Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006913.1 Hibiscus syriacus cultivar Beakdansim tig00017711_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: 61127
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:2191 original size:2 final size:2
Alignment explanation
Indices: 2184--2211 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2174 ACAGGTAATT
2184 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
2212 AAAGATGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2825 original size:18 final size:17
Alignment explanation
Indices: 2804--2850 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
2794 TTTATGTCTC
2804 TTAAATGTTAAAAT-ATA
1 TTAAAT-TTAAAATAATA
2821 TTTAAAATTTAAAATAATA
1 -TT-AAATTTAAAATAATA
2840 TTAAATATTAA
1 TTAAAT-TTAA
2851 TTTTATTAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.15
18 15 0.58
19 7 0.27
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
TTAAATTTAAAATAATA
Found at i:3659 original size:8 final size:8
Alignment explanation
Indices: 3628--3661 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
3618 TAGTTCAATT
*
3628 ATTTTATA
1 ATTTTAAA
3636 ATTTTAATA
1 ATTTTAA-A
3645 ATTTTAAA
1 ATTTTAAA
3653 ATTTTAAA
1 ATTTTAAA
3661 A
1 A
3662 ATATAAAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
ATTTTAAA
Found at i:3902 original size:2 final size:2
Alignment explanation
Indices: 3895--3922 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3885 CAGATTCCGT
3895 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3923 AAAGGGATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:7022 original size:49 final size:51
Alignment explanation
Indices: 6932--7075 Score: 211
Period size: 50 Copynumber: 2.8 Consensus size: 51
6922 TAACTCATAT
*
6932 TAAAAAAATGTAGCACTTAACATATACTTACACCGGTGTAAGTGAATAAAA
1 TAAAAAAATGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAA
* *
6983 -CAAAAAATGTAGCACTTAACACATAC-TACATCGGTGTAAGTGAATAAAA
1 TAAAAAAATGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAA
* * *
7032 TAAAAAAAGTGTAACACTTTACACATACTTACACCGATGTAAGT
1 TAAAAAAA-TGTAGCACTTAACACATACTTACACCGGTGTAAGT
7076 ATTTACATCT
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
49 22 0.27
50 30 0.37
51 17 0.21
52 13 0.16
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (51 bp):
TAAAAAAATGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAA
Found at i:7242 original size:65 final size:65
Alignment explanation
Indices: 7158--7303 Score: 167
Period size: 65 Copynumber: 2.2 Consensus size: 65
7148 TTTCAAAGAA
* *
7158 ATAAAAAATTAAAAATAATA-AAATATATATATTAAGTTATTTGTATA-CAAA-T-GTTAT-TAA
1 ATAATAAATTATAAATAATAGAAA-AT-TATATTAAGTTA--TGTATATCAAATTAGTTATGTAA
7218 AAAT
62 AAAT
* * *
7222 ATATATAAATTATAAATAATAGAAACTTATATTAAGTTATGTATATTAAATTATTTATGTAAAAA
1 ATA-ATAAATTATAAATAATAGAAAATTATATTAAGTTATGTATATCAAATTAGTTATGTAAAAA
7287 T
65 T
7288 ATAATAAATTATAAAT
1 ATAATAAATTATAAAT
7304 TTAATTGTAA
Statistics
Matches: 71, Mismatches: 5, Indels: 11
0.82 0.06 0.13
Matches are distributed among these distances:
62 6 0.08
63 3 0.04
64 16 0.23
65 33 0.46
66 13 0.18
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (65 bp):
ATAATAAATTATAAATAATAGAAAATTATATTAAGTTATGTATATCAAATTAGTTATGTAAAAAT
Found at i:17431 original size:276 final size:275
Alignment explanation
Indices: 16934--17464 Score: 823
Period size: 276 Copynumber: 1.9 Consensus size: 275
16924 ATCTTCAATC
* * * *
16934 TTTCAGCTACTTTTAGATGTCATTTATTGCAACAATAATGCACCGTTTCAACTACTTTTCAGATG
1 TTTCAGCTACTTTTAGAGGTCATTTATTGCAACAATAATACACCGTTTCAACTAATTTTCAAATG
