Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold356
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: 432500
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 4
Found at i:250840 original size:14 final size:14
Alignment explanation
Indices: 250709--250840 Score: 61
Period size: 14 Copynumber: 9.9 Consensus size: 14
250699 ATTTTGATAG
250709 ATATAA-TA-ATTT
1 ATATAATTATATTT
*
250721 ATATATTTATA-TT
1 ATATAATTATATTT
250734 ATA-AA-T-T-TTT
1 ATATAATTATATTT
250744 -TATAATTATATTT
1 ATATAATTATATTT
* * **
250757 A-AAATATTTTATAA
1 ATATA-ATTATATTT
*
250771 ATATAATT-TATAT
1 ATATAATTATATTT
250784 ATTATAATT-TATATT
1 A-TATAATTATAT-TT
* * *
250799 ATATAAATTTTAATA
1 ATAT-AATTATATTT
250814 ATATATATTATATTT
1 ATATA-ATTATATTT
250829 ATATAATTATAT
1 ATATAATTATAT
250841 ATCTAAACTT
Statistics
Matches: 91, Mismatches: 14, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
9 2 0.02
10 5 0.05
11 2 0.02
12 7 0.08
13 17 0.19
14 32 0.35
15 24 0.26
16 2 0.02
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATAATTATATTT
Found at i:251058 original size:17 final size:14
Alignment explanation
Indices: 251024--251076 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 14
251014 CTTATTAAAT
251024 AATTATATTAATCA
1 AATTATATTAATCA
251038 AATTTATATATATATCA
1 AA-TTATAT-TA-ATCA
* *
251055 AATTATATTTATTA
1 AATTATATTAATCA
251069 AA-TATATT
1 AATTATATT
251077 TTATTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 6 0.18
14 7 0.21
15 7 0.21
16 8 0.24
17 6 0.18
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (14 bp):
AATTATATTAATCA
Found at i:251071 original size:14 final size:14
Alignment explanation
Indices: 251024--251077 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
251014 CTTATTAAAT
*
251024 AATTATATTAATCA
1 AATTATATTTATCA
251038 AATTTATATATATATCA
1 AA-TTATAT-T-TATCA
*
251055 AATTATATTTATTA
1 AATTATATTTATCA
251069 AA-TATATTT
1 AATTATATTT
251078 TATTTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
13 7 0.20
14 8 0.23
15 7 0.20
16 7 0.20
17 6 0.17
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTATATTTATCA
Found at i:251272 original size:4 final size:4
Alignment explanation
Indices: 251263--251290 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
251253 TATGATTTCC
251263 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
251291 TGTTTTCACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:251867 original size:27 final size:30
Alignment explanation
Indices: 251832--251901 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
251822 AATTTAGTAT
*
251832 AATAATTATTAAT-AAAT-TATTA-AAATA
1 AATAATTATTAATGAAATATATAATAAATA
*
251859 AATAATTATTATATGTAATATATAATAAATA
1 AATAATTATTA-ATGAAATATATAATAAATA
*
251890 AATAATTTTTAA
1 AATAATTATTAA
251902 AATTTTGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 11 0.31
28 2 0.06
29 3 0.08
30 5 0.14
31 15 0.42
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (30 bp):
AATAATTATTAATGAAATATATAATAAATA
Found at i:252234 original size:18 final size:17
Alignment explanation
Indices: 252200--252252 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 17
252190 CATATAAAAT
252200 AAATAA-TTTAA-ATTA
1 AAATAATTTTAATATTA
252215 AAATAATTTTAAATATTAA
1 AAATAATTTT-AATATT-A
*
252234 AAATATTTTTAATATTA
1 AAATAATTTTAATATTA
252251 AA
1 AA
252253 TAAATAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 6 0.18
16 3 0.09
17 5 0.15
18 9 0.27
19 10 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAATTTTAATATTA
Found at i:252236 original size:19 final size:18
Alignment explanation
Indices: 252214--252252 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
252204 AATTTAAATT
252214 AAAATAATTTTAAATATTA
1 AAAAT-ATTTTAAATATTA
*
252233 AAAATATTTTTAATATTA
1 AAAATATTTTAAATATTA
252251 AA
1 AA
252253 TAAATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATATTTTAAATATTA
Found at i:252530 original size:12 final size:12
Alignment explanation
Indices: 252513--252545 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
252503 AATTTACCTA
252513 TTATATTATATT
1 TTATATTATATT
252525 TTATATTAT-TT
1 TTATATTATATT
*
252536 TAATATTATA
1 TTATATTATA
252546 ATTATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTATATTATATT
Found at i:252533 original size:17 final size:16
Alignment explanation
Indices: 252511--252646 Score: 52
Period size: 17 Copynumber: 8.1 Consensus size: 16
252501 GTAATTTACC
*
252511 TATTATATTATATTTTA
1 TATTATATTA-ATATTA
*
252528 TATTATTTTAATATTA
1 TATTATATTAATATTA
252544 TAATTATATTTAAAATATTAAA
1 T-ATTATA-TT--AATATT--A
*
252566 TATT-TATATAA-ATTT
1 TATTATAT-TAATATTA
*
252581 TGA-TGTATTAATAATTTA
1 T-ATTATATTAAT-A-TTA
252599 TATTATA-TAATA-TA
1 TATTATATTAATATTA
*
252613 T-TT-TGTGTACATATTA
1 TATTATAT-TA-ATATTA
*
252629 TATTATTTTAATATTA
1 TATTATATTAATATTA
252645 TA
1 TA
252647 ATAATCTAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 39
0.66 0.06 0.28
Matches are distributed among these distances:
12 1 0.01
13 2 0.02
14 5 0.05
15 8 0.09
16 22 0.24
17 27 0.29
18 12 0.13
19 1 0.01
20 9 0.10
21 3 0.03
22 2 0.02
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (16 bp):
TATTATATTAATATTA
Found at i:252665 original size:16 final size:16
Alignment explanation
Indices: 252646--252769 Score: 78
Period size: 16 Copynumber: 7.8 Consensus size: 16
252636 TTAATATTAT
252646 AATAATCTAAATTCAA
1 AATAATCTAAATTCAA
* *
252662 AATAAATC-ATATTCAG
1 AAT-AATCTAAATTCAA
*
252678 AATGA-CTCAAACTT-AA
1 AATAATCT-AAA-TTCAA
* *
252694 AAT-GTCTTAAATTTAA
1 AATAATC-TAAATTCAA
252710 AATAATCTCAAA-TCAA
1 AATAATCT-AAATTCAA
**
252726 AATAATCCGAATTCAA
1 AATAATCTAAATTCAA
* * *
252742 AATGATTTAAATTTAA
1 AATAATCTAAATTCAA
252758 AATAATCTAAAT
1 AATAATCTAAAT
252770 AATTAACTCG
Statistics
Matches: 81, Mismatches: 17, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
14 1 0.01
15 5 0.06
16 63 0.78
17 12 0.15
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.32
Consensus pattern (16 bp):
AATAATCTAAATTCAA
Found at i:252769 original size:64 final size:64
Alignment explanation
Indices: 252646--252769 Score: 139
Period size: 64 Copynumber: 1.9 Consensus size: 64
252636 TTAATATTAT
* *
252646 AATAATCTAAATTCAAAATAAATCATATTCAGAATGACTCAAACTTAAAATGTCTTAAATTTAA
1 AATAATCTAAATTCAAAATAAATCATATTCAAAATGACTCAAACTTAAAATATCTTAAATTTAA
* * *
252710 AATAATCTCAAA-TCAAAAT-AATCCGA-ATTCAAAATGATTTAAATTTAAAATAATC-TAAAT
1 AATAATCT-AAATTCAAAATAAAT-C-ATATTCAAAATGACTCAAACTTAAAAT-ATCTTAAAT
252770 AATTAACTCG
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
63 3 0.06
64 42 0.82
65 6 0.12
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.32
Consensus pattern (64 bp):
AATAATCTAAATTCAAAATAAATCATATTCAAAATGACTCAAACTTAAAATATCTTAAATTTAA
Found at i:254696 original size:20 final size:20
Alignment explanation
Indices: 254654--254703 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
254644 TTTAATAATG
*
254654 ATTTATTATTAAAATTATAT
1 ATTTAATATTAAAATTATAT
* * *
254674 ATTTAATATTTAAATTTTTT
1 ATTTAATATTAAAATTATAT
254694 ATTTTAATAT
1 A-TTTAATAT
254704 ATTTAATCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTAATATTAAAATTATAT
Found at i:255080 original size:18 final size:16
Alignment explanation
Indices: 255038--255110 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 16
255028 ATTATTAATT
255038 TTAATTTTTATA-AAA
1 TTAATTTTTATATAAA
*
255053 TAAATTTTTAATATAAA
1 TTAATTTTT-ATATAAA
*
255070 TTAATATTTTATTTGAAA
1 TTAAT-TTTTATAT-AAA
255088 TAATAATTTTTTATATAAA
1 T--TAA-TTTTTATATAAA
255107 TTAA
1 TTAA
255111 AAAATTATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
15 8 0.17
16 3 0.06
17 13 0.28
18 8 0.17
19 4 0.09
20 10 0.21
21 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (16 bp):
TTAATTTTTATATAAA
Found at i:259557 original size:69 final size:69
Alignment explanation
Indices: 259477--259606 Score: 190
Period size: 69 Copynumber: 1.9 Consensus size: 69
259467 TTCTATTAGA
* * *
259477 TTCATTAAATAATAATAAAA-AATTTAATTTTTATATCTGATTTTAAATTTTATTATTGAGTCAA
