Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016505.1 Corchorus olitorius cultivar O-4 contig16538, 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: 87138
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2598 original size:22 final size:24
Alignment explanation
Indices: 2567--2618 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
2557 TAGTGATTCG
*
2567 TTTTTCTTTT-GCC-ACGTGTGCC
1 TTTTTTTTTTGGCCAACGTGTGCC
*
2589 TTTTTTTTTTGGCCAAGGTGTGCC
1 TTTTTTTTTTGGCCAACGTGTGCC
2613 TTTTTT
1 TTTTTT
2619 AGTAGTCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 9 0.35
23 3 0.12
24 14 0.54
ACGTcount: A:0.06, C:0.19, G:0.19, T:0.56
Consensus pattern (24 bp):
TTTTTTTTTTGGCCAACGTGTGCC
Found at i:12057 original size:123 final size:123
Alignment explanation
Indices: 11838--12086 Score: 480
Period size: 123 Copynumber: 2.0 Consensus size: 123
11828 CCTAATCCAA
11838 CTGTACCAGAACAAAGCCTTTCAGATAAGAAGGTTAACGGTGCATCAGTCCCAGAAGCAAACCAG
1 CTGTACCAGAACAAAGCCTTTCAGATAAGAAGGTTAACGGTGCATCAGTCCCAGAAGCAAACCAG
* *
11903 CAAGAATCTTCTAATTTGACAGCGTTATCTGTTGTTCCCATTGTGAAGACACCAGTGT
66 CAAGAATCTTCTAATTTGACAGCATTATCTGTTGTTCCCACTGTGAAGACACCAGTGT
11961 CTGTACCAGAACAAAGCCTTTCAGATAAGAAGGTTAACGGTGCATCAGTCCCAGAAGCAAACCAG
1 CTGTACCAGAACAAAGCCTTTCAGATAAGAAGGTTAACGGTGCATCAGTCCCAGAAGCAAACCAG
12026 CAAGAATCTTCTAATTTGACAGCATTATCTGTTGTTCCCACTGTGAAGACACCAGTGT
66 CAAGAATCTTCTAATTTGACAGCATTATCTGTTGTTCCCACTGTGAAGACACCAGTGT
12084 CTG
1 CTG
12087 ACGGTTACAA
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 124 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (123 bp):
CTGTACCAGAACAAAGCCTTTCAGATAAGAAGGTTAACGGTGCATCAGTCCCAGAAGCAAACCAG
CAAGAATCTTCTAATTTGACAGCATTATCTGTTGTTCCCACTGTGAAGACACCAGTGT
Found at i:13512 original size:60 final size:60
Alignment explanation
Indices: 13439--13557 Score: 229
Period size: 60 Copynumber: 2.0 Consensus size: 60
13429 CGACACGGCC
13439 CACCAAGTGCTCCTCTTGTTGCTGCCGCTGCTCCTGCCTCTATGAACAACTTACAATTTT
1 CACCAAGTGCTCCTCTTGTTGCTGCCGCTGCTCCTGCCTCTATGAACAACTTACAATTTT
*
13499 CACCAAGTGCTCCTCTTGTTGCTGCCGCTGCTCCTGCCTCTATGAACAATTTACAATTT
1 CACCAAGTGCTCCTCTTGTTGCTGCCGCTGCTCCTGCCTCTATGAACAACTTACAATTT
13558 AAAAAAACAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.18, C:0.33, G:0.15, T:0.34
Consensus pattern (60 bp):
CACCAAGTGCTCCTCTTGTTGCTGCCGCTGCTCCTGCCTCTATGAACAACTTACAATTTT
Found at i:20764 original size:14 final size:13
Alignment explanation
Indices: 20745--20783 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
20735 ACTCAACACT
20745 AACTGACTCGAAAA
1 AACTGACTC-AAAA
*
20759 AACTGACTCAACA
1 AACTGACTCAAAA
20772 AACTGACT-AAAA
1 AACTGACTCAAAA
20784 CCCGATAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 3 0.13
13 11 0.48
14 9 0.39
ACGTcount: A:0.51, C:0.23, G:0.10, T:0.15
