Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008931.1 Hibiscus syriacus cultivar Beakdansim tig00112237_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: 67833
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:13043 original size:21 final size:21
Alignment explanation
Indices: 13017--13057 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
13007 AAATGTATAG
*
13017 AATTATAAAAAATTTAAAAAA
1 AATTATAAAAAAATTAAAAAA
13038 AATTATAAAAAAATTAAAAA
1 AATTATAAAAAAATTAAAAA
13058 TATTAAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AATTATAAAAAAATTAAAAAA
Found at i:13051 original size:11 final size:10
Alignment explanation
Indices: 13017--13057 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
13007 AAATGTATAG
13017 AATTATAAAAA
1 AATTA-AAAAA
*
13028 ATTTAAAAAA
1 AATTAAAAAA
13038 AATTATAAAAA
1 AATTA-AAAAA
13049 AATTAAAAA
1 AATTAAAAA
13058 TATTAAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 13 0.48
11 14 0.52
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AATTAAAAAA
Found at i:13644 original size:20 final size:21
Alignment explanation
Indices: 13613--13658 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
13603 ACTGGTAACA
*
13613 TTATTATTTCTATCGGTTTTG
1 TTATTATTTCTATCGATTTTG
*
13634 TTATT-TTTCTATCTATTTTG
1 TTATTATTTCTATCGATTTTG
13654 TTATT
1 TTATT
13659 GTTGAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.15, C:0.09, G:0.09, T:0.67
Consensus pattern (21 bp):
TTATTATTTCTATCGATTTTG
Found at i:20204 original size:15 final size:16
Alignment explanation
Indices: 20168--20207 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
20158 AAACCTATTA
*
20168 AATCATTCAGCATTTG
1 AATCATTCAGCACTTG
*
20184 AATCATTCAGCGCTT-
1 AATCATTCAGCACTTG
20199 AATCATTCA
1 AATCATTCA
20208 AATAAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.35
Consensus pattern (16 bp):
AATCATTCAGCACTTG
Found at i:20812 original size:21 final size:21
Alignment explanation
Indices: 20788--20841 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
20778 AGGAGCGGGC
20788 TGGTGACACAGAACAGGAACG
1 TGGTGACACAGAACAGGAACG
* * *
20809 TGGTGACATAGAACGGGAATG
1 TGGTGACACAGAACAGGAACG
*
20830 CGGTGACACAGA
1 TGGTGACACAGA
20842 CCTAGATACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.17, G:0.35, T:0.13
Consensus pattern (21 bp):
TGGTGACACAGAACAGGAACG
Found at i:25095 original size:23 final size:23
Alignment explanation
Indices: 25069--25122 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
25059 AGTTTTTTTT
25069 TTATGTTCGTTCATGTTAATTTA-
1 TTATGTTCGTTCAT-TTAATTTAG
*
25092 TTATGTTCGTTCATTTATTTTAG
1 TTATGTTCGTTCATTTAATTTAG
25115 TTTATGTT
1 -TTATGTT
25123 TGTTTATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 7 0.25
23 14 0.50
24 7 0.25
ACGTcount: A:0.19, C:0.07, G:0.13, T:0.61
Consensus pattern (23 bp):
TTATGTTCGTTCATTTAATTTAG
Found at i:28002 original size:12 final size:12
Alignment explanation
Indices: 27981--28023 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
27971 CGGATTATTG
*
27981 TAGATAACACCA
1 TAGATGACACCA
27993 TAGATGACACCA
1 TAGATGACACCA
*
28005 TAGATGACACCT
1 TAGATGACACCA
28017 TAGATGA
1 TAGATGA
28024 GGAAATAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (12 bp):
TAGATGACACCA
Found at i:29023 original size:37 final size:35
Alignment explanation
Indices: 28949--29023 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
28939 TTTTTATATT
*
28949 TTTAATTTTATAAAAAAATTATATAATATTATGAA
1 TTTAATTTTATAAAAAAATTATATAATATTATCAA
* *
28984 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTATAAA-AAAATTATAT-AATATTAT-CAA
29021 TTT
1 TTT
29024 GTAATATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 18 0.53
36 11 0.32
37 5 0.15
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (35 bp):
TTTAATTTTATAAAAAAATTATATAATATTATCAA
Found at i:34024 original size:5 final size:5
