Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold454
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: 169753
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5411 original size:27 final size:27
Alignment explanation
Indices: 5379--5430 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
5369 ACAAGTGAGG
5379 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
5406 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
5431 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:9607 original size:15 final size:15
Alignment explanation
Indices: 9587--9623 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
9577 ATATGTAATT
*
9587 TTTTTTTCTTTTCAA
1 TTTTTTTCCTTTCAA
9602 TTTTTTTCCTTTCAA
1 TTTTTTTCCTTTCAA
9617 TTTTTTT
1 TTTTTTT
9624 TTCGATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTTCCTTTCAA
Found at i:10016 original size:22 final size:22
Alignment explanation
Indices: 9957--10022 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
9947 GGTATTTGGG
* *
9957 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
*
9978 AATTGGTATGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
10000 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
10023 TCAAAGAGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
21 18 0.49
22 14 0.38
23 5 0.14
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.36
Consensus pattern (22 bp):
AATTGGTACGAAATGGTATGGT
Found at i:22316 original size:23 final size:22
Alignment explanation
Indices: 22265--22316 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
22255 CCTCGTCTTT
*
22265 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
22287 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
22310 TTCTTTT
1 TTCTTTT
22317 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:22331 original size:18 final size:18
Alignment explanation
Indices: 22310--22348 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
22300 TTTCTTCAAC
* *
22310 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
22328 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
22346 TTC
1 TTC
22349 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:24720 original size:4 final size:4
Alignment explanation
Indices: 24711--24738 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
24701 TTAAACTAAG
24711 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
24739 AATAAAACTT
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:26915 original size:19 final size:19
Alignment explanation
Indices: 26891--26928 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
26881 TGGCTTAGAA
26891 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
26910 AATGACTCTTGAGTTGTCC
1 AATGACTCTTGAGTTGTCC
26929 TTGGCTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
AATGACTCTTGAGTTGTCC
Found at i:40362 original size:33 final size:34
Alignment explanation
Indices: 40311--40385 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
40301 AGATTTAAAC
40311 AAATTAATTACTAACACTTATTTAAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
* *
40345 AAATTAATT-CTAACACTTATTTGAGTTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
40378 AATTTAAT
1 AAATTAAT
40386 AAACTAACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.39
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACTA
Found at i:43789 original size:20 final size:19
Alignment explanation
Indices: 43766--43830 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
43756 AAGCTCAAAC
43766 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
43786 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
43806 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
43826 GAGCT
1 GAGCT
43831 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:45645 original size:33 final size:33
Alignment explanation
Indices: 45607--45669 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
45597 GATTACTCAC
45607 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
45640 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
45670 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:45724 original size:22 final size:22
Alignment explanation
Indices: 45699--45772 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 22
45689 TCTTTTTCAA
45699 TTTT-TTTTTCATTCTCATTTCT
1 TTTTCTTTTTC-TTCTCATTTCT
*
45721 TTTTCATTTTCTTTTCTTCATTTTCT
1 TTTTC-TTTT-TCTTC-TCA-TTTCT
45747 TTTTCTCTTTT-TT-TCATTTCT
1 TTTTCT-TTTTCTTCTCATTTCT
45768 TTTTC
1 TTTTC
45773 AATCTCTTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
21 10 0.22
22 7 0.16
24 9 0.20
25 6 0.13
26 13 0.29
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTTCTTTTTCTTCTCATTTCT
Found at i:45742 original size:14 final size:14
