Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000020.1 Hibiscus syriacus cultivar Beakdansim tig00000036_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: 61799
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2912 original size:3 final size:3
Alignment explanation
Indices: 2904--2958 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
2894 CATAATTTAG
2904 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2952 TAA TAA T
1 TAA TAA T
2959 GTAAATCCGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:7658 original size:19 final size:22
Alignment explanation
Indices: 7634--7688 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
7624 AGGTTAGTTA
7634 AAAAGGATA-A-A-AACTGAGG
1 AAAAGGATATATACAACTGAGG
7653 AAAAGGAAATATATACAACTGAGG
1 AAAAGG--ATATATACAACTGAGG
*
7677 AAAAGGAAATAT
1 AAAAGGATATAT
7689 TAGACGTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 6 0.20
21 3 0.10
22 6 0.20
23 1 0.03
24 14 0.47
ACGTcount: A:0.58, C:0.05, G:0.22, T:0.15
Consensus pattern (22 bp):
AAAAGGATATATACAACTGAGG
Found at i:11463 original size:19 final size:19
Alignment explanation
Indices: 11439--11480 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
11429 CTCTCTTATT
11439 TTTATTTAAATTGCTTTTA
1 TTTATTTAAATTGCTTTTA
* *
11458 TTTATTTAAATTGTTTTTC
1 TTTATTTAAATTGCTTTTA
11477 TTTA
1 TTTA
11481 CTACTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTATTTAAATTGCTTTTA
Found at i:12081 original size:2 final size:2
Alignment explanation
Indices: 12076--12116 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
12066 CTTGTGTGTC
12076 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12117 GTTTGGTACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12298 original size:7 final size:8
Alignment explanation
Indices: 12271--12295 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12261 GAGTATCATT
12271 AATTATAA
1 AATTATAA
12279 AATTATAA
1 AATTATAA
12287 AATTATAA
1 AATTATAA
12295 A
1 A
12296 TTACTCAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AATTATAA
Found at i:16011 original size:15 final size:15
Alignment explanation
Indices: 15993--16038 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
15983 TTTTTTTAGT
*
15993 TTAATTGGTTTAGGG
1 TTAAGTGGTTTAGGG
16008 TTAAGTGGTTTA-GG
1 TTAAGTGGTTTAGGG
*
16022 TTAAGTGATTTAGGG
1 TTAAGTGGTTTAGGG
16037 TT
1 TT
16039 CAAGGTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 13 0.46
15 15 0.54
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.46
Consensus pattern (15 bp):
TTAAGTGGTTTAGGG
Found at i:16023 original size:14 final size:14
Alignment explanation
Indices: 15987--16035 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
15977 TTTAGGTTTT
* *
15987 TTTAGTTTAATTGG
1 TTTAGGTTAAGTGG
16001 TTTAGGGTTAAGTGG
1 TTTA-GGTTAAGTGG
*
16016 TTTAGGTTAAGTGA
1 TTTAGGTTAAGTGG
16030 TTTAGG
1 TTTAGG
16036 GTTCAAGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (14 bp):
TTTAGGTTAAGTGG
Found at i:17946 original size:11 final size:11
Alignment explanation
