Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009086.1 Hibiscus syriacus cultivar Beakdansim tig00112530_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: 1596699
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1572247 original size:21 final size:21
Alignment explanation
Indices: 1572223--1572262 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1572213 ACTATCGCAC
1572223 TGCGATTTTCCAAATTCGCGT
1 TGCGATTTTCCAAATTCGCGT
*
1572244 TGCGATTTTCCTAATTCGC
1 TGCGATTTTCCAAATTCGC
1572263 AATGCGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.40
Consensus pattern (21 bp):
TGCGATTTTCCAAATTCGCGT
Found at i:1572268 original size:21 final size:21
Alignment explanation
Indices: 1572217--1572269 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1572207 ATTCTGACTA
*
1572217 TCGCACTGCGATTTTCCAAAT
1 TCGCAATGCGATTTTCCAAAT
** *
1572238 TCGCGTTGCGATTTTCCTAAT
1 TCGCAATGCGATTTTCCAAAT
1572259 TCGCAATGCGA
1 TCGCAATGCGA
1572270 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAAAT
Found at i:1572284 original size:20 final size:20
Alignment explanation
Indices: 1572259--1572371 Score: 199
Period size: 20 Copynumber: 5.7 Consensus size: 20
1572249 TTTTCCTAAT
1572259 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1572279 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1572299 TCGCAATGCGAATACTTAAA
1 TCGCAATGCGAATACGTAAA
*
1572319 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
*
1572339 TCGTAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1572359 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1572372 CTGACTATCG
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 88 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1572329 original size:60 final size:60
Alignment explanation
Indices: 1572259--1572389 Score: 210
Period size: 60 Copynumber: 2.2 Consensus size: 60
1572249 TTTTCCTAAT
* *
1572259 TCGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAATCGCAATGCGAATACTTA-AA
1 TCGCAATGCGAATACATAAATCGCAATGCGAATACGTAAATCGCAATGCGAAT-CTGACAA
* *
1572319 TCGCAATGCGAATACATAAATCGTAATGCGAATACGTAAATCGCAATGCGAATCTGACTA
1 TCGCAATGCGAATACATAAATCGCAATGCGAATACGTAAATCGCAATGCGAATCTGACAA
1572379 TCGCAATGCGA
1 TCGCAATGCGA
1572390 TTTACATAGC
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
59 3 0.05
60 63 0.95
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (60 bp):
TCGCAATGCGAATACATAAATCGCAATGCGAATACGTAAATCGCAATGCGAATCTGACAA
Found at i:1572387 original size:40 final size:40
Alignment explanation
Indices: 1572259--1572389 Score: 187
Period size: 40 Copynumber: 3.3 Consensus size: 40
1572249 TTTTCCTAAT
1572259 TCGCAATGCGAATACGTAAATCGCAATGCGAATAC-GTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATACTG-AAA
*
1572299 TCGCAATGCGAATACTTAAATCGCAATGCGAATACAT-AAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATAC-TGAAA
* *
1572339 TCGTAATGCGAATACGTAAATCGCAATGCGAAT-CTGACTA
1 TCGCAATGCGAATACGTAAATCGCAATGCGAATACTGA-AA
1572379 TCGCAATGCGA
1 TCGCAATGCGA
1572390 TTTACATAGC
Statistics
Matches: 82, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
38 1 0.01
39 2 0.02
40 79 0.96
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGAATACTGAAA
Found at i:1572590 original size:22 final size:22
Alignment explanation
Indices: 1572565--1572630 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
1572555 GGCGACATCC
*
1572565 GTCCCCATCTCCGATGAAATCA
1 GTCCCCATCTCCGACGAAATCA
** *
1572587 GTCCCCATCTCAAACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
1572609 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
1572631 TTTACGGTCA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.27, C:0.36, G:0.14, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1574973 original size:34 final size:34
Alignment explanation
Indices: 1574930--1575023 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 34
1574920 ATAGTTTACT
* * *
1574930 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACAACAAA
**
1574964 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAAAATGACTATCGCAACAACAAA
**
1574997 ATCGCAACACGAAAATGACTATCGCAA
1 ATCGCAATGCGAAAATGACTATCGCAA
1575024 TACGAATTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 26 0.52
34 24 0.48
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACAACAAA
Found at i:1575011 original size:14 final size:15
Alignment explanation
