Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008098.1 Corchorus capsularis cultivar CVL-1 contig08119, 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: 12563
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:2049 original size:332 final size:331
Alignment explanation
Indices: 1--3333 Score: 3661
Period size: 332 Copynumber: 10.2 Consensus size: 331
* * *
1 AAAGAAGTTTGAAGGGCTTTTTACACTTCTATTATCGTATTTCCATTTTTTTCTAAATTAATTTC
1 AAAGAAGATTGAAGGGCTTTTTACACTTCTATTATCGTTTTTCCATTTTTTTCTGAATTAATTTC
* * * *
66 TAATAAAATCAAAACAA-ACTTCTAAT-CTTTGGAAAAACAAAACATTAAATCCATTTTGTCTGA
66 TAATAAAATCGAAACAAGA-TTCTAATGC-TCGTAAAAACAAAACATTAAATCCATTGTGTCTGA
* * ** * * * * *
129 GATTTTGTATAAAAAATATAGATAATTCATGGACCCTTCGCACCAAAAATCATATAAAACTAAGA
129 GATTTGGTATGATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCATACAAAACT-ATA
* * * **
194 T-GGGGTCCACGAACGCGTTTTTTA--AAAAAAATCATGATGGTTATTACTTGATTTCAGCTAAA
193 TCGGGG-CCAGGAACGCG-TTTTTAGCAAAAAAATCGTGATGGTTAATACACGATTTCAGCTAAA
* * * ** * *
256 ATTATGCCAAAATT-ATCCCGAAAGATAATTGCTC-ATTTGAAGCCACAATTGTCATAGAATTAT
256 ATTTTGCAAAAATTGA-CCCGAAAGATATTTGCTCAATTTTTAGCCACAATTATCATAGAAATAT
319 GTAATTCAACAT
320 GTAATTCAACAT
* * * * * *
331 AAAAAAAGATTGCAGGACTTTTTACACTTCCATTATCGTTTTTCCATTTTTTTCTGATTTAAATT
1 -AAAGAAGATTGAAGGGCTTTTTACACTTCTATTATCGTTTTTCCATTTTTTTCTGAATTAATTT
* * * *
396 CTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCGTTAAATCCATTGTGGCTGAG
65 CTAATAAAATCGAAACAAGATTCTAATGCTCGTAAAAACAAAACATTAAATCCATTGTGTCTGAG
* * * * *
461 ATTTGGTTTGATGAATATAGATATCTCATGGACTCTTGGCACCAAAAATCACACGAAACTA-AAC
130 ATTTGGTATGATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCATACAAAACTATATC
* *
525 TGGGGCGCCGGAACGCGTTTTTAGCAAAAAAATC--G-T-G---AT----GATTTCAGCGAAAAT
195 -GGGGC-CAGGAACGCGTTTTTAGCAAAAAAATCGTGATGGTTAATACACGATTTCAGCTAAAAT
*
579 TTTGCAAAAATTGAACCGAAAGATATTTGCTCAATTTTTAGCCACAATTATCATAGAAATATGTA
258 TTTGCAAAAATTGACCCGAAAGATATTTGCTCAATTTTTAGCCACAATTATCATAGAAATATGTA
*
644 ACTCAACAT
323 ATTCAACAT
* *
653 AAAGAA-ATTTCAAGGGCTTTTTACACTTCTATTATCGTATTTCCA-TTTTTTCTGAATTAATTT
1 AAAGAAGA-TTGAAGGGCTTTTTACACTTCTATTATCGTTTTTCCATTTTTTTCTGAATTAATTT
* * *
716 CTGATAAAATCAAAACAAGATTCTAGTGCTCAG-AAAAACAAAACATTAAATCCATTGTGTCTGA
65 CTAATAAAATCGAAACAAGATTCTAATGCTC-GTAAAAACAAAACATTAAATCCATTGTGTCTGA
* * * * * * * *
780 GATTTCGTATGACGAAGATAGATATTTTATGGACCCTAGGCACCAAAAATCATATAAAACTATGT
129 GATTTGGTATGATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCATACAAAACTATAT
* * *
845 TGAGGCCCAGGAACGCGTTTTT--CACAAAAAATCGTGATGGTTATTACACGATTTCAGCTAAAA
194 CG-GGGCCAGGAACGCGTTTTTAGCA-AAAAAATCGTGATGGTTAATACACGATTTCAGCTAAAA
* * * *
908 TTTTGCAAAAATTGACCCGAAAGATTTTTGCTCAATTTTTAGCCACAATAATCATAGAATTATAT
257 TTTTGCAAAAATTGACCCGAAAGATATTTGCTCAATTTTTAGCCACAATTATCATAGAAATATGT
973 AATTCAACAT
322 AATTCAACAT
* * * * * *
983 TAAGAAGATTGAAGGACTTTTAACGCTTATATTAT-GATTTTTCCA-TTTTTTATGAATTAATTT
