Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014206.1 Corchorus olitorius cultivar O-4 contig14239, 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: 56725
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:16620 original size:2 final size:2
Alignment explanation
Indices: 16615--16654 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
16605 GAGGAAATTT
16615 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16655 AAAGTAAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16948 original size:16 final size:16
Alignment explanation
Indices: 16927--16962 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
16917 CAGTTGGAAT
16927 CCTCTTTCCAATGATA
1 CCTCTTTCCAATGATA
*
16943 CCTCTTTCCAATGGTA
1 CCTCTTTCCAATGATA
16959 CCTC
1 CCTC
16963 ATTTGCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.19, C:0.36, G:0.08, T:0.36
Consensus pattern (16 bp):
CCTCTTTCCAATGATA
Found at i:19307 original size:20 final size:21
Alignment explanation
Indices: 19293--19369 Score: 100
Period size: 22 Copynumber: 3.6 Consensus size: 21
19283 TTTATGGAAT
*
19293 TTATCACAATTTTATAGGTAA
1 TTATCAAAATTTTATAGGTAA
* * *
19314 TTATCAAAATTTCATACGATAG
1 TTATCAAAATTTTATA-GGTAA
19336 TTATCAAAATTTTATAGGATAA
1 TTATCAAAATTTTATAGG-TAA
19358 TTATCAAAATTT
1 TTATCAAAATTT
19370 CATAAAAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
21 15 0.32
22 32 0.68
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (21 bp):
TTATCAAAATTTTATAGGTAA
Found at i:19315 original size:22 final size:20
Alignment explanation
Indices: 19282--19369 Score: 88
Period size: 22 Copynumber: 4.2 Consensus size: 20
19272 TATTAAAGTT
*
19282 TTTTAT-GGAATTTATCACAA
1 TTTTATAGGAA-TTATCAAAA
19302 TTTTATAGGTAATTATCAAAA
1 TTTTATAGG-AATTATCAAAA
* *
19323 TTTCATACGATAGTTATCAAAA
1 TTTTATAGGA-A-TTATCAAAA
19345 TTTTATAGGATAATTATCAAAA
1 TTTTATAGG--AATTATCAAAA
19367 TTT
1 TTT
19370 CATAAAAATA
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
20 7 0.12
21 18 0.32
22 30 0.53
23 1 0.02
24 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (20 bp):
TTTTATAGGAATTATCAAAA
Found at i:20159 original size:155 final size:155
Alignment explanation
Indices: 19929--20545 Score: 930
Period size: 155 Copynumber: 4.0 Consensus size: 155
19919 TTAATTCCAG
* * * * * * *
19929 TATCCCCAAAGTCATATACTTTATTCCCAAAATATATCTCATCATCCCCAAAGACTTATATGCAC
1 TATCCCCAACGTGATA-ACTTCATACCCAAAATATATCTCATTATACCCAAAAACTTATATGCAC
* * * *
19994 CATCCTCAATTCATTTTTTGGTATAAAGCATATTCATATATAACCAAAACCAACTTTAAACATGA
65 CATCCCCAATTCGTTTTTTGGTATAAAGCTTATTCATATATACCCAAAACCAACTTTAAACATGA
*
20059 CTTTCTCCCCAAAGTGGAGAATGAGA
130 TTTTCTCCCCAAAGTGGAGAATGAGA
* * *
20085 TATCCCCAATGTGATAACTTCATAACCAAAATATATCTCATTATACCCAAAAACCTATATGCACC
1 TATCCCCAACGTGATAACTTCATACCCAAAATATATCTCATTATACCCAAAAACTTATATGCACC
* *
20150 ATCCCCAATTCGCTTTTTGGTATAAAGCTTATTCATATATACCCAAAACCAACCTTAAACATGAT
66 ATCCCCAATTCGTTTTTTGGTATAAAGCTTATTCATATATACCCAAAACCAACTTTAAACATGAT
* * *
20215 TTTCTCCTCAAAGTGAAGAATGTGA
131 TTTCTCCCCAAAGTGGAGAATGAGA
**
20240 TATCCCCAACGTGATAACTTCATACCCCTAATATATCTCATTATACCCAAAAACTTATATGCACC
1 TATCCCCAACGTGATAACTTCATACCCAAAATATATCTCATTATACCCAAAAACTTATATGCACC
* *
20305 ATCCCCAATTCGTTTTTTGGTATAAAGCTTATTCATATATACCCAACACCATCTTTAAACATGAT
66 ATCCCCAATTCGTTTTTTGGTATAAAGCTTATTCATATATACCCAAAACCAACTTTAAACATGAT
