Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005363.1 Hibiscus syriacus cultivar Beakdansim tig00012181_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: 65524
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:332 original size:37 final size:37
Alignment explanation
Indices: 282--357 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
272 CCCAATAAGT
282 CATAATGAATTTATTTCACAAACTACGATAAAAACAA
1 CATAATGAATTTATTTCACAAACTACGATAAAAACAA
* *
319 CATAATGAATTTATTTCACAAACTACGTTAAAAGCAA
1 CATAATGAATTTATTTCACAAACTACGATAAAAACAA
356 CA
1 CA
358 ATGCAGCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.28
Consensus pattern (37 bp):
CATAATGAATTTATTTCACAAACTACGATAAAAACAA
Found at i:2685 original size:2 final size:2
Alignment explanation
Indices: 2680--2709 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2670 TTATAAACAA
2680 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
2710 TAAATTCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4470 original size:35 final size:36
Alignment explanation
Indices: 4431--4506 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
4421 CAACAATGGA
* * *
4431 AACATAATTGGGACTTG-GGCTTGAGC-ATCATTAGC
1 AACATAATTGGGACTAGAAGCTTCAGCAAT-ATTAGC
4466 AACATAATTGGGACTAGAAGCTTCAGCAATATTAGC
1 AACATAATTGGGACTAGAAGCTTCAGCAATATTAGC
4502 AACAT
1 AACAT
4507 CACTGAGACT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 16 0.44
36 18 0.50
37 2 0.06
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (36 bp):
AACATAATTGGGACTAGAAGCTTCAGCAATATTAGC
Found at i:7999 original size:20 final size:20
Alignment explanation
Indices: 7970--8008 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7960 AGAGCTCATA
*
7970 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
7990 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
8009 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:15950 original size:20 final size:20
Alignment explanation
Indices: 15921--15959 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
15911 AAAGCTCATA
*
15921 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
15941 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
15960 GTGGTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:17513 original size:17 final size:17
Alignment explanation
Indices: 17479--17514 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17469 ACTACCCTCA
* *
17479 TTGCTAGTCTTTATAGT
1 TTGCTAGTCTCTAAAGT
17496 TTGCTAGTCTCTAAAGT
1 TTGCTAGTCTCTAAAGT
17513 TT
1 TT
17515 TTTTTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (17 bp):
TTGCTAGTCTCTAAAGT
Found at i:19120 original size:20 final size:20
Alignment explanation
Indices: 19095--19208 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
19085 AATTGGGAAA
*
19095 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
19115 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
19135 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
19156 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
19176 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
19196 TTCGCAACGCGAT
1 ATCGCAACGCGAT
19209 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:19139 original size:61 final size:61
Alignment explanation
Indices: 19092--19208 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
19082 GTGAATTGGG
* * * * *
19092 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
19153 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
19209 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:19763 original size:19 final size:19
Alignment explanation
Indices: 19725--19791 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
19715 TTCGAGAATG
19725 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
19745 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
19764 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
19783 AAAATCGCA
1 AAAATCGCA
19792 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:19833 original size:20 final size:19
Alignment explanation
Indices: 19787--19952 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
19777 GAAACCAAAA
* *
19787 TCGCATTGCGATTTTCAAT
1 TCGCGTTGCGATTTTCATT
*
19806 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
19825 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
19845 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
19861 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
19878 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
19892 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
19911 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
19931 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
19951 TC
1 TC
19953 AACCAAAAGA
Statistics
