Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004995.1 Corchorus capsularis cultivar CVL-1 contig05013, 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: 2478
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:958 original size:321 final size:318
Alignment explanation
Indices: 1--2478 Score: 2936
Period size: 321 Copynumber: 7.8 Consensus size: 318
* * *
1 AAAAACACGTTCCAGAGTTCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATA
1 AAAAACGCGTTCCGGAGCTCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATA
* * * *
66 TCCATATTCATCGAACCAAATTTCAGCCATATGGGACATAAGGATTTTTTTTTAGCATCTCAATC
66 TCTATATTCATCGAACCAAATTTCAGCCATATTGGATATAAGGATTTTTTTTGAGCATCTCAATC
*
131 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAGTTGGAAAAACGATATTAGAAGCGTGAA
131 TTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAAA-TTGGAAAAACGATATTAGAAGCGTGAA
* * * * *
196 AAGCTCGCCAATC---TTGGCGTTTAATTATATATTTTTTATTAGTACTGTGGGAAAAAATTGAG
194 AAGC-CGCAAATCTTTTTGGCGTTTAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG
* * *
258 AAAAAACTTTTCGACTAAGATTTTAGCCGAAATCGTGTACGTTA-CATCACAGTTTTTGGCT
258 AAAAAACTTTTCGAGTAAGTTTTTAGCCGAAATCGTGTAC-TAACCATCACAGTTTTTGGCT
* * * *
319 AAAAACGCGTTCCGGAG-TCCGTG-TTCAATTTTGCATGAATTTTGGCGCAAATACTCCTTGAAA
1 AAAAACGCGTTCCGGAGCT-C-TGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAA
* * * ** *
382 TATCTAAATTCATCGAAGCAAATGTCTCCCACATTGGATATAAGGATTTGTTTTTACGAGCATCT
64 TATCTATATTCATCGAACCAAATTTCAGCCATATTGGATATAAGGATTT-TTTTT--GAGCATCT
* * ** *
447 AAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGGAAAACCGGGACTAGAAGCGT
126 CAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGGAAAAACGATATTAGAAGCGT
* * * * *
512 AAAAAGCAGGTTAAAATCTTTTTGACGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAA
191 GAAAAGC-CG--CAAATCTTTTTGGCGTTTAATTATATATTTTTTCTGAGTATTGTGGCAAAAAA
* * * *
576 TTGAGAAAAAACTTTTCGGGTAAGTTTTTAGCCGAAATCGTGTACTAACCGTCAAAGTTTTTTGC
253 TTGAGAAAAAACTTTTCGAGTAAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGC
641 T
318 T
*
642 AAAAACGCGTTCCTGAGCTCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATA
1 AAAAACGCGTTCCGGAGCTCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATA
* * *
707 TCCATATTCATCGAACCAAATTTCAGCCATATGGGATATAAGGATTTTTTTTATAGCATCTCAAT
66 TCTATATTCATCGAACCAAATTTCAGCCATATTGGATATAAGGATTTTTTTT-GAGCATCTCAAT
*
772 CTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAAGTTGGAAAAACGATATTAGAAGCGTGAA
130 CTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAA-TTGGAAAAACGATATTAGAAGCGTGAA
* * *
837 AAGCACGCCAATCTTTTTTGCGTTTAATTATATATTTTTTCTGAGTATTGTGGCAAAATATTGAG
194 AAGC-CGCAAATCTTTTTGGCGTTTAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG
* * * * *
902 AAAAGACTTTTCGAGTCAGTTTTTAGCCGAAATCGTGTATTAACTATCACAGTTTTTTGCT
258 AAAAAACTTTTCGAGTAAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCT
* * * * * *
