Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006496.1 Hibiscus syriacus cultivar Beakdansim tig00015797_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: 65085
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:149 original size:24 final size:19
Alignment explanation
Indices: 101--161 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 19
91 TTTCCCTTGA
101 AGTGCATCGATGCATCTAC
1 AGTGCATCGATGCATCTAC
120 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCA-TC--T-AC
143 ATGTGCATCGATGCA-CTAC
1 A-GTGCATCGATGCATCTAC
162 CCATGCATCG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
19 16 0.43
20 3 0.08
22 2 0.05
23 3 0.08
24 13 0.35
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (19 bp):
AGTGCATCGATGCATCTAC
Found at i:4977 original size:16 final size:16
Alignment explanation
Indices: 4939--4979 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
4929 GCTTATTAAA
*
4939 AATAAAAAATAAAAAT
1 AATAAAAAATAAAAAG
*
4955 AAGAAAAAATAAAAAG
1 AATAAAAAATAAAAAG
*
4971 ACTAAAAAA
1 AATAAAAAA
4980 ATATCGATGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.12
Consensus pattern (16 bp):
AATAAAAAATAAAAAG
Found at i:5439 original size:38 final size:36
Alignment explanation
Indices: 5397--5567 Score: 163
Period size: 38 Copynumber: 4.7 Consensus size: 36
5387 TTAAACTTTC
*
5397 AATTTTTTCAATTAGAACAATAAAATTTTGATTTTAGT
1 AATTTTTTCAATTAGAACACTAAAA--TTGATTTTAGT
* *
5435 AATTTTTTCAATTATAACACTAAAATTAATTTTCA-T
1 AATTTTTTCAATTAGAACACTAAAATTGATTTT-AGT
* *
5471 -ATTTTTTCAATTATAACACTAAATATTTTTATTTTAGT
1 AATTTTTTCAATTAGAACACTAAA-A--TTGATTTTAGT
* *
5509 ATTTTTTTCAATTATGAA-ACTAAAATTGATTTTCGT
1 AATTTTTTCAATTA-GAACACTAAAATTGATTTTAGT
* *
5545 -ATTTTTT-AATTATAAAACTAAAA
1 AATTTTTTCAATTAGAACACTAAAA
5568 AAATTGTTTT
Statistics
Matches: 115, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
33 2 0.02
34 12 0.10
35 29 0.25
36 18 0.16
37 2 0.02
38 32 0.28
39 18 0.16
40 2 0.02
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (36 bp):
AATTTTTTCAATTAGAACACTAAAATTGATTTTAGT
Found at i:5508 original size:74 final size:73
Alignment explanation
Indices: 5393--5567 Score: 248
Period size: 74 Copynumber: 2.4 Consensus size: 73
5383 ATTATTAAAC
* *
5393 TTTCA-ATTTTTTCAATTAGAACAATAAAATTTTGATTTTAGTAATTTTTTCAATTAT-AACACT
1 TTTCATATTTTTTCAATTATAACACTAAAATTTTGATTTTAGTAATTTTTTCAATTATGAA-ACT
5456 AAAATTAAT
65 AAAATTAAT
* *
5465 TTTCATATTTTTTCAATTATAACACTAAATATTTTTATTTTAGTATTTTTTTCAATTATGAAACT
1 TTTCATATTTTTTCAATTATAACACTAAA-ATTTTGATTTTAGTAATTTTTTCAATTATGAAACT
*
5530 AAAATTGAT
65 AAAATTAAT
* *
5539 TTTCGTATTTTTT-AATTATAAAACTAAAA
1 TTTCATATTTTTTCAATTATAACACTAAAA
5568 AAATTGTTTT
Statistics
Matches: 93, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
72 6 0.06
73 35 0.38
74 50 0.54
75 2 0.02
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (73 bp):
TTTCATATTTTTTCAATTATAACACTAAAATTTTGATTTTAGTAATTTTTTCAATTATGAAACTA
AAATTAAT
Found at i:6391 original size:217 final size:219
Alignment explanation
Indices: 5998--6426 Score: 691
Period size: 217 Copynumber: 2.0 Consensus size: 219
5988 CCATGTCCCA
* *
5998 CCAATGCTTCCCCCGGTTGTTGAATAACCCAATCCACCCTCTGTGTCTCCACCATACCCCATATT
1 CCAATGCTTCCCCCAGTTGTTGAATAACCCAATCCACCCCCTGTGTCTCCACCATACCCCATATT
* * *
6063 CATATTTTCATCCGACCTAACCTGCCTTCCCAAGTCATACCCAGTCCCAGTATCTGCTGTGGAGT
66 CATATTTTCATCCGACCTAACCTGCCTCCCCAAGTAATACCCAGTCCCAATATCTGCTGTGGAGT
* *
6128 ACCCACTGTTGGCGTCATATACGCCGCCGCCTCCATAGCCACCAGTCTCACCTCTGTTATGGGTG
