Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2497
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: 58499
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:285 original size:14 final size:14
Alignment explanation
Indices: 266--292 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
256 CTTCTGTAGC
266 TCTTTTTCCTCGCT
1 TCTTTTTCCTCGCT
280 TCTTTTTCCTCGC
1 TCTTTTTCCTCGC
293 CTCCTTTTTG
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:0.00, C:0.37, G:0.07, T:0.56
Consensus pattern (14 bp):
TCTTTTTCCTCGCT
Found at i:299 original size:15 final size:14
Alignment explanation
Indices: 267--301 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
257 TTCTGTAGCT
*
267 CTTTTTCCTCGCTT
1 CTTTTTCCTCGCTC
281 CTTTTTCCTCGCCTC
1 CTTTTTCCTCG-CTC
296 CTTTTT
1 CTTTTT
302 GGCCTTGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.00, C:0.37, G:0.06, T:0.57
Consensus pattern (14 bp):
CTTTTTCCTCGCTC
Found at i:646 original size:17 final size:16
Alignment explanation
Indices: 624--661 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
614 TTACTGATCC
624 TTCTCTT-TTTTCTTCTT
1 TTCTCTTCTTTT-TT-TT
641 TTCTCTTCTTTTTTTT
1 TTCTCTTCTTTTTTTT
657 TTCTC
1 TTCTC
662 CCCCCCCCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 9 0.45
18 4 0.20
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTCTTCTTTTTTTT
Found at i:11034 original size:16 final size:15
Alignment explanation
Indices: 11008--11038 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
10998 TAAAAAAATA
11008 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
11023 ATTTTGTTATTATTTT
1 ATTTT-TTATTATTTT
11039 TATGGAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:11552 original size:16 final size:16
Alignment explanation
Indices: 11514--11552 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
11504 AATCAATTGG
11514 AAAATAAAGAACAACA
1 AAAATAAAGAACAACA
11530 AACAATAAA-AACAAGCA
1 AA-AATAAAGAACAA-CA
11547 AAAATA
1 AAAATA
11553 GCATGAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.74, C:0.13, G:0.05, T:0.08
Consensus pattern (16 bp):
AAAATAAAGAACAACA
Found at i:20277 original size:26 final size:27
Alignment explanation
Indices: 20241--20296 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
20231 CAGGAGATTT
*
20241 TTAATATTTATA-AATATTTAA-TTAAA
1 TTAATAATTATACAA-ATTTAAGTTAAA
20267 TTAATAATTATACAAATTTAAGTTAAA
1 TTAATAATTATACAAATTTAAGTTAAA
20294 TTA
1 TTA
20297 TATTAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
TTAATAATTATACAAATTTAAGTTAAA
Found at i:20339 original size:17 final size:17
Alignment explanation
Indices: 20317--20350 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20307 TTATTATTTT
*
20317 TTTAATATTTTTTATAA
1 TTTAATATTTTATATAA
20334 TTTAATATTTTATATAA
1 TTTAATATTTTATATAA
20351 CTGAGTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAATATTTTATATAA
Found at i:20545 original size:20 final size:20
Alignment explanation
Indices: 20522--20565 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
20512 ATAAATTATT
*
20522 AATATTTAAAAATTT-ATATA
1 AATATATAAAAATTTGA-ATA
*
20542 AATATATAATAATTTGAATA
1 AATATATAAAAATTTGAATA
20562 AATA
1 AATA
20566 AAAAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AATATATAAAAATTTGAATA
Found at i:20572 original size:20 final size:20
Alignment explanation
Indices: 20539--20589 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
20529 AAAAATTTAT
* * * *
20539 ATAAATATATAATAATTTGA
1 ATAAATAAAAAATAATATAA
20559 ATAAATAAAAAATAATATAA
1 ATAAATAAAAAATAATATAA
*
20579 ATACATAAAAA
1 ATAAATAAAAA
20590 CACAAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
ATAAATAAAAAATAATATAA
Found at i:20831 original size:19 final size:19
Alignment explanation
Indices: 20790--20831 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
20780 AAATAAAATG
*
20790 AATATGATATAAATATATA
1 AATATGATATAAATATACA
*
20809 AATATGTTA-AAATATACA
1 AATATGATATAAATATACA
20827 TAATA
1 -AATA
20832 CTAATTATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (19 bp):
AATATGATATAAATATACA
Found at i:21127 original size:23 final size:21
