Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008297.1 Hibiscus syriacus cultivar Beakdansim tig00110983_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: 128232
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5506 original size:24 final size:22
Alignment explanation
Indices: 5478--5557 Score: 83
Period size: 24 Copynumber: 3.5 Consensus size: 22
5468 CACTTAACAA
5478 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CC-TTGAATG
* *
5502 TGCATCGATGTATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
*
5522 ATGCACCGATGCATGCCTTGAATG
1 -TGCATCGATGCAT-CCTTGAATG
5546 TGCATCGATGCA
1 TGCATCGATGCA
5558 CAAGATCATG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 11 0.24
22 2 0.04
23 13 0.28
24 16 0.35
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.29
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:8101 original size:21 final size:21
Alignment explanation
Indices: 8077--8116 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
8067 TTTTCAAAGG
*
8077 CATGCACCGATGCATCAATAC
1 CATGCACCGATACATCAATAC
*
8098 CATGCATCGATACATCAAT
1 CATGCACCGATACATCAAT
8117 GAATAAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.30, G:0.12, T:0.23
Consensus pattern (21 bp):
CATGCACCGATACATCAATAC
Found at i:8166 original size:19 final size:19
Alignment explanation
Indices: 8142--8180 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
8132 TCGAATGCAT
8142 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
8161 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
8180 T
1 T
8181 GATTTAATTA
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:8204 original size:64 final size:65
Alignment explanation
Indices: 8077--8242 Score: 194
Period size: 64 Copynumber: 2.5 Consensus size: 65
8067 TTTTCAAAGG
* *
8077 CATGCACCGATGCA-TCAATACCATGCATCGATACA-TCAATGAATAAATTGAAACATCGAATGC
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCACTC-ATGAATAAATTAAAACATCGAATGC
8140 ATTC
62 ATTC
* * *
8144 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTC
* * **
8208 GATGCATCGATGCACAATCCATGCATCGATGCACT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACT
8243 AGGAGTCCAA
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
64 55 0.62
65 14 0.16
66 3 0.03
67 14 0.16
68 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (65 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTC
Found at i:11838 original size:23 final size:23
Alignment explanation
Indices: 11812--11880 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
11802 TAGGGACATC
*
11812 TTATATGGCACTTCAGTGCATTT
1 TTATGTGGCACTTCAGTGCATTT
* *
11835 TTATGCGGCACTT-AGGTGCAATT
1 TTATGTGGCACTTCA-GTGCATTT
* *
11858 CTATGTGGCACTTCGGTGCATTT
1 TTATGTGGCACTTCAGTGCATTT
11881 ATACGAGCTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (23 bp):
TTATGTGGCACTTCAGTGCATTT
Found at i:14770 original size:20 final size:20
Alignment explanation
Indices: 14745--14785 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
14735 TAAAATAATT
*
14745 ATAATATATAA-ATTAATAAA
1 ATAATA-ATAATATAAATAAA
14765 ATAATAATAATATAAATAAA
1 ATAATAATAATATAAATAAA
14785 A
1 A
14786 ATATTTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAATAATAATATAAATAAA
Found at i:14860 original size:38 final size:37
Alignment explanation
Indices: 14789--14860 Score: 90
Period size: 38 Copynumber: 1.9 Consensus size: 37
14779 AATAAAAATA
*
14789 TTTTCAAAAACATATAATATATAAATTTCTAAAATGT
1 TTTTCAAAAACATATAATATACAAATTTCTAAAATGT
* * * *
14826 TTTTTAAAAACTATATATTATACATATTTTTAAAA
1 TTTTCAAAAAC-ATATAATATACAAATTTCTAAAA
14861 ACCGTTTGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 10 0.34
38 19 0.66
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.44
Consensus pattern (37 bp):
TTTTCAAAAACATATAATATACAAATTTCTAAAATGT
Found at i:15778 original size:15 final size:15
Alignment explanation
Indices: 15758--15793 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
15748 ATGTCACATT
15758 CAGAGCTAATTCTTA
1 CAGAGCTAATTCTTA
15773 CAGAGCTAATTCTTA
1 CAGAGCTAATTCTTA
15788 CAGAGC
1 CAGAGC
15794 CTCTGAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (15 bp):
CAGAGCTAATTCTTA
Found at i:16340 original size:2 final size:2