963 AAAAACGCGTTCCGGAGCCCAGGCTCAACTTTGCATGAATTTTGGCGCAAAGACTCCTTGAAATA
1 AAAAACGCGTTCCGGAGCTCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATA
* * * * * ** *
1028 TCTAAATTCATCAAATCAAATGTCACCCACGTTGGATATAAGGATTTGTTTTTACGAGCATCTAA
66 TCTATATTCATCGAACCAAATTTCAGCCATATTGGATATAAGGATTT-TTTTT--GAGCATCTCA
* * * ** *
1093 ATCTTGTTTCGATTTAATTAGAAATTAGTTCAGAAAAAATTGGAACACCGGGATTAGAAGCGTAA
128 ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGGAAAAACGATATTAGAAGCGTGA
** *
1158 AAAGCCGGTTAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAATTGA
193 AAAGCC-GCAAATCTTTTTGGCGTTTAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA
* * *
1222 GAAAAAACCTTTCG-GATAAGTTTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTTGCT
257 GAAAAAACTTTTCGAG-TAAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCT
* * * ** *
1284 AAAAATGCGTTCCGGAGCTCTGCCTAAATTTTGCATGATTTTTGGCATAAAGACTCTTTGAAGTA
1 AAAAACGCGTTCCGGAGCTCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATA
1349 TCTATATTCATCGAACCAAATTTCAGCCATATTGGATATAA-G---------GAGCATCTCAATC
66 TCTATATTCATCGAACCAAATTTCAGCCATATTGGATATAAGGATTTTTTTTGAGCATCTCAATC
* *
1404 TTGTTTCAATTTAATTAGAAATTAATTC-GGAAAAA-TGGAAAAACGATATTAGAAGCGTGAAAA
131 TTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGGAAAAACGATATTAGAAGCGTG-AAA
* * **
1467 AGCCACAAATCTTTTTGGC-TTTGAATAATATATTTTTTCTGAACATTGTGGCAAAAAATTGAGA
195 AGCCGCAAATCTTTTTGGCGTTT-AATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGA
*
1531 GAAAACTTTTCGAGTCAA-TTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCT
259 AAAAACTTTTCGAGT-AAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCT
* * *
1591 AAAAACGCGTTCCTGAGCTCTAACTCAATTTTGCATAATTTTTGGCGCAAAGACTCTTT----T-
1 AAAAACGCGTTCCGGAGCTCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATA
* * *
1651 TCCATATTCATCGAACCAAATTTCAGCCATATGGGATATAAGGATTTTTTTTTAGCATCTCAATC
66 TCTATATTCATCGAACCAAATTTCAGCCATATTGGATATAAGGATTTTTTTTGAGCATCTCAATC
*
1716 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAGTTGGAAAAACGATATTAGAAGCGTGAAA
131 TTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAA-TTGGAAAAACGATATTAGAAGCGTGAAA
* *
1781 AGCC-CGACAATCTTGTTGGCGTTTAATTATATATTTTTTCTGAGTACTGTGGCAAAAAATTGAG
195 AGCCGC-A-AATCTTTTTGGCGTTTAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG
* *
1845 AAAAAAATTTTCGAGTAAG-----A-CCGAAATCGTGTACTAACCATCACAATTTTTGGCT
258 AAAAAACTTTTCGAGTAAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCT
* * ** * * * *
1900 AAAAACGCATTCCGGAG-TCCAGGTTCAATTTTGCATAAATTTTGGCGCAAATACTCCTTGAAAT
1 AAAAACGCGTTCCGGAGCT-CTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAAT
* * * * ** * *
1964 ATCTAAATTCATCGAAGCAAATGTCACCCACGTTGGATATAAGGATTTGTTTTTACGCGCATCTA
65 ATCTATATTCATCGAACCAAATTTCAGCCATATTGGATATAAGGATTT-TTTTT--GAGCATCTC
* * ** *
2029 AATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAATTGGAAAACCGGGATTAGAAGCGTA