Consensus pattern (13 bp):
AACTGACTCAAAA
Found at i:20776 original size:13 final size:13
Alignment explanation
Indices: 20734--20779 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
20724 GTCAGACTCA
20734 GACTCAACACTAACT
1 GACTCAACA--AACT
*
20749 GACTCGAAAAAACT
1 GACTC-AACAAACT
20763 GACTCAACAAACT
1 GACTCAACAAACT
20776 GACT
1 GACT
20780 AAAACCCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 11 0.39
14 9 0.32
15 5 0.18
16 3 0.11
ACGTcount: A:0.43, C:0.28, G:0.11, T:0.17
Consensus pattern (13 bp):
GACTCAACAAACT
Found at i:31806 original size:87 final size:87
Alignment explanation
Indices: 31656--31830 Score: 341
Period size: 87 Copynumber: 2.0 Consensus size: 87
31646 GGGGAAGCTG
*
31656 TCCAGTCCAGGATCAGGGCATGTCACAGGCTTAAGGCCTCTGATCACCCACCAATGAAGACTGTT
1 TCCAGTCCAGGATCAGGGCATGTCACAGGCTTAAGGCCTCTGATCACCCACCAATGAAAACTGTT
31721 GGCACGACTCGAACCCCAAATC
66 GGCACGACTCGAACCCCAAATC
31743 TCCAGTCCAGGATCAGGGCATGTCACAGGCTTAAGGCCTCTGATCACCCACCAATGAAAACTGTT
1 TCCAGTCCAGGATCAGGGCATGTCACAGGCTTAAGGCCTCTGATCACCCACCAATGAAAACTGTT
31808 GGCACGACTCGAACCCCAAATC
66 GGCACGACTCGAACCCCAAATC
31830 T
1 T
31831 TACAAGCAAA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.28, C:0.32, G:0.21, T:0.19
Consensus pattern (87 bp):
TCCAGTCCAGGATCAGGGCATGTCACAGGCTTAAGGCCTCTGATCACCCACCAATGAAAACTGTT
GGCACGACTCGAACCCCAAATC
Found at i:32256 original size:32 final size:32
Alignment explanation
Indices: 32197--32257 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
32187 ACTCTACACT
*
32197 ATTTAATCTTTTAATTATTTTTATTTTATGCG
1 ATTTAATCTTTTAATTATATTTATTTTATGCG
* *
32229 ATTTAGTCTTTTAACTT-TATTTCTTTTAT
1 ATTTAATCTTTTAA-TTATATTTATTTTAT
32258 TAGAAAGCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 23 0.92
33 2 0.08
ACGTcount: A:0.23, C:0.08, G:0.05, T:0.64
Consensus pattern (32 bp):
ATTTAATCTTTTAATTATATTTATTTTATGCG
Found at i:34046 original size:16 final size:16
Alignment explanation
Indices: 34025--34055 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34015 TTTCATATTA
34025 ATTGAAGGTAGAACTG
1 ATTGAAGGTAGAACTG
*
34041 ATTGAAGGTGGAACT
1 ATTGAAGGTAGAACT
34056 TTTTGGTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.32, T:0.26
Consensus pattern (16 bp):
ATTGAAGGTAGAACTG
Found at i:45043 original size:2 final size:2
Alignment explanation
Indices: 45038--45064 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45028 AAAGAAAATA
45038 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
45065 ATGCAAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59951 original size:44 final size:44
Alignment explanation
Indices: 59902--59997 Score: 192
Period size: 44 Copynumber: 2.2 Consensus size: 44
59892 TTTTCAACTG
59902 CAAATTTTAAAATTCATTCGCCCTTTATTAGATCAAAACAACCC
1 CAAATTTTAAAATTCATTCGCCCTTTATTAGATCAAAACAACCC