Alignment explanation
Indices: 16333--16375 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
16323 GTATCATAAT
16333 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16375 T
1 T
16376 TTAAATAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30451 original size:22 final size:22
Alignment explanation
Indices: 30426--30546 Score: 190
Period size: 22 Copynumber: 5.5 Consensus size: 22
30416 GATTTGCATG
30426 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
* *
30448 TTATTTTAAACTAAGGATTGAT
1 TTATTTTAAAATATGGATTGAT
**
30470 TTATTTTAAAATATGGA-AAATT
1 TTATTTTAAAATATGGATTGA-T
30492 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
30514 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
30536 TTATTTTAAAA
1 TTATTTTAAAA
30547 AATTTATTAT
Statistics
Matches: 89, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
21 1 0.01
22 87 0.98
23 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.49
Consensus pattern (22 bp):
TTATTTTAAAATATGGATTGAT
Found at i:30627 original size:31 final size:31
Alignment explanation
Indices: 30570--30628 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
30560 AGTTGTATGG
* *
30570 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAATATTACAAAACTAAA
*
30601 ATTATTTAAATTTCAATATTGCAAAACT
1 ATTATTTAAATTTCAATATTACAAAACT
30629 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAATATTACAAAACTAAA
Found at i:43886 original size:21 final size:20
Alignment explanation
Indices: 43845--43886 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
43835 CAACGACTAT
*
43845 GAAAAGGGAAGGGGAATGGA
1 GAAAAGGGAAGGGGAAGGGA
*
43865 GAAAAGGGAGAGGGGAGGGGA
1 GAAAAGGGA-AGGGGAAGGGA
43886 G
1 G
43887 CATGTGTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.57, T:0.02
Consensus pattern (20 bp):
GAAAAGGGAAGGGGAAGGGA
Found at i:44056 original size:22 final size:22
Alignment explanation
Indices: 44009--44070 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 22
43999 TATCTAATTA
* *
44009 TATATATAATAATTTAGAATAG
1 TATACATAATAATATAGAATAG
* *
44031 TATAGATAATAATATA-ATATAT
1 TATACATAATAATATAGA-ATAG
44053 TATAACATACATAATATA
1 TAT-ACATA-ATAATATA
44071 TAAATGTTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 20 0.61
23 4 0.12
24 8 0.24
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (22 bp):
TATACATAATAATATAGAATAG
Found at i:46124 original size:9 final size:8
Alignment explanation
Indices: 46110--46263 Score: 84
Period size: 9 Copynumber: 18.2 Consensus size: 8
46100 GATTTATATT
46110 ATATAATTA
1 ATATAA-TA
*
46119 ATATAAAA
1 ATATAATA
46127 ATATAA-A
1 ATATAATA
*
46134 ATATTATA
1 ATATAATA
46142 TATATAATTA
1 -ATATAA-TA
*
46152 ATATAAGA
1 ATATAATA
46160 TATATAA-A
1 -ATATAATA
*
46168 ATATTATA
1 ATATAATA
46176 TATATAATTA
1 -ATATAA-TA
46186 ATATAA-A
1 ATATAATA
*
46193 ATATATAAA
1 ATATA-ATA
*
46202 ATATTATA
1 ATATAATA
46210 TATATAAGTA
1 -ATATAA-TA
46220 ATATAA-A
1 ATATAATA
46227 ATAT-ATA
1 ATATAATA
* *
46234 AAATATTA
1 ATATAATA
46242 TATATATATA
1 -ATATA-ATA
46252 TATATATATA
1 -ATATA-ATA
46262 AT
1 AT
46264 CGGGGCGGGG
Statistics
Matches: 117, Mismatches: 13, Indels: 30
0.73 0.08 0.19
Matches are distributed among these distances:
6 1 0.01
7 26 0.22
8 16 0.14
9 56 0.48
10 18 0.15
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (8 bp):
ATATAATA
Found at i:46142 original size:34 final size:34
Alignment explanation
Indices: 46103--46249 Score: 260
Period size: 34 Copynumber: 4.3 Consensus size: 34
46093 GGTTTAGGAT
46103 TTATATTATATAATTAATATAAAA-ATATAAAATA
1 TTATA-TATATAATTAATATAAAATATATAAAATA
*
46137 TTATATATATAATTAATATAAGATATATAAAATA
1 TTATATATATAATTAATATAAAATATATAAAATA
46171 TTATATATATAATTAATATAAAATATATAAAATA
1 TTATATATATAATTAATATAAAATATATAAAATA
*
46205 TTATATATATAAGTAATATAAAATATATAAAATA
1 TTATATATATAATTAATATAAAATATATAAAATA
46239 TTATATATATA
1 TTATATATATA
46250 TATATATATA
Statistics
Matches: 109, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
33 17 0.16
34 92 0.84
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (34 bp):
TTATATATATAATTAATATAAAATATATAAAATA
Found at i:46145 original size:2 final size:2
Alignment explanation
Indices: 46134--46261 Score: 67
