Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006984.1 Hibiscus syriacus cultivar Beakdansim tig00017994_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62949
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Found at i:444 original size:4 final size:4
Alignment explanation
Indices: 437--494 Score: 57
Period size: 4 Copynumber: 14.8 Consensus size: 4
427 AACGAAAGAA
* * **
437 AAAT AAAT AAAT AAAT AAAG ACAT AAA- AAAT AAAT AAA- AAGC AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
483 GAAAT AAAT AAA
1 -AAAT AAAT AAA
495 ATACTAGAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
3 5 0.11
4 35 0.80
5 4 0.09
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:448 original size:32 final size:31
Alignment explanation
Indices: 381--474 Score: 97
Period size: 32 Copynumber: 3.1 Consensus size: 31
371 AGACAAAGAG
* * * *
381 AAATAATAATAAATAACGATAACAAGTAAATT
1 AAATAAAAATAAAGAACGATAAAAAATAAA-T
*
413 AAATAAAAATAAAGAACGAAAGAAAAATAAAT
1 AAATAAAAATAAAGAACGATA-AAAAATAAAT
445 AAAT--AAATAAAG-AC-ATAAAAAATAAAT
1 AAATAAAAATAAAGAACGATAAAAAATAAAT
472 AAA
1 AAA
475 AAGCAAATGA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
27 13 0.24
28 2 0.04
29 2 0.04
30 8 0.15
32 23 0.42
33 7 0.13
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.18
Consensus pattern (31 bp):
AAATAAAAATAAAGAACGATAAAAAATAAAT
Found at i:489 original size:27 final size:27
Alignment explanation
Indices: 435--490 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
425 AGAACGAAAG
* *
435 AAAAATAAATAAATAAATAAAGACATA
1 AAAAATAAATAAATAAACAAAGAAATA
*
462 AAAAATAAATAAA-AAGCAAATGAAATA
1 AAAAATAAATAAATAAACAAA-GAAATA
489 AA
1 AA
491 TAAAATACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (27 bp):
AAAAATAAATAAATAAACAAAGAAATA
Found at i:10918 original size:19 final size:19
Alignment explanation
Indices: 10883--10931 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
10873 GTTCTTAAGG
*
10883 AGTGGTCCTT-TGGGACAT
1 AGTGGTCCTTCGGGGACAT
10901 AGTGGTCCTTCGGGGACAT
1 AGTGGTCCTTCGGGGACAT
*
10920 AGTGGTCTTTCG
1 AGTGGTCCTTCG
10932 AGACAAGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.14, C:0.18, G:0.35, T:0.33
Consensus pattern (19 bp):
AGTGGTCCTTCGGGGACAT
Found at i:11209 original size:12 final size:12
Alignment explanation
Indices: 11194--11225 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
11184 TAATAATGCT
11194 AATAATGATAAG
1 AATAATGATAAG
*
11206 AATAATAATAAG
1 AATAATGATAAG
11218 AATAATGA
1 AATAATGA
11226 AATGATATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (12 bp):
AATAATGATAAG
Found at i:13425 original size:17 final size:17
Alignment explanation
Indices: 13403--13436 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13393 TTGCCACCCT
*
13403 ACCACCCGGGTGTGGCC
1 ACCACCAGGGTGTGGCC
13420 ACCACCAGGGTGTGGCC
1 ACCACCAGGGTGTGGCC
13437 GAGAGAGAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.38, G:0.35, T:0.12
Consensus pattern (17 bp):
ACCACCAGGGTGTGGCC
Found at i:14224 original size:36 final size:36
Alignment explanation
Indices: 14153--14224 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
14143 TATATTTTTA
*
14153 ATTTTGTAAAAAAAATTATATAAATATTATGAATTT
1 ATTTTGTAAAAAAAATTATATAAATATTATCAATTT
* * *
14189 ATTTTTTAAAGAAAA-TATATAAATATTTTACAATTT
1 ATTTTGTAAAAAAAATTATATAAATATTAT-CAATTT
14225 GTAATATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 13 0.42
36 18 0.58
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (36 bp):
ATTTTGTAAAAAAAATTATATAAATATTATCAATTT
Found at i:14353 original size:3 final size:3
Alignment explanation
Indices: 14345--14381 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
