Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000123.1 Hibiscus syriacus cultivar Beakdansim tig00000222_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: 85337
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2077 original size:42 final size:42
Alignment explanation
Indices: 2023--2178 Score: 185
Period size: 42 Copynumber: 3.8 Consensus size: 42
2013 TCATCGACGG
* * *
2023 GATTCTCCACTTCGACACCGAGATCCATCACCTCATCGAGTC
1 GATTCTACACCTCGACACCGAGATCCATCACCTCATCGAGAC
* * * *
2065 AATTCT-CTACTTCGACTCCGAGATCCATCACCTCATCGAGCC
1 GATTCTAC-ACCTCGACACCGAGATCCATCACCTCATCGAGAC
* *
2107 GATTCTACACCTCGACACCGATAGCCATCACCTC-T--AGAC
1 GATTCTACACCTCGACACCGAGATCCATCACCTCATCGAGAC
*
2146 GACTCTACACCTCGACACCGAGATCCATCACCT
1 GATTCTACACCTCGACACCGAGATCCATCACCT
2179 ATTCCATCAC
Statistics
Matches: 100, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
39 33 0.33
41 2 0.02
42 64 0.64
43 1 0.01
ACGTcount: A:0.26, C:0.39, G:0.13, T:0.22
Consensus pattern (42 bp):
GATTCTACACCTCGACACCGAGATCCATCACCTCATCGAGAC
Found at i:2304 original size:21 final size:21
Alignment explanation
Indices: 2278--2468 Score: 122
Period size: 21 Copynumber: 9.1 Consensus size: 21
2268 ACCTCCATGA
*
2278 GATGAGTTAGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
*
2299 GATGAGGTCA-GTGCTTTAAGT
1 GATGAGGT-AGGTGCTTTACGT
** * * ***
2320 GATGA-CAATGATGCATGGTGT
1 GATGAGGTA-GGTGCTTTACGT
2341 GATGAGGTAGG-GTCTTTACGT
1 GATGAGGTAGGTG-CTTTACGT
* *
2362 -AGTGAGGTAGCTGTTTTACGT
1 GA-TGAGGTAGGTGCTTTACGT
***
2383 GAT-AACAATGGTGCTTTACGT
1 GATGAGGTA-GGTGCTTTACGT
* * *
2404 GGTGAGGTAGCTGTTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* *
2425 GGTGAGGTAGCTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
*
2446 GATGAGGTAGGTGCTCTACGT
1 GATGAGGTAGGTGCTTTACGT
2467 GA
1 GA
2469 GATTATTTCA
Statistics
Matches: 127, Mismatches: 33, Indels: 20
0.71 0.18 0.11
Matches are distributed among these distances:
19 1 0.01
20 4 0.03
21 116 0.91
22 6 0.05
ACGTcount: A:0.21, C:0.11, G:0.35, T:0.34
Consensus pattern (21 bp):
GATGAGGTAGGTGCTTTACGT
Found at i:2385 original size:63 final size:62
Alignment explanation
Indices: 2278--2450 Score: 172
Period size: 63 Copynumber: 2.7 Consensus size: 62
2268 ACCTCCATGA
* * **
2278 GATGAGTTA-GGTGCTTTACGTGATGAGGTCAG-TGCTTTAAGTGATGACAATGATGCATGGTGT
1 GATGAGGTAGGGT-CTTTACGTG-TGAGGT-AGCTGCTTTACGTGATGACAATGATGCATGACGT
* * * * *
2341 GATGAGGTAGGGTCTTTACGTAGTGAGGTAGCTGTTTTACGTGATAACAATGGTGCTTTACGT
1 GATGAGGTAGGGTCTTTACGT-GTGAGGTAGCTGCTTTACGTGATGACAATGATGCATGACGT
* *
2404 GGTGAGGTAGCTGT-TTTACGTGGTGAGGTAGCTGCTTTACGTGATGA
1 GATGAGGTAG-GGTCTTTACGT-GTGAGGTAGCTGCTTTACGTGATGA
2451 GGTAGGTGCT
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
62 2 0.02
63 84 0.91
64 6 0.07
ACGTcount: A:0.21, C:0.10, G:0.34, T:0.34
Consensus pattern (62 bp):
GATGAGGTAGGGTCTTTACGTGTGAGGTAGCTGCTTTACGTGATGACAATGATGCATGACGT
Found at i:2586 original size:4 final size:4
Alignment explanation
Indices: 2577--2622 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
2567 TTTTTCGACA
* * * *
2577 TTAT TTAT TTAT TTAT TTAT TTAC TGAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
2623 TTAGCGGTCG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:2785 original size:21 final size:21
Alignment explanation
Indices: 2756--2846 Score: 85
Period size: 21 Copynumber: 4.3 Consensus size: 21
2746 GAAGAAGTAT
* * *
2756 GATCTACCTCTCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
** *
2777 GATCCACCTATCATCGTTCAA
1 GATCCACCTCCCATCGTTCAG
* *
2798 GAGGCC-CCTCCCATCGTTCAT
1 GA-TCCACCTCCCATCGTTCAG
*
2819 GATCCACATCCCATCGTTCAG
1 GATCCACCTCCCATCGTTCAG
2840 GATCCAC
1 GATCCAC
2847 ATTCCATACT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
20 2 0.04
21 53 0.93
22 2 0.04
ACGTcount: A:0.22, C:0.36, G:0.14, T:0.27
Consensus pattern (21 bp):
GATCCACCTCCCATCGTTCAG
Found at i:4709 original size:20 final size:20
Alignment explanation
Indices: 4709--4922 Score: 132
Period size: 20 Copynumber: 11.3 Consensus size: 20
4699 AACACGAAAA
* *
4709 TCGCAACTCGATATTCAAAT
1 TCGCAACTCGAAAATCAAAT
*
4729 TCGCAACTCAAAAATCAAAT
1 TCGCAACTCGAAAATCAAAT
*
4749 TCGCAACGCGAAAATCAAAT
1 TCGCAACTCGAAAATCAAAT
* *
4769 TAGCAA--C-ACAA--AAA-
1 TCGCAACTCGAAAATCAAAT
* * *
4783 TCGCAACTCGATATTCAATT
1 TCGCAACTCGAAAATCAAAT
* *
4803 TCGTAACTCGAAAATCGAAT
1 TCGCAACTCGAAAATCAAAT
4823 TCGCAA-TGCG---A--AAAT
1 TCGCAACT-CGAAAATCAAAT
**
4838 T-G-ATTTCGAAAATCAAAT
1 TCGCAACTCGAAAATCAAAT
* * *
4856 TCGCAACACGATATTCAAAT
1 TCGCAACTCGAAAATCAAAT
**
4876 TCGCAACTCGAAAATGGAAT
1 TCGCAACTCGAAAATCAAAT
* *
4896 TCGCAATTCGAAAATAAAAT
1 TCGCAACTCGAAAATCAAAT
*
4916 TCACAAC
1 TCGCAAC
4923 AAGAAAATAG
Statistics
Matches: 145, Mismatches: 34, Indels: 30
0.69 0.16 0.14
Matches are distributed among these distances:
13 3 0.02
14 7 0.05
15 7 0.05
16 2 0.01
17 6 0.04
18 6 0.04
19 4 0.03
20 110 0.76
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.23
Consensus pattern (20 bp):
TCGCAACTCGAAAATCAAAT
Found at i:4787 original size:54 final size:54
Alignment explanation
Indices: 4684--4882 Score: 161
Period size: 54 Copynumber: 3.7 Consensus size: 54
4674 ATACCTTTAA
* * ** *
4684 GAAAATCAAATTCGCAACACGAAAATCGCAACTCG-ATATTC-AAATTCGCAACTC
1 GAAAATCAAATTCGCAACACGAAAATC-AAATTCGCA-ACACAAAAATCGCAACTC
* * *
4738 AAAAATCAAATTCGCAACGCGAAAATCAAATTAGCAACACAAAAATCGCAACTC
1 GAAAATCAAATTCGCAACACGAAAATCAAATTCGCAACACAAAAATCGCAACTC