* *
20370 TTTCTCCCCAAAGTGTAGAATGGGA
131 TTTCTCCCCAAAGTGGAGAATGAGA
* *
20395 TAT-CCCAACGTGATAACTTAATACCCAAAATATATCTCATTATACCCCAAAACTTATATGCACC
1 TATCCCCAACGTGATAACTTCATACCCAAAATATATCTCATTATACCCAAAAACTTATATGCACC
* * *
20459 ATCCCCAATTCGTTTTTTGGTCTAAAGCTTATTCATATATACCCAACACCGACTTTAAACATGAT
66 ATCCCCAATTCGTTTTTTGGTATAAAGCTTATTCATATATACCCAAAACCAACTTTAAACATGAT
*
20524 TTTCTCCCCAAAGTGGAAAATG
131 TTTCTCCCCAAAGTGGAGAATG
20546 TCAATCTCTA
Statistics
Matches: 421, Mismatches: 40, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
154 139 0.33
155 268 0.64
156 14 0.03
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (155 bp):
TATCCCCAACGTGATAACTTCATACCCAAAATATATCTCATTATACCCAAAAACTTATATGCACC
ATCCCCAATTCGTTTTTTGGTATAAAGCTTATTCATATATACCCAAAACCAACTTTAAACATGAT
TTTCTCCCCAAAGTGGAGAATGAGA
Found at i:20524 original size:309 final size:310
Alignment explanation
Indices: 19959--20546 Score: 946
Period size: 309 Copynumber: 1.9 Consensus size: 310
19949 TTATTCCCAA
* * *
19959 AATATATCTCATCATCCCCAAAGACTTATATGCACCATCCTCAATTCATTTTTTGGTATAAAGCA
1 AATATATCTCATCATACCCAAAAACTTATATGCACCATCCCCAATTCATTTTTTGGTATAAAGCA
20024 TATTCATATATAACCAAAACCAACTTTAAACATGACTTTCTCCCCAAAGTGGAGAATGAGATATC
66 TATTCATATATAACCAAAACCAACTTTAAACATGACTTTCTCCCCAAAGTGGAGAATGAGATATC
* *
20089 CCCAATGTGATAACTTCATAACCAAAATATATCTCATTATACCCAAAAACCTATATGCACCATCC
131 CCCAACGTGATAACTTAATAACCAAAATATATCTCATTATACCCAAAAACCTATATGCACCATCC
20154 CCAATTCGCTTTTTGGTATAAAGCTTATTCATATATACCCAAAACCAACCTTAAACATGATTTTC
196 CCAATTCGCTTTTTGGTATAAAGCTTATTCATATATACCCAAAACCAACCTTAAACATGATTTTC
*
20219 TCCTCAAAGT-GAAGAATGTGATATCCCCAACGTGATAACTTCATACCCCT
261 TCCCCAAAGTGGAA-AATGTGATATCCCCAACGTGATAACTTCATACCCCT
* * *
20269 AATATATCTCATTATACCCAAAAACTTATATGCACCATCCCCAATTCGTTTTTTGGTATAAAGCT
1 AATATATCTCATCATACCCAAAAACTTATATGCACCATCCCCAATTCATTTTTTGGTATAAAGCA
* * * * * *
20334 TATTCATATATACCCAACACCATCTTTAAACATGATTTTCTCCCCAAAGTGTAGAATGGGATAT-
66 TATTCATATATAACCAAAACCAACTTTAAACATGACTTTCTCCCCAAAGTGGAGAATGAGATATC
* * *
20398 CCCAACGTGATAACTTAATACCCAAAATATATCTCATTATACCCCAAAACTTATATGCACCATCC
131 CCCAACGTGATAACTTAATAACCAAAATATATCTCATTATACCCAAAAACCTATATGCACCATCC
* * * * *
20463 CCAATTCGTTTTTTGGTCTAAAGCTTATTCATATATACCCAACACCGACTTTAAACATGATTTTC
196 CCAATTCGCTTTTTGGTATAAAGCTTATTCATATATACCCAAAACCAACCTTAAACATGATTTTC
20528 TCCCCAAAGTGGAAAATGT
261 TCCCCAAAGTGGAAAATGT
20547 CAATCTCTAA
Statistics
Matches: 254, Mismatches: 23, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
309 134 0.53
310 120 0.47
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (310 bp):
AATATATCTCATCATACCCAAAAACTTATATGCACCATCCCCAATTCATTTTTTGGTATAAAGCA
TATTCATATATAACCAAAACCAACTTTAAACATGACTTTCTCCCCAAAGTGGAGAATGAGATATC
CCCAACGTGATAACTTAATAACCAAAATATATCTCATTATACCCAAAAACCTATATGCACCATCC
CCAATTCGCTTTTTGGTATAAAGCTTATTCATATATACCCAAAACCAACCTTAAACATGATTTTC
TCCCCAAAGTGGAAAATGTGATATCCCCAACGTGATAACTTCATACCCCT
Found at i:21748 original size:220 final size:222
Alignment explanation
Indices: 21365--22865 Score: 1772
Period size: 220 Copynumber: 6.9 Consensus size: 222
21355 AACAATCTAG
* *
21365 TATTAGATGGCACTAAAATGATATAGACGGGGTTTATTCAATTAATTAGGATGAAAAATATGGAT
1 TATTAGATGGCACTAAAATCATATAGACAGGGTTTATTCAATTAATTAGGATGAAAAATATGGAT
* *
