Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002924.1 Hibiscus syriacus cultivar Beakdansim tig00006043_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: 57526
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:9021 original size:26 final size:26
Alignment explanation
Indices: 8986--9037 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
8976 ATCTGTTTTC
*
8986 ACCCCCTTAAAATTTTATAAGTTCAT
1 ACCCCCTTAAAATTTTATAAATTCAT
*
9012 ACCCCTTTAAAATTTTATAAATTCAT
1 ACCCCCTTAAAATTTTATAAATTCAT
9038 TCCTCTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.40
Consensus pattern (26 bp):
ACCCCCTTAAAATTTTATAAATTCAT
Found at i:11733 original size:11 final size:11
Alignment explanation
Indices: 11717--11749 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
11707 GCATTGTATT
11717 TTATCTTTATC
1 TTATCTTTATC
11728 TTATCTTTA--
1 TTATCTTTATC
11737 TTATCTTTATC
1 TTATCTTTATC
11748 TT
1 TT
11750 TATTTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.45
11 11 0.55
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATCTTTATC
Found at i:11748 original size:15 final size:14
Alignment explanation
Indices: 11723--11753 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
11713 TATTTTATCT
11723 TTATCTTATCTTTA
1 TTATCTTATCTTTA
11737 TTATCTTTATCTTTA
1 TTATC-TTATCTTTA
11752 TT
1 TT
11754 TTTAATTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATCTTATCTTTA
Found at i:14532 original size:27 final size:28
Alignment explanation
Indices: 14500--14552 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
14490 TATTTTTTAA
14500 AATTTTAAATTTTTA-T-ATAATTTAAAT
1 AATTTT-AATTTTTACTAATAATTTAAAT
*
14527 AATTTTTATTTTTACTAATAATTTAA
1 AATTTTAATTTTTACTAATAATTTAA
14553 TTTTACACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 7 0.30
28 9 0.39
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (28 bp):
AATTTTAATTTTTACTAATAATTTAAAT
Found at i:15956 original size:66 final size:64
Alignment explanation
Indices: 15874--16046 Score: 247
Period size: 66 Copynumber: 2.6 Consensus size: 64
15864 CAAAACCTCC
*
15874 AGGGGGTATCGATTCCCCTACAGGGGGAATCGGTTCCCCTACAGGGAGGAATCGATTCCCCTTCA
1 AGGGGGAATCGATTCCCCTACAGGGGGAATCGGTTCCCCTACAGGGAGGAATCGATTCCCC-T-A
15939 A
64 A
* * *
15940 AGGGGGAATCGATTCCCCTTCAAGGGGAATCGGTTCCCCTACAGGGAGGAATCGATTCCCCTAC
1 AGGGGGAATCGATTCCCCTACAGGGGGAATCGGTTCCCCTACAGGGAGGAATCGATTCCCCTAA
* *
16004 AGGGAGGAATCGATTCCCCTTCAAAGGGGGAATCGATTCCCCT
1 AGGG-GGAATCGATTCCCC-T-ACAGGGGGAATCGGTTCCCCT
16047 TCAAGGTATT
Statistics
Matches: 96, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 5 0.05
65 15 0.16
66 59 0.61
67 17 0.18
ACGTcount: A:0.24, C:0.27, G:0.28, T:0.21
Consensus pattern (64 bp):
AGGGGGAATCGATTCCCCTACAGGGGGAATCGGTTCCCCTACAGGGAGGAATCGATTCCCCTAA
Found at i:16023 original size:88 final size:87
Alignment explanation
Indices: 15876--16052 Score: 318
Period size: 88 Copynumber: 2.0 Consensus size: 87
15866 AAACCTCCAG
* *
15876 GGGGTATCGATTCCCCTACAGGGGGAATCGGTTCCCCTACAGGGAGGAATCGATTCCCCTTCAAA
1 GGGGAATCGATTCCCCTACAGGGGGAATCGATTCCCCTACAGGGAGGAATCGATTCCCCTTCAAA
15941 GGGGGAATCGATTCCCCTTCAA
66 GGGGGAATCGATTCCCCTTCAA
*
15963 GGGGAATCGGTTCCCCTACAGGGAGGAATCGATTCCCCTACAGGGAGGAATCGATTCCCCTTCAA