131 ACCCACGGCTGGCGTCATATACGCCGCCGCCTCCATAGCCACCAGTCTCACCTCTGTTATGGGTG
6193 AATCCAGCACCACCACCTGCCCCT
196 AATCCAGCACCACCACCTGCCCCT
* * *
6217 CCAATGTTTCCCCCAGTTGTTGAATAACCTAATCCACCCCCTGTTTCTCCACCATACCCCATATT
1 CCAATGCTTCCCCCAGTTGTTGAATAACCCAATCCACCCCCTGTGTCTCCACCATACCCCATATT
* * * *
6282 CATA-TTTCATCCGCCCTAACCTGCC-CCCCGAGTAATACCCAGTCCCAATATCTTCTGTGGGGT
66 CATATTTTCATCCGACCTAACCTGCCTCCCCAAGTAATACCCAGTCCCAATATCTGCTGTGGAGT
* *
6345 ACCCACGGCTGGCGTCATGTACGCCGCCTCCTCCATAGCCACCAGTCTCACCTCTGTTATGGGTG
131 ACCCACGGCTGGCGTCATATACGCCGCCGCCTCCATAGCCACCAGTCTCACCTCTGTTATGGGTG
*
6410 AATCCTGCACCACCACC
196 AATCCAGCACCACCACC
6427 ACTAGGGTGG
Statistics
Matches: 193, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
217 109 0.56
218 20 0.10
219 64 0.33
ACGTcount: A:0.21, C:0.39, G:0.15, T:0.26
Consensus pattern (219 bp):
CCAATGCTTCCCCCAGTTGTTGAATAACCCAATCCACCCCCTGTGTCTCCACCATACCCCATATT
CATATTTTCATCCGACCTAACCTGCCTCCCCAAGTAATACCCAGTCCCAATATCTGCTGTGGAGT
ACCCACGGCTGGCGTCATATACGCCGCCGCCTCCATAGCCACCAGTCTCACCTCTGTTATGGGTG
AATCCAGCACCACCACCTGCCCCT
Found at i:8379 original size:64 final size:63
Alignment explanation
Indices: 8210--8387 Score: 189
Period size: 64 Copynumber: 2.8 Consensus size: 63
8200 GAATAAATTG
* * * **
8210 AACATCGAATGCATTTCATGCATCGATGCACTCTCTATGTATCGATACACTTGGGTTTTATTAA
1 AACATCGAATGCATTTCATGCATCGATGCACACT-TATGCATCGATGCACTCAGGTTTTATTAA
* * * *
8274 AACATAGAATGCATTTCATGCATCAATGCACAAGC-AATGCATCGATGCACTCAGGTTATT-TTC
1 AACATCGAATGCATTTCATGCATCGATGCAC-A-CTTATGCATCGATGCACTCAGGTT-TTATTA
8337 A
63 A
* * *
8338 AACATCGAATGCATTTTATGCATCGATACACACTTGGTGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCACACTT-ATGCATCGATGCAC
8388 ACTTGGTGCA
Statistics
Matches: 94, Mismatches: 15, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 89 0.95
65 2 0.02
66 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTTATGCATCGATGCACTCAGGTTTTATTAA
Found at i:8403 original size:19 final size:19
Alignment explanation
Indices: 8356--8406 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
8346 ATGCATTTTA
*
8356 TGCATCGATACACACTTGG
1 TGCATCGATGCACACTTGG
8375 TGCATCGATGCACACTTGG
1 TGCATCGATGCACACTTGG
*
8394 TGCACCGATGCAC
1 TGCATCGATGCAC
8407 TAAGTGTTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCACACTTGG
Found at i:13254 original size:19 final size:19
Alignment explanation
Indices: 13230--13268 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
13220 TCGAATGCAT
13230 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
13249 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
13268 T
1 T
13269 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:13364 original size:62 final size:65
Alignment explanation
Indices: 13216--13374 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
13206 GAATTAATTG
* **** *
13216 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCACCGATGCACAAGACATGCATCGATGCACTCAGAATATTTTCAA
* * *
13281 AACATCGAATGCATTTGATGCATCGATGCACAAGACATGCATC-ATGCAC-CAG-CTATTTTTC-
1 AACATCGAATGCATTTCATGCACCGATGCACAAGACATGCATCGATGCACTCAGAATA-TTTTCA
13342 A
65 A
13343 AACATCGAATGCATTTCATGCACCGATGCACA
1 AACATCGAATGCATTTCATGCACCGATGCACA
13375 CTTGGTGCAC
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
62 33 0.40
63 7 0.09
64 6 0.07
65 36 0.44
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.26
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCACCGATGCACAAGACATGCATCGATGCACTCAGAATATTTTCAA
