Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 12 of 32
Found at i:1464915 original size:78 final size:82
Alignment explanation
Indices: 1464769--1464918 Score: 191
Period size: 82 Copynumber: 1.9 Consensus size: 82
1464759 TTGTACTAAT
*
1464769 ATATAAATTAATATATTATTAATAAAATAAATACATAATACTATTAATAACAAAATATAAAATTT
1 ATATAAATTAATATATTATTAATAAAATAAATACATAATAC-ATTAATAACAAAATATAAAAGTT
1464834 TATAAGTCTTAAAAATAA
65 TATAAGTCTTAAAAATAA
* * * * * * *
1464852 ATATAAA-TAATTTTTTATTAATAAAATAAA-ATATTATA-ATTTATTA-AAAATATATAAGTTT
1 ATATAAATTAATATATTATTAATAAAATAAATACATAATACATTAATAACAAAATATAAAAGTTT
1464913 ATAAGT
66 ATAAGT
1464919 ATCAAATATA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
78 19 0.32
79 6 0.10
81 6 0.10
82 21 0.36
83 7 0.12
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (82 bp):
ATATAAATTAATATATTATTAATAAAATAAATACATAATACATTAATAACAAAATATAAAAGTTT
ATAAGTCTTAAAAATAA
Found at i:1464930 original size:78 final size:82
Alignment explanation
Indices: 1464769--1464949 Score: 190
Period size: 78 Copynumber: 2.2 Consensus size: 82
1464759 TTGTACTAAT
*
1464769 ATATAAATTAATATATTATTAATAAAATAAATACATAATACTATTAATAACAAAATATAAAATTT
1 ATATAAATTAATATATTATTAATAAAATAAATACATAATAC-ATTAATAACAAAATATAAAAGTT
* *
1464834 TATAAGTCTTAAAAATAA
65 TATAAGTATCAAAAATAA
* * * * * * *
1464852 ATATAAA-TAATTTTTTATTAATAAAATAAA-ATATTATA-ATTTATTA-AAAATATATAAGTTT
1 ATATAAATTAATATATTATTAATAAAATAAATACATAATACATTAATAACAAAATATAAAAGTTT
*
1464913 ATAAGTATCAAATATAA
66 ATAAGTATCAAAAATAA
*
1464930 ATTTTAAAATATAATATATT
1 A-TAT-AAAT-TAATATATT
1464950 TATATAAATG
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
78 28 0.35
79 8 0.10
80 3 0.04
81 6 0.08
82 28 0.35
83 7 0.09
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (82 bp):
ATATAAATTAATATATTATTAATAAAATAAATACATAATACATTAATAACAAAATATAAAAGTTT
ATAAGTATCAAAAATAA
Found at i:1465457 original size:11 final size:11
Alignment explanation
Indices: 1465414--1465461 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
1465404 TAAATAAATT
1465414 TTTAATTTTTA
1 TTTAATTTTTA
*
1465425 TTTACAATTTT-
1 TTTA-ATTTTTA
*
1465436 TTTAA-TATTA
1 TTTAATTTTTA
1465446 TTTAATTTTTA
1 TTTAATTTTTA
1465457 TTTAA
1 TTTAA
1465462 AATAAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
9 3 0.10
10 6 0.19
11 17 0.55
12 5 0.16
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTAATTTTTA
Found at i:1465473 original size:17 final size:18
Alignment explanation
Indices: 1465453--1465487 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1465443 TTATTTAATT
1465453 TTTATTTAAA-ATAAAAA
1 TTTATTTAAATATAAAAA
1465470 TTTATTTAAATATAAAAA
1 TTTATTTAAATATAAAAA
1465488 AAATAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTATTTAAATATAAAAA
Found at i:1465616 original size:23 final size:22
Alignment explanation
Indices: 1465586--1465631 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 22
1465576 ACTTATAAAA
1465586 ACTCAAAAATTAATTTTTTTATC
1 ACTCAAAAATTAA-TTTTTTATC
1465609 ACTCAAAAATTAATTTTTTATC
1 ACTCAAAAATTAATTTTTTATC
1465631 A
1 A
1465632 TACTTATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (22 bp):
ACTCAAAAATTAATTTTTTATC
Found at i:1468426 original size:2 final size:2
Alignment explanation
Indices: 1468421--1468456 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1468411 AAATCAATAA
*
1468421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1468457 TTATTCTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1470682 original size:13 final size:12
Alignment explanation
Indices: 1470618--1470686 Score: 56
Period size: 13 Copynumber: 5.8 Consensus size: 12
1470608 AAAGACTCAT
1470618 ATTTAAA-TAATA
1 ATTTAAATTAA-A
*
1470630 CATTTAAATTATTA
1 -ATTTAAATTA-AA
1470644 A-TTAAATT-AA
1 ATTTAAATTAAA
1470654 A-TTAAATTAAA
1 ATTTAAATTAAA
1470665 ATTTAAATCTAAA
1 ATTTAAAT-TAAA
*
1470678 TTTTAAATT
1 ATTTAAATT
1470687 TTTTCAGCTA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
10 9 0.19
11 3 0.06
12 14 0.29
13 19 0.40
14 3 0.06
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (12 bp):
ATTTAAATTAAA
Found at i:1470987 original size:6 final size:6
Alignment explanation
Indices: 1470930--1471020 Score: 64
Period size: 6 Copynumber: 15.3 Consensus size: 6
1470920 GTTACTCACG
* * * *
1470930 ATTTTT ATTTTT ATTTA- A-TTAT ATTTA- ATTTAT ATATAT ATTTTT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT
** *
1470975 AAATAT ATTTAT ATTTTAT ATTTAAT ATTTAT -TTTAAA ATTTAT AT
1 ATTTAT ATTTAT A-TTTAT ATTT-AT ATTTAT ATTT-AT ATTTAT AT
1471021 AAAATATTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
4 3 0.04
5 10 0.15
6 39 0.58
7 15 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTAT
Found at i:1470996 original size:13 final size:14
Alignment explanation
Indices: 1470978--1471035 Score: 52
Period size: 13 Copynumber: 4.4 Consensus size: 14
1470968 TATTTTTAAA
1470978 TATATTT-ATATTT
1 TATATTTAATATTT
1470991 TATATTTAATA-TT
1 TATATTTAATATTT
*
1471004 TAT-TTTAA-AATT
1 TATATTTAATATTT
**
1471016 TATATAAAATATTTT
1 TATATTTAATA-TTT
1471031 TATAT
1 TATAT
1471036 CAAATTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
11 1 0.03
12 10 0.27
13 15 0.41
14 4 0.11
15 7 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATATTTAATATTT
Found at i:1471020 original size:18 final size:18
Alignment explanation
Indices: 1470933--1471020 Score: 64
Period size: 19 Copynumber: 5.1 Consensus size: 18
1470923 ACTCACGATT
1470933 TTTATTTTT--ATTTA-A
1 TTTATTTTTAAATTTATA
*
1470948 -TTATATTT-AATTTATA
1 TTTATTTTTAAATTTATA
1470964 TATATATTTTTAAA--TATA
1 T-T-TATTTTTAAATTTATA
*
1470982 TTTATATTTTATATTTAATA
1 TTTAT-TTTTAAATTT-ATA
*
1471002 TTTATTTTAAAATTTATA
1 TTTATTTTTAAATTTATA
1471020 T
1 T
1471021 AAAATATTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
14 7 0.12
15 5 0.09
16 4 0.07
17 7 0.12
18 10 0.17
19 15 0.26
20 10 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTATTTTTAAATTTATA
Found at i:1471241 original size:24 final size:23
Alignment explanation
Indices: 1471208--1471288 Score: 74
Period size: 24 Copynumber: 3.5 Consensus size: 23
1471198 AAAAAATTAA
*
1471208 AAAATTTATTTTTATTATTTTTT
1 AAAATATATTTTTATTATTTTTT
* **
1471231 AAAAATATATTTTT-TTAATTAAT
1 -AAAATATATTTTTATTATTTTTT
* * *
1471254 AAAATTTATAATTTATAATTTTTT
1 AAAATATAT-TTTTATTATTTTTT
1471278 AAAATATATTT
1 AAAATATATTT
1471289 AAAAATTATC
Statistics
Matches: 43, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
22 8 0.19
23 10 0.23
24 25 0.58
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
AAAATATATTTTTATTATTTTTT
Found at i:1471276 original size:46 final size:45
Alignment explanation
Indices: 1471202--1471288 Score: 122
Period size: 46 Copynumber: 1.9 Consensus size: 45
1471192 ATTAATAAAA
* *
1471202 AATTAAAAAATTTATTTTTATTATTTTTTAAAAATATATTTTTTT
1 AATTAAAAAATTTATATTTATTAATTTTTAAAAATATATTTTTTT
*
1471247 AATTAATAAAATTTATAATTTA-TAATTTTTTAAAATATATTT
1 AATTAA-AAAATTTAT-ATTTATTAATTTTTAAAAATATATTT
1471289 AAAAATTATC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
45 6 0.16
46 27 0.73
47 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (45 bp):
AATTAAAAAATTTATATTTATTAATTTTTAAAAATATATTTTTTT
Found at i:1471594 original size:2 final size:2
Alignment explanation
Indices: 1471587--1471611 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1471577 CCTTTTTCCC
1471587 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
1471612 CAACACATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1472472 original size:3 final size:3
Alignment explanation
Indices: 1472464--1472499 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1472454 AGTCGGTTAC
1472464 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1472500 GGAGTTCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1473644 original size:111 final size:111
