Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1869
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: 105397
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:940 original size:14 final size:14
Alignment explanation
Indices: 910--953 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
900 TCTTTTCTTC
*
910 CTTTTTCTTTTCACT
1 CTTTTTCTTTT-TCT
*
925 CTTTTTGTTTTTCT
1 CTTTTTCTTTTTCT
939 CTTTTTCTTTTTCT
1 CTTTTTCTTTTTCT
953 C
1 C
954 GCCCAATAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.73
Consensus pattern (14 bp):
CTTTTTCTTTTTCT
Found at i:950 original size:15 final size:15
Alignment explanation
Indices: 899--950 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
889 ACTCTCCTCA
899 TTCTTTTCTTC-CTTT
1 TTCTTTT-TTCTCTTT
**
914 TTCTTTTCACTCTTT
1 TTCTTTTTTCTCTTT
*
929 TT-GTTTTTCTCTTT
1 TTCTTTTTTCTCTTT
943 TTCTTTTT
1 TTCTTTTT
951 CTCGCCCAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTTTCTCTTT
Found at i:2642 original size:17 final size:18
Alignment explanation
Indices: 2603--2642 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2593 CAAGTTGTAA
*
2603 AGTTTATTTATTTTATTT
1 AGTTTATTTATTTTACTT
2621 A-TTTATTTA-TTTACTT
1 AGTTTATTTATTTTACTT
2637 AGTTTA
1 AGTTTA
2643 AATTTTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 7 0.35
17 12 0.60
18 1 0.05
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.68
Consensus pattern (18 bp):
AGTTTATTTATTTTACTT
Found at i:5283 original size:14 final size:14
Alignment explanation
Indices: 5264--5296 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
5254 GTTCTTAAAA
5264 GATCCTCTCATTTT
1 GATCCTCTCATTTT
5278 GATCCTCTCATTTT
1 GATCCTCTCATTTT
5292 GATCC
1 GATCC
5297 GATTAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.15, C:0.30, G:0.09, T:0.45
Consensus pattern (14 bp):
GATCCTCTCATTTT
Found at i:8678 original size:19 final size:18
Alignment explanation
Indices: 8642--8681 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
8632 TTTCCACTCG
*
8642 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
8660 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
8679 TTT
1 TTT
8682 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:9752 original size:14 final size:14
Alignment explanation
Indices: 9733--9784 Score: 95
Period size: 14 Copynumber: 3.7 Consensus size: 14
9723 TAGCTTCTTC
9733 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
9747 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
*
9761 TTTTTTTTCAGAAT
1 TTTTTTTTCACAAT
9775 TTTTTTTTCA
1 TTTTTTTTCA
9785 ACTTGATATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:9840 original size:13 final size:13
Alignment explanation
Indices: 9822--9869 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
9812 ATGGAAACCA
9822 AATTTTTTTTTTG
1 AATTTTTTTTTTG
9835 AA-TTTTTTTTTG
1 AATTTTTTTTTTG
*
9847 AATTTTTTTTTCG
1 AATTTTTTTTTTG
9860 AATTTTTTTT
1 AATTTTTTTT
9870 GAAGAAACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
12 12 0.36
13 21 0.64
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.75
Consensus pattern (13 bp):
AATTTTTTTTTTG
Found at i:9842 original size:12 final size:12
Alignment explanation
Indices: 9825--9869 Score: 81
Period size: 12 Copynumber: 3.7 Consensus size: 12
9815 GAAACCAAAT
9825 TTTTTTTTTGAA
1 TTTTTTTTTGAA
9837 TTTTTTTTTGAA
1 TTTTTTTTTGAA
9849 TTTTTTTTTCGAA
1 TTTTTTTTT-GAA
9862 TTTTTTTT
1 TTTTTTTT
9870 GAAGAAACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 21 0.66
13 11 0.34
ACGTcount: A:0.13, C:0.02, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:9856 original size:25 final size:25
Alignment explanation
