Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001492.1 Hibiscus syriacus cultivar Beakdansim tig00002904_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: 72598
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:4929 original size:47 final size:44
Alignment explanation
Indices: 4839--4932 Score: 116
Period size: 47 Copynumber: 2.1 Consensus size: 44
4829 ACAAACCAAG
* **
4839 TGATCAGTGATTAAGCAGATGGTTATCTTTAGAAATCCCATATT
1 TGATCAGTGATTAAGCAAATGGTTATCCCTAGAAATCCCATATT
**
4883 TGATCAGTGATTAAGCAAATGGTTGTTATCCCTAGAGGTCCCATATT
1 TGATCAGTGATTAAGCAAAT-G--GTTATCCCTAGAAATCCCATATT
4930 TGA
1 TGA
4933 GCACGTCGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
44 19 0.45
45 1 0.02
47 22 0.52
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (44 bp):
TGATCAGTGATTAAGCAAATGGTTATCCCTAGAAATCCCATATT
Found at i:5246 original size:36 final size:36
Alignment explanation
Indices: 5194--5324 Score: 235
Period size: 36 Copynumber: 3.6 Consensus size: 36
5184 AGCGTCATCC
*
5194 AAGTCTGCAAAAGTATTTGAGTGTTTATCGTTGTTT
1 AAGTCTGCAAAAATATTTGAGTGTTTATCGTTGTTT
* *
5230 AAGTTTGCAAAAGTATTTGAGTGTTTATCGTTGTTT
1 AAGTCTGCAAAAATATTTGAGTGTTTATCGTTGTTT
5266 AAGTCTGCAAAAATATTTGAGTGTTTATCGTTGTTT
1 AAGTCTGCAAAAATATTTGAGTGTTTATCGTTGTTT
5302 AAGTCTGCAAAAATATTTGAGTG
1 AAGTCTGCAAAAATATTTGAGTG
5325 ATTCATCTAG
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 92 1.00
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (36 bp):
AAGTCTGCAAAAATATTTGAGTGTTTATCGTTGTTT
Found at i:7322 original size:15 final size:16
Alignment explanation
Indices: 7302--7331 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7292 ATTGAGAGAC
7302 TTTTAC-TTTTTAAAA
1 TTTTACATTTTTAAAA
7317 TTTTACATTTTTAAA
1 TTTTACATTTTTAAA
7332 TAAAAATCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTACATTTTTAAAA
Found at i:7552 original size:2 final size:2
Alignment explanation
Indices: 7545--7590 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
7535 TTATTAGATG
7545 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
7587 AT AT
1 AT AT
7591 CGTATTAGTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9623 original size:12 final size:12
Alignment explanation
Indices: 9606--9630 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9596 AAGCTGCTGG
9606 TCTCTCTTTCTT
1 TCTCTCTTTCTT
9618 TCTCTCTTTCTT
1 TCTCTCTTTCTT
9630 T
1 T
9631 ATCACCATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
TCTCTCTTTCTT
Found at i:10887 original size:6 final size:6
Alignment explanation
Indices: 10854--10885 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
10844 GATGTTATAG
*
10854 ATCTAT ATCTAT ATCTAT ATCTAT ATATAT AT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
10886 ATTCTTCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (6 bp):
ATCTAT
Found at i:14413 original size:19 final size:19
Alignment explanation
Indices: 14391--14446 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
14381 ATATTTTTTA
14391 TATTTTTATATAAATATTT
1 TATTTTTATATAAATATTT
* *
14410 TATTTTAATATTAAAAATTT
1 TATTTTTATA-TAAATATTT
* * *
14430 AATTTTTTTTTAAATAT
1 TATTTTTATATAAATAT
14447 ATCACACGGA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTTTATATAAATATTT
Found at i:14429 original size:20 final size:19
Alignment explanation
Indices: 14391--14435 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
14381 ATATTTTTTA
* *
14391 TATTTTTATATAAATATTT
1 TATTTTAATATAAAAATTT
14410 TATTTTAATATTAAAAATTT
1 TATTTTAATA-TAAAAATTT
*
14430 AATTTT
1 TATTTT
14436 TTTTTAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTTAATATAAAAATTT
Found at i:22456 original size:21 final size:21
Alignment explanation
Indices: 22431--22476 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
22421 GATTTGAGAT
22431 GATCCAGCGGCTTTCGAAGGA
1 GATCCAGCGGCTTTCGAAGGA
22452 GATCCAGCGGCTTTCGAAGGA
1 GATCCAGCGGCTTTCGAAGGA
22473 GATC
1 GATC
22477 GATACATTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.20
Consensus pattern (21 bp):
GATCCAGCGGCTTTCGAAGGA
Found at i:42215 original size:18 final size:19
Alignment explanation
Indices: 42184--42225 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
42174 AAAATTAATT
* *
42184 AAATATTATTAAAATTTTA
1 AAATATTATCAAAATTTCA
42203 AAATATT-TCAAAATTTCA
1 AAATATTATCAAAATTTCA
42221 AAATA
1 AAATA
42226 AATTAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATATTATCAAAATTTCA
Found at i:42233 original size:18 final size:17
Alignment explanation
Indices: 42191--42233 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
42181 ATTAAATATT
*
42191 ATTAAAATTTTAAAATA
1 ATTAAAATTTCAAAATA
*
42208 TTTCAAAATTTCAAAATAA
1 ATT-AAAATTTCAAAAT-A
42227 ATTAAAA
1 ATTAAAA
42234 ATAATAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.10
18 16 0.76
19 3 0.14
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTAAAATTTCAAAATA
Found at i:47471 original size:2 final size:2
Alignment explanation
Indices: 47453--47497 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
47443 TACTACAAAC
47453 TA TA TCA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47495 TA T
1 TA T
47498 CATTTCATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:48766 original size:21 final size:21
Alignment explanation
Indices: 48724--48767 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
48714 GTTTCTTTAA
* *
48724 TTTATTTATTATTTTTAGTAT
1 TTTATTTATTATATATAGTAT
48745 TTTATTCTATTATATATA-TAT
1 TTTATT-TATTATATATAGTAT
48766 TT
1 TT
48768 CTTTTATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTATTTATTATATATAGTAT
Found at i:48806 original size:2 final size:2
Alignment explanation
Indices: 48787--48833 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
48777 CATTATTTTG
* *
48787 TA TA TG TA TA TG 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
48829 TA TA T
1 TA TA T
48834 TTTTTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:48918 original size:4 final size:4
Alignment explanation
Indices: 48909--48944 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
48899 TTCCTATGTT
48909 TTTA TTTA TTTCA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTT
48945 TCTTTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:48926 original size:9 final size:9
Alignment explanation
Indices: 48912--49002 Score: 53
Period size: 9 Copynumber: 9.9 Consensus size: 9
48902 CTATGTTTTT
48912 ATTTATTTC
1 ATTTATTTC
48921 ATTTATTT-
1 ATTTATTTC
48929 ATTTATTT-
1 ATTTATTTC
48937 ATTTATTTTC
1 ATTTA-TTTC
* *
48947 TTTTCTTTTC
1 ATTT-ATTTC
* *
48957 TTTTCGTTTC
1 ATTT-ATTTC
* *
48967 GTTTATTTT
1 ATTTATTTC
48976 ATTTTATTT-
1 A-TTTATTTC
*
48985 AGTTTATTTT
1 A-TTTATTTC
48995 ATTTATTT
1 ATTTATTT
49003 ATTGTCTTTA
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
8 13 0.19
9 29 0.42
10 27 0.39
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.74
Consensus pattern (9 bp):
ATTTATTTC
Found at i:48938 original size:12 final size:13
Alignment explanation
Indices: 48909--49014 Score: 66
Period size: 13 Copynumber: 8.5 Consensus size: 13
48899 TTCCTATGTT
48909 TTTATTTATTTCA
1 TTTATTTATTTCA
48922 TTTATTTATTT-A
1 TTTATTTATTTCA
48934 TTTATTTATTTTC-
1 TTTATTTA-TTTCA
*
48947 TTT-TCT-TTTC-
1 TTTATTTATTTCA
