Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014613.1 Corchorus olitorius cultivar O-4 contig14646, 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: 66283
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:623 original size:334 final size:333
Alignment explanation
Indices: 8--4257 Score: 4511
Period size: 332 Copynumber: 12.9 Consensus size: 333
1 TTTTTTT
*
8 TTTTC-GAGTATTGTGGCAAAAAATTGAGAAAATAA-TTTTTGGGTCAGTTTTTGCAGATTTTTA
1 TTTTCTGAGTATTGTGGCAAAAAATTGAGAAAA-AACTTTTTGGGTCAGTTTTTGCAGAATTTTA
* ** * *
71 GCCGAAATCGTG---T-ACCATCACGATTTTTGGGAAAAAACGCGTTCTGGAGCCCCGTCTTAAT
65 GCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTTAAT
* * * *
132 TTTGCATGAATTTTGGCGTAATGACTCCTTGTAATATCTATATTCATTTAACCAAATCTCAACCA
130 TTTGCATGATTTTTGGCGCAATGACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGCCA
* * *
197 CTTTGGATTTAGGTATTTGTTTTTAGGAGCATCTAAATCTTGTTTCGATTTTATTAGAAATAAAT
195 CATTGGATTTAGGTATTTGTTTTTAGGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAAT
*
262 TCGGAAAAGAAATGGAAAACCATATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGCGTTGAATT
260 TCGGAAAAGAAATGGAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGCGTTGAATT
327 ATATATATA
325 ATATATATA
* * * *
336 TTTTCTGAGTACTGTGGCAAAAAATTGTGAGAAAACTTTTTGGGTTAGTTTTTGCAGAATTTTAG
1 TTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTTGGGTCAGTTTTTGCAGAATTTTAG
** * * * * *
401 CCGAAATATTGTACTAACCATCACGATTTTTGGCAAAAAAACGCGTTCGGGAGCCTCGACTTAAT
66 CCGAAATCGTGTACTAACCATCACGGTTTTTGGC-TAAAAACGCGTTCCGGAGCCCCGGCTTAAT
* *
466 TTTGCTTGAATTTTGGCGCAATGACTCCTTGTAATATCTATATTCAT-TCAACCAAATCTCAGCC
130 TTTGCATGATTTTTGGCGCAATGACTCCTTGTAATATCTATATTCATCT-AACCAAATCTCAGCC
* * * * *
530 ACTTTGGATTTAGGTAATTGTTTTAAGGAGCGTCT-AGATCTTGTTTCGATTTAATTAGATATAA
194 ACATTGGATTTAGGTATTTGTTTTTAGGAGCATCTGA-ATCTTGTTTCGATTTAATTAGAAATAA
594 ATTCGGAAAAGAAATGGAAAACGATATTAGAAGCGTGAAAAATCCTTCAATATTTTTTTGCGTTG
258 ATTCGGAAAAGAAATGGAAAACGATATTAGAAGCGTGAAAAATCCTTC-A-ATTTTTTTGCGTTG
*
659 AATTATATATATT
321 AATTATATATATA
*
672 TTTTCT-ATGTATTGTGGCAAAAAATTGAGAAAAAACTTCTTGGGTCAGTTTTTGCAGAATTTTA
1 TTTTCTGA-GTATTGTGGCAAAAAATTGAGAAAAAACTTTTTGGGTCAGTTTTTGCAGAATTTTA
* * *
736 GCCGAAATCGTGTACTAACCATCACGATTTTTGGCAAAAAACGCGTTCTGGAGCCCCGGCTTAAT
65 GCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTTAAT
* * *
801 TTTGCATGAATTTTGGTGCAATGACTCCTTGTAATATTTATATTCAT-TGAACCAAATCTCAGCC
130 TTTGCATGATTTTTGGCGCAATGACTCCTTGTAATATCTATATTCATCT-AACCAAATCTCAGCC
** * *
865 AGTTTGGATTTAGGTATTTGTTTTTAGGAGCATCTAAATCTTGTTTCGATTTTATTAGAAATAAA
194 ACATTGGATTTAGGTATTTGTTTTTAGGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAA
* *
930 TTCGGAAAAGAAATTGAAAACCATATTAGAAGCGTG-AAAATCCTTCAA-TTTTTTGCGTTGAAT
259 TTCGGAAAAGAAATGGAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGCGTTGAAT
993 TATATATATA
