Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002230.1 Hibiscus syriacus cultivar Beakdansim tig00004537_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: 63570
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:6669 original size:84 final size:82
Alignment explanation
Indices: 6570--6739 Score: 250
Period size: 84 Copynumber: 2.0 Consensus size: 82
6560 AATAAAGAAA
* * * *
6570 TAAATCCTAATTAAAATACTTAAAACTACTTAAACTAAAATACCTAAAACAAATATAAGATAAAA
1 TAAATCCGAATTAAAACACTTAAAACTACTTAAACTAAAATACCTAAAACAAAGATAAAATAAAA
6635 TATAATAAAAATAATATCC
66 TAT--TAAAAATAATATCC
* * *
6654 TAAATCCGAATTAAAACACTTAAAACTATTTAAACTAAAATTCCTAAAACAAAGATAAAATATAA
1 TAAATCCGAATTAAAACACTTAAAACTACTTAAACTAAAATACCTAAAACAAAGATAAAATAAAA
*
6719 TATTTAAAATAATATCC
66 TATTAAAAATAATATCC
6736 TAAA
1 TAAA
6740 ACATGAGTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
82 17 0.22
84 61 0.78
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (82 bp):
TAAATCCGAATTAAAACACTTAAAACTACTTAAACTAAAATACCTAAAACAAAGATAAAATAAAA
TATTAAAAATAATATCC
Found at i:10539 original size:44 final size:43
Alignment explanation
Indices: 10384--10561 Score: 160
Period size: 44 Copynumber: 4.1 Consensus size: 43
10374 TTAACGGTGT
* * *
10384 TTTTTGGATACAAACGCTGCAAAAGGTTAAGATATTTAGCGGCG
1 TTTTTGGATACAAACGCTACAAAAGG-TAAGGTATATAGCGGCG
* * * ** * *
10428 TTTTTGGATACAAA-TCTGCAACAGGTTTGGTACATAGAGGCG
1 TTTTTGGATACAAACGCTACAAAAGGTAAGGTATATAGCGGCG
* * * * *
10470 CTTTTCGGATACAAACGCCATAAAATGTGAGGTATATAGCGGCG
1 -TTTTTGGATACAAACGCTACAAAAGGTAAGGTATATAGCGGCG
* **
10514 TTTTTAGGATACAAACGCTACAAAATGTCTGGTATATAGCGGCG
1 TTTTT-GGATACAAACGCTACAAAAGGTAAGGTATATAGCGGCG
10558 TTTT
1 TTTT
10562 ATGTTACAAA
Statistics
Matches: 107, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
42 11 0.10
43 26 0.24
44 70 0.65
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (43 bp):
TTTTTGGATACAAACGCTACAAAAGGTAAGGTATATAGCGGCG
Found at i:10570 original size:87 final size:86
Alignment explanation
Indices: 10420--10581 Score: 200
Period size: 87 Copynumber: 1.9 Consensus size: 86
10410 TTAAGATATT
* * * * *
10420 TAGCGGCGTTTTTGGATACAAATCTGCAACAGGTTTGGTACATAGAGGCGCTTTTCGGATACAAA
1 TAGCGGCGTTTTTGGATACAAAGCTACAAAAGGTCTGGTACATAGAGGCGCTTTTAGGATACAAA
*
10485 CGCCATAAAATGTGAGGTATA
66 CACCATAAAATGTGAGGTATA
* * * * *
10506 TAGCGGCGTTTTTAGGATACAAACGCTACAAAATGTCTGGTATATAGCGGCG-TTTTATGTTACA
1 TAGCGGCGTTTTT-GGATACAAA-GCTACAAAAGGTCTGGTACATAGAGGCGCTTTTAGGATACA
10570 AACACCATAAAA
64 AACACCATAAAA
10582 AATCAGAATT
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
86 13 0.21
87 29 0.46
88 21 0.33
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (86 bp):
TAGCGGCGTTTTTGGATACAAAGCTACAAAAGGTCTGGTACATAGAGGCGCTTTTAGGATACAAA
CACCATAAAATGTGAGGTATA
Found at i:19827 original size:83 final size:81
Alignment explanation
Indices: 19718--19986 Score: 290
Period size: 82 Copynumber: 3.3 Consensus size: 81
19708 ATATAAGATT
* * *
19718 GCGGCGTTTGTAAAAAACGCCTCTATAGTGCTAA-TATATCGCGGCGTTTACTTAAAAAACGCCA
1 GCGGCGTTTGTACAAAACGCCTCTATAGTAC-AACTCTATCGCGGCGTTTACTT-AAAAACGCCA
*
19782 CTACTGTCCAACTCTATA
64 CTAATGTCCAACTCTATA
* * * *
19800 GCGGCGTTTGTACGAAAACGGCTCTATAGTACAACTCTATCACGGTGTTTACTTAAAATCGCCAC
