Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020401.1 Corchorus olitorius cultivar O-4 contig20434, 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: 76311
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:678 original size:330 final size:327
Alignment explanation
Indices: 3--2819 Score: 2608
Period size: 330 Copynumber: 8.5 Consensus size: 327
1 TA
* * * *
3 CTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAGTAAGAAAAAAGATATTAGAAGCGT-AA
1 CTTGTTTCGATTTAATTAGAAATTAATTC--AAAAAAATATGAAAAACGATATTAAAAGCGTGAA
** * * * *
67 AAACCCTTCAATATTTTTGGCGATGAATTATAT-TTTTT-TGAGGATTTTAGTCAAAAATTGAGG
64 AAGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGGCAAAAATTGAGG
* * * * *
130 AAATATTTTTTTTCCGTCAATTTTTGCAAAATTGTAGCCGAAATCGTGTAATAATCATCACGG-T
129 AAA-A--ATATTTCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-ATAACCATCACGGTT
* ** ** *
194 TTTTGGCTAAAAACACGTTCCAGGGCTCCAAG-TCAGTTTTGCATGATTTTTGGCGTTAAGAATC
190 TTTTGGCTAAAAACGCGTTCC-GGGC-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTC
* * * * * * *
258 CTTGAGATCTCCATATTAATCTAATCAAATCTCATCCAAATTGCATTTAATGATTTGTTTTTACG
253 CTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTG-ATTTAAGGATTTGTTTTTACG
* *
323 AAG-ATTTGTAT
317 -AGCATCTGAAT
* * *
334 CTTGTTTCGATTTAATTACAAATTAATTTAAAAAAATATGAAAAACGATATGAAAAGCGTGAAAA
1 CTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAA
* * * * * *
399 GTCCTCCAATATTTTTGGCATTAAATTATATATTTTCATGAGTATTTTAGTCAAAAATTGAGGAA
66 GTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGGCAAAAATTGAGGAA
* * * *
464 AAATTTTTCTGGTCATTTTTTTCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTT
131 AAATATTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-TAACCATCACGGTTTTTT
* * * * * * * * *
529 TGCGAAAAACGTGTTTCGGGCCCCGACTTAGTATTGCATGATTTTTGGCGTCGAGACTCCTTGAA
194 GGCTAAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAA
* * *
594 AAATCTATATTTATCTAATCAAATCTCAGCCACATTGCATTTAAGGATGTGTTTTTACGAGCATC
259 ATATCTATATTCATCTAATCAAATCTCAGCCACATTG-ATTTAAGGATTTGTTTTTACGAGCATC
659 TGAAT
323 TGAAT
* * *
664 CTTGTTTTGATTTAATTTGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAA
1 CTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAA
* *
729 GTCCTGCAATCTTTTTGGCGTTGGAATATATATATATATATATTATGAGTATTTTAGACAAAAAT
66 GTCCTTCAATCTTTTTGGCGTT-G-A-AT-TATATAT-T-T-TTATGAGTATTTTAGGCAAAAAT
* * * * *
794 TGAGGAAAAATACTTCTGGTCAATTTTTACAAAATATTAGCCGAAATCGTGTATGTTAGTCGAAA
124 TGAGGAAAAATATTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA---TA-AC--CA
* * * * *
859 TTACGGTTTTTTTTTTGCTAAAAACGCG-TCCTGCGGTCCCGG-TACAGTGTTGCTTGATTTTTG
182 TCACGG---TTTTTTGGCTAAAAACGCGTTCC-G-GGCCCCGGCT-CAGTTTTGCATGATTTTTG
**
922 GCGCTGAGACTCCTTGAAATATCTATATTCATCTAA-CTAAATCTCAGCCACATTGGATTTAAGG
241 GCGCCAAGACTCCTTGAAATATCTATATTCATCTAATC-AAATCTCAGCCACATT-GATTTAAGG
* *** *
986 ATTT-CTAAAACAAGCATCTGAAT
304 ATTTGTTTTTACGAGCATCTGAAT
** * * * *
1009 GATGTTTCGATTTAATCAGAAATTAATTCAAAAAATAATAGGAAAAACGATATTAGAAGCATGAA
1 CTTGTTTCGATTTAATTAGAAATTAATTC-AAAAA-AATATGAAAAACGATATTAAAAGCGTGAA
