Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013649.1 Corchorus capsularis cultivar CVL-1 contig13670, 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: 25262
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Found at i:622 original size:334 final size:331
Alignment explanation
Indices: 1--3401 Score: 3442
Period size: 334 Copynumber: 10.3 Consensus size: 331
* * *
1 GCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAATATGGCGGCCGGA
1 GCGTGA-AAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTCTATGAATATCGTGGCCGGA
* * * *
66 AATTGAGGAGAAATTTCTCG-GATTAATTTTGGCAAAATTTTAGCTGAAATTGTGCACTAACCAT
65 AATTGAGGAGAAATTTTTCGAG-TCAATTTTGACAAAATTTTAGCTGAAATCGTGCACTAACCAT
* *
130 CACGGTTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTAGCGCCT
129 CACGG-TTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTGGCGCCA
* *
195 AGTCTCATTGAAATATCTATATCCATCTAAACAAATCT-TTCCAACATTTGATTTAAGGATTTGT
193 AGACTCATTGAAATATCTATATCCATCTAAACAAATCTCTGCCAA-ATTTGATTTAAGGATTTGT
* * *
259 TTTTACGAGCATATAAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAATAATAGGAAAACC
257 TTTTACGAGCATATCAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAGAAAAACC
*
324 GATATTAGAA
322 AATATTAGAA
* * ** * **
334 GCGTGAATAGCCTTTCAATCTTTTAGATGTTGAATTATATATTTTCTATGATTATCGTGGCCAAA
1 GCGTGAA-AGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTCTATGAATATCGTGGCCGGA
* * * *
399 AATTGAGGA-AAATTATTTCGAGTCAATTTTCACAAAATTTTAGCCGAAATCGTGTACTGTTA-C
65 AATTGAGGAGAAATT-TTTCGAGTCAATTTTGACAAAATTTTAGCTGAAATCGTGCAC--TAACC
* * * *
462 ATCACGGTTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGC
127 ATCACGG-TTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTGGCGC
* * * ** * * *
527 CAAGAATCATTGAAATTTCCATATTTATCT-AACGAAATCTCAGCCAAATTGGATTTAAGGATCT
191 CAAGACTCATTGAAATATCTATATCCATCTAAAC-AAATCTCTGCCAAATTTGATTTAAGGATTT
** * * ** * *
591 GTTTTTACGATTATCTCCATCCGGTTTCGATTTAATTAGAAATTAATTCGGAAAATATAGAATAA
255 GTTTTTACGAGCATATCAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAGAA-AA
* *
656 AGCAATATTAGAG
319 ACCAATATTAGAA
* *
669 GCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAAATATATATTTTTTATGAATAT-GATGGCCTG
1 GCGTGA-AAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTCTATGAATATCG-TGGCC-G
* * * *
733 GAAATTGAGGAGAAATTTCTCG-GATTAATTTTGGCAAAATTTTAGCTGAAATCATGCACTAACC
63 GAAATTGAGGAGAAATTTTTCGAG-TCAATTTTGACAAAATTTTAGCTGAAATCGTGCACTAACC
* * * *
797 ATCACGGTTTTTGACTAAAAACGCGTTCTGGAGCCTCGACTCAGTTTTGCACGAGTTTTAGTGCC
127 ATCACGGTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTGGCGCC
* * *
862 TAGTCTCATTGAAATATCTATATCCATCTAAACAAATCT-TTCCAACATTTGATTTAAGGATTTG
192 AAGACTCATTGAAATATCTATATCCATCTAAACAAATCTCTGCCAA-ATTTGATTTAAGGATTTG
* * *
926 TTTTTACGAGCATATGAATCATGTTTCGATTTGATTAGGAATTAATTCGGAAAAAATAGGAAAAC
256 TTTTTACGAGCATATCAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAGAAAAAC
*
991 CGATATTAGAA
321 CAATATTAGAA
* ** * * * *
1002 GCGTGAATAGCCTTTCAATCTTTTACGTGTTGAATTATATATTTTCTATGATTATCGTAGCCGAA
1 GCGTGAA-AGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTCTATGAATATCGTGGCCGGA
* * * *