Alignment explanation
Indices: 1473446--1473667 Score: 365
Period size: 111 Copynumber: 2.0 Consensus size: 111
1473436 AATTAGCACC
* *
1473446 GCCTTAGAGAAGCCTATCTTGACTCCACCACCGCCGCCACCACTTCCACCTCCGCCAGCTCCAAA
1 GCCTTAGAGAAGCCTATCTTGACTCCACAACCGCCGCCACCACCTCCACCTCCGCCAGCTCCAAA
* *
1473511 GCAACGACGACTTTGGGAAAAACCTTTTTCATCGGTATCTTTTGCG
66 GCAACGACGACTCTGGGAAAAACCTGTTTCATCGGTATCTTTTGCG
1473557 GCCTTAGAGAAGCCTATCTTGACTCCACAACCGCCGCCACCACCTCCACCTCCGCCAGCTCCAAA
1 GCCTTAGAGAAGCCTATCTTGACTCCACAACCGCCGCCACCACCTCCACCTCCGCCAGCTCCAAA
* * *
1473622 GCAACGACCG-CTCTGGGGAAAACCTGTTTCATCGTTGTCTTTTGCG
66 GCAACGA-CGACTCTGGGAAAAACCTGTTTCATCGGTATCTTTTGCG
1473668 CAACAGATAT
Statistics
Matches: 103, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
111 101 0.98
112 2 0.02
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (111 bp):
GCCTTAGAGAAGCCTATCTTGACTCCACAACCGCCGCCACCACCTCCACCTCCGCCAGCTCCAAA
GCAACGACGACTCTGGGAAAAACCTGTTTCATCGGTATCTTTTGCG
Found at i:1475314 original size:26 final size:26
Alignment explanation
Indices: 1475295--1475347 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1475285 CAATGCTTCT
1475295 TTCCAGGGAATAGTGTCAATGCAAAA
1 TTCCAGGGAATAGTGTCAATGCAAAA
1475321 TTCCAGGGAATAGTGTCAATGCAAAA
1 TTCCAGGGAATAGTGTCAATGCAAAA
1475347 T
1 T
1475348 CCCATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.25
Consensus pattern (26 bp):
TTCCAGGGAATAGTGTCAATGCAAAA
Found at i:1476330 original size:15 final size:14
Alignment explanation
Indices: 1476310--1476358 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
1476300 CTTTGTAATC
*
1476310 TATTTTGTTTTATTA
1 TATTTTATTTT-TTA
1476325 TATTTTATTTTTTA
1 TATTTTATTTTTTA
* *
1476339 TTTTCTTATTTTTGA
1 TATT-TTATTTTTTA
1476354 TATTT
1 TATTT
1476359 GTATAAATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 7 0.24
15 22 0.76
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (14 bp):
TATTTTATTTTTTA
Found at i:1482582 original size:2 final size:2
Alignment explanation
Indices: 1482571--1482607 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1482561 GCCTACTTTT
1482571 TA TA TA -A 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
1482608 AGGTGTAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1483420 original size:34 final size:32
Alignment explanation
Indices: 1483361--1483437 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 32
1483351 TTTATATTTA
1483361 AAAATAATTTTATATTAATAAAAATTAAAATT
1 AAAATAATTTTATATTAATAAAAATTAAAATT
* * *
1483393 AAAATTA-TTTATA-TAAT--TAATTTAAATT
1 AAAATAATTTTATATTAATAAAAATTAAAATT
*
1483421 AAAA-AATTTTAAATTAA
1 AAAATAATTTTATATTAA
1483438 AAGTTCATAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 1 0.03
28 18 0.47
29 3 0.08
30 4 0.11
31 6 0.16
32 6 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
AAAATAATTTTATATTAATAAAAATTAAAATT
Found at i:1488277 original size:50 final size:54
Alignment explanation
Indices: 1488190--1488292 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 54
1488180 ATGTAAAAAT
*
1488190 TTAAATTATAATATTAAAATTTAAAAAATTATAAATTTATTGTGAATTAATTAAA
1 TTAAATTATAATATTAAAATTT-AAAAATTATAAATTTATTATGAATTAATTAAA
*
1488245 TTAAATT-T-ATATTAAAATTT-AAAATT-TAAATTTATTATGACTTAATTA
1 TTAAATTATAATATTAAAATTTAAAAATTATAAATTTATTATGAATTAATTA
1488293 CATACCATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
50 20 0.43
51 6 0.13
53 12 0.26
54 1 0.02
55 7 0.15
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.47
Consensus pattern (54 bp):
TTAAATTATAATATTAAAATTTAAAAATTATAAATTTATTATGAATTAATTAAA
Found at i:1488701 original size:27 final size:27
Alignment explanation
Indices: 1488637--1488695 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
1488627 TTTTTATATA
*
1488637 AATATATTTATTTTTTAAAAAAATTATT
1 AATATAATT-TTTTTTAAAAAAATTATT
* * *
1488665 TATTTAATTTTTTTTAAAAGAATTATT
1 AATATAATTTTTTTTAAAAAAATTATT
1488692 AATA
1 AATA
1488696 ATATTTATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
27 19 0.76
28 6 0.24
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
AATATAATTTTTTTTAAAAAAATTATT
Found at i:1493224 original size:2 final size:2
Alignment explanation
Indices: 1493214--1493249 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1493204 ATATTCACAC
*
1493214 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1493250 CTTAAATTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1495565 original size:32 final size:33
Alignment explanation
Indices: 1495504--1495584 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 33
1495494 ACGAATTAAA
1495504 ATATAATATAAATATATGAATATCATAAAATTT
1 ATATAATATAAATATATGAATATCATAAAATTT
*
1495537 ATATAATATAAAT-TATTAATAT-ATTAAAATTT
1 ATATAATATAAATATATGAATATCA-TAAAATTT
1495569 ATATAAATATAAATAT
1 ATAT-AATATAAATAT
1495585 TTTAAATGCG
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
31 1 0.02
32 20 0.45
33 22 0.50
34 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (33 bp):
ATATAATATAAATATATGAATATCATAAAATTT
Found at i:1495586 original size:18 final size:17
Alignment explanation
Indices: 1495528--1495586 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
1495518 TATGAATATC
1495528 ATAAAATTTATAT-AAT
1 ATAAAATTTATATAAAT
1495544 AT-AAA-TTAT-TAATAT
1 ATAAAATTTATATAA-AT
1495559 ATTAAAATTTATATAAAT
1 A-TAAAATTTATATAAAT
1495577 ATAAATATTT
1 ATAAA-ATTT
1495587 TAAATGCGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.14
15 6 0.17
16 3 0.08
17 7 0.19
18 11 0.31
19 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATAAAATTTATATAAAT
Found at i:1495665 original size:2 final size:2
Alignment explanation
Indices: 1495652--1495682 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1495642 CTTAAATACC
*
1495652 AT AT AC 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 A
1495683 ATTGATAACA
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:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1495708 original size:24 final size:25
Alignment explanation
Indices: 1495671--1495721 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
1495661 TATATATATA
1495671 TATATATATATAATTGATAACAAAT
1 TATATATATATAATTGATAACAAAT
*
1495696 TATAT-TATATAATTGATAACGAAT
1 TATATATATATAATTGATAACAAAT
1495720 TA
1 TA
1495722 ACTTTAAGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (25 bp):
TATATATATATAATTGATAACAAAT
Found at i:1499125 original size:17 final size:16
Alignment explanation
Indices: 1499105--1499157 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 16
1499095 ATTTATATGG
1499105 TAAAATAATTAATTTTA
1 TAAAATAA-TAATTTTA
* *
1499122 TAAATAAAATAATTTAA
1 TAAA-ATAATAATTTTA
*
1499139 TATAAATTATAATTTTA
1 TA-AAATAATAATTTTA
1499156 TA
1 TA
1499158 TTTAATCAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 24 0.83
18 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAATAATAATTTTA
Found at i:1499617 original size:17 final size:18
Alignment explanation
Indices: 1499584--1499628 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
1499574 TTATTTTAAA
*
1499584 ATATTAAAAATTATTTTT
1 ATATTAAATATTATTTTT
1499602 ATATTAAATA-TATTTTT
1 ATATTAAATATTATTTTT
1499619 ATAATTAAAT
1 AT-ATTAAAT
1499629 TTAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTAAATATTATTTTT
Found at i:1499628 original size:18 final size:16
Alignment explanation
Indices: 1499591--1499629 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 16
1499581 AAAATATTAA
1499591 AAATTATTTTTATATT
1 AAATTATTTTTATATT
1499607 AAATATATTTTTATAATT
1 AAAT-TATTTTTAT-ATT
1499625 AAATT
1 AAATT
1499630 TAAATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.19
17 10 0.48
18 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATTATTTTTATATT
Found at i:1499657 original size:20 final size:19
Alignment explanation
Indices: 1499628--1499673 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1499618 TATAATTAAA
