Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011744.1 Corchorus capsularis cultivar CVL-1 contig11765, 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: 11112
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:266 original size:31 final size:30
Alignment explanation
Indices: 228--292 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
218 GCTCAAAAAG
*
228 GCCCATGAGCT-TACACAAAACGGCCAAATAA
1 GCCCATGAACTCTACA-AAAA-GGCCAAATAA
**
259 GCCCATGAACTCTTTAAAAAGGCCAAATAA
1 GCCCATGAACTCTACAAAAAGGCCAAATAA
289 GCCC
1 GCCC
293 TTTTCTGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 14 0.47
31 14 0.47
32 2 0.07
ACGTcount: A:0.40, C:0.29, G:0.15, T:0.15
Consensus pattern (30 bp):
GCCCATGAACTCTACAAAAAGGCCAAATAA
Found at i:757 original size:30 final size:30
Alignment explanation
Indices: 723--800 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
713 CATCAGAAAA
723 GGGCTTATTTGGCCTTTTTAA-AGAGTTCAG
1 GGGCTTATTTGGCC-TTTTAATAGAGTTCAG
**
753 GGGCTTATTTGG-C-TGCAATTAGAGTTCAG
1 GGGCTTATTTGGCCTTTTAA-TAGAGTTCAG
782 GGGCTTATTTGGCCGTTTT
1 GGGCTTATTTGGCC-TTTT
801 GTGTAAGTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.08
29 22 0.56
30 13 0.33
32 1 0.03
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40
Consensus pattern (30 bp):
GGGCTTATTTGGCCTTTTAATAGAGTTCAG
Found at i:1698 original size:321 final size:320
Alignment explanation
Indices: 837--2556 Score: 2182
Period size: 321 Copynumber: 5.4 Consensus size: 320
827 AATAAGCCGT
* * * * *
837 TTTTTCGAGCATCTCAATTTTGTTTCGATTTAATCAGAAATTAATTCGGAAAAAAAATGGAAAAA
1 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GCAAAAAAATGGAAAAA
* * * * *
902 TGATATTAGAAGCGTGAAAGGCCCGTCAATTTTTTTGGCATTGAATTATATATCTTTTCTGTGTA
65 TGATATTAGAAGCGTGAAAAGCCC-TTAATCTTTTTGGCATTGAATTATATATCTTTTATGAGTA
** ** *
967 TTGTGGCAAAAAATTGAGAAAAAAAAAAATTCGGGTCGGTTTTTAGCCGAAATCGTGTACTAACC
129 TTGTGGCAAAAAATTGAG--AAAAAAATTTTCGGGTTAGTTTTTGGCCGAAATCGTGTACTAACC
* * *
1032 ATCATGG-TTTTGGCTAAAAACGCG-TCTCGGAGCCCCGACTCAATTTTGCGTGATTTTTGGCGT
192 ATCACGGTTTTTGGCTAAAAACGCGTTC-CGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGC
* * * *
1095 AAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCCACATTGGATATAGGGATTTG
256 AAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAAGGATTTG
* *
1160 CTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATTAATTCGCAAAAAAATGAAAAAA
1 -TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATG---GAA
*
1225 AAATGATATTAGAAGTGTGAAAAGCCCGTTAA-CATTTTTGGCATTGAATTATATATCTTTTATG
62 AAATGATATTAGAAGCGTGAAAAGCCC-TTAATC-TTTTTGGCATTGAATTATATATCTTTTATG
* * * *
1289 AGTATTTTGGCAAAAAAATTGAGAAAAAGATTTTCGAGTTAGTTTTTAGCCGAAATCGTGTACTA
125 AGTATTGTGGC-AAAAAATTGAGAAAAAAATTTTCGGGTTAGTTTTTGGCCGAAATCGTGTACTA
* * * *
1354 ACCATAACGGTTTTTGACTAAAAAGGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGC
189 ACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGC
*
1419 GCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAATATTGGATATAAGGATT
254 GCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAAGGATT
1484 T-
319 TG
** * * * *
1485 TTTTTTGAGCATCTCAATCTTGTTTCAATTTAATCAGAAATTAATTCGGAAAAAAATGGAAAAAT
1 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATGGAAAAAT
* * * * * * *
1550 GATTTTAGAAGCGTTAAAGGCCCTTCAATCTTTTTGACGTTGAATTATATATCTTTTCTGTGTAT
66 GATATTAGAAGCGTGAAAAGCCCTT-AATCTTTTTGGCATTGAATTATATATCTTTTATGAGTAT
* ** *
1615 TATGGCAAAAAATTGAGGAAAAAAATTTTCAAGTCAGTTTTTGGCCGAAATCGTGTACTAACC-T
130 TGTGGCAAAAAATTGA-GAAAAAAATTTTCGGGTTAGTTTTTGGCCGAAATCGTGTACTAACCAT
* * * *
1679 CCACGGTTTTTGGCTAAAAAAGCGTTCCGGAGCCAC-AGTTCAATTTTGCATGATTTTTGGTGC-
194 -CACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGA-CTCAATTTTGCATGATTTTTGGCGCA
* * * * *
1742 -AGACTCCTTGAAATATCTATATTTATCAAACCAAATGTCAGCTACATTGGATATAAGCATTTG
257 AAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAAGGATTTG
1805 CTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGC-----AA---AAAAA
1 -TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATGGAAAAA
* *
1862 TGATATTAGAAGCGTGAAAAGCCCGTTAATATTTTTGGCACTGAATTATATATCTTTTATGAGTA
65 TGATATTAGAAGCGTGAAAAGCCC-TTAATCTTTTTGGCATTGAATTATATATCTTTTATGAGTA
*
1927 TTGTGGCAAAAAATTGA-AAAAAAAATTTCGGGTTAGTTTTTGGGGCCGAAATCGTGTACTAACC
129 TTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTTAGTTTTT--GGCCGAAATCGTGTACTAACC
* * * * *
1991 ATCACGGTTTTTGGCTAAAAAAGCGTTCCGGAGCCCCGATTAAATTTTGCAGGATTTTTTGCGCA
192 ATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCA
* * * *
2056 AAGACACCTTGAAATATCTATATTCATCGAATCAAATGTCAGCCACATTGGATATAAGGATTTG
257 AAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAAGGATTTG
* *
2120 CTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATTAATTCGCAAAAAAATGAAAAAA
1 -TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATG-GAAAA
* *
2185 ATGATATTAGAAGCATGAAAAGCCCGTTAA-CATTTTTGGCATTGAATTATATATCTTTTTTGAG
64 ATGATATTAGAAGCGTGAAAAGCCC-TTAATC-TTTTTGGCATTGAATTATATATCTTTTATGAG
* ** *
2249 TATTGTGGCAAAAAATTGAGAAAAAAATTTTCGTGTTAGTTTTTAACCGAAATCGTGTACTAACA
127 TATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTTAGTTTTTGGCCGAAATCGTGTACTAACC
* * * * *
2314 ATCACAGTTTTTGGTTAAAAAGGCATTCAGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCA
192 ATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCA
* * * * * *
2379 AAGACTCCCTGAAATATCTACATTGAACGAACCAAATCTCAGTAATATTGGATATAAGGATTTG
257 AAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAAGGATTTG
* * * *
2443 TTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAACTCG-GAAAAAATGGAAAAA
1 -TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATGGAAAAA
** * *
2507 TGATATTAGAAGCGTGAAGGGCCCGTCAATCTTTTTGGCGTTGAATTATA
65 TGATATTAGAAGCGTGAAAAGCCC-TTAATCTTTTTGGCATTGAATTATA
2557 AGGATTTGTT
Statistics
Matches: 1225, Mismatches: 138, Indels: 69
0.86 0.10 0.05
Matches are distributed among these distances:
311 20 0.02
313 150 0.12
314 4 0.00
315 106 0.09
316 2 0.00
319 56 0.05
320 15 0.01