Found at i:20363 original size:31 final size:31
Alignment explanation
Indices: 20292--20371 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
20282 ATTTAACAAA
* * **
20292 AAGGGGGAGAAAATTTAAGATGTGATATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGATATAGT
*
20323 AAGGGGGAGTAAGTTTTTGATGTGCTATAGT
1 AAGGGGGAGTAAGTTTTTGATGTGATATAGT
20354 AAGGGGGAGTAAGTTTTT
1 AAGGGGGAGTAAGTTTTT
20372 CCAAATCGAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.33, C:0.01, G:0.35, T:0.31
Consensus pattern (31 bp):
AAGGGGGAGTAAGTTTTTGATGTGATATAGT
Found at i:20793 original size:19 final size:19
Alignment explanation
Indices: 20749--20800 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
20739 AATTAATTGA
20749 ACATCGAATGCA-T-TCCAT
1 ACATCG-ATGCACTCTCCAT
* *
20767 GCACCGATGCACTCTCCAT
1 ACATCGATGCACTCTCCAT
20786 ACATCGATGCACTCT
1 ACATCGATGCACTCT
20801 GAATATTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 5 0.18
18 5 0.18
19 18 0.64
ACGTcount: A:0.27, C:0.35, G:0.13, T:0.25
Consensus pattern (19 bp):
ACATCGATGCACTCTCCAT
Found at i:20925 original size:64 final size:65
Alignment explanation
Indices: 20748--20910 Score: 195
Period size: 65 Copynumber: 2.5 Consensus size: 65
20738 GAATTAATTG
* * * * *
20748 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATACATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCACCGATGCACACTACATGCATCGATGCACTCAGAATATTTTCAA
* * ** * **
20813 AACATCGAATGCATTTGATGCATCGATGCACAAGACATGCATTGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCACCGATGCACACTACATGCATCGATGCACTCAGAATA-TTTTCA
20876 A
65 A
20877 AACATCGAATGCATTTCATGCACCGATGCACACT
1 AACATCGAATGCATTTCATGCACCGATGCACACT
20911 TGGTGCACCG
Statistics
Matches: 81, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
64 35 0.43
65 46 0.57
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCACCGATGCACACTACATGCATCGATGCACTCAGAATATTTTCAA
Found at i:24521 original size:21 final size:21
Alignment explanation
Indices: 24479--24522 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
24469 ACTCCGGGAG
* *
24479 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
24500 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
24521 CT
1 CT
24523 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:39021 original size:3 final size:3
Alignment explanation
Indices: 39005--39181 Score: 241
Period size: 3 Copynumber: 59.7 Consensus size: 3
38995 CATGCCAAAA
*
39005 AAT AA- AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * * * *
39051 AGT AGT AGT AGT AGT AAT AAT AAT AAT AAT ATT AAT AGT AGT AGT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39099 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39147 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
39182 AGATAGTAGG
Statistics
Matches: 164, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
2 4 0.02
3 160 0.98
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:39579 original size:134 final size:134
Alignment explanation
Indices: 39352--40019 Score: 867
Period size: 134 Copynumber: 5.0 Consensus size: 134
39342 ATCATATATA
* * * * *
39352 GGGATGTTGATCCATTCTGCTATCACTCAGGGAATATTGAATCGGTGTAGACTTGTTCCGCTGTC
1 GGGA-GTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCCGCTGTC
* * * *
39417 ACTCATGGAATATCAAATCTTGGAAAAGAGGGACTTGTTCCGCTTCTTCTGAAGGCAATATCACA
65 ACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGCTTCTTCTGAAGGGAATATCAGA
39482 TCTGG
130 TCTGG
* * * * *
