Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013498.1 Corchorus olitorius cultivar O-4 contig13531, 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: 93314
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:984 original size:331 final size:332
Alignment explanation
Indices: 1--1891 Score: 2526
Period size: 331 Copynumber: 5.7 Consensus size: 332
* ** * *
1 AAAAATGATATTTGAAGCGTGCCAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTATAC
1 AAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAC
* * * * * *
66 GAGTACTGCGATTAAAAATTAAGGAAAAATCTTTTGGGTTAA-TTTTGTAAAATTTTTGCCGAAA
66 GAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAA
* * **
130 TCGTGTACTAACCATCTA-GGTGTTTGGCT-AAAACGCGTTCAGGGGCCCAAGCTCAGTTTTGCA
131 TCGTGTA-TAACCATC-ACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCA
* * * *
193 TGATTTTTGGCGCCAAAACTCATTGAAATATCTATATTAATCTAACAAAATATCTGCCATAATGG
194 TGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAACCAAATATCAGCCACAATGG
* *
258 ATTTAAGGATTTGTTTTTACGATCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGGA
259 ATTTAAGGATTTGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGGA
*
323 AAATATTGA
324 AAAAATTGA
* * * * *
332 AAAAATGATATTTGAAGCGTGAAAAGTCCTTCAATCTTTTTAGCCTTGAATTATATATTTTTAAC
1 AAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAC
* * * *
397 GAGTATTGTGGTTAAAAATTGAGGAAAAATTTTTCGGGTCAACTTTTGCAAATTTTTTGCCGAAA
66 GAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAA
* * *
462 TCGTGTACAAACCAATCACGGTTTTTGGCTAAAAACGCATTCCGGGGCCCCGACTCAGTTTTAG-
131 TCGTGTA-TAACC-ATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTT-GC
* * *
526 ATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAATCAAATATCTGCCATAATG
193 ATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAACCAAATATCAGCCACAATG
* *
591 GATTTAAGGA-TGGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGGAATTAATTCGGG
258 GATTTAAGGATTTGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGG
655 AAAAAATTGA
323 AAAAAATTGA
*
665 AAAAATGTTATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAC
1 AAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAC
* * * *
730 GAGTATGGCGGTTAAAGATTGCGGTAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAA
66 GAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAA
* * *
795 TCGTGTATAAACCATCACGGTTTTT-GCTAAAAACGCGTTCCGAGACCCCGGCTCAGTTTTGCGT
131 TCGTGTAT-AACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCAT
*
859 GATTTTTGGCACCAAGACTCATTGAAATATCTATATTAATCTAACCAAATATCAGCCACAATGGA
195 GATTTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAACCAAATATCAGCCACAATGGA
*
924 TTTAAGGATTTGTTTTTACGATCATCTGAAT-TTGTTTCGATTTAAATAGAAATTAATTCGGG-A
260 TTTAAGGATTTGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGGAA
987 AAAATTGA
325 AAAATTGA
* * * *
995 AAAAATGATATTAGAAGCGCGAAAAGCCCATTCAATATTTTTGGTGTTGAATTATATAGTTTTAT
1 AAAAATGATATTAGAAGCGTGAAAAGCCC-TTCAATCTTTTTGGCGTTGAATTATATA-TTTTTT
* * *
1060 ACGAGTATTGCGGTTAAAAATTGAGG-AAAATATTTC-GGTCAATTTTTACAAAACTTTTGCCGA
64 ACGAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGA
* *
1123 AATCGTGTATAAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGTCTCAGTTTTGG
129 AATCGTGTAT-AACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGC
