Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010014.1 Corchorus capsularis cultivar CVL-1 contig10035, 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: 33160
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:7334 original size:15 final size:15
Alignment explanation
Indices: 7314--7344 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
7304 GTAATGAGAC
7314 TCTCTATTATTGTAT
1 TCTCTATTATTGTAT
7329 TCTCTATTATTGTAT
1 TCTCTATTATTGTAT
7344 T
1 T
7345 AGCTAAGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.61
Consensus pattern (15 bp):
TCTCTATTATTGTAT
Found at i:13132 original size:1 final size:1
Alignment explanation
Indices: 13126--13170 Score: 72
Period size: 1 Copynumber: 45.0 Consensus size: 1
13116 CAATTCAAAG
**
13126 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
13171 AAATTAAGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.04, G:0.00, T:0.96
Consensus pattern (1 bp):
T
Found at i:14570 original size:23 final size:23
Alignment explanation
Indices: 14526--14570 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
14516 AAAGAAAATT
*
14526 TATATCTATCTTATATGCCATTC
1 TATATCTATCTTATATACCATTC
* *
14549 TATATCTATCTTTTATATCATT
1 TATATCTATCTTATATACCATT
14571 TAAAGTTATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.18, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATCTATCTTATATACCATTC
Found at i:16398 original size:35 final size:35
Alignment explanation
Indices: 16339--16424 Score: 93
Period size: 35 Copynumber: 2.5 Consensus size: 35
16329 TTGTTATTTG
16339 ACGGGAACTTTCCCAAAACGAAAAAAGGAAA-CTGA
1 ACGGGAACTTTCCCAAAACGAAAAAAGGAAACCT-A
** ** **
16374 ACGGGAACTTTCCCTTAATTAAAAATTGAAACCTA
1 ACGGGAACTTTCCCAAAACGAAAAAAGGAAACCTA
*
16409 ATGGGAACTTTCCCAA
1 ACGGGAACTTTCCCAA
16425 CTTGACAACT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
35 39 0.95
36 2 0.05
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (35 bp):
ACGGGAACTTTCCCAAAACGAAAAAAGGAAACCTA
Found at i:17765 original size:168 final size:169
Alignment explanation
Indices: 17483--17809 Score: 620
Period size: 168 Copynumber: 1.9 Consensus size: 169
17473 CCAATAAGAT
*
17483 AAGAAATCTGAAGGCCCAACAGCAATTTAAGTACCCAAACGTACTAAAAGGCACAATATGGTTTT
1 AAGAAATCTAAAGGCCCAACAGCAATTTAAGTACCCAAACGTACTAAAAGGCACAATATGGTTTT
*
17548 TCCCTATTCTACCATTACTTGATTTTATTCTTATTTAATTATATTTGATTTCCAAATCCG-AATT
66 TCCCTATTCTACCATTACTTGATTTTATTCTTATTTAATCATATTTGATTTCCAAATCCGCAATT
17612 AGTCTCCTTCAATCCTACATTTTCTAGGCCCATTTTCTA
131 AGTCTCCTTCAATCCTACATTTTCTAGGCCCATTTTCTA
17651 AAGAAATCTAAAGGCCCAACAGCAATTTAAGTACCCAAACGTACTAAAAGGCACAATATGGTTTT
1 AAGAAATCTAAAGGCCCAACAGCAATTTAAGTACCCAAACGTACTAAAAGGCACAATATGGTTTT
*
17716 TCCCTATTCTACCATTACTTGATTTTATTCTTATTTAATCATCTTTGATTTCCAAATCCGCAATT
66 TCCCTATTCTACCATTACTTGATTTTATTCTTATTTAATCATATTTGATTTCCAAATCCGCAATT
17781 AGTCTCCTTCAATCCTACATTTTCTAGGC
131 AGTCTCCTTCAATCCTACATTTTCTAGGC
17810 TTAAAACTAT
Statistics
Matches: 155, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
