Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004867.1 Hibiscus syriacus cultivar Beakdansim tig00010975_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: 46642
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:1898 original size:31 final size:30
Alignment explanation
Indices: 1852--1931 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 30
1842 TTAAATTTAA
*
1852 TATAGATTTTAAAAATTTTGATAG-GGCCAAAT
1 TATA-ATTTTTAAAATTTT-A-AGAGGCCAAAT
* *
1884 TA-AATTTTTGAAAATTTTAAGAGTCTAAAT
1 TATAATTTTT-AAAATTTTAAGAGGCCAAAT
1914 TATAATTTTTAAAATTTT
1 TATAATTTTTAAAATTTT
1932 TGGGGGGCCA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
29 2 0.05
30 22 0.52
31 16 0.38
32 2 0.05
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (30 bp):
TATAATTTTTAAAATTTTAAGAGGCCAAAT
Found at i:2198 original size:7 final size:7
Alignment explanation
Indices: 2186--2211 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2176 TATTATTGAC
2186 ATCAAGA
1 ATCAAGA
2193 ATCAAGA
1 ATCAAGA
2200 ATCAAGA
1 ATCAAGA
2207 ATCAA
1 ATCAA
2212 ATCTGGGAGA
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:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (7 bp):
ATCAAGA
Found at i:7503 original size:17 final size:18
Alignment explanation
Indices: 7464--7505 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
7454 AAATATATGT
7464 GATATGATATGATATATA
1 GATATGATATGATATATA
*
7482 TATAT-ATATGATA-ATGA
1 GATATGATATGATATAT-A
7499 GATATGA
1 GATATGA
7506 GACTCTACGA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 2 0.10
17 13 0.65
18 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (18 bp):
GATATGATATGATATATA
Found at i:7865 original size:23 final size:23
Alignment explanation
Indices: 7797--7854 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
7787 ACATTTTATA
*
7797 TGGCACTTCGATGCAATTCTACG
1 TGGCACTTCGATGTAATTCTACG
* *
7820 CGGCACTTCGGTGTAATTCTACG
1 TGGCACTTCGATGTAATTCTACG
7843 TGGCACTTCGAT
1 TGGCACTTCGAT
7855 ATATTTATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGATGTAATTCTACG
Found at i:10042 original size:26 final size:26
Alignment explanation
Indices: 10007--10067 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
9997 AGTATGGATA
10007 ATAAAGTTATAAGATTTGAAGAAAAG
1 ATAAAGTTATAAGATTTGAAGAAAAG
10033 ATAAAGTTATAAGATTTGAAGAAAAG
1 ATAAAGTTATAAGATTTGAAGAAAAG
*
10059 TTAAAGTTA
1 ATAAAGTTA
10068 AGTTAATCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (26 bp):
ATAAAGTTATAAGATTTGAAGAAAAG
Found at i:13068 original size:23 final size:23
Alignment explanation
Indices: 12977--13060 Score: 116
Period size: 23 Copynumber: 3.7 Consensus size: 23
12967 ACATTTTATA
*
12977 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCAGTGCAATTCTACG
*
13000 CGGCACTTCAGTGCAATTCTACG
1 TGGCACTTCAGTGCAATTCTACG
*
13023 TGGCA-TGTTAGTGCAATTCTACG
1 TGGCACT-TCAGTGCAATTCTACG
*
13046 TGGCACTTCGGTGCA
1 TGGCACTTCAGTGCA
13061 TTTATACGAG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
22 1 0.02
23 51 0.96
24 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCAGTGCAATTCTACG
Found at i:13259 original size:21 final size:21
Alignment explanation
Indices: 13235--13277 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
13225 ATTAAGAAGG
13235 TTAAAT-ATATGTG-CTATATGA
1 TTAAATGATA-GTGACTA-ATGA
13256 TTAAATGATAGTGACTAATGA
1 TTAAATGATAGTGACTAATGA
13277 T
1 T
13278 GATTTATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (21 bp):
TTAAATGATAGTGACTAATGA
