Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013249.1 Corchorus olitorius cultivar O-4 contig13282, 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: 53519
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:263 original size:27 final size:27
Alignment explanation
Indices: 225--324 Score: 173
Period size: 27 Copynumber: 3.7 Consensus size: 27
215 ACCCGAGGCA
*
225 AAGTGGGAGGATCCACTGTTGGGGTCG
1 AAGTGGGAGGATCCACTGCTGGGGTCG
*
252 AAGTGTGAGGATCCACTGCTGGGGTCG
1 AAGTGGGAGGATCCACTGCTGGGGTCG
*
279 AAGTGGGAGGATCCACTGCTGGGGTAG
1 AAGTGGGAGGATCCACTGCTGGGGTCG
306 AAGTGGGAGGATCCACTGC
1 AAGTGGGAGGATCCACTGC
325 GGCATCAGTC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.21, C:0.17, G:0.42, T:0.20
Consensus pattern (27 bp):
AAGTGGGAGGATCCACTGCTGGGGTCG
Found at i:3378 original size:102 final size:102
Alignment explanation
Indices: 3211--3414 Score: 381
Period size: 102 Copynumber: 2.0 Consensus size: 102
3201 AAAAATATCT
3211 CTCCCTCCATATATTAATATGGCGGCGTCTTTCTGTCAAAACGCCACTAAATGGCGGCGTCTGAA
1 CTCCCTCCATATATTAATATGGCGGCGTCTTTCTGTCAAAACGCCACTAAATGGCGGCGTCTGAA
*
3276 AAATAGACGCCGCTATAGTCAATTTCAGAAAATCATA
66 AAAAAGACGCCGCTATAGTCAATTTCAGAAAATCATA
*
3313 CTCCCTCCATATATTAATATGGCGGCGTCTTTCTGTCAAAATGCCACTAAATGGCGGCGTCTGAA
1 CTCCCTCCATATATTAATATGGCGGCGTCTTTCTGTCAAAACGCCACTAAATGGCGGCGTCTGAA
*
3378 AAAAAGATGCCGCTATAGTCAATTTCAGAAAATCATA
66 AAAAAGACGCCGCTATAGTCAATTTCAGAAAATCATA
3415 TAGCGGCGTT
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 99 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (102 bp):
CTCCCTCCATATATTAATATGGCGGCGTCTTTCTGTCAAAACGCCACTAAATGGCGGCGTCTGAA
AAAAAGACGCCGCTATAGTCAATTTCAGAAAATCATA
Found at i:5017 original size:25 final size:24
Alignment explanation
Indices: 4980--5026 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
4970 CTAGAAAATT
4980 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
5006 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
5027 AATAGAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:5810 original size:65 final size:65
Alignment explanation
Indices: 5701--5830 Score: 233
Period size: 65 Copynumber: 2.0 Consensus size: 65
5691 GGAAAAACTG
* *
5701 GTCCTACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTTGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
*
5766 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCATGCCTGGGCTAGTGCAGAAAGTTGGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
5831 AATAGCAAGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.21, C:0.30, G:0.27, T:0.22
Consensus pattern (65 bp):
GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGCAGAAAGTTGGAATC
Found at i:6046 original size:21 final size:21
Alignment explanation
Indices: 6020--6061 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
6010 GCATCTTAGG
*
6020 CAACTCCGATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
6041 CAACTCCAATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
6062 TTCTTTGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.19
Consensus pattern (21 bp):
CAACTCCAATGAGCTTGAAAC
Found at i:7966 original size:15 final size:15
Alignment explanation
Indices: 7946--7977 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
7936 AAGAAAATTA
*
7946 AAGAAAACAATTAAT
1 AAGAAAACAATGAAT
7961 AAGAAAACAATGAAT
1 AAGAAAACAATGAAT
7976 AA
1 AA
7978 ACTAAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.16
Consensus pattern (15 bp):
AAGAAAACAATGAAT
