Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1144
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: 149701
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1956 original size:13 final size:12
Alignment explanation
Indices: 1923--1953 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1913 ACGAGATTGT
1923 AAAAAAATTCGA
1 AAAAAAATTCGA
1935 AAAAAAATTCGA
1 AAAAAAATTCGA
1947 AAAAAAA
1 AAAAAAA
1954 ATTATTTTTG
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:0.74, C:0.06, G:0.06, T:0.13
Consensus pattern (12 bp):
AAAAAAATTCGA
Found at i:4039 original size:15 final size:14
Alignment explanation
Indices: 4003--4047 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
3993 TCTATTGAGC
4003 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
4017 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
4031 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
4046 GA
1 GA
4048 AAGAAACGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:4053 original size:15 final size:15
Alignment explanation
Indices: 4003--4053 Score: 61
Period size: 14 Copynumber: 3.5 Consensus size: 15
3993 TCTATTGAGC
4003 GAGA-AAAAGAAAAA
1 GAGAGAAAAGAAAAA
*
4017 GAGA-AAAACAAAAA
1 GAGAGAAAAGAAAAA
*
4031 GAGTGAAAAGAAAAA
1 GAGAGAAAAGAAAAA
*
4046 GAAAGAAA
1 GAGAGAAA
4054 CGAATGATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
14 16 0.52
15 15 0.48
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (15 bp):
GAGAGAAAAGAAAAA
Found at i:8541 original size:14 final size:14
Alignment explanation
Indices: 8517--8569 Score: 99
Period size: 14 Copynumber: 3.9 Consensus size: 14
8507 GGATATCAAG
8517 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
8531 TT-TGAAAAAAAAA
1 TTGTGAAAAAAAAA
8544 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
8558 TTGTGAAAAAAA
1 TTGTGAAAAAAA
8570 CAGAGAGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.34
14 25 0.66
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:8547 original size:27 final size:28
Alignment explanation
Indices: 8517--8569 Score: 99
Period size: 27 Copynumber: 1.9 Consensus size: 28
8507 GGATATCAAG
8517 TTGTGAAAAAAAAATT-TGAAAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAAAA
8544 TTGTGAAAAAAAAATTGTGAAAAAAA
1 TTGTGAAAAAAAAATTGTGAAAAAAA
8570 CAGAGAGCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (28 bp):
TTGTGAAAAAAAAATTGTGAAAAAAAAA
Found at i:13317 original size:45 final size:45
Alignment explanation
Indices: 13268--13500 Score: 412
Period size: 45 Copynumber: 5.2 Consensus size: 45
13258 TCGGCCATGG
* * * *
13268 TGCTTCCTCAATTTATTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
13313 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
13358 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
13403 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
13448 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
13493 TGCTTCCT
1 TGCTTCCT
13501 TAATTTCATG
Statistics
Matches: 181, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 181 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:31785 original size:18 final size:18
Alignment explanation
Indices: 31745--31788 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
31735 TTTCAATCAC
31745 TTTTTTTTGTAATTCTGAA
1 TTTTTTTTGTAATTCTG-A
31764 TTTTTTTT-TAATTTCT-A
1 TTTTTTTTGTAA-TTCTGA
31781 TTTTTTTT
1 TTTTTTTT
31789 AATACCGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.38
18 3 0.12
19 12 0.50
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTTTTTTGTAATTCTGA
Found at i:32606 original size:45 final size:45
Alignment explanation
Indices: 32557--32845 Score: 400
Period size: 45 Copynumber: 6.2 Consensus size: 45
32547 TCGGCCATGG
* * * *
32557 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
32602 TGCTTCCTTAAATTCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCC----A--------TGAATTATGCATGATGTTGGTCAAA
32659 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* *
32704 TGCTTCCTTAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
32749 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
32794 TGCTTCCTCAAATTC-TCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
32838 TGCTTCCT
1 TGCTTCCT
32846 TAATTTCATG
Statistics
Matches: 222, Mismatches: 10, Indels: 25
0.86 0.04 0.10
Matches are distributed among these distances:
44 37 0.17
45 142 0.64
49 1 0.00
53 1 0.00
57 41 0.18
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:32619 original size:12 final size:12
Alignment explanation
Indices: 32599--32632 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
32589 GATGTTGGCC
*
32599 AAATGCTTCCTT
1 AAATTCTTCCTT
32611 AAATTCTTCCTT
1 AAATTCTTCCTT
32623 AAATTCTTCC
