Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008351.1 Hibiscus syriacus cultivar Beakdansim tig00111085_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 440059
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:3289 original size:45 final size:45
Alignment explanation
Indices: 3239--3326 Score: 176
Period size: 45 Copynumber: 2.0 Consensus size: 45
3229 GTCTACTTGA
3239 CCAAGAAATATAACCTTAAATCTTCATCATAGATGATTAAAACAT
1 CCAAGAAATATAACCTTAAATCTTCATCATAGATGATTAAAACAT
3284 CCAAGAAATATAACCTTAAATCTTCATCATAGATGATTAAAAC
1 CCAAGAAATATAACCTTAAATCTTCATCATAGATGATTAAAAC
3327 TTACACTTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (45 bp):
CCAAGAAATATAACCTTAAATCTTCATCATAGATGATTAAAACAT
Found at i:4406 original size:16 final size:16
Alignment explanation
Indices: 4385--4423 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
4375 ACTTTTGGTT
4385 TAAACCTAGAATCGAC
1 TAAACCTAGAATCGAC
*
4401 TAAACCTAGAATCGGC
1 TAAACCTAGAATCGAC
4417 TAAACCT
1 TAAACCT
4424 TAGCTCTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.21
Consensus pattern (16 bp):
TAAACCTAGAATCGAC
Found at i:5452 original size:18 final size:19
Alignment explanation
Indices: 5426--5470 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
5416 AATTAATCAC
5426 TTATGATCACATA-TCACAT
1 TTAT-ATCACATAGTCACAT
5445 TTATATCACATAGTCACAT
1 TTATATCACATAGTCACAT
5464 TTCATAT
1 TT-ATAT
5471 TTCACTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.33
19 12 0.50
20 4 0.17
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (19 bp):
TTATATCACATAGTCACAT
Found at i:8113 original size:38 final size:39
Alignment explanation
Indices: 8082--8154 Score: 98
Period size: 36 Copynumber: 1.9 Consensus size: 39
8072 TTAACAAGTT
*
8082 AGAAGATTTATAT-ATTTTCTTTA-AAAATTT-AAATTC
1 AGAAAATTTATATAATTTTCTTTACAAAATTTAAAATTC
* *
8118 ATAAAATTTATATAATTTTTTTTACAAAATTTAAAAT
1 AGAAAATTTATATAATTTTCTTTACAAAATTTAAAAT
8155 GTAAAAGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 11 0.35
37 9 0.29
38 7 0.23
39 4 0.13
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (39 bp):
AGAAAATTTATATAATTTTCTTTACAAAATTTAAAATTC
Found at i:14344 original size:2 final size:2
Alignment explanation
Indices: 14337--14398 Score: 57
Period size: 2 Copynumber: 34.5 Consensus size: 2
14327 CCGCCTCGAT
* *
14337 TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT TA TA TA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14376 TA TA T- TA -A T- TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
14399 TTTATTTATT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
1 7 0.14
2 44 0.86
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:14360 original size:18 final size:17
Alignment explanation
Indices: 14337--14428 Score: 72
Period size: 16 Copynumber: 5.7 Consensus size: 17
14327 CCGCCTCGAT
14337 TATATATATATA-TATA
1 TATATATATATATTATA
*
14353 TATATATA-ATATTTTA
1 TATATATATATATTATA
*
14369 TATAT-TTTATATTA-A
1 TATATATATATATTATA
*
14384 TTATATATATAATATTTTA
1 -TATATATAT-ATATTATA
* *
14403 TTTAT-TTTATATTA-A
1 TATATATATATATTATA
14418 T-TATATATATA
1 TATATATATATA
14429 ATATTTTAGG
Statistics
Matches: 60, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
14 3 0.05
15 12 0.20
16 31 0.52
17 4 0.07
18 9 0.15
19 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATATATATATTATA
Found at i:14389 original size:25 final size:25
Alignment explanation
Indices: 14341--14425 Score: 66
Period size: 25 Copynumber: 3.3 Consensus size: 25
14331 CTCGATTATA
* * *
14341 TATATATATATATATATATAATATTT
1 TATATAT-TTTATTTATATTATATTT
*
14367 TATATATTTTATATTA-ATTATA-TA
1 TATATATTTTAT-TTATATTATATTT
*
14391 TATAATATTTTATTTATTTTATATTAAT
1 TAT-ATATTTTATTTATATTATATT--T
14419 TATATAT
1 TATATAT
14426 ATAATATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
24 7 0.15
25 23 0.49
26 10 0.21
27 4 0.09
28 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TATATATTTTATTTATATTATATTT
Found at i:14394 original size:34 final size:34
Alignment explanation
Indices: 14351--14436 Score: 163
Period size: 34 Copynumber: 2.5 Consensus size: 34
14341 TATATATATA
14351 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
*
14385 TATATATATAATATTTTATTTATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
14419 TATATATATAATATTTTA
1 TATATATATAATATTTTA
14437 GGGTTCGGGT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:14433 original size:25 final size:24
Alignment explanation
Indices: 14355--14436 Score: 68
Period size: 23 Copynumber: 3.6 Consensus size: 24
14345 TATATATATA
14355 TATATAATATTTTATA-T-ATT-T
1 TATATAATATTTTATATTAATTAT
* *
14376 TATATTA-ATTATATATATAA-TAT
1 TATATAATATTTTATAT-TAATTAT
* *
14399 TTTAT-TTATTTTATATTAATTAT
1 TATATAATATTTTATATTAATTAT
14422 ATATATAATATTTTA
1 -TATATAATATTTTA
14437 GGGTTCGGGT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
20 7 0.15
21 6 0.13
22 5 0.11
23 17 0.37
24 4 0.09
25 7 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATATAATATTTTATATTAATTAT
Found at i:14475 original size:25 final size:27
Alignment explanation
Indices: 14425--14476 Score: 90
Period size: 25 Copynumber: 2.0 Consensus size: 27
14415 TAATTATATA
14425 TATAATATTTTAGGGTTCGGGTTTGAG
1 TATAATATTTTAGGGTTCGGGTTTGAG
14452 TATAATATTTT-GGG-TCGGGTTTGAG
1 TATAATATTTTAGGGTTCGGGTTTGAG
14477 GACGGGGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 11 0.44
26 3 0.12
27 11 0.44
ACGTcount: A:0.21, C:0.04, G:0.31, T:0.44
Consensus pattern (27 bp):
TATAATATTTTAGGGTTCGGGTTTGAG
Found at i:15825 original size:6 final size:6
Alignment explanation
Indices: 15816--15846 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
15806 ATTATTACTA
15816 TTATAT TTATAT TTATAT TTATAT TT-TAT TT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TT
15847 TAATTATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTATAT
Found at i:17032 original size:31 final size:31
Alignment explanation
Indices: 16995--17067 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
16985 ATATATATTT
* *
16995 AACAAATTAGTCAATAATGTTATCGATTTGA
1 AACAAATTAGTCAATAACGTTATCGATATGA
* * *
17026 AACAAATT-GTTCACTAACGTTATTGATATGT
1 AACAAATTAG-TCAATAACGTTATCGATATGA
17057 AACAAATTAGT
1 AACAAATTAGT
17068 AATTAGTGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 1 0.03
31 33 0.94
32 1 0.03
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (31 bp):
AACAAATTAGTCAATAACGTTATCGATATGA
Found at i:17346 original size:15 final size:15
Alignment explanation
Indices: 17326--17427 Score: 109
Period size: 15 Copynumber: 6.5 Consensus size: 15
17316 TAATAAGGTT
17326 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
17341 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
17356 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
17371 ATTTATTATAAAATATGAA
1 ATTTATT-TTAAA-AT--A
17390 TTGATTTATTTT-AAATA
1 ---ATTTATTTTAAAATA
17407 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
17421 ATTTATT
1 ATTTATT
17428 AGTATGGATT
Statistics
Matches: 76, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
14 21 0.28
15 35 0.46
16 4 0.05
17 3 0.04
19 3 0.04
20 2 0.03
21 1 0.01
22 7 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:17362 original size:30 final size:30
Alignment explanation
Indices: 17326--17385 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
17316 TAATAAGGTT
17326 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
17356 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
17386 TGAATTGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTTATTTTAAAATAATTTATTATAAAATA
Found at i:17412 original size:14 final size:14
Alignment explanation
Indices: 17393--17427 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
17383 ATATGAATTG
17393 ATTTATTTTAAATA
1 ATTTATTTTAAATA
17407 ATTTATTTTAAATA
1 ATTTATTTTAAATA
17421 ATTTATT
1 ATTTATT
17428 AGTATGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:17446 original size:22 final size:22
Alignment explanation
Indices: 17430--17472 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
17420 AATTTATTAG
17430 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
17452 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
17473 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:17448 original size:32 final size:32
Alignment explanation
Indices: 17407--17558 Score: 155
Period size: 32 Copynumber: 5.4 Consensus size: 32
17397 ATTTTAAATA
17407 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
17439 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
17461 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
17493 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
17515 ATTTATTTTAAATAATTTATTAGTATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
17547 ATTTATTTTAAA
1 ATTTATTTTAAA
17559 ATATGGATTG
Statistics
Matches: 99, Mismatches: 1, Indels: 40
0.71 0.01 0.29
Matches are distributed among these distances:
22 28 0.28
23 8 0.08
25 2 0.02
26 6 0.06
28 6 0.06
29 2 0.02
31 8 0.08
32 39 0.39
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:17451 original size:68 final size:66
Alignment explanation
Indices: 17326--17482 Score: 208
Period size: 68 Copynumber: 2.3 Consensus size: 66