Alignment explanation
Indices: 45723--45749 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45713 TCATTTCTTT
45723 TTCATTTTCTTTTC
1 TTCATTTTCTTTTC
45737 TTCATTTTCTTTT
1 TTCATTTTCTTTT
45750 TCTCTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (14 bp):
TTCATTTTCTTTTC
Found at i:45778 original size:25 final size:24
Alignment explanation
Indices: 45713--45781 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 24
45703 TTTTTCATTC
*
45713 TCATTTCTTTTTCATTTTCTTTTCT
1 TCATTTCTTTTTCA-TCTCTTTTCT
45738 TCATTTTCTTTTTC-TCT-TTTT-T
1 TCA-TTTCTTTTTCATCTCTTTTCT
45760 TCATTTCTTTTTCAATCTCTTT
1 TCATTTCTTTTTC-ATCTCTTT
45782 CTCCTTTTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
21 10 0.26
22 4 0.10
23 7 0.18
24 5 0.13
25 3 0.08
26 10 0.26
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (24 bp):
TCATTTCTTTTTCATCTCTTTTCT
Found at i:46947 original size:11 final size:11
Alignment explanation
Indices: 46931--46959 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
46921 CCAACTCAAA
46931 TTTTTTTTGA-
1 TTTTTTTTGAC
46941 TTTTTTTTGAC
1 TTTTTTTTGAC
46952 TTTTTTTT
1 TTTTTTTT
46960 TTACGAACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:48491 original size:20 final size:19
Alignment explanation
Indices: 48468--48532 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
48458 AAGCTCAAAC
48468 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
48488 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
48508 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
48528 GAGCT
1 GAGCT
48533 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:53766 original size:6 final size:6
Alignment explanation
Indices: 53755--53788 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
53745 AATTTTTTTC
* *
53755 TCAATA TCAATA TCAATA TCAATC TCAATC TCAA
1 TCAATA TCAATA TCAATA TCAATA TCAATA TCAA
53789 ATTCTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (6 bp):
TCAATA
Found at i:53840 original size:21 final size:20
Alignment explanation
Indices: 53796--53840 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
53786 CAAATTCTTT
*
53796 TTTCTTTTTCTCACTCTCAT
1 TTTCTTTTTCTCACTCTCAA
* *
53816 TTTCTTTTTTTCTTCTCTCAA
1 TTTCTTTTTCTC-ACTCTCAA
53837 TTTC
1 TTTC
53841 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCTTTTTCTCACTCTCAA
Found at i:54752 original size:20 final size:21
Alignment explanation
Indices: 54730--54777 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
54720 CAATCACTCT
*
54730 TTTTTTTTTTCAATTTTG-AT
1 TTTTTTTTTTCAATTTCGAAT
*
54750 TTTTTTTTTTTAATTTCGAAT
1 TTTTTTTTTTCAATTTCGAAT
54771 TTTTTTT
1 TTTTTTT
54778 CTTCTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (21 bp):
TTTTTTTTTTCAATTTCGAAT
Found at i:54786 original size:13 final size:13
Alignment explanation
Indices: 54770--54794 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54760 TAATTTCGAA
54770 TTTTTTTTCTTCT
1 TTTTTTTTCTTCT
54783 TTTTTTTTCTTC
1 TTTTTTTTCTTC
54795 AATACTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTTCTTCT
Found at i:54854 original size:14 final size:14
Alignment explanation
Indices: 54835--54882 Score: 87
Period size: 14 Copynumber: 3.4 Consensus size: 14
54825 GAATACAAAC
54835 TTTTTTTTTTGAAT
1 TTTTTTTTTTGAAT
54849 TTTTTTTTTTGAAT
1 TTTTTTTTTTGAAT
*
54863 TTTTTTTTTCGAAT
1 TTTTTTTTTTGAAT
54877 TTTTTT
1 TTTTTT
54883 ATATTTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.12, C:0.02, G:0.06, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTTGAAT
Found at i:58819 original size:23 final size:24
Alignment explanation
Indices: 58793--58838 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
58783 TTTCTTTTGT
58793 TTCTTT-TTCTAAC-TCATTTTCTC
1 TTCTTTCTTC-AACTTCATTTTCTC
*
58816 TTCTTTCTTCAACTTCTTTTTCT
1 TTCTTTCTTCAACTTCATTTTCT
58839 ATTTTCTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.11, C:0.26, G:0.00, T:0.63
Consensus pattern (24 bp):
TTCTTTCTTCAACTTCATTTTCTC
Found at i:60488 original size:30 final size:30
Alignment explanation
Indices: 60432--60488 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
60422 TGGGCTCAAA
* **
60432 TCAAGAAAATCAAGATTCGCTTTCTTGTTT
1 TCAAGAAAATCAAGAATCGCAATCTTGTTT
60462 TCAAGAAAATCAAGAAATCG-AATCTTG
1 TCAAGAAAATCAAG-AATCGCAATCTTG
60489 GCCCAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.83
31 4 0.17
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (30 bp):
TCAAGAAAATCAAGAATCGCAATCTTGTTT
Found at i:60557 original size:43 final size:44
Alignment explanation
Indices: 60471--60564 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 44
60461 TTCAAGAAAA
** **
60471 TCAAGAAATCGAATCTTGGCCCAATTTTGCTGTTCGGAGTGATT
1 TCAAGAAATCGAATCTTGGAACAATTTTGCTGAACGGAGTGATT
