Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005833.1 Corchorus capsularis cultivar CVL-1 contig05851, 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: 4560
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:113 original size:41 final size:42
Alignment explanation
Indices: 65--246 Score: 239
Period size: 41 Copynumber: 4.4 Consensus size: 42
55 ATTGAGAGCC
* *
65 CTCTCCAAATA-TTAAATTAAAAAGTGACCGATGATAGCTGT
1 CTCTCCAAACATTTAAATTAAAAAGTGACCGATGAGAGCTGT
*
106 CAT-TCCAAACATTTAAATT-AAAAGTGACCGATGAGAGATGT
1 C-TCTCCAAACATTTAAATTAAAAAGTGACCGATGAGAGCTGT
* *
147 CTCTCCAAACATTTAAA-TAAAAAGTGACCGACGAGAGCTAT
1 CTCTCCAAACATTTAAATTAAAAAGTGACCGATGAGAGCTGT
* * **
188 CTCTCCAAATATTT-AGTTAAAAAGTGACCGATGAGAGCAAT
1 CTCTCCAAACATTTAAATTAAAAAGTGACCGATGAGAGCTGT
229 CTCTCCAAACATTTAAAT
1 CTCTCCAAACATTTAAAT
247 CGATGAGAGC
Statistics
Matches: 123, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
40 3 0.02
41 110 0.89
42 10 0.08
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (42 bp):
CTCTCCAAACATTTAAATTAAAAAGTGACCGATGAGAGCTGT
Found at i:373 original size:41 final size:41
Alignment explanation
Indices: 303--487 Score: 169
Period size: 41 Copynumber: 4.5 Consensus size: 41
293 ATTAAAAAAA
* * *
303 AAAATAGTGACTGATGAGAGC--TCTGTCCAAATATTTAATT
1 AAAA-AGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* *
343 AAAAAGTGACCGATGATAGCTGTCTCTCCAAACATTTTACTT
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACA-TTTAATT
* * * *
385 -AAAAGTGACCAATGAGAGCTGTCTCTGCAAAAATTTAAAT
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
* * * * * * *
425 CAAAACTGACCAATGAGAGTTGTCTATCCAAACAATAAATT
1 AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
*
466 AAAAAAATGACCGATGAGAGCT
1 -AAAAAGTGACCGATGAGAGCT
488 ACATCTAAAT
Statistics
Matches: 117, Mismatches: 23, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
39 14 0.12
40 9 0.08
41 71 0.61
42 23 0.20
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (41 bp):
AAAAAGTGACCGATGAGAGCTGTCTCTCCAAACATTTAATT
Found at i:470 original size:260 final size:258
Alignment explanation
Indices: 1--486 Score: 672
Period size: 260 Copynumber: 1.9 Consensus size: 258
*
1 ATCTCTCCAAACATTTAATTAAAAAAGTAACCAACCTTAAAAAAAAAGTGACAAATTGAGAGCCC
1 ATCTCTCCAAACATTTAATTAAAAAAGTAACCAACATTAAAAAAAAAGTGACAAATTGAGAGCCC
66 TCTCCAAATATTAAATTAAAAAGTGACCGATGATAGCTGTCATTCCAAACATTTAAATTAAAAGT
66 TCTCCAAATATTAAATTAAAAAGTGACCGATGATAGCTGTCATTCCAAACATTTAAATTAAAAGT
* * * * *
131 GACCGATGAGAGATGTCTCTCCAAACATTTAAATAAAAAGTGACCGACGAGAGCTATCTCTCCAA
131 GACCAATGAGAGATGTCTCTCCAAAAATTTAAATAAAAACTGACCAACGAGAGCTATCTATCCAA
* * * * *
196 ATATTTAGTT-AAAAAGTGACCGATGAGAGCAATCTCTCCAAACATTTAAATCGATGAGAGCT
196 ACAATAAATTAAAAAAATGACCGATGAGAGCAATCTCTCCAAACATTTAAATCGATGAGAGCT
* * **
258 ATCTCTCCAAACATTTCATTAAAAAAGTGACCAACATTAAAAAAAAAAATAGTGACTGA-TGAGA
1 ATCTCTCCAAACATTTAATTAAAAAAGTAACCAACATT---AAAAAAAA-AGTGACAAATTGAGA
* * * * *
322 GCTCTGTCCAAATATTTAATTAAAAAGTGACCGATGATAGCTGTC-TCTCCAAACATTTTACTTA
62 GCCCTCTCCAAATATTAAATTAAAAAGTGACCGATGATAGCTGTCAT-TCCAAACATTTAAATTA