1 AAAGAAGATTGAAGGGCTTTTTACACTTCTATTATCG-TTTTTCCATTTTTTTCTGAATTAATTT
* * * * *
1046 CTTATAAAATCGAAACAAGATTCTGATACTCGTAAAAACAAATCCTTAAATCCATTGTAG-CTGA
65 CTAATAAAATCGAAACAAGATTCTAATGCTCGTAAAAACAAAACATTAAATCCATTGT-GTCTGA
* * *
1110 GATTTGATATGATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCACACAAAACTGA-G
129 GATTTGGTATGATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCATACAAAACT-ATA
* * * * * *
1174 CCGGGGCGCCGGAACGCGTTCTTAGCAAAAAACATTGTGATGGTTAGTACACGATTTCTGCTAAA
193 TCGGGGC-CAGGAACGCGTTTTTAGCAAAAAA-ATCGTGATGGTTAATACACGATTTCAGCTAAA
* *
1239 ATTTTTGCAAAAATT-ACCCTAAAGATGTTTGCTCAATTTTTAGCCACAATTATCATAGAAATAT
256 A-TTTTGCAAAAATTGACCCGAAAGATATTTGCTCAATTTTTAGCCACAATTATCATAGAAATAT
* * *
1303 GTGACTCGACAT
320 GTAATTCAACAT
* ** * *
1315 AAAGAAGTTTGAACAGCTTTTTACACTTCTATTATCGTATTTCCATTTTTTTCTTAATTAATTTC
1 AAAGAAGATTGAAGGGCTTTTTACACTTCTATTATCGTTTTTCCATTTTTTTCTGAATTAATTTC
* * * * *
1380 TAATAAAATCGAAACAAGCTTCTAATGCTTGGAAAAGCAAAACATTAAATCCATTTTGTCTGAGA
66 TAATAAAATCGAAACAAGATTCTAATGCTCGTAAAAACAAAACATTAAATCCATTGTGTCTGAGA
* * * * *
1445 TTTGGTATGACGAATATAGATATTTCATGCACCCTTGGCACCAAAAATCATATAAAACTAAGAT-
131 TTTGGTATGATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCATACAAAACT-ATATC
* * *
1509 GGGGTCCACGAACGCGTTTTTAGAAAAAAAAAATCGTGATGCTTAGA-ACACGATTTCAGCTAAA
195 GGGG-CCAGGAACGCGTTTTTAG--CAAAAAAATCGTGATGGTTA-ATACACGATTTCAGCTAAA
* * * *
1573 ATTTTGCAAAAATTAACCCGAAAGATATTTTCTC-ATTTTTAAGCCAAAATTGTCATAGAAATAT
256 ATTTTGCAAAAATTGACCCGAAAGATATTTGCTCAATTTTT-AGCCACAATTATCATAGAAATAT
*
1637 GTAATTCAATAT
320 GTAATTCAACAT
* ** * *
1649 AAAAAAGATCAAAGGGCTTTTTACACTTCCATTATCGTTTTTCCATTTTTTTCTGAATTAAATTC
1 AAAGAAGATTGAAGGGCTTTTTACACTTCTATTATCGTTTTTCCATTTTTTTCTGAATTAATTTC
* * *
1714 TAATAAAATCGAAACAAGATTTTAATGCTCATAAAAACAAAACCA-TGAATCCATTGTGTCTGAG
66 TAATAAAATCGAAACAAGATTCTAATGCTCGTAAAAACAAAA-CATTAAATCCATTGTGTCTGAG
* * * *
1778 ATTTGGTATAATGAATATTGAAATTTCATGGACTCTTGGCACAAAAAATCATACAAAACTGA-AT
130 ATTTGGTATGATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCATACAAAACT-ATAT
* * *
1842 CGGGGCCTAGGAACGCGTTTTTAGCAAAAAAATCGTGATGGTTAATACAGGATTTTAACTAAAAT
194 CGGGGCC-AGGAACGCGTTTTTAGCAAAAAAATCGTGATGGTTAATACACGATTTCAGCTAAAAT
* * * *
1907 TTTGCAAAAATTGACCCGAAAGATTTTTGCTCAATTTTTAGCCACAATAATTATAGAAATATATA
258 TTTGCAAAAATTGACCCGAAAGATATTTGCTCAATTTTTAGCCACAATTATCATAGAAATATGTA
1972 ATTCAACAT
323 ATTCAACAT
* * * ** * * *
1981 CAAGAATATTGAAGGGCTTTTCATGCTTCTAATATCGTTTTTCCTTTTTTTTTTGAATTAATTTC
1 AAAGAAGATTGAAGGGCTTTTTACACTTCTATTATCGTTTTTCCATTTTTTTCTGAATTAATTTC
* * * *
2046 TAATAAAAT-----C--GA-TCTGATACTCGTAAAAACAAAACCTTAAATCCATTGTGGCTGAGA
66 TAATAAAATCGAAACAAGATTCTAATGCTCGTAAAAACAAAACATTAAATCCATTGTGTCTGAGA
* * * *
2103 TTTGGTTTGATGAACATAGATATTTCATGGACTTTTGGCATCGAAAAA-CATAC-AAACTA-AGT
131 TTTGGTATGATGAATATAGATATTTCATGGACTCTTGGCA-CCAAAAATCATACAAAACTATA-T
* ** * * *
2165 TGCAGCCAACGAACGCGTTTTTAGC-AAAAAATCGTGATGGTTAATACACAATTTTAGCTAAAAT
