Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold73
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: 1308442
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.31
Warning! 157727 characters in sequence are not A, C, G, or T
File 1 of 9
Found at i:2649 original size:3 final size:3
Alignment explanation
Indices: 2641--2677 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2631 AAGTAGTCTT
2641 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2678 ATTGAAGATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2719 original size:15 final size:15
Alignment explanation
Indices: 2699--2728 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2689 AAGTTACATA
2699 ATTTATTAAACTAAT
1 ATTTATTAAACTAAT
*
2714 ATTTATTAAATTAAT
1 ATTTATTAAACTAAT
2729 TTTTTTTATT
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:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTATTAAACTAAT
Found at i:3461 original size:27 final size:28
Alignment explanation
Indices: 3419--3477 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
3409 TATATATATA
3419 ATAAATAAAATATTAAATA-AATTTATTT
1 ATAAATAAAATATTAAATATAATTT-TTT
* *
3447 ATAAATTAAAT-TTAAATATTATTTTTT
1 ATAAATAAAATATTAAATATAATTTTTT
3474 ATAA
1 ATAA
3478 TTCGATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
ATAAATAAAATATTAAATATAATTTTTT
Found at i:6481 original size:16 final size:16
Alignment explanation
Indices: 6460--6493 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
6450 CATCTCCTGG
6460 CAATACTTTTAATTGC
1 CAATACTTTTAATTGC
6476 CAATACTTTTAATTGC
1 CAATACTTTTAATTGC
6492 CA
1 CA
6494 CCATTTCCTG
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:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (16 bp):
CAATACTTTTAATTGC
Found at i:6668 original size:14 final size:13
Alignment explanation
Indices: 6623--6665 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
6613 TAAAAAGATT
6623 TAAA-TAAAAATAA
1 TAAATTAAAAA-AA
* *
6636 TAAACTCAAAAAA
1 TAAATTAAAAAAA
6649 TAAATTAAAAAAA
1 TAAATTAAAAAAA
6662 TAAA
1 TAAA
6666 ATTTATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 21 0.81
14 5 0.19
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (13 bp):
TAAATTAAAAAAA
Found at i:14878 original size:2 final size:2
Alignment explanation
Indices: 14871--14901 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
14861 AGAACCTGTT
*
14871 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14902 TTGTTTTATC
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:17254 original size:4 final size:4
Alignment explanation
Indices: 17245--17273 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
17235 TATTAACACA
17245 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
17274 TACCCATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:17943 original size:23 final size:23
Alignment explanation
Indices: 17917--17978 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
17907 GAGTGAGTGA
*
17917 AAGATAATGAAAAGTGGCAAATG
1 AAGATAGTGAAAAGTGGCAAATG
17940 AAGATAGTGAAAAGTGGCAAATG
1 AAGATAGTGAAAAGTGGCAAATG
17963 AAGATAGTGAAAAGTG
1 AAGATAGTGAAAAGTG
17979 TATGCAAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.50, C:0.03, G:0.29, T:0.18
Consensus pattern (23 bp):
AAGATAGTGAAAAGTGGCAAATG
Found at i:18844 original size:21 final size:20
Alignment explanation
Indices: 18788--18833 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
18778 TTTTTATTTA
*
18788 AATTGTTTTCATATTTAACATT
1 AATTGATTT-ATATTTAA-ATT
*
18810 ATTTGATTTATATTTAAATT
1 AATTGATTTATATTTAAATT
18830 AATT
1 AATT
18834 ATCTTAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 6 0.29
21 8 0.38
22 7 0.33
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (20 bp):
AATTGATTTATATTTAAATT
Found at i:19127 original size:87 final size:87
Alignment explanation
Indices: 19030--19192 Score: 229
Period size: 87 Copynumber: 1.9 Consensus size: 87
19020 TGTATATCAT
* * *
19030 TTACTGTTTATTGGTGTTTTACTAATTTC-TCAATTAAAAAGCTGTATAATATTATATATATTTT
1 TTACTGTTTATTGGTGTTTTACTAATTTCTTAAATGAAAAAG-TGTATAACATTATATATATTTT
19094 AATTCAACATTAACAAATCTTAA
65 AATTCAACATTAACAAATCTTAA
* * ** * *
19117 TTACTTTTTATTTGTGTTTTACTAATTTCTTAAATGAAAAAGTGTATGGCATTTTATATATTTTG
1 TTACTGTTTATTGGTGTTTTACTAATTTCTTAAATGAAAAAGTGTATAACATTATATATATTTTA
19182 ATTCAACATTA
66 ATTCAACATTA
19193 TTAAAAAAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
87 56 0.85
88 10 0.15
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (87 bp):
TTACTGTTTATTGGTGTTTTACTAATTTCTTAAATGAAAAAGTGTATAACATTATATATATTTTA
ATTCAACATTAACAAATCTTAA
Found at i:19934 original size:12 final size:13
Alignment explanation
Indices: 19911--19939 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
19901 AAATCCCAAA
19911 CTAATAAAATTTC
1 CTAATAAAATTTC
19924 CTAAT-AAATTTC
1 CTAATAAAATTTC
19936 CTAA
1 CTAA
19940 ACATAAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (13 bp):
CTAATAAAATTTC
Found at i:24447 original size:79 final size:83
Alignment explanation
Indices: 24359--24537 Score: 231
Period size: 79 Copynumber: 2.2 Consensus size: 83
24349 TTATTTAGAT
* * * *
24359 TTTTAATTATATTTAAATTAGTTATCGAAGATTAAGTTGAGAGATTTTTGTATTT-AA-ATTTTT
1 TTTTAATTATATTTAAATTAATGATCGAAGATTAAGTTGAAAGATTTTTGTATTTAAACATTCTT
24422 AAATTTAA-T-TGTAAAG
66 AAATTTAACTCTGTAAAG
** *
24438 TTTTAATTATATTTAAATTAATGATTTAAGATTGAGTTGAAAGATTTTTGTATTTAAAACATTCT
1 TTTTAATTATATTTAAATTAATGATCGAAGATTAAGTTGAAAGATTTTTGTATTT-AAACATTCT
*
24503 TGAATTTAACTCTGTAAAG
65 TAAATTTAACTCTGTAAAG
**
24522 TTTTGGTTATATTTAA
1 TTTTAATTATATTTAA
24538 TCACTCTTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
79 49 0.58
81 2 0.02
82 12 0.14
83 1 0.01
84 21 0.25
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.49
Consensus pattern (83 bp):
TTTTAATTATATTTAAATTAATGATCGAAGATTAAGTTGAAAGATTTTTGTATTTAAACATTCTT
AAATTTAACTCTGTAAAG
Found at i:25419 original size:30 final size:30
Alignment explanation
Indices: 25379--25439 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
25369 ATTAATATTT
*
25379 ATATATTTTTA-TAATTAAATTAAAA-TAAAA
1 ATATAATTTTATTAA-TAAA-TAAAATTAAAA
25409 ATATAATTTTATTAATAAATAAAATTAAAA
1 ATATAATTTTATTAATAAATAAAATTAAAA
25439 A
1 A
25440 AAAGATAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 5 0.18
30 20 0.71
31 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
ATATAATTTTATTAATAAATAAAATTAAAA
Found at i:25422 original size:22 final size:24
Alignment explanation
Indices: 25388--25432 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
25378 TATATATTTT
25388 TATAATTAAATT-A-AAATAAAAA
1 TATAATTAAATTAATAAATAAAAA
**
25410 TATAATTTTATTAATAAATAAAA
1 TATAATTAAATTAATAAATAAAA
25433 TTAAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 1 0.05
24 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TATAATTAAATTAATAAATAAAAA
Found at i:25471 original size:34 final size:33
Alignment explanation
Indices: 25395--25471 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 33
25385 TTTTATAATT
* *
25395 AAATTAAAATAAAAATATAATTTTATTAATAAATA
1 AAATT-AAA-AAAAAGATAATTTAATTAATAAATA
*
25430 AAATTAAAAAAAAGATAATTTAAATTTATAAA-A
1 AAATTAAAAAAAAGATAATTT-AATTAATAAATA
25463 AAACTTAAA
1 AAA-TTAAA
25472 TCAACACAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 16 0.43
34 16 0.43
35 5 0.14
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (33 bp):
AAATTAAAAAAAAGATAATTTAATTAATAAATA
Found at i:32803 original size:22 final size:22
Alignment explanation
Indices: 32772--32832 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
32762 TAATTAGTTC
*
32772 ATAAAATTAATAAAAATAATTTA
1 ATAATATTAATAAAAAT-ATTTA
*
32795 AT-TTATTAATAATAAATATTTA
1 ATAATATTAATAA-AAATATTTA
32817 ATAATATTTAATAAAA
1 ATAATA-TTAATAAAA
32833 TTTAAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 15 0.47
23 10 0.31
24 7 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAATATTAATAAAAATATTTA
Found at i:32824 original size:10 final size:10
Alignment explanation
Indices: 32804--32837 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
32794 AATTTATTAA
32804 TAATAAATATT
1 TAAT-AATATT
32815 TAATAATATT
1 TAATAATATT
*
32825 TAATAAAATT
1 TAATAATATT
32835 TAA
1 TAA
32838 ATTTTATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TAATAATATT
Found at i:32849 original size:24 final size:22
