Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003246.1 Hibiscus syriacus cultivar Beakdansim tig00006823_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: 73645
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3482 original size:15 final size:15
Alignment explanation
Indices: 3459--3495 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
3449 TGCATGGTAG
*
3459 AAACGTATCCACCCT
1 AAACCTATCCACCCT
3474 AAACCTATCCACCCT
1 AAACCTATCCACCCT
3489 AAACCTA
1 AAACCTA
3496 ACGTGGATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.41, G:0.03, T:0.19
Consensus pattern (15 bp):
AAACCTATCCACCCT
Found at i:9943 original size:6 final size:6
Alignment explanation
Indices: 9932--9962 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
9922 TTATTTATCG
9932 GATTTT GATTTT GATTTT GATTTT GATTTT G
1 GATTTT GATTTT GATTTT GATTTT GATTTT G
9963 GGTTTTTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.19, T:0.65
Consensus pattern (6 bp):
GATTTT
Found at i:17469 original size:19 final size:19
Alignment explanation
Indices: 17445--17483 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
17435 ATATAAGTAA
*
17445 ACATGACACATACATGCAT
1 ACATGACACATACATACAT
17464 ACATGACACATACATACAT
1 ACATGACACATACATACAT
17483 A
1 A
17484 TACAGTAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.26, G:0.08, T:0.21
Consensus pattern (19 bp):
ACATGACACATACATACAT
Found at i:18012 original size:16 final size:15
Alignment explanation
Indices: 17991--18020 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
17981 ATTATTTGTT
17991 TTTATTTATTTTAATA
1 TTTATTT-TTTTAATA
18007 TTTATTTTTTTAAT
1 TTTATTTTTTTAAT
18021 TTTTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATTTTTTTAATA
Found at i:18014 original size:22 final size:21
Alignment explanation
Indices: 17983--18023 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
17973 ATATCTAAAT
* *
17983 TATTTGTTTTTATTTATTTTAA
1 TATTTATTTTT-TTAATTTTAA
18005 TATTTATTTTTTTAATTTT
1 TATTTATTTTTTTAATTTT
18024 TTTAAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (21 bp):
TATTTATTTTTTTAATTTTAA
Found at i:20524 original size:20 final size:20
Alignment explanation
Indices: 20499--20540 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
20489 GCCTGCTAAG
20499 TACATGGGTTTTCCCCGCGA
1 TACATGGGTTTTCCCCGCGA
*
20519 TACATGGGTTTTTCCCGCGA
1 TACATGGGTTTTCCCCGCGA
20539 TA
1 TA
20541 GTTCGAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (20 bp):
TACATGGGTTTTCCCCGCGA
Found at i:20871 original size:205 final size:205
Alignment explanation
Indices: 20519--20972 Score: 818
Period size: 205 Copynumber: 2.2 Consensus size: 205
20509 TTCCCCGCGA
* * * *
20519 TACATGGGTTTTTCCCGCGATAGTTCGAATCTCTCAGGCGACGTTAAGTGTACCGTTTTGCCTAA
1 TACATGGGGTTTCCCCGCGAGAGTTCGAATCTCTCAGGCGACGTGAAGTGTACCGTTTTGCCTAA
20584 TCAAAACTAAAAGGGAAAATTATGCTCCAAGTCCCTAACTCTTTGTACCTTTGATGTTTGGTCCT
66 TCAAAACTAAAAGGGAAAATTATGCTCCAAGTCCCTAACTCTTTGTACCTTTGATGTTTGGTCCT
*
20649 TATAATTTTGGTTTTCTCCATATCAAGTCAACAATTGTCGCTTTGGCCGAGTGGTTAAGGCGTGT
131 TATAATTTTGGTTTTCTCCATATCAAGTCAACAATTGTCGCTCTGGCCGAGTGGTTAAGGCGTGT
20714 GCCTGCTAAG
196 GCCTGCTAAG
*