194 CGGGGCC-AGGAACGCGTTTTTAGCAAAAAAATCGTGATGGTTAATACACGATTTCAGCTAAAAT
**** * * * *
2229 TAAAAAAAAAAAATTGACCCTAAAGGTTTTTGCTCAA-TTTTAGCCACAATAATCATAGAAATAT
258 T---TTGCAAAAATTGACCCGAAAGATATTTGCTCAATTTTTAGCCACAATTATCATAGAAATAT
*
2293 ATAATTCAACAT
320 GTAATTCAACAT
* * * * * * *
2305 TAAGAAGATTGAAGTGATTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTATGAATTAATTTC
1 AAAGAAGATTGAAGGGCTTTTTACACTTCTATTATCGTTTTTCCATTTTTTTCTGAATTAATTTC
** * * * * * *
2369 TTCTAAAATCAAAACAAGAGTCTGATGCTCGTAAAAACAAATTC-TTAAATCCTTTGTGGCTGAG
66 TAATAAAATCGAAACAAGATTCTAATGCTCGTAAAAACAAA-ACATTAAATCCATTGTGTCTGAG
* * * *
2433 ATTTGGTTTGATGAATATAGATATTTCATGGACTCTTAGC-CCTTAAAATCACACAAAACTGA-A
130 ATTTGGTATGATGAATATAGATATTTCATGGACTCTTGGCACC-AAAAATCATACAAAACT-ATA
* * * *
2496 -CTGGGGCACCGGAACGCGTTTTTAGCAAAAAAAAAAATCGTAATAGTTAGTACACGATTTCAGC
193 TC-GGGGC-CAGGAACGCGTTTTTAGC----AAAAAAATCGTGATGGTTAATACACGATTTCAGC
*
2560 TAAAATTTTGCAAAAATTGACCCGAAATATATTTGCTCAATTTTTAGCCACAATTATCATAGAAA
252 TAAAATTTTGCAAAAATTGACCCGAAAGATATTTGCTCAATTTTTAGCCACAATTATCATAGAAA
*
2625 TATGTAACTCAACAT
317 TATGTAATTCAACAT
* * *
2640 AAAGAAGTTTCAAGGGCTTTTTACACTTCTATTATCGTATTTCCATTTTTTTCTGAATTAATTTC
1 AAAGAAGATTGAAGGGCTTTTTACACTTCTATTATCGTTTTTCCATTTTTTTCTGAATTAATTTC
*
2705 TAATAAAATCGAAACAAGATTCTAATGCTCGGAAAAACAAAACATTAAATCCATTGTGTCTGAGA
66 TAATAAAATCGAAACAAGATTCTAATGCTCGTAAAAACAAAACATTAAATCCATTGTGTCTGAGA
* * * * *
2770 TTTGGTATGACGAATATAGATATGTCATGGA-TCCTTGACACCAAAAATCATATAAAACTATGTC
131 TTTGGTATGATGAATATAGATATTTCATGGACT-CTTGGCACCAAAAATCATACAAAACTATATC
*
2834 GGGGCCTAGGAACGCGTTTTTAGCAAAAAAATCGTGATGGTTAGTACACGATTTCAGCTAAAATT
195 GGGGCC-AGGAACGCGTTTTTAGCAAAAAAATCGTGATGGTTAATACACGATTTCAGCTAAAATT
* ** *
2899 TTGCGAAAATTGACTTGAAAGATATTTGCTTAATTTTTAGCCACAATTATCATAGAAATATGTAA
259 TTGCAAAAATTGACCCGAAAGATATTTGCTCAATTTTTAGCCACAATTATCATAGAAATATGTAA
*
2964 CTCAACAT
324 TTCAACAT
* * *
2972 AAAGAAGTTTGAAGGACTTTTAACACTTCTATTATCGTACTTTT--ATTTTTTTCTGAATTAATT
1 AAAGAAGATTGAAGGGCTTTTTACACTTCTATTATCGT--TTTTCCATTTTTTTCTGAATTAATT
* * *
3035 TCTAATAAAATCGAAACAAGCTTCTAATGCTTGGAAAAACAAAACATTAAATCCATTGTGTCTGA
64 TCTAATAAAATCGAAACAAGATTCTAATGCTCGTAAAAACAAAACATTAAATCCATTGTGTCTGA
* * * * *
3100 GATTTGATATGACGAATATAGATATTTCATGGACCCTTGGCACCAAAAATCATATAAAACTATGT
129 GATTTGGTATGATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCATACAAAACTATAT
*
3165 CGGGGCCCAGGAACGCGTTTTTAGTAAAAAAATC------G----T----GA--T--G---AAAT
194 CGGGG-CCAGGAACGCGTTTTTAGCAAAAAAATCGTGATGGTTAATACACGATTTCAGCTAAAAT
* * * * *
3209 TTTGCAAAAATTGACCCAAAAAATATTTGCTCAAGTTTTAGCAACTATTATCATAGAAATATGTA
258 TTTGCAAAAATTGACCCGAAAGATATTTGCTCAATTTTTAGCCACAATTATCATAGAAATATGTA
*
3274 AATCAACAT
323 ATTCAACAT
* *
3283 CAAA-AAAATTGAAGGGCTTTTTACACTTCTATTATCGTATTTCCATTTTTT
1 -AAAGAAGATTGAAGGGCTTTTTACACTTCTATTATCGTTTTTCCATTTTTT
3334 AAATACCGTG
Statistics
Matches: 2557, Mismatches: 354, Indels: 202
0.82 0.11 0.06
Matches are distributed among these distances:
