Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001402.1 Hibiscus syriacus cultivar Beakdansim tig00002738_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: 50696
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:645 original size:20 final size:20
Alignment explanation
Indices: 622--676 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
612 CTGAAACTTT
622 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
*
642 AAATCGTAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
662 CTATCGCAACGCGAA
1 AAATCGCAACACGAA
677 TTTGACTATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.13
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:682 original size:20 final size:21
Alignment explanation
Indices: 659--698 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
649 AACACGAAAA
659 TGACTATCGCAACGC-GAATT
1 TGACTATCGCAACGCAGAATT
679 TGACTATCGCAACGCAGAAT
1 TGACTATCGCAACGCAGAAT
699 CGCAACGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.23
Consensus pattern (21 bp):
TGACTATCGCAACGCAGAATT
Found at i:706 original size:33 final size:32
Alignment explanation
Indices: 664--734 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
654 GAAAATGACT
* *
664 ATCGCAACGCGAATTTGACTATCGCAACG-CAGA
1 ATCGCAACGCGAA-ATGA-AATCGCAACGACAGA
697 ATCGCAACGCGAAATGAAATCGCAACGACAGA
1 ATCGCAACGCGAAATGAAATCGCAACGACAGA
729 ATCGCA
1 ATCGCA
735 TTGCGATAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
31 9 0.26
32 13 0.37
33 13 0.37
ACGTcount: A:0.38, C:0.27, G:0.21, T:0.14
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAGA
Found at i:1115 original size:22 final size:22
Alignment explanation
Indices: 1053--1118 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
1043 TGATCGTGAA
* *
1053 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
1075 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
1097 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
1119 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:1318 original size:59 final size:62
Alignment explanation
Indices: 1226--1340 Score: 209
Period size: 60 Copynumber: 1.9 Consensus size: 62
1216 CAGTGTTCTG
1226 ATATATTAATATATTCGTGTTTGGAATTTG-AAAAAAATACGCGTTGGATACGAATTGTTCC
1 ATATATTAATATATTCGTGTTTGGAATTTGAAAAAAAATACGCGTTGGATACGAATTGTTCC
1287 ATATATTAATATA-TCGTG-TTGGAATTTGAAAAAAAATACGCGTTGGATACGAAT
1 ATATATTAATATATTCGTGTTTGGAATTTGAAAAAAAATACGCGTTGGATACGAAT
1341 GACGCTATGT
Statistics
Matches: 53, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
59 10 0.19
60 30 0.57
61 13 0.25
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (62 bp):
ATATATTAATATATTCGTGTTTGGAATTTGAAAAAAAATACGCGTTGGATACGAATTGTTCC
Found at i:1395 original size:20 final size:20
Alignment explanation
Indices: 1372--1562 Score: 314
Period size: 20 Copynumber: 9.7 Consensus size: 20
1362 CGATAGTCAG
* *
1372 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
1392 ATTCGCATTGC-ATTTATGT
1 ATTCGCATTGCGATTTACGT
*
1411 ATTCGCATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1431 ATTCGCATTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
1451 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1471 A-TCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1490 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1510 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1530 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1550 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1563 ATTAGGAAAA
Statistics
Matches: 159, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
19 34 0.21
20 125 0.79
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1445 original size:59 final size:60
Alignment explanation
Indices: 1372--1562 Score: 314
Period size: 59 Copynumber: 3.2 Consensus size: 60
1362 CGATAGTCAG
* * * *
1372 ATTCGCGTTGCGATTTACATATTCGCATTGC-ATTTATGTATTCGCATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
* *
