Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017045.1 Corchorus olitorius cultivar O-4 contig17078, 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: 48255
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Found at i:1747 original size:15 final size:15
Alignment explanation
Indices: 1716--1744 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1706 AAATTTCAAC
1716 AAAATAAAATATATT
1 AAAATAAAATATATT
1731 AAAATAAAA-ATATT
1 AAAATAAAATATATT
1745 TAATTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATAAAATATATT
Found at i:4680 original size:39 final size:39
Alignment explanation
Indices: 4626--4705 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
4616 CCTCATCTTA
*
4626 ATTATCCTTTATTTTTTAAAAGTTTCTCTTTAATTACTC
1 ATTATCCTTTATTTTTTAAAAGTTTCTCTTCAATTACTC
*
4665 ATTATCTTTTATTTTTTAAAAGTTTCTCTTCAATTACTC
1 ATTATCCTTTATTTTTTAAAAGTTTCTCTTCAATTACTC
4704 AT
1 AT
4706 CAATTATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.26, C:0.15, G:0.03, T:0.56
Consensus pattern (39 bp):
ATTATCCTTTATTTTTTAAAAGTTTCTCTTCAATTACTC
Found at i:8030 original size:11 final size:11
Alignment explanation
Indices: 8016--8053 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
8006 ATTCATAACA
8016 AATTTATAATT
1 AATTTATAATT
8027 AATTTATAATT
1 AATTTATAATT
8038 -ATTTGATAATT
1 AATTT-ATAATT
*
8049 TATTT
1 AATTT
8054 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:18087 original size:55 final size:55
Alignment explanation
Indices: 18015--18156 Score: 284
Period size: 55 Copynumber: 2.6 Consensus size: 55
18005 AATTAAAATA
18015 AAAAAAAAACCCTTAACCAATGTCATGGGCCATAAAAATCAATTTAAATTTCCCT
1 AAAAAAAAACCCTTAACCAATGTCATGGGCCATAAAAATCAATTTAAATTTCCCT
18070 AAAAAAAAACCCTTAACCAATGTCATGGGCCATAAAAATCAATTTAAATTTCCCT
1 AAAAAAAAACCCTTAACCAATGTCATGGGCCATAAAAATCAATTTAAATTTCCCT
18125 AAAAAAAAACCCTTAACCAATGTCATGGGCCA
1 AAAAAAAAACCCTTAACCAATGTCATGGGCCA
18157 ATGGCCCATC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 87 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (55 bp):
AAAAAAAAACCCTTAACCAATGTCATGGGCCATAAAAATCAATTTAAATTTCCCT
Found at i:25835 original size:65 final size:65
Alignment explanation
Indices: 25757--25886 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
25747 ACATCCTTAC
*
25757 TATATTTGTTTCTGCTTTACAGTAACAACTTCTGAAGAATAGCCTAAATAAAACAACAATTTTTG
1 TATATTTGTTTCTGCTTTACAGTAACAACTTCTGAAGAATAGCCTAAACAAAACAACAATTTTTG
25822 TATATTTGTTTCTGCTTTACAGTAACAACTTCTGAAGAATAGCCTAAACAAAACAACAATTTTTG
1 TATATTTGTTTCTGCTTTACAGTAACAACTTCTGAAGAATAGCCTAAACAAAACAACAATTTTTG
25887 CCATATATAA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (65 bp):
TATATTTGTTTCTGCTTTACAGTAACAACTTCTGAAGAATAGCCTAAACAAAACAACAATTTTTG
Found at i:27354 original size:14 final size:14
Alignment explanation
Indices: 27335--27366 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
27325 ATTTCACTAT
27335 TTTTAGACTTTTAG
1 TTTTAGACTTTTAG
*
27349 TTTTAGGCTTTTAG