1 GCGGCGTTTGTAC-AAAACGCCTCTATAGTACAACTCTATCGCGGCGTTTACTTAAAAACGCCAC
19865 TAATGTCCAACTCTATA
65 TAATGTCCAACTCTATA
** * * **
19882 GTAGCGTTTGTACAAAATCGCCTCTATAGTTCAACTCTATCGCGGCATTTTGTTTAAAAACGCCA
1 GCGGCGTTTGTACAAAA-CGCCTCTATAGTACAACTCTATCGCGGC-GTTTACTTAAAAACGCCA
* *** *
19947 CTAACGTATGACTCTTTA
64 CTAATGTCCAACTCTATA
19965 GCGGCGTTTTGGTA-AAAACGCC
1 GCGGCG-TTT-GTACAAAACGCC
19987 GCTAACGTAC
Statistics
Matches: 156, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
81 4 0.03
82 75 0.48
83 67 0.43
84 7 0.04
85 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (81 bp):
GCGGCGTTTGTACAAAACGCCTCTATAGTACAACTCTATCGCGGCGTTTACTTAAAAACGCCACT
AATGTCCAACTCTATA
Found at i:19835 original size:41 final size:41
Alignment explanation
Indices: 19718--19927 Score: 132
Period size: 41 Copynumber: 5.1 Consensus size: 41
19708 ATATAAGATT
* * * *
19718 GCGGCGTTTGTA-AAAAACGCCTCTATAGTGCTAA-TATATC
1 GCGGCGTTTGTACAAAATCGCCTCTATAGTAC-AACTCTATA
* * * *
19758 GCGGCGTTTACTTA-AAAAACGCCACTACT-GTCCAACTCTATA
1 GCGGCGTTT--GTACAAAATCGCCTCTA-TAGTACAACTCTATA
*
19800 GCGGCGTTTGTACGAAAA-CGGCTCTATAGTACAACTCTATCA
1 GCGGCGTTTGTAC-AAAATCGCCTCTATAGTACAACTCTAT-A
* * *
19842 -CGGTG-TT-TACTTAAAATCGCCACTA-ATGTCCAACTCTATA
1 GCGGCGTTTGTAC--AAAATCGCCTCTATA-GTACAACTCTATA
** * *
19882 GTAGCGTTTGTACAAAATCGCCTCTATAGTTCAACTCTATC
1 GCGGCGTTTGTACAAAATCGCCTCTATAGTACAACTCTATA
19923 GCGGC
1 GCGGC
19928 ATTTTGTTTA
Statistics
Matches: 133, Mismatches: 22, Indels: 29
0.72 0.12 0.16
Matches are distributed among these distances:
39 3 0.02
40 20 0.15
41 68 0.51
42 38 0.29
43 4 0.03
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTGTACAAAATCGCCTCTATAGTACAACTCTATA
Found at i:19961 original size:42 final size:41
Alignment explanation
Indices: 19915--19995 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
19905 CTATAGTTCA
* *
19915 ACTCTATCGCGGCATTTTGTTTAAAAACGCCACTAACGTATG
1 ACTCTATAGCGGCATTTTG-GTAAAAACGCCACTAACGTATG
* * *
19957 ACTCTTTAGCGGCGTTTTGGTAAAAACGCCGCTAACGTA
1 ACTCTATAGCGGCATTTTGGTAAAAACGCCACTAACGTA
19996 CATCTATGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 18 0.53
42 16 0.47
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (41 bp):
ACTCTATAGCGGCATTTTGGTAAAAACGCCACTAACGTATG
Found at i:20576 original size:25 final size:25
Alignment explanation
Indices: 20545--20626 Score: 155
Period size: 25 Copynumber: 3.3 Consensus size: 25
20535 CTCCTACCTC
20545 TGGTTCACCAAGAAGACTCCTTGCT
1 TGGTTCACCAAGAAGACTCCTTGCT
*
20570 TGGTTCACCAAGAAGACTCATTGCT
1 TGGTTCACCAAGAAGACTCCTTGCT
20595 TGGTTCACCAAGAAGACTCCTTGCT
1 TGGTTCACCAAGAAGACTCCTTGCT
20620 TGGTTCA
1 TGGTTCA
20627 ATGCTTCACT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 55 1.00
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (25 bp):
TGGTTCACCAAGAAGACTCCTTGCT
Found at i:21788 original size:82 final size:82
Alignment explanation
Indices: 21702--21893 Score: 237
Period size: 82 Copynumber: 2.3 Consensus size: 82
21692 ACTATTGATG
*
21702 AACCCTATTATGGA-GTTTATCTAAAAACACCGCTAAAGTACA-CTTTATTCCGGCCTT-TGTTA
1 AACCCTATTAT-GACGTTTATCTAAAAACACCGCTAAAGTA-ATCTTTATTACGGCCTTAT-TTA
**
21764 AAAAAATGCCACTATAAACT
63 AAAAAACACCACTATAAACT
* * * **