1 AAATTCTTCC
32633 ATGAATTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.44
Consensus pattern (12 bp):
AAATTCTTCCTT
Found at i:38708 original size:17 final size:18
Alignment explanation
Indices: 38671--38708 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
38661 GATTGAGAGT
* *
38671 GAAAAGGAATGTGAAACA
1 GAAAAGAAATGTGAAAAA
38689 GAAAAGAAAT-TGAAAAA
1 GAAAAGAAATGTGAAAAA
38706 GAA
1 GAA
38709 GTTGAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.63, C:0.03, G:0.24, T:0.11
Consensus pattern (18 bp):
GAAAAGAAATGTGAAAAA
Found at i:38721 original size:13 final size:12
Alignment explanation
Indices: 38690--38744 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
38680 TGTGAAACAG
*
38690 AAAAGAAATTGA
1 AAAAGAAGTTGA
38702 AAAAGAAGTTGA
1 AAAAGAAGTTGA
*
38714 AGAAAGAAG-AGA
1 A-AAAGAAGTTGA
*
38726 AAATG-AGTTAGA
1 AAAAGAAGTT-GA
38738 AAAAGAA
1 AAAAGAA
38745 ACAAAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
10 2 0.06
11 3 0.09
12 21 0.62
13 8 0.24
ACGTcount: A:0.64, C:0.00, G:0.24, T:0.13
Consensus pattern (12 bp):
AAAAGAAGTTGA
Found at i:41600 original size:22 final size:22
Alignment explanation
Indices: 41572--41615 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41562 TTTTGAACCA
41572 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
41594 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
41616 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:42745 original size:19 final size:19
Alignment explanation
Indices: 42720--42772 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
42710 CAAATGAGAG
42720 AAAAAGAAAAGAGAAAAT-A
1 AAAAAGAAAAGA-AAAATGA
*
42739 CAAAAGAAAAGAAAAATGA
1 AAAAAGAAAAGAAAAATGA
42758 AAAAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
42773 TTCAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.16
19 26 0.84
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (19 bp):
AAAAAGAAAAGAAAAATGA
Found at i:42750 original size:24 final size:24
Alignment explanation
Indices: 42721--42772 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
42711 AAATGAGAGA
*
42721 AAAAGAAAAGA-GAAAATACAAAAG
1 AAAAGAAAA-ATGAAAAAACAAAAG
*
42745 AAAAGAAAAATGAAAAAAGAAAAG
1 AAAAGAAAAATGAAAAAACAAAAG
42769 AAAA
1 AAAA
42773 TTCAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.04
Consensus pattern (24 bp):
AAAAGAAAAATGAAAAAACAAAAG
Found at i:47072 original size:22 final size:22
Alignment explanation
Indices: 47044--47087 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
47034 TTTTGAACCA
47044 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
47066 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
47088 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:48378 original size:19 final size:20
Alignment explanation
Indices: 48354--48398 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
48344 CTTTTCATTC
*
48354 TCTTTTTTTGAATTTTC-TT
1 TCTTTTTTTCAATTTTCTTT
*
48373 TCTTTTTTTCATTTTTCTTT
1 TCTTTTTTTCAATTTTCTTT
48393 TCTTTT
1 TCTTTT
48399 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:48426 original size:15 final size:15
Alignment explanation
Indices: 48378--48429 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
48368 TTCTTTCTTT
*
48378 TTTTCATTTTTCTTTTC
1 TTTTC-TTTTTC-TCTC
* *
48395 TTTTGTATTTTCGCTC
1 TTTTCT-TTTTCTCTC
48411 TTTTCTTTTTCTCTC
1 TTTTCTTTTTCTCTC
48426 TTTT
1 TTTT
48430 GATCTACAGA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 12 0.41
16 8 0.28
17 9 0.31
ACGTcount: A:0.04, C:0.19, G:0.04, T:0.73
Consensus pattern (15 bp):
TTTTCTTTTTCTCTC
Found at i:49061 original size:22 final size:22
Alignment explanation
Indices: 49031--49074 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
49021 TTTGGTATTT
49031 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
49053 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
49075 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:51046 original size:21 final size:23
Alignment explanation
Indices: 51001--51047 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
50991 TCACCTGCAA
* *
51001 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
51024 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
51045 TAA
1 TAA
51048 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:51866 original size:102 final size:102
Alignment explanation
Indices: 51685--51907 Score: 401
Period size: 102 Copynumber: 2.2 Consensus size: 102
51675 TGTCACCTTT
*
51685 AACTCTCCTCCATCGTTGAGCCATTGAAGTTTGTACGGAGTTGGATGCTTGGTGGTTGGTAGATT
1 AACT-TCCTCCATCGATGAGCCATTGAAGTTTGTACGGAGTTGGATGCTTGGTGGTTGGTAGATT
*
51750 TAATTTTTCCACCATGAGAGTGCTCGCTACGTTCGTAC
65 TAATTTTTCCACCATGAGAGTGCTCGCTACGTTCCTAC
