Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1151
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: 61959
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Found at i:6231 original size:37 final size:35
Alignment explanation
Indices: 6151--6231 Score: 83
Period size: 37 Copynumber: 2.2 Consensus size: 35
6141 CTCAATCTAG
* *
6151 TTTAATTTAAATTTAAAATATTTTATTTTTATTTA
1 TTTAATTTAAATATAAAATATTTAATTTTTATTTA
*
6186 TTCATAATTTAAATCATAATATATTTAAATTTTTATTT-
1 TT--TAATTTAAAT-ATAAAATATTT-AATTTTTATTTA
6224 TATTAATT
1 T-TTAATT
6232 AAAAAAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
35 2 0.05
37 15 0.39
38 10 0.26
39 11 0.29
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (35 bp):
TTTAATTTAAATATAAAATATTTAATTTTTATTTA
Found at i:10712 original size:18 final size:18
Alignment explanation
Indices: 10686--10720 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10676 TATATTTATT
*
10686 TAATTTAATCATATTTAA
1 TAATATAATCATATTTAA
*
10704 TAATATAATTATATTTA
1 TAATATAATCATATTTA
10721 TTGTGTATTT
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:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATATAATCATATTTAA
Found at i:11899 original size:24 final size:24
Alignment explanation
Indices: 11866--11929 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
11856 TTTAAATAAT
*
11866 TAATAAAAAAT-TTAAAA-TTATTA
1 TAATATAAAATATTAAAATTTA-TA
11889 TAAATATAAAATATTAAAATTTATA
1 T-AATATAAAATATTAAAATTTATA
*
11914 TAATATAAATTATTAA
1 TAATATAAAATATTAA
11930 TATATTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 1 0.03
24 23 0.64
25 9 0.25
26 3 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
TAATATAAAATATTAAAATTTATA
Found at i:11910 original size:32 final size:33
Alignment explanation
Indices: 11872--11963 Score: 95
Period size: 32 Copynumber: 2.8 Consensus size: 33
11862 TAATTAATAA
11872 AAAATTTAAAATTATTATAAA-TA-TAAAATATT
1 AAAATTTAAAA-TATTATAAATTATTAAAATATT
* * *
11904 AAAATTT-ATATAATATAAATTATTAATATATT
1 AAAATTTAAAATATTATAAATTATTAAAATATT
11936 AAAATTTATAAATA-TATATAATT-TTAAA
1 AAAATTTA-AAATATTATA-AATTATTAAA
11964 TATAATTATA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
30 8 0.16
31 4 0.08
32 22 0.44
33 8 0.16
34 8 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
AAAATTTAAAATATTATAAATTATTAAAATATT
Found at i:11913 original size:17 final size:17
Alignment explanation
Indices: 11872--11952 Score: 66
Period size: 17 Copynumber: 4.9 Consensus size: 17
11862 TAATTAATAA
*
11872 AAAATTTA-AAATTATT
1 AAAATTTATAAAATATT
11888 ATAAA--TATAAAATATT
1 A-AAATTTATAAAATATT
*
11904 AAAATTTATATAATA-T
1 AAAATTTATAAAATATT
*
11920 -AAA-TTATTAATATATT
1 AAAATTTA-TAAAATATT
11936 AAAATTTATAAATATAT
1 AAAATTTATAAA-ATAT
11953 ATAATTTTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
14 3 0.06
15 13 0.25
16 11 0.22
17 17 0.33
18 7 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATTTATAAAATATT
Found at i:11923 original size:30 final size:31
Alignment explanation
Indices: 11887--11951 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 31
11877 TTAAAATTAT
11887 TATAAA-TA-TAAAATATTAAAATTTATATAA
1 TATAAATTATTAAAATATTAAAATTTATA-AA
*
11917 TATAAATTATTAATATATTAAAATTTATAAA
1 TATAAATTATTAAAATATTAAAATTTATAAA
11948 TATA
1 TATA
11952 TATAATTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 6 0.19
31 8 0.25
32 18 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (31 bp):
TATAAATTATTAAAATATTAAAATTTATAAA
Found at i:11924 original size:40 final size:40
Alignment explanation
Indices: 11880--11957 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 40
11870 AAAAAATTTA
*
11880 AAATTATTATAAATA-TAAAATATTA-AAATTTATATAATAT
