Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007440.1 Hibiscus syriacus cultivar Beakdansim tig00020292_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: 87319
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:5507 original size:17 final size:17
Alignment explanation
Indices: 5485--5519 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5475 AAATTTAACT
5485 AAATTTATAATGATTCA
1 AAATTTATAATGATTCA
5502 AAATTTATAATGATTCA
1 AAATTTATAATGATTCA
5519 A
1 A
5520 TTTATATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (17 bp):
AAATTTATAATGATTCA
Found at i:5523 original size:15 final size:16
Alignment explanation
Indices: 5485--5525 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
5475 AAATTTAACT
5485 AAATTTATAATGATTC
1 AAATTTATAATGATTC
5501 AAAATTTATAATGATTC
1 -AAATTTATAATGATTC
5518 -AATTTATA
1 AAATTTATA
5526 TGGTCAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.33
17 16 0.67
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (16 bp):
AAATTTATAATGATTC
Found at i:7155 original size:176 final size:176
Alignment explanation
Indices: 6861--7213 Score: 688
Period size: 176 Copynumber: 2.0 Consensus size: 176
6851 AAGCACCGGA
*
6861 TTAACCCAAAGGCCTAATCTTACTACCTTTTCGATGGATATGCTCATCTTTCCTCTGGTCTCGCT
1 TTAACCCAAAGGCCTAATCTTACTACCTATTCGATGGATATGCTCATCTTTCCTCTGGTCTCGCT
*
6926 TGTGGCCTCGCTGGTCTCTCTGCCGGCATGGCTATTGGAATCGTCGGCGATGCTGGCGTTAGGTA
66 TGTGGCCTCGCTGGTCTCTCCGCCGGCATGGCTATTGGAATCGTCGGCGATGCTGGCGTTAGGTA
6991 TTGTTATCTAATTTGATTTTAACTACTCGTTTTTGGAATTTTCCAT
131 TTGTTATCTAATTTGATTTTAACTACTCGTTTTTGGAATTTTCCAT
7037 TTAACCCAAAGGCCTAATCTTACTACCTATTCGATGGATATGCTCATCTTTCCTCTGGTCTCGCT
1 TTAACCCAAAGGCCTAATCTTACTACCTATTCGATGGATATGCTCATCTTTCCTCTGGTCTCGCT
7102 TGTGGCCTCGCTGGTCTCTCCGCCGGCATGGCTATTGGAATCGTCGGCGATGCTGGCGTTAGGTA
66 TGTGGCCTCGCTGGTCTCTCCGCCGGCATGGCTATTGGAATCGTCGGCGATGCTGGCGTTAGGTA
7167 TTGTTATCTAATTTGATTTTAACTACTCGTTTTTGGAATTTTCCAT
131 TTGTTATCTAATTTGATTTTAACTACTCGTTTTTGGAATTTTCCAT
7213 T
1 T
7214 CCAACTCTTT
Statistics
Matches: 175, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 175 1.00
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (176 bp):
TTAACCCAAAGGCCTAATCTTACTACCTATTCGATGGATATGCTCATCTTTCCTCTGGTCTCGCT
TGTGGCCTCGCTGGTCTCTCCGCCGGCATGGCTATTGGAATCGTCGGCGATGCTGGCGTTAGGTA
TTGTTATCTAATTTGATTTTAACTACTCGTTTTTGGAATTTTCCAT
Found at i:8891 original size:21 final size:21
Alignment explanation
Indices: 8854--8893 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
8844 TACAAATACA
8854 ATTATGTTCAATTTTTAAATT
1 ATTATGTTCAATTTTTAAATT
*
8875 ATTAT-TTCATTTATTTAAA
1 ATTATGTTCAATT-TTTAAA
8894 CTTCCTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (21 bp):
ATTATGTTCAATTTTTAAATT
Found at i:32918 original size:32 final size:33
Alignment explanation
Indices: 32877--32954 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
32867 TTTAAATAGT
* *
32877 TATTATTTTTTA-TATTAAT-ATATTTATGTAAA
1 TATTATTTTTTATTA-AAATAATATTTATATAAA
*
32909 TATTATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATTAAAATAATATTTATATAAA
32942 TATTATTTATTTA
1 TATTATTT-TTTA
32955 GAATTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.38
33 21 0.52
34 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTATTTTTTATTAAAATAATATTTATATAAA
Found at i:33116 original size:17 final size:17
Alignment explanation
Indices: 33094--33147 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
33084 AATGTTAATA
33094 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
33111 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
33128 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
33145 TTT
1 TTT
33148 TTATAATATA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:35605 original size:20 final size:21
Alignment explanation
Indices: 35569--35612 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
35559 TGCGATACAA
