Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000002.1 Hibiscus syriacus cultivar Beakdansim tig00000003_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: 2131600
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:2047999 original size:55 final size:55
Alignment explanation
Indices: 2047915--2048039 Score: 191
Period size: 55 Copynumber: 2.3 Consensus size: 55
2047905 ATCTTATTTC
* *
2047915 TTTT-TCTTTTC-TTTCAATTTAGGGTGCCCTTTCGGGCTTTCACCCTAAATGTT
1 TTTTCTCTTTTCTTTTCAATTTAGGGCGCCCTTTCGGACTTTCACCCTAAATGTT
* *
2047968 TTTTCTCTTTTCTTTTCAATTTAGGGCGCCCTTTCGGATTTTCACCCTAAATTTT
1 TTTTCTCTTTTCTTTTCAATTTAGGGCGCCCTTTCGGACTTTCACCCTAAATGTT
2048023 TTTTCTCTTTTTCTTTT
1 TTTTCTC-TTTTCTTTT
2048040 ATCTTTTCTT
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
53 4 0.06
54 7 0.11
55 45 0.69
56 9 0.14
ACGTcount: A:0.12, C:0.22, G:0.11, T:0.54
Consensus pattern (55 bp):
TTTTCTCTTTTCTTTTCAATTTAGGGCGCCCTTTCGGACTTTCACCCTAAATGTT
Found at i:2059694 original size:17 final size:18
Alignment explanation
Indices: 2059672--2059715 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
2059662 AAAGAAGAAA
**
2059672 CATCGATG-TAATTAGTG
1 CATCGATGATAAGGAGTG
2059689 CATCGATGCATAAGGAGTG
1 CATCGATG-ATAAGGAGTG
2059708 CATCGATG
1 CATCGATG
2059716 CACCCCCTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
19 15 0.65
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (18 bp):
CATCGATGATAAGGAGTG
Found at i:2059806 original size:20 final size:22
Alignment explanation
Indices: 2059761--2059818 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
2059751 GCATGGGTAG
2059761 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
2059785 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
2059805 TGTATCGATGCACT
1 TGCATCGATGCACT
2059819 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:2060791 original size:32 final size:34
Alignment explanation
Indices: 2060722--2060796 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 34
2060712 ATATGTGATA
*
2060722 TATAT-ATATATGTTTTGTGATATGAATTATATG
1 TATATGATATATGTTGTGTGATATGAATTATATG
*
2060755 -ATATGATATATG-TGTGTGTTAATG-ATTAT-TG
1 TATATGATATATGTTGTGTGAT-ATGAATTATATG
*
2060786 TATATGTTATA
1 TATATGATATA
2060797 AGATATATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
31 2 0.06
32 24 0.67
33 10 0.28
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (34 bp):
TATATGATATATGTTGTGTGATATGAATTATATG
Found at i:2068720 original size:22 final size:23
Alignment explanation
Indices: 2068695--2068743 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
2068685 GAAATCGATA
2068695 CCCC-TTGAAGGGGAACCGATTC
1 CCCCTTTGAAGGGGAACCGATTC
* *
2068717 CCCCTTTGAATGGGAACTGATTC
1 CCCCTTTGAAGGGGAACCGATTC
2068740 CCCC
1 CCCC
2068744 CTAGGGGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.20, C:0.35, G:0.22, T:0.22
Consensus pattern (23 bp):
CCCCTTTGAAGGGGAACCGATTC
Found at i:2068757 original size:20 final size:20
Alignment explanation
Indices: 2068728--2068782 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
2068718 CCCTTTGAAT
*
2068728 GGGAACTGATTCCCCCCTAG
1 GGGAATTGATTCCCCCCTAG
*
2068748 GGGAATTGA-TACCCCCTAG
1 GGGAATTGATTCCCCCCTAG
* *
2068767 GGGAATCGATACCCCC
1 GGGAATTGATTCCCCC
2068783 TGGGGTTCTG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.24, C:0.33, G:0.25, T:0.18
