Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016041.1 Corchorus capsularis cultivar CVL-1 contig16062, 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: 52709
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Found at i:17 original size:2 final size:2
Alignment explanation
Indices: 11--40 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1 TAGGAGGAGG
11 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41 ACCATATTTA
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):
TA
Found at i:12078 original size:29 final size:29
Alignment explanation
Indices: 12032--12087 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
12022 ACAAATAAAT
* * *
12032 GCAATTCAATTAATCAATAGCAAGATATG
1 GCAATTCAAATAAACAATAGAAAGATATG
* *
12061 GCAATTTAAATAAACAATTGAAAGATA
1 GCAATTCAAATAAACAATAGAAAGATA
12088 GAATAAGCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (29 bp):
GCAATTCAAATAAACAATAGAAAGATATG
Found at i:17128 original size:11 final size:11
Alignment explanation
Indices: 17112--17146 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
17102 TAATTTAACC
17112 ATTAATTAGAT
1 ATTAATTAGAT
*
17123 ATTAATTAGCT
1 ATTAATTAGAT
17134 ATTAATTAGAT
1 ATTAATTAGAT
17145 AT
1 AT
17147 ATATAGTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (11 bp):
ATTAATTAGAT
Found at i:18101 original size:26 final size:26
Alignment explanation
Indices: 18070--18120 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
18060 CATATCACAT
*
18070 CATATCCTATTAATTTGCATTAGAAC
1 CATATCCTATTAATTTACATTAGAAC
*
18096 CATATCCTATTAGTTTACATTAGAA
1 CATATCCTATTAATTTACATTAGAA
18121 TCATGTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.08, T:0.39
Consensus pattern (26 bp):
CATATCCTATTAATTTACATTAGAAC
Found at i:20361 original size:22 final size:22
Alignment explanation
Indices: 20335--20378 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
20325 GTTGGAACAC
20335 GGTTTCAGA-AAGAGGCTTAGAG
1 GGTTTCAGAGAAGAGGC-TAGAG
*
20357 GGTTTGAGAGAAGAGGCTAGAG
1 GGTTTCAGAGAAGAGGCTAGAG
20379 TTTTTCAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.32, C:0.07, G:0.41, T:0.20
Consensus pattern (22 bp):
GGTTTCAGAGAAGAGGCTAGAG
Found at i:21076 original size:24 final size:25
Alignment explanation
Indices: 21032--21092 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
21022 CTTTTAACCT
* * *
21032 ATTTA-TTATGCGCTTGGGCTTTTG
1 ATTTATTTATGCACTTGAGCTTATG
21056 ATTTATTTATGCACTT-AGCTTATG
1 ATTTATTTATGCACTTGAGCTTATG
* *
21080 ATTTGTTTGTGCA
1 ATTTATTTATGCA
21093 TTTGGGCCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 22 0.71
25 9 0.29
ACGTcount: A:0.18, C:0.11, G:0.20, T:0.51
Consensus pattern (25 bp):
ATTTATTTATGCACTTGAGCTTATG
Found at i:21810 original size:32 final size:31
Alignment explanation
Indices: 21740--21817 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 31
21730 CAAAAGTAGC
* *
21740 AATCAGTAATTAAGGGTCAAAGTAAAAGGGT
1 AATCAGTAATTGAGAGTCAAAGTAAAAGGGT
* * *
21771 AAGTCAGTAATTGAGAGTCAAGGTAAGAGGATT
1 AA-TCAGTAATTGAGAGTCAAAGTAAAAGG-GT
21804 AATCAGTAAATTGA
1 AATCAGT-AATTGA
21818 TAATTAAGAG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 2 0.05
32 28 0.72
33 9 0.23
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.24
Consensus pattern (31 bp):
AATCAGTAATTGAGAGTCAAAGTAAAAGGGT
Found at i:21968 original size:32 final size:32
Alignment explanation