* * * * * *
386 AAAGTGACCAATGAGAGCTGTCTCTGCAAAAATTTAAATCAAAACTGACCAATGAGAGTTGTCTA
126 AAAGTGACCAATGAGAGATGTCTCTCCAAAAATTTAAATAAAAACTGACCAACGAGAGCTATCTA
451 TCCAAACAATAAATTAAAAAAATGACCGATGAGAGC
191 TCCAAACAATAAATTAAAAAAATGACCGATGAGAGC
487 TACATCTAAA
Statistics
Matches: 197, Mismatches: 26, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
257 35 0.18
259 1 0.01
260 135 0.69
261 26 0.13
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (258 bp):
ATCTCTCCAAACATTTAATTAAAAAAGTAACCAACATTAAAAAAAAAGTGACAAATTGAGAGCCC
TCTCCAAATATTAAATTAAAAAGTGACCGATGATAGCTGTCATTCCAAACATTTAAATTAAAAGT
GACCAATGAGAGATGTCTCTCCAAAAATTTAAATAAAAACTGACCAACGAGAGCTATCTATCCAA
ACAATAAATTAAAAAAATGACCGATGAGAGCAATCTCTCCAAACATTTAAATCGATGAGAGCT
Found at i:2317 original size:332 final size:332
Alignment explanation
Indices: 751--3836 Score: 3772
Period size: 332 Copynumber: 9.3 Consensus size: 332
741 TATTTTGTCT
* * * **
751 AAAAATGAGGAAAAAT-TTT-GGGTCAATTTTTGCAAAATTTTGGCCAAATCGTATACAAAATAT
1 AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCAT
* * * * * * *
814 CGCGG-CTATGGCTAAAAATGCGATCCGGTGCACCGGTTCAGTTTTTCATGATTTTTGGCGCTAA
66 CACGGTTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGCCAA
* * * * *
878 GACTCATTGAAAATATTTGTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAAAAGATTTG
131 GACTCATTG-AAATATATATATTAATCTAACCAAATCTCAGCCACTTTGGATTT--AAGGATTTG
* * ** * * * * * * *
943 ATTTTGCAAGCATCGGAATCATGTGTCGACTTAATCAAAAATTAATTC-GAAAAAAAAAGGAAAT
193 ATTTTACGAGCATTAGAATCATGTGTCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAA
* * * * * *
1007 TCGATATTAGAAGCGTGGAAA-CCCTTCAATCTTTCTGGCGTTAAATTATA-AATCTTTTATGCG
258 TCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATACT-TTTTATGAG
* **
1070 TATTGTAGG-AA
322 TATT-TTGGCCG
* * * * * * * *
1081 AAAATAGAGGAAAAAATCTTTCGGATCAATTTTCGCAAAGTTTTAGTCGAAATCAATG---TAAC
1 AAAATTGAGG-AAAAATATTTCGGGTCAATTTTTGCAAAATTTT-GGCCAAATC-GTGTACTAAC
* * *** * * *
1143 CATCACAGTTTTTGGCT-AAAATCGCATTCTAATGCTCCGGATCAGTTTTGCATGATTTTTGGTG
63 CATCACGGTTTTTGGCTAAAAAT-GCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCG
* * * * * * * *
1207 GCAAGACTCAATG-AATA-ACTATA-TATATCTAACAAAATCTTACCCACATGGGATTTAAGAAT
127 CCAAGACTCATTGAAATATA-TATATTA-ATCTAACCAAATCTCAGCCACTTTGGATTTAAGGAT
* * * * * *
1269 TTGATTTTACGAGTATCA-TATCAAGTTTCGATTTTATCAGAAATTAACTT-GAAACAATATAGG
190 TTGATTTTACGAGCATTAGAATCATGTGTCGATTTTATCAGAAATTAA-TTCGGAACAATATAGG
* ** * * *
1332 AAAATCGATATTAGAAACGCAAAAAGTCCTTCAATCTTTTTGGCATTGAATTATATATTTTCTTA
254 AAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATACTTT-TTA
* **
1397 TAAGTATTTTGGCAAAA
318 TGAGTATTTTGGC--CG
* * * *
1414 AAAATT-AGGAAAAATATTTCGGTTCACTTTTTGCAAAATTTTGGCCAAATCGTGTACAAAAACA
1 AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTAC-TAACCA
* ** * * * * * * * * *
1478 TCACGGTTTTTGGCAAAAAAATGTTTTACAGTGCGCTGACTTAGTTTTTCATAATTTTTTGCGAC
65 TCACGGTTTTTGGC-TAAAAATGCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGCC
* * * * * * *