324 TATATATATA
1003 TTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAAACTTTTTGGGTCAGTTTTTGCAGAAT
1 --TTTTCTGAGTATTGTGGCAAAAAATTGAG---AAAAAACTTTTTGGGTCAGTTTTTGCAGAAT
* * * *
1068 TTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACACGTTCCGAAGGCCCGGCT
61 TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCT
* * * * * * * * *
1133 CATTTTTGCATGATTTTTTGCGCAAAGACTCTTTGAAATATATATATATTTTATCGAACCAAATC
126 TAATTTTGCATGATTTTTGGCGCAATGACTCCTTG-TA-ATATCTATA-TTCATCTAACCAAATC
* * * ** ** *
1198 TCAGCCACATTGGATATAAGG-ATTTGCTTTTATGAGCATCTGAAAGTTGTTTTAATTTAATTAA
188 TCAGCCACATTGGAT-TTAGGTATTTGTTTTTAGGAGCATCTGAATCTTGTTTCGATTTAATTAG
* * ** * **
1262 AAATAAACTCGTAGAAA-AAA-GGAAAAAATATATTATAAGTTTG-AAAATCCCATT-AATCTTT
252 AAATAAATTCGGA-AAAGAAATGG-AAAACGATATTAGAAGCGTGAAAAAT-CC-TTCAAT-TTT
* * * *
1323 CTAT-CATTAAATTATCTAT-T-
312 -TTTGCGTTGAATTATATATATA
* * * * *
1343 TTTT-TGAGTATTGTGGCAAAAAATTCAGAAAAAAATTTTCGGGTTAGTTTTTAGCTGAA--TT-
1 TTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTTGGGTCAGTTTTT-GCAGAATTTTA
*** * * * * *
1404 --CG---T-GT-T--T-GTTATCACGGTTTTTGGGCTAAAAACGCGTTTCGGGGTCCCGGCTCAG
65 GCCGAAATCGTGTACTAACCATCACGGTTTTT-GGCTAAAAACGCGTTCCGGAGCCCCGGCTTAA
* * *
1459 TTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTTTATTCATCTAACCAAATCTCAGC
129 TTTTGCATGATTTTTGGC-GCAATGACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGC
* * ** * *
1523 CAGATTGGATTTAAGTATTTGTTTTTAAAAGCATATGAATCTTGTTTCGATTTAATTAGAAGTAA
193 CACATTGGATTTAGGTATTTGTTTTTAGGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAA
*
1588 ATTC-GAAAA-AAATGGAAAACGATGTTAGAAGCGTGAAAAATCCTTCAA-TTTTTTGCGTTGAA
258 ATTCGGAAAAGAAATGGAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGCGTTGAA
1650 TTATATATATA
323 TTATATATATA
* * * * *
1661 TATATTTTGAGTATTGTGGCAAAAAATTGAGAAAAGACTTTTTGTGTCAGCTTTTACAGAATTTT
1 T-T-TTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTTGGGTCAGTTTTTGCAGAATTTT
* * * *
1726 AGCCGAAATCGTGTAGTAACCATCATGGTTTTTTGCTAAAAACGCGTTCCGGAACCCCGGCTTAA
64 AGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTTAA
* ** *
1791 TTTTGCATGAATTTTGATGCAATGACTCCTTGTAATAACTATATTCATCTAACCAAATCTCAGCC
129 TTTTGCATGATTTTTGGCGCAATGACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGCC
* * *
1856 ACTTTGGATTTAGCTATTTGTTTTTAGGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAA
194 ACATTGGATTTAGGTATTTGTTTTTAGGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAA
* *
1921 TTCTGAAAAGAAATGGAAAACGATATTAGAAGCGTGAAAAATCCTTTAATTTTTTTGCGTTGAAT
259 TTCGGAAAAGAAATGGAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGCGTTGAAT
1986 TATATATATA
324 TATATATATA
* * * *
1996 TTTTCTGTGTATTTTGGCAAAAAATTGAGAAAAAACTTTTTGGGTCAGATTTTGCAGAATTCTAG
1 TTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTTGGGTCAGTTTTTGCAGAATTTTAG
