Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007811.1 Hibiscus syriacus cultivar Beakdansim tig00110139_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: 68359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:67 original size:30 final size:30
Alignment explanation
Indices: 31--87 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
21 TCTAAATTGA
31 AAAATAGAAAGTTAAAGGACTAAAATAACT
1 AAAATAGAAAGTTAAAGGACTAAAATAACT
*
61 AAAATAGAAAGTTAAAGGACTTAAATA
1 AAAATAGAAAGTTAAAGGACTAAAATA
88 GAAAAAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (30 bp):
AAAATAGAAAGTTAAAGGACTAAAATAACT
Found at i:1937 original size:22 final size:23
Alignment explanation
Indices: 1909--1958 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
1899 ATGGAAAGTC
1909 TTTTTTTCTG-CTTTATGACAC-A
1 TTTTTTT-TGTCTTTATGACACGA
*
1931 TTTTTTTTGTCTTTGTGACACGA
1 TTTTTTTTGTCTTTATGACACGA
1954 TTTTT
1 TTTTT
1959 ATTATTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 2 0.08
22 17 0.68
23 6 0.24
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.60
Consensus pattern (23 bp):
TTTTTTTTGTCTTTATGACACGA
Found at i:13779 original size:17 final size:18
Alignment explanation
Indices: 13742--13782 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
13732 ATATTATGTA
*
13742 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
13760 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
13777 TTTACT
1 TTTACT
13783 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:15486 original size:18 final size:18
Alignment explanation
Indices: 15463--15502 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
15453 ACAACAGCCA
15463 CCGCAACCATTTATGATG
1 CCGCAACCATTTATGATG
15481 CCGCAACCATTTATGATG
1 CCGCAACCATTTATGATG
15499 CCGC
1 CCGC
15503 CATCGCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (18 bp):
CCGCAACCATTTATGATG
Found at i:18190 original size:16 final size:14
Alignment explanation
Indices: 18148--18193 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
18138 TAGTATTATT
18148 TATT-AAATA-AAA
1 TATTAAAATATAAA
*
18160 CATTAAAATATAAA
1 TATTAAAATATAAA
18174 TATTAAAATTAATAAA
1 TATTAAAA-T-ATAAA
18190 TATT
1 TATT
18194 TACTATAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 3 0.11
13 5 0.18
14 10 0.36
15 1 0.04
16 9 0.32
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (14 bp):
TATTAAAATATAAA
Found at i:22139 original size:202 final size:196
Alignment explanation
Indices: 21782--22319 Score: 682
Period size: 202 Copynumber: 2.7 Consensus size: 196
21772 GCCACGTAAA
* *
21782 GAATCTCTAAAGAACTCATGTTCTGCAAAACACGAG-T--TTGCCACGTCACCTCAAGAATCTTT
1 GAATCTCTGAAGAACTCATGTTCTGCAAAA-ACAAGTTGCTTGCCACGTCACCTCAAGAATCTTT
* * * *
21844 GCATGCCTATATCTCTTCCATATCATGTTAAAA-ATCTCTTTTTTGAAAAAAAAATGAGACTTTC
65 GCAGGCCCATGTC-CTTCCATATCATGTTAAAATCTCTCTTTTTTGAAAAAAAAATGAGACTTTC
* **
21908 ATTCGAATCCTTATTTCAAGCAAGTGAAGGTAAACAAGCAAACCATACAAAACTGAAATGAACGT
129 ATTCGAATACTTATTTCAAAAAAGTGAAGGTAAACAAGCAAACCATACAAAACTGAAATGAACGT
21973 TAG
194 TAG
* *
21976 GAATCTTTGAAGAACTCATGTTATGCAAAAAGCAAGTTGCTTGCCACGTCACCTCAAGAATCTTT
1 GAATCTCTGAAGAACTCATGTTCTGCAAAAA-CAAGTTGCTTGCCACGTCACCTCAAGAATCTTT
* * ***
22041 GCAGGCCCATGTCCATTTCATATCACGTTAAGAATCTCTTTCTTTTTTTTTTAAAAAAATGAGAC
