Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2272
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: 41491
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:10191 original size:382 final size:386
Alignment explanation
Indices: 9296--12216 Score: 5428
Period size: 382 Copynumber: 7.6 Consensus size: 386
9286 CTTTCCAAGG
9296 AAAATCAACTCATATTGCGAGAAATGAGTTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTT
1 AAAATCAACTCATATTGCGAGAAATGAG-TTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTT
*
9361 TTT-TAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGCCGA-GTATTTTT
65 TTTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT
9423 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAA-TTTTGTTTTTCA
130 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCA
9487 AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTA-TTTTAAATTTTT
195 AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTT
*
9551 TTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTA-TTTTAG
260 TAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
9615 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
325 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
9677 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
9742 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTTA
66 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
9806 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAA
131 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAA
9871 AATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTT
196 AATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTT
*
9936 -AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCCGAGGTATTTTTAGT
261 AAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGT
10000 TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTG-TTTTC
326 TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
10060 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTGGAGGTATTTTTAAA-TTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
* *
10124 TAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTTA
66 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
10188 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAA
131 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAA
*
10253 AATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGATATTTTTAAATTTTTT
196 AATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTT
10318 AAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTTAGT
261 AAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGT
10382 TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTG-TTTTC
326 TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
10442 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
10507 TT--AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
66 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
10570 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAA
131 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAA
10635 AATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTT
196 AATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTT
*
10700 AAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGACACGCCGAGGTA-TTTTAGT
261 AAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGT
*
10763 TTATGTTTTAAATTGATTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
326 TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
10824 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTGGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
* *
10889 TAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
66 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
10954 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAA
131 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAA
11019 AATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTT
196 AATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTT
11084 AAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGT
261 AAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGT
11149 TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
326 TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
11210 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAA-TTT
*
11275 TTTAAAAAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTT
65 TTTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT
11339 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCA
130 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCA
11404 AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTT
195 AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTT
11469 TAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
260 TAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
*
11534 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTATTTTTC
325 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
11596 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTGGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAA-TTT
*
11661 TTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT
65 TTTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT
11726 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCA
130 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCA
* * *
11791 AAATCAACTCATATTGCGAGAAATGAGTTGAGTCTCAAGACACTTTGAGGTATTTTTTAATTTTT
195 AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTA-TTTTTAA-ATTT
*** *
11856 GTTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTT
258 -TTTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTT
11921 TAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
322 TAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
11986 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
**
12051 AAAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
66 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
12116 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAA
131 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC-A
12181 AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
195 AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
12217 GGGGCACGCC
Statistics
Matches: 2482, Mismatches: 39, Indels: 29
0.97 0.02 0.01
Matches are distributed among these distances:
380 39 0.02
381 177 0.07
382 671 0.27
383 228 0.09
384 306 0.12
385 14 0.01
386 509 0.21
387 179 0.07
388 7 0.00
389 132 0.05
390 220 0.09
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (386 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAA
AATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTTTT
AAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGT
TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:11060 original size:193 final size:193
Alignment explanation
Indices: 9296--12216 Score: 5428
Period size: 193 Copynumber: 15.2 Consensus size: 193
9286 CTTTCCAAGG
9296 AAAATCAACTCATATTGCGAGAAATGAGTTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTT
1 AAAATCAACTCATATTGCGAGAAATGAG-TTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTT
*
9361 TTT-TAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGCCGA-GTATTTTT
65 TTTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT
9423 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAA-TTTTGTTTTTC
130 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
9486 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTA-TTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
*
9550 TTTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTA-TTTTA
66 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
9614 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
9677 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
9742 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTTA
66 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
9806 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
9869 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
*
9934 TT-AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGACACGCCGAGGTATTTTTA
66 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
9998 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTG-TTTTC
131 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
10060 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTGGAGGTATTTTTAAA-TTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
* *
10124 TAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTTA
66 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
10188 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
10251 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGATATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
10316 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTTA
66 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
10380 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTG-TTTTC
131 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
10442 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
10507 TT--AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
66 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
10570 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
