Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014686.1 Corchorus olitorius cultivar O-4 contig14719, 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: 10571
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1263 original size:332 final size:332
Alignment explanation
Indices: 2--3002 Score: 2920
Period size: 332 Copynumber: 9.1 Consensus size: 332
1 C
*
2 CCCTTCAATTTTTTTTGGCGTTGAATTATATAATTTTTTTTTGAGTATTGTGGCAAAAAAATTGT
1 CCCTTCAA-TTTTTTTGGCGTTGAATTATAT-A-TTTTTTCTGAGTATTGTGGC-AAAAAATTG-
*
67 A-GAAAAACTTTACGGGT-AAGTTTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACCATCAC
61 AGGAAAAACTTTTCGGGTCAA---TTTTT-CAAAATTTTAGCCGAAATCGTGTACTAACCATCAC
* * * * * *
130 TGTTTTTGGCTAAAATCGCGTTCCGGAGTCACGGCTCAAGTTTACATGATTTTTGG-TGCAAAGA
122 GGTTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATTTTTGGCAG-AAAGA
* * *
194 CTCCTTGAAATATCTATATTTATCG-AACCAATCTCAACCACATTGGATTTAAGGATTTGTTTTT
186 CTCCTTGAAATATCTATATTCATCGAAACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
* * * * * *
258 ACGAGCTTCT-GAATTTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAAATGGGAAACCGAT
251 ACGAGCATCTCGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGAT
* ** *
322 ATTAGAATCCCGAAAAG
316 ATTAGAAGCGTGAAAAA
* * * * *
339 CTCGTCAATCTTTTGGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGA-GAA
1 CCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAA
* ** * *
403 AAAGTTTTC-GG---A---TT--AGTTTTTAGCCGAAATCGTGTAC--A-CGTTACGGTTTTTGG
66 AAACTTTTCGGGTCAATTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
* * ** * * * *
456 CTAAAAACGCGTTTCGG-GGCCCGATTCAGTTTTGCATGATTTTTGGTAGAAAGAATCATTGAAA
131 CTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAA
* * * * * *
520 TATCTATATTCATCTAACCAAATCTTAGCTACATTGGATTCACGGATTTGTTTTTACGAGCATCT
196 TATCTATATTCATCGAAACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
* * * * *
585 -AAATCTTGTTTAGATTTAATTAGAAATAAATTCAGAAAAATTATGGAAAAATGATATTAGAAGC
261 CGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAA-AATGGAAAAACGATATTAGAAGC
*
649 GTTAAAAA
325 GTGAAAAA
** * * * *
657 TTCTT-AACTTTTTTTGTCGTTGAGTTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAA
1 CCCTTCAA-TTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGA
* * * * * ** * *
721 AAAAATTTGT-GTGTCAGTTTTTCGAAATTTTAACTAAAATCGTGCACTAACCATCACAGTTTTT
65 AAAACTTT-TCGGGTCAATTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-G---GT
* * * * *
785 TTTTGGCTAAAAACGTGTTTC-GAGGTCCCAAG-TCAGTTTTGCATGATTTTAGGCAGAAAGACT
125 TTTTGGCTAAAAACGCGTTCCGGA-GTCCC-GGCTCAATTTTGCATGATTTTTGGCAGAAAGACT
* * ** *
848 CCTTGAAATATCTATATTTATCTAATTAAATCTCAGCCACATTGTG-TTTAAGAATTTGTTTTTA
188 CCTTGAAATATCTATATTCATCGAAACAAATCTCAGCCACATTG-GATTTAAGGATTTGTTTTTA
* *
912 CGAGCATCT-GAATCTTGTTTCGATTTAATTAGAAATAAATTCGGGAAAAAAGGGAAAAACGATA
252 CGAGCATCTCGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATA
976 TTAGAAGCGTGAAAAA
317 TTAGAAGCGTGAAAAA
*
992 CCCTTCAATTTTTTTGGCGTTGAATTATATA-TTTTTCTGAGTATTCTGGCAAAAAATTGAGGAA
1 CCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAA
*
1056 AAACTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAGTAACCATCACGGTTTTTT
66 AAACTTTTCGGGTCAATTTTT-CAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTTT
