Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008963.1 Corchorus capsularis cultivar CVL-1 contig08984, 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: 48054
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3152 original size:104 final size:104
Alignment explanation
Indices: 2972--3169 Score: 353
Period size: 104 Copynumber: 1.9 Consensus size: 104
2962 AAGGAGATGT
* * *
2972 CATCGATGCTAGCTTGGAGGAGTATGGAGTTGGGAGCACGTGTGACCGGCCATTGCTTGGAGAAG
1 CATCGATGCTAGCTTGGAAGAGCATGGAGTTGGGAGCACGTGTGACCGGCCATTGCTTAGAGAAG
3037 CCGCGTAACACCGGCCACATGTCCGGCCATCGCATGCGA
66 CCGCGTAACACCGGCCACATGTCCGGCCATCGCATGCGA
3076 CATCGATGCTAGCTTGGAAGAGCATGGAGTTGGGAGCACGTGTGACCGGCCATTGCTTAGAGAAG
1 CATCGATGCTAGCTTGGAAGAGCATGGAGTTGGGAGCACGTGTGACCGGCCATTGCTTAGAGAAG
3141 CCGCGCT-ACACCGGCCACATGTCCGGCCA
66 CCGCG-TAACACCGGCCACATGTCCGGCCA
3170 CATGACCGGC
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
104 89 0.99
105 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.33, T:0.19
Consensus pattern (104 bp):
CATCGATGCTAGCTTGGAAGAGCATGGAGTTGGGAGCACGTGTGACCGGCCATTGCTTAGAGAAG
CCGCGTAACACCGGCCACATGTCCGGCCATCGCATGCGA
Found at i:3168 original size:12 final size:12
Alignment explanation
Indices: 3150--3181 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3140 GCCGCGCTAC
3150 ACCGGCCACATG
1 ACCGGCCACATG
*
3162 TCCGGCCACATG
1 ACCGGCCACATG
3174 ACCGGCCA
1 ACCGGCCA
3182 TCGCATGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.22, C:0.44, G:0.25, T:0.09
Consensus pattern (12 bp):
ACCGGCCACATG
Found at i:8143 original size:66 final size:68
Alignment explanation
Indices: 8059--8196 Score: 210
Period size: 71 Copynumber: 2.0 Consensus size: 68
8049 CTAACTCCAA
*
8059 AAGCAAGGCTTGGTAGGGATTTTTTAGT-A-ATTCCACTACTCTATTAAAGTCAATTGAGAAATG
1 AAGCAAGGCTTGGTAGGGATCTTTTAGTAACATTCCACTACTCTATTAAAGTCAATTGAGAAATG
8122 ACC
66 ACC
8125 AAGCAA-GCTTTGGTAGGGATCTTTTAGTAATTCCATTCCACTACTCTATTAAAGTCAATTGAGA
1 AAGCAAGGC-TTGGTAGGGATCTTTTAGTAA---CATTCCACTACTCTATTAAAGTCAATTGAGA
8189 AATGACC
62 AATGACC
8196 A
1 A
8197 TAAAGTCTAG
Statistics
Matches: 65, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
65 2 0.03
66 24 0.37
67 1 0.02
71 38 0.58
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (68 bp):
AAGCAAGGCTTGGTAGGGATCTTTTAGTAACATTCCACTACTCTATTAAAGTCAATTGAGAAATG
ACC
Found at i:11823 original size:12 final size:12
Alignment explanation
Indices: 11799--11836 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
11789 AATGGAACAC
11799 TCCAATAGCTATT
1 TCCAAT-GCTATT
11812 TCCAATGCTATT
1 TCCAATGCTATT
11824 TCCAATGCT-TT
1 TCCAATGCTATT
11835 TC
1 TC
11837 AAGAATCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 4 0.16
12 15 0.60
13 6 0.24
ACGTcount: A:0.24, C:0.26, G:0.08, T:0.42
Consensus pattern (12 bp):
TCCAATGCTATT
Found at i:13130 original size:37 final size:37
Alignment explanation
Indices: 13086--13156 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
13076 CTTGATCAAC
* * *
13086 ATACATGTCTTTTCATATAGACATAAGTTTATGATCA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
13123 ATACATGTCTTTCCAAATAGACATAACTTTATGA
1 ATACATGTCTTTCCAAATAGACATAACTTTATGA
