Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007423.1 Hibiscus syriacus cultivar Beakdansim tig00020105_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: 64953
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Found at i:2533 original size:16 final size:16
Alignment explanation
Indices: 2512--2543 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2502 ATTAAAAGAT
2512 ACATATATTTTTAAAA
1 ACATATATTTTTAAAA
*
2528 ACATATTTTTTTAAAA
1 ACATATATTTTTAAAA
2544 TTCAAAAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
ACATATATTTTTAAAA
Found at i:2755 original size:24 final size:24
Alignment explanation
Indices: 2728--2773 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
2718 GATATTAGAA
* *
2728 ATCAAAAAATAATTCAGGTCAGAT
1 ATCAAAAAAGAATTCAGATCAGAT
* *
2752 ATCAGAACAGAATTCAGATCAG
1 ATCAAAAAAGAATTCAGATCAG
2774 GTACCGGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAAAAGAATTCAGATCAGAT
Found at i:4242 original size:13 final size:13
Alignment explanation
Indices: 4224--4256 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
4214 TAGGTACGAA
4224 TTCTCATGGTACT
1 TTCTCATGGTACT
4237 TTCTCATGGTACT
1 TTCTCATGGTACT
4250 TTCTCAT
1 TTCTCAT
4257 TAAGAGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.24, G:0.12, T:0.48
Consensus pattern (13 bp):
TTCTCATGGTACT
Found at i:6099 original size:3 final size:3
Alignment explanation
Indices: 6093--6137 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
6083 CAACAACAAC
6093 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
6138 TGTGAGAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:10139 original size:31 final size:32
Alignment explanation
Indices: 10104--10179 Score: 77
Period size: 31 Copynumber: 2.4 Consensus size: 32
10094 GTAGGCCCTG
*
10104 CGGCCCTAAGATGTGTTCTT-AGTAGGC-CTCA
1 CGGCCCTAAGATGT-ATCTTGAGTAGGCTCTCA
* * * *
10135 CGGCCCCAAAATCTATCTTGGGTAGGCTCTCA
1 CGGCCCTAAGATGTATCTTGAGTAGGCTCTCA
10167 -GGCCCTAAGATGT
1 CGGCCCTAAGATGT
10180 TCCCTTAGGT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
30 4 0.11
31 27 0.77
32 4 0.11
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (32 bp):
CGGCCCTAAGATGTATCTTGAGTAGGCTCTCA
Found at i:14279 original size:42 final size:42
Alignment explanation
Indices: 14220--14304 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
14210 GGGAAACGAA
*
14220 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCGCACAC
1 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
*
14262 CAGAGCTTTGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
1 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
14304 C
1 C
14305 GGCGAGATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (42 bp):
CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
Found at i:16494 original size:23 final size:23
Alignment explanation
Indices: 16405--16513 Score: 62
Period size: 23 Copynumber: 4.5 Consensus size: 23
16395 TTGAAATAAT
*
16405 TATA-ATATATGTATATATTATA
1 TATATATATATATATATATTATA
* *
16427 TA-ATAATAATATAATATGACACTTGTA
1 TATAT-AT-ATAT-ATAT-ATA-TTATA
* *
16454 TATATGT-TATAATGTATATTATA
1 TATATATATAT-ATATATATTATA
*
16477 TATATATATATATATATAATATA
1 TATATATATATATATATATTATA
*
16500 GTATAAAGTATATA
1 -TATATA-TATATA
16514 AACAATAAAG
Statistics
Matches: 66, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
21 1 0.02
22 2 0.03
23 22 0.33
24 14 0.21
25 16 0.24
26 2 0.03
27 7 0.11
28 2 0.03
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (23 bp):
TATATATATATATATATATTATA
Found at i:16505 original size:10 final size:9
Alignment explanation
Indices: 16461--16608 Score: 53
Period size: 10 Copynumber: 15.9 Consensus size: 9
16451 GTATATATGT
*
16461 TATAATGTA
1 TATAATATA
16470 TATTATATATA
1 TA-TA-ATATA
16481 TATATATATA