* * * * * *
2061 CCGAAATCGTGTACTAATCATCACGATTTTTGACAAAAAAACGCATTCCCGAGCCCCGGCTTAAT
66 CCGAAATCGTGTACTAACCATCACGGTTTTTGGC-TAAAAACGCGTTCCGGAGCCCCGGCTTAAT
* * *
2126 TTTGCATGAATTTTGGCGCAATGAATCCTTGTAATATCTATATTCAT-TGAACCAAATATCAGCC
130 TTTGCATGATTTTTGGCGCAATGACTCCTTGTAATATCTATATTCATCT-AACCAAATCTCAGCC
* * ** *
2190 ACATTGGATTTAAGG-ATTTATTTTTACGAGCATCTGAATCTTGTTTCGATAAAAATAGAAATAA
194 ACATTGGATTT-AGGTATTTGTTTTTAGGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAA
* * ** * *
2254 ATTCGAAAAAAAAATTGGGAAAACGATATTAGAAATGTG--AAATCCTTCAATTTTTTTGCATTA
258 ATTCGGAAAAGAAA-T-GGAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGCGTTG
*
2317 AATCATATAT-T-
321 AATTATATATATA
** * * * *
2328 TTTTCTGAGTATTGTGGCATCAAATTGAGGAAAAAA-TTTTCGGTTCAGTTTTTGCAAAAATTTA
1 TTTTCTGAGTATTGTGGCAAAAAATTGA-GAAAAAACTTTTTGGGTCAGTTTTTGCAGAATTTTA
* * * * * * *
2392 GCCGAAATCATATACTAACCATCACGGTTTTTGGCTAAAAACACGTTCCGAAGGCTCGGTCTCAA
65 GCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGG-CTTAA
* * * *
2457 TTTTACATGATTTTTGGCGCAAAT-ACTCTTTGAAATATCTATATTCATCAAACCAAATCTCAGC
129 TTTTGCATGATTTTTGGCGC-AATGACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGC
* * * * * ** * *
2521 CACATTGTATATAAGG-ATTTGCTTTTATGAGGATCTGAAAGTTGTTTTGATTTAATTAAAAATA
193 CACATTGGAT-TTAGGTATTTGTTTTTAGGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATA
* * * * * *
2585 AACTCGG-AAA-AAA-GGAAAAACGATATAATAAGTGTGAAAAACCCGTT-AATCTTTTTGTCGT
257 AATTCGGAAAAGAAATGG-AAAACGATATTAGAAGCGTGAAAAATCC-TTCAATTTTTTTG-CGT
*
2646 TGAA--ATATATATT
319 TGAATTATATATATA
* * * * *
2659 TTTTCTAAGTATTGTGGAAAAAAATTCAGGAAAAATTTTTTCGGGTCAGTTTTT----AA-TTT-
1 TTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTT-GGGTCAGTTTTTGCAGAATTTTA
* * * * * * * * *
2718 ----AAATCGTGTACTAACCATCATGATTTTTTGGATAAAAACGCATTTCGGGGACCCGGCTCAG
65 GCCGAAATCGTGTACTAACCATCACG-GTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTTAA
**
2779 TTTTGCATGATTTTTGGCAG-AAACACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGC
129 TTTTGCATGATTTTTGGC-GCAATGACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGC
* * * *
2843 TACTTTGGATTTAGGTATTTGTTTGTAGGAGCAT-TCAAATCTTGTTTCGATTTAATTAGAAATA
193 CACATTGGATTTAGGTATTTGTTTTTAGGAGCATCT-GAATCTTGTTTCGATTTAATTAGAAATA
*
2907 AATTCGGAAAAGAAATGGAAAACGATATTATAAGCGTGAAAAATCCTTCAATTTTTTTGCGTTGA
257 AATTCGGAAAAGAAATGGAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGCGTTGA
*
2972 ATTATATATATT
322 ATTATATATATA
* * * *
2984 TTTTCTGAGTATTTTGGCAAAAAAAAATGAGAAAAAACTTCTTGGGCCAGTTTTTGCAGAATTTT
1 TTTTCTGAGTATTGTGGC--AAAAAATTGAGAAAAAACTTTTTGGGTCAGTTTTTGCAGAATTTT
* * **
3049 AGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAGAAACGCGTTCCAGAGCCTTGGCTTAA
64 AGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTTAA
*
3114 TTTTGCATGAATTTTGGCGCAATGACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGCC
129 TTTTGCATGATTTTTGGCGCAATGACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGCC
* *
3179 ACTTTGGATTTAGGTATTTGTTTTTAGGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAA
194 ACATTGGATTTAGGTATTTGTTTTTAGGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAA
3244 TTCGGAAAAGAAATGGAAAACGATATTAGAAGCGTGAAAAATCCTTCTAATTTTTTTGCGTTGAA
259 TTCGGAAAAGAAATGGAAAACGATATTAGAAGCGTGAAAAATCCTTC-AATTTTTTTGCGTTGAA
3309 TTATATATATA
323 TTATATATATA
* * * *
3320 CTTTTTCTGAGTATTGTGGAAAAAAATTGCGAAAAAACTTTTTGGATCAGTTTTTGCAAAATTTT
1 --TTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTTGGGTCAGTTTTTGCAGAATTTT
* * *
3385 AGCCGAAATCGT-TAACTAACCGTCACGGTTTTTGG----AAACGCGTTCCGGAGCCCCGACGTA
64 AGCCGAAATCGTGT-ACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTTA
** * * *
3445 ATTTTGCATTTTTTTTGGCGC-A--A---C---TAATATCTATATTCAT-TGAACTAAATATGAG
128 ATTTTGCATGATTTTTGGCGCAATGACTCCTTGTAATATCTATATTCATCT-AACCAAATCTCAG
* * * * *
3500 TCTCATTGGATTTAAGG-ATTTATTTTTATGAGCATCTGAATCTTGTTTCGATTTAAATAGAAAT
192 CCACATTGGATTT-AGGTATTTGTTTTTAGGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
* * * *
3564 AAATTTGGAAAAAAAAAATGGGAAAACGATATTAGAAACGTG-AAAATCCTTCAATTTTTTTTGT
256 AAATTCGG--AAAAGAAAT-GGAAAACGATATTAGAAGCGTGAAAAATCCTTCAA-TTTTTTTGC
*
3628 GCTGAATTATATAT-T-
317 GTTGAATTATATATATA
* * * * * *
3643 TTTTCTAAGTATTTTGGCAAAAAATTGAGGAAAAA-TTTTCGGGTCAGTTTTTGCAAAATATTAG
1 TTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTTGGGTCAGTTTTTGCAGAATTTTAG
* * * * * * * *
3707 GCGAAATCGTGTACTAACCATTACGGTTTTTCGCTAAAAA-ACGTTCCGAAGGCCCGGCTCATTT
66 CCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTTAATT
* ** * * * *
3771 TTGCATGATTTTTGGCGCAAAGACTATTTGAAATATATATATTCATCGAGCCAAATCTCAGCCAC
131 TTGCATGATTTTTGGCGCAATGACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGCCAC
* * * * * * * *
3836 GTTGGATATAAGG-ATTTGCTTTTATGAGCATCTGAAACATGTTTTGATTTAATTAAAAACT-AA
196 ATTGGAT-TTAGGTATTTGTTTTTAGGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA-TAAA
* * * ** * *
3899 TTCGGAAAA-AACA-GAAAAACGATACTATAAGCGTGAAAAGCCCGTT-AATCTTTTTGTCATTG
259 TTCGGAAAAGAA-ATGGAAAACGATATTAGAAGCGTGAAAAATCC-TTCAATTTTTTTG-CGTTG
3961 AATTATAT-T-T-
321 AATTATATATATA
* * * **** * * *
3971 TTTTTTGAGTATTGTGGCAAAAAATTCACAAAAAAAAAAATCGGGTCAATTTTTTGCTGAA--TT
1 TTTTCTGAGTATTGTGGCAAAAAATTGA-GAAAAAACTTTTTGGGTC-AGTTTTTGCAGAATTTT
* * *
4034 ---CG---T-GT-T-CTAACCATCACGGTTTTTGGTTTAAAAACACGTTTCGGAGCCCCGGCTTA
64 AGCCGAAATCGTGTACTAACCATCACGGTTTTTGG-CTAAAAACGCGTTCCGGAGCCCCGGCTTA
* * * * * * *
4090 GTTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATTTTTATATTAATCTATCCAAATCTCAG
128 ATTTTGCATGATTTTTGGC-GCAATGACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAG
* * *
4154 CCACATTGGATTTAAGTAATTGTTTTTAGGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