Indices: 1574979--1575012 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1574969 AATGCGAAAT
1574979 GAAAATCGCAACAAC
1 GAAAATCGCAACAAC
1574994 -AAAATCGCAAC-AC
1 GAAAATCGCAACAAC
1575007 GAAAAT
1 GAAAAT
1575013 GACTATCGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.56, C:0.24, G:0.12, T:0.09
Consensus pattern (15 bp):
GAAAATCGCAACAAC
Found at i:1575022 original size:20 final size:20
Alignment explanation
Indices: 1574997--1575044 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1574987 CAACAACAAA
1574997 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
1575017 ATCGCAATACGAATTTGACT
1 ATCGCAACACGAAAATGACT
1575037 ATCGCAAC
1 ATCGCAAC
1575045 GAAAGAATCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.21
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:1575115 original size:20 final size:20
Alignment explanation
Indices: 1575090--1575176 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
1575080 GATTCTCTTG
1575090 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
1575110 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
1575130 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
* ** *
1575150 TTGCGATAATCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
1575170 TTGCGAT
1 TTGCGAT
1575177 TTTAAGTTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:1575712 original size:42 final size:42
Alignment explanation
Indices: 1575642--1575733 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
1575632 TCCCCTATCG
* *
1575642 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGT-CCCTCCCAACA
* ** *
1575684 TTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAACA
1 TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAACA
*
1575726 TTCTAGAG
1 TTCAAGAG
1575734 CCCGATTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 40 0.95
43 2 0.05
ACGTcount: A:0.25, C:0.36, G:0.17, T:0.22
Consensus pattern (42 bp):
TTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAACA
Found at i:1577050 original size:14 final size:14
Alignment explanation
Indices: 1577031--1577066 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1577021 ATTGTTTAAT
1577031 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1577045 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1577059 TGATTTGT
1 TGATTTGT
1577067 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1577222 original size:33 final size:33
Alignment explanation
Indices: 1577172--1577267 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
1577162 AAAACAGACT
* **
1577172 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1577206 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1577239 ATCACAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
1577268 CGAAACTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1577323 original size:14 final size:14
Alignment explanation
Indices: 1577304--1577389 Score: 55
Period size: 14 Copynumber: 5.5 Consensus size: 14
1577294 TATTTTCGCA
1577304 TTGCGATTCACTCG
1 TTGCGATTCACTCG
*
1577318 TTGCGATTTTCATTTCG
1 TTGCGA--TTCA-CTCG
*
1577335 CATTGCGATTCACTCA
1 --TTGCGATTCACTCG
*
1577351 TTGCGATTTCATTTCG
1 TTGCGA-TTCA-CTCG
*
1577367 TATTGCGATTCTCTCG
1 --TTGCGATTCACTCG
1577383 TTGCGAT
1 TTGCGAT
1577390 AGTCATTTCC
Statistics
Matches: 56, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
14 19 0.34
15 4 0.07
16 11 0.20
17 10 0.18
18 6 0.11
19 6 0.11
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (14 bp):
TTGCGATTCACTCG
Found at i:1577339 original size:33 final size:33
Alignment explanation
Indices: 1577283--1577409 Score: 166
Period size: 33 Copynumber: 3.8 Consensus size: 33
1577273 CTAAATTCTT
*
1577283 GTTGCGATTTTTATTTTCGCATTGCGATTCACTC
1 GTTGCGATTTTCA-TTTCGCATTGCGATTCACTC
1577317 GTTGCGATTTTCATTTCGCATTGCGATTCACTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCACTC
* * *
1577350 ATTGCGA-TTTCATTTCGTATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCACTC
** *
1577382 GTTGCGATAGTCATTTCCGCGTTGCGAT
1 GTTGCGATTTTCATTT-CGCATTGCGAT
1577410 AGTCAATTCC
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 29 0.35
33 32 0.39
34 21 0.26
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCACTC
Found at i:1577406 original size:20 final size:20
Alignment explanation
Indices: 1577381--1577469 Score: 144
Period size: 20 Copynumber: 4.5 Consensus size: 20
1577371 GCGATTCTCT
