Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006327.1 Hibiscus syriacus cultivar Beakdansim tig00015124_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: 84560
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:3687 original size:22 final size:22
Alignment explanation
Indices: 3659--3737 Score: 113
Period size: 22 Copynumber: 3.6 Consensus size: 22
3649 ACATTTAAAT
3659 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* * *
3681 TCTTCAAATATGGTACATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
3703 TCTTCAAAGATGATAGATTATC
1 TCTTCAAAGATGATAGATTCTC
*
3725 TTTTCAAAGATGA
1 TCTTCAAAGATGA
3738 AAGCCTTATT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:4475 original size:45 final size:45
Alignment explanation
Indices: 4411--4936 Score: 730
Period size: 45 Copynumber: 11.7 Consensus size: 45
4401 TTCCCACATT
* *
4411 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCAGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* * *
4456 TGTAAGCCCTTCAATGCATGATGTTTTCAAAATCTTTGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
4501 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
* *
4546 TGTAAGCCCTTTAGTGCATGATGTTTTCAAAACCTTTGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
4591 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
4636 TGTAAGCCCCTTCAGTGCATGATG--TTC-AAACCTTCGGGTCATC
1 TGTAAG-CCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
4679 TGTAAGCCCTTCAGTGCATGATGTTTTC-AAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
4723 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
*
4768 TGTAAGCCCTTCAGTGC---ATGTTTTCAAAAAAAACCTT-AGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTC----AAAACCTTCGGGTCATC
* * *
4813 CGTAAGACCTTCAGTGCAGGA--TTTTCAAAAAAACCTTCGGGTCATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTC---AAAACCTTCGGGTCATC
* * * *
4859 CGTAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGTTATC
1 TGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGGTCATC
* *
4906 TGTAAGACCTTCAGTGCAGGATGTTTTCAAA
1 TGTAAGCCCTTCAGTGCATGATGTTTTCAAA
4937 TGAGATTTTA
Statistics
Matches: 446, Mismatches: 20, Indels: 29
0.90 0.04 0.06
Matches are distributed among these distances:
42 25 0.06
43 22 0.05
44 50 0.11
45 238 0.53
46 66 0.15
47 39 0.09
48 6 0.01
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (45 bp):
TGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATC
Found at i:4872 original size:222 final size:220
Alignment explanation
Indices: 4412--4936 Score: 727
Period size: 222 Copynumber: 2.3 Consensus size: 220
4402 TCCCACATTT
* *
4412 GTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCAGGTCATCTGTAAGCCCTTCAATGCATGA
1 GTAAGCCCTTCAGTGCATGATG-TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGA
* * *
4477 TGTTTTCAAAATCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
65 TGTTTTC-AAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
4542 CATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTG
129 CATCTGTAAGCCCTTCAGTGCA--ATGTTTTCAAAACCTTTAGGTCATCCGTAAGACCTTCAGTG
* *
4607 CATGATGTTTTCAAAACCTTCGGGTCATCT
192 CAGGA-GTTTTCAAAACCTTCGGGTCATCC
4637 GTAAGCCCCTTCAGTGCATGATG-TTCAAA-CCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGA
1 GTAAG-CCCTTCAGTGCATGATGTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGA
4700 TGTTTTCAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
65 TGTTTTCAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTC
4765 ATCTGTAAGCCCTTCAGTGC-ATGTTTTCAAAAAAAACC-TTAGGTCATCCGTAAGACCTTCAGT
