Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014477.1 Corchorus capsularis cultivar CVL-1 contig14498, 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: 42985
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:7545 original size:39 final size:39
Alignment explanation
Indices: 7491--7569 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
7481 ACAACATTGG
*
7491 TTCCTTCTTGTTGATATCCATGAGCAATTAAATACAAAC
1 TTCCTTCTTCTTGATATCCATGAGCAATTAAATACAAAC
*
7530 TTCCTTCTTCTTGATATCCATGAGTAATTAAATACAAAC
1 TTCCTTCTTCTTGATATCCATGAGCAATTAAATACAAAC
7569 T
1 T
7570 AACAAAACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (39 bp):
TTCCTTCTTCTTGATATCCATGAGCAATTAAATACAAAC
Found at i:8299 original size:16 final size:18
Alignment explanation
Indices: 8268--8300 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
8258 TTCGAGGGTT
8268 ATTTTATCTATTAAATTA
1 ATTTTATCTATTAAATTA
8286 ATTTTAT-T-TTAAATT
1 ATTTTATCTATTAAATT
8301 GAAAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTATCTATTAAATTA
Found at i:9032 original size:19 final size:20
Alignment explanation
Indices: 8989--9050 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 20
8979 TGCTCTAATC
8989 ATCTCATCTGTACAGTACCTA
1 ATCTCATCTGTACAGTA-CTA
* *
9010 ATCTAATCTGTACAGT-GTA
1 ATCTCATCTGTACAGTACTA
9029 ATCTCATCTGTACAGTTACTA
1 ATCTCATCTGTACAG-TACTA
9050 A
1 A
9051 ACAGTGCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.46
20 1 0.03
21 18 0.51
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (20 bp):
ATCTCATCTGTACAGTACTA
Found at i:9744 original size:19 final size:20
Alignment explanation
Indices: 9703--9746 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
9693 CCCTAGCGTG
*
9703 TAATTATTTTATTTGACTTA
1 TAATTAATTTATTTGACTTA
9723 TAATTAATTT-TTTG-CTTGA
1 TAATTAATTTATTTGACTT-A
9742 TAATT
1 TAATT
9747 GTAACTCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 10 0.45
20 9 0.41
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59
Consensus pattern (20 bp):
TAATTAATTTATTTGACTTA
Found at i:13143 original size:24 final size:23
Alignment explanation
Indices: 13111--13170 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 23
13101 ATTGCTTTAA
13111 TTACATTTATATCCTTT-TTTAT-T
1 TTACATTTATAT--TTTATTTATAT
13134 TTACAATTTATATTTTGATTTATAT
1 TTAC-ATTTATATTTT-ATTTATAT
13159 TTACATTTATAT
1 TTACATTTATAT
13171 ATTGAATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
22 3 0.09
23 4 0.12
24 21 0.64
25 5 0.15
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (23 bp):
TTACATTTATATTTTATTTATAT
Found at i:13278 original size:13 final size:12
Alignment explanation
Indices: 13249--13281 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
13239 ATTAAATATG
13249 TTTTTTT-ATAA
1 TTTTTTTAATAA
13260 TTTTTTTAATAA
1 TTTTTTTAATAA
13272 TTATTTTTAA
1 TT-TTTTTAA
13282 GACTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.35
12 6 0.30
13 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTTTAATAA
Found at i:13358 original size:17 final size:18
