Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010697.1 Corchorus olitorius cultivar O-4 contig10729, 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: 36199
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6740 original size:15 final size:16
Alignment explanation
Indices: 6716--6755 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
6706 AGAGGTTGAA
*
6716 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
6731 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
6747 AGAAAACAA
1 AGAAAACAA
6756 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:16027 original size:137 final size:135
Alignment explanation
Indices: 15719--16193 Score: 495
Period size: 137 Copynumber: 3.5 Consensus size: 135
15709 TGTGTAAATG
* * * * * * ** **
15719 TTGTCGTGTAAGCATTTTGGCAACAACATTTTGTCATTTTAAAAAGTAATTTGTAACCATTTTGA
1 TTGTTGTGTAAACATTTTGACAACAACATTTTGTCGTTTTAAAAAGTTATTTGCAACCAACTAAA
* * ** ** * *
15784 TGTCGTTTTAACAAACTTTA-TACAATAATTAAAATATCATT-ACGTAAAAGTATTTACACCCAA
66 TATCGTTATAA-AAACTTTAGTA-ACCAA--AAAATATTGTTGTC-TAAAAGTATTTACAACCAA
*
15847 AATAATGA--
126 AATAATAATT
* * *
15855 -TGTTCTGTAAACATTTTGACAACAACATTTTGTCGTTTTAAAAAGTTATTTGTAACCAACTAGA
1 TTGTTGTGTAAACATTTTGACAACAACATTTTGTCGTTTTAAAAAGTTATTTGCAACCAACTAAA
* *
15919 TATCGTTCTAAATACTATTAGGTAACCAAAAAATATTGTTGTCTAAAAGTATTTACAACCAAAAT
66 TATCGTTATAAAAACT-TTA-GTAACCAAAAAATATTGTTGTCTAAAAGTATTTACAACCAAAAT
15984 AATAATT
129 AATAATT
* *
15991 TTGTTGTGTAAACATTTTGACAACAACATTTTGTCGTTTTAAAAAATTATTCGCAACCAACTAAA
1 TTGTTGTGTAAACATTTTGACAACAACATTTTGTCGTTTTAAAAAGTTATTTGCAACCAACTAAA
* *
16056 TATCGTTATACAAAACTTTACATAA-CAAAAAAGTATTGTTGTCGAAAAGTATTTACAACC--AA
66 TATCGTTATA-AAAACTTTA-GTAACCAAAAAA-TATTGTTGTCTAAAAGTATTTACAACCAAAA
16118 -AATAATT
128 TAATAATT
**
16125 TTGTTGTGTAAACATTTTGACAACAACA-TTTGTATTTTTTAAAAA-TTATTTCGCAACCAACTA
1 TTGTTGTGTAAACATTTTGACAACAACATTTTGT-CGTTTTAAAAAGTTATTT-GCAACCAACTA
16188 AATATC
64 AATATC
16194 ATTGTAAATA
Statistics
Matches: 296, Mismatches: 32, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
133 10 0.03
134 99 0.33
135 70 0.24
136 10 0.03
137 102 0.34
138 5 0.02
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (135 bp):
TTGTTGTGTAAACATTTTGACAACAACATTTTGTCGTTTTAAAAAGTTATTTGCAACCAACTAAA
TATCGTTATAAAAACTTTAGTAACCAAAAAATATTGTTGTCTAAAAGTATTTACAACCAAAATAA
TAATT
Found at i:16182 original size:67 final size:67
Alignment explanation
Indices: 15984--16184 Score: 153
Period size: 67 Copynumber: 3.0 Consensus size: 67
15974 CAACCAAAAT
**
15984 AATAATTTTGTTGTGTAAACATTTTGACAACAACATTTTGTCGTTTTAAAAAATTA-TTCGCAAC
1 AATAATTTTGTTGTGTAAACATTTTGACAACAACA-TTTGTATTTTTAAAAAATTATTTCGCAAC
16048 C-A
65 CAA
* * * * ** * *** ** * *
16050 ACTAAATATCGTTATACAAA-ACTTT-ACATAACAA-AAAAGTATTGTTGTCGAAAAGTATTT-A
1 AAT-AATTTTGTTGTGTAAACATTTTGAC--AACAACATTTGTATT-TT-TAAAAAATTATTTCG
16111 CAACCAA
61 CAACCAA
*
16118 AATAATTTTGTTGTGTAAACATTTTGACAACAACATTTGTATTTTTTAAAAATTATTTCGCAACC
1 AATAATTTTGTTGTGTAAACATTTTGACAACAACATTTGTATTTTTAAAAAATTATTTCGCAACC
16183 AA
66 AA
16185 CTAAATATCA
Statistics
Matches: 94, Mismatches: 30, Indels: 21
0.65 0.21 0.14
Matches are distributed among these distances:
65 5 0.05
66 19 0.20
67 53 0.56
68 15 0.16
