Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008327.1 Hibiscus syriacus cultivar Beakdansim tig00111034_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: 76986
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:5629 original size:141 final size:142
Alignment explanation
Indices: 5370--5634 Score: 388
Period size: 141 Copynumber: 1.9 Consensus size: 142
5360 TCTATAGTAA
* * * **
5370 GAATAAGGTGGTTACCGATCGATTTTGTTTAATTCATTATTGCGTTATTGTACCGGTACATTGTG
1 GAATAAGGCGGTTACCAATCAATTTTGTTTAACGCATTATTGCGTTATTGTACCGGTACATTGTG
* *
5435 TACTTGGAGTAGTACTTTGTGTACTATAACACTATGTGTGAAATGATGTTGTTCATAATGAGCAC
66 TACTTGGAGTAGTACTATGTGTACTATAACACTATGTGTGAAATGATGGTGTTCATAATGAGCAC
5500 TTGTTAGTACAT
131 TTGTTAGTACAT
* * * *
5512 GAATAAGGCGGTTATCAATCAATTTTGTTTAACGCATTATTGTGTTATTGTACC-TTACTTTGTG
1 GAATAAGGCGGTTACCAATCAATTTTGTTTAACGCATTATTGCGTTATTGTACCGGTACATTGTG
* * * *
5576 TACTTGGAGTAGTACTATGTGTACTATGATACTATGTGTGCATTGATGGTGTTCATAAT
66 TACTTGGAGTAGTACTATGTGTACTATAACACTATGTGTGAAATGATGGTGTTCATAAT
5635 AAGTTTTGAA
Statistics
Matches: 108, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
141 61 0.56
142 47 0.44
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.41
Consensus pattern (142 bp):
GAATAAGGCGGTTACCAATCAATTTTGTTTAACGCATTATTGCGTTATTGTACCGGTACATTGTG
TACTTGGAGTAGTACTATGTGTACTATAACACTATGTGTGAAATGATGGTGTTCATAATGAGCAC
TTGTTAGTACAT
Found at i:9769 original size:15 final size:16
Alignment explanation
Indices: 9737--9769 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
9727 AAAATCTTTC
9737 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
9753 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
9768 TT
1 TT
9770 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:15818 original size:20 final size:20
Alignment explanation
Indices: 15793--15833 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
15783 TTAAACGGGT
15793 ACTAAAATAAACAAAAACTA
1 ACTAAAATAAACAAAAACTA
*
15813 ACTAAAATAAACAGAAACTA
1 ACTAAAATAAACAAAAACTA
15833 A
1 A
15834 ACCTTAAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.68, C:0.15, G:0.02, T:0.15
Consensus pattern (20 bp):
ACTAAAATAAACAAAAACTA
Found at i:18988 original size:157 final size:156
Alignment explanation
Indices: 18644--19162 Score: 704
Period size: 156 Copynumber: 3.3 Consensus size: 156
18634 CCCGATTTCA
* * * * *
18644 TTATTTATTCAATTCCTCCTTTATTTTAAGTCCGTCTTTTTACCAAACTTGAGCCACATGCTCCT
1 TTATTTCTTCAATTCGTCATTTATTTTAAGTCC-T-TTTTTACCAAATTTGAGCCACATGCTTCT
* * * *
18709 AAACCTTAATAGAATACATGTTTACTTTCAATTCCTCTTTTTGATAAC-AACTTTTTATTTTTCA
64 AAACCATAGTAGAATACATGTATACTTTCAATTCCTC-TTTTGATAACAAATTTTTTATTTTTCA
*
18773 ATTTAGTCCTTCAATTTTTCATAATCTCT
128 ATTTAGTCCTTCAATTTTTCATAATCTCC
* * * *
18802 TTATTTCTTCAATTTGTAATTTATTTTAAGTCCTTTTTTACCAAATTTTAGTCACATGCTTCTAA
1 TTATTTCTTCAATTCGTCATTTATTTTAAGTCCTTTTTTACCAAATTTGAGCCACATGCTTCTAA
* *
18867 ACCATAGTAGAATACATGTGTAATTTCAATTCCTCTCTTTGATAACAAATTTTTTATTTTTCAAT
66 ACCATAGTAGAATACATGTATACTTTCAATTCCTCT-TTTGATAACAAATTTTTTATTTTTCAAT
18932 TTAGTCCTTCAATTTTTCATAATCTCC
130 TTAGTCCTTCAATTTTTCATAATCTCC
* *
18959 TTATTTCTTCAATTCATCATTTATTTTAAGT-CTTTTTTACCAACTTTGAGCCACATG-TTCCTA
1 TTATTTCTTCAATTCGTCATTTATTTTAAGTCCTTTTTTACCAAATTTGAGCCACATGCTT-CTA
* * * *
19022 AACCATAGTAGAATACATGCATACTTTCAATTCCTCTTTTTATTACAAATTATTTATTTTTCAAT
65 AACCATAGTAGAATACATGTATACTTTCAATTCCTCTTTTGATAACAAATTTTTTATTTTTCAAT
* *
19087 TTGGTCCTTCAATTTTTCATAATCTAC
130 TTAGTCCTTCAATTTTTCATAATCTCC
* * *
19114 TTATTCCTTCAATTTGTCATTT-TTTTAAGTTCATTTTTTTACCAAATTT
1 TTATTTCTTCAATTCGTCATTTATTTTAAG-TC-CTTTTTTACCAAATTT
19163 CACATGCTCA
Statistics