*
1188 ATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAACCAAATATCAGCCAAAATG
193 ATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAACCAAATATCAGCCACAATG
* *
1253 GATTTAAGGA-TT-TTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATCAATTAGGG
258 GATTTAAGGATTTGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGG
1316 AAAAAATTGA
323 AAAAAATTGA
1326 AAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAC
1 AAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAC
* ** *
1391 GAGTATTGCGGTTAGAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAAGCTTTGTCGAAA
66 GAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAA
* * * * *
1456 TCGTG--T-ACTCATCACGGTTTTTGGCTAAAAACGCGTTTCGAGACTCCGACTCAGTTTTGCAT
131 TCGTGTATAAC-CATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCAT
* * * * *
1518 GAATTTTGGCGCCAAGACTCACTGAAATATCTATATTCATC-AACCCAAATCTCAGCCACATTTG
195 GATTTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAA-CCAAATATCAGCCACA-ATG
* * ** * *
1582 GATTTAAAGATTTGTTTTTAGGAGAATCTGAATCTTGTATCGATTTAATTAAAAATTAATTCGGG
258 GATTTAAGGATTTGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGG
1647 -AAAAATTGA
323 AAAAAATTGA
* * * * * *
1656 AAAAACGATGTTAGACGCGTGAAAAGCCCTTCAATCTTTTTGGGGTTGAATTTTATATTTTTTAT
1 AAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAC
* * * *
1721 GAGTATTGTGGCTAAAAATTGAGGAAAAATCCTTCGAGTC-A-----G-----TTTTTGCCGAAA
66 GAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAA
* * ** *
1775 TCATGTACTAACCATCACGATTTTTTTGGCTAAAAATACGTTCTGGGGCCCCGGCTCAGTTTTGC
131 TCGTGTA-TAACCATCACG--GTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGC
* * * * *
1840 ATGAATTTT-GCTCCTAAGACTCCTTGTAATATCTATATTAGTCTAACCAAAT
193 ATGATTTTTGGCGCC-AAGACTCATTGAAATATCTATATTAATCTAACCAAAT
1892 CTCAAGTCAC
Statistics
Matches: 1394, Mismatches: 138, Indels: 63
0.87 0.09 0.04
Matches are distributed among these distances:
319 13 0.01
322 8 0.01
323 6 0.00
324 74 0.05
325 2 0.00
327 4 0.00
328 99 0.07
329 62 0.04
330 259 0.19
331 475 0.34
332 94 0.07
333 199 0.14
334 98 0.07
335 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (332 bp):
AAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAC
GAGTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAA
TCGTGTATAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATG
ATTTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAACCAAATATCAGCCACAATGGAT
TTAAGGATTTGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGGAAA
AAATTGA
Found at i:1457 original size:661 final size:657
Alignment explanation
Indices: 1--1891 Score: 2569
Period size: 661 Copynumber: 2.9 Consensus size: 657
* ** * *
1 AAAAATGATATTTGAAGCGTGCCAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTATAC
1 AAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAC
* * * * * *
66 GAGTACTGCGATTAAAAATTAAGGAAAAATCTTTTGGGTTAA-TTTTGTAAAATTTTTGCCGAAA
66 GAGTATTGCGGTT-AAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAA
* * * * **
130 TCGTGTACTAACCATCTA-GGTGTTTGGCT-AAAACGCGTTCAGGGGCCCAAGCTCAGTTTTGCA
130 TCGTGTA-TAACCATC-ACGGT-TTTTGCTAAAAACGCGTTCCGAGACCCCGGCTCAGTTTTGCA
* * * *
193 TGATTTTTGGCGCCAAAACTCATTGAAATATCTATATTAATCTAACAAAATATCTGCCATAATGG
