Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006364.1 Hibiscus syriacus cultivar Beakdansim tig00015287_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: 136438
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:12786 original size:20 final size:20
Alignment explanation
Indices: 12743--12812 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
12733 TCAGTCAGGG
**
12743 GTATCGATACCAACA-GTTGG
1 GTATCGATACCAA-AGGTTCA
*
12763 GTATCGATACCAAAGGTTTA
1 GTATCGATACCAAAGGTTCA
** *
12783 GTATCGATACTGAAGGGTCA
1 GTATCGATACCAAAGGTTCA
12803 GTATCGATAC
1 GTATCGATAC
12813 TCACAAATAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.02
20 42 0.98
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (20 bp):
GTATCGATACCAAAGGTTCA
Found at i:16828 original size:18 final size:18
Alignment explanation
Indices: 16805--16843 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
16795 TATACAAGGT
16805 AATTATGGCAATATTTCG
1 AATTATGGCAATATTTCG
16823 AATTATGGCAATATTTCG
1 AATTATGGCAATATTTCG
16841 AAT
1 AAT
16844 ATATCACGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (18 bp):
AATTATGGCAATATTTCG
Found at i:25137 original size:2 final size:2
Alignment explanation
Indices: 25130--25155 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25120 TGCTTTGCTC
25130 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
25156 GTAATAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28199 original size:20 final size:21
Alignment explanation
Indices: 28153--28199 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
28143 GTCATGCAAC
28153 TAATAATAGTTGCATAATGCA
1 TAATAATAGTTGCATAATGCA
* *
28174 TAATAATGGTT-CATAATTCA
1 TAATAATAGTTGCATAATGCA
*
28194 TTATAA
1 TAATAA
28200 GTTGGCAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (21 bp):
TAATAATAGTTGCATAATGCA
Found at i:28229 original size:23 final size:24
Alignment explanation
Indices: 28194--28241 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
28184 TCATAATTCA
28194 TTATAAGTTGGCAAC-AATAATGGT
1 TTATAAGTTGGC-ACTAATAATGGT
28218 TTAT-AGTTGGCACTAATAATGGT
1 TTATAAGTTGGCACTAATAATGGT
28241 T
1 T
28242 GAAAAGTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 2 0.09
23 17 0.74
24 4 0.17
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (24 bp):
TTATAAGTTGGCACTAATAATGGT
Found at i:41590 original size:25 final size:27
Alignment explanation
Indices: 41539--41593 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
41529 CAAAATTATA
**
41539 GTATTAAAAATATTTATTTGTGTAATT
1 GTATTAAAAATATTTATTTGTCAAATT
*
41566 GTATTAAATA-ATTTATTT-TCAAATT
1 GTATTAAAAATATTTATTTGTCAAATT
41591 GTA
1 GTA
41594 GCGAGAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.32
26 8 0.32
27 9 0.36
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (27 bp):
GTATTAAAAATATTTATTTGTCAAATT
Found at i:43999 original size:19 final size:20
Alignment explanation
Indices: 43972--44009 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43962 CTGATACTGT
*
43972 TATTGATC-AGTATCGATAC
1 TATTGATCAAGTACCGATAC
*
43991 TATTTATCAAGTACCGATA
1 TATTGATCAAGTACCGATA
44010 TTGTTATTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (20 bp):
TATTGATCAAGTACCGATAC
Found at i:51929 original size:70 final size:70
Alignment explanation
Indices: 51853--51985 Score: 248
Period size: 70 Copynumber: 1.9 Consensus size: 70
51843 GAATTCCAAA
51853 AAAAAAAGAGGGGAAAAGTACATACAAAATGACTTCAAATAAACGGATGCACACTGTCGAAATTC
1 AAAAAAA-A-GGGAAAAGTACATACAAAATGACTTCAAATAAACGGATGCACACTGTCGAAATTC
51918 GAATTCT
64 GAATTCT
51925 AAAAAAAAGGGAAAAGTACATACAAAATGACTTCAAATAAACGGATGCACACTGTCGAAAT
1 AAAAAAAAGGGAAAAGTACATACAAAATGACTTCAAATAAACGGATGCACACTGTCGAAAT
51986 GATTTTTTGA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
70 53 0.87
71 1 0.02
72 7 0.11
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.18
Consensus pattern (70 bp):
AAAAAAAAGGGAAAAGTACATACAAAATGACTTCAAATAAACGGATGCACACTGTCGAAATTCGA
ATTCT
Found at i:53385 original size:25 final size:28
Alignment explanation
Indices: 53351--53413 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
53341 TAAAAAATTA
*
53351 TATTAACTT-A-TTAAATATA-TTTTAT
1 TATTAACTTAATTTAAAAATATTTTTAT
53376 TATTAACTTAATTTAAAAATATTTTTAT
1 TATTAACTTAATTTAAAAATATTTTTAT
*
53404 T-TTAATTTAA
1 TATTAACTTAA
53414 AAACATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 9 0.27
26 1 0.03
27 16 0.48
28 7 0.21
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (28 bp):
TATTAACTTAATTTAAAAATATTTTTAT
Found at i:53398 original size:22 final size:22
Alignment explanation
Indices: 53373--53425 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
53363 AAATATATTT
53373 TATTATTAACTTAATTTAAAAA
1 TATTATTAACTTAATTTAAAAA
* **
53395 TATTTTTATTTTAATTTAAAAA
1 TATTATTAACTTAATTTAAAAA
*
53417 CATATATTA
1 TAT-TATTA
53426 GGTAAAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
TATTATTAACTTAATTTAAAAA
Found at i:53493 original size:30 final size:30
Alignment explanation
Indices: 53453--53639 Score: 136
Period size: 30 Copynumber: 6.2 Consensus size: 30
53443 TTAAGATATG
*
53453 AATAAAATATATTTAATAATTTAAAATAAT
1 AATATAATATATTTAATAATTTAAAATAAT
*
53483 AATATAATATATTTAATAAATTAAAATAA-
1 AATATAATATATTTAATAATTTAAAATAAT
* * *
53512 AATAT-ATA-CTTTAAAAAGTTAAAATAAT
1 AATATAATATATTTAATAATTTAAAATAAT
* *
53540 AATAATAAATATATTTTTTTCAA-AATTT-AGATAAG
1 AAT-AT-AATATA----TTT-AATAATTTAAAATAAT
* *
53575 AATAAAATATATTTAACT-ATTTGAAATAAT
1 AATATAATATATTTAA-TAATTTAAAATAAT
* * * *
53605 ATTATAATATATTTAGTAAATTAAGATAA-
1 AATATAATATATTTAATAATTTAAAATAAT
53634 AATATA
1 AATATA
53640 TACTTTGAAA
Statistics
Matches: 124, Mismatches: 19, Indels: 29
0.72 0.11 0.17
Matches are distributed among these distances:
27 16 0.13
28 8 0.06
29 20 0.16
30 53 0.43
31 3 0.02
33 6 0.05
34 1 0.01
35 8 0.06
36 7 0.06
37 2 0.02
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (30 bp):
AATATAATATATTTAATAATTTAAAATAAT
Found at i:53534 original size:57 final size:56
Alignment explanation
Indices: 53459--53675 Score: 182
Period size: 57 Copynumber: 3.7 Consensus size: 56