1 TTTTAGACTTTTAG
27363 TTTT
1 TTTT
27367 TAATTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.06, G:0.16, T:0.62
Consensus pattern (14 bp):
TTTTAGACTTTTAG
Found at i:33112 original size:16 final size:16
Alignment explanation
Indices: 33093--33124 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
33083 AGAAGATAGT
33093 GAAGAAGGAAGAAAAA
1 GAAGAAGGAAGAAAAA
33109 GAAGAAGGAAGAAAAA
1 GAAGAAGGAAGAAAAA
33125 ATTCCTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
GAAGAAGGAAGAAAAA
Found at i:39645 original size:437 final size:436
Alignment explanation
Indices: 38736--39728 Score: 1140
Period size: 439 Copynumber: 2.2 Consensus size: 436
38726 GATCGAAATT
* * *
38736 ACAAAATTTCA-AAAGTATTTTTTAGAATTTAAACATGAAAATTAGCTTTTGAGTCTTTCATGAA
1 ACAAAATTTCAGAAA-TATTTTTTA-AATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATG-A
* * * * *
38800 ATAGTTGTAGATCATAAAATTACTTTTTAATAGACACTTGAATTACCTTAATTGGACAAATAGAA
63 A-AGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCAACTTAATCGGACAAATAGAA
* *
38865 CAGAGAAAATAAAAAATGAAGCGTTAAATCGAGTAAAATAGAATTTGTAAAGAACTAAGTAGCAT
127 CAGAGAAAATAAAAAATAAAGCGTTAAATCGAGTAAAATAGAATTTATAAAGAACTAAGTAG---
* * * * *
38930 AAAATATATAAAATAGAAAAGTATGAGGGTCATTTGATAACTAATTCAAATAAGAAATTATTTCT
189 -----ATATAAAATAGAAAAATATAAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTCT
* * * *
38995 TAATGGATATCTTGAAACATAAAAATTCCCTCCTGAACCCTTCATGAAACTCGTAGCTTAAATTA
249 TAATGGAGATCTTGAAACATAAAAACTCCCTCCTGAACCCTTCATGAAACTCGTAGATCAAATTA
* * * ** ** *
39060 ACTTTCGGCTTCTTCATGAAAGTCGTAGCTCATACAGTAACCTTTTAACCGACACTTGAATAACT
314 ACTTTCGGCTCCTTCAAGAAAGTCATAAATCATACAACAACCTTTTAACCGACACTTCAATAACT
* * * * * *
39125 TTAATCGGACATGTGGATCGAAAATTATATGGTATTAAATAGACCAACAATCGAAACG
379 TCAATCGGACATGTGGATCAAAAATTATACGATATTAAATAGACCAACAATCAAAACC
* * * *
39183 ACCAAATTT-AGGAAGCAT-TTTTTTTAATTAAAACATAAAAATTTGTTTTTGAGTCCTTCATGA
1 ACAAAATTTCA-GAA--ATATTTTTTAAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGA
* * *
39246 AAGTTGTAAATCATGAAATTACCTTTTAATAGACACATGAATCAATTTAATCGGACAAATAGAAC
63 AAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCAACTTAATCGGACAAATAGAAC
* *
39311 A-A-AAAATAAAAAAATAAATC-TTAAA-CGTTAGATGAAGATAGAATTTATAAAGAACTAAGTA
128 AGAGAAAAT-AAAAAATAAAGCGTTAAATCG--AG-T-AAAATAGAATTTATAAAGAACTAAGTA
* * *
39372 G-TATAAAATAGAAAAATATAAGGGTTATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAAT
188 GATATAAAATAGAAAAATATAAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTCTTAAT
* ** * *
39436 GGAGATCTTGAAGCATAAAAACTCCCTTTTGAGCCCTTCATGAAACTCGTAGATCAAATTTAGCT
253 GGAGATCTTGAAACATAAAAACTCCCTCCTGAACCCTTCATGAAACTCGTAGATCAAA-TTAACT
* * *
39501 TTCGGGTCCTTCAAGAAGGTCATAAATCATGCAACAACCTTTTAACCGACACTTCAATAACTTCA
317 TTCGGCTCCTTCAAGAAAGTCATAAATCATACAACAACCTTTTAACCGACACTTCAATAACTTCA
* * **
39566 ATCGGATATGTGGA-CAAAAAAATTATACGATATTAAATTGACCGGCAATCAAAACC
382 ATCGGACATGTGGATC--AAAAATTATACGATATTAAATAGACCAACAATCAAAACC
* * * *
39622 ACAAAATTTCAGAAATATTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGTTCTTCATGAAA
1 ACAAAATTTCAGAAATATTTTTTA-AATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAA
* *
39687 ATTGTAGATCATGAAATAACCTTTTAATAGACACTTGAATCA
65 GTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCA
39729 CAAATAGGGA
Statistics
Matches: 463, Mismatches: 68, Indels: 38
0.81 0.12 0.07
Matches are distributed among these distances:
437 108 0.23
438 77 0.17
439 115 0.25
440 1 0.00
442 2 0.00
443 10 0.02
444 13 0.03
445 58 0.13
446 29 0.06
447 40 0.09
448 8 0.02
449 1 0.00
450 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (436 bp):
ACAAAATTTCAGAAATATTTTTTAAATTAAAACATAAAAATTAGCTTTTGAGTCCTTCATGAAAG
TTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCAACTTAATCGGACAAATAGAACAGA
GAAAATAAAAAATAAAGCGTTAAATCGAGTAAAATAGAATTTATAAAGAACTAAGTAGATATAAA
ATAGAAAAATATAAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTCTTAATGGAGATCT
TGAAACATAAAAACTCCCTCCTGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGCTCC
TTCAAGAAAGTCATAAATCATACAACAACCTTTTAACCGACACTTCAATAACTTCAATCGGACAT
GTGGATCAAAAATTATACGATATTAAATAGACCAACAATCAAAACC
Found at i:42981 original size:22 final size:23
Alignment explanation
Indices: 42921--42987 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
42911 TTGAAGATCT
*
42921 CACTATGAAATTTTGATAACCAA
1 CACTATGAAATATTGATAACCAA
* * **
42944 CACTATGAGATGTTGATAACCTC
1 CACTATGAAATATTGATAACCAA
*
42967 CA-TATGATATATTGATAACCA
1 CACTATGAAATATTGATAACCA
42988 CGTTATGAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 16 0.43
23 21 0.57
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (23 bp):
CACTATGAAATATTGATAACCAA
Found at i:43105 original size:23 final size:23
Alignment explanation
Indices: 43056--43115 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
43046 GATAATCACA
* *
43056 CTATGAAATTGTGA-TAACCTTT
1 CTATAAAATTTTGATTAACCTTT
43078 CTATAAAATTTTGATTAACCTCTT
1 CTATAAAATTTTGATTAACCT-TT
43102 -TATAAAATTTTGAT
1 CTATAAAATTTTGAT
43116 AAGCTCCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 12 0.35
23 20 0.59
24 2 0.06
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (23 bp):
CTATAAAATTTTGATTAACCTTT
Found at i:43131 original size:22 final size:22
Alignment explanation
Indices: 42871--43285 Score: 200
Period size: 22 Copynumber: 19.0 Consensus size: 22
42861 TAATTTTTTT
* *
42871 TAACCTTCTTATGAAATTTTGT
1 TAACCTCCTTATGAAATTTTGA
* * * *
42893 TAAACTCCCTAAGGAATTTTGA
1 TAACCTCCTTATGAAATTTTGA
*
42915 -AGATCTCAC-TATGAAATTTTGA
1 TA-ACCTC-CTTATGAAATTTTGA
* * *
42937 TAACCAACAC-TATGAGATGTTGA
1 TAACC-TC-CTTATGAAATTTTGA
* * *
42960 TAACCTCCATATGATATATTGA
1 TAACCTCCTTATGAAATTTTGA
* * * *
42982 TAACCACGTTATGAAAATTTAA
1 TAACCTCCTTATGAAATTTTGA
*
43004 AAACCT-CTATATG-AATTGTT-A
1 TAACCTCCT-TATGAAATT-TTGA
* *
43025 GTAATCACAC-TATGAAATTTTGA
1 -TAACCTC-CTTATGAAATTTTGA
* * *
43048 TAATCACAC-TATGAAATTGTGA
1 TAACCTC-CTTATGAAATTTTGA