127 AATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGGAAAAACGATATTAGAAGCGTG
** * *
2094 AAAAGCCGGTTAATC-TTTTGGACGTTGAATTATAAATTTTTTCTGAGTATTGTGGC-AAAAATT
192 AAAAGCC-GCAAATCTTTTTGG-CGTTTAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT
* * *
2157 GAGAAAAAAACTTTTCGGGTAAGTTTTTAGCCGAAATCGTGTACTAACTATCATAGTTTTTGGCT
255 GAG-AAAAAACTTTTCGAGTAAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCT
** *
2222 AAAAACGCGTTCCGGAGCTCT-ACCTCAATTTTGCATGATTTTTGGCATAAAGACTCTTTAAAAG
1 AAAAACGCGTTCCGGAGCTCTGA-CTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAA-
* *
2286 TATCTNTATTCATCGAAATCAAAATTTTCAGCCATATTTGGATATAA-G---------GAGCATC
64 TATCTATATTCATCG-AA-CCAAA-TTTCAGCCATA-TTGGATATAAGGATTTTTTTTGAGCATC
* * *
2341 TCAATCTTGTTTCAATTTAATTAGAAATTAATTC-GGAAAAA-TGGAAAAACCATATTAGAAGCG
125 TCAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGGAAAAACGATATTAGAAGCG
* * **
2404 TGAAAAAGCCACAAATCTTTTTGGC-TTTGAATAATATATTTTTTCTGAACATTGTGGCAAAAAA
190 TG-AAAAGCCGCAAATCTTTTTGGCGTTT-AATTATATATTTTTTCTGAGTATTGTGGCAAAAAA
2468 TTGAGAAAAAA
253 TTGAGAAAAAA
Statistics
Matches: 1845, Mismatches: 244, Indels: 148
0.82 0.11 0.07
Matches are distributed among these distances:
302 39 0.02
303 2 0.00
305 2 0.00
306 57 0.03
307 126 0.07
308 42 0.02
309 82 0.04
310 1 0.00
311 2 0.00
312 94 0.05
313 37 0.02
314 86 0.05
315 105 0.06
316 83 0.04
317 45 0.02
318 92 0.05
319 34 0.02
320 50 0.03
321 403 0.22
322 193 0.10
323 214 0.12
324 35 0.02
325 3 0.00
326 8 0.00
327 10 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (318 bp):
AAAAACGCGTTCCGGAGCTCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATA
TCTATATTCATCGAACCAAATTTCAGCCATATTGGATATAAGGATTTTTTTTGAGCATCTCAATC
TTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAA
GCCGCAAATCTTTTTGGCGTTTAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAA
AAACTTTTCGAGTAAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCT
Found at i:1377 original size:642 final size:636
Alignment explanation
Indices: 1--2478 Score: 3033
Period size: 644 Copynumber: 3.9 Consensus size: 636
* * *
1 AAAAACACGTTCCAGAGTTCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATA
1 AAAAACGCGTTCCGGAGCTCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATA
*
66 TCCATATTCATCGAACCAAATTTCAGCCATATGGGACATAAGGATTTTTTTTTAGCATCTCAATC
66 TCCATATTCATCGAACCAAATTTCAGCCATATGGGATATAAGGATTTTTTTTTAGCATCTCAATC
131 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAGTTGGAAAAACGATATTAGAAGCGTGAA
131 TTGTTTCGATTTAATTAGAAATTAATTC-G-AAAAAA-TTGGAAAAACGATATTAGAAGCGTGAA
* * * *
196 AAGCTCGCCAATC--TTGGCGTTTAATTATATATTTTTTATTAGTACTGTGGGAAAAAATTGAGA
193 AAGC-CGCCAATCTTTTGGCGTTTAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGA
* * *
259 AAAAACTTTTCGACTAAGATTTTAGCCGAAATCGTGTACGTTAC-ATCACAGTTTTTGGCTAAAA
257 AAAAACTTTTCGAGTAAGTTTTTAGCCGAAATCGTGTAC-TAACTATCACAGTTTTTGGCTAAAA
