Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014122.1 Corchorus olitorius cultivar O-4 contig14155, 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: 5347
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:71 original size:2 final size:2
Alignment explanation
Indices: 64--93 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54 GATTAGATGA
64 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
94 TTCAAGGAGT
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):
AT
Found at i:2087 original size:652 final size:645
Alignment explanation
Indices: 170--2428 Score: 2210
Period size: 652 Copynumber: 3.4 Consensus size: 645
160 TTATTGCGAA
* * * * * * * *
170 AATACTCAGAAGAAATATATAATTCAACGTCAAAAAGATTGATGTGCTTTTCA-GGTTTCTAA-A
1 AATACTCAGAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGGTTTTTCACGCTTT-TAATA
** * * * * * * * * *
233 TTTTTTTTCCAATTTTTTCCGAATTCATTTCTGATTTAATCAAAACAAGAATCAGATGTTCGTAA
65 TCGTTTTT-CATTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAA
* * * ** * *
298 AAATAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTTTATGAATATAAATATTTCAACGAGTC
129 AAACAATTCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
* * ** * * * *
363 TT-TACAATAAAAATCATGC-AATTTGAGCGGGGGCTAC-AGAACGCGTTTTTAACCAAAAACTG
194 TTCTGC--CAAAAATCATGCAAAACTGAGC--GGGCTCCGA-AATGCGTTTTTAGCC-AAAACCG
* ** * * *
425 TGATGGTTAGTACAAGATTTCGGCTAAAATTTTG-CAAGAACTGACCCGAAAAGGTTTTCCTCAA
253 TGATGGTTAGTACATGATTTCGGCTAAAA-ACTGACAA-AA---A----AAAA-TTTTTTCTAAA
* * * * *
489 -TTTTTGCCAGAATACTTAGAAAAAATATATAATTCAACGCCAAAAA-ATTTAAAGGGTATTCAC
308 TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGATAGGCT-TTCAC
* * * * * * *
552 GCTT-TTAATATTTTTTTCCCA-TTTTTTACGAATTTATTTTTAATTAAACCGAAATAAGATTCA
372 GCTTCTAAATTTTTTTTTCCAATTTTTTTTCGAATTAATTTCTAATTAAA---AAACAAGATTCA
* * * *
615 GATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAC-ATTTGGTTAGATGCATATAGATA
434 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC-GGCGATTTGGTTTGATGAATATAGATA
* * * **
679 TTTCAAGGAGTCCTTTA-GCCTAAAATCATACAAAACTGAGTCGAGTTCCCGAAACGCGGTTTT-
498 TTTCAAGGAGTCTTTTACGACAAAAATCATAC-AAACTGAGTCG-GTTTACGAAACGC-GTTTTA
* * * * ** *
742 AGCCAGAAAACCATGATGGTTATTGCATGATTTCGGCTAAAATTTTGC-AATGCTGCCCCGAAAA
560 AGCCA-AAAACCGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCG-AAA
* *
806 ATTTTTTCCTCAATTCTTTGCCACAAAC
623 A-GTTTTCCTCAATTTTTTG-C-C--AC
* * * * * *
834 AAAACTCAGAAAAAATATATAAATCAATCCCAAAAAAATTGAAGGGATTTTTCTCGTTTTTAGTA
1 AATACTCAGAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGG-TTTTTCACGCTTTTAATA
* * * * *
899 TTGTTTTTCTTTTTTTTTGCGCGAATTTATTTCTAAGTAAATCGAAACATTATTCAGATGCTCAT
65 TCGTTTTTCATTTTTTTT---CGAATTTATTTCTAATTAAATCGAAACAATATTCAGATGCTCGT
* *
964 AAAAACAAATT-CTTAAATCCATTGTGGCTTAGATTTGATTAGATGAATATAGATATTTCAAGGA
