Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 9 of 218
Found at i:3448559 original size:30 final size:31
Alignment explanation
Indices: 3448525--3448582 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 31
3448515 AAAAGAAAAC
3448525 AAATACACTTAATAAAATC-ATAATAAATTA
1 AAATACACTTAATAAAATCGATAATAAATTA
** * *
3448555 AAATATTCTTATTAAAATCGATAGTAAA
1 AAATACACTTAATAAAATCGATAATAAA
3448583 CTATTCAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 16 0.70
31 7 0.30
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (31 bp):
AAATACACTTAATAAAATCGATAATAAATTA
Found at i:3449821 original size:26 final size:25
Alignment explanation
Indices: 3449767--3449818 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
3449757 AAAATTATTA
3449767 TTCTAATTTTTTAAATTTTTTTAAC
1 TTCTAATTTTTTAAATTTTTTTAAC
*
3449792 TTCTAATTTTTTTAATTTTTTTAAC
1 TTCTAATTTTTTAAATTTTTTTAAC
3449817 TT
1 TT
3449819 TCTTTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (25 bp):
TTCTAATTTTTTAAATTTTTTTAAC
Found at i:3456402 original size:33 final size:33
Alignment explanation
Indices: 3456360--3456426 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
3456350 CGTTTCTTTT
3456360 GTATCTTTT-CTTCTTGTGTGACCACCCCGTTGG
1 GTATCTTTTCCTT-TTGTGTGACCACCCCGTTGG
*
3456393 GTATCTTTTCCTTTTGTGTGACCACCCTGTTGG
1 GTATCTTTTCCTTTTGTGTGACCACCCCGTTGG
3456426 G
1 G
3456427 GCTTTCTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.09, C:0.25, G:0.22, T:0.43
Consensus pattern (33 bp):
GTATCTTTTCCTTTTGTGTGACCACCCCGTTGG
Found at i:3459630 original size:16 final size:17
Alignment explanation
Indices: 3459609--3459643 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3459599 AAAAATTGAC
3459609 ATTG-AAAATATTTTTT
1 ATTGAAAAATATTTTTT
3459625 ATTGAAAAATATTTTTT
1 ATTGAAAAATATTTTTT
3459642 AT
1 AT
3459644 AAATTCATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
ATTGAAAAATATTTTTT
Found at i:3460290 original size:7 final size:7
Alignment explanation
Indices: 3460278--3460302 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3460268 TAAAGGATCT
3460278 TATAATA
1 TATAATA
3460285 TATAATA
1 TATAATA
3460292 TATAATA
1 TATAATA
3460299 TATA
1 TATA
3460303 CTAGTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TATAATA
Found at i:3460536 original size:20 final size:21
Alignment explanation
Indices: 3460500--3460538 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
3460490 GATTTTTATT
3460500 AAATAAAATAATTATATTTAA
1 AAATAAAATAATTATATTTAA
*
3460521 AAATAAAA-AGTTATATTT
1 AAATAAAATAATTATATTT
3460539 TCTATTAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (21 bp):
AAATAAAATAATTATATTTAA
Found at i:3462914 original size:20 final size:20
Alignment explanation
Indices: 3462889--3462938 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
3462879 TGGCTTAAAA
3462889 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
3462909 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
3462926 GTGGTAGTGGATT
1 TTGGTAGTGGATT
3462939 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:3467552 original size:20 final size:20
Alignment explanation
Indices: 3467527--3467576 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
3467517 TGGCTTAAAA
3467527 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
3467547 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
3467564 GTGGTAGTGGATT
1 TTGGTAGTGGATT
3467577 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:3476038 original size:92 final size:92
Alignment explanation
Indices: 3475881--3476065 Score: 370
Period size: 92 Copynumber: 2.0 Consensus size: 92
3475871 ATATCTATCA
3475881 ATTTATCACATCAATGATTTGACGGTTATTCTATCATTCTCCTTAAGTCGACTCTAATAATAATA
1 ATTTATCACATCAATGATTTGACGGTTATTCTATCATTCTCCTTAAGTCGACTCTAATAATAATA
3475946 ATCTAGATTCACATTTGCCGCTCTACC
66 ATCTAGATTCACATTTGCCGCTCTACC
3475973 ATTTATCACATCAATGATTTGACGGTTATTCTATCATTCTCCTTAAGTCGACTCTAATAATAATA
1 ATTTATCACATCAATGATTTGACGGTTATTCTATCATTCTCCTTAAGTCGACTCTAATAATAATA
3476038 ATCTAGATTCACATTTGCCGCTCTACC
66 ATCTAGATTCACATTTGCCGCTCTACC
3476065 A
1 A
3476066 CCAGCATTTA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.38
Consensus pattern (92 bp):
ATTTATCACATCAATGATTTGACGGTTATTCTATCATTCTCCTTAAGTCGACTCTAATAATAATA
ATCTAGATTCACATTTGCCGCTCTACC
Found at i:3483940 original size:29 final size:31
Alignment explanation
Indices: 3483890--3483955 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
3483880 TATTAATTTT
**
3483890 AAAATAATATTAATTTACTTAT-TTCAAATA
1 AAAATAATATTAATGCACTTATCTTCAAATA
* * *
3483920 AAAATAA-ATTAATGCATTTATCTTCAATTT
1 AAAATAATATTAATGCACTTATCTTCAAATA
3483950 AAAATA
1 AAAATA
3483956 TTTTTTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.41
Consensus pattern (31 bp):
AAAATAATATTAATGCACTTATCTTCAAATA
Found at i:3483992 original size:18 final size:18
Alignment explanation
Indices: 3483945--3484004 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
3483935 ATTTATCTTC
3483945 AATTTAAAATATTTTTTT
1 AATTTAAAATATTTTTTT
*
3483963 AAATATT-TAATATTTTTTT
1 -AAT-TTAAAATATTTTTTT
**
3483982 AATTTAAAATATAATTTT
1 AATTTAAAATATTTTTTT
3484000 AATTT
1 AATTT
3484005 GATATTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 2 0.06
18 17 0.49
19 14 0.40
20 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
AATTTAAAATATTTTTTT
Found at i:3484014 original size:16 final size:16
Alignment explanation
Indices: 3483967--3484014 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 16
3483957 TTTTTTAAAT
*
3483967 ATTTAATATTTTTTTA
1 ATTTAATATTATTTTA
*
3483983 ATTTAAAATATAATTTTA
1 ATTT--AATATTATTTTA
*
3484001 ATTTGATATTATTT
1 ATTTAATATTATTT
3484015 AAAATAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTAATATTATTTTA
Found at i:3490236 original size:19 final size:20
Alignment explanation
Indices: 3490191--3490228 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3490181 CTTTTTTACT
*
3490191 CAAAAGATAAAAAAAAGTTA
1 CAAAATATAAAAAAAAGTTA
3490211 CAAAATATAAAAAAAAGT
1 CAAAATATAAAAAAAAGT
3490229 ATAAAATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.71, C:0.05, G:0.08, T:0.16
Consensus pattern (20 bp):
CAAAATATAAAAAAAAGTTA
Found at i:3492302 original size:21 final size:22
Alignment explanation
Indices: 3492255--3492296 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
3492245 AAAATAAATA
*
3492255 TAAATTTTATGGATGAATTTAAT
1 TAAATTTTATGGA-CAATTTAAT
3492278 TAAATTTTATGG-CAATTTA
1 TAAATTTTATGGACAATTTA
3492297 TCTAAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
23 12 0.67
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (22 bp):
TAAATTTTATGGACAATTTAAT
Found at i:3496411 original size:15 final size:15
Alignment explanation
Indices: 3496391--3496421 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3496381 ATTTAACAAA
*
3496391 TGTCTAATCAATATT
1 TGTCTAATAAATATT
3496406 TGTCTAATAAATATT
1 TGTCTAATAAATATT
3496421 T
1 T
3496422 TAGAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (15 bp):
TGTCTAATAAATATT
Found at i:3504138 original size:21 final size:20
Alignment explanation
Indices: 3504108--3504150 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
3504098 TTTAAAATGT
3504108 AAAAATT-AAATAAAAAATAA
1 AAAAATTAAAAT-AAAAATAA
3504128 AAAATATTAAAATAAAAATAA
1 AAAA-ATTAAAATAAAAATAA
3504149 AA
1 AA
3504151 TTGGCTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.19
21 13 0.62
22 4 0.19
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAATTAAAATAAAAATAA
Found at i:3504626 original size:14 final size:14
Alignment explanation
Indices: 3504607--3504638 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3504597 ATTTAAAAGG
3504607 GCATGTAAAGAAAA
1 GCATGTAAAGAAAA
*
3504621 GCATGTAAAGTAAA
1 GCATGTAAAGAAAA
3504635 GCAT
1 GCAT
3504639 TCAACAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.09, G:0.22, T:0.19
Consensus pattern (14 bp):
GCATGTAAAGAAAA
Found at i:3505149 original size:21 final size:20
Alignment explanation
Indices: 3505121--3505161 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
3505111 TGCTTCTTGG
*
3505121 CAAATGGATATTGCGATACC
1 CAAATGGATATCGCGATACC
3505141 CAAAGTGGATATCGCGATACC
1 CAAA-TGGATATCGCGATACC
3505162 ATTGAAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (20 bp):
CAAATGGATATCGCGATACC
Found at i:3508378 original size:30 final size:28
Alignment explanation
Indices: 3508343--3508405 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
3508333 AAAAAACCCT
3508343 TTTTTTTCAAAATTTACCGAAATGGGCCGA
1 TTTTTTT-AAAATTTACCGAAATGGGCC-A
** * *
3508373 TTTTTTTATTATTTACCGGAATGGTCCA
1 TTTTTTTAAAATTTACCGAAATGGGCCA
3508401 TTTTT
1 TTTTT
3508406 CGGGAAATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 6 0.21
29 16 0.55
30 7 0.24
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (28 bp):
TTTTTTTAAAATTTACCGAAATGGGCCA
Found at i:3508669 original size:13 final size:13
Alignment explanation
Indices: 3508651--3508692 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
3508641 ATATTCCCTA
*
3508651 AATTAAATGTAAT
1 AATTAAATATAAT
3508664 AATT-AATAATAA-
1 AATTAAAT-ATAAT
3508676 AATTAAATATAAT
1 AATTAAATATAAT
3508689 AATT
1 AATT
3508693 TTATTAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (13 bp):
AATTAAATATAAT
Found at i:3510168 original size:29 final size:30
Alignment explanation
Indices: 3510125--3510183 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