1 AAATTATTA-AAATATTAAAAT-TTATAAATATATATAATAT
*
11920 AAATTATTAATATATTAAAATTTATAAATATATATAAT
1 AAATTATTAAAATATTAAAATTTATAAATATATATAAT
11958 TTTAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 7 0.21
40 27 0.79
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (40 bp):
AAATTATTAAAATATTAAAATTTATAAATATATATAATAT
Found at i:11944 original size:18 final size:18
Alignment explanation
Indices: 11899--11952 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
11889 TAAATATAAA
11899 ATATTAAAATTTA-T-AT
1 ATATTAAAATTTATTAAT
11915 A-A-TATAAA-TTATTAAT
1 ATATTA-AAATTTATTAAT
*
11931 ATATTAAAATTTATAAAT
1 ATATTAAAATTTATTAAT
11949 ATAT
1 ATAT
11953 ATAATTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
14 5 0.16
15 5 0.16
16 4 0.13
17 4 0.13
18 13 0.42
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATTAAAATTTATTAAT
Found at i:11973 original size:18 final size:17
Alignment explanation
Indices: 11911--11988 Score: 56
Period size: 17 Copynumber: 4.4 Consensus size: 17
11901 ATTAAAATTT
11911 ATATAA-TATAAATTATTA
1 ATATAATTAT-AATT-TTA
*
11929 ATAT-ATTAAAATTTATA
1 ATATAATTATAATTT-TA
11946 A-AT-ATATATAATTTTAA
1 ATATAAT-TATAATTTT-A
11963 ATATAATTATAATAATTTA
1 ATATAATTATAAT--TTTA
11982 ATATAAT
1 ATATAAT
11989 GAAATATCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
16 6 0.12
17 17 0.34
18 14 0.28
19 10 0.20
20 3 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTATAATTTTA
Found at i:13030 original size:2 final size:2
Alignment explanation
Indices: 13025--13049 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13015 TTAATTCCTT
13025 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 T
13050 TTAGAGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14241 original size:56 final size:56
Alignment explanation
Indices: 14155--14266 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
14145 CCTTATGGTT
14155 CCAGTTTCTTATAGATTAATTGCCTGGAAATCTCATTCTCTCCATTTATAGAAGGA
1 CCAGTTTCTTATAGATTAATTGCCTGGAAATCTCATTCTCTCCATTTATAGAAGGA
* *
14211 CCAGTTTCTTATTGATTAATTGCCTGGAAATCTCATTCTCTTCATTTATAGAAGGA
1 CCAGTTTCTTATAGATTAATTGCCTGGAAATCTCATTCTCTCCATTTATAGAAGGA
14267 AGAGTGTTGT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (56 bp):
CCAGTTTCTTATAGATTAATTGCCTGGAAATCTCATTCTCTCCATTTATAGAAGGA
Found at i:17488 original size:26 final size:25
Alignment explanation
Indices: 17428--17481 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
17418 AATAATTAAT
*
17428 TATTTTATT-TTTAAATAGTTTTTA
1 TATTTTTTTATTTAAATAGTTTTTA
*
17452 TATTTTTTTATTTAAA-ATTTTTTA
1 TATTTTTTTATTTAAATAGTTTTTA
*
17476 TCTTTT
1 TATTTT
17482 AATTTATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (25 bp):
TATTTTTTTATTTAAATAGTTTTTA
Found at i:17507 original size:16 final size:16
Alignment explanation
Indices: 17482--17530 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
17472 TTTATCTTTT
* *
17482 AATTTATATTTAATTA
1 AATTTTTATTTAAATA
17498 AATTTTTATTTTAAATA
1 AATTTTTA-TTTAAATA
**
17515 AAAATTTATTTAAATA
1 AATTTTTATTTAAATA
17531 TAATAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 15 0.54
17 13 0.46
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTTTTATTTAAATA
Found at i:17516 original size:17 final size:17
Alignment explanation
Indices: 17482--17530 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
17472 TTTATCTTTT
*
17482 AATTTATATTTAATTAAA
1 AATTTAT-TTTAAATAAA
**
17500 TTTTTATTTTAAATAAA
1 AATTTATTTTAAATAAA
17517 AATTTA-TTTAAATA
1 AATTTATTTTAAATA
17531 TAATAAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 8 0.31
17 13 0.50
18 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATAAA
Found at i:17555 original size:26 final size:26
Alignment explanation