** * * * * *
1121 TTCTAAAAACGCATTCCGGAGTGCCGGCTCAATTTTGCAGGATTTTTAGCACAAAGACTCCTTGA
129 GGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGA
* * * **
1186 AATATCTATATTCATCGAAACAAATGTCAACCACATTGGATATAAGGATTTGTTTTTATTAGCAT
194 AATATCTATATTCATCGAAACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
* * * *
1251 CTCG-ATCTTGTTTTGGTTTAATTAGAAATTAATTCGGAAACAAATGGAAAAACGATATTAGAAG
259 CTCGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAG
* * *
1315 GGCGAAAAG
324 CGTGAAAAA
* * * * * * *
1324 CCCATT-AATCTTTTTGGCATTGAGTTATATATTTTTTTTCTAAATATT-TTGCAAAAAATTAAG
1 CCC-TTCAATTTTTTTGGCGTTGAATTATATA--TTTTTTCTGAGTATTGTGGCAAAAAATTGAG
* ** *
1387 AAAAAACTTTTCGGG-------TT--AGTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTT
63 GAAAAACTTTTCGGGTCAATTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTT
* * * * *
1443 TGGCTAAAAACGCGTTTCAGA-TCCCGGCTTAGTTTTGAATGATTTTTGGCAGAAAGACTCCTTG
128 TGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTG
* * * *
1507 AAATATCTATATTCATC-TAACAAAATCTCAGCCACAATGGATTTAAGAATTTGATTTTACGAGC
193 AAATATCTATATTCATCGAAAC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
1571 ATCTC-AATCTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAT-GAAAAACGATATTA
257 ATCTCGAATC-TTGTTTCGATTTAATTAGAAATAAATTCGG-AAAAAAATGGAAAAACGATATTA
* *
1634 GAAACATG-AAAA
320 GAAGCGTGAAAAA
* *
1646 CCCTTCAATTTTTTTGGCGTTAAATTTTATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAA
1 CCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAA
* * *
1711 AAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGTTTGCCAACGAAATCATGTACTAACTATCACG
66 AAACTTTTCGGGTCAATTTTT-CAAAATTTTA----G-C--CGAAATCGTGTACTAACCATCACG
* * *
1776 GTTTTTGGCAAAAAACGCGTTCCGGAGTCTCGGCTCAATTTTGCATGATTTTTGG-TGTAAAGAC
123 GTTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATTTTTGGCAG-AAAGAC
* * * *
1840 TCCTTAAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGTATATAAGGATTTGTTTTTA
187 TCCTTGAAATATCTATATTCATCGAAACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA
* * *
1905 CGAGCATC-CGAATCTTGTTTTGATTTAATTAGAAATTAATTCGG-GAAAAATGGAAAAACGATA
252 CGAGCATCTCGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATA
*
1968 TTAGAAGCG-CAAAAA
317 TTAGAAGCGTGAAAAA
* * * * *
1983 GCCTGTCAATATCTTTGGCGTTGAATTATATATTTTTTCTGAATATT-TTGCAAAAAATTGA-GA
1 CCCT-TCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGA
** * *
2046 AAAACTTTTC-GG---A---TT--AGTTTTTAGCTGAAATCGTGTACTAACCATCACGATTTTTG
65 AAAACTTTTCGGGTCAATTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
* * * * ** *
2102 GCT-AAAATGCGTTTCGGA-TCCCGACTCAGTTTTAAATGATTTTTGGTAGAAAGACTCCTTGAA
130 GCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAA
* * * * * *
2165 ATATCTATATTCATC-TAACAAAATCTCTGGCATAAATGGATTTAAGAATTTGTTTTTACGAGCA
195 ATATCTATATTCATCGAAAC-AAATCTCAGCCA-CATTGGATTTAAGGATTTGTTTTTACGAGCA
* * *
2229 TTTC-AATCTTTGTTTCGATTTAATTAGAAATAAATTCTGGAAAAAAAAGAAAAAACGATATTAG
258 TCTCGAATC-TTGTTTCGATTTAATTAGAAATAAATTC-GGAAAAAAATGGAAAAACGATATTAG
*
2293 AAGCGTGAAGAA
321 AAGCGTGAAAAA
* *
2305 CCGTTCAA-TTTTTTGGCGTTAAATTATAT-TTTTTTCCTGAGTATTGTGGCAAAAAATTGAGGA
1 CCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTT-CTGAGTATTGTGGCAAAAAATTGAGGA
* ***
2368 AAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCGTAGTTTTT
65 AAAACTTTTCGGGTCAATTTTT-CAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT
*
2433 GGCTAAAAACGCGTTCCGGAG-CCTCGGCTCAATTTTGCATGATTTTTGGC-GTAAAAACTCCTT
129 GGCTAAAAACGCGTTCCGGAGTCC-CGGCTCAATTTTGCATGATTTTTGGCAG-AAAGACTCCTT
* * * *
2496 GAAAT-TTTCATATTCATCGAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTACGAG
192 GAAATATCT-ATATTCATCGAAACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAG
* *
2560 CATCT-GAATCTTGTTTCGATATAATTAG--ATTAATTCGGAAAAAAATGGAAAAACGATATTAG
256 CATCTCGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAG
*
2622 AAGCGTGAAAAG
321 AAGCGTGAAAAA
* *
2634 GCCGTCAATATTTTTT-GCGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAATTGA-GA
1 CCCTTCAAT-TTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGA
* * * * * * *
2696 TAAACGTTTCGGGTC-A---GT-----TTTTAGCCGAAATTGTGCATTAACCATCATGGTTTTTG
65 AAAACTTTTCGGGTCAATTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
* * * * ** **
2752 ACTAAAAAAGCGTTTTCCGGCG-CCATGGCTCTGTTTTGCATGATTTTTGGC-GCTGAGACTCCT
130 GCTAAAAACGCG--TTCCGGAGTCC-CGGCTCAATTTTGCATGATTTTTGGCAG-AAAGACTCCT
** * * * *
2815 TGAAATATCGT-TATTCATATAATCAAATCGCAGTCACATTGGATTTAAGGATTTGCTTTTAC-A
191 TGAAATATC-TATATTCATCGAAACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGA
* * * * ** * **
2878 TGGATCT-TAATTTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAAATATGTGAAACGATAT
255 -GCATCTCGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAT-GGAAAAACGATAT
* *
2942 TAAAAGCGTGAAAAG
318 TAGAAGCGTGAAAAA
** * * * * * *
2957 TTCTCCTATCTTTTTGGCATTGAATTATATATATTTTATGAGTATT
1 CCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATT
3003 TTTTGCCAAA
Statistics
Matches: 2204, Mismatches: 352, Indels: 230
0.79 0.13 0.08
Matches are distributed among these distances:
316 50 0.02
317 166 0.08
318 163 0.07
319 71 0.03
320 178 0.08
321 76 0.03
322 162 0.07
323 124 0.06
324 39 0.02
326 8 0.00
327 2 0.00
328 34 0.02
329 53 0.02
330 35 0.02
331 26 0.01
332 259 0.12
333 66 0.03
334 148 0.07
335 119 0.05
336 171 0.08
337 45 0.02
338 111 0.05
339 96 0.04
340 2 0.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.36
Consensus pattern (332 bp):
CCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAA
AAACTTTTCGGGTCAATTTTTCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGG
CTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAA
TATCTATATTCATCGAAACAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
CGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCG
TGAAAAA
Found at i:5724 original size:31 final size:32
Alignment explanation
Indices: 5657--5725 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 32
5647 TTTCCCCCTA
5657 AACTTTTACAAAATAGACATTTTCTCTCCAAG
1 AACTTTTACAAAATAGACATTTTCTCTCCAAG
* *
5689 --CTTTTATAAAATGGACATTTT-TC-CCAATG
1 AACTTTTACAAAATAGACATTTTCTCTCCAA-G
5718 AACTTTTA
1 AACTTTTA
5726 ATTTTGAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
28 4 0.12
29 3 0.09
30 19 0.59
31 6 0.19
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (32 bp):
AACTTTTACAAAATAGACATTTTCTCTCCAAG
Found at i:5807 original size:59 final size:60
Alignment explanation
Indices: 5716--5829 Score: 142
Period size: 59 Copynumber: 1.9 Consensus size: 60
5706 TTTTTCCCAA
* * * *
