Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001885.1 Hibiscus syriacus cultivar Beakdansim tig00003826_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: 84887
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Found at i:1117 original size:25 final size:25
Alignment explanation
Indices: 1056--1120 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
1046 TTTAAAAAAT
*
1056 TAAATATATTTTAAATTAAATAATAA
1 TAAATAT-TTTTAATTTAAATAATAA
*
1082 TAAATCA-TTTTAATTTAAATAATAT
1 TAAAT-ATTTTTAATTTAAATAATAA
*
1107 TTAATATTTTTAAT
1 TAAATATTTTTAAT
1121 CATTTTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 1 0.03
25 27 0.79
26 5 0.15
27 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
TAAATATTTTTAATTTAAATAATAA
Found at i:1169 original size:19 final size:18
Alignment explanation
Indices: 1147--1186 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
1137 TATTTAAAAC
1147 AAAATTAATCATTTAATTAAA
1 AAAATTAA--ATTTAATT-AA
1168 AAAATTAAATTTAATTAA
1 AAAATTAAATTTAATTAA
1186 A
1 A
1187 GTTTATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.16
19 8 0.42
21 8 0.42
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTAAATTTAATTAA
Found at i:3159 original size:178 final size:180
Alignment explanation
Indices: 2758--3657 Score: 1720
Period size: 180 Copynumber: 5.0 Consensus size: 180
2748 GAAAGAAATT
2758 ACTACCCTAATGGATAGTAAAGATATAATTATTAGGCATATTTTTTAGAGCTGCTAATTGGAAAT
1 ACTACCCTAATGGATAGTAAAGATATAATTATTAGGCATA-TTTTTAGAGCTGCTAATTGGAAAT
2823 CGGATAAAATTAGCTAAAGAAGGAATAGGTTGATTAATAGG-TGTG-GTTTAGGTTGTTAAGTTT
65 CGGAT-AAATTAGCTAAAGAAGGAATAGGTTGATTAATAGGTTGTGTGTTTAGGTTGTTAAGTTT
2886 CTGAGTTGGTTGTATTAGTGTAGTTAGTTTGGTGTTTAAGTGTTATGTTGTA
129 CTGAGTTGGTTGTATTAGTGTAGTTAGTTTGGTGTTTAAGTGTTATGTTGTA
2938 ACTACCCTAATGGATAGTAAAGATATAATTATTAGGCATATTTTTAGAGCTGCTAATTGGAAATC
1 ACTACCCTAATGGATAGTAAAGATATAATTATTAGGCATATTTTTAGAGCTGCTAATTGGAAATC
3003 GGATAAATTAGCTAAAGAAGGAATAGGTTGATTAATAGGTTGTGTGTTTAGGTTGTTAAGTTTCT
66 GGATAAATTAGCTAAAGAAGGAATAGGTTGATTAATAGGTTGTGTGTTTAGGTTGTTAAGTTTCT
3068 GAGTTGGTTGTATTAGTGTAGTTAGTTTGGTGTTTAAGTGTTATGTTGTA
131 GAGTTGGTTGTATTAGTGTAGTTAGTTTGGTGTTTAAGTGTTATGTTGTA
3118 ACTACCCTAATGGATAGTAAAGATATAA-T-TTAGGCATATTTTTAGAGCTGCTAATTGGAAATC
1 ACTACCCTAATGGATAGTAAAGATATAATTATTAGGCATATTTTTAGAGCTGCTAATTGGAAATC
*
3181 GGATAAATTAGCTAAAGAAGGAATATGTTGATTAATAGGTTGTGTGTTTAGGTTGTTAAGTTTCT
66 GGATAAATTAGCTAAAGAAGGAATAGGTTGATTAATAGGTTGTGTGTTTAGGTTGTTAAGTTTCT
3246 GAGTTGGTTGTATTAGTGTAGTTAGTTTGGTGTTTAAGTGTTATGTTGTA
131 GAGTTGGTTGTATTAGTGTAGTTAGTTTGGTGTTTAAGTGTTATGTTGTA
3296 ACTACCCTAATGGATAGTAAAGATATAATTATTAGGCATATTTTTAGAGCTGCTAATTGGAAATC
1 ACTACCCTAATGGATAGTAAAGATATAATTATTAGGCATATTTTTAGAGCTGCTAATTGGAAATC
3361 GGATAAATTAGCTAAAGAAGGAATAGG-TGATTAATAGGTTGTGTGTTTAGGTTGTTAAGTTTCT
66 GGATAAATTAGCTAAAGAAGGAATAGGTTGATTAATAGGTTGTGTGTTTAGGTTGTTAAGTTTCT
3425 GAGTTGGTTGTATTAGTGTAGTTAGTTTGGTGTTTAAGTGTTATGTTGTA
131 GAGTTGGTTGTATTAGTGTAGTTAGTTTGGTGTTTAAGTGTTATGTTGTA
3475 ACTACCCTAATGGATAGTAAAGATATAATTATTAGGCATATTTTTAGAGCTGCTAATTGGAAATC