Consensus pattern (20 bp):
GGGAATTGATTCCCCCCTAG
Found at i:2068781 original size:18 final size:19
Alignment explanation
Indices: 2068740--2068787 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
2068730 GAACTGATTC
*
2068740 CCCCCTAGGGGAATTGATA
1 CCCCCTAGGGGAATCGATA
2068759 CCCCCTAGGGGAATCGATA
1 CCCCCTAGGGGAATCGATA
2068778 CCCCCT-GGGG
1 CCCCCTAGGGG
2068788 TTCTGGTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.21, C:0.33, G:0.29, T:0.17
Consensus pattern (19 bp):
CCCCCTAGGGGAATCGATA
Found at i:2074330 original size:18 final size:17
Alignment explanation
Indices: 2074309--2074371 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 17
2074299 AATTCACGAG
*
2074309 AAAAATAAAATAAAGAA
1 AAAAATAAAATAAAAAA
*
2074326 AAAAA-GAAATGAAAAAA
1 AAAAATAAAAT-AAAAAA
*
2074343 ATAAAATAAATTAAAAAA
1 A-AAAATAAAATAAAAAA
2074361 TAAAAATAAAA
1 -AAAAATAAAA
2074372 CAGGACGAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
16 4 0.11
17 11 0.30
18 18 0.49
19 4 0.11
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (17 bp):
AAAAATAAAATAAAAAA
Found at i:2074455 original size:23 final size:21
Alignment explanation
Indices: 2074412--2074455 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2074402 TAAGGAAGAA
2074412 GAAAAAAATAAACAAATAAAC
1 GAAAAAAATAAACAAATAAAC
*
2074433 GAAAAACATAAAACAAAATAAAC
1 GAAAAAAAT-AAAC-AAATAAAC
2074456 AGTAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 4 0.20
23 8 0.40
ACGTcount: A:0.75, C:0.11, G:0.05, T:0.09
Consensus pattern (21 bp):
GAAAAAAATAAACAAATAAAC
Found at i:2074484 original size:25 final size:25
Alignment explanation
Indices: 2074434--2074504 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 25
2074424 CAAATAAACG
*
2074434 AAAAACATAAAACAAAATAAACAGTAA
1 AAAAAAATAAAA-AAAA-AAACAGTAA
2074461 TAAAAAAATAAAAAAAAAAA-AGTAA
1 -AAAAAAATAAAAAAAAAAACAGTAA
* *
2074486 AAAGAAAAGAGAAAAAAAA
1 AAA-AAAATAAAAAAAAAA
2074505 CACATACAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
24 3 0.08
25 18 0.46
26 3 0.08
27 4 0.10
28 11 0.28
ACGTcount: A:0.80, C:0.04, G:0.07, T:0.08
Consensus pattern (25 bp):
AAAAAAATAAAAAAAAAAACAGTAA
Found at i:2074501 original size:14 final size:13
Alignment explanation
Indices: 2074462--2074504 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2074452 AAACAGTAAT
*
2074462 AAAAAAATAAAAA
1 AAAAAAAGAAAAA
2074475 AAAAAAAGTAAAAA
1 AAAAAAAG-AAAAA
* *
2074489 GAAAAGAGAAAAA
1 AAAAAAAGAAAAA
2074502 AAA
1 AAA
2074505 CACATACAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.05
Consensus pattern (13 bp):
AAAAAAAGAAAAA
Found at i:2074709 original size:2 final size:2
Alignment explanation
Indices: 2074702--2074753 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
2074692 GAATGAAATA
2074702 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2074743 AT AT AC AT AT A
1 AT AT AT AT AT A
2074754 ATGGAATATA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2078013 original size:16 final size:15
Alignment explanation
Indices: 2077986--2078015 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2077976 AAATGAAAGA
2077986 TTTTATTTTTTAGTT
1 TTTTATTTTTTAGTT
2078001 TTTTATGTTTTTAGT
1 TTTTAT-TTTTTAGT
2078016 AAAACATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (15 bp):
TTTTATTTTTTAGTT
Found at i:2078076 original size:21 final size:21
