Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012998.1 Corchorus capsularis cultivar CVL-1 contig13019, 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: 19881
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Found at i:1353 original size:15 final size:14
Alignment explanation
Indices: 1335--1381 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
1325 CTAAATTGAC
1335 ATTATTAAAATTTA
1 ATTATTAAAATTTA
*
1349 TATTATTTAAATATTA
1 -ATTATTAAAAT-TTA
1365 ATTA-TAAAATTTCA
1 ATTATTAAAATTT-A
1379 ATT
1 ATT
1382 TAGACTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 2 0.07
14 9 0.32
15 14 0.50
16 3 0.11
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTATTAAAATTTA
Found at i:1663 original size:20 final size:20
Alignment explanation
Indices: 1626--1664 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1616 TACTATTATT
1626 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
1646 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
1665 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:4484 original size:22 final size:22
Alignment explanation
Indices: 4458--4654 Score: 100
Period size: 22 Copynumber: 8.9 Consensus size: 22
4448 AAAAAAAAAA
4458 TCATAAGGAGGTTATCAAAATT
1 TCATAAGGAGGTTATCAAAATT
* * * *
4480 CCATAATGTGGTTACCAAAATT
1 TCATAAGGAGGTTATCAAAATT
* * * *
4502 CCATATGTAAGTTATCAAAATT
1 TCATAAGGAGGTTATCAAAATT
*
4524 TCAT-GGGAAGGTTATCAAAATT
1 TCATAAGG-AGGTTATCAAAATT
* *
4546 TCAT-AGTGTGGTTACCAAAATT
1 TCATAAG-GAGGTTATCAAAATT
* *
4568 TCAT-AGGATCAAGTTATTAAAATT
1 TCATAAGG---AGGTTATCAAAATT
* **
4592 TC-TTAGGAAGGTTATTGAAATT
1 TCATAAGG-AGGTTATCAAAATT
* *
4614 TCAT-AGTGTGGTTATCATAATT
1 TCATAAG-GAGGTTATCAAAATT
* *
4636 TTAT-AGAAAGGTTATCAAA
1 TCATAAG-GAGGTTATCAAA
4655 GGGATTATCA
Statistics
Matches: 134, Mismatches: 33, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
21 2 0.01
22 113 0.84
23 4 0.03
24 15 0.11
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TCATAAGGAGGTTATCAAAATT
Found at i:4605 original size:46 final size:44
Alignment explanation
Indices: 4490--5006 Score: 122
Period size: 44 Copynumber: 11.9 Consensus size: 44
4480 CCATAATGTG
* * * * *
4490 GTTACCAAAATTCCATA-TGTAAGTTATCAAAATTTCATGGGAAG
1 GTTATCAAAATTTCATAGTG-AGGTTATCAAAATTTCATAGGAAA
* *
4534 GTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATCAA
1 GTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGA--AA
* * ** **
4580 GTTATTAAAATTTCTTAG-GAAGGTTATTGAAATTTCATAGTG-TG
1 GTTATCAAAATTTCATAGTG-AGGTTATCAAAATTTCATAG-GAAA
* * ** *
4624 GTTATCATAATTTTATAGAAAGGTTATC---A----A-AGG-GA
1 GTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGAAA
* * **
4659 -TTATCAAAATGTCATAGCGAGGTTAT-AAGAATTTCATAGTGTGA
1 GTTATCAAAATTTCATAGTGAGGTTATCAA-AATTTCATAG-GAAA
* * * * *
4703 -TTAACAAAATTTCATAAG-GAGGTTA-CTAATATTTCATGGGGAG
1 GTTATCAAAATTTCAT-AGTGAGGTTATC-AAAATTTCATAGGAAA
