Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017552.1 Corchorus olitorius cultivar O-4 contig17585, 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: 19363
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:794 original size:333 final size:329
Alignment explanation
Indices: 1--1839 Score: 2293
Period size: 333 Copynumber: 5.6 Consensus size: 329
* * *
1 GAATTAATTTCTGATTAAATCGAAACATGATTCGAATGCTCGTAAAATCAAATACTTAAATCCAA
1 GAATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAA
* *
66 TGTGGTTGAGATTTGGAATGATGAATAAGGATAATTCAATGAGTCTTGGCAACCAAAAATCATGC
66 TGTGGCTGAGATTTGGAATGATGAATAAGGATAATTCAATGAGTCTTGGC--GCAAAAATCATGC
* * * *
131 CAATCTGAGCCGGGGCCCCGGAATGCGTTTTCAGCCAAGAATCGTGATGGTTAGTACACGATTTC
129 AAAACTGAGCCGGGGCCCTGGAACGCGTTTTCAGCCAAGAATCGTGA-GGTTAGTACACGATTTC
* *
196 GGCATAAACTTTGCAAAAATAGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACACGTAA
193 GGCA-AAAATTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACACGTAA
*
261 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTCCACGCTTCTAATGTCATTTTTTTAA
257 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTCCACGCTTCTAATATCATTTTTTT-A
*
326 AATTTTTCCC
321 TATTTTT-CC
* *
336 GAATTAATTTCCGATTAAATCGAAACATGATTCGAATGCTCGTAAAATCAAATCCTTAAATCTAA
1 GAATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAA
* * *
401 CGTGGCTGAGATTTGGAATGATGAATAAGGATAATTCAATGAGTCTTGACACCAAAAATCATGCA
66 TGTGGCTGAGATTTGGAATGATGAATAAGGATAATTCAATGAGTCTTGGC-GCAAAAATCATGCA
* * * * * *
466 AAGCTGAGCCGAGGCCCTGGAACGCG-TTTCAGGGCCCCAG-TTCAGTTAAGTATAGTACACGAT
130 AAACTGAGCCGGGGCCCTGGAACGCGTTTTCA--G-CCAAGAATC-GTGAGGT-TAGTACACGAT
* * ** **
529 TTCGGCAAAATATTTTCAAAAATTGACCCGAGAGATTTTTCCTCAA-TTTTAACAACAATACTTG
190 TTCGGCAAAA-ATTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACACG
* * *
593 TAAAAAGTATATAATTCAACGCCAAAAATATTGAAGGGCTTTGCACGCTTCTAATATCATTTTTT
254 TAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTCCACGCTTCTAATATCATTTTTT
*
658 TTTATTTTTCC
319 TATATTTTTCC
* * * * *
669 GAATTAATTTTCGATTAAATTGAAATATGATTCAAAAGC-CTGTAAAATCAAATCTTTAAATCCA
1 GAATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTC-GTAAAATCAAATCCTTAAATCCA
* * *
733 ATGTGGCTGAGATTTGGGATGATGAATATA-GATATTTCAATGAGTTTTGGCGCATAAAATCATG
65 ATGTGGCTGAGATTTGGAATGATGAATA-AGGATAATTCAATGAGTCTTGGCGCA-AAAATCATG
* * * * *
797 CTAAACTGAGCTGGGGCCCTGAAACGCGTTTTCAGACAAGAATCGTGATGGTTAGTACAGGATTT
128 CAAAACTGAGCCGGGGCCCTGGAACGCGTTTTCAGCCAAGAATCGTGA-GGTTAGTACACGATTT
** ** *
862 CGGCAAAAACTTTATAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCTTAATACACGTT
192 CGGCAAAAA-TTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACACGTA
* *
927 AAAAATATATAATTCAACGCCAAAAATATTGAAGGGCTTTCCACGCTTATAATATCATTTTTTTA
256 AAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTCCACGCTTCTAATATCATTTTTTTA
*
992 AATTTTTCC