1577381 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1577401 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
1577421 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1577441 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
1577461 CGTTGCGAT
1 CGTTGCGAT
1577470 TTCCGCGTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 62 0.97
21 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1579928 original size:24 final size:24
Alignment explanation
Indices: 1579894--1579947 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1579884 TTGAAAAATC
1579894 ATCAAAATCCGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
1579918 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
1579942 ATCAAA
1 ATCAAA
1579948 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:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:1580814 original size:20 final size:20
Alignment explanation
Indices: 1580789--1580835 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1580779 AAATTCAGTA
*
1580789 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
1580809 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
1580829 TTGCGAT
1 TTGCGAT
1580836 TTACATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:1580845 original size:20 final size:20
Alignment explanation
Indices: 1580822--1580955 Score: 196
Period size: 20 Copynumber: 6.7 Consensus size: 20
1580812 CGATAGTCAG
* *
1580822 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
1580842 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1580862 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1580882 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
1580902 AATCGCATTGCGATTTTTCAA
1 ATTCGCATTGCGA-TTTACGT
*
1580923 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1580943 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1580956 ATTAGGAAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
20 86 0.85
21 15 0.15
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1580979 original size:21 final size:21
Alignment explanation
Indices: 1580953--1580992 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1580943 ATTCGCATTG
1580953 CGAATTAGGAAAATCACAACT
1 CGAATTAGGAAAATCACAACT
*
1580974 CGAATTTGGAAAATCACAA
1 CGAATTAGGAAAATCACAA
1580993 TGCGATAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.20
Consensus pattern (21 bp):
CGAATTAGGAAAATCACAACT
Found at i:1581566 original size:14 final size:15
Alignment explanation
Indices: 1581538--1581584 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 15
1581528 AATAACGATG
*
1581538 AATATTAT-TAATTT
1 AATATTATAAAATTT
1581552 AAT-TTATAAAATTT
1 AATATTATAAAATTT
*
1581566 AATATTTTAAAGATTT
1 AATATTATAAA-ATTT
1581582 AAT
1 AAT
1581585 GGATAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 4 0.14
14 11 0.39
15 6 0.21
16 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
AATATTATAAAATTT
Found at i:1581618 original size:22 final size:21
Alignment explanation
Indices: 1581593--1581643 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
1581583 ATGGATAATT
1581593 ATAAATTAATTAAAATTTAAA-A
1 ATAAATTAATTAAAA--TAAAGA
*
1581615 ATAAATTATTTAAAATAAAGA
1 ATAAATTAATTAAAATAAAGA
1581636 ATAAATTA
1 ATAAATTA
1581644 TATAAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 4 0.15
21 9 0.33
22 14 0.52
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAAATTAATTAAAATAAAGA
Found at i:1581640 original size:21 final size:21
Alignment explanation
Indices: 1581593--1581649 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
1581583 ATGGATAATT
*
1581593 ATAAATTAATTAAAATTTAAAA
1 ATAAATTATTTAAAA-TTAAAA
1581615 ATAAATTATTTAAAA-TAAAGA
1 ATAAATTATTTAAAATTAAA-A
*
1581636 ATAAATTATATAAA
1 ATAAATTATTTAAA
1581650 TGATTACTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 4 0.12
21 14 0.44
22 14 0.44
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
ATAAATTATTTAAAATTAAAA
Found at i:1586829 original size:21 final size:21
Alignment explanation
Indices: 1586805--1587012 Score: 174
Period size: 21 Copynumber: 10.1 Consensus size: 21
1586795 GCAAATTCGC
1586805 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* *
1586826 GTTGAAATTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* ** **
1586847 GTTGAAAATCGCAATGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
1586867 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
1586888 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
