Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019772.1 Corchorus olitorius cultivar O-4 contig19805, 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: 108068
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1889 original size:17 final size:16
Alignment explanation
Indices: 1863--1911 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 16
1853 CGGACAAAAA
1863 TATTATTTTATAGAGAT
1 TATTATTTTATAGAG-T
*
1880 TATTAATTTATAGAG-
1 TATTATTTTATAGAGT
1895 TATTATTTTATAGAGT
1 TATTATTTTATAGAGT
1911 T
1 T
1912 TATACTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 14 0.48
16 1 0.03
17 14 0.48
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (16 bp):
TATTATTTTATAGAGT
Found at i:1899 original size:18 final size:17
Alignment explanation
Indices: 1863--1914 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
1853 CGGACAAAAA
*
1863 TATTATTTTATAGAGAT
1 TATTAATTTATAGAGAT
1880 TATTAATTTATAGAG--
1 TATTAATTTATAGAGAT
* *
1895 TATTATTTTATAGAGTT
1 TATTAATTTATAGAGAT
1912 TAT
1 TAT
1915 ACTTTATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 14 0.45
17 17 0.55
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (17 bp):
TATTAATTTATAGAGAT
Found at i:1904 original size:32 final size:31
Alignment explanation
Indices: 1863--1922 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
1853 CGGACAAAAA
1863 TATTATTTTATAGAGATTATTAATTTATAGAG
1 TATTATTTTATAGAGATTA-TAATTTATAGAG
* *
1895 TATTATTTTATAGAGTTTATACTTTATA
1 TATTATTTTATAGAGATTATAATTTATA
1923 CAGAACACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 8 0.31
32 18 0.69
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATTTTATAGAGATTATAATTTATAGAG
Found at i:2209 original size:28 final size:29
Alignment explanation
Indices: 2143--2209 Score: 66
Period size: 31 Copynumber: 2.2 Consensus size: 29
2133 TACTATATAT
2143 ATAAAGTAGTAAGCAAAAAAAAAAAGTACCA
1 ATAAA-TAGTAAGCAAAAAAAAAAAGTA-CA
* *
2174 AAACAATAGTAAG-AAAAAAAAATGAGTA-A
1 ATA-AATAGTAAGCAAAAAAAAA-AAGTACA
2203 ATAAATA
1 ATAAATA
2210 ATCTCATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
28 4 0.13
29 3 0.10
30 9 0.29
31 13 0.42
32 2 0.06
ACGTcount: A:0.67, C:0.06, G:0.12, T:0.15
Consensus pattern (29 bp):
ATAAATAGTAAGCAAAAAAAAAAAGTACA
Found at i:10500 original size:473 final size:474
Alignment explanation
Indices: 9542--10601 Score: 1655
Period size: 473 Copynumber: 2.2 Consensus size: 474
9532 TAGCCGGTGA
* *
9542 TGGCATCCAAGATTTCATAGGTTATTACTCTCTAGATTCAAGGAGATATGGACCTGTAGCTCACT
1 TGGCATCCAAGATTTCTTAGGTCATTACTCTCTAGATTCAAGGAGATATGGACCTGTAGCTCACT
** * * * *
9607 TATTAGATTTGGAAAAGTATTTAACATAAGATTCATATATATTCTGGATTATTATAGCAAATCCA
66 TATCGGATTTGGAAAAGTATTTAACATAGGATTCATATATATTATGGATTACTACAGCAAATCCA
* *
9672 AATTCAATGCAAGTTGGATCGGTGATAGCATATAAACCAAAGTCGTTTGGATTCTATTTATCGGG
131 AATTCAATGCAAGTTGGATCGGTGATAGCA-ATAAACCAAAGTCGTTTGGATTCTATCTATCGAG
* *
9737 CATATGTCATAGTCACTCTGTTCAACTATATTTTCTATGCTTATGTCGCCACCAAATATTCTTAT
195 CATATGTCATAGTCACTCTATTCAACTATATTGTCTATGCTTATGTCGCCACCAAATATTCTTAT
* *
9802 GACATTATCATAAGAATACTAGAAGAAGAAATACCATTCTTGGAAGTGAAACAAGATGAACCAGC
260 GACAATATCATAAGAATACCAGAAGAAGAAATACCATTCTTGGAAGTGAAACAAGATGAACCAGC
* * *
9867 GGGGCAGACCAACAGAACAACCAAGTACAAGTGAATGTTGAGCTGCAAATGATTTCAGTGTGTAA
325 GGGGCAGACCAACAGAACAACCAAATACAAGTGAATGTTGAGCTCCAAATAATTTCAGTGTGTAA
* *
9932 TTAACGTGATGATTAATCATCAAGAAACGTCATTATGTCTTTTTAGTTTATGCAACATTATGTTT
390 TTAACGTGATGATTAATCATCAAGAAACGTCATTATGTATTTTTAGTCTATGCAACATTATGTTT
9997 TCCGTTAGTGTACATATGTAT
455 TCCGTTAGTGTA-ATATGTAT
* * *
10018 T-GTATCCAAGATTTCTTACGTCATTACTCTCCAGATTCAAGGAGATATGGACCTGTAGCTCACT
1 TGGCATCCAAGATTTCTTAGGTCATTACTCTCTAGATTCAAGGAGATATGGACCTGTAGCTCACT
10082 TATCGGATTTGGAAAAGTATTTAACATAGGATTCATATATATTATGGATTACTACAGCAAATCCA
66 TATCGGATTTGGAAAAGTATTTAACATAGGATTCATATATATTATGGATTACTACAGCAAATCCA
*
10147 AATTCAATGCAAGTTGGATCGGTGATGGC-ATAAACCAAAGTCGTTTGGATTCTATCTATCGAGC
131 AATTCAATGCAAGTTGGATCGGTGATAGCAATAAACCAAAGTCGTTTGGATTCTATCTATCGAGC
* * *
10211 ATATGTCATAGTCGCTCTATTCAACTGTATTGTCTATGCTTATGTCGCCACCTAATATTCTTATG
196 ATATGTCATAGTCACTCTATTCAACTATATTGTCTATGCTTATGTCGCCACCAAATATTCTTATG
* *
10276 ACAATATCATAAGAATACCAGAAGAGGAAATACCATTCTTGGAAGTGAAACAAGATGAATCAGCA
261 ACAATATCATAAGAATACCAGAAGAAGAAATACCATTCTTGGAAGTGAAACAAGATGAACCAGC-
* * *
10341 GGGGCAGACCAACAGATCAACCAAATGCATA-TGAATGTTGAGCTCCAAATAATTTTAGTGTGTA
325 GGGGCAGACCAACAGAACAACCAAATACA-AGTGAATGTTGAGCTCCAAATAATTTCAGTGTGTA
*
10405 ATTAACGTGATGATTAATCATCAAGAAACGTCATTATGTATTTTTAGTCTATGCAACATTTTGTT
389 ATTAACGTGATGATTAATCATCAAGAAACGTCATTATGTATTTTTAGTCTATGCAACATTATGTT
10470 TTCCGTTAGTGT-ATATGTAT
454 TTCCGTTAGTGTAATATGTAT
* *
10490 TGGCATCCAAGATTTCTTAGGCCATTACTCTCTAGATTCAAGGAGATATGGACATGTATTTACTG
1 TGGCATCCAAGATTTCTTAGGTCATTACTCTCTAGATTCAAGGAGATATGGACCTG----TA---
* *
10555 GCTCACTTATCGAAATTGGAAAAGTATTT-A-ATAGGATTCATATATAT
59 GCTCACTTATCGGATTTGGAAAAGTATTTAACATAGGATTCATATATAT
10602 CTTACTATCT
Statistics
Matches: 535, Mismatches: 39, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
472 9 0.02
473 202 0.38
474 130 0.24
475 146 0.27
476 1 0.00
477 2 0.00
478 17 0.03
479 1 0.00
480 27 0.05
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (474 bp):
TGGCATCCAAGATTTCTTAGGTCATTACTCTCTAGATTCAAGGAGATATGGACCTGTAGCTCACT
TATCGGATTTGGAAAAGTATTTAACATAGGATTCATATATATTATGGATTACTACAGCAAATCCA
AATTCAATGCAAGTTGGATCGGTGATAGCAATAAACCAAAGTCGTTTGGATTCTATCTATCGAGC
ATATGTCATAGTCACTCTATTCAACTATATTGTCTATGCTTATGTCGCCACCAAATATTCTTATG
ACAATATCATAAGAATACCAGAAGAAGAAATACCATTCTTGGAAGTGAAACAAGATGAACCAGCG
GGGCAGACCAACAGAACAACCAAATACAAGTGAATGTTGAGCTCCAAATAATTTCAGTGTGTAAT
TAACGTGATGATTAATCATCAAGAAACGTCATTATGTATTTTTAGTCTATGCAACATTATGTTTT
CCGTTAGTGTAATATGTAT
Found at i:10771 original size:43 final size:41