1 GGGGAATCGATTCCCCTACAGGG-GGAATCGATTCCCCTACAGGGAGGAATCGATTCCCCTTCAA
16028 AGGGGGAATCGATTCCCCTTCAA
65 AGGGGGAATCGATTCCCCTTCAA
16051 GG
1 GG
16053 TATTTTTCTA
Statistics
Matches: 86, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
87 21 0.24
88 65 0.76
ACGTcount: A:0.24, C:0.27, G:0.28, T:0.21
Consensus pattern (87 bp):
GGGGAATCGATTCCCCTACAGGGGGAATCGATTCCCCTACAGGGAGGAATCGATTCCCCTTCAAA
GGGGGAATCGATTCCCCTTCAA
Found at i:16052 original size:22 final size:21
Alignment explanation
Indices: 15873--16046 Score: 222
Period size: 22 Copynumber: 8.0 Consensus size: 21
15863 ACAAAACCTC
*
15873 CAGGGGGTATCGATTCCCCTA
1 CAGGGGGAATCGATTCCCCTA
*
15894 CAGGGGGAATCGGTTCCCCTA
1 CAGGGGGAATCGATTCCCCTA
15915 CAGGGAGGAATCGATTCCCCTTCA
1 CAGGG-GGAATCGATTCCCC-T-A
* *
15939 AAGGGGGAATCGATTCCCCTT
1 CAGGGGGAATCGATTCCCCTA
* *
15960 CAAGGGGAATCGGTTCCCCTA
1 CAGGGGGAATCGATTCCCCTA
15981 CAGGGAGGAATCGATTCCCCTA
1 CAGGG-GGAATCGATTCCCCTA
16003 CAGGGAGGAATCGATTCCCCTTCA
1 CAGGG-GGAATCGATTCCCC-T-A
*
16027 AAGGGGGAATCGATTCCCCT
1 CAGGGGGAATCGATTCCCCT
16047 TCAAGGTATT
Statistics
Matches: 135, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
21 45 0.33
22 50 0.37
23 30 0.22
24 10 0.07
ACGTcount: A:0.24, C:0.28, G:0.28, T:0.21
Consensus pattern (21 bp):
CAGGGGGAATCGATTCCCCTA
Found at i:22198 original size:31 final size:31
Alignment explanation
Indices: 22163--22234 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 31
22153 ATTAATGATA
*
22163 TGACATGTTTCATGTCATCA-AAGTGATGGCG
1 TGACATGTTTCATGTCA-CAGAAGTGATAGCG
*
22194 TGACATGTTTCATGTCACAGAAGTGATAGTG
1 TGACATGTTTCATGTCACAGAAGTGATAGCG
22225 TGACATGTTT
1 TGACATGTTT
22235 TATATCACCC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 2 0.05
31 36 0.95
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (31 bp):
TGACATGTTTCATGTCACAGAAGTGATAGCG
Found at i:22402 original size:15 final size:15
Alignment explanation
Indices: 22382--22410 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
22372 ATTAATTTGA
22382 TCAAAAATTAAAATT
1 TCAAAAATTAAAATT
22397 TCAAAAATTAAAAT
1 TCAAAAATTAAAAT
22411 ACCTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (15 bp):
TCAAAAATTAAAATT
Found at i:25381 original size:42 final size:42
Alignment explanation
Indices: 25335--25427 Score: 177
Period size: 42 Copynumber: 2.2 Consensus size: 42
25325 AAACGAACAC
25335 GAATATAAACGAACACGAACATAAATGAACACGAACATAAAT
1 GAATATAAACGAACACGAACATAAATGAACACGAACATAAAT
*
25377 GAATATAAACGAACATGAACATAAATGAACACGAACATAAAT
1 GAATATAAACGAACACGAACATAAATGAACACGAACATAAAT
25419 GAATATAAA
1 GAATATAAA
25428 TGTTGAAGAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.58, C:0.14, G:0.12, T:0.16
Consensus pattern (42 bp):
GAATATAAACGAACACGAACATAAATGAACACGAACATAAAT
Found at i:25402 original size:26 final size:26
Alignment explanation
Indices: 25355--25405 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
25345 GAACACGAAC
*
25355 ATAAATGAACACGAACATAAATGAAT
1 ATAAACGAACACGAACATAAATGAAT
*
25381 ATAAACGAACATGAACATAAATGAA
1 ATAAACGAACACGAACATAAATGAA
25406 CACGAACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.18
Consensus pattern (26 bp):
ATAAACGAACACGAACATAAATGAAT