Alignment explanation
Indices: 2078052--2078091 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2078042 AACTTTTTTC
2078052 TTTTT-TTAATTAAAAATAATA
1 TTTTTATT-ATTAAAAATAATA
2078073 TTTTTATTATTAAAAATAA
1 TTTTTATTATTAAAAATAA
2078092 AAATTAAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTTATTATTAAAAATAATA
Found at i:2079500 original size:260 final size:260
Alignment explanation
Indices: 2079029--2079553 Score: 818
Period size: 260 Copynumber: 2.0 Consensus size: 260
2079019 TCAGATCAGG
* *
2079029 TTGGGTCCATGTCAAATCAATTCGGGTCATTTTCAGATTGATTTGACATCAGATTCAGTTCGGGT
1 TTGGGTCCAAGTCAAATCAATTCGGGTCATTTTCAGATTGATTTGACATCAGATTCAATTCGGGT
* * *
2079094 TCAGGTCAAATTAACTTCAGTTCGGAATGATGTCAGTTCATGTCATAACAGTTAAGGTCTGAAGT
66 TCAGGTCAAATTAACTTCAGTTCGGAATGATGTCAGTTCATATCAAAACAGTTAAGGTCTGAAGC
* * * *
2079159 AGCTAAATACCAGGTTAATTCAAGTTTAGATGGACTTCAGTCGGATTTCATTCAGATTAGGTTAC
131 AGCTAAATACCAGGTTAATTCAAGTTTAGATGGACTTCAATCGAATTTCATTCAGATCAGGTCAC
* * * *
2079224 ATTATTGACATACAAAATTCAGGTAAGATCTTACCGGATACGGATTGACTTTAGGTTGCGTCATT
196 ATCATTGACATACAAAATTCAGGTAAGATCTTACAGGATACAGATTGACTTCAGGTTGCGTCATT
* *
2079289 TTGGGTTCAAGTCAAATCAATTCGGGTCATTTTCAGGTTGATTTGACATCAGATTCAATTCGGGT
1 TTGGGTCCAAGTCAAATCAATTCGGGTCATTTTCAGATTGATTTGACATCAGATTCAATTCGGGT
* * * *
2079354 TTAGGTCAAGTTAACTTCAGTTCGG-ATCGATTTCAGTTCATATCAAAACAGTTAAGGTGTGAAG
66 TCAGGTCAAATTAACTTCAGTTCGGAAT-GATGTCAGTTCATATCAAAACAGTTAAGGTCTGAAG
* *
2079418 CAGCTAAATACCAGGTTAATTCAAGTTTAGATGGACTTCAATTGAATTTCGTTCAGATCAGGTCA
130 CAGCTAAATACCAGGTTAATTCAAGTTTAGATGGACTTCAATCGAATTTCATTCAGATCAGGTCA
** *
2079483 CATCATTGACATACAAAATTCAGGTCGGATCTTACAGGATACAGATTGACTTCAGGTTGTGTCAT
195 CATCATTGACATACAAAATTCAGGTAAGATCTTACAGGATACAGATTGACTTCAGGTTGCGTCAT
2079548 T
260 T
2079549 TTGGG
1 TTGGG
2079554 GTTAATTATT
Statistics
Matches: 240, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
259 2 0.01
260 238 0.99
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (260 bp):
TTGGGTCCAAGTCAAATCAATTCGGGTCATTTTCAGATTGATTTGACATCAGATTCAATTCGGGT
TCAGGTCAAATTAACTTCAGTTCGGAATGATGTCAGTTCATATCAAAACAGTTAAGGTCTGAAGC
AGCTAAATACCAGGTTAATTCAAGTTTAGATGGACTTCAATCGAATTTCATTCAGATCAGGTCAC
ATCATTGACATACAAAATTCAGGTAAGATCTTACAGGATACAGATTGACTTCAGGTTGCGTCATT
Found at i:2079778 original size:24 final size:24
Alignment explanation
Indices: 2079751--2079797 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2079741 ACAGATCAAA
*
2079751 TTGAAA-TAATTATAAAATATGAAG
1 TTGAAATTAA-TATAAAAAATGAAG
2079775 TTGAAATTAATATAAAAAATGAA
1 TTGAAATTAATATAAAAAATGAA
2079798 CTAGATTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (24 bp):
TTGAAATTAATATAAAAAATGAAG
Found at i:2080173 original size:14 final size:14
Alignment explanation
Indices: 2080154--2080196 Score: 63
Period size: 12 Copynumber: 3.1 Consensus size: 14
2080144 ATGCATACTC
2080154 TATAAGTATACTTA
1 TATAAGTATACTTA
2080168 TATAAGTATA--TA
1 TATAAGTATACTTA
2080180 TATAAGTATACATTA
1 TATAAGTATAC-TTA
2080195 TA
1 TA
2080197 CTTATAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 12 0.46
14 10 0.38
15 4 0.15
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (14 bp):
TATAAGTATACTTA
Found at i:2080181 original size:12 final size:13
Alignment explanation
Indices: 2080148--2080190 Score: 61
Period size: 12 Copynumber: 3.3 Consensus size: 13
2080138 ATACTTATGC
*
2080148 ATACTCTATAAGT
