Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005591.1 Corchorus capsularis cultivar CVL-1 contig05609, 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: 13265
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:72 original size:33 final size:33
Alignment explanation
Indices: 26--113 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 33
16 CCCATGGTGA
* * * *
26 AGCCGCCCCAGTGGGGAGGCTCCGCCGTGGTTG
1 AGCCTCCCTAGTGGGGAGGCTCCACCGTGGCTG
59 AGCCTCCCTAGTGGGGAGGCTCCACCGTGGCTG
1 AGCCTCCCTAGTGGGGAGGCTCCACCGTGGCTG
92 AGCCGT-CCTAGTGGGGAGGCTC
1 AGCC-TCCCTAGTGGGGAGGCTC
114 AGTGTAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
33 49 0.98
34 1 0.02
ACGTcount: A:0.11, C:0.32, G:0.40, T:0.17
Consensus pattern (33 bp):
AGCCTCCCTAGTGGGGAGGCTCCACCGTGGCTG
Found at i:160 original size:15 final size:15
Alignment explanation
Indices: 119--160 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
109 GGCTCAGTGT
*
119 AAAAGTGTAAAAAGGGT
1 AAAAGTGT--AAAGGGC
136 AAAA-TGTAAAGGGC
1 AAAAGTGTAAAGGGC
150 AAAAGTGTAAA
1 AAAAGTGTAAA
161 AAGTGGGGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.43
15 6 0.26
16 3 0.13
17 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.26, T:0.17
Consensus pattern (15 bp):
AAAAGTGTAAAGGGC
Found at i:588 original size:21 final size:23
Alignment explanation
Indices: 562--608 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
552 AAAAGTTAAC
*
562 AAACCGAATCCG-CCCAACCC-G
1 AAACCGAAACCGCCCCAACCCAG
*
583 AAACCGAAACTGCCCCAACCCAG
1 AAACCGAAACCGCCCCAACCCAG
606 AAA
1 AAA
609 TGACCCGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 8 0.36
23 4 0.18
ACGTcount: A:0.40, C:0.43, G:0.13, T:0.04
Consensus pattern (23 bp):
AAACCGAAACCGCCCCAACCCAG
Found at i:1006 original size:41 final size:41
Alignment explanation
Indices: 944--1202 Score: 360
Period size: 41 Copynumber: 6.3 Consensus size: 41
934 ATGGCCGCCT
*
944 GAAGATGTTGTTTACTTTTCCCAGTTTGTCCTTCCCCACCG
1 GAAGGTGTTGTTTACTTTTCCCAGTTTGTCCTTCCCCACCG
* * *
985 GAAGGTGTTGTTTACTTTTCCCAATCTGCCCTTCCCCACCG
1 GAAGGTGTTGTTTACTTTTCCCAGTTTGTCCTTCCCCACCG
*
1026 GAAGGTGTTGTTTACTTTTCCCAGTCTGTCCTTCCCCACCG
1 GAAGGTGTTGTTTACTTTTCCCAGTTTGTCCTTCCCCACCG
* *
1067 GAAGGTGTTGTTTACATTTACCAGTTT-TCCCTTCCCCACCG
1 GAAGGTGTTGTTTACTTTTCCCAGTTTGT-CCTTCCCCACCG
* * ** * **
1108 GAAGGTGTTTTTTACATTTCCTGGTTTGCCCTTCCCCATTG
1 GAAGGTGTTGTTTACTTTTCCCAGTTTGTCCTTCCCCACCG
*
1149 GAAGGTGTTGTTTAC-TTTCCCAGTTTGTCCTTCCCCATCG
1 GAAGGTGTTGTTTACTTTTCCCAGTTTGTCCTTCCCCACCG
1189 GAAGGTGTTGTTTA
1 GAAGGTGTTGTTTA
1203 TTGTTTTTTA
Statistics
Matches: 195, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