Matches: 321, Mismatches: 34, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
154 7 0.02
155 73 0.23
156 127 0.40
157 86 0.27
158 28 0.09
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.49
Consensus pattern (156 bp):
TTATTTCTTCAATTCGTCATTTATTTTAAGTCCTTTTTTACCAAATTTGAGCCACATGCTTCTAA
ACCATAGTAGAATACATGTATACTTTCAATTCCTCTTTTGATAACAAATTTTTTATTTTTCAATT
TAGTCCTTCAATTTTTCATAATCTCC
Found at i:19217 original size:155 final size:148
Alignment explanation
Indices: 18746--19217 Score: 459
Period size: 155 Copynumber: 3.0 Consensus size: 148
18736 TCAATTCCTC
* *
18746 TTTTTGATAACAACTT-TTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCTTTATTTCT
1 TTTTTTATAACAAATTATTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTC-TTATTTCT
* *
18810 TCAATTTGTAATTTATTTTAAGTCCTTTTTTACCAAATTTTAGTCACATGCTTCTA-AACCATAG
65 TCAATTTGTCATTTATTTTAAGT-CTTTTTTACCAAA--TT--TCACATGC-TC-ACTACCATAG
* * * *
18874 TAGAATACATGTGTAATTTCAATTCCTC
123 TAGAATAC-TATGTAACTTCAATT-TTT
* * *
18902 TCTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCCTTATTTCT
1 TTTTTTATAACAAATTATTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCT-CTTATTTCT
** * *
18967 TCAATTCATCATTTATTTTAAGTCTTTTTTACCAACTTTGAGCCACATGTTC-CTAAACCATAGT
65 TCAATTTGTCATTTATTTTAAGTCTTTTTTACCAAATTT----CACATGCTCACT--ACCATAGT
* **
19031 AGAATAC-ATGCATACTTTCAATTCCT
124 AGAATACTATGTA-AC-TTCAATTTTT
* * * *
19057 CTTTTTATTACAAATTATTTATTTTTCAATTTGGTCCTTCAATTTTTCATAATCTACTTATTCCT
1 TTTTTTATAACAAATTATTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCT-CTTATTTCT
*
19122 TCAATTTGTCATTT-TTTTAAGTTCATTTTTTTACCAAATTTCACATGCTCACGTACCATAATAG
65 TCAATTTGTCATTTATTTTAAG-TC--TTTTTTACCAAATTTCACATGCTCAC-TACCATAGTAG
19186 AATACTTATGTAACTTCAATTGTTAT
126 AATAC-TATGTAACTTCAATT-TT-T
19212 TTTTTT
1 TTTTTT
19218 TACTAAAGAT
Statistics
Matches: 266, Mismatches: 30, Indels: 41
0.79 0.09 0.12
Matches are distributed among these distances:
152 1 0.00
153 29 0.11
154 15 0.06
155 86 0.32
156 54 0.20
157 80 0.30
158 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (148 bp):
TTTTTTATAACAAATTATTTATTTTTCAATTTAGTCCTTCAATTTTTCATAATCTCTTATTTCTT
CAATTTGTCATTTATTTTAAGTCTTTTTTACCAAATTTCACATGCTCACTACCATAGTAGAATAC
TATGTAACTTCAATTTTT
Found at i:20474 original size:29 final size:29
Alignment explanation
Indices: 20431--20513 Score: 121
Period size: 29 Copynumber: 2.9 Consensus size: 29
20421 TAAACTCAAA
*
20431 GTGGTAGACACGTTTCTTCATATTAAACT
1 GTGGTAGACAAGTTTCTTCATATTAAACT
* *
20460 GTGGTAGACAAGTTTCTTCACATTAAATT
1 GTGGTAGACAAGTTTCTTCATATTAAACT
* *
20489 GTGGTAGACAATTTTATTCATATTA
1 GTGGTAGACAAGTTTCTTCATATTA
20514 GCATCTTGAG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (29 bp):
GTGGTAGACAAGTTTCTTCATATTAAACT
Found at i:28093 original size:13 final size:14
Alignment explanation
Indices: 28074--28107 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
28064 TTGGATGATA
*
28074 TTTATTTATTTTAC
1 TTTATTTAATTTAC
28088 -TTATTTAATTTAC
1 TTTATTTAATTTAC
28101 TTTATTT
1 TTTATTT
28108 TGTACTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATTTAATTTAC
Found at i:30614 original size:27 final size:25
Alignment explanation
Indices: 30583--30639 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 25
30573 ATAGATAAAA
30583 TTTATTTAAATTCAAATTAAAAAACAT
1 TTTATTTAAATTCAAATT--AAAACAT
*
30610 TTTATTTAAATTCAAATTTAAACAT
1 TTTATTTAAATTCAAATTAAAACAT
30635 TTTAT
1 TTTAT
30640 ATGTTGGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 11 0.38
27 18 0.62
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTATTTAAATTCAAATTAAAACAT
Found at i:32849 original size:29 final size:29