20724 TACATGGGGTTTCCCCGCGAGAGTTCGAATCTCTCAGGCGACGTGAAGTTTACCGTTTTGCCTAA
1 TACATGGGGTTTCCCCGCGAGAGTTCGAATCTCTCAGGCGACGTGAAGTGTACCGTTTTGCCTAA
*
20789 TCAAAACTAAAAGGGAAAATTATGCTCCAATTCCCTAACTCTTTGTACCTTTGATGTTTGGTCCT
66 TCAAAACTAAAAGGGAAAATTATGCTCCAAGTCCCTAACTCTTTGTACCTTTGATGTTTGGTCCT
* *
20854 TATAATTTTGGTTTTCTCCATATTAAGTCAACAATTGTTGCTCTGGCCGAGTGGTTAAGGCGTGT
131 TATAATTTTGGTTTTCTCCATATCAAGTCAACAATTGTCGCTCTGGCCGAGTGGTTAAGGCGTGT
20919 GCCTGCTAAG
196 GCCTGCTAAG
*
20929 TACATGGGGTTTCCCCGCGAGAGTTTGAATCTCTCAGGCGACGT
1 TACATGGGGTTTCCCCGCGAGAGTTCGAATCTCTCAGGCGACGT
20973 ATTAGTTTTT
Statistics
Matches: 239, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
205 239 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (205 bp):
TACATGGGGTTTCCCCGCGAGAGTTCGAATCTCTCAGGCGACGTGAAGTGTACCGTTTTGCCTAA
TCAAAACTAAAAGGGAAAATTATGCTCCAAGTCCCTAACTCTTTGTACCTTTGATGTTTGGTCCT
TATAATTTTGGTTTTCTCCATATCAAGTCAACAATTGTCGCTCTGGCCGAGTGGTTAAGGCGTGT
GCCTGCTAAG
Found at i:21791 original size:95 final size:94
Alignment explanation
Indices: 21597--21778 Score: 292
Period size: 95 Copynumber: 1.9 Consensus size: 94
21587 GGTGAACAAC
* *
21597 TTTTTTCTGGTCGAGTCGAGTCAAATACTTTTCATCTTAAACCCAAACCCGACCTGACTCGAACA
1 TTTTTTCTGGTCGAGTCGAGTCAAATACTTTTCATCCTAAACCCAAACCCGACCTGACCCGAACA
*
21662 TAATCCCTCTAAAAACTGACCCTAAAATA
66 TAACCCCTCTAAAAACTGACCCTAAAATA
* * *
21691 TTTTTTCTTGGTCGAGTCGAGTCAAATACTTTTCATCCTAAACTCAAACTCGATCTGACCCGAAC
1 TTTTTTC-TGGTCGAGTCGAGTCAAATACTTTTCATCCTAAACCCAAACCCGACCTGACCCGAAC
*
21756 ATAACCCCTCTAAAAGCTGACCC
65 ATAACCCCTCTAAAAACTGACCC
21779 GAATTCATTT
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 7 0.09
95 73 0.91
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (94 bp):
TTTTTTCTGGTCGAGTCGAGTCAAATACTTTTCATCCTAAACCCAAACCCGACCTGACCCGAACA
TAACCCCTCTAAAAACTGACCCTAAAATA
Found at i:33021 original size:14 final size:14
Alignment explanation
Indices: 33002--33048 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
32992 TTCCATCAGT
33002 TAAATAATTTAAAA
1 TAAATAATTTAAAA
*
33016 TAAAT-ATGTTAAAT
1 TAAATAAT-TTAAAA
33030 TAAAATAATTTAAAA
1 T-AAATAATTTAAAA
33045 TAAA
1 TAAA
33049 ATTAGTCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 2 0.07
14 14 0.50
15 10 0.36
16 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
TAAATAATTTAAAA
Found at i:33042 original size:15 final size:15
Alignment explanation
Indices: 33003--33050 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
32993 TCCATCAGTT
33003 AAATAATTTAAAAT-
1 AAATAATTTAAAATA
*
33017 AAAT-ATGTTAAATTA
1 AAATAAT-TTAAAATA
33032 AAATAATTTAAAATA
1 AAATAATTTAAAATA
33047 AAAT
1 AAAT
33051 TAGTCCTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 2 0.07
14 10 0.34
15 15 0.52
16 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
AAATAATTTAAAATA
Found at i:33146 original size:30 final size:30
Alignment explanation
Indices: 33111--33177 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
33101 AATTTATATT
*
33111 AATATATTAAAAGTAAGACTAAATTAAGAA
1 AATATATTAAAAGTAAAACTAAATTAAGAA
*
33141 AATATATTAAAAGTAAAACTAAATTGAGAA
1 AATATATTAAAAGTAAAACTAAATTAAGAA
33171 AATATAT
1 AATATAT