1067 AATTGAGGA-AAATTATTTCGAGTCAATTTTCACAAAATTTTAGCCGACATCGTGTACTAACCAT
65 AATTGAGGAGAAATT-TTTCGAGTCAATTTTGACAAAATTTTAGCTGAAATCGTGCACTAACCAT
* * * * *
1131 CACGGATTTTTTTGGCTAAAAACGCGTTCGGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGC
129 CACGG---TTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTGGCGC
* ** * * *
1196 CAAGACTCATTGAAATTTCTATATTTATCT-AACGAAATCTCAGCCAAATTGGATTTAAGGATCT
191 CAAGACTCATTGAAATATCTATATCCATCTAAAC-AAATCTCTGCCAAATTTGATTTAAGGATTT
* * * ** * * *
1260 GTTTTTACGATCATCTCCATCCGGTTTCGATTTAATTAGAAATTAATTCGGAAAATATATAATAA
255 GTTTTTACGAGCATATCAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAGAA-AA
* *
1325 AGCAATATTAGAG
319 ACCAATATTAGAA
* * * * *
1338 GCGTGAGAAGCCCTTGAATCTTTTTGACGTTGAAATATATATTTTTTATGAATATGGTGGCCGGA
1 GCGTGA-AAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTCTATGAATATCGTGGCCGGA
* * **
1403 AATTGAGGAGAAATTTCTCG-GTTTAATTTTGGTAAAATTTTAGCTGAAATCGTGCACTAACCAT
65 AATTGAGGAGAAATTTTTCGAG-TCAATTTTGACAAAATTTTAGCTGAAATCGTGCACTAACCAT
* *
1467 CACGGTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTAGCGCCTA
129 CACGGTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTGGCGCCAA
* * * * *
1532 GTCTCATTGAAATATCTATATCCATCTAAACAAATCTTTCCCACATTTGATATAAGGATTTGTTT
194 GACTCATTGAAATATCTATATCCATCTAAACAAATCTCTGCCAAATTTGATTTAAGGATTTGTTT
* * * * *
1597 TTACGAGCATATGAATCATGTTTCAATTTGATTAGGAATTAATTCGGAAAAAATAGGAAAACCGA
259 TTACGAGCATATCAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAGAAAAACCAA
1662 TATTAGAA
324 TATTAGAA
* * ** * * * *
1670 GCGTGAATAGCCTTTCAAACTTTTACGTGTTGAATAATATATTTTCTATGATTATCGTGGCC-AA
1 GCGTGAA-AGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTCTATGAATATCGTGGCCGGA
* *
1734 GAATTGAGGA-AAATTATTTCGAGTCAATTTTCACAAAATTTTAGCTGAAATCGTGTACTAACCA
65 -AATTGAGGAGAAATT-TTTCGAGTCAATTTTGACAAAATTTTAGCTGAAATCGTGCACTAACCA
* * * * * * *
1798 TCACGGTTTTTTTGGCTTAAAACGCGTTCAGG-GACCCCGGCTCGGTTTTGCATGATTTTTGGCA
128 TCACGG--TTTTTGACTAAAAACGCGTTCTGGAG-CCCCGACTCAGTTTTGCACGATTTTTGGCG
* * * * *
1862 CCAAGACTCATTGAAATTTCTATATCCATCTAAACAAATATTTCCCACATTTGATTTAAGGATTT
190 CCAAGACTCATTGAAATATCTATATCCATCTAAACAAATCTCTGCCAAATTTGATTTAAGGATTT
* *
1927 GTTTTTACGAGCATATGAATCATGTTTCGATTTGATTAGGAATTAATTCGG-AAAAATAGAAATA
255 GTTTTTACGAGCATATCAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAGAAA-A
* *
1991 AACATTATTAGAA
319 ACCAATATTAGAA
* *
2004 GCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAAATATATATTTTTTATGAATA-CGGTGGCCGG
1 GCGTGA-AAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTCTATGAATATC-GTGGCCGG
* ** * *
2068 AAATTGAGGAGAAATTTCTCGAGTTTATTTTGGCAAAATTTTAGCTGAAATCGTGCACAAACCAT
64 AAATTGAGGAGAAATTTTTCGAGTCAATTTTGACAAAATTTTAGCTGAAATCGTGCACTAACCAT
* * * * *
2133 CACGGTTTTTGACTAAAAACGCTTTCTGAAGCCCTGACTCAGTTTTTCACGATTTTCGGCGCCAA
129 CACGGTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTGGCGCCAA
* * * * * *
2198 GTCTCATTGAAATATCTATATCCATATAAACAAATCTTTTCCACATTTGATTTAAGGATTTATTT
194 GACTCATTGAAATATCTATATCCATCTAAACAAATCTCTGCCAAATTTGATTTAAGGATTTGTTT
* * ** * * *
2263 TTACGAGCATATGAATCATGTTTCGATTCAATTAAAAATTAATTCGGAAAAAATAGGAAAACTAC
