Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002850.1 Hibiscus syriacus cultivar Beakdansim tig00005863_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: 62605
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:8685 original size:14 final size:14
Alignment explanation
Indices: 8666--8692 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8656 TACATTTTCA
8666 TTCTTCATTCTTTT
1 TTCTTCATTCTTTT
8680 TTCTTCATTCTTT
1 TTCTTCATTCTTT
8693 ACATTCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCTTCATTCTTTT
Found at i:12133 original size:8 final size:8
Alignment explanation
Indices: 12110--12197 Score: 62
Period size: 8 Copynumber: 11.5 Consensus size: 8
12100 ATGCTTGAAA
12110 AAAAAATG
1 AAAAAATG
**
12118 AATGAATG
1 AAAAAATG
12126 AAAAAATG
1 AAAAAATG
*
12134 AAAAAGTG
1 AAAAAATG
12142 -AAAAA-G
1 AAAAAATG
**
12148 AAAATGAAAA
1 AAAA--AATG
12158 AAAAAATG
1 AAAAAATG
12166 AAAAAA--
1 AAAAAATG
*
12172 AAAAGA--
1 AAAAAATG
12178 AAAAAATG
1 AAAAAATG
12186 AAAAAATG
1 AAAAAATG
12194 AAAA
1 AAAA
12198 GAAAAAAGAA
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
6 11 0.17
7 7 0.11
8 39 0.62
9 2 0.03
10 4 0.06
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (8 bp):
AAAAAATG
Found at i:12143 original size:16 final size:16
Alignment explanation
Indices: 12110--12213 Score: 52
Period size: 13 Copynumber: 7.1 Consensus size: 16
12100 ATGCTTGAAA
*
12110 AAAAAATGAATGAATG
1 AAAAAATGAATAAATG
12126 AAAAAATGAA-AAAGTG
1 AAAAAATGAATAAA-TG
12142 -AAAAA-G-A-AAATG
1 AAAAAATGAATAAATG
**
12154 AAAAAAAAAATGAAA--
1 AAAAAATGAAT-AAATG
* *
12169 AAAAAAAGAAAAAAATG
1 AAAAAATG-AATAAATG
12186 AAAAAATG-A-AAA-G
1 AAAAAATGAATAAATG
12199 AAAAAA-GAA-AAATG
1 AAAAAATGAATAAATG
12213 A
1 A
12214 GGGTTCGAGA
Statistics
Matches: 72, Mismatches: 5, Indels: 24
0.71 0.05 0.24
Matches are distributed among these distances:
12 3 0.04
13 20 0.28
14 6 0.08
15 19 0.26
16 14 0.19
17 10 0.14
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (16 bp):
AAAAAATGAATAAATG
Found at i:12154 original size:32 final size:30
Alignment explanation
Indices: 12131--12209 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 30
12121 GAATGAAAAA
**
12131 ATGAAAAAGTGAAAAAGAAAATGAAAAAAAAA
1 ATGAAAAA--GAAAAAGAAAATGAATGAAAAA
*
12163 ATGAAAAA-AAAAAGAAAA-AAATGAAAAA
1 ATGAAAAAGAAAAAGAAAATGAATGAAAAA
12191 ATG-AAAAGAAAAAAGAAAA
1 ATGAAAAAG-AAAAAGAAAA
12210 ATGAGGGTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 4 0.10
28 10 0.24
29 20 0.48
32 8 0.19
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (30 bp):
ATGAAAAAGAAAAAGAAAATGAATGAAAAA
Found at i:12157 original size:12 final size:12
Alignment explanation
Indices: 12135--12209 Score: 61
Period size: 12 Copynumber: 6.3 Consensus size: 12
12125 GAAAAAATGA
12135 AAAAGTGAAAAAG
1 AAAA-TGAAAAAG
*
12148 AAAATGAAAAAA
