Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015395.1 Corchorus olitorius cultivar O-4 contig15428, 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: 20716
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:762 original size:336 final size:333
Alignment explanation
Indices: 2--1420 Score: 1532
Period size: 336 Copynumber: 4.2 Consensus size: 333
1 C
* * * * ** *
2 GATATTAGAAGTGTGAAATGCCCTTCTATCTTATTGGAATTGAATT-TATATATTTTTATGAGAA
1 GATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATAT-TTTTTATGAGTA
* ** * * ** *
66 TTAT-GCCAAAAATTGAG-TGAAACTTTTTCACTTCACTTTTTTGCAAAATTTTAGCCGAAATCG
65 TTGTGGCCAAAAATTGAGAAAAAAATCTTTCAGGTCA-ATTTTTGCAAAATTTTAGCCGAAATCG
* ** *
129 TGTACTAACCATCACAGTTTTTGGGTAAAAACGCGTTCC-GGAGTCCCGACTCAGTTTTGCATGA
129 TGT--TAAACATCACAGTTTCCGGCTAAAAACGCGTTCCGGGA-TCCCGACTCAGTTTTGCATGA
** * * * * * *
193 TTTAGGGCGCCAAGATTCGTTGAAATATATGTATTCATCTAATCAAATTTTAGCCATATAGGACT
191 TTTTTGGCACCAAGACTCGTTGAAATATATGTATTCATCTAACCAAATCTCAGCCACATAGGACT
* * * * *
258 GAAGGATTTGCTTTTACGAGAATCAGAATCTTGTTTCGGTTTAATTAGAAATTAATTAAAAAAAA
256 TAAGGATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTGAAAAAAA
*
323 TAGGATAATAAAT
321 TAAGATAATAAAT
* *
336 GATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTCGGCTTTGAATTATATATTTTCTATGAGTAT
1 GATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATATTTTTTATGAGTAT
* * *
401 TGTGGCCAAAAATTGAGGGAAAAAATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGT
66 TGTGGCCAAAAATTGA-GAAAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGT
* * * * *
466 GTACTAAACATCACAGTTT-TGTGCTAAAAACGCGTTCCAGGATCCTGACTTAGTTTTGCAAGAT
130 GT--TAAACATCACAGTTTCCG-GCTAAAAACGCGTTCCGGGATCCCGACTCAGTTTTGCATGAT
** * * ** * * * *
530 TTTTAACATCAAGACTCGTGGAAATACCTGTAATCTTCAAACCAAATCTCAACCACATAGGACTT
192 TTTTGGCACCAAGACTCGTTGAAATATATGTATTCATCTAACCAAATCTCAGCCACATAGGACTT
*
595 AAGGATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAACTA-AAAGTTAATTCGAAAAAA
257 AAGGATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAA-TTAATT-GAAAAAA
659 ATAAGATAATAAAT
320 ATAAGATAATAAAT
* *
673 GATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGTTTTGAATTATATATTTTTTATAAGTAT
1 GATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATATTTTTTATGAGTAT
* * *
738 TGTTGCCGAAAATTGAGAAAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAT--T-
66 TGTGGCCAAAAATTGAGAAAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG
** * * *
800 TTAGCCATCACAGTTTCCGACT-AAAACTGCGTTTCGGGGAT-CC-ACCTTAGTTTTGCATGATT
131 TTAAACATCACAGTTTCCGGCTAAAAAC-GCG-TTCCGGGATCCCGA-CTCAGTTTTGCATGATT
* * * * * *
862 TTTGGCGA-CAAGACTCGTTGCAATATATGTATTCATTTGACCAAATATCAGCCACAT-TGAATT
193 TTTGGC-ACCAAGACTCGTTGAAATATATGTATTCATCTAACCAAATCTCAGCCACATAGGACTT
** * *
925 CAAGGACATGTTTTTACGAGCATCAGAATCTTGTATCGATTTAATTA-AAAGTTAGTTAGAAAAA
257 -AAGGATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAA-TTAATT-GAAAAA
989 AATAAGATAATAAAT
319 AATAAGATAATAAAT
* * *
1004 GGTATTAGAAGCGTGAAAAGCCCGTCAATCGTTTTGGCTTTGAATTATATATTTTTTATGAGTAT
1 GATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATATTTTTTATGAGTAT
* * *
1069 TGTGGCTAAAAATTGAGAAAAAAATCTTTCAGGTCAATTTTTGCTAAATTTTAGCCGAAATTGTG
66 TGTGGCCAAAAATTGAGAAAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG
* *