Indices: 17930--17956 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
17920 CATTAAAAAT
17930 ATAAACATAAA
1 ATAAACATAAA
17941 ATAAACATAAA
1 ATAAACATAAA
17952 ATAAA
1 ATAAA
17957 GTCCTAGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (11 bp):
ATAAACATAAA
Found at i:19473 original size:44 final size:44
Alignment explanation
Indices: 19260--19998 Score: 316
Period size: 44 Copynumber: 16.9 Consensus size: 44
19250 TGAAAAACTC
* * * * * * *
19260 GATCCACCTCATTCTGTGATGGAATCGAACGAGATGTCGATGAT
1 GATCCACCTCCTTCTGTGATGGAATCGAGCAAAAAGTTGATGCT
* * * *
19304 GATCTACCTCCTTCTGTGATAGAATCAAGCAAAAACTTGAT-CT
1 GATCCACCTCCTTCTGTGATGGAATCGAGCAAAAAGTTGATGCT
* * * * * * *
19347 GATCCAACTTCTTCTGCGATGGATTTGAACGAAAAA-ATG-T-CT
1 GATCCACCTCCTTCTGTGATGGAATCGAGC-AAAAAGTTGATGCT
* * * * * * *
19389 -ATTCATCTCCTTCTGTGATAGAATCGAACGAGATGTTGATGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAGCAAAAAGTTGATGCT
* * * *
19432 GATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGATGTT
1 GATCCACCTCCTTCTGTGATGGAATCGAGCAAAAAGTTGATGCT
* ** * * ***
19476 GATCCAACTCCTTCTACGATGGATTTGAGCGAAAATA-AAAATG-T
1 GATCCACCTCCTTCTGTGATGGAATCGAGC-AAAA-AGTTGATGCT
* * * *
19520 CGATCCACCTCCTTCTTTGATGGAATC-A--AAAGAGATATTGGTACT
1 -GATCCACCTCCTTCTGTGATGGAATCGAGCAAA-A-A-GTTGATGCT
* * * *
19565 GATCTACCTCCTT-TGTGATAGAATCGAGCTAAAAGTTAATGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAGCAAAAAGTTGATGCT
* * ** * * * ***
19608 GATTCAACTCCTTCTACGATGGATTTGAGTGAAAATA-AAAATG-T
1 GATCCACCTCCTTCTGTGATGGAATCGAG-CAAAA-AGTTGATGCT
* *
19652 CGATCCACCTCCTTCTGTGATGGAATC-A--AAAGAGATATTGGTGCT
1 -GATCCACCTCCTTCTGTGATGGAATCGAGCAAA-A-A-GTTGATGCT
* * * *
19697 GATCTACCTCCTTTTGTGATAGAATCGAGCAAAAAGTTGATGTT
1 GATCCACCTCCTTCTGTGATGGAATCGAGCAAAAAGTTGATGCT
* * * * * *
19741 GATCCAACTCCTTTTGTTATGGATTTGAGCGAAATAA-ATG-T-C-
1 GATCCACCTCCTTCTGTGATGGAATCGAGC-AAA-AAGTTGATGCT
* * * * * * *
19783 GACCCATCTCCTTCTGTGATGGAATCAAACATAATGTTGATGTT
1 GATCCACCTCCTTCTGTGATGGAATCGAGCAAAAAGTTGATGCT
** * * *
19827 GATATACCTCATTCTGTGATAGAATCGAGCAAAAAATTGATGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAGCAAAAAGTTGATGCT
* * * ***
19871 GATCCAACTCCTTCTGCGATGGATTCGAGCAAAATA-AAAATG-T
1 GATCCACCTCCTTCTGTGATGGAATCGAGCAAAA-AGTTGATGCT
* * * * *
19914 CGATCCACCTCCTTCTGTGATGGAATCAAACGAGATGTTGATGCT
1 -GATCCACCTCCTTCTGTGATGGAATCGAGCAAAAAGTTGATGCT
* * * * *
19959 GATCTACCTCATTCTGTGATAGATTCGAGCAAACAGTTGA
1 GATCCACCTCCTTCTGTGATGGAATCGAGCAAAAAGTTGA
19999 ACAATATCTT
Statistics
Matches: 496, Mismatches: 163, Indels: 72
0.68 0.22 0.10
Matches are distributed among these distances:
40 3 0.01
41 34 0.07
42 31 0.06
43 52 0.10
44 299 0.60
45 67 0.14
46 7 0.01
47 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (44 bp):
GATCCACCTCCTTCTGTGATGGAATCGAGCAAAAAGTTGATGCT
Found at i:19627 original size:132 final size:132
Alignment explanation
Indices: 19215--19998 Score: 1019
Period size: 132 Copynumber: 6.0 Consensus size: 132
19205 TTGATGATAT
* * * *
19215 TGATCCAACTCCGTATGCGATGGATTTGAGCGAAATGAAAAA-CTCGATCCACCTCATTCTGTGA