* * *
323 ACGCGTTCCGGAG-TCCGTGTTCAATTTTGCATGAATTTTGGCGCAAATACTCCTTGAAATATCT
321 ACGCGTTCCGGAGCTCC-AGCTCAATTTTGCATGAATTTTGGCGCAAAGACTCCTTGAAATATCT
* * *
387 AAATTCATCGAAGCAAATGTCTCCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTAAATC
385 AAATTCATCAAATCAAATGTCACCCACATTGGATATAAGGATTTGTTTTT--GAGCATCTAAATC
* *
452 TTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGGAAAACCGGGACTAGAAGCGTAAAAA
448 TTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGGAAAACCGAGATTAGAAGCGTAAAAA
* *
517 GCAGGTTAAAATCTTTTTGACGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAATTGAG
513 GCCGGTT--AATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG
* * *
581 AAAAAACTTTTCGGGTAAGTTTTTAGCCGAAATCGTGTACTAACCGTCAAAGTTTTTTGCT
576 AAAAAACTTTTCGGATAAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTTGCT
*
642 AAAAACGCGTTCCTGAGCTCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATA
1 AAAAACGCGTTCCGGAGCTCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATA
707 TCCATATTCATCGAACCAAATTTCAGCCATATGGGATATAAGGATTTTTTTTATAGCATCTCAAT
66 TCCATATTCATCGAACCAAATTTCAGCCATATGGGATATAAGGATTTTTTTT-TAGCATCTCAAT
772 CTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAAGTTGGAAAAACGATATTAGAAGCGTGAA
130 CTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAA-TTGGAAAAACGATATTAGAAGCGTGAA
* *
837 AAGCACGCCAATCTTTTTTGCGTTTAATTATATATTTTTTCTGAGTATTGTGGCAAAATATTGAG
193 AAGC-CGCCAATC-TTTTGGCGTTTAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG
* * * *
902 AAAAGACTTTTCGAGTCAGTTTTTAGCCGAAATCGTGTATTAACTATCACAGTTTTTTGCTAAAA
256 AAAAAACTTTTCGAGTAAGTTTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTGGCTAAAA
*
967 ACGCGTTCCGGAGC-CCAGGCTCAACTTTGCATGAATTTTGGCGCAAAGACTCCTTGAAATATCT
321 ACGCGTTCCGGAGCTCCA-GCTCAATTTTGCATGAATTTTGGCGCAAAGACTCCTTGAAATATCT
*
1031 AAATTCATCAAATCAAATGTCACCCACGTTGGATATAAGGATTTGTTTTTACGAGCATCTAAATC
385 AAATTCATCAAATCAAATGTCACCCACATTGGATATAAGGATTTGTTTTT--GAGCATCTAAATC
* * *
1096 TTGTTTCGATTTAATTAGAAATTAGTTCAGAAAAAATTGGAACACCGGGATTAGAAGCGTAAAAA
448 TTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGGAAAACCGAGATTAGAAGCGTAAAAA
1161 GCCGGTTAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAATTGAGAA
513 GCCGGTTAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAA
* *
1225 AAAACCTTTCGGATAAGTTTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTTGCT
578 AAAACTTTTCGGATAAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTTGCT
* * * ** *
1284 AAAAATGCGTTCCGGAGCTCTGCCTAAATTTTGCATGATTTTTGGCATAAAGACTCTTTGAAGTA
1 AAAAACGCGTTCCGGAGCTCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATA
* *
1349 TCTATATTCATCGAACCAAATTTCAGCCATATTGGATATAAGG----------AGCATCTCAATC
66 TCCATATTCATCGAACCAAATTTCAGCCATATGGGATATAAGGATTTTTTTTTAGCATCTCAATC
* *
1404 TTGTTTCAATTTAATTAGAAATTAATTCGGAAAAA-TGGAAAAACGATATTAGAAGCGTGAAAAA
