 A
1 A
2507761 ATAGAATGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 13 0.41
12 18 0.56
13 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:2507942 original size:47 final size:47
Alignment explanation
Indices: 2507888--2507977 Score: 128
Period size: 47 Copynumber: 1.9 Consensus size: 47
2507878 GTAATGTTGA
*
2507888 AAACATCATACACT-AAAGGGCTTACAGATGACCCGAAGGCTTTTTGG
1 AAACATCATACACTGAAA-GACTTACAGATGACCCGAAGGCTTTTTGG
* * *
2507935 AAACATCATGCACTGCAAGACTTACAGATGACCCTAAGGCTTT
1 AAACATCATACACTGAAAGACTTACAGATGACCCGAAGGCTTT
2507978 GAAAACATCA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
47 36 0.95
48 2 0.05
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (47 bp):
AAACATCATACACTGAAAGACTTACAGATGACCCGAAGGCTTTTTGG
Found at i:2508045 original size:76 final size:76
Alignment explanation
Indices: 2507919--2508139 Score: 424
Period size: 76 Copynumber: 2.9 Consensus size: 76
2507909 TTACAGATGA
*
2507919 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAAGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
2507984 ATCAAAAAGCT
66 ATCAAAAAGCT
*
2507995 CCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
2508060 ATCAAAAAGCT
66 ATCAAAAAGCT
2508071 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
2508136 ATCA
66 ATCA
2508140 TGCACTGAAG
Statistics
Matches: 142, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 142 1.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:2508141 original size:45 final size:45
Alignment explanation
Indices: 2508071--2508184 Score: 174
Period size: 45 Copynumber: 2.5 Consensus size: 45
2508061 TCAAAAAGCT
* *
2508071 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGA
1 CCCGAAGGC--TTTGAAAACATCATGCACTGAAGGACTTACAGATGA
* *
2508118 CCCTAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
2508163 CCCGAAGGCTTTGAAAACATCA
1 CCCGAAGGCTTTGAAAACATCA
2508185 AAAAGCTCCC
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
45 54 0.87
47 8 0.13
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (45 bp):
CCCGAAGGCTTTGAAAACATCATGCACTGAAGGACTTACAGATGA
Found at i:2508159 original size:121 final size:121
Alignment explanation
Indices: 2508006--2508260 Score: 467
Period size: 121 Copynumber: 2.1 Consensus size: 121
2507996 CCGAAGGCTT
* *
2508006 TTTGGAAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGAAAACATCATGCACTACAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
2508071 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGC
*
2508127 TTTGAAAACATCATGCACTGA-AGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
1 TTTGAAAACATCATGCACT-ACAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
2508191 TCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGC
65 TCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGC
2508248 TTTGAAAACATCA
1 TTTGAAAACATCA
2508261 AAAAGCTCCC
Statistics
Matches: 130, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
121 129 0.99
122 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (121 bp):
TTTGAAAACATCATGCACTACAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGC
Found at i:2508212 original size:76 final size:76
Alignment explanation
Indices: 2508127--2508866 Score: 1349
Period size: 76 Copynumber: 9.8 Consensus size: 76
2508117 ACCCTAAGGC
* * * *
2508127 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2508192 CCCGAAGGCTT
66 CCCGAAGGCTT
2508203 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2508268 CCCGAAGGCTT
66 CCCGAAGGCTT
2508279 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAA-CT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2508343 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
2508354 TTTGGAAACATCATGCACTGTAAGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2508419 CCCGAAGGCTT
66 CCCGAAGGCTT
*
