Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold127
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: 4281254
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 2 of 26
Found at i:235089 original size:3 final size:3
Alignment explanation
Indices: 235081--235111 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
235071 CACCCTTTAG
235081 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
235112 GCATTTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:235181 original size:29 final size:29
Alignment explanation
Indices: 235131--235187 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
235121 TATTTATTGC
* * *
235131 TATTTTTAATATATAATTTATTTTTAAAT
1 TATTTTTAATAAATAATCTATTTATAAAT
235160 TATTTTTAATAAAT-ATACTATTTATAAA
1 TATTTTTAATAAATAAT-CTATTTATAAA
235188 AATATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (29 bp):
TATTTTTAATAAATAATCTATTTATAAAT
Found at i:235192 original size:17 final size:18
Alignment explanation
Indices: 235160--235193 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
235150 ATTTTTAAAT
*
235160 TATTTTTAATAAATATAC
1 TATTTATAATAAATATAC
235178 TATTTATAA-AAATATA
1 TATTTATAATAAATATA
235194 TTTTAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTTATAATAAATATAC
Found at i:236399 original size:17 final size:16
Alignment explanation
Indices: 236361--236409 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
236351 ATGGGTACTT
*
236361 TTTATTAAAAAAATAA
1 TTTATTTAAAAAATAA
*
236377 TTTATTTAAAAAATTA
1 TTTATTTAAAAAATAA
*
236393 TTGTATTTTAAAAATAA
1 TT-TATTTAAAAAATAA
236410 GTATAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 16 0.57
17 12 0.43
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
TTTATTTAAAAAATAA
Found at i:236458 original size:19 final size:20
Alignment explanation
Indices: 236434--236471 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
236424 AAAATATTTT
236434 AAATAAAAT-TAATTAAATC
1 AAATAAAATATAATTAAATC
*
236453 AAATAAAATATATTTAAAT
1 AAATAAAATATAATTAAAT
236472 ATAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATAAAATATAATTAAATC
Found at i:236492 original size:15 final size:15
Alignment explanation
Indices: 236423--236494 Score: 56
Period size: 15 Copynumber: 4.5 Consensus size: 15
236413 TAATAATATA
*
236423 AAAAATATTTTAAAT
1 AAAAATAATTTAAAT
*
236438 AAAATTAA-TTAAAT
1 AAAAATAATTTAAAT
236452 CAAATAAAATATATTTAAAT
1 ---A-AAAATA-ATTTAAAT
* *
236472 ATAAATAATTTATAT
1 AAAAATAATTTAAAT
236487 AAAAATAA
1 AAAAATAA
236495 ATATATATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
14 6 0.13
15 20 0.44
16 5 0.11
17 2 0.04
18 5 0.11
19 1 0.02
20 6 0.13
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAAATAATTTAAAT
Found at i:236497 original size:35 final size:34
Alignment explanation
Indices: 236414--236505 Score: 96
Period size: 35 Copynumber: 2.6 Consensus size: 34
236404 AAATAAGTAT
* *
236414 AATAATATAAAAAATATTTTAAATAAAATTAATTA
1 AATAAAATAAAATATA-TTTAAATAAAATTAATTA
*
236449 AATCAAATAAAATATATTTAAATATAAA-TAATTTA
1 AATAAAATAAAATATATTTAAATA-AAATTAA-TTA
*
236484 TATAAAAATAAATATATATTTA
1 AAT-AAAATAAA-ATATATTTA
236506 TTTATGTATG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
34 11 0.23
35 21 0.44
36 7 0.15
37 9 0.19
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (34 bp):
AATAAAATAAAATATATTTAAATAAAATTAATTA
Found at i:239888 original size:2 final size:2
Alignment explanation
Indices: 239881--239908 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
239871 CTCAATTGAA
239881 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
239909 GGATAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:242458 original size:12 final size:12
Alignment explanation
Indices: 242441--242470 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
242431 TCTTCAGAAT
242441 AAATAAGTAAAC
1 AAATAAGTAAAC
*
242453 AAATAAGTAAAT
1 AAATAAGTAAAC
242465 AAATAA
1 AAATAA
242471 AAAGGTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (12 bp):
AAATAAGTAAAC
Found at i:250507 original size:31 final size:29
Alignment explanation
Indices: 250447--250530 Score: 91
Period size: 31 Copynumber: 2.9 Consensus size: 29
250437 AGTAATTATA
*
250447 TTTAAGATATTATATATATTTATAAAAAT
1 TTTAAAATATTATATATATTTATAAAAAT
*
250476 TTTAAAATATTAATAATTTATTT-TAATAAAT
1 TTTAAAATATT-AT-ATATATTTATAA-AAAT
* *
250507 TTTAATATATT-TATATATTCATAA
1 TTTAAAATATTATATATATTTATAA
250531 TATTATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
28 6 0.13
29 14 0.30
30 5 0.11
31 21 0.46
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (29 bp):
TTTAAAATATTATATATATTTATAAAAAT
Found at i:250531 original size:19 final size:18
Alignment explanation
Indices: 250443--250557 Score: 54
Period size: 20 Copynumber: 5.9 Consensus size: 18
250433 ATATAGTAAT
*
250443 TATATT-TAAGATATTATA
1 TATATTATAATATATT-TA
*
250461 TATATTTATAA-AAATTTTAA
1 TATA-TTATAATATA-TTT-A
* *
250481 AATATTAATAATTTATTTTAA
1 TATATT-ATAATATA-TTT-A
* *
250502 TAAATTTTAATATATTTA
1 TATATTATAATATATTTA
*
250520 TATATTCATAATATTATTTTT
1 TATATT-ATAATA-TA-TTTA
*
250541 TATATTATATTATATTT
1 TATATTATAATATATTT
250558 TAATTATTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
18 13 0.17
19 17 0.22
20 26 0.34
21 20 0.26
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.56
Consensus pattern (18 bp):
TATATTATAATATATTTA
Found at i:250550 original size:17 final size:16
Alignment explanation
Indices: 250505--250564 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
250495 ATTTTAATAA
250505 ATTTTAA-TATATTTAT
1 ATTTTAATTATA-TTAT
* * *
250521 ATATTCATAATATTAT
1 ATTTTAATTATATTAT
*
250537 TTTTTATATTATATTAT
1 ATTTTA-ATTATATTAT
250554 ATTTTAATTAT
1 ATTTTAATTAT
250565 TTTAATGTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
16 17 0.50
17 17 0.50
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAATTATATTAT
Found at i:251086 original size:31 final size:31
Alignment explanation
Indices: 251027--251094 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
251017 TGTATTATGG
* * **
251027 TTAAA-ATATTTTTATTTTTTTATTATTAAA
1 TTAAATATATTTTTATATATTTAAAATTAAA
251057 TTAAATATATTTTTATATATTTAAAATTAAA
1 TTAAATATATTTTTATATATTTAAAATTAAA
*
251088 ATAAATA
1 TTAAATA
251095 AAAAATTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
TTAAATATATTTTTATATATTTAAAATTAAA
Found at i:251177 original size:13 final size:13
Alignment explanation
Indices: 251161--251191 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
251151 ATATAACATG
251161 TAAATTAAATTTT
1 TAAATTAAATTTT
251174 TAAA-TAAATTTT
1 TAAATTAAATTTT
251186 TAAATT
1 TAAATT
251192 TTAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAATTAAATTTT
Found at i:251534 original size:11 final size:13
Alignment explanation
Indices: 251499--251562 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
251489 ATTTTAATTT
*
251499 TAATATTTAAATA
1 TAATATATAAATA
*
251512 CAATCATAATAAAT-
1 TAAT-AT-ATAAATA
251526 T-ATATATAAATA
1 TAATATATAAATA
*
251538 TAATATATATATA
1 TAATATATAAATA
*
251551 TATGTATATAAA
1 TA-ATATATAAA
251563 AAAATGTTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
11 6 0.15
12 3 0.08
13 17 0.43
14 9 0.22
15 5 0.12
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.41