3510115 TTAAGTTTAA
*
3510125 TGTGCAATTTTATACATG-AATGTTGATTT
1 TGTGCAATTTCATACATGAAATGTTGATTT
* *
3510154 TGTGTAATTTCATACATGAAATTTTGATTT
1 TGTGCAATTTCATACATGAAATGTTGATTT
3510184 GATTCAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (30 bp):
TGTGCAATTTCATACATGAAATGTTGATTT
Found at i:3510748 original size:18 final size:21
Alignment explanation
Indices: 3510725--3510763 Score: 57
Period size: 18 Copynumber: 2.0 Consensus size: 21
3510715 ATTTTTATGC
3510725 TTCACT-AAAA-AA-AAAGAA
1 TTCACTCAAAATAATAAAGAA
3510743 TTCACTCAAAATAATAAAGAA
1 TTCACTCAAAATAATAAAGAA
3510764 GAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 2 0.11
21 6 0.33
ACGTcount: A:0.62, C:0.13, G:0.05, T:0.21
Consensus pattern (21 bp):
TTCACTCAAAATAATAAAGAA
Found at i:3511878 original size:9 final size:9
Alignment explanation
Indices: 3511866--3511897 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
3511856 TATAATAAAT
3511866 ATTTTTTTA
1 ATTTTTTTA
3511875 ATTTTTTTA
1 ATTTTTTTA
3511884 ATTTTTTTA
1 ATTTTTTTA
3511893 ATTTT
1 ATTTT
3511898 AAAATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:3511907 original size:18 final size:19
Alignment explanation
Indices: 3511862--3511908 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
3511852 CGAATATAAT
*
3511862 AAATATTTTTTTAATTTTTT
1 AAATA-TTTTTTAATTTTTA
*
3511882 TAAT-TTTTTTAA-TTTTA
1 AAATATTTTTTAATTTTTA
3511899 AAATATTTTT
1 AAATATTTTT
3511909 AAAATAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 7 0.30
18 13 0.57
20 3 0.13
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
AAATATTTTTTAATTTTTA
Found at i:3515424 original size:18 final size:16
Alignment explanation
Indices: 3515348--3515450 Score: 72
Period size: 18 Copynumber: 6.2 Consensus size: 16
3515338 CGTGATCTGA
3515348 TTAAAACACGAAAAATTT
1 TTAAAACACG--AAATTT
3515366 AATTAAAACACGAGAA-TT
1 --TTAAAACACGA-AATTT
*
3515384 TTAAAGCAC--AATTT
1 TTAAAACACGAAATTT
*
3515398 TT--TACACGATAATTT
1 TTAAAACACGA-AATTT
3515413 TTGAAAACACGAGAATTT
1 TT-AAAACACGA-AATTT
3515431 TTAAAACACGGAAATTT
1 TTAAAACAC-GAAATTT
3515448 TTA
1 TTA
3515451 CAAGACACAG
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
12 3 0.04
13 2 0.03
14 4 0.06
15 7 0.10
16 8 0.12
17 15 0.22
18 18 0.26
19 2 0.03
20 10 0.14
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.32
Consensus pattern (16 bp):
TTAAAACACGAAATTT
Found at i:3515516 original size:18 final size:18
Alignment explanation
Indices: 3515493--3515565 Score: 58
Period size: 18 Copynumber: 3.9 Consensus size: 18
3515483 AATCACCGGA
*
3515493 ATTTTTGGAAACACGAAG
1 ATTTTTGAAAACACGAAG
*
3515511 ATTTTTGAAAACATGAAGAG
1 ATTTTTGAAAACACG-A-AG
* *
3515531 ATTTTTTAAAAAACACGAAA
1 A-TTTTT-GAAAACACGAAG
*
3515551 ATTTTT-AAAATACGA
1 ATTTTTGAAAACACGA
3515566 GAAATTTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
17 8 0.18
18 13 0.29
19 6 0.13
20 5 0.11
21 6 0.13
22 7 0.16
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.32
Consensus pattern (18 bp):
ATTTTTGAAAACACGAAG
Found at i:3515569 original size:19 final size:19
Alignment explanation
Indices: 3515501--3515560 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
3515491 GAATTTTTGG
* *
3515501 AAACACGAAGATTTTT-GA
1 AAACACGAAAATTTTTAAA
*
3515519 AAACATGAAGAGATTTTTTAAA
1 AAACACGAA-A-A-TTTTTAAA
3515541 AAACACGAAAATTTTTAAA
1 AAACACGAAAATTTTTAAA
3515560 A
1 A
3515561 TACGAGAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 8 0.24
19 9 0.26
20 2 0.06
21 6 0.18
22 9 0.26
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.28
Consensus pattern (19 bp):
AAACACGAAAATTTTTAAA
Found at i:3515678 original size:18 final size:17
Alignment explanation
Indices: 3515637--3515695 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
3515627 GCGAAAAGTC
*
3515637 AAAAATTTTGAAATACG
1 AAAATTTTTGAAATACG
*
3515654 AGTAATTTTTGAAAATACG
1 A-AAATTTTTG-AAATACG
*
3515673 AAAA--TTTGAAACACG
1 AAAATTTTTGAAATACG
3515688 -AAATTTTT
1 AAAATTTTT
3515696 TTATTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
14 3 0.09
15 6 0.18
16 7 0.21
17 1 0.03
18 9 0.26
19 8 0.24
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (17 bp):
AAAATTTTTGAAATACG
Found at i:3516660 original size:20 final size:21
Alignment explanation
Indices: 3516628--3516678 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
3516618 TTCTCTTCTC
*
3516628 TTTTTCTTCTTTGCTTG-TTTT
1 TTTTTCTT-TTTGCTTGCTGTT
3516649 TTTTTCTTTTTGCTTGCTGTT
1 TTTTTCTTTTTGCTTGCTGTT
3516670 TTTTTCTTT
1 TTTTTCTTT
3516679 GACTTTGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.76
Consensus pattern (21 bp):
TTTTTCTTTTTGCTTGCTGTT
Found at i:3516691 original size:20 final size:18
Alignment explanation
Indices: 3516627--3516693 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 18
3516617 CTTCTCTTCT
*
3516627 CTTTTTCTTCTTTGCTTG
1 CTTTTTTTTCTTTGCTTG
*
3516645 TTTTTTTTTCTTTTTGCTTG
1 CTTTTTTTTC--TTTGCTTG
3516665 CTGTTTTTTTCTTTGACTTTG
1 CT-TTTTTTTCTTTG-C-TTG
3516686 CTTTTTTT
1 CTTTTTTT
3516694 ATTTATTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
18 8 0.20
19 4 0.10
20 16 0.39
21 13 0.32
ACGTcount: A:0.01, C:0.15, G:0.10, T:0.73
Consensus pattern (18 bp):
CTTTTTTTTCTTTGCTTG
Found at i:3517161 original size:59 final size:59
Alignment explanation
Indices: 3517087--3517243 Score: 165
Period size: 59 Copynumber: 2.7 Consensus size: 59
3517077 TGGGGCTAAT
* * * *
3517087 ATGTAATTTAT-AGAAAGTTTAGGGGCCCAAATGAAATTTAGAAAATTTTAGGAGTAGAA
1 ATGTAATTT-TGAGAAAGTTTAGGGGCCAAAATGTAATTTAGAAAAGTTCAGGAGTAGAA
* *** * * * *
3517146 ATGTAATTTTGAGAAAGTTTAAGGGTTGAAATGTAATTTTGAAAAGTTCAGGGGTTGAG
1 ATGTAATTTTGAGAAAGTTTAGGGGCCAAAATGTAATTTAGAAAAGTTCAGGAGTAGAA
* *
3517205 ATGTAATTTAGA-AAAGTTCAGGGGCCAAAATGTAATTTA
1 ATGTAATTTTGAGAAAGTTTAGGGGCCAAAATGTAATTTA
3517244 TATTTTTGTA
Statistics
Matches: 79, Mismatches: 18, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
58 22 0.28
59 57 0.72
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (59 bp):
ATGTAATTTTGAGAAAGTTTAGGGGCCAAAATGTAATTTAGAAAAGTTCAGGAGTAGAA
Found at i:3517220 original size:29 final size:29
Alignment explanation
Indices: 3517087--3517243 Score: 134
Period size: 29 Copynumber: 5.3 Consensus size: 29
3517077 TGGGGCTAAT
* * ***
3517087 ATGTAATTTATAGAAAGTTTAGGGGCCCAA
1 ATGTAATTTAGA-AAAGTTCAGGGGTTGAA
* * * * *
3517117 ATGAAATTTAGAAAATTTTAGGAGTAGAA
1 ATGTAATTTAGAAAAGTTCAGGGGTTGAA
* * *
3517146 ATGTAATTTTGAGAAAGTTTAAGGGTTGAA
1 ATGTAATTTAGA-AAAGTTCAGGGGTTGAA
* *
3517176 ATGTAATTTTGAAAAGTTCAGGGGTTGAG
1 ATGTAATTTAGAAAAGTTCAGGGGTTGAA
***
3517205 ATGTAATTTAGAAAAGTTCAGGGGCCAAA
1 ATGTAATTTAGAAAAGTTCAGGGGTTGAA
3517234 ATGTAATTTA
1 ATGTAATTTA
3517244 TATTTTTGTA
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
29 70 0.67
30 35 0.33
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (29 bp):
ATGTAATTTAGAAAAGTTCAGGGGTTGAA
Found at i:3518343 original size:29 final size:31
Alignment explanation
Indices: 3518303--3518370 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 31
3518293 AAGTTATAGA
*
3518303 TTTAGTCCTTGTACTTTT-AA-TTGATCACT
1 TTTAGTCCTTGTACTTTTCAAGTCGATCACT
* * *
3518332 TTTAGTCTTTGTATTTTTCAAGTCGGTCACT
1 TTTAGTCCTTGTACTTTTCAAGTCGATCACT
3518363 TTTAGTCC
1 TTTAGTCC
3518371 CAATACTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 16 0.50
30 2 0.06
31 14 0.44
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.51
Consensus pattern (31 bp):
TTTAGTCCTTGTACTTTTCAAGTCGATCACT
Found at i:3519126 original size:3 final size:3
Alignment explanation
Indices: 3519118--3519155 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3519108 CTGGTACTCG
3519118 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
3519156 GCTATTATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:3542483 original size:13 final size:13
Alignment explanation
Indices: 3542465--3542489 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3542455 AATATATTTG
3542465 TTAATTAAAAATA
1 TTAATTAAAAATA
3542478 TTAATTAAAAAT
1 TTAATTAAAAAT
3542490 TAAAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TTAATTAAAAATA
Found at i:3548309 original size:23 final size:25
Alignment explanation
Indices: 3548265--3548311 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
3548255 CAGAAAAACC
*
3548265 AAAAGAGCGTGTCAACAAGACAGAG
1 AAAAAAGCGTGTCAACAAGACAGAG
3548290 AAAAAAGC-TGTCAA-AAGACAGA
1 AAAAAAGCGTGTCAACAAGACAGA
3548312 TCTAAGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 6 0.29
25 7 0.33
ACGTcount: A:0.53, C:0.15, G:0.23, T:0.09
Consensus pattern (25 bp):
AAAAAAGCGTGTCAACAAGACAGAG
Found at i:3550093 original size:27 final size:28
Alignment explanation
Indices: 3550063--3550129 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 28
3550053 ATTAATTAAT
3550063 TTTTTAAAATTAAAAATAT-TAAAAATA
1 TTTTTAAAATTAAAAATATATAAAAATA
* * *
3550090 TTTTTAAAAAT-AAAATGTATAAAATTA
1 TTTTTAAAATTAAAAATATATAAAAATA
*
3550117 TTTTAAAAATTAA
1 TTTTTAAAATTAA
3550130 TTAATTGCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 6 0.18
27 26 0.79
28 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
TTTTTAAAATTAAAAATATATAAAAATA
Found at i:3553700 original size:15 final size:16
Alignment explanation
Indices: 3553675--3553710 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
3553665 TCAGGTTTTC
3553675 TTGTTTGGTTTTTTGT
1 TTGTTTGGTTTTTTGT
*
3553691 TTGTTT-GTTTTTTTT