33178 AAACAACAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.28
Consensus pattern (30 bp):
AATATATTAAAAGTAAAACTAAATTAAGAA
Found at i:34206 original size:28 final size:27
Alignment explanation
Indices: 34119--34210 Score: 103
Period size: 28 Copynumber: 3.3 Consensus size: 27
34109 CCATAACTTA
*
34119 AAACCACAACCCACAACCCTAAACCTT
1 AAACCATAACCCACAACCCTAAACCTT
* ** *
34146 AAAACCCTAACTTACAAACCCTAAACCCT
1 -AAACCATAACCCAC-AACCCTAAACCTT
*
34175 AAACTATAACCCACAACCTCTAAACCTT
1 AAACCATAACCCACAACC-CTAAACCTT
34203 AAACCATA
1 AAACCATA
34211 TCTTAGAATT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
27 4 0.08
28 35 0.69
29 12 0.24
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.16
Consensus pattern (27 bp):
AAACCATAACCCACAACCCTAAACCTT
Found at i:35385 original size:18 final size:20
Alignment explanation
Indices: 35359--35399 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
35349 ATATTTTTTG
*
35359 TATAAAA-TT-AATGAATTT
1 TATAAAATTTAAATGAATAT
*
35377 TATATAATTTAAATGAATAT
1 TATAAAATTTAAATGAATAT
35397 TAT
1 TAT
35400 CCATGGGCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 6 0.32
19 2 0.11
20 11 0.58
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
TATAAAATTTAAATGAATAT
Found at i:38978 original size:40 final size:40
Alignment explanation
Indices: 38784--38980 Score: 123
Period size: 40 Copynumber: 5.0 Consensus size: 40
38774 AAAGATATAT
* * * * *
38784 TATTTGGCGGCGTTTATATACAAACGTCACTAAAATACGAG
1 TATTTAGCGGCGTTTAGATAAAAACGCCACTAAAATAC-AA
* ** ** * * *
38825 TATTTACCGATGTTTTTA-AAAAATGCCACGAAAGTACAA
1 TATTTAGCGGCGTTTAGATAAAAACGCCACTAAAATACAA
* * * * * * *
38864 TATTTAGCGACGTTTAGAT-AAAACACCAATAGAGTATAG
1 TATTTAGCGGCGTTTAGATAAAAACGCCACTAAAATACAA
* * * *
38903 TATTTACCGGCGTTTTA-A-AAAATAAGTCACGAAAATACAA
1 TATTTAGCGGCG-TTTAGATAAAA-ACGCCACTAAAATACAA
38943 TATTTAGCGGCGTTTAGATAAAAACGCCACTAAAATAC
1 TATTTAGCGGCGTTTAGATAAAAACGCCACTAAAATAC
38981 TAGGCATTTA
Statistics
Matches: 113, Mismatches: 37, Indels: 13
0.69 0.23 0.08
Matches are distributed among these distances:
39 46 0.41
40 50 0.44
41 17 0.15
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (40 bp):
TATTTAGCGGCGTTTAGATAAAAACGCCACTAAAATACAA
Found at i:41563 original size:27 final size:27
Alignment explanation
Indices: 41531--41586 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
41521 TTATTATTTC
*
41531 TACCGGTTTTGTTATTATTGGGCGCTT
1 TACCGGTTTTGTTATTATTGGGCACTT
*
41558 TACCGGTTTTGTTATTGTTGGGCACTT
1 TACCGGTTTTGTTATTATTGGGCACTT
41585 TA
1 TA
41587 TCGAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.12, C:0.14, G:0.25, T:0.48
Consensus pattern (27 bp):
TACCGGTTTTGTTATTATTGGGCACTT
Found at i:46967 original size:165 final size:164
Alignment explanation
Indices: 46695--47723 Score: 956
Period size: 165 Copynumber: 6.2 Consensus size: 164
46685 GAATATAATT
* * * * *
46695 GAACTCGGAGGTCTTCGGTTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTGAATGATGTGC
1 GAACTCGAAGGTCTTTGG-T-ACAGATAACCCTTCTAGCCTTAAGTTATACTGTAAATGATGTGC
* * * * * *
46760 CCTCCAAGCTGAGAGTAATTGAACTCGAGGGTC-TTTGGCAGATAGCCCTTCTCGACTTAAGCTA
64 CCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAGCTA
46824 TACTGCAAATGATGTGCCTT-AGAGCTGAGCGTAGTC
129 TACTGCAAATGATGTGCCTTGA-AGCTGAGCGTAGTC
* *
46860 GAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
1 GAACTCGAAGGTC-TTTGGT-ACAGATAACCCTTCTAGCCTTAAGTTATACTGTAAATGATGTGC
* ** * *
46925 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTGGCAGATAGCCCTTCTCGACTTAAGCTA
64 CCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAGCTA
*
46989 TACTGCAAATGATGTGCCGTTG-AGCTGAGCATAGTC
129 TACTGCAAATGATGTGCC-TTGAAGCTGAGCGTAGTC
* * * * * *
47025 GAACTCAAAGGTCTTTGGTGGCAGACAACCCTTCTAGATCC--AAGTTGTGCTGTAAATGATATG
1 GAACTCGAAGGTCTTTGGT-ACAGATAACCCTTCTAG--CCTTAAGTTATACTGTAAATGATGTG
* * * * * *
47088 -CCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTGA
63 CCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGG---CAGATAACCCTTCTAGACTTAA
** * * * * *
47152 TTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATC
125 GCTATACTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTC
** * * * * * * *
47193 GAACTCGGGGGTCTTTGG--CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGTCG
1 GAACTCGAAGGTCTTTGGTACAGATAACCCTTCTAGCCTTAAGTTATACTGTAAATGATGTGCCC
* * * * * *
47256 TTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTT
66 TCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGG---CAGATAACCCTTCTAGACTTAAGCT
* * * *
47320 ATACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATC
128 ATACTGCAAATGATGTG-CCTTGAAGCTGAGCGTAGTC
** * * * * * *
47358 GAACTCGGGGGTCTTTGG--CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCG
1 GAACTCGAAGGTCTTTGGTACAGATAACCCTTCTAGCCTTAAGTTATACTGTAAATGATGTGCCC
* * * * * *
47421 TTG-AGCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGA-TTCAAGT
66 TCGAAGCTGAGCGTAATCGAACTCGAAGGTC-TT--TTGGCAGATAACCCTTCTAGACTT-AAGC
* * * *
47484 TGTGCTGCAAATGATATGCCTTGAAGCTGAGCGTACTC
127 TATACTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTC
* * *
47522 GAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
1 GAACTCGAAGGTC-TTTGGT-ACAGATAACCCTTCTAGCCTTAAGTTATACTGTAAATGATGTGC
* ** *
47587 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTTGGCAGATAACCCTTCTTGACTTAAGCTA
64 CCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAGCTA
*
47651 TACTGCAAATGATGTACCGTTG-AGCTGAGCGTAGTC
129 TACTGCAAATGATGTGCC-TTGAAGCTGAGCGTAGTC
* *
47687 GAACTCAAAGGTCTTTGGTGGCAGATAACCCTTCTAG
1 GAACTCGAAGGTCTTTGGT-ACAGATAACCCTTCTAG
47724 ATCCAAGTTG
Statistics
Matches: 743, Mismatches: 96, Indels: 51
0.83 0.11 0.06
Matches are distributed among these distances:
163 27 0.04
164 96 0.13
165 472 0.64
166 19 0.03
167 37 0.05
168 71 0.10
169 21 0.03
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (164 bp):
GAACTCGAAGGTCTTTGGTACAGATAACCCTTCTAGCCTTAAGTTATACTGTAAATGATGTGCCC
TCGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGACTTAAGCTATA
CTGCAAATGATGTGCCTTGAAGCTGAGCGTAGTC
Found at i:47210 original size:413 final size:413
Alignment explanation
Indices: 46716--47723 Score: 1777
Period size: 413 Copynumber: 2.4 Consensus size: 413
46706 TCTTCGGTTG
** * * * *
46716 ACAGATAACCCTTCTAGCCTTGAGTTATATTGTGAATGATGTGCCCTCCAAGCTGAGAGTAATTG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
*