168 122 0.79
169 33 0.21
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (169 bp):
AAGAAATCTAAAGGCCCAACAGCAATTTAAGTACCCAAACGTACTAAAAGGCACAATATGGTTTT
TCCCTATTCTACCATTACTTGATTTTATTCTTATTTAATCATATTTGATTTCCAAATCCGCAATT
AGTCTCCTTCAATCCTACATTTTCTAGGCCCATTTTCTA
Found at i:20055 original size:3 final size:3
Alignment explanation
Indices: 20037--20073 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
20027 GAAATCAGTT
*
20037 TTC TCTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
20074 AAAAAATTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:21121 original size:2 final size:2
Alignment explanation
Indices: 21116--21152 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
21106 ACGAGTTCTA
*
21116 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21153 CACACACACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:25533 original size:37 final size:37
Alignment explanation
Indices: 25386--26473 Score: 790
Period size: 37 Copynumber: 29.4 Consensus size: 37
25376 CTAGGTCATC
** * * *
25386 ATAA-ACACCTAAACAGGGATTTTGAATAAGAATTTG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
* * * * ** * *
25422 ACAAGAAAACTAAATAGTCACCTTAAATAAAGATTTG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
* * * * *
25459 ATAAGAAAGCTAAACAGTGATCTTGAAC--GTGATTTTG
1 ATAAGACACCTAAACAGGGACCTTAAACAAG-GA-TTTG
*
25496 ATGAGACACCTAAACAGGGACCTTAAACAAGGATTTG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
* *
25533 ATAAGACACCTAAACA-GGACCTTAAATAAGGA---A
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
* * * * * *
25566 ATAAGAAATCTAAATAGGAATCTTGAACAA-GATTTTG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGA-TTTG
*
25603 ATGAA-ACACCTAAACAGGGACCTTAAACAAGGATTTA
1 AT-AAGACACCTAAACAGGGACCTTAAACAAGGATTTG
* * *
25640 ATAAGAAACCTAAACAGGAATCTTAAACAA-GATTTTG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGA-TTTG
* * * *
25677 ATGAGACACTTAAACAGGGATCTTAAACCA-GATTTCG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGATTT-G
* *
25714 ATGAGACACCTAAACAGGGACATTAAACAAGGATTTG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
*
25751 ATAAGACACCTAAACAGGGACCTTAAATAAGGATTTG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
* * * * * *
25788 CTAAGAAACTTAAACAGGAATCTTTTAACAA-GATTTTG
1 ATAAGACACCTAAACAGGGA-CCTTAAACAAGGA-TTTG
* * *
25826 ATGAGACACCTGAACAGGGACCTTAAATAAGGATTTG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
* * * *
25863 ACAAGAAACCTAAATAGGGATCTTAAACAA-GATTTTG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGA-TTTG
* * * * *
25900 ATGAA-ATACCTAAACAGGTACTTTAAATAAAGATTTG
1 AT-AAGACACCTAAACAGGGACCTTAAACAAGGATTTG
* * * *
25937 -CAAGAAACCTAAACAGGGATCTTGAACAA-GATTTCG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGATTT-G
** * *
25973 ACGAGACACCTAAATAGGGATCTTAAATC-A-GATTTCG
1 ATAAGACACCTAAACAGGGACCTTAAA-CAAGGATTT-G
* * *
26010 ATGAGACACCAAAATAGGGACCTTAAACAAGGATTTG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
* *
