Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009449.1 Hibiscus syriacus cultivar Beakdansim tig00113550_pilon, whole genome shotgun sequence
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: 86258
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:5652 original size:17 final size:17
Alignment explanation
Indices: 5630--5676 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 17
5620 AAAAGTTGAC
*
5630 CGTTGACCATTGACCGT
1 CGTTGACCATTGACCAT
5647 CGTTGACCACTATTGACCAT
1 CGTTGA-C-C-ATTGACCAT
5667 CGTTGACCAT
1 CGTTGACCAT
5677 AACTTTGACC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 8 0.31
18 2 0.08
19 2 0.08
20 14 0.54
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.30
Consensus pattern (17 bp):
CGTTGACCATTGACCAT
Found at i:5663 original size:20 final size:20
Alignment explanation
Indices: 5638--5675 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5628 ACCGTTGACC
*
5638 ATTGACCGTCGTTGACCACT
1 ATTGACCATCGTTGACCACT
5658 ATTGACCATCGTTGACCA
1 ATTGACCATCGTTGACCA
5676 TAACTTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (20 bp):
ATTGACCATCGTTGACCACT
Found at i:6535 original size:31 final size:31
Alignment explanation
Indices: 6500--6558 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
6490 TAGGCTTTGC
* *
6500 GGCCCTGAGATCAT-TCTCGGGTAGGCCCTAT
1 GGCCCTAAGAT-ATGTCTCAGGTAGGCCCTAT
*
6531 GGCCCTAAGATATGTCTTAGGTAGGCCC
1 GGCCCTAAGATATGTCTCAGGTAGGCCC
6559 CAAATCTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 22 0.92
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.25
Consensus pattern (31 bp):
GGCCCTAAGATATGTCTCAGGTAGGCCCTAT
Found at i:12358 original size:12 final size:12
Alignment explanation
Indices: 12341--12377 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
12331 TAGAGTTGAT
12341 AAGTTGAATTTG
1 AAGTTGAATTTG
12353 AAGTTGAATTTG
1 AAGTTGAATTTG
*
12365 AAGTTAAATTTG
1 AAGTTGAATTTG
12377 A
1 A
12378 CTTGTCATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.41
Consensus pattern (12 bp):
AAGTTGAATTTG
Found at i:12683 original size:22 final size:21
Alignment explanation
Indices: 12642--12681 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12632 AGATTATGCA
12642 GGGGGGTACAGATTCCCCCTT
1 GGGGGGTACAGATTCCCCCTT
**
12663 GGGGGGTATTGATTCCCCC
1 GGGGGGTACAGATTCCCCC
12682 CTAATGGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.28, G:0.35, T:0.25
Consensus pattern (21 bp):
GGGGGGTACAGATTCCCCCTT
Found at i:13773 original size:31 final size:31
Alignment explanation
Indices: 13735--13921 Score: 243
Period size: 31 Copynumber: 6.0 Consensus size: 31
13725 AGAGTCGAGG
13735 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
* *
13766 GTTTACCTATGTTC-TCCGAGACATATGGATT
1 GTTTACCTATGTTCTTCAG-GACATATGGACT
** *
13797 GTTTACCTATGTTCTTTGGGATATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
* *
13828 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
13859 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACT
* * * *
13890 GTTTACATAGGTTATTC-GGAATATATGGACT
1 GTTTACCTATGTTCTTCAGG-ACATATGGACT
13921 G
1 G
13922 GTCATTCAGG
Statistics
Matches: 140, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
30 5 0.04
31 133 0.95
32 2 0.01
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCAGGACATATGGACT
Found at i:13894 original size:93 final size:93
Alignment explanation
Indices: 13735--13921 Score: 277
Period size: 93 Copynumber: 2.0 Consensus size: 93
13725 AGAGTCGAGG
* *
13735 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTCCGAGACATATGGATTGTT
1 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTCAGAGACATATGGACTGTT
* * * * *
13800 TACCTATGTTCTTTGGGATATATGGACT
66 TACATAGGTTATTCGGAATATATGGACT
* *
13828 GTTTACCTATGTTCTTCGGGATATATGGACTGTTTACCTATGTTCTTCAG-GACATATGGACTGT
1 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTC-TCAGAGACATATGGACTGT
13892 TTACATAGGTTATTCGGAATATATGGACT
65 TTACATAGGTTATTCGGAATATATGGACT
13921 G
1 G
13922 GTCATTCAGG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
93 81 0.96
94 3 0.04
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.40
Consensus pattern (93 bp):
GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTCAGAGACATATGGACTGTT
TACATAGGTTATTCGGAATATATGGACT
Found at i:13908 original size:62 final size:62
Alignment explanation
Indices: 13735--13921 Score: 275
Period size: 62 Copynumber: 3.0 Consensus size: 62