309 3 0.00
311 105 0.04
312 3 0.00
314 1 0.00
316 1 0.00
318 4 0.00
319 8 0.00
320 138 0.05
321 82 0.03
322 78 0.03
323 53 0.02
324 152 0.06
325 36 0.01
326 2 0.00
327 1 0.00
328 2 0.00
329 8 0.00
330 268 0.10
331 257 0.10
332 622 0.24
333 190 0.07
334 282 0.11
335 84 0.03
336 139 0.05
337 38 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (331 bp):
AAAGAAGATTGAAGGGCTTTTTACACTTCTATTATCGTTTTTCCATTTTTTTCTGAATTAATTTC
TAATAAAATCGAAACAAGATTCTAATGCTCGTAAAAACAAAACATTAAATCCATTGTGTCTGAGA
TTTGGTATGATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCATACAAAACTATATCG
GGGCCAGGAACGCGTTTTTAGCAAAAAAATCGTGATGGTTAATACACGATTTCAGCTAAAATTTT
GCAAAAATTGACCCGAAAGATATTTGCTCAATTTTTAGCCACAATTATCATAGAAATATGTAATT
CAACAT
Found at i:2534 original size:991 final size:982
Alignment explanation
Indices: 1--3204 Score: 3754
Period size: 991 Copynumber: 3.2 Consensus size: 982
* * * * * *
1 AAAGAAGT-TTGAAGGGCTTTTTACACTTCTATTATCGTATTTCCATTTTTTTCTAAATTAATTT
1 AAAGAA-TATTGAAGGACTTTTAACGCTTCTATTATCGTTTTTCC-TTTTTTTATGAATTAATTT
* * * * * * *
65 CTAATAAAATCAAAACAAACTTCTAAT-CTTTGGAAAAACAAAACATTAAATCCATTTTGTCTGA
64 CTAATAAAAT-----C-GA-TTCTGATAC-TCGTAAAAACAAAACCTTAAATCCATTGTGGCTGA
* ** * * * *
129 GATTTTG-TATAAAAAATATAGATAATTCATGGACCCTTCGCACCAAAAATCATATAAAACTAAG
121 GA-TTTGATATGATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCATA-CAAACTAAG
* * * *** *
193 AT-GGGGTCCACGAACGCGTTTTTTA-AAAAAAATCATGATGGTTATTACTTGATTTCAGCTAAA
184 -TCGGGG-CCACGAACGCG-TTTTTAGCAAAAAATCGTGATGGTTAATACACAATTTCTGCTAAA
**** * ** ** * *
256 ATT-ATGCCAAAATTATCCCGAAAGATAATTGCTC-ATTTGAAGCCACAATTGTCATAGAATTAT
246 ATTAAAAAAAAAATTA-CCCTAAAGATGTTTGCTCAATTTTTAGCCACAATTATCATAGAAATAT
* * *
319 GTAATTCAACATAAAAAAAGATTGCAGGACTTTTTACACTTCCATTATCGTTTTTCCATTTTTTT
310 GTAATTCAACAT-AAAGAAGATTGAAGGA-TTTTTACACTTCTATTATCGTTTTTCCATTTTTTT
* * *
384 CTGATTTAAATTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCGTTAAATCC
373 CTGAATTAATTTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCATTAAATCC
* *
449 ATTGTGGCTGAGATTTGGTTTGATGAATATAGATATCTCATGGACTCTTGGCACCAAAAATCACA
438 TTTGTGGCTGAGATTTGGTTTGATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCACA
*
514 CGAAACTAAACTGGGGCGCCGGAACGCGTTTTTAGC---AAAAAAATCGTGA---T------GAT
503 CAAAACT-AACTGGGGC-CCGGAACGCGTTTTTAGCAAAAAAAAAATCGTGATGTTAGACACGAT
*
567 TTCAGCGAAAATTTTGCAAAAATTGAA-CCGAAAGATATTTGCTCAATTTTTAGCCACAATTATC
566 TTCAGCTAAAATTTTGCAAAAATT-AACCCGAAAGATATTTGCTCAATTTTTAGCCACAATTATC
*
631 ATAGAAATATGTAACTCAACATAAAGAAATTTCAAGGGCTTTTTACACTTCTATTATCGTATTTC
630 ATAGAAATATGTAACTCAACATAAA-AAAGTTCAAGGGCTTTTTACACTTCTATTATCGTATTTC
* * *
696 CA-TTTTTTCTGAATTAATTTCTGATAAAATCAAAACAAGATTCTAGTGCTCAGAAAAACAAAAC
694 CATTTTTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCTAATGCTCAGAAAAACAAAAC
* * * * *
760 ATTAAATCCATTGTGTCTGAGATTTCGTATGACGAAGATAGATATTTTATGGACCCTAGGCACCA
759 ATTAAATCCATTGTGTCTGAGATTTGGTATGACGAATATAGATATTTCATGGACTCTTGGCACCA