* * * * **
4746 GCTATCAAAATTTTATAGTGTGGTTATCAAAACTTT-TTAGTG-TG
1 GTTATCAAAATTTCATAGTGAGGTTATCAAAA-TTTCATAG-GAAA
***
4790 GTTATCAAAATTTCATA-TGAAGGTTAT-AAAAGTTTCAATTTCATAA
1 GTTATCAAAATTTCATAGTG-AGGTTATCAAAA-TTTC-ATAGGA-AA
* * * * * * **
4836 G-GAGTACCAAATTTGATAG-AAGGTTATC-AAATCTCATA-TAGT
1 GTTA-T-CAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGAAA
* *
4878 GATTAT-AGAAATTTCATAGAGATCAGATTATCAAAATTT-ATAGG-AA
1 G-TTATCA-AAATTTCAT--AG-TGAGGTTATCAAAATTTCATAGGAAA
** * *
4924 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCG-AG
1 G-TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAG-GAAA
* * * *
4969 GTTATC-AAATTACATAATGTGATTATCAAAATTTCATA
1 GTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATA
5007 TAGGGTTCAA
Statistics
Matches: 345, Mismatches: 82, Indels: 93
0.66 0.16 0.18
Matches are distributed among these distances:
34 21 0.06
35 1 0.00
36 2 0.01
37 2 0.01
41 2 0.01
42 11 0.03
43 55 0.16
44 144 0.42
45 20 0.06
46 70 0.20
47 17 0.05
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (44 bp):
GTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGAAA
Found at i:4613 original size:68 final size:66
Alignment explanation
Indices: 4458--4654 Score: 227
Period size: 68 Copynumber: 3.0 Consensus size: 66
4448 AAAAAAAAAA
* * * *
4458 TCATAAGG-AGGTTATCAAAATTCCATAATGTGGTTACCAAAATTCCATATGTAAGTTATCAAAA
1 TCAT-AGGAAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGTAAGTTATCAAAA
4522 TT
65 TT
* *
4524 TCATGGGAAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATCAAGTTATTAAA
1 TCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGG-T-AAGTTATCAAA
4589 ATT
64 ATT
* ** * * * *
4592 TCTTAGGAAGGTTATTGAAATTTCATAGTGTGGTTATCATAATTTTATA-GAAAGGTTATCAAA
1 TCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGTAA-GTTATCAAA
4655 GGGATTATCA
Statistics
Matches: 112, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
65 4 0.04
66 51 0.46
67 2 0.02
68 55 0.49
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (66 bp):
TCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGTAAGTTATCAAAAT
T
Found at i:4684 original size:22 final size:22
Alignment explanation
Indices: 4659--5072 Score: 153
Period size: 22 Copynumber: 18.7 Consensus size: 22
4649 ATCAAAGGGA
* *
4659 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
4681 TTAT-AAGAATTTCATAGTGTGA
1 TTATCAA-AATTTCATAGTGAGG
*
4703 TTAACAAAATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAGG
* * *
4725 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* * *
4747 CTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* *
4769 TTATCAAAACTTT-TTAGTGTGG
1 TTATCAAAA-TTTCATAGTGAGG
4791 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
*
4813 TTAT-AAAAGTTTCAATTTCA-TAAGG
1 TTATCAAAA-TTTC-A--T-AGTGAGG
* * * *
4838 AGTA-CCAAATTTGATAG-AAGG