** * * * *
1074 AAG-CCATTCAATCTGATTGGCGTTGAATTATATAATTTTAATGAGTGTTGT-GGCTAAAACTTG
64 AAGTCC-TTCAATCTTTTTGGCGTTGAATTATAT-ATTTTTATGAGTATTTTAGGC-AAAAATTG
* * * * *
1137 A-G-AAAATAACTTTCGAGTCAATTTTTGTAAAATTCTAGTCGAAATCGTTTGATAATCATCACG
126 AGGAAAAAT-A-TTTCG-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-ATAACCATCACG
** * * *
1200 G-TTTTTGGCTAAAGTCGCGTTTCGGGACCCCGGCTCAATTTTGCATGATTTTTGGCGCCGAGAC
187 GTTTTTTGGCTAAAAACGCGTTCCGGG-CCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGAC
* *
1264 TTCTTGAAATATCTATATTCATCTAATCAAATCTCAACCACATTGAATTTAAGGATTTGTTTTTA
251 TCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTG-ATTTAAGGATTTGTTTTTA
*
1329 CGAGCCTCTGAAT
315 CGAGCATCTGAAT
* *
1342 CTTGTTTCGATTTAATTAAAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAA
1 CTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAA
* * ** * * *
1407 GTCCTCCAGTCTTTTTGATGTTGAATTATATATATATTATGAGT-GTTGAGGCTAAAAATTGA-G
66 GTCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTTTAGGC-AAAAATTGAGG
*
1470 ACAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG--T-ACCATCACAGTTTT
129 A-AAAATATTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATAACCATCACGGTTTT
* * * * * * *
1532 TTCGCTCAAAACGCGTTCCGGGATCCCGGGTCAGTTTTGCATGATTTTTGGTGGCAAAACTCCTT
192 TTGGCTAAAAACGCGTTCCGGG-CCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT
* * * **
1597 GAAATATCTATATTCATCTAACCAAATCTTAACCACACTTGATTTAAGGATTTGTTTTTGTGAGC
256 GAAATATCTATATTCATCTAATCAAATCTCAGCCACA-TTGATTTAAGGATTTGTTTTTACGAGC
*
1662 ATTTGAAT
320 ATCTGAAT
* * * * *
1670 CATGTTTTGATTTAATTAGAAATTAATTTGAAAAAAAAAATAGGAAAGACGATATTAAAAGCGTG
1 CTTGTTTCGATTTAATTAGAAATTAA-TT---CAAAAAAATATGAAAAACGATATTAAAAGCGTG
* * * *
1735 AGAAGCCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTATGAGTATTAT-GGCTAAAAATT
62 AAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGGC-AAAAATT
* * * ***
1799 GA-GAAAAATATTTCGGGTTAATTTTTGCAAAATTTTAGCCGAAATCGTGTATTATCATTGTTTT
125 GAGGAAAAATATTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATAACCA---TCAC
** * * * * * *
1863 TTTTTTTTTGCTAAAAATGCGTTCCAGGGTCCTGGGTCAGTTTTGCATGATTTTTGGCACCAAGA
186 GGTTTTTTGGCTAAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGA
* * * *
1928 TTCCTTAAAATATATCTATATTCATCTAACCAAATCTCAGCCACATTGTATTTAAGGATTTATTT
250 CTCCTT-GAA-ATATCTATATTCATCTAATCAAATCTCAGCCACATTG-ATTTAAGGATTTGTTT
*** *
1993 TTCACGAATTTCTAAAT
312 TT-ACGAGCATCTGAAT
* * * * *
2010 CTTGTTTTGATTTAATTAGAAATTAATTTGGAAAGAAAATAAGGAAAACGATATTAGAAGCGTGA
1 CTTGTTTCGATTTAATTAGAAATTAA-TT-CAAA-AAAATATGAAAAACGATATTAAAAGCGTG-
* * * * * *
2075 AAAAGGCTTTC-ATTTTTTTGGCGTTGAATTATATATTTTTAATGAGTATTTT-CGCTAGAAATC
62 AAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTT-ATGAGTATTTTAGGC-AAAAATT
* * * *
2138 GAGGAAAAATTTTTCAGGTCAATTTTTGGAAAATTTTAGCTGAAATCGTG--T-ACCATCACAG-
125 GAGGAAAAATATTTC-GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATAACCATCACGGT
* ** *
2199 TTTTCGGCTAAAAACGCGTTCCGGGGTCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCC
189 TTTTTGGCTAAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
* * **