Matches: 118, Mismatches: 16, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 40 0.34
20 49 0.42
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:19868 original size:39 final size:39
Alignment explanation
Indices: 19792--19868 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
19782 CAAAATCGCA
* **
19792 TTGCGATTTTCAATTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCAATTCGCGTTGCGATTTCTAGGTCGCGG
*
19831 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCAATTCGCGTTGCGATT-TCTAGGTCGCG
19869 ATAGTCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.10, C:0.19, G:0.26, T:0.44
Consensus pattern (39 bp):
TTGCGATTTTCAATTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:19877 original size:33 final size:33
Alignment explanation
Indices: 19840--19927 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
19830 GTTGCGATTT
* *
19840 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
19873 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
19906 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
19928 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:22228 original size:24 final size:24
Alignment explanation
Indices: 22194--22247 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
22184 CTGAAACATC
* *
22194 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
22218 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
22242 ATCAAA
1 ATCAAA
22248 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:23363 original size:20 final size:20
Alignment explanation
Indices: 23307--23364 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
23297 ATTCATTTGA
* *
23307 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
23327 CTATCGCAAC-ACAAAAATGG
1 CTATCGCAACGA-GAAAATGG
*
23347 TTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
23365 CGCATTGCGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:23422 original size:19 final size:19
Alignment explanation
Indices: 23395--23450 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
23385 GCATTGCGAT
*
23395 TTTCTCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
23414 TTTCGCATTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
23433 TTTCGCATTGCGATTTTC
1 TTTCGCATTGCGATTTTC
23451 TCGTTGCGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:23426 original size:52 final size:52
Alignment explanation
Indices: 23364--23478 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 52
23354 AACGAGAAAA
***
23364 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCATTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCATTGCGATAGCCATT
** ** ** *
23416 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCATTGCGATAGCCATT
*
23468 TCGCGTTGCGA
1 TCGCATTGCGA
23479 TAGTCTGTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCATTGCGATAGCCATT
Found at i:23434 original size:12 final size:14
Alignment explanation
Indices: 23386--23412 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23376 ATGAAAATCG
23386 CATTGCGATTTTCT
1 CATTGCGATTTTCT
23400 CATTGCGATTTTC
1 CATTGCGATTTTC
23413 ATTTCGCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (14 bp):
CATTGCGATTTTCT
Found at i:23586 original size:14 final size:14
Alignment explanation
Indices: 23567--23603 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
23557 CATCAATTAA
23567 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
23581 ACAAATCATCTTTT
1 ACAAATCAACATTT
23595 ACAAATCAA
1 ACAAATCAA
23604 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:25505 original size:20 final size:19
Alignment explanation
Indices: 25470--25536 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
25460 GAAACTTAAA
25470 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
25489 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
25509 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
25528 ATCGCAACG
1 ATCGCAACG
25537 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:25544 original size:14 final size:14
Alignment explanation
Indices: 25525--25582 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
25515 ATGCGAAATG
25525 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
25539 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
25555 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
25571 AAAATCGCAACG
1 AAAATCGCAACG
25583 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:25567 original size:32 final size:33
Alignment explanation
Indices: 25509--25587 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
25499 GGAAATGGCT
*
25509 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
25542 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
25574 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