Consensus pattern (13 bp):
TAATATATAAATA
Found at i:251789 original size:21 final size:21
Alignment explanation
Indices: 251765--251806 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
251755 TAACCAGTAA
* *
251765 TTTTAGACTTTTATTGAGGTT
1 TTTTAGACATTTAATGAGGTT
251786 TTTTAGACATTTAATGAGGTT
1 TTTTAGACATTTAATGAGGTT
251807 AATTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.19, T:0.52
Consensus pattern (21 bp):
TTTTAGACATTTAATGAGGTT
Found at i:251849 original size:22 final size:23
Alignment explanation
Indices: 251823--251865 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
251813 AATTATTATT
*
251823 TATAATCATAT-TTTATTTAAAA
1 TATAATAATATATTTATTTAAAA
*
251845 TATAATAATATATTTTTTTAA
1 TATAATAATATATTTATTTAA
251866 GAAAATATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATAATAATATATTTATTTAAAA
Found at i:252136 original size:2 final size:2
Alignment explanation
Indices: 252131--252166 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
252121 AAAAGAAGTT
252131 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
252167 ATGTTATTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:252417 original size:6 final size:6
Alignment explanation
Indices: 252406--252432 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
252396 TTTCTATTCC
252406 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
252433 TTGATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:254710 original size:21 final size:21
Alignment explanation
Indices: 254671--254721 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
254661 TTTTATTATG
254671 ATATAATTATATTAAAAATTATTT
1 ATAT-ATT-TATTAAAAATT-TTT
*
254695 -TATATTTATTATAAATTTTT
1 ATATATTTATTAAAAATTTTT
254715 ATATATT
1 ATATATT
254722 AATAATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 16 0.64
22 3 0.12
23 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATATATTTATTAAAAATTTTT
Found at i:267845 original size:2 final size:2
Alignment explanation
Indices: 267838--267879 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
267828 TATCTCCAAA
267838 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
267880 CCTTCTGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:272551 original size:2 final size:2
Alignment explanation
Indices: 272477--272531 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
272467 TGTTGACGTT
*
272477 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
272519 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
272532 CTTCTTTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:281157 original size:29 final size:29
Alignment explanation
Indices: 281098--281157 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
281088 TTTATCAAAT
*
281098 AATTATTAAAAATAATTTTTCAATCCTTAA
1 AATTATTAAAAATAATTTTT-AATCCCTAA
*
281128 AATTTTTAAAAATAATTTTT-ATCTCCTAA
1 AATTATTAAAAATAATTTTTAATC-CCTAA
281157 A
1 A
281158 TATAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 3 0.11
29 5 0.19
30 19 0.70
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (29 bp):
AATTATTAAAAATAATTTTTAATCCCTAA
Found at i:281611 original size:2 final size:2
Alignment explanation
Indices: 281600--281641 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
281590 GCGAAAAAAG
* *
281600 AT AT AG AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
281642 TACATAAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:287981 original size:2 final size:2
Alignment explanation
Indices: 287974--288018 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
287964 TCACACCACC
287974 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
288016 AT A
1 AT A
288019 AAGGCTTGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:294444 original size:2 final size:2
Alignment explanation
Indices: 294437--294468 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
294427 TGAAAAGTAA
294437 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
294469 CATCTAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:295522 original size:3 final size:3
Alignment explanation
Indices: 295474--295512 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
295464 GTCTGCTATG
295474 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
295513 ACATATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:298826 original size:2 final size:2
Alignment explanation
Indices: 298819--298856 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
298809 TCAAGGTATC
*
298819 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
298857 GTTTTTCCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:300208 original size:2 final size:2
Alignment explanation
Indices: 300201--300227 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
300191 TAAGAAGACA
300201 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
300228 CATGATCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:306407 original size:24 final size:24
Alignment explanation
Indices: 306351--306408 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
306341 AAAATAAAAA
* *
306351 ATAAGAAATATAATAATTATTTAT
1 ATAAAAAATTTAATAATTATTTAT
*
306375 TTAAAAAATTTAATATATTATTT-T
1 ATAAAAAATTTAATA-ATTATTTAT
*
306399 ATAATAAATT
1 ATAAAAAATT
306409 ATAAAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
ATAAAAAATTTAATAATTATTTAT
Found at i:307026 original size:18 final size:17
Alignment explanation
Indices: 306985--307032 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
306975 AATTAAATTT
* *
306985 AATAATTTTAAATATAA
1 AATAATTATAAATAAAA
*
307002 TATAATTATAACATAAAA
1 AATAATTATAA-ATAAAA
307020 AATAATTA-AAATA
1 AATAATTATAAATA
307033 TAATATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 3 0.12
17 11 0.42
18 12 0.46
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AATAATTATAAATAAAA
Found at i:307044 original size:21 final size:21
Alignment explanation
Indices: 307018--307090 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
307008 TATAACATAA
307018 AAAATAATTAAAATATAATAT
1 AAAATAATTAAAATATAATAT
*
307039 AAAATAA-AAATAATATAAATATCT
1 AAAATAATTAA-AATAT-AATA--T
* *
307063 AAAAT-ATCAAAAT-TTATAT
1 AAAATAATTAAAATATAATAT
307082 AAAATAATT
1 AAAATAATT
307091 CATAAAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
19 6 0.14
20 4 0.10
21 15 0.36
22 5 0.12
23 4 0.10
24 8 0.19
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATAATTAAAATATAATAT
Found at i:307051 original size:16 final size:17
Alignment explanation
Indices: 306994--307057 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 17
306984 TAATAATTTT
*
306994 AAATATAATATAATTATA
1 AAATATAATATAA-AATA
* * * *
307012 ACATAAAAAAT-AATTA
1 AAATATAATATAAAATA
307028 AAATATAATATAAAATA
1 AAATATAATATAAAATA
307045 AAA-ATAATATAAA
1 AAATATAATATAAA
307058 TATCTAAAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
16 20 0.56
17 8 0.22
18 8 0.22
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATATAATATAAAATA
Found at i:312149 original size:17 final size:16
Alignment explanation
Indices: 312126--312168 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
312116 TTATATTATT
312126 ATATAAATATTATAAA
1 ATATAAATATTATAAA
* * *
312142 ATTATAAAAAATATACA