1 AAAATGAAAAAG
12160 AAAATGAAAAA-
1 AAAATGAAAAAG
*
12171 AAAA--AGAAA-
1 AAAATGAAAAAG
12180 AAAATGAAAAAATG
1 AAAATG-AAAAA-G
12194 AAAA-GAAAAAAG
1 AAAATG-AAAAAG
12206 AAAA
1 AAAA
12210 ATGAGGGTTC
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
9 8 0.15
11 4 0.07
12 27 0.50
13 11 0.20
14 4 0.07
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (12 bp):
AAAATGAAAAAG
Found at i:12171 original size:20 final size:20
Alignment explanation
Indices: 12122--12210 Score: 89
Period size: 20 Copynumber: 4.5 Consensus size: 20
12112 AAAATGAATG
12122 AATGAAAAAATGAAAAAGTGAAA
1 AATGAAAAAATGAAAAA---AAA
12145 AA-G--AAAATGAAAAAAAA
1 AATGAAAAAATGAAAAAAAA
*
12162 AATGAAAAAA-AAAAGAAAAA
1 AATGAAAAAATGAAA-AAAAA
12182 AATGAAAAAATGAAAAGAAAA
1 AATGAAAAAATGAAAA-AAAA
12203 AA-GAAAAA
1 AATGAAAAA
12211 TGAGGGTTCG
Statistics
Matches: 58, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
17 5 0.09
18 1 0.02
19 3 0.05
20 37 0.64
21 9 0.16
22 1 0.02
23 2 0.03
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (20 bp):
AATGAAAAAATGAAAAAAAA
Found at i:13303 original size:105 final size:105
Alignment explanation
Indices: 13121--13849 Score: 1170
Period size: 105 Copynumber: 6.9 Consensus size: 105
13111 TCAACAACAA
* ** *
13121 TCAAATCCACCACAGAAGGAGGTGGCCCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
13186 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
13226 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
13291 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
* * * *
13331 TCAAATCCACCACAAAAGGAGGTGACCCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
*
13396 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
* *
13436 TCAAATCCACCGCAGAATGAGGTGAACTAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
13501 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
*
13541 TCAAATCCACCGCAGAAGGAGGTGAACCAATATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* * *
13606 CTTAAAGGAGAAGGTTCATAATGAGAAGAGTATGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
*
13646 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAAAACTCGT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* * *
13711 CTTAAAAGAGAAGGTTCGTAATGAGAAGAGCCTGTTCCTT
66 CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
* * * * * *
13751 TCAAATTCACCCCAGAAGGAGGTGAATCGACATTTCCAGAAGAGTTCATAATGATAAGAACTCAT
1 TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
* *
13816 CCGATAAAAGAAGAAGAAGTTCATAATGAGAAGA
66 CC--T-AAAGGAGAAG--GTTCGTAATGAGAAGA
13850 ACTTGTTCAA
Statistics
Matches: 580, Mismatches: 39, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
105 556 0.96
107 1 0.00
108 8 0.01
110 15 0.03
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.22
Consensus pattern (105 bp):
TCAAATCCACCGCAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGT
CCTAAAGGAGAAGGTTCGTAATGAGAAGAGCATGTTCCTT
Found at i:17285 original size:23 final size:23
Alignment explanation
Indices: 17259--17341 Score: 139
Period size: 23 Copynumber: 3.6 Consensus size: 23
17249 AATCTTATAT
*
17259 GGCACTTCGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
17282 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
17305 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
17328 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
17342 TTTATATGAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.19, C:0.29, G:0.28, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:32669 original size:18 final size:19
Alignment explanation
Indices: 32622--32671 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
32612 ACCTAAAAAA
*
32622 TAAA-AAAAAATAAACGAG
1 TAAATAAAAAATAAACAAG
*
32640 TAAAT-AATAATAAACAAG
1 TAAATAAAAAATAAACAAG
32658 -AAATAAAAAATAAA
1 TAAATAAAAAATAAA
32672 ATACTACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.16
Consensus pattern (19 bp):
TAAATAAAAAATAAACAAG
Found at i:32816 original size:33 final size:33
Alignment explanation
Indices: 32683--32814 Score: 102
Period size: 33 Copynumber: 4.2 Consensus size: 33
32673 TACTACATAT
*
32683 AAAAATGTTTTAAAACTATA---TATA--TTTC
1 AAAAACGTTTTAAAACTATATGTTATAGTTTTC
** * * *
32711 AAAAATATTTTCAAAACCATATACTATATAATTTT-
1 AAAAACGTTTT-AAAACTATAT-GT-TATAGTTTTC
*
32746 AAAAATGTTTTAAAACTATATGTTATAGTTTTC
1 AAAAACGTTTTAAAACTATATGTTATAGTTTTC
32779 AAAAACGTTTTAAAACTATA--TTATA-TGTTTC
1 AAAAACGTTTTAAAACTATATGTTATAGT-TTTC
32810 AAAAA
1 AAAAA
32815 AAATTTCAAC
Statistics
Matches: 87, Mismatches: 7, Indels: 17
0.78 0.06 0.15
Matches are distributed among these distances:
28 10 0.11
29 8 0.09
30 1 0.01
31 14 0.16
32 8 0.09
33 20 0.23
34 13 0.15
35 10 0.11
36 3 0.03
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (33 bp):
AAAAACGTTTTAAAACTATATGTTATAGTTTTC
Found at i:32868 original size:35 final size:35
Alignment explanation
Indices: 32699--33097 Score: 213
Period size: 38 Copynumber: 11.2 Consensus size: 35
32689 GTTTTAAAAC
* *
32699 TATAT-ATATTTCAAAAAT-ATTTTCAAAACCATATAC
1 TATATAAT-TTTC-AAAATGATTTT-AAAACTATATAT
* *
32735 TATATAATTTTAAAAATG-TTTTAAAACTATAT-G
1 TATATAATTTTCAAAATGATTTTAAAACTATATAT
* *
32768 T-TATAGTTTTCAAAAACG-TTTTAAAAC--TATAT
1 TATATAATTTTC-AAAATGATTTTAAAACTATATAT
* ** * *
32800 TATAT--GTTTCAAAAAAAATTT-CAACTATATAT
1 TATATAATTTTCAAAATGATTTTAAAACTATATAT
* *
32832 TATATAAATTTCAAAATGATTTTAAAACTATTTAT
1 TATATAATTTTCAAAATGATTTTAAAACTATATAT
* *
32867 TATATAAGTTTTCAAAATGGTTTTAAAAACTATATAA
1 TATATAA-TTTTCAAAATGATTTT-AAAACTATATAT
* *
32904 TATAT-ATGGTTTCAAAAAT-ATCTTCAAAAACTATATAA
1 TATATAAT--TTTC-AAAATGAT-TT-TAAAACTATATAT
*
32942 TATATATGTTTTCAAAAAAAATG-TTTTCAAAACTATA-A-
1 TATATA-ATTTTC----AAAATGATTTT-AAAACTATATAT