130 ATCTGTAAGCCCTTCAGTGCAATGTTTTC----AAAACCTTTAGGTCATCCGTAAGACCTTCAGT
4828 GCAGGA-TTTTCAAAAAAACCTTCGGGTCATCC
191 GCAGGAGTTTTC---AAAACCTTCGGGTCATCC
* * * * *
4860 GTAAGACCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGTTATCTGTAAGACCTTCAGTGCAG
1 GTAAGCCCTTCAGTGCATGATG-TTTC--AAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCAT
4925 GATGTTTTCAAA
63 GATGTTTTCAAA
4937 TGAGATTTTA
Statistics
Matches: 271, Mismatches: 16, Indels: 24
0.87 0.05 0.08
Matches are distributed among these distances:
219 8 0.03
220 5 0.02
222 116 0.43
223 67 0.25
224 9 0.03
225 5 0.02
226 20 0.07
227 41 0.15
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (220 bp):
GTAAGCCCTTCAGTGCATGATGTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGAT
GTTTTCAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCA
TCTGTAAGCCCTTCAGTGCAATGTTTTCAAAACCTTTAGGTCATCCGTAAGACCTTCAGTGCAGG
AGTTTTCAAAACCTTCGGGTCATCC
Found at i:5208 original size:20 final size:20
Alignment explanation
Indices: 5186--5262 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
5176 TTTTTTCATT
5186 TTATTATTATTATA--ATTA
1 TTATTATTATTATATTATTA
* *
5204 TT-TTATAAATATATTATTA
1 TTATTATTATTATATTATTA
5223 TTATTATTATTATATTATTA
1 TTATTATTATTATATTATTA
5243 TTATTATTATTATATTATTA
1 TTATTATTATTATATTATTA
5263 CTATAAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
17 9 0.17
18 2 0.04
19 6 0.12
20 35 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTATTATTATATTATTA
Found at i:5278 original size:20 final size:20
Alignment explanation
Indices: 5207--5283 Score: 61
Period size: 20 Copynumber: 4.0 Consensus size: 20
5197 ATAATTATTT
* *
5207 TATAAATATATTATTATTAT
1 TATAAAAATATTATTATTAC
* **
5227 TATTATTATATTATTATTA-
1 TATAAAAATATTATTATTAC
** *
5246 T-TATTATTA-TATTATTAC
1 TATAAAAATATTATTATTAC
5264 TATAAAAATATTATTATTAC
1 TATAAAAATATTATTATTAC
5284 AGGCCAAATA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
17 8 0.18
18 5 0.11
19 6 0.13
20 26 0.58
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
TATAAAAATATTATTATTAC
Found at i:5282 original size:3 final size:3
Alignment explanation
Indices: 5186--5262 Score: 99
Period size: 3 Copynumber: 27.0 Consensus size: 3
5176 TTTTTTCATT
* * *
5186 TTA TTA TTA TTA TAA TTA TT- TTA TAA ATA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5232 TTA -TA TTA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5263 CTATAAAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
2 8 0.12
3 57 0.88
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5345 original size:21 final size:21
Alignment explanation
Indices: 5320--5380 Score: 97
Period size: 21 Copynumber: 3.0 Consensus size: 21
5310 AAATTAAAAT
5320 GGCCCAGATCTAGAACCCGAA
1 GGCCCAGATCTAGAACCCGAA
* *
5341 GGCCCAGATCCAGAACCCGGA
1 GGCCCAGATCTAGAACCCGAA
5362 GGCCCAGATCTAG-ACCCGA
1 GGCCCAGATCTAGAACCCGA
5381 CCCAACACCC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 5 0.14
21 31 0.86
ACGTcount: A:0.30, C:0.36, G:0.26, T:0.08
Consensus pattern (21 bp):
GGCCCAGATCTAGAACCCGAA
Found at i:5442 original size:23 final size:23
Alignment explanation
Indices: 5412--5511 Score: 173
Period size: 23 Copynumber: 4.3 Consensus size: 23
5402 TTAGCATCTT
5412 CTCCGCCGCCTCTACTCCAACTG
1 CTCCGCCGCCTCTACTCCAACTG
5435 CTCCGCCGCCTCTACTCCAACTG
1 CTCCGCCGCCTCTACTCCAACTG
*
5458 CTCCACCGCCTCTACTCCAACTG
1 CTCCGCCGCCTCTACTCCAACTG
* *
5481 CTCCGCCACCTCTACTTCAACTG
1 CTCCGCCGCCTCTACTCCAACTG
5504 CTCCGCCG
1 CTCCGCCG
5512 TCATGTTCCC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.14, C:0.52, G:0.12, T:0.22
Consensus pattern (23 bp):