131 TTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATTGGAAAAACGATATTAGAAGCGTG-AAAA
* * * ** *
1468 GCCACAAATCTTTTTGGC-TTTGAATAATATATTTTTTCTGAACATTGTGGCAAAAAATTGAGAG
195 GCCGCCAATC-TTTTGGCGTTT-AATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAA
*
1532 AAAACTTTTCGAGTCAA-TTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAA
258 AAAACTTTTCGAGT-AAGTTTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTGGCTAAAAA
* * * * *
1596 CGCGTTCCTGAGCTCTAACTCAATTTTGCAT-AATTTTTGGCGCAAAGACT-CTT----TTTCCA
322 CGCGTTCCGGAGCTCCAGCTCAATTTTGCATGAA-TTTTGGCGCAAAGACTCCTTGAAATATCTA
* * * * * * * * *
1655 TATTCATCGAACCAAATTTCAGCCATATGGGATATAAGGATTT-TTTTTTAGCATCTCAATCTTG
386 AATTCATCAAATCAAATGTCACCCACATTGGATATAAGGATTTGTTTTTGAGCATCTAAATCTTG
* * * *
1719 TTTCGATTTAATTAGAAATTAATTCGGAAAAAAGTTGGAAAAACGATATTAGAAGCGTGAAAAGC
451 TTTCGATTTAATTAGAAATTAATTCAGAAAAAA-TTGGAAAACCGAGATTAGAAGCGTAAAAAGC
* ** * * *
1784 CCGACAATCTTGTTGGCGTTTAATTATATATTTTTTCTGAGTACTGTGGCAAAAAATTGAGAAAA
515 CGGTTAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAA
* * *
1849 AAATTTTC-GAGTAAG-----A-CCGAAATCGTGTACTAACCATCACAATTTTTGGCT
580 AACTTTTCGGA-TAAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTTGCT
* * ** * * * *
1900 AAAAACGCATTCCGGAG-TCCAGGTTCAATTTTGCATAAATTTTGGCGCAAATACTCCTTGAAAT
1 AAAAACGCGTTCCGGAGCT-CTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAAT
* * * * * ** * * *
1964 ATCTAAATTCATCGAAGCAAATGTCACCCACGTTGGATATAAGGATTTGTTTTTACGCGCATCTA
65 ATCCATATTCATCGAACCAAATTTCAGCCATATGGGATATAAGGATTTTTTTTTA---GCATCTC
* * ** *
2029 AATCTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAAATTGGAAAACCGGGATTAGAAGCGTA
127 AATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAATTGGAAAAACGATATTAGAAGCGTG
** * *
2094 AAAAGCCGGTTAATCTTTTGGACGTTGAATTATAAATTTTTTCTGAGTATTGTGGC-AAAAATTG
191 AAAAGCC-GCCAATCTTTTGG-CGTTTAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTG
* *
2158 AGAAAAAAACTTTTCGGGTAAGTTTTTAGCCGAAATCGTGTACTAACTATCATAGTTTTTGGCTA
254 AG-AAAAAACTTTTCGAGTAAGTTTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTGGCTA
* * * ** * *
2223 AAAACGCGTTCCGGAGCTCTACCTCAATTTTGCATGATTTTTGGCATAAAGACTCTTTAAAAGTA
318 AAAACGCGTTCCGGAGCTCCAGCTCAATTTTGCATGAATTTTGGCGCAAAGACTCCTTGAAA-TA
** * * *
2288 TCTNTATTCATCGAAATCAAAATTTTCAGCCATATTTGGATAT-A--A---G-----GAGCATCT
382 TCTAAATTCATC-AAATC-AAA-TGTCACCCACA-TTGGATATAAGGATTTGTTTTTGAGCATCT
* * * *
2342 CAATCTTGTTTCAATTTAATTAGAAATTAATTC-GGAAAAA-TGGAAAAACC-ATATTAGAAGCG
443 AAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATTGG-AAAACCGAGATTAGAAGCG
*** * * **
2404 TGAAAAAGCC-ACAAATCTTTTTGGCTTTGAATAATATATTTTTTCTGAACATTGTGGCAAAAAA
507 T-AAAAAGCCGGTTAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAA
2468 TTGAGAAAAAA
571 TTGAGAAAAAA
Statistics
Matches: 1626, Mismatches: 161, Indels: 113
0.86 0.08 0.06
Matches are distributed among these distances:
615 1 0.00
616 119 0.07
