Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold198
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: 3915534
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 240068 characters in sequence are not A, C, G, or T
File 3 of 13
Found at i:564968 original size:14 final size:14
Alignment explanation
Indices: 564940--564968 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
564930 CCTTAGTGGC
564940 TTTTGACTTGATTT
1 TTTTGACTTGATTT
564954 TTTTG-CTTGATTT
1 TTTTGACTTGATTT
564967 TT
1 TT
564969 AAGGAATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.10, C:0.07, G:0.14, T:0.69
Consensus pattern (14 bp):
TTTTGACTTGATTT
Found at i:567769 original size:19 final size:18
Alignment explanation
Indices: 567745--567780 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
567735 AACAAACAAA
*
567745 AAATTAGAATATAAAAATT
1 AAATTA-AAAATAAAAATT
567764 AAATTAAAAATAAAAAT
1 AAATTAAAAATAAAAAT
567781 GACTAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAATTAAAAATAAAAATT
Found at i:567773 original size:12 final size:14
Alignment explanation
Indices: 567743--567774 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
567733 CAAACAAACA
567743 AAAAATTAGAATAT
1 AAAAATTAGAATAT
567757 AAAAATTA-AAT-T
1 AAAAATTAGAATAT
567769 AAAAAT
1 AAAAAT
567775 AAAAATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (14 bp):
AAAAATTAGAATAT
Found at i:571667 original size:75 final size:75
Alignment explanation
Indices: 571544--571693 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
571534 TTGTAAATAA
*
571544 TTAACTTGTTTGAGGTAAGACTCTATTTACTTTTGTTTAGCTTAGGTTTTGAATTTGTTGCATGT
1 TTAACTTATTTGAGGTAAGACTCTATTTACTTTTGTTTAGCTTAGGTTTTGAATTTGTTGCATGT
571609 TTAAATTTAG
66 TTAAATTTAG
571619 TTAACTTATTTGAGGTAAGACTCTATTTACTTTTGTTTAGCTTAGGTTTTGAATTTGTTGCATGT
1 TTAACTTATTTGAGGTAAGACTCTATTTACTTTTGTTTAGCTTAGGTTTTGAATTTGTTGCATGT
571684 TTAAATTTAG
66 TTAAATTTAG
571694 GACTTTGTAT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.51
Consensus pattern (75 bp):
TTAACTTATTTGAGGTAAGACTCTATTTACTTTTGTTTAGCTTAGGTTTTGAATTTGTTGCATGT
TTAAATTTAG
Found at i:571670 original size:39 final size:39
Alignment explanation
Indices: 571552--571670 Score: 97
Period size: 39 Copynumber: 3.1 Consensus size: 39
571542 AATTAACTTG
571552 TTTGAGGTAAGACTCTATTTACTTTTGTTTAGCTTAGGT
1 TTTGAGGTAAGACTCTATTTACTTTTGTTTAGCTTAGGT
* ** * * * * *
571591 TTTGA-ATTTG-TTGCATGTTTAAATTTAG-TTAACTTA---
1 TTTGAGGTAAGACT-C-TATTT-ACTTTTGTTTAGCTTAGGT
571627 TTTGAGGTAAGACTCTATTTACTTTTGTTTAGCTTAGGT
1 TTTGAGGTAAGACTCTATTTACTTTTGTTTAGCTTAGGT
571666 TTTGA
1 TTTGA
571671 ATTTGTTGCA
Statistics
Matches: 55, Mismatches: 16, Indels: 18
0.62 0.18 0.20
Matches are distributed among these distances:
35 5 0.09
36 16 0.29
37 4 0.07
38 4 0.07
39 21 0.38
40 5 0.09
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.50
Consensus pattern (39 bp):
TTTGAGGTAAGACTCTATTTACTTTTGTTTAGCTTAGGT
Found at i:571949 original size:10 final size:10
Alignment explanation
Indices: 571934--571972 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
571924 TCACGTCATT
571934 TTTCAAAAAA
1 TTTCAAAAAA
*
571944 TTTCAAAAAT
1 TTTCAAAAAA
571954 TTTCAAAAAAA
1 TTTC-AAAAAA
571965 TTTCAAAA
1 TTTCAAAA
571973 TTGTTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (10 bp):
TTTCAAAAAA
Found at i:571974 original size:20 final size:20
Alignment explanation
Indices: 571933--571972 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
571923 TTCACGTCAT
571933 TTTTCAAAAAATTTCAAAAA
1 TTTTCAAAAAATTTCAAAAA
571953 TTTTCAAAAAAATTTCAAAA
1 TTTTC-AAAAAATTTCAAAA
571973 TTGTTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (20 bp):
TTTTCAAAAAATTTCAAAAA
Found at i:574836 original size:40 final size:40
Alignment explanation
Indices: 574792--575159 Score: 450
Period size: 40 Copynumber: 9.2 Consensus size: 40
574782 TTTGGTATCA
* *
574792 TGAATGCACATGCGTGCCCCTGTTTATACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * *
574832 TGAATGCACATACGTGCCCCTATTTGTACTTCGATACCAC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
574872 TAAATGCACATACGTGGCCTTGTTTATACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * *
574912 TGAATGCACATACGTGCCCCTATTTGTACTTCGATACCAC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * *
574952 TAAATGCACATACGTGGCCTTGTTTGTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
574992 TGAATGCACATACATGCCCCTGTTTGCACTTTGATACCCC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * *
575032 TAAATGCACATACGTGCCCCTGTTTGTACTTCGATACACC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
575072 TGAATGCTCATACGTGCCCTTGTTTGTAGTTCAGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
575112 TGAATGCACATACAG-GCCTCTATTTGTCCTTCGGTACTCC
1 TGAATGCACATAC-GTGCCCCTGTTTGTACTTCGGTACCCC
575152 TGAATGCA
1 TGAATGCA
575160 TTATAATGTC
Statistics
Matches: 275, Mismatches: 52, Indels: 2
0.84 0.16 0.01
Matches are distributed among these distances:
40 274 1.00
41 1 0.00
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.31
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:575013 original size:20 final size:20
Alignment explanation
Indices: 574988--575053 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
574978 TACTTCGGTA
574988 CCCCTGAATGCACATACATG
1 CCCCTGAATGCACATACATG
** * ** *
575008 CCCCTGTTTGCACTTTGATA
1 CCCCTGAATGCACATACATG
* *
575028 CCCCTAAATGCACATACGTG
1 CCCCTGAATGCACATACATG
575048 CCCCTG
1 CCCCTG
575054 TTTGTACTTC
Statistics
Matches: 31, Mismatches: 15, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (20 bp):
CCCCTGAATGCACATACATG
Found at i:579958 original size:41 final size:41
Alignment explanation
Indices: 579906--580157 Score: 256
Period size: 41 Copynumber: 6.1 Consensus size: 41
579896 GCTTTTTCTT
* *
579906 ATAAACTCTGCAAAAGGTAAAGCAATAGCGGTG-TTTCTCCC
1 ATAAACACTGCAAAAGGTAAAGCAATAGCAGTGTTTTC-CCC
*
579947 ATAAACACTGCAAAAGGTAAGGCAATAGCAGTGTTTTCCCC
1 ATAAACACTGCAAAAGGTAAAGCAATAGCAGTGTTTTCCCC
* * * * *
579988 ATAAACTCCGCAAAAGGTAAAGTAATAACGGTG-TTTCTCCC
1 ATAAACACTGCAAAAGGTAAAGCAATAGCAGTGTTTTC-CCC
580029 ATAAACACTGCAAAAGGTAAAGCAATAGCAGTGTTTTCCCC
1 ATAAACACTGCAAAAGGTAAAGCAATAGCAGTGTTTTCCCC
** ** * * ** *
580070 ATAAATGCCACAAAACGTAAGGCAATAGTGGCGTTTTCCCC
1 ATAAACACTGCAAAAGGTAAAGCAATAGCAGTGTTTTCCCC
* ** * * * *
580111 ATAAATACAACAAAAGGTAAGGCAATAGTATTGTTTTTCCC
1 ATAAACACTGCAAAAGGTAAAGCAATAGCAGTGTTTTCCCC
580152 ATAAAC
1 ATAAAC
580158 GCCACGAATT
Statistics
Matches: 177, Mismatches: 31, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
40 4 0.02
41 165 0.93
42 8 0.05
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (41 bp):
ATAAACACTGCAAAAGGTAAAGCAATAGCAGTGTTTTCCCC
Found at i:580043 original size:82 final size:82
Alignment explanation
Indices: 579906--580157 Score: 337
Period size: 82 Copynumber: 3.1 Consensus size: 82
579896 GCTTTTTCTT
*
579906 ATAAACTCTGCAAAAGGTAAAGCAATAGCGGTGTTTCTCCCATAAACACTGCAAAAGGTAAGGCA
1 ATAAACTCCGCAAAAGGTAAAGCAATAGCGGTGTTTCTCCCATAAACACTGCAAAAGGTAAGGCA
579971 ATAGCAGTGTTTTCCCC
66 ATAGCAGTGTTTTCCCC
* * *
579988 ATAAACTCCGCAAAAGGTAAAGTAATAACGGTGTTTCTCCCATAAACACTGCAAAAGGTAAAGCA
1 ATAAACTCCGCAAAAGGTAAAGCAATAGCGGTGTTTCTCCCATAAACACTGCAAAAGGTAAGGCA
580053 ATAGCAGTGTTTTCCCC
66 ATAGCAGTGTTTTCCCC
* * * * * * **
580070 ATAAA-TGCCACAAAACGTAAGGCAATAGTGGCGTTT-TCCCCATAAATACAACAAAAGGTAAGG
1 ATAAACT-CCGCAAAAGGTAAAGCAATAGCGGTGTTTCT-CCCATAAACACTGCAAAAGGTAAGG
* * *
580133 CAATAGTATTGTTTTTCCC
64 CAATAGCAGTGTTTTCCCC
580152 ATAAAC
1 ATAAAC
580158 GCCACGAATT
Statistics
Matches: 149, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
81 2 0.01
82 147 0.99
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (82 bp):
ATAAACTCCGCAAAAGGTAAAGCAATAGCGGTGTTTCTCCCATAAACACTGCAAAAGGTAAGGCA
ATAGCAGTGTTTTCCCC
Found at i:580125 original size:123 final size:123
Alignment explanation
Indices: 579906--580130 Score: 310
Period size: 123 Copynumber: 1.8 Consensus size: 123
579896 GCTTTTTCTT
* * ** *
579906 ATAAACTCTGCAAAAGGTAAAGCAATAGCGGTGTTTCTCCCATAAACACTGCAAAAGGTAAGGCA
1 ATAAACACTGCAAAAGGTAAAGCAATAGCAGTGTTTCTCCCATAAACACCACAAAACGTAAGGCA
* **
579971 ATAGCAGTGTTTTCCCCATAAACTCCGCAAAAGGTAAAGTAATAACGGTGTTTCTCCC
66 ATAGCAGCGTTTTCCCCATAAACTCAACAAAAGGTAAAGTAATAACGGTGTTTCTCCC
**
580029 ATAAACACTGCAAAAGGTAAAGCAATAGCAGTGTTT-TCCCCATAAATGCCACAAAACGTAAGGC
1 ATAAACACTGCAAAAGGTAAAGCAATAGCAGTGTTTCT-CCCATAAACACCACAAAACGTAAGGC
**
580093 AATAGTGGCGTTTTCCCCATAAA-TACAACAAAAGGTAA
65 AATAGCAGCGTTTTCCCCATAAACT-CAACAAAAGGTAA
580131 GGCAATAGTA
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
122 2 0.02
123 86 0.98
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (123 bp):
ATAAACACTGCAAAAGGTAAAGCAATAGCAGTGTTTCTCCCATAAACACCACAAAACGTAAGGCA
ATAGCAGCGTTTTCCCCATAAACTCAACAAAAGGTAAAGTAATAACGGTGTTTCTCCC
Found at i:580146 original size:123 final size:123
Alignment explanation
Indices: 579906--580157 Score: 301
Period size: 123 Copynumber: 2.0 Consensus size: 123
579896 GCTTTTTCTT
* * ** *
579906 ATAAACTCTGCAAAAGGTAAAGCAATAGCGGTGTTTCTCCCATAAACACTGCAAAAGGTAAGGCA
1 ATAAACACTGCAAAAGGTAAAGCAATAGCAGTGTTTCTCCCATAAACACCACAAAACGTAAGGCA
* ** * *
579971 ATAGCAGTGTTTTCCCCATAAACTCCGCAAAAGGTAAAGTAATAACGGTGTTTCTCCC
66 ATAGCAGCGTTTTCCCCATAAACTCAACAAAAGGTAAAGCAATAACAGTGTTTCTCCC
**
580029 ATAAACACTGCAAAAGGTAAAGCAATAGCAGTGTTT-TCCCCATAAATGCCACAAAACGTAAGGC
1 ATAAACACTGCAAAAGGTAAAGCAATAGCAGTGTTTCT-CCCATAAACACCACAAAACGTAAGGC
** * ** * *
580093 AATAGTGGCGTTTTCCCCATAAA-TACAACAAAAGGTAAGGCAATAGTATTGTTTTTCCC
65 AATAGCAGCGTTTTCCCCATAAACT-CAACAAAAGGTAAAGCAATAACAGTGTTTCTCCC
580152 ATAAAC
1 ATAAAC
580158 GCCACGAATT
Statistics
Matches: 108, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
122 2 0.02
123 106 0.98