1134 TTATAACGATCACAGTTTCCGGCTAAAACCGCGTTCCGGGGA-CCCGACACAGTTTTGCATGATT
131 TTA-AAC-ATCACAGTTTCCGGCTAAAAACGCGTTCC-GGGATCCCGACTCAGTTTTGCATGATT
* * * *
1198 TTTGGCGCCAAGACTCGTTCAAATATATATATTCATCTAACCAAATCAT-AGCCACATTGGA-TA
193 TTTGGCACCAAGACTCGTTGAAATATATGTATTCATCTAACCAAATC-TCAGCCACATAGGACT-
*
1261 CAAGGATTAT-TTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAA
256 TAAGGATT-TGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAA-TTGAAAAA
* ** *
1325 AA-AATACGATAAAC
319 AATAAGATAATAAAT
* * * ** * * * *
1339 GATATTAGAAGTGTTAAAAGCCCTTCTAT-TTTATTGGGATTGAATTTATATCTTTTTTTTTAGA
1 GATATTAGAAGCGTGAAAAGCCCTTCAATCTTT-TTGGCTTTGAA-TTATATATTTTTTATGAGT
*
1403 ATTAT-GCCAAAAATTGAG
64 ATTGTGGCCAAAAATTGAG
1421 GGAAATGTCC
Statistics
Matches: 919, Mismatches: 134, Indels: 63
0.82 0.12 0.06
Matches are distributed among these distances:
330 10 0.01
331 265 0.29
332 9 0.01
333 2 0.00
334 58 0.06
335 79 0.09
336 374 0.41
337 122 0.13
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (333 bp):
GATATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCTTTGAATTATATATTTTTTATGAGTAT
TGTGGCCAAAAATTGAGAAAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG
TTAAACATCACAGTTTCCGGCTAAAAACGCGTTCCGGGATCCCGACTCAGTTTTGCATGATTTTT
GGCACCAAGACTCGTTGAAATATATGTATTCATCTAACCAAATCTCAGCCACATAGGACTTAAGG
ATTTGTTTTTACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTGAAAAAAATAAGA
TAATAAAT
Found at i:3157 original size:330 final size:331
Alignment explanation
Indices: 2576--3187 Score: 890
Period size: 330 Copynumber: 1.9 Consensus size: 331
2566 AGTTTTTTGC
* * * *
2576 AAAATTTTAGCCGAAATCTTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGTCT
1 AAAATTTTAGCCGAAATCGTGTACTAAACATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGACC
* ** * * * *
2641 CGACTTAGTTTTGCATAATTTTTGGCGCCATGATTCGTTGAAATATCTATATTCATCCAACGAAA
66 CGACTCAGTTTTGCATAATTTTTAACGCCAAGACTCATTGAAATATCTATATTCATCCAACCAAA
* * * * * *
2706 TCCCAGCCACATTGGATTTAATGATTTGTTTTTACGAGTATCGGAATCTTGTTTCGATTTAATTA
131 TCCCAGCCACATAGGACTTAAGGATTTGTTTTGACGAGCATCAGAATCTTGTTTCGATTTAATTA
* *
2771 GAAATTAATTCGAATAAAATAGGGTAAATGATATTACAAGCGTGAAAAGCCCTTCAATCTTTTTG
196 GAAATTAATTCGAAAAAAATAGGATAAATGATATTACAAGCGTGAAAAGCCCTTCAATCTTTTTG
2836 GAC-TTGAATTATAT-TTTTTTAAGAATATTTTGGTCAAAATTAGGGAAAAATCTATCGGGTCAA
261 G-CGTTGAATTATATATTTTTTAAGAATATTTTGGTCAAAATTAGGGAAAAATCTATCGGGTCAA
2899 TTTTCGA
325 TTTTCGA
* * * *
2906 AAAATTTTAGCCGAAATCGTGTACTAAACATCACAGTTTTTTGCTAAAAACGTGTTCTGGGGACC
1 AAAATTTTAGCCGAAATCGTGTACTAAACATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGACC
* * * *
2971 CGACTCAGTTTTGCATGATTTTTAACGTCAAGACTCATTGAAATATCTGTATTCATCGAACCAAA
66 CGACTCAGTTTTGCATAATTTTTAACGCCAAGACTCATTGAAATATCTATATTCATCCAACCAAA
*
3036 TCTCAGCCA-ATAGGACTTAAGGATTTGTTTTGACGAGCATCAGAATCTTGTTTCGATTTAATTA
131 TCCCAGCCACATAGGACTTAAGGATTTGTTTTGACGAGCATCAGAATCTTGTTTCGATTTAATT-
* *
3100 AGAAA-TAATTCGAAAAAAATAGGATAAATGATATTATAAGCGTGAAAAAGGCCTTCAATCTTTT
195 AGAAATTAATTCGAAAAAAATAGGATAAATGATATTACAAGCGTG-AAAAGCCCTTCAATCTTTT
*
3164 TTGCGTTGAATTATATATTTTTTA
259 TGGCGTTGAATTATATATTTTTTA
3188 TGAGTTTTGC
Statistics
Matches: 247, Mismatches: 31, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
329 85 0.34
330 155 0.63
331 7 0.03
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (331 bp):
