Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1177
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: 42623
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3114 original size:15 final size:15
Alignment explanation
Indices: 3094--3123 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3084 AGACCGTATA
3094 CAATTTTTTTCATTT
1 CAATTTTTTTCATTT
*
3109 CAATTTTTTTGATTT
1 CAATTTTTTTCATTT
3124 TTTTTTCGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.10, G:0.03, T:0.67
Consensus pattern (15 bp):
CAATTTTTTTCATTT
Found at i:3127 original size:12 final size:13
Alignment explanation
Indices: 3097--3143 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
3087 CCGTATACAA
*
3097 TTTTTTTCATTTC
1 TTTTTTTGATTTC
3110 AATTTTTTTGATTT-
1 --TTTTTTTGATTTC
*
3124 TTTTTTCGATTTC
1 TTTTTTTGATTTC
3137 TTTTTTT
1 TTTTTTT
3144 TTCAAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 11 0.39
13 6 0.21
15 11 0.39
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.77
Consensus pattern (13 bp):
TTTTTTTGATTTC
Found at i:3153 original size:27 final size:26
Alignment explanation
Indices: 3095--3158 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
3085 GACCGTATAC
*
3095 AATTTTTTTCATTTCAATTTTTTTGA
1 AATTTTTTTCATTTCAATTTTTTTCA
** **
3121 TTTTTTTTTCGATTTCTTTTTTTTTCA
1 AATTTTTTTC-ATTTCAATTTTTTTCA
3148 AATTTTTTTCA
1 AATTTTTTTCA
3159 CGAATCTACT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
26 9 0.30
27 21 0.70
ACGTcount: A:0.17, C:0.09, G:0.03, T:0.70
Consensus pattern (26 bp):
AATTTTTTTCATTTCAATTTTTTTCA
Found at i:9696 original size:24 final size:25
Alignment explanation
Indices: 9643--9696 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
9633 AACAAATTCT
* *
9643 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
9668 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
9691 TTTTTT
1 TTTTTT
9697 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:11969 original size:13 final size:13
Alignment explanation
Indices: 11950--12023 Score: 75
Period size: 13 Copynumber: 5.8 Consensus size: 13
11940 CGTATGCAAT
11950 TTTTTTTTTGCAAA
1 TTTTTTTTT-CAAA
11964 TTTTTTTTTC---
1 TTTTTTTTTCAAA
*
11974 TTTTTTTTTCAGA
1 TTTTTTTTTCAAA
11987 TTTTTTTTTCGAAA
1 TTTTTTTTTC-AAA
*
12001 CTTTTTTTTT-AAC
1 -TTTTTTTTTCAAA
12014 TTTTTTTTTC
1 TTTTTTTTTC
12024 GAAGCTACGA
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
10 10 0.19
12 9 0.17
13 13 0.25
14 11 0.21
15 9 0.17
ACGTcount: A:0.14, C:0.09, G:0.04, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTCAAA
Found at i:11981 original size:23 final size:23
Alignment explanation
Indices: 11951--11996 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
11941 GTATGCAATT
11951 TTTTTTTTGCAAATTTTTTTTTC
1 TTTTTTTTGCAAATTTTTTTTTC
* *
11974 TTTTTTTTTCAGATTTTTTTTTC
1 TTTTTTTTGCAAATTTTTTTTTC
11997 GAAACTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.09, G:0.04, T:0.76
Consensus pattern (23 bp):
TTTTTTTTGCAAATTTTTTTTTC
Found at i:12005 original size:27 final size:27
Alignment explanation
Indices: 11975--12026 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
11965 TTTTTTTTCT
11975 TTTTTTTTCAGA-TTTTTTTTTCGAAAC
1 TTTTTTTTCA-ACTTTTTTTTTCGAAAC
*
12002 TTTTTTTTTAACTTTTTTTTTCGAA
1 TTTTTTTTCAACTTTTTTTTTCGAA
12027 GCTACGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.17, C:0.10, G:0.06, T:0.67
Consensus pattern (27 bp):
TTTTTTTTCAACTTTTTTTTTCGAAAC
Found at i:12014 original size:12 final size:13
Alignment explanation
Indices: 11950--12023 Score: 68
Period size: 12 Copynumber: 5.8 Consensus size: 13
11940 CGTATGCAAT
*
11950 TTTTTTTTTGCAAA
1 TTTTTTTTT-CAAC
11964 TTTTTTTTT---C
1 TTTTTTTTTCAAC
11974 TTTTTTTTTCAGA-
1 TTTTTTTTTCA-AC
11987 TTTTTTTTTCGAAAC
1 TTTTTTTTTC--AAC
12002 TTTTTTTTT-AAC
1 TTTTTTTTTCAAC
12014 TTTTTTTTTC
1 TTTTTTTTTC
12024 GAAGCTACGA
Statistics
Matches: 51, Mismatches: 1, Indels: 17
0.74 0.01 0.25
Matches are distributed among these distances:
10 9 0.18
12 12 0.24
13 10 0.20
14 10 0.20
15 10 0.20