26047 ATAAGACACCTAAACAGGGGCCTTAAATAAGGATTTG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
* * *
26084 ATAAGAAACCTAAACAGGAATCTTTAAACAA-GATTTTG
1 ATAAGACACCTAAACAGGGA-CCTTAAACAAGGA-TTTG
* * * *
26122 ATGAGACACCTGAACAGGGATCTTAAATAAGGATTTG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
* * *
26159 ACAAGAAACCTAAACAGGGATCTTAAACAA-GATTTTG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGA-TTTG
* *** * * *
26196 ATGAA-ATACCTAAACATCTACTTTAAATAAAGATTTG
1 AT-AAGACACCTAAACAGGGACCTTAAACAAGGATTTG
* * * *
26233 -CAAGAAACCTAAACAGGGATCTTGAACAA-GATTTCG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGATTT-G
*
26269 ACT-AGACACCTAAACAGGGACCTTAAATAAGGATTTG
1 A-TAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
* * * * * * *
26306 ACAAGAAATCTAAACAGGGATCTTAAA-TAGGTTTTA
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
* *
26342 ATGAGACACCTAAATAGGGACACGATTTTAAACAAGGATTTG
1 ATAAGACACCTAAACAGGGAC-C----TTAAACAAGGATTTG
* * * * ** *
26384 ATAAGACACCTAAAGAAGAATCTTGGAC-ACGATTTTG
1 ATAAGACACCTAAACAGGGACCTTAAACAAGGA-TTTG
26421 ATGAA-ACACCTAAACAGGGACCTTAAACAAGGATTTG
1 AT-AAGACACCTAAACAGGGACCTTAAACAAGGATTTG
26458 ATAAGACACCTAAACA
1 ATAAGACACCTAAACA
26474 TAAATCTTGA
Statistics
Matches: 824, Mismatches: 178, Indels: 99
0.75 0.16 0.09
Matches are distributed among these distances:
33 15 0.02
34 9 0.01
35 14 0.02
36 96 0.12
37 569 0.69
38 92 0.11
39 1 0.00
41 6 0.01
42 22 0.03
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (37 bp):
ATAAGACACCTAAACAGGGACCTTAAACAAGGATTTG
Found at i:25994 original size:296 final size:295
Alignment explanation
Indices: 25492--26471 Score: 1267
Period size: 296 Copynumber: 3.3 Consensus size: 295
25482 TGAACGTGAT
* * * * *
25492 TTTGATGAGACACCTAAACAGGGA-CCTTAAACAAGGA-TTTGATAAGACACCTAAACA-GGACC
1 TTTGATAAGAAACCTAAACAGGAATCTTTAAACAA-GATTTTGATGAGACACCTAAACAGGGACC
* * * * * *
25554 TTAAATAAGGA---AATAAGAAATCTAAATAGGAATCTTGAACAAGATTTTGATGAAACACCTAA
65 TTAAATAAGGATTTGACAAGAAACCTAAATAGGGATCTTAAACAAGATTTTGATGAAATACCTAA
* * * * ** * * * *
25616 ACAGGGACCTTAAACAAGGATTTAATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGA
130 ACAGGTACTTTAAATAAAGATTT-GCAAGAAACCTAAACAGGGATCTTGAACAAGATTTCGACGA
* *
25681 GACACTTAAACAGGGATCTTAAACCAGATTTCGATGAGACACCTAAACAGGGACATTAAACAAGG
194 GACACCTAAACAGGGATCTTAAATCAGATTTCGATGAGACACCTAAACAGGGAC-TTAAACAAGG
25746 ATTTGATAAGACACCTAAACAGGGACCTTAAATAAGGA
258 ATTTGATAAGACACCTAAACAGGGACCTTAAATAAGGA
* * * *
25784 TTTGCTAAGAAACTTAAACAGGAATCTTTTAACAAGATTTTGATGAGACACCTGAACAGGGACCT
1 TTTGATAAGAAACCTAAACAGGAATCTTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCT
25849 TAAATAAGGATTTGACAAGAAACCTAAATAGGGATCTTAAACAAGATTTTGATGAAATACCTAAA
66 TAAATAAGGATTTGACAAGAAACCTAAATAGGGATCTTAAACAAGATTTTGATGAAATACCTAAA
25914 CAGGTACTTTAAATAAAGATTTGCAAGAAACCTAAACAGGGATCTTGAACAAGATTTCGACGAGA
131 CAGGTACTTTAAATAAAGATTTGCAAGAAACCTAAACAGGGATCTTGAACAAGATTTCGACGAGA
* * *
25979 CACCTAAATAGGGATCTTAAATCAGATTTCGATGAGACACCAAAATAGGGACCTTAAACAAGGAT
196 CACCTAAACAGGGATCTTAAATCAGATTTCGATGAGACACCTAAACAGGGA-CTTAAACAAGGAT
