Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold530
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: 160147
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.30
Warning! 14133 characters in sequence are not A, C, G, or T
Found at i:1536 original size:10 final size:10
Alignment explanation
Indices: 1502--1557 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 10
1492 ACTAAATCCT
1502 TTCTCTC-AA
1 TTCTCTCAAA
1511 TCTCTCTCTAATA
1 T-TCTCTC-AA-A
1524 TTCTCTCAAA
1 TTCTCTCAAA
*
1534 TTCCTTTCAAA
1 TT-CTCTCAAA
1545 TTCCTCTCAAA
1 TT-CTCTCAAA
1556 TT
1 TT
1558 TCTATTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 1 0.03
10 9 0.22
11 21 0.52
12 7 0.17
13 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (10 bp):
TTCTCTCAAA
Found at i:1545 original size:11 final size:11
Alignment explanation
Indices: 1526--1557 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1516 CTCTAATATT
1526 CTCTCAAATTC
1 CTCTCAAATTC
*
1537 CTTTCAAATTC
1 CTCTCAAATTC
1548 CTCTCAAATT
1 CTCTCAAATT
1558 TCTATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:2679 original size:43 final size:43
Alignment explanation
Indices: 2642--2752 Score: 150
Period size: 43 Copynumber: 2.6 Consensus size: 43
2632 CACAAATGTT
* *
2642 ACTAAAGAATATGACCTTTAGCGGCGCGTTCATCACAAACGCC
1 ACTAAAGAACATGACCTTTAGCGGCGCATTCATCACAAACGCC
* * * * *
2685 GCTAAAGAACATGACATTTAGTGACGCATTCATCATAAACGCC
1 ACTAAAGAACATGACCTTTAGCGGCGCATTCATCACAAACGCC
*
2728 ACTAAAGAACATGACCTTAAGCGGC
1 ACTAAAGAACATGACCTTTAGCGGC
2753 ACTTTTTCAG
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (43 bp):
ACTAAAGAACATGACCTTTAGCGGCGCATTCATCACAAACGCC
Found at i:3835 original size:30 final size:30
Alignment explanation
Indices: 3801--3885 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
3791 ATCAATATTT
3801 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
3831 ATGGAAAGTCAAAGATATAGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
3861 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
3886 GAGATATTAG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:3842 original size:15 final size:16
Alignment explanation
Indices: 3800--3880 Score: 73
Period size: 15 Copynumber: 5.3 Consensus size: 16
3790 CATCAATATT
3800 TATGGAAAGTCAAAGA
1 TATGGAAAGTCAAAGA
** *
3816 TATGGGTA-TCAAATA
1 TATGGAAAGTCAAAGA
3831 -ATGGAAAGTCAAAGA
1 TATGGAAAGTCAAAGA
* *
3846 TATAGG-TA-TCAAATA
1 TAT-GGAAAGTCAAAGA
3861 T-TGGAAAGTCAAAGA
1 TATGGAAAGTCAAAGA
3876 TATGG
1 TATGG
3881 GTATCGAGAT
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
13 2 0.04
14 7 0.14
15 26 0.53
16 12 0.24
17 2 0.04
ACGTcount: A:0.46, C:0.06, G:0.23, T:0.25
Consensus pattern (16 bp):
TATGGAAAGTCAAAGA
Found at i:9526 original size:13 final size:13
Alignment explanation
Indices: 9503--9538 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
9493 AAATAATAAA
9503 TAAATTAAAATATT
1 TAAA-TAAAATATT
9517 TAAATAAAATATT
1 TAAATAAAATATT
*
9530 AAAATAAAA
1 TAAATAAAA
9539 AAATGAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAATAAAATATT
Found at i:9542 original size:21 final size:21
Alignment explanation
Indices: 9491--9547 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
9481 TTCAATTGAC
*
9491 AAAAATAATAAATAAATTAAAAT
1 AAAAA-AATAAA-ATATTAAAAT
***
9514 ATTTAAATAAAATATTAAAAT
1 AAAAAAATAAAATATTAAAAT
*
9535 AAAAAAATGAAAT
1 AAAAAAATAAAAT
9548 TAGATTTATT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 18 0.69
22 6 0.23
23 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAAAAATAAAATATTAAAAT
Found at i:9664 original size:55 final size:56
Alignment explanation
Indices: 9603--9750 Score: 262
Period size: 55 Copynumber: 2.7 Consensus size: 56
9593 CTAAAAAACC
* *
9603 AAAAAAAGGGTGTTAGATGTAGAAAAATAAAACTGAAATAAATGAGTTTGAATG-A
1 AAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTGAAATAAATGAGATTGAATGAA
*
9658 AAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTAAAATAAATGAGATTGAATGAA
1 AAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTGAAATAAATGAGATTGAATGAA
9714 AAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTGAA
1 AAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTGAA
9751 TGAAAATAAA
Statistics
Matches: 88, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
55 51 0.58
56 37 0.42
ACGTcount: A:0.55, C:0.01, G:0.21, T:0.23
Consensus pattern (56 bp):
AAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTGAAATAAATGAGATTGAATGAA
Found at i:9753 original size:41 final size:41
Alignment explanation
Indices: 9704--9791 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 41
9694 AATAAATGAG
*** *
9704 ATTGAATGAAAAAAAAAGGGTGTTAGATGTAGAAAAATAAA
1 ATTGAATGAAAAAAAAAGGAAATTAGATGTAAAAAAATAAA
*
9745 ATTGAATGAAAATAAAAGGAAATTAGATGTAAAAAAATAAA
1 ATTGAATGAAAAAAAAAGGAAATTAGATGTAAAAAAATAAA
9786 ATTGAA
1 ATTGAA
9792 ATAAATGAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.23
Consensus pattern (41 bp):
ATTGAATGAAAAAAAAAGGAAATTAGATGTAAAAAAATAAA
Found at i:9763 original size:97 final size:94
Alignment explanation
Indices: 9650--9857 Score: 301
Period size: 97 Copynumber: 2.2 Consensus size: 94
9640 ATAAATGAGT
*** *
9650 TTGAATGAAAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTAAAATAAATGAGATTGAATGAAA
1 TTGAATGAAAAAAAAGGAAATTAGATGTAAAAAAATAAAATTAAAATAAATGAGATTGAATG-AA
9715 AAAAAAGGGTGTTAGATGTAGAAAAATAAAA
65 AAAAAA-GGTGTTAGATGTAGAAAAATAAAA
*
9746 TTGAATGAAAATAAAAGGAAATTAGATGTAAAAAAATAAAATTGAAATAAATGAGATTGAATGAA
1 TTGAATGAAAA-AAAAGGAAATTAGATGTAAAAAAATAAAATTAAAATAAATGAGATTGAATGAA
9811 AAAAAAGGTGTTAGATGTAGAAAAA-AATTGAA
65 AAAAAAGGTGTTAGATGTAGAAAAATAA---AA
*
9843 ATGAATGAAAAAAAA
1 TTGAATGAAAAAAAA
9858 AGTGTTTCAG
Statistics
Matches: 102, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
94 2 0.02
95 19 0.19
96 23 0.23
97 58 0.57
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (94 bp):
TTGAATGAAAAAAAAGGAAATTAGATGTAAAAAAATAAAATTAAAATAAATGAGATTGAATGAAA
AAAAAGGTGTTAGATGTAGAAAAATAAAA
Found at i:11129 original size:108 final size:111
Alignment explanation
Indices: 10919--11138 Score: 311
Period size: 108 Copynumber: 2.0 Consensus size: 111
10909 CACCACCAAT
*
10919 TTTTTTTTTTACATTTTGGCTATCATAGGCCGACACCAGTATACGAAAAAAATAAAAAAACAATT
1 TTTTTTTTTTACATTTTGGCTATCATAGGCCGACAACAGTATACGAAAAAAAT-AAAAAACAATT
* *
10984 TTTTTTTGGTGGTGGCCTGGCAATGGCCGGCATCACCTTTATGTAAA
65 TTTTTTTGGTGGTGGCCTGGCAATGGCCGACACCACCTTTATGTAAA
* ** * * **
11031 TTTTTTTTTTACATTTTGGCTGTCATTTGCTGGCAACAGTATACG-AAAAAAT-TCAAA-AATTT
1 TTTTTTTTTTACATTTTGGCTATCATAGGCCGACAACAGTATACGAAAAAAATAAAAAACAATTT
*
11093 TTTTTTGGTGGTGGCTTGGCAATGGCCGACACCACCTTTATGTAAA
66 TTTTTTGGTGGTGGCCTGGCAATGGCCGACACCACCTTTATGTAAA
11139 AAAAAAATTC
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
108 48 0.49
109 3 0.03
111 7 0.07
112 39 0.40
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.37
Consensus pattern (111 bp):
TTTTTTTTTTACATTTTGGCTATCATAGGCCGACAACAGTATACGAAAAAAATAAAAAACAATTT
TTTTTTGGTGGTGGCCTGGCAATGGCCGACACCACCTTTATGTAAA
Found at i:11257 original size:54 final size:54
Alignment explanation
Indices: 11158--11383 Score: 375
Period size: 54 Copynumber: 4.2 Consensus size: 54
11148 CATGAAGTTA
* * *
11158 AAATAAATGACATTGAATGAAAAAAAAGGGTGTTAGATGTAGAAAAATAAAACTG
1 AAATAAATGAGATTGAATG-AAAAAAAGGGTGTTAGATATAGAAAAATAAAATTG
11213 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATATAGAAAAATAAAATTG
1 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATATAGAAAAATAAAATTG
11267 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATATAGAAAAATAAAATTG
1 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATATAGAAAAATAAAATTG
*
11321 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATGTA-AAAAA-AAAATTTG
1 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATATAGAAAAATAAAA-TTG
*
11374 AAATGAATGA
1 AAATAAATGA
11384 TAAAAAAAGT
Statistics
Matches: 165, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
52 4 0.02
53 17 0.10
54 126 0.76
55 18 0.11
ACGTcount: A:0.55, C:0.01, G:0.20, T:0.23
Consensus pattern (54 bp):
AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATATAGAAAAATAAAATTG
Found at i:12751 original size:108 final size:111
Alignment explanation
Indices: 12533--12752 Score: 295