CTCCGCCGCCTCTACTCCAACTG
Found at i:5932 original size:19 final size:19
Alignment explanation
Indices: 5908--5959 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 19
5898 GGCCACTGTG
5908 AATAGTGACCGATGGCCGA
1 AATAGTGACCGATGGCCGA
* *
5927 AATAGTGATCGACGATGGTCGG
1 AATAGTGA-C--CGATGGCCGA
5949 AATAGTGACCG
1 AATAGTGACCG
5960 GTGGTAATCG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 10 0.36
20 1 0.04
21 1 0.04
22 16 0.57
ACGTcount: A:0.31, C:0.17, G:0.33, T:0.19
Consensus pattern (19 bp):
AATAGTGACCGATGGCCGA
Found at i:8573 original size:6 final size:7
Alignment explanation
Indices: 8556--8581 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
8546 TTAAAAGTTA
8556 AAAAAAT
1 AAAAAAT
8563 AAAAAAT
1 AAAAAAT
8570 AAAAAAT
1 AAAAAAT
8577 AAAAA
1 AAAAA
8582 CAGAGATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:9088 original size:15 final size:15
Alignment explanation
Indices: 9065--9094 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9055 AAGGTTGACG
9065 GTCTCGTATAGTTAA
1 GTCTCGTATAGTTAA
*
9080 GTCTTGTATAGTTAA
1 GTCTCGTATAGTTAA
9095 ATCTATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (15 bp):
GTCTCGTATAGTTAA
Found at i:9323 original size:29 final size:29
Alignment explanation
Indices: 9287--9351 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
9277 TTAAAGGATG
*
9287 ACAAATTCATAAAATTTTATGGGGTGAAA
1 ACAAATTCATAAAATTTTATAGGGTGAAA
9316 ACAAATTCATAAAATTTTATAGGGTGAAA
1 ACAAATTCATAAAATTTTATAGGGTGAAA
9345 ACAAATT
1 ACAAATT
9352 TTCAATCGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.31
Consensus pattern (29 bp):
ACAAATTCATAAAATTTTATAGGGTGAAA
Found at i:10467 original size:19 final size:19
Alignment explanation
Indices: 10443--10479 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
10433 ATGACCAACG
*
10443 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
10462 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
10480 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:10732 original size:22 final size:22
Alignment explanation
Indices: 10707--10748 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
10697 GGCGACATCC
10707 GTCCCCATCTCCGACGAAATAT
1 GTCCCCATCTCCGACGAAATAT
*
10729 GTCCCCATCTCCGGCGAAAT
1 GTCCCCATCTCCGACGAAAT
10749 CCGTCTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.38, G:0.17, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATAT
Found at i:11577 original size:20 final size:20
Alignment explanation
Indices: 11552--11638 Score: 140
Period size: 20 Copynumber: 4.4 Consensus size: 20
11542 GAAATTCAGT
11552 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
11572 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* * *
11592 GTTGCAATAGTCAAAATCAC
1 GTTGCGATAGTCAGAATCGC
11612 GTTGCGAT-GTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
11631 GTTGCGAT
1 GTTGCGAT
11639 TTACATATTC
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
19 17 0.28
20 44 0.72
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:11678 original size:21 final size:21
Alignment explanation
Indices: 11654--11700 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
11644 TATTCGCATT
*
11654 GCGATTTTCTAAAATCGCAAC
1 GCGATTTTCGAAAATCGCAAC
* * *
11675 GCGAATTTGGAAAATCGCAAT
1 GCGATTTTCGAAAATCGCAAC
11696 GCGAT
1 GCGAT
11701 AGTCAAAATC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (21 bp):
GCGATTTTCGAAAATCGCAAC
Found at i:11720 original size:41 final size:41
Alignment explanation
Indices: 11566--11721 Score: 122
Period size: 39 Copynumber: 3.9 Consensus size: 41