2508430 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
2508495 CCCGAAGACTT
66 CCCGAAGGCTT
*
2508506 TTTGGAAACATCATGCACTCCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2508571 CCCGAAGGCTT
66 CCCGAAGGCTT
2508582 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
* *
2508647 CCCGAATGTTT
66 CCCGAAGGCTT
*
2508658 TTTGGAAACATCATGCACTGCAGGACTTACATATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2508723 CCCGAAGGCTT
66 CCCGAAGGCTT
2508734 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTT-AAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
2508798 TCCGAAGGCTT
66 CCCGAAGGCTT
2508809 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
1 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
2508867 TGCACTGAAG
Statistics
Matches: 643, Mismatches: 19, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
75 147 0.23
76 496 0.77
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:2508229 original size:197 final size:197
Alignment explanation
Indices: 2507888--2508336 Score: 783
Period size: 197 Copynumber: 2.3 Consensus size: 197
2507878 GTAATGTTGA
* ** * * *
2507888 AAACATCATACACTAAAGGGCTTACAGATGACCCGAAGGCTTTTTGGAAACATCATGCACTGCAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGC--TTTGAAAACATCATGCACTGCAA
*
2507953 GACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATC
64 GACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATC
2508018 ATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTT
129 ATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTT
2508083 TTGG
194 TTGG
2508087 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCATGCACTG-AAGG
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCATGCACTGCAA-G
*
2508151 GCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
65 ACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
*
2508216 TGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTT
130 TGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTT
2508281 TGG
195 TGG
2508284 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
2508337 AAAACTCCCG
Statistics
Matches: 240, Mismatches: 9, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
196 2 0.01
197 203 0.85
199 35 0.15
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (197 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCATGCACTGCAAGA
CTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
GCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTT
GG
Found at i:2508391 original size:227 final size:228
Alignment explanation
Indices: 2508127--2508866 Score: 1333
Period size: 227 Copynumber: 3.3 Consensus size: 228
2508117 ACCCTAAGGC
* * *
2508127 TTTGAAAACATCATGCACTG-AAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGCAA-GACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGC
2508191 TCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAA
65 TCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAA
2508256 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAA
130 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAA
2508321 GGCTTTGAAAACATCAAAAA-CTCCCGAAGGCTT
195 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
*
2508354 TTTGGAAACATCATGCACTGTAAGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAAGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
2508419 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
* *
2508484 ATCAAAAAGCTCCCGAAGACTTTTTGGAAACATCATGCACTCCAGGACTTACAGATGACCCTAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
2508549 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
*
2508582 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGCAAGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
* * *
2508647 CCCGAATGTTTTTTGGAAACATCATGCACTGCAGGACTTACATATGACCCTAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
