Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016359.1 Corchorus olitorius cultivar O-4 contig16392, 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: 46132
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:4725 original size:11 final size:11
Alignment explanation
Indices: 4709--4738 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
4699 GAATGAATTT
4709 TAGCTACGGAC
1 TAGCTACGGAC
4720 TAGCTACGGAC
1 TAGCTACGGAC
4731 TAGCTACG
1 TAGCTACG
4739 ATTGCTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (11 bp):
TAGCTACGGAC
Found at i:6331 original size:323 final size:323
Alignment explanation
Indices: 5344--6490 Score: 1396
Period size: 322 Copynumber: 3.5 Consensus size: 323
5334 TTTTTTTGGT
* * *
5344 TTTTGCATGATTTTTGACGTAAATACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCC
1 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCC
* ** *
5409 ACGTTCGATTTAAATATTTGTTTTTATGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAA
66 ACATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAA
* *
5474 TTCGGAAAAAAATCATAGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTT
131 TTCAGAAAAAAA--ATAGAAAAACGATATTAAAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTT
** * *
5539 GAATTATATTTTTTT-T-AGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCTGATCAGCTTTTA
194 GAATTATATTTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCCGATCAGTTTTTA
* * * * *
5602 GCTG-AAATCGTGTACTTACCATCACGGTTTTTGGCTAAAAACGCATTCCCGAGCCCCGACTAAA
259 GCCGAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCCGAGGCCCGACTCAA
* *
5666 TTTTGCATGATTTTTGGCGCAAAGATTCCTTGAAATATCTAGATTCATCGAACAAAATCCCAGCC
1 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCC
*
5731 ACGA-TCGATTTAAGTATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTA
66 AC-ATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTA
* ** *
5795 ATTCAGAAAAAAAAATGGAAAAACGATATTCGAAGCATGAAAAGCCCGTCAATCTTTTTGGCGTT
130 ATTCAG-AAAAAAAATAGAAAAACGATATTAAAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTT
* *
5860 GAATTATATGTTTTTTCTGAGTACTGTGGCAAAAAATTGAG-AAAAAACTTCTCCGATCAGTTTT
194 GAATTATAT-TTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATT-TCCGATCAGTTTT
* * * *
5924 TAGCCGAAAATCGTTTACTAACCATCACGGTTTTTTGCTAAAAACGCGTTCCCAATGCCCGACTC
257 TAGCCGAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCCGAGGCCCGACTC
5989 AA
322 AA
* * * * ** *
5991 TTTTGCATGATTTTTGGCGCAAAGACTCCTTTAGATATCTATATTCATCAAACCAAATATCAACC
1 TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCC
* * * * *
6056 ACATTGGATATAAGGATTTCTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
66 ACATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAA
* * * * * * * * *
6121 TTCAG-AAAAAATTGGAAAAATGATATTAAAAACGTTAAAAGACCATCAATCTTTTTGGTGTTGT
131 TTCAGAAAAAAAATAGAAAAACGATATTAAAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGA
* * * * *
6185 ATTATATATTTTTTCTGAGTATTGTGGCAAAATATTCAGAAAAAAAAATT-GGGTCAGTTTTTAG
196 ATTATAT-TTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCCGATCAGTTTTTAG
* * * * *
6249 CCGAAAATCGTGTACTAACCATCATGGTTTTTGGGCTAAAAACGCGTTTCGGGGGCCCGACTCAG
260 CCGAAAATCGTGTACTAACCATCACGGTTTTT-GGCTAAAAACGCGTTCCCGAGGCCCGACTCAA
* * * * *
6314 TTTTGAATGATTTTTGGCAG-AAAGAATCCGTGAAATATCTATATTCATCTAACCAATCTCAGGC
1 TTTTGCATGATTTTTGGC-GCAAAGACTCCTTGAAATATCTATATTCATCGAA-CAA----A--A
* * * *
6378 TCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTA
58 TCCCAGCCACATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTA
* * * *
6443 GAAA-TAGATTC-GGAAAAAAATAGAAAAATGATATTAAAAGCGAGAAAA
123 AAAATTA-ATTCAGAAAAAAAATAGAAAAACGATATTAAAAGCGTGAAAA
6491 ATATTTCTTT
Statistics
Matches: 717, Mismatches: 88, Indels: 32
0.86 0.11 0.04
Matches are distributed among these distances:
321 57 0.08
322 173 0.24
323 168 0.23
324 48 0.07
325 170 0.24
328 1 0.00
329 3 0.00
330 97 0.14
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (323 bp):
TTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGCC
ACATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTAA
TTCAGAAAAAAAATAGAAAAACGATATTAAAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGA
ATTATATTTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAAAATTTCCGATCAGTTTTTAGC
CGAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCCGAGGCCCGACTCAA
Found at i:7353 original size:331 final size:322
Alignment explanation
Indices: 6542--7800 Score: 1265
Period size: 325 Copynumber: 3.9 Consensus size: 322
6532 ATTTTTTTTT
* * * * * * * *
6542 GTTTTGCATGATTTTTTATGTAAATACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGC
1 GTTTTGCATGATTTTTGACGCAAAGATTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGC
* ** * * *
6607 CACGTTCGATTTAAATATTTGTTTTTATGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTA
66 CACATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * *
6672 ATTCGGAAAAAAATCATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGT
131 ATTCGGAAAAAAATGA--GAAAAACGATATTAGAAGCGTGAAAAGACCTTCAATCTTTTTGGCGT
* * ** * *
6737 TGAATTATATATTTTTTTTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCTGATC-AGTTT
194 TGAATTATATATTTTTTCTGACTATTGTGGCAAAAAATTGAGAAAAAA--AATCGGGTCTAGTTT
* * * * * *
6801 TTAGCTGAAAA-CGTGTACTTACCATCACGGTTTTTGGCTAAAAACGCATTCCCGAGCCCCGACT
257 TTAGCCGAAAATCGTGTAC-TAACATCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCCCCGGCT
*
6865 AA
321 CA
* * *
6867 ATTTTGCATGATTTTTGGCGCAAAGATTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGC
1 GTTTTGCATGATTTTTGACGCAAAGATTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGC
*
6932 CACATT-GAATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
66 CACATTCG-ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * * * *
6996 AATTCAGAAAAAAATTGA-AAAAATGATATTACAAGCGTGAAAAGACCATCAATCTTTTTGGTGT