39487 GGGAGTTGATCCATTCCGTTATCACTCATGGAAGATTGAATCGGGGCAAACTTGTTCCGCTATCA
1 GGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCCGCTGTCA
* *
39552 CTCCA-GGAATATCAAATCTTGGAAAAGAGGGACAAGTTCCGCGTT-TTCTGAAGGGAATATTAG
66 CT-CAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGC-TTCTTCTGAAGGGAATATCAG
39615 ATCTGG
129 ATCTGG
* * * *
39621 GGGAGTTGATCCATTTCACTGTCACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCTGCTCTCA
1 GGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCCGCTGTCA
* * *
39686 CTCAGGGAATATCAAATATTGGAAAAGAGGGACATGTTCCGCTTATTTTGAAGGGAATATCAGAT
66 CTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGCTTCTTCTGAAGGGAATATCAGAT
*
39751 TTGG
131 CTGG
* * * * * *
39755 AGGAGTTTATCTATTCTGATGTCACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCTGCTGTCA
1 GGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCCGCTGTCA
* * ** *
39820 CTTAGGGAATATCAAGTCTTGGAAAAGAGGGACATGTTCAACTTCTTCTGAAGGGAATATTAGAT
66 CTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGCTTCTTCTGAAGGGAATATCAGAT
39885 CTGG
131 CTGG
* ** * * * * **
39889 AGGAGTTGATTTATTACACTGTCACTTAGGGAAGATTGAATCGGGGAAGACTTGTT--ATTGTCA
1 GGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCCGCTGTCA
* *
39952 CTCAGGGAATATCAAATCTTAGAAAATAGGGACATGTTCCGCTTCTTCTGAAGGGAATATCAGAT
66 CTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGCTTCTTCTGAAGGGAATATCAGAT
40017 CTG
131 CTG
40020 CAAATTAAAC
Statistics
Matches: 469, Mismatches: 60, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
132 66 0.14
133 4 0.01
134 391 0.83
135 8 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (134 bp):
GGGAGTTGATCCATTCCGCTGTCACTCAGGGAAGATTGAATCGGGGCAGACTTGTTCCGCTGTCA
CTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGCTTCTTCTGAAGGGAATATCAGAT
CTGG
Found at i:41651 original size:20 final size:20
Alignment explanation
Indices: 41626--41693 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
41616 ATCTTGAGCC
*
41626 CCTTTTCAATTTTCCTTATT
1 CCTTTTCAATATTCCTTATT
*
41646 CCTTTTCTTATATATTCTTTATT
1 CCTTTTC--A-ATATTCCTTATT
*
41669 --TTTTCAATCTTCCTTATT
1 CCTTTTCAATATTCCTTATT
*
41687 CTTTTTC
1 CCTTTTC
41694 TTATCTATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
18 10 0.26
19 1 0.03
20 12 0.31
21 5 0.13
22 1 0.03
23 10 0.26
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (20 bp):
CCTTTTCAATATTCCTTATT
Found at i:41673 original size:21 final size:21
Alignment explanation
Indices: 41648--41713 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
41638 TCCTTATTCC
41648 TTTTCTTATATATTCTTTATT
1 TTTTCTTATATATTCTTTATT
* *
41669 TTTTC--A-ATCTTCCTTATTCT
1 TTTTCTTATATATTCTTTA-T-T
* *
41689 TTTTCTTATCTATTCTTTCTT
1 TTTTCTTATATATTCTTTATT
41710 TTTT
1 TTTT
41714 TTCTCTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
18 8 0.24
19 2 0.06
20 6 0.18
21 10 0.29
22 2 0.06
23 6 0.18
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTTATATATTCTTTATT
Found at i:41675 original size:41 final size:41
Alignment explanation
Indices: 41628--41713 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
41618 CTTGAGCCCC
*
41628 TTTTCAATTTTCCTTATTCCTTTTCTTATATATTCTTTATT
1 TTTTCAATCTTCCTTATTCCTTTTCTTATATATTCTTTATT
* * *
41669 TTTTCAATCTTCCTTATTCTTTTTCTTATCTATTCTTTCTT
1 TTTTCAATCTTCCTTATTCCTTTTCTTATATATTCTTTATT
41710 TTTT
1 TTTT
41714 TTCTCTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (41 bp):
TTTTCAATCTTCCTTATTCCTTTTCTTATATATTCTTTATT
Found at i:41708 original size:20 final size:19
Alignment explanation
