Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 191 of 240
Found at i:58420401 original size:55 final size:57
Alignment explanation
Indices: 58420274--58420408 Score: 159
Period size: 55 Copynumber: 2.4 Consensus size: 57
58420264 AAATATTATT
* * * * *
58420274 AATAATTATATTAGTAATGTTATTAAATTATATATTATTTTATTAAATTGTATTTAAC
1 AATAATTATATTA-AAATATAATTAAATTATATATTATTTTATTAAAATATATTTAAC
* *
58420332 AATAATTATGTTAAAATATAATTAAATTATTTA-T-TTTTATTAAAATATATTTAAC
1 AATAATTATATTAAAATATAATTAAATTATATATTATTTTATTAAAATATATTTAAC
*
58420387 AATAATCT-TATTAAAATTTAAT
1 AATAAT-TATATTAAAATATAAT
58420409 AACAATAACC
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
55 37 0.55
56 2 0.03
57 16 0.24
58 12 0.18
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (57 bp):
AATAATTATATTAAAATATAATTAAATTATATATTATTTTATTAAAATATATTTAAC
Found at i:58420454 original size:9 final size:9
Alignment explanation
Indices: 58420432--58420751 Score: 258
Period size: 9 Copynumber: 36.4 Consensus size: 9
58420422 CACTTGTACA
*
58420432 TTACAAAAC
1 TTACATAAC
58420441 TTACATAAC
1 TTACATAAC
*
58420450 CTACATAAC
1 TTACATAAC
58420459 TTACATAA-
1 TTACATAAC
* *
58420467 -TACAAAAT
1 TTACATAAC
58420475 TTACATAAC
1 TTACATAAC
58420484 TTACATAAC
1 TTACATAAC
58420493 TTACATAA-
1 TTACATAAC
*
58420501 -TACAAAAC
1 TTACATAAC
*
58420509 TCACATAAC
1 TTACATAAC
* *
58420518 TTAAATATC
1 TTACATAAC
*
58420527 TTACACAAC
1 TTACATAAC
58420536 TTACATAAC
1 TTACATAAC
*
58420545 CTACATAA-
1 TTACATAAC
58420553 -TACATTTAAC
1 TTACA--TAAC
58420563 TTACATAAC
1 TTACATAAC
* *
58420572 TTAAATATC
1 TTACATAAC
*
58420581 TTACACAAC
1 TTACATAAC
58420590 TTACATAAC
1 TTACATAAC
*
58420599 CTACATAA-
1 TTACATAAC
58420607 -TACATTTAAC
1 TTACA--TAAC
58420617 TTACATAAC
1 TTACATAAC
58420626 TTACATAA-
1 TTACATAAC
58420634 -TACAAAATAAC
1 TTAC---ATAAC
58420645 TTAC--AAC
1 TTACATAAC
58420652 TTACATAAC
1 TTACATAAC
* *
58420661 ATACATTAC
1 TTACATAAC
**
58420670 TTTGATAAC
1 TTACATAAC
58420679 TTACATAAC
1 TTACATAAC
*
58420688 TTACATAGC
1 TTACATAAC
*
58420697 TTACTTAA-
1 TTACATAAC
58420705 -TACATAAC
1 TTACATAAC
58420713 TTACATAAC
1 TTACATAAC
58420722 TT--ATACAC
1 TTACATA-AC
*
58420730 GTACATAAC
1 TTACATAAC
*
58420739 TTACATAAT
1 TTACATAAC
58420748 TTAC
1 TTAC
58420752 TTAATACATA
Statistics
Matches: 248, Mismatches: 39, Indels: 48
0.74 0.12 0.14
Matches are distributed among these distances:
7 39 0.16
8 3 0.01
9 188 0.76
10 7 0.03
11 8 0.03
12 3 0.01
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (9 bp):
TTACATAAC
Found at i:58420708 original size:43 final size:43
Alignment explanation
Indices: 58420433--58420751 Score: 134
Period size: 43 Copynumber: 7.5 Consensus size: 43
58420423 ACTTGTACAT
* * * * **
58420433 TACAAAACTTACATAACCTACATAACTTACATA-ATACAAAATT
1 TACATAACTTACATAACTTACATAACTTACA-ACTTACATAACA
* *
58420476 TACATAACTTACATAACTTACATAA--TACAAAACTCACATAACT
1 TACATAACTTACATAACTTACATAACTTAC--AACTTACATAACA
* * * * * *
58420519 TAAATATCTTACACAACTTACATAACCTACATA-ATACATTTAACT
1 TACATAACTTACATAACTTACATAACTTACA-ACTTACA--TAACA
* * * *
58420564 TACATAACTTAAATATCTTACACAACTTACATAACCTACAT-A-A
1 TACATAACTTACATAACTTACATAACTTAC--AACTTACATAACA
*
58420607 TACATTTAACTTACATAACTTACATAA--TACAA---A-ATAACT
1 TACA--TAACTTACATAACTTACATAACTTACAACTTACATAACA
* * * *
58420646 TAC--AACTTACATAACATACATTACTTTGATAACTTACATAACT
1 TACATAACTTACATAACTTACATAAC-TT-ACAACTTACATAACA
* * *
58420689 TACATAGCTTACTTAA--TACATAACTTACATAACTT--ATACACG
1 TACATAACTTACATAACTTACATAACTTAC--AACTTACATA-ACA
*
58420731 TACATAACTTACATAATTTAC
1 TACATAACTTACATAACTTAC
58420752 TTAATACATA
Statistics
Matches: 212, Mismatches: 34, Indels: 59
0.70 0.11 0.19
Matches are distributed among these distances:
35 18 0.08
37 2 0.01
38 3 0.01
39 6 0.03
41 9 0.04
42 20 0.09
43 84 0.40
44 5 0.02
45 59 0.28
46 1 0.00
47 5 0.02
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (43 bp):
TACATAACTTACATAACTTACATAACTTACAACTTACATAACA
Found at i:58420740 original size:51 final size:52
Alignment explanation
Indices: 58420653--58420762 Score: 152
Period size: 51 Copynumber: 2.1 Consensus size: 52
58420643 ACTTACAACT
* * *
58420653 TACATAACATACATTACTTTGATAACTTACATAACTTACATAGCTTACTTAA
1 TACATAACATACATAACTTTGATAACGTACATAACTTACATAACTTACTTAA
* *
58420705 TACATAACTTACATAAC-TT-ATACACGTACATAACTTACATAATTTACTTAA
1 TACATAACATACATAACTTTGATA-ACGTACATAACTTACATAACTTACTTAA
58420756 TACATAA
1 TACATAA
58420763 ATATATATCA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
50 3 0.06
51 34 0.65
52 15 0.29
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.35
Consensus pattern (52 bp):
TACATAACATACATAACTTTGATAACGTACATAACTTACATAACTTACTTAA
Found at i:58426281 original size:21 final size:21
Alignment explanation
Indices: 58426255--58426325 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
58426245 CTACAACTTA
58426255 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
58426276 AAGCAGCGGCTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
58426297 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
*
58426318 AAGTAGAG
1 AAGCAGAG
58426326 TAGAGCAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.31, C:0.18, G:0.45, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:58426677 original size:42 final size:42
Alignment explanation
Indices: 58426625--58426782 Score: 255
Period size: 42 Copynumber: 3.8 Consensus size: 42
58426615 ATCCCAAAAA
*
58426625 TTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTC
1 TTTAGAGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTC
* *
58426667 TTTAGAGGCGCTTA-AACAAAAATGCCGCTAAAAACCATGTTC
1 TTTAGAGGCGCTTAGAA-AAAAACGCCGCTAAAGACCATGTTC
*
58426709 TTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTC
1 TTTAGAGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTC
*
58426751 TTTAGAGGCGCTTAGAGAAAAACGCCGCTAAA
1 TTTAGAGGCGCTTAGAAAAAAACGCCGCTAAA
58426783 TTTAGCGGCA
Statistics
Matches: 106, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
41 2 0.02
42 102 0.96
43 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (42 bp):
TTTAGAGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTC
Found at i:58426714 original size:84 final size:84
Alignment explanation
Indices: 58426625--58426782 Score: 289
Period size: 84 Copynumber: 1.9 Consensus size: 84
58426615 ATCCCAAAAA
*
58426625 TTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAAACAAAAAT
1 TTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAAACAAAAAC
58426690 GCCGCTAAAAACCATGTTC
66 GCCGCTAAAAACCATGTTC
* *
58426709 TTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAGAGAAAAAC
1 TTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAAACAAAAAC
58426774 GCCGCTAAA
66 GCCGCTAAA
58426783 TTTAGCGGCA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 71 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (84 bp):
TTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAAACAAAAAC
GCCGCTAAAAACCATGTTC
Found at i:58426847 original size:42 final size:43
Alignment explanation
Indices: 58426783--58426881 Score: 157
Period size: 42 Copynumber: 2.3 Consensus size: 43
58426773 CGCCGCTAAA
*
58426783 TTTAGCGGCA-CTTTTTCTTAAGCGCCGCTAAAGAACATGGTC
1 TTTAGCGGCATTTTTTTCTTAAGCGCCGCTAAAGAACATGGTC
*
58426825 TTTAGCGGCATTTTTTTC-TAAGCGCCGCTCAAGAACATGGTC
1 TTTAGCGGCATTTTTTTCTTAAGCGCCGCTAAAGAACATGGTC
*
58426867 TTTAGCGGCGTTTTT
1 TTTAGCGGCATTTTT
58426882 GTTTGTAAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
42 47 0.89
43 6 0.11
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (43 bp):
TTTAGCGGCATTTTTTTCTTAAGCGCCGCTAAAGAACATGGTC
Found at i:58427613 original size:27 final size:27
Alignment explanation
Indices: 58427575--58427628 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
58427565 TCCGCAAGGT
58427575 ATGATTTCCTCACATTTTGATCTAATC
1 ATGATTTCCTCACATTTTGATCTAATC
*
58427602 ATGATTTTCTCACATTTTGATCTAATC
1 ATGATTTCCTCACATTTTGATCTAATC
58427629 CATTATATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.46
Consensus pattern (27 bp):
ATGATTTCCTCACATTTTGATCTAATC
Found at i:58430943 original size:27 final size:26
Alignment explanation
Indices: 58430903--58430953 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
58430893 AATACTCATA
58430903 TTTATATAATTAAAATAT-TCATATT
1 TTTATATAATTAAAATATGTCATATT
58430928 TTTATAGTAGATTAAAATATGTCATA
1 TTTATA-TA-ATTAAAATATGTCATA
58430954 AGTCCTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.26
26 2 0.09
27 10 0.43
28 5 0.22
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (26 bp):
TTTATATAATTAAAATATGTCATATT
Found at i:58431640 original size:43 final size:43
Alignment explanation
Indices: 58431587--58431762 Score: 232
Period size: 43 Copynumber: 4.1 Consensus size: 43
58431577 TTTTTAAAAG
* *
58431587 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTCTTTACACAAA
1 CGCCGCTAAAGTACATGTTCTTTAGCGGCGCTCTTAACACAAA
*
58431630 CGCCACTAAAGGT-CATGTTCTTTAGCGGCGCTCTTAACACAAA
1 CGCCGCTAAA-GTACATGTTCTTTAGCGGCGCTCTTAACACAAA
* * *
58431673 CGCTGCTAAAGTTCATGTTCTTTAGCGGCGCT-TCTAACAGAAA
1 CGCCGCTAAAGTACATGTTCTTTAGCGGCGCTCT-TAACACAAA
* *
58431716 CGCCGCTAAAGCTA-ATGTTCTTTAGCGGCGCTTTTTACACAAA
1 CGCCGCTAAAG-TACATGTTCTTTAGCGGCGCTCTTAACACAAA
58431759 CGCC
1 CGCC
58431763 ACTTTTGTTT
Statistics
Matches: 118, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
42 3 0.03
43 112 0.95
44 3 0.03
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (43 bp):
CGCCGCTAAAGTACATGTTCTTTAGCGGCGCTCTTAACACAAA
Found at i:58432201 original size:66 final size:66
Alignment explanation
Indices: 58432113--58432243 Score: 208
Period size: 66 Copynumber: 2.0 Consensus size: 66
58432103 CGCTGCAGCC
* * * *
58432113 TCTGCTTCTCTGGATGCCGCATCAGCTTTAAGTTGTCGCTGGAGTTCTTCATATTTCTTTTGAAC
1 TCTGCTTCTCTCGATGACGCATCAGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGAAC
58432178 A
66 A
* *
58432179 TCTGCTTCTCTCGCTGACGCATCTGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGAAC
1 TCTGCTTCTCTCGATGACGCATCAGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGAAC
58432244 TTCAACTGTG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 59 1.00
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (66 bp):