127 AAAAAC-AATTCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGA
* * * ** *
1028 ATATTCCTGCCAAAAATCATGCAAAACTGAGCCGGCGTCCCCCAATGTGTTTTTAGCCAAGAACC
191 GTCTT-CTGCCAAAAATCATGCAAAACTGAGCGGGC-T-CCGAAATGCGTTTTTAGCCAA-AACC
**
1093 GTGATGGTTAGTACATGATTTCGGCTAAAAACTGACAAAAAAAAATTTTTTCTAAATTTTTTGTG
252 GTGATGGTTAGTACATGATTTCGGCTAAAAACTGACAAAAAAAAATTTTTTCTAAATTTTTTGCC
* * * *
1158 ACAAAACTCAGAAAAAATATATAATTCAACGCCAGAAAGATTGATGGGCTTTTCAGGCTTCTAAA
317 ACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGATAGGC-TTTCACGCTTCTAAA
* * * * * *
1223 -TTTTGTTTCCATTTTTTTTTCCGAATTCATTCCTTATTTAATCAAAACAAGATTCAGATGTTCG
381 TTTTTTTTTCCAATTTTTTTT-CGAATTAATTTC-TAATTAA--AAAACAAGATTCAGATGCTCG
** * * * * *
1287 TAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTTGTTTTATGAATATAAATATTTCAAGAA
442 TAAAAACAAATCCTTAAATCCAATGTGGCGGCGATTTGGTTTGATGAATATAGATATTTCAAGGA
* * ** * ** * *
1352 GTCTTTT-CAACAAAAATCATGCAATTTGAGCTGGGGCTACGGAGCGCGTTTTTAA-CCAAAAAC
507 GTCTTTTACGACAAAAATCATACAAACTGAG-TCGGTTTACGAAACGCG-TTTTAAGCCAAAAAC
* * *
1415 TGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTCCTCAA
570 CGTGATGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTCCTCAA
1480 TTTTTTGCCAC
635 TTTTTTGCCAC
* ** *
1491 AATACTCAGAATAAATATATAATTCAATGCCAAAAATTTTGAAGGGTTTTTCACGCTTCTAATAT
1 AATACTCAGAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGGTTTTTCACGCTTTTAATAT
*
1556 CGTTTTTCAATTTTCTTTTCGAATTTATTTCTAATTAAATTGAAACAATATTCAGATGCTCGTAA
66 CGTTTTTC-ATTTT-TTTTCGAATTTATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAA
** * * * * *
1621 AAACAATTCCTTAAATGAATAGTGGCTGACACTTGGTTAGATGAATAAAGATATTTAAAGGAGTC
129 AAACAATTCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
* * *
1686 TATCTGCGAAAAATCACGCAAAACTGAGCGGGCTCCGAAATGCGTTTTTAG-GATAAAGCCGTGA
194 T-TCTGCCAAAAATCATGCAAAACTGAGCGGGCTCCGAAATGCGTTTTTAGCCA-AAA-CCGTGA
* *** *** *
1750 TGGTTAGTACACGATTTCGGCTAAAAACTGACCCCGAAATTTTTTTTTCTGAATTTTTTGCCACA
256 TGGTTAGTACATGATTTCGGCTAAAAACTGA-CAAAAAAAAATTTTTTCTAAATTTTTTGCCACA
*
1815 ATACTCAGAAAAAATATATTATTCAACGCCAAAAAGATTGATAGGCTTCTCACGCTTCTAAAAGT
320 ATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGATAGGCTT-TCACGCTTCT-AAA-T
*
1880 TTTTTTTTTCAATTTTTTTTCAGAATTAATTTCTAATT-AAAAA-AAGATTCAGATGCTCGTAAA
382 TTTTTTTTCCAATTTTTTTTC-GAATTAATTTCTAATTAAAAAACAAGATTCAGATGCTCGTAAA
* * *
1943 AACAAATTCTTAAAACCAATGTGGCGGCGATTTGGTTTGATGAATATAGATATTTCAAGGA-TTT
446 AACAAATCCTTAAATCCAATGTGGCGGCGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCT
*
2007 TTTACGACAAAAATCATTCAAACTGAGTCAGGTTTACGAAACGCGTTTTAAGCCAAAAACCGTGA
511 TTTACGACAAAAATCATACAAACTGAGTC-GGTTTACGAAACGCGTTTTAAGCCAAAAACCGTGA
* * * *
2072 TAGTTAATACACGATTTCGGCTAAAGTTTTGCAAAAACTGACCCCAAAGGTTTTTCCTCAAATTT