321 TATTTTTCC
* * *
1001 GAATTAATTTCCGATTAAATCGAAACATGATTCGACTGCTCGTAAAATCAAATCCTTAAATCAAA
1 GAATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAA
* * * *
1066 CGTGGATGAGATTTGGAATGATGAATAAGGATAATTCAATGAGTCTTGGGGCCAAAAATCTTGCA
66 TGTGGCTGAGATTTGGAATGATGAATAAGGATAATTCAATGAGTCTTGGCG-CAAAAATCATGCA
* * * * ** *
1131 AAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAATCG-G-GATGCGTATACGATTTC-G
130 AAACTGAGCCGGGGCCCTGGAACGCGTTTTCAGCCAAGAATCGTGAGGTTAGTACACGATTTCGG
* *
1193 ---------GCAAAAATTGACCCGAAAGATTTTTCCTCAATTGTTAACCGCAATA-ATTGTAAAA
195 CAAAAATTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACA-CGT-AAA
* * * * *
1248 AAATAGATAATTCAACGACAAAAAAAATTTTAAGGGCTTTGCACGCTTCTAATATCATTTTTTT-
258 AAATATATAATTCAACG-CCAAAAAGA-TTGAAGGGCTTTCCACGCTTCTAATATCATTTTTTTA
1312 TATTTTTCC
321 TATTTTTCC
* ** * * *
1321 GAATTAATTTCCGAATAAATTTAAATATGATTTAAAAGCTCGTAAAATCAAATCCTTAAATCCAA
1 GAATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAA
* * * *
1386 TGTGGCTGAGATTTGGGATGATGAATATA-GATACTTCAAAGAGTCTTGGCGCAAAAAATCACGC
66 TGTGGCTGAGATTTGGAATGATGAATA-AGGATAATTCAATGAGTCTTGGCGC-AAAAATCATGC
* ** * * *
1450 AAAACTGAACTAGTGCCCTGAAACGCGTTTTCAGCCAAGAATCGTGATGGGTTAGTACAGGATTT
129 AAAACTGAGCCGGGGCCCTGGAACGCGTTTTCAGCCAAGAATCGTGA--GGTTAGTACACGATTT
*
1515 CGGCAAAAACTTTGCAAAAAATGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACACGTA
192 CGGCAAAAA-TTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACACGT-
**
1580 AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTCCACGCTTCTAATATCATTTTTAA
255 AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTCCACGCTTCTAATATCATTTTTTT
1645 AT-TTTTTCC
320 ATATTTTTCC
* *
1654 GAATTAATTCCCGATTAAATCAAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAA
1 GAATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAA
* * * *
1719 TGTGGTTGATATTTGGGATGATGAATATA-GATATTTCAATGAGTCTTGGCGCCAAAAATCATGC
66 TGTGGCTGAGATTTGGAATGATGAATA-AGGATAATTCAATGAGTCTTGGCG-CAAAAATCATGC
* *
1783 AAAACTGAGCCGGGCCCCTGGAACGCGTTTTCAGCCCAA-AATAGTGATGGTTAGTAC
129 AAAACTGAGCCGGGGCCCTGGAACGCGTTTTCAG-CCAAGAATCGTGA-GGTTAGTAC
1840 CTTATTCATC
Statistics
Matches: 1294, Mismatches: 168, Indels: 87
0.84 0.11 0.06
Matches are distributed among these distances:
317 1 0.00
318 43 0.03
319 19 0.01
320 159 0.12
321 35 0.03
324 12 0.01
325 1 0.00
328 1 0.00
329 12 0.01
330 1 0.00
331 59 0.05
332 244 0.19
333 330 0.26
334 61 0.05
335 259 0.20
336 57 0.04
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (329 bp):
GAATTAATTTCCGATTAAATCGAAACATGATTCAAATGCTCGTAAAATCAAATCCTTAAATCCAA
TGTGGCTGAGATTTGGAATGATGAATAAGGATAATTCAATGAGTCTTGGCGCAAAAATCATGCAA
AACTGAGCCGGGGCCCTGGAACGCGTTTTCAGCCAAGAATCGTGAGGTTAGTACACGATTTCGGC
AAAAATTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACACGTAAAAAA
TATATAATTCAACGCCAAAAAGATTGAAGGGCTTTCCACGCTTCTAATATCATTTTTTTATATTT