69 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.37
Consensus pattern (67 bp):
AATAATTTTGTTGTGTAAACATTTTGACAACAACATTTGTATTTTTAAAAAATTATTTCGCAACC
AA
Found at i:16188 original size:134 final size:134
Alignment explanation
Indices: 15829--16193 Score: 497
Period size: 137 Copynumber: 2.7 Consensus size: 134
15819 ATCATTACGT
* ** * *
15829 AAAAGTATTTACACCCAAAATAATGATGTTCTGTAAACATTTTGACAACAACATTTTGTCGTTTT
1 AAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACAACATTTTGTCTTTTT
* * * * **
15894 AAAAAGTTATTT-GTAACCAACTAGATATCGTTCTAAATACTATTAGGTAACCAAAAAATATTGT
66 AAAAA-TTATTTCGCAACCAACTAAATATCGTTATAAAAACTATTACATAACCAAAAAATATTGT
*
15958 TGTCT
130 TGTCG
15963 AAAAGTATTTACAACCAAAATAATAATTTTGTTGTGTAAACATTTTGACAACAACATTTTGTCGT
1 AAAAGTATTTACAACC--AA-AATAATTTTGTTGTGTAAACATTTTGACAACAACATTTTGTC-T
*
16028 TTTAAAAAATTA-TTCGCAACCAACTAAATATCGTTATACAAAACT-TTACATAA-CAAAAAAGT
62 TTTTAAAAATTATTTCGCAACCAACTAAATATCGTTATA-AAAACTATTACATAACCAAAAAA-T
16090 ATTGTTGTCG
125 ATTGTTGTCG
*
16100 AAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACAACA-TTTGTATTTTT
1 AAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACAACATTTTGT-CTTTT
16164 TAAAAATTATTTCGCAACCAACTAAATATC
65 TAAAAATTATTTCGCAACCAACTAAATATC
16194 ATTGTAAATA
Statistics
Matches: 207, Mismatches: 15, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
133 17 0.08
134 70 0.34
135 2 0.01
136 11 0.05
137 94 0.45
138 13 0.06
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.36
Consensus pattern (134 bp):
AAAAGTATTTACAACCAAAATAATTTTGTTGTGTAAACATTTTGACAACAACATTTTGTCTTTTT
AAAAATTATTTCGCAACCAACTAAATATCGTTATAAAAACTATTACATAACCAAAAAATATTGTT
GTCG
Found at i:16346 original size:41 final size:41
Alignment explanation
Indices: 16300--16427 Score: 98
Period size: 41 Copynumber: 3.3 Consensus size: 41
16290 ATATTGTTGT
16300 TACAATATTTTTACGCAACAATATTGAGTTGTTGCGTAAAA
1 TACAATATTTTTACGCAACAATATTGAGTTGTTGCGTAAAA
* *
16341 TACAAT-TCTTTTA-ACAACAATAAAATGACGTTG-T---T---A
1 TACAATAT-TTTTACGCAACAAT--ATTGA-GTTGTTGCGTAAAA
* *
16377 -A-AATATTTTTACGCAACCATATTGGGTTGTTGCGTAAAA
1 TACAATATTTTTACGCAACAATATTGAGTTGTTGCGTAAAA
16416 TACAATTATTTT
1 TACAA-TATTTT
16428 AACAACAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 31
0.64 0.06 0.30
Matches are distributed among these distances:
32 4 0.06
33 4 0.06
34 8 0.12
35 8 0.12
36 2 0.03
39 2 0.03
40 9 0.14
41 13 0.20
42 11 0.17
43 4 0.06
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.38
Consensus pattern (41 bp):
TACAATATTTTTACGCAACAATATTGAGTTGTTGCGTAAAA
Found at i:16374 original size:75 final size:75
Alignment explanation
Indices: 16295--16440 Score: 256
Period size: 75 Copynumber: 1.9 Consensus size: 75
16285 AATATATATT
* *
16295 GTTGTTACAATATTTTTACGCAACAATATTGAGTTGTTGCGTAAAATACAATTCTTTTAACAACA
1 GTTGTTAAAATATTTTTACGCAACAATATTGAGTTGTTGCGTAAAATACAATTATTTTAACAACA
16360 ATAAAATGAC
66 ATAAAATGAC
* *
16370 GTTGTTAAAATATTTTTACGCAACCATATTGGGTTGTTGCGTAAAATACAATTATTTTAACAACA
1 GTTGTTAAAATATTTTTACGCAACAATATTGAGTTGTTGCGTAAAATACAATTATTTTAACAACA
16435 ATAAAA
66 ATAAAA
16441 GGCGTAACAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (75 bp):
GTTGTTAAAATATTTTTACGCAACAATATTGAGTTGTTGCGTAAAATACAATTATTTTAACAACA
ATAAAATGAC