617 1 0.00
620 45 0.03
621 72 0.04
622 29 0.02
623 39 0.02
626 1 0.00
627 8 0.00
628 242 0.15
629 57 0.04
630 43 0.03
631 230 0.14
632 5 0.00
637 11 0.01
638 4 0.00
639 3 0.00
640 12 0.01
641 166 0.10
642 251 0.15
643 3 0.00
644 284 0.17
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (636 bp):
AAAAACGCGTTCCGGAGCTCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATA
TCCATATTCATCGAACCAAATTTCAGCCATATGGGATATAAGGATTTTTTTTTAGCATCTCAATC
TTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAG
CCGCCAATCTTTTGGCGTTTAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAA
ACTTTTCGAGTAAGTTTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTGGCTAAAAACGCG
TTCCGGAGCTCCAGCTCAATTTTGCATGAATTTTGGCGCAAAGACTCCTTGAAATATCTAAATTC
ATCAAATCAAATGTCACCCACATTGGATATAAGGATTTGTTTTTGAGCATCTAAATCTTGTTTCG
ATTTAATTAGAAATTAATTCAGAAAAAATTGGAAAACCGAGATTAGAAGCGTAAAAAGCCGGTTA
ATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTT
TCGGATAAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTTGCT
Found at i:2421 original size:943 final size:939
Alignment explanation
Indices: 24--2478 Score: 3469
Period size: 943 Copynumber: 2.6 Consensus size: 939
14 AGAGTTCTGA
* * * * *
24 CTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATATCCATATTCATCGAACCAAATTT
1 CTCAATTTTGCATGAATTTTGGCGCAAAGACTCCTTGAAATATCTAAATTCATCGAACCAAATGT
* ** * * * *
89 CAGCCATATGGGACATAAGGATTTTTTTTTA--GCATCTCAATCTTGTTTCGATTTAATTAGAAA
66 CACCCACGTTGGATATAAGGATTTGTTTTTACGGCATCTAAATCTTGTTTCGATTTAATTAGAAA
* * ** * **
152 TTAATTCGGAAAAAAAGTTGGAAAAACGATATTAGAAGCGTGAAAAGCTC-GCCAATC--TTGGC
131 TTAATTCAG-AAAAAA-TTGGAAAACCGGGATTAGAAGCGTAAAAAGC-CGGTTAATCTTTTGGC
* * * * * *
214 GTTTAATTATATATTTTTTATTAGTACTGTGGGAAAAAATTGAGAAAAAACTTTTC-GACTAAGA
193 GTTGAATTATATATTTTTTCTGAGTATTGT-GGCAAAAATTGAGAAAAAACTTTTCGGA-TAAGT
*
278 TTTTAGCCGAAATCGTGTACGTTAC-ATCACAGTTTTTGGCTAAAAACGCGTTCCGGAG-TCCGT
256 TTTTAGCCGAAATCGTGTAC-TAACTATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCT-C-T
** * ** * * *
341 GTTCAATTTTGCATGAATTTTGGCGCAAATACTCCTTGAAA-TATCTAAATTCATCGAAGCAAAT
318 CCTCAATTTTGCATGATTTTTGGCATAAAGACT-CTTTAAAGTATCTATATTCATCGAA-CAAAT
* * * *
405 GTCTC--CCACATTGGATATAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATT
381 -TTTCAGCCATATTGGATAT-A--A---G-------GAGCATCTCAATCTTGTTTCAATTTAATT
* ** * *
468 AGAAATTAATTCAGAAAAAATTGG-AAAACCGGGACTAGAAGCGT-AAAAAG-CAGGTTAAAATC
432 AGAAATTAATTC-GGAAAAA-TGGAAAAACC-ATATTAGAAGCGTGAAAAAGCCA----CAAATC
* * * **
530 TTTTTGACGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAATTGAGAAAAAACTTTTCG
490 TTTTTGGCTTTGAATAATATATTTTTTCTGAACATTGTGGCAAAAAATTGAGAAAAAACTTTTCG
* * *
594 GGTAAGTTTTTAGCCGAAATCGTGTACTAACCGTCAAAGTTTTTTGCTAAAAACGCGTTCCTGAG
555 AGTAAGTTTTTAGCCGAAATCGTGTACTAACCATCAAAGTTTTTGGCTAAAAACGCGTTCCTGAG
* *
659 CTCTGACTCAATTTTGCATGATTTTTGGCGCAAAGACTCTTTGAAATATCCATATTCATCGAACC