51788 AACTTCCTCCATCGATGAGCCATTGAAGTTTGTACGGAGTTGGATGCTTGGTGGTTGGTAGATTT
1 AACTTCCTCCATCGATGAGCCATTGAAGTTTGTACGGAGTTGGATGCTTGGTGGTTGGTAGATTT
51853 AATTTTTCCACCATGAGAGTGCTCGCTACGTTCCTAC
66 AATTTTTCCACCATGAGAGTGCTCGCTACGTTCCTAC
* *
51890 AGCTTCCTCTATCGATGA
1 AACTTCCTCCATCGATGA
51908 TGACACTACA
Statistics
Matches: 116, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
102 112 0.97
103 4 0.03
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (102 bp):
AACTTCCTCCATCGATGAGCCATTGAAGTTTGTACGGAGTTGGATGCTTGGTGGTTGGTAGATTT
AATTTTTCCACCATGAGAGTGCTCGCTACGTTCCTAC
Found at i:55522 original size:40 final size:40
Alignment explanation
Indices: 55492--55741 Score: 394
Period size: 40 Copynumber: 6.3 Consensus size: 40
55482 GGACTAAGAT
* * * **
55492 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
55532 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
55572 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
55612 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
55652 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
* ** * * *
55692 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
55731 CCGAAGGCATT
1 CCGAAGGCATT
55742 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 11, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
39 33 0.17
40 166 0.83
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
Found at i:55652 original size:120 final size:119
Alignment explanation
Indices: 55439--55741 Score: 401
Period size: 120 Copynumber: 2.5 Consensus size: 119
55429 TTGAATGCTG
* * * * * * * * *
55439 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAAACCGGGCTAAG-TCCCGAAGGCATT
*
55503 TGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
64 CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
** * *
55559 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
* **
55624 GTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
65 GTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
* *
55679 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
55742 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
119 34 0.21
120 123 0.76
121 4 0.02
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
Found at i:63479 original size:40 final size:40
Alignment explanation
Indices: 63449--63691 Score: 313
Period size: 40 Copynumber: 6.3 Consensus size: 40
63439 GGACTAAGAT
* *
63449 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* **
63489 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* **
63529 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
63569 CCGAAGGCATTCGTGC--GAT--TAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
63605 CCGAAGGCATTCGTGCGAG-T--TAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
63642 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
63681 CCGAAGGCATT
1 CCGAAGGCATT
63692 TGAACGAGGA
Statistics
Matches: 188, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
36 39 0.21
37 30 0.16
38 3 0.02
39 25 0.13
40 91 0.48
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:63533 original size:80 final size:76
Alignment explanation
Indices: 63449--63691 Score: 323
Period size: 76 Copynumber: 3.1 Consensus size: 76
63439 GGACTAAGAT
* *
63449 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAG-T--TAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTA
63514 AATCCGGGTTAAGTC
62 AATCCGGGTTAAGTC
63529 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGA---TTAA
1 CCGAAGGCATTCGTGCGA---GTTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAA
63591 ATCCGGGTTAAGTC
63 ATCCGGGTTAAGTC
* * *
63605 CCGAAGGCATTCGTGCGAGTTAAATCCGGGTTAAGTCCCGAAGGCATT-GTGTGAGTTACTAAAA
1 CCGAAGGCATTCGTGCGAGTTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAT
* *
63669 CCGGGCTATGTC
65 CCGGGTTAAGTC
63681 CCGAAGGCATT
1 CCGAAGGCATT
63692 TGAACGAGGA
Statistics
Matches: 149, Mismatches: 7, Indels: 18
0.86 0.04 0.10
Matches are distributed among these distances:
72 5 0.03
73 30 0.20
76 61 0.41
80 51 0.34
82 1 0.01
83 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (76 bp):
CCGAAGGCATTCGTGCGAGTTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAATC
CGGGTTAAGTC
Found at i:63673 original size:76 final size:76
Alignment explanation
Indices: 63396--63691 Score: 325
Period size: 80 Copynumber: 3.8 Consensus size: 76
63386 TTGAATGCTG
* * * * * * *
63396 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCCT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGT-TATAAATCCGGGCTAAG-TCCCGAAGGCAT
*
63459 TTGTGCGAGATACTAAA
63 TCGTGCGAG-T--TAAA
* *
63476 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-ATAAATCCGGGCTAAGTCCCGAAGGCATTC
63541 GTGCGAGTTGTTAAA
65 GTGCGA---GTTAAA
*