17316 TAATAAGGTT
17326 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATATGAAT
1 ATTTATTTT-AAATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATATGAAT
17391 TG
65 TG
* ** * * * *
17393 ATTTATTTTAAATAATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGG
1 ATTTATTTTAAATAATTTATTATAAAATAATTTATT--T-TAAAATAATTTATTATAAAATATGA
17457 ATTG
63 ATTG
17461 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
17483 GTATGGATTG
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
65 13 0.16
66 12 0.15
67 10 0.13
68 44 0.56
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (66 bp):
ATTTATTTTAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTATTATAAAATATGAATT
G
Found at i:17473 original size:54 final size:54
Alignment explanation
Indices: 17407--18003 Score: 619
Period size: 54 Copynumber: 11.1 Consensus size: 54
17397 ATTTTAAATA
17407 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
17461 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
17515 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
17569 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * * ***
17613 ATTTGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
17675 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
17729 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * *** **
17773 A-TTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATAAATTG
1 ATTTA-TTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
*
17835 ATTTATTTTAAATAATTTATTAGTATGCATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
17889 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
17943 ATTTATTTTAAATAATTTATTTGTATGGATTGGTTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
17997 ATTTATT
1 ATTTATT
18004 ATTGTAGTTG
Statistics
Matches: 455, Mismatches: 48, Indels: 80
0.78 0.08 0.14
Matches are distributed among these distances:
43 3 0.01
44 11 0.02
46 2 0.00
47 10 0.02
48 45 0.10
49 4 0.01
50 10 0.02
51 4 0.01
52 4 0.01
54 273 0.60
55 6 0.01
56 8 0.02
57 4 0.01
58 29 0.06
59 4 0.01
60 4 0.01
62 31 0.07
63 3 0.01
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:17509 original size:22 final size:22
Alignment explanation
Indices: 17484--17526 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
17474 AATTTATTAG
17484 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
17506 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
17527 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:17602 original size:80 final size:80
Alignment explanation
Indices: 17506--17895 Score: 719
Period size: 80 Copynumber: 4.9 Consensus size: 80
17496 TATTTTAAAA
17506 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-AGATTGATTTATTTTAAAATATGGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGA-ATTGATTTATTTTAAAATATGGATTGA
17570 TTTATTATTGTAGTTG
65 TTTATTATTGTAGTTG
*
17586 TATGGATTGATTTATTTTAAATAATTTATTTGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
17651 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
*
17666 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
17731 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
17746 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
17811 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
** *
17826 TATAAATTGATTTATTTTAAATAATTTATTAGTATGCATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
17891 TTATT
66 TTATT
17896 TTAAATAATT
Statistics
Matches: 302, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
80 301 1.00
81 1 0.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTG
Found at i:17630 original size:18 final size:18
Alignment explanation
Indices: 17583--17634 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
17573 ATTATTGTAG
*
17583 TTGTATGGATTGATTTAT
1 TTGTATGAATTGATTTAT
*
17601 TT-TA--AA-TAATTTAT
1 TTGTATGAATTGATTTAT
17615 TTGTATGAATTGATTTAT
1 TTGTATGAATTGATTTAT
17633 TT
1 TT
17635 TAAAATATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
14 9 0.33
15 3 0.11
17 4 0.15
18 11 0.41
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (18 bp):
TTGTATGAATTGATTTAT
Found at i:17712 original size:18 final size:18
Alignment explanation
Indices: 17689--17736 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
17679 ATTTTAAATA
*
17689 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
17707 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
17729 ATTTATTA
1 ATTTATTA
17737 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:17814 original size:134 final size:134
Alignment explanation
Indices: 17666--18098 Score: 605
Period size: 134 Copynumber: 3.2 Consensus size: 134
17656 ATTGTAGTTG
17666 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
17731 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
17796 AAAA
131 AAAA
* ** *
17800 TATGGATTGATTTA--TT--AT--TGTAGTT-GTATAAATTGATTTATTTTAAATAATTTAT-TA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT-AA-AA--TATGGA
* * *** *
17857 GTATGCATTGATTTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
61 -T-TG-ATTTA-TTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTG
17921 ATTTATTTTAAAA
122 ATTTATTTTAAAA
* *
17934 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGGTTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
17999 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
66 TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
18064 AAAA
131 AAAA
*
18068 TATAGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
18099 TTGTAGTTGT
Statistics
Matches: 258, Mismatches: 23, Indels: 36
0.81 0.07 0.11
Matches are distributed among these distances:
128 20 0.08
129 4 0.02
130 4 0.02
131 1 0.00
132 6 0.02
133 9 0.03
134 171 0.66
135 9 0.03
136 6 0.02
137 1 0.00
138 4 0.02
139 4 0.02
140 19 0.07
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (134 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
AAAA
Found at i:17872 original size:32 final size:30
Alignment explanation
Indices: 17831--17986 Score: 137
Period size: 32 Copynumber: 5.5 Consensus size: 30
17821 AGTTGTATAA
17831 ATTGATTTATTTTAAATAATTTATTAGTATG
1 ATTGATTTATTTTAAATAATTTATT-GTATG
17862 CATTGATTTATTTT-AA-AA--TA-TG---G
1 -ATTGATTTATTTTAAATAATTTATTGTATG
17885 ATTGATTTATTTTAAATAATTTATTAGTATGG
1 ATTGATTTATTTTAAATAATTTATT-GTAT-G
17917 ATTGATTTATTTT-AA-AA--TA-TG---G
1 ATTGATTTATTTTAAATAATTTATTGTATG
17939 ATTGATTTATTTTAAATAATTTATTTGTATGG
1 ATTGATTTATTTTAAATAATTTA-TTGTAT-G
*
17971 ATTGGTTTATTTTAAA
1 ATTGATTTATTTTAAA
17987 ATATGGATTG
Statistics
Matches: 103, Mismatches: 1, Indels: 40
0.72 0.01 0.28
Matches are distributed among these distances:
22 27 0.26
23 5 0.05
24 4 0.04
26 6 0.06
27 3 0.03
28 7 0.07
30 4 0.04
31 4 0.04
32 43 0.42
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (30 bp):
ATTGATTTATTTTAAATAATTTATTGTATG
Found at i:17883 original size:22 final size:22
Alignment explanation
Indices: 17858--17900 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
17848 AATTTATTAG
17858 TATGCATTGATTTATTTTAAAA
1 TATGCATTGATTTATTTTAAAA
*
17880 TATGGATTGATTTATTTTAAA
1 TATGCATTGATTTATTTTAAA
17901 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGCATTGATTTATTTTAAAA
Found at i:17937 original size:22 final size:22
Alignment explanation
Indices: 17912--17954 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
17902 AATTTATTAG
17912 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
17934 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
17955 TAATTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:18033 original size:80 final size:80
Alignment explanation
Indices: 17934--18083 Score: 264
Period size: 80 Copynumber: 1.9 Consensus size: 80
17924 TATTTTAAAA
* * * *
17934 TATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGGTTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
17999 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
18014 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
18079 TTATT
66 TTATT
18084 TTAAATAATT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
TTATTATTGTAGTTG
Found at i:22687 original size:18 final size:18
Alignment explanation
Indices: 22664--22738 Score: 97
Period size: 18 Copynumber: 4.4 Consensus size: 18
22654 ACCGGTCACA
22664 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
22682 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
*
22700 ACCTGACCC-A----TTG
1 ACCCGACCCGACCCGTTG
22713 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
22731 ACCCGACC
1 ACCCGACC
22739 GTTGACCGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
13 10 0.21
14 1 0.02
17 1 0.02
18 36 0.75
ACGTcount: A:0.19, C:0.49, G:0.19, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:22714 original size:31 final size:31
Alignment explanation
Indices: 22668--22738 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
22658 GTCACAACCC
*
22668 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCATTGACCCGACCCGACCCGTT
* *
22699 TACCTGACCCATTGACCCGACCCGACCCGTT
1 GACCCGACCCATTGACCCGACCCGACCCGTT
22730 GACCCGACC
1 GACCCGACC
22739 GTTGACCGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.18, C:0.48, G:0.20, T:0.14
Consensus pattern (31 bp):