1543 AAAACTCTTTGAAAATATCTTTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGCTTTG
129 AAGACTCATTG-AAATATATATATTAATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTG
* * * * * *
1608 ATTTGACAAGCATTAGAATCATGTGTCGATTTTATTAGAAAATAATTCGGAATAATATAAGAAAA
193 ATTTTACGAGCATTAGAATCATGTGTCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAA
* * *
1673 TTGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAACTATAAACTTTTTATGAGT
258 TCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATACTTTTTATGAGT
* *
1738 ATTTTGGTCA
323 ATTTTGGCCG
* * *
1748 AAAATTG-TG-AAAATATTTCGGGGCAATTTTTGCAAAATTTTGGCCAAATCGTG-A--AACTAT
1 AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCAT
* ** * *
1808 CACGGTTTTTGGCTAAACATGCGTTATGGTGCTCTGGCTCAGTTTTTTCATGATTTTTGGTGCCA
66 CACGGTTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGCTCAG-TTTTTCATGATTTTTGGCGCCA
* * * * ** * *
1873 TGACTCATTGAAAATATCTTTATTTATCTAACCAAATCTCAGGTACATCGGATTTAAGGATTTGA
130 AGACTCATTG-AAATATATATATTAATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGA
* *
1938 TTTTACGAGCATTAGAATCATGTGTCGATTTTATCTGAAATTAATTCGGAACAATATAGAAAAAT
194 TTTTACGAGCATTAGAATCATGTGTCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAAT
*
2003 CGATATTAGAAGCGTGAAAAGCTCTTCAATCTTTTTGGCTTTGAATTATATACTTTTTATGAGTA
259 CGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATACTTTTTATGAGTA
2068 TTTTGGCCG
324 TTTTGGCCG
* * *
2077 AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCTTATACAAACCAT
1 AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCAT
* * *
2142 CACGGTTTTTGTCTAAAAATGCGTTCCGGTGCTCCGGCTCGGTTTTTCATGATTTTTGACGCCAA
66 CACGGTTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGCCAA
* *
2207 GATTCATTGAAATATATATATTAATCTAACCAGATCTCAGCCACTTTGGATTTAAGGATTTGATT
131 GACTCATTGAAATATATATATTAATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATT
* *
2272 TTACGAGCATTAGAATCATGTATCAATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCG
196 TTACGAGCATTAGAATCATGTGTCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCG
* *
2337 ATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTTAGCTTTGAATTATATACTTTTTATGAGTATT
261 ATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATACTTTTTATGAGTATT
*
2402 TTGGCTG
326 TTGGCCG
* *
2409 AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCTAAATCGTGTACTAAGCAT
1 AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCAT
* * * *
2474 CACGGTTTTTGACTAAAAATGCGTTCCGGTGCTCCGGCTAAGATTTTCATGATTTTTGGTGCCAA
66 CACGGTTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGCCAA
* * * * * *
2539 GAATCATTAAAATATATACATTCATCTAACTAAATCTCAGCCACTTTGGAGTTAAGGATTTGATT
131 GACTCATTGAAATATATATATTAATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATT
* *
2604 TTACGAGCATTAGAATTATGTGTCGATTTTATCAGAAATTAAGTCGGAACAATATAGGAAAATCG
196 TTACGAGCATTAGAATCATGTGTCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCG
* * * *
2669 ATATTAGAATCTTGAAAAGCCCTTCAATCTTTTTGGATTTGACTTATATACTTTTTATGAGTATT
261 ATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATACTTTTTATGAGTATT
2734 TTGGCCG
326 TTGGCCG
* * *
2741 AAAATTGAGGAAAATTATTTCGGGTCAATTTTTGCAAAATTTTGGCCGAATCGTGCACTAACCAT
1 AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCAT
* * * *
2806 CACGGTTTTTGGTTAAAAATGCGTTCCGGTGCTCCGGCTCAGTTTCTCATGATTTTGGGCGTCAA
66 CACGGTTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGCCAA
* *
2871 GACTCATTGAAATATTTATATTAATCTAACCAAATCTCAGCCACTTTAGATTTAAGGATTTGATT
131 GACTCATTGAAATATATATATTAATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATT
*
2936 TTTCGAGCATTAGAATC---T-TC-----TATCAGAAATTAATTCGGAACAATATAGGAAAATCG
196 TTACGAGCATTAGAATCATGTGTCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCG
* * *
2992 ATATTAGAAGCGTGAAAAACCCTGTCAATCTTTTTGACTTTGAATTATATA-TTTTTCATGAATA
261 ATATTAGAAGCGTGAAAAGCCCT-TCAATCTTTTTGGCTTTGAATTATATACTTTTT-ATGAGTA
3056 TTTTGGCCG
324 TTTTGGCCG
* * * *
3065 AAAATTGAGGAAAATTATTTCAGGTCAATTTTTGCAAAATTTTGTCCAAATCGTGTACTAACCGT
1 AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCAT
* * * *
3130 CACAGTTTTTAGCTAAAAATGCGTTCCGGTGCTTCGGCTCAGTTTTTCATGCTTTTTGGCGCCAA
66 CACGGTTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGCCAA
* * * *
3195 GAATCATTAAAATATATACATTTATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATT
131 GACTCATTGAAATATATATATTAATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATT
* *
3260 TTACGAGCATTAGAATTATGTATCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCG
196 TTACGAGCATTAGAATCATGTGTCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCG
* * *
3325 ATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTTGGCTTTGGATTATATACTTTTAATGAGTATT
261 ATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATACTTTTTATGAGTATT
3390 TTGGCCG
326 TTGGCCG
* * * *
3397 AAAATTAAGGAAAAATATTTCGGGTCAATTTTCGCAAAACTTTGGCCAAATCGTGTAGTAACCAT
1 AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCAT
* * * *
3462 CACGGTTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGCTCAGTTTCTCCTGACTTTTGGCGTCAA
66 CACGGTTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGCCAA
* *
3527 GACTCATTGAAATATCTATATTAATCTGACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATT
131 GACTCATTGAAATATATATATTAATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATT
3592 TTACGAGCATTAGAATC---T-TC-----TATCAGAAATTAATTCGGAACAATATAGGAAAATCG
196 TTACGAGCATTAGAATCATGTGTCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCG
* *
3648 ATATTGGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATA-TTTTTCTTGAGTAT
261 ATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATACTTTTT-ATGAGTAT
3712 TTTGGCCG
325 TTTGGCCG
* * *
3720 AAAATTGAGAAAAAATATTTCGGGTCAATTTTTGTAAAATTTTGGCCAAATCATGTACTAACCAT
1 AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCAT
* * * *
3785 TACGGATTTTGGACTAAAAAGTGCGTTCTGGTGCTCCGGCTAAGTTTTTCAT
66 CACGGTTTTTGG-CTAAAAA-TGCGTTCCGGTGCTCCGGCTCAGTTTTTCAT
3837 TTGATTTTAC
Statistics
Matches: 2377, Mismatches: 328, Indels: 107
0.85 0.12 0.04
Matches are distributed among these distances:
322 4 0.00
323 226 0.10
324 237 0.10
325 27 0.01
327 1 0.00