1 A-TATAAATATTATAAA
312159 ATATAAATAT
1 ATATAAATAT
312169 ATTATTAAAG
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATAAATATTATAAA
Found at i:312172 original size:27 final size:27
Alignment explanation
Indices: 312142--312199 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
312132 ATATTATAAA
312142 ATTA-TAAAAAATATACAATATAAATAT
1 ATTATTAAAAAATATACAATATAAAT-T
*** *
312169 ATTATTAAAGTTTATATAATATAAATT
1 ATTATTAAAAAATATACAATATAAATT
312196 ATTA
1 ATTA
312200 ATATATCTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 9 0.35
28 17 0.65
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (27 bp):
ATTATTAAAAAATATACAATATAAATT
Found at i:312527 original size:18 final size:16
Alignment explanation
Indices: 312504--312549 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
312494 TAGATGTTAA
312504 AAATTTTAAATTATATT
1 AAATTTTAAATTAT-TT
*
312521 CAAATTTTAAATCATTT
1 -AAATTTTAAATTATTT
*
312538 TAATTTTAAATT
1 AAATTTTAAATT
312550 TAAATCACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 10 0.40
17 2 0.08
18 13 0.52
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (16 bp):
AAATTTTAAATTATTT
Found at i:312643 original size:37 final size:38
Alignment explanation
Indices: 312602--312681 Score: 87
Period size: 37 Copynumber: 2.1 Consensus size: 38
312592 TTGATTAATC
312602 AAATTTA-ATATTTAAAT-TTATAAAATTT-ATTCATTTT
1 AAATTTATATATTTAAATATT-TAAAATTTAATT-ATTTT
* *
312639 AAA-TTATTTATTTAAATATTTTAAATTTAAATTATTTT
1 AAATTTATATATTTAAATATTTAAAATTT-AATTATTTT
312677 AAATT
1 AAATT
312682 AAAATAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
36 3 0.08
37 19 0.53
38 10 0.28
39 4 0.11
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (38 bp):
AAATTTATATATTTAAATATTTAAAATTTAATTATTTT
Found at i:312676 original size:16 final size:16
Alignment explanation
Indices: 312636--312692 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
312626 ATTTATTCAT
312636 TTTAAATTA-TTT--A
1 TTTAAATTATTTTAAA
312649 TTTAAA-TATTTTAAA
1 TTTAAATTATTTTAAA
312664 TTTAAATTATTTTAAA
1 TTTAAATTATTTTAAA
* *
312680 TTAAAATAATTTT
1 TTTAAATTATTTT
312693 GAGTTCGGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
12 2 0.05
13 9 0.24
15 7 0.18
16 20 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:314071 original size:3 final size:3
Alignment explanation
Indices: 314065--314093 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
314055 TGACTACTAT
314065 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
314094 GGATGATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:314835 original size:18 final size:19
Alignment explanation
Indices: 314810--314859 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
314800 AAATAAGTAC
*
314810 TAATAAATTTA-TTTTTAA
1 TAATAAATTAATTTTTTAA
*
314828 TTATAAA-TAATTTTTTAA
1 TAATAAATTAATTTTTTAA
*
314846 TAATAAATAAATTT
1 TAATAAATTAATTT
314860 ATATATTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 2 0.08
18 19 0.73
19 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATAAATTAATTTTTTAA
Found at i:315272 original size:22 final size:23
Alignment explanation
Indices: 315228--315278 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
315218 TAATTAATTT
315228 TATTTATTTTTAGATATCGATTA
1 TATTTATTTTTAGATATCGATTA
*
315251 TATTT-TTTTATAGATAT-TATTA
1 TATTTATTTT-TAGATATCGATTA
315273 TATTTA
1 TATTTA
315279 AATCCAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (23 bp):
TATTTATTTTTAGATATCGATTA
Found at i:317285 original size:5 final size:5
Alignment explanation
Indices: 317275--317299 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
317265 CGTCCAAACA
317275 CATGC CATGC CATGC CATGC CATGC
1 CATGC CATGC CATGC CATGC CATGC
317300 ATCTAAAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (5 bp):
CATGC
Found at i:318631 original size:3 final size:3
Alignment explanation
Indices: 318584--318619 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
318574 TGTGGAGCAG
318584 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
318620 GATCATCTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:321327 original size:3 final size:3
Alignment explanation
Indices: 321319--321348 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
321309 CACCTGCCAA
321319 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
321349 GTAAATGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:323577 original size:16 final size:16
Alignment explanation
Indices: 323552--323583 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
323542 TGCGTTAGAA
*
323552 TAAGTTATTTTAAATT
1 TAAGTAATTTTAAATT
323568 TAAGTAATTTTAAATT
1 TAAGTAATTTTAAATT
323584 ATTTTATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
TAAGTAATTTTAAATT
Found at i:346565 original size:3 final size:3
Alignment explanation
Indices: 346557--346603 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
346547 CTTAAGAAAT
346557 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
346604 TGTGAAAAGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:353002 original size:2 final size:2
Alignment explanation
Indices: 352995--353019 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
352985 ACTCGAAATA
352995 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
353020 ATTATTGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:357547 original size:1 final size:1
Alignment explanation
Indices: 357543--357567 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
357533 TTTACCCAAC
357543 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
357568 GAGAGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:357860 original size:22 final size:22
Alignment explanation
Indices: 357834--357881 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
357824 TTTGAGAATA
*
357834 AAAAAATTATAAATATTAAAATT
1 AAAAAATTA-AAAAATTAAAATT
*
357857 AAAAAATTAAAAAATTAAATTT
1 AAAAAATTAAAAAATTAAAATT
357879 AAA
1 AAA
357882 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAAAATTAAAAAATTAAAATT
Found at i:357862 original size:8 final size:8
Alignment explanation
Indices: 357834--357875 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
357824 TTTGAGAATA
357834 AAAAAATT
1 AAAAAATT
*
357842 ATAAATATT
1 A-AAAAATT
357851 --AAAATT
1 AAAAAATT
357857 AAAAAATT
1 AAAAAATT
357865 AAAAAATT
1 AAAAAATT
357873 AAA
1 AAA
357876 TTTAAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 5 0.17
8 18 0.62
9 6 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAAAATT
Found at i:373081 original size:5 final size:5
Alignment explanation
Indices: 373071--373101 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
373061 AAAGCATTCA
373071 TTTCT TTTCT TTTCT TTTCT TTTGCT TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTT-CT TTTCT
373102 AGCACATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:383816 original size:2 final size:2
Alignment explanation
Indices: 383809--383837 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
383799 TTTCTACATA
383809 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
383838 AAATTTTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:390087 original size:11 final size:11
Alignment explanation