25588 CACAAATCAC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:25635 original size:14 final size:14
Alignment explanation
Indices: 25616--25673 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
25606 TTTCATTTCG
25616 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
25630 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
25646 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
25662 CGTTGCGATTTT
1 CGTTGCGATTTT
25674 CATTTCGTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:25680 original size:33 final size:33
Alignment explanation
Indices: 25599--25689 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
25589 ACAAATCACA
*
25599 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
25632 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
25664 TTGCGATTTTCATTTCGTATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
25690 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:25708 original size:20 final size:20
Alignment explanation
Indices: 25683--25728 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
25673 TCATTTCGTA
25683 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
25703 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
25723 TTGCGA
1 TTGCGA
25729 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:26229 original size:18 final size:18
Alignment explanation
Indices: 26203--26247 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
26193 GTCGATCAGA
*
26203 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
26221 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
26239 TGATGGCTC
1 TGATGGCTC
26248 CTGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:27887 original size:22 final size:22
Alignment explanation
Indices: 27860--27903 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
27850 GATGGAGATA
*
27860 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCATCGGAGATGGG
27882 GACGGATTTCATCGGAGATGGG
1 GACGGATTTCATCGGAGATGGG
27904 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.14, G:0.43, T:0.23
Consensus pattern (22 bp):
GACGGATTTCATCGGAGATGGG
Found at i:28116 original size:20 final size:20
Alignment explanation
Indices: 28091--28184 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
28081 GATTATGTAT
28091 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
28111 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
28131 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
28152 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
28172 TATCGCATTGCGA
1 TATCGCGTTGCGA
28185 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:28185 original size:20 final size:20
Alignment explanation
Indices: 28071--28185 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
28061 CGCTTTGAAA
*
28071 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
28092 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
28112 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
28132 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
28153 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
28173 ATCGCATTGCGAT
1 ATCGCATTGCGAT
28186 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:28203 original size:21 final size:21
Alignment explanation
Indices: 28174--28266 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
28164 ATAGTCAGTA
28174 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
28195 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
28215 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
28236 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
28256 TCGCATTGCGA
1 TCGCATTGCGA
28267 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:28204 original size:41 final size:41
Alignment explanation
Indices: 28113--28247 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
28103 AAAGTCAGTA
* * * ** *
28113 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
28153 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
28195 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
28236 TCGCGTTGCGAT
1 TCGCGTTGCGAT
28248 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:28248 original size:41 final size:41
Alignment explanation
Indices: 28174--28266 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
28164 ATAGTCAGTA
28174 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
28215 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
28256 TCGCATTGCGA
1 TCGCATTGCGA
28267 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:29161 original size:29 final size:29
Alignment explanation
Indices: 29088--29161 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
29078 ATGAAATTAT
*
29088 AAAAATTAGAGGACCC-AATTACAAATATA