Alignment explanation
Indices: 13325--13358 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13315 AACAGAAAAA
13325 GTTATAGAATAAAATAAG
1 GTTATAGAATAAAATAAG
*
13343 GTTATA-AATAATATAA
1 GTTATAGAATAAAATAA
13359 AATAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (18 bp):
GTTATAGAATAAAATAAG
Found at i:13366 original size:15 final size:15
Alignment explanation
Indices: 13348--13383 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
13338 ATAAGGTTAT
13348 AAATAATATAAAATA
1 AAATAATATAAAATA
*
13363 AAATAATATAGAATA
1 AAATAATATAAAATA
13378 AAATAA
1 AAATAA
13384 GGGGTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (15 bp):
AAATAATATAAAATA
Found at i:40781 original size:335 final size:332
Alignment explanation
Indices: 37761--41278 Score: 3135
Period size: 335 Copynumber: 10.7 Consensus size: 332
37751 GAATTTAACT
* * * *
37761 TTTAAGGATTTGTTTTTACGGGCATCTGAATCATGTTTCGATTTAATCAAAAATTAATT--TGAA
1 TTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATTTAATCAGAAATTAATTCGGGAA
* * * *
37824 AAAAATATAAAAAACGATATTAGAAGCG-CGAAAAGCCCTTCAATCATTTTGGCGTTGAATTATG
66 AAAAA-ATAAAAAACGATATTAGAAGCGTCGAAAA-TCCTTCAATCTTTTTGGCATTAAATTAT-
* * * * * * *
37888 CAT-TTTTTTATGAGTATTGTTGCCAAAAATTGAGGAGAAATTCTAT-GGGTTAATTTTTGCAAA
128 -ATATTTTTTATGAGTATTGTGGCCAGAAATTAAGGA-AAAATCTTTCGGGTCATTTTTTGCAAA
* * * * * * * * *
37951 AGTTTAGCCGAAATCGTGT--T--CATCATGGTTTTTAGTTAAAAACGTGTTCCTG-GATCCCGG
191 ATTTTAGCCGAAATCGTGTGCTAACATCACGGATTTTGGCTAAAAACGCGTTCCAGAGGT-CCGA
* ** * * * *
38011 CTCTGTTTTATATGATTTTTGGCGCCAAGACTCATT--GA-A-C---ATTCA-CCAGATCAAATC
255 CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTA-ACCAAATC
* * ** *
38068 TCAACAACATTGGA
319 TCAGCCATGTTAGA
* * * * * * *
38082 TTTAACGATTTGTGTTTACGAGCATCAGAAAC-CG-GTTACGATTT-ATTAGAAATAAATTC-GG
1 TTTAAGGATTTGTTTTTACGGGCATCTG--ACTCGTGTTTCGATTTAATCAGAAATTAATTCGGG
* *** * * ** * * * *
38143 AAAAAATAGGTAAATCTATATTATTAGCGT-GAAAAGCCCTTCAATCATTTTGGCGTTGAATTAT
64 AAAAAAAATAAAAAACGATATTAGAAGCGTCGAAAA-TCCTTCAATCTTTTTGGCATTAAATTAT
* *
38207 ATA-TTTTTATGAGTATTGTGGCTAGAAATTAAGGAAAAATCTTTCGGGCCATTTTTTTGCAAAA
128 ATATTTTTTATGAGTATTGTGGCCAGAAATTAAGGAAAAATCTTTCGGGTCA-TTTTTTGCAAAA
** * ** **
38271 TTTTAGCCGAAATCGTGTGCT-A-ATCTA-GTTTTTTAGCCTAGCAACGCGTTCC-GAAGACCCG
192 TTTTAGCCGAAATCGTGTGCTAACATC-ACGGATTTT-GGCTAAAAACGCGTTCCAG-AGGTCCG
* * * *
38332 ACTCAGTCTTGCATGATTTTTGGTGCCAAGACAT-CTTCAAATATCTATAGTCATCTAATCAAAT
254 ACTCAGTTTTGCATGATTTTTGGCGCCAAGAC-TCCTTCAAATATCTATATTCATCTAACCAAAT
* * *
38396 GTTAGCCATGTTGGA
318 CTCAGCCATGTTAGA
* * * * * * * *
38411 TTAAAAGATTTGTTTTTACGGGCATCTTAATCATGTTTCGATTTATTTAGAAATTATTTCGGG--
1 TTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATTTAATCAGAAATTAATTCGGGAA
* * * * *
38474 AAAAAATAGAAAA--A-ATTAGAAGC-ACGAACAATCCTTCAAT-TTTTTCCGCGTTGAATTATA
66 AAAAAATAAAAAACGATATTAGAAGCGTCGAA-AATCCTTCAATCTTTTT-GGCATTAAATTATA
* * *
38534 AATTTTTTGTGAGTATTGTGGCCAGAAATTAAGG--AAATCTTTCGAGTCATTTTTTGCAAAATT
129 TATTTTTTATGAGTATTGTGGCCAGAAATTAAGGAAAAATCTTTCGGGTCATTTTTTGCAAAATT