Period size: 108 Copynumber: 2.0 Consensus size: 111
12523 CACCACCAAT
*
12533 TTTTTTTTTTACATTTTGGCTATCATAGGCCGACACCAGTATACGAAAAAAATAAAAAAACAATT
1 TTTTTTTTTTACATTTTGGCTATCATAGGCCGACAACAGTATACGAAAAAAAT-AAAAAACAATT
* *
12598 TTTTTTTGGTGGTGGCCTGGCAATGGCCGGCATCACCTTTATGTAAA
65 TTTTTTTGGTGGTGGCCTGGCAATGGCCGACACCACCTTTATGTAAA
* ** * * **
12645 TTTTTTTTTTACATTTTGGCTGTCATTTGCTGGCAACAGTATACG-AAAAAAT-TCAAA-AATTT
1 TTTTTTTTTTACATTTTGGCTATCATAGGCCGACAACAGTATACGAAAAAAATAAAAAACAATTT
*
12707 TTTTTTGGTGGT-GCTTGGCAATTGGCCGACACCACCTTTATGTAAA
66 TTTTTTGGTGGTGGCCTGGCAA-TGGCCGACACCACCTTTATGTAAA
12753 AAAAATTTTA
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
107 8 0.08
108 39 0.41
109 3 0.03
111 7 0.07
112 39 0.41
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (111 bp):
TTTTTTTTTTACATTTTGGCTATCATAGGCCGACAACAGTATACGAAAAAAATAAAAAACAATTT
TTTTTTGGTGGTGGCCTGGCAATGGCCGACACCACCTTTATGTAAA
Found at i:12870 original size:54 final size:54
Alignment explanation
Indices: 12771--13050 Score: 483
Period size: 54 Copynumber: 5.2 Consensus size: 54
12761 TAAGAAGTTA
* * *
12771 AAATAAATGACATTGAATGAAAAAAAAGGGTGTTAGATGTAGAAAAATAAAACTG
1 AAATAAATGAGATTGAATG-AAAAAAAGGGTGTTAGATATAGAAAAATAAAATTG
12826 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATATAGAAAAATAAAATTG
1 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATATAGAAAAATAAAATTG
12880 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATATAGAAAAATAAAATTG
1 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATATAGAAAAATAAAATTG
12934 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATATAGAAAAATAAAATTG
1 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATATAGAAAAATAAAATTG
*
12988 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATGTA-AAAAA-AAAATTTG
1 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATATAGAAAAATAAAA-TTG
*
13041 AAATGAATGA
1 AAATAAATGA
13051 TAAAAAAAGT
Statistics
Matches: 219, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
52 4 0.02
53 17 0.08
54 180 0.82
55 18 0.08
ACGTcount: A:0.55, C:0.01, G:0.20, T:0.24
Consensus pattern (54 bp):
AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATATAGAAAAATAAAATTG
Found at i:14837 original size:109 final size:112
Alignment explanation
Indices: 14631--14849 Score: 327
Period size: 113 Copynumber: 2.0 Consensus size: 112
14621 CCACCACCAA
*** *
14631 TTTTTTTTTACATTTTTTTTGTCATAGGCCGGCACCAGTATACGAAAAAATTCAAAAACAATTTT
1 TTTTTTTTTACATTTTGGCTGTCATAGGCCGGCAACAGTATACGAAAAAATTC-AAAACAATTTT
*
14696 TTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTG
65 TTTTTGGTGGTGGCCTGGCAATGGCCGACACCACCTTTATGTAAATTG
** *
14744 TTTTTTTTTACATTTTGGCTGTCATTTGCCGGCAACAGTATACGAAAAAATTC-AAA-TA-TTTT
1 TTTTTTTTTACATTTTGGCTGTCATAGGCCGGCAACAGTATACGAAAAAATTCAAAACAATTTTT
*
14806 TTTTGGTGGTGGCTTGGCAATGGCCGACACCACCTTTATGTAAA
66 TTTTGGTGGTGGCCTGGCAATGGCCGACACCACCTTTATGTAAA
14850 AAAAATTTTA
Statistics
Matches: 97, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
109 46 0.47
110 1 0.01
111 3 0.03
113 47 0.48
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (112 bp):
TTTTTTTTTACATTTTGGCTGTCATAGGCCGGCAACAGTATACGAAAAAATTCAAAACAATTTTT
TTTTGGTGGTGGCCTGGCAATGGCCGACACCACCTTTATGTAAATTG
Found at i:14969 original size:54 final size:54
Alignment explanation
Indices: 14868--15039 Score: 240
Period size: 54 Copynumber: 3.2 Consensus size: 54
14858 TAAGAAGTTA
* *
14868 AAATAAATGACATTGAATGAAAAAAAAGGGTGTTAGATGTAGAAAAATAATACTT-
1 AAATAAATGAGATTGAATG-AAAAAAAGGGTGTTAGATGTAGAAAAATAA-AATTG
* * *
14923 AAATAAATGAGATTGAAAGAAAAAAAGGGTGTTATATATAGAAAAATAAAATTG
1 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTG
*
14977 AAATAAATGAGATTGAATGAAAAAAAGCGTGTTAGATGTAGAAATAA-AAAATTG
1 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATGTAGAAA-AATAAAATTG
*
15031 AAATGAATG
1 AAATAAATG
15040 GTAAAAAAAG
Statistics
Matches: 105, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
53 3 0.03
54 83 0.79
55 19 0.18
ACGTcount: A:0.55, C:0.02, G:0.19, T:0.24
Consensus pattern (54 bp):
AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTG
Found at i:16252 original size:107 final size:107
Alignment explanation
Indices: 16133--16346 Score: 306
Period size: 107 Copynumber: 2.0 Consensus size: 107
16123 CCACCACCAT
* * *
16133 TTTTTTTTTACATTTTGGCTATCATAGGCCGGCACCAGTATACGAAAAAA-T-AAAAAAACAATT
1 TTTTTTTTTACATTTTGGCTATAATAGGCCGGCAACAGTATACGAAAAAATTCAAAAAAA-AA-A
*
16196 TTTTTGTGGTGGCCTGGCAATGGCCGACACCACCTTTATGTAAA
64 TTTTGGTGGTGGCCTGGCAATGGCCGACACCACCTTTATGTAAA
* ** *
16240 TTTTTTTTTACATTTTGGCTGTAATTTGCCGGCAACAGTATATGAAAAAATTCAAAAAAAAAATT
1 TTTTTTTTTACATTTTGGCTATAATAGGCCGGCAACAGTATACGAAAAAATTCAAAAAAAAAATT
* *
16305 TTGGTGGTGGCTTGGCAATGGTCGACACCACCTTTATGTAAA
66 TTGGTGGTGGCCTGGCAATGGCCGACACCACCTTTATGTAAA
16347 AAAAAATTCA
Statistics
Matches: 95, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 85 0.89
108 3 0.03
109 7 0.07
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Consensus pattern (107 bp):
TTTTTTTTTACATTTTGGCTATAATAGGCCGGCAACAGTATACGAAAAAATTCAAAAAAAAAATT
TTGGTGGTGGCCTGGCAATGGCCGACACCACCTTTATGTAAA
Found at i:16525 original size:55 final size:54
Alignment explanation
Indices: 16365--16536 Score: 283
Period size: 54 Copynumber: 3.2 Consensus size: 54
16355 CAAGAAGTTA
* *
16365 AAATAAATGACATTGAATGAAAAAAAGGGTGTTAGATGTAGAAAAATAAAACTG
1 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTG
*
16419 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATATAGAAAAATAAAATTG
1 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTG
16473 AAATAAATGAGATTGAATGAAAAAAAGGGGTGTTAGATGTAGAAATAA-AAAATTG
1 AAATAAATGAGATTGAATGAAAAAAA-GGGTGTTAGATGTAGAAA-AATAAAATTG
*
16528 AAATGAATG
1 AAATAAATG
16537 TGTGTCATAA
Statistics
Matches: 111, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
54 77 0.69
55 32 0.29
56 2 0.02
ACGTcount: A:0.54, C:0.01, G:0.22, T:0.23
Consensus pattern (54 bp):
AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTG
Found at i:17797 original size:54 final size:54
Alignment explanation
Indices: 17728--17899 Score: 276
Period size: 54 Copynumber: 3.2 Consensus size: 54
17718 CAAAAAGTTA
17728 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTG
1 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTG
* *
17782 AAATAAATGAGATTGAATGAAAAGAAGGGTGTTAGATATAGAAAAATAAAATTG
1 AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTG
*
17836 AAATAAATGAGATTGAATGAAAAAAAAAGGGTGTTAGATGTAG-AAAA-AACATTG
1 AAATAAATGAGATTGAATG--AAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTG
*
17890 AAATGAATGA
1 AAATAAATGA
17900 AAAAAAAAAG
Statistics
Matches: 110, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
54 86 0.78
55 4 0.04
56 20 0.18
ACGTcount: A:0.54, C:0.01, G:0.22, T:0.23
Consensus pattern (54 bp):
AAATAAATGAGATTGAATGAAAAAAAGGGTGTTAGATGTAGAAAAATAAAATTG
Found at i:18512 original size:10 final size:10
Alignment explanation
Indices: 18497--18526 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
18487 TTCCTCCATT
18497 GTCCCATGAG
1 GTCCCATGAG
18507 GTCCCATGAG
1 GTCCCATGAG
18517 GTCCCATGAG
1 GTCCCATGAG
18527 ATACCTTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.30, T:0.20
Consensus pattern (10 bp):
GTCCCATGAG
Found at i:18667 original size:35 final size:36
Alignment explanation
Indices: 18610--18714 Score: 86
Period size: 45 Copynumber: 2.7 Consensus size: 36
18600 GCTCTAGATG
* * * *
18610 TTGTCTTCTTGTACTCGTAGCGAAG-ATAGCAAATC
1 TTGTCTTCCTGTATTGGCAGCGAAGAATAGCAAATC
18645 TTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAAATAGCAAATC
1 TTGTCTTCCTGTATTGGCAGC---G-A-A--G--AATAGCAAATC
18690 TTGTCTTCCTGTATTGGCAGCGAAG
1 TTGTCTTCCTGTATTGGCAGCGAAG
18715 TAGATTGAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
35 17 0.30
38 2 0.04
39 1 0.02
40 2 0.04
41 1 0.02
42 2 0.04
45 31 0.55
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (36 bp):
TTGTCTTCCTGTATTGGCAGCGAAGAATAGCAAATC
Found at i:18699 original size:45 final size:45
Alignment explanation
Indices: 18630--18785 Score: 222
Period size: 45 Copynumber: 3.5 Consensus size: 45
18620 GTACTCGTAG
18630 CGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
1 CGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