1 TTCATTAAATAATAA-AAAATAATTTAATTTTCATATCTGAATTTAAATTTTATTACTGAGTCAA
259541 CTAAG
65 CTAAG
* * *
259546 TTCATTAAATAATAAAAAATAATTTCATTTTCATGTTTGAATTTAAATTTTATTACTGAGT
1 TTCATTAAATAATAAAAAATAATTTAATTTTCATATCTGAATTTAAATTTTATTACTGAGT
259607 TCATAGGTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
68 4 0.07
69 50 0.93
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (69 bp):
TTCATTAAATAATAAAAAATAATTTAATTTTCATATCTGAATTTAAATTTTATTACTGAGTCAAC
TAAG
Found at i:261229 original size:2 final size:2
Alignment explanation
Indices: 261218--261248 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
261208 TAAATATATA
*
261218 TG TG TC TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
261249 AATAGTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:262561 original size:22 final size:22
Alignment explanation
Indices: 262526--262568 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
262516 CATTTGAATT
262526 ATAATATAACTTAATAATAATA
1 ATAATATAACTTAATAATAATA
* * *
262548 ATAATTTAATTTAATAGTAAT
1 ATAATATAACTTAATAATAAT
262569 TAAAAATAAT
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:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
ATAATATAACTTAATAATAATA
Found at i:262806 original size:30 final size:28
Alignment explanation
Indices: 262735--262827 Score: 82
Period size: 30 Copynumber: 3.2 Consensus size: 28
262725 ACTCTGAATA
*
262735 TTTTTTAAATATTAAAAGATAAATATATT
1 TTTTTTAAATTTTAAAA-ATAAATATATT
* *
262764 TTTTATAAAAATTTTAAAAATAAATATCTT
1 TTTT-T-TAAATTTTAAAAATAAATATATT
*
262794 TTACTTTTAAATTTAAATAAAT-AATA-ATT
1 TT--TTTTAAATTTTAA-AAATAAATATATT
262823 TTTTT
1 TTTTT
262828 ATTATTTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
27 3 0.06
29 8 0.15
30 25 0.47
31 15 0.28
32 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (28 bp):
TTTTTTAAATTTTAAAAATAAATATATT
Found at i:263072 original size:2 final size:2
Alignment explanation
Indices: 263065--263108 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
263055 ATTAAGGGCT
* * * *
263065 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA CA CA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
263107 TA
1 TA
263109 CGTGAGGATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (2 bp):
TA
Found at i:265187 original size:50 final size:51
Alignment explanation
Indices: 265127--265415 Score: 270
Period size: 50 Copynumber: 5.8 Consensus size: 51
265117 TATACTTAGA
* *
265127 GTCAATAATTATGGTCACTTCTCTT-TATTGTCAAAGATTGGTGAAGAATC
1 GTCAACAATTATGGTCACCTCTCTTCTATTGTCAAAGATTGGTGAAGAATC
* * * *
265177 ATCAATAATTATGGCCACCTC-CTTCTATTGTCAAA-AGTTGGTAAAGAATC
1 GTCAACAATTATGGTCACCTCTCTTCTATTGTCAAAGA-TTGGTGAAGAATC
* * * * * *
265227 GTCAACAATTACGTTCACCT-TTTTCTATTATCAAAGGTTGGAGAAGAATC
1 GTCAACAATTATGGTCACCTCTCTTCTATTGTCAAAGATTGGTGAAGAATC
* ** * *
265277 GTCAACAATTATGGTCAACC-CTC-TCTATTGTCAAAGGTCAGTGAATAATT
1 GTCAACAATTATGGTC-ACCTCTCTTCTATTGTCAAAGATTGGTGAAGAATC
* * *
265327 GTCAACAATTATGATCACCTC-CTTCTATTGTCAAAGATTGATGAAGAATA
1 GTCAACAATTATGGTCACCTCTCTTCTATTGTCAAAGATTGGTGAAGAATC
* * ** *
265377 GTCAATAATTACGACCACCTTTC-TCTATTTGTCAAAGAT
1 GTCAACAATTATGGTCACCTCTCTTCTA-TTGTCAAAGAT
265416 ACTTTTCACC
Statistics
Matches: 195, Mismatches: 34, Indels: 19
0.79 0.14 0.08
Matches are distributed among these distances:
49 8 0.04
50 171 0.88
51 16 0.08
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.34
Consensus pattern (51 bp):
GTCAACAATTATGGTCACCTCTCTTCTATTGTCAAAGATTGGTGAAGAATC
Found at i:265398 original size:150 final size:150
Alignment explanation
Indices: 265127--265405 Score: 355
Period size: 150 Copynumber: 1.9 Consensus size: 150
265117 TATACTTAGA
* * * ** * *
265127 GTCAATAATTATGGTCACTTCTCTTTATTGTCAAAGATTGGTGAAGAATCATCAATAATTATGGC
1 GTCAACAATTATGGTCACTCCTCTCTATTGTCAAAGATCAGTGAAGAATCATCAACAATTATGAC
* * ** *
265192 CACCTCCTTCTATTGTCAAAAGTTGGTAAAGAATCGTCAACAATTACGTTCACCTTTTTCTATTA
66 CACCTCCTTCTATTGTCAAAAGTTGATAAAGAATAGTCAACAATTACGACCACCTTTCTCTATTA
265257 TCAAAGGTTGGAGAAGAATC
131 TCAAAGGTTGGAGAAGAATC
* * **
265277 GTCAACAATTATGGTCAAC-CCTCTCTATTGTCAAAGGTCAGTGAATAATTGTCAACAATTATGA
1 GTCAACAATTATGGTC-ACTCCTCTCTATTGTCAAAGATCAGTGAAGAATCATCAACAATTATGA
* * *
265341 TCACCTCCTTCTATTGTC-AAAGATTGATGAAGAATAGTCAATAATTACGACCACCTTTCTCTAT
65 CCACCTCCTTCTATTGTCAAAAG-TTGATAAAGAATAGTCAACAATTACGACCACCTTTCTCTAT
265405 T
129 T
265406 TGTCAAAGAT
Statistics
Matches: 108, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
149 4 0.04
150 102 0.94
151 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (150 bp):
GTCAACAATTATGGTCACTCCTCTCTATTGTCAAAGATCAGTGAAGAATCATCAACAATTATGAC
CACCTCCTTCTATTGTCAAAAGTTGATAAAGAATAGTCAACAATTACGACCACCTTTCTCTATTA
TCAAAGGTTGGAGAAGAATC
Found at i:265738 original size:21 final size:21
Alignment explanation
Indices: 265714--265755 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
265704 AATACATAGT
265714 AAATAAAT-TAAAAAAATTTAA
1 AAATAAATAT-AAAAAATTTAA
*
265735 AAATAAATATAAATAATTTAA
1 AAATAAATATAAAAAATTTAA
265756 TTTTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATAAATATAAAAAATTTAA
Found at i:268760 original size:25 final size:24
Alignment explanation
Indices: 268727--268775 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
268717 TATTTATATA
*
268727 TAAATATATATACATGTATGTAAT
1 TAAATATATATACATGTATATAAT
* *
268751 TAAATTATATTTGCATGTATATAAT
1 TAAA-TATATATACATGTATATAAT
268776 ATATATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (24 bp):
TAAATATATATACATGTATATAAT
Found at i:269447 original size:25 final size:22
Alignment explanation
Indices: 269419--269466 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 22
269409 TTATATAAAT
*
269419 TAAATTATTAATAATTTATATATTA
1 TAAATT-TTAA-AATATATAT-TTA
269444 TAAATTTTAAAATATATATTTA
1 TAAATTTTAAAATATATATTTA
269466 T
1 T
269467 GTTATATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 4 0.18
23 8 0.36
24 4 0.18
25 6 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAATTTTAAAATATATATTTA
Found at i:269476 original size:5 final size:5
Alignment explanation
Indices: 269458--269512 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
269448 TTTTAAAATA
* * *
269458 TATATT TATGT TATAT TATAT TATA- TATTT TATAT TTTA- TATAT TATATT
1 TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA-T
269508 TATAT
1 TATAT
269513 AATCATATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
4 6 0.15
5 26 0.65
6 8 0.20
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (5 bp):
TATAT
Found at i:269482 original size:23 final size:23
Alignment explanation
Indices: 269455--269506 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
269445 AAATTTTAAA
*
269455 ATATATATTTATGTTATATTATATT
1 ATATAT-TTTATATTATA-TATATT
*
269480 ATATATTTTATATTTTATATATT
1 ATATATTTTATATTATATATATT
269503 ATAT
1 ATAT
269507 TTATATAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
24 9 0.36
25 6 0.24
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
ATATATTTTATATTATATATATT
Found at i:269520 original size:28 final size:28
Alignment explanation
Indices: 269469--269522 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
269459 ATATTTATGT
* *
269469 TATATTATATTATATATTTTATATTTTA
1 TATATTATATTATATATATCATATTTTA
269497 TATATTATATT-TATATAATCATATTT
1 TATATTATATTATATAT-ATCATATTT
269523 AAAATTACCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (28 bp):
TATATTATATTATATATATCATATTTTA
Found at i:271617 original size:48 final size:47
Alignment explanation
Indices: 271559--271659 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 47
271549 AAAATAATAT
*
271559 TAAAAATTTATT-TTTATATTAAT-ATTTATGATTAAATTTAATTAAAAA
1 TAAAAATTTATTATTTATA-TAATAATTTA-AATT-AATTTAATTAAAAA
* * *
271607 TAAAATTTTATTATTTATATAATAATTTAAATTAATTTAATTTAAAT
1 TAAAAATTTATTATTTATATAATAATTTAAATTAATTTAATTAAAAA
271654 TAAAAA
1 TAAAAA
271660 ACCCATATCT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
47 17 0.37
48 18 0.39
49 11 0.24