Found at i:10128 original size:33 final size:31
Alignment explanation
Indices: 10078--10145 Score: 75
Period size: 31 Copynumber: 2.1 Consensus size: 31
10068 TTCTCCTCTT
10078 ATCATGAAAATACTTTTTCATATCACAACTACA
1 ATCATGAAAATACTTTTT-A-ATCACAACTACA
* * *
10111 ATCAT-AACATACTTTTTTAATCATAACTTCA
1 ATCATGAAAATAC-TTTTTAATCACAACTACA
10142 ATCA
1 ATCA
10146 AGATTCAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
31 14 0.45
32 7 0.23
33 10 0.32
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (31 bp):
ATCATGAAAATACTTTTTAATCACAACTACA
Found at i:15719 original size:16 final size:16
Alignment explanation
Indices: 15698--15728 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15688 AGGAATAAGC
*
15698 AATCAATCGAAGCAAT
1 AATCAATCAAAGCAAT
15714 AATCAATCAAAGCAA
1 AATCAATCAAAGCAA
15729 CAATGCAAAG
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:0.55, C:0.19, G:0.10, T:0.16
Consensus pattern (16 bp):
AATCAATCAAAGCAAT
Found at i:17653 original size:31 final size:29
Alignment explanation
Indices: 17617--17684 Score: 75
Period size: 29 Copynumber: 2.2 Consensus size: 29
17607 AATGCAAAGA
17617 AGAAAAGAGAAGAAAGAAAT-TTTTTTTTTTT
1 AGAAAA-AGAAG-AA-AAATCTTTTTTTTTTT
* *
17648 AGAAAACGAAGAAAACTCTTTTTTTTTTT
1 AGAAAAAGAAGAAAAATCTTTTTTTTTTT
17677 AGATAAAA
1 AGA-AAAA
17685 AGCGCAGGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 3 0.09
29 16 0.50
30 7 0.22
31 6 0.19
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.37
Consensus pattern (29 bp):
AGAAAAAGAAGAAAAATCTTTTTTTTTTT
Found at i:26509 original size:13 final size:13
Alignment explanation
Indices: 26491--26520 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
26481 ATCAATAGTT
26491 TAGTTTAAGTTTC
1 TAGTTTAAGTTTC
26504 TAGTTTAAGTTTC
1 TAGTTTAAGTTTC
26517 -AGTT
1 TAGTT
26521 CAGACAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.53
Consensus pattern (13 bp):
TAGTTTAAGTTTC
Found at i:28077 original size:30 final size:30
Alignment explanation
Indices: 28006--28982 Score: 1279
Period size: 30 Copynumber: 32.2 Consensus size: 30
27996 AAATTAATTT
* * * *
28006 ATAATGCAATAATCCTAAATCAGGATTAACTG
1 ATAAAGCAATGATCCTAAACCAGGATTAA--A
* *
28038 ATGAAGCAATGATCCTAAACCATGATTAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
*
28068 CTAAAGCAATGATCCTAAACCAGGATTAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* *
28098 ATAAAGCAAAGATCCTAAACCAAGATTAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
*
28128 ATAAAGCAATGACCCTAAACCAGGATTAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* *
28158 ATAAAGCAATGATCCTCAACTAGGATTAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* * *
28188 ATAAAGTAATGATCCTCAACCAGGATTAAG
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* *
28218 ATGAAGCAATGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* * *
28248 ATAATGCAATGATCCTAAAGCAGGATAAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* * *
28278 ATGAAGCAATGATCCTCAACCAGGATTGAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
*
28308 ATAAAGCAATGATCCTAAACCAGGATTGAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* *
28338 ATGAAGCAATGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* * *
28368 ATAATGCAATGATCCTCAACCAGGATTGAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
*
28398 ATAAAGCAATGATCCTAAACTAGGATTAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
*
28428 ATAAAGCAATGATCCTAAACCAGGATAAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
*