Indices: 21926--22008 Score: 139
Period size: 32 Copynumber: 2.6 Consensus size: 32
21916 AAGAGAAGAG
* *
21926 GAAGTGATCAGTAGAATGGAGTGAAAGTAAAA
1 GAAGTAATCAGTAAAATGGAGTGAAAGTAAAA
*
21958 GAAGTAATCAGTAAAATTGAGTGAAAGTAAAA
1 GAAGTAATCAGTAAAATGGAGTGAAAGTAAAA
21990 GAAGTAATCAGTAAAATGG
1 GAAGTAATCAGTAAAATGG
22009 TAATTAAGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.49, C:0.04, G:0.27, T:0.20
Consensus pattern (32 bp):
GAAGTAATCAGTAAAATGGAGTGAAAGTAAAA
Found at i:21970 original size:16 final size:15
Alignment explanation
Indices: 21951--22046 Score: 66
Period size: 16 Copynumber: 6.5 Consensus size: 15
21941 ATGGAGTGAA
21951 AGTAAAAGAAGTAATC
1 AGTAAAAG-AGTAATC
21967 AGTAAAATTGAGTGAA--
1 AGTAAAA--GAGT-AATC
21983 AGTAAAAGAAGTAATC
1 AGTAAAAG-AGTAATC
21999 AGTAAAATG-GTAAT-
1 AGTAAAA-GAGTAATC
22013 --T--AAGAGTAA-C
1 AGTAAAAGAGTAATC
22023 AGTAAAAGAAGTAATC
1 AGTAAAAG-AGTAATC
22039 AGTAAAAG
1 AGTAAAAG
22047 TAAAGAAAAG
Statistics
Matches: 65, Mismatches: 0, Indels: 30
0.68 0.00 0.32
Matches are distributed among these distances:
9 1 0.02
10 6 0.09
12 2 0.03
14 6 0.09
15 13 0.20
16 30 0.46
17 4 0.06
18 3 0.05
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.21
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:22181 original size:21 final size:21
Alignment explanation
Indices: 22157--22216 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
22147 AAAGTAAAGA
22157 GTAATCAGTAAAAGAAGAATG
1 GTAATCAGTAAAAGAAGAATG
**
22178 GTAAAAAGT---A-AAG-A--
1 GTAATCAGTAAAAGAAGAATG
22192 GTAATCAGTAAAAGAAGAATG
1 GTAATCAGTAAAAGAAGAATG
22213 GTAA
1 GTAA
22217 AAAGTAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 14
0.61 0.09 0.30
Matches are distributed among these distances:
14 7 0.25
16 1 0.04
17 4 0.14
18 4 0.14
19 1 0.04
21 11 0.39
ACGTcount: A:0.55, C:0.03, G:0.23, T:0.18
Consensus pattern (21 bp):
GTAATCAGTAAAAGAAGAATG
Found at i:22183 original size:35 final size:35
Alignment explanation
Indices: 22144--22273 Score: 226
Period size: 35 Copynumber: 3.7 Consensus size: 35
22134 TAATCAGTAC
22144 TAAAAAGTAAAGAGTAATCAGTAAAAGAAGAATGG
1 TAAAAAGTAAAGAGTAATCAGTAAAAGAAGAATGG
22179 TAAAAAGTAAAGAGTAATCAGTAAAAGAAGAATGG
1 TAAAAAGTAAAGAGTAATCAGTAAAAGAAGAATGG
*
22214 TAAAAAGTAAAGAGTAATCAGTAAAGGAAGAATGG
1 TAAAAAGTAAAGAGTAATCAGTAAAAGAAGAATGG
* *
22249 T-AAGAGTAAAGGGTAATCAGTAAAA
1 TAAAAAGTAAAGAGTAATCAGTAAAA
22274 AGATAATCAG
Statistics
Matches: 91, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
34 21 0.23
35 70 0.77
ACGTcount: A:0.55, C:0.03, G:0.24, T:0.18
Consensus pattern (35 bp):
TAAAAAGTAAAGAGTAATCAGTAAAAGAAGAATGG
Found at i:22185 original size:59 final size:59
Alignment explanation
Indices: 22085--22201 Score: 141
Period size: 59 Copynumber: 2.0 Consensus size: 59
22075 GGTAAAATGG
* * *
22085 TAAAGAGTAAAGAGTAATTAGCAGAAAGTGAAATGGTAAAAGGAAATGA-TAATCAGTAC
1 TAAAAAGTAAAGAGTAATCAGCAGAAAGAGAAATGGTAAAAGGAAA-GAGTAATCAGTAC
* *
22144 TAAAAAGTAAAGAGTAATCAGTA-AAAGA-AGAATGGTAAAAAGTAAAGAGTAATCAGTA
1 TAAAAAGTAAAGAGTAATCAGCAGAAAGAGA-AATGGT-AAAAGGAAAGAGTAATCAGTA
22202 AAAGAAGAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
57 1 0.02
58 12 0.24
59 37 0.74
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.20
Consensus pattern (59 bp):
TAAAAAGTAAAGAGTAATCAGCAGAAAGAGAAATGGTAAAAGGAAAGAGTAATCAGTAC
Found at i:22282 original size:15 final size:15
Alignment explanation
