Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019685.1 Corchorus olitorius cultivar O-4 contig19718, 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: 220974
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2598 original size:649 final size:645
Alignment explanation
Indices: 954--2888 Score: 1942
Period size: 649 Copynumber: 3.0 Consensus size: 645
944 TAATATAACC
* * * *
954 ATCACAATTTTTGGCTAAAAAAGCGTTCTAGGGTCCCGGCTCAGTTTTGCATGATTTTTTACGCC
1 ATCACAGTTTTTGGCTAAAAAAGCGTTC-AGGGACCCGGCTCAGTTTTGCATGATTTTTGATG-C
* * ** * * *
1019 AAGACTCCTTGAGATATCCATATTCATAAAATCAAATTTCAGCCACATTGGATTTAAGAATTTGT
64 -AGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAG-CACATT-GATTTAAGGATTT-T
*
1084 TTTTACAAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAATAT-GAAAAA
125 TTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAT-TGGAAAAA
* * * * * * *
1147 CGATATTAAAAGCGTGAAGAGTCCTCCAATTTTTTTGCGT-TAAATTATATATATATATATATAT
189 CAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTG-GTGTAGA--AT-TATATAT-T-T-T-T
* * * * * * *
1211 TATGAGTATTTTATCCAAAAATTG-GGAAAAAAATTTAGGT-TATTTTTTACAAAATTTTAGTCA
246 TATGAGTA-TTTAGCAAAAAATTGAGGAAATATATTTAGGTCAATTTTTGA-AAAATTTTA-ACA
* * ** * *
1274 AAAATCGTGTATTAACCCATCATGGTTTTTTGGCCAAAAACATGTTTCGGGGCTTCGGCTTAGTT
308 GAAATCGTG--TTAA-CCATCATGGTTTTTTGGCTAAAAACGCGTTTCGGGGCCTCAGCTTAGTT
* * *
1339 TTGCATGGTTTTTGCGCCGACACTCCTTGAAATATCTATATTCATCTAATAAAATCTTAGCCACA
370 TTGCATGATTTTTGCG-CGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTTAGCCACA
* * * * *
1404 TTGCATTTAAGGATATGTTTTTACGAGCATCTAAATCTTATTTCAATTTAATTAGAAATTAATTT
434 TTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTC
*
1469 AGAAAAAATATGAAAAACGATATT-AAAGCGTGAAAA-GCACTTCAATCTTTTTGGTATTGAATT
499 A-AAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGGC-CTTCAATCTTTTTGGCATTGAATT
* * *
1532 ATATATTTTTTATGAGTATTATGGATATAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAA
562 ATAT-TTTTTTATGAGTATTTTCGATATAAATTGAGGAAACATCTTTCGGGTCAATTTTTGCAAA
*
1597 ATTTTAGCTGAAATCATGTAATA
626 ATTTTAGCCGAAATCA-G--ATA
* * * ** * ** * *
1620 ATCATTAGGGTTTTTGGCTAAAAACGCGTTCTGGGACCTAGTTCAACTTTGAATTATTTTTGGCG
1 ATCA-CA--GTTTTTGGCTAAAAAAGCGTTCAGGGACCCGGCTCAGTTTTGCATGATTTTT---G
* *
1685 TTG-AGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAG--C----A-TT---G----T
60 ATGCAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCACATTGATTTAAGGATTTT
* * * * *
1735 TTTTACAAACATCTGAATCATGTTTCGTTTTAATTAGAACTTAATTCGGAAAAAATAGGAAAAAC
125 TTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATTGGAAAAAC
* * * * *
1800 AATATTAGAAACGTGAAAAGCCCTTCAATATTTTTAGTGTTGAATTATATATATTTTATGAGTGT
190 AATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGTGTAGAATTATATATTTTTTATGAGTAT
* ** * * * * * *
1865 TGTGGTTAAAAATTGAGG-AATAATTTTTTTGGTCATTTTTTTGCAAAATTTTAGCTGAAATCGT
255 T-TAGCAAAAAATTGAGGAAAT-A-TATTTAGGTCA-ATTTTTGAAAAATTTTAACAGAAATCGT
1929 GTACTAACCATCATGGTTTTTTTCGGCTAAAAACGCGTTTCGGGGCCTCAGCTTAGTTTTGCATG
316 GT--TAACCATCATGG-TTTTTT-GGCTAAAAACGCGTTTCGGGGCCTCAGCTTAGTTTTGCATG
*
1994 ATTTTTAGCGTCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATTTTAGCCACATTGAAT
377 ATTTTT-GCG-CGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTTAGCCACATTGAAT
* * *
2059 ATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCACAAAA
440 TTAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAAAAAA
* *
2124 ATATGAAAAACGATATTAAAAGCGAGAAAAAGGCTTTCAAT-TTTTTGGCATTGAATTATATGTT
505 ATATGAAAAACGATATTAAAAGCGTG-AAAAGGCCTTCAATCTTTTTGGCATTGAATTATAT-TT
* *
2188 TTTTATGAGTATTTTCGTTATAAATTGAGGAAACATCTTTCGGGTCAATTTTTGCAGAATTTTAG
568 TTTTATGAGTATTTTCGATATAAATTGAGGAAACATCTTTCGGGTCAATTTTTGCAAAATTTTAG
2253 CCGAAATC-G-T-
633 CCGAAATCAGATA
* * * * * *
2263 GTCACAGTTTTCGGCTAAAAATGCGTTCCGGGGCCCGGCTCAGTTTTGCATGATTTATGATGCA-
1 ATCACAGTTTTTGGCTAAAAAAGCGTTCAGGGACCCGGCTCAGTTTTGCATGATTTTTGATGCAG
*
2327 A-TCCTTGAAATATCTATATTCGTCTAACCAAATCTCAGACACATTAGATTTAAGGATTTATTTT
66 ACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAG-CACATT-GATTTAAGGATTT-TTTT
*
2391 TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGGAAAAAATTGGAAAAACAA
128 TACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GGAAAAAATTGGAAAAACAA
* * *
2456 TATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGGTGTCGAATTATATATTTTTTATGAGTATGT
192 TATTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGTGTAGAATTATATATTTTTTATGAGTAT-T
* *
2521 TAGCAAAAAATTGAGGAAATATCTTTCAGGTCAATTTTTGAAAAATTTTAACCGAAATCGTG-T-
256 TAGCAAAAAATTGAGGAAATATATTT-AGGTCAATTTTTGAAAAATTTTAACAGAAATCGTGTTA
* * * * * * *
2584 ACCATTACGG-TTTTTGGCTAAAAACGCGTTCCAGGACCACAACTCT-GTTTTGCATGATTTTTT
320 ACCATCATGGTTTTTTGGCTAAAAACGCGTTTCGGGGCCTCAGCT-TAGTTTTGCATGA-TTTTT
* * * * * * * *