2508712 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
*
2508777 GCTTT-AAAACATCAAAAAGCTTCCGAAGGCTT
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
*
2508809 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
1 TTTGGAAACATCATGCACTGCAAGACTTACAGATGACCCTAAGGCTTTGAAAACATCA
2508867 TGCACTGAAG
Statistics
Matches: 496, Mismatches: 15, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
227 289 0.58
228 207 0.42
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (228 bp):
TTTGGAAACATCATGCACTGCAAGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAG
GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:2508918 original size:46 final size:46
Alignment explanation
Indices: 2508799--2509003 Score: 288
Period size: 45 Copynumber: 4.5 Consensus size: 46
2508789 CAAAAAGCTT
* *
2508799 CCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGAC
1 CCGAAGG-TTTTTGAAAACATCATGCACTGAAGGACTTACAGATGAC
* * *
2508846 CCTAAGG-CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGAC
1 CCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGAC
* * * *
2508891 CCGAAGGTTTTTGAAAACATTATGCACTGAAAGATTTACAGATTAC
1 CCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGAC
*
2508937 CCGAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGAC
1 CCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGAC
*
2508982 CCGAAGGTTTTTAAAAACATCA
1 CCGAAGGTTTTTGAAAACATCA
2509004 AAAAGCTCCC
Statistics
Matches: 138, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
45 80 0.58
46 52 0.38
47 6 0.04
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (46 bp):
CCGAAGGTTTTTGAAAACATCATGCACTGAAGGACTTACAGATGAC
Found at i:2508962 original size:91 final size:91
Alignment explanation
Indices: 2508799--2509003 Score: 320
Period size: 91 Copynumber: 2.2 Consensus size: 91
2508789 CAAAAAGCTT
* * * *
2508799 CCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACA
1 CCGAAGG-TTTTTGAAAACATCATGCACTGAAAGACTTACAGATGACCCGAAGGCTTTGAAAACA
2508864 TCATGCACTGAAGGGCTTACAGATGAC
65 TCATGCACTGAAGGGCTTACAGATGAC
* * * *
2508891 CCGAAGGTTTTTGAAAACATTATGCACTGAAAGATTTACAGATTACCCGAAGGTTTTGAAAACAT
1 CCGAAGGTTTTTGAAAACATCATGCACTGAAAGACTTACAGATGACCCGAAGGCTTTGAAAACAT
2508956 CATGCACTGAAGGGCTTACAGATGAC
66 CATGCACTGAAGGGCTTACAGATGAC
*
2508982 CCGAAGGTTTTTAAAAACATCA
1 CCGAAGGTTTTTGAAAACATCA
2509004 AAAAGCTCCC
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
91 96 0.93
92 7 0.07
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (91 bp):
CCGAAGGTTTTTGAAAACATCATGCACTGAAAGACTTACAGATGACCCGAAGGCTTTGAAAACAT
CATGCACTGAAGGGCTTACAGATGAC
Found at i:2509749 original size:22 final size:22
Alignment explanation
Indices: 2509724--2509802 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
2509714 AATAAAGCTT
2509724 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
2509746 TCATTTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
2509768 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2509790 TCATCTTTGAAAA
1 TCATCTTTGAAAA
2509803 ATGTAGATGT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2514615 original size:17 final size:16
Alignment explanation
Indices: 2514593--2514646 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
2514583 CTTGATTCAA
2514593 TTTCTCCCATTTTTCTT
1 TTTCT-CCATTTTTCTT
2514610 TTTCT-CATTTTTTCTTT
1 TTTCTCCA-TTTTTC-TT
*
2514627 TTTTTCTCATTTTTCTT
1 TTTCTC-CATTTTTCTT
2514644 TTT
1 TTT
2514647 ACATCTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
15 2 0.06
16 6 0.19
17 16 0.50
18 6 0.19
19 2 0.06
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTCCATTTTTCTT
Found at i:2514623 original size:10 final size:10
Alignment explanation
Indices: 2514608--2514640 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2514598 CCCATTTTTC
2514608 TTTTTCTCAT
1 TTTTTCTCAT
*
2514618 TTTTTCT-TT
