Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007521.1 Corchorus capsularis cultivar CVL-1 contig07542, 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: 44692
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:5407 original size:26 final size:26
Alignment explanation
Indices: 5378--5428 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
5368 ACATAAGAAG
*
5378 TCATGACTAAATAAGCATGTTGAATA
1 TCATGACTAAATAAGCATGATGAATA
5404 TCATGACTAAATAAGCATGATGAAT
1 TCATGACTAAATAAGCATGATGAAT
5429 GGTAAGAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (26 bp):
TCATGACTAAATAAGCATGATGAATA
Found at i:7296 original size:22 final size:22
Alignment explanation
Indices: 7247--7303 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
7237 GAGGGAAAAC
7247 GGGTACCAAA-ATGA-GGGATGT
1 GGGTACCAAATA-GAGGGGATGT
7268 --GTACCAAATAGAGGGGATGT
1 GGGTACCAAATAGAGGGGATGT
7288 GGGTACCAAATAGAGG
1 GGGTACCAAATAGAGG
7304 AAATCCACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 10 0.31
20 8 0.25
22 14 0.44
ACGTcount: A:0.35, C:0.11, G:0.37, T:0.18
Consensus pattern (22 bp):
GGGTACCAAATAGAGGGGATGT
Found at i:7384 original size:3 final size:3
Alignment explanation
Indices: 7376--7402 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
7366 ATAAGGTAAG
7376 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
7403 TGAAGTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:8448 original size:26 final size:26
Alignment explanation
Indices: 8419--8471 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
8409 GGTTAGAGCT
**
8419 GTTGAAGAATAATAAAGGTGAAAATA
1 GTTGAAGAATAATAAAGGCAAAAATA
** *
8445 GTTGTTGGATAATAAAGGCAAAAATA
1 GTTGAAGAATAATAAAGGCAAAAATA
8471 G
1 G
8472 ATGTTGGATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.25, T:0.25
Consensus pattern (26 bp):
GTTGAAGAATAATAAAGGCAAAAATA
Found at i:8476 original size:26 final size:26
Alignment explanation
Indices: 8427--8481 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
8417 CTGTTGAAGA
** *
8427 ATAATAAAGGTGAAAATAGTTGTTGG
1 ATAATAAAGGCAAAAATAGATGTTGG
8453 ATAATAAAGGCAAAAATAGATGTTGG
1 ATAATAAAGGCAAAAATAGATGTTGG
8479 ATA
1 ATA
8482 GTTAATGCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.47, C:0.02, G:0.24, T:0.27
Consensus pattern (26 bp):
ATAATAAAGGCAAAAATAGATGTTGG
Found at i:16980 original size:75 final size:75
Alignment explanation
Indices: 16857--17280 Score: 577
Period size: 75 Copynumber: 5.7 Consensus size: 75
16847 GCAAGAGAAG
* * * *
16857 CAGAAAGTTGAAGAGGAGAAAAGGAAGTTGATGGAAGAACATGGTAAAATAAGTCTTGAGAAAGA
1 CAGAAATTTGAAGAGGAGAAAAGGAAGCTAATGGAAGAACATGGTAAAAGAAGTCTTGAGAAAGA
16922 ATTAGAATTA
66 ATTAGAATTA
* *
16932 CAGAAATTTGAAGAGGAGAAAAGGAAGCTAATGAAAGAACATGGTAAAATAAGTCTTGAGAAAGA
1 CAGAAATTTGAAGAGGAGAAAAGGAAGCTAATGGAAGAACATGGTAAAAGAAGTCTTGAGAAAGA
16997 ATTAGAATTA
66 ATTAGAATTA
17007 CAGAAATTTGAAGAGGAGAAAAGGAAGCTAATGGAAGAACATGGTAAAAGAAGTCTTGAGAAAGA
1 CAGAAATTTGAAGAGGAGAAAAGGAAGCTAATGGAAGAACATGGTAAAAGAAGTCTTGAGAAAGA
17072 ATTAGAATTA
66 ATTAGAATTA
17082 CAGAAATTTGAAGAGGAGAAAAGGAAGCTAATGGAAGAACATGAG-AAAAGAAGTCTTGAGAAAG
1 CAGAAATTTGAAGAGGAGAAAAGGAAGCTAATGGAAGAACATG-GTAAAAGAAGTCTTGAGAAAG
*
17146 CATTAGAATTA
65 AATTAGAATTA
* * * * * * *
17157 CAGAAAGTTGAAGAGGAGAAAAGAAAGTTAATGGAAGAAAATGATAAAAAAATTCTTGA-AAAGG
1 CAGAAATTTGAAGAGGAGAAAAGGAAGCTAATGGAAGAACATGGTAAAAGAAGTCTTGAGAAA-G