1 TTGTTTGGTTTTTTGT
3553706 TTGTT
1 TTGTT
3553711 ACTGCCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (16 bp):
TTGTTTGGTTTTTTGT
Found at i:3555530 original size:2 final size:2
Alignment explanation
Indices: 3555523--3555551 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3555513 ATACAAAGTG
3555523 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3555552 GAAACTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3558302 original size:20 final size:21
Alignment explanation
Indices: 3558279--3558326 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
3558269 TAGACTTTAG
3558279 TTTTTGTTTTT-TTT-TTAGAA
1 TTTTTGTTTTTATTTATTA-AA
3558299 TTTTT-TTTTTATTTATTAAA
1 TTTTTGTTTTTATTTATTAAA
3558319 TTATTTGT
1 TT-TTTGT
3558327 AATTTTTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 5 0.21
20 12 0.50
21 6 0.25
22 1 0.04
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (21 bp):
TTTTTGTTTTTATTTATTAAA
Found at i:3560647 original size:29 final size:28
Alignment explanation
Indices: 3560590--3560648 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
3560580 ATATTTTTAT
* *
3560590 TTTAAATAATTAATATAGAGTAATAATA
1 TTTAAAAAATTAATATAGAGTAAAAATA
*
3560618 TTTAAAAAATTTAATATA-ATTAAAATATA
1 TTTAAAAAA-TTAATATAGAGTAAAA-ATA
3560647 TT
1 TT
3560649 AATTATTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (28 bp):
TTTAAAAAATTAATATAGAGTAAAAATA
Found at i:3568270 original size:43 final size:43
Alignment explanation
Indices: 3568222--3568377 Score: 246
Period size: 43 Copynumber: 3.7 Consensus size: 43
3568212 TGCGGCGTTC
3568222 CTTTAGCGGCGCATT-TTACACAAACGCCGCTAAAGAACATGTT
1 CTTTAGCGGCGC-TTCTTACACAAACGCCGCTAAAGAACATGTT
3568265 CTTTAGCGGCGCTTCTTACACAAACGCCGCTAAAGAACATGTT
1 CTTTAGCGGCGCTTCTTACACAAACGCCGCTAAAGAACATGTT
* *
3568308 CTTTAGCGGCGCTTCTTACAC-AACGCCACTAAAGCTA-ATGTT
1 CTTTAGCGGCGCTTCTTACACAAACGCCGCTAAAG-AACATGTT
*
3568350 CTTTAGCGGCGCTTTTTACACAAACGCC
1 CTTTAGCGGCGCTTCTTACACAAACGCC
3568378 ACTTTTTGTT
Statistics
Matches: 107, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
42 39 0.36
43 68 0.64
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGCTTCTTACACAAACGCCGCTAAAGAACATGTT
Found at i:3568805 original size:66 final size:66
Alignment explanation
Indices: 3568728--3568863 Score: 220
Period size: 66 Copynumber: 2.1 Consensus size: 66
3568718 CTCGCTGTAG
* * *
3568728 CCTCTGCTTCTCTGGA-TGCCGCATCAGCTTTAAGTTGTCGCTGGAGTTCTTCATATTTCTTTTG
1 CCTCTGCTTCTCT-CACTGCCGCATCAGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTG
3568792 AA
65 AA
*
3568794 CCTCTGCTTCTCTCACTGCCGCATCTGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGA
1 CCTCTGCTTCTCTCACTGCCGCATCAGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGA
3568859 A
66 A
3568860 CCTC
1 CCTC
3568864 AACTGTGGTC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
65 1 0.02
66 64 0.98
ACGTcount: A:0.15, C:0.27, G:0.18, T:0.40
Consensus pattern (66 bp):
CCTCTGCTTCTCTCACTGCCGCATCAGCTCTAAGTTGTAGCTGGAGTTCTTCATATTTCTTTTGA
A
Found at i:3574255 original size:9 final size:9
Alignment explanation
Indices: 3574227--3574653 Score: 437
Period size: 9 Copynumber: 47.0 Consensus size: 9
3574217 ATTTGCACGG
3574227 GTAAGTTACT
1 GTAAGTTA-T
*
3574237 -TAATTTAT
1 GTAAGTTAT
3574245 GTAAGTTAT
1 GTAAGTTAT
3574254 GTAAGTTAT
1 GTAAGTTAT
* *
3574263 TTAATTTAT
1 GTAAGTTAT
* *
3574272 ATAGGTTAT
1 GTAAGTTAT
3574281 GTAAGTTAT
1 GTAAGTTAT
***
3574290 GTAACCCATT
1 GTAAGTTA-T
* *
3574300 GAAATTTAT
1 GTAAGTTAT
*
3574309 GTAGGTTAT
1 GTAAGTTAT
3574318 GTAAGTTAT
1 GTAAGTTAT
3574327 GTAAGTTAT
1 GTAAGTTAT
* *
3574336 TTAATTTAT
1 GTAAGTTAT
*
3574345 GTACGTTAT
1 GTAAGTTAT
3574354 GTAAGTTAT
1 GTAAGTTAT
3574363 GTAAGTTAT
1 GTAAGTTAT
* *
3574372 TTAATTTAT
1 GTAAGTTAT
*
3574381 GCAAGTTTAT
1 GTAAG-TTAT
*
3574391 GTACGTTAT
1 GTAAGTTAT
3574400 GTAAGTTAT
1 GTAAGTTAT
3574409 GTAAGTTAT
1 GTAAGTTAT
3574418 GTAAGTTAT
1 GTAAGTTAT
3574427 GTAAGTTAT
1 GTAAGTTAT
* * *
3574436 TTTATTTAT
1 GTAAGTTAT
*
3574445 GTAGGTTAT
1 GTAAGTTAT
3574454 GTAAGTTAT
1 GTAAGTTAT
3574463 GTAAGTTACT
1 GTAAGTTA-T
* *
3574473 -TAATTTAC
1 GTAAGTTAT
3574481 GTAAGTTAT
1 GTAAGTTAT
*
3574490 GTAGGTTAT
1 GTAAGTTAT
3574499 GTAAGTTAT
1 GTAAGTTAT
**
3574508 GTAAGTTCC
1 GTAAGTTAT
3574517 GTAAAGTTACT
1 GT-AAGTTA-T
*
3574528 -TAATTTAT
1 GTAAGTTAT
3574536 GTAAGTTAT
1 GTAAGTTAT
*
3574545 GTAGGTTAT
1 GTAAGTTAT
3574554 GTAAGTTAT
1 GTAAGTTAT
3574563 GTAAGTTAT
1 GTAAGTTAT
* *
3574572 TTAATTTAT
1 GTAAGTTAT
*
3574581 GCAAGTTAT
1 GTAAGTTAT
* *
3574590 TTAATTTAT
1 GTAAGTTAT
*
3574599 GCAAGTTTAT
1 GTAAG-TTAT
3574609 GTAAGTTAT
1 GTAAGTTAT
3574618 GTAAGTTAT
1 GTAAGTTAT
* *
3574627 TTAATTTAT
1 GTAAGTTAT
3574636 GTAAGTTAT
1 GTAAGTTAT
3574645 GTAAGTTAT
1 GTAAGTTAT
3574654 TGTTTTTGTG
Statistics
Matches: 336, Mismatches: 72, Indels: 19
0.79 0.17 0.04
Matches are distributed among these distances:
8 2 0.01
9 307 0.91
10 27 0.08
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:3574409 original size:100 final size:99
Alignment explanation
Indices: 3574227--3574653 Score: 489
Period size: 100 Copynumber: 4.3 Consensus size: 99
3574217 ATTTGCACGG
* * * * ** *
3574227 GTAAGTTACTTAATTTATGTAAGTTATGTAAGTTATTTAATTTATATAGGTTATGTAAGTTATGT
1 GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGCAAGTTATGT
** * * *
3574292 AAC-CCATTGAAATTTATGTAGGTTATGTAAGTTAT
66 -ACGTTA-TGTAAGTTATGTAAGTTATGTAAGTTAT
*
3574327 GTAAGTTATTTAATTTATGTACGTTATGTAAGTTATGTAAGTTATTTAATTTATGCAAGTTTATG
1 GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGCAAG-TTATG
3574392 TACGTTATGTAAGTTATGTAAGTTATGTAAGTTAT
65 TACGTTATGTAAGTTATGTAAGTTATGTAAGTTAT
* * * * *
3574427 GTAAGTTATTTTATTTATGTAGGTTATGTAAGTTATGTAAGTTACTTAATTTACGTAAGTTATGT
1 GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGCAAGTTATGT
* **
3574492 AGGTTATGTAAGTTATGTAAGTTCCGTAAAGTTACT
66 ACGTTATGTAAGTTATGTAAGTTATGT-AAGTTA-T
* * * * *
3574528 -TAATTTATGTAAGTTATGTAGGTTATGTAAGTTATGTAAGTTATTTAATTTATGCAAGTTATTT
1 GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGCAAGTTATGT
** *
3574592 AATTTATGCAAGTTTATGTAAGTTATGTAAGTTAT
66 ACGTTATGTAAG-TTATGTAAGTTATGTAAGTTAT
* * * *
3574627 TTAATTTATGTAAGTTATGTAAGTTAT
1 GTAAGTTATTTAATTTATGTAAGTTAT
3574654 TGTTTTTGTG
Statistics
Matches: 286, Mismatches: 35, Indels: 12
0.86 0.11 0.04
Matches are distributed among these distances:
99 31 0.11
100 234 0.82
101 21 0.07
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (99 bp):
GTAAGTTATTTAATTTATGTAAGTTATGTAAGTTATGTAAGTTATTTAATTTATGCAAGTTATGT
ACGTTATGTAAGTTATGTAAGTTATGTAAGTTAT
Found at i:3574730 original size:12 final size:12
Alignment explanation
Indices: 3574707--3574776 Score: 81
Period size: 12 Copynumber: 6.0 Consensus size: 12
3574697 TTATGTATTG
*
3574707 TTATATAAGTTA
1 TTATGTAAGTTA
*
3574719 TTATGTAGGTTA
1 TTATGTAAGTTA
3574731 TTATGTAAGTT-
1 TTATGTAAGTTA
3574742 TT-TGTAAGTTA
1 TTATGTAAGTTA
* *
3574753 TTATGTACGATA
1 TTATGTAAGTTA
*
3574765 CTATGTAAGTTA
1 TTATGTAAGTTA
3574777 GGATATTATG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
10 8 0.17
11 4 0.08
12 36 0.75
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:3574883 original size:9 final size:9
Alignment explanation
Indices: 3574869--3574925 Score: 66
Period size: 9 Copynumber: 6.7 Consensus size: 9
3574859 ATTATATATT
*
3574869 TAAATTTTG
1 TAAATTATG
3574878 TAAATTATG
1 TAAATTATG
3574887 --AATTATG
1 TAAATTATG
3574894 TAAATTATG
1 TAAATTATG
*
3574903 TAAAATATG
1 TAAATTATG
*
3574912 TAAGTTATG
1 TAAATTATG
3574921 -AAATT
1 TAAATT
3574926 TGAACTTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
7 7 0.17
8 4 0.10
9 30 0.73
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (9 bp):
TAAATTATG
Found at i:3574913 original size:18 final size:16
Alignment explanation
Indices: 3574876--3574924 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
3574866 ATTTAAATTT
*
3574876 TGTAAATTATGAATTA
1 TGTAAATTATGAAATA
3574892 TGTAAATTATGTAAAATA
1 TGTAAATTATG--AAATA
*
3574910 TGTAAGTTATGAAAT
1 TGTAAATTATGAAAT
3574925 TTGAACTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 15 0.52
18 14 0.48
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (16 bp):
TGTAAATTATGAAATA
Found at i:3575095 original size:29 final size:29
Alignment explanation
Indices: 3575054--3575111 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3575044 CAAAATATAT
3575054 TTTTGGAAATGAAATAGTTGACAAATGGA
1 TTTTGGAAATGAAATAGTTGACAAATGGA
3575083 TTTTGGAAATGAAATAGTTGACAAATGGA
1 TTTTGGAAATGAAATAGTTGACAAATGGA
3575112 AGAAGATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (29 bp):
TTTTGGAAATGAAATAGTTGACAAATGGA
Found at i:3579258 original size:22 final size:21
Alignment explanation
Indices: 3579219--3579259 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
3579209 ACTCTGACTA
3579219 TAAAAACTAAACTCCAAACTT
1 TAAAAACTAAACTCCAAACTT
3579240 TAAAACACTAAA-TCACAAAC
1 TAAAA-ACTAAACTC-CAAAC
3579260 CCAATATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (21 bp):
TAAAAACTAAACTCCAAACTT
Found at i:3579303 original size:23 final size:23
Alignment explanation
Indices: 3579276--3579350 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
3579266 TAACAAACCC
*
3579276 TAAACCATAAACTATAAAACCTT
1 TAAACCATAAACTATAAAACCAT
* * *
3579299 TAAACTACATACTATAGTAAA-CAT
1 TAAACCATAAACTATA--AAACCAT
* *
3579323 TAAACCTTAAACTATAAAACCCT
1 TAAACCATAAACTATAAAACCAT