1 TTTTTCTCAT
2514627 TTTTTCTCAT
1 TTTTTCTCAT
2514637 TTTT
1 TTTT
2514641 CTTTTTACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTCTCAT
Found at i:2514639 original size:18 final size:19
Alignment explanation
Indices: 2514608--2514646 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
2514598 CCCATTTTTC
2514608 TTTTTCTCATTTTTTCTTT
1 TTTTTCTCATTTTTTCTTT
2514627 TTTTTCTCA-TTTTTCTTT
1 TTTTTCTCATTTTTTCTTT
2514645 TT
1 TT
2514647 ACATCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCTCATTTTTTCTTT
Found at i:2514656 original size:17 final size:15
Alignment explanation
Indices: 2514602--2514658 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 15
2514592 ATTTCTCCCA
2514602 TTTTTCTTTTTCTCAT
1 TTTTTCTTTTTCTC-T
*
2514618 TTTTTCTTTTTTTTCTCA
1 TTTTTC---TTTTTCTCT
2514636 TTTTTCTTTTTACATCT
1 TTTTTCTTTTT-C-TCT
2514653 TTTTTC
1 TTTTTC
2514659 ATCTTCTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
15 5 0.15
16 7 0.21
17 8 0.24
18 6 0.18
19 8 0.24
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTCTTTTTCTCT
Found at i:2517585 original size:36 final size:36
Alignment explanation
Indices: 2517508--2517597 Score: 94
Period size: 36 Copynumber: 2.5 Consensus size: 36
2517498 TAAATGCGAA
* *
2517508 AAATGCATAA-ATGCAAAAATAAGAATGCAAACTGTG
1 AAATGCA-AAGATGCAAAAATAAGAATACAAAATGTG
* *
2517544 TAATGCAAAGATGTAAAAAGTAAGAATACAAAATG-G
1 AAATGCAAAGATGCAAAAA-TAAGAATACAAAATGTG
* *
2517580 AAATGCACAGATACAAAA
1 AAATGCAAAGATGCAAAA
2517598 TGTAAATGCA
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
35 2 0.05
36 29 0.66
37 13 0.30
ACGTcount: A:0.56, C:0.10, G:0.17, T:0.18
Consensus pattern (36 bp):
AAATGCAAAGATGCAAAAATAAGAATACAAAATGTG
Found at i:2522091 original size:3 final size:3
Alignment explanation
Indices: 2522083--2522140 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
2522073 ATTTTTTATT
* *
2522083 TAA TAA TAA TAA T-A TGTA TAG TAA T-A TAAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
2522127 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
2522141 GAATGAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
2 6 0.13
3 37 0.79
4 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2522138 original size:27 final size:27
Alignment explanation
Indices: 2522084--2522134 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
2522074 TTTTTTATTT
* *
2522084 AATAATAATAATATGTATAGTAATATA
1 AATAATAATAATATGAATAATAATATA
2522111 AATAATAATAATAT-AATAATAATA
1 AATAATAATAATATGAATAATAATA
2522135 ATAATAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (27 bp):
AATAATAATAATATGAATAATAATATA
Found at i:2522327 original size:13 final size:13
Alignment explanation
Indices: 2522311--2522335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2522301 TATGATTTTC
2522311 TTATATATATATA
1 TTATATATATATA
2522324 TTATATATATAT
1 TTATATATATAT
2522336 TAGGTTTAAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATATATATATA
Found at i:2522521 original size:13 final size:14
Alignment explanation
Indices: 2522505--2522534 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2522495 TTTTTAAAAT
2522505 AAAAT-TTTATTTA
1 AAAATATTTATTTA
2522518 AAAATATTTATTTA
1 AAAATATTTATTTA
2522532 AAA
1 AAA
2522535 TAATCTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAAATATTTATTTA
Found at i:2522535 original size:13 final size:13
Alignment explanation
Indices: 2522504--2522536 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2522494 TTTTTTAAAA
2522504 TAAAAT-TTTATT
1 TAAAATATTTATT
2522516 TAAAAATATTTATT
1 T-AAAATATTTATT
2522530 TAAAATA
1 TAAAATA
2522537 ATCTAAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 11 0.58
14 7 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAAATATTTATT
Found at i:2524762 original size:25 final size:25
Alignment explanation