21784 AACCCTATTATGACATTTTTCTAAAAACACCGCTAAAGTAATCTTTATTACGGCGTTATTTGGAA
1 AACCCTATTATGACGTTTATCTAAAAACACCGCTAAAGTAATCTTTATTACGGCCTTATTTAAAA
21849 AAACACCACTATAAACT
66 AAACACCACTATAAACT
* *
21866 AACCATATTACGACGTTTATGCTAAAAA
1 AACCCTATTATGACGTTTAT-CTAAAAA
21894 TGTCCCTAAT
Statistics
Matches: 94, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
81 3 0.03
82 83 0.88
83 8 0.09
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (82 bp):
AACCCTATTATGACGTTTATCTAAAAACACCGCTAAAGTAATCTTTATTACGGCCTTATTTAAAA
AAACACCACTATAAACT
Found at i:21893 original size:42 final size:41
Alignment explanation
Indices: 21772--21893 Score: 97
Period size: 42 Copynumber: 3.0 Consensus size: 41
21762 TAAAAAAATG
* * * *
21772 CCACTATAAACTAACCCTATTATGACATTTTTCTAAAAACA
1 CCACTATAAACTAACCATATTACGACGTTTTGCTAAAAACA
* * ** * *
21813 CCGC--TAAAGTAATCTTTATTACGGCGTTATTTG-GAAAAACA
1 CCACTATAAACTAA-CCATATTACGACG-T-TTTGCTAAAAACA
21854 CCACTATAAACTAACCATATTACGACGTTTATGCTAAAAA
1 CCACTATAAACTAACCATATTACGACGTTT-TGCTAAAAA
21894 TGTCCCTAAT
Statistics
Matches: 59, Mismatches: 15, Indels: 13
0.68 0.17 0.15
Matches are distributed among these distances:
39 7 0.12
40 10 0.17
41 17 0.29
42 18 0.31
43 7 0.12
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (41 bp):
CCACTATAAACTAACCATATTACGACGTTTTGCTAAAAACA
Found at i:22174 original size:11 final size:11
Alignment explanation
Indices: 22140--22196 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
22130 ACTAGGGCTA
*
22140 GGGTTAGGTTT
1 GGGTTGGGTTT
* *
22151 AGGGTAGGCTTT
1 -GGGTTGGGTTT
22163 GGGTTGGGTTT
1 GGGTTGGGTTT
* *
22174 GGTTTGGGCTCT
1 GGGTTGGG-TTT
22186 GGGTTGGGTTT
1 GGGTTGGGTTT
22197 TGTTTGGGCT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
11 18 0.51
12 17 0.49
ACGTcount: A:0.05, C:0.05, G:0.47, T:0.42
Consensus pattern (11 bp):
GGGTTGGGTTT
Found at i:22183 original size:23 final size:23
Alignment explanation
Indices: 22157--22262 Score: 97
Period size: 23 Copynumber: 4.6 Consensus size: 23
22147 GTTTAGGGTA
*
22157 GGCTTTGGGTTGGGT-TTGGTTTG
1 GGCTTTGGGTTGGGTACT-GTTTG
* **
22180 GGCTCTGGGTTGGGTTTTGTTTG
1 GGCTTTGGGTTGGGTACTGTTTG
* *
22203 GGCTCTGGGTCGGGTACTGTTTG
1 GGCTTTGGGTTGGGTACTGTTTG
* * *
22226 GGTTTTAGGTTGGGTCCTGTTTG
1 GGCTTTGGGTTGGGTACTGTTTG
* *
22249 GGTTTTAGGTTGGG
1 GGCTTTGGGTTGGG
22263 GCATGTTTGG
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
23 71 0.97
24 2 0.03
ACGTcount: A:0.03, C:0.08, G:0.44, T:0.44
Consensus pattern (23 bp):
GGCTTTGGGTTGGGTACTGTTTG
Found at i:22269 original size:23 final size:23
Alignment explanation
Indices: 22220--22277 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
22210 GGTCGGGTAC
* *
22220 TGTTTGGGTTTTAGGTTGGGTCC
1 TGTTTGGGTTTTAGGTTGGGGCA
22243 TGTTTGGGTTTTAGGTTGGGGCA
1 TGTTTGGGTTTTAGGTTGGGGCA
22266 TGTTTGGGTTTT
1 TGTTTGGGTTTT
22278 TCGGGTATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.05, C:0.05, G:0.40, T:0.50
Consensus pattern (23 bp):
TGTTTGGGTTTTAGGTTGGGGCA
Found at i:24033 original size:23 final size:23
Alignment explanation
Indices: 23974--24025 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
23964 TTTGGCTTGG
23974 TTTGGGCTCAAGGTCAGGTTCAA
1 TTTGGGCTCAAGGTCAGGTTCAA
*
23997 TTTGGGCTCAAGGTCGGGTTCAA