575 TGGTTAATACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAG-TTTTCCTC-AATTT
2137 TTT-CCAC
638 TTTGCCAC
* * *
2144 AATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGG-TTTTCACGCTTTTAATAT
1 AATACTCAGAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGGTTTTTCACGCTTTTAATAT
* * * * *
2208 CGTTTTCCCA-TTTTTTCCGAATTTATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTTAA
66 CGTTTT-TCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAAA
*
2272 AACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCT
130 AACAATTCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC-
** * * * *
2337 TTCAACCTAAAATCATGCAAAACTGAGTCGGGCCGCCGAAACGCGTTTTTAGCCAAAAAACCATG
194 TTCTGCCAAAAATCATGCAAAACTGAG-CGGG-CTCCGAAATGCGTTTTTAGCC--AAAACCGTG
*
2402 ATGGTTAGTGCATGATTTCGGCTAAAA
255 ATGGTTAGTACATGATTTCGGCTAAAA
2429 TTTTGCAATG
Statistics
Matches: 1314, Mismatches: 227, Indels: 119
0.79 0.14 0.07
Matches are distributed among these distances:
650 123 0.09
651 20 0.02
652 201 0.15
653 140 0.11
654 91 0.07
655 124 0.09
656 28 0.02
657 72 0.05
658 4 0.00
659 1 0.00
660 9 0.01
661 60 0.05
662 63 0.05
663 39 0.03
664 136 0.10
665 21 0.02
666 12 0.01
667 4 0.00
668 106 0.08
669 58 0.04
670 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (645 bp):
AATACTCAGAAAAAATATATAATTCAATGCCAAAAAAATTGAAGGGTTTTTCACGCTTTTAATAT
CGTTTTTCATTTTTTTTCGAATTTATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAAAA
ACAATTCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT
CTGCCAAAAATCATGCAAAACTGAGCGGGCTCCGAAATGCGTTTTTAGCCAAAACCGTGATGGTT
AGTACATGATTTCGGCTAAAAACTGACAAAAAAAAATTTTTTCTAAATTTTTTGCCACAATACTC
AGAAAAAATATATAATTCAACGCCAAAAAGATTGATAGGCTTTCACGCTTCTAAATTTTTTTTTC
CAATTTTTTTTCGAATTAATTTCTAATTAAAAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
TAAATCCAATGTGGCGGCGATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTTACGACAA
AAATCATACAAACTGAGTCGGTTTACGAAACGCGTTTTAAGCCAAAAACCGTGATGGTTAATACA
CGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTCCTCAATTTTTTGCCAC
Found at i:2459 original size:330 final size:327
Alignment explanation
Indices: 170--2734 Score: 2227
Period size: 330 Copynumber: 7.8 Consensus size: 327
160 TTATTGCGAA
* * * * * *
170 AATACTCAGAAGAAATATATAATTCAACGTCAAAAAGATTGATGTGCTTTTCA-GGTTTCTAA-A
1 AATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGATTTTCACGCTTT-TAATA
* * * * * * *
233 TTTTTTTTCCAATTTTTTCCGAATTCATTTCTGATTTAATCAAAACAAGAATCAGATGTTCGTAA
65 -TTGTTTTCCAATTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* * ** * *
298 AAATAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTTTATGAATATAAATATTTCAACGAGTC
129 AAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
* ** ** * *
363 TTTACAA-TAAAAATCATGC-AATTTGAGCGGGGGCTAC-AGAACGCGTTTTTAACCAAAAACTG
194 TTT-CAACCAAAAATCATGCAAAACTGAGC--GGGCCCCGA-AACGCGTTTTTAGCCAAAAACCG