11556 CGATAGTCAG
* * *
11566 AATCGCGTTGCGATAGTCAGAATCGCGTTGC-AA-TAGTCAA
1 AATCGCATTGCGATAGTCAAAATCGCGTTGCGAATTTG-CAA
* * * * *
11606 AATCACGTTGCGAT-GTCAGAATCGCGTTGCG-ATTTACAT
1 AATCGCATTGCGATAGTCAAAATCGCGTTGCGAATTTGCAA
* ** *** *
11645 ATTCGCATTGCGATTTTCTAAAATCGCAACGCGAATTTGGAA
1 AATCGCATTGCGATAGTC-AAAATCGCGTTGCGAATTTGCAA
*
11687 AATCGCAATGCGATAGTCAAAATCGCGTTGCGAAT
1 AATCGCATTGCGATAGTCAAAATCGCGTTGCGAAT
11722 CTGGAAACTG
Statistics
Matches: 89, Mismatches: 22, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
39 30 0.34
40 16 0.18
41 24 0.27
42 19 0.21
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (41 bp):
AATCGCATTGCGATAGTCAAAATCGCGTTGCGAATTTGCAA
Found at i:20507 original size:21 final size:21
Alignment explanation
Indices: 20481--20548 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 21
20471 TTTGAAATTA
20481 CTCCCCCTTACTCTAACACTT
1 CTCCCCCTTACTCTAACACTT
*
20502 CT-CCCCTT--T-AAACACTTT
1 CTCCCCCTTACTCTAACAC-TT
20520 AACATCCCCCTTACTCTAACACTT
1 --C-TCCCCCTTACTCTAACACTT
20544 CTCCC
1 CTCCC
20549 ATTCAAACAC
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
17 5 0.14
18 3 0.08
20 7 0.19
21 7 0.19
22 7 0.19
24 3 0.08
25 5 0.14
ACGTcount: A:0.22, C:0.46, G:0.00, T:0.32
Consensus pattern (21 bp):
CTCCCCCTTACTCTAACACTT
Found at i:20541 original size:42 final size:42
Alignment explanation
Indices: 20482--20566 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
20472 TTGAAATTAC
* *
20482 TCCCCCTTACTCTAACACTTCTCCCCTTTAAACACTTTAACA
1 TCCCCCTTACTCTAACACTTCTCCCATTCAAACACTTTAACA
20524 TCCCCCTTACTCTAACACTTCTCCCATTCAAACACTTTAACA
1 TCCCCCTTACTCTAACACTTCTCCCATTCAAACACTTTAACA
20566 T
1 T
20567 TTCTCCCCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.40, G:0.00, T:0.33
Consensus pattern (42 bp):
TCCCCCTTACTCTAACACTTCTCCCATTCAAACACTTTAACA
Found at i:20873 original size:17 final size:17
Alignment explanation
Indices: 20820--20885 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 17
20810 TAAATATAAG
*
20820 TTCAAA-AATCCATAAA
1 TTCAAACAATCCACAAA
*
20836 TTCAAACAAAT--TCAAA
1 TTCAAAC-AATCCACAAA
*
20852 GTCAAACAATCCACAAA
1 TTCAAACAATCCACAAA
*
20869 TTCAAACATTCCA-AAA
1 TTCAAACAATCCACAAA
20885 T
1 T
20886 GTTAAAACAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 3 0.08
16 19 0.47
17 15 0.38
18 3 0.08
ACGTcount: A:0.53, C:0.23, G:0.02, T:0.23
Consensus pattern (17 bp):
TTCAAACAATCCACAAA
Found at i:21164 original size:18 final size:18
Alignment explanation
Indices: 21141--21179 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
21131 GCATTTGATA
*
21141 CTCTGGACGAGGTTGTTC
1 CTCTGGACGAGCTTGTTC
* *
21159 CTCTGGAGGTGCTTGTTC
1 CTCTGGACGAGCTTGTTC
21177 CTC
1 CTC
21180 GTGCTGCTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.26, G:0.31, T:0.36
Consensus pattern (18 bp):
CTCTGGACGAGCTTGTTC
Found at i:22838 original size:22 final size:22
Alignment explanation
Indices: 22749--22851 Score: 93
Period size: 22 Copynumber: 4.7 Consensus size: 22
22739 AGAATCCCAG
* * *
22749 GGGGGTATCGATTCCCCTGCAG
1 GGGGGAATCGATTCCCCTTCAA
* *
22771 GGGGGTATCGATTCCCCTAC-A
1 GGGGGAATCGATTCCCCTTCAA
* **
22792 GGGGGAATCGGTTCATCTTCAAA
1 GGGGGAATCGATTCCCCTTC-AA
*
22815 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
22837 -GGGGATATCGATTCC
1 GGGGGA-ATCGATTCC
22852 TTCAGCACTA
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
21 20 0.29
22 29 0.43
23 19 0.28
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.24
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:26685 original size:21 final size:21
