Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014921.1 Corchorus olitorius cultivar O-4 contig14954, 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: 33562
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:609 original size:332 final size:331
Alignment explanation
Indices: 3--1209 Score: 1812
Period size: 330 Copynumber: 3.7 Consensus size: 331
1 CT
*
3 ATCACTGTTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTTCTTGATTTTTGGCGC
1 ATCACTGTTTTTT-GCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGCGC
* * * * **
68 AAAGTCTCCTTAAAATATCTATATTCGTTTAAGAAAATCTTAGCCACAATC-GATTTAAGGATTT
65 AAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTTAGCCACAA-CGGATTTAAGGATTT
* ** **
132 A-TTTTACGAGCATGTGAATCTTGTTTCGATTTAATTAAAAATATTTTCGAAAAAAAAAAATAAA
129 ATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCG--AAAAAAAAAGGAA
* * * *
196 AAACGATATTGGAAGCGTGAAAAA-CATTTTAAGTTTTT-TGGGTTCAATAATATAGTTTTTTTA
192 AAACGATATTGGAAGCGTGAAAAACCATTTTAA-TTTTTCAGGGTTGAATAATATAGTTTTTCTG
*
259 AGTATTTTGGCAAAAAATTGAGGAAAAA-TTTTTCGGGTCAGTTTTTG-AAAATTTTAGCCGAAA
256 AGTATTGTGGCAAAAAATTGAGGAAAAACTTTTT-GGGTCAGTTTTTGTAAAATTTTAGCCGAAA
322 TCGTGTATTTACC
320 TCGTGTA-TTACC
*
335 ATCACTGTTTTTTGCTACAAAACGCGTTCCGGAGCCACGGCTCAATTTTGCTTGATTTTTGGC-C
1 ATCACTGTTTTTTGCTA-AAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGCGC
399 GAAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTTAGCCACAACGGATTTAAGGATTT
65 -AAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTTAGCCACAACGGATTTAAGGATTT
*
464 ATTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAAAAATAAATTCGAAAAAAAAAGGAAAA
129 ATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCGAAAAAAAAAGGAAAA
*
529 ACGATATTGGATGCGTGAAAAACCATTTTAATTTTTCAGGGTTGAATAATATAGTTTTTCTGAGT
194 ACGATATTGGAAGCGTGAAAAACCATTTTAATTTTTCAGGGTTGAATAATATAGTTTTTCTGAGT
594 ATTGTGGCAAAAAATTGAGGAAAAACTTTTTGGGTCAGTTTTTGTAAAATTTTAGCCGAAATCGT
259 ATTGTGGCAAAAAATTGAGGAAAAACTTTTTGGGTCAGTTTTTGTAAAATTTTAGCCGAAATCGT
659 GTATTA-C
324 GTATTACC
* *
666 ATCAC-GAATTTTTGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTAATTTTTGGCTG
1 ATCACTG-TTTTTTGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGC-G
*
730 -AAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTTAACCACAACGGATTTAAGGATTT
64 CAAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTTAGCCACAACGGATTTAAGGATTT
*
794 ATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCGAAAAAAAATGGAAAA
129 ATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCGAAAAAAAAAGGAAAA
* * *
859 ACGATATTGGATGCGTGAAAAACCATTTTAATTTTTCGGGGTTGAATAATATACTTTTTCTGAGT
194 ACGATATTGGAAGCGTGAAAAACCATTTTAATTTTTCAGGGTTGAATAATATAGTTTTTCTGAGT
* *
924 ATTGTGGCAAAAAATTTGAGAAAAAACTTTTTGGGTCAGTTTTTGTAAAATTTTAGCTGAAATCG
259 ATTGTGGCAAAAAA-TTGAGGAAAAACTTTTTGGGTCAGTTTTTGTAAAATTTTAGCCGAAATCG
*
989 TGTA-TGCC
323 TGTATTACC
* *
997 ATCACTATTTTTTGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTAGCGCA
1 ATCACTGTTTTTTGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGCGCA
* * * * *
1062 AAGACTCCTTGAAATATCTATATTCGTTTAACCAAATCTTAGCCACAATGGATTTAAGGATTT-G
66 AAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTTAGCCACAACGGATTTAAGGATTTAT
* ** * * * *
1126 TTTTACGAGCATCTAAATCTTGTTTC-AAATAATTAGAAATAAATTCG-AAAAAAATGGAATATC
131 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCGAAAAAAAAAGGAAAAAC
1189 GATATTGGAAGCGTGAAAAAC
196 GATATTGGAAGCGTGAAAAAC
1210 ATCACGGTTT
Statistics
Matches: 812, Mismatches: 48, Indels: 34
0.91 0.05 0.04
Matches are distributed among these distances:
328 34 0.04
329 18 0.02
330 274 0.34
331 229 0.28
332 185 0.23
333 72 0.09
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (331 bp):
ATCACTGTTTTTTGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTGGCGCA
AAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTTAGCCACAACGGATTTAAGGATTTAT
TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAAATAAATTCGAAAAAAAAAGGAAAAAC
GATATTGGAAGCGTGAAAAACCATTTTAATTTTTCAGGGTTGAATAATATAGTTTTTCTGAGTAT
TGTGGCAAAAAATTGAGGAAAAACTTTTTGGGTCAGTTTTTGTAAAATTTTAGCCGAAATCGTGT
ATTACC
Found at i:1713 original size:545 final size:546
Alignment explanation
Indices: 698--1756 Score: 1626
Period size: 545 Copynumber: 1.9 Consensus size: 546
688 GCGTTCCGGA
* ** *
698 GCCCCGGCTCAATTTTGCTTAATTTTTGGCTGAAAGACTCCTTCAAATATCTATATTCATCTAAC
1 GCCCCGGCTCAATTTTGCATAATTTTTGGAAGAAAGACTCCTTCAAATATCTATAGTCATCTAAC
*
763 CAAATCTTAACCACAACGGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTA
66 CAAATCTCAACCACAACGGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTA
* *
828 ATTAAAAATAAATTCGAAAAAAAATGGAAAAACGATATTGGATGCGTGAAAAACCATTTTAATTT
