Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002000.1 Hibiscus syriacus cultivar Beakdansim tig00004092_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: 65602
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:4060 original size:15 final size:15
Alignment explanation
Indices: 4037--4066 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4027 AATATTTTTG
*
4037 TTTTCATATTATAAT
1 TTTTAATATTATAAT
4052 TTTTAATATTATAAT
1 TTTTAATATTATAAT
4067 AGTATTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTAATATTATAAT
Found at i:5355 original size:20 final size:20
Alignment explanation
Indices: 5330--5367 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5320 TTTGGTTCAT
5330 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
5350 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
5368 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:5438 original size:35 final size:35
Alignment explanation
Indices: 5397--5476 Score: 151
Period size: 35 Copynumber: 2.3 Consensus size: 35
5387 GTTATATTTT
*
5397 GTGTTTGGTTGGTTTAGCAGGAATGTAAGATTATC
1 GTGTTTGGTTGGCTTAGCAGGAATGTAAGATTATC
5432 GTGTTTGGTTGGCTTAGCAGGAATGTAAGATTATC
1 GTGTTTGGTTGGCTTAGCAGGAATGTAAGATTATC
5467 GTGTTTGGTT
1 GTGTTTGGTT
5477 AAAGGAATAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.20, C:0.06, G:0.33, T:0.41
Consensus pattern (35 bp):
GTGTTTGGTTGGCTTAGCAGGAATGTAAGATTATC
Found at i:9938 original size:4 final size:4
Alignment explanation
Indices: 9916--9970 Score: 83
Period size: 4 Copynumber: 13.8 Consensus size: 4
9906 GTGATTAAGT
* * *
9916 TATA GATA TACA TACA TATA TATA TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
9964 TATA TAT
1 TATA TAT
9971 GAAAAAGCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (4 bp):
TATA
Found at i:9940 original size:6 final size:6
Alignment explanation
Indices: 9916--9970 Score: 83
Period size: 6 Copynumber: 9.2 Consensus size: 6
9906 GTGATTAAGT
* * *
9916 TATAGA TATACA TACATA TATATA TATATA TATATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
9964 TATATA T
1 TATATA T
9971 GAAAAAGCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (6 bp):
TATATA
Found at i:9944 original size:10 final size:10
Alignment explanation
Indices: 9916--9970 Score: 83
Period size: 10 Copynumber: 5.5 Consensus size: 10
9906 GTGATTAAGT
*
9916 TATAGATATA
1 TATATATATA
* *
9926 CATACATATA
1 TATATATATA
9936 TATATATATA
1 TATATATATA
9946 TATATATATA
1 TATATATATA
9956 TATATATATA
1 TATATATATA
9966 TATAT
1 TATAT
9971 GAAAAAGCAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (10 bp):
TATATATATA
Found at i:25432 original size:27 final size:27
Alignment explanation
Indices: 25401--25495 Score: 167
Period size: 27 Copynumber: 3.6 Consensus size: 27
25391 TCTATTTACA
25401 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
25428 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
*
25455 AAATCATATCTCTATAGGAATGTTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
25482 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
25496 ATTCCTACAC
Statistics
Matches: 67, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
25 9 0.13
27 58 0.87
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:29207 original size:27 final size:27
Alignment explanation
Indices: 29176--29243 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
29166 TCTATTTACA
29176 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
29203 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
29230 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