* *
38597 TTAGCCGAAAT-GTTGTGCTAAACATCACAGATTTTGGCTAAAAACGCGTTCCAGAGGTCCAACT
194 TTAGCCGAAATCG-TGTGCT-AACATCACGGATTTTGGCTAAAAACGCGTTCCAGAGGTCCGACT
* * *
38661 CAGTTTTGCATAATTTTTGGCGCCAAGACTCCGTCAAATATCTTTATTCATCTAACCAAATCTCA
257 CAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTCA
38726 GCCATGTTAGA
322 GCCATGTTAGA
* * * * *
38737 TTTAAGGATTTGTCTTTACGGGCATCTGACTTGTGTTTCAATTTAATTAGAAATTAATTCAGGAA
1 TTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATTTAATCAGAAATTAATTC-GGGA
* * * *
38802 AAAAAAATAAAAAAACGATATTAGAAGCGT-GAAAACCCTTCAATTTTTTTTGCGTTAAATTATA
65 AAAAAAAT-AAAAAACGATATTAGAAGCGTCGAAAATCCTTCAATCTTTTTGGCATTAAATTATA
* * * * * * *
38866 TATTTTTTTATGAATAATATGGCCAGAGATTAAAGAAAAATCTTTCAGGTCATTTTTTGCAAAAA
129 TA-TTTTTTATGAGTATTGTGGCCAGAAATTAAGGAAAAATCTTTCGGGTCATTTTTTGCAAAAT
* * * * * * * * ** **
38931 TTAAGCCGAAA-CTGTATGCTAATCATCA-AGCTTTTAGCCTAACAGCCCGTAT-TGGAGACCCG
193 TTTAGCCGAAATC-GTGTGCTAA-CATCACGGATTTT-GGCTAAAAACGCGT-TCCAGAGGTCCG
* * * *
38993 ACTCAGTTTTG-ATTGATTTTTGGCGCCAAGACACCTTCTAATATCTATAGTCATCTAACTAAAT
254 ACTCAGTTTTGCA-TGATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAAT
* *
39057 CTTAGCCATGTTGGA
318 CTCAGCCATGTTAGA
* * * * * * * * **
39072 TTAAAAGATTTGTTTTTACGGGCAACTTAATCATGTTTCGATTTATTTAGAAATT-ATTTTGGAA
1 TTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATTTAATCAGAAATTAATTCGGGAA
* * * * * * * *
39136 AAAAATAGAAAAAATGATATTAGAAGC-ACGAACAA-CTGTTCAATATTTTTAGCTTTGAATTAT
66 AAAAA-ATAAAAAACGATATTAGAAGCGTCGAA-AATC-CTTCAATCTTTTTGGCATTAAATTAT
* * * * *
39199 ATATTTTTTTGTGAGCATTGTAGCCAGAAATTAAGTAAAAATATTTCGGGTCA-TTTTTGCAAAA
128 ATA-TTTTTTATGAGTATTGTGGCCAGAAATTAAGGAAAAATCTTTCGGGTCATTTTTTGCAAAA
* * * *
39263 TTTTAGCCGAAACCGTGTGCTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCAGAGGCCCGAC
192 TTTTAGCCGAAATCGTGTGCTAA-CATCACGGATTTTGGCTAAAAACGCGTTCCAGAGGTCCGAC
*
39328 TCAGTTTTGCATAATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTC
256 TCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTC
39393 AGCCATGTTAGA
321 AGCCATGTTAGA
* *
39405 TTTAAGTATTT-TTTTTCACGGGCATCTGACTCGTCTTTCGATTTAATCAGAAATTAATTCGGG-
1 TTTAAGGATTTGTTTTT-ACGGGCATCTGACTCGTGTTTCGATTTAATCAGAAATTAATTCGGGA
* * * *
39468 --AAAAACAAAAAATGATATTAGATGCG-CGAAAATCCCTTCCA--TTTTTGGCATTAAATTATA
65 AAAAAAATAAAAAACGATATTAGAAGCGTCGAAAAT-CCTTCAATCTTTTTGGCATTAAATTATA
* * *
39528 TATTTTTATATAAGTATTGTGGCTAGAAATTAAGG-AAAATATTTCGGGTCATTTTTTTGCAAAA
129 TATTTTT-TATGAGTATTGTGGCCAGAAATTAAGGAAAAATCTTTCGGGTCA-TTTTTTGCAAAA
* * *
39592 TTTTTGCCGAAATCATGTGCTAATCATCAC-GATTTTTGGCTAAAAACGCGTT-C-TAGGTCCCC
192 TTTTAGCCGAAATCGTGTGCTAA-CATCACGGA-TTTTGGCTAAAAACGCGTTCCAGAGGT--CC
* * * * ** *
39654 GACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTCGAATATTTACATTCATCTAAATAGAT
253 GACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAAT
** ** *
39719 CTCAGTTACATTGGA
318 CTCAGCCATGTTAGA
* * * *
39734 TTTAAGGATTGGCTTTTACGGGCAACTGACTCGTGTTTCGATTTAATCAGAAATTAATTTGGG--
1 TTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATTTAATCAGAAATTAATTCGGGAA