328 49 0.02
329 276 0.12
330 47 0.02
331 119 0.05
332 917 0.39
333 222 0.09
334 92 0.04
335 6 0.00
336 67 0.03
337 87 0.04
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (332 bp):
AAAATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCAT
CACGGTTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGCCAA
GACTCATTGAAATATATATATTAATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATT
TTACGAGCATTAGAATCATGTGTCGATTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCG
ATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATACTTTTTATGAGTATT
TTGGCCG
Found at i:3324 original size:656 final size:657
Alignment explanation
Indices: 509--3836 Score: 3927
Period size: 656 Copynumber: 5.0 Consensus size: 657
499 AATAGTCATA
* * * * *
509 GGCTCAGTTTTGCATGATTTTTAGTGGCAAGACTCATTGAAATA-ACTATATTTATC-CACCAAA
1 GGCTCAGTTTTTCATGATTTTTGGTGCCAAGACTCATTAAAATATA-TATATTTATCTAACC-AA
* * * * *
572 ATCTTAGCCACATGGGATTTGAGGATTTGATTTTACAAGC-TTCAG-ATCAAGTTTCGATTTTAT
64 ATCTCAGCCACATGGGATTTAAGGATTTGATTTTACGAGCATT-AGAATCATGTGTCGATTTTAT
* * * *
635 TAGAAATTAATTCGGAACAATATAGGAAAATTGATATTAAAAGCGTGAAAAGTCCTTCAATCTTT
128 CAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTT
* * * * *
700 TTGGCGA-TTGAATTATATATATATATATATATATATTTAAGTATTTT-GTCTAAAAATGAGGAA
193 TT-G-GATTTG-A--AT-TATATA-CT-T-T-T-TA--TGAGTATTTTGGCCGAAAATTGAGGAA
* ** * * *
763 AAAT-TTT-GGGTCAATTTTTGCAAAATTTTGGCCAAATCGTATACAAAATATCGCGG-CTATGG
245 AAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACAAACCATCACGGTTTTTGG
* * *
825 CTAAAAATGCGATCCGGTGCACCGGTTCAGTTTTTCATGATTTTTGGCG-CTAAGACTCATTGAA
310 CTAAAAATGCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTC-AAGACTCATTG-A
* * * * * *
889 AATATTTGTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAAAAGATTTGATTTTGCAAGC
373 AATATTTATATTAATCTAACCAAATCTCAGCCACTTTGGATTT--AAGGATTTGATTTTACGAGC
** * * * * *
954 ATCGGAATCATGTGTCGACTTAATCAAAAATTAATTC-GAAAAAAAAAGGAAATTCGATATTAGA
436 ATTAGAATCA--TGT---CTT-ATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGA
* * * * * * * **
1018 AGCGTGGAAA-CCCTTCAATCTTTCTGGCGTTAAATTATAAATCTTTTATGCGTATTGTAGG-AA
495 AGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATAT-TTTTATGAGTATT-TTGGCCG
* * * * * * * *
1081 AAAATAGAGGAAAAAATCTTTCGGATCAATTTTCGCAAAGTTTTAGTCGAAATCAATG---TAAC
558 AAAATTGAGG-AAAAATATTTCGGGTCAATTTTTGCAAAATTTT-GGCCAAATC-GTGTACTAAC
* * **
1143 CATCACAGTTTTTGGCT-AAAATCGCATTCTAATGCTCC
620 CATCACGGTTTTTGGCTAAAAAT-GCGTTCTGGTGCTCC
* * * * * * *
1181 GGATCAGTTTTGCATGATTTTTGGTGGCAAGACTCAAT-GAATA-ACTATATATATCTAACAAAA
1 GGCTCAGTTTTTCATGATTTTTGGTGCCAAGACTCATTAAAATATA-TATATTTATCTAACCAAA
* * * * * * * *
1244 TCTTACCCACATGGGATTTAAGAATTTGATTTTACGAGTATCA-TATCAAGTTTCGATTTTATCA
65 TCTCAGCCACATGGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGTGTCGATTTTATCA
* * ** *
1308 GAAATTAACTT-GAAACAATATAGGAAAATCGATATTAGAAACGCAAAAAGTCCTTCAATCTTTT
130 GAAATTAA-TTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTT
* * **
1372 TGGCA-TTGAATTATATATTTTCTTATAAGTATTTTGGCAAAAAAAATT-AGGAAAAATATTTCG