* *
17221 CATTAGAAAT-
65 AATTAGAATTA
* * * * * * *
17231 CAAGAAACTTGAAGAAGA-AAACAGAAAGTTAATGAAAGAAAATGATAAAA
1 C-AGAAATTTGAAGAGGAGAAA-AGGAAGCTAATGGAAGAACATGGTAAAA
17281 ACAATCTTGA
Statistics
Matches: 326, Mismatches: 18, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
74 7 0.02
75 318 0.98
76 1 0.00
ACGTcount: A:0.52, C:0.05, G:0.25, T:0.18
Consensus pattern (75 bp):
CAGAAATTTGAAGAGGAGAAAAGGAAGCTAATGGAAGAACATGGTAAAAGAAGTCTTGAGAAAGA
ATTAGAATTA
Found at i:24879 original size:19 final size:19
Alignment explanation
Indices: 24855--24891 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
24845 CCTATCTATT
*
24855 TGTTGGATTTGAATTCTTC
1 TGTTGGATTTGAAATCTTC
24874 TGTTGGATTTGAAATCTT
1 TGTTGGATTTGAAATCTT
24892 ATTCAAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.08, G:0.22, T:0.51
Consensus pattern (19 bp):
TGTTGGATTTGAAATCTTC
Found at i:34357 original size:5 final size:5
Alignment explanation
Indices: 34340--34385 Score: 78
Period size: 5 Copynumber: 9.6 Consensus size: 5
34330 ATGGACAAAA
34340 ATAAT AT-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
34386 TGGTAATTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
4 8 0.21
5 31 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:34418 original size:24 final size:24
Alignment explanation
Indices: 34391--34436 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
34381 ATATATGGTA
* *
34391 ATTTATTAATTGATTTGTTTGTTG
1 ATTTATCAATTGATATGTTTGTTG
* *
34415 ATTTCTCATTTGATATGTTTGT
1 ATTTATCAATTGATATGTTTGT
34437 GTATATAGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.20, C:0.04, G:0.15, T:0.61
Consensus pattern (24 bp):
ATTTATCAATTGATATGTTTGTTG
Found at i:35354 original size:29 final size:29
Alignment explanation
Indices: 35321--35383 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
35311 AGTTTGAACG
*
35321 TTTTGTCCCT-TAAATTTCAATTTTG-GAC
1 TTTTGT-CCTATAAACTTCAATTTTGTGAC
*
35349 ATTTTGTCCTATGAACTTCAATTTTGTGAC
1 -TTTTGTCCTATAAACTTCAATTTTGTGAC
35379 TTTTG
1 TTTTG
35384 CCCCCTCAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 3 0.10
29 24 0.80
30 3 0.10
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.51
Consensus pattern (29 bp):
TTTTGTCCTATAAACTTCAATTTTGTGAC
Found at i:35633 original size:29 final size:28
Alignment explanation
Indices: 35557--35633 Score: 66
Period size: 29 Copynumber: 2.6 Consensus size: 28
35547 CGTTAGCCTG
*
35557 AGGGGACAAAACGCCCAAAATTGAAATTT
1 AGGGG-CAAAACGTCCAAAATTGAAATTT
* * * *
35586 AGAGGACGAAATGTTCAAAATT-AAAGTTT
1 AG-GGGCAAAACGTCCAAAATTGAAA-TTT
35615 ATGGGGCAAAACGTCCAAA
1 A-GGGGCAAAACGTCCAAA
35634 CGCTACAAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 6
0.71 0.18 0.12
Matches are distributed among these distances:
28 3 0.08
29 30 0.83
30 3 0.08
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.19
Consensus pattern (28 bp):
AGGGGCAAAACGTCCAAAATTGAAATTT
Found at i:38331 original size:6 final size:6
Alignment explanation
Indices: 38313--38386 Score: 80
Period size: 6 Copynumber: 12.3 Consensus size: 6
38303 AGGAGAAAAT
* *
38313 AAGAAA AATGAAA AAGAAA AAGAAA AAGAAA AAG-AA AGGAAA ACGAAA
1 AAGAAA AA-GAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
* *
38361 ATGAAA ATGAAA AA-AGAA AAGAAA AA
1 AAGAAA AAGAAA AAGA-AA AAGAAA AA
38387 AAAGCCACGT