Indices: 9822--9869 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
9812 ATGGAAACCA
*
9822 AATTTTTTTTTTGAATTTTTTTTTG
1 AATTTTTTTTTCGAATTTTTTTTTG
9847 AATTTTTTTTTCGAATTTTTTTT
1 AATTTTTTTTTCGAATTTTTTTT
9870 GAAGAAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.75
Consensus pattern (25 bp):
AATTTTTTTTTCGAATTTTTTTTTG
Found at i:21929 original size:15 final size:15
Alignment explanation
Indices: 21909--21963 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
21899 ACTCTCCTCA
*
21909 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
21924 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
21939 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
21953 TTCTTTT-TCTC
1 TTCTTTTCTCTC
21964 GATCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:23513 original size:18 final size:18
Alignment explanation
Indices: 23479--23515 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
23469 CACTTCTCTT
*
23479 TTTTTTTTTAATTCTGAA
1 TTTTTTTTTAATACTGAA
23497 TTTTTTTTTAATACTGAA
1 TTTTTTTTTAATACTGAA
23515 T
1 T
23516 ACACAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTTTTTTTAATACTGAA
Found at i:30437 original size:19 final size:18
Alignment explanation
Indices: 30401--30440 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
30391 TTTCCACTCG
*
30401 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
30419 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
30438 TTT
1 TTT
30441 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:31508 original size:14 final size:14
Alignment explanation
Indices: 31489--31542 Score: 101
Period size: 14 Copynumber: 3.9 Consensus size: 14
31479 ACTAGCTCTC
31489 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
31503 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
31517 TTTTTTTTCA-AAT
1 TTTTTTTTCACAAT
31530 TTTTTTTTCACAA
1 TTTTTTTTCACAA
31543 CTTGATATCC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.33
14 26 0.67
ACGTcount: A:0.22, C:0.13, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:31520 original size:27 final size:27
Alignment explanation
Indices: 31489--31542 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
31479 ACTAGCTCTC
31489 TTTTTTTTCACAATTTTTTTTTCACAAT
1 TTTTTTTTCA-AATTTTTTTTTCACAAT
31517 TTTTTTTTCAAATTTTTTTTTCACAA
1 TTTTTTTTCAAATTTTTTTTTCACAA
31543 CTTGATATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.22, C:0.13, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTTTTTCAAATTTTTTTTTCACAAT
Found at i:31594 original size:10 final size:10
Alignment explanation
Indices: 31579--31619 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 10
31569 ATGGAAACCA
31579 AATTTTTTTT
1 AATTTTTTTT
31589 AA-TTTTTTT
1 AATTTTTTTT
31598 AATTTTTTTTT
1 AA-TTTTTTTT
31609 GAATTTTTTTT
1 -AATTTTTTTT
31620 TCGAGTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.32
10 2 0.07
11 15 0.54
12 2 0.07
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (10 bp):
AATTTTTTTT
Found at i:31617 original size:9 final size:9
Alignment explanation
Indices: 31582--31606 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
31572 GAAACCAAAT
31582 TTTTTTTAA
1 TTTTTTTAA
31591 TTTTTTTAA
1 TTTTTTTAA
31600 TTTTTTT
1 TTTTTTT
31607 TTGAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:31628 original size:13 final size:12
Alignment explanation
Indices: 31591--31631 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
31581 TTTTTTTTAA
31591 TTTTTTT-AATT
1 TTTTTTTGAATT
31602 TTTTTTTGAATT
1 TTTTTTTGAATT
*
31614 TTTTTTTCGAGTT
1 TTTTTTT-GAATT
31627 TTTTT
1 TTTTT
31632 CGAGAAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 7 0.26
12 11 0.41
13 9 0.33