* * * **
425 TGATGGTTAGTACAAGATTTCGGCTAAAATTTTGCAAGAACTGACCCGAAAAGGTTTTCCTCAA-
255 TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAG--CTGCCCCAAAAAATTTTTCCTCAAT
*
489 TTTTTGCCAG
318 TTTTTGCCAC
* * *
499 AATACTTAGAAAAAATATATAATTCAACGCCAAAAA-ATTTAAAGGG-TATTCACGCTTTTAATA
1 AATACTCAGAAAAAATATATAATTCAACGCCAAAAAGA-TTGAAGGGATTTTCACGCTTTTAATA
* * * * * *
562 TTTTTTTCCCATTTTTTACGAATTTATTTTTAATTAAACCGAAATAAGATTCAGATGCTCGTAAA
65 TTGTTTTCCAATTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* *
627 AACAAATCCTTAAATCCATTGTGGCTGACATTTGGTTAGATGCATATAGATATTTCAAGGAGTCC
130 AACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT-C
* * * ** * *
692 TTT-AGCCTAAAATCATACAAAACTGAGTCGAGTTCCCGAAACGCGGTTTTAGCCAGAAAACCAT
194 TTTCAACCAAAAATCATGCAAAACTGAG-CG-GGCCCCGAAACGCGTTTTTAGCCA-AAAACCGT
* * * *
756 GATGGTTATTGCATGATTTCGGCTAAAATTTTGCAATGCTGCCCCGAAAAATTTTTTCCTCAATT
256 GATGGTTAGTACACGATTTCGGCTAAAATTTTGCAA-GCTGCCCC-AAAAAATTTTTCCTCAATT
*
821 CTTTGCCACAAAC
319 TTTTG-C-C--AC
* * * * * *
834 AAAACTCAGAAAAAATATATAAATCAATC-CCAAAAAAATTGAAGGGATTTTTCTCGTTTTTAGT
1 AATACTCAGAAAAAATATATAATTCAA-CGCCAAAAAGATTGAAGGGA-TTTTCACGCTTTTAAT
*** * ** *
898 ATTGTTTTTCTTTTTTTTTGCGCGAATTTATTTCTAAGTAAATCGAAACATTATTCAGATGCTCA
64 ATTG-TTTTCCAATTTTTT-C-CGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* * *
963 TAAAAACAAATTCTTAAATCCATTGTGGCTTAGATTTGATTAGATGAATATAGATATTTCAAGGA
126 TAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGA
* * * ** * * * *
1028 ATATTCCTGCCAAAAATCATGCAAAACTGAGCCGGCGTCCCC-CAATGTGTTTTTAGCCAAGAAC
191 GTCTTTCAACCAAAAATCATGCAAAACTGAG-CGG-G-CCCCGAAACGCGTTTTTAGCCAAAAAC
* *** * *
1092 CGTGATGGTTAGTACATGATTTCGGCT-AAA------AA-CTGACAAAAAAAAATTTTTTCTAAA
253 CGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAGCTG-CCCCAAAAAATTTTTCCTCAA
**
1149 TTTTTTGTGAC
317 TTTTTTGCCAC
* * * * * *
1160 AAAACTCAGAAAAAATATATAATTCAACGCCAGAAAGATTGATGGGCTTTTCAGGCTTCTAA-AT
1 AATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGATTTTCACGCTTTTAATAT
* * * * * * * *
1224 TTTGTTTCCATTTTTTTTTCCGAATTCATTCCTTATTTAATCAAAACAAGATTCAGATGTTCGTA
66 TGT-TTTCCA--ATTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * * ** * *
1289 AAAACAAATCCTTAAATCCAATGTGGTTGAGATTTTGTTTTATGAATATAAATATTTCAAGAAGT
128 AAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT
** ** * * * *
1354 CTTTTCAA-CAAAAATCATGC-AATTTGAGCTGGGGCTACGGAGCGCGTTTTTAACCAAAAACTG
193 C-TTTCAACCAAAAATCATGCAAAACTGAGC--GGGCCCCGAAACGCGTTTTTAGCCAAAAACCG
* * * * *
1417 TGATGGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAACTGACCC-GAAAAGTTTTCCTCAAT
255 TGATGGTTAGTACACGATTTCGGCTAAAATTTTGC--AAGCTGCCCCAAAAAATTTTTCCTCAAT
1481 TTTTTGCCAC
318 TTTTTGCCAC
* * ** * *
1491 AATACTCAGAATAAATATATAATTCAATGCCAAAAATTTTGAAGGGTTTTTCACGCTTCTAATAT