53449 TATGAATAAA
* *
53459 ATATATTTAATAATTTAAAATAATAATATAATATATTTAATAAATTAAAATAAAAT
1 ATATATTTAAAAAGTTAAAATAATAATATAATATATTTAATAAATTAAAATAAAAT
** *
53515 ATATACTTTAAAAAGTTAAAATAATAATAATAAATATATTTTTTTCAAAATTTAGATAAGAATAA
1 ATATA-TTTAAAAAGTTAAAATAATAAT-AT-AATATA-TTTAAT--AAA-TTA-A-AATAA-AA
*
53580 A
56 T
** * * * * *
53581 ATATATTTAACTATTTGAAATAATATTATAATATATTTAGTAAATTAAGATAAAAT
1 ATATATTTAAAAAGTTAAAATAATAATATAATATATTTAATAAATTAAAATAAAAT
* * * *
53637 ATATACTTTGAAAAGTTGAAACAATAATAAAATATATTT
1 ATATA-TTTAAAAAGTTAAAATAATAATATAATATATTT
53676 TTCAAAGTTT
Statistics
Matches: 127, Mismatches: 23, Indels: 21
0.74 0.13 0.12
Matches are distributed among these distances:
56 12 0.09
57 49 0.39
58 3 0.02
59 9 0.07
60 7 0.06
62 7 0.06
63 9 0.07
64 3 0.02
65 21 0.17
66 7 0.06
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (56 bp):
ATATATTTAAAAAGTTAAAATAATAATATAATATATTTAATAAATTAAAATAAAAT
Found at i:53712 original size:122 final size:121
Alignment explanation
Indices: 53446--53704 Score: 375
Period size: 122 Copynumber: 2.2 Consensus size: 121
53436 TTTGAAGTTA
*
53446 AGATATGAATAAAATATATTTAA-TAATTTAAAATAATAATATAATATATTTAATAAATTAAAAT
1 AGATAAGAATAAAATATATTTAACT-ATTTAAAATAATAATATAATATATTTAATAAATTAAAAT
*
53510 AAAATATATACTTTAAAAAGTTAAAATAATAATAATAAATATATTTTTTTCAAAATTT
65 AAAATATATACTTTAAAAAGTTAAAACAATAATAATAAATATA-TTTTTTCAAAATTT
* * * *
53568 AGATAAGAATAAAATATATTTAACTATTTGAAATAATATTATAATATATTTAGTAAATTAAGATA
1 AGATAAGAATAAAATATATTTAACTATTTAAAATAATAATATAATATATTTAATAAATTAAAATA
* * *
53633 AAATATATACTTTGAAAAGTTGAAACAATAAT-A-AAATATA-TTTTTCAAAGTTT
66 AAATATATACTTTAAAAAGTTAAAACAATAATAATAAATATATTTTTTCAAAATTT
53686 CA-ATAAGAATAAAATATAT
1 -AGATAAGAATAAAATATAT
53705 ACTTTTAAAT
Statistics
Matches: 126, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
118 29 0.23
119 1 0.01
120 7 0.06
121 1 0.01
122 87 0.69
123 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (121 bp):
AGATAAGAATAAAATATATTTAACTATTTAAAATAATAATATAATATATTTAATAAATTAAAATA
AAATATATACTTTAAAAAGTTAAAACAATAATAATAAATATATTTTTTCAAAATTT
Found at i:53722 original size:31 final size:32
Alignment explanation
Indices: 53621--53733 Score: 101
Period size: 31 Copynumber: 3.6 Consensus size: 32
53611 ATATATTTAG
* *
53621 TAAATTAAG-ATAAAATATATACTTTGAAAAGT
1 TAAAATAAGAATAAAATATATACTTT-TAAAGT
* * *
53653 TGAAACAATAATAAAATATAT--TTTTCAAAGT
1 TAAAATAAGAATAAAATATATACTTTT-AAAGT
**
53684 TTCAATAAGAATAAAATATATACTTTTAAA-T
1 TAAAATAAGAATAAAATATATACTTTTAAAGT
53715 TAAAATAA-ATATAAAATAT
1 TAAAATAAGA-ATAAAATAT
53734 TTTTATATTA
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
30 1 0.02
31 41 0.63
32 8 0.12
33 15 0.23
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.35
Consensus pattern (32 bp):
TAAAATAAGAATAAAATATATACTTTTAAAGT
Found at i:53756 original size:122 final size:120
Alignment explanation
Indices: 53446--53759 Score: 324
Period size: 122 Copynumber: 2.6 Consensus size: 120
53436 TTTGAAGTTA
* * *
53446 AGATATGAATAAAATATAT-TTAATAATTTAAAATAATAATATAATATATTTA-ATAAATTAAAA
1 AGATAAGAATAAAATATATATT-TTAAATTAAAATAAT-ATATAATATATTTATAT-AATTAAAA
*
53509 TAAAATATATACTTTAAAAAGTTAAAATAATAATAATAAATATATTTTTTTCAAAATTT
63 TAAAATATATACTTTAAAAAGTTAAAACAATAATAATAAATATA-TTTTTTCAAAATTT
*
53568 AGATAAGAAT-AAA-ATATA-TTTAACTATTTGAAATAATATTATAATATATTTAGTA-AATTAA
1 AGATAAGAATAAAATATATATTTTAA--A-TTAAAATAATA-TATAATATATTTA-TATAATTAA
* * * *
53629 GATAAAATATATACTTTGAAAAGTTGAAACAATAAT-A-AAATATA-TTTTTCAAAGTTT
61 AATAAAATATATACTTTAAAAAGTTAAAACAATAATAATAAATATATTTTTTCAAAATTT
* *
53686 CA-ATAAGAATAAAATATATACTTTTAAATTAAAATAAATATAAAATATTTTTATATTAAGTTAA
1 -AGATAAGAATAAAATATATA-TTTTAAATTAAAAT-AATATATAATATATTTATA-TAA-TTAA
53750 TAATAAAATA
61 -AATAAAATA
53760 CATTTAATAA
Statistics
Matches: 162, Mismatches: 13, Indels: 34
0.78 0.06 0.16
Matches are distributed among these distances:
118 22 0.14
119 24 0.15
120 24 0.15
121 9 0.06
122 82 0.51
124 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (120 bp):
AGATAAGAATAAAATATATATTTTAAATTAAAATAATATATAATATATTTATATAATTAAAATAA
AATATATACTTTAAAAAGTTAAAACAATAATAATAAATATATTTTTTCAAAATTT
Found at i:53807 original size:25 final size:26
Alignment explanation
Indices: 53723--53807 Score: 97
Period size: 25 Copynumber: 3.3 Consensus size: 26
53713 ATTAAAATAA
53723 ATATAAAATATTTTTATATTAAGTTAAT
1 ATATAAAATATTTTTA-A-TAAGTTAAT
**
53751 A-ATAAAATACATTTAATAAGTTAAT
1 ATATAAAATATTTTTAATAAGTTAAT
53776 ATA-AAAATATTTCTTAA-AA-TTAAT
1 ATATAAAATATTT-TTAATAAGTTAAT
53800 ATATAAAA
1 ATATAAAA
53808 AAATATTATA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
24 8 0.16
25 23 0.46
26 6 0.12
27 12 0.24
28 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
ATATAAAATATTTTTAATAAGTTAAT
Found at i:54838 original size:54 final size:54
Alignment explanation
Indices: 54780--54882 Score: 170
Period size: 54 Copynumber: 1.9 Consensus size: 54
54770 CCTAGGTGGA
*
54780 ACAAGGAATATCCTTGATGAATTATTAAGACAAGAGACCAAAAACCTATGTACG
1 ACAAGGAATATCCTTGATGAATTATTAAGAAAAGAGACCAAAAACCTATGTACG
* * *
54834 ACAAGGAATATCCTTTATGAATTATTAAGAAAAGAGACCCAAATCCTAT
1 ACAAGGAATATCCTTGATGAATTATTAAGAAAAGAGACCAAAAACCTAT
54883 AAGGTTGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.24
Consensus pattern (54 bp):
ACAAGGAATATCCTTGATGAATTATTAAGAAAAGAGACCAAAAACCTATGTACG
Found at i:55148 original size:37 final size:37
Alignment explanation
Indices: 55071--55339 Score: 207
Period size: 37 Copynumber: 7.4 Consensus size: 37
55061 CGGTTTTGAA
* * * **
55071 AATAAATAG-TTTTTAAAATA-ATTTTAAAAATGTAT
1 AATATATAGTTTTTTAAAATAGTTTTTGAAAACATAT
* *
55106 AAATATATAGTTTTTTTAAATAGTTTTCGAAAACATAT
1 -AATATATAGTTTTTTAAAATAGTTTTTGAAAACATAT
*
55144 AATATATAGTTTTTTAAAA-CGATTTTTGAAAACATAT
1 AATATATAGTTTTTTAAAATAG-TTTTTGAAAACATAT
* * * *
55181 AGTCTATAGTTTTTTAAAAAAGGTTTTGAAAACATAT
1 AATATATAGTTTTTTAAAATAGTTTTTGAAAACATAT
* * * *** **
55218 AGTATATAG-CTTTTAAAATAATTTAAAAAAATGTAT
1 AATATATAGTTTTTTAAAATAGTTTTTGAAAACATAT
55254 AATATATAG-TTTTTAAAATA-TTTTTGAAAACATAT
1 AATATATAGTTTTTTAAAATAGTTTTTGAAAACATAT
