Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007481.1 Hibiscus syriacus cultivar Beakdansim tig00020608_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: 55553
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:708 original size:37 final size:36
Alignment explanation
Indices: 655--750 Score: 129
Period size: 37 Copynumber: 2.6 Consensus size: 36
645 CCTTTTCGTC
*
655 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATA-AATT
* * *
692 TTGCTAGGATTTAAACTCCTAAAAATAGGATAAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAAATT
**
728 CTACTATAATTTAAACTCCTAAA
1 CTACTAGGATTTAAACTCCTAAA
751 GATATCCACA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 22 0.43
37 29 0.57
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (36 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAAATT
Found at i:1319 original size:9 final size:9
Alignment explanation
Indices: 1305--1338 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1295 TTTGCATTTT
1305 TATTATTAC
1 TATTATTAC
*
1314 TATTATTAT
1 TATTATTAC
*
1323 TATTTTTAC
1 TATTATTAC
1332 TATTATT
1 TATTATT
1339 TTCCTTTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (9 bp):
TATTATTAC
Found at i:1335 original size:12 final size:12
Alignment explanation
Indices: 1300--1462 Score: 67
Period size: 11 Copynumber: 13.5 Consensus size: 12
1290 TTTTCTTTGC
1300 ATTTTTATTATT
1 ATTTTTATTATT
* *
1312 ACTATTATTATT
1 ATTTTTATTATT
*
1324 ATTTTTACTATT
1 ATTTTTATTATT
**
1336 ATTTTCCTT-TT
1 ATTTTTATTATT
1347 ATTCTACTTATTTATAT
1 ATT-T--TTA-TTAT-T
* *
1364 ATATGTA-TATT
1 ATTTTTATTATT
1375 -TTTTATATT-TT
1 ATTTT-TATTATT
*
1386 ATTATTATTATT
1 ATTTTTATTATT
1398 -TTTTTACTTTATCT
1 ATTTTTA--TTAT-T
1412 -TTTTT-TTATT
1 ATTTTTATTATT
1422 ATTCTTGTATTATT
1 ATT-TT-TATTATT
*
1436 A-CTTTATTATT
1 ATTTTTATTATT
*
1447 -TTTATATTA-T
1 ATTTTTATTATT
1457 ATTTTT
1 ATTTTT
1463 TAATTATATA
Statistics
Matches: 112, Mismatches: 20, Indels: 39
0.65 0.12 0.23
Matches are distributed among these distances:
10 4 0.04
11 42 0.38
12 39 0.35
13 5 0.04
14 15 0.13
15 2 0.02
16 2 0.02
17 3 0.03
ACGTcount: A:0.24, C:0.06, G:0.01, T:0.69
Consensus pattern (12 bp):
ATTTTTATTATT
Found at i:1380 original size:23 final size:23
Alignment explanation
Indices: 1354--1459 Score: 60
Period size: 24 Copynumber: 4.5 Consensus size: 23
1344 TTTATTCTAC
1354 TTAT-TTATATATATGTA-TATTTT
1 TTATATTATAT-TAT-TATTATTTT
*
1377 TTATATTTTATTATTATTATTTT
1 TTATATTATATTATTATTATTTT
* * *
1400 TT-TACTTTATCTTTTTTTTATTATT
1 TTATA--TTATATTATTATTATT-TT
* *
1425 CTTGTATTATTACT-TTATTA-TTT
1 -TTATATTA-TATTATTATTATTTT
1448 TTATATTATATT
1 TTATATTATATT
1460 TTTTAATTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
21 3 0.05
22 11 0.17
23 17 0.26
24 18 0.28
25 10 0.15
26 4 0.06
27 2 0.03
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.70
Consensus pattern (23 bp):
TTATATTATATTATTATTATTTT
Found at i:1419 original size:33 final size:31
Alignment explanation
Indices: 1377--1463 Score: 92
Period size: 33 Copynumber: 2.8 Consensus size: 31
1367 TGTATATTTT
1377 TTATATTTTATTATTATTATTTTTTTACTTTA
1 TTAT-TTTTATTATTATTATTTTTTTACTTTA
*
1409 TCT-TTTTT-TTATTATTCTTGTATTATTACTTTA
1 T-TATTTTTATTATTATTATT-T-TT-TTACTTTA
1442 TTATTTTTA-TATTA-TATTTTTT
1 TTATTTTTATTATTATTATTTTTT
1464 AATTATATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
29 1 0.02
30 12 0.26
31 6 0.13
32 8 0.17
33 20 0.43
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (31 bp):
TTATTTTTATTATTATTATTTTTTTACTTTA
Found at i:1930 original size:4 final size:4
Alignment explanation
