Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004391.1 Hibiscus syriacus cultivar Beakdansim tig00009635_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: 61815
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:884 original size:24 final size:23
Alignment explanation
Indices: 857--908 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
847 ATATAATGAA
857 AATAAATAATATATAAATAAAAAT
1 AATAAA-AATATATAAATAAAAAT
* *
881 AAT-AAAATTTATATATAAAAAT
1 AATAAAAATATATAAATAAAAAT
903 -ATAAAA
1 AATAAAA
909 TGTATGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 2 0.08
22 18 0.72
23 2 0.08
24 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
AATAAAAATATATAAATAAAAAT
Found at i:927 original size:21 final size:20
Alignment explanation
Indices: 877--930 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
867 ATATAAATAA
*
877 AAATAATAAAATTTATATAT
1 AAATAATAAAATGTATATAT
* *
897 AAAAATATAAAATGTATGTAT
1 AAATA-ATAAAATGTATATAT
918 AATATAATAAAAT
1 AA-ATAATAAAAT
931 ACTAATAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 4 0.14
21 22 0.79
22 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (20 bp):
AAATAATAAAATGTATATAT
Found at i:1166 original size:14 final size:14
Alignment explanation
Indices: 1147--1196 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
1137 AAAGAGAACT
1147 ATATAATAAATAAA
1 ATATAATAAATAAA
*
1161 ATATAATAAAT-AT
1 ATATAATAAATAAA
*
1174 ATATAATAACATATA
1 ATATAATAA-ATAAA
1189 A-ATAATAA
1 ATATAATAA
1197 GGGTTAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
13 10 0.32
14 20 0.65
15 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (14 bp):
ATATAATAAATAAA
Found at i:1671 original size:34 final size:36
Alignment explanation
Indices: 1633--1717 Score: 102
Period size: 35 Copynumber: 2.4 Consensus size: 36
1623 GGATCCTATC
* *
1633 TTTAGGAGTTT-AATAATAGTAGAACTCTATCATA-
1 TTTAGGAGTTTGAATAATAGCAAAACTCTATCATAT
* ** *
1667 TTTAGGATTTTGAATCCTAGCAAAATTCTATCATAT
1 TTTAGGAGTTTGAATAATAGCAAAACTCTATCATAT
1703 TTTAGGAGTTTGAAT
1 TTTAGGAGTTTGAAT
1718 CCTAGTAGAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 10 0.24
35 18 0.43
36 14 0.33
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.41
Consensus pattern (36 bp):
TTTAGGAGTTTGAATAATAGCAAAACTCTATCATAT
Found at i:3137 original size:106 final size:106
Alignment explanation
Indices: 2467--3717 Score: 1775
Period size: 106 Copynumber: 11.9 Consensus size: 106
2457 GAATTGTTCC
* * * * * *
2467 GAGTCC-ATATCCTCCGTCGTGAAGTTGAAATTAGCTCTGGAATCGGGAAATTGTTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTTGTTGACA
* * * * *
2531 ACCAGCCG-CCCTTCATTGTG-AGTTGAACTTGTG-TGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
2570 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCT-TCGAAATTGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAGTTGTTTGTTGACA
* *
2634 ACCAGCGATCCCTTCGTCGTGAA-TTGAACTTGCGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
2675 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT-TCGAAATTGGGAAGTTGTTTTGTTGAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAGTTG-TTTGTTGAC
*
2739 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
64 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2782 GAGTCCAATA----TCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
2843 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC---GTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