AAAATTTTAGCCGAAATCGTGTACTAAACATCACAGTTTTTGGCTAAAAACGCGTTCCGGAGACC
CGACTCAGTTTTGCATAATTTTTAACGCCAAGACTCATTGAAATATCTATATTCATCCAACCAAA
TCCCAGCCACATAGGACTTAAGGATTTGTTTTGACGAGCATCAGAATCTTGTTTCGATTTAATTA
GAAATTAATTCGAAAAAAATAGGATAAATGATATTACAAGCGTGAAAAGCCCTTCAATCTTTTTG
GCGTTGAATTATATATTTTTTAAGAATATTTTGGTCAAAATTAGGGAAAAATCTATCGGGTCAAT
TTTCGA
Found at i:4722 original size:330 final size:331
Alignment explanation
Indices: 3669--4951 Score: 1570
Period size: 332 Copynumber: 3.9 Consensus size: 331
3659 GTTTCAGGGA
** **** * * *
3669 CCCGACTCAGTTTTTAATGATTTTTGGTGTCAAGATTCGTTGAAATATCTGTATTCATCTAACCA
1 CCCGACTCAGTTTTGCATGATTTTTAACATCAAGACTCGTGGAAATACCTGTATTCATCTAACCA
* * ** * * * *
3734 AATTTCATCCACATTTGATTTAAGGATTTGCTTTTACAAGAATAAGAATCATGTTTCGATTTAAT
66 AATCTCAACCACATAGGACTTAAGGATTTGCTTTTACGAGAATCAGAATCTTGTTTCGATTTAAT
* * *
3799 TAGAGATTAATTCGAAAGAAAATATG-ATAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTT
131 TAAAAATTAATTCGAAAGAAAATAGGAATAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTT
* * ** * *
3863 TTTGGCATTGAATTCTATATTTTTTATGAGTGCTGTGACCAAAAACTGAGGAAAAATATTTCGAT
196 TTTGGCTTTGAATTATATATTTTTTATGAGTATTGTGACCAAAAACTGAGAAAAAATATTTCGAG
*
3928 TCAATTTTTGTAAAATTTT-GCCCGAAATCATATACTTATCATCACAGTTTTGTGCTAAAAACGC
261 TCAATTTTTGCAAAATTTTAG-CCGAAATCATATAC-T-TCATCACAGTTTTGTGCTAAAAACGC
3992 GATCCGGGT
323 GATCCGGGT
*
4001 CCCGACTCAGTTTTGCATGATTTTTAACATCAAGACTCGTGGAAATACCTGTATTCATCTAACCG
1 CCCGACTCAGTTTTGCATGATTTTTAACATCAAGACTCGTGGAAATACCTGTATTCATCTAACCA
* ** *
4066 AATCTCAACCACATAGGACTTAAGGATTTGTTTTTACGATCATTAGAATCTTGTTTCGATTTAAT
66 AATCTCAACCACATAGGACTTAAGGATTTGCTTTTACGAGAATCAGAATCTTGTTTCGATTTAAT
4131 TAAAAATTAATTCGAAA-AAAATAGGATAATAAATGATATTAGAAGCGTGAAAAGCCCTTCAATC
131 TAAAAATTAATTCGAAAGAAAATAGG--AATAAATGATATTAGAAGCGTGAAAAGCCCTTCAATC
* * * * *
4195 TTTTTGGCTTTGAATTATGTATTTTTTATGGGTATTGTGGCCAAAAATTGAGAAAAAAATCTTTC
194 TTTTTGGCTTTGAATTATATATTTTTTATGAGTATTGTGACCAAAAACTGAG-AAAAAATATTTC
* * * * *
4260 -AGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACGT--T---AGTTTCCG-GCTAAAACC
258 GA-GTCAATTTTTGCAAAATTTTAGCCGAAATCATATACTTCATCACAGTTT-TGTGCTAAAAAC
*
4318 GCG-TCCCGAGGA
321 GCGAT-CCG-GGT
** ** * * *
4330 CCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGATTCGTTGAAATAGCTGTATTCATCTAACCA
1 CCCGACTCAGTTTTGCATGATTTTTAACATCAAGACTCGTGGAAATACCTGTATTCATCTAACCA
* * * * * * *
4395 AATTTCAGCCACGTTGCATTTAAGGATTTGCTTTTACGAGAATCAGAATCTTGTTTCGGTTTAAT
66 AATCTCAACCACATAGGACTTAAGGATTTGCTTTTACGAGAATCAGAATCTTGTTTCGATTTAAT
* * * *
4460 TAGAGATTAATTTGAAAGAAAATAGG-ATAAATGATATTAGAAACGTGAAAAGCCCTTCAATCTT
131 TAAAAATTAATTCGAAAGAAAATAGGAATAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTT
* * * * * * *
4524 TTTGGCGTTGGATTATATATTTTTTATGAGTGTTGTGACCAAGAACTGAGGAAAAATCTTTCGAT
196 TTTGGCTTTGAATTATATATTTTTTATGAGTATTGTGACCAAAAACTGAGAAAAAATATTTCGAG
*
4589 TCAATTTTTGTAAAATTTT-GCCCGAAATCATATAC-TCATCACAGTTTTGTGCTAAAAACGCGA
261 TCAATTTTTGCAAAATTTTAG-CCGAAATCATATACTTCATCACAGTTTTGTGCTAAAAACGCGA
*
4652 TCTAGGGT
325 TC-CGGGT
* *
4660 CCCGACTCAATTTTGCATGATTTTTAACATCAAGACTCGTGGAAATACCTGTATTCATCTAACCG
1 CCCGACTCAGTTTTGCATGATTTTTAACATCAAGACTCGTGGAAATACCTGTATTCATCTAACCA
* * **
4725 AATCTCAACCTCATAGGACTTAAGGATTTGTTTTTACGATCATCAGAATCTTGTTTCGATTTAAT
