Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008920.1 Hibiscus syriacus cultivar Beakdansim tig00112224_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: 1287743
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:376038 original size:15 final size:17
Alignment explanation
Indices: 376013--376046 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
376003 TAAAGGTCCT
376013 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
376029 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
376045 AA
1 AA
376047 CATATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:379927 original size:10 final size:10
Alignment explanation
Indices: 379914--379977 Score: 69
Period size: 10 Copynumber: 6.5 Consensus size: 10
379904 TTTTTTGAAA
*
379914 TTTTAGCTTT
1 TTTTGGCTTT
379924 TTTTGGCTTT
1 TTTTGGCTTT
* *
379934 TTTTTGTTTT
1 TTTTGGCTTT
379944 TTTTGGCTTTT
1 TTTTGGC-TTT
*
379955 TTTTGGCTCT
1 TTTTGGCTTT
379965 TTTT-G-TTT
1 TTTTGGCTTT
379973 TTTTG
1 TTTTG
379978 AAAAAACAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
8 6 0.13
9 1 0.02
10 28 0.62
11 10 0.22
ACGTcount: A:0.02, C:0.08, G:0.16, T:0.75
Consensus pattern (10 bp):
TTTTGGCTTT
Found at i:379953 original size:30 final size:30
Alignment explanation
Indices: 379914--379976 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
379904 TTTTTTGAAA
*
379914 TTTTAGC-TTTTTTTGGCTTTTTTTTGTTTT
1 TTTTAGCTTTTTTTTGGC-TCTTTTTGTTTT
*
379944 TTTTGGCTTTTTTTTGGCTCTTTTTGTTTT
1 TTTTAGCTTTTTTTTGGCTCTTTTTGTTTT
379974 TTT
1 TTT
379977 GAAAAAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.02, C:0.08, G:0.14, T:0.76
Consensus pattern (30 bp):
TTTTAGCTTTTTTTTGGCTCTTTTTGTTTT
Found at i:379958 original size:20 final size:20
Alignment explanation
Indices: 379921--379959 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
379911 AAATTTTAGC
379921 TTTTTTTGGCTTTTTTTTGT
1 TTTTTTTGGCTTTTTTTTGT
379941 TTTTTTTGGCTTTTTTTTG
1 TTTTTTTGGCTTTTTTTTG
379960 GCTCTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.05, G:0.15, T:0.79
Consensus pattern (20 bp):
TTTTTTTGGCTTTTTTTTGT
Found at i:379966 original size:13 final size:11
Alignment explanation
Indices: 379921--379968 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
379911 AAATTTTAGC
379921 TTTTTTTGGCT
1 TTTTTTTGGCT
379932 TTTTTTT-G-T
1 TTTTTTTGGCT
379941 TTTTTTTGGCT
1 TTTTTTTGGCT
379952 TTTTTTTGGCT
1 TTTTTTTGGCT
379963 CTTTTT
1 -TTTTT
379969 GTTTTTTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 8 0.24
10 2 0.06
11 19 0.56
12 5 0.15
ACGTcount: A:0.00, C:0.08, G:0.15, T:0.77
Consensus pattern (11 bp):
TTTTTTTGGCT
Found at i:380757 original size:15 final size:17
Alignment explanation
Indices: 380732--380765 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
380722 TAAAGGTCCT
380732 AAATAACTAATAAA-TA
1 AAATAACTAATAAACTA
380748 AAATAA-TAATAAACTA
1 AAATAACTAATAAACTA
380764 AA
1 AA
380766 CATATATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAACTAATAAACTA
Found at i:380854 original size:25 final size:22
Alignment explanation
Indices: 380825--380870 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
380815 TTTTTAACCC
380825 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
380850 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
380871 GCATCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:381748 original size:17 final size:17
Alignment explanation
Indices: 381723--381762 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
381713 CCTTAGAATG
*
381723 ATATGTAATATAATAGT
1 ATATATAATATAATAGT
381740 ATATATAATATAATAGT
1 ATATATAATATAATAGT
381757 ATATAT
1 ATATAT
381763 TATAAGGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (17 bp):
ATATATAATATAATAGT
Found at i:388576 original size:29 final size:30
Alignment explanation
Indices: 388542--388603 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
388532 TAAGATATAT
* *
388542 ACAACTAAGTGGAACATTTTGGA-AGACAA
1 ACAACTAAGTGGAACATTTGGGAGACACAA
* * *
388571 ACAACTTATTGGAGCATTTGGGAGACACAA
1 ACAACTAAGTGGAACATTTGGGAGACACAA
388601 ACA
1 ACA
388604 GCTCATAAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (30 bp):
ACAACTAAGTGGAACATTTGGGAGACACAA
Found at i:392854 original size:24 final size:23
Alignment explanation
Indices: 392826--392886 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
392816 ACTTTTCTTT
392826 CTTTCTTTTTCTTTTTTTCAAGTG
1 CTTTCTTTTTCTTTTTTT-AAGTG
** * *
392850 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCTTTTTCTTTTTTTAAGTG
392873 CTTT-TGTTTTCTTT
1 CTTTCT-TTTTCTTT
392887 GCTGAATTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
23 14 0.48
24 15 0.52
ACGTcount: A:0.08, C:0.16, G:0.10, T:0.66
Consensus pattern (23 bp):
CTTTCTTTTTCTTTTTTTAAGTG
Found at i:393874 original size:90 final size:90
Alignment explanation
Indices: 393700--393876 Score: 230
Period size: 90 Copynumber: 2.0 Consensus size: 90
393690 AATGATGTTT
**
393700 GGCCGAATAGGGAGAGAGTTCTTCATCTTGGTGCCTAAATAAACCACACGCAAGGCACATGGGGC
1 GGCCGAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATAAACCACACGCAAGGCACATGGGGC
* **
393765 TGTTCACATGTAAAACACATGGCTA
66 TGGTCACATACAAAACACATGGCTA
* * * *
393790 GGCCGAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATGATCCTCATGCAAGGCACATGGGGG
1 GGCCGAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATAAACCACACGCAAGGCACAT-GGGG
* **
393855 CTGGT-ATATACAAGGCACATGG
65 CTGGTCACATACAAAACACATGG
393877 GTGTTCTAGG
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
90 66 0.89
91 8 0.11
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.21
Consensus pattern (90 bp):
GGCCGAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATAAACCACACGCAAGGCACATGGGGC
TGGTCACATACAAAACACATGGCTA
Found at i:395229 original size:2 final size:2
Alignment explanation
Indices: 395222--395255 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
395212 ATATCACCCA
395222 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
395256 GCTTCCATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:399773 original size:10 final size:10
Alignment explanation
Indices: 399758--399813 Score: 51
Period size: 10 Copynumber: 5.2 Consensus size: 10
399748 TTTTTTATTC
399758 AAAAAAACAA
1 AAAAAAACAA
399768 AAAAAAACAA
1 AAAAAAACAA
399778 AAAAAGGAA-AGA
1 AAAAA--AACA-A
*
399790 AAAAAAAGGAAA
1 AAAAAAA--CAA
399802 AAAAAAACAA
1 AAAAAAACAA
399812 AA
1 AA
399814 CAAATGCCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
10 21 0.54
11 1 0.03
12 16 0.41
13 1 0.03
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:399795 original size:14 final size:13
Alignment explanation
Indices: 399758--399808 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
399748 TTTTTTATTC
*
399758 AAAAAAACAAAA-A
1 AAAAAAA-AAAAGG
399771 AAAACAAAAAAAGG
1 AAAA-AAAAAAAGG
399785 AAAGAAAAAAAAGG
1 AAA-AAAAAAAAGG
399799 AAAAAAAAAA
1 AAAAAAAAAA
399809 CAAAACAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
13 15 0.44
14 18 0.53
15 1 0.03
ACGTcount: A:0.86, C:0.04, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGG
Found at i:409837 original size:9 final size:10
Alignment explanation
Indices: 409815--409847 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
409805 ATTGGAGTGC
409815 AAAAAGAAAG
1 AAAAAGAAAG
*
409825 AAAAAGACA-
1 AAAAAGAAAG
409834 AAAAAGAAAG
1 AAAAAGAAAG
409844 AAAA
1 AAAA
409848 TTAGAAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:409856 original size:13 final size:12
Alignment explanation
Indices: 409833--409874 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
409823 AGAAAAAGAC
409833 AAAAAAG-AAAG
1 AAAAAAGAAAAG
*
409844 AAAATTAGAAAAG
1 AAAA-AAGAAAAG
409857 AAGAAAAGAAAAG
1 AA-AAAAGAAAAG
409870 AAAAA
1 AAAAA
409875 TTCAAAAAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 4 0.15
12 5 0.19
13 15 0.58
14 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:409881 original size:26 final size:26
Alignment explanation
Indices: 409826--409881 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
409816 AAAAGAAAGA
*
409826 AAAAGACAAAAAAGAAAGAAAATTAG
1 AAAAGACAAAAAAGAAAGAAAATTAC
*
409852 AAAAGA-AGAAAAGAAAAGAAAAATT-C
1 AAAAGACAAAAAAG-AAAG-AAAATTAC
409878 AAAA
1 AAAA
409882 AGAGAAAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 6 0.23
26 14 0.54
27 6 0.23
ACGTcount: A:0.75, C:0.04, G:0.14, T:0.07
Consensus pattern (26 bp):
AAAAGACAAAAAAGAAAGAAAATTAC
Found at i:414633 original size:18 final size:18
Alignment explanation
Indices: 414589--414627 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
414579 ACGGTGCAAC
* *
414589 TCTCCAGTTAAAATGAGG
1 TCTCCAGCTGAAATGAGG
414607 TCTCCAGCTGAAATGAGG
1 TCTCCAGCTGAAATGAGG
414625 TCT
1 TCT
414628 TTAGCTAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (18 bp):
TCTCCAGCTGAAATGAGG
Found at i:434829 original size:19 final size:20
Alignment explanation
Indices: 434787--434838 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
434777 GAAACCCCTT
*
434787 TGAAAATACATGATTTTTTGA
1 TGAAAATACATGA-TTTTTAA
434808 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
434827 TGAAGATACATG
1 TGAAAATACATG
434839 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.55