Alignment explanation
Indices: 26661--26700 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
26651 AAAACTATTT
26661 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTT-ATATTTTGAAACA
26682 TCATTTTTATATTTTGAAA
1 TCATTTTTATATTTTGAAA
26701 ATAGAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (21 bp):
TCATTTTTATATTTTGAAACA
Found at i:29013 original size:2 final size:2
Alignment explanation
Indices: 29006--29037 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28996 TAACAATCTT
29006 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
29038 AATAAAAATT
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):
TA
Found at i:32139 original size:59 final size:59
Alignment explanation
Indices: 32018--32139 Score: 158
Period size: 59 Copynumber: 2.1 Consensus size: 59
32008 TCGGGTGGTA
* * * *
32018 ATTTTGTAACTTTTAATAATCGGAGGACTCAACAAAGTAACACCCTATAGTTGGGGATC
1 ATTTTATAACTTTTAATAATCAGAGGACTCAACAAAGTAACACCCTATAGTTGGAGACC
* *
32077 ATTTTATAACTTTTAAT-AGCTAGAGGACTCAACAAAGTAACGCCCTATA-TTCGGAGACC
1 ATTTTATAACTTTTAATAATC-AGAGGACTCAACAAAGTAACACCCTATAGTT-GGAGACC
32136 ATTT
1 ATTT
32140 GTGTAATTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
58 4 0.07
59 51 0.93
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (59 bp):
ATTTTATAACTTTTAATAATCAGAGGACTCAACAAAGTAACACCCTATAGTTGGAGACC
Found at i:33075 original size:18 final size:17
Alignment explanation
Indices: 33041--33080 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
33031 TTTCTAAATT
33041 TTTTAAATTATTATATA
1 TTTTAAATTATTATATA
* *
33058 TTTTAAATATTTTTTATA
1 TTTTAAAT-TATTATATA
33076 TTTTA
1 TTTTA
33081 TATTGATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAAATTATTATATA
Found at i:37636 original size:2 final size:2
Alignment explanation
Indices: 37631--37666 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
37621 ATATGAAGAA
*
37631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37667 GATTATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38641 original size:29 final size:29
Alignment explanation
Indices: 38609--38669 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
38599 ATAGTCAAGT
38609 GATCATTTTATAACTTTTAATAGTTGAGA
1 GATCATTTTATAACTTTTAATAGTTGAGA
*
38638 GATCATTTTGTAACTTTTAATAGTTGAGA
1 GATCATTTTATAACTTTTAATAGTTGAGA
38667 GAT
1 GAT
38670 TTAACAAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (29 bp):
GATCATTTTATAACTTTTAATAGTTGAGA
Found at i:39912 original size:26 final size:27
Alignment explanation
Indices: 39883--39944 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
39873 TATGTTAATA
*
39883 TTATTTT-TTTAAGAGAATGATATTTT
1 TTATTTTATTGAAGAGAATGATATTTT
*
39909 TTATTTTGATTGAAGATAATGATATTTT
1 TTATTTT-ATTGAAGAGAATGATATTTT
39937 TCTATTTT
1 T-TATTTT
39945 GGTTGGAGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 7 0.23
28 18 0.58
29 6 0.19
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.58
Consensus pattern (27 bp):
TTATTTTATTGAAGAGAATGATATTTT
Found at i:53880 original size:32 final size:32
Alignment explanation
Indices: 53813--53880 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
53803 ACTCTGTCAT
* *
53813 TAGATCTTCAACGTCGTTAAATTATAGATAGA
1 TAGATCTTCAACGTCGTTAAATTATACATAAA
*
53845 TAGATCTTCAACGTCGTTAAATTATACCTAAA
1 TAGATCTTCAACGTCGTTAAATTATACATAAA
53877 TAGA
1 TAGA
53881 CAGATTGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (32 bp):
TAGATCTTCAACGTCGTTAAATTATACATAAA
Found at i:59430 original size:23 final size:23
Alignment explanation
Indices: 59404--59464 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