29244 ATTCCTACAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:30399 original size:3 final size:3
Alignment explanation
Indices: 30393--30460 Score: 86
Period size: 3 Copynumber: 23.0 Consensus size: 3
30383 TTTTTTTCCG
** *
30393 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
30440 TT- TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA
30461 CAATTTTTGC
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 3 0.05
3 50 0.89
4 3 0.05
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:30608 original size:25 final size:25
Alignment explanation
Indices: 30579--30700 Score: 192
Period size: 25 Copynumber: 4.9 Consensus size: 25
30569 GCAACCCGTT
*
30579 AGATTAGGGTTTCAAACCCTAAATC
1 AGATTAGGGTTTCAAACCCTAAAAC
* *
30604 AGATTAGGGTTTTAAACCCTAAATC
1 AGATTAGGGTTTCAAACCCTAAAAC
*
30629 TGATTAGGGTTTCAAACCCTAAAAC
1 AGATTAGGGTTTCAAACCCTAAAAC
30654 A-ATTTAGGGTTTCAAACCCTAAAAC
1 AGA-TTAGGGTTTCAAACCCTAAAAC
30679 AGATTAGGGTTTCAAACCCTAA
1 AGATTAGGGTTTCAAACCCTAA
30701 TCCCCTACTC
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
24 1 0.01
25 88 0.98
26 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (25 bp):
AGATTAGGGTTTCAAACCCTAAAAC
Found at i:32353 original size:16 final size:16
Alignment explanation
Indices: 32332--32365 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
32322 CTTATAGAAA
32332 TTATTTTATTGTTATT
1 TTATTTTATTGTTATT
*
32348 TTATTTTTTTGTTATT
1 TTATTTTATTGTTATT
32364 TT
1 TT
32366 TGATTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (16 bp):
TTATTTTATTGTTATT
Found at i:41105 original size:92 final size:92
Alignment explanation
Indices: 40955--41252 Score: 431
Period size: 92 Copynumber: 3.2 Consensus size: 92
40945 CCAGACTTCC
* * * *
40955 TCATCACGTAGGAGTCGTGTCAACATTAGGATAACCAGCCGTCCTTATCACGTAGGAACCGAGTT
1 TCATCACGTAAGAGCCGTGTCAAC-CT--GATAACCAGCCGTCCTCATCACGTAGGAACCGAGTT
41020 ATCACCCTTCCTTTAGATGGCCAGATCTCT
63 ATCACCCTTCCTTTAGATGGCCAGATCTCT
41050 TCATCACGTAAGAGCCGTGTCAACCTGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATC
1 TCATCACGTAAGAGCCGTGTCAACCTGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATC
41115 ACCCTTCCTTTAGATGGCCAGATCTCT
66 ACCCTTCCTTTAGATGGCCAGATCTCT
* *
41142 TCATCACGTAAGAGCCGTGTCAACCTGATAACCAGTCGTCCTCATTACGTAGGAACCGAGTTATC
1 TCATCACGTAAGAGCCGTGTCAACCTGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATC
* ** * *
41207 A---TCCCTAAAGATGACCAGATCTCC
66 ACCCTTCCTTTAGATGGCCAGATCTCT
* *
41231 TCATCACGTAGGAGCCATGTCA
1 TCATCACGTAAGAGCCGTGTCA
41253 CCCTTAGACG
Statistics
Matches: 190, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
89 38 0.20
92 129 0.68
94 1 0.01
95 22 0.12
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (92 bp):
TCATCACGTAAGAGCCGTGTCAACCTGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATC
ACCCTTCCTTTAGATGGCCAGATCTCT
Found at i:41461 original size:3 final size:3
Alignment explanation
Indices: 41455--41513 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
41445 TTTTTTTCCG
** *
41455 TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41501 TTA TTTA TTA TTA
1 TTA -TTA TTA TTA
41514 CAATTTTTGC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 3 0.06
3 41 0.87
4 3 0.06
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:41661 original size:25 final size:25
Alignment explanation
Indices: 41632--41753 Score: 185
Period size: 25 Copynumber: 4.9 Consensus size: 25
41622 GCAACCCGTT
41632 AGATTAGGGTTTCAAACCCTAAATC
1 AGATTAGGGTTTCAAACCCTAAATC
*
41657 AGATTAGGGTTTTAAACCCTAAATC
1 AGATTAGGGTTTCAAACCCTAAATC
* *
41682 TGATTAGGGTTTCAAACCCTAAAAC
1 AGATTAGGGTTTCAAACCCTAAATC