14335 AACACAAAAT
14345 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA A
14382 AACCCAATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:19574 original size:32 final size:33
Alignment explanation
Indices: 19506--19576 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
19496 TAAACCCAAA
* * *
19506 ACCCGACCCGAATATTATACTTAAAAAAACCTG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
*
19539 ACCCGACTCGAATATCACACTT-AAAAAACCCG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
19571 ACCCGA
1 ACCCGA
19577 GTAAAATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.44
33 19 0.56
ACGTcount: A:0.41, C:0.32, G:0.10, T:0.17
Consensus pattern (33 bp):
ACCCGACCCGAATATCACACTTAAAAAAACCCG
Found at i:21871 original size:75 final size:72
Alignment explanation
Indices: 21710--21885 Score: 219
Period size: 74 Copynumber: 2.4 Consensus size: 72
21700 TAAAATTTAA
* * **
21710 ACTACCTATTACATTAAAATACCTAATC-GTTTTTTTAAGGTTGTTAATAATGTAAACAGTAAAA
1 ACTACCTATTACATTAAAATACCT-ACCGGTTTTTTTAAAGTTACTAATAATGTAAACAGTAAAA
21774 AAAAAGGC
65 AAAAAGGC
* **
21782 ATTACCTATTACATTAAAATACCTACCGGTTTTTTTTTAAAGTTACTAATAATGTAAATGGTAAA
1 ACTACCTATTACATTAAAATACCTACCGG--TTTTTTTAAAGTTACTAATAATGTAAACAGTAAA
*
21847 AAAAATAGGG
64 AAAAA-AGGC
* *
21857 GCTACCTATTACATTAAACTACCTACCGG
1 ACTACCTATTACATTAAAATACCTACCGG
21886 ATATGTTGAA
Statistics
Matches: 89, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
71 2 0.02
72 24 0.27
74 34 0.38
75 29 0.33
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (72 bp):
ACTACCTATTACATTAAAATACCTACCGGTTTTTTTAAAGTTACTAATAATGTAAACAGTAAAAA
AAAAGGC
Found at i:22137 original size:91 final size:89
Alignment explanation
Indices: 21991--22182 Score: 312
Period size: 91 Copynumber: 2.1 Consensus size: 89
21981 TATAAAAATA
*
21991 TATCGATACTTTACAAATAACATGTAAAAATATGAAAAATCAGTTTCACTATGACAAAATTGGTA
1 TATCGATACTTTACAAATAACATGTAAAAATATGAAAAATCAGTTTCACTATGACAAAATCGGTA
*
22056 AAGAGCTACCTGATATTTTGAAAG
66 AAGAGCTACCTGATATGTTGAAAG
* *
22080 TATCGATATTTTACAATATAACATGTAAAAATATGACAAAATCAGTTTCATTATGACAAAATCGG
1 TATCGATACTTTACAA-ATAACATGTAAAAATATGA-AAAATCAGTTTCACTATGACAAAATCGG
22145 TAAAGAGCTACCTGATATGTTGAAAG
64 TAAAGAGCTACCTGATATGTTGAAAG
* *
22171 TATTGATCCTTT
1 TATCGATACTTT
22183 TTATAAAAAT
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 15 0.16
90 19 0.20
91 60 0.64
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (89 bp):
TATCGATACTTTACAAATAACATGTAAAAATATGAAAAATCAGTTTCACTATGACAAAATCGGTA
AAGAGCTACCTGATATGTTGAAAG
Found at i:22279 original size:114 final size:112
Alignment explanation
Indices: 22079--22432 Score: 512
Period size: 114 Copynumber: 3.1 Consensus size: 112
22069 TATTTTGAAA
* * *
22079 GTATCGATATTTTACAATATAACATGTAAAAATATGACAAAATCAGTTTCATTATGACAAAATCG
1 GTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAATCAGTTTCATTATGACAAAA-CC
*
22144 GTAAAGAGCTACCTGATATGTTGAAAGTATTGATCCTTTTTATAAAAAT
65 GTAAAGAGCTACTTGATATGTTGAAAGTATTGATCCTTTTTAT-AAAAT
*
22193 GTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAATCAGTTTCATTATAACAAAACCA
1 GTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAATCAGTTTCATTATGACAAAACC-
*
22258 GTAAAGAGCTACTTGATATGTTGAAAGTATTGATCATTTTTATTAAAAT
65 GTAAAGAGCTACTTGATATGTTGAAAGTATTGATCCTTTTTA-TAAAAT
* * *
22307 GTATCGATACTTTATAATATAACAGGTAAAAATATAACAAAATCAGTTTCATTATGACAAAACCG
1 GTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAATCAGTTTCATTATGACAAAACCG
** * * * * *
22372 ATAAAGAAATATTTGATATGTTGAAAGTATAGATACTTTTTGT-ACAT
66 -TAAAGAGCTACTTGATATGTTGAAAGTATTGATCCTTTTTATAAAAT
22419 GTATCGATACTTTA
1 GTATCGATACTTTA
22433 TTGAAAGTTG
Statistics