Alignment explanation
Indices: 10724--10841 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 41
10714 TCATTCAACT
* * *
10724 TTTTTTATTAATTATGCAAAGATATTGTAAATCCAATATTTAA
1 TTTTTTATTAATTATGGAAAGATATTTTAAATCC-AT-CTTAA
*
10767 TTTTTTA-AAATTATGGAAAGATATTTTAAATCCATCTTAA
1 TTTTTTATTAATTATGGAAAGATATTTTAAATCCATCTTAA
* *
10807 TTTTATTTTTGAATTATGGAAATATATTTTAAATC
1 TTTT-TTATT-AATTATGGAAAGATATTTTAAATC
10842 TATATATTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
40 8 0.12
41 4 0.06
42 23 0.35
43 30 0.46
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (41 bp):
TTTTTTATTAATTATGGAAAGATATTTTAAATCCATCTTAA
Found at i:11758 original size:21 final size:21
Alignment explanation
Indices: 11732--11772 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
11722 TTGTTAATAC
*
11732 CATTATAACTTTTTTGATAAT
1 CATTATAACTTCTTTGATAAT
11753 CATTATAACTTCTTTGATAA
1 CATTATAACTTCTTTGATAA
11773 AATTATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.12, G:0.05, T:0.49
Consensus pattern (21 bp):
CATTATAACTTCTTTGATAAT
Found at i:12552 original size:22 final size:22
Alignment explanation
Indices: 12507--12555 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
12497 CTTTCTAAGG
* *
12507 TTTTCATATAAAAAATGATGAA
1 TTTTTATATAAAAAAAGATGAA
* *
12529 TTTTTATATAAAAAAAGCTTAA
1 TTTTTATATAAAAAAAGATGAA
12551 TTTTT
1 TTTTT
12556 TATTCGTGAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (22 bp):
TTTTTATATAAAAAAAGATGAA
Found at i:12820 original size:30 final size:31
Alignment explanation
Indices: 12746--12842 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
12736 GATTCAACAT
* * * *
12746 TTTTAGTAGGGTCAATACTATAAAATTTTGA
1 TTTTAGAAGGGTTAATACTATAAAACTTTCA
*
12777 TTTTA-AGGGGTTAATA-TATAAAACTTTCA
1 TTTTAGAAGGGTTAATACTATAAAACTTTCA
* *
12806 TTTTAGAAGGGTTAATATTGTAAAAC-TTCAA
1 TTTTAGAAGGGTTAATACTATAAAACTTTC-A
12837 TTTTAG
1 TTTTAG
12843 TGGAGTCAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
29 16 0.29
30 21 0.38
31 19 0.34
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.42
Consensus pattern (31 bp):
TTTTAGAAGGGTTAATACTATAAAACTTTCA
Found at i:16683 original size:22 final size:22
Alignment explanation
Indices: 16649--16767 Score: 100
Period size: 22 Copynumber: 5.4 Consensus size: 22
16639 ACAATCAAAC
*
16649 CAAAATTACATAGGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * * *
16671 CAGAATTTAATAGTG-TGGTTAC
1 CAAAATTTCATAG-GAAGGTTAT
16693 CAAAATTTCATATGG-AGGTTAT
1 CAAAATTTCATA-GGAAGGTTAT
* *
16715 CAAAACTTCATAGTATA-GTTAT
1 CAAAATTTCATAGGA-AGGTTAT
* **
16737 CAAAATTTTATAAAAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
16759 CAAAATTTC
1 CAAAATTTC
16768 TTAGACTCCC
Statistics
Matches: 76, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
21 2 0.03
22 71 0.93
23 3 0.04
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:16712 original size:44 final size:44
Alignment explanation
Indices: 16647--16763 Score: 128
Period size: 44 Copynumber: 2.7 Consensus size: 44
16637 TGACAATCAA
* * * * *
16647 ACCAAAATTACATAGGAAGGTTATCAGAATTTAATAGTGTGGTT
1 ACCAAAATTTCATAGGAAGGTTATCAAAACTTAATAGTATAGTT
*
16691 ACCAAAATTTCATATGG-AGGTTATCAAAACTTCATAGTATAGTT
1 ACCAAAATTTCATA-GGAAGGTTATCAAAACTTAATAGTATAGTT
* * **
16735 ATCAAAATTTTATAAAAAGGTTATCAAAA
1 ACCAAAATTTCATAGGAAGGTTATCAAAA
16764 TTTCTTAGAC
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
44 59 0.97
45 2 0.03
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (44 bp):
ACCAAAATTTCATAGGAAGGTTATCAAAACTTAATAGTATAGTT
Found at i:17003 original size:22 final size:22
Alignment explanation
Indices: 16977--17060 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 22
16967 AGCCTTAGGG
*
16977 AGGTTAACAAAATTTCATACGA
1 AGGTTAACAAAATTTCATAAGA
* * * *
16999 AGGTTATCGAAACTTT-ATAGTGT
1 AGGTTAAC-AAAATTTCATA-AGA
*
17022 A-GTTATCAAAATTTCATAAGA
1 AGGTTAACAAAATTTCATAAGA
* *
17043 ATGTTAACAAAATATCAT
1 AGGTTAACAAAATTTCAT
17061 TGGGAGGGAG
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
21 8 0.16
22 33 0.67
23 8 0.16
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (22 bp):
AGGTTAACAAAATTTCATAAGA
Found at i:17160 original size:22 final size:21
Alignment explanation
Indices: 17088--17172 Score: 66
Period size: 22 Copynumber: 4.0 Consensus size: 21
17078 ATATTCGTGC
*
17088 TTATCAAAATTTCCTGGAG-G
1 TTATCAAAATTTCATGGAGAG
*
17108 TTAACAAAATTTCATAGG-GATG
1 TTATCAAAATTTCAT-GGAGA-G
* * *
17130 GTATGAAAATTTTATGGAGAAG
1 TTATCAAAATTTCATGGAG-AG
* *
17152 TTATCAAAATTACATAGAGAG
1 TTATCAAAATTTCATGGAGAG
17173 GATATCACAA
Statistics
Matches: 49, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
20 14 0.29
21 6 0.12
22 28 0.57
23 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (21 bp):
TTATCAAAATTTCATGGAGAG
Found at i:17285 original size:22 final size:22
Alignment explanation
Indices: 17209--17419 Score: 133
Period size: 22 Copynumber: 9.6 Consensus size: 22
17199 CATAAGGACG
* * * *
17209 TTATCGAAATTTCATGGTGTGT
1 TTATCAAAATTTCATAGTGAGA
* *
17231 TTATCAAAATTTTCATAGTGCGG
1 TTATCAAAA-TTTCATAGTGAGA
* * **
17254 TTA-C-CAATTTTATAGTTTGA
1 TTATCAAAATTTCATAGTGAGA
*
17274 TTATCAAAATTTCATAGGGAGA
1 TTATCAAAATTTCATAGTGAGA
* * *
17296 TTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGTGAGA
* *
17318 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGA
* * * *
17340 TTATCAAAATTTCACAATGTGG
1 TTATCAAAATTTCATAGTGAGA
* * *
17362 TTATCAAACTTTCATAGGGAGG
1 TTATCAAAATTTCATAGTGAGA
* *
17384 TTAT-AGAAA-TTCTATAATGAGG
1 TTATCA-AAATTTC-ATAGTGAGA
*
17406 TTATCAAATTTTCA
1 TTATCAAAATTTCA
17420 GTATGGTTAT
Statistics
Matches: 150, Mismatches: 32, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
20 12 0.08
21 7 0.05
22 114 0.76
23 17 0.11
