Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2258
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: 84157
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:4303 original size:17 final size:16
Alignment explanation
Indices: 4261--4337 Score: 77
Period size: 17 Copynumber: 4.8 Consensus size: 16
4251 AAAGAAAAGA
*
4261 AAATTTTGATATATAT
1 AAATTTTAATATATAT
* **
4277 ATATCATAATTATATAT
1 AAATTTTAA-TATATAT
4294 AAATTTTAATATAT-T
1 AAATTTTAATATATAT
4309 -AATTATTAATATAATAT
1 AAATT-TTAATAT-ATAT
4326 AAATTTTAATAT
1 AAATTTTAATAT
4338 TTTTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
14 4 0.08
15 8 0.16
16 12 0.24
17 21 0.43
18 4 0.08
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (16 bp):
AAATTTTAATATATAT
Found at i:4319 original size:15 final size:14
Alignment explanation
Indices: 4288--4337 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 14
4278 TATCATAATT
4288 ATATATAAATTTTA
1 ATATATAAATTTTA
*
4302 ATATATTAATTATTAA
1 ATATATAAATT-TT-A
4318 TATAATATAAATTTTA
1 -AT-ATATAAATTTTA
4334 ATAT
1 ATAT
4338 TTTTATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 12 0.40
15 4 0.13
16 2 0.07
17 4 0.13
18 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATAAATTTTA
Found at i:4325 original size:20 final size:17
Alignment explanation
Indices: 4290--4337 Score: 66
Period size: 15 Copynumber: 2.9 Consensus size: 17
4280 TCATAATTAT
4290 ATATAAATTTTAATAT-
1 ATATAAATTTTAATATA
4306 AT-T-AATTATTAATATA
1 ATATAAATT-TTAATATA
4322 ATATAAATTTTAATAT
1 ATATAAATTTTAATAT
4338 TTTTATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
14 4 0.14
15 8 0.29
16 4 0.14
17 8 0.29
18 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATAAATTTTAATATA
Found at i:4362 original size:41 final size:40
Alignment explanation
Indices: 4317--4397 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
4307 TTAATTATTA
* * *
4317 ATATAATATAAATTTTAATATTTTTAT-TTTTATTTATTTTT
1 ATATAATATAAATATT-A-ATTTTTATGTTATATATATTTTT
* *
4358 ATATAGTATTAATATTAATTTTTATGTTATATATATTTTT
1 ATATAATATAAATATTAATTTTTATGTTATATATATTTTT
4398 TATTTATTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
39 8 0.24
40 13 0.38
41 13 0.38
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (40 bp):
ATATAATATAAATATTAATTTTTATGTTATATATATTTTT
Found at i:5450 original size:13 final size:13
Alignment explanation
Indices: 5432--5464 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
5422 CATCCACATC
*
5432 TTCCTTTTTCTTT
1 TTCCTTTTTCCTT
5445 TTCCTTTTTCCTT
1 TTCCTTTTTCCTT
5458 TT-CTTTT
1 TTCCTTTT
5465 ATTTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTCCTTTTTCCTT
Found at i:10312 original size:2 final size:2
Alignment explanation
Indices: 10307--10345 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
10297 TCGGGAGATA
10307 AT AT AT AT AT 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 AT AT AT AT AT A
10346 CTGCTCTGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11781 original size:3 final size:3
Alignment explanation
Indices: 11773--11803 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
11763 GAAATAATTT
*
11773 TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
11804 CATACTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11992 original size:2 final size:2
Alignment explanation
Indices: 11985--12022 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11975 TGGGGAGAGG
11985 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
12023 CAATGAGCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12325 original size:9 final size:8
Alignment explanation
Indices: 12299--12362 Score: 51
Period size: 8 Copynumber: 7.8 Consensus size: 8
12289 TATTATTTTT
*
12299 TAATTTAA
1 TAATTAAA
12307 TAATTAAA
1 TAATTAAA
12315 TAATATAAA
1 TAAT-TAAA
12324 TATATTAAA
1 TA-ATTAAA
12333 T--TTAAA
1 TAATTAAA
*
12339 TTAATTTAA
1 -TAATTAAA
*
12348 TAATTTAA
1 TAATTAAA
12356 TACATTA
1 TA-ATTA
12363 TATCAAATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
6 5 0.11
7 1 0.02
8 21 0.45
9 18 0.38
10 2 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (8 bp):
TAATTAAA
Found at i:13083 original size:22 final size:22
Alignment explanation
