Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010121.1 Corchorus capsularis cultivar CVL-1 contig10142, 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: 62604
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4279 original size:18 final size:18
Alignment explanation
Indices: 4258--4390 Score: 113
Period size: 18 Copynumber: 7.4 Consensus size: 18
4248 TGTTGAACAA
*
4258 GTGCGGCCAGTTGGTGCG
1 GTGCGGCCACTTGGTGCG
4276 GTGCGGCCACTTGGTGCG
1 GTGCGGCCACTTGGTGCG
*** *
4294 GTGCAATCACTTGGTGTG
1 GTGCGGCCACTTGGTGCG
* **
4312 GTGCGACCACTTGGTATG
1 GTGCGGCCACTTGGTGCG
* * *
4330 GTGCGGCTACTGGGTGTG
1 GTGCGGCCACTTGGTGCG
** *
4348 GTGCGATCACTTGGTGTG
1 GTGCGGCCACTTGGTGCG
* **
4366 GTGCGACCACTTGGTATG
1 GTGCGGCCACTTGGTGCG
4384 GTGCGGC
1 GTGCGGC
4391 TATTCGGTGT
Statistics
Matches: 96, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 96 1.00
ACGTcount: A:0.11, C:0.21, G:0.41, T:0.27
Consensus pattern (18 bp):
GTGCGGCCACTTGGTGCG
Found at i:4315 original size:36 final size:35
Alignment explanation
Indices: 4268--4388 Score: 125
Period size: 36 Copynumber: 3.4 Consensus size: 35
4258 GTGCGGCCAG
* * * *
4268 TTGGTGCGGTGCGGCCACTTGGTGCGGTGCAATCAC
1 TTGGTGTGGTGCGACCACTTGGTGTGGTGC-ACCAC
* * *
4304 TTGGTGTGGTGCGACCACTTGGTATGGTGCGGCTAC
1 TTGGTGTGGTGCGACCACTTGGTGTGGTGC-ACCAC
* *
4340 TGGGTGTGGTGCGATCACTTGGTGTGGTGCGACCAC
1 TTGGTGTGGTGCGACCACTTGGTGTGGTGC-ACCAC
*
4376 TTGGTATGGTGCG
1 TTGGTGTGGTGCG
4389 GCTATTCGGT
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 70 1.00
ACGTcount: A:0.11, C:0.20, G:0.40, T:0.29
Consensus pattern (35 bp):
TTGGTGTGGTGCGACCACTTGGTGTGGTGCACCAC
Found at i:4351 original size:54 final size:54
Alignment explanation
Indices: 4275--4402 Score: 202
Period size: 54 Copynumber: 2.4 Consensus size: 54
4265 CAGTTGGTGC
* * *
4275 GGTGCGGCCACTTGGTGCGGTGCAATCACTTGGTGTGGTGCGACCACTTGGTAT
1 GGTGCGGCTACTCGGTGTGGTGCAATCACTTGGTGTGGTGCGACCACTTGGTAT
* *
4329 GGTGCGGCTACTGGGTGTGGTGCGATCACTTGGTGTGGTGCGACCACTTGGTAT
1 GGTGCGGCTACTCGGTGTGGTGCAATCACTTGGTGTGGTGCGACCACTTGGTAT
*
4383 GGTGCGGCTATTCGGTGTGG
1 GGTGCGGCTACTCGGTGTGG
4403 CGCCTGGTGC
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 68 1.00
ACGTcount: A:0.11, C:0.20, G:0.41, T:0.29
Consensus pattern (54 bp):
GGTGCGGCTACTCGGTGTGGTGCAATCACTTGGTGTGGTGCGACCACTTGGTAT
Found at i:9481 original size:2 final size:2
Alignment explanation
Indices: 9474--9498 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9464 AATATTATAG
9474 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
9499 TAATTTAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9991 original size:24 final size:24
Alignment explanation
Indices: 9964--10012 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
9954 AATTATAGGG
9964 TAAATATTAAAATTTAAGATTTAT