Alignment explanation
Indices: 32804--32877 Score: 80
Period size: 24 Copynumber: 3.3 Consensus size: 22
32794 AATTTATTAA
*
32804 TAATAAATATTTAATA--ATATT
1 TAATAAA-ATTTAATATTAAATT
*
32825 TAATAAAATTTAAATTTTATAATT
1 TAATAAAATTT-AATATTA-AATT
32849 TATATAAAATTTAATATTAAATT
1 TA-ATAAAATTTAATATTAAATT
32872 TAATAA
1 TAATAA
32878 CTCAAAATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
20 4 0.09
21 10 0.22
22 4 0.09
23 7 0.16
24 11 0.24
25 9 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATAAAATTTAATATTAAATT
Found at i:34664 original size:12 final size:12
Alignment explanation
Indices: 34636--34679 Score: 61
Period size: 13 Copynumber: 3.5 Consensus size: 12
34626 AAAATTTATA
34636 TAATATAAATTAT
1 TAATATAAA-TAT
*
34649 TAATATAAAAAT
1 TAATATAAATAT
34661 TAATATAAATAT
1 TAATATAAATAT
34673 ATAATAT
1 -TAATAT
34680 TTTAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 13 0.46
13 15 0.54
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATATAAATAT
Found at i:34713 original size:12 final size:13
Alignment explanation
Indices: 34632--34713 Score: 68
Period size: 12 Copynumber: 6.5 Consensus size: 13
34622 TATTAAAATT
34632 TATATAATATAAA
1 TATATAATATAAA
34645 T-TATTAATATAAA
1 TATA-TAATATAAA
*
34658 AAT-TAATATAAA
1 TATATAATATAAA
*
34670 TATATAATATTTTAA
1 TATATAATA--TAAA
*
34685 -ATATAAT-TATA
1 TATATAATATAAA
34696 -ATATAATA-AAA
1 TATATAATATAAA
34707 TATATAA
1 TATATAA
34714 ATATGATATA
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
11 11 0.20
12 19 0.34
13 15 0.27
14 8 0.14
15 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TATATAATATAAA
Found at i:34726 original size:18 final size:17
Alignment explanation
Indices: 34632--34729 Score: 65
Period size: 18 Copynumber: 5.3 Consensus size: 17
34622 TATTAAAATT
34632 TATATAATATAAATTATTAA
1 TATATAATAT-AA-TA-TAA
*
34652 TATA-AAAATTAATATAAA
1 TATATAATA-TAATAT-AA
34670 TATATAATATTTTAAATATAA
1 TATATAATA---T-AATATAA
*
34691 T-TATAATATAATAAAA
1 TATATAATATAATATAA
*
34707 TATATAAATATGATATAA
1 TATAT-AATATAATATAA
34725 TATAT
1 TATAT
34730 GAATTATCAA
Statistics
Matches: 65, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
16 7 0.11
17 5 0.08
18 23 0.35
19 8 0.12
20 12 0.18
21 5 0.08
22 5 0.08
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (17 bp):
TATATAATATAATATAA
Found at i:38751 original size:8 final size:8
Alignment explanation
Indices: 38738--38765 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
38728 TGTTAATATA
38738 ATATAAAT
1 ATATAAAT
38746 ATATAAAT
1 ATATAAAT
38754 ATATAAAT
1 ATATAAAT
38762 ATAT
1 ATAT
38766 TAAAATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAAAT
Found at i:38886 original size:31 final size:32
Alignment explanation
Indices: 38828--38891 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
38818 TAATTATAAT
* * *
38828 AAAAATAATTTAAATATAAATTTAATAT-TTA
1 AAAAATAATATAAATATAAAATAAATATATTA
38859 AAAAATAATATAAATATAAAATAAATATATTA
1 AAAAATAATATAAATATAAAATAAATATATTA
38891 A
1 A
38892 TATTAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (32 bp):
AAAAATAATATAAATATAAAATAAATATATTA
Found at i:38893 original size:19 final size:18
Alignment explanation
Indices: 38857--38906 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
38847 ATTTAATATT
*
38857 TAAA-AAATAATATAAATA
1 TAAATAAAT-ATATTAATA
38875 TAAAATAAATATATTAATA
1 T-AAATAAATATATTAATA
*
38894 TTAATAAAT-TATT
1 TAAATAAATATATT
38907 TTATTGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 4 0.14
18 8 0.29
19 12 0.43
20 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAATAAATATATTAATA
Found at i:42279 original size:18 final size:18
Alignment explanation
Indices: 42256--42291 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
42246 GAGTGCGGAC
*
42256 TAACAATAGCTGCTGCAA
1 TAACAACAGCTGCTGCAA
42274 TAACAACAGCTGCTGCAA
1 TAACAACAGCTGCTGCAA
42292 ATGCCTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (18 bp):
TAACAACAGCTGCTGCAA
Found at i:43819 original size:12 final size:12
Alignment explanation
Indices: 43804--43842 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
43794 AATAATAATA
43804 TAAATATTTATT
1 TAAATATTTATT
* *
43816 TAAATTTTTTTT
1 TAAATATTTATT
*
43828 TAAATATTTAAT
1 TAAATATTTATT
43840 TAA
1 TAA
43843 CAAAAATGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TAAATATTTATT
Found at i:46188 original size:29 final size:29
Alignment explanation
Indices: 46153--46209 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
46143 AAAATTATTA
*
46153 TTTAAATAATAAACATTAA-TTTTAAATAT
1 TTTAAATAATAAA-ATAAATTTTTAAATAT
46182 TTTAAATAATAAAATAAATTTTTAAATA
1 TTTAAATAATAAAATAAATTTTTAAATA
46210 AATTAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (29 bp):
TTTAAATAATAAAATAAATTTTTAAATAT
Found at i:46215 original size:29 final size:29
Alignment explanation
Indices: 46154--46217 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
46144 AAATTATTAT
* **
46154 TTAAATAATAAACATTAATTTTAAATATT
1 TTAAATAATAAACATAAATTTTAAATAAA
46183 TTAAATAATAAA-ATAAATTTTTAAATAAA
1 TTAAATAATAAACATAAA-TTTTAAATAAA
46212 TTAAAT
1 TTAAAT
46218 TTAAAAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
TTAAATAATAAACATAAATTTTAAATAAA
Found at i:46225 original size:17 final size:17
Alignment explanation
Indices: 46182--46225 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
46172 TTTTAAATAT
46182 TTTAAATAATAAAATAAA
1 TTTAAA-AATAAAATAAA
** *
46200 TTTTTAAATAAATTAAA
1 TTTAAAAATAAAATAAA
46217 TTTAAAAAT
1 TTTAAAAAT
46226 GTTCGTCGTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTAAAAATAAAATAAA
Found at i:46386 original size:36 final size:36
Alignment explanation
Indices: 46346--46417 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
46336 AAAAATCATT
* **
46346 ATTTTATTAAATAAATAATAAATTAAATTAAATCAA
1 ATTTTATTAAATAAATAAAAAAAAAAATTAAATCAA
*
46382 ATTTTATTAAATAAATAAAAAAAAAAATTAATTCAA
1 ATTTTATTAAATAAATAAAAAAAAAAATTAAATCAA
46418 TCTGATATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (36 bp):
ATTTTATTAAATAAATAAAAAAAAAAATTAAATCAA
Found at i:53301 original size:21 final size:21
Alignment explanation
Indices: 53277--53354 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 21
53267 TTTAAATAAT
53277 TAATTTTATTATATTATTTAC
1 TAATTTTATTATATTATTTAC
* * *
53298 TAATTTTAATATTTTA-TTAT
1 TAATTTTATTATATTATTTAC
* *
53318 TAATATTTACTATTAATATTTATC
1 TAAT-TTTATTA-TATTATTTA-C
53342 ATAA-TTTATTATA
1 -TAATTTTATTATA
53355 ATAATATTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
20 7 0.16
21 20 0.45
22 5 0.11
23 9 0.20
25 3 0.07
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATTTTATTATATTATTTAC
Found at i:53331 original size:13 final size:13
Alignment explanation
Indices: 53303--53339 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
53293 TTTACTAATT
*
53303 TTAATATTTTATTA
1 TTAATA-TTTACTA
53317 TTAATATTTACTA
1 TTAATATTTACTA
53330 TTAATATTTA
1 TTAATATTTA
53340 TCATAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (13 bp):
TTAATATTTACTA
Found at i:53333 original size:27 final size:28
Alignment explanation
Indices: 53279--53346 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 28
53269 TAAATAATTA
*
53279 ATTTTATTATATTATTTACTAATTTTAAT
1 ATTTTATTATAATATTTACTAA-TTTAAT
53308 ATTTTATTATTAATATTTACT-A-TTAAT
1 ATTTTATTA-TAATATTTACTAATTTAAT
*
53335 A-TTTATCATAAT
1 ATTTTATTATAAT
53347 TTATTATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
25 4 0.11
26 6 0.17
27 6 0.17
29 10 0.28
30 10 0.28
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTTTATTATAATATTTACTAATTTAAT
Found at i:54703 original size:18 final size:18
Alignment explanation
Indices: 54680--54714 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
54670 ATTAAAAATT
54680 AATTAAATT-AATATTATG
1 AATT-AATTAAATATTATG
54698 AATTAATTAAATATTAT
1 AATTAATTAAATATTAT
54715 TTATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
AATTAATTAAATATTATG
Found at i:58812 original size:32 final size:32
Alignment explanation
Indices: 58772--58838 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
58762 CTTATAAATT
*
58772 ATTATTAAAATATTTAAATTTAAA-TAATTTA
1 ATTATTAAAATATTTAAATTAAAATTAATTTA
*
58803 ATTACTTAAAATATTTTAATTAAAATTTAATTTA
1 ATTA-TTAAAATATTTAAATTAAAA-TTAATTTA
58837 AT
1 AT
58839 AATAAGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 4 0.13