ACGTcount: A:0.14, C:0.09, G:0.04, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTCAAC
Found at i:14439 original size:20 final size:20
Alignment explanation
Indices: 14393--14439 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
14383 AGCTCGTTTC
*
14393 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
14413 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
14433 CAGCTCA
1 CAGCTCA
14440 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:15055 original size:24 final size:23
Alignment explanation
Indices: 15001--15078 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
14991 GGATAATTAA
**
15001 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
15024 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
15048 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
15069 GAAATAGTAT
1 GAAATGGTAT
15079 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:15063 original size:21 final size:21
Alignment explanation
Indices: 15037--15103 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
15027 TTGGTATTTG
15037 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
15058 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
15079 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
15102 GG
1 GG
15104 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:19370 original size:17 final size:17
Alignment explanation
Indices: 19345--19399 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
19335 TCTCTTTTCA
*
19345 TTCTCTTTTTTTGAATT
1 TTCTTTTTTTTTGAATT
* *
19362 TTCTTTTTTTTATCATTT
1 TTCTTTTTTTT-TGAATT
* *
19380 TTCTTTTCTTTTGTATT
1 TTCTTTTTTTTTGAATT
19397 TTC
1 TTC
19400 GTCTTTTCTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 16 0.53
18 14 0.47
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.75
Consensus pattern (17 bp):
TTCTTTTTTTTTGAATT
Found at i:19397 original size:18 final size:19
Alignment explanation
Indices: 19360--19411 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
19350 TTTTTTTGAA
19360 TTTTCTTTT-TTTTATCAT
1 TTTTCTTTTCTTTTATCAT
*
19378 TTTTCTTTTCTTTTGT-AT
1 TTTTCTTTTCTTTTATCAT
19396 TTTCGTCTTTTCTTTT
1 TTT--TCTTTTCTTTT
19412 TCTCTCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 14 0.47
19 5 0.17
20 11 0.37
ACGTcount: A:0.06, C:0.13, G:0.04, T:0.77
Consensus pattern (19 bp):
TTTTCTTTTCTTTTATCAT
Found at i:21603 original size:14 final size:14
Alignment explanation
Indices: 21584--21635 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
21574 AAACCGTATG
21584 CAATTTTTTTTTTT
1 CAATTTTTTTTTTT
21598 CAA--TTTTTTTTT
1 CAATTTTTTTTTTT
21610 CAATTTTTTTTTTT
1 CAATTTTTTTTTTT
*
21624 GAACTTTTTTTT
1 CAA-TTTTTTTT
21636 ACGCACCTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
12 12 0.35
14 14 0.41
15 8 0.24
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (14 bp):
CAATTTTTTTTTTT
Found at i:21606 original size:12 final size:12
Alignment explanation
Indices: 21589--21621 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
21579 GTATGCAATT
21589 TTTTTTTTTCAA
1 TTTTTTTTTCAA
21601 TTTTTTTTTCAA
1 TTTTTTTTTCAA
21613 TTTTTTTTT
1 TTTTTTTTT
21622 TTGAACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:21613 original size:26 final size:26
Alignment explanation
Indices: 21584--21635 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
21574 AAACCGTATG
*
21584 CAATTTTTTTTTTTCAATTTTTTTTT
1 CAATTTTTTTTTTTCAACTTTTTTTT
*
21610 CAATTTTTTTTTTTGAACTTTTTTTT
1 CAATTTTTTTTTTTCAACTTTTTTTT
21636 ACGCACCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (26 bp):
CAATTTTTTTTTTTCAACTTTTTTTT
Found at i:21952 original size:24 final size:23
Alignment explanation
Indices: 21898--21975 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 23
21888 GGATAATTAA
**
21898 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
21921 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
*
21945 GAAATGGTA--TGGAATTGGTAT
1 GAAATGGTATTTGGAATTGGTAC
*
21966 GAAATAGTAT
1 GAAATGGTAT
21976 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:21960 original size:21 final size:21
