Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005820.1 Hibiscus syriacus cultivar Beakdansim tig00013637_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: 123224
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7062 original size:64 final size:64
Alignment explanation
Indices: 6988--7150 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
6978 CGGTGCACCA
*
6988 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAACCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAACCAGAGTGCATCGATGCATGG
** * **
7052 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAACCAGAGTGCATCGATGCATGG
* * *
7117 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
7151 CAATTAATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 39 0.46
65 46 0.54
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAACCAGAGTGCATCGATGCATGG
Found at i:7122 original size:19 final size:19
Alignment explanation
Indices: 7098--7148 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
7088 GAAAATATTC
7098 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
7117 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
7136 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
7149 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:7190 original size:65 final size:65
Alignment explanation
Indices: 6992--7199 Score: 207
Period size: 65 Copynumber: 3.2 Consensus size: 65
6982 GCACCAAGTG
* * ** *
6992 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAACCTG-GTGCATCGATGCATGG-CTT
1 TGCATCGGTGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-T
7055 G-
64 GA
* * *
7056 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
7119 A
65 A
* *
7120 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGA
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGA
7182 CTGA
62 CTGA
7186 TGCATCGGTGCATG
1 TGCATCGGTGCATG
7200 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 10, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
62 3 0.02
63 8 0.06
64 51 0.41
65 60 0.48
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (65 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA
Found at i:12098 original size:22 final size:21
Alignment explanation
Indices: 12072--12118 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
12062 AAGGTCAAAA
*
12072 ATCAAATTGTTTGAAAATTG-AT
1 ATCAAATGGTTT-AAAA-TGAAT
12094 ATC-AATGGTTTAAAATGAAT
1 ATCAAATGGTTTAAAATGAAT
12114 ATCAA
1 ATCAA
12119 TTACGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 8 0.36
22 3 0.14
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
ATCAAATGGTTTAAAATGAAT
Found at i:14271 original size:64 final size:65
Alignment explanation
Indices: 14185--14347 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 65
14175 CGGCGCACCA
*
14185 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTAAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTAAAAAATAGCCAGAGTGCATCGATGCATGG
** * ** **
14249 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTAAAAAATAGCCAGAGTGCATCGATGCATGG
* * * *
14314 AGAGTGTATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
14348 CAATTAATTC
Statistics
Matches: 83, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
64 40 0.48
65 43 0.52
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (65 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTAAAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:14319 original size:19 final size:19
Alignment explanation
Indices: 14295--14345 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
14285 GAAAATATTC
14295 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
* *
14314 AGAGTGTATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
14333 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
14346 TTCAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 3 0.11
18 6 0.22
19 18 0.67
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.25
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:14390 original size:65 final size:63
Alignment explanation
Indices: 14189--14396 Score: 192
Period size: 65 Copynumber: 3.2 Consensus size: 63
14179 GCACCAAGTG
* * * *
14189 TGCATCGATGCATGAAATGCATTCGATGTTTAAAAAATAGCCTGGTGCATCGATGCATGG-CTTG
1 TGCATCGATGCATGAAATGCATTCGATG-TTCAAAAAT-TCATGATGCATCGATGCATGGAC-TG
14253 -
63 A
* *
14253 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG--TTCAAAA-ATTCATGA-TGCATCGATGCATGGACT
14315 GA
62 GA
* * * *
14317 GTGTATCGGTGCATGGAATGCATTCGATGTTCAATTAATTCATCGATGCATCGATGCATGGACTG