620 CTCTAACTCAATTTTGCATAATTTTTGGCGCAAAGACTCTTT---ATATCCATATTCATCGAACC
724 AAATTTCAGCCATATGGGATATAAGGATTTTTTTTATAGCATCTCAATCTTGTTTCGATTTAATT
682 AAATTTCAGCCATATGGGATATAAGGATTTTTTTTATAGCATCTCAATCTTGTTTCGATTTAATT
* * *
789 AGAAATTAATTCTGAAAAAAGTTGGAAAAACGATATTAGAAGCGTGAAAAGCACGCCAATCTTTT
747 AGAAATTAATTCGGAAAAAAGTTGGAAAAACGATATTAGAAGCGTGAAAAGCACGACAATCTTGT
* * * * * *
854 TTGCGTTTAATTATATATTTTTTCTGAGTATTGTGGCAAAATATTGAGAAAAGACTTTTCGAGTC
812 TGGCGTTTAATTATATATTTTTTCTGAGTACTGTGGCAAAAAATTGAGAAAAAAATTTTCGAGTA
* * * * *
919 AGTTTTTAGCCGAAATCGTGTATTAACTATCACAGTTTTTTGCTAAAAACGCGTTCCGGAGCCCA
877 AG----TAGCCGAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAACGCATTCCGGAGCCCA
984 GG
938 GG
* * *
986 CTCAACTTTGCATGAATTTTGGCGCAAAGACTCCTTGAAATATCTAAATTCATCAAATCAAATGT
1 CTCAATTTTGCATGAATTTTGGCGCAAAGACTCCTTGAAATATCTAAATTCATCGAACCAAATGT
1051 CACCCACGTTGGATATAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAA
66 CACCCACGTTGGATATAAGGATTTGTTTTTACG-GCATCTAAATCTTGTTTCGATTTAATTAGAA
* *
1116 ATTAGTTCAGAAAAAATTGGAACACCGGGATTAGAAGCGTAAAAAGCCGGTTAATCTTTTTGGCG
130 ATTAATTCAGAAAAAATTGGAAAACCGGGATTAGAAGCGTAAAAAGCCGGTTAATC-TTTTGGCG
*
1181 TTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAATTGAGAAAAAACCTTTCGGATAAGTTTT
194 TTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAATTGAGAAAAAACTTTTCGGATAAGTTTT
* * *
1246 TAGCCGAAATCGTGTACTAACTATCACAGTTTTTTGCTAAAAATGCGTTCCGGAGCTCTGCCTAA
259 TAGCCGAAATCGTGTACTAACTATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCTCT-CCTCA
*
1311 ATTTTGCATGATTTTTGGCATAAAGACTCTTTGAAGTATCTATATTCATCGAACCAAA-TTTCAG
323 ATTTTGCATGATTTTTGGCATAAAGACTCTTTAAAGTATCTATATTCATCGAA-CAAATTTTCAG
1375 CCATATTGGATATAAGGAGCATCTCAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAT
387 CCATATTGGATATAAGGAGCATCTCAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAT
*
1440 GGAAAAACGATATTAGAAGCGTGAAAAAGCCACAAATCTTTTTGGCTTTGAATAATATATTTTTT
452 GGAAAAACCATATTAGAAGCGTGAAAAAGCCACAAATCTTTTTGGCTTTGAATAATATATTTTTT
*
1505 CTGAACATTGTGGCAAAAAATTGAGAGAAAACTTTTCGAGTCAA-TTTTTAGCCGAAATCGTGTA
517 CTGAACATTGTGGCAAAAAATTGAGAAAAAACTTTTCGAGT-AAGTTTTTAGCCGAAATCGTGTA
*
1569 CTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCTGAGCTCTAACTCAATTTTGCATAATTTTT
581 CTAACCATCAAAGTTTTTGGCTAAAAACGCGTTCCTGAGCTCTAACTCAATTTTGCATAATTTTT
1634 GGCGCAAAGACTCTTT-T-TCCATATTCATCGAACCAAATTTCAGCCATATGGGATATAAGGATT
646 GGCGCAAAGACTCTTTATATCCATATTCATCGAACCAAATTTCAGCCATATGGGATATAAGGATT
1697 TTTTTT-TAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAGTTGGAAAA
711 TTTTTTATAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAGTTGGAAAA
*
1761 ACGATATTAGAAGCGTGAAAAGCCCGACAATCTTGTTGGCGTTTAATTATATATTTTTTCTGAGT
776 ACGATATTAGAAGCGTGAAAAGCACGACAATCTTGTTGGCGTTTAATTATATATTTTTTCTGAGT
1826 ACTGTGGCAAAAAATTGAGAAAAAAATTTTCGAGTAAG-A-CCGAAATCGTGTACTAACCATCAC
841 ACTGTGGCAAAAAATTGAGAAAAAAATTTTCGAGTAAGTAGCCGAAATCGTGTACTAACCATCAC