66 AATCTCAACCACATAGGACTTAAGGATTTGCTTTTACGAGAATCAGAATCTTGTTTCGATTTAAT
* * *
4790 TAAAAATTAATTCGAAAAAAAATAGGATAATAAATTATATTAGAAGCCTGAAAAGCCCTTCAATC
131 TAAAAATTAATTCGAAAGAAAATAGG--AATAAATGATATTAGAAGCGTGAAAAGCCCTTCAATC
* * * * *
4855 TTTTCGGCTTTGAATTATATATTTTTTATGAGTATTGTGGCC-AAAATTGAGAAAAAAAATTTTG
194 TTTTTGGCTTTGAATTATATATTTTTTATGAGTATTGTGACCAAAAACTGAGAAAAAATATTTCG
*
4919 GGTCAATTTTTGCAAAATTTTAGCCGAAATCAT
259 AGTCAATTTTTGCAAAATTTTAGCCGAAATCAT
4952 GTATTTTTAT
Statistics
Matches: 804, Mismatches: 123, Indels: 48
0.82 0.13 0.05
Matches are distributed among these distances:
325 2 0.00
326 41 0.05
327 82 0.10
328 19 0.02
329 129 0.16
330 159 0.20
331 10 0.01
332 168 0.21
333 72 0.09
334 81 0.10
335 40 0.05
336 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (331 bp):
CCCGACTCAGTTTTGCATGATTTTTAACATCAAGACTCGTGGAAATACCTGTATTCATCTAACCA
AATCTCAACCACATAGGACTTAAGGATTTGCTTTTACGAGAATCAGAATCTTGTTTCGATTTAAT
TAAAAATTAATTCGAAAGAAAATAGGAATAAATGATATTAGAAGCGTGAAAAGCCCTTCAATCTT
TTTGGCTTTGAATTATATATTTTTTATGAGTATTGTGACCAAAAACTGAGAAAAAATATTTCGAG
TCAATTTTTGCAAAATTTTAGCCGAAATCATATACTTCATCACAGTTTTGTGCTAAAAACGCGAT
CCGGGT
Found at i:4996 original size:121 final size:122
Alignment explanation
Indices: 4865--5108 Score: 481
Period size: 122 Copynumber: 2.0 Consensus size: 122
4855 TTTTCGGCTT
4865 TGAATTATATATTTTTTATGAGTATTGTGGCCAAAATTGAGAAAAAAAATTTT-GGGTCAATTTT
1 TGAATTATATATTTTTTATGAGTATTGTGGCCAAAATTGAGAAAAAAAATTTTAGGGTCAATTTT
4929 TGCAAAATTTTAGCCGAAATCATGTATTTTTATTTTTATTTTCTATTTTTACCCTTA
66 TGCAAAATTTTAGCCGAAATCATGTATTTTTATTTTTATTTTCTATTTTTACCCTTA
4986 TGAATTATATATTTTTTATGAGTATTGTGGCCAAAATTGAGAAAAAAAATTTTAGGGTCAATTTT
1 TGAATTATATATTTTTTATGAGTATTGTGGCCAAAATTGAGAAAAAAAATTTTAGGGTCAATTTT
5051 TGCAAAATTTTAGCCGAAATCATGTATTTTTATTTTTATTTTCTATTTTTACCCTTA
66 TGCAAAATTTTAGCCGAAATCATGTATTTTTATTTTTATTTTCTATTTTTACCCTTA
5108 T
1 T
5109 CTTTTTCCCC
Statistics
Matches: 122, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
121 53 0.43
122 69 0.57
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (122 bp):
TGAATTATATATTTTTTATGAGTATTGTGGCCAAAATTGAGAAAAAAAATTTTAGGGTCAATTTT
TGCAAAATTTTAGCCGAAATCATGTATTTTTATTTTTATTTTCTATTTTTACCCTTA
Found at i:10240 original size:11 final size:10
Alignment explanation
Indices: 10224--10250 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
10214 ACTTGTTTTT
10224 AAAAAAAAAG
1 AAAAAAAAAG
10234 AAAAAAAAAG
1 AAAAAAAAAG
10244 AAAAAAA
1 AAAAAAA
10251 TATACTATAT
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:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:19130 original size:332 final size:328
Alignment explanation
Indices: 18443--20716 Score: 2003
Period size: 332 Copynumber: 6.9 Consensus size: 328
18433 ATATTTTACA
* *
18443 TCATCTAACCAAATCTCAGCAACATTGGATTTAA--ATTTTTTTTACGAGCATCTGAATCTTGTT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGA-TTTTTTTACGAGCATCTGAATCTTGTT
*** * * * *
18506 TCGATTTAATTAGAAATTAATTTTTAAAAAATAAGAAATACGATATTAGAAGCGTGAAAAGTCCA
65 TCGATTTAATTAGAAATTAATTCGGAAAAAATATGAAAAACGATATTAGAAACGTGAAAAGTCCT
* * * * *
18571 CCAATCTTTTTGGCGTTGAATTATATATTCTCATGAATATTTTAGCCAAAAATTGAGGAGAAATA
130 CCAATCTTTTTGGCGTTAAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGA-AAATC
* * * * * * * *