Found at i:14024 original size:59 final size:59
Alignment explanation
Indices: 13961--14086 Score: 252
Period size: 59 Copynumber: 2.1 Consensus size: 59
13951 ATTTTCAAAG
13961 TGAAATATTCACCATTGAGTTTGACGGTGAAGCGGTGAAGTTTGATGTTTACAAAGCCA
1 TGAAATATTCACCATTGAGTTTGACGGTGAAGCGGTGAAGTTTGATGTTTACAAAGCCA
14020 TGAAATATTCACCATTGAGTTTGACGGTGAAGCGGTGAAGTTTGATGTTTACAAAGCCA
1 TGAAATATTCACCATTGAGTTTGACGGTGAAGCGGTGAAGTTTGATGTTTACAAAGCCA
14079 TGAAATAT
1 TGAAATAT
14087 CCTAATTCTA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 67 1.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.31
Consensus pattern (59 bp):
TGAAATATTCACCATTGAGTTTGACGGTGAAGCGGTGAAGTTTGATGTTTACAAAGCCA
Found at i:15581 original size:23 final size:21
Alignment explanation
Indices: 15530--15581 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 21
15520 ATACGGTTTA
15530 AGAATTTGTTATTACAAATTT
1 AGAATTTGTTATTACAAATTT
15551 AGAGATTTGTTAATT-CAATATTT
1 AGA-ATTTGTT-ATTACAA-ATTT
15574 ATGAATTT
1 A-GAATTT
15582 TAGGGTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 3 0.11
22 10 0.37
23 12 0.44
24 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.12, T:0.48
Consensus pattern (21 bp):
AGAATTTGTTATTACAAATTT
Found at i:16047 original size:20 final size:21
Alignment explanation
Indices: 16001--16047 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
15991 ATAATATTCA
*
16001 TTAAATT--TTTATATATTTT
1 TTAAATTAATTTATATATTTC
16020 TTAAATTAATTTATA-ATTTC
1 TTAAATTAATTTATATATTTC
*
16040 TTATATTA
1 TTAAATTA
16048 TAAATTTACG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.29
20 11 0.46
21 6 0.25
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTAAATTAATTTATATATTTC
Found at i:16096 original size:2 final size:2
Alignment explanation
Indices: 16089--16113 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16079 AATAACGTTA
16089 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
16114 GTTAATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17798 original size:2 final size:2
Alignment explanation
Indices: 17791--17816 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17781 CAACATTTGA
17791 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
17817 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19014 original size:4 final size:4
Alignment explanation
Indices: 19005--19043 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
18995 TTTCTTTACC
19005 ATTT ATTT ATTT A-TT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
19044 CTATTTTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:19051 original size:23 final size:23
Alignment explanation
Indices: 19005--19049 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
18995 TTTCTTTACC
*
19005 ATTTATTTATTTATTATTTATTT
1 ATTTATTTATTTATTATCTATTT
19028 ATTTATTTATTTATT-TCTATTT
1 ATTTATTTATTTATTATCTATTT
19050 TACTAACCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (23 bp):
ATTTATTTATTTATTATCTATTT
Found at i:21348 original size:4 final size:4
Alignment explanation
Indices: 21325--21361 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
21315 TTCATGTCTG
*
21325 TTTA TTT- TATA TTT- TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
21362 CTATTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 5 0.17
4 24 0.83
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:23664 original size:4 final size:4
Alignment explanation
Indices: 23644--23680 Score: 56
Period size: 4 Copynumber: 8.8 Consensus size: 4
23634 TTCATGTCTG