Matches: 219, Mismatches: 18, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
112 17 0.08
113 3 0.01
114 198 0.90
115 1 0.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (112 bp):
GTATCGATACTTTACAATATAACAAGTAAAAATATGACAAAATCAGTTTCATTATGACAAAACCG
TAAAGAGCTACTTGATATGTTGAAAGTATTGATCCTTTTTATAAAAT
Found at i:28480 original size:24 final size:25
Alignment explanation
Indices: 28459--28517 Score: 95
Period size: 24 Copynumber: 2.4 Consensus size: 25
28449 TTATAATAAC
28459 TGACCTGGATTCTGATC-GAATACT
1 TGACCTGGATTCTGATCTGAATACT
*
28483 TGACCTGGATTTTGATCTG-ATACT
1 TGACCTGGATTCTGATCTGAATACT
28507 TGACCTGGATT
1 TGACCTGGATT
28518 ATGTTTTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
24 32 0.97
25 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (25 bp):
TGACCTGGATTCTGATCTGAATACT
Found at i:29621 original size:22 final size:22
Alignment explanation
Indices: 29570--29628 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
29560 ACGCGATTCT
29570 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * * *
29592 AAAT-TCGCGTTGCGATTTTTC
1 GACTATCGCATTGCGATTTTCC
*
29613 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
29629 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:29750 original size:20 final size:20
Alignment explanation
Indices: 29617--29748 Score: 212
Period size: 20 Copynumber: 6.6 Consensus size: 20
29607 TTTTTCGACT
29617 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
29637 ATCGCAATGCAAATATGTAA
1 ATCGCAATGCGAATATGTAA
29657 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
29677 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
29697 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* * *
29717 ATCACAATGCGATTATG-ACT
1 ATCGCAATGCGAATATGTA-A
29737 ATCGCAATGCGA
1 ATCGCAATGCGA
29749 TTCTGACTAT
Statistics
Matches: 105, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
19 1 0.01
20 104 0.99
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:29755 original size:20 final size:20
Alignment explanation
Indices: 29721--29803 Score: 130
Period size: 20 Copynumber: 4.2 Consensus size: 20
29711 ATGTAAATCA
*
29721 CAATGCGATTATGACTATCG
1 CAATGCGATTCTGACTATCG
29741 CAATGCGATTCTGACTATCG
1 CAATGCGATTCTGACTATCG
*
29761 CAATGAGATTCTGACTATCG
1 CAATGCGATTCTGACTATCG
* *
29781 CAACGCGATTCTGACTGTCG
1 CAATGCGATTCTGACTATCG
29801 CAA
1 CAA
29804 CACTAAATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (20 bp):
CAATGCGATTCTGACTATCG
Found at i:29765 original size:40 final size:40
Alignment explanation
Indices: 29677--29803 Score: 132
Period size: 40 Copynumber: 3.2 Consensus size: 40
29667 GAATATGTAA
* * * * *
29677 ATCGCAATGCGAATATGTA-AATCGCAATGCGAATATGTA-A
1 ATCGCAATGCGATTATG-ACTATCGCAATGCGATTCTG-ACT
*
29717 ATCACAATGCGATTATGACTATCGCAATGCGATTCTGACT
1 ATCGCAATGCGATTATGACTATCGCAATGCGATTCTGACT
* * *
29757 ATCGCAATGAGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAATGCGATTATGACTATCGCAATGCGATTCTGACT
*
29797 GTCGCAA
1 ATCGCAA
29804 CACTAAATTT
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
39 2 0.03
40 72 0.97
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (40 bp):
ATCGCAATGCGATTATGACTATCGCAATGCGATTCTGACT
Found at i:31809 original size:12 final size:12
Alignment explanation
Indices: 31794--31823 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
31784 CAAGAAAAAG
31794 GCAATCAAAATC
1 GCAATCAAAATC
31806 GCAATCAAAATC
1 GCAATCAAAATC
*
31818 ACAATC
1 GCAATC
31824 GGCTTCACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.27, G:0.07, T:0.17
Consensus pattern (12 bp):
GCAATCAAAATC
Found at i:32128 original size:139 final size:139
Alignment explanation
