Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007094.1 Hibiscus syriacus cultivar Beakdansim tig00018530_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: 60917
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3383 original size:6 final size:7
Alignment explanation
Indices: 3366--3391 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3356 ATGCAATGAA
3366 AAAAATT
1 AAAAATT
3373 AAAAATT
1 AAAAATT
3380 AAAAATT
1 AAAAATT
3387 AAAAA
1 AAAAA
3392 GTTTAAATGT
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAAATT
Found at i:5162 original size:42 final size:43
Alignment explanation
Indices: 5098--5178 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 43
5088 GAATTTGAAC
5098 ATTTTTAGCCTTAGCAACTTTTATTTACTTACTCTTGCAATTA
1 ATTTTTAGCCTTAGCAACTTTTATTTACTTACTCTTGCAATTA
* * **
5141 ATTTTT-GCCTTAGCGATTTTTATTTGTTTACTCTTGCA
1 ATTTTTAGCCTTAGCAACTTTTATTTACTTACTCTTGCA
5179 TATTTTTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 28 0.82
43 6 0.18
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (43 bp):
ATTTTTAGCCTTAGCAACTTTTATTTACTTACTCTTGCAATTA
Found at i:5191 original size:42 final size:41
Alignment explanation
Indices: 5098--5191 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 41
5088 GAATTTGAAC
5098 ATTTTTAGCCTTAGCAACTTTTATTTACTTACTCTTGCAATT
1 ATTTTT-GCCTTAGCAACTTTTATTTACTTACTCTTGCAATT
* * **
5140 AATTTTTGCCTTAGCGATTTTTATTTGTTTACTCTTGCATATT
1 -ATTTTTGCCTTAGCAACTTTTATTTACTTACTCTTGCA-ATT
5183 -TTTCTTGCC
1 ATTT-TTGCC
5192 ACGAAAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
41 3 0.07
42 33 0.73
43 9 0.20
ACGTcount: A:0.19, C:0.18, G:0.10, T:0.53
Consensus pattern (41 bp):
ATTTTTGCCTTAGCAACTTTTATTTACTTACTCTTGCAATT
Found at i:23976 original size:81 final size:81
Alignment explanation
Indices: 23838--24129 Score: 399
Period size: 81 Copynumber: 3.6 Consensus size: 81
23828 CAGTTTTAAC
* * * * * * *
23838 CGTTCATCTAACTGACCTAATTGGCACCTTTCTACCAATTGTACAATTAGGCCATTATTCCTTTA
1 CGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCACAGTTAGACTATTATTCCTTTG
23903 CTCAACGGTATTAAAT
66 CTCAACGGTATTAAAT
* * *
23919 CATTCATCTAACTGGCATAATTGGTACCTTTCTACCAATTGTACAGTTAGACTATTATTCCTTTG
1 CGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCACAGTTAGACTATTATTCCTTTG
*
23984 CTCAACAGTATTAAAT
66 CTCAACGGTATTAAAT
* * * * *
24000 TGTTCATCTAACTGCCATAATTGGTACCTTTTTACCAATTGCATAGTTAGGA-TATTATTCCTTT
1 CGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCACAGTTA-GACTATTATTCCTTT
*
24064 GCTCAACGGTATTAAAC
65 GCTCAACGGTATTAAAT
*
24081 CGTTCATCTTACTGGCATAATTGGCACCTTT-TACCAATTGCACAGTTAG
1 CGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCACAGTTAG
24130 GCCTTAAAGG
Statistics
Matches: 188, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
79 1 0.01
80 16 0.09
81 169 0.90
82 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (81 bp):
CGTTCATCTAACTGGCATAATTGGCACCTTTCTACCAATTGCACAGTTAGACTATTATTCCTTTG
CTCAACGGTATTAAAT
Found at i:24212 original size:68 final size:67
Alignment explanation
Indices: 24123--24334 Score: 325
Period size: 68 Copynumber: 3.1 Consensus size: 67
24113 ACCAATTGCA
* * *
24123 CAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAATTAGCTTATATGATACCTTTCTGTCATAA