40 36 0.18
41 159 0.82
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.39
Consensus pattern (41 bp):
GAAGGTGTTGTTTACTTTTCCCAGTTTGTCCTTCCCCACCG
Found at i:1263 original size:49 final size:49
Alignment explanation
Indices: 1210--1731 Score: 558
Period size: 49 Copynumber: 10.7 Consensus size: 49
1200 TTATTGTTTT
* * *
1210 TTATTCCAAAAATGCCCCTTCCCGGTCGAAAGGTCCCAGTGTTCCTTAC
1 TTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCCTTAC
* * * * *
1259 TTATTTGC-AAAATGCCCCTTCCCGGTCGGAAGGTCATAGTTTTCTTTTC
1 TTA-TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCCTTAC
* * *
1308 TTATTCCCAAAATGCCCCTTCCCGATCGGAAGGTCACAGT-TTCCTTTTC
1 TTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCC-TTAC
**
1357 TTATTCCGAAAAATGCCCCTTCCCGGTCGGACTGTCACAGTCTT-CTTCAC
1 TTATTCC-AAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCCTT-AC
* * *
1407 TTATTCCAAAGATGCCCCTTCCCGGTCGGAAGGTCGCAGTC-T--TTAT
1 TTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCCTTAC
* * * *
1453 TTATTCCAAAAATGCCCTTTCCCGATCGGAAGGTCACAGTCTTCTTTAT
1 TTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCCTTAC
* * * * * *
1502 TTATTCCAAAAATGCCCCTTCTCGATCGGACGGTCATAGTCTTCTTTAT
1 TTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCCTTAC
* * * *
1551 TTAATACAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCTTTAT
1 TTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCCTTAC
* * * * *
1600 TTATTCGAAAAATACCCCTTCCTGGTCGGAAGGTCACAGT-TTTCTTCTC
1 TTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCCTT-AC
* * * * *
1649 TTATTCCAAAAATGCTCATTCCCGGTCGGAAGGTCACAATATT-CTTCAT
1 TTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCCTT-AC
1698 TTATTCCAAAAAATG-CCCTTCCCGGTCGGAAGGT
1 TTATTCC-AAAAATGCCCCTTCCCGGTCGGAAGGT
1732 GCCAGATCTG
Statistics
Matches: 407, Mismatches: 54, Indels: 24
0.84 0.11 0.05
Matches are distributed among these distances:
46 38 0.09
47 3 0.01
48 11 0.03
49 303 0.74
50 50 0.12
51 2 0.00
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (49 bp):
TTATTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGTCTTCCTTAC
Found at i:1678 original size:147 final size:145
Alignment explanation
Indices: 1210--1731 Score: 633
Period size: 147 Copynumber: 3.6 Consensus size: 145
1200 TTATTGTTTT
* * * * * *
1210 TTATTCCAAAAATGCCCCTTCCCGGTCGAAAGGTCCCAGTGTTCCTT-ACTTATTTGC-AAAATG
1 TTATTCCAAAAATGCCCCTTCCCGGTCGGACGGTCACAGTCTT-CTTCATTTA-TTCCAAAAATG
* *
1273 CCCCTTCCCGGTCGGAAGGTCATAGTTTTCTTT-TCTTATTCCCAAAATGCCCCTTCCCGATCGG
64 CCCCTTCCCGGTCGGAAGGTCACAG-TTTCTTTAT-TTATTCCAAAAATGCCCCTTCCCGATCGG
*
