Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007887.1 Hibiscus syriacus cultivar Beakdansim tig00110267_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: 327798
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:218745 original size:37 final size:39
Alignment explanation
Indices: 218703--218775 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 39
218693 TTATTAAATC
*
218703 ATTTTAT-ATTTTTAATTTTGTAAAAAAAAT-TATATAA
1 ATTTTATGATTTTAAATTTTGTAAAAAAAATGTATATAA
* *
218740 ATTTTATGATTTTAAATTTTTTAAAGAAAATGTATA
1 ATTTTATGATTTTAAATTTTGTAAAAAAAATGTATA
218776 AATAGTTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 7 0.23
38 20 0.65
39 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (39 bp):
ATTTTATGATTTTAAATTTTGTAAAAAAAATGTATATAA
Found at i:224896 original size:23 final size:23
Alignment explanation
Indices: 224867--224912 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
224857 AGTCTTTAAA
* *
224867 AAAACTCATCGTCTCTATTGAAT
1 AAAACTCATCGTCACTATCGAAT
*
224890 AAAACTCATTGTCACTATCGAAT
1 AAAACTCATCGTCACTATCGAAT
224913 GACACGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.33
Consensus pattern (23 bp):
AAAACTCATCGTCACTATCGAAT
Found at i:227583 original size:21 final size:21
Alignment explanation
Indices: 227557--227606 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
227547 GGAGCGTGGG
227557 GGGAATCGGTACCCCCTCATA
1 GGGAATCGGTACCCCCTCATA
227578 GGGAATCGGTACCCCCTCATA
1 GGGAATCGGTACCCCCTCATA
227599 GGGAATCG
1 GGGAATCG
227607 ATTCCCTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.30, G:0.28, T:0.18
Consensus pattern (21 bp):
GGGAATCGGTACCCCCTCATA
Found at i:242309 original size:16 final size:16
Alignment explanation
Indices: 242288--242318 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
242278 CTATATGTGT
*
242288 CACTCGTAGTCGAGTG
1 CACTCGTACTCGAGTG
242304 CACTCGTACTCGAGT
1 CACTCGTACTCGAGT
242319 CTAATGCACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (16 bp):
CACTCGTACTCGAGTG
Found at i:250608 original size:105 final size:106
Alignment explanation
Indices: 250481--251202 Score: 1195
Period size: 105 Copynumber: 6.9 Consensus size: 106
250471 GGGAAATTAC
* *
250481 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCT
1 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCT
* *
250546 TCGTTGGGAAGTTGAAATTGGCTCTGAAA-TGGAGAAATGT
66 TCGTTGTGAAGTTGAAATTGGCTCTGAAATTTGAGAAATGT
* * *
250586 TTGGTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCT
1 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCT
250651 TCGTTGTGAAGTTGAAATTGGCTCTGAAA-TTGAGAAATTGT
66 TCGTTGTGAAGTTGAAATTGGCTCTGAAATTTGAGAAA-TGT
* * * *
250692 TTATTGACAACCAGCGGTCCCTTCATCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCT
1 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCT
* *
250757 TCGCTGTGAAGTTGAAATTGGCTCT-AAATTTGAGCAATGT
66 TCGTTGTGAAGTTGAAATTGGCTCTGAAATTTGAGAAATGT
*
250797 TTGTTGATAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCT
1 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCT
* *
250862 TCGTGGTGAAGTTGAAATTGGATCTG-AATTTGAGAAATGT
66 TCGTTGTGAAGTTGAAATTGGCTCTGAAATTTGAGAAATGT
250902 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCT
1 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCT
* *
250967 TCGCTGTGAAGTTGAAATTGGCTCT-AAATTTGAGCAATGT
66 TCGTTGTGAAGTTGAAATTGGCTCTGAAATTTGAGAAATGT
251007 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCT
1 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCT
* * *
251072 TCGTGGTGAAGTTGAAATTAGCTCT-AAATTTGAGCAATGT
66 TCGTTGTGAAGTTGAAATTGGCTCTGAAATTTGAGAAATGT
*
251112 TTGTTGACAACAAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCT
1 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCT
251177 TCGTTGTGAAGTTGAAATTGGCTCTG
66 TCGTTGTGAAGTTGAAATTGGCTCTG
251203 GGTAAAACCT
Statistics
Matches: 582, Mismatches: 30, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
105 488 0.84
106 94 0.16