Alignment explanation
Indices: 34004--34042 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
33994 CAATATTCTG
* *
34004 TTAAT TTAAG TGAAT TTAAT TT-AT TTAAT TTAAT TTAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT
34043 GAACCCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (5 bp):
TTAAT
Found at i:34067 original size:21 final size:21
Alignment explanation
Indices: 34041--34080 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34031 ATTTAATTTA
34041 ATGAACCCTAAACCCTAAACC
1 ATGAACCCTAAACCCTAAACC
* *
34062 ATGAACTCTAAACCTTAAA
1 ATGAACCCTAAACCCTAAA
34081 TCCTAAAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.30, G:0.05, T:0.20
Consensus pattern (21 bp):
ATGAACCCTAAACCCTAAACC
Found at i:34086 original size:14 final size:14
Alignment explanation
Indices: 34069--34192 Score: 60
Period size: 14 Copynumber: 8.9 Consensus size: 14
34059 ACCATGAACT
34069 CTAAACCTTAAATC
1 CTAAACCTTAAATC
* *
34083 CTAAAACCATAAAAC
1 CT-AAACCTTAAATC
* *
34098 TTGAATCC-TAAATTC
1 CT-AAACCTTAAA-TC
*
34113 CTACAATCTTAAA-C
1 CTA-AACCTTAAATC
* *
34127 CTTGAACCCTAAATC
1 C-TAAACCTTAAATC
*
34142 CTAAACCATAAAT-
1 CTAAACCTTAAATC
* * *
34155 CAAAACCCTAAATT
1 CTAAACCTTAAATC
*
34169 C-AAA-CTTAAACC
1 CTAAACCTTAAATC
34181 CTAAACCTTAAA
1 CTAAACCTTAAA
34193 ATCAAAATGA
Statistics
Matches: 82, Mismatches: 19, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
12 6 0.07
13 17 0.21
14 33 0.40
15 22 0.27
16 4 0.05
ACGTcount: A:0.46, C:0.27, G:0.02, T:0.25
Consensus pattern (14 bp):
CTAAACCTTAAATC
Found at i:36786 original size:27 final size:26
Alignment explanation
Indices: 36715--36787 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 26
36705 GTTCTAATTG
* ** *
36715 TATTTTTATTATTGTTTATTTATGTTT
1 TATTTTTATTATT-TATATTTAAATAT
* *
36742 TAATTTTACTTGTTTATATTTAAATAT
1 TATTTTTA-TTATTTATATTTAAATAT
36769 TATTTTTATTATTATATAT
1 TATTTTTATTATT-TATAT
36788 AGTCATATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 4 0.11
27 28 0.78
28 4 0.11
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.67
Consensus pattern (26 bp):
TATTTTTATTATTTATATTTAAATAT
Found at i:48664 original size:16 final size:16
Alignment explanation
Indices: 48645--48675 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
48635 TATTTTCTCT
48645 AAATTCAATTTATTTG
1 AAATTCAATTTATTTG
48661 AAATTCAATTTATTT
1 AAATTCAATTTATTT
48676 TCAAAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (16 bp):
AAATTCAATTTATTTG
Found at i:48685 original size:19 final size:17
Alignment explanation
Indices: 48645--48693 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
48635 TATTTTCTCT
*
48645 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTA
48661 AAATTCAATTTATTTTCAA
1 AAATTCAATTTATTTT--A
48680 AAATTCAATTTATT
1 AAATTCAATTTATT
48694 CTTTTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 12 0.41
17 3 0.10
19 14 0.48
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (17 bp):
AAATTCAATTTATTTTA
Found at i:49186 original size:114 final size:114
Alignment explanation
Indices: 48986--49437 Score: 742
Period size: 114 Copynumber: 4.0 Consensus size: 114
48976 GTGATACGTT
48986 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
*
49051 ATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
66 ATTTAGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
* *
49100 CTCATAGTAGGAATACGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
49165 ATTTAGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
66 ATTTAGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
* *
49214 CTCATAGTAGGAATACGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* *
49279 ATTTGGTATGAACCCTAAAATCAATCATTGGATTTGAAAGATGAATTTG
66 ATTTAGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
* * *
49328 CTCATAGTAGAAATAAAAAGACCCAATAGCATCTTCTGGAAGTTTTCTTTGAGTCATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * * * * * * *
49393 GTTCAATAGGAACCACAAAACCAATCATTGGAATTAAAAGATGAA
66 ATTTAGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAA
49438 CTGCATGATC
Statistics
Matches: 318, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 318 1.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
ATTTAGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTG
Found at i:50528 original size:16 final size:16
Alignment explanation
Indices: 50509--50569 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
50499 GTTCATAATG
50509 AGAAGAACTCATCTGAAGA
1 AGAAGAACTCATCT---GA
* *
50528 AGAAGAAGTTCATAATG-
1 AGAAGAA-CTCAT-CTGA
50545 AGAAGAACTCATCTGA
1 AGAAGAACTCATCTGA
50561 AGAAGAACT
1 AGAAGAACT
50570 TGTTCAACTT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
15 2 0.06
16 13 0.37
17 7 0.20
18 1 0.03
19 7 0.20
20 4 0.11
21 1 0.03
ACGTcount: A:0.48, C:0.13, G:0.21, T:0.18
Consensus pattern (16 bp):
AGAAGAACTCATCTGA
Found at i:50544 original size:36 final size:36
Alignment explanation
Indices: 50497--50567 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
50487 TTTCCAGGTA
50497 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
50533 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
50568 CTTGTTCAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.20
Consensus pattern (36 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
Found at i:50685 original size:112 final size:112
Alignment explanation
Indices: 50561--50806 Score: 363
Period size: 112 Copynumber: 2.2 Consensus size: 112
50551 ACTCATCTGA
* * *
50561 AGAAGAACTTGTTCAACTTTTTGCTT-GAATTCATCA-TTCGATGGATCAGCATTTCCAGA-AGA
1 AGAAGAACTTGTTCAACTTTTTG-TTCAAATTCATCACTT-GATGGATCAACATTTCCAGAGAAA
*
50623 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATG
64 GTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATG
* *
50673 AGAAGAACTTGTTTAACCTTTTGTTCAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGT
1 AGAAGAACTTGTTCAACTTTTTGTTCAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGT
*
50738 TCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATG
66 TCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
*
50785 AGAATAACTTGTTCAATCTTTT
1 AGAAGAACTTGTTCAA-CTTTT
50807 GCATGATTCT
Statistics
Matches: 120, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
111 2 0.02
112 83 0.69
113 35 0.29
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (112 bp):
AGAAGAACTTGTTCAACTTTTTGTTCAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGT
TCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
Found at i:50697 original size:237 final size:241
Alignment explanation
Indices: 50323--50793 Score: 763
Period size: 237 Copynumber: 2.0 Consensus size: 241
50313 GTTCATAATG
* **
50323 AGAATAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGTCGAGT
1 AGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGAAGAGT
* * *
50388 TCATAATGAGAAGAATTCATCTGAAGAATGAAGAAGAAGTTTATAATGAGAAGAACTTGTTCAAC
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* *
50453 TTTTTGTTCAAATCCATCACTTGATGGATCAATATTTCCAG-GTAAAGTTCATAATGAGAAGAAC
131 CTTTTGTTCAAATCCATCACTTGATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAAC
50517 TCATCTG-A-A-GAAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
195 TCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
* *
50561 AGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCA-GAAGAGT
1 AGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGAAGAGT
* *
50625 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTTAAC
66 TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
*
50690 CTTTTGTTCAAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACT
131 CTTTTGTTCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACT
* *
50755 TATCTGAAGAGGAAGAAGAAGTTCATAATGAGAATAACT