13725 AGAGTCGAGG
* * * *
13735 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTCCGAGACATATGGATT
1 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTTCGGGATATATGGACT
** *
13797 GTTTACCTATGTTCTTTGGGATATATGGACTGTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTTCGGGATATATGGACT
* * * *
13859 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACATAGGTTATTCGGAATATATGGACT
1 GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTTCGGGATATATGGACT
13921 G
1 G
13922 GTCATTCAGG
Statistics
Matches: 111, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 111 1.00
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.40
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCAGGACATATGGACTGTTTACCTATGTTCTTCGGGATATATGGACT
Found at i:15975 original size:31 final size:31
Alignment explanation
Indices: 15935--16056 Score: 79
Period size: 31 Copynumber: 3.9 Consensus size: 31
15925 CTAATGTGAC
* *
15935 TCTTAGGTAGGCTCTACGGCCTTGAGATCAT
1 TCTTAGGTAGGCTCTACGGCCCTAAGATCAT
* * * **
15966 TCTTGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCTCTACGGCCCTAAGAT-CAT
* * *
15998 TCTTAGGTAGGC-CTCATGGCCCCGAA-ATCTT
1 TCTTAGGTAGGCTCT-ACGG-CCCTAAGATCAT
* *
16029 TCTTGGGTAGGCTCT-CAGGCCTTAAGAT
1 TCTTAGGTAGGCTCTAC-GGCCCTAAGAT
16057 GTTCCCTTAG
Statistics
Matches: 68, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
30 4 0.06
31 41 0.60
32 18 0.26
33 5 0.07
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (31 bp):
TCTTAGGTAGGCTCTACGGCCCTAAGATCAT
Found at i:16003 original size:63 final size:63
Alignment explanation
Indices: 15935--16058 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
15925 CTAATGTGAC
** *
15935 TCTTAGGTAGG-CTCTACGGCCTTGAGATCATTCTTGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCATTCTTGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* * * *
15998 TCTTAGGTAGGCCTCATGGCCCCGAAATCTTTCTTGGGTAGGCTCTCAGGCCTTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCATTCTTGGGTAGGCCCTCAGGCCCTAAGATGT
16059 TCCCTTAGGT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 48 0.92
64 3 0.06
ACGTcount: A:0.17, C:0.24, G:0.28, T:0.31
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCATTCTTGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:16123 original size:25 final size:25
Alignment explanation
Indices: 16075--16124 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
16065 AGGTTAACTC
*
16075 TTTTATGAGATTTACTACAGTATGA
1 TTTTATGAGATTTACTACACTATGA
**
16100 TTTTATGAGATTTACTGGACTATGA
1 TTTTATGAGATTTACTACACTATGA
16125 CTTGTTTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (25 bp):
TTTTATGAGATTTACTACACTATGA
Found at i:18680 original size:19 final size:19
Alignment explanation
Indices: 18637--18680 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
18627 AAATGACCAA
*
18637 CAAATTCGCAACACGATCT
1 CAAATTCGCAACACGAACT
**
18656 CAAATTCGCAATGCGAACT
1 CAAATTCGCAACACGAACT
*
18675 CCAATT
1 CAAATT
18681 TTGCAACACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.23
Consensus pattern (19 bp):
CAAATTCGCAACACGAACT
Found at i:18766 original size:20 final size:19
Alignment explanation
Indices: 18738--18786 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
18728 GCGAATTTGT
18738 AAATTGCAACACAGAAGTC
1 AAATTGCAACACAGAAGTC
*
18757 AAATTCGCAACACATAAGTC
1 AAATT-GCAACACAGAAGTC
18777 AAATTTGCAA
1 AAA-TTGCAA
18787 AGCGCGTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 20 0.74
21 2 0.07
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.20
Consensus pattern (19 bp):
AAATTGCAACACAGAAGTC
Found at i:19344 original size:20 final size:20
Alignment explanation
Indices: 19293--19344 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
19283 TTTGAAACTT
*
19293 AAATTCGCAACACGAAAATGA
1 AAATT-GCAACGCGAAAATGA
*
19314 AAATCGCAACGCGAAAATGA
1 AAATTGCAACGCGAAAATGA
19334 AAATTGCAACG
1 AAATTGCAACG
19345 TTGCGATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.50, C:0.19, G:0.17, T:0.13
Consensus pattern (20 bp):
AAATTGCAACGCGAAAATGA
Found at i:21139 original size:21 final size:22
Alignment explanation
Indices: 21115--21227 Score: 67
Period size: 21 Copynumber: 5.4 Consensus size: 22
21105 TGGTGCATGG
21115 CGTGATGAGGTATGGT-CTTTA
1 CGTGATGAGGTATGGTACTTTA
* *
21136 CGTGGTGAGGTAGAGGT--TTTA
1 CGTGATGAGGTA-TGGTACTTTA
** ** *
21157 CACGATGA-CAATGGTGCTTTA
1 CGTGATGAGGTATGGTACTTTA
* *
21178 CGTGGTGAGGTAT-CTACTTTA