131 ATTAAAAATAAATTCGAAAAAAAATGGAAAAACGATATTGGAAGCGTGAAAAACCAATTTAATTT
* * *
893 TTCGGGGTTGAATAATATACTTTTTCTGAGTATTGTGGCAAAAAATTTGAGAAAAAACTTTTTGG
196 TTCGAGGTTGAATAATATACTTCTTCTGAGTATTGTGGCAAAAAATTTGAGAAAAAACTTTTCGG
* * * * * *
958 GTCAGTTTTTGTAAAATTTTAGCTGAAATCGTGTATGCCATCACTATTTTTTGCTAAAAACGCGT
261 GTAAGTTTTTGCAAAATTTTAGCCGAAATCGTGTATACCATCACGATTTTTAGCTAAAAACGCGT
* * * *
1023 TCCGGAGCCCCGGCTCAATTTTGCTTGATTTTTAGCGCAAAGACTCCTTGAAATATCTATATTCG
326 TCAGCAGCCCCGACTCAATTTTGCTTGATTTTTAGCGCAAAGACTCCTTGAAATATCTATATTCA
* * *
1088 TTTAACCAAATCTTAGCCACAATGGATTTAAGGATTTGTTTTACGAGCATCTAAATCTTGTTTCA
391 TCTAACCAAATCTTAGCCACAATGGATTTAAGGATTTGTTTTAAGAGCATCCAAATCTTGTTTCA
* *
1153 AATAATTAGAAATAAATTCG-AAAAAAATGGAATA-TCGATATTGGAAGCGTGAAAAACATCACG
456 AATAATTAAAAATAAATTCGAAAAAAAATGGAA-AGACGATATTGGAAGCGTGAAAAACATCACG
1216 GTTTTTGACAAAAAAAGGCGTTTCAGG
520 GTTTTTGACAAAAAAAGGCGTTTCAGG
* *
1243 GCCCCGGCTCAGTTTTGCATGATTTTTGGAAGAAAGACTCCTGT-AAATATCTATAGTCATCTAA
1 GCCCCGGCTCAATTTTGCATAATTTTTGGAAGAAAGACTCCT-TCAAATATCTATAGTCATCTAA
* * * *
1307 CCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTT
65 CCAAATCTCAACCACAACGGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTT
* *
1372 AATTAAAAATAACTTCG-AAAAAAATGGAAAAACGATATTGGAAGTGTGAAAAACCAATTTAATT
130 AATTAAAAATAAATTCGAAAAAAAATGGAAAAACGATATTGGAAGCGTGAAAAACCAATTTAATT
* * *
1436 TTTTGAGGTTGAATAATATAGTTCTTCTGAGTATTGTGGC-AAAAA-TTGAGGAAAAACTTTTCG
195 TTTCGAGGTTGAATAATATACTTCTTCTGAGTATTGTGGCAAAAAATTTGAGAAAAAACTTTTCG
* *
1499 GGTAAGTTTTTGCAAAATTTTAGCCGAAATCGTGTATAACTATCACGGTTTTTAGCTAAAAACGC
260 GGTAAGTTTTTGCAAAATTTTAGCCGAAATCGTGTAT-ACCATCACGATTTTTAGCTAAAAACGC
*
1564 GTTCAGCAGCCCCGACTCAATTTTGCTTGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATT
324 GTTCAGCAGCCCCGACTCAATTTTGCTTGATTTTTAGCGCAAAGACTCCTTGAAATATCTATATT
* *
1629 CATCTAACCAAATCTTATCCACAATGGATTTAAGGATTTGTTTTTAAGAGCATCCGAATCTTGTT
389 CATCTAACCAAATCTTAGCCACAATGGATTTAAGGATTTG-TTTTAAGAGCATCCAAATCTTGTT
* **
1694 TTACTTTAATTAAAAATAAATTCGAAAAAAAAATGGAAAGACGATATTGGAAGCGTGAAAAAC
453 TCA-AATAATTAAAAATAAATTCG-AAAAAAAATGGAAAGACGATATTGGAAGCGTGAAAAAC
1757 CATTTTAATT
Statistics
Matches: 463, Mismatches: 44, Indels: 12
0.89 0.08 0.02
Matches are distributed among these distances:
542 50 0.11
543 125 0.27
544 103 0.22