1 -TGCATCGATGCATGAAATGCATTCGATGTTCAA-AAATTCAT-GATGCATCGATGCATGGACTG
14382 A
63 A
*
14383 TGCATCGGTGCATG
1 TGCATCGATGCATG
14397 CCTTTGAATA
Statistics
Matches: 121, Mismatches: 12, Indels: 21
0.79 0.08 0.14
Matches are distributed among these distances:
63 10 0.08
64 45 0.37
65 62 0.51
66 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (63 bp):
TGCATCGATGCATGAAATGCATTCGATGTTCAAAAATTCATGATGCATCGATGCATGGACTGA
Found at i:14855 original size:13 final size:13
Alignment explanation
Indices: 14837--14875 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
14827 GGATTTATCT
14837 TTATTTTTAGGAA
1 TTATTTTTAGGAA
* *
14850 TTATTTTAAAGAA
1 TTATTTTTAGGAA
14863 TTATATTTTAGGA
1 TTAT-TTTTAGGA
14876 TTTTTATGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 15 0.71
14 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (13 bp):
TTATTTTTAGGAA
Found at i:20202 original size:37 final size:37
Alignment explanation
Indices: 20154--20227 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
20144 TTTCTTTTAA
* *
20154 AAAAATTTAAATTTAATCTTAATTCTACTTGAAAAAG
1 AAAAATTTAAATCTAATCTTAATTCTACGTGAAAAAG
* *
20191 AAAATTTTAAATCTAATCTTAATTCTCCGTGAAAAAG
1 AAAAATTTAAATCTAATCTTAATTCTACGTGAAAAAG
20228 GAGAAACGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (37 bp):
AAAAATTTAAATCTAATCTTAATTCTACGTGAAAAAG
Found at i:22908 original size:2 final size:2
Alignment explanation
Indices: 22901--22933 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
22891 TGACTAGTTC
22901 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22934 TCATAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30158 original size:11 final size:11
Alignment explanation
Indices: 30142--30176 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
30132 TTTTATTTTA
30142 TATTTTTAAAT
1 TATTTTTAAAT
30153 TATTTTTTACAAT
1 TA-TTTTTA-AAT
30166 TATTTTTAAAT
1 TATTTTTAAAT
30177 GAGTTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.23
12 12 0.55
13 5 0.23
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (11 bp):
TATTTTTAAAT
Found at i:30749 original size:2 final size:2
Alignment explanation
Indices: 30678--30735 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
30668 CCGACCCGAA
30678 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30720 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
30736 TTTACCCTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31534 original size:271 final size:268
Alignment explanation
Indices: 31054--31589 Score: 831
Period size: 271 Copynumber: 2.0 Consensus size: 268
31044 GGTGGTGACA
* *
31054 TGTCACCACTTTATTGGTGAAAAAAATTATTTAGTTAAAATATTAAAATTAATTAAAAATTATTT
1 TGTCACCACTTTATTGGTGAAAAAAATTATTTAATTAAAATATTAAAATTAATTAAAAACTATTT
* *
31119 TATCAAGTTATGGCATGTATTAATATTAAAATATATCTTAATAATCAGTTAACATGTAGTATATC
66 TATCAAGTTATGGCATGTATTAATATTAAAATATATCTTAATAATCAGTTAACATGTAGCACATC
*
31184 TTGATTGAAGGGTTAATTTATAGAATTAAATTTATATTTAAACTAAATTAACAGAATATACAAAT
131 TTGATTGAAGGGTTAATTTATAGAATTAAATTTATATTAAAACTAAATTAACAGAATATACAAAT
* * *
31249 ATTAAGGATCAAATGTGTAATTATATAATTTTGTGTTAACTGCCACATAATCCCTCCGTTAGATT
196 ATTAAGGATCAAATGTGTAATTATATAATTTTGTGTTAACTACCACATAATCCATCCGTTAAATT
31314 TTAATTGT
261 TTAATTGT
*
31322 TGTCACCACTTTATTGGTG-AGAAAATTCATTTAATTAAAATATTAAAATTAATTTAAAAAAACT
1 TGTCACCACTTTATTGGTGAAAAAAATT-ATTTAATTAAAATATTAAAATTAA-TT--AAAAACT
* * * * * **
31386 CTTTTATTAAGTTATGGCATGTATTACTATTAAAATATGTCTTAATAATTAGTTCTCATGTAGCA
62 ATTTTATCAAGTTATGGCATGTATTAATATTAAAATATATCTTAATAATCAGTTAACATGTAGCA
* * *
31451 CATCTTGATTGGAGGGTTAATTTATAGAATTAAATTTATATTAAAACTAAGTTAATAGAATATAC
127 CATCTTGATTGAAGGGTTAATTTATAGAATTAAATTTATATTAAAACTAAATTAACAGAATATAC
* * *
31516 AAGTATTAAGGATCAAATGTGTAATTATATAATTTTGTGTTAACTACCACGTAATTCATCCGTTA
192 AAATATTAAGGATCAAATGTGTAATTATATAATTTTGTGTTAACTACCACATAATCCATCCGTTA
31581 AATTTTAAT
257 AATTTTAAT
31590 GGTTAGTGAT
Statistics
Matches: 242, Mismatches: 22, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
267 7 0.03
268 42 0.17
269 2 0.01
271 191 0.79
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (268 bp):
TGTCACCACTTTATTGGTGAAAAAAATTATTTAATTAAAATATTAAAATTAATTAAAAACTATTT
TATCAAGTTATGGCATGTATTAATATTAAAATATATCTTAATAATCAGTTAACATGTAGCACATC
TTGATTGAAGGGTTAATTTATAGAATTAAATTTATATTAAAACTAAATTAACAGAATATACAAAT
ATTAAGGATCAAATGTGTAATTATATAATTTTGTGTTAACTACCACATAATCCATCCGTTAAATT
TTAATTGT
Found at i:40641 original size:6 final size:6
Alignment explanation
Indices: 40630--40681 Score: 59