32 18 0.58
34 9 0.29
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (32 bp):
ATTATTAAAATATTTAAATTAAAATTAATTTA
Found at i:63777 original size:17 final size:18
Alignment explanation
Indices: 63741--63779 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
63731 ATTTTATGAA
63741 AATTTTATTTACTAAATT
1 AATTTTATTTACTAAATT
* *
63759 AATTTT-TTTATTAATTT
1 AATTTTATTTACTAAATT
63776 AATT
1 AATT
63780 AAATTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
AATTTTATTTACTAAATT
Found at i:64117 original size:20 final size:20
Alignment explanation
Indices: 64094--64147 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
64084 TAAATACATT
64094 TTTAAATTAAATAAAAATAA
1 TTTAAATTAAATAAAAATAA
* *
64114 TTTAAATGATA-AAAAATAA
1 TTTAAATTAAATAAAAATAA
* *
64133 TCCTAAATTTAATAA
1 T-TTAAATTAAATAA
64148 CAAAGTAAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
19 9 0.35
20 15 0.58
21 2 0.08
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (20 bp):
TTTAAATTAAATAAAAATAA
Found at i:64621 original size:22 final size:24
Alignment explanation
Indices: 64586--64631 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
64576 ATTAATTTTA
64586 AAAAATTAATATTTAAT-ATATTT
1 AAAAATTAATATTTAATGATATTT
* *
64609 AAAATTTAA-ATTTTATGATATTT
1 AAAAATTAATATTTAATGATATTT
64632 TGTATTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
AAAAATTAATATTTAATGATATTT
Found at i:65706 original size:13 final size:13
Alignment explanation
Indices: 65690--65714 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65680 TACTTAAATC
65690 AAATTTGTTTAAA
1 AAATTTGTTTAAA
65703 AAATTTGTTTAA
1 AAATTTGTTTAA
65715 TTTTATTGTT
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
AAATTTGTTTAAA
Found at i:67262 original size:18 final size:18
Alignment explanation
Indices: 67235--67278 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
67225 TTTAAGTTAC
* * *
67235 TAATTTAATTAATTTGGT
1 TAATTAAATTAAATTAGT
*
67253 TAATTAAATTAAATTATT
1 TAATTAAATTAAATTAGT
67271 TAATTAAA
1 TAATTAAA
67279 AAAATTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TAATTAAATTAAATTAGT
Found at i:67910 original size:3 final size:3
Alignment explanation
Indices: 67902--67932 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
67892 CAGTCCTTCG
67902 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
67933 GATTTTCTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:71008 original size:33 final size:33
Alignment explanation
Indices: 70918--71027 Score: 102
Period size: 33 Copynumber: 3.4 Consensus size: 33
70908 AGCCCATGTA
* * * * *
70918 ACTGCAGGTCCTGCTCCAACTGTGGCTTACCTG
1 ACTGCAGGTCATGCTGCAACTGTAGCTCATCTG
* * * *
70951 ACTGCAGTTCA---TGCAAATGCAGCTCATTTG
1 ACTGCAGGTCATGCTGCAACTGTAGCTCATCTG
70981 ACTGCAGGTCATGCTGCAACTGTAGCTCATCTG
1 ACTGCAGGTCATGCTGCAACTGTAGCTCATCTG
71014 ACTGC-GGTTCATGC
1 ACTGCAGG-TCATGC
71028 AAATGCGGTA
Statistics
Matches: 60, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
30 22 0.37
32 2 0.03
33 36 0.60
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (33 bp):
ACTGCAGGTCATGCTGCAACTGTAGCTCATCTG
Found at i:71034 original size:15 final size:15
Alignment explanation
Indices: 71016--71063 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
71006 CTCATCTGAC
71016 TGCGGTTCATGCAAA
1 TGCGGTTCATGCAAA
* * *
71031 TGCGGTACATGCGAC
1 TGCGGTTCATGCAAA
* *
71046 TGCAGTTCATGTAAA
1 TGCGGTTCATGCAAA
71061 TGC
1 TGC
71064 AGCTCTTGCG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (15 bp):
TGCGGTTCATGCAAA
Found at i:71047 original size:63 final size:63
Alignment explanation
Indices: 70918--71116 Score: 174
Period size: 63 Copynumber: 3.2 Consensus size: 63
70908 AGCCCATGTA
* * * **
70918 ACTGCAGGTCCTGCTCCAACTGTGGCTTACCTGACTGCAGTTCATGCAAATGCAGCTCATTTG
1 ACTGCAGGTCATGCTCCAACTGTAGCTCACCTGACTGCAGTTCATGCAAATGCAGCTCATGCG
* * * *
70981 ACTGCAGGTCATGCTGCAACTGTAGCTCATCTGACTGCGGTTCATGCAAATGC-GGTACATGCG
1 ACTGCAGGTCATGCTCCAACTGTAGCTCACCTGACTGCAGTTCATGCAAATGCAGCT-CATGCG
* * * ** * * *
71044 ACTGCAGTTCATG-T--AAATGCAGCTCTTGC-GACTTCAGTTCATGTAAATGCAGCTCTTGCG
1 ACTGCAGGTCATGCTCCAACTGTAGCTC-ACCTGACTGCAGTTCATGCAAATGCAGCTCATGCG
* *
71104 ACTTCAGTTCATG
1 ACTGCAGGTCATG
71117 TAAATGCAGC
Statistics
Matches: 113, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
60 44 0.39
61 3 0.03
62 3 0.03
63 63 0.56
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (63 bp):
ACTGCAGGTCATGCTCCAACTGTAGCTCACCTGACTGCAGTTCATGCAAATGCAGCTCATGCG
Found at i:71064 original size:15 final size:15
Alignment explanation
Indices: 71046--71125 Score: 52
Period size: 15 Copynumber: 5.3 Consensus size: 15
71036 TACATGCGAC
71046 TGCAGTTCATGTAAA
1 TGCAGTTCATGTAAA
* * ** *
71061 TGCAGCTCTTGCGAC
1 TGCAGTTCATGTAAA
*
71076 TTCAGTTCATGTAAA
1 TGCAGTTCATGTAAA
* * ** *
71091 TGCAGCTCTTGCGAC
1 TGCAGTTCATGTAAA
*
71106 TTCAGTTCATGTAAA
1 TGCAGTTCATGTAAA
71121 TGCAG
1 TGCAG
71126 CTCTTGCGGC
Statistics
Matches: 41, Mismatches: 24, Indels: 0
0.63 0.37 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (15 bp):
TGCAGTTCATGTAAA
Found at i:71159 original size:33 final size:33
Alignment explanation
Indices: 71040--71392 Score: 284
Period size: 33 Copynumber: 11.2 Consensus size: 33
71030 ATGCGGTACA
*
71040 TGCGACTGCAGTTCA--T-GTAAATGCAGCTCT
1 TGCGACTGTAGTTCATGTGGTAAATGCAGCTCT
71070 TGCGACT-TCAGTTCA--T-GTAAATGCAGCTCT
1 TGCGACTGT-AGTTCATGTGGTAAATGCAGCTCT
71100 TGCGACT-TCAGTTCA--T-GTAAATGCAGCTCT
1 TGCGACTGT-AGTTCATGTGGTAAATGCAGCTCT
* * *
71130 TGCGGCTGTAGTTCATGTGCTAAATGCAGCTCG
1 TGCGACTGTAGTTCATGTGGTAAATGCAGCTCT
* * * *
71163 TGTGGCTGTAGTTCATGTGGTAAATGCAACTCG
1 TGCGACTGTAGTTCATGTGGTAAATGCAGCTCT
* * * *
71196 TGCGGCGGTAGTTCATGTGGTAAATGCAACTCG
1 TGCGACTGTAGTTCATGTGGTAAATGCAGCTCT
* *
71229 TGCGGCTGTAGTTCATGTGGTAAATGCAACT-T
1 TGCGACTGTAGTTCATGTGGTAAATGCAGCTCT
71261 GTGCGACTGTAGTTCATGTGGTAAATGCAGCT-T
1 -TGCGACTGTAGTTCATGTGGTAAATGCAGCTCT
* *
71294 GTGCGACTGCAGTTC--CT-GTAAATGCAGCTCT
1 -TGCGACTGTAGTTCATGTGGTAAATGCAGCTCT
** * *
71325 TGTAACT-TCAATTCA--T-GTAAATGCAGCTCG
1 TGCGACTGT-AGTTCATGTGGTAAATGCAGCTCT
* * * *
71355 TACAACTGCAGTTCA--T-GTAAATGCAGCTCG
1 TGCGACTGTAGTTCATGTGGTAAATGCAGCTCT
71385 TGCGACTG
1 TGCGACTG
71393 CAATGCATGT
Statistics
Matches: 287, Mismatches: 26, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
30 136 0.47
31 3 0.01
32 1 0.00
33 147 0.51
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (33 bp):
TGCGACTGTAGTTCATGTGGTAAATGCAGCTCT
Found at i:71319 original size:15 final size:15
Alignment explanation
Indices: 71301--71380 Score: 65
Period size: 15 Copynumber: 5.3 Consensus size: 15
71291 CTTGTGCGAC
*
71301 TGCAGTTCCTGTAAA
1 TGCAGTTCATGTAAA
* * *
71316 TGCAGCTCTTGTAAC
1 TGCAGTTCATGTAAA
* *
71331 TTCAATTCATGTAAA
1 TGCAGTTCATGTAAA
*
71346 TGCAGCTC--GTACAA
1 TGCAGTTCATGTA-AA
71360 CTGCAGTTCATGTAAA
1 -TGCAGTTCATGTAAA
71376 TGCAG
1 TGCAG
71381 CTCGTGCGAC
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
13 3 0.06
14 2 0.04
15 39 0.80
16 2 0.04
17 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (15 bp):
TGCAGTTCATGTAAA
Found at i:71402 original size:30 final size:30
Alignment explanation
Indices: 70950--71394 Score: 327
Period size: 30 Copynumber: 14.2 Consensus size: 30
70940 TGGCTTACCT
* * **
70950 GACTGCAGTTCATGCAAATGCAGCTCATTT
1 GACTGCAGTTCATGTAAATGCAGCTCGTGC
* * * *
70980 GACTGCAGGTCATGCTGCAACTGTAGCTCAT-C
1 GACTGCAGTTCATG-T--AAATGCAGCTCGTGC
* * * *
71012 TGACTGCGGTTCATGCAAATGC-GGTACATGC
1 -GACTGCAGTTCATGTAAATGCAGCT-CGTGC
*
71043 GACTGCAGTTCATGTAAATGCAGCTCTTGC
1 GACTGCAGTTCATGTAAATGCAGCTCGTGC
* *
71073 GACTTCAGTTCATGTAAATGCAGCTCTTGC
1 GACTGCAGTTCATGTAAATGCAGCTCGTGC
* *
71103 GACTTCAGTTCATGTAAATGCAGCTCTTGC
1 GACTGCAGTTCATGTAAATGCAGCTCGTGC
* * *
71133 GGCTGTAGTTCATGTGCTAAATGCAGCTCGTGT
1 GACTGCAGTTCA--TG-TAAATGCAGCTCGTGC
* * *
71166 GGCTGTAGTTCATGTGGTAAATGCAACTCGTGC
1 GACTGCAGTTCA--T-GTAAATGCAGCTCGTGC
* * * *
71199 GGCGGTAGTTCATGTGGTAAATGCAACTCGTGC
1 GACTGCAGTTCA--T-GTAAATGCAGCTCGTGC
* * * *
71232 GGCTGTAGTTCATGTGGTAAATGCAACTTGTGC
1 GACTGCAGTTCA--T-GTAAATGCAGCTCGTGC
* *
71265 GACTGTAGTTCATGTGGTAAATGCAGCTTGTGC
1 GACTGCAGTTCA--T-GTAAATGCAGCTCGTGC
* * *
71298 GACTGCAGTTCCTGTAAATGCAGCTCTTGT
1 GACTGCAGTTCATGTAAATGCAGCTCGTGC
* * * *
71328 AACTTCAATTCATGTAAATGCAGCTCGTAC
1 GACTGCAGTTCATGTAAATGCAGCTCGTGC