46781 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTT-G
* *
46846 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGC
130 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATAC
46911 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTC
195 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTC
*
46976 TCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCATAGTCGAACTCAAAGGTCTTT
260 TCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCATAGTCAAACTCAAAGGTCTTT
* *
47041 GG-TGGCAGACAACCCTTCTAGATCCAAGTTGTGCTGTAAATGATATGCCTTGGAGCTGAGCGTA
325 GGTTGGCAGACAACCCTTCTAGATCCAAGTTGTGCTGCAAATGATATGCCTTGAAGCTGAGCGTA
*
47105 GTCGAACTCGAAGATCTTTTGGTC
390 CTCGAACTCGAAGATCTTTTGGTC
*
47129 ACAGATAACCCTTCTAGCCTTGATTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
*
47194 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGTCGTTG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTG
47259 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATAC
130 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATAC
47324 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTC
195 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTC
*
47389 TCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCAAACTCAAAGGTCTTT
260 TCGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCATAGTCAAACTCAAAGGTCTTT
*
47454 GGTTGGCAGACAACCCTTCTAGATTCAAGTTGTGCTGCAAATGATATGCCTTGAAGCTGAGCGTA
325 GGTTGGCAGACAACCCTTCTAGATCCAAGTTGTGCTGCAAATGATATGCCTTGAAGCTGAGCGTA
47519 CTCGAACTCGAAGATCTTTTGGTC
390 CTCGAACTCGAAGATCTTTTGGTC
47543 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
* * *
47608 AACTCGGGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATACTGCAAATGATGTACCGTTG
66 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCC-TTG
**
47673 AGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTGGCAGATAACCCTTCTAG
130 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAG
47724 ATCCAAGTTG
Statistics
Matches: 568, Mismatches: 24, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
413 333 0.59
414 235 0.41
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (413 bp):
ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
AACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGA
GCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATACT
GTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCT
CGACTTAAGCTATACTGCAAATGATGTGCCGTTGAGCTGAGCATAGTCAAACTCAAAGGTCTTTG
GTTGGCAGACAACCCTTCTAGATCCAAGTTGTGCTGCAAATGATATGCCTTGAAGCTGAGCGTAC
TCGAACTCGAAGATCTTTTGGTC
Found at i:47514 original size:249 final size:248
Alignment explanation
Indices: 46798--47749 Score: 946
Period size: 249 Copynumber: 3.8 Consensus size: 248
46788 GGGTCTTTGG
* * * * * * * * * * *
46798 CAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAG-AGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
** * * * * * *
46862 ACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
66 ACTCGGGGGTC-TTTGG---CAGATAACCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCG
* * * *** * * *
46927 TCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTT-AAGC
127 TTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGA-TTCAAGT
