Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013922.1 Corchorus olitorius cultivar O-4 contig13955, 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: 28965
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:295 original size:2 final size:2
Alignment explanation
Indices: 283--313 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
273 AGTTTAGACT
283 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
314 AGTTAATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:472 original size:5 final size:5
Alignment explanation
Indices: 462--495 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
452 ATAAATACAG
462 ATAGT ATAGT ATAGT ATAGT ATAGAT ATA-T ATAG
1 ATAGT ATAGT ATAGT ATAGT ATAG-T ATAGT ATAG
496 AATTATAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 19 0.70
6 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38
Consensus pattern (5 bp):
ATAGT
Found at i:496 original size:10 final size:11
Alignment explanation
Indices: 462--510 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 11
452 ATAAATACAG
462 ATAG-TATAGT
1 ATAGATATAGT
472 ATAG-TATAGT
1 ATAGATATAGT
482 ATAGATATA-T
1 ATAGATATAGT
492 ATAGAATTATAG-
1 ATAG-A-TATAGT
504 ATAGATA
1 ATAGATA
511 GATAGATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 21 0.60
11 6 0.17
12 8 0.23
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (11 bp):
ATAGATATAGT
Found at i:3705 original size:11 final size:14
Alignment explanation
Indices: 3671--3701 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3661 GCCGATCCAC
3671 TTGTGTATAATAAG
1 TTGTGTATAATAAG
3685 TTGTGTATAATAAG
1 TTGTGTATAATAAG
3699 TTG
1 TTG
3702 ATAACAAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (14 bp):
TTGTGTATAATAAG
Found at i:6916 original size:13 final size:13
Alignment explanation
Indices: 6900--6925 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6890 TATAATTTAC
6900 CTATATATAAAGT
1 CTATATATAAAGT
6913 CTATATATAAAGT
1 CTATATATAAAGT
6926 AGTAATGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
CTATATATAAAGT
Found at i:7052 original size:126 final size:126
Alignment explanation
Indices: 6914--7156 Score: 459
Period size: 126 Copynumber: 1.9 Consensus size: 126
6904 ATATAAAGTC
*
6914 TATATATAAAGTAGTAATGAAATTAATATTTTTTTCTTAAAAAGTAAAGATTTAGCCATCATTAC
1 TATATATAAAGTAGTAATGAAATTAAAATTTTTTTCTTAAAAAGTAAAGATTTAGCCATCATTAC
6979 CACAGAATCGCACATCTTTTCTAGAGTTGACAATGTGAGAAGTTATCATATAAAGTCTATA
66 CACAGAATCGCACATCTTTTCTAGAGTTGACAATGTGAGAAGTTATCATATAAAGTCTATA
7040 TATATATAAAGTAGTAATGAAATTAAAATTTTTTTCTTAAAAAGTAAAGATTTAGCCATCATTAC
1 TATATATAAAGTAGTAATGAAATTAAAATTTTTTTCTTAAAAAGTAAAGATTTAGCCATCATTAC
* *
7105 CACAGAATTGCATATCTTTTCTAGAGTTGACAATGTGAGAAGTTATCATATA
66 CACAGAATCGCACATCTTTTCTAGAGTTGACAATGTGAGAAGTTATCATATA