1 ATACTATATAAGT
2080161 ATACTTATATAAGT
1 ATAC-TATATAAGT
2080175 ATA-TATATAAGT
1 ATACTATATAAGT
2080187 ATAC
1 ATAC
2080191 ATTATACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 12 0.44
13 4 0.15
14 11 0.41
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (13 bp):
ATACTATATAAGT
Found at i:2080197 original size:33 final size:33
Alignment explanation
Indices: 2080179--2080333 Score: 278
Period size: 33 Copynumber: 4.8 Consensus size: 33
2080169 ATAAGTATAT
2080179 ATATAAGTATACATTATACTTATAATATAATAC
1 ATATAAGTATACATTATACTTATAATATAATAC
*
2080212 ATATAAGTATACATTATTCTTATAATATAATAC
1 ATATAAGTATACATTATACTTATAATATAATAC
2080245 ATATAAGTATACATTATACTTAT-A-ATAATAC
1 ATATAAGTATACATTATACTTATAATATAATAC
*
2080276 ATATAAGTATACATTATTCTTATAATATAATAC
1 ATATAAGTATACATTATACTTATAATATAATAC
2080309 ATATAAGTATACATTATACTTATAA
1 ATATAAGTATACATTATACTTATAA
2080334 AATGTACTTT
Statistics
Matches: 116, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
31 29 0.25
32 2 0.02
33 85 0.73
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (33 bp):
ATATAAGTATACATTATACTTATAATATAATAC
Found at i:2080201 original size:6 final size:7
Alignment explanation
Indices: 2080186--2080332 Score: 58
Period size: 6 Copynumber: 22.6 Consensus size: 7
2080176 TATATATAAG
2080186 TATACAT
1 TATACAT
2080193 TATAC-T
1 TATACAT
2080199 TATA-AT
1 TATACAT
2080205 ATAATACA-
1 -T-ATACAT
*
2080213 TATA-AG
1 TATACAT
2080219 TATACAT
1 TATACAT
*
2080226 TATTC-T
1 TATACAT
2080232 TATA-AT
1 TATACAT
2080238 ATAATACA-
1 -T-ATACAT
*
2080246 TATA-AG
1 TATACAT
2080252 TATACAT
1 TATACAT
2080259 TATAC-T
1 TATACAT
2080265 TATA-AT
1 TATACAT
*
2080271 AATACA-
1 TATACAT
*
2080277 TATA-AG
1 TATACAT
2080283 TATACAT
1 TATACAT
*
2080290 TATTC-T
1 TATACAT
2080296 TATA-AT
1 TATACAT
2080302 ATAATACA-
1 -T-ATACAT
*
2080310 TATA-AG
1 TATACAT
2080316 TATACAT
1 TATACAT
2080323 TATAC-T
1 TATACAT
2080329 TATA
1 TATA
2080333 AAATGTACTT
Statistics
Matches: 108, Mismatches: 10, Indels: 45
0.66 0.06 0.28
Matches are distributed among these distances:
5 4 0.04
6 58 0.54
7 34 0.31
8 9 0.08
9 3 0.03
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (7 bp):
TATACAT
Found at i:2080284 original size:64 final size:64
Alignment explanation
Indices: 2080179--2080333 Score: 292
Period size: 64 Copynumber: 2.4 Consensus size: 64
2080169 ATAAGTATAT
2080179 ATATAAGTATACATTATACTTATAATATAATACATATAAGTATACATTATTCTTATAATATAATA
1 ATATAAGTATACATTATACTTAT-A-ATAATACATATAAGTATACATTATTCTTATAATATAATA
2080244 C
64 C
2080245 ATATAAGTATACATTATACTTATAATAATACATATAAGTATACATTATTCTTATAATATAATAC
1 ATATAAGTATACATTATACTTATAATAATACATATAAGTATACATTATTCTTATAATATAATAC
2080309 ATATAAGTATACATTATACTTATAA
1 ATATAAGTATACATTATACTTATAA
2080334 AATGTACTTT
Statistics
Matches: 89, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
64 65 0.73
65 1 0.01
66 23 0.26
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (64 bp):
ATATAAGTATACATTATACTTATAATAATACATATAAGTATACATTATTCTTATAATATAATAC
Found at i:2080860 original size:30 final size:30
Alignment explanation
Indices: 2080824--2080889 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
2080814 TATTAAATTG
*
2080824 TCATTTGCCGCTCAATCCTCCCTCTTTTTC
1 TCATTTGCCGCCCAATCCTCCCTCTTTTTC
* *
2080854 TCATTTGCCGCCCAATTCTCTCTCTTTTTC
1 TCATTTGCCGCCCAATCCTCCCTCTTTTTC
2080884 TCATTT