259 TTACGAGCATATCAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAGAAAAACCAA
2328 TATTAGAA
324 TATTAGAA
* * * * **
2336 GCATGAATAGCCTTTCAATCTTTTAT-GTGTTGAATTATATATTTTCTATGAGTATCGTGGCCAA
1 GCGTGAA-AGCCCTTCAATCTTTT-TGGCGTTGAATTATATATTTTCTATGAATATCGTGGCCGG
* * * * ** *
2400 AAACTGAGGA-AAACTCTTTCGAGTCAATTTTTACAAAATTTTAGCCG--ATCGTTTACTAAACA
64 AAATTGAGGAGAAA-TTTTTCGAGTCAATTTTGACAAAATTTTAGCTGAAATCGTGCACTAACCA
* * * * * * *
2462 TCACTGTTTTTGGCTAAAAATGCGTTCTGGTGCCCCGATTCAGTTTTGCATGATTTTTGGCGTCA
128 TCACGGTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTGGCGCCA
* * ** * * *
2527 AGACTCGTTGAAATTTCTATATTTATCT-AACAAAATCTCAGTCAAATTGGATTTAAGGATTTGT
193 AGACTCATTGAAATATCTATATCCATCTAAAC-AAATCTCTGCCAAATTTGATTTAAGGATTTGT
* * * * ** * * *
2591 GTTTACGATCATCTCCATCCGGTTTCGATTTAATTAGGAATTATTTC-GAAAAAATTGAAAAAAA
257 TTTTACGAGCATATCAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAG-AAAAAC
*
2655 CAATATTTGAA
321 CAATATTAGAA
* * * * * *
2666 ACGAGAGAAGCCCTTCAATCTTTTTGGCATTGAAATGTATATTTT-TATGAATATTGTGGCCGGA
1 GCGTGA-AAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTCTATGAATATCGTGGCCGGA
* * *
2730 AATTGAGGAGAAATTTCTT-GGGTCAATTTTGACTAATTTTTAGCTGAAATCGTGCACTAACCAT
65 AATTGAGGAGAAATTT-TTCGAGTCAATTTTGACAAAATTTTAGCTGAAATCGTGCACTAACCAT
* * * * *
2794 CACTGTTTTTGACTAAAAATGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTAGCTCCTA
129 CACGGTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTGGCGCCAA
* * *
2859 GACTCATTGAAATATCTATATCCATCTAAACAAATCTTTCCCACATTTGATTTAAGGA-TTGTTT
194 GACTCATTGAAATATCTATATCCATCTAAACAAATCTCTGCCAAATTTGATTTAAGGATTTGTTT
** * *
2923 TTATAAGCATAT-GA--A----TC-------TT--G---T--TTCGGAAAAAATAGAAAAACCGA
259 TTACGAGCATATCAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAGAAAAACCAA
2967 TATTAGAA
324 TATTAGAA
* * * * **
2975 GCGTGAATAGCCTTTCAATCTTTTAGGTGTTGAATTATATATTTTCT-T-AGTATCGTGGCCAAA
1 GCGTGAA-AGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTCTATGAATATCGTGGCCGGA
* * * * * * *
3038 AATTGAGGA-AAATTCTTTCAAGGCAAAATTT-ACAAAATTTTTGCCG--ATCGTGTACTAACTA
65 AATTGAGGAGAAATT-TTTCGAGTC-AATTTTGACAAAATTTTAGCTGAAATCGTGCACTAACCA
* * * * * * * * * ** **
3099 TCATGATTTTTGGCTAAAAACACGTTCCGGGGTCCCGGCTCAGTTTTGCATGATTTTTTACTTCA
128 TCACGGTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTGGCGCCA
* ** * * *
3164 AGACTCATTGAAATTTCTATATTTATCT-AACAAAAT-T-TGAACTAAATTGGATTTCAGGATTT
193 AGACTCATTGAAATATCTATATCCATCTAAAC-AAATCTCTG--CCAAATTTGATTTAAGGATTT
* * * * * * * *
3226 ATTTTTACGATCATCTCCATTC-GGTTTCGATTTAATTAGAAATTAGTTCGAAAAAAATAGAAAA
255 GTTTTTACGAGCATAT-CAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAG-AAA
*
3290 AAACAATATTAGAA
318 AACCAATATTAGAA
* * * * * * *
3304 ACGAGAAAAACCCTTCAATCTTTTTGGCATTGAAATGTATATTTTTTTTATGAATATCGTGGCCA
1 GCGTG-AAAGCCCTTCAATCTTTTTGGCGTTG-AAT-TATATATTTTCTATGAATATCGTGGCCG
*
3369 GAAATTGAGGAGAAATTTCTC-ATGTCAATTTTG
63 GAAATTGAGGAGAAATTTTTCGA-GTCAATTTTG
3402 GCTAAAGCTA
Statistics
Matches: 2507, Mismatches: 463, Indels: 196
0.79 0.15 0.06
Matches are distributed among these distances:
304 1 0.00
305 4 0.00
306 106 0.04
307 20 0.01
308 35 0.01
309 58 0.02
310 10 0.00