2881 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCT-TCGAAATTGAGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGGGAAGTTGTTTGTTGACA
2945 ACCA-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
2986 GAG-CACAATATCTTTCTTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 GAGTC-CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * *
3050 ACCAGCGATCCCTTCGTCATGAAGTTGAACTTACGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3092 AAGTCTAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
3157 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
3198 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAAG-ATTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** *
3262 CCAGCGGTCCCTTCGTAATGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3303 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTTTTTATTAACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
3368 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
3409 GAGTCCAATATACTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
3474 CAAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3515 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
3580 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3621 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
3686 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTG
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTG
3718 TGTTATCTCA
Statistics
Matches: 1039, Mismatches: 87, Indels: 41
0.89 0.07 0.04
Matches are distributed among these distances:
99 15 0.01
102 72 0.07
103 107 0.10
104 61 0.06
105 222 0.21
106 534 0.51
107 28 0.03
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:3314 original size:317 final size:315
Alignment explanation
Indices: 2486--3730 Score: 1787
Period size: 317 Copynumber: 4.0 Consensus size: 315
2476 TCCTCCGTCG
* * * * * * *
2486 TGAAGTTGAAATTAGCTCTGGAATCGGGAAATTGTTTTGTTGACAACCAGCCG-CCCTTCATTGT
1 TGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG-TTTATTGACAACCAGCGGTCCCTTCGTCGT
* * *
2550 G-AGTTGAACTTGTGTGTCTCGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTTCGAAAT
65 GAAGTTGAACTTGCGTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTCGAAAT
* * *
2614 TGGGAAATTGTTTGTTGACAACCAGCGATCCCTTCGTCGTGAA-TTGAACTTGCGTTGTCTCGAG
130 TGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG
*
2678 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTCGAAATTGGGAAGTTGTTTTGTTGACAACC
195 TCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTG-TTTGTTGACAACC
* * ** *
2743 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCGTTG--
259 AGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTCAAGTCCAATATCCTTGCT
* * *
2798 TGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
1 TGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
*
2863 AAGTTGAACTTGC--GTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTCGAAATT
66 AAGTTGAACTTGCGTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTCGAAATT
2926 GAGAAATTGTTTGTTGACAACCA-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAG-
131 GAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
2989 CACAATATCTTTCTTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAACCA
196 C-CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTTGTTGACAACCA
* * *
3054 GCGATCCCTTCGTCATGAAGTTGAACTTACGTTGTCTCAAGTCTAATATCCTTCGCT
260 GCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTCAAGTCCAATATCCTT-GCT
* *
3111 ATGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