*
55289 -ATAATATACTTTTTTTGAAAA-AGTATTTTTGAAAAC--AT
1 AAT-ATATA-GTTTTTT-AAAATAG--TTTTTGAAAACATAT
*
55327 AATATATGGTTTT
1 AATATATAGTTTT
55340 GAAAATATAA
Statistics
Matches: 187, Mismatches: 34, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
34 2 0.01
35 15 0.08
36 45 0.24
37 91 0.49
38 21 0.11
39 2 0.01
40 11 0.06
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (37 bp):
AATATATAGTTTTTTAAAATAGTTTTTGAAAACATAT
Found at i:55154 original size:73 final size:71
Alignment explanation
Indices: 55071--55302 Score: 252
Period size: 74 Copynumber: 3.2 Consensus size: 71
55061 CGGTTTTGAA
* *
55071 AATAAATAGTTTTTAAAATAATTTTAAAAATGTATAAATATATAGTTTTTTTAAATAGTTTTCGA
1 AATATATAGTTTTTAAAATAATTTTAAAAATGTAT-AATATATAGTTTTTTAAAATAGTTTT-GA
55136 AAACATAT
64 AAACATAT
* * * ** * * *
55144 AATATATAGTTTTTTAAAACGATTTTTGAAAACATATAGTCTATAGTTTTTTAAAAAAGGTTTTG
1 AATATATAG-TTTTTAAAA-TAATTTTAAAAATGTATAATATATAGTTTTTTAAAATA-GTTTTG
55209 AAAACATAT
63 AAAACATAT
* * * *
55218 AGTATATAGCTTTTAAAATAATTTAAAAAAATGTATAATATATAG-TTTTTAAAATATTTTTGAA
1 AATATATAGTTTTTAAAATAATTT-TAAAAATGTATAATATATAGTTTTTTAAAATAGTTTTGAA
55282 AACATAT
65 AACATAT
*
55289 -ATAATATACTTTTT
1 AAT-ATATAGTTTTT
55303 TTGAAAAAGT
Statistics
Matches: 129, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
70 1 0.01
71 23 0.18
72 14 0.11
73 30 0.23
74 44 0.34
75 17 0.13
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (71 bp):
AATATATAGTTTTTAAAATAATTTTAAAAATGTATAATATATAGTTTTTTAAAATAGTTTTGAAA
ACATAT
Found at i:55341 original size:21 final size:21
Alignment explanation
Indices: 55315--55354 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
55305 GAAAAAGTAT
55315 TTTTGAAAACATAATATATGG
1 TTTTGAAAACATAATATATGG
*
55336 TTTTGAAAATATAATATAT
1 TTTTGAAAACATAATATAT
55355 TATATAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTTGAAAACATAATATATGG
Found at i:55380 original size:3 final size:3
Alignment explanation
Indices: 55372--55416 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
55362 TTTTAAATAG
55372 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
55417 TATTTTCTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:55430 original size:15 final size:15
Alignment explanation
Indices: 55376--55443 Score: 68
Period size: 15 Copynumber: 4.5 Consensus size: 15
55366 AAATAGATTA
*
55376 TTATTATTA-TTATT
1 TTATTTTTATTTATT
*
55390 ATTATTATTA-TTATT
1 -TTATTTTTATTTATT
*
55405 ATTATTATTATTTATT
1 -TTATTTTTATTTATT
*
55421 TTCTTTTTATTTATT
1 TTATTTTTATTTATT
55436 TTATTTTT
1 TTATTTTT
55444 CCCTCGTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
15 44 0.90
16 5 0.10
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTTTATTTATT
Found at i:56603 original size:19 final size:21
Alignment explanation
Indices: 56581--56622 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
56571 AGTGTTTTTA
56581 TTAAC-TTTTTTCCTTTC-TT
1 TTAACATTTTTTCCTTTCATT
*
56600 TTAACATTTTTTCTTTTCATT
1 TTAACATTTTTTCCTTTCATT
56621 TT
1 TT
56623 TCCTATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 11 0.55
21 4 0.20
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (21 bp):
TTAACATTTTTTCCTTTCATT
Found at i:56854 original size:18 final size:20
Alignment explanation
Indices: 56819--56857 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
56809 AAAGGTAATT
56819 AATTCGAATTGAATCTTTAA
1 AATTCGAATTGAATCTTTAA
*
56839 AATTC-AATTTAA-CTTTAA
1 AATTCGAATTGAATCTTTAA
56857 A
1 A
56858 TTTTCACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 6 0.33
20 5 0.28
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (20 bp):
AATTCGAATTGAATCTTTAA
Found at i:76137 original size:24 final size:24
Alignment explanation
Indices: 76105--76192 Score: 122
Period size: 24 Copynumber: 3.7 Consensus size: 24
76095 ATCATAGCAT
* * *
76105 AATCCAGGTCAAGTATTATATCAA
1 AATCCAGGTCAAGTATCAGATCAG
*
76129 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAGATCAG
*
76153 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAGATCAG
*
76177 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
76193 TATAAGAGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAG
Found at i:78698 original size:13 final size:13
Alignment explanation
Indices: 78680--78706 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
78670 GTCAACGCCA
78680 GTCAACGGGTCGG
1 GTCAACGGGTCGG
78693 GTCAACGGGTCGG
1 GTCAACGGGTCGG
78706 G
1 G
78707 ACGGGTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.48, T:0.15
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:78706 original size:18 final size:18
Alignment explanation
Indices: 78685--78730 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
78675 CGCCAGTCAA
*
78685 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
*
78703 CGGGACGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
78721 CGGGTCGGGT
1 CGGGTCGGGT
78731 TATGACCGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.20, G:0.52, T:0.15
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:80888 original size:24 final size:24
Alignment explanation
Indices: 80859--80946 Score: 97
Period size: 24 Copynumber: 3.7 Consensus size: 24
80849 ATCATAACAT
* *
80859 AATCCATGTCAAGTATCATATCA-
1 AATCCAGGTCAAGTATCAGATCAG
*
80882 AACTCCAGGTCAAGTATCCGATCAG
1 AA-TCCAGGTCAAGTATCAGATCAG
* *
80907 AATCCAGGTCAAGTATCCGATGAG
1 AATCCAGGTCAAGTATCAGATCAG
* *
80931 AATCCAGATCAGGTAT
1 AATCCAGGTCAAGTAT
80947 TATAAGAGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
23 2 0.04
24 53 0.93
25 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAG
Found at i:95543 original size:41 final size:41
Alignment explanation
Indices: 95461--95553 Score: 107
Period size: 41 Copynumber: 2.3 Consensus size: 41
95451 GCACAATTTC
* **
95461 AACTTCACAACGAAGGATATCGTACCTAAAAAGTTTTACTT
1 AACTTCACAACGAAGGATATCGTACCTAAAAAGATCGACTT
* * *
95502 AACTTTACGACGAAGGATATCGTA-CTCAATAAGATCGACTT
1 AACTTCACAACGAAGGATATCGTACCT-AAAAAGATCGACTT
*
95543 AAATTCACAAC
1 AACTTCACAAC
95554 AAATGAGCCA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
