Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014692.1 Corchorus olitorius cultivar O-4 contig14725, 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: 33942
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:1010 original size:329 final size:328
Alignment explanation
Indices: 3--1545 Score: 1415
Period size: 329 Copynumber: 4.7 Consensus size: 328
1 AG
* * * *
3 TTTTGCATGATTTTTTGGCAGAAAGACTCCTTGAGATATCTATATTCAT-GTAACCAAATTTAAG
1 TTTTGCATGATTTTTGGGC--AAAGACTCCTTGAAATATCAATATTCATCG-AACCAAATGTAAG
* * *
67 CCGCAATGGATTTAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCAATTTAATAAGAAATA
63 CCACAATGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATAAGAAATA
* ** * **
132 AATTC-AAAAAAAAAGAAACACGATATTAGAAGCGTGAAAAACAC-TTTATTTTTTTGGTGTTGA
128 AATTCGAAAAAAATA-AAA-ACGATATTAGAAGCGTGAAAAACACGTCAATCTTTTTGGCATTGA
* * *
195 ATTATATTTTTTTTCTGAGTATTGTGGC--AAAAAATTGAAGAAAAACTTTTCGGGTCAATTTTT
191 ATTATATATTTTTTCTGAGTATTG-CGCAAAAAAAATAG-AGAAAAACTTTTCGGGTCAATTTTT
*
258 GCAAAATTTTGGCAGAAATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACGCATTCCGAAGT
254 GCAAAATTTTGGTAGAAATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACGCATTCCGAAGT
* *
323 GTCAGCTCAA
319 GCCGGCTCAA
*
333 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATGTCAGCC
1 TTTTGCATGATTTTTGG-GCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATGTAAGCC
* ** * * *
398 ACATTGGATATAAGGATTTGTTTTTACGAGCA-CATGAATCTTGTTTTGATTTAGTTAGAAATTA
65 ACAATGGATATAAGGATTTGTTTTTACGAGCATC-TGAATCTTGTTTCAATTTAATAAGAAATAA
*
462 ATTCGGAAAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAACCCGTCAATCTTTTTGGCATTG
129 ATTC-GAAAAAAA-T--AAAAACGATATTAGAAGCGTGAAAAACACGTCAATCTTTTTGGCATTG
* * * ** * * * * *
527 AATTATATA-TTTTTCTGATTATTTCACAATGAAATTGGAAAAAAACTTTTCTGGTCAGTTTTT-
190 AATTATATATTTTTTCTGAGTATTGCGCAAAAAAAATAGAGAAAAACTTTTCGGGTCAATTTTTG
* * * * * ** **
590 ----A-----GTCGAAATCGTGTACTAACCATCACGGTTTTCGGCTAAAAACGCGTTTCGGGGCC
255 CAAAATTTTGGTAGAAATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACGCATTCCGAAGTG
*
646 CCGGCTCAG
320 CCGGCTCAA
* * *
655 TTTTGCATGATTTTT-GGCAGAAAGACTCCTTGAGATATCTATATTCAT-GTAACCAAATTTAAG
1 TTTTGCATGATTTTTGGGC--AAAGACTCCTTGAAATATCAATATTCATCG-AACCAAATGTAAG
* *
718 CCACAATGGATTTAAGGATTAGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATAAGAAATA
63 CCACAATGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATAAGAAATA
* * * * *
783 AATTC-AAAAACA-AAAAACGATATTAGAAGCGTGAAAAACACTTTAATTTTTTTGGTCGTTGAA
128 AATTCGAAAAAAATAAAAACGATATTAGAAGCGTGAAAAACACGTCAATCTTTTTGG-CATTGAA
*
846 TTATGTATTTTTTCTGAGTATTGCGCAAAAAAAATAGAGGAAAAACTTTTCGGGTCAATTTTTGC
192 TTATATATTTTTTCTGAGTATTGCGCAAAAAAAATAGA-GAAAAACTTTTCGGGTCAATTTTTGC
* *
911 AAAATTTTGGTAGATATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACGCATTCCGATGTGC
256 AAAATTTTGGTAGAAATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACGCATTCCGAAGTGC
976 CGGCTCAA
321 CGGCTCAA
*
984 TTTTGCATGATTTTTGGTGCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATGTCAGCC
1 TTTTGCATGATTTTTGG-GCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATGTAAGCC
* * ** * * *
1049 ACATTGGATATAAGGATTTGTTTTTACGAGCACCTGAATCTTGTTTTGATTTAGTTAGAAATTAA
65 ACAATGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATAAGAAATAAA
* * *
1114 TTCGGAAAAAATTTGAAAAGCGATATTAGAAGCGTGAAAAACCCGTCAATCTTTTTGGCATTGAA
130 TTC-GAAAAAA-AT-AAAAACGATATTAGAAGCGTGAAAAACACGTCAATCTTTTTGGCATTGAA
* * * * * ** * * * * *
1179 TTATATATTTTTTCGGATTATTTCACTATGAAATTGGAAAAAAAAAACTTTTCTGGTCAGTTTTT
192 TTATATATTTTTTCTGAGTATTGCGCAAAAAAAAT---AGAGAAAAACTTTTCGGGTCAATTTTT
* * * * ** *
1244 -----A----GGT-GAAATCGTGTACTAACCATCACGG-TTTTCGCTAAAACCGCGTTCCGGGGC
254 GCAAAATTTTGGTAGAAATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACGCATTCCGAAGT
* *
1298 CCCGGCTCAG
319 GCCGGCTCAA
*
1308 TTTTGCATGATTTTT-GGCATAAAGACTCCTTGAAATATTTATATTCATCCTCATCGAACCAAAT
1 TTTTGCATGATTTTTGGGC--AAAGACTCCTTGAAATA-TCA-A-T-AT--TCATCGAACCAAAT
*** * * ** * ** * * * * *
1372 CCCAGCCACATTGGATTTAATTATTTGTTTTTACAAGCATCTGGTTTTTGTTTCGATTGAGTTAG
58 GTAAGCCACAATGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATAAG
* * * * * **
1437 AAATTAATTCGGAAAAAAAAATGGAAAAATGATATTAGAAGCGTGATAAACCCTTCAAAATTTTT
123 AAATAAATTC-G--AAAAAAAT--AAAAACGATATTAGAAGCGTGAAAAACACGTCAATCTTTTT
* * * *
1502 GGCGTTGAAATATATATTATTTTTATGAGTATTGTGGCAAAAAA
183 GGCATTGAATTATATA-T-TTTTTCTGAGTATTG-CGCAAAAAA
1546 TTGAGAATTT
Statistics
Matches: 999, Mismatches: 161, Indels: 101
0.79 0.13 0.08
Matches are distributed among these distances:
316 39 0.04
317 12 0.01
318 23 0.02
319 21 0.02
320 8 0.01
321 2 0.00
322 165 0.17
323 2 0.00
324 60 0.06
325 25 0.03
326 4 0.00
327 2 0.00
328 3 0.00
329 262 0.26
330 99 0.10
331 18 0.02
332 115 0.12
333 62 0.06
334 50 0.05
335 25 0.03
336 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Consensus pattern (328 bp):
TTTTGCATGATTTTTGGGCAAAGACTCCTTGAAATATCAATATTCATCGAACCAAATGTAAGCCA
CAATGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATAAGAAATAAAT
TCGAAAAAAATAAAAACGATATTAGAAGCGTGAAAAACACGTCAATCTTTTTGGCATTGAATTAT
ATATTTTTTCTGAGTATTGCGCAAAAAAAATAGAGAAAAACTTTTCGGGTCAATTTTTGCAAAAT
TTTGGTAGAAATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACGCATTCCGAAGTGCCGGCT
CAA
Found at i:2057 original size:224 final size:221
Alignment explanation
Indices: 1629--2065 Score: 547
Period size: 224 Copynumber: 2.0 Consensus size: 221
1619 GGGGCCTCGA
* * * * *
1629 CTCAGTTTTGCATGGTTTTTGTCATAAGACTCTTTGAAATATATATCTTCATCTAACCGAAACTC
1 CTCAATTTTGAATGGTTTTTGTCATAAGACTCCTTGAAATATATATATTCATCAAACCGAAACTC
* * *
1694 CGCCAAATTAGATTTAAGGATCTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTATAAA
66 AGCCAAATTAGATATAAGGATCTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAA
* * * * *
1759 TTAATTCGGAAAAAAATGGAAAAACGATATTAGAATCGTGAAAAACCCCTTTAATTTTAGTGGTG
