Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015212.1 Corchorus olitorius cultivar O-4 contig15245, 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: 75526
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:1306 original size:332 final size:330
Alignment explanation
Indices: 687--2749 Score: 2520
Period size: 332 Copynumber: 6.3 Consensus size: 330
677 CGTTACGACA
* * *
687 GGAATATATAATTCGATGCCAAAAAGATTGAAGAGCGTTTCACGCTTCTAATATCGTTTTTCCTA
1 GGAATATATAATTCAACGCCAAAAAGATTGAAG-GCTTTTCACGCTTCTAATATCGTTTTTCCTA
* * *
752 TATTTTCTGAATTAATTTTTAATGATATCGAAAGAAAATTTAAATGCCCGTAAAAACAAATTCTC
65 TATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCCTC
*
817 AAGTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATTATTGGCGCAAAAA
130 AACTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATTATTGGCGCAAAAA
** * * * *
882 ATCATGCAAAACTGAGTTGGGGCCCCGAAACGTGTTTTTAGCCAAAAATTGTTATGGTTAGTACA
195 ATCATGCAAAACTGAGTCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACA
* * * * * * *
947 CCATTTCGACTAAAATATTGTAAAAATTGATCCGTAAGATTTTTCCTCATACTCTTACCGCAATA
260 CGATTTCGGCTAAAATTTTGCAAAAATTGA-CCGTAAGATTTTTCCTCATATTTTTACCACAATA
*
1012 GTCATAT
324 CTCATAT
* *
1019 GGAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCCAATATAGTTTTTCCTA
1 GGAATATATAATTCAACGCCAAAAAGATTG-AAGGCTTTTCACGCTTCTAATATCGTTTTTCCTA
1084 TATTTTCTGAATTAATTTTTAATTATA-CTGAAAGAAAATTTAAATGCTCGTAAAAACAAATCCT
65 TATTTTCTGAATTAATTTTTAATTATATC-GAAAGAAAATTTAAATGCTCGTAAAAACAAATCCT
* * *
1148 CAACTCCATTGAGGTTGAGATTTGGTTAGATTAATATAGATATTTTAAGGATTATTAGCGCAAAA
129 CAACTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATTATTGGCGCAAAA
* * *
1213 AATCATGCAAAACTGAGTCAGGGCCCGGGAACGCGTTTTTAGCCAAAAACTATGATGGTTAGTAC
194 AATCATGCAAAACTGAGTCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTAC
* *
1278 ACGATTTCGGCTAAACTTTTGCAAAAATTGACCCGTAAGATTTTTCCTCATTTTTTTACCACAAT
259 ACGATTTCGGCTAAAATTTTGCAAAAATTGA-CCGTAAGATTTTTCCTCATATTTTTACCACAAT
*
1343 AGTCATAT
323 ACTCATAT
* * *
1351 GGAATATATAATTCGACGCCAAAAAGATTGAAGAGCGTTTCACGCTTCTAATATTGTTTTTCCTA
1 GGAATATATAATTCAACGCCAAAAAGATTGAAG-GCTTTTCACGCTTCTAATATCGTTTTTCCTA
1416 TATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCCTC
65 TATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCCTC
* *
1481 TACTCCA-T-T-G-TG-G--TT-G--AGATT--T-T-G----TT--A-GATTATTGACGCAAAAA
130 AACTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATTATTGGCGCAAAAA
* * * *
1525 ATCATGCAAAACTGAGTCGGGGCCCCGGAATGAGTTTTTAGCCAAAAACTGTGATGGTTAGTTCA
195 ATCATGCAAAACTGAGTCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACA
*
1590 CGATTTCGGCTAAAATTTTGCAAATATTGACCCGTAAGATTTTTCCTCAT-TTTTTAACCACAAT
260 CGATTTCGGCTAAAATTTTGCAAAAATTGA-CCGTAAGATTTTTCCTCATATTTTT-ACCACAAT
**
1654 TGTCATAT
323 ACTCATAT
* *
1662 GGAATATATAATTCTACGCCAAAAAGATTGAAGAGCGTTTCACGCTTCTAATATCGTTTTTCCTA
1 GGAATATATAATTCAACGCCAAAAAGATTGAAG-GCTTTTCACGCTTCTAATATCGTTTTTCCTA
*
1727 TATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCATAAAAACAAATCCTC
65 TATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCCTC
* *
1792 AAGTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATTATTGGCGTAAAAA
130 AACTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATTATTGGCGCAAAAA
* * * *
1857 ATCGTGCAAAACTGAG-CCGAGGCCCTGTAACGCGATTTTAGCCAAAAACTGTGATGGTTAGTAC
195 ATCATGCAAAACTGAGTCCG-GGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTAC
* *
1921 ACGATTTCGGCGAAAATTTTGCAGAAATTGACCTGTAAGATTTTTCCTCAT-TTTTTAGCCACAA
259 ACGATTTCGGCTAAAATTTTGCAAAAATTGACC-GTAAGATTTTTCCTCATATTTTTA-CCACAA
*
1985 TACTCATAA
322 TACTCATAT
* *
1994 GGAATATATAATTCAACGCCTAAAAGATTGAAAGGCTTTTCACGCTTCCAATATCGTTTTTCCTA
1 GGAATATATAATTCAACGCCAAAAAGATTG-AAGGCTTTTCACGCTTCTAATATCGTTTTTCCTA
*
2059 TATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCCGC
65 TATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCCTC
* * *
2124 AATTCAATTGTGGTTGAGATTTGGTTAGATTAATATAG--A--T--A-GATTATTGGCACAAAAA
130 AACTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATTATTGGCGCAAAAA
* *
2182 ATCATGCAAAACTGAG-CCGGGCCGCGGAACGCGTTTTTAGCCAAAAACTATGATGGTTAGTACA
195 ATCATGCAAAACTGAGTCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACA
** * * *
2246 CGATTTCGGCTGAAAA-TTTGCAAAAAAAAGACCAGTAAGATTTTTCCATCA-ATTTTTGGCTAA
260 CGATTTCGGCT-AAAATTTTGC-AAAAATTGACC-GTAAGATTTTTCC-TCATATTTTT-ACCAC
*
2309 AATACTCGT-T
320 AATACTCATAT
** * * * * *
2319 AAATATATATAATTTAACGTCAAAAAGAATGAAGGACTTTTCACGCTTTTAATATCATTTTT-C-
1 GGA-ATATATAATTCAACGCCAAAAAGATTGAAGG-CTTTTCACGCTTCTAATATCGTTTTTCCT
* * * * * * * *
2382 ATATTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAATAAATTCT
64 ATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCCT
* * * * * * * * * * * * *
2447 TAAATCCAATGTAGCTAAGATTTGATTAGATTAATATGGATATCTCAAAGAGTATTGGTGCCAAA
129 CAACTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATTATTGGCGCAAAA
* * * * * *
2512 AATCATGCAAAACTTAGT-CGGGCCTTCGGAACGGGTTTTTATCCAAAAAACCGTGATGATT-GT
194 AATCATGCAAAACTGAGTCCGGGCC-CCGGAACGCGTTTTTAGCC-AAAAACTGTGATGGTTAG-
* * * *
2575 TACACGATTTCGGCTAGAATTTTGCAAAAATTGATTCGAAAG-TTATGTCCTCA-ATTTTTAGCC
256 TACACGATTTCGGCTAAAATTTTGCAAAAATTGA-CCGTAAGATT-TTTCCTCATATTTTTA-CC
2638 ACAATACTCATA-
318 ACAATACTCATAT
** * * *
2650 AAAACTATATAATTCAACGCCAAAAAGATTGAAAAGTTTTTCATGCTTCTAATATCGTTTTTCCT
1 GGAA-TATATAATTCAACGCCAAAAAGATTG-AAGGCTTTTCACGCTTCTAATATCGTTTTTCCT
* * *
2715 ATTATTTGCTGAATTAATTTCTAATTAAATCGAAA
64 A-TATTTTCTGAATTAATTTTTAATTATATCGAAA
2750 CATGATTCAG
Statistics
Matches: 1522, Mismatches: 151, Indels: 114
0.85 0.08 0.06
Matches are distributed among these distances:
310 5 0.00
311 269 0.18
312 2 0.00
313 1 0.00
314 3 0.00
315 2 0.00
316 1 0.00
318 3 0.00
319 2 0.00
320 1 0.00
321 5 0.00
322 5 0.00
323 1 0.00
324 143 0.09
325 67 0.04
326 66 0.04
327 1 0.00
328 4 0.00
329 3 0.00
330 3 0.00
331 114 0.07
332 747 0.49
333 42 0.03
334 32 0.02
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (330 bp):
GGAATATATAATTCAACGCCAAAAAGATTGAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTAT
ATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCCTCA
ACTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATTATTGGCGCAAAAAA
TCATGCAAAACTGAGTCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACAC
GATTTCGGCTAAAATTTTGCAAAAATTGACCGTAAGATTTTTCCTCATATTTTTACCACAATACT
CATAT
Found at i:2091 original size:643 final size:647