1 CGTGATGAGGTATGGTACTTTA
* * *
21199 CATGGTGAGGTAT-CTACTTTA
1 CGTGATGAGGTATGGTACTTTA
21220 CGTGATGA
1 CGTGATGA
21228 AGTAGCCGCT
Statistics
Matches: 70, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
19 3 0.04
20 1 0.01
21 61 0.87
22 5 0.07
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.35
Consensus pattern (22 bp):
CGTGATGAGGTATGGTACTTTA
Found at i:21557 original size:21 final size:21
Alignment explanation
Indices: 21531--21643 Score: 122
Period size: 21 Copynumber: 5.4 Consensus size: 21
21521 CCTGTCATCA
*
21531 TTCAAGAGGCCTCTCCTATCG
1 TTCAAGAGGCCCCTCCTATCG
* *
21552 TTCAAGAGGCCCCT-ATCATCC
1 TTCAAGAGGCCCCTCCT-ATCG
* *
21573 TTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCCCCTCCTATCG
*
21594 TTCAAGAGGCCCCT-GTCATCG
1 TTCAAGAGGCCCCTCCT-ATCG
* *
21615 TTCAAGAGGTCCCTCCTACCG
1 TTCAAGAGGCCCCTCCTATCG
21636 TTCAAGAG
1 TTCAAGAG
21644 ACCGATTCAC
Statistics
Matches: 75, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.01
21 73 0.97
22 1 0.01
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCTATCG
Found at i:21571 original size:42 final size:41
Alignment explanation
Indices: 21525--21643 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 41
21515 GATTCACCTG
*
21525 TCATCATTCAAGAGGCCTCTCCTATCGTTCAAGAGGCCCCTA
1 TCATCATTCAAGAGGCC-CTCCTACCGTTCAAGAGGCCCCTA
* * *
21567 TCATCCTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTCAAGAGG-CCCTCCTACCGTTCAAGAGGCCCCTA
*
21609 TCATCGTTCAAGAGGTCCCTCCTACCGTTCAAGAG
1 TCATCATTCAAGAGG-CCCTCCTACCGTTCAAGAG
21644 ACCGATTCAC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 67 0.97
43 2 0.03
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (41 bp):
TCATCATTCAAGAGGCCCTCCTACCGTTCAAGAGGCCCCTA
Found at i:22990 original size:13 final size:13
Alignment explanation
Indices: 22950--22994 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
22940 TTTTTTTTGC
22950 TTGTTTAATTGAT
1 TTGTTTAATTGAT
**
22963 TTGTAAAAGTTGAT
1 TTGTTTAA-TTGAT
22977 TTGTTTAATTGAT
1 TTGTTTAATTGAT
22990 TTGTT
1 TTGTT
22995 GTTTAATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (13 bp):
TTGTTTAATTGAT
Found at i:23085 original size:14 final size:14
Alignment explanation
Indices: 23066--23095 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
23056 GAAAGTCAAA
*
23066 TTCGCGTTGCGATT
1 TTCGCGATGCGATT
23080 TTCGCGATGCGATT
1 TTCGCGATGCGATT
23094 TT
1 TT
23096 GACTTTTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.20, G:0.27, T:0.43
Consensus pattern (14 bp):
TTCGCGATGCGATT
Found at i:23161 original size:20 final size:20
Alignment explanation
Indices: 23079--23163 Score: 73
Period size: 20 Copynumber: 4.3 Consensus size: 20
23069 GCGTTGCGAT
* *
23079 TTTCGCGATGCGATTTTGAC
1 TTTCGCGTTGCGAATTTGAC
* * * *
23099 TTTTGCTTTACGAATTTAAC
1 TTTCGCGTTGCGAATTTGAC
* * *
23119 -TTCGTGTTGCGATTTTGAA
1 TTTCGCGTTGCGAATTTGAC
*
23138 TTTCGCGTTGCGAATTTGTC
1 TTTCGCGTTGCGAATTTGAC
23158 TTTCGC
1 TTTCGC
23164 AACAATCGCA
Statistics
Matches: 47, Mismatches: 17, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
19 12 0.26
20 35 0.74
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.46
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:23378 original size:20 final size:20
Alignment explanation
Indices: 23354--23539 Score: 176
Period size: 20 Copynumber: 9.3 Consensus size: 20
23344 ACTCGAAAAT
*
23354 GTTGCGATTTTGACTTTCGT
1 GTTGCGATTTTGACTTTCGC
* *
23374 GTTGCGATTTTTACTTTCGT
1 GTTGCGATTTTGACTTTCGC
*
23394 GTTGCGATTTTTACTTTCGC
1 GTTGCGATTTTGACTTTCGC
* * *
23414 GTTGCGAATTTGATTTTCGT
1 GTTGCGATTTTGACTTTCGC
* * *
23434 GTTGCGAATTTGATTTTTGC
1 GTTGCGATTTTGACTTTCGC
*
23454 GTTGCGGTTTTGACTTTCGC
1 GTTGCGATTTTGACTTTCGC
* *
23474 GTTGC-AATTTGACTTTTGC
1 GTTGCGATTTTGACTTTCGC
* * * *
23493 GTTGCGAATTTAATTTTTGC
1 GTTGCGATTTTGACTTTCGC
* * * *
23513 CTTGCGGTTTTGAATTTCGT
1 GTTGCGATTTTGACTTTCGC
23533 GTTGCGA
1 GTTGCGA
23540 AAGTGTACCA
Statistics
Matches: 139, Mismatches: 26, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
19 16 0.12
20 123 0.88
ACGTcount: A:0.12, C:0.15, G:0.24, T:0.49
Consensus pattern (20 bp):
GTTGCGATTTTGACTTTCGC
Found at i:23509 original size:59 final size:60
Alignment explanation
Indices: 23354--23540 Score: 225
Period size: 60 Copynumber: 3.1 Consensus size: 60
23344 ACTCGAAAAT
* * * * * * * * *
23354 GTTGCGATTTTGACTTTCGTGTTGCGATTTTTACTTTCGTGTTGCGATTTTTACTTTCGC