2264 TTGAAATATCTATATTCATCTAACCAAATCTTAGCCACATTAGATTTAAGGATCCGTTTTTACGA
254 TTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT-GATTTAAGGATTTGTTTTTACGA
*
2329 GAATCTGAAT
318 GCATCTGAAT
* * * * * * * *
2339 GTTGTTTCGATTTAATTGGAAATTAATTCGGAAAGAAATAGGAAAAACAATATTAGAATCGTTAA
1 CTTGTTTCGATTTAATTAGAAATTAATTC--AAAAAAATATGAAAAACGATATTAAAAGCGTGAA
* *** * * *
2404 AAGCCCTTCAATCTTTTTGATATCGAATAATATATTTTTTTATGAGTATTTTAGCCAAAAATTGA
64 AAGTCCTTCAATCTTTTTGGCGTTGAAT--TATATATTTTTATGAGTATTTTAGGCAAAAATTGA
* * * * *
2469 AGAAATATCTTTCGTGTCAATTTTTGCAAAATTTTAGCCAAAATCGTG--T-ACTCATCAC-GAT
127 GGAAAAATATTTCG-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATAAC-CATCACGGTT
* * * * *
2530 TTTTGGCTAAAAACGCGTTCCAAGACCACGGCTCTGTTTTGCATGATTTTTGGCGCCGAGACTCC
190 TTTTGGCTAAAAACGCGTTCC-GGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
* * * * * * *
2595 TTGAAATAGCTTTATTCATCTAATAAAATTTCAGCCACATTGGATTTAACGATTTGTTTTTATGT
254 TTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATT-GATTTAAGGATTTGTTTTTACGA
2660 GCATCTGAAT
318 GCATCTGAAT
* *
2670 CTTGTATCGATTTAATTAGAAATTAATTCAGAAAAAA-ATG-AAAATGATATTAAAAGCGTGAAA
1 CTTGTTTCGATTTAATTAGAAATTAATTCA-AAAAAATATGAAAAACGATATTAAAAGCGTGAAA
* * * * * * * *
2733 ATTCCTCCAATTTTTTTGGCATTGAATTATATATATTTTGTGATTATTTTTGTCAAAAATTGAGG
65 AGTCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTTTAGGCAAAAATTGAGG
*
2798 AAAAATCTTTCGGATC-ATTTTT
129 AAAAATATTTCGG-TCAATTTTT
2820 ACCATCATGG
Statistics
Matches: 2059, Mismatches: 341, Indels: 177
0.80 0.13 0.07
Matches are distributed among these distances:
326 13 0.01
327 55 0.03
328 219 0.11
329 143 0.07
330 337 0.16
331 326 0.16
332 254 0.12
333 71 0.03
334 11 0.01
335 1 0.00
336 7 0.00
337 128 0.06
338 17 0.01
339 125 0.06
340 91 0.04
341 49 0.02
342 8 0.00
343 6 0.00
344 6 0.00
345 59 0.03
346 88 0.04
347 45 0.02
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (327 bp):
CTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAA
GTCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGGCAAAAATTGAGGAA
AAATATTTCGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTATAACCATCACGGTTTTTTGG
CTAAAAACGCGTTCCGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
ATCTATATTCATCTAATCAAATCTCAGCCACATTGATTTAAGGATTTGTTTTTACGAGCATCTGA
AT
Found at i:2668 original size:331 final size:328
Alignment explanation
Indices: 3--2809 Score: 2447
Period size: 331 Copynumber: 8.4 Consensus size: 328
1 TA
* * * *
3 CTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAGTAAGAAAAAAGATATTAGAAGCGT-AA
1 CTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAAAAGCGTGAA
* * * * * *
67 AAACCCTTCAATATTTTTGGCGATGAA-T-TATATTTTTT-TGAGGATTTTAGTCAAAAATTGAG
66 AAGCCCTTCAATCTTTTTGG-TATGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAA
* * ** * * *
129 GAAATATTTTTTTTCCGTCAATTTTTGCAAAATTGTAGCCGAAATCGTGTAATAATCATCACGGT
130 GAAAAATCTTTCGT--GTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---TACTCATCACGTT
* * * ** *
194 TTTTGGCTAAAAACACGTTCCAGGGCTCCAAG-TCAGTTTTGCATGATTTTTGGCGTTAAGAATC