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (106 bp):
TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATCCT
TCGTTGTGAAGTTGAAATTGGCTCTGAAATTTGAGAAATGT
Found at i:261448 original size:20 final size:20
Alignment explanation
Indices: 261410--261453 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
261400 ACGGTTAGTA
*
261410 AAATAAAAATAAATGGAAAT
1 AAATAAAAATAAATAGAAAT
261430 AAATAAAAATAACA-AGAAAT
1 AAATAAAAATAA-ATAGAAAT
261450 AAAT
1 AAAT
261454 GGTAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (20 bp):
AAATAAAAATAAATAGAAAT
Found at i:262903 original size:20 final size:19
Alignment explanation
Indices: 262878--262922 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
262868 TGTTTATATA
262878 TAAAAAAAATAATAAGATAC
1 TAAAAAAAATAATAA-ATAC
**
262898 TAAAAAGTATAATAAATAC
1 TAAAAAAAATAATAAATAC
262917 -AAAAAA
1 TAAAAAA
262923 CGCAAAGGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 5 0.23
19 4 0.18
20 13 0.59
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20
Consensus pattern (19 bp):
TAAAAAAAATAATAAATAC
Found at i:275033 original size:20 final size:21
Alignment explanation
Indices: 275010--275089 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 21
275000 TTGGTACAGA
*
275010 GGGAATCGATACCCCCATGA-
1 GGGAACCGATACCCCCATGAG
* *
275030 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-ATG-AG
*
275053 GGGAACCGATTCCCCCCAT-AG
1 GGGAACCGA-TACCCCCATGAG
*
275074 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
275090 TTGGGGTTCT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 20 0.41
21 12 0.24
22 1 0.02
23 10 0.20
24 6 0.12
ACGTcount: A:0.25, C:0.34, G:0.25, T:0.16
Consensus pattern (21 bp):
GGGAACCGATACCCCCATGAG
Found at i:275077 original size:21 final size:21
Alignment explanation
Indices: 275021--275089 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
275011 GGAATCGATA
275021 CCCCCAT-GAGGGAACCGATTC
1 CCCCCATAG-GGGAACCGATTC
**
275042 CCCCTTTGAAGGGGAACCGATTC
1 CCCCCAT--AGGGGAACCGATTC
* *
275065 CCCCCATAGGGGAATCGATAC
1 CCCCCATAGGGGAACCGATTC
275086 CCCC
1 CCCC
275090 TTGGGGTTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 21 0.54
23 17 0.44
24 1 0.03
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.16
Consensus pattern (21 bp):
CCCCCATAGGGGAACCGATTC
Found at i:284672 original size:63 final size:62
Alignment explanation
Indices: 284597--284755 Score: 192
Period size: 63 Copynumber: 2.5 Consensus size: 62
284587 TTTGTTGAAG
* * ** * * *
284597 GTGCATCGATGCATATGAAGTACATCGATGCATTAATTTTAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
** **
284660 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
284723 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
284756 GCCTCCATTA
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
63 82 0.99
64 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:285768 original size:102 final size:103
Alignment explanation
Indices: 285578--285779 Score: 298
Period size: 102 Copynumber: 2.0 Consensus size: 103
285568 GGGTCTATGT
* * *
285578 GGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATATATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATACTTGAT
285643 CCCTAGCATATGTATATGATTCTTAAGGAATGATACGC
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATACGC
* * * * * *
285681 GGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCT-TTGAGGCACATACTTGGT
1 GGTCCTTCGGGACATATATATATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATACTTGAT
* *
285745 CCTTAGTATATGTATATGATTCTTAAGGAATGATA
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATA
285780 TGTGGTTCTG
Statistics
Matches: 88, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
102 48 0.55
103 40 0.45
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATATATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATACGC
Found at i:285796 original size:102 final size:102
Alignment explanation
Indices: 285586--285805 Score: 271
Period size: 102 Copynumber: 2.1 Consensus size: 102
