Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009421.1 Corchorus capsularis cultivar CVL-1 contig09442, 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: 65723
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3997 original size:12 final size:12
Alignment explanation
Indices: 3980--4009 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3970 AAATTGGAAT
*
3980 AATTTTTTCGGA
1 AATTTTTTCGAA
3992 AATTTTTTCGAA
1 AATTTTTTCGAA
4004 AATTTT
1 AATTTT
4010 GATTTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (12 bp):
AATTTTTTCGAA
Found at i:4314 original size:18 final size:18
Alignment explanation
Indices: 4291--4326 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4281 GGGTAGTTAA
4291 AAAAAAAATCTTTTTCAT
1 AAAAAAAATCTTTTTCAT
* *
4309 AAAAAAAGTGTTTTTCAT
1 AAAAAAAATCTTTTTCAT
4327 GCAAGAGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (18 bp):
AAAAAAAATCTTTTTCAT
Found at i:6561 original size:6 final size:6
Alignment explanation
Indices: 6550--6590 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
6540 ATTCTGCTTC
6550 AGATTT AGATTT AGATTT AGATTT AGATTT AGATTT A-ATTT
1 AGATTT AGATTT AGATTT AGATTT AGATTT AGATTT AGATTT
6591 TCTTTGCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (6 bp):
AGATTT
Found at i:7290 original size:3 final size:3
Alignment explanation
Indices: 7279--7349 Score: 117
Period size: 3 Copynumber: 23.3 Consensus size: 3
7269 TTTTAAAAAA
7279 AAT AA- AAT AAT AAAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT -AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
7325 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
7350 CAGAAATTAC
Statistics
Matches: 65, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.03
3 57 0.88
4 6 0.09
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10590 original size:56 final size:55
Alignment explanation
Indices: 10528--10640 Score: 172
Period size: 56 Copynumber: 2.0 Consensus size: 55
10518 TTGATAATTA
* * *
10528 AGAGTCAAGATAATAGTAATCAGTAAATTAGTAATTAAGTGAAAAAGAGATTAATC
1 AGAGTCAAGATAATAGTAATCAGTAAATCAGTAATCAAGT-AAAAAGAGAGTAATC
* *
10584 AGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGATAGTAATC
1 AGAGTCAAGATAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGAGAGTAATC
10639 AG
1 AG
10641 TAAATTGGTA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
55 15 0.29
56 37 0.71
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.25
Consensus pattern (55 bp):
AGAGTCAAGATAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGAGAGTAATC
Found at i:10635 original size:34 final size:34
Alignment explanation
Indices: 10596--10748 Score: 118
Period size: 34 Copynumber: 4.5 Consensus size: 34
10586 AGTCAAGGTA
10596 ATAGTAATCAGTAAATCAGTAATCAAGTAAAAAG
1 ATAGTAATCAGTAAATCAGTAATCAAGTAAAAAG
** *
10630 ATAGTAATCAGTAAATTGGTAATCAAG-AATCAAG
1 ATAGTAATCAGTAAATCAGTAATCAAGTAA-AAAG
* * * * * * *
10664 ---GTAA-GAGATTAATAAGTAATTAAGGAGTCAAGG