TCTGCTTCTCTCGATGACGCATCAGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGAAC
A
Found at i:58434981 original size:9 final size:9
Alignment explanation
Indices: 58434967--58435088 Score: 125
Period size: 9 Copynumber: 14.4 Consensus size: 9
58434957 TAAGGGATAT
58434967 TTATGTAAG
1 TTATGTAAG
58434976 TTATGTAAG
1 TTATGTAAG
58434985 TTATGT-A-
1 TTATGTAAG
* *
58434992 TTAAGTAAA
1 TTATGTAAG
58435001 TTATGTAAG
1 TTATGTAAG
58435010 TTATGT-A-
1 TTATGTAAG
*
58435017 TTATGTAAA
1 TTATGTAAG
*
58435026 TTATGTAAA
1 TTATGTAAG
58435035 TTATGT-A-
1 TTATGTAAG
* *
58435042 TTAAGTAGG
1 TTATGTAAG
58435051 TTATGTAAG
1 TTATGTAAG
*
58435060 TTATGT--C
1 TTATGTAAG
58435067 TTATGTAAG
1 TTATGTAAG
58435076 TTATGTAAG
1 TTATGTAAG
58435085 TTAT
1 TTAT
58435089 TGTTTTTGTG
Statistics
Matches: 96, Mismatches: 9, Indels: 16
0.79 0.07 0.13
Matches are distributed among these distances:
7 22 0.23
8 5 0.05
9 69 0.72
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:58434999 original size:25 final size:25
Alignment explanation
Indices: 58434971--58435088 Score: 173
Period size: 25 Copynumber: 4.7 Consensus size: 25
58434961 GGATATTTAT
58434971 GTAAGTTATGTAAGTTATGTATTAA
1 GTAAGTTATGTAAGTTATGTATTAA
* *
58434996 GTAAATTATGTAAGTTATGTATTAT
1 GTAAGTTATGTAAGTTATGTATTAA
* *
58435021 GTAAATTATGTAAATTATGTATTAA
1 GTAAGTTATGTAAGTTATGTATTAA
* * *
58435046 GTAGGTTATGTAAGTTATGTCTTAT
1 GTAAGTTATGTAAGTTATGTATTAA
58435071 GTAAGTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTAT
58435089 TGTTTTTGTG
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 83 1.00
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.46
Consensus pattern (25 bp):
GTAAGTTATGTAAGTTATGTATTAA
Found at i:58435042 original size:50 final size:50
Alignment explanation
Indices: 58434967--58435088 Score: 199
Period size: 50 Copynumber: 2.4 Consensus size: 50
58434957 TAAGGGATAT
58434967 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
* * ** *
58435017 TTATGTAAATTATGTAAATTATGTATTAAGTAGGTTATGTAAGTTATGTC
1 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
58435067 TTATGTAAGTTATGTAAGTTAT
1 TTATGTAAGTTATGTAAGTTAT
58435089 TGTTTTTGTG
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (50 bp):
TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
Found at i:58435070 original size:16 final size:17
Alignment explanation
Indices: 58434967--58435088 Score: 112
Period size: 16 Copynumber: 7.2 Consensus size: 17
58434957 TAAGGGATAT
58434967 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGTAA
*
58434984 GTTATGT-A-TTAAGTAAA
1 -TTATGTAAGTTATGT-AA
58435001 TTATGTAAGTTATGT-A
1 TTATGTAAGTTATGTAA
*
58435017 TTATGTAAATTATGTAAA
1 TTATGTAAGTTATGT-AA
* *
58435035 TTATGT-A-TTAAGTAGG
1 TTATGTAAGTTATGTA-A
*
58435051 TTATGTAAGTTATGT-C
1 TTATGTAAGTTATGTAA
58435067 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGTAA
58435084 GTTAT
1 -TTAT
58435089 TGTTTTTGTG
Statistics
Matches: 86, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
15 1 0.01
16 52 0.60
17 6 0.07
18 27 0.31
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.47
Consensus pattern (17 bp):
TTATGTAAGTTATGTAA
Found at i:58435105 original size:50 final size:49
Alignment explanation
Indices: 58434967--58435219 Score: 184
Period size: 50 Copynumber: 5.1 Consensus size: 49
58434957 TAAGGGATAT
*
58434967 TTATGTAAGTTATGTAAGTTATGTATTAAGTAAATTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTATTAAGT-GATTATGTAAGTTATGTA
* * * *
58435017 TTATGTAAATTATGTAAATTATGTATTAAGTAGGTTATGTAAGTTATGTC
1 TTATGTAAGTTATGTAAGTTATGTATTAAGT-GATTATGTAAGTTATGTA
** * * *
58435067 TTATGTAAGTTATGTAAGTTATTGT-TTTTGTGTATTATGTAACTTTTTTAA
1 TTATGTAAGTTATGTAAGTTA-TGTATTAAGTG-ATTATGTAAGTTATGT-A
* * * *
58435118 TTTATGTAGGTTATGT-A-TTGT-TATATAAGTTATTATGT-AG--GT-TA
1 -TTATGTAAGTTATGTAAGTTATGTAT-TAAGTGATTATGTAAGTTATGTA
* * *
58435162 TTATGTAAGTTTTTGTAAGTTAT-TATGTACGAT-ATTATGTAAGTTAGGATA
1 TTATGTAAG-TTATGTAAGTTATGTAT-TAAG-TGATTATGTAAGTTATG-TA
58435213 TTATGTA
1 TTATGTA
58435220 GGATATATAA
Statistics
Matches: 160, Mismatches: 28, Indels: 29
0.74 0.13 0.13
Matches are distributed among these distances:
43 8 0.05
44 6 0.04
45 2 0.01
46 17 0.11
47 3 0.02
48 2 0.01
49 10 0.06
50 85 0.53
51 13 0.08
52 14 0.09
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.50
Consensus pattern (49 bp):
TTATGTAAGTTATGTAAGTTATGTATTAAGTGATTATGTAAGTTATGTA
Found at i:58435161 original size:12 final size:12
Alignment explanation
Indices: 58435138--58435207 Score: 90
Period size: 12 Copynumber: 6.0 Consensus size: 12
58435128 TTATGTATTG
*
58435138 TTATATAAGTTA
1 TTATGTAAGTTA
*
58435150 TTATGTAGGTTA
1 TTATGTAAGTTA
58435162 TTATGTAAGTT-
1 TTATGTAAGTTA
58435173 TT-TGTAAGTTA
1 TTATGTAAGTTA
* *
58435184 TTATGTACGATA
1 TTATGTAAGTTA
58435196 TTATGTAAGTTA
1 TTATGTAAGTTA
58435208 GGATATTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
10 8 0.16
11 4 0.08
12 37 0.76
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.50
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:58435166 original size:34 final size:33
Alignment explanation
Indices: 58435128--58435202 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 33
58435118 TTTATGTAGG
* *
58435128 TTATGTA-TTGTTATATAAGTTATTATGTAGGTTA
1 TTATGTAGTT-TT-TATAAGTTATTATGTACGATA
*
58435162 TTATGTAAGTTTTTGTAAGTTATTATGTACGATA
1 TTATGT-AGTTTTTATAAGTTATTATGTACGATA
58435196 TTATGTA
1 TTATGTA
58435203 AGTTAGGATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 1 0.03
34 30 0.83
35 3 0.08
36 2 0.06
ACGTcount: A:0.29, C:0.01, G:0.17, T:0.52
Consensus pattern (33 bp):
TTATGTAGTTTTTATAAGTTATTATGTACGATA
Found at i:58435330 original size:9 final size:9
Alignment explanation
Indices: 58435307--58435356 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
58435297 ATTTAAATGT
58435307 TGTAAATTA
1 TGTAAATTA
58435316 TG--AATTA
1 TGTAAATTA
58435323 TGTAAATTA
1 TGTAAATTA
*
58435332 TGTAAAATA
1 TGTAAATTA
* *
58435341 CGTAAGTTA
1 TGTAAATTA
58435350 TG-AAATT
1 TGTAAATT
58435357 TGAACTTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
7 7 0.21
8 4 0.12
9 22 0.67
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.40
Consensus pattern (9 bp):
TGTAAATTA
Found at i:58439832 original size:16 final size:16
Alignment explanation
Indices: 58439811--58439879 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
58439801 CCCTAAACCA
58439811 TAAACTATAAAACCCT
1 TAAACTATAAAACCCT
* * **
58439827 TAAACTA-CATACTAT
1 TAAACTATAAAACCCT
58439842 AGTAAAC-AT-AAA-CCT
1 --TAAACTATAAAACCCT
58439857 TAAACTATAAAACCCT
1 TAAACTATAAAACCCT
58439873 TAAACTA
1 TAAACTA
58439880 CATACTATAG
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
13 5 0.12
14 2 0.05
15 8 0.20
16 20 0.50
17 5 0.12
ACGTcount: A:0.51, C:0.22, G:0.01, T:0.26
Consensus pattern (16 bp):
TAAACTATAAAACCCT
Found at i:58439840 original size:23 final size:23
Alignment explanation
Indices: 58439814--58439888 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
58439804 TAAACCATAA
58439814 ACTATAAAACCCTTAAACTACAT
1 ACTATAAAACCCTTAAACTACAT
*
58439837 ACTATAGTAAA--CATAAACCTTA-A-
1 ACTATA--AAACCCTTAAA-C-TACAT
58439860 ACTATAAAACCCTTAAACTACAT
1 ACTATAAAACCCTTAAACTACAT
58439883 ACTATA
1 ACTATA
58439889 GCCCTTAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
21 5 0.12
22 2 0.05
23 28 0.67
24 2 0.05
25 5 0.12
ACGTcount: A:0.49, C:0.23, G:0.01, T:0.27
Consensus pattern (23 bp):
ACTATAAAACCCTTAAACTACAT
Found at i:58440341 original size:41 final size:41
Alignment explanation
Indices: 58440290--58440473 Score: 239
Period size: 41 Copynumber: 4.5 Consensus size: 41
58440280 GCGTTTTTTA
* * *
58440290 AAAAAGCGCCGCTAAAGGCCTGAGA-ATTAGCGGCGCAT-CAAT
1 AAAAA-CGCCGCTAAAGCCCAGA-ACATTAGCGGCGCTTAC-AT
58440332 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTA-ATT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACA-T
* *
58440373 AAAAACGCCACTAAATCCCAGAACATTAGCGGCGCTTACAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
* * *
58440414 ACAAACGCCACTAAATCCCAGAACATTAGCGGCGCTTACAT
1 AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
58440455 AAAAACGCCGCTAAAGCCC
1 AAAAACGCCGCTAAAGCCC
58440474 CCGAAAAGTC
Statistics
Matches: 129, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
40 2 0.02
41 121 0.94
42 6 0.05
ACGTcount: A:0.38, C:0.29, G:0.18, T:0.15
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGCCCAGAACATTAGCGGCGCTTACAT
Found at i:58443433 original size:25 final size:25
Alignment explanation
Indices: 58443405--58443463 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
58443395 CATAGCTTGC
58443405 GTGAGCATTTATAGTCACAGCTCAT
1 GTGAGCATTTATAGTCACAGCTCAT
* * **
58443430 GTGAGCATTTATCGTCAGAGCTTGT
1 GTGAGCATTTATAGTCACAGCTCAT
58443455 GTGAGCATT
1 GTGAGCATT
58443464 GTTCTCGCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (25 bp):
GTGAGCATTTATAGTCACAGCTCAT
Found at i:58444894 original size:25 final size:25
Alignment explanation
Indices: 58444848--58444927 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
58444838 TCCAGCTCTT
*
58444848 ATGAGCTTCCCGATACTCAGCTCGC
1 ATGAGCTTCCCGTTACTCAGCTCGC
* * * *
58444873 ATGAGCTTCCCGTTATTTAGCTTGG
1 ATGAGCTTCCCGTTACTCAGCTCGC
* *
58444898 ATGAGCTTACCGTT--TACAGCTCGT
1 ATGAGCTTCCCGTTACT-CAGCTCGC
58444922 ATGAGC
1 ATGAGC
58444928 AAACATGTAC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 1 0.02
24 11 0.24
25 33 0.73
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (25 bp):
ATGAGCTTCCCGTTACTCAGCTCGC
Found at i:58457477 original size:18 final size:17
Alignment explanation
Indices: 58457444--58457482 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
58457434 TTTTATAAAT
58457444 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
58457462 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
58457479 TGTG
1 TGTG
58457483 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:58457734 original size:23 final size:23
Alignment explanation
Indices: 58457708--58457829 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
58457698 AGTGTTATTG
58457708 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
58457731 ATCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