23644 TTTA TTTTA TATTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA -TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTT
23681 CTATTTTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 23 0.74
5 8 0.26
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:33114 original size:46 final size:48
Alignment explanation
Indices: 33046--33136 Score: 132
Period size: 46 Copynumber: 1.9 Consensus size: 48
33036 AATACTTCGC
* * *
33046 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGA-AAAA-AAAACGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAACGT
*
33092 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAA
33137 AGAAAAAGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 31 0.79
47 4 0.10
48 4 0.10
ACGTcount: A:0.43, C:0.15, G:0.26, T:0.15
Consensus pattern (48 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAACGT
Found at i:33162 original size:18 final size:19
Alignment explanation
Indices: 33139--33177 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
33129 AAAGAAAAAG
*
33139 AAAAAGAGGAAAA-AAGAA
1 AAAAAGAAGAAAATAAGAA
33157 AAAAAGAAGAAAATAAGAA
1 AAAAAGAAGAAAATAAGAA
33176 AA
1 AA
33178 TAAGGTGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (19 bp):
AAAAAGAAGAAAATAAGAA
Found at i:33169 original size:16 final size:16
Alignment explanation
Indices: 33133--33177 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
33123 TTGAGAAAAG
*
33133 AAAAAGAAAAAGAGGA
1 AAAAAGAAAAAGAAGA
33149 AAAAAGAAAAAAAGAAGA
1 AAAAAG--AAAAAGAAGA
33167 AAATAAGAAAA
1 AAA-AAGAAAA
33178 TAAGGTGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.24
17 4 0.16
18 12 0.48
19 3 0.12
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAAGAAGA
Found at i:33948 original size:105 final size:105
Alignment explanation
Indices: 33766--34444 Score: 1277
Period size: 105 Copynumber: 6.5 Consensus size: 105
33756 AACTTCAAGC
33766 TCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
1 TCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
33831 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
66 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
*
33871 TCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTTGACTCCAGACAACGCAAGTTC
1 TCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
33936 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
66 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
* *
33976 TCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTC
1 TCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
34041 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
66 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
*
34081 TCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTTGACTCCAGACAACGCAAGTTC
1 TCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
34146 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
66 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
*
34186 TCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
1 TCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
34251 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
66 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
*
34291 TCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTTGACTCCAGACAACGCAAGTTC
1 TCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
*
34356 AACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACATT
66 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
* *