* * * * * * ** * * **
4792 GATATTCAATTTCGTAACTCGAAAATCGAATTCGCAATGCGAAAATTG-ATTTC
1 GAAAATCAAATTCGCAACACGAAAATCAAATTCGCAACACAAAAATCGCAACTC
* *
4845 GAAAATCAAATTCGCAACACGATATTCAAATTCGCAAC
1 GAAAATCAAATTCGCAACACGAAAATCAAATTCGCAAC
4883 TCGAAAATGG
Statistics
Matches: 112, Mismatches: 31, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
53 38 0.34
54 74 0.66
ACGTcount: A:0.44, C:0.23, G:0.12, T:0.22
Consensus pattern (54 bp):
GAAAATCAAATTCGCAACACGAAAATCAAATTCGCAACACAAAAATCGCAACTC
Found at i:4887 original size:40 final size:40
Alignment explanation
Indices: 4709--4901 Score: 151
Period size: 40 Copynumber: 5.2 Consensus size: 40
4699 AACACGAAAA
* *
4709 TCGCAACTCGATATTCAAATTCGCAACTCAAAAATCAAAT
1 TCGCAACGCGATATTCAAATTCGCAACTCGAAAATCAAAT
* * * *
4749 TCGCAACGCGAAAATCAAATTAGCAA--C-ACAA--AAA-
1 TCGCAACGCGATATTCAAATTCGCAACTCGAAAATCAAAT
* * * *
4783 TCGCAACTCGATATTCAATTTCGTAACTCGAAAATCGAAT
1 TCGCAACGCGATATTCAAATTCGCAACTCGAAAATCAAAT
* **
4823 TCGCAATGCG--A---AAATT-G-ATTTCGAAAATCAAAT
1 TCGCAACGCGATATTCAAATTCGCAACTCGAAAATCAAAT
* **
4856 TCGCAACACGATATTCAAATTCGCAACTCGAAAATGGAAT
1 TCGCAACGCGATATTCAAATTCGCAACTCGAAAATCAAAT
4896 TCGCAA
1 TCGCAA
4902 TTCGAAAATA
Statistics
Matches: 115, Mismatches: 25, Indels: 26
0.69 0.15 0.16
Matches are distributed among these distances:
33 21 0.18
34 21 0.18
35 8 0.07
36 1 0.01
37 6 0.05
38 7 0.06
39 3 0.03
40 48 0.42
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.23
Consensus pattern (40 bp):
TCGCAACGCGATATTCAAATTCGCAACTCGAAAATCAAAT
Found at i:4965 original size:74 final size:74
Alignment explanation
Indices: 4684--4964 Score: 320
Period size: 74 Copynumber: 3.8 Consensus size: 74
4674 ATACCTTTAA
* * * *
4684 GAAAATCAAATTCGCAACACGAAAATCGCAACTCGATATTCAAATTCGCAACTCAAAAATCAAAT
1 GAAAATCAAATTCACAACAAGAAAATCGCAACTCGATATTCAAATTCGCAACTCGAAAATCGAAT
*
4749 TCGCAACGC
66 TCGCAATGC
* *
4758 GAAAATCAAATT-AGCAACACA-AAAATCGCAACTCGATATTCAATTTCGTAACTCGAAAATCGA
1 GAAAATCAAATTCA-CAACA-AGAAAATCGCAACTCGATATTCAAATTCGCAACTCGAAAATCGA
4821 ATTCGCAATGC
64 ATTCGCAATGC
** * ** * * *
4832 GAAAATTGATTTCGA-AA-ATCAAATTCGCAACACGATATTCAAATTCGCAACTCGAAAATGGAA
1 GAAAATCAAATTC-ACAACAAGAAAATCGCAACTCGATATTCAAATTCGCAACTCGAAAATCGAA
*
4895 TTCGCAATTC
65 TTCGCAATGC
* * *
4905 GAAAATAAAATTCACAACAAGAAAATAGCAACTCGATATTTAAATTCGCAACGT-GAAAAT
1 GAAAATCAAATTCACAACAAGAAAATCGCAACTCGATATTCAAATTCGCAAC-TCGAAAAT
4965 GAAAATCGAA
Statistics
Matches: 173, Mismatches: 26, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
72 1 0.01
73 60 0.35
74 110 0.64
75 1 0.01
76 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.22
Consensus pattern (74 bp):
GAAAATCAAATTCACAACAAGAAAATCGCAACTCGATATTCAAATTCGCAACTCGAAAATCGAAT
TCGCAATGC
Found at i:5008 original size:20 final size:20
Alignment explanation
Indices: 4980--5032 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
4970 TCGAAATCGA
4980 TTTCGAGTTGCGAATT-TCAT
1 TTTCGAGTTGCGAATTAT-AT
*
5000 TTTCAAGTTGCGAATTATAT
1 TTTCGAGTTGCGAATTATAT
5020 TTTCGAGTTGCGA
1 TTTCGAGTTGCGA
5033 TTTTTGTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.43
Consensus pattern (20 bp):
TTTCGAGTTGCGAATTATAT
Found at i:5325 original size:18 final size:18
Alignment explanation
Indices: 5302--5337 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5292 AAGGCAGTTG
*
5302 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTAATTT
*
5320 TGATTGCGATTTTAATTT
1 TGATTGAGATTTTAATTT
5338 CCCTTTGCTT
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:0.22, C:0.03, G:0.19, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTAATTT
Found at i:7536 original size:24 final size:24
Alignment explanation
Indices: 7502--7555 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
7492 CTAAAACATC
*
7502 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
*
7526 ATCAAAGTCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
7550 ATCAAA
1 ATCAAA
7556 TTTCGAATAC
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:0.44, C:0.20, G:0.15, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:8528 original size:20 final size:20
Alignment explanation
Indices: 8479--8608 Score: 88
Period size: 20 Copynumber: 6.5 Consensus size: 20
8469 CAAAACATTT
* *
8479 GTGTTACGAAAATAAAAGTT-
1 GTGTTGCGAAATTAAAA-TTC
*
8499 GTTTTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAATTC
*
8519 GTGTTACG-AATTCGAAAA-TC
1 GTGTTGCGAAATT--AAAATTC
**
8539 AAGTTGCGAAA-TAAAATTC
1 GTGTTGCGAAATTAAAATTC
* * *
8558 GCGTTGCGAATTTAAAAATC
1 GTGTTGCGAAATTAAAATTC
** *
8578 GTGTTGCGAAAAAAGAAATTT
1 GTGTTGCGAAATTA-AAATTC
8599 GTGTTGCGAA
1 GTGTTGCGAA
8609 TTGTCAAATT
Statistics
Matches: 85, Mismatches: 18, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
18 4 0.05
19 16 0.19
20 45 0.53
21 20 0.24
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (20 bp):
GTGTTGCGAAATTAAAATTC
Found at i:8568 original size:39 final size:40
Alignment explanation
Indices: 8502--8588 Score: 113
Period size: 39 Copynumber: 2.2 Consensus size: 40
8492 AAAAGTTGTT
* *
8502 TTGCGAAATTAAAATTCGTGTTACGAATTCGAAAATCAAG
1 TTGCGAAATTAAAATTCGCGTTACGAATTCAAAAATCAAG
* * **
8542 TTGCGAAA-TAAAATTCGCGTTGCGAATTTAAAAATCGTG
1 TTGCGAAATTAAAATTCGCGTTACGAATTCAAAAATCAAG
8581 TTGCGAAA
1 TTGCGAAA
8589 AAAGAAATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
39 33 0.80
40 8 0.20
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (40 bp):