Found at i:16461 original size:75 final size:75
Alignment explanation
Indices: 16306--16470 Score: 217
Period size: 75 Copynumber: 2.2 Consensus size: 75
16296 TTGTTACAAT
*
16306 ATTTTTACGCAACAATATTGAGTTGTTGCGTAAAATACAATTCTTTTAACAACAATAAAATGACG
1 ATTTTTACGCAACAATATTGAGTTGTTGCGTAAAATACAATTATTTTAACAACAATAAAATGACG
**** *
16371 TTGTTAAAAT
66 TAACAAAAAG
* * *
16381 ATTTTTACGCAACCATATTGGGTTGTTGCGTAAAATACAATTATTTTAACAACAATAAAA-GGCG
1 ATTTTTACGCAACAATATTGAGTTGTTGCGTAAAATACAATTATTTTAACAACAATAAAATGACG
16445 TAACAAAAAG
66 TAACAAAAAG
16455 ACTTTTTTA-GCAACAA
1 A--TTTTTACGCAACAA
16471 CCACCTTAAG
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
74 9 0.12
75 63 0.81
76 6 0.08
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (75 bp):
ATTTTTACGCAACAATATTGAGTTGTTGCGTAAAATACAATTATTTTAACAACAATAAAATGACG
TAACAAAAAG
Found at i:19288 original size:101 final size:101
Alignment explanation
Indices: 19113--19314 Score: 291
Period size: 101 Copynumber: 2.0 Consensus size: 101
19103 AATATTTCCT
19113 TCCATTTAACTTAATTGTTATTACATAAAATAAAAATTTAACTAAAAATTGAAATTACGCAGTTC
1 TCCATTTAACTTAATTGTTATTACATAAAATAAAAATTTAACTAAAAATTGAAATTACGCAGTTC
*
19178 CAATCATAAATCGAAAAA-TCCGACGAGAATGCGCGG
66 CAATCATAAACCGAAAAACT-CGACGAGAATGCGCGG
* * * * * *
19214 TCCA-TTAACTTAATTGTTATTACATAAAATAAAATTTTTTACTTAGAATTGAAATTACTCCGTT
1 TCCATTTAACTTAATTGTTATTACATAAAATAAAA-ATTTAACTAAAAATTGAAATTACGCAGTT
* *
19278 CCAATCATAAACCGAAAAACTTGACGCGAATGCGCGG
65 CCAATCATAAACCGAAAAACTCGACGAGAATGCGCGG
19315 GATAATATCT
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
100 30 0.33
101 59 0.66
102 1 0.01
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.31
Consensus pattern (101 bp):
TCCATTTAACTTAATTGTTATTACATAAAATAAAAATTTAACTAAAAATTGAAATTACGCAGTTC
CAATCATAAACCGAAAAACTCGACGAGAATGCGCGG
Found at i:23129 original size:41 final size:41
Alignment explanation
Indices: 23057--23146 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
23047 ATCAGGGGCG
* *
23057 AAATTGAATCAATAAATAAATATTACTCTAAATCAAGGACA
1 AAATTGAATCAATAAAAAAATATAACTCTAAATCAAGGACA
* *
23098 AAATTGAATCAATCAACAAAAATA-AAC-CTAAATCAGGGACT
1 AAATTGAATCAAT-AA-AAAAATATAACTCTAAATCAAGGACA
*
23139 ATATTGAA
1 AAATTGAA
23147 AATGGGAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 32 0.76
42 4 0.10
43 6 0.14
ACGTcount: A:0.53, C:0.13, G:0.09, T:0.24
Consensus pattern (41 bp):
AAATTGAATCAATAAAAAAATATAACTCTAAATCAAGGACA
Found at i:25235 original size:27 final size:27
Alignment explanation
Indices: 25205--25304 Score: 155
Period size: 27 Copynumber: 3.7 Consensus size: 27
25195 TGTGAACTTA
* *
25205 AAATGACCAAAATGCCCCTGAATATGC
1 AAATGACCAAAATGCCCCTGGATGTGC
25232 AAATGACCAAAATGCCCCTGGATGTGC
1 AAATGACCAAAATGCCCCTGGATGTGC
* *
25259 AAATGACTAAGATGCCCCTGGATGTGC
1 AAATGACCAAAATGCCCCTGGATGTGC
*
25286 AAATGACTAAAATGCCCCT
1 AAATGACCAAAATGCCCCT
25305 AGGTGACCCT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 68 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (27 bp):
AAATGACCAAAATGCCCCTGGATGTGC
Found at i:25876 original size:30 final size:30
Alignment explanation
Indices: 25802--26139 Score: 381
Period size: 30 Copynumber: 11.1 Consensus size: 30
25792 TTAACTGATG
*
25802 AAGCAATGATCCTAAACTAGGATTGAAATGGATA