41707 A-ATTTAGGGTTTCAAACCCTAAAAT-
1 AGA-TTAGGGTTTCAAACCCT-AAATC
41732 AGATTAGGGTTTCAAACCCTAA
1 AGATTAGGGTTTCAAACCCTAA
41754 TCCCCTACTC
Statistics
Matches: 88, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
24 3 0.03
25 81 0.92
26 4 0.05
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.30
Consensus pattern (25 bp):
AGATTAGGGTTTCAAACCCTAAATC
Found at i:43407 original size:16 final size:16
Alignment explanation
Indices: 43386--43419 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
43376 CTTATAGAAA
43386 TTATTTTATTGTTATT
1 TTATTTTATTGTTATT
*
43402 TTATTTTTTTGTTATT
1 TTATTTTATTGTTATT
43418 TT
1 TT
43420 TTGATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (16 bp):
TTATTTTATTGTTATT
Found at i:46636 original size:18 final size:18
Alignment explanation
Indices: 46598--46649 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
46588 ATTATGTAAA
46598 TATTAAAAAGTATAATAATT
1 TATTAAAAA-T-TAATAATT
* *
46618 TATTTAAAATTAATCATT
1 TATTAAAAATTAATAATT
46636 TATTAAAAATTAAT
1 TATTAAAAATTAAT
46650 TATAATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 20 0.69
19 1 0.03
20 8 0.28
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TATTAAAAATTAATAATT
Found at i:48019 original size:21 final size:22
Alignment explanation
Indices: 47981--48024 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
47971 GTATCTATAG
*
47981 TGGTTGAAGAGAAAATTATATT
1 TGGTTGAAGAGAAAATTAAATT
* *
48003 TGGTTGAA-ATAAGATTAAATT
1 TGGTTGAAGAGAAAATTAAATT
48024 T
1 T
48025 TGATTTTAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (22 bp):
TGGTTGAAGAGAAAATTAAATT
Found at i:49080 original size:18 final size:18
Alignment explanation
Indices: 49057--49106 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
49047 GCGTAGAATT
49057 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
49075 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
49093 TGTCCCGAAAGACC
1 TGTCCCGAAGGACC
49107 GCGTAGAACC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.28, C:0.34, G:0.22, T:0.16
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:50498 original size:10 final size:10
Alignment explanation
Indices: 50483--50537 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
50473 CTTAGTGTTT
50483 TAAGCTTATA
1 TAAGCTTATA
* *
50493 TAAGCTTTCTT
1 TAAGC-TTATA
50504 TAAGCTTATA
1 TAAGCTTATA
* *
50514 TAAGCTTTCTT
1 TAAGC-TTATA
50525 TAAGCTTATA
1 TAAGCTTATA
50535 TAA
1 TAA
50538 CACCCAAATA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
10 19 0.54
11 16 0.46
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (10 bp):
TAAGCTTATA
Found at i:50507 original size:21 final size:21
Alignment explanation
Indices: 50481--50537 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
50471 CTCTTAGTGT
50481 TTTAAGCTTATATAAGCTTTC
1 TTTAAGCTTATATAAGCTTTC
50502 TTTAAGCTTATATAAGCTTTC
1 TTTAAGCTTATATAAGCTTTC
50523 TTTAAGCTTATATAA
1 TTTAAGCTTATATAA
50538 CACCCAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (21 bp):
TTTAAGCTTATATAAGCTTTC
Found at i:50509 original size:11 final size:11
Alignment explanation
Indices: 50493--50531 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
50483 TAAGCTTATA
50493 TAAGCTTTCTT
1 TAAGCTTTCTT
* *
50504 TAAGC-TTATA
1 TAAGCTTTCTT
50514 TAAGCTTTCTT
1 TAAGCTTTCTT
50525 TAAGCTT
1 TAAGCTT
50532 ATATAACACC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (11 bp):
TAAGCTTTCTT
Found at i:51869 original size:16 final size:16
Alignment explanation
Indices: 51848--51916 Score: 56
Period size: 16 Copynumber: 4.5 Consensus size: 16
51838 ATCATTTATG
51848 TATATCATATAACACT
