Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007151.1 Corchorus capsularis cultivar CVL-1 contig07172, 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: 88056
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:778 original size:31 final size:29
Alignment explanation
Indices: 709--780 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
699 TAAATGTTAC
* *
709 GCTCAATTTAGTATCTAACTTTCACAATT
1 GCTCAATTTAGTATCTAAATCTCACAATT
738 GCTCAATTTAGTA-CTAAATCTCATCAAATT
1 GCTCAATTTAGTATCTAAATCTCA-C-AATT
*
768 GATTCAATTTAGT
1 G-CTCAATTTAGT
781 CCTTTCCAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 8 0.22
29 14 0.38
30 5 0.14
31 10 0.27
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.40
Consensus pattern (29 bp):
GCTCAATTTAGTATCTAAATCTCACAATT
Found at i:965 original size:2 final size:2
Alignment explanation
Indices: 954--1006 Score: 67
Period size: 2 Copynumber: 28.0 Consensus size: 2
944 CTTTTCATAC
* *
954 AT AT -T AT AT AT AT AT AT AT AT GT GT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
994 AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT
1007 CAATTTGAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9416 original size:125 final size:128
Alignment explanation
Indices: 9214--9442 Score: 392
Period size: 126 Copynumber: 1.8 Consensus size: 128
9204 AAAATGATAA
*
9214 ATTAAACCTCTTCCTCTGGCAAAAAAAAAAACTCCTTTCTTCTTTGTATTATTTTTCTTATTTCT
1 ATTAAACCTCTTCCTCTGGCAAAAAAAAAAACTCCTTTCTTCTTTGTATTATTTTTCTTATTGCT
9279 CCTTCTTCTTTGTTTAAC-AAAACTCCCAAAACCAAAGTTTTTTTCTACGGTGATTTGTATAT
66 CCTTCTTCTTTGTTTAACAAAAACTCCCAAAACCAAAGTTTTTTTCTACGGTGATTTGTATAT
* * *
9341 ATTAAACCTCTTCCTCTGGCCAAAAAAAAAA-TCTTTTCTTCTTTGTATT-TTTTTGTTATTGCT
1 ATTAAACCTCTTCCTCTGGCAAAAAAAAAAACTCCTTTCTTCTTTGTATTATTTTTCTTATTGCT
*
9404 CCTTCTTCTTTGTTTAACAAAAACTCCCAACACCAAAGT
66 CCTTCTTCTTTGTTTAACAAAAACTCCCAAAACCAAAGT
9443 ACAATCACAT
Statistics
Matches: 96, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
125 30 0.31
126 36 0.38
127 30 0.31
ACGTcount: A:0.28, C:0.22, G:0.07, T:0.43
Consensus pattern (128 bp):
ATTAAACCTCTTCCTCTGGCAAAAAAAAAAACTCCTTTCTTCTTTGTATTATTTTTCTTATTGCT
CCTTCTTCTTTGTTTAACAAAAACTCCCAAAACCAAAGTTTTTTTCTACGGTGATTTGTATAT
Found at i:10632 original size:21 final size:21
Alignment explanation
Indices: 10589--10633 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
10579 AATGGAGATA
* * *
10589 ATGTCTCGGATAAACATGGAG
1 ATGTCTCGGACAAACAAGAAG
*
10610 ATGTCTCGGACAATCAAGAAG
1 ATGTCTCGGACAAACAAGAAG
10631 ATG
1 ATG
10634 CCAAGGTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.22
Consensus pattern (21 bp):
ATGTCTCGGACAAACAAGAAG
Found at i:17179 original size:21 final size:21
Alignment explanation
Indices: 17136--17180 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
17126 AATGGAGATA
* * *