Alignment explanation
Indices: 686--2749 Score: 2491
Period size: 643 Copynumber: 3.2 Consensus size: 647
676 ACGTTACGAC
* * *
686 AGGAATATATAATTCGATGCCAAAAAGATTG-AAGAGCGTTTCACGCTTCTAATATCGTTTTTCC
1 AGGAATATATAATTCAACGCCAAAAAGATTGAAAG-GCTTTTCACGCTTCTAATATCGTTTTTCC
* * *
750 TATATTTTCTGAATTAATTTTTAATGATATCGAAAGAAAATTTAAATGCCCGTAAAAACAAATTC
65 TATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCC
* * *
815 TCAAGTCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATTATTGGCGCAAA
130 GCAACTCAATTGTGGTTGAGA--T--TT-G-----T-TAGATA--T--A-GATTATTGGCGCAAA
* * * * *
880 AAATCATGCAAAACTGAGTTGGGGCCCCGAAACGTGTTTTTAGCCAAAAATTGTTATGGTTAGTA
179 AAATCATGCAAAACTGAGTCGGGGCCCCGGAACGAGTTTTTAGCCAAAAACTGTGATGGTTAGTA
* * * * * * * *
945 CACCATTTCGACTAAAATATTGTAAAAATTGATCCGTAAGATTTTTCCTCATACTCTTACCGCAA
244 CACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGTAAGATTTTTCCTCAT-TTTTTACCACAA
* * *
1010 TAGTCATATGGAATATATAATTCAACGCCAAAAAGATTGAA-AGGCTTTTCACGCTTCCAATATA
308 TAGTCATATGGAATATATAATTCTACGCCAAAAAGATTGAAGA-GCTTTTCACGCTTCTAATATC
1074 GTTTTTCCTATATTTTCTGAATTAATTTTTAATTATA-CTGAAAGAAAATTTAAATGCTCGTAAA
372 GTTTTTCCTATATTTTCTGAATTAATTTTTAATTATATC-GAAAGAAAATTTAAATGCTCGTAAA
* * *
1138 AACAAATCCTCAACTCCATTGAGGTTGAGATTTGGTTAGATTAATATAGATATTTTAAGGATTAT
436 AACAAATCCTCAAATCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATTAT
* * *
1203 TAGCGCAAAAAATCATGCAAAACTGAGTC-AGGGCCCGGGAACGCGTTTTTAGCCAAAAACTATG
501 TGGCGCAAAAAATCATGCAAAACTGAGTCGA-GGCCCTGGAACGCGTTTTTAGCCAAAAACTGTG
* *
1267 ATGGTTAGTACACGATTTCGGCTAAACTTTTGCAAAAATTGACCCGTAAGATTTTTCCTCATTTT
565 ATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGTAAGATTTTTCCTCA-TTT
*
1332 TTTA-CCACAATAGTCATA
629 TTTAGCCACAATACTCATA
* * * *
1350 TGGAATATATAATTCGACGCCAAAAAGATTG-AAGAGCGTTTCACGCTTCTAATATTGTTTTTCC
1 AGGAATATATAATTCAACGCCAAAAAGATTGAAAG-GCTTTTCACGCTTCTAATATCGTTTTTCC
1414 TATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCC
65 TATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCC
* * * *
1479 TCTACTCCATTGTGGTTGAGA-TT-TT-G-T-TAGATTATTGACGCAAAAAATCATGCAAAACTG
130 GCAACTCAATTGTGGTTGAGATTTGTTAGATATAGATTATTGGCGCAAAAAATCATGCAAAACTG
* *
1539 AGTCGGGGCCCCGGAATGAGTTTTTAGCCAAAAACTGTGATGGTTAGTTCACGATTTCGGCTAAA
195 AGTCGGGGCCCCGGAACGAGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAA
* *
1604 ATTTTGCAAATATTGACCCGTAAGATTTTTCCTCATTTTTTAACCACAATTGTCATATGGAATAT
260 ATTTTGCAAAAATTGACCCGTAAGATTTTTCCTCATTTTTT-ACCACAATAGTCATATGGAATAT
*
1669 ATAATTCTACGCCAAAAAGATTGAAGAGCGTTTCACGCTTCTAATATCGTTTTTCCTATATTTTC
324 ATAATTCTACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAATATCGTTTTTCCTATATTTTC
* *
1734 TGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCATAAAAACAAATCCTCAAGTCCA
389 TGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCCTCAAATCCA
* *
1799 TTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATTATTGGCGTAAAAAATCGTGC
454 TTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATTATTGGCGCAAAAAATCATGC
* * *
1864 AAAACTGAGCCGAGGCCCTGTAACGCGATTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTC
519 AAAACTGAGTCGAGGCCCTGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTC
* *