* * * *
39797 ----GA-AAAAAACGATATTAGAAGCGT-GAAAAGTACTTCAATCTTATTGGTATTAAATTATAT
66 AAAAAATAAAAAACGATATTAGAAGCGTCGAAAA-TCCTTCAATCTTTTTGGCATTAAATTATAT
* * *
39856 AATTTTTATGAGTATTGTGGCCGGAAATTAAGGAAAAATTCTATCGGGTCATTTTTTGCAAAATT
130 ATTTTTTATGAGTATTGTGGCCAGAAATTAAGGAAAAA-TCTTTCGGGTCATTTTTTGCAAAATT
** * *
39921 TTAGTTGAAATCGTTTGCTAACCATCACGGATTTTGACTAAAAACGCGTTCCAGAGGTCCGACTC
194 TTAGCCGAAATCGTGTGCTAA-CATCACGGATTTTGGCTAAAAACGCGTTCCAGAGGTCCGACTC
* ** * * * *
39986 AGTTTTGCATAATTTTTGATGCCAAGACTTCTTCAAATACCTATATTCATATAACCAAATCACAG
258 AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTCAG
40051 CCATGTTAGA
323 CCATGTTAGA
* * *
40061 TTTAAGGATTTATTTTTACGAGCATCTGACTCGTGTTTCGATTTAATCAGATATTAATTCGGGAA
1 TTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATTTAATCAGAAATTAATTCGGGAA
* * * * *
40126 AAAATA-AAAAAATGATATTAGATGCG-CGGAAATCCCTTCAATCTTTTTGGCGTTAAATTATAT
66 AAAAAATAAAAAACGATATTAGAAGCGTCGAAAAT-CCTTCAATCTTTTTGGCATTAAATTATAT
* *
40189 ATTTTTTATGAGTATTGTGGCCAAAAATTAAGGAAAAATTCTTTTGGGTCATTTTTTTTTGCAAA
130 ATTTTTTATGAGTATTGTGGCCAGAAATTAAGGAAAAA-TCTTTCGGGTCA---TTTTTTGCAAA
* * ** *
40254 ATTTTTGCGGAAATCGTGTGCTAATCATCAC-GATTTTTGGCTAAAAACGCGTTGTAG-GGCCCC
191 ATTTTAGCCGAAATCGTGTGCTAA-CATCACGGA-TTTTGGCTAAAAACGCGTTCCAGAGG-TCC
* * * * * * *
40317 GACTCAGTTTTGCTTGATTTTTGGCACCAAGACTCCTTCGAATATTTACATTCATCTAACTAATT
253 GACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAAT
** ** *
40382 CTCAGTTACATTGGA
318 CTCAGCCATGTTAGA
* ** * * *
40397 TGTAAGGATTTCCTTTTACAGGCATCTGACTCGTGTTTCAATTTAATCAGAAATTGATTCGGGAA
1 TTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATTTAATCAGAAATTAATTCGGG-A
* * *
40462 AAAAAAATAAAAAACGATATTAGAAGCGTGGAAAGTTCTTCAATCTTTTTGGCATTAAATTATAT
65 AAAAAAATAAAAAACGATATTAGAAGCGTCGAAAATCCTTCAATCTTTTTGGCATTAAATTATAT
* * *
40527 ATTTTTTATGAGTATTATGGTCC-GAAATTAAGGAAAAATTCTTTCAGGTCATTTTTTGTAAAAT
130 ATTTTTTATGAGTATTGTGG-CCAGAAATTAAGGAAAAA-TCTTTCGGGTCATTTTTTGCAAAAT
* * * *
40591 TTTAGCTGAAATCGTGTGCTAACAATCACGGATTTTGACGAAAACCGCGTTCCAGAGGTCCGACT
193 TTTAGCCGAAATCGTGTGCTAAC-ATCACGGATTTTGGCTAAAAACGCGTTCCAGAGGTCCGACT
* * * ** * *
40656 CAGTTTTGCATAATTTTTGGCGCCAAGCCTTCTTCAAATGCCTATATTCATATAACCAAATCACA
257 CAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTCA
*
40721 ACCATGTTAGA
322 GCCATGTTAGA
*
40732 TTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATCTAATCAGAAATTAATTC-GG-A
1 TTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATTTAATCAGAAATTAATTCGGGAA
* * * *
40795 AAAAAATAAAAAAATGATATTAGATGCG-CGAAAATCGCTTTAATCTTTTTGGCCTTAAATTATA
66 AAAAAAT-AAAAAACGATATTAGAAGCGTCGAAAATC-CTTCAATCTTTTTGGCATTAAATTATA
** *
40859 TATTTTTATAGTG-GTATTGTGGTTAGAAATTAAGGAAAAATATTTCGGGTCATTTTTTTTGCAA
129 TATTTTT-TA-TGAGTATTGTGGCCAGAAATTAAGGAAAAATCTTTCGGGTCA--TTTTTTGCAA
* *
40923 AATTTTTGTCGAAATCGTGTGCTAATCATCAC-GATTTTTGGCT--AAA--------A-A--T--
190 AATTTTAGCCGAAATCGTGTGCTAA-CATCACGGA-TTTTGGCTAAAAACGCGTTCCAGAGGTCC
** * * * * **
40972 --CTCAGTTTTGCATGATTTTTGGCATCAAGACTCCTTCGAATATTTACATTCATTTAACCAGTT
