Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014926.1 Corchorus olitorius cultivar O-4 contig14959, 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: 83583
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:997 original size:333 final size:333
Alignment explanation
Indices: 1--2254 Score: 3362
Period size: 333 Copynumber: 6.8 Consensus size: 333
* * *
1 AAAAATTGACCCGAATGATTTTTCCTCAAGTCTTGGCCGAAATACTCATAAAAAATATATAAATC
1 AAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATC
* * * *
66 ATAGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATA--ATGTTTGTTCTATATTTTTCTGAA
66 ATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCAT-TTT-TCCTATACTTTTCCGAA
* * * * * * *
129 TGAATTTCCAATTAAATCGAAAC-GGAATTGTCATGCTTGTAAAACCAAATTTTTAAAACTTATG
129 TTAATTTCCAATTAAATCGAAACTGG-ATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATG
* *
193 TGGCTGAGATTTGGGTAGATGAATATAGATATTCCAACGAGTCTTGGCGCAAAAAAATCATACAA
193 TGGCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGC-CAAAAATCATACAA
* * * *
258 AATTGAGCTG-GTGCCCCGGAACGCGTTTTTTAGTCGAAAAATGTGATGGTTAGCACACGATTTC
257 AACTGAGCCGAG-GCCCCGGAACGCG-TTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTC
*
322 GGTCAAGAATTTGC
320 GGTCAAGATTTTGC
* *
336 AAAAATTGACCCGAATGATTTTTCCT-ACATTTTTAGCCAAAATACTCATAAAAAATATATGAAT
1 AAAAATTGACCCGAATGATTTTTCCTCA-ATTTTTGGCCAAAATACTCATAAAAAATATATAAAT
* *
400 CATCGCCAAAAAGATTGATGGATTTTTAAAGCTTCGAATATCATTTTTCCTATACTTTTCCGAAT
65 CATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCATTTTTCCTATACTTTTCCGAAT
* * *
465 TAATTTCCAATTAAATCGAAACTGGATTCTGAAGCTCGTAAAAGAAAAATCTTTAAATCATATGT
130 TAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAA-ACAAATCTTTAAATCTTATGT
* * * * *
530 GGCTGAGATTTAGGCAGATGAATATAGATATTCAAAGGATTCTTGGCACCAAAAATCATACAAAA
194 GGCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAA
* **
595 CTGAGCCG-GAGCCCCGGAACGTGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCATT
259 CTGAGCCGAG-GCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGT
659 CAAGATTTTGC
323 CAAGATTTTGC
* *
670 AAAAATTGAGCCGAATGATTTTTCCTAAATTTTTGGCCAAAATACTCAT-AAAAATAATATAAAT
1 AAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAAT-ATATAAAT
* * * *
734 CATAGCCAAAAATATTGAAGGGTTTTTCACA-CTTCGAATATCATTTTTCCTATGCTTTTCCGAA
65 CATCGCCAAAAAGATTGAAGGGTTTTT-AAAGCTTCGAATATCATTTTTCCTATACTTTTCCGAA
798 TTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGT
129 TTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGT
863 GGCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAA
194 GGCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAA
* * *
928 CTGAGCCGAGGCCCTGGAACACATTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTC
259 CTGAGCCGAGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTC
993 AAGATTTTGC
324 AAGATTTTGC
1003 AAAAATTGACCCGAATGATTTTTCCTCCAA-TTTTGGCCAAAATACTCATAAAAAATATATAAAT
1 AAAAATTGACCCGAATGATTTTTCCT-CAATTTTTGGCCAAAATACTCATAAAAAATATATAAAT
* * **
1067 CATCGCCAAAAAGATTGAAGGGTTTTTAAAGCATCGAATATCGTTTTTCCTATACTTTTATGAAT
65 CATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCATTTTTCCTATACTTTTCCGAAT
* *
1132 TAATTTCCAATTAAATCGAAACTGGATTCTCATGCTCGTAAAAACAAATCTTTAAATCATATGTG