1499628 TTTAAATAAAAATTTATTAT
1 TTTAAATAAAAA-TTATTAT
*
1499648 TTTAACTAAAAATTATTAT
1 TTTAAATAAAAATTATTAT
1499667 TTTAAAT
1 TTTAAAT
1499674 TACTATGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAAATAAAAATTATTAT
Found at i:1500319 original size:17 final size:19
Alignment explanation
Indices: 1500279--1500320 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1500269 AATTAAACAC
*
1500279 AATTAATATGATCTAATCA
1 AATTAATATGATCTAATAA
1500298 AATTAATATGA-CTAA-AA
1 AATTAATATGATCTAATAA
1500315 AATTAA
1 AATTAA
1500321 AATAATAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.32
18 4 0.18
19 11 0.50
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (19 bp):
AATTAATATGATCTAATAA
Found at i:1500473 original size:6 final size:6
Alignment explanation
Indices: 1500462--1500499 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
1500452 AACTTAAAAA
*
1500462 AAATTT AAATTTT AAA-TT AAATTT AAATTT AATTTT AA
1 AAATTT AAA-TTT AAATTT AAATTT AAATTT AAATTT AA
1500500 TTGATTTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 5 0.17
6 18 0.62
7 6 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:1500476 original size:18 final size:18
Alignment explanation
Indices: 1500455--1500491 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1500445 AAGTCAAAAC
1500455 TTAAAAAAAATTTAAATT
1 TTAAAAAAAATTTAAATT
**
1500473 TTAAATTAAATTTAAATT
1 TTAAAAAAAATTTAAATT
1500491 T
1 T
1500492 AATTTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAAAAAAATTTAAATT
Found at i:1500483 original size:12 final size:12
Alignment explanation
Indices: 1500466--1500499 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1500456 TAAAAAAAAT
1500466 TTAAATTTTAAA
1 TTAAATTTTAAA
1500478 TTAAA-TTTAAA
1 TTAAATTTTAAA
*
1500489 TTTAATTTTAA
1 TTAAATTTTAA
1500500 TTGATTTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAATTTTAAA
Found at i:1500988 original size:4 final size:4
Alignment explanation
Indices: 1500979--1501013 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
1500969 TCGATAATCT
1500979 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1501014 TAAATACCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1515167 original size:32 final size:31
Alignment explanation
Indices: 1515069--1515182 Score: 113
Period size: 33 Copynumber: 3.5 Consensus size: 31
1515059 TAAGATAAAA
* * *
1515069 ATATTAAAAGAAATATATTTTTTATTTTAATT
1 ATATTAAAAAAAAT-TAATTTTTAATTTAATT
*
1515101 ATATTAAAAATAAATTTTATTTTTAATTTAATT
1 ATATTAAAAA-AAA-TTAATTTTTAATTTAATT
*
1515134 ATCTTAAAAAAAATTAATTTTTAAAATTT-ATT
1 ATATTAAAAAAAATTAATTTTT--AATTTAATT
*
1515166 ATTTTAAAAAATAATTA
1 ATATTAAAAAA-AATTA
1515183 TTAATCTTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
31 8 0.11
32 25 0.36
33 36 0.51
34 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (31 bp):
ATATTAAAAAAAATTAATTTTTAATTTAATT
Found at i:1515182 original size:16 final size:16
Alignment explanation
Indices: 1515129--1515184 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
1515119 ATTTTTAATT
*
1515129 TAATTATCTTAAAAAA
1 TAATTATTTTAAAAAA
* *
1515145 -AATTAATTTTTAAAAT
1 TAATT-ATTTTAAAAAA
*
1515161 TTATTATTTTAAAAAA
1 TAATTATTTTAAAAAA
1515177 TAATTATT
1 TAATTATT
1515185 AATCTTTTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
15 4 0.13
16 24 0.77
17 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTATTTTAAAAAA
Found at i:1515438 original size:13 final size:13
Alignment explanation
Indices: 1515420--1515445 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1515410 TTAAGCGTTC
1515420 ATTAATTTTTTTA
1 ATTAATTTTTTTA
1515433 ATTAATTTTTTTA
1 ATTAATTTTTTTA
1515446 TGAAATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTAATTTTTTTA
Found at i:1521597 original size:14 final size:15
Alignment explanation
Indices: 1521578--1521616 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
1521568 AGTTTTATAT
*
1521578 ATTAATTTTGA-TTG
1 ATTAATTTAGATTTG
1521592 ATTAATTTAGATTTG
1 ATTAATTTAGATTTG
1521607 ATTATATTTA
1 ATTA-ATTTA
1521617 AAATATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
15 7 0.32
16 5 0.23
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (15 bp):
ATTAATTTAGATTTG
Found at i:1524094 original size:16 final size:16
Alignment explanation
Indices: 1524073--1524106 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1524063 TGGTAGTATA
1524073 TTTCACACGTGGATTT
1 TTTCACACGTGGATTT
1524089 TTTCACACGTGGATTT
1 TTTCACACGTGGATTT
1524105 TT
1 TT
1524107 GAGCTAGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (16 bp):
TTTCACACGTGGATTT
Found at i:1525324 original size:17 final size:17
Alignment explanation
Indices: 1525305--1525338 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
1525295 AATATTTCAT
1525305 AAATGATTAAATATATTA
1 AAAT-ATTAAATATATTA
1525323 AAATATTAAATATATT
1 AAATATTAAATATATT
1525339 GTATCGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
AAATATTAAATATATTA
Found at i:1525328 original size:8 final size:9
Alignment explanation
Indices: 1525310--1525338 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1525300 TTCATAAATG
1525310 ATTAAATAT
1 ATTAAATAT
1525319 ATTAAA-AT
1 ATTAAATAT
1525327 ATTAAATAT
1 ATTAAATAT
1525336 ATT
1 ATT
1525339 GTATCGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
ATTAAATAT
Found at i:1529708 original size:2 final size:2
Alignment explanation
Indices: 1529703--1529736 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1529693 TGTGTAAAAA
1529703 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
1529737 CAGCTTCTGT
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:1531935 original size:17 final size:18
Alignment explanation
Indices: 1531894--1531935 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1531884 ATTAATATTC
*
1531894 ATTATTTATCATTTCAAA
1 ATTATTTTTCATTTCAAA
*
1531912 ATT-TTTTTCATTT-ATA
1 ATTATTTTTCATTTCAAA
1531928 ATTATTTT
1 ATTATTTT
1531936 ATAAAATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 13 0.62
18 3 0.14
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTATTTTTCATTTCAAA
Found at i:1532698 original size:18 final size:17
Alignment explanation
Indices: 1532648--1532761 Score: 69
Period size: 17 Copynumber: 6.5 Consensus size: 17
1532638 AAATAATATA
* *
1532648 ATATAAATATATATTTT
1 ATATAAATATAAAATTT
1532665 ATAT-AATAT-AAA-TT
1 ATATAAATATAAAATTT
1532679 AT-TAATATAGTAAAATTT
1 ATATAA-ATA-TAAAATTT
1532697 ATATAAATATAAAATATT
1 ATATAAATATAAAAT-TT
* *
1532715 -T-TAAATATAATTATAAT
1 ATATAAATATAA-AAT-TT
1532732 ATAATAAAATATATAAATATT
1 AT-AT-AAATATA-AAAT-TT
1532753 ATATAAATA
1 ATATAAATA
1532762 CACAAATTGT
Statistics
Matches: 78, Mismatches: 6, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
13 1 0.01
14 5 0.06
15 4 0.05
16 15 0.19
17 18 0.23
18 10 0.13
19 8 0.10
20 3 0.04
21 13 0.17
22 1 0.01
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (17 bp):
ATATAAATATAAAATTT
Found at i:1532707 original size:47 final size:43
Alignment explanation
Indices: 1532625--1532756 Score: 112
Period size: 49 Copynumber: 3.0 Consensus size: 43
1532615 ACAATATAAA
*
1532625 TAAA-ATAATTA-AA-A-AATAATATAATATAAATAT-ATATTTT
1 TAAATATAATTATAATATAATAAAAT-ATATAAATATAATA-TTT
*
1532665 ATATAATATAAATTATTAATATAGTAAAATTTATATAAATATAAAATATTT
1 -TA-AATAT-AATTA-TAATATAATAAAA--TATATAAATAT--AATATTT
*
1532716 TAAATATAATTATAATATAATAAAATATATAAATATTATAT
1 TAAATATAATTATAATATAATAAAATATATAAATATAATAT
1532757 AAATACACAA
Statistics
Matches: 75, Mismatches: 4, Indels: 22
0.74 0.04 0.22
Matches are distributed among these distances:
41 2 0.03
42 2 0.03
43 6 0.08
44 5 0.07
45 11 0.15
46 2 0.03
47 13 0.17
48 10 0.13
49 15 0.20
50 3 0.04
51 3 0.04
52 3 0.04
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.42
Consensus pattern (43 bp):
TAAATATAATTATAATATAATAAAATATATAAATATAATATTT