* *
43070 TAACCT-TTCTATAAAATTTTGA
1 TAACCTCCT-TATGAAATTTTGA
* *
43092 TTAACCTCTTTATAAAATTTTGA
1 -TAACCTCCTTATGAAATTTTGA
* * *
43115 TAAGCTCCTTATGAAATCTTAA
1 TAACCTCCTTATGAAATTTTGA
*
43137 TAA----C-TA-CAAATTTTGA
1 TAACCTCCTTATGAAATTTTGA
* **
43153 TAACCTCCCTATGATTTTTTGA
1 TAACCTCCTTATGAAATTTTGA
* *
43175 TAACCTCATTATGAAATTTTGT
1 TAACCTCCTTATGAAATTTTGA
* *
43197 TAATCTCCCTATGAAATTTTGA
1 TAACCTCCTTATGAAATTTTGA
43219 TAAACCT-CTTATGAAATTTTGA
1 T-AACCTCCTTATGAAATTTTGA
* *
43241 -AAACTAAAC-TATGAAATTTTGA
1 TAACCT--CCTTATGAAATTTTGA
* *
43263 TAACCTTCATATGAAATTTTGA
1 TAACCTCCTTATGAAATTTTGA
43285 T
1 T
43286 TTCCTTCCTG
Statistics
Matches: 304, Mismatches: 61, Indels: 56
0.72 0.14 0.13
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
18 1 0.00
20 5 0.02
21 10 0.03
22 219 0.72
23 54 0.18
24 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TAACCTCCTTATGAAATTTTGA
Found at i:43291 original size:22 final size:21
Alignment explanation
Indices: 43144--43308 Score: 79
Period size: 22 Copynumber: 7.6 Consensus size: 21
43134 TAATAACTAC
* *
43144 AAATTTTGATAACCTCCCTATG
1 AAATTTTGATTACCT-TCTATG
** *
43166 ATTTTTTGATAACC-TCATTATG
1 AAATTTTGATTACCTTC--TATG
* *
43188 AAATTTTG-TTAATCTCCCTATG
1 AAATTTTGATT-ACCT-TCTATG
*
43210 AAATTTTGATAAACC-TCTTATG
1 AAATTTTGAT-TACCTTC-TATG
* * *
43232 AAATTTTGA-AAACTAAACTATG
1 AAATTTTGATTACCT--TCTATG
*
43254 AAATTTTGATAACCTTCATATG
1 AAATTTTGATTACCTTC-TATG
* *
43276 AAATTTTGATTTCCTTC-CTG
1 AAATTTTGATTACCTTCTATG
43296 AAATTTTGATTAC
1 AAATTTTGATTAC
43309 TCCATAGTAA
Statistics
Matches: 111, Mismatches: 19, Indels: 28
0.70 0.12 0.18
Matches are distributed among these distances:
20 18 0.16
21 3 0.03
22 81 0.73
23 8 0.07
24 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (21 bp):
AAATTTTGATTACCTTCTATG
Found at i:43463 original size:22 final size:22
Alignment explanation
Indices: 43411--43829 Score: 209
Period size: 22 Copynumber: 18.9 Consensus size: 22
43401 AATCACATTT
* * *
43411 TGAAAATTTAATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
43433 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
43455 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
***
43477 TGAAATTTTGATATTTTCAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * *
43499 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTCTCTA
** *
43521 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTCTA
* * *
43543 CGAAATTTTGATGATCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
43565 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTCTA
** * *
43589 TGAAATTTCAATAATCACTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
43611 TGAGA-TTTGATAACC-ATCTA
1 TGAAATTTTGATAACCTCTCTA
* *
43631 TCAAATTTTGGT-A-CTC-CTTA
1 TGAAATTTTGATAACCTCTC-TA
*
43651 TGAAATTAAGACTTTTATAACCT-TCATA
1 TGAAA-T-----TTTGATAACCTCTC-TA
* *
43679 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