130 TAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTG
** *
1197 GCTGAGATTTGGACAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCATACAAAAC
195 GCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAAC
* * * * * * *
1262 TGAGTCGGGGCCCTGGAACGCGTTTTTAACCGAAAATTGTAATAGTTAGCACACGATTTCGGTCA
260 TGAGCCGAGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCA
1327 AGATTTTGC
325 AGATTTTGC
*
1336 AAAAATTGACCGGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATC
1 AAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATC
* * * * *
1401 ATCGCCAAAAA-AATGAAGGGTTTTTTACA-CTTC-CA-AT-A----T-CGATGCTTTTCCGAAT
66 ATCGCCAAAAAGATTGAAGGG-TTTTTAAAGCTTCGAATATCATTTTTCCTATACTTTTCCGAAT
** * * * *
1456 TAATTTCTTATTAAATCGAAATTGGATTCTGATGCTCGTAAAAACAAATATTTAAATCTTTTATG
130 TAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTG
* *
1521 GCTGAGATTTGGGTATATGAATATAGATATTCCAAGGAATCTTGGCGCCAAAAATCATACAAAAC
195 GCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAAC
* *
1586 TGAGCCGAGGCCCCGGAACACATTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCA
260 TGAGCCGAGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCA
1651 AGATTTTGC
325 AGATTTTGC
* *
1660 AAAAATTGACCCGAATTATTTTTCCTCAAATTTTGGCCAAAATACTCATAAAAAATATATAAATC
1 AAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATC
*
1725 ATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCGTTTTTCCTATACTTTTCCGAATT
66 ATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCATTTTTCCTATACTTTTCCGAATT
* * *
1790 AATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAATAAATCTTCAAATCATATGTGG
131 AATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTGG
* * * *
1855 ATGAGATTTAGGCAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCATACAAAACT
196 CTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACT
* *
1920 GAGCCGAGGCCCAGGAACGCGTTTTTAGCCGAAAATTGTGATGGTTAGCACACGATTTCGGTCAA
261 GAGCCGAGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAA
1985 GATTTTGC
326 GATTTTGC
1993 AAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATC
1 AAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATC
* * * *
2058 ATCGCCAAAAAAATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCCTATACTTTTCCGAATT
66 ATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCATTTTTCCTATACTTTTCCGAATT
* *
2123 AATTTCCTATTAAATCGAAATTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTGG
131 AATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTGG
* *
2188 CTGAGATTTGGGTAGGA-GAATATAGATATTCCAAGGAGTCTTGGCGCAAAAAATCATA-AAAAT
196 CTGAGATTTGGGTA-GATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAAC
2251 TGAG
260 TGAG
2255 ATTTGGGTAA
Statistics
Matches: 1735, Mismatches: 159, Indels: 53
0.89 0.08 0.03
Matches are distributed among these distances:
324 274 0.16
325 13 0.01
326 1 0.00
327 2 0.00
330 2 0.00
331 1 0.00
332 25 0.01
333 961 0.55
334 209 0.12
335 181 0.10
336 64 0.04
337 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Consensus pattern (333 bp):
AAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATC
ATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCATTTTTCCTATACTTTTCCGAATT
AATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTGG
CTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACT
GAGCCGAGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAA
GATTTTGC
Found at i:1646 original size:657 final size:660
Alignment explanation
Indices: 1--2254 Score: 3427
Period size: 657 Copynumber: 3.4 Consensus size: 660
* * *
1 AAAAATTGACCCGAATGATTTTTCCTCAAGTCTTGGCCGAAATACTCATAAAAAATATATAAATC
1 AAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATC
* * * *
66 ATAGCCAAAAAGATTGAAGGGTTTTT-AAAGCTTCGAATAAT-GTTTGTTCTATATTTTTCTGAA
66 ATAGCCAAAAAGAATGAAGGGTTTTTCACA-CTTCGAATAATCGTATG--C-----TTTTCCGAA
* * * * * * * *
129 TGAATTTCCAATTAAATCGAAA-CGGAATTGTCATGCTTGTAAAACCAAATTTTTAAAACTTATG
123 TTAATTTCCAATTAAATCGAAATTGG-ATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATG
*
193 TGGCTGAGATTTGGGTAGATGAATATAGATATTCCAACGAGTCTTGGCGCAAAAAAATCATACAA
187 TGGCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGC-AAAAAATCATACAA
* * * * * *
258 AATTGAGCTG-GTGCCCCGGAACGCGTTTTTTAGTCGAAAAATGTGATGGTTAGCACACGATTTC
251 AACTGAGCCGAG-GCCCCGGAACAC-ATTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTC
* * * *
322 GGTCAAGAATTTGCAAAAATTGACCCGAATGATTTTTCCTACATTTTTAGCCAAAATACTCATAA
314 GGTCAAGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCCAATTTTGGCCAAAATACTCATAA
* * * *
387 AAAATATATGAATCATCGCCAAAAAGATTGATGGATTTTTAAAGCTTCGAATATCATTTTTCCTA
379 AAAATATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCGTTTTTCCTA
*
452 TACTTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGAAGCTCGTAAAAGAAAAATCT
444 TACTTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAA-AAAAATCT
* *
517 TTAAATCATATGTGGCTGAGATTTAGGCAGATGAATATAGATATTCAAAGGATTCTTGGCACCAA
508 TTAAATCATATGTGGCTGAGATTTAGGCAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAA
* * * *
582 AAATCATACAAAACTGAGCCGGAGCCCCGGAACGTGTTTTTAGCCGAAAACTGTGATGGTTAGCA
573 AAATCATACAAAACTGAGCCGGGGCCCAGGAACGCGTTTTTAGCCGAAAATTGTGATGGTTAGCA
**
647 CACGATTTCATTCAAGATTTTGC
638 CACGATTTCGGTCAAGATTTTGC
* *
670 AAAAATTGAGCCGAATGATTTTTCCTAAATTTTTGGCCAAAATACTCAT-AAAAATAATATAAAT
1 AAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAAT-ATATAAAT
* * *
734 CATAGCCAAAAATATTGAAGGGTTTTTCACACTTCGAATATCATTTTTCCTATGCTTTTCCGAAT
65 CATAGCCAAAAAGAATGAAGGGTTTTTCACACTTCGAATA--A----TCGTATGCTTTTCCGAAT
*
799 TAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTG
124 TAATTTCCAATTAAATCGAAATTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTG
*
864 GCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAAC
189 GCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCAAAAAATCATACAAAAC
*
929 TGAGCCGAGGCCCTGGAACACATTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCA
254 TGAGCCGAGGCCCCGGAACACATTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCA
994 AGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCCAATTTTGGCCAAAATACTCATAAAAAAT
319 AGATTTTGCAAAAATTGACCCGAATGATTTTTCCTCCAATTTTGGCCAAAATACTCATAAAAAAT
*
1059 ATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTAAAGCATCGAATATCGTTTTTCCTATACTT
384 ATATAAATCATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCGTTTTTCCTATACTT
** * *
1124 TTATGAATTAATTTCCAATTAAATCGAAACTGGATTCTCATGCTCGTAAAAACAAATCTTTAAAT
449 TTCCGAATTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAAAAAATCTTTAAAT
1189 CATATGTGGCTGAGATTT-GGACAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATC
514 CATATGTGGCTGAGATTTAGG-CAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATC
* * * * *
1253 ATACAAAACTGAGTCGGGGCCCTGGAACGCGTTTTTAACCGAAAATTGTAATAGTTAGCACACGA
578 ATACAAAACTGAGCCGGGGCCCAGGAACGCGTTTTTAGCCGAAAATTGTGATGGTTAGCACACGA
1318 TTTCGGTCAAGATTTTGC
643 TTTCGGTCAAGATTTTGC
*
1336 AAAAATTGACCGGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATC
1 AAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATC
* * *
1401 ATCGCCAAAAA-AATGAAGGGTTTTTTACACTTCCAAT-ATCG-ATGCTTTTCCGAATTAATTTC
66 ATAGCCAAAAAGAATGAAGGGTTTTTCACACTTCGAATAATCGTATGCTTTTCCGAATTAATTTC
** * * *
1463 TTATTAAATCGAAATTGGATTCTGATGCTCGTAAAAACAAATATTTAAATCTTTTATGGCTGAGA
131 CAATTAAATCGAAATTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTGGCTGAGA
* * *
1528 TTTGGGTATATGAATATAGATATTCCAAGGAATCTTGGCGCCAAAAATCATACAAAACTGAGCCG
196 TTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCAAAAAATCATACAAAACTGAGCCG
1593 AGGCCCCGGAACACATTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAGATTTT
261 AGGCCCCGGAACACATTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAGATTTT
* *
1658 GCAAAAATTGACCCGAATTATTTTTCCTCAAATTTTGGCCAAAATACTCATAAAAAATATATAAA
326 GCAAAAATTGACCCGAATGATTTTTCCTCCAATTTTGGCCAAAATACTCATAAAAAATATATAAA
1723 TCATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCGTTTTTCCTATACTTTTCCGAA
391 TCATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCGTTTTTCCTATACTTTTCCGAA
* *
1788 TTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAATAAATCTTCAAATCATATGT
456 TTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAAAAAATCTTTAAATCATATGT
*
1853 GGATGAGATTTAGGCAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCATACAAAA
521 GGCTGAGATTTAGGCAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCATACAAAA
*
1918 CTGAGCCGAGGCCCAGGAACGCGTTTTTAGCCGAAAATTGTGATGGTTAGCACACGATTTCGGTC
586 CTGAGCCGGGGCCCAGGAACGCGTTTTTAGCCGAAAATTGTGATGGTTAGCACACGATTTCGGTC
1983 AAGATTTTGC
651 AAGATTTTGC
1993 AAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATC
1 AAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATC
* * *
2058 ATCGCCAAAAA-AATTGAAGGGTTTTTCACGCTTCGAAT-ATCGTTTTTCCTATACTTTTCCGAA
66 ATAGCCAAAAAGAA-TGAAGGGTTTTTCACACTTCGAATAATCG-------TATGCTTTTCCGAA
*
2121 TTAATTTCCTATTAAATCGAAATTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGT
123 TTAATTTCCAATTAAATCGAAATTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGT
2186 GGCTGAGATTTGGGTAGGA-GAATATAGATATTCCAAGGAGTCTTGGCGCAAAAAATCATA-AAA
188 GGCTGAGATTTGGGTA-GATGAATATAGATATTCCAAGGAGTCTTGGCGCAAAAAATCATACAAA
*
2249 ATTGAG
252 ACTGAG
2255 ATTTGGGTAA
Statistics
Matches: 1463, Mismatches: 98, Indels: 52
0.91 0.06 0.03
Matches are distributed among these distances:
657 601 0.41
658 29 0.02
662 1 0.00
665 33 0.02
666 338 0.23
667 216 0.15
668 37 0.03
669 198 0.14
670 4 0.00
671 1 0.00
674 1 0.00
675 1 0.00
676 3 0.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Consensus pattern (660 bp):
AAAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATC
ATAGCCAAAAAGAATGAAGGGTTTTTCACACTTCGAATAATCGTATGCTTTTCCGAATTAATTTC
CAATTAAATCGAAATTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTGGCTGAGA
TTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCAAAAAATCATACAAAACTGAGCCG
AGGCCCCGGAACACATTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAGATTTT
GCAAAAATTGACCCGAATGATTTTTCCTCCAATTTTGGCCAAAATACTCATAAAAAATATATAAA
TCATCGCCAAAAAGATTGAAGGGTTTTTAAAGCTTCGAATATCGTTTTTCCTATACTTTTCCGAA
TTAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAAAAAATCTTTAAATCATATGT
GGCTGAGATTTAGGCAGATGAATATAGATATTCAAAGGAGTCTTGGCGCCAAAAATCATACAAAA
CTGAGCCGGGGCCCAGGAACGCGTTTTTAGCCGAAAATTGTGATGGTTAGCACACGATTTCGGTC
AAGATTTTGC
Found at i:11124 original size:10 final size:10
Alignment explanation
Indices: 11101--11137 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
11091 GGTATGATGT
11101 CAAAAA-AAA
1 CAAAAAGAAA
*
11110 AAAAAAGAAA
1 CAAAAAGAAA
11120 CAAAAAGAAA
1 CAAAAAGAAA
11130 CAAAAAGA
1 CAAAAAGA
11138 GGTAAGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 5 0.20
10 20 0.80
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (10 bp):
CAAAAAGAAA
Found at i:20715 original size:49 final size:49
Alignment explanation
Indices: 20564--20716 Score: 122
Period size: 49 Copynumber: 3.1 Consensus size: 49
20554 AATCTATGAG
*
20564 AATAAATCATCTAAATGAGAATTCAACTCAAACTAGAAACTATACCATA
1 AATAAATCATCTAAATGAGAATTCAACTCAAACTAGAAACTATACTATA
* ** * * *
20613 AATAAA-CTACCTACCT-ACCAAAT-AA-ACAAAC-A-AAACGCTA-ATCTATGA
1 AATAAATC-ATCTAAATGA-GAATTCAACTCAAACTAGAAA--CTATA-CTAT-A
*
20661 GAATAAATCATCTAAATGAGAATTCAACTCAAGCTAGAAACTATACTATA
1 -AATAAATCATCTAAATGAGAATTCAACTCAAACTAGAAACTATACTATA
20711 AATAAA
1 AATAAA
20717 CTACCTACCT
Statistics
Matches: 76, Mismatches: 14, Indels: 28
0.64 0.12 0.24
Matches are distributed among these distances:
45 3 0.04
46 2 0.03
47 11 0.14
48 5 0.07
49 34 0.45
50 5 0.07
51 11 0.14
52 2 0.03
53 3 0.04
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.23
Consensus pattern (49 bp):
AATAAATCATCTAAATGAGAATTCAACTCAAACTAGAAACTATACTATA
Found at i:20716 original size:98 final size:98
Alignment explanation
Indices: 20547--20740 Score: 370
Period size: 98 Copynumber: 2.0 Consensus size: 98
20537 TACAGTACCG
20547 AAACGCTAATCTATGAGAATAAATCATCTAAATGAGAATTCAACTCAAACTAGAAACTATACCAT
1 AAACGCTAATCTATGAGAATAAATCATCTAAATGAGAATTCAACTCAAACTAGAAACTATACCAT
20612 AAATAAACTACCTACCTACCAAATAAACAAACA
66 AAATAAACTACCTACCTACCAAATAAACAAACA
* *
20645 AAACGCTAATCTATGAGAATAAATCATCTAAATGAGAATTCAACTCAAGCTAGAAACTATACTAT
1 AAACGCTAATCTATGAGAATAAATCATCTAAATGAGAATTCAACTCAAACTAGAAACTATACCAT
20710 AAATAAACTACCTACCTACCAAATAAACAAA
66 AAATAAACTACCTACCTACCAAATAAACAAA
20741 TAAATTACAA
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.51, C:0.21, G:0.07, T:0.22
Consensus pattern (98 bp):
AAACGCTAATCTATGAGAATAAATCATCTAAATGAGAATTCAACTCAAACTAGAAACTATACCAT
AAATAAACTACCTACCTACCAAATAAACAAACA
Found at i:26398 original size:7 final size:7
Alignment explanation
Indices: 26386--26410 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
26376 TTTTCTATCA
26386 TGAAATT
1 TGAAATT
26393 TGAAATT
1 TGAAATT
26400 TGAAATT
1 TGAAATT
26407 TGAA
1 TGAA
26411 TTTAGTTAAA
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:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (7 bp):
TGAAATT
Found at i:32393 original size:6 final size:6
Alignment explanation