21430 TAAAACACTTTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGACAATCTCTAAAGAATTTGGG
66 TAAAACACTGTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGTCAATCTCTAAAGAATTTGGG
* * * *
21495 GATGATGCATATGATTATTTGGAGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGG
131 GATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATTACTTTGGG
21560 GATACTGAATTTTGCATTTT-TTTAAT
196 GATACTGAATTTTGCATTTTGTTTAAT
*
21586 TATTAGATGGAACTAAAATCATATAGACAGGGTTTATTCAATTAATTAGGATG-AAAATATGGAT
1 TATTAGATGGCACTAAAATCATATAGACAGGGTTTATTCAATTAATTAGGATGAAAAATATGGAT
* * * **
21650 TAAAACACTTTTTAAAGCCAATTTTGGGTATCTGAGAAAAAATGTCAATCTTTAAAGAAAATGGG
66 TAAAACACTGTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGTCAATCTCTAAAGAATTTGGG
* * * * *
21715 GATGGTGCATATGATTATTTTGGAATGATGAGAAATGATTTGGGTATAAACTATATCAGTTTGGG
131 GATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATTACTTTGGG
21780 GATACTGAATTTTGCATTTTGTTTAAT
196 GATACTGAATTTTGCATTTTGTTTAAT
*
21807 TATTACATGGCACTAAAATCATATAGAC-GGGTTTATTCAATTAATTAGGATGAAAAATATGGAT
1 TATTAGATGGCACTAAAATCATATAGACAGGGTTTATTCAATTAATTAGGATGAAAAATATGGAT
* * * * *
21871 TAAAGCACTTTTTAAAGCCAATTTTGGGTAAATGAGAAAAAGTTGTCAATCTCTAAAGAATTTAG
66 TAAAACACTGTTTAAAGCCAATTTTGGGTATATGAGAAAAA-ATGTCAATCTCTAAAGAATTTGG
*
21936 GGATTGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATTACTTT-G
130 GGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATTACTTTGG
* *
22000 GGACACTGAATTTTGCTTTTTGTTT-A-
195 GGATACTGAATTTTGCATTTTGTTTAAT
*
22026 -ATTAGATGGCACTAAAATCATATAGACAGGGTTTATTCAATTAATTAGAATGAAAAATATGGAT
1 TATTAGATGGCACTAAAATCATATAGACAGGGTTTATTCAATTAATTAGGATGAAAAATATGGAT
* * *
22090 TAAAACA-TGTTTGAAGCCAATTTTGGGTATATGAGAAAAAAAAAGTCAATCTTTAAAGAATTTG
66 TAAAACACTGTTTAAAGCCAATTTTGGGTATATGAG--AAAAAATGTCAATCTCTAAAGAATTTG
* * *
22154 GGGATGGTGCATATGATTATTTAGGGATTATGAGAAATGATTTGGGTATAAAGTATATTACTGTG
129 GGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATTACTTTG
22219 GGGATACTGAATTTTGCATTTTGTTTAAT
194 GGGATACTGAATTTTGCATTTTGTTTAAT
* ** * ** *
22248 TATTAAATGATACTAAATTCATATAGATTGGGTTTATATTCAATTAATTAGGATG-AAAATAT-T
1 TATTAGATGGCACTAAAATCATATAGACAGGG-TT-TATTCAATTAATTAGGATGAAAAATATGG
* * * * *
22311 ATTAAAACAC-GTTTAAAGCCAATTTTGGGTTTAT-A-AAAAATTGTTAATCTCTAAAAAATTTA
64 ATTAAAACACTGTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGTCAATCTCTAAAGAATTTG
* * * * * * **
22373 GGGATGATG-AGCA--ATTATTTGGGTAT-A-AAGTATATTACTTTTGGG-ATACTG-A-A-T--
129 GGGATGGTGCA-TATGATTATTTGGGGATGATGAG-AAATGA--TTTGGGTATAAAGTATATTAC
**
22427 TTT---G---C---ATTTTG---TTTAATT-AT
190 TTTGGGGATACTGAATTTTGCATTTTGTTTAAT
* * ** * * * * * *
22447 TAGATGGCACT-AAAATCATAT-AGAT-G---GGGTTTATTCAATTAGTTAGAATGAAAAATATG
1 TA-TTAG-A-TGGCACTAAAATCATATAGACAGGGTTTATTCAATTAATTAGGATGAAAAATATG
* * *
22506 GATTAAAACAC-GTTTGAAGCCAATTTTGGGTATATGAGAAAAAATGTAAATCTCTAAATAATTT
63 GATTAAAACACTGTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGTCAATCTCTAAAGAATTT
* *
22570 GTGGATGGTGCATATGATTATTTGGGGATAATGAGAAATGATTTGGGTATAAAGTATATTACTGT
128 GGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATTACT-T
22635 T-GGGATACTGAATTTTGCATTTTGTTTAAT
192 TGGGGATACTGAATTTTGCATTTTGTTTAAT
* *
22665 TATTAGATGGCACTAAATTCATATAGACTGGGTTTATTCAATTAATTAGGATG-AAAATAT-GAT
1 TATTAGATGGCACTAAAATCATATAGACAGGGTTTATTCAATTAATTAGGATGAAAAATATGGAT