* * *
825 AAAATCATATAAAACTATGTTGAGGCCCAGGAACGCGTTTTT--CACAAAAAATCGTGATGGTTA
824 AAAATCATATAAAACTATGTCGGGGCCTAGGAACGCGTTTTTAGCA-AAAAAATCGTGATGGTTA
*
888 TTACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTGCTCAATTTTTAGCCA
888 ATACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTGCTCAATTTTTAGCCA
*
953 CAATAATCATAGAATTATATAATTCAACAT
953 CAATAATCATAGAAATATATAATTCAACAT
* * * *
983 TAAGAAGATTGAAGGACTTTTAACGCTTATATTAT-GATTTTTCCATTTTTTATGAATTAATTTC
1 AAAGAATATTGAAGGACTTTTAACGCTTCTATTATCG-TTTTTCCTTTTTTTATGAATTAATTTC
* * *
1047 TTATAAAATCGAAACAAGATTCTGATACTCGTAAAAACAAATCCTTAAATCCATTGTAGCTGAGA
65 TAATAAAAT-----C--GATTCTGATACTCGTAAAAACAAAACCTTAAATCCATTGTGGCTGAGA
* * *
1112 TTTGATATGATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCACACAAAACTGAGCCG
123 TTTGATATGATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCATAC-AAACTAAGTCG
* * * *
1177 GGGCGC-CGGAACGCGTTCTTAGCAAAAAACATTGTGATGGTTAGTACACGATTTCTGCTAAAAT
187 GGGC-CAC-GAACGCGTTTTTAGC-AAAAA-ATCGTGATGGTTAATACACAATTTCTGCTAAAAT
***** *
1241 TTTTGCAAAAATTACCCTAAAGATGTTTGCTCAATTTTTAGCCACAATTATCATAGAAATATGTG
248 TAAAAAAAAAATTACCCTAAAGATGTTTGCTCAATTTTTAGCCACAATTATCATAGAAATATGTA
* * * * * * *
1306 ACTCGACATAAAGAAGTTTGAACAGCTTTTTACACTTCTATTATCGTATTTCCATTTTTTTCTTA
313 ATTCAACATAAAGAAGATTGAA-GGATTTTTACACTTCTATTATCGTTTTTCCATTTTTTTCTGA
* * * * * *
1371 ATTAATTTCTAATAAAATCGAAACAAGCTTCTAATGCTTGGAAAAGCAAAACATTAAATCCATTT
377 ATTAATTTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCATTAAATCC-TTT
* * * * * * *
1436 -TGTCTGAGATTTGGTATGACGAATATAGATATTTCATGCACCCTTGGCACCAAAAATCATATAA
441 GTGGCTGAGATTTGGTTTGATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCACACAA
*
1500 AACTAAGATGGGGTCCAC-GAACGCGTTTTTAG-AAAAAAAAAATCGTGATGCTTAGAACACGAT
506 AACTAA-CTGGGG-CC-CGGAACGCGTTTTTAGCAAAAAAAAAATCGTGATG-TTAG-ACACGAT
* * *
1563 TTCAGCTAAAATTTTGCAAAAATTAACCCGAAAGATATTTTCTC-ATTTTTAAGCCAAAATTGTC
566 TTCAGCTAAAATTTTGCAAAAATTAACCCGAAAGATATTTGCTCAATTTTT-AGCCACAATTATC
* * * * *
1627 ATAGAAATATGTAATTCAATATAAAAAAGATCAAAGGGCTTTTTACACTTCCATTATCGTTTTTC
630 ATAGAAATATGTAACTCAACATAAAAAAGTTC-AAGGGCTTTTTACACTTCTATTATCGTATTTC
* * *
1692 CATTTTTTTCTGAATTAAATTCTAATAAAATCGAAACAAGATTTTAATGCTCATAAAAACAAAAC
694 CATTTTTTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCTAATGCTCAGAAAAACAAAA-
* * * * * *
1757 CA-TGAATCCATTGTGTCTGAGATTTGGTATAATGAATATTGAAATTTCATGGACTCTTGGCACA
758 CATTAAATCCATTGTGTCTGAGATTTGGTATGACGAATATAGATATTTCATGGACTCTTGGCACC
* *
1821 AAAAATCATACAAAACTGA-ATCGGGGCCTAGGAACGCGTTTTTAGCAAAAAAATCGTGATGGTT
823 AAAAATCATATAAAACT-ATGTCGGGGCCTAGGAACGCGTTTTTAGCAAAAAAATCGTGATGGTT
* * *
1885 AATACAGGATTTTAACTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTGCTCAATTTTTAGCC
887 AATACACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTGCTCAATTTTTAGCC
*
1950 ACAATAATTATAGAAATATATAATTCAACAT
952 ACAATAATCATAGAAATATATAATTCAACAT
* * * * * *