35569 TATATGAATTTATTTTGATTT
1 TATATGAATTTATTTTGATTT
35590 TATAT-AA-TTATATTTGATTT
1 TATATGAATTTAT-TTTGATTT
35610 TAT
1 TAT
35613 TTATATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.18
20 13 0.59
21 5 0.23
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (21 bp):
TATATGAATTTATTTTGATTT
Found at i:51106 original size:74 final size:74
Alignment explanation
Indices: 51020--51242 Score: 288
Period size: 74 Copynumber: 2.9 Consensus size: 74
51010 TAATAAGGTT
51020 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTA
1 ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTA
51085 TTATAAAAA
66 TTATAAAAA
* * *
51094 ATTTATTATAAAA-AATTTTATTTTAAAAAAATTTATTATAAAATAATATATTTTAAAATAATTT
1 ATTTATTTTAAAATAA-TTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTT
*
51158 ATTATAAAAT
65 ATTATAAAAA
* * *
51168 ATATTATTTTAAAATAAATTATTATAAAATATGGATTGATTTATTTTAAAATAATTTATTTT-AA
1 AT-TTATTTTAAAATAATTTATT-TTAAA-AT--A---ATTTATTATAAAATAATTTATTTTAAA
51232 ATAATTTATTA
58 ATAATTTATTA
51243 GTATGGATTG
Statistics
Matches: 129, Mismatches: 10, Indels: 13
0.85 0.07 0.09
Matches are distributed among these distances:
73 2 0.02
74 69 0.53
75 15 0.12
76 6 0.05
77 1 0.01
79 1 0.01
81 13 0.10
82 22 0.17
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (74 bp):
ATTTATTTTAAAATAATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAATTTA
TTATAAAAA
Found at i:51211 original size:22 final size:22
Alignment explanation
Indices: 51186--51286 Score: 94
Period size: 22 Copynumber: 4.5 Consensus size: 22
51176 TTAAAATAAA
*
51186 TTATTATAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
** * *
51208 TTATTTTAAAATAATTTATTTTAA
1 TTATTTTAAAAT-ATGGA-TTGAT
* * * *
51232 ATAATTTATTAGTATGGATTGAT
1 TTATTTTA-AAATATGGATTGAT
51255 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
51277 TTATTTTAAA
1 TTATTTTAAA
51287 TAATTTATTA
Statistics
Matches: 59, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
22 33 0.56
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (22 bp):
TTATTTTAAAATATGGATTGAT
Found at i:51235 original size:14 final size:15
Alignment explanation
Indices: 51020--51241 Score: 254
Period size: 15 Copynumber: 14.5 Consensus size: 15
51010 TAATAAGGTT
51020 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
51035 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
51050 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
51065 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
51080 ATTTATTATAAAA-A
1 ATTTATTTTAAAATA
*
51094 ATTTATTATAAAA-A
1 ATTTATTTTAAAATA
*
51108 ATTTTATTTTAAAAAA
1 A-TTTATTTTAAAATA
*
51124 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
51139 ATATATTTTAAAATA
1 ATTTATTTTAAAATA
*
51154 ATTTATTATAAAAT-
1 ATTTATTTTAAAATA
51168 ATATTATTTTAAAATA
1 AT-TTATTTTAAAATA
* *
51184 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
51203 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
51221 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
51235 ATTTATT
1 ATTTATT
51242 AGTATGGATT
Statistics
Matches: 181, Mismatches: 15, Indels: 23
0.83 0.07 0.11
Matches are distributed among these distances:
14 30 0.17
15 128 0.71
16 7 0.04
17 2 0.01
18 1 0.01
19 1 0.01
20 2 0.01
21 4 0.02
22 6 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:51259 original size:32 final size:32
Alignment explanation
Indices: 51221--51318 Score: 126
Period size: 32 Copynumber: 3.4 Consensus size: 32
51211 TTTTAAAATA
51221 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
51253 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
51275 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
51307 ATTTATTTTAAA
1 ATTTATTTTAAA
51319 ATATGGATTG
Statistics
Matches: 56, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
22 14 0.25
23 4 0.07
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.07
32 26 0.46