311 1 0.00
314 3 0.00
316 2 0.00
321 2 0.00
323 2 0.00
326 1 0.00
328 13 0.01
329 98 0.04
330 215 0.09
331 141 0.06
332 431 0.17
333 367 0.15
334 588 0.23
335 234 0.09
336 164 0.07
337 11 0.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (331 bp):
GCGTGAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTCTATGAATATCGTGGCCGGAA
ATTGAGGAGAAATTTTTCGAGTCAATTTTGACAAAATTTTAGCTGAAATCGTGCACTAACCATCA
CGGTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTGGCGCCAAGA
CTCATTGAAATATCTATATCCATCTAAACAAATCTCTGCCAAATTTGATTTAAGGATTTGTTTTT
ACGAGCATATCAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAGAAAAACCAATA
TTAGAA
Found at i:1410 original size:668 final size:666
Alignment explanation
Indices: 1--3389 Score: 4938
Period size: 668 Copynumber: 5.1 Consensus size: 666
* *
1 GCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAATATGGCGGCCGGA
1 GCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAAATATATATTTTTTATGAATATGGTGGCCGGA
*
66 AATTGAGGAGAAATTTCTCGGATTAATTTTGGCAAAATTTTAGCTGAAATTGTGCACTAACCATC
66 AATTGAGGAGAAATTTCTCGGATTAATTTTGGCAAAATTTTAGCTGAAATCGTGCACTAACCATC
131 ACGGTTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTAGCGCCTA
131 ACGG-TTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTAGCGCCTA
196 GTCTCATTGAAATATCTATATCCATCTAAACAAATCTTTCCAACATTTGATTTAAGGATTTGTTT
195 GTCTCATTGAAATATCTATATCCATCTAAACAAATCTTTCCAACATTTGATTTAAGGATTTGTTT
* *
261 TTACGAGCATATAAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAATAATAGGAAAACCGA
260 TTACGAGCATATGAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAGGAAAACCGA
326 TATTAGAAGCGTGAATAGCCTTTCAATCTTTTA-GATGTTGAATTATATATTTTCTATGATTATC
325 TATTAGAAGCGTGAATAGCCTTTCAATCTTTTACG-TGTTGAATTATATATTTTCTATGATTATC
390 GTGGCCAAAAATTGAGGAAAATTATTTCGAGTCAATTTTCACAAAATTTTAGCCGAAATCGTGTA
389 GTGGCCAAAAATTGAGGAAAATTATTTCGAGTCAATTTTCACAAAATTTTAGCCG-AATCGTGTA
*
455 CTGTTA-CATCACGG-TTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGAT
453 C--TAACCATCACGGTTTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGAT
* * *
518 TTTTGGCGCCAAGAATCATTGAAATTTCCATATTTATCTAACGAAATCTCAGCCAAATTGGATTT
516 TTTTGGCGCCAAGACTCATTGAAATTTCTATATTTATCTAACAAAATCTCAGCCAAATTGGATTT
* * *
583 AAGGATCTGTTTTTACGATTATCTCCATCCGGTTTCGATTTAATTAGAAATTAATTCGGAAAATA
581 AAGGATTTGTTTTTACGATCATCTCCATCCGGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA
* *
648 TAGAATAAAGCAATATTAGAG
646 TAGAATAAAACAATATTAGAA
*
669 GCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAAATATATATTTTTTATGAATATGATGGCCTGG
1 GCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAAATATATATTTTTTATGAATATGGTGGCC-GG
*
734 AAATTGAGGAGAAATTTCTCGGATTAATTTTGGCAAAATTTTAGCTGAAATCATGCACTAACCAT
65 AAATTGAGGAGAAATTTCTCGGATTAATTTTGGCAAAATTTTAGCTGAAATCGTGCACTAACCAT
* * *
799 CACGGTTTTTGACTAAAAACGCGTTCTGGAGCCTCGACTCAGTTTTGCACGAGTTTTAGTGCCTA
130 CACGGTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTAGCGCCTA
864 GTCTCATTGAAATATCTATATCCATCTAAACAAATCTTTCCAACATTTGATTTAAGGATTTGTTT
195 GTCTCATTGAAATATCTATATCCATCTAAACAAATCTTTCCAACATTTGATTTAAGGATTTGTTT
*
929 TTACGAGCATATGAATCATGTTTCGATTTGATTAGGAATTAATTCGGAAAAAATAGGAAAACCGA