1431 ATTCGCATTACGATTTACGTATTCGTATTGCGATTTACGTA-TCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
1490 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
1550 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1563 ATTAGGAAAA
Statistics
Matches: 122, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
59 83 0.68
60 39 0.32
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (60 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
Found at i:1486 original size:79 final size:80
Alignment explanation
Indices: 1372--1562 Score: 314
Period size: 79 Copynumber: 2.4 Consensus size: 80
1362 CGATAGTCAG
* * * *
1372 ATTCGCGTTGCGATTTACATATTCGCATTGC-ATTTATGTATTCGCATTGTGATTTACGTATTCG
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCG
1436 CATTACGATTTACGT
66 CATTACGATTTACGT
*
1451 ATTCGTATTGCGATTTACGTA-TCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCG
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCG
*
1515 CATTGCGATTTACGT
66 CATTACGATTTACGT
1530 ATTCGCATTGCGATTTACGTATTCGCATTGCGA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGA
1563 ATTAGGAAAA
Statistics
Matches: 103, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
78 9 0.09
79 83 0.81
80 11 0.11
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (80 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCG
CATTACGATTTACGT
Found at i:1582 original size:21 final size:20
Alignment explanation
Indices: 1552--1603 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1542 ATTTACGTAT
*
1552 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAA-TAGGAAAA
* *
1573 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATAGGAAAA
1593 TCGCAATGCGA
1 TCGCAATGCGA
1604 TAGTCAGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATAGGAAAA
Found at i:4233 original size:7 final size:7
Alignment explanation
Indices: 4221--4270 Score: 100
Period size: 7 Copynumber: 7.1 Consensus size: 7
4211 AAACATTAAG
4221 ATGCGAA
1 ATGCGAA
4228 ATGCGAA
1 ATGCGAA
4235 ATGCGAA
1 ATGCGAA
4242 ATGCGAA
1 ATGCGAA
4249 ATGCGAA
1 ATGCGAA
4256 ATGCGAA
1 ATGCGAA
4263 ATGCGAA
1 ATGCGAA
4270 A
1 A
4271 AAATACACTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.44, C:0.14, G:0.28, T:0.14
Consensus pattern (7 bp):
ATGCGAA
Found at i:18499 original size:126 final size:126
Alignment explanation
Indices: 18274--18525 Score: 504
Period size: 126 Copynumber: 2.0 Consensus size: 126
18264 AAAGAGCTAT
18274 AACTTTGAAAACATTAGAGAGCTATTGATTCTTTTGATATTTTGTGAACTCATGTTTATAATTCG
1 AACTTTGAAAACATTAGAGAGCTATTGATTCTTTTGATATTTTGTGAACTCATGTTTATAATTCG
18339 ATTCGATTGTGAGCCTGAATTAAGGGGCAATGTTTTATAAAATTCTTTCATTCTTTGATTC
66 ATTCGATTGTGAGCCTGAATTAAGGGGCAATGTTTTATAAAATTCTTTCATTCTTTGATTC
18400 AACTTTGAAAACATTAGAGAGCTATTGATTCTTTTGATATTTTGTGAACTCATGTTTATAATTCG
1 AACTTTGAAAACATTAGAGAGCTATTGATTCTTTTGATATTTTGTGAACTCATGTTTATAATTCG
18465 ATTCGATTGTGAGCCTGAATTAAGGGGCAATGTTTTATAAAATTCTTTCATTCTTTGATTC
66 ATTCGATTGTGAGCCTGAATTAAGGGGCAATGTTTTATAAAATTCTTTCATTCTTTGATTC
18526 CTAAAATAAG
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 126 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.43
Consensus pattern (126 bp):
AACTTTGAAAACATTAGAGAGCTATTGATTCTTTTGATATTTTGTGAACTCATGTTTATAATTCG
ATTCGATTGTGAGCCTGAATTAAGGGGCAATGTTTTATAAAATTCTTTCATTCTTTGATTC
Found at i:21519 original size:13 final size:13
Alignment explanation
Indices: 21501--21538 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
21491 ATAAATTGAG
**
21501 AAGAAAAAATGTT
1 AAGAAAAAATGAA
21514 AAG-AAAAATGAA
1 AAGAAAAAATGAA
21526 AAGAAAAAATGAA
1 AAGAAAAAATGAA
21539 GAAAATGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (13 bp):
AAGAAAAAATGAA
Found at i:21622 original size:17 final size:16
Alignment explanation
Indices: 21602--21658 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
21592 AAAACATATT
21602 AAAATTAAAATCAATAA
1 AAAATTAAAAT-AATAA
21619 AAAATATGAAAA-AAT-A
1 AAAAT-T-AAAATAATAA
21635 AAAA--AAAATAAGTAA
1 AAAATTAAAATAA-TAA