Indices: 17510--17562 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
17500 TTTTTATTTT
*
17510 AAATAAAAATTTATTTAAATATAATA
1 AAATAAAAATTTATTGAAATATAATA
*
17536 AAATATAAAATTTA-TGAAATTTAATA
1 AAATA-AAAATTTATTGAAATATAATA
17562 A
1 A
17563 TTTTAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
AAATAAAAATTTATTGAAATATAATA
Found at i:19074 original size:2 final size:2
Alignment explanation
Indices: 19069--19104 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
19059 AAAAAAACTC
19069 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
19105 TTGGAAGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19283 original size:1 final size:1
Alignment explanation
Indices: 19277--19310 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
19267 GTAAGCTCTG
19277 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19311 CTAGACAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20502 original size:18 final size:17
Alignment explanation
Indices: 20475--20509 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20465 TGATTTAAGG
*
20475 TATTTTTAAAATTATTT
1 TATTTTTAAAAATATTT
20492 TATTATTTAAAAATATTT
1 TATT-TTTAAAAATATTT
20510 AAAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTTTAAAAATATTT
Found at i:22169 original size:3 final size:3
Alignment explanation
Indices: 22161--22243 Score: 62
Period size: 3 Copynumber: 28.3 Consensus size: 3
22151 ATTGCCCAAG
* * * * * *
22161 TAA TAA TAA TAA TAA TAA TAA TTA TTA TTA TTA TTA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
22209 TTA TAA TAA T-T TAA TTA TAA -AA AAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
22244 TTGTTCACTC
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
2 3 0.04
3 64 0.96
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:22439 original size:15 final size:16
Alignment explanation
Indices: 22414--22446 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
22404 TCTCTGAAGC
22414 ATTTCTTCTTCTACTT
1 ATTTCTTCTTCTACTT
*
22430 ATTT-TTCTTCTTCTT
1 ATTTCTTCTTCTACTT
22445 AT
1 AT
22447 CAAATATTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTCTTCTTCTACTT
Found at i:24258 original size:14 final size:15
Alignment explanation
Indices: 24231--24259 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24221 GTAAGATAGT
24231 TTTATTTTTCTAAAC
1 TTTATTTTTCTAAAC
24246 TTTATTTTT-TAAAC
1 TTTATTTTTCTAAAC
24260 CAAAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATTTTTCTAAAC
Found at i:25161 original size:21 final size:21
Alignment explanation
Indices: 25137--25177 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
25127 AATTAAGAAT
* *
25137 AATAAATAATTATTTTTAAAA
1 AATAAAAAAATATTTTTAAAA
25158 AATAAAAAAATATTTTTAAA
1 AATAAAAAAATATTTTTAAA
25178 TATTTTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AATAAAAAAATATTTTTAAAA
Found at i:25956 original size:44 final size:45
Alignment explanation
Indices: 25908--25993 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 45
25898 TTCCTCACTG
* *
25908 AAAATCCCCAATTTACTCCTACCTTTATT-TTATTTTTTTTCCTT
1 AAAATACCCAATCTACTCCTACCTTTATTCTTATTTTTTTTCCTT
* * *
25952 AAAATACCCAATCTACTCTTACCTTTTTTCTTTTTTTTTTTC
1 AAAATACCCAATCTACTCCTACCTTTATTCTTATTTTTTTTC
25994 TATTTTTCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 25 0.69
45 11 0.31
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.53
Consensus pattern (45 bp):
AAAATACCCAATCTACTCCTACCTTTATTCTTATTTTTTTTCCTT
Found at i:31133 original size:3 final size:3
Alignment explanation
Indices: 31125--31168 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
31115 AGATGTTTTG
31125 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