3579346 TAAAC
1 TAAAC
3579351 TACATACTAT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
22 3 0.08
23 20 0.50
24 14 0.35
25 3 0.08
ACGTcount: A:0.51, C:0.21, G:0.01, T:0.27
Consensus pattern (23 bp):
TAAACCATAAACTATAAAACCAT
Found at i:3579359 original size:23 final size:23
Alignment explanation
Indices: 3579286--3579361 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
3579276 TAAACCATAA
*
3579286 ACTATAAAACCTTTAAACTACAT
1 ACTATAAAACCATTAAACTACAT
3579309 ACTATAGTAAA-CATTAAACCTTA-A-
1 ACTATA--AAACCATTAAA-C-TACAT
*
3579333 ACTATAAAACCCTTAAACTACAT
1 ACTATAAAACCATTAAACTACAT
3579356 ACTATA
1 ACTATA
3579362 GCCCTTAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
21 2 0.05
22 5 0.11
23 18 0.41
24 12 0.27
25 5 0.11
26 2 0.05
ACGTcount: A:0.49, C:0.21, G:0.01, T:0.29
Consensus pattern (23 bp):
ACTATAAAACCATTAAACTACAT
Found at i:3586683 original size:34 final size:32
Alignment explanation
Indices: 3586623--3586686 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 32
3586613 TACTTTTTAA
**
3586623 ATAAATTTATTGATTTTTAATTTTTAAAAATT
1 ATAAATTTATTGATTTTTAAAATTTAAAAATT
*
3586655 ATAAATGTTCTTGAATTTTTAAAATTTAAAAA
1 ATAAAT-TTATTG-ATTTTTAAAATTTAAAAA
3586687 ATGAATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 6 0.22
33 5 0.19
34 16 0.59
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (32 bp):
ATAAATTTATTGATTTTTAAAATTTAAAAATT
Found at i:3587152 original size:11 final size:11
Alignment explanation
Indices: 3587126--3587158 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
3587116 TTGTATACTG
3587126 TAAAAATAAAA
1 TAAAAATAAAA
3587137 T-AAAATAAAA
1 TAAAAATAAAA
*
3587147 TAAAAATCAAA
1 TAAAAATAAAA
3587158 T
1 T
3587159 TAAATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:3587152 original size:21 final size:21
Alignment explanation
Indices: 3587126--3587168 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3587116 TTGTATACTG
3587126 TAAAAATAAAATAAAATAAAA
1 TAAAAATAAAATAAAATAAAA
* * *
3587147 TAAAAATCAAATTAAATTAAA
1 TAAAAATAAAATAAAATAAAA
3587168 T
1 T
3587169 CGTTGAAGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAAAATAAAATAAAATAAAA
Found at i:3597131 original size:16 final size:16
Alignment explanation
Indices: 3597110--3597140 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3597100 TATCCAGAGG
3597110 GAAAAAAAAAGAAAAA
1 GAAAAAAAAAGAAAAA
*
3597126 GAAAAAGAAAGAAAA
1 GAAAAAAAAAGAAAA
3597141 GTCAATAACC
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
GAAAAAAAAAGAAAAA
Found at i:3602012 original size:21 final size:21
Alignment explanation
Indices: 3601986--3602026 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3601976 AGACGAGCAA
* *
3601986 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
3602007 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
3602027 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:3607338 original size:78 final size:78
Alignment explanation
Indices: 3607209--3607367 Score: 291
Period size: 78 Copynumber: 2.0 Consensus size: 78
3607199 CTATTGACAA
*
3607209 TAACTGTAGCTTGTAGGTGATAATGCTAAATACTAAAACTCACCCTAAACAATGTTTACTTTCAT
1 TAACTGTAGCTTGTAGGTGATAATGCTAAATACGAAAACTCACCCTAAACAATGTTTACTTTCAT
3607274 CTACATTCAGAAC
66 CTACATTCAGAAC
**
3607287 TAACTGTAGCTTGTAGGTGATAATGCTAAATACGAAAGTTCACCCTAAACAATGTTTACTTTCAT
1 TAACTGTAGCTTGTAGGTGATAATGCTAAATACGAAAACTCACCCTAAACAATGTTTACTTTCAT
3607352 CTACATTCAGAAC
66 CTACATTCAGAAC
3607365 TAA
1 TAA
3607368 GTCCAATAAC
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (78 bp):
TAACTGTAGCTTGTAGGTGATAATGCTAAATACGAAAACTCACCCTAAACAATGTTTACTTTCAT
CTACATTCAGAAC
Found at i:3618825 original size:32 final size:33
Alignment explanation
Indices: 3618784--3618859 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 33
3618774 ATCTTAATAT
* *
3618784 ATATATATGGTAATTGC-TTTTTATTAATTTTA
1 ATATATATGGTAATTACTTTTTTATTAACTTTA
*
3618816 ATATATATGGTAATTACTTTTTTTATTACCTTTA
1 ATATATATGGTAATTAC-TTTTTTATTAACTTTA
3618850 ATATATATGG
1 ATATATATGG
3618860 CAATAATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
32 16 0.41
34 23 0.59
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.54
Consensus pattern (33 bp):
ATATATATGGTAATTACTTTTTTATTAACTTTA
Found at i:3618901 original size:47 final size:47
Alignment explanation
Indices: 3618835--3618950 Score: 189
Period size: 47 Copynumber: 2.5 Consensus size: 47
3618825 GTAATTACTT
* *
3618835 TTTTTATTACCTTTAATATATATGGCAATAATATTATGGTAATGTTC
1 TTTTCATTGCCTTTAATATATATGGCAATAATATTATGGTAATGTTC
*
3618882 TTTTCATTGCCTTTAATATATATGGTAATAATATTATGGTAATGTTC
1 TTTTCATTGCCTTTAATATATATGGCAATAATATTATGGTAATGTTC
*
3618929 TTTTCATTGCCTTCAATA-ATAT
1 TTTTCATTGCCTTTAATATATAT
3618951 TATGGTAATT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
46 4 0.06
47 61 0.94
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.49
Consensus pattern (47 bp):
TTTTCATTGCCTTTAATATATATGGCAATAATATTATGGTAATGTTC
Found at i:3618921 original size:14 final size:15
Alignment explanation
Indices: 3618895--3618924 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3618885 TCATTGCCTT
3618895 TAATATATATGGTAA
1 TAATATATATGGTAA
3618910 TAATAT-TATGGTAA
1 TAATATATATGGTAA
3618924 T
1 T
3618925 GTTCTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (15 bp):
TAATATATATGGTAA
Found at i:3619479 original size:14 final size:14
Alignment explanation
Indices: 3619460--3619501 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
3619450 TTATATTTTA
3619460 AAAAAATTTAATAT
1 AAAAAATTTAATAT
**
3619474 AAAAAATAAAATTAT
1 AAAAAATTTAA-TAT
3619489 AAAAAA-TTAATAT
1 AAAAAATTTAATAT
3619502 GGGTCGAGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAAATTTAATAT
Found at i:3622185 original size:27 final size:27
Alignment explanation
Indices: 3622155--3622218 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
3622145 ATTTATATAT
*
3622155 TTTTTTAAAAAATATAAATTTTGAAAA
1 TTTTTTAAAAAATATAAATTTTAAAAA
* * * * *
3622182 TTTTATAAATATTCTGAATTTTAAAAA
1 TTTTTTAAAAAATATAAATTTTAAAAA
3622209 TTATTTTAAA
1 TT-TTTTAAA
3622219 TTTTTTTTGT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
27 23 0.79
28 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (27 bp):
TTTTTTAAAAAATATAAATTTTAAAAA
Found at i:3622220 original size:19 final size:18
Alignment explanation
Indices: 3622179--3622222 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
3622169 TAAATTTTGA
*
3622179 AAATTTTATAAATATTCT
1 AAATTTTAAAAATATTCT
* *
3622197 GAATTTTAAAAATTATTTT
1 AAATTTTAAAAA-TATTCT
3622216 AAATTTT
1 AAATTTT
3622223 TTTTGTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
AAATTTTAAAAATATTCT
Found at i:3634329 original size:15 final size:14
Alignment explanation
Indices: 3634309--3634338 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
3634299 AAACCCTGAA
3634309 TAAATATTCTTTTTT
1 TAAATATT-TTTTTT
3634324 TAAATATTTTTTTT
1 TAAATATTTTTTTT
3634338 T
1 T
3634339 CTTATTATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (14 bp):
TAAATATTTTTTTT
Found at i:3642220 original size:20 final size:20
Alignment explanation
Indices: 3642195--3642232 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3642185 CACTTCCACC
* *
3642195 TTTTATATTTTCTGAATTGA
1 TTTTATATATTCTCAATTGA
3642215 TTTTATATATTCTCAATT
1 TTTTATATATTCTCAATT
3642233 TAATTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTATATATTCTCAATTGA
Found at i:3643763 original size:16 final size:16
Alignment explanation
Indices: 3643742--3643772 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3643732 CGCTCTCCAA
3643742 CCTCACAAGAATAAAC
1 CCTCACAAGAATAAAC
3643758 CCTCACAAGAATAAA
1 CCTCACAAGAATAAA
3643773 TGGTGTATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.29, G:0.06, T:0.13
Consensus pattern (16 bp):
CCTCACAAGAATAAAC
Found at i:3648047 original size:22 final size:22
Alignment explanation
Indices: 3648022--3648079 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
3648012 ATATAGGCAA
*
3648022 AAATTAAAATATATGTATATAT
1 AAATTAAAATATATGTATATAC
* *
3648044 AAA-TATATATATATGTATTTAC
1 AAATTA-AAATATATGTATATAC
3648066 AAAGGTTAAAATAT
1 AAA--TTAAAATAT
3648080 GTACATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 2 0.07
22 19 0.68
24 5 0.18
25 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.40
Consensus pattern (22 bp):
AAATTAAAATATATGTATATAC
Found at i:3648356 original size:3 final size:3
Alignment explanation
Indices: 3648348--3648384 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
3648338 AAAAACAATT
*
3648348 ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3648385 AATTGCTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:3650079 original size:44 final size:43
Alignment explanation
Indices: 3649972--3650605 Score: 294
Period size: 44 Copynumber: 14.6 Consensus size: 43
3649962 TTTAAGTCTA
** * ** *
3649972 CTCCACTGTAATATCAGGGAGATAAGA-CCTGA-TGCGATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTTGATTTTGATCTG
** * * * *
3650013 CTCTGCTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCG
1 CTCCACTGTAACCTCAGGGAGATAAGAT-CTTGATTTTGATCTG
* * ** *
3650057 CTCCACTGTAACTTCAGGGAGATAGGATAGTG-TCTTCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTTGAT-TTTGATCTG
* ** **
3650100 CTCCGCTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCT-TGATTTTGATCTG
* * *