Alignment explanation
Indices: 21068--21127 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
21058 ACACGATATG
*
21068 AATATAACATATATAAAATAT
1 AATATAACATATATAAAAAAT
* *
21089 AATTAAAACACAATATAAAAAAT
1 AA-TATAACA-TATATAAAAAAT
21112 AATATGAACATGATAT
1 AATAT-AACAT-ATAT
21128 GAATATACAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
21 2 0.07
22 8 0.27
23 20 0.67
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (21 bp):
AATATAACATATATAAAAAAT
Found at i:21389 original size:12 final size:12
Alignment explanation
Indices: 21359--21415 Score: 62
Period size: 12 Copynumber: 4.5 Consensus size: 12
21349 TCATATAAAA
21359 TTTTCTTTCTCTCT
1 TTTTCTTTCT-T-T
21373 TTTTCTTTCTTT
1 TTTTCTTTCTTT
21385 TTTTCTTT-TTT
1 TTTTCTTTCTTT
*
21396 TCTTTCTTTTCTTC
1 T-TTTC-TTTCTTT
21410 TTTTCT
1 TTTTCT
21416 CTCTCTCTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 4 0.10
12 14 0.36
13 8 0.21
14 13 0.33
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTTTCTTT
Found at i:21397 original size:20 final size:20
Alignment explanation
Indices: 21360--21413 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
21350 CATATAAAAT
*
21360 TTTC-TTTC-TCTCTTTTTC
1 TTTCTTTTCTTCTTTTTTTC
*
21378 TTTCTTTTTTTCTTTTTTTC
1 TTTCTTTTCTTCTTTTTTTC
21398 TTTCTTTTCTTCTTTT
1 TTTCTTTTCTTCTTTT
21414 CTCTCTCTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 4 0.13
19 3 0.10
20 24 0.77
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTCTTTTCTTCTTTTTTTC
Found at i:22667 original size:34 final size:34
Alignment explanation
Indices: 22602--22820 Score: 244
Period size: 34 Copynumber: 6.5 Consensus size: 34
22592 GTAAAAACCA
* *
22602 CCATTTAATCAACAATGGCAA-CCTACTAAATCTC
1 CCATTTAATCAACAATGGTAAGCC-ACCAAATCTC
* * * *
22636 CCATTTAGTCAATAATAGTAAGCCACCAAATCAC
1 CCATTTAATCAACAATGGTAAGCCACCAAATCTC
** *
22670 CCATTTAATCAACAATGGTAAGCTGCCAAATTTC
1 CCATTTAATCAACAATGGTAAGCCACCAAATCTC
* *
22704 CCATTTAATCAACAATGGTAAGCTACCAAATCTT
1 CCATTTAATCAACAATGGTAAGCCACCAAATCTC
* * * *
22738 CCATTTAGTCAACAATGGCAAACCACCAAATCAC
1 CCATTTAATCAACAATGGTAAGCCACCAAATCTC
* * * *
22772 CCATTTAATCAACAATGGTAAACTATCAAATC-A
1 CCATTTAATCAACAATGGTAAGCCACCAAATCTC
22805 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
22821 TCTCCCACTT
Statistics
Matches: 157, Mismatches: 27, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
33 16 0.10
34 139 0.89
35 2 0.01
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAAGCCACCAAATCTC
Found at i:22725 original size:68 final size:67
Alignment explanation
Indices: 22600--22820 Score: 280
Period size: 68 Copynumber: 3.3 Consensus size: 67
22590 TGGTAAAAAC
* * * * * *
22600 CACCATTTAATCAACAATGGCAACCTACTAAATCTCCCATTTAGTCAATAATAGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
22665 AT
66 AT
* * * *
22667 CACCCATTTAATCAACAATGGTAAGCTGCCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
22732 AAT
65 AAT
* * * * * *
22735 CTTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTATCA
1 C-ACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
22800 AAT
65 AAT
22803 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
22821 TCTCCCACTT
Statistics
Matches: 131, Mismatches: 21, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
67 17 0.13
68 114 0.87
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:22744 original size:102 final size:101
Alignment explanation
Indices: 22600--22820 Score: 318
Period size: 102 Copynumber: 2.2 Consensus size: 101
22590 TGGTAAAAAC
* * * *
22600 CACCATTTAATCAACAATGGCAACCTACTAAATCTCCCATTTAGTCAATAATAGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATAGCAAACCACCAA
* *
22665 ATCACCCATTTAATCAACAATGGTAAGCTGCCAAATTT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAA--T
* * * *
22703 C-CCATTTAATCAACAATGGTAAGCTACCAAATCTTCCATTTAGTCAACAATGGCAAACCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATAGCAAACCACCAA
*
22767 ATCACCCATTTAATCAACAATGGTAAACTATCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
22803 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
22821 TCTCCCACTT
Statistics
Matches: 106, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
