Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001374.1 Hibiscus syriacus cultivar Beakdansim tig00002686_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: 68510
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:59 original size:40 final size:40
Alignment explanation
Indices: 15--90 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
5 ATTTCGCTTG
* * * *
15 TCCATCACATTAGGATTTGGATCAGCATCACCTTGGCTCT
1 TCCATCACATAAGAAGTTAGATCAGCATCACCTTGGCTCT
*
55 TCCATCATATAAGAAGTTAGATCAGCATCACCTTGG
1 TCCATCACATAAGAAGTTAGATCAGCATCACCTTGG
91 GTTAACCATC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (40 bp):
TCCATCACATAAGAAGTTAGATCAGCATCACCTTGGCTCT
Found at i:897 original size:3 final size:3
Alignment explanation
Indices: 889--917 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
879 GAATATGGTT
889 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
918 AGGTTCGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:2924 original size:18 final size:18
Alignment explanation
Indices: 2883--2944 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
2873 TTCATTTACA
* *
2883 TTGTGACACTTCGATGCA
1 TTGTGTCACTTCGATGCC
2901 TTGTGTCACTTCGATGCC
1 TTGTGTCACTTCGATGCC
* *
2919 TTGTGTAGTATTTCGATGCC
1 TTGTGT--CACTTCGATGCC
2939 TTGTGT
1 TTGTGT
2945 AGCATTTCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
18 22 0.58
20 16 0.42
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (18 bp):
TTGTGTCACTTCGATGCC
Found at i:2935 original size:20 final size:20
Alignment explanation
Indices: 2892--2956 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
2882 ATTGTGACAC
* *
2892 TTCGATGCATTGTGT--CAC
1 TTCGATGCCTTGTGTAGCAT
*
2910 TTCGATGCCTTGTGTAGTAT
1 TTCGATGCCTTGTGTAGCAT
2930 TTCGATGCCTTGTGTAGCAT
1 TTCGATGCCTTGTGTAGCAT
2950 TTCGATG
1 TTCGATG
2957 TTGGAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.34
20 27 0.66
ACGTcount: A:0.15, C:0.18, G:0.25, T:0.42
Consensus pattern (20 bp):
TTCGATGCCTTGTGTAGCAT
Found at i:7847 original size:17 final size:16
Alignment explanation
Indices: 7806--7847 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
7796 AAATATCTTT
7806 TAAAATAATTTTAAGA
1 TAAAATAATTTTAAGA
7822 -AAAATAATTTTAAAAGA
1 TAAAATAATTTT--AAGA
7839 TAAAA-AATT
1 TAAAATAATT
7848 GATCTTCGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTTAAGA
Found at i:12887 original size:22 final size:21
Alignment explanation
Indices: 12853--12893 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
12843 TTAATTATTT
12853 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAATATA
*
12874 AAAAACATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
12894 GTTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATA
Found at i:18707 original size:24 final size:24
Alignment explanation
Indices: 18671--18737 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
18661 GGAAAAAATG
* *
18671 AATAAATGAAAAAATAAAGAATAAA
1 AATAAATAAAAAAATAAA-AAGAAA
* *
18696 AATAAGTAAAAAAATAAAAGGAAA
1 AATAAATAAAAAAATAAAAAGAAA
*
18720 AATAAATAAATAAATAAA
1 AATAAATAAAAAAATAAA
18738 TAAATGAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
24 20 0.56
25 16 0.44
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.16
Consensus pattern (24 bp):
AATAAATAAAAAAATAAAAAGAAA
Found at i:18728 original size:4 final size:4
Alignment explanation
Indices: 18666--18748 Score: 55
Period size: 4 Copynumber: 20.2 Consensus size: 4
18656 TAGAGGGAAA
* * * * *
18666 AAAT GAAT AAAT GAAA- AAAT AAAG AATAA AAAT AAGT AAAA AAAT AAA-
1 AAAT AAAT AAAT -AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT
18714 AGGAA- AAAT AAAT AAAT AAAT AAAT AAAT GAAAT A