58457754 ATTAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
58457777 TTCAGTGATAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
58457800 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
58457823 ATCAGTG
1 ATCAGTG
58457830 TGGCACTTAT
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 86 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:58474865 original size:15 final size:16
Alignment explanation
Indices: 58474845--58474876 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
58474835 AGGCCCACTA
58474845 TCTCAGCCC-AACTGG
1 TCTCAGCCCAAACTGG
58474860 TCTCAGCCCAAACTGG
1 TCTCAGCCCAAACTGG
58474876 T
1 T
58474877 TCATGGGTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.22
Consensus pattern (16 bp):
TCTCAGCCCAAACTGG
Found at i:58482580 original size:56 final size:50
Alignment explanation
Indices: 58482513--58482655 Score: 169
Period size: 50 Copynumber: 2.7 Consensus size: 50
58482503 AGGAATGAGA
* * * *
58482513 TCCCATATAAGAACATATCTGGGATATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCA-C--CGAGA-TA--AGAGG
* *
58482569 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATAAGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATAAGAGG
*
58482619 TCCCATGTAAGACCATGTATGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCA
58482656 GTATAGGAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
50 39 0.50
52 2 0.03
53 4 0.05
55 1 0.01
56 32 0.41
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATAAGAGG
Found at i:58482924 original size:12 final size:12
Alignment explanation
Indices: 58482907--58482957 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
58482897 ATGAGTTATT
58482907 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
58482919 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
58482931 TAAGTGAGTAAG
1 TAAGTAAGCAAG
58482943 TAAAG-AAGCAAG
1 T-AAGTAAGCAAG
58482955 TAA
1 TAA
58482958 AGATTCTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.06
12 27 0.84
13 3 0.09
ACGTcount: A:0.53, C:0.06, G:0.24, T:0.18
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:58482955 original size:20 final size:20
Alignment explanation
Indices: 58482917--58482955 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
58482907 TAAGTAAGCA
*
58482917 AGTAAGTAAACAAGTAAGTG
1 AGTAAGTAAACAAGCAAGTG
*
58482937 AGTAAGTAAAGAAGCAAGT
1 AGTAAGTAAACAAGCAAGT
58482956 AAAGATTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.05, G:0.26, T:0.18
Consensus pattern (20 bp):
AGTAAGTAAACAAGCAAGTG
Found at i:58485257 original size:36 final size:36
Alignment explanation
Indices: 58485194--58485264 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
58485184 GAGGAGTGCC
* *
58485194 TCAGTCAGAATAGATTCGAAATGCTGCTGAACTGAG
1 TCAGTCAGAATAGATTCGAAAAGCTGCTAAACTGAG
* *
58485230 TCAGTTAGAATAGA-TCTAAAAGACTGCTAAACTGA
1 TCAGTCAGAATAGATTCGAAAAG-CTGCTAAACTGA
58485265 ATAGAGTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 6 0.20
36 24 0.80
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.25
Consensus pattern (36 bp):
TCAGTCAGAATAGATTCGAAAAGCTGCTAAACTGAG
Found at i:58487826 original size:25 final size:25
Alignment explanation
Indices: 58487799--58488010 Score: 119
Period size: 25 Copynumber: 8.5 Consensus size: 25
58487789 AAGCTCTTTT
*
58487799 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCATGA
* * * **
58487824 GAGCTATGTAACGGGAAGATCCGGA
1 GAGCCATATAACGGGAAGCTCATGA
*
58487849 GAGCCAT-TAACGGGAAGCTCATAA
1 GAGCCATATAACGGGAAGCTCATGA
* ** *
58487873 GAGCCATTTATTGGGAAGCTC-CGAA
1 GAGCCATATAACGGGAAGCTCATG-A
* *
58487898 GAGCAATA-AACGGGAAGCTCAAAAGA
1 GAGCCATATAACGGGAAGCTC--ATGA
* * ***
58487924 GAGCCAT-TAATCAGGAAACTCGCAA
1 GAGCCATATAA-CGGGAAGCTCATGA
* * * *
58487949 GAACCATTTAACGGGAAGCTCGTAA
1 GAGCCATATAACGGGAAGCTCATGA
* * *
58487974 GAGCCAAATATCAGGAAGCTCATGA
1 GAGCCATATAACGGGAAGCTCATGA
*
58487999 GAGCTA-ATAACG
1 GAGCCATATAACG
58488011 AGACACTCTT
Statistics
Matches: 139, Mismatches: 40, Indels: 17
0.71 0.20 0.09
Matches are distributed among these distances:
24 34 0.24
25 84 0.60
26 12 0.09
27 9 0.06
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.17
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATGA
Found at i:58487862 original size:49 final size:49
Alignment explanation
Indices: 58487799--58487979 Score: 152
Period size: 49 Copynumber: 3.6 Consensus size: 49
58487789 AAGCTCTTTT
** * *
58487799 GAGCCATATAACGGGAAGCTCATGTGAGCTATGTAACGGGAAGATCCGGA
1 GAGCCAT-TAACGGGAAGCTCATAAGAGCCATGTAACGGGAAGATCCGAA
* ** *
58487849 GAGCCATTAACGGGAAGCTCATAAGAGCCATTTATTGGGAAGCTCCGAA
1 GAGCCATTAACGGGAAGCTCATAAGAGCCATGTAACGGGAAGATCCGAA
* * * *
58487898 GAGCAATAAACGGGAAGCTCAAAAGAGAGCCAT-TAATCAGGAA-A-CTCGCAA
1 GAGCCATTAACGGGAAGCTC-ATA-AGAGCCATGTAA-CGGGAAGATC-CG-AA
* *
58487949 GAACCATTTAACGGGAAGCTCGTAAGAGCCA
1 GAGCCA-TTAACGGGAAGCTCATAAGAGCCA
58487980 AATATCAGGA
Statistics
Matches: 105, Mismatches: 20, Indels: 12
0.77 0.15 0.09
Matches are distributed among these distances:
49 53 0.50
50 20 0.19
51 19 0.18
52 13 0.12
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.17
Consensus pattern (49 bp):
GAGCCATTAACGGGAAGCTCATAAGAGCCATGTAACGGGAAGATCCGAA
Found at i:58487917 original size:24 final size:24
Alignment explanation
Indices: 58487832--58487917 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
58487822 GTGAGCTATG
* * *
58487832 TAACGGGAAGATCCGGAGAGCCAT
1 TAACGGGAAGCTCCGAAGAGCAAT
** *
58487856 TAACGGGAAGCTCATAAGAGCCATT
1 TAACGGGAAGCTCCGAAGAG-CAAT
**
58487881 TATTGGGAAGCTCCGAAGAGCAAT
1 TAACGGGAAGCTCCGAAGAGCAAT
*
58487905 AAACGGGAAGCTC
1 TAACGGGAAGCTC
58487918 AAAAGAGAGC
Statistics
Matches: 47, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
24 29 0.62
25 18 0.38
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.16
Consensus pattern (24 bp):
TAACGGGAAGCTCCGAAGAGCAAT
Found at i:58493177 original size:18 final size:19
Alignment explanation
Indices: 58493137--58493180 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
58493127 TATTGAAATT
58493137 TATATTATATAAATTTAGAA
1 TATATTATATAAATTTA-AA
58493157 TAT-TTATAT--ATTTAAA
1 TATATTATATAAATTTAAA
58493173 TATATTAT
1 TATATTAT
58493181 TATCGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.22
17 9 0.39
19 6 0.26
20 3 0.13
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATATTATATAAATTTAAA
Found at i:58494388 original size:23 final size:23
Alignment explanation
Indices: 58494360--58494409 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
58494350 TAAGAATGTT
58494360 TTTGATGTTTTAAATTATGATCC
1 TTTGATGTTTTAAATTATGATCC
58494383 TTTGATGTTTTAAATTATGATCC
1 TTTGATGTTTTAAATTATGATCC
58494406 TTTG
1 TTTG
58494410 CCCTCTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.08, G:0.14, T:0.54
Consensus pattern (23 bp):
TTTGATGTTTTAAATTATGATCC
Found at i:58500792 original size:3 final size:3
Alignment explanation
Indices: 58500784--58500809 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
58500774 ATTTTGTGTC
58500784 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
58500810 TGTTAGGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:58509051 original size:3 final size:3
Alignment explanation
Indices: 58509043--58509072 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
58509033 CAGCCATAGC
58509043 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
58509073 TTGAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:58512146 original size:13 final size:13
Alignment explanation
Indices: 58512128--58512156 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
58512118 GTTAAGAGTA
58512128 AAACTTTATTTGT
1 AAACTTTATTTGT
58512141 AAACTTTATTTGT
1 AAACTTTATTTGT
58512154 AAA
1 AAA
58512157 AAAGTCCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
AAACTTTATTTGT
Found at i:58514077 original size:33 final size:33
Alignment explanation
Indices: 58514034--58514100 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
58514024 TTGGACCTTC
58514034 AGCGTATCATAGAACTAATGTTTTGTACTGTTA
1 AGCGTATCATAGAACTAATGTTTTGTACTGTTA
*
58514067 AGCGTGTCATAGAACTAATGTTTTGTACTGTTA
1 AGCGTATCATAGAACTAATGTTTTGTACTGTTA
58514100 A
1 A
58514101 TTTATGTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (33 bp):
AGCGTATCATAGAACTAATGTTTTGTACTGTTA
Found at i:58516822 original size:27 final size:27
Alignment explanation
Indices: 58516784--58516839 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
58516774 TTCTTTCCTT
58516784 TCATTTTCTGTTTTTGTTTAGCAGCAA
1 TCATTTTCTGTTTTTGTTTAGCAGCAA
58516811 TCATTTTCTGTTTTTGTTTAGCAGCAA
1 TCATTTTCTGTTTTTGTTTAGCAGCAA
58516838 TC
1 TC
58516840 TTTGGCCTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.16, G:0.14, T:0.52
Consensus pattern (27 bp):
TCATTTTCTGTTTTTGTTTAGCAGCAA
Found at i:58523747 original size:6 final size:7
Alignment explanation
Indices: 58523720--58523745 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
58523710 ATAAATATAT
58523720 ATTTTTA
1 ATTTTTA
58523727 ATTTTTA
1 ATTTTTA
58523734 ATTTTTA
1 ATTTTTA
58523741 ATTTT
1 ATTTT
58523746 AAAATACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTTA
Found at i:58523769 original size:29 final size:29
Alignment explanation
Indices: 58523735--58523799 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
58523725 TAATTTTTAA
*
58523735 TTTTTAATTTTAAAATACTTTTAAAATAT
1 TTTTTAATTTTAAAATAATTTTAAAATAT
* **
58523764 TTTTTATTTTTAAAATAATTTTTTAATAT
1 TTTTTAATTTTAAAATAATTTTAAAATAT
*
58523793 TTATTAA
1 TTTTTAA
58523800 AAAATGGGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTTAATTTTAAAATAATTTTAAAATAT
Found at i:58523774 original size:18 final size:19
Alignment explanation
Indices: 58523753--58523788 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
58523743 TTTAAAATAC
58523753 TTTTAAAAT-ATTTTTTAT
1 TTTTAAAATAATTTTTTAT
58523771 TTTTAAAATAATTTTTTA
1 TTTTAAAATAATTTTTTA
58523789 ATATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTAAAATAATTTTTTAT
Found at i:58546083 original size:38 final size:40
Alignment explanation
Indices: 58546017--58546106 Score: 112
Period size: 38 Copynumber: 2.3 Consensus size: 40
58546007 ATATTAAAAA
* * *
58546017 TATATCATATTAAAAAAACTACCATAAATATAATAAATCT