100 2 0.02
101 16 0.15
102 87 0.82
103 1 0.01
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATAGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:26914 original size:19 final size:19
Alignment explanation
Indices: 26892--26928 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
26882 GTACAGTAAC
*
26892 TGTATACTTGAATAGTACA
1 TGTATACGTGAATAGTACA
26911 TGTATACGTGAATAGTAC
1 TGTATACGTGAATAGTAC
26929 CTCGACAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (19 bp):
TGTATACGTGAATAGTACA
Found at i:27280 original size:34 final size:34
Alignment explanation
Indices: 27237--27384 Score: 156
Period size: 34 Copynumber: 4.4 Consensus size: 34
27227 TAAAAACCAC
* * * *
27237 CATTTAATCAATAATAGCAACCTACCAAATCTCT
1 CATTTAATCAACAATGGCAAACTACCAAATCACT
* * * *
27271 CATTTAATCAATAAGGGTAAACTACCAAATC-TT
1 CATTTAATCAACAATGGCAAACTACCAAATCACT
* * * *
27304 CTATTTAGTCAACAATGACAAACCACCAAATCACC
1 C-ATTTAATCAACAATGGCAAACTACCAAATCACT
*
27339 CATTTAATCAACAATGGTAAACTACCAAATCAC-
1 CATTTAATCAACAATGGCAAACTACCAAATCACT
27372 CATTTAATCAACA
1 CATTTAATCAACA
27385 CTAATTAAAC
Statistics
Matches: 95, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
33 15 0.16
34 79 0.83
35 1 0.01
ACGTcount: A:0.43, C:0.25, G:0.05, T:0.26
Consensus pattern (34 bp):
CATTTAATCAACAATGGCAAACTACCAAATCACT
Found at i:27396 original size:68 final size:68
Alignment explanation
Indices: 27235--27384 Score: 187
Period size: 68 Copynumber: 2.2 Consensus size: 68
27225 GGTAAAAACC
* * * * *
27235 ACCATTTAATCAATAATAGC-AACCTACCAAATCTCTCATTTAATCAATAAGGGTAAACTACCAA
1 ACCATTTAATCAACAATAACAAACC-ACCAAATCACCCATTTAATCAACAAGGGTAAACTACCAA
27299 ATCT
65 ATCT
* * * * *
27303 TCTATTTAGTCAACAATGACAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAA
1 ACCATTTAATCAACAATAACAAACCACCAAATCACCCATTTAATCAACAAGGGTAAACTACCAAA
27368 TC-
66 TCT
27370 ACCATTTAATCAACA
1 ACCATTTAATCAACA
27385 CTAATTAAAC
Statistics
Matches: 68, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
67 12 0.18
68 52 0.76
69 4 0.06
ACGTcount: A:0.43, C:0.25, G:0.05, T:0.26
Consensus pattern (68 bp):
ACCATTTAATCAACAATAACAAACCACCAAATCACCCATTTAATCAACAAGGGTAAACTACCAAA
TCT
Found at i:28455 original size:2 final size:2
Alignment explanation
Indices: 28448--28483 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28438 TTATTATTAT
28448 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28484 AATTTGTTAT
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):
TA
Found at i:29634 original size:36 final size:37
Alignment explanation
Indices: 29560--29642 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 37
29550 TGAAAATATT
* * *
29560 ATATTTTTAATTTATTTTTAAAATATTAAATAACTTA
1 ATATTTTTTATTAAATTTTAAAATATTAAATAACTTA
*
29597 ATATTTTTTATTAAATTTTAAAATA-TAAATAATTTA
1 ATATTTTTTATTAAATTTTAAAATATTAAATAACTTA
29633 ATATTTTTTA
1 ATATTTTTTA
29643 ACGTTTATAC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 20 0.48
37 22 0.52
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (37 bp):
ATATTTTTTATTAAATTTTAAAATATTAAATAACTTA
Found at i:30088 original size:23 final size:24
Alignment explanation
Indices: 30049--30095 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
30039 ATTATATTTT
*
30049 TAAAATTTTTATTTA-TTTAAAAA
1 TAAAATTTTTATATATTTTAAAAA
30072 TAAAATATTTT-TATATTTTAAAAA
1 TAAAAT-TTTTATATATTTTAAAAA
30096 ATTATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TAAAATTTTTATATATTTTAAAAA
Found at i:30170 original size:21 final size:21
Alignment explanation
Indices: 30146--30221 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 21
30136 TTAATTAATG
30146 AATTAAAAATTAAATTATACT
1 AATTAAAAATTAAATTATACT
* *
30167 AATTATATA-T-AATTATAATCT
1 AATTAAAAATTAAATTAT-A-CT
* *
30188 AAATT-AAAATTAAATTAAATT
1 -AATTAAAAATTAAATTATACT
*
30209 AAATAAAAATTAA
1 AATTAAAAATTAA
30222 TTAATCAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
19 6 0.14
20 5 0.12
21 20 0.48
22 6 0.14
23 5 0.12
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTAAAAATTAAATTATACT
Found at i:30203 original size:11 final size:11
Alignment explanation