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (123 bp):
ATAAACACTGCAAAAGGTAAAGCAATAGCAGTGTTTCTCCCATAAACACCACAAAACGTAAGGCA
ATAGCAGCGTTTTCCCCATAAACTCAACAAAAGGTAAAGCAATAACAGTGTTTCTCCC
Found at i:583190 original size:28 final size:28
Alignment explanation
Indices: 583158--583214 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
583148 GATAGTACAA
583158 TGTGGGTCT-TAGCCCAATACAGTAACAG
1 TGTGGG-CTATAGCCCAATACAGTAACAG
*
583186 TGTGGGCTATAGCCCAATACAGTATCAG
1 TGTGGGCTATAGCCCAATACAGTAACAG
583214 T
1 T
583215 ACAGTCCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (28 bp):
TGTGGGCTATAGCCCAATACAGTAACAG
Found at i:583346 original size:26 final size:26
Alignment explanation
Indices: 583317--583371 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
583307 AACACACCAA
*
583317 TATCGCAGCAAAGCTGCCAGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
* *
583343 TATCGTAGCAAAGCTGCTAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
583369 TAT
1 TAT
583372 ATGTGGCAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.24
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAACAG
Found at i:583567 original size:27 final size:26
Alignment explanation
Indices: 583534--583606 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 26
583524 CATCTCCTAG
583534 GGGTATTTCGGTCATTTTACACTAT-
1 GGGTATTTCGGTCATTTTACACTATA
* *
583559 GGGCATATTTCAGTCATTTTACCCTATAA
1 GGG--TATTTCGGTCATTTTACACTAT-A
583588 GGGTATTTCGGTCATTTTA
1 GGGTATTTCGGTCATTTTA
583607 TTGACTTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 3 0.07
27 35 0.85
29 3 0.07
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.42
Consensus pattern (26 bp):
GGGTATTTCGGTCATTTTACACTATA
Found at i:584678 original size:38 final size:37
Alignment explanation
Indices: 584585--584686 Score: 104
Period size: 38 Copynumber: 2.7 Consensus size: 37
584575 TTCGCCAACA
584585 GAAA-AGAGAAGAG-GGGAAAAGAGAATGGAGGATTCG
1 GAAACAGAGAAGAGAGGGAAAAGAGAAT-GAGGATTCG
* * *
584621 GCAACA-AGAGGAGAGGGGAAAAGAGAAT-AGTATTCG
1 GAAACAGAGAAGAGA-GGGAAAAGAGAATGAGGATTCG
584657 GTAAACAGAGAAGAGAAGGGAAAAGTAGAA
1 G-AAACAGAGAAGAG-AGGGAAAAG-AGAA
584687 AAGGAAAACG
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
36 17 0.31
37 5 0.09
38 27 0.50
39 5 0.09
ACGTcount: A:0.49, C:0.05, G:0.37, T:0.09
Consensus pattern (37 bp):
GAAACAGAGAAGAGAGGGAAAAGAGAATGAGGATTCG
Found at i:585433 original size:154 final size:154
Alignment explanation
Indices: 585153--585452 Score: 582
Period size: 154 Copynumber: 1.9 Consensus size: 154
585143 CTATTTTTGT
585153 GTCATAAAACAAACACTATTATTTAAAAGGTCTATATGCCAGTGTCCAGATTCATTTAAGAGCAA
1 GTCATAAAACAAACACTATTATTTAAAAGGTCTATATGCCAGTGTCCAGATTCATTTAAGAGCAA
* *
585218 AACTAAAAATTCTGCAAAAGCCAAGACTTGAACCCAGGCTTCTCAAACACTCCCATACAAACCCA
66 AACTAAAAATTCTGCAAAAGCCAAGACTTAAACCCAGGCTTCTCAAACACTCACATACAAACCCA
585283 AATCATTTAGCCATTATTTAAAAG
131 AATCATTTAGCCATTATTTAAAAG
585307 GTCATAAAACAAACACTATTATTTAAAAGGTCTATATGCCAGTGTCCAGATTCATTTAAGAGCAA
1 GTCATAAAACAAACACTATTATTTAAAAGGTCTATATGCCAGTGTCCAGATTCATTTAAGAGCAA
585372 AACTAAAAATTCTGCAAAAGCCAAGACTTAAACCCAGGCTTCTCAAACACTCACATACAAACCCA
66 AACTAAAAATTCTGCAAAAGCCAAGACTTAAACCCAGGCTTCTCAAACACTCACATACAAACCCA
585437 AATCATTTAGCCATTA
131 AATCATTTAGCCATTA
585453 AAGCAAACAA
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 144 1.00
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (154 bp):
GTCATAAAACAAACACTATTATTTAAAAGGTCTATATGCCAGTGTCCAGATTCATTTAAGAGCAA
AACTAAAAATTCTGCAAAAGCCAAGACTTAAACCCAGGCTTCTCAAACACTCACATACAAACCCA
AATCATTTAGCCATTATTTAAAAG
Found at i:586188 original size:13 final size:13
Alignment explanation
Indices: 586155--586196 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
586145 AGCTTGACCA
*
586155 AATATTTATAACT
1 AATATTTGTAACT
586168 AATATTTGTAACT
1 AATATTTGTAACT
*
586181 AACT-TTTGTAATT
1 AA-TATTTGTAACT
586194 AAT
1 AAT
586197 TAGGTTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 1 0.04
13 24 0.92
14 1 0.04
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (13 bp):
AATATTTGTAACT
Found at i:586574 original size:35 final size:35
Alignment explanation
Indices: 586529--586595 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
586519 ATATTTAAAG
*
586529 ATGATAATCATGACTTACATAAACATTTAAAGTTT
1 ATGATAATCATAACTTACATAAACATTTAAAGTTT
*
586564 ATGATTATCATAACTTACATAAACATTTAAAG
1 ATGATAATCATAACTTACATAAACATTTAAAG
586596 AATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (35 bp):
ATGATAATCATAACTTACATAAACATTTAAAGTTT
Found at i:591543 original size:11 final size:11
Alignment explanation
Indices: 591527--591575 Score: 80
Period size: 11 Copynumber: 4.5 Consensus size: 11
591517 TCCTTCATTC
591527 ATCATCCCTCA
1 ATCATCCCTCA
*
591538 ATCATCCCTCC
1 ATCATCCCTCA
591549 ATCATCCCTCA
1 ATCATCCCTCA
*
591560 AGCATCCCTCA
1 ATCATCCCTCA
591571 ATCAT
1 ATCAT
591576 TTCTCATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.27, C:0.45, G:0.02, T:0.27
Consensus pattern (11 bp):
ATCATCCCTCA
Found at i:594594 original size:43 final size:42
Alignment explanation
Indices: 594546--594641 Score: 120
Period size: 43 Copynumber: 2.3 Consensus size: 42
594536 TCGCTACAGG
* **
594546 TCATGTTCTTTAGCAGCATTTATGTGAAAAGCGCTGCTAAAGA
1 TCATGTTCTTTAGCAGCATTTATGGGAAAAGCGCCACT-AAGA
* * * *
594589 TCATGTTCTTTAGCAGCGTTTGTGGGAAAAGTGCCACTAAGG
1 TCATGTTCTTTAGCAGCATTTATGGGAAAAGCGCCACTAAGA
594631 TCATGTTCTTT
1 TCATGTTCTTT
594642 GGTGGCATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 14 0.30
43 32 0.70
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (42 bp):
TCATGTTCTTTAGCAGCATTTATGGGAAAAGCGCCACTAAGA
Found at i:601159 original size:32 final size:32
Alignment explanation
Indices: 601090--601159 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
601080 TTGCTTCAAT
601090 AAAAAA-ATATATGTAGTGTATTTTAAAAATA
1 AAAAAATATATATGTAGTGTATTTTAAAAATA
601121 AAAAAATATATATGTAGTGTATTTTAAAAATA
1 AAAAAATATATATGTAGTGTATTTTAAAAATA
601153 AAAAAAT
1 AAAAAAT
601160 TTAATCTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 6 0.16
32 32 0.84
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (32 bp):
AAAAAATATATATGTAGTGTATTTTAAAAATA
Found at i:604402 original size:23 final size:24
Alignment explanation
Indices: 604359--604408 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
604349 AAAAGTTTGA
604359 AAATTTTTATATTTTCATAATTTT
1 AAATTTTTATATTTTCATAATTTT
*
604383 AAATTATTTAT-TTTT-TTAATTTT
1 AAATT-TTTATATTTTCATAATTTT
604406 AAA
1 AAA
604409 GAGTTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 10 0.42
24 9 0.38
25 5 0.21
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
AAATTTTTATATTTTCATAATTTT
Found at i:604473 original size:19 final size:19
Alignment explanation
Indices: 604427--604484 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
604417 AATAATTTCA
*
604427 AAAATATTTTTT-A-TTTA
1 AAAATATTTTTTAATTTTT
604444 AAAATTGATTTTTTAATTTTT
1 AAAA-T-ATTTTTTAATTTTT
604465 AAAATA-TTTTTAATTGTTT
1 AAAATATTTTTTAATT-TTT
604484 A
1 A
604485 GGTACTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 4 0.11
18 10 0.29
19 12 0.34
20 2 0.06
21 7 0.20
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
AAAATATTTTTTAATTTTT
Found at i:604593 original size:23 final size:23
Alignment explanation
Indices: 604549--604592 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
604539 TAATAGTCAC
*
604549 ATCAACATTTTTAAAGGTAAAATG
1 ATCAAAATTTTTAAA-GTAAAATG
604573 ATCAAAATTTTTAAA-TAAAA
1 ATCAAAATTTTTAAAGTAAAA
604593 AAGAAAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
24 14 0.74
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (23 bp):
ATCAAAATTTTTAAAGTAAAATG
Found at i:605268 original size:28 final size:29
Alignment explanation
Indices: 605232--605297 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 29
605222 TGTAATGGTT
605232 GATGACCAAAA-AAAAA-TATGAATAGTTG
1 GATGACCAAAAGAAAAAGT-TGAATAGTTG
*
605260 GGTGACCAAAAGGAAAAAGTTGAATAGTTG
1 GATGACCAAAA-GAAAAAGTTGAATAGTTG
605290 GATGACCA
1 GATGACCA
605298 TTTTGTAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 10 0.30
30 22 0.67
31 1 0.03
ACGTcount: A:0.47, C:0.09, G:0.24, T:0.20
Consensus pattern (29 bp):
GATGACCAAAAGAAAAAGTTGAATAGTTG
Found at i:608680 original size:63 final size:63
Alignment explanation
Indices: 608613--608773 Score: 207
Period size: 63 Copynumber: 2.6 Consensus size: 63
608603 AAATCTAAAA
* * *
608613 TCAGTGAGTTACACGGCTTGGACACACACCCGTGTCTCTTGCTTGTGTGACTCTAATACGAAG
1 TCAGTGAGTTACACGGCTTGGACACACACCCGTGTCTCATGCTTGTGCGACTCTAATACAAAG
* * * * *
608676 TCAGTGAGTTACATGGCTTAGACACACGCCCATGTGTCATGCTTGTGCGACTCTAATACAAAG
1 TCAGTGAGTTACACGGCTTGGACACACACCCGTGTCTCATGCTTGTGCGACTCTAATACAAAG
* * *
608739 TCAATGAGTAACACGG-TCTGGACACACATCCGTGT
1 TCAGTGAGTTACACGGCT-TGGACACACACCCGTGT
608774 ATTTCACCCA
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
62 1 0.01
63 81 0.99
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (63 bp):
TCAGTGAGTTACACGGCTTGGACACACACCCGTGTCTCATGCTTGTGCGACTCTAATACAAAG
Found at i:626144 original size:13 final size:13
Alignment explanation
Indices: 626126--626153 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
626116 AAGTGCGAAC
626126 ACTCTCTTTAGAG
1 ACTCTCTTTAGAG
626139 ACTCTCTTTAGAG
1 ACTCTCTTTAGAG
626152 AC
1 AC
626154 ATTGGGGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (13 bp):
ACTCTCTTTAGAG
Found at i:627134 original size:6 final size:6
Alignment explanation
Indices: 627123--627152 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
627113 TTATAATTTC
627123 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
627153 TTATAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:628276 original size:140 final size:143
