Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005721.1 Hibiscus syriacus cultivar Beakdansim tig00013376_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: 96963
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4804 original size:2 final size:2
Alignment explanation
Indices: 4797--4828 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4787 GATTACAATA
4797 AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4829 GTAGAGAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4818 original size:13 final size:13
Alignment explanation
Indices: 4800--4825 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4790 TACAATAATA
4800 TATATATATATAT
1 TATATATATATAT
4813 TATATATATATAT
1 TATATATATATAT
4826 ATAGTAGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:4818 original size:15 final size:15
Alignment explanation
Indices: 4798--4827 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4788 ATTACAATAA
4798 TATATATATATATAT
1 TATATATATATATAT
4813 TATATATATATATAT
1 TATATATATATATAT
4828 AGTAGAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:12842 original size:14 final size:15
Alignment explanation
Indices: 12812--12845 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
12802 TATATTTTAA
12812 AAAATTAATGATTTTT
1 AAAATTAAT-ATTTTT
12828 AAAATTAAT-TTTTT
1 AAAATTAATATTTTT
12842 AAAA
1 AAAA
12846 ATATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
16 9 0.50
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AAAATTAATATTTTT
Found at i:15580 original size:25 final size:26
Alignment explanation
Indices: 15532--15593 Score: 99
Period size: 25 Copynumber: 2.4 Consensus size: 26
15522 TGACCAAATC
*
15532 ATAAAATTTTAATGATAAATATATTT
1 ATAAAATTTTAATCATAAATATATTT
*
15558 ATAAAATTTTAA-CATAAGTATATTT
1 ATAAAATTTTAATCATAAATATATTT
15583 ATAAAATTTTA
1 ATAAAATTTTA
15594 GAGGAATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 22 0.65
26 12 0.35
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (26 bp):
ATAAAATTTTAATCATAAATATATTT
Found at i:18362 original size:20 final size:21
Alignment explanation
Indices: 18337--18388 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
18327 TTTTCCCAAT
*
18337 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
18357 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
18378 TCGCAATGCGA
1 TCGCAATGCGA
18389 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:19043 original size:19 final size:19
Alignment explanation
Indices: 19007--19048 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
18997 ACGAGAGAAT
**
19007 CGCAACGCGAAATGAAAAA
1 CGCAACGCGAAACAAAAAA
*
19026 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
19045 CGCA
1 CGCA
19049 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.26, G:0.19, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:19066 original size:19 final size:19
Alignment explanation
Indices: 19044--19133 Score: 144
Period size: 19 Copynumber: 4.7 Consensus size: 19
19034 GAAACAAAAA
* *
19044 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
19063 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
19082 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
19101 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
19121 TCGCGTTGCGATT
1 TCGCGTTGCGATT
19134 GTCTGGTCGC
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
19 48 0.73
20 18 0.27
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:19121 original size:39 final size:38
Alignment explanation
Indices: 19044--19133 Score: 162
Period size: 39 Copynumber: 2.3 Consensus size: 38
19034 GAAACAAAAA
*
19044 TCGCATTGCGATTTTTATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
19082 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGC-GTTGCGATTTTCATT
19121 TCGCGTTGCGATT
1 TCGCGTTGCGATT
19134 GTCTGGTCGC
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 22 0.44
39 28 0.56
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (38 bp):
TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
Found at i:19144 original size:39 final size:39
Alignment explanation
Indices: 19044--19144 Score: 116
Period size: 39 Copynumber: 2.6 Consensus size: 39
19034 GAAACAAAAA
* * **
19044 TCGCATTGCGATTTTTATTTCGC-GTTGCGATTTTCATT
1 TCGCGTTGCGATTTCTAGGTCGCGGTTGCGATTTTCATT
* **
19082 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTCTAGGTCGCGGTTGCGATTTTCATT