545 149 0.32
546 2 0.00
547 34 0.07
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (546 bp):
GCCCCGGCTCAATTTTGCATAATTTTTGGAAGAAAGACTCCTTCAAATATCTATAGTCATCTAAC
CAAATCTCAACCACAACGGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTA
ATTAAAAATAAATTCGAAAAAAAATGGAAAAACGATATTGGAAGCGTGAAAAACCAATTTAATTT
TTCGAGGTTGAATAATATACTTCTTCTGAGTATTGTGGCAAAAAATTTGAGAAAAAACTTTTCGG
GTAAGTTTTTGCAAAATTTTAGCCGAAATCGTGTATACCATCACGATTTTTAGCTAAAAACGCGT
TCAGCAGCCCCGACTCAATTTTGCTTGATTTTTAGCGCAAAGACTCCTTGAAATATCTATATTCA
TCTAACCAAATCTTAGCCACAATGGATTTAAGGATTTGTTTTAAGAGCATCCAAATCTTGTTTCA
AATAATTAAAAATAAATTCGAAAAAAAATGGAAAGACGATATTGGAAGCGTGAAAAACATCACGG
TTTTTGACAAAAAAAGGCGTTTCAGG
Found at i:2208 original size:334 final size:329
Alignment explanation
Indices: 1241--2964 Score: 1818
Period size: 329 Copynumber: 5.2 Consensus size: 329
1231 AGGCGTTTCA
* * * * * * *
1241 GGGCCCCGGCTCAGTTTTGCATGATTTTTGGAAG-AAAGACTCCTGTAAATATCTATAGTCATCT
1 GGGCTCCGGCTCAGTTTTGTATGATTTTTGG-CGCCAAGACTCCTTTGAATATCTATATTCATCT
* * * *
1305 AACCAAATCTCAGCCACA-ATGGATTTAAGGATTTGTTTTTACGAGTATCTGAATCTTGTTTCGA
65 -ACCAAATCTCAGCCATATAT-GATTTAA-GATTTGTTTTTACGAGCATCAGAATCTAGTTTCGA
* * * * * *
1369 TTTAATT-AAAAATAACTTCGAAAAAAAT-GGAAAAACGATATTGGAAGTGTGAAAAACCAATTT
127 TTTAATTGGAAATTAA-TTCGAAAAAAATAGGAAAAACGATATTCGAAGCGTGAAAAACC-CTTC
* * * *
1432 AATTTTTTGAGGT-TGAATAATATAGTTCTTC--TGAGTATTGTGG-CAAAAATTGAGGAAAAAC
190 AATTTTTTG-GCTATGATTAATATA-TT-TTCTATGAGTATTTTGGCCAAAAATTTAGGAAAAA-
* * * * **
1493 TT-TTCGGGT-AAGTTTTTGCAAAAT-TTTAGCCGAAATCGTGT-ATAACTATCACGGTTTTTAG
251 TTATTCGGGTCAA-TTTTTGCAAAATCTTGA-CCGAAATCGTGTGCTAACCATCACAGTTTTCGG
* *
1554 CTAAAAACGCGTTCAG
314 CTAAAAACACGTTCCG
** * * * *
1570 CAGCCCCGACTCAATTTTGCT-TGATTTTTGGCGCAAAGACTCC-TTGAAATATCTATATTCATC
1 GGGCTCCGGCTCAGTTTTG-TATGATTTTTGGCGCCAAGACTCCTTTG-AATATCTATATTCATC
* * * * * * *
1633 TAACCAAATCTTATCCACA-ATGGATTTAAGGATTTGTTTTTAAGAGCATCCGAATCTTGTTT-T
64 T-ACCAAATCTCAGCCATATAT-GATTTAA-GATTTGTTTTTACGAGCATCAGAATCTAGTTTCG
** * * * * *
1696 ACTTTAATTAAAAATAAATTCGAAAAAAAAATGGAAAGACGATATTGGAAGCGTGAAAAACCATT
126 A-TTTAATTGGAAATTAATTCGAAAAAAATA-GGAAAAACGATATTCGAAGCGTGAAAAACC-CT
* * * * * * * * *
1761 TTAATTTTTCGGGGT-TGAATAATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAAC
188 TCAATTTTT-TGGCTATGATTAATATATTTTCTATGAGTATTTTGGCCAAAAATTTAGGAAAAA-