GACCCGACCCATTGACCCGACCCGACCCGTT
Found at i:22742 original size:12 final size:13
Alignment explanation
Indices: 22717--22760 Score: 54
Period size: 12 Copynumber: 3.3 Consensus size: 13
22707 CCATTGACCC
22717 GACCCGACCCGTT
1 GACCCGACCCGTT
22730 GACCCGA-CCGTT
1 GACCCGACCCGTT
*
22742 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
22757 GACC
1 GACC
22761 ATTGACCGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 9 0.33
13 7 0.26
14 2 0.07
15 9 0.33
ACGTcount: A:0.16, C:0.41, G:0.25, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:22747 original size:7 final size:7
Alignment explanation
Indices: 22735--22768 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
22725 CCGTTGACCC
22735 GACCGTT
1 GACCGTT
22742 GACCGTT
1 GACCGTT
22749 GACCCGTT
1 GA-CCGTT
*
22757 GACCATT
1 GACCGTT
22764 GACCG
1 GACCG
22769 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:22757 original size:15 final size:15
Alignment explanation
Indices: 22737--22767 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
22727 GTTGACCCGA
*
22737 CCGTTGACCGTTGAC
1 CCGTTGACCATTGAC
22752 CCGTTGACCATTGAC
1 CCGTTGACCATTGAC
22767 C
1 C
22768 GGAGTTGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.35, G:0.23, T:0.26
Consensus pattern (15 bp):
CCGTTGACCATTGAC
Found at i:24080 original size:18 final size:18
Alignment explanation
Indices: 24054--24088 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24044 TCGAAAGGAC
*
24054 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
24072 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
24089 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:27887 original size:18 final size:18
Alignment explanation
Indices: 27864--27938 Score: 97
Period size: 18 Copynumber: 4.4 Consensus size: 18
27854 ACCGGTCACA
27864 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
27882 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
*
27900 ACCTGACCC-A----TTG
1 ACCCGACCCGACCCGTTG
27913 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
27931 ACCCGACC
1 ACCCGACC
27939 GTTGACCGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
13 10 0.21
14 1 0.02
17 1 0.02
18 36 0.75
ACGTcount: A:0.19, C:0.49, G:0.19, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:27914 original size:31 final size:31
Alignment explanation
Indices: 27868--27938 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
27858 GTCACAACCC
*
27868 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCATTGACCCGACCCGACCCGTT
* *
27899 TACCTGACCCATTGACCCGACCCGACCCGTT
1 GACCCGACCCATTGACCCGACCCGACCCGTT
27930 GACCCGACC
1 GACCCGACC
27939 GTTGACCGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.18, C:0.48, G:0.20, T:0.14
Consensus pattern (31 bp):
GACCCGACCCATTGACCCGACCCGACCCGTT
Found at i:27942 original size:12 final size:13
Alignment explanation
Indices: 27917--27960 Score: 54
Period size: 12 Copynumber: 3.3 Consensus size: 13
27907 CCATTGACCC
27917 GACCCGACCCGTT
1 GACCCGACCCGTT
27930 GACCCGA-CCGTT
1 GACCCGACCCGTT
*
27942 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
27957 GACC
1 GACC
27961 ATTGACCGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 9 0.33
13 7 0.26
14 2 0.07
15 9 0.33
ACGTcount: A:0.16, C:0.41, G:0.25, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:27947 original size:7 final size:7
Alignment explanation
Indices: 27935--27968 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
27925 CCGTTGACCC
27935 GACCGTT
1 GACCGTT
27942 GACCGTT
1 GACCGTT
27949 GACCCGTT
1 GA-CCGTT
*
27957 GACCATT
1 GACCGTT
27964 GACCG
1 GACCG
27969 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:27957 original size:15 final size:15
Alignment explanation
Indices: 27937--27967 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27927 GTTGACCCGA
*
27937 CCGTTGACCGTTGAC
1 CCGTTGACCATTGAC
27952 CCGTTGACCATTGAC
1 CCGTTGACCATTGAC
27967 C
1 C
27968 GGAGTTGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.35, G:0.23, T:0.26
Consensus pattern (15 bp):
CCGTTGACCATTGAC
Found at i:29283 original size:18 final size:18
Alignment explanation
Indices: 29257--29291 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29247 TCGAAAGGAC
*
29257 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
29275 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
29292 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:34613 original size:2 final size:2
Alignment explanation
Indices: 34606--34657 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
34596 AAGAGGAAAC
34606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34648 TA TA TA TA TA
1 TA TA TA TA TA
34658 GCATAAAAGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34830 original size:20 final size:20
Alignment explanation
Indices: 34725--34824 Score: 121
Period size: 20 Copynumber: 5.0 Consensus size: 20
34715 GTTAAGGGCA
34725 CGAATTCGGAATTAGCGTCG
1 CGAATTCGGAATTAGCGTCG
*
34745 TGAATTCGGAATTAGCGTCG
1 CGAATTCGGAATTAGCGTCG
* * * * *
34765 CGAATTTGAAAATCGCGTTG
1 CGAATTCGGAATTAGCGTCG
*
34785 CGAAATT-GAAATTAGCGTCG
1 CG-AATTCGGAATTAGCGTCG
34805 CGAATTCGGAATTAGCGTCG
1 CGAATTCGGAATTAGCGTCG
34825 TAAATTTGGA
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
19 4 0.06
20 59 0.88
21 4 0.06
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (20 bp):
CGAATTCGGAATTAGCGTCG
Found at i:34846 original size:60 final size:60
Alignment explanation
Indices: 34734--34854 Score: 170
Period size: 60 Copynumber: 2.0 Consensus size: 60
34724 ACGAATTCGG
* * *
34734 AATTAGCGTCGTGAATTCGGAATTAGCGTCGCGAATTTGAAAATCGCGTTGCGAAATTGA
1 AATTAGCGTCGCGAATTCGGAATTAGCGTCGCAAATTTGAAAATCGCATTGCGAAATTGA
* * ** *
34794 AATTAGCGTCGCGAATTCGGAATTAGCGTCGTAAATTTGGAGTTCGCATTGCGAATTTGA
1 AATTAGCGTCGCGAATTCGGAATTAGCGTCGCAAATTTGAAAATCGCATTGCGAAATTGA
34854 A
1 A
34855 TAATCGCATT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (60 bp):
AATTAGCGTCGCGAATTCGGAATTAGCGTCGCAAATTTGAAAATCGCATTGCGAAATTGA
Found at i:35073 original size:17 final size:18
Alignment explanation
Indices: 35039--35073 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35029 ATTTTTTAAA
*
35039 AAAATATCCTCTAATCAT
1 AAAATATCCTCAAATCAT
35057 AAAATATCCT-AAATCAT
1 AAAATATCCTCAAATCAT
35074 CTATCATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATATCCTCAAATCAT
Found at i:57264 original size:28 final size:28
Alignment explanation
Indices: 57229--57287 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
57219 GGATGTTACA
*
57229 TAACTAAACTCAAATTCATACATATGTT
1 TAACTAAACTCAAATTCATACATATATT
*
57257 TAACTAAACTCAAATTCATGCATATATT
1 TAACTAAACTCAAATTCATACATATATT
57285 TAA
1 TAA
57288 AATATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (28 bp):
TAACTAAACTCAAATTCATACATATATT
Found at i:57381 original size:3 final size:3
Alignment explanation
Indices: 57373--57424 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
57363 TAAGTCTCCA
*
57373 TTC TTC TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
57421 TTC T
1 TTC T
57425 CCTCATCCTC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:59350 original size:60 final size:60
Alignment explanation
Indices: 59235--59351 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
59225 ATTATATGAC
** * * * *
59235 CCTCAAACTATAATTCTCATTCTGAATTAGTCCTTAAACGTTCGAATATTTTAATTTCAT
1 CCTCAAACTATAACCCTCATTCTAAATTAGTCCTTAAACATTCGAACATTCTAATTTCAT
* * * * *
59295 CCTCAAACTATGACCCTTATTCTAAATTAGTCTTTAAATATTTGAACATTCTAATTT
1 CCTCAAACTATAACCCTCATTCTAAATTAGTCCTTAAACATTCGAACATTCTAATTT
59352 TATTCCGTAA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (60 bp):
CCTCAAACTATAACCCTCATTCTAAATTAGTCCTTAAACATTCGAACATTCTAATTTCAT
Found at i:60856 original size:29 final size:29
Alignment explanation
Indices: 60821--60902 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
60811 AAACTAAATT
*
60821 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
60850 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
60879 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
60903 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:65620 original size:29 final size:29
Alignment explanation
Indices: 65585--65666 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
65575 AAACTAAATT
*
65585 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
65614 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
65643 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
65667 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:69325 original size:21 final size:21
Alignment explanation
Indices: 69299--69338 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
69289 ATGCGTGCAG
69299 TGAATTGTGGCAATATTAGAT
1 TGAATTGTGGCAATATTAGAT
* *
69320 TGAATTGTGGTACTATTAG
1 TGAATTGTGGCAATATTAG
69339 GGATGGCAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.40
Consensus pattern (21 bp):
TGAATTGTGGCAATATTAGAT
Found at i:69839 original size:13 final size:13
Alignment explanation
Indices: 69823--69848 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
69813 TTAATTACTG
69823 AGATAAATTGATT
1 AGATAAATTGATT
69836 AGATAAATTGATT
1 AGATAAATTGATT
69849 GTATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (13 bp):