7157 GAAACATGTT
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 114 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (126 bp):
TATATATAAAGTAGTAATGAAATTAAAATTTTTTTCTTAAAAAGTAAAGATTTAGCCATCATTAC
CACAGAATCGCACATCTTTTCTAGAGTTGACAATGTGAGAAGTTATCATATAAAGTCTATA
Found at i:9725 original size:178 final size:177
Alignment explanation
Indices: 9360--9737 Score: 501
Period size: 178 Copynumber: 2.1 Consensus size: 177
9350 TCATAAGCTC
* * *
9360 AAATTATGTAATATTAAGTAGACCGTCTATTCCTGTTAACCAAAACAACTAATTCTTTGGAAGCA
1 AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTCTTTGGAAGCA
* *
9425 TTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAAC
66 TTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATAGAAC
* * * * *
9490 AACCTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTGGAGCA
131 AACCTTTCAAGAGAAACTTAAATCACCTCAATCAGACAACCGGAGCA
* *
9537 AAAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATT-TTTCGGAAG
1 AAA-TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTCTTT-GGAAG
9601 CATTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATAG
64 CATTTTTGATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATAG
* * * * ** *
9665 AACAATCTTTTAATAGAAACTTAAATCACCTTAATTGGATAACCGAAGAG-A
128 AACAACCTTTCAAGAGAAACTTAAATCACCTCAATCAGACAACCG--GAGCA
* *
9716 AAATTATATAATTTTAAATAGA
1 AAATTATATAATATTAAGTAGA
9738 TCGTTTAACC
Statistics
Matches: 174, Mismatches: 22, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
177 10 0.06
178 157 0.90
179 4 0.02
180 3 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (177 bp):
AAATTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCAAAACAACAAATTCTTTGGAAGCA
TTTTTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATAGAAC
AACCTTTCAAGAGAAACTTAAATCACCTCAATCAGACAACCGGAGCA
Found at i:10592 original size:178 final size:178
Alignment explanation
Indices: 10279--10599 Score: 484
Period size: 178 Copynumber: 1.8 Consensus size: 178
10269 TTTTCACCAT
* * *
10279 AAGCACAAATTATGTAATATTAAGTAGACAGTCTATTTCCGTTAACCGAAACAACTAATTCTTTG
1 AAGCACAAATTATATAATATTAAGTAGACAGTCTATTCCCGTTAACCGAAACAACAAATTCTTTG
* * *
10344 GAAGCATTTTTTATACCTTGAACATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTAGATAA
66 GAAGCATTTTTTATACCTTAAACATTAAATTTAGTTTTCAAGACCTTCATAAAAGTTGTAGATAA
10409 TGGAACAACCTTTCAAGACACACTTGAATAATCTCAATCAGACATTTG
131 TGGAACAACCTTTCAAGACACACTTGAATAATCTCAATCAGACATTTG
* * *
10457 AAGCA-AAAGTTATATAATATTAAGTTGACCGTCTATTCCCGTTAATCGAAACAACAAATT-TTT
1 AAGCACAAA-TTATATAATATTAAGTAGACAGTCTATTCCCGTTAACCGAAACAACAAATTCTTT
* **
10520 CGGAAGCATTTTTTATACTTTAAACATTAAATTTAGTTTTTGAGACCTTCATAAAAGTTGTAGAT
65 -GGAAGCATTTTTTATACCTTAAACATTAAATTTAGTTTTCAAGACCTTCATAAAAGTTGTAGAT
* *
10585 CATGGAACAATCTTT
129 AATGGAACAACCTTT
10600 AAATAGACAC
Statistics