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTTAATTTTTGCGTTGCGGTTTTGACTTTCGC
*
23414 GTTGCGAATTTGA-TTTTCGTGTTGCGAATTTGATTTTTGCGTTGCGGTTTTGACTTTCGC
1 GTTGCGAATTTGACTTTT-GTGTTGCGAATTTAATTTTTGCGTTGCGGTTTTGACTTTCGC
* * * *
23474 GTTGC-AATTTGACTTTTGCGTTGCGAATTTAATTTTTGCCTTGCGGTTTTGAATTTCGT
1 GTTGCGAATTTGACTTTTGTGTTGCGAATTTAATTTTTGCGTTGCGGTTTTGACTTTCGC
23533 GTTGCGAA
1 GTTGCGAA
23541 AGTGTACCAT
Statistics
Matches: 110, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
59 52 0.47
60 58 0.53
ACGTcount: A:0.13, C:0.14, G:0.24, T:0.49
Consensus pattern (60 bp):
GTTGCGAATTTGACTTTTGTGTTGCGAATTTAATTTTTGCGTTGCGGTTTTGACTTTCGC
Found at i:26182 original size:24 final size:24
Alignment explanation
Indices: 26148--26201 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
26138 CTGATGCATC
26148 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
26172 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
26196 ATCAAA
1 ATCAAA
26202 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:26215 original size:24 final size:24
Alignment explanation
Indices: 26148--26215 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
26138 CTGATGCATC
* * *
26148 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAGTCTGAATACTGACCAAG
** *
26172 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAGTCTGAATACTGACCAAG
* *
26196 ATCAAATTTTGAATACTGAC
1 ATCAAAGTCTGAATACTGAC
26216 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (24 bp):
ATCAAAGTCTGAATACTGACCAAG
Found at i:27211 original size:20 final size:20
Alignment explanation
Indices: 27142--27211 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
27132 AAATAAAAGC
* * *
27142 TGTTGCGAATTTAAAATTCG
1 TGTTGCGAAATCAAAATTCA
27162 TGTTGCG-AATCCGAAAA-TCGA
1 TGTTGCGAAAT-C-AAAATTC-A
*
27183 -GTTGTGAAATCAAAATTCA
1 TGTTGCGAAATCAAAATTCA
27202 TGTTGCGAAA
1 TGTTGCGAAA
27212 AGGAAACTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
19 7 0.18
20 25 0.64
21 7 0.18
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (20 bp):
TGTTGCGAAATCAAAATTCA
Found at i:27269 original size:21 final size:20
Alignment explanation
Indices: 27235--27456 Score: 68
Period size: 20 Copynumber: 11.0 Consensus size: 20
27225 GATGAAAAAT
27235 AAATTCGCGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
*
27255 AAATTCCGTGTTGCGAATTTG
1 AAATT-CGCGTTGCGAATTTG
* * * *
27276 -ACTTATGTGTTGCG-ATTTAC
1 AAATT-CGCGTTGCGAATTT-G
27296 AAATTCGCGTTGCG-ATTT-
1 AAATTCGCGTTGCGAATTTG
* *
27314 ACATATTCGTGTTACG-ATTT-
1 A-A-ATTCGCGTTGCGAATTTG
**
27334 ACATATTTTCGTTGCGAATTTGG
1 A-A-ATTCGCGTTGCGAATTT-G
*
27357 AAAATT-GCGTTGCGATTTTG
1 -AAATTCGCGTTGCGAATTTG
* * * *
27377 GAA-CCTGTGTTGCGAAATT-
1 AAATTC-GCGTTGCGAATTTG
* *
27396 AGAGTTCGCGTTGCGATTTTG
1 A-AATTCGCGTTGCGAATTTG
* * * *
27417 GAA-CCTGTGTTGCGAAATTG
1 AAATTC-GCGTTGCGAATTTG
* *
27437 GAGTTCGCGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTTG
27457 TTGGTCATTT
Statistics
Matches: 149, Mismatches: 37, Indels: 32
0.68 0.17 0.15
Matches are distributed among these distances:
18 1 0.01
19 8 0.05
20 101 0.68
21 34 0.23
22 3 0.02
23 1 0.01
24 1 0.01
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.38
Consensus pattern (20 bp):
AAATTCGCGTTGCGAATTTG
Found at i:27415 original size:40 final size:40
Alignment explanation
Indices: 27363--27456 Score: 170
Period size: 40 Copynumber: 2.4 Consensus size: 40
27353 TTGGAAAATT
27363 GCGTTGCGATTTTGGAACCTGTGTTGCGAAATTAGAGTTC
1 GCGTTGCGATTTTGGAACCTGTGTTGCGAAATTAGAGTTC
*
27403 GCGTTGCGATTTTGGAACCTGTGTTGCGAAATTGGAGTTC
1 GCGTTGCGATTTTGGAACCTGTGTTGCGAAATTAGAGTTC
*
27443 GCGTTGCGAATTTG
1 GCGTTGCGATTTTG
27457 TTGGTCATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.18, C:0.15, G:0.32, T:0.35
Consensus pattern (40 bp):
GCGTTGCGATTTTGGAACCTGTGTTGCGAAATTAGAGTTC
Found at i:38503 original size:29 final size:29
Alignment explanation
Indices: 38468--38549 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
38458 AAACTAAATT
*
38468 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
38497 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
38526 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
38550 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:43255 original size:29 final size:29
Alignment explanation
Indices: 43220--43301 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
43210 AAACTAAATT
*
43220 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