1337 AAGGTCACAGTTTCCTTTTC
127 AAGGTCACAGTTTTC-TTTC
* * *
1357 TTATTCCGAAAAATGCCCCTTCCCGGTCGGACTGTCACAGTCTTCTTCACTTATTCCAAAGATGC
1 TTATTCC-AAAAATGCCCCTTCCCGGTCGGACGGTCACAGTCTTCTTCATTTATTCCAAAAATGC
* *
1422 CCCTTCCCGGTCGGAAGGTCGCAG--TCTTTATTTATTCCAAAAATGCCCTTTCCCGATCGGAAG
65 CCCTTCCCGGTCGGAAGGTCACAGTTTCTTTATTTATTCCAAAAATGCCCCTTCCCGATCGGAAG
* *
1485 GTCACAGTCTTCTTTAT
130 GTCACAGTTTTCTTT-C
* * * * * *
1502 TTATTCCAAAAATGCCCCTTCTCGATCGGACGGTCATAGTCTTCTTTATTTAATACAAAAATGCC
1 TTATTCCAAAAATGCCCCTTCCCGGTCGGACGGTCACAGTCTTCTTCATTTATTCCAAAAATGCC
* * * *
1567 CCTTCCCGGTCGGAAGGTCACAGTCTTCTTTATTTATTCGAAAAATACCCCTTCCTGGTCGGAAG
66 CCTTCCCGGTCGGAAGGTCACAGT-TTCTTTATTTATTCCAAAAATGCCCCTTCCCGATCGGAAG
1632 GTCACAGTTTTCTTCTC
130 GTCACAGTTTTCTT-TC
* * * * *
1649 TTATTCCAAAAATGCTCATTCCCGGTCGGAAGGTCACAATATTCTTCATTTATTCCAAAAAATG-
1 TTATTCCAAAAATGCCCCTTCCCGGTCGGACGGTCACAGTCTTCTTCATTTATTCC-AAAAATGC
1713 CCCTTCCCGGTCGGAAGGT
65 CCCTTCCCGGTCGGAAGGT
1732 GCCAGATCTG
Statistics
Matches: 323, Mismatches: 42, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
144 74 0.23
145 52 0.16
146 1 0.00
147 124 0.38
148 72 0.22
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (145 bp):
TTATTCCAAAAATGCCCCTTCCCGGTCGGACGGTCACAGTCTTCTTCATTTATTCCAAAAATGCC
CCTTCCCGGTCGGAAGGTCACAGTTTCTTTATTTATTCCAAAAATGCCCCTTCCCGATCGGAAGG
TCACAGTTTTCTTTC
Found at i:4905 original size:24 final size:24
Alignment explanation
Indices: 4878--4923 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
4868 GGGTTCTTTA
*
4878 GCTAGAATCTAACATCTCAATTTG
1 GCTAGAATCTAACATCCCAATTTG
* * *
4902 GCTATAATTTCACATCCCAATT
1 GCTAGAATCTAACATCCCAATT
4924 GCCAAGAACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.35
Consensus pattern (24 bp):
GCTAGAATCTAACATCCCAATTTG
Found at i:6576 original size:13 final size:13
Alignment explanation
Indices: 6558--6583 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6548 TCACTAACAA
6558 CAGGTTGAGACAG
1 CAGGTTGAGACAG
6571 CAGGTTGAGACAG
1 CAGGTTGAGACAG
6584 GAAAATTTCT
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:0.31, C:0.15, G:0.38, T:0.15
Consensus pattern (13 bp):
CAGGTTGAGACAG
Found at i:7519 original size:32 final size:31
Alignment explanation
Indices: 7461--7524 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 31
7451 ATGTTTTCCG
*
7461 ATTGTACCCTTATTTTTAAAACATATTTCTA
1 ATTGTACCCTTATTTTAAAAACATATTTCTA
7492 ATTGTACCCTT-TTTTAAAAAAACATATTTCTA
1 ATTGTACCCTTATTTT--AAAAACATATTTCTA
7524 A
1 A
7525 ATTGCCATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 4 0.13
31 11 0.37
32 15 0.50
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.45
