Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000400.1 Hibiscus syriacus cultivar Beakdansim tig00000736_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: 71705
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Found at i:628 original size:18 final size:21
Alignment explanation
Indices: 592--630 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
582 GTCGGAGAGA
592 TAAGGAATGATTTATAGATAT
1 TAAGGAATGATTTATAGATAT
613 TAAGGAA-G-TTTA-AGATAT
1 TAAGGAATGATTTATAGATAT
631 AATTGAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 1 0.06
21 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.36
Consensus pattern (21 bp):
TAAGGAATGATTTATAGATAT
Found at i:1067 original size:21 final size:21
Alignment explanation
Indices: 1034--1084 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
1024 CTAAAATGTA
1034 AATTTTG-AAACTTTTTGCTC
1 AATTTTGAAAACTTTTTGCTC
*
1054 AATTTTGAAAACTTTTTGCTT
1 AATTTTGAAAACTTTTTGCTC
*
1075 GATTTTGAAA
1 AATTTTGAAA
1085 TAAGTTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.49
Consensus pattern (21 bp):
AATTTTGAAAACTTTTTGCTC
Found at i:2405 original size:20 final size:20
Alignment explanation
Indices: 2374--2417 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2364 GGGTGTTAAT
2374 TTATGTTAATGATATATGGA
1 TTATGTTAATGATATATGGA
*
2394 GTTATG-TAATGATATCTGGA
1 -TTATGTTAATGATATATGGA
2414 TTAT
1 TTAT
2418 AAGCTATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.18
20 13 0.59
21 5 0.23
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.45
Consensus pattern (20 bp):
TTATGTTAATGATATATGGA
Found at i:5483 original size:226 final size:226
Alignment explanation
Indices: 4967--6054 Score: 1573
Period size: 223 Copynumber: 4.9 Consensus size: 226
4957 TGTGGATAAA
* * * * *
4967 GGTTGA-AACAAATCAAGTAATTAAGCTG-TTATGTTATCGTTGGATTTCTAGGGCTCCATCAAC
1 GGTTGATAACAAATCAAGTAATTAA-CCGATTATGTTATAGTCGGATTTCTAAGGCTCCATCAGC
* *
5030 TTAAAC-TTGGTAACA-TTTAGGTGTTACATAATA--TTGATAATACTGATAACAAATTAAGTAA
65 TTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAA
* *
5091 TTAACCTA-TTTGTTATCGTCTGCTTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTA
130 TTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTA
* * *
5155 CGTTACAT--GTGCTACCTAATATGTTGATAAA
195 CGTTACATAAGCGCTACCTAATATGTT-ATTAT
* *
5186 GGTTGATAACAAATCAAATAATTAACCGATTACGTTATCA-TCGGATTTCTAAGGCTCCATCAGC
1 GGTTGATAACAAATCAAGTAATTAACCGATTATGTTAT-AGTCGGATTTCTAAGGCTCCATCAGC
* * *
5250 TTAAACTTTGGTAACATTTTAGGTGTTACCTAATATGTTGATAACACTGATAACAAATTTAGTAA
65 TTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAA
* *
5315 TTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGACACTACCTATTA
130 TTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTA
5380 CGTTACATAAG-GACTACCTAATATGTTATTAT
195 CGTTACATAAGCG-CTACCTAATATGTTATTAT
*
5412 GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATAGTCGGATTTCTAAGGCTCCATCAGCA
1 GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATAGTCGGATTTCTAAGGCTCCATCAGCT
*
5477 TAAACTTTGGTAATATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
66 TAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* * * * **
5542 TAACCTATTTTGTTATTGTCGGATTTCTAAGACCCCATCAACTTT-AAAAGGCGTTATATATTAC
131 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTAC
* *
5606 GTTACATAAGCTCTACCTAATATGCTATTAT
196 GTTACATAAGCGCTACCTAATATGTTATTAT
* * * * *
5637 GGTTGATAACAAATCAAGTAATTAACTGATTATGTTATCGTCGAATTTCTATGGCTCCATCAGGT
1 GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATAGTCGGATTTCTAAGGCTCCATCAGCT
*
5702 TAAACTTTGGTATCA-TTTAGGCGTTACCTAATATGTTGATAATA-TGATAACAAATTAAGTAAT
66 TAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* ** * * *
5765 TAACCTATTTTGTTATCTTCAAATTTCTAAGGCCCCATCATCCTTAAAAAGACGCTACCTATTAC
131 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTAC
*
5830 GTTACATAAGCGTTACCTAATATGTTATTAT
196 GTTACATAAGCGCTACCTAATATGTTATTAT
* * * *
5861 GGTTGATAACAAATCAAGTAATTAA-CGGTTATGTTATAGTCAGATTTCTGAGGCTCCATCAACT
1 GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATAGTCGGATTTCTAAGGCTCCATCAGCT
* * *
5925 TAAACTTTGGTAACATTTTAGGCG-TACTTAATATGTTGATAAT-TTGGTAACAAATTAAGTAAT
66 TAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
5988 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTT-AAAAGGCGCTACCTATTAC
131 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTAC
6052 GTT
196 GTT
6055 CCCAGTTAAT
Statistics
Matches: 780, Mismatches: 73, Indels: 29
0.88 0.08 0.03
Matches are distributed among these distances:
219 8 0.01
220 52 0.07
221 9 0.01
222 38 0.05
223 177 0.23
224 139 0.18
225 175 0.22
226 167 0.21
227 15 0.02
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (226 bp):
GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATAGTCGGATTTCTAAGGCTCCATCAGCT
TAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTAC
GTTACATAAGCGCTACCTAATATGTTATTAT
Found at i:5833 original size:106 final size:105
Alignment explanation
Indices: 5639--6054 Score: 270
Period size: 106 Copynumber: 3.8 Consensus size: 105
5629 GCTATTATGG
* * * * **
5639 TTGATAACAAATCAAGTAATTAA-CTGATTATGTTATCGTC-GAATTTCTATGGCTCCATCAGGT
1 TTGATAACAAATTAAGTAATTAACCT-ATTTTGTTATCGTCAG-ATTTCTAAGGCCCCATCAACT