Period size: 2 Copynumber: 72.5 Consensus size: 2
46124 AAAATATAAA
* *
46134 AT AT -T AT AT AT AT A- AT -T A- AT AT A- AG AT AT AT A- AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
46170 AT -T AT AT AT AT A- AT -T A- AT AT A- AA AT AT AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
46206 -T AT AT AT AT A- AGT A- AT AT A- AA AT AT AT A- AA AT AT -T AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46243 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
46262 ATCGGGGCGG
Statistics
Matches: 101, Mismatches: 6, Indels: 38
0.70 0.04 0.26
Matches are distributed among these distances:
1 18 0.18
2 82 0.81
3 1 0.01
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:47392 original size:29 final size:30
Alignment explanation
Indices: 47359--47426 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
47349 ACAAGCTTTA
* *
47359 GAAAATTTGGGGACC-ATTCTGTAATTTTT-
1 GAAAAGTTGGGGACCAATTC-ATAATTTTTG
47388 GAAAAGTTGGGGACCAATTCATAATTTTTG
1 GAAAAGTTGGGGACCAATTCATAATTTTTG
47418 GAAAAGTTG
1 GAAAAGTTG
47427 TAAATGGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (30 bp):
GAAAAGTTGGGGACCAATTCATAATTTTTG
Found at i:49247 original size:24 final size:24
Alignment explanation
Indices: 49220--49266 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
49210 TACGGTGCAT
*
49220 TTCTACGCGGCACTTCGATGCAAA
1 TTCTACACGGCACTTCGATGCAAA
*
49244 TTCTACATGGCACTTCGATGCAA
1 TTCTACACGGCACTTCGATGCAA
49267 TTTATACGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (24 bp):
TTCTACACGGCACTTCGATGCAAA
Found at i:50146 original size:22 final size:22
Alignment explanation
Indices: 50098--50138 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
50088 CTGAAGTTAG
*
50098 TGTAGCAAGGGTATCGGTACAC
1 TGTAGCAAGGGTATCGATACAC
50120 TGTAGC-AGGGTATCGATAC
1 TGTAGCAAGGGTATCGATAC
50139 CCCTGTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (22 bp):
TGTAGCAAGGGTATCGATACAC
Found at i:50215 original size:22 final size:22
Alignment explanation
Indices: 50175--50218 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
50165 TAGCATTCGG
* *
50175 TACTGTTCATGATATTGTTCAT
1 TACTGTTCACGATACTGTTCAT
*
50197 TACTGTTCACGGTACTGTTCAT
1 TACTGTTCACGATACTGTTCAT
50219 ACCGTATAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.45
Consensus pattern (22 bp):
TACTGTTCACGATACTGTTCAT
Found at i:50507 original size:15 final size:14
Alignment explanation
Indices: 50483--50529 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
50473 GTAATTGGTT
*
50483 TTCTTGAAATTGAA
1 TTCTGGAAATTGAA
*
50497 TTCTGGAAAATGAA
1 TTCTGGAAATTGAA
*
50511 TTACTGGAATTTGAA
1 TT-CTGGAAATTGAA
50526 TTCT
1 TTCT
50530 ATAAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (14 bp):
TTCTGGAAATTGAA
Found at i:50584 original size:14 final size:14
Alignment explanation
Indices: 50545--50585 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
50535 ATAAATTACA
* *
50545 TTTCTGGAAAACGT
1 TTTCCGGAAAATGT
50559 TTTCCGGAAAATGT
1 TTTCCGGAAAATGT
*
50573 TTTCCGTAAAATG
1 TTTCCGGAAAATG
50586 AATTACATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (14 bp):
TTTCCGGAAAATGT
Found at i:50960 original size:22 final size:21
Alignment explanation
Indices: 50884--50963 Score: 67
Period size: 22 Copynumber: 3.7 Consensus size: 21
50874 AATAATAGTG
*
50884 TTATATT-ATATTTTTAAATA
1 TTATATTAATATTATTAAATA
50904 TTA-ATTAGTATATT-TTAAATA
1 TTATATTA--ATATTATTAAATA
*
50925 TCTTTATTAAAATATTATTAAATTA
1 T-TATATT--AATATTATTAAA-TA
50950 TTATATTAATATTA
1 TTATATTAATATTA
50964 AATATATAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
19 3 0.06
20 3 0.06
21 8 0.16
22 13 0.27
23 8 0.16
24 10 0.20
25 4 0.08
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (21 bp):
TTATATTAATATTATTAAATA
Found at i:51149 original size:25 final size:26
Alignment explanation
Indices: 51113--51187 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 26
51103 TTGATTATTT
*
51113 TATTATAATATTAAAAATA-TAATAA
1 TATTATATTATTAAAAATATTAATAA
*
51138 TATTATATTATTAGAAATATTAATAA
1 TATTATATTATTAAAAATATTAATAA
* *
51164 -A-TATATT-TTAAATATTTTAATAA
1 TATTATATTATTAAAAATATTAATAA
51187 T
1 T
51188 TAAATTTGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