5716 TGAACTTTTAATTTTGAAATTTAAAGCCATAAACCGTCAAAATGGGGACAATTTCATTCT
1 TGAACTTTTAATTTTGAAATTTAAACCCATAAACCATCAAAATCGAGACAATTTCATTCT
* * *
5776 TGAATTTTTAA-TTTGAAACTTT-CACCCATAAACTATCAAAATCGAGACAATTTC
1 TGAACTTTTAATTTTGAAA-TTTAAACCCATAAACCATCAAAATCGAGACAATTTC
5830 CTCCATAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
59 33 0.72
60 13 0.28
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (60 bp):
TGAACTTTTAATTTTGAAATTTAAACCCATAAACCATCAAAATCGAGACAATTTCATTCT
Found at i:5996 original size:31 final size:31
Alignment explanation
Indices: 5961--6039 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
5951 TTCCGAAATA
5961 AAAGTTTGAGGGGGAAAATGTTCATATTATG
1 AAAGTTTGAGGGGGAAAATGTTCATATTATG
5992 AAAGTTTGAGGGGGAAAATGTTCATATTATG
1 AAAGTTTGAGGGGGAAAATGTTCATATTATG
*
6023 AAAGTTTAAGGGGGAAA
1 AAAGTTTGAGGGGGAAA
6040 TAATATTAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.38, C:0.03, G:0.30, T:0.29
Consensus pattern (31 bp):
AAAGTTTGAGGGGGAAAATGTTCATATTATG
Found at i:6736 original size:324 final size:320
Alignment explanation
Indices: 6163--7778 Score: 1568
Period size: 324 Copynumber: 5.0 Consensus size: 320
6153 TAAAATTTTG
* * *
6163 TAAAAACTGTCCCGGAAA-ATTTTTCCTT-AATTCTTTGCGACAATACTCAGAAAAAATATATAA
1 TAAAAACTGACCC-GAAATATTTTTTCTTGAATT-TTTGCCACAATACTCAGAAAAAATATATAA
* *
6226 TTCAACGCCAAAAAAATTGAAGGGGTTTTCACGCTTCTAATATCGGTTTTCCATTTTTTTCCAAA
64 TTCAACGCCAAAAAAATTGAAGGGTTTTTCACACTTCTAATATC-GTTTTCCATTTTTTTCCAAA
* * * * * *
6291 TTTTTTTTAACTAAAGCGAAACAAGATACAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
128 TTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTG
* * * *
6356 GCTGAGATTTGGTTAGATGAATATTGATATTTCAAGGAGCCTTTCTACCAAAAATCATGCAAAAC
193 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAAC
* *
6421 TGAGCCGGTTCCCCGAAACGTGTTTTTAGCCCAAAAACTGTGATGATTAGTACACAATTTCGGC
258 TGAGCCGG-GCCCCGAAACGCGTTTTTAGCCCAAAAACTGTGATGATTAGTACACAATTTCGGC
* * * * * *
6485 TAAAAACAGACCCGAAATTTTTTTTTCTTGAATTTTTGCCACGATACTCAGGAAAAATATACAAA
1 TAAAAACTGACCCGAAA-TATTTTTTCTTGAATTTTTGCCACAATACTCAGAAAAAATATATAAT
* *
6550 TCAACGCAAAAAAAATTGAAGGGTTTTTCACACTTCTAATATCGTTCTTCCATTTTTTTCCGAAT
65 TCAACGCCAAAAAAATTGAAGGGTTTTTCACACTTCTAATATCGTT-TTCCATTTTTTTCCAAAT
* * * *
6615 TAATTTCTAATTAAATCGAAACGAGATTCAGATGCTCGTAAAAACAAATCATTAAATTGATTGTG
129 T-ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTG
* *
6680 GCTGGGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAAC
193 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAAC
* * * * *
6745 TGAGGCGGGGCCCCGAAACACGTTTTTAGCCAAAAAAATGTGATGTTTAGTACACGACTTCACTA
258 TGA-GCCGGGCCCCGAAACGCGTTTTTAGCCCAAAAACTGTGATGATTAGTACAC-A----A-T-
**
6810 AAATTTTGC
315 ---TTCGGC
* * *
6819 -AAAAACTGACTCGAAA-ATTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
1 TAAAAACTGACCCGAAATATTTTTTCTTGAA-TTTTTGCCACAATACTCAGAAAAAATATATAAT
* * * * *
6882 TCAAAGCC-AAAAAATTGAAGAGTTTTTCACGCTTTTAATATCGTTTTTCCATTTTTTTCCGAAT
65 TCAACGCCAAAAAAATTGAAGGGTTTTTCACACTTCTAATATCG-TTTTCCATTTTTTTCCAAAT
* * * * * * * *
6946 TATTTCCAATTAAATCGAAACAAGATTTAAATGCTTGCAAAAACAAATTCTTAATTTTAATGTGG
129 TATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGG
* * * *
7011 CTGAGATTTTGTTAGATGAATATAAATATTTCAAGGAGT-TTT-TTCTCACAAAATTCATGCAAT