**** * *
5702 TAAACTTTGGTATC-ATTTAGGCGTTACCTAATATGTTGATAAT
64 TAAAAGACGCTACCTA-TTA-GCGTTACCTAATATGTTGATAAT
* * * *
5745 ATGATAACAAATTAAGTAATTAACCTATTTTGTTATCTTCAAATTTCTAAGGCCCCATCATCCTT
1 TTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCA-ACTT
*
5810 AAAAAGACGCTACCTATTACGTTACATAAGCGTTACCTAATATGTT-ATTAT
65 -AAAAGACGCTACC---TA---T---T-AGCGTTACCTAATATGTTGATAAT
* ** * * * *
5861 GGTTGATAACAAATCAAGTAATTAA-CGGTTATGTTATAGTCAGATTTCTGAGGCTCCATCAACT
1 --TTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCAACT
**** * * * *
5925 TAAACTTTGGTAACATTTTAGGCG-TACTTAATATGTTGATAAT
64 TAAAAGACGCT-ACCTATTA-GCGTTACCTAATATGTTGATAAT
* * *
5968 TTGGTAACAAATTAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTT
1 TTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCAAC-TT
*
6033 AAAAGGCGCTACCTATTA-CGTT
65 AAAAGACGCTACCTATTAGCGTT
6055 CCCAGTTAAT
Statistics
Matches: 235, Mismatches: 53, Indels: 45
0.71 0.16 0.14
Matches are distributed among these distances:
104 2 0.01
105 22 0.09
106 98 0.42
107 19 0.08
108 7 0.03
110 1 0.00
112 1 0.00
113 1 0.00
114 2 0.01
115 5 0.02
116 9 0.04
117 46 0.20
118 22 0.09
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (105 bp):
TTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAGATTTCTAAGGCCCCATCAACTTA
AAAGACGCTACCTATTAGCGTTACCTAATATGTTGATAAT
Found at i:5918 original size:223 final size:224
Alignment explanation
Indices: 4967--6054 Score: 1515
Period size: 225 Copynumber: 4.9 Consensus size: 224
4957 TGTGGATAAA
* * * *
4967 GGTTGA-AACAAATCAAGTAATTAAGCTG-TTATGTTATCGTTGGATTTCTAGGGCTCCATCAAC
1 GGTTGATAACAAATCAAGTAATTAA-CCGATTATGTTATAGTCGGATTTCTA-GGCTCCATCAGC
* *
5030 TTAAAC-TTGGTAACA-TTTAGGTGTTACATAATA--TTGATAATACTGATAACAAATTAAGTAA
64 TTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAA
* * *
5091 TTAACCTA-TTTGTTATCGTCTGCTTTCTAAGGCCCCATCAGCTTTAAAAAGGCGCTACCTATTA
129 TTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCA-CCTTAAAAAGGCGCTACCTATTA
* * *
5155 CGTTACAT--GTGCTACCTAATATGTTGATAAA
193 CGTTACATAAGCGCTACCTAATATGTT-ATTAT
* *
5186 GGTTGATAACAAATCAAATAATTAACCGATTACGTTATCA-TCGGATTTCTAAGGCTCCATCAGC
1 GGTTGATAACAAATCAAGTAATTAACCGATTATGTTAT-AGTCGGATTTCT-AGGCTCCATCAGC
* * *
5250 TTAAACTTTGGTAACATTTTAGGTGTTACCTAATATGTTGATAACACTGATAACAAATTTAGTAA
64 TTAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAA
* * *
5315 TTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAAGACACTACCTATTA
129 TTAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCA-CCTTAAAAAGGCGCTACCTATTA
5380 CGTTACATAAG-GACTACCTAATATGTTATTAT
193 CGTTACATAAGCG-CTACCTAATATGTTATTAT
*
5412 GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATAGTCGGATTTCTAAGGCTCCATCAGCA
1 GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATAGTCGGATTTCT-AGGCTCCATCAGCT
*
5477 TAAACTTTGGTAATATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
65 TAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* * * * * **
5542 TAACCTATTTTGTTATTGTCGGATTTCTAAGACCCCATCAACTTTAAAAGGCGTTATATATTACG
130 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCACCTTAAAAAGGCGCTACCTATTACG
* *
5607 TTACATAAGCTCTACCTAATATGCTATTAT
195 TTACATAAGCGCTACCTAATATGTTATTAT
* * * *
5637 GGTTGATAACAAATCAAGTAATTAACTGATTATGTTATCGTCGAATTTCTATGGCTCCATCAGGT
1 GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATAGTCGGATTTCTA-GGCTCCATCAGCT
*
5702 TAAACTTTGGTATCA-TTTAGGCGTTACCTAATATGTTGATAATA-TGATAACAAATTAAGTAAT
65 TAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* ** *
5765 TAACCTATTTTGTTATCTTCAAATTTCTAAGGCCCCATCATCCTTAAAAAGACGCTACCTATTAC
130 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCA-CCTTAAAAAGGCGCTACCTATTAC
*
5830 GTTACATAAGCGTTACCTAATATGTTATTAT
194 GTTACATAAGCGCTACCTAATATGTTATTAT
* * *
5861 GGTTGATAACAAATCAAGTAATTAA-CGGTTATGTTATAGTCAGATTTCTGAGGCTCCATCAACT
1 GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATAGTCGGATTTCT-AGGCTCCATCAGCT
* * *
5925 TAAACTTTGGTAACATTTTAGGCG-TACTTAATATGTTGATAAT-TTGGTAACAAATTAAGTAAT
65 TAAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAAT
* *
5988 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCAGCTTTAAAAGGCGCTACCTATTACG
130 TAACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCACCTTAAAAAGGCGCTACCTATTACG
6053 TT
195 TT
6055 CCCAGTTAAT
Statistics
Matches: 779, Mismatches: 71, Indels: 35
0.88 0.08 0.04
Matches are distributed among these distances:
219 8 0.01
220 51 0.07
221 10 0.01
222 41 0.05
223 171 0.22
224 144 0.18
225 176 0.23
226 163 0.21
227 15 0.02
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (224 bp):
GGTTGATAACAAATCAAGTAATTAACCGATTATGTTATAGTCGGATTTCTAGGCTCCATCAGCTT
AAACTTTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAGTAATT
AACCTATTTTGTTATCGTCGGATTTCTAAGGCCCCATCACCTTAAAAAGGCGCTACCTATTACGT
TACATAAGCGCTACCTAATATGTTATTAT
Found at i:7008 original size:54 final size:54
Alignment explanation
Indices: 6925--7116 Score: 176
Period size: 54 Copynumber: 3.5 Consensus size: 54
6915 CCACAGTCGC
* *
6925 CCATTACCATGATTTAGCACATGGATTTTTAACCCTATGAATATATGCTCGTAT
1 CCATTAGCATCATTTAGCACATGGATTTTTAACCCTATGAATATATGCTCGTAT
* * * * * * *
6979 CCATTAGCATCATTTAGCATATGGGTTTTTAACTCTGTTAACGATATGCTC-TCGT
1 CCATTAGCATCATTTAGCACATGGATTTTTAACCCTATGAA-TATATGCTCGT-AT
* * * * *