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (47 bp):
TAAAAATTTATTATTTATATAATAATTTAAATTAATTTAATTAAAAA
Found at i:281951 original size:2 final size:2
Alignment explanation
Indices: 281944--281987 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
281934 ATGAGGTTTG
281944 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
281986 AT
1 AT
281988 TCGTTTAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:285851 original size:2 final size:2
Alignment explanation
Indices: 285844--285875 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
285834 AAGTTTTCAT
285844 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
285876 ATCTGTATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:289125 original size:10 final size:10
Alignment explanation
Indices: 289095--289127 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
289085 ATTAAATATA
289095 AATTTAAATTT
1 AATTTAAA-TT
289106 AA-TTAAATT
1 AATTTAAATT
289115 AATTTAAATT
1 AATTTAAATT
289125 AAT
1 AAT
289128 AAAAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.19
10 15 0.71
11 2 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
AATTTAAATT
Found at i:290459 original size:15 final size:15
Alignment explanation
Indices: 290439--290492 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 15
290429 AATCATTGTG
*
290439 TTATATTTATATTTT
1 TTATATTTATATATT
290454 TTATA-TTATA-ATT
1 TTATATTTATATATT
* *
290467 TTAT-TTAAAATATT
1 TTATATTTATATATT
290481 TTATATTTATAT
1 TTATATTTATAT
290493 TATATTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 9 0.29
14 12 0.39
15 10 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATTTATATATT
Found at i:290486 original size:27 final size:28
Alignment explanation
Indices: 290439--290517 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 28
290429 AATCATTGTG
* *
290439 TTATATTT-ATATTTTTTATATTATA-A
1 TTATATTTAAAATATTTTATATTATATA
*
290465 TTTTATTTAAAATATTTTATATT-TATA
1 TTATATTTAAAATATTTTATATTATATA
* *
290492 TTATATTTTAATTATTTTAT-TTATAT
1 TTATATTTAAAATATTTTATATTATAT
290518 TATAATTATA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 11 0.25
27 33 0.75
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (28 bp):
TTATATTTAAAATATTTTATATTATATA
Found at i:290507 original size:20 final size:20
Alignment explanation
Indices: 290481--290526 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
290471 TTAAAATATT
290481 TTATATTTATATTATATTTTAA
1 TTAT-TTTAT-TTATATTTTAA
*
290503 TTATTTTATTTATATTATAA
1 TTATTTTATTTATATTTTAA
290523 TTAT
1 TTAT
290527 ATAATTCGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.61
21 5 0.22
22 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTTATTTATATTTTAA
Found at i:291096 original size:16 final size:18
Alignment explanation
Indices: 291071--291107 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
291061 TTTATTTAAA
291071 ATTAATTATAAAAAT-AT
1 ATTAATTATAAAAATAAT
291088 ATTAA-TATAAAAATAAT
1 ATTAATTATAAAAATAAT
291105 ATT
1 ATT
291108 TTAAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTAATTATAAAAATAAT
Found at i:291750 original size:30 final size:28
Alignment explanation
Indices: 291673--291755 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 28
291663 AATCTTTTGG
291673 ATATTAATAT-TAAA--TATATAATATA
1 ATATTAATATATAAATTTATATAATATA
*
291698 ATATAAATATATCTTAAAATTTATATAATATAA
1 ATATTAATATA---T-AAATTTATATAATAT-A
291731 ATTATTAATATATAAATTTATATAA
1 A-TATTAATATATAAATTTATATAA
291756 AAATAAAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
25 9 0.19
29 1 0.02
30 15 0.32
31 1 0.02
32 10 0.21
33 2 0.04
34 9 0.19
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (28 bp):
ATATTAATATATAAATTTATATAATATA
Found at i:291825 original size:20 final size:19
Alignment explanation
Indices: 291673--291826 Score: 82
Period size: 18 Copynumber: 8.3 Consensus size: 19
291663 AATCTTTTGG
291673 ATATTAATATTAAATATAT-A
1 ATATT-ATA-TAAATATATAA
*
291693 ATATAATATAAATATATCTTAA
1 ATATTATATAAATATA---TAA
*
291715 A-ATT-TATATA-ATAT-A
1 ATATTATATAAATATATAA
291730 A-ATTAT-T-AATATATAA
1 ATATTATATAAATATATAA
*
291746 AT-TTATATAAAAATA-AA
1 ATATTATATAAATATATAA
*
291763 ATATT-T-TTAATATAATTATA
1 ATATTATATAAATAT-A-TA-A
* *
291783 ATATAATA-AAATTTATAA
1 ATATTATATAAATATATAA
291801 ATATTATATAAATATATAA
1 ATATTATATAAATATATAA
291820 ATTATTA
1 A-TATTA
291827 AATTTAGAGC
Statistics
Matches: 103, Mismatches: 12, Indels: 38
0.67 0.08 0.25
Matches are distributed among these distances:
14 1 0.01
15 10 0.10
16 13 0.13
17 7 0.07
18 23 0.22
19 19 0.18
20 20 0.19
21 8 0.08
22 2 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATTATATAAATATATAA
Found at i:294124 original size:21 final size:21
Alignment explanation
Indices: 294089--294150 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
294079 AATATAAAAA
*
294089 AATAATATAACAAAATATATTT
1 AATAA-ATAATAAAATATATTT
*
294111 AATTAATAATAAAA-ATAATTT
1 AATAAATAATAAAATAT-ATTT
* *
294132 AATAAATATTAAATTATAT
1 AATAAATAATAAAATATAT
294151 GTAAATGTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
20 2 0.06
21 25 0.76
22 6 0.18
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
AATAAATAATAAAATATATTT
Found at i:294361 original size:27 final size:27
Alignment explanation
Indices: 294331--294386 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
294321 GTAATAATTT
294331 TTAACATCACTTGTAAAATTAAAAAAA
1 TTAACATCACTTGTAAAATTAAAAAAA
*
294358 TTAACATCACTTGTAAAATTTAAAAAA
1 TTAACATCACTTGTAAAATTAAAAAAA
294385 TT
1 TT
294387 TAAGTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.34
Consensus pattern (27 bp):
TTAACATCACTTGTAAAATTAAAAAAA
Found at i:297586 original size:17 final size:17
Alignment explanation
Indices: 297564--297598 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
297554 TTGTGTTATC
297564 ATTTTATCACAGTGCTA
1 ATTTTATCACAGTGCTA
297581 ATTTTATCACAGTGCTA
1 ATTTTATCACAGTGCTA
297598 A
1 A
297599 CACCTTGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.40
Consensus pattern (17 bp):
ATTTTATCACAGTGCTA
Found at i:299671 original size:25 final size:24
Alignment explanation
Indices: 299641--299721 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 24
299631 AAAAATAATT
299641 TATATTTATTTTTAATTTAAT-TA
1 TATATTTATTTTTAATTTAATATA
*
299664 TATATATTAATTTTAATATTAATATA
1 TATAT-TTATTTTTAAT-TTAATATA
*
299690 T-TATGTTATTTTT-ATTTAA-AAA
1 TATAT-TTATTTTTAATTTAATATA
*
299712 TAAATTTATT
1 TATATTTATT
299722 ATTATTCAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
22 8 0.16
23 11 0.22
24 12 0.24
25 15 0.31
26 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (24 bp):
TATATTTATTTTTAATTTAATATA
Found at i:299700 original size:24 final size:24
Alignment explanation
Indices: 299636--299708 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
299626 TATAAAAAAA
*
299636 TAATT-TATAT-TTATTTTTAATT
1 TAATTATATATATTAATTTTAATT
299658 TAATTATATATATTAATTTTAATAT
1 TAATTATATATATTAATTTTAAT-T
* *
299683 TAA-TATAT-TATGTTATTTTTATT
1 TAATTATATATAT-TAATTTTAATT
299706 TAA
1 TAA
299709 AAATAAATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 5 0.11
23 12 0.27
24 23 0.52
25 4 0.09
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (24 bp):
TAATTATATATATTAATTTTAATT
Found at i:299750 original size:16 final size:16
Alignment explanation
Indices: 299729--299769 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
299719 ATTATTATTC
299729 AAAAATT-TTAAAAATA
1 AAAAATTATT-AAAATA
299745 AAAAATTAATTAAAAT-
1 AAAAATT-ATTAAAATA
299761 AAAAATTAT
1 AAAAATTAT
299770 ATTTTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.09
16 14 0.61
17 5 0.22
18 2 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATTATTAAAATA
Found at i:299827 original size:19 final size:19
Alignment explanation
Indices: 299794--299834 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
299784 AAATAAAATT
*
299794 TTAATAAATATTTATTTAA
1 TTAATAAATATTTATATAA
299813 TTAATCAAATA-TTATATAA
1 TTAAT-AAATATTTATATAA
299832 TTA
1 TTA