1 A--AAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT A
18749 TTAAAATATA
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
3 6 0.10
4 44 0.70
5 13 0.21
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:18761 original size:2 final size:2
Alignment explanation
Indices: 18754--18784 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18744 AAATATTAAA
18754 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18785 AATGAGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19062 original size:2 final size:2
Alignment explanation
Indices: 19057--19084 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19047 TTAAAAAAAG
19057 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19085 AAATAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19677 original size:37 final size:37
Alignment explanation
Indices: 19636--19739 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 37
19626 GTGCTTGTGG
* * * *
19636 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
* *
19673 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
*
19710 ATCCTATTTTTAGGAGTTTGAATCCTAGCA
1 ATCCTATTTTTAGGAGTTTGAATCATAGCA
19740 GGACGAAAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTCT
Found at i:20660 original size:106 final size:106
Alignment explanation
Indices: 20470--21564 Score: 1713
Period size: 106 Copynumber: 10.3 Consensus size: 106
20460 GCATTGTTCC
* * * *
20470 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTATGGAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* *
20535 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* ** *
20576 GAGTCCAATATCCTTCGCTGTGAAGTCAAAATTGACTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * *
20641 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTTCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
20682 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
20747 CCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
20788 GAGTCCAACATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
20853 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGCTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
20894 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
20959 CCAGTGGTCCCTTCATCGTGAAGTTAAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * ** *
21000 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTTTGAAATTAAGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
21065 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
21106 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
21171 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCTTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
21212 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
21277 CTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
21318 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
*
21383 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCTTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
21424 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
* * * *
21489 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
21530 GAGTGGCACGATATCCTCCGTTGTGGAGTTGAAAT
1 GAGT--C-CAATATCCTTCGTTGTGAAGTTGAAAT
21565 CGTGGATGGC
Statistics
Matches: 913, Mismatches: 73, Indels: 3
0.92 0.07 0.00
Matches are distributed among these distances:
106 888 0.97
108 1 0.00
109 24 0.03
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:23171 original size:20 final size:19
Alignment explanation
Indices: 23135--23210 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 19
23125 TTTTTGTCCC
**
23135 TTTTTCTTTTTGATTTTTG