7034 CCATTA-CTGTCGTAT-GCACACGGATTTTTATTCCC-ATGAAATATATGCTCGTAT
1 CCATTAGC-ATCATTTAGCACATGGATTTTTA-ACCCTATG-AATATATGCTCGTAT
*
7088 CCATTAGCATCTTTTAGCACATGGATTTT
1 CCATTAGCATCATTTAGCACATGGATTTT
7117 AACTATAGCG
Statistics
Matches: 105, Mismatches: 25, Indels: 15
0.72 0.17 0.10
Matches are distributed among these distances:
54 68 0.65
55 37 0.35
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.39
Consensus pattern (54 bp):
CCATTAGCATCATTTAGCACATGGATTTTTAACCCTATGAATATATGCTCGTAT
Found at i:7196 original size:55 final size:55
Alignment explanation
Indices: 7076--7319 Score: 151
Period size: 55 Copynumber: 4.5 Consensus size: 55
7066 CCCATGAAAT
* * * * * *
7076 ATATGCTCGTATCCATTAGCATCTTTTAGCACATGGAT-TTTAA-CTATAG-CGGTG
1 ATATACTCGTGTCTATTAACATCATTTAGCACATGAATCTTTAATCT-T-GCCGGTG
*
7130 ATATACTCGTGT-TCATTCTAACATCATTT-TCACATGAAT-TTTAATCTTGCCGGTG
1 ATATACTCGTGTCT-A-T-TAACATCATTTAGCACATGAATCTTTAATCTTGCCGGTG
* * * * *
7185 ATATA-TACGTGTCTATTAATATCATTTAGCACATGAATCTTTAATCATACCAGCG
1 ATATACT-CGTGTCTATTAACATCATTTAGCACATGAATCTTTAATCTTGCCGGTG
* * * * * * * * * *
7240 ATATGCTCGTGTCCATTAATATCATCTAACACGTGAATTTTTAACCATGCCGGTA
1 ATATACTCGTGTCTATTAACATCATTTAGCACATGAATCTTTAATCTTGCCGGTG
* * * *
7295 ATATATTTGTATCTATTAATATCAT
1 ATATACTCGTGTCTATTAACATCAT
7320 ATGACACAAA
Statistics
Matches: 151, Mismatches: 29, Indels: 19
0.76 0.15 0.10
Matches are distributed among these distances:
53 10 0.07
54 23 0.15
55 105 0.70
56 13 0.09
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (55 bp):
ATATACTCGTGTCTATTAACATCATTTAGCACATGAATCTTTAATCTTGCCGGTG
Found at i:7393 original size:76 final size:78
Alignment explanation
Indices: 7262--7418 Score: 183
Period size: 76 Copynumber: 2.0 Consensus size: 78
7252 CCATTAATAT
* * * *** **
7262 CATCTAACACGTGAATTTTTAACCATGCCGGTAATATATTTGTATCTATTAATATCATAT-G-AC
1 CATCTAACACATGAATCTTTAACCATACCAAAAATATATTCATATCTATTAATATCATATGGTAC
7325 ACAAATTTTTAAC
66 ACAAATTTTTAAC
* * *
7338 CATCTAACACATGAATCTTTAACCATACCAAAAATATATTCATGTCTATTTATATCATCTGGTAC
1 CATCTAACACATGAATCTTTAACCATACCAAAAATATATTCATATCTATTAATATCATATGGTAC
**
7403 ATGAATTTTTAAC
66 ACAAATTTTTAAC
7416 CAT
1 CAT
7419 GCCGGGGCTA
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
76 49 0.74
77 1 0.02
78 16 0.24
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (78 bp):
CATCTAACACATGAATCTTTAACCATACCAAAAATATATTCATATCTATTAATATCATATGGTAC
ACAAATTTTTAAC
Found at i:8058 original size:25 final size:26
Alignment explanation
Indices: 8007--8062 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
7997 ATCAAATCAC
* * **
8007 AAGGGTATTCTGGTAATTTTCTCTAT
1 AAGGGTATTATAGTAATTTTCAATAT
8033 AAGGGTATTATAGTAA-TTTCAATAT
1 AAGGGTATTATAGTAATTTTCAATAT
8058 AAGGG
1 AAGGG
8063 CATTTTTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.39
Consensus pattern (26 bp):
AAGGGTATTATAGTAATTTTCAATAT
Found at i:12167 original size:31 final size:30
Alignment explanation
Indices: 12129--12293 Score: 170
Period size: 31 Copynumber: 5.3 Consensus size: 30
12119 AATGTGATTA
*
12129 TTGGGTAGGCTCTGTTGGCCC-GAGATCATTC
1 TTGGGTAGGC-CTG-TGGCCCTGAGATCTTTC
* * * *
12160 TTGGGTAGGCCCTGCGGCCTTGGGATTTTTC
1 TTGGGTAGG-CCTGTGGCCCTGAGATCTTTC
*
12191 TTGGGTAGGCCTCGTGGCCCTGAGATCATTC
1 TTGGGTAGGCCT-GTGGCCCTGAGATCTTTC
***
12222 TTGGGTAGGCCCTACAGCCCTGAGATCTTTC
1 TTGGGTAGG-CCTGTGGCCCTGAGATCTTTC
* *
12253 TTGGGTAAGCCTCGTGGCCCTGAGAACTTTC
1 TTGGGTAGGCCT-GTGGCCCTGAGATCTTTC
12284 TTGGGTAGGC
1 TTGGGTAGGC
12294 TCTCAGACCC
Statistics
Matches: 109, Mismatches: 20, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
30 10 0.09
31 95 0.87
32 4 0.04
ACGTcount: A:0.13, C:0.24, G:0.32, T:0.31
Consensus pattern (30 bp):
TTGGGTAGGCCTGTGGCCCTGAGATCTTTC
Found at i:12216 original size:62 final size:62
Alignment explanation
Indices: 12129--12293 Score: 226
Period size: 62 Copynumber: 2.7 Consensus size: 62
12119 AATGTGATTA
* * * * *
12129 TTGGGTAGG-CTCTGTTGGCCC-GAGATCATTCTTGGGTAGGCCCTGCGGCCTTGGGATTTTTC
1 TTGGGTAGGCCTC-G-TGGCCCTGAGATCATTCTTGGGTAGGCCCTACAGCCCTGAGATCTTTC
12191 TTGGGTAGGCCTCGTGGCCCTGAGATCATTCTTGGGTAGGCCCTACAGCCCTGAGATCTTTC
1 TTGGGTAGGCCTCGTGGCCCTGAGATCATTCTTGGGTAGGCCCTACAGCCCTGAGATCTTTC
* * *
12253 TTGGGTAAGCCTCGTGGCCCTGAGAACTTTCTTGGGTAGGC
1 TTGGGTAGGCCTCGTGGCCCTGAGATCATTCTTGGGTAGGC
12294 TCTCAGACCC
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
61 6 0.06
62 84 0.90
63 3 0.03
ACGTcount: A:0.13, C:0.24, G:0.32, T:0.31
Consensus pattern (62 bp):
TTGGGTAGGCCTCGTGGCCCTGAGATCATTCTTGGGTAGGCCCTACAGCCCTGAGATCTTTC
Found at i:15277 original size:48 final size:48
Alignment explanation
Indices: 15223--15318 Score: 122
Period size: 49 Copynumber: 2.0 Consensus size: 48
15213 TTCACACTCC
* *
15223 GATTTT-CCTTTTCATTACGATTAAGAGGGCTAGTTAGAGAAAATTATT
1 GATTTTCCCTTTTCATTACGACTAAGAGGGCTAGATA-AGAAAATTATT
* * * *
15271 GATTTTCCCTTTTCATTGCGACTAGGAGGGTTCGATAAGAAAATTATT
1 GATTTTCCCTTTTCATTACGACTAAGAGGGCTAGATAAGAAAATTATT
15319 CCATCTATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
48 17 0.41
49 24 0.59
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (48 bp):
GATTTTCCCTTTTCATTACGACTAAGAGGGCTAGATAAGAAAATTATT
Found at i:18294 original size:2 final size:2
Alignment explanation