2647 GCGCTAAGACTCCTTCAAATATATTTATTCATCTAATTC-AATCTCAGGCACATTGGATTTAAAG
383 GCGC-GAGACTCCTTGAAATATCTATATTCATCTAA-TCAAATCTTAGCCACATTGAATTTAAGG
* * * *
2711 ATTTGTTTTTATGTGCATCTGAATCTTTTTTCGATTTAATTAGAAATTAATTTAGAAAAAAATAT
446 ATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAA-TT-CAAAAAAATAT
* * * * *
2776 GAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCCTTTTGGCATTGAATTATATATATTTAT
509 GAAAAACGATATTAAAAGCGTGAAAAGGCCTTCAATCTTTTTGGCATTGAATTATATTTTTTTAT
* * * * * *
2841 GAGTAGTTTTGCCAAAAAAAATGAGGAAAAATCTTTCGGATC-ATTTTT
574 GAGTA-TTTT-CGATATAAATTGAGGAAACATCTTTCGGGTCAATTTTT
2889 ACCATTATGG
Statistics
Matches: 1056, Mismatches: 159, Indels: 126
0.79 0.12 0.09
Matches are distributed among these distances:
636 35 0.03
637 4 0.00
638 1 0.00
639 1 0.00
640 40 0.04
642 1 0.00
643 3 0.00
644 4 0.00
645 23 0.02
646 144 0.14
647 63 0.06
648 131 0.12
649 246 0.23
650 13 0.01
651 49 0.05
652 43 0.04
653 72 0.07
654 94 0.09
655 4 0.00
659 2 0.00
660 1 0.00
665 1 0.00
666 4 0.00
667 1 0.00
668 55 0.05
669 20 0.02
671 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (645 bp):
ATCACAGTTTTTGGCTAAAAAAGCGTTCAGGGACCCGGCTCAGTTTTGCATGATTTTTGATGCAG
ACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCACATTGATTTAAGGATTTTTTTTAC
AAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATTGGAAAAACAATATT
AGAAGCGTGAAAAGCCCTTCAATATTTTTGGTGTAGAATTATATATTTTTTATGAGTATTTAGCA
AAAAATTGAGGAAATATATTTAGGTCAATTTTTGAAAAATTTTAACAGAAATCGTGTTAACCATC
ATGGTTTTTTGGCTAAAAACGCGTTTCGGGGCCTCAGCTTAGTTTTGCATGATTTTTGCGCGAGA
CTCCTTGAAATATCTATATTCATCTAATCAAATCTTAGCCACATTGAATTTAAGGATTTGTTTTT
ACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATAT
TAAAAGCGTGAAAAGGCCTTCAATCTTTTTGGCATTGAATTATATTTTTTTATGAGTATTTTCGA
TATAAATTGAGGAAACATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCAGATA
Found at i:4895 original size:35 final size:35
Alignment explanation
Indices: 4845--4918 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
4835 AATACCATTC
4845 ATTT-CATTCTTCATATTTCTCAGATAAAAATTAG
1 ATTTACATTCTTCATATTTCTCAGATAAAAATTAG
*
4879 ATTTACATTCTTCATATTTCTTAGATAAAAATTAG
1 ATTTACATTCTTCATATTTCTCAGATAAAAATTAG
4914 ATTTA
1 ATTTA
4919 AGTGTTCAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 4 0.11
35 34 0.89
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.46
Consensus pattern (35 bp):
ATTTACATTCTTCATATTTCTCAGATAAAAATTAG
Found at i:5528 original size:29 final size:30
Alignment explanation
Indices: 5490--5547 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
5480 ATAAATAATA
* *
5490 TAATATAATTAAATAA-TTATATTTATACG
1 TAATAAAATTAAATAATTTATATATATACG
*
5519 TAATAAAATTGAATAATTTATATATATAC
1 TAATAAAATTAAATAATTTATATATATAC
5548 ATTAATTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (30 bp):
TAATAAAATTAAATAATTTATATATATACG
Found at i:7017 original size:17 final size:16
Alignment explanation
Indices: 6967--7013 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
6957 TTAAGATCAC
6967 CACTAGTGATCTAAGAT
1 CACTAGTGATC-AAGAT
*
6984 CACCAGTGATGCAAGAT
1 CACTAGTGAT-CAAGAT
*
7001 CACTGGTGATCAA
1 CACTAGTGATCAA
7014 AGATTACATG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 3 0.12
17 22 0.85
18 1 0.04
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (16 bp):
CACTAGTGATCAAGAT
Found at i:11534 original size:2 final size:2
Alignment explanation
Indices: 11527--11556 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11517 ATGTAGCAAA
11527 AT AT 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 AT AT
11557 TGTAATGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12516 original size:25 final size:26
Alignment explanation
Indices: 12488--12540 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
12478 TAAACAGGTC
12488 TCGTATCCCATGTATC-TGTTT-AATT
1 TCGTATCCCATGT-TCGTGTTTCAATT
* *
12513 TCGTGTCTCATGTTCGTGTTTCAATT
1 TCGTATCCCATGTTCGTGTTTCAATT
12539 TC
1 TC
12541 ATGACACGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 2 0.08
25 16 0.67
26 6 0.25
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.49
Consensus pattern (26 bp):
TCGTATCCCATGTTCGTGTTTCAATT
Found at i:13956 original size:21 final size:21
Alignment explanation
Indices: 13923--13966 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
13913 TAGAACAAAC
* * *
13923 TAAAGTGAAACAAAGTGTACA
1 TAAAATGAAACAAAATCTACA
*
13944 TAAAATGACACAAAATCTACA
1 TAAAATGAAACAAAATCTACA
13965 TA
1 TA
13967 TACTATACAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.14, G:0.11, T:0.20
Consensus pattern (21 bp):
TAAAATGAAACAAAATCTACA
Found at i:14428 original size:2 final size:2
Alignment explanation
Indices: 14421--14466 Score: 65
Period size: 2 Copynumber: 21.5 Consensus size: 2
14411 TTGTCGAGGG
14421 AT AT AT AT AT AT AT AGT AGT AT AT AT AT AT AT AT AT AT AGT AT