65 GCAGGCCCATGTCC-TTCCATATCATGTTAA-AATCTC--TC-TTTTTTGAAAAAAAAATGAGAC
*
22106 TTTCATTCGAATACTTATTTCAAAAAAGTGAAGGTAAACAAGCAAACCATACAGAACTGAAATGA
125 TTTCATTCGAATACTTATTTCAAAAAAGTGAAGGTAAACAAGCAAACCATACAAAACTGAAATGA
*
22171 ACGTTAT
190 ACGTTAG
* *
22178 GAATCTCTGAATAACTCATGTTCTG-AAAAACACGAGTTGCTTGCCACGTCCCCTCAAGAATCTT
1 GAATCTCTGAAGAACTCATGTTCTGCAAAAACA--AGTTGCTTGCCACGTCACCTCAAGAATCTT
* * *
22242 TGCAGACCCATGTCCCTTCCATATCATGTTAATAA--TCTATTTTTTG-AAAAAACAT--GACTT
64 TGCAGGCCCATGT-CCTTCCATATCATGTTAA-AATCTCTCTTTTTTGAAAAAAAAATGAGACTT
*
22302 TCATTCGAATCCTTATTT
127 TCATTCGAATACTTATTT
22320 AAGCAAGTGG
Statistics
Matches: 300, Mismatches: 31, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
193 1 0.00
194 52 0.17
195 1 0.00
196 8 0.03
197 55 0.18
198 3 0.01
199 2 0.01
200 4 0.01
201 7 0.02
202 165 0.55
203 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (196 bp):
GAATCTCTGAAGAACTCATGTTCTGCAAAAACAAGTTGCTTGCCACGTCACCTCAAGAATCTTTG
CAGGCCCATGTCCTTCCATATCATGTTAAAATCTCTCTTTTTTGAAAAAAAAATGAGACTTTCAT
TCGAATACTTATTTCAAAAAAGTGAAGGTAAACAAGCAAACCATACAAAACTGAAATGAACGTTA
G
Found at i:27617 original size:110 final size:110
Alignment explanation
Indices: 27484--27703 Score: 413
Period size: 110 Copynumber: 2.0 Consensus size: 110
27474 TTATGACACT
*
27484 ATGGGAATGCTCAGCGTATTCAAGCAATTGGACTGTGGGATCTCTCGGCGTCTTCTGCATGCTAC
1 ATGGGAATGCTCAGCGTATTCAAGCAATTAGACTGTGGGATCTCTCGGCGTCTTCTGCATGCTAC
27549 AAGGAATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTG
66 AAGGAATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTG
* *
27594 ATGGGAATGCTCGGCGTCTTCAAGCAATTAGACTGTGGGATCTCTCGGCGTCTTCTGCATGCTAC
1 ATGGGAATGCTCAGCGTATTCAAGCAATTAGACTGTGGGATCTCTCGGCGTCTTCTGCATGCTAC
27659 AAGGAATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTG
66 AAGGAATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTG
27704 GCGGGAATCT
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 107 1.00
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (110 bp):
ATGGGAATGCTCAGCGTATTCAAGCAATTAGACTGTGGGATCTCTCGGCGTCTTCTGCATGCTAC
AAGGAATGCCAAGGTGGATCTCTCGGCGTCTTCACCTGTCGTCTG
Found at i:28007 original size:18 final size:18
Alignment explanation
Indices: 27984--28048 Score: 130
Period size: 18 Copynumber: 3.6 Consensus size: 18
27974 CTTTGTGGCC
27984 GAAGCGTGAGATTCGTCT
1 GAAGCGTGAGATTCGTCT
28002 GAAGCGTGAGATTCGTCT
1 GAAGCGTGAGATTCGTCT
28020 GAAGCGTGAGATTCGTCT
1 GAAGCGTGAGATTCGTCT
28038 GAAGCGTGAGA
1 GAAGCGTGAGA
28049 CTAATAATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.25, C:0.15, G:0.35, T:0.25
Consensus pattern (18 bp):
GAAGCGTGAGATTCGTCT
Found at i:31429 original size:8 final size:8
Alignment explanation
Indices: 31405--31823 Score: 126
Period size: 8 Copynumber: 56.5 Consensus size: 8
31395 TATTTTATAA
31405 TAATTATT
1 TAATTATT
31413 TAA--ATT
1 TAATTATT
31419 TAATTATT
1 TAATTATT
*
31427 TAA--CTT
1 TAATTATT
*
31433 TAATGATT
1 TAATTATT
*
31441 TAA-TA-A
1 TAATTATT
31447 TAATTATT
1 TAATTATT
*
31455 TAA--CTT
1 TAATTATT
*
31461 TAATGATT
1 TAATTATT
*
31469 TAA-TA-A
1 TAATTATT
31475 TAATTACTT
1 TAATTA-TT
*
31484 TAATGATT
1 TAATTATT
*
31492 TAA--CTT
1 TAATTATT
*
31498 TAATGATT
1 TAATTATT
*
31506 TAA-TA-A
1 TAATTATT
31512 TAATTACTT
1 TAATTA-TT
*
31521 TAATGATT
1 TAATTATT
31529 TAA-T-TT
