Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002127.1 Hibiscus syriacus cultivar Beakdansim tig00004356_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: 55843
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:2894 original size:28 final size:29
Alignment explanation
Indices: 2863--2928 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
2853 AAAATATTAC
* *
2863 TAAAATTAAAA-TATTAAAGA-TTAGGGAT
1 TAAAATTAAAATTATCAAA-ATTTAGGAAT
*
2891 TAAAATAAAAATTATCAAAATTTAGGAAT
1 TAAAATTAAAATTATCAAAATTTAGGAAT
*
2920 TAAATTTAA
1 TAAAATTAA
2929 TATTTACCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 11 0.35
29 20 0.65
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (29 bp):
TAAAATTAAAATTATCAAAATTTAGGAAT
Found at i:4041 original size:14 final size:13
Alignment explanation
Indices: 4022--4068 Score: 69
Period size: 14 Copynumber: 3.5 Consensus size: 13
4012 AATAATATTT
4022 ATAATAATAATACA
1 ATAATAATAATA-A
4036 ATAATAATATATAA
1 ATAATAATA-ATAA
4050 ATAATAAT-ATAA
1 ATAATAATAATAA
4062 ATAATAA
1 ATAATAA
4069 CATGATGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 11 0.34
14 18 0.56
15 3 0.09
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAATAATAATAA
Found at i:4043 original size:26 final size:26
Alignment explanation
Indices: 4011--4068 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
4001 TTTTATCTAT
* *
4011 TAATAATATTTATAATAATAATA-CAA
1 TAATAATATATA-AATAATAATATAAA
4037 TAATAATATATAAATAATAATATAAA
1 TAATAATATATAAATAATAATATAAA
4063 TAATAA
1 TAATAA
4069 CATGATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 10 0.34
26 19 0.66
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
TAATAATATATAAATAATAATATAAA
Found at i:4660 original size:134 final size:136
Alignment explanation
Indices: 4217--4860 Score: 878
Period size: 134 Copynumber: 4.8 Consensus size: 136
4207 AAACTAGTGT
* *
4217 ATGACATTGTTCCTTCGTGATGAGGATGTCT-AGCCATCTTTAAAGATATTTGAGATAACTCGGT
1 ATGACATTGTTCCTTCGTGATGAGGAAGTCTGA-CCATCTTTAAAGATATTTGAGATAACACGGT
* ** *
4281 TCCTTCGTGATGAGGATATCT-GTCTATCTAAGGATGATGCTGCTCCTTTATGATGAGGAATTTT
65 TCCTTCGTGATGAGGACATCTGGT-TATCTAAGGATGATGCTGCTCCTTCGTGATGAGG-ATTCT
4345 GATCAATGG
128 GATCAATGG
* *
4354 AT---ATTGTTCCTTCGTGATGA-GAACGTCT-AGCCATCTTTAAAGATATTTGAGATAATACAG
1 ATGACATTGTTCCTTCGTGATGAGGAA-GTCTGA-CCATCTTTAAAGATATTTGAGATAACACGG
* * *
4414 TTCATTCGTGATGAGGACATCTGG-TATCTAAGGATGATGATGCTTCTTCGTGATGAGGATTTCT
64 TTCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGCTGCTCCTTCGTGATGAGGA-TTCT
**
4478 GATCGGTGG
128 GATCAATGG
* * * * * *
4487 ATGACATTGTTCATTCATGATGAGGACGCCTGACCATCTTAAAAGATATTTGAGATAACACGGAT
1 ATGACATTGTTCCTTCGTGATGAGGAAGTCTGACCATCTTTAAAGATATTTGAGATAACACGGTT
* *
4552 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGCTACTTCTTCGTGATGAGG-TTCTGAT
66 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGCTGCTCCTTCGTGATGAGGATTCTGAT
*
4616 C-GTGG
131 CAATGG
*
4621 ATGACATTGTTCCTTCGTGATGAGGAAATCTGACCATCTTTAAAGATATTTGAGATAACACGGTT