299835 TTTTGTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATAAATATTTATATAA
Found at i:299856 original size:20 final size:22
Alignment explanation
Indices: 299822--299864 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
299812 ATTAATCAAA
299822 TATTATATAATTATTTTGTATT
1 TATTATATAATTATTTTGTATT
*
299844 TATTATAT-A-TATTTTTTATT
1 TATTATATAATTATTTTGTATT
299864 T
1 T
299865 TTTGAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 1 0.05
22 8 0.40
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATATAATTATTTTGTATT
Found at i:299930 original size:22 final size:20
Alignment explanation
Indices: 299902--299944 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
299892 TCATTAAATT
*
299902 TTTAAATAATAATACTAATTAA
1 TTTAAATAAAAATA-T-ATTAA
299924 TTTAAATAAAAATATATTAA
1 TTTAAATAAAAATATATTAA
299944 T
1 T
299945 AAATTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 1 0.05
22 13 0.65
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTAAATAAAAATATATTAA
Found at i:300006 original size:37 final size:39
Alignment explanation
Indices: 299960--300040 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 39
299950 TATTTTAAAA
*
299960 TTAATATATAATTGAACTAAAAATA-AATTTAA-AAT-AT
1 TTAATATATAATT-AAATAAAAATATAATTTAATAATAAT
* *
299997 TTAATATATACTTAAATTAAAATATAATTTAATAATAAT
1 TTAATATATAATTAAATAAAAATATAATTTAATAATAAT
300036 TTAAT
1 TTAAT
300041 TTAATAGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 9 0.24
37 19 0.50
38 3 0.08
39 7 0.18
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.42
Consensus pattern (39 bp):
TTAATATATAATTAAATAAAAATATAATTTAATAATAAT
Found at i:300040 original size:16 final size:16
Alignment explanation
Indices: 300021--300051 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
300011 AATTAAAATA
300021 TAATTTAATAATAATT
1 TAATTTAATAATAATT
*
300037 TAATTTAATAGTAAT
1 TAATTTAATAATAAT
300052 CAAAAATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TAATTTAATAATAATT
Found at i:300252 original size:26 final size:26
Alignment explanation
Indices: 300193--300270 Score: 86
Period size: 26 Copynumber: 2.8 Consensus size: 26
300183 AAATAATAAT
* *
300193 TTAATAAAATAAACATATTTTTGTTAAATT
1 TTAAAAAAAT-AA-ATA-TTTT-TTAAATG
300223 TTAAAAAAATAAATATTTTTTAAATG
1 TTAAAAAAATAAATATTTTTTAAATG
300249 TT-AAAAAATAAATATATTTTTA
1 TTAAAAAAATAAATAT-TTTTTA
300271 TAAAAATTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
25 13 0.29
26 14 0.31
27 4 0.09
28 3 0.07
29 2 0.04
30 9 0.20
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (26 bp):
TTAAAAAAATAAATATTTTTTAAATG
Found at i:300281 original size:29 final size:28
Alignment explanation
Indices: 300185--300281 Score: 85
Period size: 30 Copynumber: 3.4 Consensus size: 28
300175 TAATTTAAAA
*
300185 ATAATAATTTAATAAAATAAACATATTTTT
1 ATAAAAATTTAA-AAAATAAA-ATATTTTT
* * *
300215 GTTAAATTTTAAAAAA-ATAAATATTTTT
1 ATAAAAATTTAAAAAATA-AAATATTTTT
300243 -T--AAATGTTAAAAAATAAATATATTTTT
1 ATAAAAAT-TTAAAAAATAAA-ATATTTTT
300270 ATAAAAATTTAA
1 ATAAAAATTTAA
300282 GTAAATATCT
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
25 3 0.05
26 10 0.18
27 10 0.18
28 10 0.18
29 10 0.18
30 12 0.22
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (28 bp):
ATAAAAATTTAAAAAATAAAATATTTTT
Found at i:305207 original size:34 final size:34
Alignment explanation
Indices: 305169--305384 Score: 118
Period size: 34 Copynumber: 6.4 Consensus size: 34
305159 GTAAAAATCA
**
305169 TCATTTAATCAACAATGGTAACTTACCAAATCTC
1 TCATTTAATCAACAATAATAACTTACCAAATCTC
* * * * * * *
305203 TCATTTAGTGAACAATAGTAAATCACAAAATC-A
1 TCATTTAATCAACAATAATAACTTACCAAATCTC
* * * ***
305236 TCATTTAATCAATAATAGTAAGTTGTTAAATCTC
1 TCATTTAATCAACAATAATAACTTACCAAATCTC
* * *
305270 CCGTTTAATCAACAATAATAAAC-TATCAAATCTC
1 TCATTTAATCAACAATAAT-AACTTACCAAATCTC
* * * * * * *
305304 TCAATTAGTCAATAATGATAAATCATCAAATCATC
1 TCATTTAATCAACAATAATAACTTACCAAATC-TC
* * *
305339 -CATTTAATCAATAATGATAAAC-TACCAAATC-A
1 TCATTTAATCAACAATAAT-AACTTACCAAATCTC
305371 TCATTTAATCAACA
1 TCATTTAATCAACA
305385 TTTATTTGAT
Statistics
Matches: 138, Mismatches: 38, Indels: 13
0.73 0.20 0.07
Matches are distributed among these distances:
33 38 0.28
34 94 0.68
35 6 0.04
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.32
Consensus pattern (34 bp):
TCATTTAATCAACAATAATAACTTACCAAATCTC
Found at i:305284 original size:67 final size:67
Alignment explanation
Indices: 305162--305384 Score: 168
Period size: 67 Copynumber: 3.3 Consensus size: 67
305152 AGGTTTAGTA
* * * * *
305162 AAAATCATCATTTAATCAACAATGGTAACTTACCAAATCTCTCATTTAGTGAACAATAGTAAATC
1 AAAATCATCATTTAATCAACAATAGTAACTTACCAAATCTCCCATTTAATCAACAATAATAAATC
305227 AC
66 AC
* * *** *
305229 AAAATCATCATTTAATCAATAATAGTAAGTTGTTAAATCTCCCGTTTAATCAACAATAATAAA-C
1 AAAATCATCATTTAATCAACAATAGTAACTTACCAAATCTCCCATTTAATCAACAATAATAAATC
305293 TATC
66 -A-C
* * * * * * * * *
305297 -AAATCTCTCAATTAGTCAATAAT-GATAAATCATCAAATCAT-CCATTTAATCAATAATGATAA
1 AAAATC-ATCATTTAATCAACAATAG-TAACTTACCAAATC-TCCCATTTAATCAACAATAATAA
305359 A-CTAC
63 ATC-AC
*
305364 CAAATCATCATTTAATCAACA
1 AAAATCATCATTTAATCAACA
305385 TTTATTTGAT
Statistics
Matches: 125, Mismatches: 25, Indels: 12
0.77 0.15 0.07
Matches are distributed among these distances:
66 1 0.01
67 71 0.57
68 52 0.42
69 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.31
Consensus pattern (67 bp):
AAAATCATCATTTAATCAACAATAGTAACTTACCAAATCTCCCATTTAATCAACAATAATAAATC
AC
Found at i:305378 original size:101 final size:100
Alignment explanation
Indices: 305163--305384 Score: 238
Period size: 101 Copynumber: 2.2 Consensus size: 100
305153 GGTTTAGTAA
** * *
305163 AAATCATCATTTAATCAACAATGGTAACTTACCAAATCTCTCATTTAGTGAACAATAGTAAATCA
1 AAATCATCATTTAATCAACAATAATAACTTACCAAATCTCTCAATTAGTCAACAATAGTAAATCA
** ***
305228 CAAAATCATCATTTAATCAATAATAGTAAGTTGTT
66 CAAAATCATCATTTAATCAATAATAGTAAACTACC
* * *
305263 AAATC-TCCCGTTTAATCAACAATAATAAAC-TATCAAATCTCTCAATTAGTCAATAAT-GATAA
1 AAATCAT--CATTTAATCAACAATAAT-AACTTACCAAATCTCTCAATTAGTCAACAATAG-TAA
305325 ATCATC-AAATCATCCATTTAATCAATAAT-GATAAACTACC
62 ATCA-CAAAATCAT-CATTTAATCAATAATAG-TAAACTACC
305365 AAATCATCATTTAATCAACA
1 AAATCATCATTTAATCAACA
305385 TTTATTTGAT
Statistics
Matches: 101, Mismatches: 13, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
99 1 0.01
100 6 0.06
101 65 0.64
102 28 0.28
103 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (100 bp):
AAATCATCATTTAATCAACAATAATAACTTACCAAATCTCTCAATTAGTCAACAATAGTAAATCA
CAAAATCATCATTTAATCAATAATAGTAAACTACC
Found at i:305614 original size:24 final size:25
Alignment explanation
Indices: 305567--305634 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 25
305557 TCATGAGAAT
*
305567 TAATTAGATTTAAATT-TAAATATTT-
1 TAATTA-A-TTAAATTAAAAATATTTA
305592 TAAATT-ATTAAATTAAAAATATTTA
1 T-AATTAATTAAATTAAAAATATTTA
305617 TAATTAGATTAAATTAAA
1 TAATTA-ATTAAATTAAA
305635 TTAAATTTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
23 7 0.19
24 13 0.35
25 2 0.05
26 15 0.41
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (25 bp):
TAATTAATTAAATTAAAAATATTTA
Found at i:305635 original size:24 final size:23
Alignment explanation
Indices: 305566--305635 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 23
305556 ATCATGAGAA
305566 TTAATTAGATTTAAATTTAAATATT
1 TTAATTAGA-TTAAA-TTAAATATT
305591 TTAAATT--ATTAAATTAAAAATATT
1 TT-AATTAGATTAAATT--AAATATT
305615 TATAATTAGATTAAATTAAAT
1 T-TAATTAGATTAAATTAAAT
305636 TAAATTTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
22 2 0.05
23 5 0.13
24 17 0.44
25 3 0.08
26 12 0.31
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (23 bp):
TTAATTAGATTAAATTAAATATT
Found at i:305893 original size:13 final size:13
Alignment explanation
Indices: 305877--305929 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
305867 TTTAATTTAA
*
305877 TAAAAATATTTTT
1 TAAAAATAATTTT
*
305890 TAAATATAATTTT
1 TAAAAATAATTTT
**
305903 TAAAAATAATAAT
1 TAAAAATAATTTT
305916 T--AAATAATTTT
1 TAAAAATAATTTT
305927 TAA
1 TAA
