Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold402
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: 85460
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:474 original size:20 final size:22
Alignment explanation
Indices: 449--493 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
439 ACTATTTTAA
449 ATATG-AT-TATGATAT-AAAAT
1 ATATGAATATATGAT-TGAAAAT
469 ATATGAATATATGATTGAAAAT
1 ATATGAATATATGATTGAAAAT
491 ATA
1 ATA
494 GCAAATGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.23
21 3 0.14
22 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (22 bp):
ATATGAATATATGATTGAAAAT
Found at i:2788 original size:16 final size:16
Alignment explanation
Indices: 2764--2816 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2754 AATAATATAT
*
2764 AATTTTTATATATTTA
1 AATTATTATATATTTA
*
2780 AATTATTATATTTTTA
1 AATTATTATATATTTA
* * *
2796 TATTAATATAAATATTA
1 AATTATTATATAT-TTA
2813 AATT
1 AATT
2817 TAAATATTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 23 0.79
17 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTATTATATATTTA
Found at i:2811 original size:25 final size:23
Alignment explanation
Indices: 2757--2817 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 23
2747 TATCAAAAAT
*
2757 AATA-TATAATTTTTATATATTTA
1 AATATTAT-ATTTTTATATATATA
2780 AATTATTATATTTTTATATTAATATA
1 AA-TATTATATTTTTATA-T-ATATA
*
2806 AATATTAAATTT
1 AATATTATATTT
2818 AAATATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 2 0.06
24 11 0.34
25 13 0.41
26 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AATATTATATTTTTATATATATA
Found at i:2822 original size:13 final size:13
Alignment explanation
Indices: 2775--2833 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
2765 ATTTTTATAT
*
2775 ATTTAAATTATTAT
1 ATTTAAA-TATTAA
**
2789 ATTTTTATATT-A
1 ATTTAAATATTAA
*
2801 ATATAAATATTAA
1 ATTTAAATATTAA
*
2814 ATTTAAATATTTA
1 ATTTAAATATTAA
2827 ATTTAAA
1 ATTTAAA
2834 AAATAAAAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
12 8 0.22
13 23 0.64
14 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTTAAATATTAA
Found at i:6133 original size:26 final size:25
Alignment explanation
Indices: 6088--6141 Score: 58
Period size: 26 Copynumber: 2.1 Consensus size: 25
6078 ACTCATAAAT
*
6088 TAAATAAATTAAATATATATATAT-A
1 TAAATAAATTAAATAGATAT-TATGA
6113 TAAATAAAATTAACA-AGATATTATGA
1 TAAAT-AAATTAA-ATAGATATTATGA
6139 TAA
1 TAA
6142 TATTTTCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 8 0.32
26 16 0.64
27 1 0.04
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
TAAATAAATTAAATAGATATTATGA
Found at i:6823 original size:16 final size:15
Alignment explanation
Indices: 6791--6819 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6781 TATTTATGAA
6791 TAAAAAAATTATTAT
1 TAAAAAAATTATTAT
6806 TAAAAAAATT-TTAT
1 TAAAAAAATTATTAT
6820 ATTAGAAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAAAAAATTATTAT
Found at i:6871 original size:18 final size:18
Alignment explanation
Indices: 6848--6897 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
6838 TAGTTTGAAT
6848 TAAATTAATTAAAATTAA
1 TAAATTAATTAAAATTAA
*
6866 TAAATT-TTTAAATATTAA
1 TAAATTAATTAAA-ATTAA
* *
6884 -AATTTAAATAAAAT
1 TAAATTAATTAAAAT
6898 ATATATATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATTAATTAAAATTAA
Found at i:7226 original size:27 final size:27
Alignment explanation
Indices: 7196--7284 Score: 69
Period size: 27 Copynumber: 3.4 Consensus size: 27
7186 TGATAAATAT
7196 AATTTAATTATAA-TATTTTATTATTTA
1 AATTTAATTA-AACTATTTTATTATTTA
* * * **
7223 AATTGATTTAAATTAAATTATTATTT-
1 AATTTAATTAAACTATTTTATTATTTA
*
7249 -ATTTAATTAAACAATATTT-TTATTTA
1 AATTTAATTAAACTAT-TTTATTATTTA
*
7275 ATTTTAATTA
1 AATTTAATTA
7285 TAAAATATAT
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
25 16 0.34
26 4 0.09
27 27 0.57
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (27 bp):
AATTTAATTAAACTATTTTATTATTTA
Found at i:7254 original size:21 final size:20
Alignment explanation
Indices: 7228--7285 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