60515 TCAAGAAATCGAATCTTGGAACAA-TTTGCTGAACGGAGTGATT
1 TCAAGAAATCGAATCTTGGAACAATTTTGCTGAACGGAGTGATT
60558 TCAAGAA
1 TCAAGAA
60565 TCAAGAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
43 24 0.52
44 22 0.48
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (44 bp):
TCAAGAAATCGAATCTTGGAACAATTTTGCTGAACGGAGTGATT
Found at i:66922 original size:21 final size:19
Alignment explanation
Indices: 66874--66934 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
66864 AACTCCGACC
* *
66874 AGCTCAATTGAGCTTATTT
1 AGCTCAATTCAGCTCATTT
66893 CAGCTCAA-TCGAGCTCAATTT
1 -AGCTCAATTC-AGCTC-ATTT
66914 AGCTACAATTCAGCTCATTT
1 AGCT-CAATTCAGCTCATTT
66934 A
1 A
66935 TTTTATTGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
19 1 0.03
20 20 0.57
21 12 0.34
22 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (19 bp):
AGCTCAATTCAGCTCATTT
Found at i:66928 original size:11 final size:10
Alignment explanation
Indices: 66873--66930 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
66863 CAACTCCGAC
66873 CAGCTCAATT
1 CAGCTCAATT
* * *
66883 GAGCTTATTT
1 CAGCTCAATT
66893 CAGCTCAA-T
1 CAGCTCAATT
66902 CGAGCTCAATT
1 C-AGCTCAATT
*
66913 TAGCTACAATT
1 CAGCT-CAATT
66924 CAGCTCA
1 CAGCTCA
66931 TTTATTTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
9 2 0.05
10 25 0.68
11 10 0.27
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:69229 original size:18 final size:18
Alignment explanation
Indices: 69208--69242 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
69198 AGAAAAGAAA
69208 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
69226 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
69243 AGAAGAAAAG
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:71327 original size:10 final size:10
Alignment explanation
Indices: 71311--71368 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
71301 CAACTCCGAC
71311 CAGCTCAATT
1 CAGCTCAATT
* *
71321 GAGCTCATTT
1 CAGCTCAATT
71331 CAGCTCAA-T
1 CAGCTCAATT
71340 CGAGCTCAATT
1 C-AGCTCAATT
*
71351 TAGCTACAATT
1 CAGCT-CAATT
71362 CAGCTCA
1 CAGCTCA
71369 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:71334 original size:20 final size:20
Alignment explanation
Indices: 71311--71371 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
71301 CAACTCCGAC
71311 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
71331 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
71352 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
71372 ATTTTATTGG
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:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:73766 original size:20 final size:19
Alignment explanation
Indices: 73743--73807 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
73733 AAGCTCAAAC
73743 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
73763 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
73783 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
73803 GAGCT
1 GAGCT
73808 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:75653 original size:23 final size:23
Alignment explanation
Indices: 75627--75690 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
75617 TTGAACCATA
*
75627 ACCATTTCGTACCAAAT-AGTATT
1 ACCATTTCGTACCAAATCA-CATT
*
75650 ACCATTTCGAACCAAATCACATT
1 ACCATTTCGTACCAAATCACATT
*
75673 ACCATTTCGTAACAAATC
1 ACCATTTCGTACCAAATC
75691 CAAAACCGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.38, C:0.27, G:0.06, T:0.30
Consensus pattern (23 bp):
ACCATTTCGTACCAAATCACATT
Found at i:79744 original size:11 final size:11
Alignment explanation
Indices: 79728--79758 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
79718 TAGTTTCTTC
79728 AAAAAAATTGA
1 AAAAAAATTGA
79739 AAAAAAATTGA
1 AAAAAAATTGA
79750 AAAAAAATT
1 AAAAAAATT
79759 TGGTTTCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:79820 original size:17 final size:16
Alignment explanation
Indices: 79796--79853 Score: 107
Period size: 16 Copynumber: 3.6 Consensus size: 16
79786 GATATCAAGT
79796 TGAAAAAAAAAATTTG
1 TGAAAAAAAAAATTTG
79812 TGAAAAAAAAAATTTG
1 TGAAAAAAAAAATTTG
79828 TGAAAAAAAAAATTTCG
1 TGAAAAAAAAAATTT-G
79845 TGAAAAAAA
1 TGAAAAAAA
79854 GAAGAAGCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
16 31 0.76
17 10 0.24
ACGTcount: A:0.64, C:0.02, G:0.12, T:0.22
Consensus pattern (16 bp):
TGAAAAAAAAAATTTG
Found at i:94925 original size:10 final size:10
Alignment explanation
Indices: 94910--94992 Score: 76
Period size: 10 Copynumber: 7.9 Consensus size: 10
94900 TTTGAACCAT
*
94910 TACCAATTCG
1 TACCAATTCA
*
94920 TACCAAATACCA
1 TACC-AAT-TCA
*
94932 TACCATTTCA
1 TACCAATTCA
94942 TACCAATTCCA
1 TACCAATT-CA
*
94953 TACCATTTCA
1 TACCAATTCA
94963 TACCAATTCCA
1 TACCAATT-CA
* *