1 ATGACATTGTTCCTTCGTGATGAGGAAGTCTGACCATCTTTAAAGATATTTGAGATAACACGGTT
* *
4686 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGTTGCTCCTTCGTGATGAGGAGTTCTGA
66 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGCTGCTCCTTCGTGATGAGGA-TTCTGA
4751 TCAATGG
130 TCAATGG
* * *
4758 ATGACATTGTTCCTTCGTGATG-CGAATGTCTGGCCATCTTTAAAGATATTTGAGATAACTCGGT
1 ATGACATTGTTCCTTCGTGATGAGGAA-GTCTGACCATCTTTAAAGATATTTGAGATAACACGGT
*
4822 TCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATG
65 TCCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATG
4861 TTTCCTAAAA
Statistics
Matches: 454, Mismatches: 40, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
132 1 0.00
133 44 0.10
134 186 0.41
135 9 0.02
136 79 0.17
137 135 0.30
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (136 bp):
ATGACATTGTTCCTTCGTGATGAGGAAGTCTGACCATCTTTAAAGATATTTGAGATAACACGGTT
CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGCTGCTCCTTCGTGATGAGGATTCTGAT
CAATGG
Found at i:4698 original size:270 final size:270
Alignment explanation
Indices: 4217--4860 Score: 915
Period size: 270 Copynumber: 2.4 Consensus size: 270
4207 AAACTAGTGT
4217 ATGACATTGTTCCTTCGTGATGAGGATGTCT-AGCCATCTTTAAAGATATTTGAGATAACTCGGT
1 ATGACATTGTTCCTTCGTGATGAGGATGTCTGA-CCATCTTTAAAGATATTTGAGATAACTCGGT
* * * *
4281 TCCTTCGTGATGAGGATATCT-GTCTATCTAAGGATGATGCTGCTCCTTTATGATGAGGAATTTT
65 TCCTTCGTGATGAGGACATCTGGT-TATCTAAGGATGATGCTACTCCTTCATGATGAGG-ATTCT
* *
4345 GATCAATGGATATTGTTCCTTCGTGATGAGAACGTCTAGCCATCTTTAAAGATATTTGAGATAAT
128 GATCAATGGATATTGTTCCTTCGTGATGAGAACATCTAGCCATCTTTAAAGATATTTGAGATAAC
* *
4410 ACAGTTCATTCGTGATGAGGACATCTGG-TATCTAAGGATGATGATGCTTCTTCGTGATGAGGAT
193 ACAGTTCATTCGTGATGAGGACATCTGGTTATCTAAGGATGATGATGCTCCTTCGTGATGAGGAG
**
4474 TTCTGATCGGTGG
258 TTCTGATCAATGG
* * * * * * *
4487 ATGACATTGTTCATTCATGATGAGGACGCCTGACCATCTTAAAAGATATTTGAGATAACACGGAT
1 ATGACATTGTTCCTTCGTGATGAGGATGTCTGACCATCTTTAAAGATATTTGAGATAACTCGGTT
* *
4552 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGCTACTTCTTCGTGATGAGG-TTCTGAT
66 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGCTACTCCTTCATGATGAGGATTCTGAT
*
4616 C-GTGGATGACATTGTTCCTTCGTGATGAGGAA-ATCT-GACCATCTTTAAAGATATTTGAGATA
131 CAATGGAT---ATTGTTCCTTCGTGATGA-GAACATCTAG-CCATCTTTAAAGATATTTGAGATA
* * * *
4678 ACACGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGTTGCTCCTTCGTGATGAGG
191 ACACAGTTCATTCGTGATGAGGACATCTGGTTATCTAAGGATGATGATGCTCCTTCGTGATGAGG
4743 AGTTCTGATCAATGG
256 AGTTCTGATCAATGG
* * *
4758 ATGACATTGTTCCTTCGTGATGCGAATGTCTGGCCATCTTTAAAGATATTTGAGATAACTCGGTT
1 ATGACATTGTTCCTTCGTGATGAGGATGTCTGACCATCTTTAAAGATATTTGAGATAACTCGGTT
*
4823 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATG
66 CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATG
4861 TTTCCTAAAA
Statistics
Matches: 331, Mismatches: 35, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
267 5 0.02
268 7 0.02
269 1 0.00
270 176 0.53
271 142 0.43