1 TTTGGGCTCAAGGTCAGGTTCAA
24020 TTTGGG
1 TTTGGG
24026 TTTTAGGTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.17, C:0.15, G:0.35, T:0.33
Consensus pattern (23 bp):
TTTGGGCTCAAGGTCAGGTTCAA
Found at i:27811 original size:114 final size:114
Alignment explanation
Indices: 27609--27820 Score: 327
Period size: 114 Copynumber: 1.9 Consensus size: 114
27599 TGTCATTGAG
*
27609 TGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATCAGCACTGAGTGTGCAAA
1 TGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCATATCAGCACTGAGTGTGCAAA
* * *
27674 AAGTTAAGAAATTCATAATTTGTTTATGGATTTCAGTATGGGCACTAAA
66 AAGTTAAGAAATTAATAAATTGTTTATGAATTTCAGTATGGGCACTAAA
* * *
27723 TGTGCAAAAAGTTAAGAAATTTATAATTTGTTTATGAATTTCTATAT-AGGCACTGAGTGTTCAA
1 TGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCATATCA-GCACTGAGTGTGCAA
**
27787 AATTTTAAGAAATTAATAAATTGTTTATGAATTT
65 AAAGTTAAGAAATTAATAAATTGTTTATGAATTT
27821 TTGTATAAGA
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
113 1 0.01
114 87 0.99
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (114 bp):
TGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCATATCAGCACTGAGTGTGCAAA
AAGTTAAGAAATTAATAAATTGTTTATGAATTTCAGTATGGGCACTAAA
Found at i:27843 original size:114 final size:114
Alignment explanation
Indices: 27611--27872 Score: 312
Period size: 114 Copynumber: 2.3 Consensus size: 114
27601 TCATTGAGTG
* *
27611 TGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATCAGCACTGAGTGTGCAAAAA
1 TGCAAAAAGTTAAGAAATTTATAATTTGTTTATGAATTTCCATATCAGCACTGAGTGTGCAAAAA
* * * ** * *
27676 GTTAAGAAATTCATAATTTGTTTATGGATTTCAGTATGGGCACTAAATG
66 GTTAAGAAATTAATAAATTGTTTATGAATTTCAGTATAAGAACTAAATA
* *
27725 TGCAAAAAGTTAAGAAATTTATAATTTGTTTATGAATTTCTATAT-AGGCACTGAGTGTTCAAAA
1 TGCAAAAAGTTAAGAAATTTATAATTTGTTTATGAATTTCCATATCA-GCACTGAGTGTGCAAAA
** ** **
27789 TTTTAAGAAATTAATAAATTGTTTATGAATTTTTGTATAAGAACTTTATA
65 AGTTAAGAAATTAATAAATTGTTTATGAATTTCAGTATAAGAACTAAATA
* *
27839 TGCAAAAA-CTAAGAAATTATATGAATTTCTTTAT
1 TGCAAAAAGTTAAGAAATT-TAT-AATTTGTTTAT
27873 TGGTATTATG
Statistics
Matches: 126, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
113 10 0.08
114 106 0.84
115 10 0.08
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.39
Consensus pattern (114 bp):
TGCAAAAAGTTAAGAAATTTATAATTTGTTTATGAATTTCCATATCAGCACTGAGTGTGCAAAAA
GTTAAGAAATTAATAAATTGTTTATGAATTTCAGTATAAGAACTAAATA
Found at i:27845 original size:57 final size:57
Alignment explanation
Indices: 27605--27829 Score: 297
Period size: 57 Copynumber: 3.9 Consensus size: 57
27595 ATAATGTCAT
* *
27605 TGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCCGTATCAGCAC
1 TGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCTGTATAAGCAC
* * **
27662 TGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGGATTTCAGTATGGGCAC
1 TGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCTGTATAAGCAC
* * * * *
27719 TAAATGTGCAAAAAGTTAAGAAATTTATAATTTGTTTATGAATTTCTATATAGGCAC
1 TGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCTGTATAAGCAC
* ** * * *
27776 TGAGTGTTCAAAATTTTAAGAAATTAATAAATTGTTTATGAATTTTTGTATAAG
1 TGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCTGTATAAG
27830 AACTTTATAT
Statistics