21 13 0.45
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:438235 original size:8 final size:8
Alignment explanation
Indices: 438222--438266 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
438212 ATCTTTTTCT
438222 TTTTCTTC
1 TTTTCTTC
438230 TTTTCTTC
1 TTTTCTTC
438238 TTTTCTTC
1 TTTTCTTC
438246 TTTT-TGTC
1 TTTTCT-TC
438254 TTTTCTTTC
1 TTTTC-TTC
438263 TTTT
1 TTTT
438267 TGTACTCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 1 0.03
8 26 0.76
9 6 0.18
10 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTCTTC
Found at i:438268 original size:17 final size:16
Alignment explanation
Indices: 438213--438269 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
438203 CTTTTTGAAA
*
438213 TCTTTTTCT-TTTTCT
1 TCTTTTTGTCTTTTCT
438228 TCTTTTCT-TCTTTTCT
1 TCTTTT-TGTCTTTTCT
438244 TCTTTTTGTCTTTTCTT
1 TCTTTTTGTCTTTTC-T
438261 TCTTTTTGT
1 TCTTTTTGT
438270 ACTCCAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.21
16 20 0.53
17 10 0.26
ACGTcount: A:0.00, C:0.19, G:0.04, T:0.77
Consensus pattern (16 bp):
TCTTTTTGTCTTTTCT
Found at i:439023 original size:20 final size:19
Alignment explanation
Indices: 438992--439041 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
438982 GAAACCCCTT
438992 TGAAAA-ACATGATTTTTAA
1 TGAAAATACATGA-TTTTAA
439011 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
*
439030 TGAAGATACATG
1 TGAAAATACATG
439042 CTCTTTGCCG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 23 0.79
20 6 0.21
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:442010 original size:19 final size:21
Alignment explanation
Indices: 441986--442037 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
441976 CGGCCAAGAG
*
441986 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
442005 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
442026 CATGTATTTTCA
1 CATGTATTTTCA
442038 AAGGGGATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:442719 original size:11 final size:11
Alignment explanation
Indices: 442703--442729 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
442693 TCATTGGCGT
442703 GAAAAGCAAAA
1 GAAAAGCAAAA
442714 GAAAAGCAAAA
1 GAAAAGCAAAA
442725 GAAAA
1 GAAAA
442730 TACTCCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (11 bp):
GAAAAGCAAAA
Found at i:444593 original size:16 final size:16
Alignment explanation
Indices: 444568--444600 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
444558 TAGTTAGCTC
*
444568 ATTTGCATTCTAACAT
1 ATTTGAATTCTAACAT
444584 ATTTGAATTCTAACAT
1 ATTTGAATTCTAACAT
444600 A
1 A
444601 GGTGGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.15, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGAATTCTAACAT
Found at i:449200 original size:36 final size:36
Alignment explanation
Indices: 449153--449236 Score: 150
Period size: 36 Copynumber: 2.3 Consensus size: 36
449143 GATACAATTT
449153 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
449189 GTCCATCACCATTATCACGTCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
449225 TTCCATCACCAT
1 GTCCATCACCAT
449237 ATCTTTCTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:451737 original size:22 final size:22
Alignment explanation
Indices: 451712--451754 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
451702 TTCTTTGGAG
*
451712 TGTATTGGTGAGATTTTTTTTT
1 TGTATTGGTGAGATTTATTTTT
*
451734 TGTATTGGTGAGGTTTATTTT
1 TGTATTGGTGAGATTTATTTT
451755 CATCTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.14, C:0.00, G:0.26, T:0.60
Consensus pattern (22 bp):
TGTATTGGTGAGATTTATTTTT
Found at i:453480 original size:18 final size:18
Alignment explanation
Indices: 453457--453502 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
453447 ATTCATGCAT
*
453457 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAATA
453475 TTAGTTCATTGAATAATA
1 TTAGTTCATTGAATAATA
*
453493 TTAATTCATT
1 TTAGTTCATT
453503 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAATA
Found at i:454709 original size:19 final size:20
Alignment explanation
Indices: 454662--454712 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
454652 GAAACCCCTT
*
454662 TGAAAATACATGATTTGTGA
1 TGAAAATACATGATTTGTAA
454682 TGAAAATACATGATTT-TAA
1 TGAAAATACATGATTTGTAA
*
454701 TGAAGATACATG
1 TGAAAATACATG
454713 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTGTAA
Found at i:457043 original size:26 final size:26
Alignment explanation
Indices: 457005--457059 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
456995 GGAAATATAA
457005 ATAAGAAATGGAAAAAGAAAGGAAATG
1 ATAAGAAATGGAAAAAGAAA-GAAATG
**
457032 ATAAG-AATGGAAATGGAAAGAAATG
1 ATAAGAAATGGAAAAAGAAAGAAATG
457057 ATA
1 ATA
457060 TCAAAGTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 9 0.35
26 12 0.46
27 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.25, T:0.15
Consensus pattern (26 bp):
ATAAGAAATGGAAAAAGAAAGAAATG
Found at i:457227 original size:35 final size:35
Alignment explanation
Indices: 457188--457263 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
457178 GAAGAAATGG
* * *
457188 GATGGTGATTATATAAGCGTGAAATGTAGATAGAA
1 GATGGTGATGATATAAGCGCGAAATGAAGATAGAA
* * *
457223 GATGGTGATGATATAGGCGCGATATGAAGATGGAA
1 GATGGTGATGATATAAGCGCGAAATGAAGATAGAA
457258 GATGGT
1 GATGGT
457264 ATAGATAGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.36, C:0.04, G:0.34, T:0.26
Consensus pattern (35 bp):
GATGGTGATGATATAAGCGCGAAATGAAGATAGAA
Found at i:460384 original size:20 final size:20
Alignment explanation
Indices: 460341--460391 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
460331 CGGCCAGGAG
* *
460341 CATGTATTTTC-TTTAAAGT
1 CATGTATTTTCATTAAAAAT
460360 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
460380 CATGTATTTTCA
1 CATGTATTTTCA
460392 AAGGGATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:462862 original size:16 final size:16
Alignment explanation
Indices: 462841--462880 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
462831 TAAGGGGGAT
462841 TTTCTTTAAATTAATC
1 TTTCTTTAAATTAATC
462857 TTTCTTTAAATTAATC
1 TTTCTTTAAATTAATC
*
462873 ATTCTTTA
1 TTTCTTTA
462881 TACCATAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTCTTTAAATTAATC
Found at i:464532 original size:16 final size:16
Alignment explanation
Indices: 464491--464534 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 16
464481 TGCTACAATA
464491 AAAACAAAAGAAAGAAG
1 AAAA-AAAAGAAAGAAG
464508 AAACAAAAAGAAA-AAG
1 AAA-AAAAAGAAAGAAG
464524 AAAAGAAAAGA
1 AAAA-AAAAGA
464535 CTCATACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.04
16 12 0.48
17 11 0.44
18 1 0.04
ACGTcount: A:0.80, C:0.05, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAGAAG
Found at i:464532 original size:17 final size:17
Alignment explanation
Indices: 464492--464526 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
464482 GCTACAATAA
464492 AAAC-AAAAGAAAGAAG
1 AAACAAAAAGAAAGAAG
464508 AAACAAAAAGAAA-AAG
1 AAACAAAAAGAAAGAAG
464524 AAA
1 AAA
464527 AGAAAAGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (17 bp):
AAACAAAAAGAAAGAAG
Found at i:464749 original size:16 final size:16
Alignment explanation
Indices: 464710--464762 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
464700 GAGTTGTAAG
*
464710 TTATCTTCACTTTCTTA
1 TTAT-TTCATTTTCTTA
*
464727 CTATTTCATTTTCTTA
1 TTATTTCATTTTCTTA
*
464743 TTCTTTCATCTATTCTTA
1 TTATTTCAT-T-TTCTTA
464761 TT
1 TT
464763 TCATTACCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 18 0.60
17 4 0.13
18 8 0.27
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATTTCATTTTCTTA
Found at i:465646 original size:18 final size:18
Alignment explanation
Indices: 465575--465646 Score: 51
Period size: 18 Copynumber: 4.2 Consensus size: 18
465565 AGGATTAGAT
465575 TTATTATTTTATTAGGAA
1 TTATTATTTTATTAGGAA
* ** *
465593 TTAATATTTGGTTA-AAA
1 TTATTATTTTATTAGGAA
* * **
465610 ATATTA-TCT-TTAGTTA
1 TTATTATTTTATTAGGAA
465626 TTATTATTTTATTAGGAA
1 TTATTATTTTATTAGGAA
465644 TTA
1 TTA
465647 GAGTTAAGAT
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
15 3 0.08
16 7 0.19
17 8 0.22
18 19 0.51
ACGTcount: A:0.35, C:0.01, G:0.10, T:0.54
Consensus pattern (18 bp):
TTATTATTTTATTAGGAA
Found at i:467697 original size:25 final size:22
Alignment explanation
Indices: 467668--467713 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
467658 TTTTTAACCC
467668 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
467693 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
467714 GCATCATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:472953 original size:16 final size:16
Alignment explanation
Indices: 472932--472964 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
472922 GTCTTCCACC
472932 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
472948 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
472964 T
1 T
472965 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:476554 original size:16 final size:16
Alignment explanation
Indices: 476533--476565 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
476523 GTCTTCCACC
476533 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