7218 ATTTAAATTG
7228 ATTTAAATTAAATTATTATTT
1 ATTTAAATTAAATTATT-TTT
*
7249 ATTT-AATTAAACAATATTTTT
1 ATTTAAATT-AA-ATTATTTTT
* *
7270 ATTTAATTTTAATTAT
1 ATTTAAATTAAATTAT
7286 AAAATATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 8 0.27
21 14 0.47
22 8 0.27
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTAAATTAAATTATTTTT
Found at i:7291 original size:27 final size:25
Alignment explanation
Indices: 7243--7292 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 25
7233 AATTAAATTA
7243 TTATTTATTTAATTAAACAATATTT
1 TTATTTATTTAATTAAACAATATTT
7268 TTATTTAATTTTAATTATAA-AATAT
1 TTATTT-A-TTTAATTA-AACAATAT
7293 ATAAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.27
26 1 0.05
27 13 0.59
28 2 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
TTATTTATTTAATTAAACAATATTT
Found at i:8241 original size:3 final size:3
Alignment explanation
Indices: 8228--8270 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
8218 TATATTATAG
8228 ATT ACTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
8271 TAGGATGTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:9221 original size:20 final size:20
Alignment explanation
Indices: 9195--9240 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
9185 ATACATTTGT
9195 ATATTTTTATCATATT-TATA
1 ATATTTTT-TCATATTATATA
* *
9215 TTATTTTTTTATATTATATA
1 ATATTTTTTCATATTATATA
9235 ATATTT
1 ATATTT
9241 CAATCAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
ATATTTTTTCATATTATATA
Found at i:9624 original size:7 final size:8
Alignment explanation
Indices: 9609--9654 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
9599 TTAAAAAATA
9609 AATATATT
1 AATATATT
9617 AATA-ATT
1 AATATATT
9624 AATATA-T
1 AATATATT
*
9631 -ATATTTT
1 AATATATT
9638 AATATATT
1 AATATATT
*
9646 TATATATT
1 AATATATT
9654 A
1 A
9655 TATCAATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
6 4 0.13
7 9 0.29
8 18 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
AATATATT
Found at i:9649 original size:18 final size:18
Alignment explanation
Indices: 9628--9683 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
9618 ATAATTAATA
9628 TATATATTTTAATATATT
1 TATATATTTTAATATATT
*
9646 TATATATTAT-ATCA-ATT
1 TATATATTTTAAT-ATATT
9663 ATATATATTTTAATTATATT
1 -TATATATTTTAA-TATATT
9683 T
1 T
9684 TTTTATGTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
17 5 0.16
18 19 0.61
19 3 0.10
20 4 0.13
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATATTTTAATATATT
Found at i:10920 original size:11 final size:11
Alignment explanation
Indices: 10887--10920 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
10877 ATAATAATAT
10887 TTATTA-TATA
1 TTATTATTATA
10897 TTATTATTATA
1 TTATTATTATA
*
10908 TTATTTTTATA
1 TTATTATTATA
10919 TT
1 TT
10921 GATATGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATTATTATA
Found at i:11381 original size:20 final size:22
Alignment explanation
Indices: 11339--11390 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 22
11329 TTTCATATTT
*
11339 ATTATTTATTAACATATTTTTA
1 ATTATTTATTAACATAATTTTA
11361 ATTATTTATT-A-ATAATTTTA
1 ATTATTTATTAACATAATTTTA
*
11381 ATTATATATT
1 ATTATTTATT
11391 TTTAATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 17 0.61
21 1 0.04
22 10 0.36
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTATTTATTAACATAATTTTA
Found at i:12930 original size:32 final size:32
Alignment explanation
Indices: 12877--12940 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
12867 TTATTATATG
*
12877 TTTATATAAATTTTAAAATATTAATAATTTAT
1 TTTATATAAATTATAAAATATTAATAATTTAT
* * * *
12909 TTTATATAAATTATGACATATTATTTATTTAT
1 TTTATATAAATTATAAAATATTAATAATTTAT
12941 ATAATATTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (32 bp):
TTTATATAAATTATAAAATATTAATAATTTAT
Found at i:12959 original size:26 final size:28
Alignment explanation
Indices: 12898--12959 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 28
12888 TTTAAAATAT
*
12898 TAATAATTTATTTTATATAAATTATGACA
1 TAAT-ATTTATTTTATATAAATTATCACA
*
12927 TATTATTTA-TTTATAT-AA-TATTCACA