Alignment explanation
Indices: 32806--32888 Score: 121
Period size: 29 Copynumber: 2.9 Consensus size: 29
32796 TAAACTCAAA
*
32806 GTGGTAGACACGTTTCTTCATATTAAACT
1 GTGGTAGACAAGTTTCTTCATATTAAACT
* *
32835 GTGGTAGACAAGTTTCTTCACATTAAATT
1 GTGGTAGACAAGTTTCTTCATATTAAACT
* *
32864 GTGGTAGACAAGTTTATTTATATTA
1 GTGGTAGACAAGTTTCTTCATATTA
32889 GCATCTTGAG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (29 bp):
GTGGTAGACAAGTTTCTTCATATTAAACT
Found at i:39803 original size:21 final size:20
Alignment explanation
Indices: 39779--39855 Score: 59
Period size: 21 Copynumber: 3.8 Consensus size: 20
39769 ATAAAAATAA
*
39779 TTTATTTTTATTTTTAGTATT
1 TTTATTTTTATTTTTAG-AAT
* *
39800 TTTATATTTAATTTTTA-ACAA
1 TTTAT-TTTTATTTTTAGA-AT
*
39821 TTTATTCTTA-TTTTAGAAAT
1 TTTATTTTTATTTTTAG-AAT
*
39841 TTTATATTTATTTTT
1 TTTATTTTTATTTTT
39856 TTGAATATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
19 5 0.12
20 13 0.30
21 15 0.35
22 10 0.23
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTTATTTTTATTTTTAGAAT
Found at i:39857 original size:42 final size:42
Alignment explanation
Indices: 39777--39856 Score: 117
Period size: 41 Copynumber: 1.9 Consensus size: 42
39767 TAATAAAAAT
* * *
39777 AATTTATTTTTATTTTTAGTATTTTTATATTTAATTTTTAAC
1 AATTTATTCTTATTTTTAGAAATTTTATATTTAATTTTTAAC
*
39819 AATTTATTCTTA-TTTTAGAAATTTTATATTTATTTTTT
1 AATTTATTCTTATTTTTAGAAATTTTATATTTAATTTTT
39857 TGAATATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
41 23 0.68
42 11 0.32
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (42 bp):
AATTTATTCTTATTTTTAGAAATTTTATATTTAATTTTTAAC
Found at i:40459 original size:13 final size:14
Alignment explanation
Indices: 40440--40473 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
40430 TTGGATGATA
*
40440 TTTATTTATTTTAC
1 TTTATTTAATTTAC
40454 -TTATTTAATTTAC
1 TTTATTTAATTTAC
40467 TTTATTT
1 TTTATTT
40474 TGTACTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATTTAATTTAC
Found at i:42264 original size:35 final size:35
Alignment explanation
Indices: 42191--42265 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
42181 CGTCACTAAC
**
42191 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
42226 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
42261 AGTAA
1 AGTAA
42266 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:42404 original size:23 final size:23
Alignment explanation
Indices: 42344--42418 Score: 105
Period size: 24 Copynumber: 3.2 Consensus size: 23
42334 CATAATTCAA
*
42344 GTCAAGTATCATATCAGAATCCAG
1 GTCAA-TATCAGATCAGAATCCAG
* *
42368 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAG
42392 GTCAATATCAGATCAGAATCCAG
1 GTCAATATCAGATCAGAATCCAG
42415 GTCA
1 GTCA
42419 GGATCATAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.47
24 24 0.53
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAG
Found at i:42424 original size:23 final size:23
Alignment explanation
Indices: 42348--42433 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
42338 ATTCAAGTCA
*
42348 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
42371 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
42395 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
* * *
42418 AGGATCATAACAGAAT
1 AGTATCAGATCAGAAT
42434 TCAAGTCGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 33 0.61
24 21 0.39
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:42451 original size:47 final size:47
Alignment explanation
Indices: 42327--42440 Score: 131
Period size: 47 Copynumber: 2.4 Consensus size: 47
42317 TATATCAAAA
* * * * *
42327 ATCAAAACATAATTCAAGTCAAGTATCATATCAGAATCCAGGTCATGT