1 -TGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
3176 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC-TCTGAA
65 GAAGTTGAACTTGCG-TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTC-GAA
* * ** *
3240 ATTAAG-ATTTGTTTGTTGACAACCAGCGGTCCCTTCGTAATGAAGTTGAACTTGCGTTGTCTAG
128 ATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
3304 AGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTTTTTATTAACAAC
193 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTTGTTGACAAC
** *
3369 CAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATACTTTGCT
258 CAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTCAAGTCCAATAT-CCTTGCT
*
3428 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACAAGCGGTCCCTTCGTCGT
1 -TGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
*
3493 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGC-TCTGAA
65 GAAGTTGAACTTGCG-TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTC-GAA
* * *
3557 ATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTGG
128 ATTGAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
3622 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAAC
193 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTTGTTGACAAC
** * *
3687 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCAAGT
258 CAG-CGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTCAAGT
3731 GGCACGATAT
Statistics
Matches: 842, Mismatches: 74, Indels: 28
0.89 0.08 0.03
Matches are distributed among these distances:
310 77 0.09
311 151 0.18
312 38 0.05
313 11 0.01
314 75 0.09
316 20 0.02
317 316 0.38
318 153 0.18
319 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (315 bp):
TGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTG
AAGTTGAACTTGCGTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTCGAAATT
GAGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAGTTGTTTGTTGACAACCAG
CGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTCAAGTCCAATATCCTTGCT
Found at i:5338 original size:16 final size:15
Alignment explanation
Indices: 5301--5356 Score: 71
Period size: 13 Copynumber: 3.7 Consensus size: 15
5291 TTTTTGTCCC
5301 TTTTTCTTTTTGA--
1 TTTTTCTTTTTGATT
5314 TTTTTCTTTTTGATT
1 TTTTTCTTTTTGATT
*
5329 TTTCTTCTTTTTTGCTT
1 TTT-TTC-TTTTTGATT
5346 TTTTTCTTTTT
1 TTTTTCTTTTT
5357 TGTTTTTGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
13 13 0.34
15 8 0.21
16 6 0.16
17 11 0.29
ACGTcount: A:0.04, C:0.11, G:0.05, T:0.80
Consensus pattern (15 bp):
TTTTTCTTTTTGATT
Found at i:5357 original size:16 final size:15
Alignment explanation
Indices: 5301--5363 Score: 69
Period size: 16 Copynumber: 4.2 Consensus size: 15
5291 TTTTTGTCCC
*
5301 TTTTTC-TTTTTG-A
1 TTTTTCTTTTTTGTT
5314 TTTTTC-TTTTTGATT
1 TTTTTCTTTTTTG-TT
5329 TTTCTTCTTTTTTGCTT
1 TTT-TTCTTTTTTG-TT
5346 TTTTTCTTTTTTGTT
1 TTTTTCTTTTTTGTT
5361 TTT
1 TTT
5364 GCCCTTATTG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
13 12 0.27
15 8 0.18
16 13 0.30
17 11 0.25
ACGTcount: A:0.03, C:0.10, G:0.06, T:0.81
Consensus pattern (15 bp):
TTTTTCTTTTTTGTT
Found at i:9829 original size:17 final size:16
Alignment explanation
Indices: 9800--9948 Score: 53
Period size: 17 Copynumber: 8.8 Consensus size: 16
9790 AATATAATGA
9800 AAATAAATAAATAGTAT
1 AAATAAATAAATA-TAT
9817 AAATAAA-ATAATATAT
1 AAATAAATA-AATATAT
* *
9833 --ATATATATATATAT
1 AAATAAATAAATATAT
* *
9847 AAATATAAAAAATGTATGT
1 AAATA-AATAAA--TATAT
9866 ATAATATAATAAA-ATACT
1 A-AATA-AATAAATATA-T