ACGTcount: A:0.12, C:0.02, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:38038 original size:20 final size:20
Alignment explanation
Indices: 38013--38057 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
38003 GTCTTAACCG
38013 AATTAATTAG-GTTTTAG-TTT
1 AATTAATT-GTGTTTT-GTTTT
38033 AATTAATTGTGTTTTGTTTT
1 AATTAATTGTGTTTTGTTTT
38053 AATTA
1 AATTA
38058 TAAGGATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (20 bp):
AATTAATTGTGTTTTGTTTT
Found at i:39819 original size:21 final size:21
Alignment explanation
Indices: 39774--39836 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
39764 TTTGAACCAT
* *
39774 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
39796 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
39817 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
39837 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:42396 original size:17 final size:16
Alignment explanation
Indices: 42376--42430 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 16
42366 AAGAAAAGAG
42376 AGAAAATACAAAAGAAA
1 AGAAAATACAAAA-AAA
42393 AGAAAAATGA-AAAAAAA
1 AG-AAAAT-ACAAAAAAA
*
42410 AGAAAATTCAAAAAAA
1 AGAAAATACAAAAAAA
42426 GAGAA
1 -AGAA
42431 TGAAAAGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
16 12 0.36
17 11 0.33
18 9 0.27
19 1 0.03
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (16 bp):
AGAAAATACAAAAAAA
Found at i:42409 original size:16 final size:17
Alignment explanation
Indices: 42364--42430 Score: 62
Period size: 17 Copynumber: 3.7 Consensus size: 17
42354 AAATGAGAGA
42364 AAAAGAAAAGAGAGAAAATAC
1 AAAA-AAAA-AGA-AAAAT-C
* *
42385 AAAAGAAAAGAAAAATG
1 AAAAAAAAAGAAAAATC
*
42402 AAAAAAAAAGAAAATTC
1 AAAAAAAAAGAAAAATC
*
42419 AAAAAAAGAGAA
1 AAAAAAAAAGAA
42431 TGAAAAGGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
17 25 0.62
18 5 0.12
19 3 0.08
20 3 0.08
21 4 0.10
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAGAAAAATC
Found at i:43855 original size:13 final size:12
Alignment explanation
Indices: 43830--43868 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
43820 CTCGCAAGAC
*
43830 TTTTCACTTTTT
1 TTTTTACTTTTT
43842 TTTGTT-CTTTTT
1 TTT-TTACTTTTT
43854 TTTTTACTTTTT
1 TTTTTACTTTTT
43866 TTT
1 TTT
43869 CTTTTTTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 2 0.08
12 21 0.88
13 1 0.04
ACGTcount: A:0.05, C:0.10, G:0.03, T:0.82
Consensus pattern (12 bp):
TTTTTACTTTTT
Found at i:43862 original size:24 final size:23
Alignment explanation
Indices: 43830--43876 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
43820 CTCGCAAGAC
*
43830 TTTTCACTTTTTTTTGTTCTTTTT
1 TTTTCACTTTTTTTTCTT-TTTTT
*
43854 TTTTTACTTTTTTTTCTTTTTTT
1 TTTTCACTTTTTTTTCTTTTTTT
43877 GCTCACTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.04, C:0.11, G:0.02, T:0.83
Consensus pattern (23 bp):
TTTTCACTTTTTTTTCTTTTTTT
Found at i:43884 original size:22 final size:21
Alignment explanation
Indices: 43839--43895 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
43829 CTTTTCACTT
* *
43839 TTTTTTGTTCTTTTTTTTTTAC
1 TTTTTT-TTCTTTTTTTCTCAC
43861 TTTTTTTTCTTTTTTTGCTCAC
1 TTTTTTTTCTTTTTTT-CTCAC
*
43883 TTCTTTTT-TTTTT
1 TTTTTTTTCTTTTT
43896 GAATTTTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.81
Consensus pattern (21 bp):
TTTTTTTTCTTTTTTTCTCAC
Found at i:43889 original size:24 final size:22
Alignment explanation
Indices: 43833--43892 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 22
43823 GCAAGACTTT
*
43833 TCACTTTTTTTTGTTCTTTTTTTT
1 TCAC-TTTTTTT-TTCTTTTTTTC
*
43857 TTAC-TTTTTTTTCTTTTTTTGC
1 TCACTTTTTTTTTCTTTTTTT-C
43879 TCACTTCTTTTTTT
1 TCACTT-TTTTTTT