*
26044 TTGATAAGACACCTAAACAGGGGCCTTAAATAAGGA
260 TTGATAAGACACCTAAACAGGGACCTTAAATAAGGA
* *
26080 TTTGATAAGAAACCTAAACAGGAATCTTTAAACAAGATTTTGATGAGACACCTGAACAGGGATCT
1 TTTGATAAGAAACCTAAACAGGAATCTTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCT
*
26145 TAAATAAGGATTTGACAAGAAACCTAAACAGGGATCTTAAACAAGATTTTGATGAAATACCTAAA
66 TAAATAAGGATTTGACAAGAAACCTAAATAGGGATCTTAAACAAGATTTTGATGAAATACCTAAA
** *
26210 CATCTACTTTAAATAAAGATTTGCAAGAAACCTAAACAGGGATCTTGAACAAGATTTCGACTAGA
131 CAGGTACTTTAAATAAAGATTTGCAAGAAACCTAAACAGGGATCTTGAACAAGATTTCGACGAGA
* * ** * * * *
26275 CACCTAAACAGGGACCTTAAATAAGGATTT-GACAAGAAATCTAAACAGGGATCTTAAA-TAGGT
196 CACCTAAACAGGGATCTTAAATCA-GATTTCGATGAGACACCTAAACAGGGA-CTTAAACAAGGA
* * * *
26338 TTTAATGAGACACCTAAATAGGGACACGATTTTAAACAAGGA
259 TTTGATAAGACACCTAAACAGGGAC-C----TTAAATAAGGA
* * * ** * *
26380 TTTGATAAGACACCTAAAGAAGAATC-TTGGACACGATTTTGATGAAACACCTAAACAGGGACCT
1 TTTGATAAGAAACCTAAACAGGAATCTTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCT
* * *
26444 TAAACAAGGATTTGATAAGACACCTAAA
66 TAAATAAGGATTTGACAAGAAACCTAAA
26472 CATAAATCTT
Statistics
Matches: 607, Mismatches: 68, Indels: 19
0.87 0.10 0.03
Matches are distributed among these distances:
292 21 0.03
293 26 0.04
294 16 0.03
295 24 0.04
296 360 0.59
297 70 0.12
299 57 0.09
300 33 0.05
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (295 bp):
TTTGATAAGAAACCTAAACAGGAATCTTTAAACAAGATTTTGATGAGACACCTAAACAGGGACCT
TAAATAAGGATTTGACAAGAAACCTAAATAGGGATCTTAAACAAGATTTTGATGAAATACCTAAA
CAGGTACTTTAAATAAAGATTTGCAAGAAACCTAAACAGGGATCTTGAACAAGATTTCGACGAGA
CACCTAAACAGGGATCTTAAATCAGATTTCGATGAGACACCTAAACAGGGACTTAAACAAGGATT
TGATAAGACACCTAAACAGGGACCTTAAATAAGGA
Found at i:26495 original size:37 final size:35
Alignment explanation
Indices: 26380--26501 Score: 93
Period size: 37 Copynumber: 3.3 Consensus size: 35
26370 TAAACAAGGA
* * *
26380 TTTGATAAGACACCTAAAGAAGAATCTTGGACACGAT
1 TTTGATAAGACACCTAAACAA-AATCTTGAACA-GGT
** * * *
26417 TTTGATGAA-ACACCTAAACAGGGACCTTAAACAAGGA
1 TTTGAT-AAGACACCTAAACA-AAATCTTGAAC-AGGT
26454 TTTGATAAGACACCTAAACATAAATCTTGAACTAGGT
1 TTTGATAAGACACCTAAACA-AAATCTTGAAC-AGGT
*
26491 TTTGATGAGAC
1 TTTGATAAGAC
26502 TGAATTTCAT
Statistics
Matches: 65, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
36 2 0.03
37 60 0.92
38 3 0.05
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (35 bp):
TTTGATAAGACACCTAAACAAAATCTTGAACAGGT
Found at i:26498 original size:74 final size:74
Alignment explanation
Indices: 25492--26473 Score: 1008
Period size: 74 Copynumber: 13.3 Consensus size: 74
25482 TGAACGTGAT
* * *
25492 TTTGATGAGACACCTAAACAGGGACCTTAAACAAGGA-TTTGAT-AAGACACCTAAACA-GGACC
1 TTTGATAAGAAACCTAAACAGGGATCTTAAACAA-GATTTTGATGAA-ACACCTAAACAGGGACC
25554 TTAAATAAGGA
64 TTAAATAAGGA
* * * * *
25565 ---AATAAGAAATCTAAATAGGAATCTTGAACAAGATTTTGATGAAACACCTAAACAGGGACCTT
1 TTTGATAAGAAACCTAAACAGGGATCTTAAACAAGATTTTGATGAAACACCTAAACAGGGACCTT
*
25627 AAACAAGGA
66 AAATAAGGA
* * * * *
