Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014529.1 Corchorus capsularis cultivar CVL-1 contig14550, 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: 27617
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4462 original size:32 final size:32
Alignment explanation
Indices: 4403--4538 Score: 166
Period size: 33 Copynumber: 4.2 Consensus size: 32
4393 GTCTCCCCAC
* * *
4403 TGGGGCAGCTTCACCATGGGCAGGCCGCCC-CA
1 TGGGGCGGCTTCGCCA-AGGCAGGCCGCCCTCA
*
4435 CCGGGGCGGCTTCGCCAAGGCAGGCCGCCCTCA
1 -TGGGGCGGCTTCGCCAAGGCAGGCCGCCCTCA
*
4468 TGGGACGGCTTCGCTCAAGGCAGGCCGCCCTCA
1 TGGGGCGGCTTCGC-CAAGGCAGGCCGCCCTCA
* **
4501 TGGGGCGGCTTCGCCACGGCAAACCGCCCTCA
1 TGGGGCGGCTTCGCCAAGGCAGGCCGCCCTCA
4533 TGGGGC
1 TGGGGC
4539 AACCGGGGCG
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
32 45 0.49
33 46 0.51
ACGTcount: A:0.14, C:0.38, G:0.35, T:0.12
Consensus pattern (32 bp):
TGGGGCGGCTTCGCCAAGGCAGGCCGCCCTCA
Found at i:4639 original size:34 final size:33
Alignment explanation
Indices: 4543--4681 Score: 165
Period size: 34 Copynumber: 4.2 Consensus size: 33
4533 TGGGGCAACC
* * *
4543 GGGGCGGCCTGCCC-TGGCGAAGTCGCCCGAGT
1 GGGGCGGCCTGCCCATGGTGAAGCCGCCCTAGT
*** * *
4575 GGGGCGGCCTATTCATAGTGAAGCCACCCTAGT
1 GGGGCGGCCTGCCCATGGTGAAGCCGCCCTAGT
4608 GGGGCGGCCTGCCCAATGGTGAAGCCGCCCTAGT
1 GGGGCGGCCTGCCC-ATGGTGAAGCCGCCCTAGT
**
4642 GGGGCGGCCTGCCCATGGT-AAGCCGCCCTCTT
1 GGGGCGGCCTGCCCATGGTGAAGCCGCCCTAGT
4674 GGGGCGGC
1 GGGGCGGC
4682 ACGGGTCATC
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
32 30 0.33
33 29 0.32
34 31 0.34
ACGTcount: A:0.13, C:0.32, G:0.39, T:0.16
Consensus pattern (33 bp):
GGGGCGGCCTGCCCATGGTGAAGCCGCCCTAGT
Found at i:5317 original size:21 final size:21
Alignment explanation
Indices: 5272--5317 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5262 TTCTCATCAG
* * **
5272 TACAGTAACAAATTTTATATG
1 TACAGTAACAAATCTAATACA
5293 TACAGTAACAAATCTAATACA
1 TACAGTAACAAATCTAATACA
5314 TACA
1 TACA
5318 ATAATCAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (21 bp):
TACAGTAACAAATCTAATACA
Found at i:9584 original size:29 final size:29
Alignment explanation
Indices: 9542--9612 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
9532 TTTAGGGGAT
*
9542 AAAACGTTCCAAAATTGAA-GTTCAGAGGGT
1 AAAACG-TCCAAAATT-AATGTTCAGAGGGC
* * *
9572 AAAATGTCCAAAATTAATGTTTAGGGGGC
1 AAAACGTCCAAAATTAATGTTCAGAGGGC
9601 AAAACGTCCAAA
1 AAAACGTCCAAA
9613 CGGAACAAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.06
29 28 0.80
30 5 0.14
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (29 bp):
AAAACGTCCAAAATTAATGTTCAGAGGGC
Found at i:11982 original size:14 final size:14
Alignment explanation
Indices: 11963--11995 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