*
71358 AACTGCAGTTCATGTAAATGCAGCTCGTGC
1 GACTGCAGTTCATGTAAATGCAGCTCGTGC
71388 GACTGCA
1 GACTGCA
71395 ATGCATGTTT
Statistics
Matches: 360, Mismatches: 44, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
29 2 0.01
30 181 0.50
31 4 0.01
32 2 0.01
33 170 0.47
34 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACTGCAGTTCATGTAAATGCAGCTCGTGC
Found at i:72107 original size:9 final size:8
Alignment explanation
Indices: 72083--72112 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
72073 AATTGATGTA
72083 TTTAATTT
1 TTTAATTT
72091 TTTAATTT
1 TTTAATTT
72099 TTTATATTT
1 TTTA-ATTT
72108 TTTAA
1 TTTAA
72113 AAAAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTAATTT
Found at i:72160 original size:27 final size:27
Alignment explanation
Indices: 72106--72160 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
72096 TTTTTTATAT
*
72106 TTTTTAAAAAAAAATTAAAAAATTATA
1 TTTTTAAAAAAAAATTAAAAAATAATA
* *
72133 TTTTTAAAAATATATTAAATAAA-AATA
1 TTTTTAAAAAAAAATTAAA-AAATAATA
72160 T
1 T
72161 AAATATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
TTTTTAAAAAAAAATTAAAAAATAATA
Found at i:72454 original size:19 final size:19
Alignment explanation
Indices: 72432--72471 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
72422 TTAATGTGAA
* *
72432 TATATATTTTAAAATTTTT
1 TATATATTTAAAAATATTT
72451 TATATATTTAAAAATATTT
1 TATATATTTAAAAATATTT
72470 TA
1 TA
72472 ATAAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATATTTAAAAATATTT
Found at i:74479 original size:27 final size:28
Alignment explanation
Indices: 74429--74485 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 28
74419 AACTCTCGAT
74429 TGCTTAAACTTAAAGCTCCACTCAATAA
1 TGCTTAAACTTAAAGCTCCACTCAATAA
74457 TGCTTAAACTT-AAGCTCCACTCAATAA
1 TGCTTAAACTTAAAGCTCCACTCAATAA
74484 TG
1 TG
74486 AACATGCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 18 0.62
28 11 0.38
ACGTcount: A:0.37, C:0.25, G:0.09, T:0.30
Consensus pattern (28 bp):
TGCTTAAACTTAAAGCTCCACTCAATAA
Found at i:78943 original size:24 final size:25
Alignment explanation
Indices: 78897--78947 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
78887 ATTTTATGAT
*
78897 TAAAATTATTATTTAATAATTTAAA
1 TAAAATGATTATTTAATAATTTAAA
* *
78922 TAAAATGATT-TTTATTATTTTAAA
1 TAAAATGATTATTTAATAATTTAAA
78946 TA
1 TA
78948 TTTTTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
TAAAATGATTATTTAATAATTTAAA
Found at i:79567 original size:20 final size:20
Alignment explanation
Indices: 79514--79569 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
79504 TTTTTTTTTA
* * *
79514 AATTCTATATATAATTTATT
1 AATTTTATATTTAATTTACT
*
79534 AGATTTAAATATTTAATTTACT
1 A-ATTT-TATATTTAATTTACT
79556 AATTTTATATTTAA
1 AATTTTATATTTAA
79570 AAATAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 9 0.31
21 7 0.24
22 13 0.45
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (20 bp):
AATTTTATATTTAATTTACT
Found at i:79592 original size:15 final size:15
Alignment explanation
Indices: 79574--79626 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
79564 ATTTAAAAAT
*
79574 AATATTATTAAATTA
1 AATATTATTATATTA
*
79589 AATA-TATTTTTATTA
1 AATATTA-TTATATTA
*
79604 AATATTAATTATATTT
1 AATATT-ATTATATTA
79620 AATATTA
1 AATATTA
79627 AGATTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
14 2 0.06
15 15 0.48
16 13 0.42
17 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATATTATTATATTA
Found at i:79620 original size:20 final size:20
Alignment explanation
Indices: 79570--79620 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
79560 TTATATTTAA
79570 AAATA-ATA-TTATTAAATT
1 AAATATATATTTATTAAATT
*
79588 AAATATATTTTTATTAAATAT
1 AAATATATATTTATTAAAT-T
*
79609 TAAT-TATATTTA
1 AAATATATATTTA
79621 ATATTAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 5 0.19
19 2 0.07
20 16 0.59
21 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATATATATTTATTAAATT
Found at i:79623 original size:16 final size:16
Alignment explanation
Indices: 79574--79627 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
79564 ATTTAAAAAT
*
79574 AATATT-ATTAAATTA
1 AATATTAATTATATTA
* *
79589 AATA-TATTTTTATTA
1 AATATTAATTATATTA
*
79604 AATATTAATTATATTT
1 AATATTAATTATATTA
79620 AATATTAA
1 AATATTAA
79628 GATTATTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 1 0.03
15 14 0.45
16 16 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATTAATTATATTA
Found at i:79663 original size:17 final size:19
Alignment explanation
Indices: 79643--79686 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
79633 TTTTTTAAAT
79643 ATTAAAATTT-T-AATTAA
1 ATTAAAATTTATCAATTAA
79660 ATTAATAATTTAATCAATTAA
1 ATTAA-AATTT-ATCAATTAA
79681 ATTAAA
1 ATTAAA
79687 TCCATTAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 5 0.22
20 2 0.09
21 11 0.48
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTAAAATTTATCAATTAA
Found at i:82280 original size:21 final size:22
Alignment explanation
Indices: 82255--82303 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
82245 ATTTTATATC
* *
82255 TTTATATTTTTACATATTATAA
1 TTTATATTTTAAAATATTATAA
82277 -TTATA-TTTAAAATATTATAA
1 TTTATATTTTAAAATATTATAA
82297 TTTATAT
1 TTTATAT
82304 AAATTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTATATTTTAAAATATTATAA
Found at i:82293 original size:20 final size:20
Alignment explanation
Indices: 82268--82324 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
82258 ATATTTTTAC
82268 ATATTATAATTATATTTAAA
1 ATATTATAATTATATTTAAA
*
82288 ATATTATAATT-TATAT-AA
1 ATATTATAATTATATTTAAA
* *
82306 ATTTTATTATATATATTTA
1 ATATTATAAT-TATATTTA
82325 TATTATATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 10 0.33
19 5 0.17
20 15 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATTATAATTATATTTAAA
Found at i:82317 original size:14 final size:15
Alignment explanation
Indices: 82277--82332 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 15
82267 CATATTATAA
82277 TTATATT-TA-AAAT
1 TTATATTATATAAAT
82290 ATTATAATTTATATAAAT
1 -TTAT-A-TTATATAAAT
*
82308 TT-TATTATATATAT
1 TTATATTATATAAAT
82322 TTATATTATAT
1 TTATATTATAT
82333 TTATATTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
14 15 0.42
15 10 0.28
16 3 0.08
17 4 0.11
18 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATTATATAAAT
Found at i:82327 original size:24 final size:26
Alignment explanation
Indices: 82292--82354 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
82282 TTTAAAATAT
82292 TATA-ATTTATA-TAAATTT-TATTA
1 TATATATTTATATTAAATTTATATTA
*
82315 TATATATTTATATTATATTTATATTA
1 TATATATTTATATTAAATTTATATTA
82341 TATCATATTT-TATT
1 TAT-ATATTTATATT
82355 CTTTATTTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
23 4 0.11
24 7 0.20
25 6 0.17
26 12 0.34
27 6 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TATATATTTATATTAAATTTATATTA
Found at i:82331 original size:11 final size:11
Alignment explanation
Indices: 82288--82343 Score: 60
Period size: 11 Copynumber: 4.8 Consensus size: 11
82278 TATATTTAAA
82288 ATATTATAATTT
1 ATATTAT-ATTT
*
82300 ATA-TAAATTTT
1 ATATTATA-TTT
82311 ATTATATATATTT
1 A-TAT-TATATTT
82324 ATATTATATTT
1 ATATTATATTT
82335 ATATTATAT
1 ATATTATAT
82344 CATATTTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 1 0.03
11 22 0.58
12 8 0.21
13 4 0.11
14 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATATTATATTT
Found at i:84551 original size:174 final size:174
Alignment explanation
Indices: 84261--84612 Score: 704
Period size: 174 Copynumber: 2.0 Consensus size: 174
84251 ATATATTTAT
84261 AAATATTTTTTACTTTTGATAAAGTTTCATTATTAAATAGGTATGGATCAAAATACTTGTCATTT
1 AAATATTTTTTACTTTTGATAAAGTTTCATTATTAAATAGGTATGGATCAAAATACTTGTCATTT
84326 CAAAAATAAGTTTGATTTTTTAAAAAATAATTAATTTATGTAGTAATATTTAGTTGAAAAATTCA
66 CAAAAATAAGTTTGATTTTTTAAAAAATAATTAATTTATGTAGTAATATTTAGTTGAAAAATTCA
84391 TAAATCTCACCTAAAAGGTCCATATAATAATTGTTGGGAAAGTG
131 TAAATCTCACCTAAAAGGTCCATATAATAATTGTTGGGAAAGTG
84435 AAATATTTTTTACTTTTGATAAAGTTTCATTATTAAATAGGTATGGATCAAAATACTTGTCATTT
1 AAATATTTTTTACTTTTGATAAAGTTTCATTATTAAATAGGTATGGATCAAAATACTTGTCATTT
84500 CAAAAATAAGTTTGATTTTTTAAAAAATAATTAATTTATGTAGTAATATTTAGTTGAAAAATTCA
66 CAAAAATAAGTTTGATTTTTTAAAAAATAATTAATTTATGTAGTAATATTTAGTTGAAAAATTCA
84565 TAAATCTCACCTAAAAGGTCCATATAATAATTGTTGGGAAAGTG