TTCC
Found at i:1709 original size:653 final size:651
Alignment explanation
Indices: 1--1824 Score: 2565
Period size: 653 Copynumber: 2.8 Consensus size: 651
* * * * * *
1 GAATTAATTTCTGATTAAATCGAAACATGATTCGAATGCTCGTAAAATCAAATACTTAAATCCAA
1 GAATTAATTTCCGATTAAATTGAAATATGATTCAAAAGCTCGTAAAATCAAATCCTTAAATCCAA
* * * *
66 TGTGGTTGAGATTTGGAATGATGAATA-AGGATAATTCAATGAGTCTTGGCAACCAAAAATCATG
66 TGTGGCTGAGATTTGGGATGATGAATATA-GATAATTCAATGAGTCTTGGC-GCAAAAAATCATG
* * * * * * *
130 CCAATCTGAGCCGGGGCCCCGGAATGCGTTTTCAGCCAAGAATCGTGATGGTTAGTACACGATTT
129 CAAAACTGAGCTGGGGCCCTGAAACGCGTTTTCAGCCAAGAATCGTGATGGTTAGTACAGGATTT
*
195 CGGCATAAACTTTGC-AAAAATAGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACACGT
194 CGGCAAAAACTTTGCAAAAAAT-GACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACACGT
*
259 AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTCCACGCTTCTAATGTCATTTTTTT
258 AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTCCACGCTTCTAATATCA-TTTTTT
*
324 AAAATTTTTCCCGAATTAATTTCCGATTAAATCGAAACATGATTCGAATGCTCGTAAAATCAAAT
322 -AAATTTTTTCCGAATTAATTTCCGATTAAATCGAAACATGATTCGAATGCTCGTAAAATCAAAT
* * * *
389 CCTTAAATCTAACGTGGCTGAGATTTGGAATGATGAATAAGGATAATTCAATGAGTCTTGACACC
386 CCTTAAATCAAACGTGGATGAGATTTGGAATGATGAATAAGGATAATTCAATGAGTCTTGGCGCC
* * * * ** *
454 AAAAATCATGCAAAGCTGAGCCGAGGCCCTGGAACGCG-TTTCAGGGCCCCAGTTCAGTTAAGTA
451 AAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTCA--GCCCAAAATCAG---AGGA
*
518 TAGTACACGATTTCGGCAAAATATTTTCAAAAATTGACCCGAGAGATTTTTCCTCAATTTTAACA
511 TAGTACACGATTTCGG------A----CAAAAATTGACCCGAAAGATTTTTCCTCAATTTTAACA
* * * * *
583 ACAATACTTGTAAAAAGTATATAATTCAACGCCAAAAATATTGAAGGGCTTTGCACGCTTCTAAT
566 ACAATAATTGTAAAAAATAGATAATTCAACGCAAAAAAAATTGAAGGGCTTTGCACGCTTCTAAT
648 ATCATTTTTTTTTATTTTTCC
631 ATCATTTTTTTTTATTTTTCC
* *
669 GAATTAATTTTCGATTAAATTGAAATATGATTCAAAAGC-CTGTAAAATCAAATCTTTAAATCCA
1 GAATTAATTTCCGATTAAATTGAAATATGATTCAAAAGCTC-GTAAAATCAAATCCTTAAATCCA
* * *
733 ATGTGGCTGAGATTTGGGATGATGAATATAGATATTTCAATGAGTTTTGGCGCATAAAATCATGC
65 ATGTGGCTGAGATTTGGGATGATGAATATAGATAATTCAATGAGTCTTGGCGCAAAAAATCATGC
* *
798 TAAACTGAGCTGGGGCCCTGAAACGCGTTTTCAGACAAGAATCGTGATGGTTAGTACAGGATTTC
130 AAAACTGAGCTGGGGCCCTGAAACGCGTTTTCAGCCAAGAATCGTGATGGTTAGTACAGGATTTC
** * ** *
863 GGCAAAAACTTTATAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCTTAATACACGTTA
195 GGCAAAAACTTTGCAAAAAATGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACACGTAA
* *
928 AAAATATATAATTCAACGCCAAAAATATTGAAGGGCTTTCCACGCTTATAATATCATTTTTTTAA
260 AAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTCCACGCTTCTAATATCA-TTTTTTAA
*
993 A-TTTTTCCGAATTAATTTCCGATTAAATCGAAACATGATTCGACTGCTCGTAAAATCAAATCCT
324 ATTTTTTCCGAATTAATTTCCGATTAAATCGAAACATGATTCGAATGCTCGTAAAATCAAATCCT
*
1057 TAAATCAAACGTGGATGAGATTTGGAATGATGAATAAGGATAATTCAATGAGTCTTGGGGCCAAA