Indices: 390071--390099 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
390061 AAAATTTTTC
390071 TCTCTATTCTT
1 TCTCTATTCTT
390082 TCTCTATTCTT
1 TCTCTATTCTT
390093 TCTCTAT
1 TCTCTAT
390100 GCATTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.28, G:0.00, T:0.62
Consensus pattern (11 bp):
TCTCTATTCTT
Found at i:406238 original size:24 final size:24
Alignment explanation
Indices: 406211--406257 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
406201 GGGAGAAACT
* *
406211 GCTGGTGGTGGTGGCGGAGGTGGC
1 GCTGGCGGTGGGGGCGGAGGTGGC
406235 GCTGGCGGTGGGGGCGGAGGTGG
1 GCTGGCGGTGGGGGCGGAGGTGG
406258 AGGGGGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.04, C:0.13, G:0.66, T:0.17
Consensus pattern (24 bp):
GCTGGCGGTGGGGGCGGAGGTGGC
Found at i:406560 original size:33 final size:33
Alignment explanation
Indices: 406523--406587 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
406513 TCACGGATTG
*
406523 GGTGGAGGAAATGGAGGGGGAGGAGGTGGGGGA
1 GGTGGAGGAAATGGAGGAGGAGGAGGTGGGGGA
* * *
406556 GGTGGTGGGAATGGTGGAGGAGGAGGTGGGGG
1 GGTGGAGGAAATGGAGGAGGAGGAGGTGGGGG
406588 TGGAGGCAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.68, T:0.12
Consensus pattern (33 bp):
GGTGGAGGAAATGGAGGAGGAGGAGGTGGGGGA
Found at i:406639 original size:135 final size:139
Alignment explanation
Indices: 406430--406710 Score: 462
Period size: 135 Copynumber: 2.0 Consensus size: 139
406420 GGGTGGAGGT
406430 GGAGGAGGTGGGAGTGGAGGCAGTGGTGGTGGTGGTGGCGGCGGCGGCGGAAGCAGCGGTGGAGG
1 GGAGGAGGTGGGAGTGGAGGCA--GGTGGTGGTGGT-G-GGCGGCGGCGG-AGCAGCGGTGGAGG
*
406495 AGGAGGAAATGGTAAAGGTCACGGATTGGGTGGAGGAAATGGAGGGGGAGGAGGTGGGGGAGGTG
61 AGGAGGAAATGGTAAAGGTCACGGATGGGGTGGAGGAAATGGAGGGGGAGGAGGTGGGGGAGGTG
406560 GTGGGAATGGTGGA
126 GTGGGAATGGTGGA
* *
406574 GGAGGAGGTGGGGGTGGAGGCA-GTGGTGGTGGT-GGCGGCGGC-G-GCAGTGGTGGAGGAGGAG
1 GGAGGAGGTGGGAGTGGAGGCAGGTGGTGGTGGTGGGCGGCGGCGGAGCAGCGGTGGAGGAGGAG
406635 GAAATGGTAAAGGTCACGGATGGGGTGGAGGAAATGGAGGGGGAGGAGGTGGGGGAGGTGGTGGG
66 GAAATGGTAAAGGTCACGGATGGGGTGGAGGAAATGGAGGGGGAGGAGGTGGGGGAGGTGGTGGG
406700 AATGGTGGA
131 AATGGTGGA
406709 GG
1 GG
406711 CAACGGTGGG
Statistics
Matches: 134, Mismatches: 3, Indels: 9
0.92 0.02 0.06
Matches are distributed among these distances:
135 92 0.69
137 1 0.01
138 9 0.07
141 11 0.08
144 21 0.16
ACGTcount: A:0.20, C:0.06, G:0.60, T:0.14
Consensus pattern (139 bp):
GGAGGAGGTGGGAGTGGAGGCAGGTGGTGGTGGTGGGCGGCGGCGGAGCAGCGGTGGAGGAGGAG
GAAATGGTAAAGGTCACGGATGGGGTGGAGGAAATGGAGGGGGAGGAGGTGGGGGAGGTGGTGGG
AATGGTGGA
Found at i:406740 original size:30 final size:30
Alignment explanation
Indices: 406706--406825 Score: 79
Period size: 30 Copynumber: 4.0 Consensus size: 30
406696 TGGGAATGGT
406706 GGAGGCAACGGTGGGCGAGGTGGAGGTGGA
1 GGAGGCAACGGTGGGCGAGGTGGAGGTGGA
*
406736 GGAGGCAA---T-GGCAGAGGTCATGGATGG-GGT
1 GGAGGCAACGGTGGGC-GAGG---TGGA-GGTGGA
* * * * * * *
406766 GGAGGAAATGGAGGGGGAGGTGGTGGGGGT
1 GGAGGCAACGGTGGGCGAGGTGGAGGTGGA
*
406796 GGAGGCAACGGTGGGGGAGGTGGAGGTGGA
1 GGAGGCAACGGTGGGCGAGGTGGAGGTGGA
406826 TGGGGTGGAG
Statistics
Matches: 69, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
26 3 0.04
27 5 0.07
29 2 0.03
30 51 0.74
31 2 0.03
33 4 0.06
34 2 0.03
ACGTcount: A:0.21, C:0.07, G:0.60, T:0.12
Consensus pattern (30 bp):
GGAGGCAACGGTGGGCGAGGTGGAGGTGGA
Found at i:406770 original size:135 final size:133
Alignment explanation
Indices: 406463--406776 Score: 386
Period size: 135 Copynumber: 2.3 Consensus size: 133
406453 TGGTGGTGGT
* * * * * *
406463 GGTGGCGGCGGCGGCGGAAGCAGCGGTGGAGGAGGAGGAAATGGTAAAGGTCACGGATTGGGTGG
1 GGTGGAGGAGGCGGCAGAGGCAGTGGTGGAGGAGGAGGAAATGGTAAAGGTCACGGATGGGGTGG
* *
406528 AGGAAATGGAGGGGGAGGAGGTGGGGGAGGTGGTGGGAATGGTGGAGGAGGAGGTGGGGGTGGAG
66 AGGAAATGGAGGGGGAGGAGGTGGGGGAGGTGGTGGGAATGGTGGAGGA-GAGGTGGGCGAGGAG
406593 GCAG
130 GCAG
* * * *
406597 TGGTGGTGGTGGCGGCGGCGGCAGTGGTGGAGGAGGAGGAAATGGTAAAGGTCACGGATGGGGTG
1 -GGTGGAGGAGGCGGCAGAGGCAGTGGTGGAGGAGGAGGAAATGGTAAAGGTCACGGATGGGGTG
406662 GAGGAAATGGAGGGGGAGGAGGTGGGGGAGGTGGTGGGAATGGTGGAGGCA-ACGGTGGGCGAGG
65 GAGGAAATGGAGGGGGAGGAGGTGGGGGAGGTGGTGGGAATGGTGGAGG-AGA-GGTGGGCGAGG
*
406726 TGG-A-
128 AGGCAG
*
406730 GGTGGAGGAGGCAATGGCAGAGGTCA-TGGATGG-GGTGGAGGAAATGG
1 GGTGGAGGAGGC---GGCAGAGG-CAGTGG-TGGAGGAGGAGGAAATGG
406777 AGGGGGAGGT
Statistics
Matches: 158, Mismatches: 14, Indels: 14
0.85 0.08 0.08
Matches are distributed among these distances:
132 10 0.06
134 2 0.01
135 140 0.89
136 6 0.04
ACGTcount: A:0.22, C:0.07, G:0.58, T:0.13
Consensus pattern (133 bp):
GGTGGAGGAGGCGGCAGAGGCAGTGGTGGAGGAGGAGGAAATGGTAAAGGTCACGGATGGGGTGG
AGGAAATGGAGGGGGAGGAGGTGGGGGAGGTGGTGGGAATGGTGGAGGAGAGGTGGGCGAGGAGG
CAG
Found at i:406799 original size:15 final size:15
Alignment explanation
Indices: 406781--406862 Score: 51
Period size: 15 Copynumber: 5.1 Consensus size: 15
406771 AAATGGAGGG
406781 GGAGGTGGTGGGGGT
1 GGAGGTGGTGGGGGT
*
406796 GGAGGCAACGGTGGGGGAGGT
1 GGAGG---TGGT--GGG-GGT
406817 GGAGGTGGAT-GGGGT
1 GGAGGTGG-TGGGGGT
**
406832 GGAGGAAGTGGAGGG-
1 GGAGGTGGTGG-GGGT
406847 GGAGGTGGTGGGGGT
1 GGAGGTGGTGGGGGT
406862 G
1 G
406863 AAGGCAACGG
Statistics
Matches: 51, Mismatches: 6, Indels: 20
0.66 0.08 0.26
Matches are distributed among these distances:
14 4 0.08
15 25 0.49
16 5 0.10
18 5 0.10
19 1 0.02
20 3 0.06
21 8 0.16
ACGTcount: A:0.15, C:0.02, G:0.68, T:0.15
Consensus pattern (15 bp):
GGAGGTGGTGGGGGT
Found at i:406815 original size:36 final size:36
Alignment explanation
Indices: 406775--406881 Score: 138
Period size: 36 Copynumber: 3.1 Consensus size: 36
406765 TGGAGGAAAT
406775 GGAGGGGGAGGTGGTGGGGGTGGAGGCAACGGTGGG
1 GGAGGGGGAGGTGGTGGGGGTGGAGGCAACGGTGGG
*
406811 GGAGGTGGAGGTGGAT-GGGGTGGAGG-AA--GT---
1 GGAGGGGGAGGTGG-TGGGGGTGGAGGCAACGGTGGG
*
406841 GGAGGGGGAGGTGGTGGGGGTGAAGGCAACGGTGGG
1 GGAGGGGGAGGTGGTGGGGGTGGAGGCAACGGTGGG
406877 GGAGG
1 GGAGG
406882 TGGCGGCGGG
Statistics
Matches: 60, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
29 1 0.02
30 22 0.37
31 2 0.03
33 4 0.07
35 2 0.03
36 28 0.47
37 1 0.02
ACGTcount: A:0.17, C:0.04, G:0.67, T:0.12
Consensus pattern (36 bp):
GGAGGGGGAGGTGGTGGGGGTGGAGGCAACGGTGGG
Found at i:406830 original size:18 final size:18
Alignment explanation
Indices: 406808--406854 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
406798 AGGCAACGGT
*
406808 GGGGGAGGTGGAGGTGGA
1 GGGGGAGGTGGAAGTGGA
* * *
406826 TGGGGTGGAGGAAGTGGA
1 GGGGGAGGTGGAAGTGGA
406844 GGGGGAGGTGG
1 GGGGGAGGTGG
406855 TGGGGGTGAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.00, G:0.70, T:0.13
Consensus pattern (18 bp):
GGGGGAGGTGGAAGTGGA
Found at i:406845 original size:30 final size:29
Alignment explanation
Indices: 406760--406938 Score: 117
Period size: 30 Copynumber: 5.8 Consensus size: 29
406750 AGGTCATGGA
*
406760 TGGGGTGGAGGAAATGGAGGGGGAGGTGG
1 TGGGGTGGAGGAAGTGGAGGGGGAGGTGG
*
406789 TGGGGGTGGAGGCAACGGTGGGGGAGGTGGAGGTGG
1 T-GGGGTGGAGG-AA--GT---GGAGGGGGAGGTGG
406825 ATGGGGTGGAGGAAGTGGAGGGGGAGGTGG
1 -TGGGGTGGAGGAAGTGGAGGGGGAGGTGG
* * *
406855 TGGGGGTGAAGGCAA-CGGTGGGGGAGGTGG
1 T-GGGGTGGAGG-AAGTGGAGGGGGAGGTGG
* * * * *
406885 CGGCGGGGGTGGAGGTGGAGGTGGAGGTGG
1 TGG-GGTGGAGGAAGTGGAGGGGGAGGTGG
* * * *
406915 AGGTGGAGGAGGAGGAGGAGGGGG
