Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004419.1 Hibiscus syriacus cultivar Beakdansim tig00009690_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: 55122
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Found at i:645 original size:12 final size:12
Alignment explanation
Indices: 615--639 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
605 TACCCATTTT
615 ATATTTAATTGA
1 ATATTTAATTGA
627 ATATTTAATTGA
1 ATATTTAATTGA
639 A
1 A
640 AGTTTATCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATATTTAATTGA
Found at i:1305 original size:158 final size:156
Alignment explanation
Indices: 1121--1515 Score: 463
Period size: 158 Copynumber: 2.5 Consensus size: 156
1111 AATGATTTCA
* * * *
1121 TTATTTCTTCAATTCCTCCTTCATTTTAAGTTCATTTTTTACCAAATTTGAACTACATGCTCCTA
1 TTATTTCTTCAATTCATCATTTATTTTAAGTTC-TTTTTTACCAAATTTGAACCACATGCTCCTA
* * *
1186 AACCATAGTAGGATACATGTGTACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTTAA
65 AACCATAGTAGAATACATGTATACTTTCAATTCATCTTTTTGATAACAAA-TTTTTATTTTTCAA
** *
1251 TTTAGTCCTTCAATTTTTCATAATCTCC
129 TTTAGTCCTTCAAAGTTTCATAATATCC
* * * * *
1279 TTATTTCTTCAATTCATCATTTATTTTAAGTCTGTTTTTTTACAAAATTTGAGCCACAAGCTTCT
1 TTATTTCTTCAATTCATCATTTATTTTAAGT-T-CTTTTTTACCAAATTTGAACCACATGCTCCT
* * *
1344 AAACCATAGTATAATACATGTATACTTTCAATTCCTTTTTTTGATAACAAATTTTTATTTTTCAA
64 AAACCATAGTAGAATACATGTATACTTTCAATTCATCTTTTTGATAACAAATTTTTATTTTTCAA
* *
1409 TTTAGTTCTTCAAAGTTTCATAATATTC
129 TTTAGTCCTTCAAAGTTTCATAATATCC
* * ** * * * *
1437 TTATTCCATCAATTTGTGATTTATTTT-AG-TC-TCTTTACCAAATTTGAACCACATGCTCATAT
1 TTATTTCTTCAATTCATCATTTATTTTAAGTTCTTTTTTACCAAATTTGAACCACATGCTCCTAA
* *
1499 ACCACAATAGAATACAT
66 ACCATAGTAGAATACAT
1516 ATGTAACTTC
Statistics
Matches: 199, Mismatches: 36, Indels: 9
0.82 0.15 0.04
Matches are distributed among these distances:
153 38 0.19
155 1 0.01
157 2 0.01
158 86 0.43
159 72 0.36
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.46
Consensus pattern (156 bp):
TTATTTCTTCAATTCATCATTTATTTTAAGTTCTTTTTTACCAAATTTGAACCACATGCTCCTAA
ACCATAGTAGAATACATGTATACTTTCAATTCATCTTTTTGATAACAAATTTTTATTTTTCAATT
TAGTCCTTCAAAGTTTCATAATATCC
Found at i:2698 original size:64 final size:64
Alignment explanation
Indices: 2584--2721 Score: 199
Period size: 64 Copynumber: 2.2 Consensus size: 64
2574 CTAAGGGTGA
* * *
2584 ATCGATGCATAAAATACATTCGATGTTTTAAACAAGCCTGGAGTGCATCGATGCATGGTCTGTGC
1 ATCGATGCATAAAATACATTCAATGTTTCAAAAAAGCCTGGAGTGCATCGATGCATGG-CTGTGC
* *
2649 ATCGATGCAT-AAATGCATTCAATGTTTCAATAAAATCCT-GAGTGCATCGATGCATGGCTGTGC
1 ATCGATGCATAAAATACATTCAATGTTTCAA-AAAAGCCTGGAGTGCATCGATGCATGGCTGTGC
2712 ATCGATGCAT
1 ATCGATGCAT
2722 CCCTTCACAA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
63 16 0.24
64 35 0.52
65 16 0.24
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (64 bp):
ATCGATGCATAAAATACATTCAATGTTTCAAAAAAGCCTGGAGTGCATCGATGCATGGCTGTGC
Found at i:3332 original size:2 final size:2
Alignment explanation
Indices: 3325--3401 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
3315 ACCAAACCAA
3325 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
3367 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3402 ATAAGTTCAA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4915 original size:2 final size:2
Alignment explanation
Indices: 4908--4959 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
4898 GAAAATCATA
4908 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
4950 AT AT AT AT AT
1 AT AT AT AT AT
4960 TCATGAAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5445 original size:23 final size:23
Alignment explanation
Indices: 5419--5501 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
5409 ATGAACTGCT
*
5419 GAGTGCATTGATGCACATTCAAG
1 GAGTGCATCGATGCACATTCAAG
* * *
5442 GAGTGCATCGGTGCACCTTC-AT