13157 ATAATTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (37 bp):
ATACATGTCTTTCCAAATAGACATAACTTTATGATCA
Found at i:13715 original size:3 final size:3
Alignment explanation
Indices: 13702--13750 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
13692 TATATGTATG
* *
13702 TAA TTA TAA TAA T-A TAA TAA TTA TAA TAA TAA T-A TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
13747 TAA T
1 TAA T
13751 TGTTATGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 6 0.15
3 33 0.85
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:13719 original size:8 final size:8
Alignment explanation
Indices: 13706--13750 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
13696 TGTATGTAAT
13706 TATAATAA
1 TATAATAA
13714 TATAATAA
1 TATAATAA
13722 T-T-ATAA
1 TATAATAA
13728 TAATAAT-A
1 T-ATAATAA
13736 TAATAATAA
1 T-ATAATAA
13745 TATAAT
1 TATAAT
13751 TGTTATGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
6 5 0.15
7 1 0.03
8 23 0.70
9 4 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TATAATAA
Found at i:13724 original size:17 final size:17
Alignment explanation
Indices: 13702--13750 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
13692 TATATGTATG
13702 TAATTATAATAATATAA
1 TAATTATAATAATATAA
13719 TAATTATAAT-A-ATAA
1 TAATTATAATAATATAA
*
13734 T-ATAATAATAATATAA
1 TAATTATAATAATATAA
13750 T
1 T
13751 TGTTATGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 7 0.24
15 6 0.21
16 6 0.21
17 10 0.34
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATTATAATAATATAA
Found at i:13737 original size:11 final size:11
Alignment explanation
Indices: 13707--13750 Score: 74
Period size: 11 Copynumber: 4.2 Consensus size: 11
13697 GTATGTAATT
13707 ATAATAATATA
1 ATAATAATATA
13718 ATAAT--TATA
1 ATAATAATATA
13727 ATAATAATATA
1 ATAATAATATA
13738 ATAATAATATA
1 ATAATAATATA
13749 AT
1 AT
13751 TGTTATGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.29
11 22 0.71
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATAATAATATA
Found at i:21155 original size:46 final size:46
Alignment explanation
Indices: 21088--21179 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
21078 ATTTTCAAGG
* *
21088 CATAATAGTAACTCTTTTGGGGAAAAACATTTAACCCAGTAATATA
1 CATAATAGTAACTCTTTTGGGGAAAAACATTCAAACCAGTAATATA
21134 CATAATAGTAACTCTTTTGGGGAAAAACATTCAAACCAGTAATATA
1 CATAATAGTAACTCTTTTGGGGAAAAACATTCAAACCAGTAATATA
21180 GGCTTCTAGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.29
Consensus pattern (46 bp):
CATAATAGTAACTCTTTTGGGGAAAAACATTCAAACCAGTAATATA
Found at i:21875 original size:30 final size:30
Alignment explanation
Indices: 21808--22153 Score: 327
Period size: 30 Copynumber: 11.7 Consensus size: 30
21798 CATGGTGTAT
* * *
21808 ATGACAAGTTCTAGTGTCAATTGAATAAAATC
1 ATGACAACTTCTGGTGTCAATTG--CAAAATC
* **
21840 ATGACATCTTCAAGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * * *
21870 GTGACAACTTCTGGTTTTAGTTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
21900 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
21930 GTGACAACTTCTGGTGTCAATTGC-AAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
21959 ATGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * * *
21989 ATGACAACTTCTGGTGTCATTTGTAAGATT
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
*
22019 ATTGACAA---C---T-T--A-TGTAAAATC
1 A-TGACAACTTCTGGTGTCAATTGCAAAATC
* * * *
22040 ATGACAACTTCTGGTGTCATTTGTAAGATT
1 ATGACAACTTCTGGTGTCAATTGCAAAATC
* * * *
22070 ATTGACAATTTCTGGTGTCAATTGTAACACC
1 A-TGACAACTTCTGGTGTCAATTGCAAAATC
* *
22101 ATTGACAACTTCTGGTGTCAATTGTAACATC
1 A-TGACAACTTCTGGTGTCAATTGCAAAATC
22132 ATTGACAACTTCTGGTGTCAAT
1 A-TGACAACTTCTGGTGTCAAT
22154 GGAGATTTAT
Statistics
Matches: 267, Mismatches: 34, Indels: 27
0.81 0.10 0.08
Matches are distributed among these distances:
20 6 0.02
21 8 0.03
23 1 0.00
24 1 0.00
25 1 0.00
26 1 0.00
27 1 0.00
28 1 0.00
29 28 0.10
30 118 0.44
31 81 0.30
32 20 0.07
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (30 bp):
ATGACAACTTCTGGTGTCAATTGCAAAATC
Found at i:21987 original size:59 final size:61
Alignment explanation
Indices: 21808--22153 Score: 351
Period size: 62 Copynumber: 5.9 Consensus size: 61
21798 CATGGTGTAT
* * * * **
21808 ATGACAAGTTCTAGTGTCAATTGAATAAAATCA-TGACATCTTCAAGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTG--TAAGATCATTGACAACTTCTGGTGTCAATTGCAAAATC
* * * * * *
21870 GTGACAACTTCTGGTTTTAGTTGCAAAATCA-TGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATCATTGACAACTTCTGGTGTCAATTGCAAAATC
* *
21930 GTGACAACTTCTGGTGTCAATTGCAA-ATCA-TGACAACTTCTGGTGTCAATTGCAAAATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATCATTGACAACTTCTGGTGTCAATTGCAAAATC
* * *
21989 ATGACAACTTCTGGTGTCATTTGTAAGATTATTGACAA---C---T-T--A-TGTAAAATC
1 ATGACAACTTCTGGTGTCAATTGTAAGATCATTGACAACTTCTGGTGTCAATTGCAAAATC
* * * * * *
22040 ATGACAACTTCTGGTGTCATTTGTAAGATTATTGACAATTTCTGGTGTCAATTGTAACACC
1 ATGACAACTTCTGGTGTCAATTGTAAGATCATTGACAACTTCTGGTGTCAATTGCAAAATC
*
22101 ATTGACAACTTCTGGTGTCAATTGTAACATCATTGACAACTTCTGGTGTCAAT
1 A-TGACAACTTCTGGTGTCAATTGTAAGATCATTGACAACTTCTGGTGTCAAT
22154 GGAGATTTAT
Statistics
Matches: 247, Mismatches: 24, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
51 46 0.19
52 1 0.00
54 2 0.01
55 1 0.00
57 1 0.00
58 2 0.01
59 56 0.23
60 60 0.24
61 14 0.06
62 64 0.26
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (61 bp):
ATGACAACTTCTGGTGTCAATTGTAAGATCATTGACAACTTCTGGTGTCAATTGCAAAATC
Found at i:22076 original size:31 final size:31
Alignment explanation
Indices: 22031--22153 Score: 185
Period size: 31 Copynumber: 4.0 Consensus size: 31
22021 TGACAACTTA
* *
22031 TGTAAAATCA-TGACAACTTCTGGTGTCATT
1 TGTAACATCATTGACAACTTCTGGTGTCAAT
* * *
22061 TGTAAGATTATTGACAATTTCTGGTGTCAAT
1 TGTAACATCATTGACAACTTCTGGTGTCAAT
*
22092 TGTAACACCATTGACAACTTCTGGTGTCAAT
1 TGTAACATCATTGACAACTTCTGGTGTCAAT
22123 TGTAACATCATTGACAACTTCTGGTGTCAAT
1 TGTAACATCATTGACAACTTCTGGTGTCAAT
22154 GGAGATTTAT
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 8 0.10
31 75 0.90
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (31 bp):
TGTAACATCATTGACAACTTCTGGTGTCAAT
Found at i:23816 original size:18 final size:19
Alignment explanation
Indices: 23780--23826 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
23770 ACTCAGACTC
*
23780 AAACT-AACTGACTCAAAA
1 AAACTGAACTAACTCAAAA
23798 AAACTGAACTAACTC-AAA
1 AAACTGAACTAACTCAAAA
23816 AAACTG-ACTAA