18636 TTTCGTGTCAATTTTTACAAAATTTTAGCTGACATCGTGTACTAACTATCACGGTTTTTGGCTAA
194 TTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCTAA
* * ** * * * ** ** * *
18701 AAATGCATTCTGGGGATCCGCCTCAATTTTGCCTAATTTTTTACTCCGAGACTACTTGAAATATC
259 AAACGCGTTCTGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGACAAGACTCCTTGAAATATC
*
18766 TATAT
324 CATAT
* * * * * *
18771 TTATCTACTTAAATCTCGGCCACATTGGATTTAAGGATGTATTTTTACGAGCATTTGAATCTTAT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGAT-T-TTTTTACGAGCATCTGAATCTTGT
* * * *
18836 TTCGATTTAATTAGTAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAACGTCAAAAGCCC
64 TTCGATTTAATTAGAAATTAATTCGGAAAAAATATGAAAAACGATATTAGAAACGTGAAAAGTCC
* * *
18901 TTCAATCTTTTTGACGTTAAAATATATAATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATA
129 TCCAATCTTTTTGGCGTTAAATTATAT-ATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA-A
* *
18966 TCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCT
192 TCTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCT
* * * * * * * *
19031 AAAAAAGCGTTTTGGGCCCCCAACTTAGTTTTGCGTGATTTTTGGCGACAAGACTCCTTGACATA
257 AAAAACGCGTTCTGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGACAAGACTCCTTGAAATA
19096 TCCATAT
322 TCCATAT
* * * * *
19103 TCATATAATCAAATCTTAGCTACATTGGATTTAAGAATTTGTTTTTACGAGCATTTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGA-TT-TTTTTACGAGCATCTGAATCTTGT
* * * *
19168 TTCGATGTAATTAGAAATTCATTCGGAAAAAATATGAAAAACGATATT-TAAA-GTGGAGAAGTC
64 TTCGATTTAATTAGAAATTAATTCGGAAAAAATATGAAAAACGATATTAGAAACGT-GAAAAGTC
* * *
19231 CTCCAATCTTTTTGGTGTTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTAAGGAAAA
128 CTCCAATCTTTTTGGCGTTAAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGGAAAA
* * * *
19296 TTTTTCGGGTCATTTTTTGTAAAATTTTAGTCAAAATC--GT-AT-ACCATCAC-GATTTTTGGC
192 TCTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAG-TTTTTGGC
* * * * *
19356 TAAAAATGCGTT-TCGGGGCCTCGACTCAGTTTTGCATGATTCTTGGC-ACCGAGACTCCTTGAA
256 TAAAAACGCGTTCT-GGGGCCCCGACTCAATTTTGCATGATTTTTGGCGA-CAAGACTCCTTGAA
*
19419 ATATCTATAT
319 ATATCCATAT
* * * *
19429 TCATCTAAT-AAAGTCTAAGCCACATTGCATTTAAGGA-TTTTTTATGAGCATCTGAATCTTATT
1 TCATCTAATCAAA-TCTCAGCCACATTGGATTTAAGGATTTTTTTACGAGCATCTGAATCTTGTT
* * * * *
19492 TCGATTTAATTAGAAATTGATTC-AAAAAAATATGAAAAACGATATTTGAAGCGTGAAAAGCCCT
65 TCGATTTAATTAGAAATTAATTCGGAAAAAATATGAAAAACGATATTAGAAACGTGAAAAGTCCT
* ** * * *
19556 TCAAAATTTTTGGCG-TAGAATTATATAAATTTTTTATGAATGTTTTAGCCAAAAATTGGGGAAA
130 CCAATCTTTTTGGCGTTA-AATTATAT--A-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA
* * * * *
19620 TATATTTCGGGTCAATTTTTGCAAAATGTTAGCCGAAAATCGTATAATAATCATCACAGTTTTTG
191 -ATCTTTCGGGTCATTTTTTGCAAAATTTTAGCCG-AAATCGTGTAATAACCATCACAGTTTTTG
*** ** * * * *
19685 GCTAAAAACGCGTTCCAAGG-CCCGTGTCAATTTTGCATGATTTTTGCCGCCAAGACTCCTTTAC
254 GCTAAAAACGCGTTCTGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGACAAGACTCCTTGAA
*
19749 ATATCCATGT
319 ATATCCATAT
* * *
19759 TCATCTAATCAAATCTCAGCCACAATGCATTTAAGGATTTCTTTTTACGAGCATCTGAATCTTAT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGA-TT-TTTTTACGAGCATCTGAATCTTGT
* * *
19824 TTCGATTT-A--AGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGAAAAGTGTGTAA
64 TTCGATTTAATTAGAAATTAATTCGGAAAAAATATGAAAAACGATATT---AG-AAA-CGTGAAA
* * * * * * * * *