Indices: 32384--32439 Score: 55
Period size: 6 Copynumber: 9.2 Consensus size: 6
32374 TTGGGGTTGG
32384 TTTTTC TTTTTTC TTCTTCTC TTTTTC -TTTTC TTTTTC TTTCTT- TTTTT-
1 TTTTTC -TTTTTC TT-TT-TC TTTTTC TTTTTC TTTTTC TTT-TTC TTTTTC
32433 TTTTTC T
1 TTTTTC T
32440 CTTCTTCTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
5 12 0.27
6 16 0.36
7 12 0.27
8 4 0.09
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:34301 original size:21 final size:22
Alignment explanation
Indices: 34277--34319 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
34267 ACGTAATAAT
*
34277 TGTTGACA-TTAACAAAAAAAA
1 TGTTGAAATTTAACAAAAAAAA
*
34298 TGTTTAAATTTAACAAAAAAAA
1 TGTTGAAATTTAACAAAAAAAA
34320 ATCACCACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.28
Consensus pattern (22 bp):
TGTTGAAATTTAACAAAAAAAA
Found at i:37831 original size:1 final size:1
Alignment explanation
Indices: 37825--37853 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
37815 CTAAGATAAG
37825 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
37854 AAATGTTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:46755 original size:2 final size:2
Alignment explanation
Indices: 46748--46777 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
46738 CTAGTATAAC
46748 TA TA TA TA 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
46778 GATTATTAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60039 original size:6 final size:6
Alignment explanation
Indices: 60028--60063 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
60018 GGACAGAGGG
60028 AGGCGA AGGCGA AGGCGA AGGCGA AGGCGA AGGCGA
1 AGGCGA AGGCGA AGGCGA AGGCGA AGGCGA AGGCGA
60064 TGGTTTTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.50, T:0.00
Consensus pattern (6 bp):
AGGCGA
Found at i:63901 original size:42 final size:43
Alignment explanation
Indices: 63842--63926 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 43
63832 ATGAAAGGCC
* * *
63842 CTTAATTGAGCCGATTTTGTTATATTGGACCCTGATTT-AGTT
1 CTTAATTGAACCGATTTTGTAATATTGGACCATGATTTGAGTT
* *
63884 CTTAATTGAATCGATTTTGTAATGTTGGACCATGATTTGAGTT
1 CTTAATTGAACCGATTTTGTAATATTGGACCATGATTTGAGTT
63927 TTTGAATAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 33 0.89
43 4 0.11
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.45
Consensus pattern (43 bp):
CTTAATTGAACCGATTTTGTAATATTGGACCATGATTTGAGTT
Found at i:64751 original size:25 final size:24
Alignment explanation
Indices: 64714--64760 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
64704 CAATTCTCGA
*
64714 TTTTAGATTTCTGGGTTTATGGGG
1 TTTTAGATGTCTGGGTTTATGGGG
64738 TTTTCAGATGTCTGGGTTTATGG
1 TTTT-AGATGTCTGGGTTTATGG
64761 ATTTTCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.13, C:0.06, G:0.32, T:0.49
Consensus pattern (24 bp):
TTTTAGATGTCTGGGTTTATGGGG
Found at i:83229 original size:21 final size:21
Alignment explanation
Indices: 83203--83245 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
83193 AAAAAGGGTA
*
83203 TTACTAAATACCGCCCCCCTT
1 TTACTAAACACCGCCCCCCTT
**
83224 TTACTAGCCACCGCCCCCCTT
1 TTACTAAACACCGCCCCCCTT
83245 T
1 T
83246 GGACTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.47, G:0.07, T:0.28
Consensus pattern (21 bp):
TTACTAAACACCGCCCCCCTT
Done.