Matches: 127, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
177 6 0.05
178 121 0.95
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (178 bp):
AAGCACAAATTATATAATATTAAGTAGACAGTCTATTCCCGTTAACCGAAACAACAAATTCTTTG
GAAGCATTTTTTATACCTTAAACATTAAATTTAGTTTTCAAGACCTTCATAAAAGTTGTAGATAA
TGGAACAACCTTTCAAGACACACTTGAATAATCTCAATCAGACATTTG
Found at i:10650 original size:178 final size:177
Alignment explanation
Indices: 10279--10662 Score: 457
Period size: 178 Copynumber: 2.2 Consensus size: 177
10269 TTTTCACCAT
* * *
10279 AAGCACAAATTATGTAATATTAAGTAGACAGTCTATTTCCGTTAACCGAAACAACTAATTCTTTG
1 AAGCA-AAATTATATAATATTAAGTAGACAGTCTATTCCCGTTAACCGAAACAACAAATTCTTTG
* * *
10344 GAAGCATTTTTTATACCTTGAACATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTAGATAA
65 GAAGCATTTTTTATACCTTAAACATTAAATTTAGTTTTCAAGACCTTCATAAAAGTTGTAGATAA
* * * * ***
10409 TGGAACAACCTTTCAAGACACACTTGAATAATCTCAATCAGACATTTG
130 TGGAACAACCTTTAAAGACACACTTAAATAACCTCAATCAGAAACCGG
* * *
10457 AAGCAAAAGTTATATAATATTAAGTTGACCGTCTATTCCCGTTAATCGAAACAACAAATT-TTTC
1 AAGCAAAA-TTATATAATATTAAGTAGACAGTCTATTCCCGTTAACCGAAACAACAAATTCTTT-
* ** *
10521 GGAAGCATTTTTTATACTTTAAACATTAAATTTAGTTTTTGAGACCTTCATAAAAGTTGTAGATC
64 GGAAGCATTTTTTATACCTTAAACATTAAATTTAGTTTTCAAGACCTTCATAAAAGTTGTAGATA
* * * * * *
10586 ATGGAACAATCTTTAAATAGACACTTAAATCACCTTAATCGGATAACCGG
129 ATGGAACAACCTTTAAAGACACACTTAAATAACCTCAATCAGA-AACCGG
* *
10636 AGAG-AAAATTATATAATGTTAAATAGA
1 A-AGCAAAATTATATAATATTAAGTAGA
10663 TCGTTTAGGC
Statistics
Matches: 173, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
177 6 0.03
178 158 0.91
179 7 0.04
180 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (177 bp):
AAGCAAAATTATATAATATTAAGTAGACAGTCTATTCCCGTTAACCGAAACAACAAATTCTTTGG
AAGCATTTTTTATACCTTAAACATTAAATTTAGTTTTCAAGACCTTCATAAAAGTTGTAGATAAT
GGAACAACCTTTAAAGACACACTTAAATAACCTCAATCAGAAACCGG
Found at i:10802 original size:925 final size:922
Alignment explanation
Indices: 9024--10870 Score: 2973
Period size: 925 Copynumber: 2.0 Consensus size: 922
9014 TTATAGTTAC
* * * *
9024 TAGGTAAGAGCCCGCGCGTTTCATAGCGCGAATATGTTCTTGCACTTGATATGCAATATTCCACA
1 TAGGTAAGAGCCAGCGCGTTTCATAGCGCGAACATGTTCTTGCACTTGATATACAATAGTCCACA
* * * * *
9089 ATCAGTTTTCAACATATTATTGGTGACTTATGGGTTTGTCATATAAGGACGATGACCGATTGCTT
66 ATCAGTTTTCAAAATATTATTGGTGACTTATGGGTTTGCCAAATAAGGACGATGACCAATTACTT
* * *
9154 TAGGTCATGTGTTTTGAAAGATTTGGACTTAAGGATCTGACAAAAAAACCAGTCTAAAGAATTAG
131 TAGCTAATGTGTTTTGAAAGATTTGGACTTAAGGATCCGACAAAAAAACCAGTCTAAAGAATTAG
* *
9219 CGTCATTAATCTAAGAACAAATTGATAGGGGTATTTCGGTTATTTCATGCTTGATCTTTTTGTTA
196 CCTCATTAATCTAAGAACAAATTGATAGGGGTATTTCGGTCATTTCATGCTTGATCTTTTTGTTA
* *
9284 TTTGAGTTAAAAACCGAGGGTATTTTGGGAAGTTTGAAAAAAAACTCTCCATGGGTCCAATTTCC
261 TTTGAGTTAAAAACCGAGGGTATTTTGGGAAGTTTGAAAAAAAACCCTCCATGGATCCAATTTCC