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (270 bp):
ATGACATTGTTCCTTCGTGATGAGGATGTCTGACCATCTTTAAAGATATTTGAGATAACTCGGTT
CCTTCGTGATGAGGACATCTGGTTATCTAAGGATGATGCTACTCCTTCATGATGAGGATTCTGAT
CAATGGATATTGTTCCTTCGTGATGAGAACATCTAGCCATCTTTAAAGATATTTGAGATAACACA
GTTCATTCGTGATGAGGACATCTGGTTATCTAAGGATGATGATGCTCCTTCGTGATGAGGAGTTC
TGATCAATGG
Found at i:4772 original size:40 final size:42
Alignment explanation
Indices: 4683--4779 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 42
4673 AGATAACACG
**
4683 GTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGTT
1 GTTCCTTCGTGATGAGGACGTCTGG-TATCTAAGGATGACATT
*
4726 GCTCCTTCGTGATGAGGA-GTTCT-G-ATC-AATGGATGACATT
1 GTTCCTTCGTGATGAGGACG-TCTGGTATCTAA-GGATGACATT
4766 GTTCCTTCGTGATG
1 GTTCCTTCGTGATG
4780 CGAATGTCTG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
39 2 0.04
40 24 0.50
42 2 0.04
43 20 0.42
ACGTcount: A:0.19, C:0.16, G:0.29, T:0.36
Consensus pattern (42 bp):
GTTCCTTCGTGATGAGGACGTCTGGTATCTAAGGATGACATT
Found at i:14464 original size:119 final size:122
Alignment explanation
Indices: 14221--14497 Score: 402
Period size: 119 Copynumber: 2.3 Consensus size: 122
14211 CTATGGAATA
* * ** *
14221 TTTAAAAATAATTGTTTTTTCAAAGTTTCAACTAAT-AGAGCTCATTTTCTCAAACCCCATGCAA
1 TTTAAAATTAATTGATTAATCAAAGTTTCAACTAATCAGAGCTAATTTTCTCAAACCCCATGCAA
* * * *
14285 TACCCACGAAAAATTTAAAATTCACGGAAAGAATCCCACGCAAATCTCCATGGAACT
66 TACCCACGAAAAAATTAAAATTCACGCAAAGAATCCCACGCAAATCTCCAAGGAAAT
14342 TTTAAAATTAATTGATTAATCAAAGTTTCAACTAATCAG-GCTAATTTT-TCAAACCCCATGCAA
1 TTTAAAATTAATTGATTAATCAAAGTTTCAACTAATCAGAGCTAATTTTCTCAAACCCCATGCAA
* *
14405 TACCCA-TAAAAAATTAAAATTCATGCAAAGAATCCC-CTGCAAATCTCCAAGGAAAT
66 TACCCACGAAAAAATTAAAATTCACGCAAAGAATCCCAC-GCAAATCTCCAAGGAAAT
*
14461 TTTAAAATTAATTGATTAGTCAAAGTTTCAACTAATC
1 TTTAAAATTAATTGATTAATCAAAGTTTCAACTAATC
14498 TCCACTTCTT
Statistics
Matches: 142, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
118 1 0.01
119 78 0.55
120 21 0.15
121 40 0.28
122 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (122 bp):
TTTAAAATTAATTGATTAATCAAAGTTTCAACTAATCAGAGCTAATTTTCTCAAACCCCATGCAA
TACCCACGAAAAAATTAAAATTCACGCAAAGAATCCCACGCAAATCTCCAAGGAAAT
Found at i:15485 original size:22 final size:22
Alignment explanation
Indices: 15459--15509 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
15449 ATATTACTAA
*
15459 AATTAAAATATTAAAGA-TTAGG
1 AATTAAAATATCAAA-ATTTAGG
*
15481 GATTAAAATATCAAAATTTAGG
1 AATTAAAATATCAAAATTTAGG
15503 AATTAAA
1 AATTAAA
15510 TTTAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.55, C:0.02, G:0.12, T:0.31
Consensus pattern (22 bp):
AATTAAAATATCAAAATTTAGG
Found at i:16187 original size:22 final size:22
Alignment explanation
Indices: 16160--16262 Score: 170
Period size: 22 Copynumber: 4.7 Consensus size: 22
16150 GCAAAATTTA
* *
16160 GCGGCGGAGCAATTGGATGTAG
1 GCGGCGGAGCAGTTGGATATAG
*
16182 GCGGCGGAGCAGTTGGATGTAG
1 GCGGCGGAGCAGTTGGATATAG
16204 GCGGCGGAGCAGTTGGATATAG