305930 CCGTAAAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
11 9 0.29
13 22 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TAAAAATAATTTT
Found at i:305899 original size:22 final size:21
Alignment explanation
Indices: 305849--305899 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
305839 ATATAAATAA
* *
305849 AAATATAATTAATAATTTTTT
1 AAATATAATAAAAAATTTTTT
*
305870 -AATTTAATAAAAATATTTTTT
1 AAATATAATAAAAA-ATTTTTT
305891 AAATATAAT
1 AAATATAAT
305900 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 10 0.42
21 7 0.29
22 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATATAATAAAAAATTTTTT
Found at i:305913 original size:35 final size:36
Alignment explanation
Indices: 305860--305929 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 36
305850 AATATAATTA
* ** *
305860 ATAATTTTTTAATTTAATAA-AAATATTTTTTAAAT
1 ATAATTTTTAAAAATAATAATAAATAATTTTTAAAT
305895 ATAATTTTTAAAAATAATAATTAAATAATTTTTAA
1 ATAATTTTTAAAAATAATAA-TAAATAATTTTTAA
305930 CCGTAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 17 0.59
37 12 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (36 bp):
ATAATTTTTAAAAATAATAATAAATAATTTTTAAAT
Found at i:306357 original size:7 final size:7
Alignment explanation
Indices: 306345--306374 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
306335 AATTATTGAG
306345 TTAAATT
1 TTAAATT
306352 TTAAATT
1 TTAAATT
306359 TTAAATT
1 TTAAATT
306366 TTAAATT
1 TTAAATT
306373 TT
1 TT
306375 TTTAAATCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTAAATT
Found at i:308206 original size:2 final size:2
Alignment explanation
Indices: 308199--308233 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
308189 TGTGGTTTAA
308199 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 A
308234 GAGAGAGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:309005 original size:2 final size:2
Alignment explanation
Indices: 308998--309033 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
308988 GTTAGAAAAG
308998 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
309034 TAGATAACAG
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:317934 original size:36 final size:36
Alignment explanation
Indices: 317860--317957 Score: 118
Period size: 39 Copynumber: 2.8 Consensus size: 36
317850 ATTTTTTTTA
317860 TTATTCTA-TTATAATATAATTAATATTATTATTTATATT
1 TTATT-TATTTATAATATAATTAA-A--ATTATTTATATT
317899 TTATTTATTTATAATATAATTAAAATTATTTATATT
1 TTATTTATTTATAATATAATTAAAATTATTTATATT
317935 TTA-TTATTT-T-ATAT--TTAAAATTA
1 TTATTTATTTATAATATAATTAAAATTA
317958 ATAAATATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
31 9 0.16
33 4 0.07
34 1 0.02
35 6 0.10
36 15 0.26
38 3 0.05
39 20 0.34
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (36 bp):
TTATTTATTTATAATATAATTAAAATTATTTATATT
Found at i:317951 original size:14 final size:14
Alignment explanation
Indices: 317885--317950 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 14
317875 ATAATTAATA
317885 TTATTATTTATATT
1 TTATTATTTATATT
317899 TTATTTATTTATAATAT
1 TTA-TTATTTAT-AT-T
317916 AATTAAAATTATTTATATT
1 --TT---ATTATTTATATT
317935 TTATTATTTTATATT
1 TTATTA-TTTATATT
317950 T
1 T
317951 AAAATTAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 17
0.72 0.00 0.28
Matches are distributed among these distances:
14 7 0.16
15 17 0.40
16 2 0.05
17 3 0.07
19 3 0.07
20 2 0.05
21 8 0.19
22 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTATTTATATT
Found at i:318627 original size:23 final size:23
Alignment explanation
Indices: 318576--318627 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 23
318566 ATAATTGAAA
318576 TTAATAGTTAATAATAAAAATTT
1 TTAATAGTTAATAATAAAAATTT
318599 TATAATA-TTAAT-ATAAAAATACTT
1 T-TAATAGTTAATAATAAAAAT--TT
318623 TTAAT
1 TTAAT
318628 TAATTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 8 0.31
23 10 0.38
24 8 0.31
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
TTAATAGTTAATAATAAAAATTT
Found at i:318906 original size:13 final size:13
Alignment explanation
Indices: 318888--318951 Score: 59
Period size: 13 Copynumber: 5.3 Consensus size: 13
318878 TTCTTTATTT
318888 ATTAATATTTATA
1 ATTAATATTTATA
*
318901 ATTAATATATAT-
1 ATTAATATTTATA
*
318913 AGTAATATATTATA
1 ATTAATAT-TTATA
318927 A-TAATA--T-TA
1 ATTAATATTTATA
318936 ATT-ATATTTATA
1 ATTAATATTTATA
318948 ATTA
1 ATTA
318952 TAATAAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
9 6 0.15
10 2 0.05
11 1 0.02
12 12 0.29
13 19 0.46
14 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (13 bp):
ATTAATATTTATA
Found at i:319443 original size:36 final size:36
Alignment explanation
Indices: 319402--319499 Score: 112
Period size: 35 Copynumber: 2.8 Consensus size: 36
319392 TATTAAGAAA
* *
319402 TAATTTTTATATTAATATTTATATATTA-TTATAAT
1 TAATTTTTATATTAATATTTATATAATATTTAAAAT
** * *
319437 TAAATTTAAATATAAATATTT-TTTAATATTTAAAAT
1 T-AATTTTTATATTAATATTTATATAATATTTAAAAT
319473 TAATTTTTATATTAATATTTATA-AATA
1 TAATTTTTATATTAATATTTATATAATA
319500 AAATTTAAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
35 26 0.52
36 24 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (36 bp):
TAATTTTTATATTAATATTTATATAATATTTAAAAT
Found at i:319472 original size:25 final size:27
Alignment explanation
Indices: 319407--319503 Score: 74
Period size: 25 Copynumber: 4.0 Consensus size: 27
319397 AGAAATAATT
*
319407 TTTATATTAATATTT---ATAT-ATTA
1 TTTATATTAATATTTAAAATATAAATA
319430 -TTATAATTAA-ATTT-AAATATAAATA
1 TTTAT-ATTAATATTTAAAATATAAATA
*
319455 TTT-T-TTAATATTTAAAAT-T-AATT
1 TTTATATTAATATTTAAAATATAAATA
319478 TTTATATTAATATTTATAAATA-AAAT
1 TTTATATTAATATTTA-AAATATAAAT
319504 TTAAATAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
22 8 0.13
23 15 0.25
24 10 0.17
25 18 0.30
26 6 0.10
27 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTATATTAATATTTAAAATATAAATA
Found at i:319519 original size:62 final size:60
Alignment explanation
Indices: 319410--319541 Score: 169
Period size: 62 Copynumber: 2.2 Consensus size: 60
319400 AATAATTTTT
* * *
319410 ATATTAATATTTATATATTATTATAATTAAATTTAAATATAAATATTTTTTAATATTTAA
1 ATATTAATTTTTATATAATATTATAATAAAATTTAAATATAAATATTTTTTAATATTTAA
*
319470 A-ATTAATTTTTATATTAATATTTATAAATAAAATTTAAATA-AAATTATTTTTTATTATTTAA
1 ATATTAATTTTTATA-TAATA-TTAT-AATAAAATTTAAATATAAA-TATTTTTTAATATTTAA
*
319532 ATAATAATTT
1 ATATTAATTT
319542 ATATCTATTC
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
59 12 0.19
60 5 0.08
61 7 0.11
62 31 0.50
63 7 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (60 bp):
ATATTAATTTTTATATAATATTATAATAAAATTTAAATATAAATATTTTTTAATATTTAA
Found at i:324124 original size:18 final size:17
Alignment explanation
Indices: 324101--324148 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 17
324091 TAAATATTTA
*
324101 AAAATATTATAATGTAAT
1 AAAATA-TATAATATAAT
324119 AAAATATATAAATATAAT
1 AAAATATAT-AATATAAT
324137 ATAAATATATAA
1 A-AAATATATAA
324149 ATTTTAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 3 0.11
18 16 0.59
19 8 0.30
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AAAATATATAATATAAT
Found at i:324124 original size:28 final size:29
Alignment explanation
Indices: 324086--324140 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
324076 AAAATTTATA
* *
324086 TAATATAAATATTTAAAAATATTATAATG
1 TAATATAAATATATAAAAATAATATAATG
*
324115 TAATA-AAATATATAAATATAATATAA
1 TAATATAAATATATAAAAATAATATAA
324141 ATATATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (29 bp):
TAATATAAATATATAAAAATAATATAATG
Found at i:324149 original size:19 final size:18
Alignment explanation
Indices: 324088--324150 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 18
324078 AATTTATATA
*
324088 ATATAAATAT-TTAAAA-
1 ATATAAATATAATAAAAT
*
324104 ATATTATAATGTAATAAAAT
1 ATA-TA-AATATAATAAAAT
324124 ATATAAATATAATATAAAT
1 ATATAAATATAATA-AAAT
324143 ATATAAAT
1 ATATAAAT
324151 TTTAATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 3 0.08
17 2 0.05
18 12 0.31
19 19 0.49