59946 CAAATTTTAAAATTCATTCGCCCTTTATTAGATCAAAACAACCC
1 CAAATTTTAAAATTCATTCGCCCTTTATTAGATCAAAACAACCC
59990 CAAATTTT
1 CAAATTTT
59998 GTTACCCAGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (44 bp):
CAAATTTTAAAATTCATTCGCCCTTTATTAGATCAAAACAACCC
Found at i:64110 original size:30 final size:30
Alignment explanation
Indices: 64038--64154 Score: 137
Period size: 30 Copynumber: 3.9 Consensus size: 30
64028 ACACGTGATG
* * *
64038 TGCCACGTGTCATTTTTGTGTACACGCGGCA
1 TGCCACATGTCATTTTTG-GTACACGTGGAA
* * *
64069 TGCCACGTGTCATTTTTGGTACATGTGGTA
1 TGCCACATGTCATTTTTGGTACACGTGGAA
* * *
64099 TGCTACATGTCATTTTTTGTACACAT-GAA
1 TGCCACATGTCATTTTTGGTACACGTGGAA
64128 TGCCACATGTCATTTTTGGTACACGTG
1 TGCCACATGTCATTTTTGGTACACGTG
64155 ACGGTACACA
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
29 25 0.34
30 30 0.41
31 18 0.25
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.38
Consensus pattern (30 bp):
TGCCACATGTCATTTTTGGTACACGTGGAA
Found at i:65187 original size:31 final size:31
Alignment explanation
Indices: 65149--65222 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
65139 TTTGCCTCCT
*
65149 AAAATATCTTTAATTTGAGAAGTTCA-GGGGC
1 AAAATATCTTGAATTTG-GAAGTTCATGGGGC
* *
65180 AAAATATCCTGAATTTGGAAGTTCATTGGGC
1 AAAATATCTTGAATTTGGAAGTTCATGGGGC
*
65211 AAAATGTCTTGA
1 AAAATATCTTGA
65223 TTAATTTGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 8 0.22
31 29 0.78
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (31 bp):
AAAATATCTTGAATTTGGAAGTTCATGGGGC
Found at i:68105 original size:47 final size:47
Alignment explanation
Indices: 68050--68162 Score: 199
Period size: 47 Copynumber: 2.4 Consensus size: 47
68040 GACTAATAGC
68050 GAGGAGGAGCAAATAAAGAACATTCATTGAGACTAATACCCAAAGAG
1 GAGGAGGAGCAAATAAAGAACATTCATTGAGACTAATACCCAAAGAG
* *
68097 GAGGAGGAGCAAATAAGGAACATTCATTGAGACTAATAGCCAAAGAG
1 GAGGAGGAGCAAATAAAGAACATTCATTGAGACTAATACCCAAAGAG
*
68144 GAGGAGGAGTAAATAAAGA
1 GAGGAGGAGCAAATAAAGA
68163 GCTAAAAGAG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 62 1.00
ACGTcount: A:0.47, C:0.12, G:0.27, T:0.14
Consensus pattern (47 bp):
GAGGAGGAGCAAATAAAGAACATTCATTGAGACTAATACCCAAAGAG
Found at i:68145 original size:44 final size:44
Alignment explanation
Indices: 68030--68149 Score: 167
Period size: 47 Copynumber: 2.8 Consensus size: 44
68020 AATCAACCCC
68030 CATTCATTGAGACTAATAG-C---GAGGAGGAGCAAATAAAGAA
1 CATTCATTGAGACTAATAGCCAAAGAGGAGGAGCAAATAAAGAA
* *
68070 CATTCATTGAGACTAATACCCAAAGAGGAGGAGGAGCAAATAAGGAA
1 CATTCATTGAGACTAATAGCC-AA-A-GAGGAGGAGCAAATAAAGAA
68117 CATTCATTGAGACTAATAGCCAAAGAGGAGGAG
1 CATTCATTGAGACTAATAGCCAAAGAGGAGGAG
68150 GAGTAAATAA
Statistics
Matches: 70, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
40 18 0.26
41 1 0.01
44 9 0.13
45 1 0.01
46 2 0.03