1 GCGGCGGAGCAGTTGGATATAG
*
16226 GCGGCGGAGCAGTTAGATATAG
1 GCGGCGGAGCAGTTGGATATAG
16248 GCGGCGGAGCAGTTG
1 GCGGCGGAGCAGTTG
16263 TAGGCATCAC
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 77 1.00
ACGTcount: A:0.21, C:0.15, G:0.47, T:0.17
Consensus pattern (22 bp):
GCGGCGGAGCAGTTGGATATAG
Found at i:16306 original size:16 final size:16
Alignment explanation
Indices: 16281--16319 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
16271 ACCAAAGTCT
*
16281 CCCTAAGGTTGGTGAA
1 CCCTAGGGTTGGTGAA
16297 CCCTAGGGTTGGTGAA
1 CCCTAGGGTTGGTGAA
*
16313 CCTTAGG
1 CCCTAGG
16320 ATTTCTGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (16 bp):
CCCTAGGGTTGGTGAA
Found at i:23160 original size:81 final size:81
Alignment explanation
Indices: 23026--23180 Score: 283
Period size: 81 Copynumber: 1.9 Consensus size: 81
23016 AATGAGGGGT
* *
23026 AAAATCAAAATAAATTAAAATTTAAAGGTCTAAATAGGTAATTGTCCCATTATTCTTTAATGATA
1 AAAATCAAAATAAATTAAAATTTAAAGGCCTAAATAGGTAATTATCCCATTATTCTTTAATGATA
23091 AAAAATTTTGGGAGGC
66 AAAAATTTTGGGAGGC
23107 AAAATCAAAATAAATTAAAATTTAAAGGCCTAAATAGGTAATTATCCCATTATTCTTTAATGATA
1 AAAATCAAAATAAATTAAAATTTAAAGGCCTAAATAGGTAATTATCCCATTATTCTTTAATGATA
*
23172 AAATATTTT
66 AAAAATTTT
23181 TGGGGAGGTG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 71 1.00
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (81 bp):
AAAATCAAAATAAATTAAAATTTAAAGGCCTAAATAGGTAATTATCCCATTATTCTTTAATGATA
AAAAATTTTGGGAGGC
Found at i:26985 original size:21 final size:21
Alignment explanation
Indices: 26959--27003 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
26949 AACGCGATCT
*
26959 CGAATTCGGAAAATCGCAACG
1 CGAATTCGGAAAATCACAACG
26980 CGAATTCGGAAAATCACAACG
1 CGAATTCGGAAAATCACAACG
27001 CGA
1 CGA
27004 TTTACATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.13
Consensus pattern (21 bp):
CGAATTCGGAAAATCACAACG
Found at i:28978 original size:42 final size:42
Alignment explanation
Indices: 28932--29035 Score: 108
Period size: 42 Copynumber: 2.4 Consensus size: 42
28922 ATGTTAGATA
28932 AAAAATACTAAATAAATATAA-AATAAATC-AAA-GAATAAACAT
1 AAAAATA-TAAATAAATATAATAATAAATCAAAAGGAA-AAA-AT
* *
28974 AAAAA-ATAAAAATAATAAAATAATAAATCAAAAGGAAAAAAT
1 AAAAATATAAATA-AATATAATAATAAATCAAAAGGAAAAAAT
29016 AAAAATAAATAAATAAATAT
1 AAAAAT--ATAAATAAATAT
29036 TATATACTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
40 5 0.10
41 7 0.14
42 20 0.39
43 6 0.12
44 7 0.14
45 6 0.12
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.20
Consensus pattern (42 bp):
AAAAATATAAATAAATATAATAATAAATCAAAAGGAAAAAAT
Found at i:28999 original size:30 final size:33
Alignment explanation
Indices: 28940--29000 Score: 83
Period size: 30 Copynumber: 1.9 Consensus size: 33
28930 TAAAAAATAC
*
28940 TAAATAAATATAAAATAAATCAAAGAATAAACA
1 TAAATAAATATAAAATAAATAAAAGAATAAACA
*
28973 TAAA-AAATA-AAAAT-AATAAAATAATAAA
1 TAAATAAATATAAAATAAATAAAAGAATAAA
29001 TCAAAAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 5 0.19