1 ATAGTAATCAG-TAAATCAGTAATCAAGTA--AAAAG
10697 TAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAG
1 --ATAGTAATCAGTAAATCAGTAATCAAGTAAAAAG
*
10733 ATAATAATCAGTAAAT
1 ATAGTAATCAGTAAAT
10749 TGATAATCAA
Statistics
Matches: 89, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
30 2 0.02
31 16 0.18
32 1 0.01
33 4 0.04
34 43 0.48
36 3 0.03
38 18 0.20
39 2 0.02
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.25
Consensus pattern (34 bp):
ATAGTAATCAGTAAATCAGTAATCAAGTAAAAAG
Found at i:10699 original size:103 final size:103
Alignment explanation
Indices: 10585--10785 Score: 375
Period size: 103 Copynumber: 2.0 Consensus size: 103
10575 AGATTAATCA
* *
10585 GAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGATAGTAATCAGTAAATTGGT
1 GAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGATAATAATCAGTAAATTGAT
10650 AATCAAGAATCAAGGTAAGAGATTAATAAGTAATTAAG
66 AATCAAGAATCAAGGTAAGAGATTAATAAGTAATTAAG
10688 GAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGATAATAATCAGTAAATTGAT
1 GAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGATAATAATCAGTAAATTGAT
*
10753 AATCAAGAATCAAGGTAAGAGATTAATCAGTAA
66 AATCAAGAATCAAGGTAAGAGATTAATAAGTAA
10786 AGTCAGTAAT
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 95 1.00
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.25
Consensus pattern (103 bp):
GAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGATAATAATCAGTAAATTGAT
AATCAAGAATCAAGGTAAGAGATTAATAAGTAATTAAG
Found at i:11018 original size:15 final size:15
Alignment explanation
Indices: 10982--11021 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
10972 AGTAAGATAG
10982 AAAGTAAAAAAGGTA
1 AAAGTAAAAAAGGTA
* *
10997 ATTAGTAAAAATGGTA
1 A-AAGTAAAAAAGGTA
11013 AAAGTAAAA
1 AAAGTAAAA
11022 GAAGCAGTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (15 bp):
AAAGTAAAAAAGGTA
Found at i:11211 original size:26 final size:25
Alignment explanation
Indices: 11170--11246 Score: 95
Period size: 24 Copynumber: 3.1 Consensus size: 25
11160 TAAAAAAATG
11170 AAGAGTAAAAATGGTATTAAGTAAAA
1 AAGAGTAAAAATGGTATTAAG-AAAA
* *
11196 AAG-GTTATAAATGGTATTAA-ACAA
1 AAGAG-TAAAAATGGTATTAAGAAAA
*
11220 AAGAGTAAAAATGGTATTAAGCAAA
1 AAGAGTAAAAATGGTATTAAGAAAA
11245 AA
1 AA
11247 TGGTATTAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
24 20 0.47
25 6 0.14
26 17 0.40
ACGTcount: A:0.56, C:0.03, G:0.18, T:0.23
Consensus pattern (25 bp):
AAGAGTAAAAATGGTATTAAGAAAA
Found at i:11247 original size:16 final size:18
Alignment explanation
Indices: 11226--11271 Score: 69
Period size: 16 Copynumber: 2.6 Consensus size: 18
11216 ACAAAAGAGT
11226 AAAAATGGTATTAA-G-C
1 AAAAATGGTATTAAGGTC
11242 AAAAATGGTATTAAGGGTC
1 AAAAATGGTATTAA-GGTC
11261 AAAAATGGTAT
1 AAAAATGGTAT
11272 CAAGTAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.52
18 1 0.04
19 12 0.44
ACGTcount: A:0.48, C:0.04, G:0.22, T:0.26
Consensus pattern (18 bp):
AAAAATGGTATTAAGGTC
Found at i:11341 original size:18 final size:19