1 TAAATATTAAAATTTAAGATTTAT
9988 TAAATATTAAAATTTAAGATTTAT
1 TAAATATTAAAATTTAAGATTTAT
10012 T
1 T
10013 CTTATAGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
TAAATATTAAAATTTAAGATTTAT
Found at i:32591 original size:21 final size:21
Alignment explanation
Indices: 32565--32606 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
32555 TCCTCTGAGA
*
32565 AGAGTTGTTTTAGACCTGGAG
1 AGAGTTATTTTAGACCTGGAG
32586 AGAGTTATTTTAGACCTGGAG
1 AGAGTTATTTTAGACCTGGAG
32607 TCTAAGTTGT
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:0.26, C:0.10, G:0.31, T:0.33
Consensus pattern (21 bp):
AGAGTTATTTTAGACCTGGAG
Found at i:39252 original size:22 final size:22
Alignment explanation
Indices: 39146--39245 Score: 78
Period size: 22 Copynumber: 4.5 Consensus size: 22
39136 TATGATCCCA
*
39146 TTATGAAATTTTGATAACCTTC
1 TTATGAAATTTTAATAACCTTC
* * *
39168 CTATGAAATTTTAATAACGATAC
1 TTATGAAATTTTAATAAC-CTTC
* * * *
39191 -TATGGAATTTCAAAAACCTTT
1 TTATGAAATTTTAATAACCTTC
**
39212 TTAT-AAATTTTTTTTAACCTTC
1 TTATGAAA-TTTTAATAACCTTC
39234 TTATGAAATTTT
1 TTATGAAATTTT
39246 GTTAACCGCC
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
21 3 0.05
22 50 0.86
23 5 0.09
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (22 bp):
TTATGAAATTTTAATAACCTTC
Found at i:39491 original size:22 final size:22
Alignment explanation
Indices: 39283--39697 Score: 198
Period size: 22 Copynumber: 19.2 Consensus size: 22
39273 CCTCAATTTG
* *
39283 TCCCAATGAAATTTTAATAACC
1 TCCCTATGAAATTTTGATAACC
* * * *
39305 AACACTATGAGATGTTGATAACC
1 -TCCCTATGAAATTTTGATAACC
* * *
39328 TCCATATGATATATTGATAACC
1 TCCCTATGAAATTTTGATAACC
* ** * * *
39350 ACGTTATGAAAATTTAAAAACC
1 TCCCTATGAAATTTTGATAACC
* * *
39372 TCCATATG-AATTGTGTTAGTAATC
1 TCCCTATGAAATT-T-TGA-TAACC
* * *
39396 ACACTATGAAATTTTGATAAATC
1 TCCCTATGAAATTTTGAT-AACC
* *
39419 TTCCTATAAAATTTTGATAACC
1 TCCCTATGAAATTTTGATAACC
*
39441 TCCCTATG-ATTTTTGATAACC
1 TCCCTATGAAATTTTGATAACC
** * *
39462 TCTTTATGAAATTTTGTTAATC
1 TCCCTATGAAATTTTGATAACC
* *
39484 TCCCTATGAAATTTTGATCTACA
1 TCCCTATGAAATTTTGAT-AACC
*
39507 T-ACTATGAAATTTTGATAACC
1 TCCCTATGAAATTTTGATAACC
* *
39528 -CTCTTATGAAATTTTGA-AAAC
1 TC-CCTATGAAATTTTGATAACC
** *
39549 TAAACTATGAAATTTTGATAGCC
1 T-CCCTATGAAATTTTGATAACC
* * *
39572 TTCATATGAAATTTTGATATCC
1 TCCCTATGAAATTTTGATAACC
*
39594 TCCC--TG-AATTTTGATATCC
1 TCCCTATGAAATTTTGATAACC
*
39613 T-CCT-TGAAATTTTGATTA-C
1 TCCCTATGAAATTTTGATAACC
* * *
39632 TCCATAATAAAATTTTAATAACC
1 TCCCT-ATGAAATTTTGATAACC
* *
39655 TTCC--T--AA-TTTGGTAACC
1 TCCCTATGAAATTTTGATAACC
*
39672 AT-ACTATGAAATTTTGATAACC
1 -TCCCTATGAAATTTTGATAACC
39694 TCCC
1 TCCC
39698 CATAAATACC
Statistics
Matches: 288, Mismatches: 79, Indels: 51
0.69 0.19 0.12
Matches are distributed among these distances:
17 9 0.03
18 5 0.02