Indices: 41685--41731 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
41675 ATCTTCCTTA
41685 TTCTTTTTCTTATCTATTCT
1 TTCTTTTTCTTATCT-TTCT
* * *
41705 TTCTTTTTTTTCTCTTTTT
1 TTCTTTTTCTTATCTTTCT
41724 TTCTTTTT
1 TTCTTTTT
41732 TTTTCTAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (19 bp):
TTCTTTTTCTTATCTTTCT
Found at i:41722 original size:10 final size:9
Alignment explanation
Indices: 41685--41734 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
41675 ATCTTCCTTA
41685 TTCTTTTTCT
1 TTCTTTTT-T
* *
41695 TATCTATTCT
1 T-TCTTTTTT
41705 TTCTTTTTT
1 TTCTTTTTT
41714 TTCTCTTTTT
1 TTCT-TTTTT
41724 TTCTTTTTT
1 TTCTTTTTT
41733 TT
1 TT
41735 TCTAGTGTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
9 17 0.50
10 12 0.35
11 5 0.15
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:41726 original size:19 final size:20
Alignment explanation
Indices: 41685--41738 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
41675 ATCTTCCTTA
*
41685 TTCTTTTTCTTATCTATTCT
1 TTCTTTTTTTTATCTATTCT
* *
41705 TTCTTTTTTTTCTCT-TTTT
1 TTCTTTTTTTTATCTATTCT
41724 TTCTTTTTTTT-TCTA
1 TTCTTTTTTTTATCTA
41739 GTGTGATATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.10
19 14 0.47
20 13 0.43
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.78
Consensus pattern (20 bp):
TTCTTTTTTTTATCTATTCT
Found at i:41735 original size:10 final size:10
Alignment explanation
Indices: 41704--41737 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
41694 TTATCTATTC
41704 TTTC-TTTTT
1 TTTCTTTTTT
*
41713 TTTCTCTTTT
1 TTTCTTTTTT
41723 TTTCTTTTTT
1 TTTCTTTTTT
41733 TTTCT
1 TTTCT
41738 AGTGTGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:52556 original size:31 final size:31
Alignment explanation
Indices: 52518--52626 Score: 166
Period size: 31 Copynumber: 3.5 Consensus size: 31
52508 GGGTCGAGGG
52518 TTTACCTATGTTCTTCGGGACATATGGACTA
1 TTTACCTATGTTCTTCGGGACATATGGACTA
* * *
52549 TTTACCTATGTTCTTCAGGATATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTA
52580 TTTACCTATGTTCTTCGGGACATATGGACTGA
1 TTTACCTATGTTCTTCGGGACATATGGACT-A
*
52612 -TTACCTAGGTTCTTC
1 TTTACCTATGTTCTTC
52627 AGAATCTATG
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
31 70 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACTA
Found at i:52588 original size:62 final size:62
Alignment explanation
Indices: 52517--52641 Score: 207
Period size: 62 Copynumber: 2.0 Consensus size: 62
52507 AGGGTCGAGG
* *
52517 GTTTACCTATGTTCTTCGGGACATATGGACT-ATTTACCTATGTTCTTCAGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGA-TTACCTAGGTTCTTCAGAATATATGGACT
*
52579 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAATCTATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAATATATGGACT
52641 G
1 G
52642 GTCCTTCGGG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 58 0.98
63 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.38
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAATATATGGACT
Found at i:52637 original size:31 final size:31
Alignment explanation
Indices: 52519--52641 Score: 144
Period size: 31 Copynumber: 4.0 Consensus size: 31
52509 GGTCGAGGGT
*
52519 TTACCTATGTTCTTCGGGA-CATATGGACT-A
1 TTACCTATGTTCTTCAGGATC-TATGGACTGA
* *
52549 TTTACCTATGTTCTTCAGGATATATGGACTGT
1 -TTACCTATGTTCTTCAGGATCTATGGACTGA
*
52581 TTACCTATGTTCTTCGGGA-CATATGGACTGA
1 TTACCTATGTTCTTCAGGATC-TATGGACTGA
* *
52612 TTACCTAGGTTCTTCAGAATCTATGGACTG
1 TTACCTATGTTCTTCAGGATCTATGGACTG