130 AATTCGGAAAAAAA-TGAGAAAAACGATATTAGAAGCGTGAAAAGACCTTCAATCTTTTTGGCGT
* * * *
7060 TGAATTTTATATTTTTTCTGAGTATTGTGGCAAAATATTCAGAAAAAAAATCGGGT-TAGTTTTT
194 TGAATTATATATTTTTTCTGACTATTGTGGCAAAAAATTGAGAAAAAAAATCGGGTCTAGTTTTT
* * ** *
7124 AGCCGAAAATCGTGTACTAACAATCATGGTTTTTCGGCTAAAAAGGCGTTTCGGGGGCCGCGGCT
259 AGCCGAAAATCGTGTACTAAC-ATCACGGTTTTT-GGCTAAAAACGCG-TTCCAGGGCCCCGGCT
7189 CA
321 CA
* * *
7191 GTTTTGCATGATTTTTGCCAG-AAAGACTCCTTGAAATATCTATATTCATCTAACCAATCTCAGG
1 GTTTTGCATGATTTTTGAC-GCAAAGATTCCTTGAAATATCTATATTCATCAAACCAA----A--
* * * *
7255 CTCTCAGCCACATTAGATTTAAGGATTTTTTTTTACGAGCATCTGATTATTGTTTCGATTTAATT
59 -TCTCAGCCACATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
* * * * *
7320 AGAAA-TAGATTCGGAAAAAAATGAGAAAAATGATATTTA-AAGCGAGAAAATA-TTTCAATTTT
123 AGAAATTA-ATTCGGAAAAAAATGAGAAAAACGATA-TTAGAAGCGTGAAAAGACCTTCAATCTT
* ** *
7382 TTTTGCGTTGAATTGCATATTTTTTCTGACTATTGTGGCAAAAAAATTGAGGAAAAAAATTTTCG
186 TTTGGCGTTGAATTATATATTTTTTCTGACTATTGTGGC-AAAAAATTGA-GAAAAAAA--ATCG
* * * * * * * *
7447 AGTCT-GTTTTTGCAAAACTTTCGCTGAAATCCTGTACTAACATCACGGTTTTTTGCTTAAACCA
247 GGTCTAGTTTTT----AGC---CG--AAAATCGTGTACTAACATCACGGTTTTTGGCTAAAAACG
*
7511 CGTTCCAGGACCCCGGCTCA
303 CGTTCCAGGGCCCCGGCTCA
* * * *
7531 GTTTTTCATGA-TTTTGACGTAAAGATTCCTTGAAATATCTATATTCATCGAACCAAATCCCAGC
1 GTTTTGCATGATTTTTGACGCAAAGATTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGC
* * * * *
7595 CAAATTCGATTTAACGAGTTATTTTTACGAGCATCTGAATCTTGTTTCGTTTTAATTAGAAATTA
66 CACATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * *
7660 ATTCTGAAAAAAATG-GAAAAACGATATTAGAAGTGTGAAAA-ATCCTTCAATTTTTTTGGCGTT
131 ATTCGGAAAAAAATGAGAAAAACGATATTAGAAGCGTGAAAAGA-CCTTCAATCTTTTTGGCGTT
* * * ** *
7723 AAATTATATATTTTTTATGACTATTGTCGC--AAAATTGAG-AAAAAAATCTCGTCTCAATTTTT
195 GAATTATATATTTTTTCTGACTATTGTGGCAAAAAATTGAGAAAAAAAATCGGGTCT-AGTTTTT
7785 AGCCG-AAATCGTGTAC
259 AGCCGAAAATCGTGTAC
7801 ATTTGGCTAA
Statistics
Matches: 783, Mismatches: 111, Indels: 88
0.80 0.11 0.09
Matches are distributed among these distances:
317 10 0.01
320 2 0.00
321 22 0.03
322 18 0.02
323 98 0.13
324 64 0.08
325 129 0.16
326 2 0.00
327 11 0.01
328 2 0.00
329 8 0.01
330 50 0.06
331 122 0.16
332 128 0.16
333 2 0.00
334 11 0.01
335 2 0.00
338 3 0.00
339 40 0.05
340 24 0.03
341 10 0.01
342 11 0.01
343 14 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (322 bp):
GTTTTGCATGATTTTTGACGCAAAGATTCCTTGAAATATCTATATTCATCAAACCAAATCTCAGC
CACATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
ATTCGGAAAAAAATGAGAAAAACGATATTAGAAGCGTGAAAAGACCTTCAATCTTTTTGGCGTTG
AATTATATATTTTTTCTGACTATTGTGGCAAAAAATTGAGAAAAAAAATCGGGTCTAGTTTTTAG
CCGAAAATCGTGTACTAACATCACGGTTTTTGGCTAAAAACGCGTTCCAGGGCCCCGGCTCA
Found at i:7655 original size:332 final size:322
Alignment explanation
Indices: 6542--7769 Score: 1250
Period size: 332 Copynumber: 3.7 Consensus size: 322
