Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3666
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: 123533
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1793 original size:22 final size:22
Alignment explanation
Indices: 1768--1809 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1758 TTTCTTTGTT
1768 TTCTT-TTCTAATTCATTTTCTC
1 TTCTTCTTC-AATTCATTTTCTC
*
1790 TTCTTCTTCAATTCTTTTTC
1 TTCTTCTTCAATTCATTTTC
1810 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (22 bp):
TTCTTCTTCAATTCATTTTCTC
Found at i:11229 original size:22 final size:21
Alignment explanation
Indices: 11195--11237 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
11185 GGCTGTTAAA
*
11195 AAAAGGAGCTTAAAGATCATT
1 AAAAGGAGCTTAAAGAGCATT
*
11216 AAAAGGAGTTTTAAAGAGCATT
1 AAAAGGAG-CTTAAAGAGCATT
11238 TTATGCCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (21 bp):
AAAAGGAGCTTAAAGAGCATT
Found at i:15096 original size:23 final size:22
Alignment explanation
Indices: 15045--15097 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
15035 CCTCGTCTAT
*
15045 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTTTTTCTTTTTCTAAC
15067 -TCATTTTTTCTTCTTTCTTC-AAC
1 TTC-TTTTTT-TTCTTT-TTCTAAC
15090 TTCTTTTT
1 TTCTTTTT
15098 CAATTTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.19
23 14 0.54
24 5 0.19
ACGTcount: A:0.09, C:0.21, G:0.02, T:0.68
Consensus pattern (22 bp):
TTCTTTTTTTTCTTTTTCTAAC
Found at i:15097 original size:24 final size:21
Alignment explanation
Indices: 15045--15097 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 21
15035 CCTCGTCTAT
15045 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTT-TTTCTTTTTCTAAC
*
15067 -TCATTTTTTCTTCTTTCTTCAAC
1 TTCTTTTTTTCTT-TTTC-T-AAC
15090 TTCTTTTT
1 TTCTTTTT
15098 CAATTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 6 0.24
21 9 0.36
22 1 0.04
23 3 0.12
24 6 0.24
ACGTcount: A:0.09, C:0.21, G:0.02, T:0.68
Consensus pattern (21 bp):
TTCTTTTTTTCTTTTTCTAAC
Found at i:18682 original size:12 final size:13
Alignment explanation
Indices: 18665--18709 Score: 76
Period size: 12 Copynumber: 3.6 Consensus size: 13
18655 ACGAGATTGT
18665 AAAAAAAA-TCGA
1 AAAAAAAATTCGA
18677 AAAAAAAATTCGA
1 AAAAAAAATTCGA
18690 AAAAAAAATTC-A
1 AAAAAAAATTCGA
18702 AAAAAAAA
1 AAAAAAAA
18710 AGTTTGTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 17 0.53
13 15 0.47
ACGTcount: A:0.78, C:0.07, G:0.04, T:0.11
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:18683 original size:13 final size:13
Alignment explanation
Indices: 18665--18710 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
18655 ACGAGATTGT
18665 AAAAAAAATCGAA
1 AAAAAAAATCGAA
*
18678 AAAAAAATTCGAA
1 AAAAAAAATCGAA
*
18691 AAAAAAATTC-AA
1 AAAAAAAATCGAA
18703 AAAAAAAA
1 AAAAAAAA
18711 GTTTGTATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 9 0.29
13 22 0.71
ACGTcount: A:0.78, C:0.07, G:0.04, T:0.11
Consensus pattern (13 bp):
AAAAAAAATCGAA
Found at i:20803 original size:14 final size:14
Alignment explanation
Indices: 20784--20836 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
20774 TCTATTGAGC
20784 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
* *
20798 GAGAAAAACAAAGA
1 GAGAAAAAGAAAAA
*
20812 GTG-AAAAGAAAAA
1 GAGAAAAAGAAAAA
*
20825 GAAAGAAAAGAA
1 GAGA-AAAAGAA
20837 TGAGGAGAGT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
13 9 0.30
14 14 0.47
15 7 0.23
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:21926 original size:22 final size:22
Alignment explanation
Indices: 21875--21940 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
21865 GGTATTTGGG
* *
21875 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
21896 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
21918 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