19 19 0.07
20 14 0.05
21 29 0.10
22 153 0.53
23 46 0.16
24 9 0.03
25 4 0.01
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.38
Consensus pattern (22 bp):
TCCCTATGAAATTTTGATAACC
Found at i:39634 original size:19 final size:20
Alignment explanation
Indices: 39578--39628 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
39568 AGCCTTCATA
39578 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
*
39598 TG-AATTTTGATATCCTCCT
1 TGAAATTTTGATATCCTCCC
39617 TGAAATTTTGAT
1 TGAAATTTTGAT
39629 TACTCCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:39762 original size:22 final size:22
Alignment explanation
Indices: 39737--39941 Score: 105
Period size: 22 Copynumber: 9.3 Consensus size: 22
39727 CACATTTTGG
*
39737 AATTTTGATAACCTCTTTATAA
1 AATTTTGATAACCTCTTTATGA
* * * *
39759 AATTTTGTTGACCCCTCTATGA
1 AATTTTGATAACCTCTTTATGA
* * * * *
39781 ATTTTTGATAATCACATTATGT
1 AATTTTGATAACCTCTTTATGA
*
39803 AATTTTGATAACCTCGCTT-TGA
1 AATTTTGATAACCTC-TTTATGA
** **
39825 AATTTTGATAACAACACTATGA
1 AATTTTGATAACCTCTTTATGA
* *
39847 AATTTTGATAA-TTTTTCTAT-A
1 AATTTTGATAACCTCTT-TATGA
*
39868 AATTTTGATAATCCGATCTCTATGA
1 AATTTTGATAA-CC--TCTTTATGA
* * * *
39893 AATTTCGATAATCACTCTATGA
1 AATTTTGATAACCTCTTTATGA
* * *
39915 GA-TTTGATAACCT-TCTATCA
1 AATTTTGATAACCTCTTTATGA
39935 AATTTTG
1 AATTTTG
39942 GTACTCCTTA
Statistics
Matches: 135, Mismatches: 39, Indels: 19
0.70 0.20 0.10
Matches are distributed among these distances:
20 7 0.05
21 25 0.19
22 84 0.62
23 2 0.01
24 4 0.03
25 13 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (22 bp):
AATTTTGATAACCTCTTTATGA
Found at i:39828 original size:66 final size:66
Alignment explanation
Indices: 39707--39858 Score: 182
Period size: 66 Copynumber: 2.3 Consensus size: 66
39697 CCATAAATAC
* * * *
39707 CACTATGAAATTTTTG-TAATCACATTTTGGAATTTTGATAACCTCTTTATAAAATTTTGTTGAC
1 CACTATG-AATTTTTGATAATCACATTATGGAATTTTGATAACCTCCTTATAAAATTTTGATAAC
**
39771 CC
65 AA
* * *
39773 CTCTATGAATTTTTGATAATCACATTATGTAATTTTGATAACCTCGCTT-TGAAATTTTGATAAC
1 CACTATGAATTTTTGATAATCACATTATGGAATTTTGATAACCTC-CTTATAAAATTTTGATAAC
39837 AA
65 AA
*
39839 CACTATGAAATTTTGATAAT
1 CACTATGAATTTTTGATAAT
39859 TTTTCTATAA
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
65 8 0.11
66 63 0.86
67 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43
Consensus pattern (66 bp):
CACTATGAATTTTTGATAATCACATTATGGAATTTTGATAACCTCCTTATAAAATTTTGATAACA
A
Found at i:40007 original size:22 final size:22
Alignment explanation
Indices: 39964--40321 Score: 131
Period size: 22 Copynumber: 16.5 Consensus size: 22
39954 AAAATGAGAC
39964 TTTT-ATAACCTTCA-TATGAAA
1 TTTTGATAACC-TCACTATGAAA
* *
39985 TTTTGATAACCACACTATAAAA
1 TTTTGATAACCTCACTATGAAA
* *
40007 TTTTGATAACCTCCCAATGAAA
1 TTTTGATAACCTCACTATGAAA
*