52642 GTCCTTCGGG
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
31 78 0.99
32 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCAGGATCTATGGACTGA
Found at i:53372 original size:20 final size:21
Alignment explanation
Indices: 53335--53375 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
53325 TCGAAGTTTT
*
53335 ATGCATCGGTGTACTGTAGCA
1 ATGCATCGGTGCACTGTAGCA
53356 ATGCATC-GTGCACTGTAGCA
1 ATGCATCGGTGCACTGTAGCA
53376 GGTTACTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (21 bp):
ATGCATCGGTGCACTGTAGCA
Found at i:57395 original size:31 final size:30
Alignment explanation
Indices: 57357--57469 Score: 165
Period size: 31 Copynumber: 3.7 Consensus size: 30
57347 AGGTTCGAGG
57357 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTC-GGACATATGGACT
57388 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGG-ACATATGGACT
*
57419 ATTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTC-GGACATATGGACT
*
57450 -TATTACCTAGGTTCTTCGGA
1 GT-TTACCTATGTTCTTCGGA
57470 ATCTATGGAC
Statistics
Matches: 77, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
30 6 0.08
31 69 0.90
32 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (30 bp):
GTTTACCTATGTTCTTCGGACATATGGACT
Found at i:57434 original size:62 final size:62
Alignment explanation
Indices: 57358--57480 Score: 196
Period size: 62 Copynumber: 2.0 Consensus size: 62
57348 GGTTCGAGGG
*
57358 TTTACCTATGTTCTTCAGGACATATGGACTGT-TTACCTATGTTCTTCGGAA-CATATGGACTA
1 TTTACCTATGTTCTTCAGGACATATGGACT-TATTACCTAGGTTCTTCGGAATC-TATGGACTA
*
57420 TTTACCTATGTTCTTCGGGACATATGGACTTATTACCTAGGTTCTTCGGAATCTATGGACT
1 TTTACCTATGTTCTTCAGGACATATGGACTTATTACCTAGGTTCTTCGGAATCTATGGACT
57481 GGTCCTTCGG
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
61 1 0.02
62 55 0.96
63 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.39
Consensus pattern (62 bp):
TTTACCTATGTTCTTCAGGACATATGGACTTATTACCTAGGTTCTTCGGAATCTATGGACTA
Found at i:58190 original size:21 final size:21
Alignment explanation
Indices: 58164--58203 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
58154 TCGAAGTTTT
*
58164 ATGCATCGGTGCACTGTAGCA
1 ATGCATCGATGCACTGTAGCA
58185 ATGCATCGATGCACTGTAG
1 ATGCATCGATGCACTGTAG
58204 TTATGTAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (21 bp):
ATGCATCGATGCACTGTAGCA
Found at i:64163 original size:3 final size:3
Alignment explanation
Indices: 64150--64238 Score: 62
Period size: 3 Copynumber: 31.3 Consensus size: 3
64140 TCTGCCAAAA
* *
64150 AAT AA- AAT AAT AAT AAT AAT AAT AAT -AT AAT AGT AAT AGT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** * * * *
64195 AAT AGT TGT AGT AGT AGT -AT AGT -AT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
64239 GTAGGACGAA
Statistics
Matches: 71, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
2 8 0.11
3 63 0.89
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:64192 original size:17 final size:17
Alignment explanation
Indices: 64159--64241 Score: 71
Period size: 17 Copynumber: 4.9 Consensus size: 17
64149 AAATAAAATA
* *
64159 ATAATAATAATAATAAT
1 ATAATAGTAATAGTAAT
64176 ATAATAGTAATAGTAAT
1 ATAATAGTAATAGTAAT
** *
64193 ATAATAGTTGTAGTAGT
1 ATAATAGTAATAGTAAT
*
64210 AGT-ATAGT-ATAATAAT
1 A-TAATAGTAATAGTAAT
*
64226 AATAATAATAATAGTA
1 -ATAATAGTAATAGTA
64242 GGACGAAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
16 6 0.12
17 40 0.77
18 6 0.12
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (17 bp):
ATAATAGTAATAGTAAT
Done.