** * *
43701 AAAAATTTTAATAACCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
43723 TGAAATTTTGATAACCT-TCCTA
1 TGAAATTTTGATAACCTCT-CTA
*
43745 TGAAATATT-AGTAACCTC-CTTA
1 TGAAATTTTGA-TAACCTCTC-TA
* * *
43767 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTCTCTA
*
43789 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTCTCTA
* *
43811 TGACATTTTGATAATCTCT
1 TGAAATTTTGATAACCTCT
43830 TTGATAACCT
Statistics
Matches: 294, Mismatches: 72, Indels: 62
0.69 0.17 0.14
Matches are distributed among these distances:
19 2 0.01
20 15 0.05
21 28 0.10
22 211 0.72
23 5 0.02
24 6 0.02
25 11 0.04
26 4 0.01
27 2 0.01
28 10 0.03
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:43725 original size:44 final size:44
Alignment explanation
Indices: 43677--43973 Score: 186
Period size: 44 Copynumber: 6.4 Consensus size: 44
43667 ATAACCTTCA
*
43677 TATGAAATTTTGATAACCACACTAAAAAATTTTAATAACCACAT
1 TATGAAATTTTGATAACCACACTATAAAATTTTAATAACCACAT
* * * * * *
43721 TATGAAATTTTGATAACCTTC-CTATGAAATATTAGTAACCTCCT
1 TATGAAATTTTGATAACC-ACACTATAAAATTTTAATAACCACAT
* *
43765 TATGAAATTTTGTTAACCACACTATGAAATTCTT-ATAACCTCGCTATGACAT
1 TATGAAATTTTGATAACCACACTATAAAATT-TTAATAA---C-C----ACAT
* *** * * *
43817 TTTGATAATCTCTTTGATAACCTTTCTATAAAATTGTGATAACCACAC
1 TATGA-AA--T-TTTGATAACCACACTATAAAATTTTAATAACCACAT
** * * **
43865 TATGAAATTTCAATAACCTTC-CTAAAAGAATTTTAATAACCTGAT
1 TATGAAATTTTGATAACC-ACACTATAA-AATTTTAATAACCACAT
* * *
43910 CCTATGAAATTTTGGTAACCACACTATAAAATTTTGATAACCACAC
1 --TATGAAATTTTGATAACCACACTATAAAATTTTAATAACCACAT
43956 TATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
43974 TTCCCATGAT
Statistics
Matches: 191, Mismatches: 41, Indels: 42
0.70 0.15 0.15
Matches are distributed among these distances:
43 1 0.01
44 94 0.49
45 17 0.09
46 14 0.07
47 23 0.12
48 8 0.04
52 7 0.04
53 3 0.02
55 2 0.01
56 22 0.12
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (44 bp):
TATGAAATTTTGATAACCACACTATAAAATTTTAATAACCACAT
Found at i:43867 original size:22 final size:22
Alignment explanation
Indices: 43842--44087 Score: 117
Period size: 22 Copynumber: 11.0 Consensus size: 22
43832 GATAACCTTT
*
43842 CTATAAAATTGTGATAACCACA
1 CTATAAAATTTTGATAACCACA
* ** *
43864 CTATGAAATTTCAATAACCTTC-
1 CTATAAAATTTTGATAACC-ACA
* *
43886 CTAAAAGAATTTTAATAACCTGATC-
1 CTATAA-AATTTTGATAACC--A-CA
* *
43911 CTATGAAATTTTGGTAACCACA
1 CTATAAAATTTTGATAACCACA
43933 CTATAAAATTTTGATAACCACA
1 CTATAAAATTTTGATAACCACA
* *
43955 CTATGAAATTTTGATAACCTTC-
1 CTATAAAATTTTGATAACC-ACA
* * ** **
43977 CCATGATGTTTTGATAACTTTCA
1 CTATAAAATTTTGATAAC-CACA
* *
44000 -TATGAAATTTTGGTAACCACA
1 CTATAAAATTTTGATAACCACA
** **
44021 CTATGGAATTTTGATAACTTC-
1 CTATAAAATTTTGATAACCACA
* * *
44042 CTCATGAAATTATAATAACCATC-
1 CT-ATAAAATTTTGATAACCA-CA
* *
44065 TTATGAAATTTTGATAACCACA
1 CTATAAAATTTTGATAACCACA
44087 C
1 C
44088 AGAGAAAAGA
Statistics
Matches: 171, Mismatches: 41, Indels: 24
0.72 0.17 0.10
Matches are distributed among these distances:
