Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007756.1 Corchorus capsularis cultivar CVL-1 contig07777, 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: 36513
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:4154 original size:15 final size:16
Alignment explanation
Indices: 4125--4154 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4115 GTGTGAAGTC
4125 AAATTGATCTTTTGAA
1 AAATTGATCTTTTGAA
4141 AAATTGAT-TTTTGA
1 AAATTGATCTTTTGA
4155 TTAACTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (16 bp):
AAATTGATCTTTTGAA
Found at i:19440 original size:96 final size:97
Alignment explanation
Indices: 19317--19521 Score: 297
Period size: 97 Copynumber: 2.1 Consensus size: 97
19307 TGGTTTCAAT
* * *
19317 GTTGAATATTTTTGGTGTTGTTGATGAGTTCACAAAAAAGATGGGG-TTTGATCTTATTTTGGGA
1 GTTGAATATTCTTGGTGTTCTTGATGAGTTCACAAAAAAGAGGGGGCTTTGATCTTATTTTGGGA
*
19381 TAAATTTTTGGAAAATTTGTGTTTTTGGTTGA
66 TAAATTTCTGGAAAATTTGTGTTTTTGGTTGA
* * ** *
19413 GTTGAATGTTCTTGTTGTTCTTGATGAGTTCATGAAAAGGAGGGGGCTTTGATCTTATTTTGGGA
1 GTTGAATATTCTTGGTGTTCTTGATGAGTTCACAAAAAAGAGGGGGCTTTGATCTTATTTTGGGA
*
19478 TGAATTTCTGGAAAATTTGTGTTTTTGGTTGA
66 TAAATTTCTGGAAAATTTGTGTTTTTGGTTGA
*
19510 G-TGAAAATTCTT
1 GTTGAATATTCTT
19522 TAAATGGATA
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
96 47 0.49
97 49 0.51
ACGTcount: A:0.23, C:0.05, G:0.27, T:0.45
Consensus pattern (97 bp):
GTTGAATATTCTTGGTGTTCTTGATGAGTTCACAAAAAAGAGGGGGCTTTGATCTTATTTTGGGA
TAAATTTCTGGAAAATTTGTGTTTTTGGTTGA
Found at i:21312 original size:34 final size:37
Alignment explanation
Indices: 21255--21356 Score: 165
Period size: 34 Copynumber: 2.8 Consensus size: 37
21245 TTCCTTTCTT
*
21255 TGATGACAATCCTAAAAGTCTCATTGCCAGCAAAG-C
1 TGATGACAATCCTAAAAGTCTCATTGCCAGCAAAGTA
21291 T-ATGACAATCCT-AAAGTCTCATTGCCAGCAAAGTTA
1 TGATGACAATCCTAAAAGTCTCATTGCCAGCAAAG-TA
21327 TGATGACAATCCTAAAAGTCTCATTGCCAG
1 TGATGACAATCCTAAAAGTCTCATTGCCAG
21357 GCATAATCAG
Statistics
Matches: 61, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
34 21 0.34
35 11 0.18
36 2 0.03
37 11 0.18
38 16 0.26
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (37 bp):
TGATGACAATCCTAAAAGTCTCATTGCCAGCAAAGTA
Found at i:34660 original size:22 final size:22
Alignment explanation
Indices: 34635--35212 Score: 229
Period size: 22 Copynumber: 26.6 Consensus size: 22
34625 ATGATCCCAT
34635 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** *
34657 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * * **
34679 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* *
34701 TAT-AAATTTT-TTAACCTTCT
1 TATGAAATTTTGATAACCTTCC
* *
34721 TATGAAATTTGGTTAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * *
34743 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
34765 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * **
34787 AATGAAATTTTGATGACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* *
34810 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * * *
34831 ATATGATATATTGATAACC-ACGT
1 -TATGAAATTTTGATAACCTTC-C
* * *
34854 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
34875 ATATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * *
34898 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
* *
34920 TCTGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
*
34942 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
34965 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
34988 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
35010 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
35027 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** * *
35048 T-T-ATTTTTTGATAATC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
35068 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
35090 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
