Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001012.1 Hibiscus syriacus cultivar Beakdansim tig00002018_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: 53619
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2762 original size:13 final size:13
Alignment explanation
Indices: 2744--2777 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2734 AGTTTGATGG
*
2744 TTTAACCATGGAC
1 TTTAACCATGAAC
2757 TTTAACCATGAAC
1 TTTAACCATGAAC
2770 TTTAACCA
1 TTTAACCA
2778 GACAAAGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.32
Consensus pattern (13 bp):
TTTAACCATGAAC
Found at i:5727 original size:18 final size:19
Alignment explanation
Indices: 5688--5731 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
5678 TCTTAGATTA
*
5688 TTTATTTAATTATTTTTCT
1 TTTATTTAATTATTTATCT
*
5707 TTTATTTAGTT-TTTATCT
1 TTTATTTAATTATTTATCT
5725 TTTATTT
1 TTTATTT
5732 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTATTTAATTATTTATCT
Found at i:5825 original size:15 final size:15
Alignment explanation
Indices: 5799--5862 Score: 53
Period size: 15 Copynumber: 4.2 Consensus size: 15
5789 TTATTTCCCC
5799 TTTATATTTATTATTA
1 TTTAT-TTTATTATTA
*
5815 TTTATTTTATTATTT
1 TTTATTTTATTATTA
*
5830 TTTCTTTTTAAATTATTA
1 TTT-ATTTT--ATTATTA
5848 -TTA-TTTATT-TTA
1 TTTATTTTATTATTA
5860 TTT
1 TTT
5863 TATTATATCT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
12 3 0.08
13 5 0.12
15 15 0.38
16 9 0.22
17 2 0.05
18 6 0.15
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATTTTATTATTA
Found at i:9913 original size:134 final size:133
Alignment explanation
Indices: 9673--10568 Score: 809
Period size: 134 Copynumber: 6.7 Consensus size: 133
9663 TCAAGATTTG
* * * ** * * * * *
9673 ACAAGTCTGCCCTGATTCAATCTTCCATGAGTGACAGCTAAATGAATCAACGTCTCTATATCTTA
1 ACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACATCCCCATATCTGA
* * * * * *
9738 TATTCCCTTAAGAAGAAGCGAAATATATCCCTTTCTTTCAAGATTTGATA-TCCTCTTAGTGTCA
66 TATTCCC-TCAGAAGAAGCGAAACAAATCCCTCTCTTTCAAGATTTGATATTCC-CTGAGTGACA
*
9802 GTGGA
129 GCGGA
* * * * * * *
9807 ACAAGTCTGCCCCAATTCAATCTTCCCTAAGTGATAGCGGAATGGATCAATATCCCCAGATATGA
1 ACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACATCCCCATATCTGA
* * * * *
9872 TATTCCCTCAAAATGAAGCGGAACAAATCCCCCTATTTCAAGATTTGACATTCCCTGAGTGACAG
66 TATTCCCTCAGAA-GAAGCGAAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAG
*
9937 CGAA
130 CGGA
* * * * * * ** *
9941 ACAAGTCTGCCCCGATTTAATCTTTCCTGAGTGATAGCGGAATGAATCAACGTCTTCAAATCTGA
1 ACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACATCCCCATATCTGA
* * * * * * *
10006 TATTCCCTTTAGATGAAGCGAAACATATACCTCTTTTTCAAGATTTGATATTACCTGAGTAACAG
66 TATTCCC-TCAGAAGAAGCGAAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAG
10071 CGGA
130 CGGA
* * * * * * **
10075 ACAAGTTTACCACGATTCAATCTTCCATCAGTGACAGCGAAATAGATCAAC-TCCCCCGGATCTG
1 ACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACAT-CCCCATATCTG
* * *
10139 ATATTCCCTTCAGAAGAAGTGAAACAAAT--CTCTCTTTCAAGATTTTATATTCCATGAGTGACA
65 ATATTCCC-TCAGAAGAAGCGAAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACA
* *
10202 ACGAA
129 GCGGA
* * * * * * * * *
10207 ACAAGTTTGCCCCTATTCAATCTTCTCTGAGTGATAGTGGAATAGACCAAC-TCCCCCATATTTG
1 ACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACAT-CCCCATATCTG
* * *
10271 ATATTCCTTTCAGAAGAAGCGAAACATATCCATCTCTTTCAAGATTTGATATTCCCTGAGTGACA
65 ATATTCC-CTCAGAAGAAGCGAAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACA
10336 G-GGA
129 GCGGA
* * * * * * *
10340 ACAAGTCTACCCTGATTTAATCTTTCCTGAGTGACAACGAAATGGATCAACAACCCTATATCTGA
1 ACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACATCCCCATATCTGA
* * * * * * *
10405 TATTCCCTCCAGAAGAAGCAAAACAAATTCATTTCTTTCAATATTTGATATTCTCTGAGTGATAG
66 TATTCCCT-CAGAAGAAGCGAAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAG
10470 CGGA
130 CGGA
* * * * *
10474 ACAAGTCTACCCCGATTCAATTTTCCCTAAGTAACAACAGAATGGATCAACAT-CCCATATCTGA
1 ACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACATCCCCATATCTGA
* * *
10538 TATTCCCTAAG-TGACAGCGAAACATATCCCT
66 TATTCCCTCAGAAGA-AGCGAAACAAATCCCT
10569 TATCATAATT
Statistics
Matches: 613, Mismatches: 138, Indels: 24
0.79 0.18 0.03
Matches are distributed among these distances:
131 2 0.00
132 123 0.20
133 128 0.21
134 354 0.58
135 6 0.01
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (133 bp):
ACAAGTCTACCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACATCCCCATATCTGA
TATTCCCTCAGAAGAAGCGAAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGC
GGA
Found at i:10524 original size:399 final size:399
Alignment explanation
Indices: 9673--10545 Score: 913
Period size: 399 Copynumber: 2.2 Consensus size: 399
9663 TCAAGATTTG
* * * * * * * *
9673 ACAAGTCTGCC-CTGATTCAATCTTCCATGAGTGACAGCTAAAT-GAATCAACGTCTCTATATCT
1 ACAAGTCTACCAC-GATTCAATCTTCCATAAGTAACAACGAAATAG-ATCAACATC-CCAGATCT
* * * * * * * * * *
9736 TATATTCCCTTAAGAAGAAGCGAAATATATCCCTTTCTTTCAAGATTTGATA-TCCTCTTAGTGT
63 GATATTCCCTTCAGAAGAAGTGAAACAAAT--CTCTCTTTCAAGATTTTATATTCC-ATGAGTGA
** * * * *
9800 CAGTGGAACAAGTCTGCCCCAATTCAATCTTCCCTAAGTGATAGCGGAATGGATCAATATCCCCA
125 CAACGAAACAAGTCTGCCCCAATTCAATCTTCCCTAAGTGATAGCGGAATAGACCAATACCCCCA
* *
9865 GATATGATATTCCCTCAAAATGAAGCGGAACAAATCCCCCTATTTCAAGATTTGACATTCCCTGA
190 GATATGATATTCCCTCAAAATGAAGCGAAACAAATCCACCTATTTCAAGATTTGACATTCCCTGA
* * * * **
9930 GTGACAGCGAAACAAGTCTGCCCCGATTTAATCTTTCCTGAGTGATAGCGGAATGAATCAACGTC
255 GTGACAGCGAAACAAGTCTACCCCGATTTAATCTTTCCTGAGTGACAACGAAATGAATCAACACC
* ** * * * *
9995 TTCAAATCTGATATTCCCTTTAGATGAAGCGAAACATATACCTCTTTTTCAAGATTTGATATTAC
320 CTCAAATCTGATATTCCCTCCAGAAGAAGCAAAACAAATACATCTTTTTCAAGATTTGATATTAC
10060 CTGAGTAACAGCGGA
385 CTGAGTAACAGCGGA
* * * * *
10075 ACAAGTTTACCACGATTCAATCTTCCATCAGTGACAGCGAAATAGATCAAC-TCCCCCGGATCTG
1 ACAAGTCTACCACGATTCAATCTTCCATAAGTAACAACGAAATAGATCAACAT--CCCAGATCTG
10139 ATATTCCCTTCAGAAGAAGTGAAACAAATCTCTCTTTCAAGATTTTATATTCCATGAGTGACAAC
64 ATATTCCCTTCAGAAGAAGTGAAACAAATCTCTCTTTCAAGATTTTATATTCCATGAGTGACAAC
* * * * * *
10204 GAAACAAGTTTGCCCCTATTCAATCTTCTCTGAGTGATAGTGGAATAGACCAACT-CCCCCATAT
129 GAAACAAGTCTGCCCCAATTCAATCTTCCCTAAGTGATAGCGGAATAGACCAA-TACCCCCAGAT
* * * * * * *
10268 TTGATATTCCTTTCAGAA-GAAGCGAAACATATCCATCTCTTTCAAGATTTGATATTCCCTGAGT
193 ATGATATTCC-CTCAAAATGAAGCGAAACAAATCCACCTATTTCAAGATTTGACATTCCCTGAGT
* * *
10332 GACAG-GGAACAAGTCTACCCTGATTTAATCTTTCCTGAGTGACAACGAAATGGATCAACAACCC
257 GACAGCGAAACAAGTCTACCCCGATTTAATCTTTCCTGAGTGACAACGAAATGAATCAAC-ACCC
* * *
10396 T-ATATCTGATATTCCCTCCAGAAGAAGCAAAACAAATTCAT-TTCTTTCAATATTTGATATT-C
321 TCAAATCTGATATTCCCTCCAGAAGAAGCAAAACAAATACATCTT-TTTCAAGATTTGATATTAC
* *
10458 TCTGAGTGATAGCGGA
385 -CTGAGTAACAGCGGA
* * * * *
10474 ACAAGTCTACCCCGATTCAATTTTCCCTAAGTAACAAC-AGAATGGATCAACATCCCATATCTGA
1 ACAAGTCTACCACGATTCAATCTTCCATAAGTAACAACGA-AATAGATCAACATCCCAGATCTGA
10538 TATTCCCT
65 TATTCCCT
10546 AAGTGACAGC
Statistics
Matches: 390, Mismatches: 69, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
398 21 0.05
399 149 0.38
400 134 0.34
401 10 0.03
402 73 0.19
403 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (399 bp):
ACAAGTCTACCACGATTCAATCTTCCATAAGTAACAACGAAATAGATCAACATCCCAGATCTGAT
ATTCCCTTCAGAAGAAGTGAAACAAATCTCTCTTTCAAGATTTTATATTCCATGAGTGACAACGA