19121 TCGCGTTGCGATTGTCT-GGTCGCG
1 TCGCGTTGCGATT-TCTAGGTCGCG
19145 ATAGTCATTT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
38 22 0.39
39 33 0.58
40 2 0.04
ACGTcount: A:0.10, C:0.20, G:0.25, T:0.46
Consensus pattern (39 bp):
TCGCGTTGCGATTTCTAGGTCGCGGTTGCGATTTTCATT
Found at i:19174 original size:14 final size:14
Alignment explanation
Indices: 19157--19193 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
19147 AGTCATTTCG
*
19157 CGTTGCGATTCTCT
1 CGTTGCGATTCTAT
19171 CGTTGCGATTCTAT
1 CGTTGCGATTCTAT
19185 CGTTGCGAT
1 CGTTGCGAT
19194 AGTCATTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.11, C:0.24, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTAT
Found at i:19179 original size:33 final size:33
Alignment explanation
Indices: 19106--19179 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
19096 TTATTTCGCG
** * *
19106 GTTGCGATTTTCATTTCGCGTTGCGATTGTCTG
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
*
19139 GTCGCGATAGTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
19172 GTTGCGAT
1 GTTGCGAT
19180 TCTATCGTTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.22, G:0.27, T:0.41
Consensus pattern (33 bp):
GTTGCGATAGTCATTTCGCGTTGCGATTCTCTC
Found at i:19193 original size:47 final size:48
Alignment explanation
Indices: 19124--19217 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 48
19114 TTTCATTTCG
* * *
19124 CGTTGCGATTGTCTGGTCGCGATAGTCATTT-CGCGTTGCGATTCTCT
1 CGTTGCGATTCTATCGTCGCGATAGTCATTTCCGCGTTGCGATTCTCT
* *
19171 CGTTGCGATTCTATCGTTGCGATAGTCATTTCCGTGTTGCGATTCTC
1 CGTTGCGATTCTATCGTCGCGATAGTCATTTCCGCGTTGCGATTCTC
19218 ATTATCTCGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 27 0.66
48 14 0.34
ACGTcount: A:0.12, C:0.23, G:0.26, T:0.39
Consensus pattern (48 bp):
CGTTGCGATTCTATCGTCGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:19219 original size:20 final size:20
Alignment explanation
Indices: 19184--19242 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
19174 TGCGATTCTA
**
19184 TCGTTGCGATAGTCATTTCC
1 TCGTTGCGATTCTCATTTCC
19204 GT-GTTGCGATTCTCATTAT-C
1 -TCGTTGCGATTCTCATT-TCC
*
19224 TCGTTGCGATTTTCATTTC
1 TCGTTGCGATTCTCATTTC
19243 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (20 bp):
TCGTTGCGATTCTCATTTCC
Found at i:21328 original size:21 final size:21
Alignment explanation
Indices: 21304--21370 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
21294 TCATTCCTCG
21304 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
21325 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
21346 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
21367 AGAG
1 AGAG
21371 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:21328 original size:42 final size:42
Alignment explanation
Indices: 21252--21370 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 42
21242 GACTAGCCTG
* * * *
21252 TCATCCCTC-AAGA-GTCCACTCCTATCATTGAAGAGGCCCCTA
1 TCAT-CCTCGAAGAGGTCC-CTCCCACCATTCAAGAGGCCACTA
* *
21294 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTCGAAGAGGT-CCCTCCCACCATTCAAGAGGCCACTA
* *
21336 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAG
21371 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
41 4 0.06
42 54 0.86
43 5 0.08
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCCTCGAAGAGGTCCCTCCCACCATTCAAGAGGCCACTA
Found at i:22749 original size:14 final size:14
Alignment explanation
Indices: 22730--22765 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
22720 ATTGTTTAAT
22730 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
22744 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
22758 TGATTTGT
1 TGATTTGT
22766 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:22956 original size:19 final size:19
Alignment explanation
Indices: 22924--23074 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
22914 CGAAATTAAA
* *
22924 TTCGCGTTGTGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
22943 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
22959 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
22976 TTTGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
22990 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
23009 TTCGCATTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
*
23024 -TCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
** *
23042 TTCGCATTGCGATAGTAAT
1 TTCGCATTGCGATTTTCAT