40 2 0.05
41 40 0.95
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (41 bp):
AACTTCACAACGAAGGATATCGTACCTAAAAAGATCGACTT
Found at i:96288 original size:28 final size:28
Alignment explanation
Indices: 96239--96293 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
96229 AATATATAAT
* ** *
96239 ATATGGTTTTTAAAACGGTTTTGAAAAC
1 ATATAGTTTTTAAAACAATTTTAAAAAC
*
96267 ATATAGTTTTTAAAATAATTTTAAAAA
1 ATATAGTTTTTAAAACAATTTTAAAAA
96294 TGTATAAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.42
Consensus pattern (28 bp):
ATATAGTTTTTAAAACAATTTTAAAAAC
Found at i:96340 original size:36 final size:36
Alignment explanation
Indices: 96267--96675 Score: 155
Period size: 36 Copynumber: 10.9 Consensus size: 36
96257 TTTTGAAAAC
**
96267 ATATAGTTTTTAAAATAATTTTAAAAATGTATAAAT
1 ATATAGTTTTTAAAATAATTTTAAAAACATATAAAT
*
96303 ATATAGGTTTTT-AAATAGTTTTCAAAAACATAT--A-
1 ATATA-GTTTTTAAAATAATTTT-AAAAACATATAAAT
* *
96337 ATATA-TTTTTAAAATTATTTTTGAAAACATATAGTATAT
1 ATATAGTTTTTAAAA-TAATTTTAAAAACATATA--A-AT
* * * *
96376 AGTTTTGTAAACGATTTTTGAAAATGATTTTTGAAAACATAT-AGT
1 A------TATA-G-TTTTT-AAAAT-AATTTTAAAAACATATAAAT
* * * *
96421 TTATAGTTTTTTAAAATATTTTTGAAAACTTAT-AAT
1 ATATAG-TTTTTAAAATAATTTTAAAAACATATAAAT
*
96457 ATATAGTTTTTTATAAA-AATGGTTTTAAAAACATAT-AGT
1 ATATAG-TTTTTA-AAATAA---TTTTAAAAACATATAAAT
* * *
96496 ATATAGTTTTTTAAAATATTTTTGAAAACGTAT-AAT
1 ATATAG-TTTTTAAAATAATTTTAAAAACATATAAAT
* * *
96532 ATATAGTTTTTTTAAAA-AACGGTTTTGAAAATATAT-AGT
1 ATATAG--TTTTTAAAATAA---TTTTAAAAACATATAAAT
* * *
96571 ACATAGTTTCTAAAATAA-TTTAAAAA-ATGTATAAT
1 ATATAGTTTTTAAAATAATTTTAAAAACATATA-AAT
* *
96606 ATATAGTTTTTAAAAT-ATATTTGAAAACGTATATAAT
1 ATATAGTTTTTAAAATAAT-TTTAAAAACATATA-AAT
** * *
96643 ATATTTTTTTTAAAACGTATTTTTGAAAACATA
1 ATATAGTTTTTAAAA--TAATTTTAAAAACATA
96676 GTATATGGTT
Statistics
Matches: 295, Mismatches: 39, Indels: 75
0.72 0.10 0.18
Matches are distributed among these distances:
32 5 0.02
33 15 0.05
34 19 0.06
35 17 0.06
36 72 0.24
37 60 0.20
38 12 0.04
39 63 0.21
40 1 0.00
45 4 0.01
46 1 0.00
48 6 0.02
49 20 0.07
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (36 bp):
ATATAGTTTTTAAAATAATTTTAAAAACATATAAAT
Found at i:96404 original size:13 final size:13
Alignment explanation
Indices: 96378--96413 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
96368 TAGTATATAG
*
96378 TTTTGTAAACGAT
1 TTTTGAAAACGAT
*
96391 TTTTGAAAATGAT
1 TTTTGAAAACGAT
96404 TTTTGAAAAC
1 TTTTGAAAAC
96414 ATATAGTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (13 bp):
TTTTGAAAACGAT
Found at i:96406 original size:49 final size:49
Alignment explanation
Indices: 96341--96448 Score: 164
Period size: 49 Copynumber: 2.2 Consensus size: 49
96331 CATATAATAT
* *
96341 ATTTTT-AAAATTATTTTTGAAAACATATAGTATATAGTTTTGTAAACG
1 ATTTTTGAAAATGATTTTTGAAAACATATAGTATATAGTTTTGTAAAAG
* * *
96389 ATTTTTGAAAATGATTTTTGAAAACATATAGTTTATAGTTTTTTAAAAT
1 ATTTTTGAAAATGATTTTTGAAAACATATAGTATATAGTTTTGTAAAAG
96438 ATTTTTGAAAA
1 ATTTTTGAAAA
96449 CTTATAATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 6 0.11
49 48 0.89
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (49 bp):
ATTTTTGAAAATGATTTTTGAAAACATATAGTATATAGTTTTGTAAAAG
Found at i:96493 original size:75 final size:75
Alignment explanation
Indices: 96404--96616 Score: 297
Period size: 75 Copynumber: 2.9 Consensus size: 75
96394 TGAAAATGAT
*
96404 TTTTGAAAACATATAGTTTATAGTTTTTTAAAATATTTTTGAAAACTTATAATATATAG-TTTTT
1 TTTTGAAAACATATAGTATATAGTTTTTTAAAATATTTTTGAAAACTTATAATATATAGTTTTTT
*
96468 TATAAAAATGG
66 TA-AAAAACGG
* *
96479 TTTTAAAAACATATAGTATATAGTTTTTTAAAATATTTTTGAAAACGTATAATATATAGTTTTTT
1 TTTTGAAAACATATAGTATATAGTTTTTTAAAATATTTTTGAAAACTTATAATATATAGTTTTTT
96544 TAAAAAACGG
66 TAAAAAACGG
* * * * * *
96554 TTTTGAAAATATATAGTACATAG-TTTCTAAAATA-ATTTAAAAAATGTATAATATATAGTTTTT
1 TTTTGAAAACATATAGTATATAGTTTTTTAAAATATTTTTGAAAACT-TATAATATATAGTTTTT
96617 AAAATATATT
Statistics
Matches: 124, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
73 7 0.06
74 27 0.22
75 83 0.67
76 7 0.06
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (75 bp):
TTTTGAAAACATATAGTATATAGTTTTTTAAAATATTTTTGAAAACTTATAATATATAGTTTTTT
TAAAAAACGG
Found at i:96577 original size:39 final size:36
Alignment explanation
Indices: 96404--96687 Score: 195
Period size: 39 Copynumber: 7.8 Consensus size: 36
96394 TGAAAATGAT
* * *
96404 TTTTGAAAACATATAGTTTATAGTTTTTTAAAATAT
1 TTTTGAAAACATATAGTATATAGTTTTTTAAAAAAG
* *
96440 TTTTGAAAACTTATAATATATAGTTTTTTATAAAAATGG
1 TTTTGAAAACATATAGTATATAGTTTTTTA-AAAAA--G
* * *
96479 TTTTAAAAACATATAGTATATAGTTTTTTAAAATAT
1 TTTTGAAAACATATAGTATATAGTTTTTTAAAAAAG
* *
96515 TTTTGAAAACGTATAATATATAGTTTTTTTAAAAAACGG
1 TTTTGAAAACATATAGTATATAG-TTTTTTAAAAAA--G
* * *
96554 TTTTGAAAATATATAGTACATAG-TTTCTAAAATAA-
1 TTTTGAAAACATATAGTATATAGTTTTTTAAAA-AAG
** ** * *
96589 TTTAAAAAATGTATAATATATAG-TTTTTAAAATA-
1 TTTTGAAAACATATAGTATATAGTTTTTTAAAAAAG
* * * *
96623 TATTTGAAAACGTATA-TAATATATTTTTTTTAAAACGTAT
1 T-TTTGAAAACATATAGT-ATATA-GTTTTTTAAAA--AAG
*
96663 TTTTGAAAAC--ATAGTATATGGTTTT
1 TTTTGAAAACATATAGTATATAGTTTT
96688 GAAAATATAA
Statistics
Matches: 200, Mismatches: 33, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
34 3 0.01
35 42 0.21
36 51 0.25
37 39 0.19
38 7 0.04
39 57 0.28
40 1 0.00
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (36 bp):
TTTTGAAAACATATAGTATATAGTTTTTTAAAAAAG
Found at i:96612 original size:35 final size:37
Alignment explanation
Indices: 96559--96646 Score: 108
Period size: 35 Copynumber: 2.4 Consensus size: 37
96549 AACGGTTTTG
* *
96559 AAAATATATAGTACATAGTTTCTAAAATA-ATTT-AA
1 AAAATATATAATATATAGTTTCTAAAATATATTTGAA
* *
96594 AAAATGTATAATATATAGTTTTTAAAATATATTTGAA
1 AAAATATATAATATATAGTTTCTAAAATATATTTGAA
**
96631 AACGTATATAATATAT
1 AAAATATATAATATAT
96647 TTTTTTTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 25 0.57
36 4 0.09
37 15 0.34
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (37 bp):
AAAATATATAATATATAGTTTCTAAAATATATTTGAA
Found at i:96653 original size:37 final size:36
Alignment explanation