** *
48957 -TT-TTCGTTTCG
1 TTTATTTATTTCA
*
48968 TTTATTTTATTTTA
1 TTTA-TTTATTTCA
*
48982 TTTAGTTTATTTTA
1 TTTA-TTTATTTCA
48996 TTTATTTATTGTC-
1 TTTATTTATT-TCA
49009 TTTATT
1 TTTATT
49015 CTCGTATTCT
Statistics
Matches: 76, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
9 3 0.04
10 8 0.11
12 13 0.17
13 29 0.38
14 23 0.30
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.74
Consensus pattern (13 bp):
TTTATTTATTTCA
Found at i:48990 original size:14 final size:13
Alignment explanation
Indices: 48968--49005 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
48958 TTTCGTTTCG
48968 TTTATTTTATTTTA
1 TTTA-TTTATTTTA
48982 TTTAGTTTATTTTA
1 TTTA-TTTATTTTA
48996 TTTATTTATT
1 TTTATTTATT
49006 GTCTTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:49005 original size:4 final size:5
Alignment explanation
Indices: 48908--49002 Score: 53
Period size: 5 Copynumber: 20.6 Consensus size: 5
48898 TTTCCTATGT
* * *
48908 TTTTA -TTTA TTTCA -TTTA -TTTA -TTTA -TTTA -TTTA TTTTC TTTTC
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
* * * * * *
48952 TTTTC TTTTC GTTTC GTTTA TTTTA TTTTA -TTTA GTTTA TTTTA -TTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
49000 TTT
1 TTT
49003 ATTGTCTTTA
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
4 31 0.39
5 48 0.61
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:49070 original size:59 final size:55
Alignment explanation
Indices: 48973--49099 Score: 150
Period size: 59 Copynumber: 2.3 Consensus size: 55
48963 TTTCGTTTAT
* * *
48973 TTTATTTT-ATTTAGTTTATTTTATTTATTTATTGTCTTTATTCTCGTATTCTTGTTTC
1 TTTATTTTCATTTAGTTTATGTTATTTACTTATTATCTTTATT-T-GTATTC-T-TTTC
* *
49031 TTTATTTTCATTTTGTTTATGTTATTTACTTGTTATCTTTATTTGTATTCTTTTC
1 TTTATTTTCATTTAGTTTATGTTATTTACTTATTATCTTTATTTGTATTCTTTTC
49086 TTTATCTTTC-TTTA
1 TTTAT-TTTCATTTA
49100 CTCGTTTTGT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
55 12 0.20
56 5 0.08
57 6 0.10
58 9 0.15
59 29 0.48
ACGTcount: A:0.15, C:0.09, G:0.06, T:0.69
Consensus pattern (55 bp):
TTTATTTTCATTTAGTTTATGTTATTTACTTATTATCTTTATTTGTATTCTTTTC
Found at i:58083 original size:21 final size:20
Alignment explanation
Indices: 58049--58097 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
58039 TAAGTCGAAG
58049 AAGAAAAAGAA-AAAAAG-AA
1 AAGAAAAA-AATAAAAAGAAA
58068 AAGAACAAAAATAAAAAGAAA
1 AAGAA-AAAAATAAAAAGAAA
58089 AAGAAAAAA
1 AAGAAAAAA
58098 TGTTTAGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 7 0.26
20 13 0.48
21 7 0.26
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (20 bp):
AAGAAAAAAATAAAAAGAAA
Found at i:58084 original size:15 final size:13
Alignment explanation
Indices: 58052--58097 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
58042 GTCGAAGAAG
58052 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
*
58065 GAAAAGAACAAAAA
1 AAAAAGAA-AAAAA
58079 TAAAAAGAAAAAGAA
1 -AAAAAGAAAAA-AA
58094 AAAA
1 AAAA
58098 TGTTTAGGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 7 0.25
14 12 0.43
15 9 0.32
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:58149 original size:8 final size:8
Alignment explanation
Indices: 58136--58181 Score: 83
Period size: 8 Copynumber: 5.6 Consensus size: 8
58126 CCTAAATTGA
58136 AAAAAAGG
1 AAAAAAGG
58144 AAAAAAGG
1 AAAAAAGG
58152 AAAAAAGG
1 AAAAAAGG
58160 AAAAAAGG
1 AAAAAAGG
58168 AAAAAAGAG
1 AAAAAAG-G
58177 AAAAA
1 AAAAA
58182 GAGAAAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 31 0.84
9 6 0.16
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:58182 original size:24 final size:25
Alignment explanation