194 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGTGC-CA-AAAA-TCATGCAAA
* * * * * *
7074 ACTGAGCCAGGGCCGCGGAATGCGTTTTCAGCCCAAAAACCGTGATGGTTAGTACACAATTTCGG
256 ACTGAGCC-GGGCCCCGAAACGCGTTTTTAGCCCAAAAACTGTGATGATTAGTACACAATTTCGG
7139 C
320 C
* *
7140 TAAAAACTGACCCG-AATATTTTTT-TAGAATTTTTGCCACAATACTCATAAAAAATATATAATT
1 TAAAAACTGACCCGAAATATTTTTTCTTGAATTTTTGCCACAATACTCAGAAAAAATATATAATT
* * * *
7203 CAACGCCAAAAAGATTGACGGGATTTTCACACTTCTAATATCATTTTCCA--TTTTTCCAAATTA
66 CAACGCCAAAAAAATTGAAGGGTTTTTCACACTTCTAATATCGTTTTCCATTTTTTTCCAAATT-
*
7266 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG-GAAAACAAATCCTTAAATTCAATGTGGC
130 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGC
* * ** * * * **
7330 TGAGATTTGATTAGATGAATATAGATCTTTCAAGGAGTCTCGGCGCAAAAAATCATTCAAAACAA
195 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAACTG
* * * * *
7395 AGTCGGGACCCAAAACGCGTTTTTAGCCAAAAAAATCGTGATTATACGATTTCAGCTA-A-AATT
260 AGCCGGGCCCCGAAACGCGTTTTTAGCC-CAAAAA-C-TG-TGAT--GA-TT-AG-TACACAATT
*
7458 TTGG-
316 TCGGC
* * * * * * * * * * *
7462 -AAAAAATGACCC-AAA-AGTTGTTCCTAAATTTTTGGCTAAAATACTAATAAAATATATAAAAT
1 TAAAAACTGACCCGAAATATTTTTTCTTGAATTTTT-GCCACAATACTCAGAAAAAATATATAAT
* * * * * ** * * * *
7524 TTAACGTCAAACATATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCA-TTTTTTCCTGAAT
65 TCAACGCCAAAAAAATTGAAGGGTTTTTCACACTTCTAATATCGTTTTCCATTTTTTTCC-AAAT
* * *
7588 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAAAATTCTTAAATCCAATG
129 T-ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT--AAAAACAAATCCTTAAATTCAATG
* * * * * * * *
7653 TAGCTGAGATTTGATTAGATGAGTATGGATAGCTT-AAAGAGTCTTGGTGTCAAAAATCATGCAA
191 TGGCTGAGATTTGGTTAGATGAATATAGATA-TTTCAAGGAGTCTTTGTGCCAAAAATCATGCAA
* * ** * *
7717 AACTTAGCCGGGGCCTC-AGAACGCG-TTTTAG-CCAAAAAAAGTGATGATTATTACACGATTTC
255 AACTGAGCC-GGGCCCCGA-AACGCGTTTTTAGCCCAAAAACTGTGATGATTAGTACACAATTTC
7779 TGATAATATT
Statistics
Matches: 1065, Mismatches: 179, Indels: 103
0.79 0.13 0.08
Matches are distributed among these distances:
316 18 0.02
317 19 0.02
318 76 0.07
319 41 0.04
320 57 0.05
321 60 0.06
322 99 0.09
323 109 0.10
324 203 0.19
325 13 0.01
326 2 0.00
327 83 0.08
328 15 0.01
329 6 0.01
330 96 0.09
331 113 0.11
332 37 0.03
333 14 0.01
334 4 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (320 bp):
TAAAAACTGACCCGAAATATTTTTTCTTGAATTTTTGCCACAATACTCAGAAAAAATATATAATT
CAACGCCAAAAAAATTGAAGGGTTTTTCACACTTCTAATATCGTTTTCCATTTTTTTCCAAATTA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCT
GAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAACTGA
GCCGGGCCCCGAAACGCGTTTTTAGCCCAAAAACTGTGATGATTAGTACACAATTTCGGC
Found at i:7493 original size:654 final size:651
Alignment explanation
Indices: 6152--7778 Score: 1792
Period size: 655 Copynumber: 2.5 Consensus size: 651
6142 ACGATTTCGG
* * * * *
6152 CTAAAATTTTGTAAAAACTGTC-CCGGAAAA-TTTTTCCTTAATTCTTTGCGACAATACTCAGAA
1 CTAAAATTTTGCAAAAAATGACTCC--AAAATTTTTTCCTCAATTCTTTGCCACAATACTCAGAA
* *
6215 AAAATATATAATTCAACGCCAAAAAAATTGAAGGGGTTTTCACGCTTCTAATATCGGTTTTCCAT
64 AAAATATATAATTCAAAGCCAAAAAAATTGAAGAGGTTTTCACGCTTCTAATATCGGTTTTCCAT
* ** * *
6280 TTTTTTCCAAATTTTTTTTAACTAAAGCGAAACAAGATACAGATGCTCGTAAAAACAAATCCTTA
129 TTTTTTCCAAATTATTTCCAACTAAAGCGAAACAAGATACAAATGCTCGCAAAAACAAATCCTTA