* *
35112 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* * **
35134 TGTGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
35156 TATGAAATTTTGAATAACCTTCA
1 TATGAAATTTTG-ATAACCTTCC
*
35179 TATGAAATTTTGATATCC-TCC
1 TATGAAATTTTGATAACCTTCC
35200 T-TGAAATTTTGAT
1 TATGAAATTTTGAT
35213 TACTCCATAA
Statistics
Matches: 418, Mismatches: 102, Indels: 74
0.70 0.17 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
19 1 0.00
20 34 0.08
21 32 0.08
22 254 0.61
23 78 0.19
24 6 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:34845 original size:45 final size:45
Alignment explanation
Indices: 34765--34850 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
34755 AAGACCTCAA
* * * *
34765 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATGACCAACAC
1 TATGAAATGTTGATAACCTCCCAATGAAATATTGATAACCAACAC
* *
34810 TATGAGATGTTGATAACCT-CCATATGATATATTGATAACCA
1 TATGAAATGTTGATAACCTCCCA-ATGAAATATTGATAACCA
34851 CGTTATGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 3 0.09
45 31 0.91
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (45 bp):
TATGAAATGTTGATAACCTCCCAATGAAATATTGATAACCAACAC
Found at i:34972 original size:23 final size:23
Alignment explanation
Indices: 34941--35025 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
34931 GATAACCTCG
*
34941 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
34964 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
34987 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
35009 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
35026 CTACAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:35024 original size:45 final size:45
Alignment explanation
Indices: 34922--35025 Score: 122
Period size: 46 Copynumber: 2.3 Consensus size: 45
34912 AATCACACTC
* *
34922 TGAAATTGTGAT-AACCTCGCTATGAAATTTTGATAAATCTTCCTA
1 TGAAATT-TGATAAACCTCCCTATAAAATTTTGATAAATCTTCCTA
* * *
34967 TAAAATTTTGATAAACCTCCCTATAAAATTTTGATAACT-TTCTTA
1 TGAAA-TTTGATAAACCTCCCTATAAAATTTTGATAAATCTTCCTA
35012 TGAAATCTTGATAA
1 TGAAAT-TTGATAA
35026 CTACAAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
44 1 0.02
45 24 0.48
46 25 0.50
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (45 bp):
TGAAATTTGATAAACCTCCCTATAAAATTTTGATAAATCTTCCTA
Found at i:35070 original size:19 final size:20
Alignment explanation
Indices: 35033--35070 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
35023 TAACTACAAA
*
35033 TTTTGATAACCTCCCTTATT
1 TTTTGATAACCTCCATTATT
*
35053 TTTTGATAATCT-CATTAT
1 TTTTGATAACCTCCATTAT
35071 GAAATTTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.24, C:0.18, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTTGATAACCTCCATTATT
Found at i:35372 original size:44 final size:44
Alignment explanation
Indices: 35318--35572 Score: 187
Period size: 44 Copynumber: 5.8 Consensus size: 44
35308 AATCACATTT
* *
35318 TGAAAATTTGATAACCCTTTTATGAAATTTTGATAACCTTTTTA
1 TGAAATTTTGATAACCCTTTTATGAAATTTTGATAACCTTTCTA
* * * * * **
35362 TGGAATTTTGATAACCTTTTTATAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCCTTTTATGAAATTTTGATAACCTTTCTA
* * * * * *
35406 TGAAATTCTGATAATCAC-ATTATGTAATTTTGATAACCTTGCTT
1 TGAAATTTTGATAA-CCCTTTTATGAAATTTTGATAACCTTTCTA
* ** *
35450 TGAAATTTTGATAACAAC-ACTATGAAATTTTGATAATCTTTCTA
1 TGAAATTTTGATAAC-CCTTTTATGAAATTTTGATAACCTTTCTA
* * * **
35494 T-AAATTTTGATAATCCTATCTCTATGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCCT-T-T-TATGAAATTTTGATAACCTTTCTA
* * *
35540 TGAGA-TTTGATAA-CCTTCTATCAAATTTTGATA
1 TGAAATTTTGATAACCCTTTTATGAAATTTTGATA
35573 CTCCCTATGA
Statistics
Matches: 165, Mismatches: 39, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
42 14 0.08
43 13 0.08
44 102 0.62
45 4 0.02
46 30 0.18
47 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (44 bp):