1 AATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGATTTTCACGCTTTTAATAT
* * * * *
1556 CGTTTTTCAATTTTCTTTTCGAATTTATTTCTAATTAAATTGAAACAATATTCAGATGCTCGTAA
66 TGTTTTCCAA-TTT-TTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* ** * * * * *
1621 AAACAATTCCTTAAATGAATAGTGGCTGACACTTGGTTAGATGAATAAAGATATTTAAAGGAGTC
129 AAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
* ** * * * * * *
1686 TATCTGCGAAAAATCACGCAAAACTGAGCGGGCTCCGAAATGCGTTTTTAG-GATAAAGCCGTGA
194 TTTCAACCAAAAATCATGCAAAACTGAGCGGGCCCCGAAACGCGTTTTTAGCCA-AAAACCGTGA
** * *** * *
1750 TGGTTAGTACACGATTTCGGCTAAAA-ACTG--A-C--CCCGAAATTTTTTTTTCTGAATTTTTT
258 TGGTTAGTACACGATTTCGGCTAAAATTTTGCAAGCTGCCCCAAAAAATTTTTCCTCAATTTTTT
1809 GCCAC
323 GCCAC
* * * *
1814 AATACTCAGAAAAAATATATTATTCAACGCCAAAAAGATTGATA-GGCTTCTCACGCTTCTAAAA
1 AATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGA-AGGGATTTTCACGCTT-T-TAA
* * * * *
1878 GTTTTTTTTTTCAATTTTTTTTCAGAATTAATTTCTAATT-AA---AAA-AAGATTCAGATGCTC
63 -TATTGTTTTCCAA--TTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * * * *
1938 GTAAAAACAAATTCTTAAAACCAATGTGGCGGCGATTTGGTTTGATGAATATAGATATTTCAAGG
125 GTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGG
* * * * **** *
2003 ATTTTTTACGA-CAAAAATCATTC-AAACTGAGTCAGGTTTACGAAACGCGTTTTAAGCCAAAAA
190 AGTCTTT-CAACCAAAAATCATGCAAAACTGAG-C-GGGCCCCGAAACGCGTTTTTAGCCAAAAA
* * * * **
2066 CCGTGATAGTTAATACACGATTTCGGCTAAAGTTTTGCAAAAACTGACCCC-AAAGGTTTTTCCT
252 CCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGC--AAGCTG-CCCCAAAAAATTTTTCCT
2130 CAAATTTTTT-CCAC
314 C-AATTTTTTGCCAC
*
2144 AATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTAAAGGG-TTTTCACGCTTTTAATAT
1 AATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGATTTTCACGCTTTTAATAT
* * * *
2208 CGTTTTCCCATTTTTTCCGAATTTATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTTAAA
66 TGTTTTCCAATTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
2273 ACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT
131 ACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT
* *
2338 TCAACCTAAAATCATGCAAAACTGAGTCGGGCCGCCGAAACGCGTTTTTAGCCAAAAAACCATGA
196 TCAACCAAAAATCATGCAAAACTGAG-CGGGCC-CCGAAACGCGTTTTTAGCC-AAAAACCGTGA
* * * *
2403 TGGTTAGTGCATGATTTCGGCTAAAATTTTGCAATGCTGCCCCAAAAAAATTTTCCTTAATTCTT
258 TGGTTAGTACACGATTTCGGCTAAAATTTTGCAA-GCTGCCCCAAAAAATTTTTCCTCAATT-TT
*
2468 TTCCACAAAC
321 TTGC-C--AC
* * * * *
2478 AATACTCAGAAAAAATATATAAATCAA-TCCAAATAAAATTGAAGGGATTTTCTCG-TTTTAGTA
1 AATACTCAGAAAAAATATATAATTCAACGCCAAA-AAGATTGAAGGGATTTTCACGCTTTTAATA
* ** * * *
2541 TCGTTTT----TTTTCCCCGAATTTATTTCTAAGTAAATCGAAACAATATTCAGATGCTCATAAA
65 TTGTTTTCCAATTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * * *
2602 AACAAATTCTTAAATCCATTGTGGCTGAGATTTGATTAGTTGAATATAGATATTTCAAGGAATAT
130 AACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCT
* ** * * *
2667 TCCTGCCAAAAATCATGCAAAACTGAGCCGGGACCCAGAAATGCGTTTTTTAGCCAAGAACCGTG
195 TTCAACCAAAAATCATGCAAAACTGAG-CGGG-CCCCGAAACGCG-TTTTTAGCCAAAAACCGTG
2732 ATG
257 ATG
2735 TTTATCTAAA
Statistics
Matches: 1795, Mismatches: 348, Indels: 185
0.77 0.15 0.08
Matches are distributed among these distances:
320 8 0.00
321 79 0.04
322 58 0.03
323 120 0.07
324 137 0.08
325 22 0.01
326 85 0.05
327 8 0.00
328 135 0.08
329 189 0.11
330 386 0.22
331 247 0.14
332 16 0.01
333 9 0.01
334 52 0.03
335 46 0.03
336 2 0.00
337 15 0.01
338 14 0.01
339 31 0.02
340 133 0.07
341 3 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (327 bp):
AATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGATTTTCACGCTTTTAATAT
TGTTTTCCAATTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
ACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT
TCAACCAAAAATCATGCAAAACTGAGCGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGG
TTAGTACACGATTTCGGCTAAAATTTTGCAAGCTGCCCCAAAAAATTTTTCCTCAATTTTTTGCC
AC
Found at i:5145 original size:328 final size:330
Alignment explanation
Indices: 3970--5311 Score: 1169
Period size: 328 Copynumber: 4.1 Consensus size: 330
3960 CCTTTTTGGC
* * * * **
3970 CAAAAATTGAGGAAAAATTTTTCGGGTCATTTTTTGAAAAATTTTAGCCGAAATCGTGTGTTAAC
1 CAAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCATGTACTAAC
* ** ** * * *
4035 CATCACGGTTTTTGGCTTAAAACGCGTTCCATAAACCCGACTCAG-TTTGATTGATTTTTTGTCG
66 CATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAGTTTTGAATGATTTTTAG-CA
* * *
4099 TAAA-GAATCCTTGAAATATCTATATTCATCAAACCAAATCTCAGA-CACATTGGATTTAAGGAT
130 TAAATGAATCCTTAAAATATCTATATTCATCAAACCAAATCTCA-ACCACAATGGATTTAAGAAT
* *
4162 TTGTTTTTACGAGCATCTGAATCTTGTTTTGATTAAATTAGAAAA-GAATTCGG-AAAAAT---A
194 TTGTTTTTATGAGCATCTGAATCTTGTTTCGATTAAATTA-AAAATGAATTCGGAAAAAATGGGA
* * *
4222 AAAAAT-TTAGAAGCCTGAAAAAGCCCATCAATCTTTTTGGCGTTGAATTATATATTTTTTATGA
258 AAAGATATTAAAAGCCTG-AAAAGCCCATCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGA
**
4286 GTATTGTCG
322 GTATTGTTT
** *
4295 CAAAAAATTTAGAAAAAAAAAAATTT-GGGTCAGTTTTT-----A----A-CCGAAATCATGTAC
1 C-AAAAA-TT-G-AGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCATGTAC
* * ** * * *
4349 TAACCATCACGGTTCTTGGCTAAAAATGTATTCCGGGGCCCCGACTCAGTTTTGCATGATTTTTG
62 TAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAGTTTTGAATGATTTTTA
* * * * * * *
4414 GCAGAAATTG-GTCCTTGAAAATATCTATATTCCATCTAATCAAATCTCAGCCTCAATGGGTTTA
127 GCATAAA-TGAATCCTT-AAAATATCTATATT-CATCAAACCAAATCTCAACCACAATGGATTTA
* * * *
4478 AGAATTTGTTTTTATGAGCATCTGAATATTGTTTCGATTTACTTAGAAAT-AATTCGGGGAAAAA
189 AGAATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTAAATTAAAAATGAATTC--GG---AA
* ** * * ** * * * *
4542 AAAAAGCAAAAACGATACTAAAAACGAGAAAATCCCTTCAATTTTTTTGG-GATTGATTTATATT