63556 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGA--T-TAAATCCGGGTTAAGTCCCGAAGGCATTCG
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATAAATCCGGGCTAAGTCCCGAAGGCATTCG
63618 TGCGAGTTAAA
66 TGCGAGTTAAA
* * *
63629 TCCGGGTTAAGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTA-TAAATCCGGGCTAAGTCCCGAAGGCATT
63692 TGAACGAGGA
Statistics
Matches: 192, Mismatches: 14, Indels: 24
0.83 0.06 0.10
Matches are distributed among these distances:
72 5 0.03
73 30 0.16
74 1 0.01
76 60 0.31
78 1 0.01
79 1 0.01
80 86 0.45
81 6 0.03
82 1 0.01
83 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (76 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATAAATCCGGGCTAAGTCCCGAAGGCATTCG
TGCGAGTTAAA
Found at i:65249 original size:12 final size:12
Alignment explanation
Indices: 65232--65271 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
65222 TTGTAGATTC
65232 AAAAAAATCAAA
1 AAAAAAATCAAA
*
65244 AAAAAAATC-GA
1 AAAAAAATCAAA
65255 AAAAAAATCGAAA
1 AAAAAAATC-AAA
65268 AAAA
1 AAAA
65272 TATTTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.42
12 9 0.38
13 5 0.21
ACGTcount: A:0.80, C:0.07, G:0.05, T:0.07
Consensus pattern (12 bp):
AAAAAAATCAAA
Found at i:67844 original size:20 final size:21
Alignment explanation
Indices: 67821--67867 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
67811 GGGTTAAGAT
67821 TGAGCTGAA-TTGAGCTCGAA-
1 TGAGCTGAACTTGAGCTC-AAG
67841 TGAGCT-AACTTGAGCTCAAG
1 TGAGCTGAACTTGAGCTCAAG
67861 TGAGCTG
1 TGAGCTG
67868 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (21 bp):
TGAGCTGAACTTGAGCTCAAG
Found at i:68859 original size:18 final size:18
Alignment explanation
Indices: 68836--68871 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
68826 TTTCATTCTC
*
68836 TTTTTTGAATTTTCTTTT
1 TTTTTTCAATTTTCTTTT
*
68854 TTTTTTCATTTTTCTTTT
1 TTTTTTCAATTTTCTTTT
68872 CTTTGTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.81
Consensus pattern (18 bp):
TTTTTTCAATTTTCTTTT
Found at i:71116 original size:15 final size:13
Alignment explanation
Indices: 71083--71107 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71073 ATCGTATGCA
71083 TTTTTTTTTCAAT
1 TTTTTTTTTCAAT
71096 TTTTTTTTTCAA
1 TTTTTTTTTCAA
71108 AATTTTTTTA
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTCAAT
Found at i:71355 original size:14 final size:14
Alignment explanation
Indices: 71336--71369 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
71326 TTTAAGTCGA
71336 AATGGTATGACTAG
1 AATGGTATGACTAG
71350 AATGGTATGACTAG
1 AATGGTATGACTAG
71364 AATGGT
1 AATGGT
71370 CGAGTCCGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (14 bp):
AATGGTATGACTAG
Found at i:71404 original size:14 final size:13
Alignment explanation
Indices: 71385--71440 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
71375 CCGTGCAAAC
71385 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
*
71398 TTTTTTTTCGAAT
1 TTTTTTTTTGAAT
* * *
71411 TTTTCTTTTCAAG
1 TTTTTTTTTGAAT
71424 TTTTTTTTT--AT
1 TTTTTTTTTGAAT
71435 TTTTTT
1 TTTTTT
71441 ACTATACCGT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
11 7 0.19
13 29 0.81
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:76816 original size:12 final size:12
Alignment explanation
Indices: 76801--76832 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
76791 ATTTTTATTT
76801 TTATTTATTTAC
1 TTATTTATTTAC
76813 TTATTTATTTAC
1 TTATTTATTTAC
76825 TTAGTTTA
1 TTA-TTTA
76833 ATTTTTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.25, C:0.06, G:0.03, T:0.66
Consensus pattern (12 bp):
TTATTTATTTAC
Found at i:84363 original size:18 final size:19
Alignment explanation
Indices: 84339--84380 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
84329 ATCTTATAAT
84339 GAAAAGA-AATTGAAAAAGA
1 GAAAAGAGAA-TGAAAAAGA
84358 -AAAAGAGAATGAAAAAGA
1 GAAAAGAGAATGAAAAAGA
84376 GAAAA
1 GAAAA
84381 AAGAGATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.07
Consensus pattern (19 bp):
GAAAAGAGAATGAAAAAGA
Found at i:84378 original size:20 final size:20
Alignment explanation
Indices: 84351--84392 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
84341 AAAGAAATTG
84351 AAAAAG-AAAAAGAGAATGA
1 AAAAAGAAAAAAGAGAATGA
*
84370 AAAAGAGAAAAAAGAGATTGA
1 AAAA-AGAAAAAAGAGAATGA
84391 AA
1 AA
84393 GTGAAATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 2 0.10
21 14 0.70
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.07
Consensus pattern (20 bp):
AAAAAGAAAAAAGAGAATGA
Found at i:87617 original size:22 final size:22
Alignment explanation
Indices: 87587--87630 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
87577 TTTGGTATTT
*
87587 GGGAATTGGTACGAATTGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