Indices: 31878--32146 Score: 520
Period size: 139 Copynumber: 1.9 Consensus size: 139
31868 AAACGTTGTA
31878 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
31943 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGTGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACATGAATTTGACTAT
32008 TATGTGTTT
131 TATGTGTTT
32017 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
32082 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACATGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACATGAATTTGACTAT
32147 CGCAACGCGA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
139 128 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (139 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACATGAATTTGACTAT
TATGTGTTT
Found at i:32140 original size:20 final size:20
Alignment explanation
Indices: 32117--32261 Score: 149
Period size: 20 Copynumber: 7.5 Consensus size: 20
32107 TTACACATTC
* **
32117 ATTTGAATATCGCAACATGA
1 ATTTGACTATCGCAACGCGA
32137 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
32157 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
32176 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
32191 ATTTGACTATTGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
32211 ATATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
32231 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
32251 ATTTGATTATC
1 ATTTGACTATC
32262 TGTAACCCCC
Statistics
Matches: 102, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
14 9 0.09
15 3 0.03
19 3 0.03
20 87 0.85
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:33041 original size:24 final size:24
Alignment explanation
Indices: 33007--33113 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
32997 AAACGGAGAT
* *
33007 ATCAGAAATCAAAATATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
33031 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
33055 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
33079 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
33103 ATCAGAAATCA
1 ATCAGAAATCA
33114 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:33113 original size:48 final size:48
Alignment explanation
Indices: 33007--33115 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
32997 AAACGGAGAT
* * * * *
33007 ATCAGAAATCAAAATATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
33055 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
33103 ATCAGAAATCAGA
1 ATCAGAAATCAGA
33116 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:34259 original size:18 final size:18
Alignment explanation
Indices: 34238--34275 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
34228 TCCTTCCATC
*
34238 CAATCTTATTATTTAATT
1 CAATCTTATCATTTAATT
*
34256 CAATCTTATCATTTACTT
1 CAATCTTATCATTTAATT
34274 CA
1 CA
34276 GTCCTTTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (18 bp):
CAATCTTATCATTTAATT
Found at i:35607 original size:8 final size:8
Alignment explanation
Indices: 35587--35641 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
35577 GGTCAACTCC
35587 GGTCAAC-
1 GGTCAACG
35594 GGTCAACG
1 GGTCAACG
35602 GGTCAAC-
1 GGTCAACG
35609 GGTCAACG
1 GGTCAACG
35617 GGT---CG
1 GGTCAACG
35622 GGTCAACG
1 GGTCAACG
35630 GGTCAACG
1 GGTCAACG
35638 GGTC
1 GGTC
35642 GGGTAAATGG
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.12
7 14 0.33
8 24 0.56
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:35607 original size:15 final size:15
Alignment explanation
Indices: 35587--35638 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
35577 GGTCAACTCC
35587 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