* * * *
22728 TAAAACAC-GTTTAAAGCCAATTTTGAGTTTAT-A-AAAAATTGTTAATCTCTCAAA-AATTTGG
66 TAAAACACTGTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGTCAATCTCT-AAAGAATTTGG
* * * *
22789 GGATGGTGCTTATGATTATTTGGGGATGATGAGAAATTATTTGGGAATAAAGTATATAACTTTGG
130 GGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATTACTTTGG
*
22854 GGATACTTAATT
195 GGATACTGAATT
22866 GAATTTATAG
Statistics
Matches: 1097, Mismatches: 127, Indels: 116
0.82 0.09 0.09
Matches are distributed among these distances:
194 17 0.02
195 9 0.01
196 35 0.03
197 1 0.00
198 31 0.03
199 12 0.01
200 25 0.02
201 12 0.01
202 4 0.00
203 7 0.01
205 1 0.00
206 3 0.00
208 1 0.00
209 1 0.00
211 1 0.00
212 2 0.00
214 7 0.01
215 4 0.00
216 13 0.01
217 114 0.10
218 67 0.06
219 181 0.16
220 212 0.19
221 178 0.16
222 76 0.07
223 56 0.05
224 9 0.01
225 18 0.02
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.37
Consensus pattern (222 bp):
TATTAGATGGCACTAAAATCATATAGACAGGGTTTATTCAATTAATTAGGATGAAAAATATGGAT
TAAAACACTGTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGTCAATCTCTAAAGAATTTGGG
GATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATTACTTTGGG
GATACTGAATTTTGCATTTTGTTTAAT
Found at i:22194 original size:441 final size:432
Alignment explanation
Indices: 21365--22865 Score: 1981
Period size: 441 Copynumber: 3.5 Consensus size: 432
21355 AACAATCTAG
*
21365 TATTAGATGGCACTAAAATGATATAGACGGGGTTTATTCAATTAATTAGGATGAAAAATATGGAT
1 TATTAGATGGCACTAAAATCATATAGACGGGGTTTATTCAATTAATTAGGATG-AAAATAT-GAT
* * * *
21430 TAAAACACTTTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGACAATCTCTAAAGAATTTGGG
64 TAAAACAC-GTTTAAAGCCAATTTTGGGTATAT-A-AAAAATTGTCAATCTCTAAA-AATTTAGG
* * *
21495 GATGATGCATATGATTATTTGGAGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGG
125 GATG-TGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATTACTTT-GG
* *
21560 GATACTGAATTTTGCATTTTT-TTAATTATTAGATGGAACTAAAATCATATAGACAGGGTTTATT
188 GATACTGAATTTTGC-TTTTTGTT--TAATTAGATGGCACTAAAATCATATAGACAGGGTTTATT
* * * *
21624 CAATTAATTAGGATG-AAAATATGGATTAAAACACTTTTTAAAGCCAATTTTGGGTATCTGAGAA
250 CAATTAATTAGAATGAAAAATATGGATTAAAACA-TGTTTGAAGCCAATTTTGGGTATATGAGAA
** * * *
21688 AAAATGTCAATCTTTAAAGAAAATGGGGATGGTGCATATGATTATTTTGGAATGATGAGAAATGA
314 AAAATGTCAATCTTTAAAGAATTTGGGGATGGTGCATATGATTATTTAGGGATAATGAGAAATGA
* * *
21753 TTTGGGTATAAACTATATCAGTTTGGGGATACTGAATTTTGCATTTTGTTTAAT
379 TTTGGGTATAAAGTATATTACTTTGGGGATACTGAATTTTGCATTTTGTTTAAT
*
21807 TATTACATGGCACTAAAATCATATAGAC-GGGTTTATTCAATTAATTAGGATGAAAAATATGGAT
1 TATTAGATGGCACTAAAATCATATAGACGGGGTTTATTCAATTAATTAGGATG-AAAATAT-GAT
* * *
21871 TAAAGCACTTTTTAAAGCCAATTTTGGGTAAATGAGAAAAAGTTGTCAATCTCTAAAGAATTTAG
64 TAAAACAC-GTTTAAAGCCAATTTTGGGTATAT-A-AAAAA-TTGTCAATCTCTAAA-AATTTAG
21936 GGATTGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATTACTTTGG
124 GGA-TGTGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATTACTTTGG
*
22001 GACACTGAATTTTGCTTTTTGTTTAATTAGATGGCACTAAAATCATATAGACAGGGTTTATTCAA
188 GATACTGAATTTTGCTTTTTGTTTAATTAGATGGCACTAAAATCATATAGACAGGGTTTATTCAA
22066 TTAATTAGAATGAAAAATATGGATTAAAACATGTTTGAAGCCAATTTTGGGTATATGAGAAAAAA
253 TTAATTAGAATGAAAAATATGGATTAAAACATGTTTGAAGCCAATTTTGGGTATATGAG--AAAA
* *
22131 AAAGTCAATCTTTAAAGAATTTGGGGATGGTGCATATGATTATTTAGGGATTATGAGAAATGATT