192 TGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAACCAAATATCAGCCACAATGG
* *
258 ATTTAAGGATTTGTTTTTACGATCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGGA
257 ATTTAAGGATTTGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGGA
* * * *
323 AAATATTGAAAAAATGATATTTGAAGCGTGAAAAGTCCTTCAATCTTTTTAGCCTTGAATTATAT
322 AAA-ATTGAAAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATAT
* *
388 ATTTT-TAACGAGTATTGTGGTTAAAAATTGAGGAAAAATTTTTCGGGTCAACTTTTGCAAATTT
386 ATTTTAT-ACGAGTATTGTGGTTAAAAATTGAGG-AAAATATTTC-GGTCAA-TTTT-CAAAATT
* *
452 TTTGCCGAAATCGTGTACAAACCAATCACGGTTTTTGGCTAAAAACGCATTCCGGGGCCCCGACT
446 TTTGCCGAAATCGTGTATAAACC-ATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACT
* * *
517 CAGTTTTAGATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAATCAAATATCT
510 CAGTTTTGGATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAACCAAATATCA
* * *
582 GCCATAATGGATTTAAGGATGGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGGAATT
575 GCCAAAATGGATTTAAGGATGGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATC
*
647 AATTCGGGAAAAAATTGA
640 AATTAGGGAAAAAATTGA
*
665 AAAAATGTTATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAC
1 AAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAC
* * *
730 GAGTATGGCGGTTAAAGATTGCGGTAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAA
66 GAGTATTGCGGTTAAA-ATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAA
*
795 TCGTGTATAAACCATCACGGTTTTTGCTAAAAACGCGTTCCGAGACCCCGGCTCAGTTTTGCGTG
130 TCGTGTAT-AACCATCACGGTTTTTGCTAAAAACGCGTTCCGAGACCCCGGCTCAGTTTTGCATG
*
860 ATTTTTGGCACCAAGACTCATTGAAATATCTATATTAATCTAACCAAATATCAGCCACAATGGAT
194 ATTTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAACCAAATATCAGCCACAATGGAT
*
925 TTAAGGATTTGTTTTTACGATCATCTGAAT-TTGTTTCGATTTAAATAGAAATTAATTCGGGAAA
259 TTAAGGATTTGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGGAAA
* * *
989 AATTGAAAAAATGATATTAGAAGCGCGAAAAGCCCATTCAATATTTTTGGTGTTGAATTATATAG
324 AATTGAAAAAATGATATTAGAAGCGTGAAAAGCCC-TTCAATCTTTTTGGCGTTGAATTATATA-
* *
1054 TTTTATACGAGTATTGCGGTTAAAAATTGAGGAAAATATTTCGGTCAATTTTTACAAAACTTTTG
387 TTTTATACGAGTATTGTGGTTAAAAATTGAGGAAAATATTTCGGTCAA-TTTT-CAAAATTTTTG
*
1119 CCGAAATCGTGTATAAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGTCTCAGTT
450 CCGAAATCGTGTATAAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAGTT
1184 TTGGATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAACCAAATATCAGCCAA
515 TTGGATGATTTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAACCAAATATCAGCCAA
*
1249 AATGGATTTAAGGAT-TTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATCAATTA
580 AATGGATTTAAGGATGGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATCAATTA
1313 GGGAAAAAATTGA
645 GGGAAAAAATTGA
1326 AAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAC
1 AAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAC
** *
1391 GAGTATTGCGGTTAGAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAAGCTTTGTCGAAA
66 GAGTATTGCGGTTA-AAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAA
* * *
1456 TCGTG--T-ACTCATCACGGTTTTTGGCTAAAAACGCGTTTCGAGACTCCGACTCAGTTTTGCAT
130 TCGTGTATAAC-CATCACGGTTTTT-GCTAAAAACGCGTTCCGAGACCCCGGCTCAGTTTTGCAT
* * * * *
1518 GAATTTTGGCGCCAAGACTCACTGAAATATCTATATTCATC-AACCCAAATCTCAGCCACATTTG