TGAAATTTTGATAACCCTTTTATGAAATTTTGATAACCTTTCTA
Found at i:35409 original size:66 final size:66
Alignment explanation
Indices: 35338--35506 Score: 180
Period size: 66 Copynumber: 2.6 Consensus size: 66
35328 ATAACCCTTT
* * * * * **
35338 TATGAAATTTTGATAACCTTTTTATGGAATTTTGATAACCTT-TTTATAAAATTTTGTTGACCCC
1 TATGAAATTTTGATAATCTTTTTATGAAATTTTGATAACCTTGCTT-TAAAATTTTGATAACAAC
*
35402 TC
65 AC
* *** * *
35404 TATGAAATTCTGATAATCACATTATGTAATTTTGATAACCTTGCTTTGAAATTTTGATAACAACA
1 TATGAAATTTTGATAATCTTTTTATGAAATTTTGATAACCTTGCTTTAAAATTTTGATAACAACA
35469 C
66 C
*
35470 TATGAAATTTTGATAATCTTTCTAT-AAATTTTGATAA
1 TATGAAATTTTGATAATCTTTTTATGAAATTTTGATAA
35507 TCCTATCTCT
Statistics
Matches: 83, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
65 11 0.13
66 70 0.84
67 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (66 bp):
TATGAAATTTTGATAATCTTTTTATGAAATTTTGATAACCTTGCTTTAAAATTTTGATAACAACA
C
Found at i:35456 original size:22 final size:22
Alignment explanation
Indices: 35318--35645 Score: 147
Period size: 22 Copynumber: 14.8 Consensus size: 22
35308 AATCACATTT
* *
35318 TGAAAATTTGATAACCCTT-TTA
1 TGAAATTTTGATAA-CCTTACTA
**
35340 TGAAATTTTGATAACCTTTTTA
1 TGAAATTTTGATAACCTTACTA
* **
35362 TGGAATTTTGATAACCTTTTTA
1 TGAAATTTTGATAACCTTACTA
* * * *
35384 TAAAATTTTGTTGACCCCT-CTA
1 TGAAATTTTGAT-AACCTTACTA
* * ** *
35406 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTTACTA
* * *
35428 TGTAATTTTGATAACCTTGCTT
1 TGAAATTTTGATAACCTTACTA
***
35450 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTTACTA
* *
35472 TGAAATTTTGATAATCTTTCTA
1 TGAAATTTTGATAACCTTACTA
*
35494 T-AAATTTTGATAATCCTATCTCTA
1 TGAAATTTTGATAA-CCT-T-ACTA
*
35518 TGAAATTTCGATAATCAC-T-CTA
1 TGAAATTTTGATAA-C-CTTACTA
*
35540 TGAGA-TTTGATAACCTT-CTA
1 TGAAATTTTGATAACCTTACTA
* **
35560 TCAAATTTTGAT-A-CTCCCTA
1 TGAAATTTTGATAACCTTACTA
*
35580 TGAAATTGAGACTTTTATAACCTT-CATA
1 TGAAA-T-----TTTGATAACCTTAC-TA
**
35608 TG-AATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTTACTA
*
35629 TAAAATTTTGATAACCT
1 TGAAATTTTGATAACCT
35646 CCCCATTAAA
Statistics
Matches: 234, Mismatches: 50, Indels: 44
0.71 0.15 0.13
Matches are distributed among these distances:
19 3 0.01
20 16 0.07
21 44 0.19
22 130 0.56
23 5 0.02
24 6 0.03
25 13 0.06
26 7 0.03
27 4 0.02
28 6 0.03
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTACTA
Found at i:35500 original size:21 final size:22
Alignment explanation
Indices: 35318--35572 Score: 153
Period size: 22 Copynumber: 11.6 Consensus size: 22
35308 AATCACATTT
* *
35318 TGAAAATTTGATAACCCTTT-TA
1 TGAAATTTTGATAA-TCTTTCTA
* *
35340 TGAAATTTTGATAACCTTTTTA
1 TGAAATTTTGATAATCTTTCTA
* * *
35362 TGGAATTTTGATAACCTTTTTA
1 TGAAATTTTGATAATCTTTCTA
* * * * **
35384 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAATCTTTCTA
* **
35406 TGAAATTCTGATAATCACAT-TA
1 TGAAATTTTGATAATC-TTTCTA
* * * *
35428 TGTAATTTTGATAACCTTGCTT
1 TGAAATTTTGATAATCTTTCTA
***
35450 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAATC-TTTCTA
35472 TGAAATTTTGATAATCTTTCTA
1 TGAAATTTTGATAATCTTTCTA
35494 T-AAATTTTGATAATCCTATCTCTA
1 TGAAATTTTGATAAT-CT-T-TCTA
* **
35518 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAATCTTTCTA
* *
35540 TGAGA-TTTGATAA-CCTTCTA
1 TGAAATTTTGATAATCTTTCTA
*
35560 TCAAATTTTGATA
1 TGAAATTTTGATA
35573 CTCCCTATGA
Statistics
Matches: 184, Mismatches: 39, Indels: 21
0.75 0.16 0.09
Matches are distributed among these distances:
20 8 0.04
21 33 0.18
22 121 0.66
23 4 0.02
24 6 0.03
25 12 0.07
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAATCTTTCTA
Found at i:35580 original size:68 final size:68
Alignment explanation
Indices: 35403--35572 Score: 176
Period size: 66 Copynumber: 2.5 Consensus size: 68
35393 GTTGACCCCT
* * * *
35403 CTATGAAATTCTGATAATCACAT-TATGTAATTTTGATAA-CCT-TGCT-T-TGAAATTTTGATA
