Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005013.1 Hibiscus syriacus cultivar Beakdansim tig00011254_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: 73194
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:4658 original size:2 final size:2
Alignment explanation
Indices: 4651--4684 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4641 TCAAATTCGA
4651 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4685 GGACTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5680 original size:11 final size:11
Alignment explanation
Indices: 5664--5697 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
5654 AAAAAGGAAT
*
5664 TAAATAAATAA
1 TAAATAAAAAA
5675 TAAATAAAAAA
1 TAAATAAAAAA
5686 TAAATATAAAAA
1 TAAATA-AAAAA
5698 ATTTGAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAATAAAAAA
Found at i:6377 original size:14 final size:13
Alignment explanation
Indices: 6334--6380 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
6324 GTTTTGATCC
6334 ATCTACTGTACTTA
1 ATCTA-TGTACTTA
*
6348 AT-TTTGGTACTTA
1 ATCTAT-GTACTTA
6361 ATCTATGTACTTTA
1 ATCTATGTAC-TTA
6375 ATCTAT
1 ATCTAT
6381 CATAAGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 1 0.04
13 14 0.50
14 13 0.46
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.49
Consensus pattern (13 bp):
ATCTATGTACTTA
Found at i:6473 original size:26 final size:26
Alignment explanation
Indices: 6430--6496 Score: 116
Period size: 26 Copynumber: 2.5 Consensus size: 26
6420 GGGAATGAAC
6430 TTATAAAATTTTTAGAGGAGAGCAAAA
1 TTATAAAA-TTTTAGAGGAGAGCAAAA
*
6457 TTATAAAAATTTAGAGGAGAGCAAAA
1 TTATAAAATTTTAGAGGAGAGCAAAA
6483 TTATAAAATTTTAG
1 TTATAAAATTTTAG
6497 GTGACAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 30 0.79
27 8 0.21
ACGTcount: A:0.49, C:0.03, G:0.16, T:0.31
Consensus pattern (26 bp):
TTATAAAATTTTAGAGGAGAGCAAAA
Found at i:8844 original size:20 final size:20
Alignment explanation
Indices: 8819--8856 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
8809 TTTTTTCCAA
8819 TGATGATATGGTATTATCTT
1 TGATGATATGGTATTATCTT
8839 TGATGATATGGTATTATC
1 TGATGATATGGTATTATC
8857 ACTATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.47
Consensus pattern (20 bp):
TGATGATATGGTATTATCTT
Found at i:13329 original size:59 final size:57
Alignment explanation
Indices: 12973--13403 Score: 284
Period size: 59 Copynumber: 7.4 Consensus size: 57
12963 TCTGAAAGAT
* * *
12973 CATACACTTAGTATGATTTCTCTT-TCATTTTAGTACATGAAGTGCCCTATTC-GAAAATC
1 CATACACTCAGTATGATTTCT-TTACCATTTTAGCACAT-AAGTGCCCTA-TCAG-AAATC
* * * * **
13032 CATAC-CATTAGTATGAATTCATTACCATTTTAGCACACGAAGTGCCCTATGTGAAAATC
1 CATACAC-TCAGTATGATTTCTTTACCATTTTAGCACA-TAAGTGCCCTATCAG-AAATC
* * * * * * ** *
13091 CATACCCTTAGTATGATTTCCTTATCC-TTGTAGCACCCTTAGTGCTTTATCTGGAAATC
1 CATACACTCAGTATGATTTCTTTA-CCATTTTAGCA-CATAAGTGCCCTATC-AGAAATC
* * * **
13150 CATACACTCAGTTTGATTCCTTTACCATTTTAGCACATAAAATGCCCTATGTGAAAATC
1 CATACACTCAGTATGATTTCTTTACCATTTTAGCACAT-AAGTGCCCTATCAG-AAATC
* * * * * **
13209 CATACCCTTAGTATGATTTC-TTATCC-TTGTAGCACCCTTAGTGCTTTATCTAGAAATC
1 CATACACTCAGTATGATTTCTTTA-CCATTTTAGCA-CATAAGTGCCCTATC-AGAAATC
13267 CATACACTCAGTATGATTTCTTTACCATTTTAGCACATAAAGTGCCCTATCCAGAAATC
1 CATACACTCAGTATGATTTCTTTACCATTTTAGCACAT-AAGTGCCCTAT-CAGAAATC
* * * * * * * *
13326 CATATATTCATTATGATCTCCTTATCA-TTTAGCACACTCAGTGCTCCATAT-GGAAATC