17136 ATGTCTCGGATAAACATGGAG
1 ATGTCTCGGACAAACAAGAAG
*
17157 ATGTCTCGGACAATCAAGAAG
1 ATGTCTCGGACAAACAAGAAG
17178 ATG
1 ATG
17181 CCAAGGTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.22
Consensus pattern (21 bp):
ATGTCTCGGACAAACAAGAAG
Found at i:19555 original size:21 final size:21
Alignment explanation
Indices: 19522--19723 Score: 237
Period size: 21 Copynumber: 9.7 Consensus size: 21
19512 GAAACTTTAA
* *
19522 GGTTAGACTATCAATATTTGG
1 GGTTTGACTATCAAGATTTGG
* *
19543 GGTTTGACCATCAAAATTTGG
1 GGTTTGACTATCAAGATTTGG
*
19564 GATTTGACTATCAAGATTTGG
1 GGTTTGACTATCAAGATTTGG
*
19585 GGTTAGACTATCAAGATTTGG
1 GGTTTGACTATCAAGATTTGG
19606 GGTTTGACTATCAA-ATTTGG
1 GGTTTGACTATCAAGATTTGG
*
19626 GGTTTGATTATCAAGATTTGG
1 GGTTTGACTATCAAGATTTGG
* * *** *
19647 GGTGTGACCATTTTGATTTTG
1 GGTTTGACTATCAAGATTTGG
*
19668 GGTTTGACAATCAA-ACTTTGG
1 GGTTTGACTATCAAGA-TTTGG
*
19689 GGTTTGACCATCAAGATTTGG
1 GGTTTGACTATCAAGATTTGG
*
19710 GGTTTGACCATCAA
1 GGTTTGACTATCAA
19724 AAAGTTTTGT
Statistics
Matches: 154, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
20 20 0.13
21 133 0.86
22 1 0.01
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (21 bp):
GGTTTGACTATCAAGATTTGG
Found at i:22042 original size:196 final size:196
Alignment explanation
Indices: 21708--22098 Score: 764
Period size: 196 Copynumber: 2.0 Consensus size: 196
21698 TGAGAATCAC
*
21708 ATTTAAGTATTTAACCTATATAGCTATCTTAATGAAAGTTTATGTTTTTATTCTTTAAAAGTGGG
1 ATTTAAGTATTTAACCTATATAGCTATCTTAATGAAAGTTTATGTTTTTATTCTTTAAAAATGGG
21773 AGAGGAAGAAGATAAGTCAAATAAAATTTCTAAAACTCTTACCAATTATATTAATTACTTTTTTC
66 AGAGGAAGAAGATAAGTCAAATAAAATTTCTAAAACTCTTACCAATTATATTAATTACTTTTTTC
*
21838 TAATTATGTACTATACTCTGGAAAAATTTTATATTATTTTTAAATTTAATATTTGGATAATATTA
131 TAATTATGTACTATACTCTGGAAAAATTTTATATTATTTTTAAATTTAATATTTGGATAACATTA
21903 A
196 A
21904 ATTTAAGTATTTAACCTATATAGCTATCTTAATGAAAGTTTATGTTTTTATTCTTTAAAAATGGG
1 ATTTAAGTATTTAACCTATATAGCTATCTTAATGAAAGTTTATGTTTTTATTCTTTAAAAATGGG
21969 AGAGGAAGAAGATAAGTCAAATAAAATTTCTAAAACTCTTACCAATTATATTAATTACTTTTTTC
66 AGAGGAAGAAGATAAGTCAAATAAAATTTCTAAAACTCTTACCAATTATATTAATTACTTTTTTC
22034 TAATTATGTACTATACTCTGGAAAAATTTTATATTATTTTTAAATTTAATATTTGGATAACATTA
131 TAATTATGTACTATACTCTGGAAAAATTTTATATTATTTTTAAATTTAATATTTGGATAACATTA
22099 TCAAATATAC
Statistics
Matches: 193, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
196 193 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.43
Consensus pattern (196 bp):
ATTTAAGTATTTAACCTATATAGCTATCTTAATGAAAGTTTATGTTTTTATTCTTTAAAAATGGG
AGAGGAAGAAGATAAGTCAAATAAAATTTCTAAAACTCTTACCAATTATATTAATTACTTTTTTC
TAATTATGTACTATACTCTGGAAAAATTTTATATTATTTTTAAATTTAATATTTGGATAACATTA
A
Found at i:22748 original size:21 final size:21
Alignment explanation
Indices: 22695--22843 Score: 126
Period size: 21 Copynumber: 7.2 Consensus size: 21