Consensus pattern (31 bp):
ATTGTACCCTTATTTTAAAAACATATTTCTA
Found at i:7722 original size:38 final size:37
Alignment explanation
Indices: 7662--7757 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 37
7652 AATTTGACTT
7662 TTTGTTTCCAACGTCTTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACGTCTTATTTAATTTTGCCTTTTGTC
* *
7699 TTTGTTTTCAATCGT-TGTATTTAATTTTGCTTTTTGTC
1 TTTGTTTCCAA-CGTCT-TATTTAATTTTGCCTTTTGTC
* *
7737 TTTGTCTCCAACGTCCTATTT
1 TTTGTTTCCAACGTCTTATTT
7758 GGGCTTAGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
37 19 0.37
38 32 0.63
ACGTcount: A:0.14, C:0.18, G:0.11, T:0.57
Consensus pattern (37 bp):
TTTGTTTCCAACGTCTTATTTAATTTTGCCTTTTGTC
Found at i:8882 original size:164 final size:164
Alignment explanation
Indices: 8576--8901 Score: 403
Period size: 164 Copynumber: 2.0 Consensus size: 164
8566 TATATAAAAG
* *
8576 TACGAATAATGGAAAATTTATGTTTTCCGATTGTACCCTTTTTTAAAATATATTTCTAAATTGAA
1 TACGAATAATGGAAAATTTATGTTTTCCAATTGCACCCTTTTTTAAAATATATTTCTAAATTGAA
8641 ATTATTAAAATTTATCATTTAAAAATTAATTATAAAATTTATATTTAGACCAAATTATAAGTTTG
66 ATTATTAAAATTTATCATTT-AAAATTAATTATAAAATTTATATTTAGACCAAATTATAAGTTTG
*
8706 TAAAATTGATTTTCA-TTAATGAATATGCAAATCTC
130 TAAAATTGATTTT-AGTTAATGAACATGCAAATCTC
* *** **
8741 TACGAATAATGGGAAACTTTATGTTTTCCAATTGCACCC-TTTTTCCCATATATTTCTAAATTTT
1 TACGAATAAT-GGAAAATTTATGTTTTCCAATTGCACCCTTTTTTAAAATATATTTCTAAATTGA
* ** * *
8805 CATTATTAAAATTTAGT-ATAATT-TTATTATTTA-AAAATTT-TAATTTAGACCGAATTATAAG
65 AATTATTAAAATTTA-TCAT--TTAAAATTAATTATAAAATTTAT-ATTTAGACCAAATTATAAG
* *
8866 TTTGTCAAATTGATTTTAGTTGATGAACATGCAAAT
126 TTTGTAAAATTGATTTTAGTTAATGAACATGCAAAT
8902 TTCCTTTACT
Statistics
Matches: 139, Mismatches: 16, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
163 2 0.01
164 56 0.40
165 53 0.38
166 26 0.19
167 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.44
Consensus pattern (164 bp):
TACGAATAATGGAAAATTTATGTTTTCCAATTGCACCCTTTTTTAAAATATATTTCTAAATTGAA
ATTATTAAAATTTATCATTTAAAATTAATTATAAAATTTATATTTAGACCAAATTATAAGTTTGT
AAAATTGATTTTAGTTAATGAACATGCAAATCTC
Found at i:9180 original size:22 final size:21
Alignment explanation
Indices: 9128--9306 Score: 133
Period size: 22 Copynumber: 8.0 Consensus size: 21
9118 CTATGTGGTC
*
9128 ATCAAAATTTCATAAGATGGTT
1 ATCAAAATTTCATAGGA-GGTT
* *
9150 ATTATAATTTCATGAGGAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
* *
9172 ATCAAAATTCCATAGTGTGGTT
1 ATCAAAATTTCATAG-GAGGTT
** *
9194 CGCAAAATTTCATATGGAAGTT
1 ATCAAAATTTCATA-GGAGGTT
*
9216 ATCAAAATTTCATAGTATGGTT
1 ATCAAAATTTCATAGGA-GGTT
* *
9238 ACCAAAATATCATAGGATCAGGTT
1 ATCAAAATTTCATAGG---AGGTT