253 GACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAAT
* **
41035 CTCAGTCACATTAGA
318 CTCAGCCATGTTAGA
* * * * * *
41050 TTTAAGAATTTGTTTTAAGGGGCATCTAACTCGTGTTTCGATTTAAACTGAAATTAATTCGGG--
1 TTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATTTAATCAGAAATTAATTCGGGAA
* * * *
41113 AAAAAATAAAAAACAATATTAGACGAG-CGAAAAGCCCTTCAATCTTTTTGGCATTAAATTATAT
66 AAAAAATAAAAAACGATATTAGAAGCGTCGAAAA-TCCTTCAATCTTTTTGGCATTAAATTATAT
* * * * *
41177 ATTTTTTATGAATACTGTGGCCAAAAATTAAGGAGAAATTCTTTCGGGTCTTTTTTTTTGCAAAA
130 ATTTTTTATGAGTATTGTGGCCAGAAATTAAGGA-AAAATCTTTCGGGTC--ATTTTTTGCAAAA
** *
41242 TTTTAGTTGAAATCATGTGCTAACCATCACGGATTTT
192 TTTTAGCCGAAATCGTGTGCTAA-CATCACGGATTTT
41279 CAGTTTTGCA
Statistics
Matches: 2620, Mismatches: 456, Indels: 246
0.79 0.14 0.07
Matches are distributed among these distances:
315 2 0.00
316 20 0.01
317 116 0.04
318 157 0.06
319 30 0.01
320 60 0.02
321 51 0.02
322 45 0.02
323 5 0.00
324 33 0.01
325 48 0.02
326 196 0.07
327 267 0.10
328 55 0.02
329 249 0.10
330 50 0.02
331 7 0.00
332 44 0.02
333 389 0.15
334 121 0.05
335 391 0.15
336 182 0.07
337 7 0.00
338 89 0.03
339 6 0.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (332 bp):
TTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATTTAATCAGAAATTAATTCGGGAA
AAAAAATAAAAAACGATATTAGAAGCGTCGAAAATCCTTCAATCTTTTTGGCATTAAATTATATA
TTTTTTATGAGTATTGTGGCCAGAAATTAAGGAAAAATCTTTCGGGTCATTTTTTGCAAAATTTT
AGCCGAAATCGTGTGCTAACATCACGGATTTTGGCTAAAAACGCGTTCCAGAGGTCCGACTCAGT
TTTGCATGATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTCAGCCA
TGTTAGA
Found at i:42332 original size:337 final size:333
Alignment explanation
Indices: 41278--42985 Score: 2054
Period size: 337 Copynumber: 5.1 Consensus size: 333
41268 TCACGGATTT
*
41278 TCAGTTTTGCATAATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTC
1 TCAGTTTTGCATAATTTTTGGCACCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTC
* * * * *
41343 ATCCATGTTAGATTTAAGGATTTGTTTTTATGGGCATCTGACTCGTCTTTCGATTTAATCATAAA
66 AACCAAGTTAGATTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATTTAATCAGAAA
** * * * *
41408 TTAATTC-ATAAAAAGCA-AAAAAATGATATTAGCTGCGTGAAAATCTCTTCAATCTTTTTGGCG
131 TTAATTCGGGAAAAA-AATAAAAAATGATATTAGATGCGTGAAAATCCCTTCAATCTTTTTGACG
*
41471 TTAAATTATATATTTTTATATGAGTATTGTGGCTAGAAATTAAGGAAAAATATTTTGGGTCATTT
195 TTAAATTATATATTTTTATATGAGTATTGTGGCTAGAAATTAAGGGAAAATATTTTGGGTCATTT
* * * * *
41536 TTTTTCAAAATTTTTGTCGAAGTCGTGTGGTAATCATCATGATTTTGGCTAAAAACGCGTTCTAG
260 TTTTGCAAAATTTTTGCCGAAATCGTGTGCTAATCATCACGATTTTGGCTAAAAACGCGTTCTAG
41601 GGCCCCGAC
325 GGCCCCGAC
* * * * * * * **
41610 TAAGTTTTGCATGATTTTTTGCACCAAGACTCCTTCGAATATTTACATTCATCTAACTAGTTCTC
1 TCAGTTTTGCATAATTTTTGGCACCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTC
*** * * * *
41675 AGTTACA-TTGGGTTTAAGGATTTGCTTTCACGGGCATCTGACTCGTGTTTCGATTTAATCAGAA
66 AACCA-AGTTAGATTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATTTAATCAGAA
* * * * *
41739 ATTAATTCGGGAAAAAAATAAAAAACGATATTAGAAGCGCGAAAAGT-ACTTCAATCTTTTTGCC