Indices: 13053--13110 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
13043 AAATTTTTTG
* *
13053 TATTGATAATAATATTTATTAT
1 TATTTATAATAATATTTAATAT
*
13075 TATTTATAATATTATTTAATAT
1 TATTTATAATAATATTTAATAT
*
13097 CA-TTATAATAATAT
1 TATTTATAATAATAT
13111 ATTTTTTTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 11 0.35
22 20 0.65
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TATTTATAATAATATTTAATAT
Found at i:14300 original size:41 final size:40
Alignment explanation
Indices: 14224--14307 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 40
14214 TACATAAAAA
** *
14224 TAAAAATAAAAATTATTTGATAAAAATACGATAATTTTTT
1 TAAAAATAAAAATTACATGATAAAAATAAGATAATTTTTT
14264 TAAAAATATAAAATTACATGAGTAAAAATAAG-TAATTTTTT
1 TAAAAATA-AAAATTACATGA-TAAAAATAAGATAATTTTTT
14305 TAA
1 TAA
14308 TTAAATTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
40 8 0.21
41 22 0.56
42 9 0.23
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (40 bp):
TAAAAATAAAAATTACATGATAAAAATAAGATAATTTTTT
Found at i:19105 original size:2 final size:2
Alignment explanation
Indices: 19098--19130 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
19088 AGTCACATGC
19098 AG AG 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 AG AG A
19131 ATAGAATTAC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21947 original size:79 final size:78
Alignment explanation
Indices: 21812--21975 Score: 181
Period size: 79 Copynumber: 2.1 Consensus size: 78
21802 ATAAAAAAGA
* * *
21812 ATAAAATCTTAAAAACTAAGGGGCTGATTCATCTTTGTTTCCCACTCGAACGTATTTACGGGT-A
1 ATAAAATCTTAAAAACTAAGGGGCTGATTCATCTTTATTTCCAACTCGAAC-TATTTACGGATGA
*
21876 AAGTTGAATTAGATT
65 AA-TTAAATTAGATT
* * ** * *
21891 ATAAAATCTTAAAAATTAAGGGGTTGATTCATCTTTATTTTTAATTCAGATA-TATTTATGGATG
1 ATAAAATCTTAAAAACTAAGGGGCTGATTCATCTTTATTTCCAACTC-GA-ACTATTTACGGATG
21955 AAATTAAATTAGATT
64 AAATTAAATTAGATT
21970 -TAAAAT
1 ATAAAAT
21976 TTTATTTATA
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
78 6 0.08
79 60 0.83
80 5 0.07
81 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (78 bp):
ATAAAATCTTAAAAACTAAGGGGCTGATTCATCTTTATTTCCAACTCGAACTATTTACGGATGAA
ATTAAATTAGATT
Found at i:21982 original size:35 final size:35
Alignment explanation
Indices: 21943--22017 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
21933 AATTCAGATA
* *
21943 TATTTAT-GGATGAAATTAAATTAGATTTAAAATTT
1 TATTTATAGG-TGAAATTAAATCAAATTTAAAATTT
* * *
21978 TATTTATAGGTGTAGTTGAATCAAATTTAAAATTT
1 TATTTATAGGTGAAATTAAATCAAATTTAAAATTT
22013 TATTT
1 TATTT
22018 TATTTTTATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 32 0.94
36 2 0.06
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.48
Consensus pattern (35 bp):
TATTTATAGGTGAAATTAAATCAAATTTAAAATTT
Found at i:22071 original size:19 final size:20
Alignment explanation
Indices: 22047--22088 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
22037 AAATTATGTT
22047 AAATTTAAGTT-TGATTTAA
1 AAATTTAAGTTATGATTTAA
* *
22066 AAATTTAATTTATTATTTAA
1 AAATTTAAGTTATGATTTAA
22086 AAA
1 AAA
22089 GATAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
AAATTTAAGTTATGATTTAA
Found at i:31392 original size:19 final size:18
Alignment explanation
Indices: 31346--31400 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 18
31336 AAAATAAAAT
*
31346 TTATTAATTTAATTTCTTA
1 TTATTAAATTAATTT-TTA
31365 TTAATTAAATTAATTTTTAA
1 TT-ATTAAATTAATTTTT-A
31385 TTATTAAA-TAATTTTT
1 TTATTAAATTAATTTTT
31401 TATTTTAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 8 0.24
19 10 0.30
20 15 0.45
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATTAAATTAATTTTTA
Found at i:31401 original size:19 final size:21
Alignment explanation
Indices: 31343--31402 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 21
31333 ATAAAAATAA
* * *
31343 AATTTATTAATTTAATTTCTT
1 AATTAATTAAATTAATTTTTT
31364 -ATTAATTAAATTAA-TTTTT
1 AATTAATTAAATTAATTTTTT
31383 AATT-ATTAAA-TAATTTTTT
1 AATTAATTAAATTAATTTTTT
31402 A
1 A
31403 TTTTAAGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.09
19 16 0.47
20 15 0.44
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
AATTAATTAAATTAATTTTTT