3650144 CTCCACTGTAACCTCAGGGAGATAAGATC-TGAAATTCTCCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTTG--ATT-T-TGATCTG
* * * *
3650190 CTCCACTGTAACCTCAGGGAAATAAGA-CCTGA-TGTGATCTT
1 CTCCACTGTAACCTCAGGGAGATAAGATCTTGATTTTGATCTG
* * * * * *
3650231 CTCTACTGTAACTTCAGAGAGATAAGATC----CTTTAATCCG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTTGATTTTGATCTG
* * * *
3650270 CTCCATTGTAATCTCAAGGAGATAGGAT-TACT-ATCTTTGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCT--TGAT-TTTGATCTG
* * ** **
3650314 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCT-TGATTTTGATCTG
* *
3650358 CTCCACTGTAACCTCAGGGAGATAAGATC-TGAAATTCTTCGGTCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTTG--ATT-TT-GATCTG
* * * ** *
3650404 CTCCAATGTAACCTCAGGGTGATAAGA-CCTGA-TGCGATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGATCTTGATTTTGATCTG
** * * * * *
3650445 CTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCG
1 CTCCACTGTAACCTCAGGGAGATAAGAT-CTTGATTTTGATCTG
* * * * ** *
3650489 CTCCACTGTAATCTCAGGGAGATAGGATTACTAG-CTTCAATCTA
1 CTCCACTGTAACCTCAGGGAGATAAGA-T-CTTGATTTTGATCTG
** * *
3650533 CTCCGTTGTAATCTCAGGGAGATAAGATC-TGAAATTCTTTGGTCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCTTG--A-T-TTTGATCTG
* *
3650579 TTCCACTGTAATCTCAGGGAGATAAGA
1 CTCCACTGTAACCTCAGGGAGATAAGA
3650606 CCTGTATAAT
Statistics
Matches: 440, Mismatches: 118, Indels: 65
0.71 0.19 0.10
Matches are distributed among these distances:
39 26 0.06
41 76 0.17
42 7 0.02
43 41 0.09
44 191 0.43
45 8 0.02
46 91 0.21
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (43 bp):
CTCCACTGTAACCTCAGGGAGATAAGATCTTGATTTTGATCTG
Found at i:3650122 original size:87 final size:87
Alignment explanation
Indices: 3649962--3650561 Score: 358
Period size: 87 Copynumber: 6.9 Consensus size: 87
3649952 AGGTTTTAGG
* * * * *
3649962 TTTAAGTCTACTCCACTGTAA-TATCAGGGAGATAAGA-CCTGATGCGATCTACTCTGCTGTAAC
1 TTTAA-TCTGCTCCACTGTAACT-TCAGGGAGATAAGATACTGCTTCGATCTACTCCGCTGTAAC
*
3650025 CTCAGAGAGATAAGATCCT-TTAT
64 CTCAGGGAGATAAGATCCTATTAT
* * * *
3650048 TTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAACC
1 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATACTG-CTTCGATCTACTCCGCTGTAACC
* ***
3650113 TCAGGGAGATAAGAT-CTCTGGC
65 TCAGGGAGATAAGATCCTATTAT
* * * * *
3650135 TTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTCCGGTCTACTCCACTGT
1 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATACTG-----CTTCGATCTACTCCGCTGT
* *
3650199 AACCTCAGGGAAATAAGA-CC--TGA-
61 AACCTCAGGGAGATAAGATCCTATTAT
* * * * * ** ** ** *
3650222 TGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGAT-C--CTTTAATCCGCTCCATTGTAATCT
1 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATACTGCTTCGATCTACTCCGCTGTAACCT
* * *
3650284 CAAGGAGATAGGAT--TACTAT
66 CAGGGAGATAAGATCCTATTAT
* * * * * *
3650304 CTTTGATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTA
1 -TTTAATCTGCTCCACTGTAACT-TCAGGGAGATAAGAT-ACT-GCTTCGATCTACTCCGCTGTA
*
3650368 ACCTCAGGGAGATAAGAT-CTGA-AAT
62 ACCTCAGGGAGATAAGATCCT-ATTAT
** * * * * * * * *
3650393 TCTTCGGTCTACTCCAATGTAACCTCAGGGTGATAAGA-CCTGATGCGATCTACTCTGCTGTAAC
1 T-TT-AATCTGCTCCACTGTAACTTCAGGGAGATAAGATACTGCTTCGATCTACTCCGCTGTAAC
* *
3650457 TTCAGAGAGATAAGATCCT-TTAT
64 CTCAGGGAGATAAGATCCTATTAT
* * * *
3650480 TTTAATCCGCTCCACTGTAA-TCTCAGGGAGATAGGATTACTAGCTTCAATCTACTCCGTTGTAA
1 TTTAATCTGCTCCACTGTAACT-TCAGGGAGATAAGA-TACT-GCTTCGATCTACTCCGCTGTAA
*
3650544 TCTCAGGGAGATAAGATC
63 CCTCAGGGAGATAAGATC
3650562 TGAAATTCTT
Statistics
Matches: 394, Mismatches: 89, Indels: 60
0.73 0.16 0.11
Matches are distributed among these distances:
80 26 0.07
81 1 0.00
82 1 0.00
83 30 0.08
85 51 0.13
86 14 0.04
87 134 0.34
88 71 0.18
89 5 0.01
90 61 0.15
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (87 bp):
TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATACTGCTTCGATCTACTCCGCTGTAACCT
CAGGGAGATAAGATCCTATTAT
Found at i:3650372 original size:214 final size:215
Alignment explanation
Indices: 3649967--3650562 Score: 910
Period size: 214 Copynumber: 2.7 Consensus size: 215
3649957 TTAGGTTTAA
** *
3649967 GTCTACTCCACTGTAATATCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACCTCAGAG
1 GTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAG
* *
3650032 AGATAAGATCCTTTATTTTAATCCGCTCCACTGTAA-CTTCAGGGAGATAGGA-TAGTGTCTTCG
66 AGATAAGATCC----TTTTAATCCGCTCCACTGTAATC-TCAGGGAGATAGGATTACTATCTTCG
*
3650095 ATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCA
126 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCA
3650160 GGGAGATAAGATCTGAAATTCTCCG
191 GGGAGATAAGATCTGAAATTCTCCG
* * * *
3650185 GTCTACTCCACTGTAACCTCAGGGAAATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAG
1 GTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAG
* * *
3650250 AGATAAGATCC-TTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTG
66 AGATAAGATCCTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCGATCTG
3650314 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
131 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
*
3650379 ATAAGATCTGAAATTCTTCG
196 ATAAGATCTGAAATTCTCCG
* *
3650399 GTCTACTCCAATGTAACCTCAGGGTGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAG
1 GTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAG
* *
3650464 AGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAA
66 AGATAAGATCC----TTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCGA
* *
3650529 TCTACTCCGTTGTAATCTCAGGGAGATAAGATCT
127 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
3650563 GAAATTCTTT
Statistics
Matches: 344, Mismatches: 27, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
213 32 0.09
214 167 0.49
218 69 0.20
219 76 0.22
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (215 bp):
GTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAG
AGATAAGATCCTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCGATCTG
CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
ATAAGATCTGAAATTCTCCG
Found at i:3659521 original size:50 final size:49
Alignment explanation
Indices: 3659452--3659596 Score: 185
Period size: 49 Copynumber: 3.0 Consensus size: 49
3659442 AATCAACAAA
* *
3659452 TCACATACCG-TGCCA-AGCCCAAGCTATGGGTCTTAACACGAAATCACATA-
1 TCACTTACCGATGCCATAGCCC-AGCTAT-GGTCTT--CACGGAATCACATAT
3659502 TCAC-TA-CGATGCCATAGCCCAGCTA-GGTCTTCACGGAATCACATAT
1 TCACTTACCGATGCCATAGCCCAGCTATGGTCTTCACGGAATCACATAT
3659548 TCACTTACTCGATGCCATAGCCCAGCTATGGTCTTCACGGAATCACATA
1 TCACTTAC-CGATGCCATAGCCCAGCTATGGTCTTCACGGAATCACATA
3659597 ATCAATGTCA
Statistics
Matches: 87, Mismatches: 1, Indels: 14
0.85 0.01 0.14
Matches are distributed among these distances:
45 13 0.15
46 4 0.05
47 8 0.09
48 2 0.02
49 31 0.36
50 29 0.33
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (49 bp):
TCACTTACCGATGCCATAGCCCAGCTATGGTCTTCACGGAATCACATAT
Found at i:3660903 original size:37 final size:37
Alignment explanation
Indices: 3660844--3660990 Score: 228
Period size: 37 Copynumber: 4.0 Consensus size: 37
3660834 TACGTATGAT
*
3660844 CACTTATCAC-TTG-TCCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
3660879 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
3660916 CACTTATCACTTTGTTTCTTTGATCAGAT-AGTGTAGC
1 CACTTATCACTTTGTTTC-TTGATCAGATAAGTGTAGC
*
3660953 CACTTATCACTTATGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTT-TGTTTCTTGATCAGATAAGTGTAGC
3660991 TAAAGCTATA
Statistics
Matches: 103, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 68 0.66
38 23 0.22
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:3660977 original size:75 final size:72
Alignment explanation
Indices: 3660844--3660990 Score: 224
Period size: 75 Copynumber: 2.0 Consensus size: 72
3660834 TACGTATGAT
*
3660844 CACTTATCACTTGTCCTTGATCAGATAAGTGTAGCCACCTATCACTTTGTTTCTTGATCAGATAA
1 CACTTATCACTTGTCCTTGATCAGATAAGTGTAGCCACCTATCACTTTGTCTCTTGATCAGATAA
3660909 GTGTAGC
66 GTGTAGC
* *
3660916 CACTTATCACTTTGTTTCTTTGATCAGAT-AGTGTAGCCACTTATCACTTATGTCTCTTGATCAG
1 CACTTATCAC-TTG--TCCTTGATCAGATAAGTGTAGCCACCTATCACTT-TGTCTCTTGATCAG
3660980 ATAAGTGTAGC
62 ATAAGTGTAGC
3660991 TAAAGCTATA
Statistics
Matches: 68, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
72 10 0.15
73 3 0.04
74 19 0.28
75 36 0.53
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.38
Consensus pattern (72 bp):
CACTTATCACTTGTCCTTGATCAGATAAGTGTAGCCACCTATCACTTTGTCTCTTGATCAGATAA
GTGTAGC
Found at i:3661008 original size:45 final size:48
Alignment explanation
Indices: 3660954--3661171 Score: 181
Period size: 45 Copynumber: 4.6 Consensus size: 48
3660944 TAGTGTAGCC
*
3660954 ACTTATCAC-TT-ATGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 ACTTATCACTTTCATGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
* * * *
3661000 AC-TATCACTGT--TGTCTCTTGATCA-ATAAGT-AAGC-GAAGCTAT
1 ACTTATCACTTTCATGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
* * *
3661042 CACTTATCACTTTTCCTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTTT
1 -ACTTATCAC-TTT-CATGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
*
3661093 ACTTATTCCACTTTCCACTTGTCACTTGATCAGATAA-TGTAGCTAAAGCTACC
1 ACTTA-T-CACTTT-CA--TGTCACTTGATCAGATAAGTGTAGCTAAAGCTA-T
*
3661146 ACTTTTCACTTT-A--TCACTTGATCAGA
1 ACTTATCACTTTCATGTCACTTGATCAGA
3661172 AGTACTCAAA
Statistics
Matches: 145, Mismatches: 12, Indels: 31
0.77 0.06 0.16
Matches are distributed among these distances:
42 7 0.05
43 5 0.03
44 12 0.08