9884 AAATAGTAAT-AATAATAAT
1 AAATA--AATAAAT-AT-AT
9903 AAATAAATGAAA-A-AT
1 AAATAAAT-AAATATAT
9918 AAATATACATATAATAT-T
1 AAATA-A-ATA-AATATAT
*
9936 AAATAAAAAAATA
1 AAATAAATAAATA
9949 GTAATCATAG
Statistics
Matches: 103, Mismatches: 9, Indels: 42
0.67 0.06 0.27
Matches are distributed among these distances:
14 10 0.10
15 12 0.12
16 11 0.11
17 31 0.30
18 13 0.13
19 15 0.15
20 11 0.11
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATAAATAAATATAT
Found at i:9839 original size:22 final size:22
Alignment explanation
Indices: 9786--9839 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
9776 GCAAAGAAAC
*
9786 TAAAAATAT-AATGAAAATAAA
1 TAAATATATAAATGAAAATAAA
9807 TAAATAGTATAAAT-AAAATAATA
1 TAAATA-TATAAATGAAAATAA-A
*
9830 TATATATATA
1 TAAATATATA
9840 TATATATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 5 0.18
22 14 0.50
23 9 0.32
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (22 bp):
TAAATATATAAATGAAAATAAA
Found at i:9852 original size:14 final size:14
Alignment explanation
Indices: 9806--9853 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
9796 ATGAAAATAA
9806 ATAAATAGTATA-A-
1 ATAAATA-TATATAT
9819 ATAAA-ATA-ATAT
1 ATAAATATATATAT
*
9831 ATATATATATATAT
1 ATAAATATATATAT
9845 ATAAATATA
1 ATAAATATA
9854 AAAAATGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
10 1 0.03
11 3 0.10
12 5 0.17
13 8 0.28
14 12 0.41
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
ATAAATATATATAT
Found at i:9981 original size:89 final size:91
Alignment explanation
Indices: 9821--9986 Score: 193
Period size: 89 Copynumber: 1.8 Consensus size: 91
9811 TAGTATAAAT
* * *
9821 AAAATAATATATATATATATATATATAAATATAAAAAATGTATGTATAATATAATAAAATACTAA
1 AAAATAATATATACATATATATATATAAATATAAAAAATGTATGCATAAAATAATAAAATAC-AA
*
9886 ATAGTAATAATAATAATAAATAAATGA
65 ATAGTAAGAATAATAATAAATAAATGA
9913 AAAATAA-ATATACATATA-ATAT-TAAATA-AAAAAATAGTAAT-CATAGAAAT-ATAAAATA-
1 AAAATAATATATACATATATATATATAAATATAAAAAAT-GT-ATGCATA-AAATAATAAAATAC
9971 AAATGAAGTAAGAATA
63 AAAT--AGTAAGAATA
9987 TATATATATA
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
87 4 0.06
88 7 0.11
89 28 0.43
90 9 0.14
91 10 0.15
92 7 0.11
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (91 bp):
AAAATAATATATACATATATATATATAAATATAAAAAATGTATGCATAAAATAATAAAATACAAA
TAGTAAGAATAATAATAAATAAATGA
Found at i:9991 original size:2 final size:2
Alignment explanation
Indices: 9984--10012 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9974 TGAAGTAAGA
9984 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 A
10013 ACGTTAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10729 original size:37 final size:37
Alignment explanation
Indices: 10636--10737 Score: 141
Period size: 37 Copynumber: 2.8 Consensus size: 37
10626 ATGCTTGTGG
* * * ** *
10636 ATCCTATCTTTAGAAGTTTAAATAATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
10673 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
10710 ATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
10738 TAGTACGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:16427 original size:3 final size:3
Alignment explanation
Indices: 16419--16488 Score: 61
Period size: 3 Copynumber: 22.7 Consensus size: 3
16409 TTTTAATTGT
* * *
16419 TTA TTA TTA GTTA TTA TAA TTA TTA TT- TTAA TTA TTA TCA CTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
* *
16465 TTA GTA TTA TTA TTTA CTA TTA TT
1 TTA TTA TTA TTA -TTA TTA TTA TT
16489 TTTCTTTTAC