Matches: 147, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 147 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (57 bp):
TGAGTGTGCAAAAAGTTAAGAAATTCATAATTTGTTTATGAATTTCTGTATAAGCAC
Found at i:28138 original size:67 final size:67
Alignment explanation
Indices: 28030--28485 Score: 664
Period size: 67 Copynumber: 6.8 Consensus size: 67
28020 TAAAAGTTTA
*
28030 TGAGGCCTAACTGTGCATTTACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 TGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
28095 TT
66 TT
* * ** * *
28097 TGAGGCCTAACTATGCATTGACAAAAATATGTCAATTATGCCAGTTAGATGAAATGCTAAGCGCC
1 TGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
28162 TT
66 TT
* * * * *
28164 TCAGGCCTAACTGTGCATTGACAGAAAGGTATTAATTATGCTAGTTAGATGAAAGGCTAAGTTCC
1 TGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
28229 TT
66 TT
* *
28231 TGAGGGCTAATTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 TGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
28296 TT
66 TT
* * *
28298 TTAGGCCTAATTGTGCATTCG-CAGAAAGGTGTCAATTATGCCAGTTAGATAAAAGGCTAAGTGC
1 TGAGGCCTAACTGTGCATT-GACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGC
28362 CTT
65 CTT
* *
28365 TGAGGCCTAACTGTGCATTGACAGATAGGTGTCAATTATTCCAGTTAGATGAAAGGCTAAGTGCC
1 TGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
28430 TT
66 TT
* * * *
28432 TGAGACCTAGA-TGTGCATTTGGCAGAAAGGTGTCAATTATGCAAGTAAGATGAA
1 TGAGGCCTA-ACTGTGCA-TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
28486 CGATTAAAGA
Statistics
Matches: 346, Mismatches: 39, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
66 1 0.00
67 312 0.90
68 33 0.10
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (67 bp):
TGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
TT
Found at i:28572 original size:81 final size:80
Alignment explanation
Indices: 28437--28724 Score: 368
Period size: 81 Copynumber: 3.6 Consensus size: 80
28427 GCCTTTGAGA
* * *
28437 CCTAGATGTGCATTTGGCAGAAAGGTGTCAATTATGCAAGTAAGATGAACGATTAAAGACCGTTG
1 CCTAGCTGTGCATTT-ACAGAAAGGTGTCAATTATGCAAGTTAGATGAACGATTAAAGACCGTTG
*
28502 AGTAAAAGTTAAATGG
65 AGTAAAAGATAAATGG
* * *
28518 CCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGATCGTTG
1 CCTAGCTGTGCATTT-ACAGAAAGGTGTCAATTATGCAAGTTAGATGAACGATTAAAGACCGTTG
28583 AGTAAAAGATAAATGG
65 AGTAAAAGATAAATGG
* * * *
28599 CCTAGCTGTTCATTT--TG-CAGGTGTCAATTATATC-AGTTAGATGAACGATTAAAGACCGTTG
1 CCTAGCTGTGCATTTACAGAAAGGTGTCAATTAT-GCAAGTTAGATGAACGATTAAAGACCGTTG
28660 AGTAAAAGATAAATGG
65 AGTAAAAGATAAATGG
* * * * *
28676 CCTAACTATGCATTTAGCAGAAAAGTATCAATCATGCAAGTTAGATGAA
1 CCTAGCTGTGCATTTA-CAGAAAGGTGTCAATTATGCAAGTTAGATGAA
28725 AGGTTAAATG
Statistics
Matches: 180, Mismatches: 21, Indels: 12
0.85 0.10 0.06
Matches are distributed among these distances:
77 67 0.37
78 2 0.01
80 2 0.01
81 109 0.61
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (80 bp):
CCTAGCTGTGCATTTACAGAAAGGTGTCAATTATGCAAGTTAGATGAACGATTAAAGACCGTTGA
GTAAAAGATAAATGG
Found at i:28747 original size:158 final size:158
Alignment explanation
Indices: 28459--28754 Score: 402
Period size: 158 Copynumber: 1.9 Consensus size: 158
28449 TTTGGCAGAA
* *
28459 AGGTGTCAATTATGCAAGTAAGATGAACGATTAAAGACCGTTGAGTAAAAGTTAAATGGCCTAGC