31169 AAGATCATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:37078 original size:27 final size:27
Alignment explanation
Indices: 37048--37109 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
37038 AATGAAGTAC
37048 AATATAAAA-AAATAATTAAAATAATAT
1 AATATAAAATAAATAATTAAAATAA-AT
* *
37075 AATATAAAAATAAATATTTAATATAAAT
1 AATAT-AAAATAAATAATTAAAATAAAT
37103 -ATATAAA
1 AATATAAA
37110 TATTTCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 3 0.10
27 9 0.29
28 6 0.19
29 13 0.42
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
AATATAAAATAAATAATTAAAATAAAT
Found at i:37090 original size:17 final size:17
Alignment explanation
Indices: 37065--37112 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
37055 AAAAATAATT
37065 AAAAT-AATATAATATA
1 AAAATAAATATAATATA
37081 AAAATAAATATTTAATATA
1 AAAATAAATA--TAATATA
37100 AATATATAAATAT
1 AA-A-ATAAATAT
37113 TTCAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 5 0.19
17 4 0.15
19 10 0.37
20 1 0.04
21 7 0.26
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAATAAATATAATATA
Found at i:37096 original size:19 final size:21
Alignment explanation
Indices: 37074--37114 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
37064 TAAAATAATA
37074 TAATATAAA-A-ATAAATATT
1 TAATATAAATATATAAATATT
37093 TAATATAAATATATAAATATT
1 TAATATAAATATATAAATATT
37114 T
1 T
37115 CAAAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.45
20 1 0.05
21 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATATAAATATATAAATATT
Found at i:37108 original size:8 final size:8
Alignment explanation
Indices: 37095--37169 Score: 53
Period size: 8 Copynumber: 8.8 Consensus size: 8
37085 TAAATATTTA
37095 ATATAAAT
1 ATATAAAT
37103 ATATAAAT
1 ATATAAAT
*
37111 ATTTCAAAAT
1 ATAT--AAAT
*
37121 ATATAAAA
1 ATATAAAT
37129 ATATAAAT
1 ATATAAAT
37137 A-ATTAATATT
1 ATA-TAA-A-T
* *
37147 TTAAAAATT
1 ATATAAA-T
37156 ATATAAAT
1 ATATAAAT
37164 ATATAA
1 ATATAA
37170 TATTTTAATT
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
7 1 0.02
8 32 0.60
9 9 0.17
10 10 0.19
11 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAAAT
Found at i:37164 original size:33 final size:34
Alignment explanation
Indices: 37096--37201 Score: 96
Period size: 33 Copynumber: 3.2 Consensus size: 34
37086 AAATATTTAA
*
37096 TATAAATATATAAATATTTCAAAATATATAAAAA
1 TATAAATATATAAATATTTAAAAATATATAAAAA
* *
37130 TATAAATA-ATTAATATTTTAAAAAT-TATATAAA
1 TATAAATATATAAATA-TTTAAAAATATATAAAAA
* * *
37163 TATATAATATTTTAAT-TTT-AATATA-ATAAAATA
1 TATA-AATATATAAATATTTAAAAATATATAAAA-A
37196 TATAAA
1 TATAAA
37202 ATAATATGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
32 11 0.18
33 25 0.41
34 20 0.33
35 5 0.08
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.42
Consensus pattern (34 bp):
TATAAATATATAAATATTTAAAAATATATAAAAA
Found at i:37188 original size:27 final size:28
Alignment explanation
Indices: 37092--37177 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 28
37082 AAATAAATAT
* *
37092 TTAATATAAATATATAAATATTTCAAAATA
1 TTAATATAAATA-ATTAATATTTTAAAA-A
37122 TATAAAAATATAAATAATTAATATTTTAAAAA
1 T-T---AATATAAATAATTAATATTTTAAAAA
37154 TT-ATATAAAT-ATATAATATTTTAA
1 TTAATATAAATAAT-TAATATTTTAA
37178 TTTTAATATA
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
26 2 0.04
27 19 0.39
30 1 0.02
31 2 0.04
32 2 0.04
33 13 0.27
34 10 0.20
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (28 bp):
TTAATATAAATAATTAATATTTTAAAAA
Found at i:37914 original size:15 final size:15
Alignment explanation
Indices: 37896--37926 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
37886 TATAAGATCC
37896 AATAAAATAAAATAT
1 AATAAAATAAAATAT
37911 AATAAAATAAAATAT
1 AATAAAATAAAATAT
37926 A
1 A