1 TAATATTTATTTTATATAAATTA-TCACA
12953 TAATATT
1 TAATATT
12960 ATATAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 2 0.07
26 12 0.41
27 7 0.24
28 5 0.17
29 3 0.10
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (28 bp):
TAATATTTATTTTATATAAATTATCACA
Found at i:14784 original size:21 final size:21
Alignment explanation
Indices: 14758--14797 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
14748 AAATTTTTAT
14758 TTTAATTAA-ATTATATTATAA
1 TTTAATTAATATTA-ATTATAA
14779 TTTAATTAATATTAATTAT
1 TTTAATTAATATTAATTAT
14798 CATATTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAATTAATATTAATTATAA
Found at i:14832 original size:26 final size:26
Alignment explanation
Indices: 14750--14832 Score: 60
Period size: 30 Copynumber: 3.0 Consensus size: 26
14740 ATGTTTAAAA
* * *
14750 ATTTTTATTTTAATTAAATTATATTAT
1 ATTTTAATTTTTATTACATT-TATTAT
* *
14777 AATTTAATTAATATTAATTATCATAT-TTAT
1 ATTTTAATT--T-TT-ATTA-CATTTATTAT
14807 ATTTTAATTTTTATTACATTTATTAT
1 ATTTTAATTTTTATTACATTTATTAT
14833 TAATTTTATC
Statistics
Matches: 43, Mismatches: 7, Indels: 13
0.68 0.11 0.21
Matches are distributed among these distances:
25 4 0.09
26 8 0.19
27 9 0.21
28 1 0.02
29 1 0.02
30 13 0.30
31 5 0.12
32 2 0.05
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTTAATTTTTATTACATTTATTAT
Found at i:15336 original size:21 final size:21
Alignment explanation
Indices: 15308--15360 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
15298 TGTAATTATA
*
15308 TTATATTATATTT-ATATATT
1 TTATATTATATTTAAAATATT
15328 TTAATATTATATTTAAAATATT
1 TT-ATATTATATTTAAAATATT
15350 TTATATTATAT
1 TTATATTATAT
15361 AAATTTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 2 0.07
21 20 0.67
22 8 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATATTATATTTAAAATATT
Found at i:15438 original size:16 final size:18
Alignment explanation
Indices: 15302--15429 Score: 65
Period size: 18 Copynumber: 7.0 Consensus size: 18
15292 TAATTATGTA
15302 ATTATATTATA--TT-AT
1 ATTATATTATATTTTAAT
15317 ATT-TA-TATATTTTAAT
1 ATTATATTATATTTTAAT
15333 ATTATATTTAAAATATTTT-AT
1 ATTATA-TT---ATATTTTAAT
*
15354 ATTATA-TAAATTTTAAT
1 ATTATATTATATTTTAAT
* * *
15371 AAAATAATAATTTATATTATAAA
1 ---ATTAT-A-TTATATTTTAAT
*
15394 ATT-TAAATATATTTTAAT
1 ATTAT-ATTATATTTTAAT
15412 ATTATATTATATTTTAAT
1 ATTATATTATATTTTAAT
15430 TATTTTATAC
Statistics
Matches: 86, Mismatches: 10, Indels: 31
0.68 0.08 0.24
Matches are distributed among these distances:
13 4 0.05
14 2 0.02
15 5 0.06
16 11 0.13
17 4 0.05
18 24 0.28
19 6 0.07
20 6 0.07
21 9 0.10
22 7 0.08
23 8 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTATATTATATTTTAAT
Found at i:15636 original size:19 final size:19
Alignment explanation
Indices: 15604--15642 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
15594 ATAATATATA
15604 TTTTATTATATTTTAATTTT
1 TTTTATTATATTTT-ATTTT
*
15624 TTTTA-TATTTTTTATTTT
1 TTTTATTATATTTTATTTT
15642 T
1 T
15643 AATTATCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 7 0.39
20 5 0.28
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTATTATATTTTATTTT
Found at i:15648 original size:19 final size:18
Alignment explanation
Indices: 15604--15653 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
15594 ATAATATATA
15604 TTTTATTATA-TTTTAAT
1 TTTTATTATATTTTTAAT
* *
15621 TTTTTTTATATTTTTTAT
1 TTTTATTATATTTTTAAT
15639 TTTTAATTATCATTT
1 TTTT-ATTAT-ATTT
15654 ATTTTTACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 9 0.33
18 10 0.37
19 4 0.15
20 4 0.15
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATTATATTTTTAAT
Found at i:16197 original size:24 final size:25
Alignment explanation
Indices: 16147--16201 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
16137 GTTAGCTGAA
*
16147 ATAAAAAATATTATGATAATTAAATT
1 ATAAAAAATATTAT-ATAAATAAATT
16173 ATAAAAAATA-TAT-TAAATAATATT
1 ATAAAAAATATTATATAAATAA-ATT
16197 ATAAA
1 ATAAA
16202 TTATGAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 6 0.22
24 8 0.30
25 3 0.11
26 10 0.37
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (25 bp):