43249 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
43278 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
43302 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:49124 original size:23 final size:23
Alignment explanation
Indices: 49098--49166 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
49088 CACCATAGCT
*
49098 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
49121 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
49144 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
49167 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:49353 original size:103 final size:103
Alignment explanation
Indices: 49182--49495 Score: 565
Period size: 103 Copynumber: 3.0 Consensus size: 103
49172 TAATGTCCAT
* * * *
49182 AAGGACTACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
49247 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
49285 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTATCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
49350 GACTTCACACATGTTCCAAAGAATACATATATGTCCCA
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
49388 AAGGACCACATATCATTCCTTAAGAATCATATACATATGTCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
49453 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
49491 AAGGA
1 AAGGA
49496 TCGCGTAGAC
Statistics
Matches: 202, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 202 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:54998 original size:34 final size:34
Alignment explanation
Indices: 54960--55029 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
54950 TAATTTTAAA
54960 ATTATGTAGATTGAGTATACCATTCACAACATGG
1 ATTATGTAGATTGAGTATACCATTCACAACATGG
54994 ATTATGTAGATTGAGTATACCATTCACAACATGG
1 ATTATGTAGATTGAGTATACCATTCACAACATGG
55028 AT
1 AT
55030 ACGTAATTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (34 bp):
ATTATGTAGATTGAGTATACCATTCACAACATGG
Found at i:55099 original size:14 final size:14
Alignment explanation
Indices: 55076--55108 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
55066 ATTATATTAT
*
55076 TAAAATATTAATTG
1 TAAAAAATTAATTG
55090 TAAAAAATTAATTG
1 TAAAAAATTAATTG
55104 TAAAA
1 TAAAA
55109 TTATATACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (14 bp):
TAAAAAATTAATTG
Found at i:56008 original size:29 final size:29
Alignment explanation
Indices: 55977--56070 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 29
55967 ATCAATTATA
55977 GGGTTTAATTTTTTTAATACTTATTATTAG
1 GGGTTTAATTTTTTTAATA-TTATTATTAG
* *
56007 GGGTTCAATATTTTCTTAATATATATTATTAT
1 GGGTTTAAT-TTTT-TTAATAT-TATTATTAG
* * *
56039 AGGCTTAGTTTTTTCTAATATTTATTATTAG
1 GGGTTTAATTTTTT-TAATA-TTATTATTAG
56070 G
1 G
56071 AGCATACTCT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
30 9 0.18
31 22 0.43
32 20 0.39
ACGTcount: A:0.28, C:0.05, G:0.13, T:0.54
Consensus pattern (29 bp):
GGGTTTAATTTTTTTAATATTATTATTAG
Found at i:58153 original size:2 final size:2
Alignment explanation
Indices: 58146--58173 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
58136 GTCATTGGAT
58146 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58174 AACTACTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59398 original size:2 final size:2
Alignment explanation
Indices: 59391--59416 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59381 AAATAATTAA
59391 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
59417 TGACTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60529 original size:14 final size:16
Alignment explanation
Indices: 60500--60531 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
60490 GCCTTCAGGC
60500 TTTACAAATAATAATA
1 TTTACAAATAATAATA
60516 TTTA-AAAT-ATAATA
1 TTTACAAATAATAATA
60530 TT
1 TT
60532 ATTATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTACAAATAATAATA
Found at i:60547 original size:18 final size:16
Alignment explanation
Indices: 60507--60562 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
60497 GGCTTTACAA
* *
60507 ATAATAATATTTAAAAT
1 ATAATAATATAT-ATAT
*
60524 ATAATATTAT-TATAT
1 ATAATAATATATATAT
60539 ATAATAATATATATAT
1 ATAATAATATATATAT
60555 ATAATAAT
1 ATAATAAT
60563 CATCATCACT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
15 12 0.34
16 14 0.40
17 9 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATAATATATATAT
Found at i:61901 original size:18 final size:18