321 250 0.20
322 10 0.01
323 182 0.15
324 175 0.14
325 66 0.05
326 176 0.14
327 13 0.01
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (320 bp):
TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATGGAAAAAT
GATATTAGAAGCGTGAAAAGCCCTTAATCTTTTTGGCATTGAATTATATATCTTTTATGAGTATT
GTGGCAAAAAATTGAGAAAAAAATTTTCGGGTTAGTTTTTGGCCGAAATCGTGTACTAACCATCA
CGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAGA
CTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAAGGATTTG
Found at i:2108 original size:634 final size:633
Alignment explanation
Indices: 836--2498 Score: 2255
Period size: 634 Copynumber: 2.6 Consensus size: 633
826 CAATAAGCCG
*
836 TTTTTTCGAGCATCTCAATTTTGTTTCGATTTAATCAGAAATTAATTCGGAAAAAAAATGGAAAA
1 TTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATCAGAAATTAATTCGG-AAAAAAATGGAAAA
* *
901 ATGATATTAGAAGCGTGAAAGGCCCGTCAATTTTTTTGGCATTGAATTATATATCTTTTCTGTGT
65 ATGATATTAGAAGCGTGAAAGGCCCTTCAATCTTTTTGGCATTGAATTATATATCTTTTCTGTGT
* ** * *
966 ATTGTGGCAAAAAATTGAGAAAAAAAAAAATTCGGGTCGGTTTTTAGCCGAAATCGTGTACTAAC
130 ATTGTGGCAAAAAATTGAG-GAAAAAAATTTTCGAGTCAGTTTTTAGCCGAAATCGTGTACTAAC
* * *
1031 CATCATGG-TTTTGGCTAAAAACGCG-TCTCGGAGCCCCGACTCAATTTTGCGTGATTTTTGGCG
194 C-TCACGGTTTTTGGCTAAAAAAGCGTTC-CGGAGCCCCGACTCAATTTTGCATGATTTTT-G-G
** * *
1094 TAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCCACATTGGATATAGGGATTT
255 TGCAGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCTACATTGGATATAAGGATTT
*
1159 GCTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATTAATTCGCAAAAAAATGAAAAA
320 GCTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGC-----------AAA
* *
1224 AAAATGATATTAGAAGTGTGAAAAGCCCGTTAACATTTTTGGCATTGAATTATATATCTTTTATG
374 AAAATGATATTAGAAGCGTGAAAAGCCCGTTAACATTTTTGGCACTGAATTATATATCTTTTATG
* * *
1289 AGTATTTTGGCAAAAAAATTGAGAAAAAGATTTTCGAGTTAGTTTTTAGCCGAAATCGTGTACTA
439 AGTATTGTGGCAAAAAAATTGAGAAAAAAAATTTCGAGTTAGTTTTTAGCCGAAATCGTGTACTA
* * * *
1354 ACCATAACGGTTTTTGACTAAAAAGGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGC
504 ACCATAACGGTTTTTGACTAAAAAAGCGTTCCGGAGCCCCGACTAAATTTTGCAGGATTTTTGGC
* *
1419 GCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAATATTGGATATAAGGATT
569 GCAAAGACACCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAAGGATT
* *
1484 TTTTTTTGAGCATCTCAATCTTGTTTCAATTTAATCAGAAATTAATTCGGAAAAAAATGGAAAAA
1 TTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATCAGAAATTAATTCGGAAAAAAATGGAAAAA
* * * *
1549 TGATTTTAGAAGCGTTAAAGGCCCTTCAATCTTTTTGACGTTGAATTATATATCTTTTCTGTGTA
66 TGATATTAGAAGCGTGAAAGGCCCTTCAATCTTTTTGGCATTGAATTATATATCTTTTCTGTGTA
* * *
1614 TTATGGCAAAAAATTGAGGAAAAAAATTTTCAAGTCAGTTTTTGGCCGAAATCGTGTACTAACCT
131 TTGTGGCAAAAAATTGAGGAAAAAAATTTTCGAGTCAGTTTTTAGCCGAAATCGTGTACTAACCT
* *
1679 CCACGGTTTTTGGCTAAAAAAGCGTTCCGGAGCCAC-AGTTCAATTTTGCATGATTTTTGGTGCA
196 -CACGGTTTTTGGCTAAAAAAGCGTTCCGGAGCCCCGA-CTCAATTTTGCATGATTTTTGGTGCA
* *
1743 GACTCCTTGAAATATCTATATTTATCAAACCAAATGTCAGCTACATTGGATATAAGCATTTGCTT