389 TAAATCAAACGTGGATGAGATTTGGAATGATGAATAAGGATAATTCAATGAGTCTTGGCGCCAAA
* * * * *
1122 AATCTTGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAATC-G-GGATGCGTATA
454 AATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTCAGCCCAAAATCAGAGGAT-AGTACA
**
1185 CGATTTCGG-CAAAAATTGACCCGAAAGATTTTTCCTCAATTGTTAACCGCAATAATTGTAAAAA
518 CGATTTCGGACAAAAATTGACCCGAAAGATTTTTCCTCAATT-TTAACAACAATAATTGT-AAAA
*
1249 AATAGATAATTCAACGACAAAAAAAATTTTAAGGGCTTTGCACGCTTCTAATATCA-TTTTTTTT
581 AATAGATAATTCAACG-CAAAAAAAA-TTGAAGGGCTTTGCACGCTTCTAATATCATTTTTTTTT
1313 ATTTTTCC
644 ATTTTTCC
* * *
1321 GAATTAATTTCCGAATAAATTTAAATATGATTTAAAAGCTCGTAAAATCAAATCCTTAAATCCAA
1 GAATTAATTTCCGATTAAATTGAAATATGATTCAAAAGCTCGTAAAATCAAATCCTTAAATCCAA
* * *
1386 TGTGGCTGAGATTTGGGATGATGAATATAGATACTTCAAAGAGTCTTGGCGCAAAAAATCACGCA
66 TGTGGCTGAGATTTGGGATGATGAATATAGATAATTCAATGAGTCTTGGCGCAAAAAATCATGCA
* * *
1451 AAACTGAACTAGTGCCCTGAAACGCGTTTTCAGCCAAGAATCGTGATGGGTTAGTACAGGATTTC
131 AAACTGAGCTGGGGCCCTGAAACGCGTTTTCAGCCAAGAATCGTGAT-GGTTAGTACAGGATTTC
1516 GGCAAAAACTTTGCAAAAAATGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACACGTAA
195 GGCAAAAACTTTGCAAAAAATGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACACGT-A
1581 AAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTCCACGCTTCTAATATCA-TTTTTAA
259 AAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTCCACGCTTCTAATATCATTTTTTAA
* * *
1645 ATTTTTTCCGAATTAATTCCCGATTAAATCAAAACATGATTCAAATGCTCGTAAAATCAAATCCT
324 ATTTTTTCCGAATTAATTTCCGATTAAATCGAAACATGATTCGAATGCTCGTAAAATCAAATCCT
* * * * * *
1710 TAAATCCAATGTGGTTGATATTTGGGATGATGAATATA-GATATTTCAATGAGTCTTGGCGCCAA
389 TAAATCAAACGTGGATGAGATTTGGAATGATGAATA-AGGATAATTCAATGAGTCTTGGCGCCAA
1774 AAATCATGCAAAACTGAGCC-GGGCCCCTGGAACGCGTTTTCAGCCCAAAAT
453 AAATCATGCAAAACTGAGCCGGGGCCCC-GGAACGCGTTTTCAGCCCAAAAT
1825 AGTGATGGTT
Statistics
Matches: 1043, Mismatches: 98, Indels: 45
0.88 0.08 0.04
Matches are distributed among these distances:
649 31 0.03
650 14 0.01
651 18 0.02
652 198 0.19
653 258 0.25
654 56 0.05
659 3 0.00
660 13 0.01
663 1 0.00
664 6 0.01
665 152 0.15
666 7 0.01
667 181 0.17
668 104 0.10
669 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (651 bp):
GAATTAATTTCCGATTAAATTGAAATATGATTCAAAAGCTCGTAAAATCAAATCCTTAAATCCAA
TGTGGCTGAGATTTGGGATGATGAATATAGATAATTCAATGAGTCTTGGCGCAAAAAATCATGCA
AAACTGAGCTGGGGCCCTGAAACGCGTTTTCAGCCAAGAATCGTGATGGTTAGTACAGGATTTCG
GCAAAAACTTTGCAAAAAATGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACACGTAAA
AAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTCCACGCTTCTAATATCATTTTTTAAAT
TTTTTCCGAATTAATTTCCGATTAAATCGAAACATGATTCGAATGCTCGTAAAATCAAATCCTTA
AATCAAACGTGGATGAGATTTGGAATGATGAATAAGGATAATTCAATGAGTCTTGGCGCCAAAAA
TCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTCAGCCCAAAATCAGAGGATAGTACACGA