1 TGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAT-AAAAATGTCGATCCACCTCCTTCTGTGA
* * * * * * *
19279 TGGAATCGAACGAGATGTCGATGATGATCTACCTCCTTCTGTGATAGAATCAAGCAAAAACTTGA
65 TGGAATCAAAAGAGATGTTGATGCTGATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGA
19344 T-C
130 TGC
* * * * *
19346 TGATCCAACTTCTTCTGCGATGGATTTGAACG--A-AAAAATGTCTATTCATCTCCTTCTGTGAT
1 TGATCCAACTCCTTCTGCGATGGATTTGAGCGAAATAAAAATGTCGATCCACCTCCTTCTGTGAT
* * *
19408 AGAATCGAACGAGATGTTGATGCTGATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGAT
66 GGAATCAAAAGAGATGTTGATGCTGATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGAT
*
19473 GT
131 GC
* *
19475 TGATCCAACTCCTTCTACGATGGATTTGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTTTGA
1 TGATCCAACTCCTTCTGCGATGGATTTGAGCG-AAATAAAAATGTCGATCCACCTCCTTCTGTGA
* * * * * *
19540 TGGAATCAAAAGAGATATTGGTACTGATCTACCTCCTT-TGTGATAGAATCGAGCTAAAAGTTAA
65 TGGAATCAAAAGAGATGTTGATGCTGATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGA
19604 TGC
130 TGC
* * *
19607 TGATTCAACTCCTTCTACGATGGATTTGAGTGAAAATAAAAATGTCGATCCACCTCCTTCTGTGA
1 TGATCCAACTCCTTCTGCGATGGATTTGAGCG-AAATAAAAATGTCGATCCACCTCCTTCTGTGA
* * * *
19672 TGGAATCAAAAGAGATATTGGTGCTGATCTACCTCCTTTTGTGATAGAATCGAGCAAAAAGTTGA
65 TGGAATCAAAAGAGATGTTGATGCTGATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGA
*
19737 TGT
130 TGC
* ** * *
19740 TGATCCAACTCCTTTTGTTATGGATTTGAGCGAAAT--AAATGTCGACCCATCTCCTTCTGTGAT
1 TGATCCAACTCCTTCTGCGATGGATTTGAGCGAAATAAAAATGTCGATCCACCTCCTTCTGTGAT
* * * *
19803 GGAATCAAACATA-ATGTTGATGTTGATATACCTCATTCTGTGATAGAATCGAGCAAAAAATTGA
66 GGAATCAAA-AGAGATGTTGATGCTGATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGA
19867 TGC
130 TGC
* *
19870 TGATCCAACTCCTTCTGCGATGGATTCGAGCAAAATAAAAATGTCGATCCACCTCCTTCTGTGAT
1 TGATCCAACTCCTTCTGCGATGGATTTGAGCGAAATAAAAATGTCGATCCACCTCCTTCTGTGAT
* * *
19935 GGAATCAAACGAGATGTTGATGCTGATCTACCTCATTCTGTGATAGATTCGAGCAAACAGTTGA
66 GGAATCAAAAGAGATGTTGATGCTGATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGA
19999 ACAATATCTT
Statistics
Matches: 571, Mismatches: 71, Indels: 21
0.86 0.11 0.03
Matches are distributed among these distances:
127 5 0.01
128 77 0.13
129 30 0.05
130 111 0.19
131 31 0.05
132 210 0.37
133 107 0.19
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (132 bp):
TGATCCAACTCCTTCTGCGATGGATTTGAGCGAAATAAAAATGTCGATCCACCTCCTTCTGTGAT
GGAATCAAAAGAGATGTTGATGCTGATCTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGAT
GC
Found at i:19674 original size:45 final size:45
Alignment explanation
Indices: 19471--19675 Score: 106
Period size: 45 Copynumber: 4.6 Consensus size: 45
19461 CAAAAAGTTG
* * * *
19471 ATGTTGATCCAACTCCTTCTACGATGGATTTGAGCGAAAATAAAA
1 ATGTCGATCCACCTCCTTCTATGATGGATTTGAGTGAAAATAAAA
* * * *
19516 ATGTCGATCCACCTCCTTCTTTGATGGA----A-TCAAAAGAGATA
1 ATGTCGATCCACCTCCTTCTATGATGGATTTGAGTGAAAATA-AAA
* * * * * * *
19557 TTGGTACTGATCTACCTCCTT-TGTGATAGAATCGAGCT-AAAAGT--TA
1 AT-GT-C-GATCCACCTCCTTCTATGATGGATTTGAG-TGAAAA-TAAAA
* * *
19603 ATG-CTGATTCAACTCCTTCTACGATGGATTTGAGTGAAAATAAAA