Indices: 2524733--2524780 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
2524723 ACATATATGG
*
2524733 TTACCCATTATTAGGGTTTTTTTTC
1 TTACCCATTATTAGGGGTTTTTTTC
2524758 TTACCCATTATTAGGGGTTTTTT
1 TTACCCATTATTAGGGGTTTTTT
2524781 GTCATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.54
Consensus pattern (25 bp):
TTACCCATTATTAGGGGTTTTTTTC
Found at i:2526047 original size:49 final size:49
Alignment explanation
Indices: 2525993--2526091 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
2525983 TTAAAATTAG
2525993 ACAAAACTAAATAAAATAATCATAATTACTATTATAAGACATTTTTAAA
1 ACAAAACTAAATAAAATAATCATAATTACTATTATAAGACATTTTTAAA
2526042 ACAAAACTAAATAAAATAATCATAATTACTATTATAAGACATTTTTAAA
1 ACAAAACTAAATAAAATAATCATAATTACTATTATAAGACATTTTTAAA
2526091 A
1 A
2526092 TAATCTTGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.32
Consensus pattern (49 bp):
ACAAAACTAAATAAAATAATCATAATTACTATTATAAGACATTTTTAAA
Found at i:2526236 original size:25 final size:25
Alignment explanation
Indices: 2526207--2526264 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
2526197 TGTTGGCAAG
* *
2526207 CTTCTCACTTCATGACCTCTACTTT
1 CTTCTAACCTCATGACCTCTACTTT
*
2526232 CTTCTAACCTCATTACCTCTACTTT
1 CTTCTAACCTCATGACCTCTACTTT
2526257 CTTCTAAC
1 CTTCTAAC
2526265 ATACGCATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.19, C:0.36, G:0.02, T:0.43
Consensus pattern (25 bp):
CTTCTAACCTCATGACCTCTACTTT
Found at i:2526632 original size:71 final size:71
Alignment explanation
Indices: 2526537--2526672 Score: 238
Period size: 71 Copynumber: 1.9 Consensus size: 71
2526527 TTCAGAACCA
*
2526537 GACCGGTTAGCAAACCGACTATGCTACCGGTTCACTGGTTCAACCGGTCGAACCA-GTCGGAAGA
1 GACCGGTTAGCAAACCGACCATGCTACCGGTTCACTGGTTCAACCGGTCGAA-CAGGTCGGAAGA
2526601 AGAATCG
65 AGAATCG
*
2526608 GACCGGTTAGCGAACCGACCATGCTACCGGTTCACTGGTTCAACCGGTCGAACAGGTCGGAAGAA
1 GACCGGTTAGCAAACCGACCATGCTACCGGTTCACTGGTTCAACCGGTCGAACAGGTCGGAAGAA
2526673 CCGGACGACG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
70 2 0.03
71 60 0.97
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.18
Consensus pattern (71 bp):
GACCGGTTAGCAAACCGACCATGCTACCGGTTCACTGGTTCAACCGGTCGAACAGGTCGGAAGAA
GAATCG
Found at i:2528815 original size:71 final size:72
Alignment explanation
Indices: 2528699--2528842 Score: 281
Period size: 71 Copynumber: 2.0 Consensus size: 72
2528689 AGTCACTTAT
2528699 TACCATTTTAACTCCGCCACTGGCTCATCGCAAGCCAATGTTTGTACGAGAACAAAAACAAATTA
1 TACCATTTTAACTCCGCCACTGGCTCATCGCAAGCCAATGTTTGTACGAGAACAAAAACAAATTA
2528764 AA-GCAC
66 AATGCAC
2528770 TACCATTTTAACTCCGCCACTGGCTCATCGCAAGCCAATGTTTGTACGAGAACAAAAACAAATTA
1 TACCATTTTAACTCCGCCACTGGCTCATCGCAAGCCAATGTTTGTACGAGAACAAAAACAAATTA
2528835 AATGCAC
66 AATGCAC
2528842 T
1 T
2528843 TATATTTACC
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 67 0.93
72 5 0.07
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (72 bp):
TACCATTTTAACTCCGCCACTGGCTCATCGCAAGCCAATGTTTGTACGAGAACAAAAACAAATTA
AATGCAC
Found at i:2535225 original size:14 final size:14
Alignment explanation
Indices: 2535206--2535245 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
2535196 ACCAAACCAT
2535206 GAAAAGAATTTGTC
1 GAAAAGAATTTGTC
2535220 GAAAAGAATTTGTC
1 GAAAAGAATTTGTC
2535234 GAAAAGAATTTG
1 GAAAAGAATTTG
2535246 GAGGTCACGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.28
Consensus pattern (14 bp):
GAAAAGAATTTGTC
Found at i:2540672 original size:33 final size:33
Alignment explanation
Indices: 2540630--2540736 Score: 136
Period size: 33 Copynumber: 3.4 Consensus size: 33
2540620 AACCCGAACC
*
2540630 CGACCCGACCCGAATATCACACTTAAAAAAACT
1 CGACCCAACCCGAATATCACACTTAAAAAAACT
* *
2540663 CGACCCGACCCGAATATCACATTTAAAAAAA-T
1 CGACCCAACCCGAATATCACACTTAAAAAAACT
*
2540695 ----CCAACCCGAATATCACACTT-AAAAAACC
1 CGACCCAACCCGAATATCACACTTAAAAAAACT
2540723 CGACCCAACCCGAA
1 CGACCCAACCCGAA