1 TATATTATATTAAAAAAACTAACATAAATATAATAAATAT
* *
58546057 TTTATTATATTAAAAACAC-AAC-TAAATATAATAAATAT
1 TATATTATATTAAAAAAACTAACATAAATATAATAAATAT
*
58546095 TATATTGTATTA
1 TATATTATATTA
58546107 GATATAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 25 0.58
39 2 0.05
40 16 0.37
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.38
Consensus pattern (40 bp):
TATATTATATTAAAAAAACTAACATAAATATAATAAATAT
Found at i:58546833 original size:18 final size:20
Alignment explanation
Indices: 58546803--58546843 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
58546793 TATTATTAAA
58546803 TAAAATATTAAAAATATT-T
1 TAAAATATTAAAAATATTAT
*
58546822 TAAAAT-TTAAAATTATTAT
1 TAAAATATTAAAAATATTAT
58546841 TAA
1 TAA
58546844 TGCTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAAATATTAAAAATATTAT
Found at i:58547087 original size:80 final size:80
Alignment explanation
Indices: 58546938--58547088 Score: 207
Period size: 81 Copynumber: 1.9 Consensus size: 80
58546928 TATAAATATA
* * *
58546938 TATGTTTAATAATATAAACTTATGAGAAAATATTTGGTGCACCATCGGTGGCAAGTTTTAGACTC
1 TATGATTAATAATATAAAATTATGAGAAAATATTTGGTGCACCATCAGTGGCAAGTTTTAGACTC
58547003 CACAAGCTAATCATG
66 CACAAGCTAATCATG
* * * *
58547018 TATGATTAATGATATTAAAATTATGAGAAAATATTTGGTGTACTATCAGT-G-AAGGTTTTATAC
1 TATGATTAATAATA-TAAAATTATGAGAAAATATTTGGTGCACCATCAGTGGCAA-GTTTTAGAC
58547081 TCCACAAG
64 TCCACAAG
58547089 TAAGTTTAGG
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
79 2 0.03
80 29 0.47
81 31 0.50
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (80 bp):
TATGATTAATAATATAAAATTATGAGAAAATATTTGGTGCACCATCAGTGGCAAGTTTTAGACTC
CACAAGCTAATCATG
Found at i:58550588 original size:6 final size:6
Alignment explanation
Indices: 58550577--58550639 Score: 63
Period size: 6 Copynumber: 10.2 Consensus size: 6
58550567 AGGTAAATTG
** * * *
58550577 ATAAAA ATAAAA ATAAAA ATAAAA ATACTA ATAATA ATAATA ATAATA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
58550625 ATAATAA ACTAAAA A
1 ATAA-AA A-TAAAA A
58550640 ATGCAAAAGG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
6 43 0.84
7 5 0.10
8 3 0.06
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (6 bp):
ATAAAA
Found at i:58550600 original size:18 final size:18
Alignment explanation
Indices: 58550577--58550639 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
58550567 AGGTAAATTG
*
58550577 ATAAAAATAAAAATAAAA
1 ATAAAAATAATAATAAAA
* *
58550595 ATAAAAATACTAATAATA
1 ATAAAAATAATAATAAAA
*
58550613 ATAATAATAATAATAATAA
1 ATAAAAATAATAATAA-AA
58550632 ACTAAAAA
1 A-TAAAAA
58550640 ATGCAAAAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
18 29 0.81
19 2 0.06
20 5 0.14
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAAAAATAATAATAAAA
Found at i:58552133 original size:89 final size:89
Alignment explanation
Indices: 58551982--58552452 Score: 567
Period size: 89 Copynumber: 5.3 Consensus size: 89
58551972 TTTCACTTTT
* *
58551982 CAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGCAAATCAGATCGAAGACACCAGCTT
1 CAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGACACCAGCTT
*
58552047 GGCCTCTCTGAGTTTGCAGCGGAG
66 GGCCTCTCTGAGTTTGCAGTGGAG
* * * *
58552071 CAGACTGAAGATAACAGATCTTGTCTTCCTTTATTGGCAGCAAAGTAGATCGAAGACACCAGCCT
1 CAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGACACCAGCTT
* * *
58552136 GACCT-TATTGAGTTTGCAGTGAAG
66 GGCCTCT-CTGAGTTTGCAGTGGAG
* * * *
58552160 TAGACTAAAGATAGCAGATCTTGTCTTTCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGTCT
1 CAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGACACCAG-CT
* *
58552225 T-GCCTC-CTTGAGTTTGTAGCGGAG
65 TGGCCTCTC-TGAGTTTGCAGTGGAG
* * *
58552249 CAGACTAGAA-ATAGCAGATCTTGTCTTCCTATATTGGCAGCAAAGCAGATCGAAGGCACCAGCC
1 CAGACT-GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGACACCAGCT
* *
58552313 TGACCTCCCTGAGTTTGCAGTGGAG
65 TGGCCTCTCTGAGTTTGCAGTGGAG
* * * * *
58552338 CATAGTAAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAA-CAGATCGAAAACACCAGCC
1 CAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGC-AAAGCAGATCGAAGACACCAG-C
58552402 TT-GCCTCTCTGAGTTTGCAGTGGAG
64 TTGGCCTCTCTGAGTTTGCAGTGGAG
* ** * *
58552427 TAGGTTGAAGATTGTAGATCTTGTCT
1 CAGACTGAAGATAGCAGATCTTGTCT
58552453 CCCTAAGTAG
Statistics
Matches: 323, Mismatches: 49, Indels: 20
0.82 0.12 0.05
Matches are distributed among these distances:
88 5 0.02
89 308 0.95
90 10 0.03
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (89 bp):
CAGACTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCAAAGCAGATCGAAGACACCAGCTT
GGCCTCTCTGAGTTTGCAGTGGAG
Found at i:58552301 original size:178 final size:177
Alignment explanation
Indices: 58551982--58552426 Score: 644
Period size: 178 Copynumber: 2.5 Consensus size: 177
58551972 TTTCACTTTT
* *
58551982 CAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGCAGC-AAATCAGATCGAAGACACCAGCT
1 CAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAA-CAGATCGAAGACACCAGCT
*
58552046 TGGCCTCTCTGAGTTTGCAGCGGAGCAGACTGAAGATAACAGATCTTGTCTTCCTTTATTGGCAG
65 T-GCCTCTCTGAGTTTGCAGCGGAGCAGACTGAAGATAACAGATCTTGTCTTCCTATATTGGCAG
* * *
58552111 CAAAGTAGATCGAAGACACCAGCCTGACCTTATTGAGTTTGCAGTGAAG
129 CAAAGCAGATCGAAGACACCAGCCTGACCTCACTGAGTTTGCAGTGAAG
* * *
58552160 TAGACTAAAGATAGCAGATCTTGTCTTTCTGTATTGGCAGCGAAGCAGATCGAAGACACCAGTCT
1 CAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAACAGATCGAAGACACCAG-CT
* *
58552225 TGCCTC-CTTGAGTTTGTAGCGGAGCAGACTAGAA-ATAGCAGATCTTGTCTTCCTATATTGGCA
65 TGCCTCTC-TGAGTTTGCAGCGGAGCAGACT-GAAGATAACAGATCTTGTCTTCCTATATTGGCA
* * *
58552288 GCAAAGCAGATCGAAGGCACCAGCCTGACCTCCCTGAGTTTGCAGTGGAG
128 GCAAAGCAGATCGAAGACACCAGCCTGACCTCACTGAGTTTGCAGTGAAG
* * * *
58552338 CATAGTAAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAACAGATCGAAAACACCAGCCT
1 CAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAACAGATCGAAGACACCAG-CT
*
58552403 TGCCTCTCTGAGTTTGCAGTGGAG
65 TGCCTCTCTGAGTTTGCAGCGGAG
58552427 TAGGTTGAAG
Statistics
Matches: 238, Mismatches: 24, Indels: 10
0.88 0.09 0.04
Matches are distributed among these distances:
177 1 0.00
178 228 0.96
179 9 0.04
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (177 bp):
CAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAACAGATCGAAGACACCAGCTT
GCCTCTCTGAGTTTGCAGCGGAGCAGACTGAAGATAACAGATCTTGTCTTCCTATATTGGCAGCA
AAGCAGATCGAAGACACCAGCCTGACCTCACTGAGTTTGCAGTGAAG
Found at i:58552743 original size:97 final size:97
Alignment explanation
Indices: 58552627--58552968 Score: 463
Period size: 97 Copynumber: 3.5 Consensus size: 97
58552617 CGAATCTTAT
* * * * * * *
58552627 TTTCC-TGGCGTTGCAGTGGAACAGATTAAATCTGAAGGTAGCGAGTCTTATTTCCCTGGCGTCA
1 TTTCCTTGGCGTTGCAGTGGAGCAGATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGTGTCG
*
58552691 CAGCAGATTAAAGCTGAAGGCAGCAAGTCTCA
66 CAGTAGATTAAAGCTGAAGGCAGCAAGTCTCA
* * *
58552723 TTTCCTTGGCGTTGGAGTGGAGCAGATTAAAGCTAAAGGCAGCAAATCTTATCTT-TCTGGTGTC
1 TTTCCTTGGCGTTGCAGTGGAGCAGATTAAAGCTGAAGGCAGCAAATCTTAT-TTCCCTGGTGTC
* * * *
58552787 GTAGTAGATTAAAGCTAAAGGCAGCAAATTTCA
65 GCAGTAGATTAAAGCTGAAGGCAGCAAGTCTCA
* * * *
58552820 TTTCCTTAGTGTTGCAGTGGAGCAGATTAAAGCTTAAGGCAGCAAATCTTATCTCCCTGGTGTCG
1 TTTCCTTGGCGTTGCAGTGGAGCAGATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGTGTCG
*
58552885 CAATAGATTAAAGCTGAAGGCAGCAAGTCTCA
66 CAGTAGATTAAAGCTGAAGGCAGCAAGTCTCA
* *
58552917 TTTCCTTGGCATTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCAAATCTTAT
1 TTTCCTTGGCGTTGCAGTGGAGCAGATTAAAGCTGAAGGCAGCAAATCTTAT
58552969 ATCCTTGGAG
Statistics
Matches: 212, Mismatches: 31, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
96 6 0.03
97 204 0.96
98 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (97 bp):
TTTCCTTGGCGTTGCAGTGGAGCAGATTAAAGCTGAAGGCAGCAAATCTTATTTCCCTGGTGTCG
CAGTAGATTAAAGCTGAAGGCAGCAAGTCTCA
Found at i:58552974 original size:51 final size:51
Alignment explanation
Indices: 58552619--58552976 Score: 302
Period size: 51 Copynumber: 7.3 Consensus size: 51
58552609 GAAGACAACG
** * * *
58552619 AATCTTATTTTCC-TGGCGTTGCAGTGGAACAGATTAAATCTGAAGGTAGCG
1 AATCTTA-TTTCCTTGGCGTTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
* * * *
58552670 AGTCTTATTTCCCTGGCG-T-CA---CAGCAGATTAAAGCTGAAGGCAGCA
1 AATCTTATTTCCTTGGCGTTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
* * * * *
58552716 AGTCTCATTTCCTTGGCGTTGGAGTGGAGCAGATTAAAGCTAAAGGCAGCA
1 AATCTTATTTCCTTGGCGTTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
* * *
58552767 AATCTTATCTTTC-TGGTG-T-C-GT--AGTAGATTAAAGCTAAAGGCAGCA
1 AATCTTAT-TTCCTTGGCGTTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
* * * *
58552813 AAT-TTCATTTCCTTAGTGTTGCAGTGGAGCAGATTAAAGCTTAAGGCAGCA
1 AATCTT-ATTTCCTTGGCGTTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
* * * *
58552864 AATCTTATCTCCCTGGTGTCGCA----A-TAGATTAAAGCTGAAGGCAGCA
1 AATCTTATTTCCTTGGCGTTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
* * *
58552910 AGTCTCATTTCCTTGGCATTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
1 AATCTTATTTCCTTGGCGTTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
*
58552961 AATCTTATATCCTTGG
1 AATCTTATTTCCTTGG
58552977 AGTTAAGATT
Statistics
Matches: 250, Mismatches: 37, Indels: 40
0.76 0.11 0.12
Matches are distributed among these distances:
45 5 0.02
46 104 0.42
47 3 0.01
48 4 0.02
49 4 0.02
50 8 0.03
51 117 0.47
52 5 0.02
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (51 bp):
AATCTTATTTCCTTGGCGTTGCAGTGGAGTAGATTAAAGCTGAAGGCAGCA
Found at i:58555116 original size:22 final size:23
Alignment explanation
Indices: 58555047--58555128 Score: 89
Period size: 22 Copynumber: 3.7 Consensus size: 23
58555037 CTTAACTATG
**
58555047 TTTTAAATTTATCATTAGCATTA
1 TTTTAAATTTATCATTAATATTA
* * *
58555070 TTTT-AATATATAATATACTATTA
1 TTTTAAATTTATCAT-TAATATTA
58555093 TTTTAAA-TTATCATTAATATTA
1 TTTTAAATTTATCATTAATATTA
58555115 -TTTAAATTTATCAT
1 TTTTAAATTTATCAT
58555129 ACATCATAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
21 6 0.12
22 22 0.45
23 19 0.39
24 2 0.04
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (23 bp):
TTTTAAATTTATCATTAATATTA
Found at i:58555146 original size:45 final size:45
Alignment explanation
Indices: 58555048--58555147 Score: 103