1 AAACTGAACTAA
23827 ACCCAACAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 14 0.52
19 8 0.30
ACGTcount: A:0.55, C:0.21, G:0.06, T:0.17
Consensus pattern (19 bp):
AAACTGAACTAACTCAAAA
Found at i:25227 original size:72 final size:72
Alignment explanation
Indices: 25106--25253 Score: 253
Period size: 72 Copynumber: 2.1 Consensus size: 72
25096 GTAAGTAAAG
*
25106 TAAA-GTCATTAACAAAGTAAAATTCGATGTTAATGGAAGCCAATTTCAGAAACAAATTGTATAA
1 TAAATGTCATTAACAAAGTAAAATTAGATGTTAATGGAAGCCAATTTCAGAAACAAATTGTATAA
25170 CAATGCA
66 CAATGCA
**
25177 TAAATGTCATTAACAAAGTAAAATTAGATGTTAATGGAAGCCAATTTCAGAAATTAATTGTATAA
1 TAAATGTCATTAACAAAGTAAAATTAGATGTTAATGGAAGCCAATTTCAGAAACAAATTGTATAA
*
25242 CAGTGCA
66 CAATGCA
25249 TAAAT
1 TAAAT
25254 ATTTTTTTTA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 4 0.06
72 68 0.94
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (72 bp):
TAAATGTCATTAACAAAGTAAAATTAGATGTTAATGGAAGCCAATTTCAGAAACAAATTGTATAA
CAATGCA
Found at i:29473 original size:22 final size:22
Alignment explanation
Indices: 29426--29473 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
29416 TAACAAACTG
* *
29426 TTTTAACTAAAATTAGTTACTG
1 TTTTAACTAAAATTAGCTACTA
*
29448 TTTTAACTAACTATT-GCTACTA
1 TTTTAACTAA-AATTAGCTACTA
29470 TTTT
1 TTTT
29474 CAATTTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (22 bp):
TTTTAACTAAAATTAGCTACTA
Found at i:40968 original size:11 final size:11
Alignment explanation
Indices: 40952--41047 Score: 79
Period size: 11 Copynumber: 8.3 Consensus size: 11
40942 TCTTCCCCAA
40952 TTTCTTAATTT
1 TTTCTTAATTT
40963 TTTCTTAAGTTT
1 TTTCTTAA-TTT
*
40975 TTATACGTTGTATTTT
1 TT-T-C--T-TAATTT
40991 TTTCTTAAATTT
1 TTTCTT-AATTT
41003 TTTCTTAATTT
1 TTTCTTAATTT
***
41014 CACCTT--TTT
1 TTTCTTAATTT
41023 TTTCTTAATTT
1 TTTCTTAATTT
41034 TTTCTTAATTT
1 TTTCTTAATTT
41045 TTT
1 TTT
41048 TCAGTATCCC
Statistics
Matches: 68, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
9 6 0.09
11 34 0.50
12 16 0.24
13 1 0.01
14 2 0.03
15 1 0.01
16 6 0.09
17 2 0.03
ACGTcount: A:0.18, C:0.10, G:0.03, T:0.69
Consensus pattern (11 bp):
TTTCTTAATTT
Found at i:41004 original size:13 final size:12
Alignment explanation
Indices: 40952--41049 Score: 55
Period size: 12 Copynumber: 8.3 Consensus size: 12
40942 TCTTCCCCAA
40952 TTTCTT-AATTT
1 TTTCTTAAATTT
*
40963 TTTCTTAAGTTT
1 TTTCTTAAATTT
* *
40975 TTATACGTTGTATTTT
1 TT-T-C-TT-AAATTT
40991 TTTCTTAAATTT
1 TTTCTTAAATTT
41003 TTTCTT-AATTT
1 TTTCTTAAATTT
***
41014 CACCTT---TTT
1 TTTCTTAAATTT
41023 TTTCTT-AATTT
1 TTTCTTAAATTT
*
41034 TTTCTTAATTTT
1 TTTCTTAAATTT
41046 TTTC
1 TTTC
41050 AGTATCCCCA
Statistics
Matches: 67, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
9 6 0.09
11 23 0.34
12 24 0.36
13 3 0.04
14 2 0.03
15 3 0.04
16 6 0.09
ACGTcount: A:0.17, C:0.11, G:0.03, T:0.68
Consensus pattern (12 bp):
TTTCTTAAATTT
Found at i:41429 original size:220 final size:220
Alignment explanation
Indices: 41047--41451 Score: 652
Period size: 220 Copynumber: 1.8 Consensus size: 220
41037 CTTAATTTTT
41047 TTCAGTATCCCCAAAATGATATACTTTATACCAAAATCATTTCTCATCATCCCCAATGAATCTTA
1 TTCAGTATCCCCAAAATGATATACTTTATACCAAAATCATTTCTCATCATCCCCAATGAATCTTA