* *
32980 TATATATGTTTTCAAAAATGATTTTAAAAATTATATAT
1 TATATA-ATTTTC-AAAATGATTTT-AAAACTATATAT
* *
33018 TATATATATTTTCTAAAATGTTTTTTTTTAAACTATATAT
1 TATATA-ATTTTC-AAAATG---ATTTTAAAACTATATAT
* * *
33058 TATATAGTTTTAAAAACT-A-TTAAAAACTATATAT
1 TATATAATTTTCAAAA-TGATTTTAAAACTATATAT
33092 TATATA
1 TATATA
33098 CGTAGTTTCA
Statistics
Matches: 293, Mismatches: 38, Indels: 66
0.74 0.10 0.17
Matches are distributed among these distances:
30 7 0.02
31 10 0.03
32 19 0.06
33 18 0.06
34 40 0.14
35 33 0.11
36 35 0.12
37 23 0.08
38 63 0.22
39 6 0.02
40 28 0.10
41 11 0.04
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (35 bp):
TATATAATTTTCAAAATGATTTTAAAACTATATAT
Found at i:33051 original size:76 final size:73
Alignment explanation
Indices: 32840--33111 Score: 236
Period size: 76 Copynumber: 3.6 Consensus size: 73
32830 ATTATATAAA
*
32840 TTTC-AAAATGATTTT-AAAACTATTTATTATATA-AGTTTTCAAAATG-GTTTTAAAAACTATA
1 TTTCAAAAAT-ATTTTAAAAACTATATATTATATATA-TTTTCAAAATGTGTTTTAAAAAC--TA
*
32901 TAATATATATGG
62 TAATATATATGT
* * * ** *
32913 TTTCAAAAATATCTTCAAAAACTATATAATATATATGTTTTCAAAAAAAATGTTTTCAAAACTAT
1 TTTCAAAAATAT-TTTAAAAACTATATATTATATATATTTTC--AAAATGTGTTTTAAAAACTAT
32978 AATATATATGT
63 AATATATATGT
* * **
32989 TTTCAAAAATGATTTTAAAAATTATATATTATATATATTTTCTAAAATGTTTTTTTTTAAACTAT
1 TTTCAAAAAT-ATTTTAAAAACTATATATTATATATATTTTC-AAAATG-TGTTTTAAAAACTAT
33054 -ATATTATATAGT
63 AATA-TATAT-GT
*
33066 TTT-AAAAACTA--TTAAAAACTATATATTATATACGTAGTTTCAAAAT
1 TTTCAAAAA-TATTTTAAAAACTATATATTATATA--TATTTTCAAAAT
33112 ATGTATATAT
Statistics
Matches: 165, Mismatches: 20, Indels: 26
0.78 0.09 0.12
Matches are distributed among these distances:
73 6 0.04
74 27 0.16
75 33 0.20
76 77 0.47
77 12 0.07
78 10 0.06
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (73 bp):
TTTCAAAAATATTTTAAAAACTATATATTATATATATTTTCAAAATGTGTTTTAAAAACTATAAT
ATATATGT
Found at i:34135 original size:248 final size:244
Alignment explanation
Indices: 33686--34308 Score: 755
Period size: 248 Copynumber: 2.5 Consensus size: 244
33676 GACAATTTTA
* * * * * *
33686 TTGACAAATAGCCCTTCTTGCCTTGAGCTATGTTGTAACTGATATGACCTCGAAGTTGAGTGTAA
1 TTGACAGATAACCCTTCTTGCCTTGAGCTATGATGTAAATGATATG-CCTTGAAGCTGAGTGTAA
* * *
33751 TCGAACCCAGGGGTCTTTGGCAGATAGCCCTTTTTGACTTAAGCTATGCTGCAAATGATGTGCCT
65 TCGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCT
* * *
33816 TAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGATGACAGATAACCCTTCTAGCCTTGAGTTAT
130 TAGAGCTGAGCGTAGTCGAACCCAAAGGTCTTTGATAACAGATAACCCTTCTAGCCTTGAGTTAT
* * *
33881 GCTGTAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCAAAAGTCTT
195 GCTGTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCAAAAGTC-T
* * *
33931 TTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGATGTAAATGTTATGCCCTTGAAGCTGAGTG
1 TTG---ACAGATAACCCTTCTTGCCTTGAGCTATGATGTAAATGATATG-CCTTGAAGCTGAGTG