Indices: 18287--18311 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18277 ATTATTCAAT
18287 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 T
18312 TAAACACGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19018 original size:55 final size:55
Alignment explanation
Indices: 18837--19471 Score: 773
Period size: 55 Copynumber: 11.6 Consensus size: 55
18827 GTACCCAAGA
* * * * * * * * *
18837 CCAATATGAAAATTCACAAACTCTTTTTGAAATCCTTGGGG-TGCAAATATAGTG
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTG
* * *
18891 CCAATAC-AGAAATTCATAAACTCATTATGAATTTCAT-AGGTTGCACACATACTG
1 CCAATACGA-AAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTG
* *
18945 CCAATAC-AGAAATTCATAAATTCATTATGAATTTCGTGGGGTTACACACATAGTG
1 CCAATACGA-AAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTG
* * *
19000 CCAATTCGAAAATTCATAAACTCATTATGAATTTGGTGGGGTTGCACCCATAGTG
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTG
* *
19055 CCAATAC-ATAAATTCATAAACTAATTATGAATTTCGTGGGGTTGCACAAATAGTG
1 CCAATACGA-AAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTG
** * *
19110 CCAATACGAAAATTCATAAACTCATTATGAATTTCGCAGGGTCGCACACATAGTT
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTG
* * ** *
19165 CCAATACGGAAATTCATAAACTTATTATGAATTTC-TTAGGTTGCACAGATAGTG
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTG
* * * *
19219 CCAATACAAAAATTCATAAACTCATTATGAATTTAGT-GGATTGCACACGTAGTG
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTG
*
19273 CCAATACGAAAATTCATAAACTCATTATGAATTTCATGGGGTTGCACACATAGTG
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTG
* * * *
19328 CCAATACGGAGATTCATAAACTCATTATGAATTTCATGGGGTTGCACATATAGTG
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTG
* * * * **
19383 GCAATACGGAAATTCTTAAACTCATTATCAATTTC-TTAGGTTGCACACATAGTG
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTG
* * *
19437 CCAATATGGAAATTCATGAACTCATTATGAATTTC
1 CCAATACGAAAATTCATAAACTCATTATGAATTTC
19472 TTATGAATTT
Statistics
Matches: 505, Mismatches: 68, Indels: 16
0.86 0.12 0.03
Matches are distributed among these distances:
53 3 0.01
54 211 0.42
55 289 0.57
56 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (55 bp):
CCAATACGAAAATTCATAAACTCATTATGAATTTCGTGGGGTTGCACACATAGTG
Found at i:19335 original size:218 final size:219
Alignment explanation
Indices: 18837--19470 Score: 841
Period size: 218 Copynumber: 2.9 Consensus size: 219
18827 GTACCCAAGA
* * * * * * *
18837 CCAATATGAAAATTCACAAACTCTTTTTGAAATCCTTGGGG-TGCA-AATATAGTGCCAATAC-A
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCATGGGGTTGCACAA-ATAGTGCCAATACGA
* *
18899 GAAATTCATAAACTCATTATGAATTTCATA-GGTTGCACACATACTGCCAATACAGAAATTCATA
65 -AAATTCATAAACTCATTATGAATTTCATAGGGTTGCACACATAGTGCCAATACGGAAATTCATA
** * *
18963 AA-TTCATTATGAATTTCGTGGGGTTACACACATAGTGCCAATTCGAAAATTCATAAACTCATTA
129 AACTT-ATTATGAATTTC-TTAGGTTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTA
* * *
19027 TGAATTTGGTGGGGTTGCACCCATAGTG
192 TGAATTTAGTGGGATTGCACACATAGTG
* *
19055 CCAATAC-ATAAATTCATAAACTAATTATGAATTTCGTGGGGTTGCACAAATAGTGCCAATACGA
1 CCAATACGA-AAATTCATAAACTCATTATGAATTTCATGGGGTTGCACAAATAGTGCCAATACGA
** * *
19119 AAATTCATAAACTCATTATGAATTTCGCAGGGTCGCACACATAGTTCCAATACGGAAATTCATAA
65 AAATTCATAAACTCATTATGAATTTCATAGGGTTGCACACATAGTGCCAATACGGAAATTCATAA
* *
19184 ACTTATTATGAATTTCTTAGGTTGCACAGATAGTGCCAATACAAAAATTCATAAACTCATTATGA
130 ACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGA
*
19249 ATTTAGT-GGATTGCACACGTAGTG
195 ATTTAGTGGGATTGCACACATAGTG
* *
19273 CCAATACGAAAATTCATAAACTCATTATGAATTTCATGGGGTTGCACACATAGTGCCAATACGGA
1 CCAATACGAAAATTCATAAACTCATTATGAATTTCATGGGGTTGCACAAATAGTGCCAATACGAA
* * * * *
19338 GATTCATAAACTCATTATGAATTTCATGGGGTTGCACATATAGTGGCAATACGGAAATTCTTAAA
66 AATTCATAAACTCATTATGAATTTCATAGGGTTGCACACATAGTGCCAATACGGAAATTCATAAA
* * * * *
19403 CTCATTATCAATTTCTTAGGTTGCACACATAGTGCCAATATGGAAATTCATGAACTCATTATGAA
131 CTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAA
19468 TTT
196 TTT
19471 CTTATGAATT
Statistics
Matches: 365, Mismatches: 44, Indels: 14
0.86 0.10 0.03
Matches are distributed among these distances:
217 1 0.00
218 221 0.61
219 94 0.26
220 47 0.13
221 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (219 bp):
CCAATACGAAAATTCATAAACTCATTATGAATTTCATGGGGTTGCACAAATAGTGCCAATACGAA
AATTCATAAACTCATTATGAATTTCATAGGGTTGCACACATAGTGCCAATACGGAAATTCATAAA
CTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAA
TTTAGTGGGATTGCACACATAGTG
Found at i:19846 original size:20 final size:20
Alignment explanation
Indices: 19821--19874 Score: 54
Period size: 22 Copynumber: 2.6 Consensus size: 20
19811 AAACTTAATA
*
19821 GTATCGATACCCCTCCTTTG
1 GTATCGATACCCCTCCTATG
* * *
19841 GTATCGGTACTTCTCTTCTATG
1 GTATCGATAC--CCCTCCTATG
19863 GTATCGATACCC
1 GTATCGATACCC
19875 ACTTCAATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
20 10 0.38
22 16 0.62
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.37
Consensus pattern (20 bp):
GTATCGATACCCCTCCTATG
Found at i:19975 original size:21 final size:21
Alignment explanation
Indices: 19946--19999 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
19936 CTTCTTCCTG
* *
19946 ATATCGATACTACTTGCATCA
1 ATATTGATACTACATGCATCA
19967 ATATTGATACTACATGCATCA
1 ATATTGATACTACATGCATCA