1 CATACACTCAGTATGATTTCTTTACCATTTTAGCACA-TAAGTGC-CC-TATCAGAAATC
13384 CATACACTCAGTATGATTTC
1 CATACACTCAGTATGATTTC
13404 CTGATCCTTT
Statistics
Matches: 291, Mismatches: 60, Indels: 43
0.74 0.15 0.11
Matches are distributed among these distances:
58 89 0.31
59 193 0.66
60 9 0.03
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (57 bp):
CATACACTCAGTATGATTTCTTTACCATTTTAGCACATAAGTGCCCTATCAGAAATC
Found at i:13402 original size:117 final size:117
Alignment explanation
Indices: 13027--13403 Score: 492
Period size: 117 Copynumber: 3.2 Consensus size: 117
13017 CCCTATTCGA
* * * **
13027 AAATCCATAC-CATTAGTATGAATTCATTACCATTTTAGCACACGAAGTGCCCTATGTGAAAATC
1 AAATCCATACAC-TCAGTATGATTTCTTTACCATTTTAGCACATAAAGTGCCCTATGTGAAAATC
13091 CATACCCTTAGTATGATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTATCTGG
65 CATACCCTTAGTATGA-TTCCTTATCCTTGTAGCACCCTTAGTGCTTTATCTGG
* * *
13145 AAATCCATACACTCAGTTTGATTCCTTTACCATTTTAGCACATAAAATGCCCTATGTGAAAATCC
1 AAATCCATACACTCAGTATGATTTCTTTACCATTTTAGCACATAAAGTGCCCTATGTGAAAATCC
* *
13210 ATACCCTTAGTATGATTTCTTATCCTTGTAGCACCCTTAGTGCTTTATCTAG
66 ATACCCTTAGTATGATTCCTTATCCTTGTAGCACCCTTAGTGCTTTATCTGG
**
13262 AAATCCATACACTCAGTATGATTTCTTTACCATTTTAGCACATAAAGTGCCCTAT-CCAGAAATC
1 AAATCCATACACTCAGTATGATTTCTTTACCATTTTAGCACATAAAGTGCCCTATGTGA-AAATC
** * * * * ** *
13326 CATA-TATTCATTATGATCTCCTTATCATT-TAGCACACTCAGTGCTCCATATGG
65 CATACCCTT-AGTATGAT-TCCTTATCCTTGTAGCACCCTTAGTGCTTTATCTGG
13379 AAATCCATACACTCAGTATGATTTC
1 AAATCCATACACTCAGTATGATTTC
13404 CTGATCCTTT
Statistics
Matches: 229, Mismatches: 26, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
116 3 0.01
117 146 0.64
118 79 0.34
119 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (117 bp):
AAATCCATACACTCAGTATGATTTCTTTACCATTTTAGCACATAAAGTGCCCTATGTGAAAATCC
ATACCCTTAGTATGATTCCTTATCCTTGTAGCACCCTTAGTGCTTTATCTGG
Found at i:20078 original size:14 final size:14
Alignment explanation
Indices: 20061--20096 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
20051 TCACGTAATT
*
20061 TGTTTTTCGGAAAA
1 TGTTTTCCGGAAAA
20075 TGTTTTCCGGAAAA
1 TGTTTTCCGGAAAA
20089 TGTTTTCC
1 TGTTTTCC
20097 CATGTTTGTT
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:0.22, C:0.14, G:0.19, T:0.44
Consensus pattern (14 bp):
TGTTTTCCGGAAAA
Found at i:20360 original size:31 final size:30
Alignment explanation
Indices: 20315--20395 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 30
20305 ATTATTTATT
*
20315 TATT-TATTTATTAATATTTATAATAACATAA
1 TATTATATTTATTAATA-TTAT-ATAAAATAA
20346 TATTATATTT-TTAATATTATATAAAATAA
1 TATTATATTTATTAATATTATATAAAATAA
*
20375 TCAATTATATTATAATAATAT
1 T--ATTATATT-TATTAATAT
20396 ATGATATGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
29 9 0.21
30 4 0.09
31 18 0.42
32 6 0.14
33 6 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (30 bp):
TATTATATTTATTAATATTATATAAAATAA
Found at i:20916 original size:21 final size:21
Alignment explanation
Indices: 20892--20934 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20882 AGAATTCAAA
**
20892 TTCCACTAATTCATTTTCCAG
1 TTCCACTAATTCAAATTCCAG
*
20913 TTCCAGTAATTCAAATTCCAG
1 TTCCACTAATTCAAATTCCAG
20934 T
1 T
20935 AATTTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.26, G:0.07, T:0.40
Consensus pattern (21 bp):
TTCCACTAATTCAAATTCCAG
Found at i:21047 original size:59 final size:57