40029 TATT-AGTAACCTC-CTAATGAAA
1 TTTTGA-TAACCTCACT-ATGAAA
* *
40051 TTTTGTTAACCACACTATGAAA
1 TTTTGATAACCTCACTATGAAA
* * * *
40073 TTTTTATTACCTCGCTATGACA
1 TTTTGATAACCTCACTATGAAA
* * ** *
40095 TTTTGATAATCTC-TTGGGTAACC
1 TTTTGATAACCTCACTATG-AA-A
* * *
40118 TTTCT-ATAA---AATTGTGATAA
1 TTT-TGATAACCTCACTATGA-AA
* *
40138 ---T--TAACCACCCTATGAAA
1 TTTTGATAACCTCACTATGAAA
** * *
40155 TTTCAATAACC-AACCTAAGAAA
1 TTTTGATAACCTCA-CTATGAAA
* * *
40177 TTTTAATAACCTGATCCTAAGAAA
1 TTTTGATAACCTCA--CTATGAAA
* *
40201 TTTTGGTAACCACACTATGAAA
1 TTTTGATAACCTCACTATGAAA
*
40223 TTTTGATAACTTC-CATATGAAA
1 TTTTGATAACCTCAC-TATGAAA
* * *
40245 TTTTGGTAACCACACTATGGAA
1 TTTTGATAACCTCACTATGAAA
40267 TTTTGATAACCTC-CTCATGAAA
1 TTTTGATAACCTCACT-ATGAAA
** * *
40289 TCATAATAACCATC-TTATGAAA
1 TTTTGATAACC-TCACTATGAAA
40311 TTTTGATAACC
1 TTTTGATAACC
40322 ACATAGAGAT
Statistics
Matches: 251, Mismatches: 60, Indels: 51
0.69 0.17 0.14
Matches are distributed among these distances:
15 3 0.01
16 1 0.00
17 2 0.01
18 4 0.02
20 1 0.00
21 18 0.07
22 188 0.75
23 14 0.06
24 20 0.08
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
TTTTGATAACCTCACTATGAAA
Found at i:40322 original size:22 final size:22
Alignment explanation
Indices: 40139--40322 Score: 151
Period size: 22 Copynumber: 8.3 Consensus size: 22
40129 TTGTGATAAT
* **
40139 TAACCACCCTATGAAATTTCAA
1 TAACCATCCTATGAAATTTTGA
* * *
40161 TAACCAACCTAAGAAATTTTAA
1 TAACCATCCTATGAAATTTTGA
* *
40183 TAACCTGATCCTAAGAAATTTTGG
1 TAACC--ATCCTATGAAATTTTGA
40207 TAACCA-CACTATGAAATTTTGA
1 TAACCATC-CTATGAAATTTTGA
* *
40229 TAA-CTTCCATATGAAATTTTGG
1 TAACCATCC-TATGAAATTTTGA
*
40251 TAACCA-CACTATGGAATTTTGA
1 TAACCATC-CTATGAAATTTTGA
** *
40273 TAACC-TCCTCATGAAATCATAA
1 TAACCATCCT-ATGAAATTTTGA
*
40295 TAACCATCTTATGAAATTTTGA
1 TAACCATCCTATGAAATTTTGA
40317 TAACCA
1 TAACCA
40323 CATAGAGATA
Statistics
Matches: 131, Mismatches: 21, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
21 5 0.04
22 102 0.78
23 5 0.04
24 19 0.15
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (22 bp):
TAACCATCCTATGAAATTTTGA
Found at i:40525 original size:19 final size:20
Alignment explanation
Indices: 40494--40531 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
40484 TATTGACATT
40494 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
40513 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
40532 AATAATAGTA
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:40736 original size:31 final size:31
Alignment explanation
Indices: 40701--40766 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
40691 TGGCAATTTA
*
40701 GAAATATGTTTTAAAAAAAAGGGTACAATTG
1 GAAATATGTTTCAAAAAAAAGGGTACAATTG
*
40732 GAAATATGTTTCAAAAATAAGGGTACAATTG
1 GAAATATGTTTCAAAAAAAAGGGTACAATTG
40763 GAAA
1 GAAA