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGA
Found at i:17324 original size:44 final size:44
Alignment explanation
Indices: 17274--17419 Score: 188
Period size: 44 Copynumber: 3.3 Consensus size: 44
17264 TATAGTTTGA
* *
17274 TTATCAAAATTTCATAGGGAGATTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACAATGAGG
* * *
17318 TTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAATGTGG
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACAATGAGG
* *
17362 TTATCAAACTTTCATAGGGAGGTTAT-AGAAA-TTCTATAATGAGG
1 TTATCAAAATTTCATAGGGAGGTTATCA-AAATTTC-ACAATGAGG
*
17406 TTATCAAATTTTCA
1 TTATCAAAATTTCA
17420 GTATGGTTAT
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
43 4 0.04
44 85 0.96
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCACAATGAGG
Found at i:17366 original size:66 final size:66
Alignment explanation
Indices: 17259--17419 Score: 155
Period size: 66 Copynumber: 2.4 Consensus size: 66
17249 TGCGGTTACC
* * * * * *
17259 AATTTTATAGTTTGATTATCAAAATTTCATAGGGAGATTATCAAAATTTCACACTGAGGTTATCA
1 AATTTCATAGTGTGGTTATCAAAATTTCACAAGGAGATTATCAAAATTTCACACGGAGGTTAT-A
17324 -A
65 GA
* * * * * *
17325 AATTTCATAGTGTGGTTATCAAAATTTCACAATGTGGTTATCAAACTTTCATAGGGAGGTTATAG
1 AATTTCATAGTGTGGTTATCAAAATTTCACAAGGAGATTATCAAAATTTCACACGGAGGTTATAG
17390 A
66 A
* * *
17391 AA-TTCTATAATGAGGTTATCAAATTTTCA
1 AATTTC-ATAGTGTGGTTATCAAAATTTCA
17420 GTATGGTTAT
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
65 4 0.05
66 74 0.95
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (66 bp):
AATTTCATAGTGTGGTTATCAAAATTTCACAAGGAGATTATCAAAATTTCACACGGAGGTTATAG
A
Found at i:18944 original size:12 final size:12
Alignment explanation
Indices: 18929--18953 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18919 ATATATATTA
18929 CTATAGCAAATT
1 CTATAGCAAATT
18941 CTATAGCAAATT
1 CTATAGCAAATT
18953 C
1 C
18954 AATGCAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (12 bp):
CTATAGCAAATT
Found at i:19818 original size:27 final size:27
Alignment explanation
Indices: 19788--19853 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
19778 TTAAATTTTA
19788 TTTTAAATATATCATTAATAATAT-TAT
1 TTTTAAATAT-TCATTAATAATATATAT
*
19815 TTTTATAATATTTATTAATAATATATAT
1 TTTTA-AATATTCATTAATAATATATAT
* *
19843 TATTAATTATT
1 TTTTAAATATT
19854 AATATAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 22 0.65
28 12 0.35
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTTAAATATTCATTAATAATATATAT
Found at i:19837 original size:13 final size:13
Alignment explanation
Indices: 19801--19849 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
19791 TAAATATATC
19801 ATTAATAATATTAT
1 ATTAATAATATT-T
* *
19815 TTTTATAATATTT
1 ATTAATAATATTT
*
19828 ATTAATAATATAT
1 ATTAATAATATTT
*
19841 ATTATTAAT
1 ATTAATAAT
19850 TATTAATATA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTAATAATATTT
Found at i:19846 original size:20 final size:20
Alignment explanation
Indices: 19818--19859 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
19808 ATATTATTTT
*
19818 TATAATATTTATTAATAATA
1 TATAATATTAATTAATAATA
* *
19838 TATATTATTAATTATTAATA
1 TATAATATTAATTAATAATA
19858 TA
1 TA
19860 AAACGAATAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATAATATTAATTAATAATA
Found at i:23782 original size:16 final size:16
Alignment explanation
Indices: 23777--23823 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
23767 TTATTCGGGT
23777 TTCGGGTCTCGGGTCA
1 TTCGGGTCTCGGGTCA
* *
23793 TACGGGTTTCGGGTCA
1 TTCGGGTCTCGGGTCA
23809 TTCGGGTCTCGGGTC
1 TTCGGGTCTCGGGTC
23824 TCAGGTTGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.06, C:0.23, G:0.38, T:0.32
Consensus pattern (16 bp):
TTCGGGTCTCGGGTCA
Found at i:23788 original size:23 final size:23
Alignment explanation
Indices: 23762--23816 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
23752 TCATTTTGGT
* *
23762 TCGGGTTATTCGGGTTTCGGGTC
1 TCGGGTCATACGGGTTTCGGGTC
23785 TCGGGTCATACGGGTTTCGGGTC
1 TCGGGTCATACGGGTTTCGGGTC
23808 ATTCGGGTC
1 --TCGGGTC
23817 TCGGGTCTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 21 0.75
25 7 0.25
ACGTcount: A:0.07, C:0.20, G:0.38, T:0.35
Consensus pattern (23 bp):
TCGGGTCATACGGGTTTCGGGTC
Found at i:23823 original size:7 final size:7
Alignment explanation
Indices: 23771--23825 Score: 56
Period size: 7 Copynumber: 7.3 Consensus size: 7
23761 TTCGGGTTAT
*
23771 TCGGGTT
1 TCGGGTC
23778 TCGGGTC
1 TCGGGTC
23785 TCGGGTC
1 TCGGGTC
*
23792 ATACGGGTT
1 -T-CGGGTC
23801 TCGGGTC
1 TCGGGTC
23808 ATTCGGGTC
1 --TCGGGTC
23817 TCGGGTC
1 TCGGGTC
23824 TC
1 TC
23826 AGGTTGAGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
7 27 0.66
8 2 0.05
9 12 0.29
ACGTcount: A:0.05, C:0.24, G:0.38, T:0.33
Consensus pattern (7 bp):
TCGGGTC
Found at i:24096 original size:39 final size:39
Alignment explanation
Indices: 24053--24129 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
24043 TTGATATTAA
24053 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGG
* *
24092 TTTTGAATATTATATACATAATTAATTATCATGTGGGG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGG
24130 TATGTGTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (39 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGG
Found at i:25114 original size:42 final size:42
Alignment explanation
Indices: 25052--25131 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
25042 GCTAAGTCTT
25052 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATAATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATAATA
* *
25094 GAAAATTCTTTGTAATTTAAGAAATACTCAACTCAAAT
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAAT
25132 CCTAATCCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.47, C:0.14, G:0.07, T:0.31
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATAATA
Found at i:25268 original size:55 final size:56
Alignment explanation
Indices: 25198--25310 Score: 194
Period size: 56 Copynumber: 2.0 Consensus size: 56
25188 TTTATTCTGT
25198 AGAATAACTAAGTAGAGATA-GGGGATAGGATTTATTATAACATTTATTATGTGAA
1 AGAATAACTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTATGTGAA
*
25253 AGAATAA-TCAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAACT-AAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTATGTGAA
25309 AG
1 AG
25311 GAAACGGATA
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
54 1 0.02
55 18 0.33
56 36 0.65
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.32
Consensus pattern (56 bp):
AGAATAACTAAGTAGAGATAGGGGGATAGGATTTATTATAACATTTATTATGTGAA
Found at i:25606 original size:22 final size:23
Alignment explanation
Indices: 25576--25621 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
25566 TTTTAGTTTA
25576 TAATATTCTCGGATCATTCGGGT
1 TAATATTCTCGGATCATTCGGGT
* *
25599 TAAT-TTCTCGGGTTATTCGGGT
1 TAATATTCTCGGATCATTCGGGT
25621 T
1 T
25622 TCGGGTCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.17, C:0.15, G:0.24, T:0.43
Consensus pattern (23 bp):
TAATATTCTCGGATCATTCGGGT
Found at i:25658 original size:16 final size:16
Alignment explanation
Indices: 25639--25699 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
25629 ATATAAGTCT
25639 CGGGTCACTCGGGTCA
1 CGGGTCACTCGGGTCA
* *
25655 CGGGTCATTCGGGTCT
1 CGGGTCACTCGGGTCA
**
25671 CGGGTCAACT-GGGTTG
1 CGGGTC-ACTCGGGTCA
*
25687 CGGGTCATTCGGG
1 CGGGTCACTCGGG
25700 ACGGGTTCGT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
15 2 0.05
16 33 0.89
17 2 0.05
ACGTcount: A:0.10, C:0.25, G:0.41, T:0.25
Consensus pattern (16 bp):
CGGGTCACTCGGGTCA
Found at i:25671 original size:32 final size:32
Alignment explanation
Indices: 25635--25699 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
25625 GGTCATATAA
25635 GTCTCGGGTC-ACTCGGGTCACGGGTCATTCGG
1 GTCTCGGGTCAACT-GGGTCACGGGTCATTCGG
**
25667 GTCTCGGGTCAACTGGGTTGCGGGTCATTCGG
1 GTCTCGGGTCAACTGGGTCACGGGTCATTCGG
25699 G
1 G
25700 ACGGGTTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 27 0.90
33 3 0.10
ACGTcount: A:0.09, C:0.25, G:0.40, T:0.26
Consensus pattern (32 bp):
GTCTCGGGTCAACTGGGTCACGGGTCATTCGG
Found at i:27516 original size:16 final size:16
Alignment explanation
Indices: 27495--27526 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27485 AAAAGGAGAT
27495 TAATATAATGAATTTA
1 TAATATAATGAATTTA
*
27511 TAATATAATGACTTTA
1 TAATATAATGAATTTA
27527 ATACCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (16 bp):
TAATATAATGAATTTA
Found at i:31747 original size:16 final size:19
Alignment explanation
Indices: 31704--31741 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
31694 TGGAACTCCT
*
31704 TTCCTTCTCTTCTTGTTGA
1 TTCCTTCTCTTCTTCTTGA
31723 TTCCTTCTCTT-TTCTTGA
1 TTCCTTCTCTTCTTCTTGA
31741 T
1 T
31742 CCTCTCAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.05, C:0.26, G:0.08, T:0.61
Consensus pattern (19 bp):
TTCCTTCTCTTCTTCTTGA
Found at i:33024 original size:20 final size:18
Alignment explanation
Indices: 32978--33027 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
32968 ACTTACAATG
32978 TGACTTTTTTTTAATAAA
1 TGACTTTTTTTTAATAAA
**
32996 TTTCATTTTTTCTTAATAACA
1 TGAC-TTTTTT-TTAATAA-A
33017 TGACTTTTTTT
1 TGACTTTTTTT
33028 CACATTAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 2 0.08
19 7 0.28
20 13 0.52
21 3 0.12
ACGTcount: A:0.26, C:0.10, G:0.04, T:0.60
Consensus pattern (18 bp):
TGACTTTTTTTTAATAAA
Found at i:34106 original size:23 final size:23
Alignment explanation
Indices: 34080--34125 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
34070 GAGTAGAGAA
*
34080 TTGAAGTATAGAAAA-GACAAGAG
1 TTGAACTAT-GAAAAGGACAAGAG
34103 TTGAACTATGAAAAGGACAAGAG
1 TTGAACTATGAAAAGGACAAGAG
34126 AATGTAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.50, C:0.07, G:0.26, T:0.17
Consensus pattern (23 bp):
TTGAACTATGAAAAGGACAAGAG
Found at i:39211 original size:29 final size:29
Alignment explanation
Indices: 39166--39222 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
39156 TCATCCTTAA
* *
39166 TATGACAACTTCGGGTGTCAAAATGATAT
1 TATGACAACATCAGGTGTCAAAATGATAT
*
39195 TATGACAACATCAGGTGTCAAAGTGATA
1 TATGACAACATCAGGTGTCAAAATGATA
39223 CTATATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (29 bp):
TATGACAACATCAGGTGTCAAAATGATAT
Found at i:39273 original size:33 final size:33
Alignment explanation
Indices: 39231--39296 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
39221 TACTATATTT
39231 TTGATGTGACAACTTCAGGTGCCACAAATATGC
1 TTGATGTGACAACTTCAGGTGCCACAAATATGC
**
39264 TTGATGTGACAACTTCAGGTGCCAGTAATATGC
1 TTGATGTGACAACTTCAGGTGCCACAAATATGC
39297 AAAGTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (33 bp):
TTGATGTGACAACTTCAGGTGCCACAAATATGC
Found at i:39396 original size:32 final size:34
Alignment explanation
Indices: 39331--39404 Score: 107
Period size: 32 Copynumber: 2.2 Consensus size: 34
39321 ATTTTTTTTA
* *
39331 ATGATAAAGAAAAGGTAGAAGGAGGAGATTATGC
1 ATGATAAAGAAAAGGTAGAAGCAAGAGATTATGC
39365 ATGATAAAG-AAAGGTAGAA-CAAGAGATTATGC
1 ATGATAAAGAAAAGGTAGAAGCAAGAGATTATGC
*
39397 ATGTTAAA
1 ATGATAAA
39405 TAAACTTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 18 0.49
33 10 0.27
34 9 0.24
ACGTcount: A:0.49, C:0.04, G:0.27, T:0.20
Consensus pattern (34 bp):
ATGATAAAGAAAAGGTAGAAGCAAGAGATTATGC
Found at i:40536 original size:13 final size:14
Alignment explanation
Indices: 40497--40538 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
40487 CCTCACAAAG
*
40497 TTATCTAATTGTATTT
1 TTATCTAA-T-TATGT
40513 TTATCTAATTATGT
1 TTATCTAATTATGT
40527 TTAT-TAATTATG
1 TTATCTAATTATG