1 ACTACCCTAATGGATAGTAAAGATATAATTATTAGGCATATTTTTAGAGCTGCTAATTGGAAATC
3540 GGATAAATTAGCTAAAGAAGGAATAGGTTGATTAATAGGTTGTGTGTTTAGGTTGTTAAGTTTCT
66 GGATAAATTAGCTAAAGAAGGAATAGGTTGATTAATAGGTTGTGTGTTTAGGTTGTTAAGTTTCT
* *
3605 GAGTTGGTTGTATCAGTGTAGTTAGTTTGGTGTTTAAGTGCTATGTTGTA
131 GAGTTGGTTGTATTAGTGTAGTTAGTTTGGTGTTTAAGTGTTATGTTGTA
3655 ACT
1 ACT
3658 GAAGTTTGTT
Statistics
Matches: 711, Mismatches: 4, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
178 211 0.30
179 214 0.30
180 286 0.40
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.40
Consensus pattern (180 bp):
ACTACCCTAATGGATAGTAAAGATATAATTATTAGGCATATTTTTAGAGCTGCTAATTGGAAATC
GGATAAATTAGCTAAAGAAGGAATAGGTTGATTAATAGGTTGTGTGTTTAGGTTGTTAAGTTTCT
GAGTTGGTTGTATTAGTGTAGTTAGTTTGGTGTTTAAGTGTTATGTTGTA
Found at i:3792 original size:67 final size:67
Alignment explanation
Indices: 3684--3818 Score: 216
Period size: 67 Copynumber: 2.0 Consensus size: 67
3674 TGACTTTGTA
* * ** *
3684 TTATTCTTATATTAATAAATTCTTAAGCACTCTTTTCCTCCTTTCAATGTCTTTCATGTTAATGT
1 TTATTCTTACATTAATAAATTCTTAAGCACTCTTTTCCTCCTTCCAACATCCTTCATGTTAATGT
3749 TG
66 TG
*
3751 TTATTCTTACATTAATAAATTCTTAGGCACTCTTTTCCTCCTTCCAACATCCTTCATGTTAATGT
1 TTATTCTTACATTAATAAATTCTTAAGCACTCTTTTCCTCCTTCCAACATCCTTCATGTTAATGT
3816 TG
66 TG
3818 T
1 T
3819 AACATGGAGG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.24, C:0.21, G:0.07, T:0.48
Consensus pattern (67 bp):
TTATTCTTACATTAATAAATTCTTAAGCACTCTTTTCCTCCTTCCAACATCCTTCATGTTAATGT
TG
Found at i:11281 original size:32 final size:32
Alignment explanation
Indices: 11245--11313 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
11235 TGTCACACCA
11245 AATTCCCCCTTCACTCTCCACCCCCTCAATCC
1 AATTCCCCCTTCACTCTCCACCCCCTCAATCC
**** *
11277 AATTCTTTTTTCACTCTCCACCCCCTCAATCT
1 AATTCCCCCTTCACTCTCCACCCCCTCAATCC
11309 AATTC
1 AATTC
11314 TTTTTGCGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.20, C:0.46, G:0.00, T:0.33
Consensus pattern (32 bp):
AATTCCCCCTTCACTCTCCACCCCCTCAATCC
Found at i:11314 original size:32 final size:32
Alignment explanation
Indices: 11254--11318 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
11244 AAATTCCCCC
11254 TTCACTCTCCACCCCCTCAATCCAATTCTTTT
1 TTCACTCTCCACCCCCTCAATCCAATTCTTTT
*
11286 TTCACTCTCCACCCCCTCAATCTAATTCTTTT
1 TTCACTCTCCACCCCCTCAATCCAATTCTTTT
11318 T
1 T
11319 GCGACGCCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.18, C:0.42, G:0.00, T:0.40
Consensus pattern (32 bp):
TTCACTCTCCACCCCCTCAATCCAATTCTTTT
Found at i:20305 original size:29 final size:29
Alignment explanation
Indices: 20260--20317 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
20250 GTGTTAGTCG
*
20260 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
20289 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
20318 AAGAGATTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:20379 original size:14 final size:14
Alignment explanation
Indices: 20360--20406 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