1 AAGCAATGATCCTAAACCAGGATT-AAA---ATA
** * * *
25836 AAATAAAGATCCTAAACCAGGATTGAAATG
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
25866 AAGCAAAGATCCTAAACCAGGATTGAAAAGTA
1 AAGCAATGATCCTAAACCAGGATT-AAAA-TA
* * * * *
25898 CA-CAACGATCGTAAACCAGGATTGAGATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
25927 AAGCGATGATCCTAAACCAGGATTAAGAATA
1 AAGCAATGATCCTAAACCAGGATTAA-AATA
*
25958 AAGCAATGATCCTAAAACAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
*
25988 AAGCAATGATCCTAAACCAGGATTAAAATG
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* * *
26018 AAGCAACGATCCTCAACCAGGATTAAAACA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* *
26048 AAGCAACGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* * *
26078 AGGCAACGATCCTCAACCAGGATTAAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
* *
26108 AAGCAATGATCCTCAACCAGGATTGAAATA
1 AAGCAATGATCCTAAACCAGGATTAAAATA
26138 AA
1 AA
26140 CTAATAAGCA
Statistics
Matches: 266, Mismatches: 34, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
29 3 0.01
30 190 0.71
31 49 0.18
32 2 0.01
33 2 0.01
34 20 0.08
ACGTcount: A:0.47, C:0.18, G:0.17, T:0.18
Consensus pattern (30 bp):
AAGCAATGATCCTAAACCAGGATTAAAATA
Found at i:26236 original size:20 final size:20
Alignment explanation
Indices: 26211--26252 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
26201 AGGAAAATAA
*
26211 CAAATGCCCGGAGGTCTTAT
1 CAAATGCCCGGAGGACTTAT
*
26231 CAAATGCTCGGAGGACTTAT
1 CAAATGCCCGGAGGACTTAT
26251 CA
1 CA
26253 GAATTAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (20 bp):
CAAATGCCCGGAGGACTTAT
Found at i:26613 original size:172 final size:170
Alignment explanation
Indices: 26217--26737 Score: 715
Period size: 169 Copynumber: 3.1 Consensus size: 170
26207 ATAACAAATG
* * * *
26217 CCCGGAGGTCTTATCAAATGCTCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAAATTG
1 CCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTG
* * * * *
26282 TACCCGAAGGTCTCACCAATGCAAACTCTGAATAGAGACCTTGACCAAGGATTTTAAA-TATAAA
66 TGCCCGGAGGACTTACCAATGCAAACTCTGAATAGAGACCTTGACCAAGGATTTTAAACTTTAAA
* *
26346 CATGGATTTTTAATGAAAAACTTGATAAAATGAAATGGTA
131 AATGGATTTTTAATGAAAAACTTGATGAAATGAAATGGTA
* *
26386 CCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCGGAATTAATACCCGGAGGTTTCTGGATTTG
1 CCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTG
* * * *
26451 TGCCCGGAGGACTTACCAGTGCAAACTTTGAATTGAGACCTTGAACAAGGATTTTAAACTTTAAA
66 TGCCCGGAGGACTTACCAATGCAAACTCTGAATAGAGACCTTGACCAAGGATTTTAAACTTTAAA
* * * * * *
26516 TATGAATCTTTGATGAAAAACTTGATGAAATGGAATGTTA
131 AATGGATTTTTAATGAAAAACTTGATGAAATGAAATGGTA
* *
26556 CCCGGAGGTTTT-TGAATTTGTGCCGAGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAAT
1 CCCGGAGGTTTTATCAA-TTG-CCCG-GAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAAT
**
26620 TTGTGCCCGGAGGACTTACCAATGTGAACTCTGAATAGAGACCTTGACCAAGGATTTTAAAC-TT
63 TTGTGCCCGGAGGACTTACCAATGCAAACTCTGAATAGAGACCTTGACCAAGGATTTTAAACTTT
* * *
26684 AAAAATGGATTTTTAATGAAAAACTTAATGAAATGAGATAGTA
128 AAAAATGGATTTTTAATGAAAAACTTGATGAAATGAAATGGTA
*
26727 CCCGGGGGTTT
1 CCCGGAGGTTT
26738 CAACAATGCA
Statistics
Matches: 306, Mismatches: 42, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
169 112 0.37
170 53 0.17
171 49 0.16