130 ATTAATTCGGGAAAAAAATAAAAAATGATATTAGATGCGTGAAAA-TCCCTTCAATCTTTTTGAC
** * *
41803 AATAAATTATATATTTTT-TATGAGTATTGCGGCTGGAAATTAA-GGAAAAT-TCTATTGGGTCA
194 GTTAAATTATATATTTTTATATGAGTATTGTGGCTAGAAATTAAGGGAAAATAT-T-TTGGGTCA
* * *
41865 -TTTTTTGCAAAATTTTTGCTGAAATCGTGTGCTAAGCATCACGGATTTTGGCTGAAAACGCGTT
257 TTTTTTTGCAAAATTTTTGCCGAAATCGTGTGCTAATCATCAC-GATTTTGGCTAAAAACGCGTT
* *
41929 CCAGAGG-ACCGAC
321 CTAG-GGCCCCGAC
* * *
41942 TCAGTTTTGCATAATTTTTTGCGCCAAGACTCCTTCAAATATCTATATTCATCTTACCAAATCTC
1 TCAGTTTTGCATAATTTTTGGCACCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTC
* *
42007 AACGAAGTTAGATTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCTATTTAATCAGAAA
66 AACCAAGTTAGATTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATTTAATCAGAAA
42072 TTAATTCGGGAAAAAAATAAAAAAAAATGATATTAGATGCGTGAAAATCCCTTCAATCTTTTTGA
131 TTAATTCGGGAAAAAAAT---AAAAAATGATATTAGATGCGTGAAAATCCCTTCAATCTTTTTGA
* *
42137 CATTAAATTATATATTTTTATATGAGTATTGTGGCTACAAATTAAGGGAAAATATTTTGGGTCAT
193 CGTTAAATTATATATTTTTATATGAGTATTGTGGCTAGAAATTAAGGGAAAATATTTTGGGTCAT
* * *
42202 TTTTTTGCAAAATTTTTACCGAAATCGTGTGCTAATCATCACGATTTTTGGCTAAAAGCGCGTTG
258 TTTTTTGCAAAATTTTTGCCGAAATCGTGTGCTAATCATCACGA-TTTTGGCTAAAAACGCGTTC
42267 TAGGGCCCCGAC
322 TAGGGCCCCGAC
* * * * ** ** *
42279 TCAGTTTTGCATGATTTTTGGCACCAAGACACCTTCCAATATTTACCTTCATCTAACCAGTTCTT
1 TCAGTTTTGCATAATTTTTGGCACCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTC
** * * *
42344 AGTCACA-TTTGATTTAAGGATTTGATTTTACGGGCATCTGACTCGTGTTTCGATTTAATCTGAA
66 AACCA-AGTTAGATTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATTTAATCAGAA
* * * * * * *
42408 ATTAATTCGGGGAAAAAAT-AAAAGTGATATTGGAAGAGTGAAAAACCCTTCAATCTTTTTGGCG
130 ATTAATTCGGGAAAAAAATAAAAAATGATATTAGATGCGTGAAAATCCCTTCAATCTTTTTGACG
* * * *
42472 TTAAATTATA-A-TTTT-TATGAGTATTGTGGCCAAAAATTAAGGAAAAAT-TCTTTCGGGACTA
195 TTAAATTATATATTTTTATATGAGTATTGTGGCTAGAAATTAAGGGAAAATAT-TTT-GGGTC-A
* * * * * *
42533 TTTTTTTTTTTTGCAAAATTATAGCTGAAATCATGTGCTAACCATCACGGATTCTGGCTAAAAAC
257 -----TTTTTTTGCAAAATTTTTGCCGAAATCGTGTGCTAATCATCAC-GATTTTGGCTAAAAAC
* *
42598 GCGTTCCAGAGG-TCCGAC
316 GCGTTCTAG-GGCCCCGAC
* * * * *
42616 TCAGTTTTGCATAATTTTTGGCGCCAAGACTTCTTCAAATACCTATATTCATATAACCAAATCAC
1 TCAGTTTTGCATAATTTTTGGCACCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTC
* * * * * *
42681 AACCATGTTAGATTTAAGGAGTT-TTTTTATGGGTACCTGACTCGTGTTTCGATTTAATTAGAAA
66 AACCAAGTTAGATTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATTTAATCAGAAA
* * *
42745 TTAATTCGGG--AAAAATAAAAAATGATATTAGATGCGCGAAAATCCCTTCAATCCTTTTGATGT
131 TTAATTCGGGAAAAAAATAAAAAATGATATTAGATGCGTGAAAATCCCTTCAATCTTTTTGACGT
* *
42808 TAAATTATATATTTTTATATGAGTATTGTGGCTAGAAATTAAGGGAAAATATTTTGGGCCATCTT
196 TAAATTATATATTTTTATATGAGTATTGTGGCTAGAAATTAAGGGAAAATATTTTGGGTCATTTT
* * *
42873 TTTGC-AAATTTTTGCCGAAATCGTGTGCTAGTCATCATGATTTTTGGCTAAAAACGCGTTGTAG
261 TTTGCAAAATTTTTGCCGAAATCGTGTGCTAATCATCACGA-TTTTGGCTAAAAACGCGTTCTAG
42937 GGCCCCGAC
325 GGCCCCGAC
* *
42946 TCAGTTTTGCATGA-TTTTGGCACCAAGACTCCTTCGAATA