Indices: 22262--22318 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
22252 GAGTAAAGGG
22262 TAATCAGTAAAAAGA
1 TAATCAGTAAAAAGA
*
22277 TAATCAGTAAAGAGTA
1 TAATCAGTAAAAAG-A
* *
22293 AAAT-AGT-AAAAGG
1 TAATCAGTAAAAAGA
22306 TAATCAGTAAAAA
1 TAATCAGTAAAAA
22319 AAGTAATGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 3 0.09
14 7 0.21
15 20 0.59
16 4 0.12
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.21
Consensus pattern (15 bp):
TAATCAGTAAAAAGA
Found at i:22286 original size:22 final size:21
Alignment explanation
Indices: 22261--22490 Score: 177
Period size: 22 Copynumber: 10.6 Consensus size: 21
22251 AGAGTAAAGG
*
22261 GTAATCAGTAAAAAGATAATCA
1 GTAATCAGTAAAAAGAAAAT-A
** *
22283 GTAAAGAGTAAAATAGTAAAA-G
1 GTAATCAGTAAAA-AG-AAAATA
22305 GTAATCAGTAAAAA-AAGTAAT-
1 GTAATCAGTAAAAAGAA--AATA
*
22326 GATAATCAGTAAAAGGTAAAATA
1 G-TAATCAGTAAAAAG-AAAATA
* *
22349 GTAATCAGT-AAGAGCAAAATG
1 GTAATCAGTAAAAAG-AAAATA
*
22370 GTAATCAGT-AAAAGCAAAATG
1 GTAATCAGTAAAAAG-AAAATA
*
22391 GTAATCAGT-AAAAGAAAAATG
1 GTAATCAGTAAAAAG-AAAATA
*
22412 GTAATCAGTAAAGAATAAAATA
1 GTAATCAGTAAA-AAGAAAATA
*
22434 GTAATCAGTAAAAAGTAAGA-A
1 GTAATCAGTAAAAAG-AAAATA
22455 GATAATCAGTAAAAAGTAAAATA
1 G-TAATCAGTAAAAAG-AAAATA
*
22478 GTAATTAGTAAAA
1 GTAATCAGTAAAA
22491 GGTAATCAGT
Statistics
Matches: 175, Mismatches: 19, Indels: 28
0.79 0.09 0.13
Matches are distributed among these distances:
19 2 0.01
21 65 0.37
22 96 0.55
23 7 0.04
24 5 0.03
ACGTcount: A:0.56, C:0.05, G:0.17, T:0.21
Consensus pattern (21 bp):
GTAATCAGTAAAAAGAAAATA
Found at i:22286 original size:29 final size:28
Alignment explanation
Indices: 22253--22316 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
22243 GAATGGTAAG
*
22253 AGTAAAGGGT-AATCAGTAAAAAGATAATC
1 AGTAAAGAGTAAAT-AGT-AAAAGATAATC
*
22282 AGTAAAGAGTAAAATAGTAAAAGGTAATC
1 AGTAAAGAGT-AAATAGTAAAAGATAATC
22311 AGTAAA
1 AGTAAA
22317 AAAAGTAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 25 0.81
30 3 0.10
31 3 0.10
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (28 bp):
AGTAAAGAGTAAATAGTAAAAGATAATC
Found at i:22308 original size:44 final size:42
Alignment explanation
Indices: 22267--22599 Score: 215
Period size: 44 Copynumber: 7.7 Consensus size: 42
22257 AAGGGTAATC
22267 AGTAAAAAGATAATCAGTAAAGAGTAAAATAGTAAAAGGTAATCAGTAAA
1 AGTAAAAAGATAATCAGTAAA-AGT-AAA-A-T---A-GTAATCAGTAAA
*
22317 A--AAAGTAATGATAATCAGTAAAAGGTAAAATAGTAATCAGTAAG
1 AGTAAA--AA-GATAATCAGTAAAA-GTAAAATAGTAATCAGTAAA
* * * * *
22361 AGCAAAATGGTAATCAGTAAAAGCAAAATGGTAATCAGTAAA
1 AGTAAAAAGATAATCAGTAAAAGTAAAATAGTAATCAGTAAA
* *
22403 AG-AAAAATGGTAATCAGTAAAGAATAAAATAGTAATCAGTAAAA
1 AGTAAAAA-GATAATCAGTAAA-AGTAAAATAGTAATCAGT-AAA
*
22447 AGTAAGAAGATAATCAGTAAAAAGTAAAATAGTAAT---T---
1 AGTAAAAAGATAATCAGT-AAAAGTAAAATAGTAATCAGTAAA
* * * *
22484 AGT-AAAAGGTAATCAGTAAGAGTAAAATAGTAATCGGCAAAAA
1 AGTAAAAAGATAATCAGTAAAAGTAAAATAGTAATCAG--TAAA
* *
22527 AGTAAAGAG-TAATCAATAAGAAGTCAAAAT-GTAATCAGTAAAA
1 AGTAAAAAGATAATCAGTAA-AAGT-AAAATAGTAATCAGT-AAA
* *
22570 ATGTGAAAAG-CAATCAGTAAAGAGTAAAAT
1 A-GTAAAAAGATAATCAGTAAA-AGTAAAAT
22600 GATAAAAAGT
Statistics
Matches: 232, Mismatches: 26, Indels: 57
0.74 0.08 0.18
Matches are distributed among these distances:
35 16 0.07
36 12 0.05
37 3 0.01
41 5 0.02
42 32 0.14
43 50 0.22
44 71 0.31
45 13 0.06
46 3 0.01
48 4 0.02
49 1 0.00
50 7 0.03
51 15 0.06