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
2 2 0.04
3 43 0.81
4 8 0.15
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:18659 original size:18 final size:18
Alignment explanation
Indices: 18622--18659 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
18612 TGAATAATTG
* *
18622 AATCGAATATAATATTTT
1 AATCGAATATAAAATATT
18640 AATCGAATATAAAATATT
1 AATCGAATATAAAATATT
18658 AA
1 AA
18660 AATTAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (18 bp):
AATCGAATATAAAATATT
Found at i:19066 original size:18 final size:18
Alignment explanation
Indices: 19045--19083 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19035 ACCAATCATT
19045 AAAAAC-ATACAAATATCC
1 AAAAACAAT-CAAATATCC
*
19063 AAAAACAATCAAATATTC
1 AAAAACAATCAAATATCC
19081 AAA
1 AAA
19084 CAACCAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAAACAATCAAATATCC
Found at i:21154 original size:22 final size:21
Alignment explanation
Indices: 21129--21185 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
21119 ATTCTATGCT
21129 AGTAGTATCGATACCTA-GAAAG
1 AGTAGTATCGATACCTATG--AG
*
21151 AGTAGTATCGATA-CTATGTG
1 AGTAGTATCGATACCTATGAG
21171 AGTAGTATCGATACC
1 AGTAGTATCGATACC
21186 AAGTGCACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 14 0.44
21 4 0.12
22 14 0.44
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (21 bp):
AGTAGTATCGATACCTATGAG
Found at i:26154 original size:18 final size:18
Alignment explanation
Indices: 26133--26167 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
26123 CGAATAATTG
* *
26133 AATCGAATATAATATTTA
1 AATCGAACATAAAATTTA
26151 AATCGAACATAAAATTT
1 AATCGAACATAAAATTT
26168 TAAAATTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (18 bp):
AATCGAACATAAAATTTA
Found at i:28013 original size:35 final size:35
Alignment explanation
Indices: 27966--28083 Score: 123
Period size: 35 Copynumber: 3.3 Consensus size: 35
27956 GTCTCTGCAA
*
27966 GTTCAGTTCGATCAAATTGGTAATTCCTTATATAG
1 GTTCAGTCCGATCAAATTGGTAATTCCTTATATAG
*
28001 GTTCAGTCCGATCGAATTGGTAATTACC-TATATTAG
1 GTTCAGTCCGATCAAATTGGTAATT-CCTTATA-TAG
* * * * *
28037 GTTTAG-CTTGGTTAAATTGGTAATTCTTTATATAG
1 GTTCAGTC-CGATCAAATTGGTAATTCCTTATATAG
*
28072 GTTCAGACCGAT
1 GTTCAGTCCGAT
28084 GGAGGTGTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
35 39 0.58
36 28 0.42
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (35 bp):
GTTCAGTCCGATCAAATTGGTAATTCCTTATATAG
Found at i:31169 original size:27 final size:26
Alignment explanation
Indices: 31118--31169 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
31108 TCTGACGTAC
*
31118 CAATTTTTAGAAGGTCCAGTCAGCGG
1 CAATTTTTAGAAGATCCAGTCAGCGG
* *
31144 CAATTTTCTAGAAGATCTAGTGAGCG
1 CAATTTT-TAGAAGATCCAGTCAGCG
31170 CCTTTTGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (26 bp):
CAATTTTTAGAAGATCCAGTCAGCGG
Found at i:47400 original size:19 final size:19
Alignment explanation
Indices: 47376--47416 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
47366 AACATCAAAC
47376 AAAAAAGGTTTTCGTAACA
1 AAAAAAGGTTTTCGTAACA
* *
47395 AAAAAATGTTTTCGTGACA
1 AAAAAAGGTTTTCGTAACA
47414 AAA
1 AAA
47417 TGACATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.27
Consensus pattern (19 bp):
AAAAAAGGTTTTCGTAACA
Found at i:47960 original size:22 final size:22
Alignment explanation
Indices: 47935--47977 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
47925 ATTTTATTTA
*
47935 AATTTGTTATTATAACTAAAAT
1 AATTTGTTATGATAACTAAAAT
*
47957 AATTTGTTCTGATAACTAAAA