41112 TGCACCATCCCCAAATTCTTTAGAGATTGACATTTTCTCATATACACAAATTTGACTTAAAAAAG
66 TGCACCATCCCCAAATTCTTTAGAGATTGACATTTTCTCATATACACAAATTTGACTTAAAAAAG
* * *
41177 TGCTTTAAACCATATTTTTCATTCTAATTAATTGAATAAACCACGTCTATATGATTTTAGCGCCG
131 TGCTTTAAACCATATTTTGCAATCTAATTAATTGAATAAACCACGTATATATGATTTTAGCGCCG
41242 TCTCATAATTAAACAAAATGCAAAA
196 TCTCATAATTAAACAAAATGCAAAA
* * * *
41267 TTCAGTATCCCCAAAATGATATAGTTTATACCCAAATCATTTTTCATCATCCCCAATTAATCTTA
1 TTCAGTATCCCCAAAATGATATACTTTATACCAAAATCATTTCTCATCATCCCCAATGAATCTTA
** **
41332 TGCACCAT-CCCAAATTCTTTAGAGATTGACAATTTT-TTGTATACACAAATTTGACTTTCAAAA
66 TGCACCATCCCCAAATTCTTTAGAGATTGAC-ATTTTCTCATATACACAAATTTGACTTAAAAAA
* * *
41395 GTGCTTTAATCCATATTTTAGGAATCTAATTAATTGAATAAACCACGTATATTTGAT
130 GTGCTTTAAACCATATTTT-GCAATCTAATTAATTGAATAAACCACGTATATATGAT
41452 GGTGGAAAAT
Statistics
Matches: 169, Mismatches: 14, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
219 63 0.37
220 106 0.63
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (220 bp):
TTCAGTATCCCCAAAATGATATACTTTATACCAAAATCATTTCTCATCATCCCCAATGAATCTTA
TGCACCATCCCCAAATTCTTTAGAGATTGACATTTTCTCATATACACAAATTTGACTTAAAAAAG
TGCTTTAAACCATATTTTGCAATCTAATTAATTGAATAAACCACGTATATATGATTTTAGCGCCG
TCTCATAATTAAACAAAATGCAAAA
Found at i:41510 original size:11 final size:11
Alignment explanation
Indices: 41496--41584 Score: 63
Period size: 11 Copynumber: 7.5 Consensus size: 11
41486 GGAAAAAGAA
41496 AAGAAAAAATT
1 AAGAAAAAATT
*
41507 AAGAAAAAA-A
1 AAGAAAAAATT
***
41517 AAGGTGAAATT
1 AAGAAAAAATT
41528 AAGAAAAAATTT
1 AAGAAAAAA-TT
*
41540 AAGAAAAAAATAC
1 AAG-AAAAAAT-T
41553 AACGTATAAAAACTT
1 AA-G-A-AAAAA-TT
41568 AAGAAAAAATT
1 AAGAAAAAATT
41579 AAGAAA
1 AAGAAA
41585 TTGGGGAAGA
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 6 0.10
11 23 0.38
12 11 0.18
13 9 0.15
14 3 0.05
15 7 0.12
16 1 0.02
ACGTcount: A:0.69, C:0.03, G:0.11, T:0.17
Consensus pattern (11 bp):
AAGAAAAAATT
Found at i:41513 original size:21 final size:21
Alignment explanation
Indices: 41487--41536 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
41477 TTAAGAAAAG
41487 GAAAAAGAAAAGAAAAAATTAA
1 GAAAAA-AAAAGAAAAAATTAA
***
41509 GAAAAAAAAAGGTGAAATTAA
1 GAAAAAAAAAGAAAAAATTAA
41530 GAAAAAA
1 GAAAAAA
41537 TTTAAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.10
Consensus pattern (21 bp):
GAAAAAAAAAGAAAAAATTAA
Found at i:42344 original size:41 final size:41
Alignment explanation
Indices: 42283--42360 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
42273 TTTATAACTA
*
42283 GGGGCTAAACCTGAATTTAATTTCTTACCTTAATTATCATG
1 GGGGCTAAACCTGAACTTAATTTCTTACCTTAATTATCATG
* * *
42324 GGGGCTAAACCTGGACTTAATTTGTTTCCTTAATTAT
1 GGGGCTAAACCTGAACTTAATTTCTTACCTTAATTAT
42361 TTAGGAGGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (41 bp):
GGGGCTAAACCTGAACTTAATTTCTTACCTTAATTATCATG
Found at i:47175 original size:19 final size:18
Alignment explanation
Indices: 47151--47186 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
47141 TGAAGATTTC
47151 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
47170 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
47187 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.