6532 ATTTTTTTTT
* * * *
6542 GTTTTGCATGATTTTTTATGTAAATACTCCTTGAAATATCTATATTCATCGAACAAAATCCCAGC
1 GTTTTGCATGATTTTTGACGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCCCAGC
* ** * * *
6607 CACGTTCGATTTAAATATTTGTTTTTATGAGCATCTGAATCTTGTTTCAATTTAATTAAAAATTA
66 CACATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * *
6672 ATTCGGAAAAAAATCATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGT
131 ATTCGGAAAAAAATGA--GAAAAACGATATTAGAAGCGTGAAAA--ACTTCAATCTTTTTGGCGT
* * * *
6737 TGAATTATATATTTTTTTTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCTGA-TCAGTTT
192 TGAATTATATATTTTTTCTGACTATTGTGGCAAAAAATTGAGAAAAAAATTTTC-GAGTCTGTTT
* * * * *
6801 TT-A--GCTGAAAACGTGTACTTACCATCACGGTTTTTGGCTAAAAACGCATTCCCGAGCCCCGA
256 TTAACCGCTGAAATCGTGTAC-TAACATCACGGTTTTTGGCTAAAAACGCGTTCCGGA-CCCCGG
*
6863 CTAA
319 CTCA
* * * * * **
6867 ATTTTGCATGATTTTTGGCGCAAAGATTCCTTGAAATATCTATATTCATCAAACCAAATGTCAGC
1 GTTTTGCATGATTTTTGACGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCCCAGC
*
6932 CACATT-GAATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
66 CACATTCG-ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * * * *
6996 AATTCAGAAAAAAATTGA-AAAAATGATATTACAAGCGTGAAAAGACCATCAATCTTTTTGGTGT
130 AATTCGGAAAAAAA-TGAGAAAAACGATATTAGAAGCGTGAAAA-A-CTTCAATCTTTTTGGCGT
* * * * * *
7060 TGAATTTTATATTTTTTCTGAGTATTGTGGCAAAATATTCAGAAAAAAA--ATCGGGT-TAGTTT
192 TGAATTATATATTTTTTCTGACTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGAGTCT-GTTT
* * * * * * *
7122 TTAGCCG--AAAATCGTGTACTAACAATCATGGTTTTTCGGCTAAAAAGGCGTTTCGGGGGCCGC
256 TTAACCGCTGAAATCGTGTACTAAC-ATCACGGTTTTT-GGCTAAAAACGCG-TTC-CGGACCCC
7185 GGCTCA
317 GGCTCA
* *
7191 GTTTTGCATGATTTTTGCCAG-AAAGACTCCTTGAAATATCTATATTCATCTAACCAATCTCAGG
1 GTTTTGCATGATTTTTGAC-GTAAAGACTCCTTGAAATATCTATATTCATCGAACCAA----A--
* * * * *
7255 CTCTCAGCCACATTAGATTTAAGGATTTTTTTTTACGAGCATCTGATTATTGTTTCGATTTAATT
59 -TCCCAGCCACATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
* * * *
7320 AGAAA-TAGATTCGGAAAAAAATGAGAAAAATGATATTTA-AAGCGAGAAAATATTTCAATTTTT
123 AGAAATTA-ATTCGGAAAAAAATGAGAAAAACGATA-TTAGAAGCGTGAAAA-ACTTCAATCTTT
* **
7383 TTTGCGTTGAATTGCATATTTTTTCTGACTATTGTGGCAAAAAAATTGAGGAAAAAAATTTTCGA
185 TTGGCGTTGAATTATATATTTTTTCTGACTATTGTGGC-AAAAAATTGA-GAAAAAAATTTTCGA
* * * * *
7448 GTCTGTTTTTGCAAAACTTTCGCTGAAATCCTGTACTAACATCACGGTTTTTTGCTTAAACCACG
248 GTCTGTTTTT----AAC---CGCTGAAATCGTGTACTAACATCACGGTTTTTGGCTAAAAACGCG
7513 TTCCAGGACCCCGGCTCA
306 TTCC-GGACCCCGGCTCA
* *
7531 GTTTTTCATGA-TTTTGACGTAAAGATTCCTTGAAATATCTATATTCATCGAACCAAATCCCAGC
1 GTTTTGCATGATTTTTGACGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCCCAGC
* * * * *
7595 CAAATTCGATTTAACGAGTTATTTTTACGAGCATCTGAATCTTGTTTCGTTTTAATTAGAAATTA
66 CACATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * *
7660 ATTCTGAAAAAAATG-GAAAAACGATATTAGAAGTGTGAAAAATCCTTCAATTTTTTTGGCGTTA