Alignment explanation
Indices: 628021--628301 Score: 428
Period size: 140 Copynumber: 2.0 Consensus size: 143
628011 CCATTTGTCC
* * *
628021 AGGTTCATTGTACATGCAAAATAAAAATAAATAAATTTCCTAATTCTTAATTTCTAAAAAAAATT
1 AGGTTCACTATACATGCAAAATAAAAATAAATAAATCTCCTAATTCTTAATTTCTAAAAAAAATT
*
628086 AATATTTCATATCACGTGTCAACATTATAGGATGGCAGCTTAAAATCTCATGGTGTTAGTCAGGT
66 AATATTTCATATCACGTGTCAACATTATAGGATGGCAGCTTAAAATCTCATGGTGTTAGTCAAGT
628151 ACCAATAAAAACT
131 ACCAATAAAAACT
628164 AGGTTCACTATACATGCAAAAT-AAAA-AAA-AAA-CTCCTAATTCTTAATTT-TCAAAAAGAAA
1 AGGTTCACTATACATGCAAAATAAAAATAAATAAATCTCCTAATTCTTAATTTCT-AAAAA-AAA
* * * * *
628224 TTAATATTTCATATCTCGTGTTAACATTATATGATGTCAGCTTAAAATCTCATGGTGTTAGTTAA
64 TTAATATTTCATATCACGTGTCAACATTATAGGATGGCAGCTTAAAATCTCATGGTGTTAGTCAA
628289 GTACCAATAAAAA
129 GTACCAATAAAAA
628302 GTACCAACTT
Statistics
Matches: 127, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
138 1 0.01
139 21 0.17
140 78 0.61
141 3 0.02
142 4 0.03
143 20 0.16
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (143 bp):
AGGTTCACTATACATGCAAAATAAAAATAAATAAATCTCCTAATTCTTAATTTCTAAAAAAAATT
AATATTTCATATCACGTGTCAACATTATAGGATGGCAGCTTAAAATCTCATGGTGTTAGTCAAGT
ACCAATAAAAACT
Found at i:628837 original size:19 final size:20
Alignment explanation
Indices: 628796--628840 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
628786 TTTAACCCAA
* *
628796 TTCAACTAGTTTTTAGTATG
1 TTCAATTAGTTTTTAGTAGG
*
628816 TTCAATTAGTTTTTAG-CGG
1 TTCAATTAGTTTTTAGTAGG
628835 TTCAAT
1 TTCAAT
628841 CATTTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.49
Consensus pattern (20 bp):
TTCAATTAGTTTTTAGTAGG
Found at i:630008 original size:5 final size:5
Alignment explanation
Indices: 629998--630031 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
629988 AAATACACAT
*
629998 ATATC ATATC ATATC ATATC ATATC ATAAC ATAT
1 ATATC ATATC ATATC ATATC ATATC ATATC ATAT
630032 TAGAGGTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATC
Found at i:635703 original size:23 final size:23
Alignment explanation
Indices: 635647--635705 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
635637 TGTACGGGCT
* * *
635647 AATTAGATTAGTTTGTTGAGTTG
1 AATTAGTTTATTTTTTTGAGTTG
635670 AATTAGTTTATTTTTTTGAGTTG
1 AATTAGTTTATTTTTTTGAGTTG
635693 AATTAAG-TTATTT
1 AATT-AGTTTATTT
635706 AGTTTAGTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 30 0.94
24 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (23 bp):
AATTAGTTTATTTTTTTGAGTTG
Found at i:636781 original size:6 final size:6
Alignment explanation
Indices: 636764--636801 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
636754 ACCCTTCTTC
*
636764 TCCCCTT TCCCCT TCCCCT TCCCTT TCCCCT TCCCCT T
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT T
636802 GGGTTGCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (6 bp):
TCCCCT
Found at i:636801 original size:18 final size:18
Alignment explanation
Indices: 636766--636801 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
636756 CCTTCTTCTC
636766 CCCTTTCCCCTTCCCCTT
1 CCCTTTCCCCTTCCCCTT
636784 CCCTTTCCCCTTCCCCTT
1 CCCTTTCCCCTTCCCCTT
636802 GGGTTGCAAA
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:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (18 bp):
CCCTTTCCCCTTCCCCTT
Found at i:640208 original size:21 final size:21
Alignment explanation
Indices: 640184--640236 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
640174 CACTGTTTCT
*
640184 AATCTCACTGCTACAGTACCC
1 AATCTCACTGCTACAGTAACC
** *
640205 AATCTCACCACTACAGTAACT
1 AATCTCACTGCTACAGTAACC
640226 AATCTCACTGC
1 AATCTCACTGC
640237 CACCACTGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.32, C:0.36, G:0.08, T:0.25
Consensus pattern (21 bp):
AATCTCACTGCTACAGTAACC
Found at i:640796 original size:5 final size:5
Alignment explanation
Indices: 640786--640810 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
640776 AATGAATAGG
640786 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
640811 TTAACATGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:641260 original size:14 final size:13
Alignment explanation
Indices: 641237--641291 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 13
641227 TTATTAATTA
641237 TAAATATTGAAAAT
1 TAAA-ATTGAAAAT
*
641251 TAAAATTTGAAGAT
1 TAAAA-TTGAAAAT
*
641265 TGAAGATTGAAAAT
1 T-AAAATTGAAAAT
641279 ATAAAATTGAAAA
1 -TAAAATTGAAAA
641292 ATGGGGATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 1 0.03
14 29 0.85
15 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (13 bp):
TAAAATTGAAAAT
Found at i:641291 original size:7 final size:7
Alignment explanation
Indices: 641242--641291 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
641232 AATTATAAAT
641242 ATTGAAA
1 ATTGAAA
641249 ATT-AAA
1 ATTGAAA
*
641255 ATTTGAAG
1 A-TTGAAA
*
641263 ATTGAAG
1 ATTGAAA
641270 ATTGAAA
1 ATTGAAA
641277 ATAT-AAA
1 AT-TGAAA
641284 ATTGAAA
1 ATTGAAA
641291 A
1 A
641292 ATGGGGATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 5 0.14
7 28 0.76
8 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.30
Consensus pattern (7 bp):
ATTGAAA
Found at i:641300 original size:28 final size:28
Alignment explanation
Indices: 641242--641303 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
641232 AATTATAAAT
* *
641242 ATTGAAAATTAAAATTTGAAGATTGAAG
1 ATTGAAAATTAAAATTTGAAAAATGAAG
**
641270 ATTGAAAATATAAAA-TTGAAAAATGGGG
1 ATTGAAAAT-TAAAATTTGAAAAATGAAG
641298 ATTGAA
1 ATTGAA
641304 GATTGAGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.29
Consensus pattern (28 bp):
ATTGAAAATTAAAATTTGAAAAATGAAG
Found at i:644420 original size:16 final size:15
Alignment explanation
Indices: 644393--644422 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
644383 ACACACCATC
644393 AATAAAATAATTAAA
1 AATAAAATAATTAAA
644408 AATAAATATAATTAA
1 AATAAA-ATAATTAA
644423 TATAGTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAAAATAATTAAA
Found at i:645601 original size:22 final size:22
Alignment explanation
Indices: 645576--645618 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
645566 ACACCAAAAC
*
645576 AGGCTTTTAGTGGCGCTTTTTT
1 AGGCCTTTAGTGGCGCTTTTTT
645598 AGGCCTTTAGTGGCGCTTTTT
1 AGGCCTTTAGTGGCGCTTTTT
645619 AGCGCCACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (22 bp):
AGGCCTTTAGTGGCGCTTTTTT
Found at i:645919 original size:43 final size:43
Alignment explanation
Indices: 645671--645907 Score: 314
Period size: 43 Copynumber: 5.5 Consensus size: 43
645661 AAAAACGCCG
*
645671 CATGACCTTTAGCGGCGCTTTCCCGACAAACGCCGCTAAAGAC
1 CATGACCTTTAGCGGCGCTTTTCCGACAAACGCCGCTAAAGAC
* * *
645714 CATGACCTTTAGCGGCGCTTATCCGACAAATGCCGCTGAAGAC
1 CATGACCTTTAGCGGCGCTTTTCCGACAAACGCCGCTAAAGAC
*
645757 CATGACCTTTAGCGGCGCTTATCCGACAAACGCCGCTAAAGAC
1 CATGACCTTTAGCGGCGCTTTTCCGACAAACGCCGCTAAAGAC
* * ** *
645800 CATGACCTTTAGCAGCGTTTTTCAAACAAATGCCGCTAAAGAC
1 CATGACCTTTAGCGGCGCTTTTCCGACAAACGCCGCTAAAGAC
* ** *
645843 CCTGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGC-ATAAGAC
1 CATGACCTTTAGCGGCGCTTTTCCGACAAACGCCGCTA-AAGAC
* *
645886 CATGACCTTTAGTGGCGTTTTT
1 CATGACCTTTAGCGGCGCTTTT
645908 TTTAAAAACG
Statistics
Matches: 168, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
42 1 0.01
43 167 0.99
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (43 bp):
CATGACCTTTAGCGGCGCTTTTCCGACAAACGCCGCTAAAGAC
Found at i:646325 original size:66 final size:66
Alignment explanation
Indices: 646249--646409 Score: 189
Period size: 66 Copynumber: 2.4 Consensus size: 66
646239 ACGCTGCTCT
* * *
646249 GCTTCCCTCGCTGCAGCCTCTGCTTTAAGCTACAATTGGAGTTCTTCATA-CTTTCGTTGAACCT
1 GCTTCTCTCGCTGCTGCCTCTGCTTTAAGCTACAACTGGAGTTCTTCATATCTTT-GTTGAACCT
646313 CA
65 CA
* * * ** * * *
646315 GCTTTTCTCGCTGCTGCATCTGCTTTAAGTTTTAGCTGGAGTTCTTTATATCTTTTTTGAACCTC
1 GCTTCTCTCGCTGCTGCCTCTGCTTTAAGCTACAACTGGAGTTCTTCATATCTTTGTTGAACCTC
646380 A
66 A
* *
646381 GCTTCTCTCGATGCTGCCTCCGCTTTAAG
1 GCTTCTCTCGCTGCTGCCTCTGCTTTAAG
646410 TTGTGTAATT
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
66 75 0.95
67 4 0.05
ACGTcount: A:0.16, C:0.27, G:0.17, T:0.40
Consensus pattern (66 bp):
GCTTCTCTCGCTGCTGCCTCTGCTTTAAGCTACAACTGGAGTTCTTCATATCTTTGTTGAACCTC
A
Found at i:651458 original size:25 final size:25
Alignment explanation
Indices: 651413--651464 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
651403 GCCTAAAAAT
* **
651413 TTATGTATTATATAAATTATGTAAG
1 TTATGTATTATGTAAGCTATGTAAG
* *
651438 TTACGTATTATGTAAGCTATGGAAG
1 TTATGTATTATGTAAGCTATGTAAG
651463 TT
1 TT
651465 GTATTTTATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (25 bp):
TTATGTATTATGTAAGCTATGTAAG
Found at i:651499 original size:25 final size:25
Alignment explanation
Indices: 651471--651550 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
651461 AGTTGTATTT
651471 TATGTTAGTTATTTATTATGTAAGC
1 TATGTTAGTTATTTATTATGTAAGC
* * *
651496 TATGTAAGTTGTGTATTATGTAAGC
1 TATGTTAGTTATTTATTATGTAAGC
* *
651521 TATG-TA-TTATGTTAGTTATGTCAGT
1 TATGTTAGTTAT-TTA-TTATGTAAGC
651546 TATGT
1 TATGT
651551 ATTATGTATG
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
23 3 0.07
24 3 0.07
25 38 0.86
ACGTcount: A:0.26, C:0.04, G:0.20, T:0.50
Consensus pattern (25 bp):
TATGTTAGTTATTTATTATGTAAGC
Found at i:651517 original size:16 final size:16
Alignment explanation
Indices: 651496--651692 Score: 91
Period size: 16 Copynumber: 11.9 Consensus size: 16
651486 TTATGTAAGC
*
651496 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
*
651512 TATGTAAGCTATGTAT
1 TATGTAAGTTATGTAT
*
651528 TATGTTAGTTATGTCAGT
1 TATGTAAGTTATGT-A-T
651546 TATGT-A-TTATGTAT
1 TATGTAAGTTATGTAT
* *
651560 GTCATGTAAGTTGTGTAG
1 -T-ATGTAAGTTATGTAT
* *
651578 AATGTAAGCTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