1 TATA-ATATA
16491 TATAATATA
1 TATAATATA
16500 GTATAA-AGTA
1 -TATAATA-TA
*
16510 TATAA-ACA
1 TATAATATA
16518 -ATAAAGTATAAA
1 TAT-AA-TAT--A
16530 TATAAGTATA
1 TATAA-TATA
16540 TA-AAT-TA
1 TATAATATA
16547 TATAA-ACTA
1 TATAATA-TA
16556 TATAA-ATA
1 TATAATATA
*
16564 TA-AGTATA
1 TATAATATA
*
16572 TA-AGTATA
1 TATAATATA
*
16580 TATAAGTGTA
1 TATAA-TATA
*
16590 TATAAGTGTA
1 TATAA-TATA
16600 TATAGATAT
1 TATA-ATAT
16609 TGTTCTTACA
Statistics
Matches: 115, Mismatches: 7, Indels: 33
0.74 0.05 0.21
Matches are distributed among these distances:
7 7 0.06
8 23 0.20
9 25 0.22
10 44 0.38
11 7 0.06
12 7 0.06
13 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.39
Consensus pattern (9 bp):
TATAATATA
Found at i:16513 original size:2 final size:2
Alignment explanation
Indices: 16468--16504 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
16458 TGTTATAATG
16468 TA TA T- TA TA TA TA TA TA TA TA TA TA TA -A TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
16505 AAGTATATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.06
2 28 0.88
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:16520 original size:23 final size:22
Alignment explanation
Indices: 16479--16533 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
16469 ATATTATATA
* * * *
16479 TATATATATATATATAATATAG
1 TATAAATATATAAACAATAAAG
16501 TATAAAGTATATAAACAATAAAG
1 TATAAA-TATATAAACAATAAAG
16524 TATAAATATA
1 TATAAATATA
16534 AGTATATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.36
Consensus pattern (22 bp):
TATAAATATATAAACAATAAAG
Found at i:16541 original size:14 final size:14
Alignment explanation
Indices: 16524--16579 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
16514 AACAATAAAG
16524 TATAAATATAAGTA
1 TATAAATATAAGTA
*
16538 TATAAATTATATAAACTA
1 TAT-AA--ATAT-AAGTA
16556 TATAAATATAAGTA
1 TATAAATATAAGTA
*
16570 TATAAGTATA
1 TATAAATATA
16580 TATAAGTGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.46
15 6 0.17
17 6 0.17
18 7 0.20
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (14 bp):
TATAAATATAAGTA
Found at i:16542 original size:8 final size:8
Alignment explanation
Indices: 16529--16581 Score: 56
Period size: 8 Copynumber: 6.6 Consensus size: 8
16519 TAAAGTATAA
16529 ATATAAGT
1 ATATAAGT
*
16537 ATATAAATT
1 ATAT-AAGT
*
16546 ATATAAACT
1 ATAT-AAGT
16555 ATATAA--
1 ATATAAGT
16561 ATATAAGT
1 ATATAAGT
16569 ATATAAGT
1 ATATAAGT
16577 ATATA
1 ATATA
16582 TAAGTGTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
6 6 0.15
8 19 0.47
9 15 0.38
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (8 bp):
ATATAAGT
Found at i:16990 original size:50 final size:50
Alignment explanation
Indices: 16916--17028 Score: 165
Period size: 50 Copynumber: 2.3 Consensus size: 50
16906 AATGTTTTTG
*
16916 CGAATAGTATTG-TACTGTATGAATAGTATCGATAATGTGTGAACAACAA
1 CGAATAGTACTGATACTGTATGAATAGTATCGATAATGTGTGAACAACAA
* * **
16965 CGAATAGTACTGATATTGTATGAATAGTATTGATAATGTGTGAACAGTAA
1 CGAATAGTACTGATACTGTATGAATAGTATCGATAATGTGTGAACAACAA
*
17015 CGAACAGTACTGAT
1 CGAATAGTACTGAT
17029 GCTCAAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 11 0.19
50 46 0.81
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (50 bp):
CGAATAGTACTGATACTGTATGAATAGTATCGATAATGTGTGAACAACAA
Found at i:16991 original size:20 final size:20
Alignment explanation
Indices: 16966--17013 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
16956 GAACAACAAC
*
16966 GAATAGTACTGATATTGTAT
1 GAATAGTACTGATAATGTAT
* *
16986 GAATAGTATTGATAATGTGT
1 GAATAGTACTGATAATGTAT
*
17006 GAACAGTA
1 GAATAGTA
17014 ACGAACAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (20 bp):
GAATAGTACTGATAATGTAT
Found at i:17080 original size:20 final size:20
Alignment explanation