1 CAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACT-GCTTATATGAAACCTTTCTGTCATAA
24188 GCG
65 GCG
* *
24191 TAGTTAGGCCTCAAAGTCACTTAGCCTTTCATCTAACTGACTTATATGAAACCTTTCTGTCATAA
1 CAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTG-CTTATATGAAACCTTTCTGTCATAA
24256 GCG
65 GCG
*
24259 CAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCTTATATGACACCTTTCTGTCATAA
1 CAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACT-GCTTATATGAAACCTTTCTGTCATAA
*
24324 GTG
65 GCG
*
24327 CATTTAGG
1 CAGTTAGG
24335 TCTCTTAGTC
Statistics
Matches: 132, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
67 1 0.01
68 130 0.98
69 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (67 bp):
CAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGCTTATATGAAACCTTTCTGTCATAAG
CG
Found at i:24959 original size:34 final size:34
Alignment explanation
Indices: 24916--24994 Score: 158
Period size: 34 Copynumber: 2.3 Consensus size: 34
24906 CCCCCGTCGG
24916 GTATCGATACCAAAAATAGGTTCGATGTTGCCTA
1 GTATCGATACCAAAAATAGGTTCGATGTTGCCTA
24950 GTATCGATACCAAAAATAGGTTCGATGTTGCCTA
1 GTATCGATACCAAAAATAGGTTCGATGTTGCCTA
24984 GTATCGATACC
1 GTATCGATACC
24995 CTTACCATGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (34 bp):
GTATCGATACCAAAAATAGGTTCGATGTTGCCTA
Found at i:26666 original size:39 final size:39
Alignment explanation
Indices: 26623--26737 Score: 140
Period size: 39 Copynumber: 2.9 Consensus size: 39
26613 AAAAAGGAAG
*
26623 ATAATACCTAAGGTGAGGATGTTGAGTCCAATAAAGGCA
1 ATAATGCCTAAGGTGAGGATGTTGAGTCCAATAAAGGCA
* * *
26662 ATAATGCCTAAAGTGAGGATGTTGAGTGCAATAAAGGCG
1 ATAATGCCTAAGGTGAGGATGTTGAGTCCAATAAAGGCA
* * * ** *
26701 ATAACGCCTGAGGTGAGGGTAATGAGTTCAATAAAGG
1 ATAATGCCTAAGGTGAGGATGTTGAGTCCAATAAAGG
26738 TGGTAGTGCA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.23
Consensus pattern (39 bp):
ATAATGCCTAAGGTGAGGATGTTGAGTCCAATAAAGGCA
Found at i:28425 original size:22 final size:22
Alignment explanation
Indices: 28397--28440 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28387 CTTACAGATC
28397 TTCCAAGGAAAGAAGAGAGGAG
1 TTCCAAGGAAAGAAGAGAGGAG
28419 TTCCAAGGAAAGAAGAGAGGAG
1 TTCCAAGGAAAGAAGAGAGGAG
28441 AAAATCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.09, G:0.36, T:0.09
Consensus pattern (22 bp):
TTCCAAGGAAAGAAGAGAGGAG
Found at i:28690 original size:42 final size:42
Alignment explanation
Indices: 28616--28708 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
28606 TCAAAGGTTT
28616 CATGATGATTAAATCCTTCGAGTAATCAATAAGTCTTTCGAG
1 CATGATGATTAAATCCTTCGAGTAATCAATAAGTCTTTCGAG
* * * * * * *
28658 CATGGTGATTAAATCTTTTGGGTCATCTATAAGTCTTTCGAA
1 CATGATGATTAAATCCTTCGAGTAATCAATAAGTCTTTCGAG
*
28700 CAAGATGAT
1 CATGATGAT
28709 AAGTCATTTG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35
Consensus pattern (42 bp):
CATGATGATTAAATCCTTCGAGTAATCAATAAGTCTTTCGAG
Found at i:28917 original size:42 final size:42
Alignment explanation
Indices: 28858--28969 Score: 165
Period size: 42 Copynumber: 2.7 Consensus size: 42
28848 AAGTAAGTTT
28858 TTCGGGTCATCAGTAAGTCTTTCGAGCATA-ATGATTAAATCC
1 TTCGGGTCATCAGTAAGTCTTTCGAGCA-AGATGATTAAATCC
*
28900 TTCGGGTCATCAGTAAGTCTTTCAAGCAAGATGATTAAATCC
1 TTCGGGTCATCAGTAAGTCTTTCGAGCAAGATGATTAAATCC
* *
28942 TTCGGATCAT-ATATAAGTCTTTCGAGCA