1 AT AT AT AT AT AT AT A-T A-T AT AT AT AT AT AT AT AT AT A-T AT
14464 AT A
1 AT A
14467 AAATTACTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 35 0.83
3 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (2 bp):
AT
Found at i:14453 original size:24 final size:23
Alignment explanation
Indices: 14421--14466 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
14411 TTGTCGAGGG
14421 ATATATATATATATAGTAGTATAT
1 ATATATATATATATAGTA-TATAT
14445 ATATATATATATATAGTATATA
1 ATATATATATATATAGTATATA
14467 AAATTACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (23 bp):
ATATATATATATATAGTATATAT
Found at i:14810 original size:56 final size:56
Alignment explanation
Indices: 14630--14797 Score: 320
Period size: 56 Copynumber: 3.0 Consensus size: 56
14620 TGTGTTTCCT
14630 TTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTC
1 TTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTC
*
14686 TTTCACACAATAAATGTTATAATAAATACTATCCCCCTATCTCTACTTAATTATTC
1 TTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTC
14742 TTTCACACAATAAATGTTATAATAAATCCTAT-CCCCTATCTCTACTTAATTATTC
1 TTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTC
14797 T
1 T
14798 ACAAAATAAA
Statistics
Matches: 110, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
55 24 0.22
56 86 0.78
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.40
Consensus pattern (56 bp):
TTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTC
Found at i:14920 original size:42 final size:42
Alignment explanation
Indices: 14861--14943 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
14851 GTTAAGGATC
14861 ATGATTTGAGTTGAGTATTTCTTAATTAACAAAGAATTTTCT
1 ATGATTTGAGTTGAGTATTTCTTAATTAACAAAGAATTTTCT
* * *
14903 ATGATTTGAGTTGAGTATTTTTTAATTTACAGAGAATTTTC
1 ATGATTTGAGTTGAGTATTTCTTAATTAACAAAGAATTTTC
14944 AAGACTTAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (42 bp):
ATGATTTGAGTTGAGTATTTCTTAATTAACAAAGAATTTTCT
Found at i:15736 original size:23 final size:24
Alignment explanation
Indices: 15702--15748 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
15692 ATGGTTGAAT
15702 GAGAAGAAGAAGATCGAAAA-AACA
1 GAGAAGAAGAAGATC-AAAACAACA
15726 GAGAA-AAGAAGATCAAAACAACA
1 GAGAAGAAGAAGATCAAAACAACA
15749 AAAAATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.18
23 13 0.59
24 5 0.23
ACGTcount: A:0.64, C:0.11, G:0.21, T:0.04
Consensus pattern (24 bp):
GAGAAGAAGAAGATCAAAACAACA
Found at i:17935 original size:32 final size:34
Alignment explanation
Indices: 17859--17932 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 34
17849 CAAAGAAGAG
17859 TTATAAG-ATAAGTACACTTAAGATTATTAGCTAA
1 TTATAAGTA-AAGTACACTTAAGATTATTAGCTAA
*
17893 TTAAGGTAAGTAAAGTACACTTCAGATTATTAGCTAA
1 TT-A--TAAGTAAAGTACACTTAAGATTATTAGCTAA
17930 TTA
1 TTA
17933 AGTTTATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
34 2 0.06
35 1 0.03
36 1 0.03
37 30 0.86
38 1 0.03
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (34 bp):
TTATAAGTAAAGTACACTTAAGATTATTAGCTAA
Found at i:18821 original size:2 final size:2
Alignment explanation
Indices: 18814--18843 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18804 AGGTTACACA
18814 AT AT 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 AT AT
18844 GGAGTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25241 original size:2 final size:2
Alignment explanation
Indices: 25234--25258 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25224 TATCCAAAAT
25234 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
25259 TTGTATGCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:42088 original size:11 final size:11
Alignment explanation
Indices: 42064--42098 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
42054 TTGACAGCGC
42064 AACAAAAACAA
1 AACAAAAACAA
* *
42075 AACGAAAACGA
1 AACAAAAACAA
42086 AACAAAAACAA
1 AACAAAAACAA
42097 AA
1 AA
42099 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:43231 original size:55 final size:55
Alignment explanation
Indices: 43146--43249 Score: 163
Period size: 55 Copynumber: 1.9 Consensus size: 55
43136 TCCACCTTGT
* * *
43146 GTTATGATCCACTATTGGCACGCTTTACTACTGCCTGCAGGTTTGCCCCCCTCAC
1 GTTATGATCCACTATTGGCACGCTTCACTACTGCCCGCAAGTTTGCCCCCCTCAC
* *
43201 GTTATGATCCATTCTTGGCACGCTTCACTACTGCCCGCAAGTTTGCCCC
1 GTTATGATCCACTATTGGCACGCTTCACTACTGCCCGCAAGTTTGCCCC
43250 TCGCCATGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.16, C:0.35, G:0.18, T:0.31
Consensus pattern (55 bp):
GTTATGATCCACTATTGGCACGCTTCACTACTGCCCGCAAGTTTGCCCCCCTCAC
Found at i:43310 original size:39 final size:40
Alignment explanation
Indices: 43267--43343 Score: 129
Period size: 39 Copynumber: 1.9 Consensus size: 40
43257 GAAATCACTA
43267 CCATGAATCACTGGAGTTT-AAGAGGGAGCAGGGGACTCG