1 TATATCATATAACACT
* *
51864 TATATCATTTCACA-T
1 TATATCATATAACACT
* * *
51879 AACATCATAT---ATT
1 TATATCATATAACACT
51892 GTATATCATATAACACT
1 -TATATCATATAACACT
51909 TATATCAT
1 TATATCAT
51917 TTCACATAAC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
12 1 0.03
13 1 0.03
14 8 0.20
15 8 0.20
16 20 0.50
17 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.01, T:0.41
Consensus pattern (16 bp):
TATATCATATAACACT
Found at i:51880 original size:21 final size:21
Alignment explanation
Indices: 51856--51927 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
51846 TGTATATCAT
51856 ATAACACTTATATCATTTCAC
1 ATAACACTTATATCATTTCAC
* * * *
51877 ATAACATCATATATTGTATATCAT
1 ATAACA-CTTATA-T-CATTTCAC
51901 ATAACACTTATATCATTTCAC
1 ATAACACTTATATCATTTCAC
51922 ATAACA
1 ATAACA
51928 TCATGGCATT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
21 17 0.43
22 6 0.15
23 6 0.15
24 11 0.28
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (21 bp):
ATAACACTTATATCATTTCAC
Found at i:51896 original size:45 final size:44
Alignment explanation
Indices: 51838--51931 Score: 170
Period size: 45 Copynumber: 2.1 Consensus size: 44
51828 TCTTGTACTT
*
51838 ATCATTTATGTATATCATATAACACTTATATCATTTCACATAAC
1 ATCATATATGTATATCATATAACACTTATATCATTTCACATAAC
51882 ATCATATATTGTATATCATATAACACTTATATCATTTCACATAAC
1 ATCATATA-TGTATATCATATAACACTTATATCATTTCACATAAC
51927 ATCAT
1 ATCAT
51932 GGCATTTCAA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 7 0.15
45 41 0.85
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.40
Consensus pattern (44 bp):
ATCATATATGTATATCATATAACACTTATATCATTTCACATAAC
Found at i:52181 original size:22 final size:22
Alignment explanation
Indices: 52155--52218 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
52145 GTTCAGTATT
*
52155 CGTCCCGAAGGACCACTATATA
1 CGTCCCGAAGGACTACTATATA
* **
52177 CGTCCCGTAGGACTACTGGATA
1 CGTCCCGAAGGACTACTATATA
52199 CGTCCCGAAGGACTACTATA
1 CGTCCCGAAGGACTACTATA
52219 CCCTCGACTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (22 bp):
CGTCCCGAAGGACTACTATATA
Found at i:56141 original size:2 final size:2
Alignment explanation
Indices: 56134--56165 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
56124 ATCATCTATC
56134 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
56166 CATAAATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57011 original size:16 final size:16
Alignment explanation
Indices: 56990--57060 Score: 65
Period size: 16 Copynumber: 4.5 Consensus size: 16
56980 ATCATTTATG
56990 TATATCATATAACACT
1 TATATCATATAACACT
* *
57006 TATATCATTTCACA-T
1 TATATCATATAACACT
* * * *
57021 AACATCATAT-ATATT
1 TATATCATATAACACT
57036 GTATATCATATAACACT
1 -TATATCATATAACACT
57053 TATATCAT
1 TATATCAT
57061 TTCACATAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
14 2 0.05
15 9 0.21
16 28 0.67
17 3 0.07
ACGTcount: A:0.41, C:0.17, G:0.01, T:0.41
Consensus pattern (16 bp):
TATATCATATAACACT
Found at i:57022 original size:21 final size:21
Alignment explanation
Indices: 56998--57071 Score: 76
Period size: 21 Copynumber: 3.3 Consensus size: 21
56988 TGTATATCAT
56998 ATAACACTTATATCATTTCAC
1 ATAACACTTATATCATTTCAC
* * *
57019 ATAACATCATATATATTGTATATCAT
1 ATAACA-C-T-TATA-T-CATTTCAC
57045 ATAACACTTATATCATTTCAC
1 ATAACACTTATATCATTTCAC
57066 ATAACA
1 ATAACA
57072 TCATGACATT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
21 17 0.40
22 2 0.05
23 5 0.12
24 5 0.12
25 2 0.05
26 11 0.26
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (21 bp):
ATAACACTTATATCATTTCAC
Found at i:57350 original size:22 final size:22
Alignment explanation