20 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
ATATAAATATAATAAAAT
Found at i:324171 original size:42 final size:37
Alignment explanation
Indices: 324131--324206 Score: 127
Period size: 36 Copynumber: 2.1 Consensus size: 37
324121 AATATATAAA
*
324131 TATAATATAAATATATAAATTTTAA-TTTTTTTAATT
1 TATAATAAAAATATATAAATTTTAATTTTTTTTAATT
*
324167 TATAATAAAAATATATAATTTTTAATTTTTTTTAATT
1 TATAATAAAAATATATAAATTTTAATTTTTTTTAATT
324204 TAT
1 TAT
324207 GGTAGGGTGC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
36 23 0.62
37 14 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (37 bp):
TATAATAAAAATATATAAATTTTAATTTTTTTTAATT
Found at i:324400 original size:17 final size:18
Alignment explanation
Indices: 324378--324425 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 18
324368 TATAAATGTT
324378 AAAATATAAAATA-TTTA
1 AAAATATAAAATATTTTA
*
324395 AAAATAAAAAATATTTTA
1 AAAATATAAAATATTTTA
324413 AAACATAATAAAA
1 AAA-AT-ATAAAA
324426 AATATATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 12 0.46
18 7 0.27
19 2 0.08
20 5 0.19
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATATAAAATATTTTA
Found at i:325069 original size:27 final size:28
Alignment explanation
Indices: 325022--325100 Score: 108
Period size: 27 Copynumber: 2.9 Consensus size: 28
325012 ATATAATATA
325022 ATATAAAA-ATATTAATATATTAAAATTT
1 ATATAAAATATA-TAATATATTAAAATTT
*
325050 ATATAATATA-ATAATATATTAAAATTT
1 ATATAAAATATATAATATATTAAAATTT
* *
325077 TTATAAAATATATAATATTTTAAA
1 ATATAAAATATATAATATATTAAA
325101 TATAATTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 24 0.53
28 20 0.44
29 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
ATATAAAATATATAATATATTAAAATTT
Found at i:325098 original size:19 final size:22
Alignment explanation
Indices: 325056--325097 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
325046 ATTTATATAA
325056 TATAATAATATATTAAAATTTT
1 TATAATAATATATTAAAATTTT
*
325078 TATAA-AATATA-TAATATTTT
1 TATAATAATATATTAAAATTTT
325098 AAATATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TATAATAATATATTAAAATTTT
Found at i:325101 original size:27 final size:27
Alignment explanation
Indices: 325027--325122 Score: 90
Period size: 29 Copynumber: 3.5 Consensus size: 27
325017 ATATAATATA
*
325027 AAAATAT-TAATATATTAAA-ATTTAT
1 AAAATATATAATATTTTAAATATTTAT
* * *
325052 ATAATATAATAATATATTAAAATTTTTAT
1 AAAATAT-ATAATAT-TTTAAATATTTAT
325081 AAAATATATAATATTTTAAATATAATTAT
1 AAAATATATAATATTTTAAATAT--TTAT
*
325110 AATATATA-AATAT
1 AAAATATATAATAT
325123 ATATATATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
25 6 0.11
27 13 0.23
28 16 0.28
29 22 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATATTTTAAATATTTAT
Found at i:325110 original size:20 final size:19
Alignment explanation
Indices: 325087--325147 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 19
325077 TTATAAAATA
*
325087 TATAATATTTTAAATATAAT
1 TATAATA-TATAAATATAAT
325107 TATAATATATAAATAT-AT
1 TATAATATATAAATATAAT
325125 ATATATATATATACAACTATAAT
1 -TATA-ATATATA-AA-TATAAT
325148 AATTGTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
18 2 0.06
19 12 0.34
20 14 0.40
21 2 0.06
22 3 0.09
23 2 0.06
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
TATAATATATAAATATAAT
Found at i:325132 original size:29 final size:29
Alignment explanation
Indices: 325016--325133 Score: 74
Period size: 29 Copynumber: 4.2 Consensus size: 29
325006 ATTATAATAT
325016 AATATAA-TATAAAA-ATATTAATA-TATTA
1 AATATAATTATAAAATATA-TAATATTA-TA
*
325044 AA-AT--TTATATAATATAATAATA-TATTA
1 AATATAATTATAAAATAT-ATAATATTA-TA
** *
325071 AA-ATTTTTATAAAATATATAATATTTTA
1 AATATAATTATAAAATATATAATATTATA
*
325099 AATATAATTATAATATATA-AATATATATA
1 AATATAATTATAAAATATATAATAT-TATA
*
325128 TATATA
1 AATATA
325134 TATACAACTA
Statistics
Matches: 74, Mismatches: 8, Indels: 15
0.76 0.08 0.15
Matches are distributed among these distances:
26 6 0.08
27 18 0.24
28 18 0.24
29 32 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AATATAATTATAAAATATATAATATTATA
Found at i:325137 original size:27 final size:27
Alignment explanation
Indices: 325008--325137 Score: 63
Period size: 27 Copynumber: 5.1 Consensus size: 27
324998 AAAGAATAAT
* * *
325008 TATAATATA-ATATA-ATATAAAAATA
1 TATAATATATAAATATATATATATATA
*
325033 T-TAATATATTAAA-ATTTATATA-ATA
1 TATAATATA-TAAATATATATATATATA
325058 TAATAATATATTAAA-AT-T-T-T-TATA
1 T-ATAATATA-TAAATATATATATATATA
* *
325082 -A-AATATAT-AATATTTTAAATATA-A
1 TATAATATATAAATA-TATATATATATA
325106 TTATAATATATAAATATATATATATATA
1 -TATAATATATAAATATATATATATATA
325134 TATA
1 TATA
325138 CAACTATAAT
Statistics
Matches: 82, Mismatches: 6, Indels: 32
0.68 0.05 0.27
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 7 0.09
22 2 0.02
24 13 0.16
25 9 0.11
26 9 0.11
27 33 0.40
28 5 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TATAATATATAAATATATATATATATA
Found at i:326353 original size:16 final size:17
Alignment explanation
Indices: 326323--326364 Score: 70
Period size: 16 Copynumber: 2.6 Consensus size: 17
326313 AAAAATAATG
326323 ATAAAATTAATTATTTT
1 ATAAAATTAATTATTTT
326340 ATAAAATT-ATTATTTT
1 ATAAAATTAATTATTTT
326356 AT-AAATTAA
1 ATAAAATTAA
326365 ATAATTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.21
16 11 0.46
17 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATAAAATTAATTATTTT
Found at i:330700 original size:17 final size:17
Alignment explanation
Indices: 330680--330715 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
330670 TATTTATTAC
330680 ATATCTAAATTTACTAA
1 ATATCTAAATTTACTAA
*
330697 ATATCTAAATTTATTAA
1 ATATCTAAATTTACTAA
330714 AT
1 AT
330716 TATTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATCTAAATTTACTAA
Found at i:333394 original size:2 final size:2
Alignment explanation
Indices: 333387--333414 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
333377 CCAACCCAAC
333387 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
333415 GGCTTAGTAC
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:333853 original size:33 final size:33
Alignment explanation
Indices: 333811--333876 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
333801 CAAGTGCATC
333811 TTACAGAATACATACATACATATATATATATAG
1 TTACAGAATACATACATACATATATATATATAG
333844 TTACAGAATACATACATACATATATATATATAG
1 TTACAGAATACATACATACATATATATATATAG
333877 GAGTTTGGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.33
Consensus pattern (33 bp):
TTACAGAATACATACATACATATATATATATAG
Found at i:336933 original size:22 final size:22
Alignment explanation
Indices: 336887--336935 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
336877 AAAATTAGTG
* ** *
336887 TTAAAAATAATTTTTTATTTTT
1 TTAAAAATAATTTTTAACCTCT
336909 TTAAAAATAATTTTTAACCTCT
1 TTAAAAATAATTTTTAACCTCT
336931 TTAAA
1 TTAAA
336936 TTTTATAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAAAATAATTTTTAACCTCT
Found at i:340111 original size:13 final size:14
Alignment explanation
Indices: 340089--340117 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
340079 AAAAATATCG
340089 TAAATATTAAAATT
1 TAAATATTAAAATT
340103 TAAAT-TTAAAATT
1 TAAATATTAAAATT
340116 TA
1 TA
340118 TTGAATGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAATATTAAAATT
Found at i:342137 original size:7 final size:7
Alignment explanation
Indices: 342118--342159 Score: 54
Period size: 6 Copynumber: 6.3 Consensus size: 7
342108 AAAAAAATAA
342118 TAAAATAT
1 TAAAAT-T
342126 TAAAATT
1 TAAAATT
342133 TAAAATT
1 TAAAATT
342140 T-AAATT
1 TAAAATT
342146 T-AAATT
1 TAAAATT
342152 T-AAATT
1 TAAAATT
342158 TA
1 TA
342160 TTAACATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 18 0.55
7 9 0.27
8 6 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TAAAATT
Found at i:342146 original size:6 final size:6
Alignment explanation
Indices: 342128--342159 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
342118 TAAAATATTA
342128 AAATTT AAAATTT AAATTT AAATTT AAATTT A
1 AAATTT -AAATTT AAATTT AAATTT AAATTT A