1 GAGTGCATCGATGCACATTCAAG
* *
5464 G-GTGTATCGATGCATATTCAAAG
1 GAGTGCATCGATGCACATTC-AAG
5487 GA-TGCATCGATGCAC
1 GAGTGCATCGATGCAC
5502 TGACGAGTGT
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
21 14 0.30
22 2 0.04
23 30 0.65
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (23 bp):
GAGTGCATCGATGCACATTCAAG
Found at i:6654 original size:30 final size:30
Alignment explanation
Indices: 6620--6713 Score: 179
Period size: 30 Copynumber: 3.1 Consensus size: 30
6610 CCCGAAGAAC
6620 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
6650 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
6680 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
6710 CTAT
1 CTAT
6714 TCATATGTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:6798 original size:32 final size:32
Alignment explanation
Indices: 6715--6803 Score: 105
Period size: 32 Copynumber: 2.8 Consensus size: 32
6705 AGTAACTATT
* *
6715 CATATGTTCCTTAGAACATAGGT-ATACTGTC
1 CATATGTTCCGTAGAACATAGGTAAAACTGTC
6746 CATATG-TCTCG-A-AAGGCATAGGTAAAACTGTC
1 CATATGTTC-CGTAGAA--CATAGGTAAAACTGTC
6778 CATATGTTCCGTAGAACATAGGTAAA
1 CATATGTTCCGTAGAACATAGGTAAA
6804 CCCTCGACTC
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
29 2 0.04
30 3 0.06
31 14 0.29
32 25 0.51
33 3 0.06
34 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (32 bp):
CATATGTTCCGTAGAACATAGGTAAAACTGTC
Found at i:7705 original size:21 final size:21
Alignment explanation
Indices: 7681--7725 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
7671 TGTTGTTCGT
* *
7681 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
7702 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
7723 TTG
1 TTG
7726 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:10575 original size:30 final size:30
Alignment explanation
Indices: 10537--10630 Score: 170
Period size: 30 Copynumber: 3.1 Consensus size: 30
10527 GAAGAACCTG
10537 TCCAGAGGTCATAAAGATCCTCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTA
*
10567 TCCTGAGGTCATAAAGATCCTCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTA
*
10597 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTA
10627 TCCA
1 TCCA
10631 TATGTTCCTT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTA
Found at i:10661 original size:31 final size:30
Alignment explanation
Indices: 10619--10716 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 30
10609 AAAGATCCTC
*
10619 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* *
10649 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
*
10680 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
10712 GGTAA
1 GGTAA
10717 ACCCTTGACT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
30 6 0.11
31 25 0.44
32 25 0.44
33 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:11638 original size:21 final size:21
Alignment explanation
Indices: 11595--11639 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
11585 TGTTGTTCGT
* *
11595 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
* *
11616 TTGAATGGGTACCGATTCGCC
1 TTGAAGGGGTACCGATTCCCC
11637 TTG
1 TTG
11640 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:19015 original size:46 final size:46
Alignment explanation
Indices: 18916--19020 Score: 122
Period size: 46 Copynumber: 2.3 Consensus size: 46
18906 ACACTAAGGG
* * *
18916 TGAATCGATGTATAAAATACATTCAATGTTTTAAACAAGCCTGGAA
1 TGAATCGATGCATAAAATACATTCAATGTTTCAAAAAAGCCTGGAA
* * * *
18962 TGAATCGATGCATAAAATGCATTCGATGTTTCAATAAAATCCT-GAG
1 TGAATCGATGCATAAAATACATTCAATGTTTCAA-AAAAGCCTGGAA
*
19008 TGTATCGATGCAT
1 TGAATCGATGCAT
19021 GGCTGTGCAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
46 44 0.88
47 6 0.12
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (46 bp):
TGAATCGATGCATAAAATACATTCAATGTTTCAAAAAAGCCTGGAA