TTGCGAAATTAAAATTCGCGTTACGAATTCAAAAATCAAG
Found at i:8617 original size:21 final size:19
Alignment explanation
Indices: 8593--8693 Score: 76
Period size: 21 Copynumber: 5.0 Consensus size: 19
8583 GCGAAAAAAG
8593 AAATTTGTGTTGCGAATTGT
1 AAATTTGTGTTGCGAATT-T
* * *
8613 CAAATTCGAGTTGTGAATTT
1 -AAATTTGTGTTGCGAATTT
* * *
8633 GACTTATGTGTTGCGAATTCC
1 AAATT-TGTGTTGCGAATT-T
*
8654 AAATTTTGTGTTACGAATTCT
1 AAA-TTTGTGTTGCGAATT-T
*
8675 AAATTCGTGTTGCGAATTT
1 AAATTTGTGTTGCGAATTT
8694 GAAAACTTTG
Statistics
Matches: 62, Mismatches: 15, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
19 4 0.06
20 24 0.39
21 32 0.52
22 2 0.03
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.43
Consensus pattern (19 bp):
AAATTTGTGTTGCGAATTT
Found at i:8690 original size:20 final size:19
Alignment explanation
Indices: 8502--8693 Score: 87
Period size: 20 Copynumber: 9.5 Consensus size: 19
8492 AAAAGTTGTT
*
8502 TTGCGAAATTAAAATTCGTG
1 TTGCG-AATTTAAATTCGTG
* * * **
8522 TTACGAATTCGAAAATCAAG
1 TTGCGAATT-TAAATTCGTG
* * *
8542 TTGCGAAATAAAATTCGCG
1 TTGCGAATTTAAATTCGTG
*
8561 TTGCGAATTTAAAAATCGTG
1 TTGCGAATTT-AAATTCGTG
*** *
8581 TTGCGAAAAAAGAAATTTGTG
1 TTGCG--AATTTAAATTCGTG
*
8602 TTGCGAATTGTCAAATTCGAG
1 TTGCGAATT-T-AAATTCGTG
* * * *
8623 TTGTGAATTTGACTTATGTG
1 TTGCGAATTTAAATT-CGTG
* *
8643 TTGCGAATTCCAAATTTTGTG
1 TTGCGAATT-TAAA-TTCGTG
*
8664 TTACGAATTCTAAATTCGTG
1 TTGCGAATT-TAAATTCGTG
8684 TTGCGAATTT
1 TTGCGAATTT
8694 GAAAACTTTG
Statistics
Matches: 125, Mismatches: 38, Indels: 19
0.69 0.21 0.10
Matches are distributed among these distances:
19 24 0.19
20 53 0.42
21 44 0.35
22 4 0.03
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.36
Consensus pattern (19 bp):
TTGCGAATTTAAATTCGTG
Found at i:12878 original size:44 final size:43
Alignment explanation
Indices: 12814--12937 Score: 167
Period size: 44 Copynumber: 2.8 Consensus size: 43
12804 AGCTTCATCA
*
12814 AGATGTTGACTAAAAGAATCAGATACAAGATTCAAGTTTTATTT
1 AGATGTTGAC-AAAAGAATCAGATACAAGATTCAAGTTTCATTT
* * *
12858 GGATGTTGAGCAAAAGAATCAGATACAAGATTCAAATTTCGTTT
1 AGATGTTGA-CAAAAGAATCAGATACAAGATTCAAGTTTCATTT
* *
12902 AGATGTTGAACAAAATAACCAGATACAAGATTCAAG
1 AGATGTTG-ACAAAAGAATCAGATACAAGATTCAAG
12938 CTTCTAGTTG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
44 68 0.97
45 2 0.03
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.28
Consensus pattern (43 bp):
AGATGTTGACAAAAGAATCAGATACAAGATTCAAGTTTCATTT
Found at i:15729 original size:49 final size:49
Alignment explanation
Indices: 15657--15776 Score: 186
Period size: 49 Copynumber: 2.4 Consensus size: 49
15647 TTGTATCCTA
* *
15657 AAATAATGTTTTAAAAATAAATTTTAACCTTAAAATATCAGGGTTTATT
1 AAATAATGTTTTAAAAATAAATTTTAACCCTAAAATATCAGGATTTATT
*
15706 AAATAATGTTTTAAAAATAAATTTTAGCCCTAAAATATCAGGATTTATT
1 AAATAATGTTTTAAAAATAAATTTTAACCCTAAAATATCAGGATTTATT
* * *
15755 AAATAGTATTTTGAAAATAAAT
1 AAATAATGTTTTAAAAATAAAT
15777 GTACATAACT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 65 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (49 bp):
AAATAATGTTTTAAAAATAAATTTTAACCCTAAAATATCAGGATTTATT
Found at i:24581 original size:2 final size:2
Alignment explanation
Indices: 24576--24601 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24566 AAAATAGACA
24576 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
24602 TAAATTTTTA
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:25717 original size:26 final size:26
Alignment explanation
Indices: 25696--25745 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
25686 ACTTTTTTTT
*
25696 AAATAAAAACA-AAAACCATTTTCTGA
1 AAATAAAAACATAAAA-CATTTTTTGA
*
25722 AAATAAAAACATAAAATATTTTTT
1 AAATAAAAACATAAAACATTTTTT
25746 AGAACCAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (26 bp):
AAATAAAAACATAAAACATTTTTTGA
Found at i:27221 original size:20 final size:20
Alignment explanation
Indices: 27192--27244 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
27182 GATTTTCCAT
*
27192 AATCGAAACGCGAATATGA-A
1 AATCGAAACGCGAACAT-ATA
*
27212 AATCGTAACGCGAACATATA
1 AATCGAAACGCGAACATATA
*
27232 AATCGCAACGCGA
1 AATCGAAACGCGA
27245 TTCTGACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGAAACGCGAACATATA
Found at i:27300 original size:20 final size:20
Alignment explanation
Indices: 27253--27418 Score: 128
Period size: 20 Copynumber: 8.6 Consensus size: 20
27243 GATTCTGACT
27253 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGT-AA
* *
27274 ATTGCAACGTGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* *
27294 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGTATCCGTAA
* *
27314 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
*
27334 ATCGCAAC--G----CGGAA
1 ATCGCAACGAGTATCCGTAA
* *
27348 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
* * * *
27368 ATCGCAATGCGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
* * * *
27388 ATCGCAATGCGAATCTGTAA
1 ATCGCAACGAGTATCCGTAA
27408 ATCGCAACGAG
1 ATCGCAACGAG
27419 ATTCTGACTA
Statistics
Matches: 122, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
14 12 0.10
16 1 0.01
18 1 0.01
20 92 0.75
21 16 0.13
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:27333 original size:40 final size:39
Alignment explanation
Indices: 27253--27416 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 39
27243 GATTCTGACT
* * * * *
27253 ATCGCAACGAGTATCCGTAAAATTGCAACGTGTATCCGTAA