249 AAAATGGGAAAA-GATATTAAAAGCCTGAAAAGCCCATCAATCTTTTTGGCG-TTGAATTATA--
*
4606 TTTTTTTTCTGAGTATTGTTTGT
310 TATTTTTTCTGAGTATTG-TT-T
* * ** * * *
4629 GGCACAGAATTGAGGAAAAAATTTTCGGGGCAG-CATTGCAAATTTTTAGCCGAAATCATGCAAT
1 --CA-AAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCATGTACT
* * * * * * *
4693 GATCATCATGGTTTATTGGCTAAAACCGCGTTTCGGGGCCCCGACTCAGTTTTGTATGA-TTTTA
63 AACCATCACGGTTT-TTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAGTTTTGAATGATTTTTA
* * * * * *
4757 GGC-TAAAGGACTCCTTGAAATATCTATATTCATCTAACCAAATGTCAGCCACAATGGATTTAAG
127 -GCATAAATGAATCCTTAAAATATCTATATTCATCAAACCAAATCTCAACCACAATGGATTTAAG
* * * * *
4821 AATTTGTTTTTAGGAGCATCTGAATCTTATTTCGGTTTAATTAAAAATAAATTCGGAAAAAATGG
191 AATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTAAATTAAAAATGAATTCGGAAAAAATGG
* * * * *
4886 GAAAACGATATTAAAAGCGTGAATA-CCCTTTAATTTTTTTGGCGTTGAATTATATATTTTTTCT
256 GAAAA-GATATTAAAAGCCTGAAAAGCCCATCAATCTTTTTGGCGTTGAATTATATATTTTTTCT
*
4950 AAGTATTGTTT
320 GAGTATTGTTT
* ** *
4961 CAAAAAGTGAGGAAAACCTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC
1 CAAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCATGTACTAAC
* * * * * *
5026 CATCACAGTTTTTGGTTAAAAACGCGTTCCGTAGCCCCGACTCA-ATTTGAATGATTTTCATCAT
66 CATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAGTTTTGAATGATTTTTAGCAT
* * *
5090 AAA-GAATCATTAAAATATCTATATTCATCAAACCAAATCTCAACCACATTGGATTTAAGGATTT
131 AAATGAATCCTTAAAATATCTATATTCATCAAACCAAATCTCAACCACAATGGATTTAAGAATTT
* * * * *
5154 GTTTTTATAAACATCTGAATCTTGTTTTGATTAAATTAGAAATGAATTCCGAAAAAATGGGAAAA
196 GTTTTTATGAGCATCTGAATCTTGTTTCGATTAAATTAAAAATGAATTCGGAAAAAATGGGAAAA
* * * * *
5219 -ACTTTTAGAAGCCTGAAAAGCCCATCAATCTTTCTGGCGTTGAATTTTATATTTTTCCTGAGTA
261 GA-TATTAAAAGCCTGAAAAGCCCATCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTA
**
5283 TTGTCG
325 TTGTTT
* *
5289 CAAAAAATTTAGAAAAAAATTTT
1 C-AAAAATTGAGGAAAAAATTTT
5312 TTGTTCAGTT
Statistics
Matches: 806, Mismatches: 159, Indels: 100
0.76 0.15 0.09
Matches are distributed among these distances:
318 54 0.07
319 19 0.02
320 22 0.03
321 64 0.08
322 2 0.00
323 1 0.00
325 1 0.00
326 11 0.01
327 15 0.02
328 171 0.21
329 89 0.11
330 67 0.08
331 6 0.01
332 17 0.02
333 15 0.02
334 23 0.03
335 3 0.00
336 29 0.04
337 28 0.03
340 2 0.00
341 72 0.09
342 20 0.02
343 35 0.04
344 40 0.05
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (330 bp):
CAAAAATTGAGGAAAAAATTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCATGTACTAAC
CATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAGTTTTGAATGATTTTTAGCAT
AAATGAATCCTTAAAATATCTATATTCATCAAACCAAATCTCAACCACAATGGATTTAAGAATTT
GTTTTTATGAGCATCTGAATCTTGTTTCGATTAAATTAAAAATGAATTCGGAAAAAATGGGAAAA
GATATTAAAAGCCTGAAAAGCCCATCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTAT
TGTTT
Done.