476549 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
476565 T
1 T
476566 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:495437 original size:35 final size:35
Alignment explanation
Indices: 495359--495442 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 35
495349 ACATCACCAT
* * *
495359 ATTTTACGCCTATAACATCACCATCTTCCATTAAT
1 ATTTCACGCCTATAACATCACCATCTTCCATCAAC
* * * * *
495394 ATTGCACGCCTATAACCTTACCATCTTCTATCACC
1 ATTTCACGCCTATAACATCACCATCTTCCATCAAC
495429 ATTTCACGCCTATA
1 ATTTCACGCCTATA
495443 TAACCACCAA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.29, C:0.32, G:0.05, T:0.35
Consensus pattern (35 bp):
ATTTCACGCCTATAACATCACCATCTTCCATCAAC
Found at i:502663 original size:15 final size:15
Alignment explanation
Indices: 502652--502680 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
502642 ACTCAAAAAG
502652 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
502667 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
502681 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:503959 original size:24 final size:21
Alignment explanation
Indices: 503925--503968 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
503915 TCAACAAGAC
*
503925 ATGTCCTTTGACATTTCAAAAT
1 ATGTCCTTTGA-AATTCAAAAT
503947 ATGTACCTCTTGAAATTCAAAA
1 ATGT-CCT-TTGAAATTCAAAA
503969 GAATGTGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAAT
Found at i:513694 original size:20 final size:21
Alignment explanation
Indices: 513672--513715 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
513662 GTAGGAGTTC
513672 TTTCTT-TTGTTTTTGATTTCT
1 TTTCTTCTT-TTTTTGATTTCT
*
513693 TTTCTTCTTTTTTTG-TTTAT
1 TTTCTTCTTTTTTTGATTTCT
513713 TTT
1 TTT
513716 GTTGTAGCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 12 0.57
22 2 0.10
ACGTcount: A:0.05, C:0.09, G:0.07, T:0.80
Consensus pattern (21 bp):
TTTCTTCTTTTTTTGATTTCT
Found at i:514872 original size:192 final size:192
Alignment explanation
Indices: 514545--514931 Score: 711
Period size: 192 Copynumber: 2.0 Consensus size: 192
514535 GAGCATGGCC
514545 ATTCGGTTGGGATTGAAGATGCATCCCCCTTGACTGAATGATTAGATGCATCTTCACTTTGGCGC
1 ATTCGGTTGGGATTGAAGATGCATCCCCCTTGACTGAATGATTAGATGCATCTTCACTTTGGCGC
*
514610 CAAGCATTGGGTATGTTCTAGGCGTGTGCCAAGGCTGTGGCTGAATGGTTGTAAGGGTTGCCTCA
66 CAAGCATTGGGTATGTTCTAGGCGTGTGCCAAGGCTGTAGCTGAATGGTTGTAAGGGTTGCCTCA
* *
514675 TGTCTCCTCGCAAATTAGGCTCCCTTTGGCTACAACAAGCTCACCAACGTGCATCTAGGTTT
131 TGTCTCCTCGCAAATTAGGCTCCCGTTGGCTACAACAAGCTCACCAACGTGCATCTAGGTGT
** *
514737 ATTCGGTTGGGATTGAAGATGCATCCCCCTTGGTTGAATGATTAGATGCATCTTCACTTTGGTGC
1 ATTCGGTTGGGATTGAAGATGCATCCCCCTTGACTGAATGATTAGATGCATCTTCACTTTGGCGC
*
514802 CAAGCATTGGGTATGTTCTAGGTGTGTGCCAAGGCTGTAGCTGAATGGTTGTAAGGGTTGCCTCA
66 CAAGCATTGGGTATGTTCTAGGCGTGTGCCAAGGCTGTAGCTGAATGGTTGTAAGGGTTGCCTCA
514867 TGTCTCCTCGCAAATTAGGCTCCCGTTGGCTACAACAAGCTCACCAACGTGCATCTAGGTGT
131 TGTCTCCTCGCAAATTAGGCTCCCGTTGGCTACAACAAGCTCACCAACGTGCATCTAGGTGT
514929 ATT
1 ATT
514932 AGCATCTAAT
Statistics
Matches: 188, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
192 188 1.00
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (192 bp):
ATTCGGTTGGGATTGAAGATGCATCCCCCTTGACTGAATGATTAGATGCATCTTCACTTTGGCGC
CAAGCATTGGGTATGTTCTAGGCGTGTGCCAAGGCTGTAGCTGAATGGTTGTAAGGGTTGCCTCA
TGTCTCCTCGCAAATTAGGCTCCCGTTGGCTACAACAAGCTCACCAACGTGCATCTAGGTGT
Found at i:516024 original size:16 final size:15
Alignment explanation
Indices: 515995--516031 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
515985 TGAAGCACTC
*
515995 AAAAAAAAGTAAAGA
1 AAAAAAAAGAAAAGA
516010 AAAAGAAAAGAAAAGA
1 AAAA-AAAAGAAAAGA
516026 AAAAAA
1 AAAAAA
516032 GAAAAGTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (15 bp):
AAAAAAAAGAAAAGA
Found at i:517226 original size:24 final size:21
Alignment explanation
Indices: 517192--517234 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
517182 CCCACAAGAC
*
517192 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AGTTCAAAGG
517214 ATGTACCTCTTGAAGTTCAAA
1 ATGT-CCT-TTGAAGTTCAAA
517235 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAGTTCAAAGG
Found at i:518671 original size:17 final size:17
Alignment explanation
Indices: 518646--518685 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
518636 GTATGTTGTT
*
518646 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
518663 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
518680 CATTTA
1 CATTTA
518686 GGGAAGTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:518765 original size:18 final size:18
Alignment explanation
Indices: 518742--518783 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
518732 ATGCATTTAG
518742 TTCATTGAATAAAGTTAT
1 TTCATTGAATAAAGTTAT
*
518760 TTCATTGAATAATGTTAT
1 TTCATTGAATAAAGTTAT
518778 TTCATT
1 TTCATT
518784 AATCAAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (18 bp):
TTCATTGAATAAAGTTAT
Found at i:522289 original size:17 final size:17
Alignment explanation
Indices: 522264--522303 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
522254 GTATGTTGTT
*
522264 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
522281 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
522298 CATTTA
1 CATTTA
522304 GGGAAGTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:522382 original size:18 final size:18
Alignment explanation
Indices: 522359--522404 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
522349 ATTAATGCAT
522359 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
522377 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
522395 TTATTTCATT
1 TTAGTTCATT
522405 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:532619 original size:26 final size:26
Alignment explanation
Indices: 532582--532678 Score: 149
Period size: 26 Copynumber: 3.7 Consensus size: 26
532572 TCCTAGAACA
532582 CCCATGTGCCTTGCATATGACCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
*
532608 CCCATGTACCTTGCATATGACCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
** * *
532634 CCCATGTGTTTTGCATGTGATCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
532660 CCCATGTGCCTTGCATATG
1 CCCATGTGCCTTGCATATG
532679 GTTCATTTAG
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 62 1.00
ACGTcount: A:0.19, C:0.34, G:0.20, T:0.28
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAGCC
Found at i:536249 original size:11 final size:13
Alignment explanation
Indices: 536217--536246 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
536207 TGGCCAAAGA
536217 TGAAAAGGTATGT
1 TGAAAAGGTATGT
536230 TGAAAAGGTATG-
1 TGAAAAGGTATGT
536242 TGAAA
1 TGAAA
536247 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:540889 original size:24 final size:21
Alignment explanation
Indices: 540854--540896 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
540844 AGCACATTCT
*
540854 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
540877 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
540897 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:542123 original size:15 final size:14
Alignment explanation
Indices: 542102--542139 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 14
542092 AGTTCCTCAA
542102 CTTTCTTTCTTTTT
1 CTTTCTTTCTTTTT
542116 CTTTTCTTTTCTTTTT
1 C-TTTC-TTTCTTTTT
542132 CTTTCTTT
1 CTTTCTTT
542140 GAGTGATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.18
15 8 0.36
16 10 0.45
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CTTTCTTTCTTTTT
Found at i:547547 original size:18 final size:19
Alignment explanation
Indices: 547526--547565 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
547516 TTTTTTTGGC
547526 TTTTTG-ATATTTCTTTTT
1 TTTTTGCATATTTCTTTTT
* *
547544 TTTTTGCCTTTTTCTTTTT
1 TTTTTGCATATTTCTTTTT
547563 TTT
1 TTT
547566 GAAAAATAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.80
Consensus pattern (19 bp):
TTTTTGCATATTTCTTTTT
Found at i:551218 original size:20 final size:22
Alignment explanation
Indices: 551193--551232 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
551183 GTGTAAGACC
551193 TATGAGCT-A-AAATGAATGCA
1 TATGAGCTAACAAATGAATGCA
551213 TATGAGCTAACAAATGAATG
1 TATGAGCTAACAAATGAATG
551233 ATTAAGCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (22 bp):
TATGAGCTAACAAATGAATGCA
Found at i:551512 original size:113 final size:114
Alignment explanation
Indices: 551372--551609 Score: 462
Period size: 113 Copynumber: 2.1 Consensus size: 114
551362 CATGGTATTC
551372 ATAA-ATGATAAATGGAAACATGTAATAATAATATCCTAAGAAATGATATGTAATCAAAGCATAT
1 ATAATATGATAAATGGAAACATGTAATAATAATATCCTAAGAAATGATATGTAATCAAAGCATAT
551436 A-TTTGAATGATATGAAAGACTTGATCAACTAAGCATACGATGGAAATA
66 ATTTTGAATGATATGAAAGACTTGATCAACTAAGCATACGATGGAAATA
551484 ATAATATGATAAATGGAAACATGTAATAATAATATCCTAAGAAATGATATGTAATCAAAGCATAT
1 ATAATATGATAAATGGAAACATGTAATAATAATATCCTAAGAAATGATATGTAATCAAAGCATAT
551549 ATTTTGAATGATATGAAAGACTTGATCAACTAAGCATACGATGGAAATA
66 ATTTTGAATGATATGAAAGACTTGATCAACTAAGCATACGATGGAAATA
551598 ATAATATGATAA
1 ATAATATGATAA
551610 CTTATACTAA
Statistics
Matches: 124, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
112 4 0.03
113 61 0.49
114 59 0.48
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (114 bp):