21941 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:22709 original size:20 final size:20
Alignment explanation
Indices: 22663--22709 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
22653 AGCTCGTTTC
*
22663 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
22683 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
22703 CAGCTCA
1 CAGCTCA
22710 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:24872 original size:11 final size:10
Alignment explanation
Indices: 24847--24907 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
24837 ACCAATAAAA
24847 TAAA-TGAGC
1 TAAATTGAGC
*
24856 TGAATTGTAGC
1 TAAATTG-AGC
24867 TAAATTGAGC
1 TAAATTGAGC
**
24877 TCGATTGAGC
1 TAAATTGAGC
24887 TGAAA-TGAGC
1 T-AAATTGAGC
*
24897 TCAATTGAGC
1 TAAATTGAGC
24907 T
1 T
24908 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:24908 original size:20 final size:20
Alignment explanation
Indices: 24848--24908 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
24838 CCAATAAAAT
*
24848 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
24868 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
24889 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
24909 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:26996 original size:18 final size:18
Alignment explanation
Indices: 26975--27009 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
26965 TTTTTCTTTT
26975 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
26993 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
27010 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:27006 original size:6 final size:6
Alignment explanation
Indices: 26997--27101 Score: 52
Period size: 6 Copynumber: 17.2 Consensus size: 6
26987 TCAATCTCAA
* * * ** **
26997 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTAT TTTGAT
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCT-T TTTCTT
* ** * *
27049 TT-CTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
27095 TTTCTT T
1 TTTCTT T
27102 CAATTTCTTT
Statistics
Matches: 69, Mismatches: 25, Indels: 10
0.66 0.24 0.10
Matches are distributed among these distances:
5 7 0.10
6 49 0.71
7 10 0.14
8 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:27114 original size:6 final size:6
Alignment explanation
Indices: 27048--27101 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
27038 ACTATTTTGA
* ** * *
27048 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
27095 TTTCTT T
1 TTTCTT T
27102 CAATTTCTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:28159 original size:40 final size:36
Alignment explanation
Indices: 28115--28203 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 36
28105 GCAAGACTTT
*
28115 TCACTTTTTTTTTCTTCTTTTTTTTAACTCGATTTTTTTG
1 TCACTTTTTTTTT-TTCTTTGTTTT---TCGATTTTTTTG
*
28155 TCACTTCTTTTTTTTTCTTTGTTTTTCGATTTTTTTT
1 TCACTT-TTTTTTTTTCTTTGTTTTTCGATTTTTTTG
*
28192 TGA-TTTTTTTTT
1 TCACTTTTTTTTT
28204 GAATTTCTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
35 7 0.16
36 2 0.04
37 13 0.29
40 16 0.36
41 7 0.16
ACGTcount: A:0.08, C:0.12, G:0.06, T:0.74
Consensus pattern (36 bp):
TCACTTTTTTTTTTTCTTTGTTTTTCGATTTTTTTG
Found at i:28209 original size:12 final size:11
Alignment explanation
Indices: 28162--28205 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
28152 TTGTCACTTC
*
28162 TTTTTTTTT-C
1 TTTTTTTTTGA
*
28172 TTTGTTTTTCGA
1 TTT-TTTTTTGA
28184 TTTTTTTTTGA
1 TTTTTTTTTGA
28195 TTTTTTTTTGA
1 TTTTTTTTTGA
28206 ATTTCTTCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 3 0.10
11 23 0.79
12 3 0.10
ACGTcount: A:0.07, C:0.05, G:0.09, T:0.80
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:29593 original size:11 final size:10
Alignment explanation
Indices: 29568--29628 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
29558 ACCAATAAAA
29568 TAAA-TGAGC
1 TAAATTGAGC
*