Period size: 6 Copynumber: 8.0 Consensus size: 6
40620 GATTCTGCTA
*
40630 TATTTT TATTTT TATTTT TATTGTTTT TGTTTT TATTTT TATTTTT TATTTT
1 TATTTT TATTTT TATTTT TA---TTTT TATTTT TATTTT TA-TTTT TATTTT
40682 AGTTTTTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 29 0.73
7 6 0.15
9 5 0.12
ACGTcount: A:0.13, C:0.00, G:0.04, T:0.83
Consensus pattern (6 bp):
TATTTT
Found at i:40656 original size:21 final size:19
Alignment explanation
Indices: 40632--40681 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 19
40622 TTCTGCTATA
40632 TTTTTATTTTTATTTTTATT
1 TTTTTATTTTTATTTTTA-T
*
40652 GTTTTTGTTTTTATTTTTAT
1 -TTTTTATTTTTATTTTTAT
40672 TTTTTATTTT
1 TTTTTATTTT
40682 AGTTTTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 9 0.33
20 1 0.04
21 17 0.63
ACGTcount: A:0.12, C:0.00, G:0.04, T:0.84
Consensus pattern (19 bp):
TTTTTATTTTTATTTTTAT
Found at i:40667 original size:33 final size:31
Alignment explanation
Indices: 40632--40692 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 31
40622 TTCTGCTATA
40632 TTTTTATTTTTA-TTTTTA--TT-GTTTTTG
1 TTTTTATTTTTATTTTTTATTTTAGTTTTTG
40659 TTTTTATTTTTATTTTTTATTTTAGTTTTTG
1 TTTTTATTTTTATTTTTTATTTTAGTTTTTG
40690 TTT
1 TTT
40693 CGACAAGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 12 0.40
28 6 0.20
30 2 0.07
31 10 0.33
ACGTcount: A:0.11, C:0.00, G:0.07, T:0.82
Consensus pattern (31 bp):
TTTTTATTTTTATTTTTTATTTTAGTTTTTG
Found at i:40682 original size:12 final size:14
Alignment explanation
Indices: 40628--40681 Score: 60
Period size: 13 Copynumber: 4.0 Consensus size: 14
40618 TCGATTCTGC
40628 TATATTTTTA-TTT
1 TATATTTTTATTTT
40641 T-TATTTTTATTGTT
1 TATATTTTTATT-TT
* *
40655 TTTGTTTTTATTTT
1 TATATTTTTATTTT
40669 TAT-TTTTTATTTT
1 TATATTTTTATTTT
40682 AGTTTTTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
12 8 0.22
13 12 0.33
14 7 0.19
15 9 0.25
ACGTcount: A:0.15, C:0.00, G:0.04, T:0.81
Consensus pattern (14 bp):
TATATTTTTATTTT
Found at i:40687 original size:12 final size:13
Alignment explanation
Indices: 40632--40688 Score: 64
Period size: 12 Copynumber: 4.4 Consensus size: 13
40622 TTCTGCTATA
40632 TTTTTATTTTTA-
1 TTTTTATTTTTAG
*
40644 TTTTTATTGTTTTTG
1 TTTTTA-T-TTTTAG
*
40659 TTTTTATTTTTAT
1 TTTTTATTTTTAG
40672 TTTTTA-TTTTAG
1 TTTTTATTTTTAG
40684 TTTTT
1 TTTTT
40689 GTTTCGACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
12 16 0.42
13 11 0.29
14 5 0.13
15 6 0.16
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.82
Consensus pattern (13 bp):
TTTTTATTTTTAG
Found at i:45815 original size:3 final size:3
Alignment explanation
Indices: 45807--45876 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
45797 CGCACATGTT
45807 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
45855 TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
45877 ATAGGAAAAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:47364 original size:19 final size:19
Alignment explanation
Indices: 47319--47355 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
47309 GCGTTTGGAT
47319 GGGGAATGTGGGATTCCTC
1 GGGGAATGTGGGATTCCTC
47338 GGGGAATGTGGGATTCCT
1 GGGGAATGTGGGATTCCT
47356 TTGGGAATGG
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:0.16, C:0.14, G:0.43, T:0.27
Consensus pattern (19 bp):
GGGGAATGTGGGATTCCTC
Found at i:56301 original size:3 final size:3
Alignment explanation
Indices: 56293--56355 Score: 99
Period size: 3 Copynumber: 20.0 Consensus size: 3
56283 CTGTGCAAGC
56293 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGAA AGAA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AG-A AGA
56340 AGGA AGA AGA AGA AGA
1 A-GA AGA AGA AGA AGA
56356 CCGGGGGAGG
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
3 48 0.83
4 10 0.17
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:58555 original size:15 final size:13
Alignment explanation
Indices: 58536--58611 Score: 77
Period size: 13 Copynumber: 5.8 Consensus size: 13
58526 TCTACAAAAA
58536 TATTTTATTATATT
1 TATTTTATT-TATT
58550 ATATTTTATTTATT
1 -TATTTTATTTATT
58564 TA-TTTATTTATT
1 TATTTTATTTATT
58576 TATTATTA-TTATT
1 TATT-TTATTTATT
* *
58589 TTTTTTACTT-TT
1 TATTTTATTTATT
58601 TATTTTTATTT
1 TA-TTTTATTT
58612 TTGTAGGCCC
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
12 18 0.33
13 20 0.37
14 7 0.13
15 9 0.17
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (13 bp):
TATTTTATTTATT
Found at i:58563 original size:4 final size:4
Alignment explanation
Indices: 58539--58579 Score: 55