190 TTTTGGCTAAAAACGCGTTCCAGGAC-CC-GGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTC
* * * * * * * *
258 CTTGAGATCTCCATATTAATCTAATCAAATCTCATCCAAATTGCATTTAATGATTTGTTTTTACG
253 CTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
* *
323 AAG-ATTTGTAT
318 -AGCATCTGAAT
* * * *
334 CTTGTTTCGATTTAATTACAAATTAATT--TAAAAAAATATGAAAAACGATATGAAAAGCGTGAA
1 CTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAAAAGCGTGAA
* * * * * * * *
397 AAGTCCTCCAATATTTTTGGCATTAAATTATATA-TTTTCATGAGTATTTTAGTCAAAAATTGAG
66 AAGCCCTTCAATCTTTTTGGTA-TGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAA
* * * *
461 GAAAAATTTTTC-TGGTCATTTTTTTCAAAATTTTAGCCAAAATCGTGTACTAACCATCACGGTT
130 GAAAAATCTTTCGT-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT---CATCAC-GTT
* * * * * * * * * * *
525 TTTTTGCGAAAAACGTGTTTCGGGCCCCGACTTAGTATTGCATGATTTTTGGCGTCGAGACTCCT
190 TTTTGGCTAAAAACGCGTTCCAGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCT
* * * *
590 TGAAAAATCTATATTTATCTAATCAAATCTCAGCCACATTGCATTTAAGGATGTGTTTTTACGAG
255 TGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
655 CATCTGAAT
320 CATCTGAAT
* * * *
664 CTTGTTTTGATTTAATTTGAAATTAATTC--AGAAAAATATGAAAAACGATATTAAAAGCGTGAA
1 CTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAAAAGCGTGAA
* * *
727 AAGTCCTGCAATCTTTTTGGCGT-TGGAATATATATATATATATATTATGAGTATTTTAGACAAA
66 AAGCCCTTCAATCTTTTT-G-GTAT-GAAT-TATATAT-T-T-T-TTATGAGTATTTTAGCCAAA
* * * *
791 AATTGAGGAAAAATAC-TTC-TGGTCAATTTTTACAAAATATTAGCCGAAATCGTGTATGTTAGT
123 AATTGAAGAAAAAT-CTTTCGT-GTCAATTTTTGCAAAATTTTAGCCGAAATC--G--TG-TACT
* * * * * *
854 CGAAATTACGGTTTTTTTTTTGCTAAAAACGCG-TCCTGCGGTCCCGG-TACAGTGTTGCTTGAT
181 C---ATCAC-G---TTTTTTGGCTAAAAACGCGTTCC--AGGACCCGGCT-CAGTTTTGCATGAT
**
917 TTTTGGCGCTGAGACTCCTTGAAATATCTATATTCATCTAA-CTAAATCTCAGCCACATTGGATT
236 TTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATC-AAATCTCAGCCACATTGGATT
* *** *
981 TAAGGATTT-CTAAAACAAGCATCTGAAT
300 TAAGGATTTGTTTTTACGAGCATCTGAAT
** * * * *
1009 GATGTTTCGATTTAATCAGAAATTAATTC-AAAAAATAATAGGAAAAACGATATTAGAAGCATGA
1 CTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAA-AATAGGAAAAACGATATTAAAAGCGTGA
* * * * * * * * * *
1073 AAAGCCATTCAATCTGATTGGCGT-TGAATTATATAATTTTAATGAGTGTTGTGGCTAAAACTTG
65 AAAGCCCTTCAATCT-TTTTG-GTATGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTG
* * * * * * *
1137 -AGAAAATAACTTTCGAGTCAATTTTTGTAAAATTCTAGTCGAAATCGTTTGATAATCATCACGG
128 AAGAAAA-ATCTTTCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCG--TG-TACTCATCACGT
** * * * * *
1201 TTTTTGGCTAAAGTCGCGTTTCGGGACCCCGGCTCAATTTTGCATGATTTTTGGCGCCGAGACTT
189 TTTTTGGCTAAAAACGCGTTCCAGGA-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTC
* *
1266 CTTGAAATATCTATATTCATCTAATCAAATCTCAACCACATTGAATTTAAGGATTTGTTTTTACG
253 CTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
*
1331 AGCCTCTGAAT
318 AGCATCTGAAT
* * *
1342 CTTGTTTCGATTTAATTAAAAATTAATTC--AGAAAAATATGAAAAACGATATTAAAAGCGTGAA
1 CTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAAAAGCGTGAA
* * * * * * * *
1405 AAGTCCTCCAGTCTTTTTGATGT-TGAATTATATATATATTATGAGT-GTTGAGGCTAAAAATTG