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:51286 original size:54 final size:54
Alignment explanation
Indices: 51221--51748 Score: 440
Period size: 54 Copynumber: 9.8 Consensus size: 54
51211 TTTTAAAATA
51221 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
51275 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* **
51329 ATTTA--TT--AT--TGTTGTT-GTATGGATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAAT-TTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** ** * * * **
51378 TATGGA-TTTATTTATTTTA-AAATATGGATTGATTTATTTT-AAATAATTTATTAG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * **
51432 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTT-AAATAATTTATTAG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * ****
51486 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTATTGTTGTTGTATGGATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGA--T-TTATT-TTAAAATATGGATTG
* * *
51543 ATTTATTTTAAATAATTTATTAGTATGAATTTATTTACTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * *
51597 ATTTATATTAAATAATTTATTAGTATAGATTGATTTATTTTAAACTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
51651 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
51705 ATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
51749 TAATTTATTT
Statistics
Matches: 417, Mismatches: 40, Indels: 34
0.85 0.08 0.07
Matches are distributed among these distances:
47 4 0.01
48 25 0.06
49 5 0.01
50 5 0.01
51 2 0.00
52 2 0.00
53 1 0.00
54 331 0.79
55 5 0.01
56 5 0.01
57 15 0.04
58 16 0.04
59 1 0.00
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:51361 original size:80 final size:80
Alignment explanation
Indices: 51266--51415 Score: 291
Period size: 80 Copynumber: 1.9 Consensus size: 80
51256 TATTTTAAAA
51266 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
51331 TTATTATTGTTGTTG
66 TTATTATTGTTGTTG
*
51346 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
51411 TTATT
66 TTATT
51416 TTAAATAATT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTTGTTG
Found at i:51394 original size:22 final size:22
Alignment explanation
Indices: 51378--51420 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
51368 AATTTATTAG
*
51378 TATGGATTTATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
51400 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
51421 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:51423 original size:188 final size:188
Alignment explanation
Indices: 51221--51797 Score: 985
Period size: 188 Copynumber: 3.0 Consensus size: 188
51211 TTTTAAAATA
51221 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
51286 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTTGTTGTATGG
66 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTTGTTGTATGG
51351 ATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTATTTTAAAATATGGATTG
131 ATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTATTTTAAAATATGGATTG
51409 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
51474 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTTGTTGTATGG
66 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTTGTTGTATGG
* *
51539 ATTGATTTATTTTAAATAATTTATTAGTATGAATTTATTTACTTTAAAATATGGATTG
131 ATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTATTTTAAAATATGGATTG
* * *
51597 ATTTATATTAAATAATTTATTAGTATAGATTGATTTATTTTAAACTATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
* *
51662 ATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAAT-TTATT
66 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTTGTT
* * * *
51726 AGTATGTATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGAATTG
125 -GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTATTTTAAAATATGGATTG
51791 ATTTATT
1 ATTTATT
51798 ATTGTAGTTG
Statistics
Matches: 368, Mismatches: 14, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
188 295 0.80
190 2 0.01