Found at i:32665 original size:2 final size:2
Alignment explanation
Indices: 32654--32687 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
32644 AGCATTGAAT
32654 TA TA -A 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 T
32688 TTGTTGGTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:32846 original size:21 final size:21
Alignment explanation
Indices: 32778--32836 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
32768 TTAAATTTAT
*
32778 AAATTATTTTATTAATTACAT-A
1 AAATTA-TTTATT-ATTAAATAA
*
32800 ATATTATTTATTATTAAATAA
1 AAATTATTTATTATTAAATAA
32821 AAATTATTTATATATT
1 AAATTATTTAT-TATT
32837 TTAAAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 6 0.19
21 17 0.53
22 9 0.28
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
AAATTATTTATTATTAAATAA
Found at i:32847 original size:18 final size:19
Alignment explanation
Indices: 32826--32892 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 19
32816 AATAAAAATT
32826 ATTTATATATTTTAAA-AA
1 ATTTATATATTTTAAACAA
*
32844 ATTT-TA-ATTTTATAACTA
1 ATTTATATATTTTA-AACAA
* *
32862 ATTTAT-TAATATTAAATAA
1 ATTTATAT-ATTTTAAACAA
*
32881 ATTTATGTATTT
1 ATTTATATATTT
32893 ATATTTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
16 6 0.16
17 4 0.11
18 9 0.24
19 13 0.34
20 6 0.16
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (19 bp):
ATTTATATATTTTAAACAA
Found at i:33019 original size:21 final size:20
Alignment explanation
Indices: 32987--33062 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 20
32977 ATATTTAAAA
*
32987 AATATAAAAATA-ATATAAT
1 AATATAATAATATATATAAT
*
33006 AATATATCATAATATATA-ATT
1 AATATA--ATAATATATATAAT
33027 AATATAATAAATATATTATAAT
1 AATATAAT-AATATA-TATAAT
33049 -ATATAATTAATATA
1 AATATAA-TAATATA
33063 ATTAAAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
19 8 0.17
20 6 0.13
21 27 0.57
22 6 0.13
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (20 bp):
AATATAATAATATATATAAT
Found at i:33032 original size:40 final size:39
Alignment explanation
Indices: 32987--33067 Score: 110
Period size: 40 Copynumber: 2.1 Consensus size: 39
32977 ATATTTAAAA
*
32987 AATATAA-AAATAATATAATAATATATCATAATATATAATT
1 AATATAATAAAT-ATATAATAATATATAATAA-ATATAATT
* *
33027 AATATAATAAATATATTATAATATATAATTAATATAATT
1 AATATAATAAATATATAATAATATATAATAAATATAATT
33066 AA
1 AA
33068 AATTTAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 10 0.27
40 23 0.62
41 4 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (39 bp):
AATATAATAAATATATAATAATATATAATAAATATAATT
Found at i:33042 original size:30 final size:29
Alignment explanation
Indices: 32987--33064 Score: 120
Period size: 30 Copynumber: 2.7 Consensus size: 29
32977 ATATTTAAAA
* *
32987 AATATAAAAATAATATAATAATATATCAT
1 AATATATAATTAATATAATAATATATCAT
*
33016 AATATATAATTAATATAATAAATATATTAT
1 AATATATAATTAATATAAT-AATATATCAT
33046 AATATATAATTAATATAAT
1 AATATATAATTAATATAAT
33065 TAAAATTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 17 0.38
30 28 0.62
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (29 bp):
AATATATAATTAATATAATAATATATCAT
Found at i:33462 original size:28 final size:26
Alignment explanation
Indices: 33413--33464 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
33403 ATATCATTTA
33413 ATTTTTTTATTTTTTTAAAAAATTAT
1 ATTTTTTTATTTTTTTAAAAAATTAT
*
33439 ATTTTATTTATTATTTTTATAAAATT
1 ATTTT-TTTATT-TTTTTAAAAAATT
33465 TAAAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 5 0.22
27 6 0.26
28 12 0.52
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
ATTTTTTTATTTTTTTAAAAAATTAT
Found at i:34722 original size:26 final size:25
Alignment explanation
Indices: 34678--34726 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
34668 TATATAAATA
* *
34678 TAATAAAAATAAATTATTTTAAAAAC
1 TAATAAAAATAAA-AAATTTAAAAAC
*
34704 TAATATAAATAAAAAATTTAAAA
1 TAATAAAAATAAAAAATTTAAAA
34727 TTTTTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
TAATAAAAATAAAAAATTTAAAAAC
Found at i:39938 original size:22 final size:22
Alignment explanation
Indices: 39913--39955 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
39903 TATGTCCATC
39913 TTATATGTGGATATGATTGTAT
1 TTATATGTGGATATGATTGTAT
39935 TTATATGTGGATATGATTGTA