AACAAGTCTGCCCCAATTCAATCTTCCCTAAGTGATAGCGGAATAGACCAATACCCCCAGATATG
ATATTCCCTCAAAATGAAGCGAAACAAATCCACCTATTTCAAGATTTGACATTCCCTGAGTGACA
GCGAAACAAGTCTACCCCGATTTAATCTTTCCTGAGTGACAACGAAATGAATCAACACCCTCAAA
TCTGATATTCCCTCCAGAAGAAGCAAAACAAATACATCTTTTTCAAGATTTGATATTACCTGAGT
AACAGCGGA
Found at i:12505 original size:3 final size:3
Alignment explanation
Indices: 12499--12550 Score: 88
Period size: 3 Copynumber: 17.3 Consensus size: 3
12489 TTATTACCGC
12499 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT
12544 TAT TAT T
1 TAT TAT T
12551 GCAGGCTTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:15825 original size:30 final size:30
Alignment explanation
Indices: 15791--15923 Score: 230
Period size: 30 Copynumber: 4.4 Consensus size: 30
15781 GGTTCTTCGG
* *
15791 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
15821 GACCTCTGGATAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
15851 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
15881 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
15911 GACCTCTAGATAG
1 GACCTCTGGATAG
15924 GTCCTTCGAG
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 98 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:20522 original size:2 final size:2
Alignment explanation
Indices: 20515--20586 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
20505 AACATGTGAC
20515 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
20557 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
20587 AAGGATAAGA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21034 original size:30 final size:30
Alignment explanation
Indices: 20994--21053 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
20984 TATGGACAGT
*
20994 TTACCTAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
21024 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
21054 GTCCTTCAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (30 bp):
TTACCGAGGATCTTTATGACCTCTGGATAG
Found at i:26503 original size:2 final size:2
Alignment explanation
Indices: 26496--26527 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
26486 TTTATCTTAA
26496 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
26528 GCAGTAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27685 original size:3 final size:3
Alignment explanation
Indices: 27677--27727 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
27667 AACCATTAAG
27677 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AA- ATAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
27721 AAT AAT A
1 AAT AAT A
27728 TATATATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 3 0.07
3 41 0.91
4 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:27985 original size:36 final size:36
Alignment explanation
Indices: 27945--28091 Score: 267
Period size: 36 Copynumber: 4.1 Consensus size: 36
27935 TGAATACTGA
27945 ATTTGCATTGCTTCACTACTCTTTTGTGAAGGCTTG
1 ATTTGCATTGCTTCACTACTCTTTTGTGAAGGCTTG
*
27981 ATTTGCATTACTTCACTACTCTTTTGTGAAGGCTTG
1 ATTTGCATTGCTTCACTACTCTTTTGTGAAGGCTTG
*
28017 ATTTGCATTGTTTCACTACTCTTTTGTGAAGGCTTG
1 ATTTGCATTGCTTCACTACTCTTTTGTGAAGGCTTG
*
28053 ATTTACATTGCTTCACTACTCTTTTGTGAAGGCTTG
1 ATTTGCATTGCTTCACTACTCTTTTGTGAAGGCTTG
28089 ATT
1 ATT
28092 AACTTGAGAA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 106 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.46
Consensus pattern (36 bp):
ATTTGCATTGCTTCACTACTCTTTTGTGAAGGCTTG
Found at i:40223 original size:19 final size:21
Alignment explanation
Indices: 40183--40225 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
40173 ATTTTCTCTG
40183 TTGGTTGTTGTGTCTCTGTTGC
1 TTGGTTGTTGTGTCTC-GTTGC