* * * *
16999 TCATTTAATGCATAATTCAAGAAAGTATTCAGAAAACGGGTCAAAATAGTGTTGCATTATCATCT
66 TAATTTAATGCAGAATTCAAGAAACTATTCAGAAAACGGGTCAAAATAATGTTGCATTATCATCT
17064 TCTGCAACTTCTCAGTGATATATCAACTCAAATCAGAAAAAAAATTCAGTGTTGAATTGTCACTT
131 TCTGCAACTTCTCAGTGATATATCAACTCAAATCAGAAAAAAAATTCAGTGTTGAATTGTCACTT
* * *
17129 CAAATCATAAAAAAGTGTAGTTTAACCAGGCCAAATTATTCACTGCTTCAACTACTTTTCGATGC
196 CAAATCATAAAAAAATGTAGTTTAACCAGACCAAATTATTCACTGATTCAACTACTTTTCGATGC
17194 TCAATTAATACATCG
261 TCAATTAATACATCG
* * *
17209 TTTCAGCTACTTTTCAGAGGTCATTTATTGTAGCAATAATACACCGTTTCACCTAATTTTCAAAT
1 TTTCAGCTACTTTT-AGAGGTCATTTATTGCAACAATAATACACCGTTTCAACTAATTTTCAAAT
* *
17274 GTAATTTAATGCAGAATTCAAGCAACTATTCAGAAAACGGGTGAAAATAATGTTGCATTATCATC
65 GTAATTTAATGCAGAATTCAAGAAACTATTCAGAAAACGGGTCAAAATAATGTTGCATTATCATC
* * * *
17339 TTTTGCAACTTCTTAGTGATATATCAACTCAAAT-A-AAAAAAAATTTCATTGTTTAATTGTCAC
130 TTCTGCAACTTCTCAGTGATATATCAACTCAAATCAGAAAAAAAA-TTCAGTGTTGAATTGTCAC
* *
17402 TTCAAATCATAAAAAATATGTATTTTAACCAGACCAAATTATTCACTTATTCAACTACTTTTC
194 TTCAAATCATAAAAAA-ATGTAGTTTAACCAGACCAAATTATTCACTGATTCAACTACTTTTC
17465 ATAGGTCATT
Statistics
Matches: 231, Mismatches: 22, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
274 8 0.03
275 48 0.21
276 175 0.76
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (275 bp):
TTTCAGCTACTTTTAGAGGTCATTTATTGCAACAATAATACACCGTTTCAACTAATTTTCAAATG
TAATTTAATGCAGAATTCAAGAAACTATTCAGAAAACGGGTCAAAATAATGTTGCATTATCATCT
TCTGCAACTTCTCAGTGATATATCAACTCAAATCAGAAAAAAAATTCAGTGTTGAATTGTCACTT
CAAATCATAAAAAAATGTAGTTTAACCAGACCAAATTATTCACTGATTCAACTACTTTTCGATGC
TCAATTAATACATCG
Found at i:17568 original size:46 final size:45
Alignment explanation
Indices: 17451--17568 Score: 121
Period size: 46 Copynumber: 2.6 Consensus size: 45
17441 TATTCACTTA
* * * **
17451 TTCAACTACTTTTCATAGGTCATTTATTGCAGCAATAATGCATCGT
1 TTCAGCTACTTTTCAGAGGTCATTTATTACAAAAATAAT-CATCGT
* *
17497 TTCAGCTACTTTTCAGATGTAATTTATTACAAAAATAAT-ATACTGT
1 TTCAGCTACTTTTCAGAGGTCATTTATTACAAAAATAATCAT-C-GT
* *
17543 TTTAGCTACTTTTTAGAGGTCATTTA
1 TTCAGCTACTTTTCAGAGGTCATTTA
17569 ATGCAGAATT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
44 2 0.03
45 1 0.02
46 56 0.95
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (45 bp):
TTCAGCTACTTTTCAGAGGTCATTTATTACAAAAATAATCATCGT
Found at i:18976 original size:19 final size:19
Alignment explanation
Indices: 18952--18989 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
18942 CAAATCCTAT
18952 AATTT-ACCTTAATTTTTAA
1 AATTTAACC-TAATTTTTAA
*
18971 AATTTAACCTATTTTTTAA
1 AATTTAACCTAATTTTTAA
18990 CTGGAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53
Consensus pattern (19 bp):
AATTTAACCTAATTTTTAA
Found at i:21009 original size:23 final size:23
Alignment explanation
Indices: 20973--21050 Score: 113
Period size: 23 Copynumber: 3.4 Consensus size: 23
20963 AAAACTACCA
* * *
20973 AAAGACAAAGATAAACGTGTCAC
1 AAAGATAAATATAAACGTATCAC
20996 AAAGATAAATATAAACGTATCAC
1 AAAGATAAATATAAACGTATCAC
21019 -AAGAATAAATATAAACGTATCAC
1 AAAG-ATAAATATAAACGTATCAC
21042 AAAGATAAA
1 AAAGATAAA
21051 ATTATTTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
22 3 0.06
23 44 0.88
24 3 0.06
ACGTcount: A:0.58, C:0.13, G:0.12, T:0.18
Consensus pattern (23 bp):
AAAGATAAATATAAACGTATCAC
Found at i:26605 original size:14 final size:14
Alignment explanation
Indices: 26586--26615 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
26576 TTTATATTTT
*
26586 TTAAAATTACATTA
1 TTAAAAATACATTA
26600 TTAAAAATACATTA
1 TTAAAAATACATTA
26614 TT
1 TT