66 AAGCCCTTCAATCTTTTTG--GTATGAATTATATATTTTTTATGAGTATTTTA-GCCAAAAATTG
* *
1468 -AGACAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC-CATCACAGTTT
128 AAGA-AAAATCTTTCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTCATCAC-GTTT
* * * * * * *
1531 TTTCGCTCAAAACGCGTTCCGGGATCCCGGGTCAGTTTTGCATGATTTTTGGTGGCAAAACTCCT
191 TTTGGCTAAAAACGCGTTCCAGGA-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCT
* * * **
1596 TGAAATATCTATATTCATCTAACCAAATCTTAACCACACTT-GATTTAAGGATTTGTTTTTGTGA
255 TGAAATATCTATATTCATCTAATCAAATCTCAGCCACA-TTGGATTTAAGGATTTGTTTTTACGA
*
1660 GCATTTGAAT
319 GCATCTGAAT
* * * * *
1670 CATGTTTTGATTTAATTAGAAATTAATTTGAAAAAAAAAATAGGAAAGACGATATTAAAAGCGTG
1 CTTGTTTCGATTTAATTAGAAATTAATTCG--GAAAAAAATAGGAAAAACGATATTAAAAGCGTG
* * * *
1735 AGAAGCCCTTCAATCTTTTTTGCGT-TGAATTATATATTTTTTATGAGTATTATGGCTAAAAATT
64 AAAAGCCCTTCAATC-TTTTTG-GTATGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATT
* * * * *
1799 G-AGAAAAATATTTCGGGTTAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-TTATCATTGTTT
127 GAAGAAAAATCTTTCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTCATCA-CG---
* * * * * *
1862 TTTTTTTTTTGCTAAAAATGCGTTCCAGGGTCCTGGGTCAGTTTTGCATGATTTTTGGCACCAAG
188 ---TTTTTTGGCTAAAAACGCGTTCCA-GGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAG
* * * * *
1927 ATTCCTTAAAATATATCTATATTCATCTAACCAAATCTCAGCCACATTGTATTTAAGGATTTATT
249 ACTCCTT-GAA-ATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTT
*** *
1992 TTTCACGAATTTCTAAAT
312 TTT-ACGAGCATCTGAAT
* * *
2010 CTTGTTTTGATTTAATTAGAAATTAATTTGGAAAGAAAATAAGG-AAAACGATATTAGAAGCGTG
1 CTTGTTTCGATTTAATTAGAAATTAATTCGGAAA-AAAAT-AGGAAAAACGATATTAAAAGCGTG
* * * * * * *
2074 AAAAAGGCTTTC-ATTTTTTTGGCGT-TGAATTATATATTTTTAATGAGTATTTTCGCTAGAAAT
64 -AAAAGCCCTTCAATCTTTTT-G-GTATGAATTATATATTTTTTATGAGTATTTTAGCCAAAAAT
* * * * *
2137 CGAGGAAAAATTTTTCAG-GTCAATTTTTGGAAAATTTTAGCTGAAATCGTGTAC-CATCACAG-
126 TGAAGAAAAATCTTTC-GTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTCATCAC-GT
* * ** *
2199 TTTTCGGCTAAAAACGCGTTCCGGGGTCCGGCTCAGTTTTGCATGATTTTTGGTGCCAAGACTCC
189 TTTTTGGCTAAAAACGCGTTCCAGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCC
* * * **
2264 TTGAAATATCTATATTCATCTAACCAAATCTTAGCCACATTAGATTTAAGGATCCGTTTTTACGA
254 TTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGA
*
2329 GAATCTGAAT
319 GCATCTGAAT
* * * * * * *
2339 GTTGTTTCGATTTAATTGGAAATTAATTCGGAAAGAAATAGGAAAAACAATATTAGAATCGTTAA
1 CTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAAAAGCGTGAA
* *
2404 AAGCCCTTCAATCTTTTTGATATCGAATAATATATTTTTTTATGAGTATTTTAGCCAAAAATTGA
66 AAGCCCTTCAATCTTTTTGGTAT-GAATTATATA-TTTTTTATGAGTATTTTAGCCAAAAATTGA
* * *
2469 AGAAATATCTTTCGTGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTACTCATCACGATTTTT
129 AGAAAAATCTTTCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTCATCACGTTTTTT
* * *
2534 GGCTAAAAACGCGTTCCAAGACCACGGCTCTGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGA
194 GGCTAAAAACGCGTTCCAGGACC-CGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
* * * * * * *
2599 AATAGCTTTATTCATCTAATAAAATTTCAGCCACATTGGATTTAACGATTTGTTTTTATGTGCAT