Indices: 96427--96672 Score: 171
Period size: 37 Copynumber: 6.6 Consensus size: 36
96417 TAGTTTATAG
96427 TTTTTTAAAATATTTTTGAAAACT-TATAATATATAGT
1 TTTTTTAAAATATTTTTGAAAACTATATAATATAT--T
* * *
96464 TTTTTATAAAA-ATGGTTTTAAAAAC-ATATAGTATATAG
1 TTTTT-TAAAATAT--TTTTGAAAACTATATAATATAT-T
*
96502 TTTTTTAAAATATTTTTGAAAACGTATA-ATATATAGT
1 TTTTTTAAAATATTTTTGAAAAC-TATATA-ATATATT
* * * * *
96539 TTTTTTAAAAAACGGTTTTGAAAA-TATATAGTACATA
1 TTTTTTAAAATA--TTTTTGAAAACTATATAATATATT
* * * * * * *
96576 GTTTCTAAAATA-ATTTAAAAAATGTATAATATATA
1 TTTTTTAAAATATTTTTGAAAACTATATAATATATT
* *
96611 GTTTTTAAAATATATTTGAAAACGTATATAATATATT
1 TTTTTTAAAATATTTTTGAAAAC-TATATAATATATT
96648 TTTTTTAAAACGTATTTTTGAAAAC
1 TTTTTTAAAA--TATTTTTGAAAAC
96673 ATAGTATATG
Statistics
Matches: 164, Mismatches: 29, Indels: 30
0.74 0.13 0.13
Matches are distributed among these distances:
34 7 0.04
35 21 0.13
36 17 0.10
37 60 0.37
38 20 0.12
39 39 0.24
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (36 bp):
TTTTTTAAAATATTTTTGAAAACTATATAATATATT
Found at i:96689 original size:21 final size:21
Alignment explanation
Indices: 96663--96702 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
96653 TAAAACGTAT
*
96663 TTTTGAAAACATAGTATATGG
1 TTTTGAAAACATAATATATGG
*
96684 TTTTGAAAATATAATATAT
1 TTTTGAAAACATAATATAT
96703 TATATAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (21 bp):
TTTTGAAAACATAATATATGG
Found at i:96733 original size:11 final size:11
Alignment explanation
Indices: 96717--96748 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
96707 TAGTTTTAAA
96717 TATATTATTAT
1 TATATTATTAT
96728 TATATTATTAT
1 TATATTATTAT
96739 T-TATT-TTAT
1 TATATTATTAT
96748 T
1 T
96749 TTTTTCCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 5 0.24
10 4 0.19
11 12 0.57
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TATATTATTAT
Found at i:97236 original size:24 final size:26
Alignment explanation
Indices: 97209--97257 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
97199 TCACCTGCAT
97209 CATCCATCCACCCAT-TA-ATATATC
1 CATCCATCCACCCATATATATATATC
*
97233 CATCCATCCATCCATATATATATAT
1 CATCCATCCACCCATATATATATAT
97258 ATATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.64
25 2 0.09
26 6 0.27
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (26 bp):
CATCCATCCACCCATATATATATATC
Found at i:97249 original size:20 final size:20
Alignment explanation
Indices: 97210--97251 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
97200 CACCTGCATC
*
97210 ATCCATCCACCCATTAATAT
1 ATCCATCCACCCATCAATAT
* *
97230 ATCCATCCATCCATCCATAT
1 ATCCATCCACCCATCAATAT
97250 AT
1 AT
97252 ATATATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (20 bp):
ATCCATCCACCCATCAATAT
Found at i:97253 original size:2 final size:2
Alignment explanation
Indices: 97246--97271 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
97236 CCATCCATCC
97246 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
97272 TATCCCATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:97383 original size:11 final size:11
Alignment explanation
Indices: 97367--97393 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
97357 AAAATTACAT
97367 TATTAAAAATG
1 TATTAAAAATG
97378 TATTAAAAATG
1 TATTAAAAATG
97389 TATTA
1 TATTA
97394 TTGATAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (11 bp):
TATTAAAAATG
Found at i:97427 original size:11 final size:11
Alignment explanation
Indices: 97367--97429 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
97357 AAAATTACAT
*
97367 TATTAAAAATG
1 TATTAAAAATA
*
97378 TATTAAAAATG
1 TATTAAAAATA
***
97389 TATTATTGATA
1 TATTAAAAATA
97400 -ATTATAAAAT-
1 TATTA-AAAATA
97410 T-TTAAAAATA
1 TATTAAAAATA
97420 TATTAAAAAT
1 TATTAAAAAT
97430 TCTATAATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:97577 original size:7 final size:7
Alignment explanation
Indices: 97562--97730 Score: 104
Period size: 7 Copynumber: 24.4 Consensus size: 7
97552 CCTAACCTTA
97562 AAACC-T
1 AAACCAT
97568 AAACCAT
1 AAACCAT
97575 AAATCC-T
1 AAA-CCAT
*
97582 AAACC-G
1 AAACCAT
97588 AAA-CACT
1 AAACCA-T
97595 AAACC-T
1 AAACCAT
97601 AAACCAT
1 AAACCAT
97608 AAACCAT
1 AAACCAT
97615 AAA-CACT
1 AAACCA-T
*
97622 AAA-TACT
1 AAACCA-T
97629 AAACCAT
1 AAACCAT
97636 AAACCAT
1 AAACCAT
*
97643 AAACCCT
1 AAACCAT
97650 AAATCCA-
1 AAA-CCAT
* *
97657 ATACCCT
1 AAACCAT
*
97664 AAACCAAA
1 AAACC-AT
*
97672 AAACCCT
1 AAACCAT
*
97679 AAACCCT
1 AAACCAT
*
97686 AAACCCT
1 AAACCAT
*
97693 AAACCCT
1 AAACCAT
97700 AAACC-T
1 AAACCAT
97706 AAAACCAT
1 -AAACCAT
**
97714 AAACCCC
1 AAACCAT
97721 AAACCAT
1 AAACCAT
97728 AAA
1 AAA
97731 TCCGATTATA
Statistics
Matches: 133, Mismatches: 17, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
5 1 0.01
6 21 0.16
7 99 0.74
8 12 0.09
ACGTcount: A:0.53, C:0.33, G:0.01, T:0.14
Consensus pattern (7 bp):
AAACCAT
Found at i:97719 original size:21 final size:20
Alignment explanation
Indices: 97562--97730 Score: 138
Period size: 21 Copynumber: 8.4 Consensus size: 20
97552 CCTAACCTTA
*
97562 AAACCTAAACCATAAATCCT
1 AAACCTAAACCATAAACCCT
*
97582 AAACCGAAA-CACTAAA-CCT
1 AAACCTAAACCA-TAAACCCT
*
97601 AAACCATAAACCATAAACACT
1 AAACC-TAAACCATAAACCCT
* *
97622 AAATACTAAACCATAAACCAT
1 AAA-CCTAAACCATAAACCCT
*
97643 AAACCCTAAATCCA-ATACCCT
1 AAA-CCTAAA-CCATAAACCCT
97664 AAACC--AA--A-AAACCCT
1 AAACCTAAACCATAAACCCT
*
97679 AAACCCTAAACCCTAAACCCT
1 AAA-CCTAAACCATAAACCCT
*
97700 AAACCTAAAACCATAAACCCC
1 AAACCT-AAACCATAAACCCT
97721 AAACCATAAA
1 AAACC-TAAA
97731 TCCGATTATA
Statistics
Matches: 121, Mismatches: 14, Indels: 27
0.75 0.09 0.17
Matches are distributed among these distances:
15 10 0.08
16 2 0.02
18 4 0.03
19 10 0.08
20 24 0.20
21 66 0.55
22 5 0.04
ACGTcount: A:0.53, C:0.33, G:0.01, T:0.14
Consensus pattern (20 bp):
AAACCTAAACCATAAACCCT
Found at i:97724 original size:14 final size:14
Alignment explanation
Indices: 97549--97730 Score: 160
Period size: 14 Copynumber: 13.1 Consensus size: 14
97539 ATTTGTAATG
*
97549 AACCCT-AACCTTA
1 AACCCTAAACCATA
*
97562 AAACCTAAACCATA
