Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020786.1 Corchorus olitorius cultivar O-4 contig20819, 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: 5113
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Found at i:744 original size:323 final size:323
Alignment explanation
Indices: 63--869 Score: 1097
Period size: 323 Copynumber: 2.5 Consensus size: 323
53 TCTCGCTTTA
* * * * *
63 AATATCATTTTTCTATTTTTTTCCGAACCT-ATTTCTAATTAAATCGAAACAATATTCAGATGCT
1 AATATCATTTTTCCATTTTTTTCCGAA-TTAATTTTTAATTAAATTGAAACAAGATTCAGATGCT
* * * * * *
127 CATAAAAACAAATCCTTAAATCTAAT-GTGGCTGAGAGCCTGAGATTGGTTAGATGAATATGGAT
65 CGTAAAAACAAATACTTAAATCGAATCGTGGCT--G-G---GA-TTTTGTTAGATGAATATAGAT
*
191 ATTTCAAGGAGTCTTTGCGCCAAAATTCATGCAAAATTGAGTCGGGGCTCGGGAACGCGTTTTTA
123 ATTTCAAGGAGTCTTTGCGCCAAAATTCATGCAAAATTGAGTCGGGGCTCGGGAACACGTTTTTA
* * * * *
256 GCCAAAAACAGTGATGGTTAGTTCACGATTTCGGCAAAAAACTTATCGGAAAAGATTTTTCTCAA
188 GCCAAAAACAGTGATGATTAATACACGATTTCGGCAAAAAACTGATCGGAAAAAATTTTTCTCAA
*
321 TTTTTTGCCACAATTCTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCAC
253 TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCAC
386 ACTTCT
318 ACTTCT
*
392 AATATCGTTTTTCCATTTTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCT
1 AATATCATTTTTCCA-TTTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCT
* * *
457 TGTAAAAACAAATATTTAAATC-AATCGTGGCTGGGATTTTGTTTGATGAATATAGATATTTCAA
65 CGTAAAAACAAATACTTAAATCGAATCGTGGCTGGGATTTTGTTAGATGAATATAGATATTTCAA
*
521 GGAGTCTTTGCGCCAAAATTCATGCAAAATTGTGTCGGGGCTCGGGAACACGTTTTTAGCCAAAA
130 GGAGTCTTTGCGCCAAAATTCATGCAAAATTGAGTCGGGGCTCGGGAACACGTTTTTAGCCAAAA
*
586 ACAGTGATGATTAATACACTATTTCGGCAAAAAAAACTGATC-GAAAAAATTTTT-TCTAATTTT
195 ACAGTGATGATTAATACACGATTTCGGC--AAAAAACTGATCGGAAAAAATTTTTCTC-AA-TTT
* * *
649 TTTGCCACAATACTCAGAAAAAATATATTATTCAACGCCAAAAGGATTGACGGGCTTTTCACGCT
256 TTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACACT
714 TCT
321 TCT
* * * *
717 TATATCATTTTTCCA-TTTTTCCCGAATTAATTTTTAATTAAATTGAAACAAGATTTAGATTCTC
1 AATATCATTTTTCCATTTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCTC
* * * *
781 GTAAAAACAAATACTTAAATCGAA-CGTGACTGGCATTTTGTTCGATGAATATAGATATTTTAAG
66 GTAAAAACAAATACTTAAATCGAATCGTGGCTGGGATTTTGTTAGATGAATATAGATATTTCAAG
* * * *
845 AACTCTTTGTGCCAAAAATCATGCA
131 GAGTCTTTGCGCCAAAATTCATGCA
870 CAAAAAAATA
Statistics
Matches: 429, Mismatches: 41, Indels: 22
0.87 0.08 0.04
Matches are distributed among these distances:
323 235 0.55
324 17 0.04
325 91 0.21
327 1 0.00
328 1 0.00
329 17 0.04
330 67 0.16
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (323 bp):
AATATCATTTTTCCATTTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCTC
GTAAAAACAAATACTTAAATCGAATCGTGGCTGGGATTTTGTTAGATGAATATAGATATTTCAAG
GAGTCTTTGCGCCAAAATTCATGCAAAATTGAGTCGGGGCTCGGGAACACGTTTTTAGCCAAAAA
CAGTGATGATTAATACACGATTTCGGCAAAAAACTGATCGGAAAAAATTTTTCTCAATTTTTTGC
CACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACACTTCT
Found at i:3188 original size:322 final size:328
Alignment explanation
Indices: 2477--3273 Score: 884
Period size: 322 Copynumber: 2.4 Consensus size: 328
2467 TCTATTTTTT
* *