94974 TACCATTTCG
1 TACCAATTCA
94984 TACCAATTC
1 TACCAATTC
94993 CCAAATACCA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
10 31 0.53
11 23 0.39
12 5 0.08
ACGTcount: A:0.34, C:0.33, G:0.02, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:94955 original size:21 final size:21
Alignment explanation
Indices: 94910--94993 Score: 123
Period size: 21 Copynumber: 4.0 Consensus size: 21
94900 TTTGAACCAT
* * *
94910 TACCAATTCGTACCAAATACCA
1 TACCATTTCATACC-AATTCCA
94932 TACCATTTCATACCAATTCCA
1 TACCATTTCATACCAATTCCA
94953 TACCATTTCATACCAATTCCA
1 TACCATTTCATACCAATTCCA
*
94974 TACCATTTCGTACCAATTCC
1 TACCATTTCATACCAATTCC
94994 CAAATACCAA
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
21 46 0.79
22 12 0.21
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.31
Consensus pattern (21 bp):
TACCATTTCATACCAATTCCA
Found at i:97679 original size:23 final size:23
Alignment explanation
Indices: 97653--97714 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
97643 TTGAACCATA
**
97653 ACCATTTCGTACCAAATCGTATT
1 ACCATTTCGTACCAAATCACATT
*
97676 ACCATTTCGAACCAAATCACATT
1 ACCATTTCGTACCAAATCACATT
* *
97699 ATCATTTCGTAACAAA
1 ACCATTTCGTACCAAA
97715 CCCAAAACCG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (23 bp):
ACCATTTCGTACCAAATCACATT
Found at i:104288 original size:46 final size:46
Alignment explanation
Indices: 104236--104329 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
104226 ATAGTGTGGC
*
104236 GTTCATCATATACCAAGGTTCTTATCA-TCATTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTC-TTGATAGTGGGTCGAG
104282 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
104328 GT
1 GT
104330 CTTTTCTTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 44 0.96
47 2 0.04
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
Found at i:104663 original size:10 final size:11
Alignment explanation
Indices: 104643--104686 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
104633 ATAGTAGTTT
104643 CTCGAAAAAAA
1 CTCGAAAAAAA
104654 CTCGAAAAAAA
1 CTCGAAAAAAA
* *
104665 TTCAAAAAAAA
1 CTCGAAAAAAA
*
104676 TTCGAAAAAAA
1 CTCGAAAAAAA
104687 ACTAGTTTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.66, C:0.14, G:0.07, T:0.14
Consensus pattern (11 bp):
CTCGAAAAAAA
Found at i:104749 original size:14 final size:14
Alignment explanation
Indices: 104725--104763 Score: 71
Period size: 13 Copynumber: 2.9 Consensus size: 14
104715 GGATATCAAG
104725 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
104739 TT-TGAAAAAAAAA
1 TTGTGAAAAAAAAA
104752 TTGTGAAAAAAA
1 TTGTGAAAAAAA
104764 GAGAGCTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:109631 original size:19 final size:19
Alignment explanation
Indices: 109609--109646 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
109599 AACTAGCCAA
109609 GGACAACTCAAGAGTCATT
1 GGACAACTCAAGAGTCATT
109628 GGACAACTCAAGAGTCATT
1 GGACAACTCAAGAGTCATT
109647 TTCTAAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
GGACAACTCAAGAGTCATT
Found at i:110023 original size:46 final size:47
Alignment explanation
Indices: 109971--110065 Score: 158
Period size: 47 Copynumber: 2.0 Consensus size: 47
109961 ATAGTGTGGC
*
109971 GTTCATCATATACCAAGGTT-CTTATCA-TCATTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTAATCATTC-TTGATAGTGGGTCGAG
110017 GTTCATCATATACCAAGGTTCCTAATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTAATCATTCTTGATAGTGGGTCGAG
110064 GT
1 GT
110066 CTTTTCTTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
46 20 0.43
47 24 0.52
48 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (47 bp):
GTTCATCATATACCAAGGTTCCTAATCATTCTTGATAGTGGGTCGAG
Found at i:110471 original size:22 final size:22
Alignment explanation
Indices: 110441--110484 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
110431 TTTGGTATTT
110441 GGGAATTGGTAAGAAATGGTAA
1 GGGAATTGGTAAGAAATGGTAA
* *
110463 GGGACTTGGTACGAAATGGTAA
1 GGGAATTGGTAAGAAATGGTAA
110485 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.36, T:0.23
Consensus pattern (22 bp):
GGGAATTGGTAAGAAATGGTAA
Found at i:114702 original size:17 final size:17
Alignment explanation
Indices: 114677--114730 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
114667 TCTCTTTTCA
*
114677 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
114694 TTCTTTTTTTTTCATTT
1 TTCTTTTTTTTTGAATT
* *
114711 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
114728 TTC
1 TTC
114731 GCTCTTTTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.07, C:0.13, G:0.04, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:117286 original size:22 final size:22
Alignment explanation
Indices: 117256--117299 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