47 39 0.56
ACGTcount: A:0.43, C:0.14, G:0.26, T:0.17
Consensus pattern (44 bp):
CATTCATTGAGACTAATAGCCAAAGAGGAGGAGCAAATAAAGAA
Found at i:71769 original size:30 final size:30
Alignment explanation
Indices: 71735--71802 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
71725 AGCTATCTGT
71735 TTATCTTCATCTTCATCTTCTGAATCTGAC
1 TTATCTTCATCTTCATCTTCTGAATCTGAC
71765 TTATCTTCATCTTCATCTTCTGAATCTGAC
1 TTATCTTCATCTTCATCTTCTGAATCTGAC
71795 TTATCTTC
1 TTATCTTC
71803 CTCAAACCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.19, C:0.26, G:0.06, T:0.49
Consensus pattern (30 bp):
TTATCTTCATCTTCATCTTCTGAATCTGAC
Found at i:75362 original size:29 final size:30
Alignment explanation
Indices: 75303--75366 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
75293 AAAAAGGTTA
* * *
75303 ATTTGGCCAAAATTAGGAGTTTAGGGGCTT
1 ATTTGGCCAAAATTAGAAGTTTAAGGACTT
75333 ATTTGGCCAAAATT-GAAGTTTAAGGACTT
1 ATTTGGCCAAAATTAGAAGTTTAAGGACTT
75362 ATTTG
1 ATTTG
75367 ACCATTACCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 17 0.55
30 14 0.45
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (30 bp):
ATTTGGCCAAAATTAGAAGTTTAAGGACTT
Found at i:78172 original size:18 final size:18
Alignment explanation
Indices: 78132--78179 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
78122 AGTAATAAAA
*
78132 AATAAATATTAATTAGTC
1 AATAAATATTAATTAATC
78150 AATAAATATTTAATTAAT-
1 AATAAATA-TTAATTAATC
*
78168 TATAAAT-TTAAT
1 AATAAATATTAAT
78180 ATTTTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 5 0.19
18 14 0.52
19 8 0.30
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
AATAAATATTAATTAATC
Found at i:78365 original size:25 final size:24
Alignment explanation
Indices: 78320--78369 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
78310 TTCTAAATTA
* **
78320 TCATTGTTAAAATATTTTTTTTATG
1 TCATTATTAAAATA-TAATTTTATG
78345 TCATTATTAAAATATAATTTTATG
1 TCATTATTAAAATATAATTTTATG
78369 T
1 T
78370 ATTTTGTTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (24 bp):
TCATTATTAAAATATAATTTTATG
Found at i:78408 original size:97 final size:99
Alignment explanation
Indices: 78295--78474 Score: 258
Period size: 97 Copynumber: 1.8 Consensus size: 99
78285 ATTATACCCC
* ** *
78295 TTTTTTTAAATATATTTCTAAATTATCATTGTTAAAATAT-TTTT-TTTATGTCATTATTAAAAT
1 TTTTTTTAAATATATTTCTAAATTATCATTATTAAAATATATTTTAACTATGCCATTATTAAAAT
78358 ATAATTTTATGTA-TTTTGTTCTGATTGTACTAT
66 ATAATTTTATGTACTTTTGTTCTGATTGTACTAT
* * *
78391 TTTTTTTCAAATGTATTTTTAAATTGTCATTATTAAAATATATTTTAACTATGCCATTATTAAAA
1 TTTTTTT-AAATATATTTCTAAATTATCATTATTAAAATATATTTTAACTATGCCATTATTAAAA
*
78456 TATAATTTTGTGTACTTTT
65 TATAATTTTATGTACTTTT
78475 TTCAAATATA
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
96 7 0.10
97 29 0.40
98 4 0.06
99 28 0.39
100 4 0.06