43893 TTTGAATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 10 0.33
22 9 0.30
23 1 0.03
24 10 0.33
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (22 bp):
TCACTTTTTTTTTCTTTTTTTC
Found at i:45454 original size:20 final size:20
Alignment explanation
Indices: 45411--45454 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
45401 AGGTTAAGAT
*
45411 TGAGTTGAATTGAGCTTGAA
1 TGAGTTGAATTGAGCTCGAA
* *
45431 TGAGTTGACTTGAGCTCGAG
1 TGAGTTGAATTGAGCTCGAA
45451 TGAG
1 TGAG
45455 CTGGAAACGA
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:0.25, C:0.09, G:0.34, T:0.32
Consensus pattern (20 bp):
TGAGTTGAATTGAGCTCGAA
Found at i:48806 original size:21 final size:21
Alignment explanation
Indices: 48761--48823 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
48751 TTTGAACCAT
* *
48761 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
48783 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
48804 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
48824 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:49666 original size:23 final size:23
Alignment explanation
Indices: 49640--49711 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
49630 AATTTGGTTT
49640 ATTTCGTACCAAAATCTC-ATACC
1 ATTTCGTACCAAAATC-CAATACC
* *
49663 ATTTCGTACCAACATCCAATTCC
1 ATTTCGTACCAAAATCCAATACC
* * *
49686 ATTTCTTACCAAAAACCAAAACC
1 ATTTCGTACCAAAATCCAATACC
49709 ATT
1 ATT
49712 ACCTAATTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 1 0.02
23 40 0.98
ACGTcount: A:0.38, C:0.31, G:0.03, T:0.29
Consensus pattern (23 bp):
ATTTCGTACCAAAATCCAATACC
Found at i:52875 original size:18 final size:18
Alignment explanation
Indices: 52854--52893 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
52844 GATTGAGAGT
* * *
52854 GAAAAGGAATGTGAAACA
1 GAAAAGAAAAGTGAAAAA
52872 GAAAAGAAAAGTGAAAAA
1 GAAAAGAAAAGTGAAAAA
52890 GAAA
1 GAAA
52894 TTGAAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (18 bp):
GAAAAGAAAAGTGAAAAA
Found at i:55814 original size:28 final size:28
Alignment explanation
Indices: 55762--55817 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
55752 TAAATGTGTT
* *
55762 TTTTATTATATGTTATTAATGTGTCTAA
1 TTTTATTAAATGCTATTAATGTGTCTAA
55790 TTTTATTAAATGCT-TTAATGATGTCTAA
1 TTTTATTAAATGCTATTAATG-TGTCTAA
55818 GTCAAGCCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.54
Consensus pattern (28 bp):
TTTTATTAAATGCTATTAATGTGTCTAA
Found at i:59103 original size:21 final size:23
Alignment explanation
Indices: 59058--59104 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
59048 TCACCTACAA
* *
59058 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
59081 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
59102 TAA
1 TAA
59105 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:65712 original size:12 final size:12
Alignment explanation
Indices: 65695--65725 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
65685 GTATGCAATT
65695 TTTTTTTCTCGA
1 TTTTTTTCTCGA
65707 TTTTTTTCTCGA
1 TTTTTTTCTCGA
65719 TTTTTTT
1 TTTTTTT
65726 TGAATCTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.13, G:0.06, T:0.74
Consensus pattern (12 bp):
TTTTTTTCTCGA
Found at i:69307 original size:21 final size:21
Alignment explanation
Indices: 69281--69321 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
69271 GACCGTATAT
69281 ATTTTTTTTTCAATTTTTTTG
1 ATTTTTTTTTCAATTTTTTTG
*
69302 ATTTTTTTTTTAATTTTTTT
1 ATTTTTTTTTCAATTTTTTT
69322 ACGAACCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.80
Consensus pattern (21 bp):
ATTTTTTTTTCAATTTTTTTG
Found at i:69905 original size:10 final size:10
Alignment explanation