28458 ATAAAGCAATGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* *
28488 ATAAAGCAATGATCCTAAACTAGGATAAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* * *
28518 ATGAAGCAATGATCCTAAACCAAGATTGAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* *
28548 ATGAAGCAATGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* * *
28578 ATAATGCAATGATCCTCAACCAGGATTGAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* *
28608 ATAAAGCAATGATCCTTAACTAGGATTAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
*
28638 ATAAAGTAATGATCCTAAACCAGGATTAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
*
28668 ATAAAGCAATGATCCTAAACTAGGATTGAAAGTAAA
1 ATAAAGCAATGATCCTAAACCAGGA-T-----TAAA
*
28704 CTGATAAAGCAATGATCCTAAACCAGGATTGAA
1 ---ATAAAGCAATGATCCTAAACCAGGATTAAA
* * *
28737 ATGAAGTAATGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* * *
28767 ATAATGCAATGATCCTCAACCAGGATTGAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* *
28797 ATAAAGCAATGATCCTTAACTAGGATTAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* * *
28827 ATCAAGTAATGATCCTAAACCAGGATAAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
* *
28857 ATAAAGCAATGATCCTCAACCAGGATCAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
*
28887 ATAAAGCAATGATCCTAAACCAGGATAAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
28917 ATAAAGCAATGATCCTAAACCAGGATTAAA
1 ATAAAGCAATGATCCTAAACCAGGATTAAA
*
28947 ATAAAGCAATTATCCTAAACCAGGATTGAAA
1 ATAAAGCAATGATCCTAAACCAGGATT-AAA
*
28978 GTAAA
1 ATAAA
28983 TTGATAAAGC
Statistics
Matches: 833, Mismatches: 102, Indels: 21
0.87 0.11 0.02
Matches are distributed among these distances:
30 769 0.92
31 8 0.01
32 24 0.03
33 3 0.00
36 4 0.00
38 1 0.00
39 24 0.03
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (30 bp):
ATAAAGCAATGATCCTAAACCAGGATTAAA
Found at i:29005 original size:39 final size:39
Alignment explanation
Indices: 28947--29030 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 39
28937 CAGGATTAAA
* * * *
28947 ATAAAGCAATTATCCTAAACCAGGATTGAAAGTAAATTG
1 ATAAAGCAATGATACTAAACCAGGATCGAAAATAAATTG
*
28986 ATAAAGCAATGATATTAAACCAGGATCGAAAATAAATTG
1 ATAAAGCAATGATACTAAACCAGGATCGAAAATAAATTG
*
29025 AAAAAG
1 ATAAAG
29031 TAGAATAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.51, C:0.11, G:0.15, T:0.23
Consensus pattern (39 bp):
ATAAAGCAATGATACTAAACCAGGATCGAAAATAAATTG
Found at i:29093 original size:20 final size:20
Alignment explanation
Indices: 29056--29096 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29046 AGAAAATATG
* *
29056 AAATGCCCAGATGTCTTATC
1 AAATGCCCAGAGGACTTATC
*
29076 AAATGCCCGGAGGACTTATC
1 AAATGCCCAGAGGACTTATC
29096 A
1 A
29097 GAATTAATAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (20 bp):
AAATGCCCAGAGGACTTATC
Found at i:29373 original size:170 final size:170
Alignment explanation
Indices: 29071--29577 Score: 680
Period size: 170 Copynumber: 3.0 Consensus size: 170
29061 CCCAGATGTC
* **
29071 TTATCAAATGCCCGGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAATTTGTGCCCAAAGG
1 TTATCAATTGCCCGGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAATTTGTGCCCGGAGG
* * * * * **
29136 ACATACCAATGCAAACTTTTAATTGAGATCTTAAACAAGGATCTTAAGTTTAAACATGAACTTTT
66 ACTTACCAATGCAAACTTTAAATTGAGACCTTGAACAAGGATTTTAAACTTAAACATGAA-TTTT
*
29201 TGATGAAAAACTTGATGAAATTAAATTGTACCCGGAGG-TT
130 TGATGAAAAACTTGATGAAATCAAATTGTACCCGGAGGCTT
* * *
29241 TTATCAATTGCCCGAAGGACTTATCAGAATTAATACCC-GAAGGTTTTTGCATTTTGTGCCCGGA