Period size: 4 Copynumber: 9.5 Consensus size: 4
58529 ACAAAAATAT
58539 TTTA TTATA TTATA TTTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TT-TA TT-TA -TTTA TTTA TTTA TTTA TTTA TTTA TT
58580 ATTATTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 24 0.69
5 9 0.26
6 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:58584 original size:22 final size:22
Alignment explanation
Indices: 58555--58611 Score: 53
Period size: 25 Copynumber: 2.5 Consensus size: 22
58545 ATATTATATT
*
58555 TTATTTATTTATTTATTTATTTA
1 TTATTTATTTATTTACTT-TTTA
*
58578 TTATTATTATTTTTTTTACTTTTTA
1 TTA-T-TTA-TTTATTTACTTTTTA
58603 TT-TTTATTT
1 TTATTTATTT
58612 TTGTAGGCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
21 3 0.10
22 3 0.10
23 4 0.14
24 1 0.03
25 9 0.31
26 9 0.31
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (22 bp):
TTATTTATTTATTTACTTTTTA
Found at i:58611 original size:35 final size:35
Alignment explanation
Indices: 58539--58605 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
58529 ACAAAAATAT
58539 TTTATTATATTATATTTTATTTATTTATTTATTTA
1 TTTATTATATTATATTTTATTTATTTATTTATTTA
*
58574 TTTATTATTATTAT-TTTT-TTTACTT-TTTATTT
1 TTTATTA-TATTATATTTTATTTATTTATTTATTT
58606 TTATTTTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 7 0.23
34 6 0.20
35 11 0.37
36 6 0.20
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (35 bp):
TTTATTATATTATATTTTATTTATTTATTTATTTA
Found at i:58613 original size:12 final size:13
Alignment explanation
Indices: 58538--58610 Score: 71
Period size: 12 Copynumber: 5.5 Consensus size: 13
58528 TACAAAAATA
58538 TTTTATTATATTAT
1 TTTTATTAT-TTAT
58552 ATTTTATTTATTTAT
1 -TTTTA-TTATTTAT
*
58567 TTAT-TTATTTAT
1 TTTTATTATTTAT
*
58579 TATTATTATTT-T
1 TTTTATTATTTAT
58591 TTTTACTT-TTTAT
1 TTTTA-TTATTTAT
58604 TTTTATT
1 TTTTATT
58611 TTTGTAGGCC
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
12 20 0.40
13 14 0.28
14 3 0.06
15 9 0.18
16 4 0.08
ACGTcount: A:0.23, C:0.01, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:58706 original size:33 final size:33
Alignment explanation
Indices: 58660--58746 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 33
58650 TTCAAAAAAT
*
58660 AAATCAACATATTTGAGTCCTATTGAAACACTA
1 AAATCAACATATTTGAGTCCTATTAAAACACTA
*
58693 AAATCAACGTATTTGAGTCCTATTAAAACACTA
1 AAATCAACATATTTGAGTCCTATTAAAACACTA
*
58726 AAACCGAAGCAT-TTTGAGTCC
1 AAATC-AA-CATATTTGAGTCC
58747 AAGTATGACT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
33 35 0.73
34 11 0.23
35 2 0.04
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (33 bp):
AAATCAACATATTTGAGTCCTATTAAAACACTA
Found at i:59033 original size:12 final size:12
Alignment explanation
Indices: 59010--59040 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
59000 AACTTTTGAC
59010 TTATTCTTTTTAT
1 TTATT-TTTTTAT
59023 TTATTTTTTTAT
1 TTATTTTTTTAT
59035 TTATTT
1 TTATTT
59041 ACTTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (12 bp):
TTATTTTTTTAT
Found at i:63251 original size:106 final size:105
Alignment explanation
Indices: 63110--63472 Score: 492
Period size: 106 Copynumber: 3.4 Consensus size: 105
63100 TTCAGTTTCA
* * *
63110 TTCAGAGTCAATTTCAACTTCACAGTGAAGAATATTGGACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* *
63175 CAGCGAAGGGACGGCTGGCTGTCAACAAACAATTTCCTAGT
66 CAGCGAAGGGGCGGTTGGCTGTCAACAAACAATTTCC-AGT
* *
63216 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
* * * *
63281 CAGCGAAGGGGTGATTGACTGTCAACAAACAACTTTTCAGTTT
66 CAGCGAAGGGGCGGTTGGCTGTCAACAAACAA-TTTCCAG--T
* * * *
63324 CATTCAGAGTCAATTTCAACTTCACAGTGAAAGATATTAGACTCGAGACAACACAAGCTCAACTT
1 --TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTT
63389 CACAGCGAAGGGGCGGTTGGCTGTCAACAAACAATTTCCCAGT
64 CACAGCGAAGGGGCGGTTGGCTGTCAACAAACAATTT-CCAGT
* * * *
63432 TCCAGAGCCAATTTTAACTTCACGGCGGAGGATATTGGACT
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
63473 GGGAACAATA
Statistics
Matches: 222, Mismatches: 29, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
106 122 0.55
107 4 0.02
108 2 0.01
109 3 0.01
110 91 0.41
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (105 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCA
CAGCGAAGGGGCGGTTGGCTGTCAACAAACAATTTCCAGT
Found at i:63382 original size:110 final size:110
Alignment explanation
Indices: 63216--63454 Score: 335
Period size: 110 Copynumber: 2.2 Consensus size: 110
63206 ATTTCCTAGT
* *
63216 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAAGATATTAGACTCAAGACAACACAAGCTCAACTTCA
*