ACGTcount: A:0.56, C:0.06, G:0.18, T:0.21
Consensus pattern (42 bp):
AGTAAAAAGATAATCAGTAAAAGTAAAATAGTAATCAGTAAA
Found at i:22495 original size:22 final size:21
Alignment explanation
Indices: 22328--22491 Score: 186
Period size: 21 Copynumber: 7.6 Consensus size: 21
22318 AAAGTAATGA
22328 TAATCAGTAAAAGGTAAAATAG
1 TAATCAGTAAAA-GTAAAATAG
* * *
22350 TAATCAGTAAGAGCAAAATGG
1 TAATCAGTAAAAGTAAAATAG
* *
22371 TAATCAGTAAAAGCAAAATGG
1 TAATCAGTAAAAGTAAAATAG
* *
22392 TAATCAGTAAAAGAAAAATGG
1 TAATCAGTAAAAGTAAAATAG
*
22413 TAATCAGTAAAGAATAAAATAG
1 TAATCAGTAAA-AGTAAAATAG
*
22435 TAATCAGTAAAAAGTAAGA-AG
1 TAATCAGT-AAAAGTAAAATAG
22456 ATAATCAGTAAAAAGTAAAATAG
1 -TAATCAGT-AAAAGTAAAATAG
*
22479 TAATTAGTAAAAG
1 TAATCAGTAAAAG
22492 GTAATCAGTA
Statistics
Matches: 126, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
21 65 0.52
22 56 0.44
23 5 0.04
ACGTcount: A:0.55, C:0.05, G:0.18, T:0.21
Consensus pattern (21 bp):
TAATCAGTAAAAGTAAAATAG
Found at i:22502 original size:21 final size:21
Alignment explanation
Indices: 22297--22491 Score: 198
Period size: 22 Copynumber: 9.1 Consensus size: 21
22287 AGAGTAAAAT
22297 AGTAAAA-GGTAATCAGTAAA
1 AGTAAAATGGTAATCAGTAAA
* *
22317 A-AAAGTAATGATAATCAGTAAA
1 AGTAA--AATGGTAATCAGTAAA
* *
22339 AGGTAAAATAGTAATCAGTAAG
1 A-GTAAAATGGTAATCAGTAAA
*
22361 AGCAAAATGGTAATCAGTAAA
1 AGTAAAATGGTAATCAGTAAA
*
22382 AGCAAAATGGTAATCAGTAAA
1 AGTAAAATGGTAATCAGTAAA
*
22403 AGAAAAATGGTAATCAGTAAA
1 AGTAAAATGGTAATCAGTAAA
* *
22424 GAATAAAATAGTAATCAGTAAAA
1 -AGTAAAATGGTAATCAGT-AAA
*
22447 AGTAAGAA-GATAATCAGTAAAA
1 AGTAA-AATGGTAATCAGT-AAA
* *
22469 AGTAAAATAGTAATTAGTAAA
1 AGTAAAATGGTAATCAGTAAA
22490 AG
1 AG
22492 GTAATCAGTA
Statistics
Matches: 147, Mismatches: 19, Indels: 17
0.80 0.10 0.09
Matches are distributed among these distances:
19 2 0.01
20 1 0.01
21 67 0.46
22 70 0.48
23 5 0.03
24 2 0.01
ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21
Consensus pattern (21 bp):
AGTAAAATGGTAATCAGTAAA
Found at i:22516 original size:21 final size:21
Alignment explanation
Indices: 22504--22599 Score: 54
Period size: 22 Copynumber: 4.4 Consensus size: 21
22494 AATCAGTAAG
* *
22504 AGTAAAATAGTAATCGGCAAAAA
1 AGTAAAATAGTAATCAG--TAAA
* *
22527 AGT-AAAGAGTAATCAATAAGA
1 AGTAAAATAGTAATCAGTAA-A
22548 AGTCAAAAT-GTAATCAGTAAAA
1 AGT-AAAATAGTAATCAGT-AAA
* *
22570 ATGTGAAA-AGCAATCAGTAAA
1 A-GTAAAATAGTAATCAGTAAA
22591 GAGTAAAAT
1 -AGTAAAAT
22600 GATAAAAAGT
Statistics
Matches: 56, Mismatches: 9, Indels: 17
0.68 0.11 0.21
Matches are distributed among these distances:
20 2 0.04
21 12 0.21
22 32 0.57
23 10 0.18
ACGTcount: A:0.55, C:0.07, G:0.18, T:0.20
Consensus pattern (21 bp):
AGTAAAATAGTAATCAGTAAA
Found at i:22538 original size:101 final size:102
Alignment explanation
Indices: 22385--22570 Score: 236
Period size: 101 Copynumber: 1.8 Consensus size: 102
22375 CAGTAAAAGC
* * * * *
22385 AAAATGGTAATCAGTAAAAGAAAAATGGTAATCAGTAAAGAATAAAATAGTAATCAGTAAAAAGT
1 AAAATGGTAATCAGTAAAAGAAAAATAGTAATCAGCAAAAAATAAAAGAGTAATCAATAAAAAGT
22450 -AAGAA-GATAATCAGTAAAAAGTAAAATAGTAATTAGT
66 CAA-AATG-TAATCAGTAAAAAGTAAAATAGTAATTAGT
* * * *
22487 AAAA-GGTAATCAGTAAGAGTAAAATAGTAATCGGCAAAAAAGT-AAAGAGTAATCAATAAGAAG
1 AAAATGGTAATCAGTAAAAGAAAAATAGTAATCAGCAAAAAA-TAAAAGAGTAATCAATAAAAAG
22550 TCAAAATGTAATCAGTAAAAA
65 TCAAAATGTAATCAGTAAAAA
22571 TGTGAAAAGC
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