2477 TTTTTCCGAATCT-ATTTCTAATTAAACCGAAACAATATTCAGATGCTCGTAAAAACAAATCCTT
1 TTTTTCCGAAT-TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * * *
2541 AAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAGATGAATATAGATATTTCAAGGAATCTTTCT
65 AAATCCAATGTGGCT--GAG-C--A-TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCA
* ** *
2606 GCCAAACATCATGCAAAACTAAGTCGGGGCCCCCGAAACGCGTTTTTAGCTAAAAACCATGATGA
124 GCCAAACATCATGCAAAACTAAGTCGGGACCCAAGAAACGCGTTTTTAGCCAAAAACCATGATGA
* * ***** *
2671 TTTAGTACACGATTTTCGGCTAAAAACTGACCCGAAGTTTTTTTTCTGAATTTTTTTACCACAAT
189 GTTAGTACACGATTTTCAGCTAAAAACTGACCCGAAGAAGACTTTCTCAATTTTTTTACCACAAT
* * ** * * *
2736 AACTTGAAAAAAATGTATAATTCAACTTCAAAAAGATTGATGGTCTTTTCACGCTTTTAACATCA
254 AACTTCAAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAACATCA
*
2801 TTTTTTCCAA
319 GTTTTTCCAA
*
2811 TTTTTCTGAATTAA-TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
1 TTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
* * *
2875 TATCCAATGTGGCTGA-CATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGAGCCAAA-
66 AATCCAATGTGGCTGAGCATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCAGCCAAAC
* * * *
2938 ATTCATGCAAAATTGAGTCGGGACTCAAG-AACGCGTTTTTAGCCAAAAACCGTGATG-GTTAGT
131 A-TCATGCAAAACTAAGTCGGGACCCAAGAAACGCGTTTTTAGCCAAAAACCATGATGAGTTAGT
* * *
3001 ACACGA-TTTCAGCTAAAAACTGATCGGAA-AAGACTTTCTCAA-TTTTTTGCCACAAT-AC-TC
195 ACACGATTTTCAGCTAAAAACTGACCCGAAGAAGACTTTCTCAATTTTTTTACCACAATAACTTC
* *
3061 AAAATAAATATATAATTCAAGGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATC-GTTTT
260 AAAA-AAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAACATCAGTTTT
*
3125 TCCAT
324 TCCAA
* * * * *
3130 TTTTTCCCCGAATTAATTTTTAATTAAATTGAAACAAGATTTAGATTCTCGTAAAAACAAATACT
1 TTTTT--CCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
* * ** * * * * *
3195 TAAAGCGAGCGTGGCT-AGGATTTTGTTCGATGAATATAGATATTTCAAGGAGTATTT-ACGTCA
64 TAAATCCAATGTGGCTGAGCATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCA-GCCA
*
3258 AAAATCATGCACAAAC
128 AACATCATGCA-AAAC
3274 AAAAAAATAT
Statistics
Matches: 396, Mismatches: 57, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
319 18 0.05
320 48 0.12
321 23 0.06
322 108 0.27
323 24 0.06
324 11 0.03
325 27 0.07
326 61 0.15
327 1 0.00
329 1 0.00
331 2 0.01
333 61 0.15
334 11 0.03
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (328 bp):
TTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
AATCCAATGTGGCTGAGCATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCAGCCAAAC
ATCATGCAAAACTAAGTCGGGACCCAAGAAACGCGTTTTTAGCCAAAAACCATGATGAGTTAGTA
CACGATTTTCAGCTAAAAACTGACCCGAAGAAGACTTTCTCAATTTTTTTACCACAATAACTTCA
AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAACATCAGTTTTTC
CAA
Found at i:3804 original size:563 final size:550
Alignment explanation
Indices: 2780--3831 Score: 1351
Period size: 563 Copynumber: 1.9 Consensus size: 550
2770 GATTGATGGT
*
2780 CTTTTCACGCTTTTAACATCATTTTTTCCAATTTTTCTGAATTAATTCTAATTAAATCGAAACAA
1 CTTTTCACGCTTTAAACATCATTTTTTCCAATTTTTCTGAATTAATTCTAATTAAATCGAAACAA
* * *
2845 GATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATAT
66 GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGACAATTGGTTAGATGAATAT
* * * * * *
2910 AGATATTTCAAGGAGTCTTTGAGCCAAAATTCATGCAAAATTGAGTCGGGACTCAAGAACGCGTT
131 AGATATTTCAAGGAGTCTTTCAGCCAAAAATCATGCAAAACTAAGCCGGGACCCAAGAACGCGTT
* * *
2975 TTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGATCGGAAAAGACTTTCT
196 TTTAGCCAAAAACCATGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAAAGACTTTCT
* * *
3040 CAATTTTTTGCCACAATACTCAAAATAAATATATAATTCAAGGCCAAAAAGATTGAAGGACTTTT
261 CAATCTTTTGCCACAATACCCAAAATAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTT
* * * *
3105 CACGCTTCTAATATCGTTTTTCCATTTTTTCCCCGAATTAATTTTTAATTAAATTGAAACAAGAT
326 CACGCTTCTAACATCATTTTTCCATTTTTT-CCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * * * *
3170 TTAGATTCTCGTAAAAACAAATACTTAAAGCGAGCGTGGCTAGGATTTTGTTCGATGAATATAGA
390 TCAGATGCTCGTAAAAACAAATACTTAAAGCGAACGTGGCTAGCATTTGGTTCGATGAATATAGA
*
3235 TATTTCAAGGAGTATTTACGTCAAAAATCATGCACAAACAAAAAAATATTTTCGGCAAAAAATAC
455 TATTTCAAGGAGTATTTACGCCAAAAATCATGCACAAACAAAAAAATATTTTCGGCAAAAAATAC
3300 ACAATTCAACGCTAAAAAGAAAATTGAAATA
520 ACAATTCAACGCTAAAAAGAAAATTGAAATA
* * * *
3331 CTTTTCTCGCTTTAAATATCA-TTTTTCTATTTTTTTCTGAATCT-ATCTCTAATTAAATCGAAA
1 CTTTTCACGCTTTAAACATCATTTTTTCCA-ATTTTTCTGAAT-TAAT-TCTAATTAAATCGAAA
* * *
3394 CAATATTCAGATGCTCGTAAAAACAAATCTTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTT
63 CAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT--GA--C--A-ATTGGTT
* * * *
3459 AGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTCAAAACTAAGCCGGGGCCCC
121 AGATGAATATAGATATTTCAAGGAGTCTTTCAGCCAAAAATCATGCAAAACTAAGCCGGGACCCA
* *
3524 CGAAACGCGTTTTTAGCCCAAAAACCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCC
186 AG-AACGCGTTTTTAG-CCAAAAACCATGATGGTTAGTACACGA-TTTCAGCTAAAAACTGACCC
***** * **
3589 GAATTTTTTTTTTCTGAATCTTTTGCCACAATACCCAGAAA-AAATATATAATTCAACTTCAAAA
248 GAA--AAGACTTTCTCAATCTTTTGCCACAATACCCA-AAATAAATATATAATTCAACGCCAAAA
* * *
3653 AGATTGATGGTCTTTTCACGCTTTTAACATCATTTTTCCAATTTTTT-CCGAATTAATTTCTAAT
310 AGATTGAAGGACTTTTCACGCTTCTAACATCATTTTTCC-ATTTTTTCCCGAATTAATTTCTAAT
* * ** *
3717 TAAATCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTATATTC-AATGTGGCT-GACATT
374 TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTA-AAGCGAACGTGGCTAG-CATT
* * **
3780 TGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCA
437 TGGTTCGATGAATATAGATATTTCAAGGAGTATTTACGCCAAAAATCATGCA
3832 AAATTGAGTC
Statistics
Matches: 423, Mismatches: 59, Indels: 26
0.83 0.12 0.05
Matches are distributed among these distances:
550 7 0.02
551 31 0.07
552 60 0.14
554 2 0.00
556 1 0.00
558 1 0.00
559 61 0.14
560 13 0.03
561 26 0.06
562 21 0.05
563 110 0.26
564 80 0.19
565 10 0.02
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (550 bp):
CTTTTCACGCTTTAAACATCATTTTTTCCAATTTTTCTGAATTAATTCTAATTAAATCGAAACAA
GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGACAATTGGTTAGATGAATAT
AGATATTTCAAGGAGTCTTTCAGCCAAAAATCATGCAAAACTAAGCCGGGACCCAAGAACGCGTT
TTTAGCCAAAAACCATGATGGTTAGTACACGATTTCAGCTAAAAACTGACCCGAAAAGACTTTCT
CAATCTTTTGCCACAATACCCAAAATAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTT
CACGCTTCTAACATCATTTTTCCATTTTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATT
CAGATGCTCGTAAAAACAAATACTTAAAGCGAACGTGGCTAGCATTTGGTTCGATGAATATAGAT
ATTTCAAGGAGTATTTACGCCAAAAATCATGCACAAACAAAAAAATATTTTCGGCAAAAAATACA
CAATTCAACGCTAAAAAGAAAATTGAAATA
Found at i:3806 original size:885 final size:885
Alignment explanation
Indices: 1891--5020 Score: 4346
Period size: 885 Copynumber: 3.5 Consensus size: 885
1881 ATTGAAATAT
* * * * * * *
1891 TTTTCTCGCTTTAAATATCATTTTT-CTATTTTTTCCTAATCTATGTATAATTAAATCGAAACAA
1 TTTTCACGCTTTTAACATCATTTTTCCAATTTTTTCCGAATCTATTTCTAATTAAATCGAAACAA
* * *
1955 TATTAAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTCGCTGAGAGCCTGAGATTGGTTAGA
66 GATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCT-AGA-CC-GAGATTGGTTAGA
* * *
2020 TGAATATTGATATTTCAAGGAGTCTTTGCGCCAAAATTCATGCAAAATTGAGTCGGGGCTCGGGA
128 TGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGA
* * * * *
2085 ATGCGTTTTTAGCCAAAAACAGTGATGGTTAGTTCACGATTTCGGCAAAAAACTTATCGGAAAAG
193 ACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAG
* *
2150 ATTTTCTCAATTTTTTGCCACAATACTCAGGAAAAATATATAATT-AACGGCCAAGAAGATTGAC
258 ATTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAA-GGCCAAAAAGATTGA-
*
2214 A-GACTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCCGAACTAATTTTTAATTAAATTG
321 AGGACTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTCCCGAATTAATTTTTAATTAAATTG
* * *
2278 AAACAAGATTTAGATTCTCGTAAAAACAAATACTTAAATCGAACATGGCTGGCATTTTGTTCGAT
385 AAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCGAACGTGGCTGG-ATTTTGTTCGAT
2343 GAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATG--C--A-AAAAAAATATTTTCGGC
449 GAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCACAAACAAAAAAATATTTTCGGC
* *
2403 AAAAAATACACAATTCAACGCAAAAA-AAATTTTGAAATACTTTTCTTGCTTTAAATATCATTTT
514 AAAAAATACACAATTCAACGCAAAAAGAAA-ATTGAAATACTTTTCTCGCTTTAAATATCATTTT
*
2467 TCTATTTTTTTTTTTCCGAATCTATTTCTAATTAAACCGAAACAATATTCAGATGCTCGTAAAAA
578 TCTA---TTTTTTTTCCGAATCTATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAAAAA
2532 CAAATCCTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAGATGAATATAGATATTTCAAGG
640 CAAATCCTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAGATGAATATAGATATTTCAAGG
* * * * *
2597 AATCTTTCTGCCAAACATCATGCAAAACTAAGTCGGGGCCCCCGAAACGCGTTTTTAG-CTAAAA
705 AGTCTTTCTGCCAAAAATCATTCAAAACTAAGCCGGGGCCCCCGAAACGCGTTTTTAGCCCAAAA
*
2661 ACCATGATGATTTAGTACACGATTTTCGGCTAAAAACTGACCCGAAGTTTTTTTTCTGAATTTTT
770 ACCATGATG-CTTAGTACACGATTTTCGGCTAAAAACTGACCCGAA-TTTTTTTTCTGAA-TTTT
* * ** *
2726 TTACCACAATAACTTGAAAAAAATGTATAATTCAACTTCAAAAAGATTGATGGTC
832 TTGCCACAATACCCAG-AAAAAATATATAATTCAACTTCAAAAAGATTGATGGTC
* *
2781 TTTTCACGCTTTTAACATCATTTTTTCCAA-TTTTTCTGAAT-TAATTCTAATTAAATCGAAACA
1 TTTTCACGCTTTTAACATCA-TTTTTCCAATTTTTTCCGAATCTATTTCTAATTAAATCGAAACA
* * * *
2844 AGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCT-GA-C-A-TTTGGTTTGATG
65 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTAGACCGAGATTGGTTAGATG
* * * **
2905 AATATAGATATTTCAAGGAGTCTTTGAGCCAAAATTCATGCAAAATTGAGTCGGGACTCAAGAAC
130 AATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAAC
* *
2970 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGATCGGAAAAGAC
195 GCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAGAT
3035 TTTCTCAATTTTTTGCCACAATACTCA-AAATAAATATATAATTCAAGGCCAAAAAGATTGAAGG
260 TTTCTCAATTTTTTGCCACAATACTCAGAAA-AAATATATAATTCAAGGCCAAAAAGATTGAAGG
3099 ACTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCCCGAATTAATTTTTAATTAAATTGAAA
324 ACTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT-CCCGAATTAATTTTTAATTAAATTGAAA
* * * *
3164 CAAGATTTAGATTCTCGTAAAAACAAATACTTAAAGCGAGCGTGGCTAGGATTTTGTTCGATGAA
388 CAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCGAACGTGGCT-GGATTTTGTTCGATGAA
3229 TATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCACAAACAAAAAAATATTTTCGGCAAA
452 TATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCACAAACAAAAAAATATTTTCGGCAAA
3294 AAATACACAATTCAACGCTAAAAAGAAAATTGAAATACTTTTCTCGCTTTAAATATCATTTTTCT
517 AAATACACAATTCAACGC-AAAAAGAAAATTGAAATACTTTTCTCGCTTTAAATATCATTTTTCT
* *
3359 A-TTTTTTTCTGAATCTATCTCTAATTAAATCGAAACAATATTCAGATGCTCGTAAAAACAAATC
581 ATTTTTTTTCCGAATCTATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAAAAACAAATC
*
3423 TTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAGATGAATATAGATATTTCAAGGAGTCTT
646 CTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAGATGAATATAGATATTTCAAGGAGTCTT
3488 TCTGCCAAAAATCATTCAAAACTAAGCCGGGGCCCCCGAAACGCGTTTTTAGCCCAAAAACCATG
711 TCTGCCAAAAATCATTCAAAACTAAGCCGGGGCCCCCGAAACGCGTTTTTAGCCCAAAAACCATG
* *
3553 ATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGAATTTTTTTTTTCTGAATCTTTTGCCAC
776 ATGCTTAGTACACGATTTTCGGCTAAAAACTGACCCGAA--TTTTTTTTCTGAATTTTTTGCCAC
3618 AATACCCAGAAAAAATATATAATTCAACTTCAAAAAGATTGATGGTC
839 AATACCCAGAAAAAATATATAATTCAACTTCAAAAAGATTGATGGTC
3665 TTTTCACGCTTTTAACATCATTTTTCCAATTTTTTCCGAAT-TAATTTCTAATTAAATCGAAACA
1 TTTTCACGCTTTTAACATCATTTTTCCAATTTTTTCCGAATCT-ATTTCTAATTAAATCGAAACA
* * * *
3729 AGATTCAGATGCTCGTAAAAATAAATCCTTATAT-TCAATGTGGCT-GA-C-A-TTTGGTTTGAT
65 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCT-AATGTGGCTAGACCGAGATTGGTTAGAT
3789 GAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAA
129 GAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAA
* *
3854 CGCGTTTTTAGCCAAAAACCGTGATTGTTAGTACACGATTTCGGCTAAAAACTGATCCGAAAAGT
194 CGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAG-
* * *
3919 TTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACG
258 ATTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAGGCCAAAAAGATTGAAG
* * *
3984 GGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCTAATTAATTTTTAATTAAATTGAAA
323 GACTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCCGAATTAATTTTTAATTAAATTGAAA
* * *
4049 CAAGATTCATATGCTTGTAAAAACAAATACTTAAATCGAATGTGGCTGGGATTTTGTTCGATGAA
388 CAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCGAACGTGGCT-GGATTTTGTTCGATGAA
* * * *
4114 TATGGATATTTCAATGAGTATTTACGTCAAAAATCATTCAAAAACAAAATAAATATTTTCGGCAA
452 TATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCACAAACAAAA-AAATATTTTCGGCAA
* *
4179 AAAATACACAATTCAACGCAAAAA-AGAAATTGAAATATTTTTCTGGCTTTAAATATCATTTTTC
516 AAAATACACAATTCAACGCAAAAAGA-AAATTGAAATACTTTTCTCGCTTTAAATATCATTTTTC
* *