* *
33996 TAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTG
62 TAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG
**
34061 CC-TAGGAGCTGAGCGTAGTCGAACCCAAAGGTCTTTTCTAACAGATAACCCTTCTAGCCTTGAG
127 CCTTA-GAGCTGAGCGTAGTCGAACCCAAAGGTCTTTGATAACAGATAACCCTTCTAGCCTTGAG
* * * **
34125 TTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCT
191 TTATGCTGTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCAAAAGTCT
* * * ** * * * * *
34179 TTGGCAGATAACCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGACAGATAACCCTTCTTGCCTTGAGCTATGATGTAAATGATATGCCTTGAAGCTGAGTGTAAT
* * * *
34244 CGAACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTTAAGTTATGCTGCAAATGATGT
66 CGAACTCAAGGGTC--T--TTGGCAGATAGCCCTTCTTGAC-TTAAGCTATGCTGCAAATGATGT
34309 TCCCTCGAAG
Statistics
Matches: 321, Mismatches: 47, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
244 28 0.09
245 36 0.11
246 1 0.00
247 2 0.01
248 211 0.66
249 43 0.13
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (244 bp):
TTGACAGATAACCCTTCTTGCCTTGAGCTATGATGTAAATGATATGCCTTGAAGCTGAGTGTAAT
CGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTT
AGAGCTGAGCGTAGTCGAACCCAAAGGTCTTTGATAACAGATAACCCTTCTAGCCTTGAGTTATG
CTGTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCAAAAGTCT
Found at i:34143 original size:164 final size:163
Alignment explanation
Indices: 33819--34304 Score: 679
Period size: 164 Copynumber: 2.9 Consensus size: 163
33809 TGTGCCTTAG
* * * * * * * *
33819 AGCTGAGCGTAGTCGAACTCGAA-GGTCTTTGATGACAGATAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGTGTAATCGAACT-TAAGGGTCTTTG--G-CAGATAACCCTTCTTGACTTAAGCTATTC
* * *
33883 TGTAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAAGTCTTTTGCTAACAGATAACCC
62 TGCAAATGATGTGCC-TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTT-CTAACAGATAACCC
*
33948 TTCTAGCCTTGAGTTATGATGTAAATGTTATGCCCTTGA
125 TTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGA
*
33987 AGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGCA
1 AGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATTCTGCA
*
34052 AATGATGTGCCTAGGAGCTGAGCGTAGTCGAACCCAAAGGTCTTTTCTAACAGATAACCCTTCTA
66 AATGATGTGCCT-GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTCTAACAGATAACCCTTCTA
34117 GCCTTGAGTTATGCTGTAAATGTTATGCCCTTGA
130 GCCTTGAGTTATGCTGTAAATGTTATGCCCTTGA
34151 AGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATTCTGCA
1 AGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATTCTGCA
**
34216 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGT-TGGCAGATAACCCTTC
66 AATGATGTGCC-TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT--TCTAACAGATAACCCTTC
* * * *
34280 TCGACTTTAAGTTATGCTGCAAATG
128 TAG-CCTTGAGTTATGCTGTAAATG
34305 ATGTTCCCTC
Statistics