1 TCATTT
2080890 CCATTGTGCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.11, C:0.36, G:0.06, T:0.47
Consensus pattern (30 bp):
TCATTTGCCGCCCAATCCTCCCTCTTTTTC
Found at i:2081061 original size:20 final size:20
Alignment explanation
Indices: 2081038--2081089 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2081028 AACGCGATCC
2081038 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
2081058 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
2081078 CCAAAATCGCAA
1 CCAGAATCGCAA
2081090 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:2081208 original size:20 final size:20
Alignment explanation
Indices: 2081144--2081491 Score: 409
Period size: 20 Copynumber: 17.4 Consensus size: 20
2081134 GATTTTCCAT
* ** *
2081144 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
2081164 AATCGCAACGCG-AACACAT-
1 AATCGCAACGCGTATC-CGTA
2081183 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2081203 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
2081223 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
2081243 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2081263 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
2081283 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2081303 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2081323 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
2081343 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2081363 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
2081383 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
2081403 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2081423 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2081443 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
2081463 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
2081483 AATCACAAC
1 AATCGCAAC
2081492 ACTGAAATTT
Statistics
Matches: 283, Mismatches: 36, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
19 17 0.06
20 265 0.94
21 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:2082205 original size:24 final size:24
Alignment explanation
Indices: 2082166--2082212 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2082156 AAATTTGGTC
2082166 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
2082190 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
2082213 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:2082405 original size:12 final size:12
Alignment explanation
Indices: 2082388--2082412 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2082378 ATATAATCCT
2082388 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2082400 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2082412 G
1 G
2082413 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:2087737 original size:121 final size:121
Alignment explanation
Indices: 2087583--2087824 Score: 394
Period size: 121 Copynumber: 2.0 Consensus size: 121
2087573 AATAGCTTAC
* * * * * *
2087583 CCTCGAATAAATTTTACGTTGAGTCCTTTAAATTTCTTTGAATATTTGTGAAACCGAAACTTAAA
1 CCTCAAATAAATTATACGTCGAATCATTTAAATTTCTTTAAATATTTGTGAAACCGAAACTTAAA
* * *
2087648 TTATGTACACTCTAAGTGCTAACTATCCATTTATATCATTCATCTTTAAATACAAA
66 CTATGCACACTCTAAGTGCTAACTATCAATTTATATCATTCATCTTTAAATACAAA
*
2087704 CCTCAAATAAATTATACGTCGAATCATTTAAATTTCTTTAAATATTTGTGAAACCGAATCTTAAA