316 AATGTCAATCTTTAAAGAATTTGGGGATGGTGCATATGATTATTTAGGGATAATGAGAAATGATT
*
22196 TGGGTATAAAGTATATTACTGTGGGGATACTGAATTTTGCATTTTGTTTAAT
381 TGGGTATAAAGTATATTACTTTGGGGATACTGAATTTTGCATTTTGTTTAAT
* ** * * * *
22248 TATTAAATGATACTAAATTCATATAGATTGGGTTTATATTCAATTAATTAGGATGAAAATATTAT
1 TATTAGATGGCACTAAAATCATATAGA-CGGGGTT-TATTCAATTAATTAGGATGAAAATATGAT
* *
22313 TAAAACACGTTTAAAGCCAATTTTGGGTTTATAAAAAATTGTTAATCTCT---AA---A---A--
64 TAAAACACGTTTAAAGCCAATTTTGGGTATATAAAAAATTGTCAATCTCTAAAAATTTAGGGATG
* *
22367 ---A-AT--TTA----GGGATGATGAGCAATTATTTGGGTATAAAGTATATTACTTTTGGGATAC
129 TGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATTAC-TTTGGGATAC
* **
22422 TGAATTTTGCATTTTGTTTAATTATTAGATGGCACTAAAATCATATAGATGGGGTTTATTCAATT
193 TGAATTTTGCTTTTTGTTT-A--ATTAGATGGCACTAAAATCATATAGACAGGGTTTATTCAATT
* *
22487 AGTTAGAATGAAAAATATGGATTAAAACACGTTTGAAGCCAATTTTGGGTATATGAGAAAAAATG
255 AATTAGAATGAAAAATATGGATTAAAACATGTTTGAAGCCAATTTTGGGTATATGAGAAAAAATG
* * * * *
22552 TAAATCTCTAAATAATTTGTGGATGGTGCATATGATTATTTGGGGATAATGAGAAATGATTTGGG
320 TCAATCTTTAAAGAATTTGGGGATGGTGCATATGATTATTTAGGGATAATGAGAAATGATTTGGG
22617 TATAAAGTATATTACTGTT-GGGATACTGAATTTTGCATTTTGTTTAAT
385 TATAAAGTATATTACT-TTGGGGATACTGAATTTTGCATTTTGTTTAAT
* *
22665 TATTAGATGGCACTAAATTCATATAGACTGGGTTTATTCAATTAATTAGGATGAAAATATGATTA
1 TATTAGATGGCACTAAAATCATATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGATTA
* * * *
22730 AAACACGTTTAAAGCCAATTTTGAGTTTATAAAAAATTGTTAATCTCTCAAAAATTTGGGGATGG
66 AAACACGTTTAAAGCCAATTTTGGGTATATAAAAAATTGTCAATCTCT-AAAAATTTAGGGAT-G
* * * *
22795 TGCTTATGATTATTTGGGGATGATGAGAAATTATTTGGGAATAAAGTATATAACTTTGGGGATAC
129 TGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATTACTTT-GGGATAC
*
22860 TTAATT
193 TGAATT
22866 GAATTTATAG
Statistics
Matches: 952, Mismatches: 69, Indels: 80
0.86 0.06 0.07
Matches are distributed among these distances:
415 113 0.12
416 31 0.03
417 136 0.14
418 1 0.00
419 100 0.11
421 2 0.00
422 1 0.00
425 1 0.00
428 1 0.00
431 1 0.00
432 2 0.00
434 5 0.01
437 3 0.00
438 58 0.06
439 81 0.09
440 24 0.03
441 248 0.26
442 112 0.12
443 13 0.01
444 19 0.02
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.37
Consensus pattern (432 bp):
TATTAGATGGCACTAAAATCATATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGATTA
AAACACGTTTAAAGCCAATTTTGGGTATATAAAAAATTGTCAATCTCTAAAAATTTAGGGATGTG
CATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATTACTTTGGGATACTGA
ATTTTGCTTTTTGTTTAATTAGATGGCACTAAAATCATATAGACAGGGTTTATTCAATTAATTAG
AATGAAAAATATGGATTAAAACATGTTTGAAGCCAATTTTGGGTATATGAGAAAAAATGTCAATC
TTTAAAGAATTTGGGGATGGTGCATATGATTATTTAGGGATAATGAGAAATGATTTGGGTATAAA
GTATATTACTTTGGGGATACTGAATTTTGCATTTTGTTTAAT
Found at i:22513 original size:196 final size:198
Alignment explanation
Indices: 22172--22569 Score: 588
Period size: 196 Copynumber: 2.0 Consensus size: 198
22162 GCATATGATT
*
22172 ATTTAGGGATTATGAGAAATGATTTGGGTATAAAGTATATTACTGTGGGGATACTGAATTTTGCA
1 ATTTAGGGATGATGAGAAATGATTTGGGTATAAAGTATATTACTGTGGGGATACTGAATTTTGCA
* * * *
22237 TTTTGTTTAATTATTAAATGATACTAAATTCATATAGATTGGGTTTATATTCAATTAATTAGGAT
66 TTTTGTTTAATTATTAAATGACACTAAAATCATATAGATTGGGGTTATATTCAATTAATTAGAAT
* * * *
22302 GAAAATATTATTAAAACACGTTTAAAGCCAATTTTGGGTTTAT-A-AAAAATTGTTAATCTCTAA
131 GAAAATATGATTAAAACACGTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGTAAATCTCTAA
22365 AAA
196 AAA
* * * *
22368 ATTTAGGGATGATGAGCAATTATTTGGGTATAAAGTATATTACTTTTGGGATACTGAATTTTGCA
1 ATTTAGGGATGATGAGAAATGATTTGGGTATAAAGTATATTACTGTGGGGATACTGAATTTTGCA
* * *
22433 TTTTGTTTAATTATTAGATGGCACTAAAATCATATAGA-TGGGGTT-TATTCAATTAGTTAGAAT
66 TTTTGTTTAATTATTAAATGACACTAAAATCATATAGATTGGGGTTATATTCAATTAATTAGAAT
*
22496 GAAAAATATGGATTAAAACACGTTTGAAGCCAATTTTGGGTATATGAGAAAAAATGTAAATCTCT
131 G-AAAATAT-GATTAAAACACGTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGTAAATCTCT
*
22561 AAATA
194 AAAAA
22566 ATTT
1 ATTT
22570 GTGGATGGTG
Statistics
Matches: 180, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
194 17 0.09
195 13 0.07
196 126 0.70
197 1 0.01
198 23 0.13
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.39
Consensus pattern (198 bp):
ATTTAGGGATGATGAGAAATGATTTGGGTATAAAGTATATTACTGTGGGGATACTGAATTTTGCA
TTTTGTTTAATTATTAAATGACACTAAAATCATATAGATTGGGGTTATATTCAATTAATTAGAAT
GAAAATATGATTAAAACACGTTTAAAGCCAATTTTGGGTATATGAGAAAAAATGTAAATCTCTAA
AAA
Found at i:25207 original size:13 final size:13
Alignment explanation
Indices: 25185--25226 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
25175 TATCATAATT
*
25185 AAAGTCATAAACC
1 AAAGTAATAAACC
*
25198 AAAGTAATAAATC
1 AAAGTAATAAACC
25211 AGAA-TAATAAACC
1 A-AAGTAATAAACC
25224 AAA
1 AAA
25227 CAGTCAGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 2 0.08
13 21 0.84
14 2 0.08
ACGTcount: A:0.62, C:0.14, G:0.07, T:0.17
Consensus pattern (13 bp):
AAAGTAATAAACC
Found at i:31572 original size:70 final size:70
Alignment explanation
Indices: 31459--31599 Score: 264
Period size: 70 Copynumber: 2.0 Consensus size: 70
31449 TATATAGGGC
31459 CTCCTTGTACGGGTCGCACGCGCGATGTCAAATGTGGAGGTGTCCGTGGGAGGTCACGTGTGAGG
1 CTCCTTGTACGGGTCGCACGCGCGATGTCAAATGTGGAGGTGTCCGTGGGAGGTCACGTGTGAGG
31524 TCGTA
66 TCGTA
* *
31529 CTCCTTGTACGGGTCGCACGCGCGATGTCACATGTGGAGGTGTCCGTTGGAGGTCACGTGTGAGG
1 CTCCTTGTACGGGTCGCACGCGCGATGTCAAATGTGGAGGTGTCCGTGGGAGGTCACGTGTGAGG
31594 TCGTA
66 TCGTA
31599 C
1 C
31600 GTTTGAGGTC
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.15, C:0.23, G:0.38, T:0.25
Consensus pattern (70 bp):
CTCCTTGTACGGGTCGCACGCGCGATGTCAAATGTGGAGGTGTCCGTGGGAGGTCACGTGTGAGG
TCGTA
Found at i:31595 original size:12 final size:12
Alignment explanation
Indices: 31578--31616 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
31568 GTGTCCGTTG
31578 GAGGTCACGTGT
1 GAGGTCACGTGT
*
31590 GAGGTCGTACGTTT
1 GAGGTC--ACGTGT
31604 GAGGTCACGTGT
1 GAGGTCACGTGT
31616 G
1 G
31617 GGGTGCTAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 12 0.52
14 11 0.48
ACGTcount: A:0.15, C:0.15, G:0.41, T:0.28
Consensus pattern (12 bp):
GAGGTCACGTGT
Found at i:31602 original size:26 final size:25
Alignment explanation
Indices: 31555--31621 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
31545 CACGCGCGAT
* *
31555 GTCACATGTGGAGGTGTCCGTTGGAG
1 GTCACGTGT-GAGGTGTACGTTGGAG
*
31581 GTCACGTGTGAGGTCGTACGTTTGAG
1 GTCACGTGTGAGGT-GTACGTTGGAG
*
31607 GTCACGTGTGGGGTG
1 GTCACGTGTGAGGTG
31622 CTAGCTGGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 6 0.17
26 30 0.83
ACGTcount: A:0.13, C:0.15, G:0.43, T:0.28
Consensus pattern (25 bp):
GTCACGTGTGAGGTGTACGTTGGAG
Found at i:31752 original size:23 final size:23
Alignment explanation