Indices: 30177--30225 Score: 57
Period size: 10 Copynumber: 4.5 Consensus size: 11
30167 AATTATATAT
*
30177 AATTATAATCTA
1 AATTAAAAT-TA
30189 AATTAAAATTA
1 AATTAAAATTA
30200 AATT-AAATTA
1 AATTAAAATTA
*
30210 AATAAAAATT-
1 AATTAAAATTA
30220 AATTAA
1 AATTAA
30226 TCAAATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 14 0.42
11 11 0.33
12 8 0.24
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
AATTAAAATTA
Found at i:30208 original size:16 final size:18
Alignment explanation
Indices: 30177--30211 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
30167 AATTATATAT
30177 AATTATAATCTAAATTAA
1 AATTATAATCTAAATTAA
30195 AATTA-AAT-TAAATTAA
1 AATTATAATCTAAATTAA
30211 A
1 A
30212 TAAAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 3 0.18
18 5 0.29
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AATTATAATCTAAATTAA
Found at i:30810 original size:75 final size:75
Alignment explanation
Indices: 30685--30836 Score: 214
Period size: 75 Copynumber: 2.0 Consensus size: 75
30675 GATGAAACGA
* * ** *
30685 TAATCCGAGATAATCTGCATGATATTTACAATCAACAAATGTTTCAGCATATTTCACAGTACTAC
1 TAATCCGAGATAATCTACACGATAACTACAATCAACAAATGTTTCAGCATATTCCACAGTACTAC
30750 TATCAACAAC
66 TATCAACAAC
* * * *
30760 TAATCTGAGATAATCTACACGATAACTACAATCAACAAATGTTTCTGCATATTCCACATTGCTAC
1 TAATCCGAGATAATCTACACGATAACTACAATCAACAAATGTTTCAGCATATTCCACAGTACTAC
*
30825 TATCAATAAC
66 TATCAACAAC
30835 TA
1 TA
30837 TAATCAACAA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.31
Consensus pattern (75 bp):
TAATCCGAGATAATCTACACGATAACTACAATCAACAAATGTTTCAGCATATTCCACAGTACTAC
TATCAACAAC
Found at i:31302 original size:15 final size:15
Alignment explanation
Indices: 31265--31304 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
31255 GGGTAAACAG
*
31265 GTGGTGGATGCACGG
1 GTGGTGGATGCACGA
**
31280 GTTATGGATGCACGA
1 GTGGTGGATGCACGA
31295 GTGGTGGATG
1 GTGGTGGATG
31305 GACAGGATCA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.17, C:0.10, G:0.47, T:0.25
Consensus pattern (15 bp):
GTGGTGGATGCACGA
Found at i:36202 original size:14 final size:14
Alignment explanation
Indices: 36183--36221 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
36173 TTATAGGCTT
36183 TAAACTAATTACCC
1 TAAACTAATTACCC
*
36197 TAAACTAATTACGC
1 TAAACTAATTACCC
36211 TAAACCTAATT
1 TAAA-CTAATT
36222 CCACATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.44, C:0.23, G:0.03, T:0.31
Consensus pattern (14 bp):
TAAACTAATTACCC
Found at i:37446 original size:32 final size:32
Alignment explanation
Indices: 37405--37474 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
37395 AATAATATAA
*
37405 ATATAATATGAATAAATAGATGTATT-AAATTT
1 ATATAATATGAATAAATA-ATATATTAAAATTT
* * *
37437 ATATGATATGAATTATTAATATATTAAAATTT
1 ATATAATATGAATAAATAATATATTAAAATTT
37469 ATATAA
1 ATATAA
37475 ATATATGATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 6 0.19
32 26 0.81
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (32 bp):
ATATAATATGAATAAATAATATATTAAAATTT
Found at i:39203 original size:16 final size:16
Alignment explanation
Indices: 39184--39215 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39174 TGGAGATAGA
39184 ATCAATTGAATTATCT
1 ATCAATTGAATTATCT
*
39200 ATCAATTTAATTATCT
1 ATCAATTGAATTATCT
39216 TATTATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (16 bp):
ATCAATTGAATTATCT
Found at i:39247 original size:8 final size:8
Alignment explanation
Indices: 39234--39283 Score: 64
Period size: 8 Copynumber: 6.0 Consensus size: 8
39224 TTAATAATTA
39234 AAAAAAAT
1 AAAAAAAT
39242 AAAAAAAT
1 AAAAAAAT
39250 AAAAAAATTT
1 AAAAAAA--T
39260 AAAAAAAT
1 AAAAAAAT
*
39268 AAAAAATT
1 AAAAAAAT
*
39276 ATAAAAAT
1 AAAAAAAT
39284 TAAAGATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
8 29 0.78
10 8 0.22
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (8 bp):
AAAAAAAT
Found at i:39256 original size:18 final size:18
Alignment explanation
Indices: 39233--39273 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
39223 TTTAATAATT
39233 AAAAAAAATAAAAAAATA
1 AAAAAAAATAAAAAAATA
**
39251 AAAAAATTTAAAAAAATA