45 34 0.23
46 3 0.02
48 12 0.08
49 7 0.05
50 8 0.06
51 19 0.13
52 16 0.11
53 22 0.15
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.37
Consensus pattern (48 bp):
ACTTATCACTTTCATGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
Found at i:3661120 original size:53 final size:51
Alignment explanation
Indices: 3660966--3661157 Score: 190
Period size: 53 Copynumber: 3.9 Consensus size: 51
3660956 TTATCACTTA
* * *
3660966 TGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT-AC-TATCAC--T--GT
1 TGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCCT
* * *
3661011 TGTCTCTTGATCA-ATAAGT-AAGC-GAAGCTATCACTTATCACTTTTCCT
1 TGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCCT
*
3661059 TGTCACTTGATCAGATAAGTGTAGCTGAAGCT-TTACTTATTCCACTTTCCACT
1 TGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTA-T-CACTTTCC-CT
* * *
3661112 TGTCACTTGATCAGATAA-TGTAGCTAAAGCTACCACTTTTCACTTT
1 TGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTT
3661158 ATCACTTGAT
Statistics
Matches: 123, Mismatches: 11, Indels: 20
0.80 0.07 0.13
Matches are distributed among these distances:
42 7 0.06
43 5 0.04
44 12 0.10
45 13 0.11
46 1 0.01
48 13 0.11
49 6 0.05
50 9 0.07
51 13 0.11
52 20 0.16
53 24 0.20
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (51 bp):
TGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTCCCT
Found at i:3661164 original size:52 final size:51
Alignment explanation
Indices: 3661010--3661165 Score: 178
Period size: 52 Copynumber: 3.1 Consensus size: 51
3661000 ACTATCACTG
* *
3661010 TTGTCTCTTGATCA-ATAA-GTAAGC-GAAGCTATCACTTATCACTTTTC-C
1 TTGTCACTTGATCAGATAATGT-AGCTGAAGCTATCACTTTTCACTTTTCAC
* *
3661058 TTGTCACTTGATCAGATAAGTGTAGCTGAAGCT-TTACTTATTCCACTTTCCAC
1 TTGTCACTTGATCAGATAA-TGTAGCTGAAGCTATCACTT-TT-CACTTTTCAC
* *
3661111 TTGTCACTTGATCAGATAATGTAGCTAAAGCTACCACTTTTCACTTTATCAC
1 TTGTCACTTGATCAGATAATGTAGCTGAAGCTATCACTTTTCACTTT-TCAC
3661163 TTG
1 TTG
3661166 ATCAGAAGTA
Statistics
Matches: 91, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
48 13 0.14
49 4 0.04
50 8 0.09
51 15 0.16
52 27 0.30
53 24 0.26
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.38
Consensus pattern (51 bp):
TTGTCACTTGATCAGATAATGTAGCTGAAGCTATCACTTTTCACTTTTCAC
Found at i:3665792 original size:1 final size:1
Alignment explanation
Indices: 3665761--3665785 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3665751 TGATCACATG
3665761 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
3665786 GCTTTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3667651 original size:19 final size:17
Alignment explanation
Indices: 3667624--3667664 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 17
3667614 AAAAAATTTA
3667624 TTTTAGTCTTTTATTTAAT
1 TTTTAGTC-TTT-TTTAAT
*
3667643 TTTTCGTCTTTTTTAAT
1 TTTTAGTCTTTTTTAAT
3667660 TTTTA
1 TTTTA
3667665 AAATTTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 10 0.50
18 3 0.15
19 7 0.35
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (17 bp):
TTTTAGTCTTTTTTAAT
Found at i:3670468 original size:16 final size:15
Alignment explanation
Indices: 3670440--3670469 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3670430 ACGTTTACGA
3670440 ATAAAATAAATATAT
1 ATAAAATAAATATAT
3670455 ATAAAATAAA-ATAT
1 ATAAAATAAATATAT
3670469 A
1 A
3670470 AATAGAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAAAATAAATATAT
Found at i:3672544 original size:56 final size:55
Alignment explanation
Indices: 3672468--3672590 Score: 133
Period size: 56 Copynumber: 2.2 Consensus size: 55
3672458 TTTAAAAAAA
* * *
3672468 TTTGGTTGTCGTCGGTATGTCAGGCAACACCAGTAAATATTTAATAAAAAA-A-ATTT
1 TTTGG-TGTCGCCGGAATGTCAGACAACACCAGTAAA-ATTTAA-AAAAAATATATTT
* * *
3672524 TGTTGGTGTCGCCGGAATGTCAGACGACACCCGTTAAATTTAAAAAAAATATATTT
1 T-TTGGTGTCGCCGGAATGTCAGACAACACCAGTAAAATTTAAAAAAAATATATTT
3672580 TTTAGGTGTCG
1 TTT-GGTGTCG
3672591 TTGTCATGTC
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
54 6 0.11
55 9 0.16
56 38 0.67
57 4 0.07
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (55 bp):
TTTGGTGTCGCCGGAATGTCAGACAACACCAGTAAAATTTAAAAAAAATATATTT
Found at i:3672659 original size:11 final size:11
Alignment explanation
Indices: 3672643--3672669 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3672633 TTGCAGAAAG
3672643 AATATTTAAAA
1 AATATTTAAAA
3672654 AATATTTAAAA
1 AATATTTAAAA
3672665 AATAT
1 AATAT
3672670 ATATTGCAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AATATTTAAAA
Found at i:3673134 original size:47 final size:46
Alignment explanation
Indices: 3673056--3673234 Score: 135
Period size: 47 Copynumber: 4.0 Consensus size: 46
3673046 ATTTAATATT
* * *
3673056 TTATTATTTTCCACATCTGATATTTTATTTCC-TTTCTCATATTTGA
1 TTATTATTTTCCATATATGATATTCTATTTCCTTTTCT-ATATTTGA
* *
3673102 TTATGTATTTTCCATATATGTTATTCTCTTTCCTTTTCTATATTTGA
1 TTAT-TATTTTCCATATATGATATTCTATTTCCTTTTCTATATTTGA
* * **
3673149 TTCTCTATTTTCCATA-A-AATATTAAATTTCC-TTTC-ATA--T--
1 TTAT-TATTTTCCATATATGATATTCTATTTCCTTTTCTATATTTGA
* * * * *
3673188 CT-CTATTTTCCATATTTGTTATTCTATTTCCTTTCCTATATTTGA
1 TTATTATTTTCCATATATGATATTCTATTTCCTTTTCTATATTTGA
3673233 TT
1 TT
3673235 CTCCATTTTC
Statistics
Matches: 102, Mismatches: 21, Indels: 21
0.71 0.15 0.15
Matches are distributed among these distances:
37 11 0.11
39 11 0.11
40 3 0.03
41 4 0.04
43 4 0.04
44 4 0.04
45 10 0.10
46 5 0.05
47 45 0.44
48 5 0.05
ACGTcount: A:0.22, C:0.17, G:0.04, T:0.57
Consensus pattern (46 bp):
TTATTATTTTCCATATATGATATTCTATTTCCTTTTCTATATTTGA
Found at i:3673210 original size:84 final size:84
Alignment explanation
Indices: 3673107--3673315 Score: 267
Period size: 84 Copynumber: 2.5 Consensus size: 84
3673097 TTTGATTATG
* * * * *
3673107 TATTTTCCATATATGTTATTCTCTTTCCTTTTCTATATTTGATTCTCTATTTTCCATAAAATATT
1 TATTTTCCATATTTGTTATTCTCTTTCCTTTCCTATATTTGATTCTCCATTTTCAACAAAATATT
3673172 AAATT-TCCTTTCATATCTC
66 AAATTCT-CTTTCATATCTC
*
3673191 TATTTTCCATATTTGTTATTCTATTTCCTTTCCTATATTTGATTCTCCATTTTCAACAAAATATT
1 TATTTTCCATATTTGTTATTCTCTTTCCTTTCCTATATTTGATTCTCCATTTTCAACAAAATATT
* *
3673256 CAATTCTCTTTCATATTTC
66 AAATTCTCTTTCATATCTC
* * * * *
3673275 TATTGTACATATAGTTGTTATTCTCTTGCATTTCCCATATT
1 TATTTTCCATAT--TTGTTATTCTCTTTCCTTTCCTATATT
3673316 GACATTCATT
Statistics
Matches: 108, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
84 84 0.78
85 1 0.01
86 23 0.21
ACGTcount: A:0.23, C:0.19, G:0.04, T:0.54
Consensus pattern (84 bp):
TATTTTCCATATTTGTTATTCTCTTTCCTTTCCTATATTTGATTCTCCATTTTCAACAAAATATT
AAATTCTCTTTCATATCTC
Found at i:3676309 original size:9 final size:9
Alignment explanation
Indices: 3676261--3676389 Score: 70
Period size: 9 Copynumber: 14.6 Consensus size: 9
3676251 ATCCAAAGTT
3676261 TTATGTAAG
1 TTATGTAAG
*
3676270 TTATGATATG
1 TTATG-TAAG
* * *
3676280 ATATAT-AT
1 TTATGTAAG
3676288 TTATGT-A-
1 TTATGTAAG
3676295 TTATGTAAG
1 TTATGTAAG
3676304 TTATGTAAG
1 TTATGTAAG
*
3676313 TTATGATATG
1 TTATG-TAAG
* * *
3676323 ATATAT-AT
1 TTATGTAAG
*
3676331 TTTTGTAAG
1 TTATGTAAG
*
3676340 TTACGTAAG
1 TTATGTAAG
*
3676349 TTATGATATG
1 TTATG-TAAG
* * *
3676359 ATATAT-AC
1 TTATGTAAG
3676367 TTATGTAAG
1 TTATGTAAG
3676376 TTATGTAAG
1 TTATGTAAG
3676385 TTATG
1 TTATG
3676390 AAATTTGAAC
Statistics
Matches: 86, Mismatches: 27, Indels: 14
0.68 0.21 0.11
Matches are distributed among these distances:
7 6 0.07
8 13 0.15
9 49 0.57
10 18 0.21
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:3676311 original size:43 final size:42
Alignment explanation
Indices: 3676261--3676389 Score: 171
Period size: 36 Copynumber: 3.1 Consensus size: 42
3676251 ATCCAAAGTT
3676261 TTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAG
1 TTATGTAAGTTATGATATGATATATA-TTATGTATTATGTAAG
3676304 TTATGTAAGTTATGATATG--ATATA-TAT-T-TT-TGTAAG
1 TTATGTAAGTTATGATATGATATATATTATGTATTATGTAAG
*
3676340 TTACGTAAGTTATGATATGATATATACTTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGATATGATATATA-TTATGT-A-TTATGTAAG
3676385 TTATG
1 TTATG
3676390 AAATTTGAAC
Statistics
Matches: 75, Mismatches: 2, Indels: 16
0.81 0.02 0.17
Matches are distributed among these distances:
36 24 0.32
37 2 0.03
38 6 0.08
39 3 0.04
40 3 0.04
41 6 0.08
43 19 0.25
44 2 0.03
45 10 0.13
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (42 bp):
TTATGTAAGTTATGATATGATATATATTATGTATTATGTAAG
Found at i:3677844 original size:12 final size:11
Alignment explanation
Indices: 3677817--3677842 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3677807 ATATTTTTTA
3677817 TTTTAAAGTAT
1 TTTTAAAGTAT
3677828 TTTTAAAGTAT
1 TTTTAAAGTAT
3677839 TTTT
1 TTTT
3677843 TATTTTTTAT
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:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (11 bp):
TTTTAAAGTAT
Found at i:3678513 original size:23 final size:23
Alignment explanation
Indices: 3678483--3678527 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
3678473 AGTTTGCAAG
3678483 TATAGGACAATGAAGGCTTTAAA
1 TATAGGACAATGAAGGCTTTAAA
3678506 TATAGGACAATGAAGGCTTTAA
1 TATAGGACAATGAAGGCTTTAA
3678528 CAGTTTGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (23 bp):
TATAGGACAATGAAGGCTTTAAA
Found at i:3682200 original size:30 final size:30
Alignment explanation
Indices: 3682133--3682223 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 30
3682123 TCCATATTTA
* *
3682133 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