192 CCACATTGGATTTAGGTATTTGTTTTTAGGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATA
* * *
4219 GATTCTGAAAA-AAATGGAAAAACGATATTAGAAGTGTGA
257 AATTCGGAAAAGAAATGG-AAAACGATATTAGAAGCGTGA
4258 GAAGCCCGTT
Statistics
Matches: 3316, Mismatches: 460, Indels: 297
0.81 0.11 0.07
Matches are distributed among these distances:
315 2 0.00
316 15 0.00
317 3 0.00
318 25 0.01
319 12 0.00
320 147 0.04
321 98 0.03
322 277 0.08
323 231 0.07
324 48 0.01
325 68 0.02
326 38 0.01
327 24 0.01
328 78 0.02
329 95 0.03
330 43 0.01
331 93 0.03
332 457 0.14
333 163 0.05
334 438 0.13
335 408 0.12
336 375 0.11
337 24 0.01
338 29 0.01
339 94 0.03
340 11 0.00
341 3 0.00
342 15 0.00
343 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (333 bp):
TTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTTGGGTCAGTTTTTGCAGAATTTTAG
CCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTTAATT
TTGCATGATTTTTGGCGCAATGACTCCTTGTAATATCTATATTCATCTAACCAAATCTCAGCCAC
ATTGGATTTAGGTATTTGTTTTTAGGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATT
CGGAAAAGAAATGGAAAACGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGCGTTGAATTA
TATATATA
Found at i:4393 original size:109 final size:109
Alignment explanation
Indices: 4177--4396 Score: 284
Period size: 109 Copynumber: 2.0 Consensus size: 109
4167 AAGTAATTGT
* ** *
4177 TTTTAGGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTGATTCTGAAAAAAATGGAAAAAC
1 TTTTAGGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAAC
* ** * * *
4242 GATATTAGAAGTGTGAGAAGCCCGTTACTCTTTTTGTTGTTGAA
66 GATATTAGAAGCGTGAGAAAACCATTAATCTTTTTGTCGTTGAA
*
4286 TTTTAGGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAGAAATTG-AAAA
1 TTTTAGGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAA-AAATGGAAAAA
*
4350 CGATATTAGAAGCGTGA-AAAACCATTCAATTTCTTTTG-CGTTGAA
65 CGATATTAGAAGCGTGAGAAAACCATT-AATCT-TTTTGTCGTTGAA
4395 TT
1 TT
4397 ATATATATAT
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
108 6 0.06
109 80 0.83
110 10 0.10
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.36
Consensus pattern (109 bp):
TTTTAGGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAAC
GATATTAGAAGCGTGAGAAAACCATTAATCTTTTTGTCGTTGAA
Found at i:5666 original size:21 final size:22
Alignment explanation
Indices: 5637--5679 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
5627 GTTTCGATTT
5637 AAATAGAAATAA-ATAC-GGAAA
1 AAATAGAAA-AAGATACTGGAAA
*
5658 AAATGGAAAAAGATACTGGAAA
1 AAATAGAAAAAGATACTGGAAA
5680 CGTGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 2 0.11
21 12 0.63
22 5 0.26
ACGTcount: A:0.63, C:0.05, G:0.19, T:0.14
Consensus pattern (22 bp):
AAATAGAAAAAGATACTGGAAA
Found at i:24327 original size:50 final size:50
Alignment explanation
Indices: 24252--24351 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