1929 GGCGAAAATTTTGCAGAAATTGACCTGTAAGATTTTTCCTCATTTTTTAGCCACAATACTCATA
584 GGCTAAAATTTTGCAAAAATTGACCTGTAAGATTTTTCCTCATTTTTTAGCCACAATACTCATA
* *
1993 AGGAATATATAATTCAACGCCTAAAAGATTGAAAGGCTTTTCACGCTTCCAATATCGTTTTTCCT
1 AGGAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCT
2058 ATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCCG
66 ATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCCG
* *
2123 CAATTCAATTGTGGTTGAGATTTGGTTAGATTAATATAGATAGATTATTGGCACAAAAAATCATG
131 CAACTCAATTGTGGTTGAGATTT-GTTAG------AT--ATAGATTATTGGCGCAAAAAATCATG
* * * *
2188 CAAAACTGAG-CCGGGCCGCGGAACGCGTTTTTAGCCAAAAACTATGATGGTTAGTACACGATTT
187 CAAAACTGAGTCGGGGCCCCGGAACGAGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTT
** * ** * * *
2252 CGGCTGAAAA-TTTGCAAAAAAAAGACCAGTAAGATTTTTCCATCAATTTTTGGCTAAAATACTC
252 CGGCT-AAAATTTTGC-AAAAATTGACCCGTAAGATTTTTCC-TC-ATTTTTTACCACAATAGTC
* ** * * * *
2316 GT-TAAATATATATAATT-TAACGTCAAAAAGAATGAAG-GACTTTTCACGCTTTTAATATCATT
313 ATATGGA-ATATATAATTCT-ACGCCAAAAAGATTGAAGAG-CTTTTCACGCTTCTAATATCGTT
* * * * * * *
2378 TTT-C-ATATTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAATA
375 TTTCCTATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACA
* * * * * * * * * * * *
2441 AATTCTTAAATCCAATGTAGCTAAGATTTGATTAGATTAATATGGATATCTCAAAGAGTATTGGT
440 AATCCTCAAATCCATTGTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATTATTGGC
* * * * * *
2506 GCCAAAAATCATGCAAAACTTAGTCG-GGCCTTCGGAACGGGTTTTTATCCAAAAAACCGTGATG
505 GCAAAAAATCATGCAAAACTGAGTCGAGGCCCT-GGAACGCGTTTTTAGCC-AAAAACTGTGATG
* * * * * *
2570 ATT-GTTACACGATTTCGGCTAGAATTTTGCAAAAATTGA-TTCGAAAG-TTATGTCCTCAATTT
568 GTTAG-TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCT-GTAAGATT-TTTCCTCATTTT
2632 TTAGCCACAATACTCATA
630 TTAGCCACAATACTCATA
* * * *
2650 A-AAACTATATAATTCAACGCCAAAAAGATTGAAAAGTTTTTCATGCTTCTAATATCGTTTTTCC
1 AGGAA-TATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCC
* * *
2714 TATTATTTGCTGAATTAATTTCTAATTAAATCGAAA
65 TA-TATTTTCTGAATTAATTTTTAATTATATCGAAA
2750 CATGATTCAG
Statistics
Matches: 1234, Mismatches: 132, Indels: 74
0.86 0.09 0.05
Matches are distributed among these distances:
642 10 0.01
643 564 0.46
644 9 0.01
646 3 0.00
647 1 0.00
649 1 0.00
650 1 0.00
651 1 0.00
652 1 0.00
654 1 0.00
655 5 0.00
656 201 0.16
657 197 0.16
658 89 0.07
659 8 0.01
664 142 0.12
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (647 bp):
AGGAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCT
ATATTTTCTGAATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCCG
CAACTCAATTGTGGTTGAGATTTGTTAGATATAGATTATTGGCGCAAAAAATCATGCAAAACTGA
GTCGGGGCCCCGGAACGAGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAA
TTTTGCAAAAATTGACCCGTAAGATTTTTCCTCATTTTTTACCACAATAGTCATATGGAATATAT
AATTCTACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAATATCGTTTTTCCTATATTTTCTG
AATTAATTTTTAATTATATCGAAAGAAAATTTAAATGCTCGTAAAAACAAATCCTCAAATCCATT
GTGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGATTATTGGCGCAAAAAATCATGCAA
AACTGAGTCGAGGCCCTGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGG
CTAAAATTTTGCAAAAATTGACCTGTAAGATTTTTCCTCATTTTTTAGCCACAATACTCATA
Found at i:3181 original size:15 final size:16
Alignment explanation