* * * * **
46987 TATACTGCAAATGATGTGCCGTTGAGCTGAGCATAGTCGAACTCAAAGGTC-TTTGGTGG
190 TGTGCTGCAAATGATATGCC-TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
* * * * * * * *
47046 CAGACAACCCTTCTAGATCC--AAGTTGTGCTGTAAATGATATG-CCTTGGAGCTGAGCGTAGTC
1 CAGATAACCCTTCTAG--CCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATC
** * * * ** * *
47108 GAACTCGAAGATCTTTTGGTCACAGATAACCCTTCTAGCCTTGATTTATGCTGTAAATGATGTGC
64 GAACTCGGGGGTC-TTTGG---CAGATAACCCTTCTAGACTTAAGCTATACTGCAAATGATGTGC
* * * * *** * *
47173 CCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTT-AA
125 CGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGA-TTCAA
* * * * *
47233 GCTATACTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
188 GTTGTGCTGCAAATGATATG-CCTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
*
47295 CAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
* *
47360 ACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTTGA
66 ACTCGGGGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCGTTGA
* *
47425 GCTGAGCGTAGTCAAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGATTCAAGTTGTGCT
131 GCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGATTCAAGTTGTGCT
* * *
47490 GCAAATGATATGCCTTGAAGCTGAGCGTACTCGAACTCGAAGATCTTTTGGTCA
196 GCAAATGATATGCCTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
47544 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
* *
47609 ACTCGGGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATACTGCAAATGATGTACCGTTGA
66 ACTCGGGGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCGTTGA
*
47674 GCTGAGCGTAGTCGAACTCAAAGGTCTTTGG-TGGCAGATAACCCTTCTAGATCCAAGTTGTGCT
131 GCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGATTCAAGTTGTGCT
*
47738 GTAAATGATATG
196 GCAAATGATATG
47750 TTTAAAAAAT
Statistics
Matches: 626, Mismatches: 64, Indels: 28
0.87 0.09 0.04
Matches are distributed among these distances:
245 21 0.03
246 38 0.06
247 6 0.01
248 264 0.42
249 270 0.43
250 27 0.04
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (248 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
ACTCGGGGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATACTGCAAATGATGTGCCGTTGA
GCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTAGATTCAAGTTGTGCT
GCAAATGATATGCCTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
Found at i:50845 original size:18 final size:19
Alignment explanation
Indices: 50804--50848 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
50794 AGTTAATGTG
50804 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
50823 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
50841 AATGCAAA
1 AATGCAAA
50849 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:53996 original size:31 final size:31
Alignment explanation
Indices: 53961--54025 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
53951 TACAAAATGA
53961 TCACCAGACTATTCATTTTGTTCCAAACTCG
1 TCACCAGACTATTCATTTTGTTCCAAACTCG
*
53992 TCACCAGACTATTCATTTTTTTCCAAACTCG
1 TCACCAGACTATTCATTTTGTTCCAAACTCG
54023 TCA
1 TCA
54026 TTTTCAGTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.26, C:0.29, G:0.08, T:0.37