20350 CGCTGGGCAT
*
20360 CCGAGGACATCCGA
1 CCGAGGCCATCCGA
*
20374 CCGAGGCCATCTGA
1 CCGAGGCCATCCGA
20388 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
20402 ACGAG
1 CCGAG
20407 CTATGCGAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.26, C:0.36, G:0.30, T:0.09
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:20425 original size:33 final size:33
Alignment explanation
Indices: 20388--20459 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
20378 GGCCATCTGA
* * *
20388 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGCCAACCGAACGAGCTATGCGAGAGAAT
** **
20421 CCGAGGGTAACCGGGCGAGCTATGCGAGAGAAT
1 CCGAGGCCAACCGAACGAGCTATGCGAGAGAAT
20454 CCGAGG
1 CCGAGG
20460 GAAGCCGAGC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.25, C:0.26, G:0.38, T:0.11
Consensus pattern (33 bp):
CCGAGGCCAACCGAACGAGCTATGCGAGAGAAT
Found at i:20472 original size:33 final size:33
Alignment explanation
Indices: 20398--20472 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 33
20388 CCGAGGCCAT
* * *
20398 CCGAACGAGCTATGCGAGGGCATCCGAGGGTAA
1 CCGAGCGAGCTATGCGAGAGAATCCGAGGGTAA
*
20431 CCGGGCGAGCTATGCGAGAGAATCCGAGGG-AA
1 CCGAGCGAGCTATGCGAGAGAATCCGAGGGTAA
20463 GCCGAGCGAG
1 -CCGAGCGAG
20473 GGTAGGTCGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
32 2 0.06
33 34 0.94
ACGTcount: A:0.27, C:0.24, G:0.40, T:0.09
Consensus pattern (33 bp):
CCGAGCGAGCTATGCGAGAGAATCCGAGGGTAA
Found at i:20509 original size:29 final size:29
Alignment explanation
Indices: 20476--20589 Score: 192
Period size: 29 Copynumber: 3.9 Consensus size: 29
20466 GAGCGAGGGT
*
20476 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
*
20505 AGGTCGTCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
*
20534 AGGTCGTCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
*
20563 AGGTCGCCCAGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
20590 TGTGTTGGGA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.21, C:0.29, G:0.37, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:25564 original size:55 final size:55
Alignment explanation
Indices: 25472--25579 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 55
25462 TAAGCTAGTT
* *
25472 TTCTTTTGACTGCTAGCTAGTAGGTATTAATTCTATTGAGTTTCTAATTAAACCA
1 TTCTTTTGACTGCTAGCTAGTAAGTATTAATTCTATTGAATTTCTAATTAAACCA
* *
25527 TTCTTTTGACTGCTAGCTAGTAAGTATTACTTTTATTGAATTTCTAATTAAAC
1 TTCTTTTGACTGCTAGCTAGTAAGTATTAATTCTATTGAATTTCTAATTAAAC
25580 TATACGATCG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (55 bp):
TTCTTTTGACTGCTAGCTAGTAAGTATTAATTCTATTGAATTTCTAATTAAACCA
Found at i:38480 original size:105 final size:105
Alignment explanation
Indices: 38370--39272 Score: 1572
Period size: 105 Copynumber: 8.6 Consensus size: 105
38360 TTTGTCGGAT
* * * *
38370 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTCGATTCACCTCCTTCTGGGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* *
38435 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
38475 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