1 TAATTATT
*
31535 TAATGATT
1 TAATTATT
*
31543 TAA-TA-A
1 TAATTATT
31549 TAATTACTT
1 TAATTA-TT
*
31558 TAATGATT
1 TAATTATT
31566 TAA-T-TT
1 TAATTATT
*
31572 TAATGATT
1 TAATTATT
*
31580 TAATGATT
1 TAATTATT
*
31588 TAA--CTT
1 TAATTATT
*
31594 TAATGATT
1 TAATTATT
*
31602 TAA-TA-A
1 TAATTATT
31608 TAATTACTT
1 TAATTA-TT
*
31617 TAATGATT
1 TAATTATT
*
31625 TAATGATT
1 TAATTATT
*
31633 TAA-TA-A
1 TAATTATT
31639 TAATTATTT
1 TAATTA-TT
*
31648 TAATGATT
1 TAATTATT
*
31656 TAATGATT
1 TAATTATT
*
31664 TAATGATT
1 TAATTATT
*
31672 TAA-TA-A
1 TAATTATT
31678 TAATTACTT
1 TAATTA-TT
*
31687 TAATGATT
1 TAATTATT
*
31695 TAA--CTT
1 TAATTATT
**
31701 TAATGCTT
1 TAATTATT
*
31709 TAA-TA-A
1 TAATTATT
31715 TAATTACTT
1 TAATTA-TT
*
31724 TAATGATT
1 TAATTATT
*
31732 TAATGATT
1 TAATTATT
*
31740 TAATGATT
1 TAATTATT
*
31748 TAATAATT
1 TAATTATT
*
31756 TAATGATT
1 TAATTATT
31764 TAA-T-TT
1 TAATTATT
*
31770 TAATAATT
1 TAATTATT
*
31778 TAA-TA-A
1 TAATTATT
*
31784 TAATTACT
1 TAATTATT
31792 TAA-T-TT
1 TAATTATT
*
31798 TAATGATT
1 TAATTATT
31806 TAA-T-TT
1 TAATTATT
*
31812 TAATGATT
1 TAATTATT
31820 TAAT
1 TAAT
31824 AATAATTACT
Statistics
Matches: 308, Mismatches: 56, Indels: 94
0.67 0.12 0.21
Matches are distributed among these distances:
6 82 0.27
7 27 0.09
8 164 0.53
9 35 0.11
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (8 bp):
TAATTATT
Found at i:31494 original size:37 final size:37
Alignment explanation
Indices: 31447--31605 Score: 259
Period size: 37 Copynumber: 4.3 Consensus size: 37
31437 GATTTAATAA
* *
31447 TAATTATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
*
31484 TAATGATTTAACTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
31521 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
1 TAATGATTTAATTTTAATGATTTAATAATAATTACTT
*
31558 TAATGATTTAATTTTAATGATTTAATGAT--TTAACTT
1 TAATGATTTAATTTTAATGATTTAATAATAATT-ACTT
31594 TAATGATTTAAT
1 TAATGATTTAAT
31606 AATAATTACT
Statistics
Matches: 118, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
35 2 0.02
36 16 0.14
37 100 0.85
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.51
Consensus pattern (37 bp):
TAATGATTTAATTTTAATGATTTAATAATAATTACTT
Found at i:31697 original size:31 final size:31
Alignment explanation
Indices: 31603--31667 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
31593 TTAATGATTT
31603 AATAATAATTACTTTAATGATTTAATGATTT
1 AATAATAATTACTTTAATGATTTAATGATTT
*
31634 AATAATAATTATTTTAATGATTTAATGATTT
1 AATAATAATTACTTTAATGATTTAATGATTT
31665 AAT
1 AAT
31668 GATTTAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (31 bp):
AATAATAATTACTTTAATGATTTAATGATTT
Found at i:31703 original size:76 final size:76
Alignment explanation
Indices: 31623--31834 Score: 280
Period size: 76 Copynumber: 2.8 Consensus size: 76
31613 ACTTTAATGA
31623 TTTAATGATTTAATAATAATTATTTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTT
1 TTTAATGATTTAATAATAATTATTTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTT
31688 AATGATTTAAC
66 AATGATTTAAC
* *
31699 TTTAATGCTTTAATAATAATTACTTTAATGATTTAATGATTTAATGA-TT--TAAT-A--A-TTT
1 TTTAATGATTTAATAATAATTATTTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTT
*
31757 AATGATTTAAT
66 AATGATTTAAC
*
31768 TTTAATAATTTAATAATAATTACTTAATTTTAATGATTTAAT--TTTAATGATTTAATAATAATT