Indices: 1894--1989 Score: 52
Period size: 4 Copynumber: 23.0 Consensus size: 4
1884 TCTTTTCGTC
* * * * *
1894 ATTT AATTT ATTA ATTT ATAT ATTT ACTT ATTT ATTT ATTT ATAT ATAT
1 ATTT -ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
* * *
1943 A-TT ATTCGT ATTT -TGTT ATAT ATTTT GTTT ATTT GTTTT ATTT ATTT
1 ATTT ATT--T ATTT AT-TT ATTT A-TTT ATTT ATTT -ATTT ATTT ATTT
1990 CTTTTTCTTT
Statistics
Matches: 70, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
3 3 0.04
4 53 0.76
5 10 0.14
6 4 0.06
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (4 bp):
ATTT
Found at i:2010 original size:22 final size:22
Alignment explanation
Indices: 1959--2012 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1949 CGTATTTTGT
*
1959 TATATATTTTGTTTATTTGTTT
1 TATATATTTTGTTTATTTGTTA
* * *
1981 TATTTATTTCTTTTTCTTT-TTA
1 TATATATTT-TGTTTATTTGTTA
2003 TATATATTTT
1 TATATATTTT
2013 ATTATTGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.04
22 18 0.69
23 7 0.27
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.74
Consensus pattern (22 bp):
TATATATTTTGTTTATTTGTTA
Found at i:5087 original size:38 final size:38
Alignment explanation
Indices: 5043--5145 Score: 109
Period size: 38 Copynumber: 2.7 Consensus size: 38
5033 AGATAAAGTT
* * *
5043 GGTTTCTAGAGAAAC-ATTCTTATGAAAGACAAGACTGA
1 GGTTTCTAGAGAAACGA-TCTTAAGAAAGACAAAACTAA
* * *
5081 GGTTTCTAGGGAAACGATCTTAAGATAGACAAAATTAA
1 GGTTTCTAGAGAAACGATCTTAAGAAAGACAAAACTAA
* * *
5119 GGTTTCCAGAGAAACGAGCCTAAGAAA
1 GGTTTCTAGAGAAACGATCTTAAGAAA
5146 ATCAAGAATG
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
38 52 0.98
39 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (38 bp):
GGTTTCTAGAGAAACGATCTTAAGAAAGACAAAACTAA
Found at i:5789 original size:45 final size:44
Alignment explanation
Indices: 5721--6260 Score: 464
Period size: 45 Copynumber: 12.0 Consensus size: 44
5711 AGTCAAGTTG
** * *
5721 AGAATGACATTACTAAAA-AGTTGACTCATTTTCCTAAGAAAGTCA
1 AGAATGACAACACTAAAAGA-TTGACTCCTTTTCC-GAGAAAGTCA
* * * * * *
5766 AGAATGACATCATTAAAAGGTTGACTACTCTTCGAGAGAAAGTCA
1 AGAATGACAACACTAAAAGATTGACTCCTTTTC-CGAGAAAGTCA
* * * *
5811 AGAATGACATCACTAAAAGGTTGACTCCTCTTCGCAAGAAAGTCA
1 AGAATGACAACACTAAAAGATTGACTCCTTTTC-CGAGAAAGTCA
*
5856 AGAATGACAACACTAAAATG-TTGACTCCTCTTTGCGAGAAAGTCA
1 AGAATGACAACACTAAAA-GATTGACTCCT-TTTCCGAGAAAGTCA
* * *
5901 AGAAGGACAACACTAAAAGATCGAATCCTTTTCGCGAGAAAGTCA
1 AGAATGACAACACTAAAAGATTGACTCCTTTTC-CGAGAAAGTCA
* * * * * * *
5946 AGAATAATATCACTAAAAGGTTGATTCCTCTTCATGAGAAAGTCA
1 AGAATGACAACACTAAAAGATTGACTCCTTTTC-CGAGAAAGTCA
* *
5991 AGAATGACAACACTAAAA-ATTGACTCCTCTTCACGAGAAATTCA
1 AGAATGACAACACTAAAAGATTGACTCCTTTTC-CGAGAAAGTCA
* * * *
6035 AGAATGATAACACTGAAAGATT--CTCTCTTCTTCATGAGAAATTCA
1 AGAATGACAACACTAAAAGATTGACTC-CTT-TTC-CGAGAAAGTCA
* * *
6080 AGAATGATAACACTAAAAGATTGACTCCTCTTTACGAGAAATTCA
1 AGAATGACAACACTAAAAGATTGACTCCT-TTTCCGAGAAAGTCA
* * * *
6125 AGAATGACAACACTAAAAGATTCATTCCTCTTCATGAGAAAGTCA
1 AGAATGACAACACTAAAAGATTGACTCCTTTTC-CGAGAAAGTCA
* * *
6170 AGAATGACAACACT-AAAGATTGACTCATTTTCAAGAGAAAGCCA
1 AGAATGACAACACTAAAAGATTGACTCCTTTTC-CGAGAAAGTCA
* * * * *
6214 AGAATGGCATCACTAAAATATTTACT-CTTCTTCATGAGAAAGTCA
1 AGAATGACAACACTAAAAGATTGACTCCTT-TTC-CGAGAAAGTCA
6259 AG
1 AG
6261 TTGAGGTTTT
Statistics
Matches: 416, Mismatches: 64, Indels: 30
0.82 0.13 0.06
Matches are distributed among these distances:
43 3 0.01
44 84 0.20
45 318 0.76
46 7 0.02
47 4 0.01
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (44 bp):
AGAATGACAACACTAAAAGATTGACTCCTTTTCCGAGAAAGTCA
Found at i:5834 original size:90 final size:90