1 TTTTTCTTTTTTCTTTTTG
23154 TTCTTTCTTTTTTC-TTTTG
1 TT-TTTCTTTTTTCTTTTTG
*
23173 TTTCTCTTTTTTCTTTATT-
1 TTTTTCTTTTTTCTTT-TTG
*
23192 TTTTGCTTCTTTTCTTTTT
1 TTTTTCTT-TTTTCTTTTT
23211 TGTTCTTGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 10 0.21
19 19 0.40
20 19 0.40
ACGTcount: A:0.03, C:0.13, G:0.05, T:0.79
Consensus pattern (19 bp):
TTTTTCTTTTTTCTTTTTG
Found at i:23182 original size:18 final size:19
Alignment explanation
Indices: 23149--23188 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
23139 TCTTTTTGAT
*
23149 TTTTGTTCTTTCTTTTTTC
1 TTTTGTTCTCTCTTTTTTC
23168 TTTTGTT-TCTCTTTTTTC
1 TTTTGTTCTCTCTTTTTTC
23186 TTT
1 TTT
23189 ATTTTTTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (19 bp):
TTTTGTTCTCTCTTTTTTC
Found at i:23205 original size:29 final size:30
Alignment explanation
Indices: 23149--23217 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
23139 TCTTTTTGAT
* *
23149 TTTTGTTCTTTCTTTTTTCTTTTGTTTCTC
1 TTTTGTTCTTTATTTTTTCTTCTGTTTCTC
*
23179 TTTT-TTCTTTATTTTTTGCTTCT-TTTCTT
1 TTTTGTTCTTTATTTTTT-CTTCTGTTTCTC
23208 TTTTGTTCTT
1 TTTTGTTCTT
23218 GATTGGATCT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.01, C:0.14, G:0.06, T:0.78
Consensus pattern (30 bp):
TTTTGTTCTTTATTTTTTCTTCTGTTTCTC
Found at i:27661 original size:4 final size:4
Alignment explanation
Indices: 27609--27677 Score: 52
Period size: 4 Copynumber: 17.0 Consensus size: 4
27599 TGTTAGAGGG
* * * **
27609 AATA AATG AATA AATGA AA-A AATA AGTA AAAA AATGA AAGG AA-A AATA
1 AATA AATA AATA AAT-A AATA AATA AATA AATA AAT-A AATA AATA AATA
27657 AATA AATA AATA AATGA AATA
1 AATA AATA AATA AAT-A AATA
27678 TTAATATATA
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
3 5 0.10
4 36 0.71
5 10 0.20
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (4 bp):
AATA
Found at i:27818 original size:29 final size:30
Alignment explanation
Indices: 27751--27818 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
27741 AGTAATATGA
*
27751 AAATAT-AATATAATATAAATAAAAAAACC
1 AAATATAAAAATAATATAAATAAAAAAACC
* * * *
27780 AAAAACAAAAATAA-ATAAATATATAAACC
1 AAATATAAAAATAATATAAATAAAAAAACC
27809 AAATATAAAA
1 AAATATAAAA
27819 GTATACATAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (30 bp):
AAATATAAAAATAATATAAATAAAAAAACC
Found at i:27976 original size:2 final size:2
Alignment explanation
Indices: 27971--28001 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
27961 TAAAAAAAAG
*
27971 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28002 TATTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 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):
TA
Found at i:28579 original size:37 final size:37
Alignment explanation
Indices: 28538--28640 Score: 143
Period size: 37 Copynumber: 2.8 Consensus size: 37
28528 GTGCTTGTGG
* * * *
28538 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
* *
28575 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
*
28612 ATCTTATTTTTAGGAGTTTGAATCCTAGT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGT
28641 TGGACGAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:29297 original size:3 final size:3
Alignment explanation
Indices: 29289--29333 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
29279 GGTACCCAGT
*
29289 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTT TTA TT- TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29334 AATTTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 6 0.16
3 31 0.84
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:29338 original size:18 final size:19
Alignment explanation