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (99 bp):
TTTTTTTAAATATATTTCTAAATTATCATTATTAAAATATATTTTAACTATGCCATTATTAAAAT
ATAATTTTATGTACTTTTGTTCTGATTGTACTAT
Found at i:79529 original size:334 final size:327
Alignment explanation
Indices: 78518--79702 Score: 1380
Period size: 331 Copynumber: 3.6 Consensus size: 327
78508 AAATATAATT
* * * *
78518 TTTAATTAGAAATTAATTCGGAAAAAGGTAGGAAAAGCGATATTAGAAACGTGAGAAGCCCTTCA
1 TTTAATTAGAAATTAATTCGGAAAAA-TTAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCA
** * * *
78583 GCCTTTTTGGCGTTGAGTTATATATTTTTTATTAGTATTGTGGCCCAAAATTGA-GAAGACAT-T
65 ATCTTTTTGGCGTT-AATTATATATTTTTTATGAGTATCGTGG-CCAAAATTGAGGAA-A-ATCT
** * * * * *
78646 TCTTGGGTCAATTTTTGCACAATTTTAGCTGAAATCGTGTACTAACCATCACGGATTTTCACTAA
126 T-TCAGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAA
* *
78711 AAACGCG-TTCCGGAACCCCGACTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAAAAT
190 AAACGCGATTCC-G--TCCCGACTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATAT
* * * * * *
78775 CTATATCCATCTAACCAAATCTTACCCACATTCGATTTAAGAATTTGTTTTTACGAGGATATGAA
252 CTATATCCATCTAACAAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATATGAA
*
78840 TAATGTTTCGA
317 TCATGTTTCGA
* * *
78851 TTAAATTAGGAATTAATTCGGAAAAATTAGGAAAAACGATATTAGAAGCGT-AAATAGCCTTTCA
1 TTTAATTAGAAATTAATTCGGAAAAATTAGGAAAAACGATATTAGAAGCGTGAAA-AGCCCTTCA
* * *
78915 ATCTTTTTGGTGTTGAATTATATATTTTTTAAGAGTATCGTGGCCAAAAGTTGAGGTAAATTCTT
65 ATCTTTTTGGCGTT-AATTATATATTTTTTATGAGTATCGTGGCCAAAA-TTGAGG-AAAATCTT
* *
78980 TCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACTATCACGGTTTTTTG-CTAAA
127 TCAGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTTTGACTAAA
** * *
79044 AACGC-ATTCCGTGGCCCGACTCAATTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATATTT
191 AACGCGATTCCGT--CCCGACTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCT
** * * * *
79108 ATATTTATCTAACGAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTCAATC
254 ATATCCATCTAACAAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATATGAATC
79173 -TGGTTTCGA
319 AT-GTTTCGA
* * *
79182 TTTAATTAGAAATTAATTCGGAAAAATTAGAAAAAAAAAAACAATATTAGAAGCATGAGAAA-CC
1 TTTAATTAGAAATTAATTCGGAAAAATTAG-----GAAAAACGATATTAGAAGCGTGA-AAAGCC
* * *
79246 CTTCAATCTTTTTGGCGTTAAGTTATATATTTTTTATGAATATGGTGGCCGGAAATTGAGGAGAA
60 CTTCAATCTTTTTGGCGTTAA-TTATATATTTTTTATGAGTATCGTGGCC-AAAATTGAGGA-AA
* * ** *
79311 ATGTTCCCTGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGAC
122 ATCTTTCAGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGAC
* *
79376 TAAAAACGCGATT-CGTCCCGGCTCTGTTTTGTATGATTTTTGGCGCCAAGTCTCATTGAAATAT
187 TAAAAACGCGATTCCGTCCCGACTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATAT
* *
79440 CTATATCCATCTCACAAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAA
252 CTATATCCATCTAACAAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATATGAA
**
79505 TCATGTTTTAA
317 TCATGTTTCGA
* ** * * *
79516 TTTAATTAGAAATTAATTCGGAAAAAATAGGAAAATTGATATTAGAAGCTTGAAAATCCTTTCAA
1 TTTAATTAGAAATTAATTCGGAAAAATTAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAA
* * *
79581 TCTTTTTGGCGTTTAATTATATATTTTTTATGAGTATCATGGCTAAAAATTTAGGAAAATTCTTT
66 TCTTTTTGGCG-TTAATTATATATTTTTTATGAGTATCGTGGC-CAAAATTGAGGAAAA-TCTTT
* * * * *
79646 CAGGTAAATTTTTGCAAAATTTTAACCGAAATCGTGTATTAATCATCACGGTTTTTG
128 CAGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
79703 GTAACAAAGG
Statistics
Matches: 730, Mismatches: 95, Indels: 58
0.83 0.11 0.07
Matches are distributed among these distances:
328 6 0.01
329 121 0.17
330 5 0.01
331 143 0.20
332 132 0.18
333 32 0.04
334 138 0.19
335 10 0.01
336 133 0.18
337 8 0.01
338 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (327 bp):
TTTAATTAGAAATTAATTCGGAAAAATTAGGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAA
TCTTTTTGGCGTTAATTATATATTTTTTATGAGTATCGTGGCCAAAATTGAGGAAAATCTTTCAG
GTCAATTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACTAAAAACGC
GATTCCGTCCCGACTCTGTTTTGCATGATTTTTGGCGCCAAGTCTCATTGAAATATCTATATCCA
TCTAACAAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACGAGCATATGAATCATGTTTC
GA
Found at i:80109 original size:21 final size:21
Alignment explanation
Indices: 80083--80132 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
80073 TCGCTGATTA
80083 TAATCTCATCTGTACAGTATC
1 TAATCTCATCTGTACAGTATC
* * *
80104 TAATCTAATCTGTACAGTGTT
1 TAATCTCATCTGTACAGTATC
80125 TAATCTCA
1 TAATCTCA
80133 CAACTCCAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (21 bp):
TAATCTCATCTGTACAGTATC
Found at i:81161 original size:31 final size:31
Alignment explanation
Indices: 81100--81156 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
81090 TTCGTTAGAG
*
81100 GGTAAAATCTCCTGAATTTGGAAGTTCAGGA
1 GGTAAAATCTCCTGAATTTGAAAGTTCAGGA
*
81131 GGTAAAATGTCCTG-ATTT-AAAGTTCA
1 GGTAAAATCTCCTGAATTTGAAAGTTCA
81157 CAGGACAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.29
30 4 0.17
31 13 0.54
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (31 bp):
GGTAAAATCTCCTGAATTTGAAAGTTCAGGA
Found at i:83637 original size:15 final size:15
Alignment explanation
Indices: 83615--83681 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 15
83605 GATATGTCCA
83615 TAGTTTTTTTCGAGT
1 TAGTTTTTTTCGAGT
*
83630 TTG-TTTTTT-GAGT
1 TAGTTTTTTTCGAGT
*
83643 T-GTTTTGATTC-AGT
1 TAGTTTT-TTTCGAGT
*
83657 TAGTTTTTATCGAGT
1 TAGTTTTTTTCGAGT
*
83672 CAGTTTTTTT
1 TAGTTTTTTT
83682 TTTTTCTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
12 1 0.02
13 8 0.20
14 14 0.34
15 18 0.44
ACGTcount: A:0.13, C:0.06, G:0.19, T:0.61
Consensus pattern (15 bp):
TAGTTTTTTTCGAGT
Done.