1 CCATGAATCACTGGAGTTTAAAGAGGGAGCAGGGGACTCG
* *
43306 CCATGAATCACTGGGGTTTAAAGAGGGAGCGGGGGACT
1 CCATGAATCACTGGAGTTTAAAGAGGGAGCAGGGGACT
43344 TAGAGCCTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 18 0.51
40 17 0.49
ACGTcount: A:0.27, C:0.17, G:0.38, T:0.18
Consensus pattern (40 bp):
CCATGAATCACTGGAGTTTAAAGAGGGAGCAGGGGACTCG
Found at i:49369 original size:12 final size:12
Alignment explanation
Indices: 49352--49404 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
49342 CGACACGTAC
*
49352 GCATGTATGCAT
1 GCATGTATGTAT
49364 GCATGTATGTAT
1 GCATGTATGTAT
*
49376 GTATGTATGTAT
1 GCATGTATGTAT
* * *
49388 GTATGTAGGGAT
1 GCATGTATGTAT
49400 GCATG
1 GCATG
49405 AGATTAGCTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.25, C:0.08, G:0.30, T:0.38
Consensus pattern (12 bp):
GCATGTATGTAT
Found at i:49373 original size:4 final size:4
Alignment explanation
Indices: 49354--49394 Score: 64
Period size: 4 Copynumber: 10.2 Consensus size: 4
49344 ACACGTACGC
* *
49354 ATGT ATGC ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
49395 GGGATGCATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.27, C:0.05, G:0.24, T:0.44
Consensus pattern (4 bp):
ATGT
Found at i:52989 original size:18 final size:19
Alignment explanation
Indices: 52962--53003 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
52952 ACAACCCTAC
*
52962 TTTTT-TTTTTTCCTTTCT
1 TTTTTCTTTTTTCATTTCT
52980 TTTTTCTTTTTTCATTT-T
1 TTTTTCTTTTTTCATTTCT
52998 TTTTTC
1 TTTTTC
53004 ATGAGGTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTCTTTTTTCATTTCT
Found at i:60504 original size:1 final size:1
Alignment explanation
Indices: 60498--60554 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
60488 GTTTGTTGTG
* * * * * * *
60498 TTTTTTTTTTTTTTTTTTGTTTTTCTTGTTTCTTGTTTTTTGTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
60555 CCCAATTATG
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:61229 original size:13 final size:13
Alignment explanation
Indices: 61211--61235 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61201 TGACTAAAGT
61211 TAGATTTATTAAC
1 TAGATTTATTAAC
61224 TAGATTTATTAA
1 TAGATTTATTAA
61236 GTGTGCATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TAGATTTATTAAC
Found at i:74822 original size:250 final size:250
Alignment explanation
Indices: 74381--74831 Score: 796
Period size: 250 Copynumber: 1.8 Consensus size: 250
74371 CTGTTGCATG
* * *
74381 TAATTAATTTTAGACAAATTATATAATACACCGGCGTTGGAGTTTAGCAGACTACACAAGCGGGT
1 TAATTAATATTAGACAAATTATACAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCGGGT
74446 CCTGAAGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTCAAAA
66 CCTGAAGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTCAAAA
* * *
74511 AATGGACATGTGTCAACTCCATAACCCGCTTGTGGAATCCAAAATTTATACCGCTGGTGTATCAA
131 AATGGACATGTGTCAACTCCACAACCCGCTTATGGAATCCAAAATTTACACCGCTGGTGTATCAA
74576 ATAATTTGCATTCAGATAGCGACATTAACATCTTTTTTTCATTACCCTTACTTAA
196 ATAATTTGCATTCAGATAGCGACATTAACATCTTTTTTTCATTACCCTTACTTAA
*
74631 TAATTAATATTAGGCAAATTATACAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCGGGT
1 TAATTAATATTAGACAAATTATACAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCGGGT
74696 CCTGAAGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATT-AAAA
66 CCTGAAGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTCAAAA
* * *
74760 AATTGGACGTGTGTCAACTCCACAACCCGCTTATGGAGTCCAAAATTTACACCGTTGGTGTATCA
131 AA-TGGACATGTGTCAACTCCACAACCCGCTTATGGAATCCAAAATTTACACCGCTGGTGTATCA
74825 AATAATT
195 AATAATT
74832 ACCCTTAACA
Statistics
Matches: 190, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
249 6 0.03
250 184 0.97
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (250 bp):
TAATTAATATTAGACAAATTATACAATACACCGGCGGTGGAGTTTAGCAGACTACACAAGCGGGT
CCTGAAGGGTGACATGTGTCCTCTAGGGACTAGATTGAAATATTTAAAACTTAATTAATTCAAAA
AATGGACATGTGTCAACTCCACAACCCGCTTATGGAATCCAAAATTTACACCGCTGGTGTATCAA
ATAATTTGCATTCAGATAGCGACATTAACATCTTTTTTTCATTACCCTTACTTAA
Found at i:75923 original size:95 final size:95
Alignment explanation
Indices: 75760--75940 Score: 362
Period size: 95 Copynumber: 1.9 Consensus size: 95
75750 TTAATTGTTG
75760 GATATTGGTAGTGGGGGGTTTAGTAGTACTTGTAACCTTATAAAAAAAAGGTGAATCTCCAAAGT
1 GATATTGGTAGTGGGGGGTTTAGTAGTACTTGTAACCTTATAAAAAAAAGGTGAATCTCCAAAGT
75825 AATTGATGGACTGATTCACTACCAATATTT
66 AATTGATGGACTGATTCACTACCAATATTT
75855 GATATTGGTAGTGGGGGGTTTAGTAGTACTTGTAACCTTATAAAAAAAAGGTGAATCTCCAAAGT
1 GATATTGGTAGTGGGGGGTTTAGTAGTACTTGTAACCTTATAAAAAAAAGGTGAATCTCCAAAGT
75920 AATTGATGGACTGATTCACTA
66 AATTGATGGACTGATTCACTA
75941 AAATCTTATT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 86 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (95 bp):