131 TTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCATGAAAAA--CCGTCAATTTTAGTGGCG
1824 CTAAATTATATATTTTTTATGATCCTGT
194 CTAAATTATATATTTTTTATGATCCTGT
* *
1852 CTCAATTTTGAATGGTTTTTTTCGCA-AAGACTCCTTGAAATATCTATATTCATCAAACC-AAAT
1 CTCAATTTTGAATGGTTTTTGT--CATAAGACTCCTTGAAATATATATATTCATCAAACCGAAA-
* * * *
1915 CTCATCCACATTGGATATAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAG
63 CTCAGCCAAATTAGATATAAGGATCTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAG
* * * **
1980 AAATTAATTCGGAAAATTAATGGAAAAACGATATTAGTAGCATGAAAGGA-CGTCAATCTTTTTT
128 AAATTAATTCGGAAAA-AAATGGAAAAACGATATTAGAAGCATGAAA-AACCGTCAAT-TTTAGT
* *
2044 GGCGTTGAATTATATATTTTTT
190 GGCGCTAAATTATATATTTTTT
2066 TTGAATATTT
Statistics
Matches: 182, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
223 27 0.15
224 126 0.69
225 28 0.15
226 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.39
Consensus pattern (221 bp):
CTCAATTTTGAATGGTTTTTGTCATAAGACTCCTTGAAATATATATATTCATCAAACCGAAACTC
AGCCAAATTAGATATAAGGATCTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAA
TTAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCATGAAAAACCGTCAATTTTAGTGGCGCT
AAATTATATATTTTTTATGATCCTGT
Found at i:2374 original size:543 final size:545
Alignment explanation
Indices: 1328--2385 Score: 1196
Period size: 543 Copynumber: 1.9 Consensus size: 545
1318 TTTTTGGCAT
* * *
1328 AAAGACTCCTTGAAATATTTATATTCATCCTCATCGAACCAAATCCCAGCCACATTGGATTTAAT
1 AAAGACTCCTTGAAATATCTATATTCA--CTCA-C-AACCAAATCCCAGCCACATTGGATATAAG
* ** * *
1393 TATTTGTTTTTACAAGCATCTGGTTTTTGTTTCGATTGAGTTAGAAATTAATTCGGAAAAAAAAA
62 GATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTGAATTAGAAATTAATTCGGAAAAAAAAA
* * * *
1458 TGGAAAAATGATATTAGAAGCGTGATAAACCCTTCAAAATTTTTGGCGTTGAAATATATATTATT
127 TGGAAAAACGATATTAGAAGCATGATAAACACGTCAAAATTTTTGGCGTTGAAATATATATTATT
* * * * * *
1523 TTTATGAGTATTGTGGCAAAAAATTGAGAATTTTCGGGTCAGTTTCTAGTCGAAATCATGTACGT
192 TTTATGAATATTGTGACAAAAAATTGAGAACTTTCGGGTCAGTTTCTAGCCAAAATCATGTACGC
* * * * * *
1588 TAATCACAATTTTTGGTTAAAAACGCGTTTCGGGGCCTCGACTCAGTTTTGCATGGTTTTTGTCA
257 TAATCACAATTTTTGGCTAAAAACACGTTTCGAGGCCCCGACTCAGTTTTCCATAGTTTTTGTCA
* ** **
1653 TAAGACTCTTTGAAATATATATCTTCATCTAACCGAAACTCCGCCAAATTAGATTTAAGGATCTG
322 AAAGACTCCCTGAAATATATATCTTCATCTAACCGAAACTCAACCAAATTAGATTTAAGGATCTG
* * * * *
1718 TTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTATAAATTAATTCGGAAAAAAATGGAAAAA
387 TTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATAAATTC-AAAAAAAATGGAAAAA
* * **
1783 CGATATTAGAATCGTGAAAAACCCCTTTAATTTTAGTGGTGCTAAATTATATATT-TTTTATGAT
451 CGATATTAGAAGCGTGAAAAACCCCTTCAATTTTAGTGACGCTAAATTATATATTCTTTTATGAT
1847 CCTGTCTCAATTTTGAATGGTTTTTTTCGC
516 CCTGTCTCAATTTTGAATGGTTTTTTTCGC
* *
1877 AAAGACTCCTTGAAATATCTATATTCA-TCA-AACCAAATCTCATCCACATTGGATATAAGGATT
1 AAAGACTCCTTGAAATATCTATATTCACTCACAACCAAATCCCAGCCACATTGGATATAAGGATT