1 AAAAATTA-AGGACCCTAATTACAAATACA
* *
29117 AAAAAAT-AGGATCCCTAATTATAAATACA
1 AAAAATTAAGGA-CCCTAATTACAAATACA
29146 AAAAATTAAGGACCCT
1 AAAAATTAAGGACCCT
29162 GAGCGGTTGC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
27 4 0.11
28 3 0.08
29 27 0.71
30 4 0.11
ACGTcount: A:0.54, C:0.15, G:0.09, T:0.22
Consensus pattern (29 bp):
AAAAATTAAGGACCCTAATTACAAATACA
Found at i:29609 original size:20 final size:20
Alignment explanation
Indices: 29554--29609 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
29544 TTATATAAAA
29554 TATATTTTTATTATAA---T
1 TATATTTTTATTATAATTTT
*
29571 TATATTTTTATT-TGTATTTT
1 TATATTTTTATTAT-AATTTT
29591 TATATTTTTATTATAATTT
1 TATATTTTTATTATAATTT
29610 AACTTGATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 1 0.03
17 13 0.41
20 17 0.53
21 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (20 bp):
TATATTTTTATTATAATTTT
Found at i:40081 original size:117 final size:117
Alignment explanation
Indices: 39950--40160 Score: 264
Period size: 117 Copynumber: 1.8 Consensus size: 117
39940 AAAAACAGAG
* * * * * *
39950 AAAAATGTGATTAAATTTAATTCCAAATTAAATGAA-TAAGTACGATAAATGAAAAAAGAGGGTC
1 AAAAATGTGATTAAAATTAATTCAAAATTAAATGAATTAA-TAAGAGAAATGAAAAAAGAGGATA
* *
40014 AAAATTAAACATTTTATGAAATTATAAAAATTAGGTGCTTTGATTAGAAATATA
65 AAAACTAAA-AATTTATGAAATTATAAAAATTAGGTGCTTTGATTAGAAATATA
* * * * **
40068 AAAAAT-TGGTTAAAATTAATTCAAAATTGAATGAATTAATAAGAGAGATGGATGAAGAGGATAA
1 AAAAATGTGATTAAAATTAATTCAAAATTAAATGAATTAATAAGAGAAATGAAAAAAGAGGATAA
40132 AAACTAAAAATTTATGAAATTATAAAAAT
66 AAACTAAAAATTTATGAAATTATAAAAAT
40161 CAGAGGACCT
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
116 20 0.26
117 49 0.63
118 9 0.12
ACGTcount: A:0.52, C:0.04, G:0.14, T:0.30
Consensus pattern (117 bp):
AAAAATGTGATTAAAATTAATTCAAAATTAAATGAATTAATAAGAGAAATGAAAAAAGAGGATAA
AAACTAAAAATTTATGAAATTATAAAAATTAGGTGCTTTGATTAGAAATATA
Found at i:40228 original size:29 final size:29
Alignment explanation
Indices: 40168--40228 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
40158 AATCAGAGGA
* *
40168 CCTAATTACTAATATAAAAAATTAGGATC
1 CCTAATTACTAATACAAAAAATTAGGACC
*
40197 CCTAATTA-TAAATACAAAAAATTAGGGCC
1 CCTAATTACT-AATACAAAAAATTAGGACC
40226 CCT
1 CCT
40229 GAGTGGTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (29 bp):
CCTAATTACTAATACAAAAAATTAGGACC
Found at i:40678 original size:20 final size:21
Alignment explanation
Indices: 40617--40679 Score: 76
Period size: 20 Copynumber: 3.0 Consensus size: 21
40607 TTATATAAAA
40617 TATATTTTTATTATAATTATAAT
1 TATATTTTTATTATAATT-T-AT
*
40640 TATATTTTTATT-TGTATTT-T
1 TATATTTTTATTAT-AATTTAT
40660 TATATTTTTATTATAATTTA
1 TATATTTTTATTATAATTTA
40680 ACTTGTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
20 17 0.49
21 1 0.03
22 2 0.06
23 15 0.43
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TATATTTTTATTATAATTTAT
Found at i:43488 original size:18 final size:18
Alignment explanation
Indices: 43467--43520 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
43457 TAAATAATAT
43467 AATAAATAAAAATTAAAA
1 AATAAATAAAAATTAAAA
*
43485 AATAAAAAATAAATTAAAA
1 AATAAATAA-AAATTAAAA
* * *
43504 ATTTAATAAAAAGTAAA
1 AATAAATAAAAATTAAA
43521 GTTAAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AATAAATAAAAATTAAAA
Found at i:43494 original size:21 final size:19
Alignment explanation
Indices: 43467--43504 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
43457 TAAATAATAT
*
43467 AATAAATAA-AAATTAAAA
1 AATAAAAAATAAATTAAAA
43485 AATAAAAAATAAATTAAAA
1 AATAAAAAATAAATTAAAA
43504 A
1 A
43505 TTTAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (19 bp):
AATAAAAAATAAATTAAAA
Found at i:45002 original size:36 final size:36
Alignment explanation
Indices: 44944--45038 Score: 111
Period size: 36 Copynumber: 2.6 Consensus size: 36
44934 CTGCGATGAG
* * * * * *
44944 AGCTTGAGCAACAATGGAAACATAATTGGGACTTGG
1 AGCTTGAGCAATATTAGCAACATAATTGGGACTAGA
*
44980 GGCTTGAGC-ATCATTAGCAACATAATTGGGACTAGA
1 AGCTTGAGCAAT-ATTAGCAACATAATTGGGACTAGA
45016 AGCTTGAGCAATATTAGCAACAT
1 AGCTTGAGCAATATTAGCAACAT
45039 CACTGAGACT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
35 1 0.02
36 46 0.94
37 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (36 bp):
AGCTTGAGCAATATTAGCAACATAATTGGGACTAGA
Found at i:53178 original size:61 final size:60
Alignment explanation
Indices: 53084--53259 Score: 160
Period size: 64 Copynumber: 2.8 Consensus size: 60
53074 AATTAAATTG
* * * *
53084 AACATCGAATGCATTTCATGCAT-GCACT-TACCATGCACCGATGCATTGAGGAT-TTTATGAA
1 AACATCGAATGCATTTGATGCATCG-A-TGCACCATGCACCGATGCACTCAGGATATTT-TG-A
* * *
53145 AACATCGAATGCATTTGATGCATCGATGCACCATCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATG---CA-CCATGCACCGATGCACTCAGGATATTTTGA