1 ATGTC-GATCCACCTCCTTCTATGATGGATTTGAGTGAAAATAAAA
*
19648 ATGTCGATCCACCTCCTTCTGTGATGGA
1 ATGTCGATCCACCTCCTTCTATGATGGA
19676 ATCAAAAGAG
Statistics
Matches: 117, Mismatches: 27, Indels: 32
0.66 0.15 0.18
Matches are distributed among these distances:
40 5 0.04
41 4 0.03
42 2 0.02
43 22 0.19
44 26 0.22
45 48 0.41
46 4 0.03
47 1 0.01
48 4 0.03
49 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (45 bp):
ATGTCGATCCACCTCCTTCTATGATGGATTTGAGTGAAAATAAAA
Found at i:20452 original size:36 final size:36
Alignment explanation
Indices: 20361--20435 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
20351 CTCAAGCAAT
* *
20361 AAAACTCGTTTCAAGGGAAACTGTCTCAAGAGAGAC
1 AAAAGTCGTTTCAAGAGAAACTGTCTCAAGAGAGAC
*
20397 AAAAGTCATTTCAAGAGAAACTGTCTCAAGAGAGAC
1 AAAAGTCGTTTCAAGAGAAACTGTCTCAAGAGAGAC
20433 AAA
1 AAA
20436 CTTTGTTTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.19
Consensus pattern (36 bp):
AAAAGTCGTTTCAAGAGAAACTGTCTCAAGAGAGAC
Found at i:20670 original size:21 final size:21
Alignment explanation
Indices: 20639--20692 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
20629 TATGGATGGC
*
20639 TCGAAGGACTTATCATCA-TGT
1 TCGAAAGACTTATCAT-ATTGT
*
20660 TTGAAAGACTTATCATATTGT
1 TCGAAAGACTTATCATATTGT
20681 TCGAAAGACTTA
1 TCGAAAGACTTA
20693 CAGATGACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (21 bp):
TCGAAAGACTTATCATATTGT
Found at i:20848 original size:39 final size:39
Alignment explanation
Indices: 20794--21309 Score: 753
Period size: 39 Copynumber: 13.2 Consensus size: 39
20784 TAGTTTCTTT
* * * *
20794 AAATCTTTTGTTTCGAGGGAAACTGTCTCAAGCTAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACA
*
20833 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCAAGACA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACA
20872 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACA
* * * *
20911 AACTCTTATGTTTCAAAGGAAACTATCTCAAGCGAGACA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACA
* *
20950 AAATTTTCTGTTTCGAGGGAAACTATCTCAAGTGAGACA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACA
* * *
20989 AAATGTTCTGTTTCAAGGGAAACTATCTCCAGCGAGACA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACA
** *
21028 AAATCTTCTGTTTTAAGGGAAACTATCTCAAGCAAGACA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACA
* * *
21067 AAATCTTTTGTTTCGAGGGAAACTATCTCAAGCGAAATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACA
*
21106 AAATCTTCTGTTTCGAGGGACACTATCTCAAGCGAGACA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACA
*
21145 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACA
*
21184 AAATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAGACA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACA
* * * *
21223 AAATCTTCTGTTTCAAGGGAAACCATATCAAGTGAGACA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACA
* * *
21262 AAATCTTTTGTTTCAAGGGAAACTATCTCAAGCGAGATA
1 AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACA
*
21301 TAATCTTCT
1 AAATCTTCT
21310 TTAAAAATAA
Statistics