* * *
9349 ATCATAAGCTCAAATTATGTAATATTAAGTAGACCGTCTATTCCTGTTAACCAAAACAACTAATT
326 ACCATAAGCACAAATTATGTAATATTAAGTAGACAGTCTATTCCTGTTAACCAAAACAACTAATT
*
9414 CTTTGGAAGCATTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTA
391 CTTTGGAAGCATTTTTTATACCTTGAACATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTA
* * * *
9479 GATCATGGAACAACCTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTGGAGCAAAAGTTA
456 GATAATGGAACAACCTTTCAAGACACACTTGAATAATCTCAATCAGACATCTGAAGCAAAAGTTA
9544 TATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATTTTTCGGAAGCATTTTTG
521 TATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATTTTTCGGAAGCATTTTTG
* *
9609 ATACTTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATAGAACAATCTT
586 ATACTTGAAACATTAAATTTAGTTTTCGAGACCTTCATAAAAGTTGTAGATCATAGAACAATCTT
* * *
9674 TTAATAGAAACTTAAATCACCTTAATTGGATAACCGAAGAGAAAATTATATAATTTTAAATAGAT
651 TAAATAGAAACTTAAATCACCTTAATCGGATAACCGAAGAGAAAATTATATAATGTTAAATAGAT
9739 CGTTTAACCAAACCACTTATAAATATGTTATATTATATTAAATTGTTAGAAAGTCAAAAATACCC
716 CGTTTAACCAAACCACTTATAAATATGTTATATTATATTAAATTGTTAGAAAGTCAAAAATACCC
* *
9804 TTTGAAGTTTGTGAGAATAACGAAAAAACCAATATCAAAATGATGAAAAAACCAAGCTAAATAGT
781 TTAGAAGTTTGTAAGAATAACGAAAAAACCAATATCAAAATGATGAAAAAACCAAGCTAAATAGT
* * * *
9869 AATCAAATTGATAAGATTAAATCTTTTGACTGG-TTTTTTAGTACTTTCACTTCCTATAATTATT
846 AATCAAATTAATAAGATTAAATCTCTTGACTGGTTTTTTTAGTACATTCACATCCTATAATTATT
9933 GTTTTTTTATAAT
911 G-TTTTTTATAAT
* * * *
9946 TAGGTAAGAGCCAGCGCGTTTCATTGTGCGAACATGTTCTTGCACTTGATATACAATAGTCCCCG
1 TAGGTAAGAGCCAGCGCGTTTCATAGCGCGAACATGTTCTTGCACTTGATATACAATAGTCCACA
* * * *
10011 ATTATTTTTCAAAATATTATTGGTGACTTATGGGTTTGCCAAATGAGGATGATGACCAATTACTT
66 ATCAGTTTTCAAAATATTATTGGTGACTTATGGGTTTGCCAAATAAGGACGATGACCAATTACTT
* * *
10076 TAGCTAATGTGTTTTGAAAGATTTGGATTTAAGTAAGGATCCGACCAAAAAACCGGTCTAAAGAA
131 TAGCTAATGTGTTTTGAAAGATTTGGA-CT---TAAGGATCCGACAAAAAAACCAGTCTAAAGAA
* *
10141 TTAGCCTCATTAATCT-AGAAACAAATTGATAGGGGTATTTTGGTCATTTCATGCTTGATTTTTT
192 TTAGCCTCATTAATCTAAG-AACAAATTGATAGGGGTATTTCGGTCATTTCATGCTTGATCTTTT
* **
10205 TGTTATTTGAGTTAAAGACCGAGGGTATTTTGGGAAGTTTG-AAAAAAACCCTCTGTGGATCCAA
256 TGTTATTTGAGTTAAAAACCGAGGGTATTTTGGGAAGTTTGAAAAAAAACCCTCCATGGATCCAA
* *
10269 TTTTCACCATAAGCACAAATTATGTAATATTAAGTAGACAGTCTATTTCC-GTTAACCGAAACAA
321 TTTCCACCATAAGCACAAATTATGTAATATTAAGTAGACAGTCTA-TTCCTGTTAACCAAAACAA
10333 CTAATTCTTTGGAAGCATTTTTTATACCTTGAACATTAAATTTAGTTTTCAAGTCCTTCATGAAA
385 CTAATTCTTTGGAAGCATTTTTTATACCTTGAACATTAAATTTAGTTTTCAAGTCCTTCATGAAA
*
10398 GTTGTAGATAATGGAACAACCTTTCAAGACACACTTGAATAATCTCAATCAGACATTTGAAGCAA
450 GTTGTAGATAATGGAACAACCTTTCAAGACACACTTGAATAATCTCAATCAGACATCTGAAGCAA
* *
10463 AAGTTATATAATATTAAGTTGACCGTCTATTCCCGTTAATCGAAACAACAAATTTTTCGGAAGCA