258 AATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
2664 CTGAAT
323 CTGAAT
* * *
2670 CTTGTATCGATTTAATTAGAAATTAATTCAGAAAAAAAT--G-AAAATGATATTAAAAGCGTGAA
1 CTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAAAAGCGTGAA
** * * * * * * * * *
2732 AATTCCTCCAATTTTTTTGGCATTGAATTATATATATTTTGTGATTATTTTTGTCAAAAATTGAG
66 AAGCCCTTCAATCTTTTTGGTA-TGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAA
2797 GAAAAATCTTTCG
130 GAAAAATCTTTCG
2810 GATCATTTTT
Statistics
Matches: 2039, Mismatches: 347, Indels: 184
0.79 0.14 0.07
Matches are distributed among these distances:
326 1 0.00
327 60 0.03
328 226 0.11
329 144 0.07
330 305 0.15
331 347 0.17
332 263 0.13
333 68 0.03
334 1 0.00
335 2 0.00
336 5 0.00
337 118 0.06
338 14 0.01
339 123 0.06
340 101 0.05
341 50 0.02
342 10 0.00
343 1 0.00
344 3 0.00
345 63 0.03
346 90 0.04
347 42 0.02
348 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (328 bp):
CTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAAAAGCGTGAA
AAGCCCTTCAATCTTTTTGGTATGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAAG
AAAAATCTTTCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTCATCACGTTTTTTGG
CTAAAAACGCGTTCCAGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
ATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTG
AAT
Found at i:10118 original size:35 final size:37
Alignment explanation
Indices: 10068--10144 Score: 113
Period size: 35 Copynumber: 2.1 Consensus size: 37
10058 AGCGACAACA
* *
10068 AAACCGTTCCTTGATTATTATA-G-CAAAATATAACT
1 AAACCGTTCCCTGATTATTATAGGAAAAAATATAACT
10103 AAACCGTTCCCTGATTATTATAGTGAAAAAATATAACT
1 AAACCGTTCCCTGATTATTATAG-GAAAAAATATAACT
10141 AAAC
1 AAAC
10145 ATGTACATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 21 0.57
37 1 0.03
38 15 0.41
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (37 bp):
AAACCGTTCCCTGATTATTATAGGAAAAAATATAACT
Found at i:31606 original size:14 final size:14
Alignment explanation
Indices: 31589--31615 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31579 TTACAACAGA
31589 TTACAATTTTAAAT
1 TTACAATTTTAAAT
31603 TTACAATTTTAAA
1 TTACAATTTTAAA
31616 AAAAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
TTACAATTTTAAAT
Found at i:39056 original size:10 final size:10
Alignment explanation
Indices: 39043--39069 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
39033 TACAAAAATT
39043 TCAAAAATCA
1 TCAAAAATCA
39053 TCAAAAATCA
1 TCAAAAATCA
39063 TCAAAAA
1 TCAAAAA
39070 GGAAAGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.19, G:0.00, T:0.19
Consensus pattern (10 bp):
TCAAAAATCA
Found at i:41661 original size:13 final size:13
Alignment explanation
Indices: 41645--41670 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41635 GATAAGTGTA
41645 TAGGTTAAGAGAT
1 TAGGTTAAGAGAT
41658 TAGGTTAAGAGAT
1 TAGGTTAAGAGAT
41671 ATACATGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
TAGGTTAAGAGAT
Found at i:46141 original size:13 final size:13
Alignment explanation
Indices: 46125--46150 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46115 GATAAGTGTA