Indices: 29288--29344 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
29278 TGGTACCCAG
*
29288 TTTATTATT--ATTATTAT
1 TTTATTATTAAATTTTTAT
*
29305 TATTATTATTATATTTTTAT
1 T-TTATTATTAAATTTTTAT
29325 TTTA-TATTAAATTTTTAT
1 TTTATTATTAAATTTTTAT
29343 TT
1 TT
29345 ATAATTCTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 1 0.03
18 23 0.66
19 3 0.09
20 8 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATTATTAAATTTTTAT
Found at i:29410 original size:38 final size:39
Alignment explanation
Indices: 29354--29458 Score: 137
Period size: 38 Copynumber: 2.7 Consensus size: 39
29344 TATAATTCTC
29354 AAATTATTTCAC-TCTAACATTCTAAATTCCTAATTTCGT
1 AAATTATTTCACAT-TAACATTCTAAATTCCTAATTTCGT
* *
29393 -AATT-TTTCCACCA-TAACATTCTAAATTCTTAATTTCTT
1 AAATTATTT-CA-CATTAACATTCTAAATTCCTAATTTCGT
29431 AAATTATTTCACATTAACATTCTAAATT
1 AAATTATTTCACATTAACATTCTAAATT
29459 ATTTTTTAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
37 3 0.05
38 31 0.53
39 21 0.36
40 3 0.05
ACGTcount: A:0.35, C:0.19, G:0.01, T:0.45
Consensus pattern (39 bp):
AAATTATTTCACATTAACATTCTAAATTCCTAATTTCGT
Found at i:29661 original size:18 final size:18
Alignment explanation
Indices: 29640--29677 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
29630 TATATTTTTT
* *
29640 AAAAATAATATAATTATA
1 AAAAATAAAAAAATTATA
29658 AAAAATAAAAAAATTATA
1 AAAAATAAAAAAATTATA
29676 AA
1 AA
29678 TTGGGTATCG
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATAAAAAAATTATA
Found at i:35805 original size:16 final size:16
Alignment explanation
Indices: 35784--35816 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
35774 TAATAAATAA
35784 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
35800 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
35816 A
1 A
35817 AAATTTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:35898 original size:10 final size:10
Alignment explanation
Indices: 35883--35973 Score: 65
Period size: 10 Copynumber: 9.7 Consensus size: 10
35873 CATTTAATAA
35883 ATAAACGAAC
1 ATAAACGAAC
35893 ATAAACGAAC
1 ATAAACGAAC
* **
35903 ACGAAAATAA-
1 A-TAAACGAAC
35913 ATGAACACGAAC
1 AT-AA-ACGAAC
35925 ATAAACGAAC
1 ATAAACGAAC
35935 ----ACGAAC
1 ATAAACGAAC
35941 ATAAACGAAC
1 ATAAACGAAC
35951 ----ACGAAC
1 ATAAACGAAC
35957 ATAAACGAAC
1 ATAAACGAAC
35967 ATAAACG
1 ATAAACG
35974 TTGGAAACCC
Statistics
Matches: 63, Mismatches: 6, Indels: 24
0.68 0.06 0.26
Matches are distributed among these distances:
6 12 0.19
10 39 0.62
11 10 0.16
12 2 0.03
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:35912 original size:16 final size:16
Alignment explanation
Indices: 35887--35967 Score: 144
Period size: 16 Copynumber: 5.1 Consensus size: 16
35877 TAATAAATAA
35887 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
35903 ACGAAAATAAATGAAC
1 ACGAACATAAACGAAC
35919 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
35935 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
35951 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
35967 A
1 A
35968 TAAACGTTGG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 61 1.00
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.07
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:36812 original size:24 final size:24
Alignment explanation
Indices: 36752--36801 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
36742 TAAATGAATG
36752 AACATAAACGAACATAACCGAACA
1 AACATAAACGAACATAACCGAACA
36776 AACATAAACGAACATAACCGAACA
1 AACATAAACGAACATAACCGAACA
36800 AA
1 AA
36802 TATAGCTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.60, C:0.24, G:0.08, T:0.08
Consensus pattern (24 bp):
AACATAAACGAACATAACCGAACA