40539 CCATGTGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 8 0.32
14 8 0.32
15 1 0.04
16 8 0.32
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.60
Consensus pattern (14 bp):
TTATCTAATTATGT
Found at i:43664 original size:21 final size:21
Alignment explanation
Indices: 43635--43676 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
43625 TCGCTCGGTC
*
43635 TCTACAAACCAATC-ATCACA
1 TCTACAAACCAAACAATCACA
43655 TCTACCAAACCAAACAATCACA
1 TCTA-CAAACCAAACAATCACA
43677 CACACCCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (21 bp):
TCTACAAACCAAACAATCACA
Found at i:47840 original size:19 final size:19
Alignment explanation
Indices: 47812--47868 Score: 96
Period size: 19 Copynumber: 3.0 Consensus size: 19
47802 CCCGTTCTGG
*
47812 TTCAGAAAAAGTTAAAGGC
1 TTCAGTAAAAGTTAAAGGC
47831 TTCAGTAAAAGTTAAAGGC
1 TTCAGTAAAAGTTAAAGGC
*
47850 TTCAGTAAAAGTTCAAGGC
1 TTCAGTAAAAGTTAAAGGC
47869 AAGGATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (19 bp):
TTCAGTAAAAGTTAAAGGC
Found at i:58775 original size:30 final size:30
Alignment explanation
Indices: 58741--58799 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
58731 TTTTATCTTG
58741 ACTTTCCTCTTATACCCTCAAATTTTAATA
1 ACTTTCCTCTTATACCCTCAAATTTTAATA
* *
58771 ACTTTTCTCTTATACTCTCAAATTTTAAT
1 ACTTTCCTCTTATACCCTCAAATTTTAAT
58800 GGCTTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (30 bp):
ACTTTCCTCTTATACCCTCAAATTTTAATA
Found at i:62293 original size:16 final size:16
Alignment explanation
Indices: 62254--62299 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
62244 GAAAACTGCA
*
62254 AAAAGAGGAAAAGAAG
1 AAAAGAGAAAAAGAAG
62270 AAAA-A-AAAAA-AAG
1 AAAAGAGAAAAAGAAG
62283 AAAAGAGAAAAAGAAG
1 AAAAGAGAAAAAGAAG
62299 A
1 A
62300 TATTTGCTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 7 0.27
14 5 0.19
15 6 0.23
16 8 0.31
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (16 bp):
AAAAGAGAAAAAGAAG
Found at i:64643 original size:42 final size:43
Alignment explanation
Indices: 64596--64678 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
64586 CGTGTTTGGC
*
64596 TTATCGTGTCTCGTGT-CTGAATCGTGTC-GGACACGATTAAGA
1 TTATCGTGTCTCGTGTCCT-AATCGTGTCAAGACACGATTAAGA
*
64638 TTATCGTGTTTCGTGTCCTAATCGTGTCAAGACACGATTAA
1 TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAA
64679 CACGTTTAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 24 0.65
43 13 0.35
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (43 bp):
TTATCGTGTCTCGTGTCCTAATCGTGTCAAGACACGATTAAGA
Found at i:64691 original size:20 final size:21
Alignment explanation
Indices: 64666--64708 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
64656 TAATCGTGTC
*
64666 AAGACACGATTAACACG-TTT
1 AAGACACGAGTAACACGCTTT
*
64686 AAGACACGAGTGACACGCTTT
1 AAGACACGAGTAACACGCTTT
64707 AA
1 AA
64709 TTAACGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGACACGAGTAACACGCTTT
Found at i:65173 original size:12 final size:12
Alignment explanation
Indices: 65156--65182 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
65146 CTATATAAAT
65156 ACGACACGAAAC
1 ACGACACGAAAC
65168 ACGACACGAAAC
1 ACGACACGAAAC
65180 ACG
1 ACG
65183 GATTGTCAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.33, G:0.19, T:0.00
Consensus pattern (12 bp):
ACGACACGAAAC
Found at i:69986 original size:41 final size:41
Alignment explanation
Indices: 69940--70022 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
69930 TTGATAGCAA
69940 TTGAAGTGTATTACATATACAGATTACATAATCTTGACAGT
1 TTGAAGTGTATTACATATACAGATTACATAATCTTGACAGT
*
69981 TTGAAGTGTATTACATATACATATTACATAATCTTGACAGT
1 TTGAAGTGTATTACATATACAGATTACATAATCTTGACAGT
70022 T
1 T
70023 ATATTTAAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (41 bp):
TTGAAGTGTATTACATATACAGATTACATAATCTTGACAGT
Found at i:70376 original size:24 final size:24
Alignment explanation
Indices: 70344--70394 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
70334 TAGTGAGAGG
*
70344 TTTAGTCTTTC-CCTGGTGCAAATT
1 TTTAGTCTTGCTCC-GGTGCAAATT
*
70368 TTTAGTCTTGCTCCGGTGCAAGTT
1 TTTAGTCTTGCTCCGGTGCAAATT
70392 TTT
1 TTT
70395 TTTCCTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.47
Consensus pattern (24 bp):
TTTAGTCTTGCTCCGGTGCAAATT
Found at i:72846 original size:60 final size:61
Alignment explanation
Indices: 72766--72907 Score: 187
Period size: 60 Copynumber: 2.3 Consensus size: 61
72756 TTGCTCAATC
* *
72766 CCTAACGTATGCGAACATGCTAAATTTAGGACCCATGCTTTAAATTTG-GTTAAATAGGGG
1 CCTAACGTATGCGAAAATGCTAAATTTAGGACCCATACTTTAAATTTGTGTTAAATAGGGG
* * * * * *
72826 CCTAACGTATGCAAAAATGCTCAATTTAGGACCCATACTTTTATTTTGTTTTAAATAGGGT
1 CCTAACGTATGCGAAAATGCTAAATTTAGGACCCATACTTTAAATTTGTGTTAAATAGGGG
**
72887 CCTAATATATGCGAAAATGCT
1 CCTAACGTATGCGAAAATGCT
72908 CAGATTAGAG
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
60 42 0.60
61 28 0.40
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (61 bp):
CCTAACGTATGCGAAAATGCTAAATTTAGGACCCATACTTTAAATTTGTGTTAAATAGGGG
Found at i:73049 original size:31 final size:32
Alignment explanation
Indices: 73009--73074 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
72999 TAATTTGGTT
*
73009 AATTAAGTCCCGAATATTGCAAAATCGGCTCA
1 AATTAAGTCCCGAACATTGCAAAATCGGCTCA
**
73041 AATT-AGTCCTTAACATTGCAAAATCGGCTCA
1 AATTAAGTCCCGAACATTGCAAAATCGGCTCA
73072 AAT
1 AAT
73075 CAATGTCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (32 bp):
AATTAAGTCCCGAACATTGCAAAATCGGCTCA
Found at i:73798 original size:16 final size:17
Alignment explanation
Indices: 73767--73799 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
73757 ACATATTTTA
*
73767 TTTGCTTTTCTTCCTTT
1 TTTGATTTTCTTCCTTT
73784 TTTGATTTT-TTCCTTT
1 TTTGATTTTCTTCCTTT
73800 AGTTAAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.03, C:0.18, G:0.06, T:0.73