342160 TTAACATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:342247 original size:2 final size:2
Alignment explanation
Indices: 342240--342275 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
342230 TAAAAGAGGA
342240 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
342276 GCACTTTCTT
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:342449 original size:15 final size:15
Alignment explanation
Indices: 342425--342486 Score: 58
Period size: 15 Copynumber: 4.2 Consensus size: 15
342415 AAAAATATTT
342425 TTTATAATTATTTTAA
1 TTTAT-ATTATTTTAA
*
342441 TTTATATTATTTAAA
1 TTTATATTATTTTAA
342456 TTTA-ATATATTTT-A
1 TTTATAT-TATTTTAA
* *
342470 TATAT-TTATATTAA
1 TTTATATTATTTTAA
342484 TTT
1 TTT
342487 TTTATTATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
13 5 0.13
14 10 0.26
15 18 0.47
16 5 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATATTATTTTAA
Found at i:342502 original size:31 final size:30
Alignment explanation
Indices: 342420--342504 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 30
342410 TTAATAAAAA
* *
342420 TATTTTTTATAAT-TATTTTA-ATTTATAT
1 TATTTTTTATTATATATTATATATTTATAT
* *
342448 TATTTAAATTTAATATATTTTATATATTTATAT
1 TATTT---TTTATTATATATTATATATTTATAT
342481 TAATTTTTTATTATATATTATATA
1 T-ATTTTTTATTATATATTATATA
342505 ATTACATCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
28 5 0.11
31 22 0.49
32 5 0.11
33 9 0.20
34 4 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
TATTTTTTATTATATATTATATATTTATAT
Found at i:342727 original size:3 final size:3
Alignment explanation
Indices: 342721--342767 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
342711 ATTATTATTA
* * *
342721 TTG TTG TTG TTA TTG TTG TTG TTG TTG TTG TTG CTG TCG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
342768 ACAGCAGTCG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.02, C:0.04, G:0.30, T:0.64
Consensus pattern (3 bp):
TTG
Found at i:343020 original size:2 final size:2
Alignment explanation
Indices: 343013--343046 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
343003 TTTCATTTTA
343013 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
343047 TTTACAAATG
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:343333 original size:3 final size:3
Alignment explanation
Indices: 343327--343351 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
343317 AATATTGTTG
343327 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
343352 TATGGATCTT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:349854 original size:2 final size:2
Alignment explanation
Indices: 349847--349881 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
349837 ATAAACTCTT
349847 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
349882 CAACTTCTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:352087 original size:3 final size:3
Alignment explanation
Indices: 352079--352112 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
352069 TTGTATGTCT
352079 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
352113 ATAATTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:352271 original size:14 final size:14
Alignment explanation
Indices: 352221--352262 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
352211 AAGTCGATTA
*
352221 AAATTGATTTAATT
1 AAATTAATTTAATT
*
352235 AAA--ATTTTAATT
1 AAATTAATTTAATT
352247 AAATTAATTTAATT
1 AAATTAATTTAATT
352261 AA
1 AA
352263 TTTGATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 10 0.43
14 13 0.57
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
AAATTAATTTAATT
Found at i:352434 original size:23 final size:23
Alignment explanation
Indices: 352408--352458 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
352398 TTAAATCTAT
* *
352408 TTAAACTTAACCTAAAAATTTAG
1 TTAAACTTAAACTAAAAATTTAA
* *
352431 TTAAACTTAAATTAAAAGTTTAA
1 TTAAACTTAAACTAAAAATTTAA
352454 TTAAA
1 TTAAA
352459 ATAAAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.37
Consensus pattern (23 bp):
TTAAACTTAAACTAAAAATTTAA
Found at i:352518 original size:19 final size:19
Alignment explanation
Indices: 352460--352533 Score: 71
Period size: 19 Copynumber: 3.8 Consensus size: 19
352450 TTAATTAAAA
*
352460 TAAAAAATAAAAAAACTAA-T
1 TAAAAAA-ATAAAAA-TAATT
*
352480 TAAAATAAA-AAATATAAATT
1 TAAAA-AAATAAAAAT-AATT
*
352500 TAACAAAATAAAAATAATT
1 TAAAAAAATAAAAATAATT
352519 TAAAAAAATAAAAAT
1 TAAAAAAATAAAAAT
352534 TTGATCAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
18 1 0.02
19 27 0.59
20 16 0.35
21 2 0.04
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAAAAAATAAAAATAATT
Found at i:352534 original size:16 final size:16
Alignment explanation
Indices: 352486--352535 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
352476 TAATTAAAAT
*
352486 AAAAAATATAAATTTA
1 AAAAAATAAAAATTTA
*
352502 ACAAAATAAAAATAATTTA
1 A-AAAA-ATAAA-AATTTA
352521 AAAAAATAAAAATTT
1 AAAAAATAAAAATTT
352536 GATCAAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 6 0.21
17 8 0.29
18 7 0.25
19 7 0.25
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAAATAAAAATTTA
Found at i:352626 original size:26 final size:27
Alignment explanation
Indices: 352574--352626 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
352564 TTAATTATTA
*
352574 TAATTTTAATATTAAAATTAATTAAAT
1 TAATTTTAATATTAAAATTAATCAAAT
*
352601 TAATTTTTA-ATTAAAA-TATATCAAAT
1 TAATTTTAATATTAAAATTA-ATCAAAT
352627 CGAGTAATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 2 0.09
26 13 0.57
27 8 0.35
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
TAATTTTAATATTAAAATTAATCAAAT
Found at i:352887 original size:25 final size:24
Alignment explanation
Indices: 352839--352890 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
352829 AGTATAATTT
* *
352839 TATTTATAATATATATTATATTAA
1 TATTAATAATACATATTATATTAA
*
352863 TATTAATAATACATTATTATTTTAA
1 TATTAATAATACA-TATTATATTAA
352888 TAT
1 TAT
352891 ATTATTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTAATAATACATATTATATTAA
Found at i:352894 original size:16 final size:17
Alignment explanation
Indices: 352855--352906 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
352845 TAATATATAT
*
352855 TATATTAATATTAATAA
1 TATATTATTATTAATAA
* *
352872 TACATTATTATT-TTAA
1 TATATTATTATTAATAA
352888 TATATTATTTATTATATAA
1 TATATTA-TTATTA-ATAA
352907 AAGAGAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 9 0.33
17 15 0.56
19 3 0.11
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
TATATTATTATTAATAA
Found at i:352966 original size:11 final size:11
Alignment explanation
Indices: 352942--352975 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
352932 TCTTTTATAA
352942 TATATTACATAT
1 TATATTA-ATAT
352954 TATATTAATAT
1 TATATTAATAT
*
352965 TATTTTAATAT
1 TATATTAATAT
352976 ATTATATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATTAATAT
Found at i:353323 original size:5 final size:5
Alignment explanation
Indices: 353313--353348 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
353303 GGAATGACTA
353313 AATTT AATTT AATTT AATTT AATGTT AAATTT AATT
1 AATTT AATTT AATTT AATTT AAT-TT -AATTT AATT
353349 GATATGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 22 0.76
6 4 0.14
7 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (5 bp):
AATTT
Found at i:353372 original size:10 final size:10
Alignment explanation
Indices: 353313--353374 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
353303 GGAATGACTA
*
353313 AATTTAATTT
1 AATTTAAATT
*
353323 AATTTAATTT
1 AATTTAAATT
353333 AATGTTAAATTT
1 AAT-TTAAA-TT
* * *
353345 AATTGATATG
1 AATTTAAATT
*
353355 ATTTTAAATT
1 AATTTAAATT
353365 AATTTAAATT
1 AATTTAAATT
353375 TAAATTTAGT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
10 29 0.71
11 7 0.17
12 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (10 bp):
AATTTAAATT
Found at i:353376 original size:16 final size:16
Alignment explanation
Indices: 353311--353380 Score: 63