1 ATCGCAACGCGTAT-CGT-AAATCGCAACGAGAATACGTAA
27294 ATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATC-GTAAATCGCAACGAGAATACGTAA
27334 ATCGCAACGCG----G-AAATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCGTAAATCGCAACGAGAATACGTAA
* * * *
27368 ATCGCAATGCGAATACGTAAATCGCAATGCGAAT-CTGTAA
1 ATCGCAACGCGTAT-CGTAAATCGCAACGAGAATAC-GTAA
27408 ATCGCAACG
1 ATCGCAACG
27417 AGATTCTGAC
Statistics
Matches: 106, Mismatches: 9, Indels: 17
0.80 0.07 0.13
Matches are distributed among these distances:
34 32 0.30
35 1 0.01
39 2 0.02
40 56 0.53
41 15 0.14
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.20
Consensus pattern (39 bp):
ATCGCAACGCGTATCGTAAATCGCAACGAGAATACGTAA
Found at i:27374 original size:54 final size:54
Alignment explanation
Indices: 27292--27394 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
27282 GTGTATCCGT
* *
27292 AAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAACGCGG
1 AAATCGCAACGAGAATCTGTAAATCGCAACGAGAATACGTAAATCGCAACGCGG
* *
27346 AAATCGCAACGAGAATAC-GTAAATCGCAATGCGAATACGTAAATCGCAA
1 AAATCGCAACGAGAAT-CTGTAAATCGCAACGAGAATACGTAAATCGCAA
27395 TGCGAATCTG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 43 0.98
55 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.17
Consensus pattern (54 bp):
AAATCGCAACGAGAATCTGTAAATCGCAACGAGAATACGTAAATCGCAACGCGG
Found at i:27424 original size:20 final size:19
Alignment explanation
Indices: 27230--27422 Score: 96
Period size: 20 Copynumber: 9.9 Consensus size: 19
27220 CGCGAACATA
*
27230 TAAATCGCAACGCGATTC-
1 TAAATCGCAACGAGATTCG
* *
27248 TGACTATCGCAACGAGTATCCG
1 T-A-AATCGCAACGAG-ATTCG
* * *
27270 TAAAATTGCAACGTGTATCCG
1 T-AAATCGCAACGAG-ATTCG
*
27291 TAAATCGCAACGCG-TATCTG
1 TAAATCGCAACGAGAT-TC-G
*
27311 TAAATCGCAACGAGAATACG
1 TAAATCGCAACGAG-ATTCG
27331 TAAATCGCAAC--G---CG
1 TAAATCGCAACGAGATTCG
* *
27345 GAAATCGCAACGAGAATACG
1 TAAATCGCAACGAG-ATTCG
*
27365 TAAATCGCAATGCGA-ATACG
1 TAAATCGCAA--CGAGATTCG
* * *
27385 TAAATCGCAATGCGAATCTG
1 TAAATCGCAACGAGATTC-G
27405 TAAATCGCAACGAGATTC
1 TAAATCGCAACGAGATTC
27423 TGACTATCGC
Statistics
Matches: 136, Mismatches: 21, Indels: 34
0.71 0.11 0.18
Matches are distributed among these distances:
14 12 0.09
16 1 0.01
18 4 0.03
19 4 0.03
20 89 0.65
21 20 0.15
22 6 0.04
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (19 bp):
TAAATCGCAACGAGATTCG
Found at i:39408 original size:22 final size:21
Alignment explanation
Indices: 39366--39405 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
39356 GAGTTTGTTT
*
39366 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
39387 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
39406 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:42759 original size:14 final size:14
Alignment explanation
Indices: 42730--42766 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
42720 AGAAAAAGAA
42730 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
42745 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
42759 GAAGAAAA
1 GAAGAAAA
42767 TGACACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:44985 original size:33 final size:34
Alignment explanation
Indices: 44932--45021 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 34
44922 ATGTTTATCG
* ** *
44932 CAACGCGGAAATTACTATCGCAACGAGAGAATCA
1 CAACGCGGAAATGAAAATCGCAACGAGAAAATCA
* * *
44966 CAATGC-GAAATGAAAATCGCAACGTGAAAATCG
1 CAACGCGGAAATGAAAATCGCAACGAGAAAATCA
**
44999 CAACGCGGAAATGACTATCGCAA
1 CAACGCGGAAATGAAAATCGCAA
45022 TGCGAAATGA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
33 26 0.58
34 19 0.42
ACGTcount: A:0.42, C:0.22, G:0.21, T:0.14
Consensus pattern (34 bp):
CAACGCGGAAATGAAAATCGCAACGAGAAAATCA
Found at i:44995 original size:14 final size:14
Alignment explanation
Indices: 44976--45003 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
44966 CAATGCGAAA
44976 TGAAAATCGCAACG
1 TGAAAATCGCAACG
44990 TGAAAATCGCAACG
1 TGAAAATCGCAACG
45004 CGGAAATGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
TGAAAATCGCAACG
Found at i:45010 original size:14 final size:14
Alignment explanation
Indices: 44977--45010 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
44967 AATGCGAAAT
*
44977 GAAAATCGCAACGT
1 GAAAATCGCAACGC
44991 GAAAATCGCAACGC
1 GAAAATCGCAACGC
*
45005 GGAAAT
1 GAAAAT
45011 GACTATCGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (14 bp):
GAAAATCGCAACGC
Found at i:45020 original size:20 final size:19
Alignment explanation
Indices: 44970--45075 Score: 79
Period size: 19 Copynumber: 6.1 Consensus size: 19
44960 GAATCACAAT
44970 GCGAAATGAAAATCGCAA-
1 GCGAAATGAAAATCGCAAC
44988 -CG---TGAAAATCGCAAC
1 GCGAAATGAAAATCGCAAC
** *
45003 GCGGAAATGACTATCGCAAT
1 GC-GAAATGAAAATCGCAAC
45023 GCGAAATGAAAATCGCAA-
1 GCGAAATGAAAATCGCAAC
* * *
45041 -CG--A-GAGAATCACAAT
1 GCGAAATGAAAATCGCAAC
45056 GCGAAATGAAAATCGCAAC
1 GCGAAATGAAAATCGCAAC
45075 G
1 G
45076 AGGGAATCGC
Statistics
Matches: 67, Mismatches: 10, Indels: 21
0.68 0.10 0.21
Matches are distributed among these distances:
14 21 0.31
15 1 0.01
16 3 0.04
17 5 0.07
18 1 0.01
19 24 0.36
20 12 0.18
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GCGAAATGAAAATCGCAAC
Found at i:45025 original size:53 final size:52
Alignment explanation
Indices: 44961--45073 Score: 154
Period size: 53 Copynumber: 2.2 Consensus size: 52
44951 GCAACGAGAG
* * * *
44961 AATCACAATGCGAAATGAAAATCGCAACGTGAAAATCGCAACGCGGAAATGAC