26616 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:26705 original size:7 final size:7
Alignment explanation
Indices: 26693--26736 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
26683 AATTATGTAA
26693 TAGGGTT
1 TAGGGTT
26700 TAGGGTT
1 TAGGGTT
*
26707 TAGGATT
1 TAGGGTT
*
26714 TAGTGTT
1 TAGGGTT
*
26721 TAAGGTT
1 TAGGGTT
*
26728 TAAGGTT
1 TAGGGTT
26735 TA
1 TA
26737 AGTTATGCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (7 bp):
TAGGGTT
Found at i:29487 original size:11 final size:11
Alignment explanation
Indices: 29471--29574 Score: 136
Period size: 11 Copynumber: 9.5 Consensus size: 11
29461 ACTTAACCTG
*
29471 TCGAGCTTAAA
1 TCGAGCTTGAA
*
29482 TCGAGCTTGAG
1 TCGAGCTTGAA
*
29493 TCGAGCTTAAA
1 TCGAGCTTGAA
*
29504 TCGAGCTTGAG
1 TCGAGCTTGAA
*
29515 TCGAGCTTAAA
1 TCGAGCTTGAA
*
29526 TCGAGCTTGAG
1 TCGAGCTTGAA
29537 TCGAGCTTGAA
1 TCGAGCTTGAA
*
29548 TCGAGCTTGAG
1 TCGAGCTTGAA
*
29559 TCAAGCTTGAA
1 TCGAGCTTGAA
29570 TCGAG
1 TCGAG
29575 TTCGAGTCTT
Statistics
Matches: 78, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 78 1.00
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:29495 original size:22 final size:22
Alignment explanation
Indices: 29470--29582 Score: 183
Period size: 22 Copynumber: 5.1 Consensus size: 22
29460 AACTTAACCT
29470 GTCGAGCTTAAATCGAGCTTGA
1 GTCGAGCTTAAATCGAGCTTGA
29492 GTCGAGCTTAAATCGAGCTTGA
1 GTCGAGCTTAAATCGAGCTTGA
29514 GTCGAGCTTAAATCGAGCTTGA
1 GTCGAGCTTAAATCGAGCTTGA
*
29536 GTCGAGCTTGAATCGAGCTTGA
1 GTCGAGCTTAAATCGAGCTTGA
* *
29558 GTCAAGCTTGAATCGAG-TTCGA
1 GTCGAGCTTAAATCGAGCTT-GA
29580 GTC
1 GTC
29583 TTGAGTTTCA
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
21 2 0.02
22 86 0.98
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (22 bp):
GTCGAGCTTAAATCGAGCTTGA
Found at i:36884 original size:43 final size:42
Alignment explanation
Indices: 36831--37200 Score: 327
Period size: 43 Copynumber: 8.6 Consensus size: 42
36821 TGACAACATA
* *
36831 TAGCAGCGTTTGTTGAACAAACGCCGCAATAGGTGTTGATATT
1 TAGCGGCGTTT-TTCAACAAACGCCGCAATAGGTGTTGATATT
* * *
36874 TAGCGACGTTTGTCAGACAAACACCGCAATAGGTGTTGATATT
1 TAGCGGCGTTTTTCA-ACAAACGCCGCAATAGGTGTTGATATT
* * *
36917 TAGCGGCATTTGTCAGACAAACGCCGCAATAGGTGTTGATGTT
1 TAGCGGCGTTTTTCA-ACAAACGCCGCAATAGGTGTTGATATT
* * * *
36960 TAGCGGCATTTTTCTCACAAACGTCGCAGTAGGTGTTGATGATT
1 TAGCGGCGTTTTTC-AACAAACGCCGCAATAGGTGTTGAT-ATT
* ** * *
37004 T-GCGGCGTTTTCCCCTCAAACGCCGCAGTAGGTGTTGATGTT
1 TAGCGGCGTTTT-TCAACAAACGCCGCAATAGGTGTTGATATT
* * * * *
37046 TAGCGGCGTTTTATC-ATAAACGTCGTAGTAGGTGTTGATGTTT
1 TAGCGGCGTTTT-TCAACAAACGCCGCAATAGGTGTTGAT-ATT
* * * *
37089 TA-CTGCGTTTTTGCCTA-AAACGCCGCAGTAGGTGTTGATGTT
1 TAGCGGCGTTTTT--CAACAAACGCCGCAATAGGTGTTGATATT
* *
37131 TAGCGGCGTTTTT-ATCGCAAACGCCGCAATAGGTGTTGAAATT
1 TAGCGGCGTTTTTCA--ACAAACGCCGCAATAGGTGTTGATATT
*
37174 TCGCGGCGTTTTTCATACAAACGCCGC
1 TAGCGGCGTTTTTCA-ACAAACGCCGC
37201 TAAAGGTCGA
Statistics
Matches: 274, Mismatches: 39, Indels: 28
0.80 0.11 0.08
Matches are distributed among these distances:
41 1 0.00
42 37 0.14
43 230 0.84
44 6 0.02
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (42 bp):
TAGCGGCGTTTTTCAACAAACGCCGCAATAGGTGTTGATATT
Found at i:37127 original size:128 final size:128
Alignment explanation
Indices: 36847--37200 Score: 373
Period size: 128 Copynumber: 2.8 Consensus size: 128
36837 CGTTTGTTGA
* * * *
36847 ACAAACGCCGCAATAGGTGTTGAT-ATTTAGCGACGTTTGTCAGACAAACACCGCAATAGGTGTT
1 ACAAACGCCGCAGTAGGTGTTGATGATTTAGCGGCGTTT-TCACACAAACGCCGCAATAGGTGTT
* * *
36911 GATATTTAGCGGCATTTGTCA-GACAAACGCCGCAATAGGTGTTGATGTTTAGCGGCATTTTTCT