131 TAAATCTCACCTAAAAGGTCCATATAATAATTGTTGGGAAAGTG
84609 AAAT
1 AAAT
84613 TATGATTAGA
Statistics
Matches: 178, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 178 1.00
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (174 bp):
AAATATTTTTTACTTTTGATAAAGTTTCATTATTAAATAGGTATGGATCAAAATACTTGTCATTT
CAAAAATAAGTTTGATTTTTTAAAAAATAATTAATTTATGTAGTAATATTTAGTTGAAAAATTCA
TAAATCTCACCTAAAAGGTCCATATAATAATTGTTGGGAAAGTG
Found at i:84705 original size:47 final size:50
Alignment explanation
Indices: 84654--84746 Score: 129
Period size: 47 Copynumber: 1.9 Consensus size: 50
84644 TTTAAATTTT
* * **
84654 TTAAATTTTTATTTAAATTT-AA-AATGTTA-TTTTATTATTTAAAAATA
1 TTAAATATATATTTAAATTTAAATAAAATTATTTTTATTATTTAAAAATA
84701 TTAAATATATATTTAAATTTAAATAAAATTATTTTTATTATTTAAA
1 TTAAATATATATTTAAATTTAAATAAAATTATTTTTATTATTTAAA
84747 TTTTAATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
47 18 0.46
48 2 0.05
49 5 0.13
50 14 0.36
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (50 bp):
TTAAATATATATTTAAATTTAAATAAAATTATTTTTATTATTTAAAAATA
Found at i:84715 original size:28 final size:25
Alignment explanation
Indices: 84658--84746 Score: 62
Period size: 26 Copynumber: 3.6 Consensus size: 25
84648 AATTTTTTAA
**
84658 ATTT-TTATTTAAATTTAAAATGT-T
1 ATTTATTATTTAAAAATAAAAT-TAT
84682 ATTTTATTATTTAAAAATATTAAATATAT
1 A-TTTATTATTTAAAAATA--AAAT-TAT
*
84711 ATTTA-AATTT--AAATAAAATTAT
1 ATTTATTATTTAAAAATAAAATTAT
*
84733 TTTTATTATTTAAA
1 ATTTATTATTTAAA
84747 TTTTAATTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
22 7 0.14
23 8 0.16
24 1 0.02
25 9 0.18
26 11 0.22
27 4 0.08
28 9 0.18
29 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (25 bp):
ATTTATTATTTAAAAATAAAATTAT
Found at i:87626 original size:22 final size:22
Alignment explanation
Indices: 87586--87627 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
87576 ATTAAAATAT
*
87586 TATTTTTATTTTAATATTTATA
1 TATTTTTATATTAATATTTATA
87608 TATTTTTATAATTAA-ATTTA
1 TATTTTTAT-ATTAATATTTA
87628 AATAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTTATATTAATATTTATA
Found at i:90755 original size:13 final size:12
Alignment explanation
Indices: 90735--90765 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
90725 TTATTGATAG
90735 TTTAAATTAATT
1 TTTAAATTAATT
90747 TTATAAATTAATT
1 TT-TAAATTAATT
90760 TTTAAA
1 TTTAAA
90766 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTAAATTAATT
Found at i:91418 original size:23 final size:23
Alignment explanation
Indices: 91387--91451 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 23
91377 AATTGATATA
*
91387 ATATATATTAAATATATTAAATT
1 ATATTTATTAAATATATTAAATT
* *
91410 ATATTTATTAAATATTTTTATATT
1 ATATTTATTAAATA-TATTAAATT
91434 ATATTTA--AAAT-TATTAAA
1 ATATTTATTAAATATATTAAA
91452 ATTAAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 5 0.14
22 4 0.11
23 13 0.36
24 14 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATTTATTAAATATATTAAATT
Found at i:91621 original size:14 final size:15
Alignment explanation
Indices: 91593--91624 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
91583 TTTGGTAATT
91593 TATATATTATTATTA
1 TATATATTATTATTA
91608 TATATATT-TTATTA
1 TATATATTATTATTA
91622 TAT
1 TAT
91625 CATAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATATTATTATTA
Found at i:91727 original size:5 final size:5
Alignment explanation
Indices: 91705--91772 Score: 50
Period size: 5 Copynumber: 13.0 Consensus size: 5
91695 TTAAAATTTT
* * *
91705 TTATA TTCATA TCATA TTATA TTTTAA TTATT TTATA TTATA TT-TA -TATAA
1 TTATA TT-ATA TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA TTAT-A
91756 TTATA TTTAATA TTATA
1 TTATA -TT-ATA TTATA
91773 ACAGTAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
3 1 0.02
4 3 0.06
5 28 0.56
6 15 0.30
7 3 0.06
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:91748 original size:26 final size:26
Alignment explanation
Indices: 91718--91772 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 26
91708 TATTCATATC
91718 ATATTATA-TT-T-TAATTAT-TTT-
1 ATATTATATTTATATAATTATATTTA
91739 ATATTATATTTATATAATTATATTTA
1 ATATTATATTTATATAATTATATTTA
91765 ATATTATA
1 ATATTATA
91773 ACAGTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 8 0.28
22 2 0.07
23 1 0.03
24 7 0.24
25 3 0.10
26 8 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
ATATTATATTTATATAATTATATTTA
Found at i:92619 original size:17 final size:17
Alignment explanation
Indices: 92579--92620 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
92569 AATTAAACTT
*
92579 AAAATTTA-ATAGATAA
1 AAAATTTATATAGAAAA
* *
92595 ATAATTTATATATAAAA
1 AAAATTTATATAGAAAA
92612 AAAATTTAT
1 AAAATTTAT
92621 TTTAATTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
AAAATTTATATAGAAAA
Found at i:95506 original size:26 final size:24
Alignment explanation
Indices: 95455--95533 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 24
95445 TGAAATATAA
* * *
95455 ATATTTTGATTATTTTTAATTTTT
1 ATATTTTTATTATTTTTAAATATT
95479 ATATTTTTATATATTTTTAAAATATT
1 ATATTTTTAT-TATTTTT-AAATATT
*
95505 AT-TTTTATATTTATATTTAAATA-T
1 ATATTTT-TA-TTATTTTTAAATATT
95529 ATATT
1 ATATT
95534 AAATATAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
24 12 0.26
25 18 0.39
26 15 0.33
27 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (24 bp):
ATATTTTTATTATTTTTAAATATT
Found at i:96891 original size:27 final size:27
Alignment explanation
Indices: 96868--96925 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
96858 TATATAAGAT
*
96868 TAAAAT-ATTATTTAAATATAATAAAA
1 TAAAATAATTATTTAAATAAAATAAAA
*
96894 TAAAATAATTATTTGAATAAAAT--AA
1 TAAAATAATTATTTAAATAAAATAAAA
96919 TAAAATA
1 TAAAATA
96926 TAGAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 9 0.31
26 6 0.21
27 14 0.48
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
TAAAATAATTATTTAAATAAAATAAAA
Found at i:98093 original size:2 final size:2
Alignment explanation
Indices: 98086--98118 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
98076 ATGAACTGAT
98086 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
98119 TTATTTATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:98497 original size:16 final size:16
Alignment explanation
Indices: 98476--98509 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
98466 AAAGAAATTT
98476 ATATAACACAGGCTTA
1 ATATAACACAGGCTTA
98492 ATATAACACAGGCTTA
1 ATATAACACAGGCTTA
98508 AT
1 AT
98510 CAACCCAGTA
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:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (16 bp):
ATATAACACAGGCTTA
Found at i:100282 original size:1 final size:1
Alignment explanation
Indices: 100247--100272 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
100237 TTGCTATGGG
100247 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
100273 AAGTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:101713 original size:24 final size:23
Alignment explanation
Indices: 101656--101738 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 23
101646 GAAAGAGAAA
*
101656 AAAATAAATATT-ATATTAATAT
1 AAAATAAATATTAAAATTAATAT
* *
101678 ATAA-AAATATTAAAATTTATAT
1 AAAATAAATATTAAAATTAATAT
*
101700 AAAATAAATTATTAATATGTGAATATT
1 AAAATAAA-TATTAAAAT-T-AATA-T
101727 AAAATAAATATT
1 AAAATAAATATT
101739 TAATATATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
21 7 0.14
22 14 0.29
23 3 0.06
24 8 0.16
25 1 0.02
26 7 0.14
27 9 0.18
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
AAAATAAATATTAAAATTAATAT
Found at i:109729 original size:19 final size:18
Alignment explanation
Indices: 109698--109741 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
109688 TATTAAACTT
109698 AAAAATAACTTTAAATAA
1 AAAAATAACTTTAAATAA
* **
109716 AAAAATGAAGTTTATTTAA
1 AAAAAT-AACTTTAAATAA
109735 AAAAATA
1 AAAAATA
109742 GCCATGCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAAATAACTTTAAATAA
Found at i:110349 original size:82 final size:81
Alignment explanation
Indices: 110259--110430 Score: 236
Period size: 82 Copynumber: 2.1 Consensus size: 81
110249 ACCATGTGAT
* * *
110259 ATTCAACTGTCCTAAAATTAAAAATTTAACATTTACTATCTCTTTCCTAGTTTGTAAGCTACAGT
1 ATTCAACTGTCCTAAAATTAAAAATTTAACATTTACTACCTCTTTACTAGTTTGTAAACTACAGT
*
110324 CAAATATAATTTTAAA
66 CAAATATAATCTTAAA
* * * *
110340 ATTCAAACTGTCCTAAAATTAAAAATTTAACATTTATTACCTCTTTATTTGTTTGTAAATTACAG