23061 TTCCGCATTGCGAT
1 TT-CGCATTGCGAT
23075 AGACATTAAG
Statistics
Matches: 98, Mismatches: 18, Indels: 31
0.67 0.12 0.21
Matches are distributed among these distances:
14 27 0.28
16 9 0.09
17 8 0.08
19 43 0.44
20 11 0.11
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:22971 original size:33 final size:32
Alignment explanation
Indices: 22928--23054 Score: 166
Period size: 33 Copynumber: 3.9 Consensus size: 32
22918 ATTAAATTCG
*
22928 CGTTGTGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
22961 CGTTGCGATTTTCATTTTGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
22994 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
23027 CATTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
23055 AGTAATTTCC
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
31 3 0.04
33 76 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:23007 original size:66 final size:66
Alignment explanation
Indices: 22921--23053 Score: 221
Period size: 66 Copynumber: 2.0 Consensus size: 66
22911 ACGCGAAATT
* * * *
22921 AAATTCGCGTTGTGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTTGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
22986 G
66 G
*
22987 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
23052 G
66 G
23053 A
1 A
23054 TAGTAATTTC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
G
Found at i:25568 original size:24 final size:24
Alignment explanation
Indices: 25534--25587 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
25524 CTGAAACATC
* *
25534 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
25558 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
25582 ATCAAA
1 ATCAAA
25588 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:26658 original size:20 final size:20
Alignment explanation
Indices: 26633--26710 Score: 129
Period size: 20 Copynumber: 3.9 Consensus size: 20
26623 ATTCATTTGA
*
26633 CTATCGCAACGCAAAAATGG
1 CTATCGCAACGCGAAAATGG
26653 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
26673 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
26693 CTATCGTAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
26711 CGCAATGCGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:26753 original size:14 final size:14
Alignment explanation
Indices: 26734--26787 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
26724 GAAAATCGCA
26734 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
26748 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
26765 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
26781 TTGCGAT
1 TTGCGAT
26788 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:26753 original size:33 final size:33
Alignment explanation
Indices: 26716--26786 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
26706 AAAATCGCAA
26716 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
26749 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
26782 TGCGA
1 TGCGA
26787 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:26787 original size:33 final size:33
Alignment explanation
Indices: 26729--26806 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
26719 GAAATGAAAA
***
26729 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
26762 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
26795 TCGCGTTGCGAT
1 TCGCATTGCGAT
26807 AGTCTGTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:26915 original size:14 final size:14
Alignment explanation
Indices: 26896--26930 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
26886 TCAATTAAAT
26896 AAATCAACATTTAC
1 AAATCAACATTTAC
* *
26910 AAATCATCTTTTAC
1 AAATCAACATTTAC
26924 AAATCAA
1 AAATCAA
26931 TTAAACAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACATTTAC
Found at i:28760 original size:26 final size:27
Alignment explanation
Indices: 28694--28762 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
28684 ATGCTCAGAT
*
28694 AACATTCCAGAAGTAAGCACTTATATAA
1 AACATTCCAGAAG-AAGCACATATATAA
* *
28722 AACATT-TAAAAGAA-CAACATATAT-A
1 AACATTCCAGAAGAAGC-ACATATATAA
28747 AACATTCCAGAAGAAG
1 AACATTCCAGAAGAAG
28763 AATAGTTTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
25 8 0.24
26 15 0.45
27 4 0.12
28 6 0.18
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.22
Consensus pattern (27 bp):
AACATTCCAGAAGAAGCACATATATAA
Found at i:28818 original size:19 final size:19