Alignment explanation
Indices: 5721--6260 Score: 556
Period size: 90 Copynumber: 6.0 Consensus size: 90
5711 AGTCAAGTTG
** * * *
5721 AGAATGACATTACTAAAA-AGTTGACTCATTTTC-CTAAGAAAGTCAAGAATGACATCATTAAAA
1 AGAATGACAACACTAAAAGA-TTGACTCCTTTTCGC-AAGAAAGTCAAGAATGACAACACTAAAA
*
5784 GGTTGACTACTCTTCGA-GAGAAAGTCA
64 GGTTGACTCCTCTTC-ATGAGAAAGTCA
* * * *
5811 AGAATGACATCACTAAAAGGTTGACTCCTCTTCGCAAGAAAGTCAAGAATGACAACACTAAAATG
1 AGAATGACAACACTAAAAGATTGACTCCTTTTCGCAAGAAAGTCAAGAATGACAACACTAAAAGG
***
5876 TTGACTCCTCTTTGCGAGAAAGTCA
66 TTGACTCCTCTTCATGAGAAAGTCA
* * * * * * *
5901 AGAAGGACAACACTAAAAGATCGAATCCTTTTCGCGAGAAAGTCAAGAATAATATCACTAAAAGG
1 AGAATGACAACACTAAAAGATTGACTCCTTTTCGCAAGAAAGTCAAGAATGACAACACTAAAAGG
*
5966 TTGATTCCTCTTCATGAGAAAGTCA
66 TTGACTCCTCTTCATGAGAAAGTCA
* * * * * * *
5991 AGAATGACAACACTAAAA-ATTGACTCCTCTTCACGAGAAATTCAAGAATGATAACACTGAAAGA
1 AGAATGACAACACTAAAAGATTGACTCCTTTTCGCAAGAAAGTCAAGAATGACAACACTAAAAGG
** * *
6055 TTCTCTCTTCTTCATGAGAAATTCA
66 TTGACTCCTCTTCATGAGAAAGTCA
* *
6080 AGAATGATAACACTAAAAGATTGACTCCTCTTTACG--AGAAATTCAAGAATGACAACACTAAAA
1 AGAATGACAACACTAAAAGATTGACTCCT-TTT-CGCAAGAAAGTCAAGAATGACAACACTAAAA
* * *
6143 GATTCATTCCTCTTCATGAGAAAGTCA
64 GGTTGACTCCTCTTCATGAGAAAGTCA
* * * * * *
6170 AGAATGACAACACT-AAAGATTGACTCATTTTC-AAGAGAAAGCCAAGAATGGCATCACTAAAAT
1 AGAATGACAACACTAAAAGATTGACTCCTTTTCGCA-AGAAAGTCAAGAATGACAACACTAAAAG
* * *
6233 ATTTACTCTTCTTCATGAGAAAGTCA
65 GTTGACTCCTCTTCATGAGAAAGTCA
6259 AG
1 AG
6261 TTGAGGTTTT
Statistics
Matches: 382, Mismatches: 59, Indels: 19
0.83 0.13 0.04
Matches are distributed among these distances:
87 1 0.00
88 3 0.01
89 135 0.35
90 239 0.63
91 3 0.01
92 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (90 bp):
AGAATGACAACACTAAAAGATTGACTCCTTTTCGCAAGAAAGTCAAGAATGACAACACTAAAAGG
TTGACTCCTCTTCATGAGAAAGTCA
Found at i:6128 original size:179 final size:178
Alignment explanation
Indices: 5757--6260 Score: 609
Period size: 179 Copynumber: 2.8 Consensus size: 178
5747 CATTTTCCTA
* * * *
5757 AGAAAGTCAAGAATGACATCATTAAAAGGTTGACTACTCTTCGA-GAGAAAGTCAAGAATGACAT
1 AGAAAGTCAAGAATGACATCACTAAAAGGTTGATTCCTCTTC-ATGAGAAAGTCAAGAATGACAA
* * * * *
5821 CACTAAAAGGTTGACTCCTCTTCGCAAGAAAGTCAAGAATGACAACACTAAAATG-TTGACTCCT
65 CACTAAAA-ATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACTAAAA-GATT-TCTCTT
*** *
5885 CTTTGCGAGAAAGTCAAGAAGGACAACACTAAAAGATCGAATCCTTTTCGCG
127 CTTCATGAGAAAGTCAAGAAGGACAACACTAAAAGATCGAATCCTTTTCACG
* *
5937 AGAAAGTCAAGAATAATATCACTAAAAGGTTGATTCCTCTTCATGAGAAAGTCAAGAATGACAAC
1 AGAAAGTCAAGAATGACATCACTAAAAGGTTGATTCCTCTTCATGAGAAAGTCAAGAATGACAAC
* * *
6002 ACTAAAAATTGACTCCTCTTCACGAGAAATTCAAGAATGATAACACTGAAAGATTCTCTCTTCTT
66 ACTAAAAATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACTAAAAGATT-TCTCTTCTT
* * * * *
6067 CATGAGAAATTCAAGAATGATAACACTAAAAGATTGACTCCTCTTT-ACG
130 CATGAGAAAGTCAAGAAGGACAACACTAAAAGATCGAATCCT-TTTCACG
* * * *
6116 AGAAATTCAAGAATGACAACACTAAAAGATTCATTCCTCTTCATGAGAAAGTCAAGAATGACAAC
1 AGAAAGTCAAGAATGACATCACTAAAAGGTTGATTCCTCTTCATGAGAAAGTCAAGAATGACAAC
* * * * * * * *
6181 ACTAAAGATTGACTCATTTTCAAGAGAAAGCCAAGAATGGCATCACTAAAATATTTACTCTTCTT
66 ACTAAAAATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACTAAAAGATTT-CTCTTCTT
6246 CATGAGAAAGTCAAG
130 CATGAGAAAGTCAAG
6261 TTGAGGTTTT
Statistics
Matches: 278, Mismatches: 42, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
178 2 0.01
179 209 0.75
180 67 0.24
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (178 bp):
AGAAAGTCAAGAATGACATCACTAAAAGGTTGATTCCTCTTCATGAGAAAGTCAAGAATGACAAC
ACTAAAAATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACACTAAAAGATTTCTCTTCTTC
ATGAGAAAGTCAAGAAGGACAACACTAAAAGATCGAATCCTTTTCACG
Found at i:6364 original size:34 final size:34
Alignment explanation
Indices: 6302--6367 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
6292 GACTAAGATG
*
6302 AAATTTTAAAGAAACGATCCTAAGAAGGACTAAC
1 AAATTTTAAAGAAACCATCCTAAGAAGGACTAAC
*
6336 AAATTTCTAGAGAAACCATCCTAA-AAGGACTA
1 AAATTT-TAAAGAAACCATCCTAAGAAGGACTA
6368 GATTGAGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (34 bp):
AAATTTTAAAGAAACCATCCTAAGAAGGACTAAC
Found at i:7549 original size:24 final size:24
Alignment explanation
Indices: 7505--7555 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
7495 TTCTTATCGA
*
7505 GAAGAATCGATCTATCATAC-ATT
1 GAAGAATCGATCTAACATACAATT
7528 GAAGCAATCGATTCTAAC-TACAATT
1 GAAG-AATCGA-TCTAACATACAATT
7553 GAA
1 GAA
7556 ATAAGAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.17
24 9 0.38
25 11 0.46
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (24 bp):
GAAGAATCGATCTAACATACAATT
Found at i:9550 original size:3 final size:3
Alignment explanation
Indices: 9542--9603 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
9532 ATTTATTTTG
9542 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9590 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
9604 TGATAGTATC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:19030 original size:14 final size:14
Alignment explanation
Indices: 19011--19037 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19001 AATTTATGAA
19011 AAAAATAATTATTT
1 AAAAATAATTATTT
19025 AAAAATAATTATT
1 AAAAATAATTATT
19038 AGATTAGAAC
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAAATAATTATTT
Found at i:19280 original size:20 final size:21
Alignment explanation
Indices: 19255--19293 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
19245 ATAATCTATT
19255 TAATT-ATTT-TTTATATTTTC
1 TAATTAATTTATTT-TATTTTC
19275 TAATTAATTTATTTTATTT
1 TAATTAATTTATTTTATTT
19294 CAATTAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 9 0.53
22 3 0.18
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (21 bp):
TAATTAATTTATTTTATTTTC
Found at i:19418 original size:16 final size:15
Alignment explanation
Indices: 19372--19425 Score: 74
Period size: 14 Copynumber: 3.6 Consensus size: 15
19362 AACTTAACTT
*
19372 TTTAAATAATTTATA
1 TTTAAATAAATTATA
*
19387 TTTATA-AAATTATA
1 TTTAAATAAATTATA
19401 TTTAAATAAATTAGTA
1 TTTAAATAAATTA-TA
19417 TTTAAATAA
1 TTTAAATAA
19426 TTGATAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
14 12 0.35
15 11 0.32
16 11 0.32
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
TTTAAATAAATTATA
Found at i:19427 original size:15 final size:14
Alignment explanation
Indices: 19372--19427 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 14
19362 AACTTAACTT
19372 TTTAAATAATTTATA
1 TTTAAATAA-TTATA
19387 TTTATAA-AATTATA
1 TTTA-AATAATTATA
19401 TTTAAATAAATTAGTA
1 TTTAAAT-AATTA-TA
19417 TTTAAATAATT
1 TTTAAATAATT
19428 GATAATAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
13 2 0.05
14 9 0.24
15 15 0.41
16 11 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (14 bp):
TTTAAATAATTATA
Found at i:19437 original size:30 final size:29
Alignment explanation
Indices: 19374--19437 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
19364 CTTAACTTTT
* *
19374 TAAATAATTTATATTTATAAAATTATATT
1 TAAATAAATTATATTTATAAAATTATATA
19403 TAAATAAATTAGTATTTA-AATAATTGATA-A
1 TAAATAAATTA-TATTTATAA-AATT-ATATA
19433 TAAAT
1 TAAAT