*
18675 CGAAAATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
1 CGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
* * * * *
18720 TGAAGATAACAGATCTTGTCTTCATGTATTGGCAGTGAAGTAGAT
1 CGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
* * * *
18765 TGAAGATTGTAGATCTTGTCT
1 CGAAGATAGCAAATCTTGTCT
18786 CCCTAAGCAG
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 101 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (45 bp):
CGAAGATAGCAAATCTTGTCTTCCTGTATTGGCAGCGAAGTAGAT
Found at i:18994 original size:132 final size:132
Alignment explanation
Indices: 18751--19092 Score: 463
Period size: 132 Copynumber: 2.6 Consensus size: 132
18741 TCATGTATTG
* * * * **
18751 GCAGTGAAGTAGATTGAAGATTGTAGATCTTGTCTCCCTAAGCAGT-GTGGAGCAGATCGAAGAT
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGAAGTAGTGGAGCAGATCGAAGGC
* * * * * *
18815 GGTAAATCTTATATTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGT-CCTATCTCCTTGA
66 AGCAAATCTTATCTTCCCAAGGTAGTAGGGAAGCAAATTTAAGCCACCAATCCCT-TCTCCCTGA
18879 GCA
130 GCA
* *
18882 GCGGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGAAGTAGTGGACCAGATCGAAGGC
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGAAGTAGTGGAGCAGATCGAAGGC
*
18947 AGCAAATCCTATCTTCCCAAGGTAGTAGGGAAGCAAATTTAAGCCACCAATCCCTTCTCCCTGAG
66 AGCAAATCTTATCTTCCCAAGGTAGTAGGGAAGCAAATTTAAGCCACCAATCCCTTCTCCCTGAG
19012 CA
131 CA
* * * * * *
19014 GCAGTGGAGTAGGTCGAAGATTGTAGATCCTGTATCCCTAAGTAGTAATGGAGAAGATAGAAGGC
1 GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGAAGTAGTGGAGCAGATCGAAGGC
*
19079 AGCGAATCTTATCT
66 AGCAAATCTTATCT
19093 CCTTGTCATT
Statistics
Matches: 184, Mismatches: 25, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
131 41 0.22
132 140 0.76
133 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (132 bp):
GCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGAAGTAGTGGAGCAGATCGAAGGC
AGCAAATCTTATCTTCCCAAGGTAGTAGGGAAGCAAATTTAAGCCACCAATCCCTTCTCCCTGAG
CA
Found at i:19613 original size:21 final size:21
Alignment explanation
Indices: 19588--19627 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
19578 ATCTTCAAGG
19588 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
19609 ATATGCAATCTTAGATATG
1 ATATGCAATCTTAGATATG
19628 GTATGCTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:22096 original size:107 final size:106
Alignment explanation
Indices: 21952--22166 Score: 265
Period size: 103 Copynumber: 2.0 Consensus size: 106
21942 AGCCACCACA
* *
21952 AATTTATTTTTTATATTATGGCTATCTTTGGCAGGCACCAATATACGAAAAAATTCAAAAAAAAA
1 AATTTATTTTTTACATTATGGCTATCATTGGCAGGCACCAATATACGAAAAAATTC----AAAAA
* * *
22017 ATTTTTTTGGTGGTGGCCTGGCAATGG-CAGCACCACCTTTATGT
62 ATTTTTTTGGCGGTGGCCTGGAAATGGCCAGCACCACCGTTATGT
* * * * *
22061 AATTT-TTTTTTACATTTTGGCTGTCATTGG-GGGCACCAGTATACGAAAAAATTCAAAATATTT
1 AATTTATTTTTTACATTATGGCTATCATTGGCAGGCACCAATATACGAAAAAATTCAAAAAATTT
* *
22124 TTTTGGCGGTGGTCTGGAAATGGCCGGCACCACCGTTATGT
66 TTTTGGCGGTGGCCTGGAAATGGCCAGCACCACCGTTATGT
22165 AA
1 AA
22167 AAAAAAAAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
103 28 0.30
104 17 0.18
107 22 0.24
108 21 0.23
109 5 0.05
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (106 bp):
AATTTATTTTTTACATTATGGCTATCATTGGCAGGCACCAATATACGAAAAAATTCAAAAAATTT
TTTTGGCGGTGGCCTGGAAATGGCCAGCACCACCGTTATGT
Found at i:22470 original size:41 final size:40
Alignment explanation
Indices: 22408--22641 Score: 308
Period size: 41 Copynumber: 5.7 Consensus size: 40
22398 CCTTTTGGGG
*
22408 CTTTAGCGGCGTTTTTACGAAAGCGCCGCTAATGCTCAGGC
1 CTTTAGCGGCGTTTTT-GGAAAGCGCCGCTAATGCTCAGGC
* *
22449 CTTTAGCAGCGTTTTTGCGAAAGCGCAGCTAATGCTCAGGC
1 CTTTAGCGGCGTTTTTG-GAAAGCGCCGCTAATGCTCAGGC
* * *
22490 CTTCAGCGGCGTTTTTGCTAAAGCGCCGCTAATGCTCAGGG
1 CTTTAGCGGCGTTTTTG-GAAAGCGCCGCTAATGCTCAGGC
*
22531 CTTTAGCGGCGTTTTTGGATAAGCGCCGCTAATGCTCAGGG
1 CTTTAGCGGCGTTTTTGGA-AAGCGCCGCTAATGCTCAGGC
* * *
22572 CTTTAGCAGCATTTTTGGAAAAGCGCCGTTAATGCTCAAGG-
1 CTTTAGCGGCGTTTTTGG-AAAGCGCCGCTAATGCTC-AGGC
22613 CTTTAGCGGCGTTTTTGGATAAGCGCCGC
1 CTTTAGCGGCGTTTTTGGA-AAGCGCCGC
22642 AAAAACATTT
Statistics
Matches: 172, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
40 2 0.01
41 166 0.97
42 4 0.02
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (40 bp):
CTTTAGCGGCGTTTTTGGAAAGCGCCGCTAATGCTCAGGC
Found at i:22624 original size:123 final size:123
Alignment explanation
Indices: 22405--22629 Score: 348
Period size: 123 Copynumber: 1.8 Consensus size: 123
22395 TGACCTTTTG
*
22405 GGGCTTTAGCGGCGTTTTTACGAAAGCGCCGCTAATGCTCAGGCCTTTAGCAGCGTTTTTGCGAA
1 GGGCTTTAGCGGCGTTTTTACGAAAGCGCCGCTAATGCTCAGGCCTTTAGCAGCATTTTTGCGAA
22470 AGCGCAGCTAATGCTCAGGCCTTCAGCGGCGTTTTTGCTAAAGCGCCGCTAATGCTCA
66 AGCGCAGCTAATGCTCAGGCCTTCAGCGGCGTTTTTGCTAAAGCGCCGCTAATGCTCA
* *
22528 GGGCTTTAGCGGCGTTTTT-GGATAAGCGCCGCTAATGCTCAGGGCTTTAGCAGCATTTTTG-GA
1 GGGCTTTAGCGGCGTTTTTACGA-AAGCGCCGCTAATGCTCAGGCCTTTAGCAGCATTTTTGCG-
* * *
22591 AAAGCGCCGTTAATGCTCAAGG-CTTTAGCGGCGTTTTTG
64 AAAGCGCAGCTAATGCTC-AGGCCTTCAGCGGCGTTTTTG
22630 GATAAGCGCC
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
122 3 0.03
123 87 0.94
124 3 0.03
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (123 bp):
GGGCTTTAGCGGCGTTTTTACGAAAGCGCCGCTAATGCTCAGGCCTTTAGCAGCATTTTTGCGAA
AGCGCAGCTAATGCTCAGGCCTTCAGCGGCGTTTTTGCTAAAGCGCCGCTAATGCTCA
Found at i:22924 original size:14 final size:14
Alignment explanation
Indices: 22901--22937 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
22891 GGGTTTAATA
*
22901 TATATTGTTTAGGG
1 TATATGGTTTAGGG
*
22915 TTTATGGTTTAGGG
1 TATATGGTTTAGGG
22929 TATATGGTT
1 TATATGGTT
22938 AATTTAGGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (14 bp):
TATATGGTTTAGGG
Found at i:23274 original size:7 final size:7
Alignment explanation
Indices: 23251--23309 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
23241 TAAATAAGGT
*
23251 TTAGGGG
1 TTAGAGG
23258 TTAGTA-G
1 TTAG-AGG
23265 TTAGAGG
1 TTAGAGG
23272 TTA-AGGG
1 TTAGA-GG
* *
23279 TTTGGGG
1 TTAGAGG
*
23286 TTAGGGG
1 TTAGAGG
23293 TTAGAGG
1 TTAGAGG
23300 TTAGAGG
1 TTAGAGG
23307 TTA
1 TTA
23310 AGAGTTAGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
6 2 0.05
7 41 0.95
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.34
Consensus pattern (7 bp):
TTAGAGG
Found at i:23285 original size:28 final size:29
Alignment explanation
Indices: 23248--23302 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
23238 TATTAAATAA
*
23248 GGTTTAGGGGTTAGTAGTTAGAGGTTAAG
1 GGTTTAGGGGTTAGGAGTTAGAGGTTAAG
*
23277 GGTTT-GGGGTTAGGGGTTAGAGGTTA
1 GGTTTAGGGGTTAGGAGTTAGAGGTTA
23303 GAGGTTAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.20, C:0.00, G:0.45, T:0.35
Consensus pattern (29 bp):
GGTTTAGGGGTTAGGAGTTAGAGGTTAAG
Found at i:23301 original size:14 final size:14
Alignment explanation
Indices: 23264--23309 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
23254 GGGGTTAGTA
*
23264 GTTAGAGGTTAAGG
1 GTTAGAGGTTAGGG
* *
23278 GTTTGGGGTTAGGG
1 GTTAGAGGTTAGGG
*
23292 GTTAGAGGTTAGAG
1 GTTAGAGGTTAGGG
23306 GTTA
1 GTTA
23310 AGAGTTAGTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.46, T:0.33
Consensus pattern (14 bp):
GTTAGAGGTTAGGG
Found at i:23482 original size:21 final size:21
Alignment explanation
Indices: 23441--23483 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
23431 GGTTTAGGGG
**
23441 TTTAGGGTATATGTTTTATAA
1 TTTAGGGTATATGTTAAATAA
23462 TTTAGGGCT-TATGTTAAATAA
1 TTTAGGG-TATATGTTAAATAA
23483 T
1 T
23484 AAAATTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.49
Consensus pattern (21 bp):
TTTAGGGTATATGTTAAATAA
Found at i:24189 original size:23 final size:21
Alignment explanation
Indices: 24147--24189 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
24137 CCCTTCCCTC
*
24147 CAAAACCCAAATTCCTTCAAG
1 CAAAACCCAAACTCCTTCAAG
24168 CAAAACCCAAACCCTCCTTCAA
1 CAAAACCCAAA--CTCCTTCAA
24190 ATTATCCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.42, C:0.40, G:0.02, T:0.16
Consensus pattern (21 bp):
CAAAACCCAAACTCCTTCAAG
Found at i:25473 original size:19 final size:19
Alignment explanation
Indices: 25449--25532 Score: 132
Period size: 19 Copynumber: 4.3 Consensus size: 19
25439 AATTTTTGAG
*