1 -TTATCAAAATTTCATAGTGAGG
*
4859 TTATC-AAATCTCATA-T-AGTG
1 TTATCAAAATTTCATAGTGAG-G
* *
4879 ATTAT-AGAAATTTCATAGAGATCAGA
1 -TTATCA-AAATTTCAT--AG-TGAGG
*
4905 TTATCAAAATTT-ATAG-GAAGA
1 TTATCAAAATTTCATAGTG-AGG
**
4926 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAGTGAGG
* *
4948 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
4970 TTATC-AAATTACATAATGTGA
1 TTATCAAAATTTCATAGTGAGG
4991 TTATCAAAATTTCATA-T-AGGG
1 TTATCAAAATTTCATAGTGA-GG
* * **
5012 TTCAACAAAATTTTATAAAGAGG
1 TT-ATCAAAATTTCATAGTGAGG
* * * * * *
5035 TTAACAAATTTTCAAAATGCGA
1 TTATCAAAATTTCATAGTGAGG
*
5057 TTACCAAAATTTCATA
1 TTATCAAAATTTCATA
5073 TGATATTTCT
Statistics
Matches: 298, Mismatches: 57, Indels: 74
0.69 0.13 0.17
Matches are distributed among these distances:
19 2 0.01
20 11 0.04
21 57 0.19
22 181 0.61
23 14 0.05
24 5 0.02
25 17 0.06
26 9 0.03
27 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:4953 original size:43 final size:43
Alignment explanation
Indices: 4903--5004 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
4893 ATAGAGATCA
* * *
4903 GATTATCAAAATTT-ATAG-GAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGCG-AGATTATC-AAATTACATAATG-T
*
4947 G-TTATCAAAATTTCAAAGCGAGGTTATCAAATTACATAATGT
1 GATTATCAAAATTTCAAAGCGAGATTATCAAATTACATAATGT
4989 GATTATCAAAATTTCA
1 GATTATCAAAATTTCA
5005 TATAGGGTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
42 2 0.04
43 37 0.73
44 11 0.22
45 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (43 bp):
GATTATCAAAATTTCAAAGCGAGATTATCAAATTACATAATGT
Found at i:5021 original size:65 final size:65
Alignment explanation
Indices: 4924--5074 Score: 164
Period size: 65 Copynumber: 2.3 Consensus size: 65
4914 TTTATAGGAA
* * * * *
4924 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAA-TTACATAAT
1 GATTATCAAAATTTCATA-TGTGGTTAACAAAATTTCATAA-AGAGGTTAACAAATTTACAAAAT
*
4987 GT
64 GC
* *
4989 GATTATCAAAATTTCATATAG-GGTTCAACAAAATTTTATAAAGAGGTTAACAAATTTTCAAAAT
1 GATTATCAAAATTTCATAT-GTGGTT-AACAAAATTTCATAAAGAGGTTAACAAATTTACAAAAT
5053 GC
64 GC
*
5055 GATTACCAAAATTTCATATG
1 GATTATCAAAATTTCATATG
5075 ATATTTCTGG
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
64 4 0.05
65 41 0.56
66 28 0.38
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (65 bp):
GATTATCAAAATTTCATATGTGGTTAACAAAATTTCATAAAGAGGTTAACAAATTTACAAAATGC
Found at i:5288 original size:22 final size:22
Alignment explanation
Indices: 5172--5396 Score: 143
Period size: 22 Copynumber: 10.1 Consensus size: 22
5162 TCAGGGAGAA
* *
5172 TATCAAAATTTCATAGTTTAGCT
1 TATCAAAATTTCATAG-TGAGGT
* *
5195 T-TCAAAATTTTATAAG-AAGGT
1 TATCAAAATTTCAT-AGTGAGGT
*
5216 TATCAAAATTTCATAGT-ATGT
1 TATCAAAATTTCATAGTGAGGT
* * * * *
5237 AGATTAGAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAGTGAGGT
* *
5260 TAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCATAGTGAGGT
** *
5282 TATCAAAAAATCATATGAAGAGGT
1 TATCAAAATTTCATA-G-TGAGGT
* * *
5306 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAGTG-AGGT
* * *
5329 TATCAAAATTTCATTGGGAAGT
1 TATCAAAATTTCATAGTGAGGT
5351 TATCAAAATTTCATAGTGAGGT
1 TATCAAAATTTCATAGTGAGGT
* * *
5373 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATAGTGAGGT
5395 TA
1 TA
5397 AATTTCATAA
Statistics
Matches: 152, Mismatches: 40, Indels: 21
0.71 0.19 0.10
Matches are distributed among these distances:
21 10 0.07
22 101 0.66
23 24 0.16
24 17 0.11
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGAGGT
Found at i:5486 original size:22 final size:22
Alignment explanation
Indices: 5172--5499 Score: 138
Period size: 22 Copynumber: 14.9 Consensus size: 22
5162 TCAGGGAGAA
** *
5172 TATCAAAATTTCATAGTTTAGCT
1 TATCAAAATTTCATAG-GAAGGT
* *
5195 T-TCAAAATTTTATAAGAAGGT
1 TATCAAAATTTCATAGGAAGGT
* *
5216 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATAGGAAGGT
* * * * *
5237 AGATTAGAATTTCATAGGGAGAT
1 -TATCAAAATTTCATAGGAAGGT
* *
5260 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-AGGAAGGT
** *
5282 TATCAAAAAATCATATGAAGAGGT
1 TATCAAAATTTCATA-GGA-AGGT
* * **
5306 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAG-GAAGGT
*
5329 TATCAAAATTTCATTGGGAA-GT
1 TATCAAAATTTCA-TAGGAAGGT
5351 TATCAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATAG-GAAGGT
* * *
5373 CT-TCAAAATTCCTTAGGGAGG-
1 -TATCAAAATTTCATAGGAAGGT
*
5394 T-T--AAATTTCATAAGAAGGT
1 TATCAAAATTTCATAGGAAGGT
** * *
5413 TAAAAAAATTTTATA-AAAGGAT
1 TATCAAAATTTCATAGGAAGG-T
* * * * **
5435 TCTCGAAATTCCATAGTATCGT
1 TATCAAAATTTCATAGGAAGGT
*
5457 TATTAAAATTTCATAGGAAGGT
1 TATCAAAATTTCATAGGAAGGT
*
5479 CATCAAAATTTCATAAGGAAG
1 TATCAAAATTTCAT-AGGAAG
5500 TCATAAAAAA
Statistics
Matches: 221, Mismatches: 64, Indels: 40
0.68 0.20 0.12
Matches are distributed among these distances:
18 12 0.05
19 1 0.00
20 2 0.01
21 17 0.08
22 140 0.63
23 31 0.14
24 18 0.08
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (22 bp):
TATCAAAATTTCATAGGAAGGT
Found at i:5510 original size:23 final size:22
Alignment explanation
Indices: 5461--5508 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
5451 TATCGTTATT
*
5461 AAAATTTCATAGGAAGGTCATC
1 AAAATTTCATAGGAAGGTCATA
5483 AAAATTTCATAAGGAA-GTCATA
1 AAAATTTCAT-AGGAAGGTCATA
5505 AAAA
1 AAAA
5509 ATAGTGTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTCATA
Found at i:5893 original size:3 final size:3
Alignment explanation
Indices: 5885--5932 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
5875 AAATCCACTA
5885 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
5933 TCATCCGATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:15742 original size:22 final size:22
Alignment explanation
Indices: 15717--15759 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
15707 GTTAGACTAG
15717 TTAGTAACTTATATTAGTATTC