ATAATATGATAAATGGAAACATGTAATAATAATATCCTAAGAAATGATATGTAATCAAAGCATAT
ATTTTGAATGATATGAAAGACTTGATCAACTAAGCATACGATGGAAATA
Found at i:556969 original size:20 final size:22
Alignment explanation
Indices: 556944--556983 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
556934 GTGTAAGACC
556944 TATGAGCT-A-AAATGAATGCA
1 TATGAGCTAACAAATGAATGCA
556964 TATGAGCTAACAAATGAATG
1 TATGAGCTAACAAATGAATG
556984 ATTAAGCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (22 bp):
TATGAGCTAACAAATGAATGCA
Found at i:560569 original size:14 final size:14
Alignment explanation
Indices: 560552--560578 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
560542 TTAAGGATTT
560552 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
560566 ATGGTGATGGAAA
1 ATGGTGATGGAAA
560579 TAGTATCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:578322 original size:20 final size:22
Alignment explanation
Indices: 578297--578336 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
578287 GTATAAGACC
578297 TATGAGCT-A-AAATGAATGCA
1 TATGAGCTAACAAATGAATGCA
578317 TATGAGCTAACAAATGAATG
1 TATGAGCTAACAAATGAATG
578337 ATTAAGCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (22 bp):
TATGAGCTAACAAATGAATGCA
Found at i:579577 original size:21 final size:22
Alignment explanation
Indices: 579548--579588 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
579538 ATTACCACTC
*
579548 CTTGCTTTTT-AATAGTCACCT
1 CTTGCTTTTTGAAAAGTCACCT
*
579569 CTTGGTTTTTGAAAAGTCAC
1 CTTGCTTTTTGAAAAGTCAC
579589 ATTTAGTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.44
Consensus pattern (22 bp):
CTTGCTTTTTGAAAAGTCACCT
Found at i:581744 original size:14 final size:14
Alignment explanation
Indices: 581727--581753 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
581717 TTAAGGATTT
581727 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
581741 ATGGTGATGGAAA
1 ATGGTGATGGAAA
581754 TAGTATCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:585995 original size:16 final size:16
Alignment explanation
Indices: 585962--586010 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
585952 TAAGGTAATG
585962 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
585980 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* * *
585996 TAGTAAGAAAGTGAA
1 GAATAAGAAAATGAA
586011 GATAACTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:586223 original size:16 final size:16
Alignment explanation
Indices: 586204--586235 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
586194 TGTAGGAGTC
586204 TTTTTTTCTTT-TTGT
1 TTTTTTTCTTTCTTGT
586219 TTTTTTTCTTTCTTGT
1 TTTTTTTCTTTCTTGT
586235 T
1 T
586236 GCTTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.84
Consensus pattern (16 bp):
TTTTTTTCTTTCTTGT
Found at i:586464 original size:915 final size:914
Alignment explanation
Indices: 584631--586456 Score: 3433
Period size: 915 Copynumber: 2.0 Consensus size: 914
584621 GTTTTCTCTT
584631 TGATCATCCTCTATGATTTGAGTGTTTAAAGCTTTTTTAATGACAAGAACTTGTCTTGAAACTGT
1 TGATCATCCTCTATGATTTGAGTGTTTAAAGCTTTTTTAATGACAAGAACTTGTCTTGAAACTGT
584696 ATGGAAATCAAGCAATTCTTGTGACATGGTTAGTGAAATAAAATAAATTGAAACCTTACCAGGAC
66 ATGGAAATCAAGCAATTCTTGTGACATGGTTAGTGAAATAAAATAAATTGAAACCTTACCAGGAC
584761 ACTCACAAAAGCCTCTTGATCACTATAAAGAGAGTTCAGATTGCACTCCACTCACACTTGTGTTT
131 ACTCACAAAAGCCTCTTGATCACTATAAAGAGAGTTCAGATTGCACTCCACTCACACTTGTGTTT
584826 GCACTCGGGGATATGTTCATTGGCTTTTTTGATCCCCCTTGTGTCTCACCCTCTCGTTTGATTTT
196 GCACTCGGGGATATGTTCATTGGCTTTTTTGATCCCCCTTGTGTCTCACCCTCTCGTTTGATTTT
584891 TTCCACTCGATTCTCTCTTGTGGGTCCTTTTTAAGAACTAACTCAAGATTGAGCAAGTTTCTGAG
261 TTCCACTCGATTCTCTCTTGTGGGTCCTTTTTAAGAACTAACTCAAGATTGAGCAAGTTTCTGAG
584956 TTTGTGCGTCGGCTTAAAAGAAATGGTTAGGTATAAAAGTGGTTATGATAGGGTACGATAGAAAA
326 TTTGTGCGTCGGCTTAAAAGAAATGGTTAGGTATAAAAGTGGTTATGATAGGGTACGATAGAAAA
585021 AGGTTTAAGAAAATGATAAGGTAATGGAATAAGAATAGATGAAGAATAAGAAATGAAATAGTAAG
391 AGGTTTAAGAAAATGATAAGGTAATGGAATAAGAATAGATGAAGAATAAGAAATGAAATAGTAAG
585086 AAAGTGAAGATAACTTAAAACTCAAGTTGTAACACTTACTATCTTCCTTCACAAGAAACAACAAG
456 AAAGTGAAGATAACTTAAAACTCAAGTTGTAACACTTACTA-CTTCCTTCACAAGAAACAACAAG
585151 GATTACTCCTTCTAGTTTGTTGTTAGGGTAGATTCTTTTGTGCTTCTCTTTGAATGTACTTTGCA
520 GATTACTCCTTCTAGTTTGTTGTTAGGGTAGATTCTTTTGTGCTTCTCTTTGAATGTACTTTGCA
585216 ACTTTGCTTCACTTTCTTTTGCTTTGATTTTTCTTCTTTTCTTTTCTTTCTTTTGCACTCCAAAT
585 ACTTTGCTTCACTTTCTTTTGCTTTGATTTTTCTTCTTTTCTTTTCTTTCTTTTGCACTCCAAAT
*
585281 TTTTTGTAGGAGTCTTTTCTTTTTTTGTTTTTTTTCTTCTTTCTTGTTGCTTTTAATGTAGCACT
650 TTTTTGTAGGAGTCTTTTCTTTTTTTGTGTTTTTTCTTCTTTCTTGTTGCTTTTAATGTAGCACT
*
585346 TGATTGTCAATCCAACAAGCTCTGATTGCTGCTTGATGTAAGGCTAACCAGATTCTTCAATAATG
715 TGATTGTCAATCCAACAAGCTCTGATTGCCGCTTGATGTAAGGCTAACCAGATTCTTCAATAATG
585411 GAGAAGTTGGTAACCTTGTTGTTTCCCGATCTAGGAGAGACAACAAATGCTACACTTTAAATTGA
780 GAGAAGTTGGTAACCTTGTTGTTTCCCGATCTAGGAGAGACAACAAATGCTACACTTTAAATTGA
585476 TAAATAATCTACAAAATTAAAAGAAATAAATGATTAAGATGGAAATAAAAAAAGAAATGGAAGAA
845 TAAATAATCTACAAAATTAAAAGAAATAAATGATTAAGATGGAAATAAAAAAAGAAATGGAAGAA
585541 GAAAA
910 GAAAA
585546 TGATCATCCTCTATGATTTGAGTGTTTAAAGCTTTTTTAATGACAAGAACTTGTCTTGAAACTGT
1 TGATCATCCTCTATGATTTGAGTGTTTAAAGCTTTTTTAATGACAAGAACTTGTCTTGAAACTGT
585611 ATGGAAATCAAGCAATTCTTGTGACATGGTTAGTGAAATAAAATAAATTGAAACCTTACCAGGAC
66 ATGGAAATCAAGCAATTCTTGTGACATGGTTAGTGAAATAAAATAAATTGAAACCTTACCAGGAC
585676 ACTCACAAAAGCCTCACTTGATCACTATAAAGAGAGTTCAGATTGCACTCCACTCACACTTGTGT
131 ACTCACAAAAGCCT--CTTGATCACTATAAAGAGAGTTCAGATTGCACTCCACTCACACTTGTGT
585741 TTGCACTCGGGGATATGTTCATTGGC-TTTTTGAT-CCCCTTGTGTCTCACCCTCTCGTTTGATT
194 TTGCACTCGGGGATATGTTCATTGGCTTTTTTGATCCCCCTTGTGTCTCACCCTCTCGTTTGATT
585804 TTTTCCACTCGATTCTCTCTTGTGGGTCCTTTTTAAGAACTAACTCAAGATTGAGCAAGTTTCTG
259 TTTTCCACTCGATTCTCTCTTGTGGGTCCTTTTTAAGAACTAACTCAAGATTGAGCAAGTTTCTG
585869 AGTTTGTGCGTCGGCTTAAAAGAAATGGTTAGGTATAAAAGTGGTTATGATAGGGTACGATAGAA
324 AGTTTGTGCGTCGGCTTAAAAGAAATGGTTAGGTATAAAAGTGGTTATGATAGGGTACGATAGAA
585934 AAAGGTTTAAGAAAATGATAAGGTAATGGAATAAGAATAGATGAAAGAATAAGAAAATGAAATAG
389 AAAGGTTTAAGAAAATGATAAGGTAATGGAATAAGAATAGATG-AAGAATAAG-AAATGAAATAG
*
585999 TAAGAAAGTGAAGATAACTTACAACTCAAGTTGTAACACTTACTA-TTCCTTCACAAGAAACAAC
452 TAAGAAAGTGAAGATAACTTAAAACTCAAGTTGTAACACTTACTACTTCCTTCACAAGAAACAAC
*
586063 AAGGA-TAC-CCTTCTAGTTTGTTGTTAGGGTAGA-TGTTTTGTGCTTCTCTTTGAATGTACTTT
517 AAGGATTACTCCTTCTAGTTTGTTGTTAGGGTAGATTCTTTTGTGCTTCTCTTTGAATGTACTTT
586125 GCAACTTTGCTTCACTTTCTTTTGCTTTGA-TTTTCTTCTTTTC-TTTC-TTCTTTTGCACTCCA
582 GCAACTTTGCTTCACTTTCTTTTGCTTTGATTTTTCTTCTTTTCTTTTCTTTCTTTTGCACTCCA
586187 AATTTTTTGTAGGAGTCTTTT-TTTCTTTT-TGTTTTTT-TTCTTTCTTGTTGCTTTTAATTGTA
647 AATTTTTTGTAGGAGTCTTTTCTTT-TTTTGTGTTTTTTCTTCTTTCTTGTTGCTTTTAA-TGTA
586249 GCACTTGATTGTCAATCCAACAAAGCTCTGATTGCCGCTTGATGTAAGGCTAACCAGGATTCTTC
710 GCACTTGATTGTCAATCCAAC-AAGCTCTGATTGCCGCTTGATGTAAGGCTAACCA-GATTCTTC
586314 AATAATGGAGAAGTTGGTAACCTTGTTGTTTCCCGATCTAGGAGAGACAACAAATGCTACACTTT
773 AATAATGGAGAAGTTGGTAACCTTGTTGTTTCCCGATCTAGGAGAGACAACAAATGCTACACTTT
*
586379 AAATTGATAAATAATCTACAAAATTAAAAGAAATAAATGATTAAGATGGAAATATAAACAAGAAA
838 AAATTGATAAATAATCTACAAAATTAAAAGAAATAAATGATTAAGATGGAAATA-AAAAAAGAAA
586444 TGGAAGAAGAAAA
902 TGGAAGAAGAAAA
586457 GAAATGATAA
Statistics
Matches: 897, Mismatches: 5, Indels: 22
0.97 0.01 0.02
Matches are distributed among these distances:
907 20 0.02
908 35 0.04
909 73 0.08
910 131 0.15
911 35 0.04
912 58 0.06
913 25 0.03
914 3 0.00
915 370 0.41
916 17 0.02
917 130 0.14
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (914 bp):
TGATCATCCTCTATGATTTGAGTGTTTAAAGCTTTTTTAATGACAAGAACTTGTCTTGAAACTGT
ATGGAAATCAAGCAATTCTTGTGACATGGTTAGTGAAATAAAATAAATTGAAACCTTACCAGGAC
ACTCACAAAAGCCTCTTGATCACTATAAAGAGAGTTCAGATTGCACTCCACTCACACTTGTGTTT
GCACTCGGGGATATGTTCATTGGCTTTTTTGATCCCCCTTGTGTCTCACCCTCTCGTTTGATTTT
TTCCACTCGATTCTCTCTTGTGGGTCCTTTTTAAGAACTAACTCAAGATTGAGCAAGTTTCTGAG
TTTGTGCGTCGGCTTAAAAGAAATGGTTAGGTATAAAAGTGGTTATGATAGGGTACGATAGAAAA
AGGTTTAAGAAAATGATAAGGTAATGGAATAAGAATAGATGAAGAATAAGAAATGAAATAGTAAG
AAAGTGAAGATAACTTAAAACTCAAGTTGTAACACTTACTACTTCCTTCACAAGAAACAACAAGG
ATTACTCCTTCTAGTTTGTTGTTAGGGTAGATTCTTTTGTGCTTCTCTTTGAATGTACTTTGCAA
CTTTGCTTCACTTTCTTTTGCTTTGATTTTTCTTCTTTTCTTTTCTTTCTTTTGCACTCCAAATT
TTTTGTAGGAGTCTTTTCTTTTTTTGTGTTTTTTCTTCTTTCTTGTTGCTTTTAATGTAGCACTT
GATTGTCAATCCAACAAGCTCTGATTGCCGCTTGATGTAAGGCTAACCAGATTCTTCAATAATGG
AGAAGTTGGTAACCTTGTTGTTTCCCGATCTAGGAGAGACAACAAATGCTACACTTTAAATTGAT
AAATAATCTACAAAATTAAAAGAAATAAATGATTAAGATGGAAATAAAAAAAGAAATGGAAGAAG
AAAA
Found at i:586483 original size:15 final size:16
Alignment explanation
Indices: 586440--586488 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
586430 ATATAAACAA
*
586440 GAAATGGAAGAAGAAAA
1 GAAATGG-AGAAGAAAT
*
586457 GAAAT-GATAAGAAAT
1 GAAATGGAGAAGAAAT
586472 GAAATGGA-AAGAAAT
1 GAAATGGAGAAGAAAT
586487 GA
1 GA
586489 TATCAAAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 21 0.72
16 3 0.10
17 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (16 bp):
GAAATGGAGAAGAAAT
Found at i:588297 original size:14 final size:14
Alignment explanation
Indices: 588273--588307 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
588263 TAACTATTAA
588273 AACATTATATAACAT