40767 ACATAAAGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (31 bp):
GAAATATGTTTCAAAAAAAAGGGTACAATTG
Found at i:41007 original size:28 final size:28
Alignment explanation
Indices: 40968--41024 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
40958 TAACTATCCA
40968 TTTTGGGACAAATTG-GCCCATTAACTTT
1 TTTTGGGACAAATTGAGCCC-TTAACTTT
*
40996 TTTTGGGACAAATTGATCCCTTAACTTT
1 TTTTGGGACAAATTGAGCCCTTAACTTT
41024 T
1 T
41025 AAAAATGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.42
Consensus pattern (28 bp):
TTTTGGGACAAATTGAGCCCTTAACTTT
Found at i:41770 original size:27 final size:28
Alignment explanation
Indices: 41714--41770 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
41704 TCTCGTTTTT
*
41714 AAAAGTTAAGGGGCCAATTTGTCCTAAA
1 AAAAGTTAAGGGACCAATTTGTCCTAAA
*
41742 AAAAGTTAAGGGACCAATTTGTCCCAAA
1 AAAAGTTAAGGGACCAATTTGTCCTAAA
41770 A
1 A
41771 TGGATAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (28 bp):
AAAAGTTAAGGGACCAATTTGTCCTAAA
Found at i:43951 original size:41 final size:41
Alignment explanation
Indices: 43889--44061 Score: 142
Period size: 43 Copynumber: 4.2 Consensus size: 41
43879 AACGTGTTCC
* *
43889 AGTGTCAAA--TAA-TTTAA-TTTACCGGAGCGACAACTTCT
1 AGTGTCAAATGTAATTTTAATTTTACC-AAGTGACAACTTCT
*
43927 AGTGTCAAATGTAATTTTAA-TTTACCAAGGTAACAACTTCT
1 AGTGTCAAATGTAATTTTAATTTTACCAA-GTGACAACTTCT
* * *
43968 GGTGTTAAAGGTAATTTTAATTTTTACCAAAGTGACAACTTCT
1 AGTGTCAAATGTAATTTTAA-TTTTACC-AAGTGACAACTTCT
* ****
44011 TGTGTC-AATGGTAGATTTTAATTTTATTTGTGTGACAACTTCT
1 AGTGTCAAAT-GTA-ATTTTAATTTTA-CCAAGTGACAACTTCT
44054 AGTGTCAA
1 AGTGTCAA
44062 TTAAATTCAA
Statistics
Matches: 109, Mismatches: 15, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
38 9 0.08
40 4 0.04
41 38 0.35
42 2 0.02
43 46 0.42
44 10 0.09
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (41 bp):
AGTGTCAAATGTAATTTTAATTTTACCAAGTGACAACTTCT
Found at i:44008 original size:43 final size:43
Alignment explanation
Indices: 43917--44061 Score: 152
Period size: 43 Copynumber: 3.4 Consensus size: 43
43907 TTACCGGAGC
* *
43917 GACAACTTCTAGTGTCAAATGTAATTTTAA--TTTACCAAGGT
1 GACAACTTCTAGTGTCAAAGGTAATTTTAATTTTTACCAAAGT
* * *
43958 AACAACTTCTGGTGTTAAAGGTAATTTTAATTTTTACCAAAGT
1 GACAACTTCTAGTGTCAAAGGTAATTTTAATTTTTACCAAAGT
* * *****
44001 GACAACTTCTTGTGTCAATGGTAGATTTTAA-TTTTATTTGTGT
1 GACAACTTCTAGTGTCAAAGGTA-ATTTTAATTTTTACCAAAGT
44044 GACAACTTCTAGTGTCAA
1 GACAACTTCTAGTGTCAA
44062 TTAAATTCAA
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
41 26 0.30
43 53 0.62
44 7 0.08
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (43 bp):
GACAACTTCTAGTGTCAAAGGTAATTTTAATTTTTACCAAAGT
Found at i:44097 original size:47 final size:47
Alignment explanation
Indices: 44043--44438 Score: 519
Period size: 47 Copynumber: 8.7 Consensus size: 47