1 ATCAGAACAGAATCCAAGTCAA-TATCAGATCAGAATCCAGGTCATGG
* *
42375 ATCAGATCAGAATCCATGTCAATATCAGATCAGAATCCAGGTCA-GG
1 ATCAGAACAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
* *
42421 ATCATAACAGAATTCAAGTC
1 ATCAGAACAGAATCCAAGTC
42441 GGAAATCAGA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 17 0.31
47 21 0.38
48 17 0.31
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (47 bp):
ATCAGAACAGAATCCAAGTCAATATCAGATCAGAATCCAGGTCATGG
Found at i:43600 original size:18 final size:18
Alignment explanation
Indices: 43579--43613 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43569 TTCCATCAGG
*
43579 TCTTATTATTTAATTTAA
1 TCTTATCATTTAATTTAA
*
43597 TCTTATCATTTACTTTA
1 TCTTATCATTTAATTTA
43614 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (18 bp):
TCTTATCATTTAATTTAA
Found at i:47259 original size:23 final size:22
Alignment explanation
Indices: 47233--47286 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
47223 TCAAAAACTT
47233 AAATATATTAATACGAAAAA-TAA
1 AAATATATT-ATAC-AAAAATTAA
* *
47256 AAATTAAATTATTCAAAAATTAA
1 AAA-TATATTATACAAAAATTAA
47279 AAATATAT
1 AAATATAT
47287 ATTATTACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 9 0.35
23 12 0.46
24 5 0.19
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATATATTATACAAAAATTAA
Found at i:48700 original size:32 final size:33
Alignment explanation
Indices: 48618--48718 Score: 95
Period size: 32 Copynumber: 3.1 Consensus size: 33
48608 CTAAGGTGAC
*
48618 CTTTGGGTAGGCTCTT-AGGCCCC-GAGATACTGC-
1 CTTT-GGTAGGCTCTTAAGGCCCCAAAG-TACT-CT
*
48651 CTTGGGTAGGCTCTTAA-GCCCCTAAAGTACTCT
1 CTTTGGTAGGCTCTTAAGGCCCC-AAAGTACTCT
* *
48684 CTTTGGTAGGCT-TTAAGGCCCCAAGGTATTCT
1 CTTTGGTAGGCTCTTAAGGCCCCAAAGTACTCT
48716 CTT
1 CTT
48719 AGGATGGCTC
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
32 32 0.55
33 24 0.41
34 2 0.03
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.32
Consensus pattern (33 bp):
CTTTGGTAGGCTCTTAAGGCCCCAAAGTACTCT
Found at i:53127 original size:16 final size:16
Alignment explanation
Indices: 53106--53139 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
53096 TTACTATTCA
*
53106 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
53122 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
53138 CG
1 CG
53140 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:66349 original size:30 final size:30
Alignment explanation
Indices: 66313--66709 Score: 740
Period size: 30 Copynumber: 13.2 Consensus size: 30
66303 TCCGAATGAC
66313 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
66343 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
66373 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
66403 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
66433 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
66463 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
66493 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
66523 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
66553 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
66583 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
66613 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
66643 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
66673 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
66703 CTATCCA
1 CTATCCA
66710 TATTTTCCTT
Statistics
Matches: 357, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 357 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:67031 original size:20 final size:20
Alignment explanation
Indices: 67006--67106 Score: 106
Period size: 20 Copynumber: 5.3 Consensus size: 20