24242 AGTCGCTTAC
24252 ACTGCCATTGATCATCTCTTTTGAGCAGCATATCAAAGATATGCACAATT
1 ACTGCCATTGATCATCTCTTTTGAGCAGCATATCAAAGATATGCACAATT
24302 ACTGCCATTGATCATCTCTTTTGAGCAGCATATCAAAGATATGCACAATT
1 ACTGCCATTGATCATCTCTTTTGAGCAGCATATCAAAGATATGCACAATT
24352 TTGGGCTACA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (50 bp):
ACTGCCATTGATCATCTCTTTTGAGCAGCATATCAAAGATATGCACAATT
Found at i:27074 original size:1 final size:1
Alignment explanation
Indices: 27026--27057 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
27016 TTTTTAATTT
27026 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
27058 CAGTAAGCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:34804 original size:44 final size:44
Alignment explanation
Indices: 34741--34834 Score: 179
Period size: 44 Copynumber: 2.1 Consensus size: 44
34731 TTAAACCATG
*
34741 AATCAGAGTATTCTCTGATTGATGGTTTGGGTATCATTTTTTAA
1 AATCAAAGTATTCTCTGATTGATGGTTTGGGTATCATTTTTTAA
34785 AATCAAAGTATTCTCTGATTGATGGTTTGGGTATCATTTTTTAA
1 AATCAAAGTATTCTCTGATTGATGGTTTGGGTATCATTTTTTAA
34829 AATCAA
1 AATCAA
34835 TGTAAGGTTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.44
Consensus pattern (44 bp):
AATCAAAGTATTCTCTGATTGATGGTTTGGGTATCATTTTTTAA
Found at i:35214 original size:147 final size:148
Alignment explanation
Indices: 34946--35239 Score: 563
Period size: 147 Copynumber: 2.0 Consensus size: 148
34936 AAAAATTTAT
34946 GTACACGACCGGATCAAAACCAGATTATACCGAATGGGAAAAAAAAATCAGAGCATTCTCCCATA
1 GTACACGACCGGATCAAAACCAGATTATACCGAATGGGAAAAAAAAATCAGAGCATTCTCCCATA
35011 TTGCTACGATGACCATTTTAATCTTTTTCTTTTTTGTTTTGAGAATGACCATTTTAGTCTTGTCA
66 TTGCTACGATGACCATTTTAATCTTTTTCTTTTTTGTTTTGAGAATGACCATTTTAGTCTTGTCA
35076 TAATAAATAGTTTTTTTG
131 TAATAAATAGTTTTTTTG
* *
35094 GTACACGACCGGATCAAAACCGGATTATACCGGATGGG-AAAAAAAATCAGAGCATTCTCCCATA
1 GTACACGACCGGATCAAAACCAGATTATACCGAATGGGAAAAAAAAATCAGAGCATTCTCCCATA
35158 TTGCTACGATGACCATTTTAATCTTTTTCTTTTTTGTTTTGAGAATGACCATTTTAGTCTTGTCA
66 TTGCTACGATGACCATTTTAATCTTTTTCTTTTTTGTTTTGAGAATGACCATTTTAGTCTTGTCA
35223 TAATAAATAGTTTTTTT
131 TAATAAATAGTTTTTTT
35240 TTATCCCATC
Statistics
Matches: 144, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
147 108 0.75
148 36 0.25
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (148 bp):
GTACACGACCGGATCAAAACCAGATTATACCGAATGGGAAAAAAAAATCAGAGCATTCTCCCATA
TTGCTACGATGACCATTTTAATCTTTTTCTTTTTTGTTTTGAGAATGACCATTTTAGTCTTGTCA
TAATAAATAGTTTTTTTG
Found at i:48208 original size:31 final size:31
Alignment explanation
Indices: 48161--48275 Score: 131
Period size: 31 Copynumber: 3.7 Consensus size: 31
48151 CGAAGCATGC
* *
48161 CACGTGTCGCTTTTTGGTATACATGGCGTGA
1 CACGTGTCACTTTTTGGTACACATGGCGTGA
* * * * *
48192 CAGGTATCACTTTTTGGTACACGTGGCATGT
1 CACGTGTCACTTTTTGGTACACATGGCGTGA
* * *
48223 CACATGTCACTTTTTTGTACACATGGCGTGC