* *
9262 ATCAAAATTTCTTAGGTTGGTT
1 ATCAAAATTTCATAGG-AGGTT
**
9284 ATTGAAATTTCATAGGATGGTT
1 ATCAAAATTTCATAGGA-GGTT
9306 A
1 A
9307 ATTATCACAA
Statistics
Matches: 121, Mismatches: 28, Indels: 16
0.73 0.17 0.10
Matches are distributed among these distances:
21 4 0.03
22 95 0.79
23 4 0.03
24 17 0.14
25 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (21 bp):
ATCAAAATTTCATAGGAGGTT
Found at i:9193 original size:44 final size:42
Alignment explanation
Indices: 9128--10129 Score: 271
Period size: 44 Copynumber: 22.8 Consensus size: 42
9118 CTATGTGGTC
* *
9128 ATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAGGTT
1 ATCAAAATTTCAT-AGATGGTTATCAAAATTTCAT-AGGAGGTT
* * ** *
9172 ATCAAAATTCCATAGTGTGGTTCGCAAAATTTCATATGGAAGTT
1 ATCAAAATTTCATAG-ATGGTTATCAAAATTTCATA-GGAGGTT
* *
9216 ATCAAAATTTCATAGTATGGTTACCAAAATATCATAGGATCAGGTT
1 ATCAAAATTTCATAG-ATGGTTATCAAAATTTCATAGG---AGGTT
* * **
9262 ATCAAAATTTCTTAGGTTGGTTATTGAAATTTCATAGGATGGTTAATT
1 ATCAAAATTTCATA-GATGGTTATCAAAATTTCATAGGA-GG----TT
* * *
9310 ATCACAATTTTATAGAAAGGTTATCAAAGAGGTTATCATAATGTCATAGCGAGGTT
1 ATCAAAATTTCATAG-ATGGTTATC--A-A----A--AT--T-TCATAG-GAGGTT
*
9366 AT-AAGAATTTCATAGTATGGTTAACAAAATTTCATTAGGAGGTT
1 ATCAA-AATTTCATAG-ATGGTTATCAAAATTTCA-TAGGAGGTT
* * * *
9410 A-CTAATATTTCATGGGGA-GGTTATCAAAATTTTATAGTGTGGTT
1 ATC-AAAATTTCAT--AGATGGTTATCAAAATTTCATAG-GAGGTT
* * * **
9454 ATCACAATTTCATATGAAGATATAAAAGACTCAATTTCATAAGGA-G-T
1 ATCAAAATTTCATA-GATGGT-TATCA-A---AATTTCAT-AGGAGGTT
* * * * *
9501 ACCAAAATTTGATAGAAGGTTATC-CAATCTCATA-GAGTGATT
1 ATCAAAATTTCATAGATGGTTATCAAAATTTCATAGGAG-G-TT
* * *
9543 ATCGAAATTTCACAGAGATCGGATTATCAAAATTTC-TAGGAAGATT
1 ATCAAAATTT--CATAGAT-GG-TTATCAAAATTTCATAGG-AGGTT
* * *
9589 ATCAAAATTTCATAGCGTTGTTATCAAAATTTCAAAGGGAGGTT
1 ATCAAAATTTCATAG-ATGGTTATCAAAATTTCATA-GGAGGTT
* * *
9633 ATCAAAATTACATA-ATGTGATTATCAGAATTTCATAAAGG-GGTC
1 ATCAAAATTTCATAGATG-G-TTATCAAAATTTCAT--AGGAGGTT
* * * *
9677 AACGAAATTTTATAAAGA-GGTTATCAAAATTTCATAAAGAGGTT
1 ATCAAAATTTCAT--AGATGGTTATCAAAATTTCAT-AGGAGGTT
* * *
9721 ATCAAATTTTCAGA-ATGTGATTA-CAAAAATTTCATA-GTGG--
1 ATCAAAATTTCATAGATG-G-TTATC-AAAATTTCATAGGAGGTT
* *
9761 -T----ATTTC-TGGGGA-GGTTATCAAAATTTCATAGTATGGTT
1 ATCAAAATTTCAT--AGATGGTTATCAAAATTTCATAGGA-GGTT
* * * * * *
9799 A-CCAAA-TT-A-GGAAGGTTATTAAACTTTTATTATGGA-GTT
1 ATCAAAATTTCATAGATGGTTATCAAAATTTCA-TA-GGAGGTT
* ** * * * *
9838 ATCAAAATTTTAGGGA-GGATATTAAAATTTCATATGAATGTT
1 ATCAAAATTTCATAGATGGTTATCAAAATTTCATA-GGAGGTT
* * *
9880 ATCAAAATTTCATA-ATTTAGTTTTCAAAATTTCATAAGAGGGTT
1 ATCAAAATTTCATAGA--TGGTTATCAAAATTTCATAGGA-GGTT
* * *