*
38540 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* * *
38580 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTTACCTCCTTTTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* * *
38645 GGAACATACTCTTCTCATTACGAACCTTCTCCTTTAAGAT
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
38685 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
*
38750 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
38790 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
38855 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
38895 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
38960 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
39000 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCATTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* *
39065 GGAACATGCTCTTCTCATTACGAATCTTCTCTTTTAGGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
39105 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* *
39170 GGAACAGGCTCTTCTCATTACGAACCTTCTCATTTAGGAC
66 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* * *
39210 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCATCTCCTTCTGTGGTGGATTTGA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGA
39273 TTGTTGTTGA
Statistics
Matches: 766, Mismatches: 32, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
105 766 1.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.37
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
Found at i:40205 original size:12 final size:11
Alignment explanation
Indices: 40202--40258 Score: 75
Period size: 11 Copynumber: 5.4 Consensus size: 11
40192 TTTCTTTTCA
*
40202 TTTTTTCTTTT
1 TTTTTTCATTT
40213 TTTTTTCA-TT
1 TTTTTTCATTT
40223 TTTTTTCATTTT
1 TTTTTTCA-TTT
40235 TTTTTTCA--T
1 TTTTTTCATTT
40244 TTTTTTCATTT
1 TTTTTTCATTT
40255 TTTT
1 TTTT
40259 ATTTTTTATT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
9 9 0.22
10 10 0.24
11 12 0.29
12 10 0.24
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:40207 original size:8 final size:8
Alignment explanation
Indices: 40196--40298 Score: 77
Period size: 8 Copynumber: 14.0 Consensus size: 8
40186 TTCTTTTTTC
40196 TTTTCATT
1 TTTTCATT
40204 TTTTC--T
1 TTTTCATT
40210 TTTT---T
1 TTTTCATT
40215 TTTTCATTTT
1 TTTTCA--TT
40225 TTTTCA-T
1 TTTTCATT
40232 TTTT--T-
1 TTTTCATT
40237 TTTTCATTT
1 TTTTCA-TT
40246 TTTTCATT
1 TTTTCATT
*
40254 TTTTTATT
1 TTTTCATT
40262 TTTT-ATT
1 TTTTCATT
40269 TTTT-A-T
1 TTTTCATT
*
40275 TTTTCACT
1 TTTTCATT
40283 TTTTCATT
1 TTTTCATT
40291 TTTTCATT
1 TTTTCATT
40299 CATTCTTTTT
Statistics
Matches: 81, Mismatches: 2, Indels: 24
0.76 0.02 0.22
Matches are distributed among these distances:
5 9 0.11
6 10 0.12
7 14 0.17
8 35 0.43
9 6 0.07
10 7 0.09
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTCATT
Found at i:40227 original size:22 final size:22
Alignment explanation
Indices: 40183--40313 Score: 94
Period size: 22 Copynumber: 5.8 Consensus size: 22
40173 CGAACCCTCA
40183 TTTTTCTTTTTTCTTTTCA---T