Found at i:30863 original size:32 final size:32
Alignment explanation
Indices: 30827--30900 Score: 94
Period size: 33 Copynumber: 2.3 Consensus size: 32
30817 TAACGAATCG
* *
30827 GTTGATTTTCGGTTCGTATCAATATTGGATCA
1 GTTGATTTTCGGATCGGATCAATATTGGATCA
** *
30859 GTTGAATTTTTTGATCGGGTCAATATTGGATCA
1 GTTG-ATTTTCGGATCGGATCAATATTGGATCA
30892 GTTGATTTT
1 GTTGATTTT
30901 TAGGTCGGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
32 9 0.25
33 27 0.75
ACGTcount: A:0.22, C:0.09, G:0.23, T:0.46
Consensus pattern (32 bp):
GTTGATTTTCGGATCGGATCAATATTGGATCA
Found at i:30909 original size:32 final size:32
Alignment explanation
Indices: 30845--30965 Score: 118
Period size: 32 Copynumber: 3.8 Consensus size: 32
30835 TCGGTTCGTA
* *
30845 TCAATATTGGATCAGTTGAATTTTTTGATCGGG
1 TCAATATTGGATCAGTTG-ATTTTTAGGTCGGG
30878 TCAATATTGGATCAGTTGATTTTTAGGTCGGG
1 TCAATATTGGATCAGTTGATTTTTAGGTCGGG
* **** * *
30910 TTAATACCATATCGGTTAGA-TTTCAGGTCGGG
1 TCAATATTGGATCAGTT-GATTTTTAGGTCGGG
* *
30942 TCAATATAGGATCAATTGATTTTT
1 TCAATATTGGATCAGTTGATTTTT
30966 GGTTTAGGTT
Statistics
Matches: 69, Mismatches: 17, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
31 2 0.03
32 47 0.68
33 20 0.29
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.40
Consensus pattern (32 bp):
TCAATATTGGATCAGTTGATTTTTAGGTCGGG
Found at i:33387 original size:23 final size:23
Alignment explanation
Indices: 33361--33429 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
33351 CACCACAGCT
*
33361 CGTATAAATGCACCGAAGTACCA
1 CGTAGAAATGCACCGAAGTACCA
* * *
33384 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTACCA
*
33407 CGTAGAAAAGCACCGAAGTACCA
1 CGTAGAAATGCACCGAAGTACCA
33430 TATAAGGTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTACCA
Found at i:33907 original size:2 final size:2
Alignment explanation
Indices: 33900--33928 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33890 CATCTTCCTT
33900 TA TA TA TA 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 T
33929 CATTTTTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35156 original size:64 final size:64
Alignment explanation
Indices: 35047--35208 Score: 193
Period size: 64 Copynumber: 2.5 Consensus size: 64
35037 TTCCCTTGAA
* * * * *
35047 GTGCATCGATGCACTACTCATGCGTCGATACACAAATCACCTTCGATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACTCCTTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAA-GGG
** * ** *
35111 GTGCATCGATGCACTCCTTATGCATCGATGTACTAATTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCCTTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
35175 GTGCATCGATGCACTTCC-TATGCATCGATACACA
1 GTGCATCGATGCAC-TCCTTATGCATCGATACACA
35209 CTGAATAATT
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 73 0.89
65 9 0.11
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTCCTTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:37591 original size:20 final size:20
Alignment explanation
Indices: 37566--37613 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
37556 GAAGAACAAA
37566 TATCGATATTATCCTGATAG
1 TATCGATATTATCCTGATAG
37586 TATCGATATTATCCTGATAG
1 TATCGATATTATCCTGATAG
37606 TATCGATA
1 TATCGATA
37614 CTCTACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
TATCGATATTATCCTGATAG
Found at i:40232 original size:20 final size:20
Alignment explanation
Indices: 40187--40280 Score: 124
Period size: 20 Copynumber: 4.9 Consensus size: 20
40177 TGAATATTTA
40187 TCCCGAAGGACCACT-A-TG
1 TCCCGAAGGACCACTGATTG
40205 TCCCGAAGGACCACTGATTG
1 TCCCGAAGGACCACTGATTG
* *
40225 TTCCGAAGAACCACT-A-TG
1 TCCCGAAGGACCACTGATTG
* *
40243 TCCTGAAGGACCACTGTTTG
1 TCCCGAAGGACCACTGATTG
40263 TCCCGAAGGACCACTGAT
1 TCCCGAAGGACCACTGAT
40281 AATCCCTCGA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
18 29 0.45
19 2 0.03