1 CACGTGTCACTTTTTGGTACACATGGCGTGA
*
48254 CACGTGTCGCTTTTTGGTACAC
1 CACGTGTCACTTTTTGGTACAC
48276 TTGGTATGTC
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 67 1.00
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (31 bp):
CACGTGTCACTTTTTGGTACACATGGCGTGA
Found at i:48236 original size:62 final size:62
Alignment explanation
Indices: 48140--48289 Score: 176
Period size: 62 Copynumber: 2.4 Consensus size: 62
48130 GGCACATGTC
** * * * * *
48140 CTTTTT-GTACACGAAGCATGCCACGTGTCGCTTTTTGGTATACATGGCGTGACAGGTATCA
1 CTTTTTGGTACACGTGGCATGTCACATGTCACTTTTTGGTACACATGGCGTGACACGTATCA
* * * *
48201 CTTTTTGGTACACGTGGCATGTCACATGTCACTTTTTTGTACACATGGCGTGCCACGTGTCG
1 CTTTTTGGTACACGTGGCATGTCACATGTCACTTTTTGGTACACATGGCGTGACACGTATCA
* *
48263 CTTTTTGGTACACTTGGTATGTCACAT
1 CTTTTTGGTACACGTGGCATGTCACAT
48290 CGGACACCGT
Statistics
Matches: 75, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
61 6 0.08
62 69 0.92
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (62 bp):
CTTTTTGGTACACGTGGCATGTCACATGTCACTTTTTGGTACACATGGCGTGACACGTATCA
Found at i:61141 original size:19 final size:20
Alignment explanation
Indices: 61117--61175 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
61107 ACTGTTTGGC
61117 AACTGTACAGATGAGATTA-
1 AACTGTACAGATGAGATTAG
*
61136 AACTGTACAGATTAGATTAGG
1 AACTGTACAGATGAGATTA-G
*
61157 TACTGTACAGATGAGATTA
1 AACTGTACAGATGAGATTA
61176 TTAGAGCAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 18 0.51
21 17 0.49
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (20 bp):
AACTGTACAGATGAGATTAG
Found at i:61334 original size:16 final size:16
Alignment explanation
Indices: 61313--61343 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61303 CAGAATCTAG
*
61313 ACCAAAAGCAAAAAAA
1 ACCAAAAACAAAAAAA
61329 ACCAAAAACAAAAAA
1 ACCAAAAACAAAAAA
61344 CAATGAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.19, G:0.03, T:0.00
Consensus pattern (16 bp):
ACCAAAAACAAAAAAA
Found at i:63228 original size:2 final size:2
Alignment explanation
Indices: 63221--63254 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
63211 GCCGCCCAAC
63221 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
63255 CAAGATTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64097 original size:2 final size:2
Alignment explanation
Indices: 64090--64114 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
64080 AGAACATGAT
64090 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
64115 TTATGCATAG
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:66259 original size:2 final size:2
Alignment explanation
Indices: 66252--66283 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
66242 ATGACAAACC
66252 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
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.