Alignment explanation
Indices: 11303--11342 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
11293 TAAGAAGGTC
*
11303 AAAAAATGGTATTAATTTA
1 AAAAAATGGTATTAATGTA
11322 AAAAAATGGTATTAA-GTA
1 AAAAAATGGTATTAATGTA
11340 AAA
1 AAA
11343 GAGTAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.30
Consensus pattern (19 bp):
AAAAAATGGTATTAATGTA
Found at i:11370 original size:15 final size:15
Alignment explanation
Indices: 11350--11380 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11340 AAAGAGTAAG
*
11350 AAAAATGGTAAAAGT
1 AAAAATGATAAAAGT
11365 AAAAATGATAAAAGT
1 AAAAATGATAAAAGT
11380 A
1 A
11381 GCAAAAGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.19
Consensus pattern (15 bp):
AAAAATGATAAAAGT
Found at i:11474 original size:34 final size:34
Alignment explanation
Indices: 11386--11466 Score: 162
Period size: 34 Copynumber: 2.4 Consensus size: 34
11376 AAGTAGCAAA
11386 AGTAAAAATGGTAATCAATAAGAAGAGGATAATT
1 AGTAAAAATGGTAATCAATAAGAAGAGGATAATT
11420 AGTAAAAATGGTAATCAATAAGAAGAGGATAATT
1 AGTAAAAATGGTAATCAATAAGAAGAGGATAATT
11454 AGTAAAAATGGTA
1 AGTAAAAATGGTA
11467 GTTAATAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.53, C:0.02, G:0.21, T:0.23
Consensus pattern (34 bp):
AGTAAAAATGGTAATCAATAAGAAGAGGATAATT
Found at i:12293 original size:66 final size:66
Alignment explanation
Indices: 12208--12596 Score: 388
Period size: 66 Copynumber: 5.8 Consensus size: 66
12198 AAATTGAACG
* * * * * * *
12208 TAAACTTAGATGCACAAGACAAAAATGATCCTTCGACTGGAAGGGTATTTTTGGAAATGAAAATA
1 TAAACTTAAATGCAAAAGACAAAAATGACCCTTCCACCGAAAGGGTATTTTTGGAAAAGAAAATA
12273 C
66 C
* * * * ** * * *
12274 TAAACTTGAATACAAAAGACAATACTGACCCTTTGACCGAAAGGGTATTTTTGGGAATGAGAATA
1 TAAACTTAAATGCAAAAGACAAAAATGACCCTTCCACCGAAAGGGTATTTTTGGAAAAGAAAATA
12339 C
66 C
* * *
12340 CATACCTAAATGCAAAAGA-AGAAAATGACCCTTCCACCGAAAGGGTATTTTTTTTGGAAAAAGA
1 TAAACTTAAATGCAAAAGACA-AAAATGACCCTTCCACCGAAAGGGTA---TTTTTGG-AAAAGA
12404 AAATA-
61 AAATAC
* * * *
12409 TCAAACCTT-AATGCAAAAGGCGAAAATGACCCTTTCACCGAAAGGGTAATTTTGGAAAAAGAAA
1 T-AAA-CTTAAATGCAAAAGACAAAAATGACCCTTCCACCGAAAGGGTATTTTTGG-AAAAGAAA
12473 ATAC
63 ATAC
* * * * *
12477 TAAGCTTAAATGTGAGATGACAAAAAATGACCCTTCCACCGAAAGGGTACTTTTAGGAAAAGAAA
1 TAAACTTAAATG-CAAAAGAC-AAAAATGACCCTTCCACCGAAAGGGTA-TTTTTGGAAAAGAAA
12542 ATAC
63 ATAC
* *
12546 TAAACTTAAATGCAAAAGACGAAAATGACCCTTCCACCAAAAGGGTATTTT
1 TAAACTTAAATGCAAAAGACAAAAATGACCCTTCCACCGAAAGGGTATTTT
12597 CGTAAATTAA
Statistics
Matches: 264, Mismatches: 46, Indels: 26
0.79 0.14 0.08
Matches are distributed among these distances:
65 1 0.00
66 97 0.37
67 49 0.19
68 10 0.04
69 55 0.21
70 50 0.19
71 2 0.01
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (66 bp):
TAAACTTAAATGCAAAAGACAAAAATGACCCTTCCACCGAAAGGGTATTTTTGGAAAAGAAAATA
C
Found at i:12451 original size:136 final size:136
Alignment explanation
Indices: 12223--12596 Score: 397
Period size: 136 Copynumber: 2.8 Consensus size: 136