*
1889 AATTTTTGGCTAAAAACGCATTCCGGAGTCCAGG
906 AATTTTTGGCTAAAAACGCATTCCGGAGCCCAGG
* * * *
1923 TTCAATTTTGCATAAATTTTGGCGCAAATACTCCTTGAAATATCTAAATTCATCGAAGCAAATGT
1 CTCAATTTTGCATGAATTTTGGCGCAAAGACTCCTTGAAATATCTAAATTCATCGAACCAAATGT
*
1988 CACCCACGTTGGATATAAGGATTTGTTTTTACGCGCATCTAAATCTTGTTTCGATTTAATTAAAA
66 CACCCACGTTGGATATAAGGATTTGTTTTTACG-GCATCTAAATCTTGTTTCGATTTAATTAGAA
2053 ATTAATTCAGAAAAAATTGGAAAACCGGGATTAGAAGCGTAAAAAGCCGGTTAATCTTTTGGACG
130 ATTAATTCAGAAAAAATTGGAAAACCGGGATTAGAAGCGTAAAAAGCCGGTTAATCTTTTGG-CG
* *
2118 TTGAATTATAAATTTTTTCTGAGTATTGTGGCAAAAATTGAGAAAAAAACTTTTCGGGTAAGTTT
194 TTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAATTGAG-AAAAAACTTTTCGGATAAGTTT
*
2183 TTAGCCGAAATCGTGTACTAACTATCATAGTTTTTGGCTAAAAACGCGTTCCGGAGCTCTACCTC
258 TTAGCCGAAATCGTGTACTAACTATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCTCT-CCTC
*
2248 AATTTTGCATGATTTTTGGCATAAAGACTCTTTAAAAGTATCTNTATTCATCGAAATCAAAATTT
322 AATTTTGCATGATTTTTGGCATAAAGACTCTTT-AAAGTATCTATATTCATCG-AA-C-AAATTT
2313 TCAGCCATATTTGGATATAAGGAGCATCTCAATCTTGTTTCAATTTAATTAGAAATTAATTCGGA
383 TCAGCCATA-TTGGATATAAGGAGCATCTCAATCTTGTTTCAATTTAATTAGAAATTAATTCGGA
2378 AAAATGGAAAAACCATATTAGAAGCGTGAAAAAGCCACAAATCTTTTTGGCTTTGAATAATATAT
447 AAAATGGAAAAACCATATTAGAAGCGTGAAAAAGCCACAAATCTTTTTGGCTTTGAATAATATAT
2443 TTTTTCTGAACATTGTGGCAAAAAATTGAGAAAAAA
512 TTTTTCTGAACATTGTGGCAAAAAATTGAGAAAAAA
Statistics
Matches: 1361, Mismatches: 106, Indels: 71
0.88 0.07 0.05
Matches are distributed among these distances:
936 6 0.00
937 271 0.20
938 114 0.08
939 17 0.01
940 3 0.00
941 3 0.00
942 11 0.01
943 305 0.22
944 52 0.04
945 1 0.00
948 41 0.03
949 120 0.09
950 15 0.01
951 17 0.01
952 41 0.03
959 1 0.00
962 84 0.06
963 34 0.02
964 16 0.01
965 175 0.13
966 34 0.02
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (939 bp):
CTCAATTTTGCATGAATTTTGGCGCAAAGACTCCTTGAAATATCTAAATTCATCGAACCAAATGT
CACCCACGTTGGATATAAGGATTTGTTTTTACGGCATCTAAATCTTGTTTCGATTTAATTAGAAA
TTAATTCAGAAAAAATTGGAAAACCGGGATTAGAAGCGTAAAAAGCCGGTTAATCTTTTGGCGTT
GAATTATATATTTTTTCTGAGTATTGTGGCAAAAATTGAGAAAAAACTTTTCGGATAAGTTTTTA
GCCGAAATCGTGTACTAACTATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGCTCTCCTCAATT
TTGCATGATTTTTGGCATAAAGACTCTTTAAAGTATCTATATTCATCGAACAAATTTTCAGCCAT
ATTGGATATAAGGAGCATCTCAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAATGGAA
AAACCATATTAGAAGCGTGAAAAAGCCACAAATCTTTTTGGCTTTGAATAATATATTTTTTCTGA
ACATTGTGGCAAAAAATTGAGAAAAAACTTTTCGAGTAAGTTTTTAGCCGAAATCGTGTACTAAC
CATCAAAGTTTTTGGCTAAAAACGCGTTCCTGAGCTCTAACTCAATTTTGCATAATTTTTGGCGC
AAAGACTCTTTATATCCATATTCATCGAACCAAATTTCAGCCATATGGGATATAAGGATTTTTTT
TATAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAGTTGGAAAAACGAT
ATTAGAAGCGTGAAAAGCACGACAATCTTGTTGGCGTTTAATTATATATTTTTTCTGAGTACTGT
GGCAAAAAATTGAGAAAAAAATTTTCGAGTAAGTAGCCGAAATCGTGTACTAACCATCACAATTT
TTGGCTAAAAACGCATTCCGGAGCCCAGG
Done.