1 TTTAATGATTTAATAAT-A--A-TT-ATTTTAATGATTTAATGATTTAATGATTTAATAATAATT
31831 ACTT
61 ACTT
31835 GACTTTAATG
Statistics
Matches: 118, Mismatches: 6, Indels: 21
0.81 0.04 0.14
Matches are distributed among these distances:
69 28 0.24
70 2 0.02
72 10 0.08
73 8 0.07
74 15 0.13
75 6 0.05
76 46 0.39
78 1 0.01
79 2 0.02
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.51
Consensus pattern (76 bp):
TTTAATGATTTAATAATAATTATTTTAATGATTTAATGATTTAATGATTTAATAATAATTACTTT
AATGATTTAAC
Found at i:31823 original size:14 final size:14
Alignment explanation
Indices: 31405--31823 Score: 235
Period size: 14 Copynumber: 30.9 Consensus size: 14
31395 TATTTTATAA
* *
31405 TAATTATTTAAATT
1 TAATGATTTAATTT
* *
31419 TAATTATTTAACTT
1 TAATGATTTAATTT
**
31433 TAATGATTTAATAA
1 TAATGATTTAATTT
* *
31447 TAATTATTTAACTT
1 TAATGATTTAATTT
31461 TAATGATTTAA---
1 TAATGATTTAATTT
* *
31472 TAAT-AATT-ACTT
1 TAATGATTTAATTT
*
31484 TAATGATTTAACTT
1 TAATGATTTAATTT
31498 TAATGATTTAA---
1 TAATGATTTAATTT
* *
31509 TAAT-AATT-ACTT
1 TAATGATTTAATTT
31521 TAATGATTTAATTT
1 TAATGATTTAATTT
**
31535 TAATGATTTAATAA
1 TAATGATTTAATTT
*
31549 TAATTACTTTAATGATT
1 TAATGA-TTTAAT--TT
31566 TAAT--TTTAATGATT
1 TAATGATTTAAT--TT
*
31580 TAATGATTTAACTT
1 TAATGATTTAATTT
**
31594 TAATGATTTAATAA
1 TAATGATTTAATTT
*
31608 TAATTACTTTAATGATT
1 TAATGA-TTTAAT--TT
31625 TAATGATTTAA---
1 TAATGATTTAATTT
*
31636 TAAT-AATT-ATTT
1 TAATGATTTAATTT
31648 TAATGATTTAATGATT
1 TAATGATTTAAT--TT
31664 TAATGATTTAA---
1 TAATGATTTAATTT
* *
31675 TAAT-AATT-ACTT
1 TAATGATTTAATTT
*
31687 TAATGATTTAACTT
1 TAATGATTTAATTT
*
31701 TAATGCTTTAA---
1 TAATGATTTAATTT
* *
31712 TAAT-AATT-ACTT
1 TAATGATTTAATTT
31724 TAATGATTTAATGATT
1 TAATGATTTAAT--TT
31740 TAATGATTTAATAATT
1 TAATGATTTAAT--TT
31756 TAATGATTTAATTT
1 TAATGATTTAATTT
* **
31770 TAATAATTTAATAA
1 TAATGATTTAATTT
* *
31784 TAATTACTTAATTT
1 TAATGATTTAATTT
31798 TAATGATTTAATTT
1 TAATGATTTAATTT
31812 TAATGATTTAAT
1 TAATGATTTAAT
31824 AATAATTACT
Statistics
Matches: 321, Mismatches: 47, Indels: 74
0.73 0.11 0.17
Matches are distributed among these distances:
9 5 0.02
10 14 0.04
11 20 0.06
12 20 0.06
13 15 0.05
14 174 0.54
15 12 0.04
16 52 0.16
17 9 0.03
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (14 bp):
TAATGATTTAATTT
Found at i:32334 original size:6 final size:6
Alignment explanation
Indices: 32323--32347 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
32313 GGTGAGAATA
32323 ACTCCC ACTCCC ACTCCC ACTCCC A
1 ACTCCC ACTCCC ACTCCC ACTCCC A
32348 GTCCTTCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.64, G:0.00, T:0.16
Consensus pattern (6 bp):
ACTCCC
Found at i:34373 original size:171 final size:172
Alignment explanation
Indices: 34083--34439 Score: 549
Period size: 171 Copynumber: 2.1 Consensus size: 172
34073 CATCAAATAT
* *
34083 AAAATGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTTGCAATTTAATCACTAATTT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAATTT
*
34148 ATAAATTCTTTCAAATTTAACCAATTAAGCATATTAATACTAAATTCAAGCATAGTATACCAACT
66 ATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAACT
* *
34213 TTT-ATAATTTACTCTAATTTCTTAAATTCCTCAAATTTTGC
131 TTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
* *