12213 TTAGATGCAC
* * * * * * * *
12223 AAGAC-AAAAATGATCCTTCGACTGGAAGGGTA-TTTTTGGAAATGAAAATACTAAACTTGAATA
1 AAGACAAAAAATGACCCTTCCACCGAAAGGGTACTTTTAGGAAAAGAAAATACTAAACTTAAATG
* * * * *
12286 CAAAAGAC-AATACTGACCCTTTGACCGAAAGGGTATTTTTGG-GAATGAGAATACCATA-CCTA
66 CAAAAGACGAA-AATGACCCTTTCACCGAAAGGGTATTTTTGGAAAAAGAAAATACCA-AGCCTA
12348 AATG-CAA
129 AATGTCAA
* * *
12355 AAGA-AGAAAATGACCCTTCCACCGAAAGGGTATTTTTTTTGGAAAAAGAAAATA-TCAAACCTT
1 AAGACAAAAAATGACCCTTCCACCGAAAGGGTA--CTTTTAGG-AAAAGAAAATACT-AAA-CTT
* * *
12418 -AATGCAAAAGGCGAAAATGACCCTTTCACCGAAAGGGTAATTTTGGAAAAAGAAAATACTAAGC
61 AAATGCAAAAGACGAAAATGACCCTTTCACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAGC
* * *
12482 TTAAATGTGAG
126 CTAAATGTCAA
*
12493 ATGACAAAAAATGACCCTTCCACCGAAAGGGTACTTTTAGGAAAAGAAAATACTAAACTTAAATG
1 AAGACAAAAAATGACCCTTCCACCGAAAGGGTACTTTTAGGAAAAGAAAATACTAAACTTAAATG
* *
12558 CAAAAGACGAAAATGACCCTTCCACCAAAAGGGTATTTT
66 CAAAAGACGAAAATGACCCTTTCACCGAAAGGGTATTTT
12597 CGTAAATTAA
Statistics
Matches: 202, Mismatches: 26, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
132 26 0.13
135 11 0.05
136 105 0.52
137 29 0.14
138 4 0.02
139 27 0.13
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (136 bp):
AAGACAAAAAATGACCCTTCCACCGAAAGGGTACTTTTAGGAAAAGAAAATACTAAACTTAAATG
CAAAAGACGAAAATGACCCTTTCACCGAAAGGGTATTTTTGGAAAAAGAAAATACCAAGCCTAAA
TGTCAA
Found at i:14030 original size:20 final size:20
Alignment explanation
Indices: 14005--14052 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
13995 CTCCAACTAA
* *
14005 ACTGAAACGAAAATGCCTAG
1 ACTGAAAAGAAAATGCCAAG
*
14025 ACTGAAAAGAAGATGCCAAG
1 ACTGAAAAGAAAATGCCAAG
*
14045 ACTCAAAA
1 ACTGAAAA
14053 TTTCAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (20 bp):
ACTGAAAAGAAAATGCCAAG
Found at i:16533 original size:2 final size:2
Alignment explanation
Indices: 16526--16551 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16516 TGATGAAAAT
16526 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
16552 CTCGAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17316 original size:192 final size:192
Alignment explanation
Indices: 16989--17366 Score: 738
Period size: 192 Copynumber: 2.0 Consensus size: 192
16979 TAAAAAATAG
*
16989 CACTATATCAAGGTCCTAAGAATTGATATCAAAGCCTATCTAGTTTTAAGGATAAAAATCTTTTG
1 CACTATATCAAGGTCCTAACAATTGATATCAAAGCCTATCTAGTTTTAAGGATAAAAATCTTTTG
17054 GGAAAAATCTAAAAATGGCATTTACAAGCAACACTACCATGGAGGGTAAATCTATCAATAGGCCA
66 GGAAAAATCTAAAAATGGCATTTACAAGCAACACTACCATGGAGGGTAAATCTATCAATAGGCCA
17119 ACACTATTTGATGGAAGACTCTTGGTTAATATATATTTAAGAGTAAATTACATATAAAACAA
131 ACACTATTTGATGGAAGACTCTTGGTTAATATATATTTAAGAGTAAATTACATATAAAACAA
17181 CACTATATCAAGGTCCTAACAATTGATATCAAAGCCTATCTAGTTTTAAGGATAAAAATCTTTTG
1 CACTATATCAAGGTCCTAACAATTGATATCAAAGCCTATCTAGTTTTAAGGATAAAAATCTTTTG
*
17246 GGAAAAATCTAAAAATGTCATTTACAAGCAACACTACCATGGAGGGTAAATCTATCAATAGGCCA
66 GGAAAAATCTAAAAATGGCATTTACAAGCAACACTACCATGGAGGGTAAATCTATCAATAGGCCA