* * * * **
1825 TT-TTTGGGTCAGTTTTTGTAAAAT-TTTAGCCGAAATCGTGTATTAACCATCACAGTTTTCGGC
251 TTATTCGGGTCAATTTTTGCAAAATCTTGA-CCGAAATCGTGTGCTAACCATCACAGTTTTCGGC
1888 TTAAAAAACACGTTCCG
315 -T-AAAAACACGTTCCG
* * * *
1905 GGTCTCCGGCTCAGTTTTGTATGATTTTTGGGGTCAAGACTCCTTTGAATATCTATATTCATCTT
1 GGGCTCCGGCTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTTGAATATCTATATTCATCTA
* *
1970 CCTTAATCTCAGCCATATATGATTTGAAGATTTGTTTTTACGAGCATCAGAATCCAGTTTCGATT
66 CC-AAATCTCAGCCATATATGATTT-AAGATTTGTTTTTACGAGCATCAGAATCTAGTTTCGATT
** *
2035 TAATTGGAAATTAATTCGGAAAAGCATAGG-AAAACGATATTCGAAGCGTCAAAAACCCTTCAAT
129 TAATTGGAAATTAATTC-GAAAAAAATAGGAAAAACGATATTCGAAGCGTGAAAAACCCTTCAAT
* *
2099 ATTTTTGGCTATGATTTATATATTTTCTATGAGTATTTTGGCCGAAAATTTAGGAAAAATTATTC
193 -TTTTTGGCTATGATTAATATATTTTCTATGAGTATTTTGGCCAAAAATTTAGGAAAAATTATTC
*
2164 GGGTCAACTTTTGCAAAATCTTGACCGAAATCGTGTGCTAACCATCACAGTTTTCGGCTTAAAAA
257 GGGTCAATTTTTGCAAAATCTTGACCGAAATCGTGTGCTAACCATCACAGTTTTCGGC-T-AAAA
2229 ACACGTTCCG
320 ACACGTTCCG
* * *
2239 GGGCTCCGGCTCAGTTTTGTATGATTTTTGGTGCCAAGACTCCTTTGAATATCTATATTTATCTG
1 GGGCTCCGGCTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTTGAATATCTATATTCATCTA
* *
2304 CCTAAATCTCACCCATATATGATTTGAAGATTTGTTTGTACGAGCATCAGAAGTC-AGTTTCGAT
66 CC-AAATCTCAGCCATATATGATTT-AAGATTTGTTTTTACGAGCATCAGAA-TCTAGTTTCGAT
** * * *
2368 TTAATTGGAAATTAATTCAGAAAATTATAGGAAAAACGATATTCGAAGCTTTAAAAACTCTTCAA
128 TTAATTGGAAATTAATTC-GAAAAAAATAGGAAAAACGATATTCGAAGCGTGAAAAACCCTTCAA
* * * * * *
2433 TCTTTTTGGCGATGATTCACATATTTTTTATGAGTATTTTGGCTAAAAATTTAGGAAAAATCATT
192 T-TTTTTGGCTATGATTAATATATTTTCTATGAGTATTTTGGCCAAAAATTTAGGAAAAATTATT
2498 CGGGTCAATTTTTGCAAAATCTTGACCGAAATCGTGTGC--A-CATCACAGTTTTCGGCTAAAAA
256 CGGGTCAATTTTTGCAAAATCTTGACCGAAATCGTGTGCTAACCATCACAGTTTTCGGCTAAAAA
*
2560 CGCGTTCCG
321 CACGTTCCG
* *
2569 GGGC-CCGACTCAGTTTTGTATGATTTTTTGCGCCAAGACTCC-TTGAAATATCTATATTCATCT
1 GGGCTCCGGCTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTTG-AATATCTATATTCATCT
*
2632 ACCCAAATCTCAGCCATATAGGATTTAAAGATTTGTTTTTACGAGCATCAGAATCTAGTTTCGAT
65 A-CCAAATCTCAGCCATATATGATTT-AAGATTTGTTTTTACGAGCATCAGAATCTAGTTTCGAT
* * **
2697 TTAATTGGAAATTCATTTGGAAAAGCATAGGAAAAACGATATTCGAAGCGTGAAAAAACCCTTCA
128 TTAATTGGAAATT-AATTCGAAAAAAATAGGAAAAACGATATTCGAAGCGTG-AAAAACCCTTCA
* * * * * * *