2540737 CAAAATAAAG
Statistics
Matches: 65, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
27 6 0.09
28 18 0.28
32 11 0.17
33 30 0.46
ACGTcount: A:0.43, C:0.35, G:0.08, T:0.14
Consensus pattern (33 bp):
CGACCCAACCCGAATATCACACTTAAAAAAACT
Found at i:2540702 original size:28 final size:30
Alignment explanation
Indices: 2540637--2540720 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 30
2540627 ACCCGACCCG
*
2540637 ACCCGAATATCACACTTAAAAAAACTCGACCCG
1 ACCCGAATATCACACTTAAAAAAACT---CCCA
*
2540670 ACCCGAATATCACATTTAAAAAAA-T-CCA
1 ACCCGAATATCACACTTAAAAAAACTCCCA
2540698 ACCCGAATATCACACTTAAAAAA
1 ACCCGAATATCACACTTAAAAAA
2540721 CCCGACCCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
28 24 0.50
32 1 0.02
33 23 0.48
ACGTcount: A:0.48, C:0.29, G:0.06, T:0.18
Consensus pattern (30 bp):
ACCCGAATATCACACTTAAAAAAACTCCCA
Found at i:2541497 original size:28 final size:29
Alignment explanation
Indices: 2541465--2541530 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 29
2541455 TGTTATAAGT
*
2541465 AATTTTAAA-AATAATAAAATAATTATTA
1 AATTTTAAATAATAATAAAATAATCATTA
* * *
2541493 AATTTCACAAATAATTATAAAATGATCATTA
1 AATTT--TAAATAATAATAAAATAATCATTA
2541524 AATTTTA
1 AATTTTA
2541531 TTAAGCTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
28 5 0.17
29 1 0.03
30 3 0.10
31 21 0.70
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (29 bp):
AATTTTAAATAATAATAAAATAATCATTA
Found at i:2542207 original size:24 final size:24
Alignment explanation
Indices: 2542168--2542214 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2542158 TTTTTATATA
*
2542168 TAATAATATTACATATTTAATTAT
1 TAATAATATTACATATTAAATTAT
* *
2542192 TAATAATTTTATATATTAAATTA
1 TAATAATATTACATATTAAATTA
2542215 AACTAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATAATATTACATATTAAATTAT
Found at i:2548723 original size:24 final size:24
Alignment explanation
Indices: 2548676--2548728 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2548666 ATGTTTATTA
* * *
2548676 ATAAACTTATTTGTTAATATATTT
1 ATAAACTAATTTATTAATAGATTT
* *
2548700 TTAAACTAATTTATTAGTAGATTT
1 ATAAACTAATTTATTAATAGATTT
2548724 ATAAA
1 ATAAA
2548729 AATTGATATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.49
Consensus pattern (24 bp):
ATAAACTAATTTATTAATAGATTT
Found at i:2550277 original size:390 final size:389
Alignment explanation
Indices: 2549504--2550278 Score: 1379
Period size: 390 Copynumber: 2.0 Consensus size: 389
2549494 TAGAGAGTAG
2549504 AGAGTAGAAGATTGAGTGATGGGTTTTTTACATATTTAAATGTAGCATGGTATATGATGAAGTTA
1 AGAGTAGAAGATTGAGTGATGGGTTTTTTACATATTTAAATGTAGCATGGTATATGATGAAGTTA
2549569 GTGTATTATGACTTCAAAATAGACAAAATACAAGAAGAGCATCCGGATTGGCCTTGAGCAGGTAT
66 GTGTATTATGACTTCAAAATAGACAAAATACAAGAAGAGCATCCGGATTGGCCTTGAGCAGGTAT
2549634 GAAGAAAGAGTTTTCCGGATATGCCTAAGCCATCGCGACATCGGTCGTCGCCGCCAGATTCGGAG
131 GAAGAAAGAGTTTTCCGGATATGCCTAAGCCATCGCGACATCGGTCGTCGCCGCCAGATTCGGAG
*
2549699 CTTCGATACAAGGCGCGTCTCCGGCCACGACCGCGACGGTGTTCAATTGTTATTAGAGATCCATG
196 CTTCGATACAAGGCGCGTCTCCGGCCACGACCGCGAAGGTGTTCAATTGTTATTAGAGATCCATG
2549764 ATAGGATGAGAAAGGAGTTAAAAGCCATCGACGAGGAATGGGATACATGGTAATGGAAGCCGCAG
261 ATAGGATGAGAAAGGAGTTAAAAGCCATCGACGAGGAATGGGATACATGGTAATGGAAGCCGCAG
2549829 ATTCAAGGATAAATATATAGAGACGGATGAGGGCGGTCGCTTCCTTAATTTAAAATCCTAAAGT
326 ATTCAAGGATAAATATATAGAGACGGATGAGGGCGGTCGCTTCCTTAATTTAAAATCCTAAAGT
2549893 AGAGTAAGAAGATTGAGTGATGGGTTTTTTACATATTT-AATGTAGCATGGTATATGATGAAGTT
1 AGAGT-AGAAGATTGAGTGATGGGTTTTTTACATATTTAAATGTAGCATGGTATATGATGAAGTT
2549957 AGTGTATTATGACTTCAAAATAGACAAAATACAAGAAGAGCATCCGGATTGGCCTTGGAGCAGGT
65 AGTGTATTATGACTTCAAAATAGACAAAATACAAGAAGAGCATCCGGATTGGCCTT-GAGCA-G-
2550022 GTATG-A-AAAGAG-TTTCCGGATATGCCTAAAGCCATCGCGACATCGGTCGTCGCCGCCAGATT
127 GTATGAAGAAAGAGTTTTCCGGATATGCCT-AAGCCATCGCGACATCGGTCGTCGCCGCCAGATT
*