9924 ATCAAAATTTCATAGGGA-GATTAACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATA--GATGGTTATCAAAATTTCAT-AGGAGGTT
** *
9968 ATCAAAAAATCATAGGGA-GGTTATCAAAA-TT--T-GTA-GTT
1 ATCAAAATTTCATA--GATGGTTATCAAAATTTCATAGGAGGTT
* ** *
10006 ATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGAAGGTTT
1 ATCAAAATTTCAT-AGATGGTTATCAAAATTTCATAGG-AGG-TT
* * * *
10051 ATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAACGAGGTT
1 ATCAAAATTTCATA-GATG-GTTATCAAAATTTCAT-AGGAGGTT
*
10096 ATCACAATTTCATAG-TGTGATTATCAAAATTTCA
1 ATCAAAATTTCATAGATG-G-TTATCAAAATTTCA
10130 GAGTGTGATT
Statistics
Matches: 712, Mismatches: 136, Indels: 220
0.67 0.13 0.21
Matches are distributed among these distances:
34 14 0.02
35 6 0.01
36 3 0.00
37 3 0.00
38 28 0.04
39 23 0.03
40 14 0.02
41 15 0.02
42 45 0.06
43 39 0.05
44 292 0.41
45 54 0.08
46 79 0.11
47 26 0.04
48 22 0.03
49 9 0.01
50 2 0.00
51 1 0.00
53 1 0.00
54 1 0.00
55 2 0.00
56 20 0.03
57 2 0.00
59 1 0.00
60 8 0.01
61 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (42 bp):
ATCAAAATTTCATAGATGGTTATCAAAATTTCATAGGAGGTT
Found at i:9378 original size:22 final size:20
Alignment explanation
Indices: 9338--9467 Score: 80
Period size: 22 Copynumber: 6.0 Consensus size: 20
9328 GGTTATCAAA
* *
9338 GAGGTTATCATAATGTCATAG
1 GAGGTTAT-AAAATTTCATAG
9359 CGAGGTTATAAGAATTTCATAG
1 -GAGGTTATAA-AATTTCATAG
* *
9381 TATGGTTAACAAAATTTCATTAG
1 GA-GGTT-ATAAAATTTCA-TAG
* *
9404 GAGGTTACTAATATTTCATGGG
1 GAGGTTA-TAAAATTTCAT-AG
*
9426 GAGGTTATCAAAATTTTATAG
1 GAGGTTAT-AAAATTTCATAG
* *
9447 TGTGGTTATCACAATTTCATA
1 -GAGGTTAT-AAAATTTCATA
9468 TGAAGATATA
Statistics
Matches: 86, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
21 6 0.07
22 73 0.85
23 7 0.08
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (20 bp):
GAGGTTATAAAATTTCATAG
Found at i:9615 original size:22 final size:22
Alignment explanation
Indices: 9530--9668 Score: 99
Period size: 22 Copynumber: 6.2 Consensus size: 22
9520 TTATCCAATC
*
9530 TCATA-GAGTGATTATCGAAATT
1 TCATAGGA-TGATTATCAAAATT
*
9552 TCACAGAGATCGGATTATCAAAATT
1 TCATAG-GAT--GATTATCAAAATT
*
9577 TC-TAGGAAGATTATCAAAATT
1 TCATAGGATGATTATCAAAATT
*
9598 TCATAGCGTTG-TTATCAAAATT
1 TCATAG-GATGATTATCAAAATT
* *
9620 TCAAAGGGA-GGTTATCAAAATT
1 TCATA-GGATGATTATCAAAATT
* * *
9642 ACATAATG-TGATTATCAGAATT
1 TCAT-AGGATGATTATCAAAATT
9664 TCATA
1 TCATA
9669 AAGGGGTCAA
Statistics
Matches: 93, Mismatches: 14, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
21 17 0.18
22 51 0.55
23 7 0.08
24 4 0.04
25 14 0.15
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.34
Consensus pattern (22 bp):