25449 GATATGAAATCTTAGATAT
1 GATATGCAATCTTAGATAT
25468 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
25487 GATATATGCAATCTTAGTTAT
1 G--ATATGCAATCTTAGATAT
25508 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
25527 GATATG
1 GATATG
25533 TNNNNNNNNN
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
19 42 0.70
21 18 0.30
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:25494 original size:40 final size:40
Alignment explanation
Indices: 25450--25531 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
25440 ATTTTTGAGG
25450 ATATGAAATCTTAGATATGATATGCAATCTTAGATATGAT
1 ATATGAAATCTTAGATATGATATGCAATCTTAGATATGAT
* *
25490 ATATGCAATCTTAGTTATGATATGCAATCTTAGATATGAT
1 ATATGAAATCTTAGATATGATATGCAATCTTAGATATGAT
25530 AT
1 AT
25532 GTNNNNNNNN
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.39
Consensus pattern (40 bp):
ATATGAAATCTTAGATATGATATGCAATCTTAGATATGAT
Found at i:30153 original size:22 final size:23
Alignment explanation
Indices: 30101--30154 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
30091 CGTTTTTAAT
*
30101 TAAAATTAAAATTATATTTGTAA
1 TAAAATTAAAACTATATTTGTAA
*
30124 TAAAATTAAAACTA-A-TTGTTA
1 TAAAATTAAAACTATATTTGTAA
30145 TCAAAATTAA
1 T-AAAATTAA
30155 TTGTTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 6 0.21
22 9 0.32
23 13 0.46
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (23 bp):
TAAAATTAAAACTATATTTGTAA
Found at i:30155 original size:16 final size:16
Alignment explanation
Indices: 30131--30168 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
30121 TAATAAAATT
*
30131 AAAACTAATTGTTATC
1 AAAATTAATTGTTATC
*
30147 AAAATTAATTGTTATT
1 AAAATTAATTGTTATC
30163 AAAATT
1 AAAATT
30169 GTATCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (16 bp):
AAAATTAATTGTTATC
Found at i:30848 original size:9 final size:9
Alignment explanation
Indices: 30836--30861 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
30826 AACATCATCC
30836 TCATCGTCG
1 TCATCGTCG
30845 TCATCGTCG
1 TCATCGTCG
30854 TCATCGTC
1 TCATCGTC
30862 CCTTTTGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.19, T:0.35
Consensus pattern (9 bp):
TCATCGTCG
Found at i:32113 original size:22 final size:22
Alignment explanation
Indices: 32070--32144 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 22
32060 GTTATTAATA
*
32070 AAATTT-ATAAATCTTCCT-TTT
1 AAATTTAATAAAT-TTACTATTT
32091 AAATTTAATAAATTTACTATTT
1 AAATTTAATAAATTTACTATTT
* *
32113 -ATTTTAATAAAATTTATTAAATTT
1 AAATTTAAT-AAATTTACT--ATTT
32137 AAATTTAA
1 AAATTTAA
32145 ATTTTTAGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
21 17 0.39
22 17 0.39
24 4 0.09
25 6 0.14
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATTTAATAAATTTACTATTT
Found at i:34041 original size:5 final size:6
Alignment explanation
Indices: 34025--34050 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
34015 TAATCACCTA
34025 CTTTTT CTTTTT CTTTTT CTTTTT CT
1 CTTTTT CTTTTT CTTTTT CTTTTT CT
34051 GACTTGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
CTTTTT
Found at i:35553 original size:17 final size:17
Alignment explanation
Indices: 35523--35564 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
35513 ATAGAAATAA
*
35523 ATATTATTTGAAAAAAT
1 ATATTTTTTGAAAAAAT
* *
35540 ATATTTTTTTAAAAGAT
1 ATATTTTTTGAAAAAAT
35557 ATATTTTT
1 ATATTTTT
35565 AGCGGCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
ATATTTTTTGAAAAAAT
Found at i:35609 original size:43 final size:43
Alignment explanation
Indices: 35562--35915 Score: 453
Period size: 43 Copynumber: 8.3 Consensus size: 43
35552 AAGATATATT
* ** * * *
35562 TTTAGCGGCATTTGTGTCAAAAGCGTCGCTAAAAGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
** * * *
35605 TTTAGCGGCGTTTACGGGAAAATCGTCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * *
35648 TTTAGCGGTGTTTGTAGGAAAAACGCCGCTAAAGGTCTTTGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
** * * *
35691 TTTAGCGGCGTTTGTGCTAAAACCGCCGCTAAAAGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
35734 TTTAGCGGCGCTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
35777 ATTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
35820 TTTA---GCGTTTCTGGGGAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
35860 TTTAGCGGCGTTTGTGGGAAAAGAGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
35903 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
35916 ATTTCTAAAA
Statistics
Matches: 271, Mismatches: 37, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
40 39 0.14
43 232 0.86
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:36025 original size:22 final size:22
Alignment explanation
Indices: 35997--36039 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
35987 TAGCGGTGCT
* *
35997 AAAAAGCGTCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
36019 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
36040 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.21, T:0.12
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:36119 original size:54 final size:55
Alignment explanation
Indices: 36054--36174 Score: 208
Period size: 54 Copynumber: 2.2 Consensus size: 55
36044 TGGTGTAGTG
*
36054 TAGATGTAGAAAAATAAAATTGAAATAAATGAGACTGAATGAAGAAAA-GGGTGT
1 TAGATGTAGAAAAATAAAATTGAAATAAATGAGACTGAATGAAAAAAAGGGGTGT
* *
36108 TAGATATAGAAAAATAAAATTGAAATAAATGAGATTGAATGAAAAAAAGGGGTGT
1 TAGATGTAGAAAAATAAAATTGAAATAAATGAGACTGAATGAAAAAAAGGGGTGT
36163 TAGATGTAGAAA
1 TAGATGTAGAAA
36175 TTTTTTTTTG
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
54 45 0.73
55 17 0.27
ACGTcount: A:0.53, C:0.01, G:0.23, T:0.23
Consensus pattern (55 bp):
TAGATGTAGAAAAATAAAATTGAAATAAATGAGACTGAATGAAAAAAAGGGGTGT
Found at i:37445 original size:108 final size:106
Alignment explanation
Indices: 37252--37661 Score: 480
Period size: 108 Copynumber: 3.9 Consensus size: 106
37242 TTTTTTCCCG
**
37252 TAAAGGTGGTGCCGGCCATTGGTAGGCCACCACC---AAAATTTTTTTTTCAAATTTTTTCGTAT
1 TAAAGGTGGTGCCGGCCATTGCCAGGCCACCACCAAAAAAATTTTTTTTT-AAATTTTTTCGTAT
*
37314 ACTGGTGCCTGCCAATGACAGCCCGAAATGTAATTTTTTTACA
65 ACTGGTGCCGGCCAATGACAGCCC-AAATGTAATTTTTTTACA
*
37357 TATAGGTGGTGCCGGCCATTGCCAGGCCACCACCAAAAAAATTTTTTTTTTAAAATTTTTT-GTA
1 TAAAGGTGGTGCCGGCCATTGCCAGGCCACCACCAAAAAAA-TTTTTTTTT-AAATTTTTTCGTA
* *
37421 TACTGGTGCCGGCTAATGATAGCCCATAATGTAAATTTTTTTTTACA
64 TACTGGTGCCGGCCAATGACAGCCCA-AATGT-AA--TTTTTTTACA
** *
37468 TAAAGGTGGTGCCGGCCATTGCCAGGCCACCA-CAAAAAAA-----AATTCAATTTTTTCGTATA
1 TAAAGGTGGTGCCGGCCATTGCCAGGCCACCACCAAAAAAATTTTTTTTTAAATTTTTTCGTATA
* * * *
37527 CTGGTGCCGACCAATAACAGCCAAAATGTATTTTTTTTTACA
66 CTGGTGCCGGCCAATGACAGCCCAAATGTA-ATTTTTTTACA
* * * *
37569 TAAAGGTGGTGCCGGCAATTGCCAGACTACCACCAAAAAAATTTATTTTTTTAATTTTTTCGTAT
1 TAAAGGTGGTGCCGGCCATTGCCAGGCCACCACCAAAAAAATTT-TTTTTTAAATTTTTTCGTAT
* * *
37634 ACTGGTGTCAGCCAATGACAGCCAAAAT
65 ACTGGTGCCGGCCAATGACAGCCCAAAT
37662 ATAAGATTTT
Statistics
Matches: 261, Mismatches: 27, Indels: 31
0.82 0.08 0.10
Matches are distributed among these distances:
101 39 0.15
102 9 0.03
103 13 0.05
104 26 0.10
105 31 0.12
107 1 0.00
108 73 0.28
109 20 0.08
110 8 0.03
111 41 0.16
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (106 bp):
TAAAGGTGGTGCCGGCCATTGCCAGGCCACCACCAAAAAAATTTTTTTTTAAATTTTTTCGTATA
CTGGTGCCGGCCAATGACAGCCCAAATGTAATTTTTTTACA
Found at i:37690 original size:161 final size:159
Alignment explanation
Indices: 37513--37820 Score: 460
Period size: 161 Copynumber: 1.9 Consensus size: 159
37503 AAAAAAATTC
* *
37513 AATTTTTTCGTATACTGGTGCCGACCAATAACAG-CCAAAATGTATTTTTTTTTACATAAAGGTG
1 AATTTTTTCGTATACTGGTGCAG-CCAATAACAGCCCAAAATGTAATTTTTTTTACATAAAGGTG
**
37577 GTGCCGGCAATTGCCAGACTACCACCAAAAAAATTTATTTTT-TTAATTTTTTCGTATACTGGTG
65 GTGCCGGCAATTGCCAGAC-A--ACCAAAAAAATTT-TTTTTAAAAATTTTTTCGTATACTGGTG
37641 TCAGCCAATGACAG-CCAAAATATAAGATTTTTG
126 TCAGCCAATGACAGTCCAAAATATAAGATTTTTG
*
37674 AATTTTTTCGTATACTGGTGCAGCCAATGACAGCCCAAAATGTAATTTTTTTTACATAAAGGTGG
1 AATTTTTTCGTATACTGGTGCAGCCAATAACAGCCCAAAATGTAATTTTTTTTACATAAAGGTGG
* * ** *
37739 TGCCGGCCATTGCCAGGCAACCAGCAAAATTTTTTTTAAAAATTTTTTCGTATACTGGTGTCGGC
66 TGCCGGCAATTGCCAGACAACCAAAAAAATTTTTTTTAAAAATTTTTTCGTATACTGGTGTCAGC
37804 CAATGACAGTCCAAAAT
131 CAATGACAGTCCAAAAT
37821 GTAAAAAAAA