193 GATTTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAA-CCAAATATCAGCCACA-ATG
* * ** * *
1582 GATTTAAAGATTTGTTTTTAGGAGAATCTGAATCTTGTATCGATTTAATTAAAAATTAATTCGGG
256 GATTTAAGGATTTGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGG
* * * * *
1647 AAAAATTGAAAAAACGATGTTAGACGCGTGAAAAGCCCTTCAATCTTTTTGGGGTTGAATTTTAT
321 AAAAATTGAAAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATAT
* * * ** * * *
1712 ATTTTTTATGAGTATTGTGGCTAAAAATTGAGGAAAA-A--TCCTTCGA--GTC--AGTTTTTGC
386 ATTTTATACGAGTATTGTGGTTAAAAATTGAGGAAAATATTTCGGTCAATTTTCAAAATTTTTGC
* * ** * *
1770 CGAAATCATGTACT-AACCATCACGATTTTTTTGGCTAAAAATACGTTCTGGGGCCCCGGCTCAG
451 CGAAATCGTGTA-TAAACCATCACG--GTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAG
* * * * * *
1834 TTTTGCATGAATTTT-GCTCCTAAGACTCCTTGTAATATCTATATTAGTCTAACCAAAT
513 TTTTGGATGATTTTTGGCGCC-AAGACTCATTGAAATATCTATATTAATCTAACCAAAT
1892 CTCAAGTCAC
Statistics
Matches: 1102, Mismatches: 107, Indels: 48
0.88 0.09 0.04
Matches are distributed among these distances:
650 28 0.03
651 5 0.00
652 81 0.07
653 1 0.00
656 5 0.00
657 2 0.00
658 16 0.01
659 120 0.11
660 56 0.05
661 245 0.22
662 122 0.11
663 71 0.06
664 163 0.15
665 186 0.17
666 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (657 bp):
AAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTAC
GAGTATTGCGGTTAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAAT
CGTGTATAACCATCACGGTTTTTGCTAAAAACGCGTTCCGAGACCCCGGCTCAGTTTTGCATGAT
TTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAACCAAATATCAGCCACAATGGATTT
AAGGATTTGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGGAAAAA
TTGAAAAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTT
ATACGAGTATTGTGGTTAAAAATTGAGGAAAATATTTCGGTCAATTTTCAAAATTTTTGCCGAAA
TCGTGTATAAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGACTCAGTTTTGGAT
GATTTTTGGCGCCAAGACTCATTGAAATATCTATATTAATCTAACCAAATATCAGCCAAAATGGA
TTTAAGGATGGTTTTTACGATCATCTGAATCTTGTTTCGATTTAATTAGAAATCAATTAGGGAAA
AAATTGA
Found at i:3513 original size:26 final size:26
Alignment explanation
Indices: 3478--3533 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
3468 AATTCTTAGT
3478 AAAAGCTGTAAAGAAAACAAGTTCGA
1 AAAAGCTGTAAAGAAAACAAGTTCGA
3504 AAAAGCTGTAAAGAAAACAAGTTCGA
1 AAAAGCTGTAAAGAAAACAAGTTCGA
3530 AAAA
1 AAAA
3534 ACTCCTAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.57, C:0.11, G:0.18, T:0.14
Consensus pattern (26 bp):
AAAAGCTGTAAAGAAAACAAGTTCGA
Found at i:4754 original size:19 final size:19
Alignment explanation
Indices: 4727--4764 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4717 CCCATCTAAG
*
4727 GCGATAATTAAAGCAGCAA
1 GCGAGAATTAAAGCAGCAA
4746 GCGAGAATTAAAGCAGCAA
1 GCGAGAATTAAAGCAGCAA
4765 TTTCACAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.16, G:0.24, T:0.13
Consensus pattern (19 bp):
GCGAGAATTAAAGCAGCAA
Found at i:11082 original size:54 final size:54
Alignment explanation
Indices: 10980--11083 Score: 129
Period size: 54 Copynumber: 1.9 Consensus size: 54
10970 CTATCCCTAT
* * * * *
10980 TCCTTTCTCGTTCCCTTTCCCTTCTTCTATCACCCCTCATGTCCCTATCTCTGC
1 TCCTTGCTCGTTCCCTATCCCTTCTCCTATCACCCATCATATCCCTATCTCTGC
* *
11034 TCCTTGCTCGTTCCCTATCCCTTCTCCTCTCA-CCATCGATATCTCTATCT
1 TCCTTGCTCGTTCCCTATCCCTTCTCCTATCACCCATC-ATATCCCTATCT