Matches: 430, Mismatches: 47, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 430 1.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (39 bp):
AAATCTTCTGTTTCGAGGGAAACTATCTCAAGCGAGACA
Found at i:21401 original size:76 final size:75
Alignment explanation
Indices: 21312--21473 Score: 229
Period size: 76 Copynumber: 2.1 Consensus size: 75
21302 AATCTTCTTT
* * *
21312 AAAAATAATCTTGAGTGAAATGAAATGTCTTCTTTCGAGTAAAAATTGTCCCAAGCT-AGACAAA
1 AAAAACAATCTTGAGTCAAATGAAATGTCTTCTTTCGAGT-AAAACTGTCCCAAG-TGAGACAAA
*
21376 -TCTTCTTTTAAG
64 GT-ATCTTTTAAG
*
21388 AAAAACAATCTTGAGTCAAATGAAATGTCTTCTTTCGAGTAAAACTGTCTCAAGTGAGACAAAGT
1 AAAAACAATCTTGAGTCAAATGAAATGTCTTCTTTCGAGTAAAACTGTCCCAAGTGAGACAAAGT
*
21453 ATGTTTTAAG
66 ATCTTTTAAG
21463 AAAAACAATCT
1 AAAAACAATCT
21474 CAAGTGAGAT
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
74 1 0.01
75 38 0.49
76 39 0.50
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (75 bp):
AAAAACAATCTTGAGTCAAATGAAATGTCTTCTTTCGAGTAAAACTGTCCCAAGTGAGACAAAGT
ATCTTTTAAG
Found at i:21432 original size:39 final size:39
Alignment explanation
Indices: 21313--21432 Score: 88
Period size: 39 Copynumber: 3.1 Consensus size: 39
21303 ATCTTCTTTA
* *
21313 AAAATAATCTTGAGTGAAATGAAATGTCTTCTTTCGAGT
1 AAAACAATCTTGAGTCAAATGAAATGTCTTCTTTCGAGT
*** * * ** *
21352 -AAA-AA--TTGTCCCAAGCTAGACAA-ATCTTCTTTTAAGA
1 AAAACAATCTTGAGTCAA-AT-GA-AATGTCTTCTTTCGAGT
21389 AAAACAATCTTGAGTCAAATGAAATGTCTTCTTTCGAGT
1 AAAACAATCTTGAGTCAAATGAAATGTCTTCTTTCGAGT
21428 AAAAC
1 AAAAC
21433 TGTCTCAAGT
Statistics
Matches: 56, Mismatches: 17, Indels: 16
0.63 0.19 0.18
Matches are distributed among these distances:
35 5 0.09
36 1 0.02
37 14 0.25
38 10 0.18
39 19 0.34
40 1 0.02
41 6 0.11
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (39 bp):
AAAACAATCTTGAGTCAAATGAAATGTCTTCTTTCGAGT
Found at i:21877 original size:26 final size:26
Alignment explanation
Indices: 21844--21904 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
21834 GATTGTCCTA
21844 TTTGAAAATGTTTTATTTCTTTTTAT
1 TTTGAAAATGTTTTATTTCTTTTTAT
21870 TTTGAAAATGTTTTATTTCTTTTTAT
1 TTTGAAAATGTTTTATTTCTTTTTAT
21896 TTTGAAAAT
1 TTTGAAAAT
21905 ATGGAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.62
Consensus pattern (26 bp):
TTTGAAAATGTTTTATTTCTTTTTAT
Found at i:27780 original size:101 final size:99
Alignment explanation
Indices: 27621--27807 Score: 243
Period size: 101 Copynumber: 1.9 Consensus size: 99
27611 TTAAACGTAT
* * * *
27621 TCCCCTTGAACTTGAAGACATTGTTCATATGGGTTTTAAACTTACTGGTGTGTCGAAGGCATCTT
1 TCCCCTAGAACTTGAAGACATAGTTCATATGGGTTTTAAAATTACTGATGTG-CGAAGGCATCTT
**
27686 CATATTGAGGTTGAAGAAGTTAGCAAATGAATATC
65 CATATTGAGGTCAAAGAAGTTAGCAAATGAATATC
*
27721 TCCCCTAGAACTTGAAGGCATAGTGTCATATGGGTATTTAACAGATTACT-ATGTG-GAAGGCAT
1 TCCCCTAGAACTTGAAGACATAGT-TCATATGGGT-TTTAA-A-ATTACTGATGTGCGAAGGCAT
*
27784 CTTTATATTGAGGTCAAAGAAGTT
62 CTTCATATTGAGGTCAAAGAAGTT
27808 GGTAGATGGA
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
100 21 0.28
101 39 0.52
102 5 0.07
103 5 0.07
104 5 0.07
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33