40205 TTGGTTGTTGT-TCTC-TTGC
1 TTGGTTGTTGTGTCTCGTTGC
40224 TT
1 TT
40226 TCGTTGCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
21 4 0.19
22 11 0.52
ACGTcount: A:0.00, C:0.14, G:0.28, T:0.58
Consensus pattern (21 bp):
TTGGTTGTTGTGTCTCGTTGC
Found at i:40772 original size:3 final size:3
Alignment explanation
Indices: 40764--40802 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
40754 AACTATTAAG
40764 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40803 TTTATTATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40846 original size:17 final size:19
Alignment explanation
Indices: 40824--40868 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
40814 TATGTCTATA
40824 ATAATA-ATA-ATATAAAT
1 ATAATATATATATATAAAT
*
40841 ATAATATATATATATATAT
1 ATAATATATATATATAAAT
40860 AT-ATATATA
1 ATAATATATA
40869 AATGTCACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 6 0.24
18 10 0.40
19 9 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAATATATATATATAAAT
Found at i:40851 original size:2 final size:2
Alignment explanation
Indices: 40833--40868 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
40823 AATAATAATA
*
40833 AT AT AA AT AT A- 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 AT A
40869 AATGTCACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:43171 original size:6 final size:6
Alignment explanation
Indices: 43160--43199 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
43150 CCAGTCAAAC
**
43160 GCCCTA GCCCTA TTCCTA GCCCTA GCCCTA GCCCTA GCCC
1 GCCCTA GCCCTA GCCCTA GCCCTA GCCCTA GCCCTA GCCC
43200 AAACATAAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.15, C:0.50, G:0.15, T:0.20
Consensus pattern (6 bp):
GCCCTA
Found at i:43571 original size:47 final size:47
Alignment explanation
Indices: 43500--43593 Score: 170
Period size: 47 Copynumber: 2.0 Consensus size: 47
43490 TTGCATTTTC
* *
43500 CTTCGTGTGCAGGTTTGTTCTGTAGTGGAATGGTTGATTCAACACTT
1 CTTCGTGTGCAGGTTAGTTATGTAGTGGAATGGTTGATTCAACACTT
43547 CTTCGTGTGCAGGTTAGTTATGTAGTGGAATGGTTGATTCAACACTT
1 CTTCGTGTGCAGGTTAGTTATGTAGTGGAATGGTTGATTCAACACTT
43594 ATTCTAGAGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.19, C:0.14, G:0.28, T:0.39
Consensus pattern (47 bp):
CTTCGTGTGCAGGTTAGTTATGTAGTGGAATGGTTGATTCAACACTT
Found at i:43878 original size:174 final size:174
Alignment explanation
Indices: 43626--43948 Score: 427
Period size: 174 Copynumber: 1.9 Consensus size: 174
43616 GATCTACCTC
* * * *
43626 ATAAAAGAATTGTTGTTGTTTCTTAAAATCCGTGTTCGAGCACTATAAATGACAAGGGTGTGAGC
1 ATAAAAGAATTGTTGTTATTTCTGAAAATCCGTGTTCGAGCACCATAAATGACAAGGATGTGAGC
* * * * * * * *
43691 GTTTAATGTTGAAAGGTTGAGAGTTATCTTCTAACATATATTATCTTGTACT-TACCCTAGATTA
66 GTTCAATGTTGAAAGATTGAGAGTTATCTTCGAAAAGATATTACCTGGTA-TATA-CCAAGATTA
43755 TT-AAAAAAACACTTATTCTATAGCACGAACCAAGTGACATTTGTG
129 TTAAAAAAAACACTTATTCTATAGCACGAACCAAGTGACATTTGTG
* * * * *
43800 ATAAAAGAATTGTTTTTATTTCTGAAGATTCG-GATTTGAGCACCATAAATGCCAAGGATGTGAG
1 ATAAAAGAATTGTTGTTATTTCTGAAAATCCGTG-TTCGAGCACCATAAATGACAAGGATGTGAG
* *
43864 CGTTCAATGTTGAAAGATTGAGATTTATCTTCGAAAAGATATTGCCTGGTATATACCAAGATTAT
65 CGTTCAATGTTGAAAGATTGAGAGTTATCTTCGAAAAGATATTACCTGGTATATACCAAGATTAT
43929 TAAAAAAAACACTTATTCTA
130 TAAAAAAAACACTTATTCTA
43949 GAAATTTCTG
Statistics
Matches: 127, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
173 12 0.09
174 115 0.91
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (174 bp):
ATAAAAGAATTGTTGTTATTTCTGAAAATCCGTGTTCGAGCACCATAAATGACAAGGATGTGAGC
GTTCAATGTTGAAAGATTGAGAGTTATCTTCGAAAAGATATTACCTGGTATATACCAAGATTATT
AAAAAAAACACTTATTCTATAGCACGAACCAAGTGACATTTGTG
Done.