1 AACA-TATATAACAT
588288 AACATATATAACAT
1 AACATATATAACAT
588302 AACATA
1 AACATA
588308 GGAGGCTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (14 bp):
AACATATATAACAT
Found at i:596520 original size:19 final size:20
Alignment explanation
Indices: 596481--596530 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
596471 GAAACCCCTT
596481 TGAAAATACATGATATTTAA
1 TGAAAATACATGATATTTAA
596501 TGAAAATACATGAT-TTTAA
1 TGAAAATACATGATATTTAA
*
596520 TGAAGATACAT
1 TGAAAATACAT
596531 AGTCTTGGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (20 bp):
TGAAAATACATGATATTTAA
Found at i:599882 original size:6 final size:6
Alignment explanation
Indices: 599836--599879 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
599826 GACTTAGGAG
* *
599836 TTCTTT TTC-TT TTCTTT TTGTTT TTCTTCT TTCTTT TTGTTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTT-T TTCTTT TTCTTT TT
599880 GTTGCAGCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 5 0.15
6 22 0.67
7 6 0.18
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.82
Consensus pattern (6 bp):
TTCTTT
Found at i:600074 original size:12 final size:12
Alignment explanation
Indices: 600057--600101 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
600047 AAAATGGATT
600057 AATGAAATAAAA
1 AATGAAATAAAA
*
600069 AATGAAAGAAAGA
1 AATGAAATAAA-A
*
600082 AATGAAATGAAA
1 AATGAAATAAAA
600094 AATGAAAT
1 AATGAAAT
600102 GAATGAATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
AATGAAATAAAA
Found at i:600110 original size:25 final size:25
Alignment explanation
Indices: 600048--600110 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
600038 ACAATGAAAA
* *
600048 AAATGGATTAATGAAATAAAAAATG
1 AAATGAATGAATGAAATAAAAAATG
* *
600073 AAA-GAAAGAAATGAAATGAAAAATG
1 AAATGAATG-AATGAAATAAAAAATG
600098 AAATGAATGAATG
1 AAATGAATGAATG
600111 TAGATGTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
24 2 0.06
25 25 0.81
26 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (25 bp):
AAATGAATGAATGAAATAAAAAATG
Found at i:600688 original size:19 final size:20
Alignment explanation
Indices: 600638--600680 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
600628 GAAATCCCTT
600638 TGAAAATACATGATATTTAA
1 TGAAAATACATGATATTTAA
600658 TGAAAATACATGAT-TTTAA
1 TGAAAATACATGATATTTAA
600677 TGAA
1 TGAA
600681 GTTACATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATATTTAA
Found at i:613902 original size:19 final size:18
Alignment explanation
Indices: 613878--613913 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
613868 ACTTGTTGTG
*
613878 TTCTTTTTCTTTTCTTTTC
1 TTCTTTTT-TTTTATTTTC
613897 TTCTTTTTTTTTATTTT
1 TTCTTTTTTTTTATTTT
613914 GCTTTTATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (18 bp):
TTCTTTTTTTTTATTTTC
Found at i:620108 original size:41 final size:40
Alignment explanation
Indices: 620063--620303 Score: 257
Period size: 41 Copynumber: 5.9 Consensus size: 40
620053 TGAAAACATG
* * ** *
620063 CAATAGTTCACCATTCTACTCAATTGAATCATGGCAGCATA
1 CAATAATTCACCATTCAACTTGATTG-ATCATGGTAGCATA
* * * *
620104 CAATACTTCACCATGCAACTTGATTCGATCATGGTAGTATG
1 CAATAATTCACCATTCAACTTGATT-GATCATGGTAGCATA
* *
620145 CAATAAATCACTATTCAACTTGATTCGATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTGATT-GATCATGGTAGCATA
* *
620186 CAATAATTCAACATTCAACTTGATTCAATCATGGTAGCATA
1 CAATAATTCACCATTCAACTTGATT-GATCATGGTAGCATA
* * * * *
620227 CAATAATTAACCATTCAATTTAATTTGATCATGGAAGCATG
1 CAATAATTCACCATTCAACTTGA-TTGATCATGGTAGCATA
*
620268 CAATAATTCACCATTCAACTTGATTCAATCATGGTA
1 CAATAATTCACCATTCAACTTGATT-GATCATGGTA
620304 ACTGATGCAA
Statistics
Matches: 167, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
40 2 0.01
41 162 0.97
42 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (40 bp):
CAATAATTCACCATTCAACTTGATTGATCATGGTAGCATA
Found at i:620149 original size:82 final size:81
Alignment explanation
Indices: 620044--620303 Score: 313
Period size: 82 Copynumber: 3.2 Consensus size: 81
620034 TCACAATTCA
** * * * * *
620044 ATTCAATCATGAAAACATGCAATAGTTCACCATTCTACTCAATTGAATCATGGCAGCATACAATA
1 ATTCAATCATGGTAGCATGCAATAATTCACCATTCAACTTAATTG-ATCATGGAAGCATACAATA
* *
620109 CTTCACCATGCAACTTG
65 ATTCACCATTCAACTTG
* * * * * *
620126 ATTCGATCATGGTAGTATGCAATAAATCACTATTCAACTTGATTCGATCATGGTAGCATACAATA
1 ATTCAATCATGGTAGCATGCAATAATTCACCATTCAACTTAATT-GATCATGGAAGCATACAATA
*
620191 ATTCAACATTCAACTTG
65 ATTCACCATTCAACTTG
* * * *
620208 ATTCAATCATGGTAGCATACAATAATTAACCATTCAATTTAATTTGATCATGGAAGCATGCAATA
1 ATTCAATCATGGTAGCATGCAATAATTCACCATTCAACTTAA-TTGATCATGGAAGCATACAATA
620273 ATTCACCATTCAACTTG
65 ATTCACCATTCAACTTG
620290 ATTCAATCATGGTA
1 ATTCAATCATGGTA
620304 ACTGATGCAA
Statistics
Matches: 150, Mismatches: 26, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
82 147 0.98
83 3 0.02
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (81 bp):
ATTCAATCATGGTAGCATGCAATAATTCACCATTCAACTTAATTGATCATGGAAGCATACAATAA
TTCACCATTCAACTTG
Found at i:620190 original size:123 final size:123
Alignment explanation
Indices: 620044--620303 Score: 322
Period size: 123 Copynumber: 2.1 Consensus size: 123
620034 TCACAATTCA
** * * * * * *
620044 ATTCAATCATGAAAACATGCAATAGTTCACCATTCTACTCAATTGAATCATGGCAGCATACAATA
1 ATTCAATCATGGTAGCATACAATAATTCAACATTCAACTCAATTCAATCATGGCAGCATACAATA
* * * * * *
620109 CTTCACCATGCAACTTGATTCGATCATGGTAGTATGCAATAAATCACTATTCAACTTG
66 ATTAACCATGCAACTTAATTCGATCATGGAAGCATGCAATAAATCACCATTCAACTTG
* ** *
620167 ATTCGATCATGGTAGCATACAATAATTCAACATTCAACTTGATTCAATCATGGTAGCATACAATA
1 ATTCAATCATGGTAGCATACAATAATTCAACATTCAACTCAATTCAATCATGGCAGCATACAATA
* * * *
620232 ATTAACCATTCAATTTAATTTGATCATGGAAGCATGCAATAATTCACCATTCAACTTG
66 ATTAACCATGCAACTTAATTCGATCATGGAAGCATGCAATAAATCACCATTCAACTTG
620290 ATTCAATCATGGTA
1 ATTCAATCATGGTA
620304 ACTGATGCAA
Statistics
Matches: 114, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
123 114 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (123 bp):
ATTCAATCATGGTAGCATACAATAATTCAACATTCAACTCAATTCAATCATGGCAGCATACAATA
ATTAACCATGCAACTTAATTCGATCATGGAAGCATGCAATAAATCACCATTCAACTTG
Found at i:627184 original size:20 final size:22
Alignment explanation
Indices: 627144--627189 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
627134 TGCTTGAATG
627144 ATGCACATGGCAGCCTACTTG-A
1 ATGCACATGG-AGCCTACTTGCA
*
627166 ATGCACATGG-GCCTTCTTGCA
1 ATGCACATGGAGCCTACTTGCA
627187 ATG
1 ATG
627190 ATTTTCTGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 4 0.18
22 10 0.45
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (22 bp):
ATGCACATGGAGCCTACTTGCA
Found at i:631153 original size:17 final size:17
Alignment explanation
Indices: 631112--631171 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
631102 ATTAATGCCT
631112 CTAGTTCATTTAA-TAAA
1 CTAGTTCA-TTAATTAAA
631129 GCTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* * *
631147 CTTGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
631164 CTAGTTCA
1 CTAGTTCA
631172 ATTATTATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 25 0.68
18 12 0.32
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:638096 original size:19 final size:21
Alignment explanation
Indices: 638072--638115 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
638062 TCGGATTTAG
638072 TAAAAAAAGAAA-AAAAA-TT
1 TAAAAAAAGAAAGAAAAAGTT
*
638091 TAAAAAAATAAAGAAAAAGTT
1 TAAAAAAAGAAAGAAAAAGTT
638112 TAAA
1 TAAA
638116 GAGGGATGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.50
20 5 0.23
21 6 0.27
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (21 bp):
TAAAAAAAGAAAGAAAAAGTT
Found at i:640224 original size:17 final size:17
Alignment explanation
Indices: 640204--640256 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
640194 TTAATAAAGT
640204 TAGTTAATTAATTAAAC
1 TAGTTAATTAATTAAAC
* * *
640221 TAGTTCATTCATCAAAC
1 TAGTTAATTAATTAAAC
* * *
640238 TAATTTATTTATTAAAC
1 TAGTTAATTAATTAAAC
640255 TA
1 TA
640257 ACTCTTAATT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.43
Consensus pattern (17 bp):
TAGTTAATTAATTAAAC
Found at i:644394 original size:24 final size:21
Alignment explanation
Indices: 644360--644402 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
644350 TGCACAAGAT
*
644360 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
644382 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
644403 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:649725 original size:17 final size:17
Alignment explanation
Indices: 649657--649727 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 17
649647 TTCATGCATA
*
649657 TAGTTCATTTAATAAAGT
1 TAGTTCATTTAATAAA-C
* *
649675 TAGTTCACTAAATAAAC
1 TAGTTCATTTAATAAAC
** *
649692 TAGTT-AAATCATCAAAC
1 TAGTTCATTTAAT-AAAC
*
649709 TAGTTCATTTATTAAAC
1 TAGTTCATTTAATAAAC
649726 TA
1 TA
649728 ACTCTTAATT
Statistics
Matches: 40, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
16 3 0.08
17 20 0.50
18 17 0.43
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (17 bp):
TAGTTCATTTAATAAAC
Found at i:663669 original size:15 final size:15
Alignment explanation
Indices: 663649--663677 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
663639 TACTAATTCA
663649 CAATTTAATTCAATT