192 2 0.01
193 4 0.01
194 65 0.18
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (188 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTTGTTGTATGG
ATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTATTTTAAAATATGGATTG
Found at i:51457 original size:22 final size:22
Alignment explanation
Indices: 51432--51474 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
51422 AATTTATTAG
51432 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
51454 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
51475 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:51636 original size:22 final size:22
Alignment explanation
Indices: 51620--51662 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
51610 AATTTATTAG
51620 TATAGATTGATTTATTTTAAAC
1 TATAGATTGATTTATTTTAAAC
*
51642 TATGGATTGATTTATTTTAAA
1 TATAGATTGATTTATTTTAAA
51663 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (22 bp):
TATAGATTGATTTATTTTAAAC
Found at i:51646 original size:134 final size:134
Alignment explanation
Indices: 51248--51837 Score: 632
Period size: 134 Copynumber: 4.4 Consensus size: 134
51238 TATTAGTATG
* *** *
51248 GATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAT
1 GATTTATTTATTTTATTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTAT
*
51313 TTTAAAATATGGATTGA-TT-TATT--AT--TGTTGTT-GTATGGATTGATTTATTTTAAATAAT
66 TTTAAAATATGGATTGATTTATATTAAATAAT-TTATTAGTATGGATTGATTTATTTT-AA-AA-
* *
51371 TTATTAGTATG
127 -TA-T-GGATT
*** *
51382 GATTTATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAT
1 GATTTATTTATTTTATTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTAT
*
51447 TTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
66 TTTAAAATATGGATTGATTTATATTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
51512 GATT
131 GATT
* *
51516 GATTTA-TTATTGTTGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTTATTTA
1 GATTTATTTATT-TTATTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTA
* * *
51580 CTTTAAAATATGGATTGATTTATATTAAATAATTTATTAGTATAGATTGATTTATTTTAAACTAT
65 TTTTAAAATATGGATTGATTTATATTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT
51645 GGATT
130 GGATT
* * * *
51650 GATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTA-TTTT
1 GATTTA-TTT--AT--TTTATT-GTATGGATTGATTTATTTT-AAATA---ATTTA-TTAGTATG
* * * * * *
51714 AAATAATTTA--TT--AGTATGTATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTAT
55 AATTGATTTATTTTAAAATATGGATTGATTTATATTAAATAATTTATTAGTATGGATTGATTTAT
*
51775 TTTAAAATATGAATT
120 TTTAAAATATGGATT
*
51790 GATTTA-TTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATT
1 GATTTATTTATTTTA-TTGTATGGATTGATTTATTTTAAATAATTTATT
51838 TTAAATTTCA
Statistics
Matches: 403, Mismatches: 32, Indels: 47
0.84 0.07 0.10
Matches are distributed among these distances:
129 2 0.00
130 4 0.01
133 10 0.02
134 229 0.57
135 5 0.01
136 9 0.02
138 8 0.02
139 10 0.02
140 102 0.25
141 5 0.01
142 2 0.00
144 14 0.03
145 3 0.01
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (134 bp):
GATTTATTTATTTTATTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTAT
TTTAAAATATGGATTGATTTATATTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
GATT
Found at i:51791 original size:108 final size:108
Alignment explanation
Indices: 51538--51837 Score: 308
Period size: 108 Copynumber: 2.8 Consensus size: 108
51528 TTGTTGTATG
* * * * *
51538 GATTGATTTATTTTAAATAATTTATT--AGTATGAATTTATTTACTTTAAAATATGGATTGATTT
1 GATTGATTTATATGAAATAATTTATTAAAATATGAATTGATTTATTTTAAAATATGGATTGATTT
*
51601 ATATTAAATAATTTATTAGTATAGATTGATTTATTTTAAACTA
66 ATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAACTA
* * **
51644 TGGATTGATTTATTTTAAATAATTTATTAGTATA-G-ATTGATTTATTTTAAAATATGGATTGAT
1 --GATTGATTTATATGAAATAATTTATTAAAATATGAATTGATTTATTTTAAAATATGGATTGAT
51707 TTATTTTAAATAATTTATTAGTAT-GTATTGATTTATTTTAAA-TA
64 TTATTTTAAATAATTTATTAGTATAG-ATTGATTTATTTTAAACTA