* * * **
1940 TGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAAATTAATGGA
66 TGTTTTTACAAGCATCTGAATCTTGTTTCGATTGAATTAGAAATTAATTCGGAAAAAAAAATGGA
* ** ** *
2004 AAAACGATATTAGTAGCATGA-AAGGACGTCAATCTTTTTTGGCGTTGAATTATATATT-TTTTT
131 AAAACGATATTAGAAGCATGATAAACACGTCAA-AATTTTTGGCGTTGAAATATATATTATTTTT
* * * *
2067 -TGAATATT-TTACAAAAAAAATTGAGTAAAAACCTTTCTGGTCAGTTTTTAGCCAAAATCGTGT
195 ATGAATATTGTGAC--AAAAAATTGAG----AA-CTTTCGGGTCAGTTTCTAGCCAAAATCATGT
** *
2130 AC-CT-ATCACTGTTTTTTGGCTAAAAACACGTTTCGAGGCCCCGACTCAGTTTTCCATAATTTT
253 ACGCTAATCAC-AATTTTTGGCTAAAAACACGTTTCGAGGCCCCGACTCAGTTTTCCATAGTTTT
* * * *
2193 T-TGCAGAAAGAGTCCCTGAAATGTCTA-CATTCATCTAACC-AAATCTCAATCACAA-TAGATT
317 TGT-CA-AAAGACTCCCTGAAATATATATC-TTCATCTAACCGAAA-CTCAACCA-AATTAGATT
* *
2254 TAAGGATTTGTTTTTACGAGCATCTGAATCTTTATTTTGATTTAATTAGAAATAAATT-AAAAAA
377 TAAGGATCTGTTTTTACGAGCATCTGAATC-TTATTTCGATTTAATTAGAAATAAATTCAAAAAA
* ** * *
2318 AATGGAAAAACGATATTAGAAGCGTG-AATA-CCCTTCAATTTTTTTGACGTTAAATTATTTATT
441 AATGGAAAAACGATATTAGAAGCGTGAAAAACCCCTTCAATTTTAGTGACGCTAAATTATATATT
2381 CTTTT
506 CTTTT
2386 GGAGTATTGT
Statistics
Matches: 424, Mismatches: 69, Indels: 37
0.80 0.13 0.07
Matches are distributed among these distances:
539 2 0.00
540 7 0.02
541 23 0.05
542 50 0.12
543 99 0.23
544 13 0.03
545 84 0.20
546 95 0.22
547 25 0.06
549 26 0.06
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.37
Consensus pattern (545 bp):
AAAGACTCCTTGAAATATCTATATTCACTCACAACCAAATCCCAGCCACATTGGATATAAGGATT
TGTTTTTACAAGCATCTGAATCTTGTTTCGATTGAATTAGAAATTAATTCGGAAAAAAAAATGGA
AAAACGATATTAGAAGCATGATAAACACGTCAAAATTTTTGGCGTTGAAATATATATTATTTTTA
TGAATATTGTGACAAAAAATTGAGAACTTTCGGGTCAGTTTCTAGCCAAAATCATGTACGCTAAT
CACAATTTTTGGCTAAAAACACGTTTCGAGGCCCCGACTCAGTTTTCCATAGTTTTTGTCAAAAG
ACTCCCTGAAATATATATCTTCATCTAACCGAAACTCAACCAAATTAGATTTAAGGATCTGTTTT
TACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATAAATTCAAAAAAAATGGAAAAACGATA
TTAGAAGCGTGAAAAACCCCTTCAATTTTAGTGACGCTAAATTATATATTCTTTTATGATCCTGT
CTCAATTTTGAATGGTTTTTTTCGC
Found at i:4153 original size:322 final size:319
Alignment explanation
Indices: 3197--4627 Score: 1351
Period size: 322 Copynumber: 4.5 Consensus size: 319
3187 ATGGTTTTTT
* * * *
3197 TTTTG-CTAAAAACGCGTTCCAGAGTCC-CGACTCAATTTTGCATGATTTTTGGCGTAAAGACTC
1 TTTTGACTAAAAACGCGTTCCGGAG-CCACGGCTCAATTTTGCATGATTTTTAGCGCAAAGACTC
* * * * *
3260 CTTGAAATATCTATATTTATCGAACCAGATCTCAGTCACATTGTATATAAGAATTTG-TTTTACG
65 CTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACG
* * *
3324 AGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAGGAAAAACAATATTA
130 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTA
* * * **
3389 GAAACGT-AAAAAGCCCGTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAATATT-TTAC
195 GAAAAGTGAAAAA-CCCTTCAA-TTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC
* * * *
3452 AAAACATTGAGAAAAACTTTTCAGGTTCGTTTTTAGTCGAAATCGTGTACTAACCATCACGG