117246 TTTGGTATTT
117256 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
117278 GGGACTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
117300 TGGTTCAAAA
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:0.34, C:0.07, G:0.36, T:0.23
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:119250 original size:11 final size:11
Alignment explanation
Indices: 119228--119268 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
119218 AGAAGTGAGC
119228 AAAAAAAG--A
1 AAAAAAAGTAA
119237 AAAAAAAGTAA
1 AAAAAAAGTAA
*
119248 AAAAAAAGAACA
1 AAAAAAAGTA-A
119260 AAAAAAAGT
1 AAAAAAAGT
119269 GAAGTCTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
9 8 0.30
11 10 0.37
12 9 0.33
ACGTcount: A:0.83, C:0.02, G:0.10, T:0.05
Consensus pattern (11 bp):
AAAAAAAGTAA
Found at i:120278 original size:6 final size:6
Alignment explanation
Indices: 120250--120389 Score: 55
Period size: 6 Copynumber: 22.3 Consensus size: 6
120240 CCATTGAGCG
* * * * * * *
120250 AGAAAA GGAAAA AGAGAT TGAAAA AGAAAT TGAAAGA AAACAAA AAGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAA-A AGA-AAA A-GAAAA
* * * ** * * ** *
120301 CGAAAA AGAAAA AGAAAT TGCTAA AGAAAA AGAAAT CGAAAA AGTGAG
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
* *
120349 AGAAAA AGAAAA TGAAGAAA AGAAAA TTGAAAA AGAAAA AG
1 AGAAAA AGAAAA AG-A-AAA AGAAAA -AGAAAA AGAAAA AG
120390 CGAAAAAAGA
Statistics
Matches: 90, Mismatches: 38, Indels: 12
0.64 0.27 0.09
Matches are distributed among these distances:
6 70 0.78
7 13 0.14
8 7 0.08
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.09
Consensus pattern (6 bp):
AGAAAA
Found at i:120278 original size:18 final size:18
Alignment explanation
Indices: 120251--120344 Score: 77
Period size: 18 Copynumber: 5.4 Consensus size: 18
120241 CATTGAGCGA
* * *
120251 GAAAAGGAAAAAGAGATT
1 GAAAAAGAAAAAGAAATC
**
120269 GAAAAAGAAATTGAAA--
1 GAAAAAGAAAAAGAAATC
* *
120285 G-AAAACAAAAAGAAAAC
1 GAAAAAGAAAAAGAAATC
*
120302 GAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAATC
**
120320 GCTAAAGAAAAAGAAATC
1 GAAAAAGAAAAAGAAATC
120338 GAAAAAG
1 GAAAAAG
120345 TGAGAGAAAA
Statistics
Matches: 58, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
15 11 0.19
16 1 0.02
17 1 0.02
18 45 0.78
ACGTcount: A:0.68, C:0.04, G:0.19, T:0.09
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAATC
Found at i:120308 original size:12 final size:12
Alignment explanation
Indices: 120282--120401 Score: 66
Period size: 12 Copynumber: 9.6 Consensus size: 12
120272 AAAGAAATTG
120282 AAAGAAAAC-AA
1 AAAGAAAACGAA
120293 AAAGAAAACGAA
1 AAAGAAAACGAA
*
120305 AAAGAAAAAGAA
1 AAAGAAAACGAA
** *
120317 ATTGCTAAA-GAA
1 AAAG-AAAACGAA
*
120329 AAAGAAATCGAA
1 AAAGAAAACGAA
* *
120341 AAAGTGAGA-GAA
1 AAAG-AAAACGAA
*
120353 AAAGAAAATGAAGA
1 AAAGAAAACG-A-A
*
120367 AAAGAAAATTGAA
1 AAAGAAAA-CGAA
120380 AAAGAAAAAGCGAAA
1 AAAG-AAAA-CG-AA
120395 AAAGAAA
1 AAAGAAA
120402 TTGAAAGAGA
Statistics
Matches: 84, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
11 13 0.15
12 35 0.42
13 10 0.12
14 18 0.21
15 8 0.10
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:120335 original size:81 final size:83
Alignment explanation
Indices: 120250--120404 Score: 190
Period size: 81 Copynumber: 1.9 Consensus size: 83
120240 CCATTGAGCG
* ** * *
120250 AGAAAAGGAAAAAGAGATTGAAAAAGAAATTGAAAGAAAACAAAA-AGAAAACGAAAAA-G-AAA
1 AGAAAACGAAAAAGAGAGAGAAAAAGAAAATG-AAGAAAACAAAATAGAAAAAGAAAAACGAAAA
120312 AAGAAATTGCTAAAGAAAA
65 AAGAAATTGCTAAAGAAAA
* * * *
120331 AGAAATCGAAAAAGTGAGAGAAAAAGAAAATGAAGAAAAGAAAATTGAAAAAGAAAAAGCGAAAA
1 AGAAAACGAAAAAGAGAGAGAAAAAGAAAATGAAGAAAACAAAATAGAAAAAGAAAAA-CGAAAA
120396 AAGAAATTG
65 AAGAAATTG
120405 AAAGAGAGCT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
80 11 0.18
81 37 0.61
83 1 0.02
84 12 0.20
ACGTcount: A:0.68, C:0.03, G:0.20, T:0.09
Consensus pattern (83 bp):
AGAAAACGAAAAAGAGAGAGAAAAAGAAAATGAAGAAAACAAAATAGAAAAAGAAAAACGAAAAA
AGAAATTGCTAAAGAAAA
Found at i:120371 original size:14 final size:13
Alignment explanation
Indices: 120350--120387 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
120340 AAAAGTGAGA
120350 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
120362 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
120377 GAAAAAGAAAA
1 GAAAAAGAAAA
120388 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:120401 original size:21 final size:21
Alignment explanation
Indices: 120351--120401 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
120341 AAAGTGAGAG
*
120351 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
120372 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
120393 AAAAAGAAA
1 AAAAAGAAA