Consensus pattern (17 bp):
TTTGATTTTCTTCCTTT
Found at i:75502 original size:12 final size:13
Alignment explanation
Indices: 75479--75514 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
75469 AGCATCTTAT
75479 TATATA-AATATA
1 TATATATAATATA
75491 TA-ATATAATATA
1 TATATATAATATA
75503 -ATATATAATATA
1 TATATATAATATA
75515 GGGCTAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.18
12 18 0.82
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TATATATAATATA
Found at i:78192 original size:41 final size:41
Alignment explanation
Indices: 78135--78231 Score: 158
Period size: 41 Copynumber: 2.4 Consensus size: 41
78125 CTTAAGAATT
* **
78135 AATTACCCTCTTGCACCCTCTGGCAATATATATTTTATGGC
1 AATTACCCTCTTGCACCCTCTGACAATATATACCTTATGGC
78176 AATTACCCTCTTGCACCCTCTGACAATATATACCTTATGGC
1 AATTACCCTCTTGCACCCTCTGACAATATATACCTTATGGC
*
78217 AATTACACTCTTGCA
1 AATTACCCTCTTGCA
78232 AAACCATGTG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (41 bp):
AATTACCCTCTTGCACCCTCTGACAATATATACCTTATGGC
Found at i:78273 original size:27 final size:27
Alignment explanation
Indices: 78213--78273 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
78203 ATATACCTTA
78213 TGGCAATTACACTCTTGCAAAACCATG
1 TGGCAATTACACTCTTGCAAAACCATG
* * * * *
78240 TGACAATTACCCTCTTGCAATATCTTG
1 TGGCAATTACACTCTTGCAAAACCATG
78267 TGGCAAT
1 TGGCAAT
78274 ACTTTATGAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31
Consensus pattern (27 bp):
TGGCAATTACACTCTTGCAAAACCATG
Found at i:78910 original size:2 final size:2
Alignment explanation
Indices: 78898--78955 Score: 66
Period size: 2 Copynumber: 30.0 Consensus size: 2
78888 TTAAGAATGC
* * *
78898 AT AT GT AT AT AT AT AT AT GT AT -T CT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
78938 AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
78956 GTATTCTTAC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (2 bp):
AT
Found at i:78956 original size:12 final size:12
Alignment explanation
Indices: 78923--78959 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
78913 TATGTATTCT
*
78923 TATATATATATA
1 TATATATATGTA
78935 TATATATATGTA
1 TATATATATGTA
78947 TATATATATGTA
1 TATATATATGTA
78959 T
1 T
78960 TCTTACAGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (12 bp):
TATATATATGTA
Found at i:79404 original size:48 final size:44
Alignment explanation
Indices: 79281--79423 Score: 207
Period size: 45 Copynumber: 3.1 Consensus size: 44
79271 TGTTGAGAGA
*
79281 TTCAATGTCTTTGTCATGGT-GAAGACAATTTGTGTATCTCTCATG
1 TTCAATGTCTTTGTCATGGTGGAA-AC-ATTTGTGTATCTCCCATG
79326 TTCAATGTCTTTGTCATGGTGGAAACCATTTGTGTATCTCCCATG
1 TTCAATGTCTTTGTCATGGTGGAAA-CATTTGTGTATCTCCCATG
79371 TTCAATGTGATCTTTGTCATGGTGGAAATCATTTGTGTATCTCCCATG
1 TTCAA--TG-TCTTTGTCATGGTGGAAA-CATTTGTGTATCTCCCATG
79419 TTCAA
1 TTCAA
79424 CGCCTTGGAG
Statistics
Matches: 91, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
45 43 0.47
46 4 0.04
47 2 0.02
48 42 0.46
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (44 bp):
TTCAATGTCTTTGTCATGGTGGAAACATTTGTGTATCTCCCATG
Found at i:79895 original size:30 final size:30
Alignment explanation
Indices: 79859--79917 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
79849 CTGAAGATGG
*
79859 ATGCTCACATAAGAGCTACCGTGTAGAGTT
1 ATGCTCACATAAGAGCTACCGTATAGAGTT
*
79889 ATGCTCACATAAGAGCTACTGTATAGAGT
1 ATGCTCACATAAGAGCTACCGTATAGAGT
79918 ATTCTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (30 bp):
ATGCTCACATAAGAGCTACCGTATAGAGTT
Found at i:79960 original size:46 final size:46
Alignment explanation
Indices: 79890--80068 Score: 304
Period size: 46 Copynumber: 3.9 Consensus size: 46
79880 TGTAGAGTTA
*
79890 TGCTCACATAAGAGCTACTGTATAGAGTATTCTTTCTGAAGAAGGG
1 TGCTCACATAAGAGCTACCGTATAGAGTATTCTTTCTGAAGAAGGG
** *
79936 TGCTCACATAAGAGCTACTTTATAGAGTATTATTTCTGAAGAAGGG
1 TGCTCACATAAGAGCTACCGTATAGAGTATTCTTTCTGAAGAAGGG
* *
79982 TGCTCACATAAGAGCTACCATATAGAGTATTCTTTTTGAAGAAGGG
1 TGCTCACATAAGAGCTACCGTATAGAGTATTCTTTCTGAAGAAGGG
80028 TGCTCACATAAGAGCTACCGTATAGAGTATTCTTTCTGAAG
1 TGCTCACATAAGAGCTACCGTATAGAGTATTCTTTCTGAAG
80069 GGTTCTCACA
Statistics
Matches: 125, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 125 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (46 bp):
TGCTCACATAAGAGCTACCGTATAGAGTATTCTTTCTGAAGAAGGG
Found at i:80362 original size:72 final size:72
Alignment explanation
Indices: 80245--80411 Score: 271
Period size: 72 Copynumber: 2.3 Consensus size: 72
80235 ATGGCATCAA
* * * *
80245 AGGCCAGCAACATTATAGCCAAATATTGGGTGACTAAGGCCAGCGGCTTTATAGCCAATTATTGG
1 AGGCCATCAACATTATAGCCAAATATTGGGCGACTAAGGCCAGCGGCTTTATAGCCAACTATTAG
80310 GCGACTT
66 GCGACTT
* * *
80317 AGGCCATCAGCATTATAGCCAAGTATTGGGCGACTAAGGCCAGCGGCTTTATAGCCCACTATTAG
1 AGGCCATCAACATTATAGCCAAATATTGGGCGACTAAGGCCAGCGGCTTTATAGCCAACTATTAG
80382 GCGACTT
66 GCGACTT
80389 AGGCCATCAACATTATAGCCAAA
1 AGGCCATCAACATTATAGCCAAA
80412 GATAGAGAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 86 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (72 bp):
AGGCCATCAACATTATAGCCAAATATTGGGCGACTAAGGCCAGCGGCTTTATAGCCAACTATTAG
GCGACTT
Found at i:80405 original size:36 final size:36
Alignment explanation
Indices: 80244--80411 Score: 192
Period size: 36 Copynumber: 4.7 Consensus size: 36
80234 AATGGCATCA
* *
80244 AAGGCCAGCAACATTATAGCCAAATATTGGGTGACT
1 AAGGCCAGCAGCATTATAGCCAAATATTGGGCGACT
* * *
80280 AAGGCCAGCGGCTTTATAGCCAATTATTGGGCGACT
1 AAGGCCAGCAGCATTATAGCCAAATATTGGGCGACT
* * *
80316 TAGGCCATCAGCATTATAGCCAAGTATTGGGCGACT
1 AAGGCCAGCAGCATTATAGCCAAATATTGGGCGACT
* * * * *
80352 AAGGCCAGCGGCTTTATAGCCCACTATTAGGCGACT
1 AAGGCCAGCAGCATTATAGCCAAATATTGGGCGACT
* * *
80388 TAGGCCATCAACATTATAGCCAAA
1 AAGGCCAGCAGCATTATAGCCAAA
80412 GATAGAGAAA