1 CTATGAAATTTTGATAATC-CTTCTAT-AAATTTTGATAATCCTAT-CTCTATGAAATTTCGATA
35463 ACAACA
63 ACAACA
*
35469 CTATGAAATTTTGATAATCTTTCTATAAATTTTGATAATCCTATCTCTATGAAATTTCGATAATC
1 CTATGAAATTTTGATAATCCTTCTATAAATTTTGATAATCCTATCTCTATGAAATTTCGATAA-C
*
35534 -ACT
65 AACA
*
35537 CTATGAGA-TTTGATAA-CCTTCTATCAAATTTTGATA
1 CTATGAAATTTTGATAATCCTTCTAT-AAATTTTGATA
35573 CTCCCTATGA
Statistics
Matches: 89, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
65 12 0.13
66 33 0.37
67 21 0.24
68 22 0.25
69 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (68 bp):
CTATGAAATTTTGATAATCCTTCTATAAATTTTGATAATCCTATCTCTATGAAATTTCGATAACA
ACA
Found at i:35690 original size:22 final size:23
Alignment explanation
Indices: 35665--35722 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 23
35655 ATATTTAATA
35665 AAATTTTGT-TAACCACACTATG
1 AAATTTTGTATAACCACACTATG
* * *
35687 AAATTCTTATATAACCTCGCTATG
1 AAATT-TTGTATAACCACACTATG
*
35711 ACATTTTG-ATAA
1 AAATTTTGTATAA
35723 TCTCTTTGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
22 9 0.31
23 5 0.17
24 15 0.52
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (23 bp):
AAATTTTGTATAACCACACTATG
Found at i:35841 original size:22 final size:22
Alignment explanation
Indices: 35813--35887 Score: 116
Period size: 22 Copynumber: 3.4 Consensus size: 22
35803 AACCTGATCT
35813 TATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGGTAACCACAC
35835 TATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGGTAACCACAC
* *
35857 TATGAAATTTTGATAACCTC-C
1 TATGAAATTTTGGTAACCACAC
35878 TCATGAAATT
1 T-ATGAAATT
35888 ATAATAACCA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
21 2 0.04
22 48 0.96
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (22 bp):
TATGAAATTTTGGTAACCACAC
Found at i:35874 original size:44 final size:44
Alignment explanation
Indices: 35765--35920 Score: 129
Period size: 44 Copynumber: 3.5 Consensus size: 44
35755 AATTAATCAC
** * * *
35765 CCTATGAAATTTCAATAACCAACCT-AAGAGATTTTAATAACCTGAT
1 CCTATGAAATTTTGATAACC-ACCTCATGAAATTATAATAACC--AT
* * * **
35811 CTTATGAAATTTTGGTAACCACACT-ATGAAATTTTGGTAACCA-
1 CCTATGAAATTTTGATAACCAC-CTCATGAAATTATAATAACCAT
*
35854 CACTATGAAATTTTGATAACCTCCTCATGAAATTATAATAACCAT
1 C-CTATGAAATTTTGATAACCACCTCATGAAATTATAATAACCAT
* *
35899 CTTATGAAAATTTGATAACCAC
1 CCTATGAAATTTTGATAACCAC
35921 TTAGAGACAA
Statistics
Matches: 89, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
43 3 0.03
44 52 0.58
45 3 0.03
46 31 0.35
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.33
Consensus pattern (44 bp):
CCTATGAAATTTTGATAACCACCTCATGAAATTATAATAACCAT
Found at i:35905 original size:22 final size:21
Alignment explanation
Indices: 35809--35923 Score: 76
Period size: 22 Copynumber: 5.3 Consensus size: 21
35799 TAATAACCTG
*
35809 ATCTTATGAAATTTTGGTAACC
1 ATCTTATGAAA-TTTGATAACC
* *
35831 A-CACTATGAAATTTTGGTAACC
1 ATC-TTATGAAA-TTTGATAACC
*
35853 A-CACTATGAAATTTTGATAACC
1 ATC-TTATGAAA-TTTGATAACC
* *
35875 -TCCTCATGAAATTATAATAACC
1 AT-CTTATGAAATT-TGATAACC
35897 ATCTTATGAAAATTTGATAACC
1 ATCTTATG-AAATTTGATAACC
35919 A-CTTA
1 ATCTTA
35924 GAGACAAGAA
Statistics
Matches: 80, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
21 7 0.09
22 66 0.82
23 7 0.09
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (21 bp):
ATCTTATGAAATTTGATAACC
Found at i:36347 original size:19 final size:20
Alignment explanation
Indices: 36316--36358 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
36306 TATTGACATT
36316 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTAAAAAG
36335 TAAAATATT-AAATTCAAAAAG
1 TAAAA-ATTGAAATT-AAAAAG
36356 TAA
1 TAA
36359 TAGTAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 10 0.48
20 3 0.14
21 8 0.38
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (20 bp):
TAAAAATTGAAATTAAAAAG
Done.