1 AAAAAAAATAAAAAAATA
39269 AAAAA
1 AAAAA
39274 TTATAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAAAAATAAAAAAATA
Found at i:39258 original size:26 final size:26
Alignment explanation
Indices: 39229--39301 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
39219 TATATTTAAT
39229 AATTAAAAAAAATAAAAAAATAAAAA
1 AATTAAAAAAAATAAAAAAATAAAAA
* * *
39255 AATTTAAAAAAATAAAAAATTATAAA
1 AATTAAAAAAAATAAAAAAATAAAAA
* *
39281 AATTAAAGATAAATAATAAAA
1 AATTAAA-AAAAATAAAAAAA
39302 GTATCGTATG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 29 0.74
27 10 0.26
ACGTcount: A:0.77, C:0.00, G:0.01, T:0.22
Consensus pattern (26 bp):
AATTAAAAAAAATAAAAAAATAAAAA
Found at i:39280 original size:18 final size:19
Alignment explanation
Indices: 39232--39282 Score: 74
Period size: 17 Copynumber: 2.9 Consensus size: 19
39222 ATTTAATAAT
39232 TAAAAAAA--ATAAAAAAA
1 TAAAAAAATTATAAAAAAA
39249 TAAAAAAATT-TAAAAAAA
1 TAAAAAAATTATAAAAAAA
39267 T-AAAAAATTATAAAAA
1 TAAAAAAATTATAAAAA
39283 TTAAAGATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (19 bp):
TAAAAAAATTATAAAAAAA
Found at i:39287 original size:17 final size:17
Alignment explanation
Indices: 39229--39287 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
39219 TATATTTAAT
* *
39229 AATTAAAAAAAATAAAAA
1 AATT-AAAAAATTATAAA
*
39247 AATAAAAAAATT-TAAAA
1 AATTAAAAAATTAT-AAA
*
39264 AAATAAAAAATTATAAA
1 AATTAAAAAATTATAAA
39281 AATTAAA
1 AATTAAA
39288 GATAAATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
17 29 0.88
18 4 0.12
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AATTAAAAAATTATAAA
Found at i:41135 original size:18 final size:21
Alignment explanation
Indices: 41096--41135 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41086 AAAATGTAAT
41096 AAATAATTCAATTACTTTATA
1 AAATAATTCAATTACTTTATA
41117 AAATAATT-AA-TAC-TTATA
1 AAATAATTCAATTACTTTATA
41135 A
1 A
41136 TTATATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 3 0.16
20 2 0.11
21 8 0.42
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATAATTCAATTACTTTATA
Found at i:41690 original size:8 final size:8
Alignment explanation
Indices: 41676--41786 Score: 51
Period size: 9 Copynumber: 14.5 Consensus size: 8
41666 ATCTTAGTTA
41676 ATTAATAT
1 ATTAATAT
*
41684 CTTAATAT
1 ATTAATAT
41692 ATT-A-A-
1 ATTAATAT
41697 A-TAATAT
1 ATTAATAT
41704 ATTAAATAT
1 ATT-AATAT
41713 ATTAAATAT
1 ATT-AATAT
41722 ATTAA-AT
1 ATTAATAT
41729 -TTAATA-
1 ATTAATAT
*
41735 ATAAAT-T
1 ATTAATAT
*
41742 A-TAAAAT
1 ATTAATAT
*
41749 ATTAAAAT
1 ATTAATAT
**
41757 AAAAATAAT
1 ATTAAT-AT
*
41766 ACTAATAAT
1 ATTAAT-AT
*
41775 ATTAAAAT
1 ATTAATAT
41783 ATTA
1 ATTA
41787 TATTCTATAT
Statistics
Matches: 80, Mismatches: 12, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
4 1 0.01
5 2 0.03
6 8 0.10
7 12 0.15
8 27 0.34
9 30 0.38
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (8 bp):
ATTAATAT
Found at i:41701 original size:12 final size:12
Alignment explanation
Indices: 41686--41711 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41676 ATTAATATCT
41686 TAATATATTAAA
1 TAATATATTAAA
41698 TAATATATTAAA
1 TAATATATTAAA
41710 TA
1 TA
41712 TATTAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATATTAAA
Found at i:41711 original size:9 final size:9
Alignment explanation
Indices: 41699--41728 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
41689 TATATTAAAT
41699 AATATATTA
1 AATATATTA
41708 AATATATTA
1 AATATATTA
41717 AATATATTA
1 AATATATTA
41726 AAT
1 AAT
41729 TTAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AATATATTA
Found at i:41713 original size:21 final size:20
Alignment explanation
Indices: 41673--41720 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
41663 TTAATCTTAG
* *
41673 TTAATTAATATCTTAATATA
1 TTAAATAATATATTAATATA
41693 TTAAATAATATATTAAATATA
1 TTAAATAATATATT-AATATA
41714 TTAAATA
1 TTAAATA
41721 TATTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAATAATATATTAATATA
Found at i:41757 original size:20 final size:21
Alignment explanation
Indices: 41715--41759 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