Indices: 3163--3192 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3153 ATAAATAATA
3163 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
3178 ATATTATAATCTAAA
1 ATATTATAATCTAAA
3193 AATAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:12128 original size:2 final size:2
Alignment explanation
Indices: 12121--12149 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12111 AATAGATATC
12121 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12150 ACACATACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:15086 original size:25 final size:24
Alignment explanation
Indices: 15033--15087 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
15023 CAACAGTTTC
*
15033 TATTTCTCTTTTTTTTTTTTGGTCA
1 TATTT-TCTTTTTTTTTTTTGGTAA
**
15058 -ATTTTCTTTTTCTTTTTTTTTTAA
1 TATTTTCTTTTT-TTTTTTTGGTAA
15082 TATTTT
1 TATTTT
15088 TATTTGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 7 0.28
24 13 0.52
25 5 0.20
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.76
Consensus pattern (24 bp):
TATTTTCTTTTTTTTTTTTGGTAA
Found at i:20660 original size:7 final size:8
Alignment explanation
Indices: 20634--20659 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
20624 CACATAATCA
20634 TTTCCCAT
1 TTTCCCAT
20642 TTTCCCAT
1 TTTCCCAT
20650 TTTCCCAT
1 TTTCCCAT
20658 TT
1 TT
20660 CATGGCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.54
Consensus pattern (8 bp):
TTTCCCAT
Found at i:34151 original size:56 final size:56
Alignment explanation
Indices: 34046--34151 Score: 158
Period size: 56 Copynumber: 1.9 Consensus size: 56
34036 AAAGGTTTTT
* * *
34046 CGTTTTTAAGTTGGTTTCGATTCGACTTTAGATTAGTTAAAAGCAATGTAGGTTTC
1 CGTTTTTAAGTTGGTTTCAATTCGACTTCAGATTAGTTAAAACCAATGTAGGTTTC
* * *
34102 CGTTTTTAAGTTGGTTTTAATTCGACTTCGGATTAGTTAAAACCTATGTA
1 CGTTTTTAAGTTGGTTTCAATTCGACTTCAGATTAGTTAAAACCAATGTA
34152 ACTGCCATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 44 1.00
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.43
Consensus pattern (56 bp):
CGTTTTTAAGTTGGTTTCAATTCGACTTCAGATTAGTTAAAACCAATGTAGGTTTC
Found at i:43450 original size:2 final size:2
Alignment explanation
Indices: 43445--43477 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
43435 TAAAAAAAAA
43445 AT AT AT 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 AT AT AT A
43478 ATTATTAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44431 original size:45 final size:45
Alignment explanation
Indices: 44367--44458 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
44357 GACAATCGTC
44367 ATCATCAGATAGACGGTGAATGCAGCCTGATTTACCCTCCTCTTA
1 ATCATCAGATAGACGGTGAATGCAGCCTGATTTACCCTCCTCTTA
44412 ATCATCAGATAGACGGTGAATGCAGCCTGATTTACCCTCCTCTTA
1 ATCATCAGATAGACGGTGAATGCAGCCTGATTTACCCTCCTCTTA
44457 AT
1 AT
44459 AAACAATTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.29
Consensus pattern (45 bp):
ATCATCAGATAGACGGTGAATGCAGCCTGATTTACCCTCCTCTTA
Found at i:49497 original size:6 final size:6
Alignment explanation
Indices: 49482--49520 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
49472 GGCAGTAGGG
49482 TTTTTC -TTTTC TTTTTC TTTTTC TTTTTC TTTTT- TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