Statistics
Matches: 134, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
157 5 0.04
158 44 0.33
159 7 0.05
160 10 0.07
161 68 0.51
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (159 bp):
AATTTTTTCGTATACTGGTGCAGCCAATAACAGCCCAAAATGTAATTTTTTTTACATAAAGGTGG
TGCCGGCAATTGCCAGACAACCAAAAAAATTTTTTTTAAAAATTTTTTCGTATACTGGTGTCAGC
CAATGACAGTCCAAAATATAAGATTTTTG
Found at i:37725 original size:53 final size:52
Alignment explanation
Indices: 37613--37725 Score: 174
Period size: 53 Copynumber: 2.2 Consensus size: 52
37603 AAAAAAATTT
37613 ATTTTTTTAATTTTTTCGTATACTGGTGTCAGCCAATGACAGCCAAAATATA
1 ATTTTTTTAATTTTTTCGTATACTGGTGTCAGCCAATGACAGCCAAAATATA
* * *
37665 AGATTTTTGAATTTTTTCGTATACTGGTG-CAGCCAATGACAGCCCAAAATGTA
1 A-TTTTTTTAATTTTTTCGTATACTGGTGTCAGCCAATGACAG-CCAAAATATA
37718 ATTTTTTT
1 ATTTTTTT
37726 TACATAAAGG
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
52 19 0.35
53 35 0.65
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (52 bp):
ATTTTTTTAATTTTTTCGTATACTGGTGTCAGCCAATGACAGCCAAAATATA
Found at i:41018 original size:3 final size:3
Alignment explanation
Indices: 41012--41052 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
41002 ATAAAGAAGA
*
41012 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41053 CAGTACAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:41145 original size:77 final size:78
Alignment explanation
Indices: 41057--41213 Score: 307
Period size: 77 Copynumber: 2.0 Consensus size: 78
41047 TAATAACAGT
41057 ACAAAAACAACAGAAAGACTAATTTTGAAATCAAAATTGAAATTGGAGAGCCAATTCGAAATAAA
1 ACAAAAACAACAGAAAGACTAATTTTGAAATCAAAATTGAAATTGGAGAGCCAATTCGAAATAAA
41122 TAC-AATATGCGA
66 TACAAATATGCGA
41134 ACAAAAACAACAGAAAGACTAATTTTGAAATCAAAATTGAAATTGGAGAGCCAATTCGAAATAAA
1 ACAAAAACAACAGAAAGACTAATTTTGAAATCAAAATTGAAATTGGAGAGCCAATTCGAAATAAA
41199 TACAAATATGCGA
66 TACAAATATGCGA
41212 AC
1 AC
41214 CCCACTAAAC
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 68 0.86
78 11 0.14
ACGTcount: A:0.52, C:0.13, G:0.14, T:0.20
Consensus pattern (78 bp):
ACAAAAACAACAGAAAGACTAATTTTGAAATCAAAATTGAAATTGGAGAGCCAATTCGAAATAAA
TACAAATATGCGA
Found at i:42144 original size:13 final size:13
Alignment explanation
Indices: 42126--42159 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
42116 GGGTTGGTAG
42126 TTTAGGTATGGGT
1 TTTAGGTATGGGT
*
42139 TTTAGGTTTTGGGT
1 TTTAGG-TATGGGT
42153 TTTAGGT
1 TTTAGGT
42160 TTTAGGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.12, C:0.00, G:0.35, T:0.53
Consensus pattern (13 bp):
TTTAGGTATGGGT
Found at i:42148 original size:7 final size:7
Alignment explanation
Indices: 42136--42166 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
42126 TTTAGGTATG
42136 GGTTTTA
1 GGTTTTA
*
42143 GGTTTTG
1 GGTTTTA
42150 GGTTTTA
1 GGTTTTA
42157 GGTTTTA
1 GGTTTTA
42164 GGT
1 GGT
42167 AATTGTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.10, C:0.00, G:0.35, T:0.55
Consensus pattern (7 bp):
GGTTTTA
Found at i:42795 original size:44 final size:44
Alignment explanation
Indices: 42760--42894 Score: 211
Period size: 44 Copynumber: 3.1 Consensus size: 44
42750 ACTACTGCTT
*
42760 AGGGAGACAGGA-TCTACAATCTTCAACCTATTCCACTGCTGTCC
1 AGGGAGATAGGACT-TACAATCTTCAACCTATTCCACTGCTGTCC
*
42804 AGGGAGATAGGACTTACAATCTTCGACCTATTCCACTGCTGTCC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGTCC
*
42848 AGGGAGATAGGACTTACAATCTTCAACCTA-TCCATTGCCTGTCC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTG-CTGTCC
42892 AGG
1 AGG
42895 ATCTTCAACC
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
43 6 0.07
44 78 0.92
45 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (44 bp):
AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGTCC
Found at i:42856 original size:132 final size:132
Alignment explanation
Indices: 42747--43333 Score: 710
Period size: 132 Copynumber: 4.6 Consensus size: 132
42737 TTTGATCTGG
* *
42747 TCCACTACTGCTT-AGGGAGACAGGA-TCTACAATCTTCAACCTATTCCACTGCTGTCCAGGGAG
1 TCCACTACTG-TTCAGGGAGATAGGACT-TGCAATCTTCAACCTATTCCACTGCTGTCCAGGGAG
* *
42810 ATAGGACTTACAATCTTCGACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACAATCTTCAAC
64 ATAGGACTTGCAATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACAATCTTCAAC
42875 CTA-
129 CTAT
* * *
42878 TCCATTGCCTG-TC-------CA-G----G--ATCTTCAACCTATTCCACTGCTGTCCAGGGAGA
1 TCCACT-ACTGTTCAGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCTGTCCAGGGAGA
* *
42928 TAGGACTTGCAATCTTCAACCTATTCCACTACTGTCCAGGGAGATAGGACTTACAATCTTCAACG
65 TAGGACTTGCAATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACAATCTTCAACC
42993 TAT
130 TAT
* * *
42996 TCCAC-GCTGTTCAGGGAGATAGGACTTGCAATCTTCAGCCTATTCCATTGCTG-CTCAGGGAGA
1 TCCACTACTGTTCAGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCTGTC-CAGGGAGA
** ** * *
43059 TAGGACTTGCAATCTTCAACCTATAACACTGCTGTTTAGGGAGGTGGGACTTACAATCTTCAACC
65 TAGGACTTGCAATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACAATCTTCAACC
43124 TAT
130 TAT
* * * * * *
43127 TCAACTACTGTTCAGGGAGATAGGACTTGTAATCTTCAACATATTCTACTACTGTTCAGGGAGAT
1 TCCACTACTGTTCAGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCTGTCCAGGGAGAT
* * * * *
43192 AGGACTTGCAATCTTTAACCTATTCCACTGCGGTTCAGGGAGATAAGACTTGCAATCTTCAACCT
66 AGGACTTGCAATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACAATCTTCAACCT
43257 AT
131 AT
* *
43259 TCCACTACTGTTCAGGGAGATAGAACTTGCAATCTTCAACCTATTCCACTGCTGTTCAGGGAGAT
1 TCCACTACTGTTCAGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCTGTCCAGGGAGAT
*
43324 AGGATTTGCA
66 AGGACTTGCA
43334 GTTTCACCAA
Statistics
Matches: 390, Mismatches: 45, Indels: 41
0.82 0.09 0.09
Matches are distributed among these distances:
116 3 0.01
117 98 0.25
118 4 0.01
123 1 0.00
124 3 0.01
125 1 0.00
129 1 0.00
130 2 0.01
131 98 0.25
132 179 0.46
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (132 bp):
TCCACTACTGTTCAGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTGCTGTCCAGGGAGAT
AGGACTTGCAATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACAATCTTCAACCT
AT
Found at i:42918 original size:29 final size:29
Alignment explanation
Indices: 42866--42923 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
42856 AGGACTTACA
*
42866 ATCTTCAACCTATCCATTGCCTGTCCAGG
1 ATCTTCAACCTATCCACTGCCTGTCCAGG
42895 ATCTTCAACCTATTCCACTG-CTGTCCAGG
1 ATCTTCAACCTA-TCCACTGCCTGTCCAGG
42924 GAGATAGGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.31
Consensus pattern (29 bp):
ATCTTCAACCTATCCACTGCCTGTCCAGG
Found at i:42963 original size:44 final size:44
Alignment explanation
Indices: 42895--43333 Score: 637
Period size: 44 Copynumber: 10.0 Consensus size: 44
42885 CCTGTCCAGG
*
42895 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTGCA
1 ATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGCA
* * *
42939 ATCTTCAACCTATTCCACTACTGTCCAGGGAGATAGGACTTACA
1 ATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGCA
*
42983 ATCTTCAACGTATTCCAC-GCTGTTCAGGGAGATAGGACTTGCA
1 ATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGCA
* * *
43026 ATCTTCAGCCTATTCCATTGCTGCTCAGGGAGATAGGACTTGCA
1 ATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGCA
** * * * *
43070 ATCTTCAACCTATAACACTGCTGTTTAGGGAGGTGGGACTTACA
1 ATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGCA
* * *
43114 ATCTTCAACCTATTCAACTACTGTTCAGGGAGATAGGACTTGTA
1 ATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGCA
* * *
43158 ATCTTCAACATATTCTACTACTGTTCAGGGAGATAGGACTTGCA
1 ATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGCA
* * *
43202 ATCTTTAACCTATTCCACTGCGGTTCAGGGAGATAAGACTTGCA
1 ATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGCA
* *
43246 ATCTTCAACCTATTCCACTACTGTTCAGGGAGATAGAACTTGCA
1 ATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGCA
*
43290 ATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGATTTGCA
1 ATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGCA
43334 GTTTCACCAA
Statistics
Matches: 349, Mismatches: 45, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
43 37 0.11
44 312 0.89
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
ATCTTCAACCTATTCCACTGCTGTTCAGGGAGATAGGACTTGCA
Found at i:42963 original size:73 final size:73
Alignment explanation
Indices: 42822--42967 Score: 240