17311 ACACTATTTGATGGAAGACTCTTGGTTAATATATATTTAAGAGTAAATTACATATA
131 ACACTATTTGATGGAAGACTCTTGGTTAATATATATTTAAGAGTAAATTACATATA
17367 TGGTCACTTA
Statistics
Matches: 184, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
192 184 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (192 bp):
CACTATATCAAGGTCCTAACAATTGATATCAAAGCCTATCTAGTTTTAAGGATAAAAATCTTTTG
GGAAAAATCTAAAAATGGCATTTACAAGCAACACTACCATGGAGGGTAAATCTATCAATAGGCCA
ACACTATTTGATGGAAGACTCTTGGTTAATATATATTTAAGAGTAAATTACATATAAAACAA
Found at i:22852 original size:22 final size:21
Alignment explanation
Indices: 22827--22868 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
22817 GAAGTGGTTT
*
22827 ATGTGATTGAGGTTGGATTTTA
1 ATGTGATTGAAGTT-GATTTTA
*
22849 ATGTTATTGAAGTTGATTTT
1 ATGTGATTGAAGTTGATTTT
22869 GGATTTGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (21 bp):
ATGTGATTGAAGTTGATTTTA
Found at i:23758 original size:14 final size:13
Alignment explanation
Indices: 23728--23770 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
23718 TTATTACTAC
*
23728 TTTTAATAAATTGT
1 TTTTATTAAA-TGT
23742 TTTTA-TAAATGAT
1 TTTTATTAAATG-T
23755 TTTTATTAAATGT
1 TTTTATTAAATGT
23768 TTT
1 TTT
23771 GGGTGCATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 2 0.07
13 14 0.52
14 11 0.41
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (13 bp):
TTTTATTAAATGT
Found at i:25217 original size:21 final size:22
Alignment explanation
Indices: 25169--25219 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
25159 GCGTCAGAGA
*
25169 TATGGGGCCCAAGTTCCACCAT
1 TATGGGGCCCAAGGTCCACCAT
* *
25191 T-CGGGGCCCAAGGTCCATC-T
1 TATGGGGCCCAAGGTCCACCAT
25211 TATGGGGCC
1 TATGGGGCC
25220 GCCCAACCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.08
21 21 0.88
22 1 0.04
ACGTcount: A:0.18, C:0.31, G:0.29, T:0.22
Consensus pattern (22 bp):
TATGGGGCCCAAGGTCCACCAT
Found at i:30193 original size:2 final size:2
Alignment explanation
Indices: 30186--30211 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30176 TCATGCTAGA
30186 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
30212 TATGAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:32519 original size:17 final size:17
Alignment explanation
Indices: 32474--32517 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
32464 TCCAACATAT
32474 AATC-CTAATTTTACAA
1 AATCTCTAATTTTACAA
*
32490 AATCTCT-ATTTTACCA
1 AATCTCTAATTTTACAA
32506 AAT-TCTAATTTT
1 AATCTCTAATTTT
32518 TATGGAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 3 0.12
16 20 0.80
17 2 0.08
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.45
Consensus pattern (17 bp):
AATCTCTAATTTTACAA
Found at i:39503 original size:10 final size:10
Alignment explanation
Indices: 39488--39513 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
39478 AATTTAATAT
39488 GGATATTTAC
1 GGATATTTAC
39498 GGATATTTAC
1 GGATATTTAC
39508 GGATAT
1 GGATAT