1 AGGTGTCAATTATGCAAGTAAGATGAACGATTAAAGACCGTTGAGTAAAAGATAAATGGCCTAAC
* * * * * * *
28524 TGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGATCGTTGAGTAAA
66 TATGCATTTGACAGAAAAGTATCAATCATGCAAGTTAGATGAAAGATTAAAGATC-TTGAGTAAA
28589 AGA-TAAATGGCCTAGCTGTTCATTTTGC
130 AGACTAAATGGCCTAGCTGTTCATTTTGC
* *
28617 AGGTGTCAATTATATC-AGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATAAATGGCCTAA
1 AGGTGTCAATTAT-GCAAGTAAGATGAACGATTAAAGACCGTTGAGTAAAAGATAAATGGCCTAA
* *
28681 CTATGCATTT-AGCAGAAAAGTATCAATCATGCAAGTTAGATGAAAGGTTAAATGCAT-TTGGGT
65 CTATGCATTTGA-CAGAAAAGTATCAATCATGCAAGTTAGATGAAAGATTAAA-G-ATCTTGAGT
28744 AAAAGACTAAA
127 AAAAGACTAAA
28755 GGAATTATAA
Statistics
Matches: 120, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
157 1 0.01
158 111 0.93
159 6 0.05
160 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (158 bp):
AGGTGTCAATTATGCAAGTAAGATGAACGATTAAAGACCGTTGAGTAAAAGATAAATGGCCTAAC
TATGCATTTGACAGAAAAGTATCAATCATGCAAGTTAGATGAAAGATTAAAGATCTTGAGTAAAA
GACTAAATGGCCTAGCTGTTCATTTTGC
Found at i:28974 original size:43 final size:45
Alignment explanation
Indices: 28870--29000 Score: 137
Period size: 45 Copynumber: 3.0 Consensus size: 45
28860 AGGTATAAAA
* ***
28870 GGCATGAAA-AGATGCCATAAATGAAATAT--ATAATAGTGTATAAAA
1 GGCATGAAAGA-ATGCCATAAATGAAA-ATGCATAATAGTGCAT-TTT
* * *
28915 GGCATGAAAGGATGCCATCAATG-AAATGCAT-ATGGTGCATTTT
1 GGCATGAAAGAATGCCATAAATGAAAATGCATAATAGTGCATTTT
28958 GGCATGAAAGAATGCCATAAATGAAAATGCATAATAGTGCATT
1 GGCATGAAAGAATGCCATAAATGAAAATGCATAATAGTGCATT
29001 ATAAGTATGA
Statistics
Matches: 71, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
43 23 0.32
44 17 0.24
45 31 0.44
ACGTcount: A:0.43, C:0.11, G:0.21, T:0.25
Consensus pattern (45 bp):
GGCATGAAAGAATGCCATAAATGAAAATGCATAATAGTGCATTTT
Found at i:29908 original size:2 final size:2
Alignment explanation
Indices: 29901--29935 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
29891 CTTTTATTAT
29901 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 T
29936 TACTTTTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31408 original size:4 final size:4
Alignment explanation
Indices: 31399--31462 Score: 69
Period size: 4 Copynumber: 15.8 Consensus size: 4
31389 TTAATATTCT
* *
31399 TTTA TTTA TTTA TTTA TTTA TTTTA TTTG TTTCCT TTTA TTTA TTTA -TTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTT--A TTTA TTTA TTTA TTTA
31449 TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTT
31463 CTCATCTAAC
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
3 6 0.12
4 39 0.75
5 4 0.08
6 3 0.06
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:32382 original size:16 final size:16
Alignment explanation
Indices: 32361--32392 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
32351 TTTTTATGTC
32361 CGGGATATAGAGCATG
1 CGGGATATAGAGCATG
*
32377 CGGGATATAGATCATG
1 CGGGATATAGAGCATG
32393 TGGGGTAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.12, G:0.34, T:0.22
Consensus pattern (16 bp):
CGGGATATAGAGCATG
Found at i:35399 original size:110 final size:110
Alignment explanation
Indices: 35198--35767 Score: 828
Period size: 110 Copynumber: 5.2 Consensus size: 110
35188 GATGGTGGTT
* *