2550084 CGGAGCTTCGATACAAGGCGCGTCTCTGGCCACGACCGCAGAAGGTGTTCAA-TGTTATTAGAGA
191 CGGAGCTTCGATACAAGGCGCGTCTCCGGCCACGACCGC-GAAGGTGTTCAATTGTTATTAGAGA
2550148 TCCATGATAGGATGAGAAAGGAGTTAAAAGCCATCGA-GAGG-ATGGGATACATGGTAATGGAGA
255 TCCATGATAGGATGAGAAAGGAGTTAAAAGCCATCGACGAGGAATGGGATACATGGTAATGGA-A
2550211 GCCGCAGATTCAAGGATAAATATATAGGAGAGACGGATGAGGGC-GTCGCTTCCTTAATTT-AAA
319 GCCGCAGATTCAAGGATAAATATAT---AGAGACGGATGAGGGCGGTCGCTTCCTTAATTTAAAA
2550274 TCCTA
381 TCCTA
2550279 CGTCTGTTCC
Statistics
Matches: 374, Mismatches: 2, Indels: 19
0.95 0.01 0.05
Matches are distributed among these distances:
388 20 0.05
389 132 0.35
390 172 0.46
391 29 0.08
392 21 0.06
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.25
Consensus pattern (389 bp):
AGAGTAGAAGATTGAGTGATGGGTTTTTTACATATTTAAATGTAGCATGGTATATGATGAAGTTA
GTGTATTATGACTTCAAAATAGACAAAATACAAGAAGAGCATCCGGATTGGCCTTGAGCAGGTAT
GAAGAAAGAGTTTTCCGGATATGCCTAAGCCATCGCGACATCGGTCGTCGCCGCCAGATTCGGAG
CTTCGATACAAGGCGCGTCTCCGGCCACGACCGCGAAGGTGTTCAATTGTTATTAGAGATCCATG
ATAGGATGAGAAAGGAGTTAAAAGCCATCGACGAGGAATGGGATACATGGTAATGGAAGCCGCAG
ATTCAAGGATAAATATATAGAGACGGATGAGGGCGGTCGCTTCCTTAATTTAAAATCCTAAAGT
Found at i:2551093 original size:59 final size:60
Alignment explanation
Indices: 2550970--2551096 Score: 159
Period size: 59 Copynumber: 2.1 Consensus size: 60
2550960 TAGAATCGCT
* * ** * * *
2550970 CATAGTTTGAGGATGAAATTGGATTTCTTAGAAGTTTAAGGACTAATTTAGAATGAGTAT
1 CATAGTTTGAGGATGAAATTGAATATCTTAGAAAATTAAAGACTAATTTAAAATGAGTAC
*
2551030 CATAGTTTGAGGATGAAATTAGAATAT-TTA-AAAATTAAATACTAATTTAAAATGAGTAC
1 CATAGTTTGAGGATGAAATT-GAATATCTTAGAAAATTAAAGACTAATTTAAAATGAGTAC
2551089 CATAGTTT
1 CATAGTTT
2551097 AGAAATATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 31 0.53
60 23 0.40
61 4 0.07
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (60 bp):
CATAGTTTGAGGATGAAATTGAATATCTTAGAAAATTAAAGACTAATTTAAAATGAGTAC
Found at i:2555595 original size:31 final size:31
Alignment explanation
Indices: 2555560--2555656 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 31
2555550 ATTTCTTAGA
2555560 AGTTTAAGGACTAATTTAGAATGAGTATCAT
1 AGTTTAAGGACTAATTTAGAATGAGTATCAT
* * * * *
2555591 AGTTTGAGGA-TGAAATTAGAAT-A-TTTAAA
1 AGTTTAAGGACT-AATTTAGAATGAGTATCAT
* * * *
2555620 AATTTAAGTACTAATTTAAAATGAGTACCAT
1 AGTTTAAGGACTAATTTAGAATGAGTATCAT
2555651 AGTTTA
1 AGTTTA
2555657 GAAATATATG
Statistics
Matches: 47, Mismatches: 15, Indels: 8
0.67 0.21 0.11
Matches are distributed among these distances:
29 18 0.38
30 4 0.09
31 25 0.53
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.36
Consensus pattern (31 bp):
AGTTTAAGGACTAATTTAGAATGAGTATCAT
Found at i:2555626 original size:60 final size:60
Alignment explanation
Indices: 2555474--2555655 Score: 178
Period size: 60 Copynumber: 3.0 Consensus size: 60
2555464 TTTGGATGAA
* * * *
2555474 TTTGAGAATGAAATTCA-AA-AGTTTAAAAGTTTAGGGGCTAATTTAGAAT-ACG-CTCATAG
1 TTTGAGGATGAAATT-AGAATA-TTTAAAAGTTTAAGGACTAATTTAGAATGA-GTATCATAG
* * *
2555533 -TTGAGGGATGAAATT-GGATTTCTTAGAAGTTTAAGGACTAATTTAGAATGAGTATCATAG
1 TTTGA-GGATGAAATTAGAATAT-TTAAAAGTTTAAGGACTAATTTAGAATGAGTATCATAG
* * * *
2555593 TTTGAGGATGAAATTAGAATATTTAAAAATTTAAGTACTAATTTAAAATGAGTACCATAG
1 TTTGAGGATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAGAATGAGTATCATAG
2555653 TTT
1 TTT
2555656 AGAAATATAT
Statistics
Matches: 101, Mismatches: 14, Indels: 15
0.78 0.11 0.12
Matches are distributed among these distances:
58 6 0.06
59 34 0.34
60 53 0.52
61 8 0.08
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (60 bp):
TTTGAGGATGAAATTAGAATATTTAAAAGTTTAAGGACTAATTTAGAATGAGTATCATAG
Found at i:2561296 original size:30 final size:30
Alignment explanation
Indices: 2561262--2561322 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2561252 TTTTTCAAAA
*
2561262 TCATACCTAAAGTTTAATTTTTGTTTCATT