Alignment explanation
Indices: 21934--22000 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
21924 TTGGTATTTG
21934 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
21955 GGAATTGGTATGAAATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
21976 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
21999 GG
1 GG
22001 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:24576 original size:13 final size:13
Alignment explanation
Indices: 24558--24617 Score: 61
Period size: 13 Copynumber: 4.5 Consensus size: 13
24548 TTGGAGTAAC
24558 AAAAAAAAA-TC-
1 AAAAAAAAATTCA
24569 AAAAAAAAATTCGA
1 AAAAAAAAATTC-A
* *
24583 AAAAAAATTGATTGA
1 AAAAAAA--AATTCA
24598 AAAAAAAAATTCA
1 AAAAAAAAATTCA
24611 AAAAAAA
1 AAAAAAA
24618 GTGAAAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 9 0.22
12 2 0.05
13 11 0.28
14 7 0.17
15 8 0.20
16 3 0.08
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (13 bp):
AAAAAAAAATTCA
Found at i:24625 original size:12 final size:12
Alignment explanation
Indices: 24558--24628 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 12
24548 TTGGAGTAAC
*
24558 AAAAAAAAA-TC
1 AAAAAAAAATTG
24569 AAAAAAAAATTCG
1 AAAAAAAAATT-G
24582 AAAAAAAATTGATTG
1 AAAAAAAA---ATTG
24597 AAAAAAAAAATT-
1 -AAAAAAAAATTG
* *
24609 CAAAAAAAAGTG
1 AAAAAAAAATTG
24621 AAAAAAAA
1 AAAAAAAA
24629 TCGAGCAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
11 18 0.37
12 8 0.16
13 11 0.22
15 1 0.02
16 11 0.22
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:24640 original size:39 final size:40
Alignment explanation
Indices: 24558--24643 Score: 106
Period size: 39 Copynumber: 2.2 Consensus size: 40
24548 TTGGAGTAAC
* *
24558 AAAAAAAAATCAAAAAAAAATTCGAAAAAAAATTGATTG-AA
1 AAAAAAAAATCAAAAAAAAAGTCGAAAAAAAATCGA--GCAA
*
24599 AAAAAAAATTC-AAAAAAAAGT-GAAAAAAAATCGAGCAA
1 AAAAAAAAATCAAAAAAAAAGTCGAAAAAAAATCGAGCAA
24637 AAAAAAA
1 AAAAAAA
24644 GGTGAGCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
37 1 0.02
38 9 0.22
39 12 0.29
40 9 0.22
41 10 0.24
ACGTcount: A:0.73, C:0.06, G:0.08, T:0.13
Consensus pattern (40 bp):
AAAAAAAAATCAAAAAAAAAGTCGAAAAAAAATCGAGCAA
Found at i:24642 original size:16 final size:16
Alignment explanation
Indices: 24621--24658 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
24611 AAAAAAAGTG
24621 AAAAAAA-ATCGAGCAA
1 AAAAAAAGAT-GAGCAA
*
24637 AAAAAAAGGTGAGCAA
1 AAAAAAAGATGAGCAA
24653 AAAAAA
1 AAAAAA
24659 TCAAGTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.71, C:0.08, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAAAAAGATGAGCAA
Found at i:25725 original size:6 final size:6
Alignment explanation
Indices: 25692--25799 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
25682 AAAGAAATTG
* * * ** *
25692 AAAG-A AAACAA AAAGAA AACGAA GAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
25739 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
25790 AAAGAA AAAG
1 AAAGAA AAAG
25800 CGAAAAAAGA
Statistics
Matches: 73, Mismatches: 26, Indels: 7
0.69 0.25 0.07
Matches are distributed among these distances:
5 3 0.04
6 59 0.81
7 7 0.10
8 4 0.05
ACGTcount: A:0.70, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:25753 original size:18 final size:18
Alignment explanation
Indices: 25696--25754 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
25686 AAATTGAAAG
* *
25696 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAATCGA
* * *
25714 AGAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAATCGA
25732 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAATCGA
25750 AAAAG
1 AAAAG
25755 TGAGAGAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.71, C:0.07, G:0.17, T:0.05
Consensus pattern (18 bp):
AAAAGAAAAAGAAATCGA
Found at i:25781 original size:14 final size:13
Alignment explanation
Indices: 25760--25797 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
25750 AAAAGTGAGA
25760 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