194 TGG-ATTTGAATTATATACTTT-TTATGAGTATTTTGGC--CGAAAATTGAGGAAAAATATTTCG
* * * *
1435 GTTCACTTTTTGCAAAATTTTGGCCAAATCGTGTACAAAAACATCACGGTTTTTGGCAAAAAAAT
255 GGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTAC-AAACCATCACGGTTTTTGGC-TAAAAAT
** * * * * * * * * * * *
1500 GTTTTACAGTGCGCTGACTTAGTTTTTCATAATTTTTTGCGACAAAACTCTTTGAAAATATCTT-
318 GCGTTCCGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGACTCATTG-AAATAT-TTA
* * * * *
1564 TATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGCTTTGATTTGACAAGCATTAGAATCA
381 TATTAATCTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATCA
* * * * *
1629 TGTGTCGATTTTATTAGAAAATAATTCGGAATAATATAAGAAAATTGATATTAGAAGCGTGAAAA
446 --TGTC----TTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAA
* * * * *
1694 GCCCTTCAATCTTTTTGGCTTTGAACTATAAACTTTTTATGAGTATTTTGGTCAAAAATTG-TG-
505 GCCCTTCAATCTTTTTGGCTTTGAATTATATA-TTTTTATGAGTATTTTGGCCGAAAATTGAGGA
* *
1757 AAAATATTTCGGGGCAATTTTTGCAAAATTTTGGCCAAATCGTG-A--AACTATCACGGTTTTTG
569 AAAATATTTCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTG
* * *
1819 GCTAAACATGCGTTATGGTGCTCT
634 GCTAAAAATGCGTTCTGGTGCTCC
* * *
1843 GGCTCAGTTTTTTCATGATTTTTGGTGCCATGACTCATTGAAAATATCTTTATTTATCTAACCAA
1 GGCTCAG-TTTTTCATGATTTTTGGTGCCAAGACTCATT-AAAATATATATATTTATCTAACCAA
** *
1908 ATCTCAGGTACATCGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGTGTCGATTTTATC
64 ATCTCAGCCACATGGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGTGTCGATTTTATC
* * *
1973 TGAAATTAATTCGGAACAATATAGAAAAATCGATATTAGAAGCGTGAAAAGCTCTTCAATCTTTT
129 AGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTT
*
2038 TGGCTTTGAATTATATACTTTTTATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCGGGTC
194 TGGATTTGAATTATATACTTTTTATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCGGGTC
* * *
2103 AATTTTTGCAAAATTTTGGCCAAATCTTATACAAACCATCACGGTTTTTGTCTAAAAATGCGTTC
259 AATTTTTGCAAAATTTTGGCCAAATCGTGTACAAACCATCACGGTTTTTGGCTAAAAATGCGTTC
* * * * *
2168 CGGTGCTCCGGCTCGGTTTTTCATGATTTTTGACGCCAAGATTCATTGAAATATATATATTAATC
324 CGGTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGACTCATTGAAATATTTATATTAATC
*
2233 TAACCAGATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGTATCAA
389 TAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATG--TC--
*
2298 TTTTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTCCA
450 --TTATCAGAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCA
* *
2363 ATCTTTTTAGCTTTGAATTATATACTTTTTATGAGTATTTTGGCTGAAAATTGAGGAAAAATATT
513 ATCTTTTTGGCTTTGAATTATATA-TTTTTATGAGTATTTTGGCCGAAAATTGAGGAAAAATATT
* * *
2428 TCGGGTCAATTTTTGCAAAATTTTGGCTAAATCGTGTACTAAGCATCACGGTTTTTGACTAAAAA
577 TCGGGTCAATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA
*
2493 TGCGTTCCGGTGCTCC
642 TGCGTTCTGGTGCTCC
* * * * * *
2509 GGCTAAGATTTTCATGATTTTTGGTGCCAAGAATCATTAAAATATATACATTCATCTAACTAAAT
1 GGCTCAGTTTTTCATGATTTTTGGTGCCAAGACTCATTAAAATATATATATTTATCTAACCAAAT
* * * *
2574 CTCAGCCACTTTGGAGTTAAGGATTTGATTTTACGAGCATTAGAATTATGTGTCGATTTTATCAG