29577 TGAATTGTAGC
1 TAAATTG-AGC
29588 TAAATTGAGC
1 TAAATTGAGC
**
29598 TCGATTGAGC
1 TAAATTGAGC
29608 TGAAA-TGAGC
1 T-AAATTGAGC
*
29618 TCAATTGAGC
1 TAAATTGAGC
29628 T
1 T
29629 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:29629 original size:20 final size:20
Alignment explanation
Indices: 29569--29629 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
29559 CCAATAAAAT
*
29569 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
29589 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
29610 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
29630 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:30438 original size:13 final size:13
Alignment explanation
Indices: 30422--30496 Score: 59
Period size: 13 Copynumber: 5.6 Consensus size: 13
30412 AAAAAAAATC
30422 AAAAAAAATTCGA
1 AAAAAAAATTCGA
30435 AAAAAAAATT-GA
1 AAAAAAAATTCGA
30447 TTGAAAAAAACATTC-A
1 ---AAAAAAA-ATTCGA
*
30463 AAAAAAAAGT-GA
1 AAAAAAAATTCGA
30475 AAAAAAAA-TCGA
1 AAAAAAAATTCGA
30487 GCAAAAAAAA
1 --AAAAAAAA
30497 AGGTGAGCAA
Statistics
Matches: 52, Mismatches: 1, Indels: 17
0.74 0.01 0.24
Matches are distributed among these distances:
11 1 0.02
12 15 0.29
13 17 0.33
14 8 0.15
15 7 0.13
16 4 0.08
ACGTcount: A:0.71, C:0.07, G:0.09, T:0.13
Consensus pattern (13 bp):
AAAAAAAATTCGA
Found at i:30492 original size:15 final size:15
Alignment explanation
Indices: 30461--30512 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 15
30451 AAAAAACATT
30461 CAAAAAAAAAGT--G
1 CAAAAAAAAAGTGAG
30474 -AAAAAAAAA-TCGAG
1 CAAAAAAAAAGT-GAG
30488 CAAAAAAAAAGGTGAG
1 CAAAAAAAAA-GTGAG
30504 CAAAAAAAA
1 CAAAAAAAA
30513 TCAAGTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 1 0.03
12 9 0.27
14 1 0.03
15 9 0.27
16 12 0.36
17 1 0.03
ACGTcount: A:0.71, C:0.08, G:0.15, T:0.06
Consensus pattern (15 bp):
CAAAAAAAAAGTGAG
Found at i:31427 original size:18 final size:18
Alignment explanation
Indices: 31406--31440 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31396 AGAAAAGAAA
31406 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
31424 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
31441 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:34633 original size:20 final size:20
Alignment explanation
Indices: 34587--34633 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
34577 AGCTCGTTTC
*
34587 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
34607 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
34627 CAGCTCA
1 CAGCTCA
34634 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:42172 original size:12 final size:12
Alignment explanation
Indices: 42155--42212 Score: 91
Period size: 12 Copynumber: 4.9 Consensus size: 12
42145 AGACCGTATG
42155 CAATTTTTTTTT
1 CAATTTTTTTTT
42167 CAATTTTTTTTT
1 CAATTTTTTTTT
42179 CAA-TTTTTTTT
1 CAATTTTTTTTT
*
42190 CGATTTTTTTTT
1 CAATTTTTTTTT
*
42202 CGATTTTTTTT
1 CAATTTTTTTT
42213 GAATCTACAA
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
11 10 0.23
12 34 0.77
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.74
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:42189 original size:23 final size:23
Alignment explanation
Indices: 42159--42212 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
42149 CGTATGCAAT
42159 TTTTTTTTCAATTTTTTTTTCAA
1 TTTTTTTTCAATTTTTTTTTCAA
* *
42182 TTTTTTTTCGATTTTTTTTTCGA
1 TTTTTTTTCAATTTTTTTTTCAA
42205 TTTTTTTT
1 TTTTTTTT
42213 GAATCTACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.11, C:0.07, G:0.04, T:0.78
Consensus pattern (23 bp):
TTTTTTTTCAATTTTTTTTTCAA
Found at i:45493 original size:17 final size:17
Alignment explanation
Indices: 45466--45510 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
45456 CTCTCTTTCA
*
45466 TTCTCTTTTTTT-AATT
1 TTCTTTTTTTTTCAATT
*
45482 TTCTTTTTTTTTCATTT
1 TTCTTTTTTTTTCAATT