Alignment explanation
Indices: 61873--61915 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
61863 TCTTCTTATT
61873 TTTACTTTAAT-TACTTTTA
1 TTTA-TTTAATCT-CTTTTA
61892 TTTATTTAATCTCTTTTA
1 TTTATTTAATCTCTTTTA
61910 -TTATTT
1 TTTATTT
61916 TAATATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.26
18 12 0.52
19 5 0.22
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTTAATCTCTTTTA
Found at i:68362 original size:31 final size:31
Alignment explanation
Indices: 68315--68383 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
68305 AGAAAGAAGA
68315 AAAAAAATAGCAGTTCGAAAAAAGAAAAAAAG
1 AAAAAAATAGCAGTTCGAAAAAA-AAAAAAAG
* * * *
68347 AAAAAAA-AGCTGTTCGAAAGAAAAAGAGAG
1 AAAAAAATAGCAGTTCGAAAAAAAAAAAAAG
68377 AAAAAAA
1 AAAAAAA
68384 GACATGAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 13 0.39
31 13 0.39
32 7 0.21
ACGTcount: A:0.68, C:0.06, G:0.17, T:0.09
Consensus pattern (31 bp):
AAAAAAATAGCAGTTCGAAAAAAAAAAAAAG
Found at i:70006 original size:18 final size:18
Alignment explanation
Indices: 69960--70002 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
69950 TCTTCTTATT
*
69960 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATCACTTTTA
69979 TTTATTTAATCACTTTTA
1 TTTATTTAATCACTTTTA
69997 -TTATTT
1 TTTATTT
70003 TAATATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCACTTTTA
Found at i:78382 original size:32 final size:31
Alignment explanation
Indices: 78328--78427 Score: 107
Period size: 32 Copynumber: 3.2 Consensus size: 31
78318 AGAGTCAAGG
**
78328 GTTACCTATGTCTTTCAAGACATATGGACAGT
1 GTTACCTATGTC-TTCGGGACATATGGACAGT
*
78360 GTTACCTTTGTCCTTCGGGACATATGGACAG-
1 GTTACCTATGT-CTTCGGGACATATGGACAGT
* *
78391 GATTACCTATGT-TTAGGGAAATATGGACAGT
1 G-TTACCTATGTCTTCGGGACATATGGACAGT
78422 -TTACCT
1 GTTACCT
78428 TGGTTCTTTG
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
29 6 0.10
30 16 0.27
31 1 0.02
32 35 0.59
33 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (31 bp):
GTTACCTATGTCTTCGGGACATATGGACAGT
Found at i:79743 original size:18 final size:19
Alignment explanation
Indices: 79710--79746 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
79700 AATCAGATGA
*
79710 AACACCAAATTGTAGAGTC
1 AACACCAAATTATAGAGTC
79729 AACACC-AATTATAGAGTC
1 AACACCAAATTATAGAGTC
79747 GCCACCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.22
Consensus pattern (19 bp):
AACACCAAATTATAGAGTC
Found at i:81380 original size:14 final size:16
Alignment explanation
Indices: 81351--81382 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
81341 GCCTTCGGGC
81351 TTTACAAATAATAATA
1 TTTACAAATAATAATA
81367 TTTA-AAAT-ATAATA
1 TTTACAAATAATAATA
81381 TT
1 TT
81383 ATTATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTACAAATAATAATA
Found at i:81607 original size:20 final size:20
Alignment explanation
Indices: 81584--81635 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
81574 AACGCGATCC
81584 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
81604 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
81624 CCAAAATCGCAA
1 CCAGAATCGCAA
81636 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:81703 original size:21 final size:21
Alignment explanation
Indices: 81621--81703 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
81611 CGCAAATCAG
81621 TTTCCAAAATCGCAACGCGAT
1 TTTCCAAAATCGCAACGCGAT
* * *
81642 TCTT-GAAAATCGCGATGCGAT
1 T-TTCCAAAATCGCAACGCGAT
** * * **
81663 AGTACAAATTCGCATTGCGAT
1 TTTCCAAAATCGCAACGCGAT
81684 TTTCCAAAATCGCAACGCGA
1 TTTCCAAAATCGCAACGCGA
81704 ATGAAATCGC
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
20 1 0.02
21 42 0.93
22 2 0.04
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (21 bp):
TTTCCAAAATCGCAACGCGAT
Found at i:81732 original size:20 final size:20
Alignment explanation
Indices: 81690--81880 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
81680 CGATTTTCCA
*
81690 AAATCGCAACGCGAAT--G-
1 AAATCGCAACGCGTATCCGT
* *
81707 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
81727 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
81747 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
81767 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
81787 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
81807 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
81827 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
81847 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