19438 TATTTCATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
29 12 0.40
30 15 0.50
31 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (29 bp):
TAAATAAATTATATTTATAAAATTATATA
Found at i:20894 original size:96 final size:94
Alignment explanation
Indices: 20730--20907 Score: 257
Period size: 96 Copynumber: 1.9 Consensus size: 94
20720 AGAGGGAATG
* *
20730 AGATTGAGACGTCATTGTGTGAACGAAGAAAAGACAATCGATACCACATACATGACTATAGAAGC
1 AGATTGAGACGTCATTATGTGAACGAAGAAAAGACAATCGATACCACACACATGACTATAGAAGC
20795 ATCAAGCATCCATGCAATAGCGTTTTTACTA
66 ATCAAGCAT--ATGCAATAGCGTTTTTACTA
* * * * * *
20826 AGATTGAGACGTCATTATGTGAATGGAGAAAGGACATTCGATACTACACCCATGACTATAGAAGC
1 AGATTGAGACGTCATTATGTGAACGAAGAAAAGACAATCGATACCACACACATGACTATAGAAGC
*
20891 ATCATGCATATGCAATA
66 ATCAAGCATATGCAATA
20908 ACATTTTCAA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
94 8 0.11
96 65 0.89
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (94 bp):
AGATTGAGACGTCATTATGTGAACGAAGAAAAGACAATCGATACCACACACATGACTATAGAAGC
ATCAAGCATATGCAATAGCGTTTTTACTA
Found at i:21852 original size:22 final size:22
Alignment explanation
Indices: 21824--21869 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
21814 GTTAGAAGCT
*
21824 GTTGGTTTTTTTTTTCATGAAA
1 GTTGGTTTTTTTCTTCATGAAA
21846 GTTGGTTTTTTTCTTCATGAAA
1 GTTGGTTTTTTTCTTCATGAAA
21868 GT
1 GT
21870 GATTATTAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.17, C:0.07, G:0.20, T:0.57
Consensus pattern (22 bp):
GTTGGTTTTTTTCTTCATGAAA
Found at i:22150 original size:18 final size:18
Alignment explanation
Indices: 22127--22178 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
22117 ACATAGAATT
*
22127 TGTCCCAAATGACCACTA
1 TGTCCCGAATGACCACTA
22145 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
*
22163 TGTCCCGAAGGACCAC
1 TGTCCCGAATGACCAC
22179 ATATAACACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.29, C:0.35, G:0.17, T:0.19
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:25717 original size:157 final size:156
Alignment explanation
Indices: 25431--25737 Score: 470
Period size: 157 Copynumber: 2.0 Consensus size: 156
25421 TAAAATTCAG
*
25431 AAACCATAGTAATCCCTCCAGCCCAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
1 AAACCATAGTAATCCCTCCAACCCAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
* * * *
25496 CCATCACATCGAGTAAGGCATTGAGCACAAAGCCGATGAGCTTGCAAGTATACTTCCTCCAACAA
66 CCATCACATCGAGTAAGGCACTAAGCACAAAGCCGATGAGCCTACAAGTATACTTCCTCCAACAA
25561 TACCCCCCAAATAAAACATTTATAAAA
131 T-CCCCCCAAATAAAACATTTATAAAA
* ** *
25588 AAACCATAGTAATCCCTTCAACTGAACACATCATAATGTGTAGGTTCCCTAGAACCATACACCCA
1 AAACCATAGTAATCCCTCCAACCCAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
* * * * * *
25653 CCGTCACATCGAGTAAGGCCCTAAGCACAAAGCTGATGAGCCTACAAGTATTCTTTCTTCAACAA
66 CCATCACATCGAGTAAGGCACTAAGCACAAAGCCGATGAGCCTACAAGTATACTTCCTCCAACAA
25718 TCCCCCCAAATAAAACATTT
131 TCCCCCCAAATAAAACATTT
25738 TTCGTCTGTG
Statistics
Matches: 135, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
156 19 0.14
157 116 0.86
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.21
Consensus pattern (156 bp):
AAACCATAGTAATCCCTCCAACCCAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
CCATCACATCGAGTAAGGCACTAAGCACAAAGCCGATGAGCCTACAAGTATACTTCCTCCAACAA
TCCCCCCAAATAAAACATTTATAAAA
Found at i:25840 original size:24 final size:24
Alignment explanation
Indices: 25764--25842 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 24
25754 TATATCAAAA
* *
25764 ATCAAAACATAATTCAGGTCAGAT
1 ATCATAACATAATCCAGGTCAGAT
*
25788 ATCAGAACAGT-ATCCAGGTCAGAT