AGATAAATTGATT
Found at i:85203 original size:32 final size:32
Alignment explanation
Indices: 85162--85224 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
85152 ACCTAGGGCG
85162 CCTTCAGGGATCACTTAACATTGGAGCATACA
1 CCTTCAGGGATCACTTAACATTGGAGCATACA
85194 CCTTCAGGGATCACTTAACATTGGAGCATAC
1 CCTTCAGGGATCACTTAACATTGGAGCATAC
85225 GTCCAACTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (32 bp):
CCTTCAGGGATCACTTAACATTGGAGCATACA
Found at i:86001 original size:15 final size:15
Alignment explanation
Indices: 85981--86012 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
85971 TAGTGATTAT
85981 ATTGAAACCATTTAA
1 ATTGAAACCATTTAA
*
85996 ATTGAAACTATTTAA
1 ATTGAAACCATTTAA
86011 AT
1 AT
86013 AGTTCAATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (15 bp):
ATTGAAACCATTTAA
Found at i:97569 original size:3 final size:3
Alignment explanation
Indices: 97561--97616 Score: 51
Period size: 3 Copynumber: 18.0 Consensus size: 3
97551 TAGTTCATTT
* * *
97561 TTA TTA TTA TTA TAA TAA TTA TTA TTA ATA TTA TTA -TA TATA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA
97607 TTA TTTA TTA
1 TTA -TTA TTA
97617 AATATTACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 34 0.74
4 10 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:97984 original size:22 final size:22
Alignment explanation
Indices: 97925--97977 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
97915 ACGTCAAGCT
97925 CTATGGTGAGTCACCACCATAG
1 CTATGGTGAGTCACCACCATAG
97947 CTATGGTGAGTCACCACCATAG
1 CTATGGTGAGTCACCACCATAG
97969 CTATGGTGA
1 CTATGGTGA
97978 CTAACCAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
CTATGGTGAGTCACCACCATAG
Found at i:99995 original size:22 final size:21
Alignment explanation
Indices: 99943--99997 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 21
99933 TATATATACT
99943 TTTTATTTTCATAATATTTTA
1 TTTTATTTTCATAATATTTTA
99964 TATATT-TTTT-ATTAATATCTTTA
1 T-T-TTATTTTCA-TAATAT-TTTA
99987 TTTTATTTTCA
1 TTTTATTTTCA
99998 GTTATTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
21 4 0.14
22 16 0.57
23 8 0.29
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATTTTCATAATATTTTA
Found at i:102406 original size:13 final size:13
Alignment explanation
Indices: 102382--102421 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
102372 CATTTATATC
102382 TTTGCA-TTTGCA
1 TTTGCATTTTGCA
102394 TTTGCATTTTGCA
1 TTTGCATTTTGCA
*
102407 TTTGTATCTTTGCA
1 TTTGCAT-TTTGCA
102421 T
1 T
102422 AATTACATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 6 0.24
13 12 0.48
14 7 0.28
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (13 bp):
TTTGCATTTTGCA
Found at i:104771 original size:9 final size:8
Alignment explanation
Indices: 104754--104892 Score: 56
Period size: 8 Copynumber: 16.6 Consensus size: 8
104744 ATATACTCAT
104754 AAAAAGAA
1 AAAAAGAA
*
104762 AAAAAGGA
1 AAAAAGAA
*
104770 AAAAGGAA
1 AAAAAGAA
104778 AAAGGAA-AA
1 AAA--AAGAA
*
104787 GGAAAAAGGA
1 --AAAAAGAA
104797 AAAAAG-A
1 AAAAAGAA
104804 AAAAAGAA
1 AAAAAGAA
104812 AAAGGAA-AA
1 AAA--AAGAA
*
104821 AGGAAAAGGA
1 A--AAAAGAA
*
104831 AAAAGGAA
1 AAAAAGAA
*
104839 AAAGGAAAAA
1 AAA--AAGAA
*
104849 GGAAAAAG-G
1 --AAAAAGAA
*
104858 AAAAAGGA
1 AAAAAGAA
104866 AAAAAG-A
1 AAAAAGAA
104873 AAAAAG-A
1 AAAAAGAA
104880 AAAAAGAA
1 AAAAAGAA
104888 AAAAA
1 AAAAA
104893 AATTGAATCA
Statistics
Matches: 101, Mismatches: 13, Indels: 34
0.68 0.09 0.23
Matches are distributed among these distances:
7 27 0.27
8 46 0.46
9 9 0.09
10 11 0.11
11 5 0.05
12 3 0.03
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:104772 original size:7 final size:7
Alignment explanation
Indices: 104762--104890 Score: 199
Period size: 7 Copynumber: 18.7 Consensus size: 7
104752 ATAAAAAGAA
104762 AAAAAGG
1 AAAAAGG
104769 AAAAAGG
1 AAAAAGG
104776 AAAAAGG
1 AAAAAGG
104783 -AAAAGG
1 AAAAAGG
104789 AAAAAGG
1 AAAAAGG
*
104796 AAAAAAG
1 AAAAAGG
*
104803 AAAAAAG
1 AAAAAGG
104810 AAAAAGG
1 AAAAAGG
104817 AAAAAGG
1 AAAAAGG
104824 -AAAAGG
1 AAAAAGG
104830 AAAAAGG
1 AAAAAGG
104837 AAAAAGG
1 AAAAAGG
104844 AAAAAGG
1 AAAAAGG
104851 AAAAAGG
1 AAAAAGG
104858 AAAAAGG
1 AAAAAGG
*
104865 AAAAAAG
1 AAAAAGG
*
104872 AAAAAAG
1 AAAAAGG
*
104879 AAAAAAG
1 AAAAAGG
104886 AAAAA
1 AAAAA
104891 AAAATTGAAT
Statistics
Matches: 117, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
6 12 0.10
7 105 0.90
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:104815 original size:41 final size:41
Alignment explanation
Indices: 104754--104891 Score: 213
Period size: 41 Copynumber: 3.3 Consensus size: 41
104744 ATATACTCAT
104754 AAAAAGAAAAAAAGGAAAAAGGAAAAAGGAAAAGGAAAAAGGA
1 AAAAAG-AAAAAA-GAAAAAGGAAAAAGGAAAAGGAAAAAGGA
104797 AAAAAGAAAAAAGAAAAAGGAAAAAGGAAAAGGAAAAAGGA
1 AAAAAGAAAAAAGAAAAAGGAAAAAGGAAAAGGAAAAAGGA
* * * *
104838 AAAAGGAAAAAGGAAAAAGGAAAAAGGAAAAAAGAAAAAAGA
1 AAAAAGAAAAAAGAAAAAGGAAAAAGG-AAAAGGAAAAAGGA
104880 AAAAAGAAAAAA
1 AAAAAGAAAAAA
104892 AAATTGAATC
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
41 54 0.61
42 28 0.32
43 6 0.07
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (41 bp):
AAAAAGAAAAAAGAAAAAGGAAAAAGGAAAAGGAAAAAGGA
Found at i:109268 original size:22 final size:19
Alignment explanation
Indices: 109220--109269 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
109210 ATCTACATTC
109220 TTCAAAGATGATAGATTTT
1 TTCAAAGATGATAGATTTT
*
109239 CTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGA-T-T-TT
109261 TTCAAAGAT
1 TTCAAAGAT
109270 AAAAGCTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 14 0.54
20 1 0.04
21 1 0.04
22 10 0.38
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (19 bp):
TTCAAAGATGATAGATTTT
Found at i:110040 original size:46 final size:45
Alignment explanation
Indices: 109942--110353 Score: 662
Period size: 45 Copynumber: 9.1 Consensus size: 45
109932 TGTTTCCCAT
* * *
109942 ATCTGTAAGACCTTCAATGCTTGATGTTTTCAAAATCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTC
* *
109987 ATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCTTGATG-TTTTCAAAACCTTCGGGTC
*
110033 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCAGGTC
1 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTC
* * *
110078 ATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAAACCTTTGGGTC
1 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGTC
*
110124 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGTC
*
110170 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACTTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTC
110215 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTC
* *
110260 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAATCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGTC
*
110306 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAATCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTC
110351 ATC
1 ATC
110354 CATAAGACAT
Statistics
Matches: 344, Mismatches: 20, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
45 173 0.50
46 171 0.50
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (45 bp):
ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTC
Found at i:110384 original size:45 final size:45
Alignment explanation
Indices: 109942--110353 Score: 628
Period size: 46 Copynumber: 9.1 Consensus size: 45
109932 TGTTTCCCAT
* * *
109942 ATCTGTAAGACCTTCAATGCTTGATGTTTTCAAAATCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAATCTTCGGGTC
* *
109987 ATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATG-TTTTCAAAATCTTCGGGTC
* * *
110033 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCAGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAATCTTCGGGTC
* * *
110078 ATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAAACCTTTGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAATCTTCGGGTC
*
110124 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAATCTTCGGGTC
*
110170 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAA-CTTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAATC-TTCGGGTC
* *
110215 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAATCTTCGGGTC
110260 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAATCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAATCTTCGGGTC
*
110306 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAATCTTCGGGTC
1 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAATCTTCGGGTC
110351 ATC
1 ATC
110354 CATAAGACAT
Statistics
Matches: 344, Mismatches: 18, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
44 1 0.00
45 171 0.50
46 172 0.50
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (45 bp):
ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAATCTTCGGGTC
Found at i:110384 original size:91 final size:91
Alignment explanation
Indices: 109942--110353 Score: 700
Period size: 91 Copynumber: 4.5 Consensus size: 91
109932 TGTTTCCCAT
* * *
109942 ATCTGTAAGACCTTCAATGCTTGATGTTTTCAAAATCTTCGGGTCATCTGTAAGCCCTTCAGTGC
1 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
*
110007 ATGATGTTTTTAAAAACCTTCGGGTC
66 ATGATGTTTTCAAAAACCTTCGGGTC
* *
110033 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTTTAGTGC
1 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
*
110098 ATGATGTTTTCAAAAACCTTTGGGTC
66 ATGATGTTTTCAAAAACCTTCGGGTC
*
110124 ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
1 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTG
* *
110189 CTTGATGTTTTC-AAAACTTTCGGGTC
65 CATGATGTTTTCAAAAACCTTCGGGTC
110215 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
1 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
*
110280 ATGATGTTTTCAAAAATCTTCGGGTC
66 ATGATGTTTTCAAAAACCTTCGGGTC
*
110306 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAATCTTCGGGTCATC
1 ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATC
110354 CATAAGACAT
Statistics
Matches: 301, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
90 44 0.15
91 215 0.71
92 42 0.14
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (91 bp):
ATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
ATGATGTTTTCAAAAACCTTCGGGTC
Found at i:110667 original size:15 final size:16
Alignment explanation
Indices: 110647--110689 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
110637 TATTTTTATT
110647 ATTATTAAAATTAA-A
1 ATTATTAAAATTAATA
*
110662 ATTATTATAA-TAATA
1 ATTATTAAAATTAATA
*
110677 ATTATTAATATTA
1 ATTATTAAAATTA
110690 TTATATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 3 0.13
15 18 0.78
16 2 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTATTAAAATTAATA
Found at i:110683 original size:24 final size:25
Alignment explanation
Indices: 110656--110707 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
110646 TATTATTAAA
110656 ATTAAAATTATTATA-ATA-ATAATT
1 ATTAAAATTATTATATATATAT-ATT
*
110680 ATTAATATTATTATATATATATATT
1 ATTAAAATTATTATATATATATATT
110705 ATT
1 ATT
110708 TATTAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 14 0.56
25 9 0.36
26 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTAAAATTATTATATATATATATT
Found at i:110705 original size:16 final size:14
Alignment explanation
Indices: 110663--110719 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
110653 AAAATTAAAA
* *
110663 TTATTATAATAATAA
1 TTATTA-AATATTAT
110678 TTATT-AATATTAT
1 TTATTAAATATTAT
*
110691 TATATATATATATTAT
1 T-TAT-TAAATATTAT
110707 TTATTAAATATTA
1 TTATTAAATATTA
110720 CAAAGCCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
13 7 0.20
14 11 0.31
15 9 0.26
16 8 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATTAAATATTAT
Found at i:113455 original size:24 final size:25
Alignment explanation
Indices: 113421--113471 Score: 95
Period size: 24 Copynumber: 2.1 Consensus size: 25
113411 AGTAATTCCC
113421 TAATGATTTTTTCTATTAATTTGGG
1 TAATGATTTTTTCTATTAATTTGGG
113446 TAATGA-TTTTTCTATTAATTTGGG
1 TAATGATTTTTTCTATTAATTTGGG
113470 TA
1 TA
113472 TTATTTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.25, C:0.04, G:0.16, T:0.55
Consensus pattern (25 bp):
TAATGATTTTTTCTATTAATTTGGG
Found at i:123004 original size:59 final size:60
Alignment explanation
Indices: 122929--123051 Score: 160
Period size: 59 Copynumber: 2.1 Consensus size: 60
122919 TTTTTATTTC
* * * *
122929 AATTAGTCCATAAACTTTT-ACACATTTCAATTTTATTATCAAACTATGACTCTCATTCTA
1 AATTAGTCCATAAACTTTTGA-ACATTTCAATTTCATCACCAAACTATGAATCTCATTCTA
* * *
122989 AATTAGT-CATTAACTTTTGAACATTTCAATTTCATCCCCAAACTATGAATTTCATTCTA
1 AATTAGTCCATAAACTTTTGAACATTTCAATTTCATCACCAAACTATGAATCTCATTCTA
123048 AATT
1 AATT
123052 GATCACTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
59 47 0.85
60 8 0.15
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (60 bp):
AATTAGTCCATAAACTTTTGAACATTTCAATTTCATCACCAAACTATGAATCTCATTCTA
Found at i:123090 original size:60 final size:59
Alignment explanation
Indices: 122929--123090 Score: 159
Period size: 59 Copynumber: 2.7 Consensus size: 59
122919 TTTTTATTTC
* * *** *
122929 AATTAGTCCATAAACTTTT-ACACATTTCAATTTTATTATCAAACTATGACTCTCATTCTA
1 AATTAGT-CATAAACTTTTGA-ACATTCCAATTTCATCCCCAAACTATGAATCTCATTCTA
* * *
122989 AATTAGTCATTAACTTTTGAACATTTCAATTTCATCCCCAAACTATGAATTTCATTCTA
1 AATTAGTCATAAACTTTTGAACATTCCAATTTCATCCCCAAACTATGAATCTCATTCTA
* *
123048 AATT-GATCACTAAACTTTTAGATC-TTCCAATTTTATCCCCAAA
1 AATTAG-TCA-TAAACTTTT-GAACATTCCAATTTCATCCCCAAA
123091 TTCATCCAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
58 1 0.01
59 50 0.57
60 33 0.38
61 3 0.03
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (59 bp):
AATTAGTCATAAACTTTTGAACATTCCAATTTCATCCCCAAACTATGAATCTCATTCTA
Found at i:123856 original size:15 final size:16
Alignment explanation
Indices: 123821--123858 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
123811 TTTAAATTAA
123821 AAATATATTTAATATT
1 AAATATATTTAATATT
*
123837 -TATATATTTAAT-TT
1 AAATATATTTAATATT
123851 AAATATAT
1 AAATATAT
123859 ATACCCGGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATATATTTAATATT
Found at i:123857 original size:17 final size:17
Alignment explanation
Indices: 123810--123860 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
123800 AATAAATTTA
* *
123810 ATTTAAATTAAAAATAT
1 ATTTAATTTAAATATAT
123827 ATTTAATATT---TATAT
1 ATTTAAT-TTAAATATAT
123842 ATTTAATTTAAATATAT
1 ATTTAATTTAAATATAT
123859 AT
1 AT
123861 ACCCGGTCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 2 0.07
15 11 0.39
17 13 0.46
18 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAATTTAAATATAT
Found at i:131155 original size:20 final size:21
Alignment explanation
Indices: 131130--131170 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
131120 GTTGTGGACG
*
131130 TTTCTAGCCG-TTGGGGATGA
1 TTTCTAGCAGTTTGGGGATGA
*
131150 TTTCTAGTAGTTTGGGGATGA
1 TTTCTAGCAGTTTGGGGATGA
131171 AATCTCTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.17, C:0.10, G:0.34, T:0.39
Consensus pattern (21 bp):
TTTCTAGCAGTTTGGGGATGA
Found at i:140157 original size:38 final size:38
Alignment explanation
Indices: 140100--140184 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 38
140090 ATACGTCCTA
* * *
140100 CGGGACACAGATTATATCCTTCGGGATGACAGGTCTTT
1 CGGGACACAGATGACATCCTTCGGGATGACAGGTCATT
*
140138 CGGGACACAGATGACATCCTTCGGGATGATAGGTCATT
1 CGGGACACAGATGACATCCTTCGGGATGACAGGTCATT
140176 CGGGACACA
1 CGGGACACA
140185 ATTTATACGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (38 bp):
CGGGACACAGATGACATCCTTCGGGATGACAGGTCATT
Found at i:142172 original size:2 final size:2
Alignment explanation
Indices: 142165--142191 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
142155 TATCATTGGA
142165 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
142192 AAATAATTTG
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:146438 original size:38 final size:38
Alignment explanation
Indices: 146381--146465 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 38
146371 ATACGTCCTA
* * *
146381 CGGGACACAGATTATATCCTTCGGGATGACAGGTCTTT
1 CGGGACACAGATGACATCCTTCGGGATGACAGGTCATT
*
146419 CGGGACACAGATGACATCCTTCGGGATGATAGGTCATT
1 CGGGACACAGATGACATCCTTCGGGATGACAGGTCATT
146457 CGGGACACA
1 CGGGACACA
146466 ATTTATACGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (38 bp):
CGGGACACAGATGACATCCTTCGGGATGACAGGTCATT
Found at i:149594 original size:33 final size:33
Alignment explanation
Indices: 149553--149615 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
149543 TTAAATAGAT
149553 ATATAAGAGTT-A-AGAATAGAAAAAGGGATGAA
1 ATATAAGAGTTGATAGAATA-AAAAAGGGATGAA
*
149585 ATATGAAGAGTTGATAGAATAAAGAAGGGAT
1 ATAT-AAGAGTTGATAGAATAAAAAAGGGAT
149616 TTTCGTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 4 0.15
33 7 0.26
34 10 0.37
35 6 0.22
ACGTcount: A:0.52, C:0.00, G:0.27, T:0.21
Consensus pattern (33 bp):
ATATAAGAGTTGATAGAATAAAAAAGGGATGAA
Found at i:154310 original size:15 final size:15
Alignment explanation
Indices: 154290--154325 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
154280 CGCCCCGCAT
*
154290 CCGCCCCGCATCCGC
1 CCGCCCCACATCCGC
154305 CCGCCCCACATCCGC
1 CCGCCCCACATCCGC
154320 CCGCCC
1 CCGCCC
154326 AGTTAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.69, G:0.17, T:0.06
Consensus pattern (15 bp):
CCGCCCCACATCCGC
Found at i:154321 original size:11 final size:11
Alignment explanation
Indices: 154279--154306 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
154269 GAGACATTAC
154279 CCGCCCCGCAT
1 CCGCCCCGCAT
154290 CCGCCCCGCAT
1 CCGCCCCGCAT
154301 CCGCCC
1 CCGCCC
154307 GCCCCACATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.68, G:0.18, T:0.07
Consensus pattern (11 bp):
CCGCCCCGCAT
Found at i:158039 original size:28 final size:28
Alignment explanation
Indices: 158008--158062 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
157998 TTAATGGATA
158008 TTGTTT-ATAAAAATATTGTACTTTTTAT
1 TTGTTTAATAAAAATATTGTA-TTTTTAT
*
158036 TTGTTTAATAAAAATATTTTATTTTTA
1 TTGTTTAATAAAAATATTGTATTTTTA
158063 ATATAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (28 bp):
TTGTTTAATAAAAATATTGTATTTTTAT
Found at i:163692 original size:16 final size:17
Alignment explanation
Indices: 163671--163727 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 17
163661 ATGTTTTAGA
163671 TTCAGA-TTCAGATT-CC
1 TTCAGATTTCA-ATTCCC
163687 TTCAGATTTCAATTCCC
1 TTCAGATTTCAATTCCC
163704 TTCACAGATTTCAATTCCC
1 TT--CAGATTTCAATTCCC
163723 -TCAGA
1 TTCAGA
163728 AACATTCTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