34254 AAAACGATCCCTAATTACTATTTGGTTCTCAACATTTTCAAAGTTAGCAATTTAATC-CATAAAT
1 AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCAC-T-AAT
* * * *
34318 TT-TAAGTTCTTTCTAATTTAACCAATTAAGCATACTAATACTAAATTCCAGCATAGTATAGCAA
64 TTATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAA
* *
34382 CTTTTAATAATTTACTCTTATTCCTTAAATTCCTTAAATTTTAC
129 CTTTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
*
34426 AAAACGGTCCCTAA
1 AAAACGATCCCTAA
34440 AACTTTACAA
Statistics
Matches: 169, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
170 1 0.01
171 116 0.69
172 52 0.31
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.39
Consensus pattern (172 bp):
AAAACGATCCCTAATTACTATTTGCTTCTCAACATTTTCAAACTTAGCAATTTAATCACTAATTT
ATAAATTCTTTCAAATTTAACCAATTAAGCATACTAATACTAAATTCAAGCATAGTATACCAACT
TTTAATAATTTACTCTAATTCCTTAAATTCCTCAAATTTTAC
Found at i:34923 original size:23 final size:23
Alignment explanation
Indices: 34897--34940 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
34887 AGTTGCATGC
34897 CCCCCACATGCAGACGTGCAGGA
1 CCCCCACATGCAGACGTGCAGGA
34920 CCCCCACATGCAGACGTGCAG
1 CCCCCACATGCAGACGTGCAG
34941 CCCTGCAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.41, G:0.25, T:0.09
Consensus pattern (23 bp):
CCCCCACATGCAGACGTGCAGGA
Found at i:35001 original size:22 final size:22
Alignment explanation
Indices: 34971--35013 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
34961 GTGATTTCTG
*
34971 TGCTTTCTCCTTGCAGAACCCA
1 TGCTCTCTCCTTGCAGAACCCA
34993 TGCTCTCTCCTTGCAGAACCC
1 TGCTCTCTCCTTGCAGAACCC
35014 GTGATTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.40, G:0.14, T:0.30
Consensus pattern (22 bp):
TGCTCTCTCCTTGCAGAACCCA
Found at i:35023 original size:22 final size:22
Alignment explanation
Indices: 34974--35023 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
34964 ATTTCTGTGC
*
34974 TTTCTCCTTGCAGAACCCATGC
1 TTTCTCCTTGCAGAACCCATGA
* *
34996 TCTCTCCTTGCAGAACCCGTGA
1 TTTCTCCTTGCAGAACCCATGA
35018 TTTCTC
1 TTTCTC
35024 ACGTCCAGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.16, C:0.36, G:0.14, T:0.34
Consensus pattern (22 bp):
TTTCTCCTTGCAGAACCCATGA
Found at i:35088 original size:34 final size:34
Alignment explanation
Indices: 35045--35129 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
35035 CATGCACAGC
*
35045 ACTGAAGACGCCGAGATTTCCTACGAAGAATCCA
1 ACTGAAGACGCCGAGAGTTCCTACGAAGAATCCA
*
35079 ACTGAAGACGCCGAGAGTTCCTATGAAGAATCCA
1 ACTGAAGACGCCGAGAGTTCCTACGAAGAATCCA
35113 ACTGAAGACGCCGAGAG
1 ACTGAAGACGCCGAGAG
35130 ATCAATCATA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (34 bp):
ACTGAAGACGCCGAGAGTTCCTACGAAGAATCCA
Found at i:41008 original size:2 final size:2
Alignment explanation
Indices: 41001--41036 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40991 GTCATTGTTT
41001 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
41037 GAATTATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45015 original size:37 final size:37
Alignment explanation
Indices: 44969--45044 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
44959 CCACCGAAAG
44969 TGGCCTCCAAAATCCACCAAAAATTGCCCACCAATTT
1 TGGCCTCCAAAATCCACCAAAAATTGCCCACCAATTT
* * *
45006 TGGCTTCCAAAATCCACTAAAAATTGCCTACCAATTT
1 TGGCCTCCAAAATCCACCAAAAATTGCCCACCAATTT
45043 TG
1 TG