39514 ATCGAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:39641 original size:12 final size:12
Alignment explanation
Indices: 39624--39662 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
39614 GTACAGGTAT
39624 CGGATATATCGA
1 CGGATATATCGA
39636 CGGATATATCGA
1 CGGATATATCGA
39648 -GG---TATCGA
1 CGGATATATCGA
39656 CGGATAT
1 CGGATAT
39663 TTAATTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:42672 original size:114 final size:114
Alignment explanation
Indices: 42465--42672 Score: 292
Period size: 114 Copynumber: 1.8 Consensus size: 114
42455 AATTATTTTG
* * * *
42465 ATTTTGGTGATCATGAGTATAGGTAAAATTGATTGTTAATAAGTCAAAGAGAATTGTTTGGAAAG
1 ATTTTGATGATCATGAGTATAGGTAAAACTGATTGTTAACAAGTCAAACAGAATTGTTTGGAAAG
* * **
42530 AGTGAACAGAATACCTTCCTTCTGATGAATTTTAATATTGTTTTTAATT
66 AGTGAAAAGAATACCTTCCATCCAATGAATTTTAATATTGTTTTTAATT
* * * *
42579 ATTTTGATGATCATGAGTATAGGTAGAACTGATTGTTGACAAGTGAAACATAATTGTTTGGAAAG
1 ATTTTGATGATCATGAGTATAGGTAAAACTGATTGTTAACAAGTCAAACAGAATTGTTTGGAAAG
42644 AGTGAAAAGAATACGC-TCCATCCAATGAA
66 AGTGAAAAGAATAC-CTTCCATCCAATGAA
42673 CTTGCTTAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
114 80 0.99
115 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.35
Consensus pattern (114 bp):
ATTTTGATGATCATGAGTATAGGTAAAACTGATTGTTAACAAGTCAAACAGAATTGTTTGGAAAG
AGTGAAAAGAATACCTTCCATCCAATGAATTTTAATATTGTTTTTAATT
Found at i:50487 original size:2 final size:2
Alignment explanation
Indices: 50482--50508 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
50472 TTGAAGATTA
50482 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
50509 CTAGTAACTG
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:59325 original size:18 final size:18
Alignment explanation
Indices: 59304--59369 Score: 87
Period size: 18 Copynumber: 3.7 Consensus size: 18
59294 GGATTTAGAG
59304 GATGATGTTGACCCAGAT
1 GATGATGTTGACCCAGAT
*
59322 GATGGTGTTGACCCAGAT
1 GATGATGTTGACCCAGAT
* * *
59340 GATGATTTTGATCCAAAT
1 GATGATGTTGACCCAGAT
*
59358 GATGATCTTGAC
1 GATGATGTTGAC
59370 GAGGATTTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (18 bp):
GATGATGTTGACCCAGAT
Found at i:59528 original size:15 final size:15
Alignment explanation
Indices: 59498--59557 Score: 84
Period size: 15 Copynumber: 4.0 Consensus size: 15
59488 GTATCCGTCA
* *
59498 GACGGCAAGGAAGTC
1 GACGGCTAGGATGTC
* *
59513 GACTGCGAGGATGTC
1 GACGGCTAGGATGTC
59528 GACGGCTAGGATGTC
1 GACGGCTAGGATGTC
59543 GACGGCTAGGATGTC
1 GACGGCTAGGATGTC
59558 TGTCATAGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.23, C:0.20, G:0.40, T:0.17
Consensus pattern (15 bp):
GACGGCTAGGATGTC
Found at i:64554 original size:19 final size:18
Alignment explanation
Indices: 64530--64566 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
64520 TTGAAGATTT
64530 TTTGAAGATAATTTGAAGA
1 TTTGAAGATAA-TTGAAGA
*
64549 TTTGAAGATCATTGAAGA
1 TTTGAAGATAATTGAAGA
64567 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.35
Consensus pattern (18 bp):
TTTGAAGATAATTGAAGA
Done.