Period size: 73 Copynumber: 2.0 Consensus size: 73
42812 AGGACTTACA
* * *
42822 ATCTTCGACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACAATCTTCAACCTATCCATTGCC
1 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACAATCTTCAACCTATCCACTGAC
42887 TGTCCAGG
66 TGTCCAGG
*
42895 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTGCAATCTTCAACCTATTCCACT-A
1 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACAATCTTCAACCTA-TCCACTGA
42959 CTGTCCAGG
65 CTGTCCAGG
42968 GAGATAGGAC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
73 63 0.93
74 5 0.07
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (73 bp):
ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACAATCTTCAACCTATCCACTGAC
TGTCCAGG
Found at i:42984 original size:117 final size:117
Alignment explanation
Indices: 42778--42991 Score: 401
Period size: 117 Copynumber: 1.8 Consensus size: 117
42768 AGGATCTACA
* *
42778 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACAATCTTCGACCTATTCCACTGC
1 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTAC
42843 TGTCCAGGGAGATAGGACTTACAATCTTCAACCTATCCATTGCCTGTCCAGG
66 TGTCCAGGGAGATAGGACTTACAATCTTCAACCTATCCATTGCCTGTCCAGG
*
42895 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTGCAATCTTCAACCTATTCCACTAC
1 ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTAC
42960 TGTCCAGGGAGATAGGACTTACAATCTTCAAC
66 TGTCCAGGGAGATAGGACTTACAATCTTCAAC
42992 GTATTCCACG
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 94 1.00
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (117 bp):
ATCTTCAACCTATTCCACTGCTGTCCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTAC
TGTCCAGGGAGATAGGACTTACAATCTTCAACCTATCCATTGCCTGTCCAGG
Found at i:45111 original size:13 final size:13
Alignment explanation
Indices: 45088--45125 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
45078 CCGGTAGAGG
45088 TTTTTATTTCTTT-
1 TTTTT-TTTCTTTA
45101 TTTTTTGTTCTTTA
1 TTTTTT-TTCTTTA
45115 TTTTTTTTCTT
1 TTTTTTTTCTT
45126 GATTGAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.04
13 16 0.70
14 6 0.26
ACGTcount: A:0.05, C:0.08, G:0.03, T:0.84
Consensus pattern (13 bp):
TTTTTTTTCTTTA
Found at i:51353 original size:23 final size:23
Alignment explanation
Indices: 51311--51358 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
51301 AAATTTTATA
* *
51311 TAATCTTAATTATATTAAATACTT
1 TAATATTAATTATATGAAATA-TT
51335 TAATATTAA-TATATGAAATATT
1 TAATATTAATTATATGAAATATT
51357 TA
1 TA
51359 TATGTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.18
23 10 0.45
24 8 0.36
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (23 bp):
TAATATTAATTATATGAAATATT
Found at i:55961 original size:24 final size:24
Alignment explanation
Indices: 55929--55974 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
55919 AGGCGATCTA
*
55929 ATTCGGTTGCACCACACGTGTCTG
1 ATTCGGTTGCAACACACGTGTCTG
55953 ATTCGGTTGCAACACACGTGTC
1 ATTCGGTTGCAACACACGTGTC
55975 ACCTCTACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (24 bp):
ATTCGGTTGCAACACACGTGTCTG
Found at i:93483 original size:35 final size:36
Alignment explanation
Indices: 93443--93514 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
93433 TCTAGGATCA
93443 CATATC-TCAAAAGATCACTTTCCATATTTGCCAAG
1 CATATCTTCAAAAGATCACTTTCCATATTTGCCAAG
**
93478 CATATCTTCAAAAGATCACTTTCTTTATTTGCCAAG
1 CATATCTTCAAAAGATCACTTTCCATATTTGCCAAG
93514 C
1 C
93515 TCCGGAGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 6 0.18
36 28 0.82
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.35
Consensus pattern (36 bp):
CATATCTTCAAAAGATCACTTTCCATATTTGCCAAG
Found at i:99802 original size:20 final size:19
Alignment explanation
Indices: 99769--99806 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
99759 AGCTAGAAAC
99769 ACAAAAAATAAAAAGTCAAG
1 ACAAAAAATAAAAA-TCAAG
99789 ACAAGAAAAT-AAAATCAA
1 ACAA-AAAATAAAAATCAA
99807 ATACCTGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.71, C:0.11, G:0.08, T:0.11
Consensus pattern (19 bp):
ACAAAAAATAAAAATCAAG
Found at i:101281 original size:30 final size:30
Alignment explanation
Indices: 101245--101306 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
101235 TGGTTATAGA
101245 GATAATTAAGGAGGGATATTGGGATTTGAG
1 GATAATTAAGGAGGGATATTGGGATTTGAG
*
101275 GATAATTGAGGAGGGATATTGGGATTTGAG
1 GATAATTAAGGAGGGATATTGGGATTTGAG
101305 GA
1 GA
101307 GGTTGTTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.39, T:0.29
Consensus pattern (30 bp):
GATAATTAAGGAGGGATATTGGGATTTGAG
Found at i:102023 original size:27 final size:27
Alignment explanation
Indices: 101986--102241 Score: 314
Period size: 27 Copynumber: 9.5 Consensus size: 27
101976 CCCCAAAATA
* **
101986 GGTAAAATGACCAAAATACCCTTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
102013 GGTAGAATGACCGAAATACCTCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
** *
102040 GGTAAAATGATTGAAATACCCCAATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
102067 GGTAAAATTACCAAAATACCTCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
102094 GGTAAAATGACCGAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * *
102121 GGTAAAATAACTGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* * ***
102148 TGTAAACTGATTAAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
* *
102175 GGTAAAATGACCGAAATACCCTCGTAG
1 GGTAAAATGACCGAAATACCCCCATAG
*
102202 GGTAAAATGACCAAAATACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCATAG
102229 GGTAAAATGACCG
1 GGTAAAATGACCG
102242 TACTGATAAG
Statistics
Matches: 190, Mismatches: 39, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 190 1.00
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGAAATACCCCCATAG
Found at i:109921 original size:22 final size:22
Alignment explanation
Indices: 109896--109951 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
109886 AGACTTATGG
109896 AATGCGTTGACAGTAAGATTTC
1 AATGCGTTGACAGTAAGATTTC
109918 AATGCGTTGACAGTAAGATTTC
1 AATGCGTTGACAGTAAGATTTC
*
109940 AATGCGTCGACA
1 AATGCGTTGACA
109952 ATGGTACCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (22 bp):
AATGCGTTGACAGTAAGATTTC
Found at i:112827 original size:51 final size:51
Alignment explanation
Indices: 112759--113002 Score: 371
Period size: 51 Copynumber: 5.0 Consensus size: 51
112749 ATCACATTTA
*
112759 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
* *
112810 TCACTTGTCACCGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTG
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
*
112860 TCACTTATCACTGATCAGATAAGTGCAGCTAAAGCTACCAC-T-T-A----
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
112904 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
* *
112955 TCACTTATCACTAATCAAATAAGTGTAGCTAAA-CTACCACTTATCACT
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACT
113003 GATCAGATAA
Statistics
Matches: 178, Mismatches: 7, Indels: 17
0.88 0.03 0.08
Matches are distributed among these distances:
44 40 0.22
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 63 0.35
51 70 0.39
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (51 bp):
TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
Found at i:112908 original size:44 final size:44
Alignment explanation
Indices: 112854--113053 Score: 230
Period size: 44 Copynumber: 4.6 Consensus size: 44
112844 TACCACTTAT
*
112854 CACTTGTCACTTATCACTGATCAGATAAGTGCAGCTAAAGCTAC
1 CACTTATCACTTATCACTGATCAGATAAGTGCAGCTAAAGCTAC
*
112898 CACTTATCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTATCACTGATCAGATAAGTGCAGCTAAAGCTAC
* * * **
112942 CACTTATCACTTGTCACTTATCA-CTAA-T-CAAATAAGTGTAGCTA-
1 CACTTATCACTTATCACTGATCAGATAAGTGCAGCTAA----AGCTAC
* * *
112986 AAC-TACCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTATCACTGATCAGATAAGTGCAGCTAAAGCTAC
*
113029 CACTTATCACTTGTCACTGATCAGA
1 CACTTATCACTTATCACTGATCAGA
113054 AGTACTCAAA
Statistics
Matches: 128, Mismatches: 19, Indels: 18
0.78 0.12 0.11
Matches are distributed among these distances:
41 4 0.03
42 6 0.05
43 21 0.16
44 87 0.68
45 6 0.05
46 4 0.03
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (44 bp):
CACTTATCACTTATCACTGATCAGATAAGTGCAGCTAAAGCTAC
Found at i:113007 original size:87 final size:90
Alignment explanation