11953 ACCACCAAAA
11963 ATTAGACTGTGGTT
1 ATTAGACTGTGGTT
11977 ATTAGACTGTGGTT
1 ATTAGACTGTGGTT
*
11991 CTTAG
1 ATTAG
11996 TTTTTACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.09, G:0.27, T:0.42
Consensus pattern (14 bp):
ATTAGACTGTGGTT
Found at i:13743 original size:31 final size:29
Alignment explanation
Indices: 13705--13762 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
13695 AAAAAGTACT
13705 AAATTGGACCATTAATAAAACGTTTGGTATG
1 AAATTGGACCA--AATAAAACGTTTGGTATG
* *
13736 AAATTGGACGAAATAAAAGGTTTGGTA
1 AAATTGGACCAAATAAAACGTTTGGTA
13763 CCAAATTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.60
31 10 0.40
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.29
Consensus pattern (29 bp):
AAATTGGACCAAATAAAACGTTTGGTATG
Found at i:13768 original size:29 final size:29
Alignment explanation
Indices: 13700--13801 Score: 78
Period size: 31 Copynumber: 3.4 Consensus size: 29
13690 ACCTGAAAAA
* *
13700 GTACTAAATTGGACCATTAATAAAACGTTTG
1 GTACCAAATTGGACCA--AATAAAAGGTTTG
** *
13731 GTATGAAATTGGACGAAATAAAAGGTTTG
1 GTACCAAATTGGACCAAATAAAAGGTTTG
** ** *
13760 GTACCAAATTACTATTAAACATAAAGGTTTG
1 GTACCAAATT-GGACCAAATA-AAAGGTTTG
13791 GTACCAAATTG
1 GTACCAAATTG
13802 AGATTTCAGC
Statistics
Matches: 57, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
29 20 0.35
30 5 0.09
31 32 0.56
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (29 bp):
GTACCAAATTGGACCAAATAAAAGGTTTG
Found at i:17640 original size:320 final size:319
Alignment explanation
Indices: 16644--18432 Score: 871
Period size: 309 Copynumber: 5.6 Consensus size: 319
16634 CGACTCAGTT
* * * * *
16644 TTGCAT-ACTTTTTGGCA-TAAAGACTCCTTGAAATATCTATA-TCAATCTAATCAAACCTCATC
1 TTGCATGA-TTTTTGG-AGTAAAGCCTCCTTGAAATATCTATATTC-ATCGAACCAAATCTCAGC
* * * * *
16706 CACATTGGATTTAAGGATTTGTTTTTACGAGTATCTAAATCTTGTTTCGATTTAATTA-AATATA
63 CACATTGTATGTAAGGATTTGGTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTACAA-ATA
* * * * **
16770 AATTCGGAAAAAAA-ATGGAAAAATGATATTAGAAGCGTAAAAAACCCTTCAATTTTTTTACCGT
127 AATTC-GAAAAAAAGAAGGAAAAACGATATAAGAAGCGTGAAAAACCCTTCAA-TTTTTTGGCGT
* * * * ** **
16834 TAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTTTGACAA
190 TAAATTATATATTTCTTCTGAGTATTATGAC-AAAAATTCA-G-AAAGTTTTTTAGG---G-C-A
* * * ** * * * * * * * * * **
16899 AATTTTAGCCGAAATCGTGTACTAAGCAACACGATCTTTTACAAAAAAAAAACGTGTTCCGA-AA
247 GATGTTAGCCAAAATCAAGTACGATGCATCACGGTTTTTTGC----TAAAAACGCGATCCGAGGC
* *
16963 CCCTGACTCAATT
308 CCCAG-CTCAATC
* ** * * * * * *
16976 TTGAATGATTTTT-GACCCAAAGACTCCTTGGAATATCTATATTCATCTAACAAAATATCAACCA
1 TTGCATGATTTTTGGA-GTAAAGCCTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCA
* * ** * * *
17040 CATTGAATGTAAGAATTTATTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAAT
65 CATTGTATGTAAGGATTTGGTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTACAAATAAAT
* * * * *
17105 TCG----AAA-AA-CAAAAACAATATTAGAAGCGTGAAAAAAACCTTCAAATTTTTTTTTTGCGT
130 TCGAAAAAAAGAAGGAAAAACGATATAAGAAGCGTG-AAAAACCCTTC-AA---TTTTTTGGCGT
* * * * * * * * *
17164 TGAATTATATAATTT-TTTTGACTATTGTGGCCAAAAATTGAGGAAAAAAAATTTTCTA-GTCAG
190 TAAATTATAT-ATTTCTTCTGAGTATTAT-GACAAAAATTCA-G----AAAGTTTTTTAGGGCAG
* * *
17227 -TTTTTG-CAAAAT----T----T---TCACGGTTTTTTGCTAAAAAGGCGATCCGAGGCCCCAG
248 ATGTTAGCCAAAATCAAGTACGATGCATCACGGTTTTTTGCTAAAAACGCGATCCGAGGCCCCAG
*
17279 CTCAGTC
313 CTCAATC
* * *
17286 TTGCATGATTTTTGGCGTAAAGTCTCCTTGAAATATCTATATTCATCGAATCAAAT-TCCAGCCA
1 TTGCATGATTTTTGGAGTAAAGCCTCCTTGAAATATCTATATTCATCGAACCAAATCT-CAGCCA
* * * * * * *
17350 CATTCG-ATTTAAGGATTT-GTTTTTCGAGTATCTAAATCTTGTTTCGATTTAATTAGAGATTAA
65 CATT-GTATGTAAGGATTTGGTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTACAAATAAA
** * ** ** * *
17413 TTCGGGGAAGAA-ATTGAAAAACGATATAAGAAGCGTGAAAAATTCTTCAATATTTTTGGTGTTG
129 TTC-GAAAAAAAGAAGGAAAAACGATATAAGAAGCGTGAAAAACCCTTCAAT-TTTTTGGCGTTA
17477 AATTATATATTT-TTCCTGAGTATTATGACAAAAATTCAGAAAGTTTTTTAGGGCAGATGTTAGC
192 AATTATATATTTCTT-CTGAGTATTATGACAAAAATTCAGAAAGTTTTTTAGGGCAGATGTTAGC
* * * * *
17541 CAAAATCAAGTACGATGCATCACGGTTTTTGTGCTAAAAACGCGTTTCGAGGTCCCGGCTCAATT
256 CAAAATCAAGTACGATGCATCACGGTTTTT-TGCTAAAAACGCGATCCGAGGCCCCAGCTCAATC
*
17606 TTGCATGATTTTTTGTAG-AAAGACCT-CTTGAAATATCTATATTCATCGAACCAAATCTCAGCC
1 TTGCATGA-TTTTTGGAGTAAAG-CCTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCC
*
17669 ACATTGTATGTAAGGATTTGGTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTACAAATAAA
64 ACATTGTATGTAAGGATTTGGTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTACAAATAAA
* * *
17734 TTCGAAAAAAAGAAGGGAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGCGTTAAA
129 TTCGAAAAAAAGAAGGAAAAACGATATAAGAAGCGTGAAAAACCCTTCAATTTTTTGGCGTTAAA
* * ** ** * * * *
17799 TTATATATTTCTTCTGAGTATTGTGGCAAGAAATTGGGGAAAACTTTTCAGGTCAG-TTTTTG-C
194 TTATATATTTCTTCTGAGTATTATGACAA-AAATT-CAGAAAGTTTTTTAGGGCAGATGTTAGCC
** * * * * * *
17862 AAAAT--TTTA-GCTGAAATCGTCGGTTTTTGGCTAAAGACGCGTTCC-AGAGCCCC-G------
257 AAAATCAAGTACGATG-CATC-ACGGTTTTTTGCTAAAAACGCGATCCGAG-GCCCCAGCTCAAT
17916 -
319 C
* * * * * * * * *
17916 -GGCATGATTTTTGG-CTCAAAGACTCTTTCAAATATCTATATTCGTCGAACCATATCTCATCAA
1 TTGCATGATTTTTGGAGT-AAAGCCTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCA
* * * * * * **
17979 CATTGGATATAAGGATTTGGTTTTACGAGCATCTGAATCTTATTTCGATATAATTATTAATAAAT
65 CATTGTATGTAAGGATTTGGTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTACAAATAAAT
* * * * * * **
18044 TCGAAAAAAA-AA--AAAAACGATATTATAAGCTTGAAAAGCCCGTCAATTTTTTTGGCTTTGTA