Found at i:1532717 original size:20 final size:18
Alignment explanation
Indices: 1532642--1532761 Score: 85
Period size: 16 Copynumber: 6.8 Consensus size: 18
1532632 ATTAAAAAAT
*
1532642 AATATAATATAAATAT-A
1 AATATTATATAAATATAA
* *
1532659 TATTTTATAT-AATATAA
1 AATATTATATAAATATAA
*
1532676 ATTATTA-AT--ATAGTAA
1 AATATTATATAAATA-TAA
1532692 AAT-TTATATAAATATAA
1 AATATTATATAAATATAA
1532709 AATATT-T-TAAATATAA
1 AATATTATATAAATATAA
* *
1532725 TTATAATATAATAAAATATATA
1 -AATATTAT-AT-AAATATA-A
1532747 AATATTATATAAATA
1 AATATTATATAAATA
1532762 CACAAATTGT
Statistics
Matches: 80, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
15 6 0.08
16 23 0.29
17 23 0.29
18 6 0.08
19 5 0.06
20 3 0.04
21 13 0.16
22 1 0.01
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (18 bp):
AATATTATATAAATATAA
Found at i:1532737 original size:16 final size:16
Alignment explanation
Indices: 1532619--1532758 Score: 64
Period size: 16 Copynumber: 8.9 Consensus size: 16
1532609 ATGAATACAA
*
1532619 TATAA-ATAAAATAAT
1 TATAATATAATATAAT
* *
1532634 TAAAAAATAATATAA-
1 TATAATATAATATAAT
1532649 TATAA-AT-ATAT-AT
1 TATAATATAATATAAT
*
1532662 T-TTATATAATATAAAT
1 TATAATATAATAT-AAT
* *
1532678 TATTAATATAGTAAAAT
1 TA-TAATATAATATAAT
1532695 T-T-ATATAAATATAA-
1 TATAATAT-AATATAAT
* * *
1532709 AATATTTTAAATATAAT
1 TATAATAT-AATATAAT
*
1532726 TATAATATAATAAAAT
1 TATAATATAATATAAT
*
1532742 ATATAAATATTATATAA
1 -TAT-AATATAATATAA
1532759 ATACACAAAT
Statistics
Matches: 93, Mismatches: 18, Indels: 25
0.68 0.13 0.18
Matches are distributed among these distances:
12 3 0.03
13 7 0.08
14 10 0.11
15 15 0.16
16 28 0.30
17 12 0.13
18 18 0.19
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.41
Consensus pattern (16 bp):
TATAATATAATATAAT
Found at i:1535784 original size:2 final size:2
Alignment explanation
Indices: 1535777--1535823 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1535767 GCTTGTCAAG
1535777 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
1535819 AT AT A
1 AT AT A
1535824 ACCTCTCCCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1536042 original size:2 final size:2
Alignment explanation
Indices: 1536035--1536070 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1536025 GGGAGTATTT
1536035 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
1536071 GATTAGAAAT
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:1536110 original size:27 final size:27
Alignment explanation
Indices: 1536068--1536125 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
1536058 ATATATATAT
1536068 ATAGATTAGAAATTAAAAATTAATTAA
1 ATAGATTAGAAATTAAAAATTAATTAA
* *
1536095 ATAGTTTAGAAGTTAAAAATTAATTAA
1 ATAGATTAGAAATTAAAAATTAATTAA
1536122 ATAG
1 ATAG
1536126 GTTGGAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.34
Consensus pattern (27 bp):
ATAGATTAGAAATTAAAAATTAATTAA
Found at i:1536144 original size:27 final size:27
Alignment explanation
Indices: 1536068--1536138 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
1536058 ATATATATAT
* *
1536068 ATAGATTAGAAATTAAAAATTAATTAA
1 ATAGGTTAGAAGTTAAAAATTAATTAA
*
1536095 ATAGTTTAGAAGTTAAAAATTAATTAA
1 ATAGGTTAGAAGTTAAAAATTAATTAA
* *
1536122 ATAGGTTGGAATTTAAA
1 ATAGGTTAGAAGTTAAA
1536139 TTTTAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (27 bp):
ATAGGTTAGAAGTTAAAAATTAATTAA
Found at i:1537004 original size:5 final size:5
Alignment explanation
Indices: 1536994--1537023 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
1536984 AAAGACATAA
1536994 TTATT TTATT TTATT TTATTT TTATT TTAT
1 TTATT TTATT TTATT TTA-TT TTATT TTAT
1537024 AATTTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:1537018 original size:11 final size:11
Alignment explanation
Indices: 1536994--1537023 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1536984 AAAGACATAA
1536994 TTATTTTA-TT
1 TTATTTTATTT
1537004 TTATTTTATTT
1 TTATTTTATTT
1537015 TTATTTTAT
1 TTATTTTAT
1537024 AATTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TTATTTTATTT
Found at i:1537928 original size:16 final size:16
Alignment explanation
Indices: 1537909--1537939 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1537899 CACAATACTA
1537909 AAAAATA-ATATTATT
1 AAAAATATATATTATT
1537924 AAAAATATATATTATT
1 AAAAATATATATTATT
1537940 TTAAGAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAAATATATATTATT
Found at i:1540644 original size:17 final size:17
Alignment explanation
Indices: 1540624--1540657 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1540614 TAAATAGAAA
1540624 GAAAAAGGAAAAAGATT
1 GAAAAAGGAAAAAGATT
1540641 GAAAAAGGAAAAAGATT
1 GAAAAAGGAAAAAGATT
1540658 AAAGAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.12
Consensus pattern (17 bp):
GAAAAAGGAAAAAGATT
Found at i:1542967 original size:67 final size:67
Alignment explanation
Indices: 1542859--1542994 Score: 272
Period size: 67 Copynumber: 2.0 Consensus size: 67
1542849 GCAAACAGAA
1542859 AAATTAGGTTTGGTTTAGGTAAGCCCCAAATCTTTATACTCCATAATTCAGCCTGATAGAACGTG
1 AAATTAGGTTTGGTTTAGGTAAGCCCCAAATCTTTATACTCCATAATTCAGCCTGATAGAACGTG
1542924 AG
66 AG
1542926 AAATTAGGTTTGGTTTAGGTAAGCCCCAAATCTTTATACTCCATAATTCAGCCTGATAGAACGTG
1 AAATTAGGTTTGGTTTAGGTAAGCCCCAAATCTTTATACTCCATAATTCAGCCTGATAGAACGTG
1542991 AG
66 AG
1542993 AA
1 AA
1542995 GGTTCTAAGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (67 bp):
AAATTAGGTTTGGTTTAGGTAAGCCCCAAATCTTTATACTCCATAATTCAGCCTGATAGAACGTG
AG
Found at i:1547578 original size:15 final size:15
Alignment explanation
Indices: 1547554--1547599 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1547544 TTTTAATACG
1547554 TTTA-TATATTATTT
1 TTTATTATATTATTT
*
1547568 TTTATTATATT-TAT
1 TTTATTATATTATTT
*
1547582 ATTATTTATATTATTT
1 TTTA-TTATATTATTT
1547598 TT
1 TT
1547600 ATCATATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 9 0.36
15 13 0.52
16 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTATATTATTT
Found at i:1547580 original size:23 final size:22
Alignment explanation
Indices: 1547554--1547607 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
1547544 TTTTAATACG
*
1547554 TTTATATATTATTTTTTATTATA
1 TTTATATATTA-TTTATATTATA
*
1547577 -TT-TATATTATTTATATTATT
1 TTTATATATTATTTATATTATA
1547597 TTTATCATATT
1 TTTAT-ATATT
1547608 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 9 0.35
21 9 0.35
22 3 0.12
23 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTATATATTATTTATATTATA
Found at i:1547608 original size:20 final size:20
Alignment explanation
Indices: 1547558--1547601 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1547548 AATACGTTTA
*
1547558 TATATTATTTTTTATTATATT
1 TATATTA-TTTATATTATATT
*
1547579 TATATTATTTATATTATTTT
1 TATATTATTTATATTATATT
1547599 TAT
1 TAT
1547602 CATATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TATATTATTTATATTATATT
Found at i:1553890 original size:62 final size:62
Alignment explanation
Indices: 1553793--1553929 Score: 206
Period size: 62 Copynumber: 2.2 Consensus size: 62
1553783 AATCCAAATT
* * * *
1553793 TATATT-TAATAATTAAATGTAAATAAAACATAAATATTAATATA-TACATAATTTTTAAAT
1 TATATTATAATTATTAAATATAAATAAAACATAAATATTAATATATTAAATAATTTTTAAAA
*
1553853 TATTTTATAATTATTAATATATAAATAAAACATAAATATTAATATATTAAATAATTTTTAAAA
1 TATATTATAATTATTAA-ATATAAATAAAACATAAATATTAATATATTAAATAATTTTTAAAA
1553916 TATATTATAATTAT
1 TATATTATAATTAT
1553930 AAACAATAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
60 5 0.07
61 9 0.13
62 27 0.40
63 27 0.40
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.45
Consensus pattern (62 bp):
TATATTATAATTATTAAATATAAATAAAACATAAATATTAATATATTAAATAATTTTTAAAA
Found at i:1554642 original size:43 final size:45
Alignment explanation
Indices: 1554594--1554682 Score: 114
Period size: 45 Copynumber: 2.0 Consensus size: 45
1554584 TATTTTTATG