63281 CAGCGAAGGGGTGATTGACTGTCAACAAACAACTTTTCAGTTTCA
66 CAGCGAAGGGGCGATTGACTGTCAACAAACAACTTTTCAGTTTCA
* ** *
63326 TTCAGAGTCAATTTCAACTTCACAGTGAAAGATATTAGACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAAGATATTAGACTCAAGACAACACAAGCTCAACTTCA
* * *
63391 CAGCGAAGGGGCGGTTGGCTGTCAACAAACAA-TTTCCCAG-TTC-
66 CAGCGAAGGGGCGATTGACTGTCAACAAACAACTTT-TCAGTTTCA
*
63434 --CAGAGCCAATTTTAACTTCAC
1 TTCAGAGCCAATTTCAACTTCAC
63455 GGCGGAGGAT
Statistics
Matches: 116, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
106 19 0.16
109 6 0.05
110 91 0.78
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAAGATATTAGACTCAAGACAACACAAGCTCAACTTCA
CAGCGAAGGGGCGATTGACTGTCAACAAACAACTTTTCAGTTTCA
Found at i:63466 original size:216 final size:212
Alignment explanation
Indices: 63058--63472 Score: 661
Period size: 216 Copynumber: 1.9 Consensus size: 212
63048 GATGGTGGTT
*
63058 GCTCAACTTCACAGCAAAGGGGCGACTGACAATAAACAACTTTTCAGTTTCATTCAGAGTCAATT
1 GCTCAACTTCACAGCAAAGGGGCGACTGACAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
*
63123 TCAACTTCACAGTGAAGAATATTGGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGACG
66 TCAACTTCACAGTGAAGAATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGACG
* *
63188 GCTGGCTGTCAACAAACAATTTCCTAGTTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
131 GCTGGCTGTCAACAAACAATTTCCCAGTTCCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
63253 GACTCAAGACAACACAA
196 GACTCAAGACAACACAA
* * *
63270 GCTCAACTTCACAGCGAAGGGGTGATTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGC-AAAGGG-G--CGACTGACAACAAACAACTTTTCAGTTTCATTCAGAGTC
63335 AATTTCAACTTCACAGTGAA-AGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCGAAG
62 AATTTCAACTTCACAGTGAAGA-ATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCGAAG
* * * ** *
63399 GGGCGGTTGGCTGTCAACAAACAATTTCCCAGTTCCAGAGCCAATTTTAACTTCACGGCGGAGGA
126 GGACGGCTGGCTGTCAACAAACAATTTCCCAGTTCCAGAGCCAATTTCAACTTCACAACGAAGGA
63464 TATTGGACT
191 TATTGGACT
63473 GGGAACAATA
Statistics
Matches: 185, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
212 15 0.08
213 5 0.03
214 1 0.01
215 1 0.01
216 163 0.88
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (212 bp):
GCTCAACTTCACAGCAAAGGGGCGACTGACAACAAACAACTTTTCAGTTTCATTCAGAGTCAATT
TCAACTTCACAGTGAAGAATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGACG
GCTGGCTGTCAACAAACAATTTCCCAGTTCCAGAGCCAATTTCAACTTCACAACGAAGGATATTG
GACTCAAGACAACACAA
Found at i:63994 original size:2 final size:2
Alignment explanation
Indices: 63979--64034 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
63969 ATTGCAAATC
63979 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
64019 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
64035 TTATTTATTT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65706 original size:46 final size:46
Alignment explanation
Indices: 65638--65736 Score: 189
Period size: 46 Copynumber: 2.1 Consensus size: 46
65628 AGCGCAAAGA
65638 AAACACATAGAAGTCTATACTTTATGGCATGGCATGACAATTATACC
1 AAACA-ATAGAAGTCTATACTTTATGGCATGGCATGACAATTATACC
65685 AAACAATAGAAGTCTATACTTTATGGCATGGCATGACAATTATACC
1 AAACAATAGAAGTCTATACTTTATGGCATGGCATGACAATTATACC
65731 AAACAA
1 AAACAA
65737 GTTTTCACTA
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 47 0.90
47 5 0.10
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.26
Consensus pattern (46 bp):
AAACAATAGAAGTCTATACTTTATGGCATGGCATGACAATTATACC
Found at i:68000 original size:34 final size:34
Alignment explanation
Indices: 67953--68024 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
67943 AAATCATTGA
* *
67953 GTGAAATCTAAGGCCTGGAAATACTATACTAAAG
1 GTGAAATCAAAGGCCTGGAAATACTATACAAAAG
67987 GTGAAATCAAAGGCCTGGAAATACTATACAAAAG
1 GTGAAATCAAAGGCCTGGAAATACTATACAAAAG
68021 GTGA
1 GTGA
68025 GTTCATCCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.43, C:0.14, G:0.22, T:0.21
Consensus pattern (34 bp):
GTGAAATCAAAGGCCTGGAAATACTATACAAAAG
Found at i:68749 original size:2 final size:2
Alignment explanation
Indices: 68742--68824 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
68732 ACAGGGTGAT
68742 TA TA TA TA 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
68784 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
68825 TGATTGCATC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:69217 original size:18 final size:18
Alignment explanation
Indices: 69194--69231 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
69184 AGGGACTAAT
*
69194 TTAGAAAGATGGTCATAG