Indices: 17055--17095 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
17045 ATGCAAAATG
17055 AGTATCGATACCT-CTACAGT
1 AGTATCGATA-CTACTACAGT
17075 AGTATCGATACTACTACAGT
1 AGTATCGATACTACTACAGT
17095 A
1 A
17096 AAATCAAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTACTACAGT
Found at i:23403 original size:20 final size:20
Alignment explanation
Indices: 23378--23420 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
23368 TATATTAGGC
* *
23378 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
23398 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
23418 TAT
1 TAT
23421 GGAATAATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.56
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:24999 original size:24 final size:21
Alignment explanation
Indices: 24977--25019 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
24967 TAAATATTAC
24977 AAAGGTAGTACCGATACTCATT
1 AAAGG-AGTACCGATACTCATT
*
24999 AAAGGAGTACTGATACTCATT
1 AAAGGAGTACCGATACTCATT
25020 GTCCTGTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (21 bp):
AAAGGAGTACCGATACTCATT
Found at i:26001 original size:8 final size:7
Alignment explanation
Indices: 25980--26022 Score: 52
Period size: 8 Copynumber: 6.0 Consensus size: 7
25970 AAAAATGGAA
25980 ATAAT-T
1 ATAATAT
25986 ATAATAT
1 ATAATAT
25993 ATGAATAT
1 AT-AATAT
*
26001 ATATTAT
1 ATAATAT
26008 ATAATAAT
1 ATAAT-AT
26016 ATAATAT
1 ATAATAT
26023 GACACACACA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
6 5 0.16
7 13 0.41
8 14 0.44
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (7 bp):
ATAATAT
Found at i:26041 original size:2 final size:2
Alignment explanation
Indices: 26036--26283 Score: 75
Period size: 2 Copynumber: 128.5 Consensus size: 2
26026 ACACACACAC
26036 AT AT AT AT AT AT AT AT -T AT A- AT -T AT AT -T AT ACT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * *
26074 -T AT AT AT AT AT AA AGT AT -T A- AT AT -T GGT AT AT AA AT -T AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT -AT AT AT AT AT AT AT
* * *
26113 AT AA ACT AT AA AGT AT AT A- AA AT AT AT AGT AT A- AGT AT AT AT
1 AT AT A-T AT AT A-T AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT
** * * * *
26155 AT A- AT AT AT -T AT GC AT GT AT AT ACT -T A- AGT GT GT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT
* *
26195 AT AT GT -T AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * *
26235 AT GT GT AT AT CAT AT AT GT -T AT AC AT GT AT AT AT GT GT AT GT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26277 AT AT AT A
1 AT AT AT A
26284 AAAGTACATA
Statistics
Matches: 185, Mismatches: 32, Indels: 58
0.67 0.12 0.21
Matches are distributed among these distances:
1 19 0.10
2 155 0.84
3 11 0.06
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (2 bp):
AT
Found at i:26061 original size:11 final size:11
Alignment explanation
Indices: 26047--26077 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
26037 TATATATATA
26047 TATATTATAAT
1 TATATTATAAT
*
26058 TATATTATACT
1 TATATTATAAT
26069 TATATTATA
1 TATATTATA
26078 TATATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (11 bp):
TATATTATAAT
Found at i:26295 original size:43 final size:41
Alignment explanation
Indices: 26248--26330 Score: 103
Period size: 43 Copynumber: 2.0 Consensus size: 41
26238 TGTATATCAT
* * *
26248 ATATGTTATACATGTATATATGTGTATGTATATATAAAAGTAC
1 ATATGTTATACATGTACATATATGTA--TATATACAAAAGTAC
**
26291 ATATGTTATGTATGTACATATATGTATATATACAAAAGTA
1 ATATGTTATACATGTACATATATGTATATATACAAAAGTA
26331 TAGACATAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 13 0.37
43 22 0.63
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (41 bp):
ATATGTTATACATGTACATATATGTATATATACAAAAGTAC
Found at i:27093 original size:15 final size:15
Alignment explanation