**
6345 AATCCAATGTGGCTGAGATTTGGTTAGATGAATATTGATATTTCAAGGAGCCTTTCTACCAAAAA
194 AATCCAATGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAAGGAGCCTTTCTACCAAAAA
* * * *
6410 TCATGCAAAACTGAGCCGGTTCCCCGAAACGTGTTTTTAGCCCAAAAACTGTGATGATTAGTACA
259 TCATGCAAAACTGAGCCGGTGCCCCGAAACGCGTTTTCAGCCCAAAAACCGTGATGATTAGTACA
* * * *
6475 CAATTTCGGCTAAAAACAGACCCGAAATTTTTTTTTCTTGAATTTTTGCCACGATACTCAGGAAA
324 CAATTTCGGCTAAAAACAGACCCGAAATTATTTTTTCTAGAATTTTTGCCACAATACTCAGAAAA
* *
6540 AATATACAAATCAACGCAAAAAAAATTGAAGGGTTTTTCACACTTCTAATATCGTTCTTCCATTT
389 AATATACAAATCAACGCAAAAAAAATTGAAGGGATTTTCACACTTCTAATATCATTCTTCCA-TT
* *
6605 TTTTCCGAATTAATTTCTAATTAAATCGAAACGAGATTCAGATGCTCGTAAAAACAAATCATTAA
453 TTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAA
* * * * * ** * *
6670 ATTGATTGTGGCTGGGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAAT
518 ATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCAAAAAAT
** * *
6735 CATGCAAAACTGAGGCGGGGCCCCGAAACACGTTTTTAGCCAAAAAAATGTGATGTTTAGTACAC
583 CATGCAAAACAAAGGCGGGGACCCAAAACACGTTTTTAGCCAAAAAAATGTGA--TTTAGTA-AC
6800 GACTTCA
645 GACTTCA
* * *
6807 CTAAAATTTTGCAAAAACTGACTCGAAAATTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAA
1 CTAAAATTTTGCAAAAAATGACTCCAAAATTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAA
* * *
6872 AATATATAATTCAAAGCC-AAAAAATTGAAGAGTTTTTCACGCTTTTAATATCGTTTTTCCATTT
66 AATATATAATTCAAAGCCAAAAAAATTGAAGAGGTTTTCACGCTTCTAATATCGGTTTTCCATTT
* * * ** * * *
6936 TTTTCCGAATTATTTCCAATTAAATCGAAACAAGATTTAAATGCTTGCAAAAACAAATTCTTAAT
131 TTTTCCAAATTATTTCCAACTAAAGCGAAACAAGATACAAATGCTCGCAAAAACAAATCCTTAAA
** * ** *
7001 TTTAATGTGGCTGAGATTTTGTTAGATGAATATAAATATTTCAAGGAGTTTTTTCT-CACAAAAT
196 TCCAATGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAAGGAG-CCTTTCTAC-CAAAAA
* * * * *
7065 TCATGCAATACTGAGCCAGG-GCCGCGGAATGCGTTTTCAGCCCAAAAACCGTGATGGTTAGTAC
259 TCATGCAAAACTGAGCC-GGTGCCCCGAAACGCGTTTTCAGCCCAAAAACCGTGATGATTAGTAC
* *
7129 ACAATTTCGGCTAAAAACTGACCCG-AA-TATTTTTT-TAGAATTTTTGCCACAATACTCATAAA
323 ACAATTTCGGCTAAAAACAGACCCGAAATTATTTTTTCTAGAATTTTTGCCACAATACTCAGAAA
* * * * *
7191 AAATATATAATTCAACGCCAAAAAGATTGACGGGATTTTCACACTTCTAATATCATT-TTCCA-T
388 AAATATACAAATCAACGCAAAAAAAATTGAAGGGATTTTCACACTTCTAATATCATTCTTCCATT
* *
7254 TTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG-GAAAACAAATCCTTAA
453 TTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAA
*
7318 ATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATCTTTCAAGGAGTCTCGGCGCAAAAAAT
518 ATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCAAAAAAT
* * *
7383 CATTCAAAACAAAGTC-GGGACCCAAAACGCGTTTTTAGCCAAAAAAATCGTGA-TTA-T-ACGA
583 CATGCAAAACAAAGGCGGGGACCCAAAACACGTTTTTAGCCAAAAAAAT-GTGATTTAGTAACGA
*
7444 TTTCA
647 CTTCA
* * * * * * * *
7449 GCTAAAATTTTGGAAAAAATGAC-CCAAAAGTTGTTCCTAAATT-TTTGGCTAAAATACTAATAA
1 -CTAAAATTTTGCAAAAAATGACTCCAAAATTTTTTCCTCAATTCTTT-GCCACAATACTCAGAA
* * * * * * * * *
7512 AATATATAAAATTTAACGTCAAACATATTG--GAGGACTTTTCACGCTTTTAATATC-GTTTTTC
64 AAAATATATAATTCAAAGCCAAAAAAATTGAAGAGG--TTTTCACGCTTCTAATATCGGTTTTCC
* * * * * * * *
7574 A-TTTTTTCCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAAAAAA
127 ATTTTTTTCC-AAATT-ATTTCCAACTAAAGCGAAACAAGATACAAATGCTCG--CAAAAACAAA
* * * * ** * * * ** *