Found at i:37569 original size:24 final size:23
Alignment explanation
Indices: 37526--37573 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 23
37516 ATAATTTTTT
37526 ATAAATAATTTTTTTAATTAAAA
1 ATAAATAATTTTTTTAATTAAAA
37549 ATAAAT-ATTTTTTTATTATTAAAA
1 ATAAATAATTTTTTTA--ATTAAAA
37573 A
1 A
37574 ATTTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.39
23 6 0.26
24 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATAAATAATTTTTTTAATTAAAA
Found at i:41666 original size:29 final size:30
Alignment explanation
Indices: 41628--41767 Score: 105
Period size: 29 Copynumber: 4.9 Consensus size: 30
41618 CATTTTACAC
**
41628 AAATAGCACCTTTTTTTTAA-TAATTACCA
1 AAATAGCACCTTTTTTCGAATTAATTACCA
* *
41657 AAATATCACC-CTTTTCGAATTAATT-CACA
1 AAATAGCACCTTTTTTCGAATTAATTAC-CA
* ** *
41686 TAATAGCACCAATTTT-GAATTAATTCCCA
1 AAATAGCACCTTTTTTCGAATTAATTACCA
* **
41715 AAATATCA-CTTTTTTC-AAAAAATTACCA
1 AAATAGCACCTTTTTTCGAATTAATTACCA
* *
41743 AAATAGCACC-TATTTCAAATTAATT
1 AAATAGCACCTTTTTTCGAATTAATT
41768 CCCCGAATAG
Statistics
Matches: 86, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
28 33 0.38
29 48 0.56
30 5 0.06
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (30 bp):
AAATAGCACCTTTTTTCGAATTAATTACCA
Found at i:41743 original size:28 final size:28
Alignment explanation
Indices: 41707--41761 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
41697 ATTTTGAATT
* * * *
41707 AATTCCCAAAATATCACTTTTTTCAAAA
1 AATTACCAAAATAGCACCTATTTCAAAA
41735 AATTACCAAAATAGCACCTATTTCAAA
1 AATTACCAAAATAGCACCTATTTCAAA
41762 TTAATTCCCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.31
Consensus pattern (28 bp):
AATTACCAAAATAGCACCTATTTCAAAA
Found at i:41828 original size:13 final size:13
Alignment explanation
Indices: 41810--41839 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
41800 AAATAAAACC
41810 GGTCAACGGGTCG
1 GGTCAACGGGTCG
41823 GGTCAACGGGTCG
1 GGTCAACGGGTCG
41836 GGTC
1 GGTC
41840 GGGTCAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:41839 original size:18 final size:17
Alignment explanation
Indices: 41816--41855 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
41806 AACCGGTCAA
41816 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAAC-GGT
41834 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTCAACGGT
41851 CGGGT
1 CGGGT
41856 AAACGGGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.10, C:0.23, G:0.50, T:0.17
Consensus pattern (17 bp):
CGGGTCGGGTCAACGGT
Found at i:41875 original size:30 final size:31
Alignment explanation
Indices: 41810--41876 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
41800 AAATAAAACC
* *
41810 GGTCAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGGACG
* *
41841 GGTCAAC-GGTCGGGTAAACGGGTCGTGACT
1 GGTCAACGGGTCGGGTAAACGGGTCGGGACG
41871 GGTCAA
1 GGTCAA
41877 ACCGATCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 25 0.78
31 7 0.22
ACGTcount: A:0.18, C:0.21, G:0.43, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGTCGGGACG
Found at i:43728 original size:23 final size:23
Alignment explanation
Indices: 43685--43728 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
43675 TGTAGTTATG
*
43685 TTATATTTGTTTTCTTATCATAT
1 TTATATTTGTTTTATTATCATAT
*
43708 TTATATTT-TTGTTATTTTCAT
1 TTATATTTGTT-TTATTATCAT
43729 GTCAAGTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (23 bp):
TTATATTTGTTTTATTATCATAT
Found at i:44323 original size:2 final size:2
Alignment explanation
Indices: 44286--44311 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44276 TTTTTTATTA
44286 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