23 13 0.30
24 6 0.14
25 18 0.42
26 6 0.14
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (26 bp):
TATTATATTATTAAAAATATTAATAA
Found at i:55446 original size:23 final size:21
Alignment explanation
Indices: 55411--55454 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
55401 TTAATTATTT
55411 AAAAAATTAAATAAAAATATAA
1 AAAAAATTAAATAAAAA-ATAA
*
55433 AAAAACATTTAATAAAAAATAA
1 AAAAA-ATTAAATAAAAAATAA
55455 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAATTAAATAAAAAATAA
Found at i:57454 original size:20 final size:20
Alignment explanation
Indices: 57429--57482 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
57419 GACCAACAAA
57429 TTCGCAACACGAA-CTCCAAT
1 TTCGCAAC-CGAATCTCCAAT
* *
57449 TTCGCAACCCAATTTCCAAT
1 TTCGCAACCGAATCTCCAAT
57469 TTCGCAACGCGAAT
1 TTCGCAAC-CGAAT
57483 ATGTAAATCG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.10
20 22 0.76
21 4 0.14
ACGTcount: A:0.31, C:0.33, G:0.11, T:0.24
Consensus pattern (20 bp):
TTCGCAACCGAATCTCCAAT
Found at i:57493 original size:20 final size:20
Alignment explanation
Indices: 57470--57557 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
57460 ATTTCCAATT
*
57470 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATTTGTAAA
** * **
57490 TCGCATTGCGATTTTCCAAA
1 TCGCAACGCGAATTTGTAAA
* * *
57510 TTCACAACGCAAATCTGTAAA
1 -TCGCAACGCGAATTTGTAAA
57531 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
57551 TCGCAAC
1 TCGCAAC
57558 ACAGAAGTCA
Statistics
Matches: 50, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
20 38 0.76
21 12 0.24
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:57588 original size:20 final size:20
Alignment explanation
Indices: 57563--57617 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
57553 GCAACACAGA
*
57563 AGTCAAATTCACAATGCGAT
1 AGTCAAATTCACAACGCGAT
*
57583 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCACAACGCGAT
*
57603 AGTCAAATTCGCAAC
1 AGTCAAATTCACAAC
57618 TGAATTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (20 bp):
AGTCAAATTCACAACGCGAT
Found at i:57812 original size:14 final size:15
Alignment explanation
Indices: 57793--57830 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
57783 TCCCCATCTC
57793 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
57807 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
57823 TAATTTTT
1 TAATTTTT
57831 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:60869 original size:18 final size:18
Alignment explanation
Indices: 60846--60881 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
60836 AAGCAAAAGG
*
60846 AAATCAAAATCTCAATCA
1 AAATCAAAATCCCAATCA
60864 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
60882 CAACCGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:61223 original size:20 final size:20
Alignment explanation
Indices: 61198--61261 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
61188 AAACCGAAAA
*
61198 TCGCGTTGCGAATTTGGCTT
1 TCGCGTTGCGAATTTGACTT
61218 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTT
* *
61238 TCTCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTT
61258 TCGC
1 TCGC
61262 AATGCTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTT
Found at i:61741 original size:18 final size:18
Alignment explanation
Indices: 61720--61756 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
61710 GTAATTGGAG
61720 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
61738 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
61756 T
1 T
61757 ATAAATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:61763 original size:24 final size:24
Alignment explanation
Indices: 61712--61764 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
61702 TTTCATATGT
* * *
61712 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
61736 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
61760 AATTT
1 AATTT
61765 TGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:62154 original size:39 final size:39
Alignment explanation
Indices: 62067--62155 Score: 135
Period size: 39 Copynumber: 2.3 Consensus size: 39
62057 TCCGATGCTC
* *
62067 ATCAAAATCCAAAGCTCATATGGTGTCAAGCAAAAAGAA
1 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAAGAA
*
62106 ATCAAAATCTAAATCTCATATGGTGCCAAG-AAAAAGGAA
1 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAA-GAA
62145 ATCAAAATCTA
1 ATCAAAATCTA
62156 CAACTTGAGT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 5 0.11
39 41 0.89
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.20
Consensus pattern (39 bp):
ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAAGAA
Found at i:62390 original size:20 final size:20
Alignment explanation
Indices: 62367--62405 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
62357 AATAAGCGTT
* *
62367 GCGATAGTCAAATTTGCAAC
1 GCGAAAGTCAAATTCGCAAC
*
62387 GCGAAAGTTAAATTCGCAA
1 GCGAAAGTCAAATTCGCAA
62406 ACCGAAAATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:62443 original size:20 final size:20
Alignment explanation
Indices: 62414--62469 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
62404 AAACCGAAAA
*
62414 TCGCGTTGCGAATTTGGCTT
1 TCGCGTTGCGAATTTGACTT
*
62434 TCGCGATGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTT
62454 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
62470 TACCTTCAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.14, C:0.20, G:0.29, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTT
Found at i:62610 original size:28 final size:28
Alignment explanation
Indices: 62578--62631 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
62568 ATAATTTTTA
*
62578 TTTACACATCAAATTAAACAAATCAAGT
1 TTTACAAATCAAATTAAACAAATCAAGT
* **
62606 TTTACAAATCAACTTTTACAAATCAA
1 TTTACAAATCAAATTAAACAAATCAA
62632 TTAATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (28 bp):
TTTACAAATCAAATTAAACAAATCAAGT
Found at i:62612 original size:14 final size:14
Alignment explanation
Indices: 62595--62631 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
62585 ATCAAATTAA
*
62595 ACAAATCAAGTTTT
1 ACAAATCAACTTTT
62609 ACAAATCAACTTTT
1 ACAAATCAACTTTT
62623 ACAAATCAA
1 ACAAATCAA
62632 TTAATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.49, C:0.19, G:0.03, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:64102 original size:21 final size:21
Alignment explanation
Indices: 64055--64154 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
64045 GCGGGCAGGA
* **
64055 CCTCTTGAACGATGACAGAAG
1 CCTCTTGAACGATGAGAGGGG
* *
64076 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
64097 CTTCTTCGAATGATGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
**
64119 CCTCTTGAACGAT-AGGAGGCA
1 CCTCTTGAACGATGA-GAGGGG
*
64140 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
64155 TAGGTGCATC
Statistics
Matches: 62, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
20 1 0.02
21 43 0.69
22 18 0.29
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:73210 original size:10 final size:10
Alignment explanation
Indices: 73195--73254 Score: 55
Period size: 10 Copynumber: 6.7 Consensus size: 10
73185 CATTTAATAA
73195 ATAAACGAAC
1 ATAAACGAAC
73205 ATAAACGAAC
1 ATAAACGAAC
73215 ----ACGAAC
1 ATAAACGAAC
73221 ATAAAACGAAC
1 AT-AAACGAAC
73232 ----ACGAAC
1 ATAAACGAAC
73238 ATAAACGAAC
1 ATAAACGAAC
73248 ATAAACG
1 ATAAACG
73255 TTGGAGACCC
Statistics
Matches: 41, Mismatches: 0, Indels: 18
0.69 0.00 0.31
Matches are distributed among these distances:
6 12 0.29
10 23 0.56
11 6 0.15
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.08
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:73229 original size:17 final size:16
Alignment explanation
Indices: 73199--73248 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
73189 TAATAAATAA
73199 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
73215 ACGAACATAAAACGAAC
1 ACGAACAT-AAACGAAC
73232 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
73248 A
1 A
73249 TAAACGTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 17 0.52
17 16 0.48
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:73886 original size:36 final size:36
Alignment explanation
Indices: 73841--73916 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
73831 GTTATAGCAA
73841 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
73877 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
73913 AAAA
1 AAAA