Indices: 27073--27105 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
27063 AGTGTGATGA
27073 AAACCTATGGGGGAT
1 AAACCTATGGGGGAT
27088 AAACCTATGGGGGAT
1 AAACCTATGGGGGAT
27103 AAA
1 AAA
27106 AGAGCTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.12, G:0.30, T:0.18
Consensus pattern (15 bp):
AAACCTATGGGGGAT
Found at i:27227 original size:13 final size:13
Alignment explanation
Indices: 27209--27233 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27199 TAACATCACT
27209 TTTCTTTCATTTA
1 TTTCTTTCATTTA
27222 TTTCTTTCATTT
1 TTTCTTTCATTT
27234 TATGAATTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCTTTCATTTA
Found at i:28903 original size:12 final size:12
Alignment explanation
Indices: 28886--28914 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
28876 ACCTGAAAAG
28886 GTGAGTAACAGA
1 GTGAGTAACAGA
28898 GTGAGTAACAGA
1 GTGAGTAACAGA
28910 GTGAG
1 GTGAG
28915 CTTTGGGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.38, T:0.17
Consensus pattern (12 bp):
GTGAGTAACAGA
Found at i:33276 original size:16 final size:15
Alignment explanation
Indices: 33255--33285 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
33245 ATTAAAAGAT
33255 ACATATATTTTTAAAA
1 ACATAT-TTTTTAAAA
33271 ACATATTTTTTAAAA
1 ACATATTTTTTAAAA
33286 TTCAAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
ACATATTTTTTAAAA
Found at i:33497 original size:24 final size:24
Alignment explanation
Indices: 33470--33515 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
33460 GATATTAGAA
* *
33470 ATCAAAAAATAATTCAGGTCAGAT
1 ATCAAAAAAGAATTCAGATCAGAT
* *
33494 ATCAGAACAGAATTCAGATCAG
1 ATCAAAAAAGAATTCAGATCAG
33516 GTACCGGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAAAAGAATTCAGATCAGAT
Found at i:36827 original size:3 final size:3
Alignment explanation
Indices: 36821--36850 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
36811 CAACAACAAC
36821 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
36851 TGTGAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40786 original size:31 final size:32
Alignment explanation
Indices: 40751--40826 Score: 77
Period size: 31 Copynumber: 2.4 Consensus size: 32
40741 GTAGGCCCTG
*
40751 CGGCCCTAAGATGTGTTCTT-AGTAGGC-CTCA
1 CGGCCCTAAGATGT-ATCTTGAGTAGGCTCTCA
* * * *
40782 CGGCCCCAAAATCTATCTTGGGTAGGCTCTCA
1 CGGCCCTAAGATGTATCTTGAGTAGGCTCTCA
40814 -GGCCCTAAGATGT
1 CGGCCCTAAGATGT
40827 TCCCTTAGGT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
30 4 0.11
31 27 0.77
32 4 0.11
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (32 bp):
CGGCCCTAAGATGTATCTTGAGTAGGCTCTCA
Found at i:44216 original size:42 final size:42
Alignment explanation
Indices: 44157--44241 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
44147 GGGAAACGAA
*
44157 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCGCACAC
1 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
*
44199 CAGAGCTTTGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
1 CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
44241 C
1 C
44242 GGCGAGATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (42 bp):
CAGAGCTATGGAAATCAAGCTAGTTAAGAGTGCATCCCACAC
Found at i:46781 original size:23 final size:22
Alignment explanation
Indices: 46740--46794 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
46730 TAATGTATAT
* * * *
46740 TATATATATATATATAATATAG
1 TATAAATATATAAACAATAAAG
46762 TATAAAGTATATAAACAATAAAG
1 TATAAA-TATATAAACAATAAAG
46785 TATAAATATA
1 TATAAATATA
46795 AGTATATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.36
Consensus pattern (22 bp):
TATAAATATATAAACAATAAAG
Found at i:46803 original size:8 final size:8
Alignment explanation
Indices: 46790--46847 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