TCATAGGATGATTATCAAAATT
Found at i:9720 original size:22 final size:22
Alignment explanation
Indices: 9566--9732 Score: 135
Period size: 22 Copynumber: 7.6 Consensus size: 22
9556 AGAGATCGGA
9566 TTATCAAAATTTC-TAGGAAGA--
1 TTATCAAAATTTCATA--AAGAGG
** **
9587 TTATCAAAATTTCATAGCGTTG
1 TTATCAAAATTTCATAAAGAGG
*
9609 TTATCAAAATTTCA-AAGGGAGG
1 TTATCAAAATTTCATAA-AGAGG
* * * *
9631 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAAGAGG
* *
9653 TTATCAGAATTTCATAAAGGGG
1 TTATCAAAATTTCATAAAGAGG
* * * *
9675 TCAACGAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
9697 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
*
9719 TTATCAAATTTTCA
1 TTATCAAAATTTCA
9733 GAATGTGATT
Statistics
Matches: 114, Mismatches: 27, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
20 1 0.01
21 14 0.12
22 97 0.85
23 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:9861 original size:42 final size:42
Alignment explanation
Indices: 9805--9889 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
9795 GGTTACCAAA
* * * *
9805 TTAGGAAGGTTATTAAACTTTTATTATGGA-GTTATCAAAATT
1 TTAGGAAGGATATTAAAATTTCA-TATGAATGTTATCAAAATT
*
9847 TTAGGGAGGATATTAAAATTTCATATGAATGTTATCAAAATT
1 TTAGGAAGGATATTAAAATTTCATATGAATGTTATCAAAATT
9889 T
1 T
9890 CATAATTTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 5 0.14
42 32 0.86
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (42 bp):
TTAGGAAGGATATTAAAATTTCATATGAATGTTATCAAAATT
Found at i:9889 original size:22 final size:22
Alignment explanation
Indices: 9809--10396 Score: 223
Period size: 22 Copynumber: 27.0 Consensus size: 22
9799 ACCAAATTAG
* * *
9809 GAAGGTTATTAAACTTTTATTAT
1 GAAGGTTATCAAAATTTCA-TAT
* *
9832 GGA-GTTATCAAAATTT--TAG
1 GAAGGTTATCAAAATTTCATAT
* * *
9851 GGAGGATATTAAAATTTCATAT
1 GAAGGTTATCAAAATTTCATAT
*
9873 GAATGTTATCAAAATTTCATAAT
1 GAAGGTTATCAAAATTTCAT-AT
** * *
9896 TTA-GTTTTCAAAATTTCATAA
1 GAAGGTTATCAAAATTTCATAT
* *
9917 GAGGGTTATCAAAATTTCATAG
1 GAAGGTTATCAAAATTTCATAT
* * *
9939 GGAGATTAACAAAATTTCATAAT
1 GAAGGTTATCAAAATTTCAT-AT
** *
9962 G-AGGTTATCAAAAAATCATAG
1 GAAGGTTATCAAAATTTCATAT
*
9983 GGAGGTTATCAAAA--T--T-T
1 GAAGGTTATCAAAATTTCATAT
* * *
10000 GTA-GTTATCAAGATTTCATAA
1 GAAGGTTATCAAAATTTCATAT
* * *
10021 GAAAGTTATCAAAATTTTATAG
1 GAAGGTTATCAAAATTTCATAT
* *
10043 GAAGGTTTATCAAAATTTTATAG
1 GAAGG-TTATCAAAATTTCATAT
* *
10066 GAAGATTTATCAAAATTTCATAAC
1 GAAG-GTTATCAAAATTTCAT-AT
*
10090 G-AGGTTATCACAATTTCATAGT
1 GAAGGTTATCAAAATTTCATA-T
* * *
10112 G-TGATTATCAAAATTTCAGAGT
1 GAAGGTTATCAAAATTTCATA-T
* *
10134 G-TGATTA-CTAACAA-TTCATAT
1 GAAGGTTATC-AA-AATTTCATAT
* * * *