131 ATTCGGAAAAAAATGAGAAAAACGATATTAGAAGCGTGAAAAA--CTTCAATCTTTTTGGCGTTG
* *
7724 AATTATATATTTTTTATGACTATTGTCGC--AAAATTGAGAAAAAAAT
194 AATTATATATTTTTTCTGACTATTGTGGCAAAAAATTGAGAAAAAAAT
7770 CTCGTCTCAA
Statistics
Matches: 752, Mismatches: 107, Indels: 85
0.80 0.11 0.09
Matches are distributed among these distances:
320 1 0.00
321 12 0.02
322 21 0.03
323 94 0.12
324 63 0.08
325 124 0.16
326 2 0.00
328 10 0.01
329 8 0.01
330 50 0.07
331 122 0.16
332 128 0.17
333 2 0.00
334 11 0.01
335 2 0.00
338 3 0.00
339 40 0.05
340 24 0.03
341 10 0.01
342 11 0.01
343 14 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (322 bp):
GTTTTGCATGATTTTTGACGTAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCCCAGC
CACATTCGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
ATTCGGAAAAAAATGAGAAAAACGATATTAGAAGCGTGAAAAACTTCAATCTTTTTGGCGTTGAA
TTATATATTTTTTCTGACTATTGTGGCAAAAAATTGAGAAAAAAATTTTCGAGTCTGTTTTTAAC
CGCTGAAATCGTGTACTAACATCACGGTTTTTGGCTAAAAACGCGTTCCGGACCCCGGCTCA
Found at i:8443 original size:308 final size:305
Alignment explanation
Indices: 7887--8465 Score: 729
Period size: 308 Copynumber: 1.9 Consensus size: 305
7877 AATTATATAT
* * * *
7887 TTTTTCTGAGTATTGTGGGAAAGAAATGAGGAAAAATTTTTTAGGATTAGTTTTTGCAAAATTTT
1 TTTTTCTGAGTATTGAGGCAAAGAAATGAGGAAAAAATTTTTAGGATCAGTTTTTGCAAAATTTT
* * * * *
7952 AGCCGAAATAGTTTACTCATCACGGTTTATAGCTAAAAACGCGTTCTGGGCCCTAGCTCGGTTTT
66 AGCCGAAATAGTTTACTCATCACGGCTTATAGCTAAAAACGCATTCGGGGCCCCAGCTCAGTTTT
* ** *** *
8017 GAATAATTTGTAGCGTAAAGACTCCTTGATATATTCATCTAACCAAATCACAGCCACATTCGTTT
131 GAATAATTTGTAGCATAAAGACTCCTTGATATATTCATAGAACCAAATCACAGCCACATTAAATA
* * *
8082 TAATGATTTGTTTTTACAAGCATCTTAATGTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAA
196 TAATGATTTGTTTTTACAAGCATCTCAATCTTGTTTCGACTTAATTAGAAATTAATTCGGAAAAA
8146 AAAGGAAAAACTCTTCAATCTTTTTGGTGTTAAATTATATTTTTC
261 AAAGGAAAAACTCTTCAATCTTTTTGGTGTTAAATTATATTTTTC
*
8191 TTTTT-TG-GTATTGAGGCAAAGAATTGAGGAAAAAATTTTT-GGATCAGTTTTTGCAAAATTTT
1 TTTTTCTGAGTATTGAGGCAAAGAAATGAGGAAAAAATTTTTAGGATCAGTTTTTGCAAAATTTT
* * * *
8253 ATCCGAAATCGTTTACTCATCACGGCTTATGGCTAAAAACGCATTCCGGGGCCCCGGCTCAGTTT
66 AGCCGAAATAGTTTACTCATCACGGCTTATAGCTAAAAACGCATT-CGGGGCCCCAGCTCAGTTT
* * * * * * *
8318 TGCAA-GATTTTTGGCATAAAGGCTCCTTGAAATATCTATATTCATAGAACCAAATCTCAGTCAT
130 TG-AATAATTTGTAGCATAAAGACTCCTTG----A--TATATTCATAGAACCAAATCACAGCCAC
* *
8382 ATTAAATAT-ATGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGACTTAATTAGAAATTAAT
188 ATTAAATATAAT-GATTTGTTTTTACAAGCATCTCAATCTTGTTTCGACTTAATTAGAAATTAAT
*
8446 TCGGAAAAAAATGGAAAAAC
252 TCGGAAAAAAAAGGAAAAAC
8466 GATATTAGAA
Statistics
Matches: 231, Mismatches: 34, Indels: 15
0.82 0.12 0.05
Matches are distributed among these distances:
301 61 0.26
302 65 0.28
303 4 0.02
304 5 0.02
306 1 0.00
307 2 0.01
308 77 0.33
309 16 0.07
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (305 bp):