Statistics
Matches: 108, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 108 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.23
Consensus pattern (36 bp):
AAGGCCAGCAGCATTATAGCCAAATATTGGGCGACT
Found at i:80602 original size:31 final size:31
Alignment explanation
Indices: 80567--80627 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
80557 GATAGTTTGC
*
80567 CAACACCATATAGAAGATGGTGTACTTCTTA
1 CAACACCATATAGAAGAGGGTGTACTTCTTA
* *
80598 CAACATCATATGGAAGAGGGTGTACTTCTT
1 CAACACCATATAGAAGAGGGTGTACTTCTT
80628 GTTCTTGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (31 bp):
CAACACCATATAGAAGAGGGTGTACTTCTTA
Found at i:80788 original size:51 final size:51
Alignment explanation
Indices: 80669--80817 Score: 217
Period size: 51 Copynumber: 2.9 Consensus size: 51
80659 ACCCTTCGAC
* * * * * *
80669 ATTGGAAGGAGGTGATAGTTCGCCAACGCCATATACAAAAGACTTCATAAT
1 ATTGGAAAGAGGTGATATTTTGCGAACACCATATGCAAAAGACTTCATAAT
80720 ATTGGAAAGAGGTGATATTTTGCGAACACCATATGCAAAAGACTTCATAAT
1 ATTGGAAAGAGGTGATATTTTGCGAACACCATATGCAAAAGACTTCATAAT
* * *
80771 ATTGGAAAGAGGTGATATTTTGTGAACACCATATGCAAGAGGCTTCA
1 ATTGGAAAGAGGTGATATTTTGCGAACACCATATGCAAAAGACTTCA
80818 GGACTTTGGA
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 89 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (51 bp):
ATTGGAAAGAGGTGATATTTTGCGAACACCATATGCAAAAGACTTCATAAT
Found at i:80850 original size:51 final size:51
Alignment explanation
Indices: 80669--80853 Score: 203
Period size: 51 Copynumber: 3.6 Consensus size: 51
80659 ACCCTTCGAC
* * * * *
80669 ATTGGAAGGAGGTGATAGTTCGCCAACGCCATATACAAAAGACTTCATAAT
1 ATTGGAAAGAGGTGATATTTCGCTAACACCATATGCAAAAGACTTCATAAT
* *
80720 ATTGGAAAGAGGTGATATTTTGCGAACACCATATGCAAAAGACTTCATAAT
1 ATTGGAAAGAGGTGATATTTCGCTAACACCATATGCAAAAGACTTCATAAT
* * * * *
80771 ATTGGAAAGAGGTGATATTTTG-TGAACACCATATGCAAGAGGCTTCAGGACT
1 ATTGGAAAGAGGTGATATTTCGCT-AACACCATATGCAAAAGACTTCA-TAAT
* * *
80823 -TTGGAAGGAGGTGAGACTTCGCTAACACCAT
1 ATTGGAAAGAGGTGATATTTCGCTAACACCAT
80854 TGGAAGGAGG
Statistics
Matches: 116, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
51 113 0.97
52 3 0.03
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (51 bp):
ATTGGAAAGAGGTGATATTTCGCTAACACCATATGCAAAAGACTTCATAAT
Found at i:80859 original size:30 final size:30
Alignment explanation
Indices: 80823--80883 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
80813 CTTCAGGACT
*
80823 TTGGAAGGAGGTGAG-ACTTCGCTAACACCA
1 TTGGAAGGAGGTG-GTACTTCGCGAACACCA
80853 TTGGAAGGAGGTGGTACTTCGCGAACACCA
1 TTGGAAGGAGGTGGTACTTCGCGAACACCA
80883 T
1 T
80884 ATGCTTTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.28, C:0.20, G:0.31, T:0.21
Consensus pattern (30 bp):
TTGGAAGGAGGTGGTACTTCGCGAACACCA
Found at i:80920 original size:44 final size:43
Alignment explanation
Indices: 80870--81021 Score: 169
Period size: 44 Copynumber: 3.7 Consensus size: 43
80860 GAGGTGGTAC
*
80870 TTCGCGAACACCATATGCTTTTGACATTGAAAGAGGGTGATAGT
1 TTCGCGAACACCATATGCCTTTGACATTGAAAGAGGGTGAT-GT
*
80914 TTCGCGAACACAATATGCCTTTGACATTGAAAGA----G--G-
1 TTCGCGAACACCATATGCCTTTGACATTGAAAGAGGGTGATGT
* * *
80950 --CACAAACACCATATGTCTTTGACATTGAAAGAGGGTGATGGT
1 TTCGCGAACACCATATGCCTTTGACATTGAAAGAGGGTGAT-GT
*
80992 CTCGCGAACACCATATGCCTTTGACATTGA
1 TTCGCGAACACCATATGCCTTTGACATTGA
81022 CATTGAAAGA
Statistics
Matches: 89, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
34 28 0.31
37 1 0.01
38 1 0.01
40 1 0.01
41 1 0.01
44 57 0.64
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (43 bp):
TTCGCGAACACCATATGCCTTTGACATTGAAAGAGGGTGATGT
Found at i:80971 original size:78 final size:78
Alignment explanation
Indices: 80876--81021 Score: 249
Period size: 78 Copynumber: 1.9 Consensus size: 78
80866 GTACTTCGCG
*
80876 AACACCATATGCTTTTGACATTGAAAGAGGGTGATAGTTTCGCGAACACAATATGCCTTTGACAT
1 AACACCATATGCTTTTGACATTGAAAGAGGGTGATAGTCTCGCGAACACAATATGCCTTTGACAT
80941 TGAAAGAGGCACA
66 TGAAAGAGGCACA
* *
80954 AACACCATATG-TCTTTGACATTGAAAGAGGGTGATGGTCTCGCGAACACCATATGCCTTTGACA
1 AACACCATATGCT-TTTGACATTGAAAGAGGGTGATAGTCTCGCGAACACAATATGCCTTTGACA
81018 TTGA
65 TTGA
81022 CATTGAAAGA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
77 1 0.02
78 63 0.98
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (78 bp):
AACACCATATGCTTTTGACATTGAAAGAGGGTGATAGTCTCGCGAACACAATATGCCTTTGACAT
TGAAAGAGGCACA
Found at i:81066 original size:50 final size:50
Alignment explanation
Indices: 80968--81066 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 50
80958 CCATATGTCT
** *
80968 TTGACATTGAAAGAGGGTGATGGTCTCGCGAACACCATATGCCTTTGACA
1 TTGACATTGAAAGAGGGTGATAATCTCGCGAACACCATATGCCGTTGACA
* * * * *
81018 TTGACATTGAAAGAGGGTGATAATTTTGTGAACCCCATATGTCGTTGAC
1 TTGACATTGAAAGAGGGTGATAATCTCGCGAACACCATATGCCGTTGAC
81067 GTCGCAGTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (50 bp):
TTGACATTGAAAGAGGGTGATAATCTCGCGAACACCATATGCCGTTGACA
Found at i:81251 original size:19 final size:19
Alignment explanation
Indices: 81227--81301 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
81217 GCCTTTTGTG
81227 TCGCGAATACCATACCATA
1 TCGCGAATACCATACCATA
* *
81246 TCGCGAGTACCATACCTTTA
1 TCGCGAATACCATACC-ATA
* *
81266 GCGTTGCGAATACCATACCACA
1 ---TCGCGAATACCATACCATA
*
81288 TCGCGAGTACCATA
1 TCGCGAATACCATA
81302 TGCCATTTCC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
19 27 0.61
20 2 0.05
22 1 0.02
23 14 0.32
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.23
Consensus pattern (19 bp):
TCGCGAATACCATACCATA
Found at i:81506 original size:99 final size:99
Alignment explanation
Indices: 81335--81534 Score: 391
Period size: 99 Copynumber: 2.0 Consensus size: 99
81325 TCATATCGGC
81335 CAAACCATGTTGTAAGAGTGAAATATCACATCGCAAATGCCACATGCCACTGTACATGTCTTTGT