Period size: 45 Copynumber: 2.2 Consensus size: 45
58555038 TTAACTATGT
* * * * *
58555048 TTTAAATTTATCATTAGCATTATTTTAATATATAATATACTATTA
1 TTTAAAATTATCATTAACATTATTTAAATATATAATACACTATAA
* * * *
58555093 TTTTAAATTATCATTAATATTATTTAAATTTATCATACA-TCATAA
1 TTTAAAATTATCATTAACATTATTTAAATATATAATACACT-ATAA
58555138 TTTAAAATTA
1 TTTAAAATTA
58555148 ATATATTTTG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
44 1 0.02
45 43 0.98
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.50
Consensus pattern (45 bp):
TTTAAAATTATCATTAACATTATTTAAATATATAATACACTATAA
Found at i:58556749 original size:40 final size:39
Alignment explanation
Indices: 58556693--58556811 Score: 159
Period size: 40 Copynumber: 3.0 Consensus size: 39
58556683 TATTGTTAGA
*
58556693 TGTGCGAGTTATTAATTCCGGGTTAAGTCCCGAAGGCCTT
1 TGTGCGAG-TATTAATTCCGGGTTAAGTCCCGAAGGCATT
*
58556733 TGTGCGAGATACTAATTCCGGGTTAAGT-CCGAAGGCATT
1 TGTGCGAG-TATTAATTCCGGGTTAAGTCCCGAAGGCATT
* * *
58556772 CGTGCGAGTTTTAAAATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTATT-AATTCCGGGTTAAGTCCCGAAGGCATT
58556812 GTATGANNNN
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
38 2 0.03
39 31 0.44
40 37 0.53
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (39 bp):
TGTGCGAGTATTAATTCCGGGTTAAGTCCCGAAGGCATT
Found at i:58567088 original size:24 final size:24
Alignment explanation
Indices: 58567061--58567108 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
58567051 GTTCATGAAC
*
58567061 AAGCTCGTCCATTGGCTCATTTAT
1 AAGCTCGTCCATTGACTCATTTAT
* **
58567085 AAGCTCTTTTATTGACTCATTTAT
1 AAGCTCGTCCATTGACTCATTTAT
58567109 TTATTAATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (24 bp):
AAGCTCGTCCATTGACTCATTTAT
Found at i:58567251 original size:24 final size:24
Alignment explanation
Indices: 58567224--58567269 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
58567214 TTATTAACAT
*
58567224 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAAAATGTTCAATTATA
* *
58567248 TGTTCGTTAAAATGTTCGATTA
1 TGTTCGTGAAAATGTTCAATTA
58567270 AGTTAAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (24 bp):
TGTTCGTGAAAATGTTCAATTATA
Found at i:58567353 original size:26 final size:27
Alignment explanation
Indices: 58567291--58567355 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 27
58567281 CATGTTCGTG
58567291 AAAA-TTAAATAAACGAACAGGAACAC
1 AAAATTTAAATAAACGAACAGGAACAC
*
58567317 ACATAATTTTAAATAAACGAACATGAACA-
1 A-A-AA-TTTAAATAAACGAACAGGAACAC
58567346 AAAATTTAAA
1 AAAATTTAAA
58567356 ATTCTTAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
26 7 0.21
27 3 0.09
28 3 0.09
29 1 0.03
30 20 0.59
ACGTcount: A:0.60, C:0.12, G:0.08, T:0.20
Consensus pattern (27 bp):
AAAATTTAAATAAACGAACAGGAACAC
Found at i:58571840 original size:61 final size:62
Alignment explanation
Indices: 58571662--58571840 Score: 152
Period size: 61 Copynumber: 2.9 Consensus size: 62
58571652 TTAGTCTAGT
* ** * *
58571662 AACAAAATTAGCCCTCTAATGTTTAC-ATATTCTATCAATTT-GATCTTAAATATAAAAAAAATT
1 AACAAATTTAGCCCTC-AACATTTACAAAATT-TATCAATTTAG-TCTTAAATCT-AAAAAAATT
58571725 C
62 C
* * * * * *
58571726 AACAAATTTAGCTCTCAATATTTACAAAATTTTTCATTTTAAT-TCTAATTCTAAAAAAATT-
1 AACAAATTTAGCCCTCAACATTTACAAAATTTATCAATTTAGTCT-TAAATCTAAAAAAATTC
* *
58571787 AATAAATTT-GACCCTCAACATTTACAAAATTTATCAATTTAGTCTTAACTCTAA
1 AACAAATTTAG-CCCTCAACATTTACAAAATTTATCAATTTAGTCTTAAATCTAA
58571841 TTTAAAAAAA
Statistics
Matches: 94, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
60 1 0.01
61 43 0.46
62 11 0.12
63 21 0.22
64 18 0.19
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (62 bp):
AACAAATTTAGCCCTCAACATTTACAAAATTTATCAATTTAGTCTTAAATCTAAAAAAATTC
Found at i:58572322 original size:61 final size:62
Alignment explanation
Indices: 58572257--58572385 Score: 156
Period size: 61 Copynumber: 2.1 Consensus size: 62
58572247 AAGGGGAAAG
*
58572257 TTTATTGAATTTTTTAGAATTAGAACTAAAA-TGA-AAAATTTTGTAAACAAT-GAGGGCTAAA
1 TTTATTGAATTTTTTAGAATTAGAA-TAAAATTGATAAAA-TATGTAAACAATAGAGGGCTAAA
* * * * * *
58572318 TTTATTGAATTTTTTATATTTAGGATAAAATTGATAGAATATGTAAACATTAGAGGGCTAAT
1 TTTATTGAATTTTTTAGAATTAGAATAAAATTGATAAAATATGTAAACAATAGAGGGCTAAA
58572380 TTTATT
1 TTTATT
58572386 ACTAGACCAA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
60 5 0.09
61 35 0.60
62 18 0.31
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.41
Consensus pattern (62 bp):
TTTATTGAATTTTTTAGAATTAGAATAAAATTGATAAAATATGTAAACAATAGAGGGCTAAA
Found at i:58580333 original size:40 final size:40
Alignment explanation
Indices: 58580278--58580368 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
58580268 TTCAAATTAT
*
58580278 TGAAAAGGTTGAAAAGGATACATCTAAAACGAATATCTAA
1 TGAAAAGGTTGAAAAGGATACATCCAAAACGAATATCTAA
* * * *
58580318 TGAAAATGTTGAAAAGGATATATCCGAAAGGAATATCT-A
1 TGAAAAGGTTGAAAAGGATACATCCAAAACGAATATCTAA
58580357 TCGAAAAGGTTG
1 T-GAAAAGGTTG
58580369 TTACCCTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
39 2 0.05
40 42 0.95
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.24
Consensus pattern (40 bp):
TGAAAAGGTTGAAAAGGATACATCCAAAACGAATATCTAA
Found at i:58581008 original size:22 final size:23
Alignment explanation
Indices: 58580980--58581024 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
58580970 ATGCAATTTT
58580980 AGATATGA-TATGCAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
* *
58581002 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGCAATCTTAGA
58581025 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (23 bp):
AGATATGATTATGCAATCTTAGA
Found at i:58588988 original size:7 final size:7
Alignment explanation
Indices: 58588976--58589000 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
58588966 TTTAATTAAA
58588976 TTACCTT
1 TTACCTT
58588983 TTACCTT
1 TTACCTT
58588990 TTACCTT
1 TTACCTT
58588997 TTAC
1 TTAC
58589001 TAAATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (7 bp):
TTACCTT
Found at i:58598413 original size:38 final size:38
Alignment explanation
Indices: 58598361--58598439 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
58598351 AAATTTTATT
*
58598361 ACACCAACAATAAGCATGCTCGGCACAAAGCCT-AAATA
1 ACACCAACAATAAGCATGCTAGGCACAAAGCCTGAAA-A
* * *
58598399 ACACCAGCACTAAGCCTGCTAGGCACAAAGCCTGAAAA
1 ACACCAACAATAAGCATGCTAGGCACAAAGCCTGAAAA
58598437 ACA
1 ACA
58598440 ATATACTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 33 0.92
39 3 0.08
ACGTcount: A:0.43, C:0.30, G:0.15, T:0.11
Consensus pattern (38 bp):
ACACCAACAATAAGCATGCTAGGCACAAAGCCTGAAAA
Found at i:58600115 original size:3 final size:3
Alignment explanation
Indices: 58600107--58600133 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
58600097 TCCCATTAAT
58600107 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
58600134 CGTTCTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:58602281 original size:17 final size:18
Alignment explanation
Indices: 58602248--58602281 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
58602238 TATGACTTGA
*
58602248 TAAATGATAATATAATTT
1 TAAATGATAATAAAATTT
58602266 TAAATGA-AATAAAATT
1 TAAATGATAATAAAATT
58602282 AAATAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
TAAATGATAATAAAATTT
Found at i:58602283 original size:15 final size:15
Alignment explanation
Indices: 58602265--58602298 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
58602255 TAATATAATT
58602265 TTAAAT-GAAATAAAA
1 TTAAATAGAAA-AAAA
58602280 TTAAATAGAAAAAAA
1 TTAAATAGAAAAAAA
58602295 TTAA
1 TTAA
58602299 TTTTATTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (15 bp):
TTAAATAGAAAAAAA
Found at i:58608055 original size:19 final size:20
Alignment explanation
Indices: 58608011--58608057 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
58608001 TATAGATTTT
58608011 AAATTTTATTTATTAATATA
1 AAATTTTATTTATTAATATA
**
58608031 TTATTTTATTT-TTAA-ATAA
1 AAATTTTATTTATTAATAT-A
58608050 AAATTTTA
1 AAATTTTA
58608058 AAAAATATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 2 0.09
19 11 0.50
20 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AAATTTTATTTATTAATATA
Found at i:58608861 original size:33 final size:33
Alignment explanation
Indices: 58608819--58608884 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
58608809 CGTTCCTTTG
58608819 GAGGTTATAGAGGGTTTTGTTTTTGGTGGCTGC
1 GAGGTTATAGAGGGTTTTGTTTTTGGTGGCTGC
58608852 GAGGTTATAGAGGGTTTTGTTTTTGGTGGCTGC
1 GAGGTTATAGAGGGTTTTGTTTTTGGTGGCTGC
58608885 CTTAGGTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.12, C:0.06, G:0.39, T:0.42
Consensus pattern (33 bp):
GAGGTTATAGAGGGTTTTGTTTTTGGTGGCTGC
Found at i:58623436 original size:42 final size:42
Alignment explanation
Indices: 58623351--58623436 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
58623341 AAAGAGGATC
* * * *
58623351 AAGGTGAAAACTCACAAAGGGCGCTTTGAGTTCTAAACAAAT
1 AAGGTGAAAACCCACAAAGGGCGCTTGGAGTTCCAAAAAAAT
*
58623393 AAGGTGAAAACCCGCAAAGGGCGCTTGGAG-TCCAAAAATAAT
1 AAGGTGAAAACCCACAAAGGGCGCTTGGAGTTCCAAAAA-AAT
58623435 AA
1 AA
58623437 TAAAATGATG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
41 6 0.16
42 32 0.84
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.17
Consensus pattern (42 bp):
AAGGTGAAAACCCACAAAGGGCGCTTGGAGTTCCAAAAAAAT
Found at i:58624865 original size:89 final size:89
Alignment explanation
Indices: 58624700--58624884 Score: 282
Period size: 89 Copynumber: 2.1 Consensus size: 89
58624690 ATGGATTGAA
*
58624700 GAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGAGAAGTAGATCGAAGACACCAACCTCGCCTC
1 GAAGATAGCAGATCTTGTCTTCCTCTATTGGCAGAGAAGTAGATCGAAGACACCAACCTCGCCTC
*
58624765 CCTAAGTTTGCAGCGGAAC-AGACT
66 CCTAAGCTTGCAGCGGAACTA-ACT
* *
58624789 GAAGATAGCAGATCTTGTCTTCCTCTATTGGCAGTGAAGTAGATCGAAGACACCAGCCTCGCCTC
1 GAAGATAGCAGATCTTGTCTTCCTCTATTGGCAGAGAAGTAGATCGAAGACACCAACCTCGCCTC
* * * *
58624854 CTTGAGCTTGCAGTGGAGCTAACT
66 CCTAAGCTTGCAGCGGAACTAACT
58624878 GAAGATA
1 GAAGATA
58624885 ACCAACCTTA
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
89 86 0.99
90 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (89 bp):
GAAGATAGCAGATCTTGTCTTCCTCTATTGGCAGAGAAGTAGATCGAAGACACCAACCTCGCCTC
CCTAAGCTTGCAGCGGAACTAACT
Found at i:58624948 original size:44 final size:44
Alignment explanation