1 TGG-GGTGGAGGAAGTGGAGGGGG
406939 TAGTCAAGGT
Statistics
Matches: 118, Mismatches: 20, Indels: 23
0.73 0.12 0.14
Matches are distributed among these distances:
29 5 0.04
30 80 0.68
31 4 0.03
33 3 0.03
35 2 0.02
36 23 0.19
37 1 0.01
ACGTcount: A:0.17, C:0.03, G:0.67, T:0.12
Consensus pattern (29 bp):
TGGGGTGGAGGAAGTGGAGGGGGAGGTGG
Found at i:406846 original size:66 final size:66
Alignment explanation
Indices: 406756--406884 Score: 240
Period size: 66 Copynumber: 2.0 Consensus size: 66
406746 GCAGAGGTCA
*
406756 TGGATGGGGTGGAGGAAATGGAGGGGGAGGTGGTGGGGGTGGAGGCAACGGTGGGGGAGGTGGAG
1 TGGATGGGGTGGAGGAAATGGAGGGGGAGGTGGTGGGGGTGAAGGCAACGGTGGGGGAGGTGGAG
406821 G
66 G
*
406822 TGGATGGGGTGGAGGAAGTGGAGGGGGAGGTGGTGGGGGTGAAGGCAACGGTGGGGGAGGTGG
1 TGGATGGGGTGGAGGAAATGGAGGGGGAGGTGGTGGGGGTGAAGGCAACGGTGGGGGAGGTGG
406885 CGGCGGGGGT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.18, C:0.03, G:0.65, T:0.14
Consensus pattern (66 bp):
TGGATGGGGTGGAGGAAATGGAGGGGGAGGTGGTGGGGGTGAAGGCAACGGTGGGGGAGGTGGAG
G
Found at i:406909 original size:66 final size:66
Alignment explanation
Indices: 406761--406920 Score: 214
Period size: 66 Copynumber: 2.4 Consensus size: 66
406751 GGTCATGGAT
* * * *
406761 GGGGTGGAGGAAATGGAGGGGGAGGTGGTGGGGGTGGAGGCAACGGTGGGGGAGGTGGAGGTGGA
1 GGGGAGGAGGAAGTGGAGGGGGAGGTGGTGGGGGTGAAGGCAACGGTGGGGGAGGTGGAGGCGGA
*
406826 T
66 G
* *
406827 GGGGTGGAGGAAGTGGAGGGGGAGGTGGTGGGGGTGAAGGCAACGGTGGGGGAGGTGGCGGCGG-
1 GGGGAGGAGGAAGTGGAGGGGGAGGTGGTGGGGGTGAAGGCAACGGTGGGGGAGGTGGAGGCGGA
406891 G
66 G
* * *
406892 GGTGGAGGTGGAGGTGGAGGTGGAGGTGG
1 GG-GGAGGAGGAAGTGGAGGGGGAGGTGG
406921 AGGAGGAGGA
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
65 2 0.02
66 82 0.98
ACGTcount: A:0.16, C:0.04, G:0.67, T:0.13
Consensus pattern (66 bp):
GGGGAGGAGGAAGTGGAGGGGGAGGTGGTGGGGGTGAAGGCAACGGTGGGGGAGGTGGAGGCGGA
G
Found at i:406954 original size:6 final size:6
Alignment explanation
Indices: 406877--406935 Score: 73
Period size: 6 Copynumber: 9.8 Consensus size: 6
406867 CAACGGTGGG
* * * *
406877 GGAGGT GGCGGC GGGGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGA
1 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT
*
406925 GGAGGA GGAGG
1 GGAGGT GGAGG
406936 GGGTAGTCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.17, C:0.03, G:0.69, T:0.10
Consensus pattern (6 bp):
GGAGGT
Found at i:407658 original size:1 final size:1
Alignment explanation
Indices: 407652--407676 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
407642 CCATTAACAG
407652 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
407677 GGCAATCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:408127 original size:20 final size:19
Alignment explanation
Indices: 408099--408140 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
408089 AAATATGATT
*
408099 ATAATATAAAAATATTATAA
1 ATAAAATAAAAATA-TATAA
408119 ATAAAATAAAAATATATAA
1 ATAAAATAAAAATATATAA
408138 ATA
1 ATA
408141 TTAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAAATAAAAATATATAA
Found at i:420208 original size:2 final size:2
Alignment explanation
Indices: 420201--420235 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
420191 AAGAAATTAT
* *
420201 GA GA GA GA GA GA GC GA GA GA GA GG GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
420236 TGCAGCAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.03, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:421663 original size:32 final size:34
Alignment explanation
Indices: 421624--421692 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 34
421614 TTTGGAGTAG
*
421624 TAAGTTTATTTTAATAAATTT-TATAA-AATATT
1 TAAGTTTAATTTAATAAATTTATATAATAATATT
* *
421656 TAAGTTTAATTTAATTAATTTATATAATAATTTT
1 TAAGTTTAATTTAATAAATTTATATAATAATATT
421690 TAA
1 TAA
421693 AAATTAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 19 0.59
33 5 0.16
34 8 0.25
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (34 bp):
TAAGTTTAATTTAATAAATTTATATAATAATATT
Found at i:421857 original size:23 final size:20
Alignment explanation
Indices: 421820--421861 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 20
421810 AATTTATTTT
421820 AAAATATTTTTATATATTTAA
1 AAAATATTTTTATAT-TTTAA
421841 AAAATTATATTTTATATTTTA
1 AAAA-TAT-TTTTATATTTTA
421862 TATTCGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 7 0.37
23 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AAAATATTTTTATATTTTAA
Found at i:422469 original size:13 final size:13
Alignment explanation
Indices: 422453--422482 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
422443 ACAATAGAAT
422453 ATATAAATATATA
1 ATATAAATATATA
*
422466 ATATAATTATATA
1 ATATAAATATATA
422479 ATAT
1 ATAT
422483 TTATTATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATAAATATATA
Found at i:423506 original size:2 final size:2
Alignment explanation
Indices: 423499--423535 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
423489 TCGAGGTGTT
423499 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
423536 TCACACACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:424505 original size:2 final size:2
Alignment explanation
Indices: 424500--424528 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
424490 ATATATATAT
424500 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
424529 TGGGTTGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:425594 original size:17 final size:18
Alignment explanation
Indices: 425569--425602 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
425559 CCTCAAATGG
425569 CTTTGGGACC-CTAAAAC
1 CTTTGGGACCTCTAAAAC
*
425586 CTTTTGGACCTCTAAAA
1 CTTTGGGACCTCTAAAA
425603 TGGTATGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (18 bp):
CTTTGGGACCTCTAAAAC
Found at i:425762 original size:2 final size:2
Alignment explanation
Indices: 425755--425779 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
425745 TAAAATATTC
425755 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
425780 ATAATTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:426435 original size:58 final size:58
Alignment explanation
Indices: 426345--426460 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
426335 TGCTTTGCCC
426345 TAGCTTTTAGATTAAGGAATGAAAGCATTAGCTGATACCATGGCATCTTGACAGCCAA
1 TAGCTTTTAGATTAAGGAATGAAAGCATTAGCTGATACCATGGCATCTTGACAGCCAA
426403 TAGCTTTTAGATTAAGGAATGAAAGCATTAGCTGATACCATGGCATCTTGACAGCCAA
1 TAGCTTTTAGATTAAGGAATGAAAGCATTAGCTGATACCATGGCATCTTGACAGCCAA
426461 ATAACTTGTG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (58 bp):
TAGCTTTTAGATTAAGGAATGAAAGCATTAGCTGATACCATGGCATCTTGACAGCCAA
Found at i:431731 original size:2 final size:2
Alignment explanation
Indices: 431726--431753 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
431716 TTTGTGTGTG
431726 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
431754 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:431758 original size:2 final size:2
Alignment explanation
Indices: 431753--431782 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
431743 ATATATATAT
431753 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
431783 GATTTTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:437002 original size:28 final size:25