21650 AAAATTAAA
1 AAAATTAAA
21659 GGATCAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
12 4 0.12
13 2 0.06
14 1 0.03
15 5 0.15
16 5 0.15
17 11 0.33
18 1 0.03
19 4 0.12
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (16 bp):
AAAATTAAAATAATAA
Found at i:21633 original size:21 final size:21
Alignment explanation
Indices: 21608--21654 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
21598 TATTAAAATT
* *
21608 AAAATCAATAAAAAATATG-AA
1 AAAAT-AAAAAAAAATAAGTAA
21629 AAAATAAAAAAAAATAAGTAA
1 AAAATAAAAAAAAATAAGTAA
21650 AAAAT
1 AAAAT
21655 TAAAGGATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (21 bp):
AAAATAAAAAAAAATAAGTAA
Found at i:22702 original size:3 final size:3
Alignment explanation
Indices: 22670--22739 Score: 54
Period size: 3 Copynumber: 23.7 Consensus size: 3
22660 TGGACCTTTA
* * * *
22670 AAT AA- AAT AAA AAA AAT ACT AAT AA- GAT AAT AAAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * *
22714 AAT AAT AAA AAT TAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
22740 AAAATTATAT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
2 3 0.06
3 46 0.88
4 3 0.06
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:22754 original size:20 final size:19
Alignment explanation
Indices: 22673--22758 Score: 75
Period size: 18 Copynumber: 4.3 Consensus size: 19
22663 ACCTTTAAAT
*
22673 AAAATAAAAAAAATACTAATA
1 AAAAT-AAAAAATTA-TAATA
* *
22694 AGATAATAAATAATAATAATA
1 A-A-AATAAAAAATTATAATA
*
22715 ATAAT-AAAAATTATAATA
1 AAAATAAAAAATTATAATA
*
22733 AAAATAAAAAATTATATTTA
1 AAAATAAAAAATTATA-ATA
22753 AAAATA
1 AAAATA
22759 TATATTATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
18 15 0.28
19 13 0.25
20 8 0.15
21 7 0.13
22 7 0.13
23 3 0.06
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (19 bp):
AAAATAAAAAATTATAATA
Found at i:22781 original size:38 final size:37
Alignment explanation
Indices: 22739--22844 Score: 133
Period size: 38 Copynumber: 2.8 Consensus size: 37
22729 AATAAAAATA
* * *
22739 AAAAATTATATTTAAAAATATATATTATATATGATTTT-
1 AAAAATTGT-TTTAAAACTATATAATATATAT-ATTTTC
*
22777 AAAAATTGTTTTCAAAACCATATAATATATATATTTTC
1 AAAAATTGTTTT-AAAACTATATAATATATATATTTTC
22815 AAAAATTGTTTTTAAAACTATATAATATAT
1 AAAAATTG-TTTTAAAACTATATAATATAT
22845 TTTAAAAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
37 8 0.13
38 48 0.80
39 4 0.07
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (37 bp):
AAAAATTGTTTTAAAACTATATAATATATATATTTTC
Found at i:22951 original size:39 final size:38
Alignment explanation
Indices: 22920--22998 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 38
22910 TATATTTTCA
22920 AAATGATTTAAAAATATTTTCAAAAACTATATATTATAT
1 AAATGATTTAAAAATATTTTC-AAAACTATATATTATAT
* * * *
22959 ATATGTTTTCAAAATGTTTTCAAAACTATATATATATAT
1 AAATGATTTAAAAATATTTTCAAAACTATATAT-TATAT
22998 A
1 A
22999 TATATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 12 0.34
39 23 0.66
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (38 bp):
AAATGATTTAAAAATATTTTCAAAACTATATATTATAT
Found at i:22972 original size:50 final size:47
Alignment explanation
Indices: 22889--22983 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 47
22879 TTATGAAACG
22889 TTTTCAAAACTATATATTATATATATTTTCAAAATGATTTAAAAATA
1 TTTTCAAAACTATATATTATATATATTTTCAAAATGATTTAAAAATA
* *
22936 TTTTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAAA
1 TTTTC-AAAACTATATATTATATATA--TTTTCAAAATGATTTAAAAA
22984 CTATATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
47 5 0.12
48 20 0.47
50 18 0.42
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (47 bp):
TTTTCAAAACTATATATTATATATATTTTCAAAATGATTTAAAAATA
Found at i:23001 original size:50 final size:49
Alignment explanation
Indices: 22894--23013 Score: 138
Period size: 50 Copynumber: 2.4 Consensus size: 49
22884 AAACGTTTTC
*
22894 AAAACTATATATTATATATA-TTTTCAAAATGATTTAAAAATATTTTCA
1 AAAACTATATATTATATATATTTTTCAAAATGATTTAAAAATATTATCA
* *