1981 CAAGAATATTGAAGGGCTTTTCATGCTTCTAATATCGTTTTTCCTTTTTTTTTTGAATTAATTTC
1 AAAGAATATTGAAGGACTTTTAACGCTTCTATTATCGTTTTTCC-TTTTTTTATGAATTAATTTC
* *
2046 TAATAAAATCGA-TCTGATACTCGTAAAAACAAAACCTTAAATCCATTGTGGCTGAGATTTGGTT
65 TAATAAAATCGATTCTGATACTCGTAAAAACAAAACCTTAAATCCATTGTGGCTGAGATTTGATA
* * * * **
2110 TGATGAACATAGATATTTCATGGACTTTTGGCATCGAAAAA-CATACAAACTAAGTTGCAGCCAA
130 TGATGAATATAGATATTTCATGGACTCTTGGCA-CCAAAAATCATACAAACTAAGTCGGGGCC-A
2174 CGAACGCGTTTTTAGCAAAAAATCGTGATGGTTAATACACAATTT-TAGCTAAAATTAAAAAAAA
193 CGAACGCGTTTTTAGCAAAAAATCGTGATGGTTAATACACAATTTCT-GCTAAAATT--AAAAAA
* * * *
2238 AAAATTGACCCTAAAGGTTTTTGCTCAA-TTTTAGCCACAATAATCATAGAAATATATAATTCAA
255 AAAATT-ACCCTAAAGATGTTTGCTCAATTTTTAGCCACAATTATCATAGAAATATGTAATTCAA
* * * * *
2302 CATTAAGAAGATTGAAGTGATTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTATGAATTAAT
319 CATAAAGAAGATTGAAG-GATTTTTACACTTCTATTATCGTTTTTCCATTTTTTTCTGAATTAAT
** * *
2366 TTCTTCTAAAATCAAAACAAGAGTCTGATGCTCGTAAAAACAAATTC-TTAAATCCTTTGTGGCT
383 TTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAAA-TCATTAAATCCTTTGTGGCT
* *
2430 GAGATTTGGTTTGATGAATATAGATATTTCATGGACTCTTAGC-CCTTAAAATCACACAAAACTG
447 GAGATTTGGTTTGATGAATATAGATATTTCATGGACTCTTGGCACC-AAAAATCACACAAAACT-
*
2494 AACTGGGGCACCGGAACGCGTTTTTAGCAAAAAAAAAAATCGTAATAGTTAGTACACGATTTCAG
510 AACTGGGGC-CCGGAACGCGTTTTTAGC-AAAAAAAAAATCGTGAT-GTTAG-ACACGATTTCAG
* *
2559 CTAAAATTTTGCAAAAATTGACCCGAAATATATTTGCTCAATTTTTAGCCACAATTATCATAGAA
571 CTAAAATTTTGCAAAAATTAACCCGAAAGATATTTGCTCAATTTTTAGCCACAATTATCATAGAA
*
2624 ATATGTAACTCAACATAAAGAAGTTTCAAGGGCTTTTTACACTTCTATTATCGTATTTCCATTTT
636 ATATGTAACTCAACATAAAAAAG-TTCAAGGGCTTTTTACACTTCTATTATCGTATTTCCATTTT
*
2689 TTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCTAATGCTCGGAAAAACAAAACATTAAA
700 TTTCTGAATTAATTTCTAATAAAATCGAAACAAGATTCTAATGCTCAGAAAAACAAAACATTAAA
* *
2754 TCCATTGTGTCTGAGATTTGGTATGACGAATATAGATATGTCATGGA-TCCTTGACACCAAAAAT
765 TCCATTGTGTCTGAGATTTGGTATGACGAATATAGATATTTCATGGACT-CTTGGCACCAAAAAT
*
2818 CATATAAAACTATGTCGGGGCCTAGGAACGCGTTTTTAGCAAAAAAATCGTGATGGTTAGTACAC
829 CATATAAAACTATGTCGGGGCCTAGGAACGCGTTTTTAGCAAAAAAATCGTGATGGTTAATACAC
* ** * * *
2883 GATTTCAGCTAAAATTTTGCGAAAATTGACTTGAAAGATATTTGCTTAATTTTTAGCCACAATTA
894 GATTTCAGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTGCTCAATTTTTAGCCACAATAA
* *
2948 TCATAGAAATATGTAACTCAACAT
959 TCATAGAAATATATAATTCAACAT
* * *
2972 AAAGAAGT-TTGAAGGACTTTTAACACTTCTATTATCGTACTTTT-ATTTTTTTCTGAATTAATT
1 AAAGAA-TATTGAAGGACTTTTAACGCTTCTATTATCGT--TTTTCCTTTTTTTATGAATTAATT
* * * * * *
3035 TCTAATAAAATCGAAACAAGCTTCTAATGCTTGGAAAAACAAAACATTAAATCCATTGTGTCTGA
63 TCTAATAAAATCG-----A--TTCTGATACTCGTAAAAACAAAACCTTAAATCCATTGTGGCTGA
* * * *
3100 GATTTGATATGACGAATATAGATATTTCATGGACCCTTGGCACCAAAAATCATATAAAACTATGT
121 GATTTGATATGATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCATA-CAAACTAAGT
* *
3165 CGGGGCCCAGGAACGCGTTTTTAGTAAAAAAATCGTGATG