1554594 TAATAAAAGTATATT-TA-AAATATTATATATT-TTA-TTAATATAA
1 TAATAAAAGTATATTATATAAATATTA-AT-TTATTATTTAATATAA
* *
1554637 TAATAAAATTATATTATATAAATTTTAATTTATTATTTAATATAA
1 TAATAAAAGTATATTATATAAATATTAATTTATTATTTAATATAA
1554682 T
1 T
1554683 CATATTATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
43 16 0.40
44 7 0.17
45 17 0.43
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (45 bp):
TAATAAAAGTATATTATATAAATATTAATTTATTATTTAATATAA
Found at i:1554803 original size:20 final size:19
Alignment explanation
Indices: 1554778--1554844 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 19
1554768 ATTATAAAAT
1554778 AAAAATTTTAAAAATCGATA
1 AAAAATTTTAAAAATC-ATA
*
1554798 AAAAATTAATT-AAATTCATA
1 AAAAATT--TTAAAAATCATA
*
1554818 AAAAATATTATAAAAATTA-A
1 AAAAAT-TT-TAAAAATCATA
1554838 AAAAATT
1 AAAAATT
1554845 AAATTTAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
19 2 0.05
20 24 0.62
21 11 0.28
22 2 0.05
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (19 bp):
AAAAATTTTAAAAATCATA
Found at i:1555011 original size:22 final size:22
Alignment explanation
Indices: 1554979--1555030 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
1554969 TAAAAATTTT
**
1554979 AATTAACTTAACTTAATTTAATA
1 AATTAA-TTAACCAAATTTAATA
* *
1555002 ATTTAATTAACCAAATTTATTA
1 AATTAATTAACCAAATTTAATA
1555024 AATTAAT
1 AATTAAT
1555031 AATTCAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTAATTAACCAAATTTAATA
Found at i:1555806 original size:21 final size:22
Alignment explanation
Indices: 1555751--1555806 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
1555741 TTTTATTCAA
* *
1555751 TTATTTCATGTAAAATATTATT
1 TTATTTAATGAAAAATATTATT
*
1555773 TAATTTAAT-AAAAATAATT-TT
1 TTATTTAATGAAAAAT-ATTATT
1555794 TTATTT-ATGAAAA
1 TTATTTAATGAAAA
1555807 TTTTACAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 2 0.07
21 16 0.57
22 10 0.36
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (22 bp):
TTATTTAATGAAAAATATTATT
Found at i:1555955 original size:17 final size:19
Alignment explanation
Indices: 1555921--1555964 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
1555911 TTATACTCTA
1555921 AAATTATTTTATTAATATT
1 AAATTATTTTATTAATATT
1555940 AAATT-TTTTATT-ATATT
1 AAATTATTTTATTAATATT
1555957 AATATTAT
1 AA-ATTAT
1555965 AAATTAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 7 0.30
18 10 0.43
19 6 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AAATTATTTTATTAATATT
Found at i:1555982 original size:15 final size:16
Alignment explanation
Indices: 1555962--1555994 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1555952 ATATTAATAT
1555962 TATAAA-TTAATCAAA
1 TATAAATTTAATCAAA
*
1555977 TATAAATTTAATTAAA
1 TATAAATTTAATCAAA
1555993 TA
1 TA
1555995 AATTATTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TATAAATTTAATCAAA
Found at i:1556012 original size:21 final size:21
Alignment explanation
Indices: 1555988--1556039 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1555978 ATAAATTTAA
* * *
1555988 TTAAATAAATTATTTACAAAC
1 TTAAAAAAATTAATTAAAAAC
1556009 TTAAAAAAATTAATTAAAAAC
1 TTAAAAAAATTAATTAAAAAC
*
1556030 TTAAACAAAT
1 TTAAAAAAAT
1556040 AATATTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.33
Consensus pattern (21 bp):
TTAAAAAAATTAATTAAAAAC
Found at i:1556018 original size:25 final size:23
Alignment explanation
Indices: 1555990--1556051 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 23
1555980 AAATTTAATT
1555990 AAATAAATTATTTACAAACTTAAAA
1 AAATAAATTA-TTA-AAACTTAAAA
* *
1556015 AAATTAATTA--AAAACTTAAAC
1 AAATAAATTATTAAAACTTAAAA
1556036 AAATAATATTATTAAA
1 AAATAA-ATTATTAAA
1556052 GTATTTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 14 0.45
22 5 0.16
24 3 0.10
25 9 0.29
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATAAATTATTAAAACTTAAAA
Found at i:1556883 original size:10 final size:11
Alignment explanation
Indices: 1556858--1556883 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1556848 TTCCACCATT
1556858 TTTTTCCCTTA
1 TTTTTCCCTTA
1556869 TTTTTCCCTTA
1 TTTTTCCCTTA
1556880 TTTT
1 TTTT
1556884 ATATGGCCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTCCCTTA
Found at i:1558860 original size:20 final size:20
Alignment explanation
Indices: 1558808--1558862 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 20
1558798 CTATGCTGTC
1558808 ATTTTTTTTATTAATTAATT
1 ATTTTTTTTATTAATTAATT
1558828 ATTGTTATTTTTTATTAATTAATT
1 A---TT-TTTTTTATTAATTAATT
1558852 ATTTCTTTTTA
1 ATTT-TTTTTA
1558863 AATATGTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
20 2 0.07
21 8 0.27
23 2 0.07
24 18 0.60
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
ATTTTTTTTATTAATTAATT
Found at i:1562498 original size:21 final size:21
Alignment explanation
Indices: 1562464--1562503 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1562454 TATTACTAAT
*
1562464 AAAAAAATATAGTATAATATC
1 AAAAAAATATAGTAAAATATC
1562485 AAAATAAATA-AGTAAAATA
1 AAAA-AAATATAGTAAAATA
1562504 CCAATTGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (21 bp):
AAAAAAATATAGTAAAATATC
Found at i:1562817 original size:15 final size:17
Alignment explanation
Indices: 1562788--1562821 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1562778 ATAATTTTGA
1562788 TAATATATAATAATATT
1 TAATATATAATAATATT
1562805 TAATAT-TAA-AATATT
1 TAATATATAATAATATT
1562820 TA
1 TA
1562822 TAATTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 3 0.18
17 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATATAATAATATT
Found at i:1563079 original size:14 final size:15
Alignment explanation
Indices: 1563060--1563100 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
1563050 AAAAAAAGAG
1563060 TAAATTTTTAAAT-T
1 TAAATTTTTAAATAT
1563074 TAAATTTATTAAATAT
1 TAAATTT-TTAAATAT
*
1563090 T-ATTTTTTAAA
1 TAAATTTTTAAA
1563101 AATAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.50
15 10 0.42
16 2 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAAATTTTTAAATAT
Found at i:1564794 original size:30 final size:29
Alignment explanation
Indices: 1564760--1564816 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1564750 AAATATTTTT
*
1564760 ATATTAATATTTATAATTAAATTTTAAAAA
1 ATATTAATATTTA-AATGAAATTTTAAAAA
** *
1564790 ATATTTTTATTTAAATGATATTTTAAA
1 ATATTAATATTTAAATGAAATTTTAAA
1564817 TTAATTTAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 12 0.52
30 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (29 bp):
ATATTAATATTTAAATGAAATTTTAAAAA
Found at i:1565471 original size:2 final size:2
Alignment explanation
Indices: 1565450--1565487 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1565440 TAAGAAAAGC
*
1565450 AT AT AT -T AT AT -T AT AA 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
1565488 TTTACTATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1566905 original size:38 final size:38
Alignment explanation
Indices: 1566862--1566948 Score: 165
Period size: 38 Copynumber: 2.3 Consensus size: 38
1566852 AAAATAATTG
1566862 AAATATAAATATGATATAATATAAGAAATGTATTTAAA
1 AAATATAAATATGATATAATATAAGAAATGTATTTAAA
1566900 AAATATAAATATGATATAATATAAGAAATGTATTTAAA
1 AAATATAAATATGATATAATATAAGAAATGTATTTAAA
*
1566938 AAATTTAAATA
1 AAATATAAATA
1566949 AATATATAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (38 bp):
AAATATAAATATGATATAATATAAGAAATGTATTTAAA
Found at i:1566971 original size:19 final size:20
Alignment explanation
Indices: 1566940--1566977 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
1566930 TATTTAAAAA
1566940 ATTTAAATAAATA-TATAAT
1 ATTTAAATAAATATTATAAT
1566959 ATTTAAA-ATAATATTATAA
1 ATTTAAATA-AATATTATAA
1566978 AACATAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.06
19 11 0.65
20 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTTAAATAAATATTATAAT
Found at i:1571377 original size:2 final size:2