130 TCGAAAAAAAGAAGGAAAAACGATATAAGAAGCGTGAAAAACCCTTCAA-TTTTTTGGCGTTAAA
* * *** * * * *
18106 TTATATATTT-TTCTTAGTATTGT-AGCAAAAAATTCAGAAAAAATTTTCGAGTCAGTTTTTAGC
194 TTATATATTTCTTCTGAGTATTATGA-C-AAAAATTCAGAAAGTTTTTTAG-GGCAGATGTTAGC
** ** * * * * * ** **
18169 TGAAATCGTGTACTAAT-CATCACAGTTTTTGGGCTAAAAACGCGTTTC-AGGGTTCTGGCTCAA
256 CAAAATCAAGTAC-GATGCATCACGGTTTTT-TGCTAAAAACGCGATCCGA-GGCCCCAGCTCAA
*
18232 TT
318 TC
* * * * * * **
18234 TTTCATGATTTTTGACAG-AAAGACTCATTTAAATATCTATATTCATCTAACCAAATCAAAGCCA
1 TTGCATGATTTTTG-GAGTAAAGCCTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCA
* * * * * * * * *
18298 CATTGGATTTAATGATTTGTTTTTACGAGAATCTGAAA-CTTGTTTCGATTTAATAAGAAATCAA
65 CATTGTATGTAAGGATTTGGTTTTACGAGCATCT-AAATCTTGTTTCAATTTAATTACAAATAAA
* * * ** * * *
18362 TTC--AAAAAA-ATGGAAAAACGATATTACAAGCGTGAAAAAATCTTCAATTTTTT-TCCTTGAA
129 TTCGAAAAAAAGAAGGAAAAACGATATAAGAAGCGTGAAAAACCCTTCAATTTTTTGGCGTTAAA
18423 TTATATATTT
194 TTATATATTT
18433 TCTTTGACTA
Statistics
Matches: 1156, Mismatches: 219, Indels: 179
0.74 0.14 0.12
Matches are distributed among these distances:
305 18 0.02
306 56 0.05
307 32 0.03
308 20 0.02
309 161 0.14
310 123 0.11
311 34 0.03
312 2 0.00
313 2 0.00
314 22 0.02
315 19 0.02
316 1 0.00
317 28 0.02
318 29 0.03
319 149 0.13
320 137 0.12
321 96 0.08
322 14 0.01
325 5 0.00
326 23 0.02
327 15 0.01
328 3 0.00
330 42 0.04
331 8 0.01
332 104 0.09
333 13 0.01
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (319 bp):
TTGCATGATTTTTGGAGTAAAGCCTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCAC
ATTGTATGTAAGGATTTGGTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTACAAATAAATT
CGAAAAAAAGAAGGAAAAACGATATAAGAAGCGTGAAAAACCCTTCAATTTTTTGGCGTTAAATT
ATATATTTCTTCTGAGTATTATGACAAAAATTCAGAAAGTTTTTTAGGGCAGATGTTAGCCAAAA
TCAAGTACGATGCATCACGGTTTTTTGCTAAAAACGCGATCCGAGGCCCCAGCTCAATC
Found at i:18199 original size:309 final size:309
Alignment explanation
Indices: 17636--18432 Score: 774
Period size: 319 Copynumber: 2.6 Consensus size: 309
17626 AGACCTCTTG
* * *
17636 AAATATCTATATTCATCGAACCAAATCTCAGCCACATTGTATGTAAGGATTTGGTTTTACGAGCA
1 AAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAAGGATTTGGTTTTACGAGCA
* * *
17701 TCTGAATCTTGTTTCAATTTAATTACAAATAAATTCGAAAAAAAGAAGGGAAAACGATATTAGAA
66 TCTGAATCTTATTTCAATATAATTACAAATAAATTCGAAAAAAAGAA-GAAAAACGATATTAGAA
* * *
17766 GCGTGAAAAACCCTTCAATTTTTTTGCGTTAAATTATATATTTCTTCTGAGTATTGTGGCAAGAA
130 GCGTGAAAAACCCGTCAATTTTTTTGCGTTAAATTATATATTTCTTCTGAGTATTGTAGCAAAAA
** * * * * *
17831 ATTGGGGAAAACTTTTCAGGTCAGTTTTTGCAAAATTTTAGCTGAAATCGTCGGTTTTT-GGCTA
195 ATTCAGAAAAAATTTTCAGGTCAGTTTTTGCAAAATTGTAGCTGAAATCGACAGTTTTTGGGCTA
*
17895 AAGACGCGTTCCAGAGCCCCGGGCATGATTTTTGGCTCAAAGACTCTTTC