Found at i:25418 original size:16 final size:16
Alignment explanation
Indices: 25293--25421 Score: 121
Period size: 16 Copynumber: 8.6 Consensus size: 16
25283 CGTTCATTTA
25293 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
* * *
25307 ATAAACGAATACGAAT
1 ATAAATGAACACGAAC
* *
25323 ATAAACGAACACGAAT
1 ATAAATGAACACGAAC
*
25339 ATAAACGAACACGAAC
1 ATAAATGAACACGAAC
25355 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
*
25371 ATAAAT------GAAT
1 ATAAATGAACACGAAC
* *
25381 ATAAACGAACATGAAC
1 ATAAATGAACACGAAC
25397 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
25413 ATAAATGAA
1 ATAAATGAA
25422 TATAAATGTT
Statistics
Matches: 97, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
10 8 0.08
14 5 0.05
15 2 0.02
16 82 0.85
ACGTcount: A:0.58, C:0.16, G:0.12, T:0.15
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:26532 original size:10 final size:10
Alignment explanation
Indices: 26517--26550 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
26507 ATAAATGAAT
26517 GAACATAAAC
1 GAACATAAAC
26527 GAACATAAAC
1 GAACATAAAC
* *
26537 GAATATAACC
1 GAACATAAAC
26547 GAAC
1 GAAC
26551 GTTCACGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.12
Consensus pattern (10 bp):
GAACATAAAC
Found at i:26913 original size:55 final size:55
Alignment explanation
Indices: 26829--26969 Score: 239
Period size: 55 Copynumber: 2.6 Consensus size: 55
26819 TACTTTTTGG
*
26829 GTCCATTCAGTTATGTATTTCTTCAATATTTGTACTTTTTTTGGGGTCTATAACA
1 GTCCATTCAGTTATGTATTTCTTCAATATTTATACTTTTTTTGGGGTCTATAACA
*
26884 GTCCATTCAGTTATGTATTTCTTCAATATTTATACTTTTTTTTGGGTCTATAACA
1 GTCCATTCAGTTATGTATTTCTTCAATATTTATACTTTTTTTGGGGTCTATAACA
*
26939 GTCCACTCA-TCTATGTATTTCTTCAATATTT
1 GTCCATTCAGT-TATGTATTTCTTCAATATTT
26970 TTTGGGGGTC
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
54 1 0.01
55 81 0.99
ACGTcount: A:0.23, C:0.16, G:0.11, T:0.50
Consensus pattern (55 bp):
GTCCATTCAGTTATGTATTTCTTCAATATTTATACTTTTTTTGGGGTCTATAACA
Found at i:29630 original size:20 final size:20
Alignment explanation
Indices: 29602--29644 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
29592 AAATCTTGAC
*
29602 ATTTATTTAGA-AAATATAAT
1 ATTTATTTA-ATAAAAATAAT
*
29622 ATTTTTTTAATAAAAATAAT
1 ATTTATTTAATAAAAATAAT
29642 ATT
1 ATT
29645 ATGAAGAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTTATTTAATAAAAATAAT
Found at i:38845 original size:14 final size:14
Alignment explanation
Indices: 38828--38878 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
38818 ATGAATAAAT
38828 AAATGGTTTTAATG
1 AAATGGTTTTAATG
** *
38842 AAATGTGAATAAAT-
1 AAATG-GTTTTAATG
38856 AAATGGTTTTAATG
1 AAATGGTTTTAATG
38870 AAAT-GTTTT
1 AAATGGTTTT
38879 GGAGTCGCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 10 0.34
14 14 0.48
15 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (14 bp):
AAATGGTTTTAATG
Found at i:38874 original size:28 final size:28
Alignment explanation
Indices: 38813--38875 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
38803 TGACGGAAAA
*
38813 GAAATATGAATAAATAAATGGTTTTAAT
1 GAAATGTGAATAAATAAATGGTTTTAAT
38841 GAAATGTGAATAAATAAATGGTTTTAAT
1 GAAATGTGAATAAATAAATGGTTTTAAT
38869 GAAATGT
1 GAAATGT