37927 TTATGTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAAAATAAAATAT
Found at i:38275 original size:13 final size:13
Alignment explanation
Indices: 38257--38281 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38247 TTTTTTTATT
38257 TATTTATATTTAA
1 TATTTATATTTAA
38270 TATTTATATTTA
1 TATTTATATTTA
38282 TACCTTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTATATTTAA
Found at i:38657 original size:18 final size:19
Alignment explanation
Indices: 38634--38669 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
38624 CTTTAATTTA
*
38634 TATTTAAATAA-AAAAATT
1 TATTTAAAAAATAAAAATT
38652 TATTTAAAAAATAAAAAT
1 TATTTAAAAAATAAAAAT
38670 AAATCATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TATTTAAAAAATAAAAATT
Found at i:38902 original size:2 final size:2
Alignment explanation
Indices: 38895--38936 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
38885 GTTGACATTA
*
38895 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38937 CAGATCATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39277 original size:24 final size:24
Alignment explanation
Indices: 39242--39289 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
39232 AACATAATAT
39242 AATAAATATAATATAAAATATTTA
1 AATAAATATAATATAAAATATTTA
*
39266 AATATAAT-TAATATGAAATATTTA
1 AATA-AATATAATATAAAATATTTA
39290 TTATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
AATAAATATAATATAAAATATTTA
Found at i:39565 original size:3 final size:3
Alignment explanation
Indices: 39557--39597 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
39547 ATCAAGAAAG
39557 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
39598 ACCCAAACTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:40648 original size:4 final size:4
Alignment explanation
Indices: 40639--40665 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
40629 CCTCAGCATG
40639 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
40666 CTTTGATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:43256 original size:2 final size:2
Alignment explanation
Indices: 43249--43277 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43239 ATTTTAAGAG
43249 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 T
43278 GCAATTCTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46257 original size:13 final size:13
Alignment explanation
Indices: 46239--46263 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46229 TGAATGGAAT
46239 TTTTATTTTTTAC
1 TTTTATTTTTTAC
46252 TTTTATTTTTTA
1 TTTTATTTTTTA
46264 AATTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTATTTTTTAC
Found at i:46377 original size:25 final size:24
Alignment explanation
Indices: 46326--46378 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 24
46316 ATTGAATACG
46326 ATAATAAAAATATGAAATAAATAAA
1 ATAATAAAAATA-GAAATAAATAAA
*
46351 ATAATTAAAATA-AAATACAATATAA
1 ATAATAAAAATAGAAATA-AATA-AA
46376 ATA
1 ATA
46379 TATATCTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 5 0.20
24 4 0.16
25 16 0.64
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (24 bp):
ATAATAAAAATAGAAATAAATAAA
Found at i:46413 original size:29 final size:34
Alignment explanation
Indices: 46369--46442 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 34
46359 AATAAAATAC
46369 AATATAAA-TATATATC-T-TAAAATTTATA-T-
1 AATATAAATTATATATCATATAAAATTTATATTA
*
46398 AATATAAATTAT-TATCATATTAAATTTATATTA
1 AATATAAATTATATATCATATAAAATTTATATTA
46431 AATATAAATTAT
1 AATATAAATTAT
46443 CTTAAATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
29 12 0.31
30 4 0.10
31 10 0.26
32 1 0.03
33 12 0.31
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (34 bp):
AATATAAATTATATATCATATAAAATTTATATTA