21 6 0.04
22 133 0.78
23 16 0.09
24 11 0.06
25 5 0.03
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
CTATAAAATTTTGATAACCACA
Found at i:44011 original size:66 final size:66
Alignment explanation
Indices: 43925--44087 Score: 204
Period size: 66 Copynumber: 2.5 Consensus size: 66
43915 GAAATTTTGG
* ** *
43925 TAACCA-CACTATAAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCC-CATGATGTTT
1 TAACCATCA-TATGAAATTTTGATAACCACACTATGAAATTTTGATAA-CTTCCTCATGAAATTA
*
43988 TGA
64 TAA
** * *
43991 TAACTTTCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACTTCCTCATGAAATTATA
1 TAACCATCATATGAAATTTTGATAACCACACTATGAAATTTTGATAACTTCCTCATGAAATTATA
44056 A
66 A
*
44057 TAACCATCTTATGAAATTTTGATAACCACAC
1 TAACCATCATATGAAATTTTGATAACCACAC
44088 AGAGAAAAGA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
65 5 0.06
66 75 0.91
67 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (66 bp):
TAACCATCATATGAAATTTTGATAACCACACTATGAAATTTTGATAACTTCCTCATGAAATTATA
A
Found at i:44033 original size:44 final size:44
Alignment explanation
Indices: 43911--44052 Score: 141
Period size: 44 Copynumber: 3.2 Consensus size: 44
43901 TAACCTGATC
* *
43911 CTATGAAATTTTGGTAACCACACTATAAAATTTTGATAAC-CACA
1 CTATGAAATTTTGGTAACCACACTAT-GAATTTTGATAACTTACA
* * * * *
43955 CTATGAAATTTTGATAACCTTC-CCATGATGTTTTGATAACTTTCA
1 CTATGAAATTTTGGTAACC-ACACTATGA-ATTTTGATAACTTACA
44000 -TATGAAATTTTGGTAACCACACTATGGAATTTTGATAACTT-C-
1 CTATGAAATTTTGGTAACCACACTAT-GAATTTTGATAACTTACA
44042 CTCATGAAATT
1 CT-ATGAAATT
44053 ATAATAACCA
Statistics
Matches: 80, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
43 4 0.05
44 71 0.89
45 5 0.06
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (44 bp):
CTATGAAATTTTGGTAACCACACTATGAATTTTGATAACTTACA
Found at i:44290 original size:20 final size:20
Alignment explanation
Indices: 44252--44290 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
44242 TATTGACATT
44252 TAAAAAATTGAAATTAAAAG
1 TAAAAAATTGAAATTAAAAG
*
44272 TAAAATATT-AAATTCAAAA
1 TAAAAAATTGAAATT-AAAA
44291 AATAATAGTA
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:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
TAAAAAATTGAAATTAAAAG
Found at i:45535 original size:23 final size:23
Alignment explanation
Indices: 45505--45550 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
45495 ATACCATCAT
45505 AAAGGATCAACCACATTAGTGCA
1 AAAGGATCAACCACATTAGTGCA
45528 AAAGGATCAACCACATTAGTGCA
1 AAAGGATCAACCACATTAGTGCA
45551 CAATTGCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.17
Consensus pattern (23 bp):
AAAGGATCAACCACATTAGTGCA
Found at i:48239 original size:11 final size:12
Alignment explanation
Indices: 48218--48242 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48208 TGTTAAAGTG
48218 TTTCTTTTTTTT
1 TTTCTTTTTTTT
48230 TTTCTTTTTTTT
1 TTTCTTTTTTTT
48242 T
1 T
48243 AATTATAATT
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTCTTTTTTTT
Done.