Alignment explanation
Indices: 20975--21253 Score: 238
Period size: 59 Copynumber: 4.7 Consensus size: 57
20965 AAACAAACAG
* *
20975 ACCCTTAGTATGATTTCTCTTTCATTTTAGTACATGAAGTGCCCTATGTGAAAATCCAT
1 ACCCTTAGTATGATTTC-CTTTCATTTTAGCACAT-AAGTGCCTTATGTGAAAATCCAT
* * * * * * * *
21034 ACCCTTAGTATGATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTATCTGGAAATTCAT
1 ACCCTTAGTATGATTTCCTT-TCATTTTAGCA-CATAAGTGCCTTATGTGAAAATCCAT
* *
21093 ACACTCAGTATGA-TTCCTTTACCATTTTAGCACATAAAGTGCCTTATGTGAAAATCCAT
1 ACCCTTAGTATGATTTCCTTT--CATTTTAGCACAT-AAGTGCCTTATGTGAAAATCCAT
* * * * * * * *
21152 ACCCTTAGTATGATTTCCTTATCCTTGTAGCACCCTTATTGCTTTATCTGGAAATCCAT
1 ACCCTTAGTATGATTTCCTT-TCATTTTAGCA-CATAAGTGCCTTATGTGAAAATCCAT
* *
21211 ACACTCAGTATGA-TTCCTTTACCATTTTAGCACATAAAGTGCC
1 ACCCTTAGTATGATTTCCTTT--CATTTTAGCACAT-AAGTGCC
21254 ATATCCGGAA
Statistics
Matches: 171, Mismatches: 38, Indels: 22
0.74 0.16 0.10
Matches are distributed among these distances:
57 2 0.01
58 19 0.11
59 139 0.81
60 10 0.06
61 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.38
Consensus pattern (57 bp):
ACCCTTAGTATGATTTCCTTTCATTTTAGCACATAAGTGCCTTATGTGAAAATCCAT
Found at i:21189 original size:118 final size:118
Alignment explanation
Indices: 20981--21341 Score: 489
Period size: 118 Copynumber: 3.1 Consensus size: 118
20971 ACAGACCCTT
* * *
20981 AGTATGATTTCTCTTT--CATTTTAGTACATGAAGTGCCCTATGTGAAAATCCATACCCTTAGTA
1 AGTATGA-TTC-CTTTACCATTTTAGCACATAAAGTGCCATATGTGAAAATCCATACCCTTAGTA
*
21044 TGATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTATCTGGAAATTCATACACTC
64 TGATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTC
*
21099 AGTATGATTCCTTTACCATTTTAGCACATAAAGTGCCTTATGTGAAAATCCATACCCTTAGTATG
1 AGTATGATTCCTTTACCATTTTAGCACATAAAGTGCCATATGTGAAAATCCATACCCTTAGTATG
*
21164 ATTTCCTTATCCTTGTAGCACCCTTATTGCTTTATCTGGAAATCCATACACTC
66 ATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTC
** * ** *
21217 AGTATGATTCCTTTACCATTTTAGCACATAAAGTGCCATATCCGGAAATCCATA-TATTGAATAT
1 AGTATGATTCCTTTACCATTTTAGCACATAAAGTGCCATATGTGAAAATCCATACCCTT-AGTAT
* * * * ** *
21281 -ATCTCCTTATCATT-TAGCACACTTAGTTCTCCATATGGAAATCCATACACTC
65 GATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTC
21333 AGTATGATT
1 AGTATGATT
21342 TCTTAATCCT
Statistics
Matches: 220, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
116 45 0.20
117 17 0.08
118 158 0.72
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.37
Consensus pattern (118 bp):
AGTATGATTCCTTTACCATTTTAGCACATAAAGTGCCATATGTGAAAATCCATACCCTTAGTATG
ATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTC
Found at i:21264 original size:59 final size:57
Alignment explanation
Indices: 20997--21346 Score: 235
Period size: 59 Copynumber: 6.0 Consensus size: 57
20987 ATTTCTCTTT
* * * * * *
20997 CATTTTAGTACATGAAGTGCCCTATGTGAAAATCCATACCCTTAGTATGATTTCCTTATC
1 CATTTTAGCACAT-AAGTGCCATATCTGGAAATCCATACACTCAGTATGA-TTCCTTA-C
* * * ** *
21057 C-TTGTAGCACCCTTAGTGCTTTATCTGGAAATTCATACACTCAGTATGATTCCTTTAC
1 CATTTTAGCA-CATAAGTGCCATATCTGGAAATCCATACACTCAGTATGATTCC-TTAC
* * * * *
21115 CATTTTAGCACATAAAGTGCCTTATGTGAAAATCCATACCCTTAGTATGATTTCCTTATC
1 CATTTTAGCACAT-AAGTGCCATATCTGGAAATCCATACACTCAGTATGA-TTCCTTA-C
* * * * **
21175 C-TTGTAGCACCCTTATTGCTTTATCTGGAAATCCATACACTCAGTATGATTCCTTTAC
1 CATTTTAGCA-CATAAGTGCCATATCTGGAAATCCATACACTCAGTATGATTCC-TTAC