Alignment explanation
Indices: 436963--437013 Score: 59
Period size: 25 Copynumber: 1.9 Consensus size: 25
436953 AATGTATCTA
436963 AAATAATGAATAAATTTATTATTATACT
1 AAATAATGAAT--A-TTATTATTATACT
436991 AAATATAT-AATATTATTATTATA
1 AAATA-ATGAATATTATTATTATA
437014 AATAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
25 11 0.50
26 1 0.05
28 8 0.36
29 2 0.09
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
AAATAATGAATATTATTATTATACT
Found at i:437004 original size:22 final size:20
Alignment explanation
Indices: 436979--437031 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
436969 TGAATAAATT
436979 TATTATTA-TACTAAATATATAA
1 TATTATTATTA-TAAATA-AT-A
437001 TATTATTATTATAAATAATA
1 TATTATTATTATAAATAATA
437021 TATTATATATT
1 TATTAT-TATT
437032 TTAACATAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.24
21 6 0.21
22 14 0.48
23 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTATTATTATAAATAATA
Found at i:437020 original size:25 final size:25
Alignment explanation
Indices: 436978--437028 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
436968 ATGAATAAAT
*
436978 TTATTATTATACTAAATATATAATA
1 TTATTATTATAATAAATATATAATA
*
437003 TTATTATTATAA-ATAATATATTATA
1 TTATTATTATAATA-AATATATAATA
437028 T
1 T
437029 ATTTTAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (25 bp):
TTATTATTATAATAAATATATAATA
Found at i:437271 original size:19 final size:21
Alignment explanation
Indices: 437247--437288 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
437237 AAAATTATTT
437247 TAAAAAA-TTTAATTTT-TAA
1 TAAAAAATTTTAATTTTATAA
437266 TAAAAAATTTTAATTTTATAA
1 TAAAAAATTTTAATTTTATAA
437287 TA
1 TA
437289 TTTTACTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 9 0.43
21 5 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAAAAATTTTAATTTTATAA
Found at i:438172 original size:30 final size:28
Alignment explanation
Indices: 438146--438226 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 28
438136 GATAATAATT
438146 TAATTATTAAAAAAATTAAAATTAAT-A
1 TAATTATTAAAAAAATTAAAATTAATAA
* * * *
438173 TAATAATATAAATAAATAAAAATATATTAA
1 TAATTAT-TAAAAAAATTAAAAT-TAATAA
*
438203 TAATTATTAAAACAAAATAAAATT
1 TAATTATTAAAA-AAATTAAAATT
438227 CACTCATCAT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
27 6 0.14
28 13 0.31
29 8 0.19
30 15 0.36
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (28 bp):
TAATTATTAAAAAAATTAAAATTAATAA
Found at i:438192 original size:27 final size:28
Alignment explanation
Indices: 438145--438224 Score: 67
Period size: 27 Copynumber: 2.8 Consensus size: 28
438135 AGATAATAAT
* *
438145 TTAATTAT-TAAAAAAATTAAAATTA-A
1 TTAATAATATAAAAAAATTAAAAATATA
*
438171 TATAATAATATAAATAAA-TAAAAATATA
1 T-TAATAATATAAAAAAATTAAAAATATA
*
438199 TTAATAATTATTAAAACAAAATAAAA
1 TTAATAA-TA-TAAAA-AAATTAAAA
438225 TTCACTCATC
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
26 1 0.02
27 19 0.44
28 11 0.26
29 4 0.09
30 3 0.07
31 5 0.12
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (28 bp):
TTAATAATATAAAAAAATTAAAAATATA
Found at i:445285 original size:43 final size:44
Alignment explanation
Indices: 445197--445292 Score: 108
Period size: 43 Copynumber: 2.2 Consensus size: 44
445187 ACATTAAATT
* *
445197 CTTTTAGCACATATACTTTTGATACAGGAACTTTGTCATAGATA
1 CTTTTAACACAAATACTTTTGATACAGGAACTTTGTCATAGATA
* * *
445241 C-TTTAACACAAATATTTTTGGTACAGGTACTTTAG-CACTA-ATA
1 CTTTTAACACAAATACTTTTGATACAGGAACTTT-GTCA-TAGATA
445284 CTTTTAACA
1 CTTTTAACA
445293 TAGGTCTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
43 33 0.75
44 11 0.25
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (44 bp):
CTTTTAACACAAATACTTTTGATACAGGAACTTTGTCATAGATA
Found at i:445328 original size:15 final size:15
Alignment explanation
Indices: 445263--445333 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 15
445253 TATTTTTGGT
445263 ACAGGTAC-TTTAGC
1 ACAGGTACTTTTAGC
* *
445277 ACTA-ATACTTTTAAC
1 AC-AGGTACTTTTAGC
* * *
445292 ATAGGT-CTTTTGGT
1 ACAGGTACTTTTAGC
*
445306 ACATGTACTTTTAGC
1 ACAGGTACTTTTAGC
445321 ACAGGTACTTTTA
1 ACAGGTACTTTTA
445334 ACAGAGATGA
Statistics
Matches: 41, Mismatches: 12, Indels: 7
0.68 0.20 0.12
Matches are distributed among these distances:
14 15 0.37
15 26 0.63
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (15 bp):
ACAGGTACTTTTAGC
Found at i:449860 original size:2 final size:2
Alignment explanation
Indices: 449853--449887 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
449843 GTCAATTGCA
*
449853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
449888 AAAGTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:464809 original size:88 final size:88
Alignment explanation
Indices: 464657--464834 Score: 302
Period size: 88 Copynumber: 2.0 Consensus size: 88
464647 CACTAACCAG
* * *
464657 GATTAAAGCTTCGTTAACCTTGATTAAGCTAAAATACATAAACAGGGAAAGCAATAATATGAAAC
1 GATTAAAGCTTCGTTAACCTTGATTAACCTAAAATACATAAACAGGAAAAGCAATAATACGAAAC
464722 TTATTAAAAAAATTAGTTTAGTT
66 TTATTAAAAAAATTAGTTTAGTT
* *
464745 GATTAAAGCTTCGTTAACCTTGATTAACCTTAAATACATAACCAGGAAAAGCAATAATACGAAAC
1 GATTAAAGCTTCGTTAACCTTGATTAACCTAAAATACATAAACAGGAAAAGCAATAATACGAAAC
*
464810 TTATTAAAAAATTTAGTTTAGTT
66 TTATTAAAAAAATTAGTTTAGTT
464833 GA
1 GA
464835 CTTGTTAAGG
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (88 bp):
GATTAAAGCTTCGTTAACCTTGATTAACCTAAAATACATAAACAGGAAAAGCAATAATACGAAAC
TTATTAAAAAAATTAGTTTAGTT
Found at i:469145 original size:260 final size:260
Alignment explanation
Indices: 468684--469207 Score: 1021
Period size: 260 Copynumber: 2.0 Consensus size: 260
468674 AGTGCCAAAA
468684 GCAAAAAGATTTTAACATAAATTTTAGATTAGATAGATGTGCTAATGAAAGGTGATTTGTAAGAT
1 GCAAAAAGATTTTAACATAAATTTTAGATTAGATAGATGTGCTAATGAAAGGTGATTTGTAAGAT
468749 AACAATGGCGTGGGCCTTTGCCAGTATTTGATGATTAATGTTGGTTGGCTGCCTATAGTGATGGA
66 AACAATGGCGTGGGCCTTTGCCAGTATTTGATGATTAATGTTGGTTGGCTGCCTATAGTGATGGA
468814 AGGTTTTTTGCCAAAAACTAGATTAAACACATGCCTGCATGACTTGCATGTAATGAAGAGTATGA
131 AGGTTTTTTGCCAAAAACTAGATTAAACACATGCCTGCATGACTTGCATGTAATGAAGAGTATGA
468879 CTAGAAGAAGCATATCAACGAAGATAGAGTTTCTTTTCAGCAAGGTCTGCGAAGAAATTGACTTG
196 CTAGAAGAAGCATATCAACGAAGATAGAGTTTCTTTTCAGCAAGGTCTGCGAAGAAATTGACTTG
*
468944 GCAAAAAGATTTTAACATAAATTTTAGATTAGATAGATGTGCTACTGAAAGGTGATTTGTAAGAT
1 GCAAAAAGATTTTAACATAAATTTTAGATTAGATAGATGTGCTAATGAAAGGTGATTTGTAAGAT
**
469009 AACAATGGCGTGGGCCTTTGTTAGTATTTGATGATTAATGTTGGTTGGCTGCCTATAGTGATGGA
66 AACAATGGCGTGGGCCTTTGCCAGTATTTGATGATTAATGTTGGTTGGCTGCCTATAGTGATGGA
469074 AGGTTTTTTGCCAAAAACTAGATTAAACACATGCCTGCATGACTTGCATGTAATGAAGAGTATGA
131 AGGTTTTTTGCCAAAAACTAGATTAAACACATGCCTGCATGACTTGCATGTAATGAAGAGTATGA
469139 CTAGAAGAAGCATATCAACGAAGATAGAGTTTCTTTTCAGCAAGGTCTGCGAAGAAATTGACTTG
196 CTAGAAGAAGCATATCAACGAAGATAGAGTTTCTTTTCAGCAAGGTCTGCGAAGAAATTGACTTG
469204 GCAA
1 GCAA
469208 TTTTTCGTTT
Statistics
Matches: 261, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
260 261 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (260 bp):
GCAAAAAGATTTTAACATAAATTTTAGATTAGATAGATGTGCTAATGAAAGGTGATTTGTAAGAT
AACAATGGCGTGGGCCTTTGCCAGTATTTGATGATTAATGTTGGTTGGCTGCCTATAGTGATGGA
AGGTTTTTTGCCAAAAACTAGATTAAACACATGCCTGCATGACTTGCATGTAATGAAGAGTATGA