GATATTGGTAGTGGGGGGTTTAGTAGTACTTGTAACCTTATAAAAAAAAGGTGAATCTCCAAAGT
AATTGATGGACTGATTCACTACCAATATTT
Found at i:77100 original size:2 final size:2
Alignment explanation
Indices: 77093--77121 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
77083 AAATAACAAA
77093 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
77122 ATTATATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:82816 original size:60 final size:60
Alignment explanation
Indices: 82750--82862 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
82740 AATGTTTGCC
* ** *
82750 AAAATGCTTAAATAAGGATCTGATCTTTTAATTTGGCCAAATAAAGG-CCTAACTTTATCG
1 AAAATGCTCAAATAAGGATCCAATCTTTTAATTTGACCAAAT-AAGGACCTAACTTTATCG
*
82810 AAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGACCAAATAAGGACCTAAC
1 AAAATGCTCAAATAAGGATCCAATCTTTTAATTTGACCAAATAAGGACCTAAC
82863 AAAATGTTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 4 0.09
60 43 0.91
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGATCCAATCTTTTAATTTGACCAAATAAGGACCTAACTTTATCG
Found at i:83028 original size:60 final size:60
Alignment explanation
Indices: 82923--83085 Score: 222
Period size: 60 Copynumber: 2.7 Consensus size: 60
82913 TTCGATGTCA
* * * *
82923 GACCCTTAATTGAGCATTTTCGATAACGTTAGGCCATTATTTGGCCAAATTAAAAGATC-
1 GACCCTTATTTAAGCATTTTCGATAACATTAGGCCTTTATTTGGCCAAATTAAAAGATCG
*
82982 GAGCTCTTATTTAAGCATTTTCGATAACATTAGGCCTTTATTTGGCCAAATTAAAAGATCG
1 GA-CCCTTATTTAAGCATTTTCGATAACATTAGGCCTTTATTTGGCCAAATTAAAAGATCG
* * *
83043 GACCCTTATTTGAGCATTTTGGCA-AACATTAGACCTTTATTTG
1 GACCCTTATTTAAGCATTTTCG-ATAACATTAGGCCTTTATTTG
83086 AGCAATTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
59 2 0.02
60 87 0.95
61 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (60 bp):
GACCCTTATTTAAGCATTTTCGATAACATTAGGCCTTTATTTGGCCAAATTAAAAGATCG
Found at i:83610 original size:80 final size:80
Alignment explanation
Indices: 83477--83639 Score: 290
Period size: 80 Copynumber: 2.0 Consensus size: 80
83467 TCTCTGTTAC
* *
83477 AGAGCAAAAATCTAAAAAATTCCCCTGAATTCATCTATCGATCGTGCTTGAGTGATTTGAGAAGA
1 AGAGCAAAAATCTAAAAAATTCCCCTAAATTCATCTATCGATCGTGCTTGAGTGATCTGAGAAGA
83542 AAAATCATCCATTGA
66 AAAATCATCCATTGA
* *
83557 AGAGCAAAAATCTTAAAAATTCCCCTAAATTCATCTATCGATCGTGTTTGAGTGATCTGAGAAGA
1 AGAGCAAAAATCTAAAAAATTCCCCTAAATTCATCTATCGATCGTGCTTGAGTGATCTGAGAAGA
83622 AAAATCATCCATTGA
66 AAAATCATCCATTGA
83637 AGA
1 AGA
83640 CGGGTTCAAC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (80 bp):
AGAGCAAAAATCTAAAAAATTCCCCTAAATTCATCTATCGATCGTGCTTGAGTGATCTGAGAAGA
AAAATCATCCATTGA
Found at i:89644 original size:20 final size:21
Alignment explanation
Indices: 89604--89644 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
89594 ATATATGATC
*
89604 GTAATAAAAAAAAAGTCATTT
1 GTAATAAAAAAAAAGTAATTT
*
89625 GTAAT-AAAAAAACGTAATTT
1 GTAATAAAAAAAAAGTAATTT
89645 ATTTCATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.56, C:0.05, G:0.10, T:0.29
Consensus pattern (21 bp):
GTAATAAAAAAAAAGTAATTT
Found at i:94848 original size:180 final size:176
Alignment explanation
Indices: 94484--94855 Score: 541
Period size: 186 Copynumber: 2.1 Consensus size: 176
94474 TATATGATGT
*
94484 AAAAAAAAAAAAAAACAAAACACCAACAGGTGGTTGGTTCAAGTGGTTTGACACTTATTCCCCTT
1 AAAAAAAAAAAAAAACAAAACACCAACAGGTGGTTGATTCAAGTGGTTTGACACTTATTCCCCTT
* *
94549 AAACAAGGTCTCAGATTCGAGTTTTGTGAATGGAGAAAATCATTGTTGGGAAAACTTTACCCCAT
66 AAACAAGGTCTCAGATTCGAGTCTTATGAATGGAGAAAATCATTGTTGGGAAAACTTTACCCCAT
* *
94614 AGTGGACTAACCCGGCTCGAACAAGATTAACTTGTAAATATTCAAAAAA
131 AATGGACTAACCCGGCTCGAACAAGATTAACTTGTAAATAGT---AAAA
*
94663 AAAAAAAAACAAAAAACAAAACACCAACAGGTGGTTGATTCAAGTGGTTTGGCTTTGACACTTGT
1 AAAAAAAAA-AAAAAACAAAACACCAACAGGTGGTTGATTCAA---G--TGG-TTTGACACTTAT
* * * *
94728 TCCCTTTAAACAAGGTCTCGGATTCGAGTCTTATGAATGGAGAAAATCATTGTT-GGAGAGCTTT
59 TCCCCTTAAACAAGGTCTCAGATTCGAGTCTTATGAATGGAGAAAATCATTGTTGGGAAAACTTT
*
94792 ACCCCATAATGGACTAACCCGGCTCGAACAAGATTAACTTGTAAAT-GTATAA
124 ACCCCATAATGGACTAACCCGGCTCGAACAAGATTAACTTGTAAATAGTAAAA
94844 AAAAAAAAAAAA
1 AAAAAAAAAAAA
94856 TTTACTATTA
Statistics
Matches: 175, Mismatches: 11, Indels: 13
0.88 0.06 0.07
Matches are distributed among these distances:
179 9 0.05
180 35 0.20
181 12 0.07
183 1 0.01
184 1 0.01
185 56 0.32
186 61 0.35
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (176 bp):
AAAAAAAAAAAAAAACAAAACACCAACAGGTGGTTGATTCAAGTGGTTTGACACTTATTCCCCTT
AAACAAGGTCTCAGATTCGAGTCTTATGAATGGAGAAAATCATTGTTGGGAAAACTTTACCCCAT
AATGGACTAACCCGGCTCGAACAAGATTAACTTGTAAATAGTAAAA
Found at i:94848 original size:185 final size:179
Alignment explanation
Indices: 94484--94855 Score: 568
Period size: 185 Copynumber: 2.0 Consensus size: 179
94474 TATATGATGT
*
94484 AAAAAAAAAAAAAAACAAAACACCAACAGGTGGTTGGTTCAAGTGGTTTGACACTTATTCCCCTT