Indices: 58136--58188 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
58126 CCTAAATTGA
58136 AAAAAAGGAAAAAAGGAAAAAAG-G
1 AAAAAAGGAAAAAAGGAAAAAAGAG
58160 AAAAAAGGAAAAAA-GAGAAAAAGAG
1 AAAAAAGGAAAAAAGGA-AAAAAGAG
58185 AAAA
1 AAAA
58189 GAAAAAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 2 0.07
24 20 0.74
25 5 0.19
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (25 bp):
AAAAAAGGAAAAAAGGAAAAAAGAG
Found at i:59246 original size:88 final size:88
Alignment explanation
Indices: 59142--59335 Score: 225
Period size: 88 Copynumber: 2.2 Consensus size: 88
59132 ATCCACAATT
*
59142 TCAACTTCACGACGAAGGATATCGTGTTCACCAGCAACA-T-A-CAATA-CTTAGATTTCAACTT
1 TCAACTTCACGACGAAGGATATCATG--C-CCA-CAACATTCATCAATAGCTTAGATTTCAACTT
**
59203 CACGATGAAGGATATCCAATTCAAGAC
62 CACGACAAAGGATATCCAATTCAAGAC
** * ** * *
59230 TCAACTTCAAAACGAAGGATATCATGCCGACAACATTCATCTTTAGGTTGGATTTCAACTTCACG
1 TCAACTTCACGACGAAGGATATCATGCCCACAACATTCATCAATAGCTTAGATTTCAACTTCACG
*
59295 ACAAAGGATATCCAATTCAAGGC
66 ACAAAGGATATCCAATTCAAGAC
59318 TCAACTTCACGACGAAGG
1 TCAACTTCACGACGAAGG
59336 GACCATCCAC
Statistics
Matches: 89, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
84 5 0.06
85 3 0.03
86 2 0.02
87 3 0.03
88 76 0.85
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.25
Consensus pattern (88 bp):
TCAACTTCACGACGAAGGATATCATGCCCACAACATTCATCAATAGCTTAGATTTCAACTTCACG
ACAAAGGATATCCAATTCAAGAC
Found at i:61178 original size:12 final size:12
Alignment explanation
Indices: 61156--61375 Score: 62
Period size: 14 Copynumber: 18.8 Consensus size: 12
61146 TTAATTTTTC
*
61156 ATTAGTATTTAT
1 ATTATTATTTAT
61168 A-TATATATTTA-
1 ATTAT-TATTTAT
61179 ATTATTATTTAT
1 ATTATTATTTAT
* * *
61191 TTTATTTTTTCCT
1 ATTATTATTT-AT
* *
61204 TTTTTTATTT-T
1 ATTATTATTTAT
*
61215 ATTATTATATAT
1 ATTATTATTTAT
61227 A-TA-TATTTAT
1 ATTATTATTTAT
61237 -TTA-T-TTTAT
1 ATTATTATTTAT
* * *
61246 GTCATTATTTGT
1 ATTATTATTTAT
*
61258 A-TA-TATATAT
1 ATTATTATTTAT
*
61268 ATATATATATATAT
1 AT-TAT-TATTTAT
*
61282 ATATATATATATAT
1 AT-TAT-TATTTAT
*
61296 ATATATATATATAT
1 AT-TAT-TATTTAT
61310 ATATATTA-TT-T
1 AT-TATTATTTAT
*
61321 -TTATTGTTT-T
1 ATTATTATTTAT
61331 ATT-TTATTTAT
1 ATTATTATTTAT
61342 ATATATCCTATTTAT
1 AT-TAT--TATTTAT
*
61357 -TTA-TATGTAT
1 ATTATTATTTAT
61367 A-TATTATTT
1 ATTATTATTT
61376 TCACTATTAT
Statistics
Matches: 165, Mismatches: 21, Indels: 45
0.71 0.09 0.19
Matches are distributed among these distances:
9 9 0.05
10 34 0.21
11 31 0.19
12 28 0.17
13 14 0.08
14 42 0.25
15 7 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (12 bp):
ATTATTATTTAT
Found at i:61207 original size:53 final size:54
Alignment explanation
Indices: 61122--61241 Score: 129
Period size: 57 Copynumber: 2.2 Consensus size: 54
61112 TATTTTTGCC
*
61122 TATTTAAATATTATATTTTATTCTTTAA-TTTTTCA-TTAGTATT-TATATATA
1 TATTTAATTATTATATTTTATTCTTTAATTTTTTCATTTAGTATTATATATATA
* ** * *
61173 TATTTAATTATTATTTATTTTATTTTTTCCTTTTTTTATTTTATTATTATATATATA
1 TATTTAATTATTA--TATTTTATTCTTTAATTTTTTCA-TTTAGTATTATATATATA
*
61230 TATTTATTTATT
1 TATTTAATTATT
61242 TTATGTCATT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
51 12 0.21
53 12 0.21
54 6 0.11
56 7 0.12
57 19 0.34
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (54 bp):
TATTTAATTATTATATTTTATTCTTTAATTTTTTCATTTAGTATTATATATATA
Found at i:61264 original size:2 final size:2
Alignment explanation
Indices: 61257--61315 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
61247 TCATTATTTG
61257 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
61299 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