87609 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
87631 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:0.32, C:0.05, G:0.36, T:0.27
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:90929 original size:30 final size:30
Alignment explanation
Indices: 90871--90929 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
90861 TTGAAAATGT
* *
90871 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
90901 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
90930 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:94483 original size:22 final size:22
Alignment explanation
Indices: 94452--94513 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
94442 ACCTTTTTGA
*
94452 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
*
94475 ACCATACCATTTCGTACCAACT
1 ACCATACCATTTCGTACCAAAT
*
94497 TCCATACCATTTCGTAC
1 ACCATACCATTTCGTAC
94514 TAATTCCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 32 0.89
23 4 0.11
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:96745 original size:18 final size:17
Alignment explanation
Indices: 96667--96762 Score: 77
Period size: 18 Copynumber: 5.4 Consensus size: 17
96657 TATCATATCA
*
96667 CTCATTTCTTTTGCACT
1 CTCATTTCTTTTTCACT
*
96684 CTCATTTCTTTCTTCATT
1 CTCATTTCTTT-TTCACT
* *
96702 CTCAATCTCTTTTTCAGTT
1 CTC-ATTTCTTTTTCA-CT
* *
96721 CTCTTTTCTTTTTCACA
1 CTCATTTCTTTTTCACT
*
96738 CTCATTT-TTATTCTCAAT
1 CTCATTTCTT-TT-TCACT
96756 CTCATTT
1 CTCATTT
96763 TCAATTTTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
16 2 0.03
17 19 0.30
18 31 0.48
19 12 0.19
ACGTcount: A:0.15, C:0.27, G:0.02, T:0.56
Consensus pattern (17 bp):
CTCATTTCTTTTTCACT
Found at i:96754 original size:48 final size:48
Alignment explanation
Indices: 96699--96790 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
96689 TTCTTTCTTC
* * * *
96699 ATTCTCAATCTCTTTTTCAGTTCTCTTTTCTTTTTCACACTCATTTTT
1 ATTCTCAATCTCATTTTCAATTCTCTTTTCTATCTCACACTCATTTTT
*
96747 ATTCTCAATCTCATTTTCAATTTTCTTTTCTATCTCACACTCAT
1 ATTCTCAATCTCATTTTCAATTCTCTTTTCTATCTCACACTCAT
96791 CTTCTTTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.01, T:0.54
Consensus pattern (48 bp):
ATTCTCAATCTCATTTTCAATTCTCTTTTCTATCTCACACTCATTTTT
Found at i:96812 original size:15 final size:16
Alignment explanation
Indices: 96787--96818 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
96777 TATCTCACAC
96787 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
96803 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
96818 T
1 T
96819 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:97824 original size:11 final size:11
Alignment explanation
Indices: 97808--97845 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
97798 AATACAAACT
97808 TTTTTTTTGAA
1 TTTTTTTTGAA
*
97819 TTTTTTTTCAA
1 TTTTTTTTGAA
97830 -TTTTTTTG-A
1 TTTTTTTTGAA
97839 TTTTTTT
1 TTTTTTT
97846 ACAATACCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 1 0.04
10 13 0.54
11 10 0.42
ACGTcount: A:0.13, C:0.03, G:0.05, T:0.79
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:97835 original size:21 final size:20
Alignment explanation
Indices: 97809--97850 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
97799 ATACAAACTT
*
97809 TTTTTTTGAATTTTTTTTCAA
1 TTTTTTTG-ATTTTTTTACAA
97830 TTTTTTTGATTTTTTTACAA
1 TTTTTTTGATTTTTTTACAA
97850 T
1 T
97851 ACCGTAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTTTTTGATTTTTTTACAA
Found at i:108685 original size:11 final size:10
Alignment explanation
Indices: 108660--108720 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
108650 ACCAATAAAA
108660 TAAA-TGAGC
1 TAAATTGAGC
*
108669 TGAATTGTAGC
1 TAAATTG-AGC
108680 TAAATTGAGC
1 TAAATTGAGC
**
108690 TCGATTGAGC
1 TAAATTGAGC
108700 TGAAA-TGAGC
1 T-AAATTGAGC
*
108710 TCAATTGAGC
1 TAAATTGAGC
108720 T
1 T
108721 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:108721 original size:20 final size:20
Alignment explanation
Indices: 108661--108721 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
108651 CCAATAAAAT
*
108661 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
108681 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
108702 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
108722 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:111736 original size:28 final size:26
Alignment explanation
Indices: 111705--111798 Score: 73
Period size: 27 Copynumber: 3.5 Consensus size: 26
111695 GCAAGACTTT
*
111705 TCACTTTTTTTTAACTTGATTTTTTTGC
1 TCACTTTTTTTT-ACTCGATTTTTTT-C
* *
111733 TCACCTTTTTTTTTCTCGATTTTTTTT
1 TCA-CTTTTTTTTACTCGATTTTTTTC
* * *
111760 TCATTTTTTTTTCAATCAATTTTTTT-
1 TCACTTTTTTTT-ACTCGATTTTTTTC
*
111786 TCGAATTTTTTTT
1 TC-ACTTTTTTTT