66996 TTCATATTCT
67006 TTCTTATGTCCTTTTCATAC
1 TTCTTATGTCCTTTTCATAC
* * *
67026 TTCTTATTTCATATTC-T--
1 TTCTTATGTCCTTTTCATAC
67043 TTCTTATGTCCTTTTCATAC
1 TTCTTATGTCCTTTTCATAC
* * *
67063 TTCTTATTTCATATTC-T--
1 TTCTTATGTCCTTTTCATAC
67080 TTCTTATGTCCTTTTCATAC
1 TTCTTATGTCCTTTTCATAC
67100 TTCTTAT
1 TTCTTAT
67107 TTCATATTCT
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
17 26 0.41
18 2 0.03
19 2 0.03
20 33 0.52
ACGTcount: A:0.16, C:0.22, G:0.03, T:0.59
Consensus pattern (20 bp):
TTCTTATGTCCTTTTCATAC
Found at i:67035 original size:37 final size:37
Alignment explanation
Indices: 66993--67117 Score: 250
Period size: 37 Copynumber: 3.4 Consensus size: 37
66983 ATATTCTGTA
66993 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
1 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
67030 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
1 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
67067 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
1 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
67104 TATTTCATATTCTT
1 TATTTCATATTCTT
67118 ATGAAATCAT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 88 1.00
ACGTcount: A:0.17, C:0.21, G:0.02, T:0.60
Consensus pattern (37 bp):
TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
Found at i:67119 original size:13 final size:12
Alignment explanation
Indices: 66995--67117 Score: 69
Period size: 13 Copynumber: 10.0 Consensus size: 12
66985 ATTCTGTATA
66995 TTTCATATTCTT
1 TTTCATATTCTT
* *
67007 TCTT-AT-GTCCT
1 T-TTCATATTCTT
67018 TTTCATACTTCTT
1 TTTCATA-TTCTT
67031 ATTTCATATTCTT
1 -TTTCATATTCTT
* *
67044 TCTT-AT-GTCCT
1 T-TTCATATTCTT
67055 TTTCATACTTCTT
1 TTTCATA-TTCTT
67068 ATTTCATATTCTT
1 -TTTCATATTCTT
* *
67081 TCTT-AT-GTCCT
1 T-TTCATATTCTT
67092 TTTCATACTTCTT
1 TTTCATA-TTCTT
67105 ATTTCATATTCTT
1 -TTTCATATTCTT
67118 ATGAAATCAT
Statistics
Matches: 84, Mismatches: 12, Indels: 29
0.67 0.10 0.23
Matches are distributed among these distances:
10 6 0.07
11 18 0.21
12 9 0.11
13 30 0.36
14 21 0.25
ACGTcount: A:0.16, C:0.21, G:0.02, T:0.60
Consensus pattern (12 bp):
TTTCATATTCTT
Found at i:71148 original size:30 final size:30
Alignment explanation
Indices: 71110--71506 Score: 722
Period size: 30 Copynumber: 13.2 Consensus size: 30
71100 TCCGAAGGAC
71110 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
71140 CCATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
71170 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
71200 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
71230 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
71260 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
71290 CTGTCCAGAGGTCATAAAGATCCTCGGAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
71320 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
71350 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
71380 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
71410 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
71440 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
71470 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
71500 CTATCCA
1 CTATCCA
71507 TATGTTCCTT
Statistics
Matches: 353, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 353 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:71825 original size:20 final size:20
Alignment explanation
Indices: 71800--71863 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
71790 TTCATATTCT
71800 TTCTTATGTCCTTTTCATAC
1 TTCTTATGTCCTTTTCATAC
* * *
71820 TTCTTATTTCATATTC-T--
1 TTCTTATGTCCTTTTCATAC