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.08
6 48 0.80
7 7 0.12
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (6 bp):
AAGAAA
Found at i:38694 original size:6 final size:6
Alignment explanation
Indices: 38679--38720 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
38669 GTTTTGAGGG
*
38679 TTTTGTT TTTTGT TTTTGT TTTTGT TTTTTT TTTTGT ATTTT
1 TTTTG-T TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT -TTTT
38721 ATACAAGAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 23 0.72
7 9 0.28
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (6 bp):
TTTTGT
Found at i:38703 original size:19 final size:19
Alignment explanation
Indices: 38679--38720 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
38669 GTTTTGAGGG
38679 TTTTGTTTTTTGTTTTTGT-
1 TTTTGTTTTTT-TTTTTGTA
38698 TTTTGTTTTTTTTTTTGTA
1 TTTTGTTTTTTTTTTTGTA
38717 TTTT
1 TTTT
38721 ATACAAGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (19 bp):
TTTTGTTTTTTTTTTTGTA
Found at i:39252 original size:12 final size:12
Alignment explanation
Indices: 39235--39259 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39225 TTCTTTCTTC
39235 ATGATTTAAAAG
1 ATGATTTAAAAG
39247 ATGATTTAAAAG
1 ATGATTTAAAAG
39259 A
1 A
39260 GGTTTGGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGATTTAAAAG
Found at i:40185 original size:86 final size:87
Alignment explanation
Indices: 40078--40252 Score: 316
Period size: 86 Copynumber: 2.0 Consensus size: 87
40068 CGTATTTTAT
*
40078 TTCTTGTTATTTTATCATAATAATATTGATAATATCATTTAGATGATACTATCAATCAATGACTC
1 TTCTTGTTA-TTTATCATAATAATATTGATAATATCATTTAGATGATACTATCAATAAATGACTC
40143 ACAAGTAGTGTAATACATAAAAC
65 ACAAGTAGTGTAATACATAAAAC
*
40166 TTCTTGTTA-TTATCATAATAATATTGATAATATCATTTAGATGATCCTATCAATAAATGACTCA
1 TTCTTGTTATTTATCATAATAATATTGATAATATCATTTAGATGATACTATCAATAAATGACTCA
40230 CAAGTAGTGTAATACATAAAAC
66 CAAGTAGTGTAATACATAAAAC
40252 T
1 T
40253 GTTTCTTTGC
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
86 76 0.89
88 9 0.11
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (87 bp):
TTCTTGTTATTTATCATAATAATATTGATAATATCATTTAGATGATACTATCAATAAATGACTCA
CAAGTAGTGTAATACATAAAAC
Found at i:41758 original size:22 final size:22
Alignment explanation
Indices: 41733--42375 Score: 220
Period size: 22 Copynumber: 29.9 Consensus size: 22
41723 ATGATCCCAT
41733 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** *
41755 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
41777 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
41799 TAT-AAATTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* *
41820 TATGAAATTTGGTTAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
41841 TTAAGGAATTTTGA-AGACC-TCAA
1 -TATGAAATTTTGATA-ACCTTC-C
41864 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* **
41886 CATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* * *
41909 TATGAGATGTTGATAACC-TCTA
1 TATGAAATTTTGATAACCTTC-C
* * * *
41931 TATGATATATTGATAACC-ACGT
1 TATGAAATTTTGATAACCTTC-C
* * *
41953 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
41974 ATATG-AATTGTT-AGTAATCATAC
1 -TATGAAATT-TTGA-TAACCTTCC
* * *
41997 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
* *
42019 TATGAAATTGTGATAACC-TCGT
1 TATGAAATTTTGATAACCTTC-C
*
42041 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