32 5 0.19
33 4 0.15
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.21
Consensus pattern (33 bp):
TAAATAAATATAAAATAAATAAAAGAATAAACA
Found at i:29574 original size:26 final size:28
Alignment explanation
Indices: 29545--29606 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 28
29535 AACTCTTTTC
* *
29545 TTAATATATAAAA-AA-ATAACTAAATA
1 TTAATATATAAAATAATAAAAATAAATA
*
29571 TTAATA-A-AAAATAATAAAAATATATA
1 TTAATATATAAAATAATAAAAATAAATA
29597 TTAATATATA
1 TTAATATATA
29607 TAATTGATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 4 0.14
25 3 0.10
26 20 0.69
27 1 0.03
28 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (28 bp):
TTAATATATAAAATAATAAAAATAAATA
Found at i:30016 original size:29 final size:30
Alignment explanation
Indices: 29962--30020 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
29952 ATTGCAATTA
29962 AATAGTGACTAAAACATATAAAATTAAAAT
1 AATAGTGACTAAAACATATAAAATTAAAAT
* *
29992 AATAG-GATTAAAATATA-AAATATTAAAAT
1 AATAGTGACTAAAACATATAAA-ATTAAAAT
30021 GTATAGCCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (30 bp):
AATAGTGACTAAAACATATAAAATTAAAAT
Found at i:31367 original size:3 final size:3
Alignment explanation
Indices: 31359--31416 Score: 62
Period size: 3 Copynumber: 18.7 Consensus size: 3
31349 TATTTATTTA
* * *
31359 AAT AAT AAT AAT AAT AAT AAT GTAT AAT AAT AAT AAAT AAA AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT -AAT AAT AAT AAT
*
31406 AAT AAA AAT AA
1 AAT AAT AAT AA
31417 AAGTAAACTG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
3 40 0.89
4 5 0.11
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:31417 original size:6 final size:6
Alignment explanation
Indices: 31382--31423 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
31372 ATAATAATGT
* *
31382 ATAATA ATAATAA ATAAAA ATAAAA ATAAAA ATAAAA GTAAA
1 ATAAAA ATAA-AA ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
31424 CTGAAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 28 0.85
7 5 0.15
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (6 bp):
ATAAAA
Found at i:31991 original size:215 final size:215
Alignment explanation
Indices: 31620--32051 Score: 837
Period size: 215 Copynumber: 2.0 Consensus size: 215
31610 GTGTTGATGC
* *
31620 TTTATAGCACAAATTTATGCTTTGCCGTTGAAGTTTAAATTGCCCATCTTTTCATAATAGTAAAA
1 TTTATAGCACAAATTTATGCTTTGACGTTGAAGTTTAAATTGCCCATCTTTTCATAATAATAAAA
*
31685 TAATGATGAGAGCCAAGTGATGGTGTGGGACAAAGTGAGAGTGGTGGCAGAAATAGGACCAAAAT
66 CAATGATGAGAGCCAAGTGATGGTGTGGGACAAAGTGAGAGTGGTGGCAGAAATAGGACCAAAAT
31750 AACATCATTCAAAACTAGAATGGCTTAATGTAGAAATGACCCATGCGTTAAGAAATGCACTACAT
131 AACATCATTCAAAACTAGAATGGCTTAATGTAGAAATGACCCATGCGTTAAGAAATGCACTACAT
31815 ATTTAAAATCCAAACAGAAG
196 ATTTAAAATCCAAACAGAAG
31835 TTTATAGCACAAATTTATGCTTTGACGTTGAAGTTTAAATTGCCCATCTTTTCATAATAATAAAA
1 TTTATAGCACAAATTTATGCTTTGACGTTGAAGTTTAAATTGCCCATCTTTTCATAATAATAAAA
31900 CAATGATGAGAGCCAAGTGATGGTGTGGGACAAAGTGAGAGTGGTGGCAGAAATAGGACCAAAAT