1 TTATCAATTGCCCGGAGGACTTATCAGAATTAATACCCAG-AGGTTTCTG-AATTTGTGCCCGGA
* ** * * *
29305 GGACTTACCAATGTAAACACTAAATAGAGACCTTGACCAAGGATTTTAAACTAAAACATGAATTT
64 GGACTTACCAATGCAAACTTTAAATTGAGACCTTGAACAAGGATTTTAAACTTAAACATGAATTT
* * *
29370 TTGATG-AAAACTTGATAAAATGAAA-TGATACCAGGAGGCTT
129 TTGATGAAAAACTTGATGAAATCAAATTG-TACCCGGAGGCTT
* * *
29411 TTACCAATTGCCTGGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAATTTGCGCCCGGAGG
1 TTATCAATTGCCCGGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAATTTGTGCCCGGAGG
* * *
29476 ACTTACCAATGCAAACTTTGAATTGAAACCTTGAACAAGGATTTTAAACTTAAACATGAATCTTT
66 ACTTACCAATGCAAACTTTAAATTGAGACCTTGAACAAGGATTTTAAACTTAAACATGAATTTTT
*
29541 GATGAAAAACTTGATGAAATCAAATGGTACCCGGAGG
131 GATGAAAAACTTGATGAAATCAAATTGTACCCGGAGG
29578 ACTTATCAGA
Statistics
Matches: 289, Mismatches: 41, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
168 2 0.01
169 101 0.35
170 124 0.43
171 62 0.21
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.29
Consensus pattern (170 bp):
TTATCAATTGCCCGGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAATTTGTGCCCGGAGG
ACTTACCAATGCAAACTTTAAATTGAGACCTTGAACAAGGATTTTAAACTTAAACATGAATTTTT
GATGAAAAACTTGATGAAATCAAATTGTACCCGGAGGCTT
Found at i:29734 original size:149 final size:149
Alignment explanation
Indices: 29424--29726 Score: 579
Period size: 149 Copynumber: 2.0 Consensus size: 149
29414 CCAATTGCCT
29424 GGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAATTTGCGCCCGGAGGACTTACCAATGCA
1 GGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAATTTGCGCCCGGAGGACTTACCAATGCA
*
29489 AACTTTGAATTGAAACCTTGAACAAGGATTTTAAACTTAAACATGAATCTTTGATGAAAAACTTG
66 AACCTTGAATTGAAACCTTGAACAAGGATTTTAAACTTAAACATGAATCTTTGATGAAAAACTTG
29554 ATGAAATCAAATGGTACCC
131 ATGAAATCAAATGGTACCC
* *
29573 GGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAATGCA
1 GGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAATTTGCGCCCGGAGGACTTACCAATGCA
29638 AACCTTGAATTGAAACCTTGAACAAGGATTTTAAACTTAAACATGAATCTTTGATGAAAAACTTG
66 AACCTTGAATTGAAACCTTGAACAAGGATTTTAAACTTAAACATGAATCTTTGATGAAAAACTTG
29703 ATGAAATCAAATGGTACCC
131 ATGAAATCAAATGGTACCC
29722 GGAGG
1 GGAGG
29727 TTTTATCAAT
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (149 bp):
GGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAATTTGCGCCCGGAGGACTTACCAATGCA
AACCTTGAATTGAAACCTTGAACAAGGATTTTAAACTTAAACATGAATCTTTGATGAAAAACTTG
ATGAAATCAAATGGTACCC
Found at i:29870 original size:318 final size:319
Alignment explanation
Indices: 29251--29887 Score: 994
Period size: 318 Copynumber: 2.0 Consensus size: 319
29241 TTATCAATTG
* *
29251 CCCGAAGGACTTATCAGAATTAATACCCGAAGGTTTTTGCATTTTGTGCCCGGAGGACTTACCAA
1 CCCGAAGGACTTATCAGAATTAATACCCGAAGGTTTCTGCAATTTGTGCCCGGAGGACTTACCAA
* * * *
29316 TGTAAACACTAAATAGAGACCTTGACCAAGGATTTTAAACTAAAACATGAATTTTTGATGAAAAC
66 TGCAAACACTAAATAGAAACCTTGAACAAGGATTTTAAACTAAAACATGAATCTTTGATGAAAAC
* *
29381 TTGATAAAATGAAATGATACCAGGAGGCTTTTACCAATTGCCTGGAGGACTTATCAGAATTAATA
131 TTGATAAAATCAAATGATACCAGGAGGCTTTTACCAATTGCCCGGAGGACTTATCAGAATTAATA
* * * *
29446 CCCAGAGGTTTCTGAATTTGCGCCCGGAGGACTTACCAATGCAAACTTTGAATTGAAACCTTGAA
196 CCCAGAGGTTTCCGAATTTGCGCCCGGAGGACTTAACAATGCAAACCTTGAATTGAAACCTTAAA
29511 CAAGGATTTTAAACTTAAACATGAATCTTTGATGAAAAACTTGATGAAATCAAATGGTA
261 CAAGGATTTTAAACTTAAACATGAATCTTTGATGAAAAACTTGATGAAATCAAATGGTA
* *
29570 CCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTG-AATTTGTGCCCGGAGGACTTACCAA