45499 TTCTTTTCTTTT
1 TTCTTTT-TTTT
45511 GTATTTTCGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.44
17 10 0.40
18 4 0.16
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (17 bp):
TTCTTTTTTTTTCAATT
Found at i:47627 original size:12 final size:12
Alignment explanation
Indices: 47610--47646 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
47600 AAACCGTATG
47610 CAATTTTTTTTT
1 CAATTTTTTTTT
47622 CAATTTTTTTTT
1 CAATTTTTTTTT
*
47634 CAAATTTTTTTT
1 CAATTTTTTTTT
47646 C
1 C
47647 GAACTCCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:48013 original size:22 final size:22
Alignment explanation
Indices: 47962--48027 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
47952 GGTATTTGGG
* *
47962 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
47983 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
48005 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
48028 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:56703 original size:22 final size:22
Alignment explanation
Indices: 56652--56717 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
56642 GGTATTTGGG
* *
56652 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
56673 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
56695 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
56718 TCAAAGAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 19 0.49
22 15 0.38
23 5 0.13
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:58543 original size:22 final size:22
Alignment explanation
Indices: 58515--58558 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
58505 TTTTGAACCA
58515 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
58537 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
58559 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:60207 original size:10 final size:10
Alignment explanation
Indices: 60192--60229 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
60182 TTGGGTTAAG
60192 ATTGAGCTGA
1 ATTGAGCTGA
60202 ATTGAGCTCGA
1 ATTGAGCT-GA
60213 A-TGAGCTGA
1 ATTGAGCTGA
*
60222 CTTGAGCT
1 ATTGAGCT
60230 TGAGTGAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.80
11 3 0.12
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:60217 original size:20 final size:20
Alignment explanation
Indices: 60194--60240 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
60184 GGGTTAAGAT
60194 TGAGCTGAATTGAGCTCGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
60214 TGAGCTGACTTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAA
60234 TGAGCTG
1 TGAGCTG
60241 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.34, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:60663 original size:21 final size:21
Alignment explanation
Indices: 60598--60669 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
60588 AAAACAAGTG
*
60598 AGGAAAAAGAAAAAGAAGAGAA
1 AGGAAAATGAAAAAGAAGA-AA
*
60620 A-AATACAAGTGAAAAAGAAGAAA
1 AGGA-A-AA-TGAAAAAGAAGAAA
* **
60643 ATGAAAATGAAAAAGGCGAAA
1 AGGAAAATGAAAAAGAAGAAA
60664 AGGAAA
1 AGGAAA
60670 GCGAGAGAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
21 18 0.45
22 4 0.10
23 6 0.15
24 12 0.30
ACGTcount: A:0.68, C:0.03, G:0.24, T:0.06
Consensus pattern (21 bp):
AGGAAAATGAAAAAGAAGAAA
Found at i:63335 original size:21 final size:21
Alignment explanation
Indices: 63309--63352 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
63299 TTGGTATTTG
63309 GGAATTGGTACAAAATGGTAT
1 GGAATTGGTACAAAATGGTAT
**
63330 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACAAAATGGTAT
63351 GG
1 GG
63353 TATTAAAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.02, G:0.34, T:0.30
Consensus pattern (21 bp):
GGAATTGGTACAAAATGGTAT
Found at i:73866 original size:23 final size:22
Alignment explanation
Indices: 73814--73866 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