1 CAATTTAATTCAATT
663664 CAATTTAATTCAAT
1 CAATTTAATTCAAT
663678 CAAGACAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (15 bp):
CAATTTAATTCAATT
Found at i:663782 original size:41 final size:41
Alignment explanation
Indices: 663732--663905 Score: 240
Period size: 41 Copynumber: 4.2 Consensus size: 41
663722 GTCAACATGT
* * *
663732 AATACTTCACCATTCAACTTGATTCAATTATTGTAGCATAC
1 AATAATTCACCATTCAACTTGATTCAATCATGGTAGCATAC
*
663773 AATAATTCACCATTCAACTTGATTCGATCATGGTAGCATAC
1 AATAATTCACCATTCAACTTGATTCAATCATGGTAGCATAC
* *
663814 AATAATTCATCATTCAACTTGATTCTATCATGGTAGCATAC
1 AATAATTCACCATTCAACTTGATTCAATCATGGTAGCATAC
* * * *
663855 AATAATTCACCATTCAACTTTATTCGATCATCGTAACATAC
1 AATAATTCACCATTCAACTTGATTCAATCATGGTAGCATAC
* *
663896 ATTTATTCAC
1 AATAATTCAC
663906 AAATCTATTC
Statistics
Matches: 120, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 120 1.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (41 bp):
AATAATTCACCATTCAACTTGATTCAATCATGGTAGCATAC
Found at i:663926 original size:82 final size:82
Alignment explanation
Indices: 663764--663927 Score: 206
Period size: 82 Copynumber: 2.0 Consensus size: 82
663754 TTCAATTATT
* * *
663764 GTAGCATACAATAATTCACCATTCAACTTGATTCGATCATGGTAGCATACAATAATTCATCATTC
1 GTAGCATACAATAATTCACCATTCAACTTGATTCGATCATCGTAACATACAATAATTCATCAATC
* **
663829 AACTTGATTCTATCATG
66 AACTTCATTAGATCATG
* * *
663846 GTAGCATACAATAATTCACCATTCAACTTTATTCGATCATCGTAACATACATTTATTCA-CAAAT
1 GTAGCATACAATAATTCACCATTCAACTTGATTCGATCATCGTAACATACAATAATTCATC-AAT
*
663910 CTA-TTCAGTTAGATCATG
65 CAACTTCA-TTAGATCATG
663928 ATAACATGTA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
81 4 0.06
82 66 0.94
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.35
Consensus pattern (82 bp):
GTAGCATACAATAATTCACCATTCAACTTGATTCGATCATCGTAACATACAATAATTCATCAATC
AACTTCATTAGATCATG
Found at i:670429 original size:14 final size:15
Alignment explanation
Indices: 670395--670441 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
670385 GATTTGGAGT
670395 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
670410 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
670424 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
670441 G
1 G
670442 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:671722 original size:13 final size:12
Alignment explanation
Indices: 671705--671790 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
671695 AATATAGGCT
671705 GATATGGTGATG
1 GATATGGTGATG
671717 GAATATGGTGAT-
1 G-ATATGGTGATG
*
671729 GATATAGGCG-T-
1 GATAT-GGTGATG
671740 GATAATGGTGATG
1 GAT-ATGGTGATG
671753 GACTATGGTGAT-
1 GA-TATGGTGATG
*
671765 GATATAGGCG-T-
1 GATAT-GGTGATG
671776 GATAATGGTGATG
1 GAT-ATGGTGATG
671789 GA
1 GA
671791 CAGATTATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:671760 original size:36 final size:36
Alignment explanation
Indices: 671689--671791 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
671679 TTTATAAGTG
* *
671689 GGTGATAATATAGGC-TGAT-ATGGTGATGGAATAT
1 GGTGATGATATAGGCGTGATAATGGTGATGGACTAT
671723 GGTGATGATATAGGCGTGATAATGGTGATGGACTAT
1 GGTGATGATATAGGCGTGATAATGGTGATGGACTAT
671759 GGTGATGATATAGGCGTGATAATGGTGATGGAC
1 GGTGATGATATAGGCGTGATAATGGTGATGGAC
671792 AGATTATATC
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
34 14 0.22
35 4 0.06
36 47 0.72
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
GGTGATGATATAGGCGTGATAATGGTGATGGACTAT
Found at i:675751 original size:11 final size:12
Alignment explanation
Indices: 675730--675814 Score: 56
Period size: 11 Copynumber: 7.2 Consensus size: 12
675720 TTTATAAGTT
*
675730 GGTGATAATATA
1 GGTGATGATATA
675742 GGTG-TGATAT-
1 GGTGATGATATA
675752 GGTGATGGA-ATA
1 GGTGAT-GATATA
675764 TGGTGATGATATA
1 -GGTGATGATATA
*
675777 GG-GGTGATA-A
1 GGTGATGATATA
*
675787 TGGTAATGGACTAT-
1 -GGTGAT-GA-TATA
675801 GGTGATGATATA
1 GGTGATGATATA
675813 GG
1 GG
675815 CGTGATAATG
Statistics
Matches: 57, Mismatches: 5, Indels: 22
0.68 0.06 0.26
Matches are distributed among these distances:
10 5 0.09
11 19 0.33
12 15 0.26
13 16 0.28
14 2 0.04
ACGTcount: A:0.31, C:0.01, G:0.36, T:0.32
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:675773 original size:24 final size:22
Alignment explanation
Indices: 675729--675829 Score: 64
Period size: 22 Copynumber: 4.3 Consensus size: 22
675719 ATTTATAAGT
675729 TGGTGATAATATAGGTGTGATA
1 TGGTGATAATATAGGTGTGATA
675751 TGGTGATGGAATAT-GGTGATGATA
1 TGGTGAT--AATATAGGTG-TGATA
* *
675775 TAGGGGTGATAATGGTA-ATG-GACTA
1 T---GGTGATAAT-ATAGGTGTGA-TA
* *
675800 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGTGTGAT-A
675823 TGGTGAT
1 TGGTGAT
675830 GGACAGATTG
Statistics
Matches: 61, Mismatches: 6, Indels: 23
0.68 0.07 0.26
Matches are distributed among these distances:
21 2 0.03
22 17 0.28
23 14 0.23
24 13 0.21
25 6 0.10
26 3 0.05
27 6 0.10
ACGTcount: A:0.30, C:0.02, G:0.36, T:0.33
Consensus pattern (22 bp):
TGGTGATAATATAGGTGTGATA
Found at i:675802 original size:36 final size:36
Alignment explanation
Indices: 675729--675833 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
675719 ATTTATAAGT
* * *
675729 TGGTGATAATATAGGTGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
* *
675764 TGGTGATGATATAGGGGTGATAATGGTAATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
675800 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
675834 AGATTGTATC
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 19 0.30
36 44 0.70
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:683602 original size:19 final size:19
Alignment explanation
Indices: 683578--683616 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
683568 AGAAGTTTGG
683578 TGTCATGTTTTTTTCATCT
1 TGTCATGTTTTTTTCATCT
683597 TGTCATGTTTTTTTCATCT
1 TGTCATGTTTTTTTCATCT
683616 T
1 T
683617 TATTCTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.15, G:0.10, T:0.64
Consensus pattern (19 bp):
TGTCATGTTTTTTTCATCT
Found at i:685474 original size:11 final size:13
Alignment explanation
Indices: 685453--685484 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
685443 GAGTGCTTTA
685453 ATTTCTTTTC-TG
1 ATTTCTTTTCTTG
685465 ATTT-TTTTCTTG
1 ATTTCTTTTCTTG
685477 ATTTCTTT
1 ATTTCTTT
685485 GACTTTGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 10 0.56
13 3 0.17
ACGTcount: A:0.09, C:0.12, G:0.06, T:0.72
Consensus pattern (13 bp):
ATTTCTTTTCTTG
Found at i:688804 original size:46 final size:46
Alignment explanation
Indices: 688351--688798 Score: 610
Period size: 46 Copynumber: 9.8 Consensus size: 46
688341 AAATGAATGA
* *
688351 ATAAATGAAAATGTATAATGGTGCATTATCGGCAT-AAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
688396 ATAAATGAAAATGAATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
688442 ATAAATTAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * **
688488 ATAAATGAAAATGCATAACGATGCCTTATCCTCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
688534 ATAAATGAAAATGCATAACGATGCATTATCGGCATGAAAGGAAGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
688580 ATAAATGAAAATGCATAACGGCGCATTATCGGTATGAAAGGAAGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* **** *
688626 ATAAATGAAAATGCATAACGGTACATTATCAATGTGAAACGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
688672 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* ** *
688718 ATAAATTAAAATGCATAGTGGTGCATTATCGGCATGAATGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* ** * * *
688764 ACAGTTGAAAATGTACAACGGTGCATTAACGGCAT
1 ATAAATGAAAATGCATAACGGTGCATTATCGGCAT
688799 AAATGGTTCC
Statistics
Matches: 357, Mismatches: 45, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
45 33 0.09
46 324 0.91
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:691565 original size:8 final size:9
Alignment explanation
Indices: 691540--691564 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
691530 TTCAAAACAA
691540 AAGAAAAAG
1 AAGAAAAAG
691549 AAGAAAAAG
1 AAGAAAAAG
691558 AAGAAAA
1 AAGAAAA
691565 GGAATTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:696783 original size:2 final size:2
Alignment explanation
Indices: 696778--696822 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
696768 TTATAACTCT
* *
696778 AC AC AC AC AC AC AC AC AA AC AC GC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
696820 AC A
1 AC A
696823 TATATATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.47, G:0.02, T:0.00
Consensus pattern (2 bp):
AC
Found at i:698094 original size:13 final size:13
Alignment explanation
Indices: 698072--698109 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
698062 ATTCCATTAT
698072 CATCCATCATCAA
1 CATCCATCATCAA
*
698085 CATCCTTCATCAA
1 CATCCATCATCAA
*
698098 GA-CCATCATCAA
1 CATCCATCATCAA
698110 TTCCATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.37, C:0.37, G:0.03, T:0.24
Consensus pattern (13 bp):
CATCCATCATCAA
Found at i:698158 original size:18 final size:18
Alignment explanation
Indices: 698131--698182 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
698121 TGCAGCCATC
698131 TCTA-TCATTTCTTTATT
1 TCTATTCATTTCTTTATT
698148 TCTATTCATTTC-TTATCT
1 TCTATTCATTTCTTTAT-T
698166 T-TATT-ATTTCATTTATT
1 TCTATTCATTTC-TTTATT