11084 TTATCCCTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 4 0.10
54 38 0.90
ACGTcount: A:0.10, C:0.43, G:0.06, T:0.41
Consensus pattern (54 bp):
TCCTTGCTCGTTCCCTATCCCTTCTCCTATCACCCATCATATCCCTATCTCTGC
Found at i:11148 original size:24 final size:24
Alignment explanation
Indices: 11121--11166 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
11111 TCCATCTCCC
*
11121 TCTCTCTGCTTCTTTCACGGTCCT
1 TCTCTCTGCTTCGTTCACGGTCCT
* *
11145 TCTCTCTTCTTCGTTCCCGGTC
1 TCTCTCTGCTTCGTTCACGGTC
11167 TATATCCCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.02, C:0.39, G:0.13, T:0.46
Consensus pattern (24 bp):
TCTCTCTGCTTCGTTCACGGTCCT
Found at i:20209 original size:124 final size:129
Alignment explanation
Indices: 20076--20330 Score: 353
Period size: 124 Copynumber: 2.0 Consensus size: 129
20066 GATAGATTAA
* *
20076 TAATTTAATCGAGAAAAATCATAAACCTTCTAATTGTTGAAAATAAGGAAAA-AAAAAAAGAA-G
1 TAATTTAATCGAGAAAAATCATAAACCTTCTAATTGTTGAAAATAAAGAAAACAAAAAAAGAACC
*
20139 AAG-AGAA-C-C-CAATAGCCGGGACCTTAATTTCTTCAGGCCAAAAAA-ACAGCAATTGCAAAG
66 AAGTAAAATCTCTC-A-AGCCGGGACCTTAATTTCTTCAGGCCAAAAAACACAGCAATTGCAAAG
20199 T
129 T
* * ** *
20200 TAATTTAATCGAGAAAAATCATAAATCTTCTAATTTTTTTAAATAAAGAAAACAAAAATAGAACC
1 TAATTTAATCGAGAAAAATCATAAACCTTCTAATTGTTGAAAATAAAGAAAACAAAAAAAGAACC
* *
20265 TAGTAAAATCTCTCAAGCCGGGACCTTAATTTCTTCAGGCCAAAAAACCCAGCAATTGCAAAGT
66 AAGTAAAATCTCTCAAGCCGGGACCTTAATTTCTTCAGGCCAAAAAACACAGCAATTGCAAAGT
20329 TA
1 TA
20331 CGGAGAAATT
Statistics
Matches: 114, Mismatches: 10, Indels: 9
0.86 0.08 0.07
Matches are distributed among these distances:
124 47 0.41
125 9 0.08
126 2 0.02
127 3 0.03
128 33 0.29
129 19 0.17
130 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.24
Consensus pattern (129 bp):
TAATTTAATCGAGAAAAATCATAAACCTTCTAATTGTTGAAAATAAAGAAAACAAAAAAAGAACC
AAGTAAAATCTCTCAAGCCGGGACCTTAATTTCTTCAGGCCAAAAAACACAGCAATTGCAAAGT
Found at i:22375 original size:15 final size:12
Alignment explanation
Indices: 22345--22369 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22335 TTAGTAATAT
22345 TATTATAGAAAA
1 TATTATAGAAAA
22357 TATTATAGAAAA
1 TATTATAGAAAA
22369 T
1 T
22370 TATATTTAGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TATTATAGAAAA
Found at i:22433 original size:5 final size:5
Alignment explanation
Indices: 22420--22450 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
22410 ATTAACTCAG
*
22420 TTATA TTATT TTATT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT TTATT T
22451 GTCATGTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:26555 original size:11 final size:10
Alignment explanation
Indices: 26530--26567 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
26520 TCTCTTTCGC
26530 CTCTTCC-CT
1 CTCTTCCTCT
26539 CTCTTCCTCT
1 CTCTTCCTCT
26549 CCTCTTCCTCGT
1 -CTCTTCCTC-T
26561 CTCTTCC
1 CTCTTCC
26568 CATCCGTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 7 0.27
10 2 0.08
11 16 0.62
12 1 0.04
ACGTcount: A:0.00, C:0.53, G:0.03, T:0.45
Consensus pattern (10 bp):
CTCTTCCTCT
Found at i:26958 original size:24 final size:24
Alignment explanation
Indices: 26931--26979 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
26921 TCAACCCCAT
* *
26931 CTGCTCCTCCTCCTGCTCCAGCTC
1 CTGCTCCTACTCCAGCTCCAGCTC