1 ATTC-AACTGTCCTAAAATTAAAAATTTAACATTTACTACCTCTTTACTAGTTTGTAAACTACAG
**
110405 TTGAATATAATCTTAAA
65 TCAAATATAATCTTAAA
110422 ATTCGAACT
1 ATTC-AACT
110431 TAATATTTAC
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
81 4 0.05
82 75 0.95
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (81 bp):
ATTCAACTGTCCTAAAATTAAAAATTTAACATTTACTACCTCTTTACTAGTTTGTAAACTACAGT
CAAATATAATCTTAAA
Found at i:110877 original size:2 final size:2
Alignment explanation
Indices: 110870--110907 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
110860 AACTGAATAC
110870 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
110908 TATGGTACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:111933 original size:1 final size:1
Alignment explanation
Indices: 111929--111958 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
111919 TTTTTTTTTT
*
111929 GGGGGGGGGGGGGGGGGGGGGGGGGAGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
111959 CTTCATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:114314 original size:362 final size:345
Alignment explanation
Indices: 113781--114563 Score: 798
Period size: 362 Copynumber: 2.2 Consensus size: 345
113771 AAAAAATATG
* ** * *
113781 AAAAGGCATGAAAATAAGGGTTCAAAACTTTTATTATATATAGTTTGAAAAATATTAATTATAAT
1 AAAAAGCATGAAAATAACAGTCCAAAACTTTTA-T-TATA-A-TTTGAAAAACATTAATTATAAT
* ** * *
113846 TAAGAATAAAATCAGTTAATTTGATTAATGATCCATTTTTCTATGTTTTAAGTAATCTTCATCAA
62 TAA-AATAAAATCAATTAATTTGATTAATGATCCATTTCCCCATGTTTGAAGTAATCTTCATCAA
* * * ** **
113911 TGTATTTATATAGTAGGTAATGAAATATAATACGTGTATTT-ACTTGAAAAAAAATGCAAAAATA
126 TATATTCATATAATACATAATGAAATATAATACAAGTATTTAAC-TGAAAAAAAATGCAAAAATA
* * * * *
113975 ACA-ATCCAAAACTTTTATTATAGTGTGAAAAACATTAATTATATCTAAAAATAAATTTAGTTAA
190 A-AGATCCAAAACTTTCATTATAGTGTGAAAAACATTAATTATAACTAAAAATAAAATCAATTAA
* *
114039 TTTAATTAATGATCCATTTTTTTTATTTTTGAAGTAATCTCTTTCAACATATTTATTCACTACGT
254 TTTAATTAATGATCCA-ATTTTTTATGTTTGAAGTAATCTCTTTCAAC--A-TT-TTCA-TA--T
* * *
114104 AATACTACATAATGAAATATAATATATTTATTTAATTTA
311 -AT--TACATAATAAAATATAATATATGTATTTAA-TCA
* *
114143 AAAATGCATGAAAATAACAGTCCAAAACTTTTATTATAATTTGAAAAACATTAACTATAATTAAA
1 AAAAAGCATGAAAATAACAGTCCAAAACTTTTATTATAATTTGAAAAACATTAATTATAATTAAA
* * *
114208 AGTAGAATCAATTAATTTGATTAATGATCCATTTCCCCATGTTTGAAGTGATC-TCTTTCAATAT
66 A-TAAAATCAATTAATTTGATTAATGATCCATTTCCCCATGTTTGAAGTAATCTTC-ATCAATAT
* * * **
114272 ATTCATGCATAACATACATAATGAAATATGATATAAGTATTTAACTGAACAAAAATGTGAAAATA
129 ATTCAT--AT-A-ATACATAATGAAATATAATACAAGTATTTAACTGAAAAAAAATGCAAAAATA
* * * * *
114337 AAGGTCCAAAACTTTCATTATATTTTGAAAAATATTAATTATAACTAAGAATAAAATCAATTAAT
190 AAGATCCAAAACTTTCATTATAGTGTGAAAAACATTAATTATAACTAAAAATAAAATCAATTAAT
* ** ** **
114402 TTGATTAATGATTTAATTTTTTATGTTTGAAGTAATCTCTTTTGACATTTTCATATATTATGTAA
255 TTAATTAATGATCCAATTTTTTATGTTTGAAGTAATCTCTTTCAACATTTTCATATATTACATAA
**
114467 TAAAATATGCTATATGTATTTAATCA
320 TAAAATATAATATATGTATTTAATCA
* * * * * *
114493 AAAAAACTTGAAAATAGCAATCCAAAACTTTTACTATAATTTGAAAAACATTAATTATAACTAAA
1 AAAAAGCATGAAAATAACAGTCCAAAACTTTTATTATAATTTGAAAAACATTAATTATAA-TTAA
114558 AATAAA
65 AATAAA
114564 TAAATTCACT
Statistics
Matches: 353, Mismatches: 59, Indels: 30
0.80 0.13 0.07
Matches are distributed among these distances:
350 58 0.16
351 29 0.08
353 2 0.01
354 1 0.00
356 2 0.01
357 8 0.02
358 80 0.23
359 2 0.01
360 6 0.02
361 30 0.08
362 133 0.38
363 2 0.01
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (345 bp):
AAAAAGCATGAAAATAACAGTCCAAAACTTTTATTATAATTTGAAAAACATTAATTATAATTAAA
ATAAAATCAATTAATTTGATTAATGATCCATTTCCCCATGTTTGAAGTAATCTTCATCAATATAT
TCATATAATACATAATGAAATATAATACAAGTATTTAACTGAAAAAAAATGCAAAAATAAAGATC
CAAAACTTTCATTATAGTGTGAAAAACATTAATTATAACTAAAAATAAAATCAATTAATTTAATT
AATGATCCAATTTTTTATGTTTGAAGTAATCTCTTTCAACATTTTCATATATTACATAATAAAAT
ATAATATATGTATTTAATCA
Found at i:114397 original size:178 final size:176
Alignment explanation
Indices: 113789--114563 Score: 678
Period size: 178 Copynumber: 4.4 Consensus size: 176
113779 TGAAAAGGCA
** * * *
113789 TGAAAATAAGGGTTCAAAACTTTTATTATATATAGTTTGAAAAATATTAATTATAATTAAGAATA
1 TGAAAATAACAGTCCAAAACTTTTA-T-TATAT--TTTGAAAAACATTAATTATAACTAAGAATA
* * * * *
113854 AAATCAGTTAATTTGATTAATGATCCATTTTTCTATGTTTTAAGTAATCT-TCATCAATGTATTT
62 AAATCAATTAATTTGATTAATGATCCATTTTTCTATGTTTGAAGTAATCTCT-TTCAATATATTC
* ** **
113918 AT-AT-AGTAGGTAATGAAATATAATACGTGTATTT-ACTTGAAAAAAAATG
126 ATCATAAATACATAATGAAATATAATATATGTATTTAAC-TGAAAAAAAATG
** * * * * * *
113967 CAAAAATAACAATCCAAAACTTTTATTATAGTGTGAAAAACATTAATTATATCTAAAAATAAATT
1 TGAAAATAACAGTCCAAAACTTTTATTATATTTTGAAAAACATTAATTATAACTAAGAATAAAAT
* * * * *
114032 TAGTTAATTTAATTAATGATCCATTTTTTTTATTTTTGAAGTAATCTCTTTCAACATATTTATTC
66 CAATTAATTTGATTAATGATCCA-TTTTTCTATGTTTGAAGTAATCTCTTTC-A-ATA--TATTC
* * **
114097 ACTACGTAATACTACATAATGAAATATAATATATTTATTTAA-T--TTAAAAATG
126 A-T-CATAA-A-TACATAATGAAATATAATATATGTATTTAACTGAAAAAAAATG
* * * *
114149 CATGAAAATAACAGTCCAAAACTTTTATTATAATTTGAAAAACATTAACTATAATTAA-AAGTAG
1 --TGAAAATAACAGTCCAAAACTTTTATTATATTTTGAAAAACATTAATTATAACTAAGAA-TAA
** * *
114213 AATCAATTAATTTGATTAATGATCCATTTCCCCATGTTTGAAGTGATCTCTTTCAATATATTCAT
63 AATCAATTAATTTGATTAATGATCCATTTTTCTATGTTTGAAGTAATCTCTTTCAATATATTCAT
* * *
114278 GCATAACATACATAATGAAATATGATATAAGTATTTAACTGAACAAAAATG
128 -CATAA-ATACATAATGAAATATAATATATGTATTTAACTGAAAAAAAATG
* *
114329 TGAAAATAA-AGGTCCAAAACTTTCATTATATTTTGAAAAATATTAATTATAACTAAGAATAAAA
1 TGAAAATAACA-GTCCAAAACTTTTATTATATTTTGAAAAACATTAATTATAACTAAGAATAAAA
** ** * *
114393 TCAATTAATTTGATTAATGATTTAATTTTT-TATGTTTGAAGTAATCTCTTTTGACATTTTCAT-
65 TCAATTAATTTGATTAATGA-TCCATTTTTCTATGTTTGAAGTAATCTCTTTCAATATATTCATC
* ** * ** * *
114456 AT-ATTATGTAATAAAATATGCTATATGTATTTAA-TCAAAAAAACT-
129 ATAAATACATAATGAAATATAATATATGTATTTAACTGAAAAAAAATG
* * * * *
114501 TGAAAATAGCAATCCAAAACTTTTACTATAATTTGAAAAACATTAATTATAACTAAAAATAAA
1 TGAAAATAACAGTCCAAAACTTTTATTATATTTTGAAAAACATTAATTATAACTAAGAATAAA
114564 TAAATTCACT
Statistics
Matches: 485, Mismatches: 89, Indels: 52
0.77 0.14 0.08
Matches are distributed among these distances:
172 54 0.11
173 9 0.02
174 74 0.15
175 23 0.05
176 8 0.02
177 31 0.06
178 126 0.26
179 18 0.04
180 8 0.02
181 3 0.01
182 9 0.02
183 25 0.05
184 73 0.15
185 23 0.05
186 1 0.00
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.39
Consensus pattern (176 bp):
TGAAAATAACAGTCCAAAACTTTTATTATATTTTGAAAAACATTAATTATAACTAAGAATAAAAT
CAATTAATTTGATTAATGATCCATTTTTCTATGTTTGAAGTAATCTCTTTCAATATATTCATCAT
AAATACATAATGAAATATAATATATGTATTTAACTGAAAAAAAATG
Found at i:115006 original size:17 final size:17
Alignment explanation
Indices: 114984--115018 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
114974 TATATGTATT
114984 ATATATTTATATAATTTAG
1 ATAT-TTTA-ATAATTTAG
115003 ATATTTTAATAATTTA
1 ATATTTTAATAATTTA
115019 TTTTATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATATTTTAATAATTTAG
Found at i:117451 original size:2 final size:2
Alignment explanation
Indices: 117444--117487 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
117434 CTTGCTGAAA
117444 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
117486 AT
1 AT
117488 TTATCATCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:119806 original size:18 final size:16
Alignment explanation
Indices: 119778--119811 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
119768 TTTTAAATTT
119778 AAATTTTATAAATAAAA
1 AAATTTTATAAA-AAAA
119795 AAATTATTATAAAAAAA
1 AAATT-TTATAAAAAAA
119812 TTATTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTTTATAAAAAAA
Found at i:119830 original size:16 final size:14
Alignment explanation
Indices: 119789--119822 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
119779 AATTTTATAA
119789 ATAAAAAAATTATT
1 ATAAAAAAATTATT
119803 ATAAAAAAATTATT
1 ATAAAAAAATTATT
*
119817 TTAAAA
1 ATAAAA
119823 GTAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAAAAAAATTATT
Found at i:119981 original size:62 final size:62
Alignment explanation
Indices: 119904--120028 Score: 196
Period size: 62 Copynumber: 2.0 Consensus size: 62
119894 AAACAGTTTC
* * *
119904 CTTTTTCTATGAATAGTAGTAAAATATCTTTGTTTCTTCGTCTTTTTCTGCCTCTGCTTTTT
1 CTTTTTCTATGAATAGTAGTAAAATATCTTCGTTTCTTCGTCTTTCTCTACCTCTGCTTTTT
* * *
119966 CTTTTTCTATGAATAGTAGTAAGATATCTTCGTTTCTTCGTCTTTCTCTACTTGTGCTTTTT