66 CTCAGCCACATGGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGTGTCGATTTTATCAG
* * *
2639 AAATTAAGTCGGAACAATATAGGAAAATCGATATTAGAATCTTGAAAAGCCCTTCAATCTTTTTG
131 AAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTG
* *
2704 GATTTGACTTATATACTTTTTATGAGTATTTTGGCCGAAAATTGAGGAAAATTATTTCGGGTCAA
196 GATTTGAATTATATACTTTTTATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCGGGTCAA
* * * *
2769 TTTTTGCAAAATTTTGGCCGAATCGTGCACTAACCATCACGGTTTTTGGTTAAAAATGCGTTCCG
261 TTTTTGCAAAATTTTGGCCAAATCGTGTACAAACCATCACGGTTTTTGGCTAAAAATGCGTTCCG
* *
2834 GTGCTCCGGCTCAGTTTCTCATGATTTTGGGCGTCAAGACTCATTGAAATATTTATATTAATCTA
326 GTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGACTCATTGAAATATTTATATTAATCTA
* *
2899 ACCAAATCTCAGCCACTTTAGATTTAAGGATTTGATTTTTCGAGCATTAGAATC-T-TC-TATCA
391 ACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGTCTTATCA
*
2961 GAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAACCCTGTCAATCTTTT
456 GAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCT-TCAATCTTTT
* * * *
3026 TGACTTTGAATTATATATTTTTCATGAATATTTTGGCCGAAAATTGAGGAAAATTATTTCAGGTC
520 TGGCTTTGAATTATATATTTTT-ATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCGGGTC
* * * *
3091 AATTTTTGCAAAATTTTGTCCAAATCGTGTACTAACCGTCACAGTTTTTAGCTAAAAATGCGTTC
584 AATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCGTTC
* *
3156 CGGTGCTTC
649 TGGTGCTCC
* * * *
3165 GGCTCAGTTTTTCATGCTTTTTGGCGCCAAGAATCATTAAAATATATACATTTATCTAACCAAAT
1 GGCTCAGTTTTTCATGATTTTTGGTGCCAAGACTCATTAAAATATATATATTTATCTAACCAAAT
* * * *
3230 CTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATTATGTATCGATTTTATCAG
66 CTCAGCCACATGGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGTGTCGATTTTATCAG
*
3295 AAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTCCAATCTTTTTG
131 AAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTG
* * * *
3360 GCTTTGGATTATATACTTTTAATGAGTATTTTGGCCGAAAATTAAGGAAAAATATTTCGGGTCAA
196 GATTTGAATTATATACTTTTTATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCGGGTCAA
* * **
3425 TTTTCGCAAAACTTTGGCCAAATCGTGTAGTAACCATCACGGTTTTTGGCTAAAAATGCGTTCCG
261 TTTTTGCAAAATTTTGGCCAAATCGTGTACAAACCATCACGGTTTTTGGCTAAAAATGCGTTCCG
* * * * *
3490 GTGCTCCGGCTCAGTTTCTCCTGACTTTTGGCGTCAAGACTCATTGAAATATCTATATTAATCTG
326 GTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGACTCATTGAAATATTTATATTAATCTA
3555 ACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATC-T-TC-TATCA
391 ACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGTCTTATCA
*
3617 GAAATTAATTCGGAACAATATAGGAAAATCGATATTGGAAGCGTGAAAAGCCCTTCAATCTTTTT
456 GAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTT
* *
3682 GGCTTTGAATTATATATTTTTCTTGAGTATTTTGGCCGAAAATTGAGAAAAAATATTTCGGGTCA
521 GGCTTTGAATTATATATTTTT-ATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCGGGTCA
* * * *
3747 ATTTTTGTAAAATTTTGGCCAAATCATGTACTAACCATTACGGATTTTGGACTAAAAAGTGCGTT
585 ATTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGG-CTAAAAA-TGCGTT
3812 CTGGTGCTCC
648 CTGGTGCTCC
*
3822 GGCTAAGTTTTTCAT
1 GGCTCAGTTTTTCAT
3837 TTGATTTTAC