1 TTCGGGTCATCA-GTAAGTCTTTCGAGCA
28970 GGGTGATAAG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
41 2 0.03
42 62 0.97
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (42 bp):
TTCGGGTCATCAGTAAGTCTTTCGAGCAAGATGATTAAATCC
Found at i:29096 original size:21 final size:22
Alignment explanation
Indices: 29070--29111 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
29060 AATTTAATAA
*
29070 AAATAAAAATGAAAAA-AAATT
1 AAATAAAAACGAAAAATAAATT
29091 AAATAAAAACGAAAAATAAAT
1 AAATAAAAACGAAAAATAAAT
29112 GACATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (22 bp):
AAATAAAAACGAAAAATAAATT
Found at i:29118 original size:22 final size:21
Alignment explanation
Indices: 29070--29119 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
29060 AATTTAATAA
* *
29070 AAATAAAAATGAAAAAAAATT
1 AAATAAAAACGAAAAAAAATG
29091 AAATAAAAACGAAAAATAAATG
1 AAATAAAAACGAAAAA-AAATG
*
29113 ACATAAA
1 AAATAAA
29120 TAAATCCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.16
Consensus pattern (21 bp):
AAATAAAAACGAAAAAAAATG
Found at i:34202 original size:30 final size:30
Alignment explanation
Indices: 34166--34235 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
34156 ATATCATAGT
34166 AGATGATGACGTGGTAGATCCATGTGGACC
1 AGATGATGACGTGGTAGATCCATGTGGACC
34196 AGATGATGACGTGGTAGATCCATGTGGACC
1 AGATGATGACGTGGTAGATCCATGTGGACC
* *
34226 AAATGCTGAC
1 AGATGATGAC
34236 ATGGCATACC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (30 bp):
AGATGATGACGTGGTAGATCCATGTGGACC
Found at i:40795 original size:14 final size:14
Alignment explanation
Indices: 40776--40820 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
40766 TAGATCGAAA
*
40776 ATAAACGAACAAAC
1 ATAAACAAACAAAC
40790 ATAAACAAACAAAC
1 ATAAACAAACAAAC
*
40804 ATAAACAAACTAAC
1 ATAAACAAACAAAC
40818 ATA
1 ATA
40821 CATGAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.67, C:0.20, G:0.02, T:0.11
Consensus pattern (14 bp):
ATAAACAAACAAAC
Found at i:43386 original size:23 final size:23
Alignment explanation
Indices: 43360--43427 Score: 118
Period size: 23 Copynumber: 3.0 Consensus size: 23
43350 CACCACAGCT
* *
43360 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGTAGTGCCG
43383 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAATTGCACCGTAGTGCCG
43406 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGTAGTGCC
43428 ATATAATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGTAGTGCCG
Found at i:45184 original size:64 final size:63
Alignment explanation
Indices: 45081--45246 Score: 185
Period size: 64 Copynumber: 2.6 Consensus size: 63
45071 TCTTTTAATG
* * *
45081 AATGTATGCATCGATGCACTACACCATGCATCGATGCATAAATC-CTATTCGATG-TTTGTATTT
1 AATGCATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCTC-ATTCGATGTTTTCTATTT
45144 -
63 A
*
45144 AATGGGGATGCATCGATGCACTCCTTATGCATCGATGCATAAATCTCATTCGATGTTTTCTATTT
1 AAT--GCATGCATCGATGCACTCC-TATGCATCGATGCATAAATCTCATTCGATGTTTTCTATTT
45209 A
63 A
* * *
45210 AATTCATGCATCGATGCACTGCATGTGCATCGATGCA
1 AATGCATGCATCGATGCACT-CCTATGCATCGATGCA
45247 CCTTAAACAA
Statistics
Matches: 89, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
63 4 0.04
64 56 0.63
65 26 0.29
66 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