651596 TATGTGAGTTATATA-
1 TATGTAAGTTATGTAT
* ** *
651611 TAAGTTATCTTAAT-AAT
1 TATG-TAAGTT-ATGTAT
* *
651628 TATATAAGCTATGTAT
1 TATGTAAGTTATGTAT
*
651644 TATGTTAGTTATGCTAGT
1 TATGTAAGTTATG-TA-T
651662 TATGT-A-TTATGTATGT
1 TATGTAAGTTATGTA--T
*
651678 TATGTAAGTTGTGTA
1 TATGTAAGTTATGTA
651693 GAATGTAACC
Statistics
Matches: 135, Mismatches: 29, Indels: 32
0.69 0.15 0.16
Matches are distributed among these distances:
14 1 0.01
15 9 0.07
16 78 0.58
17 13 0.10
18 34 0.25
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:651524 original size:66 final size:65
Alignment explanation
Indices: 651413--651596 Score: 192
Period size: 66 Copynumber: 2.8 Consensus size: 65
651403 GCCTAAAAAT
* * ** * *
651413 TTATGTATTATATAAATTATGTAAGTTACGTATTATGTAAGCTATGGAAGTTG-TATTTTATGTT
1 TTATGTATTATGT-AAGTATGTAAGTTGTGTATTATGTAAGCTATGGAAGTTGTTA-GTTATGTC
651477 AG
64 AG
* * *
651479 TTATTTATTATGTAAGCTATGTAAGTTGTGTATTATGTAAGCTAT-GTATTATGTTAGTTATGTC
1 TTATGTATTATGTAAG-TATGTAAGTTGTGTATTATGTAAGCTATGGAAGT-TGTTAGTTATGTC
651543 AG
64 AG
* ** *
651545 TTATGTATTATGTATGTCATGTAAGTTGTGTAGAATGTAAGCTATGTAAGTT
1 TTATGTATTATGTAAGT-ATGTAAGTTGTGTATTATGTAAGCTATGGAAGTT
651597 ATGTGAGTTA
Statistics
Matches: 97, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
65 6 0.06
66 87 0.90
67 4 0.04
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (65 bp):
TTATGTATTATGTAAGTATGTAAGTTGTGTATTATGTAAGCTATGGAAGTTGTTAGTTATGTCAG
Found at i:651541 original size:41 final size:41
Alignment explanation
Indices: 651428--651567 Score: 163
Period size: 41 Copynumber: 3.4 Consensus size: 41
651418 TATTATATAA
* * *
651428 ATTATGTAAGTTACGTATTATGTAAGCTATGGAAGTTGTAT
1 ATTATGTAAGTTATGTATTATGTAAGCTATGTAAGTTGTGT
* * *
651469 TTTATGTTAGTTATTTATTATGTAAGCTATGTAAGTTGTGT
1 ATTATGTAAGTTATGTATTATGTAAGCTATGTAAGTTGTGT
* * * * *
651510 ATTATGTAAGCTATGTATTATGTTAGTTATGTCAGTTATGT
1 ATTATGTAAGTTATGTATTATGTAAGCTATGTAAGTTGTGT
* *
651551 ATTATGTATGTCATGTA
1 ATTATGTAAGTTATGTA
651568 AGTTGTGTAG
Statistics
Matches: 82, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (41 bp):
ATTATGTAAGTTATGTATTATGTAAGCTATGTAAGTTGTGT
Found at i:651566 original size:25 final size:25
Alignment explanation
Indices: 651513--651600 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
651503 GTTGTGTATT
* *
651513 ATGTAAGCTATGTATTATGTTAGTT
1 ATGTAAGTTATGTATTATGTTAGTC
*
651538 ATGTCAGTTATGTATTATG-TATGTC
1 ATGTAAGTTATGTATTATGTTA-GTC
* ** *
651563 ATGTAAGTTGTGTAGAATGTAAG-C
1 ATGTAAGTTATGTATTATGTTAGTC
651587 TATGTAAGTTATGT
1 -ATGTAAGTTATGT
651601 GAGTTATATA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
24 3 0.06
25 47 0.92
26 1 0.02
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (25 bp):
ATGTAAGTTATGTATTATGTTAGTC
Found at i:651605 original size:9 final size:8
Alignment explanation
Indices: 651470--651693 Score: 72
Period size: 9 Copynumber: 27.0 Consensus size: 8
651460 AAGTTGTATT
651470 TTATGTTAG
1 TTATG-TAG
*
651479 TTATTTA-
1 TTATGTAG
651486 TTATGTAAG
1 TTATGT-AG
*
651495 CTATGTAAG
1 TTATGT-AG
*
651504 TTGTGTA-
1 TTATGTAG
651511 TTATGTAAG
1 TTATGT-AG
*
651520 CTATGTA-
1 TTATGTAG
651527 TTATGTTAG
1 TTATG-TAG
651536 TTATGTCAG
1 TTATGT-AG
651545 TTATGTA-
1 TTATGTAG
651552 TTATGTATG
1 TTATGTA-G
*
651561 TCATGTAAG
1 TTATGT-AG
*
651570 TTGTGTAG
1 TTATGTAG
*
651578 -AATGTAAG
1 TTATGT-AG
*
651586 CTATGTAAG
1 TTATGT-AG
651595 TTATGTGAG
1 TTATGT-AG
*
651604 TTATATA-
1 TTATGTAG
* *
651611 -TAAGTTATC
1 TTATG-TA-G
* *
651620 TTA-ATAA
1 TTATGTAG
*
651627 TTATATAAG
1 TTATGT-AG
*
651636 CTATGTA-
1 TTATGTAG
651643 TTATGTTAG
1 TTATG-TAG
651652 TTATGCTAG
1 TTATG-TAG
651661 TTATGTA-
1 TTATGTAG
651668 TTATGTATG
1 TTATGTA-G
651677 TTATGTAAG
1 TTATGT-AG
*
651686 TTGTGTAG
1 TTATGTAG
651694 AATGTAACCT
Statistics
Matches: 165, Mismatches: 27, Indels: 47
0.69 0.11 0.20
Matches are distributed among these distances:
6 2 0.01
7 40 0.24
8 26 0.16
9 93 0.56
10 4 0.02
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (8 bp):
TTATGTAG
Found at i:651687 original size:25 final size:25
Alignment explanation
Indices: 651627--651692 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
651617 ATCTTAATAA
* *
651627 TTATATAAGCTATGTATTATGTTAG
1 TTATGTAAGTTATGTATTATGTTAG
651652 TTATGCT-AGTTATGTATTATG-TATG
1 TTATG-TAAGTTATGTATTATGTTA-G
*
651677 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
651693 GAATGTAACC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
24 3 0.09
25 31 0.89
26 1 0.03
ACGTcount: A:0.27, C:0.03, G:0.20, T:0.50
Consensus pattern (25 bp):
TTATGTAAGTTATGTATTATGTTAG
Found at i:651753 original size:20 final size:20
Alignment explanation
Indices: 651725--651835 Score: 115
Period size: 20 Copynumber: 5.8 Consensus size: 20
651715 GTTAGAAATT
*
651725 TTATATTAATATTATATAAG
1 TTATCTTAATATTATATAAG
651745 TTATCTTAATAATTATATAAG
1 TTATCTTAAT-ATTATATAAG
* *
651766 TTAT-GT-A-ATTAGA-AA-
1 TTATCTTAATATTATATAAG
* *
651781 TTGTCTTAATACTATATAAG
1 TTATCTTAATATTATATAAG
*
651801 TAATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
*
651821 TTATCTTAATTTTAT
1 TTATCTTAATATTAT
651836 GTAATTACAA
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
15 3 0.04
16 3 0.04
17 6 0.08
18 4 0.05
19 3 0.04
20 40 0.55
21 14 0.19
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.49
Consensus pattern (20 bp):
TTATCTTAATATTATATAAG
Found at i:651849 original size:66 final size:66
Alignment explanation
Indices: 651766--651962 Score: 229
Period size: 66 Copynumber: 3.0 Consensus size: 66
651756 ATTATATAAG
*
651766 TTATGTAATTAGAAATTG-TCT-TAATACTATATAA-GTAATCTTAATATTATATAAGTTATCTT
1 TTATGTAATTAGAAATTGATCTGTAAT--TAGA-AATGTAATCTTAATATTATATAAGTTATCTT
651828 AATT
63 AATT
* * ** * * *
651832 TTATGTAATTACAAATTGATGTGTGGTTAGAAATTTTATCTTAATATTTTATAAGTTATCTTAAT
1 TTATGTAATTAGAAATTGATCTGTAATTAGAAATGTAATCTTAATATTATATAAGTTATCTTAAT
651897 T
66 T
* ** * *
651898 TTATGTAATTAGAAATTGATGTGTGGTTAGAAATTTTATCTTAATATTATATAAGTTATCTTAAT
1 TTATGTAATTAGAAATTGATCTGTAATTAGAAATGTAATCTTAATATTATATAAGTTATCTTAAT
651963 AATTATATAA
Statistics
Matches: 118, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
65 2 0.02
66 112 0.95
67 2 0.02
68 2 0.02
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (66 bp):
TTATGTAATTAGAAATTGATCTGTAATTAGAAATGTAATCTTAATATTATATAAGTTATCTTAAT
T
Found at i:651958 original size:20 final size:20
Alignment explanation
Indices: 651933--652119 Score: 98
Period size: 20 Copynumber: 9.2 Consensus size: 20
651923 GTTAGAAATT
651933 TTATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
*
651953 TTATCTTAATAATTATATAAC
1 TTATCTTAAT-ATTATATAAG
* *
651974 TTAT-GT-A-ATTAGA-AA-
1 TTATCTTAATATTATATAAG
* * *
651989 TTGTCTTAACACTATATAAG
1 TTATCTTAATATTATATAAG
* *
652009 TAATCCTAATATTATATAAG
1 TTATCTTAATATTATATAAG
* *
652029 TTATCTTAATTTTATGTAA-
1 TTATCTTAATATTATATAAG
** * * * * *
652048 TTAGAAATTGATGTGTGGTTAGAAATT
1 TT--ATCTTAATAT-T--ATA-TAA-G
652075 TTATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
652095 TTATCTTAATAATTATATAAG
1 TTATCTTAAT-ATTATATAAG
652116 TTAT
1 TTAT
652120 GTAATTAGAA
Statistics
Matches: 122, Mismatches: 30, Indels: 29
0.67 0.17 0.16
Matches are distributed among these distances:
15 3 0.02
16 3 0.02
17 6 0.05
18 4 0.03
19 5 0.04
20 51 0.42
21 35 0.29
22 3 0.02
24 2 0.02
25 8 0.07
27 2 0.02
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.47
Consensus pattern (20 bp):
TTATCTTAATATTATATAAG
Found at i:651962 original size:208 final size:208
Alignment explanation
Indices: 651715--652104 Score: 726
Period size: 208 Copynumber: 1.9 Consensus size: 208
651705 TGTAGGTTAT
*
651715 GTTAGAAATTTTATATTAATATTATATAAGTTATCTTAATAATTATATAAGTTATGTAATTAGAA
1 GTTAGAAATTTTATATTAATATTATATAAGTTATCTTAATAATTATATAACTTATGTAATTAGAA
* *
651780 ATTGTCTTAATACTATATAAGTAATCTTAATATTATATAAGTTATCTTAATTTTATGTAATTACA
66 ATTGTCTTAACACTATATAAGTAATCCTAATATTATATAAGTTATCTTAATTTTATGTAATTACA
*
651845 AATTGATGTGTGGTTAGAAATTTTATCTTAATATTTTATAAGTTATCTTAATTTTATGTAATTAG
131 AATTGATGTGTGGTTAGAAATTTTATCTTAATATTATATAAGTTATCTTAATTTTATGTAATTAG
651910 AAATTGATGTGTG
196 AAATTGATGTGTG
*
651923 GTTAGAAATTTTATCTTAATATTATATAAGTTATCTTAATAATTATATAACTTATGTAATTAGAA
1 GTTAGAAATTTTATATTAATATTATATAAGTTATCTTAATAATTATATAACTTATGTAATTAGAA
*
651988 ATTGTCTTAACACTATATAAGTAATCCTAATATTATATAAGTTATCTTAATTTTATGTAATTAGA
66 ATTGTCTTAACACTATATAAGTAATCCTAATATTATATAAGTTATCTTAATTTTATGTAATTACA
652053 AATTGATGTGTGGTTAGAAATTTTATCTTAATATTATATAAGTTATCTTAAT
131 AATTGATGTGTGGTTAGAAATTTTATCTTAATATTATATAAGTTATCTTAAT
652105 AATTATATAA
Statistics
Matches: 176, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
208 176 1.00
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (208 bp):
GTTAGAAATTTTATATTAATATTATATAAGTTATCTTAATAATTATATAACTTATGTAATTAGAA
ATTGTCTTAACACTATATAAGTAATCCTAATATTATATAAGTTATCTTAATTTTATGTAATTACA
AATTGATGTGTGGTTAGAAATTTTATCTTAATATTATATAAGTTATCTTAATTTTATGTAATTAG
AAATTGATGTGTG
Found at i:652111 original size:21 final size:20
Alignment explanation
Indices: 652075--652119 Score: 81
Period size: 21 Copynumber: 2.2 Consensus size: 20
652065 GTTAGAAATT
652075 TTATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
652095 TTATCTTAATAATTATATAAG
1 TTATCTTAAT-ATTATATAAG
652116 TTAT
1 TTAT
652120 GTAATTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (20 bp):
TTATCTTAATATTATATAAG
Found at i:652139 original size:142 final size:142
Alignment explanation
Indices: 651873--652146 Score: 521
Period size: 142 Copynumber: 1.9 Consensus size: 142
651863 AATTTTATCT
*
651873 TAATATTTTATAAGTTATCTTAATTTTATGTAATTAGAAATTGATGTGTGGTTAGAAATTTTATC
1 TAATATTATATAAGTTATCTTAATTTTATGTAATTAGAAATTGATGTGTGGTTAGAAATTTTATC