Indices: 69889--69945 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
69879 CAACTCCGAC
69889 CAGCTCAATT
1 CAGCTCAATT
*
69899 GAGCTC-ATT
1 CAGCTCAATT
69908 CAGCTCAA-T
1 CAGCTCAATT
69917 CGAGCTCAATT
1 C-AGCTCAATT
*
69928 TAGCTACAATT
1 CAGCT-CAATT
69939 CAGCTCA
1 CAGCTCA
69946 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 10 0.26
10 19 0.49
11 10 0.26
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:69913 original size:19 final size:19
Alignment explanation
Indices: 69889--69947 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
69879 CAACTCCGAC
69889 CAGCTCAATTGAGCTCATT
1 CAGCTCAATTGAGCTCATT
*
69908 CAGCTCAATCGAGCTCAATT
1 CAGCTCAATTGAGCTC-ATT
* *
69928 TAGCTACAATTCAGCTCATT
1 CAGCT-CAATTGAGCTCATT
69948 TATTTTATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 15 0.44
20 10 0.29
21 9 0.26
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (19 bp):
CAGCTCAATTGAGCTCATT
Found at i:76554 original size:11 final size:11
Alignment explanation
Indices: 76538--76577 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
76528 GACCGTATAT
76538 ATTTTTTTTCA
1 ATTTTTTTTCA
*
76549 A-TTTTTTTGA
1 ATTTTTTTTCA
*
76559 TTTTTTTTTCA
1 ATTTTTTTTCA
76570 ATTTTTTT
1 ATTTTTTT
76578 ACGAACCTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.78
Consensus pattern (11 bp):
ATTTTTTTTCA
Found at i:77187 original size:10 final size:10
Alignment explanation
Indices: 77171--77227 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
77161 CAACTCTGAC
77171 CAGCTCAATT
1 CAGCTCAATT
*
77181 GAGCTC-ATT
1 CAGCTCAATT
77190 CAGCTCAA-T
1 CAGCTCAATT
77199 CGAGCTCAATT
1 C-AGCTCAATT
*
77210 TAGCTACAATT
1 CAGCT-CAATT
77221 CAGCTCA
1 CAGCTCA
77228 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 10 0.26
10 19 0.49
11 10 0.26
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:77195 original size:19 final size:19
Alignment explanation
Indices: 77171--77229 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
77161 CAACTCTGAC
77171 CAGCTCAATTGAGCTCATT
1 CAGCTCAATTGAGCTCATT
*
77190 CAGCTCAATCGAGCTCAATT
1 CAGCTCAATTGAGCTC-ATT
* *
77210 TAGCTACAATTCAGCTCATT
1 CAGCT-CAATTGAGCTCATT
77230 TATTTTATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 15 0.44
20 10 0.29
21 9 0.26
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (19 bp):
CAGCTCAATTGAGCTCATT
Found at i:84601 original size:17 final size:18
Alignment explanation
Indices: 84579--84619 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
84569 CATTTCTTTT
84579 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
84596 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
84614 T-TTTTG
1 TCTTTTG
84620 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:91519 original size:14 final size:13
Alignment explanation
Indices: 91500--91546 Score: 78
Period size: 14 Copynumber: 3.6 Consensus size: 13
91490 ACGAGATTGT
91500 AAAAAAAAA-TCA
1 AAAAAAAAATTCA
91512 AAAAAAAAATTCGA
1 AAAAAAAAATTC-A
91526 AAAAAAAAATTCA
1 AAAAAAAAATTCA
91539 AAAAAAAA
1 AAAAAAAA
91547 GTTTGTATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
12 9 0.27
13 11 0.33
14 13 0.39
ACGTcount: A:0.81, C:0.06, G:0.02, T:0.11
Consensus pattern (13 bp):
AAAAAAAAATTCA
Found at i:93660 original size:15 final size:14
Alignment explanation
Indices: 93624--93678 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
93614 TCTATTGAGC
93624 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
93638 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
93652 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
93667 GAAAGAAAAGAA
1 GAGA-AAAAGAA
93679 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Done.