71837 TTCTTATGTCCTTTTCATAC
1 TTCTTATGTCCTTTTCATAC
71857 TTCTTAT
1 TTCTTAT
71864 TTCATATTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 13 0.37
18 1 0.03
19 1 0.03
20 20 0.57
ACGTcount: A:0.16, C:0.22, G:0.03, T:0.59
Consensus pattern (20 bp):
TTCTTATGTCCTTTTCATAC
Found at i:71829 original size:37 final size:37
Alignment explanation
Indices: 71787--71874 Score: 176
Period size: 37 Copynumber: 2.4 Consensus size: 37
71777 ATATTCTGTA
71787 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
1 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
71824 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
1 TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
71861 TATTTCATATTCTT
1 TATTTCATATTCTT
71875 ATGAAATCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.17, C:0.20, G:0.02, T:0.60
Consensus pattern (37 bp):
TATTTCATATTCTTTCTTATGTCCTTTTCATACTTCT
Found at i:71852 original size:13 final size:12
Alignment explanation
Indices: 71789--71872 Score: 50
Period size: 13 Copynumber: 6.8 Consensus size: 12
71779 ATTCTGTATA
71789 TTTCATATT-C-
1 TTTCATATTCCT
*
71799 TTTCTTATGTCCT
1 TTTCATAT-TCCT
*
71812 TTTCATACTTCTT
1 TTTCATA-TTCCT
71825 ATTTCATATT-C-
1 -TTTCATATTCCT
*
71836 TTTCTTATGTCCT
1 TTTCATAT-TCCT
*
71849 TTTCATACTTCTT
1 TTTCATA-TTCCT
71862 ATTTCATATTC
1 -TTTCATATTC
71873 TTATGAAATC
Statistics
Matches: 57, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
10 14 0.25
11 2 0.04
12 2 0.04
13 23 0.40
14 16 0.28
ACGTcount: A:0.17, C:0.21, G:0.02, T:0.60
Consensus pattern (12 bp):
TTTCATATTCCT
Found at i:71875 original size:13 final size:13
Alignment explanation
Indices: 71812--71876 Score: 57
Period size: 13 Copynumber: 5.1 Consensus size: 13
71802 CTTATGTCCT
71812 TTTCATACTTCTTA
1 TTTCATA-TTCTTA
71826 TTTCATATTCTT-
1 TTTCATATTCTTA
* *
71838 TCTT-AT-GTCCT-
1 T-TTCATATTCTTA
71849 TTTCATACTTCTTA
1 TTTCATA-TTCTTA
71863 TTTCATATTCTTA
1 TTTCATATTCTTA
71876 T
1 T
71877 GAAATCATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
10 2 0.05
11 6 0.14
12 3 0.07
13 17 0.40
14 14 0.33
ACGTcount: A:0.18, C:0.20, G:0.02, T:0.60
Consensus pattern (13 bp):
TTTCATATTCTTA
Found at i:75240 original size:14 final size:13
Alignment explanation
Indices: 75221--75272 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
75211 GTATCTACCA
75221 AAAAAAATCAAACT
1 AAAAAAAT-AAACT
* *
75235 AAAAAAGGTAAATAT
1 AAAAAA-ATAAA-CT
75250 AAAAAAATAAACT
1 AAAAAAATAAACT
75263 -AAAAAATAAA
1 AAAAAAATAAA
75273 GCGATAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
12 10 0.31
13 1 0.03
14 13 0.41
15 8 0.25
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (13 bp):
AAAAAAATAAACT
Found at i:75281 original size:28 final size:28
Alignment explanation
Indices: 75221--75273 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
75211 GTATCTACCA
*
75221 AAAAAAATCAAACTAAAAAAGGTAAATAT
1 AAAAAAATCAAACTAAAAAA-GTAAAGAT
75250 AAAAAAAT-AAACTAAAAAA-TAAAG
1 AAAAAAATCAAACTAAAAAAGTAAAG
75274 CGATAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
28 11 0.48
29 8 0.35
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.15
Consensus pattern (28 bp):
AAAAAAATCAAACTAAAAAAGTAAAGAT
Found at i:75298 original size:24 final size:24
Alignment explanation
Indices: 75267--75315 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
75257 TAAACTAAAA
75267 AATAAAGCGATAAAATTGGGTTGC
1 AATAAAGCGATAAAATTGGGTTGC
75291 AATAAAGCGATAAAATTGGGTTGC
1 AATAAAGCGATAAAATTGGGTTGC
75315 A
1 A
75316 TCCTAGTAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.08, G:0.24, T:0.24
Consensus pattern (24 bp):
AATAAAGCGATAAAATTGGGTTGC
Done.