185 CGGGG-CCACGAACGCGTTTTTAG-CAAAAAATCGTGATG
3205 AAATTTTGCA
Statistics
Matches: 1888, Mismatches: 254, Indels: 141
0.83 0.11 0.06
Matches are distributed among these distances:
980 11 0.01
981 126 0.07
982 44 0.02
983 221 0.12
984 49 0.03
985 13 0.01
987 1 0.00
988 37 0.02
989 140 0.07
990 108 0.06
991 553 0.29
992 18 0.01
993 4 0.00
994 1 0.00
995 13 0.01
996 109 0.06
997 142 0.08
998 151 0.08
999 106 0.06
1000 25 0.01
1001 16 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (982 bp):
AAAGAATATTGAAGGACTTTTAACGCTTCTATTATCGTTTTTCCTTTTTTTATGAATTAATTTCT
AATAAAATCGATTCTGATACTCGTAAAAACAAAACCTTAAATCCATTGTGGCTGAGATTTGATAT
GATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCATACAAACTAAGTCGGGGCCACGA
ACGCGTTTTTAGCAAAAAATCGTGATGGTTAATACACAATTTCTGCTAAAATTAAAAAAAAAATT
ACCCTAAAGATGTTTGCTCAATTTTTAGCCACAATTATCATAGAAATATGTAATTCAACATAAAG
AAGATTGAAGGATTTTTACACTTCTATTATCGTTTTTCCATTTTTTTCTGAATTAATTTCTAATA
AAATCGAAACAAGATTCTGATGCTCGTAAAAACAAATCATTAAATCCTTTGTGGCTGAGATTTGG
TTTGATGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCACACAAAACTAACTGGGGCCC
GGAACGCGTTTTTAGCAAAAAAAAAATCGTGATGTTAGACACGATTTCAGCTAAAATTTTGCAAA
AATTAACCCGAAAGATATTTGCTCAATTTTTAGCCACAATTATCATAGAAATATGTAACTCAACA
TAAAAAAGTTCAAGGGCTTTTTACACTTCTATTATCGTATTTCCATTTTTTTCTGAATTAATTTC
TAATAAAATCGAAACAAGATTCTAATGCTCAGAAAAACAAAACATTAAATCCATTGTGTCTGAGA
TTTGGTATGACGAATATAGATATTTCATGGACTCTTGGCACCAAAAATCATATAAAACTATGTCG
GGGCCTAGGAACGCGTTTTTAGCAAAAAAATCGTGATGGTTAATACACGATTTCAGCTAAAATTT
TGCAAAAATTGACCCGAAAGATTTTTGCTCAATTTTTAGCCACAATAATCATAGAAATATATAAT
TCAACAT
Found at i:4806 original size:17 final size:17
Alignment explanation
Indices: 4784--4822 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
4774 GAACTTACTT
*
4784 CATTTCCAGCTGCGGAC
1 CATTTCCAGCTGCCGAC
4801 CATTTCCAGCTGCCGAC
1 CATTTCCAGCTGCCGAC
4818 CATTT
1 CATTT
4823 ACAACTTCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.36, G:0.18, T:0.28
Consensus pattern (17 bp):
CATTTCCAGCTGCCGAC
Found at i:4958 original size:84 final size:83
Alignment explanation
Indices: 4864--5102 Score: 330
Period size: 84 Copynumber: 3.0 Consensus size: 83
4854 GACGGTGGCT
*
4864 CTCAGCAGTGAGGCTCTCAAAATGGCCGCCGACTGCGAGACTCGCGACACGACACACACGAAGGT
1 CTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGACTCGCGACACGACACACACGAAGGT
4929 ACACGAGAAGGACAGCGG
66 ACACGAGAAGGACAGCGG
* **
4947 CCTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGGCTCGCGACACG--ACACACGAAAC
1 -CTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGACTCGCGACACGACACACACGAAGG
5010 TACACGAGAAGGACAGCGG
65 TACACGAGAAGGACAGCGG
* * * * * *
5029 CTC-TCA--GA--CTGTCAAAACGACCGCCGACTGCGAGTCTCGCGACACTACACACACAAAGGT
1 CTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGACTCGCGACACGACACACACGAAGGT
5089 ACACGAGAAGGACA
66 ACACGAGAAGGACA
5103 ACGGGTCTCG
Statistics
Matches: 141, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
76 34 0.24
78 25 0.18
80 2 0.01