TTTTTCTGAGTATTGAGGCAAAGAAATGAGGAAAAAATTTTTAGGATCAGTTTTTGCAAAATTTT
AGCCGAAATAGTTTACTCATCACGGCTTATAGCTAAAAACGCATTCGGGGCCCCAGCTCAGTTTT
GAATAATTTGTAGCATAAAGACTCCTTGATATATTCATAGAACCAAATCACAGCCACATTAAATA
TAATGATTTGTTTTTACAAGCATCTCAATCTTGTTTCGACTTAATTAGAAATTAATTCGGAAAAA
AAAGGAAAAACTCTTCAATCTTTTTGGTGTTAAATTATATTTTTC
Found at i:9069 original size:621 final size:618
Alignment explanation
Indices: 8307--9466 Score: 1534
Period size: 621 Copynumber: 1.9 Consensus size: 618
8297 TCCGGGGCCC
* * * *
8307 CGGCTCAGTTTTGCAAGATTTTTGGCATAAAGGCTCCTTGAAATATCTATATTCATAGAACCAAA
1 CGGCTCAATGTTGCAAGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATAGAACCAAA
* * * *
8372 TCTCAGTCATATTAAATATATGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGACTTAATTA
66 TCTCAGCCACATTAAATATATGGATTTGTTTTTACGAGCATCTCAATCTTATTTCGACTTAATTA
* *
8437 GAAATTAATTCGG-AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCGTCAATCTTTTT
131 GAAATTAATTCGGAAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAACCCATCAATCTTTTT
* *
8501 GGCGTTGAAAGATATATTTTTTCTGAGTATTGTGGCAAAAATTTGAGAAAAAAACTTTTCGGGTT
196 GGAGTTGAAAGATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG--AAAAACTTTT-GGG-T
* ** * *
8566 C-GTTTTTAGCCAAAATCGTGTACTAA-CCATCACGGTTTTTGGCTAAAAACACGTTCCGCAGCC
257 CAGTTTTCAGCCAAAATCGTGTACTAACCCATCACGAATTTTGACTAAAAACACCTTCCGCAGCC
* *
8629 CCGGCTCAATTTTGCATGATTTTTGGCACAAAGACTTCTTGAAATATCTATTT-TCA-TCGAA-C
322 ACGGCTCAATTTTGCATGATTTTTGGCACAAAGACTCCTTGAAATAT-T-TTTATCAGTCGAATC
* * * * *
8691 TAAATCTCA-GCCATATTGGATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCG-ATT
385 -AAATAT-AGGCCACATTGAATATAAGGATTTGTTTTTACGAGCATCACAATCTTGTTTCGAATT
* *
8754 TAATTAGAAATTAATTCGGGGGAAAAAAAAGGGAAAA-CAATATTACAAGCGTGAAAAGCCCAT-
448 TAATTAGAAATTAATTC---AG-AAAAAAA-GGAAAATCAATATTAAAAGCGTGAAAAGCCC-TC
8817 CAATCTTTTTGGCGTTGAATTATATAT-TTTTTCTAAGTATTTTGGCAAAAAATTGAGATAAAAT
507 CAATCTTTTTGGCGTTGAATTATATATATTTTTCTAAGTATTTTGGCAAAAAATTGAGATAAAAT
8881 TTTTTTGGGTCGGTTTTTAGCCAAAATCGTGTACTAACCATCACGGT
572 TTTTTTGGGTCGGTTTTTAGCCAAAATCGTGTACTAACCATCACGGT
* * ** *
8928 CGGCTCAATGTTGCATGATTTTTGGCGCAAAGACTCCTTGATTTATCTATATTCATCGAACCAAA
1 CGGCTCAATGTTGCAAGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATAGAACCAAA
* ** * * *
8993 TGTCAGCCACATTGGATATGA-GGATTTGTTTTTACGAGCATCTGAATCTTATTTTGATTTAATT
66 TCTCAGCCACATTAAATAT-ATGGATTTGTTTTTACGAGCATCTCAATCTTATTTCGACTTAATT
* *
9057 AGAAATTAATTCGGAAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAGCCCATTAATCTTTT
130 AGAAATTAATTCGGAAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAACCCATCAATCTTTT
** *
9122 TGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAGAAACTTTTGGGTCAG
195 TGGAGTTGAAAGATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTGGGTCAG
* * * ** *
9187 TTTTCAGCCGAAATCGTGTACTAACCCATCACGAATTTTGACTAAAAACGCCTTTCGGGGTCACG
260 TTTTCAGCCAAAATCGTGTACTAACCCATCACGAATTTTGACTAAAAACACCTTCCGCAGCCACG