* *
26955 CTGCTGCTACTTCAGCTCCAGCTC
1 CTGCTCCTACTCCAGCTCCAGCTC
26979 C
1 C
26980 ACCGAAGCCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.08, C:0.49, G:0.14, T:0.29
Consensus pattern (24 bp):
CTGCTCCTACTCCAGCTCCAGCTC
Found at i:41115 original size:107 final size:105
Alignment explanation
Indices: 40902--41114 Score: 261
Period size: 107 Copynumber: 2.0 Consensus size: 105
40892 CAATAATGAT
* * * * *
40902 AATGGAAAACTGGGACATCAGACATTTGGCCTGTGTGGTAGAGTATTGGACTCTTAGTTCAGTAG
1 AATGGAAAACAGGGACATCAGACATTTAGCCTGTGTGGTAGAGTACTGAACTCTTAATTCAGTAG
* *
40967 TAGGGTTCGATCCTAGCTAGCAGCCTGAAGTACCAAAAAAAA
66 TAGGGTTCGATCC-A-CTAACAGCCTCAAGTACCAAAAAAAA
* * * *
41009 AATGGAAAACAGGGACATCGGGCATTTAGCCTG-GTGGTAGAGTCCTGAACTCTTAATTATAGT-
1 AATGGAAAACAGGGACATCAGACATTTAGCCTGTGTGGTAGAGTACTGAACTCTTAATT-CAGTA
*
41072 GCTAGGGTTCGATCC-CTAATAGCCTCAAGTACCAAAAAAAA
65 G-TAGGGTTCGATCCACTAACAGCCTCAAGTACCAAAAAAAA
41113 AA
1 AA
41115 AGATAATGGA
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
104 25 0.27
106 22 0.24
107 45 0.49
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (105 bp):
AATGGAAAACAGGGACATCAGACATTTAGCCTGTGTGGTAGAGTACTGAACTCTTAATTCAGTAG
TAGGGTTCGATCCACTAACAGCCTCAAGTACCAAAAAAAA
Found at i:49189 original size:25 final size:25
Alignment explanation
Indices: 49155--49206 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
49145 TAATAATCAG
*
49155 TTTGACCTCCTACACATATATTTGT
1 TTTGACCTCCTACAAATATATTTGT
*
49180 TTTGATCTCCTACAAATATATTTGT
1 TTTGACCTCCTACAAATATATTTGT
49205 TT
1 TT
49207 GGAAATCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (25 bp):
TTTGACCTCCTACAAATATATTTGT
Found at i:52651 original size:9 final size:9
Alignment explanation
Indices: 52637--52665 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
52627 TGTAGGAACA
52637 GCCGCTTGT
1 GCCGCTTGT
52646 GCCGCTTGT
1 GCCGCTTGT
52655 GCCGCTTGT
1 GCCGCTTGT
52664 GC
1 GC
52666 AGGCTGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.34, G:0.34, T:0.31
Consensus pattern (9 bp):
GCCGCTTGT
Found at i:62552 original size:16 final size:16
Alignment explanation
Indices: 62510--62554 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
62500 TTGTCAGTCC
** *
62510 TTTTAAATTTGGTTTC
1 TTTTAAATTTATTTTA
62526 TTTT-AATTTATTTTA
1 TTTTAAATTTATTTTA
62541 TTTTAAATTTATTT
1 TTTTAAATTTATTT
62555 ATTGTGCTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (16 bp):
TTTTAAATTTATTTTA
Found at i:62555 original size:15 final size:15
Alignment explanation
Indices: 62510--62557 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
62500 TTGTCAGTCC
* *
62510 TTTTAAATTTGGTTTC
1 TTTTAAATTT-ATTTA
62526 TTTT-AATTTATTTTA
1 TTTTAAATTTA-TTTA
62541 TTTTAAATTTATTTA
1 TTTTAAATTTATTTA
62556 TT
1 TT
62558 GTGCTGTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 18 0.64
16 10 0.36
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (15 bp):
TTTTAAATTTATTTA
Found at i:64928 original size:27 final size:29
Alignment explanation
Indices: 64895--64953 Score: 95
Period size: 27 Copynumber: 2.1 Consensus size: 29
64885 TAAAAAATAG
*
64895 AAAAACTTGTTAATCTCT-TTTTG-AAGA
1 AAAAACTTGTTAATCTCTATTTGGCAAGA
64922 AAAAACTTGTTAATCTCTATTTGGCAAGA
1 AAAAACTTGTTAATCTCTATTTGGCAAGA
64951 AAA
1 AAA