4243 TATTTTTTTTCCGAATCTATTTCTGATTAAATCGAAATAATATTCAGATGCTCGTAAAAACAAAT
580 TATTTTTTTTCCGAATCTATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAAAAACAAAT
* * * **
4308 CCTTAAATCTAATGTTGCTGAGAGCCTGAAATT-GATATGATGAATATAGATATTTCATCGAGTC
645 CCTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTA-GATGAATATAGATATTTCAAGGAGTC
* *
4372 TTTCTGCCAAAAATCATTCAAAACTGAGCCGGGG-CCCCAAAACGCGTTTTTAGCCCAAAAACCA
709 TTTCTGCCAAAAATCATTCAAAACTAAGCCGGGGCCCCCGAAACGCGTTTTTAGCCCAAAAACCA
* * * * *
4436 TAATGCTTAGTATACGATTTTCGGCTAAAAACTGACCCG-ATTTTTTTCCTAAATTTTTTGCTAC
774 TGATGCTTAGTACACGATTTTCGGCTAAAAACTGACCCGAATTTTTTTTCTGAATTTTTTGCCAC
* * **
4500 AATACTCAG-AAAAATCTATAATTCAACACCAAAAAGATTGATGGTC
839 AATACCCAGAAAAAATATATAATTCAACTTCAAAAAGATTGATGGTC
* * * * *
4546 TTTTCATGCTTTTAATATCATTTTTCTATTTTTTTTCCGAATCTATTTCTAATTAAATTGAAACA
1 TTTTCACGCTTTTAACATCATTTTTCCA-ATTTTTTCCGAATCTATTTCTAATTAAATCGAAACA
* * * *
4611 ATATTCAGTTGCTCATAAAAACAAATCCTTAAATCTACTGTGGCTGAGAGCCTGAGATTGGTTAG
65 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCT-AGA-CC-GAGATTGGTTAG
* * * * * * *
4676 ATGGATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTCAAAACTGAGTCGGGGCCCCGA
127 ATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGG
* * * * * *
4741 AACGCGTTTTTAGCTAAAAAGCGTGAGGGTTAGTACACGATTTCGGCTAAAAAATTA-C-CAAAA
192 AACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAA
** * **** * *** * * *
4804 CTTTTTTTCTCCATTTTTTTATGCAATAGTTTTAAAGAATATATAATTTAAAGCCAAAAAGATTG
257 --GATTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAGGCCAAAAAGATTG
** * *
4869 AAGGGTTTTTTC-CCCTTCTAATATCGTTTTTCCACTTTTTT-CCGAATTAATTTCTAATTAAAT
320 AA-GGACTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTCCCGAATTAATTTTTAATTAAAT
* * * * * * * * * *
4932 CGAAACAAGATTCAGAAGCTCGTATAAATAAATCCTCAAATCCATCGTGGCTGAGATTTGGTTTG
383 TGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCGAACGTGGCTG-GATTTTGTTCG
4997 ATGAATATAGATATTTCAAGGAGT
447 ATGAATATAGATATTTCAAGGAGT
5021 CTTTCTGCAA
Statistics
Matches: 2030, Mismatches: 170, Indels: 82
0.89 0.07 0.04
Matches are distributed among these distances:
881 59 0.03
882 106 0.05
883 347 0.17
884 77 0.04
885 660 0.33
886 301 0.15
887 9 0.00
888 206 0.10
889 170 0.08
890 79 0.04
891 14 0.01
892 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (885 bp):
TTTTCACGCTTTTAACATCATTTTTCCAATTTTTTCCGAATCTATTTCTAATTAAATCGAAACAA
GATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTAGACCGAGATTGGTTAGATGA
ATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAACG
CGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAGATT
TTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAGGCCAAAAAGATTGAAGGAC
TTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCCGAATTAATTTTTAATTAAATTGAAACAA
GATTCAGATGCTCGTAAAAACAAATACTTAAATCGAACGTGGCTGGATTTTGTTCGATGAATATA
GATATTTCAAGGAGTATTTACGTCAAAAATCATGCACAAACAAAAAAATATTTTCGGCAAAAAAT
ACACAATTCAACGCAAAAAGAAAATTGAAATACTTTTCTCGCTTTAAATATCATTTTTCTATTTT
TTTTCCGAATCTATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAAAAACAAATCCTTAA
ATCTAATGTGGCTGAGAGCCTGAGATTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGC
CAAAAATCATTCAAAACTAAGCCGGGGCCCCCGAAACGCGTTTTTAGCCCAAAAACCATGATGCT