1 AAAAAAAAAAAAAAACAAAACACCAACAGGTGGTTGATTCAAGTGGTTTGACACTTATTCCCCTT
* *
94549 AAACAAGGTCTCAGATTCGAGTTTTGTGAATGGAGAAAATCATTGTTGGGAAAACTTTACCCCAT
66 AAACAAGGTCTCAGATTCGAGTCTTATGAATGGAGAAAATCATTGTTGGGAAAACTTTACCCCAT
*
94614 AGTGGACTAACCCGGCTCGAACAAGATTAACTTGTAAATATTCAAAAAA
131 AATGGACTAACCCGGCTCGAACAAGATTAACTTGTAAATATTCAAAAAA
*
94663 AAAAAAAAACAAAAAACAAAACACCAACAGGTGGTTGATTCAAGTGGTTTGGCTTTGACACTTGT
1 AAAAAAAAA-AAAAAACAAAACACCAACAGGTGGTTGATTCAA---G--TGG-TTTGACACTTAT
* * * *
94728 TCCCTTTAAACAAGGTCTCGGATTCGAGTCTTATGAATGGAGAAAATCATTGTT-GGAGAGCTTT
59 TCCCCTTAAACAAGGTCTCAGATTCGAGTCTTATGAATGGAGAAAATCATTGTTGGGAAAACTTT
*
94792 ACCCCATAATGGACTAACCCGGCTCGAACAAGATTAACTTGTAAATGTAT-AAAAAA
124 ACCCCATAATGGACTAACCCGGCTCGAACAAGATTAACTTGTAAATAT-TCAAAAAA
94848 AAAAAAAA
1 AAAAAAAA
94856 TTTACTATTA
Statistics
Matches: 175, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
179 9 0.05
180 32 0.18
183 1 0.01
185 71 0.41
186 62 0.35
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (179 bp):
AAAAAAAAAAAAAAACAAAACACCAACAGGTGGTTGATTCAAGTGGTTTGACACTTATTCCCCTT
AAACAAGGTCTCAGATTCGAGTCTTATGAATGGAGAAAATCATTGTTGGGAAAACTTTACCCCAT
AATGGACTAACCCGGCTCGAACAAGATTAACTTGTAAATATTCAAAAAA
Found at i:96844 original size:14 final size:14
Alignment explanation
Indices: 96825--96853 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
96815 CAATTATGAG
96825 TTATAGTATCAAAT
1 TTATAGTATCAAAT
96839 TTATAGTATCAAAT
1 TTATAGTATCAAAT
96853 T
1 T
96854 ATATCTTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TTATAGTATCAAAT
Found at i:100248 original size:18 final size:18
Alignment explanation
Indices: 100225--100260 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
100215 AATGAGGAAG
100225 GCTTCT-TTCTTCGTCGTA
1 GCTTCTCTTCTT-GTCGTA
100243 GCTTCTCTTCTTGTCGTA
1 GCTTCTCTTCTTGTCGTA
100261 TTTATTGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.06, C:0.28, G:0.17, T:0.50
Consensus pattern (18 bp):
GCTTCTCTTCTTGTCGTA
Found at i:101676 original size:14 final size:15
Alignment explanation
Indices: 101642--101684 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
101632 TATTTTTTAT
*
101642 ATATATAATAATATTAG
1 ATATATAAT-A-ATTAC
101659 ATATAT-ATAATTAC
1 ATATATAATAATTAC
101673 ATATATAATAAT
1 ATATATAATAAT
101685 ATATAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 10 0.42
15 6 0.25
16 2 0.08
17 6 0.25
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
ATATATAATAATTAC
Found at i:101686 original size:10 final size:10
Alignment explanation
Indices: 101642--101691 Score: 59
Period size: 10 Copynumber: 4.9 Consensus size: 10
101632 TATTTTTTAT
101642 ATATATAATA
1 ATATATAATA
101652 ATAT-TAGAT-
1 ATATATA-ATA
101661 ATATATAATTA
1 ATATATAA-TA
101672 CATATATAATA
1 -ATATATAATA
101683 ATATATAAT
1 ATATATAAT
101692 TATTAAATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
9 7 0.20
10 18 0.51
11 2 0.06
12 8 0.23
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (10 bp):
ATATATAATA
Found at i:108473 original size:72 final size:72
Alignment explanation
Indices: 108356--108499 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
108346 CCCATTGCGC
108356 AATATTGAAATTTGAACCAATCGTTAGATGGTTTAGCATCTGCAAACAAGTGGAATCTCTTTCTG
1 AATATTGAAATTTGAACCAATCGTTAGATGGTTTAGCATCTGCAAACAAGTGGAATCTCTTTCTG
108421 ATTTTGT
66 ATTTTGT
108428 AATATTGAAATTTGAACCAATCGTTAGATGGTTTAGCATCTGCAAACAAGTGGAATCTCTTTCTG
1 AATATTGAAATTTGAACCAATCGTTAGATGGTTTAGCATCTGCAAACAAGTGGAATCTCTTTCTG
108493 ATTTTGT
66 ATTTTGT
108500 TTTCTTGACA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.38
Consensus pattern (72 bp):
AATATTGAAATTTGAACCAATCGTTAGATGGTTTAGCATCTGCAAACAAGTGGAATCTCTTTCTG
ATTTTGT
Found at i:126602 original size:5 final size:5
Alignment explanation
Indices: 126589--126622 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
126579 GAGGCAGTAA
126589 TTTCAT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTC-T TTTCT TTTCT TTTCT TTTCT TTTCT TTT
126623 ACCATTAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:138827 original size:17 final size:17
Alignment explanation
Indices: 138807--138844 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
138797 ATAATCTTTG
138807 ATCACCGGTGATCTCGC
1 ATCACCGGTGATCTCGC
* *
138824 ATCACTGGTGATCTTGC
1 ATCACCGGTGATCTCGC
138841 ATCA
1 ATCA
138845 TTAGTGATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (17 bp):
ATCACCGGTGATCTCGC
Found at i:138851 original size:17 final size:17
Alignment explanation
Indices: 138814--138854 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
138804 TTGATCACCG
*
138814 GTGATCTCGCATCACTG
1 GTGATCTCGCATCACTA
* *
138831 GTGATCTTGCATCATTA
1 GTGATCTCGCATCACTA
138848 GTGATCT
1 GTGATCT
138855 GAAGGGTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (17 bp):
GTGATCTCGCATCACTA