44312 TAAGGGTATA
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:44704 original size:41 final size:41
Alignment explanation
Indices: 44659--44736 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
44649 ATAAAGAAGT
*
44659 ATTG-TGAAAAAAATGTGATATCCT-AATTTAAAATGTTTGAC
1 ATTGTTGAAAAAAA-GT-ATATCCTAAAGTTAAAATGTTTGAC
* *
44700 ATTGTTGTAAAAAAGTATATTCTAAAGTTAAAATGTT
1 ATTGTTGAAAAAAAGTATATCCTAAAGTTAAAATGTT
44737 GATTTTAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 6 0.19
41 18 0.56
42 8 0.25
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.38
Consensus pattern (41 bp):
ATTGTTGAAAAAAAGTATATCCTAAAGTTAAAATGTTTGAC
Found at i:47065 original size:17 final size:17
Alignment explanation
Indices: 47043--47086 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
47033 ATGTAAAAAT
47043 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
47060 AAATATAAAAATTTATT
1 AAATATTTAAATTTAAA
47077 AAATATTTAA
1 AAATATTTAA
47087 TCAAGTAGGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:49224 original size:31 final size:31
Alignment explanation
Indices: 49189--49262 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 31
49179 CAACCATTCC
*** *
49189 CAACTTTTTCCAAAATTTTGAATTGGTCCCT
1 CAACTTTTTCCAAAATTACAAAATGGTCCCT
*
49220 CAAC-TTTTCAAAAATTACAAAATGGTCCCT
1 CAACTTTTTCCAAAATTACAAAATGGTCCCT
*
49250 -AAATTTTTCCAAA
1 CAACTTTTTCCAAA
49263 GCCTGTAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
29 2 0.06
30 29 0.83
31 4 0.11
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.36
Consensus pattern (31 bp):
CAACTTTTTCCAAAATTACAAAATGGTCCCT
Found at i:50248 original size:30 final size:30
Alignment explanation
Indices: 50212--50270 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
50202 TTTGGTCCCT
* *
50212 AAACTTT-TCAAATTTTATACTTCGGTCACC
1 AAACTTTACCAAA-TTTATAATTCGGTCACC
*
50242 AAACTTTACCAAATTTATAATTTGGTCAC
1 AAACTTTACCAAATTTATAATTCGGTCAC
50271 TAAATAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTACCAAATTTATAATTCGGTCACC
Found at i:51283 original size:9 final size:8
Alignment explanation
Indices: 51270--51329 Score: 57
Period size: 9 Copynumber: 6.9 Consensus size: 8
51260 ATCTCTCATA
51270 TTTTTTTC
1 TTTTTTTC
51278 ATTTTTTTC
1 -TTTTTTTC
*
51287 TGTTTTTC
1 TTTTTTTC
51295 TTTTTCTTC
1 TTTTT-TTC
*
51304 TTCTTCTTC
1 TT-TTTTTC
51313 TTTTTCTTC
1 TTTTT-TTC
51322 TTCTTTTT
1 TT-TTTTT
51330 AGTTTTTTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 13 0.30
9 25 0.58
10 5 0.12
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTTTTC
Found at i:51298 original size:6 final size:6
Alignment explanation
Indices: 51289--51329 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
51279 TTTTTTTCTG
* * *
51289 TTTTTC TTTTTC TTCTTC TTCTTC TTTTTC TTCTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
51330 AGTTTTTTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:51304 original size:3 final size:3
Alignment explanation
Indices: 51292--51326 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
51282 TTTTCTGTTT
* *
51292 TTC TTT TTC TTC TTC TTC TTC TTT TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
51327 TTTAGTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (3 bp):
TTC
Found at i:51327 original size:12 final size:12
Alignment explanation
Indices: 51289--51329 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
51279 TTTTTTTCTG
*
51289 TTTTTCTTTTTC
1 TTTTTCTTCTTC
*
51301 TTCTTCTTCTTC
1 TTTTTCTTCTTC
51313 TTTTTCTTCTTC
1 TTTTTCTTCTTC
51325 TTTTT
1 TTTTT
51330 AGTTTTTTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTCTTCTTC
Found at i:54118 original size:131 final size:131