73917 TCCCGAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:74701 original size:14 final size:14
Alignment explanation
Indices: 74684--74729 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
74674 AATGAACATA
74684 AACGAACATAACCG
1 AACGAACATAACCG
74698 AACGAACATAACCG
1 AACGAACATAACCG
* *
74712 AACAAATATAACCG
1 AACGAACATAACCG
74726 AACG
1 AACG
74730 TTCATGAACG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.52, C:0.26, G:0.13, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:87836 original size:29 final size:29
Alignment explanation
Indices: 87779--87836 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
87769 ACTTCAGGAA
* *
87779 GCTTCTAACAATACTGCTAATGTATACAC
1 GCTTCTAACAACACTGCTAATGTACACAC
* *
87808 GCTTCTAACTACACTGCTAATGTGCACAC
1 GCTTCTAACAACACTGCTAATGTACACAC
87837 TGCATTAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (29 bp):
GCTTCTAACAACACTGCTAATGTACACAC
Found at i:88246 original size:15 final size:15
Alignment explanation
Indices: 88226--88255 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
88216 TGTCAAAGGT
88226 GGTAACAAGGGGTCA
1 GGTAACAAGGGGTCA
88241 GGTAACAAGGGGTCA
1 GGTAACAAGGGGTCA
88256 TATGTACTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.40, T:0.13
Consensus pattern (15 bp):
GGTAACAAGGGGTCA
Found at i:89480 original size:29 final size:29
Alignment explanation
Indices: 89425--89480 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
89415 TTCAAGAAGC
* *
89425 TTCTAACAATACTGCTAACGTATACACGT
1 TTCTAACAACACTGCTAACGTACACACGT
* * *
89454 TTCTAACTACACTGCTAATGTGCACAC
1 TTCTAACAACACTGCTAACGTACACAC
89481 TACATTAGTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (29 bp):
TTCTAACAACACTGCTAACGTACACACGT
Found at i:94181 original size:21 final size:21
Alignment explanation
Indices: 94155--94194 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
94145 CAGAACCCCA
*
94155 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
94176 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
94195 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:100781 original size:12 final size:12
Alignment explanation
Indices: 100766--100799 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
100756 GCTGGAGACA
100766 TGGGCACGACTC
1 TGGGCACGACTC
100778 TGGGCACGACTC
1 TGGGCACGACTC
100790 TGGGCACGAC
1 TGGGCACGAC
100800 ACGGTCTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.35, T:0.15
Consensus pattern (12 bp):
TGGGCACGACTC
Found at i:102638 original size:19 final size:19
Alignment explanation
Indices: 102600--102638 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
102590 TTATATTTTT
* **
102600 ATTTTATTTTTTTTGTTTC
1 ATTTTATTTTTATTCATTC
102619 ATTTTATTTTTATTCATTC
1 ATTTTATTTTTATTCATTC
102638 A
1 A
102639 AGCCTGTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.72
Consensus pattern (19 bp):
ATTTTATTTTTATTCATTC
Found at i:108239 original size:20 final size:20
Alignment explanation
Indices: 108193--108246 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
108183 GTCGAGGGTT
108193 CATAGGTCCTTCGGGACAAA
1 CATAGGTCCTTCGGGACAAA
* *
108213 CAGAGGTCCTTCGGGACATA
1 CATAGGTCCTTCGGGACAAA
* *
108233 TATAGGTCATTCGG
1 CATAGGTCCTTCGG
108247 AAAAAATTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (20 bp):
CATAGGTCCTTCGGGACAAA
Found at i:108333 original size:16 final size:17
Alignment explanation
Indices: 108312--108345 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
108302 GTGCACAACC
108312 TCTAT-GTACTCACATA
1 TCTATGGTACTCACATA
*
108328 TCTATGGTTCTCACATA
1 TCTATGGTACTCACATA
108345 T
1 T
108346 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (17 bp):
TCTATGGTACTCACATA
Found at i:117186 original size:33 final size:33
Alignment explanation
Indices: 117149--117215 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
117139 CGCAGAGGAT
*
117149 GCATCCA-CACCATCTGTTGCAGCAGACCTTCGA
1 GCATCCACCA-CATCTGTTGCAACAGACCTTCGA
117182 GCATCCACCACATCTGTTGCAACAGACCTTCGA
1 GCATCCACCACATCTGTTGCAACAGACCTTCGA
117215 G
1 G
117216 GTCGCCTGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.25, C:0.36, G:0.18, T:0.21
Consensus pattern (33 bp):
GCATCCACCACATCTGTTGCAACAGACCTTCGA
Done.