61316 TATTTTTATT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61408 original size:5 final size:5
Alignment explanation
Indices: 61398--61469 Score: 103
Period size: 5 Copynumber: 14.6 Consensus size: 5
61388 TCCTATGTTT
* *
61398 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTCG TTTT- GTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA
61448 TTTTA -TTTA TTTTA TTTTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTT
61470 ACTTATTGTC
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
4 7 0.11
5 50 0.82
6 4 0.07
ACGTcount: A:0.17, C:0.01, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:61493 original size:39 final size:39
Alignment explanation
Indices: 61394--61493 Score: 98
Period size: 39 Copynumber: 2.6 Consensus size: 39
61384 ATTTTCCTAT
* * *
61394 GTTTT-TTTATTTTATTTTATTTTATTTTATTTTATTTTC
1 GTTTTGTTTATATTATCTTA-TTTATTTTATTTTATTTAC
* *
61433 GTTTTGTTTATTTTATTTTATTTATTTTATTTTATTTAC
1 GTTTTGTTTATATTATCTTATTTATTTTATTTTATTTAC
*
61472 -TTATTGTCTT-TATTCTCTTATT
1 GTT-TTGT-TTATATTATCTTATT
61494 CTTTATTTTC
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
38 2 0.04
39 36 0.67
40 16 0.30
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (39 bp):
GTTTTGTTTATATTATCTTATTTATTTTATTTTATTTAC
Found at i:63730 original size:37 final size:37
Alignment explanation
Indices: 63681--63756 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
63671 ATCGAGTCAC
63681 CACAAGGACGAATAAAATATCAACAATAAATAAATGT
1 CACAAGGACGAATAAAATATCAACAATAAATAAATGT
* *
63718 CACAAGGTCGAATCAAATATCAACAATAAATAAATGT
1 CACAAGGACGAATAAAATATCAACAATAAATAAATGT
63755 CA
1 CA
63757 GTGGTTAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.54, C:0.16, G:0.11, T:0.20
Consensus pattern (37 bp):
CACAAGGACGAATAAAATATCAACAATAAATAAATGT
Found at i:68554 original size:46 final size:44
Alignment explanation
Indices: 68448--68554 Score: 128
Period size: 46 Copynumber: 2.4 Consensus size: 44
68438 CTACCTAAAC
* *
68448 ATTTGTTCTACCAG-AATGTAATATTGGGCACTATCTAAGCATT
1 ATTTTTTCTACCAGAAATGTAATATTGGGCACTACCTAAGCATT
* * *
68491 ATTTTTTCTACCGGAAATGTTAATATTGGGCGCTACCTAA-AATCTT
1 ATTTTTTCTACCAGAAATG-TAATATTGGGCACTACCTAAGCA--TT
68537 ATTTTTTCTACCAGAAAT
1 ATTTTTTCTACCAGAAAT
68555 TATCTAGCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
43 12 0.22
44 5 0.09
45 18 0.33
46 19 0.35
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (44 bp):
ATTTTTTCTACCAGAAATGTAATATTGGGCACTACCTAAGCATT
Found at i:69497 original size:18 final size:18
Alignment explanation
Indices: 69474--69521 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
69464 GTCTGCCCGA
69474 CGAACTGTTGACCCGACC
1 CGAACTGTTGACCCGACC
* *
69492 CGAACTATTGAACCGACC
1 CGAACTGTTGACCCGACC
* *
69510 CAAACCGTTGAC
1 CGAACTGTTGAC
69522 TTTGACCCGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.17
Consensus pattern (18 bp):
CGAACTGTTGACCCGACC
Found at i:69570 original size:16 final size:16
Alignment explanation
Indices: 69551--69588 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
69541 TGTGGTCAGA
69551 GTTGACCAGT-TAAACC
1 GTTGACCAGTCT-AACC
*
69567 GTTGACCGGTCTAACC
1 GTTGACCAGTCTAACC
69583 GTTGAC
1 GTTGAC
69589 TGAAAAAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (16 bp):
GTTGACCAGTCTAACC
Found at i:71200 original size:22 final size:21
Alignment explanation
Indices: 71160--71225 Score: 75
Period size: 22 Copynumber: 3.2 Consensus size: 21
71150 AAATGATATT
*
71160 GATACCATAGCA--TAGTATC
1 GATACCATAGTATGTAGTATC
*
71179 GGTACCATAGTATGGTAGTATC
1 GATACCATAGTAT-GTAGTATC
*
71201 GATACCATGGTATG-AGTATC