* * * * * ***
51751 -ATTTATTTGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTTGTATGGAT
1 GATTGATTTATATGAAATAATTTA--TTAAAATATGAATTGATTTA-T-TT-TA-AAATATGGAT
51815 TGATTTATTTTAAATAATTTATT
60 TGATTTATTTTAAATAATTTATT
51838 TTAAATTTCA
Statistics
Matches: 164, Mismatches: 17, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
104 16 0.10
106 6 0.04
107 4 0.02
108 100 0.61
109 2 0.01
110 4 0.02
111 2 0.01
112 30 0.18
ACGTcount: A:0.35, C:0.01, G:0.11, T:0.53
Consensus pattern (108 bp):
GATTGATTTATATGAAATAATTTATTAAAATATGAATTGATTTATTTTAAAATATGGATTGATTT
ATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAACTA
Found at i:51836 original size:14 final size:14
Alignment explanation
Indices: 51817--51843 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
51807 GTATGGATTG
51817 ATTTATTTTAAATA
1 ATTTATTTTAAATA
51831 ATTTATTTTAAAT
1 ATTTATTTTAAAT
51844 TTCAATATTG
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:55096 original size:26 final size:27
Alignment explanation
Indices: 55032--55104 Score: 98
Period size: 26 Copynumber: 2.8 Consensus size: 27
55022 ATTTTATATA
55032 TATTAACTT-A-TTAAAAATATTTTAT
1 TATTAACTTAATTTAAAAATATTTTAT
55057 TATTAACTTAATTTAAAAATATTTTAT
1 TATTAACTTAATTTAAAAATATTTTAT
** *
55084 T-TTATTTTCATTTAAAAATAT
1 TATTAACTTAATTTAAAAATAT
55105 ATAATTTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 9 0.21
26 18 0.42
27 16 0.37
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (27 bp):
TATTAACTTAATTTAAAAATATTTTAT
Found at i:56879 original size:21 final size:19
Alignment explanation
Indices: 56853--56908 Score: 51
Period size: 22 Copynumber: 2.8 Consensus size: 19
56843 AAAAATTTTA
56853 AAAATTATAATTTAAACCTTC
1 AAAATT-TAATTTAAACC-TC
*
56874 AAAATTCTTAATTCAAACCTC
1 AAAA-T-TTAATTTAAACCTC
*
56895 TAAATTT-ATTTAAA
1 AAAATTTAATTTAAA
56909 AAAATCAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 6 0.20
19 2 0.07
20 1 0.03
21 9 0.30
22 11 0.37
23 1 0.03
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTTAATTTAAACCTC
Found at i:57482 original size:2 final size:2
Alignment explanation
Indices: 57475--57500 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57465 CGTCTAGTTA
57475 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
57501 GATGTAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60930 original size:22 final size:22
Alignment explanation
Indices: 60900--60949 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
60890 ACAAATTTCA
* *
60900 GAACTAGTGAACCATGTGTGTC
1 GAACCAGTGAACCATGTATGTC
60922 GAACCAGTGAACCATGTATGTC
1 GAACCAGTGAACCATGTATGTC
60944 GAACCA
1 GAACCA
60950 TAATGTCCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (22 bp):
GAACCAGTGAACCATGTATGTC
Found at i:62983 original size:2 final size:2
Alignment explanation
Indices: 62978--63007 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
62968 ATACATACAC
62978 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
63008 TTCTTTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63884 original size:2 final size:2
Alignment explanation
Indices: 63877--63901 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63867 GACGGTCCAA
63877 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 A
63902 AACGAGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64246 original size:2 final size:2
Alignment explanation
Indices: 64235--64268 Score: 50
Period size: 2 Copynumber: 16.0 Consensus size: 2
64225 TTTATTTTTT
64235 TA TA TGA TA TA TA TA TA TA TA TA TA TGA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA T-A TA TA TA
64269 ATACATAGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 26 0.87
3 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
TA
Found at i:69629 original size:19 final size:22
Alignment explanation
Indices: 69605--69647 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 22
69595 GACGCCATCT