22685 TATTTTATAT
* *
22695 TCAAGATTTGGGGATTGACTT
1 TCAAGAATTGGGGATTGACTA
* * *
22716 TCAA-ATTTGGGGTTTGACCA
1 TCAAGAATTGGGGATTGACTA
*
22736 TCAAGAATTGGGGTTTGACTA
1 TCAAGAATTGGGGATTGACTA
* *
22757 TCAAGATTTTGGGATTGACTA
1 TCAAGAATTGGGGATTGACTA
* *
22778 TC-A-AATTTGGGATTGTACCA
1 TCAAGAATTGGGGATTG-ACTA
*
22798 TCAAG-ATTAGGGGTTTGACTA
1 TCAAGAATT-GGGGATTGACTA
* * *
22819 TCAAGGATTGTGGATTGACTT
1 TCAAGAATTGGGGATTGACTA
22840 TCAA
1 TCAA
22844 ATGTCGGGTG
Statistics
Matches: 106, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
19 11 0.10
20 23 0.22
21 63 0.59
22 9 0.08
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.36
Consensus pattern (21 bp):
TCAAGAATTGGGGATTGACTA
Found at i:22754 original size:41 final size:42
Alignment explanation
Indices: 22695--22843 Score: 160
Period size: 41 Copynumber: 3.6 Consensus size: 42
22685 TATTTTATAT
* * *
22695 TCAAGATTTGGGGATTGACTTTCAA-ATTTGGGGTTTGACCA
1 TCAAGAATTGGGGATTGACTATCAAGATTTGGGGTTTGACTA
* * *
22736 TCAAGAATTGGGGTTTGACTATCAAGATTTTGGGATTGACTA
1 TCAAGAATTGGGGATTGACTATCAAGATTTGGGGTTTGACTA
* * *
22778 TC-A-AATTTGGGATTGTACCATCAAGATTAGGGGTTTGACTA
1 TCAAGAATTGGGGATTG-ACTATCAAGATTTGGGGTTTGACTA
* * *
22819 TCAAGGATTGTGGATTGACTTTCAA
1 TCAAGAATTGGGGATTGACTATCAA
22844 ATGTCGGGTG
Statistics
Matches: 87, Mismatches: 17, Indels: 7
0.78 0.15 0.06
Matches are distributed among these distances:
40 10 0.11
41 46 0.53
42 22 0.25
43 9 0.10
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.36
Consensus pattern (42 bp):
TCAAGAATTGGGGATTGACTATCAAGATTTGGGGTTTGACTA
Found at i:22798 original size:62 final size:62
Alignment explanation
Indices: 22695--22845 Score: 218
Period size: 62 Copynumber: 2.4 Consensus size: 62
22685 TATTTTATAT
* *
22695 TCAAGATTTGGGGATTGACTTTCAAATTTGGGGTTTGACCATCAAGAATT-GGGGTTTGACTA
1 TCAAGATTTTGGGATTGACTTTCAAATTTGGGATTTGACCATCAAG-ATTAGGGGTTTGACTA
*
22757 TCAAGATTTTGGGATTGACTATCAAATTTGGGA-TTGTACCATCAAGATTAGGGGTTTGACTA
1 TCAAGATTTTGGGATTGACTTTCAAATTTGGGATTTG-ACCATCAAGATTAGGGGTTTGACTA
*
22819 TCAAGGATTGT-GGATTGACTTTCAAAT
1 TCAA-GATTTTGGGATTGACTTTCAAAT
22846 GTCGGGTGTG
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
61 6 0.07
62 70 0.86
63 5 0.06
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (62 bp):
TCAAGATTTTGGGATTGACTTTCAAATTTGGGATTTGACCATCAAGATTAGGGGTTTGACTA
Found at i:24545 original size:33 final size:33
Alignment explanation
Indices: 24503--24565 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
24493 AAAATAGTCT
* *
24503 AGCCGCCCTAGTGGGGCGGTTCCGCCGTGGCTG
1 AGCCGCCCTAGTGGGGAGGCTCCGCCGTGGCTG
*
24536 AGCCGCCCTAGTGGGGAGGCTCCGCTGTGG
1 AGCCGCCCTAGTGGGGAGGCTCCGCCGTGG
24566 TTAAGGACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.08, C:0.32, G:0.43, T:0.17
Consensus pattern (33 bp):
AGCCGCCCTAGTGGGGAGGCTCCGCCGTGGCTG