Indices: 58624877--58625367 Score: 245
Period size: 44 Copynumber: 10.9 Consensus size: 44
58624867 TGGAGCTAAC
*
58624877 TGAAGATAACCAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
1 TGAAGAT-ACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
*
58624922 TGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
1 TGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
* ** * * * * *
58624966 TGAAGCTATTAATCATATCTCCCTAAAGTTGTAATGGAG-TGGAT
1 TGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGG-T
* * *
58625010 TAGAACGAT--CAATCCTATAC-CCCTAAAGTTCCAGTGG-G-ATGGAT
1 T-GAA-GATACCAATCTTAT-CTCCCTGAAGTTGCAGTGGAGCA-GG-T
* **
58625054 TGAAG-TCATCGTGGCAAATCTTATCTCCCTGAAGTTGCAGCGGAGCAGAC
1 TGAAGAT-A-C----C-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
* * * * *
58625104 TGAAGATAGCGAATCTTATTTCCCTGAAGTTGTAGGGGAGCAGAT
1 TGAAGATA-CCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
* * * *
58625149 TGAAGCTATACACTACAGATCTTATCTCTCTAAAGTTGCAGTAGAACA---
1 TGAAG--AT--AC--CA-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
** * * * * * *
58625197 -GATCATATCAAACTTATCCCCCCTAAAGTTGCAGTAGG-GTATGT
1 TGAAGATACCAATCTTAT-CTCCCTGAAGTTGCAGT-GGAGCAGGT
* * * * *
58625241 TGAA-ATTGCAAACCTTATCTTCCTGAAGTTGCAATGGAGCAGGT
1 TGAAGA-TACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
* * *
58625285 TGAAGATA-CAATCTTACCTCCCTGAAGTTGCAGTGGAGTAGAT
1 TGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
* ** * *
58625328 TGAAGCTATTAATCCTATCTCCCTGAAGTTACAGTGGAGC
1 TGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGC
58625368 GGACTAAAAC
Statistics
Matches: 339, Mismatches: 72, Indels: 71
0.70 0.15 0.15
Matches are distributed among these distances:
40 6 0.02
41 19 0.06
42 2 0.01
43 43 0.13
44 144 0.42
45 59 0.17
46 2 0.01
47 4 0.01
48 1 0.00
49 3 0.01
50 29 0.09
51 26 0.08
52 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
TGAAGATACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGGT
Found at i:58625331 original size:43 final size:44
Alignment explanation
Indices: 58625262--58625367 Score: 133
Period size: 43 Copynumber: 2.4 Consensus size: 44
58625252 ACCTTATCTT
* * *
58625262 CCTGAAGTTGCAATGGAGCAGGTTGAAGATA-CAATCTTACCTC
1 CCTGAAGTTGCAGTGGAGCAGATTGAAGATATCAATCCTACCTC
* * * *
58625305 CCTGAAGTTGCAGTGGAGTAGATTGAAGCTATTAATCCTATCTC
1 CCTGAAGTTGCAGTGGAGCAGATTGAAGATATCAATCCTACCTC
*
58625349 CCTGAAGTTACAGTGGAGC
1 CCTGAAGTTGCAGTGGAGC
58625368 GGACTAAAAC
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 27 0.51
44 26 0.49
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (44 bp):
CCTGAAGTTGCAGTGGAGCAGATTGAAGATATCAATCCTACCTC
Found at i:58625386 original size:44 final size:44
Alignment explanation
Indices: 58625302--58625389 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
58625292 ACAATCTTAC
* * * * * * *
58625302 CTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTATTAATCCTAT
1 CTCCCTGAAGTTACAGTGGAGCAGACTAAAACGATGAATCCTAT
*
58625346 CTCCCTGAAGTTACAGTGGAGCGGACTAAAACGATGAATCCTAT
1 CTCCCTGAAGTTACAGTGGAGCAGACTAAAACGATGAATCCTAT
58625390 ACCTCTAAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
CTCCCTGAAGTTACAGTGGAGCAGACTAAAACGATGAATCCTAT
Found at i:58625756 original size:27 final size:27
Alignment explanation
Indices: 58625725--58625781 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
58625715 AAGTCAAGAA
58625725 TCTGTGAGACCGGGCAAGATTGGTCTT
1 TCTGTGAGACCGGGCAAGATTGGTCTT
58625752 TCTGTGAGACCGGGCAAGATTGGTCTT
1 TCTGTGAGACCGGGCAAGATTGGTCTT
58625779 TCT
1 TCT
58625782 TAGTTTCTGT
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:0.18, C:0.19, G:0.32, T:0.32
Consensus pattern (27 bp):
TCTGTGAGACCGGGCAAGATTGGTCTT
Found at i:58627178 original size:3 final size:3
Alignment explanation
Indices: 58627170--58627208 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
58627160 ATAGGTTTGA
* * *
58627170 TAT TAT TAT TAT TAC TAT TGT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
58627209 ATTTCTATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:58627220 original size:15 final size:15
Alignment explanation
Indices: 58627170--58627217 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
58627160 ATAGGTTTGA
58627170 TATTATTATTATTAC
1 TATTATTATTATTAC
*
58627185 TATTGTTATTATTAC
1 TATTATTATTATTAC
*
58627200 TATTATTA-TATTTC
1 TATTATTATTATTAC
58627214 TATT
1 TATT
58627218 TATATTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
14 9 0.30
15 21 0.70
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.62
Consensus pattern (15 bp):
TATTATTATTATTAC
Found at i:58632932 original size:22 final size:22
Alignment explanation
Indices: 58632888--58632932 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
58632878 AATTTATAAA
**
58632888 ATATGAAATTTTGTGATTTATT
1 ATATGAAATTTTGTGATAAATT
58632910 ATATG-AATTTTGTGCATAAATT
1 ATATGAAATTTTGTG-ATAAATT
58632932 A
1 A
58632933 AATTAATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (22 bp):
ATATGAAATTTTGTGATAAATT
Found at i:58635681 original size:25 final size:24
Alignment explanation
Indices: 58635613--58635694 Score: 64
Period size: 25 Copynumber: 3.3 Consensus size: 24
58635603 CGGACTCACC
*
58635613 ACAGCTCGTATGAGCTTACCTATTT
1 ACAGCTCGTATGAGATTA-CTATTT
58635638 ACAGCTC--ATGAGAGCTTACTGATTCT
1 ACAGCTCGTATGAGA--TTACT-ATT-T
58635664 -CAGCTCGTATGAGATTACCATATTT
1 ACAGCTCGTATGAGATTA-C-TATTT
58635689 -CAGCTC
1 ACAGCTC
58635695 AGAAAATACC
Statistics
Matches: 48, Mismatches: 1, Indels: 16
0.74 0.02 0.25
Matches are distributed among these distances:
23 5 0.10
24 2 0.04
25 29 0.60
26 5 0.10
27 7 0.15
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (24 bp):
ACAGCTCGTATGAGATTACTATTT
Found at i:58645065 original size:19 final size:15
Alignment explanation
Indices: 58645024--58645060 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
58645014 TTGTTAAATA
58645024 TTAAATATTTTCATG
1 TTAAATATTTTCATG
58645039 TTAAATATTTTCATG
1 TTAAATATTTTCATG
58645054 TTAAATA
1 TTAAATA
58645061 AATATAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.51
Consensus pattern (15 bp):
TTAAATATTTTCATG
Found at i:58651974 original size:29 final size:26
Alignment explanation
Indices: 58651937--58651994 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 26
58651927 TTTGTAAGTT
*
58651937 TTTATAATATTTTGAATTTTTATTATAA
1 TTTATAATATTTT-AACTTTT-TTATAA
*
58651965 TTTAGTAATATTTTTACTTTTTTATAA
1 TTTA-TAATATTTTAACTTTTTTATAA
58651992 TTT
1 TTT
58651995 TTAAACTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 9 0.33
28 9 0.33
29 9 0.33
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (26 bp):
TTTATAATATTTTAACTTTTTTATAA
Found at i:58658801 original size:39 final size:41
Alignment explanation
Indices: 58658747--58658868 Score: 131
Period size: 39 Copynumber: 3.0 Consensus size: 41
58658737 ATGGTCTTTG
* * *
58658747 GCGTTTGTGGGGAAAGCGTCGCTAAAGGTCATGTCTTTAGCT
1 GCGTTTGT-GAGAAAGCGCCGCTAAAGGTCATGTCTTTAGCA
* *
58658789 GTG-TT-TGAGAAAGTGCCGCTAAAGGTCATGTTCTTTAGCA
1 GCGTTTGTGAGAAAGCGCCGCTAAAGGTCATG-TCTTTAGCA
* * *
58658829 GCGTTTGTGAGAAAAGCACCACTAAAGGTCATGTTTTTAG
1 GCGTTTGTGAG-AAAGCGCCGCTAAAGGTCATGTCTTTAG
58658869 TGGCATTTAT
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
39 21 0.32
40 11 0.17
41 4 0.06
42 12 0.18
43 18 0.27
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.31
Consensus pattern (41 bp):
GCGTTTGTGAGAAAGCGCCGCTAAAGGTCATGTCTTTAGCA
Found at i:58658862 original size:43 final size:40
Alignment explanation
Indices: 58658768--58658868 Score: 116
Period size: 43 Copynumber: 2.5 Consensus size: 40
58658758 GAAAGCGTCG
* * ** *
58658768 CTAAAGGTCATG-TCTTTAGCTGTGTTTGAGAAAGTGCCG
1 CTAAAGGTCATGTTCTTTAGCAGCGTTTGAGAAAGCACCA
58658807 CTAAAGGTCATGTTCTTTAGCAGCGTTTGTGAGAAAAGCACCA
1 CTAAAGGTCATGTTCTTTAGCAGCG-TT-TGAG-AAAGCACCA
58658850 CTAAAGGTCATGTT-TTTAG
1 CTAAAGGTCATGTTCTTTAG
58658869 TGGCATTTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
39 12 0.23
40 10 0.19
41 2 0.04
42 9 0.17
43 20 0.38
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.33
Consensus pattern (40 bp):
CTAAAGGTCATGTTCTTTAGCAGCGTTTGAGAAAGCACCA
Found at i:58659787 original size:20 final size:21
Alignment explanation
Indices: 58659721--58659789 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 21
58659711 AAATTACAAA
58659721 AAAAAATTCAAAATAATTT-T
1 AAAAAATTCAAAATAATTTAT
** * *
58659741 ATGAGATTAAAAATAATTGTA-
1 AAAAAATTCAAAATAATT-TAT
58659762 AAAAAATTCAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTTAT
58659782 AAAAAATT
1 AAAAAATT
58659790 TTAAAAATAA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 2 0.05
20 25 0.66
21 11 0.29
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.33
Consensus pattern (21 bp):
AAAAAATTCAAAATAATTTAT
Found at i:58659795 original size:21 final size:21
Alignment explanation
Indices: 58659720--58659787 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
58659710 AAAATTACAA
58659720 AAAAAAATTCAAAATAATT-T
1 AAAAAAATTCAAAATAATTAT
* ** * * *
58659740 TATGAGATTAAAAATAATTGT
1 AAAAAAATTCAAAATAATTAT
*
58659761 AAAAAAATTCAAAATATTTAT
1 AAAAAAATTCAAAATAATTAT
58659782 AAAAAA
1 AAAAAA
58659788 TTTTAAAAAT
Statistics
Matches: 35, Mismatches: 12, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAAAAATTCAAAATAATTAT
Found at i:58659802 original size:28 final size:28
Alignment explanation
Indices: 58659771--58659841 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
58659761 AAAAAAATTC
*
58659771 AAAATATTTATAAAAAATTTTAAAA-ATA
1 AAAATATTTATAAAAAA-GTTAAAATATA
* * *
58659799 AAAAAATATATAAAAAAGTTAAAATTTA
1 AAAATATTTATAAAAAAGTTAAAATATA
* *
58659827 AAAATTTTTGTAAAA
1 AAAATATTTATAAAA
58659842 CAATAATTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
27 6 0.18
28 28 0.82
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAATATTTATAAAAAAGTTAAAATATA
Found at i:58659829 original size:27 final size:28
Alignment explanation
Indices: 58659764--58659830 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
58659754 TAATTGTAAA
* * * *
58659764 AAAATTCAAAATATTTATAAAAAATTTT
1 AAAATTAAAAAAATATATAAAAAATGTT
*
58659792 AAAAATAAAAAAATATATAAAAAA-GTT
1 AAAATTAAAAAAATATATAAAAAATGTT
*