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCACAACGC-GAAATGAA
* * *
45014 TATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCACAACGCGAAATGAA
45066 AATCGCAA
1 AATCGCAA
45074 CGAGGGAATC
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
52 14 0.27
53 38 0.73
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCACAACGCGAAATGAA
Found at i:45061 original size:33 final size:33
Alignment explanation
Indices: 45019--45096 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
45009 ATGACTATCG
45019 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
* *
45052 CAATGCGAAATGAAAATCGCAACGAGGGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAGAATCA
45085 CAATGCGAAATG
1 CAATGCGAAATG
45097 CGATTCTCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAGAATCA
Found at i:45255 original size:14 final size:14
Alignment explanation
Indices: 45235--45271 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
45225 ACATCAATTA
45235 ACAAATCAACTTTT
1 ACAAATCAACTTTT
* *
45249 TCAAATCATCTTTT
1 ACAAATCAACTTTT
45263 ACAAATCAA
1 ACAAATCAA
45272 TTAAACAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:46703 original size:42 final size:41
Alignment explanation
Indices: 46621--46726 Score: 97
Period size: 42 Copynumber: 2.5 Consensus size: 41
46611 AATCGGGCTC
* * *
46621 TTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGCCTA
1 TTGAACGGTGGGAGGGGA-CTC-TCAAAGATGACAGGGGCCTA
* *
46663 TTGAACGGTGGGAGGGGACTCTCAAAGAATGATAGGGGCCTC
1 TTGAACGGTGGGAGGGGACTCTCAAAG-ATGACAGGGGCCTA
* * * *
46705 TTCAACGATAGGAGTGGACTCT
1 TTGAACGGTGGGAGGGGACTCT
46727 TTAGGGATGA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
41 5 0.09
42 44 0.83
43 4 0.08
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (41 bp):
TTGAACGGTGGGAGGGGACTCTCAAAGATGACAGGGGCCTA
Found at i:48763 original size:19 final size:19
Alignment explanation
Indices: 48699--48825 Score: 122
Period size: 19 Copynumber: 6.8 Consensus size: 19
48689 TCTTTTGGTT
*
48699 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
48718 GAGAATGAAAATCGCAATGC
1 GA-AATGAAAATCGCAACGC
**
48738 AGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
48758 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
48775 G--A-GAGAATCGCGTA-GC
1 GAAATGAAAATCGC-AACGC
*
48791 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
48810 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
48826 TGCTGTTTTG
Statistics
Matches: 87, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
14 8 0.09
15 2 0.02
16 2 0.02
17 2 0.02
18 2 0.02
19 40 0.46
20 29 0.33
21 2 0.02
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:48889 original size:21 final size:21
Alignment explanation
Indices: 48863--48921 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
48853 CGCGTTGCGA
48863 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
48884 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
48905 TT-TCAT-GTTGCGATTTT
1 TTCTC-TCGTTGCGATTTT
48922 AAGTTTAGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 11 0.33
21 22 0.67
ACGTcount: A:0.12, C:0.20, G:0.17, T:0.51
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:49220 original size:22 final size:22
Alignment explanation
Indices: 49168--49220 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
49158 GTGAATGGTT
*
49168 GTGAGGGATTTCGCCGGAGATG
1 GTGAGAGATTTCGCCGGAGATG
* * *
49190 GGGACAGATTTCGCCGTAGA-G
1 GTGAGAGATTTCGCCGGAGATG
49211 AGTGAGAGAT
1 -GTGAGAGAT
49221 GGAGATGGGA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.25, C:0.13, G:0.42, T:0.21
Consensus pattern (22 bp):
GTGAGAGATTTCGCCGGAGATG
Found at i:49439 original size:40 final size:41
Alignment explanation
Indices: 49373--49540 Score: 148
Period size: 40 Copynumber: 4.1 Consensus size: 41
49363 TTAAAAATCG
* *
49373 CGTTACGATTTACGTATTCGCATTGCGA-TTTACGGATATA
1 CGTTGCGATTTACGTATTCTCATTGCGATTTTACGGATATA
* * * * **
49413 CATTGCGATTTACGTATTCTCGTTGCGA-ATTACAGATACG
1 CGTTGCGATTTACGTATTCTCATTGCGATTTTACGGATATA
* * *
49453 CGTTGCGATTTACGTATTGTCATTGCGATTTTACGTAT-TGT
1 CGTTGCGATTTACGTATTCTCATTGCGATTTTACGGATAT-A
* * *
49494 CGTTGCGATTTACGGATACGT-GTTGCGATTTTACGGATACT-
1 CGTTGCGATTTACGTATTC-TCATTGCGATTTTACGGATA-TA
49535 CGTTGC
1 CGTTGC
49541 AATAGTCAGA
Statistics
Matches: 102, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
40 57 0.56
41 43 0.42
42 1 0.01
43 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTACGTATTCTCATTGCGATTTTACGGATATA
Found at i:49512 original size:61 final size:60
Alignment explanation
Indices: 49373--49532 Score: 196
Period size: 60 Copynumber: 2.6 Consensus size: 60
49363 TTAAAAATCG
* * * *
49373 CGTTACGATTTACGTATTCGCATTGCGATTTACGGATATACATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATATACATTGCGATTTACGTATTCT
* * * * *
49433 CGTTGCGAATTACAGATACGCGTTGCGATTTACGTAT-TGTCATTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATAT-ACATTGCGA-TTTACGTATTCT
*
49494 CGTTGCGATTTACGGATACGTGTTGCGATTTTACGGATA
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGGATA
49533 CTCGTTGCAA
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
59 1 0.01
60 38 0.46
61 36 0.43
62 8 0.10
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.39
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATATACATTGCGATTTACGTATTCT
Found at i:49518 original size:20 final size:21
Alignment explanation
Indices: 49373--49540 Score: 120