1 AATTTGTTATGATAACTAAAA
47978 ATAAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (22 bp):
AATTTGTTATGATAACTAAAAT
Found at i:49449 original size:36 final size:36
Alignment explanation
Indices: 49372--49553 Score: 275
Period size: 36 Copynumber: 5.1 Consensus size: 36
49362 TTTTTTCAAA
49372 AATATATAGTTTTGAAAACATTTTTGAAAGTATATAT
1 AATATATAGTTTTGAAAACATTTTTGAAA-TATATAT
49409 AATATATAGTTTTGAAAACATTTTTGAAATATATAT
1 AATATATAGTTTTGAAAACATTTTTGAAATATATAT
49445 AATATATAGTTTTGAAAACATTTTTGAAAGTATATATAT
1 AATATATAGTTTTGAAAACATTTTTG-AA--ATATATAT
* *
49484 AATATATAGTTTTAAAAAGATTTTTG-AA-ATATAT
1 AATATATAGTTTTGAAAACATTTTTGAAATATATAT
49518 -ATATATAGTTTTGAAAACA-TTTTGAAA-ATATAT
1 AATATATAGTTTTGAAAACATTTTTGAAATATATAT
49551 AAT
1 AAT
49554 TTTTGAAAAC
Statistics
Matches: 136, Mismatches: 4, Indels: 13
0.89 0.03 0.08
Matches are distributed among these distances:
32 5 0.04
33 25 0.18
34 8 0.06
35 1 0.01
36 33 0.24
37 32 0.24
39 32 0.24
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.43
Consensus pattern (36 bp):
AATATATAGTTTTGAAAACATTTTTGAAATATATAT
Found at i:49461 original size:73 final size:71
Alignment explanation
Indices: 49372--49651 Score: 289
Period size: 73 Copynumber: 3.8 Consensus size: 71
49362 TTTTTTCAAA
*
49372 AATATATAGTTTTGAAAACATTTTTGAAAGTATATATAATATATAGTTTTGAAAACATTTTTGAA
1 AATATATAGTTTTGAAAACATTTTTGAAAGTATATATAATATATAGTTTTAAAAACATTTTTG-A
49437 ATATATAT
65 A-ATATAT
*
49445 AATATATAGTTTTGAAAACATTTTTGAAAGTATATATATAATATATAGTTTTAAAAAGATTTTTG
1 AATATATAGTTTTGAAAACATTTTTGAAAG--TATATATAATATATAGTTTTAAAAACATTTTTG
49510 AAATATAT
64 AAATATAT
*
49518 -ATATATAGTTTTGAAAACA-TTTTGAAAATATATAATTTTTGAAAACATATATAG-TTTAAAAA
1 AATATATAGTTTTGAAAACATTTTTGAAAGTATAT-A----T----A-ATATATAGTTTTAAAAA
*
49580 TGATTTTTGAAAATATAT
56 -CATTTTTG-AAATATAT
* * * * * * *
49598 AATATATAGTTTTTAAAATATTTTTTAAA-AATGTATAATATATGGTTTTTAAAA
1 AATATATAGTTTTGAAAACATTTTTGAAAGTATATATAATATATAGTTTTAAAAA
49652 GAAGGTTTTT
Statistics
Matches: 180, Mismatches: 10, Indels: 35
0.80 0.04 0.16
Matches are distributed among these distances:
69 5 0.03
70 1 0.01
71 15 0.08
72 27 0.15
73 36 0.20
74 3 0.02
75 31 0.17
76 1 0.01
78 9 0.05
79 16 0.09
80 9 0.05
81 20 0.11
82 7 0.04
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.44
Consensus pattern (71 bp):
AATATATAGTTTTGAAAACATTTTTGAAAGTATATATAATATATAGTTTTAAAAACATTTTTGAA
ATATAT
Found at i:49559 original size:17 final size:17
Alignment explanation
Indices: 49537--49600 Score: 57
Period size: 17 Copynumber: 4.0 Consensus size: 17
49527 TTTGAAAACA
49537 TTTTGAAAATATATAAT
1 TTTTGAAAATATATAAT
*
49554 TTTTGAAAACATAT-AT
1 TTTTGAAAATATATAAT
* *
49570 AGTTT--AAA-A-ATGAT
1 -TTTTGAAAATATATAAT
49584 TTTTGAAAATATATAAT
1 TTTTGAAAATATATAAT
49601 ATATAGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
13 5 0.14
14 3 0.08
15 6 0.16
16 3 0.08
17 20 0.54
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (17 bp):
TTTTGAAAATATATAAT
Found at i:49564 original size:28 final size:31
Alignment explanation
Indices: 49478--49565 Score: 101
Period size: 33 Copynumber: 2.8 Consensus size: 31
49468 TTGAAAGTAT
* *
49478 ATATATAATATATAGTTTTAAAAAGATTTTTGAA
1 ATATAT-ATATATA-TTTTGAAAACA-TTTTGAA
49512 ATATATATATATAGTTTTGAAAACATTTTGAA
1 ATATATATATATA-TTTTGAAAACATTTTGAA
49544 A-ATATATA-AT-TTTTGAAAACAT
1 ATATATATATATATTTTGAAAACAT
49566 ATATAGTTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
28 12 0.23
30 2 0.04
31 7 0.13
32 8 0.15
33 17 0.33
34 6 0.12