34396 TCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 TCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
34445 AGAACAATAC
Statistics
Matches: 559, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 559 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (105 bp):
TCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
Found at i:34726 original size:2 final size:2
Alignment explanation
Indices: 34721--34800 Score: 137
Period size: 2 Copynumber: 41.0 Consensus size: 2
34711 GTAGACACAC
34721 TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
34762 TA TA TA TA TA TA TA TA TA TA TA TA T- TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34801 AATTATTTTC
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
1 2 0.03
2 72 0.97
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38020 original size:15 final size:16
Alignment explanation
Indices: 37990--38023 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
37980 TTCTTATGTA
37990 TTTATTTATTTATTAT
1 TTTATTTATTTATTAT
*
38006 TTTATTT-TTTGTTAT
1 TTTATTTATTTATTAT
38021 TTT
1 TTT
38024 TTCTTTCTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTATTTATTTATTAT
Found at i:38199 original size:38 final size:37
Alignment explanation
Indices: 38074--38367 Score: 282
Period size: 38 Copynumber: 7.9 Consensus size: 37
38064 TGCAAATGAT
* * *
38074 TTTTG-AAATAAATACA-ATATATAGTTTTTGAAAGCA
1 TTTTGAAAATATATATATATATATAGTTTTT-AAAACA
* ** *
38110 TTTCGAAAACCTATATAT-TATATAGTCTTTAAAACA
1 TTTTGAAAATATATATATATATATAGTTTTTAAAACA
*
38146 TTTTTGGAAACATATATATA-ATATATAATTTTTAAAACA
1 -TTTT-GAAA-ATATATATATATATATAGTTTTTAAAACA
38185 TTTTGAAAATATATATATATTATATAGTTTTTAAAACA
1 TTTTGAAAATATATATATA-TATATAGTTTTTAAAACA
*
38223 TTTTGAATATATATATA-ATATATAGTTTTTAAAACAA
1 TTTTGAAAATATATATATATATATAGTTTTTAAAAC-A
* *
38260 TTTTTGAAAATATATATAT-TATATAGTTTTGAAAATTA
1 -TTTTGAAAATATATATATATATATAGTTTTTAAAA-CA
* * *
38298 TTTTTAAAA-ATATATAT-TATATAGTTTTGAAAATTA
1 TTTTGAAAATATATATATATATATAGTTTTTAAAA-CA
* * * *
38334 TTTTTAAAAAATATATAT-TATATAATTTTAAAAA
1 TTTTGAAAATATATATATATATATAGTTTTTAAAA
38368 TGTTTTATTT
Statistics
Matches: 225, Mismatches: 20, Indels: 25
0.83 0.07 0.09
Matches are distributed among these distances:
36 71 0.32
37 58 0.26
38 73 0.32
39 23 0.10
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
TTTTGAAAATATATATATATATATAGTTTTTAAAACA
Found at i:38232 original size:36 final size:36
Alignment explanation
Indices: 38045--38367 Score: 299
Period size: 36 Copynumber: 8.7 Consensus size: 36
38035 TTTATTATAT
* ** **
38045 ATATATATATTATATAATTTGCAAATGATTTTTG-AA
1 ATATATATATTATATAGTTTTTAAAACA-TTTTGAAA
* * * * *
38081 ATAAATACAATATATAGTTTTTGAAAGCATTTCGAAA
1 ATATATATATTATATAGTTTTT-AAAACATTTTGAAA
** *
38118 ACCTATATATTATATAGTCTTTAAAACATTTTTGGAAA
1 ATATATATATTATATAGTTTTTAAAACA-TTTT-GAAA
* *
38156 CATATATATAATATATAATTTTTAAAACATTTTGAAAA
1 -ATATATATATTATATAGTTTTTAAAACATTTTG-AAA
*
38194 TATATATATATTATATAGTTTTTAAAACATTTTGAAT
1 -ATATATATATTATATAGTTTTTAAAACATTTTGAAA
*
38231 ATATATATAATATATAGTTTTTAAAACAATTTTTGAAA
1 ATATATATATTATATAGTTTTTAAAAC-A-TTTTGAAA
* * *
38269 ATATATATATTATATAGTTTTGAAAATTATTTTTAAA
1 ATATATATATTATATAGTTTTTAAAA-CATTTTGAAA
* * *
38306 A-ATATATATTATATAGTTTTGAAAATTATTTTTAAA
1 ATATATATATTATATAGTTTTTAAAA-CATTTTGAAA
* * *
38342 AAATATATATTATATAATTTTAAAAA
1 ATATATATATTATATAGTTTTTAAAA
38368 TGTTTTATTT
Statistics
Matches: 243, Mismatches: 34, Indels: 19
0.82 0.11 0.06
Matches are distributed among these distances:
36 87 0.36
37 59 0.24
38 74 0.30
39 23 0.09