Alignment explanation
Indices: 28793--28881 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
28783 CGAAACTTAA
28793 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAC
* *
28812 TATCGCAACGCGGAAATGGC
1 AATCGCAACGC-GAAATGAC
* *
28832 TATCGCAATGCGAAATGA-
1 AATCGCAACGCGAAATGAC
*
28850 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAC
*
28869 AATCGCAATGCGA
1 AATCGCAACGCGA
28882 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
18 16 0.26
19 28 0.46
20 17 0.28
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.15
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAC
Found at i:28912 original size:14 final size:14
Alignment explanation
Indices: 28893--28950 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
28883 TTGTGTTTCG
28893 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
28907 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
28923 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
28939 CGTTGCAATTTT
1 CGTTGCGATTTT
28951 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:28927 original size:32 final size:33
Alignment explanation
Indices: 28888--28966 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
28878 GCGATTTGTG
*
28888 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCAATTTTCA
28920 TTTCGCGTTGCGATTTTGTCGTTGCAATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCAATTTTCA
*
28953 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
28967 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCAATTTTCA
Found at i:28985 original size:20 final size:19
Alignment explanation
Indices: 28951--29005 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
28941 TTGCAATTTT
*
28951 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
28970 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
28990 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
29006 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:29513 original size:18 final size:18
Alignment explanation
Indices: 29487--29531 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
29477 GTCGATCAGA
*
29487 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
29505 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
29523 TGATGGCTC
1 TGATGGCTC
29532 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:30876 original size:20 final size:20
Alignment explanation
Indices: 30851--30893 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
30841 AATAGTTTCT
30851 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
30871 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
30891 GAA
1 GAA
30894 TTCGACTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:31185 original size:22 final size:22
Alignment explanation
Indices: 31158--31201 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
31148 GATGGAGATA
31158 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
31180 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
31202 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:31451 original size:20 final size:20
Alignment explanation
Indices: 31389--31502 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
31379 GATTATGTAT
31389 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
31409 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
31429 TATCGCGTTGCGAAAGT-ATG
1 TATCGCGTTGCGAAAGTCA-G
* ** *
31449 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
31470 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
31490 TATCGCATTGCGA
1 TATCGCGTTGCGA
31503 TTTTCCCAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
19 4 0.05
20 62 0.77
21 11 0.14
22 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:31503 original size:20 final size:19
Alignment explanation
Indices: 31369--31503 Score: 99
Period size: 20 Copynumber: 6.7 Consensus size: 19
31359 CGCTTTGAAA
* *
31369 ATCGCATTGCGATTATGTATT
1 ATCGCGTTGCGA-TA-GTAGT
* *
31390 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGATAGT-AGT
*
31410 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGT-AGT
*
31430 ATCGCGTTGCGAAAGTATGT
1 ATCGCGTTGCGATAGTA-GT
* * *
31450 ATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGA--TAGTAGT
*
31471 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGT-AGT
*
31491 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
31504 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
19 6 0.06