285576 GTGGTCTTTC
* *
285586 GGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCTAGCA
1 GGGACATAT-TATATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATACTTGATCCCTAGCA
**
285651 TATGTATATGATTCTTAAGGAATGATACGCGGTCCTTC
65 TATGTATATGATTCTTAAGGAATGATACGCGGTCCTGA
* * * * * * *
285689 GGGACATATGTATATTCTTTGGAACATTTATGAGGTCT-TTGAGGCACATACTTGGTCCTTAGTA
1 GGGACATAT-TATATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATACTTGATCCCTAGCA
* * *
285753 TATGTATATGATTCTTAAGGAATGATATGTGGTTCTGA
65 TATGTATATGATTCTTAAGGAATGATACGCGGTCCTGA
*
285791 TGGACATTATTATAT
1 GGGACA-TATTATAT
285806 GGCACTACGG
Statistics
Matches: 100, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
102 64 0.64
103 36 0.36
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (102 bp):
GGGACATATTATATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATACTTGATCCCTAGCAT
ATGTATATGATTCTTAAGGAATGATACGCGGTCCTGA
Found at i:285860 original size:148 final size:149
Alignment explanation
Indices: 285676--285976 Score: 471
Period size: 149 Copynumber: 2.0 Consensus size: 149
285666 TAAGGAATGA
* * * * * *
285676 TACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTT-TGAGGCACATAC
1 TACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTGTAAGACACATAC
* *
285740 TTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGT-TCTGATGGACATTATTAT
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCT-TGATGGACATTATTAT
*
285804 ATGGCACTACGGTGCAATTC
130 AAGGCACTACGGTGCAATTC
* *
285824 TACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATAC
1 TACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTGTAAGACACATAC
*
285889 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCTTTATGGACATTATTATA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCTTGATGGACATTATTATA
285954 AGGCACTACGGTGCAATTC
131 AGGCACTACGGTGCAATTC
285973 TACG
1 TACG
285977 TGCACTTCGG
Statistics
Matches: 139, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
148 46 0.33
149 92 0.66
150 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (149 bp):
TACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTGTAAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCTTGATGGACATTATTATA
AGGCACTACGGTGCAATTC
Found at i:285998 original size:22 final size:22
Alignment explanation
Indices: 285956--285998 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
285946 TTATTATAAG
**
285956 GCACTACGGTGCAATTCTACGT
1 GCACTACGGTGCAATGATACGT
*
285978 GCACTTCGGTGCAATGATACG
1 GCACTACGGTGCAATGATACG
285999 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (22 bp):
GCACTACGGTGCAATGATACGT
Found at i:289818 original size:19 final size:20
Alignment explanation
Indices: 289789--289826 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
289779 AGAAATTTGT
289789 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
289809 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
289827 TAATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:289869 original size:63 final size:62
Alignment explanation
Indices: 289794--289952 Score: 201
Period size: 63 Copynumber: 2.5 Consensus size: 62
289784 TTTGTTGAAG
* ** * * *
289794 GTGCATCGATGCATATGAAGTGCATCGATGCATTAATTTTAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
** **
289857 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
289920 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
289953 GCCTCCATTA
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 83 0.99
64 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:290991 original size:102 final size:102
Alignment explanation
Indices: 290767--290982 Score: 308
Period size: 102 Copynumber: 2.1 Consensus size: 102
290757 GTTGAGGGTC
* *
290767 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATAT-TATATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
290832 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
65 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* * * * * *