16 13 0.35
17 8 0.22
18 1 0.03
19 15 0.41
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.37
Consensus pattern (17 bp):
TTCAGATTTCAATTCCC
Found at i:165572 original size:16 final size:16
Alignment explanation
Indices: 165543--165615 Score: 105
Period size: 16 Copynumber: 4.7 Consensus size: 16
165533 CGTTCATTTA
165543 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
165557 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
*
165573 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
*
165589 ATAAATGAACATGAAC
1 ATAAATGAACACGAAC
*
165605 ATAAACGAACA
1 ATAAATGAACA
165616 TAAACGTTGG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
14 6 0.11
15 2 0.04
16 45 0.85
ACGTcount: A:0.59, C:0.18, G:0.11, T:0.12
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:165587 original size:32 final size:32
Alignment explanation
Indices: 165551--165615 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
165541 TAATAAATAA
165551 ACGAACATAAATGAACACGAACATAAACGAAC
1 ACGAACATAAATGAACACGAACATAAACGAAC
*
165583 ACGAACATAAATGAACATGAACATAAACGAAC
1 ACGAACATAAATGAACACGAACATAAACGAAC
165615 A
1 A
165616 TAAACGTTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.11
Consensus pattern (32 bp):
ACGAACATAAATGAACACGAACATAAACGAAC
Found at i:166721 original size:10 final size:10
Alignment explanation
Indices: 166706--166777 Score: 63
Period size: 10 Copynumber: 6.4 Consensus size: 10
166696 ATAAATGAAT
166706 GAACATAAAC
1 GAACATAAAC
166716 GAACATAACCGAAC
1 GAACAT-A---AAC
166730 GAACATAAAC
1 GAACATAAAC
166740 GAACATAATCGAAC
1 GAACAT-A---AAC
166754 GAACATAAAC
1 GAACATAAAC
*
166764 GAACATAACC
1 GAACATAAAC
166774 GAAC
1 GAAC
166778 GTTCACGAAC
Statistics
Matches: 53, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
10 31 0.58
11 2 0.04
13 2 0.04
14 18 0.34
ACGTcount: A:0.54, C:0.24, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:166730 original size:14 final size:13
Alignment explanation
Indices: 166713--166778 Score: 63
Period size: 14 Copynumber: 5.3 Consensus size: 13
166703 AATGAACATA
166713 AACGAACATAACCG
1 AACGAACATAA-CG
166727 AACGAACAT-A--
1 AACGAACATAACG
166737 AACGAACATAATCG
1 AACGAACATAA-CG
166751 AACGAACAT-A--
1 AACGAACATAACG
166761 AACGAACATAACCG
1 AACGAACATAA-CG
166775 AACG
1 AACG
166779 TTCACGAACG
Statistics
Matches: 44, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
10 18 0.41
11 2 0.05
13 2 0.05
14 22 0.50
ACGTcount: A:0.53, C:0.24, G:0.14, T:0.09
Consensus pattern (13 bp):
AACGAACATAACG
Found at i:166787 original size:34 final size:34
Alignment explanation
Indices: 166727--166801 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 34
166717 AACATAACCG
166727 AACGAACATAAACGAACATAATCGAACG-AACATA
1 AACGAACATAAACGAACATAATCGAACGTAA-ATA
* * *
166761 AACGAACATAACCGAACGTTCA-CGAACGTAAATA
1 AACGAACATAAACGAAC-ATAATCGAACGTAAATA
166795 AACGAAC
1 AACGAAC
166802 GAGACTTATG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 32 0.89
35 4 0.11
ACGTcount: A:0.52, C:0.23, G:0.13, T:0.12
Consensus pattern (34 bp):
AACGAACATAAACGAACATAATCGAACGTAAATA
Found at i:166788 original size:24 final size:24
Alignment explanation
Indices: 166706--166778 Score: 137
Period size: 24 Copynumber: 3.0 Consensus size: 24
166696 ATAAATGAAT
166706 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
166730 GAACATAAACGAACATAATCGAAC
1 GAACATAAACGAACATAACCGAAC
166754 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
166778 G
1 G
166779 TTCACGAACG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.53, C:0.23, G:0.14, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:166801 original size:48 final size:48
Alignment explanation
Indices: 166693--166803 Score: 143
Period size: 48 Copynumber: 2.3 Consensus size: 48
166683 GATTGGGTTA
* * *
166693 AACATAAATGAATGAACATAAACGAACATAACCGAACGAACATAAACG
1 AACATAAACGAACGAACATAAACGAACATAACCGAACGAACACAAACG
* ** *
166741 AACATAATCGAACGAACATAAACGAACATAACCGAACGTTCACGAACG
1 AACATAAACGAACGAACATAAACGAACATAACCGAACGAACACAAACG
166789 TAA-ATAAACGAACGA
1 -AACATAAACGAACGA
166804 GACTTATGTT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
48 52 0.96
49 2 0.04
ACGTcount: A:0.53, C:0.21, G:0.14, T:0.13
Consensus pattern (48 bp):
AACATAAACGAACGAACATAAACGAACATAACCGAACGAACACAAACG
Found at i:167069 original size:36 final size:36
Alignment explanation
Indices: 167028--167100 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
167018 GTATGTTCAT
*
167028 AATTTTTTATAAAAATGTCTAATCATAACATCATTA
1 AATTTTTTACAAAAATGTCTAATCATAACATCATTA
*
167064 AATTTTTTACAAAAATGTTTAATCATAACATCATTA
1 AATTTTTTACAAAAATGTCTAATCATAACATCATTA
167100 A
1 A
167101 GTATTTAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.45, C:0.11, G:0.03, T:0.41
Consensus pattern (36 bp):
AATTTTTTACAAAAATGTCTAATCATAACATCATTA
Found at i:171812 original size:3 final size:3
Alignment explanation
Indices: 171804--171855 Score: 61
Period size: 3 Copynumber: 16.3 Consensus size: 3
171794 CGGGTCTTTT
171804 TTA TTA TTA TT- TATA TATA TTTA TTA TTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA T-TA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA
171852 TTA T
1 TTA T
171856 GTTTATTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.02
3 34 0.76
4 9 0.20
5 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:171861 original size:9 final size:8
Alignment explanation
Indices: 171807--171863 Score: 55
Period size: 9 Copynumber: 6.8 Consensus size: 8
171797 GTCTTTTTTA
171807 TTATTA-T
1 TTATTATT
171814 TTATATATAT
1 TTAT-TAT-T
171824 TTATTA-T
1 TTATTATT
171831 TTATTATT
1 TTATTATT
171839 ATTATTATT
1 -TTATTATT
171848 ATTATTATGT
1 -TTATTAT-T
171858 TTATTA
1 TTATTA
171864 ATTACATATT
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
7 11 0.25
8 3 0.07
9 24 0.55
10 6 0.14
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (8 bp):
TTATTATT
Found at i:178445 original size:12 final size:12
Alignment explanation
Indices: 178410--178445 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
178400 GAGCAAAGAG
178410 CAAAGAGAAAAAT
1 CAAAGA-AAAAAT
*
178423 CAAAGCAAAAAT
1 CAAAGAAAAAAT
178435 CAAAGAAAAAA
1 CAAAGAAAAAA
178446 AGAGAAAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.72, C:0.11, G:0.11, T:0.06
Consensus pattern (12 bp):
CAAAGAAAAAAT
Found at i:180124 original size:105 final size:102
Alignment explanation
Indices: 179996--180229 Score: 273
Period size: 105 Copynumber: 2.3 Consensus size: 102
179986 TGAGAATTTT
* * *
179996 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGAT-ACAAATTTTGAATTTGATTCAC
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATCA-AAATTTCGAATTTGATTCAC
*
180060 -TAAAAACAAAAG-TAATCTCACCTT-AGATTCTTGTTTCTTTC-
65 AT-AAAAC-AAAGTTAATCTCA-CTTGAGA-TC--GTTT-TCTCA
* *
180101 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCAAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATCAAAATTTCGAATTTGATTCACA
* *
180166 TTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
66 TAAAACAAAGTTAATCTCACTTGAGATCGTTTTCTCA
180203 AAAACAAACTTT-GTCTCGCTTGAGACA
1 AAAACAAA-TTTCGTCTCGCTTGAGACA
180230 ATTGCTCTAA
Statistics
Matches: 114, Mismatches: 9, Indels: 15
0.83 0.07 0.11
Matches are distributed among these distances:
101 3 0.03
102 26 0.23
103 3 0.03
104 9 0.08
105 71 0.62
106 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (102 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATCAAAATTTCGAATTTGATTCACA
TAAAACAAAGTTAATCTCACTTGAGATCGTTTTCTCA
Found at i:180225 original size:36 final size:36
Alignment explanation
Indices: 180180--180264 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 36
180170 ACAAAGTTGA
** *
180180 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTGCTCTAAAAACAAACTTTG
* *
180216 TCTCGCTTGAGACAATTGCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTGCTCTAAAAACAAACTTTG
*
180252 TCTCATTTGAGAC
1 TCTCACTTGAGAC
180265 TATATCTTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 6 0.15
36 35 0.85
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (36 bp):
TCTCACTTGAGACAATTGCTCTAAAAACAAACTTTG
Found at i:180568 original size:28 final size:28
Alignment explanation
Indices: 180537--180728 Score: 257
Period size: 28 Copynumber: 6.8 Consensus size: 28
180527 TCTTGAGACA
180537 GTTTCTCTTGAAAAAAATCTTTGAGTTT
1 GTTTCTCTTGAAAAAAATCTTTGAGTTT
*
180565 GTTTCTCTT-AAAAAAATCTTTGAGTTA
1 GTTTCTCTTGAAAAAAATCTTTGAGTTT
180592 GTTTCTCTTGAAAAAAATCTTTGAGTTT
1 GTTTCTCTTGAAAAAAATCTTTGAGTTT
180620 GTTTCTCTTG-AAAAAATCTTTGAGTTT
1 GTTTCTCTTGAAAAAAATCTTTGAGTTT
* * *
180647 GTTCCTCTTAAAAAAAAAATCTTGGAGTTT
1 GTTTCTCTT--GAAAAAAATCTTTGAGTTT
* *
180677 GTTCCTTTTGAAAAAAAATCTTTGAG-TT
1 GTTTCTCTTG-AAAAAAATCTTTGAGTTT
180705 GTTTCGT-TTGAAAAAAAATCTTTG
1 GTTTC-TCTTG-AAAAAAATCTTTG
180729 TGTCCATTTA
Statistics
Matches: 149, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
27 51 0.34
28 59 0.40
29 15 0.10
30 24 0.16
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (28 bp):
GTTTCTCTTGAAAAAAATCTTTGAGTTT
Found at i:180595 original size:55 final size:55
Alignment explanation
Indices: 180536--180728 Score: 255
Period size: 55 Copynumber: 3.4 Consensus size: 55