22942 AAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAAACTATATAT-A
1 AAAACTATATATTATATATAT-TTTTCAAAATGATTT-AAAAATAT-TATCA
* *
22993 TATA-TATATATATATATATAT
1 AAAACTATATAT-TATATATAT
23014 ATATGTATGT
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
48 20 0.32
50 21 0.34
51 19 0.31
52 2 0.03
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.45
Consensus pattern (49 bp):
AAAACTATATATTATATATATTTTTCAAAATGATTTAAAAATATTATCA
Found at i:23047 original size:2 final size:2
Alignment explanation
Indices: 22985--23031 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
22975 TTTTCAAAAC
* *
22985 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23027 TA TA T
1 TA TA T
23032 TCAAAACTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23084 original size:4 final size:4
Alignment explanation
Indices: 23077--23317 Score: 214
Period size: 4 Copynumber: 60.5 Consensus size: 4
23067 CGTCCATCTG
* *
23077 TCCA TCCA TCCG TCCA TCCA TCCG TCCA TCCA TCCA TCCA TCCA TCCA
1 TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA
* * * * * *
23125 TCCA TCCG TCCA TCCG TCCG TCCT TCCA TCCG TCCA TCCG TCCA TCCA
1 TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA
* * * * * * * *
23173 TCCG TCCC TCCC TCCA TCCA TCCA TCCA TCTA TCTA TCTA -CTA TCTA
1 TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA
* * ** *
23220 TCGA TCCA TCCA TCCA TCCA TCTA TTGA TCCA TCCA TCCA TCCA TCTA
1 TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA
* * * ** * * *
23268 TCGA TCCA TCCA TCCA TGCG TCTG TCCG TCCG TCCA TCTA TCCA TCCA
1 TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA TCCA
23316 TC
1 TC
23318 TATATTATTA
Statistics
Matches: 201, Mismatches: 35, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
3 3 0.01
4 198 0.99
ACGTcount: A:0.19, C:0.45, G:0.07, T:0.29
Consensus pattern (4 bp):
TCCA
Found at i:23468 original size:2 final size:2
Alignment explanation
Indices: 23434--23459 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23424 AAAATGAATA
23434 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
23460 GCATATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24301 original size:16 final size:15
Alignment explanation
Indices: 24279--24329 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
24269 TCTCCTCTCT
24279 TTTTTCTTTGT-TTTG
1 TTTTTCTTT-TCTTTG
24294 TGTTTTCTTTTCTTTG
1 T-TTTTCTTTTCTTTG
24310 TTTTTCACTTTT-TTTG
1 TTTTT--CTTTTCTTTG
24326 TTTT
1 TTTT
24330 GTTTTCTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 6 0.19
16 21 0.66
17 5 0.16
ACGTcount: A:0.02, C:0.10, G:0.10, T:0.78
Consensus pattern (15 bp):
TTTTTCTTTTCTTTG
Found at i:24342 original size:35 final size:37
Alignment explanation
Indices: 24280--24355 Score: 104
Period size: 35 Copynumber: 2.1 Consensus size: 37
24270 CTCCTCTCTT
* *
24280 TTTTCTTTGTTTTGTGTTTTCTTTTCTTTGTTTTTCA
1 TTTTCTTTGTTTTGTGTTTTCTCTTCTTTCTTTTTCA
24317 CTTTT-TTTG-TTT-TGTTTTCTCTTCTTTCTTTTTCA
1 -TTTTCTTTGTTTTGTGTTTTCTCTTCTTTCTTTTTCA
24352 TTTT
1 TTTT
24356 GTTTCTGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
34 4 0.11
35 21 0.58
36 3 0.08
37 4 0.11
38 4 0.11
ACGTcount: A:0.03, C:0.13, G:0.08, T:0.76
Consensus pattern (37 bp):
TTTTCTTTGTTTTGTGTTTTCTCTTCTTTCTTTTTCA
Found at i:39698 original size:60 final size:60
Alignment explanation
Indices: 39578--39714 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 60
39568 ATAGCCAAAT
* * * * *
39578 GACCATTTTGTAACTTTTAATATTCAATGAACTCAACAAAGCAACTCCCTAGAGTTGGGG
1 GACCATTTTGTAACTTTTAATAGTCAAGGAACTCAACAAAACAACTCCCTACAGTCGGGG
* * * *
39638 GACCATTTTGTAACTTTTAATAGTCAGGGGACTCAACAAAATAA-TATCCTACAGTCGGGG
1 GACCATTTTGTAACTTTTAATAGTCAAGGAACTCAACAAAACAACT-CCCTACAGTCGGGG
*
39698 GACTATTTCTGT-ACTTT
1 GACCATTT-TGTAACTTT
39715 ACTCTAAAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 1 0.02
60 61 0.94
61 3 0.05
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTCAAGGAACTCAACAAAACAACTCCCTACAGTCGGGG
Done.