111799 TGATTTTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
26 10 0.18
27 22 0.40
28 14 0.25
29 9 0.16
ACGTcount: A:0.14, C:0.14, G:0.04, T:0.68
Consensus pattern (26 bp):
TCACTTTTTTTTACTCGATTTTTTTC
Found at i:111755 original size:14 final size:13
Alignment explanation
Indices: 111724--111799 Score: 57
Period size: 15 Copynumber: 5.6 Consensus size: 13
111714 TTTAACTTGA
*
111724 TTTTTTTGCTCACCT
1 TTTTTTTTCTCA--T
111739 TTTTTTTTCTCGA-
1 TTTTTTTTCTC-AT
111752 TTTTTTTT-TCAT
1 TTTTTTTTCTCAT
*
111764 TTTTTTTTCAATCAA
1 TTTTTTTTC--TCAT
**
111779 TTTTTTTTCGAAT
1 TTTTTTTTCTCAT
111792 TTTTTTTT
1 TTTTTTTT
111800 GATTTTTTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
11 1 0.02
12 10 0.20
13 17 0.33
15 22 0.43
16 1 0.02
ACGTcount: A:0.12, C:0.13, G:0.04, T:0.71
Consensus pattern (13 bp):
TTTTTTTTCTCAT
Found at i:111765 original size:11 final size:12
Alignment explanation
Indices: 111739--111808 Score: 63
Period size: 11 Copynumber: 5.6 Consensus size: 12
111729 TTGCTCACCT
*
111739 TTTTTTTTCTCGA
1 TTTTTTTT-TCAA
111752 TTTTTTTTTC-A
1 TTTTTTTTTCAA
111763 TTTTTTTTTCAA
1 TTTTTTTTTCAA
111775 TCAATTTTTTTTCGAA
1 T---TTTTTTTTC-AA
*
111791 TTTTTTTTT-GA
1 TTTTTTTTTCAA
111802 TTTTTTT
1 TTTTTTT
111809 GTTACTCCAA
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
11 19 0.37
12 4 0.08
13 16 0.31
15 9 0.18
16 3 0.06
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.74
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:111781 original size:27 final size:25
Alignment explanation
Indices: 111738--111799 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
111728 TTTGCTCACC
*
111738 TTTTTTTTTCTCGATTTTTTTTTC-A
1 TTTTTTTTTCTC-AATTTTTTTTCAA
111763 TTTTTTTTTCAATCAATTTTTTTTCGAA
1 TTTTTTTTTC--TCAATTTTTTTTC-AA
111791 TTTTTTTTT
1 TTTTTTTTT
111800 GATTTTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 10 0.31
26 10 0.31
27 2 0.06
28 10 0.31
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.74
Consensus pattern (25 bp):
TTTTTTTTTCTCAATTTTTTTTCAA
Found at i:114175 original size:11 final size:10
Alignment explanation
Indices: 114150--114210 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
114140 ACCAATAAAA
114150 TAAA-TGAGC
1 TAAATTGAGC
*
114159 TGAATTGTAGC
1 TAAATTG-AGC
114170 TAAATTGAGC
1 TAAATTGAGC
**
114180 TCGATTGAGC
1 TAAATTGAGC
114190 TGAAA-TGAGC
1 T-AAATTGAGC
*
114200 TCAATTGAGC
1 TAAATTGAGC
114210 T
1 T
114211 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:114211 original size:20 final size:20
Alignment explanation
Indices: 114151--114211 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
114141 CCAATAAAAT
*
114151 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
114171 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
114192 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
114212 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:119099 original size:46 final size:46
Alignment explanation
Indices: 119046--119138 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 46
119036 CAAAGAAAAG
* *
119046 ACCTCGACCCACTATCAA-GAATGATAGGAATCTTGGTATATGATGA
1 ACCTCGACCCACTATCAATG-ATGATAAGAACCTTGGTATATGATGA
*
119092 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTTTATGATGA
1 ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
119138 A
1 A
119139 TGCCACACTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 42 0.98
47 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (46 bp):
ACCTCGACCCACTATCAATGATGATAAGAACCTTGGTATATGATGA
Found at i:123762 original size:23 final size:22
Alignment explanation
Indices: 123710--123762 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
123700 TCCACGTCTT
*
123710 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
123732 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
123755 TTTCTTTT
1 TTTCTTTT
123763 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:126035 original size:20 final size:20
Alignment explanation
Indices: 126012--126065 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
126002 AGTTTTTCCC
*
126012 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
126032 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
126052 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
126066 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:126047 original size:30 final size:30
Alignment explanation
Indices: 126012--126085 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
126002 AGTTTTTCCC
126012 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
126042 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
126072 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