1 TCAGTTTTGCATAATTTTTGGCACCAAGACTCCTTCAAATA
Statistics
Matches: 1162, Mismatches: 176, Indels: 79
0.82 0.12 0.06
Matches are distributed among these distances:
329 28 0.02
330 98 0.08
331 59 0.05
332 305 0.26
333 108 0.09
334 8 0.01
335 101 0.09
336 81 0.07
337 334 0.29
338 39 0.03
339 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (333 bp):
TCAGTTTTGCATAATTTTTGGCACCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTC
AACCAAGTTAGATTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCGATTTAATCAGAAA
TTAATTCGGGAAAAAAATAAAAAATGATATTAGATGCGTGAAAATCCCTTCAATCTTTTTGACGT
TAAATTATATATTTTTATATGAGTATTGTGGCTAGAAATTAAGGGAAAATATTTTGGGTCATTTT
TTTGCAAAATTTTTGCCGAAATCGTGTGCTAATCATCACGATTTTGGCTAAAAACGCGTTCTAGG
GCCCCGAC
Found at i:42767 original size:668 final size:664
Alignment explanation
Indices: 41278--42985 Score: 2516
Period size: 668 Copynumber: 2.6 Consensus size: 664
41268 TCACGGATTT
41278 TCAGTTTTGCATAATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTC
1 TCAGTTTTGCATAATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTC
* * *
41343 ATCCATGTTAGATTTAAGGATTTGTTTTTATGGGCATCTGACTCGTCTTTCGATTTAATCATAAA
66 AACCATGTTAGATTTAAGGATTTGTTTTTATGGGCATCTGACTCGTGTTTCGATTTAATCAGAAA
** * * * *
41408 TTAATTC-ATAAAAAGCAAAAAAATGATATTAGCTGCGTGAAAATCTCTTCAATCTTTTTGGCGT
131 TTAATTCGGGAAAAA--TAAAAAATGATATTAGATGCGTGAAAATCCCTTCAATCTTTTTGACGT
*
41472 TAAATTATATATTTTTATATGAGTATTGTGGCTAGAAATTAAGGAAAAATATTTTGGGTCATTTT
194 TAAATTATATATTTTTATATGAGTATTGTGGCTAGAAATTAAGGGAAAATATTTTGGGTCATTTT
* * * * *
41537 TTTTCAAAATTTTTGTCGAAGTCGTGTGGTAATCATCATGA-TTTTGGCTAAAAACGCGTTCTAG
259 TTTGCAAAATTTTTGCCGAAATCGTGTGCTAATCATCATGATTTTTGGCTAAAAACGCGTTGTAG
* *
41601 GGCCCCGACTAAGTTTTGCATGATTTTTTGCACCAAGACTCCTTCGAATATTTACATTCATCTAA
324 GGCCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTCGAATATTTACATTCATCTAA
* * * *
41666 CTAGTTCTCAGTTACATTGGGTTTAAGGATTTGCTTTCACGGGCATCTGACTCGTGTTTCGATTT
389 CCAGTTCTCAGTCACATTGGATTTAAGGATTTGATTTCACGGGCATCTGACTCGTGTTTCGATTT
* **
41731 AATCAGAAATTAATTCGGGAAAAAAATAAAAAACGATATTAGAAGCGCGAAAAGTACTTCAATCT
454 AATCAGAAATTAATTCGGGAAAAAAATAAAAAACGATATTAGAAGAGCGAAAAACACTTCAATCT
***
41796 TTTTGCCAATAAATTATATATTTTTTATGAGTATTGCGGCTGGAAATTAAGGAAAATTCTATTGG
519 TTTTGCCAATAAATTATATATTTTTTATGAGTATTGCGGCCAAAAATTAAGGAAAATTCTATTGG
* * * * * * *
41861 GTCATTTTTTGCAAAATTTTTGCTGAAATCGTGTGCTAAGCATCACGGATTTTGGCTGAAAACGC
584 GACATTTTTTGCAAAATTATAGCTGAAATCATGTGCTAACCATCACGGATTCTGGCTAAAAACGC
41926 GTTCCAGAGGACCGAC
649 GTTCCAGAGGACCGAC
* *
41942 TCAGTTTTGCATAATTTTTTGCGCCAAGACTCCTTCAAATATCTATATTCATCTTACCAAATCTC
1 TCAGTTTTGCATAATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTC
* * * *
42007 AACGAAGTTAGATTTAAGGATTTGTTTTTACGGGCATCTGACTCGTGTTTCTATTTAATCAGAAA
66 AACCATGTTAGATTTAAGGATTTGTTTTTATGGGCATCTGACTCGTGTTTCGATTTAATCAGAAA
42072 TTAATTCGGGAAAAAAATAAAAAAAAATGATATTAGATGCGTGAAAATCCCTTCAATCTTTTTGA
131 TTAATTCGGG--AAAAAT---AAAAAATGATATTAGATGCGTGAAAATCCCTTCAATCTTTTTGA
* *
42137 CATTAAATTATATATTTTTATATGAGTATTGTGGCTACAAATTAAGGGAAAATATTTTGGGTCAT