1586908 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* *
1586929 GTCTACA-GTCGCGTTGCGAT-
1 GT-TGCATTTCGCGTTGCGATA
* *
1586949 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* *
1586970 GTTGAAATTCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
1586990 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
1587011 GT
1 GT
1587013 CTACAGTTGT
Statistics
Matches: 144, Mismatches: 37, Indels: 12
0.75 0.19 0.06
Matches are distributed among these distances:
19 3 0.02
20 57 0.40
21 81 0.56
22 3 0.02
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.37
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:1586879 original size:41 final size:41
Alignment explanation
Indices: 1586833--1587012 Score: 299
Period size: 41 Copynumber: 4.4 Consensus size: 41
1586823 ATAGTTGAAA
**
1586833 TTCGCGTTGCGATAGTTGAAAATCGCAATGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1586874 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
* *
1586915 TTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCCAT
*
1586956 TTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1586997 TTCGCGTTGCGATAGT
1 TTCGCGTTGCGATAGT
1587013 CTACAGTTGT
Statistics
Matches: 131, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
40 1 0.01
41 129 0.98
42 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
Found at i:1586884 original size:20 final size:20
Alignment explanation
Indices: 1586861--1587009 Score: 147
Period size: 20 Copynumber: 7.3 Consensus size: 20
1586851 AAAATCGCAA
1586861 TGCGATTTTCCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
* ** **
1586881 TGCGATAGTTGAAAATCGCGT
1 TGCGAT-TTTCCATTTCGCGT
1586902 TGCGATTTTCCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
* * *
1586922 TGCGATAGTCTACA-GTCGCGT
1 TGCGAT--TTTCCATTTCGCGT
1586943 TGCGATTTTCCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
* ** *
1586963 TGCGATAGTTGAAATTCGCGT
1 TGCGAT-TTTCCATTTCGCGT
1586984 TGCGATTTTCCATTTCGCGT
1 TGCGATTTTCCATTTCGCGT
1587004 TGCGAT
1 TGCGAT
1587010 AGTCTACAGT
Statistics
Matches: 100, Mismatches: 24, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
19 4 0.04
20 49 0.49
21 43 0.43
22 4 0.04
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.38
Consensus pattern (20 bp):
TGCGATTTTCCATTTCGCGT
Found at i:1587016 original size:82 final size:82
Alignment explanation
Indices: 1586833--1587037 Score: 331
Period size: 82 Copynumber: 2.5 Consensus size: 82
1586823 ATAGTTGAAA
* * **
1586833 TTCGCGTTGCGATAGT-TGAAAATCGCAATGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAAT
1 TTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAAT
1586897 CGCGTTGCGATTTTCCAT
65 CGCGTTGCGATTTTCCAT
*
1586915 TTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAATTC
1 TTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATC
1586980 GCGTTGCGATTTTCCAT
66 GCGTTGCGATTTTCCAT
*
1586997 TTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCA
1 TTCGCGTTGCGATAGTCTACAGTCG-CGTTGCGATTTTCCA
1587038 AATTCGTTGT
Statistics
Matches: 115, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
82 99 0.86
83 16 0.14
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (82 bp):
TTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATC
GCGTTGCGATTTTCCAT
Found at i:1587052 original size:41 final size:40
Alignment explanation
Indices: 1586861--1587037 Score: 216
Period size: 41 Copynumber: 4.3 Consensus size: 40
1586851 AAAATCGCAA
* * *
1586861 TGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCGCGT
1 TGCGATTTTCCATTTC-CGTTGCGATAGTCT-ACAGTTGCGT
*
1586902 TGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGCGT
1 TGCGATTTTCCATTTC-CGTTGCGATAGTCTACAGTTGCGT
*
1586943 TGCGATTTTCCATTTCGCGTTGCGATAGT-TGA-AATTCGCGT
1 TGCGATTTTCCATTTC-CGTTGCGATAGTCT-ACAGTT-GCGT
1586984 TGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGT
1 TGCGATTTTCCATTTC-CGTTGCGATAGTCTACAGTTG-CGT
1587026 TGCGATTTTCCA
1 TGCGATTTTCCA
1587038 AATTCGTTGT
Statistics
Matches: 125, Mismatches: 5, Indels: 11
0.89 0.04 0.08
Matches are distributed among these distances:
40 3 0.02
41 102 0.82
42 20 0.16
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.38
Consensus pattern (40 bp):
TGCGATTTTCCATTTCCGTTGCGATAGTCTACAGTTGCGT
Found at i:1587142 original size:6 final size:6
Alignment explanation
Indices: 1587131--1587163 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1587121 GACACGTATT