59394 GTGTTGGTTA
59404 TGAACATTAAACGAACATGTTCG
1 TGAACATTAAACGAACATGTTCG
59427 TGAACATTAAACGAACATGTTCG
1 TGAACATTAAACGAACATGTTCG
*
59450 TGAACGTTAAACGAA
1 TGAACATTAAACGAA
59465 TATATTTATG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (23 bp):
TGAACATTAAACGAACATGTTCG
Found at i:59955 original size:21 final size:22
Alignment explanation
Indices: 59929--59971 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
59919 ACGGTACTTG
59929 AATCAAAT-T-AATTGATTAATA
1 AATCAAATATCAA-TGATTAATA
59950 AATCAAATATCAATGATTAATA
1 AATCAAATATCAATGATTAATA
59972 TTAAAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 10 0.50
23 2 0.10
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (22 bp):
AATCAAATATCAATGATTAATA
Found at i:61447 original size:10 final size:10
Alignment explanation
Indices: 61414--61491 Score: 57
Period size: 10 Copynumber: 7.1 Consensus size: 10
61404 GTGTTTGTGT
61414 TGTTCGTTTA
1 TGTTCGTTTA
*
61424 TGTTCCTTTATTA
1 TGTT-C-GT-TTA
61437 TGTTCGTTTA
1 TGTTCGTTTA
*
61447 TGTTTGTTCGTTTG
1 ----TGTTCGTTTA
61461 TGTTCGTTTA
1 TGTTCGTTTA
* *
61471 CGTTCTTTTA
1 TGTTCGTTTA
61481 TGTTCGTTTA
1 TGTTCGTTTA
61491 T
1 T
61492 CATTTAAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
10 33 0.62
11 2 0.04
12 2 0.04
13 7 0.13
14 9 0.17
ACGTcount: A:0.09, C:0.12, G:0.18, T:0.62
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:62905 original size:28 final size:28
Alignment explanation
Indices: 62873--62945 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
62863 TAAGTTATAC
62873 TTTTTATATTTTAGTCAATGAATTTAAT-
1 TTTTTATATTTTAGTC-ATGAATTTAATA
* * *
62901 TTTTTAATATTTTAATCCTGAATTTATTA
1 TTTTT-ATATTTTAGTCATGAATTTAATA
*
62930 TTTTTACATTTTAGTC
1 TTTTTATATTTTAGTC
62946 CCTACCTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
28 23 0.61
29 15 0.39
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (28 bp):
TTTTTATATTTTAGTCATGAATTTAATA
Found at i:63100 original size:28 final size:27
Alignment explanation
Indices: 63069--63144 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 27
63059 AATTTATAAC
63069 TATTCATTTTTTCTTTGATTTA-TTTT
1 TATTCATTTTTTCTTTGATTTATTTTT
* *
63095 TA-T-ATTTTTT-TGTG-TTT-TGTTT
1 TATTCATTTTTTCTTTGATTTATTTTT
63117 TATTTCATTTTTTTCTTTGATTTATTTT
1 TA-TTCA-TTTTTTCTTTGATTTATTTT
63145 CCTTTTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
22 8 0.21
23 3 0.08
24 8 0.21
25 2 0.05
26 8 0.21
27 3 0.08
28 3 0.08
29 3 0.08
ACGTcount: A:0.13, C:0.05, G:0.07, T:0.75
Consensus pattern (27 bp):
TATTCATTTTTTCTTTGATTTATTTTT
Found at i:63105 original size:27 final size:24
Alignment explanation
Indices: 63071--63226 Score: 66
Period size: 23 Copynumber: 6.6 Consensus size: 24
63061 TTTATAACTA
63071 TTCA-TTTTTTCTTTGATTTATTT
1 TTCATTTTTTTCTTTGATTTATTT
* * *
63094 TTATATTTTTTTGTGTTTTG-TTT-TAT
1 TT-CA-TTTTTT-T-CTTTGATTTATTT
63120 TTCATTTTTTTCTTTGATTTA-TT
1 TTCATTTTTTTCTTTGATTTATTT
* * *
63143 TTC-CTTTTTT-ATT-ATTTCTTT
1 TTCATTTTTTTCTTTGATTTATTT
*
63164 TTAATTTTTTTTCTCTT--TTTGATTT
1 TTCA-TTTTTTTCT-TTGATTT-ATTT
*
63189 ATTC-TTTTATTCTTT--TTTATTT
1 -TTCATTTTTTTCTTTGATTTATTT
*
63211 TTACATTTCTTTCTTT
1 TT-CATTTTTTTCTTT
63227 CTTTTGATTT
Statistics
Matches: 100, Mismatches: 17, Indels: 32
0.67 0.11 0.21
Matches are distributed among these distances:
20 4 0.04
21 8 0.08
22 15 0.15
23 30 0.30
24 18 0.18
25 6 0.06
26 11 0.11
27 4 0.04
28 4 0.04
ACGTcount: A:0.12, C:0.09, G:0.04, T:0.75
Consensus pattern (24 bp):
TTCATTTTTTTCTTTGATTTATTT
Found at i:63145 original size:23 final size:23
Alignment explanation