Consensus pattern (31 bp):
TCACCAGACTATTCATTTTGTTCCAAACTCG
Found at i:54609 original size:14 final size:15
Alignment explanation
Indices: 54578--54615 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
54568 GTTATTATTT
*
54578 TTTAAAAAAATATCA
1 TTTAAAAATATATCA
54593 TTTAAAAATATAT-A
1 TTTAAAAATATATCA
*
54607 TTTTAAAAT
1 TTTAAAAAT
54616 CTAAACGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTAAAAATATATCA
Found at i:54931 original size:54 final size:54
Alignment explanation
Indices: 54831--54933 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
54821 AACTCCCAGT
* * *
54831 TTTTAACTTTCCGTCTAATGCATTAGACCAATCGTGAAGTTCCACGCGCGCCCA
1 TTTTAACTTTCCGTCTAATGCATTACACCAAGCGTGAAGATCCACGCGCGCCCA
*
54885 TTTTAACTTTCCG-CTAATTGCATTACATCAAGCGTGAA-ATCGCACGCGC
1 TTTTAACTTTCCGTCTAA-TGCATTACACCAAGCGTGAAGATC-CACGCGC
54934 AACGGTTAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
53 6 0.14
54 37 0.86
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (54 bp):
TTTTAACTTTCCGTCTAATGCATTACACCAAGCGTGAAGATCCACGCGCGCCCA
Found at i:57085 original size:2 final size:2
Alignment explanation
Indices: 57078--57104 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
57068 TAGATTTTCG
57078 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 T
57105 TATTAATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:67867 original size:284 final size:279
Alignment explanation
Indices: 67349--68463 Score: 1293
Period size: 282 Copynumber: 3.9 Consensus size: 279
67339 TTAATGACTA
* * * * * * * * * *
67349 AAATGTGGAAGACGGAAATTGGAAAAATCGCTACGAGTTTTCCCGATTATATGGCTATCATATAT
1 AAATGTGGAAGATGAAAATCGGTAAAATCACTACAAGTTCTCCCGATTATATGACCATCATACAT
* * *
67414 GTTTACACTAATTATATAAGACCCCTCCATCACCATTC-GAGCCTATGACAATTAACAATGTTAA
66 GTTTACACTAATTATATAAGACCCCTCCATCACCATTCACAACCTATGACAACTAACAATGTTAA
* * *
67478 ACTACAAGCTTGAAAACTCAATCACTGTCTTTACCAATAATTCAATTTCATCGCCAAATTTACAC
131 ACTACAAGTTTGAAAACTCAATCACTGTCTTGACCAATCATTCAATTTCATCGCCAAATTTA-AC
* ** *
67543 ACACTTATCGATCCATGAGCTCGACTAACTTCAGCGACGAGAGGTTACCTAATGACTATAACTTA
195 ACACTTATCGATCCATGAGCTCGACTAACTTCAACGACGAGAAATTACCTAATGACTA-AACATA
67608 AACTAACATATCATTATACTAGC
259 AACTAAC--ATCATTATACTAGC
* * * * * *
67631 ATAATTTGGAAGATGGAAATTGGTGAAATCACTACGATTTCTCCCGATTATATGACCATCATACA
1 A-AATGTGGAAGATGAAAATCGGTAAAATCACTACAAGTTCTCCCGATTATATGACCATCATACA
* * *
67696 TGTTTACACTAACTATATAAGACCCCTCCATCACCATTCCCAACCTATGACAACTAACAATGTTC
65 TGTTTACACTAATTATATAAGACCCCTCCATCACCATTCACAACCTATGACAACTAACAATGTTA
* ** * *
67761 AACTACAAGTTTGAAAACTCAATCACTGTCTAGACCAATCATTTGATTTCATTGCCAAATTTACT
130 AACTACAAGTTTGAAAACTCAATCACTGTCTTGACCAATCATTCAATTTCATCGCCAAATTTA-A
* * *
67826 CGCACTTATCGATCCATGAGCTCAATTAACTTCAACGACGAGAAATTACCTAATGACTAAAACAT
194 CACACTTATCGATCCATGAGCTCGACTAACTTCAACGACGAGAAATTACCTAATGACT-AAACAT
*
67891 AAACTAACAGCATTATACTAGC
258 AAACTAACATCATTATACTAGC
* *
67913 ACAATGTGGAAGATGAAAATCAGTAAAATCACTACAAGTTCTCCCGATTATATGACCGTCATACA
1 A-AATGTGGAAGATGAAAATCGGTAAAATCACTACAAGTTCTCCCGATTATATGACCATCATACA
* * * *
67978 TGTTTACACTAATTATAAAAGGCCCCTCCGTCACCATTCACAACCTATGACAACGAACAATGTTA
65 TGTTTACACTAATTATATAAGACCCCTCCATCACCATTCACAACCTATGACAACTAACAATGTTA