ATAAAAAATATTATATAAATAAATT
Found at i:16513 original size:15 final size:15
Alignment explanation
Indices: 16493--16544 Score: 63
Period size: 16 Copynumber: 3.5 Consensus size: 15
16483 CAGTATTTAG
16493 ATAATATATTTTAAA
1 ATAATATATTTTAAA
16508 ATAATATTATTTTAATA
1 ATAATA-TATTTTAA-A
*
16525 ATTA-AT-TTTTAAA
1 ATAATATATTTTAAA
16538 ATAATAT
1 ATAATAT
16545 TAATTTGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 4 0.12
14 8 0.25
15 7 0.22
16 9 0.28
17 4 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAATATATTTTAAA
Found at i:16546 original size:18 final size:18
Alignment explanation
Indices: 16501--16550 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
16491 AGATAATATA
16501 TTTTAAAATAATATT-A-
1 TTTTAAAATAATATTAAT
16517 TTTT--AAT-A-ATTAAT
1 TTTTAAAATAATATTAAT
16531 TTTTAAAATAATATTAAT
1 TTTTAAAATAATATTAAT
16549 TT
1 TT
16551 GGTTAATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 3 0.11
13 2 0.07
14 7 0.25
16 7 0.25
17 1 0.04
18 8 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTAAAATAATATTAAT
Found at i:16899 original size:18 final size:18
Alignment explanation
Indices: 16872--16925 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
16862 TATAATTATA
*
16872 TTTAAAATATTATAAAAT
1 TTTAATATATTATAAAAT
16890 TTTAATATATTA-ATAAAT
1 TTTAATATATTATA-AAAT
*
16908 TAT-AT-TA-TATAAAAT
1 TTTAATATATTATAAAAT
16923 TTT
1 TTT
16926 GTATCTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
15 8 0.26
16 3 0.10
17 3 0.10
18 17 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAATATATTATAAAAT
Found at i:18164 original size:3 final size:3
Alignment explanation
Indices: 18158--18182 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18148 AAAAAAAAAA
18158 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
18183 GAAGGTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19871 original size:6 final size:6
Alignment explanation
Indices: 19860--19889 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
19850 TAATCTTAAC
19860 AATTAT AATTAT AATTAT AATTAT AATTAT
1 AATTAT AATTAT AATTAT AATTAT AATTAT
19890 TATATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTAT
Found at i:21272 original size:2 final size:2
Alignment explanation
Indices: 21265--21292 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21255 CATGAGTTAC
21265 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
21293 TACTTTAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24730 original size:38 final size:38
Alignment explanation
Indices: 24668--24746 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
24658 GAAACATAGA
* * *
24668 TTTTATTGGTTTATTTTCTAGAAGGAACGCTCATATGT
1 TTTTATTGGCTCATTTACTAGAAGGAACGCTCATATGT
* *
24706 TTTTATTGGCTCATTTACTGGAAGGAATGCTCATATGT
1 TTTTATTGGCTCATTTACTAGAAGGAACGCTCATATGT
24744 TTT
1 TTT
24747 CCCTCTGAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (38 bp):
TTTTATTGGCTCATTTACTAGAAGGAACGCTCATATGT
Found at i:32212 original size:22 final size:21
Alignment explanation
Indices: 32186--32247 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 21
32176 TATTTTTCAA
32186 ATTTAGTATAATTTAAATTATT
1 ATTTA-TATAATTTAAATTATT
*
32208 ATTTA-ATAATTTAAAAATATT
1 ATTTATATAATTT-AAATTATT
*
32229 -TTTATTTTAATTT-AATTAT
1 ATTTA-TATAATTTAAATTAT
32248 AAAATATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
20 16 0.47
21 7 0.21
22 11 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTATATAATTTAAATTATT
Found at i:34099 original size:19 final size:18
Alignment explanation
Indices: 34038--34090 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 18
34028 TTTTAAAATT
34038 AATATAATATAAATTAT-TA
1 AATATAA-A-AAATTATATA
34057 ATATATAAAAAATTATATA
1 A-ATATAAAAAATTATATA
34076 AATATAAAATAATTA
1 AATATAAAA-AATTA
34091 GTATGATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 15 0.48
19 10 0.32
20 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATATAAAAAATTATATA
Found at i:36522 original size:22 final size:22
Alignment explanation