260 AAAACGCGTTCCAGAGCCCCGGGCATGATTTTTGGCTCAAAGACTCTTTC
* * *
17945 AAATATCTATATTCGTCGAACCATATCTCATCAACATTGGATATAAGGATTTGGTTTTACGAGCA
1 AAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAAGGATTTGGTTTTACGAGCA
* ** *
18010 TCTGAATCTTATTTCGATATAATTATTAATAAATTCGAAAAAAA-AA-AAAAACGATATTATAAG
66 TCTGAATCTTATTTCAATATAATTACAAATAAATTCGAAAAAAAGAAGAAAAACGATATTAGAAG
* * * ** *
18073 CTTGAAAAGCCCGTCAATTTTTTTGGCTTTGTATTATATATTT-TTCTTAGTATTGTAGCAAAAA
131 CGTGAAAAACCCGTCAATTTTTTT-GCGTTAAATTATATATTTCTTCTGAGTATTGTAGCAAAAA
*
18137 ATTCAGAAAAAATTTTC-GAGTCAGTTTTTAGCTGAAATCGTGTA-CT-AATCATC-ACAGTTTT
195 ATTCAGAAAAAATTTTCAG-GTCAGTTTTT-GC-AAAAT--TGTAGCTGAA--ATCGACAGTTTT
* * **** * **
18198 TGGGCTAAAAACGCGTTTCAGGGTTCTGGCTCAATTTTTCATGATTTTTGACAGAAAGACTCATT
253 TGGGCTAAAAACGCGTTCCAGAG--C---C-C---CGGGCATGATTTTTGGCTCAAAGACTC-TT
18263 T-
308 TC
* ** * * * * *
18264 AAATATCTATATTCATCTAACCAAATCAAAGCCACATTGGATTTAATGATTTGTTTTTACGAGAA
1 AAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAAGGATTTGGTTTTACGAGCA
* * * * * * * *
18329 TCTGAAACTTGTTTCGATTTAATAAGAAATCAATTC-AAAAAAATG--GAAAAACGATATTACAA
66 TCTGAATCTTATTTCAATATAATTACAAATAAATTCGAAAAAAA-GAAGAAAAACGATATTAGAA
** * * *
18391 GCGTGAAAAAATCTTCAATTTTTTT-CCTTGAATTATATATTT
130 GCGTGAAAAACCCGTCAATTTTTTTGCGTTAAATTATATATTT
18433 TCTTTGACTA
Statistics
Matches: 400, Mismatches: 66, Indels: 36
0.80 0.13 0.07
Matches are distributed among these distances:
305 1 0.00
306 77 0.19
307 17 0.04
308 8 0.02
309 107 0.27
310 24 0.06
312 1 0.00
315 1 0.00
316 1 0.00
317 15 0.04
318 7 0.02
319 138 0.34
320 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (309 bp):
AAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAAGGATTTGGTTTTACGAGCA
TCTGAATCTTATTTCAATATAATTACAAATAAATTCGAAAAAAAGAAGAAAAACGATATTAGAAG
CGTGAAAAACCCGTCAATTTTTTTGCGTTAAATTATATATTTCTTCTGAGTATTGTAGCAAAAAA
TTCAGAAAAAATTTTCAGGTCAGTTTTTGCAAAATTGTAGCTGAAATCGACAGTTTTTGGGCTAA
AAACGCGTTCCAGAGCCCCGGGCATGATTTTTGGCTCAAAGACTCTTTC
Found at i:18276 original size:628 final size:616
Alignment explanation
Indices: 16652--18442 Score: 1749
Period size: 628 Copynumber: 2.8 Consensus size: 616
16642 TTTTGCATAC
* *
16652 TTTTTGGCATAAAGACTCCTTGAAATATCTATA-TCAATCTAATCAAACCTCATCCACATTGGAT
1 TTTTTGGCATAAAGACTCCTTGAAATATCTATATTC-ATCGAATCAAATCTCATCCACATTGGAT
* *
16716 TTAAGGATTTGTTTTTACGAGTATCTAAATCTTGTTTCGATTTAATTAAATATAAATTCGGAAAA
65 TTAAGGATTTGGTTTTACGAGTATCTAAATCTTGTTTCGATTTAATTAAAGATAAATTCGGAAAA
* * ** * *
16781 AAAATGGAAAAATGATATTAGAAGCGTAAAAAACCCTTCAATTTTTTTACCGTTAAATTATATAT
130 AAAA--GAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCTTTGAATTATATA-
* * *
16846 TTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTTTGACAAAATTTTAGCCGA
192 TTTTTCTGAGTATTGT-GCAAAAAATTCA-GAAAAAATTTTC-GG--T--C-AGATTTTAGCCGA
* * * *** * * *** *
16911 AATCGTGTACTAAGCAACACGATCTTTTACAAAAAAAAAACGTGTTCCGAAACCCTGACTCAATT
249 AATCGTGTACTAATCATCACG-T-TTTTGC--GCTAAAAACGCGTTTCGAGGTCCTGGCTCAATT
* ** * * * *
16976 TTGAATGATTTTTGACCCAAAGACTCCTTGGAATATCTATATTCATCTAACAAAATATCAACCAC
310 TTGCATGATTTTTGACAGAAAGACT-CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCAC
* * *
17041 ATTGAATGTAAGAATTTATTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAATT
374 ATTGAATGTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATAAATT
* *
17106 CG-AAAAACA--AAAACAATATTAGAAGCGTGAAAAAAACCTTCAAATTTTTTTTTTGCGTTGAA
439 CGAAAAAAAAGGAAAACGATATTAGAAGCGTG-AAAAAACCTTC-AA---TTTTTTTGCGTTGAA
*
17168 TTATATAATTTTTTTGACTATTGTGGCCAAAAATTGAGGAAAAAAAATTTTCTAGTCAGTTTTTG
499 TTATAT-ATTTTTCTGACTATTGTGGCCAAAAATTGAGG-AAAAAAATTTTCTAGTCAGTTTTTG
* *
17233 CAAAATTTTCACGGTTTTTTGCTAAAAAGGCGATCCGAGGCCCCAGCTCAGTCTTGCATGA
562 CAAAATTTTCACGGTTTTTGGCTAAAAACGCGATCCGAGGCCCCAG--C-G---TGCATGA
* * * *
17294 TTTTTGGCGTAAAGTCTCCTTGAAATATCTATATTCATCGAATCAAAT-TCCAGCCACATTCGAT
1 TTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGAATCAAATCT-CATCCACATTGGAT
* * *
17358 TTAAGGATTT-GTTTTTCGAGTATCTAAATCTTGTTTCGATTTAATTAGAGATTAATTCGGGGAA
65 TTAAGGATTTGGTTTTACGAGTATCTAAATCTTGTTTCGATTTAATTAAAGATAAATTC--GGAA
* ** * ** *
17422 GAAATTGAAAAACGATATAAGAAGCGTGAAAAATTCTTCAATATTTTTGG-TGTTGAATTATATA
128 AAAAAAGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCT-TTGAATTATATA
* *** * * * * **
17486 TTTTTCCTGAGTATTATG-ACAAAAATTCAGAAAGTTTTTTAGGGCAGATGTTAGCCAAAATCAA
192 TTTTT-CTGAGTATTGTGCA-AAAAATTCAGAAAAAATTTTCGGTCAGATTTTAGCCGAAATCGT
* * *
17550 GTAC-GATGCATCACGGTTTTTGTGCTAAAAACGCGTTTCGAGGTCCCGGCTCAATTTTGCATGA
255 GTACTAAT-CATCAC-GTTTTTGCGCTAAAAACGCGTTTCGAGGTCCTGGCTCAATTTTGCATGA
* * *
17614 TTTTTTG-TAGAAAGACCTCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGTAT
318 -TTTTTGACAGAAAGA-CTCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAAT
* *
17678 GTAAGGATTTGGTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTACAAATAAATTCGAAAAA
381 GTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATAAATTCG-AAAA
* *
17743 AAGAAGGGAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGCGTTAAATTATATATT
445 AA-AA-GGAAAACGATATTAGAAGCGTGAAAAAACCTTCAATTTTTTTGCGTTGAATTATATATT
* * *
17808 TCTTCTGAGTATTGTGG-CAAGAAATTG-GG-GAAAACTTTTC-AGGTCAGTTTTTGCAAAATTT
508 T-TTCTGACTATTGTGGCCAA-AAATTGAGGAAAAAAATTTTCTA-GTCAGTTTTTGCAAAATTT
* *
17869 TAGCTGAAATCGTCGGTTTTTGGCTAAAGACGCGTTCC-AGAGCCCC-G-G-GCATGA
570 T--C----A----CGGTTTTTGGCTAAAAACGCGATCCGAG-GCCCCAGCGTGCATGA
* * * * * *
17923 TTTTTGGC-TCAAAGACTCTTTCAAATATCTATATTCGTCGAACCATATCTCATCAACATTGGAT