64954 GAGAGAGGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 18 0.62
28 4 0.14
29 7 0.24
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (29 bp):
AAAAACTTGTTAATCTCTATTTGGCAAGA
Found at i:68522 original size:7 final size:7
Alignment explanation
Indices: 68510--68534 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
68500 ATCATAATCA
68510 AAAAAAT
1 AAAAAAT
68517 AAAAAAT
1 AAAAAAT
68524 AAAAAAT
1 AAAAAAT
68531 AAAA
1 AAAA
68535 TTTGGGCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:77266 original size:52 final size:51
Alignment explanation
Indices: 77167--77267 Score: 143
Period size: 52 Copynumber: 2.0 Consensus size: 51
77157 TGCTTTTTCC
*
77167 ATGTACATTGTTAAAAATCGACTCTTTCTTACCCAAAGTCTTTTTTTTTGG
1 ATGTACATTGTTAAAAATCGACTCTTTCTTACCCAAAGTCTTGTTTTTTGG
*
77218 ATGTACATTGTTAAAAAATC-ATTTCTTTCTTACCCAAAGT-TTGGTTTTTT
1 ATGTACATTGTT-AAAAATCGA-CTCTTTCTTACCCAAAGTCTT-GTTTTTT
77268 TTTTTGCAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
51 15 0.33
52 30 0.67
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.47
Consensus pattern (51 bp):
ATGTACATTGTTAAAAATCGACTCTTTCTTACCCAAAGTCTTGTTTTTTGG
Found at i:84111 original size:18 final size:18
Alignment explanation
Indices: 84091--84132 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
84081 GCAGTAACTT
84091 TTTTC-CTTTTTCTTTTC
1 TTTTCTCTTTTTCTTTTC
*
84108 TTTTCTTTTTTTCTTTTC
1 TTTTCTCTTTTTCTTTTC
84126 ATTTTCT
1 -TTTTCT
84133 TCATCACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 11 0.50
19 6 0.27
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTCTCTTTTTCTTTTC
Found at i:84115 original size:24 final size:24
Alignment explanation
Indices: 84088--84133 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
84078 TTTGCAGTAA
84088 CTTTTTTCCTTTTTC-TTTTCTTTT
1 CTTTTTTCC-TTTTCATTTTCTTTT
*
84112 CTTTTTTTCTTTTCATTTTCTT
1 CTTTTTTCCTTTTCATTTTCTT
84134 CATCACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (24 bp):
CTTTTTTCCTTTTCATTTTCTTTT
Found at i:84119 original size:13 final size:13
Alignment explanation
Indices: 84089--84130 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
84079 TTGCAGTAAC
*
84089 TTTTTTCCTTT-T
1 TTTTTTCTTTTCT
*
84101 TCTTTTCTTTTCT
1 TTTTTTCTTTTCT
84114 TTTTTTCTTTTCAT
1 TTTTTTCTTTTC-T
84128 TTT
1 TTT
84131 CTTCATCACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 9 0.36
13 12 0.48
14 4 0.16
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTTCTTTTCT
Found at i:84939 original size:21 final size:21
Alignment explanation
Indices: 84913--84952 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
84903 ATGAAATTAC
*
84913 ACTGTACAGATTAGATTATGT
1 ACTGTACAGATGAGATTATGT
84934 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
84953 TAGAGCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (21 bp):
ACTGTACAGATGAGATTATGT
Found at i:91322 original size:22 final size:20
Alignment explanation
Indices: 91283--91322 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
91273 ATTAGTAGTA
*
91283 ATATTAATATATTATAAGTT
1 ATATTAATATAGTATAAGTT
91303 ATATTATATATAAGTATAAG
1 ATATTA-ATAT-AGTATAAG
91323 CCTTGTTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 4 0.24
22 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATATTAATATAGTATAAGTT
Done.