CTAGAAGAAGCATATCAACGAAGATAGAGTTTCTTTTCAGCAAGGTCTGCGAAGAAATTGACTTG
Found at i:474566 original size:2 final size:2
Alignment explanation
Indices: 474559--474591 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
474549 AATATGTATT
474559 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
474592 TGTTGCTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:482873 original size:136 final size:136
Alignment explanation
Indices: 482627--482898 Score: 508
Period size: 136 Copynumber: 2.0 Consensus size: 136
482617 AATCAGATGA
*
482627 AACTTTGAATAGACTGGCAGAGAAAGGATTGCGAACTGAGCTAGTAATATTTTATTAGTAATGAA
1 AACTTTCAATAGACTGGCAGAGAAAGGATTGCGAACTGAGCTAGTAATATTTTATTAGTAATGAA
*
482692 ATTTACATATTATTAGACTACAGTATTCTTCTAAACCCACACATTACTTCTTTTTACCATTCTTT
66 ATTTACACATTATTAGACTACAGTATTCTTCTAAACCCACACATTACTTCTTTTTACCATTCTTT
482757 TTCTGT
131 TTCTGT
*
482763 AACTTTCAATAGACTTGCAGAGAAAGGATTGCGAACTGAGCTAGTAATATTTTATTAGTAATGAA
1 AACTTTCAATAGACTGGCAGAGAAAGGATTGCGAACTGAGCTAGTAATATTTTATTAGTAATGAA
*
482828 ATTTACACATTATTAGACTACAGTATTCTTCTAAACCCACCCATTACTTCTTTTTACCATTCTTT
66 ATTTACACATTATTAGACTACAGTATTCTTCTAAACCCACACATTACTTCTTTTTACCATTCTTT
482893 TTCTGT
131 TTCTGT
482899 TCATCGTCAG
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
136 132 1.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.38
Consensus pattern (136 bp):
AACTTTCAATAGACTGGCAGAGAAAGGATTGCGAACTGAGCTAGTAATATTTTATTAGTAATGAA
ATTTACACATTATTAGACTACAGTATTCTTCTAAACCCACACATTACTTCTTTTTACCATTCTTT
TTCTGT
Found at i:485108 original size:20 final size:22
Alignment explanation
Indices: 485085--485138 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
485075 TTTTATTATA
485085 ATATTAAAATATA-T-ATTAAT
1 ATATTAAAATATATTAATTAAT
* * *
485105 ATATTTAAATTTATTAATTTAT
1 ATATTAAAATATATTAATTAAT
*
485127 ATATAAAAATAT
1 ATATTAAAATAT
485139 TTTTAAATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 11 0.42
21 1 0.04
22 14 0.54
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATATTAAAATATATTAATTAAT
Found at i:485119 original size:18 final size:19
Alignment explanation
Indices: 485076--485122 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
485066 AAATATTATT
485076 TTTATT-ATAATATTAAAA
1 TTTATTAATAATATTAAAA
*
485094 TATATATTAAT-ATATTTAAA
1 T-T-TATTAATAATATTAAAA
485114 TTTATTAAT
1 TTTATTAAT
485123 TTATATATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 8 0.32
19 2 0.08
20 13 0.52
21 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTATTAATAATATTAAAA
Found at i:485361 original size:31 final size:29
Alignment explanation
Indices: 485306--485365 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
485296 TCAAGTTTGT
*
485306 AAAAAATTTTATTTAACTTTTTAAAATTTA
1 AAAAAATTATATTTAACTTTTT-AAATTTA
485336 AAAATAATTATATTTAA-TTTATTAAATTTA
1 AAAA-AATTATATTTAACTTT-TTAAATTTA
485366 CGATCAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 14 0.52
31 13 0.48
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (29 bp):
AAAAAATTATATTTAACTTTTTAAATTTA
Found at i:485914 original size:24 final size:23
Alignment explanation
Indices: 485859--485934 Score: 75
Period size: 24 Copynumber: 3.3 Consensus size: 23
485849 TTTTATTATA
485859 TTATTAAATT-TAATATTAATTT
1 TTATTAAATTATAATATTAATTT
**
485881 TTATCGAATTATAAATATTTAA-TT
1 TTATTAAATTAT-AATA-TTAATTT
**
485905 TTATTAAATTATTTTATTAAATTT
1 TTATTAAATTATAATATT-AATTT
485929 TTATTA
1 TTATTA
485935 TTAATAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
22 10 0.23
23 5 0.12
24 24 0.56
25 4 0.09
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (23 bp):
TTATTAAATTATAATATTAATTT
Found at i:485920 original size:13 final size:13
Alignment explanation
Indices: 485902--485983 Score: 65
Period size: 13 Copynumber: 5.8 Consensus size: 13
485892 TAAATATTTA
485902 ATTTTATTAAATT
1 ATTTTATTAAATT
485915 ATTTTATTAAATTTTT
1 ATTTTATTAAA---TT
*
485931 ATTATTAATAAATT
1 ATT-TTATTAAATT
* *
485945 ATGTTATTTATATT
1 ATTTTA-TTAAATT
*
485959 AATTTTATTAAATA
1 -ATTTTATTAAATT
*
485973 ATTTTAATAAA
1 ATTTTATTAAA
485984 AAAATTAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
13 24 0.44
14 14 0.25
15 5 0.09
16 5 0.09
17 7 0.13
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (13 bp):
ATTTTATTAAATT
Found at i:485943 original size:30 final size:30
Alignment explanation
Indices: 485892--485971 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
485882 TATCGAATTA
* *
485892 TAAATATTTAATTTTATTAAATTATTTTAT
1 TAAATATTTAATTTTAATAAATTATGTTAT
*
485922 TAAAT-TTTTATTATTAATAAATTATGTTAT
1 TAAATATTTAATT-TTAATAAATTATGTTAT
* *
485952 T-TATA-TTAATTTTATTAAAT
1 TAAATATTTAATTTTAATAAAT
485972 AATTTTAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 8 0.19
29 13 0.31
30 21 0.50
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (30 bp):
TAAATATTTAATTTTAATAAATTATGTTAT
Found at i:486247 original size:23 final size:23
Alignment explanation
Indices: 486221--486267 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
486211 AATTATGAAA
486221 TGAGTAATTTTTCATTTCAAGCT
1 TGAGTAATTTTTCATTTCAAGCT
486244 TGAGTAATTTTTCATTTCAAGCT
1 TGAGTAATTTTTCATTTCAAGCT
486267 T
1 T
486268 ATTGAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.49
Consensus pattern (23 bp):
TGAGTAATTTTTCATTTCAAGCT
Found at i:492331 original size:6 final size:6
Alignment explanation
Indices: 492322--492347 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
492312 TTATTAATTC
492322 TAATGA TAATGA TAATGA TAATGA TA
1 TAATGA TAATGA TAATGA TAATGA TA
492348 TAATCTCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (6 bp):
TAATGA
Found at i:495875 original size:16 final size:16
Alignment explanation
Indices: 495846--495890 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
495836 ATATAAATAT
*
495846 AATATATAATTTTTCA
1 AATATATATTTTTTCA
*
495862 AATATATATTTTTTTA
1 AATATATATTTTTTCA
* *
495878 AAAAAATATTTTT
1 AATATATATTTTT
495891 ACATATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
AATATATATTTTTTCA
Found at i:496203 original size:19 final size:18
Alignment explanation
Indices: 496174--496227 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
496164 GTTTTCAAGA
*
496174 TAAAATATATAAAAAAAT
1 TAAAATTTATAAAAAAAT
* **
496192 ATTAAATTTATATTAAAAT
1 -TAAAATTTATAAAAAAAT
496211 TAAAATTATATAAAAAA
1 TAAAATT-TATAAAAAA
496228 TCGACATAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATTTATAAAAAAAT
Found at i:496226 original size:17 final size:17
Alignment explanation
Indices: 496187--496226 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
496177 AATATATAAA
*
496187 AAAATATTAAATTTATAT
1 AAAA-ATTAAAATTATAT
*
496205 TAAAATTAAAATTATAT
1 AAAAATTAAAATTATAT
496222 AAAAA
1 AAAAA
496227 ATCGACATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAAATTAAAATTATAT
Found at i:497457 original size:20 final size:19
Alignment explanation
Indices: 497424--497475 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
497414 AAAATTTTGT
* *
497424 ATTAATATGTATTGGTATCA
1 ATTAATATG-ATTGATATAA
497444 ATTAATATTGATTGATATAA
1 ATTAATA-TGATTGATATAA
*
497464 ATTGATATGATT
1 ATTAATATGATT
497476 AATGTCAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.18
20 21 0.75