AATGCATGCATCGATGCACTCCTATGCATCGATGCATAAATCTCATTCGATGTTTTCTATTTA
Found at i:45508 original size:3 final size:3
Alignment explanation
Indices: 45493--45541 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
45483 AGTTAAAAAA
* *
45493 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
45540 TA
1 TA
45542 AGTGTATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 1 0.02
3 40 0.98
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:47458 original size:2 final size:2
Alignment explanation
Indices: 47451--47475 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47441 GTTAAACGTG
47451 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 T
47476 TATTTAATGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47689 original size:102 final size:98
Alignment explanation
Indices: 47460--47695 Score: 373
Period size: 102 Copynumber: 2.3 Consensus size: 98
47450 GTATATATAT
*
47460 ATATATATATATATATTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATATATATATATATT
1 ATATATATATATAT-TTGTTTAATGTGTCTTGGAAACTGATTTTTTGTTCATATATATATATATT
*
47525 TGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
65 TGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
**
47559 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTCATATATATATATATAT
1 ATATATATATATATTTGTTTAATGTGTCTTGGAAACTGATTTTTTGTTC----ATATATATATAT
47624 ATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
62 ATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
*
47661 ATATACATATATATTTGTTTAATGTGTCTTAGGAA
1 ATATATATATATATTTGTTTAATGTGTCTT-GGAA
47696 GAATAGCCAT
Statistics
Matches: 125, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
98 32 0.26
99 14 0.11
102 75 0.60
103 4 0.03
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (98 bp):
ATATATATATATATTTGTTTAATGTGTCTTGGAAACTGATTTTTTGTTCATATATATATATATTT
GTTTAACATGTCTTGGAAACTGATTCTTTGTTC
Found at i:47690 original size:49 final size:49
Alignment explanation
Indices: 47460--47682 Score: 356
Period size: 49 Copynumber: 4.4 Consensus size: 49
47450 GTATATATAT
* **
47460 ATATATATATATATATTATTTAATGTGTCTTGGAAACTGATTTTTTGTTC
1 ATATATATATATAT-TTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
47510 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
1 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
47559 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
1 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
*
47608 ATATATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
1 ----ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
*
47661 ATATACATATATATTTGTTTAA
1 ATATATATATATATTTGTTTAA
47683 TGTGTCTTAG
Statistics
Matches: 164, Mismatches: 5, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
49 102 0.62
50 14 0.09
53 48 0.29
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (49 bp):
ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
Found at i:47809 original size:52 final size:52
Alignment explanation
Indices: 47751--47863 Score: 194
Period size: 52 Copynumber: 2.2 Consensus size: 52
47741 TTGTTAAACG
47751 TATATATATTTTATTTAATGTGTCTTGGAAACTGA-TTTTTTGTTCATATATA
1 TATATATATTTT-TTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATATATA
47803 TATATATA-TTTTTTAATGTGTCTTGGAAACTGATTTTTTTTGTTCATATATA