Indices: 112810--113051 Score: 357
Period size: 87 Copynumber: 2.7 Consensus size: 90
112800 TTATCACTTG
* * *
112810 TCACTTGTCACCGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTGTCACTTATCACTGA
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTATCACTAA
*
112874 TCAGATAAGTGCAGCTAAAGCTACCAC
66 TCAAATAAGTGCAGCTAAAGCT--CAC
112901 TTATCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTATCAC
1 ---TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTATCAC
*
112966 TAATCAAATAAGTGTAGCTAAA-CT-AC
63 TAATCAAATAAGTGCAGCTAAAGCTCAC
*
112992 -CACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTGATCA
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTATCA
113052 GAAGTACTCA
Statistics
Matches: 141, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
87 59 0.42
91 2 0.01
94 30 0.21
95 50 0.35
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (90 bp):
TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTATCACTAA
TCAAATAAGTGCAGCTAAAGCTCAC
Found at i:113013 original size:36 final size:37
Alignment explanation
Indices: 112956--113039 Score: 143
Period size: 36 Copynumber: 2.3 Consensus size: 37
112946 TATCACTTGT
112956 CACTTATCACTAATCAAATAAGTGTAGCTAAA-CTAC
1 CACTTATCACTAATCAAATAAGTGTAGCTAAAGCTAC
* *
112992 CACTTATCACTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTAATCAAATAAGTGTAGCTAAAGCTAC
113029 CACTTATCACT
1 CACTTATCACT
113040 TGTCACTGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
36 30 0.67
37 15 0.33
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.29
Consensus pattern (37 bp):
CACTTATCACTAATCAAATAAGTGTAGCTAAAGCTAC
Found at i:117781 original size:7 final size:7
Alignment explanation
Indices: 117765--117796 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
117755 CTAAAGCTAC
*
117765 CACTTAT
1 CACTTGT
117772 CACTTGT
1 CACTTGT
117779 CACTTGT
1 CACTTGT
117786 CACTTGT
1 CACTTGT
117793 CACT
1 CACT
117797 GATCAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.19, C:0.31, G:0.09, T:0.41
Consensus pattern (7 bp):
CACTTGT
Found at i:117788 original size:14 final size:14
Alignment explanation
Indices: 117765--117801 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
117755 CTAAAGCTAC
117765 CACTTATCACTTGT
1 CACTTATCACTTGT
*
117779 CACTTGTCACTTGT
1 CACTTATCACTTGT
*
117793 CACTGATCA
1 CACTTATCA
117802 GATAAGTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.30, G:0.11, T:0.38
Consensus pattern (14 bp):
CACTTATCACTTGT
Found at i:117797 original size:58 final size:57
Alignment explanation
Indices: 117727--117837 Score: 213
Period size: 58 Copynumber: 1.9 Consensus size: 57
117717 ATCACATTTA
117727 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTGTCACTTG
117785 TCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGTCA
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGTCA
117838 TTGATCAGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 23 0.43
58 30 0.57
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (57 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTGTCACTTG
Found at i:124704 original size:17 final size:17
Alignment explanation
Indices: 124682--124714 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
124672 CACTAACATT
*
124682 AAAATGCAATGACAATA
1 AAAATGCAACGACAATA
124699 AAAATGCAACGACAAT
1 AAAATGCAACGACAAT
124715 GTACACGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (17 bp):
AAAATGCAACGACAATA
Found at i:138087 original size:15 final size:15
Alignment explanation
Indices: 138067--138096 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
138057 ATTTCTAATG
*
138067 TTTATCTTTTTACTC
1 TTTATCTTTTCACTC
138082 TTTATCTTTTCACTC
1 TTTATCTTTTCACTC
138097 AAGTTTACGA
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:0.13, C:0.23, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATCTTTTCACTC
Found at i:139476 original size:25 final size:25
Alignment explanation
Indices: 139448--139509 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
139438 TATAGATACA
*
139448 TATTTTATTTTCAG-TTATTTTATTT
1 TATTTTATTTTCAGATTA-TTAATTT
* **
139473 TATTTCATTTTTTGATTATTAATTT
1 TATTTTATTTTCAGATTATTAATTT
*
139498 TATTTTAATTTC
1 TATTTTATTTTC
139510 TCTTTGATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
25 26 0.90
26 3 0.10
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (25 bp):
TATTTTATTTTCAGATTATTAATTT
Found at i:143628 original size:22 final size:22
Alignment explanation
Indices: 143603--143647 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
143593 AGAATCGAAC
143603 ATATCCCATAAGTAAAGCTTTT
1 ATATCCCATAAGTAAAGCTTTT
*
143625 ATATCCCATAAGTGAAGCTTTT
1 ATATCCCATAAGTAAAGCTTTT
143647 A
1 A
143648 GCTAACACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (22 bp):
ATATCCCATAAGTAAAGCTTTT
Found at i:145968 original size:20 final size:20
Alignment explanation
Indices: 145945--145988 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
145935 AACATAACAA
*
145945 AACAAAACAAAACAAAGTAG
1 AACAAAACAAAACAAAATAG
* *
145965 AACAAACCAAATCAAAATAG
1 AACAAAACAAAACAAAATAG
145985 AACA
1 AACA
145989 GGACCAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.68, C:0.18, G:0.07, T:0.07
Consensus pattern (20 bp):
AACAAAACAAAACAAAATAG
Found at i:149448 original size:20 final size:20
Alignment explanation
Indices: 149423--149481 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
149413 GCGGTAGTAC
149423 AACATAACAGAACAAAATAA
1 AACATAACAGAACAAAATAA
* *
149443 AACATAGCAGAA-TAAATCAA
1 AACATAACAGAACAAAAT-AA
* * *
149463 ATCAAAACAGAACATAATA
1 AACATAACAGAACAAAATA
149482 GTAAATGCAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 4 0.13
20 23 0.77
21 3 0.10
ACGTcount: A:0.64, C:0.15, G:0.07, T:0.14
Consensus pattern (20 bp):
AACATAACAGAACAAAATAA
Found at i:151989 original size:15 final size:16
Alignment explanation
Indices: 151969--151999 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
151959 CTATTTTATA
151969 TAAAATAA-TATGTAC
1 TAAAATAATTATGTAC
151984 TAAAATAATTATGTAC
1 TAAAATAATTATGTAC
152000 AATACAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (16 bp):
TAAAATAATTATGTAC
Found at i:153547 original size:25 final size:25
Alignment explanation
Indices: 153518--153575 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
153508 TTTTTTAGAC
*
153518 ATATTTAAATTTATTATTAATTATT
1 ATATTTAAATGTATTATTAATTATT
*
153543 CTATTTAAATGTATTATTAATTATT
1 ATATTTAAATGTATTATTAATTATT
153568 ATATTTAA
1 ATATTTAA
153576 TTATTGATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
ATATTTAAATGTATTATTAATTATT
Found at i:153587 original size:14 final size:13
Alignment explanation
Indices: 153534--153588 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
153524 AAATTTATTA
*
153534 TTAATTATTCTAT
1 TTAATTATTATAT
153547 TTAA--ATGTAT-T
1 TTAATTAT-TATAT
153558 ATTAATTATTATAT
1 -TTAATTATTATAT
153572 TTAATTATTGATAT
1 TTAATTATT-ATAT
153586 TTA
1 TTA
153589 TATGTTATTC
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
11 3 0.09
12 6 0.17
13 16 0.46
14 10 0.29
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (13 bp):
TTAATTATTATAT
Found at i:155314 original size:136 final size:134
Alignment explanation
Indices: 155069--155732 Score: 968
Period size: 136 Copynumber: 5.0 Consensus size: 134
155059 CTAAAAATAT
* * * *
155069 AATTAAGTTCACAACCAACACAGTAGTTTACAAATACATAATTCATTTCACTGCCTTATTGAAGT
1 AATTAAGTTTACAAGCAACACAATAGTTT-CAAATACATAATTTATTTCACTGCCTTATTGAAGT
*
155134 AAAGTTTTGGACTCAAATAGTTCCAAAATGATTTGGCACTTGAAAGACGGAAATAAACTTGAAAG
65 AAAGTTTT-GACTCAAATAGTTCCAAAATGATTTGGCACTTGAAAGATGGAAATAAACTTGAAAG
155199 CAATTC
129 CAATTC
* * * *
155205 GATTAAGTTTACAAGCAACACAATAGTTTGCAAATACATGATTTATTTCACTGTCTTATTGAAAT
1 AATTAAGTTTACAAGCAACACAATAGTTT-CAAATACATAATTTATTTCACTGCCTTATTGAAGT
* * *
155270 AAAGTGTTGAACTCAAATAGTTTCAAAATGATTTGGCACTTGAAAGACGGAAATAAACTTGAAAG
65 AAAGTTTTG-ACTCAAATAGTTCCAAAATGATTTGGCACTTGAAAGATGGAAATAAACTTGAAAG
155335 CAATTC
129 CAATTC
* * * *
155341 GATTAAGTTTACAAGCAACACAATAGTTTGCAAATACATGATTTATTTCACTGTCTTATTGAAAT
1 AATTAAGTTTACAAGCAACACAATAGTTT-CAAATACATAATTTATTTCACTGCCTTATTGAAGT
* * *
155406 AAAGTCTTGAACTCAAATAGTTTCAAAATGATTTGGCACTTGAAAAATGGAAATAAACTT--AAG
65 AAAGTTTTG-ACTCAAATAGTTCCAAAATGATTTGGCACTTGAAAGATGGAAATAAACTTGAAAG