21 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.46
Consensus pattern (19 bp):
ATTAATATGATTGATATAA
Found at i:500291 original size:23 final size:24
Alignment explanation
Indices: 500245--500294 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
500235 TATTAAAAAA
500245 AATAAAAATTTAATTAATTCGATT
1 AATAAAAATTTAATTAATTCGATT
* *
500269 AATAAAATTTTGATTAATT-GATT
1 AATAAAAATTTAATTAATTCGATT
500292 AAT
1 AAT
500295 CAGATTGATG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (24 bp):
AATAAAAATTTAATTAATTCGATT
Found at i:501005 original size:2 final size:2
Alignment explanation
Indices: 500998--501026 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
500988 TGAAGGTAAG
500998 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
501027 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:502608 original size:25 final size:27
Alignment explanation
Indices: 502580--502636 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 27
502570 TTTTAAAAGG
502580 TTTTTAAAAATGATTT-AAAATT-AT-AT
1 TTTTTAAAAAT--TTTAAAAATTAATCAT
502606 TTTTTAAAAATTTTAAAAATTAATCAT
1 TTTTTAAAAATTTTAAAAATTAATCAT
502633 TTTT
1 TTTT
502637 AATATTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.11
25 6 0.21
26 13 0.46
27 6 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
TTTTTAAAAATTTTAAAAATTAATCAT
Found at i:502700 original size:32 final size:32
Alignment explanation
Indices: 502633--502701 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
502623 AATTAATCAT
* * * *
502633 TTTTAATATTATTAAATTAACACAAACATTAA
1 TTTTAATACTATTAAATTAAAACAAAAAATAA
* *
502665 TTTTAATACTATTAAATTTAAAATAAAAAATAT
1 TTTTAATACTATTAAA-TTAAAACAAAAAATAA
502698 TTTT
1 TTTT
502702 TTATCTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (32 bp):
TTTTAATACTATTAAATTAAAACAAAAAATAA
Found at i:506440 original size:2 final size:2
Alignment explanation
Indices: 506428--506456 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
506418 TACTAGTAAA
506428 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
506457 TATCAGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:507474 original size:17 final size:16
Alignment explanation
Indices: 507454--507487 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
507444 AATTTATTGA
507454 TTATAATAATTATTATT
1 TTATAATAATT-TTATT
*
507471 TTATTATAATTTTATT
1 TTATAATAATTTTATT
507487 T
1 T
507488 GATTTGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATAATAATTTTATT
Found at i:508493 original size:23 final size:22
Alignment explanation
Indices: 508463--508506 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
508453 TTTTTTATTT
508463 AAATTTAAT-TATAAAAATATAA
1 AAATTTAATATA-AAAAATATAA
508485 AAATATTAATATAAAAAATATA
1 AAAT-TTAATATAAAAAATATA
508507 TTTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 14 0.70
24 2 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AAATTTAATATAAAAAATATAA
Found at i:508515 original size:24 final size:23
Alignment explanation
Indices: 508488--508532 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
508478 AATATAAAAA
508488 TATTAATATAAAAAATATATTTTT
1 TATTAATATAAAAAATA-ATTTTT
** *
508512 TATTTTTATAAATAATAATTT
1 TATTAATATAAAAAATAATTT
508533 AAGCTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 4 0.22
24 14 0.78
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATAAAAAATAATTTTT
Found at i:509942 original size:23 final size:22
Alignment explanation
Indices: 509915--509967 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
509905 AAATTTAAAC
* *
509915 TTTAAATTTATTAATATTAATTT
1 TTTAAATTTATT-ATATAAATTA
*
509938 TTTAAAATTATTATATAAATTA
1 TTTAAATTTATTATATAAATTA
*
509960 ATTAAATT
1 TTTAAATT
509968 AAAACACCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAAATTTATTATATAAATTA
Found at i:512015 original size:23 final size:22
Alignment explanation
Indices: 511983--512025 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
511973 ATAAGTTTAA
511983 AAAATGTTGTAAAATATTTTTTT
1 AAAATGTTGTAAAA-ATTTTTTT
* *
512006 AAAATTTTGTAATAATTTTT
1 AAAATGTTGTAAAAATTTTT
512026 ATTTTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (22 bp):
AAAATGTTGTAAAAATTTTTTT
Found at i:512035 original size:17 final size:17
Alignment explanation
Indices: 512009--512066 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
511999 TTTTTTTAAA
*
512009 ATTTTGTAATAATTTTT
1 ATTTTTTAATAATTTTT
* *
512026 ATTTTTTAATATAATTTG
1 ATTTTTTAATA-ATTTTT
*
512044 ATTGTTT-ATAATTTTT
1 ATTTTTTAATAATTTTT
512060 -TTTTTTA
1 ATTTTTTA
512067 GTTTTGTAGT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
15 5 0.16
16 4 0.12
17 13 0.41
18 10 0.31
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (17 bp):
ATTTTTTAATAATTTTT
Found at i:512691 original size:23 final size:23
Alignment explanation
Indices: 512665--512710 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
512655 TGATAATAAA
* *
512665 TTTTAAATATTTAATTATTAATT
1 TTTTAAATATTAAATTATAAATT
*
512688 TTTTAGATATTAAATTATAAATT
1 TTTTAAATATTAAATTATAAATT
512711 CAATTATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTTAAATATTAAATTATAAATT
Found at i:515260 original size:14 final size:15
Alignment explanation
Indices: 515241--515276 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
515231 ATTAAATAAT
515241 AAATAAAACA-AAAA
1 AAATAAAACATAAAA
*
515255 AAATAAAATATAAAA
1 AAATAAAACATAAAA
515270 AAATAAA
1 AAATAAA
515277 TATAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (15 bp):
AAATAAAACATAAAA
Found at i:515260 original size:21 final size:20
Alignment explanation
Indices: 515234--515285 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
515224 TAAATTCATT
515234 AAATAATAAATAAAACAAA-AA
1 AAATAA-AAATAAAA-AAATAA
515255 AAATAAAATATAAAAAAATAA
1 AAATAAAA-ATAAAAAAATAA
*
515276 ATATAAAAAT
1 AAATAAAAAT
515286 TTACGTGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (20 bp):
AAATAAAAATAAAAAAATAA
Found at i:515277 original size:14 final size:15
Alignment explanation
Indices: 515241--515284 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 15
515231 ATTAAATAAT
*
515241 AAATAAAACA-AAAA
1 AAATAAAATATAAAA
515255 AAATAAAATATAAAA
1 AAATAAAATATAAAA
515270 AAAT-AAATATAAAA
1 AAATAAAATATAAAA
515284 A
1 A
515285 TTTACGTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 20 0.71
15 8 0.29
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (15 bp):
AAATAAAATATAAAA
Found at i:515285 original size:12 final size:14
Alignment explanation
Indices: 515236--515284 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
515226 AATTCATTAA
* *
515236 ATAATAAATAAAAC
1 ATAAAAAATAAAAT
*
515250 AAAAAAAATAAAAT
1 ATAAAAAATAAAAT
515264 ATAAAAAA-ATAAAT
1 ATAAAAAATA-AAAT
515278 ATAAAAA
1 ATAAAAA
515285 TTTACGTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 1 0.03
14 29 0.97
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (14 bp):
ATAAAAAATAAAAT
Found at i:516900 original size:2 final size:2
Alignment explanation
Indices: 516895--516922 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
516885 TATATATATA
516895 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
516923 GAAAGGATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Done.