*
19988 GTATTGATACTA
1 ATATTGATACTA
20000 TTATTCATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (21 bp):
ATATTGATACTACATGCATCA
Found at i:24979 original size:54 final size:54
Alignment explanation
Indices: 24858--25190 Score: 407
Period size: 54 Copynumber: 6.1 Consensus size: 54
24848 CGCCCAAGTA
* * * * * * *
24858 CCAATATGGAAATTCACAAACTCATTTTGAAATCCTT-GGGTGCACATATAGTG
1 CCAATACGGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTG
* * * *
24911 CTAATACAGAAATTCATAAACTCATAATGAATTTCTTAGGTTTCACACATAGTG
1 CCAATACGGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTG
* * *
24965 CCAATATGGAAATTCATAAACTTATTATGAATTTATTAGGTTGCACACATAGTG
1 CCAATACGGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTG
* * ** *
25019 CCAATACGGAAATTAATAAACTCAATATGAATTTCGTGGGGTTGCACGCATAGTG
1 CCAATACGGAAATTCATAAACTCATTATGAATTTC-TTAGGTTGCACACATAGTG
* *
25074 CCAATACAGAAATTCATAAACTCATTAGGAATTTCTTAGGTTGCACACATAGTG
1 CCAATACGGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTG
* ** *
25128 CTAATACGGAAATTCATAAACTCATTATGAATTTCATGGGGTTGCACATATAGTG
1 CCAATACGGAAATTCATAAACTCATTATGAATTTC-TTAGGTTGCACACATAGTG
*
25183 TCAATACG
1 CCAATACG
25191 ATAAATGAAA
Statistics
Matches: 236, Mismatches: 41, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
53 29 0.12
54 138 0.58
55 69 0.29
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (54 bp):
CCAATACGGAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTG
Found at i:25117 original size:109 final size:108
Alignment explanation
Indices: 24866--25189 Score: 418
Period size: 109 Copynumber: 3.0 Consensus size: 108
24856 TACCAATATG
* * * * * * *
24866 GAAATTCACAAACTCATTTTGAAATCCTT-GGGTGCACATATAGTGCTAATACAGAAATTCATAA
1 GAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCTAATACGGAAATTCATAA
** * **
24930 ACTC-ATAATGAATTTCTTAGGTTTCACACATAGTGCCAATATG
66 ACTCAAT-ATGAATTTCTGGGGTTGCACACATAGTGCCAATACA
* * * *
24973 GAAATTCATAAACTTATTATGAATTTATTAGGTTGCACACATAGTGCCAATACGGAAATTAATAA
1 GAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCTAATACGGAAATTCATAA
*
25038 ACTCAATATGAATTTCGTGGGGTTGCACGCATAGTGCCAATACA
66 ACTCAATATGAATTTC-TGGGGTTGCACACATAGTGCCAATACA
*
25082 GAAATTCATAAACTCATTAGGAATTTCTTAGGTTGCACACATAGTGCTAATACGGAAATTCATAA
1 GAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCTAATACGGAAATTCATAA
* * *
25147 ACTCATTATGAATTTCATGGGGTTGCACATATAGTGTCAATAC
66 ACTCAATATGAATTTC-TGGGGTTGCACACATAGTGCCAATAC
25190 GATAAATGAA
Statistics
Matches: 187, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
107 23 0.12
108 43 0.23
109 121 0.65
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (108 bp):
GAAATTCATAAACTCATTATGAATTTCTTAGGTTGCACACATAGTGCTAATACGGAAATTCATAA
ACTCAATATGAATTTCTGGGGTTGCACACATAGTGCCAATACA
Found at i:39042 original size:60 final size:59
Alignment explanation
Indices: 38942--39071 Score: 170
Period size: 60 Copynumber: 2.2 Consensus size: 59
38932 CAGCAGGTTG
** * ** *
38942 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCAGGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGAAACGACCTTATGTGT
** *
39001 CATATTCGGGAACTGTACTTAAGGATACCTAGTACAGATGGTGGAAACGACCTTATGTGT
1 CATATTCGGGAA-TACACTAAAGGATACCTAGTACAGATGGTGGAAACGACCTTATGTGT
39061 CATATTCGGGA
1 CATATTCGGGA
39072 TTGCACTACG
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
59 12 0.20
60 49 0.80
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGAAACGACCTTATGTGT
Found at i:39170 original size:20 final size:20
Alignment explanation
Indices: 39147--39215 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
39137 GTTTATTGTT
39147 TATGGTTATTATCTATGGTA
1 TATGGTTATTATCTATGGTA
* *
39167 TATGGTTATGGAAT-AATGGTA
1 TATGGTTAT--TATCTATGGTA
*
39188 -ATGGTTATTGTCTATGGTA
1 TATGGTTATTATCTATGGTA
39207 TATGGTTAT
1 TATGGTTAT
39216 GGAATAATGG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
18 1 0.03
19 6 0.15
20 25 0.62
21 6 0.15
22 2 0.05
ACGTcount: A:0.26, C:0.03, G:0.25, T:0.46
Consensus pattern (20 bp):
TATGGTTATTATCTATGGTA
Found at i:39176 original size:13 final size:13
Alignment explanation
Indices: 39160--39217 Score: 64
Period size: 13 Copynumber: 4.4 Consensus size: 13
39150 GGTTATTATC
39160 TATGGTATATGGT
1 TATGGTATATGGT
*
39173 TATGGAATAATGGT
1 TATGGTAT-ATGGT
* *
39187 AATGGT-TATTGT
1 TATGGTATATGGT
39199 CTATGGTATATGGT
1 -TATGGTATATGGT
39213 TATGG
1 TATGG
39218 AATAATGGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
12 4 0.11
13 18 0.50
14 14 0.39
ACGTcount: A:0.26, C:0.02, G:0.29, T:0.43
Consensus pattern (13 bp):
TATGGTATATGGT
Found at i:39193 original size:40 final size:40
Alignment explanation
Indices: 39148--39228 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
39138 TTTATTGTTT
39148 ATGGTTATTATCTATGGTATATGGTTATGGAATAATGGTA
1 ATGGTTATTATCTATGGTATATGGTTATGGAATAATGGTA
*
39188 ATGGTTATTGTCTATGGTATATGGTTATGGAATAATGGTA
1 ATGGTTATTATCTATGGTATATGGTTATGGAATAATGGTA
39228 A
1 A
39229 GTGTATTGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (40 bp):
ATGGTTATTATCTATGGTATATGGTTATGGAATAATGGTA
Found at i:39275 original size:44 final size:44
Alignment explanation
Indices: 39212--39405 Score: 302
Period size: 44 Copynumber: 4.4 Consensus size: 44
39202 TGGTATATGG
* *