1 CCCGAAGGACTTATCAGAATTAATACCCGAAGGTTTCTGCAATTTGTGCCCGGAGGACTTACCAA
* * *
29634 TGCAAAC-CTTGAATTGAAACCTTGAACAAGGATTTTAAACTTAAACATGAATCTTTGATGAAAA
66 TGCAAACAC-TAAATAGAAACCTTGAACAAGGATTTTAAACTAAAACATGAATCTTTGATG-AAA
* * * * *
29698 ACTTGATGAAATCAAATGGTACCCGGAGG-TTTTATCAATTGCCCGGAGGACTTATCATAATTAA
129 ACTTGATAAAATCAAATGATACCAGGAGGCTTTTACCAATTGCCCGGAGGACTTATCAGAATTAA
* * *
29762 TACCCGGAGGTTTCCGAATTTGTGCCCGGAGGACTTAACAATGCAAACCTTGAATTGAGACCTTA
194 TACCCAGAGGTTTCCGAATTTGCGCCCGGAGGACTTAACAATGCAAACCTTGAATTGAAACCTTA
29827 AACAAGGATTTTAAACTTAAACATGAA-CTTTTGATGAAAAACTTGATGAAATCAAATGGTA
259 AACAAGGATTTTAAACTTAAACATGAATC-TTTGATGAAAAACTTGATGAAATCAAATGGTA
29888 GCGGAGGTTT
Statistics
Matches: 290, Mismatches: 25, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
317 2 0.01
318 224 0.77
319 64 0.22
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (319 bp):
CCCGAAGGACTTATCAGAATTAATACCCGAAGGTTTCTGCAATTTGTGCCCGGAGGACTTACCAA
TGCAAACACTAAATAGAAACCTTGAACAAGGATTTTAAACTAAAACATGAATCTTTGATGAAAAC
TTGATAAAATCAAATGATACCAGGAGGCTTTTACCAATTGCCCGGAGGACTTATCAGAATTAATA
CCCAGAGGTTTCCGAATTTGCGCCCGGAGGACTTAACAATGCAAACCTTGAATTGAAACCTTAAA
CAAGGATTTTAAACTTAAACATGAATCTTTGATGAAAAACTTGATGAAATCAAATGGTA
Found at i:29992 original size:168 final size:169
Alignment explanation
Indices: 29570--30013 Score: 709
Period size: 169 Copynumber: 2.6 Consensus size: 169
29560 TCAAATGGTA
29570 CCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAAT
1 CCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAAT
*
29635 GCAAACCTTGAATTGAAACCTTGAACAAGGATTTTAAACTTAAACATGAATCTTTGATGAAAAAC
66 GCAAACCTTGAATTGAGACCTTGAACAAGGATTTTAAACTTAAACATGAATCTTTGATGAAAAAC
29700 TTGATGAAATCAAATGGTACCCGGAGGTTTTATCAATTG
131 TTGATGAAATCAAATGGTACCCGGAGGTTTTATCAATTG
* * *
29739 CCCGGAGGACTTATCATAATTAATACCCGGAGGTTTCCGAATTTGTGCCCGGAGGACTTAACAAT
1 CCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAAT
*
29804 GCAAACCTTGAATTGAGACCTTAAACAAGGATTTTAAACTTAAACATGAA-CTTTTGATGAAAAA
66 GCAAACCTTGAATTGAGACCTTGAACAAGGATTTTAAACTTAAACATGAATC-TTTGATGAAAAA
*
29868 CTTGATGAAATCAAATGGTA-GCGGAGGTTTTATCAATTG
130 CTTGATGAAATCAAATGGTACCCGGAGGTTTTATCAATTG
* * *
29907 CTCGGAGGACTTATCAGAATTAATACCCAGAGGTTTCTGAAATTGTGCCC-GACGGACTTACCAA
1 CCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGA-GGACTTACCAA
* ** *
29971 TGTAAA-CTCTGAAAAGAGACCTTGACCAAGGATTTT-AACTTAA
65 TGCAAACCT-TGAATTGAGACCTTGAACAAGGATTTTAAACTTAA
30014 CTTATATGGA
Statistics
Matches: 255, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
167 11 0.04
168 102 0.40
169 142 0.56
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (169 bp):
CCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTACCAAT
GCAAACCTTGAATTGAGACCTTGAACAAGGATTTTAAACTTAAACATGAATCTTTGATGAAAAAC
TTGATGAAATCAAATGGTACCCGGAGGTTTTATCAATTG
Found at i:31734 original size:19 final size:19
Alignment explanation
Indices: 31710--31747 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
31700 AGGTCTATTC
31710 TTTCCTTCTTTT-CTTTTTT
1 TTTCCTT-TTTTCCTTTTTT
31729 TTTCCTTTTTTCCTTTTTT
1 TTTCCTTTTTTCCTTTTTT
31748 CATTTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTCCTTTTTTCCTTTTTT
Found at i:31737 original size:7 final size:8
Alignment explanation
Indices: 31726--31755 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
31716 TCTTTTCTTT
31726 TTTTTTCC
1 TTTTTTCC
31734 TTTTTTCC
1 TTTTTTCC
*
31742 TTTTTTCA
1 TTTTTTCC
31750 TTTTTT
1 TTTTTT
31756 GTGCACTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTCC
Found at i:32073 original size:20 final size:20
Alignment explanation
Indices: 32050--32088 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
32040 TTCTTTTTCA
32050 ATTTTGATTT-TGATTTTTTG
1 ATTTT-ATTTATGATTTTTTG
*
32070 ATTTTTTTTATGATTTTTT
1 ATTTTATTTATGATTTTTT
32089 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.74
Consensus pattern (20 bp):
ATTTTATTTATGATTTTTTG
Found at i:32084 original size:26 final size:25
Alignment explanation
Indices: 32053--32130 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 25
32043 TTTTTCAATT
32053 TTGATTTTGATTTTTTGATTTTTTTTA
1 TTGATTTT--TTTTTTGATTTTTTTTA
* ** *
32080 -TGATTTTTTTTTTAAAATTTTTGA
1 TTGATTTTTTTTTTGATTTTTTTTA
32104 TTGATTTTTTTATTTTTGATTTTTTTT
1 TTGA--TTTTT-TTTTTGATTTTTTTT
32131 GGAATTTCTT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
24 13 0.33
25 3 0.08
26 7 0.18
27 5 0.13
28 11 0.28
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (25 bp):
TTGATTTTTTTTTTGATTTTTTTTA
Found at i:32137 original size:19 final size:17
Alignment explanation
Indices: 32064--32130 Score: 50
Period size: 19 Copynumber: 3.9 Consensus size: 17
32054 TGATTTTGAT
32064 TTTTTGATTTTTTTT-A
1 TTTTTGATTTTTTTTAA
**
32080 TGATTTT--TTTTTTAAAA
1 T--TTTTGATTTTTTTTAA
*
32097 TTTTTGATTGATTTTTTTA
1 TTTTTGATT--TTTTTTAA
32116 TTTTTGATTTTTTTT
1 TTTTTGATTTTTTTT
32131 GGAATTTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 13
0.68 0.09 0.23
Matches are distributed among these distances:
15 4 0.10
16 7 0.18
17 10 0.26
18 4 0.10
19 14 0.36
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.76
Consensus pattern (17 bp):
TTTTTGATTTTTTTTAA
Found at i:32539 original size:16 final size:16
Alignment explanation
Indices: 32512--32579 Score: 77
Period size: 16 Copynumber: 4.2 Consensus size: 16
32502 AGTGCCTTTA
32512 TTTTCA-TTTTTTCAT
1 TTTTCATTTTTTTCAT
32527 TTTTCATTTTTTTCAT
1 TTTTCATTTTTTTCAT
* *
32543 TCATTC-TTTTCTTCATT
1 T-TTTCATTTTTTTCA-T
*
32560 TTTTCATTTTTTTTAT
1 TTTTCATTTTTTTCAT
32576 TTTT
1 TTTT
32580 ATGGGAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
15 6 0.14
16 26 0.59
17 12 0.27
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTCATTTTTTTCAT
Found at i:32565 original size:20 final size:17
Alignment explanation
Indices: 32526--32579 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
32516 CATTTTTTCA
*
32526 TTTTTCATTTTTTTCAT
1 TTTTTCATTTTTTTTAT
** * *
32543 TCATTC-TTTTCTTCAT
1 TTTTTCATTTTTTTTAT
32559 TTTTTCATTTTTTTTAT
1 TTTTTCATTTTTTTTAT
32576 TTTT
1 TTTT
32580 ATGGGAATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCATTTTTTTTAT
Found at i:32579 original size:8 final size:8
Alignment explanation
Indices: 32512--32571 Score: 70
Period size: 8 Copynumber: 7.5 Consensus size: 8
32502 AGTGCCTTTA
32512 TTTTCATT
1 TTTTCATT
32520 TTTTCA-T
1 TTTTCATT
32527 TTTTCATTT
1 TTTTCA-TT
32536 TTTTCATT
1 TTTTCATT
**
32544 CATTC-TT
1 TTTTCATT
32551 TTCTTCATT
1 TT-TTCATT
32560 TTTTCATT
1 TTTTCATT
32568 TTTT
1 TTTT
32572 TTATTTTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
7 9 0.20
8 24 0.55
9 11 0.25
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTCATT
Found at i:35848 original size:14 final size:15
Alignment explanation
Indices: 35825--35858 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
35815 GCAATAAAAC
*
35825 ACCAAGACAAAC-AA
1 ACCAAAACAAACAAA
35839 ACCAAAACAAACAAA
1 ACCAAAACAAACAAA
35854 ACCAA
1 ACCAA
35859 GCAACCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.68, C:0.29, G:0.03, T:0.00