* * ** ** * *
9252 GCTCTATTTTGCATGGTTTTTGGTGCTGAGACTCCTTGAAATATTTTTATTAGTCTAATCAAATA
325 GCTCAATTTTGCATGATTTTTGGCACAAAGACTCCTTGAAATATTTTTATCAGTCGAATCAAATA
* * *
9317 TAGGCCACATTGAATTTAAGGATTTGTTTTTACGTGCATCAGAATCTTGTTTCGAATTTAATTAG
390 TAGGCCACATTGAATATAAGGATTTGTTTTTACGAGCATCACAATCTTGTTTCGAATTTAATTAG
* * * *
9382 AAATTAATTCAGAAAAATATGAAAATCGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGC
455 AAATTAATTCAGAAAAAAAGGAAAATCAATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGC
9447 GTTGAATTATATATATTTTT
520 GTTGAATTATATATATTTTT
9467 ATGAGTGTTT
Statistics
Matches: 464, Mismatches: 63, Indels: 27
0.84 0.11 0.05
Matches are distributed among these distances:
616 6 0.01
617 54 0.12
618 11 0.02
619 30 0.06
620 129 0.28
621 143 0.31
622 91 0.20
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (618 bp):
CGGCTCAATGTTGCAAGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATAGAACCAAA
TCTCAGCCACATTAAATATATGGATTTGTTTTTACGAGCATCTCAATCTTATTTCGACTTAATTA
GAAATTAATTCGGAAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAACCCATCAATCTTTTT
GGAGTTGAAAGATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTTTTGGGTCAGT
TTTCAGCCAAAATCGTGTACTAACCCATCACGAATTTTGACTAAAAACACCTTCCGCAGCCACGG
CTCAATTTTGCATGATTTTTGGCACAAAGACTCCTTGAAATATTTTTATCAGTCGAATCAAATAT
AGGCCACATTGAATATAAGGATTTGTTTTTACGAGCATCACAATCTTGTTTCGAATTTAATTAGA
AATTAATTCAGAAAAAAAGGAAAATCAATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCG
TTGAATTATATATATTTTTCTAAGTATTTTGGCAAAAAATTGAGATAAAATTTTTTTGGGTCGGT
TTTTAGCCAAAATCGTGTACTAACCATCACGGT
Found at i:19585 original size:8 final size:8
Alignment explanation
Indices: 19572--19599 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
19562 TACATTGATA
19572 ATGTGTGT
1 ATGTGTGT
19580 ATGTGTGT
1 ATGTGTGT
19588 ATGTGTGT
1 ATGTGTGT
19596 ATGT
1 ATGT
19600 CTTAATGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.36, T:0.50
Consensus pattern (8 bp):
ATGTGTGT
Found at i:19607 original size:16 final size:17
Alignment explanation
Indices: 19570--19609 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
19560 CTTACATTGA
*
19570 TAATGTGTGTATGTGTG
1 TAATGTGTGTATGTCTG
19587 T-ATGTGTGTATGTCT-
1 TAATGTGTGTATGTCTG
19602 TAATGTGT
1 TAATGTGT
19610 TGATGGCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 19 0.90
17 1 0.05
ACGTcount: A:0.17, C:0.03, G:0.30, T:0.50
Consensus pattern (17 bp):
TAATGTGTGTATGTCTG
Found at i:22910 original size:4 final size:4
Alignment explanation
Indices: 22901--22937 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
22891 AGAATCTTAA
22901 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG A
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG A
22938 CAGACAAGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
ATAG
Found at i:31340 original size:21 final size:22
Alignment explanation