2762 ATCTTTTTGGCGATAATTTATATATTTT-TACGAGTATTTTGGCCAAAGATTTAGGAAAAATCAA
191 AT-TTTTTGGCTATGATTAATATATTTTCTATGAGTATTTTGGCCAAAAATTTAGGAAAAATTAT
** *
2826 TCGGGTCAATTTTCACAAAATCTTGACCGAAATCGTGTGCGT----TTCACAGTTTTCGGCTAAA
255 TCGGGTCAATTTTTGCAAAATCTTGACCGAAATCGTGTGC-TAACCATCACAGTTTTCGGCTAAA
*
2887 AACACGTTTCG
319 AACACGTTCCG
* **
2898 GGGCTCTGGCTTTGTTTTGTATGATTTTTGGCGCCAAGACTCCTTTGAATATCTATATTCATCTA
1 GGGCTCCGGCTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTTGAATATCTATATTCATCTA
2963 CC
66 CC
2965 CATCACGGTT
Statistics
Matches: 1220, Mismatches: 138, Indels: 74
0.85 0.10 0.05
Matches are distributed among these distances:
328 8 0.01
329 376 0.31
330 117 0.10
331 69 0.06
332 70 0.06
333 28 0.02
334 285 0.23
335 252 0.21
336 15 0.01
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (329 bp):
GGGCTCCGGCTCAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTTGAATATCTATATTCATCTA
CCAAATCTCAGCCATATATGATTTAAGATTTGTTTTTACGAGCATCAGAATCTAGTTTCGATTTA
ATTGGAAATTAATTCGAAAAAAATAGGAAAAACGATATTCGAAGCGTGAAAAACCCTTCAATTTT
TTGGCTATGATTAATATATTTTCTATGAGTATTTTGGCCAAAAATTTAGGAAAAATTATTCGGGT
CAATTTTTGCAAAATCTTGACCGAAATCGTGTGCTAACCATCACAGTTTTCGGCTAAAAACACGT
TCCG
Found at i:3294 original size:24 final size:24
Alignment explanation
Indices: 3262--3309 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3252 AATCGTGTAC
3262 TAATCATCACGGTTTTTGGTTAAA
1 TAATCATCACGGTTTTTGGTTAAA
3286 TAATCATCACGGTTTTTGGTTAAA
1 TAATCATCACGGTTTTTGGTTAAA
3310 AACGCGTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (24 bp):
TAATCATCACGGTTTTTGGTTAAA
Found at i:4061 original size:327 final size:323
Alignment explanation
Indices: 3290--4129 Score: 889
Period size: 326 Copynumber: 2.6 Consensus size: 323
3280 GTTAAATAAT
**
3290 CATCACGGTTTTTGGTTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGC
1 CATCACGGTTTTTGACTAAAAACGCGTTCCGGGG-CCC-GCTCAGTTTTGCATGATTTTTGGCGC
* * * *
3355 CAAGACTCATTGAAATGTCTATATTCGT-TCAATGAAATTTCAGCCACATTGGATTGAAGGATTT
64 CAAGACTCATTGAAATATCTATATTCATCT-AATGAAATCTCAGCCACATTGGATTTAAGGATTT
* * **
3419 GTTTTTACGAGCATCTCAATCCAGTTTCGATTTAATTAGAAATTAATTCGAAAAAAAAAACGGTA
128 GTTTTTACGAGCATCTCAATCCTGTTTCGATTTAATAAGAAATTAATTCGAAAAAAAAAACGAAA
* * *
3484 TAAGAAGCGTGAGAAATCCTTCAATCTTTTTGGCGTTGGATTATATTTATTTTATGAGTATTGTG
193 TAAGAAGCGTAAGAAACCCTTCAATCTTTTTGGCGTTGGATTATATTTATTTTATGAGTATCGTG