44033 TTTATTTGTG
* * *
44043 TGACAACTTCTAGTGTCAATTAAATTCAATAAAGTAGAATTTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
** *
44090 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAGGTTTTGATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
*
44137 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGCAAAATTTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
*
44184 TGACAACTTCTAGTGTC-----AA--T--T-AAGTAGAA-TTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
* *
44220 TGATAACTTCTAGTGTCAATTAAATTTACTAAAGCAAAATTTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
* *
44267 TGACAACTTTTAGTGTCAATTAAATTTACTTAAGTAAAATTTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
* ** *
44314 TGACAACTTCTAGTGTCAATTAAATTTACTAAAATAAAAACTAAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
*
44361 TGACAACTTCTAGTGTCAATTAAA-TTACTAATGTAAAATTTTAATT
1 TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
* * *
44407 TGATAACTCCTGGTGTCAATTAAAATTTACTA
1 TGACAACTTCTAGTGTCAATT-AAATTTACTA
44439 GAGCTCTCGT
Statistics
Matches: 303, Mismatches: 33, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
36 23 0.08
37 6 0.02
38 1 0.00
40 1 0.00
41 2 0.01
42 2 0.01
43 1 0.00
45 1 0.00
46 41 0.14
47 219 0.72
48 6 0.02
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (47 bp):
TGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAAATTTTAATT
Found at i:44237 original size:130 final size:131
Alignment explanation
Indices: 44068--44438 Score: 467
Period size: 130 Copynumber: 2.8 Consensus size: 131
44058 TCAATTAAAT
* * **
44068 TCAATAAAGTAGAATTTTAATTTGACAACTTCTAGTGTCAATTAAATTTACTAAAGTAAGGTTTT
1 TCAATTAAGTAGAATTTTAATTTGACAACTTCTAGTGTCAATTAAATTTACTAAAGCAAAATTTT
*
44133 GATTTGACAACTTCTAGTGTCAATTAAATTTACTAAAGCAAAATTTTAATTTGACAACTTCTAGT
66 AATTTGACAACTTCTAGTGTCAATTAAATTTACTAAAGCAAAATTTTAATTTGACAACTTCTAGT
44198 G
131 G
*
44199 TCAATTAAGTAGAA-TTTAATTTGATAACTTCTAGTGTCAATTAAATTTACTAAAGCAAAATTTT
1 TCAATTAAGTAGAATTTTAATTTGACAACTTCTAGTGTCAATTAAATTTACTAAAGCAAAATTTT
* * *
44263 AATTTGACAACTTTTAGTGTCAATTAAATTTACTTAAGTAAAATTTTAATTTGACAACTTCTAGT
66 AATTTGACAACTTCTAGTGTCAATTAAATTTACTAAAGCAAAATTTTAATTTGACAACTTCTAGT
44328 G
131 G
* * * * *
44329 TCAATTAAATTTACTAAAATAAAAACTAAATTTGACAACTTCTAGTGTCAATTAAA-TTACTAAT
1 TCAATT--A---AGTAGAAT-----TTTAATTTGACAACTTCTAGTGTCAATTAAATTTACTAAA
* * * *
44393 GTAAAATTTTAATTTGATAACTCCTGGTGTCAATTAAAATTTACTA
56 GCAAAATTTTAATTTGACAACTTCTAGTGTCAATT-AAATTTACTA
44439 GAGCTCTCGT
Statistics
Matches: 207, Mismatches: 21, Indels: 14
0.86 0.09 0.06
Matches are distributed among these distances:
130 114 0.55
131 13 0.06
132 1 0.00
135 5 0.02
140 37 0.18
141 37 0.18
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (131 bp):
TCAATTAAGTAGAATTTTAATTTGACAACTTCTAGTGTCAATTAAATTTACTAAAGCAAAATTTT