Indices: 31724--31807 Score: 113
Period size: 23 Copynumber: 3.8 Consensus size: 23
31714 CGTTGCGTTA
31724 TGGAAGTGGTCGGTCGCCAGGTT
1 TGGAAGTGGTCGGTCGCCAGGTT
* *
31747 TGGAAGTGGTCGG--G-C-GCTA
1 TGGAAGTGGTCGGTCGCCAGGTT
31766 TGGAAGTGGTCGGTCGCCAGGTT
1 TGGAAGTGGTCGGTCGCCAGGTT
*
31789 TGGAAGTGGTCGGGCGCCA
1 TGGAAGTGGTCGGTCGCCA
31808 AGCAATTGTG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
19 15 0.29
20 1 0.02
21 2 0.04
22 1 0.02
23 33 0.63
ACGTcount: A:0.14, C:0.18, G:0.45, T:0.23
Consensus pattern (23 bp):
TGGAAGTGGTCGGTCGCCAGGTT
Found at i:31781 original size:42 final size:42
Alignment explanation
Indices: 31722--31805 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
31712 AGCGTTGCGT
31722 TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGGCGC
1 TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGGCGC
31764 TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGGCGC
1 TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGGCGC
31806 CAAGCAATTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.14, C:0.17, G:0.45, T:0.24
Consensus pattern (42 bp):
TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGGCGC
Found at i:33374 original size:16 final size:16
Alignment explanation
Indices: 33353--33392 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
33343 TCCCGAAGAC
*
33353 GGCGCCAAATCTTGCG
1 GGCGCCAAATATTGCG
33369 GGCGCCAAATATTGCG
1 GGCGCCAAATATTGCG
*
33385 GGCACCAA
1 GGCGCCAA
33393 GTCGCCGGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.15
Consensus pattern (16 bp):
GGCGCCAAATATTGCG
Found at i:33755 original size:70 final size:70
Alignment explanation
Indices: 33633--33773 Score: 246
Period size: 70 Copynumber: 2.0 Consensus size: 70
33623 TATATAGGGC
33633 CTCCTTGTACGGGTCGCACACGCGATGTCAAATGTGGAGGTGTCCGTGGGAGGTCACGTGTGAGG
1 CTCCTTGTACGGGTCGCACACGCGATGTCAAATGTGGAGGTGTCCGTGGGAGGTCACGTGTGAGG
33698 TCGTA
66 TCGTA
* * * *
33703 CTCCTTGTACGGGTCGCACGCGCGATGTCACATGTGGAGGTGTTCGTTGGAGGTCACGTGTGAGG
1 CTCCTTGTACGGGTCGCACACGCGATGTCAAATGTGGAGGTGTCCGTGGGAGGTCACGTGTGAGG
33768 TCGTA
66 TCGTA
33773 C
1 C
33774 GTTTGAGGTC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 67 1.00
ACGTcount: A:0.16, C:0.22, G:0.37, T:0.26
Consensus pattern (70 bp):
CTCCTTGTACGGGTCGCACACGCGATGTCAAATGTGGAGGTGTCCGTGGGAGGTCACGTGTGAGG
TCGTA
Found at i:33769 original size:12 final size:12
Alignment explanation
Indices: 33752--33794 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 12
33742 GTGTTCGTTG
33752 GAGGTCACGTGT
1 GAGGTCACGTGT
*
33764 GAGGTCGTACGTTT
1 GAGGTC--ACGTGT
33778 GAGGTCACGTGT
1 GAGGTCACGTGT
33790 GAGGT
1 GAGGT
33795 GCCAGCTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 16 0.59
14 11 0.41
ACGTcount: A:0.16, C:0.14, G:0.42, T:0.28
Consensus pattern (12 bp):
GAGGTCACGTGT
Found at i:33776 original size:26 final size:25
Alignment explanation
Indices: 33729--33795 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 25
33719 CACGCGCGAT
* *
33729 GTCACATGTGGAGGTGTTCGTTGGAG
1 GTCACGTGT-GAGGTGTACGTTGGAG
*
33755 GTCACGTGTGAGGTCGTACGTTTGAG
1 GTCACGTGTGAGGT-GTACGTTGGAG
33781 GTCACGTGTGAGGTG
1 GTCACGTGTGAGGTG
33796 CCAGCTAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.16
26 31 0.84
ACGTcount: A:0.15, C:0.13, G:0.42, T:0.30