1587131 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1587164 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1587812 original size:20 final size:19
Alignment explanation
Indices: 1587787--1587933 Score: 74
Period size: 20 Copynumber: 7.6 Consensus size: 19
1587777 ACTGTAGACT
1587787 ATCGCAACGCGCAATGGAAA
1 ATCGCAACGCG-AATGGAAA
* **
1587807 ATCGCAACGCGACTGTAGACT
1 ATCGCAACGCGAATG--GAAA
*
1587828 ATCGCAACGCGAAATCGAAA
1 ATCGCAACGCG-AATGGAAA
*
1587848 ATCGCAA-TC-AACT-----
1 ATCGCAACGCGAA-TGGAAA
*
1587861 ATCGCAATGCGAAATGGAAA
1 ATCGCAACGCG-AATGGAAA
* ** *
1587881 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-ATGGAA-A
1587902 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCG-AATGGAAA
1587922 ATCGCAACGCGA
1 ATCGCAACGCGA
1587934 TTTTCAACTA
Statistics
Matches: 94, Mismatches: 18, Indels: 31
0.66 0.13 0.22
Matches are distributed among these distances:
13 7 0.07
14 1 0.01
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 6 0.06
20 44 0.47
21 27 0.29
22 3 0.03
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAATGGAAA
Found at i:1587833 original size:21 final size:21
Alignment explanation
Indices: 1587762--1587839 Score: 79
Period size: 21 Copynumber: 3.7 Consensus size: 21
1587752 CTTTTTTTTA
* *
1587762 ACTATCGTAACGACAACTGTAG
1 ACTATCGCAACG-CGACTGTAG
*
1587784 ACTATCGCAACGCGCAATG--G
1 ACTATCGCAACGCG-ACTGTAG
**
1587804 AAAATCGCAACGCGACTGTAG
1 ACTATCGCAACGCGACTGTAG
1587825 ACTATCGCAACGCGA
1 ACTATCGCAACGCGA
1587840 AATCGAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
19 3 0.07
20 13 0.29
21 15 0.33
22 14 0.31
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.17
Consensus pattern (21 bp):
ACTATCGCAACGCGACTGTAG
Found at i:1587834 original size:41 final size:41
Alignment explanation
Indices: 1587784--1587999 Score: 288
Period size: 41 Copynumber: 5.5 Consensus size: 41
1587774 ACAACTGTAG
* * *
1587784 ACTATCGCAACGCGCAATGGAAAATCGCAACGCGACTGT-A
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
1587824 GACTATCGCAACGCGAAATCGAAAATCGC-A----A---TCA
1 -ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
1587858 ACTATCGCAATGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1587899 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* * *
1587940 ACTATCGCAATGCGAAATGGAAAACCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1587981 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
1588000 CAACGCGAAT
Statistics
Matches: 157, Mismatches: 9, Indels: 18
0.85 0.05 0.10
Matches are distributed among these distances:
33 27 0.17
34 2 0.01
36 1 0.01
38 1 0.01
40 1 0.01
41 125 0.80
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:1587905 original size:74 final size:77
Alignment explanation
Indices: 1587784--1587998 Score: 285
Period size: 74 Copynumber: 2.8 Consensus size: 77
1587774 ACAACTGTAG
* * * *
1587784 ACTATCGCAACGCGCAATGGAAAATCGCAACGCGACTGT-AGACTATCGCAACGCGAAATCGAAA
1 ACTATCGCAATGCGAAATGGAAAATCGCAACGCGATTTTCA-ACTATCGCAACGCGAAATCGAAA
1587848 ATCGC-A-A-TCA
65 ATCGCAACATTCA
*
1587858 ACTATCGCAATGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAATGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATCGAAAA
1587923 TCGCAACGCGATTTTCA
66 TCGCAA--C-A--TTCA
* *
1587940 ACTATCGCAATGCGAAATGGAAAACCACAACGCGATTTTCAACTATCGCAACGCGAAAT
1 ACTATCGCAATGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAAT
1587999 GCAACGCGAA
Statistics
Matches: 125, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
74 62 0.50
75 2 0.02
79 1 0.01
82 60 0.48
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (77 bp):
ACTATCGCAATGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATCGAAAA
TCGCAACATTCA
Found at i:1587907 original size:21 final size:21
Alignment explanation
Indices: 1587881--1587995 Score: 99
Period size: 21 Copynumber: 5.6 Consensus size: 21
1587871 GAAATGGAAA
1587881 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
1587902 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
1587922 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* ** ** *
1587943 ATCGCAATGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
* *
1587963 ACCACAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
1587984 ATCGCAACGCGA
1 ATCGCAACGCGA
1587996 AATGCAACGC
Statistics
Matches: 66, Mismatches: 26, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
20 27 0.41
21 39 0.59