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
ATATATATATTATATAGTTTTTAAAACATTTTGAAA
Found at i:38273 original size:74 final size:72
Alignment explanation
Indices: 38045--38367 Score: 326
Period size: 74 Copynumber: 4.4 Consensus size: 72
38035 TTTATTATAT
* ** ** * * *
38045 ATATATATATTATATAATTTGCAAATGATTTTTGAAATAAATACAATATATAGTTTTTGAAAGCA
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAATATATATAATATATAGTTTTT-AAAACA
*
38110 TTTCGAAA
65 TTTTGAAA
** * *
38118 ACCTATATATTATATAGTCTTTAAAACATTTTTGGAAACATATATATAATATATAATTTTTAAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTT-G-AA-ATATATATAATATATAGTTTTTAAAA
38183 CATTTTGAAAA
63 CATTTTG-AAA
38194 TATATATATATTATATAGTTTTTAAAACA-TTTTGAATATATATATAATATATAGTTTTTAAAAC
1 -ATATATATATTATATAGTTTTTAAAACATTTTTGAA-ATATATATAATATATAGTTTTTAAAAC
38258 AATTTTTGAAA
64 -A-TTTTGAAA
* * * * * *
38269 ATATATATATTATATAGTTTTGAAAATTATTTTT-AAAAATATATATTATATAGTTTTGAAAATT
1 ATATATATATTATATAGTTTTTAAAA-CATTTTTGAAATATATATAATATATAGTTTTTAAAA-C
*
38333 ATTTTTAAA
64 ATTTTGAAA
* * *
38342 AAATATATATTATATAATTTTAAAAA
1 ATATATATATTATATAGTTTTTAAAA
38368 TGTTTTATTT
Statistics
Matches: 212, Mismatches: 28, Indels: 20
0.82 0.11 0.08
Matches are distributed among these distances:
73 55 0.26
74 78 0.37
75 19 0.09
76 35 0.17
77 25 0.12
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (72 bp):
ATATATATATTATATAGTTTTTAAAACATTTTTGAAATATATATAATATATAGTTTTTAAAACAT
TTTGAAA
Found at i:38412 original size:4 final size:4
Alignment explanation
Indices: 38371--38440 Score: 56
Period size: 4 Copynumber: 17.2 Consensus size: 4
38361 TTAAAAATGT
* * *
38371 TTTA TTTTA ATTA TTTA -TTA TTT- TTCTA CTTC TTTA TTTA TTTTA TTTTA
1 TTTA -TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA -TTTA -TTTA
38421 TTTA TTTA -TTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA T
38441 CGTTTTAGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
3 8 0.15
4 32 0.59
5 14 0.26
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:38422 original size:14 final size:13
Alignment explanation
Indices: 38371--38440 Score: 56
Period size: 13 Copynumber: 5.4 Consensus size: 13
38361 TTAAAAATGT
*
38371 TTTATTTTAATTA
1 TTTATTTTATTTA
*
38384 TTTATTATTTTTCTA
1 TTTATT-TTATT-TA
* *
38399 CTT-CTTTATTTA
1 TTTATTTTATTTA
38411 TTTTATTTTATTTA
1 -TTTATTTTATTTA
38425 TTTA--TTATTTA
1 TTTATTTTATTTA
38436 TTTAT
1 TTTAT
38441 CGTTTTAGGT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
11 11 0.24
12 2 0.04
13 16 0.36
14 12 0.27
15 4 0.09
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:39236 original size:33 final size:33
Alignment explanation
Indices: 39194--39264 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
39184 CACCGTGGGT
* **
39194 GGTGGCCGGAGCGATTTCCGGTAAGCAGCTGGC
1 GGTGGCCGGAGCAATTTCCGACAAGCAGCTGGC
*
39227 GGTGGCCGGAGCAATTTCCGACAAGCGGCTGGC
1 GGTGGCCGGAGCAATTTCCGACAAGCAGCTGGC
39260 GGTGG
1 GGTGG
39265 GGTTCCTATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.17
Consensus pattern (33 bp):
GGTGGCCGGAGCAATTTCCGACAAGCAGCTGGC
Found at i:42322 original size:20 final size:21
Alignment explanation
Indices: 42247--42323 Score: 61
Period size: 20 Copynumber: 3.8 Consensus size: 21
42237 TTTTTGGCTC
*
42247 AAAGGATCGATCCC-TTAACA
1 AAAGGATCGATCCCTTTGACA
* * *
42267 AAAGGATTGGTCCATTTGATC-
1 AAAGGATCGATCCCTTTGA-CA
* *
42288 AAAGGATCAACCCCTTTGA-A
1 AAAGGATCGATCCCTTTGACA
*
42308 AAAGGATTGATCCCTT
1 AAAGGATCGATCCCTT
42324 ATATTCCAGA
Statistics