Alignment explanation
Indices: 53884--54148 Score: 503
Period size: 131 Copynumber: 2.0 Consensus size: 131
53874 ACAAAGTTCT
*
53884 CCAACTTATAATTTGACCGAATTTTACATAATAATTTCTAGAAAGATCGAACATGTTTTAACCAT
1 CCAACTTATAATTTGACAGAATTTTACATAATAATTTCTAGAAAGATCGAACATGTTTTAACCAT
*
53949 AAATCATGCTTGGAAATGAATCTATAACCTTTGATTAATCAAGATTTATCATCAATTTCATGAAT
66 AAATCATGCTTGGAAATGAATCTATAACCTCTGATTAATCAAGATTTATCATCAATTTCATGAAT
54014 C
131 C
*
54015 CCAACTTATAATTTGACAGAATTTTACATAATAATTTCTAGAAAGATCGATCATGTTTTAACCAT
1 CCAACTTATAATTTGACAGAATTTTACATAATAATTTCTAGAAAGATCGAACATGTTTTAACCAT
54080 AAATCATGCTTGGAAATGAATCTATAACCTCTGATTAATCAAGATTTATCATCAATTTCATGAAT
66 AAATCATGCTTGGAAATGAATCTATAACCTCTGATTAATCAAGATTTATCATCAATTTCATGAAT
54145 C
131 C
54146 CCA
1 CCA
54149 TCATGAACAT
Statistics
Matches: 131, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 131 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (131 bp):
CCAACTTATAATTTGACAGAATTTTACATAATAATTTCTAGAAAGATCGAACATGTTTTAACCAT
AAATCATGCTTGGAAATGAATCTATAACCTCTGATTAATCAAGATTTATCATCAATTTCATGAAT
C
Found at i:60498 original size:23 final size:22
Alignment explanation
Indices: 60472--60544 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
60462 GCATGTTATT
60472 TACCTTTATGACAAGTTTATCTA
1 TACCTTTATGACAA-TTTATCTA
* * * *
60495 TACCTTTGTGGC-ATGT-TCTC
1 TACCTTTATGACAATTTATCTA
*
60515 TGCCTTTATGACACATTTATCTA
1 TACCTTTATGACA-ATTTATCTA
60538 TACCTTT
1 TACCTTT
60545 GTGGCACGTT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
20 12 0.32
21 2 0.05
22 4 0.11
23 19 0.51
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (22 bp):
TACCTTTATGACAATTTATCTA
Found at i:60521 original size:43 final size:43
Alignment explanation
Indices: 60455--60564 Score: 150
Period size: 43 Copynumber: 2.6 Consensus size: 43
60445 ATAATTATGT
* *
60455 CTTTGTAGCATGTTATTTACCTTTATGACA-AGTTTATCTATAC
1 CTTTGTGGCATGTTATTTGCCTTTATGACACA-TTTATCTATAC
* *
60498 CTTTGTGGCATGTTCTCTGCCTTTATGACACATTTATCTATAC
1 CTTTGTGGCATGTTATTTGCCTTTATGACACATTTATCTATAC
* *
60541 CTTTGTGGCACGTTTTTTGCCTTT
1 CTTTGTGGCATGTTATTTGCCTTT
60565 TGGTAGTTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 58 0.98
44 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.47
Consensus pattern (43 bp):
CTTTGTGGCATGTTATTTGCCTTTATGACACATTTATCTATAC
Found at i:61502 original size:19 final size:19
Alignment explanation
Indices: 61463--61502 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
61453 TGACCAGAAG
61463 TTTTCGAAACTTCTACAAGA
1 TTTTCGAAACTTC-ACAAGA
61483 TTTTCGAAACATTC-CAAGA
1 TTTTCGAAAC-TTCACAAGA
61502 T
1 T
61503 AGTTTCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 10 0.53
21 3 0.16
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (19 bp):
TTTTCGAAACTTCACAAGA
Found at i:64152 original size:19 final size:20
Alignment explanation
Indices: 64128--64179 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
64118 TTCCCAAAAT
64128 GTTTCGATACTTTA-C-AAGA
1 GTTTCGATACTTTACCTAA-A
*
64147 GTTTCGAAACTTTACCTAAA
1 GTTTCGATACTTTACCTAAA
64167 GTTTCGATACTTT
1 GTTTCGATACTTT
64180 GTGTCCAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 13 0.45
20 14 0.48
21 2 0.07
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (20 bp):
GTTTCGATACTTTACCTAAA
Found at i:67882 original size:17 final size:17
Alignment explanation
Indices: 67856--67889 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
67846 AAACAGAAGT
* *
67856 AAATACTGAAATTTAAA
1 AAATAATGAAATATAAA
67873 AAATAATGAAATATAAA
1 AAATAATGAAATATAAA
67890 TATTGGAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (17 bp):
AAATAATGAAATATAAA
Done.