Found at i:46417 original size:15 final size:16
Alignment explanation
Indices: 46370--46442 Score: 57
Period size: 15 Copynumber: 4.7 Consensus size: 16
46360 ATAAAATACA
46370 ATATAAA-TATATATC
1 ATATAAATTATATATC
* *
46385 TTA-AAATT-TATATA
1 ATATAAATTATATATC
46399 ATATAAATTAT-TATC
1 ATATAAATTATATATC
*
46414 ATATTAAATT-TATATTAA
1 ATA-TAAATTATATA-T-C
46432 ATATAAATTAT
1 ATATAAATTAT
46443 CTTAAATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
14 10 0.22
15 15 0.33
16 9 0.20
17 7 0.16
18 4 0.09
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATAAATTATATATC
Found at i:46426 original size:17 final size:16
Alignment explanation
Indices: 46388--46488 Score: 52
Period size: 15 Copynumber: 6.2 Consensus size: 16
46378 ATATATCTTA
46388 AAATTTA-TATAATAT
1 AAATTTATTATAATAT
*
46403 AAA-TTATTATCATATT
1 AAATTTATTATAATA-T
46419 AAATTTA-TATTAAATAT
1 AAATTTATTA-T-AATAT
*
46436 AAATTATCTTA-AATAT
1 AAATT-TATTATAATAT
* *
46452 -AATTATAATATAA-AA
1 AAATT-TATTATAATAT
46467 AAATTTATGAATATAATAT
1 AAATTTAT---TATAATAT
46486 AAA
1 AAA
46489 ATAACAAGCT
Statistics
Matches: 65, Mismatches: 8, Indels: 22
0.68 0.08 0.23
Matches are distributed among these distances:
14 3 0.05
15 20 0.31
16 17 0.26
17 10 0.15
18 9 0.14
19 6 0.09
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (16 bp):
AAATTTATTATAATAT
Found at i:46442 original size:16 final size:16
Alignment explanation
Indices: 46398--46458 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
46388 AAATTTATAT
*
46398 AATATAAATTATTATCA
1 AATATAAATTA-TATTA
*
46415 TAT-TAAATTTATATTA
1 AATATAAA-TTATATTA
*
46431 AATATAAATTATCTTA
1 AATATAAATTATATTA
46447 AATAT-AATTATA
1 AATATAAATTATA
46459 ATATAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
15 6 0.16
16 22 0.59
17 9 0.24
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
AATATAAATTATATTA
Found at i:47896 original size:18 final size:18
Alignment explanation
Indices: 47875--47916 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
47865 ATATGTATCG
* *
47875 TATATTAAATTATGTAAA
1 TATATAAAATTATATAAA
*
47893 TATATAAAATTATATATA
1 TATATAAAATTATATAAA
47911 TATATA
1 TATATA
47917 TATGAAGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TATATAAAATTATATAAA
Found at i:48482 original size:35 final size:37
Alignment explanation
Indices: 48406--48483 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 37
48396 TTCTGCTCCG
* * *
48406 TTATAATAACTTTAAATATATATTTTTACTATTAATG
1 TTATAATAACTTTAAATATATATTATTACCATTAATA
*
48443 TTATAGTAAC-TTAAATATATA-TATTACCATTAATA
1 TTATAATAACTTTAAATATATATTATTACCATTAATA
48478 TTATAA
1 TTATAA
48484 ATAGCTGTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
35 16 0.44
36 11 0.31
37 9 0.25
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (37 bp):
TTATAATAACTTTAAATATATATTATTACCATTAATA
Found at i:50988 original size:2 final size:2
Alignment explanation
Indices: 50983--51012 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
50973 TATACGGTTA
*
50983 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51013 CTTCAGCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:53745 original size:23 final size:23
Alignment explanation
Indices: 53715--53760 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
53705 TCTCGAGGCA
53715 AAGGTCGATACTAATGCTGTAAG
1 AAGGTCGATACTAATGCTGTAAG
* *
53738 AAGGTCGATATTAATTCTGTAAG
1 AAGGTCGATACTAATGCTGTAAG
53761 CGAGTTAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (23 bp):
AAGGTCGATACTAATGCTGTAAG
Found at i:53807 original size:9 final size:9
Alignment explanation
Indices: 53785--53843 Score: 55
Period size: 10 Copynumber: 6.1 Consensus size: 9
53775 TGATAATATT