10633 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
*
10698 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGACACGCCGAGGTA-TTTTA
66 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
*
10761 GTTTATGTTTTAAATTGATTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
10824 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTGGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
* *
10889 TAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
66 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
10954 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
11017 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
11082 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
66 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
11147 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
11210 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAA-TTT
*
11275 TTTAAAAAAAATCAACTCATATTGTGAGAAGTGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTT
65 TTTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT
11339 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
130 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
11403 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
11468 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
66 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
*
11533 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTATTTTTC
131 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
11596 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTGGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAA-TTT
*
11661 TTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT
65 TTTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT
11726 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
130 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* * *
11790 AAAATCAACTCATATTGCGAGAAATGAGTTGAGTCTCAAGACACTTTGAGGTATTTTTTAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTA-TTTTTAA-ATT
*** *
11855 TGTTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTT
64 T-TTTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTT
11920 TTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTT
128 TTAGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTT
11985 C
193 C
11986 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
**
12051 AAAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
66 TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
12116 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
12179 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
1 -AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
12217 GGGGCACGCC
Statistics
Matches: 2664, Mismatches: 44, Indels: 42
0.97 0.02 0.02
Matches are distributed among these distances:
188 13 0.00
189 103 0.04
190 254 0.10
191 605 0.23
192 461 0.17
193 768 0.29
194 266 0.10
195 17 0.01
196 177 0.07
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (193 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
TTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:11921 original size:73 final size:73
Alignment explanation
Indices: 11772--11968 Score: 231
Period size: 74 Copynumber: 2.7 Consensus size: 73
11762 GAGTTAAGCC
* ***
11772 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGTCTCAAGACACTTT
1 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCC
11837 GAGGTATT
66 GAGGTATT
** *
11845 TTTTAATTTTTGTTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGC
1 TTTTAATTTTTGTTTTTC-AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGC
11910 CGAGGTA-T
65 CGAGGTATT
* * ** ** *
11918 TTTTAGTTTATG-TTTT--AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCT
11969 TTTAATTTTT
Statistics
Matches: 109, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
69 30 0.28
72 4 0.04
73 29 0.27
74 46 0.42
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (73 bp):
TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCC
GAGGTATT
Found at i:12197 original size:54 final size:54
Alignment explanation
Indices: 12133--12338 Score: 160
Period size: 54 Copynumber: 3.5 Consensus size: 54
12123 TTTTAAATTG
12133 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCA
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCA
** * *** ***
12187 ACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTATGTTTTAA
1 ACTCATATTGCGAGAGGTGAGTTAAGCCT---------TTTA---ATTTTT-GTTT-T-TCAAAA
**
12252 ATTG
51 ATCA
12256 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCA
1 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCA
* *