651938 TTAATATTATATAAGTTATCTTAATAATTATATAACTTATGTAATTAGAAATTGTCTTAACACTA
66 TTAATATTATATAAGTTATCTTAATAATTATATAACTTATGTAATTAGAAATTGTCTTAACACTA
652003 TATAAGTAATCC
131 TATAAGTAATCC
652015 TAATATTATATAAGTTATCTTAATTTTATGTAATTAGAAATTGATGTGTGGTTAGAAATTTTATC
1 TAATATTATATAAGTTATCTTAATTTTATGTAATTAGAAATTGATGTGTGGTTAGAAATTTTATC
* *
652080 TTAATATTATATAAGTTATCTTAATAATTATATAAGTTATGTAATTAGAAATTGTCTTAATACTA
66 TTAATATTATATAAGTTATCTTAATAATTATATAACTTATGTAATTAGAAATTGTCTTAACACTA
652145 TA
131 TA
652147 CAAATAAAAA
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
142 129 1.00
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (142 bp):
TAATATTATATAAGTTATCTTAATTTTATGTAATTAGAAATTGATGTGTGGTTAGAAATTTTATC
TTAATATTATATAAGTTATCTTAATAATTATATAACTTATGTAATTAGAAATTGTCTTAACACTA
TATAAGTAATCC
Found at i:652215 original size:15 final size:15
Alignment explanation
Indices: 652195--652225 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
652185 TTACGTAAAC
652195 TAAATAACTTTGAAT
1 TAAATAACTTTGAAT
652210 TAAATAACTTTGAAT
1 TAAATAACTTTGAAT
652225 T
1 T
652226 CCGTCGTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (15 bp):
TAAATAACTTTGAAT
Found at i:659928 original size:21 final size:21
Alignment explanation
Indices: 659902--659943 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
659892 GAGAGTGATG
* *
659902 CATTTTTAAAAAATAATTACA
1 CATTTTAAAAAAATAAATACA
659923 CATTTTAAAAAAATAAATACA
1 CATTTTAAAAAAATAAATACA
659944 TCAATATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (21 bp):
CATTTTAAAAAAATAAATACA
Found at i:660175 original size:15 final size:16
Alignment explanation
Indices: 660145--660180 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
660135 TTTTTTTAAA
*
660145 ATATTAATTTATATTT
1 ATATTAATTTACATTT
660161 ATATT-ATTTACATTT
1 ATATTAATTTACATTT
660176 ATATT
1 ATATT
660181 CTTTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTAATTTACATTT
Found at i:660342 original size:21 final size:22
Alignment explanation
Indices: 660318--660373 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
660308 CCGTAAATCT
660318 TAAACCCTAAACT-ATAAACCC
1 TAAACCCTAAACTCATAAACCC
* * *
660339 TAAACCCCAAA-TCGTAAACCT
1 TAAACCCTAAACTCATAAACCC
*
660360 TAAACCTTAAACTC
1 TAAACCCTAAACTC
660374 GTCAATTAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.04
21 25 0.89
22 2 0.07
ACGTcount: A:0.45, C:0.32, G:0.02, T:0.21
Consensus pattern (22 bp):
TAAACCCTAAACTCATAAACCC
Found at i:660370 original size:14 final size:14
Alignment explanation
Indices: 660302--660371 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 14
660292 ATACTGTAAG
*
660302 CCTT-AACCGTAAA
1 CCTTAAACCCTAAA
*
660315 TCTTAAACCCTAAA
1 CCTTAAACCCTAAA
660329 -CTATAAACCCTAAA
1 CCT-TAAACCCTAAA
** * *
660343 CCCCAAATCGTAAA
1 CCTTAAACCCTAAA
*
660357 CCTTAAACCTTAAA
1 CCTTAAACCCTAAA
660371 C
1 C
660372 TCGTCAATTA
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
13 5 0.11
14 38 0.86
15 1 0.02
ACGTcount: A:0.43, C:0.31, G:0.03, T:0.23
Consensus pattern (14 bp):
CCTTAAACCCTAAA
Found at i:660720 original size:7 final size:7
Alignment explanation
Indices: 660700--660782 Score: 67
Period size: 7 Copynumber: 11.4 Consensus size: 7
660690 TACCCTTGAC
*
660700 ACCCTAA
1 ACCCCAA
*
660707 ACACCAA
1 ACCCCAA
660714 ACCCCAA
1 ACCCCAA
660721 ACCCCTAA
1 ACCCC-AA
*
660729 ATCCCAA
1 ACCCCAA
*
660736 ACCCTAA
1 ACCCCAA
660743 ACCCCAA
1 ACCCCAA
660750 ACCCCTAA
1 ACCCC-AA
* *
660758 ATCCCTA
1 ACCCCAA
* *
660765 ACACCTA
1 ACCCCAA
660772 ACCCCTAA
1 ACCCC-AA
660780 ACC
1 ACC
660783 AATAAACCTT
Statistics
Matches: 60, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
7 44 0.73
8 16 0.27
ACGTcount: A:0.41, C:0.48, G:0.00, T:0.11
Consensus pattern (7 bp):
ACCCCAA
Found at i:660729 original size:22 final size:21
Alignment explanation
Indices: 660701--660753 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
660691 ACCCTTGACA
660701 CCCTAAACACCAAACCCCAAAC
1 CCCTAAAC-CCAAACCCCAAAC
*
660723 CCCTAAATCCCAAACCCTAAAC
1 CCCTAAA-CCCAAACCCCAAAC
660745 CCC-AAACCC
1 CCCTAAACCC
660754 CTAAATCCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 3 0.10
21 3 0.10
22 22 0.76
23 1 0.03
ACGTcount: A:0.42, C:0.51, G:0.00, T:0.08
Consensus pattern (21 bp):
CCCTAAACCCAAACCCCAAAC
Found at i:660736 original size:15 final size:15
Alignment explanation
Indices: 660716--660772 Score: 80
Period size: 15 Copynumber: 3.9 Consensus size: 15
660706 AACACCAAAC
660716 CCCAAACCCCTAAAT
1 CCCAAACCCCTAAAT
*
660731 CCCAAA-CCCTAAAC
1 CCCAAACCCCTAAAT
660745 CCCAAACCCCTAAAT
1 CCCAAACCCCTAAAT
* *
660760 CCCTAACACCTAA
1 CCCAAACCCCTAA
660773 CCCCTAAACC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
14 13 0.35
15 24 0.65
ACGTcount: A:0.40, C:0.47, G:0.00, T:0.12
Consensus pattern (15 bp):
CCCAAACCCCTAAAT
Found at i:660747 original size:29 final size:30
Alignment explanation
Indices: 660705--660782 Score: 117
Period size: 29 Copynumber: 2.7 Consensus size: 30
660695 TTGACACCCT
660705 AAACACC-AAACCCCAAACCCCTAAATCCC
1 AAACACCTAAACCCCAAACCCCTAAATCCC
660734 AAAC-CCTAAACCCCAAACCCCTAAATCCC
1 AAACACCTAAACCCCAAACCCCTAAATCCC
*
660763 TAACACCT-AACCCCTAAACC
1 AAACACCTAAACCCC-AAACC
660783 AATAAACCTT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
28 2 0.04
29 35 0.78
30 8 0.18
ACGTcount: A:0.42, C:0.47, G:0.00, T:0.10
Consensus pattern (30 bp):
AAACACCTAAACCCCAAACCCCTAAATCCC
Found at i:660765 original size:8 final size:7
Alignment explanation
Indices: 660700--660796 Score: 65
Period size: 7 Copynumber: 13.3 Consensus size: 7
660690 TACCCTTGAC
660700 ACCCTAA
1 ACCCTAA
660707 ACACC-AA
1 AC-CCTAA
*
660714 ACCCCAA
1 ACCCTAA
660721 ACCCCTAA
1 A-CCCTAA
660729 ATCCC-AA
1 A-CCCTAA
660736 ACCCTAA
1 ACCCTAA
*
660743 ACCCCAA
1 ACCCTAA
660750 ACCCCTAA
1 A-CCCTAA
660758 ATCCCT-A
1 A-CCCTAA
660765 ACACCTAA
1 AC-CCTAA
*
660773 CCCCTAA
1 ACCCTAA
*
660780 ACCAATAA
1 ACC-CTAA
*
660788 ACCTTAA
1 ACCCTAA
660795 AC
1 AC
660797 TTTTAACTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
6 6 0.08
7 38 0.52
8 29 0.40
ACGTcount: A:0.43, C:0.44, G:0.00, T:0.12
Consensus pattern (7 bp):
ACCCTAA
Found at i:660880 original size:14 final size:15
Alignment explanation
Indices: 660863--660900 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
660853 CTTAAATCAG
660863 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
660877 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
660892 AATCCCTAA
1 AATCCCTAA
660901 ACCTTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.37, C:0.34, G:0.00, T:0.29
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:661205 original size:41 final size:41
Alignment explanation
Indices: 661154--661425 Score: 359
Period size: 41 Copynumber: 6.6 Consensus size: 41
661144 TTTGCGGTGT
* * * *
661154 TTCTTCAAAAACGCCGCTAAAGGCCCCAGCATTAACGGTGA
1 TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
* *
661195 TTCTTTAAAAACGCTGCTAAAGGCCCGAGCATTAGCGGCGC
1 TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
* * *
661236 TTCTTCAAAAACACTGCTAAAGGCCCGAGCATTAGTGGCGC
1 TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
* * * *
661277 TTCGTCAAAAACGCCGCTAAAGGCCCGAGCATTAGTGGTGT
1 TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
* *
661318 TTCTAT-AAAAACGCCGCTAAAGGACCAAGCATTAGCGGCGC
1 TTCT-TCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
*
661359 ATT-TTCAAAAACGCCGCTAAATGCCCGAGCATTAGCGGCGC
1 -TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
*
661400 TTCTTTAAAAACGCCGCTAAAGGCCC
1 TTCTTCAAAAACGCCGCTAAAGGCCC
661426 CAAAAACCCA
Statistics
Matches: 202, Mismatches: 25, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
40 3 0.01
41 196 0.97
42 3 0.01
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.21
Consensus pattern (41 bp):
TTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGC
Found at i:661378 original size:123 final size:123
Alignment explanation
Indices: 661158--661427 Score: 398
Period size: 123 Copynumber: 2.2 Consensus size: 123
661148 CGGTGTTTCT
* * * *
661158 TCAAAAACGCCGCTAAAGGCCCCAGCATTAACGGTGATTCTTTAAAAACGCTGCTAAAGGCCCGA
1 TCAAAAACGCCGCTAAAGGCCCCAGCATTAACGGTGATTCTATAAAAACGCCGCTAAAGGACCAA
* *
661223 GCATTAGCGGCGCTTCTTCAAAAACACTGCTAAAGGCCCGAGCATTAGTGGCGCTTCG
66 GCATTAGCGGCGCTTCTTCAAAAACACCGCTAAAGGCCCGAGCATTAGCGGCGCTTCG
* ** *
661281 TCAAAAACGCCGCTAAAGGCCCGAGCATTAGTGGTGTTTCTATAAAAACGCCGCTAAAGGACCAA
1 TCAAAAACGCCGCTAAAGGCCCCAGCATTAACGGTGATTCTATAAAAACGCCGCTAAAGGACCAA
* * *
661346 GCATTAGCGGCGCATT-TTCAAAAACGCCGCTAAATGCCCGAGCATTAGCGGCGCTTCT
66 GCATTAGCGGCGC-TTCTTCAAAAACACCGCTAAAGGCCCGAGCATTAGCGGCGCTTCG
*
661404 TTAAAAACGCCGCTAAAGGCCCCA
1 TCAAAAACGCCGCTAAAGGCCCCA
661428 AAAACCCAGA
Statistics
Matches: 131, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
123 129 0.98
124 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (123 bp):
TCAAAAACGCCGCTAAAGGCCCCAGCATTAACGGTGATTCTATAAAAACGCCGCTAAAGGACCAA
GCATTAGCGGCGCTTCTTCAAAAACACCGCTAAAGGCCCGAGCATTAGCGGCGCTTCG
Found at i:667124 original size:36 final size:35
Alignment explanation
Indices: 667062--667133 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 35
667052 CAAAATACCT
* *
667062 CCCAATTTAATGTTTTAAGAACTTGTCGAATACTCG
1 CCCAATTTAAAGTTTGAAGAACTTGTCGAAT-CTCG
* *
667098 CCCAATTTAAAGTTTGAA-AATGTTGTCGTATCTCG
1 CCCAATTTAAAGTTTGAAGAA-CTTGTCGAATCTCG
667133 C
1 C
667134 TTTGGCTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 7 0.23
36 24 0.77
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.36
Consensus pattern (35 bp):
CCCAATTTAAAGTTTGAAGAACTTGTCGAATCTCG
Found at i:668171 original size:15 final size:16
Alignment explanation
Indices: 668144--668173 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
668134 GATAACAATT