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:1588055 original size:20 final size:20
Alignment explanation
Indices: 1588032--1588137 Score: 65
Period size: 20 Copynumber: 5.2 Consensus size: 20
1588022 AGATCGCGTT
1588032 GCGATTTCAACTATCGCAAC
1 GCGATTTCAACTATCGCAAC
* *
1588052 GCGAAATGT-AA-AATCGCAAC
1 GCG--ATTTCAACTATCGCAAC
*
1588072 GCGATCTCCAACTATCGCAAC
1 GCGAT-TTCAACTATCGCAAC
* ** * *
1588093 GCGAAATGGAA-AAACGCAAC
1 GCG-ATTTCAACTATCGCAAC
*
1588113 GCGATTTTCAACTATCGCAAT
1 GCGA-TTTCAACTATCGCAAC
1588134 GCGA
1 GCGA
1588138 AATGCAACGT
Statistics
Matches: 62, Mismatches: 16, Indels: 15
0.67 0.17 0.16
Matches are distributed among these distances:
18 2 0.03
19 1 0.02
20 29 0.47
21 26 0.42
22 4 0.06
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
GCGATTTCAACTATCGCAAC
Found at i:1588089 original size:41 final size:41
Alignment explanation
Indices: 1588039--1588141 Score: 161
Period size: 41 Copynumber: 2.5 Consensus size: 41
1588029 GTTGCGATTT
* *
1588039 CAACTATCGCAACGCGAAATGTAAAATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
* *
1588080 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
*
1588121 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
1588142 CAACGTGAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.17
Consensus pattern (41 bp):
CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
Found at i:1588177 original size:142 final size:143
Alignment explanation
Indices: 1587881--1588177 Score: 472
Period size: 142 Copynumber: 2.1 Consensus size: 143
1587871 GAAATGGAAA
* * *
1587881 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATC
1 ATCGCAATGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATC
* *
1587946 GCAATGCGAAATGGAAAACCACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATT
66 GCAACGCGAAATGGAAAAACACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATT
1588011 TGCGATGATGGAG
131 TGCGATGATGGAG
** *
1588024 ATCGCGTTGCGA-TTTCAACTATCGCAACGCGAAATGTAAAATCGCAACGCGATCTCCAACTATC
1 ATCGCAATGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATC
* * *
1588088 GCAACGCGAAATGGAAAAACGCAACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTGAATT
66 GCAACGCGAAATGGAAAAACACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATT
1588153 TGCGAT-AGTGGAG
131 TGCGATGA-TGGAG
1588166 ATCGCAATGCGA
1 ATCGCAATGCGA
1588178 ATTAGAGATC
Statistics
Matches: 140, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
141 1 0.01
142 130 0.93
143 9 0.06
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.21
Consensus pattern (143 bp):
ATCGCAATGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCAACTATC
GCAACGCGAAATGGAAAAACACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATT
TGCGATGATGGAG
Found at i:1588374 original size:35 final size:34
Alignment explanation
Indices: 1588289--1588375 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
1588279 TCTCTAATTT
*
1588289 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
1588323 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
1588361 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1588376 ACTGAAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:1592694 original size:30 final size:30
Alignment explanation
Indices: 1592658--1592726 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
1592648 CGTGGATTGG
*
1592658 TCGATTTGTAACAAACAATAACGTTAGTAA
1 TCGATTTGTAACAAACAATAACATTAGTAA
*
1592688 TCGATTTGTAACAAACAATAACATTAGTTA
1 TCGATTTGTAACAAACAATAACATTAGTAA
*
1592718 TCGGTTTGT
1 TCGATTTGT
1592727 GACTTTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (30 bp):
TCGATTTGTAACAAACAATAACATTAGTAA
Found at i:1594390 original size:16 final size:17
Alignment explanation
Indices: 1594369--1594403 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1594359 TTACTATTCA
1594369 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
1594385 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
1594402 CG
1 CG
1594404 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:1595155 original size:15 final size:16
Alignment explanation
Indices: 1595137--1595169 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1595127 GTGGCAGATC
1595137 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
1595152 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
1595168 AA
1 AA
1595170 GAAAGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Done.