12310 ACTCATATTGCAAGAGGTGAGTTGAGCCT
1 ACTCATATTGCGAGAGGTGAGTTAAGCCT
12339 CGGCTCACAT
Statistics
Matches: 113, Mismatches: 24, Indels: 30
0.68 0.14 0.18
Matches are distributed among these distances:
54 58 0.51
55 1 0.01
56 4 0.04
57 6 0.05
60 1 0.01
63 1 0.01
66 6 0.05
67 4 0.04
68 1 0.01
69 31 0.27
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (54 bp):
ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAAAATCA
Found at i:12202 original size:123 final size:123
Alignment explanation
Indices: 12056--12374 Score: 548
Period size: 123 Copynumber: 2.6 Consensus size: 123
12046 ATTTTAAAAA
12056 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
12121 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
66 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
12179 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
12244 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
66 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* * ** * * *
12302 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCAC--GCCGAGGTATTTTTAGTT
12367 TATGTTTT
64 TATGTTTT
12375 TTTCAATCTA
Statistics
Matches: 185, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
123 162 0.88
125 23 0.12
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (123 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTA
TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:12379 original size:16 final size:17
Alignment explanation
Indices: 12358--12391 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12348 TGCTGAGGTA
*
12358 TTTTCAATTTATG-TTT
1 TTTTCAATCTATGCTTT
12374 TTTTCAATCTATGCTTT
1 TTTTCAATCTATGCTTT
12391 T
1 T
12392 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTCAATCTATGCTTT
Found at i:12502 original size:176 final size:182
Alignment explanation
Indices: 12297--12710 Score: 477
Period size: 194 Copynumber: 2.2 Consensus size: 182
12287 TAATTTTTGT
*
12297 TTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGC-CACACGCTGAGGTATTT
* *
12361 TC-AA-TTT-A-TGTTTTTTTCAATCTATGCT-TTTC-AAAAATCAACTTATATTGCGAGAGGTG
64 TCAAATTTTAATTGTTTTTTTCAATCTATG-TGTTTCAAAAAATCAACTCATATTGCAAGAGGTG
*
12420 AGTTGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTGCTTTACTAA-TTCTAC
128 AGTTGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTACTTTAC-AATTTCTAC
* *
12475 TTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACACGCTGAGGTCTTTTC
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
* * *
12539 AAATTCTGTTTTTAATTTCTGTTTTTTTTAATTTCTGTGTTTCAAAAAAAAAATCAACTCATATT
66 AAA------TTTTAA--T-TGTTTTTTTCAATCTATGTGTTTC----AAAAAATCAACTCATATT
* * **
12604 GCAAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGT
118 GCAAGAGGTGAGTTGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTACTTTACAATTTCTAC
*
12669 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT
12711 TTTAATTTCT
Statistics
Matches: 198, Mismatches: 15, Indels: 28
0.82 0.06 0.12
Matches are distributed among these distances:
176 52 0.26
177 5 0.03
178 5 0.03
184 3 0.02
185 1 0.01
188 1 0.01
189 19 0.10
193 2 0.01
194 77 0.39
196 33 0.17
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.37
Consensus pattern (182 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
AAATTTTAATTGTTTTTTTCAATCTATGTGTTTCAAAAAATCAACTCATATTGCAAGAGGTGAGT
TGAGCCTCAAGGCACGCTGAGGTATTTTCAATTTCTACTTTACAATTTCTAC
Found at i:12555 original size:85 final size:88
Alignment explanation
Indices: 12297--12555 Score: 309
Period size: 91 Copynumber: 2.9 Consensus size: 88
12287 TAATTTTTGT
*
12297 TTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGC-CACACGCTGAGGTATTT
*
12361 TCAATTTATGTTTTTTTCAA-TCTATGC
64 TCAATTTCTG-TTTTTT-AATTCTA-GC
* *
12388 TTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG---CACGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGCCACACGCTGAGGTATTT
**
12450 TCAATTTCTGCTTTACTAATTCTA-C
64 TCAATTTCTG-TTTTTTAATTCTAGC
* *
12475 TTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACACGCTGAGGTCTTTTC
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
*
12539 AAATTCTG-TTTTTAATT
66 AATTTCTGTTTTTTAATT
12556 TCTGTTTTTT
Statistics
Matches: 148, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
84 3 0.02
85 40 0.27
87 29 0.20
88 2 0.01
89 31 0.21
91 41 0.28
93 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (88 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
AATTTCTGTTTTTTAATTCTAGC
Found at i:12738 original size:54 final size:54
Alignment explanation
Indices: 12654--12820 Score: 234
Period size: 54 Copynumber: 3.1 Consensus size: 54
12644 TCAATTTCTA
*