1 TTAGAAAGATGATCATAG
69212 TTAGAAAGATGATCATAG
1 TTAGAAAGATGATCATAG
69230 TT
1 TT
69232 TAGAGATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (18 bp):
TTAGAAAGATGATCATAG
Found at i:69319 original size:60 final size:60
Alignment explanation
Indices: 69224--69358 Score: 164
Period size: 60 Copynumber: 2.2 Consensus size: 60
69214 AGAAAGATGA
* * * * *
69224 TCATAGTTTAGAGATGAAATTAGAATGTCCAAAAGTTTAAGAACTAATTGAAAATGAGAG
1 TCATAGTTTGGGGATGAAATTAGAATATCCAAAAGTTTAAGAACTAATTCAAAATGAAAG
* * *
69284 TCATAGTTTGGGGATGTAATTAGAATAT-TATAAAGTTTAAGGACTAATTCAAAATGAAAG
1 TCATAGTTTGGGGATGAAATTAGAATATCCA-AAAGTTTAAGAACTAATTCAAAATGAAAG
* *
69344 TTATTGTTTGGGGAT
1 TCATAGTTTGGGGAT
69359 CTATGATGCA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 1 0.02
60 63 0.98
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.33
Consensus pattern (60 bp):
TCATAGTTTGGGGATGAAATTAGAATATCCAAAAGTTTAAGAACTAATTCAAAATGAAAG
Found at i:69706 original size:18 final size:18
Alignment explanation
Indices: 69691--69758 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 18
69681 TATCAGAATC
69691 CGAAAAAGAAAAAGAAAA
1 CGAAAAAGAAAAAGAAAA
* * *
69709 GGAAAAGGAAAAGGAAAA
1 CGAAAAAGAAAAAGAAAA
*
69727 GGAAAAAGAAAAAG-AAA
1 CGAAAAAGAAAAAGAAAA
69744 C-AAAAAG-AAAAGAAA
1 CGAAAAAGAAAAAGAAA
69759 CAAAACCTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
15 5 0.12
16 8 0.19
17 3 0.07
18 27 0.63
ACGTcount: A:0.75, C:0.03, G:0.22, T:0.00
Consensus pattern (18 bp):
CGAAAAAGAAAAAGAAAA
Found at i:69754 original size:6 final size:6
Alignment explanation
Indices: 69692--69743 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
69682 ATCAGAATCC
* * * *
69692 GAAAAA GAAAAA GAAAAG GAAAAG GAAAAG GAAAAG GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA
69740 GAAA
1 GAAA
69744 CAAAAAGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:69754 original size:15 final size:16
Alignment explanation
Indices: 69693--69763 Score: 65
Period size: 15 Copynumber: 4.2 Consensus size: 16
69683 TCAGAATCCG
69693 AAAAAGAAAAAGAAA-
1 AAAAAGAAAAAGAAAC
* *
69708 AGGAAAAGGAAAAGGAAAAGG
1 A--AAAA-GAAAAAG-AAA-C
69729 AAAAAGAAAAAGAAAC
1 AAAAAGAAAAAGAAAC
69745 AAAAAG-AAAAGAAAC
1 AAAAAGAAAAAGAAAC
69760 AAAA
1 AAAA
69764 CCTCAACCTC
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
15 14 0.30
16 6 0.13
17 7 0.15
18 12 0.26
19 7 0.15
21 1 0.02
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAGAAAC
Found at i:84760 original size:20 final size:20
Alignment explanation
Indices: 84732--84800 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
84722 TTGATCCTCT
* *
84732 TTGGAAAAGTATAGATGCTC
1 TTGGGAAAGCATAGATGCTC
84752 TTGGGAAAGCATAGATGCTC
1 TTGGGAAAGCATAGATGCTC
* * *
84772 TTTGGAAAGCATGGATACTC
1 TTGGGAAAGCATAGATGCTC
84792 TTGGGAAAG
1 TTGGGAAAG
84801 TATCGATACT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.28
Consensus pattern (20 bp):
TTGGGAAAGCATAGATGCTC
Found at i:84808 original size:20 final size:20
Alignment explanation
Indices: 84732--84812 Score: 90
Period size: 20 Copynumber: 4.0 Consensus size: 20
84722 TTGATCCTCT
* * *
84732 TTGGAAAAGTATAGATGCTC
1 TTGGGAAAGCATAGATACTC
*
84752 TTGGGAAAGCATAGATGCTC
1 TTGGGAAAGCATAGATACTC
* *
84772 TTTGGAAAGCATGGATACTC
1 TTGGGAAAGCATAGATACTC
* *
84792 TTGGGAAAGTATCGATACTC
1 TTGGGAAAGCATAGATACTC
84812 T
1 T
84813 CTGCTAGAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (20 bp):
TTGGGAAAGCATAGATACTC
Found at i:85790 original size:3 final size:3
Alignment explanation
Indices: 85782--85822 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
85772 AGAGTGAAAC
85782 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
85823 ATTAAGAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:86423 original size:10 final size:10
Alignment explanation
Indices: 86404--86486 Score: 76
Period size: 10 Copynumber: 7.6 Consensus size: 10
86394 CATTTAAATG
86404 ATAAACGAAC
1 ATAAACGAAC
*
86414 ATAAATGAAC
1 ATAAACGAAC
86424 ATAAACGAAC
1 ATAAACGAAC
86434 GGATGTAAACGAAC
1 --A--TAAACGAAC
86448 ATAAACGAACAC
1 ATAAACG-A-AC
*
86460 AATAAACTAAC
1 -ATAAACGAAC
86471 ATAAACGAAC
1 ATAAACGAAC
*
86481 ACAAAC
1 ATAAAC
86487 AAATGACCGT
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
10 38 0.62
11 3 0.05
12 5 0.08
13 6 0.10
14 9 0.15
ACGTcount: A:0.58, C:0.19, G:0.11, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:86513 original size:23 final size:23
Alignment explanation
Indices: 86414--86523 Score: 114
Period size: 24 Copynumber: 4.7 Consensus size: 23