81868 AAATCGCAACGCG
1 AAATCGCAACGCG
81881 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
16 1 0.01
17 13 0.09
19 1 0.01
20 113 0.77
21 17 0.12
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:81777 original size:60 final size:60
Alignment explanation
Indices: 81690--81880 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
81680 CGATTTTCCA
* *
81690 AAATCGCAACGCGAAT--G-AAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
81747 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
81807 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
81868 AAATCGCAACGCG
1 AAATCGCAACGCG
81881 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
57 14 0.12
59 1 0.01
60 66 0.59
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:82298 original size:33 final size:33
Alignment explanation
Indices: 82259--82329 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
82249 TTCACTTAGA
*
82259 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
82292 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
82325 TTTCA
1 TTTCA
82330 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:82462 original size:14 final size:14
Alignment explanation
Indices: 82424--82497 Score: 67
Period size: 14 Copynumber: 4.7 Consensus size: 14
82414 AGATAATGAA
82424 AATCGCAACGAGAG
1 AATCGCAACGAGAG
82438 AACTGTCGCAACGAGAG
1 AA---TCGCAACGAGAG
*
82455 AATCGCAACGCGAAATGG
1 AATCGCAA--CGAGA--G
82473 AAATCGCAACGAGAG
1 -AATCGCAACGAGAG
82488 AATCGCAACG
1 AATCGCAACG
82498 CGAAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
14 18 0.36
15 1 0.02
16 4 0.08
17 18 0.36
18 1 0.02
19 8 0.16
ACGTcount: A:0.41, C:0.23, G:0.27, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:82510 original size:33 final size:33
Alignment explanation
Indices: 82443--82513 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
82433 GAGAGAACTG
***
82443 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
82476 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
82509 TCGCA
1 TCGCA
82514 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:82531 original size:19 final size:19
Alignment explanation
Indices: 82509--82606 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
82499 GAAACCAAAA
*
82509 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
82528 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
82542 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
82561 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
82575 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
82594 TCGCGTTGCGATT
1 TCGCGTTGCGATT
82607 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:82550 original size:14 final size:14
Alignment explanation
Indices: 82531--82620 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
82521 TTTCATTTCG
82531 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
82545 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
82564 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
82578 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
82595 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
82611 CGTTGCGATT
1 CGTTGCGATT
82621 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:82556 original size:33 final size:33
Alignment explanation
Indices: 82514--82628 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
82504 CAAAATCGCA
82514 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
82547 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
82580 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
82613 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
82629 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:84499 original size:90 final size:93
Alignment explanation
Indices: 84310--84774 Score: 842
Period size: 90 Copynumber: 5.1 Consensus size: 93
84300 TAGATTGCTT
84310 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AAACTGTGTATTCTTTAACACTGTGAAATAGT
84375 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
84404 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AA-A-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
84466 TTTGTCGTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84494 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84558 TTTGTCTTTGTTTTGTC--TTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84584 AGTAAATTTGTTCGGTTGCTG-CAATTCTGCTAAAC--TGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84646 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84673 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