12654 CTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTT-AATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
12709 CTTTTAATTTCTATTTGTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
12763 C--TT--TTTCTATTTTTCAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGC
1 CTTTTAATTTCTATTTTTC---AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
12816 CTTTT
1 CTTTT
12821 GTAAATTTCT
Statistics
Matches: 101, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
50 11 0.11
52 2 0.02
53 34 0.34
54 47 0.47
55 7 0.07
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (54 bp):
CTTTTAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:13278 original size:17 final size:17
Alignment explanation
Indices: 13235--13282 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
13225 AGAAAAAAAT
13235 CGTGTTTCAAAAATTTTCA
1 CGTGTTTC-AAAA-TTTCA
13254 --TGTCTTCAAAATTTCA
1 CGTGT-TTCAAAATTTCA
13270 CGTGTTTCAAAAT
1 CGTGTTTCAAAAT
13283 AATAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 5 0.19
17 15 0.58
18 6 0.23
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (17 bp):
CGTGTTTCAAAATTTCA
Found at i:13365 original size:17 final size:18
Alignment explanation
Indices: 13345--13409 Score: 64
Period size: 17 Copynumber: 3.8 Consensus size: 18
13335 TAAAAAAATC
13345 CGTG-TTTCAAAAATTCT
1 CGTGATTTCAAAAATTCT
* **
13362 CGTGAATAAAAAAATT-T
1 CGTGATTTCAAAAATTCT
*
13379 CGTGTTTTCAAAAATTCT
1 CGTGATTTCAAAAATTCT
*
13397 CGTG-TTTTAAAAA
1 CGTGATTTCAAAAA
13410 AAAAATTTCG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 25 0.66
18 13 0.34
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
CGTGATTTCAAAAATTCT
Found at i:13388 original size:35 final size:36
Alignment explanation
Indices: 13335--13426 Score: 118
Period size: 39 Copynumber: 2.6 Consensus size: 36
13325 TTTCTTTCTT
*
13335 TAAAAAAA-TCCGTG-TTTCAAAAATTCTCGTG-AA
1 TAAAAAAATTTCGTGTTTTCAAAAATTCTCGTGTAA
13368 TAAAAAAATTTCGTGTTTTCAAAAATTCTCGTGTTTTAA
1 TAAAAAAATTTCGTGTTTTCAAAAATTCTCGTG---TAA
*
13407 AAAAAAAATTTCGTGTTTTC
1 TAAAAAAATTTCGTGTTTTC
13427 GTGTTTTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
33 8 0.16
34 5 0.10
35 17 0.33
39 21 0.41
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (36 bp):
TAAAAAAATTTCGTGTTTTCAAAAATTCTCGTGTAA
Found at i:13448 original size:28 final size:29
Alignment explanation
Indices: 13396--13452 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
13386 TCAAAAATTC
*
13396 TCGTGTTTTAAAAAAAAAATTTCGTGTTT
1 TCGTGTTTTAAAAAAAAAATCTCGTGTTT
13425 TCGTGTTTT-AAAAAAAAATCTCGTGTTT
1 TCGTGTTTTAAAAAAAAAATCTCGTGTTT
13453 CAAAAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 18 0.67
29 9 0.33
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (29 bp):
TCGTGTTTTAAAAAAAAAATCTCGTGTTT
Found at i:13471 original size:18 final size:18
Alignment explanation
Indices: 13422--13684 Score: 108
Period size: 17 Copynumber: 14.1 Consensus size: 18
13412 AAATTTCGTG
*
13422 TTTTCGTGTTTTAAAAAAAA
1 TTTTCGTGTTTT--CAAAAA
* *
13442 ATCTCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
13459 TTTTCGTGTTTTCAAAATTTTCA
1 TTTTCGTGTTTTCAAAA-----A
13482 TGTTTTCGTGTTTTCAAAAAA
1 --TTTTCGTGTTTTC-AAAAA
* *
13503 TTCTCGTGTTTTTTTAAAAA
1 TTTTCGTG--TTTTCAAAAA
** * *
13523 AATTCATGTTTTAAAAAA
1 TTTTCGTGTTTTCAAAAA
** * *
13541 AATTCATGTTTTC-GAAA
1 TTTTCGTGTTTTCAAAAA
13558 TTTTCGTGTTTTC-AAAA
1 TTTTCGTGTTTTCAAAAA
* *
13575 TTTT-TTG-TGTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* * * *
13592 TTCTCATG-TATCGAAAA
1 TTTTCGTGTTTTCAAAAA
* *
13609 TTTCCTTGTTTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* *
13628 ATTCCGTGTTTTCAAAAAAA
1 TTTTCGTGTTTTC--AAAAA
*
13648 ATTTCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
13665 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
13683 TT
1 TT
13685 ATTATTGTGT
Statistics
Matches: 190, Mismatches: 35, Indels: 38
0.72 0.13 0.14
Matches are distributed among these distances:
15 3 0.02
16 2 0.01
17 58 0.31
18 47 0.25
19 29 0.15
20 28 0.15
21 5 0.03
23 1 0.01
25 13 0.07
26 4 0.02
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:13630 original size:20 final size:20
Alignment explanation
Indices: 13605--13682 Score: 87
Period size: 20 Copynumber: 4.1 Consensus size: 20
13595 TCATGTATCG
*
13605 AAAATTTCCTTGTTTTCAAA
1 AAAATTTCCGTGTTTTCAAA
13625 AAAA-TTCCGTGTTTTCAAAA
1 AAAATTTCCGTGTTTTC-AAA
13645 AAAATTT-CGTG-TTTC--A
1 AAAATTTCCGTGTTTTCAAA
13661 AAAATCTT-CGTGTTTTCAAA
1 AAAAT-TTCCGTGTTTTCAAA
13681 AA
1 AA
13683 TTATTATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
16 6 0.12
17 6 0.12
18 4 0.08
19 15 0.29
20 18 0.35
21 2 0.04