Found at i:25500 original size:22 final size:21
Alignment explanation
Indices: 25475--25515 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25465 TTAAATATAT
* *
25475 ATTATTTATTTATTTTAAATTC
1 ATTATATA-TTATTTAAAATTC
25497 ATTATATATTATTTAAAAT
1 ATTATATATTATTTAAAAT
25516 ATATTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTATATATTATTTAAAATTC
Found at i:25525 original size:25 final size:24
Alignment explanation
Indices: 25497--25547 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
25487 TTTTAAATTC
*
25497 ATTATATATTATTTAAAATATAT-TT
1 ATTATATA-TA-TAAAAATATATATT
*
25522 ATTATTTATATAAAAATATATATT
1 ATTATATATATAAAAATATATATT
25546 AT
1 AT
25548 ATCTAAGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 10 0.43
24 6 0.26
25 7 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATTATATATATAAAAATATATATT
Found at i:31164 original size:184 final size:184
Alignment explanation
Indices: 30855--31218 Score: 692
Period size: 184 Copynumber: 2.0 Consensus size: 184
30845 ATTACCTCAA
*
30855 TACAAATGACTCTTTTAGTCTTGGTGAAATTGTGTGTCACCAAAAGATGCACCTTCTTCAGCCAT
1 TACAAATGACTCTTTTAGTCTTGGTGAAACTGTGTGTCACCAAAAGATGCACCTTCTTCAGCCAT
*
30920 CCTACATATAACAATTTCTCCCAAATACATACCAGGTATTTCCTTGTCATAAATCTGTGGTATAT
66 CCTACATATAACAATTTCTCCCAAATACATACCAGATATTTCCTTGTCATAAATCTGTGGTATAT
30985 GAAAAATTAAACAAATTTAATCATATAACACAAACGTACAAATTTTAAAAAACG
131 GAAAAATTAAACAAATTTAATCATATAACACAAACGTACAAATTTTAAAAAACG
* *
31039 TACAAATGACTCTTTTAGTCTTGGTGGAACTGTGTGTCACCAAAAGATGCACCTTCTTCAGTCAT
1 TACAAATGACTCTTTTAGTCTTGGTGAAACTGTGTGTCACCAAAAGATGCACCTTCTTCAGCCAT
31104 CCTACATATAACAATTTCTCCCAAATACATACCAGATATTTCCTTGTCATAAATCTGTGGTATAT
66 CCTACATATAACAATTTCTCCCAAATACATACCAGATATTTCCTTGTCATAAATCTGTGGTATAT
31169 GAAAAATTAAACAAATTTAATCATATAACACAAACGTACAAATTTTAAAA
131 GAAAAATTAAACAAATTTAATCATATAACACAAACGTACAAATTTTAAAA
31219 GACGCGAATG
Statistics
Matches: 176, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 176 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.32
Consensus pattern (184 bp):
TACAAATGACTCTTTTAGTCTTGGTGAAACTGTGTGTCACCAAAAGATGCACCTTCTTCAGCCAT
CCTACATATAACAATTTCTCCCAAATACATACCAGATATTTCCTTGTCATAAATCTGTGGTATAT
GAAAAATTAAACAAATTTAATCATATAACACAAACGTACAAATTTTAAAAAACG
Found at i:36378 original size:21 final size:21
Alignment explanation
Indices: 36341--36383 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
36331 TAACAATTAT
*
36341 AAATAAAAGCAATTAAACTAA
1 AAATAAAAGCAACTAAACTAA
*
36362 AAAT-AAAGCAAACTAAATTAA
1 AAATAAAAGC-AACTAAACTAA
36383 A
1 A
36384 TTTAAATCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.67, C:0.09, G:0.05, T:0.19
Consensus pattern (21 bp):
AAATAAAAGCAACTAAACTAA
Found at i:39304 original size:16 final size:16
Alignment explanation
Indices: 39283--39313 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39273 ACGAATAGGC