126086 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:126075 original size:20 final size:20
Alignment explanation
Indices: 126012--126076 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
126002 AGTTTTTCCC
* * * *
126012 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
126032 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
126051 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
126072 AGCTC
1 AGCTC
126077 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:132080 original size:15 final size:15
Alignment explanation
Indices: 132060--132112 Score: 88
Period size: 15 Copynumber: 3.5 Consensus size: 15
132050 TAGCTTCTTC
132060 TTTTTTTCACGAAAT
1 TTTTTTTCACGAAAT
*
132075 TTTTTTTCACGAATTT
1 TTTTTTTCACGAA-AT
132091 TTTTTTTCACGAAAT
1 TTTTTTTCACGAAAT
132106 TTTTTTT
1 TTTTTTT
132113 TCAACTTGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 21 0.60
16 14 0.40
ACGTcount: A:0.21, C:0.11, G:0.06, T:0.62
Consensus pattern (15 bp):
TTTTTTTCACGAAAT
Found at i:132081 original size:16 final size:16
Alignment explanation
Indices: 132060--132115 Score: 96
Period size: 16 Copynumber: 3.6 Consensus size: 16
132050 TAGCTTCTTC
132060 TTTTTTTCACGAAA-T
1 TTTTTTTCACGAAATT
*
132075 TTTTTTTCACGAATTT
1 TTTTTTTCACGAAATT
132091 TTTTTTTCACGAAATT
1 TTTTTTTCACGAAATT
132107 TTTTTTTCA
1 TTTTTTTCA
132116 ACTTGATATC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 13 0.34
16 25 0.66
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTTTTTCACGAAATT
Found at i:132170 original size:12 final size:12
Alignment explanation
Indices: 132153--132197 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
132143 ATGGAAACCA
132153 AATTTTTTTTTG
1 AATTTTTTTTTG
*
132165 AATTTTTTTTTT
1 AATTTTTTTTTG
132177 AA-TTTTTTTTG
1 AATTTTTTTTTG
132188 AATTTTTTTT
1 AATTTTTTTT
132198 CGAGAAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 10 0.33
12 20 0.67
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:132172 original size:11 final size:11
Alignment explanation
Indices: 132156--132197 Score: 66
Period size: 11 Copynumber: 3.7 Consensus size: 11
132146 GAAACCAAAT
132156 TTTTTTTTGAA
1 TTTTTTTTGAA
*
132167 TTTTTTTTTTAA
1 -TTTTTTTTGAA
132179 TTTTTTTTGAA
1 TTTTTTTTGAA
132190 TTTTTTTT
1 TTTTTTTT
132198 CGAGAAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:132600 original size:45 final size:46
Alignment explanation
Indices: 132509--132601 Score: 163
Period size: 46 Copynumber: 2.0 Consensus size: 46
132499 CAAAGAAAAG
132509 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
132555 ACCTCGACCCACTATCAATG-ATGATA-GAACCTTGGTATATGATGA
1 ACCTCGACCCACTATCAA-GAATGATAGGAACCTTGGTATATGATGA
132600 AC
1 AC
132602 GCCACACTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
45 21 0.46
46 24 0.52
47 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (46 bp):
ACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATGA
Found at i:135610 original size:498 final size:498
Alignment explanation
Indices: 134673--135672 Score: 1894
Period size: 498 Copynumber: 2.0 Consensus size: 498
134663 GGAGATGGAG
*
134673 ATGCTCATTTAGAGAGCTAATGTGGAGGAGGATGAGGAAACAACTATGGTTCGATTTATTGATGG
1 ATGCTCATTCAGAGAGCTAATGTGGAGGAGGATGAGGAAACAACTATGGTTCGATTTATTGATGG
134738 TTTGAACAGGCCGATAGCTAATACATTGAGGCTACAAACTTACATTAATTTGGAAGAAGCAGTTC
66 TTTGAACAGGCCGATAGCTAATACATTGAGGCTACAAACTTACATTAATTTGGAAGAAGCAGTTC
134803 ATAAAGCCATTGAGATCGAGCAACAACTAAAGGAACAAAGGTTTGGTTCCTTCTCGACTTCACAA
131 ATAAAGCCATTGAGATCGAGCAACAACTAAAGGAACAAAGGTTTGGTTCCTTCTCGACTTCACAA
134868 TATTACCTAGGTAACAACTCCAATTCTGATTTTAAGAGTTCGAAATCCCCTTTTGTTACTAACAA
196 TATTACCTAGGTAACAACTCCAATTCTGATTTTAAGAGTTCGAAATCCCCTTTTGTTACTAACAA
*
134933 GTCTTCTTTGAGTAATGGAAGTAAGCAATCAGATTGGAAAAAAGGGGCTCCTGCTAAAACACAAA
261 GTCTTCTTTGAGTAATGGAAGTAAGCAATCAGATTGGAAAAAAGGGGCTCCTACTAAAACACAAA
134998 CACCTTCTAAGAAGCCCAATTTAGGTGATTCGAGTGCGAAGAGGACTCGTGAGATTGAATGCTTT
326 CACCTTCTAAGAAGCCCAATTTAGGTGATTCGAGTGCGAAGAGGACTCGTGAGATTGAATGCTTT
135063 AAGTGCAAAGGGCATGGTCATTATAGTAGAGAATGCCCTAACACGAGATTACTTCTTCTAAAAGA
391 AAGTGCAAAGGGCATGGTCATTATAGTAGAGAATGCCCTAACACGAGATTACTTCTTCTAAAAGA
*
135128 TAACGGTGAGTACACTTCC-AGCTCTGATAATACAGATCCAGAT
456 TAACGGTGAGTACACTTCCGA-CTCTAATAATACAGATCCAGAT
*
135171 ATGCTCATTCAGCGAGCTAATGTGGAGGAGGATGAGGAAACAACTATGGTTCGATTTATTGATGG
1 ATGCTCATTCAGAGAGCTAATGTGGAGGAGGATGAGGAAACAACTATGGTTCGATTTATTGATGG
* *
135236 TTTGAACAGGCCGATAGCTAATACATTGAGGCTACAAACTTACATTGATTTGGAAGAAGTAGTTC
66 TTTGAACAGGCCGATAGCTAATACATTGAGGCTACAAACTTACATTAATTTGGAAGAAGCAGTTC
135301 ATAAAGCCATTGAGATCGAGCAACAACTAAAGGAACAAAGGTTTGGTTCCTTCTCGACTTCACAA
131 ATAAAGCCATTGAGATCGAGCAACAACTAAAGGAACAAAGGTTTGGTTCCTTCTCGACTTCACAA
135366 TATTACCTAGGTAACAACTCCAATTCTGATTTTAAGAGTTCGAAATCCCCTTTTGTTACTAACAA