1 ATCATAACA-TAATCCAGGTCAGAT
* *
25812 ATCATAACATAATCCATGTCAGGT
1 ATCATAACATAATCCAGGTCAGAT
25836 ATCATAA
1 ATCATAA
25843 AAGAATTCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
23 1 0.02
24 46 0.96
25 1 0.02
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (24 bp):
ATCATAACATAATCCAGGTCAGAT
Found at i:28148 original size:37 final size:37
Alignment explanation
Indices: 28106--28177 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
28096 GGTCAAAGTA
*
28106 AACGGTCAACGGGTTGACTCGGTCAAAGTTAACGATC
1 AACGGTCAACGGGTTGACTCGGTCAAAGTCAACGATC
* *
28143 AACGGTCAGCGGGTTGACTCGTTCAAAGTCAACGA
1 AACGGTCAACGGGTTGACTCGGTCAAAGTCAACGA
28178 GTTGACCAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (37 bp):
AACGGTCAACGGGTTGACTCGGTCAAAGTCAACGATC
Found at i:30142 original size:13 final size:13
Alignment explanation
Indices: 30124--30148 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30114 AAAGATATAA
30124 ATCTTTTTAAAAC
1 ATCTTTTTAAAAC
30137 ATCTTTTTAAAA
1 ATCTTTTTAAAA
30149 TTCAGAAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
ATCTTTTTAAAAC
Found at i:30438 original size:156 final size:156
Alignment explanation
Indices: 30154--30460 Score: 497
Period size: 156 Copynumber: 2.0 Consensus size: 156
30144 TAAAATTCAG
* *
30154 AAACCATAGTAATCCCTGCAGCCCAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
1 AAACCATAGTAATCCCTCCAACCCAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
* * *
30219 CCGTCACATCGAGTTAGGCCCTAAGCACAAAGCCGAGGAGCCTGCAAGTATACTTCCTCCAACAA
66 CCGTCACATCGAGTAAGGCCCTAAGCACAAAGCCGAGCAGCCTACAAGTATACTTCCTCCAACAA
*
30284 TACCCCCCAAATAAAACATTTATCAA
131 TACCACCCAAATAAAACATTTATCAA
*
30310 AAACCATAGTAATCCCTCCAACCGAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
1 AAACCATAGTAATCCCTCCAACCCAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
* * * * * *
30375 TCGTCACATTGAGTAAGGCTCTGAGCACAAAGCCGAGCAGCTTACAAGTATTCTTCCTCCAACAA
66 CCGTCACATCGAGTAAGGCCCTAAGCACAAAGCCGAGCAGCCTACAAGTATACTTCCTCCAACAA
30440 TACCACCCAAATAAAACATTT
131 TACCACCCAAATAAAACATTT
30461 TCCGTTCGTA
Statistics
Matches: 138, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
156 138 1.00
ACGTcount: A:0.36, C:0.32, G:0.13, T:0.20
Consensus pattern (156 bp):
AAACCATAGTAATCCCTCCAACCCAACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCA
CCGTCACATCGAGTAAGGCCCTAAGCACAAAGCCGAGCAGCCTACAAGTATACTTCCTCCAACAA
TACCACCCAAATAAAACATTTATCAA
Found at i:30549 original size:24 final size:24
Alignment explanation
Indices: 30481--30549 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
30471 AATGGATATA
* * *
30481 TCAAAAATCAAAACATAATTCAGG
1 TCAAATATCAGAACATAATCCAGG
*
30505 TCAAATATCAGAATAGT-ATCCAGG
1 TCAAATATCAGAACA-TAATCCAGG
* *
30529 TCAGATATTAGAACATAATCC
1 TCAAATATCAGAACATAATCC
30550 TTGTGAGGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
23 1 0.03
24 34 0.94
25 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (24 bp):
TCAAATATCAGAACATAATCCAGG
Found at i:32692 original size:7 final size:7
Alignment explanation
Indices: 32679--32715 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
32669 GTCAAAGGAA
32679 GTCAACG
1 GTCAACG
*
32686 ATCAACG
1 GTCAACG
32693 GTCAA-G
1 GTCAACG
32699 GTCAACG
1 GTCAACG
32706 GTCAACG
1 GTCAACG
32713 GTC
1 GTC
32716 GGGTCGGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:32705 original size:13 final size:14
Alignment explanation
Indices: 32679--32715 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
32669 GTCAAAGGAA
*
32679 GTCAACGATCAACG
1 GTCAACGGTCAACG
32693 GTCAA-GGTCAACG
1 GTCAACGGTCAACG