25772 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
25787 GAAAAAGAAAA
1 GAAAAAGAAAA
25798 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:25811 original size:21 final size:21
Alignment explanation
Indices: 25761--25811 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
25751 AAAGTGAGAG
*
25761 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
25782 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
25803 AAAAAGAAA
1 AAAAAGAAA
25812 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:25815 original size:27 final size:27
Alignment explanation
Indices: 25713--25817 Score: 77
Period size: 27 Copynumber: 3.8 Consensus size: 27
25703 AAAGAAAACG
* *
25713 AAGAAGAAAAAGAAATTGCAAAAGAAA
1 AAGAAGAAAAAAAAATTGAAAAAGAAA
*** **
25740 AAGAAATCGAAAAAGTGAGAGAAAAAGAAA
1 AAG-AA--GAAAAAAAAATTGAAAAAGAAA
* *
25770 ATGAAGAAAAGAAAATTGAAAAAGAAA
1 AAGAAGAAAAAAAAATTGAAAAAGAAA
*
25797 AAG-CGAAAAAAGAAATTGAAA
1 AAGAAGAAAAAA-AAATTGAAA
25818 GAGAGCTTGA
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
26 6 0.10
27 30 0.51
28 2 0.03
29 2 0.03
30 19 0.32
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.09
Consensus pattern (27 bp):
AAGAAGAAAAAAAAATTGAAAAAGAAA
Found at i:25959 original size:48 final size:47
Alignment explanation
Indices: 25880--25985 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
25870 GAGTGTCATG
*
25880 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
25928 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
25976 GAAAAAGAAA
1 GAAAAAGAAA
25986 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:29281 original size:20 final size:20
Alignment explanation
Indices: 29235--29281 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
29225 AGCTCGTTTC
*
29235 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
29255 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
29275 CAGCTCA
1 CAGCTCA
29282 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:35659 original size:19 final size:19
Alignment explanation
Indices: 35635--35672 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
35625 TAAGCATGTG
35635 TGGA-CTTCTTGATTGGGCT
1 TGGACCTTCTT-ATTGGGCT
35654 TGGACTCTTCTTATTGGGC
1 TGGAC-CTTCTTATTGGGC
35673 CTTGCCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 7 0.41
21 6 0.35
ACGTcount: A:0.11, C:0.18, G:0.29, T:0.42
Consensus pattern (19 bp):
TGGACCTTCTTATTGGGCT
Found at i:39344 original size:20 final size:20
Alignment explanation
Indices: 39321--39374 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
39311 AGTTTTTCCC
*
39321 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
39341 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
39361 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
39375 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:39356 original size:30 final size:30
Alignment explanation
Indices: 39321--39394 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
39311 AGTTTTTCCC
39321 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
39351 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
39381 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
39395 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:39384 original size:20 final size:20
Alignment explanation
Indices: 39321--39385 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
39311 AGTTTTTCCC
* * * *
39321 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
39341 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
39360 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
39381 AGCTC
1 AGCTC
39386 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:41956 original size:17 final size:18
Alignment explanation
Indices: 41924--41958 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
41914 AAGTATGAAC
41924 GAATTTCTTGATTGGGCT
1 GAATTTCTTGATTGGGCT
*
41942 GAATTTGTT-ATTGGGCT
1 GAATTTCTTGATTGGGCT
41959 CGCCTTCGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.09, G:0.29, T:0.46
Consensus pattern (18 bp):
GAATTTCTTGATTGGGCT
Done.