3682163 T---AAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
3682190 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
3682221 TGG
1 TGG
3682224 CATAATAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 25 0.46
30 21 0.39
31 8 0.15
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:3686836 original size:27 final size:28
Alignment explanation
Indices: 3686798--3686871 Score: 105
Period size: 27 Copynumber: 2.6 Consensus size: 28
3686788 TTATGGAAAA
3686798 TCAAAGATATGGGTATCAAATAAT-AAG
1 TCAAAGATATGGGTATCAAATAATGAAG
* *
3686825 TCAAATATATGGGTATCAAATATTGGAAAG
1 TCAAAGATATGGGTATCAAATAAT-G-AAG
3686855 TCAAAGATATGGGTATC
1 TCAAAGATATGGGTATC
3686872 GAGATATTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 22 0.54
30 19 0.46
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.28
Consensus pattern (28 bp):
TCAAAGATATGGGTATCAAATAATGAAG
Found at i:3697946 original size:28 final size:27
Alignment explanation
Indices: 3697901--3697963 Score: 108
Period size: 28 Copynumber: 2.3 Consensus size: 27
3697891 AATTTTGATT
*
3697901 CAAACTTTCAAGTTTGACTTGATCAAC
1 CAAATTTTCAAGTTTGACTTGATCAAC
3697928 CAGAATTTTCAAGTTTGACTTGATCAAC
1 CA-AATTTTCAAGTTTGACTTGATCAAC
3697956 CAAATTTT
1 CAAATTTT
3697964 AACATGAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 8 0.24
28 26 0.76
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (27 bp):
CAAATTTTCAAGTTTGACTTGATCAAC
Found at i:3699981 original size:13 final size:13
Alignment explanation
Indices: 3699963--3699992 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3699953 AATATTTATA
3699963 AAAGATCGAACCC
1 AAAGATCGAACCC
3699976 AAAGATCGAACCC
1 AAAGATCGAACCC
3699989 AAAG
1 AAAG
3699993 GAAAAGATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.27, G:0.17, T:0.07
Consensus pattern (13 bp):
AAAGATCGAACCC
Found at i:3700363 original size:19 final size:18
Alignment explanation
Indices: 3700335--3700370 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3700325 AAGCAGCTAT
3700335 AAAAGTAAAACTTAAGAA
1 AAAAGTAAAACTTAAGAA
*
3700353 AAAATGTAAAAGTTAAGA
1 AAAA-GTAAAACTTAAGA
3700371 TTTTCATGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.64, C:0.03, G:0.14, T:0.19
Consensus pattern (18 bp):
AAAAGTAAAACTTAAGAA
Found at i:3700699 original size:11 final size:11
Alignment explanation
Indices: 3700669--3700710 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
3700659 ACCTAAGTGC
*
3700669 AGAGAAAAACT
1 AGAGAAAACCT
*
3700680 AAAGAAAACCT
1 AGAGAAAACCT
*
3700691 AGAGAAAACTT
1 AGAGAAAACCT
3700702 AGAGAAAAC
1 AGAGAAAAC
3700711 TAAACCTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.62, C:0.12, G:0.17, T:0.10
Consensus pattern (11 bp):
AGAGAAAACCT
Found at i:3701527 original size:41 final size:41
Alignment explanation
Indices: 3701443--3701533 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
3701433 ACATGGACCG
* *
3701443 ATTCAATTGGATCAATGGTTGTACGATTAATTATACAATTT
1 ATTCAATTGGATCAATGGTTATACGATTAATTATACAAATT
* *
3701484 ATTCAATTGGATCATTGGTTATACGATTAGTGTA-ACAAATT
1 ATTCAATTGGATCAATGGTTATACGATTAAT-TATACAAATT
*
3701525 ATTCGATTG
1 ATTCAATTG
3701534 CGCTACAAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (41 bp):
ATTCAATTGGATCAATGGTTATACGATTAATTATACAAATT
Found at i:3704191 original size:12 final size:12
Alignment explanation
Indices: 3704172--3704200 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3704162 TATGATTAAA
3704172 AATA-TTATCTT
1 AATATTTATCTT
3704183 AATATTTATCTT
1 AATATTTATCTT
3704195 AATATT
1 AATATT
3704201 AATTAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (12 bp):
AATATTTATCTT
Found at i:3709598 original size:22 final size:21
Alignment explanation
Indices: 3709573--3709621 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
3709563 TTTTATTTTT
*
3709573 ATTTATGTTT-ATTGCCTATTTA
1 ATTT-TGTTTAATTG-CAATTTA
3709595 ATTTTGTTTTAATTGCAATTTA
1 ATTTTG-TTTAATTGCAATTTA
3709617 ATTTT
1 ATTTT
3709622 TGTTCCTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 2 0.08
22 18 0.75
23 4 0.17
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.61
Consensus pattern (21 bp):
ATTTTGTTTAATTGCAATTTA
Found at i:3718166 original size:26 final size:26
Alignment explanation
Indices: 3718095--3718166 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 26
3718085 TTAGGGCTAG
*
3718095 TTTAACAA-TACTTTTGAAAAGTGCT
1 TTTAAAAAGTACTTTTGAAAAGTGCT
* * *
3718120 TTTAAAAAGT-GTTGTGAAAAAGTGTT
1 TTTAAAAAGTACTTTTG-AAAAGTGCT
* *
3718146 TTTTAGAAGTACTTTTGAAAA
1 TTTAAAAAGTACTTTTGAAAA
3718167 TTTTTGAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
25 11 0.31
26 21 0.58
27 4 0.11
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (26 bp):
TTTAAAAAGTACTTTTGAAAAGTGCT
Found at i:3741144 original size:15 final size:15
Alignment explanation
Indices: 3741124--3741174 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
3741114 ACAACATGAT
3741124 AACGTAAATGACTAA
1 AACGTAAATGACTAA
* *
3741139 AACGTAACAT--TTCA
1 AACGTAA-ATGACTAA
*
3741153 AACATAAATGACTAA
1 AACGTAAATGACTAA
3741168 AACGTAA
1 AACGTAA
3741175 CCTAAGGTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 15 0.56
16 2 0.07
ACGTcount: A:0.53, C:0.16, G:0.10, T:0.22
Consensus pattern (15 bp):
AACGTAAATGACTAA
Found at i:3743173 original size:2 final size:2
Alignment explanation
Indices: 3743166--3743195 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3743156 GTGCAATCTC
3743166 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
3743196 TAAAAAAGCC
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3745261 original size:12 final size:12
Alignment explanation
Indices: 3745233--3745264 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3745223 TATTTTTTAT
3745233 GAGAT-AATTAA
1 GAGATAAATTAA
3745244 -AGATAAATTAA
1 GAGATAAATTAA
3745255 GAGATAAATT
1 GAGATAAATT
3745265 CAACTTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.21
11 6 0.32
12 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (12 bp):
GAGATAAATTAA
Found at i:3745456 original size:8 final size:8
Alignment explanation
Indices: 3745443--3745474 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
3745433 ATTATCGTAC
3745443 ATGTTGGT
1 ATGTTGGT
3745451 ATGTTGGT
1 ATGTTGGT
3745459 ATGTTGGT
1 ATGTTGGT
3745467 ATGTTGGT
1 ATGTTGGT
3745475 GGGAGTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (8 bp):
ATGTTGGT
Found at i:3746402 original size:7 final size:7
Alignment explanation
Indices: 3746390--3746422 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
3746380 TCGTATTGTA
3746390 GCCTTCT
1 GCCTTCT
3746397 GCCTTCT
1 GCCTTCT
3746404 GCCTTCT
1 GCCTTCT
*
3746411 GCCTTCC
1 GCCTTCT
3746418 GCCTT
1 GCCTT
3746423 TTACATTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.45, G:0.15, T:0.39
Consensus pattern (7 bp):
GCCTTCT
Found at i:3749055 original size:23 final size:22
Alignment explanation
Indices: 3749025--3749069 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
3749015 TGTTAAGAGT
*
3749025 TATATTTT-TAATTGATATTTAA
1 TATATTTTATAA-TGAAATTTAA
3749047 TATACTTTTATAATGAAATTTAA
1 TATA-TTTTATAATGAAATTTAA
3749070 ATTTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 13 0.65
24 3 0.15
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (22 bp):
TATATTTTATAATGAAATTTAA
Found at i:3751138 original size:25 final size:25
Alignment explanation
Indices: 3751103--3751178 Score: 109
Period size: 25 Copynumber: 3.0 Consensus size: 25
3751093 CAAAGTCCCG
*
3751103 ATTCACAGCTCGTGTGAGTAATT-T
1 ATTCACAGCTCGTGTGAGCAATTAT
*
3751127 ATTTCACAGCTCGTGTTAGCAATTAT
1 A-TTCACAGCTCGTGTGAGCAATTAT
3751153 ATTCACAGCTCGTGTGAGCAAATTAT
1 ATTCACAGCTCGTGTGAGC-AATTAT
3751179 GTCATGTGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
24 1 0.02
25 37 0.80
26 8 0.17
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (25 bp):
ATTCACAGCTCGTGTGAGCAATTAT
Found at i:3751304 original size:22 final size:21
Alignment explanation
Indices: 3751263--3751310 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
3751253 GAAAGATTAA
3751263 ATATGAAATCAATGGTTATAT
1 ATATGAAATCAATGGTTATAT
*
3751284 GTATGAAATGCTAA-GGTTATAT
1 ATATGAAAT-C-AATGGTTATAT
3751306 ATATG
1 ATATG
3751311 CATGTATGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 13 0.57
23 2 0.09
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (21 bp):
ATATGAAATCAATGGTTATAT
Found at i:3753410 original size:15 final size:16
Alignment explanation
Indices: 3753376--3753422 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
3753366 CAGTTATTCG
*
3753376 GAACAACCTCAATATTGA
1 GAACAA-CTC-ATGTTGA
3753394 GAACAACT-ATGTTGA
1 GAACAACTCATGTTGA
3753409 GAACAACTCATGTT
1 GAACAACTCATGTT
3753423 TGGAACAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 14 0.52
16 5 0.19
17 2 0.07
18 6 0.22
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (16 bp):
GAACAACTCATGTTGA
Found at i:3759680 original size:24 final size:24
Alignment explanation
Indices: 3759625--3759682 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
3759615 GTTACATAAA
* * *
3759625 AATTCAAAATACTAATTTAAAAAT
1 AATTTAAAATAATAATTCAAAAAT
** *
3759649 AAGATAAAATAATAATTCAAAATT
1 AATTTAAAATAATAATTCAAAAAT
3759673 AATTTAAAAT
1 AATTTAAAAT
3759683 CAAGATAATA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (24 bp):
AATTTAAAATAATAATTCAAAAAT
Found at i:3759681 original size:35 final size:37