260 TTACGAGCATATGAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAGGAAAACCGA
994 TATTAGAAGCGTGAATAGCCTTTCAATCTTTTACGTGTTGAATTATATATTTTCTATGATTATCG
325 TATTAGAAGCGTGAATAGCCTTTCAATCTTTTACGTGTTGAATTATATATTTTCTATGATTATCG
* *
1059 TAGCCGAAAATTGAGGAAAATTATTTCGAGTCAATTTTCACAAAATTTTAGCCGACATCGTGTAC
390 TGGCCAAAAATTGAGGAAAATTATTTCGAGTCAATTTTCACAAAATTTTAGCCGA-ATCGTGTAC
*
1124 TAACCATCACGGATTTTTTTGGCTAAAAACGCGTTCGGGGGCCCCGGCTCAGTTTTGCATGATTT
454 TAACCATCACGG-TTTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGATTT
*
1189 TTGGCGCCAAGACTCATTGAAATTTCTATATTTATCTAACGAAATCTCAGCCAAATTGGATTTAA
518 TTGGCGCCAAGACTCATTGAAATTTCTATATTTATCTAACAAAATCTCAGCCAAATTGGATTTAA
* *
1254 GGATCTGTTTTTACGATCATCTCCATCCGGTTTCGATTTAATTAGAAATTAATTCGGAAAATATA
583 GGATTTGTTTTTACGATCATCTCCATCCGGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATA
* * *
1319 TAATAAAGCAATATTAGAG
648 GAATAAAACAATATTAGAA
* *
1338 GCGTGAGAAGCCCTTGAATCTTTTTGACGTTGAAATATATATTTTTTATGAATATGGTGGCCGGA
1 GCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAAATATATATTTTTTATGAATATGGTGGCCGGA
* *
1403 AATTGAGGAGAAATTTCTCGGTTTAATTTTGGTAAAATTTTAGCTGAAATCGTGCACTAACCATC
66 AATTGAGGAGAAATTTCTCGGATTAATTTTGGCAAAATTTTAGCTGAAATCGTGCACTAACCATC
1468 ACGGTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTAGCGCCTAG
131 ACGGTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTAGCGCCTAG
* *
1533 TCTCATTGAAATATCTATATCCATCTAAACAAATCTTTCCCACATTTGATATAAGGATTTGTTTT
196 TCTCATTGAAATATCTATATCCATCTAAACAAATCTTTCCAACATTTGATTTAAGGATTTGTTTT
* *
1598 TACGAGCATATGAATCATGTTTCAATTTGATTAGGAATTAATTCGGAAAAAATAGGAAAACCGAT
261 TACGAGCATATGAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAGGAAAACCGAT
* *
1663 ATTAGAAGCGTGAATAGCCTTTCAAACTTTTACGTGTTGAATAATATATTTTCTATGATTATCGT
326 ATTAGAAGCGTGAATAGCCTTTCAATCTTTTACGTGTTGAATTATATATTTTCTATGATTATCGT
* *
1728 GGCCAAGAATTGAGGAAAATTATTTCGAGTCAATTTTCACAAAATTTTAGCTGAAATCGTGTACT
391 GGCCAAAAATTGAGGAAAATTATTTCGAGTCAATTTTCACAAAATTTTAGCCG-AATCGTGTACT
* * * *
1793 AACCATCACGGTTTTTTTGGCTTAAAACGCGTTCAGGGACCCCGGCTCGGTTTTGCATGATTTTT
455 AACCATCACGGTTTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGATTTTT
* ** * * *
1858 GGCACCAAGACTCATTGAAATTTCTATATCCATCTAAACAAATATTTC--CCACATTTGATTTAA
520 GGCGCCAAGACTCATTGAAATTTCTATATTTATCT-AACAAA-ATCTCAGCCAAATTGGATTTAA
* * ** ** * *
1921 GGATTTGTTTTTACGAGCATATGAATCATGTTTCGATTTGATTAGGAATTAATTCGG-AAAAATA
583 GGATTTGTTTTTACGATCATCTCCATCCGGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATA
*
1985 GAA-ATAAACATTATTAGAA
648 GAATA-AAACAATATTAGAA
*
2004 GCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAAATATATATTTTTTATGAATACGGTGGCCGGA
1 GCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAAATATATATTTTTTATGAATATGGTGGCCGGA
* *
2069 AATTGAGGAGAAATTTCTC-GAGTTTATTTTGGCAAAATTTTAGCTGAAATCGTGCACAAACCAT
66 AATTGAGGAGAAATTTCTCGGA-TTAATTTTGGCAAAATTTTAGCTGAAATCGTGCACTAACCAT
* * * * ** *
2133 CACGGTTTTTGACTAAAAACGCTTTCTGAAGCCCTGACTCAGTTTTTCACGATTTTCGGCGCCAA
130 CACGGTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTAGCGCCTA
* *
2198 GTCTCATTGAAATATCTATATCCATATAAACAAATCTTTTCC-ACATTTGATTTAAGGATTTATT