290870 TACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCT-TTGAGGCACATAC
1 TATGTGGTCCTTCGGGACATAT-TATATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
* * *
290934 TTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGA
65 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
290972 TATGTGGTCCT
1 TATGTGGTCCT
290983 GATGGACATT
Statistics
Matches: 99, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
102 55 0.56
103 44 0.44
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (102 bp):
TATGTGGTCCTTCGGGACATATTATATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATACT
TGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:291139 original size:149 final size:148
Alignment explanation
Indices: 290870--291170 Score: 485
Period size: 149 Copynumber: 2.0 Consensus size: 148
290860 TAAGGAATGA
* * * * * *
290870 TACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATACT
1 TACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATACT
* * *
290935 TGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTGATGGACATTATTATAT
66 TGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTGATGGACATTATTATAA
291000 GGCACTACGGTGCAATTC
131 GGCACTACGGTGCAATTC
* *
291018 TACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATAC
1 TACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACATAC
*
291083 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTATA
65 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTGATGGACATTATTATA
291148 AGGCACTACGGTGCAATTC
130 AGGCACTACGGTGCAATTC
291167 TACG
1 TACG
291171 TGGCACTACG
Statistics
Matches: 140, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
148 46 0.33
149 94 0.67
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (148 bp):
TACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATACT
TGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTGATGGACATTATTATAA
GGCACTACGGTGCAATTC
Found at i:291215 original size:22 final size:23
Alignment explanation
Indices: 291149--291209 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
291139 ATTATTATAA
291149 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGT
291172 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGT
*
291195 -GCACTTCGGTGCAAT
1 GGCACTACGGTGCAAT
291210 GATACGAGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 14 0.38
23 23 0.62
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGT
Found at i:294626 original size:124 final size:126
Alignment explanation
Indices: 294493--294788 Score: 346
Period size: 134 Copynumber: 2.3 Consensus size: 126
294483 TCCCTAAAGG
* *
294493 CTCTGCATATATGTATGTACTCATTCTAGTTTGCTTCT-TCA-AAATGCATCATCGGGCGTACTT
1 CTCTGCATATATGTATGTACTCATTCTAGTTTGCTTCTATCATAAATGCATCACCGGGCATACTT
** * *
294556 ACAGTAAGCGGGATGCTCTGAATGACGCTTATGACAAAACCAAACTATGTTTTCCCAAGAA
66 ACAGTAAGCGCAATGCTCCGAATCACGCTTATGACAAAACCAAACTATGTTTTCCCAAGAA
*
294617 CTCTGCATATATGTATGTACTCATTCTAGTATGCTTCTGAATCACTTTTTGAAATGCATCACCGG
1 CTCTGCATATATGTATGTACTCATTCTAGTTTGCTTCT--ATCA-----T-AAATGCATCACCGG
* * *
294682 GCATACTTACAGTAAGCGCAATGCTCCGAATCACGCTTATGACGAAATCAAACTATGTTTTCCTA
58 GCATACTTACAGTAAGCGCAATGCTCCGAATCACGCTTATGACAAAACCAAACTATGTTTTCCCA
*
294747 AGAG
123 AGAA
* * * *
294751 C-CTGATCATATTTGTATTTGCTCATTCTAGCTTGCTTC
1 CTCTG--CATATATGTATGTACTCATTCTAGTTTGCTTC
294789 AGAATTGCCT
Statistics
Matches: 144, Mismatches: 16, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
124 37 0.26
127 3 0.02
133 3 0.02
134 74 0.51
135 27 0.19
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (126 bp):
CTCTGCATATATGTATGTACTCATTCTAGTTTGCTTCTATCATAAATGCATCACCGGGCATACTT
ACAGTAAGCGCAATGCTCCGAATCACGCTTATGACAAAACCAAACTATGTTTTCCCAAGAA
Found at i:295889 original size:2 final size:2
Alignment explanation
Indices: 295882--295956 Score: 69
Period size: 2 Copynumber: 36.0 Consensus size: 2
295872 AATTCTACAT
* * * *
295882 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA AA CA TGA AA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T-A TA TA TA