53785 AAATATTAAA
1 AAATATT-AA
53795 AAATATTAA
1 AAATATTAA
53804 AAATAATATAA
1 AAAT-AT-TAA
* *
53815 ATATAATAA
1 AAATATTAA
53824 AAATATATAA
1 AAATAT-TAA
*
53834 ATATATTAA
1 AAATATTAA
53843 A
1 A
53844 TTTTATATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
9 17 0.41
10 18 0.44
11 6 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAATATTAA
Found at i:53825 original size:19 final size:19
Alignment explanation
Indices: 53801--53890 Score: 75
Period size: 20 Copynumber: 4.9 Consensus size: 19
53791 TAAAAAATAT
53801 TAAAAATAATATAAATATAA
1 TAAAAAT-ATATAAATATAA
53821 TAAAAATATATAAATAT-A
1 TAAAAATATATAAATATAA
* *
53839 T-TAAAT-T-T-TATATAA
1 TAAAAATATATAAATATAA
* * *
53854 TATAAAT-TATTAATATAT
1 TAAAAATATATAAATATAA
53872 TAAAAATTATATAAATATA
1 TAAAAA-TATATAAATATA
53891 TTACATTTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
14 4 0.07
15 3 0.05
16 7 0.12
17 5 0.09
18 12 0.21
19 11 0.19
20 16 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAAATATATAAATATAA
Found at i:53852 original size:20 final size:20
Alignment explanation
Indices: 53780--53893 Score: 90
Period size: 19 Copynumber: 6.3 Consensus size: 20
53770 AAATATGATA
53780 ATATTAAATATTA-A-AAA-
1 ATATTAAATATTATATAAAT
* *
53797 ATATTAAAAATAATATAAAT
1 ATATTAAATATTATATAAAT
* *
53817 ATAATAAA-AATATATAAAT
1 ATATTAAATATTATATAAAT
*
53836 ATATTAAAT-TT-TATATA-
1 ATATTAAATATTATATAAAT
53853 ATA-T-AA-ATTAT-T-AAT
1 ATATTAAATATTATATAAAT
*
53868 ATATTAAAAATTATATAAAT
1 ATATTAAATATTATATAAAT
53888 ATATTA
1 ATATTA
53894 CATTTTAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
14 1 0.01
15 8 0.11
16 3 0.04
17 16 0.21
18 11 0.14
19 21 0.28
20 16 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATTAAATATTATATAAAT
Found at i:53869 original size:18 final size:18
Alignment explanation
Indices: 53814--53881 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
53804 AAATAATATA
*
53814 AATATAATAAAAATATATA
1 AATATAATAAAAAT-TATT
*
53833 AATAT-AT-TAAATT-TT
1 AATATAATAAAAATTATT
*
53848 -ATATAATATAAATTATT
1 AATATAATAAAAATTATT
*
53865 AATATATTAAAAATTAT
1 AATATAATAAAAATTAT
53882 ATAAATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
14 4 0.10
15 3 0.07
16 7 0.17
17 6 0.15
18 16 0.39
19 5 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATAATAAAAATTATT
Found at i:53872 original size:32 final size:33
Alignment explanation
Indices: 53815--53890 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 33
53805 AATAATATAA
* **
53815 ATATAATAAAAATATATAAATATATTAAATTTT
1 ATATAATATAAATATATAAATATATTAAAAATT
*
53848 ATATAATATAAAT-TATTAATATATTAAAAATT
1 ATATAATATAAATATATAAATATATTAAAAATT
53880 ATATAAATATA
1 ATAT-AATATA
53891 TTACATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 20 0.53
33 18 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
ATATAATATAAATATATAAATATATTAAAAATT
Found at i:53901 original size:27 final size:26
Alignment explanation
Indices: 53821--53905 Score: 88
Period size: 27 Copynumber: 3.3 Consensus size: 26
53811 ATAAATATAA
53821 TAAAAA-TATATAAATATATTAAATTT
1 TAAAAATTATATAAATATATT-AATTT
* *
53847 T--ATATAATATAAAT-TATTAATATAT
1 TAAAAATTATATAAATATATTAAT-T-T
53872 TAAAAATTATATAAATATATTACATTT
1 TAAAAATTATATAAATATATTA-ATTT
53899 TAAAAAT
1 TAAAAAT
53906 AATAAAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
23 3 0.06
24 7 0.15
25 10 0.21
26 1 0.02
27 19 0.40
28 6 0.12
29 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (26 bp):
TAAAAATTATATAAATATATTAATTT
Found at i:53911 original size:52 final size:51
Alignment explanation
Indices: 53814--53911 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 51
53804 AAATAATATA
*
53814 AATATAATAAAAATATATAAATATATTAAATTTTATATAATATAAATTATT