39283 AATCAATAAAAGCAAT
1 AATCAATAAAAGCAAT
*
39299 AATCAATCAAAGCAA
1 AATCAATAAAAGCAA
39314 AGCAAGAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.16, G:0.06, T:0.16
Consensus pattern (16 bp):
AATCAATAAAAGCAAT
Found at i:42606 original size:51 final size:51
Alignment explanation
Indices: 42454--42657 Score: 295
Period size: 51 Copynumber: 4.0 Consensus size: 51
42444 AGGAGTCTTG
* * **
42454 ATAATTACCATAATTATCTCTAATAATATAAAAAGATAATATGGTTAATAAAT
1 ATAATCACCATAATTATCTCTAAT-ATATATATGGATAATATGGTTAAT-AAT
42507 ATAATCACCATAATTATCTCT-A-ATATATATGGATAATATGGTTAATAAT
1 ATAATCACCATAATTATCTCTAATATATATATGGATAATATGGTTAATAAT
* *
42556 ATAATCACCATAATTATCTCTAATTTATATATTGATAATATGGTTAATAAT
1 ATAATCACCATAATTATCTCTAATATATATATGGATAATATGGTTAATAAT
* * *
42607 ATAATCACCATAATTATCTCTAATATATTTGTGGATATTATGGTTAATAAT
1 ATAATCACCATAATTATCTCTAATATATATATGGATAATATGGTTAATAAT
42658 GGTAACTGGT
Statistics
Matches: 138, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
49 24 0.17
50 22 0.16
51 71 0.51
52 1 0.01
53 20 0.14
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.40
Consensus pattern (51 bp):
ATAATCACCATAATTATCTCTAATATATATATGGATAATATGGTTAATAAT
Found at i:43301 original size:32 final size:34
Alignment explanation
Indices: 43234--43302 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 34
43224 CGAGGTGTTT
* *
43234 CCAGTTCACAGGGTATTACCAAGAACATGTATTA
1 CCAGTTCACAAGGTATTACCAACAACATGTATTA
* *
43268 CCAG-TCACAAGGTA-TACTAACAACATGTCTTA
1 CCAGTTCACAAGGTATTACCAACAACATGTATTA
43300 CCA
1 CCA
43303 ATTACATGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 18 0.58
33 9 0.29
34 4 0.13
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (34 bp):
CCAGTTCACAAGGTATTACCAACAACATGTATTA
Found at i:44380 original size:18 final size:18
Alignment explanation
Indices: 44353--44389 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
44343 TTATCCGCTT
44353 AGAAAAAGGAAAAGGAAA
1 AGAAAAAGGAAAAGGAAA
* *
44371 AGAAATAGGAAAGGGAAA
1 AGAAAAAGGAAAAGGAAA
44389 A
1 A
44390 ACAATGGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03
Consensus pattern (18 bp):
AGAAAAAGGAAAAGGAAA
Found at i:44908 original size:18 final size:18
Alignment explanation
Indices: 44885--44923 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
44875 ATAGATATAG
* *
44885 TGTGGGCCTAATTTGTAA
1 TGTGGGCCTAAATCGTAA
44903 TGTGGGCCTAAATCGTAA
1 TGTGGGCCTAAATCGTAA
44921 TGT
1 TGT
44924 AAGCTTTGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (18 bp):
TGTGGGCCTAAATCGTAA
Found at i:54962 original size:16 final size:19
Alignment explanation
Indices: 54928--54965 Score: 55
Period size: 16 Copynumber: 2.2 Consensus size: 19
54918 TACTATAAGG
54928 AAAATGTAATTAAAGTAAA
1 AAAATGTAATTAAAGTAAA
54947 AAAAT-TAA-TAAA-TAAA
1 AAAATGTAATTAAAGTAAA
54963 AAA