35602 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
35617 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
35630 GGTCAACGG
1 GGTCAACGG
35639 GTCGGGTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.36
15 21 0.64
ACGTcount: A:0.23, C:0.25, G:0.38, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:35635 original size:21 final size:21
Alignment explanation
Indices: 35600--35654 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
35590 CAACGGTCAA
35600 CGGGTCAAC-GGTCAACGGGT
1 CGGGTCAACGGGTCAACGGGT
35620 CGGGTCAACGGGTCAACGGGT
1 CGGGTCAACGGGTCAACGGGT
* *
35641 CGGGTAAATGGGTC
1 CGGGTCAACGGGTC
35655 GGTTCGGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 9 0.28
21 23 0.72
ACGTcount: A:0.20, C:0.22, G:0.42, T:0.16
Consensus pattern (21 bp):
CGGGTCAACGGGTCAACGGGT
Found at i:35663 original size:18 final size:18
Alignment explanation
Indices: 35615--35681 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
35605 CAACGGTCAA
*
35615 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
*
35633 CAACGGGTCGGGTAAATGGGT
1 ---CGGGTCGGGTAAACGGGT
*
35654 CGGTTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
35672 CGGGTCGGGT
1 CGGGTCGGGT
35682 TGTGACCGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 25 0.61
21 16 0.39
ACGTcount: A:0.15, C:0.18, G:0.48, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:37837 original size:24 final size:24
Alignment explanation
Indices: 37803--37909 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
37793 AAACGGAGAT
* *
37803 ATCAGAAATCAAAATATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
37827 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
37851 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** * *
37875 ATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
37899 ATCAGAAATCA
1 ATCAGAAATCA
37910 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:37909 original size:48 final size:48
Alignment explanation
Indices: 37803--37911 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
37793 AAACGGAGAT
* * * * *
37803 ATCAGAAATCAAAATATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
37851 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
37899 ATCAGAAATCAGA
1 ATCAGAAATCAGA
37912 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:39052 original size:18 final size:18
Alignment explanation
Indices: 39031--39068 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
39021 TCCTTCCATC
*
39031 CAATCTTATTATTTAATT
1 CAATCTTATCATTTAATT
*
39049 CAATCTTATCATTTACTT
1 CAATCTTATCATTTAATT
39067 CA
1 CA
39069 GTCCTTTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (18 bp):
CAATCTTATCATTTAATT
Found at i:40391 original size:8 final size:8
Alignment explanation
Indices: 40371--40425 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
40361 GGTCAACTCC
40371 GGTCAAC-
1 GGTCAACG
40378 GGTCAACG
1 GGTCAACG
40386 GGTCAAC-
1 GGTCAACG
40393 GGTCAACG
1 GGTCAACG
40401 GGT---CG
1 GGTCAACG
40406 GGTCAACG
1 GGTCAACG
40414 GGTCAACG
1 GGTCAACG
40422 GGTC
1 GGTC
40426 GGGTAAATGG
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.12
7 14 0.33
8 24 0.56
ACGTcount: A:0.22, C:0.25, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:40391 original size:15 final size:15
Alignment explanation
Indices: 40371--40422 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
40361 GGTCAACTCC
40371 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
40386 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
40401 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
40414 GGTCAACGG
1 GGTCAACGG
40423 GTCGGGTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.36