Indices: 36503--36545 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
36493 TAATATTATA
36503 TTTAAAATAAATTAAAATTAAT
1 TTTAAAATAAATTAAAATTAAT
* * *
36525 TTTTAAATATATTTAAATTAA
1 TTTAAAATAAATTAAAATTAA
36546 GTCGTTATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTAAAATAAATTAAAATTAAT
Found at i:37063 original size:17 final size:18
Alignment explanation
Indices: 37043--37077 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
37033 AAATTATATT
*
37043 ATATTTAAAAA-TAATAA
1 ATATTAAAAAATTAATAA
37060 ATATTAAAAAATTAATAA
1 ATATTAAAAAATTAATAA
37078 TAATATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATTAAAAAATTAATAA
Found at i:37079 original size:17 final size:17
Alignment explanation
Indices: 37032--37079 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
37022 AATATTATCT
* *
37032 AAAATTATATTATATTTA
1 AAAATTA-ATAATATTAA
37050 AAAA-TAATAAATATTAA
1 AAAATTAAT-AATATTAA
37067 AAAATTAATAATA
1 AAAATTAATAATA
37080 ATATTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 2 0.08
17 16 0.62
18 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATTAATAATATTAA
Found at i:38701 original size:19 final size:20
Alignment explanation
Indices: 38657--38714 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
38647 TATTTTATAT
* *
38657 TTATATAAATTTTATATATTAA
1 TTATATATA-TTTATATA-AAA
38679 TTAT-TCATA-TTATATAAAA
1 TTATAT-ATATTTATATAAAA
38698 TTATATATATTTATATA
1 TTATATATATTTATATA
38715 TCTATGTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
19 9 0.29
20 15 0.48
21 1 0.03
22 6 0.19
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATATATATTTATATAAAA
Found at i:38764 original size:28 final size:29
Alignment explanation
Indices: 38726--38808 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 29
38716 CTATGTCATG
*
38726 TTTATATTATTTTTCATATTATATTA-TA
1 TTTATTTTATTTTTCATATTATATTAGTA
** *
38754 TTT-TTTATATTTTAAATTTTATATTAGTA
1 TTTATTT-TATTTTTCATATTATATTAGTA
**
38783 TTTATTTTATATAATCATATTATATT
1 TTTATTTTAT-TTTTCATATTATATT
38809 TAAAATTATC
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
27 2 0.05
28 19 0.45
29 8 0.19
30 13 0.31
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (29 bp):
TTTATTTTATTTTTCATATTATATTAGTA
Found at i:39224 original size:18 final size:19
Alignment explanation
Indices: 39190--39226 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
39180 AAATTTTTAA
*
39190 TAAATTAATTTAAATAATT
1 TAAATTAATTAAAATAATT
39209 TAAATT-ATTAAAATAATT
1 TAAATTAATTAAAATAATT
39227 GATAATTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATTAATTAAAATAATT
Found at i:40314 original size:25 final size:22
Alignment explanation
Indices: 40285--40333 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
40275 TTTATGTAAA
40285 TAAAAGGAATATTATATGTTATTTG
1 TAAAA-GAATATT-TAT-TTATTTG
*
40310 TAAAATAATATTTATTTATTTG
1 TAAAAGAATATTTATTTATTTG
40332 TA
1 TA
40334 TATTTCAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 9 0.39
23 3 0.13
24 6 0.26
25 5 0.22
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (22 bp):
TAAAAGAATATTTATTTATTTG
Found at i:48962 original size:2 final size:2
Alignment explanation
Indices: 48957--48990 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
48947 TGCACTCAAA
48957 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
48991 TAAAAGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49157 original size:18 final size:19
Alignment explanation
Indices: 49130--49168 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
49120 TAGATTATTG
49130 TTTTTCTTATTATTTA-AT
1 TTTTTCTTATTATTTACAT
* *
49148 TTTTTTTTATTTTTTACAT
1 TTTTTCTTATTATTTACAT
49167 TT
1 TT
49169 CTTATTGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTCTTATTATTTACAT
Found at i:50005 original size:21 final size:21
Alignment explanation
Indices: 49965--50005 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
49955 TATATATAAT
*
49965 ATAATATACAATTAGTTTTAC
1 ATAATATACAATTAGATTTAC
49986 ATAATAATACAATTA-ATTTA
1 ATAAT-ATACAATTAGATTTA
50006 TTTTTTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (21 bp):