1 AAA
54966 CAGACAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 4 0.21
18 3 0.16
19 5 0.26
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAATGTAATTAAAGTAAA
Found at i:55426 original size:12 final size:13
Alignment explanation
Indices: 55396--55420 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55386 TACTTATTTT
55396 ATTTGTATGTTTA
1 ATTTGTATGTTTA
55409 ATTTGTATGTTT
1 ATTTGTATGTTT
55421 CATTGTTTAG
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:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (13 bp):
ATTTGTATGTTTA
Found at i:57946 original size:22 final size:22
Alignment explanation
Indices: 57901--57958 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
57891 TTCTATGAAC
* *
57901 TTTTGGTAACTACAATATGAAA
1 TTTTGGTAACCACAATAAGAAA
* *
57923 TTTTGGTAACCACACTAAGGAA
1 TTTTGGTAACCACAATAAGAAA
*
57945 TTTTGATAACCACA
1 TTTTGGTAACCACA
57959 TAAAGACTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (22 bp):
TTTTGGTAACCACAATAAGAAA
Found at i:58266 original size:26 final size:26
Alignment explanation
Indices: 58187--58267 Score: 69
Period size: 26 Copynumber: 3.1 Consensus size: 26
58177 TTTGCATGTA
* *
58187 TATATACTTTTATATACAGTCTAGAA
1 TATATACTTTTATATATAGTCTAGAT
* * *
58213 TATATA-TATCTA-A-ATAATCTCAAAAT
1 TATATACT-TTTATATATAGTCT--AGAT
58239 TATATACTTTTATATATAGTCTAGAT
1 TATATACTTTTATATATAGTCTAGAT
58265 TAT
1 TAT
58268 TGAGATATAT
Statistics
Matches: 41, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
24 5 0.12
25 2 0.05
26 26 0.63
27 2 0.05
28 6 0.15
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (26 bp):
TATATACTTTTATATATAGTCTAGAT
Found at i:58279 original size:2 final size:2
Alignment explanation
Indices: 58272--58321 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
58262 GATTATTGAG
* *
58272 AT AT AT AT AT AT AT AT AT AT -T AT CT AG 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
58313 AT AT AT AT A
1 AT AT AT AT A
58322 CACAACAACC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:68081 original size:36 final size:34
Alignment explanation
Indices: 67998--68081 Score: 105
Period size: 36 Copynumber: 2.4 Consensus size: 34
67988 GGCCTGGCAC
*
67998 GGCCCAAGTGCCCAGGCAAGGCGCGGGCCAGCTAT
1 GGCCCAA-TGCCCAGGCAAGGCGCGGGCCAGCCAT
** *
68033 GGCCCAGCGCCCAGGCCTAGTGCGCGGGCCAGCCAT
1 GGCCCAATGCCCAGG-CAAG-GCGCGGGCCAGCCAT
68069 GGCCCAATGCCCA
1 GGCCCAATGCCCA
68082 AGCTTGGGCT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
34 7 0.17
35 9 0.22
36 25 0.61
ACGTcount: A:0.18, C:0.39, G:0.35, T:0.08
Consensus pattern (34 bp):
GGCCCAATGCCCAGGCAAGGCGCGGGCCAGCCAT
Found at i:68211 original size:18 final size:17
Alignment explanation
Indices: 68162--68213 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 17
68152 AATAAAGTAA
*
68162 AGAAAAAAGGAAA-AAG