42064 TATAAAATTTCGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* *
42087 TAT-AATATTTTGATAACTTTCT
1 TATGAA-ATTTTGATAACCTTCC
* *
42109 TATGAAATCTTAATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
42126 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
42147 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
42169 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
42191 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
*
42213 TATGAAATTTTGATAA-CTCTCT
1 TATGAAATTTTGATAACCT-TCC
* * *
42235 TGTGAAATTTTGATAACATTCA
1 TATGAAATTTTGATAACCTTCC
* *
42257 TATGGAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
42278 -CTG-AATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
*
42297 T-TGAAATTTTGATTA-C-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
42316 ATAATAAAAGTTTAATAACCTTCC
1 -T-ATGAAATTTTGATAACCTTCC
* * *
42340 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACCTTCC
42357 TATGAAATTTTGATAACCT
1 TATGAAATTTTGATAACCT
42376 CCCCAAAAAT
Statistics
Matches: 457, Mismatches: 121, Indels: 86
0.69 0.18 0.13
Matches are distributed among these distances:
16 10 0.02
17 12 0.03
18 2 0.00
19 23 0.05
20 13 0.03
21 33 0.07
22 295 0.65
23 64 0.14
24 5 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:42073 original size:23 final size:23
Alignment explanation
Indices: 42001--42102 Score: 82
Period size: 23 Copynumber: 4.5 Consensus size: 23
41991 TCATACTCTG
* * * *
42001 AAATTTTGAT-AATCACACTATG
1 AAATTTTGATAAACCTCCCTATA
* ** *
42023 AAATTGTGAT-AACCTCGTTATG
1 AAATTTTGATAAACCTCCCTATA
* *
42045 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
*
42068 AAATTTCGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
*
42091 ATATTTTGATAA
1 AAATTTTGATAA
42103 CTTTCTTATG
Statistics
Matches: 63, Mismatches: 16, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
22 26 0.41
23 37 0.59
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:42285 original size:19 final size:19
Alignment explanation
Indices: 42261--42309 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 19
42251 CATTCATATG
42261 GAATTTTGATATCCTCCCT
1 GAATTTTGATATCCTCCCT
*
42280 GAATTTTGATATCCTCCTT
1 GAATTTTGATATCCTCCCT
42299 GAAATTTTGAT
1 G-AATTTTGAT
42310 TACTCCATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.45
Consensus pattern (19 bp):
GAATTTTGATATCCTCCCT
Found at i:42482 original size:24 final size:22
Alignment explanation
Indices: 42415--42562 Score: 120
Period size: 22 Copynumber: 6.6 Consensus size: 22
42405 AATCACATTT
*
42415 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
42437 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * *
42459 TAAAATTTTGTTGACCCCTCTTTA
1 TGAAATTTTGAT-A-ACCTCTTTA
* * * *
42483 TGAAATTCTGATAAATCACGTTA
1 TGAAATTTTGAT-AACCTCTTTA
* ** **
42506 TGTAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
*
42528 TGAAATTTTGATAATCT-TTCTA
1 TGAAATTTTGATAACCTCTT-TA
42550 T-AAATTTTGATAA
1 TGAAATTTTGATAA
42563 TCCGATCTCT
Statistics
Matches: 99, Mismatches: 24, Indels: 7
0.76 0.18 0.05
Matches are distributed among these distances:
21 12 0.12
22 53 0.54
23 16 0.16
24 18 0.18
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:42625 original size:21 final size:22
Alignment explanation
Indices: 42525--42625 Score: 77
Period size: 21 Copynumber: 4.6 Consensus size: 22