20 65 0.68
21 22 0.23
22 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATAGTAGT
Found at i:31521 original size:21 final size:21
Alignment explanation
Indices: 31492--31584 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
31482 ATAGTCAGTA
31492 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
31513 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
31533 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
31554 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
31574 TCGCATTGCGA
1 TCGCATTGCGA
31585 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:31522 original size:41 final size:41
Alignment explanation
Indices: 31492--31584 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
31482 ATAGTCAGTA
* *
31492 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* *
31533 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
31574 TCGCATTGCGA
1 TCGCATTGCGA
31585 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:32472 original size:30 final size:30
Alignment explanation
Indices: 32438--32494 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
32428 TTAATGTTGT
*
32438 AATCAATCAATTGAGTGATTTAATTATTAC
1 AATCAATCAATTGAGTGACTTAATTATTAC
* *
32468 AATCAATTAATTGAGTGACTTGATTAT
1 AATCAATCAATTGAGTGACTTAATTAT
32495 AACTCTGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (30 bp):
AATCAATCAATTGAGTGACTTAATTATTAC
Found at i:34543 original size:15 final size:15
Alignment explanation
Indices: 34525--34556 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
34515 TAGAAATCAT
34525 ATTATTAAAAATAGA
1 ATTATTAAAAATAGA
34540 ATTATTAAAAATAGA
1 ATTATTAAAAATAGA
34555 AT
1 AT
34557 GGAATATTGA
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:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (15 bp):
ATTATTAAAAATAGA
Found at i:37310 original size:14 final size:14
Alignment explanation
Indices: 37291--37317 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
37281 TTAATCTAAT
37291 TGTTGACACCTTAG
1 TGTTGACACCTTAG
37305 TGTTGACACCTTA
1 TGTTGACACCTTA
37318 ATGATATTTT
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:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (14 bp):
TGTTGACACCTTAG
Found at i:38460 original size:15 final size:15
Alignment explanation
Indices: 38440--38472 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
38430 TAAGGCCCTA
*
38440 AGCACAAAGTCGAGG
1 AGCACAAAGCCGAGG
38455 AGCACAAAGCCGAGG
1 AGCACAAAGCCGAGG
38470 AGC
1 AGC
38473 TTGCAAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.33, T:0.03
Consensus pattern (15 bp):
AGCACAAAGCCGAGG
Found at i:39412 original size:28 final size:29
Alignment explanation
Indices: 39360--39543 Score: 196
Period size: 29 Copynumber: 6.4 Consensus size: 29
39350 AATTTTACAT
* *
39360 AAATAACACCTTTTTTTTAAA-TAATT-ACA
1 AAATAACACC--TTTTTCAAATTAATTCCCA
*
39389 AAA-AACACCCTTTTTCGAATTAATTCCCA
1 AAATAACA-CCTTTTTCAAATTAATTCCCA
*
39418 AAATAGCACCTTTTTCAAATTAATTCCCA
1 AAATAACACCTTTTTCAAATTAATTCCCA
* *
39447 AAATAGCACCATTTTCAAATTAATTCCCA
1 AAATAACACCTTTTTCAAATTAATTCCCA
* *
39476 AAATAACA-CTATTTCGAATTAATTCCCA
1 AAATAACACCTTTTTCAAATTAATTCCCA
* * * *
39504 AAATAGCACCTATTTCGAATAAATTCCCA
1 AAATAACACCTTTTTCAAATTAATTCCCA
*
39533 AAATAGCACCT
1 AAATAACACCT
39544 GGTCAACGGT
Statistics
Matches: 138, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
27 7 0.05
28 33 0.24
29 95 0.69
30 3 0.02
ACGTcount: A:0.41, C:0.23, G:0.04, T:0.32
Consensus pattern (29 bp):
AAATAACACCTTTTTCAAATTAATTCCCA
Found at i:39419 original size:29 final size:29
Alignment explanation
Indices: 39397--39543 Score: 224
Period size: 29 Copynumber: 5.1 Consensus size: 29
39387 CAAAAAACAC
39397 CCTTTTTCGAATTAATTCCCAAAATAGCA
1 CCTTTTTCGAATTAATTCCCAAAATAGCA
*
39426 CCTTTTTCAAATTAATTCCCAAAATAGCA
1 CCTTTTTCGAATTAATTCCCAAAATAGCA
* * *
39455 CCATTTTCAAATTAATTCCCAAAATAACA
1 CCTTTTTCGAATTAATTCCCAAAATAGCA
*
39484 -CTATTTCGAATTAATTCCCAAAATAGCA
1 CCTTTTTCGAATTAATTCCCAAAATAGCA
* *
39512 CCTATTTCGAATAAATTCCCAAAATAGCA
1 CCTTTTTCGAATTAATTCCCAAAATAGCA
39541 CCT
1 CCT
39544 GGTCAACGGT
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
28 24 0.22
29 85 0.78
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.32
Consensus pattern (29 bp):
CCTTTTTCGAATTAATTCCCAAAATAGCA
Found at i:39513 original size:57 final size:57
Alignment explanation
Indices: 39400--39543 Score: 209