668144 AATATATATTATATAA
1 AATATATATTATATAA
668160 AATATA-ATTATATA
1 AATATATATTATATA
668174 TTAGTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATATTATATAA
Found at i:668514 original size:15 final size:16
Alignment explanation
Indices: 668494--668523 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
668484 CAATCTCCTA
668494 GACATA-ATTTATTTT
1 GACATACATTTATTTT
668509 GACATACATTTATTT
1 GACATACATTTATTT
668524 AAAAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (16 bp):
GACATACATTTATTTT
Found at i:678916 original size:15 final size:15
Alignment explanation
Indices: 678896--678972 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
678886 TTATGGAAAG
*
678896 TCAAATATATGGTTA
1 TCAAATATATGGATA
*
678911 TCAAATA-ATGGAAA
1 TCAAATATATGGATA
* *
678925 GTCAAAGATATGGGTA
1 -TCAAATATATGGATA
*
678941 TCAAATAT-TGGAAAA
1 TCAAATATATGG-ATA
* *
678956 TCAAAGATATGGGTA
1 TCAAATATATGGATA
678971 TC
1 TC
678973 GAGATATTGG
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
14 8 0.17
15 31 0.66
16 8 0.17
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (15 bp):
TCAAATATATGGATA
Found at i:678924 original size:30 final size:30
Alignment explanation
Indices: 678888--678972 Score: 134
Period size: 30 Copynumber: 2.8 Consensus size: 30
678878 ATCCGTATTT
* *
678888 ATGGAAAGTCAAATATATGGTTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
678918 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
* *
678948 TTGGAAAATCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
678973 GAGATATTGG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.27
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:683672 original size:15 final size:15
Alignment explanation
Indices: 683606--683707 Score: 66
Period size: 15 Copynumber: 6.7 Consensus size: 15
683596 TTATAGAAAG
683606 TCAAAGATATGGGTA
1 TCAAAGATATGGGTA
* *
683621 TCAGAAAGTATATGGTTG
1 TC--AAAG-ATATGGGTA
* **
683639 TCAAATA-ATGGAAA
1 TCAAAGATATGGGTA
683653 GTCAAAGATATGGGTA
1 -TCAAAGATATGGGTA
* **
683669 TCAAATAT-TGGAAAA
1 TCAAAGATATGG-GTA
683684 TCAAAGATATGGGTA
1 TCAAAGATATGGGTA
683699 TC-AAGATAT
1 TCAAAGATAT
683708 TGGCATAAGA
Statistics
Matches: 65, Mismatches: 15, Indels: 15
0.68 0.16 0.16
Matches are distributed among these distances:
14 14 0.22
15 27 0.42
16 11 0.17
17 4 0.06
18 9 0.14
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (15 bp):
TCAAAGATATGGGTA
Found at i:683706 original size:14 final size:14
Alignment explanation
Indices: 683657--683707 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
683647 TGGAAAGTCA
683657 AAGATATGGGTATC
1 AAGATATGGGTATC
**
683671 AA-ATATTGGAAAATC
1 AAGATA-TGG-GTATC
683686 AAAGATATGGGTATC
1 -AAGATATGGGTATC
683701 AAGATAT
1 AAGATAT
683708 TGGCATAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
13 3 0.10
14 12 0.41
15 6 0.21
16 5 0.17
17 3 0.10
ACGTcount: A:0.45, C:0.06, G:0.22, T:0.27
Consensus pattern (14 bp):
AAGATATGGGTATC
Found at i:683729 original size:36 final size:30
Alignment explanation
Indices: 683625--683710 Score: 118
Period size: 30 Copynumber: 2.8 Consensus size: 30
683615 TGGGTATCAG
* * * *
683625 AAAGTATATGGTTGTCAAATAATGGAAAGTC
1 AAAG-ATATGGGTATCAAATATTGGAAAATC
683656 AAAGATATGGGTATCAAATATTGGAAAATC
1 AAAGATATGGGTATCAAATATTGGAAAATC
683686 AAAGATATGGGTATCAAGATATTGG
1 AAAGATATGGGTATCAA-ATATTGG
683711 CATAAGAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 39 0.78
31 11 0.22
ACGTcount: A:0.43, C:0.06, G:0.23, T:0.28
Consensus pattern (30 bp):
AAAGATATGGGTATCAAATATTGGAAAATC
Found at i:685116 original size:15 final size:15
Alignment explanation
Indices: 685091--685125 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
685081 AACTCTATTT
*
685091 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
685105 TAATTAATATTAAGA
1 TAATTAATATTAAGA
685120 TAATTA
1 TAATTA
685126 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:686596 original size:23 final size:23
Alignment explanation
Indices: 686569--686642 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
686559 AATTGGCTTA
* *
686569 GTATACTTGGTTGTGTTCGGAGG
1 GTATAATTGGTTGTGTTCGAAGG
* *
686592 TTATATATATGGTTGTGTTTGAAGG
1 GTATA-AT-TGGTTGTGTTCGAAGG
*
686617 GTATATTTGGTTGTGTTCGAAGG
1 GTATAATTGGTTGTGTTCGAAGG
686640 GTA
1 GTA
686643 CATATGGCTG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
23 22 0.52
24 2 0.05
25 18 0.43
ACGTcount: A:0.19, C:0.04, G:0.34, T:0.43
Consensus pattern (23 bp):
GTATAATTGGTTGTGTTCGAAGG
Found at i:686598 original size:25 final size:24
Alignment explanation
Indices: 686570--686647 Score: 95
Period size: 25 Copynumber: 3.2 Consensus size: 24
686560 ATTGGCTTAG
* *
686570 TATACTTGGTTGTGTTCGGAGGTTA
1 TATA-TTGGTTGTGTTCGAAGGGTA
*
686595 TATATATGGTTGTGTTTGAAGGGTA
1 TATAT-TGGTTGTGTTCGAAGGGTA
686620 TAT-TTGGTTGTGTTCGAAGGGTA
1 TATATTGGTTGTGTTCGAAGGGTA
*
686643 CATAT
1 TATAT
686648 GGCTGTATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
23 20 0.43
24 3 0.07
25 23 0.50
ACGTcount: A:0.21, C:0.05, G:0.31, T:0.44
Consensus pattern (24 bp):
TATATTGGTTGTGTTCGAAGGGTA
Found at i:689302 original size:2 final size:2
Alignment explanation
Indices: 689295--689339 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
689285 ACATACAAAT
689295 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
689337 AC A
1 AC A
689340 TAGTATTCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:693960 original size:20 final size:20
Alignment explanation
Indices: 693903--693963 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
693893 CATTACAACA
*
693903 AAAATTACTAAAATTT-TGAC
1 AAAATTAC-AAAATTTCTTAC
** *
693923 AAAATTATTAAATCTCTTAC
1 AAAATTACAAAATTTCTTAC
693943 AAAATTACAAAATTTCTTAC
1 AAAATTACAAAATTTCTTAC
693963 A
1 A
693964 GCTTTATTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
19 5 0.15
20 28 0.85
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAATTACAAAATTTCTTAC
Found at i:694028 original size:20 final size:20
Alignment explanation
Indices: 694003--694047 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
693993 ACTTTGGATA
694003 TCTTATAAAATTATTAAACT
1 TCTTATAAAATTATTAAACT
* * *
694023 TCTTATAAGATTGTTAAATT
1 TCTTATAAAATTATTAAACT
694043 TCTTA
1 TCTTA
694048 CAACATTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (20 bp):
TCTTATAAAATTATTAAACT
Found at i:694055 original size:20 final size:20
Alignment explanation
Indices: 694016--694056 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
694006 TATAAAATTA
* *
694016 TTAAACTTCTTATAAGATTG
1 TTAAACTTCTTACAACATTG
*
694036 TTAAATTTCTTACAACATTG
1 TTAAACTTCTTACAACATTG
694056 T
1 T
694057 AAAGCTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.46
Consensus pattern (20 bp):
TTAAACTTCTTACAACATTG
Found at i:699680 original size:24 final size:22
Alignment explanation
Indices: 699653--699712 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
699643 TGAGTGAAAA
699653 TTCTCTTTGAGTTCTCCAAGAATT
1 TTCTCTTTGAGTTCT-CAA-AATT
**
699677 TTCTC-TTGAGGATTCTTTAAATT
1 TTCTCTTTGA-G-TTCTCAAAATT
699700 TTCTCTTTGAGTT
1 TTCTCTTTGAGTT
699713 TTCTTAGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
22 2 0.06
23 14 0.45
24 11 0.35
25 4 0.13
ACGTcount: A:0.18, C:0.17, G:0.13, T:0.52
Consensus pattern (22 bp):
TTCTCTTTGAGTTCTCAAAATT
Found at i:709977 original size:20 final size:20
Alignment explanation
Indices: 709951--710023 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
709941 TACCTCAAGA
709951 AAGGTATCGATACTTCAATC
1 AAGGTATCGATACTTCAATC
* *
709971 AAAGTATCAATA-TT-ATAGTC
1 AAGGTATCGATACTTCA-A-TC
709991 AAGGTATCGATACTTCAAT-
1 AAGGTATCGATACTTCAATC
710010 ATAGGTATCGATAC
1 A-AGGTATCGATAC
710024 ATGTTGAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
18 1 0.02
19 4 0.09
20 35 0.80
21 3 0.07
22 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (20 bp):
AAGGTATCGATACTTCAATC
Found at i:714264 original size:13 final size:13
Alignment explanation
Indices: 714221--714268 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
714211 TTTGTTTTTA
714221 AAAAAATATAAAT
1 AAAAAATATAAAT
*
714234 AAATAAATGA-AAAC
1 AAA-AAAT-ATAAAT
714248 AAAAAATATAAAT
1 AAAAAATATAAAT
714261 AAAAAATA
1 AAAAAATA
714269 ATTACAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 1 0.03
13 18 0.60
14 10 0.33
15 1 0.03
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (13 bp):
AAAAAATATAAAT
Found at i:720710 original size:13 final size:15
Alignment explanation
Indices: 720692--720723 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
720682 CCTTTATTTC
720692 CTTT-CCCTCT-TCT
1 CTTTCCCCTCTCTCT
720705 CTTTCCCCTCTCTCT
1 CTTTCCCCTCTCTCT
720720 CTTT
1 CTTT
720724 TTATAATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.24
14 6 0.35
15 7 0.41
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (15 bp):
CTTTCCCCTCTCTCT
Found at i:721742 original size:3 final size:3
Alignment explanation
Indices: 721736--721786 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
721726 GTTTAACAAC
721736 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
721784 AGA
1 AGA
721787 TGATGATATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:724031 original size:15 final size:17
Alignment explanation
Indices: 723994--724032 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
723984 GAAGTTTGAG
723994 ATATTTTTTAATACTTT
1 ATATTTTTTAATACTTT
724011 ATTATTTTTT-ATA-TTT
1 A-TATTTTTTAATACTTT
724027 ATATTT
1 ATATTT
724033 CTAAGGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 5 0.24
16 4 0.19
17 4 0.19
18 8 0.38
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
ATATTTTTTAATACTTT
Found at i:724724 original size:39 final size:40
Alignment explanation