Indices: 31299--31347 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
31289 GTGAGTGATA
*
31299 GTAATTTTTTTTTAAAGAAAAT
1 GTAATTTTTATTTAAAGAAAAT
*
31321 GTAATTTTTATTTATA-AAAAT
1 GTAATTTTTATTTAAAGAAAAT
*
31342 GAAATT
1 GTAATT
31348 ACAATGACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (22 bp):
GTAATTTTTATTTAAAGAAAAT
Found at i:31802 original size:29 final size:29
Alignment explanation
Indices: 31760--31832 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
31750 CGGCTGTAAT
*
31760 AAAAAAAAAATGGTGTGGTATTTCTGGAG
1 AAAAAAAACATGGTGTGGTATTTCTGGAG
31789 AAAAAAAACATGGTGTGGTATTTCTGGAG
1 AAAAAAAACATGGTGTGGTATTTCTGGAG
31818 AAAAAAAACAATGGT
1 AAAAAAAAC-ATGGT
31833 ATTAGAGTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 37 0.88
30 5 0.12
ACGTcount: A:0.45, C:0.05, G:0.25, T:0.25
Consensus pattern (29 bp):
AAAAAAAACATGGTGTGGTATTTCTGGAG
Found at i:31917 original size:28 final size:28
Alignment explanation
Indices: 31874--31967 Score: 136
Period size: 30 Copynumber: 3.3 Consensus size: 28
31864 TGCGGCTGTG
31874 GAAAAAAA-ATGGTGTGGTATTTCTGGA
1 GAAAAAAACATGGTGTGGTATTTCTGGA
*
31901 GAAAAAAACATGATGTGGTATTTCTTGAGA
1 GAAAAAAACATGGTGTGGTATTTC-TG-GA
*
31931 AAAAAAAACATGGTGTGGTATTTCTGGA
1 GAAAAAAACATGGTGTGGTATTTCTGGA
31959 GAAGAAAAA
1 GAA-AAAAA
31968 ACAATTGGGT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
27 8 0.14
28 18 0.31
29 9 0.15
30 24 0.41
ACGTcount: A:0.43, C:0.05, G:0.26, T:0.27
Consensus pattern (28 bp):
GAAAAAAACATGGTGTGGTATTTCTGGA
Found at i:31938 original size:116 final size:114
Alignment explanation
Indices: 31711--31940 Score: 365
Period size: 116 Copynumber: 2.0 Consensus size: 114
31701 CTTTCCTACA
31711 AATGATATTAGAGTTAGGTTCGATTGGAGTTTGGTGGTGCGGCTGTAATAAAAAAAAAATGGTGT
1 AATGATATTAGAGTTAGGTTCGATTGGAGTTTGGTGGTGCGGCTG--ATAAAAAAAAAATGGTGT
* *
31776 GGTATTTCTGGAGAAAAAAAACATGGTGTGGTATTTCTGGAGAAAAAAAAC
64 GGTATTTCTGGAGAAAAAAAACATGATGTGGTATTTCTGGAAAAAAAAAAC
* **
31827 AATGGTATTAGAGTTAGGTTCGATTGGAGTTTGGTGGTGCGGCTG-TGGAAAAAAAATGGTGTGG
1 AATGATATTAGAGTTAGGTTCGATTGGAGTTTGGTGGTGCGGCTGATAAAAAAAAAATGGTGTGG
*
31891 TATTTCTGGAG-AAAAAAACATGATGTGGTATTTCTTGAGAAAAAAAAAC
66 TATTTCTGGAGAAAAAAAACATGATGTGGTATTTCTGGA-AAAAAAAAAC
31940 A
1 A
31941 TGGTGTGGTA
Statistics
Matches: 107, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
112 25 0.23
113 38 0.36
116 44 0.41
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.30
Consensus pattern (114 bp):
AATGATATTAGAGTTAGGTTCGATTGGAGTTTGGTGGTGCGGCTGATAAAAAAAAAATGGTGTGG
TATTTCTGGAGAAAAAAAACATGATGTGGTATTTCTGGAAAAAAAAAAC
Found at i:45947 original size:12 final size:12
Alignment explanation
Indices: 45930--45956 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
45920 GGTCAAGACT
45930 TTAAATTTATAA
1 TTAAATTTATAA
45942 TTAAATTTATAA
1 TTAAATTTATAA
45954 TTA
1 TTA
45957 TTTTCTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAATTTATAA
Done.