120402 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:120441 original size:33 final size:33
Alignment explanation
Indices: 120404--120466 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
120394 AAAAGAAATT
120404 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
120437 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
120467 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:129674 original size:22 final size:22
Alignment explanation
Indices: 129623--129688 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 22
129613 GGTATTTGGG
* *
129623 AATTGGTTCGAAATAGTATGG-
1 AATTGGTACGAAATGGTATGGT
129644 AATTGGTACGAAATGGTATGGT
1 AATTGGTACGAAATGGTATGGT
* *
129666 ATTTGGTACGAATTGGTAATGGT
1 AATTGGTACGAAATGGT-ATGGT
129689 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:132191 original size:16 final size:16
Alignment explanation
Indices: 132170--132210 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
132160 ATGATCTTTA
132170 AGCTCCTTTTTTTAAC
1 AGCTCCTTTTTTTAAC
132186 AGCTCCTTTTTTTAAC
1 AGCTCCTTTTTTTAAC
*
132202 AGCCCCTTT
1 AGCTCCTTT
132211 AATTGTAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.17, C:0.29, G:0.07, T:0.46
Consensus pattern (16 bp):
AGCTCCTTTTTTTAAC
Found at i:132455 original size:20 final size:20
Alignment explanation
Indices: 132432--132485 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
132422 AGTTTTTCCC
*
132432 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
132452 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
132472 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
132486 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:132467 original size:30 final size:30
Alignment explanation
Indices: 132432--132505 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
132422 AGTTTTTCCC
132432 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
132462 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
132492 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
132506 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:132495 original size:20 final size:20
Alignment explanation
Indices: 132432--132496 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
132422 AGTTTTTCCC
* * * *
132432 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
132452 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
132471 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
132492 AGCTC
1 AGCTC
132497 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:134122 original size:10 final size:11
Alignment explanation
Indices: 134100--134135 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
134090 AAAAGAGAAG
134100 AAATTCAAAAA
1 AAATTCAAAAA
134111 AAATTCAAAAAA
1 AAATTC-AAAAA
*
134123 AAATTGAAAAA
1 AAATTCAAAAA
134134 AA
1 AA
134136 GGAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.75, C:0.06, G:0.03, T:0.17
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:134123 original size:12 final size:12
Alignment explanation
Indices: 134100--134135 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
134090 AAAAGAGAAG
134100 AAATTC-AAAAA
1 AAATTCAAAAAA
134111 AAATTCAAAAAA
1 AAATTCAAAAAA
*
134123 AAATTGAAAAAA
1 AAATTCAAAAAA
134135 A
1 A
134136 GGAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.75, C:0.06, G:0.03, T:0.17
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:135189 original size:18 final size:18
Alignment explanation
Indices: 135139--135192 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
135129 AAAGAGATTG
*
135139 AAAAAGAAATTGAAAGAAA
1 AAAAAGAAATCGAAA-AAA
*
135158 ACAAAA-AAAACGAAAAAA
1 A-AAAAGAAATCGAAAAAA
135176 AAAAAGAAATCGAAAAA
1 AAAAAGAAATCGAAAAA
135193 GTGAGAGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 4 0.13
18 14 0.47
19 8 0.27
20 4 0.13
ACGTcount: A:0.78, C:0.06, G:0.11, T:0.06
Consensus pattern (18 bp):
AAAAAGAAATCGAAAAAA
Found at i:135289 original size:33 final size:33
Alignment explanation
Indices: 135252--135314 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
135242 AAAAGAAATT
135252 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
135285 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
135315 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:137113 original size:20 final size:20
Alignment explanation
Indices: 137090--137143 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
137080 AGTTTTTCCC
*
137090 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
137110 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
137130 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
137144 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:137125 original size:30 final size:30
Alignment explanation