19885 TGTCCTCCAATATTTTTTGCATTAAAATATATATATTT-CGATTATTTTAGCCAAAAATTAAGGA
124 AGTCCTCCAATCTTTTTGGCGTTAAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGG-
* *
19949 AAAAAATCTTTTCAGGTCATTTTTTGGAAAATTTTA---G----C-TG----AA--AT-AGCA--
188 --AAAATC-TTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCA-CAGT
* * * * * * *
19997 -TTTGGTTAAAAACGCGTT-TCGGGGCCTCGGCTTAGTTTAGCATGATTTTTGGCGACGAGACTC
249 TTTTGGCTAAAAACGCGTTCT-GGGGCCCCGACTCAATTTTGCATGATTTTTGGCGACAAGACTC
**
20060 CTTGAAATATGTATAT
313 CTTGAAATATCCATAT
* * * **** * *
20076 TCATTTAATCAAATCTCGGCCAAATTGGATTTAAGGATTTGCAAAACAAGCATCTGAATCATGTT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTT-TTTTACGAGCATCTGAATCTTGTT
* * * * *
20141 TCGATTTAATTAGAAATTAGTTCGAAAAATAATA-GGAAAATGATATTAGAAACGT-AAAATTCC
65 TCGATTTAATTAGAAATTAATTCGGAAAA-AATATGAAAAACGATATTAGAAACGTGAAAAGT-C
* * * * * * *
20204 CTTCAATCTTCTTGGCGTTGAATTATATACTTTTTATGAGTATTATGGCTAAAAAATGAGGAAAT
128 CTCCAATCTTTTTGGCGTTAAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAA-
* * * * * * *
20269 AACTTTCAGGTCATTTTTTGCAAAA-TTTAGCTGAAATCGTGTAATAAATCATAACGGATTTTGG
191 ATCTTTCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAAT-AACCATCACAGTTTTTGG
* ** * * *
20333 CTAAAAACGCATTCCT-GGGCCCCGTGTCAATTTTGCATGATTTATGGCGCCAAGACTCCTTGAG
255 CTAAAAACGCGTT-CTGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGACAAGACTCCTTGAA
*
20397 ATATGCATAT
319 ATATCCATAT
* * * * * *
20407 TCATCTGATCACATCTCTGCCAAATTGAATTCAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGA-TT-TTTTTACGAGCATCTGAATCTTGT
* * * * *
20472 TTCGATTTAATTGGAAATTAATTCAGAAAAAATATGAAAAACGATATGAAAAACGTAAAAAGTCC
64 TTCGATTTAATTAGAAATTAATTCGGAAAAAATATGAAAAACGATATTAGAAACGTGAAAAGTCC
* * * *
20537 TCCAACCTTTTTGGCGTTATATTATATATATTTCAAGAGTATTTTAGCCAAAAAATTGAGGAAAA
129 TCCAATCTTTTTGGCGTTAAATTATATAT-TTTTATGAGTATTTTAGCC-AAAAATTGAGGAAAA
* * *
20602 GT-TTTACAGGTCATTTTTTGCAAAATTTTAGCCAAAATCGTGTAGTAACCATCAC-GTTTTTTA
192 -TCTTT-CGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAG-----T-
* * * * *
20665 TTTTGGCTAAAAACGCATTATGGGGCCCCGATTCAGTGTTGCATGATTTTTG
249 TTTTGGCTAAAAACGCGTTCTGGGGCCCCGACTCAATTTTGCATGATTTTTG
Statistics
Matches: 1570, Mismatches: 283, Indels: 176
0.77 0.14 0.09
Matches are distributed among these distances:
313 4 0.00
314 27 0.02
315 28 0.02
316 53 0.03
317 93 0.06
318 1 0.00
319 15 0.01
320 15 0.01
321 8 0.01
322 24 0.02
323 72 0.05
324 3 0.00
325 36 0.02
326 135 0.09
327 7 0.00
328 33 0.02
329 3 0.00
330 145 0.09
331 316 0.20
332 351 0.22
333 82 0.05
334 45 0.03
335 27 0.02
336 2 0.00
337 1 0.00
338 44 0.03
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (328 bp):
TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTTTTTACGAGCATCTGAATCTTGTTT
CGATTTAATTAGAAATTAATTCGGAAAAAATATGAAAAACGATATTAGAAACGTGAAAAGTCCTC
CAATCTTTTTGGCGTTAAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAATCTT
TCGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAA
ACGCGTTCTGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGACAAGACTCCTTGAAATATCCA
TAT
Found at i:20629 original size:647 final size:644
Alignment explanation
Indices: 18443--20633 Score: 2264
Period size: 647 Copynumber: 3.3 Consensus size: 644
18433 ATATTTTACA
* * *
18443 TCATCTAACCAAATCTCAG-CAACATTGGATTTAA--ATTT-TTTTTACGAGCATCTGAATCTTG