Consensus pattern (99 bp):
TCCCCTAGAACTTGAAGACATAGTTCATATGGGTTTTAAAATTACTGATGTGCGAAGGCATCTTC
ATATTGAGGTCAAAGAAGTTAGCAAATGAATATC
Found at i:28875 original size:169 final size:170
Alignment explanation
Indices: 28497--28997 Score: 490
Period size: 169 Copynumber: 2.9 Consensus size: 170
28487 TGGAAATAAT
* * *
28497 GGAACTATTCACGTCAACCTTATTTATGTTTGATGGGACGAGACACTATGACATGCCAGAGATTC
1 GGAACTATTCACATCAACCCTATTTATGTTTGATGGGACGAGACACTATGACATGACAGAGATTC
* * *
28562 TCTAAAACCTTTGAAAACCACTTCTTATGGAACGAGCCTTTCATTTTTTTTAGAATTTATCTGCA
66 TCTAAAACCTTTGAAAACCACTTCTTATGGAACGAGCCTTT-ATTTTTGTCACAATTTATCTGCA
* * * * * * *
28627 TATTTCAATCAAGTATATGTAGATATGATGTTTCTAGTTGG
130 TATTTCAATAAAGTACATGCAGATATGATGTTGCTAATCGA
* * *
28668 GGAACTATTCACATCAACTCTATTTATGTTTGATGGGACAAGATACTATGACATGACAGAGATTC
1 GGAACTATTCACATCAACCCTATTTATGTTTGATGGGACGAGACACTATGACATGACAGAGATTC
* *** * *
28733 TCTAAACACCTTTGGAAAGTGCTTCTTGTGGAACGAGCC-TT-TTTTTGTCACAATTTATCTTCA
66 TCTAAA-ACCTTTGAAAACCACTTCTTATGGAACGAGCCTTTATTTTTGTCACAATTTATCTGCA
* * * *
28796 TATTTCATTAAATTACATGCATATATGTTGTTGGC-AATCGA
130 TATTTCAATAAAGTACATGCAGATATGATGTT-GCTAATCGA
* * ** *
28837 GGAACTATTCACTTCAACCCTATTTATATTAAATGGGACGAGACACTATGATATGACAGAGATTC
1 GGAACTATTCACATCAACCCTATTTATGTTTGATGGGACGAGACACTATGACATGACAGAGATTC
* **** * * * * * *
28902 TTTGAAAA-GAGGGAAAA-CGCTTCTTGTGGAACTAGTCTTTTGTTTTTGTCAGAATTTATCTGC
66 TCT-AAAACCTTTGAAAACCACTTCTTATGGAACGAG-CCTTTATTTTTGTCACAATTTATCTGC
* * * * * *
28965 ATATTTTAGTCAAGTATATGCAAATATAATGTT
129 ATATTTCAATAAAGTACATGCAGATATGATGTT
28998 CCCATTTTGG
Statistics
Matches: 271, Mismatches: 53, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
167 16 0.06
168 5 0.02
169 108 0.40
170 48 0.18
171 67 0.25
172 27 0.10
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (170 bp):
GGAACTATTCACATCAACCCTATTTATGTTTGATGGGACGAGACACTATGACATGACAGAGATTC
TCTAAAACCTTTGAAAACCACTTCTTATGGAACGAGCCTTTATTTTTGTCACAATTTATCTGCAT
ATTTCAATAAAGTACATGCAGATATGATGTTGCTAATCGA
Found at i:30442 original size:13 final size:13
Alignment explanation
Indices: 30436--30509 Score: 71
Period size: 13 Copynumber: 5.8 Consensus size: 13
30426 CATAAACACT
30436 AAACATAATACAA
1 AAACATAATACAA
*
30449 AAACATAATATAA
1 AAACATAATACAA
*
30462 AGACATAATA-AA
1 AAACATAATACAA
* *
30474 AAAGCA-AACAAAA
1 AAA-CATAATACAA
* *
30487 AAACTTAATATAA
1 AAACATAATACAA
30500 AAACATAATA
1 AAACATAATA
30510 AAATATAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
12 8 0.16
13 42 0.84
ACGTcount: A:0.69, C:0.11, G:0.03, T:0.18
Consensus pattern (13 bp):
AAACATAATACAA
Found at i:30519 original size:7 final size:7
Alignment explanation
Indices: 30507--30533 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
30497 TAAAAACATA
30507 ATAAAAT
1 ATAAAAT
30514 ATAAAAT
1 ATAAAAT
30521 ATAAAAT
1 ATAAAAT
30528 ATAAAA
1 ATAAAA
30534 CAAACATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
ATAAAAT
Found at i:36124 original size:31 final size:31
Alignment explanation
Indices: 36089--36152 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