Indices: 63071--63152 Score: 69
Period size: 23 Copynumber: 3.4 Consensus size: 23
63061 TTTATAACTA
63071 TTCA-TTTTTTCTTTGATTTATTT
1 TTCATTTTTTTCTTTGATTTA-TT
* * *
63094 TTATATTTTTTTGTGTTTTGTTTTA-T
1 TT-CA-TTTTTT-T-CTTTGATTTATT
63120 TTCATTTTTTTCTTTGATTTATT
1 TTCATTTTTTTCTTTGATTTATT
*
63143 TTCCTTTTTT
1 TTCATTTTTT
63153 ATTATTTCTT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
22 8 0.17
23 13 0.28
24 7 0.15
25 1 0.02
26 8 0.17
27 1 0.02
28 8 0.17
ACGTcount: A:0.11, C:0.07, G:0.06, T:0.76
Consensus pattern (23 bp):
TTCATTTTTTTCTTTGATTTATT
Found at i:63194 original size:32 final size:31
Alignment explanation
Indices: 63136--63196 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
63126 TTTTTCTTTG
*
63136 ATTTATTTTCCTTTTTTATTATTTCTTTTTA
1 ATTTATTTTCCTTTTTGATTATTTCTTTTTA
*
63167 ATTTTTTTTCTCTTTTTGATT-TATTCTTTT
1 ATTTATTTTC-CTTTTTGATTAT-TTCTTTT
63197 ATTCTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.13, C:0.10, G:0.02, T:0.75
Consensus pattern (31 bp):
ATTTATTTTCCTTTTTGATTATTTCTTTTTA
Found at i:63197 original size:31 final size:30
Alignment explanation
Indices: 63128--63206 Score: 74
Period size: 31 Copynumber: 2.6 Consensus size: 30
63118 ATTTCATTTT
* * *
63128 TTTC-TTTGATTTATTTTCCTTTTTTATTA
1 TTTCTTTTTATTTTTTTTCCTTTTTGATTA
63157 TTTCTTTTTAATTTTTTTTCTCTTTTTGATT-
1 TTTCTTTTT-ATTTTTTTTC-CTTTTTGATTA
63188 TATTC-TTTTATTCTTTTTT
1 T-TTCTTTTTATT-TTTTTT
63207 ATTTTTACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
29 4 0.10
30 6 0.14
31 20 0.48
32 12 0.29
ACGTcount: A:0.11, C:0.10, G:0.03, T:0.76
Consensus pattern (30 bp):
TTTCTTTTTATTTTTTTTCCTTTTTGATTA
Found at i:63286 original size:37 final size:40
Alignment explanation
Indices: 63227--63338 Score: 133
Period size: 44 Copynumber: 2.8 Consensus size: 40
63217 TTCTTTCTTT
*
63227 CTTTTGATTTA-T-TTAATATATTTTTATTTTATTTTC-C-
1 CTTTTGATTTATTATTATTAT-TTTTTATTTTATTTTCTCA
*
63264 CTTTTGATTTATTATTATTATTTATTTATTGTTTTTTTCTTCA
1 CTTTTGATTTATTATTATTATTT-TTTATT-TTATTTTC-TCA
63307 TCTTTTGATTTATTATTATTATTTTTTATTTT
1 -CTTTTGATTTATTATTATTATTTTTTATTTT
63339 CATTCTTATG
Statistics
Matches: 65, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
37 11 0.17
38 3 0.05
39 12 0.18
40 7 0.11
42 3 0.05
43 6 0.09
44 23 0.35
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.71
Consensus pattern (40 bp):
CTTTTGATTTATTATTATTATTTTTTATTTTATTTTCTCA
Found at i:64409 original size:18 final size:18
Alignment explanation
Indices: 64375--64409 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
64365 ACTAAATATT
*
64375 TGTCCCGATGGAACACTA
1 TGTCCCGAAGGAACACTA
*
64393 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGAACACT
64410 GATTATTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGAACACTA
Found at i:70951 original size:18 final size:18
Alignment explanation
Indices: 70928--70962 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
70918 ACTGAATATT
70928 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
70946 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
70963 GATAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:71561 original size:19 final size:19
Alignment explanation
Indices: 71537--71581 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
71527 CCTTAACGGG
71537 TGCATCGATGCACTAACTA
1 TGCATCGATGCACTAACTA
71556 TGCATCGATGCACTAACTA
1 TGCATCGATGCACTAACTA
71575 TGCATCG
1 TGCATCG
71582 GTACATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (19 bp):
TGCATCGATGCACTAACTA
Found at i:73107 original size:22 final size:22
Alignment explanation