46780 TAAAGTATAA
46790 ATATAAGT
1 ATATAAGT
*
46798 ATATAAATT
1 ATAT-AAGT
46807 ATATAA--
1 ATATAAGT
46813 ACTAT-A-T
1 A-TATAAGT
46820 ATATAAGT
1 ATATAAGT
46828 ATATAAGT
1 ATATAAGT
*
46836 ATATATGT
1 ATATAAGT
46844 ATAT
1 ATAT
46848 GTTGAACAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
6 5 0.12
7 5 0.12
8 26 0.60
9 7 0.16
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (8 bp):
ATATAAGT
Found at i:46824 original size:30 final size:28
Alignment explanation
Indices: 46740--46840 Score: 107
Period size: 30 Copynumber: 3.5 Consensus size: 28
46730 TAATGTATAT
*
46740 TATATATATATATATAATATAGTATA-AAG
1 TATATAAATATATA-AATATA-TATATAAG
* *
46769 TATATAAACA-ATAAAGTATAAATATAAG
1 TATATAAATATATAAA-TATATATATAAG
46797 TATATAAATTATATAAACTATATATATAAG
1 TATATAAA-TATATAAA-TATATATATAAG
*
46827 TATATAAGTATATA
1 TATATAAATATATA
46841 TGTATATGTT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
27 5 0.08
28 18 0.30
29 15 0.25
30 23 0.38
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (28 bp):
TATATAAATATATAAATATATATATAAG
Found at i:47360 original size:50 final size:50
Alignment explanation
Indices: 47286--47398 Score: 147
Period size: 50 Copynumber: 2.3 Consensus size: 50
47276 AATGTTTTTG
47286 CGAATAGTATTG-TACTGTATGAATAGTACCAATAATGTGTGAACAACAA
1 CGAATAGTATTGATACTGTATGAATAGTACCAATAATGTGTGAACAACAA
* * *** **
47335 CGAATAGTACTGATATTGTATGAATAGTATTGATAATGTGTGAACAGTAA
1 CGAATAGTATTGATACTGTATGAATAGTACCAATAATGTGTGAACAACAA
*
47385 CGAACAGTATTGAT
1 CGAATAGTATTGAT
47399 GCTCAAAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 11 0.20
50 43 0.80
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (50 bp):
CGAATAGTATTGATACTGTATGAATAGTACCAATAATGTGTGAACAACAA
Found at i:47361 original size:20 final size:20
Alignment explanation
Indices: 47336--47383 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
47326 GAACAACAAC
*
47336 GAATAGTACTGATATTGTAT
1 GAATAGTACTGATAATGTAT
* *
47356 GAATAGTATTGATAATGTGT
1 GAATAGTACTGATAATGTAT
*
47376 GAACAGTA
1 GAATAGTA
47384 ACGAACAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (20 bp):
GAATAGTACTGATAATGTAT
Found at i:53749 original size:20 final size:20
Alignment explanation
Indices: 53724--53766 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
53714 TATATTGGGC
* *
53724 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
53744 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
53764 TAT
1 TAT
53767 GGAATAATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.56
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:56344 original size:15 final size:15
Alignment explanation
Indices: 56315--56358 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
56305 AAAAAATGGA
*
56315 AATAATTATAATATAT
1 AATAA-TATATTATAT
56331 GAAT-ATATATTATAT
1 -AATAATATATTATAT
56346 AATAATATATTAT
1 AATAATATATTAT
56359 GACACACACA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 3 0.12
15 18 0.72
16 1 0.04
17 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
AATAATATATTATAT
Found at i:56413 original size:11 final size:11
Alignment explanation
Indices: 56372--56414 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
56362 ACACACACAC
56372 ATATATATATT
1 ATATATATATT
56383 ATA-ATTATATT
1 ATATA-TATATT
56394 ATACT-TATATT
1 ATA-TATATATT
56405 ATATATATAT
1 ATATATATAT
56415 AAAGTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 2 0.07
11 26 0.93
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
ATATATATATT
Found at i:56490 original size:37 final size:36
Alignment explanation
Indices: 56449--56548 Score: 98
Period size: 37 Copynumber: 2.8 Consensus size: 36
56439 GTATATAAAA
*
56449 TATATAGTATAAGTATATATATAATATATTATGCATG
1 TATATA-TATAAGTATATATATAATATATTATACATG
* * * *