180526 CTCTTGAGAC
180536 AGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTTCTCTTAAAAAAATCTTTGAGTT
1 AGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTTCTCTTAAAAAAATCTTTGAGTT
*
180591 AGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTTCTCTTGAAAAAATCTTTGAGTT
1 AGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTTCTCTTAAAAAAATCTTTGAGTT
* * * * * *
180646 TGTTCCTCTTAAAAAAAAAATCTTGGAGTTTGTTCCTTTTGAAAAAAAATCTTTGAGTT
1 AGTTTCTCTT--GAAAAAAATCTTTGAGTTTGTTTCTCTT--AAAAAAATCTTTGAGTT
180705 -GTTTCGT-TTGAAAAAAAATCTTTG
1 AGTTTC-TCTTG-AAAAAAATCTTTG
180729 TGTCCATTTA
Statistics
Matches: 121, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
55 62 0.51
57 36 0.30
58 6 0.05
59 17 0.14
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.44
Consensus pattern (55 bp):
AGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTTCTCTTAAAAAAATCTTTGAGTT
Found at i:180743 original size:29 final size:28
Alignment explanation
Indices: 180682--180746 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
180672 AGTTTGTTCC
** *
180682 TTTTGAAAAAAAATCTTTGAGTTGTTTC
1 TTTTGAAAAAAAATCTTTGAGTCATTTA
* *
180710 GTTTGAAAAAAAATCTTTGTGTCCATTTA
1 TTTTGAAAAAAAATCTTTGAGT-CATTTA
180739 TTTTGAAA
1 TTTTGAAA
180747 CAAAGTTTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 20 0.67
29 10 0.33
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.45
Consensus pattern (28 bp):
TTTTGAAAAAAAATCTTTGAGTCATTTA
Found at i:180948 original size:65 final size:65
Alignment explanation
Indices: 180841--180996 Score: 221
Period size: 65 Copynumber: 2.4 Consensus size: 65
180831 AAAAAAAAAA
*
180841 TCTTAAGATAATTTCTTTTGAAACAAAAGTCTTTGAGTTTGTTT-CTTTGGAAACAAAATTTTGT
1 TCTTAAGACAATTTCTTTTG-AA-AAAAGTCTTTGAGTTTGTTTCCTTT-GAAACAAAATTTTGT
180905 CTC
63 CTC
180908 TCTTAAAGACAATTTCTTTTGAAAAAA-TCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCT
1 TCTT-AAGACAATTTCTTTTGAAAAAAGTCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCT
180972 C
65 C
* *
180973 TC--GAGACAACTTCTTTTGAAAAAA
1 TCTTAAGACAATTTCTTTTGAAAAAA
180997 AAAACAAAAA
Statistics
Matches: 84, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
62 20 0.24
65 35 0.42
66 8 0.10
67 6 0.07
68 15 0.18
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.42
Consensus pattern (65 bp):
TCTTAAGACAATTTCTTTTGAAAAAAGTCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
Found at i:181009 original size:13 final size:13
Alignment explanation
Indices: 180991--181023 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
180981 ACTTCTTTTG
180991 AAAAAAAAAACAA
1 AAAAAAAAAACAA
*
181004 AAAAAAAAAACCA
1 AAAAAAAAAACAA
181017 AAAAAAA
1 AAAAAAA
181024 CACCTTTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:181010 original size:14 final size:14
Alignment explanation
Indices: 180991--181023 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
180981 ACTTCTTTTG
180991 AAAAAAAAAACAAA
1 AAAAAAAAAACAAA
*
181005 AAAAAAAAACCAAA
1 AAAAAAAAAACAAA
181019 AAAAA
1 AAAAA
181024 CACCTTTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAA
Found at i:181530 original size:30 final size:28
Alignment explanation
Indices: 181496--181557 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 28
181486 TTTTGTCTCA
* *
181496 TTTGAGACGGTTTCCCATGAAAAACCAAT
1 TTTGAGAAGGTTTCCC-TGAAAAACAAAT
* *
181525 CTTTGAGAATGTTTCCCTTAAAAACAAAT
1 -TTTGAGAAGGTTTCCCTGAAAAACAAAT
181554 TTTG
1 TTTG
181558 TCTCGCTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.14
29 10 0.36
30 14 0.50
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (28 bp):
TTTGAGAAGGTTTCCCTGAAAAACAAAT
Found at i:181789 original size:40 final size:40
Alignment explanation
Indices: 181734--182178 Score: 236
Period size: 40 Copynumber: 10.4 Consensus size: 40
181724 TGGCCATCCG
* * *
181734 TCCTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCTAGACCAGATC
* * * *
181774 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCTG
1 TCCTCATCACGTAGGAGCCGTGTCATCCCTAG---ACCAGATC
* * *
181817 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 TCCTCATCACGTAGGAGCCGTGTCATC-CC--TAGA---CCAGATC
* *
181863 TCTTCATCACGTATGAGCCGTGTCATTCCC-AGACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCA-TCCCTAGACCAGATC
* *
181903 TCCTTATCACGTAGGAGCCGTGTCA-CCCTTAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATCCC-TAG---ACCAGATC
* * * *
181945 GTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCATC-CC--TAGA---CC-AGATC
* *
181993 TCTTCATCACGTAGGAGCCGTGTCATCAGCT-GACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATC-CCTAGACCAGATC
*
182033 TCCTCATCACGTAGGAGCCGTGTCA-CCCTTAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATCCC-TAG---ACCAGATC
* * * *
182075 GTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCATC-CC--TAGA---CC-AGATC
* * * * * *
182123 TCTTCATCATGTATGAGCAGTGTCATCCCTTGACCAGATT
1 TCCTCATCACGTAGGAGCCGTGTCATCCCTAGACCAGATC
* *
182163 TCCTTATCATGTAGGA
1 TCCTCATCACGTAGGA
182179 ACCTTGTCGC
Statistics
Matches: 314, Mismatches: 53, Indels: 76
0.71 0.12 0.17
Matches are distributed among these distances:
38 4 0.01
39 2 0.01
40 102 0.32
41 4 0.01
42 2 0.01
43 89 0.28
44 8 0.03
45 5 0.02
46 44 0.14
47 52 0.17
48 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (40 bp):
TCCTCATCACGTAGGAGCCGTGTCATCCCTAGACCAGATC
Found at i:181825 original size:43 final size:43
Alignment explanation
Indices: 181766--182091 Score: 256
Period size: 43 Copynumber: 7.6 Consensus size: 43
181756 TCATCCCCAG
*
181766 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCATAGATA
1 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATA
* * * * *
181809 ACCAGCTGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATG
1 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCA--ACC-TTAGATA
* * * * * *
181855 GCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCC-CAG---
1 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCA-ACCTTAGATA
* *
181895 ACCAGATCTCCTTATCACGTAGGAGCCGTGTCACCCTTAGATA
1 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATA
* * * * *
181938 ACCAG-CCGTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATG
1 ACCAGATC-TCCTCATCACGTAGGAGCCGTGTCA--ACC-TTAGATA
* * * * * *
181984 GCCAAGAACTCTTCATCACGTAGGAGCCGTGTC-A--TCAGCTG
1 ACC-AGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATA
*
182025 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCCTTAGATA
1 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATA
*
182068 ACCAG-CCGTCCTCATCACGTAGGA
1 ACCAGATC-TCCTCATCACGTAGGA
182092 ACTGTGTTAT
Statistics
Matches: 219, Mismatches: 47, Indels: 34
0.73 0.16 0.11
Matches are distributed among these distances:
39 2 0.01
40 57 0.26
41 7 0.03
42 2 0.01
43 82 0.37
44 1 0.00
45 7 0.03
46 38 0.17
47 22 0.10
48 1 0.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (43 bp):
ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTTAGATA
Found at i:182218 original size:130 final size:129
Alignment explanation
Indices: 181737--182178 Score: 688
Period size: 130 Copynumber: 3.4 Consensus size: 129
181727 CCATCCGTCC
* * * * * *
181737 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCAT-CCCTGACCAGATCTCCTTATCACGTAGGAGCCGTGTCACCC
* * *
181802 ATAGATAACCAGCTGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCC-AGAACTCT
65 TTAGATAACCAGCCGTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAAGAACTCT
*
181866 TCATCACGTATGAGCCGTGTCATTCCCAGACCAGATCTCCTTATCACGTAGGAGCCGTGTCACCC
1 TCATCACGTATGAGCCGTGTCA-TCCCTGACCAGATCTCCTTATCACGTAGGAGCCGTGTCACCC
181931 TTAGATAACCAGCCGTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAAGAACTCT
65 TTAGATAACCAGCCGTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAAGAACTCT
* * *
181996 TCATCACGTAGGAGCCGTGTCATCAGCTGACCAGATCTCCTCATCACGTAGGAGCCGTGTCACCC
1 TCATCACGTATGAGCCGTGTCATC-CCTGACCAGATCTCCTTATCACGTAGGAGCCGTGTCACCC
182061 TTAGATAACCAGCCGTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAAGAACTCT
65 TTAGATAACCAGCCGTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAAGAACTCT
* * * *
182126 TCATCATGTATGAGCAGTGTCATCCCTTGACCAGATTTCCTTATCATGTAGGA
1 TCATCACGTATGAGCCGTGTCATCCC-TGACCAGATCTCCTTATCACGTAGGA
182179 ACCTTGTCGC
Statistics
Matches: 290, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
129 114 0.39
130 176 0.61
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (129 bp):
TCATCACGTATGAGCCGTGTCATCCCTGACCAGATCTCCTTATCACGTAGGAGCCGTGTCACCCT
TAGATAACCAGCCGTCCTCATCACGTAGGAACTGTGTTATCACCTTTAGATGGCCAAGAACTCT
Found at i:182388 original size:3 final size:3
Alignment explanation
Indices: 182380--182431 Score: 61
Period size: 3 Copynumber: 16.3 Consensus size: 3
182370 CGGGTCTTTT
182380 TTA TTA TTA TT- TATA TATA TTTA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA T-TA -TTA TTA TTA -TTA TTA TTA TTA TTA TTA
182428 TTA T
1 TTA T
182432 GTTTATTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.02
3 34 0.76
4 9 0.20
5 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:182400 original size:10 final size:10
Alignment explanation
Indices: 182379--182429 Score: 79
Period size: 10 Copynumber: 5.2 Consensus size: 10
182369 CCGGGTCTTT
182379 TTTATTATTA
1 TTTATTATTA
182389 TTTA-TATATA