15 21 0.64
ACGTcount: A:0.23, C:0.25, G:0.38, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:40419 original size:21 final size:21
Alignment explanation
Indices: 40384--40438 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
40374 CAACGGTCAA
40384 CGGGTCAAC-GGTCAACGGGT
1 CGGGTCAACGGGTCAACGGGT
40404 CGGGTCAACGGGTCAACGGGT
1 CGGGTCAACGGGTCAACGGGT
* *
40425 CGGGTAAATGGGTC
1 CGGGTCAACGGGTC
40439 GGTTCGGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 9 0.28
21 23 0.72
ACGTcount: A:0.20, C:0.22, G:0.42, T:0.16
Consensus pattern (21 bp):
CGGGTCAACGGGTCAACGGGT
Found at i:40447 original size:18 final size:18
Alignment explanation
Indices: 40399--40465 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
40389 CAACGGTCAA
*
40399 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
*
40417 CAACGGGTCGGGTAAATGGGT
1 ---CGGGTCGGGTAAACGGGT
*
40438 CGGTTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
40456 CGGGTCGGGT
1 CGGGTCGGGT
40466 TGTGACCGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 25 0.61
21 16 0.39
ACGTcount: A:0.15, C:0.18, G:0.48, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:41285 original size:34 final size:34
Alignment explanation
Indices: 41235--41371 Score: 132
Period size: 34 Copynumber: 3.9 Consensus size: 34
41225 GTGTTACATT
41235 ATCGCAACG-GCTATTTGACTATCGCAACGAGAAA
1 ATCGCAACGCG-TATTTGACTATCGCAACGAGAAA
** * **
41269 ATCGCAACGCAAATTTGAGTATCGCAACTTGAATTTTA
1 ATCGCAACGCGTATTTGACTATCGCAACGAGAA----A
*
41307 TTATCGCAACGGGTATTTGACTATCGCAACGAGAAA
1 --ATCGCAACGCGTATTTGACTATCGCAACGAGAAA
* *
41343 ATCGCAAAGCGTATTAGACTATCGCAACG
1 ATCGCAACGCGTATTTGACTATCGCAACG
41372 CGAATTGACT
Statistics
Matches: 82, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
34 53 0.65
36 1 0.01
38 1 0.01
40 27 0.33
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (34 bp):
ATCGCAACGCGTATTTGACTATCGCAACGAGAAA
Found at i:41294 original size:20 final size:20
Alignment explanation
Indices: 41269--41381 Score: 69
Period size: 20 Copynumber: 6.0 Consensus size: 20
41259 CAACGAGAAA
* *
41269 ATCGCAACGCAAATTTGAGT
1 ATCGCAACGCGAATTTGACT
** * *
41289 ATCGCAACTTGAATTTTATT
1 ATCGCAACGCGAATTTGACT
* *
41309 ATCGCAACGGGTATTTGACT
1 ATCGCAACGCGAATTTGACT
*
41329 ATCGCAACGAGAA----A--
1 ATCGCAACGCGAATTTGACT
* * *
41343 ATCGCAAAGCGTATTAGACT
1 ATCGCAACGCGAATTTGACT
41363 ATCGCAACGCGAA-TTGACT
1 ATCGCAACGCGAATTTGACT
41382 TTCACGTTGC
Statistics
Matches: 69, Mismatches: 18, Indels: 13
0.69 0.18 0.13
Matches are distributed among these distances:
14 10 0.14
16 1 0.01
18 1 0.01
19 5 0.07
20 52 0.75
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:41366 original size:74 final size:74
Alignment explanation
Indices: 41232--41370 Score: 224
Period size: 74 Copynumber: 1.9 Consensus size: 74
41222 GGGGTGTTAC
* * *
41232 ATTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATCGCAACGCAAATTTGAGTATCGCAAC
1 ATTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATCGCAAAGCAAATTAGACTATCGCAAC
41297 TTGAATTTT
66 TTGAATTTT
* **
41306 ATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAATCGCAAAGCGTATTAGACTATCGCAAC
1 ATTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATCGCAAAGCAAATTAGACTATCGCAAC
41371 GCGAATTGAC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 59 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (74 bp):
ATTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATCGCAAAGCAAATTAGACTATCGCAAC
TTGAATTTT
Found at i:41431 original size:20 final size:20
Alignment explanation
Indices: 41376--41433 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
41366 GCAACGCGAA
41376 TTGACTTTCA-CGTTGCGATT