ATAATATACAATTAGATTTAC
Found at i:50315 original size:5 final size:5
Alignment explanation
Indices: 50305--50330 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
50295 TAGAATTGAA
50305 AATTT AATTT AATTT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT A
50331 TATCTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:50367 original size:15 final size:14
Alignment explanation
Indices: 50340--50387 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
50330 ATATCTTTAT
50340 TTTTAAAATTTAATA
1 TTTTAAAA-TTAATA
*
50355 TTTTATAAATTAAAA
1 TTTTA-AAATTAATA
*
50370 TTTTAAATTTTAATA
1 TTTTAAA-ATTAATA
50385 TTT
1 TTT
50388 ATAATTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 2 0.07
15 23 0.82
16 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTTAAAATTAATA
Found at i:50400 original size:18 final size:17
Alignment explanation
Indices: 50377--50410 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
50367 AAATTTTAAA
50377 TTTTAATATTTATAATTT
1 TTTTAATATTTA-AATTT
50395 TTTTAATATTTAAATT
1 TTTTAATATTTAAATT
50411 ACGATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAATATTTAAATTT
Found at i:52505 original size:25 final size:24
Alignment explanation
Indices: 52473--52519 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
52463 TATCATATTA
**
52473 ATATATATTTTTTATTTTTAAATT
1 ATATATATAATTTATTTTTAAATT
52497 ATATAATATAATTTATTTTTAAA
1 ATAT-ATATAATTTATTTTTAAA
52520 AAATAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATATATATAATTTATTTTTAAATT
Found at i:52527 original size:18 final size:19
Alignment explanation
Indices: 52504--52576 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 19
52494 ATTATATAAT
52504 ATAATTTATTT-TTAAAAA
1 ATAATTTATTTATTAAAAA
*
52522 ATAA-TTATTTATTATAAA
1 ATAATTTATTTATTAAAAA
*
52540 ATAATTAATAAATTATTAAAATA
1 ATAATT--T-ATTTATTAAAA-A
52563 A-ATATTTATTTATT
1 ATA-ATTTATTTATT
52577 GTATATAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
17 6 0.14
18 14 0.32
19 1 0.02
20 6 0.14
21 2 0.05
22 10 0.23
23 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATAATTTATTTATTAAAAA
Found at i:52833 original size:21 final size:21
Alignment explanation
Indices: 52808--52872 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 21
52798 TTTTAATAAA
52808 ATAATTTAATATAATTTAT-T
1 ATAATTTAATATAATTTATAT
**
52828 GATAATAAAATA-AATTTATAT
1 -ATAATTTAATATAATTTATAT
*
52849 ATAA-TTAATAT-A-TTAAAT
1 ATAATTTAATATAATTTATAT
52867 ATAATT
1 ATAATT
52873 AAAAATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 9 0.25
19 6 0.17
20 11 0.31
21 10 0.28
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATAATTTAATATAATTTATAT
Found at i:52867 original size:9 final size:10
Alignment explanation
Indices: 52804--52875 Score: 53
Period size: 10 Copynumber: 7.4 Consensus size: 10
52794 AAATTTTTAA
52804 TAAA-ATAAT
1 TAAATATAAT
*
52813 TTAATATAAT
1 TAAATATAAT
* *
52823 TTATTGATAAT
1 TAAAT-ATAAT
*
52834 AAAATA-AATT
1 TAAATATAA-T
*
52844 TATATATAAT
1 TAAATATAAT
52854 T-AATAT-AT
1 TAAATATAAT
52862 TAAATATAAT
1 TAAATATAAT
52872 TAAA
1 TAAA
52876 AATTATTAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
8 3 0.06
9 14 0.29
10 23 0.47
11 9 0.18
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (10 bp):
TAAATATAAT
Found at i:52872 original size:29 final size:29
Alignment explanation
Indices: 52801--52872 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 29
52791 TATAAATTTT
*
52801 TAATAAAATAATTTAATATAATTTATTGA
1 TAATAAAATAATTTAATATAATTTAATGA
52830 TAATAAAATAAATTTATATATAA-TTAAT-A
1 TAATAAAAT-AATTTA-ATATAATTTAATGA
*
52859 TATTAAATATAATT
1 TAATAAA-ATAATT
52873 AAAAATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 20 0.53
30 12 0.32
31 6 0.16
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (29 bp):
TAATAAAATAATTTAATATAATTTAATGA
Found at i:52884 original size:20 final size:18
Alignment explanation
Indices: 52847--52880 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52837 ATAAATTTAT
*
52847 ATATAATTAATATATTAA
1 ATATAATTAAAATATTAA
52865 ATATAATTAAAA-ATTA