Period size: 16 Copynumber: 4.4 Consensus size: 16
353301 TTGGAATGAC
353311 TAAATTTAATTT-AATT
1 TAAA-TTAATTTAAATT
*
353327 TAATTTAATGTTAAATT
1 TAAATTAAT-TTAAATT
* * * *
353344 T-AATTGATATGATTT
1 TAAATTAATTTAAATT
353359 TAAATTAATTTAAATT
1 TAAATTAATTTAAATT
353375 TAAATT
1 TAAATT
353381 TAGTTAAAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
15 10 0.24
16 26 0.63
17 5 0.12
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (16 bp):
TAAATTAATTTAAATT
Found at i:353496 original size:16 final size:15
Alignment explanation
Indices: 353475--353529 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 15
353465 AGTCTAATTG
353475 ATTTAAATTAAAAATA
1 ATTTAAATT-AAAATA
*
353491 ATTTAAAGTTAAAGTA
1 ATTTAAA-TTAAAATA
*
353507 ATTTAAATTCGAAATA
1 ATTTAAATT-AAAATA
353523 ATATTAA
1 AT-TTAA
353530 TTCAAAATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
15 2 0.06
16 25 0.76
17 6 0.18
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (15 bp):
ATTTAAATTAAAATA
Found at i:353741 original size:16 final size:16
Alignment explanation
Indices: 353722--353774 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
353712 TTCAAACACG
353722 AAATATTTAAAAATTA
1 AAATATTTAAAAATTA
** * *
353738 AAATAAATCAAATTTA
1 AAATATTTAAAAATTA
353754 AAATATTTAAAAATTA
1 AAATATTTAAAAATTA
353770 AAATA
1 AAATA
353775 AATTAAACCC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATATTTAAAAATTA
Found at i:353743 original size:32 final size:32
Alignment explanation
Indices: 353707--353788 Score: 101
Period size: 32 Copynumber: 2.6 Consensus size: 32
353697 TTGATTCTAT
* *
353707 AATAATTCAAACACGAAATATTTAAAAATTAA
1 AATAAATCAAACACAAAATATTTAAAAATTAA
***
353739 AATAAATCAAATTTAAAATATTTAAAAATTAA
1 AATAAATCAAACACAAAATATTTAAAAATTAA
* *
353771 AATAAATTAAACCCAAAA
1 AATAAATCAAACACAAAA
353789 ATAATTCACA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.62, C:0.09, G:0.01, T:0.28
Consensus pattern (32 bp):
AATAAATCAAACACAAAATATTTAAAAATTAA
Found at i:354695 original size:38 final size:38
Alignment explanation
Indices: 354653--354745 Score: 123
Period size: 38 Copynumber: 2.4 Consensus size: 38
354643 GCCGCTAATC
* * *
354653 AAATTTAAATTAAATTTACTAGCCGTAAGCTATTAGTT
1 AAATTTAAATTGAATTTACTAACCGTAAGCTACTAGTT
* * * *
354691 AAATTCAAATTGAATTTACTAACTGTCAGTTACTAGTT
1 AAATTTAAATTGAATTTACTAACCGTAAGCTACTAGTT
354729 AAATTTAAATTGAATTT
1 AAATTTAAATTGAATTT
354746 GATTTATCTA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.41
Consensus pattern (38 bp):
AAATTTAAATTGAATTTACTAACCGTAAGCTACTAGTT
Found at i:354958 original size:19 final size:19
Alignment explanation
Indices: 354934--354980 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
354924 TATTTTTTAA
354934 ATATAAAATTTTTACATTT
1 ATATAAAATTTTTACATTT
354953 ATATAAAATTTTTACATTT
1 ATATAAAATTTTTACATTT
354972 ATATAAAAT
1 ATATAAAAT
354981 AATTATTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATAAAATTTTTACATTT
Found at i:355345 original size:2 final size:2
Alignment explanation
Indices: 355338--355382 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
355328 TTTTCACCTT
355338 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
355380 TA T
1 TA T
355383 TGAATATTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:356271 original size:19 final size:19
Alignment explanation
Indices: 356247--356292 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
356237 TAATTTTATT
*
356247 TATAAAATTTTTATATTTA
1 TATAAAATTTTTACATTTA
*
356266 TATAAAATTTTTACGTTTA
1 TATAAAATTTTTACATTTA
356285 TATAAAAT
1 TATAAAAT
356293 AATTATTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TATAAAATTTTTACATTTA
Found at i:356658 original size:2 final size:2
Alignment explanation
Indices: 356651--356682 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
356641 TTTTCACCTT
356651 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
356683 GAATATTCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:356926 original size:11 final size:12
Alignment explanation
Indices: 356910--356942 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
356900 ATTAGATTGA
356910 TTAAATTAA-AT
1 TTAAATTAATAT
356921 TTAAATTAATAT
1 TTAAATTAATAT
356933 TT-AATTAATA
1 TTAAATTAATA
356943 AAAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TTAAATTAATAT
Found at i:356981 original size:38 final size:38
Alignment explanation
Indices: 356919--356993 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 38
356909 ATTAAATTAA
356919 ATTTAAATTAATATTTAATTAATAA-AAATAAATTTTTT
1 ATTTAAATTAATATTTAA-TAATAACAAATAAATTTTTT
356957 ATTTAAATTTAATATTTTAA-AATAATCAAATAAATTT
1 ATTTAAA-TTAATA-TTTAATAATAA-CAAATAAATTT
356994 ATGAACCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
38 12 0.36
39 6 0.18
40 15 0.45
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (38 bp):
ATTTAAATTAATATTTAATAATAACAAATAAATTTTTT
Found at i:357321 original size:11 final size:11
Alignment explanation
Indices: 357305--357363 Score: 68
Period size: 11 Copynumber: 5.4 Consensus size: 11
357295 AATATAGTTT
357305 TATAAATATAA
1 TATAAATATAA
*
357316 TATAAATAAAA
1 TATAAATATAA
357327 TATTAAATAT-A
1 TA-TAAATATAA
*
357338 TAAATAATATAA
1 TATA-AATATAA
357350 TATAAATAT-A
1 TATAAATATAA
357360 TATA
1 TATA
357364 TTAAAATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
10 6 0.15
11 25 0.61
12 10 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TATAAATATAA
Found at i:357329 original size:16 final size:16
Alignment explanation
Indices: 357308--357357 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
357298 ATAGTTTTAT
357308 AAATATAATATAAATA
1 AAATATAATATAAATA
357324 AAATATTAAATATATAA-A
1 AAATA-T-AATATA-AATA
*
357342 TAATATAATATAAATA
1 AAATATAATATAAATA
357358 TATATATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
15 2 0.07
16 12 0.41
17 2 0.07
18 11 0.38
19 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAATATAATATAAATA
Found at i:357340 original size:20 final size:20
Alignment explanation
Indices: 357315--357391 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 20
357305 TATAAATATA
357315 ATATAAATAAAATATTAAAT
1 ATATAAATAAAATATTAAAT
*
357335 ATATAAATAATATAATATAAAT
1 ATATAAATAAAAT-AT-TAAAT
*
357357 ATATATATTAAAAT-TT--AT
1 ATATA-AATAAAATATTAAAT
*
357375 ATA-AAATAAATTATTAA
1 ATATAAATAAAATATTAA
357392 TATTAAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
16 6 0.13
17 3 0.07
18 5 0.11
20 13 0.28
21 3 0.07
22 10 0.22
23 6 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATATAAATAAAATATTAAAT
Found at i:357412 original size:29 final size:29
Alignment explanation
Indices: 357315--357418 Score: 101
Period size: 29 Copynumber: 3.6 Consensus size: 29
357305 TATAAATATA
*
357315 ATATAA-ATAAAATATTAA-ATATATAAA-TA
1 ATATAATAT-AAATATTAATAT-TA-AAATTT
357344 ATATAATATAAATA-TATATATTAAAATTT
1 ATATAATATAAATATTA-ATATTAAAATTT
*
357373 ATATAAAATAAATTATTAATATTAAAATTT
1 ATATAATATAAA-TATTAATATTAAAATTT
357403 ATA-AATATAAAATATT
1 ATATAATAT-AAATATT
357419 TTAAATATGT
Statistics
Matches: 65, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
28 5 0.08
29 34 0.52
30 24 0.37
31 2 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
ATATAATATAAATATTAATATTAAAATTT
Found at i:357416 original size:34 final size:32
Alignment explanation
Indices: 357303--357416 Score: 112
Period size: 34 Copynumber: 3.5 Consensus size: 32
357293 TAAATATAGT
* *
357303 TTTATAAATATAATATAAATAAAATATT-AAA
1 TTTATAAATATAAAATAAATATAATATTAAAA
*
357334 TATATAAATAATATAATATAAATATATATATTAAAA
1 TTTATAAAT-ATA-AA-ATAAATATA-ATATTAAAA
357370 -TT-T--ATATAAAATAAATTATTAATATTAAAA
1 TTTATAAATATAAAATAAA-TA-TAATATTAAAA
357400 TTTATAAATATAAAATA
1 TTTATAAATATAAAATA
357417 TTTTAAATAT
Statistics
Matches: 68, Mismatches: 4, Indels: 19
0.75 0.04 0.21
Matches are distributed among these distances:
29 5 0.07
30 13 0.19
31 15 0.22
32 6 0.09
33 1 0.01
34 19 0.28
35 6 0.09
36 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (32 bp):
TTTATAAATATAAAATAAATATAATATTAAAA
Done.