1 TTGACTTT-AGCGTTGCGATT
* * *
41396 TTGTCTTTCGCATTGCGATT
1 TTGACTTTAGCGTTGCGATT
*
41416 TTGAGTTTAGCGTTGCGA
1 TTGACTTTAGCGTTGCGA
41434 AAGTGTACCT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.45
Consensus pattern (20 bp):
TTGACTTTAGCGTTGCGATT
Found at i:41589 original size:14 final size:14
Alignment explanation
Indices: 41555--41593 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
41545 TCAATATTAA
* *
41555 ACAAATAAACTTTT
1 ACAAATCAATTTTT
41569 ACAAATCAATTTTT
1 ACAAATCAATTTTT
*
41583 ATAAATCAATT
1 ACAAATCAATT
41594 AAACAAGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:43094 original size:42 final size:42
Alignment explanation
Indices: 43015--43096 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
43005 CCTCTTCAAC
* * *
43015 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* *
43057 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGA
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGA
43097 ACAATGACAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.21, C:0.17, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:43633 original size:20 final size:20
Alignment explanation
Indices: 43605--43680 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
43595 TCGCAACACG
* *
43605 AATGGCTATCGCAACGCAAA
1 AATGACTATCGCAACGCGAA
*
43625 AATGACTATCGCAATGCGAA
1 AATGACTATCGCAACGCGAA
43645 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
43665 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
43681 AGAGAATCGC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:43748 original size:20 final size:20
Alignment explanation
Indices: 43723--43770 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
43713 GTGATTCTTT
43723 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
43743 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
43763 CGTTGCGA
1 CGTTGCGA
43771 AAGTAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:45705 original size:20 final size:20
Alignment explanation
Indices: 45682--45788 Score: 119
Period size: 20 Copynumber: 5.5 Consensus size: 20
45672 TATGAAACTT
*
45682 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
*
45702 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** **
45722 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
**
45742 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
*
45761 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
45780 AAAATCGCA
1 AAAATCGCA
45789 TTGAGATTCT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
19 24 0.32
20 52 0.68
ACGTcount: A:0.46, C:0.23, G:0.17, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:46399 original size:20 final size:20
Alignment explanation
Indices: 46369--46446 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
46359 GCGCTTTGAA
*
46369 AATCGCATTGCGACAGTCAG
1 AATCGCGTTGCGACAGTCAG
*
46389 CATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGACAGTCAG
*
46409 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGACAGTCAG
* *
46429 AATTGCGTTGCGATAGTC
1 AATCGCGTTGCGACAGTC
46447 GGAAAATCGC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (20 bp):
AATCGCGTTGCGACAGTCAG
Found at i:59189 original size:14 final size:14
Alignment explanation
Indices: 59139--59201 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
59129 AACTTAAAAA
59139 TATATTTAA-TT-T
1 TATATTTAACTTAT
*
59151 TTTATCTTAAC-TAT
1 TATAT-TTAACTTAT
*
59165 TACATTCTAACTTAT
1 TATATT-TAACTTAT
59180 TATATTTAACTTAT
1 TATATTTAACTTAT
*
59194 TACATTTA
1 TATATTTA
59202 TTACATTCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
12 4 0.10
13 6 0.15
14 23 0.56
15 8 0.20