1 ATATAATTAAAATATTA
52881 TTAATTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAATTAAAATATTAA
Found at i:54072 original size:2 final size:2
Alignment explanation
Indices: 54065--54098 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
54055 GTAATAGAAT
*
54065 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54099 GTCATTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:56551 original size:2 final size:2
Alignment explanation
Indices: 56544--56568 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56534 CTAATGTCAA
56544 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
56569 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:57102 original size:2 final size:2
Alignment explanation
Indices: 57095--57120 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57085 AAATTTACAA
57095 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
57121 CATGATTAAA
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):
AT
Found at i:57551 original size:19 final size:19
Alignment explanation
Indices: 57527--57563 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
57517 ATATTTAAAA
*
57527 AATTAAACTTCTATAATTT
1 AATTAAAATTCTATAATTT
*
57546 AATTAAAATTTTATAATT
1 AATTAAAATTCTATAATT
57564 AAAAAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTAAAATTCTATAATTT
Found at i:58683 original size:2 final size:2
Alignment explanation
Indices: 58676--58711 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
58666 TTCAAATACC
58676 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
58712 CATACACTAA
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:58756 original size:13 final size:13
Alignment explanation
Indices: 58728--58760 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
58718 CTAATGATAA
58728 AATAAA-AAAATT
1 AATAAATAAAATT
58740 -ATAAATAAAATT
1 AATAAATAAAATT
58752 AATAAATAA
1 AATAAATAA
58761 TATGTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.26
12 6 0.32
13 8 0.42
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AATAAATAAAATT
Found at i:59807 original size:13 final size:14
Alignment explanation
Indices: 59738--59808 Score: 56
Period size: 14 Copynumber: 5.0 Consensus size: 14
59728 AGATACAGAA
*
59738 TTATAAATATTAAAAT
1 TTATAAATA-T-AATT
* *
59754 TTA-AAATTTAAAT
1 TTATAAATATAATT
*
59767 TTATTAAATATTATT
1 TTA-TAAATATAATT
*
59782 TTTTAAATATAATT
1 TTATAAATATAATT
59796 TTATAAAT-TAATT
1 TTATAAATATAATT
59809 AAGATAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
13 12 0.26
14 18 0.39
15 13 0.28
16 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTATAAATATAATT
Found at i:60480 original size:26 final size:26
Alignment explanation
Indices: 60440--60489 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
60430 TTGGAATTGA
* *
60440 TAAAGTTCAACTTTACCTGTGATTAC
1 TAAAGTTCAAATTTACCTGAGATTAC
* *
60466 TAAAGTTGAAATTTATCTGAGATT
1 TAAAGTTCAAATTTACCTGAGATT
60490 CTGAATAAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (26 bp):
TAAAGTTCAAATTTACCTGAGATTAC
Found at i:65461 original size:2 final size:2
Alignment explanation
Indices: 65454--65490 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
65444 GCATCTGTAC
65454 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 A
65491 GGCAACTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:65986 original size:14 final size:14
Alignment explanation
Indices: 65967--65998 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
65957 TACTAAAAAA
65967 ATTATTTTTATATT
1 ATTATTTTTATATT
65981 ATTATTTTTATATT
1 ATTATTTTTATATT
65995 -TTAT
1 ATTAT
65999 AATTAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTATTTTTATATT
Found at i:68784 original size:57 final size:58
Alignment explanation
Indices: 68682--68794 Score: 192
Period size: 57 Copynumber: 1.9 Consensus size: 58
68672 CATCAACAGT
68682 GGATGCCATAAATGATACAGCAGCCAAAAATTTCAGAATAGATGCTAGGAATTATGCAGC
1 GGATGCCATAAATGATACAGCA--CAAAAATTTCAGAATAGATGCTAGGAATTATGCAGC
*
68742 GGATGTCATAAATGATACAGCA-AAAAATTTCAGAATAGATGCTAGGAATTATG
1 GGATGCCATAAATGATACAGCACAAAAATTTCAGAATAGATGCTAGGAATTATG