Found at i:145116 original size:4 final size:4
Alignment explanation
Indices: 145109--145135 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
145099 TAAAAAAAAA
145109 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
145136 CAATACACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:149169 original size:22 final size:22
Alignment explanation
Indices: 149135--149195 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 22
149125 CAAAATGGCA
* *
149135 CGGCACGACACGACTCACGTGC
1 CGGCACAACACGACCCACGTGC
*
149157 CGGCACAATACGACCCACGTGC
1 CGGCACAACACGACCCACGTGC
* * *
149179 CGACGCAGCACGACCCA
1 CGGCACAACACGACCCA
149196 TTTTTAATGT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.26, C:0.43, G:0.25, T:0.07
Consensus pattern (22 bp):
CGGCACAACACGACCCACGTGC
Found at i:155355 original size:21 final size:21
Alignment explanation
Indices: 155329--155368 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
155319 CATCAATAAC
155329 TTTACTACAACAATAGTAAAG
1 TTTACTACAACAATAGTAAAG
155350 TTTACTACAACAATAGTAA
1 TTTACTACAACAATAGTAA
155369 GAGGGAGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTACTACAACAATAGTAAAG
Found at i:156703 original size:44 final size:44
Alignment explanation
Indices: 156640--156723 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
156630 AATTTGAAAA
*
156640 TGAAACCATGAATTAAAAACTAATGAATTATTCATTTCTACATC
1 TGAAACCATGAATTAAAAACTAATAAATTATTCATTTCTACATC
*
156684 TGAAACCATGAATTAAAAACTCATAAATTATTCATTTCTA
1 TGAAACCATGAATTAAAAACTAATAAATTATTCATTTCTA
156724 GGCATCTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (44 bp):
TGAAACCATGAATTAAAAACTAATAAATTATTCATTTCTACATC
Found at i:160936 original size:17 final size:16
Alignment explanation
Indices: 160884--160932 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
160874 AATCCCCCAA
*
160884 ATCACTAGTGATCTAAG
1 ATCACCAGTGATC-AAG
160901 ATCACCAGTGATGCAAG
1 ATCACCAGTGAT-CAAG
*
160918 ATCACCGGTGATCAA
1 ATCACCAGTGATCAA
160933 AGATTACATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (16 bp):
ATCACCAGTGATCAAG
Found at i:176068 original size:40 final size:43
Alignment explanation
Indices: 176004--176098 Score: 142
Period size: 40 Copynumber: 2.3 Consensus size: 43
175994 CCTTTCCCAG
*
176004 TTGGGCCTTGTCTTACTATTTCAATTT-A-A-TTATTTTGATC
1 TTGGGCCTCGTCTTACTATTTCAATTTAATAGTTATTTTGATC
*
176044 TTGTGCCTCGTCTTACTATTTCAATTTAATTAGTTATTTTGATC
1 TTGGGCCTCGTCTTACTATTTCAATTTAA-TAGTTATTTTGATC
176088 TTGGGCCTCGT
1 TTGGGCCTCGT
176099 TTGAAGCTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
40 25 0.52
41 1 0.02
43 1 0.02
44 21 0.44
ACGTcount: A:0.18, C:0.17, G:0.15, T:0.51
Consensus pattern (43 bp):
TTGGGCCTCGTCTTACTATTTCAATTTAATAGTTATTTTGATC
Found at i:177201 original size:2 final size:2
Alignment explanation
Indices: 177194--177230 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
177184 TGTTTTAATC
177194 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
177231 TGATAACAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:177484 original size:107 final size:107
Alignment explanation
Indices: 177363--177570 Score: 407
Period size: 107 Copynumber: 1.9 Consensus size: 107
177353 TAATTTAATT
177363 TATAAAATTAAATTAATTCTAAGCATTAACAATTGATTTGATTTAGTAATTGTTACCAATTGTTA
1 TATAAAATTAAATTAATTCTAAGCATTAACAATTGATTTGATTTAGTAATTGTTACCAATTGTTA
*
177428 TATATGGTTTAATAATTCATGAAAAAAATAATTGATTAATAG
66 TATACGGTTTAATAATTCATGAAAAAAATAATTGATTAATAG
177470 TATAAAATTAAATTAATTCTAAGCATTAACAATTGATTTGATTTAGTAATTGTTACCAATTGTTA
1 TATAAAATTAAATTAATTCTAAGCATTAACAATTGATTTGATTTAGTAATTGTTACCAATTGTTA
177535 TATACGGTTTAATAATTCATGAAAAAAATAATTGAT
66 TATACGGTTTAATAATTCATGAAAAAAATAATTGAT
177571 GGTTTGAAAA
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 100 1.00
ACGTcount: A:0.43, C:0.06, G:0.10, T:0.41
Consensus pattern (107 bp):
TATAAAATTAAATTAATTCTAAGCATTAACAATTGATTTGATTTAGTAATTGTTACCAATTGTTA
TATACGGTTTAATAATTCATGAAAAAAATAATTGATTAATAG
Found at i:181170 original size:59 final size:60
Alignment explanation
Indices: 181078--181206 Score: 165
Period size: 59 Copynumber: 2.2 Consensus size: 60
181068 GGTTTTATGG
* * **
181078 AATAAGGGTCCGATCTTTTAATTTGTCAAATAAGGGTTTAACGTT-TGC-CAAAATGCTCA
1 AATAAGGGCCCGATCTTTTAATTTGCCAAATAAGGGCCTAACGTTAT-CACAAAATGCTCA
* *
181137 AATAAGGGCCCGCTC-TTTAATTTGGCCAAATAAGGGCCTAACGTTATCAGAAAATGCTCA
1 AATAAGGGCCCGATCTTTTAATTT-GCCAAATAAGGGCCTAACGTTATCACAAAATGCTCA
181197 AATAAGGGCC
1 AATAAGGGCC
181207 TGACATACGC
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
58 8 0.13
59 32 0.52
60 21 0.34
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (60 bp):
AATAAGGGCCCGATCTTTTAATTTGCCAAATAAGGGCCTAACGTTATCACAAAATGCTCA
Found at i:181270 original size:31 final size:31
Alignment explanation