73804 TCCACGTCTT
*
73814 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
73836 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
73859 TTTCTTTT
1 TTTCTTTT
73867 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:76181 original size:4 final size:4
Alignment explanation
Indices: 76172--76199 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
76162 TTAAACTAAG
76172 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
76200 ATTAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:81862 original size:18 final size:18
Alignment explanation
Indices: 81841--81875 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
81831 AGAAAAGAAA
81841 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
81859 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
81876 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:83731 original size:21 final size:23
Alignment explanation
Indices: 83686--83732 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
83676 TCACCTGCAA
* *
83686 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
83709 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
83730 TAA
1 TAA
83733 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:90615 original size:12 final size:12
Alignment explanation
Indices: 90597--90638 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
90587 CAGTTTAATG
90597 ATTTTTTT-TTT
1 ATTTTTTTATTT
90608 ATTTTTTTATTT
1 ATTTTTTTATTT
* *
90620 ATTTATTTACTT
1 ATTTTTTTATTT
90632 AGTTTTT
1 A-TTTTT
90639 AAGTTAGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 8 0.31
12 14 0.54
13 4 0.15
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (12 bp):
ATTTTTTTATTT
Found at i:91418 original size:13 final size:13
Alignment explanation
Indices: 91400--91428 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
91390 AGGAAATTTG
91400 AAAAAAAAAATTC
1 AAAAAAAAAATTC
91413 AAAAAAAAAATTC
1 AAAAAAAAAATTC
91426 AAA
1 AAA
91429 TTTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAAAAAAATTC
Found at i:96071 original size:20 final size:20
Alignment explanation
Indices: 96046--96100 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
96036 TGTGGTTCAA
*
96046 CTCATTCGAGCTCAAGTTAG
1 CTCATTCGAGCTCAAGTCAG
*
96066 CTCATTCGTGCTCAAGTCAG
1 CTCATTCGAGCTCAAGTCAG
*
96086 CTCATTCAAGCTCAA
1 CTCATTCGAGCTCAA
96101 TTTAACTCGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
CTCATTCGAGCTCAAGTCAG
Found at i:98265 original size:21 final size:23
Alignment explanation
Indices: 98220--98266 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
98210 TCACCTGCAA
* *
98220 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
98243 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
98264 TAA
1 TAA
98267 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:101114 original size:11 final size:11
Alignment explanation
Indices: 101098--101137 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
101088 GTTTCTCAAA
*
101098 AAAAAAACTCG
1 AAAAAAATTCG
*
101109 AAAAAAATTCA
1 AAAAAAATTCG
101120 AAAAAAATTCG
1 AAAAAAATTCG
101131 AAAAAAA
1 AAAAAAA
101138 ACTAGTTTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.72, C:0.10, G:0.05, T:0.12
Consensus pattern (11 bp):
AAAAAAATTCG
Found at i:101195 original size:14 final size:14
Alignment explanation
Indices: 101176--101215 Score: 73
Period size: 13 Copynumber: 2.9 Consensus size: 14
101166 GGATATCAAG
101176 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
101190 TTGTG-AAAAAAAA
1 TTGTGAAAAAAAAA
101203 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
101216 GAGAGCTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:108666 original size:19 final size:20
Alignment explanation
Indices: 108642--108686 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
108632 CTTTTCATTC
*