258 AAAAAATTGAGAAAAACTTTTCGGGTTAGTTTTTAGCCGAAATCGTGTACTAACCATCACGG
* * * * * *
3514 TTTTTAGCTAAAAACGCATTTCGG-GCCCCGGCTC-AGTTTGCATGATTTTT-G-GC--AGAAT-
1 TTTTGA-CTAAAAACGCGTTCCGGAGCCACGGCTCAATTTTGCATGATTTTTAGCGCAAAGACTC
* * * * * * *
3572 -TTTAAATATCTATATTTATCTAACCAAATCTCAGCAACAATGGGTTTAAGGATTTGTTTTTACG
65 CTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACG
* * *
3636 AGCATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATTTGGAAAGAAAA-GGAAAAACGATAT
130 AGCATCTGAATC-TTGTTTCGATTTAATTAGAAATTAATTCGGAAA-AAAATGGAAAAACGATAT
* * *
3700 TAGAAGAGTG--AAACCCTTCAATTCTTTTGACGTTAAATTATATATTTTTT-TGAGTATTGTGG
193 TAGAAAAGTGAAAAACCCTTCAATT-TTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGG
* * * *
3762 AAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTGTAAAATTTTAGCCAAAATCGTGTACTAA
257 CAAAAAATT-GAGAAAAACTTTTC-GG---G--TTAGT----TTTTAGCCGAAATCGTGTACTAA
3827 CCATCACGG
311 CCATCACGG
* *
3836 CTTTTGACTAAAAACGCGTTCCGGAGCCACGGTTCAATTTTGCATAATTTTTAGCGCAAAGACTC
1 -TTTTGACTAAAAACGCGTTCCGGAGCCACGGCTCAATTTTGCATGATTTTTAGCGCAAAGACTC
* * * * * *
3901 ATTGAAATATCTCTATTCATCGAAACAAATGTCGGCCACATTGGATACAAGGATTTGTTTTTACG
65 CTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACG
*
3966 AGCATATGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTA
130 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTA
** * * *
4031 GAAGCGTGAAAAACCCATCAATATTTTTGGTGTTGAATTATATTTTTTTTCTGAGTATTGTGGCA
195 GAAAAGTGAAAAACCCTTCAAT-TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCA
* * *
4096 AAAAATTGAGAATAAACGTTTCGGGTTAGTTTTTAGCCGAAATTGTTTACTAACCATCACGG
259 AAAAATTGAGAA-AAACTTTTCGGGTTAGTTTTTAGCCGAAATCGTGTACTAACCATCACGG
* * * * ** * *
4158 TTTTTGACTAAAAATGTGTTCTGGGGCCACGGCTCTGTTTTGCATGATTTTTAGCACAGAGACTC
1 -TTTTGACTAAAAACGCGTTCCGGAGCCACGGCTCAATTTTGCATGATTTTTAGCGCAAAGACTC
* * * *
4223 CTTGAAATATCTTTATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
65 CTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACG
* * * *
4288 TGCATCTGAAT-ATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAT-AAAAAACGATATT
130 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA-ATGGAAAAACGATATT
* * * * * * * *
4351 AAAAAAGTGAAAAGCCTTTCAATCTTTTTAGCGTTGAATTATATATATTTTATGAGTATTTTTGC
194 AGAAAAGTGAAAAACCCTTCAAT-TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC
* *
4416 CAAAAATTGATGAAAAA-TCTTTCGGATTA-TTTTTA--C-----C----A-T-A--AT---GG
258 AAAAAATTGA-GAAAAACT-TTTCGGGTTAGTTTTTAGCCGAAATCGTGTACTAACCATCACGG
* * * * * **
4460 TTTTTGGCTAAAAGCGCGTTCCGGA-CCCCAGCTCAATTTTGCATGATTTTTTGCGCCGAGACTC
1 -TTTTGACTAAAAACGCGTTCCGGAGCCACGGCTCAATTTTGCATGATTTTTAGCGCAAAGACTC
* * * * * * * * *
4524 CTTGAAATGTCTATATT-ATCTAATCGAATCTCAGACATATTAGATTTAAGAATTTGTTTTTACG
65 CTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACG
* * * * **
4588 AGTATTTAAATCTTGTTTTGATTTAATTACTAATTAATTC
130 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC
4628 AAAAAATATG
Statistics
Matches: 930, Mismatches: 145, Indels: 94
0.80 0.12 0.08
Matches are distributed among these distances:
300 49 0.05
301 71 0.08
302 21 0.02
305 2 0.00
307 1 0.00
308 1 0.00
309 1 0.00
310 9 0.01
311 85 0.09
312 34 0.04
313 54 0.06
314 4 0.00
315 1 0.00
316 2 0.00
317 21 0.02
318 11 0.01
319 14 0.02
320 6 0.01
321 118 0.13
322 199 0.21
323 13 0.01
324 14 0.02
325 1 0.00
326 6 0.01
328 9 0.01
329 53 0.06
330 62 0.07
331 39 0.04
332 29 0.03
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (319 bp):
TTTTGACTAAAAACGCGTTCCGGAGCCACGGCTCAATTTTGCATGATTTTTAGCGCAAAGACTCC
TTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGA
GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAACGATATTAG
AAAAGTGAAAAACCCTTCAATTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAA
AAATTGAGAAAAACTTTTCGGGTTAGTTTTTAGCCGAAATCGTGTACTAACCATCACGG
Found at i:5906 original size:40 final size:40
Alignment explanation
Indices: 5851--5938 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
5841 GAACTTTTAT
* *
5851 TGGGCCTTTGCAATAACAATTTAGGCCTTATACAACTTAA
1 TGGGCTTTTGCAATAACAAATTAGGCCTTATACAACTTAA
* *
5891 TGGGCTTTTGTAATAACAAATTAGGCCTTCTACAACTTAA
1 TGGGCTTTTGCAATAACAAATTAGGCCTTATACAACTTAA
*
5931 TGTGCTTT
1 TGGGCTTT
5939 CTTTATGTGC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (40 bp):
TGGGCTTTTGCAATAACAAATTAGGCCTTATACAACTTAA
Found at i:6882 original size:62 final size:62
Alignment explanation
Indices: 6785--7185 Score: 777
Period size: 62 Copynumber: 6.5 Consensus size: 62
6775 ACACGACAGA
6785 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
6847 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
6909 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
*
6971 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGA-GCGGGGCCAGCAGG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
7032 CACGAAGGTACACGAGAAGACAAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
1 CACGAAGGTACACGAGAAGAC-AGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
7095 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
1 CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
7157 CACGAAGGTACACGAGAAGACAGAGGAAG
1 CACGAAGGTACACGAGAAGACAGAGGAAG
7186 ACAGACACGA
Statistics
Matches: 335, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
61 34 0.10
62 267 0.80
63 34 0.10
ACGTcount: A:0.35, C:0.22, G:0.40, T:0.03
Consensus pattern (62 bp):
CACGAAGGTACACGAGAAGACAGAGGAAGGAAGAGGCCTCCGCAGGAGGCGAGGCCAGCAGG
Found at i:7200 original size:34 final size:34
Alignment explanation
Indices: 7157--7280 Score: 221
Period size: 34 Copynumber: 3.6 Consensus size: 34
7147 GGCCAGCAGG
7157 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
*
7191 CACGAAGGTAAACGAGAAGACAGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
*
7225 CACGAAGGTACACGAGAAGACCGAGGAAGACAGA