* * *
3549 GCTAAAAATTTAGGCAGAAACTTTCGTTTAAATTTTTGCAGAAATTTAGCCGAAATCGTGTACTA
258 GCTAAAAATTGAGGCAGAAACTTTCGGTCAAATTTTTGCAGAAATTTAGCCGAAATCG-GTACTA
3614 AC
322 AC
* * * *
3616 CATCACGATTTTT-AGCTAAAAACGTGTTTCGGGGTCCCGTCTCAGTTTTGAATGATTTTTGGCG
1 CATCACGGTTTTTGA-CTAAAAACGCGTTCCGGGG-CCCG-CTCAGTTTTGCATGATTTTTGGCG
*
3680 CCAAGACTCATTGAAATATCTATATTCATCTAATGAAATCTCAGCCTCATTGGATTTAAGGATTT
63 CCAAGACTCATTGAAATATCTATATTCATCTAATGAAATCTCAGCCACATTGGATTTAAGGATTT
* *
3745 GTTTTTACGAGCATCTCAATCCTGTTTTGCTTT-ATAAGAAATTAATTCGGAAAAAAATAGGAAA
128 GTTTTTACGAGCATCTCAATCCTGTTTCGATTTAATAAGAAATTAATTC-G--AAAAA-A--AAA
* * * *
3809 ATCGAAATTAGAAATC-TAAGAAACCCTTCAATTTTTTTGGCGTT-GAGTTATATATTCTTTT-T
187 A-CGAAATAAG-AAGCGTAAGAAACCCTTCAATCTTTTTGGCGTTGGA-TTATAT-TTATTTTAT
* * * * * *
3871 GAGTATCGTGGC-AGAAAATTGAGTC-GAAATTTTTGGGGTCAATTTTTTGTA-AAATTTTAGCT
248 GAGTATCGTGGCTA-AAAATTGAGGCAGAAA-CTTT-CGGTCAAATTTTTGCAGAAA-TTTAGCC
3933 GAAATC-GTA-T-A-
309 GAAATCGGTACTAAC
* ** * * *
3944 CATTACGGTTTTTGACTAAAAACGCGTTCCGAAGCCTCAGCTCTGTTTCGCCTGATTTTTGGCGC
1 CATCACGGTTTTTGACTAAAAACGCGTTCCGGGGCC-C-GCTCAGTTTTGCATGATTTTTGGCGC
* * * ** * *
4009 CAAG-TTTATTGAAATATCTATATCCATCTAACCAAATCTCACCCACATTGGATTTAAGCATTTG
64 CAAGACTCATTGAAATATCTATATTCATCTAATGAAATCTCAGCCACATTGGATTTAAGGATTTG
* * * * * *
4073 TTTTTACGAGAATCTAAATCATGTTTCAATTTAATTAGAAAGTAAATTCAGAAAAAA
129 TTTTTACGAGCATCTCAATCCTGTTTCGATTTAATAAGAAA-TTAATTC-GAAAAAA
4130 TTAGGAAAAC
Statistics
Matches: 431, Mismatches: 61, Indels: 44
0.80 0.11 0.08
Matches are distributed among these distances:
325 15 0.03
326 144 0.33
327 86 0.20
328 64 0.15
329 11 0.03
330 1 0.00
331 14 0.03
332 64 0.15
333 32 0.07
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (323 bp):
CATCACGGTTTTTGACTAAAAACGCGTTCCGGGGCCCGCTCAGTTTTGCATGATTTTTGGCGCCA
AGACTCATTGAAATATCTATATTCATCTAATGAAATCTCAGCCACATTGGATTTAAGGATTTGTT
TTTACGAGCATCTCAATCCTGTTTCGATTTAATAAGAAATTAATTCGAAAAAAAAAACGAAATAA
GAAGCGTAAGAAACCCTTCAATCTTTTTGGCGTTGGATTATATTTATTTTATGAGTATCGTGGCT
AAAAATTGAGGCAGAAACTTTCGGTCAAATTTTTGCAGAAATTTAGCCGAAATCGGTACTAAC
Found at i:11382 original size:9 final size:9
Alignment explanation
Indices: 11368--11398 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
11358 GCCATTAGTT
11368 CTAAAAGTC
1 CTAAAAGTC
*
11377 CTAAAACTC