39212 TTATGGA-ATAATGGTAAGTGTATTGGTAAAATAAGCTTGCGAGC
1 TTATGGATA-AATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* *
39256 TTATGGATAAATGGCAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
39300 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACCAGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
39344 TTATGGATAAATGGTAAG-ATATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
39387 TTATGGTATTAAATGGTAA
1 TTATGG-A-TAAATGGTAA
39406 AATATTGCAC
Statistics
Matches: 141, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
43 30 0.21
44 100 0.71
45 11 0.08
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (44 bp):
TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:39756 original size:12 final size:12
Alignment explanation
Indices: 39737--39771 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
39727 ATAATGCTTA
39737 AATTACTGTAGC
1 AATTACTGTAGC
*
39749 AGTTACTGTAGC
1 AATTACTGTAGC
39761 AATTACTGTAG
1 AATTACTGTAG
39772 TGTATCGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (12 bp):
AATTACTGTAGC
Found at i:42939 original size:17 final size:17
Alignment explanation
Indices: 42917--42952 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
42907 TTTAAGTAAG
42917 GATTAAAATTGGCATTT
1 GATTAAAATTGGCATTT
42934 GATTAAAATTGGCATTT
1 GATTAAAATTGGCATTT
42951 GA
1 GA
42953 AAACTTGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (17 bp):
GATTAAAATTGGCATTT
Found at i:43457 original size:23 final size:24
Alignment explanation
Indices: 43431--43480 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
43421 CAAACCATTC
*
43431 AAACAAACATATCCAAAA-ATCCA
1 AAACAAACAAATCCAAAACATCCA
* *
43454 AAACATACAAATCCAAAACATTCA
1 AAACAAACAAATCCAAAACATCCA
43478 AAA
1 AAA
43481 TGTTTTAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.14
Consensus pattern (24 bp):
AAACAAACAAATCCAAAACATCCA
Found at i:43467 original size:15 final size:15
Alignment explanation
Indices: 43447--43479 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
43437 ACATATCCAA
43447 AAATCCAAAACATAC
1 AAATCCAAAACATAC
*
43462 AAATCCAAAACATTC
1 AAATCCAAAACATAC
43477 AAA
1 AAA
43480 ATGTTTTAAC
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:0.61, C:0.24, G:0.00, T:0.15
Consensus pattern (15 bp):
AAATCCAAAACATAC
Found at i:52168 original size:10 final size:10
Alignment explanation
Indices: 52153--52191 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
52143 ACAAATAAAG
52153 TTTGTTAATA
1 TTTGTTAATA
52163 TTTGTT-ATAA
1 TTTGTTAAT-A
*
52173 ATTGTTAATA
1 TTTGTTAATA
52183 TTTGTTAAT
1 TTTGTTAAT
52192 TTTATACCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (10 bp):
TTTGTTAATA
Found at i:52325 original size:32 final size:33
Alignment explanation
Indices: 52237--52325 Score: 83
Period size: 32 Copynumber: 2.7 Consensus size: 33
52227 TTGTCCTCCA
* * * *
52237 ATAATTTTTTATATTGAGAAATTAATATTTGTT
1 ATAAATTTTTATTTTGAGAAAATAATATTTGTC
* * **
52270 ATAAATTGTTATTATGACTAAATAA-ATTTGTC
1 ATAAATTTTTATTTTGAGAAAATAATATTTGTC
52302 A-AAAGTTTTTATTTTGAGAAAATA
1 ATAAA-TTTTTATTTTGAGAAAATA
52326 TTGTGACAAA
Statistics
Matches: 43, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
31 3 0.07
32 22 0.51
33 18 0.42
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.47
Consensus pattern (33 bp):
ATAAATTTTTATTTTGAGAAAATAATATTTGTC
Found at i:52592 original size:195 final size:195
Alignment explanation
Indices: 52243--52621 Score: 573
Period size: 195 Copynumber: 1.9 Consensus size: 195
52233 TCCAATAATT
* **
52243 TTTTATATTGAGAAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGT
1 TTTTATATTGAGAAATTAATATTTATTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAAA
* *
52308 TTTTATTTTGAGAAAATATTGTGACAAAATAATTGTAACATAATTTTTTATTTTGACTAATGTTA
66 ATTTATTTTGAGAAAATATTGTGACAAAATAATTGTAACATAATTTTTTATTTTCACTAATGTTA
* * * *
52373 ATATGTTAGTGTGGCTAAATAAATTTGTTACAATTTGTTAATGTGAAAGAATATATGTCCTGATA
131 ATATGGTAGTGTGACTAAATAAATTTGTTACAATTTATTAATGTGAAAAAATATATGTCCTGATA
*
52438 TTTTATATTGAGAAATTATTATTTATTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAAA
1 TTTTATATTGAGAAATTAATATTTATTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAAA
* *
52503 ATTTATTTTGAGAAAATATTGTGACAAAATAAATT-TGATATAATTTTTTATTTTCACTAAAT-T
66 ATTTATTTTGAGAAAATATTGTGACAAAAT-AATTGTAACATAATTTTTTATTTTCACT-AATGT
* * * * *
52566 TACTATGGTATTGTGATTAGATAAATTTGTTACAATTTATTATTGTGAAAAAATAT
129 TAATATGGTAGTGTGACTAAATAAATTTGTTACAATTTATTAATGTGAAAAAATAT
52622 TTTTCATGAA
Statistics
Matches: 165, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
195 158 0.96
196 7 0.04
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (195 bp):
TTTTATATTGAGAAATTAATATTTATTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAAA
ATTTATTTTGAGAAAATATTGTGACAAAATAATTGTAACATAATTTTTTATTTTCACTAATGTTA
ATATGGTAGTGTGACTAAATAAATTTGTTACAATTTATTAATGTGAAAAAATATATGTCCTGATA
Found at i:52958 original size:145 final size:144
Alignment explanation
Indices: 52676--52958 Score: 298
Period size: 145 Copynumber: 2.0 Consensus size: 144
52666 ATTTTGAGAT
* *
52676 AATATTGTGAATAAATAAATTTGACACAATTTTTTATTTTAATTAAATTTAACATAATAGTATTA
1 AATATTGTGAATAAATAAATTTGACACAATTTCTTATTTTAATTAAATTTAACATAATAGTATGA
* * **** * * *