Matches: 42, Mismatches: 12, Indels: 6
0.70 0.20 0.10
Matches are distributed among these distances:
20 24 0.57
21 17 0.40
22 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (21 bp):
AAAGGATCGATCCCTTTGACA
Found at i:42549 original size:14 final size:14
Alignment explanation
Indices: 42530--42562 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
42520 TGTCATATCC
42530 ATATTTTTTAAATA
1 ATATTTTTTAAATA
42544 ATA--TTTTAAATA
1 ATATTTTTTAAATA
42556 ATATTTT
1 ATATTTT
42563 ATTTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.71
14 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATATTTTTTAAATA
Found at i:42552 original size:12 final size:12
Alignment explanation
Indices: 42535--42563 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
42525 TATCCATATT
42535 TTTTAAATAATA
1 TTTTAAATAATA
42547 TTTTAAATAATA
1 TTTTAAATAATA
42559 TTTTA
1 TTTTA
42564 TTTTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTTAAATAATA
Found at i:44039 original size:42 final size:42
Alignment explanation
Indices: 44002--44088 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
43992 TATCATAAGT
* *
44002 ATGCAACAAGTTTCTTACATCTAGCGAAGGAGTATCATATAC
1 ATGCAACAAGTTACTTACACCTAGCGAAGGAGTATCATATAC
* * *
44044 ATGCTATAAGTTACTTATACCTAGCGAAGGAGTATCATATAC
1 ATGCAACAAGTTACTTACACCTAGCGAAGGAGTATCATATAC
44086 ATG
1 ATG
44089 TAGTTATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (42 bp):
ATGCAACAAGTTACTTACACCTAGCGAAGGAGTATCATATAC
Found at i:45754 original size:15 final size:14
Alignment explanation
Indices: 45722--45769 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
45712 ATACATATAT
*
45722 GCATGCTGATTAGC
1 GCATGGTGATTAGC
45736 GCATGGTGATTAGGC
1 GCATGGTGATTA-GC
**
45751 GCATGGTGACAAGC
1 GCATGGTGATTAGC
45765 GCATG
1 GCATG
45770 ATAATTTGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (14 bp):
GCATGGTGATTAGC
Found at i:46002 original size:14 final size:15
Alignment explanation
Indices: 45971--46003 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
45961 TTAATCATGA
45971 TATTGTTCATGATAT
1 TATTGTTCATGATAT
*
45986 TATTGTT-ATGGTAT
1 TATTGTTCATGATAT
46000 TATT
1 TATT
46004 ATCATATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (15 bp):
TATTGTTCATGATAT
Found at i:46418 original size:58 final size:58
Alignment explanation
Indices: 46344--46633 Score: 342
Period size: 58 Copynumber: 5.0 Consensus size: 58
46334 AATCTTATGT
* **
46344 TGATTCTAACTTTGTAAGGAAAATAGTTTGTTGAATTTA-TTTCATTGAGAATCTTAAA
1 TGATTCTAACTTTGTAAGAAAAATAAATTGTTGAATTTATTTTC-TTGAGAATCTTAAA
* *
46402 TGATTCTAACTTTGTAAGAAAAATAAATTGTTGAATTTATTTCCTTG-GAAATCTTGAA
1 TGATTCTAACTTTGTAAGAAAAATAAATTGTTGAATTTATTTTCTTGAG-AATCTTAAA
* *
46460 TGATTTTAACTTTGTAAGAAAAATAAATTGTCGAATTTATTTTCTTGAGAATCTTAAA
1 TGATTCTAACTTTGTAAGAAAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAA
* * *
46518 TAATTCT-ATTTTGTAA-AAATTAATAAATTGTTAAATTTATTTTCTTGAGAATCTTAAA
1 TGATTCTAACTTTGTAAGAAA--AATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAA
* * * * *
46576 CGATTCT-ATTTTGTTAA-AGGAAATGAATTGTTAAATTTATTTTCTTG-GAATCTTAAA
1 TGATTCTAACTTTG-TAAGA-AAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAA
46633 T
1 T
46634 AAAGAAATA
Statistics
Matches: 206, Mismatches: 19, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
56 3 0.01
57 19 0.09
58 175 0.85
59 8 0.04
60 1 0.00
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.44
Consensus pattern (58 bp):
TGATTCTAACTTTGTAAGAAAAATAAATTGTTGAATTTATTTTCTTGAGAATCTTAAA
Done.