10155 GGAGGTTTTTAAATTTTCATAAT
1 GAAGGTTATCAAAATTTCAT-AT
* * *
10178 G-TGGTTATCAATATATCATAT
1 GAAGGTTATCAAAATTTCATAT
* * *
10199 GGAGGTTATCAACATCTCATAGT
1 GAAGGTTATCAAAATTTCATA-T
**
10222 GTTGGTTATCAAAATTTCAT-T
1 GAAGGTTATCAAAATTTCATAT
*
10243 GGGAA-GTTATCAAAATTTTATATT
1 --GAAGGTTATCAAAATTTCATA-T
* * * *
10267 G-AGATCT-TCAAAATTCCTTAG
1 GAAGGT-TATCAAAATTTCATAT
* * * * *
10288 GGAGGCTAACAAAATTTTATAA
1 GAAGGTTATCAAAATTTCATAT
* *
10310 GAAGGTTATAAAAAATTT-ATAA
1 GAAGGTTAT-CAAAATTTCATAT
* * * *
10332 AAAGGTTCTCGAAATTCCATAAT
1 GAAGGTTATCAAAATTTCAT-AT
** * *
10355 -ATCGTTATTAAAATTTCATAG
1 GAAGGTTATCAAAATTTCATAT
10376 GAAGGTTATCAAAATTTCATA
1 GAAGGTTATCAAAATTTCATA
10397 ATGGGATCAT
Statistics
Matches: 425, Mismatches: 103, Indels: 75
0.70 0.17 0.12
Matches are distributed among these distances:
16 9 0.02
17 2 0.00
18 2 0.00
19 5 0.01
20 13 0.03
21 23 0.05
22 292 0.69
23 76 0.18
24 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
GAAGGTTATCAAAATTTCATAT
Found at i:10054 original size:23 final size:23
Alignment explanation
Indices: 10004--10083 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
9994 AAATTTGTAG
* * * *
10004 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTTATAGGAAGGT
10026 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGAAGGT
*
10049 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTTATAGGAAGGT
10072 TTATCAAAATTT
1 TTATCAAAATTT
10084 CATAACGAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
22 18 0.35
23 34 0.65
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGGT
Found at i:10219 original size:44 final size:45
Alignment explanation
Indices: 10149--10256 Score: 114
Period size: 45 Copynumber: 2.4 Consensus size: 45
10139 TACTAACAAT
* * * *
10149 TCATATGGAGGTTTTTAAATTTTCATAATG-TGGTTATCAATATA
1 TCATATGGAGGTTATCAAATTCTCATAATGTTGGTTATCAAAATA
* *
10193 TCATATGGAGGTTATCAACA-TCTCATAGTGTTGGTTATCAAAATT
1 TCATATGGAGGTTATCAA-ATTCTCATAATGTTGGTTATCAAAATA
*
10238 TCAT-TGGGAAGTTATCAAA
1 TCATAT-GGAGGTTATCAAA
10257 ATTTTATATT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
44 26 0.48
45 28 0.52
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (45 bp):
TCATATGGAGGTTATCAAATTCTCATAATGTTGGTTATCAAAATA
Found at i:11857 original size:18 final size:18
Alignment explanation
Indices: 11834--11873 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
11824 AACAAAAAAA
*
11834 ATTAGAAGAGATGAACCC
1 ATTAGAAGACATGAACCC
*
11852 ATTAGAAGACATGGACCC
1 ATTAGAAGACATGAACCC
11870 ATTA
1 ATTA
11874 AATAAGTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (18 bp):
ATTAGAAGACATGAACCC
Done.