69605 AAAATATT-TAAA-AA-TAAAA
1 AAAATATTATAAACAAGTAAAA
69624 AAAATATTATAAACAAGTAAAA
1 AAAATATTATAAACAAGTAAAA
69646 AA
1 AA
69648 TAATTAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
20 4 0.19
21 2 0.10
22 7 0.33
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (22 bp):
AAAATATTATAAACAAGTAAAA
Found at i:79211 original size:141 final size:139
Alignment explanation
Indices: 78959--79238 Score: 524
Period size: 141 Copynumber: 2.0 Consensus size: 139
78949 ACTGATCTAA
78959 GAATTTTCTTTAAACAAATGTCGTTTTGTACTTACCTCATATAAAAAAAAGTTAATATATAACAT
1 GAATTTTCTTTAAACAAATGTCGTTTTGTACTTACCTCATATAAAAAAAAGTTAATATATAACAT
*
79024 AAAGATCCTATAATTTAGCCACAACGAATTACAATCATTCCTATAATCGGTTTATCAGATGATGA
66 AAAGATCCTATAATTTAGCCACAACGAATTACAATCATTCATATAATCGGTTTATCAGATGATGA
79089 TATACGATT
131 TATACGATT
*
79098 GAATTTTCTTTAAACAAATGTCGTTTTGTACTTACCTCATATAAAAAAAAAAGTTAATATGTAAC
1 GAATTTTCTTTAAACAAATGTCGTTTTGTACTTACCTCATAT--AAAAAAAAGTTAATATATAAC
79163 ATAAAGATCCTATAATTTAGCCACAACGAATTACAATCATTCATATAATCGGTTTATCAGATGAT
64 ATAAAGATCCTATAATTTAGCCACAACGAATTACAATCATTCATATAATCGGTTTATCAGATGAT
79228 GATATACGATT
129 GATATACGATT
79239 TTAGCTCGCA
Statistics
Matches: 137, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
139 42 0.31
141 95 0.69
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (139 bp):
GAATTTTCTTTAAACAAATGTCGTTTTGTACTTACCTCATATAAAAAAAAGTTAATATATAACAT
AAAGATCCTATAATTTAGCCACAACGAATTACAATCATTCATATAATCGGTTTATCAGATGATGA
TATACGATT
Found at i:82534 original size:38 final size:38
Alignment explanation
Indices: 82484--82614 Score: 149
Period size: 38 Copynumber: 3.5 Consensus size: 38
82474 ACTCGATCTG
*
82484 AAAA-TATGTATCTTTCATCCGAATCCGTCACGATTTA
1 AAAATTATATATCTTTCATCCGAATCCGTCACGATTTA
** * ** * ***
82521 AAAATTATATATCTTTCAT-ATAACCCAACTCGACCCA
1 AAAATTATATATCTTTCATCCGAATCCGTCACGATTTA
*
82558 AAAAATATATATCTTTCATCCGAATCCGTCACGATTTA
1 AAAATTATATATCTTTCATCCGAATCCGTCACGATTTA
82596 AAAATTATATATCTTTCAT
1 AAAATTATATATCTTTCAT
82615 ATAACCCAAC
Statistics
Matches: 71, Mismatches: 21, Indels: 3
0.75 0.22 0.03
Matches are distributed among these distances:
37 31 0.44
38 40 0.56
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35
Consensus pattern (38 bp):
AAAATTATATATCTTTCATCCGAATCCGTCACGATTTA
Found at i:82589 original size:75 final size:75
Alignment explanation
Indices: 82467--82645 Score: 315
Period size: 75 Copynumber: 2.4 Consensus size: 75
82457 GTTTTTTGGT
* ** *
82467 TAACCCAACTCGA-TCTGAAAATATGTATCTTTCATCCGAATCCGTCACGATTTAAAAATTATAT
1 TAACCCAACTCGACCCAAAAAATATATATCTTTCATCCGAATCCGTCACGATTTAAAAATTATAT
82531 ATCTTTCATA
66 ATCTTTCATA
82541 TAACCCAACTCGACCCAAAAAATATATATCTTTCATCCGAATCCGTCACGATTTAAAAATTATAT
1 TAACCCAACTCGACCCAAAAAATATATATCTTTCATCCGAATCCGTCACGATTTAAAAATTATAT
82606 ATCTTTCATA
66 ATCTTTCATA
82616 TAACCCAACTCGACCCAAAAAATATATATC
1 TAACCCAACTCGACCCAAAAAATATATATC
82646 CTTTATTCGA
Statistics
Matches: 100, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
74 13 0.13
75 87 0.87
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (75 bp):
TAACCCAACTCGACCCAAAAAATATATATCTTTCATCCGAATCCGTCACGATTTAAAAATTATAT
ATCTTTCATA
Found at i:82637 original size:38 final size:37
Alignment explanation
Indices: 82520--82645 Score: 144
Period size: 37 Copynumber: 3.4 Consensus size: 37
82510 GTCACGATTT
*
82520 AAAAATTATATATCTTTCATATAACCCAACTCGACCC
1 AAAAAATATATATCTTTCATATAACCCAACTCGACCC
** * ** * ***
82557 AAAAAATATATATCTTTCATCCGAATCCGTCACGATTT
1 AAAAAATATATATCTTTCAT-ATAACCCAACTCGACCC
*
82595 AAAAATTATATATCTTTCATATAACCCAACTCGACCC
1 AAAAAATATATATCTTTCATATAACCCAACTCGACCC
82632 AAAAAATATATATC
1 AAAAAATATATATC
82646 CTTTATTCGA
Statistics
Matches: 67, Mismatches: 21, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
37 40 0.60
38 27 0.40
ACGTcount: A:0.42, C:0.23, G:0.04, T:0.31
Consensus pattern (37 bp):
AAAAAATATATATCTTTCATATAACCCAACTCGACCC
Done.