Indices: 724589--724725 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 40
724579 CGTTTGGATA
* * *
724589 AAAAATGCCGCTAAAAATCGAGCATTAGCGGCGCTTTACG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTAGG
* * * **
724629 TAAAACGCTGCTAAAGATCGAGCATTAGCGGCGCTTCCAGG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCG-TTTTAGG
* ** *
724670 -AAAGCGCCGAGAAAAAT-GAGCATTAGCGGCGTTTTTTGG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCG-TTTTAGG
*
724709 AAAAACGCCGCAAAAAA
1 AAAAACGCCGCTAAAAA
724726 CCTAAGCCCA
Statistics
Matches: 75, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
39 18 0.24
40 54 0.72
41 3 0.04
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGTTTTAGG
Found at i:724821 original size:18 final size:18
Alignment explanation
Indices: 724795--724830 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
724785 CGCCACTAAT
*
724795 GCTCGGGTCTTTAGCGGC
1 GCTCAGGTCTTTAGCGGC
*
724813 GCTCAGGTCTTTCGCGGC
1 GCTCAGGTCTTTAGCGGC
724831 ATTTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.31, G:0.36, T:0.28
Consensus pattern (18 bp):
GCTCAGGTCTTTAGCGGC
Found at i:728366 original size:28 final size:28
Alignment explanation
Indices: 728334--728472 Score: 172
Period size: 28 Copynumber: 5.0 Consensus size: 28
728324 AACCGTGTGT
* * *
728334 CCACTACTTTTCAGATTTTATAGTTTTG
1 CCACTATTTTTTAGATTTTACAGTTTTG
* *
728362 CCACT-TTTTTTCAAATTTTACAATTTTG
1 CCACTATTTTTT-AGATTTTACAGTTTTG
*
728390 CCATTATTTTTTAGATTTTACAGTTTTG
1 CCACTATTTTTTAGATTTTACAGTTTTG
**
728418 CCACTGGTTTTTAGATTTTACAGTTTTG
1 CCACTATTTTTTAGATTTTACAGTTTTG
* *
728446 ACACTATTTTTTAGATTTTATAGTTTT
1 CCACTATTTTTTAGATTTTACAGTTTT
728473 ATCTTATTTT
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
27 4 0.04
28 84 0.89
29 6 0.06
ACGTcount: A:0.22, C:0.14, G:0.10, T:0.54
Consensus pattern (28 bp):
CCACTATTTTTTAGATTTTACAGTTTTG
Found at i:733560 original size:41 final size:41
Alignment explanation
Indices: 733499--733642 Score: 207
Period size: 41 Copynumber: 3.5 Consensus size: 41
733489 AAAGTAATCT
*
733499 AGACATTACGTCTAGCAGGCTTGATGCCGATGAAACATACC
1 AGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATACC
* *
733540 AGTCATTACGTCTAGTAGGCTTGATGCCGGTGAAACATACC
1 AGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATACC
* * *
733581 AAACTTTACGTCTAGCAGGCTTGATGCCGGTGAAACATATC
1 AGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATACC
* * *
733622 AGACTTTATGTCTAGAAGGCT
1 AGACATTACGTCTAGCAGGCT
733643 AAGTGCCGGT
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (41 bp):
AGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACATACC
Found at i:733678 original size:82 final size:82
Alignment explanation
Indices: 733510--733683 Score: 190
Period size: 82 Copynumber: 2.1 Consensus size: 82
733500 GACATTACGT
* * *
733510 CTAGCAGGCTTGATGCCGATGAAACATACCAGTCATTACGTCTAGTAGGCTTGATGCCGGTGAAA
1 CTAGCAGGCTTGATGCCGATGAAACATACCAGACATTACGTCTAGAAGGCTAGATGCCGGTGAAA
* * * *
733575 CATACCAAACTTTACGT
66 CAAAACAAACTTTAAGC
* * * * *
733592 CTAGCAGGCTTGATGCCGGTGAAACATATCAGACTTTATGTCTAGAAGGCTA-AGTGCCGGTG-T
1 CTAGCAGGCTTGATGCCGATGAAACATACCAGACATTACGTCTAGAAGGCTAGA-TGCCGGTGAA
**
733655 ACTAAAACAGGCTTTAAGC
65 AC-AAAACAAACTTTAAGC
733674 CTAGCAGGCT
1 CTAGCAGGCT
733684 AAGTGCCGGT
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
81 3 0.04
82 73 0.96
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (82 bp):
CTAGCAGGCTTGATGCCGATGAAACATACCAGACATTACGTCTAGAAGGCTAGATGCCGGTGAAA
CAAAACAAACTTTAAGC
Found at i:734382 original size:13 final size:13
Alignment explanation
Indices: 734364--734388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
734354 NNNTATATGA
734364 TATTTATGTGTTT
1 TATTTATGTGTTT
734377 TATTTATGTGTT
1 TATTTATGTGTT
734389 GTTTTAGTTA
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:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (13 bp):
TATTTATGTGTTT
Found at i:737099 original size:130 final size:129
Alignment explanation
Indices: 736820--737100 Score: 348
Period size: 129 Copynumber: 2.2 Consensus size: 129
736810 AAGCTTATTA
* * **
736820 ATGATCATGAACATTTTCTTCTGAGTTAGCTTATTTACGATCACAACTTCAAACAACTCATTGGT
1 ATGATCATGAACATTTTCTTCTAAGTTAGCTTATTTACGATCACAACTCCAAACAACTCATTAAT
* * *
736885 TTACAATCATGATTGATATTATCAAGGCTCGCTATTTAGGATCACAACCTATGTTCATTGATTT
66 TTACAATCATGAGTGATATTATCAAGGCTCGCTATTTACGATCACAACCTAAGTTCATTGATTT
* * * * **
736949 ACGATCATGAACATTTTCTTCTAAGTTAG-TTGATTTACGATCGCAACTCCAACCAGCTTGTTAA
1 ATGATCATGAACATTTTCTTCTAAGTTAGCTT-ATTTACGATCACAACTCCAAACAACTCATTAA
* * * * * * *
737013 TTTACGATCATGAGTGCTATTATTAAGGTTCGTTGATTTACGATCATAGCCTAAGTTCATTGATT
65 TTTACAATCATGAGTGATATTATCAAGGCTCGCT-ATTTACGATCACAACCTAAGTTCATTGATT
737078 T
129 T
*
737079 ATGATCATGAACAATTTCTTCT
1 ATGATCATGAACATTTTCTTCT
737101 TAAATTCAAA
Statistics
Matches: 128, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
128 2 0.02
129 79 0.62
130 47 0.37
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (129 bp):
ATGATCATGAACATTTTCTTCTAAGTTAGCTTATTTACGATCACAACTCCAAACAACTCATTAAT
TTACAATCATGAGTGATATTATCAAGGCTCGCTATTTACGATCACAACCTAAGTTCATTGATTT
Found at i:737367 original size:3 final size:3
Alignment explanation
Indices: 737354--737394 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
737344 ATTAGTGAGG
*
737354 TTC TT- TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
737395 CACTTCTCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:747052 original size:54 final size:54
Alignment explanation
Indices: 747019--747173 Score: 156
Period size: 54 Copynumber: 2.9 Consensus size: 54
747009 GGTTTGTCAT
*
747019 ATGGCCTAGCACACGACCGTGTGACTCAAGTCAAAGAGTTACATGGTCAGACAC
1 ATGGCCTAGCACACGACCGTGTGACTCAAGTCAAAGAGTTACACGGTCAGACAC
* * * **
747073 ATGGCCT-GACACACGCCCGTGTGACTCAAGTCAGAGAGTTACACTGCTTGGGACAC
1 ATGGCCTAG-CACACGACCGTGTGACTCAAGTCAAAGAGTTACAC-G-GTCAGACAC
* * * *
747129 --GGCTTAGCACGC-ACCCATGTGACTCAAGACAAAGAGTTACACGGT
1 ATGGCCTAGCACACGA-CCGTGTGACTCAAGTCAAAGAGTTACACGGT
747174 TTGACACACA
Statistics
Matches: 83, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
52 1 0.01
53 2 0.02
54 72 0.87
55 2 0.02
56 6 0.07
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (54 bp):
ATGGCCTAGCACACGACCGTGTGACTCAAGTCAAAGAGTTACACGGTCAGACAC
Found at i:747740 original size:19 final size:20
Alignment explanation
Indices: 747698--747745 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
747688 GCGGTAGGAA
747698 ATAA-AAGAAAAAGGTAAAC
1 ATAAGAAGAAAAAGGTAAAC
747717 A-AAGAAGAAAAA-G-AAAC
1 ATAAGAAGAAAAAGGTAAAC
747734 GATAAGAAGAAA
1 -ATAAGAAGAAA
747746 GATAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.15
18 4 0.15
19 18 0.69
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (20 bp):
ATAAGAAGAAAAAGGTAAAC
Found at i:754355 original size:13 final size:13
Alignment explanation
Indices: 754339--754364 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
754329 CTAGTCAGTT
754339 TTACATTAAAAAG
1 TTACATTAAAAAG
754352 TTACATTAAAAAG
1 TTACATTAAAAAG
754365 GCCTAGCAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
TTACATTAAAAAG
Found at i:770121 original size:40 final size:40
Alignment explanation
Indices: 770076--770187 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 40
770066 GCGTTTGGAA
* *
770076 AAAAACGCCGCCAAAAATTGAGCATTACCAGCGC-TTTAC
1 AAAAACGCCGCTAAAAATTGAGCATTAGCAGCGCATTTAC
* * * * * * *
770115 GTAAAACGCTGGTAAAGATCGAGCATTAGCGGCGCATTTTC
1 -AAAAACGCCGCTAAAAATTGAGCATTAGCAGCGCATTTAC
770156 AAAAACGCCGCTAAAAA-TGAGCATTAGCAGCG
1 AAAAACGCCGCTAAAAATTGAGCATTAGCAGCG
770188 TTTTTTGGAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
39 13 0.23
40 39 0.70
41 4 0.07
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATTGAGCATTAGCAGCGCATTTAC
Found at i:770200 original size:40 final size:38
Alignment explanation
Indices: 770076--770201 Score: 99
Period size: 40 Copynumber: 3.2 Consensus size: 38
770066 GCGTTTGGAA
* * * *
770076 AAAAACGCCGCCAAAAATTGAGCATTACCAGCGCTTTACG
1 AAAAACGCCGCTAAAAA-TGAGCATTAGCAGCGATTT-TG
* * * * * *
770116 TAAAACGCTGGTAAAGATCGAGCATTAGCGGCGCATTTTC
1 AAAAACGCCGCTAAAAAT-GAGCATTAGCAGCG-ATTTTG
*
770156 AAAAACGCCGCTAAAAATGAGCATTAGCAGCGTTTTTTGG
1 AAAAACGCCGCTAAAAATGAGCATTAGCAGCG-ATTTT-G
770196 AAAAAC
1 AAAAAC
770202 ACCTCAAAAA
Statistics
Matches: 65, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
39 18 0.28
40 44 0.68
41 3 0.05
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (38 bp):
AAAAACGCCGCTAAAAATGAGCATTAGCAGCGATTTTG
Found at i:770690 original size:14 final size:15
Alignment explanation
Indices: 770660--770692 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
770650 AAGGTTTATA
*
770660 GATTATGGAATTAGG
1 GATTATGGAAGTAGG
770675 GATTATGG-AGTAGG
1 GATTATGGAAGTAGG
770689 GATT
1 GATT
770693 CTGATTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.33
Consensus pattern (15 bp):
GATTATGGAAGTAGG
Found at i:770842 original size:7 final size:7
Alignment explanation
Indices: 770830--770899 Score: 60
Period size: 7 Copynumber: 10.7 Consensus size: 7
770820 TAAATAACGT
770830 TTAGGGG
1 TTAGGGG
770837 TTAGGGG
1 TTAGGGG
*
770844 TTAGGGA
1 TTAGGGG
*
770851 TTCGGGG
1 TTAGGGG
*
770858 -T-CGGG
1 TTAGGGG
770863 TTA-GGG
1 TTAGGGG
770869 TTA-GGG
1 TTAGGGG
770875 TTA-GGG
1 TTAGGGG
*
770881 TTAGGGT
1 TTAGGGG
*
770888 TTAGGGT
1 TTAGGGG
770895 TTAGG
1 TTAGG
770900 ATTTAGATTA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
5 3 0.05
6 20 0.36
7 32 0.58
ACGTcount: A:0.14, C:0.03, G:0.50, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:770869 original size:6 final size:6
Alignment explanation
Indices: 770834--770895 Score: 70
Period size: 6 Copynumber: 9.8 Consensus size: 6
770824 TAACGTTTAG
* * *