81 3 0.02
82 28 0.20
84 49 0.35
ACGTcount: A:0.31, C:0.32, G:0.27, T:0.10
Consensus pattern (83 bp):
CTCAGCAGTGAGGCTCTCAAAACGGCCGCCGACTGCGAGACTCGCGACACGACACACACGAAGGT
ACACGAGAAGGACAGCGG
Found at i:5070 original size:76 final size:78
Alignment explanation
Indices: 4876--5111 Score: 278
Period size: 76 Copynumber: 2.9 Consensus size: 78
4866 CAGCAGTGAG
* *
4876 GCTCTCAAAATGGCCGCCGACTGCGAGACTCGCGACACGACACACACGAAGGTACACGAGAAGGA
1 GCTCTCAAAACGGCCGCCGACTGCGAGACTCGCGACACG--ACACACGAAAGTACACGAGAAGGA
*
4941 CAGCGGCCTCAGCAGTGA
64 CAGCGG-CTC-TCAG-GA
* *
4959 GGCTCTCAAAACGGCCGCCGACTGCGAGGCTCGCGACACGACACACGAAACTACACGAGAAGGAC
1 -GCTCTCAAAACGGCCGCCGACTGCGAGACTCGCGACACGACACACGAAAGTACACGAGAAGGAC
5024 AGCGGCTCTCA-GA
65 AGCGGCTCTCAGGA
* * * * *
5037 -CTGTCAAAACGACCGCCGACTGCGAGTCTCGCGACACTACACACACAAAGGTACACGAGAAGGA
1 GCTCTCAAAACGGCCGCCGACTGCGAGACTCGCGACACGACACAC-GAAA-GTACACGAGAAGGA
* *
5101 CAACGGGTCTC
64 CAGCGGCTCTC
5112 GCGACACTAC
Statistics
Matches: 137, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
76 40 0.29
77 3 0.02
78 24 0.18
80 2 0.01
81 3 0.02
82 28 0.20
84 37 0.27
ACGTcount: A:0.31, C:0.32, G:0.27, T:0.10
Consensus pattern (78 bp):
GCTCTCAAAACGGCCGCCGACTGCGAGACTCGCGACACGACACACGAAAGTACACGAGAAGGACA
GCGGCTCTCAGGA
Found at i:5126 original size:45 final size:45
Alignment explanation
Indices: 5062--5147 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
5052 CCGACTGCGA
5062 GTCTCGCGACACTACACACACAAAGGTACACGAGAAGGACAACGG
1 GTCTCGCGACACTACACACACAAAGGTACACGAGAAGGACAACGG
* *
5107 GTCTCGCGACACTACACACACGAAGGTACAGGAGAAGGACA
1 GTCTCGCGACACTACACACACAAAGGTACACGAGAAGGACA
5148 GCAGCTTCAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.37, C:0.28, G:0.26, T:0.09
Consensus pattern (45 bp):
GTCTCGCGACACTACACACACAAAGGTACACGAGAAGGACAACGG
Found at i:5250 original size:84 final size:84
Alignment explanation
Indices: 5109--5375 Score: 410
Period size: 84 Copynumber: 3.2 Consensus size: 84
5099 GACAACGGGT
* * *
5109 CTCGCGACACTACACACACGAAGGTACAGGAGAAGGACAGCAGCTTCAGCAGTGAGGCTCTCAAA
1 CTCGCGACACGACACACACGAAGGTACACGAGAAGGACAGCAGCCTCAGCAGTGAGGCTCTCAAA
5174 ACGGCCGCCGACTACGAGG
66 ACGGCCGCCGACTACGAGG
* * *
5193 CTCGCGACACTACACACACGAAGGTACACGAGAAAGACAGCGGCCTCAGCAGTGAGGCTCTCAAA
1 CTCGCGACACGACACACACGAAGGTACACGAGAAGGACAGCAGCCTCAGCAGTGAGGCTCTCAAA
*
5258 ACGGCTGCCGACTACGAGG
66 ACGGCCGCCGACTACGAGG
* *
5277 CTCGCGACACGACACACGCGAAGGTACACGAGAAGGACAGCAACCTCAGCAGTGAGGCTCTCAAA
1 CTCGCGACACGACACACACGAAGGTACACGAGAAGGACAGCAGCCTCAGCAGTGAGGCTCTCAAA
* * *
5342 AC-ACCGCCGACTGCAAGG
66 ACGGCCGCCGACTACGAGG
*
5360 GTCGCGACACGACACA
1 CTCGCGACACGACACA
5376 ATGGGAGCAG
Statistics
Matches: 168, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
83 27 0.16
84 141 0.84
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.10
Consensus pattern (84 bp):
CTCGCGACACGACACACACGAAGGTACACGAGAAGGACAGCAGCCTCAGCAGTGAGGCTCTCAAA
ACGGCCGCCGACTACGAGG
Done.