195 GTCTCATTGAAATATCTATATCCATCTAAACAAATC-TTTCCAACATTTGATTTAAGGATTTGTT
* ** *
2262 TTTACGAGCATATGAATCATGTTTCGATTCAATTAAAAATTAATTCGGAAAAAATAGGAAAA-CT
259 TTTACGAGCATATGAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAGGAAAACCG
* * *
2326 ACTATTAGAAGCATGAATAGCCTTTCAATCTTTTATGTGTTGAATTATATATTTTCTATGAGTAT
324 A-TATTAGAAGCGTGAATAGCCTTTCAATCTTTTACGTGTTGAATTATATATTTTCTATGATTAT
* * * * *
2391 CGTGGCCAAAAACTGAGGAAAACTCTTTCGAGTCAATTTTTACAAAATTTTAGCCG-ATCGTTTA
388 CGTGGCCAAAAATTGAGGAAAATTATTTCGAGTCAATTTTCACAAAATTTTAGCCGAATCGTGTA
* * * * **
2455 CTAAACATCAC--TGTTTTTGGCTAAAAATGCGTTCTGGTGCCCCGATTCAGTTTTGCATGATTT
453 CTAACCATCACGGTTTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGATTT
* * *
2518 TTGGCGTCAAGACTCGTTGAAATTTCTATATTTATCTAACAAAATCTCAGTCAAATTGGATTTAA
518 TTGGCGCCAAGACTCATTGAAATTTCTATATTTATCTAACAAAATCTCAGCCAAATTGGATTTAA
* * * *
2583 GGATTTGTGTTTACGATCATCTCCATCCGGTTTCGATTTAATTAGGAATTATTTC-GAAAAAATT
583 GGATTTGTTTTTACGATCATCTCCATCCGGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATA
* *
2647 GAAAAAAACAATATTTGAA
648 GAATAAAACAATATTAGAA
* * * * *
2666 ACGAGAGAAGCCCTTCAATCTTTTTGGCATTGAAATGTATA-TTTTTATGAATATTGTGGCCGGA
1 GCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAAATATATATTTTTTATGAATATGGTGGCCGGA
* * * * * *
2730 AATTGAGGAGAAATTTCTTGGGTCAATTTTGACTAATTTTTAGCTGAAATCGTGCACTAACCATC
66 AATTGAGGAGAAATTTCTCGGATTAATTTTGGCAAAATTTTAGCTGAAATCGTGCACTAACCATC
* * *
2795 ACTGTTTTTGACTAAAAATGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTAGCTCCTAG
131 ACGGTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTAGCGCCTAG
* *
2860 ACTCATTGAAATATCTATATCCATCTAAACAAATCTTTCCCACATTTGATTTAAGGA-TTGTTTT
196 TCTCATTGAAATATCTATATCCATCTAAACAAATCTTTCCAACATTTGATTTAAGGATTTGTTTT
** *
2924 TATAAGCATATG-A--A----TC-------TT--G---T--TTCGGAAAAAATAGAAAAACCGAT
261 TACGAGCATATGAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAGGAAAACCGAT
* *
2968 ATTAGAAGCGTGAATAGCCTTTCAATCTTTTAGGTGTTGAATTATATATTTTCT-T-AGTATCGT
326 ATTAGAAGCGTGAATAGCCTTTCAATCTTTTACGTGTTGAATTATATATTTTCTATGATTATCGT
* * * * *
3031 GGCCAAAAATTGAGGAAAATTCTTTCAAGGCAAAATTT-ACAAAATTTTTGCCG-ATCGTGTACT
391 GGCCAAAAATTGAGGAAAATTATTTCGAGTC-AATTTTCACAAAATTTTAGCCGAATCGTGTACT
* * * * * *
3094 AACTATCA-TG-ATTTTTGGCTAAAAACACGTTCCGGGGTCCCGGCTCAGTTTTGCATGATTTTT
455 AACCATCACGGTTTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGATTTTT
** ** * * * * *
3157 TACTTCAAGACTCATTGAAATTTCTATATTTATCTAACAAAATTTGAACTAAATTGGATTTCAGG
520 GGCGCCAAGACTCATTGAAATTTCTATATTTATCTAACAAAATCTCAGCCAAATTGGATTTAAGG
* * * *
3222 ATTTATTTTTACGATCATCTCCATTCGGTTTCGATTTAATTAGAAATTAGTTCGAAAAAAATAGA
585 ATTTGTTTTTACGATCATCTCCATCCGGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGA
*
3287 AAAAAACAATATTAGAA
650 ATAAAACAATATTAGAA
* * * * * * * *
3304 ACGAGAAAAACCCTTCAATCTTTTTGGCATTGAAATGTATATTTTTTTTATGAATATCGTGGCCA
1 GCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAAA--TATATATTTTTTATGAATATGGTGGCCG
3369 GAAATTGAGGAGAAATTTCTC
64 GAAATTGAGGAGAAATTTCTC
3390 ATGTCAATTT
Statistics
Matches: 2490, Mismatches: 204, Indels: 81
0.90 0.07 0.03
Matches are distributed among these distances:
637 212 0.09
638 64 0.03
639 71 0.03
640 6 0.00
641 40 0.02
646 2 0.00
653 2 0.00
657 1 0.00
659 1 0.00
660 25 0.01
661 187 0.08
662 192 0.08
663 1 0.00
664 17 0.01
665 4 0.00
666 419 0.17
667 157 0.06
668 759 0.30
669 330 0.13
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (666 bp):
GCGTGAGAAGCCCTTCAATCTTTTTGGCGTTGAAATATATATTTTTTATGAATATGGTGGCCGGA
AATTGAGGAGAAATTTCTCGGATTAATTTTGGCAAAATTTTAGCTGAAATCGTGCACTAACCATC
ACGGTTTTTGACTAAAAACGCGTTCTGGAGCCCCGACTCAGTTTTGCACGATTTTTAGCGCCTAG
TCTCATTGAAATATCTATATCCATCTAAACAAATCTTTCCAACATTTGATTTAAGGATTTGTTTT
TACGAGCATATGAATCATGTTTCGATTTAATTAGGAATTAATTCGGAAAAAATAGGAAAACCGAT
ATTAGAAGCGTGAATAGCCTTTCAATCTTTTACGTGTTGAATTATATATTTTCTATGATTATCGT
GGCCAAAAATTGAGGAAAATTATTTCGAGTCAATTTTCACAAAATTTTAGCCGAATCGTGTACTA
ACCATCACGGTTTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGGCTCAGTTTTGCATGATTTTTG
GCGCCAAGACTCATTGAAATTTCTATATTTATCTAACAAAATCTCAGCCAAATTGGATTTAAGGA
TTTGTTTTTACGATCATCTCCATCCGGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGAA
TAAAACAATATTAGAA
Found at i:4532 original size:49 final size:49
Alignment explanation
Indices: 4476--4817 Score: 529
Period size: 49 Copynumber: 7.1 Consensus size: 49
4466 CAACACACAC
* * * *
4476 GAAGACATAGCCTCCACAGTGAGGGGAGGCCAAACACAAAGATACAAGA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACAAGA
*
4525 GAAGACATAGCCTCCGAAGTGAGGCGAGGCCAGACACGAAGATACAAGA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACAAGA
*
4574 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACACGA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACAAGA
4623 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACAAGA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACAAGA
*
4672 GAAGAC--AGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACATGA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACAAGA
*
4719 GAAGAC--AGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACACGA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACAAGA
** *
4766 GAAGACATAGCCTCCGC----AGGCGAGGCCAGACACGAATCTACATGA
1 GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACAAGA
4811 GAAGACA
1 GAAGACA
4818 CACAACACAC
Statistics
Matches: 278, Mismatches: 13, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
45 32 0.12
47 92 0.33
49 154 0.55
ACGTcount: A:0.37, C:0.25, G:0.30, T:0.08
Consensus pattern (49 bp):
GAAGACATAGCCTCCGCAGTGAGGCGAGGCCAGACACGAAGATACAAGA
Found at i:10181 original size:2 final size:2
Alignment explanation
Indices: 10174--10214 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
10164 TGGATTGGAC
*
10174 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10215 CACAAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:13534 original size:121 final size:121
Alignment explanation
Indices: 13320--13565 Score: 492
Period size: 121 Copynumber: 2.0 Consensus size: 121
13310 GCTATCATAG
13320 TTATTCATCTCCCAATGTAGCAACCAAAGAAAAGGAAGGCAGCTACGTGTAAGATGTCAATGCAA
1 TTATTCATCTCCCAATGTAGCAACCAAAGAAAAGGAAGGCAGCTACGTGTAAGATGTCAATGCAA
13385 CTTATTGTTATGTCTATTTATCTAGTAAATTCTCATCCAGTACTATTACCTTCCAT