698183 CTTTCTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
16 5 0.16
17 13 0.42
18 13 0.42
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.65
Consensus pattern (18 bp):
TCTATTCATTTCTTTATT
Found at i:698163 original size:17 final size:19
Alignment explanation
Indices: 698131--698181 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
698121 TGCAGCCATC
698131 TCTA-TCATTTCTTTAT-T
1 TCTATTCATTTCTTTATCT
698148 TCTATTCATTTC-TTATCT
1 TCTATTCATTTCTTTATCT
698166 T-TATT-ATTTCATTTAT
1 TCTATTCATTTC-TTTAT
698182 TCTTTCTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.17
17 12 0.40
18 13 0.43
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.65
Consensus pattern (19 bp):
TCTATTCATTTCTTTATCT
Found at i:698170 original size:23 final size:24
Alignment explanation
Indices: 698140--698217 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 24
698130 CTCTATCATT
698140 TCTTTATT-TCTATTCATTTCTTA
1 TCTTTATTATCTATTCATTTCTTA
* *
698163 TCTTTATTATTTCATTTA-TTCTT-
1 TCTTTATTATCT-ATTCATTTCTTA
698186 TCTTTATTAATCATATTCATTTTCTTA
1 TCTTTATT-ATC-TATTCA-TTTCTTA
698213 TCTTT
1 TCTTT
698218 GTTGCAGCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
23 16 0.36
24 13 0.30
25 5 0.11
26 5 0.11
27 5 0.11
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.65
Consensus pattern (24 bp):
TCTTTATTATCTATTCATTTCTTA
Found at i:698407 original size:19 final size:18
Alignment explanation
Indices: 698383--698449 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 18
698373 TGTGAAAAAC
698383 AAAAGAAAATAAAAAGAA
1 AAAAGAAAATAAAAAGAA
*
698401 GAAAAG--AAGAAAAA-AA
1 -AAAAGAAAATAAAAAGAA
*
698417 TAAA-AAAATCAGAAAAGAA
1 AAAAGAAAAT-A-AAAAGAA
698436 TAAAAGAAAATAAA
1 -AAAAGAAAATAAA
698450 TTCAAAAGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
15 3 0.08
16 4 0.11
17 8 0.22
18 4 0.11
19 9 0.24
20 4 0.11
21 5 0.14
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.07
Consensus pattern (18 bp):
AAAAGAAAATAAAAAGAA
Found at i:698423 original size:27 final size:29
Alignment explanation
Indices: 698383--698449 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
698373 TGTGAAAAAC
698383 AAAAGAAAAT--AAAAAGAAGAAAAGAA-
1 AAAAGAAAATAAAAAAAGAAGAAAAGAAT
* **
698409 GAAA-AAAATAAAAAAATCAGAAAAGAAT
1 AAAAGAAAATAAAAAAAGAAGAAAAGAAT
698437 AAAAGAAAATAAA
1 AAAAGAAAATAAA
698450 TTCAAAAGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
25 5 0.15
26 3 0.09
27 14 0.42
28 3 0.09
29 8 0.24
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.07
Consensus pattern (29 bp):
AAAAGAAAATAAAAAAAGAAGAAAAGAAT
Found at i:702321 original size:195 final size:195
Alignment explanation
Indices: 701989--702379 Score: 737
Period size: 195 Copynumber: 2.0 Consensus size: 195
701979 ATTCGGCCAA
701989 GGGAGATGTTCCCTCATCATTGTCGAATCATCAAGCCCCTTCATGAAGGGTTAGCCAAGCTATCA
1 GGGAGATGTTCCCTCATCATTGTCGAATCATCAAGCCCCTTCATGAAGGGTTAGCCAAGCTATCA
*
702054 CAAGCCCAAAGGACTTAATCATTCATTTGAAGCGTTATGACCATTCGACCAAGCCCTCTCATTTC
66 CAAGCCCAAAGGACTTAATCATTCATTTGAAGCATTATGACCATTCGACCAAGCCCTCTCATTTC
702119 CTATGAATAGAGTGGATTGCCTTCATTTGTACTTATCTCATCTCAAATATAAAAATTACTCTTGT
131 CTATGAATAGAGTGGATTGCCTTCATTTGTACTTATCTCATCTCAAATATAAAAATTACTCTTGT
*
702184 GGGAGATGTTCCCTCATCATTGTTGAATCATCAAGCCCCTTCATGAAGGGTTAGCCAAGCTATCA
1 GGGAGATGTTCCCTCATCATTGTCGAATCATCAAGCCCCTTCATGAAGGGTTAGCCAAGCTATCA
702249 CAAGCCCAAAGGACTTAATCATTCATTTGAAGCATTATGACCATTCGACCAAGCCCTCTCATTTC
66 CAAGCCCAAAGGACTTAATCATTCATTTGAAGCATTATGACCATTCGACCAAGCCCTCTCATTTC
* * *
702314 CTATGAATAGAGTGGCTTGCCTTCATTTGTACTTATCTCGTCTCATATATAAAAATTACTCTTGT
131 CTATGAATAGAGTGGATTGCCTTCATTTGTACTTATCTCATCTCAAATATAAAAATTACTCTTGT
702379 G
1 G
702380 TGTTATTTCT
Statistics
Matches: 191, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
195 191 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (195 bp):
GGGAGATGTTCCCTCATCATTGTCGAATCATCAAGCCCCTTCATGAAGGGTTAGCCAAGCTATCA
CAAGCCCAAAGGACTTAATCATTCATTTGAAGCATTATGACCATTCGACCAAGCCCTCTCATTTC
CTATGAATAGAGTGGATTGCCTTCATTTGTACTTATCTCATCTCAAATATAAAAATTACTCTTGT
Found at i:703060 original size:24 final size:24
Alignment explanation
Indices: 703004--703067 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
702994 TTCATCTCTT
* *
703004 TCATTTCATTACTTATATTATTTATC
1 TCATTTC-TTA-TTTTATTATTAATC
703030 -CATTTCTTATTTTATTATTAATC
1 TCATTTCTTATTTTATTATTAATC
703053 TCATTTCTT-TTTTAT
1 TCATTTCTTATTTTAT
703068 CTTTGTTGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 18 0.51
24 11 0.31
25 6 0.17
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.62
Consensus pattern (24 bp):
TCATTTCTTATTTTATTATTAATC
Found at i:706392 original size:20 final size:20
Alignment explanation
Indices: 706350--706398 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
706340 TGAAAGGGAT
* *
706350 TATCGGTACCATGATATAAG
1 TATCGATACCATGATAGAAG
**
706370 TATCGATACCATGATAGGGG
1 TATCGATACCATGATAGAAG
706390 TATCGATAC
1 TATCGATAC
706399 TATTGAATCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (20 bp):
TATCGATACCATGATAGAAG
Found at i:706856 original size:46 final size:46
Alignment explanation
Indices: 706806--707109 Score: 387
Period size: 46 Copynumber: 6.6 Consensus size: 46
706796 AGTTGAATGA
* *
706806 ATAAATGAAAATGCCTAACGGTA-ACTTATCGGCATGAAATGATGCC
1 ATAAATGAAAATGCATAACGGTACA-TTATCGGCATGAAAGGATGCC
* * * *
706852 ATAAATGAAAATGCATAATGGTGCATTATCGGCGTGAAAGGATGTC
1 ATAAATGAAAATGCATAACGGTACATTATCGGCATGAAAGGATGCC
* * *
706898 ATAAATGAAAATGCATAACGGTGCATTATCAGCATGAAAGGATGCT
1 ATAAATGAAAATGCATAACGGTACATTATCGGCATGAAAGGATGCC
* * **
706944 ATAAATGAAAATGCATAACGATACATTATTGGCATGAAAGGATTTC
1 ATAAATGAAAATGCATAACGGTACATTATCGGCATGAAAGGATGCC
* * *
706990 ATAAATGAAAATGCATAACGGTGA-ATTATCGGCCTGAAAAGATGTC
1 ATAAATGAAAATGCATAACGGT-ACATTATCGGCATGAAAGGATGCC
* *
707036 ATAAATGAAAATGCATAACAGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTACATTATCGGCATGAAAGGATGCC
* * *
707082 AAAAATGAAAAAGCATAACGGTCCATTA
1 ATAAATGAAAATGCATAACGGTACATTA
707110 ACGACATAAA
Statistics
Matches: 223, Mismatches: 32, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
46 221 0.99
47 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTACATTATCGGCATGAAAGGATGCC
Found at i:706998 original size:138 final size:138
Alignment explanation
Indices: 706806--707101 Score: 441
Period size: 138 Copynumber: 2.1 Consensus size: 138
706796 AGTTGAATGA
* * * *
706806 ATAAATGAAAATGCCTAACGGTAACTTATCGGCATGAAATGATGCCATAAATGAAAATGCATAAT
1 ATAAATGAAAATGCATAACGATAACTTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
* * * *
706871 GGTGCATTATCGGCGTGAAAGGATGTCATAAATGAAAATGCATAACGGTGCATTATCAGCATGAA
66 GGTGAATTATCGGCCTGAAAAGATGTCATAAATGAAAATGCATAACAGTGCATTATCAGCATGAA
*
706936 AGGATGCT
131 AGGATGCC
* **
706944 ATAAATGAAAATGCATAACGAT-ACATTATTGGCATGAAAGGATTTCATAAATGAAAATGCATAA
1 ATAAATGAAAATGCATAACGATAAC-TTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAA
*
707008 CGGTGAATTATCGGCCTGAAAAGATGTCATAAATGAAAATGCATAACAGTGCATTATCGGCATGA
65 CGGTGAATTATCGGCCTGAAAAGATGTCATAAATGAAAATGCATAACAGTGCATTATCAGCATGA
707073 AAGGATGCC
130 AAGGATGCC
* *
707082 AAAAATGAAAAAGCATAACG
1 ATAAATGAAAATGCATAACG
707102 GTCCATTAAC
Statistics
Matches: 142, Mismatches: 15, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
137 2 0.01
138 140 0.99
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (138 bp):
ATAAATGAAAATGCATAACGATAACTTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAAC
GGTGAATTATCGGCCTGAAAAGATGTCATAAATGAAAATGCATAACAGTGCATTATCAGCATGAA
AGGATGCC
Found at i:713731 original size:23 final size:23
Alignment explanation
Indices: 713700--713743 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
713690 TTTATGTTTA
713700 GGATGATGAAGATGATTTAAAAAT
1 GGATGATG-AGATGATTTAAAAAT
*
713724 GGAT-ATGATATGATTTAAAA
1 GGATGATGAGATGATTTAAAA
713744 GCCCATTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 3 0.16
24 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (23 bp):
GGATGATGAGATGATTTAAAAAT
Found at i:717405 original size:20 final size:20
Alignment explanation
Indices: 717382--717434 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
717372 CTTATAATGT
*
717382 TATCGATACTACTTCAA-CGG
1 TATCGATACTA-TTCAATCAG
*
717402 TATCGATACTGATTGAATCAG
1 TATCGATACT-ATTCAATCAG
717423 TATCGATACTAT
1 TATCGATACTAT
717435 CCAGCATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (20 bp):
TATCGATACTATTCAATCAG
Found at i:723235 original size:45 final size:45
Alignment explanation
Indices: 723173--723457 Score: 256
Period size: 45 Copynumber: 6.4 Consensus size: 45
723163 AATGTACCAT
* ***
723173 TATGCATTTTAAACTATAGCATACTTTTCTATTGATAATTTTCCCA
1 TATGCA-TTTCAACTATAGCATACTTTTCTATTGATAATACACCCA
* * *
723219 TATACATATCAACTATAGCATACTTTTCTATTGAGAATACACCCA
1 TATGCATTTCAACTATAGCATACTTTTCTATTGATAATACACCCA
* * * *
723264 TATGCATTTCAACTATCGCATATTTTTC-GTTGATAATGCACCCA
1 TATGCATTTCAACTATAGCATACTTTTCTATTGATAATACACCCA
* * * * * **
723308 TATGTATTTCAACTATCGCATATTTTTCTGTTGATAATGCATACA
1 TATGCATTTCAACTATAGCATACTTTTCTATTGATAATACACCCA
* * * *
723353 TATGCATTTCATCTAT-GCCATGA-TTTTCTGTTGAAAATGCACCCA
1 TATGCATTTCAACTATAG-CAT-ACTTTTCTATTGATAATACACCCA
* * ** *