101 64 0.89
102 8 0.11
ACGTcount: A:0.56, C:0.05, G:0.17, T:0.21
Consensus pattern (102 bp):
AAAATGGTAATCAGTAAAAGAAAAATAGTAATCAGCAAAAAATAAAAGAGTAATCAATAAAAAGT
CAAAATGTAATCAGTAAAAAGTAAAATAGTAATTAGT
Found at i:24178 original size:12 final size:12
Alignment explanation
Indices: 24161--24186 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
24151 ACAAATACGT
24161 ATCATATAGAAA
1 ATCATATAGAAA
24173 ATCATATAGAAA
1 ATCATATAGAAA
24185 AT
1 AT
24187 TTGAGCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.27
Consensus pattern (12 bp):
ATCATATAGAAA
Found at i:33449 original size:2 final size:2
Alignment explanation
Indices: 33442--33526 Score: 67
Period size: 2 Copynumber: 45.5 Consensus size: 2
33432 TTAAATTTTA
* *
33442 AT AT AT AT -T AA AT AT TT AT -T AT AT -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
* * *
33481 AT AT A- AC GT AT GAT AT AT CT AT -T AT -T AT AT AT AT A- AT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33520 AT AT AT A
1 AT AT AT A
33527 ATTGTTTTAT
Statistics
Matches: 66, Mismatches: 9, Indels: 16
0.73 0.10 0.18
Matches are distributed among these distances:
1 7 0.11
2 57 0.86
3 2 0.03
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33465 original size:9 final size:11
Alignment explanation
Indices: 33442--33525 Score: 68
Period size: 11 Copynumber: 7.7 Consensus size: 11
33432 TTAAATTTTA
*
33442 ATATATATTAA
1 ATATATATTAT
*
33453 ATATTTATTAT
1 ATATATATTAT
33464 AT-TATA-TAT
1 ATATATATTAT
33473 ATATATA-TAT
1 ATATATATTAT
*
33483 ATA-ACGTATGAT
1 ATATA--TATTAT
*
33495 ATATCTATTATT
1 ATATATATTA-T
*
33507 ATATATATAAT
1 ATATATATTAT
33518 ATATATAT
1 ATATATAT
33526 AATTGTTTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
9 6 0.10
10 13 0.22
11 26 0.44
12 14 0.24
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (11 bp):
ATATATATTAT
Found at i:34561 original size:27 final size:28
Alignment explanation
Indices: 34526--34584 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
34516 AAAAAAAAAC
* *
34526 AATATTTTTACAAT-ATTTTAATGTAAA
1 AATATTTTTAAAATAATTTAAATGTAAA
*
34553 AATATTTTTAAAATAATTTAAATTTAAA
1 AATATTTTTAAAATAATTTAAATGTAAA
34581 AATA
1 AATA
34585 ATAGCTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 13 0.46
28 15 0.54
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (28 bp):
AATATTTTTAAAATAATTTAAATGTAAA
Found at i:35964 original size:63 final size:61
Alignment explanation
Indices: 35893--36019 Score: 209
Period size: 63 Copynumber: 2.0 Consensus size: 61
35883 TACCTATCGC
*
35893 CCTTTACTTCATTTTCTTTAAACTTTCTAACTTCAAAGATCCTCTAAAACCTTCAAAATAAAA
1 CCTTTACTTCATTTTCTTCAAACTTTCTAACTTC-AA-ATCCTCTAAAACCTTCAAAATAAAA
* *
35956 CCTTTACTTCATTTTCTTCAAACTTTCTAACTTCAAATCCTCTAAAACCTTCAAACTCAAA
1 CCTTTACTTCATTTTCTTCAAACTTTCTAACTTCAAATCCTCTAAAACCTTCAAAATAAAA
36017 CCT
1 CCT
36020 CAAATTTTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 26 0.43
62 2 0.03
63 33 0.54
ACGTcount: A:0.34, C:0.28, G:0.01, T:0.38
Consensus pattern (61 bp):
CCTTTACTTCATTTTCTTCAAACTTTCTAACTTCAAATCCTCTAAAACCTTCAAAATAAAA
Found at i:36334 original size:10 final size:10
Alignment explanation
Indices: 36307--36394 Score: 84
Period size: 10 Copynumber: 9.4 Consensus size: 10
36297 ATTGTTAAAT
36307 TTAATTAAG-G
1 TTAATT-AGTG
36317 TTAATTAGTG
1 TTAATTAGTG
36327 TTAATTAGT-
1 TTAATTAGTG
36336 TT-ATTAGT-
1 TTAATTAGTG
36344 TTCAATTAGT-