Period size: 57 Copynumber: 2.5 Consensus size: 57
39390 AAAACACCCT
* *
39400 TTTTCGAATTAATTCCCAAAATAGCACCTTTTTCAAATTAATTCCCAAAATAGCACC
1 TTTTCGAATTAATTCCCAAAATAACACCTATTTCAAATTAATTCCCAAAATAGCACC
* *
39457 ATTTTCAAATTAATTCCCAAAATAACA-CTATTTCGAATTAATTCCCAAAATAGCACC
1 -TTTTCGAATTAATTCCCAAAATAACACCTATTTCAAATTAATTCCCAAAATAGCACC
* *
39514 TATTTCGAATAAATTCCCAAAATAGCACCT
1 T-TTTCGAATTAATTCCCAAAATAACACCT
39544 GGTCAACGGT
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
56 1 0.01
57 50 0.65
58 26 0.34
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.32
Consensus pattern (57 bp):
TTTTCGAATTAATTCCCAAAATAACACCTATTTCAAATTAATTCCCAAAATAGCACC
Found at i:46644 original size:28 final size:28
Alignment explanation
Indices: 46613--46678 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
46603 CATTTTACAG
*
46613 AAATAACACATTTTTAAAATAATTACCA
1 AAATAACACATTTTCAAAATAATTACCA
* * * *
46641 AAATAGCACCCTTTTCAAATTAATTCCCA
1 AAATAACA-CATTTTCAAAATAATTACCA
46670 AAATAACAC
1 AAATAACAC
46679 CCATTTCGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 8 0.26
29 23 0.74
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (28 bp):
AAATAACACATTTTCAAAATAATTACCA
Found at i:46739 original size:29 final size:29
Alignment explanation
Indices: 46633--46739 Score: 135
Period size: 29 Copynumber: 3.7 Consensus size: 29
46623 TTTTTAAAAT
* * *
46633 AATTACCAAAATAGCACCC-TTTTCAAATT
1 AATTCCCAAAATAGCACCCGTTTT-GAATA
* * *
46662 AATTCCCAAAATAACACCCATTTCGAATA
1 AATTCCCAAAATAGCACCCGTTTTGAATA
*
46691 AATTCCCAAAAAAGCACCCGTTTTGAATA
1 AATTCCCAAAATAGCACCCGTTTTGAATA
46720 AATTCCCAAAATAGCACCCG
1 AATTCCCAAAATAGCACCCG
46740 GTCAACGGTC
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
29 64 0.96
30 3 0.04
ACGTcount: A:0.42, C:0.27, G:0.07, T:0.24
Consensus pattern (29 bp):
AATTCCCAAAATAGCACCCGTTTTGAATA
Found at i:46761 original size:17 final size:18
Alignment explanation
Indices: 46739--46779 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
46729 AATAGCACCC
46739 GGTCAAC-GGTCGAGTAG
1 GGTCAACAGGTCGAGTAG
*
46756 GGTCAACAGGTCGGGTAG
1 GGTCAACAGGTCGAGTAG
46774 GGTCAA
1 GGTCAA
46780 AATCGGTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.24, C:0.17, G:0.41, T:0.17
Consensus pattern (18 bp):
GGTCAACAGGTCGAGTAG
Found at i:47515 original size:2 final size:2
Alignment explanation
Indices: 47508--47587 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
47498 AATTACAATT
47508 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
47550 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
47588 AAATTTCTGG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47919 original size:12 final size:12
Alignment explanation
Indices: 47902--47927 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
47892 TTGCACTGAT
47902 ACGGATACGGGG
1 ACGGATACGGGG
47914 ACGGATACGGGG
1 ACGGATACGGGG
47926 AC
1 AC
47928 AGGAAAAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.19, G:0.46, T:0.08
Consensus pattern (12 bp):
ACGGATACGGGG
Found at i:57591 original size:14 final size:14
Alignment explanation
Indices: 57566--57594 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
57556 TATATATATA
57566 TATATATATATTGT
1 TATATATATATTGT
57580 TATATATATATTGT
1 TATATATATATTGT
57594 T
1 T
57595 GTACCCTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TATATATATATTGT
Found at i:60583 original size:23 final size:23
Alignment explanation
Indices: 60555--60617 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
60545 AAGAGAGAAG
60555 AAAGGAGCAAAGGAATTGTGGGA
1 AAAGGAGCAAAGGAATTGTGGGA
60578 AAAGGAGCAAAGGAATTGTGGGA
1 AAAGGAGCAAAGGAATTGTGGGA
*
60601 AAAGGACCAAAGAGAAT
1 AAAGGAGCAAAG-GAAT
60618 CACATACTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 34 0.89
24 4 0.11
ACGTcount: A:0.48, C:0.06, G:0.35, T:0.11
Consensus pattern (23 bp):
AAAGGAGCAAAGGAATTGTGGGA
Found at i:62741 original size:21 final size:21
Alignment explanation
Indices: 62699--62741 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
62689 TTTCTGGGCT
* * *
62699 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
62720 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
62741 A
1 A
62742 ACAAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:64362 original size:23 final size:23
Alignment explanation
Indices: 64329--64396 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
64319 ATTATTATAT