49521 GGTATTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 10 0.31
6 22 0.69
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTC
Found at i:49520 original size:11 final size:11
Alignment explanation
Indices: 49482--49520 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
49472 GGCAGTAGGG
*
49482 TTTTTCTTTTC
1 TTTTTCTTTTT
49493 TTTTTCTTTTT
1 TTTTTCTTTTT
49504 CTTTTTCTTTTT
1 -TTTTTCTTTTT
49516 TTTTT
1 TTTTT
49521 GGTATTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:56327 original size:27 final size:27
Alignment explanation
Indices: 56297--56426 Score: 125
Period size: 27 Copynumber: 4.6 Consensus size: 27
56287 CTTGCCGGTT
*
56297 GGACTTGAAGGCCTATGCCATTTCTCA
1 GGACTGGAAGGCCTATGCCATTTCTCA
* * * * *
56324 GGACTGGAAGGCTTGTTATTCCACTTGCCGGCT
1 GGACTGGAAGGC---CTATGCCA-TT-TC-TCA
56357 GGACTGGAAGGCCTATGCCATTTCTCA
1 GGACTGGAAGGCCTATGCCATTTCTCA
* *
56384 GGACTGGAAGGCCTACGCCATTTCTCG
1 GGACTGGAAGGCCTATGCCATTTCTCA
*
56411 GGACTTGAAGGCCTAT
1 GGACTGGAAGGCCTAT
56427 TCCACTTACC
Statistics
Matches: 82, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
27 51 0.62
28 1 0.01
29 2 0.02
30 12 0.15
31 2 0.02
32 1 0.01
33 13 0.16
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (27 bp):
GGACTGGAAGGCCTATGCCATTTCTCA
Found at i:56334 original size:60 final size:60
Alignment explanation
Indices: 56237--56395 Score: 273
Period size: 60 Copynumber: 2.6 Consensus size: 60
56227 ATAACGAACA
* * * *
56237 GGACTGGAAGGCTTACGCCATTTCTCAGGACTTGAAGGCTTGTTATTCCACTTGCCGGTT
1 GGACTGGAAGGCCTATGCCATTTCTCAGGACTGGAAGGCTTGTTATTCCACTTGCCGGCT
*
56297 GGACTTGAAGGCCTATGCCATTTCTCAGGACTGGAAGGCTTGTTATTCCACTTGCCGGCT
1 GGACTGGAAGGCCTATGCCATTTCTCAGGACTGGAAGGCTTGTTATTCCACTTGCCGGCT
56357 GGACTGGAAGGCCTATGCCATTTCTCAGGACTGGAAGGC
1 GGACTGGAAGGCCTATGCCATTTCTCAGGACTGGAAGGC
56396 CTACGCCATT
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 93 1.00
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.28
Consensus pattern (60 bp):
GGACTGGAAGGCCTATGCCATTTCTCAGGACTGGAAGGCTTGTTATTCCACTTGCCGGCT
Found at i:56366 original size:33 final size:33
Alignment explanation
Indices: 56264--56368 Score: 96
Period size: 33 Copynumber: 3.4 Consensus size: 33
56254 CCATTTCTCA
* *
56264 GGACTTGAAGGCTTGTTATTCCACTTGCCGGTT
1 GGACTGGAAGGCTTGTTATTCCACTTGCCGGCT
* * * * * *
56297 GGACTTGAAGGC---CTATGCCA-TT-TC-TCA
1 GGACTGGAAGGCTTGTTATTCCACTTGCCGGCT
56324 GGACTGGAAGGCTTGTTATTCCACTTGCCGGCT
1 GGACTGGAAGGCTTGTTATTCCACTTGCCGGCT
56357 GGACTGGAAGGC
1 GGACTGGAAGGC
56369 CTATGCCATT
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
27 11 0.20
28 1 0.02
29 2 0.04
30 12 0.22
31 2 0.04
32 1 0.02
33 25 0.46
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.30
Consensus pattern (33 bp):
GGACTGGAAGGCTTGTTATTCCACTTGCCGGCT
Found at i:61225 original size:21 final size:21
Alignment explanation
Indices: 61199--61240 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
61189 GGATCACCTG
*
61199 ATAGAAGCAGCAATATAAGAA
1 ATAGAAGCAGAAATATAAGAA
61220 ATAGAAGCAGAAATATAAGAA
1 ATAGAAGCAGAAATATAAGAA
61241 CAACCTCACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.07, G:0.19, T:0.14
Consensus pattern (21 bp):
ATAGAAGCAGAAATATAAGAA
Done.