1 CTTTTTCTATGAATAGTAGTAAAATATCTTCGTTTCTTCGTCTTTCTCTACCTCTGCTTTTT
120028 C
1 C
120029 CAGCGTTCCC
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.16, C:0.18, G:0.12, T:0.54
Consensus pattern (62 bp):
CTTTTTCTATGAATAGTAGTAAAATATCTTCGTTTCTTCGTCTTTCTCTACCTCTGCTTTTT
Found at i:120410 original size:5 final size:5
Alignment explanation
Indices: 120400--120430 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
120390 TATTTTAATA
*
120400 TATAT TATAT TATAT TATAT TATAT CATAT T
1 TATAT TATAT TATAT TATAT TATAT TATAT T
120431 TGTTAATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:122343 original size:27 final size:27
Alignment explanation
Indices: 122283--122348 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
122273 TTATAATATT
122283 TTTATATAATATTTAAAATATTCAATA
1 TTTATATAATATTTAAAATATTCAATA
* *
122310 TTCATATAA-ATTTTAATATATT-AATAA
1 TTTATATAATA-TTTAAAATATTCAAT-A
*
122337 TTTATATTATAT
1 TTTATATAATAT
122349 AAAATTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
26 4 0.12
27 27 0.84
28 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTATATAATATTTAAAATATTCAATA
Found at i:122354 original size:16 final size:16
Alignment explanation
Indices: 122307--122357 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
122297 AAAATATTCA
122307 ATATTCATAT-AAATTT
1 ATATT-ATATAAAATTT
*
122323 -TAATATATTAATAATTT
1 ATATTATA-TAA-AATTT
122340 ATATTATATAAAATTT
1 ATATTATATAAAATTT
122356 AT
1 AT
122358 TAAAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 3 0.10
15 4 0.14
16 8 0.28
17 8 0.28
18 6 0.21
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATTATATAAAATTT
Found at i:124867 original size:177 final size:176
Alignment explanation
Indices: 124089--124913 Score: 672
Period size: 183 Copynumber: 4.6 Consensus size: 176
124079 CATAATGGTT
* * * * * * *
124089 TAAAATTTTTATTATAATTTGAAAAATATTAACTGA-AACTAAAATTACAATCAATTAATTCGAT
1 TAAAACTTTTATTATAGTTTGAAAAACATTAA-TTATAACTAAAAATAAAATC-ATTAATTTGAT
* * * ** * ** * *
124153 TAATGATCTATTTTT-TCATGTTTGAGGTAATCTCCTTCAACATATGCATACACTCATGCACTAT
64 TAATGATCCATTTTTCT-ATGTTTGAAGTAATCTCCTTCAATATATTTATGCACAAAT-TAC-GT
* * * * *
124217 ACAGTGAAGTATAATATGTTTATTTAATTGGAAAAAAATGAAAAGGTACGAAAATAACGGCC
126 A-A-TGAAATATGATATATGTATTTAATT--AAAAAAA-G---A-GT--GAAAATAACAGCC
* *
124279 TAATACTTTTATTATATATAGTTTGAAAAACATTAATTATAATTAAAAATAAAATCAGTTAATTT
1 TAAAAC--TT-TTAT-TATAGTTTGAAAAACATTAATTATAACTAAAAATAAAATCA-TTAATTT
* * * * * * *
124344 AATTAATGATCTATTTTTCTATGTTTGTAGTAAACTCCGTCAATGTATTTATG--C-AA-TAGGT
61 GATTAATGATCCATTTTTCTATGTTTGAAGTAATCTCCTTCAATATATTTATGCACAAATTACGT
* * *
124405 AATGAAATAT-ACTATGTGTATTTAATTGAAAAAA-A-TGCAAAAGTAACAATCC
126 AATGAAATATGA-TATATGTATTTAATTAAAAAAAGAGTG-AAAA-TAAC-AGCC
*
124457 -AAAACTTTTATTATAGTTTGAAAAACATTAATTATAACTAAAAATAAAATTAATTAATTTGATT
1 TAAAACTTTTATTATAGTTTGAAAAACATTAATTATAACTAAAAATAAAA-TCATTAATTTGATT
* * *
124521 AATGATTCATTTTTCTATGTTTGAAGTAATCT-CTCTC-ATCATATTCATTCACTATGTAATACT
65 AATGATCCATTTTTCTATGTTTGAAGTAATCTCCT-TCAAT-ATATTTATGCAC-A---AAT--T
* * * * * * *
124584 ACGCAATGACATGTGATATATTTATTTTATTAAAAAAAG-GTGAAAATAATAGTC
122 ACGTAATGAAATATGATATATGTATTTAATTAAAAAAAGAGTGAAAATAACAGCC
* *
124638 TAAAACTTTTATTATAGTTTGAAAAACATTAACTACTAACTAAAAGTAAAATCACTTAATTTGAT
1 TAAAACTTTTATTATAGTTTGAAAAACATTAATTA-TAACTAAAAATAAAATCA-TTAATTTGAT
* ** *
124703 TAATGATCCATTTCTCCCTGTTTGAAGTAATTTCCTTCAATATATTTATGCACAACATTA-GTAA
64 TAATGATCCATTTTTCTATGTTTGAAGTAATCTCCTTCAATATATTTATGCACAA-ATTACGTAA
*
124767 TAAAATATGATATATGTATTTAATTAAAAAAAGACGTGAAAATAACAGCC
128 TGAAATATGATATATGTATTTAATTAAAAAAAGA-GTGAAAATAACAGCC
* * * * *
124817 TAAAA-TTTCATTATAATTTGAAAAATATTAATTATAACTAAAAATAAAATCAATATATTTTATT
1 TAAAACTTTTATTATAGTTTGAAAAACATTAATTATAACTAAAAATAAAATCATTA-ATTTGATT
*
124881 AATGATCTATTTTTCTATGTTTGAAGTAATCTC
65 AATGATCCATTTTTCTATGTTTGAAGTAATCTC
124914 ATTTGAGTCT
Statistics
Matches: 518, Mismatches: 81, Indels: 85
0.76 0.12 0.12
Matches are distributed among these distances:
172 3 0.01
173 83 0.16
174 6 0.01
175 4 0.01
176 6 0.01
177 92 0.18
178 29 0.06
179 20 0.04
180 4 0.01
181 2 0.00
182 39 0.08
183 97 0.19
184 13 0.03
185 1 0.00
186 21 0.04
187 1 0.00
188 2 0.00
189 1 0.00
190 4 0.01
191 1 0.00
192 3 0.01
193 7 0.01
194 78 0.15
195 1 0.00
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.38
Consensus pattern (176 bp):
TAAAACTTTTATTATAGTTTGAAAAACATTAATTATAACTAAAAATAAAATCATTAATTTGATTA
ATGATCCATTTTTCTATGTTTGAAGTAATCTCCTTCAATATATTTATGCACAAATTACGTAATGA
AATATGATATATGTATTTAATTAAAAAAAGAGTGAAAATAACAGCC
Found at i:125580 original size:22 final size:23
Alignment explanation
Indices: 125546--125588 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
125536 ATTTTGACAC
*
125546 ATGTATATATTCGTGTTATATTT
1 ATGTATATATTCGTGTCATATTT
*
125569 ATGT-TATTTTCGTGTCATAT
1 ATGTATATATTCGTGTCATAT
125589 CCTATAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.23, C:0.07, G:0.14, T:0.56
Consensus pattern (23 bp):
ATGTATATATTCGTGTCATATTT
Found at i:125940 original size:20 final size:20
Alignment explanation
Indices: 125917--125954 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
125907 CAATAAATTA
*
125917 TTAATATTATTATTATATTT
1 TTAAAATTATTATTATATTT
*
125937 TTAAAATTATTTTTATAT
1 TTAAAATTATTATTATAT
125955 AAAATATTAA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTAAAATTATTATTATATTT
Found at i:127121 original size:2 final size:2
Alignment explanation
Indices: 127114--127145 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
127104 TTCTTAACTT
127114 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
127146 ATTAAAAACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:128162 original size:2 final size:2
Alignment explanation
Indices: 128155--128194 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
128145 CTTGCTGAAA
128155 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
128195 TTATCATCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128813 original size:20 final size:20
Alignment explanation
Indices: 128788--128834 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
128778 TAAAATTTAA
*
128788 AATATTTTTATTTT-TATATT
1 AATATTTATATTTTATA-ATT
128808 AATATTTATATTTTATAATT
1 AATATTTATATTTTATAATT
128828 AA-ATTTA
1 AATATTTA
128835 AATAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 5 0.20
20 18 0.72
21 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
AATATTTATATTTTATAATT
Found at i:130037 original size:22 final size:21
Alignment explanation
Indices: 130006--130052 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
129996 AAACTAAAAG
*
130006 AATTTTTAT-TTTTAT-ATTA
1 AATTTATATATTTTATAATTA
130025 ATATTTATATATTTTATAATTA
1 A-ATTTATATATTTTATAATTA
130047 AATTTA
1 AATTTA
130053 AATAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.04
20 7 0.29
21 11 0.46
22 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
AATTTATATATTTTATAATTA
Found at i:131858 original size:16 final size:16
Alignment explanation
Indices: 131834--131891 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
131824 TTTATATTAG
131834 TAAAAATATAATATGA
1 TAAAAATATAATATGA
* **
131850 TAAATATATTTTATGA
1 TAAAAATATAATATGA
* *
131866 TAGAAAT-TAATATAA
1 TAAAAATATAATATGA
131881 TAAAAATATAA
1 TAAAAATATAA
131892 AATTTATTCT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 11 0.34
16 21 0.66
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (16 bp):
TAAAAATATAATATGA
Found at i:132677 original size:27 final size:28
Alignment explanation
Indices: 132647--132707 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
132637 TTATATCATA
132647 ATAATATTTTAA-ATATTTAAT-ATTTAT
1 ATAATATTTTAATATA-TTAATAATTTAT
132674 ATAA-ATTTTAATATATTAATAATTTAT
1 ATAATATTTTAATATATTAATAATTTAT
*
132701 ATTATAT
1 ATAATAT
132708 AAAATTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 12 0.40
27 16 0.53
28 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
ATAATATTTTAATATATTAATAATTTAT
Found at i:132685 original size:18 final size:18
Alignment explanation
Indices: 132656--132715 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
132646 AATAATATTT
132656 TAAATATTTAATATTTATA
1 TAAAT-TTTAATATTTATA
132675 TAAATTTTAATATATTA-A
1 TAAATTTTAATAT-TTATA
132693 T-AA-TTT-ATA-TTATA
1 TAAATTTTAATATTTATA
*
132707 TAAAATTTA
1 TAAATTTTA