66 CTTATTGTTATGTCTATTTATCTAGTAAATTCTCATCCAGTACTATTACCTTCCAT
13441 TTATTCATCTCCCAATGTAGCAACCAAAGAAAAGGAAGGCAGCTACGTGTAAGATGTCAATGCAA
1 TTATTCATCTCCCAATGTAGCAACCAAAGAAAAGGAAGGCAGCTACGTGTAAGATGTCAATGCAA
13506 CTTATTGTTATGTCTATTTATCTAGTAAATTCTCATCCAGTACTATTACCTTCCAT
66 CTTATTGTTATGTCTATTTATCTAGTAAATTCTCATCCAGTACTATTACCTTCCAT
13562 TTAT
1 TTAT
13566 AGCTTGCTCT
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 125 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (121 bp):
TTATTCATCTCCCAATGTAGCAACCAAAGAAAAGGAAGGCAGCTACGTGTAAGATGTCAATGCAA
CTTATTGTTATGTCTATTTATCTAGTAAATTCTCATCCAGTACTATTACCTTCCAT
Found at i:23236 original size:331 final size:332
Alignment explanation
Indices: 22634--23380 Score: 1207
Period size: 331 Copynumber: 2.3 Consensus size: 332
22624 TCGAGGGAAA
* * * *
22634 CTAAATCCTAAACTTTGGA-AGAGCGTGAGAAACGAATAAATAATCATCGGCTCCC-AAAGAAAT
1 CTAAATCCTAAACTTTCGACAGAACGTGAGAAGCGAATGAATAATCATCGGCTCCCGAAAGAAAT
* *
22697 CGAAGAATGTTCTGGTTAATGTCTAGATAAAGAGTAACCCCTCATTTATTGCTCCATATTCTGAA
66 CGAAGAATGTTTTGGTTAATGCCTAGATAAAGAGTAACCCCTCATTTATTGCTCCATATTCTGAA
* * *
22762 ACTCTTGACCTAATACTCTTAGCATCCTCTTAACTATTTCGAGGATTCGACACTGACTTGACTGT
131 ACTCTTGACCTAATACTCTTAGCATCCTCCTAACTACTTCGAGGATTCGACACTGACTTGAATGT
* *
22827 CGGAGTGCTAACGCCTGATTCCATCCCCGCACTCCTAGGTGTTCTTCCACTTGCAGGTCCTTCAT
196 CGGAGTGCTAACGCCGGATTCCATCCCCGCACTCCTAGGTGTTCTTCCACTTGCAAGTCCTTCAT
* *
22892 CTCACAGGTCTAAGAGATTC-AGAGAGACAGTCGTCGTCGGCCGTCTTGTTGAATATTTTGCCTT
261 CTCACAGGTCTAAGAGATTCGA-AGAGACAGTCGTCGCCAGCCGTCTTGTTGAATATTTTGCCTT
*
22956 CAACGGTT
325 CAACAGTT
*
22964 CTAAATCCTAAAC-TTCGACAGAACGTGAGAAGCGAATGAATAATCATCGGCTCCCGGAAGAAAT
1 CTAAATCCTAAACTTTCGACAGAACGTGAGAAGCGAATGAATAATCATCGGCTCCCGAAAGAAAT
*
23028 CAAAGAATGTTTTGGTTAATGCCTAGATAAAGAGTAACCCCTCATTTATTGCTCCATATTCTGAA
66 CGAAGAATGTTTTGGTTAATGCCTAGATAAAGAGTAACCCCTCATTTATTGCTCCATATTCTGAA
* *
23093 ACTCTTGACCTAATATTCTTAGCATCCTCCTAACTACTTCGAGGATTCGACACTGACTTTAATGT
131 ACTCTTGACCTAATACTCTTAGCATCCTCCTAACTACTTCGAGGATTCGACACTGACTTGAATGT
* * *
23158 CGGAGTGCTAATGCGGGATTCCATTCCCGCACTCCTAGGTGTTCTTCCACTTGCAAGTCCTTCAT
196 CGGAGTGCTAACGCCGGATTCCATCCCCGCACTCCTAGGTGTTCTTCCACTTGCAAGTCCTTCAT
*
23223 CTCAC-GAGTCTAAGAGATTCGAAGAGACGGTCGTCGCCAGCCGTCTTGTTGAATATTTTGCCTT
261 CTCACAG-GTCTAAGAGATTCGAAGAGACAGTCGTCGCCAGCCGTCTTGTTGAATATTTTGCCTT
23287 CAACAGTT
325 CAACAGTT
* * *
23295 CTAAATCCTAAACTTTTGACAGAACGTGAGAAGCGAATGAATAATCATCGGCTCCTGTAAGAAAT
1 CTAAATCCTAAACTTTCGACAGAACGTGAGAAGCGAATGAATAATCATCGGCTCCCGAAAGAAAT
*
23360 CGAAGAATTTTTTGGTTAATG
66 CGAAGAATGTTTTGGTTAATG
23381 TCTCCATTGA
Statistics
Matches: 385, Mismatches: 27, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
329 4 0.01
330 47 0.12
331 266 0.69
332 68 0.18
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (332 bp):
CTAAATCCTAAACTTTCGACAGAACGTGAGAAGCGAATGAATAATCATCGGCTCCCGAAAGAAAT
CGAAGAATGTTTTGGTTAATGCCTAGATAAAGAGTAACCCCTCATTTATTGCTCCATATTCTGAA
ACTCTTGACCTAATACTCTTAGCATCCTCCTAACTACTTCGAGGATTCGACACTGACTTGAATGT
CGGAGTGCTAACGCCGGATTCCATCCCCGCACTCCTAGGTGTTCTTCCACTTGCAAGTCCTTCAT
CTCACAGGTCTAAGAGATTCGAAGAGACAGTCGTCGCCAGCCGTCTTGTTGAATATTTTGCCTTC
AACAGTT
Done.