196 CATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACT
50794 TGTTCAATCT
Statistics
Matches: 214, Mismatches: 15, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
237 130 0.61
238 56 0.26
239 1 0.00
240 27 0.13
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (241 bp):
AGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAGGAAGAGT
TCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
CTTTTGTTCAAATCCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACT
CATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTCATCTGA
Found at i:50807 original size:112 final size:111
Alignment explanation
Indices: 50124--50808 Score: 717
Period size: 113 Copynumber: 6.0 Consensus size: 111
50114 AGCAAAGTTC
* * ***
50124 AAATCCATCATTCAATGGATCAACA-TTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCATTCGATGGATCAACATTTCCA-GAAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
50188 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGTTT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTT-GCTT
* * * * **
50236 GAATTCATCATTCGATAGATCAGCATTACCAGGTCGAA-TTCATAATGAGAAGAACTCATCTGAA
1 AAATTCATCATTCGATGGATCAACATTTCCA-G-AAAAGTTCATAATGAGAAGAACTCATCTGAA
*
50300 GAAGGAAGAAGAAGTTCATAATGAGAATAACTTGTTCAACTTTTCGCTT
64 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTT-GCTT
* * * *** *
50349 GAATTCATCATTCGATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAATTCATCTGAAG
1 AAATTCATCATTCGATGGATCAACATTTCCA-GAAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
50414 AATGAAGAAGAAGTTTATAATGAGAAGAACTTGTTCAACTTTTTG-TT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC-TTTTGCTT
* * *
50461 CAAATCCATCACTT-GATGGATCAATATTTCCAGGTAAAGTTCATAATGAGAAGAACTCATCT--
1 -AAATTCATCA-TTCGATGGATCAACATTTCCA-GAAAAGTTCATAATGAGAAGAACTCATCTGA
50523 -GAA-GAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAACTTGTTCAACTTTTTGCT
63 AGAAGGAAGAAGAAGTTCATAATGAGAAGAA--C-T-T------G----T--TCAAC-TTTTGCT
50586 T
111 T
* * *
50587 GAATTCATCATTCGATGGATCAGCATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AAATTCATCATTCGATGGATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
50652 AGGAAGAGGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTG-TT
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTGCTT
*
50698 CAAATTCATCACTT-GATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
1 -AAATTCATCA-TTCGATGGATCAACATTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGA
*
50762 AG-AGGAAGAAGAAGTTCATAATGAGAATAACTTGTTCAATCTTTTGC
63 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTGC
50809 ATGATTCTAT
Statistics
Matches: 496, Mismatches: 44, Indels: 65
0.82 0.07 0.11
Matches are distributed among these distances:
109 25 0.05
110 3 0.01
111 3 0.01
112 100 0.20
113 257 0.52
114 8 0.02
118 1 0.00
119 1 0.00
123 1 0.00
124 30 0.06
125 36 0.07
126 3 0.01
127 3 0.01
128 25 0.05
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (111 bp):
AAATTCATCATTCGATGGATCAACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTGCTT
Found at i:51088 original size:3 final size:3
Alignment explanation
Indices: 51080--51199 Score: 163
Period size: 3 Copynumber: 40.0 Consensus size: 3
51070 ACTTATTTAT
* * *
51080 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TAA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
51128 TTA TTA TTA -TA TATA TTA TTA TTA TTA TTA TTA TTA TAA TAA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
51173 TTA TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA
51200 AAAAAATAAT
Statistics
Matches: 107, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
2 4 0.04
3 97 0.91
4 6 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:51209 original size:42 final size:42
Alignment explanation
Indices: 51085--51199 Score: 205
Period size: 42 Copynumber: 2.7 Consensus size: 42
51075 TTTATTTATT
*