Period size: 20 Copynumber: 8.3 Consensus size: 21
49363 TTAAAAATCG
* * *
49373 CGTTACGATTTACGTATTCG-
1 CGTTGCGATTTACGGATACGT
*
49393 CATTGCGATTTACGGATA--T
1 CGTTGCGATTTACGGATACGT
* * *
49412 ACATTGCGATTTACGTATTC-T
1 -CGTTGCGATTTACGGATACGT
* *
49433 CGTTGCGAATTACAGATACG-
1 CGTTGCGATTTACGGATACGT
* *
49453 CGTTGCGATTTACGTAT-TGT
1 CGTTGCGATTTACGGATACGT
* * *
49473 CATTGCGATTTTACGTAT-TGT
1 CGTTGCGA-TTTACGGATACGT
49494 CGTTGCGATTTACGGATACGT
1 CGTTGCGATTTACGGATACGT
49515 -GTTGCGATTTTACGGATAC-T
1 CGTTGCGA-TTTACGGATACGT
49535 CGTTGC
1 CGTTGC
49541 AATAGTCAGA
Statistics
Matches: 120, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
19 1 0.01
20 81 0.68
21 38 0.32
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.39
Consensus pattern (21 bp):
CGTTGCGATTTACGGATACGT
Found at i:51299 original size:2 final size:2
Alignment explanation
Indices: 51292--51341 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
51282 CAATTATTTA
51292 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
51334 AT AT AT AT
1 AT AT AT AT
51342 TCTTGGATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52835 original size:51 final size:52
Alignment explanation
Indices: 52730--52852 Score: 203
Period size: 51 Copynumber: 2.4 Consensus size: 52
52720 AAACACCTTA
* * *
52730 AAGACGCCGGGAGATCCCAAGCAAGATCGAAAAAAAATCTGATTCAACCCTG
1 AAGACGCCGAGATATCCCAAGCAAGATCAAAAAAAAATCTGATTCAACCCTG
*
52782 AAGACGCCGAGATATCCCAAGCAAGA-CAAAAAAAAATCTGGTTCAACCCTG
1 AAGACGCCGAGATATCCCAAGCAAGATCAAAAAAAAATCTGATTCAACCCTG
52833 AAGACGCCGAGATATCCCAA
1 AAGACGCCGAGATATCCCAA
52853 ATCTACTATT
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
51 43 0.64
52 24 0.36
ACGTcount: A:0.41, C:0.26, G:0.20, T:0.13
Consensus pattern (52 bp):
AAGACGCCGAGATATCCCAAGCAAGATCAAAAAAAAATCTGATTCAACCCTG
Found at i:55604 original size:13 final size:14
Alignment explanation
Indices: 55586--55614 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
55576 ATTATTTTAA
55586 AAATTTTAAA-AAT
1 AAATTTTAAATAAT
55599 AAATTTTAAATAAT
1 AAATTTTAAATAAT
55613 AA
1 AA
55615 TAAGTCAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATTTTAAATAAT
Found at i:60288 original size:7 final size:7
Alignment explanation
Indices: 60276--60300 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
60266 TATAATTGTG
60276 TTTTATA
1 TTTTATA
60283 TTTTATA
1 TTTTATA
60290 TTTTATA
1 TTTTATA
60297 TTTT
1 TTTT
60301 TTTTCATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTATA
Found at i:60768 original size:50 final size:50
Alignment explanation
Indices: 60671--60768 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 50
60661 CATCCTTAGC
* * * *
60671 AGGAAAGCGCGACCCTGCACCGCGCTATATGCTGATTTGGCGCCACGTAT
1 AGGAAAGCGCGACCCTGAACCGCGCTATACGCTGATCTGGCGACACGTAT
*
60721 AGGAAAGCGCGCACCCTGAACCGCGCTATACGTTGA-CTGG-GTACACGT
1 AGGAAAGCGCG-ACCCTGAACCGCGCTATACGCTGATCTGGCG-ACACGT
60769 GGGGTATAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
49 1 0.02
50 19 0.46
51 21 0.51
ACGTcount: A:0.23, C:0.30, G:0.29, T:0.18
Consensus pattern (50 bp):
AGGAAAGCGCGACCCTGAACCGCGCTATACGCTGATCTGGCGACACGTAT
Found at i:64682 original size:6 final size:6
Alignment explanation
Indices: 64666--64722 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
64656 ACTCCTCACT
* * * * * *
64666 GTCATC ATCATC GTCATC GTCGTC GTCACC ATCATC ATCGTC GTCATC
1 GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC GTCATC
*
64714 GTCGTC GTC
1 GTCATC GTC
64723 CTGAGCAGGT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.16, C:0.35, G:0.18, T:0.32
Consensus pattern (6 bp):
GTCATC
Found at i:66728 original size:111 final size:111
Alignment explanation
Indices: 66592--66813 Score: 381
Period size: 111 Copynumber: 2.0 Consensus size: 111
66582 ATTACAAAAA
* * * *
66592 TTAATTTTTAATCTAATAATTATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* * *
66657 AATTAAAACGTTAAAATGTTACCGTATCAGTAAATTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66703 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
66768 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66814 ATGATTTCCA
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:67194 original size:50 final size:50
Alignment explanation
Indices: 67103--67215 Score: 120
Period size: 50 Copynumber: 2.3 Consensus size: 50
67093 TAACACGGAT
* * *
67103 CAGGGGGAGCGCTATACCCACGTGGAACCAGATCACTATATATCGCGGGG
1 CAGGGGGCGCGCTATACCCACGTGGAACCAAATCACTATATAACGCGGGG
* *** **
67153 CAGGGGGCGCGCTATATCCACGTGGCGTCAAATCAAC-ATATAACGCGGTT
1 CAGGGGGCGCGCTATACCCACGTGGAACCAAATC-ACTATATAACGCGGGG
*
67203 CAGGAGGCGCGCT
1 CAGGGGGCGCGCT
67216 TTCCTGCTAA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 50 0.96
51 2 0.04
ACGTcount: A:0.25, C:0.27, G:0.32, T:0.17
Consensus pattern (50 bp):
CAGGGGGCGCGCTATACCCACGTGGAACCAAATCACTATATAACGCGGGG
Found at i:71896 original size:63 final size:63
Alignment explanation
Indices: 71797--71926 Score: 260
Period size: 63 Copynumber: 2.1 Consensus size: 63
71787 GTCTATTCCA
71797 GACGTTGCTTGTCTTACTTGATGAATGATAAGCCACAACAGGCTCTCAGGCTCTCGGGTATGC
1 GACGTTGCTTGTCTTACTTGATGAATGATAAGCCACAACAGGCTCTCAGGCTCTCGGGTATGC
71860 GACGTTGCTTGTCTTACTTGATGAATGATAAGCCACAACAGGCTCTCAGGCTCTCGGGTATGC
1 GACGTTGCTTGTCTTACTTGATGAATGATAAGCCACAACAGGCTCTCAGGCTCTCGGGTATGC
71923 GACG
1 GACG
71927 CAAGCGCAGG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (63 bp):