132716 TTAAATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.08
14 2 0.06
15 5 0.14
16 6 0.17
17 2 0.06
18 10 0.28
19 8 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TAAATTTTAATATTTATA
Found at i:132699 original size:34 final size:32
Alignment explanation
Indices: 132648--132715 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
132638 TATATCATAA
* *
132648 TAATATTTTAAATATTTAATATTTATATAAATTT
1 TAATATATTAAATATTT-ATA-TTATATAAAATT
132682 TAATATATT-AATAATTTATATTATATAAAATT
1 TAATATATTAAAT-ATTTATATTATATAAAATT
132714 TA
1 TA
132716 TTAAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 13 0.42
33 6 0.19
34 12 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TAATATATTAAATATTTATATTATATAAAATT
Found at i:134276 original size:24 final size:25
Alignment explanation
Indices: 134210--134270 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
134200 AGATTAATTT
* * *
134210 TAATAAAATTAAAAATAATATTATA
1 TAATAAAAATAAAATTAAAATTATA
*
134235 TAATAATAATAAAATTAAAATTA-A
1 TAATAAAAATAAAATTAAAATTATA
134259 TAATAAAAATAA
1 TAATAAAAATAA
134271 TTTTAATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
24 12 0.39
25 19 0.61
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
TAATAAAAATAAAATTAAAATTATA
Found at i:135250 original size:32 final size:33
Alignment explanation
Indices: 135186--135264 Score: 128
Period size: 32 Copynumber: 2.5 Consensus size: 33
135176 CTACCATTGA
*
135186 AGGTACTT-AAAGGT-CTTTTTGGTTCAGGGTG
1 AGGTACTTAAAAAGTCCTTTTTGGTTCAGGGTG
135217 AGGTACTTAAAAAGTCCTTTTTGG-TCAGGGTG
1 AGGTACTTAAAAAGTCCTTTTTGGTTCAGGGTG
135249 AGGTACTTAAAAAGTC
1 AGGTACTTAAAAAGTC
135265 TTTCCATTAG
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
31 8 0.18
32 29 0.64
33 8 0.18
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.34
Consensus pattern (33 bp):
AGGTACTTAAAAAGTCCTTTTTGGTTCAGGGTG
Found at i:136465 original size:18 final size:19
Alignment explanation
Indices: 136442--136492 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
136432 TGATAATTAT
136442 AAAAATTTATGATTTTT-A
1 AAAAATTTATGATTTTTAA
**
136460 AAAAATTTAAAATTTTTAA
1 AAAAATTTATGATTTTTAA
*
136479 AAAAATTTGTGATT
1 AAAAATTTATGATT
136493 GATGTTGATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (19 bp):
AAAAATTTATGATTTTTAA
Found at i:139593 original size:16 final size:16
Alignment explanation
Indices: 139544--139594 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
139534 AAAATATTCG
*
139544 ATATTCATATAAATATTA
1 ATATT-ATATAAA-ATTT
139562 ATA-TAT-TAATAATTT
1 ATATTATATAA-AATTT
139577 ATATTATATAAAATTT
1 ATATTATATAAAATTT
139593 AT
1 AT
139595 TAAAATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
15 9 0.31
16 13 0.45
17 4 0.14
18 3 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTATATAAAATTT
Found at i:140024 original size:2 final size:2
Alignment explanation
Indices: 140017--140047 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
140007 TTATCGACAG
140017 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
140048 CAGGAACAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:141653 original size:21 final size:21
Alignment explanation
Indices: 141627--141673 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
141617 ATCTGCTCTG
*
141627 TTTATTTTATTTTTTAAA-AT
1 TTTATTTTACTTTTTAAATAT
141647 TATTATTTTACTTTTTAAATAT
1 T-TTATTTTACTTTTTAAATAT
141669 TTTAT
1 TTTAT
141674 ATATTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 20 0.83
22 3 0.12
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTATTTTACTTTTTAAATAT
Found at i:144058 original size:20 final size:19
Alignment explanation
Indices: 144028--144068 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
144018 AGCTTTTTTA
*
144028 AATAAAAAGTTAATATTAT
1 AATAAAAAGTTAATAATAT
144047 AATAATAAAGTTAATAATAT
1 AATAA-AAAGTTAATAATAT
144067 AA
1 AA
144069 ACAAAAACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
AATAAAAAGTTAATAATAT
Found at i:155849 original size:40 final size:40
Alignment explanation
Indices: 155804--155884 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
155794 TGTTTAGCAA
* *
155804 ATATTATTCATATTCAAATTTAAATCTAAATAATATAATT
1 ATATTATTCATATTCAAATCTAAATCTAAATAACATAATT
* * * *
155844 ATATTATTTATATTTAAATCTGAATTTAAATAACATAATT
1 ATATTATTCATATTCAAATCTAAATCTAAATAACATAATT
155884 A
1 A
155885 CGTATTACTC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (40 bp):
ATATTATTCATATTCAAATCTAAATCTAAATAACATAATT
Found at i:157921 original size:18 final size:18
Alignment explanation
Indices: 157898--157943 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
157888 TTTAAAATAA
157898 TAATTTAAATCATTAAAT
1 TAATTTAAATCATTAAAT
157916 TAATTTAAATCATTAAAT
1 TAATTTAAATCATTAAAT
157934 TAATTTAAAT
1 TAATTTAAAT
157944 TTAAATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATTTAAATCATTAAAT
Found at i:157957 original size:18 final size:17
Alignment explanation
Indices: 157898--157950 Score: 81
Period size: 18 Copynumber: 3.1 Consensus size: 17
157888 TTTAAAATAA
157898 TAATTTAAATCATTAAAT
1 TAATTTAAAT-ATTAAAT
157916 TAATTTAAATCATTAAAT
1 TAATTTAAAT-ATTAAAT
157934 TAATTTAAAT-TTAAAT
1 TAATTTAAATATTAAAT
157950 T
1 T
157951 TAAATTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.20
18 28 0.80
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATTTAAATATTAAAT
Found at i:157961 original size:7 final size:6
Alignment explanation
Indices: 157899--157957 Score: 54
Period size: 6 Copynumber: 9.8 Consensus size: 6
157889 TTAAAATAAT
157899 AATTTA AATCATTA AA-TT- AATTTA AATCATTA AA-TT- AATTTA AATTTA
1 AATTTA AAT--TTA AATTTA AATTTA AAT--TTA AATTTA AATTTA AATTTA
157947 AATTTA AATTT
1 AATTTA AATTT
157958 TAAAATTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
4 4 0.09
5 8 0.18
6 23 0.51
8 10 0.22
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (6 bp):
AATTTA
Found at i:160736 original size:39 final size:39
Alignment explanation
Indices: 160682--160760 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
160672 AATCATATGT
*
160682 ATGCTACTTGTATGAGTGGGAATCTTTCTCAAGAACTTC
1 ATGCTACTTGTATGAGTGAGAATCTTTCTCAAGAACTTC
160721 ATGCTACTTGTATGAGTGAGAATCTTTCTCAAGAACTTC
1 ATGCTACTTGTATGAGTGAGAATCTTTCTCAAGAACTTC
160760 A
1 A
160761 AAAGGTGGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (39 bp):
ATGCTACTTGTATGAGTGAGAATCTTTCTCAAGAACTTC
Found at i:161500 original size:17 final size:17
Alignment explanation
Indices: 161464--161508 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
161454 ATAAATTTTA
*
161464 AATTT-TATTTA-AATT
1 AATTTATATTTATAAAT
161479 AATTTATATTTATAAAT
1 AATTTATATTTATAAAT
*
161496 AATTTAAATTTAT
1 AATTTATATTTAT
161509 TAAAGTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 5 0.19
16 6 0.23
17 15 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTATATTTATAAAT
Found at i:161557 original size:14 final size:13
Alignment explanation
Indices: 161540--161584 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
161530 AAAATATTTT
161540 TTAAAATTTAATAA
1 TTAAAATTTAAT-A
161554 TTAATAATTTAATA
1 TTAA-AATTTAATA
*
161568 TTAAAAATATAATA
1 TT-AAAATTTAATA
161582 TTA
1 TTA
161585 TATATATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 1 0.04
14 17 0.61
15 10 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAAATTTAATA
Found at i:161606 original size:33 final size:32
Alignment explanation
Indices: 161561--161623 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
161551 TAATTAATAA
* *
161561 TTTAATATTAAAAA-TATAATATTATATATATT
1 TTTAATAATAAAAATTAT-ATAATATATATATT
161593 TTTATATAATAAAAATTATATAATATATATA
1 TTTA-ATAATAAAAATTATATAATATATATA
161624 AATAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 4 0.15
33 20 0.74
34 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
TTTAATAATAAAAATTATATAATATATATATT
Found at i:161622 original size:31 final size:32
Alignment explanation
Indices: 161561--161622 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
161551 TAATTAATAA
* *
161561 TTTAATATTAAAAATATAATATTATATATATT
1 TTTAATAATAAAAATATAATATAATATATATT
161593 TTTATATAATAAAAAT-T-ATATAATATATAT
1 TTTA-ATAATAAAAATATAATATAATATATAT
161623 AAATAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 12 0.44
32 5 0.19
33 10 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
TTTAATAATAAAAATATAATATAATATATATT
Done.