41705 TTAAATATAT
*
41715 TAAATATATTAAATTTAATAA
1 TAAATATATAAAATTTAATAA
41736 TAAAT-TATAAAATATTAA-AA
1 TAAATATATAAAAT-TTAATAA
41756 TAAA
1 TAAA
41760 AATAATACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATATATAAAATTTAATAA
Found at i:41875 original size:12 final size:12
Alignment explanation
Indices: 41820--41922 Score: 75
Period size: 12 Copynumber: 8.3 Consensus size: 12
41810 CCATCATATT
*
41820 TTATATTAAAAA
1 TTATATTTAAAA
* * *
41832 TTACATATAATA
1 TTATATTTAAAA
*
41844 TTATTTTAATAAATA
1 TTATATT--TAAA-A
41859 TTATATTTAAAA
1 TTATATTTAAAA
*
41871 CTATA-TTAAAA
1 TTATATTTAAAA
*
41882 GTTAAATTTAAAA
1 -TTATATTTAAAA
41895 TTA-ATTTAAAAA
1 TTATATTT-AAAA
*
41907 TAATATTTAAAA
1 TTATATTTAAAA
41919 TTAT
1 TTAT
41923 TTCAAACATA
Statistics
Matches: 70, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
11 10 0.14
12 36 0.51
13 14 0.20
14 3 0.04
15 7 0.10
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (12 bp):
TTATATTTAAAA
Found at i:41876 original size:51 final size:48
Alignment explanation
Indices: 41821--41943 Score: 124
Period size: 51 Copynumber: 2.5 Consensus size: 48
41811 CATCATATTT
* * *
41821 TATATTAAAAATTACATATAATATTATTTTAATAAATATTATATTTAAAAC
1 TATATTAAAAATTAAATATAAAATTAATTTAA-AAATA--ATATTTAAAAC
* * *
41872 TATATTAAAAGTTAAATTTAAAATTAATTTAAAAATAATATTTAAAAT
1 TATATTAAAAATTAAATATAAAATTAATTTAAAAATAATATTTAAAAC
*
41920 TAT-TTCAAACA-TAAATAATAAAAT
1 TATATT-AAAAATTAAAT-ATAAAAT
41944 ATTTAATATT
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
47 7 0.11
48 22 0.36
50 5 0.08
51 27 0.44
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (48 bp):
TATATTAAAAATTAAATATAAAATTAATTTAAAAATAATATTTAAAAC
Found at i:41881 original size:11 final size:12
Alignment explanation
Indices: 41860--41918 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 12
41850 TAATAAATAT
41860 TATATTTAAAAC
1 TATATTTAAAAC
*
41872 TATA-TTAAAAGT
1 TATATTTAAAA-C
* *
41884 TAAATTTAAAAT
1 TATATTTAAAAC
*
41896 TA-ATTTAAAAA
1 TATATTTAAAAC
41907 TAATATTTAAAA
1 T-ATATTTAAAA
41919 TTATTTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
11 15 0.38
12 11 0.28
13 14 0.35
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (12 bp):
TATATTTAAAAC
Found at i:41894 original size:13 final size:12
Alignment explanation
Indices: 41853--41921 Score: 61
Period size: 13 Copynumber: 5.7 Consensus size: 12
41843 ATTATTTTAA
*
41853 TAAATATTATATT
1 TAAA-ATTAAATT
* *
41866 TAAAACTATA-T
1 TAAAATTAAATT
41877 TAAAAGTTAAATT
1 TAAAA-TTAAATT
41890 TAAAATT-AATT
1 TAAAATTAAATT
*
41901 TAAAAATAATATT
1 TAAAATTAA-ATT
41914 TAAAATTA
1 TAAAATTA
41922 TTTCAAACAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
11 16 0.34
12 11 0.23
13 20 0.43
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (12 bp):
TAAAATTAAATT
Found at i:41933 original size:24 final size:23
Alignment explanation
Indices: 41820--41949 Score: 77
Period size: 24 Copynumber: 5.3 Consensus size: 23
41810 CCATCATATT
* * * *
41820 TTATATTAAAAATTACATATAATA
1 TTAT-TTAAAAATAATATTTAAAA
41844 TTATTTTAATAAATATTATATTTAAAA
1 TTA-TTTAA-AAATA--ATATTTAAAA
* *
41871 CTATATTAAAAGTTAA-ATTTAAAA
1 TTAT-TTAAAA-ATAATATTTAAAA
41895 TTAATTTAAAAATAATATTTAAAA
1 TT-ATTTAAAAATAATATTTAAAA
* *
41919 TTATTTCAAACATAA-ATAATAAAA
1 TTATTT-AAAAATAATAT-TTAAAA
41943 -TATTTAA
1 TTATTTAA
41950 TATTAAAAAT
Statistics
Matches: 86, Mismatches: 10, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
22 2 0.02
23 14 0.16
24 44 0.51
25 8 0.09
26 3 0.03
27 15 0.17
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (23 bp):
TTATTTAAAAATAATATTTAAAA
Found at i:42031 original size:2 final size:2
Alignment explanation
Indices: 42026--42055 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42016 GAACCCCCCT
42026 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
42056 AAGGTTTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:43280 original size:21 final size:21
Alignment explanation
Indices: 43233--43281 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
43223 ATTTAATTTG
43233 ATTTAAAATAATATTTTTTAA
1 ATTTAAAATAATATTTTTTAA
* *
43254 AATTAAAATAATATATTTTT-T