38876 TTTGGAGTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.35
Consensus pattern (28 bp):
GAAATGTGAATAAATAAATGGTTTTAAT
Found at i:41887 original size:124 final size:124
Alignment explanation
Indices: 41346--41888 Score: 682
Period size: 124 Copynumber: 4.4 Consensus size: 124
41336 TTTTTCTTAT
* * * *
41346 TATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTTATTACGAACTCCT-TATGGAAATGTTGA
1 TATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATTACGAACTCCTGTCTGGAAATGCTGA
* * * * * *
41410 TGCTGCTTTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATACGTTCTTCAGAT
66 TGTTACTCTATCTCCTTCTGCGATAGAGTCAAGAAAAAGGTTGAATAAGTTCTTCAGAC
* * **
41469 TATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATTACAAACT-CTTTCTGGAAATATTGA
1 TATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATTACGAACTCCTGTCTGGAAATGCTGA
* * * *
41533 TGTTACTCTATCTCCTTCTGCGATAGAATCGAGCAAAAAGGTTGAATACA-TCCTTCAGAT
66 TGTTACTCTATCTCCTTCTGCGATAGAGTCAAG-AAAAAGGTTGAATA-AGTTCTTCAGAC
* * ** * * * *
41593 TATGAACTTCTTCTTCATATTCAGACGAGTTCTTCAGATTATGAAATCATGTTTGGAAATGGCT-
1 TATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATTACGAACTCCTGTCTGGAAAT-GCTG
* * * *
41657 CTGTTGCTCTATCTCCTTCTGCAATAGAGTCAAGCAAAAGGTTGAATAAGTTCTTCAGAC
65 ATGTTACTCTATCTCCTTCTGCGATAGAGTCAAGAAAAAGGTTGAATAAGTTCTTCAGAC
* ** *
41717 TATGAACTTCTTATTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTGTCTGGAAATGGCT-
1 TATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATTACGAACTCCTGTCTGGAAAT-GCTG
*
41781 CTGTTACTCTATCTCCTTCTGCGATAGAGTCAAGAAAAAGGTTGAATAAGTTCTTCAGAC
65 ATGTTACTCTATCTCCTTCTGCGATAGAGTCAAGAAAAAGGTTGAATAAGTTCTTCAGAC
* *
41841 TATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTC
1 TATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATTACGAACTC
41889 TATAAATCAA
Statistics
Matches: 366, Mismatches: 48, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
122 2 0.01
123 85 0.23
124 240 0.66
125 38 0.10
126 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.37
Consensus pattern (124 bp):
TATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTTATTACGAACTCCTGTCTGGAAATGCTGA
TGTTACTCTATCTCCTTCTGCGATAGAGTCAAGAAAAAGGTTGAATAAGTTCTTCAGAC
Found at i:42188 original size:177 final size:177
Alignment explanation
Indices: 41892--42609 Score: 1114
Period size: 177 Copynumber: 4.1 Consensus size: 177
41882 CGAACTCTAT
41892 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAACT
1 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAACT
** ** * * *
41957 TCCTTTAACATCTCTTTTGAGATAATTAGTAAACCCTTGCAGTCTTGGTTTCTAAAATCTTATTT
66 TCCTTTAACAGATCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTT
* * *
42022 GAAAACATCCTGCACTGAAGGTCTTATGGATAATCTGTAGGACTTAC
131 GAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGTAGGACTTAC
*
42069 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAGCT
1 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAACT
*
42134 TCCTTTAACAGATCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTTATTT
66 TCCTTTAACAGATCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTT
* *
42199 GAAAACATCCTGCACTGAAGGTCTTATGGATGACCCATAGGACTTAT
131 GAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGTAGGACTTAC
* * ** * *
42246 AAATCAAGAAACCCCTGAAGGATTAGTTTCTTAGTTGTCAATAAACCCCTTTGTTAGACTTAACT
1 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAACT
* *
42311 TCCTTTAACA-ACTATTTTGAGATTATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATT
66 TCCTTTAACAGA-TCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATT
* *
42375 TGAAAACATCCTGCACTAAAGGTCTTATGGATGTCCCGTAGGACTTAC
130 TGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGTAGGACTTAC
* * * * * *
42423 AAATCTAGAAACCCCCGAAGGTTTGGTTTCTTAGTTGTTAAGGAACCCCTTTGTTAGGCTTAGCT
1 AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAACT
*
42488 TCCTTTAACAGCTCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTT
66 TCCTTTAACAGATCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTT
* * *
42553 GAAAACATCCTGCACTGAAGGTCTTTTGGATGGCCCGTAGGACTTAT
131 GAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGTAGGACTTAC
42600 AAATCAAGAA
1 AAATCAAGAA
42610 TATAGATGTA
Statistics
Matches: 496, Mismatches: 43, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
176 1 0.00
177 495 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (177 bp):
AAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAACT
TCCTTTAACAGATCTTTTGAGATAATTAGTAAACCCCCGAAGGCTTGGTTTCTAAAATCTCATTT
GAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGTAGGACTTAC
Found at i:43055 original size:54 final size:54
Alignment explanation
Indices: 42968--43076 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
42958 TAATCATTGG
*
42968 TTCGTAAAACATTTAACAACACATTCATTCTTTCCTGTGGCTTCTGCCCAGATT
1 TTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGATT
* *
43022 TTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCTAGATT
1 TTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGATT
43076 T
1 T
43077 CTTGTCAGTA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.38
Consensus pattern (54 bp):
TTCGTAAAACATTTAACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGATT
Found at i:43617 original size:52 final size:52
Alignment explanation
Indices: 43541--43743 Score: 255
Period size: 52 Copynumber: 3.9 Consensus size: 52
43531 TATCCCAACC
* *
43541 TTTTCATGCTGGTATGAGCCTTCAAGATGCCCCACATGGATTACTTCTGTCT
1 TTTTCATGCTGATATGAGCCTTCAAGATGCCCCAGATGGATTACTTCTGTCT
* * *
43593 TTTTCATGCTGATGTGAGCCTTCAAGATACCCCAGATGGATTACTTATGTCT
1 TTTTCATGCTGATATGAGCCTTCAAGATGCCCCAGATGGATTACTTCTGTCT
* ** * *
43645 TTTTTATGCTGATGCGAGCCTTCAATATGCCCCAGATGGATTACTTCTATC-
1 TTTTCATGCTGATATGAGCCTTCAAGATGCCCCAGATGGATTACTTCTGTCT
* * * * * *
43696 TTTTCATACTGACATGATCCTTCAAGATTCCCCAAATAGATTACTTCT
1 TTTTCATGCTGATATGAGCCTTCAAGATGCCCCAGATGGATTACTTCT
43744 ATGTTGATGT
Statistics
Matches: 130, Mismatches: 21, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
51 38 0.29
52 92 0.71
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (52 bp):
TTTTCATGCTGATATGAGCCTTCAAGATGCCCCAGATGGATTACTTCTGTCT
Found at i:45253 original size:19 final size:19
Alignment explanation
Indices: 45229--45317 Score: 103
Period size: 18 Copynumber: 4.7 Consensus size: 19
45219 CTTGATTCAA
45229 TTTTTTCTTTTTTTCTTTC
1 TTTTTTCTTTTTTTCTTTC
*
45248 TTTTTTCCTTTTTTT-TCTC
1 TTTTTT-CTTTTTTTCTTTC
*
45267 TTTTTCCTTTTTTTC-TTC
1 TTTTTTCTTTTTTTCTTTC