86404 ATAAACGAAC
**
86414 ATAAATGAACATAAACGAACGGA
1 ATAAATGAACATAAACGAACACA
* *
86437 TGTAAACGAACATAAACGAACACA
1 -ATAAATGAACATAAACGAACACA
86461 ATAAACT-AACATAAACGAACACAA
1 ATAAA-TGAACATAAACGAACAC-A
* * *
86485 ACAAATGACCGTAAACGAACACA
1 ATAAATGAACATAAACGAACACA
*
86508 ATAAATGGACATAAAC
1 ATAAATGAACATAAAC
86524 AAACGTATTA
Statistics
Matches: 70, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
23 33 0.47
24 37 0.53
ACGTcount: A:0.56, C:0.19, G:0.12, T:0.13
Consensus pattern (23 bp):
ATAAATGAACATAAACGAACACA
Found at i:88338 original size:16 final size:16
Alignment explanation
Indices: 88314--88355 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
88304 AACAAAACAG
* *
88314 AATAGAAATAAAATAT
1 AATAAAAATAAAATAA
*
88330 CATAAAAATAAAATAA
1 AATAAAAATAAAATAA
88346 AATAAAAATA
1 AATAAAAATA
88356 TTACTATCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (16 bp):
AATAAAAATAAAATAA
Found at i:96341 original size:48 final size:49
Alignment explanation
Indices: 96274--96369 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 49
96264 ATATACCAAT
* **
96274 TTTTTTACTAAACCTACCAAAAGATTGGTGTAATGATTATGTTTTTTCA
1 TTTTTTACTAAAACTACCAAAAGATTAATGTAATGATTATGTTTTTTCA
*
96323 TTTTTTATTAAAAC-ACCAAAAGATTAATGTAATGATTATGTTTTTTC
1 TTTTTTACTAAAACTACCAAAAGATTAATGTAATGATTATGTTTTTTC
96370 TTTATATGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 31 0.72
49 12 0.28
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (49 bp):
TTTTTTACTAAAACTACCAAAAGATTAATGTAATGATTATGTTTTTTCA
Found at i:98976 original size:73 final size:73
Alignment explanation
Indices: 98889--99034 Score: 292
Period size: 73 Copynumber: 2.0 Consensus size: 73
98879 TCATAATTAA
98889 ATTACACTTTGATTATTTGAAAATAAAAAAGTCAAAATATAAAGGAAACAGAAAAAGATGTGTAA
1 ATTACACTTTGATTATTTGAAAATAAAAAAGTCAAAATATAAAGGAAACAGAAAAAGATGTGTAA
98954 TGTTTTAC
66 TGTTTTAC
98962 ATTACACTTTGATTATTTGAAAATAAAAAAGTCAAAATATAAAGGAAACAGAAAAAGATGTGTAA
1 ATTACACTTTGATTATTTGAAAATAAAAAAGTCAAAATATAAAGGAAACAGAAAAAGATGTGTAA
99027 TGTTTTAC
66 TGTTTTAC
99035 CTGCATCGTA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.30
Consensus pattern (73 bp):
ATTACACTTTGATTATTTGAAAATAAAAAAGTCAAAATATAAAGGAAACAGAAAAAGATGTGTAA
TGTTTTAC
Found at i:99725 original size:5 final size:5
Alignment explanation
Indices: 99707--99773 Score: 50
Period size: 5 Copynumber: 13.8 Consensus size: 5
99697 TTCCTGCAAC
* * * * *
99707 AAAAT -AAA- AAAAT AGAAT AAAAT ACATT TATAT AAAAT AAAAT AAAAGT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T
*
99756 -ATAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
99774 AATCAGACCC
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
4 7 0.15
5 38 0.83
6 1 0.02
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:99747 original size:20 final size:20
Alignment explanation
Indices: 99735--99773 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
99725 AAAATACATT
99735 TATATAAAATAAAATAAAAG
1 TATATAAAATAAAATAAAAG
99755 TATATAAAATAAAATAAAA
1 TATATAAAATAAAATAAAA
99774 AATCAGACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
TATATAAAATAAAATAAAAG
Found at i:102349 original size:3 final size:3
Alignment explanation
Indices: 102341--102384 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
102331 TATAAATTAA
102341 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
102385 ATGAAACAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:103320 original size:24 final size:24
Alignment explanation
Indices: 103266--103353 Score: 70
Period size: 24 Copynumber: 3.7 Consensus size: 24
103256 GAAATTGGGC
* *
103266 TGAAAATAAACGAACGAACATATA
1 TGAACATAAACGAACGAACATAAA
* * *
103290 CGGACATAAACGAACGAACTTAAA
1 TGAACATAAACGAACGAACATAAA
* * * *
103314 TGAACATACACGGAC-ATAAATGAA
1 TGAACATAAACGAACGA-ACATAAA
*
103338 CGAACATAAACGAACG
1 TGAACATAAACGAACG
103354 GATTATCGAA
Statistics
Matches: 47, Mismatches: 15, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
23 1 0.02
24 46 0.98
ACGTcount: A:0.52, C:0.18, G:0.16, T:0.14
Consensus pattern (24 bp):
TGAACATAAACGAACGAACATAAA
Found at i:103327 original size:34 final size:34
Alignment explanation
Indices: 103278--103352 Score: 114
Period size: 34 Copynumber: 2.2 Consensus size: 34
103268 AAAATAAACG
* *
103278 AACGAACATATACGGACATAAACGAACGAACTTA
1 AACGAACATACACGGACATAAACGAACGAACATA
* *
103312 AATGAACATACACGGACATAAATGAACGAACATA
1 AACGAACATACACGGACATAAACGAACGAACATA
103346 AACGAAC
1 AACGAAC