1 CTAAAAGTC
11386 CTAAAAGTC
1 CTAAAAGTC
11395 CTAA
1 CTAA
11399 CTGACTTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.26, G:0.06, T:0.23
Consensus pattern (9 bp):
CTAAAAGTC
Found at i:11949 original size:261 final size:261
Alignment explanation
Indices: 11479--11999 Score: 889
Period size: 261 Copynumber: 2.0 Consensus size: 261
11469 CCACTCTTTG
* * *
11479 CTACTTGATGAATCATCATTGTTGCTGTCACAGAATTCGTTCAATTCTTCCTCAAACCCTTTCCT
1 CTACTTGATGAATCATCATTGTTGCTATCACAGAATTCCTTCAATTCTTCCTCAAACCATTTCCT
11544 TGCATGTATCCCCAACAAGGAGCCATCACTATACTGCCGAGAATGTGCTGCACTCATTGAAGCTT
66 TGCATGTATCCCCAACAAGGAGCCATCACTATACTGCCGAGAATGTGCTGCACTCATTGAAGCTT
* *
11609 TAGTGCTACTCACTGGTTTCGGTATTGGTGCTGAACCAGGAGGAAAAGACTGGCGGGGACTCCTT
131 TAGTACTACTCACTGGTTTCGGTATTGGTGCTGAACCAGGAGGAAAAGACCGGCGGGGACTCCTT
*
11674 TCCTTTGTCAATTCACTCAATTTGGACTTAGGTGAATCTGAAGAATTGGAGTGTGAAGGAGACAG
196 TCCTTTGCCAATTCACTCAATTTGGACTTAGGTGAATCTGAAGAATTGGAGTGTGAAGGAGACAG
11739 C
261 C
* *
11740 CTACTTGATGAATCATCATTTTTGCTATCACAGAATTCCTTCAATTCTTCCTCAAAGCATTTCCT
1 CTACTTGATGAATCATCATTGTTGCTATCACAGAATTCCTTCAATTCTTCCTCAAACCATTTCCT
* *
11805 TGCATGTGTCCCCAACAAGGAGCCATCACTATACTGCCTAGAATGTGCTGCACTCATTGAAGCTT
66 TGCATGTATCCCCAACAAGGAGCCATCACTATACTGCCGAGAATGTGCTGCACTCATTGAAGCTT
* * * * *
11870 TAGTACTAGTCATTGGTTTCGGTATTGGTGCTGCAGCAGGAGGAAAAGACCGGTGGGGACTCCTT
131 TAGTACTACTCACTGGTTTCGGTATTGGTGCTGAACCAGGAGGAAAAGACCGGCGGGGACTCCTT
* *
11935 TCCTTTGCCAATTCACTCAATTTGGACTTGGGTGAATCTGAAGAATTGGAGTGTGAAGGCGACAG
196 TCCTTTGCCAATTCACTCAATTTGGACTTAGGTGAATCTGAAGAATTGGAGTGTGAAGGAGACAG
12000 GCTGCTAGGC
Statistics
Matches: 243, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
261 243 1.00
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (261 bp):
CTACTTGATGAATCATCATTGTTGCTATCACAGAATTCCTTCAATTCTTCCTCAAACCATTTCCT
TGCATGTATCCCCAACAAGGAGCCATCACTATACTGCCGAGAATGTGCTGCACTCATTGAAGCTT
TAGTACTACTCACTGGTTTCGGTATTGGTGCTGAACCAGGAGGAAAAGACCGGCGGGGACTCCTT
TCCTTTGCCAATTCACTCAATTTGGACTTAGGTGAATCTGAAGAATTGGAGTGTGAAGGAGACAG
C
Found at i:33533 original size:1 final size:1
Alignment explanation
Indices: 33529--33561 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
33519 TTCAAGCTGC
33529 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33562 C
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.