Consensus pattern (15 bp):
ACCAAAACAAACAAA
Found at i:36629 original size:12 final size:12
Alignment explanation
Indices: 36612--36657 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
36602 GATTTTTCCA
36612 TTTTTTCATTTT
1 TTTTTTCATTTT
*
36624 TTTTTTCTTTTTT
1 TTTTTTC-ATTTT
36637 TCTTTTTCATTTT
1 T-TTTTTCATTTT
*
36650 TTTCTTCA
1 TTTTTTCA
36658 AATTTGACCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 13 0.45
13 10 0.34
14 6 0.21
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTCATTTT
Found at i:36642 original size:15 final size:16
Alignment explanation
Indices: 36620--36655 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
36610 CATTTTTTCA
36620 TTTT-TTTTTTC-TTT
1 TTTTCTTTTTTCATTT
36634 TTTTC-TTTTTCATTT
1 TTTTCTTTTTTCATTT
36649 TTTTCTT
1 TTTTCTT
36656 CAAATTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 10 0.53
15 8 0.42
16 1 0.05
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTCTTTTTTCATTT
Found at i:36649 original size:20 final size:20
Alignment explanation
Indices: 36612--36649 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
36602 GATTTTTCCA
*
36612 TTTTTTCATTTTTTTTTTCT
1 TTTTTTCATTTTTATTTTCT
36632 TTTTTTC-TTTTTCATTTT
1 TTTTTTCATTTTT-ATTTT
36650 TTTCTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTTTCATTTTTATTTTCT
Found at i:38329 original size:17 final size:17
Alignment explanation
Indices: 38275--38330 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
38265 AAAGTGTGAA
38275 GAGAGAGAGAGGTTCTG
1 GAGAGAGAGAGGTTCTG
* * *
38292 GAGGGAGAAGAGTTGTGTG
1 GAGAGAG-AGAGGT-TCTG
38311 GAGAGAGAGAGGTTCTG
1 GAGAGAGAGAGGTTCTG
38328 GAG
1 GAG
38331 GCTGAGACTC
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
17 12 0.39
18 10 0.32
19 9 0.29
ACGTcount: A:0.29, C:0.04, G:0.50, T:0.18
Consensus pattern (17 bp):
GAGAGAGAGAGGTTCTG
Found at i:38937 original size:15 final size:16
Alignment explanation
Indices: 38913--38952 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
38903 AGAGGTTGAA
*
38913 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
38928 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
38944 AGAAAACAA
1 AGAAAACAA
38953 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:48850 original size:19 final size:18
Alignment explanation
Indices: 48826--48861 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
48816 TGAAGATTTA
48826 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
48845 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
48862 ATTATCCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:49461 original size:13 final size:13
Alignment explanation
Indices: 49445--49469 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49435 CATACACACA
49445 ATTTTCTCTTCTT
1 ATTTTCTCTTCTT
49458 ATTTTCTCTTCT
1 ATTTTCTCTTCT
49470 AGTTCTAGTT
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:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTTCTCTTCTT
Found at i:51116 original size:21 final size:21
Alignment explanation
Indices: 51086--51140 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
51076 ATTGAAATAG
* *
51086 TTTAGATTTAATTTATTTTGC-
1 TTTATATTTAATTTA-ATTGCT
* *
51107 TTTATTTTTAGTTTAATTGCT
1 TTTATATTTAATTTAATTGCT
51128 TTTATATTTAATT
1 TTTATATTTAATT
51141 GTTTTAATCC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.24, C:0.04, G:0.07, T:0.65
Consensus pattern (21 bp):
TTTATATTTAATTTAATTGCT
Done.