32706 GTCAACGGTC
1 GTCAACGGTC
32716 GGGTCGGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:32722 original size:5 final size:5
Alignment explanation
Indices: 32712--32749 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
32702 AACGGTCAAC
**
32712 GGTCG GGTCG GGTCG GGTC- AATCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
32750 AGTCCGGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
4 2 0.07
5 26 0.93
ACGTcount: A:0.05, C:0.21, G:0.53, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:32736 original size:19 final size:19
Alignment explanation
Indices: 32714--32750 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
32704 CGGTCAACGG
32714 TCGGGTCGGGTCGGGTCAA
1 TCGGGTCGGGTCGGGTCAA
32733 TCGGGTCGGGTCGGGTCA
1 TCGGGTCGGGTCGGGTCA
32751 GTCCGGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.08, C:0.22, G:0.49, T:0.22
Consensus pattern (19 bp):
TCGGGTCGGGTCGGGTCAA
Found at i:32739 original size:24 final size:22
Alignment explanation
Indices: 32705--32749 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 22
32695 CAAGGTCAAC
32705 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
32727 GGTCAATCGGGTCGGGTCGGGTC
1 GGTCAA-C-GGTCGGGTCGGGTC
32750 AGTCCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.29
23 1 0.05
24 14 0.67
ACGTcount: A:0.09, C:0.22, G:0.49, T:0.20
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:32758 original size:19 final size:19
Alignment explanation
Indices: 32717--32758 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
32707 TCAACGGTCG
*
32717 GGTCGGGTCGGGTCAATCG
1 GGTCGGGTCGGGTCAATCC
*
32736 GGTCGGGTCGGGTCAGTCC
1 GGTCGGGTCGGGTCAATCC
32755 GGTC
1 GGTC
32759 AAATCGGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.07, C:0.24, G:0.48, T:0.21
Consensus pattern (19 bp):
GGTCGGGTCGGGTCAATCC
Found at i:32765 original size:19 final size:19
Alignment explanation
Indices: 32743--32780 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
32733 TCGGGTCGGG
*
32743 TCGGGTCAGTCCGGTCAAA
1 TCGGGTCAGACCGGTCAAA
*
32762 TCGGTTCAGACCGGTCAAA
1 TCGGGTCAGACCGGTCAAA
32781 CCGGTTCGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (19 bp):
TCGGGTCAGACCGGTCAAA
Found at i:32777 original size:28 final size:28
Alignment explanation
Indices: 32753--32847 Score: 88
Period size: 29 Copynumber: 3.4 Consensus size: 28
32743 TCGGGTCAGT
*
32753 CCGG-TCAAATCGGTTCAGACCGGTCAAA
1 CCGGTTCAAATCGG-TCAAACCGGTCAAA
* *
32781 CCGGTTCGAATCGGTCAAACCGGTTCGAA
1 CCGGTTCAAATCGGTCAAACCGG-TCAAA
* *
32810 CCGG-TCAAAACCGGTCAAACAGGTCAGAA
1 CCGGTTC-AAATCGGTCAAACCGGTCA-AA
32839 CCGG-TCAAA
1 CCGGTTCAAA
32848 CCGATTTCCA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
28 19 0.34
29 37 0.66
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.16
Consensus pattern (28 bp):
CCGGTTCAAATCGGTCAAACCGGTCAAA
Found at i:32785 original size:19 final size:19
Alignment explanation
Indices: 32748--32843 Score: 90
Period size: 19 Copynumber: 5.0 Consensus size: 19
32738 TCGGGTCGGG
* *
32748 TCAGTCCGGTCAAATCGGT
1 TCAGACCGGTCAAACCGGT
32767 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
32786 TC-GAATCGGTCAAACCGGT
1 TCAG-ACCGGTCAAACCGGT
32805 TC-GAACCGGTCAAAACCGG-
1 TCAG-ACCGGTC-AAACCGGT
* *
32824 TCAAACAGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
32844 CAAACCGATT
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.03
19 57 0.86
20 7 0.11
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:32821 original size:10 final size:9
Alignment explanation
Indices: 32753--32850 Score: 97