Statistics
Matches: 2328, Mismatches: 283, Indels: 105
0.86 0.10 0.04
Matches are distributed among these distances:
655 175 0.08
656 608 0.26
657 28 0.01
659 2 0.00
660 13 0.01
661 175 0.08
662 93 0.04
663 115 0.05
664 479 0.21
665 151 0.06
666 176 0.08
667 134 0.06
668 4 0.00
669 2 0.00
670 5 0.00
671 128 0.05
672 40 0.02
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (657 bp):
GGCTCAGTTTTTCATGATTTTTGGTGCCAAGACTCATTAAAATATATATATTTATCTAACCAAAT
CTCAGCCACATGGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGTGTCGATTTTATCAG
AAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTG
GATTTGAATTATATACTTTTTATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCGGGTCAA
TTTTTGCAAAATTTTGGCCAAATCGTGTACAAACCATCACGGTTTTTGGCTAAAAATGCGTTCCG
GTGCTCCGGCTCAGTTTTTCATGATTTTTGGCGTCAAGACTCATTGAAATATTTATATTAATCTA
ACCAAATCTCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTAGAATCATGTCTTATCA
GAAATTAATTCGGAACAATATAGGAAAATCGATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTT
GGCTTTGAATTATATATTTTTATGAGTATTTTGGCCGAAAATTGAGGAAAAATATTTCGGGTCAA
TTTTTGCAAAATTTTGGCCAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAATGCGTTCTG
GTGCTCC
Found at i:4030 original size:251 final size:249
Alignment explanation
Indices: 3584--4085 Score: 842
Period size: 251 Copynumber: 2.0 Consensus size: 249
3574 GGATTTAAGG
3584 ATTTGATTTTACGAGCATTAGAATCTTCTATCAGAAATTAATTCGGAACAATATAGGAAAATCGA
1 ATTTGATTTTACGAGCATTAGAATCTTCTATCAGAAATTAATTCGGAACAATATAGGAAAATCGA
* * *
3649 TATTGGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATATTTTTCTTGAGTATTT
66 TATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATATTTTTCATGAATATTT
* *
3714 TGGCCGAAAATTGAGAAAAAATATTTCGGGTCAATTTTTGTAAAATTTTGGCCAAATCATGTACT
131 TGGCCGAAAATTGAGAAAAAATATTTCAGGTCAATTTTTGCAAAATTTTGGCCAAATCATGTACT
* * *
3779 AACCATTACGGATTTTGGACTAAAAAGTGCGTTCTGGTGCTCCGGCTAAGTTTTTC
196 AACCATCACGGATTTTGG-CTAAAAA-TGCGTTCCGGTGCTCCGGCTAAGTTTCTC
* *
3835 ATTTGATTTTACGAGCATTAGAATCTTCTATCAGAAATTAATTCGGTACAATATATGAAAATCGA
1 ATTTGATTTTACGAGCATTAGAATCTTCTATCAGAAATTAATTCGGAACAATATAGGAAAATCGA
3900 TATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATATTTTTCATGAATATTT
66 TATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATATTTTTCATGAATATTT
* * * *
3965 TGGCCGAAAATTGAGGAAAATTATTTCAGGTCAATTTTTGCAAAATTTTGGCCGAATCGTGTACT
131 TGGCCGAAAATTGAGAAAAAATATTTCAGGTCAATTTTTGCAAAATTTTGGCCAAATCATGTACT
* *
4030 AACCATCACGGTTTTTGGCTAAAAATGCGTTCCGGTGCTCCGGCTCAGTTTCTC
196 AACCATCACGGATTTTGGCTAAAAATGCGTTCCGGTGCTCCGGCTAAGTTTCTC
4084 AT
1 AT
4086 GATTTTTGGC
Statistics
Matches: 235, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
249 28 0.12
250 7 0.03
251 200 0.85
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (249 bp):
ATTTGATTTTACGAGCATTAGAATCTTCTATCAGAAATTAATTCGGAACAATATAGGAAAATCGA
TATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATATTTTTCATGAATATTT
TGGCCGAAAATTGAGAAAAAATATTTCAGGTCAATTTTTGCAAAATTTTGGCCAAATCATGTACT
AACCATCACGGATTTTGGCTAAAAATGCGTTCCGGTGCTCCGGCTAAGTTTCTC
Done.