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (14 bp):
TATATTTAACTTAT
Found at i:59234 original size:30 final size:30
Alignment explanation
Indices: 59185--59261 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
59175 CTTATTATAT
* * * *
59185 TTAACTTATTACATTTATTACATTCTTAAA
1 TTAAATTATTAAATATATTACAGTCTTAAA
* **
59215 TTAAATTATTAAATATATTATAGTCTTACC
1 TTAAATTATTAAATATATTACAGTCTTAAA
59245 TTAAATTATTAAATATA
1 TTAAATTATTAAATATA
59262 ATTTATCCCT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.42, C:0.09, G:0.01, T:0.48
Consensus pattern (30 bp):
TTAAATTATTAAATATATTACAGTCTTAAA
Found at i:59360 original size:26 final size:26
Alignment explanation
Indices: 59321--59386 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
59311 AATATTTATA
59321 TATATTTTTATTTTAAATTAAAAATG
1 TATATTTTTATTTTAAATTAAAAATG
*
59347 TATATTATTT-TTTTAATTTTAAAATAT-
1 TATATT-TTTATTTTAA-ATTAAAA-ATG
*
59374 TTTATTTTTATTT
1 TATATTTTTATTT
59387 GAATGTTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
26 15 0.44
27 17 0.50
28 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
TATATTTTTATTTTAAATTAAAAATG
Found at i:59379 original size:27 final size:27
Alignment explanation
Indices: 59323--59401 Score: 65
Period size: 27 Copynumber: 3.0 Consensus size: 27
59313 TATTTATATA
* * *
59323 TATTTTTATTTTAA-ATTAAAA-ATGTA
1 TATTTTTATTTGAATGTTAAAATAT-TT
* *
59349 TATTATTT-TTTTAATTTTAAAATATTT
1 TATT-TTTATTTGAATGTTAAAATATTT
*
59376 TATTTTTATTTGAATGTTGAAATATT
1 TATTTTTATTTGAATGTTAAAATATT
59402 ATAAGAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
26 13 0.30
27 29 0.66
28 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (27 bp):
TATTTTTATTTGAATGTTAAAATATTT
Found at i:59508 original size:25 final size:27
Alignment explanation
Indices: 59402--59535 Score: 94
Period size: 30 Copynumber: 4.8 Consensus size: 27
59392 TTGAAATATT
*
59402 ATAAGAATAAAATAAATATTTAAGCTAAG
1 ATAAGAATAAAATATATATTTAA--TAAG
* * *
59431 GTAAGAAT-AAAT-TATTTTTTA-AAG
1 ATAAGAATAAAATATATATTTAATAAG
* * * * *
59455 TTAATAAAAAAATATATTTTATAAGTTAAA
1 ATAAGAATAAAATATATATT-TAA--TAAG
59485 ATAAGAATAAAATATAATATTTAAGTTAAG
1 ATAAGAATAAAATAT-ATATTTAA--TAAG
59515 ATAAGAATAAAATATATATTT
1 ATAAGAATAAAATATATATTT
59536 TTAATGTTAA
Statistics
Matches: 84, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
24 8 0.10
25 4 0.05
26 6 0.07
27 8 0.10
28 4 0.05
29 13 0.15
30 37 0.44
31 4 0.05
ACGTcount: A:0.55, C:0.01, G:0.08, T:0.36
Consensus pattern (27 bp):
ATAAGAATAAAATATATATTTAATAAG
Found at i:59545 original size:32 final size:31
Alignment explanation
Indices: 59461--59551 Score: 130
Period size: 30 Copynumber: 2.9 Consensus size: 31
59451 AAAGTTAATA
* *
59461 AAAAAATATATTTTATAAGTTAAAATAAGAAT
1 AAAATATATATTTT-TAAGTTAAGATAAGAAT
*
59493 AAAATATA-ATATTTAAGTTAAGATAAGAAT
1 AAAATATATATTTTTAAGTTAAGATAAGAAT
59523 AAAATATATATTTTTAATGTTAAGATAAG
1 AAAATATATATTTTTAA-GTTAAGATAAG
59552 TTTAGACTAG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
30 24 0.45
31 11 0.21
32 18 0.34
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (31 bp):
AAAATATATATTTTTAAGTTAAGATAAGAAT
Found at i:61700 original size:36 final size:36
Alignment explanation
Indices: 61625--61700 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
61615 CTACATTTTG
* * *
61625 TTCAACAGTCGGTTGCATGTCATCACTGCTGCATTC
1 TTCAACAGTCGGTTGCATGTCATAACTGCTACATCC
* *
61661 TTCAACAGTCGGTTGCATGTTATAATTTGCTACA-CC
1 TTCAACAGTCGGTTGCATGTCATAA-CTGCTACATCC
61697 TTCA
1 TTCA
61701 GTTTTGCAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 28 0.82
37 6 0.18
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (36 bp):
TTCAACAGTCGGTTGCATGTCATAACTGCTACATCC
Done.