Matches: 290, Mismatches: 22, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
164 159 0.55
165 84 0.29
166 20 0.07
167 2 0.01
168 25 0.09
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (163 bp):
AGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATTCTGCA
AATGATGTGCCTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTCTAACAGATAACCCTTCTAG
CCTTGAGTTATGCTGTAAATGTTATGCCCTTGA
Found at i:40793 original size:18 final size:18
Alignment explanation
Indices: 40753--40795 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
40743 AAAAAAAAAT
*
40753 AAATAAACGAGTAAATAA
1 AAATAAACAAGTAAATAA
*
40771 TAATAAACAAG-AAATAAA
1 AAATAAACAAGTAAAT-AA
40789 AAATAAA
1 AAATAAA
40796 ATACTACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.72, C:0.05, G:0.07, T:0.16
Consensus pattern (18 bp):
AAATAAACAAGTAAATAA
Found at i:40940 original size:33 final size:33
Alignment explanation
Indices: 40807--40938 Score: 102
Period size: 33 Copynumber: 4.2 Consensus size: 33
40797 TACTACATAT
*
40807 AAAAATGTTTTAAAACTATA---TATA--TTTC
1 AAAAACGTTTTAAAACTATATGTTATAGTTTTC
** * * *
40835 AAAAATATTTTCAAAACCATATACTATATAATTTT-
1 AAAAACGTTTT-AAAACTATAT-GT-TATAGTTTTC
*
40870 AAAAATGTTTTAAAACTATATGTTATAGTTTTC
1 AAAAACGTTTTAAAACTATATGTTATAGTTTTC
40903 AAAAACGTTTTAAAACTATA--TTATA-TGTTTC
1 AAAAACGTTTTAAAACTATATGTTATAGT-TTTC
40934 AAAAA
1 AAAAA
40939 AAATTTCAAC
Statistics
Matches: 87, Mismatches: 7, Indels: 17
0.78 0.06 0.15
Matches are distributed among these distances:
28 10 0.11
29 8 0.09
30 1 0.01
31 14 0.16
32 8 0.09
33 20 0.23
34 13 0.15
35 10 0.11
36 3 0.03
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (33 bp):
AAAAACGTTTTAAAACTATATGTTATAGTTTTC
Found at i:40992 original size:35 final size:35
Alignment explanation
Indices: 40823--41221 Score: 222
Period size: 38 Copynumber: 11.2 Consensus size: 35
40813 GTTTTAAAAC
* *
40823 TATAT-ATATTTCAAAAAT-ATTTTCAAAACCATATAC
1 TATATAAT-TTTC-AAAATGATTTT-AAAACTATATAT
* *
40859 TATATAATTTTAAAAATG-TTTTAAAACTATAT-G
1 TATATAATTTTCAAAATGATTTTAAAACTATATAT
* *
40892 T-TATAGTTTTCAAAAACG-TTTTAAAAC--TATAT
1 TATATAATTTTC-AAAATGATTTTAAAACTATATAT
* ** * *
40924 TATAT--GTTTCAAAAAAAATTT-CAACTATATAT
1 TATATAATTTTCAAAATGATTTTAAAACTATATAT
* *
40956 TATATAAATTTCAAAATGATTTTAAAACTATTTAT
1 TATATAATTTTCAAAATGATTTTAAAACTATATAT
* *
40991 TATATAAGTTTTCAAAATGGTTTTAAAAACTATATAA
1 TATATAA-TTTTCAAAATGATTTT-AAAACTATATAT
* *
41028 TATAT-ATGGTTTCAAAAAT-ATCTTCAAAAACTATATAA
1 TATATAAT--TTTC-AAAATGAT-TT-TAAAACTATATAT
*
41066 TATATATGTTTTCAAAAAAATG-TTTTCAAAACTATA-A-
1 TATATA-ATTTTC---AAAATGATTTT-AAAACTATATAT
* *
41103 TATATATGTTTTCAAAAATGATTTTAAAAATTATATAT
1 TATATA-ATTTTC-AAAATGATTTT-AAAACTATATAT
*
41141 TATATATATTTTCTAAAATGTTTTTTTTTAAAACTATATAT
1 TATATA-ATTTTC-AAAATG----ATTTTAAAACTATATAT
* * *
41182 TATATAGTTTTAAAAACT-A-TTAAAAACTATATAT
1 TATATAATTTTCAAAA-TGATTTTAAAACTATATAT