* * **
68043 AACTACAAGTTTGAAAACTCGATCACTATCTTGACCAATCATTTGATTTCATCGCCAAATTT-AC
130 AACTACAAGTTTGAAAACTCAATCACTGTCTTGACCAATCATTCAATTTCATCGCCAAATTTAAC
*
68107 ACACTTA-CTGATCCATGAGCTCGATTAACTTCAACGACGAGAAATTACCTAATG-----AC-T-
195 ACACTTATC-GATCCATGAGCTCGACTAACTTCAACGACGAGAAATTACCTAATGACTAAACATA
*
68164 --CGAACATCATTATACTAGC
259 AACTAACATCATTATACTAGC
* * *
68183 AACATGTGGAAGATGAAAATCGGTAAAATCAGTATAAGTTCTCCCGATTATATGACCA-CTGTAC
1 AA-ATGTGGAAGATGAAAATCGGTAAAATCACTACAAGTTCTCCCGATTATATGACCATC-ATAC
68247 ATGTTTACACTAATATATAAGAGTATAAGACCCCTCCATCACCATTCACAACCTCTGAGGCTATG
64 ATGTTTACACT-A-AT-T---A-TATAAGACCCCTCCATCACCATTCACAA---C-----CTATG
* ** * * *
68312 ACAGCTAACAATGTTAAACTACAAGTTTGAAAACTCGGTCGCTGTCTTGACTAATCATTCAATAT
114 ACAACTAACAATGTTAAACTACAAGTTTGAAAACTCAATCACTGTCTTGACCAATCATTCAATTT
* * * * * *
68377 CATTGCCAAATTTGAACACACTTATCGATCCATAAGCTCGACTAACATCAACTATGAGAAGTTAC
179 CATCGCCAAATTT-AACACACTTATCGATCCATGAGCTCGACTAACTTCAACGACGAGAAATTAC
*
68442 CCAATGACTAGAACATAAACTA
243 CTAATGACTA-AACATAAACTA
68464 GCATAATTTG
Statistics
Matches: 717, Mismatches: 82, Indels: 53
0.84 0.10 0.06
Matches are distributed among these distances:
269 2 0.00
270 83 0.12
271 1 0.00
272 2 0.00
273 2 0.00
274 2 0.00
276 1 0.00
277 25 0.03
279 1 0.00
280 52 0.07
282 186 0.26
283 91 0.13
284 142 0.20
285 74 0.10
287 47 0.07
288 1 0.00
293 2 0.00
294 1 0.00
297 2 0.00
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.28
Consensus pattern (279 bp):
AAATGTGGAAGATGAAAATCGGTAAAATCACTACAAGTTCTCCCGATTATATGACCATCATACAT
GTTTACACTAATTATATAAGACCCCTCCATCACCATTCACAACCTATGACAACTAACAATGTTAA
ACTACAAGTTTGAAAACTCAATCACTGTCTTGACCAATCATTCAATTTCATCGCCAAATTTAACA
CACTTATCGATCCATGAGCTCGACTAACTTCAACGACGAGAAATTACCTAATGACTAAACATAAA
CTAACATCATTATACTAGC
Found at i:69791 original size:15 final size:17
Alignment explanation
Indices: 69760--69791 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
69750 TATTAATGTA
69760 TGAATCATTTATATTTT
1 TGAATCATTTATATTTT
69777 TGAAT-ATTT-TATTTT
1 TGAATCATTTATATTTT
69792 AATAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.62
Consensus pattern (17 bp):
TGAATCATTTATATTTT
Found at i:70965 original size:33 final size:35
Alignment explanation
Indices: 70902--70975 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 35
70892 AATTGAATTT
*
70902 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAATTTAGGGTTTAGAATGA
*
70937 AATTGAA-TACTTTGGAA-TTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAATTTAGGGTTTAGAATGA
70970 AATTGA
1 AATTGA
70976 GGACTGTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 21 0.57
34 9 0.24
35 7 0.19
ACGTcount: A:0.35, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAATTTAGGGTTTAGAATGA
Found at i:73612 original size:20 final size:21
Alignment explanation
Indices: 73556--73613 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
73546 GTTGATCGTT
*
73556 ACGGTGCTGACGTGGTAATTC
1 ACGGTGCTGACGTGGCAATTC
* * **
73577 ACAGTGATGATATGGCAA-TC
1 ACGGTGCTGACGTGGCAATTC
73597 ACGGTGCTGACGTGGCA
1 ACGGTGCTGACGTGGCA
73614 TTCCACAATG
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (21 bp):
ACGGTGCTGACGTGGCAATTC
Done.