770834 GGGTTA GGGGTTA GGGATTC GGGGTC GGGTTA GGGTTA GGGTTA GGGTTA
1 GGGTTA -GGGTTA GGG-TTA GGGTTA GGGTTA GGGTTA GGGTTA GGGTTA
770884 GGGTTTA GGGTT
1 GGG-TTA GGGTT
770896 TAGGATTTAG
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
6 32 0.65
7 17 0.35
ACGTcount: A:0.13, C:0.03, G:0.52, T:0.32
Consensus pattern (6 bp):
GGGTTA
Found at i:770904 original size:7 final size:7
Alignment explanation
Indices: 770828--770905 Score: 58
Period size: 7 Copynumber: 11.9 Consensus size: 7
770818 ATTAAATAAC
770828 GTTTAGG
1 GTTTAGG
*
770835 GGTTAGG
1 GTTTAGG
*
770842 GGTTAGG
1 GTTTAGG
* *
770849 GATTCGG
1 GTTTAGG
* *
770856 G-GTCGG
1 GTTTAGG
770862 G-TTAGG
1 GTTTAGG
770868 G-TTAGG
1 GTTTAGG
770874 G-TTAGG
1 GTTTAGG
770880 G-TTAGG
1 GTTTAGG
770886 GTTTAGG
1 GTTTAGG
770893 GTTTAGG
1 GTTTAGG
*
770900 ATTTAG
1 GTTTAG
770906 ATTAATTAGT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
6 27 0.43
7 36 0.57
ACGTcount: A:0.15, C:0.03, G:0.47, T:0.35
Consensus pattern (7 bp):
GTTTAGG
Found at i:772011 original size:21 final size:21
Alignment explanation
Indices: 771985--772030 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
771975 AAAAATCCCC
*
771985 TCCCCCC-GAAATCCCCAACTT
1 TCCCCCCTAAAATCCCCAA-TT
*
772006 TCCCCCCTAAAATCCCTAATT
1 TCCCCCCTAAAATCCCCAATT
772027 TCCC
1 TCCC
772031 ACATCCCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.24, C:0.50, G:0.02, T:0.24
Consensus pattern (21 bp):
TCCCCCCTAAAATCCCCAATT
Found at i:776180 original size:43 final size:43
Alignment explanation
Indices: 776125--776355 Score: 345
Period size: 43 Copynumber: 5.3 Consensus size: 43
776115 TAAAAGTCAA
* * * * *
776125 TCTTATAGCGGCGTTTGTAATAGAAACGCCGCTAAAGGTCCTAG
1 TCTT-TAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGGTCTTGG
* * * *
776169 TTTTTAACGGCGTTTGTAAGAAAAGCGCCGCTAAAGGTCTTGG
1 TCTTTAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGGTCTTGG
*
776212 TCTTTAGCGGCGTTTGTGAGAGAAGGGCCGCTAAAGGTCTTGG
1 TCTTTAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGGTCTTGG
776255 TCTTTAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGGTCTTGG
1 TCTTTAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGGTCTTGG
* *
776298 TCTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGC
1 TCTTTAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGGTCTTGG
776341 TCTTTAGCGGCGTTT
1 TCTTTAGCGGCGTTT
776356 TTTTCTATAA
Statistics
Matches: 172, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
43 169 0.98
44 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.29
Consensus pattern (43 bp):
TCTTTAGCGGCGTTTGTGAGAGAAGCGCCGCTAAAGGTCTTGG
Found at i:779797 original size:26 final size:27
Alignment explanation
Indices: 779752--779803 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
779742 TTATTTAATC
*
779752 AATTAATTTATTTAATTAAATAAACTA
1 AATTAATTTACTTAATTAAATAAACTA
779779 AATTAATTT-CTTAATTAAATAAACT
1 AATTAATTTACTTAATTAAATAAACT
779804 TCTCAACTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (27 bp):
AATTAATTTACTTAATTAAATAAACTA
Found at i:782182 original size:114 final size:114
Alignment explanation
Indices: 781996--782562 Score: 881
Period size: 114 Copynumber: 5.0 Consensus size: 114
781986 CGCAACCGAT
781996 TGAGTATTAGCGGCGTTTCTATAAAAACGCCGCAAAAAACT-AAACCCAGACGACGTCGTTTGGA
1 TGAGTATTAGCGGCGTTTCTATAAAAACGCCGC-AAAAACTAAAACCCAGACGACGTCGTTTGGA
*
782060 GACACTTCGGTGACTTTAGTGGCGTTTTTCTAATAGCGCCGCTAATAATA
65 GACACTTCGGTGACATTAGTGGCGTTTTTCTAATAGCGCCGCTAATAATA
* *
782110 TGAGTATTAGCGGCGTTTCTGTAAAAATGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
1 TGAGTATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
*
782175 ACACTTCGGTGACATTAGTGGCGTTTTT-TGAATAGCACCGCTAATAATA
66 ACACTTCGGTGACATTAGTGGCGTTTTTCT-AATAGCGCCGCTAATAATA
* * *
782224 TGAGTATTAGCGACGTTTCTATAAAAATGCCGCAAAAACTAAACCCCAGACGACGTCGTTTGGAG
1 TGAGTATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
*
782289 ACACTTCGGTGACTTTAGTGGCGTTTTTCTAATAGCGCCGCTAATAATA
66 ACACTTCGGTGACATTAGTGGCGTTTTTCTAATAGCGCCGCTAATAATA
* * *
782338 TGAGTATTAGCGGCGTTTCTACAAAAACGCCAG-AAAAACTAAAACCCAAACGACTTCGTTTGGA
1 TGAGTATTAGCGGCGTTTCTATAAAAACGCC-GCAAAAACTAAAACCCAGACGACGTCGTTTGGA
* * * *
782402 GACACTTCGGTGACATTAGTGGCGTTTTTCGAGTAGTGCCACTAATAATA
65 GACACTTCGGTGACATTAGTGGCGTTTTTCTAATAGCGCCGCTAATAATA
* * * *
782452 TGAGTATTAGTGGCGTTTTTTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTTGTCTGGA
1 TGAGTATTAGCGGCG-TTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGA
*
782517 GACACTTCGGTGACATTAGTGGC-TTTTTTTGAATAGCGCCGCTAAT
65 GACACTTCGGTGACATTAGTGGCGTTTTTCT-AATAGCGCCGCTAAT
782563 TGATGCGGAA
Statistics
Matches: 414, Mismatches: 32, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
113 8 0.02
114 328 0.79
115 78 0.19
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (114 bp):
TGAGTATTAGCGGCGTTTCTATAAAAACGCCGCAAAAACTAAAACCCAGACGACGTCGTTTGGAG
ACACTTCGGTGACATTAGTGGCGTTTTTCTAATAGCGCCGCTAATAATA
Found at i:801353 original size:43 final size:43
Alignment explanation
Indices: 801220--801471 Score: 234
Period size: 43 Copynumber: 5.8 Consensus size: 43
801210 ATCTGCCAAA
* * * * *
801220 TTTAGTGGCGTTTTTTGGTAAAAGCACCGCTAAAGATAAGGGTC
1 TTTAGCGGCG-TTTGTGGGAAAAGCGCCGCTAAAGATCAGGGTC
* * *
801264 TTTAGCGGCGTTTGTGGAAAAAAGCGCCACTAAAGATCATGGTC
1 TTTAGCGGCGTTTGTGG-GAAAAGCGCCGCTAAAGATCAGGGTC
* * * *
801308 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAAATTAGGATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGTC
* *** * *
801351 TTTAGTGGCGTTTGTGGTCTAGGCGCCGCTATAGATCAGGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGTC
* * ****
801394 TTTTGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCCTAATC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGTC
* * * *
801437 TTTAGCGGCGCTTGTTGCAAAAACGCCGCTAAAGA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGA
801472 CCCTGATCTT
Statistics
Matches: 167, Mismatches: 40, Indels: 3
0.80 0.19 0.01
Matches are distributed among these distances:
43 120 0.72
44 47 0.28
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCAGGGTC
Found at i:801464 original size:86 final size:86
Alignment explanation
Indices: 801262--801575 Score: 292
Period size: 86 Copynumber: 3.6 Consensus size: 86
801252 AAGATAAGGG
* * * *
801262 TCTTTAGCGGCGTTTGTGGAAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTGTGGGG
1 TCTTTAGCGGCGCTTGTGGCAAAAA-CGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGGGA
**
801327 AAAGCGCCGCTAAA-A-ATTAGGA
65 AAAGCGCCGCTAAAGACCCTA--A
* * * ** * * *
801349 TCTTTAGTGGCGTTTGTGGTC-TAGGCGCCGCTATAGATCAGGGTCTTTTGCGGCGTTTGTGGGA
1 TCTTTAGCGGCGCTTGTGG-CAAAAACGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGGGA
801413 AAAGCGCCGCTAAAGACCCTAA
65 AAAGCGCCGCTAAAGACCCTAA
* * * * * ** * * *
801435 TCTTTAGCGGCGCTTGTTGCAAAAACGCCGCTAAAGACCCTGATCTTCAGCGGCGACTCTCGAAA
1 TCTTTAGCGGCGCTTGTGGCAAAAACGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGGGAA
*
801500 AAACGCCGCTAAAGACCCTAA
66 AAGCGCCGCTAAAGACCCTAA
* * * * * *
801521 TCTTTAGCGGCGCTTCTAGCAAAAACGTCGCTAAAGACCCTGATCTTTAGCGGCG
1 TCTTTAGCGGCGCTTGTGGCAAAAACGCCGCTAAAGATCATGGTCTTTAGCGGCG
801576 CTTCCACTAA
Statistics
Matches: 188, Mismatches: 35, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
85 1 0.01
86 165 0.88
87 20 0.11
88 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.25
Consensus pattern (86 bp):
TCTTTAGCGGCGCTTGTGGCAAAAACGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGGGAA
AAGCGCCGCTAAAGACCCTAA
Found at i:801472 original size:43 final size:43
Alignment explanation
Indices: 801412--801598 Score: 243
Period size: 43 Copynumber: 4.4 Consensus size: 43
801402 CGTTTGTGGG
* * *
801412 AAAAGCGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTGTTGC
1 AAAAACGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTCTAGC
* * * *
801455 AAAAACGCCGCTAAAGACCCTGATCTTCAGCGGCGAC-TCTCGA
1 AAAAACGCCGCTAAAGACCCTAATCTTTAGCGGCG-CTTCTAGC
801498 AAAAACGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTCTAGC
1 AAAAACGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTCTAGC
* * *
801541 AAAAACGTCGCTAAAGACCCTGATCTTTAGCGGCGCTTCCA-C
1 AAAAACGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTCTAGC
* *
801583 TAAAGCGCCGCTAAAG
1 AAAAACGCCGCTAAAG
801599 GTCTTAGTCT
Statistics
Matches: 126, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
42 15 0.12
43 110 0.87
44 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACCCTAATCTTTAGCGGCGCTTCTAGC
Found at i:801785 original size:22 final size:22
Alignment explanation
Indices: 801757--801799 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
801747 TTGCGGCGCT
*
801757 AAAAAGCACCGCTAAAGGCCTA
1 AAAAAGCACCGCTAAAAGCCTA
*
801779 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCACCGCTAAAAGCCT
801800 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.28, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAAGCACCGCTAAAAGCCTA
Found at i:802174 original size:28 final size:27
Alignment explanation
Indices: 802130--802183 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
802120 GAAGTAGGGA
* *
802130 AGAAAAAGAGGGAAAATATAAAAAGGAG
1 AGAAAAAAAGGGAAAAT-GAAAAAGGAG
*
802158 AGAAAAAAAGGGGAAATGAAAAAGGA
1 AGAAAAAAAGGGAAAATGAAAAAGGA
802184 AATAGCAGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.65, C:0.00, G:0.30, T:0.06
Consensus pattern (27 bp):
AGAAAAAAAGGGAAAATGAAAAAGGAG
Found at i:808277 original size:13 final size:13
Alignment explanation
Indices: 808259--808283 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
808249 GGGGGATTTG
808259 ATTTTTATTTTTT
1 ATTTTTATTTTTT
808272 ATTTTTATTTTT
1 ATTTTTATTTTT
808284 CTTTGTTCGG
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTTATTTTTT
Done.