52741 TTAAATAAATTTTTTACAATTAGTTATAAATAATTGCTATTATAATTATATAAATTTGTCATAAT
66 CTAAATAAATTTGTTACAATTAGTTATAAATAAAAAATATTAT-ATTATATAAATTTATAATAAC
* *
52806 TAGTTATTTAAAGAA
130 AAATTATTTAAAGAA
* * * * ** **
52821 AATATTGTGACTAAATAAATTTGACATAATTTCTTATTTTGATTAAATTTAATATGTTTTTATGA
1 AATATTGTGAATAAATAAATTTGACACAATTTCTTATTTTAATTAAATTTAACATAATAGTATGA
* * * * *
52886 CTAAATAAATTTGTTACAATTTGTTATTATTAAAAAAATATTAT-TTTTATAATTTTTATAATAA
66 CTAAATAAATTTGTTACAATTAGTTATAAAT-AAAAAATATTATATTATATAA-ATTTATAATAA
52950 CAAATTATT
129 CAAATTATT
52959 ATTTTCTATA
Statistics
Matches: 110, Mismatches: 26, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
144 7 0.06
145 95 0.86
146 8 0.07
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.47
Consensus pattern (144 bp):
AATATTGTGAATAAATAAATTTGACACAATTTCTTATTTTAATTAAATTTAACATAATAGTATGA
CTAAATAAATTTGTTACAATTAGTTATAAATAAAAAATATTATATTATATAAATTTATAATAACA
AATTATTTAAAGAA
Found at i:58240 original size:3 final size:3
Alignment explanation
Indices: 58234--58284 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
58224 AAATTATTAG
*
58234 TAA TAA TAA TAA TAA T-A TAT TAA T-A TAA TAA TAA TAA TAA TCAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
58278 T-A TAA TA
1 TAA TAA TA
58285 TATATTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 6 0.14
3 33 0.79
4 3 0.07
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:58816 original size:55 final size:55
Alignment explanation
Indices: 58556--59312 Score: 1071
Period size: 55 Copynumber: 13.8 Consensus size: 55
58546 ATAGAACTAG
* ** *
58556 ATCTTCAACAAACGTGTAC-GCTCCCTATTCCTTCAGAGAGTATTGGACTTGAACAA
1 ATCTTCAACAATCGTGT-CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAC-A
* ** *
58612 ATCTTCAACAAACGTGTCCCCTCCCTATTCCTTCAGAGAGTATAGGACTCG----
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* *
58663 ATCTTCAACAAACGTGT-TCGCTCCCTATTCCTTCAAAGAGTATAAGACTCGAACA
1 ATCTTCAACAATCGTGTCT-GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* * *
58718 ATCTTCAACAAATCGTGTCTACTCCCTATTCCTCCAGAGAGTATAAGACTCGAATA
1 ATCTTCAAC-AATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* * * *
58774 ATCTTCAACAAAT-GTGTCTACTCCATATTTCTTCAGAGAGTATAAGACTTGAACA
1 ATCTTCAAC-AATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* *
58829 ATCTTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCAAAC-
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
** *
58883 ATCTTCTTCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAATA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* *
58938 ATCTTCAACAATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACTCGAATA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* * *
58993 ATCTTCAACAAACGTGTCTACTCCCTATTTCTTCAGAGAGTATAAGACTCGAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
** *
59048 ATCTTCAACAATCGTGTCTGCTCCCTATTGTTTCAGAGAGTATAAGACTCGAGCA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
59103 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* *
59158 ATATTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* *
59213 ATCTTCAACAATCGTGTCTGCTCTCTATTCCTTCAGAGAGTATAAGACTCAAACA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
* * * *
59268 ATTTTCAACAATCGTATTTGCTCTCTATTCCTTCAGAGAGTATAA
1 ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAA
59313 TAAATCCTAC
Statistics
Matches: 640, Mismatches: 51, Indels: 21
0.90 0.07 0.03
Matches are distributed among these distances:
51 46 0.07
54 52 0.08
55 443 0.69
56 98 0.15
57 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (55 bp):
ATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
Found at i:59389 original size:89 final size:89
Alignment explanation
Indices: 59238--59401 Score: 283
Period size: 89 Copynumber: 1.8 Consensus size: 89
59228 GTCTGCTCTC
* *
59238 TATTCCTTCAGAGAGTATAAGACTCAAACAATTTTCAACAATCGTATTTGCTCTCTATTCCTTCA
1 TATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCAACAATCGTATCTGCTCTCTATTCCTTCA
59303 GAGAGTATAATAAATCCTACTCCA
66 GAGAGTATAATAAATCCTACTCCA
* * *
59327 TATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGTTCTCTATTCCTTCA
1 TATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCAACAATCGTATCTGCTCTCTATTCCTTCA
59392 GAGAGTATAA
66 GAGAGTATAA
59402 GACTCGAACA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 70 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (89 bp):
TATTCCTTCAGAGAGTATAAGACTCAAACAATCTTCAACAATCGTATCTGCTCTCTATTCCTTCA
GAGAGTATAATAAATCCTACTCCA
Found at i:59463 original size:54 final size:53
Alignment explanation
Indices: 59394--59526 Score: 162
Period size: 54 Copynumber: 2.5 Consensus size: 53
59384 TTCCTTCAGA
* *
59394 GAGTATA-AGACTCGAACATCTTCTTCATACGGGTTTGCTCCCTCTTTCTTTAGG
1 GAGTATAGA-ACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTT-TTTAGG
* * * *
59448 GAGTATAGAATTCGAATAATCTT-TCGCAAATGGGTTCGCTCCCTCTTTTTTAGG
1 GAGTATAGAACTCGAA-CATCTTCT-TCAAACGGGTTCGCTCCCTCTTTTTTAGG
59502 GAGTATAGAACTCGAACATCTTCTT
1 GAGTATAGAACTCGAACATCTTCTT
59527 TTTCTTCACT
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
53 5 0.08
54 36 0.55
55 25 0.38
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (53 bp):
GAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTTTTAGG
Found at i:68150 original size:17 final size:17