1 CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
*
7259 CAAGAAGGTACACGAGAAGACA
1 CACGAAGGTACACGAGAAGACA
7281 CGGTGGTGCT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 85 1.00
ACGTcount: A:0.48, C:0.18, G:0.31, T:0.03
Consensus pattern (34 bp):
CACGAAGGTACACGAGAAGACAGAGGAAGACAGA
Found at i:7398 original size:2 final size:2
Alignment explanation
Indices: 7393--7424 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7383 ACACACACAC
7393 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
7425 GTAGGAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8191 original size:41 final size:44
Alignment explanation
Indices: 8134--8230 Score: 137
Period size: 45 Copynumber: 2.2 Consensus size: 44
8124 AAGTTAGAAT
*
8134 CCATGACTGCCAAATGCTTCAA-G-GA-AAAGAGAGCTTTGGCC
1 CCATGATTGCCAAATGCTTCAAGGAGACAAAGAGAGCTTTGGCC
* *
8175 CCATGATTGCCAAATGCTTTAAGGAGATCAAAGAGAGCTTTGGCT
1 CCATGATTGCCAAATGCTTCAAGGAGA-CAAAGAGAGCTTTGGCC
8220 CCATGATTGCC
1 CCATGATTGCC
8231 GAGTGCACAA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
41 20 0.41
42 1 0.02
43 2 0.04
45 26 0.53
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.24
Consensus pattern (44 bp):
CCATGATTGCCAAATGCTTCAAGGAGACAAAGAGAGCTTTGGCC
Found at i:12682 original size:72 final size:71
Alignment explanation
Indices: 12482--12695 Score: 358
Period size: 71 Copynumber: 3.0 Consensus size: 71
12472 AAAATAAAGC
12482 GAAGTTAAAACTGAAGAAACGAAATCAAGAAAAGAAGATGAAAAGAAATACAAGAAATCAGATCT
1 GAAGTTAAAACTGAAGAAACGAAATCAAGAAAAGAAGATGAAAAGAAATACAAGAAATCAGATCT
12547 AGAAGG
66 AGAAGG
* *
12553 GAAGTTAAAACTGAAGAAACGATATCAAGAAAACG-AGATGAAAAGAAATACAAGAAATCGGATC
1 GAAGTTAAAACTGAAGAAACGAAATCAAGAAAA-GAAGATGAAAAGAAATACAAGAAATCAGATC
*
12617 TGGAAGG
65 TAGAAGG
*
12624 GAAGTTAAAACTGAAGAAAACGAAATCAAGAAAAGAAGATGAAAAGAATTACAAGAAATCAGATC
1 GAAGTTAAAACTGAAG-AAACGAAATCAAGAAAAGAAGATGAAAAGAAATACAAGAAATCAGATC
*
12689 TAAAAGG
65 TAGAAGG
12696 AAGAGAAAGA
Statistics
Matches: 132, Mismatches: 8, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
71 83 0.63
72 49 0.37
ACGTcount: A:0.56, C:0.09, G:0.21, T:0.14
Consensus pattern (71 bp):
GAAGTTAAAACTGAAGAAACGAAATCAAGAAAAGAAGATGAAAAGAAATACAAGAAATCAGATCT
AGAAGG
Found at i:14270 original size:2 final size:2
Alignment explanation
Indices: 14263--14289 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14253 GTACAGGAAA
14263 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
14290 AGAAGGATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17285 original size:7 final size:7
Alignment explanation
Indices: 17269--17327 Score: 95
Period size: 7 Copynumber: 8.7 Consensus size: 7
17259 AACAAGCTAG
17269 TTTTTC-
1 TTTTTCT
17275 TTTTTCT
1 TTTTTCT
17282 TTTTTCT
1 TTTTTCT
17289 TTTTTCT
1 TTTTTCT
17296 TTTTTCT
1 TTTTTCT
17303 TTTTTCT
1 TTTTTCT
*
17310 TTCTT-T
1 TTTTTCT
17316 TTTTTCT
1 TTTTTCT
17323 TTTTT
1 TTTTT