103353 GGATTATCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.52, C:0.20, G:0.15, T:0.13
Consensus pattern (34 bp):
AACGAACATACACGGACATAAACGAACGAACATA
Found at i:110714 original size:21 final size:21
Alignment explanation
Indices: 110690--110731 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
110680 AGTTTATTTT
110690 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
110711 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
110732 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:110780 original size:33 final size:32
Alignment explanation
Indices: 110726--110824 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 32
110716 TTTGTTTCAA
110726 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
110758 TTATCGAACTTGAAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTG-AAGTTTTTAAGTATTTGAAT
* * *
110791 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
110824 T
1 T
110825 ATGTTGAGTT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
32 12 0.19
33 49 0.79
34 1 0.02
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (32 bp):
TTATCGAACTTGAAGTTTTTAAGTATTTGAAT
Found at i:111544 original size:21 final size:21
Alignment explanation
Indices: 111518--111557 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
111508 TCGACCGTTG
111518 AATGGGGGAATCGGTTCCCCC
1 AATGGGGGAATCGGTTCCCCC
111539 AATGGGGGAATCGGTTCCC
1 AATGGGGGAATCGGTTCCC
111558 TCCGAGCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.35, T:0.20
Consensus pattern (21 bp):
AATGGGGGAATCGGTTCCCCC
Found at i:111990 original size:21 final size:18
Alignment explanation
Indices: 111945--111978 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
111935 GGTTTTTTAT
111945 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
111962 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
111979 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:112098 original size:15 final size:17
Alignment explanation
Indices: 112072--112103 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
112062 TTCTATGGGA
112072 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
112088 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
112104 CGGATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:112101 original size:21 final size:21
Alignment explanation
Indices: 112077--112129 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
112067 TGGGAAAAAA
112077 CCGGATCGGATAAAAACCGAT
1 CCGGATCGGATAAAAACCGAT
112098 CCGGATCGGATAAAAACCGAT
1 CCGGATCGGATAAAAACCGAT
112119 CCGGATCGGAT
1 CCGGATCGGAT
112130 TGAAATCCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.25, G:0.26, T:0.15
Consensus pattern (21 bp):
CCGGATCGGATAAAAACCGAT
Found at i:115357 original size:117 final size:118
Alignment explanation
Indices: 115129--115416 Score: 470
Period size: 117 Copynumber: 2.4 Consensus size: 118
115119 GAATATGATG
115129 CTAAAGCTCAAACAACTTTTACTTAAAACCTTGACATGTTACATTCTAAGTACATGTCTATAACC
1 CTAAAGCTCAAACAACTTTTACTTAAAACCTTGACATGTTACATTCTAAGTACATGTCTATAACC
*
115194 TAACAATATGGCATACATCATAAAGACCTAAAATTATGTAACAC-AGAATATT
66 TAACAATATGGCATACATCACAAAGACCTAAAATTATGTAACACAAGAATATT
* * *
115246 TTAAAGCTCAAACAACTTTTACTTAAAACCTTGACATGTTACATTCTAAGTAGATGTCTATAGCC
1 CTAAAGCTCAAACAACTTTTACTTAAAACCTTGACATGTTACATTCTAAGTACATGTCTATAACC
*
115311 TAACATTATATGGCATACATCACAAAGACCTAAAATTATGTAACAGAGAGAATATT
66 TAACA--ATATGGCATACATCACAAAGACCTAAAATTATGTAACACA-AGAATATT
* *
115367 CTAAAGCTCAAACAACTTTTTCTTAAAACCTTGACATGTTTACATCCTAA
1 CTAAAGCTCAAACAACTTTTACTTAAAACCTTGACATG-TTACATTCTAA
115417 CATACGGCAT
Statistics
Matches: 158, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
117 67 0.42
119 37 0.23
121 44 0.28
122 10 0.06
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.31
Consensus pattern (118 bp):
CTAAAGCTCAAACAACTTTTACTTAAAACCTTGACATGTTACATTCTAAGTACATGTCTATAACC
TAACAATATGGCATACATCACAAAGACCTAAAATTATGTAACACAAGAATATT
Found at i:118617 original size:39 final size:40
Alignment explanation
Indices: 118534--118619 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
118524 AGTTTTTTTT
*
118534 ATTTTCTAATAAGGTAATTTTAATAGTATTTCTTAAAATA
1 ATTTTCTAATAAGGTAATTTTAATAATATTTCTTAAAATA
*
118574 ATTTTCTAATAAGGTACTTTTAATAATA-TTCTT-AAATAA
1 ATTTTCTAATAAGGTAATTTTAATAATATTTCTTAAAAT-A
118613 ATTTTCT
1 ATTTTCT
118620 GGATAATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
38 4 0.09
39 13 0.30
40 26 0.60
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (40 bp):
ATTTTCTAATAAGGTAATTTTAATAATATTTCTTAAAATA
Done.