* *
155469 TAGTTC
129 CAATTC
155475 AATTAAGTTTACAAGCAACACAATAG--TCAAATACATAATTTATTTCACTGCCTTATTGAAGTA
1 AATTAAGTTTACAAGCAACACAATAGTTTCAAATACATAATTTATTTCACTGCCTTATTGAAGTA
155538 AAGTCTTTGACTCAAATAGTTCCAAAATGATTTGGCACTTGAACA-ATGGAAATAAACTT--AAG
66 AAGT-TTTGACTCAAATAGTTCCAAAATGATTTGGCACTTGAA-AGATGGAAATAAACTTGAAAG
* *
155600 TAGTTC
129 CAATTC
155606 AATTAAGTTTACAAGCAACACAATAG--TCAAATACATAATTTATTTCACTGCCTTATTGAAGTA
1 AATTAAGTTTACAAGCAACACAATAGTTTCAAATACATAATTTATTTCACTGCCTTATTGAAGTA
*
155669 AAGTCTTTGACTCAAATAGTTCCAAAATGATTTGGCACTTAAAAGATGGAAATAAACTTGAAAG
66 AAGT-TTTGACTCAAATAGTTCCAAAATGATTTGGCACTTGAAAGATGGAAATAAACTTGAAAG
155733 TAGTTTGACT
Statistics
Matches: 499, Mismatches: 23, Indels: 15
0.93 0.04 0.03
Matches are distributed among these distances:
130 1 0.00
131 212 0.42
132 5 0.01
133 3 0.01
134 32 0.06
135 1 0.00
136 245 0.49
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (134 bp):
AATTAAGTTTACAAGCAACACAATAGTTTCAAATACATAATTTATTTCACTGCCTTATTGAAGTA
AAGTTTTGACTCAAATAGTTCCAAAATGATTTGGCACTTGAAAGATGGAAATAAACTTGAAAGCA
ATTC
Found at i:156883 original size:154 final size:152
Alignment explanation
Indices: 156678--157137 Score: 581
Period size: 154 Copynumber: 3.0 Consensus size: 152
156668 TCAAAGCTTT
* * *
156678 AAATATAA-ATAACTAATTTTTTT-TCCTGTGTGATGCATGGGTTG-TAAGTGTGCTTTATAAAA
1 AAATATAATAT-ACTAGTTTTTTTATCC-GTGTGATGCACGGGTTGCT-AGTGTGTTTTATAAAA
* * *
156740 TTATTATTTAAATAATGATATGTTAAATAAAATTATTGATTAAA-AATATTTAAAAGATATAATC
63 TTATTATTTAAATAAAGATATATTAAATAAAATTATTGATAAAACAATATTTAAAAGATATAA-C
*
156804 AAAATTTAAAATATACTTAAGTTTTTG
127 -AAATTAAAAATATACTTAAGTTTTTG
* * *
156831 AAATATAATATACTAGTTTTTTTATCTCGCGTGATGCACGGGTTGCTTGTGTGTTTTATAAAATC
1 AAATATAATATACTAGTTTTTTTATC-CGTGTGATGCACGGGTTGCTAGTGTGTTTTATAAAATT
156896 ATTATTTAAATAAAGATATATTAAATAAAATTATTGATAAAACAATATTTAAAAGATATAAACAA
65 ATTATTTAAATAAAGATATATTAAATAAAATTATTGATAAAACAATATTTAAAAGATAT-AACAA
*
156961 ATTAAAAAATATACTTAAGTTTTCG
129 ATT-AAAAATATACTTAAGTTTTTG
* * * * * *
156986 AGATATAATATACTAG-TTTTTTATCCCATGTGATGTACGGATTGCTCGTATGTTTTATAAAATT
1 AAATATAATATACTAGTTTTTTTAT-CCGTGTGATGCACGGGTTGCTAGTGTGTTTTATAAAATT
* * * * *
157050 GTTATTT-AATAACGATATATTAAATAAAATTATTAATAAAATAATATTTAAAACATATAACCAA
65 ATTATTTAAATAAAGATATATTAAATAAAATTATTGATAAAACAATATTTAAAAGATATAA-CAA
157114 ATTAAAAATTATACTTAAGTTTTT
129 ATTAAAAA-TATACTTAAGTTTTT
157138 AAAAANNNNN
Statistics
Matches: 272, Mismatches: 25, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
152 7 0.03
153 86 0.32
154 123 0.45
155 54 0.20
156 2 0.01
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (152 bp):
AAATATAATATACTAGTTTTTTTATCCGTGTGATGCACGGGTTGCTAGTGTGTTTTATAAAATTA
TTATTTAAATAAAGATATATTAAATAAAATTATTGATAAAACAATATTTAAAAGATATAACAAAT
TAAAAATATACTTAAGTTTTTG
Found at i:156958 original size:20 final size:18
Alignment explanation
Indices: 156931--156973 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
156921 TAAAATTATT
156931 GATA-AAACAATATTTAAAA
1 GATATAAACAA-A-TTAAAA
156950 GATATAAACAAATTAAAA
1 GATATAAACAAATTAAAA
*
156968 AATATA
1 GATATA
156974 CTTAAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
19 5 0.23
20 6 0.27
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (18 bp):
GATATAAACAAATTAAAA
Found at i:156968 original size:19 final size:20
Alignment explanation
Indices: 156931--156973 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
156921 TAAAATTATT
*
156931 GATA-AAACAATATTTAAAA
1 GATATAAACAATATTAAAAA
156950 GATATAAACAA-ATTAAAAA
1 GATATAAACAATATTAAAAA
156969 -ATATA
1 GATATA
156974 CTTAAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 5 0.23
19 11 0.50
20 6 0.27
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (20 bp):
GATATAAACAATATTAAAAA
Found at i:159004 original size:630 final size:630
Alignment explanation
Indices: 157802--159061 Score: 2511
Period size: 630 Copynumber: 2.0 Consensus size: 630
157792 AAACATTAAA
157802 ATATTTTTAATATTAGGATAGATATTATTTAACTTTATTTATATTTATGATAAATGTTTTATTAT
1 ATATTTTTAATATTAGGATAGATATTATTTAACTTTATTTATATTTATGATAAATGTTTTATTAT
157867 GAAATTTAAGCTATATTTTTAATACAGTTTTGTTGGTTCTGGATATTTGTGATTCTGTGGTCTAA
66 GAAATTTAAGCTATATTTTTAATACAGTTTTGTTGGTTCTGGATATTTGTGATTCTGTGGTCTAA
157932 GTGAGAAACACAACATTTTTTCACTGCATGCAGTATCCAAAGGCTTTTTGCAGAACCCGTGTGGT
131 GTGAGAAACACAACATTTTTTCACTGCATGCAGTATCCAAAGGCTTTTTGCAGAACCCGTGTGGT
157997 TTTCTACCGTGACATTTTCGGGTAGGTTTTGATCATAAAAGCCGCTGATGGGTTTTCTTTTGAAT
196 TTTCTACCGTGACATTTTCGGGTAGGTTTTGATCATAAAAGCCGCTGATGGGTTTTCTTTTGAAT
158062 GTGTCCTGTCTGAAATTTCCGCCACTTTTTTTTTTAGTTTTACGACAATAATTGCTCTACTTCAA
261 GTGTCCTGTCTGAAATTTCCGCCACTTTTTTTTTTAGTTTTACGACAATAATTGCTCTACTTCAA
158127 ATGTCTCCATGTTCAGGCTAACAAAAGGCAATAGATTTGGTTTCTTTTTGTTTTCCTCAGGCTAA
326 ATGTCTCCATGTTCAGGCTAACAAAAGGCAATAGATTTGGTTTCTTTTTGTTTTCCTCAGGCTAA
158192 GACCCCTAAGTCACAGTCTATGAATGTGATTGGTTGGTAGAGAAATCGTTTGAGAAAAAACAGGA
391 GACCCCTAAGTCACAGTCTATGAATGTGATTGGTTGGTAGAGAAATCGTTTGAGAAAAAACAGGA
158257 GACGAGAAAGCCCCATGCCCCAATCCATCATCACCCAAATACTTATGGATTTTCATAAAAGGATT
456 GACGAGAAAGCCCCATGCCCCAATCCATCATCACCCAAATACTTATGGATTTTCATAAAAGGATT
158322 TTAAATTATATTTTTATTTTATGATCGCAATATTTGTTTAAGGGTCTGAAATTTTATTTTTCATT
521 TTAAATTATATTTTTATTTTATGATCGCAATATTTGTTTAAGGGTCTGAAATTTTATTTTTCATT
*
158387 TTTATGGTAGTAAAAATATAATTTTATTATTTGAGTAGTTTATAT
586 TTTATGGTAGTAAAAATATAATTTTATTATTTGAATAGTTTATAT
158432 ATATTTTTAATATTAGGATAGATATTATTTAACTTTATTTATATTTATGATAAATGTTTTATTAT
1 ATATTTTTAATATTAGGATAGATATTATTTAACTTTATTTATATTTATGATAAATGTTTTATTAT
158497 GAAATTTAAGCTATATTTTTAATACAGTTTTGTTGGTTCTGGATATTTGTGATTCTGTGGTCTAA
66 GAAATTTAAGCTATATTTTTAATACAGTTTTGTTGGTTCTGGATATTTGTGATTCTGTGGTCTAA
158562 GTGAGAAACACAACATTTTTTCACTGCATGCAGTATCCAAAGGCTTTTTGCAGAACCCGTGTGGT
131 GTGAGAAACACAACATTTTTTCACTGCATGCAGTATCCAAAGGCTTTTTGCAGAACCCGTGTGGT
158627 TTTCTACCGTGACATTTTCGGGTAGGTTTTGATCATAAAAGCCGCTGATGGGTTTTCTTTTGAAT
196 TTTCTACCGTGACATTTTCGGGTAGGTTTTGATCATAAAAGCCGCTGATGGGTTTTCTTTTGAAT
158692 GTGTCCTGTCTGAAATTTCCGCCACTTTTTTTTTTAGTTTTACGACAATAATTGCTCTACTTCAA
261 GTGTCCTGTCTGAAATTTCCGCCACTTTTTTTTTTAGTTTTACGACAATAATTGCTCTACTTCAA
158757 ATGTCTCCATGTTCAGGCTAACAAAAGGCAATAGATTTGGTTTCTTTTTGTTTTCCTCAGGCTAA
326 ATGTCTCCATGTTCAGGCTAACAAAAGGCAATAGATTTGGTTTCTTTTTGTTTTCCTCAGGCTAA
158822 GACCCCTAAGTCACAGTCTATGAATGTGATTGGTTGGTAGAGAAATCGTTTGAGAAAAAACAGGA
391 GACCCCTAAGTCACAGTCTATGAATGTGATTGGTTGGTAGAGAAATCGTTTGAGAAAAAACAGGA
158887 GACGAGAAAGCCCCATGCCCCAATCCATCATCACCCAAATACTTATGGATTTTCATAAAAGGATT
456 GACGAGAAAGCCCCATGCCCCAATCCATCATCACCCAAATACTTATGGATTTTCATAAAAGGATT
158952 TTAAATTATATTTTTATTTTATGATCGCAATATTTGTTTAAGGGTCTGAAATTTTATTTTTCATT
521 TTAAATTATATTTTTATTTTATGATCGCAATATTTGTTTAAGGGTCTGAAATTTTATTTTTCATT
159017 TTTATGGTAGTAAAAATATAATTTTATTATTTGAATAGTTTATAT
586 TTTATGGTAGTAAAAATATAATTTTATTATTTGAATAGTTTATAT
159062 TTTTATAATT
Statistics
Matches: 629, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
630 629 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.41
Consensus pattern (630 bp):
ATATTTTTAATATTAGGATAGATATTATTTAACTTTATTTATATTTATGATAAATGTTTTATTAT
GAAATTTAAGCTATATTTTTAATACAGTTTTGTTGGTTCTGGATATTTGTGATTCTGTGGTCTAA
GTGAGAAACACAACATTTTTTCACTGCATGCAGTATCCAAAGGCTTTTTGCAGAACCCGTGTGGT
TTTCTACCGTGACATTTTCGGGTAGGTTTTGATCATAAAAGCCGCTGATGGGTTTTCTTTTGAAT
GTGTCCTGTCTGAAATTTCCGCCACTTTTTTTTTTAGTTTTACGACAATAATTGCTCTACTTCAA
ATGTCTCCATGTTCAGGCTAACAAAAGGCAATAGATTTGGTTTCTTTTTGTTTTCCTCAGGCTAA
GACCCCTAAGTCACAGTCTATGAATGTGATTGGTTGGTAGAGAAATCGTTTGAGAAAAAACAGGA
GACGAGAAAGCCCCATGCCCCAATCCATCATCACCCAAATACTTATGGATTTTCATAAAAGGATT
TTAAATTATATTTTTATTTTATGATCGCAATATTTGTTTAAGGGTCTGAAATTTTATTTTTCATT
TTTATGGTAGTAAAAATATAATTTTATTATTTGAATAGTTTATAT
Found at i:159115 original size:31 final size:30
Alignment explanation
Indices: 159062--159127 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 30
159052 TAGTTTATAT
* * *
159062 TTTTATAATTTTTAAAAGATTAAATTAAAA
1 TTTTATAATTTATAAAAAATTAAAGTAAAA
* *
159092 TTTTATTATTTATAAGAAAATTAAAGTACAA
1 TTTTATAATTTATAA-AAAATTAAAGTAAAA
159123 TTTTA
1 TTTTA
159128 ACTTTATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 13 0.43
31 17 0.57
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (30 bp):
TTTTATAATTTATAAAAAATTAAAGTAAAA
Done.