1 AGAAATAAGGAAATAAG
68178 AGAGAATAAGGAAAATAAGG
1 AGA-AATAAGG-AAATAA-G
68198 AGAAATAAGGAAATAA
1 AGAAATAAGGAAATAA
68214 AAAAGGGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 3 0.10
17 6 0.19
18 9 0.29
19 9 0.29
20 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.25, T:0.08
Consensus pattern (17 bp):
AGAAATAAGGAAATAAG
Found at i:68451 original size:27 final size:28
Alignment explanation
Indices: 68393--68466 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
68383 TATGGGCATA
* *
68393 AAATTACCGTTTTACCCTAAGTATGAGT
1 AAATTACCGTTTTACCCTTAGTAAGAGT
68421 -AATTACCGTTTTACCCTTAG-AAG-GTT
1 AAATTACCGTTTTACCCTTAGTAAGAG-T
*
68447 AAATTTACAGTTTTACCCTT
1 AAA-TTACCGTTTTACCCTT
68467 TTTAATCATG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 1 0.03
26 3 0.08
27 21 0.52
28 15 0.38
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (28 bp):
AAATTACCGTTTTACCCTTAGTAAGAGT
Found at i:74883 original size:63 final size:63
Alignment explanation
Indices: 74784--74915 Score: 264
Period size: 63 Copynumber: 2.1 Consensus size: 63
74774 ATGGCCCAGT
74784 GCCCAAGCTTGGGCTCCAAGCACAAGTTTAAAAAAATAAAAAAAATGAAAATGAATGGACTAG
1 GCCCAAGCTTGGGCTCCAAGCACAAGTTTAAAAAAATAAAAAAAATGAAAATGAATGGACTAG
74847 GCCCAAGCTTGGGCTCCAAGCACAAGTTTAAAAAAATAAAAAAAATGAAAATGAATGGACTAG
1 GCCCAAGCTTGGGCTCCAAGCACAAGTTTAAAAAAATAAAAAAAATGAAAATGAATGGACTAG
74910 GCCCAA
1 GCCCAA
74916 TTTTGAAATA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 69 1.00
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (63 bp):
GCCCAAGCTTGGGCTCCAAGCACAAGTTTAAAAAAATAAAAAAAATGAAAATGAATGGACTAG
Found at i:74981 original size:18 final size:17
Alignment explanation
Indices: 74926--74983 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
74916 TTTTGAAATA
*
74926 AAATAA-AGAAAAAAGG
1 AAATAAGAGAAATAAGG
*
74942 AAA-AAGAGAGAATAAGAA
1 AAATAAGAGA-AATAAG-G
74960 AAATAAGGAGAAATAAGG
1 AAATAA-GAGAAATAAGG
74978 AAATAA
1 AAATAA
74984 AAAAGGGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 2 0.06
16 6 0.18
17 5 0.15
18 9 0.26
19 8 0.24
20 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.09
Consensus pattern (17 bp):
AAATAAGAGAAATAAGG
Found at i:74982 original size:8 final size:9
Alignment explanation
Indices: 74926--74983 Score: 52
Period size: 8 Copynumber: 6.7 Consensus size: 9
74916 TTTTGAAATA
74926 AAATAA-AG
1 AAATAAGAG
*
74934 AAAAAAG-G
1 AAATAAGAG
74942 AAA-AAGAG
1 AAATAAGAG
*
74950 AGAATAAGAA
1 A-AATAAGAG
74960 AAATAAGGAG
1 AAATAA-GAG
74970 AAATAAG-G
1 AAATAAGAG
74978 AAATAA
1 AAATAA
74984 AAAAGGGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
7 3 0.07
8 18 0.43
9 8 0.19
10 13 0.31
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.09
Consensus pattern (9 bp):
AAATAAGAG
Found at i:75198 original size:27 final size:28
Alignment explanation