259 GACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCTACATTGGATATAAGGATTTGCTT
1808 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATGATATTAGAA
324 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATGATATTAGAA
*
1873 GCGTGAAAAGCCCGTTAATATTTTTGGCACTGAATTATATATCTTTTATGAGTATTGTGGC-AAA
389 GCGTGAAAAGCCCGTTAACATTTTTGGCACTGAATTATATATCTTTTATGAGTATTGTGGCAAAA
* * *
1937 AAATTGA-AAAAAAAATTTCGGGTTAGTTTTTGGGGCCGAAATCGTGTACTAACCATCACGGTTT
454 AAATTGAGAAAAAAAATTTCGAGTTAGTTTTT--AGCCGAAATCGTGTACTAACCATAACGGTTT
* * *
2001 TTGGCTAAAAAAGCGTTCCGGAGCCCCGATTAAATTTTGCAGGATTTTTTGCGCAAAGACACCTT
517 TTGACTAAAAAAGCGTTCCGGAGCCCCGACTAAATTTTGCAGGATTTTTGGCGCAAAGACACCTT
* * *
2066 GAAATATCTATATTCATCGAATCAAATGTCAGCCACATTGGATATAAGGATT
582 GAAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAAGGATT
* * * * * *
2118 TGCTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTATAAATTAATTCGCAAAAAAATGAAAA
1 T--TTTTTCGAGCATCTCAATCTTGTTTCGATTTAATCAGAAATTAATTCGGAAAAAAATG-GAA
* * *
2183 AAATGATATTAGAAGCATGAAAAGCCCGTT-AA-CATTTTTGGCATTGAATTATATATCTTTTTT
63 AAATGATATTAGAAGCGTGAAAGGCCC-TTCAATC-TTTTTGGCATTGAATTATATATCTTTTCT
* * * *
2246 GAGTATTGTGGCAAAAAATTGA-GAAAAAAATTTTCGTGTTAGTTTTTAACCGAAATCGTGTACT
126 GTGTATTGTGGCAAAAAATTGAGGAAAAAAATTTTCGAGTCAGTTTTTAGCCGAAATCGTGTACT
* * * * * *
2310 AACAATCACAGTTTTTGGTTAAAAAGGCATTCAGGAGCCCCGACTCAATTTTGCATGATTTTTGG
191 AAC-CTCACGGTTTTTGGCTAAAAAAGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGG
* * * * * * * *
2375 CGCAAAGACTCCCTGAAATATCTACATTGAACGAACCAAATCTCAG-TAATATTGGATATAAGGA
255 TGC--AGACTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCT-ACATTGGATATAAGGA
* * * * *
2439 TTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAACTCGGAAAAAA
317 TTTGCTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAA
2499 TGGAAAAATG
Statistics
Matches: 905, Mismatches: 94, Indels: 42
0.87 0.09 0.04
Matches are distributed among these distances:
632 21 0.02
633 10 0.01
634 210 0.23
636 144 0.16
637 76 0.08
638 106 0.12
645 111 0.12
646 45 0.05
647 133 0.15
648 49 0.05
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (633 bp):
TTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATCAGAAATTAATTCGGAAAAAAATGGAAAAA
TGATATTAGAAGCGTGAAAGGCCCTTCAATCTTTTTGGCATTGAATTATATATCTTTTCTGTGTA
TTGTGGCAAAAAATTGAGGAAAAAAATTTTCGAGTCAGTTTTTAGCCGAAATCGTGTACTAACCT
CACGGTTTTTGGCTAAAAAAGCGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGTGCAGA
CTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGCTACATTGGATATAAGGATTTGCTTTT
ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATGATATTAGAAGC
GTGAAAAGCCCGTTAACATTTTTGGCACTGAATTATATATCTTTTATGAGTATTGTGGCAAAAAA
ATTGAGAAAAAAAATTTCGAGTTAGTTTTTAGCCGAAATCGTGTACTAACCATAACGGTTTTTGA
CTAAAAAAGCGTTCCGGAGCCCCGACTAAATTTTGCAGGATTTTTGGCGCAAAGACACCTTGAAA
TATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAAGGATT
Found at i:3748 original size:325 final size:323
Alignment explanation
Indices: 2692--5581 Score: 3209