1 TTTTTCTTTTTT-TTTTCATTTT
40203 TTTTTCTTTTTTTTTTCA-TTT
1 TTTTTCTTTTTTTTTTCATTTT
40224 TTTTTCATTTTTTTTTTCATTTT
1 TTTTTC-TTTTTTTTTTCATTTT
*
40247 TTTCATT-TTTTTATTTTTTATTTT
1 TTT--TTCTTTTT-TTTTTCATTTT
***
40271 TTATTT-TTCACTTTTTCATTTT
1 TT-TTTCTTTTTTTTTTCATTTT
*
40293 TTCATTCATTCTTTTTTTTCA
1 TT-TTTC-TT-TTTTTTTTCA
40314 AGCATAGTAC
Statistics
Matches: 90, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
19 6 0.07
20 12 0.13
21 7 0.08
22 26 0.29
23 15 0.17
24 14 0.16
25 10 0.11
ACGTcount: A:0.10, C:0.11, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTCTTTTTTTTTTCATTTT
Found at i:40228 original size:29 final size:28
Alignment explanation
Indices: 40196--40295 Score: 114
Period size: 29 Copynumber: 3.5 Consensus size: 28
40186 TTCTTTTTTC
40196 TTTTCATTTTTTCTTTTTTTTTTCATTTT
1 TTTTCATTTTTTCTTTTTTTTTTCA-TTT
*
40225 TTTTCATTTTTTTTTTCATTTTTTTCATTT
1 TTTTCATTTTTTCTTT--TTTTTTTCATTT
* *
40255 TTTT-ATTTTTTATTTTTTATTTTTCA-CT
1 TTTTCATTTTTT-CTTTTT-TTTTTCATTT
40283 TTTTCATTTTTTC
1 TTTTCATTTTTTC
40296 ATTCATTCTT
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
28 7 0.11
29 36 0.57
30 11 0.17
31 9 0.14
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (28 bp):
TTTTCATTTTTTCTTTTTTTTTTCATTT
Found at i:40270 original size:12 final size:11
Alignment explanation
Indices: 40202--40277 Score: 66
Period size: 11 Copynumber: 6.5 Consensus size: 11
40192 TTTCTTTTCA
*
40202 TTTTTTCTTTT
1 TTTTTTATTTT
40213 TTTTTTCA-TTT
1 TTTTTT-ATTTT
*
40224 TTTTTCATTTT
1 TTTTTTATTTT
40235 TTTTTTCATTTT
1 TTTTTT-ATTTT
40247 TTTCATTT-TTTT
1 TTT--TTTATTTT
40259 ATTTTTTATTTT
1 -TTTTTTATTTT
40271 TTATTTT
1 TT-TTTT
40278 TCACTTTTTC
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
10 1 0.02
11 27 0.50
12 20 0.37
13 3 0.06
14 3 0.06
ACGTcount: A:0.09, C:0.07, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:40286 original size:9 final size:8
Alignment explanation
Indices: 40235--40298 Score: 80
Period size: 8 Copynumber: 8.2 Consensus size: 8
40225 TTTTCATTTT
40235 TTTTTTCA
1 TTTTTTCA
40243 TTTTTTTCA
1 -TTTTTTCA
*
40252 TTTTTTTA
1 TTTTTTCA
40260 TTTTTT-A
1 TTTTTTCA
40267 TTTTTT-A
1 TTTTTTCA
40274 -TTTTTCA
1 TTTTTTCA
*
40281 CTTTTTCA
1 TTTTTTCA
40289 TTTTTTCA
1 TTTTTTCA
40297 TT
1 TT
40299 CATTCTTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
6 5 0.10
7 9 0.18
8 29 0.57
9 8 0.16
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTCA
Found at i:40308 original size:37 final size:37
Alignment explanation
Indices: 40231--40311 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 37
40221 TTTTTTTTCA
* * **
40231 TTTTTTTTTTCATTTTTTTCATTTTTTTATTTTTTAT
1 TTTTTTTTTTCATCTTTTTCATTTTTTCATTCATTAT
*
40268 TTTTTATTTTTCA-CTTTTTCATTTTTTCATTCATTCT
1 TTTTT-TTTTTCATCTTTTTCATTTTTTCATTCATTAT
40305 TTTTTTT
1 TTTTTTT
40312 CAAGCATAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
36 2 0.05
37 29 0.76
38 7 0.18
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.79
Consensus pattern (37 bp):
TTTTTTTTTTCATCTTTTTCATTTTTTCATTCATTAT