723398 TATGCATTTTAACTATAGCATAC-TTTC-AGTTAACCATTCACCCA
1 TATGCATTTCAACTATAGCATACTTTTCTA-TTGATAATACACCCA
723442 TATGCATTTCAACTAT
1 TATGCATTTCAACTAT
723458 GGTATCCTTT
Statistics
Matches: 203, Mismatches: 30, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
44 72 0.35
45 124 0.61
46 7 0.03
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.40
Consensus pattern (45 bp):
TATGCATTTCAACTATAGCATACTTTTCTATTGATAATACACCCA
Found at i:723329 original size:89 final size:88
Alignment explanation
Indices: 723173--723494 Score: 283
Period size: 89 Copynumber: 3.6 Consensus size: 88
723163 AATGTACCAT
* * *** * *
723173 TATGCATTTTAAACTATAGCATACTTTTCTATTGATAATTTTCCCATATACATATCAACTATAGC
1 TATGCA-TTTCAACTAT-GCATA-TTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGC
*
723238 ATACTTTTCTATTGAGAATACACCCA
63 ATACTTTTCTATTGACAATACACCCA
* *
723264 TATGCATTTCAACTATCGCATATTTT-TCGTTGATAATGCACCCATATGTATTTCAACTATCGCA
1 TATGCATTTCAACTAT-GCATATTTTCT-GTTGATAATGCACCCATATGCATTTCAACTATAGCA
* * * * **
723328 TATTTTTCTGTTGATAATGCATACA
64 TACTTTTCTATTGACAATACACCCA
* * *
723353 TATGCATTTCATCTATGCCATGATTTTCTGTTGAAAATGCACCCATATGCATTTTAACTATAGCA
1 TATGCATTTCAACTATG-CAT-ATTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCA
* * *
723418 TAC-TTTC-AGTTAACCATTCACCCA
64 TACTTTTCTA-TTGACAATACACCCA
* ** *
723442 TATGCATTTCAACTATG-GTATCCTTTCATGTCAATAATGCATCCATATGCATT
1 TATGCATTTCAACTATGCATAT--TTTC-TGTTGATAATGCACCCATATGCATT
723495 ATTATTTTCA
Statistics
Matches: 188, Mismatches: 35, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
86 2 0.01
87 1 0.01
88 6 0.03
89 119 0.63
90 53 0.28
91 7 0.04
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (88 bp):
TATGCATTTCAACTATGCATATTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGCATA
CTTTTCTATTGACAATACACCCA
Found at i:723342 original size:134 final size:134
Alignment explanation
Indices: 723173--723457 Score: 308
Period size: 134 Copynumber: 2.1 Consensus size: 134
723163 AATGTACCAT
* ** *
723173 TATGCATTTTAAACTATAGCATACTTTTCTATTGATAAT-TTTCCCATATACATATCAACTATAG
1 TATGCA-TTTCAACTATAGCATACTTTTCTATTGATAATGCAT-ACATATACATATCAACTAT-G
* * * * *
723237 -CAT-ACTTTTCTATTGAGAATACACCCATATGCATTTCAACTATCGCATATTTTTC-GTTGATA
63 CCATGA-TTTTCTATTGAAAATACACCCATATGCATTTCAACTATAGCATA-CTTTCAGTTAACA
723299 ATGCACCCA
126 ATGCACCCA
* * * * * * *
723308 TATGTATTTCAACTATCGCATATTTTTCTGTTGATAATGCATACATATGCATTTCATCTATGCCA
1 TATGCATTTCAACTATAGCATACTTTTCTATTGATAATGCATACATATACATATCAACTATGCCA
* * * * *
723373 TGATTTTCTGTTGAAAATGCACCCATATGCATTTTAACTATAGCATACTTTCAGTTAACCATTCA
66 TGATTTTCTATTGAAAATACACCCATATGCATTTCAACTATAGCATACTTTCAGTTAACAATGCA
723438 CCCA
131 CCCA
723442 TATGCATTTCAACTAT
1 TATGCATTTCAACTAT
723458 GGTATCCTTT
Statistics
Matches: 124, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
133 5 0.04
134 112 0.90
135 7 0.06
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.40
Consensus pattern (134 bp):
TATGCATTTCAACTATAGCATACTTTTCTATTGATAATGCATACATATACATATCAACTATGCCA
TGATTTTCTATTGAAAATACACCCATATGCATTTCAACTATAGCATACTTTCAGTTAACAATGCA
CCCA
Found at i:723479 original size:134 final size:134
Alignment explanation
Indices: 723242--723494 Score: 314
Period size: 134 Copynumber: 1.9 Consensus size: 134
723232 TATAGCATAC
* * * * *
723242 TTTTCTATTGAGAATACACCCATATGCATTTCAACTATCGCATATTTTTCGTTGATAATGCACCC
1 TTTTCTATTGAAAATACACCCATATGCATTTCAACTATAGCATATCTTTCGTTAACAATGCACCC
* * **
723307 ATATGTATTTCAACTATCGCATATTTTTCTGTTGATAATGCATACATATGCATTTCATCTATGCC
66 ATATGCATTTCAACTATCGCATATCTTTCTGTCAATAATGCATACATATGCATTTCATCTATGCC
723372 ATGA
131 ATGA
* * * * *
723376 TTTTCTGTTGAAAATGCACCCATATGCATTTTAACTATAGCATA-CTTTCAGTTAACCATTCACC
1 TTTTCTATTGAAAATACACCCATATGCATTTCAACTATAGCATATCTTTC-GTTAACAATGCACC
* *
723440 CATATGCATTTCAACTAT-G-GTATCCTTTCATGTCAATAATGCATCCATATGCATT
65 CATATGCATTTCAACTATCGCATAT-CTTTC-TGTCAATAATGCATACATATGCATT
723495 ATTATTTTCA
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
132 3 0.03
133 9 0.09
134 88 0.88
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (134 bp):
TTTTCTATTGAAAATACACCCATATGCATTTCAACTATAGCATATCTTTCGTTAACAATGCACCC
ATATGCATTTCAACTATCGCATATCTTTCTGTCAATAATGCATACATATGCATTTCATCTATGCC
ATGA
Found at i:738643 original size:66 final size:66
Alignment explanation
Indices: 738565--738689 Score: 169
Period size: 66 Copynumber: 1.9 Consensus size: 66
738555 GTTTTAATTT
* *
738565 TTAGAGTCGTTGTTAATGGAGTATCGAGGATTATGGCTTTATATTTTATTATCAGAGTCGTTATT
1 TTAGAGTCGTTGTTAATGGAGTATCGAGGATTAGGGCATTATATTTTATTATCAGAGTCGTTATT
738630 G
66 G
* * * * * * *
738631 TTAGAGTTGTTGTTATTGGAGTATTGGGGGTTAGGGGATTGTATTTTATTATCAGAGTC
1 TTAGAGTCGTTGTTAATGGAGTATCGAGGATTAGGGCATTATATTTTATTATCAGAGTC
738690 ATTGTTATTT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 50 1.00
ACGTcount: A:0.22, C:0.06, G:0.28, T:0.44
Consensus pattern (66 bp):
TTAGAGTCGTTGTTAATGGAGTATCGAGGATTAGGGCATTATATTTTATTATCAGAGTCGTTATT
G
Found at i:743215 original size:5 final size:5
Alignment explanation
Indices: 743205--743253 Score: 62
Period size: 5 Copynumber: 9.6 Consensus size: 5
743195 AATTAAAACT
** *
743205 AAATA AAATA AAATA ATGTA AAATA AATAAA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AA-ATA AAATA AAATA AAATA AAA
743254 ATAGAAACTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
5 33 0.89
6 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:745743 original size:66 final size:68
Alignment explanation
Indices: 745552--745755 Score: 231
Period size: 66 Copynumber: 3.0 Consensus size: 68
745542 TTTAATTTTT
* * * * * *
745552 TGGA-GTCGTTGTTAATGGAGTATC-GGGGATTAGGGGTT-TATATTTTATTATCAGAATCATTA
1 TGGAGGTCGTTGTTATTGGAGTATCAGGGGGTTAGGGATTGTAT-TTTTATTATCGGAGTCACTA
*
745614 TTAT
65 TTAA
** *
745618 TGGAGG-CACTGTTATTGGAGTATCCAGGGGGTTAGGGTATTGTATTTTTATTATTGGAGTCACT
1 TGGAGGTCGTTGTTATTGGAGTAT-CAGGGGGTTAGGG-ATTGTATTTTTATTATCGGAGTCACT
745682 ATTAA
64 ATTAA
* *
745687 TGG-GGTCGTTGGTATTGGAGTATCAGGGGGTTA-GGATTGTATTTTTATTATCGGAGTCACTGT
1 TGGAGGTCGTTGTTATTGGAGTATCAGGGGGTTAGGGATTGTATTTTTATTATCGGAGTCACTAT
745750 TAA
66 TAA
745753 TGG
1 TGG
745756 TTGTTGTTAA
Statistics
Matches: 117, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
66 50 0.43
67 4 0.03
68 22 0.19
69 38 0.32
70 3 0.03
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.40
Consensus pattern (68 bp):
TGGAGGTCGTTGTTATTGGAGTATCAGGGGGTTAGGGATTGTATTTTTATTATCGGAGTCACTAT
TAA
Found at i:756456 original size:43 final size:44
Alignment explanation
Indices: 756336--756471 Score: 111
Period size: 43 Copynumber: 3.1 Consensus size: 44
756326 AAAATAGTTG
*
756336 TTATGACTAAATAAGA-TT-TTATAATTTTTTATTTTGAGAAAATA
1 TTATGACTAAATAA-ATTTATTA-AATTTCTTATTTTGAGAAAATA
** * **
756380 TTGCGACTAAATAAATTTGACTT-AGTTTCTTATTTT-A-ACTATA
1 TTATGACTAAATAAATTT-A-TTAAATTTCTTATTTTGAGAAAATA
* * *
756423 TTATGACTAAATAAATTTATTAAAATTTGTTATTGTGAAAAAATA
1 TTATGACTAAATAAATTTATT-AAATTTCTTATTTTGAGAAAATA
756468 TTAT
1 TTAT
756472 TTGTCATAAT
Statistics
Matches: 71, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
41 2 0.03
42 1 0.01
43 31 0.44
44 16 0.23
45 19 0.27
47 2 0.03
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (44 bp):
TTATGACTAAATAAATTTATTAAATTTCTTATTTTGAGAAAATA
Found at i:756760 original size:23 final size:23
Alignment explanation
Indices: 756703--756760 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
756693 TTGTGACATG
*
756703 TTCTCTGCCTTAGTGACACATTT
1 TTCTCTGCCTTTGTGACACATTT
* * *
756726 ATCTCTACCTTTGTGGCACATTT
1 TTCTCTGCCTTTGTGACACATTT
756749 TTCTCTGCCTTT
1 TTCTCTGCCTTT
756761 TGGTAACTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.14, C:0.28, G:0.12, T:0.47
Consensus pattern (23 bp):
TTCTCTGCCTTTGTGACACATTT
Found at i:757592 original size:172 final size:177
Alignment explanation
Indices: 757248--757592 Score: 411
Period size: 172 Copynumber: 2.0 Consensus size: 177
757238 TATTTGTTAG
* * *
757248 AAATTGTTATTATGACTAAATAAATTTGTCAAAATTTTTTATTTTGAGAAAATATTGTGAACAAA
1 AAATTGTTATTATGACTAAATAAATTTGTCAAAATTTGTTATTTTAAGAAAATATTATGAACAAA
* *
757313 TAAATTTGACATAATTTCTTATTTTGACTAAATTTAATATCTTATTGTGACTACATAAATTTGTT
66 TAAATTTGACATAA-TTCTTATTTTGACTAAATTTAATATCTTATTGTGACTAAATAAATTTATT
* * *
757378 ACAATTCATTATTGTTAAAAAAGCATTATTTGTCATAATTTTTTTTAT
130 ACAATTCATTATTGCTAAAAAAGCATGATTTGTCACAATTTTTTTTAT
* * * *
757426 AAATTTTTATTATGATTAAA-AAATTAT-T-ATAATTTGTTATTTTAAGAAACTATTATG-ACTA
1 AAATTGTTATTATGACTAAATAAATT-TGTCAAAATTTGTTATTTTAAGAAAATATTATGAAC-A
* * *
757487 AATAAATTTGACATAA-T-TT-TTTTGACTAAATTTAATATTTTGTTGTGATTAAATAAATTTAT
64 AATAAATTTGACATAATTCTTATTTTGACTAAATTTAATATCTTATTGTGACTAAATAAATTTAT
* * * *
757549 TACAATTTATTATAT-CTGACAAA-TATGATTTGTCACCAATTTTT
129 TACAATTCATTAT-TGCTAAAAAAGCATGATTTGTCA-CAATTTTT
757593 ATATTTGTAA
Statistics
Matches: 144, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
171 10 0.07
172 62 0.43
173 3 0.02
174 1 0.01
175 2 0.01
176 41 0.28
177 6 0.04
178 19 0.13
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.47
Consensus pattern (177 bp):
AAATTGTTATTATGACTAAATAAATTTGTCAAAATTTGTTATTTTAAGAAAATATTATGAACAAA
TAAATTTGACATAATTCTTATTTTGACTAAATTTAATATCTTATTGTGACTAAATAAATTTATTA
CAATTCATTATTGCTAAAAAAGCATGATTTGTCACAATTTTTTTTAT
Done.