1 TTTATTAT-TA
182399 TTTATTATTA
1 TTTATTATTA
182409 TTTATTATTA
1 TTTATTATTA
182419 -TTATTATTA
1 TTTATTATTA
182428 TT
1 TT
182430 ATGTTTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 12 0.32
10 23 0.61
11 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATTATTA
Found at i:187860 original size:6 final size:6
Alignment explanation
Indices: 187849--187886 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
187839 CTTAAGGACT
*
187849 CTGGAA CTGGAA CTGGAA CTGGAA CTGGAA CTGAAA CT
1 CTGGAA CTGGAA CTGGAA CTGGAA CTGGAA CTGGAA CT
187887 CCTCATGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.34, C:0.18, G:0.29, T:0.18
Consensus pattern (6 bp):
CTGGAA
Found at i:191667 original size:13 final size:15
Alignment explanation
Indices: 191649--191680 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
191639 AATTAGATTG
191649 AAAAAT-AAA-AGAA
1 AAAAATCAAATAGAA
191662 AAAAATCAAATAGAA
1 AAAAATCAAATAGAA
191677 AAAA
1 AAAA
191681 TACAATAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 3 0.18
15 8 0.47
ACGTcount: A:0.81, C:0.03, G:0.06, T:0.09
Consensus pattern (15 bp):
AAAAATCAAATAGAA
Found at i:216674 original size:28 final size:28
Alignment explanation
Indices: 216634--216691 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
216624 GTTTTTTTTT
*
216634 TTTTTTTTGATAAATCGAGATGGGTTTA
1 TTTTTTTTGATAAATCGAGACGGGTTTA
216662 TTTTTTTTGATAAATCGAGACGGGTTTA
1 TTTTTTTTGATAAATCGAGACGGGTTTA
216690 TT
1 TT
216692 GAGAGAAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.24, C:0.05, G:0.21, T:0.50
Consensus pattern (28 bp):
TTTTTTTTGATAAATCGAGACGGGTTTA
Found at i:220771 original size:15 final size:15
Alignment explanation
Indices: 220751--220786 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
220741 CTATTGGCGA
220751 GTGAGTAAACTACTG
1 GTGAGTAAACTACTG
220766 GTGAGTAAACTACTG
1 GTGAGTAAACTACTG
220781 GTGAGT
1 GTGAGT
220787 CTCAGAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.28
Consensus pattern (15 bp):
GTGAGTAAACTACTG
Found at i:226524 original size:89 final size:89
Alignment explanation
Indices: 226391--226570 Score: 315
Period size: 89 Copynumber: 2.0 Consensus size: 89
226381 ATAAATAAAG
*
226391 CCATCATCCTCCTTAGTTAATCATCCCACAAATATAAGCATTCTTCTATATTAAAGGCTATTTGT
1 CCATCATCCTCCTTAGTTAATCATCCCACAAATATAAGCATTCTTCTATATTAAAGGCTATTTAT
* *
226456 ATTCTTTCTCTTTTTGTAATATTT
66 ATTCTTTCTCTCTTTATAATATTT
* *
226480 CCATCATCCTCTTTAGTTAATCATCCCACAAATATAAGCCTTCTTCTATATTAAAGGCTATTTAT
1 CCATCATCCTCCTTAGTTAATCATCCCACAAATATAAGCATTCTTCTATATTAAAGGCTATTTAT
226545 ATTCTTTCTCTCTTTATAATATTT
66 ATTCTTTCTCTCTTTATAATATTT
226569 CC
1 CC
226571 TCTATTAGTG
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.27, C:0.23, G:0.06, T:0.44
Consensus pattern (89 bp):
CCATCATCCTCCTTAGTTAATCATCCCACAAATATAAGCATTCTTCTATATTAAAGGCTATTTAT
ATTCTTTCTCTCTTTATAATATTT
Found at i:231603 original size:21 final size:23
Alignment explanation
Indices: 231579--231625 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
231569 ATTGAAATTT
231579 TATT-GAAAAAA-TATTATTAAA
1 TATTCGAAAAAATTATTATTAAA
*
231600 TATTCCTAAAAAATTATTATTAAA
1 TATT-CGAAAAAATTATTATTAAA
231624 TA
1 TA
231626 ATTTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
23 6 0.27
24 12 0.55
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
TATTCGAAAAAATTATTATTAAA
Found at i:236243 original size:21 final size:22
Alignment explanation
Indices: 236214--236255 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
236204 GTATAATATA
236214 TAAATAAATTTAAAATTAAAAT
1 TAAATAAATTTAAAATTAAAAT
**
236236 TAAA-AAATTTTTAATTAAAA
1 TAAATAAATTTAAAATTAAAA
236256 AAATGTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATAAATTTAAAATTAAAAT
Found at i:238698 original size:226 final size:226
Alignment explanation
Indices: 238304--238763 Score: 796
Period size: 226 Copynumber: 2.0 Consensus size: 226
238294 AAGAGTTGTG
*
238304 ATTTTCTTCCGCTTTTAGGGTTGTTTTGGTGATTTTGTGATTGAATTGGTGTCTTCAAATGCTTG
1 ATTTTCTTCCGCTTTTAGGGTTGTTTTGGTGATTTTGCGATTGAATTGGTGTCTTCAAATGCTTG
* *
238369 TTCTTTGATTAAGGAAAATAGACTCTGTTGAAATATGCTGTTTAGATGTATGCGTTATTATTCAG
66 TTCTATGATTAAGGAAAATAGACTCTGTTGAAATATGCTGTCTAGATGTATGCGTTATTATTCAG
*
238434 GGAAATAGAATACAAAATTTTCCATCTTTTCTTTTAACCTGAAATTCAGGCTTTTCATAAATATT
131 GGAAATAGAATACAAAATTTTCCATCTTTTCTTTTAACCTGAAAATCAGGCTTTTCATAAATATT
* *
238499 TTTGAAAAGTTGGAGGCGTTTGTCATAGTAT
196 TTTCAAAAGCTGGAGGCGTTTGTCATAGTAT
** *
238530 ATTTTCTTCCGCTTTTAGTTTTGTTTTGGTGATTTTGCGATTGAATTGGCT-TCTTCGAATGCTT
1 ATTTTCTTCCGCTTTTAGGGTTGTTTTGGTGATTTTGCGATTGAATTGG-TGTCTTCAAATGCTT
238594 GTTCTATGATTAAGGAAAATAGACTCTGTTGAAATATGCTGTCTAGATGTATGCGTTATTATTCA
65 GTTCTATGATTAAGGAAAATAGACTCTGTTGAAATATGCTGTCTAGATGTATGCGTTATTATTCA
* * *
238659 GGGAAATAGAATGCAAAATTTTCCTTCTTTTCTTTTAACCTGAAAATCAGGCTTTTCGTAAATAT
130 GGGAAATAGAATACAAAATTTTCCATCTTTTCTTTTAACCTGAAAATCAGGCTTTTCATAAATAT
238724 TTTTCAAAAGCTGGAGGCGTTTGTCATAGTAT
195 TTTTCAAAAGCTGGAGGCGTTTGTCATAGTAT
238756 ATTTTCTT
1 ATTTTCTT
238764 GTAAATTTGG
Statistics
Matches: 221, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
226 220 1.00
227 1 0.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.43
Consensus pattern (226 bp):
ATTTTCTTCCGCTTTTAGGGTTGTTTTGGTGATTTTGCGATTGAATTGGTGTCTTCAAATGCTTG
TTCTATGATTAAGGAAAATAGACTCTGTTGAAATATGCTGTCTAGATGTATGCGTTATTATTCAG
GGAAATAGAATACAAAATTTTCCATCTTTTCTTTTAACCTGAAAATCAGGCTTTTCATAAATATT
TTTCAAAAGCTGGAGGCGTTTGTCATAGTAT
Found at i:243804 original size:173 final size:176
Alignment explanation
Indices: 243515--243866 Score: 539
Period size: 173 Copynumber: 2.0 Consensus size: 176
243505 TGGTTTGACA
* * *
243515 TCTGATATTTTATCTTTCAAAGTAACAACTTTATATGAAAATTTTGGCTCGCTGCAAAAGCATTT
1 TCTGATATTTTATCTTTCAAAGTAACAACTTTACATGAAAATTTTGACTCGCTGCAAAAGAATTT
* *
243580 CATCTGATATGAATATGCAGTTGAAGCTTTAGGTTGAACTCTGTGGAAAATCTTCAATGTAAATC
66 CATCTGATATGAATATGCAGTTGAAGCTTTAGATTGAACTCTGTGGAAAATCTTCAATATAAATC
*
243645 GTTC-AT-ATC-ATGCATTCATTTTATGTCAAAACCACTTTATATG
131 GTTCAATAATCTATGCAATCATTTTATGTCAAAACCACTTTATATG
* * * *
243688 TCTGATATTTTATCTTTTAAATTAACAGCTTTACATGAAAATTTTTACTCGCTGCAAAAGAATTT
1 TCTGATATTTTATCTTTCAAAGTAACAACTTTACATGAAAATTTTGACTCGCTGCAAAAGAATTT
*
243753 CATCTGATATGAATATGCAGTTGAAGCTTTAGATTGAACTCTGTGGAAAATCTTCAATATAAATG
66 CATCTGATATGAATATGCAGTTGAAGCTTTAGATTGAACTCTGTGGAAAATCTTCAATATAAATC
243818 GTTCATATAATCATATTATGCAATCATTTTATGTCAAAACCACTTTATA
131 GTTCA-ATAATC----TATGCAATCATTTTATGTCAAAACCACTTTATA
243867 CATAGCAAAA
Statistics
Matches: 160, Mismatches: 11, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
173 124 0.77
175 2 0.01
176 3 0.02
181 31 0.19
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Consensus pattern (176 bp):
TCTGATATTTTATCTTTCAAAGTAACAACTTTACATGAAAATTTTGACTCGCTGCAAAAGAATTT
CATCTGATATGAATATGCAGTTGAAGCTTTAGATTGAACTCTGTGGAAAATCTTCAATATAAATC
GTTCAATAATCTATGCAATCATTTTATGTCAAAACCACTTTATATG
Found at i:264224 original size:33 final size:32
Alignment explanation
Indices: 264176--264241 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 32
264166 GTCGAAGATG
*
264176 TTAGGAAAAAAAATAACAAATAAGT-AATGAA
1 TTAGGAAAAAAAATAACAAATAAATAAATGAA
*
264207 TTAGGAAGAATAAAATAATAAATAAATAAATGAA
1 TTAGGAA-AA-AAAATAACAAATAAATAAATGAA
264241 T
1 T
264242 ATAAATCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 7 0.23
32 2 0.07
33 14 0.47
34 7 0.23
ACGTcount: A:0.64, C:0.02, G:0.12, T:0.23
Consensus pattern (32 bp):
TTAGGAAAAAAAATAACAAATAAATAAATGAA
Found at i:264472 original size:14 final size:14
Alignment explanation
Indices: 264440--264469 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
264430 TATGGGAAAG
264440 AAATAACAATAATA
1 AAATAACAATAATA
264454 AAATAA-AATAATA
1 AAATAACAATAATA
264467 AAA
1 AAA
264470 ATAGATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAACAATAATA
Found at i:264477 original size:13 final size:14
Alignment explanation
Indices: 264440--264472 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
264430 TATGGGAAAG
264440 AAATAACAATAAT-A
1 AAATAA-AATAATAA
264454 AAATAAAATAATAA
1 AAATAAAATAATAA
264468 AAATA
1 AAATA
264473 GATAAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAATAATAA
Found at i:265700 original size:10 final size:10
Alignment explanation
Indices: 265667--265705 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
265657 TTAAGTTAAT
*
265667 AAATGAAATG
1 AAATGAAATA
*
265677 AAACGAAATA
1 AAATGAAATA
265687 AAATGAAATA
1 AAATGAAATA
265697 AAAT-AAATA
1 AAATGAAATA
265706 TTAATAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 5 0.19
10 21 0.81
ACGTcount: A:0.69, C:0.03, G:0.10, T:0.18
Consensus pattern (10 bp):
AAATGAAATA
Found at i:265870 original size:34 final size:32
Alignment explanation
Indices: 265800--265870 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
265790 AACTATATAT
* *
265800 TATATAGTTTTCAAAAATGATTTTAAAAATAT
1 TATATAGTTTTCAAAAATGATTTTAAAAACAA
* * *
265832 TATATAAGTTTTCCAAAATGTTTTGTTAAAACAA
1 TATAT-AGTTTTCAAAAATGATTT-TAAAAACAA
265866 TATAT
1 TATAT
265871 TATATAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 5 0.16
33 16 0.50
34 11 0.34
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (32 bp):
TATATAGTTTTCAAAAATGATTTTAAAAACAA
Done.