Indices: 181235--181338 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 31
181225 AACTGATGTC
181235 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
** *
181266 AGGCCCTTATTTG-GCCAAATT--AAAGACCG--
1 AGGCCCTTATTTGAG-CATTTTGGCAA-A-CGTT
181295 -GGCCCTTATTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTT
181325 AGGCCCTTATTTGA
1 AGGCCCTTATTTGA
181339 ACAATTAGCC
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
28 18 0.31
29 4 0.07
30 4 0.07
31 32 0.55
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (31 bp):
AGGCCCTTATTTGAGCATTTTGGCAAACGTT
Found at i:186339 original size:40 final size:40
Alignment explanation
Indices: 186284--186364 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
186274 ACACGGCCAC
186284 GGTCAGGGCATTCATGCCACAAGCCCCAGAGAGGTTTATA
1 GGTCAGGGCATTCATGCCACAAGCCCCAGAGAGGTTTATA
186324 GGTCAGGGCATTCATGCCACAAGCCCCAGAGAGGTTTATA
1 GGTCAGGGCATTCATGCCACAAGCCCCAGAGAGGTTTATA
186364 G
1 G
186365 AGGTACTTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (40 bp):
GGTCAGGGCATTCATGCCACAAGCCCCAGAGAGGTTTATA
Found at i:186457 original size:76 final size:76
Alignment explanation
Indices: 186324--186546 Score: 351
Period size: 76 Copynumber: 3.0 Consensus size: 76
186314 GAGGTTTATA
* * *
186324 GGTCAGGGCATTCA-TGCCACAAGCCCCAGAGA-GGTTTATAGAGGTACTTACAGATCACCAACC
1 GGTCAGGGCATTCATTTCCACAAGCCTCAGAGAGGGCTTATAGAGGTACTTACAGATCACCAACC
*
186387 AACAAGGACAC
66 AACGAGGACAC
* * *
186398 GGTCAAGGCATTCATTTCCACAAGCCTCAGAGAGGGCTTATAGAGGTGCTTATAGATCACCAACC
1 GGTCAGGGCATTCATTTCCACAAGCCTCAGAGAGGGCTTATAGAGGTACTTACAGATCACCAACC
186463 AACGAGGACAC
66 AACGAGGACAC
* *
186474 GGCCAGGGCATTCATTTCCACAAGCCTCAGAGAGGGCTTATAGTGGTACTTACAGATCACCAACC
1 GGTCAGGGCATTCATTTCCACAAGCCTCAGAGAGGGCTTATAGAGGTACTTACAGATCACCAACC
186539 AACGAGGA
66 AACGAGGA
186547 TCGTTGGCAG
Statistics
Matches: 135, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
74 13 0.10
75 16 0.12
76 106 0.79
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (76 bp):
GGTCAGGGCATTCATTTCCACAAGCCTCAGAGAGGGCTTATAGAGGTACTTACAGATCACCAACC
AACGAGGACAC
Found at i:195105 original size:18 final size:19
Alignment explanation
Indices: 195067--195109 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
195057 ACTGAGACTC
*
195067 AAACT-AACTGCCTCAACA
1 AAACTGAACTGACTCAACA
195085 AAACTGAACTGACTCAA-A
1 AAACTGAACTGACTCAACA
195103 AAACTGA
1 AAACTGA
195110 CTAAACCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.49, C:0.26, G:0.09, T:0.16
Consensus pattern (19 bp):
AAACTGAACTGACTCAACA
Found at i:197441 original size:21 final size:19
Alignment explanation
Indices: 197416--197469 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
197406 GCTGCTCTAA
197416 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* * *
197437 TAATCTAATATGTACAGTG
1 TAATCTCATCTGTACAGTC
197456 TAATCTCATCTGTA
1 TAATCTCATCTGTA
197470 AAGTTGCTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 12 0.43
21 16 0.57
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:198939 original size:11 final size:11
Alignment explanation
Indices: 198896--198933 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
198886 TTCTTATATA
*
198896 AAATAAATTAT
1 AAATTAATTAT
198907 CAAA-TAATTAT
1 -AAATTAATTAT
198918 AAATTAATTAT
1 AAATTAATTAT
198929 AAATT
1 AAATT
198934 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:204714 original size:43 final size:43
Alignment explanation
Indices: 204653--204740 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
204643 ATGAGCTACA
*
204653 CAATAAGAGGTAGTGATCTTTTTTCCCATAATCCCATCCCGCC
1 CAATAAGAGGTAGTGATCTTTTTTCCCATAATCCCACCCCGCC
204696 CAATAAGAGGTAGTGATCTTTTTTCCCATAATCCCACCCCGCC
1 CAATAAGAGGTAGTGATCTTTTTTCCCATAATCCCACCCCGCC
204739 CA
1 CA
204741 TTTCAGGATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.26, C:0.32, G:0.14, T:0.28
Consensus pattern (43 bp):
CAATAAGAGGTAGTGATCTTTTTTCCCATAATCCCACCCCGCC
Found at i:209951 original size:29 final size:29
Alignment explanation
Indices: 209909--209968 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
209899 ATTCAATATT
209909 TCGATGTCTGTATATCTGGTTTAAGTTGA
1 TCGATGTCTGTATATCTGGTTTAAGTTGA
209938 TCGATGTCTGTATATCTGGTTTAAGTTGA
1 TCGATGTCTGTATATCTGGTTTAAGTTGA
209967 TC
1 TC
209969 CTTTACAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.20, C:0.12, G:0.23, T:0.45
Consensus pattern (29 bp):
TCGATGTCTGTATATCTGGTTTAAGTTGA
Found at i:214540 original size:14 final size:15
Alignment explanation
Indices: 214512--214542 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
214502 CTATTTTTTA
214512 TTTCAAAAAATAATT
1 TTTCAAAAAATAATT
214527 TTTCAAAAAA-AATT
1 TTTCAAAAAATAATT
214541 TT
1 TT
214543 AAACATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTCAAAAAATAATT
Done.