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (20 bp):
AAAATTTCCGTGTTTTCAAA
Found at i:13660 original size:38 final size:38
Alignment explanation
Indices: 13618--13700 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 38
13608 ATTTCCTTGT
13618 TTTCAAAAAAATTCCGTGTTTTCAAAAAAAATT-TCGTG
1 TTTCAAAAAAATT-CGTGTTTTCAAAAAAAATTATCGTG
** ** *
13656 TTTCAAAAATCTTCGTGTTTTCAAAAATTATTATTGTG
1 TTTCAAAAAAATTCGTGTTTTCAAAAAAAATTATCGTG
13694 TTTCAAA
1 TTTCAAA
13701 GTTCTCGTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 17 0.44
38 22 0.56
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (38 bp):
TTTCAAAAAAATTCGTGTTTTCAAAAAAAATTATCGTG
Found at i:16617 original size:172 final size:172
Alignment explanation
Indices: 16326--16670 Score: 665
Period size: 172 Copynumber: 2.0 Consensus size: 172
16316 AAGAAGCCTT
16326 AATCATATCCTGGCATGACACTGATGGTCTTGGTATATTCAGATTTTCTTTTATATCTAATTCAT
1 AATCATATCCTGGCATGACACTGATGGTCTTGGTATATTCAGATTTTCTTTTATATCTAATTCAT
*
16391 GAAGGTGCAGTTATTTTTTTAAATTTTTTTTATATAAAATTAGGGTACGGGATGGAGTCACTCAA
66 GAAGGTGCAGTTATCTTTTTAAATTTTTTTTATATAAAATTAGGGTACGGGATGGAGTCACTCAA
16456 TTTGAACCCATGTTAGACAAATGTCTAACAAAAGTTTTGATC
131 TTTGAACCCATGTTAGACAAATGTCTAACAAAAGTTTTGATC
16498 AATCATATCCTGGCATGACACTGATGGTCTTGGTATATTCAGATTTTCTTTTATATCTAATTCAT
1 AATCATATCCTGGCATGACACTGATGGTCTTGGTATATTCAGATTTTCTTTTATATCTAATTCAT
16563 GAAGGTGCAGTTATCTTTTTAAATTTTTTTTATATAAAATTAGGGTGA-GGGATGGAGTCACTCA
66 GAAGGTGCAGTTATCTTTTTAAATTTTTTTTATATAAAATTAGGGT-ACGGGATGGAGTCACTCA
16627 ATTTGAACCCATGTTAGACAAATGTCTAACAAAAGTTTTGATC
130 ATTTGAACCCATGTTAGACAAATGTCTAACAAAAGTTTTGATC
16670 A
1 A
16671 CCGCTCTGTA
Statistics
Matches: 171, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
172 170 0.99
173 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.39
Consensus pattern (172 bp):
AATCATATCCTGGCATGACACTGATGGTCTTGGTATATTCAGATTTTCTTTTATATCTAATTCAT
GAAGGTGCAGTTATCTTTTTAAATTTTTTTTATATAAAATTAGGGTACGGGATGGAGTCACTCAA
TTTGAACCCATGTTAGACAAATGTCTAACAAAAGTTTTGATC
Found at i:19779 original size:5 final size:5
Alignment explanation
Indices: 19769--19794 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
19759 TCTAAGTTTG
19769 TATTA TATTA TATTA TATTA TATTA T
1 TATTA TATTA TATTA TATTA TATTA T
19795 GTAATTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATTA
Found at i:20111 original size:18 final size:18
Alignment explanation
Indices: 20088--20131 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
20078 GGTGGACACA
* **
20088 TTAAAAAATTAATTTTTT
1 TTAAAAAATAAATTAATT
20106 TTAAAAAATAAATTAATT
1 TTAAAAAATAAATTAATT
20124 TTAAAAAA
1 TTAAAAAA
20132 GTATAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAAAAATAAATTAATT
Found at i:21886 original size:23 final size:23
Alignment explanation
Indices: 21859--21902 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
21849 TGATATTGCG
* *
21859 AAAATTTAATTATAATTTTATAA
1 AAAATTAAAATATAATTTTATAA
21882 AAAATTAAAATATAATTTTAT
1 AAAATTAAAATATAATTTTAT
21903 CATTTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAATTAAAATATAATTTTATAA
Found at i:25288 original size:22 final size:22
Alignment explanation
Indices: 25263--25304 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
25253 ATATAATAGC
*
25263 AAAATGACAGTAAAACAACAGT
1 AAAATGACAGCAAAACAACAGT
*
25285 AAAATGGCAGCAAAACAACA
1 AAAATGACAGCAAAACAACA
25305 ACAAGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.17, G:0.14, T:0.10
Consensus pattern (22 bp):
AAAATGACAGCAAAACAACAGT
Found at i:30805 original size:20 final size:21
Alignment explanation
Indices: 30769--30809 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
30759 AATTTTAAAA
30769 TATTTTTAAAATAAATTTTTT
1 TATTTTTAAAATAAATTTTTT
30790 TATTTTTAAAAT-AATTTTTT
1 TATTTTTAAAATAAATTTTTT
30810 GGTGTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTT
Found at i:30817 original size:20 final size:21
Alignment explanation
Indices: 30773--30817 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
30763 TTAAAATATT
* *
30773 TTTAAAATAAATTTTTTTATT
1 TTTAAAATAAATTTTTTGATG
*
30794 TTTAAAAT-AATTTTTTGGTG
1 TTTAAAATAAATTTTTTGATG
30814 TTTA
1 TTTA
30818 TTAAAAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
TTTAAAATAAATTTTTTGATG
Found at i:31634 original size:12 final size:12
Alignment explanation
Indices: 31614--31646 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
31604 TTGTTTCAGG
31614 TTGTATTATTAA
1 TTGTATTATTAA
*
31626 TTGTGTTATTAA
1 TTGTATTATTAA
31638 TT-TATTATT
1 TTGTATTATT
31647 TTAAATTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (12 bp):
TTGTATTATTAA
Found at i:31955 original size:43 final size:42