35198 GCTCAACTTCACAACGAAGGGG---C-GATTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCAACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * * * *
35259 AATTTCAACTTCACATCGAATGATAATGGACTTGAGACAACATAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* * * * * *
35304 GCTCAACTACACAGCGAAGGGGCAACTGAATGTCAGCAAATAACTTTTCATTTTCATTTAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCAACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
35369 AATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
*
35414 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCAACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
*
35479 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAAAACACAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
*
35524 GCTCAACTTCACAGCGAAGGGGCAACTGACTGTCAACAAACAATTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCAACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * * * *
35589 AATTTCAATTTCACAGCGAAGAATATTAGACTTGAGACAACAAAA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
* *
35634 GCTCAAATTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCAACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
* * *
35699 AATTTCAACTTCACAGCGAAGTAAATTAGACTCGAGACAATTCA-AA
66 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAA--CACAA
35745 GCTCAACTTCAC-GACGAAGGGGC
1 GCTCAACTTCACAG-CGAAGGGGC
35768 TTCCTAGTTT
Statistics
Matches: 420, Mismatches: 37, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
106 20 0.05
109 1 0.00
110 375 0.89
111 22 0.05
112 2 0.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCAACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAA
Found at i:36026 original size:240 final size:240
Alignment explanation
Indices: 35735--36247 Score: 821
Period size: 240 Copynumber: 2.1 Consensus size: 240
35725 TAGACTCGAG
* * * *
35735 ACAATTCAAAGCTCAACTTCACGACGAAGGGGCTTCCTAGTTTTATTCAGAGCCACTTTCAACTT
1 ACAATTCAAAGCTCAACTTCACGACGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTT
*
35800 CACGGCAAAGGATATTGGACTTGAAACAATACAAGCTTGGATTTCAACTTCACGACAAAGGATAT
66 CACGGCAAAGGATATTGGACTTGAAACAATACAAGCTTGGATTTCAACTTAACGACAAAGGATAT
* *
35865 TCAAGTCAAGGCTCAACTTTACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATA
131 TCAACTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATA
** * *
35930 TTGTGCCAA-CTCTAGATTGGATTTCAACTTCATGATGAAGGATAT
196 TCAT-ACAACCTCTAGATTGGATTTCAACTTCACGATGAAGGATAT
35975 ACAATTCAAAGCTCAACTTCACGACGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTT
1 ACAATTCAAAGCTCAACTTCACGACGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTT
* ** *
36040 CAGGGTGAAGGATATTGGACTTGAAACAATACAAGCTTGGATTTCAACTTAACGACGAAGGATAT
66 CACGGCAAAGGATATTGGACTTGAAACAATACAAGCTTGGATTTCAACTTAACGACAAAGGATAT
* * *
36105 TCAACTCAAGGCTCAACTTCACAACGAATGGGCCATCCACGATTTCAACTTCATGACGAATGATA
131 TCAACTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATA
36170 TCATACAACCTCTAGATTGGATTTCAACTTCACGATGAAGGATAT
196 TCATACAACCTCTAGATTGGATTTCAACTTCACGATGAAGGATAT
* * *
36215 CCAATTCAAGGCTCAACTTCACAACGAAGGGGC
1 ACAATTCAAAGCTCAACTTCACGACGAAGGGGC
36248 CATCCACGGT
Statistics
Matches: 251, Mismatches: 21, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
239 3 0.01
240 248 0.99