Consensus pattern (25 bp):
GTCACGTGTGAGGTGTACGTTGGAG
Found at i:33928 original size:23 final size:25
Alignment explanation
Indices: 33877--33939 Score: 89
Period size: 23 Copynumber: 2.6 Consensus size: 25
33867 TTGTGGTCAC
33877 AAGTGGTCGAG-CGCC-GCGTTATGG
1 AAGTGGTCG-GTCGCCAGCGTTATGG
33901 AAGTGGTCGGTCGCCAG-GTT-TGG
1 AAGTGGTCGGTCGCCAGCGTTATGG
33924 AAGTGGTCGGTCGCCA
1 AAGTGGTCGGTCGCCA
33940 AGCAATTGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
23 20 0.54
24 16 0.43
25 1 0.03
ACGTcount: A:0.16, C:0.21, G:0.41, T:0.22
Consensus pattern (25 bp):
AAGTGGTCGGTCGCCAGCGTTATGG
Found at i:35564 original size:14 final size:15
Alignment explanation
Indices: 35545--35575 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
35535 TCTTGTTCTA
35545 AAAAAGAA-AAAAAT
1 AAAAAGAAGAAAAAT
35559 AAAAAGAAGAAAAAT
1 AAAAAGAAGAAAAAT
35574 AA
1 AA
35576 GAACGGAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (15 bp):
AAAAAGAAGAAAAAT
Found at i:43659 original size:38 final size:38
Alignment explanation
Indices: 43608--43684 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
43598 TCATTGCCAC
43608 GAGCATTCCAACAAAGCATATGACAGTACCTATAATAT
1 GAGCATTCCAACAAAGCATATGACAGTACCTATAATAT
43646 GAGCATTCCAACAAAGCATATGACAGTACCTATAATAT
1 GAGCATTCCAACAAAGCATATGACAGTACCTATAATAT
43684 G
1 G
43685 TAGGTTTCCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (38 bp):
GAGCATTCCAACAAAGCATATGACAGTACCTATAATAT
Found at i:56310 original size:27 final size:27
Alignment explanation
Indices: 56267--56344 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
56257 AAATGACGAG
* *
56267 ATGCCCTTGAACGTGCAAATGACCAAA
1 ATGCCCCTGAACATGCAAATGACCAAA
* *
56294 ATGCCCCTGGACATGCAAATGACTAAA
1 ATGCCCCTGAACATGCAAATGACCAAA
56321 ATGCCCCTGAACATGCAAATGACC
1 ATGCCCCTGAACATGCAAATGACC
56345 CCAAAATTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (27 bp):
ATGCCCCTGAACATGCAAATGACCAAA
Found at i:56667 original size:52 final size:50
Alignment explanation
Indices: 56597--56718 Score: 174
Period size: 50 Copynumber: 2.4 Consensus size: 50
56587 CGATCAATTT
* *
56597 CTTTGAATTGTTCT-CCAATCTAACATATTAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTG-TCTACCAAT-TAA-ATATTAAAAGGACCGTCTCCCGCTTATC
* *
56649 CTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTCCCGCTTATC
1 CTTTGAACTGTCTACCAATTAAATATTAAAAGGACCGTCTCCCGCTTATC
56699 CTTTGAACTGTCTACCAATT
1 CTTTGAACTGTCTACCAATT
56719 CAATCTC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
50 46 0.71
51 5 0.08
52 14 0.22
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.35
Consensus pattern (50 bp):
CTTTGAACTGTCTACCAATTAAATATTAAAAGGACCGTCTCCCGCTTATC
Found at i:56685 original size:50 final size:50
Alignment explanation
Indices: 56624--56724 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
56614 ATCTAACATA
*
56624 TTAAAAGGACCGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
1 TTAAAAGGACCGTCTCCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
56674 TTAAAAGGACCGTCTCCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
1 TTAAAAGGACCGTCTCCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
56724 T
1 T
56725 C
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.34
Consensus pattern (50 bp):
TTAAAAGGACCGTCTCCCGCTTATCCTTTGAACTGTCTACCAATTCAATC
Done.