1 TTATATGTGGATATGATTGTA
39956 AAAGTATGAT
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:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (22 bp):
TTATATGTGGATATGATTGTAT
Found at i:39963 original size:22 final size:22
Alignment explanation
Indices: 39915--39963 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
39905 TGTCCATCTT
**
39915 ATATGTGGATATGATTGTATTT
1 ATATGTGGATATGATTGTATAA
39937 ATATGTGGATATGATTGTA-AA
1 ATATGTGGATATGATTGTATAA
39958 AGTATG
1 A-TATG
39964 ATCTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (22 bp):
ATATGTGGATATGATTGTATAA
Found at i:40057 original size:77 final size:77
Alignment explanation
Indices: 39932--40094 Score: 310
Period size: 77 Copynumber: 2.1 Consensus size: 77
39922 GATATGATTG
39932 TATTTATATGTGGATATGATTGTAAAAGTATGATCTTTTAAATT-AAAAAAAATTAAATATATTT
1 TATTTATATGTGGATATGATTGTAAAAGTATGATCTTTTAAATTAAAAAAAAATTAAATATATTT
39996 ATATCAAACACA
66 ATATCAAACACA
40008 TATCTTATATGTGGATATGATTGTAAAAGTATGATCTTTTAAATTAAAAAAAAATTAAATATATT
1 TAT-TTATATGTGGATATGATTGTAAAAGTATGATCTTTTAAATTAAAAAAAAATTAAATATATT
40073 TATATCAAACACA
65 TATATCAAACACA
40086 TATTTATAT
1 TATTTATAT
40095 TTGACACCTT
Statistics
Matches: 85, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
76 3 0.04
77 47 0.55
78 35 0.41
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (77 bp):
TATTTATATGTGGATATGATTGTAAAAGTATGATCTTTTAAATTAAAAAAAAATTAAATATATTT
ATATCAAACACA
Found at i:42659 original size:24 final size:24
Alignment explanation
Indices: 42617--42690 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 24
42607 GAAAAATAAA
* *
42617 TAAAAAATATTCATATAATTATTTT
1 TAAAAAATAAT-ATTTAATTATTTT
**
42642 TAAAAAATAATATTTAA-TAAATT
1 TAAAAAATAATATTTAATTATTTT
*
42665 TAAAATATAATATTT-ATATATTTT
1 TAAAAAATAATATTTAAT-TATTTT
42689 TA
1 TA
42691 TTTATCATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
22 1 0.03
23 18 0.45
24 11 0.28
25 10 0.25
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAAAAATAATATTTAATTATTTT
Found at i:42841 original size:9 final size:9
Alignment explanation
Indices: 42818--42873 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
42808 TATTTATTTA
42818 AAATTTAAT
1 AAATTTAAT
42827 -AATTTAAT
1 AAATTTAAT
*
42835 AAATTTAAA
1 AAATTTAAT
*
42844 AAATTTATT
1 AAATTTAAT
42853 AATAATTTATAT
1 -A-AATTTA-AT
*
42865 AAAATTAAT
1 AAATTTAAT
42874 TTAATTCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
8 8 0.21
9 16 0.42
10 6 0.16
11 7 0.18
12 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AAATTTAAT
Found at i:42856 original size:21 final size:22
Alignment explanation
Indices: 42830--42870 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
42820 ATTTAATAAT
42830 TTAATAAATTTA-A-AAAATTTA
1 TTAAT-AATTTATATAAAATTTA
42851 TTAATAATTTATATAAAATT
1 TTAATAATTTATATAAAATT
42871 AATTTAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 6 0.33
22 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAATAATTTATATAAAATTTA
Found at i:44322 original size:20 final size:22
Alignment explanation
Indices: 44293--44334 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
44283 CAATGTAAAA
44293 TTTTATTATTTAA-GTATTATT
1 TTTTATTATTTAATGTATTATT
44314 TTTTA-TATTTAATGTATTATT
1 TTTTATTATTTAATGTATTATT
44335 ATTAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (22 bp):
TTTTATTATTTAATGTATTATT
Found at i:46361 original size:14 final size:14
Alignment explanation
Indices: 46342--46369 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46332 TTTTTTAATT
46342 TTAAATATATTTTA
1 TTAAATATATTTTA
46356 TTAAATATATTTTA
1 TTAAATATATTTTA
46370 AATATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:47059 original size:23 final size:22
Alignment explanation
Indices: 47033--47089 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
47023 GATATAAAAA
47033 ATAATTAAAATATAATATTATAT
1 ATAATTAAAATATAAT-TTATAT
* *
47056 ATAAATAATATA-AATTTATAT
1 ATAATTAAAATATAATTTATAT
47077 A-AATATAAAATAT
1 ATAAT-TAAAATAT
47090 TTTAAATATG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 2 0.07
21 13 0.46
22 3 0.11
23 10 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAATTAAAATATAATTTATAT
Found at i:47067 original size:21 final size:20
Alignment explanation
Indices: 47038--47134 Score: 80
Period size: 19 Copynumber: 5.0 Consensus size: 20
47028 AAAAAATAAT
47038 TAAA-ATATAATATTATATA
1 TAAATATATAATATTATATA
47057 TAAATAATATAA-ATT-TATA
1 TAAAT-ATATAATATTATATA
* * *
47076 TAAATATAAAATATTTTAAA
1 TAAATATATAATATTATATA
*
47096 TATGATA-ATAATAATTA-ATA
1 TA-AATATATAAT-ATTATATA
*
47116 TGAATATATAA-ATTATATA
1 TAAATATATAATATTATATA
47135 AATATATCTG
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
18 9 0.15
19 22 0.35
20 19 0.31
21 12 0.19
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TAAATATATAATATTATATA
Found at i:47068 original size:9 final size:8
Alignment explanation
Indices: 47052--47141 Score: 69
Period size: 9 Copynumber: 10.8 Consensus size: 8
47042 ATATAATATT
47052 ATATATAA
1 ATATATAA
47060 ATAATATAA
1 AT-ATATAA
47069 ATTTATATAA
1 A--TATATAA
47079 ATATA-AA
1 ATATATAA
*
47086 ATATTTTAA
1 ATA-TATAA
47095 ATATGAT-A
1 ATAT-ATAA
47103 ATA-ATAA
1 ATATATAA
* *
47110 TTAATATGA
1 AT-ATATAA
47119 ATATATAA
1 ATATATAA
47127 ATTATATAA
1 A-TATATAA
47136 ATATAT
1 ATATAT
47142 CTGTGAGCAA
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
6 2 0.03
7 7 0.11
8 24 0.36
9 25 0.38
10 7 0.11
11 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (8 bp):
ATATATAA
Found at i:47070 original size:27 final size:27
Alignment explanation
Indices: 47031--47138 Score: 70
Period size: 26 Copynumber: 4.2 Consensus size: 27
47021 ATGATATAAA
47031 AAATAAT-TAAAATATAATATTATATAT
1 AAATAATATAAAATATAATA-TATATAT
* *
47058 AAATAATAT-AAAT-TTATATAAATAT
1 AAATAATATAAAATATAATATATATAT
* * *
47083 AAA-ATATTTTAAATATGATA-ATA-AT
1 AAATA-ATATAAAATATAATATATATAT
* *
47108 AATTAATATGAATATATAA-AT-TATAT
1 AAATAATAT-AAAATATAATATATATAT
47134 AAATA
1 AAATA
47139 TATCTGTGAG
Statistics
Matches: 62, Mismatches: 11, Indels: 17
0.69 0.12 0.19
Matches are distributed among these distances:
24 1 0.02
25 22 0.35
26 23 0.37
27 15 0.24
28 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
AAATAATATAAAATATAATATATATAT
Found at i:50593 original size:2 final size:2
Alignment explanation
Indices: 50586--50611 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50576 ATCATCCAAT
50586 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
50612 CAGGTACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53633 original size:12 final size:12
Alignment explanation
Indices: 53616--53676 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 12
53606 ATAAGATTTA
53616 TTTAATTATTAT
1 TTTAATTATTAT
*
53628 TTTAATTTTTAT
1 TTTAATTATTAT
53640 ATTTAATATATTAAT
1 -TTTAAT-TATT-AT
* **
53655 TTTTATTAAAATT
1 TTTAATTATTA-T
53668 TTTAATTAT
1 TTTAATTAT
53677 AAAAATTATC
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
12 12 0.32
13 16 0.42
14 8 0.21
15 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTAATTATTAT
Found at i:55774 original size:14 final size:14
Alignment explanation
Indices: 55755--55781 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55745 AAATATATCA
55755 AAACTTCAACGATC
1 AAACTTCAACGATC
55769 AAACTTCAACGAT
1 AAACTTCAACGAT
55782 TCCTATCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.22
Consensus pattern (14 bp):
AAACTTCAACGATC
Found at i:57367 original size:9 final size:9
Alignment explanation
Indices: 57339--57375 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
57329 TCCACCGCAC
57339 CCACCACAG
1 CCACCACAG
57348 CCA-C-CAG
1 CCACCACAG
57355 -CACCACAG
1 CCACCACAG
57363 CCACCACAG
1 CCACCACAG
57372 CCAC
1 CCAC
57376 TGCTATTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
6 2 0.08
7 4 0.16
8 4 0.16
9 15 0.60
ACGTcount: A:0.32, C:0.57, G:0.11, T:0.00
Consensus pattern (9 bp):
CCACCACAG
Found at i:57375 original size:15 final size:15
Alignment explanation
Indices: 57340--57368 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
57330 CCACCGCACC
57340 CACCACAGCCACCAG
1 CACCACAGCCACCAG
57355 CACCACAGCCACCA
1 CACCACAGCCACCA
57369 CAGCCACTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.55, G:0.10, T:0.00
Consensus pattern (15 bp):
CACCACAGCCACCAG
Found at i:57389 original size:72 final size:72
Alignment explanation