1 GATACCATAGTATGTAGTATC
71221 GATAC
1 GATAC
71226 TGAGGAGCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 10 0.25
20 11 0.28
21 1 0.03
22 18 0.45
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.29
Consensus pattern (21 bp):
GATACCATAGTATGTAGTATC
Found at i:71624 original size:54 final size:54
Alignment explanation
Indices: 71538--71819 Score: 426
Period size: 54 Copynumber: 5.3 Consensus size: 54
71528 TTACCAATTA
* ** *
71538 GGCACTAAGTGTACATTTCATGGAATTTATCCTACGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTACGTGGATGAATAACCGTTTC
71592 GGCACTAAGTGTGCATTTCACAGAATTCATCCTACGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTACGTGGATGAATAACCGTTTC
* * *
71646 GGCAATAAGTGTGCATTTCACAGAATTCATCATACGTGGATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTACGTGGATGAATAACCGTTTC
* * * *
71700 GGCACTAAGTGTGCATTTCACGGAATTCATCATACGTGGATAAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTACGTGGATGAATAACCGTTTC
71754 GGCACTAAGTGTGCA-TTCA-AGAATTCATCCTACGTGGATGAATAACCG-TTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTACGTGGATGAATAACCGTTTC
* *
71805 GACACTATGTGTGCA
1 GGCACTAAGTGTGCA
71820 ATCTACGAAA
Statistics
Matches: 212, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
51 16 0.08
52 25 0.12
53 4 0.02
54 167 0.79
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACAGAATTCATCCTACGTGGATGAATAACCGTTTC
Found at i:71993 original size:54 final size:55
Alignment explanation
Indices: 71790--72407 Score: 720
Period size: 53 Copynumber: 11.6 Consensus size: 55
71780 ATCCTACGTG
* * * *
71790 GATGAATAACCGTTCGA-CACTATGTGTGC-AATCTACGAAATTCATCATGAGTT
1 GATGAATAACCGTACAAGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTT
* * *
71843 -ATGAATAACCGTACAAGCACTACGTGTGC-AATACACAGAATTCATCATGA-TT
1 GATGAATAACCGTACAAGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTT
71895 GATTGAAT-ACCGTACAAGCACTATGT-TGCAAATCCACGGAATTCATCATGAGTT
1 GA-TGAATAACCGTACAAGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTT
* * ** * *
71949 GATG-ATAATCGTACATGCACTATACGTGTAAATACACGGAATTCATCATGAG-T
1 GATGAATAACCGTACAAGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTT
* *
72002 --TGAATAACCGTA-AGGCATTATGTGTGCAAATCCACGGAATTCATCATGA-TT
1 GATGAATAACCGTACAAGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTT
* *
72053 GATGAATAACCGTACAAACACTATGTGTGCAAATCCACGAAATTCATCATGAGTT
1 GATGAATAACCGTACAAGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTT
* *
72108 GATGAATAACCGTACATGCACTATGTGTGCAAATCCATGGAATTCATCATGAGTT
1 GATGAATAACCGTACAAGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTT
* * * * *
72163 AATGTATAACCGTACATGCACTATGTGTGC-AATCCATGAAATTCATCATGAGTT
1 GATGAATAACCGTACAAGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTT
* * *
72217 GATGAAT-ACCGTACATGCACTATGTGTGCAAATCCATGAAATTCATCATGAGTT
1 GATGAATAACCGTACAAGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTT
*
72271 -TTGAATAACCGTACAAGCACTATGTGTGC-AATCCACGGAATTCATCATGAGTT
1 GATGAATAACCGTACAAGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTT
* * * * * **
72324 GATAAATAACCGTACCA-TACGATGTGTG-TAA-CCGAAAGAATTCATCATGAGTT
1 GATGAATAACCGTACAAGCACTATGTGTGCAAATCC-ACGGAATTCATCATGAGTT
* * *
72377 GATGAACT-ACCGTATAGGCACTACGTGTGCA
1 GATGAA-TAACCGTACAAGCACTATGTGTGCA
72408 TCTTAATAAA
Statistics
Matches: 489, Mismatches: 55, Indels: 40
0.84 0.09 0.07
Matches are distributed among these distances:
51 34 0.07
52 31 0.06
53 182 0.37
54 161 0.33
55 81 0.17
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (55 bp):
GATGAATAACCGTACAAGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTT
Done.