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (240 bp):
ACAATTCAAAGCTCAACTTCACGACGAAGGGGCTTCCCAATTTCATTCAGAGCCAATTTCAACTT
CACGGCAAAGGATATTGGACTTGAAACAATACAAGCTTGGATTTCAACTTAACGACAAAGGATAT
TCAACTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTTCAACTTCACGACGAAGGATA
TCATACAACCTCTAGATTGGATTTCAACTTCACGATGAAGGATAT
Found at i:36274 original size:110 final size:110
Alignment explanation
Indices: 36076--36283 Score: 317
Period size: 110 Copynumber: 1.9 Consensus size: 110
36066 CAATACAAGC
* *
36076 TTGGATTTCAACTTAACGACGAAGGATATTCAACTCAAGGCTCAACTTCACAACGAATGGGCCAT
1 TTGGATTTCAACTTAACGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* ** * *
36141 CCACGATTTCAACTTCATGACGAATGATATCATACAACCTCTAGA
66 CCACGATTTCAACATCACAACGAAGGAAATCATACAACCTCTAGA
* * *
36186 TTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTAACGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGAAGGGGCCAT
*
36251 CCACGGTTTCAACATCACAACGAAGGAAATCAT
66 CCACGATTTCAACATCACAACGAAGGAAATCAT
36284 GCTCACCAGC
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
110 87 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (110 bp):
TTGGATTTCAACTTAACGACGAAGGATATCCAACTCAAGGCTCAACTTCACAACGAAGGGGCCAT
CCACGATTTCAACATCACAACGAAGGAAATCATACAACCTCTAGA
Found at i:36713 original size:3 final size:3
Alignment explanation
Indices: 36685--36740 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
36675 TTTAAAAAAA
* * *
36685 TAT TA- TAT TTT TAT TTT TATT TAT TAT TAT TAT TAT TAT TAG TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
36730 TAT TAT TAT TA
1 TAT TAT TAT TA
36741 ATATATATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:38248 original size:12 final size:12
Alignment explanation
Indices: 38231--38275 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
38221 TTTAATATTC
38231 TTTTATTTTTTA
1 TTTTATTTTTTA
38243 TTTTATTTTTTA
1 TTTTATTTTTTA
*
38255 TTGTATTTTTTTA
1 TTTTA-TTTTTTA
*
38268 TTTAATTT
1 TTTTATTT
38276 ATACTTTTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:39560 original size:16 final size:16
Alignment explanation
Indices: 39541--39572 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39531 ACATGTAAAC
39541 AAAATGACAAATGCAT
1 AAAATGACAAATGCAT
*
39557 AAAATGTCAAATGCAT
1 AAAATGACAAATGCAT
39573 CAACCCAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.22
Consensus pattern (16 bp):
AAAATGACAAATGCAT
Found at i:41776 original size:26 final size:26
Alignment explanation
Indices: 41747--41800 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
41737 AAATGAGGTT
*
41747 TAAAAATTAAAATTAAAAGATGAGGA
1 TAAAAATAAAAATTAAAAGATGAGGA
* ** *
41773 TAAAGATAAAAATTGGAAGGTGAGGA
1 TAAAAATAAAAATTAAAAGATGAGGA
41799 TA
1 TA
41801 GAGTAAGGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (26 bp):
TAAAAATAAAAATTAAAAGATGAGGA
Found at i:60945 original size:18 final size:18
Alignment explanation
Indices: 60922--60963 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
60912 GGCAAGGCTG
60922 ACTCCCAGATGCTGGAGC
1 ACTCCCAGATGCTGGAGC
60940 ACTCCCAGATGCTGGAGC
1 ACTCCCAGATGCTGGAGC
60958 ACTCCC
1 ACTCCC
60964 CCGCTCGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.21, C:0.38, G:0.24, T:0.17
Consensus pattern (18 bp):
ACTCCCAGATGCTGGAGC
Done.