20 33 0.52
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (20 bp):
TCCCGAAGGACCACTGATTG
Found at i:40232 original size:38 final size:38
Alignment explanation
Indices: 40187--40277 Score: 146
Period size: 38 Copynumber: 2.4 Consensus size: 38
40177 TGAATATTTA
40187 TCCCGAAGGACCACTATGTCCCGAAGGACCACTGATTG
1 TCCCGAAGGACCACTATGTCCCGAAGGACCACTGATTG
* * * *
40225 TTCCGAAGAACCACTATGTCCTGAAGGACCACTGTTTG
1 TCCCGAAGGACCACTATGTCCCGAAGGACCACTGATTG
40263 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
40278 GATAATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.21
Consensus pattern (38 bp):
TCCCGAAGGACCACTATGTCCCGAAGGACCACTGATTG
Found at i:43481 original size:14 final size:14
Alignment explanation
Indices: 43462--43491 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43452 TTGATCTTTT
43462 AAGTTTTATTAAGA
1 AAGTTTTATTAAGA
*
43476 AAGTTTTATTGAGA
1 AAGTTTTATTAAGA
43490 AA
1 AA
43492 CTCAATGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (14 bp):
AAGTTTTATTAAGA
Found at i:44080 original size:32 final size:32
Alignment explanation
Indices: 44039--44112 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
44029 TAAAGTCGGT
* * * * *
44039 TTGCTTTCGGTTCAGATTAATTTCTGTTTAGG
1 TTGCTTTCGGGTCAGATTAAATTCAGTTCAAG
*
44071 TTGCTTTCGGGTCGGATTAAATTCAGTTCAAG
1 TTGCTTTCGGGTCAGATTAAATTCAGTTCAAG
44103 TTGCTTTCGG
1 TTGCTTTCGG
44113 ATTGGGTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.16, C:0.15, G:0.24, T:0.45
Consensus pattern (32 bp):
TTGCTTTCGGGTCAGATTAAATTCAGTTCAAG
Found at i:44194 original size:16 final size:16
Alignment explanation
Indices: 44161--44202 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
44151 AGTTTCTTTT
44161 GGTTCGGGTT-GATTC
1 GGTTCGGGTTAGATTC
*
44176 GGTTCGGGTTAGTTTC
1 GGTTCGGGTTAGATTC
*
44192 GGTTCAGGTTA
1 GGTTCGGGTTA
44203 ATTTTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.10, C:0.12, G:0.38, T:0.40
Consensus pattern (16 bp):
GGTTCGGGTTAGATTC
Found at i:45266 original size:22 final size:22
Alignment explanation
Indices: 45241--45292 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
45231 TATTATTATT
45241 TTTA-AAATATTAAAATAGTTTA
1 TTTATAAATATTAAAAT-GTTTA
* * *
45263 TTTATTATTATTAAAATGTTTT
1 TTTATAAATATTAAAATGTTTA
45285 TTCTATAA
1 TT-TATAA
45293 TTTTATTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTATAAATATTAAAATGTTTA
Found at i:49687 original size:2 final size:2
Alignment explanation
Indices: 49680--49706 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49670 ATAGCTAGGG
49680 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
49707 ATATATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:49711 original size:2 final size:2
Alignment explanation
Indices: 49706--49756 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
49696 TCTCTCTCTC
49706 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
49748 TA TA TA TA T
1 TA TA TA TA T
49757 TGAGAAATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52138 original size:74 final size:70
Alignment explanation
Indices: 52013--52161 Score: 253
Period size: 74 Copynumber: 2.1 Consensus size: 70
52003 GTAGATAGAT
52013 AACCCAAATTCATGTTTGGTAAAAAGGTCTTAACCTGAGTAGAGTGGTAAAGATTCAAAATGTCG
1 AACCCAAATTCATGTTTGGTAAAAAGGTCTTAACCTGAGTAGAGTGGTAAAGATTC-AAATGTC-
52078 GAATTCA
64 GAATTCA
*
52085 AACCCTAAATTCATGTTTTGGTAAAAAGTTCTTAACCTGAGTAGAGTGGTAAAGATTCAAATGTC
1 AACCC-AAATTCATG-TTTGGTAAAAAGGTCTTAACCTGAGTAGAGTGGTAAAGATTCAAATGTC
52150 GAATTCA
64 GAATTCA
52157 AACCC
1 AACCC
52162 CAAACCTTCT
Statistics
Matches: 74, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
72 17 0.23
73 16 0.22
74 41 0.55
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (70 bp):
AACCCAAATTCATGTTTGGTAAAAAGGTCTTAACCTGAGTAGAGTGGTAAAGATTCAAATGTCGA
ATTCA
Done.