25636 TTTAATAAGAAACCTAAACAGGAATCTTAAACAAGATTTTGATGAGACACTTAAACAGGGATCTT
1 TTTGATAAGAAACCTAAACAGGGATCTTAAACAAGATTTTGATGAAACACCTAAACAGGGACCTT
**
25701 AAACCA-GA
66 AAATAAGGA
* *
25709 TTTCGATGAGACACCTAAACAGGGA-CATTAAACAAGGA-TTTGAT-AAGACACCTAAACAGGGA
1 TTT-GATAAGAAACCTAAACAGGGATC-TTAAACAA-GATTTTGATGAA-ACACCTAAACAGGGA
25771 CCTTAAATAAGGA
62 CCTTAAATAAGGA
* * * * * *
25784 TTTGCTAAGAAACTTAAACAGGAATCTTTTAACAAGATTTTGATGAGACACCTGAACAGGGACCT
1 TTTGATAAGAAACCTAAACAGGGATC-TTAAACAAGATTTTGATGAAACACCTAAACAGGGACCT
25849 TAAATAAGGA
65 TAAATAAGGA
* * * * *
25859 TTTGACAAGAAACCTAAATAGGGATCTTAAACAAGATTTTGATGAAATACCTAAACAGGTACTTT
1 TTTGATAAGAAACCTAAACAGGGATCTTAAACAAGATTTTGATGAAACACCTAAACAGGGACCTT
*
25924 AAATAAAGA
66 AAATAAGGA
* * * * * * *
25933 TTTG-CAAGAAACCTAAACAGGGATCTTGAACAAGATTTCGACGAGACACCTAAATAGGGATCTT
1 TTTGATAAGAAACCTAAACAGGGATCTTAAACAAGATTTTGATGAAACACCTAAACAGGGACCTT
*
25997 AAATCA-GA
66 AAATAAGGA
* * * * * *
26005 TTTCGATGAGACACCAAAATAGGGACCTTAAACAAGGA-TTTGAT-AAGACACCTAAACAGGGGC
1 TTT-GATAAGAAACCTAAACAGGGATCTTAAACAA-GATTTTGATGAA-ACACCTAAACAGGGAC
26068 CTTAAATAAGGA
63 CTTAAATAAGGA
* * * *
26080 TTTGATAAGAAACCTAAACAGGAATCTTTAAACAAGATTTTGATGAGACACCTGAACAGGGATCT
1 TTTGATAAGAAACCTAAACAGGGATC-TTAAACAAGATTTTGATGAAACACCTAAACAGGGACCT
26145 TAAATAAGGA
65 TAAATAAGGA
* * *** *
26155 TTTGACAAGAAACCTAAACAGGGATCTTAAACAAGATTTTGATGAAATACCTAAACATCTACTTT
1 TTTGATAAGAAACCTAAACAGGGATCTTAAACAAGATTTTGATGAAACACCTAAACAGGGACCTT
*
26220 AAATAAAGA
66 AAATAAGGA
* * * *
26229 TTTG-CAAGAAACCTAAACAGGGATCTTGAACAAGATTTCGACT-AGACACCTAAACAGGGACCT
1 TTTGATAAGAAACCTAAACAGGGATCTTAAACAAGATTTTGA-TGAAACACCTAAACAGGGACCT
26292 TAAATAAGGA
65 TAAATAAGGA
* * * * * * *
26302 TTTGACAAGAAATCTAAACAGGGATCTTAAA-TAGGTTTTAATGAGACACCTAAATAGGGACACG
1 TTTGATAAGAAACCTAAACAGGGATCTTAAACAAGATTTTGATGAAACACCTAAACAGGGAC-C-
*
26366 ATTTTAAACAAGGA
64 ---TTAAATAAGGA
* * * * ** *
26380 TTTGATAAGACACCTAAAGAAGAATCTTGGACACGATTTTGATGAAACACCTAAACAGGGACCTT
1 TTTGATAAGAAACCTAAACAGGGATCTTAAACAAGATTTTGATGAAACACCTAAACAGGGACCTT
*
26445 AAACAAGGA
66 AAATAAGGA
*
26454 TTTGATAAGACACCTAAACA
1 TTTGATAAGAAACCTAAACA
26474 TAAATCTTGA
Statistics
Matches: 754, Mismatches: 124, Indels: 61
0.80 0.13 0.06
Matches are distributed among these distances:
69 2 0.00
70 40 0.05
71 17 0.02
72 6 0.01
73 149 0.20
74 341 0.45
75 139 0.18
76 2 0.00
78 34 0.05
79 24 0.03
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (74 bp):
TTTGATAAGAAACCTAAACAGGGATCTTAAACAAGATTTTGATGAAACACCTAAACAGGGACCTT
AAATAAGGA
Found at i:28122 original size:14 final size:14
Alignment explanation
Indices: 28101--28150 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
28091 ACTCAAAACC
28101 TTTTTGAAAGTCAT
1 TTTTTGAAAGTCAT
*
28115 TGTTTGAAAG-CAGT
1 TTTTTGAAAGTCA-T
*
28129 TTTTTGAAAATC-T
1 TTTTTGAAAGTCAT
28142 TTTTTGAAA
1 TTTTTGAAA
28151 AACATCTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 12 0.39
14 18 0.58
15 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48
Consensus pattern (14 bp):
TTTTTGAAAGTCAT
Done.