1 TT-AATTAGTG
36354 TT-ATTAGTG
1 TTAATTAGTG
36363 TTAATTAGT-
1 TTAATTAGTG
*
36372 TT-ATTAGGG
1 TTAATTAGTG
*
36381 TTAATTATTG
1 TTAATTAGTG
36391 TTAA
1 TTAA
36395 ATTAACTAAG
Statistics
Matches: 68, Mismatches: 3, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
8 19 0.28
9 10 0.15
10 39 0.57
ACGTcount: A:0.31, C:0.01, G:0.16, T:0.52
Consensus pattern (10 bp):
TTAATTAGTG
Found at i:36343 original size:18 final size:18
Alignment explanation
Indices: 36320--36387 Score: 111
Period size: 18 Copynumber: 3.8 Consensus size: 18
36310 ATTAAGGTTA
36320 ATTAGTGTTAATTAGTTT
1 ATTAGTGTTAATTAGTTT
36338 ATTAGT-TTCAATTAGTTT
1 ATTAGTGTT-AATTAGTTT
36356 ATTAGTGTTAATTAGTTT
1 ATTAGTGTTAATTAGTTT
*
36374 ATTAGGGTTAATTA
1 ATTAGTGTTAATTA
36388 TTGTTAAATT
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
17 2 0.04
18 43 0.91
19 2 0.04
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (18 bp):
ATTAGTGTTAATTAGTTT
Found at i:36459 original size:17 final size:17
Alignment explanation
Indices: 36439--36471 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
36429 CCAGATTACT
36439 AGTGATCCAAGATCACC
1 AGTGATCCAAGATCACC
*
36456 AGTGATGCAAGATCAC
1 AGTGATCCAAGATCAC
36472 TGGTAATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (17 bp):
AGTGATCCAAGATCACC
Found at i:38444 original size:21 final size:21
Alignment explanation
Indices: 38420--38460 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
38410 GTCATTGTCT
*
38420 ACTTCCACCAGTGCCTTTGAG
1 ACTTCCACCAGTGCATTTGAG
38441 ACTTCCACCAGTGCATTTGA
1 ACTTCCACCAGTGCATTTGA
38461 TTTGGCCTTC
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:0.22, C:0.32, G:0.17, T:0.29
Consensus pattern (21 bp):
ACTTCCACCAGTGCATTTGAG
Found at i:39046 original size:25 final size:25
Alignment explanation
Indices: 39018--39073 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
39008 CTGCATATAT
*
39018 ATGTTTAAACTTTAATATCAAATAC
1 ATGTTTAAACTTTAACATCAAATAC
* *
39043 ATGTTTAAATTTTAACATGAAATAC
1 ATGTTTAAACTTTAACATCAAATAC
39068 ATGTTT
1 ATGTTT
39074 CCAACTACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (25 bp):
ATGTTTAAACTTTAACATCAAATAC
Found at i:39130 original size:34 final size:34
Alignment explanation
Indices: 39056--39140 Score: 91
Period size: 34 Copynumber: 2.5 Consensus size: 34
39046 TTTAAATTTT
* * *
39056 AACATGAAATACATG-TTTCCAACTACAAACAAC
1 AACATCAAATACATGTTTTCCAACTAAAAACAAA
* * *
39089 AATATCAAATACATGTTTTCCAAGTAAAAAGAAA
1 AACATCAAATACATGTTTTCCAACTAAAAACAAA
* *
39123 AACATCAATTTCATGTTT
1 AACATCAAATACATGTTT
39141 AACAATACAT
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
33 13 0.31
34 29 0.69
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (34 bp):
AACATCAAATACATGTTTTCCAACTAAAAACAAA
Found at i:42695 original size:33 final size:33
Alignment explanation
Indices: 42577--42700 Score: 108
Period size: 32 Copynumber: 3.7 Consensus size: 33
42567 AATAGTGCAT
* *
42577 ATGACAACTTCTTGTGTCATTTTGAAAAGTAAAATC
1 ATGACAACTTCTGGTGTCA-ATTG-AAA-TAAAATC
* *
42613 GTGACAACTTCTGGTGTCAATT-AAATAAAATT
1 ATGACAACTTCTGGTGTCAATTGAAATAAAATC
* ** * **
42645 ATGACATCTTCAAGTGTCTATTGGAAAT-TTATC
1 ATGACAACTTCTGGTGTCAATT-GAAATAAAATC
42678 ATGACAACTTCTGGTGTCAATTG
1 ATGACAACTTCTGGTGTCAATTG
42701 TAAGACCATT
Statistics
Matches: 70, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
32 24 0.34
33 23 0.33
34 4 0.06
35 2 0.03