1 ATTTAAAATAATAT-TTTTTAA
43275 ATTTAAA
1 ATTTAAA
43282 TTTAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTAAAATAATATTTTTTAA
Found at i:43452 original size:28 final size:27
Alignment explanation
Indices: 43418--43471 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
43408 TTTAAAATTT
43418 TAATTTGAATATTTGTAATTAAAATAAA
1 TAATTTG-ATATTTGTAATTAAAATAAA
* * *
43446 TAATTTGATTTTTTTTATTAAAATAA
1 TAATTTGATATTTGTAATTAAAATAA
43472 CAGTGACGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (27 bp):
TAATTTGATATTTGTAATTAAAATAAA
Found at i:46590 original size:22 final size:22
Alignment explanation
Indices: 46562--46603 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
46552 ATTTGATAAA
46562 ATTAAT-ATAAATAATTTAATTT
1 ATTAATAATAAA-AATTTAATTT
46584 ATTAATAATAAAAATTTAAT
1 ATTAATAATAAAAATTTAAT
46604 AATATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTAATAATAAAAATTTAATTT
Found at i:46605 original size:30 final size:30
Alignment explanation
Indices: 46571--46638 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
46561 AATTAATATA
*
46571 AATAATTTAATTTATTAATAA-TAAAAATTT
1 AATAATTTAATTTAATAA-AATTAAAAATTT
* *
46601 AATAATATAATTTAATAAAATTAAATATTT
1 AATAATTTAATTTAATAAAATTAAAAATTT
46631 -ATAATTTA
1 AATAATTTA
46639 TACGATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 9 0.27
30 24 0.73
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
AATAATTTAATTTAATAAAATTAAAAATTT
Found at i:46614 original size:13 final size:14
Alignment explanation
Indices: 46585--46618 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
46575 ATTTAATTTA
46585 TTAATAATAAAAAT
1 TTAATAATAAAAAT
*
46599 TTAATAAT-ATAAT
1 TTAATAATAAAAAT
46612 TTAATAA
1 TTAATAA
46619 AATTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAATAATAAAAAT
Found at i:46633 original size:24 final size:24
Alignment explanation
Indices: 46589--46638 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
46579 AATTTATTAA
*
46589 TAATAAAAATTTAATAATATAATT
1 TAATAAAAATTAAATAATATAATT
*
46613 TAAT-AAAATTAAATATTTATAATT
1 TAATAAAAATTAAATA-ATATAATT
46637 TA
1 TA
46639 TACGATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAATAAAAATTAAATAATATAATT
Found at i:46861 original size:19 final size:19
Alignment explanation
Indices: 46829--46865 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
46819 AGGTTATTAA
*
46829 ATTAAGTATTAATTTTTAT
1 ATTAAGTATAAATTTTTAT
*
46848 ATTAATTATAAATTTTTA
1 ATTAAGTATAAATTTTTA
46866 ATTTTATTAA
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:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
ATTAAGTATAAATTTTTAT
Found at i:46866 original size:26 final size:25
Alignment explanation
Indices: 46837--46886 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
46827 AAATTAAGTA
*
46837 TTAATTTTTATATTAATTATA-AATTT
1 TTAA-TTTTAT-TAAATTATATAATTT
46863 TTAATTTTATTAAATTATATAATT
1 TTAATTTTATTAAATTATATAATT
46887 AAATGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 10 0.45
26 4 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTAATTTTATTAAATTATATAATTT
Found at i:47090 original size:24 final size:23
Alignment explanation
Indices: 47058--47135 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 23
47048 AGTAAATTTA
*
47058 TTAAAAAAATTTTAATAATATAAT
1 TTAATAAAA-TTTAATAATATAAT
* *
47082 TTAATAAAATTAAATATTTATAAT
1 TTAATAAAATTTAATA-ATATAAT
* *
47106 TTACATAAAACTTAAT-ATAAAAT
1 TTA-ATAAAATTTAATAATATAAT
47129 TTAATAA
1 TTAATAA
47136 TCTACTCCGT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
22 4 0.09
23 14 0.31
24 17 0.38
25 10 0.22
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (23 bp):
TTAATAAAATTTAATAATATAAT
Found at i:47122 original size:25 final size:24
Alignment explanation
Indices: 47076--47135 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
47066 ATTTTAATAA
47076 TATAATTTAATAAAATTAAATATT
1 TATAATTTAATAAAATTAAATATT
47100 TATAATTTACATAAAACTT-AATA--
1 TATAATTTA-ATAAAA-TTAAATATT
*
47123 TAAAATTTAATAA
1 TATAATTTAATAA
47136 TCTACTCCGT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 4 0.12
23 8 0.24
24 9 0.27
25 10 0.30