1 CAAACCATGTTGTAAGAGTGAAATATCACATCGCAAATGCCACATGCCACTGTACATGTCTTTGT
81400 CGTTGGAAGAAGGAATACTATATTCCGAATACCA
66 CGTTGGAAGAAGGAATACTATATTCCGAATACCA
81434 CAAACCATGTTGTAAGAGTGAAATATCACATCGCAAATGCCACATGCCACTGTACATGTCTTTGT
1 CAAACCATGTTGTAAGAGTGAAATATCACATCGCAAATGCCACATGCCACTGTACATGTCTTTGT
*
81499 CGTTGGAAGAAGGAATACTATATTGCGAATACCA
66 CGTTGGAAGAAGGAATACTATATTCCGAATACCA
81533 CA
1 CA
81535 TTGCGAATAC
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (99 bp):
CAAACCATGTTGTAAGAGTGAAATATCACATCGCAAATGCCACATGCCACTGTACATGTCTTTGT
CGTTGGAAGAAGGAATACTATATTCCGAATACCA
Found at i:81530 original size:14 final size:14
Alignment explanation
Indices: 81520--81563 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
81510 GGAATACTAT
81520 ATTGCGAATACCAC
1 ATTGCGAATACCAC
81534 ATTGCGAATACCAC
1 ATTGCGAATACCAC
* *
81548 ATCGCGAATGCCAC
1 ATTGCGAATACCAC
81562 AT
1 AT
81564 GCCTTTAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (14 bp):
ATTGCGAATACCAC
Found at i:81654 original size:42 final size:42
Alignment explanation
Indices: 81608--81688 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
81598 CACCACATGC
* *
81608 CTTTT-ACGTTGGAAGAGAGTAATATTTCGCAAACACCATATA
1 CTTTTCACATTGGAAGA-AGTAATAATTCGCAAACACCATATA
** *
81650 CTTTTCACATTGGAAGAAGTGGTAATTCGCCAACACCAT
1 CTTTTCACATTGGAAGAAGTAATAATTCGCAAACACCAT
81689 GAGGATGTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 23 0.70
43 10 0.30
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (42 bp):
CTTTTCACATTGGAAGAAGTAATAATTCGCAAACACCATATA
Found at i:83974 original size:114 final size:112
Alignment explanation
Indices: 83784--84011 Score: 352
Period size: 114 Copynumber: 2.0 Consensus size: 112
83774 TTTCAAGCTG
* *
83784 CATAGGCTAGAAGTATCAACAAGGAAGGGCACTCCTGAAGGTGCAACCAGTGCAGCACTCCGAAG
1 CATAGGCCAGAAGTATCAACAAGGAAGGGCACTCCTGAAGGTGCAACCAGTGCAACACTCCGAAG
*
83849 GGTGCATTCACTCCAAGTCAAAATATA-GATTCTTTTTTTTAATGGGCTA
66 GGTGCACTCACTCCAAGTCAAAATATAGGA---TTTTTTTTAATGGGCTA
* * *
83898 CATAGGCCAGAA-TCATCAACAAGGAAGGGCACTCCTGGAGGTGCAACTAGTGCAACACTCCTAA
1 CATAGGCCAGAAGT-ATCAACAAGGAAGGGCACTCCTGAAGGTGCAACCAGTGCAACACTCCGAA
83962 GGGTGCACTCACTCCAAGTCAAAATATAGGATTTTTTTTAATGGGCTA
65 GGGTGCACTCACTCCAAGTCAAAATATAGGATTTTTTTTAATGGGCTA
84010 CA
1 CA
84012 ATCCTTGTTG
Statistics
Matches: 106, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
112 19 0.18
113 1 0.01
114 84 0.79
115 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (112 bp):
CATAGGCCAGAAGTATCAACAAGGAAGGGCACTCCTGAAGGTGCAACCAGTGCAACACTCCGAAG
GGTGCACTCACTCCAAGTCAAAATATAGGATTTTTTTTAATGGGCTA
Found at i:86923 original size:19 final size:19
Alignment explanation
Indices: 86899--86935 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
86889 TGTATTTGTA
86899 ACCGTTTCACCACCATTTG
1 ACCGTTTCACCACCATTTG
*
86918 ACCGTTTCACTACCATTT
1 ACCGTTTCACCACCATTT
86936 TGGGCCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (19 bp):
ACCGTTTCACCACCATTTG
Found at i:87011 original size:21 final size:19
Alignment explanation
Indices: 86986--87043 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 19
86976 GCTGCTCTAA
86986 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
87007 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
*
87026 TAATCTCATATGTACAGT
1 TAATCTCATCTGTACAGT
87044 TACTAAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:92711 original size:30 final size:31
Alignment explanation
Indices: 92658--92726 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 31
92648 TGATTTTATC
* *
92658 CTGAATTGACACAACCCGATAACGTTATATA
1 CTGAATTGACACAACACGATAACGGTATATA
* * *
92689 CTGAATTGACACAA-ATGATAACGGTGTATC
1 CTGAATTGACACAACACGATAACGGTATATA
92719 CTGAATTG
1 CTGAATTG
92727 CATTTTCGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 19 0.58
31 14 0.42
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (31 bp):
CTGAATTGACACAACACGATAACGGTATATA
Found at i:96837 original size:18 final size:18
Alignment explanation
Indices: 96814--96850 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
96804 CTTCTCTTGC
96814 ATGAAAAC-ATTTCTTTTT
1 ATGAAAACAATTT-TTTTT
96832 ATGAAAACAATTTTTTTT
1 ATGAAAACAATTTTTTTT
96850 A
1 A
96851 AGACTATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (18 bp):
ATGAAAACAATTTTTTTT
Found at i:100866 original size:35 final size:36
Alignment explanation
Indices: 100799--100869 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 36
100789 CTTTTTTTTC
*
100799 AAAACGCAAAAACAAAATTTTTTCTTTTAAATTAAAT
1 AAAACGCAAAAAC-AAATTTTTTCTTTGAAATTAAAT
*
100836 AAAACGCAGAAAC-AATTTTTT-TTTAGAAATTAAA
1 AAAACGCAAAAACAAATTTTTTCTTT-GAAATTAAA
100870 AACGCAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 3 0.10
35 16 0.52
37 12 0.39
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.34
Consensus pattern (36 bp):
AAAACGCAAAAACAAATTTTTTCTTTGAAATTAAAT
Found at i:104203 original size:27 final size:27
Alignment explanation
Indices: 104172--104250 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
104162 CACATTAATG
104172 AATAATGTGATTATTCATGAATCAATT
1 AATAATGTGATTATTCATGAATCAATT
* *
104199 AATAACGTGATTATTCATGAATTAATT
1 AATAATGTGATTATTCATGAATCAATT
* *
104226 AGTATTGTGATTATTCATGAATCAA
1 AATAATGTGATTATTCATGAATCAA
104251 GAGTTGTCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.41
Consensus pattern (27 bp):
AATAATGTGATTATTCATGAATCAATT
Found at i:106463 original size:13 final size:13
Alignment explanation
Indices: 106445--106470 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
106435 AAGGTAACAA
106445 CAAAAATCATCAC
1 CAAAAATCATCAC
106458 CAAAAATCATCAC
1 CAAAAATCATCAC
106471 TCATGCCAAG
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:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Done.