58659819 AAAATTTAAAAA
1 AAAATTAAAAAA
58659831 TTTTTGTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 12 0.38
28 20 0.62
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (28 bp):
AAAATTAAAAAAATATATAAAAAATGTT
Found at i:58661599 original size:11 final size:11
Alignment explanation
Indices: 58661579--58661621 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
58661569 AGATAAATGT
*
58661579 TATTTAATTAA
1 TATTTTATTAA
58661590 TATTTTATTAA
1 TATTTTATTAA
* * *
58661601 GATTTTAGTAT
1 TATTTTATTAA
58661612 TATTTTATTA
1 TATTTTATTA
58661622 TTAAATGATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:58667377 original size:9 final size:9
Alignment explanation
Indices: 58667339--58667375 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
58667329 CTATTTTTTG
58667339 ATATTATTA
1 ATATTATTA
58667348 ATATTATTTA
1 ATATTA-TTA
58667358 ATATTATTA
1 ATATTATTA
*
58667367 TTATTATTA
1 ATATTATTA
58667376 TTTCATTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
ATATTATTA
Found at i:58667700 original size:16 final size:16
Alignment explanation
Indices: 58667679--58667712 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58667669 CGTTTTATAA
* *
58667679 TACATATGCATTTTTT
1 TACATATACATGTTTT
58667695 TACATATACATGTTTT
1 TACATATACATGTTTT
58667711 TA
1 TA
58667713 GAAATTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (16 bp):
TACATATACATGTTTT
Found at i:58679789 original size:132 final size:132
Alignment explanation
Indices: 58679490--58679949 Score: 735
Period size: 132 Copynumber: 3.5 Consensus size: 132
58679480 ATCATAAAGC
*
58679490 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCT-AAGGTTATA
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAA-GTTACA
58679554 GTGGAGTACATTGAAGCCAGTAATTCTATCT-CCTGGGCAGCAGTGGAATAGATTGAAGATTACA
65 GTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACA
58679618 GAT
130 GAT
* * * * *
58679621 CTTATCTCCCTAAACAGTAGTGGAGTAGATCAAAGATGGTGGATTTTACCTCCCTGAAGTTACAA
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAG
* * * * *
58679686 TGGAGTACATTGAAGCCAGTAATTCTATCTCCCTAGGTAGCAGTGGAATATATTGAAGTTTACGG
66 TGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAG
58679751 AT
131 AT
* * *
58679753 CTTATCCCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTATCTCCCTGAGGTTACAG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAG
*
58679818 TGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGTAGTGGAATAGATTGAAGATTACAG
66 TGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAG
58679883 AT
131 AT
* * *
58679885 CTTATCTCCCTAAGCAATAGTGGAACAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAG
1 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAG
58679950 CTATTATACC
Statistics
Matches: 298, Mismatches: 29, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
131 86 0.29
132 212 0.71
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTACAG
TGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAG
AT
Found at i:58679891 original size:44 final size:44
Alignment explanation
Indices: 58679580--58679921 Score: 137
Period size: 44 Copynumber: 7.8 Consensus size: 44
58679570 CCAGTAATTC
* *
58679580 TATCT-CCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTAGGCAGTAGTGGAATAGATTGAAGATTACAGATCT
** * ** **** *
58679623 TATCTCCCTAAACAGTAGTGGAGTAGATCAAAGATGGTGGATTT
1 TATCTCCCTAGGCAGTAGTGGAATAGATTGAAGATTACAGATCT
* * * * * * *
58679667 TACCTCCCT--GAAGTTACAATGGAGTACATTGAAGCCAGTA-A-TTC-
1 TATCTCCCTAGGCAG-T--AGTGGAATAGATTGAAG--ATTACAGATCT
* * * * *
58679711 TATCTCCCTAGGTAGCAGTGGAATATATTGAAGTTTACGGATCT
1 TATCTCCCTAGGCAGTAGTGGAATAGATTGAAGATTACAGATCT
* * ** * ** * *
58679755 TATCCCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTT
1 TATCTCCCTAGGCAGTAGTGGAATAGATTGAAGATTACAGATCT
* * * * * *
58679799 TATCTCCCTGAGGTTA-CAGTGGAGTACATTGAAGCCAGTA-A-TTC-
1 TATCTCCCT-AGG-CAGTAGTGGAATAGATTGAAG--ATTACAGATCT
*
58679843 TATCTCCCTGGGCAGTAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTAGGCAGTAGTGGAATAGATTGAAGATTACAGATCT
* * * *
58679887 TATCTCCCTAAGCAATAGTGGAACAGATCGAAGAT
1 TATCTCCCTAGGCAGTAGTGGAATAGATTGAAGAT
58679922 GGCGGATTTT
Statistics
Matches: 208, Mismatches: 72, Indels: 37
0.66 0.23 0.12
Matches are distributed among these distances:
41 5 0.02
42 4 0.02
43 41 0.20
44 121 0.58
45 31 0.15
46 4 0.02
47 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (44 bp):
TATCTCCCTAGGCAGTAGTGGAATAGATTGAAGATTACAGATCT
Found at i:58684894 original size:18 final size:18
Alignment explanation
Indices: 58684852--58684887 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
58684842 ATACCATTAA
58684852 CACCCCTTGTTGGGCAAC
1 CACCCCTTGTTGGGCAAC
58684870 CACCCCTTGTTGGGCAAC
1 CACCCCTTGTTGGGCAAC
58684888 GGCCCCTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.39, G:0.22, T:0.22
Consensus pattern (18 bp):
CACCCCTTGTTGGGCAAC
Found at i:58685300 original size:101 final size:101
Alignment explanation
Indices: 58685128--58685324 Score: 286
Period size: 101 Copynumber: 2.0 Consensus size: 101
58685118 AACCTGACTT
* * * * *
58685128 GTTTCTTAGGCCTTTGAATAGAACTAGAGGGCTCTAAATCCCTCTTGCTCTTACCCCTCTCAAGG
1 GTTTCTTAGGCCTCTAAACAGAACTAGAGGGCTCCAAATCCCTCTTACTCTTACCCCTCTCAAGG
*
58685193 TCCCTATTTTCGCATTGAGAGCGTTTAACCTAGCTC
66 TCCCTATTTTCGCATTGAGAGCGCTTAACCTAGCTC
* * *
58685229 GTTTCTTAGGCCTCTAAACAGAACTAGAGGGCTCCAAATCCCTCTTACTCTTACCCTTTTCATGG
1 GTTTCTTAGGCCTCTAAACAGAACTAGAGGGCTCCAAATCCCTCTTACTCTTACCCCTCTCAAGG
* * *
58685294 TTCCTATTTTTGCATTGAGAGTGCTTAACCT
66 TCCCTATTTTCGCATTGAGAGCGCTTAACCT
58685325 CATCGGTAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 84 1.00
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (101 bp):
GTTTCTTAGGCCTCTAAACAGAACTAGAGGGCTCCAAATCCCTCTTACTCTTACCCCTCTCAAGG
TCCCTATTTTCGCATTGAGAGCGCTTAACCTAGCTC
Found at i:58689214 original size:22 final size:22
Alignment explanation
Indices: 58689186--58689233 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
58689176 CTTGAATTTT
*
58689186 TAAATTC-AAAAAATATAAATA
1 TAAATTCTAAAAAATAAAAATA
*
58689207 CTAAATTCTTAAAAATAAAAATA
1 -TAAATTCTAAAAAATAAAAATA
58689230 TAAA
1 TAAA
58689234 AATTAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAATTCTAAAAAATAAAAATA
Found at i:58689540 original size:76 final size:76
Alignment explanation
Indices: 58689453--58689604 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
58689443 CACATATGTT
58689453 GATATATTAGACGATTATAAGTTTTTATTATTATTTACATGTGATCAATAATGGGTTTTGTATTA
1 GATATATTAGACGATTATAAGTTTTTATTATTATTTACATGTGATCAATAATGGGTTTTGTATTA
58689518 TTTAAATAAAC
66 TTTAAATAAAC
58689529 GATATATTAGACGATTATAAGTTTTTATTATTATTTACATGTGATCAATAATGGGTTTTGTATTA
1 GATATATTAGACGATTATAAGTTTTTATTATTATTTACATGTGATCAATAATGGGTTTTGTATTA
58689594 TTTAAATAAAC
66 TTTAAATAAAC
58689605 ACTACTATTA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (76 bp):
GATATATTAGACGATTATAAGTTTTTATTATTATTTACATGTGATCAATAATGGGTTTTGTATTA
TTTAAATAAAC
Found at i:58691884 original size:3 final size:3
Alignment explanation
Indices: 58691871--58691906 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
58691861 TTTTAAATAT
*
58691871 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
58691907 CTATACATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:58695706 original size:18 final size:18
Alignment explanation
Indices: 58695683--58695744 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 18
58695673 AAGTTAATTC
58695683 TAAAATTATAAAAAAAAT
1 TAAAATTATAAAAAAAAT
58695701 TAAAATTTATAAAAAAATCAT
1 TAAAA-TTATAAAAAAA--AT
*
58695722 TAAAATTAT-AAAAATAT
1 TAAAATTATAAAAAAAAT
58695739 TAAAAT
1 TAAAAT
58695745 ATTTAAAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 8 0.20
18 5 0.12
19 16 0.40
20 4 0.10
21 7 0.17
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAATTATAAAAAAAAT
Found at i:58695752 original size:17 final size:18
Alignment explanation
Indices: 58695683--58695763 Score: 69
Period size: 18 Copynumber: 4.4 Consensus size: 18
58695673 AAGTTAATTC
*
58695683 TAAAAT-TATAAAAAAAAT
1 TAAAATATAT-AAAAATAT
*
58695701 TAAAATTTATAAAAAAATCAT
1 TAAAA--TATATAAAAAT-AT
58695722 TAAAAT-TATAAAAATAT
1 TAAAATATATAAAAATAT
* *
58695739 TAAAATATTTAAAATTA-
1 TAAAATATATAAAAATAT
58695756 TAAAATAT
1 TAAAATAT
58695764 CAAAGAAGGT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
17 16 0.30
18 21 0.40
19 1 0.02
20 6 0.11
21 9 0.17
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATATATAAAAATAT
Found at i:58696076 original size:19 final size:18
Alignment explanation
Indices: 58696051--58696092 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
58696041 TGAACTTGAA
*
58696051 TTTTTTAAAAAATATATT
1 TTTTTTAAAAAAAATATT
58696069 TATTTTTAAAAAAAATATT
1 T-TTTTTAAAAAAAATATT
58696088 TTTTT
1 TTTTT
58696093 CTGATGTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTTTAAAAAAAATATT
Found at i:58696527 original size:45 final size:45
Alignment explanation
Indices: 58696421--58696614 Score: 173
Period size: 45 Copynumber: 4.3 Consensus size: 45
58696411 AATTTTTCTA
* * *
58696421 TATTGGCAGCGAAGTAGATTAAAGAACACCAGCCTTGCCTCCCTG
1 TATTGGCAGCGAAGCAGACTGAAGAACACCAGCCTTGCCTCCCTG
* * * * * *
58696466 -AGTTTGCAGTGGAGCAGACTGAA-AACAGCAGATCTTGCCTTCCTG
1 TA-TTGGCAGCGAAGCAGACTGAAGAACACCAG-CCTTGCCTCCCTG
58696511 TATTGGCAGCGAAGCAGA-TCGAAGAACACCAGCCTTGCCTCCCTG
1 TATTGGCAGCGAAGCAGACT-GAAGAACACCAGCCTTGCCTCCCTG
* * ** * *
58696556 -AGTTTGCAGCGGAGCAGACTGAA-AACAATAGATCTTGCCTTCCTG
1 TA-TTGGCAGCGAAGCAGACTGAAGAACACCAG-CCTTGCCTCCCTG
58696601 TATTGGCAGCGAAG
1 TATTGGCAGCGAAG
58696615 TAGATCGAAG
Statistics
Matches: 117, Mismatches: 23, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
44 16 0.14
45 91 0.78
46 10 0.09
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (45 bp):
TATTGGCAGCGAAGCAGACTGAAGAACACCAGCCTTGCCTCCCTG
Found at i:58696574 original size:90 final size:90
Alignment explanation
Indices: 58696421--58696925 Score: 518
Period size: 90 Copynumber: 5.7 Consensus size: 90
58696411 AATTTTTCTA
* **
58696421 TATTGGCAGCGAAGTAGATTAAAGAACACCAGCCTTGCCTCCCTGAGTTTGCAGTGGAGCAGACT
1 TATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTCCCTGAGTTTGCAGTGGAGCAGACT
*
58696486 GAAAACAGCAGATCTTGCCTTCCTG