36079 AAAACATAAT
**
36089 ATATGACCACTTTCTTTTTTATATAATTAAG
1 ATATGACCACTTTCGGTTTTATATAATTAAG
* *
36120 ATATGATCACTTTCGGTTTTATTTAATTAAG
1 ATATGACCACTTTCGGTTTTATATAATTAAG
36151 AT
1 AT
36153 GTGGTCAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.48
Consensus pattern (31 bp):
ATATGACCACTTTCGGTTTTATATAATTAAG
Found at i:39813 original size:23 final size:22
Alignment explanation
Indices: 39782--39850 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
39772 CACCATAGCT
*
39782 CGTATAATTGCACCTAAGTGCCA
1 CGTAGAATTGCACC-AAGTGCCA
* * *
39805 CTTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACC-AAGTGCCA
39828 CGTAGAATTGCACCATAGTGCCA
1 CGTAGAATTGCACCA-AGTGCCA
39851 TATAATAATG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (22 bp):
CGTAGAATTGCACCAAGTGCCA
Found at i:39991 original size:103 final size:103
Alignment explanation
Indices: 39866--40083 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
39856 TAATGTCCAT
*
39866 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
39931 TACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
39969 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
40034 GACCTCACACATGTTCCAAATAATACATATATGTTCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
40072 AAGGACCACATA
1 AAGGACCACATA
40084 GACCCTCTAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:40601 original size:19 final size:20
Alignment explanation
Indices: 40564--40601 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40554 TTTTTCATTA
*
40564 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
40584 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
40602 TCTAGCATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:40653 original size:21 final size:21
Alignment explanation
Indices: 40629--40671 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
40619 TCATATTCGT
* *
40629 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
40650 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
40671 T
1 T
40672 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:46701 original size:23 final size:23
Alignment explanation
Indices: 46670--46738 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
46660 CACCACAACT
* * *
46670 CGTATAATTGCACCTAAGTTCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
46693 CTTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
46716 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
46739 TATAATAATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:46925 original size:103 final size:103
Alignment explanation
Indices: 46746--46971 Score: 409
Period size: 103 Copynumber: 2.2 Consensus size: 103
46736 CCATATAATA
*
46746 ATGT-CCATAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
1 ATGTCCCA-AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
46810 GTCTCACAAGACCTCACACATGTTCCAAAGAATACATAT
65 GTCTCACAAGACCTCACACATGTTCCAAAGAATACATAT
46849 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
1 ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
*