Indices: 57283--57569 Score: 312
Period size: 72 Copynumber: 4.0 Consensus size: 72
57273 CTGCCACACC
* * * *
57283 CACCACAGCCGCCACAGCCACTGCTACTT-GCCATGCTTCCACAACCTCCACCGCACCCACCACA
1 CACCACAACCACCACAGCCACTGCTA-TTCACCATGCTTCCACAACCTCCACCACACCCACCACA
57347 GCCACCAG
65 GCCACCAG
* *
57355 CACCACAGCCACCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCGCCACACCCACCACAG
1 CACCACAACCACCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCACCACACCCACCACAG
*
57420 ---CCTG
66 CCACCAG
* * * * *
57424 CACCACAACCGCCACAACCACTGCTATTCACCATGCTTCCACAACCACCCCCGCACCCACCACCA
1 CACCACAACCACCACAGCCACTGCTATTCACCATGCTTCCACAACC-TCCAC-CACAC-CCACCA
* *
57489 CAACCACCTG
63 CAGCCACCAG
** * * * * * *
57499 CACCACAACCACCACAGCCACCACTCTTCACCATGTTTCCGCAGCCTGCACCACAACCACCACAG
1 CACCACAACCACCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCACCACACCCACCACAG
57564 CCACCA
66 CCACCA
57570 CTTTTTGTTG
Statistics
Matches: 181, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
69 46 0.25
70 3 0.02
71 6 0.03
72 79 0.44
73 3 0.02
74 2 0.01
75 42 0.23
ACGTcount: A:0.28, C:0.52, G:0.09, T:0.11
Consensus pattern (72 bp):
CACCACAACCACCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCACCACACCCACCACAG
CCACCAG
Found at i:57417 original size:21 final size:21
Alignment explanation
Indices: 57393--57442 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
57383 CACCATGCTT
* *
57393 CCACAACCTCCGCCACACCCA
1 CCACAACCTCCACCACAACCA
* * *
57414 CCACAGCCTGCACCACAACCG
1 CCACAACCTCCACCACAACCA
57435 CCACAACC
1 CCACAACC
57443 ACTGCTATTC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.58, G:0.08, T:0.04
Consensus pattern (21 bp):
CCACAACCTCCACCACAACCA
Found at i:57465 original size:69 final size:70
Alignment explanation
Indices: 57283--57486 Score: 286
Period size: 69 Copynumber: 2.9 Consensus size: 70
57273 CTGCCACACC
*
57283 CACCACAGCCGCCACAGCCACTGCTACTT-GCCATGCTTCCACAACCTCCACCGCACCCACCACA
1 CACCACAGCCGCCACAGCCACTGCTA-TTCACCATGCTTCCACAACCTCCACCGCACCCACCACA
57347 GCCACCAG
65 G-C-CCAG
* * *
57355 CACCACAGCCACCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCGCCACACCCACCACAG
1 CACCACAGCCGCCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCACCGCACCCACCACAG
*
57420 -CCTG
66 CCCAG
* * * *
57424 CACCACAACCGCCACAACCACTGCTATTCACCATGCTTCCACAACCACCCCCGCACCCACCAC
1 CACCACAGCCGCCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCACCGCACCCACCAC
57487 CACAACCACC
Statistics
Matches: 120, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
69 60 0.50
71 2 0.02
72 58 0.48
ACGTcount: A:0.26, C:0.52, G:0.10, T:0.12
Consensus pattern (70 bp):
CACCACAGCCGCCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCACCGCACCCACCACAG
CCCAG
Found at i:57513 original size:69 final size:68
Alignment explanation
Indices: 57300--57513 Score: 182
Period size: 69 Copynumber: 3.1 Consensus size: 68
57290 GCCGCCACAG
* * * *
57300 CCACTGCTACTT-GCCATGCTTCCACAACCTCCACCGCACCCACCACAGCCACCAGCACCACAGC
1 CCACTGCTA-TTCACCATGCTTCCACAACCTCCACCGCACCCA-C-CA-CCACAACCACCGCA-C
*
57364 CACCA-CA
61 CACAACCA
* * *** * *
57371 GCCACTGCTATTCACCATGCTTCCACAACCTCCGCCACACCCACCA-CAGCCTGCACCACAACCG
1 -CCACTGCTATTCACCATGCTTCCACAACCTCCACCGCACCCACCACCA-CAACCACCGC-ACCA
* *
57435 CCACAA
63 CAACCA
* *
57441 CCACTGCTATTCACCATGCTTCCACAACCACCCCCGCACCCACCACCACAACCACCTGCACCACA
1 CCACTGCTATTCACCATGCTTCCACAACCTCCACCGCACCCACCACCACAACCACC-GCACCACA
57506 ACCA
65 ACCA
57510 CCAC
1 CCAC
57514 AGCCACCACT
Statistics
Matches: 120, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
68 2 0.02
69 72 0.60
70 7 0.06
71 3 0.03
72 36 0.30
ACGTcount: A:0.28, C:0.52, G:0.08, T:0.12
Consensus pattern (68 bp):
CCACTGCTATTCACCATGCTTCCACAACCTCCACCGCACCCACCACCACAACCACCGCACCACAA
CCA
Found at i:57570 original size:75 final size:75
Alignment explanation
Indices: 57313--57561 Score: 219
Period size: 75 Copynumber: 3.4 Consensus size: 75
57303 CTGCTACTTG
* * * * * *
57313 CCATGCTTCCACAACCTCCACCGC-A-C-CCACCACAGCCACCAGCACCACAGCCACCACAGCCA
1 CCATGCTTCCACAACCACCACCACAACCACCACCACAACCACCTGCACCACAACCACCACAACCA
**
57375 CTGCTATTCA
66 CCACTATTCA
* * * *
57385 CCATGCTTCCACAACCTCCGCCAC-A-C-CCACCAC-A--GCCTGCACCACAACCGCCACAACCA