191 CGTTAAATTATATATTTTTATATGAGTATTGTGGCTAGAAATTAAGGGAAAATATTTTGGGTCAT
* * *
42202 TTTTTTGCAAAATTTTTACCGAAATCGTGTGCTAATCATCACGATTTTTGGCTAAAAGCGCGTTG
256 TTTTTTGCAAAATTTTTGCCGAAATCGTGTGCTAATCATCATGATTTTTGGCTAAAAACGCGTTG
* * *
42267 TAGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACACCTTCCAATATTTACCTTCATC
321 TAGGGCCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTCGAATATTTACATTCATC
* * *
42332 TAACCAGTTCTTAGTCACATTTGATTTAAGGATTTGATTTTACGGGCATCTGACTCGTGTTTCGA
386 TAACCAGTTCTCAGTCACATTGGATTTAAGGATTTGATTTCACGGGCATCTGACTCGTGTTTCGA
* * ** * * *
42397 TTTAATCTGAAATTAATTCGGGGAAAAAAT-AAAAGTGATATTGGAAGAGTGAAAAACCCTTCAA
451 TTTAATCAGAAATTAATTCGGGAAAAAAATAAAAAACGATATTAGAAGAGCGAAAAACACTTCAA
* ** *
42461 TCTTTTTGGCGTTAAATTATA-A-TTTTTATGAGTATTGTGGCCAAAAATTAAGGAAAAATTCT-
516 TCTTTTTGCCAATAAATTATATATTTTTTATGAGTATTGCGGCCAAAAATTAAGG-AAAATTCTA
42523 TTCGGGACTATTTTTTTTTTTTGCAAAATTATAGCTGAAATCATGTGCTAACCATCACGGATTCT
580 TT-GGGAC-A------TTTTTTGCAAAATTATAGCTGAAATCATGTGCTAACCATCACGGATTCT
*
42588 GGCTAAAAACGCGTTCCAGAGGTCCGAC
637 GGCTAAAAACGCGTTCCAGAGGACCGAC
* * * *
42616 TCAGTTTTGCATAATTTTTGGCGCCAAGACTTCTTCAAATACCTATATTCATATAACCAAATCAC
1 TCAGTTTTGCATAATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTC
* * * *
42681 AACCATGTTAGATTTAAGGAGTT-TTTTTATGGGTACCTGACTCGTGTTTCGATTTAATTAGAAA
66 AACCATGTTAGATTTAAGGATTTGTTTTTATGGGCATCTGACTCGTGTTTCGATTTAATCAGAAA
* * *
42745 TTAATTCGGGAAAAATAAAAAATGATATTAGATGCGCGAAAATCCCTTCAATCCTTTTGATGTTA
131 TTAATTCGGGAAAAATAAAAAATGATATTAGATGCGTGAAAATCCCTTCAATCTTTTTGACGTTA
* *
42810 AATTATATATTTTTATATGAGTATTGTGGCTAGAAATTAAGGGAAAATATTTTGGGCCATCTTTT
196 AATTATATATTTTTATATGAGTATTGTGGCTAGAAATTAAGGGAAAATATTTTGGGTCATTTTTT
*
42875 TGC-AAATTTTTGCCGAAATCGTGTGCTAGTCATCATGATTTTTGGCTAAAAACGCGTTGTAGGG
261 TGCAAAATTTTTGCCGAAATCGTGTGCTAATCATCATGATTTTTGGCTAAAAACGCGTTGTAGGG
42939 CCCCGACTCAGTTTTGCATGA-TTTTGGCACCAAGACTCCTTCGAATA
326 CCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTCGAATA
Statistics
Matches: 938, Mismatches: 90, Indels: 30
0.89 0.09 0.03
Matches are distributed among these distances:
664 128 0.14
666 53 0.06
667 96 0.10
668 296 0.32
669 164 0.17
671 6 0.01
673 46 0.05
674 149 0.16
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (664 bp):
TCAGTTTTGCATAATTTTTGGCGCCAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTC
AACCATGTTAGATTTAAGGATTTGTTTTTATGGGCATCTGACTCGTGTTTCGATTTAATCAGAAA
TTAATTCGGGAAAAATAAAAAATGATATTAGATGCGTGAAAATCCCTTCAATCTTTTTGACGTTA
AATTATATATTTTTATATGAGTATTGTGGCTAGAAATTAAGGGAAAATATTTTGGGTCATTTTTT
TGCAAAATTTTTGCCGAAATCGTGTGCTAATCATCATGATTTTTGGCTAAAAACGCGTTGTAGGG
CCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTCGAATATTTACATTCATCTAACC
AGTTCTCAGTCACATTGGATTTAAGGATTTGATTTCACGGGCATCTGACTCGTGTTTCGATTTAA
TCAGAAATTAATTCGGGAAAAAAATAAAAAACGATATTAGAAGAGCGAAAAACACTTCAATCTTT
TTGCCAATAAATTATATATTTTTTATGAGTATTGCGGCCAAAAATTAAGGAAAATTCTATTGGGA
CATTTTTTGCAAAATTATAGCTGAAATCATGTGCTAACCATCACGGATTCTGGCTAAAAACGCGT
TCCAGAGGACCGAC
Done.