1 AATATAATAAAAATATATAAATATATTAAATTTTATAAAATATAAATTATT
* *
53865 AATATATTAAAAATTATATAAATATATTACATTTTA-AAAATAATAAA
1 AATATAATAAAAA-TATATAAATATATTAAATTTTATAAAAT-ATAAA
53912 AAATAATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
51 16 0.38
52 26 0.62
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (51 bp):
AATATAATAAAAATATATAAATATATTAAATTTTATAAAATATAAATTATT
Found at i:54828 original size:34 final size:34
Alignment explanation
Indices: 54736--54917 Score: 260
Period size: 34 Copynumber: 5.4 Consensus size: 34
54726 AAGAAAAAAC
* * *
54736 TGTTGATTAAAT-GGTGATTTGGTAGTTTATCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
54769 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
54802 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
54836 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
54870 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
54904 TGTTGATTAAATGG
1 TGTTGATTAAATGG
54918 TGGTTTTTAC
Statistics
Matches: 133, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 40 0.30
34 93 0.70
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:55276 original size:19 final size:19
Alignment explanation
Indices: 55220--55282 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
55210 TGGTTGTCGA
**
55220 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
55239 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
55258 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
55277 GTTACT
1 GGTACT
55283 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:59442 original size:34 final size:34
Alignment explanation
Indices: 59348--59531 Score: 273
Period size: 34 Copynumber: 5.5 Consensus size: 34
59338 AAGTGGGAGA
* *
59348 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
59381 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
59414 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
59448 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
59482 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
59516 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
59532 TGGTTTTTAC
Statistics
Matches: 136, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 43 0.32
34 93 0.68
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:60615 original size:45 final size:45
Alignment explanation
Indices: 60547--60633 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
60537 CTATTACAAT
60547 GATGTTCTTATCTCACCCGCCAAATGGAACTACTAAATCTTATCC
1 GATGTTCTTATCTCACCCGCCAAATGGAACTACTAAATCTTATCC
* *
60592 GATGTTCTTATCTCGCCCTCCAAATGGAACTACTAAATCTTA
1 GATGTTCTTATCTCACCCGCCAAATGGAACTACTAAATCTTA
60634 GCCTGGAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (45 bp):
GATGTTCTTATCTCACCCGCCAAATGGAACTACTAAATCTTATCC
Found at i:61259 original size:98 final size:98
Alignment explanation
Indices: 61073--61263 Score: 285
Period size: 98 Copynumber: 1.9 Consensus size: 98
61063 ATTTACTCAC
* *
61073 TTCTTGGTGCATTTTTTTGCCTTGTGTAACAAATCTTGCCTAAATCAGTATGCTCTTCCTATATC
1 TTCTTGGTGCACTTTTTTGCCTTGTGTAACAAATCTTGCCTAAATCAATATGCTCTTCCTATATC
*
61138 TTAGAAAACTTGTAAGCTACTAGATTTGCCCAT
66 TTAGAAAACGTGTAAGCTACTAGATTTGCCCAT
* * *
61171 TTCTTGGTGCACTTTTTTGCCTTGTGTAGACAAGTCTTGGCTAAATCAATCTGCTCTTCCTATAT
1 TTCTTGGTGCACTTTTTTGCCTTGTGTA-ACAAATCTTGCCTAAATCAATATGCTCTTCCTATAT
* * *
61236 CTTAG-CAACGTGTAAGTTGCTAGATTTG
65 CTTAGAAAACGTGTAAGCTACTAGATTTG
61264 GTCCTATGTA
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
98 46 0.55
99 37 0.45
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.41
Consensus pattern (98 bp):
TTCTTGGTGCACTTTTTTGCCTTGTGTAACAAATCTTGCCTAAATCAATATGCTCTTCCTATATC
TTAGAAAACGTGTAAGCTACTAGATTTGCCCAT
Done.