68795 TACCTATTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
57 31 0.60
60 21 0.40
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (58 bp):
GGATGCCATAAATGATACAGCACAAAAATTTCAGAATAGATGCTAGGAATTATGCAGC
Found at i:71794 original size:64 final size:64
Alignment explanation
Indices: 71674--71796 Score: 151
Period size: 64 Copynumber: 1.9 Consensus size: 64
71664 AAATAATATA
* *
71674 ATTAGCAGTGATTTCAAACTAAAGCTAATCATTAGTAGGCTGCGAATAAAACACACACACAATC
1 ATTAGCAGTGATTTCAAACTAAAGCAAATCATTAGTAGACTGCGAATAAAACACACACACAATC
* * *
71738 ATTAGCAGTGATTTCAGACTACCA-CAAATGGCATTAGTAGATTGC-AATTAAAACACACA
1 ATTAGCAGTGATTTCAAACTA-AAGCAAAT--CATTAGTAGACTGCGAA-TAAAACACACA
71797 TACACACACA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
64 24 0.48
65 3 0.06
66 23 0.46
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (64 bp):
ATTAGCAGTGATTTCAAACTAAAGCAAATCATTAGTAGACTGCGAATAAAACACACACACAATC
Found at i:73027 original size:21 final size:21
Alignment explanation
Indices: 72985--73028 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
72975 CATATTTGTA
*
72985 ATTAAAAAAATAGTATAGAACT
1 ATTAAAAAAATAG-ATACAACT
73007 ATTAAAAAAATTA-ATACAACT
1 ATTAAAAAAA-TAGATACAACT
73028 A
1 A
73029 GGAAAAGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 10 0.50
23 2 0.10
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.27
Consensus pattern (21 bp):
ATTAAAAAAATAGATACAACT
Found at i:73904 original size:170 final size:170
Alignment explanation
Indices: 73614--74050 Score: 552
Period size: 170 Copynumber: 2.6 Consensus size: 170
73604 AAAATAAACG
* * * * *
73614 CTTTATACATTTGCCA-AGTGCTGATCAACTATAAGATAATTATCCTATATAGAATGATAGAGGA
1 CTTTATACATTTGCCACA-TGCTGATTAACTATAATATAATTATCCTATATACACTGATAGTGGA
* * *
73678 ATTCAGAAACGCCACAAGGAAGTTAACTGATAAAAGAATCAATAATTACGAAGAAAAAGACAATT
65 ATTCAGAAACGCCACAAGCAAGTTAACTGATAAAAGAATCAATAATCACAAAGAAAAAGACAATT
* * * *
73743 ACACGATACACTACTGGTGAAGCCAAAAGCTCCACAAGCGA
130 ACACGATACACCACCGATGAAGCCAAAAACTCCACAAGCGA
* * * *
73784 CTTTATACATTTGCCACATGCTGATTAACTAGAATATAATTATCTTAGATACACTGATAGTGGAG
1 CTTTATACATTTGCCACATGCTGATTAACTATAATATAATTATCCTATATACACTGATAGTGGAA
* * * * * * *
73849 TTTAGAAACGCTACAAGCAAGTCAACTGATAAAAGAATCTATTATCACAAAGAAAAGGACTATTA
66 TTCAGAAACGCCACAAGCAAGTTAACTGATAAAAGAATCAATAATCACAAAGAAAAAGACAATTA
* ** *
73914 CACGATACACCACCGATGAAGCTAAAAACTCTGCTAGCGA
131 CACGATACACCACCGATGAAGCCAAAAACTCCACAAGCGA
* * * * * *
73954 CTTTATGCATTTGCCACGTGCTGAATAACTATAATATAAGTATCCTCTATACACTGATAATGGAA
1 CTTTATACATTTGCCACATGCTGATTAACTATAATATAATTATCCTATATACACTGATAGTGGAA
*
74019 TTCAGAAATGCCACAAGCAAGTTAACTGATAA
66 TTCAGAAACGCCACAAGCAAGTTAACTGATAA
74051 CCACGTATAC
Statistics
Matches: 225, Mismatches: 41, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
170 224 1.00
171 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (170 bp):
CTTTATACATTTGCCACATGCTGATTAACTATAATATAATTATCCTATATACACTGATAGTGGAA
TTCAGAAACGCCACAAGCAAGTTAACTGATAAAAGAATCAATAATCACAAAGAAAAAGACAATTA
CACGATACACCACCGATGAAGCCAAAAACTCCACAAGCGA
Found at i:75039 original size:3 final size:3
Alignment explanation
Indices: 75031--75080 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
75021 TTTTATAAAA
75031 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
75079 TA
1 TA
75081 CTCATTCTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:77780 original size:55 final size:54
Alignment explanation
Indices: 77692--77806 Score: 178
Period size: 55 Copynumber: 2.1 Consensus size: 54
77682 TGTTCTAAAT
*
77692 GTTGAACATTTCATCCAATAAAATGACGCATCTTAATTAGAAAAGGT-GAAAGGG
1 GTTGAACATTTCATCCAAAAAAATGACGCATCTTAATTAGAAAAGGTCG-AAGGG
* *
77746 GTTGGACATTTCATCCACAAAAAATGAGGCATCTTAATTAGAAAAGGTCGAAGGG
1 GTTGAACATTTCATCCA-AAAAAATGACGCATCTTAATTAGAAAAGGTCGAAGGG
77801 GTTGAA
1 GTTGAA
77807 AATTGTGATG
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
54 16 0.29
55 38 0.69
56 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25
Consensus pattern (54 bp):
GTTGAACATTTCATCCAAAAAAATGACGCATCTTAATTAGAAAAGGTCGAAGGG
Done.