Indices: 75140--75213 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
75130 TATGGGCATA
* *
75140 AAATTACCGTTTTACCCTAAGTATGAGT
1 AAATTACCGTTTTACCCTTAGTAAGAGT
75168 -AATTACCGTTTTACCCTTAG-AAG-GTT
1 AAATTACCGTTTTACCCTTAGTAAGAG-T
*
75194 AAATTTACAGTTTTACCCTT
1 AAA-TTACCGTTTTACCCTT
75214 TTTAATCATG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 1 0.03
26 3 0.08
27 21 0.52
28 15 0.38
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (28 bp):
AAATTACCGTTTTACCCTTAGTAAGAGT
Found at i:77098 original size:134 final size:131
Alignment explanation
Indices: 76721--77108 Score: 584
Period size: 134 Copynumber: 2.9 Consensus size: 131
76711 AGGTTGCAAG
* * * * * *
76721 ACCCACACGAGTTTGAATGTGAGATCAATCATATCAA-ATATACAGTACTTCAATACATAGTTTG
1 ACCCACATGAGTTTGAATGTGAGATCATTCATGTGAACTTATACAGTTCTTCAATACATAGTTTG
76785 ATATATATAACCAAATTTAAATTAACCATGTTTTGAAACAAAGACATATTTTAGAAGACGTAATT
66 ATATATATAACCAAATTTAAATTAACCATGTTTTGAAACAAAGACATATTTTAGAAGACGTAATT
76850 A
131 A
* *
76851 ACCCACCTGAGTTTGAATGTGAGTTCATTCATGTGAACTTATACA-TTACTTCAATACATAGTTT
1 ACCCACATGAGTTTGAATGTGAGATCATTCATGTGAACTTATACAGTT-CTTCAATACATAGTTT
76915 GATATATATAACCAAATTTAAATTAACCATGTTTTGAAACAAAGACATATTTTAGAAGACGTAAT
65 GATATATATAACCAAATTTAAATTAACCATGTTTTGAAACAAAGACATATTTTAGAAGACGTAAT
76980 TAA
130 T-A
* * *
76983 ATCCCACATGATTATTGAATGTGAGATCTTTCATGTGAACTTATACAGTTCTTTAATACATA-TT
1 A-CCCACATGAGT-TTGAATGTGAGATCATTCATGTGAACTTATACAGTTCTTCAATACATAGTT
* * *
77047 CTGATATATAGAACCAAATTTAAATTAACCATGCTTTGAAACAAAGACATATTTCAGAAGAC
64 -TGATATATATAACCAAATTTAAATTAACCATGTTTTGAAACAAAGACATATTTTAGAAGAC
77109 ATAACTTATA
Statistics
Matches: 235, Mismatches: 16, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
130 32 0.14
131 88 0.37
132 2 0.01
133 11 0.05
134 100 0.43
135 2 0.01
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (131 bp):
ACCCACATGAGTTTGAATGTGAGATCATTCATGTGAACTTATACAGTTCTTCAATACATAGTTTG
ATATATATAACCAAATTTAAATTAACCATGTTTTGAAACAAAGACATATTTTAGAAGACGTAATT
A
Found at i:79893 original size:2 final size:2
Alignment explanation
Indices: 79886--79912 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
79876 ACAATTTAAA
79886 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 A
79913 ACAAAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:85199 original size:27 final size:27
Alignment explanation
Indices: 85169--85239 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 27
85159 ATTAGGGTCG
*
85169 CCCAGGGGCATTTTGGTCATTTTTGCA
1 CCCAGGGGCATTTTGGTCATTTTCGCA
85196 CCCAGGGGCATTTTGGTCATTTTCGCA
1 CCCAGGGGCATTTTGGTCATTTTCGCA
*
85223 CCC-GAGGGCATCTTGGT
1 CCCAG-GGGCATTTTGGT
85240 AAATCGGTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
26 1 0.02
27 40 0.98
ACGTcount: A:0.14, C:0.25, G:0.28, T:0.32
Consensus pattern (27 bp):
CCCAGGGGCATTTTGGTCATTTTCGCA
Done.