1 TCATCTAATCAAATCTCTGCCAA-ATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
*** * * * **
18504 TTTCGATTTAATTAGAAATTAATTTTTAAAAAATAAGAAATACGATATTAGAAGCGTGAAAAGTC
65 TTTCGATTTAATT-GAAATTAATTCAGAAAAAATATGAAAAACGATATGA-AAAAGTGAAAAGTC
* * * * *
18569 CACCAATCTTTTTGGCGTTGAATTATATAT-TCTCATGAATATTTTAGCCAAAAATTGAGGAGAA
128 CTCCAATCTTTTTGGCGTTAAATTATATATATTTCA-GAGTATTTTAGCCAAAAATTAAGGA-AA
* * * *
18633 ATATTTC-GTGTCAATTTTTACAAAATTTTAGCTGACATCGTGTACTAACTATCACGGTTTTTGG
191 ATTTTTCAG-GTCATTTTTTGCAAAATTTTA---G-CATC--GTA-T-AC-ATCAC-GATTTTGG
* * * * * * * * * ** * *
18697 CTAAAAATGC-ATTCTGGGG-ATCCGCCTCAATTTTGCCTAATTTTTTACTCCGAGACTACTTGA
245 CTAAAAACGCGTTTC-GGGGCCT-CGACTCAGTTTAGCATGATTCTTGGCACCGAGACTCCTTGA
* *
18760 AATATCTATATTTATCTACTTAAATCTCGGCCACATTGGATTTAAGGATGTATTTTTACGAGCAT
308 AATATCTATATTCATCTA-ATAAATCTCGGCCACATTGGATTTAAGGA--T-TTTTTACGAGCAT
* * * *
18825 TTGAATCTTATTTCGATTTAATTAGTAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAAC
369 CTGAATCTTATTTCGATTTAATTAGAAATTAGTTCGAAAAAAATAGG-AAAACGATATTAGAAAC
* * *
18890 GTCAAAAGCCCTTCAATCTTTTTGACGTTAAAATATATAATTTTTATGAGTATTTTAGCCAAAAA
433 GTCAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTTTAGCCAAAAA
* * *
18955 TTGAGGAAATATCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCAC
498 TTGAGGAAATAACTTTCGGGTCAATTTTTGCAAAA-TTTAGCCGAAATCGTGTAATAATCATCAC
* * *** * * * *
19020 AGTTTTTGGCTAAAAAAGCGTT-TTGGGCCCCCAACTTAGTTTTGCGTGATTTTTGGCGACAAGA
562 AGTTTTTGGCTAAAAACGCGTTCCTGGG-CCCCGTGTCAATTTTGCATGATTTTTGGCGCCAAGA
19084 CTCCTTGACATATCCATAT
626 CTCCTTGACATATCCATAT
* * * * * *
19103 TCATATAATCAAATCT-TAGCTACATTGGATTTAAGAATTTGTTTTTACGAGCATTTGAATCTTG
1 TCATCTAATCAAATCTCT-GCCAAATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * * ** *
19167 TTTCGATGTAATTAGAAATTCATTCGGAAAAAATATGAAAAACGATAT-TTAAAGTGGAGAAGTC
65 TTTCGATTTAATT-GAAATTAATTCAGAAAAAATATGAAAAACGATATGAAAAAGT-GAAAAGTC
* * *
19231 CTCCAATCTTTTTGGTGTTAAATTATATATATTTTATGAGTATTTTATCCAAAAATTAAGGAAAA
128 CTCCAATCTTTTTGGCGTTAAATTATATATATTTCA-GAGTATTTTAGCCAAAAATTAAGGAAAA
* *
19296 TTTTTCGGGTCATTTTTTGTAAAATTTTAGTCAAAATCGTATACCATCACGATTTTTGGCTAAAA
192 TTTTTCAGGTCATTTTTTGCAAAATTTTAG-C---ATCGTATA-CATCACGA-TTTTGGCTAAAA
* *
19361 ATGCGTTTCGGGGCCTCGACTCAGTTTTGCATGATTCTTGGCACCGAGACTCCTTGAAATATCTA
251 ACGCGTTTCGGGGCCTCGACTCAGTTTAGCATGATTCTTGGCACCGAGACTCCTTGAAATATCTA
** * *
19426 TATTCATCTAATAAAGTCTAAGCCACATTGCATTTAAGGATTTTTTATGAGCATCTGAATCTTAT
316 TATTCATCTAATAAA-TCTCGGCCACATTGGATTTAAGGATTTTTTACGAGCATCTGAATCTTAT
* * * *
19491 TTCGATTTAATTAGAAATT-GATTC-AAAAAAATATGAAAAACGATATTTGAAGCGTGAAAAGCC
380 TTCGATTTAATTAGAAATTAG-TTCGAAAAAAATA-GGAAAACGATATTAGAAACGTCAAAAGCC
** * * * *
19554 CTTCAAAATTTTTGGCGTAGAATTATATAAATTTTTTATGAATGTTTTAGCCAAAAATTGGGGAA
443 CTTCAATCTTTTTGGCGTTGAATTATAT-AA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAA
*
19619 ATATA-TTTCGGGTCAATTTTTGCAAAATGTTAGCCGAAAATCGTATAATAATCATCACAGTTTT
506 ATA-ACTTTCGGGTCAATTTTTGCAAAAT-TTAGCCG-AAATCGTGTAATAATCATCACAGTTTT
** * *
19683 TGGCTAAAAACGCGTTCCAAGG-CCCGTGTCAATTTTGCATGATTTTTGCCGCCAAGACTCCTTT
568 TGGCTAAAAACGCGTTCCTGGGCCCCGTGTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTG
*
19747 ACATATCCATGT
633 ACATATCCATAT
* * * *
19759 TCATCTAATCAAATCTCAGCCACAA-TGCATTTAAGGATTTCTTTTTACGAGCATCTGAATCTTA