172 92 0.30
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (170 bp):
CCCGGAGGTTTTATCAATTGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTG
TGCCCGGAGGACTTACCAATGCAAACTCTGAATAGAGACCTTGACCAAGGATTTTAAACTTTAAA
AATGGATTTTTAATGAAAAACTTGATGAAATGAAATGGTA
Found at i:26628 original size:22 final size:22
Alignment explanation
Indices: 26556--26632 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
26546 TGGAATGTTA
*
26556 CCCGGAGGTTTTTGAATTTGTG
1 CCCGGAGGTTTCTGAATTTGTG
* ** *
26578 -CCGAGAGGACTTATCAGAATTAATA
1 CCCG-GAGG--TT-TCTGAATTTGTG
26603 CCCGGAGGTTTCTGAATTTGTG
1 CCCGGAGGTTTCTGAATTTGTG
26625 CCCGGAGG
1 CCCGGAGG
26633 ACTTACCAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
21 3 0.07
22 20 0.49
23 2 0.05
24 2 0.05
25 11 0.27
26 3 0.07
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (22 bp):
CCCGGAGGTTTCTGAATTTGTG
Found at i:26957 original size:69 final size:69
Alignment explanation
Indices: 26873--27304 Score: 618
Period size: 69 Copynumber: 6.3 Consensus size: 69
26863 CTCATTAAAC
* * * * * * * *
26873 TTGGCTTATGGAAAAGCCTCTGTTG-TATGGATGGAACTAATGTTTAAACTGACTTGCATGGAAA
1 TTGGCTTGTGGAAAAGCCTATGTGGCT-TGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAA
*
26937 TGAGT
65 CGAGT
* * * * *
26942 TTGACTTATGGAAAAGTCTATATGGCTTGGATGGAACCAAGACTTAAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
27007 GAGT
66 GAGT
* * *
27011 TTTGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAAACAAGGCTTAAACTGACTCGTATGGAAAT
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
27076 GAGT
66 GAGT
*
27080 TTGGCTTATGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
27145 GAGT
66 GAGT
* * * *
27149 TTGGCTTGTGGAAAAGCCTATGTGTCTTGGACGGAACCAA--CGTAAACTGACTCATATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
27212 GAGT
66 GAGT
*
27216 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGGTTAAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
27281 GAGT
66 GAGT
*
27285 TTGGCTTGTCGAAAAGCCTA
1 TTGGCTTGTGGAAAAGCCTA
27305 ACCATTCGGA
Statistics
Matches: 325, Mismatches: 35, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
67 63 0.19
69 261 0.80
70 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (69 bp):
TTGGCTTGTGGAAAAGCCTATGTGGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
GAGT
Found at i:32718 original size:16 final size:16
Alignment explanation
Indices: 32697--32739 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
32687 TTACTCTGCT
32697 TTGTTTTT-TAGTTTAA
1 TTGTTTTTCT-GTTTAA
32713 TTGTTTTTCTGTTTAA
1 TTGTTTTTCTGTTTAA
32729 TTG-TTTTCTGT
1 TTGTTTTTCTGT
32740 CAACCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.31
16 17 0.65
17 1 0.04
ACGTcount: A:0.12, C:0.05, G:0.14, T:0.70
Consensus pattern (16 bp):
TTGTTTTTCTGTTTAA
Found at i:35810 original size:21 final size:21
Alignment explanation
Indices: 35767--35818 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
35757 CCCATTACCA
**
35767 TGCCACCACCGGTTAAGCCCG
1 TGCCACCACCGGCCAAGCCCG
* *
35788 TGCCACCACCGGCCATGCTCG
1 TGCCACCACCGGCCAAGCCCG
*
35809 TGCCATCACC
1 TGCCACCACC
35819 ATTCCAAACC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.46, G:0.21, T:0.15
Consensus pattern (21 bp):
TGCCACCACCGGCCAAGCCCG
Done.