196 TATTACCTAGGTAACAACTCCAATTCTGATTTTAAGAGTTCGAAATCCCCTTTTGTTACTAACAA
*
135431 GTCTTCTTTGAGTAATGGAAGTAAGCAATCAGATTGGAAAAAAGGGGCTCCTACTAAAACGCAAA
261 GTCTTCTTTGAGTAATGGAAGTAAGCAATCAGATTGGAAAAAAGGGGCTCCTACTAAAACACAAA
*
135496 CACCTTCTAAGCAGCCCAATTTAGGTGATTCGAGTGCGAAGAGGACTCGTGAGATTGAATGCTTT
326 CACCTTCTAAGAAGCCCAATTTAGGTGATTCGAGTGCGAAGAGGACTCGTGAGATTGAATGCTTT
**
135561 AAGTGCAAAGGGTGTGGTCATTATAGTAGAGAATGCCCTAACACGAGATTACTTCTTCTAAAAGA
391 AAGTGCAAAGGGCATGGTCATTATAGTAGAGAATGCCCTAACACGAGATTACTTCTTCTAAAAGA
135626 TAACGGTGAGTACACTTCCGACTCTAATAATACAGATCCAGAT
456 TAACGGTGAGTACACTTCCGACTCTAATAATACAGATCCAGAT
135669 ATGC
1 ATGC
135673 CAGAACTTGT
Statistics
Matches: 491, Mismatches: 10, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
498 490 1.00
499 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (498 bp):
ATGCTCATTCAGAGAGCTAATGTGGAGGAGGATGAGGAAACAACTATGGTTCGATTTATTGATGG
TTTGAACAGGCCGATAGCTAATACATTGAGGCTACAAACTTACATTAATTTGGAAGAAGCAGTTC
ATAAAGCCATTGAGATCGAGCAACAACTAAAGGAACAAAGGTTTGGTTCCTTCTCGACTTCACAA
TATTACCTAGGTAACAACTCCAATTCTGATTTTAAGAGTTCGAAATCCCCTTTTGTTACTAACAA
GTCTTCTTTGAGTAATGGAAGTAAGCAATCAGATTGGAAAAAAGGGGCTCCTACTAAAACACAAA
CACCTTCTAAGAAGCCCAATTTAGGTGATTCGAGTGCGAAGAGGACTCGTGAGATTGAATGCTTT
AAGTGCAAAGGGCATGGTCATTATAGTAGAGAATGCCCTAACACGAGATTACTTCTTCTAAAAGA
TAACGGTGAGTACACTTCCGACTCTAATAATACAGATCCAGAT
Found at i:137473 original size:59 final size:63
Alignment explanation
Indices: 137410--137551 Score: 166
Period size: 70 Copynumber: 2.2 Consensus size: 63
137400 ATTTAAAGGG
*
137410 AAGCAAAGACATG-AATTAA-A-T-CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
1 AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
* *
137469 AAGCATAGACATGCATTTAAGGTGATGTTCAACAGCAGCAATAAAGGAGGTTTTGGCCGAATTTA
1 AAGCATAGACATGCAATTAA---GA--TT--ACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTA
137534 ATGTA
59 ATGTA
137539 AAGCATAGACATG
1 AAGCATAGACATG
137552 TATTTAAGGT
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
59 12 0.17
60 5 0.07
64 1 0.01
67 1 0.01
70 50 0.72
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (63 bp):
AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
Found at i:137514 original size:70 final size:70
Alignment explanation
Indices: 137431--137567 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 70
137421 TGAATTAAAT
137431 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
1 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
137496 TTCAA
66 TTCAA
* * *
137501 CAGCAGCAATAAAGGAGGTTTTGGCCGAATTTAATGTAAAGCATAGACATGTATTTAAGGTGCTG
1 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
137566 TT
66 TT
137568 GGGCATGCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (70 bp):
CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
TTCAA
Found at i:138538 original size:21 final size:21
Alignment explanation
Indices: 138512--138574 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
138502 TTGGTATTTG
138512 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
138533 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
138554 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
138575 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:147889 original size:22 final size:22
Alignment explanation
Indices: 147858--147922 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
147848 ACCTTTTTGA
147858 ACCATTACCATTTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
*
147881 ACCATACCATTTCGTACCAACT
1 ACCATACCATTTCGTACCAAAT
*
147903 TCCATACCATTTCGTACCAA
1 ACCATACCATTTCGTACCAA
147923 TTCCTAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 36 0.90
23 4 0.10
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:148255 original size:19 final size:20
Alignment explanation
Indices: 148230--148276 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
148220 TAGACTTGTG
148230 AAAAAAATTGAAAAAAA-AA
1 AAAAAAATTGAAAAAAATAA
148249 TAAAAAAATTTGAAAAAAATAA
1 -AAAAAAA-TTGAAAAAAATAA
148271 AAAAAA
1 AAAAAA
148277 TTGTATACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 7 0.28
21 16 0.64
22 2 0.08
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (20 bp):
AAAAAAATTGAAAAAAATAA
Found at i:148255 original size:20 final size:19
Alignment explanation
Indices: 148230--148279 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 19
148220 TAGACTTGTG
148230 AAAAAAATTGAAAAAAAAA
1 AAAAAAATTGAAAAAAAAA
*
148249 TAAAAAAATTTGAAAAAAATA
1 -AAAAAAA-TTGAAAAAAAAA
148270 AAAAAAATTG
1 AAAAAAATTG
148280 TATACAGTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 3 0.11
20 14 0.50
21 11 0.39
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (19 bp):
AAAAAAATTGAAAAAAAAA
Done.