Alignment explanation
Indices: 68128--68160 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
68118 CAAAATCGTT
68128 TTCATTTTAAATAAAAA
1 TTCATTTTAAATAAAAA
*
68145 TTCATTTTAATTAAAA
1 TTCATTTTAAATAAAA
68161 CAACAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TTCATTTTAAATAAAAA
Found at i:69159 original size:18 final size:18
Alignment explanation
Indices: 69100--69167 Score: 70
Period size: 18 Copynumber: 3.7 Consensus size: 18
69090 AAACCGAAAC
69100 CGGTTTTATCGGTTCGGTT
1 CGGTTTT-TCGGTTCGGTT
*
69119 CAGTTTTT---TTAACGGTT
1 CGGTTTTTCGGTT--CGGTT
69136 CGGGTTTTTCGGTTCGGTT
1 C-GGTTTTTCGGTTCGGTT
69155 CGGTTTTTCGGTT
1 CGGTTTTTCGGTT
69168 TTTCAATGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
15 2 0.05
17 6 0.15
18 19 0.46
19 12 0.29
21 2 0.05
ACGTcount: A:0.06, C:0.15, G:0.29, T:0.50
Consensus pattern (18 bp):
CGGTTTTTCGGTTCGGTT
Found at i:70825 original size:13 final size:13
Alignment explanation
Indices: 70791--70836 Score: 65
Period size: 13 Copynumber: 3.4 Consensus size: 13
70781 ATTAAACAAC
70791 ACTTATTACTTTAT
1 ACTTA-TACTTTAT
*
70805 ATTATATACTTTAT
1 ACT-TATACTTTAT
70819 ACTTATACTTTAT
1 ACTTATACTTTAT
70832 ACTTA
1 ACTTA
70837 GATGACACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 15 0.52
14 12 0.41
15 2 0.07
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (13 bp):
ACTTATACTTTAT
Found at i:70826 original size:6 final size:7
Alignment explanation
Indices: 70797--70835 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
70787 CAACACTTAT
70797 TACTTTA
1 TACTTTA
70804 TA-TTATA
1 TACTT-TA
70811 TACTTTA
1 TACTTTA
70818 TAC-TTA
1 TACTTTA
70824 TACTTTA
1 TACTTTA
70831 TACTT
1 TACTT
70836 AGATGACACC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 8 0.28
7 19 0.66
8 2 0.07
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (7 bp):
TACTTTA
Found at i:70913 original size:16 final size:17
Alignment explanation
Indices: 70874--70919 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
70864 ATACATACAT
70874 TAATCACACATTATGCATA
1 TAAT-ACACA-TATGCATA
70893 T-ATACACATATG-ATA
1 TAATACACATATGCATA
*
70908 TAATACATATAT
1 TAATACACATAT
70920 TAGGGTTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 4 0.16
16 13 0.52
17 5 0.20
18 2 0.08
19 1 0.04
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (17 bp):
TAATACACATATGCATA
Found at i:70931 original size:7 final size:7
Alignment explanation
Indices: 70919--70996 Score: 70
Period size: 7 Copynumber: 11.4 Consensus size: 7
70909 AATACATATA
70919 TTAGGGT
1 TTAGGGT
70926 TTAGGGT
1 TTAGGGT
*
70933 TTATGG-
1 TTAGGGT
* *
70939 TTATGGC
1 TTAGGGT
**
70946 TTAAAGT
1 TTAGGGT
70953 TTAGGGT
1 TTAGGGT
*
70960 TTA-TGT
1 TTAGGGT
70966 TTAGGGT
1 TTAGGGT
**
70973 TTAAAGT
1 TTAGGGT
70980 TTAGGGT
1 TTAGGGT
70987 TTAGGGT
1 TTAGGGT
70994 TTA
1 TTA
70997 TATAAACTAT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
6 11 0.19
7 46 0.81
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.46
Consensus pattern (7 bp):
TTAGGGT
Found at i:70962 original size:27 final size:27
Alignment explanation
Indices: 70924--70994 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
70914 ATATATTAGG
*
70924 GTTTAGGGTTTATGGTTATGGCTTAAA
1 GTTTAGGGTTTATGGTTAGGGCTTAAA
* *
70951 GTTTAGGGTTTATGTTTAGGGTTTAAA
1 GTTTAGGGTTTATGGTTAGGGCTTAAA
*
70978 GTTTAGGGTTTAGGGTT
1 GTTTAGGGTTTATGGTT
70995 TATATAAACT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.20, C:0.01, G:0.32, T:0.46
Consensus pattern (27 bp):
GTTTAGGGTTTATGGTTAGGGCTTAAA
Found at i:71097 original size:19 final size:18
Alignment explanation
Indices: 71073--71109 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
71063 TATTATAGTT
71073 TATATATAGGTTATATATA
1 TATATATAGGTTAT-TATA
*
71092 TATATATAGTTTATTATA
1 TATATATAGGTTATTATA
71110 CATGGTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (18 bp):
TATATATAGGTTATTATA
Found at i:71271 original size:16 final size:18
Alignment explanation
Indices: 71250--71292 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
71240 TAGTACATGT
71250 CATATTA-ATTTTA-TTG
1 CATATTAGATTTTATTTG
71266 CATATTAGTATTTTATTTG
1 CATATTAG-ATTTTATTTG
*
71285 CATGTTAG
1 CATATTAG
71293 GTTAATTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
18 6 0.26
19 10 0.43
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.53
Consensus pattern (18 bp):
CATATTAGATTTTATTTG
Found at i:71280 original size:18 final size:19
Alignment explanation
Indices: 71257--71292 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
71247 TGTCATATTA
71257 ATTTTA-TTGCATATTAGT
1 ATTTTATTTGCATATTAGT
*
71275 ATTTTATTTGCATGTTAG
1 ATTTTATTTGCATATTAG
71293 GTTAATTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.25, C:0.06, G:0.14, T:0.56
Consensus pattern (19 bp):
ATTTTATTTGCATATTAGT
Found at i:71490 original size:21 final size:21
Alignment explanation
Indices: 71461--71512 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
71451 GTCCATTATA
*
71461 TTAGGGTTTGTGGTTTAAAGT
1 TTAGGGTTTATGGTTTAAAGT
*
71482 TTAGTGTTTATGGTTTAAAGT
1 TTAGGGTTTATGGTTTAAAGT
*
71503 TTAGGATTTA
1 TTAGGGTTTA
71513 GGAGTTATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (21 bp):
TTAGGGTTTATGGTTTAAAGT
Done.