1 CCATGCTTCCACAACCACCACCACAACCACCACCACAACCACCTGCACCACAACCACCACAACCA
**
57444 CTGCTATTCA
66 CCACTATTCA
* * * *
57454 CCATGCTTCCACAACCACCCCCGCACCCACCACCACAACCACCTGCACCACAACCACCACAGCCA
1 CCATGCTTCCACAACCACCACCACAACCACCACCACAACCACCTGCACCACAACCACCACAACCA
*
57519 CCACTCTTCA
66 CCACTATTCA
* * * **
57529 CCATGTTTCCGCAGCCTGCACCACAACCACCAC
1 CCATGCTTCCACAACCACCACCACAACCACCAC
57562 AGCCACCACT
Statistics
Matches: 145, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
69 51 0.35
71 1 0.01
72 38 0.26
73 1 0.01
75 54 0.37
ACGTcount: A:0.28, C:0.52, G:0.08, T:0.12
Consensus pattern (75 bp):
CCATGCTTCCACAACCACCACCACAACCACCACCACAACCACCTGCACCACAACCACCACAACCA
CCACTATTCA
Found at i:62992 original size:17 final size:17
Alignment explanation
Indices: 62970--63061 Score: 53
Period size: 17 Copynumber: 5.1 Consensus size: 17
62960 ATTTGATGTT
62970 AAAATAATATAATATAA
1 AAAATAATATAATATAA
*
62987 AAAATAAATTTAAAATTGATATA
1 AAAAT-AA--TATAA-T-ATA-A
* *
63010 AAAATATTATAAAAATAAA
1 AAAATAATAT-AATAT-AA
63029 AAAATAA-AT-ATATAA
1 AAAATAATATAATATAA
* *
63044 AAATTTATATAATATAA
1 AAAATAATATAATATAA
63061 A
1 A
63062 TTATTGATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
15 7 0.12
16 5 0.09
17 12 0.21
18 4 0.07
19 9 0.16
20 7 0.12
21 3 0.05
22 4 0.07
23 6 0.11
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (17 bp):
AAAATAATATAATATAA
Found at i:63350 original size:49 final size:49
Alignment explanation
Indices: 63252--63347 Score: 115
Period size: 50 Copynumber: 1.9 Consensus size: 49
63242 ATTTAAAAAT
* *
63252 ATTTTTATTTAAATATAATTATAAAATATTAATATAAATATAATTTTAAA
1 ATTTTTATTTAAATATAATAATAAAATAATAATATAAATATAA-TTTAAA
*
63302 ATTTTTA-TTAATTATAAATAATAAATATAAATAATATAAAT-TAATT
1 ATTTTTATTTAAATAT-AATAATAAA-AT-AATAATATAAATATAATT
63348 AAATTAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
49 7 0.17
50 17 0.43
51 5 0.12
52 11 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (49 bp):
ATTTTTATTTAAATATAATAATAAAATAATAATATAAATATAATTTAAA
Found at i:63773 original size:17 final size:17
Alignment explanation
Indices: 63753--63791 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
63743 GAATATATAA
63753 ATATATATTTTATAAAT
1 ATATATATTTTATAAAT
* * *
63770 ATATTTATTTTTTAATT
1 ATATATATTTTATAAAT
63787 ATATA
1 ATATA
63792 AAGATCATAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATATATTTTATAAAT
Found at i:63833 original size:17 final size:16
Alignment explanation
Indices: 63806--63837 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
63796 TCATATTTTT
63806 AATATTTATATTTAAA
1 AATATTTATATTTAAA
63822 AATATATTATATTTAA
1 AATAT-TTATATTTAA
63838 TATTTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATATTTATATTTAAA
Found at i:64086 original size:18 final size:18
Alignment explanation
Indices: 64047--64112 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
64037 GTTAATAATT
64047 TATATTATATAAATTTTAA
1 TATATT-TATAAATTTTAA
*
64066 TATATTTATATATTATT-A
1 TATATTTATAAATT-TTAA
* *
64084 TATATTTATTAATTTT-T
1 TATATTTATAAATTTTAA
64101 TATATTATATAA
1 TATATT-TATAA
64113 TTATATTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
17 8 0.20
18 24 0.60
19 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATTTATAAATTTTAA
Found at i:64096 original size:30 final size:27
Alignment explanation
Indices: 64049--64108 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 27
64039 TAATAATTTA
64049 TATTATATAAATTTTAATATATTTATATAT
1 TATTATATAAATTTTAAT-T-TTT-TATAT
*
64079 TATTATAT-ATTTATTAATTTTTTATAT
1 TATTATATAAATT-TTAATTTTTTATAT
64106 TAT
1 TAT
64109 ATAATTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 8 0.29
28 3 0.11
29 4 0.14
30 13 0.46
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TATTATATAAATTTTAATTTTTTATAT
Found at i:64118 original size:30 final size:29
Alignment explanation
Indices: 64045--64127 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 29
64035 AGGTTAATAA
64045 TTTATATTATATAA-AT-TTTAATATATT
1 TTTATATTATATAATATATTTAATATATT
* *
64072 TATATATTAT-T-ATATATTTATTA-ATTT
1 TTTATATTATATAATATATTTAATATA-TT
64099 TTTATATTATATAATTATATTTAAATATA
1 TTTATATTATATAA-TATATTT-AATATA