36 17 0.24
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (33 bp):
ATGACAACTTCTGGTGTCAATTGAAATAAAATC
Found at i:43032 original size:153 final size:151
Alignment explanation
Indices: 42789--43168 Score: 503
Period size: 153 Copynumber: 2.5 Consensus size: 151
42779 TGCAAAATCA
* * * *
42789 TGACAACTTCTGGTGTCAAGTGCAAAATCATGACAACTTCTT-GTGTCAATTGTAAGATCATGAC
1 TGACAACTTCTGATGTCAATTGGAAGATCATGACAACTT-TTGGTGTCAATTGTAAGATCATGAC
* * * * *
42853 AACTTCTAGTGTCAATTGTAAGATCATGACAACTTCTAGTGTCAATTGTAAGACCATGACAACTT
65 AACTTCTGGTGTAAATTGCAAAATCATGACAACTTCGAGTGTCAATTGTAAGACCATGACAACTT
* *
42918 CTGGTGTTATTTGTAAGATCA-
130 CTGGTGTCATTTGTAAGACCAT
* * * * *
42939 TGACAACTTCTGATGTCATTTGGAGATTTATCATGACAACTTTTGGTGTAAATTGCAAAATCATG
1 TGACAACTTCTGATGTCAATTGGA-A--GATCATGACAACTTTTGGTGTCAATTGTAAGATCATG
* *
43004 ACAACTTCTGGTGTAAATTGCAAAATCATGACAACTTCGGGTGTCATTTGTAAGACCATGACAAC
63 ACAACTTCTGGTGTAAATTGCAAAATCATGACAACTTCGAGTGTCAATTGTAAGACCATGACAAC
43069 TTCTGGTGTCATTTGTAAGACCAT
128 TTCTGGTGTCATTTGTAAGACCAT
* * * * *
43093 TGACAACTTCTGGTGTCAATTGTAAGATCATGACAACTTCTGGTGTCATTTGTAAGACCATGACA
1 TGACAACTTCTGATGTCAATTGGAAGATCATGACAACTTTTGGTGTCAATTGTAAGATCATGACA
43158 ACTTCTGGTGT
66 ACTTCTGGTGT
43169 CATTATATAT
Statistics
Matches: 198, Mismatches: 27, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
150 20 0.10
151 45 0.23
152 2 0.01
153 110 0.56
154 21 0.11
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (151 bp):
TGACAACTTCTGATGTCAATTGGAAGATCATGACAACTTTTGGTGTCAATTGTAAGATCATGACA
ACTTCTGGTGTAAATTGCAAAATCATGACAACTTCGAGTGTCAATTGTAAGACCATGACAACTTC
TGGTGTCATTTGTAAGACCAT
Found at i:43172 original size:30 final size:30
Alignment explanation
Indices: 42755--43170 Score: 501
Period size: 30 Copynumber: 13.7 Consensus size: 30
42745 TTTGAATAAA
* * * *
42755 ATCATGACATCTTCAT-GTGTCAGTTGCAAA
1 ATCATGACAACTTC-TGGTGTCAATTGTAAG
* * *
42785 ATCATGACAACTTCTGGTGTCAAGTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGTAAG
*
42815 ATCATGACAACTTCTTGTGTCAATTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGTAAG
*
42845 ATCATGACAACTTCTAGTGTCAATTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGTAAG
*
42875 ATCATGACAACTTCTAGTGTCAATTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGTAAG
* * *
42905 ACCATGACAACTTCTGGTGTTATTTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGTAAG
* * * *
42935 ATCATGACAACTTCTGATGTCATTTGGAGATTT
1 ATCATGACAACTTCTGGTGTCAATTGTA-A--G
* * * *
42968 ATCATGACAACTTTTGGTGTAAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGTAAG
* * *
42998 ATCATGACAACTTCTGGTGTAAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGTAAG
* *
43028 ATCATGACAACTTCGGGTGTCATTTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGTAAG
* *
43058 ACCATGACAACTTCTGGTGTCATTTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGTAAG
*
43088 ACCATTGACAACTTCTGGTGTCAATTGTAAG
1 ATCA-TGACAACTTCTGGTGTCAATTGTAAG
*
43119 ATCATGACAACTTCTGGTGTCATTTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGTAAG
*
43149 ACCATGACAACTTCTGGTGTCA
1 ATCATGACAACTTCTGGTGTCA
43171 TTATATATTA
Statistics
Matches: 346, Mismatches: 35, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
29 1 0.00
30 292 0.84
31 29 0.08
32 1 0.00
33 23 0.07
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (30 bp):
ATCATGACAACTTCTGGTGTCAATTGTAAG
Found at i:44188 original size:17 final size:19