53209 AACATCGAATGCATTTGATGCATCGATGCACTCTTATTGCACCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCAC-C--A-TGCACCGATGCACT
53260 AAGGGTTCAA
Statistics
Matches: 96, Mismatches: 8, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
60 2 0.02
61 26 0.27
62 1 0.01
63 1 0.01
64 43 0.45
65 20 0.21
66 3 0.03
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (60 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:53232 original size:64 final size:63
Alignment explanation
Indices: 53035--53239 Score: 199
Period size: 64 Copynumber: 3.2 Consensus size: 63
53025 TTTATCAAAG
* **
53035 TGATGCACGATGCACCAATCCATGCATCGATGCAC-CATGAATTAAATTG-AACATCGAATGCAT
1 TGATGCACGATGCACC-ATCCATGCATCGATGCACTC-TGGA-TATTTTGAAACATCGAATGCAT
53098 T
63 T
* * * * **
53099 TCATG--C-ATGCA-CTTACCATGCACCGATGCATTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCACGATGCACCAT-CCATGCATCGATGCACTCTGGATATTT-TG-AAACATCGAATGCAT
53159 T
63 T
*
53160 TGATGCATCGATGCACCATCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCATT
1 TGATGCA-CGATGCACCATCCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
53224 TGATGCATCGATGCAC
1 TGATGCA-CGATGCAC
53240 TCTTATTGCA
Statistics
Matches: 114, Mismatches: 16, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
58 1 0.01
59 4 0.04
60 17 0.15
61 24 0.21
62 1 0.01
64 37 0.32
65 25 0.22
66 5 0.04
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (63 bp):
TGATGCACGATGCACCATCCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
Found at i:59037 original size:20 final size:20
Alignment explanation
Indices: 58973--59043 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
58963 TTGTGGTTCA
*
58973 TGCATCGATACACCT-AACAG
1 TGCATCGATACACATGAA-AG
* * *
58993 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA--CATGAAAG
*
59015 TGCATCGATACACATGAAGG
1 TGCATCGATACACATGAAAG
59035 TGCATCGAT
1 TGCATCGAT
59044 GCACGCCTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 26 0.62
22 14 0.33
23 2 0.05
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (20 bp):
TGCATCGATACACATGAAAG
Found at i:59038 original size:42 final size:43
Alignment explanation
Indices: 58973--59071 Score: 139
Period size: 42 Copynumber: 2.3 Consensus size: 43
58963 TTGTGGTTCA
* *
58973 TGCATCGATACACCTAACAGTGCATCGATGCA-TCCTTGAATG
1 TGCATCGATACACATAACAGTGCATCGATGCACGCCTTGAATG
*
59015 TGCATCGATACACATGAA-GGTGCATCGATGCACGCCTTGAATG
1 TGCATCGATACACAT-AACAGTGCATCGATGCACGCCTTGAATG
*
59058 TGCATCGATGCACA
1 TGCATCGATACACA
59072 GGGTCATGCA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
42 27 0.53
43 24 0.47
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.24
Consensus pattern (43 bp):
TGCATCGATACACATAACAGTGCATCGATGCACGCCTTGAATG
Found at i:59060 original size:23 final size:22
Alignment explanation
Indices: 58992--59070 Score: 99
Period size: 23 Copynumber: 3.6 Consensus size: 22
58982 ACACCTAACA
*
58992 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCACCCTTGAAT
* * *
59014 GTGCATCGAT--ACACATGAAG
1 GTGCATCGATGCACCCTTGAAT
59034 GTGCATCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
59057 GTGCATCGATGCAC
1 GTGCATCGATGCAC
59071 AGGGTCATGC
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 16 0.34
22 12 0.26
23 19 0.40
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:59082 original size:43 final size:42
Alignment explanation
Indices: 58973--59089 Score: 128
Period size: 43 Copynumber: 2.8 Consensus size: 42
58963 TTGTGGTTCA
** *
58973 TGCATCGATACAC-CTAACAGTGCATCGATGCATCCTTGAATG
1 TGCATCGATACACAGGAACA-TGCATCGATGCAGCCTTGAATG
* **
59015 TGCATCGATACACATGAAGGTGCATCGATGCACGCCTTGAATG
1 TGCATCGATACACAGGAACATGCATCGATGCA-GCCTTGAATG
* **
59058 TGCATCGATGCACAGGGTCATGCATCGATGCA
1 TGCATCGATACACAGGAACATGCATCGATGCA
59090 TCCGTCAGGT
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
42 25 0.40
43 37 0.60
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (42 bp):
TGCATCGATACACAGGAACATGCATCGATGCAGCCTTGAATG
Found at i:61790 original size:65 final size:63
Alignment explanation
Indices: 61721--61879 Score: 187
Period size: 62 Copynumber: 2.5 Consensus size: 63
61711 AATTAAATTG
* * *
61721 AACATCGAATGCATTTCATGCATCGATGCACTTA-CCATGCACCGATGCACTGAGGATTTTATGA
1 AACATCGAATGCATTTGATGCATC-ATGCACTCAGCCATGCACCGATGCACTGAGGATATT-TG-
61785 A
63 A
* * ** *
61786 AACATCGAATGCATTTGATGCATCAAGCAC-CAGCCATGCATCGATGCACTTTGGCTATTTGA
1 AACATCGAATGCATTTGATGCATCATGCACTCAGCCATGCACCGATGCACTGAGGATATTTGA
* *
61848 AACACCGAATGCACTTGATGCATCATGCACTC
1 AACATCGAATGCATTTGATGCATCATGCACTC
61880 TTAGTGCACC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
62 28 0.35
63 4 0.05
64 26 0.32
65 23 0.28
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCATGCACTCAGCCATGCACCGATGCACTGAGGATATTTGA
Done.