Indices: 57299--57381 Score: 84
Period size: 22 Copynumber: 4.0 Consensus size: 22
57289 GTTCAGTATT
*
57299 CGTCCCGAATGACTA-T-TAT-
1 CGTCCCGAAGGACTACTATATA
* *
57318 -GTCCTGAAGGACCACTATATA
1 CGTCCCGAAGGACTACTATATA
* **
57339 CGTCCCGTAGGACTACTGGATA
1 CGTCCCGAAGGACTACTATATA
57361 CGTCCCGAAGGACTACTATAT
1 CGTCCCGAAGGACTACTATAT
57382 CCTCGACTCT
Statistics
Matches: 49, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
18 11 0.22
19 1 0.02
20 3 0.06
22 34 0.69
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (22 bp):
CGTCCCGAAGGACTACTATATA
Found at i:57565 original size:41 final size:41
Alignment explanation
Indices: 57514--57591 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
57504 ACCATGTATT
* *
57514 TCATATCATATCACATGTATCACATATTGCATATTCATATG
1 TCATATCATATAACATATATCACATATTGCATATTCATATG
* * *
57555 TCATTTCATATAACATATATCATATATTGCATTTTCA
1 TCATATCATATAACATATATCACATATTGCATATTCA
57592 CGTAGATCGT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (41 bp):
TCATATCATATAACATATATCACATATTGCATATTCATATG
Found at i:60845 original size:21 final size:21
Alignment explanation
Indices: 60820--60859 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
60810 TAATGAGGTT
*
60820 TTAGTTGATTTAAT-ATTTACA
1 TTAGTT-ATATAATGATTTACA
60841 TTAGTTATATAATGATTTA
1 TTAGTTATATAATGATTTA
60860 TAAAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (21 bp):
TTAGTTATATAATGATTTACA
Found at i:61592 original size:6 final size:6
Alignment explanation
Indices: 61581--61605 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
61571 GTGATGTAGG
61581 TGGGGT TGGGGT TGGGGT TGGGGT T
1 TGGGGT TGGGGT TGGGGT TGGGGT T
61606 TGGATCAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (6 bp):
TGGGGT
Found at i:63683 original size:155 final size:161
Alignment explanation
Indices: 63375--63683 Score: 384
Period size: 155 Copynumber: 2.0 Consensus size: 161
63365 AGATAATCGA
* *
63375 TTCTTCATTTCTTAAATTGATTTTATAGAATAGATTTGATTAAATGAAGTCCCTTTTTTAACCTT
1 TTCTTCATTTCTTAAATTGATTTTAGAGAATAGATTCGATTAAATGAAGTCCCTTTTTTAACCTT
* * * *
63440 GGAATTGATAAACTAGACTTTGTAGAGACATTAAAGTTGAATGTGCTTCTATTTAATATTAATGA
66 GGAACTGATAAACTAGACTTTGTACAGACATCAAAGTTGAATGTGCTTCTATTGAATATTAATGA
* * *
63505 TGTCAACTAAGGGTTGATTTTTAGGGTTCAG
131 TGACAAATAAGGGTTAATTTTTAGGGTTCAG
*
63536 TTCTTCATTTCTT-AATTGATTTTAGAGAATAGCTTCGATTAAATGAA-T-CC-TTTTT-A-CTT
1 TTCTTCATTTCTTAAATTGATTTTAGAGAATAGATTCGATTAAATGAAGTCCCTTTTTTAACCTT
* ** * *
63595 ATGAACTGATACGCTAGACTTTGTACTGACATCAAA-TTGAATGTGCTTTTATTGAACT-TTAAT
66 -GGAACTGATAAACTAGACTTTGTACAGACATCAAAGTTGAATGTGCTTCTATTGAA-TATTAAT
*
63658 GATGACAAAT-CGGGTTTAATTTTTAG
129 GATGACAAATAAGGG-TTAATTTTTAG
63684 AATTTCGACT
Statistics
Matches: 129, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
154 3 0.02
155 44 0.34
156 30 0.23
157 5 0.04
158 2 0.02
159 1 0.01
160 31 0.24
161 13 0.10
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.42
Consensus pattern (161 bp):
TTCTTCATTTCTTAAATTGATTTTAGAGAATAGATTCGATTAAATGAAGTCCCTTTTTTAACCTT
GGAACTGATAAACTAGACTTTGTACAGACATCAAAGTTGAATGTGCTTCTATTGAATATTAATGA
TGACAAATAAGGGTTAATTTTTAGGGTTCAG
Found at i:65551 original size:32 final size:32
Alignment explanation
Indices: 65509--65573 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
65499 TTTTTTCTGA
* *
65509 TGTTTAGTGATTTTCCCAATGAAATGTGTTAT
1 TGTTTAGTGATTTTCCCAAGGAAATGTCTTAT
* *
65541 TGTTTGGTGATTTTCCCGAGGAAATGTCTTAT
1 TGTTTAGTGATTTTCCCAAGGAAATGTCTTAT
65573 T
1 T
65574 CTTGGTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.46
Consensus pattern (32 bp):
TGTTTAGTGATTTTCCCAAGGAAATGTCTTAT
Done.