1 TTAGTAACTTATATTAGTATTC
15739 TTAGTAACTTATATTAGTATT
1 TTAGTAACTTATATTAGTATT
15760 TTTTTTGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (22 bp):
TTAGTAACTTATATTAGTATTC
Found at i:15804 original size:61 final size:62
Alignment explanation
Indices: 15739--15859 Score: 226
Period size: 62 Copynumber: 2.0 Consensus size: 62
15729 ATTAGTATTC
*
15739 TTAGTAACTTATATTAGTATT-TTTTTTGTTAGTATCTTTTGGAAAATTGATCCTAATTTAG
1 TTAGTAACTTATATTAGTATTCTTTTTGGTTAGTATCTTTTGGAAAATTGATCCTAATTTAG
15800 TTAGTAACTTATATTAGTATTCTTTTTGGTTAGTATCTTTTGGAAAATTGATCCTAATTT
1 TTAGTAACTTATATTAGTATTCTTTTTGGTTAGTATCTTTTGGAAAATTGATCCTAATTT
15860 GGTGTTAAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
61 21 0.36
62 37 0.64
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.52
Consensus pattern (62 bp):
TTAGTAACTTATATTAGTATTCTTTTTGGTTAGTATCTTTTGGAAAATTGATCCTAATTTAG
Found at i:15861 original size:33 final size:33
Alignment explanation
Indices: 15766--15862 Score: 94
Period size: 33 Copynumber: 3.1 Consensus size: 33
15756 TATTTTTTTT
*
15766 GTTAGTATCTTTTGGAAAATTGATCCTAATTTA
1 GTTAGTATCTTTTGGAAAATTGATCCTAATTTG
* * ** * * *
15799 GTTAGTAACTTAT--ATTAGT-ATTCT-TTTTG
1 GTTAGTATCTTTTGGAAAATTGATCCTAATTTG
15828 GTTAGTATCTTTTGGAAAATTGATCCTAATTTG
1 GTTAGTATCTTTTGGAAAATTGATCCTAATTTG
15861 GT
1 GT
15863 GTTAAATAAC
Statistics
Matches: 45, Mismatches: 15, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
29 14 0.31
30 4 0.09
31 6 0.13
32 4 0.09
33 17 0.38
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.48
Consensus pattern (33 bp):
GTTAGTATCTTTTGGAAAATTGATCCTAATTTG
Found at i:18851 original size:29 final size:29
Alignment explanation
Indices: 18819--19002 Score: 156
Period size: 29 Copynumber: 6.3 Consensus size: 29
18809 TGCGGCACCC
* * *
18819 TCTTCAAAGGTGGTGTGTGTACGACGCTT
1 TCTTCCAAGATGGTGGGTGTACGACGCTT
** *
18848 TCTTCCAAGATGGTGGGTGTACGGTGCTG
1 TCTTCCAAGATGGTGGGTGTACGACGCTT
* *
18877 TCTTCCAAGATGGTGGGCGTACGACGCCCT
1 TCTTCCAAGATGGTGGGTGTACGACG-CTT
* * *
18907 T-TTCCAAGATGGTGAGTGTACGACACCT
1 TCTTCCAAGATGGTGGGTGTACGACGCTT
* * * * *
18935 TCATCTAAGATGGTGGGTATACGATGCTC
1 TCTTCCAAGATGGTGGGTGTACGACGCTT
* * * *
18964 ACGTCCAAGATGGTGGGCGTACGACGGCAT
1 TCTTCCAAGATGGTGGGTGTACGAC-GCTT
18994 T-TTCCAAGA
1 TCTTCCAAGA
19003 AGATGAGCAT
Statistics
Matches: 120, Mismatches: 32, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
28 4 0.03
29 112 0.93
30 4 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (29 bp):
TCTTCCAAGATGGTGGGTGTACGACGCTT
Found at i:18945 original size:87 final size:87
Alignment explanation
Indices: 18829--19002 Score: 240
Period size: 87 Copynumber: 2.0 Consensus size: 87
18819 TCTTCAAAGG
* * * * * * ** *
18829 TGGTGTGTGTACGACGCTTTCTTCCAAGATGGTGGGTGTACGGTGCTGTCTTCCAAGATGGTGGG
1 TGGTGAGTGTACGACACCTTCATCCAAGATGGTGGGTATACGATGCTCACGTCCAAGATGGTGGG