7638 TTCTTAAATCCAATGTAGCTGAGATTTGATTAGATGAGTATGGATAGCTT-AAAGAGTCTTGGTG
188 TCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAAATA-TTTCAAGGAGCCTTTCTA
* * * * **
7702 TCAAAAATCATGCAAAACTTAGCCGGGGCCTC-AGAACGCGTTTT-AG-CCAAAAAAAGTGATGA
252 CCAAAAATCATGCAAAACTGAGCCGGTGCCCCGA-AACGCGTTTTCAGCCCAAAAACCGTGATGA
* *
7764 TTATTACACGATTTC
316 TTAGTACACAATTTC
7779 TGATAATATT
Statistics
Matches: 825, Mismatches: 128, Indels: 51
0.82 0.13 0.05
Matches are distributed among these distances:
641 14 0.02
642 88 0.11
643 82 0.10
644 38 0.05
645 53 0.06
646 2 0.00
647 29 0.04
648 85 0.10
649 47 0.06
651 5 0.01
652 73 0.09
653 7 0.01
654 144 0.17
655 155 0.19
656 3 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (651 bp):
CTAAAATTTTGCAAAAAATGACTCCAAAATTTTTTCCTCAATTCTTTGCCACAATACTCAGAAAA
AATATATAATTCAAAGCCAAAAAAATTGAAGAGGTTTTCACGCTTCTAATATCGGTTTTCCATTT
TTTTCCAAATTATTTCCAACTAAAGCGAAACAAGATACAAATGCTCGCAAAAACAAATCCTTAAA
TCCAATGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAAGGAGCCTTTCTACCAAAAATC
ATGCAAAACTGAGCCGGTGCCCCGAAACGCGTTTTCAGCCCAAAAACCGTGATGATTAGTACACA
ATTTCGGCTAAAAACAGACCCGAAATTATTTTTTCTAGAATTTTTGCCACAATACTCAGAAAAAA
TATACAAATCAACGCAAAAAAAATTGAAGGGATTTTCACACTTCTAATATCATTCTTCCATTTTT
TCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAAATT
CAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCAAAAAATCAT
GCAAAACAAAGGCGGGGACCCAAAACACGTTTTTAGCCAAAAAAATGTGATTTAGTAACGACTTC
A
Found at i:9449 original size:308 final size:307
Alignment explanation
Indices: 8888--9469 Score: 775
Period size: 308 Copynumber: 1.9 Consensus size: 307
8878 ATGTGGCTGA
* * * *
8888 GATTTGATTAGAAGAATATAGATATTTCAAGGAGTCTTGGAGTCAAAAATCATGCAAAACTGATC
1 GATTTGATTAGAAGAATATAAATATTTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAACTGAAC
** * *
8953 TGGGGCCCGGAACGCGTTTTTAGCCCCAAAGAAAACCGTGATGGTACACGATTTCAACTAATATT
66 CAGCGCCCGGAACGCGTTTTTAG-CCC-AAGAAAACCGTGATGGTACACGATTTCAACTAAAATT
* * * **
9018 TTGCAAAAATTGACCCGGAATATTTTTCCTCATTTTTAGCCACAATACTCATAAAAATATATAAT
129 TTACAAAAATTGACCCGAAAGATAATTCCTCATTTTTAGCCACAATACTCATAAAAATATATAAT
* * *
9083 TTAATGCAAAAAAGATTGAAGGGCTTTTCACGTTTCTAATATCGTTTTTCCTATTTTTTC-GAAT
194 TCAATACAAAAAAGATTGAAGGGCTTTTCACGTTTCTAATATCGTTTTTCATATTTTTTCTGAAT
9147 TAATTTT-TAATTAAGTCAAAGCTCAAATCCTTGTAAAAAGAATGGCTAG
259 T-ATTTTCTAATTAAGTCAAAGCTCAAATCCTTGTAAAAAGAATGGCTAG
* * *
9196 GATTTGGTTAGATGAATATAAATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAAC
1 GATTTGATTAGAAGAATATAAATATTTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAACTGAAC
* ** **
9261 CAGCTCTTGGAACGCGTTTTTAG-CC-A-AAAA-CGTGATGATTGATACACGATTTCGGCTAAAA
66 CAGCGCCCGGAACGCGTTTTTAGCCCAAGAAAACCGTGATG---G-TACACGATTTCAACTAAAA
9322 TTTTACAAAAATTGACCCGAAAGATAATTCCTCAATTTTTAGCCACAATACTCATAAAAAATATA
127 TTTTACAAAAATTGACCCGAAAGATAATTCCTC-ATTTTTAGCCACAATACTCAT-AAAAATATA
* *
9387 TAATTCAATACCAAAAAGATTGAAGGGC-TTTCACGCTTT-TAATGTCGTTTTTCATAATTTTTT
190 TAATTCAATACAAAAAAGATTGAAGGGCTTTTCACG-TTTCTAATATCGTTTTTCAT-ATTTTTT
9450 CTGAATTATTTTCTAATTAA
253 CTGAATTATTTTCTAATTAA
9470 ATCGAAATAA
Statistics
Matches: 238, Mismatches: 26, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
302 7 0.03
303 4 0.02
304 1 0.00
305 1 0.00
306 46 0.19
307 42 0.18
308 125 0.53
309 12 0.05
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (307 bp):
GATTTGATTAGAAGAATATAAATATTTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAACTGAAC
CAGCGCCCGGAACGCGTTTTTAGCCCAAGAAAACCGTGATGGTACACGATTTCAACTAAAATTTT
ACAAAAATTGACCCGAAAGATAATTCCTCATTTTTAGCCACAATACTCATAAAAATATATAATTC
AATACAAAAAAGATTGAAGGGCTTTTCACGTTTCTAATATCGTTTTTCATATTTTTTCTGAATTA
TTTTCTAATTAAGTCAAAGCTCAAATCCTTGTAAAAAGAATGGCTAG
Found at i:10412 original size:336 final size:333
Alignment explanation
Indices: 9732--10556 Score: 1023
Period size: 336 Copynumber: 2.5 Consensus size: 333
9722 TATATATATG
* * * *
9732 TATAAAATTTAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTT
1 TATATAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTT
* * * **
9797 TTCAGAATTAATTTCTAATTAAATCAAAACAAGATTCAGTTATTCGTAAAAA-AAATTCTTAAAT
66 TTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAAT
** ** * * * * * *
9861 CCAATGTATCTGAGATTTGACCAGAAGAATATGGAT-ATCTCAAGGT-GTCTTGGCGCCCAAAAC
131 CCAATGTGGCTGAGATTTGATTAGATGAATATAGATAAT-TCAAGGTAGTCTCGGAGCCAAAAAT
* ** * * * * *
9924 CATGAAAAACTGAGCCGGGGCTCCGGAACGCTTTTTTTGGCAAAAAACTGTGATGGTTA-TTACA
195 CATGCAAAACTGAGCCGGATCCCCGGAACGC-GTTTTTAGCAAAAAACCGTGATGGTTAGATACA
* *
9988 CGATTTCGGCTAAAATTTTATAAAAATTGACCCGAAAGATATCTCCTCAATTTTTGACTAAAATA
259 CGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAGATATCTCCTCAATTTTTGGCTAAAATA
10053 CTCATAAAAA
324 CTCATAAAAA
* * ** *
10063 TATATATTTCAACGCCAAAAAGATTGAAGGGCTTTTCACG-TTTCTAATATAATTTTTCCTATTT
1 TATATAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTT-TAATATCGTTTTTCATATTT
* *
10127 TTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCATATGCTCGTAAAAACAAATGCTTAAA
65 TTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAA
*
10192 TCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAATTCAA-GTAGTCTCGGAGTCAAAAAT
130 TCCAATGTGGCTGAGATTTGATTAGATGAATATAGATAATTCAAGGTAGTCTCGGAGCCAAAAAT
* * * *
10256 CATGCGAAATTGAGGCGGATCCCCAGAACGCGTTTTTAGCGAAAAAACCGTGATGGTTAGTTAGT
195 CATGCAAAACTGAGCCGGATCCCCGGAACGCGTTTTTAGC-AAAAAACCGTGATGGTTAG--A-T
* * * * *
10321 ACAGGATTTCGGCTAAAATTTTGCAAAAATTGACACGAAAGATTTCTCCTCAATTGTTGGCTAAA
256 ACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAGATATCTCCTCAATTTTTGGCTAAA
10386 ATACTCATAAAAA
321 ATACTCATAAAAA
* * * * *
10399 TATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCATGCTTTTAATATCGTATTTCTTATTTT
1 TATATAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTT
* *
10464 TTCTAAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAAT
66 TTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAAT
* * * * *
10529 CCAATATTGTTGAAATTTGGTTAGATGA
131 CCAATGTGGCTGAGATTTGATTAGATGA
10557 TGTAAAGTAT
Statistics
Matches: 422, Mismatches: 62, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
330 3 0.01
331 107 0.25
332 97 0.23
333 2 0.00
336 210 0.50
337 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (333 bp):
TATATAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTT
TTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAAT
CCAATGTGGCTGAGATTTGATTAGATGAATATAGATAATTCAAGGTAGTCTCGGAGCCAAAAATC
ATGCAAAACTGAGCCGGATCCCCGGAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGATACACG
ATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAGATATCTCCTCAATTTTTGGCTAAAATACT
CATAAAAA
Done.