1 TCATCTAATCAAATCTCTGCCA-AATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* *
19823 TTTCGATTTAA--GAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGAAAAGTGTGTAA
65 TTTCGATTTAATTGAAATTAATTCAGAAAAAATATGAAAAACGATA-T----GAAAA-AGTGAAA
* * * * * *
19885 TGTCCTCCAATATTTTTTGCATTAAAATATATATATTTC-GATTATTTTAGCCAAAAATTAAGGA
124 AGTCCTCCAATCTTTTTGGCGTTAAATTATATATATTTCAGAGTATTTTAGCCAAAAATTAAGG-
* *
19949 AAAAAATCTTTTCAGGTCATTTTTTGGAAAATTTTAGC-T-G-A-A-AT-A-GCA-TTTGGTTAA
188 --AAAAT-TTTTCAGGTCATTTTTTGCAAAATTTTAGCATCGTATACATCACG-ATTTTGGCTAA
* * *
20006 AAACGCGTTTCGGGGCCTCGGCTTAGTTTAGCATGATTTTTGGCGA-CGAGACTCCTTGAAATAT
249 AAACGCGTTTCGGGGCCTCGACTCAGTTTAGCATGATTCTTGGC-ACCGAGACTCCTTGAAATAT
* * * *** *
20070 GTATATTCATTTAATCAAATCTCGGCCAAATTGGATTTAAGGATTTGCAAAACAAGCATCTGAAT
313 CTATATTCATCTAAT-AAATCTCGGCCACATTGGATTTAAGGATTT--TTTACGAGCATCTGAAT
* * *
20135 CATGTTTCGATTTAATTAGAAATTAGTTCGAAAAATAATAGGAAAATGATATTAGAAACGT-AAA
375 CTTATTTCGATTTAATTAGAAATTAGTTCGAAAAA-AATAGGAAAACGATATTAGAAACGTCAAA
* * * * * * *
20199 ATTCCCTTCAATCTTCTTGGCGTTGAATTATATACTTTTTATGAGTATTATGGCTAAAAAATGAG
439 A-GCCCTTCAATCTTTTTGGCGTTGAATTATATAATTTTTATGAGTATTTTAGCCAAAAATTGAG
* * * * * *
20264 GAAATAACTTTCAGGTCATTTTTTGCAAAATTTAGCTGAAATCGTGTAATAAATCATAACGGATT
503 GAAATAACTTTCGGGTCAATTTTTGCAAAATTTAGCCGAAATCGTGTAAT-AATCATCACAGTTT
* *
20329 TTGGCTAAAAACGCATTCCTGGGCCCCGTGTCAATTTTGCATGATTTATGGCGCCAAGACTCCTT
567 TTGGCTAAAAACGCGTTCCTGGGCCCCGTGTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTT
* *
20394 GAGATATGCATAT
632 GACATATCCATAT
* * *
20407 TCATCTGATCACATCTCTGCCAAATTGAATTCAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCTGCCAAATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
*
20472 TTCGATTTAATTGGAAATTAATTCAGAAAAAATATGAAAAACGATATGAAAAACGTAAAAAGTCC
66 TTCGATTTAATT-GAAATTAATTCAGAAAAAATATGAAAAACGATATGAAAAA-GTGAAAAGTCC
* * *
20537 TCCAACCTTTTTGGCGTTATATTATATATATTTCAAGAGTATTTTAGCCAAAAAATTGAGGAAAA
129 TCCAATCTTTTTGGCGTTAAATTATATATATTTC-AGAGTATTTTAGCC-AAAAATTAAGGAAAA
*
20602 GTTTTACAGGTCATTTTTTGCAAAATTTTAGC
192 -TTTTTCAGGTCATTTTTTGCAAAATTTTAGC
20634 CAAAATCGTG
Statistics
Matches: 1287, Mismatches: 185, Indels: 131
0.80 0.12 0.08
Matches are distributed among these distances:
646 11 0.01
647 214 0.17
648 169 0.13
649 56 0.04
650 61 0.05
651 18 0.01
652 39 0.03
653 13 0.01
654 55 0.04
655 48 0.04
656 190 0.15
657 46 0.04
658 134 0.10
659 16 0.01
660 56 0.04
661 4 0.00
662 67 0.05
663 90 0.07
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (644 bp):
TCATCTAATCAAATCTCTGCCAAATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATTGAAATTAATTCAGAAAAAATATGAAAAACGATATGAAAAAGTGAAAAGTCCTC
CAATCTTTTTGGCGTTAAATTATATATATTTCAGAGTATTTTAGCCAAAAATTAAGGAAAATTTT
TCAGGTCATTTTTTGCAAAATTTTAGCATCGTATACATCACGATTTTGGCTAAAAACGCGTTTCG
GGGCCTCGACTCAGTTTAGCATGATTCTTGGCACCGAGACTCCTTGAAATATCTATATTCATCTA
ATAAATCTCGGCCACATTGGATTTAAGGATTTTTTACGAGCATCTGAATCTTATTTCGATTTAAT
TAGAAATTAGTTCGAAAAAAATAGGAAAACGATATTAGAAACGTCAAAAGCCCTTCAATCTTTTT
GGCGTTGAATTATATAATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATAACTTTCGGGTCA
ATTTTTGCAAAATTTAGCCGAAATCGTGTAATAATCATCACAGTTTTTGGCTAAAAACGCGTTCC
TGGGCCCCGTGTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTGACATATCCATAT
Done.