56486 TATATACT-TAAGTGTGTGTATATATATGTTATACATG
1 TATATA-TATAAGTATATATATA-ATATATTATACATG
*
56523 TATATATAT-A-TATATATATATTATAT
1 TATATATATAAGTATATATATAATATAT
56549 GTGTATATCA
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
34 4 0.08
35 7 0.14
36 13 0.26
37 26 0.52
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (36 bp):
TATATATATAAGTATATATATAATATATTATACATG
Found at i:56509 original size:2 final size:2
Alignment explanation
Indices: 56504--56593 Score: 51
Period size: 2 Copynumber: 46.0 Consensus size: 2
56494 TAAGTGTGTG
* * *
56504 TA TA TA TA TG T- TA TA CA TG TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * *
56544 TA TA TG TG TA TA TCA TA TG T- TA TA CA TG TA TA TA TG TG TA TG
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56586 TA TA TA TA
1 TA TA TA TA
56594 AAAGTACATA
Statistics
Matches: 68, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
1 3 0.04
2 63 0.93
3 2 0.03
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (2 bp):
TA
Found at i:56562 original size:49 final size:48
Alignment explanation
Indices: 56500--56592 Score: 150
Period size: 49 Copynumber: 1.9 Consensus size: 48
56490 TACTTAAGTG
56500 TGTGTATATATATGTTATACATGTATATATATATATATATATATTATA
1 TGTGTATATATATGTTATACATGTATATATATATATATATATATTATA
* * *
56548 TGTGTATATCATATGTTATACATGTATATATGTGTATGTATATAT
1 TGTGTATAT-ATATGTTATACATGTATATATATATATATATATAT
56593 AAAAGTACAT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 9 0.22
49 32 0.78
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.49
Consensus pattern (48 bp):
TGTGTATATATATGTTATACATGTATATATATATATATATATATTATA
Found at i:56622 original size:14 final size:15
Alignment explanation
Indices: 56597--56625 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
56587 ATATATAAAA
56597 GTACATATTATGTAT
1 GTACATATTATGTAT
56612 GTACATA-TATGTAT
1 GTACATATTATGTAT
56626 ATATACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (15 bp):
GTACATATTATGTAT
Found at i:57398 original size:15 final size:15
Alignment explanation
Indices: 57378--57410 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
57368 AGTGTGATGA
57378 AAACCTATGGGGGAT
1 AAACCTATGGGGGAT
57393 AAACCTATGGGGGAT
1 AAACCTATGGGGGAT
57408 AAA
1 AAA
57411 AGAGCTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.12, G:0.30, T:0.18
Consensus pattern (15 bp):
AAACCTATGGGGGAT
Found at i:57532 original size:13 final size:13
Alignment explanation
Indices: 57514--57538 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57504 TAACATCACT
57514 TTTCTTTCATTTA
1 TTTCTTTCATTTA
57527 TTTCTTTCATTT
1 TTTCTTTCATTT
57539 TATGAATTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCTTTCATTTA
Found at i:59196 original size:12 final size:12
Alignment explanation
Indices: 59179--59207 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
59169 ACCTGAAAAG
59179 GTGAGTAACAGA
1 GTGAGTAACAGA
59191 GTGAGTAACAGA
1 GTGAGTAACAGA
59203 GTGAG
1 GTGAG
59208 CTTTGGGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.38, T:0.17
Consensus pattern (12 bp):
GTGAGTAACAGA
Found at i:63506 original size:16 final size:15
Alignment explanation
Indices: 63485--63515 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
63475 ATTAAAAGAT
63485 ACATATATTTTTAAAA
1 ACATAT-TTTTTAAAA
63501 ACATATTTTTTAAAA
1 ACATATTTTTTAAAA
63516 TTCAAAACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
ACATATTTTTTAAAA
Found at i:63723 original size:24 final size:24
Alignment explanation
Indices: 63696--63741 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
63686 GATATTAGAA
* *
63696 ATCAAAAAATAATTCAGGTCAGAT
1 ATCAAAAAAGAATTCAGATCAGAT
* *
63720 ATCAGAACAGAATTCAGATCAG
1 ATCAAAAAAGAATTCAGATCAG
63742 GTACCGGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAAAAGAATTCAGATCAGAT
Done.