*
18894 CGTACGACGCCCTTTTCCAAGA
66 CGTACGACGCCATTTTCCAAGA
*
18916 TGGTGAGTGTACGACACCTTCATCTAAGATGGTGGGTATACGATGCTCACGTCCAAGATGGTGGG
1 TGGTGAGTGTACGACACCTTCATCCAAGATGGTGGGTATACGATGCTCACGTCCAAGATGGTGGG
*
18981 CGTACGACGGCATTTTCCAAGA
66 CGTACGACGCCATTTTCCAAGA
19003 AGATGAGCAT
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
87 75 1.00
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (87 bp):
TGGTGAGTGTACGACACCTTCATCCAAGATGGTGGGTATACGATGCTCACGTCCAAGATGGTGGG
CGTACGACGCCATTTTCCAAGA
Found at i:19021 original size:87 final size:87
Alignment explanation
Indices: 18853--19037 Score: 228
Period size: 87 Copynumber: 2.1 Consensus size: 87
18843 CGCTTTCTTC
* * ** * * *
18853 CAAGATGGTGGGTGTACGGTGCTGTCTTCCAAGATGGTGGGCGTACGACGCCCTTTTCCAAGATG
1 CAAGATGGTGGGTATACGATGCTCACGTCCAAGATGGTGGGCGTACGACGCCATTTTCCAAGAAG
* ** *
18918 GTGAGTGTACGACACCTTCATCT
66 ATGAGCATACCACACCTTC-TCT
*
18941 -AAGATGGTGGGTATACGATGCTCACGTCCAAGATGGTGGGCGTACGACGGCATTTTCCAAGAAG
1 CAAGATGGTGGGTATACGATGCTCACGTCCAAGATGGTGGGCGTACGACGCCATTTTCCAAGAAG
* *
19005 ATGAGCATACCTCACCTTCTTT
66 ATGAGCATACCACACCTTCTCT
19027 CAAGATGGTGG
1 CAAGATGGTGG
19038 ACGTGCGGCG
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
86 2 0.02
87 80 0.98
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.26
Consensus pattern (87 bp):
CAAGATGGTGGGTATACGATGCTCACGTCCAAGATGGTGGGCGTACGACGCCATTTTCCAAGAAG
ATGAGCATACCACACCTTCTCT
Found at i:19097 original size:29 final size:29
Alignment explanation
Indices: 19073--19175 Score: 127
Period size: 29 Copynumber: 3.6 Consensus size: 29
19063 GGTGTACCGT
**
19073 GCCCTCTTCCAAGATGGTGGCTGTATAAC
1 GCCCTCTTCCAAGATGGTGGCTGTACGAC
* *
19102 GCCCTC-TCCAAAGATGGTGGTTGTACGCC
1 GCCCTCTTCC-AAGATGGTGGCTGTACGAC
* *
19131 GCCCTCTCCCAAGATGGTTGCTGTACGAC
1 GCCCTCTTCCAAGATGGTGGCTGTACGAC
*
19160 GCCTTCTTCCAAGATG
1 GCCCTCTTCCAAGATG
19176 CTTGGCGCGC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 57 0.92
30 2 0.03
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.26
Consensus pattern (29 bp):
GCCCTCTTCCAAGATGGTGGCTGTACGAC
Found at i:19328 original size:28 final size:28
Alignment explanation
Indices: 19296--19433 Score: 163
Period size: 28 Copynumber: 5.0 Consensus size: 28
19286 AGCGTTCTAT
* *
19296 GCTTTGTAATCTTTGGGGGCGTACTACC
1 GCTTTGTGATCTTTGAGGGCGTACTACC
*
19324 GCTTTGTGATCTTCGAGGGCGTACTACC
1 GCTTTGTGATCTTTGAGGGCGTACTACC
* * *
19352 GCTTTATAATCCTTT-AGGGCATACTACC
1 GCTTTGTGAT-CTTTGAGGGCGTACTACC
*
19380 GCTTTGTGATCCTTGAGGGCGTACTACC
1 GCTTTGTGATCTTTGAGGGCGTACTACC
* * *
19408 GTTTTGCGATCTTTGA-GGCGAACTAC
1 GCTTTGTGATCTTTGAGGGCGTACTAC
19434 GCCCTTTCCA
Statistics
Matches: 93, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
27 12 0.13
28 78 0.84
29 3 0.03
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.34
Consensus pattern (28 bp):
GCTTTGTGATCTTTGAGGGCGTACTACC
Done.