Alignment explanation
Indices: 3759620--3759695 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
3759610 AGATAGTTAC
3759620 ATAAAAATTCAAAATACTAATTTAAAAAT-AAGATAA-A
1 ATAAAAATTCAAAATA-TAATTT-AAAATCAAGATAATA
*
3759657 ATAATAATTCAAAAT-TAATTTAAAATCAAGATAATA
1 ATAAAAATTCAAAATATAATTTAAAATCAAGATAATA
3759693 ATA
1 ATA
3759696 GCTAATCTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
34 5 0.14
35 13 0.36
36 4 0.11
37 14 0.39
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (37 bp):
ATAAAAATTCAAAATATAATTTAAAATCAAGATAATA
Found at i:3761478 original size:28 final size:28
Alignment explanation
Indices: 3761428--3761481 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
3761418 AACTTAACCT
**
3761428 TTCTCTTCCCTTTTTTTTTTCTTTTCCA
1 TTCTCTTCCCTTTTTTAGTTCTTTTCCA
3761456 TTCT-TTCCCTTTTATTAGTTCTTTTC
1 TTCTCTTCCCTTTT-TTAGTTCTTTTC
3761482 TTCAGCTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.06, C:0.26, G:0.02, T:0.67
Consensus pattern (28 bp):
TTCTCTTCCCTTTTTTAGTTCTTTTCCA
Found at i:3762152 original size:22 final size:22
Alignment explanation
Indices: 3762110--3762152 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3762100 AAATATTAAA
* *
3762110 ATATATTTTTATTTGATATTTT
1 ATATATTTTTAATTGAAATTTT
3762132 ATATATTTTATAATT-AAATTT
1 ATATATTTT-TAATTGAAATTT
3762153 AAAAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
ATATATTTTTAATTGAAATTTT
Found at i:3772228 original size:106 final size:106
Alignment explanation
Indices: 3772043--3772243 Score: 384
Period size: 106 Copynumber: 1.9 Consensus size: 106
3772033 AAGCTTTAAG
3772043 AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACATTTTCTCGA
1 AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACATTTTCTCGA
3772108 TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
66 TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
* *
3772149 AGGATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTCGA
1 AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACATTTTCTCGA
3772214 TTTTCCAAACGCGAAATATTGCCTTATTTA
66 TTTTCCAAACGCGAAATATTGCCTTATTTA
3772244 GAAAAATTTT
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 93 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (106 bp):
AGGATATTTGGCTATTTAGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACATTTTCTCGA
TTTTCCAAACGCGAAATATTGCCTTATTTAAAAGTTTAAAA
Found at i:3772764 original size:38 final size:38
Alignment explanation
Indices: 3772705--3772810 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 38
3772695 TATTTTTAAG
*
3772705 AATAT-AAAGAATATATATAAGTATGTATATG-ATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAGAAT-TAGA
* *
3772742 AATATGTATAAATATATGTAAGTA--TATAAGAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAGAATTA-GA
*
3772780 AATATGAAAAATATATTTAAGTATGTATAAG
1 AATATGAAAAATATATATAAGTATGTATAAG
3772811 TACGTATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.12
37 22 0.39
38 20 0.35
39 8 0.14
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (38 bp):
AATATGAAAAATATATATAAGTATGTATAAGAATTAGA
Found at i:3773152 original size:22 final size:23
Alignment explanation
Indices: 3773096--3773152 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
3773086 AGTTTAAAAT
3773096 AAAATATATAAAAGAAAGTCTTA
1 AAAATATATAAAAGAAAGTCTTA
*
3773119 AATAATA-A-AAAAGACAGT-TTA
1 AA-AATATATAAAAGAAAGTCTTA
3773140 AAAATATATAAAA
1 AAAATATATAAAA
3773153 ATAGTGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 13 0.43
23 3 0.10
24 4 0.13
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.25
Consensus pattern (23 bp):
AAAATATATAAAAGAAAGTCTTA
Found at i:3773882 original size:13 final size:13
Alignment explanation
Indices: 3773864--3773888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3773854 AAATGCGTAG
3773864 ATAAATAAATGAA
1 ATAAATAAATGAA
3773877 ATAAATAAATGA
1 ATAAATAAATGA
3773889 TAGATGATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
ATAAATAAATGAA
Found at i:3779625 original size:16 final size:16
Alignment explanation
Indices: 3779604--3779637 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3779594 TTGGACTTTC
3779604 TTAGGTGTAAAATAAT
1 TTAGGTGTAAAATAAT
3779620 TTAGGTGTAAAATAAT
1 TTAGGTGTAAAATAAT
3779636 TT
1 TT
3779638 GTAGGATAGT
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:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (16 bp):
TTAGGTGTAAAATAAT
Found at i:3783500 original size:45 final size:45
Alignment explanation
Indices: 3783445--3784119 Score: 816
Period size: 45 Copynumber: 15.2 Consensus size: 45
3783435 GGAAAGTAAA
* *
3783445 ATCTGTTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACCAG
1 ATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAG
*
3783490 ATCTGCTATCTTCAGTCTACTTTGCTGCCAATACAGGAAGACAAG
1 ATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAG
* * *
3783535 A-CTTGCTATATTC-GATCTACTTCGCTGCCAGTACAGGAAGACAGG
1 ATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAG
* *
3783580 ATCTGCTATCTTCAGTCTACTTTGCTGCCAATACAGGAAGACGAG
1 ATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAG
*
3783625 A-CTTGCTATCTTC-GATCTACTTCGTTGCCAATACAGGAAGACAAG
1 ATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAG
*
3783670 ATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGATAAG
1 ATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAG
*
3783715 A-CTTGCTATCTT-TGATCTACTTCGCTGCCAATACAGGAAGACAAG
1 ATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAG
* * *
3783760 ATTTGCTATCTTCAATCTACTTCGCTGCCAATACAAGAAGACAAG
1 ATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAG
*
3783805 A-CTTGCTATCTTC-GATCTACTTCGCTGCCAATACAGGAAGACAAT
1 ATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAG
* * * * *
3783850 ATATGTTATCTTCAGTCTATTTTGCTGCCAATACAGGAAGATAAG
1 ATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAG
* *
3783895 A-CTTGCTATCTT-TGATCTACTTCGCTGCCAATACAGGAAGATAAG
1 ATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAG
* *
3783940 ATTTGCTATCTTCAGTCTACTTCGTTGCCAATACAGGAAGACAAG
1 ATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAG
* *
3783985 A-CT--TA-C-T-A-TCT--TTCTCTGCCAATACAGGAAGACAAT
1 ATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAG
* * *
3784021 ATCTGTTATCTTCAGTCTACTTTGTTGCCAATACAGGAAGACAAG
1 ATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAG
*
3784066 A-CTTGCTATCTTC-GATCTACTTCGTTGCCAATACAGGAAGACAAG
1 ATC-TGCTATCTTCAG-TCTACTTCGCTGCCAATACAGGAAGACAAG
*
3784111 ATCTACTAT
1 ATCTGCTAT
3784120 AATGACTTCA
Statistics
Matches: 545, Mismatches: 53, Indels: 64
0.82 0.08 0.10
Matches are distributed among these distances:
36 23 0.04
37 2 0.00
38 3 0.01
39 3 0.01
40 2 0.00
41 2 0.00
42 3 0.01
43 3 0.01
44 10 0.02
45 487 0.89
46 7 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (45 bp):
ATCTGCTATCTTCAGTCTACTTCGCTGCCAATACAGGAAGACAAG
Found at i:3783573 original size:90 final size:90
Alignment explanation
Indices: 3783451--3784119 Score: 998
Period size: 90 Copynumber: 7.5 Consensus size: 90
3783441 TAAAATCTGT
*
3783451 TATCTTC-AGTCTACTTCGCTGCCAATACAGGAAGACCAGATCTGCTATCTTCAGTCTACTTTGC
1 TATCTTCGA-TCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTTGC
3783515 TGCCAATACAGGAAGACAAGACTTGC
65 TGCCAATACAGGAAGACAAGACTTGC
* * *
3783541 TATATTCGATCTACTTCGCTGCCAGTACAGGAAGACAGGATCTGCTATCTTCAGTCTACTTTGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTTGCT
*
3783606 GCCAATACAGGAAGACGAGACTTGC
66 GCCAATACAGGAAGACAAGACTTGC
* *
3783631 TATCTTCGATCTACTTCGTTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTTGCT
*
3783696 GCCAATACAGGAAGATAAGACTTGC
66 GCCAATACAGGAAGACAAGACTTGC
* * * *
3783721 TATCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATTTGCTATCTTCAATCTACTTCGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTTGCT
*
3783786 GCCAATACAAGAAGACAAGACTTGC
66 GCCAATACAGGAAGACAAGACTTGC
* * * *
3783811 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAATATATGTTATCTTCAGTCTATTTTGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTTGCT
*
3783876 GCCAATACAGGAAGATAAGACTTGC
66 GCCAATACAGGAAGACAAGACTTGC
* * * * *
3783901 TATCTTTGATCTACTTCGCTGCCAATACAGGAAGATAAGATTTGCTATCTTCAGTCTACTTCGTT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTTGCT
3783966 GCCAATACAGGAAGACAAGAC-T--
66 GCCAATACAGGAAGACAAGACTTGC
* * * *
3783988 TA-C-T--ATCT--TTCTCTGCCAATACAGGAAGACAATATCTGTTATCTTCAGTCTACTTTGTT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTTGCT
3784047 GCCAATACAGGAAGACAAGACTTGC
66 GCCAATACAGGAAGACAAGACTTGC
* *
3784072 TATCTTCGATCTACTTCGTTGCCAATACAGGAAGACAAGATCTACTAT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTAT
3784120 AATGACTTCA
Statistics
Matches: 522, Mismatches: 47, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
81 66 0.13
82 1 0.00
83 4 0.01
84 2 0.00
85 2 0.00
86 2 0.00
87 2 0.00
88 4 0.01
89 1 0.00
90 437 0.84
91 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (90 bp):
TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAGTCTACTTTGCT
GCCAATACAGGAAGACAAGACTTGC
Found at i:3788093 original size:10 final size:10
Alignment explanation
Indices: 3788078--3788103 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3788068 GAGATGGAAT
3788078 TCGAATTGAA
1 TCGAATTGAA
3788088 TCGAATTGAA
1 TCGAATTGAA
3788098 TCGAAT
1 TCGAAT
3788104 ATATTTGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (10 bp):
TCGAATTGAA
Done.