42515 GATAACAACA
* *
42525 CTATGAAATTTTGATAATCTTT
1 CTATCAAATTTTGATAATCCTT
42547 CTAT-AAATTTTGATAATCCGATCT
1 CTATCAAATTTTGATAATCC--T-T
*
42571 CTA-CAAAATTTCGATAATCAC-T
1 CTATC-AAATTTTGATAATC-CTT
* *
42593 CTATGAGA-TTTGATAA-CCTT
1 CTATCAAATTTTGATAATCCTT
42613 CTATCAAATTTTG
1 CTATCAAATTTTG
42626 GTACTTCTTA
Statistics
Matches: 63, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
19 1 0.02
20 8 0.13
21 25 0.40
22 10 0.16
23 1 0.02
24 4 0.06
25 13 0.21
26 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.42
Consensus pattern (22 bp):
CTATCAAATTTTGATAATCCTT
Found at i:42713 original size:22 final size:22
Alignment explanation
Indices: 42663--42713 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
42653 TAACCTTCAT
*
42663 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACACC
* *
42685 ATAAAATTTTGATAATCTAC-CC
1 ATGAAATTTTGATAA-CCACACC
42707 ATGAAAT
1 ATGAAAT
42714 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:42877 original size:24 final size:22
Alignment explanation
Indices: 42820--42877 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
42810 AATTAATCAC
42820 CCTATGAAATTTCAATAACCAA
1 CCTATGAAATTTCAATAACCAA
* * *
42842 CCTAAGAGATTTCAATAACCTGAT
1 CCTATGAAATTTCAATAACC--AA
42866 CCTATGAAATTT
1 CCTATGAAATTT
42878 TGGTATCCAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 18 0.62
24 11 0.38
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.31
Consensus pattern (22 bp):
CCTATGAAATTTCAATAACCAA
Found at i:42893 original size:22 final size:22
Alignment explanation
Indices: 42867--42976 Score: 107
Period size: 22 Copynumber: 5.0 Consensus size: 22
42857 TAACCTGATC
*
42867 CTATGAAATTTTGGTATCCACA
1 CTATGAAATTTTGGTAACCACA
42889 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* * *
42911 CTATGGAATTTTGATAACCTCA
1 CTATGAAATTTTGGTAACCACA
* ** *
42933 -TCATGAAATTATAATAACCA-T
1 CT-ATGAAATTTTGGTAACCACA
*
42954 CTCATGAAATTTTGATAACCACA
1 CT-ATGAAATTTTGGTAACCACA
42977 TAGAGAGAAG
Statistics
Matches: 73, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
21 1 0.01
22 72 0.99
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:43171 original size:19 final size:20
Alignment explanation
Indices: 43140--43177 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
43130 TATTGACATT
43140 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
43159 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
43178 ATAATAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:43553 original size:31 final size:31
Alignment explanation
Indices: 43489--43553 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
43479 GGTAATTTAG
* * *
43489 AAATATGTTTTAAAGAAAAGGGTACAATTGA
1 AAATATATTTTAAAGAAAAGAGTACAATCGA
*
43520 AAATATATTTTAAA-AATAAGAGTATAATCGA
1 AAATATATTTTAAAGAA-AAGAGTACAATCGA
43551 AAA
1 AAA
43554 ACATAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.07
31 27 0.93
ACGTcount: A:0.54, C:0.03, G:0.14, T:0.29
Consensus pattern (31 bp):
AAATATATTTTAAAGAAAAGAGTACAATCGA
Found at i:44638 original size:2 final size:2
Alignment explanation
Indices: 44631--44678 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
44621 ACAAAAGAAT
44631 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
44673 GA GA GA
1 GA GA GA
44679 ATAGTAGTAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Done.