* *
45285 TTTTTTCTCTTTTTCCTT-
1 TTTTTTCTTTTTTTCTTTC
45303 TTTTTTCTTCTTTTT
1 TTTTTTCTT-TTTTT
45318 TCTCTAAGGG
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
18 31 0.52
19 21 0.35
20 8 0.13
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTTCTTTTTTTCTTTC
Found at i:45259 original size:17 final size:16
Alignment explanation
Indices: 45239--45288 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 16
45229 TTTTTTCTTT
45239 TTTTCTTTCTTTTTTCC
1 TTTT-TTTCTTTTTTCC
45256 TTTTTTTTCTCTTTTTCC
1 -TTTTTTTCT-TTTTTCC
45274 TTTTTTTCTTCTTTT
1 TTTTTTTCTT-TTTT
45289 TTCTCTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.03
17 18 0.60
18 11 0.37
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTTCTTTTTTCC
Found at i:45259 original size:18 final size:18
Alignment explanation
Indices: 45238--45320 Score: 87
Period size: 20 Copynumber: 4.4 Consensus size: 18
45228 ATTTTTTCTT
45238 TTTTTCTTTCTTTTTTCC
1 TTTTTCTTTCTTTTTTCC
45256 TTTTT-TTTCTCTTTTTCC
1 TTTTTCTTTCT-TTTTTCC
*
45274 TTTTTTTCTTCTTTTTTCTC
1 TTTTTCT-TTCTTTTTTC-C
* *
45294 TTTTTCCTTTTTTTTCTTCT
1 TTTTT-CTTTCTTTT-TTCC
45314 TTTTTCT
1 TTTTTCT
45321 CTAAGGGATG
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
17 5 0.09
18 17 0.30
19 9 0.16
20 21 0.38
21 4 0.07
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTCTTTCTTTTTTCC
Found at i:45259 original size:27 final size:26
Alignment explanation
Indices: 45229--45322 Score: 109
Period size: 28 Copynumber: 3.4 Consensus size: 26
45219 CTTGATTCAA
*
45229 TTTTTTCT-TTTTTTCTTTCTTTTTTCC
1 TTTTTTCTCTTTTTCCTTT-TTTTTT-C
45256 TTTTTTTTCTCTTTTTCCTTTTTTTCTTC
1 --TTTTTTCTCTTTTTCCTTTTTTT-TTC
45285 TTTTTTCTCTTTTTCCTTTTTTTTCTTC
1 TTTTTTCTCTTTTTCC-TTTTTTT-TTC
45313 TTTTTTCTCT
1 TTTTTTCTCT
45323 AAGGGATGAG
Statistics
Matches: 61, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
27 16 0.26
28 21 0.34
29 13 0.21
30 11 0.18
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTTTTCTCTTTTTCCTTTTTTTTTC
Found at i:49069 original size:14 final size:15
Alignment explanation
Indices: 49035--49067 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
49025 ATGTAAAATG
49035 AAAATGCAAAAAAAA
1 AAAATGCAAAAAAAA
49050 AAAATGCAAAAAAAA
1 AAAATGCAAAAAAAA
49065 AAA
1 AAA
49068 TGTAAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.82, C:0.06, G:0.06, T:0.06
Consensus pattern (15 bp):
AAAATGCAAAAAAAA
Found at i:53228 original size:3 final size:3
Alignment explanation
Indices: 53220--53254 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
53210 ATTTATCATT
53220 TAA TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53255 ATGGGACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:54090 original size:27 final size:27
Alignment explanation
Indices: 54038--54100 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
54028 ACAAAGGCTA
**
54038 CCTTCATTTGCATAATCAGCCTGGTTC
1 CCTTCATTTGCATAATCAGAATGGTTC
* *
54065 CCTTCATTTGCATGATCA-AATAGGTTT
1 CCTTCATTTGCATAATCAGAAT-GGTTC
*
54092 CCTTGATTT
1 CCTTCATTT
54101 CCACAACAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 1 0.03
27 29 0.97
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (27 bp):
CCTTCATTTGCATAATCAGAATGGTTC
Done.