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (31 bp):
ATATATATATATATTTTGAAAACATTTTGAA
Found at i:49603 original size:35 final size:36
Alignment explanation
Indices: 49564--49672 Score: 114
Period size: 36 Copynumber: 3.0 Consensus size: 36
49554 TTTTGAAAAC
49564 ATATATAG-TTTAAAAATGATTTTTGAAAATATATA
1 ATATATAGTTTTAAAAATGATTTTTGAAAATATATA
* * *
49599 ATATATAGTTTTTAAAAT-ATTTTTTAAAAATGTATA
1 ATATATAGTTTTAAAAATGA-TTTTTGAAAATATATA
* * * *
49635 ATATATGGTTTTTAAAAGAAGGTTTTTGAAAACATATA
1 ATATATAG-TTTTAAAA-ATGATTTTTGAAAATATATA
49673 GCATATAGAT
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
35 9 0.15
36 29 0.49
37 7 0.12
38 14 0.24
ACGTcount: A:0.45, C:0.01, G:0.10, T:0.44
Consensus pattern (36 bp):
ATATATAGTTTTAAAAATGATTTTTGAAAATATATA
Found at i:49623 original size:36 final size:36
Alignment explanation
Indices: 49564--49651 Score: 117
Period size: 36 Copynumber: 2.5 Consensus size: 36
49554 TTTTGAAAAC
* *
49564 ATATATAG-TTTAAAAATGATTTTTGAAAATATATA
1 ATATATAGTTTTTAAAATGATTTTTAAAAATATATA
*
49599 ATATATAGTTTTTAAAAT-ATTTTTTAAAAATGTATA
1 ATATATAGTTTTTAAAATGA-TTTTTAAAAATATATA
*
49635 ATATATGGTTTTTAAAA
1 ATATATAGTTTTTAAAA
49652 GAAGGTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
35 9 0.19
36 38 0.81
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (36 bp):
ATATATAGTTTTTAAAATGATTTTTAAAAATATATA
Found at i:49814 original size:23 final size:22
Alignment explanation
Indices: 49786--49831 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
49776 TTCAAATATG
49786 TATTTATTATCATTTATTTTCTT
1 TATTTATT-TCATTTATTTTCTT
* *
49809 TATTTATTTTATTTTTTTTCTT
1 TATTTATTTCATTTATTTTCTT
49831 T
1 T
49832 TTCAGGCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (22 bp):
TATTTATTTCATTTATTTTCTT
Found at i:50981 original size:5 final size:5
Alignment explanation
Indices: 50971--51017 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
50961 GATTTGAATA
* *
50971 TTATT TTATT TTACT TTATC TTATT TT-TT TTATT TTAATTT TTATT T
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT-A-TT TTATT T
51018 GTTTTATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 4 0.11
5 25 0.71
6 2 0.06
7 4 0.11
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:51011 original size:15 final size:14
Alignment explanation
Indices: 50971--51024 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
50961 GATTTGAATA
*
50971 TTATTTTATTTTACT
1 TTATTTTATTTT-TT
*
50986 TTATCTTATTTTTT
1 TTATTTTATTTTTT
51000 TTATTTTAATTTTTAT
1 TTATTTT-ATTTTT-T
*
51016 TTGTTTTAT
1 TTATTTTAT
51025 ATTAACCCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 7 0.21
15 19 0.58
16 7 0.21
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.76
Consensus pattern (14 bp):
TTATTTTATTTTTT
Found at i:51132 original size:6 final size:6
Alignment explanation
Indices: 51121--51145 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
51111 ATTGAATCTA
51121 TAAATT TAAATT TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
51146 TTACAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:60863 original size:18 final size:19
Alignment explanation
Indices: 60827--60864 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
60817 ATTAGGAGAG
60827 AATTGTTGATAATTGTGCT
1 AATTGTTGATAATTGTGCT
* *
60846 AATT-TTGATGATTTTGCT
1 AATTGTTGATAATTGTGCT
60864 A
1 A
60865 TGAATTTGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.26, C:0.05, G:0.18, T:0.50
Consensus pattern (19 bp):
AATTGTTGATAATTGTGCT
Done.