Alignment explanation
Indices: 31868--32096 Score: 209
Period size: 43 Copynumber: 5.5 Consensus size: 42
31858 TTTTTGCTAG
* * * * * *
31868 AAGCGCCGCTAAAGGT-TTGTTCTTTAGCGGCATTTATAATAA
1 AAGCGCCGCTAAAGGTCATG-CCTTTAGCGGCGTTTGTGACAA
* * *
31910 AAGCGACGCTAAAGGTCATGACCTTTAGTGGCATTTGTGACAA
1 AAGCGCCGCTAAAGGTCATG-CCTTTAGCGGCGTTTGTGACAA
* * *
31953 AAGCGCCACTAAAGTTCATGGTCTTTTAGCGGCGTTTGTGACAA
1 AAGCGCCGCTAAAGGTCAT-G-CCTTTAGCGGCGTTTGTGACAA
* * * *
31997 AAGCGCAGCTAAAGCTCATGGTCTTTAGCGGCGTTTGTGACAG
1 AAGCGCCGCTAAAGGTCAT-GCCTTTAGCGGCGTTTGTGACAA
*
32040 ACGCGCCGCTAAAGG---T--CTTTAGCGGCGTTTGTGACAA
1 AAGCGCCGCTAAAGGTCATGCCTTTAGCGGCGTTTGTGACAA
*
32077 ATGCGCCGCTAAAGGTCATG
1 AAGCGCCGCTAAAGGTCATG
32097 GTATTTAGCG
Statistics
Matches: 155, Mismatches: 26, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
37 34 0.22
40 2 0.01
42 15 0.10
43 66 0.43
44 38 0.25
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (42 bp):
AAGCGCCGCTAAAGGTCATGCCTTTAGCGGCGTTTGTGACAA
Found at i:32009 original size:87 final size:80
Alignment explanation
Indices: 31888--32096 Score: 213
Period size: 87 Copynumber: 2.5 Consensus size: 80
31878 AAAGGTTTGT
* * * * *
31888 TCTTTAGCGGCATTTATAATAAAAGCG-ACGCTAAAGGTCATGACCTTTAGTGGCATTTGTGACA
1 TCTTTAGCGGCGTTTGTGACAAAAGCGCA-GCTAAAGGTCATGACCTTTAGCGGCATTTGTGACA
31952 AAAGCGCCACTAAAGTTCATGG
65 AAAGCGCCACT-AA----A-GG
* ** *
31974 TCTTTTAGCGGCGTTTGTGACAAAAGCGCAGCTAAAGCTCATGGTCTTTAGCGGCGTTTGTGACA
1 TC-TTTAGCGGCGTTTGTGACAAAAGCGCAGCTAAAGGTCATGACCTTTAGCGGCATTTGTGACA
* * *
32039 GACGCGCCGCTAAAGG
65 AAAGCGCCACTAAAGG
* *
32055 TCTTTAGCGGCGTTTGTGACAAATGCGCCGCTAAAGGTCATG
1 TCTTTAGCGGCGTTTGTGACAAAAGCGCAGCTAAAGGTCATG
32097 GTATTTAGCG
Statistics
Matches: 106, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
80 37 0.35
81 4 0.04
82 1 0.01
86 4 0.04
87 59 0.56
88 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (80 bp):
TCTTTAGCGGCGTTTGTGACAAAAGCGCAGCTAAAGGTCATGACCTTTAGCGGCATTTGTGACAA
AAGCGCCACTAAAGG
Found at i:32066 original size:37 final size:37
Alignment explanation
Indices: 31972--32093 Score: 145
Period size: 37 Copynumber: 3.1 Consensus size: 37
31962 TAAAGTTCAT
* *
31972 GGTCTTTTAGCGGCGTTTGTGACAAAAGCGCAGCTAAAGCTCA
1 GGTC-TTTAGCGGCGTTTGTGACAAACGCGCCGCT-AA----A
*
32015 TGGTCTTTAGCGGCGTTTGTGACAGACGCGCCGCTAAA
1 -GGTCTTTAGCGGCGTTTGTGACAAACGCGCCGCTAAA
*
32053 GGTCTTTAGCGGCGTTTGTGACAAATGCGCCGCTAAA
1 GGTCTTTAGCGGCGTTTGTGACAAACGCGCCGCTAAA
32090 GGTC
1 GGTC
32094 ATGGTATTTA
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
37 39 0.53
38 1 0.01
42 2 0.03
43 27 0.37
44 4 0.05
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.26
Consensus pattern (37 bp):
GGTCTTTAGCGGCGTTTGTGACAAACGCGCCGCTAAA
Found at i:35171 original size:50 final size:50
Alignment explanation
Indices: 35047--35295 Score: 284
Period size: 50 Copynumber: 4.8 Consensus size: 50
35037 GATAATAACA
* * ** * *
35047 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
35098 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
35148 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
35198 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
35253 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
35296 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 92 0.54
51 33 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:35225 original size:100 final size:104
Alignment explanation
Indices: 35046--35295 Score: 357
Period size: 100 Copynumber: 2.4 Consensus size: 104
35036 TGATAATAAC
**
35046 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
* *
35111 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* *
35148 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
35211 TCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
35253 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
35296 TTACCCAAAT
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 50 0.38
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:35411 original size:13 final size:13
Alignment explanation
Indices: 35390--35421 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
35380 GCTTGGATCA
*
35390 TCATCAAATAAAT
1 TCATAAAATAAAT
35403 TCATAAAATAAAT
1 TCATAAAATAAAT
35416 TCATAA
1 TCATAA
35422 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:35668 original size:30 final size:30
Alignment explanation
Indices: 35633--35690 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
35623 CCTCGACTCT
*
35633 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
35663 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
35691 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Done.