46125 TAGGTTAAGAGAT
1 TAGGTTAAGAGAT
46138 TAGGTTAAGAGAT
1 TAGGTTAAGAGAT
46151 ATACATGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
TAGGTTAAGAGAT
Found at i:47185 original size:19 final size:19
Alignment explanation
Indices: 47161--47198 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
47151 AGTCTGATTC
*
47161 CACTCAATATCAGGTTTAG
1 CACTCAATATCAAGTTTAG
47180 CACTCAATATCAAGTTTAG
1 CACTCAATATCAAGTTTAG
47199 TTATGTTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (19 bp):
CACTCAATATCAAGTTTAG
Found at i:53226 original size:19 final size:20
Alignment explanation
Indices: 53202--53240 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
53192 TAGCAGAATC
*
53202 ATTGAT-TTCTAAATAATAT
1 ATTGATCTTCGAAATAATAT
53221 ATTGATGCTTCGAAATAATA
1 ATTGAT-CTTCGAAATAATA
53241 GGCAACTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (20 bp):
ATTGATCTTCGAAATAATAT
Found at i:56943 original size:32 final size:34
Alignment explanation
Indices: 56887--56954 Score: 95
Period size: 32 Copynumber: 2.0 Consensus size: 34
56877 TCTGACATTG
* *
56887 TTTTTTTTATTTCACCAATTATTGAAGGGTAATTC
1 TTTTTTTTATTTCAACAA-TATTGAAAGGTAATTC
56922 TTTTTTTT-TTTCAACAA-ATTGAAAGGTAATTC
1 TTTTTTTTATTTCAACAATATTGAAAGGTAATTC
56954 T
1 T
56955 ATTAGTTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 15 0.48
34 8 0.26
35 8 0.26
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (34 bp):
TTTTTTTTATTTCAACAATATTGAAAGGTAATTC
Found at i:65958 original size:4 final size:4
Alignment explanation
Indices: 65949--65991 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
65939 CGCAATAACA
65949 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
65992 ACAACCACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:67975 original size:18 final size:18
Alignment explanation
Indices: 67952--67990 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
67942 AGTAATAGGT
67952 ATAGTTAGTTATTGTCAC
1 ATAGTTAGTTATTGTCAC
67970 ATAGTTAGTTATTGTCAC
1 ATAGTTAGTTATTGTCAC
67988 ATA
1 ATA
67991 ACCTTATCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (18 bp):
ATAGTTAGTTATTGTCAC
Found at i:73618 original size:22 final size:22
Alignment explanation
Indices: 73601--73644 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
73591 TAATTACTAT
73601 CCCCTCAGTCCCATATTATCTG
1 CCCCTCAGTCCCATATTATCTG
73623 CCCCTCAGTCCCATATTATCTG
1 CCCCTCAGTCCCATATTATCTG
73645 TAAGCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.41, G:0.09, T:0.32
Consensus pattern (22 bp):
CCCCTCAGTCCCATATTATCTG
Found at i:76302 original size:22 final size:23
Alignment explanation
Indices: 76247--76308 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
76237 ATTGACAGCG
**
76247 CAAAAAAAAAATAAAAACAACAA
1 CAAAAAAAAAACGAAAACAACAA
**
76270 C-AAAACGAAACGAAAACAA-AA
1 CAAAAAAAAAACGAAAACAACAA
76291 CAAAAAAAAAACGAAAAC
1 CAAAAAAAAAACGAAAAC
76309 GAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 3 0.09
22 28 0.88
23 1 0.03
ACGTcount: A:0.77, C:0.16, G:0.05, T:0.02
Consensus pattern (23 bp):
CAAAAAAAAAACGAAAACAACAA
Done.