1 TATATATATTTTTTTAATGTGTCTTGGAAACTGA-TTTTTTTGTTCATATATA
47855 TATATATAT
1 TATATATAT
47864 ATATTTGTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
50 22 0.38
51 3 0.05
52 33 0.57
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (52 bp):
TATATATATTTTTTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATATATA
Found at i:47818 original size:50 final size:52
Alignment explanation
Indices: 47751--47869 Score: 199
Period size: 50 Copynumber: 2.3 Consensus size: 52
47741 TTGTTAAACG
47751 TATATATAT-TTTATTTAATGTGTCTTGGAAACTGA-TTTTTTGTTCATATA
1 TATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATATA
47801 TATATATATATTT-TTTAATGTGTCTTGGAAACTGATTTTTTTTGTTCATATA
1 TATATATATATTTATTTAATGTGTCTTGGAAACTGA-TTTTTTTGTTCATATA
*
47853 TATATATATATATATTT
1 TATATATATATTTATTT
47870 GTTTAACATG
Statistics
Matches: 64, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
50 31 0.48
51 3 0.05
52 27 0.42
53 3 0.05
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.55
Consensus pattern (52 bp):
TATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTTGTTCATATA
Found at i:47894 original size:193 final size:188
Alignment explanation
Indices: 47562--47933 Score: 518
Period size: 193 Copynumber: 1.9 Consensus size: 188
47552 TTTGTTCATA
*
47562 TATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTCATATATATATATATATATT
1 TATATATATATTTATTTAACATGTCTTGGAAACTGATTTTTTGTTCA-ATATATATATATATATT
**
47627 TGTTTAACATGTCTTGGAAACTGATTCTTTGTTCATATACATATATATTTGTTTAATGTGTCTTA
65 TGTTTAACATGTCTTGGAAACTGATTCTTTGTTCATATACATATATATTTGTTTAACATGTCTTA
*
47692 GGAAGAATAGCCAT-TATTTATTTGTTTAACATATAGCTTAGTTGGATATTTGTTAAACG
130 GGAAGAATAGCCATAT-TTTATTTGTTTAACATATAGCTTAGCTGGATATTTGTTAAACG
**
47751 TATATATAT-TTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTC-ATATATATATATATATTT
1 TATATATATATTTATTTAACATGTCTTGGAAACTGATTTTTTGTTCAATATATATATATATATTT
** * *
47814 -TTTAATGTGTCTTGGAAACTGATTTTTTTTGTTCATATATATATATATATATATTTGTTTAACA
66 GTTTAACATGTCTTGGAAACTGA--TTCTTTGTTC------ATATACATATATATTTGTTTAACA
* *
47878 TGTCTTAGGAAGAATAGGCATATTTTATTTGTTTAACGTATAGCTTAGCTGGATAT
123 TGTCTTAGGAAGAATAGCCATATTTTATTTGTTTAACATATAGCTTAGCTGGATAT
47934 ATATATATTT
Statistics
Matches: 162, Mismatches: 12, Indels: 14
0.86 0.06 0.07
Matches are distributed among these distances:
185 20 0.12
186 18 0.11
187 9 0.06
188 33 0.20
189 9 0.06
193 72 0.44
194 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (188 bp):
TATATATATATTTATTTAACATGTCTTGGAAACTGATTTTTTGTTCAATATATATATATATATTT
GTTTAACATGTCTTGGAAACTGATTCTTTGTTCATATACATATATATTTGTTTAACATGTCTTAG
GAAGAATAGCCATATTTTATTTGTTTAACATATAGCTTAGCTGGATATTTGTTAAACG
Found at i:59838 original size:17 final size:17
Alignment explanation
Indices: 59775--59844 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 17
59765 GAACAAATAA
* *
59775 AAATAAAAATGAAAAAG
1 AAATGAAAATAAAAAAG
*
59792 AAA--AAAATGAAAAA-
1 AAATGAAAATAAAAAAG
59806 AAATGAAAAATGAAAAAAG
1 AAATG-AAAAT-AAAAAAG
*
59825 AAATGAAAATAAAAGAG
1 AAATGAAAATAAAAAAG
59842 AAA
1 AAA
59845 AAGGAGGGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
14 3 0.07
15 11 0.24
17 17 0.37
18 10 0.22
19 5 0.11
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (17 bp):
AAATGAAAATAAAAAAG
Done.