46914 TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
66 TCTCACAAGACCTCACACATGTTCCAAAGAATACATAT
*
46952 ATGTCCCGAAGGACCACATA
1 ATGTCCCAAAGGACCACATA
46972 GACCCTCTAC
Statistics
Matches: 119, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
103 116 0.97
104 3 0.03
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.25
Consensus pattern (103 bp):
ATGTCCCAAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTG
TCTCACAAGACCTCACACATGTTCCAAAGAATACATAT
Found at i:47537 original size:21 final size:21
Alignment explanation
Indices: 47513--47555 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
47503 TCATATTCGT
* *
47513 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
47534 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
47555 T
1 T
47556 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:49776 original size:3 final size:3
Alignment explanation
Indices: 49762--49799 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
49752 CAGTTTTCTT
*
49762 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
49800 TAAATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:51195 original size:29 final size:30
Alignment explanation
Indices: 51147--51205 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
51137 AGGGCTGTAA
51147 ATTTTAATATTTTATATTTTAATC-CTATT
1 ATTTTAATATTTTATATTTTAATCACTATT
* *
51176 ATTTTAAT-TTTATATGTTTTAGTCACTATT
1 ATTTTAATATTT-TATATTTTAATCACTATT
51206 TAATTGCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (30 bp):
ATTTTAATATTTTATATTTTAATCACTATT
Found at i:51269 original size:12 final size:11
Alignment explanation
Indices: 51252--51286 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
51242 TTCAATATGT
51252 TTTAATTATTA
1 TTTAATTATTA
51263 CTTTAATTATTA
1 -TTTAATTATTA
*
51275 TTTTATTATTA
1 TTTAATTATTA
51286 T
1 T
51287 ATTAGCCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTAATTATTA
Found at i:54188 original size:12 final size:12
Alignment explanation
Indices: 54155--54189 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
54145 GTCTACTGGT
* *
54155 AAATGCTCTATA
1 AAATTCTCTCTA
54167 AAATTCTCTCTA
1 AAATTCTCTCTA
54179 AAATTCTCTCT
1 AAATTCTCTCT
54190 CCCGTTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (12 bp):
AAATTCTCTCTA
Found at i:55957 original size:22 final size:22
Alignment explanation
Indices: 55929--55972 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
55919 TGTTTCACTA
55929 CTTTCGAATAGAAAAATAATAG
1 CTTTCGAATAGAAAAATAATAG
*
55951 CTTTCGAATAGGAAAATAATAG
1 CTTTCGAATAGAAAAATAATAG
55973 TTTTTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.27
Consensus pattern (22 bp):
CTTTCGAATAGAAAAATAATAG
Found at i:60016 original size:16 final size:16
Alignment explanation
Indices: 59985--60018 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
59975 CTTGCTCCCA
59985 TAAAATTTTATCAATT
1 TAAAATTTTATCAATT
60001 TAAAAGTTTTAT-AATT
1 TAAAA-TTTTATCAATT
60017 TA
1 TA
60019 GGACTGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (16 bp):
TAAAATTTTATCAATT
Done.