* * * * * *
21233 CATTTTAGCACATAAAGTGCCATATCCGGAAATCCATATATTGAATAT-ATCTCCTTAT
1 CATTTTAGCACAT-AAGTGCCATATCTGGAAATCCATACACTCAGTATGAT-TCCTTAC
* * *
21291 CA-TTTAGCACACTTAGTTCTCCATA--TGGAAATCCATACACTCAGTATGATTTCTTA
1 CATTTTAGCACA-TAAG-T-GCCATATCTGGAAATCCATACACTCAGTATGATTCCTTA
21347 ATCCTTTATC
Statistics
Matches: 226, Mismatches: 49, Indels: 33
0.73 0.16 0.11
Matches are distributed among these distances:
57 33 0.15
58 27 0.12
59 155 0.69
60 11 0.05
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.37
Consensus pattern (57 bp):
CATTTTAGCACATAAGTGCCATATCTGGAAATCCATACACTCAGTATGATTCCTTAC
Found at i:21726 original size:20 final size:20
Alignment explanation
Indices: 21703--21741 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21693 CCCTAACTGA
*
21703 GGTATAGATACCCTTTCTAG
1 GGTATAGATACCCTATCTAG
21723 GGTATAGATACCCTATCTA
1 GGTATAGATACCCTATCTA
21742 CATTCTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (20 bp):
GGTATAGATACCCTATCTAG
Found at i:23089 original size:21 final size:21
Alignment explanation
Indices: 23063--23104 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
23053 TCAATAAGTG
23063 TCAATGATATTCATGTCTCTA
1 TCAATGATATTCATGTCTCTA
23084 TCAATGATATTCATGTCTCTA
1 TCAATGATATTCATGTCTCTA
23105 GAGTGTCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
TCAATGATATTCATGTCTCTA
Found at i:23970 original size:17 final size:17
Alignment explanation
Indices: 23951--24009 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
23941 ATTAAGTTAG
*
23951 TTCATTAATCAAACTAG
1 TTCATTAATCAAACTAA
* *
23968 TTCATTCATTAAACTAA
1 TTCATTAATCAAACTAA
* *
23985 TGCATTAATCGAACTAA
1 TTCATTAATCAAACTAA
24002 TT-ATTAAT
1 TTCATTAAT
24010 TGTTTCATGC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
16 6 0.18
17 28 0.82
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (17 bp):
TTCATTAATCAAACTAA
Found at i:25796 original size:20 final size:21
Alignment explanation
Indices: 25768--25806 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
25758 AGTTTAGGAA
*
25768 TTATCTTTAGGATTTATCTCT
1 TTATCTTTAGGAATTATCTCT
25789 TTAT-TTTAGGAATTATCT
1 TTATCTTTAGGAATTATCT
25807 TTTCCTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.56
Consensus pattern (21 bp):
TTATCTTTAGGAATTATCTCT
Found at i:35060 original size:36 final size:36
Alignment explanation
Indices: 35013--35101 Score: 178
Period size: 36 Copynumber: 2.5 Consensus size: 36
35003 TATAGTTATT
35013 TCATGCTTTTGTTGATAGAGATAAACTTAATATGCA
1 TCATGCTTTTGTTGATAGAGATAAACTTAATATGCA
35049 TCATGCTTTTGTTGATAGAGATAAACTTAATATGCA
1 TCATGCTTTTGTTGATAGAGATAAACTTAATATGCA
35085 TCATGCTTTTGTTGATA
1 TCATGCTTTTGTTGATA
35102 TAAACCTTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (36 bp):
TCATGCTTTTGTTGATAGAGATAAACTTAATATGCA
Found at i:36525 original size:18 final size:18
Alignment explanation
Indices: 36502--36536 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
36492 GATTTATCTC
36502 TTTA-TTTTAGGAATTTTT
1 TTTATTTTTAGG-ATTTTT
36520 TTTATTTTTAGGATTTT
1 TTTATTTTTAGGATTTT
36537 GAAGGCTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.20, C:0.00, G:0.11, T:0.69
Consensus pattern (18 bp):
TTTATTTTTAGGATTTTT
Found at i:38092 original size:20 final size:21
Alignment explanation
Indices: 38064--38102 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
38054 AGTTTAGGAA
*