41216 TATATA
1 TATATA
41222 CGTAGTTTCA
Statistics
Matches: 295, Mismatches: 36, Indels: 66
0.74 0.09 0.17
Matches are distributed among these distances:
30 7 0.02
31 10 0.03
32 19 0.06
33 18 0.06
34 41 0.14
35 33 0.11
36 35 0.12
37 36 0.12
38 47 0.16
39 15 0.05
40 13 0.04
41 17 0.06
42 4 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (35 bp):
TATATAATTTTCAAAATGATTTTAAAACTATATAT
Found at i:41077 original size:75 final size:74
Alignment explanation
Indices: 40946--41221 Score: 246
Period size: 75 Copynumber: 3.7 Consensus size: 74
40936 AAAAAATTTC
* ** * * *
40946 AACTATATATTATATA-AATTTC-AAAATGATTTTAAAACTATTTATTATATAAGTTTTC-AAAA
1 AACTATATAATATATATGGTTTCAAAAAT-ATTTAAAAACTATATATTATATATGTTTTCAAAAA
41008 TGGTTTTAAA
65 TGGTTTTAAA
*
41018 AACTATATAATATATATGGTTTCAAAAATATCTTCAAAAACTATATAATATATATGTTTTCAAAA
1 AACTATATAATATATATGGTTTCAAAAATAT-TT-AAAAACTATATATTATATATGTTTTC--AA
*
41083 AAAT-GTTTTCAA
62 AAATGGTTTTAAA
* * * *
41095 AAC--TATAATATATATGTTTTCAAAAATGATTTTAAAAATTATATATTATATATATTTTCTAAA
1 AACTATATAATATATATGGTTTCAAAAAT-A-TTTAAAAACTATATATTATATATGTTTTCAAAA
* *
41158 ATGTTTTTTTTTAA
64 ATG---GTTTTAAA
* *
41172 AACTATAT-AT-TATATAGTTTTAAAAACTA-TTAAAAACTATATATTATATA
1 AACTATATAATATATATGGTTTCAAAAA-TATTTAAAAACTATATATTATATA
41222 CGTAGTTTCA
Statistics
Matches: 169, Mismatches: 19, Indels: 29
0.78 0.09 0.13
Matches are distributed among these distances:
72 15 0.09
73 11 0.07
74 7 0.04
75 88 0.52
76 3 0.02
77 34 0.20
78 8 0.05
79 3 0.02
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (74 bp):
AACTATATAATATATATGGTTTCAAAAATATTTAAAAACTATATATTATATATGTTTTCAAAAAT
GGTTTTAAA
Found at i:41100 original size:77 final size:75
Alignment explanation
Indices: 40823--41221 Score: 242
Period size: 75 Copynumber: 5.6 Consensus size: 75
40813 GTTTTAAAAC
* * * * *
40823 TATATAT-ATTTCAAAAATATTTTCAAAACCATATACTATATA-ATTTT---AAAAATGTTTT-A
1 TATATATGGTTTCAAAAATA-TTTAAAAACTATATATTATATATGTTTTCAAAAAAATGTTTTAA
*
40882 AAACTATAT-G
65 AAACTATATAA
* ** * * *
40892 T-TATA-GTTTTCAAAAACGTTTTAAAAC--TATA-T-TATATG-TTTCAAAAAAA--ATTT--C
1 TATATATGGTTTCAAAAATATTTAAAAACTATATATTATATATGTTTTCAAAAAAATGTTTTAAA
*
40946 AACTATATAT
66 AACTATATAA
** * * *
40956 TATATA-AATTTC-AAAATGATTTTAAAACTATTTATTATATAAGTTTTC---AAAATGGTTTTA
1 TATATATGGTTTCAAAAAT-ATTTAAAAACTATATATTATATATGTTTTCAAAAAAAT-GTTTTA
41016 AAAACTATATAA
64 AAAACTATATAA
* *
41028 TATATATGGTTTCAAAAATATCTTCAAAAACTATATAATATATATGTTTTCAAAAAAATGTTTTC
1 TATATATGGTTTCAAAAATAT-TT-AAAAACTATATATTATATATGTTTTCAAAAAAATGTTTTA
41093 AAAAC--TATAA
64 AAAACTATATAA
* * * *** *
41103 TATATATGTTTTCAAAAATGATTTTAAAAATTATATATTATATATATTTTCTAAAATGTTTTTTT
1 TATATATGGTTTCAAAAAT-A-TTTAAAAACTATATATTATATATGTTTTC-AAAA-AAATGTTT
*
41168 TTAAAACTATAT-A
62 TAAAAACTATATAA
* *
41181 T-TATATAGTTTTAAAAACTA-TTAAAAACTATATATTATATA