66 GAAAATAGCAGATCTTGCCTTCCTG
*
58696511 TATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTCCCTGAGTTTGCAGCGGAGCAGACT
1 TATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTCCCTGAGTTTGCAGTGGAGCAGACT
* **
58696576 GAAAACAATAGATCTTGCCTTCCTG
66 GAAAATAGCAGATCTTGCCTTCCTG
* ** * ** * ** *
58696601 TATTGGCAGCGAAGTAGATCGAAGATAGCA--AGCCTTATCTCTCTGAG-CAGCGGTGGAATAGG
1 TATTGGCAGCGAAGCAGATCGAAGA-A-CACCAGCCTTGCCTCCCTGAGTTTGCAGTGGAGCAGA
* **
58696663 TTGAAAATAGCAGATCTTATCTTCCTG
64 CTGAAAATAGCAGATCTTGCCTTCCTG
* * * * * ** ** * * **
58696690 TATTAGCAGCGAAGTAGATTGAAG-ACCCCAACCTTATCTCCCTGAG-CAGCAGTGGTGTAGGTT
1 TATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTCCCTGAGTTTGCAGTGGAGCAGACT
**
58696753 GAAAATAGCAGATCTTGCCTTATTG
66 GAAAATAGCAGATCTTGCCTTCCTG
* *
58696778 TATTAGCAGCGAAGCAGATCGAAGAACACTAGCCTTGCCTCCCTGAGTTTGCAGTGGAGCAGACT
1 TATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTCCCTGAGTTTGCAGTGGAGCAGACT
* * * *
58696843 AAAAATAGCATATCTTGTCTTTCTG
66 GAAAATAGCAGATCTTGCCTTCCTG
* * * * **
58696868 TACTGGCAACGAAGCAGATC-AACAACACTAGCCTTGCCTCTTTGAGTTTGCAGTGGAG
1 TATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTCCCTGAGTTTGCAGTGGAG
58696926 TAGGTTGAAG
Statistics
Matches: 350, Mismatches: 59, Indels: 13
0.83 0.14 0.03
Matches are distributed among these distances:
86 1 0.00
87 1 0.00
88 72 0.21
89 103 0.29
90 170 0.49
91 1 0.00
92 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (90 bp):
TATTGGCAGCGAAGCAGATCGAAGAACACCAGCCTTGCCTCCCTGAGTTTGCAGTGGAGCAGACT
GAAAATAGCAGATCTTGCCTTCCTG
Found at i:58697130 original size:50 final size:50
Alignment explanation
Indices: 58696985--58697148 Score: 179
Period size: 50 Copynumber: 3.3 Consensus size: 50
58696975 CAAAGAAAGG
* * *
58696985 AAATCTTACTTCCCCGACATTGCAATTAAATAGATTGAAGCTACAATAGC
1 AAATCTTACTCCCCCGACATTGCAGTTAAACAGATTGAAGCTACAATAGC
** * * ** *
58697035 AAATCTTACTTCCCTGGAGA-TGTAGTGGAACAGATTGAAGCTACAATGGC
1 AAATCTTAC-TCCCCCGACATTGCAGTTAAACAGATTGAAGCTACAATAGC
*
58697085 AAATCTTACTCCCCCGACATTGCAGTTAAAACAGATTGAAG-TACAACAGC
1 AAATCTTACTCCCCCGACATTGCAGTT-AAACAGATTGAAGCTACAATAGC
*
58697135 AAATCCTATCTCCC
1 AAATCTTA-CTCCC
58697149 TGACGTTGTA
Statistics
Matches: 91, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
49 7 0.08
50 61 0.67
51 23 0.25
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (50 bp):
AAATCTTACTCCCCCGACATTGCAGTTAAACAGATTGAAGCTACAATAGC
Found at i:58697374 original size:15 final size:15
Alignment explanation
Indices: 58697354--58697383 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
58697344 CTCGGCCCAT
*
58697354 AACCAAATTAATAAA
1 AACCAAAATAATAAA
58697369 AACCAAAATAATAAA
1 AACCAAAATAATAAA
58697384 TTAAATGTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.13, G:0.00, T:0.17
Consensus pattern (15 bp):
AACCAAAATAATAAA
Found at i:58698569 original size:3 final size:3
Alignment explanation
Indices: 58698563--58698602 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
58698553 AAAAAATTAA
58698563 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
58698603 GCGTAAGTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:58701636 original size:18 final size:18
Alignment explanation
Indices: 58701613--58701674 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 18
58701603 AAGTTAATTC
58701613 TAAAATTATAAAAAAAAT
1 TAAAATTATAAAAAAAAT
58701631 TAAAATTTATAAAAAAATCAT
1 TAAAA-TTATAAAAAAA--AT
*
58701652 TAAAATTAT-AAAAATAT
1 TAAAATTATAAAAAAAAT
58701669 TAAAAT
1 TAAAAT
58701675 ATTTAAAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 8 0.20
18 5 0.12
19 16 0.40
20 4 0.10
21 7 0.17
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAAAATTATAAAAAAAAT
Found at i:58701682 original size:17 final size:18
Alignment explanation
Indices: 58701613--58701693 Score: 69
Period size: 18 Copynumber: 4.4 Consensus size: 18
58701603 AAGTTAATTC
*
58701613 TAAAAT-TATAAAAAAAAT
1 TAAAATATAT-AAAAATAT
*
58701631 TAAAATTTATAAAAAAATCAT
1 TAAAA--TATATAAAAAT-AT
58701652 TAAAAT-TATAAAAATAT
1 TAAAATATATAAAAATAT
* *
58701669 TAAAATATTTAAAATTA-
1 TAAAATATATAAAAATAT
58701686 TAAAATAT
1 TAAAATAT
58701694 CAAAGAAGGT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
17 16 0.30
18 21 0.40
19 1 0.02
20 6 0.11
21 9 0.17
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATATATAAAAATAT
Found at i:58704336 original size:3 final size:3
Alignment explanation
Indices: 58704328--58704352 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
58704318 AAATATTGTT
58704328 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
58704353 TTGGTATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:58710425 original size:15 final size:15
Alignment explanation
Indices: 58710405--58710434 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
58710395 CATGCCACAC
58710405 ACTTCAACTTATTTA
1 ACTTCAACTTATTTA
58710420 ACTTCAACTTATTTA
1 ACTTCAACTTATTTA
58710435 TCGTCCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (15 bp):
ACTTCAACTTATTTA
Found at i:58716291 original size:31 final size:31
Alignment explanation
Indices: 58716249--58716307 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
58716239 TTGTCATCAC
*
58716249 TGGTTTTAAAGATATAAGAAAATTTTGTCAA
1 TGGTTTGAAAGATATAAGAAAATTTTGTCAA
* *
58716280 TGGTTTGAAAGATATGAGAAACTTTTGT
1 TGGTTTGAAAGATATAAGAAAATTTTGT
58716308 TTCCATACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.39
Consensus pattern (31 bp):
TGGTTTGAAAGATATAAGAAAATTTTGTCAA
Found at i:58717437 original size:12 final size:12
Alignment explanation
Indices: 58717422--58717460 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
58717412 TTACATAATT
58717422 ATATACATAAAA
1 ATATACATAAAA
*
58717434 ATATCCATAAAA
1 ATATACATAAAA
*
58717446 ATGTACATAAAA
1 ATATACATAAAA
58717458 ATA
1 ATA
58717461 CATGTGTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.26
Consensus pattern (12 bp):
ATATACATAAAA
Found at i:58724675 original size:18 final size:18
Alignment explanation
Indices: 58724652--58724693 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
58724642 TTCTATTCTA
58724652 AATAAA-AACAACAATAAT
1 AATAAAGAA-AACAATAAT
* *
58724670 ATTAAAGAAACCAATAAT
1 AATAAAGAAAACAATAAT
58724688 AATAAA
1 AATAAA
58724694 TATATAAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.69, C:0.10, G:0.02, T:0.19
Consensus pattern (18 bp):
AATAAAGAAAACAATAAT
Found at i:58725908 original size:34 final size:34
Alignment explanation
Indices: 58725870--58726002 Score: 115
Period size: 29 Copynumber: 4.2 Consensus size: 34
58725860 TGCACAATCT
* *
58725870 TAGGGTTCACATGGGATATATGTTCGCATGTTCC
1 TAGGGTTCACATGGGATATAGGCTCGCATGTTCC
* * *
58725904 TAGGGTT--C--GTG-TATAGGCTCGTATGATCC
1 TAGGGTTCACATGGGATATAGGCTCGCATGTTCC
* * *
58725933 TAGGGTACGCATGGCATATAGGCTCGCATGTTCC
1 TAGGGTTCACATGGGATATAGGCTCGCATGTTCC
*
58725967 TAGGGTTCACA---G--ATAGGCTCGCAAGTTCC
1 TAGGGTTCACATGGGATATAGGCTCGCATGTTCC
58725996 TAGGGTT
1 TAGGGTT
58726003 TGCATGAGCC
Statistics
Matches: 80, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
29 43 0.54
30 2 0.03
31 1 0.01
32 1 0.01
33 1 0.01
34 32 0.40
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (34 bp):
TAGGGTTCACATGGGATATAGGCTCGCATGTTCC
Found at i:58725909 original size:63 final size:63
Alignment explanation
Indices: 58725827--58725989 Score: 191
Period size: 63 Copynumber: 2.6 Consensus size: 63
58725817 TGATCACATG
* * * * *
58725827 GGCTCGCATGTACCTAGGGTTCGCATATAGGCTTGCACAATCTTAGGGTTCACATGGGATATA
1 GGCTCGCATGTTCCTAGGGTTCGCATATAGGCTCGCACAATCCTAGGGTACACATGGCATATA
* * ** * ** *
58725890 TGTTCGCATGTTCCTAGGGTTCGTGTATAGGCTCGTATGATCCTAGGGTACGCATGGCATATA
1 GGCTCGCATGTTCCTAGGGTTCGCATATAGGCTCGCACAATCCTAGGGTACACATGGCATATA
* *
58725953 GGCTCGCATGTTCCTAGGGTTCACAGATAGGCTCGCA
1 GGCTCGCATGTTCCTAGGGTTCGCATATAGGCTCGCA
58725990 AGTTCCTAGG
Statistics
Matches: 80, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
63 80 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (63 bp):
GGCTCGCATGTTCCTAGGGTTCGCATATAGGCTCGCACAATCCTAGGGTACACATGGCATATA
Found at i:58726008 original size:63 final size:62
Alignment explanation
Indices: 58725809--58726008 Score: 186
Period size: 63 Copynumber: 3.2 Consensus size: 62
58725799 CACGTTTGAA
* * * * * * *
58725809 GGTTCGCATGATCACATGGGCTCGCATGTACCTAGGGTTCGCATATAGGCTTGCACA-ATCTTAG
1 GGTTCGCATG-GCATATAGGCTCGCATGTTCCTAGGGTTC-CAGATAGGCTCGCA-AGATCCTAG
* * * * ** * *
58725873 GGTTCACATGGGATATATGTTCGCATGTTCCTAGGGTTCGTGTATAGGCTCGTATGATCCTAG
1 GGTTCGCATGGCATATAGGCTCGCATGTTCCTAGGGTTCCAG-ATAGGCTCGCAAGATCCTAG
* *
58725936 GGTACGCATGGCATATAGGCTCGCATGTTCCTAGGGTTCACAGATAGGCTCGCAAGTTCCTAG
1 GGTTCGCATGGCATATAGGCTCGCATGTTCCTAGGGTTC-CAGATAGGCTCGCAAGATCCTAG
*
58725999 GGTTTGCATG
1 GGTTCGCATG
58726009 AGCCTAGGGT
Statistics
Matches: 106, Mismatches: 27, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
63 96 0.91
64 10 0.09
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.30
Consensus pattern (62 bp):
GGTTCGCATGGCATATAGGCTCGCATGTTCCTAGGGTTCCAGATAGGCTCGCAAGATCCTAG
Found at i:58726511 original size:21 final size:20
Alignment explanation
Indices: 58726487--58726529 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
58726477 TATGGGGTAT
58726487 GCACATAATAACCTAGGGTTC
1 GCACAT-ATAACCTAGGGTTC
* * *
58726508 GCACGTATAATCTAGGTTTC
1 GCACATATAACCTAGGGTTC
58726528 GC
1 GC
58726530 TTAGTTTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (20 bp):
GCACATATAACCTAGGGTTC
Found at i:58728695 original size:20 final size:20
Alignment explanation
Indices: 58728670--58728709 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
58728660 AATATTTTCC
*
58728670 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
58728690 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
58728710 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:58728715 original size:34 final size:35
Alignment explanation
Indices: 58728658--58728724 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
58728648 CAAACACCAG
*
58728658 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
58728693 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
58728725 TATTACGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Done.