17328 ATTATTATTA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
6 11 0.22
7 38 0.78
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTCT
Found at i:17294 original size:20 final size:20
Alignment explanation
Indices: 17269--17327 Score: 93
Period size: 20 Copynumber: 2.9 Consensus size: 20
17259 AACAAGCTAG
17269 TTTTTCTTTTTCTTTTTTCT
1 TTTTTCTTTTTCTTTTTTCT
17289 TTTTTCTTTTTTCTTTTTTCT
1 TTTTTC-TTTTTCTTTTTTCT
17310 TTCTTT-TTTTTCTTTTTT
1 TT-TTTCTTTTTCTTTTTT
17328 ATTATTATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.49
21 16 0.43
22 3 0.08
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (20 bp):
TTTTTCTTTTTCTTTTTTCT
Found at i:17332 original size:3 final size:3
Alignment explanation
Indices: 17326--17351 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17316 TTTTTCTTTT
17326 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
17352 TTTGCAAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:17809 original size:2 final size:2
Alignment explanation
Indices: 17802--17826 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17792 ACTTTCGATT
17802 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
17827 GCATTAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26344 original size:2 final size:2
Alignment explanation
Indices: 26337--26372 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
26327 CTAAATGTTC
26337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26373 TTTGTATTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28752 original size:129 final size:129
Alignment explanation
Indices: 28473--28812 Score: 357
Period size: 129 Copynumber: 2.7 Consensus size: 129
28463 GCTAATTCTG
* * * *
28473 TCTTCTGCAAGAGAATGTCCTACGCCAGGGCTGTGTCCTGGGCT-GCTAGGGCGGAAATCTTCCT
1 TCTTCTGCAAAAGAATGTCCTACGCCAGGGCTGTGTCCTGGGGTAG-TTGGTCGGAAATCTTCCT
* * *
28537 TGTCACCTCCTGCAATAGAATGCCTGCTAATGCTTTCTGGTGAATTGTGTTCAACATCTTCACTA
65 TGTCACCACCTGCAATAGAATGCCTGCTAATGCTTCCTAGTGAATTGTGTTCAACATCTTCACTA
* * * * *
28602 CCTTCTTCAAATGAGTGTCCTACGCCAGGGCTGTGTCCTGGGGTAGTTGGTTGGAAATCTTCCTT
1 TCTTCTGCAAAAGAATGTCCTACGCCAGGGCTGTGTCCTGGGGTAGTTGGTCGGAAATCTTCCTT
* * * * ** *
28667 GTTACCACCTGCAATGGAATGCCTGCTAATGCTTCCTAGTGACTTTTGTTCAGTATCTTC-GTCA
66 GTCACCACCTGCAATAGAATGCCTGCTAATGCTTCCTAGTGAATTGTGTTCAACATCTTCACT-A
* * * * *** * * *
28731 TCTTCTGGAAAAGAATTTCCTACACCAGGACTGACCCCTGGTGTAGTTGGTCGAAAATCATCCTT
1 TCTTCTGCAAAAGAATGTCCTACGCCAGGGCTGTGTCCTGGGGTAGTTGGTCGGAAATCTTCCTT
*
28796 GT-A-C-CCTGCAACAGAAT
66 GTCACCACCTGCAATAGAAT
28813 CATCATCAAA
Statistics
Matches: 173, Mismatches: 36, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
126 11 0.06
127 1 0.01
128 2 0.01
129 158 0.91
130 1 0.01
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.31
Consensus pattern (129 bp):
TCTTCTGCAAAAGAATGTCCTACGCCAGGGCTGTGTCCTGGGGTAGTTGGTCGGAAATCTTCCTT
GTCACCACCTGCAATAGAATGCCTGCTAATGCTTCCTAGTGAATTGTGTTCAACATCTTCACTA
Done.