TAGTACACGATTTTCGGCTAAAAACTGACCCGAATTTTTTTTCTGAATTTTTTGCCACAATACCC
AGAAAAAATATATAATTCAACTTCAAAAAGATTGATGGTC
Found at i:3995 original size:322 final size:326
Alignment explanation
Indices: 3331--4156 Score: 1052
Period size: 322 Copynumber: 2.5 Consensus size: 326
3321 AATTGAAATA
* * * * *
3331 CTTTTCTCGCTTTAAATATCATTTTTCTATTTTTTTCTGAATCT-ATCTCTAATTAAATCGAAAC
1 CTTTTCACGCTTTTAATATCATTTTTCCATTTTTTTCCGAAT-TAATTTCTAATTAAATCGAAAC
* * * *
3395 AATATTCAGATGCTCGTAAAAACAAATCTTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTA
65 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCGAATGTGGCT--GA--C--A-TTTGGTTA
*
3460 GATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTCAAAACTAAGCCGGGGCCCCC
123 GATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATTCAAAACTAAGCCGGGGCCCCC
3525 GAAACGCGTTTTTAGCCCAAAAACCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCG
188 GAAACGCGTTTTTAGCCCAAAAACCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCG
*** * **
3590 AATTTTTTTTTTCTGAATCTTTTGCCACAATACCCAGAAAAAATATATAATTCAACTTCAAAAAG
253 AATAAGTTTTTTCTCAATCTTTTGCCACAATACCCAGAAAAAATATATAATTCAACGCCAAAAAG
* *
3655 ATTGATGGT
318 ATTGACGGG
* *
3664 CTTTTCACGCTTTTAACATCATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
1 CTTTTCACGCTTTTAATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * *
3729 AGATTCAGATGCTCGTAAAAATAAATCCTTATATTC-AATGTGGCTGACATTTGGTTTGATGAAT
66 AGATTCAGATGCTCGTAAAAACAAATCCTTA-AATCGAATGTGGCTGACATTTGGTTAGATGAAT
* * * * * * * *
3793 ATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGG-CTCGGGAACGC
130 ATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATTCAAAACTAAGCCGGGGCCCCCGAAACGC
* * *
3857 GTTTTTAG-CCAAAAACCGTGATTGTTAGTACACGA-TTTCGGCTAAAAACTGATCCGAA-AAGT
195 GTTTTTAGCCCAAAAACCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGAATAAGT
* *
3919 TTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACG
260 TTTTTCTCAATCTTTTGCCACAATACCCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACG
3984 GG
325 GG
* * * * *
3986 CTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCTAATTAATTTTTAATTAAATTGAAACA
1 CTTTTCACGCTTTTAATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * * ** * *
4051 AGATTCATATGCTTGTAAAAACAAATACTTAAATCGAATGTGGCTGGGATTTTGTTCGATGAATA
66 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGACATTTGGTTAGATGAATA
* * * * *
4116 TGGATATTTCAATGAGTATTTACGTCAAAAATCATTCAAAA
131 TAGATATTTCAAGGAGTCTTTATGCCAAAAATCATTCAAAA
4157 ACAAAATAAA
Statistics
Matches: 433, Mismatches: 57, Indels: 17
0.85 0.11 0.03
Matches are distributed among these distances:
321 3 0.01
322 205 0.47
323 22 0.05
324 25 0.06
325 16 0.04
326 61 0.14
327 1 0.00
329 1 0.00
331 2 0.00
332 1 0.00
333 93 0.21
334 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (326 bp):
CTTTTCACGCTTTTAATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGACATTTGGTTAGATGAATA
TAGATATTTCAAGGAGTCTTTATGCCAAAAATCATTCAAAACTAAGCCGGGGCCCCCGAAACGCG
TTTTTAGCCCAAAAACCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGAATAAGTT
TTTTCTCAATCTTTTGCCACAATACCCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGG
G
Done.