Alignment explanation
Indices: 1571319--1571361 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
1571309 ATTTGAATGC
* * *
1571319 AT AT CT AT AT CT AT AT AT TT 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
1571361 A
1 A
1571362 ATTTCCATTC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1571706 original size:20 final size:20
Alignment explanation
Indices: 1571667--1571706 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1571657 TTATGATGGT
* *
1571667 TTTATATTTATAATTGAATA
1 TTTATAATTATAATTAAATA
*
1571687 TTTATAATTATTATTAAATA
1 TTTATAATTATAATTAAATA
1571707 CTTTTAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTATAATTATAATTAAATA
Found at i:1572040 original size:23 final size:21
Alignment explanation
Indices: 1572014--1572159 Score: 79
Period size: 22 Copynumber: 6.8 Consensus size: 21
1572004 GTATGACTTA
*
1572014 ATAATATGAAATATGGTATAAAT
1 ATAATAT-AAATAT-ATATAAAT
* *
1572037 ATAATATTAAAAATAAATATAAT
1 ATAATA-TAAATATATATA-AAT
*
1572060 ATAATAT-AATATAATATAAAA
1 ATAATATAAATAT-ATATAAAT
*
1572081 ATAATATAAATATTATATGAAT
1 ATAATATAAATA-TATATAAAT
* *
1572103 ATATTA-AAAT-TA-ATATGAT
1 ATAATATAAATATATATA-AAT
*
1572122 ATTAAATATAAATTTAT-TAAA-
1 A-T-AATATAAATATATATAAAT
*
1572143 ATTTATATAAATATATA
1 A-TAATATAAATATATA
1572160 ATATTTTAAA
Statistics
Matches: 96, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
18 2 0.02
19 5 0.05
20 12 0.12
21 23 0.24
22 28 0.29
23 25 0.26
24 1 0.01
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (21 bp):
ATAATATAAATATATATAAAT
Found at i:1572052 original size:18 final size:16
Alignment explanation
Indices: 1572034--1572089 Score: 78
Period size: 16 Copynumber: 3.4 Consensus size: 16
1572024 ATATGGTATA
1572034 AATATAATATTAAAAAT
1 AATATAATA-TAAAAAT
*
1572051 AAATATAATAT-AATAT
1 -AATATAATATAAAAAT
1572067 AATATAATATAAAAAT
1 AATATAATATAAAAAT
1572083 AATATAA
1 AATATAA
1572090 ATATTATATG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 10 0.29
16 15 0.43
17 1 0.03
18 9 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AATATAATATAAAAAT
Found at i:1572060 original size:5 final size:5
Alignment explanation
Indices: 1572034--1572123 Score: 71
Period size: 5 Copynumber: 18.0 Consensus size: 5
1572024 ATATGGTATA
*
1572034 AATAT AATATT AA-A- AATA- AATAT AATAT AATAT AATAT AATAT AAAAAT
1 AATAT AATA-T AATAT AATAT AATAT AATAT AATAT AATAT AATAT -AATAT
* * * *
1572083 AATAT AAATAT TATAT GAATAT ATTAA AAT-T AATAT GATAT
1 AATAT -AATAT AATAT -AATAT AATAT AATAT AATAT AATAT
1572124 TAAATATAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
3 2 0.03
4 8 0.12
5 43 0.62
6 16 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:1572076 original size:33 final size:33
Alignment explanation
Indices: 1572013--1572118 Score: 112
Period size: 32 Copynumber: 3.2 Consensus size: 33
1572003 CGTATGACTT
** *
1572013 AATAATATGAAATATGGTATAAATATAATATTAAA
1 AATAATAT-AAATATAATATGAATATAATA-TAAA
1572048 AATAA-ATATAATATAATAT-AATATAATATAAA
1 AATAATATA-AATATAATATGAATATAATATAAA
*
1572080 AATAATATAAATATTATATGAATAT-AT-TAAA
1 AATAATATAAATATAATATGAATATAATATAAA
*
1572111 ATTAATAT
1 AATAATAT
1572119 GATATTAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
31 11 0.17
32 20 0.31
33 18 0.28
34 10 0.16
35 5 0.08
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (33 bp):
AATAATATAAATATAATATGAATATAATATAAA
Found at i:1572082 original size:28 final size:28
Alignment explanation
Indices: 1572034--1572132 Score: 73
Period size: 28 Copynumber: 3.4 Consensus size: 28
1572024 ATATGGTATA
1572034 AATATAATATTAA-A-AATAAATATAATAT
1 AATATAATA-TAATATAA-AAATATAATAT
1572062 AATATAATATAATAT-AAAA-ATAATAT
1 AATATAATATAATATAAAAATATAATAT
*
1572088 AAATATTATATGAATATATTAAAAT-TAATAT
1 -AATATAATAT-AATATA--AAAATATAATAT
*
1572119 GATATTAAATATAA
1 AATA-T-AATATAA
1572133 ATTTATTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
26 7 0.12
27 15 0.26
28 16 0.28
30 3 0.05
31 13 0.22
32 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (28 bp):
AATATAATATAATATAAAAATATAATAT
Found at i:1572604 original size:2 final size:2
Alignment explanation
Indices: 1572597--1572626 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1572587 CTTAACCATG
1572597 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1572627 TATATATATA
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:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1572631 original size:2 final size:2
Alignment explanation
Indices: 1572626--1572654 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1572616 ACACACACAC
1572626 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1572655 CAGTAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1584653 original size:252 final size:249
Alignment explanation
Indices: 1584206--1584686 Score: 725
Period size: 252 Copynumber: 1.9 Consensus size: 249
1584196 CACCTAGATG
*
1584206 CAATGGTATTTCATAATAGGACCAAAAGATACAAGAAAACTTAGACCCCACAACAGGCATGAAAA
1 CAATGGTATTTCATAATAGGACCAAAAGATACAAGAAAACTTAGACCCCACAACAGACATGAAAA
* ** * *
1584271 GTAGCAAGACACCCTTGAGGAGATAAACCCACAAATGAGTTAGAGCACAACATTGCTTTGATTGA
66 CTAGCAAGACACCCTCAAGGAGATAAACCCAAAAATGAGTTAGAGCACAACATTGCCTTGATTGA
*
1584336 ATTGAAATAAGAGCAGAGGTTCATAGCATCACAAATCAAAATAACTATGGCCCAGTCCCGGGCAG
131 ATTGAAATAAGAACAGAGGTTCATAGCATCACAAATCAAAATAACTATGGCCCAGTCCCGGGCAG
1584401 CTCCAATTCTTACAGGTGTTCTAACATTAGATGTGTTCTAACAAATCAAAATCA
196 CTCCAATTCTTACAGGTGTTCTAACATTAGATGTGTTCTAACAAATCAAAATCA
* * * *
1584455 CAATGGTATTTCATAATATGACCAAAAGATGCAAGAAAACTTGGACCCCACAACAGACGTGAAAA
1 CAATGGTATTTCATAATAGGACCAAAAGATACAAGAAAACTTAGACCCCACAACAGACATGAAAA
* *
1584520 CTAGCAAGACA-CCTCAAGGGGATAATAACCCAAAAATGAGTTGTAGAGCGCAACATTGCCTTGA
66 CTAGCAAGACACCCTCAAGGAGAT-A-AACCCAAAAATGAG-T-TAGAGCACAACATTGCCTTGA
* * * *
1584584 TTGAATTGAAATGAGAACAGAGGTTCAT-GATATCACAAATC-AAATCCACTATGGCCCAGTCCT
127 TTGAATTGAAATAAGAACAGAGGTTCATAG-CATCACAAATCAAAAT-AACTATGGCCCAGTCCC
*
1584647 GGGCAGCTCCGATTCTTACAGGTGTTCTAACATTAGATGT
190 GGGCAGCTCCAATTCTTACAGGTGTTCTAACATTAGATGT
1584687 CTTCACTATT
Statistics
Matches: 208, Mismatches: 18, Indels: 9
0.89 0.08 0.04
Matches are distributed among these distances:
248 9 0.04
249 71 0.34
250 13 0.06
251 6 0.03
252 109 0.52
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (249 bp):
CAATGGTATTTCATAATAGGACCAAAAGATACAAGAAAACTTAGACCCCACAACAGACATGAAAA
CTAGCAAGACACCCTCAAGGAGATAAACCCAAAAATGAGTTAGAGCACAACATTGCCTTGATTGA
ATTGAAATAAGAACAGAGGTTCATAGCATCACAAATCAAAATAACTATGGCCCAGTCCCGGGCAG
CTCCAATTCTTACAGGTGTTCTAACATTAGATGTGTTCTAACAAATCAAAATCA
Found at i:1588072 original size:17 final size:16
Alignment explanation
Indices: 1588050--1588094 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
1588040 ATGTATATAT
1588050 TAATATAAAATAATTTA
1 TAATATAAAA-AATTTA
*
1588067 TAATATATTAAAATTTA
1 TAATATA-AAAAATTTA
1588084 T-ATATAAAAAA
1 TAATATAAAAAA
1588095 ATATATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 4 0.16
16 5 0.20
17 14 0.56
18 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATATAAAAAATTTA
Found at i:1588173 original size:15 final size:17
Alignment explanation
Indices: 1588160--1588208 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1588150 TTATTTATTT
1588160 TTATTAAAAATATTATA
1 TTATTAAAAATATTATA
* **
1588177 TTTTTAATTATATTATAA
1 TTATTAAAAATATTAT-A
*
1588195 TTATTAAAATTATT
1 TTATTAAAAATATT
1588209 TTAATTAAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTAAAAATATTATA
Found at i:1588189 original size:17 final size:17
Alignment explanation
Indices: 1588133--1588193 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 17
1588123 TCTACTTAAA
1588133 TAATTCATATTATATTTT
1 TAATT-ATATTATATTTT
*
1588151 T-ATT-TATT-T-TTAT
1 TAATTATATTATATTTT
**
1588164 TAAAAATATTATATTTT
1 TAATTATATTATATTTT
1588181 TAATTATATTATA
1 TAATTATATTATA