Period size: 321 Copynumber: 8.9 Consensus size: 323
2682 TATTTTATGT
* *
2692 AGAAAAAAATTTTCGGGTCAGTTTTGGCCGAAATCGTGTACTAAACATCACGGTTTTTGGCTAAA
1 AGAAAAAAATTTTCGGGTCAGTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAA
* * * * *
2757 AACGCGTTCCAGAGCCCCGGCTCAATTTTGCATTATTTTTGGCGCAAAAACTCCTTGGAATATCA
66 AACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCT
* * * * *
2822 ATATTCTTCGAACCAAATGTTAGCGACATTGGATATAAGGATTTGCTTTTACGAGTATTTGAATC
131 ATATTCATCGAACCAAATGTCAGCAACATTGGATATAAGGATTTGCTTTTACGAGCATCTGAATC
* **
2887 TTGTTTCGATTTAATTAGAAATTAGTTCGCAAAAAAATGAGAAAAAAATGATATTAGAAGAATGA
196 TTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATGA-AAAAAAATGATATTAGAAGCGTGA
* * * *
2952 AAAGCCCGTTAATTTTTTTGGCATTGAATTATATATCTTTTAAGAGTATTGTGACAAAAAATTG
260 AAAGCCCTTTAATATTTTTGGCATTGAATTATATATCTTTTATGAGTATTGTGGCAAAAAATTG
* * * *
3016 AGAAAAAAAATTTCGGGTTAGTTTTTAGCCGAAATCATGTACTAACCATCACGATTTTTGGCTAA
1 AGAAAAAAATTTTCGGGTCAGTTTTT-GCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA
**
3081 AAACGCGTTCCGGAGCCCCATCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATC
65 AAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATC
* * * * *
3146 TAAATTCATCAAACCAAATGCCAGCTACATTGGATATAAGCATTTGCTTTTACGAGCATCTGAAT
130 TATATTCATCGAACCAAATGTCAGCAACATTGGATATAAGGATTTGCTTTTACGAGCATCTGAAT
3211 CTTGTTTCGATTTAATTAGAAATTAATTCGC---------AAAAAAAATGATATTAGAAGCGTGA
195 CTTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATGAAAAAAAATGATATTAGAAGCGTGA
* * * * * * *
3267 AAAGCTCGTTAATATTTTTGGCAATGAATTATAAATCTTTGATGAGTATTGTTGCAAGAAATTG
260 AAAGCCCTTTAATATTTTTGGCATTGAATTATATATCTTTTATGAGTATTGTGGCAAAAAATTG
* * * *
3331 AGAAAAAAAATTTCGGGTTAGTTTTTGGCCGAAATCGTGTACTAACCATAACTGTTTTTGGCTAA
1 AGAAAAAAATTTTCGGGTCAGTTTTT-GCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA
* * * * *
3396 AAACGCGTTCCAGAGCCCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGGAATATG
65 AAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATC
* * *
3461 TATATTCATCGAACCAAATGTCAGCCACATTGGATATAAGGATTTGCTTTTACGAGTATTTGAAT
130 TATATTCATCGAACCAAATGTCAGCAACATTGGATATAAGGATTTGCTTTTACGAGCATCTGAAT
* * *
3526 CTTGTTTCGATTTAATTGGAAATTAATTTGCAAAAAATTGTAAAAAAAATGATATTAGAAGCGTG
195 CTTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATG-AAAAAAAATGATATTAGAAGCGTG
* * *
3591 AAAAGCCCTTTAATATTTTTGGCGTTGAATTATATATCTTTTCTGTGTATTGTGGCAAAAAATTG
259 AAAAGCCCTTTAATATTTTTGGCATTGAATTATATATCTTTTATGAGTATTGTGGCAAAAAATTG
* * *
3656 AGGAAAAAAATTTTCGGATCAGTTTTTGGCGAAACCGTGTACTAACCATCACGGTTTTTGGCTAA
1 A-GAAAAAAATTTTCGGGTCAGTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA
* * * *
3721 AAACGCGTTCCGGAGCGCCGGCTCAATTTTGCATGATTTTTGGCCCAAAGACTCCTTGAATTATT
65 AAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATC
* * *
3786 TATATTCATCAAACCAAATGTCAGCCACATTGGATATAAGGATTTGCTTTTACGAGCATATGAAT
130 TATATTCATCGAACCAAATGTCAGCAACATTGGATATAAGGATTTGCTTTTACGAGCATCTGAAT
*
3851 CTTGTTTTGA--T--TTAGAAATTAATTCGCAAAACAAATGAAAAAAAATGATATTAGAAGCGTG