64329 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
64352 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
64375 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
64397 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:67665 original size:14 final size:14
Alignment explanation
Indices: 67631--67662 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
67621 GTTTTTTCGG
67631 TTCGGTTCGGGTTT
1 TTCGGTTCGGGTTT
67645 TTCGGTTC-GGTTT
1 TTCGGTTCGGGTTT
67658 TTCGG
1 TTCGG
67663 GTTTTCAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.00, C:0.16, G:0.34, T:0.50
Consensus pattern (14 bp):
TTCGGTTCGGGTTT
Found at i:71600 original size:2 final size:2
Alignment explanation
Indices: 71595--71624 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
71585 TGCACACACC
*
71595 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
71625 ATAAGCATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:71679 original size:2 final size:2
Alignment explanation
Indices: 71667--71701 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
71657 TTATTGAAAG
*
71667 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
71702 TAATATCACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:72307 original size:18 final size:18
Alignment explanation
Indices: 72273--72328 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
72263 AACCTAAAGA
*
72273 AAATGTTATTTTAATAAT
1 AAATATTATTTTAATAAT
72291 AAATATTATTCTT-ATAATT
1 AAATATTATT-TTAATAA-T
* * *
72310 AAACAATATTTTACTAAT
1 AAATATTATTTTAATAAT
72328 A
1 A
72329 CACGTATGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 17 0.55
19 14 0.45
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (18 bp):
AAATATTATTTTAATAAT
Found at i:81043 original size:18 final size:19
Alignment explanation
Indices: 81016--81051 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
81006 GCTATGTTAA
*
81016 AAATACTTTTAAAGTTATT
1 AAATACTTTTAAAATTATT
81035 AAATA-TTTTAAAATTAT
1 AAATACTTTTAAAATTAT
81052 AAAACTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
AAATACTTTTAAAATTATT
Found at i:85630 original size:6 final size:6
Alignment explanation
Indices: 85619--85673 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
85609 CTATTTTTTT
* * *
85619 CAAAAA CAAAAA AAAAAA AAAAAA AAAAAGA GCAAAAA C-AAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAA-A -CAAAAA CAAAAA CAAAAA
85668 CAAAAA
1 CAAAAA
85674 AGCCAAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
5 5 0.11
6 33 0.75
7 2 0.05
8 4 0.09
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:85665 original size:11 final size:11
Alignment explanation
Indices: 85619--85672 Score: 60
Period size: 11 Copynumber: 5.0 Consensus size: 11
85609 CTATTTTTTT
85619 CAAAAACAAAA
1 CAAAAACAAAA
85630 -AAAAA-AAAA
1 CAAAAACAAAA
*
85639 -AAAAAAAAAGA
1 CAAAAACAAA-A
85650 GCAAAAACAAAA
1 -CAAAAACAAAA
85662 CAAAAACAAAA
1 CAAAAACAAAA
85673 AAGCCAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
9 9 0.24
10 8 0.21
11 12 0.32
12 1 0.03
13 8 0.21
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (11 bp):
CAAAAACAAAA
Found at i:85680 original size:26 final size:26
Alignment explanation
Indices: 85625--85681 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
85615 TTTTCAAAAA
*
85625 CAAAAAAAAAAAAAAAAAAAAAAGAG
1 CAAAAAAAAAAAAAAAAAAAAAAGAC
* *
85651 CAAAAACAAAACAAAAACAAAAAAG-C
1 CAAAAA-AAAAAAAAAAAAAAAAAGAC
85677 CAAAA
1 CAAAA
85682 TTTCAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.82, C:0.12, G:0.05, T:0.00
Consensus pattern (26 bp):
CAAAAAAAAAAAAAAAAAAAAAAGAC
Found at i:85681 original size:25 final size:26
Alignment explanation
Indices: 85625--85675 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
85615 TTTTCAAAAA
85625 CAAAAAAAAAAAAAAAAAAAAAAGAG
1 CAAAAAAAAAAAAAAAAAAAAAAGAG
* *
85651 CAAAAACAAAACAAAAACAAAAAAG
1 CAAAAA-AAAAAAAAAAAAAAAAAG
85676 CCAAAATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (26 bp):
CAAAAAAAAAAAAAAAAAAAAAAGAG
Found at i:95764 original size:15 final size:15
Alignment explanation
Indices: 95744--95772 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
95734 ATAACATCTA
95744 AAAACTTTCATAACT
1 AAAACTTTCATAACT
95759 AAAACTTTCATAAC
1 AAAACTTTCATAAC
95773 CGGCTTGAAA
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:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAACTTTCATAACT
Done.