515 AAGTTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATTTTTCGGAAGCA
* * * *
10528 TTTTTTATACTTTAAACATTAAATTTAGTTTTTGAGACCTTCATAAAAGTTGTAGATCATGGAAC
580 TTTTTGATACTTGAAACATTAAATTTAGTTTTCGAGACCTTCATAAAAGTTGTAGATCATAGAAC
* *
10593 AATCTTTAAATAGACACTTAAATCACCTTAATCGGATAACCGGAGAGAAAATTATATAATGTTAA
645 AATCTTTAAATAGAAACTTAAATCACCTTAATCGGATAACCGAAGAGAAAATTATATAATGTTAA
**
10658 ATAGATCGTTTAGGCAAACCACTTATAAATATGTTATATTATATTAAATTGTTAGAAAGTCAAAA
710 ATAGATCGTTTAACCAAACCACTTATAAATATGTTATATTATATTAAATTGTTAGAAAGTCAAAA
* ** *
10723 ATGCCCTTAGAAGTTTGTAAGAATAACGAAAAAACCAATATTGAAATGATGAAAAAACCAAGCTG
775 ATACCCTTAGAAGTTTGTAAGAATAACGAAAAAACCAATATCAAAATGATGAAAAAACCAAGCTA
* *
10788 AATAGTATTCAAATTAATAAGGTTAAATCTCTTGACTGGTTTTTTTAGTACATTCACATCCTATA
840 AATAGTAATCAAATTAATAAGATTAAATCTCTTGACTGGTTTTTTTAGTACATTCACATCCTATA
10853 ATTATTGTTTTTTATAAT
905 ATTATTGTTTTTTATAAT
10871 AGGCGGGAAG
Statistics
Matches: 848, Mismatches: 70, Indels: 11
0.91 0.08 0.01
Matches are distributed among these distances:
922 138 0.16
923 1 0.00
925 549 0.65
926 160 0.19
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (922 bp):
TAGGTAAGAGCCAGCGCGTTTCATAGCGCGAACATGTTCTTGCACTTGATATACAATAGTCCACA
ATCAGTTTTCAAAATATTATTGGTGACTTATGGGTTTGCCAAATAAGGACGATGACCAATTACTT
TAGCTAATGTGTTTTGAAAGATTTGGACTTAAGGATCCGACAAAAAAACCAGTCTAAAGAATTAG
CCTCATTAATCTAAGAACAAATTGATAGGGGTATTTCGGTCATTTCATGCTTGATCTTTTTGTTA
TTTGAGTTAAAAACCGAGGGTATTTTGGGAAGTTTGAAAAAAAACCCTCCATGGATCCAATTTCC
ACCATAAGCACAAATTATGTAATATTAAGTAGACAGTCTATTCCTGTTAACCAAAACAACTAATT
CTTTGGAAGCATTTTTTATACCTTGAACATTAAATTTAGTTTTCAAGTCCTTCATGAAAGTTGTA
GATAATGGAACAACCTTTCAAGACACACTTGAATAATCTCAATCAGACATCTGAAGCAAAAGTTA
TATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATTTTTCGGAAGCATTTTTG
ATACTTGAAACATTAAATTTAGTTTTCGAGACCTTCATAAAAGTTGTAGATCATAGAACAATCTT
TAAATAGAAACTTAAATCACCTTAATCGGATAACCGAAGAGAAAATTATATAATGTTAAATAGAT
CGTTTAACCAAACCACTTATAAATATGTTATATTATATTAAATTGTTAGAAAGTCAAAAATACCC
TTAGAAGTTTGTAAGAATAACGAAAAAACCAATATCAAAATGATGAAAAAACCAAGCTAAATAGT
AATCAAATTAATAAGATTAAATCTCTTGACTGGTTTTTTTAGTACATTCACATCCTATAATTATT
GTTTTTTATAAT
Found at i:13047 original size:27 final size:26
Alignment explanation
Indices: 13017--13087 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 26
13007 GTATAGCCAT
13017 CGGTAAGTTCATCT-CAAGCTATTCCTG
1 CGGTAA-TTCATCTCCAA-CTATTCCTG
* *
13044 CGGTGAATTCATCTCCAATTTTTCCTG
1 CGGT-AATTCATCTCCAACTATTCCTG
*
13071 CGGTAATTGATTCTCCA
1 CGGTAATTCA-TCTCCA
13088 GATCTTCCTG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
26 5 0.13
27 28 0.74
28 5 0.13
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (26 bp):
CGGTAATTCATCTCCAACTATTCCTG
Found at i:13095 original size:27 final size:27
Alignment explanation
Indices: 13038--13099 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