65 GATATTTAGCGGCGTTT-T-ATCATAAACGCCGCAATAGGTGTTGATGTTTAGCGGCATTTTTCT
36975 C
128 C
* * * *
36976 ACAAACGTCGCAGTAGGTGTTGATGATTT-GCGGCGTTTTCCCCTCAAACGCCGCAGTAGGTGTT
1 ACAAACGCCGCAGTAGGTGTTGATGATTTAGCGGCGTTTT-CACACAAACGCCGCAATAGGTGTT
* * * * * *
37040 GATGTTTAGCGGCGTTTTATCATAAACGTCGTAGTAGGTGTTGATGTTTTA-CTGCGTTTTTGC-
65 GATATTTAGCGGCGTTTTATCATAAACGCCGCAATAGGTGTTGATG-TTTAGCGGCATTTTT-CT
37103 C
128 C
* *
37104 TA-AAACGCCGCAGTAGGTGTTGATG-TTTAGCGGCGTTTTTATCGCAAACGCCGCAATAGGTGT
1 -ACAAACGCCGCAGTAGGTGTTGATGATTTAGCGGCGTTTTCA-CACAAACGCCGCAATAGGTGT
* *
37167 TGAAATTTCGCGGCGTTTT-TCATACAAACGCCGC
64 TGATATTTAGCGGCGTTTTATCAT--AAACGCCGC
37201 TAAAGGTCGA
Statistics
Matches: 188, Mismatches: 27, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
127 8 0.04
128 99 0.53
129 77 0.41
130 4 0.02
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (128 bp):
ACAAACGCCGCAGTAGGTGTTGATGATTTAGCGGCGTTTTCACACAAACGCCGCAATAGGTGTTG
ATATTTAGCGGCGTTTTATCATAAACGCCGCAATAGGTGTTGATGTTTAGCGGCATTTTTCTC
Found at i:37634 original size:21 final size:20
Alignment explanation
Indices: 37610--37676 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
37600 GTTGATATGT
*
37610 TGCTTCTGTCTGTGCTGTCGC
1 TGCTTCTCTCTGTGCT-TCGC
* *
37631 TGCTTCTCTCTGTACTACCGC
1 TGCTTCTCTCTGTGCT-TCGC
* *
37652 TGCTTCTTTCTCTGCTTCTGC
1 TGCTTCTCTCTGTGCTTC-GC
37673 TGCT
1 TGCT
37677 GCTTCCACTG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 1 0.03
21 36 0.97
ACGTcount: A:0.03, C:0.33, G:0.19, T:0.45
Consensus pattern (20 bp):
TGCTTCTCTCTGTGCTTCGC
Found at i:44944 original size:12 final size:12
Alignment explanation
Indices: 44927--44951 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44917 AATTAAAGTC
44927 ACCACTTTGTGA
1 ACCACTTTGTGA
44939 ACCACTTTGTGA
1 ACCACTTTGTGA
44951 A
1 A
44952 GTTTCACATA
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:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (12 bp):
ACCACTTTGTGA
Found at i:46954 original size:3 final size:3
Alignment explanation
Indices: 46929--46975 Score: 67
Period size: 3 Copynumber: 15.0 Consensus size: 3
46919 TTGGGTTTTG
*
46929 TAA TAT TAA TAAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
46976 ATTTTAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 34 0.85
4 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:47323 original size:124 final size:123
Alignment explanation
Indices: 47190--47416 Score: 346
Period size: 124 Copynumber: 1.8 Consensus size: 123
47180 GACCTATTTC
* * * * * * * *
47190 CTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGTTCTTCTTATTTTGAACTTCTTCTTTCTTT
1 CTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC-TTCCTC
* *
47255 TTCAGATGAGTTCTTCTTATTATGAACTTTCTCTGGAAAGGTTTATGCTAATCTATCTG
65 TTCAAATAAGTTCTTCTTATTATGAACTTTCTCTGGAAAGGTTTATGCTAATCTATCTG
*
47314 CTTCTGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCT
1 CTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCT
47379 TCAAATAAGTTCTTCTTATTATGAACTTTCTCTGGAAA
66 TCAAATAAGTTCTTCTTATTATGAACTTTCTCTGGAAA
47417 TGTTGATCCA
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
123 41 0.45
124 51 0.55
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (123 bp):
CTTCTGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCT
TCAAATAAGTTCTTCTTATTATGAACTTTCTCTGGAAAGGTTTATGCTAATCTATCTG
Found at i:47662 original size:116 final size:113
Alignment explanation
Indices: 47332--47982 Score: 887
Period size: 116 Copynumber: 5.7 Consensus size: 113
47322 ATAGAATTAT
** * * * * *
47332 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCT-CTTCAAATAAGTTCTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTC
* ** * * *
47396 ATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGA
66 ATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * * * *
47444 ACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAATTCTTCT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTCCTTCAGATGAGTTCTTCT
*
47508 CATTATGAACTCTAACTGGAAAAACTGATCCATCAAGTGATGGATTTGA
65 CATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
47557 GCATAAGGTTGACCAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAAGTAATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTC-AG--ATGAGTTCTT
47622 CTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
63 CTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
47673 GCATAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAAGTAATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTC-AG--ATGAGTTCTT
* *
47738 CTCATTATGAACTCTACCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
63 CTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * *
47789 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTGTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTC
* ** * *
47854 ATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGA
66 ATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * *
47902 GCAAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTT-CTCTCTTCAGATGAGTTCTTCT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTC-CTTCAGATGAGTTCTTCT
47965 CATTATGAACTCTAACTG
65 CATTATGAACTCTAACTG
47983 ACAATGTTGA
Statistics
Matches: 486, Mismatches: 46, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
111 2 0.00
112 103 0.21
113 158 0.33
114 2 0.00
115 2 0.00
116 219 0.45
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTC
ATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
Found at i:47696 original size:229 final size:225
Alignment explanation
Indices: 47332--47982 Score: 923
Period size: 229 Copynumber: 2.9 Consensus size: 225
47322 ATAGAATTAT
** * * *
47332 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTCTTCCTCTTCA-AATAAGTTCTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGAATGAGTTCTTCTT
* * * * *
47396 ATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAG
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGC-AAAGGTTGAACAAG
*
47461 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACTCTAACTG
130 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTG
*
47526 GAAAAACTGATCCATCAAGTGATGGATTTGA
195 GAAAAACTGATCCATCAAATGATGGATTTGA
* *
47557 GCATAAGGTTGACCAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAAGTAATGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCT-CTTC-AG-AATGAGTTCTT
* * **
47622 CTCATTATGAACTCTAACTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCATAAGGTTGAAC
63 CTTATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCA-AAGGTTGAAC
* *
47687 AAATTCTTCTCATTATGAA-TTTCTTCTTCCTCCTTCAAGTAATGAGTTCTTCTCATTATGAACT
127 AAGTTCTTCTCATTATGAACTTT-TTCTTCCTTCTTC-AG--ATGAGTTCTTCTCATTATGAACT
* *
47751 CTACCTGGAAAAGCTGATCCATCAAATGATGGATTTGA
188 CTAACTGGAAAAACTGATCCATCAAATGATGGATTTGA
*
47789 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTGTTCTTCCTTCTTCAG-ATGAGTTCTTCT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGAATGAGTTCTTCT
* * *
47853 TATTATGAACTTTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGTTGAACAAG
65 TATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAGGTTGAACAAG
* *
47918 TTCTTCTTATTATGAACTTCTTCTT-CTCTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACT
130 TTCTTCTCATTATGAACTTTTTCTTCCT-TCTTCAGATGAGTTCTTCTCATTATGAACTCTAACT
47982 G
194 G
47983 ACAATGTTGA
Statistics
Matches: 377, Mismatches: 37, Indels: 24
0.86 0.08 0.05
Matches are distributed among these distances:
225 68 0.18
226 4 0.01
227 5 0.01
228 39 0.10
229 154 0.41
230 2 0.01
231 2 0.01
232 102 0.27
233 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (225 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGAATGAGTTCTTCTT
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAGGTTGAACAAGT
TCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAACTGG
AAAAACTGATCCATCAAATGATGGATTTGA
Found at i:48473 original size:95 final size:95
Alignment explanation
Indices: 48310--48507 Score: 387
Period size: 95 Copynumber: 2.1 Consensus size: 95
48300 CAACATGTTA
*
48310 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACATATATCGATAGT
1 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGT
48375 TCTTTTAATACCGAGAAATCTTGAATTCTG
66 TCTTTTAATACCGAGAAATCTTGAATTCTG
48405 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGT
1 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGT
48470 TCTTTTAATACCGAGAAATCTTGAATTCTG
66 TCTTTTAATACCGAGAAATCTTGAATTCTG
48500 ATTCTGAT
1 ATTCTGAT
48508 GAGGAGAATA
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 102 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (95 bp):
ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCACAGATATCGATAGT
TCTTTTAATACCGAGAAATCTTGAATTCTG
Found at i:49063 original size:83 final size:83
Alignment explanation
Indices: 48924--49311 Score: 713
Period size: 83 Copynumber: 4.7 Consensus size: 83
48914 CTGTGGTTCA
* *
48924 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCAATGAGCACATTCCTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCC
48989 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
*
49007 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCC
49072 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
*
49090 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCC
49155 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
*
49173 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGAACATTACTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCC
49238 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
* *
49256 TACCAAACTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACAT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
49312 GGAATTTGTT
Statistics
Matches: 297, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 297 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.26
Consensus pattern (83 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCC
AAATTCAATGATTGATTT
Found at i:49155 original size:166 final size:166
Alignment explanation
Indices: 48835--49311 Score: 749
Period size: 166 Copynumber: 2.8 Consensus size: 166
48825 GGTTTTATAT
* * * *
48835 CAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCCAAA
*
48900 TTCAATAACTGGTTCTG-TGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
66 TTC---AA-T-GAT-TGAT--TT--TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
* *
48964 GATGCAATGAGCACATTCCTCTTCCAAATTCAATGATTGATTTTAC
121 GATGCTATGAGCACATTACTCTTCCAAATTCAATGATTGATTTTAC
*
49010 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCCAAA
49075 TTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
*
49140 GCACATTATTCTTCCAAATTCAATGATTGATTTTAC
131 GCACATTACTCTTCCAAATTCAATGATTGATTTTAC
*
49176 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGAACATTACTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCCAAA
* *
49241 TTCAATGATTGATTTTACCAAACTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTA
66 TTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
49306 GCACAT
131 GCACAT
49312 GGAATTTGTT
Statistics
Matches: 288, Mismatches: 13, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
166 215 0.75
168 2 0.01
169 2 0.01
170 3 0.01
171 1 0.00
172 2 0.01
175 63 0.22
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (166 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCCAAA
TTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
GCACATTACTCTTCCAAATTCAATGATTGATTTTAC
Found at i:49282 original size:249 final size:254
Alignment explanation
Indices: 48835--49311 Score: 768
Period size: 249 Copynumber: 1.9 Consensus size: 254
48825 GGTTTTATAT
* *
48835 CAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCCAAA
*
48900 TTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
66 TTC-A-AACTGGATCTGT-GTT-ATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* *
48965 ATGCAATGAGCACATTCCTCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTC
127 ATGCAATGAGAACATTACTCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTC
49030 AAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAATGATTGATTTTAC
192 AAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAATGATTGATTTTAC
* * *
49093 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAA
1 CAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCCAAA
49158 TTC-AA-T-GAT-TGAT-TT-TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
66 TTCAAACTGGATCTG-TGTTATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
* *
49217 CTATGAGAACATTACTCTTCCAAATTCAATGATTGATTTTACCAAACTAGATCAGATAACTCAAA
130 CAATGAGAACATTACTCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAA
*
49282 GAACACTTCCAGAAGATGCTATTAGCACAT
195 GAACACTTCCAGAAGATGCTATGAGCACAT
49312 GGAATTTGTT
Statistics
Matches: 207, Mismatches: 11, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
249 134 0.65
251 2 0.01
252 2 0.01
253 3 0.01
254 1 0.00
255 2 0.01
258 63 0.30
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (254 bp):
CAAACCAAATCAGAGAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCCAAA
TTCAAACTGGATCTGTGTTATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
AATGAGAACATTACTCTTCCAAATTCAATGATTGATTTTACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATGAGCACATTATTCTTCCAAATTCAATGATTGATTTTAC
Found at i:50551 original size:7 final size:7
Alignment explanation
Indices: 50539--50576 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
50529 CTTGACCCCC
50539 CTTTTTT
1 CTTTTTT
50546 CTTTTTT
1 CTTTTTT
*
50553 CTTTCTT
1 CTTTTTT
50560 -TTTTTT
1 CTTTTTT
50566 CTTTTTCT
1 CTTTTT-T
50574 CTT
1 CTT
50577 CAAGCATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
6 5 0.19
7 18 0.67
8 4 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
CTTTTTT
Found at i:57920 original size:15 final size:15
Alignment explanation
Indices: 57897--57928 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
57887 TGAAATGAAT
57897 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
57912 AATGCATGTATGCAA
1 AATGAATGTATGCAA
57927 AA
1 AA
57929 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:60654 original size:9 final size:9
Alignment explanation
Indices: 60640--60664 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
60630 TAAACATGCT
60640 TTTAAATAA
1 TTTAAATAA
60649 TTTAAATAA
1 TTTAAATAA
60658 TTTAAAT
1 TTTAAAT
60665 TCACATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTAAATAA
Done.