* *
295926 TA TA TA TA TA TA TA TA TG TA CA TCA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
295957 ATAATAATAA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
2 57 0.93
3 4 0.07
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (2 bp):
TA
Found at i:300073 original size:30 final size:31
Alignment explanation
Indices: 300008--300099 Score: 104
Period size: 30 Copynumber: 3.1 Consensus size: 31
299998 ATATATATGT
300008 TTAATTGATTATTTTTAAAAAAATTTGAGGAC
1 TTAATTGATTATTTTT-AAAAAATTTGAGGAC
* *
300040 TTAATTGATTCTTTTT-AAAAGTTTGAAGG-C
1 TTAATTGATTATTTTTAAAAAATTTG-AGGAC
*
300070 TTAATTG---ATTTTTAAAAAATTTAAGGAC
1 TTAATTGATTATTTTTAAAAAATTTGAGGAC
300098 TT
1 TT
300100 GGTTGATACT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
27 8 0.15
28 10 0.19
30 16 0.31
31 3 0.06
32 15 0.29
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (31 bp):
TTAATTGATTATTTTTAAAAAATTTGAGGAC
Found at i:301684 original size:6 final size:6
Alignment explanation
Indices: 301673--301751 Score: 140
Period size: 6 Copynumber: 13.2 Consensus size: 6
301663 GACACGTATT
* *
301673 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
301721 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
301752 GCCGAGCCGA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.32, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:301759 original size:5 final size:5
Alignment explanation
Indices: 301749--301787 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
301739 ACCACGACCA
* * *
301749 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
301788 ACGGACGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:307668 original size:6 final size:6
Alignment explanation
Indices: 307657--307693 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
307647 GACACGTATT
307657 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
307694 GCCGAGCCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:307701 original size:5 final size:5
Alignment explanation
Indices: 307691--307734 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
307681 ACCACGACCA
* * *
307691 CGAGC CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
307735 ACGGACGGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.23, C:0.34, G:0.41, T:0.02
Consensus pattern (5 bp):
CGAGC
Found at i:310590 original size:31 final size:31
Alignment explanation
Indices: 310555--310624 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
310545 AATTTGAGTC
*
310555 TTAAACTTT-AGATGAAATATCATTTTGATAA
1 TTAAA-TTTCAGATAAAATATCATTTTGATAA
* *
310586 TTAAATTTCAGATAAAATATTATTTTGATAT
1 TTAAATTTCAGATAAAATATCATTTTGATAA
*
310617 TTGAATTT
1 TTAAATTT
310625 GACGAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 3 0.09
31 31 0.91
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (31 bp):
TTAAATTTCAGATAAAATATCATTTTGATAA
Found at i:312709 original size:28 final size:29
Alignment explanation
Indices: 312646--312716 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 29
312636 ACAAGAGATC
*
312646 AAATTGATATTTT-ATAAAATTTATGAATT
1 AAATTAATATTTTAATAAAATTTATG-ATT
312675 AAATTAATATTTTAACTAAAATTTA-G-TT
1 AAATTAATATTTTAA-TAAAATTTATGATT
312703 AAATTAATATTTTA
1 AAATTAATATTTTA
312717 TATTAGAATC
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
28 16 0.41
29 12 0.31
30 2 0.05
31 9 0.23
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (29 bp):
AAATTAATATTTTAATAAAATTTATGATT
Found at i:326099 original size:2 final size:2
Alignment explanation
Indices: 326092--326169 Score: 142
Period size: 2 Copynumber: 40.0 Consensus size: 2
326082 TAGAAACTTC
326092 AT AT AT AT AT -T AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
326132 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
326170 GAGATTTGGT
Statistics
Matches: 74, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 72 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.