Period size: 10 Copynumber: 10.3 Consensus size: 9
32743 TCGGGTCAGT
32753 CCGGTCAAA
1 CCGGTCAAA
* *
32762 TCGGTTCAGA
1 CCGG-TCAAA
32772 CCGGTCAAA
1 CCGGTCAAA
*
32781 CCGGTTCGAA
1 CCGG-TCAAA
*
32791 TCGGTCAAA
1 CCGGTCAAA
*
32800 CCGGTTCGAA
1 CCGG-TCAAA
32810 CCGGTCAAAA
1 CCGGTC-AAA
32820 CCGGTCAAA
1 CCGGTCAAA
*
32829 CAGGTCAGAA
1 CCGGTCA-AA
32839 CCGGTCAAA
1 CCGGTCAAA
32848 CCG
1 CCG
32851 ATTTCCAGCC
Statistics
Matches: 72, Mismatches: 12, Indels: 10
0.77 0.13 0.11
Matches are distributed among these distances:
9 34 0.47
10 38 0.53
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.15
Consensus pattern (9 bp):
CCGGTCAAA
Found at i:39982 original size:13 final size:14
Alignment explanation
Indices: 39964--39993 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
39954 GTCAAATGAA
39964 GTCAACGGTCAA-G
1 GTCAACGGTCAACG
39977 GTCAACGGTCAACG
1 GTCAACGGTCAACG
39991 GTC
1 GTC
39994 GGGTCGGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.17
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:39986 original size:7 final size:7
Alignment explanation
Indices: 39964--39993 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
39954 GTCAAATGAA
39964 GTCAACG
1 GTCAACG
39971 GTCAA-G
1 GTCAACG
39977 GTCAACG
1 GTCAACG
39984 GTCAACG
1 GTCAACG
39991 GTC
1 GTC
39994 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:43096 original size:11 final size:11
Alignment explanation
Indices: 43080--43110 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
43070 ATGAAAAATG
43080 GTAAATAAACA
1 GTAAATAAACA
43091 GTAAATAAACA
1 GTAAATAAACA
*
43102 GCAAATAAA
1 GTAAATAAA
43111 ATGAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.16
Consensus pattern (11 bp):
GTAAATAAACA
Found at i:43631 original size:23 final size:23
Alignment explanation
Indices: 43605--43651 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
43595 AAAGAAACAC
*
43605 AATAAACT-TAAATATACCATTAA
1 AATAAACTCTAAACAT-CCATTAA
*
43628 AATAAAGTCTAAACATCCATTAA
1 AATAAACTCTAAACATCCATTAA
43651 A
1 A
43652 CCAACCACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.28
Consensus pattern (23 bp):
AATAAACTCTAAACATCCATTAA
Found at i:46900 original size:20 final size:20
Alignment explanation
Indices: 46864--46908 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
46854 GATAAAAAGT
*
46864 AAAAGTTAAAAATGAAATAG
1 AAAAGTTAAAAATGAAAGAG
*
46884 AAAAGTTAATGAA-GAAAGAG
1 AAAAGTTAA-AAATGAAAGAG
46904 AAAAG
1 AAAAG
46909 AAAAAGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAAGTTAAAAATGAAAGAG
Found at i:50137 original size:45 final size:45
Alignment explanation
Indices: 50082--50178 Score: 167
Period size: 45 Copynumber: 2.2 Consensus size: 45
50072 AATCACCAGT
* * *
50082 AAAGTTTCATTGCTACCTAAGTAAATATATTTAAGATGCCCTGGC
1 AAAGTCTCATTACTACCTAAGTAAACATATTTAAGATGCCCTGGC
50127 AAAGTCTCATTACTACCTAAGTAAACATATTTAAGATGCCCTGGC
1 AAAGTCTCATTACTACCTAAGTAAACATATTTAAGATGCCCTGGC
50172 AAAGTCT
1 AAAGTCT
50179 TAAGCTCTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (45 bp):
AAAGTCTCATTACTACCTAAGTAAACATATTTAAGATGCCCTGGC
Found at i:53764 original size:22 final size:22
Alignment explanation
Indices: 53739--53784 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
53729 AAAGAACCAT
53739 AATAAA-CTAAATATACCATTAA
1 AATAAAGCTAAATAT-CCATTAA
53761 AATAAAGTCTAAATATCCATTAA
1 AATAAAG-CTAAATATCCATTAA
53784 A
1 A
53785 CCAACACCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 8 0.36
24 8 0.36
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (22 bp):
AATAAAGCTAAATATCCATTAA
Done.