51085 ATTATTATTAT-TATTATTATTATTATAATTATTATTATAATA
1 ATTATTATTATATA-TATTATTATTATTATTATTATTATAATA
51127 ATTATTATTATATATATTATTATTATTATTATTATTATAATA
1 ATTATTATTATATATATTATTATTATTATTATTATTATAATA
51169 ATTATTATTATATATATTATTATTATTATTA
1 ATTATTATTATATATATTATTATTATTATTA
51200 AAAAAATAAT
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
42 69 0.97
43 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (42 bp):
ATTATTATTATATATATTATTATTATTATTATTATTATAATA
Found at i:57896 original size:18 final size:17
Alignment explanation
Indices: 57875--57912 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
57865 ATTTTTAGTG
57875 TTTTTT-TTCCTCTATT
1 TTTTTTCTTCCTCTATT
*
57891 GTTTTTTCTTCTTCTATT
1 -TTTTTTCTTCCTCTATT
57909 TTTT
1 TTTT
57913 AGTTTACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTTTCTTCCTCTATT
Found at i:58120 original size:20 final size:20
Alignment explanation
Indices: 58097--58136 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
58087 AATCATTTTT
*
58097 ATATATTAA-TATTTATTTAA
1 ATATATAAATTATTT-TTTAA
58117 ATATATAAATTATTTTTTAA
1 ATATATAAATTATTTTTTAA
58137 TATTGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATAAATTATTTTTTAA
Found at i:58653 original size:17 final size:18
Alignment explanation
Indices: 58631--58707 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 18
58621 TCTTTAAGGT
58631 ATATTTTATTA-TATTTA
1 ATATTTTATTATTATTTA
* *
58648 ATATTTTGTTATTATTTT
1 ATATTTTATTATTATTTA
58666 AT-TTAATTATTTAAATTATTTA
1 ATATT--TTA-TT--ATTATTTA
58688 ATATTTTATTTATTTATTTA
1 ATATTTTA-TTA-TTATTTA
58708 TTTATTTTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
17 12 0.25
18 7 0.15
19 3 0.06
20 9 0.19
21 6 0.12
22 9 0.19
23 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (18 bp):
ATATTTTATTATTATTTA
Found at i:58696 original size:29 final size:31
Alignment explanation
Indices: 58631--58707 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 31
58621 TCTTTAAGGT
*
58631 ATATTTTA-TT-A-TATTTAATATTTTGTTA
1 ATATTTTATTTAATTATTTAATATTATGTTA
*
58659 TTATTTTATTTAATTATTTAA-ATTAT-TTA
1 ATATTTTATTTAATTATTTAATATTATGTTA
*
58688 ATATTTTATTTATTTATTTA
1 ATATTTTATTTAATTATTTA
58708 TTTATTTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 7 0.17
29 23 0.55
30 5 0.12
31 7 0.17
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (31 bp):
ATATTTTATTTAATTATTTAATATTATGTTA
Found at i:58701 original size:4 final size:4
Alignment explanation
Indices: 58663--58714 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
58653 TTGTTATTAT
* * *
58663 TTTA TTTA ATTA TTTAA ATTA TTTA -ATA TTTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTT-A TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA
58712 TTT
1 TTT
58715 TTGCAGATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
3 2 0.05
4 32 0.82
5 5 0.13
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (4 bp):
TTTA
Found at i:59641 original size:26 final size:25
Alignment explanation
Indices: 59602--59651 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
59592 GATTATTTTG
59602 TTTATTACCATTTAATATCAGTTAA
1 TTTATTACCATTTAATATCAGTTAA
* *
59627 TTTATTTATCATTTAATATTAGTTA
1 TTTA-TTACCATTTAATATCAGTTA
59652 TTGTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (25 bp):
TTTATTACCATTTAATATCAGTTAA
Found at i:59653 original size:21 final size:19
Alignment explanation
Indices: 59628--59688 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 19
59618 ATCAGTTAAT
59628 TTATTTATCATTTAATATTA
1 TTATTTA-CATTTAATATTA
59648 GTTATTGTA-ATTT--TATTA
1 -TTATT-TACATTTAATATTA
59666 TTATTTACCATTTAATACTTA
1 TTATTTA-CATTTAATA-TTA
59687 TT
1 TT
59689 GTAAGCTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
16 2 0.06
17 5 0.15
18 9 0.26
20 6 0.18
21 10 0.29
22 2 0.06
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.59
Consensus pattern (19 bp):
TTATTTACATTTAATATTA
Done.