Indices: 137090--137163 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
137080 AGTTTTTCCC
137090 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
137120 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
137150 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
137164 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:137153 original size:20 final size:20
Alignment explanation
Indices: 137090--137154 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
137080 AGTTTTTCCC
* * * *
137090 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
137110 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
137129 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
137150 AGCTC
1 AGCTC
137155 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:138542 original size:22 final size:22
Alignment explanation
Indices: 138512--138555 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
138502 TTTGGTATTT
138512 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
138534 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
138556 TGGTTCAAAA
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:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:142854 original size:19 final size:19
Alignment explanation
Indices: 142830--142871 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
142820 TTCATTCTCT
*
142830 TTTTTTGAATTTTCTTTTC
1 TTTTTTCAATTTTCTTTTC
*
142849 TTTTTTCATTTTTCTTTTC
1 TTTTTTCAATTTTCTTTTC
142868 TTTT
1 TTTT
142872 GTATTTTCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.07, C:0.12, G:0.02, T:0.79
Consensus pattern (19 bp):
TTTTTTCAATTTTCTTTTC
Found at i:144196 original size:30 final size:29
Alignment explanation
Indices: 144097--144198 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 29
144087 CGAGTTTAAA
*
144097 CTAAAATGAGCTAA-GTTTAGCTCGTGAG
1 CTAAATTGAGCTAAGGTTTAGCTCGTGAG
* * * * * *
144125 CTAAAGTTGAGCTGAGGCTAAACTCCTAAG
1 CTAAA-TTGAGCTAAGGTTTAGCTCGTGAG
*
144155 CTGAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CT-AAATTGAGCTAAGGTTTAGCTCGTGAG
144185 CTAAATATGAGCTA
1 CTAAAT-TGAGCTA
144199 GGAGTGAGCT
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
28 5 0.09
29 10 0.18
30 38 0.69
31 2 0.04
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (29 bp):
CTAAATTGAGCTAAGGTTTAGCTCGTGAG
Found at i:146393 original size:12 final size:12
Alignment explanation
Indices: 146378--146408 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
146368 TTCTTTTTGC
146378 TTTTCAAAGGCT
1 TTTTCAAAGGCT
146390 TTTTCAAAGGCT
1 TTTTCAAAGGCT
146402 TTTTCAA
1 TTTTCAA
146409 GTTCTCTCAA
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:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:146491 original size:27 final size:25
Alignment explanation
Indices: 146456--146524 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 25
146446 CTCTTGCCTC
146456 TCTTTTCTTTTTATTTCATTTTCTTTT
1 TCTTTTCTTTTT-TTTCATTTTC-TTT
* *
146483 TCTTCTCTTGCTTTTTCATTTTCTTT
1 TCTTTTCTT-TTTTTTCATTTTCTTT
*
146509 TCTTTTCTTTGTTTTC
1 TCTTTTCTTTTTTTTC
146525 TCTTTACAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
25 5 0.14
26 11 0.31
27 18 0.50
28 2 0.06
ACGTcount: A:0.04, C:0.19, G:0.03, T:0.74
Consensus pattern (25 bp):
TCTTTTCTTTTTTTTCATTTTCTTT
Found at i:147437 original size:11 final size:12
Alignment explanation
Indices: 147406--147436 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
147396 TTGAGAGAAC
147406 TTGAAAAAGCCT
1 TTGAAAAAGCCT
147418 TTGAAAAAGCCT
1 TTGAAAAAGCCT
147430 TTGAAAA
1 TTGAAAA
147437 GAAAAAAGAA
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:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:148510 original size:22 final size:22
Alignment explanation
Indices: 148480--148523 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
148470 TTTGGTATTT
148480 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
148502 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
148524 TGGTTCAAAA
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:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:150361 original size:21 final size:23
Alignment explanation
Indices: 150316--150362 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
150306 TCACATCAAA
* *
150316 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
150339 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
150360 TAA
1 TAA
150363 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:154261 original size:4 final size:4
Alignment explanation
Indices: 154252--154282 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
154242 TTAAACTAAG
154252 TAAA TAAA TAAA TAAA TAAA TAAA -AAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