195 CTTGTTTCGATTTAATTAGAAATTAATTCGCAAAA-AAATGAAAAAAAATGATATTAGAAGCGTG
* * *
3912 AAAAGCACATTAATATTTTTGGCATTGAATTATATATCTTTTATGAGTATTGTGGCAAAAAACTG
259 AAAAGCCCTTTAATATTTTTGGCATTGAATTATATATCTTTTATGAGTATTGTGGCAAAAAATTG
* * *
3977 AGAAAAAATTTTTCGGGTTAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGCTAA
1 AGAAAAAAATTTTCGGGTCAGTTTTT-GCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA
* * * * *
4042 AAAGGCGTTCCGGAGCCCCGGCTCAGTTTTGCCTGTTTTTTAGCGCAAAGACTCCTTGAAATATC
65 AAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATC
* * ** * *
4107 TATATTCATCGAACCAAATCTCAGCAATATTGGATATAAGGATTTATTTTTTCGAGCATCTCAAT
130 TATATTCATCGAACCAAATGTCAGCAACATTGGATATAAGGATTTGCTTTTACGAGCATCTGAAT
* * * *
4172 CTTGTTTCGATTTAATCAGAAATTAATTCGGAAAAAAATG--GAAAAATGATATTAAAAGCGTG-
195 CTTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATGAAAAAAAATGATATTAGAAGCGTGA
** * * * * *
4234 AAAGGTCTGTCAATCTTTTTGGCGTTGAATTATATATCTTTTCT-ATGTATTGTGTCAAAAAATT
260 AAAGCCCT-TTAATATTTTTGGCATTGAATTATATATCTTTTATGA-GTATTGTGGCAAAAAATT
4298 G
323 G
* **
4299 AGAAAAAAA-TTTCAGGTCAGTTTTTGGCCGAAATTATGTACTAACCATCACGGTTTTTGGCTAA
1 AGAAAAAAATTTTCGGGTCAGTTTTT-GCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA
* * ** *
4363 AAACGCATTCTGGAGCCCCTACTCAATTTTGCATGATTTTTGGCGTAAAGACTCCTTGAAATATC
65 AAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATC
* * *
4428 TATATTAATCAAACCAAATGTCAGCCACATTGGATATAAGGATTTGCTTTTACGAGCATCTGAAT
130 TATATTCATCGAACCAAATGTCAGCAACATTGGATATAAGGATTTGCTTTTACGAGCATCTGAAT
* * *
4493 CTTGTTTCGATTTAATTCGAGATTAATTCGCAAAAAAATGAAAAAAAAATGATATTAGAAGCGTA
195 CTTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATG-AAAAAAAATGATATTAGAAGCGTG
* *
4558 AAAAGCCCGTTAATATTTTTGGCATTGAATTATTTATCTTTTATGAGTATTGTGGCAAAAAATTG
259 AAAAGCCCTTTAATATTTTTGGCATTGAATTATATATCTTTTATGAGTATTGTGGCAAAAAATTG
* * ** *
4623 AGAAAAAAATTTCCGGGTTAGTTTTTAGCCGAAATCGTGTA-T--GTATCACGGTTTTTGCCT-A
1 AGAAAAAAATTTTCGGGTCAGTTTTT-GCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA
* * * * *
4684 AAAGGTGTTTCGGAGCCCCGGCTCAATTTTGCATGCTTTTTGGCGCAAAGACTCCTTGGAATATC
65 AAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATC
* * * * * * *
4749 TATATTCATCGAACCAAATCTCAACAATATTGGATATAAGGATTAGTTTTTTCGAGCATCTCAAT
130 TATATTCATCGAACCAAATGTCAGCAACATTGGATATAAGGATTTGCTTTTACGAGCATCTGAAT
* *
4814 CTTGTTTCGATTTAATTAGAAATTAATTCG-GAAAAAATG--GAAAAATGATATTAGAAGCGTGA
195 CTTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATGAAAAAAAATGATATTAGAAGCGTG-
* *
4876 AAGGCCCCCGTCAATCTTTTTGGCGCTGAATTATATATCTTTTCTTGGCGTTGAATTATATATCT
259 AA----------AA--------GCCCT---TTA-ATA---TTT-TTGGCATTGAATTATATATCT
* * * *
4941 TTTCTGTGTATTATGGCAAAAAATTC
298 TTTATGAGTATTGTGGCAAAAAATTG
*
4967 AGAAAACAAATTTTCGGATCAGTTTTTGACCGAAATCGTGTACTAACCATCACGGTTTTTGGC-A
1 AGAAAA-AAATTTTCGGGTCAGTTTTTG-CCGAAATCGTGTACTAACCATCACGGTTTTTGGCTA
* * * *
5031 AAGAAGGCGTTCCAGAGCCCCGACTCAATTTTGCATGATTTTTGGCGCAAAAACTCCTTGAAATA
64 AA-AACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATA
* * * *
5096 TCTATATTCATCGAACCAAATCTCAGCAATATTGGATATAAGGATTTGTTTTTACGAGCATTTGA
128 TCTATATTCATCGAACCAAATGTCAGCAACATTGGATATAAGGATTTGCTTTTACGAGCATCTGA
* *
5161 ATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATTG--AAAAAACGATATTAGAAGC
193 ATCTTGTTTCGATTTAATTAGAAATTAATTC-GCAAAAAAA-TGAAAAAAAATGATATTAGAAGC
* * * * * * *
5224 GTGAAATG-CCTGTTAATCTTTTTGGCTTTGAATTATATAT-TTTTCTGGGTATTGTGGTAAAAT
256 GTGAAAAGCCCT-TTAATATTTTTGGCATTGAATTATATATCTTTTATGAGTATTGTGGCAAAAA
*
5287 TTTG
320 ATTG
* * * * ** ** **
5291 AG---AAACTTTT-TGGTTAGTTTTTAGCTGAAATCGTGTAAC-AATTATCTTGGTTTTTTTTTA
1 AGAAAAAAATTTTCGGGTCAGTTTTT-GCCGAAATCGTGT-ACTAACCATCACGG---TTTTTGG
* *** * * ** * ** *
5351 CTAAAAACGCCTTTAAG-GCCACTGCTCTGTTTTGCATGGTTTTTGGCGCTTAGACTCCTTGAAT
61 CTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAA
* * * * * ** * * * * * *
5415 TATCTTTATT-AGTCTAATCAAATCTCAACCGCATCGGATTTAGGGATTTGGTTTTAGGTGCATC
126 TATCTATATTCA-TCGAACCAAATGTCAGCAACATTGGATATAAGGATTTGCTTTTACGAGCATC
* * * * * *
5479 AGAATCTTGTTTCGATTTAAATAAAAATTTATTCAG-AAAAAATATG---AAAAACGATATTAAA
190 TGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GCAAAAAA-ATGAAAAAAAATGATATTAGA
* * * * *
5540 AGCGTGAAAAGTCCTTCAATCTTTCT-GCGTTGAATTATATAT
253 AGCGTGAAAAGCCCTTTAATATTTTTGGCATTGAATTATATAT
5582 ATAAATATAT
Statistics
Matches: 2199, Mismatches: 295, Indels: 150
0.83 0.11 0.06
Matches are distributed among these distances:
315 283 0.13
316 1 0.00
317 20 0.01
318 17 0.01
319 60 0.03
320 51 0.02
321 717 0.33
322 109 0.05
323 5 0.00
324 128 0.06
325 488 0.22
326 25 0.01
328 2 0.00
329 2 0.00
330 3 0.00
332 2 0.00
333 1 0.00
336 3 0.00
339 3 0.00
340 3 0.00
341 1 0.00
343 3 0.00
344 48 0.02
345 30 0.01
346 1 0.00
348 16 0.01
349 146 0.07
350 1 0.00
351 8 0.00
352 22 0.01
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (323 bp):
AGAAAAAAATTTTCGGGTCAGTTTTTGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAA
AACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCT
ATATTCATCGAACCAAATGTCAGCAACATTGGATATAAGGATTTGCTTTTACGAGCATCTGAATC
TTGTTTCGATTTAATTAGAAATTAATTCGCAAAAAAATGAAAAAAAATGATATTAGAAGCGTGAA
AAGCCCTTTAATATTTTTGGCATTGAATTATATATCTTTTATGAGTATTGTGGCAAAAAATTG
Found at i:4930 original size:25 final size:25
Alignment explanation
Indices: 4895--4945 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
4885 GTCAATCTTT
4895 TTGGCGCTGAATTATATATCTTTTC
1 TTGGCGCTGAATTATATATCTTTTC
*
4920 TTGGCGTTGAATTATATATCTTTTC
1 TTGGCGCTGAATTATATATCTTTTC
4945 T
1 T
4946 GTGTATTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.51
Consensus pattern (25 bp):
TTGGCGCTGAATTATATATCTTTTC
Found at i:8866 original size:15 final size:15
Alignment explanation
Indices: 8846--8875 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
8836 GGAAATTAAG
8846 AAACTTCAATACTAA
1 AAACTTCAATACTAA
8861 AAACTTCAATACTAA
1 AAACTTCAATACTAA
8876 CCTTCTTGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (15 bp):
AAACTTCAATACTAA
Done.