1 TCATACCTAAAGTTAAATTTTTGTTTCATT
2561292 TCATACCTAAAGTTAAATTTTTGTTTCATT
1 TCATACCTAAAGTTAAATTTTTGTTTCATT
2561322 T
1 T
2561323 TAGTACCTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.28, C:0.13, G:0.07, T:0.52
Consensus pattern (30 bp):
TCATACCTAAAGTTAAATTTTTGTTTCATT
Found at i:2561545 original size:122 final size:121
Alignment explanation
Indices: 2561393--2561696 Score: 330
Period size: 122 Copynumber: 2.5 Consensus size: 121
2561383 AATGTCAAGT
* *
2561393 TTTG-AAAAAATTGAAAGTTTAGATATGAAAACGGATCAAAATTGATAGTTTAGTCACTAAACAT
1 TTTGAAAAAAATTGAAAGTTTAGGTATGAAAACGGATCAAAATTGATAGTTTAGTCACTAAACAC
* ** *
2561457 GTTAGGTTTTTAAC-G-ATGGGTACTAAAACGAAATAAGAACTAAATGTTAAGTATGAA
66 GTTAGGTTTTTAACGGCAT--GTACTAAAACGAAATAAAAACTAAACATCAAGTATG-A
* * * * * * * **
2561514 TTTGAAAAAAACTAAAAGTTTTGGTACGAAAATGAATC-AAATCTGATAGTTTAGGCACTAAATG
1 TTTGAAAAAAATTGAAAGTTTAGGTATGAAAACGGATCAAAAT-TGATAGTTTAGTCACTAAACA
*
2561578 CGTTAGGTTTTTAACGGCATGTACTAAAATGAAATAAAAACTAAACATCAAGTATGA
65 CGTTAGGTTTTTAACGGCATGTACTAAAACGAAATAAAAACTAAACATCAAGTATGA
* * * * * *
2561635 TTTTAAAAAAATTGAAAGTTTCGGTATTAAAGCTGACCAAAATTGATAGTTTAGGT-ACTAAA
1 TTTGAAAAAAATTGAAAGTTTAGGTATGAAAACGGATCAAAATTGATAGTTTA-GTCACTAAA
2561697 TGCATAATTT
Statistics
Matches: 149, Mismatches: 28, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
121 52 0.35
122 94 0.63
123 1 0.01
124 2 0.01
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (121 bp):
TTTGAAAAAAATTGAAAGTTTAGGTATGAAAACGGATCAAAATTGATAGTTTAGTCACTAAACAC
GTTAGGTTTTTAACGGCATGTACTAAAACGAAATAAAAACTAAACATCAAGTATGA
Found at i:2564566 original size:99 final size:99
Alignment explanation
Indices: 2564395--2564592 Score: 378
Period size: 99 Copynumber: 2.0 Consensus size: 99
2564385 AAAAGCACTA
*
2564395 AATTAACATTAATTAAGGATCGATTAGCAGATAATCCACCATGGTCAAAGCATGGAGAAGAACAC
1 AATTAACATTAATTAAGGATCGATTAGCAGACAATCCACCATGGTCAAAGCATGGAGAAGAACAC
*
2564460 GTATGCAACTCCTTTTGGAAAACCCATGCGACCT
66 ATATGCAACTCCTTTTGGAAAACCCATGCGACCT
2564494 AATTAACATTAATTAAGGATCGATTAGCAGACAATCCACCATGGTCAAAGCATGGAGAAGAACAC
1 AATTAACATTAATTAAGGATCGATTAGCAGACAATCCACCATGGTCAAAGCATGGAGAAGAACAC
2564559 ATATGCAACTCCTTTTGGAAAACCCATGCGACCT
66 ATATGCAACTCCTTTTGGAAAACCCATGCGACCT
2564593 GGAATTGCAA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.23
Consensus pattern (99 bp):
AATTAACATTAATTAAGGATCGATTAGCAGACAATCCACCATGGTCAAAGCATGGAGAAGAACAC
ATATGCAACTCCTTTTGGAAAACCCATGCGACCT
Found at i:2566714 original size:4 final size:4
Alignment explanation
Indices: 2566705--2566735 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2566695 GATAACATAA
2566705 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
2566736 CATTTAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2566952 original size:13 final size:13
Alignment explanation
Indices: 2566904--2566955 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
2566894 TAGTAAATAA
*
2566904 AATATTTCAATTT
1 AATATTTAAATTT
2566917 AATA-TTAAACTATT
1 AATATTTAAA-T-TT
2566931 AA-ATATTAAATTT
1 AATAT-TTAAATTT
2566944 AATATTTAAATT
1 AATATTTAAATT
2566956 AACACATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
12 4 0.12
13 17 0.52
14 7 0.21
15 5 0.15
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
AATATTTAAATTT
Found at i:2567716 original size:29 final size:29
Alignment explanation
Indices: 2567681--2567766 Score: 111
Period size: 29 Copynumber: 3.0 Consensus size: 29
2567671 GTTGGCTGGT
*
2567681 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
2567710 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
*
2567739 AGGTCGCCGGGCGTGCATGGCGA-CTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
2567767 CGGTACTGTA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
28 2 0.04
29 46 0.96
ACGTcount: A:0.15, C:0.29, G:0.40, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Done.