154283 AATAAAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:155393 original size:24 final size:23
Alignment explanation
Indices: 155339--155416 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
155329 GGATAATTAA
**
155339 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
155362 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
155386 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
155407 GAAATAGTAT
1 GAAATGGTAT
155417 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:155401 original size:21 final size:21
Alignment explanation
Indices: 155375--155441 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
155365 TTGGTATTTG
155375 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
155396 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
155417 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
155440 GG
1 GG
155442 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:161967 original size:14 final size:14
Alignment explanation
Indices: 161948--161998 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
161938 CGTATGCAAT
161948 TTTTTTTTTTCAAA
1 TTTTTTTTTTCAAA
161962 TTTTTTTTTTC-AA
1 TTTTTTTTTTCAAA
*
161975 -TTTTTTTTTCGAAC
1 TTTTTTTTTTC-AAA
161989 TTTTTTTTTT
1 TTTTTTTTTT
161999 TACGCACCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
12 10 0.30
13 2 0.06
14 12 0.36
15 9 0.27
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTTTTTTTTCAAA
Found at i:162315 original size:24 final size:23
Alignment explanation
Indices: 162261--162338 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
162251 GGATAATTAA
**
162261 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
162284 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
162308 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
162329 GAAATAGTAT
1 GAAATGGTAT
162339 GGTATTTGGT
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 18 0.42
22 1 0.02
23 9 0.21
24 15 0.35
ACGTcount: A:0.27, C:0.03, G:0.31, T:0.40
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:162323 original size:21 final size:21
Alignment explanation
Indices: 162297--162363 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
162287 TTGGTATTTG
162297 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
162318 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
162339 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
162362 GG
1 GG
162364 TTCAAAGAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 21 0.55
22 12 0.32
23 5 0.13
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.34
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:168417 original size:40 final size:39
Alignment explanation
Indices: 168330--168550 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
168320 TCCTCGTTCA
* * *
168330 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACT--CAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
168367 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
168406 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
168446 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
168486 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
168527 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
168551 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 20, Indels: 13
0.83 0.11 0.07
Matches are distributed among these distances:
37 30 0.19
39 8 0.05
40 106 0.68
41 12 0.08
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:168510 original size:80 final size:78
Alignment explanation
Indices: 168328--168550 Score: 238
Period size: 80 Copynumber: 2.8 Consensus size: 78
168318 GCTCCTCGTT
* * *
168328 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACT-CACAATGCCTTCGGGACTTAACCCGG-A
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTGCACAAAGCCTTCGGGACTTAACCCGGAA
168391 TTTAATAACTCGCA
65 TTTAATAACTCGCA
* * *
168405 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CT-GCACAAA-GCCTTCGGGACTTAACCCGG
* *
168470 AATTT-GTATCTCGCA
63 AATTTAATAACTCGCA
* * * *
168485 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-T-GCACAAAGCCTTCGGGACTTAACCCG
168549 GA
62 GA
168551 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
76 1 0.01
77 30 0.25
79 8 0.07
80 70 0.57
81 13 0.11
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTGCACAAAGCCTTCGGGACTTAACCCGGAAT
TTAATAACTCGCA
Found at i:168559 original size:41 final size:41
Alignment explanation
Indices: 168482--168559 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
168472 TTTGTATCTC
* * *
168482 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
168523 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
168560 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Done.