1588194 ATTATTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
13 4 0.12
14 2 0.06
15 8 0.24
16 1 0.03
17 17 0.52
18 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATTATATTATATTTT
Found at i:1589362 original size:31 final size:31
Alignment explanation
Indices: 1589291--1589385 Score: 130
Period size: 29 Copynumber: 3.2 Consensus size: 31
1589281 CAATTCAATA
1589291 TTACGTCTCTTATAAAAAT---ATAAAGAAG
1 TTACGTCTCTTATAAAAATAAAATAAAGAAG
*
1589319 ATTATGTCTCTTATAAAAATAAAATAAAGAAG
1 -TTACGTCTCTTATAAAAATAAAATAAAGAAG
1589351 TTACGTCTCTTAT-AAAATAAAATAAAG-A-
1 TTACGTCTCTTATAAAAATAAAATAAAGAAG
1589379 TTACGTC
1 TTACGTC
1589386 CAAAATTGAT
Statistics
Matches: 61, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
28 7 0.11
29 19 0.31
30 14 0.23
31 12 0.20
32 9 0.15
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (31 bp):
TTACGTCTCTTATAAAAATAAAATAAAGAAG
Found at i:1691167 original size:32 final size:32
Alignment explanation
Indices: 1691126--1691217 Score: 152
Period size: 32 Copynumber: 2.9 Consensus size: 32
1691116 TGAGACGTAA
1691126 TCTTTATTTTATTTTTATAAGAGACGTAATCT
1 TCTTTATTTTATTTTTATAAGAGACGTAATCT
*
1691158 TCTTTATTTTATTTTTATAAGAGACATAATCT
1 TCTTTATTTTATTTTTATAAGAGACGTAATCT
*
1691190 TCTTTA-TAT-TTTTTATAAGAGACGTAAT
1 TCTTTATTTTATTTTTATAAGAGACGTAAT
1691218 ATTGAATTGA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
30 18 0.32
31 2 0.04
32 37 0.65
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (32 bp):
TCTTTATTTTATTTTTATAAGAGACGTAATCT
Found at i:1692322 original size:16 final size:16
Alignment explanation
Indices: 1692302--1692369 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
1692292 ATATTTTATT
1692302 TTTTTAATTAAAAATAA
1 TTTTTAA-TAAAAATAA
**
1692319 TTTTTAATAATTATAA
1 TTTTTAATAAAAATAA
*
1692335 --TATAATTAAAATATAATA
1 TTTTTAA-TAAAA-AT-A-A
1692353 TTTTTAATAAAAATAA
1 TTTTTAATAAAAATAA
1692369 T
1 T
1692370 ATAAAAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 13
0.67 0.10 0.22
Matches are distributed among these distances:
14 4 0.10
15 3 0.08
16 11 0.28
17 9 0.23
18 3 0.08
19 5 0.13
20 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTTTAATAAAAATAA
Found at i:1692360 original size:34 final size:34
Alignment explanation
Indices: 1692306--1692385 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 34
1692296 TTTATTTTTT
**
1692306 TAATTAAAA-AT-A-ATTTTTAATAATTATAATA
1 TAATTAAAATATAATATTTTTAATAAAAATAATA
1692337 TAATTAAAATATAATATTTTTAATAAAAATAATA
1 TAATTAAAATATAATATTTTTAATAAAAATAATA
1692371 T-A--AAAATATAATATT
1 TAATTAAAATATAATATT
1692386 ATTATTTAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
31 22 0.50
32 2 0.05
33 2 0.05
34 18 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (34 bp):
TAATTAAAATATAATATTTTTAATAAAAATAATA
Found at i:1692380 original size:31 final size:33
Alignment explanation
Indices: 1692318--1692385 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 33
1692308 ATTAAAAATA
**
1692318 ATTTTTAATAATTATAATATAATTAAAATATAAT
1 ATTTTTAATAAAAATAATATAA-TAAAATATAAT
1692352 ATTTTTAATAAAAATAATAT-A-AAAATATAAT
1 ATTTTTAATAAAAATAATATAATAAAATATAAT
1692383 ATT
1 ATT
1692386 ATTATTTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 13 0.41
33 1 0.03
34 18 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
ATTTTTAATAAAAATAATATAATAAAATATAAT
Found at i:1693948 original size:19 final size:19
Alignment explanation
Indices: 1693911--1693949 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1693901 ATTAACAGTA
* **
1693911 TATAAAATAATTATTTTAT
1 TATAAAATAAATAAATTAT
1693930 TATAAAATAAATAAATTAT
1 TATAAAATAAATAAATTAT
1693949 T
1 T
1693950 TAATTATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATAAAATAAATAAATTAT
Found at i:1698075 original size:25 final size:25
Alignment explanation
Indices: 1698030--1698084 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1698020 TATTTTTAAT
* *
1698030 TTTATAATTAAATTAGATTATTTTA
1 TTTATAATTAAATTAGATTATATCA
*
1698055 TTTATAATT-AATTAGTTTTATATCA
1 TTTATAATTAAATTAG-ATTATATCA
1698080 TTTAT
1 TTTAT
1698085 TTATTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (25 bp):
TTTATAATTAAATTAGATTATATCA
Found at i:1698619 original size:3 final size:3
Alignment explanation
Indices: 1698613--1698648 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1698603 AAAAAAAGCA
1698613 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1698649 ATGATAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1698893 original size:12 final size:13
Alignment explanation
Indices: 1698816--1698913 Score: 59
Period size: 12 Copynumber: 7.9 Consensus size: 13
1698806 ATATATGTAT
1698816 ATATATATATATATA
1 ATATATATA-ATA-A
* *
1698831 ATTTATATCA-AA
1 ATATATATAATAA
1698843 ATATA-AT-ATAA
1 ATATATATAATAA
** *
1698854 ATATGATATTTTTA
1 ATAT-ATATAATAA
1698868 ATATATATAA-AA
1 ATATATATAATAA
1698880 ATA-ATATAATAA
1 ATATATATAATAA
1698892 ATATAT-T--TAA
1 ATATATATAATAA
*
1698902 ATATAAATAATA
1 ATATATATAATA
1698914 TTATAAATAT
Statistics
Matches: 65, Mismatches: 9, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
10 9 0.14
11 15 0.23
12 16 0.25
13 11 0.17
14 7 0.11
15 7 0.11
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (13 bp):
ATATATATAATAA
Found at i:1698913 original size:19 final size:18
Alignment explanation
Indices: 1698882--1698923 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1698872 ATATAAAAAT
*
1698882 AATATAATAAATATATTTA
1 AATATAATAAATAT-TATA
1698901 AATATAA-ATAATATTATA
1 AATATAATA-AATATTATA
1698919 AATAT
1 AATAT
1698924 TTAATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATAATAAATATTATA
Found at i:1698934 original size:37 final size:36
Alignment explanation
Indices: 1698893--1698973 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 36
1698883 ATATAATAAA
1698893 TATATTTAAATATAAATAATATTATAAATATTTA-ATT
1 TATATTTAAATATAAAT-ATATT-TAAATATTTATATT
* * *
1698930 TATATTTAAAATTTTAATATATTTAATTATTTATATT
1 TATATTT-AAATATAAATATATTTAAATATTTATATT
1698967 T-TATTTA
1 TATATTTA
1698974 TATAATTAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
35 1 0.03
36 14 0.36
37 16 0.41
38 8 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (36 bp):
TATATTTAAATATAAATATATTTAAATATTTATATT
Found at i:1698945 original size:19 final size:18
Alignment explanation
Indices: 1698891--1698955 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 18
1698881 TAATATAATA
*
1698891 AATATATTT-AAATA-TA
1 AATATATTTAAAATATTT
1698907 AATA-ATATTATAAATATTT
1 AATATAT-TTA-AAATATTT
1698926 AATTTATATTTAAAAT-TTT
1 AA--TATATTTAAAATATTT
1698945 AATATATTTAA
1 AATATATTTAA
1698956 TTATTTATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
15 2 0.05
16 6 0.15
17 9 0.22
18 5 0.12
19 8 0.20
20 4 0.10
21 5 0.12
22 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AATATATTTAAAATATTT
Found at i:1698960 original size:8 final size:9
Alignment explanation
Indices: 1698881--1698962 Score: 57
Period size: 9 Copynumber: 9.2 Consensus size: 9
1698871 TATATAAAAA
*
1698881 TAATATAAT
1 TAATATATT
*
1698890 AAATATATT
1 TAATATATT
1698899 TAA-ATA-T
1 TAATATATT
*
1698906 AAATAATATT
1 TAAT-ATATT
1698916 ATAA-ATATT
1 -TAATATATT
1698925 TAATTTATATT
1 TAA--TATATT
*
1698936 TAAAAT-TT
1 TAATATATT
1698944 TAATATATT
1 TAATATATT
1698953 TAAT-TATT
1 TAATATATT
1698961 TA
1 TA
1698963 TATTTTATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 17
0.71 0.09 0.21
Matches are distributed among these distances:
7 3 0.05
8 19 0.33
9 25 0.43
10 1 0.02
11 10 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TAATATATT
Found at i:1703235 original size:2 final size:2
Alignment explanation
Indices: 1703230--1703256 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1703220 ATATATATAT