Alignment explanation
Indices: 44152--44187 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44142 TGTAATCTTC
*
44152 CTTGGTTCTCTCATTAAAA
1 CTTGATTCTCTCATTAAAA
44171 CTTGATTCTCTC-TTAAA
1 CTTGATTCTCTCATTAAA
44188 CCTAAATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.44
Consensus pattern (19 bp):
CTTGATTCTCTCATTAAAA
Found at i:48361 original size:21 final size:21
Alignment explanation
Indices: 48318--48361 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
48308 AGAAAGGGGA
*
48318 TTGCTAAATATCGCCCTAGTT
1 TTGCTAAATATCGCCCCAGTT
*
48339 TTGCTAAATA-CTGCCCCATTT
1 TTGCTAAATATC-GCCCCAGTT
48360 TT
1 TT
48362 TACACTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.41
Consensus pattern (21 bp):
TTGCTAAATATCGCCCCAGTT
Found at i:48400 original size:16 final size:15
Alignment explanation
Indices: 48358--48403 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
48348 ACTGCCCCAT
48358 TTTTTACACTTTTAC
1 TTTTTACACTTTTAC
** *
48373 CCTTTACTCTTTGTAC
1 TTTTTACACTTT-TAC
48389 TTTTTACACTTTTAC
1 TTTTTACACTTTTAC
48404 ACTGAGCCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.17, C:0.24, G:0.02, T:0.57
Consensus pattern (15 bp):
TTTTTACACTTTTAC
Found at i:48449 original size:33 final size:33
Alignment explanation
Indices: 48408--48514 Score: 132
Period size: 32 Copynumber: 3.3 Consensus size: 33
48398 TTTTACACTG
* *
48408 AGCCTCCCCACTAGGACGG-TTCAGCCACGGCA
1 AGCCGCCCCACTGGGACGGCTTCAGCCACGGCA
* *
48440 GAGCCTCCCCACTGGGGCGGCTTC-GCCACGGCA
1 -AGCCGCCCCACTGGGACGGCTTCAGCCACGGCA
48473 AGCCGCCCTCA-TGGGACGGCTTCA-CCACGGCA
1 AGCCGCCC-CACTGGGACGGCTTCAGCCACGGCA
48505 AGCCGCCCCA
1 AGCCGCCCCA
48515 TCGTGGCGAA
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
31 2 0.03
32 34 0.51
33 28 0.42
34 3 0.04
ACGTcount: A:0.18, C:0.43, G:0.28, T:0.11
Consensus pattern (33 bp):
AGCCGCCCCACTGGGACGGCTTCAGCCACGGCA
Found at i:48559 original size:32 final size:32
Alignment explanation
Indices: 48516--48577 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
48506 GCCGCCCCAT
*
48516 CGTGGCGAAGCCATCCCACCGGGGCGGCCTGC
1 CGTGGCGAAGCCACCCCACCGGGGCGGCCTGC
* * **
48548 CGTGGCTAAGCCGCCCCAGTGGGGCGGCCT
1 CGTGGCGAAGCCACCCCACCGGGGCGGCCT
48578 TTTCATGGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.11, C:0.39, G:0.39, T:0.11
Consensus pattern (32 bp):
CGTGGCGAAGCCACCCCACCGGGGCGGCCTGC
Found at i:49191 original size:15 final size:16
Alignment explanation
Indices: 49158--49192 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
49148 TAAATATCAG
49158 TTTTATCAAACAAATT
1 TTTTATCAAACAAATT
*
49174 TTTTGTCAAACAAATT
1 TTTTATCAAACAAATT
49190 TTT
1 TTT
49193 CCATCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.49
Consensus pattern (16 bp):
TTTTATCAAACAAATT
Found at i:52652 original size:33 final size:33
Alignment explanation
Indices: 52554--52652 Score: 96
Period size: 33 Copynumber: 3.0 Consensus size: 33
52544 AGGTCGCGCG
*
52554 ACCC-GATCGCGACCCGGCCACGGT-TGGGTCGC
1 ACCCGGATCGCGACCC-GCCACGGTCCGGGTCGC
* * * * *
52586 GCGCGGGTCGCGACCCGCCCAC-GACCGAAGTCGC
1 ACCCGGATCGCGACCCG-CCACGGTCCG-GGTCGC
52620 ACCCGGATCGCGACCCGCCACGGTCCGGGTCGC
1 ACCCGGATCGCGACCCGCCACGGTCCGGGTCGC
52653 GTGCGATTAT
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
32 4 0.08
33 24 0.47
34 23 0.45
ACGTcount: A:0.13, C:0.43, G:0.34, T:0.09
Consensus pattern (33 bp):
ACCCGGATCGCGACCCGCCACGGTCCGGGTCGC
Done.