GACGTTGCTTGTCTTACTTGATGAATGATAAGCCACAACAGGCTCTCAGGCTCTCGGGTATGC
Found at i:74532 original size:2 final size:2
Alignment explanation
Indices: 74527--74552 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
74517 AGATTATGAC
74527 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
74553 TGGAACAGAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:79463 original size:15 final size:15
Alignment explanation
Indices: 79443--79474 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
79433 CGCACTCGCC
79443 CTCCAGTCGCCGAAT
1 CTCCAGTCGCCGAAT
79458 CTCCAGTCGCCGAAT
1 CTCCAGTCGCCGAAT
79473 CT
1 CT
79475 TCGCGGCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.41, G:0.19, T:0.22
Consensus pattern (15 bp):
CTCCAGTCGCCGAAT
Found at i:79898 original size:25 final size:25
Alignment explanation
Indices: 79859--79917 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
79849 AAAAAAATAA
79859 AAAATAAATAAATTACTAATTATTTT
1 AAAA-AAATAAATTACTAATTATTTT
* * * * *
79885 ATAAAAATATATTATTTATTTTTTT
1 AAAAAAATAAATTACTAATTATTTT
79910 AAAAAAAT
1 AAAAAAAT
79918 CTACTATTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 24 0.89
26 3 0.11
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
AAAAAAATAAATTACTAATTATTTT
Found at i:81036 original size:25 final size:25
Alignment explanation
Indices: 80998--81046 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
80988 TTTAAAATTA
80998 GATTGAACTCAATTCGAAAGTTTTT
1 GATTGAACTCAATTCGAAAGTTTTT
* *
81023 GATTGAACTTAATTTGAAAGTTTT
1 GATTGAACTCAATTCGAAAGTTTT
81047 CGAGTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (25 bp):
GATTGAACTCAATTCGAAAGTTTTT
Found at i:81683 original size:7 final size:7
Alignment explanation
Indices: 81657--81778 Score: 82
Period size: 7 Copynumber: 18.0 Consensus size: 7
81647 GACACAATTA
81657 ATATATT
1 ATATATT
81664 AT-TATAT
1 ATATAT-T
81671 AGTATATT
1 A-TATATT
81679 ATATATT
1 ATATATT
81686 ATATATT
1 ATATATT
81693 ATATGA-T
1 ATAT-ATT
*
81700 ATA-AGT
1 ATATATT
81706 ATATTATTT
1 ATA-TA-TT
*
81715 ATATTTT
1 ATATATT
81722 ATATATT
1 ATATATT
**
81729 -GGTA-T
1 ATATATT
*
81734 ATGTATT
1 ATATATT
81741 ATATATT
1 ATATATT
81748 AT-TATT
1 ATATATT
81754 AT-TATT
1 ATATATT
81760 AT-TATT
1 ATATATT
81766 AT-TATT
1 ATATATT
*
81772 ATTTATT
1 ATATATT
81779 TTTATTTATT
Statistics
Matches: 97, Mismatches: 7, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
5 2 0.02
6 36 0.37
7 46 0.47
8 6 0.06
9 7 0.07
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (7 bp):
ATATATT
Found at i:81687 original size:19 final size:19
Alignment explanation
Indices: 81658--81778 Score: 101
Period size: 19 Copynumber: 6.4 Consensus size: 19
81648 ACACAATTAA
*
81658 TATATTATTATATAGTATAT
1 TATA-TATTATATATTATAT
81678 TATATATTATATATTATAT
1 TATATATTATATATTATAT
*
81697 GATATA--AGTATATTAT-T
1 TATATATTA-TATATTATAT
* *
81714 TATATTTTATATATTGGTA-
1 TATATATTATATATT-ATAT
*
81733 TATGTATTATATATTATTAT
1 TATATATTATATATTA-TAT
81753 TAT-TATTAT-TATTATTAT
1 TATATATTATATATTA-TAT
*
81771 TATTTATT
1 TATATATT
81779 TTTATTTATT
Statistics
Matches: 85, Mismatches: 8, Indels: 17
0.77 0.07 0.15
Matches are distributed among these distances:
17 6 0.07
18 26 0.31
19 46 0.54
20 7 0.08
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TATATATTATATATTATAT
Found at i:81752 original size:3 final size:3
Alignment explanation
Indices: 81737--81784 Score: 69
Period size: 3 Copynumber: 15.3 Consensus size: 3
81727 TTGGTATATG
*
81737 TAT TAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TTT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
81784 T
1 T
81785 TATTTAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 35 0.85
4 6 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:83154 original size:9 final size:9
Alignment explanation
Indices: 83121--83161 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
83111 TTTTTTATTC
83121 TTTTA-TTA
1 TTTTATTTA
83129 TTTAATATTTA
1 TTT--TATTTA
83140 -TTTATTTA
1 TTTTATTTA
83148 TTTTATTTA
1 TTTTATTTA
83157 TTTTA
1 TTTTA
83162 CAGCTGTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 9 0.31
9 13 0.45
10 4 0.14
11 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTATTTA
Found at i:83207 original size:2 final size:2
Alignment explanation
Indices: 83200--83284 Score: 117
Period size: 2 Copynumber: 45.0 Consensus size: 2
83190 GTTATTTTGT
83200 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
* *
83242 TA TA T- TA T- TT TT TA TA TA TA TA TA TA TA TA TA -A TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
83280 -A TA TA
1 TA TA TA
83285 GTTTGTGAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
1 5 0.06
2 72 0.94
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:83401 original size:25 final size:25
Alignment explanation
Indices: 83373--83433 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 25
83363 TTGAAAATAT
83373 TTTTAAAAATATATATAATATATAG
1 TTTTAAAAATATATATAATATATAG
* *
83398 TTTTGAAAACATTTATATATTATATAG
1 TTTT-AAAA-ATATATATAATATATAG
*
83425 TTTTTAAAA
1 TTTTAAAAA
83434 CATTTTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 5 0.16
26 7 0.23
27 19 0.61
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (25 bp):
TTTTAAAAATATATATAATATATAG
Found at i:83422 original size:27 final size:27
Alignment explanation
Indices: 83384--83438 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
83374 TTTAAAAATA
83384 TATATAATATATAGTTTTGAAAACATT