1 CCTCAAATAAATTATACGTCGAATCATTTAAATTTCTTTAAATATTTGTGAAACCGAAACTTAAA
2087769 CTATGCACACTCTAAGTGCTAACTATCAATTTATATCATTCATCTTTAAATACAAA
66 CTATGCACACTCTAAGTGCTAACTATCAATTTATATCATTCATCTTTAAATACAAA
2087825 ACTTGAAAAT
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 111 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.38
Consensus pattern (121 bp):
CCTCAAATAAATTATACGTCGAATCATTTAAATTTCTTTAAATATTTGTGAAACCGAAACTTAAA
CTATGCACACTCTAAGTGCTAACTATCAATTTATATCATTCATCTTTAAATACAAA
Found at i:2090566 original size:13 final size:13
Alignment explanation
Indices: 2090548--2090572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2090538 AAATCTTAAC
2090548 ATTTAACTAAATA
1 ATTTAACTAAATA
2090561 ATTTAACTAAAT
1 ATTTAACTAAAT
2090573 TATCATTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTTAACTAAATA
Found at i:2094347 original size:7 final size:7
Alignment explanation
Indices: 2094329--2094379 Score: 77
Period size: 7 Copynumber: 7.1 Consensus size: 7
2094319 GAGCGACATT
2094329 TATATTA
1 TATATTA
2094336 TATATATAA
1 TATAT-T-A
2094345 TATATTA
1 TATATTA
2094352 TATATTA
1 TATATTA
2094359 TATATTA
1 TATATTA
2094366 TATATTA
1 TATATTA
2094373 T-TATTA
1 TATATTA
2094379 T
1 T
2094380 TATCACAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.14
7 28 0.67
8 2 0.05
9 6 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TATATTA
Found at i:2094380 original size:16 final size:16
Alignment explanation
Indices: 2094331--2094382 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
2094321 GCGACATTTA
*
2094331 TATTATATA-TATAAT
1 TATTATATATTATTAT
2094346 ATATTATATATTA-TA-
1 -TATTATATATTATTAT
2094361 TATTATATATTATTAT
1 TATTATATATTATTAT
2094377 TATTAT
1 TATTAT
2094383 CACAAGATTC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 12 0.38
15 2 0.06
16 16 0.50
17 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTATATATTATTAT
Found at i:2094422 original size:24 final size:25
Alignment explanation
Indices: 2094385--2094432 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
2094375 ATTATTATCA
2094385 CAAGATTCGAAGGCCCAATTACAAAG
1 CAAGATTC-AAGGCCCAATTACAAAG
*
2094411 CAAGATTC-AGGCCCGATTACAA
1 CAAGATTCAAGGCCCAATTACAA
2094433 CAACCAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.62
26 8 0.38
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.17
Consensus pattern (25 bp):
CAAGATTCAAGGCCCAATTACAAAG
Found at i:2096865 original size:17 final size:17
Alignment explanation
Indices: 2096839--2096880 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
2096829 GAAAAGCATG
*
2096839 TTAGTTTTTTAATTTAC
1 TTAGTATTTTAATTTAC
2096856 TTAGTATTTTAATTTAC
1 TTAGTATTTTAATTTAC
2096873 TTAGTATT
1 TTAGTATT
2096881 ACTTTACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.62
Consensus pattern (17 bp):
TTAGTATTTTAATTTAC
Found at i:2114400 original size:20 final size:20
Alignment explanation
Indices: 2114375--2114429 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
2114365 CAAAGGTAAG
2114375 GGAAGTATCGATACTCTCAA
1 GGAAGTATCGATACTCTCAA
2114395 GGAAGTATCGATACTCTCAA
1 GGAAGTATCGATACTCTCAA
*
2114415 GGTAGTATCGATACT
1 GGAAGTATCGATACT
2114430 ACCAACATTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (20 bp):
GGAAGTATCGATACTCTCAA
Found at i:2115444 original size:18 final size:17
Alignment explanation