Indices: 73082--73131 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
73072 GATCATGTCA
73082 GGGTAGGATTAATAAGTATGTG
1 GGGTAGGATTAATAAGTATGTG
73104 GGGTAGGATTAATAAGTATGTG
1 GGGTAGGATTAATAAGTATGTG
*
73126 TGGTAG
1 GGGTAG
73132 ATATCATGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.38, T:0.32
Consensus pattern (22 bp):
GGGTAGGATTAATAAGTATGTG
Found at i:75449 original size:64 final size:63
Alignment explanation
Indices: 75331--75471 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
75321 CACATTCAAT
* *
75331 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCAT-AGGTA
* * * * * * *
75394 GTGCATCGATGCATCCCTTTAAA-ATGAAAATATTGAAGGTAATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA-CCCTTTAAAGAAG-AAACATCGAAGGCAATTGGTGCATCGATGCATAGGTA
75458 GTGCATCGATGCAC
1 GTGCATCGATGCAC
75472 ATGTTAAATA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 18 0.27
64 48 0.73
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCATAGGTA
Found at i:76391 original size:36 final size:36
Alignment explanation
Indices: 76337--76415 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 36
76327 AGGGTCTACG
*
76337 TGGTCCTTCGGGATATAGTGGTCATTCGGGACATAA
1 TGGTCCTTCGGGACATAGTGGTCATTCGGGACATAA
* * *
76373 TGGTTCTTCGGGACATAGTGGTCATTCGGGATATAG
1 TGGTCCTTCGGGACATAGTGGTCATTCGGGACATAA
76409 TGGTCCT
1 TGGTCCT
76416 ACGAGATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.19, C:0.16, G:0.32, T:0.33
Consensus pattern (36 bp):
TGGTCCTTCGGGACATAGTGGTCATTCGGGACATAA
Found at i:76423 original size:18 final size:18
Alignment explanation
Indices: 76336--76415 Score: 106
Period size: 18 Copynumber: 4.4 Consensus size: 18
76326 GAGGGTCTAC
76336 GTGGTCCTTCGGGATATA
1 GTGGTCCTTCGGGATATA
* *
76354 GTGGTCATTCGGGACATA
1 GTGGTCCTTCGGGATATA
* * *
76372 ATGGTTCTTCGGGACATA
1 GTGGTCCTTCGGGATATA
*
76390 GTGGTCATTCGGGATATA
1 GTGGTCCTTCGGGATATA
76408 GTGGTCCT
1 GTGGTCCT
76416 ACGAGATAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.33
Consensus pattern (18 bp):
GTGGTCCTTCGGGATATA
Found at i:79870 original size:20 final size:20
Alignment explanation
Indices: 79825--79902 Score: 111
Period size: 20 Copynumber: 3.7 Consensus size: 20
79815 GCATGGCTAG
79825 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
79849 TGCATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
79869 TGCATCGATGCATTGTAGAA
1 TGCATCGATGCACTGTAGAA
79889 TGCATCGATGCACT
1 TGCATCGATGCACT
79903 TCAAAGGGAA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
20 36 0.69
22 1 0.02
23 2 0.04
24 13 0.25
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:80813 original size:18 final size:18
Alignment explanation
Indices: 80704--80805 Score: 161
Period size: 18 Copynumber: 5.7 Consensus size: 18
80694 GTCATTCGAC
*
80704 ACATAGTGGTCCTTCGGG
1 ACATAATGGTCCTTCGGG
80722 ACATAATGGTCCTTCGGG
1 ACATAATGGTCCTTCGGG
80740 ACATAATGGTCCTTCGGG
1 ACATAATGGTCCTTCGGG
80758 ACATAATGGTCCTTC-GG
1 ACATAATGGTCCTTCGGG
* *
80775 ACACAGTGGTCCTTCGGG
1 ACATAATGGTCCTTCGGG
*
80793 ACATAGTGGTCCT
1 ACATAATGGTCCT
80806 ATGGGACAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
17 15 0.19
18 64 0.81
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (18 bp):
ACATAATGGTCCTTCGGG
Found at i:82683 original size:2 final size:2
Alignment explanation
Indices: 82676--82714 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
82666 CCATAACAAA
82676 AT AT AT AT AT AT AT -T 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
82715 GTATTTCCCA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.