45045 ACTTTTCCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.34, C:0.30, G:0.09, T:0.26
Consensus pattern (37 bp):
TGGCCTCCAAAATCCACCAAAAATTGCCCACCAATTT
Found at i:47461 original size:37 final size:37
Alignment explanation
Indices: 47420--47501 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
47410 TTTGTTGTTT
47420 CCACCGAA-AATGGCCTCCAAAATCCACCGAAAATTAC
1 CCACC-AATAATGGCCTCCAAAATCCACCGAAAATTAC
** * *
47457 CCACCAATTTTGGCTTCCAAAATCCACCGAAAATTAT
1 CCACCAATAATGGCCTCCAAAATCCACCGAAAATTAC
*
47494 CCATCAAT
1 CCACCAAT
47502 TTTGACTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
36 2 0.05
37 37 0.95
ACGTcount: A:0.38, C:0.33, G:0.09, T:0.21
Consensus pattern (37 bp):
CCACCAATAATGGCCTCCAAAATCCACCGAAAATTAC
Found at i:47502 original size:37 final size:37
Alignment explanation
Indices: 47430--47505 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
47420 CCACCGAAAA
47430 TGGCCTCCAAAATCCACCGAAAATTACCCACCAATTT
1 TGGCCTCCAAAATCCACCGAAAATTACCCACCAATTT
* * *
47467 TGGCTTCCAAAATCCACCGAAAATTATCCATCAATTT
1 TGGCCTCCAAAATCCACCGAAAATTACCCACCAATTT
47504 TG
1 TG
47506 ACTTTTCCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.34, C:0.30, G:0.09, T:0.26
Consensus pattern (37 bp):
TGGCCTCCAAAATCCACCGAAAATTACCCACCAATTT
Found at i:50496 original size:13 final size:13
Alignment explanation
Indices: 50478--50504 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
50468 ATAGTTGAAG
50478 AGTCTTCATATGC
1 AGTCTTCATATGC
50491 AGTCTTCATATGC
1 AGTCTTCATATGC
50504 A
1 A
50505 CGTGTGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (13 bp):
AGTCTTCATATGC
Found at i:56523 original size:17 final size:17
Alignment explanation
Indices: 56501--56533 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
56491 ACATTCAAAT
*
56501 AAATAATTAGTTATAAA
1 AAATAATTAGGTATAAA
56518 AAATAATTAGGTATAA
1 AAATAATTAGGTATAA
56534 TTGAGGGGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (17 bp):
AAATAATTAGGTATAAA
Found at i:57781 original size:3 final size:3
Alignment explanation
Indices: 57773--57821 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
57763 TTCTTCACTT
* * *
57773 TAA TAA TAA TAA TAC TAA TAC TAA TAC TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57821 T
1 T
57822 TAAGGAGACG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:59264 original size:17 final size:16
Alignment explanation
Indices: 59239--59271 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
59229 TACTTTATAA
59239 TTTTTTTAAAAAATTT
1 TTTTTTTAAAAAATTT
59255 TTTTTCTTAAAAAATTT
1 TTTTT-TTAAAAAATTT
59272 CGTTTTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTTTAAAAAATTT
Found at i:65277 original size:33 final size:33
Alignment explanation
Indices: 65230--65323 Score: 81
Period size: 32 Copynumber: 2.9 Consensus size: 33
65220 GAAATTGAAA
* *
65230 TTAACCTGA-CCGAAAGA-AACTTGAACCA-AAT
1 TTAACCCGATCCGAAAGACAACTCGAA-CATAAT
65261 TGTAACCCGATCCGAAA-ACAACTCGAACATAAT
1 T-TAACCCGATCCGAAAGACAACTCGAACATAAT
* * * *
65294 TTATCCCGATCCAAAAG-CAACCCGAGCATA
1 TTAACCCGATCCGAAAGACAACTCGAACATA
65324 TTGAAATTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
31 1 0.02
32 34 0.65
33 17 0.33
ACGTcount: A:0.41, C:0.28, G:0.13, T:0.18
Consensus pattern (33 bp):
TTAACCCGATCCGAAAGACAACTCGAACATAAT
Done.