Found at i:61233 original size:26 final size:28
Alignment explanation
Indices: 61199--61259 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 28
61189 AAGAGGTATG
* *
61199 AAATT-AATTTTTTTAA-AAGAATAT-A
1 AAATTAAATTTTATTAATAAAAATATAA
61224 AAATTAAA--TTATTAATAAAAATATAA
1 AAATTAAATTTTATTAATAAAAATATAA
61250 AAATTAAATT
1 AAATTAAATT
61260 ATATGAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
24 6 0.21
25 12 0.41
26 11 0.38
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (28 bp):
AAATTAAATTTTATTAATAAAAATATAA
Found at i:76703 original size:32 final size:32
Alignment explanation
Indices: 76625--76708 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 32
76615 AGTGTCCTTC
*
76625 TGTTCCTTAGAACATAGGT-ATATTGTCCATA
1 TGTTCCCTAGAACATAGGTAATATTGTCCATA
* * *
76656 T-ATCCCAAAAGACATAGGTAAT-TATGTCCATA
1 TGTTCCCTAGA-ACATAGGTAATAT-TGTCCATA
*
76688 TGTTCCGTAGAACATAGGTAA
1 TGTTCCCTAGAACATAGGTAA
76709 ACCCTTGACT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
30 5 0.12
31 10 0.24
32 21 0.51
33 5 0.12
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (32 bp):
TGTTCCCTAGAACATAGGTAATATTGTCCATA
Found at i:77633 original size:64 final size:63
Alignment explanation
Indices: 77546--77707 Score: 157
Period size: 64 Copynumber: 2.5 Consensus size: 63
77536 CCCTTAACAT
* * * *
77546 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTT-TAATCTTAAAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCAATGTTTCCAATCTTAAA-GG
* * * ** * *
77610 GTGCATCGATGCACTCCTTATGCATAGATGCACTAATTGCATTCAATGTTTCCATTTTTAAAGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACAAATCACATTCAATGTTTCCAATCTTAAAGG
*
77674 GTGCATCGATGCACTTC-ATGTACATCGATACACA
1 GTGCATCGATGCACTCCTATG--CATCGATACACA
77708 CTGAACAATT
Statistics
Matches: 79, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
62 3 0.04
63 2 0.03
64 67 0.85
65 7 0.09
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCAATGTTTCCAATCTTAAAGG
Found at i:81408 original size:24 final size:25
Alignment explanation
Indices: 81371--81425 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
81361 TATCACATGG
81371 TTACA-ATTCATATAA-CACTTATA
1 TTACATATTCATATAATCACTTATA
* *
81394 TTACATATTCTTATAATTACTTATA
1 TTACATATTCATATAATCACTTATA
81419 TTA-ATAT
1 TTACATAT
81426 CACATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.18
24 13 0.46
25 10 0.36
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (25 bp):
TTACATATTCATATAATCACTTATA
Found at i:81433 original size:25 final size:24
Alignment explanation
Indices: 81371--81433 Score: 58
Period size: 25 Copynumber: 2.6 Consensus size: 24
81361 TATCACATGG
*
81371 TTACA-ATTCATATAACACTTATA
1 TTACATATACATATAACACTTATA
* * *
81394 TTACATATTCTTATAATTACTTATA
1 TTACATATACATATAA-CACTTATA
81419 TTA-ATATCACATATA
1 TTACATAT-ACATATA
81434 TAACAAGTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 5 0.15
24 13 0.39
25 15 0.45
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.44
Consensus pattern (24 bp):
TTACATATACATATAACACTTATA
Done.