1 AACCCTAAACCATA
* *
97576 AATCCTAAACC-GA
1 AACCCTAAACCATA
*
97589 AACACTAAACC-TA
1 AACCCTAAACCATA
*
97602 AACCATAAACCATA
1 AACCCTAAACCATA
* *
97616 AACACTAAA-TACTA
1 AACCCTAAACCA-TA
*
97630 AACCATAAACCATA
1 AACCCTAAACCATA
97644 AACCCTAAATCCA-A
1 AACCCTAAA-CCATA
* *
97658 TACCCTAAACCAAAA
1 AACCCTAAACC-ATA
*
97673 AACCCTAAACCCTA
1 AACCCTAAACCATA
*
97687 AACCCTAAACCCTA
1 AACCCTAAACCATA
97701 AA-CCTAAAACCATA
1 AACCCT-AAACCATA
*
97715 AACCCCAAACCATA
1 AACCCTAAACCATA
97729 AA
1 AA
97731 TCCGATTATA
Statistics
Matches: 138, Mismatches: 22, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
13 31 0.22
14 90 0.65
15 17 0.12
ACGTcount: A:0.52, C:0.33, G:0.01, T:0.15
Consensus pattern (14 bp):
AACCCTAAACCATA
Found at i:99295 original size:20 final size:20
Alignment explanation
Indices: 99259--99300 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
99249 AGTATTTTTA
*
99259 TTAACTTTTTTTCTTTC-TT
1 TTAACATTTTTTCTTTCATT
99278 TTAACATTTTTTCTTTTCATT
1 TTAACATTTTTTC-TTTCATT
99299 TT
1 TT
99301 TTTCCTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 4 0.20
21 4 0.20
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (20 bp):
TTAACATTTTTTCTTTCATT
Found at i:109603 original size:21 final size:20
Alignment explanation
Indices: 109517--109674 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
109507 AAATGACCAA
**
109517 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
109536 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
109556 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
109576 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
109597 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
109618 CAAATTCGCATTGCGATTTTT
1 CAAAATCGCAACGCGA-TTTT
* *
109639 CAAAATCGCAACGCGAATAT
1 CAAAATCGCAACGCGATTTT
*
109659 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
109675 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 45 0.43
22 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:109703 original size:20 final size:20
Alignment explanation
Indices: 109641--109910 Score: 242
Period size: 20 Copynumber: 13.5 Consensus size: 20
109631 CGATTTTTCA
* ** *
109641 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
109661 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
109681 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
109701 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
109721 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
109741 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
109761 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
109781 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
109801 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
* *
109821 AAATCACAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * **
109841 AAATCGCAACGAGAATCTAT
1 AAATCGCAACGCGTATCCGT
* *
109861 AAATCGCAATG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
109881 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
109901 AAATCACAAC
1 AAATCGCAAC
109911 ACTGAAATTT
Statistics
Matches: 204, Mismatches: 38, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 200 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:110632 original size:24 final size:24
Alignment explanation
Indices: 110593--110639 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
110583 AAATTTGGTC
110593 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
110617 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
110640 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:113119 original size:33 final size:34
Alignment explanation
Indices: 113068--113232 Score: 174
Period size: 33 Copynumber: 4.7 Consensus size: 34
113058 CGGAAATTAC
* *
113068 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
113101 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
113135 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* *
113173 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
113206 AATCACAATGCGAAATGAAAATCGCAA
1 AATCGCAA--C--AATGAAAATCGCAA
113233 CGAGAGAATC
Statistics
Matches: 112, Mismatches: 8, Indels: 19
0.81 0.06 0.14
Matches are distributed among these distances:
32 1 0.01
33 49 0.44
34 16 0.14
35 1 0.01
36 2 0.02
37 1 0.01
38 26 0.23
39 16 0.14
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:113151 original size:19 final size:19
Alignment explanation
Indices: 113082--113270 Score: 210
Period size: 19 Copynumber: 10.7 Consensus size: 19
113072 GCAACGAGAG
113082 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
113101 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
113115 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
113135 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
113154 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
113173 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
113187 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
113206 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
113225 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
113239 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
113258 AATCGCATTGCGA
1 AATCGCAATGCGA
113271 TTCTCCCGTT
Statistics
Matches: 144, Mismatches: 10, Indels: 32
0.77 0.05 0.17
Matches are distributed among these distances:
14 32 0.22
15 2 0.01
16 5 0.03
17 5 0.03
18 2 0.01
19 82 0.57
20 16 0.11
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:113209 original size:52 final size:52
Alignment explanation
Indices: 113068--113270 Score: 272
Period size: 52 Copynumber: 3.9 Consensus size: 52
113058 CGGAAATTAC
*
113068 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
113115 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
*
113173 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
113225 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
113271 TTCTCCCGTT
Statistics
Matches: 138, Mismatches: 7, Indels: 17
0.85 0.04 0.10
Matches are distributed among these distances:
47 8 0.06
49 1 0.01
50 1 0.01