108642 TCTTTTTTTGAATTTTC-TT
1 TCTTTTTTTCAATTTTCTTT
*
108661 TCTTTTTTTCATTTTTCTTT
1 TCTTTTTTTCAATTTTCTTT
108681 TCTTTT
1 TCTTTT
108687 GTATTTTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (20 bp):
TCTTTTTTTCAATTTTCTTT
Found at i:110918 original size:28 final size:27
Alignment explanation
Indices: 110871--110924 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
110861 CCGTATGCAA
110871 ATTTTTTTTCTTTTCAATTTTTTTTTG
1 ATTTTTTTTCTTTTCAATTTTTTTTTG
*
110898 ATTTTTTTTCGATTTT-GATTTTTTTTT
1 ATTTTTTTTC--TTTTCAATTTTTTTTT
110925 CGAACTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 10 0.42
28 10 0.42
29 4 0.17
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.78
Consensus pattern (27 bp):
ATTTTTTTTCTTTTCAATTTTTTTTTG
Found at i:111264 original size:21 final size:21
Alignment explanation
Indices: 111238--111281 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
111228 TTGGTATTTG
111238 GGAATTGGTACAAAATGGTAT
1 GGAATTGGTACAAAATGGTAT
**
111259 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACAAAATGGTAT
111280 GG
1 GG
111282 TATTAAAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.02, G:0.34, T:0.30
Consensus pattern (21 bp):
GGAATTGGTACAAAATGGTAT
Found at i:112374 original size:10 final size:10
Alignment explanation
Indices: 112359--112400 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
112349 TTTGCAAGTT
112359 TTGAGCTAAA
1 TTGAGCTAAA
* *
112369 TTGAGCTGAT
1 TTGAGCTAAA
*
112379 TTGAGCT-CA
1 TTGAGCTAAA
112388 TTGAGCTAAA
1 TTGAGCTAAA
112398 TTG
1 TTG
112401 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:112944 original size:70 final size:70
Alignment explanation
Indices: 112831--112970 Score: 262
Period size: 70 Copynumber: 2.0 Consensus size: 70
112821 AGACAAATGC
* *
112831 TGATGTGGTCCGGCCCGGGTTAATTGAGTCGTTTCACGTAATTGCCCGATCGTCGACGAGGAATA
1 TGATGTGATCCGGCCCGGATTAATTGAGTCGTTTCACGTAATTGCCCGATCGTCGACGAGGAATA
112896 GTTGA
66 GTTGA
112901 TGATGTGATCCGGCCCGGATTAATTGAGTCGTTTCACGTAATTGCCCGATCGTCGACGAGGAATA
1 TGATGTGATCCGGCCCGGATTAATTGAGTCGTTTCACGTAATTGCCCGATCGTCGACGAGGAATA
112966 GTTGA
66 GTTGA
112971 GTTATCGAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (70 bp):
TGATGTGATCCGGCCCGGATTAATTGAGTCGTTTCACGTAATTGCCCGATCGTCGACGAGGAATA
GTTGA
Found at i:117290 original size:13 final size:13
Alignment explanation
Indices: 117274--117325 Score: 72
Period size: 12 Copynumber: 4.1 Consensus size: 13
117264 TATACTTCGA
117274 TTTTTTTT-AATT
1 TTTTTTTTCAATT
*
117286 TTTTTTTTCGA-T
1 TTTTTTTTCAATT
117298 TTTTTTTTCAATT
1 TTTTTTTTCAATT
117311 TTTTTTTTCGAATT
1 TTTTTTTTC-AATT
117325 T
1 T
117326 CCTCTTCTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 19 0.54
13 11 0.31
14 5 0.14
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.77
Consensus pattern (13 bp):
TTTTTTTTCAATT
Found at i:117302 original size:25 final size:25
Alignment explanation
Indices: 117269--117358 Score: 93
Period size: 25 Copynumber: 3.8 Consensus size: 25
117259 TTTTTTATAC
117269 TTCGA-TTTTTTTT-AATTTTTTTT
1 TTCGATTTTTTTTTCAATTTTTTTT
117292 TTCGATTTTTTTTTCAATTTTTTTT
1 TTCGATTTTTTTTTCAATTTTTTTT
** *
117317 TTCGAATTTCCTCTTC--TCTTTTTTT
1 TTCG-ATTTTTTTTTCAAT-TTTTTTT
117342 TT-GA-TTTTTTTTCAATT
1 TTCGATTTTTTTTTCAATT
117359 ACAATATGCT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
22 6 0.11
23 7 0.13
24 11 0.20
25 23 0.42
26 8 0.15
ACGTcount: A:0.12, C:0.11, G:0.04, T:0.72
Consensus pattern (25 bp):
TTCGATTTTTTTTTCAATTTTTTTT
Found at i:122496 original size:21 final size:23
Alignment explanation
Indices: 122451--122497 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
122441 TCACCTGCAA
* *
122451 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
122474 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
122495 TAA
1 TAA
122498 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
Done.