AATTTGACAACTTCTAGTGTCAATTAAATTTACTAAAGCAAAATTTTAATTTGACAACTTCTAGT
G
Found at i:44242 original size:177 final size:177
Alignment explanation
Indices: 44047--44383 Score: 548
Period size: 177 Copynumber: 1.9 Consensus size: 177
44037 TTTGTGTGAC
* *
44047 AACTTCTAGTGTCAATTAAATTCAATAAAGTAGAATTTTAATTTGACAACTTCTAGTGTCAATTA
1 AACTTCTAGTGTCAATTAAATTCAATAAAGCAAAATTTTAATTTGACAACTTCTAGTGTCAATTA
** * * *
44112 AATTTACTAAAGTAAGGTTTTGATTTGACAACTTCTAGTGTCAATTAAATTTACTAAAGCAAAAT
66 AATTTACTAAAGTAAAATTTTAATTTGACAACTTCTAGTGTCAATTAAATTTACTAAAACAAAAA
* *
44177 TTTAATTTGACAACTTCTAGTGTCAATTAAGTAGAATTTAATTTGAT
131 CTAAATTTGACAACTTCTAGTGTCAATTAAGTAGAATTTAATTTGAT
* * *
44224 AACTTCTAGTGTCAATTAAATTTACTAAAGCAAAATTTTAATTTGACAACTTTTAGTGTCAATTA
1 AACTTCTAGTGTCAATTAAATTCAATAAAGCAAAATTTTAATTTGACAACTTCTAGTGTCAATTA
* *
44289 AATTTACTTAAGTAAAATTTTAATTTGACAACTTCTAGTGTCAATTAAATTTACTAAAATAAAAA
66 AATTTACTAAAGTAAAATTTTAATTTGACAACTTCTAGTGTCAATTAAATTTACTAAAACAAAAA
44354 CTAAATTTGACAACTTCTAGTGTCAATTAA
131 CTAAATTTGACAACTTCTAGTGTCAATTAA
44384 ATTACTAATG
Statistics
Matches: 146, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
177 146 1.00
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (177 bp):
AACTTCTAGTGTCAATTAAATTCAATAAAGCAAAATTTTAATTTGACAACTTCTAGTGTCAATTA
AATTTACTAAAGTAAAATTTTAATTTGACAACTTCTAGTGTCAATTAAATTTACTAAAACAAAAA
CTAAATTTGACAACTTCTAGTGTCAATTAAGTAGAATTTAATTTGAT
Found at i:48868 original size:36 final size:36
Alignment explanation
Indices: 48821--48895 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
48811 AAGTGAGTAC
48821 ATAGTTTTTATATCACATTCAAAACTCAGCTATGAT
1 ATAGTTTTTATATCACATTCAAAACTCAGCTATGAT
48857 ATAGTTTTTATATCACATTCAAAACTCAGCTATGAT
1 ATAGTTTTTATATCACATTCAAAACTCAGCTATGAT
48893 ATA
1 ATA
48896 ACAAGTATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (36 bp):
ATAGTTTTTATATCACATTCAAAACTCAGCTATGAT
Found at i:56374 original size:7 final size:7
Alignment explanation
Indices: 56362--56402 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
56352 TCCTCTCTGT
56362 GCAAAAC
1 GCAAAAC
56369 GCAAAAC
1 GCAAAAC
56376 GCAAAAC
1 GCAAAAC
56383 GCAAAAC
1 GCAAAAC
56390 GCAAAAC
1 GCAAAAC
56397 GCAAAA
1 GCAAAA
56403 TGCCTGCCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.59, C:0.27, G:0.15, T:0.00
Consensus pattern (7 bp):
GCAAAAC
Found at i:58357 original size:15 final size:15
Alignment explanation
Indices: 58337--58371 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
58327 ACGAACATTA
58337 TTATTGTTGT-TGTTG
1 TTATTGTTGTCT-TTG
58352 TTATTGTTGTCTTTG
1 TTATTGTTGTCTTTG
58367 TTATT
1 TTATT
58372 ATTGGAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 18 0.95
16 1 0.05
ACGTcount: A:0.09, C:0.03, G:0.20, T:0.69
Consensus pattern (15 bp):
TTATTGTTGTCTTTG
Done.