64128 ATTATTACAA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
25 1 0.02
26 4 0.09
27 26 0.59
28 1 0.02
29 1 0.02
30 7 0.16
31 3 0.07
32 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTATATTATATAATATATTTAATATATT
Found at i:72283 original size:9 final size:9
Alignment explanation
Indices: 72269--72307 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
72259 CTCAAATGCG
72269 AAAAAAAGA
1 AAAAAAAGA
72278 AAAAAAA-A
1 AAAAAAAGA
*
72286 AAAAAAGGA
1 AAAAAAAGA
*
72295 AAAACAAGA
1 AAAAAAAGA
72304 AAAA
1 AAAA
72308 GTAGTATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:72290 original size:16 final size:16
Alignment explanation
Indices: 72269--72308 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
72259 CTCAAATGCG
72269 AAAAAAAGAAAAAAAA
1 AAAAAAAGAAAAAAAA
* *
72285 AAAAAAAGGAAAAACA
1 AAAAAAAGAAAAAAAA
*
72301 AGAAAAAG
1 AAAAAAAG
72309 TAGTATTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAAAAA
Found at i:73355 original size:3 final size:3
Alignment explanation
Indices: 73347--73384 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
73337 AATGGTTGGA
*
73347 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
73385 AAAGATAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:73698 original size:24 final size:24
Alignment explanation
Indices: 73650--73741 Score: 69
Period size: 24 Copynumber: 3.7 Consensus size: 24
73640 TATGATTAAT
* * **
73650 AATATATAAAAATAAATAATTATA
1 AATAAATAAAAATATATAAAAATA
73674 AATAAATAAAAATATATAAAAATA
1 AATAAATAAAAATATATAAAAATA
* * * *
73698 AA-ATATATAATTATATAAGTAAATT
1 AATAAATAAAAATATATAA--AAATA
73723 AATAAATAATTAAATATAT
1 AATAAATAA--AAATATAT
73742 GATCAATTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
23 13 0.25
24 22 0.42
25 6 0.12
26 4 0.08
28 7 0.13
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (24 bp):
AATAAATAAAAATATATAAAAATA
Found at i:73922 original size:17 final size:17
Alignment explanation
Indices: 73900--73933 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
73890 TTTATTTAAT
73900 AATAATTA-ATTATATAA
1 AATAATTATA-TATATAA
73917 AATAATTATATATATAA
1 AATAATTATATATATAA
73934 TTAACAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAATTATATATATAA
Found at i:74018 original size:12 final size:11
Alignment explanation
Indices: 73990--74032 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
73980 ATAAAAATAA
*
73990 AATATATAATT
1 AATAAATAATT
74001 ATATAAATAAATT
1 A-ATAAAT-AATT
74014 AATAAATAATT
1 AATAAATAATT
74025 AAATAAAT
1 -AATAAAT
74033 TATCATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 5 0.18
12 18 0.64
13 5 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATAAATAATT
Found at i:74018 original size:20 final size:21
Alignment explanation
Indices: 73984--74044 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
73974 GTAAACATAA
* *
73984 AAATAAAATATAT-AATTATAT
1 AAATAAATTATATAAATAAT-T
74005 AAATAAATTA-ATAAATAATT
1 AAATAAATTATATAAATAATT
74025 AAATAAATTATCATTAAATA
1 AAATAAATTAT-A-TAAATA
74045 TATGATCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 13 0.38
21 14 0.41
22 1 0.03
23 6 0.18
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AAATAAATTATATAAATAATT
Found at i:81274 original size:22 final size:23
Alignment explanation
Indices: 81248--81303 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 23
81238 TCTGATACAA
*
81248 TATATTTAATTTTTAATT-TTTT
1 TATATTTAATTTATAATTATTTT
81270 TATATTTAA---ATAATTATTTT
1 TATATTTAATTTATAATTATTTT
81290 TATATTTATATTTA
1 TATATTTA-ATTTA
81304 AATATACATT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 5 0.18
20 12 0.43
21 1 0.04
22 9 0.32
24 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TATATTTAATTTATAATTATTTT
Found at i:81308 original size:14 final size:14
Alignment explanation
Indices: 81268--81308 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
81258 TTTTAATTTT
81268 TTTATATTTAAATA
1 TTTATATTTAAATA
* *
81282 ATTAT-TTT-TATA
1 TTTATATTTAAATA
81294 TTTATATTTAAATA
1 TTTATATTTAAATA
81308 T
1 T
81309 ACATTAGAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
12 7 0.33
13 6 0.29
14 8 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTATATTTAAATA
Done.