38064 TTATCTTTAGGATTTATCTCT
1 TTATCTTTAGGAATTATCTCT
38085 TTAT-TTTAGGAATTATCT
1 TTATCTTTAGGAATTATCT
38103 TTTCCTTGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.56
Consensus pattern (21 bp):
TTATCTTTAGGAATTATCTCT
Found at i:40404 original size:37 final size:37
Alignment explanation
Indices: 40353--40426 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
40343 AAAAAGCGTG
40353 ATAAAAGATATGAAGAAAGGGAGATCTTAGAGGTGTT
1 ATAAAAGATATGAAGAAAGGGAGATCTTAGAGGTGTT
*
40390 ATAAAAGATCTGAAGAAAGGGAGATCTTAGAGGTGTT
1 ATAAAAGATATGAAGAAAGGGAGATCTTAGAGGTGTT
40427 CCAAAAAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.42, C:0.04, G:0.30, T:0.24
Consensus pattern (37 bp):
ATAAAAGATATGAAGAAAGGGAGATCTTAGAGGTGTT
Found at i:46935 original size:36 final size:36
Alignment explanation
Indices: 46888--46976 Score: 160
Period size: 36 Copynumber: 2.5 Consensus size: 36
46878 TATAGTTATT
*
46888 TCATGCTTTTGTTGATAGAGATAAACTTAATATGCA
1 TCATGCTTTTGTTGATAGAGATAAAATTAATATGCA
*
46924 TCATGCTTTTGTTGATAGAGATAAAATTAATATGTA
1 TCATGCTTTTGTTGATAGAGATAAAATTAATATGCA
46960 TCATGCTTTTGTTGATA
1 TCATGCTTTTGTTGATA
46977 TAAACCTTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (36 bp):
TCATGCTTTTGTTGATAGAGATAAAATTAATATGCA
Found at i:50863 original size:17 final size:17
Alignment explanation
Indices: 50838--50890 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
50828 TGAATTAAGT
*
50838 TAGTTCATTAATCAAAC
1 TAGTCCATTAATCAAAC
* *
50855 TAGTCCATTCATTAAAC
1 TAGTCCATTAATCAAAC
* *
50872 TAGTGCATTAATCGAAC
1 TAGTCCATTAATCAAAC
50889 TA
1 TA
50891 ATTCTTAATT
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:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (17 bp):
TAGTCCATTAATCAAAC
Found at i:51880 original size:78 final size:78
Alignment explanation
Indices: 51788--51943 Score: 294
Period size: 78 Copynumber: 2.0 Consensus size: 78
51778 GTGGGTCACA
*
51788 TTCCACCCTCTTCCACTTTAAATTCATTTATTTATATTGTTGATTCCTAGCTCTTATAACTAGTG
1 TTCCACCCTCTTCCACTTTAAATCCATTTATTTATATTGTTGATTCCTAGCTCTTATAACTAGTG
51853 GATCACAATCCAT
66 GATCACAATCCAT
*
51866 TTCCACCCTCTTCCACTTTAAATCCATTTATTTATATTTTTGATTCCTAGCTCTTATAACTAGTG
1 TTCCACCCTCTTCCACTTTAAATCCATTTATTTATATTGTTGATTCCTAGCTCTTATAACTAGTG
51931 GATCACAATCCAT
66 GATCACAATCCAT
51944 AGTCCTTTAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.26, C:0.25, G:0.07, T:0.42
Consensus pattern (78 bp):
TTCCACCCTCTTCCACTTTAAATCCATTTATTTATATTGTTGATTCCTAGCTCTTATAACTAGTG
GATCACAATCCAT
Found at i:64752 original size:22 final size:22
Alignment explanation
Indices: 64716--64774 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
64706 AAGTTCCTTA
* *
64716 GCACTAATACTAAAGTGC-CTC
1 GCACTGATACAAAAGTGCACTC
* *
64737 AGCACTGGTACAAAAGTGCATTC
1 -GCACTGATACAAAAGTGCACTC
64760 GCACTGATACAAAAG
1 GCACTGATACAAAAG
64775 GGTCATAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 29 0.94
23 2 0.06
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (22 bp):
GCACTGATACAAAAGTGCACTC
Found at i:70997 original size:2 final size:2
Alignment explanation
Indices: 70990--71043 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
70980 AACTGTTTAA
70990 AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71031 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
71044 AACTATTTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.