1 TATATATGGTTTCAAAAA-TATTTAAAAACTATATATTATATA
41222 CGTAGTTTCA
Statistics
Matches: 261, Mismatches: 37, Indels: 58
0.73 0.10 0.16
Matches are distributed among these distances:
63 15 0.06
64 9 0.03
65 21 0.08
66 5 0.02
67 15 0.06
68 14 0.05
69 6 0.02
70 7 0.03
72 15 0.06
73 6 0.02
74 7 0.03
75 88 0.34
76 7 0.03
77 35 0.13
78 8 0.03
79 3 0.01
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (75 bp):
TATATATGGTTTCAAAAATATTTAAAAACTATATATTATATATGTTTTCAAAAAAATGTTTTAAA
AACTATATAA
Found at i:41752 original size:19 final size:19
Alignment explanation
Indices: 41728--41778 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
41718 TCAATTGAAC
41728 TGAAAATATTATAAATAAT
1 TGAAAATATTATAAATAAT
*
41747 TGAAAATATTATGAATAAT
1 TGAAAATATTATAAATAAT
41766 TGAAAATATTATA
1 TGAAAATATTATA
41779 CAAAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (19 bp):
TGAAAATATTATAAATAAT
Found at i:41785 original size:19 final size:18
Alignment explanation
Indices: 41728--41785 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
41718 TCAATTGAAC
41728 TGAAAATATTATAAATAAT
1 TGAAAATATTATAAA-AAT
*
41747 TGAAAATATTATGAATAAT
1 TGAAAATATTAT-AAAAAT
41766 TGAAAATATTATACAAAAT
1 TGAAAATATTATA-AAAAT
41785 T
1 T
41786 TAACATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.03
19 32 0.91
20 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (18 bp):
TGAAAATATTATAAAAAT
Found at i:42299 original size:11 final size:12
Alignment explanation
Indices: 42274--42325 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
42264 TTATTAATAG
42274 AAAATATTATAA
1 AAAATATTATAA
42286 AAAATATTAT--
1 AAAATATTATAA
*
42296 AAAATATTTTCAA
1 AAAATATTAT-AA
42309 AAAA-ATTAATAA
1 AAAATATT-ATAA
42321 AAAAT
1 AAAAT
42326 TAATATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
10 9 0.27
12 19 0.58
13 5 0.15
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATATTATAA
Found at i:42300 original size:22 final size:23
Alignment explanation
Indices: 42274--42327 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
42264 TTATTAATAG
42274 AAAATATTAT-AAAAAATATT-AT
1 AAAATATTATCAAAAAA-ATTAAT
*
42296 AAAATATTTTCAAAAAAATTAAT
1 AAAATATTATCAAAAAAATTAAT
*
42319 AAAAAATTA
1 AAAATATTA
42328 ATATTTTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATATTATCAAAAAAATTAAT
Found at i:44834 original size:44 final size:44
Alignment explanation
Indices: 44771--44859 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
44761 TAATAAATAA
*
44771 TAATATTTTTTGTACTATTAAAGTTGATTGATTCCTGATTGAAT
1 TAATATTTTTTGTACTATTAAAGTTGAGTGATTCCTGATTGAAT
*
44815 TAATATTTTTTGTAGTATTAAAGTTGAGTGATTCCTGATTGAAT
1 TAATATTTTTTGTACTATTAAAGTTGAGTGATTCCTGATTGAAT
44859 T
1 T
44860 TAGATGAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (44 bp):
TAATATTTTTTGTACTATTAAAGTTGAGTGATTCCTGATTGAAT
Done.