84738 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
84766 AGTAAATTT
1 AGTAAATTT
84775 ATCCATTCAA
Statistics
Matches: 359, Mismatches: 2, Indels: 21
0.94 0.01 0.05
Matches are distributed among these distances:
87 6 0.02
88 37 0.10
89 64 0.18
90 110 0.31
91 2 0.01
92 57 0.16
93 51 0.14
94 32 0.09
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:84857 original size:19 final size:19
Alignment explanation
Indices: 84817--84951 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
84807 TAGTTTACTT
* *
84817 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
84837 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
84856 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
84875 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
84889 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
84908 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
**
84922 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
84941 TCGCAATGCGA
1 TCGCAACGCGA
84952 TTTTCATTTC
Statistics
Matches: 94, Mismatches: 11, Indels: 21
0.75 0.09 0.17
Matches are distributed among these distances:
14 19 0.20
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 50 0.53
20 13 0.14
ACGTcount: A:0.45, C:0.27, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:84896 original size:33 final size:32
Alignment explanation
Indices: 84853--84946 Score: 152
Period size: 33 Copynumber: 2.9 Consensus size: 32
84843 CGCGAAACCA
84853 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAATGAAAATCGCAACGAC
**
84885 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAATGAAAATCGCAACGAC
84918 AAGATCGCAACGCGAAATGAAAATCGCAA
1 AA-ATCGCAACGCGAAATGAAAATCGCAA
84947 TGCGATTTTC
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.47, C:0.26, G:0.19, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAATGAAAATCGCAACGAC
Found at i:84943 original size:52 final size:51
Alignment explanation
Indices: 84817--84951 Score: 141
Period size: 52 Copynumber: 2.6 Consensus size: 51
84807 TAGTTTACTT
*
84817 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
84869 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAATGA-A-AATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
* *
84922 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAACACGAAATGAAAATCGCAACGCGA
84952 TTTTCATTTC
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
50 4 0.06
51 6 0.09
52 44 0.66
53 4 0.06
54 7 0.10
55 2 0.03
ACGTcount: A:0.45, C:0.27, G:0.19, T:0.10
Consensus pattern (51 bp):
TCGCAACACGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:84982 original size:14 final size:14
Alignment explanation
Indices: 84963--85013 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
84953 TTTCATTTCG
*
84963 CGTTGCGATTCTTT
1 CGTTGCGATTCTCT
*
84977 CGTTGCGATT-TCG
1 CGTTGCGATTCTCT
* *
84990 CATTGCGATTCTGT
1 CGTTGCGATTCTCT
85004 CGTTGCGATT
1 CGTTGCGATT
85014 TTCATTTCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
13 10 0.33
14 20 0.67
ACGTcount: A:0.10, C:0.22, G:0.25, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:85029 original size:33 final size:33
Alignment explanation
Indices: 84947--85032 Score: 112
Period size: 27 Copynumber: 2.8 Consensus size: 33
84937 AAAATCGCAA
*
84947 TGCGATTTTCATTTCGCGTTGCGATTCTTTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
*
84980 TGCG------ATTTCGCATTGCGATTCTGTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
85007 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCGTTGCGATT
85033 TTGGTTTCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
27 25 0.57
33 19 0.43
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTGTCGT
Found at i:85061 original size:20 final size:19
Alignment explanation
Indices: 85004--85069 Score: 89
Period size: 19 Copynumber: 3.4 Consensus size: 19
84994 GCGATTCTGT
85004 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
85023 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
85042 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
*
85062 TGTTGCGA
1 CGTTGCGA
85070 AAGTAAACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.11, C:0.17, G:0.27, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Done.