1703230 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1703257 AAAACTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1706381 original size:15 final size:15
Alignment explanation
Indices: 1706361--1706390 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1706351 GTGAATTTGA
1706361 ATAATATTTGTACGT
1 ATAATATTTGTACGT
*
1706376 ATAATATTTTTACGT
1 ATAATATTTGTACGT
1706391 GTCAGACCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (15 bp):
ATAATATTTGTACGT
Found at i:1715792 original size:18 final size:19
Alignment explanation
Indices: 1715769--1715805 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1715759 GCATCAACTC
*
1715769 AATT-AAAAATTAAATTAA
1 AATTAAAAAATAAAATTAA
1715787 AATTAAAAAATAAAATTAA
1 AATTAAAAAATAAAATTAA
1715806 TGGTGTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTAAAAAATAAAATTAA
Found at i:1716646 original size:20 final size:20
Alignment explanation
Indices: 1716623--1716668 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1716613 AATTAAAAAT
*
1716623 ATTTAAAATTAAAATAATTA
1 ATTTAAAATTAAAATAATCA
* *
1716643 ATTTAAATTTAAATTAATCA
1 ATTTAAAATTAAAATAATCA
1716663 ATTTAA
1 ATTTAA
1716669 TCTATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTTAAAATTAAAATAATCA
Found at i:1718402 original size:20 final size:20
Alignment explanation
Indices: 1718358--1718415 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 20
1718348 GGTTTAATAA
1718358 TTTAAACTAATAAAATTAAAATT
1 TTTAAA-TAA-AAAATT-AAATT
*
1718381 TTTAATTAAAAAATT-AATT
1 TTTAAATAAAAAATTAAATT
1718400 TTTAAATAAATAAATT
1 TTTAAATAAA-AAATT
1718416 TTAATTATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 13 0.41
20 5 0.16
21 6 0.19
22 3 0.09
23 5 0.16
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TTTAAATAAAAAATTAAATT
Found at i:1718460 original size:26 final size:28
Alignment explanation
Indices: 1718394--1718478 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 28
1718384 AATTAAAAAA
* *
1718394 TTAATTTTTAAATAAATAAATTTTAATTATTC
1 TTAATTTTT--ATAAA-ATATTTTTA-TATTC
* *
1718426 TTAATTTTTGTTATAAT-TTTTTATATT-
1 TTAATTTTT-ATAAAATATTTTTATATTC
1718453 TTAA-TTTTATAAAATATTTTTATATT
1 TTAATTTTTATAAAATATTTTTATATT
1718479 AAAATTAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
25 5 0.11
26 14 0.31
27 4 0.09
28 4 0.09
29 5 0.11
30 1 0.02
31 3 0.07
32 9 0.20
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (28 bp):
TTAATTTTTATAAAATATTTTTATATTC
Found at i:1720743 original size:12 final size:12
Alignment explanation
Indices: 1720726--1720766 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1720716 GTGTAATTAC
*
1720726 ATTTAAGTACAT
1 ATTTAAATACAT
*
1720738 ATTTAAAAAC-T
1 ATTTAAATACAT
1720749 A-TTAAATACAT
1 ATTTAAATACAT
1720760 ATTTAAA
1 ATTTAAA
1720767 AATTAAGACC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
10 7 0.29
11 4 0.17
12 13 0.54
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.39
Consensus pattern (12 bp):
ATTTAAATACAT
Found at i:1721166 original size:16 final size:17
Alignment explanation
Indices: 1721145--1721209 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 17
1721135 TAATATAAAT
*
1721145 ATAATATAT-TTAATAA
1 ATAATATATAATAATAA
1721161 ATAATA-ATAATAATAA
1 ATAATATATAATAATAA
*
1721177 ATAA-ATATAAT-ATAT
1 ATAATATATAATAATAA
*
1721192 TTAA-ATATAATTAATAA
1 ATAATATATAA-TAATAA
1721209 A
1 A
1721210 ATAAATTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
15 15 0.38
16 22 0.55
17 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATATATAATAATAA
Found at i:1721196 original size:19 final size:19
Alignment explanation
Indices: 1721139--1721207 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 19
1721129 TGACGATAAT
1721139 ATAAATATAATATATTT-A
1 ATAAATATAATATATTTAA
*
1721157 ATAAATAATAATA-ATAATAA
1 ATAAAT-ATAATATAT-TTAA
1721177 ATAAATATAATATATTTAA
1 ATAAATATAATATATTTAA
1721196 ATATAAT-TAATA
1 ATA-AATATAATA
1721208 AAATAAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
18 8 0.18
19 24 0.55
20 12 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
ATAAATATAATATATTTAA
Found at i:1721245 original size:38 final size:37
Alignment explanation
Indices: 1721134--1721234 Score: 123
Period size: 38 Copynumber: 2.6 Consensus size: 37
1721124 AATTCTGACG
*
1721134 ATAATATAAATATAATATATTTAATAAATAATAATAATA
1 ATAA-ATAAATATAATATATTTAA-ATATAATAATAATA
1721173 ATAAATAAATATAATATATTTAAATATAATTAATAA-A
1 ATAAATAAATATAATATATTTAAATATAA-TAATAATA
*
1721210 ATAAATTTAATATATATTATATTTA
1 ATAAA--TAA-ATATAATATATTTA
1721235 TATTTATAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
37 11 0.20
38 25 0.45
39 7 0.12
40 13 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (37 bp):
ATAAATAAATATAATATATTTAAATATAATAATAATA
Found at i:1721246 original size:15 final size:16
Alignment explanation
Indices: 1721142--1721247 Score: 50
Period size: 15 Copynumber: 6.9 Consensus size: 16
1721132 CGATAATATA
1721142 AATATA-AT-ATATTT
1 AATATATATAATATTT
*
1721156 AATA-A-ATAATA-AT
1 AATATATATAATATTT
* *
1721169 AATAATAAATAA-ATAT
1 AAT-ATATATAATATTT
*
1721185 AATATATTTAAATATAATT
1 AATATATAT-AATAT--TT
*
1721204 AATA-AAATAA-ATTT
1 AATATATATAATATTT
*
1721218 AATATATATTATATTT
1 AATATATATAATATTT
*
1721234 -ATATTTATAATATT
1 AATATATATAATATT
1721248 AAAAAAATTT
Statistics
Matches: 71, Mismatches: 10, Indels: 21
0.70 0.10 0.21
Matches are distributed among these distances:
13 7 0.10
14 14 0.20
15 22 0.31
16 17 0.24
17 4 0.06
18 2 0.03
19 5 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATATATATAATATTT
Found at i:1721357 original size:6 final size:6
Alignment explanation
Indices: 1721346--1721376 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1721336 GCAGAAGCAC
*
1721346 GTAGGT GTAGGT GTAGGT GCAGGT GTAGGT G
1 GTAGGT GTAGGT GTAGGT GTAGGT GTAGGT G
1721377 CGGTAGTAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.03, G:0.52, T:0.29
Consensus pattern (6 bp):
GTAGGT
Found at i:1722116 original size:30 final size:33
Alignment explanation
Indices: 1722068--1722130 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 33
1722058 TTGTGTTTAA
1722068 ATTTTATATTTACATTTTAACTT-AT-TTTTTT
1 ATTTTATATTTACATTTTAACTTAATATTTTTT
** *
1722099 ATTTTA-ATTTATTTTTTATCTTAATATTTTTT
1 ATTTTATATTTACATTTTAACTTAATATTTTTT
1722131 CAAATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 13 0.48
31 8 0.30
32 6 0.22
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (33 bp):
ATTTTATATTTACATTTTAACTTAATATTTTTT
Found at i:1722117 original size:17 final size:18
Alignment explanation
Indices: 1722081--1722115 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1722071 TTATATTTAC
*
1722081 ATTTTAACTTATTTTTTT
1 ATTTTAATTTATTTTTTT
1722099 ATTTTAATTTATTTTTT
1 ATTTTAATTTATTTTTT
1722116 ATCTTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTAATTTATTTTTTT
Found at i:1722126 original size:15 final size:16
Alignment explanation
Indices: 1722093--1722130 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
1722083 TTTAACTTAT
*
1722093 TTTTTTATTTTAATTTA
1 TTTTTTATCTTAA-TTA
1722110 TTTTTTATCTTAA-TA
1 TTTTTTATCTTAATTA
1722125 TTTTTT
1 TTTTTT
1722131 CAAATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
17 12 0.60
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTATCTTAATTA
Found at i:1725481 original size:15 final size:16
Alignment explanation
Indices: 1725463--1725530 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 16
1725453 TAAATGTATC
1725463 ATATTATTTTT-TATT
1 ATATTATTTTTATATT
1725478 ATATTATTTTTATATT
1 ATATTATTTTTATATT
*
1725494 -TATTAATATATTATATT
1 ATATT-AT-TTTTATATT
1725511 -TATGTCAATTTTTATATT
1 ATAT-T--ATTTTTATATT
1725529 AT
1 AT
1725531 GTTCAAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
15 15 0.33
16 6 0.13
17 11 0.24
18 9 0.20
19 4 0.09
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (16 bp):
ATATTATTTTTATATT
Done.