13028 TCTCAAGCTA
*
13038 TTCCTGCGGTGAATTCATCTCCAATTT
1 TTCCTGCGGTGAATTCATCTCCAATTC
*
13065 TTCCTGCGGT-AATTGATTCTCCAGA-TC
1 TTCCTGCGGTGAATTCA-TCTCCA-ATTC
13092 TTCCTGCG
1 TTCCTGCG
13100 ACATCCACTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 5 0.16
27 25 0.81
28 1 0.03
ACGTcount: A:0.16, C:0.27, G:0.18, T:0.39
Consensus pattern (27 bp):
TTCCTGCGGTGAATTCATCTCCAATTC
Found at i:18538 original size:62 final size:62
Alignment explanation
Indices: 18441--18564 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
18431 TGGTCGTCAT
18441 ATAAGAATTAAGTCTCCATTGAAATTCAAGATCGTATGAGATGACTTTAATTATTTTCTGAC
1 ATAAGAATTAAGTCTCCATTGAAATTCAAGATCGTATGAGATGACTTTAATTATTTTCTGAC
*
18503 ATAAGAATTAAGTCTCCGTTGAAATTCAAGATCGTATGAGATGACTTTAATTATTTTCTGAC
1 ATAAGAATTAAGTCTCCATTGAAATTCAAGATCGTATGAGATGACTTTAATTATTTTCTGAC
18565 CATTATTATT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (62 bp):
ATAAGAATTAAGTCTCCATTGAAATTCAAGATCGTATGAGATGACTTTAATTATTTTCTGAC
Found at i:18819 original size:12 final size:12
Alignment explanation
Indices: 18802--18834 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
18792 GTATCAACAA
18802 ATATAATATAAT
1 ATATAATATAAT
18814 ATATAATATAAT
1 ATATAATATAAT
18826 ATAATAATA
1 AT-ATAATA
18835 ACATTCCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATAATATAAT
Found at i:18823 original size:17 final size:16
Alignment explanation
Indices: 18801--18835 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
18791 GGTATCAACA
18801 AATATAATATAATATAT
1 AATATAATATAATA-AT
18818 AATATAATATAATAAT
1 AATATAATATAATAAT
18834 AA
1 AA
18836 CATTCCATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AATATAATATAATAAT
Found at i:22286 original size:51 final size:50
Alignment explanation
Indices: 22185--22289 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 50
22175 GTTCTTCATA
* **
22185 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
* *
22235 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTGTTT-AGATCTTGTCTCAGGACAAACAAACACTCGTACA-GTGT
22286 TTTT
1 TTTT
22290 ATTCAGAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
50 7 0.15
51 39 0.83
52 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCAGGACAAACAAACACTCGTACAGTGT
Found at i:23077 original size:28 final size:29
Alignment explanation
Indices: 23044--23114 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 29
23034 ATGTGATTTG
23044 CTAGTGGGATATTTTTTCTT-AATAAGTC
1 CTAGTGGGATATTTTTTCTTCAATAAGTC
* *
23072 CTAGTGGGAT-TTTTTTTTTCAATCAGTC
1 CTAGTGGGATATTTTTTCTTCAATAAGTC
23100 CTAGTGGGA-ATTTTT
1 CTAGTGGGATATTTTT
23115 ATTTTGAAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 8 0.21
28 31 0.79
ACGTcount: A:0.21, C:0.11, G:0.20, T:0.48
Consensus pattern (29 bp):
CTAGTGGGATATTTTTTCTTCAATAAGTC
Done.