Indices: 2115417--2115450 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2115407 TTATCTCCAG
2115417 AAATTCTAAATTCTTAAA
1 AAATTCTAAATT-TTAAA
*
2115435 AAATTTTAAATTTTAA
1 AAATTCTAAATTTTAA
2115451 TTAATAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTCTAAATTTTAAA
Found at i:2127416 original size:41 final size:43
Alignment explanation
Indices: 2127295--2127422 Score: 165
Period size: 43 Copynumber: 3.1 Consensus size: 43
2127285 TAGAGCATGT
* * ** *
2127295 TATATG-TGATATGAGATTAAGGGATGAAA-ATAGATGATATA
1 TATATGATGATATAAGAATAAGACATGAAACAGAGATGATATA
*
2127336 TATATGATGATATAAGAATAAGACATGAAACATAGATGATATA
1 TATATGATGATATAAGAATAAGACATGAAACAGAGATGATATA
*
2127379 TATATGATGATATAAGAATAAGACATGAATC-GA-ATGATATA
1 TATATGATGATATAAGAATAAGACATGAAACAGAGATGATATA
2127420 TAT
1 TAT
2127423 GTTTATGTGA
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
41 17 0.22
42 20 0.25
43 42 0.53
ACGTcount: A:0.48, C:0.03, G:0.19, T:0.30
Consensus pattern (43 bp):
TATATGATGATATAAGAATAAGACATGAAACAGAGATGATATA
Found at i:2127422 original size:43 final size:43
Alignment explanation
Indices: 2127295--2127407 Score: 176
Period size: 43 Copynumber: 2.7 Consensus size: 43
2127285 TAGAGCATGT
* * **
2127295 TATATG-TGATATGAGATTAAGGGATGAAA-ATAGATGATATA
1 TATATGATGATATAAGAATAAGACATGAAACATAGATGATATA
2127336 TATATGATGATATAAGAATAAGACATGAAACATAGATGATATA
1 TATATGATGATATAAGAATAAGACATGAAACATAGATGATATA
2127379 TATATGATGATATAAGAATAAGACATGAA
1 TATATGATGATATAAGAATAAGACATGAA
2127408 TCGAATGATA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
41 6 0.09
42 19 0.29
43 41 0.62
ACGTcount: A:0.49, C:0.03, G:0.19, T:0.29
Consensus pattern (43 bp):
TATATGATGATATAAGAATAAGACATGAAACATAGATGATATA
Found at i:2127652 original size:18 final size:18
Alignment explanation
Indices: 2127629--2127692 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
2127619 CGAGGGTTAC
2127629 AGTGGTCCTACGGGACAT
1 AGTGGTCCTACGGGACAT
**
2127647 AGTGGTCCTTTGGGACAAT
1 AGTGGTCCTACGGGAC-AT
*
2127666 ACAATGGTCCTACGGGACAT
1 --AGTGGTCCTACGGGACAT
2127686 AGTGGTC
1 AGTGGTC
2127693 ATTTGGGATA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 20 0.54
19 2 0.05
20 2 0.05
21 13 0.35
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.25
Consensus pattern (18 bp):
AGTGGTCCTACGGGACAT
Found at i:2127685 original size:39 final size:39
Alignment explanation
Indices: 2127626--2127700 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
2127616 AGTCGAGGGT
* *
2127626 TACAGTGGTCCTACGGGACATAGTGGTCCTTTGGGACAA
1 TACAATGGTCCTACGGGACATAGTGGTCATTTGGGACAA
2127665 TACAATGGTCCTACGGGACATAGTGGTCATTTGGGA
1 TACAATGGTCCTACGGGACATAGTGGTCATTTGGGA
2127701 TAAATTTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.27
Consensus pattern (39 bp):
TACAATGGTCCTACGGGACATAGTGGTCATTTGGGACAA
Found at i:2127700 original size:18 final size:18
Alignment explanation
Indices: 2127629--2127700 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
2127619 CGAGGGTTAC
**
2127629 AGTGGTCCTACGGGACAT
1 AGTGGTCCTTTGGGACAT
2127647 AGTGGTCCTTTGGGACAAT
1 AGTGGTCCTTTGGGAC-AT
* **
2127666 ACAATGGTCCTACGGGACAT
1 --AGTGGTCCTTTGGGACAT
*
2127686 AGTGGTCATTTGGGA
1 AGTGGTCCTTTGGGA
2127701 TAAATTTAGT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
18 25 0.60
19 2 0.05
20 2 0.05
21 13 0.31
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTTGGGACAT
Done.