52 83 0.60
53 29 0.21
55 2 0.01
56 1 0.01
58 13 0.09
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:113318 original size:53 final size:52
Alignment explanation
Indices: 113260--113376 Score: 198
Period size: 53 Copynumber: 2.2 Consensus size: 52
113250 GAAATTAAAA
113260 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
* *
113313 TCGCATTGCGATTTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
*
113365 TTGCATTGCGAT
1 TCGCATTGCGAT
113377 AGTCAATTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 29 0.48
53 32 0.52
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:113319 original size:19 final size:19
Alignment explanation
Indices: 113279--113376 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
113269 GATTCTCCCG
113279 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
113299 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
113318 TTGCGATTTTC---TCG--
1 TTGCGATTTTCATTTCGCA
113332 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
113351 TTGCGATTTTCATTTTGCA
1 TTGCGATTTTCATTTCGCA
113370 TTGCGAT
1 TTGCGAT
113377 AGTCAATTTT
Statistics
Matches: 72, Mismatches: 1, Indels: 11
0.86 0.01 0.13
Matches are distributed among these distances:
14 11 0.15
16 3 0.04
17 3 0.04
19 40 0.56
20 15 0.21
ACGTcount: A:0.14, C:0.20, G:0.17, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:113341 original size:33 final size:33
Alignment explanation
Indices: 113299--113361 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
113289 CATTTCCGCA
113299 TTGCGATTTTCATTTCGCATTGCGATTTTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCTCG
113332 TTGCGATTTTCATTTCGCATTGCGATTTTC
1 TTGCGATTTTCATTTCGCATTGCGATTTTC
113362 ATTTTGCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.13, C:0.21, G:0.17, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCTCG
Found at i:113502 original size:14 final size:14
Alignment explanation
Indices: 113483--113519 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
113473 CATCAATTAC
113483 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
113497 ACAAATCATCTTTT
1 ACAAATCAACTTTT
113511 ACAAATCAA
1 ACAAATCAA
113520 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:115517 original size:14 final size:14
Alignment explanation
Indices: 115498--115554 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
115488 GCGAAATGAA
*
115498 AATCGCAACGACAG
1 AATCGCAACGAAAG
115512 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
115529 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
115545 AATCGCAACG
1 AATCGCAACG
115555 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:115525 original size:33 final size:33
Alignment explanation
Indices: 115479--115571 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
115469 GCGAAACCAA
*
115479 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
115512 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
115545 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
115572 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:115536 original size:19 final size:19
Alignment explanation
Indices: 115442--115576 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
115432 TAGTTTACTT
* *
115442 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
115462 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
115481 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
115500 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
115514 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
115533 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
115547 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
115566 TCGCAATGCGA
1 TCGCAACGCGA
115577 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:115594 original size:19 final size:19
Alignment explanation
Indices: 115572--115700 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
115562 AAAATCGCAA
115572 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
115591 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
115605 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
115624 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
* **
115638 TGTGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
115657 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
115676 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
115696 TGCGA
1 TGCGA
115701 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 47 0.53
20 13 0.15
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:115614 original size:33 final size:33
Alignment explanation
Indices: 115572--115663 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
115562 AAAATCGCAA
115572 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
115605 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
* **
115638 TGTGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
115664 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:115864 original size:93 final size:93
Alignment explanation
Indices: 115748--116123 Score: 736
Period size: 93 Copynumber: 4.1 Consensus size: 93
115738 ATGGATTGCA
115748 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
115812 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
115840 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
115905 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
115933 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
115998 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
116026 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
116091 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
116119 TTACT
1 TTACT
116124 AAGCAATCTA
Statistics
Matches: 282, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 4 0.01
93 278 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:117842 original size:14 final size:14
Alignment explanation
Indices: 117823--117912 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
117813 TTGAAATGAA
117823 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