66 CAATGATGAGAGCCAAGTGATGGTGTGGGACAAAGTGAGAGTGGTGGCAGAAATAGGACCAAAAT
31965 AACATCATTCAAAACTAGAATGGCTTAATGTAGAAATGACCCATGCGTTAAGAAATGCACTACAT
131 AACATCATTCAAAACTAGAATGGCTTAATGTAGAAATGACCCATGCGTTAAGAAATGCACTACAT
32030 ATTTAAAATCCAAACAGAAG
196 ATTTAAAATCCAAACAGAAG
32050 TT
1 TT
32052 AAAAGGGAGC
Statistics
Matches: 214, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
215 214 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (215 bp):
TTTATAGCACAAATTTATGCTTTGACGTTGAAGTTTAAATTGCCCATCTTTTCATAATAATAAAA
CAATGATGAGAGCCAAGTGATGGTGTGGGACAAAGTGAGAGTGGTGGCAGAAATAGGACCAAAAT
AACATCATTCAAAACTAGAATGGCTTAATGTAGAAATGACCCATGCGTTAAGAAATGCACTACAT
ATTTAAAATCCAAACAGAAG
Found at i:34306 original size:39 final size:39
Alignment explanation
Indices: 34223--34306 Score: 96
Period size: 39 Copynumber: 2.2 Consensus size: 39
34213 TACTTTTGGG
* *
34223 GTCTTCTCAATTTGTCTGAAGATACCATGTAGTCGTGAA
1 GTCTTCTCAATTTGTCTGAAGACACCATGCAGTCGTGAA
* ** * * *
34262 ATCTTCTTTATTTTTCTGAAGACGCCATGCAGTCGTGGA
1 GTCTTCTCAATTTGTCTGAAGACACCATGCAGTCGTGAA
34301 GTCTTC
1 GTCTTC
34307 ATATTTAACT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (39 bp):
GTCTTCTCAATTTGTCTGAAGACACCATGCAGTCGTGAA
Found at i:35473 original size:24 final size:24
Alignment explanation
Indices: 35423--35489 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
35413 TATAACATGT
*
35423 TTTTCTCTATTCTTGTGG-TATGTA
1 TTTTCTCTATTCTTGTGGCTA-GCA
35447 TTTTCTCTATTCTTGTGGCTCA-CA
1 TTTTCTCTATTCTTGTGGCT-AGCA
*
35471 TTTTCTCTGTTCTTGTGGC
1 TTTTCTCTATTCTTGTGGC
35490 ATGATCCTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
24 37 0.95
25 1 0.03
26 1 0.03
ACGTcount: A:0.09, C:0.19, G:0.16, T:0.55
Consensus pattern (24 bp):
TTTTCTCTATTCTTGTGGCTAGCA
Found at i:50095 original size:20 final size:22
Alignment explanation
Indices: 50072--50117 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
50062 GGATGTACAA
50072 ATATAATA-T-TAAATGTTAAT
1 ATATAATATTATAAATGTTAAT
**
50092 ATATTTTATTATAAATGTTAAT
1 ATATAATATTATAAATGTTAAT
50114 ATAT
1 ATAT
50118 GACGTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 1 0.05
22 15 0.68
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
ATATAATATTATAAATGTTAAT
Found at i:52750 original size:13 final size:13
Alignment explanation
Indices: 52732--52765 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
52722 TAAGATTTTC
52732 TTTGAAAATCATT
1 TTTGAAAATCATT
52745 TTTG-AAATCATT
1 TTTGAAAATCATT
52757 TTTGAAAAT
1 TTTGAAAAT
52766 TACTTCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (13 bp):
TTTGAAAATCATT
Found at i:54542 original size:13 final size:13
Alignment explanation
Indices: 54524--54557 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
54514 AATGGGCAAA
* *
54524 TTTGAAAACTATT
1 TTTGAAAACAATG
54537 TTTGAAAACAATG
1 TTTGAAAACAATG
54550 TTTGAAAA
1 TTTGAAAA
54558 TTAATATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (13 bp):
TTTGAAAACAATG
Done.