TTTCGGACAAAAATTGACCCGAAAGATTTTTCCTCAATTTTAACAACAATAATTGTAAAAAATAG
ATAATTCAACGCAAAAAAAATTGAAGGGCTTTGCACGCTTCTAATATCATTTTTTTTTATTTTTC
C
Found at i:2452 original size:330 final size:331
Alignment explanation
Indices: 1846--3170 Score: 1783
Period size: 330 Copynumber: 4.0 Consensus size: 331
1836 GTACCTTATT
*
1846 CATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCACCGGCTCAGTTTTGCATGATTTTTGGCGC
1 CATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGC
* * **
1911 CAAGACTCATTGAATTATCATTATTTATCATTCCAAATCTCAGCCATGTTGGATTTAAGGATTTG
66 CAAGACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCACATTGGATTTAAGGATTTG
* * * *
1976 ATTTTGCGAGCATTCGAATCAAGTTTCGATTTAATCGGAAATTAATTCGGAAAAAATT-TAAAAA
131 ATTTTACAAGCATTCGAATCATGTTTCGATTTAATCGGAAATTAATTAGGAAAAAATTATAAAAA
* * * * *
2040 AATGATATTAAAAGCGTGGAAATCCGTTCAATCTTTTTGACGTTGAATTATATATTTTTTACGAG
196 AATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACAAG
* * *
2105 TATTACGGTTGAAAATTGAGGAAAAAAT-TCTCGGGTCAATTTTTGCAAAAGTTTTGCCGAAATC
261 TATTGCGGTTAAAAATTGAGG-AAAAATCTTTCGGGTCAATTTTTGCAAAAGTTTTGCCGAAATC
2169 GTGTACC
325 GTGTACC
* *
2176 CATCACGATTTTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGC
1 CATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGC
* *
2241 CAAGACTCATTGAATTATCCTTATTC-TCATTCCAAATCTCAGGCACATTGGATTTAAGGATTTA
66 CAAGACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCACATTGGATTTAAGGATTTG
*** * * *
2305 ATTTTACAAATGTTTGAATCATGTTTCGATTTAATCGGAAATTAATTAGGAAAAAATTATAATAC
131 ATTTTACAAGCATTCGAATCATGTTTCGATTTAATCGGAAATTAATTAGGAAAAAATTATAAAAA
**
2370 AATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACTTG
196 AATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACAAG
2435 TATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGC-AAAGTTTTTGCCGAAATC
261 TATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAAG-TTTTGCCGAAATC
* *
2499 GAGTATTAAC
325 --GT-GTACC
* * * *
2509 CATCACGATTCTTGGCTGAAAACGCGTTCCAGGGCCCCGGCTCAGTATTGTATGATTTTTTGCGC
1 CATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGC
* * * *
2574 CAATACTCATTGAAATAT-CTATATTCATCATCCCAAATCTCAGCCACATTGGATTTAAGAATTT
66 CAAGACTCATTGAATTATCCT-TATTCATCATTCCAAATCTCAGCCACATTGGATTTAAGGATTT
* * * * *
2638 GATTTTACAAGCATTTGAATCATATTTCAATGTAATCGGAAATTAATTCGG--AAAATTA-AAAA
130 GATTTTACAAGCATTCGAATCATGTTTCGATTTAATCGGAAATTAATTAGGAAAAAATTATAAAA
* * * * *
2700 AAATGATTTTAGAAGCGTGCAAAGCCTTTCAATCTTTTTTGCGTTGAATTATATATTTTTTACGA
195 AAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACAA
* * * * * *
2765 TTATTGCGGTTAACAATAGATGAAAAATCTTTCGGGTCAATTTTTGCAAAACTTTTGCCGAAATT
260 GTATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAAGTTTTGCCGAAATC
*
2830 GTATACTATC
325 GTGTAC---C
* * * *
2840 CATCACAATTTTTTTGCTGAAAACGCGTTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCG
1 CATCACGA-TTCTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCG
** *
2905 CCAACTCTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCACGA-AGGA-TTAAGGATT
65 CCAAGACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCAC-ATTGGATTTAAGGATT
* *
2968 TGATTTTACGAGCATTCGAATCATGTTTCGATTTAATCGGAAATTAATTCA-GAAAAAATTTTTA
129 TGATTTTACAAGCATTCGAATCATGTTTCGATTTAATCGGAAATTAATT-AGGAAAAAA-TTATA
* * *
3032 AAAAAATAATATTAGAAGCGTGGAAAGCCCTTCAAGCTTTTTAGCGTTGAATTATATATTTTTTA
192 AAAAAATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTA
* * *
3097 CAAGTATTGCGGTTAAAAATTGTGGAAAAAT-TTATCGGGTCAATTTTTACAAAAAATTTTGCCG
257 CAAGTATTGCGGTTAAAAATTGAGGAAAAATCTT-TCGGGTCAATTTTTGC-AAAAGTTTTGCCG
*
3161 AAATTGTGTA
320 AAATCGTGTA
3171 GTATACTTAA
Statistics
Matches: 872, Mismatches: 101, Indels: 38
0.86 0.10 0.04
Matches are distributed among these distances:
328 2 0.00
329 96 0.11
330 198 0.23
331 177 0.20
332 107 0.12
333 90 0.10
334 81 0.09
335 100 0.11
336 21 0.02
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (331 bp):
CATCACGATTCTTGGCTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGC
CAAGACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAGCCACATTGGATTTAAGGATTTG
ATTTTACAAGCATTCGAATCATGTTTCGATTTAATCGGAAATTAATTAGGAAAAAATTATAAAAA
AATGATATTAGAAGCGTGGAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTACAAG
TATTGCGGTTAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAAGTTTTGCCGAAATCG
TGTACC
Found at i:6822 original size:19 final size:21
Alignment explanation
Indices: 6798--6844 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
6788 AATTGTTTTT
6798 TTTTTTCATTTT-ACTTGTA-
1 TTTTTTCATTTTAACTTGTAC
* *
6817 TTTTTT-TTTTTAACTTTTAC
1 TTTTTTCATTTTAACTTGTAC
6837 TTTTTTCA
1 TTTTTTCA
6845 ATGCTTTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 4 0.18
19 12 0.55
20 6 0.27
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTTTCATTTTAACTTGTAC
Found at i:14835 original size:18 final size:18
Alignment explanation
Indices: 14812--14861 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
14802 ACTTGCTGCA
* *
14812 GCAGCAGCGGCGGCGGCG
1 GCAGCAGCAGCAGCGGCG
14830 GCAGCAGCAGCAGCGGCG
1 GCAGCAGCAGCAGCGGCG
* *
14848 GCGGCGGCAGCAGC
1 GCAGCAGCAGCAGC
14862 AGCAGCCTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.16, C:0.34, G:0.50, T:0.00
Consensus pattern (18 bp):
GCAGCAGCAGCAGCGGCG
Found at i:14841 original size:24 final size:24
Alignment explanation
Indices: 14809--14867 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
14799 TTGACTTGCT
14809 GCAGCAGCAGCGGCGGCGGCGGCA
1 GCAGCAGCAGCGGCGGCGGCGGCA
14833 GCAGCAGCAGCGGCGGCGGCGGCA
1 GCAGCAGCAGCGGCGGCGGCGGCA
14857 GCAGCAGCAGC
1 GCAGCAGCAGC
14868 CTGGGCTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.19, C:0.34, G:0.47, T:0.00
Consensus pattern (24 bp):
GCAGCAGCAGCGGCGGCGGCGGCA
Done.