117837 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
117856 AATCGCAACTAGAG
1 AATCGCAACGAGAG
*
117870 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
117889 AATCGCAACGAGAG
1 AATCGCAACGAGAG
117903 AATCGCAACG
1 AATCGCAACG
117913 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 30 0.50
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 20 0.33
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:117855 original size:33 final size:33
Alignment explanation
Indices: 117815--117929 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
117805 TCTTTTGGTT
117815 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
117848 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
117881 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
117914 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
117930 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:117861 original size:19 final size:19
Alignment explanation
Indices: 117837--117934 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
117827 GCAACGAGAG
117837 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
117856 AATCGCAA--C--TA-GAG
1 AATCGCAACGCGAAATGAA
117870 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
117889 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
117903 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
117922 AATCGCAATGCGA
1 AATCGCAACGCGA
117935 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:118010 original size:41 final size:41
Alignment explanation
Indices: 117953--118030 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
117943 TCGCGTTGCG
*
117953 ATTCTCTCGTTGCGATTTTCATTTCGCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTAGCTCGTTGCGACAGTC
*
117994 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTAGCTCGTTGCGAC
118031 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTAGCTCGTTGCGACAGTC
Found at i:118015 original size:20 final size:21
Alignment explanation
Indices: 117954--118029 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
117944 CGCGTTGCGA
117954 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
* ***
117975 TTCGCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
117995 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
118016 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
118030 CTCTTCTGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:118146 original size:33 final size:33
Alignment explanation
Indices: 118109--118179 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
118099 AATACTAACT
*
118109 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
118142 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
118175 TGAAA
1 TGAAA
118180 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:118413 original size:22 final size:22
Alignment explanation
Indices: 118361--118415 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
118351 TGGTTGTGAG
**
118361 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
** *
118383 GGAAATCTTCGGAGATGGGGAT
1 GGATTTCTTCGGAGATGGGGAC
118405 GGATTTCTTCG
1 GGATTTCTTCG
118416 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.15, G:0.40, T:0.25
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:118587 original size:20 final size:20
Alignment explanation
Indices: 118562--118715 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
118552 CTTTAAATAT
118562 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
118582 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
118604 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
118623 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
118643 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
118663 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
118683 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
118703 CGCGTTGCGATTT
1 CGCGTTGCGATTT
118716 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:118689 original size:40 final size:40
Alignment explanation
Indices: 118561--118715 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
118551 GCTTTAAATA
*
118561 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
118602 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
118642 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
118682 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
118716 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:118732 original size:21 final size:21
Alignment explanation
Indices: 118702--118784 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
118692 ATTTTCATAT
*
118702 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
118723 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
118744 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
118765 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
118785 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:118775 original size:42 final size:43
Alignment explanation
Indices: 118682--118780 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
118672 ATTTATGTGT
* *
118682 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
118723 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
118765 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
118781 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:119370 original size:8 final size:10
Alignment explanation
Indices: 119342--119376 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
119332 TTCATCACAC
119342 CAAATTCTCT
1 CAAATTCTCT
119352 CAAATTCTCT
1 CAAATTCTCT
*
119362 CAATTTCTCT
1 CAAATTCTCT
119372 CAAAT
1 CAAAT
119377 ACTATCTCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:119461 original size:17 final size:18
Alignment explanation
Indices: 119424--119464 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
119414 ATATTATGTA
*
119424 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
119442 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
119459 TTTACT
1 TTTACT
119465 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Done.