1 TATATAATATATAGTTTTGAAAACATT
* *
83411 TATATATTATATAGTTTTTAAAACATT
1 TATATAATATATAGTTTTGAAAACATT
83438 T
1 T
83439 TGAAAACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (27 bp):
TATATAATATATAGTTTTGAAAACATT
Found at i:83423 original size:38 final size:36
Alignment explanation
Indices: 83398--83658 Score: 153
Period size: 38 Copynumber: 7.3 Consensus size: 36
83388 TAATATATAG
*
83398 TTTTGAAAACATTTATATATTATATAGTTTTTAAAACA
1 TTTTGAAAACATTTATATATTATATA--TTATAAAACA
*
83436 TTTTGAAAACATTTATATATTATATAGTTTTTAAAACA
1 TTTTGAAAACATTTATATATTATATA--TTATAAAACA
83474 TTTTGAAAAC--TTATATA-TAGT-T-TT-TAAAACA
1 TTTTGAAAACATTTATATATTA-TATATTATAAAACA
* *
83505 TTTTGAAAAC--TTATATATTTATAATTCTTTTAAAACA
1 TTTTGAAAACATTTATATA-TTAT-A-TATTATAAAACA
** *
83542 TTTTTGAAAA-A-TTATATAAGATATAATTTTAAAAACA
1 -TTTTGAAAACATTTATATATTATAT-ATTAT-AAAACA
* *
83579 TTTTTGGAAAA-A-TTATATAATATATAGTTCTAAAGACA
1 -TTTT-GAAAACATTTATATATTATATA-TTATAAA-ACA
*
83617 TTTTTTGAAAAC--TTATATA--ATAT-TTTTAAAACA
1 --TTTTGAAAACATTTATATATTATATATTATAAAACA
83650 -TTTGAAAAC
1 TTTTGAAAAC
83659 TATATAATAT
Statistics
Matches: 200, Mismatches: 6, Indels: 42
0.81 0.02 0.17
Matches are distributed among these distances:
30 9 0.05
31 24 0.12
32 3 0.01
33 5 0.03
34 6 0.03
35 5 0.03
36 19 0.09
37 24 0.12
38 100 0.50
39 5 0.03
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.45
Consensus pattern (36 bp):
TTTTGAAAACATTTATATATTATATATTATAAAACA
Found at i:83428 original size:65 final size:65
Alignment explanation
Indices: 83348--83522 Score: 210
Period size: 65 Copynumber: 2.6 Consensus size: 65
83338 CGAAAGTTTG
* * *
83348 TATATTATATGGTTTTTGAAAATATTTTTAAAA-ATATATATAATATATAGTTTTGAAAACATTT
1 TATATTATATAGTTTTT-AAAACATTTTGAAAACATATATATAATATATAGTTTTGAAAACATTT
83412 A
65 A
* * *
83413 TATATTATATAGTTTTTAAAACATTTTGAAAACATTTATATATTATATAGTTTTTAAAACATTT-
1 TATATTATATAGTTTTTAAAACATTTTGAAAACATATATATAATATATAGTTTTGAAAACATTTA
* *
83477 TGAAAACTTATATATAGTTTTTAAAACATTTTGAAAACTTATATAT
1 T--ATA--T-TATATAGTTTTTAAAACATTTTGAAAACATATATAT
83523 TTATAATTCT
Statistics
Matches: 95, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
64 14 0.15
65 44 0.46
66 2 0.02
68 1 0.01
69 34 0.36
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.47
Consensus pattern (65 bp):
TATATTATATAGTTTTTAAAACATTTTGAAAACATATATATAATATATAGTTTTGAAAACATTTA
Found at i:83494 original size:31 final size:31
Alignment explanation
Indices: 83456--83522 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
83446 ATTTATATAT
83456 TATATAGTTTTTAAAACATTTTGAAAACTTA
1 TATATAGTTTTTAAAACATTTTGAAAACTTA
83487 TATATAGTTTTTAAAACATTTTGAAAACTTA
1 TATATAGTTTTTAAAACATTTTGAAAACTTA
83518 TATAT
1 TATAT
83523 TTATAATTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (31 bp):
TATATAGTTTTTAAAACATTTTGAAAACTTA
Found at i:83551 original size:107 final size:107
Alignment explanation
Indices: 83398--83597 Score: 266
Period size: 105 Copynumber: 1.9 Consensus size: 107
83388 TAATATATAG
** *
83398 TTTTGAAAACATTTATATATTATATAGTTTTTAAAACATTTTGAAAACATTTATATATTATATAG
1 TTTTGAAAACATTTATATATTATATAGTTTTTAAAACATTTTGAAAA-A-TTATATAAGATATAA
* *
83463 TTTTTAAAACA-TTTT-GAAAACTTATATATAGTTTTTAAAACA
64 TTTTAAAAACATTTTTGGAAAAATTATATATAGTTTTTAAAACA
*
83505 TTTTGAAAAC--TTATATATT-TATAATTCTTTTAAAACATTTTTGAAAAATTATATAAGATATA
1 TTTTGAAAACATTTATATATTATAT-AGT-TTTTAAAACA-TTTTGAAAAATTATATAAGATATA
83567 ATTTTAAAAACATTTTTGGAAAAATTATATA
63 ATTTTAAAAACATTTTTGGAAAAATTATATA
83598 ATATATAGTT
Statistics
Matches: 82, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
104 3 0.04
105 33 0.40
106 15 0.18
107 31 0.38
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (107 bp):
TTTTGAAAACATTTATATATTATATAGTTTTTAAAACATTTTGAAAAATTATATAAGATATAATT
TTAAAAACATTTTTGGAAAAATTATATATAGTTTTTAAAACA
Found at i:83577 original size:143 final size:144
Alignment explanation
Indices: 83398--83664 Score: 368
Period size: 143 Copynumber: 1.9 Consensus size: 144
83388 TAATATATAG
** * * *
83398 TTTTGAAAACATTTATATATTATATAGTTTTTAAAACA-TTTT-GAAAACATTTATATATTATAT
1 TTTTGAAAACATTTATATAAGATATAATTTTAAAAACATTTTTGGAAAA-A-TTATATAATATAT
*
83461 AGTTTTTAAA-ACA-TTTTGAAAACTTATAT-ATAGTTTTTAAAACATTTTGAAAACTTATATAT
64 AG-TTCTAAAGACATTTTTGAAAACTTATATAATA-TTTTTAAAACA-TTTGAAAAC-TATATAT
83523 TTATAATTCTTTTAAAACAT
125 TTATAATTCTTTTAAAACAT
83543 TTTTGAAAA-A-TTATATAAGATATAATTTTAAAAACATTTTTGGAAAAATTATATAATATATAG
1 TTTTGAAAACATTTATATAAGATATAATTTTAAAAACATTTTTGGAAAAATTATATAATATATAG
83606 TTCTAAAGACATTTTTTGAAAACTTATATAATATTTTTAAAACATTTGAAAACTATATA
66 TTCTAAAGACA-TTTTTGAAAACTTATATAATATTTTTAAAACATTTGAAAACTATATA
83665 ATATAGTTTT
Statistics
Matches: 110, Mismatches: 6, Indels: 14
0.85 0.05 0.11
Matches are distributed among these distances:
142 6 0.05
143 45 0.41
144 15 0.14
145 41 0.37
146 3 0.03
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.45
Consensus pattern (144 bp):
TTTTGAAAACATTTATATAAGATATAATTTTAAAAACATTTTTGGAAAAATTATATAATATATAG
TTCTAAAGACATTTTTGAAAACTTATATAATATTTTTAAAACATTTGAAAACTATATATTTATAA
TTCTTTTAAAACAT
Found at i:83746 original size:17 final size:16
Alignment explanation
Indices: 83720--83755 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
83710 TATTTTGAAG
83720 TATATATATTATAATT
1 TATATATATTATAATT
*
83736 TATATTATATTATTATT
1 TATA-TATATTATAATT
83753 TAT
1 TAT
83756 TCATTTTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATATATATTATAATT
Done.