1 TTTTTGGCAT-AAAGACTCCTTGAAATATCTATATTCATCGAATCAAATCTCATCCACATTGGAT
* * * * * *
17987 ATAAGGATTTGGTTTTACGAGCATCTGAATCTTATTTCGATATAATTATTA-ATAAATTC-GAAA
65 TTAAGGATTTGGTTTTACGAGTATCTAAATCTTGTTTCGATTTAATTA-AAGATAAATTCGGAAA
* * * * * *
18050 AAAAAAAAAAACGATATTATAAGCTTGAAAAGCCCGTCAATTTTTTTGGCTTTGTATTATATATT
129 AAAAAGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCTTTGAATTATATATT
* * *
18115 TTTCTTAGTATTGTAGCAAAAAATTCAGAAAAAATTTTCGAGTCAGTTTTTAGCTGAAATCGTGT
194 TTTCTGAGTATTGT-GCAAAAAATTCAGAAAAAATTTTCG-GTCAGATTTTAGCCGAAATCGTGT
* * *
18180 ACTAATCATCACAGTTTTTGGGCTAAAAACGCGTTTC-AGGGTTCTGGCTCAATTTTTCATGATT
257 ACTAATCATCAC-GTTTTTGCGCTAAAAACGCGTTTCGA-GGTCCTGGCTCAATTTTGCATGATT
* ** * *
18244 TTTGACAGAAAGACTCATTTAAATATCTATATTCATCTAACCAAATCAAAGCCACATTGGATTTA
320 TTTGACAGAAAGACTC-TTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATGTA
* * * * * * *
18309 ATGATTTGTTTTTACGAGAATCTGAAACTTGTTTCGATTTAATAAGAAATCAATTC-AAAAAAAT
384 AGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATAAATTCGAAAAAAAA
* * * *
18373 GGAAAAACGATATTACAAGCGTGAAAAAATCTTCAATTTTTTT-CCTTGAATTATATATTTTCTT
449 GG-AAAACGATATTAGAAGCGTGAAAAAACCTTCAATTTTTTTGCGTTGAATTATATATTTT-TC
18437 TGACTA
512 TGACTA
18443 GAAACGCGTT
Statistics
Matches: 954, Mismatches: 150, Indels: 108
0.79 0.12 0.09
Matches are distributed among these distances:
623 1 0.00
624 23 0.02
625 38 0.04
626 15 0.02
627 87 0.09
628 197 0.21
629 68 0.07
630 180 0.19
631 48 0.05
632 10 0.01
633 26 0.03
634 5 0.01
635 10 0.01
636 19 0.02
637 3 0.00
638 28 0.03
639 9 0.01
640 14 0.01
641 101 0.11
642 63 0.07
643 9 0.01
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (616 bp):
TTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCGAATCAAATCTCATCCACATTGGATT
TAAGGATTTGGTTTTACGAGTATCTAAATCTTGTTTCGATTTAATTAAAGATAAATTCGGAAAAA
AAAGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCTTTGAATTATATATTTT
TCTGAGTATTGTGCAAAAAATTCAGAAAAAATTTTCGGTCAGATTTTAGCCGAAATCGTGTACTA
ATCATCACGTTTTTGCGCTAAAAACGCGTTTCGAGGTCCTGGCTCAATTTTGCATGATTTTTGAC
AGAAAGACTCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGAATGTAAGGATTT
GTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATAAATTCGAAAAAAAAGGAAAAC
GATATTAGAAGCGTGAAAAAACCTTCAATTTTTTTGCGTTGAATTATATATTTTTCTGACTATTG
TGGCCAAAAATTGAGGAAAAAAATTTTCTAGTCAGTTTTTGCAAAATTTTCACGGTTTTTGGCTA
AAAACGCGATCCGAGGCCCCAGCGTGCATGA
Found at i:21999 original size:12 final size:12
Alignment explanation
Indices: 21982--22012 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21972 TCCAGCTTGA
21982 TTTTTTTTTCAT
1 TTTTTTTTTCAT
21994 TTTTTTTTTCAT
1 TTTTTTTTTCAT
*
22006 TCTTTTT
1 TTTTTTT
22013 ATTATGTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTCAT
Done.