26 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (24 bp):
TATAATTTAATAAAATTAAATATT
Found at i:47388 original size:69 final size:69
Alignment explanation
Indices: 47304--47443 Score: 280
Period size: 69 Copynumber: 2.0 Consensus size: 69
47294 TTAGGGCATC
47304 TTAACCTTTCTTTCTAGTTTAGTTGTTTCGTTCGTTCTTCATTTTCTTCCACATCCAAAGTATCG
1 TTAACCTTTCTTTCTAGTTTAGTTGTTTCGTTCGTTCTTCATTTTCTTCCACATCCAAAGTATCG
47369 AGTG
66 AGTG
47373 TTAACCTTTCTTTCTAGTTTAGTTGTTTCGTTCGTTCTTCATTTTCTTCCACATCCAAAGTATCG
1 TTAACCTTTCTTTCTAGTTTAGTTGTTTCGTTCGTTCTTCATTTTCTTCCACATCCAAAGTATCG
47438 AGTG
66 AGTG
47442 TT
1 TT
47444 CTTCTCAATT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.17, C:0.21, G:0.13, T:0.49
Consensus pattern (69 bp):
TTAACCTTTCTTTCTAGTTTAGTTGTTTCGTTCGTTCTTCATTTTCTTCCACATCCAAAGTATCG
AGTG
Found at i:51444 original size:19 final size:19
Alignment explanation
Indices: 51402--51445 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
51392 TTGAATCAAG
*
51402 TTAAATTTATTTAAATTAA
1 TTAAATTTATTTAAAATAA
*
51421 ATAAATTTATTTATAAAT-A
1 TTAAATTTATTTA-AAATAA
51440 TTAAAT
1 TTAAAT
51446 GAACATGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAATTTATTTAAAATAA
Found at i:51837 original size:22 final size:21
Alignment explanation
Indices: 51787--51837 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
51777 TAATGAAAAA
51787 TATATTTTAATTTTTGTATTAT
1 TATA-TTTAATTTTTGTATTAT
* *
51809 TAAATTTAATATTTT-TAATTTT
1 TATATTTAAT-TTTTGT-ATTAT
51831 TATATTT
1 TATATTT
51838 TAAAAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TATATTTAATTTTTGTATTAT
Found at i:51845 original size:31 final size:31
Alignment explanation
Indices: 51785--51841 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
51775 TATAATGAAA
*
51785 AATATATTTTAATTTTTGTATTATTAAATTT
1 AATATATTTTAATTTTTATATTATTAAATTT
51816 AATAT-TTTTAATTTTTATATT-TTAAA
1 AATATATTTTAATTTTTATATTATTAAA
51842 AATTATAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 5 0.20
30 15 0.60
31 5 0.20
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (31 bp):
AATATATTTTAATTTTTATATTATTAAATTT
Found at i:52100 original size:14 final size:14
Alignment explanation
Indices: 52081--52132 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
52071 TATTATAATT
52081 TTAAAATATAAAAA
1 TTAAAATATAAAAA
**
52095 TTAAAATACT-AACT
1 TTAAAATA-TAAAAA
52109 TTAATAATATAAAAA
1 TTAA-AATATAAAAA
52124 TTAAAATAT
1 TTAAAATAT
52133 TTTTTATCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 20 0.65
15 11 0.35
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAAAATATAAAAA
Found at i:52171 original size:31 final size:29
Alignment explanation
Indices: 52085--52171 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 29
52075 ATAATTTTAA
**
52085 AATATAAAAATTAAAATACTAACTTTA--AT
1 AATATAAAAATTAAAATA--ATTTTTATCAT
*
52114 AATATAAAAATTAAAATATTTTTTATCAT
1 AATATAAAAATTAAAATAATTTTTATCAT
**
52143 AATATAAAAACTTCTAATAAATTTTTATC
1 AATATAAAAA-TTAAAAT-AATTTTTATC
52172 GGATTGAAGC
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
27 4 0.08
29 30 0.62
30 5 0.10
31 9 0.19
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (29 bp):
AATATAAAAATTAAAATAATTTTTATCAT
Found at i:53544 original size:20 final size:20
Alignment explanation
Indices: 53519--53570 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
53509 AAGTTAGGTA
* *
53519 AAAAAGAAAGAAAGAAGATG
1 AAAAAGAAAGAAAGAAAAAG
53539 AAAAAGAAAGAAAGAAAAAG
1 AAAAAGAAAGAAAGAAAAAG
*
53559 AAAAAAAAAGAA
1 AAAAAGAAAGAA
53571 TAAATATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (20 bp):
AAAAAGAAAGAAAGAAAAAG
Found at i:53546 original size:16 final size:14
Alignment explanation
Indices: 53525--53561 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 14
53515 GGTAAAAAAG
53525 AAAGAAAGAAGATGAA
1 AAAGAAAGAA-A-GAA
53541 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
53555 AAAGAAA
1 AAAGAAA
53562 AAAAAAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.48
15 1 0.05
16 10 0.48
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.03
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Done.