Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006630.1 Hibiscus syriacus cultivar Beakdansim tig00016291_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: 74423
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7166 original size:25 final size:25
Alignment explanation
Indices: 7133--7195 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
7123 TTAAGGAGTG
7133 GCGAGCTAGGCGCCGAGAGGAGCTA
1 GCGAGCTAGGCGCCGAGAGGAGCTA
*
7158 GCGTGCTAGGCGCCGAGAGGAGCTA
1 GCGAGCTAGGCGCCGAGAGGAGCTA
7183 GCGAGCTAAGGCG
1 GCGAGCT-AGGCG
7196 GTTCGTGGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 30 0.86
26 5 0.14
ACGTcount: A:0.22, C:0.24, G:0.44, T:0.10
Consensus pattern (25 bp):
GCGAGCTAGGCGCCGAGAGGAGCTA
Found at i:13067 original size:12 final size:12
Alignment explanation
Indices: 13050--13078 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
13040 CTGGAGAGAG
13050 CCGCCATAAGAC
1 CCGCCATAAGAC
13062 CCGCCATAAGAC
1 CCGCCATAAGAC
13074 CCGCC
1 CCGCC
13079 TTGCTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.48, G:0.17, T:0.07
Consensus pattern (12 bp):
CCGCCATAAGAC
Found at i:16491 original size:109 final size:109
Alignment explanation
Indices: 16300--16534 Score: 420
Period size: 109 Copynumber: 2.2 Consensus size: 109
16290 AGAGGCATTG
*
16300 AAAAGTAAAATAGAAGGGGGTTTTTAATGTCCGTTGAGATACTTTTTTATTTTGACGGTTATAGA
1 AAAAGTAAAATAGAAGGGGGTTTTTAATGTCCATTGAGATACTTTTTTATTTTGACGGTTATAGA
*
16365 GGGGTTTTTTAATGAGACATTGAGACTT-CTCTTTCTTATAAAAA
66 GAGGTTTTTTAATGAGACATTGAGACTTCCT-TTTCTTATAAAAA
16409 AAAAGTAAAATAGAAGAGGGG-TTTTAATGTCCATTGAGATACTTTTTTATTTTGACGGTTATAG
1 AAAAGTAAAATAGAAG-GGGGTTTTTAATGTCCATTGAGATACTTTTTTATTTTGACGGTTATAG
16473 AGAGGTTTTTTAATGAGACATTGAGACTTCCTTTTCTTATAAAAA
65 AGAGGTTTTTTAATGAGACATTGAGACTTCCTTTTCTTATAAAAA
16518 AAAAGTAAAATAGAAGG
1 AAAAGTAAAATAGAAGG
16535 AACACCAACC
Statistics
Matches: 122, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
108 1 0.01
109 115 0.94
110 6 0.05
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (109 bp):
AAAAGTAAAATAGAAGGGGGTTTTTAATGTCCATTGAGATACTTTTTTATTTTGACGGTTATAGA
GAGGTTTTTTAATGAGACATTGAGACTTCCTTTTCTTATAAAAA
Found at i:22338 original size:21 final size:22
Alignment explanation
Indices: 22312--22360 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
22302 TATTATTTTT
*
22312 AATTTATAT-ATTTTATTTA-AA
1 AATTTATATAATTGT-TTTACAA
22333 AATTTATATAATTGTTTTACAA
1 AATTTATATAATTGTTTTACAA
22355 AATTTA
1 AATTTA
22361 AAAGATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
AATTTATATAATTGTTTTACAA
Found at i:24484 original size:63 final size:67
Alignment explanation
Indices: 24407--24559 Score: 174
Period size: 63 Copynumber: 2.3 Consensus size: 67
24397 CATTTATTTC
* *
24407 TATTTAATTTTGAATATTAAAGATGAT-TATATA-CTTTTGAATATTTCAAATT-AAA-ATAATA
1 TATTTAAATTTGAATATTAAA-ATGATGTATATATCTTTTCAATATTTCAAATTAAAAGATAATA
24468 -TA
65 TTA
* * * * *
24470 TATTTAAGTTTGAATAGT-GAATGGTGTATATATCTTTTCAATATTTCAAATTAAAAGATATTAT
1 TATTTAAATTTGAATATTAAAATGATGTATATATCTTTTCAATATTTCAAATTAAAAGATAATAT
24534 TA
66 TA
24536 TCAGTTTAAATTTGAATATTAAAA
1 T-A-TTTAAATTTGAATATTAAAA
24560 GTTATTTGAT
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
61 4 0.05
62 7 0.10
63 34 0.47
64 3 0.04
65 5 0.07
66 3 0.04
67 1 0.01
68 14 0.19
69 2 0.03
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (67 bp):
TATTTAAATTTGAATATTAAAATGATGTATATATCTTTTCAATATTTCAAATTAAAAGATAATAT
TA
Found at i:29808 original size:16 final size:17
Alignment explanation
Indices: 29781--29812 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
29771 CGAAGTTCGG
29781 GGACTAAAAAGGTCAAA
1 GGACTAAAAAGGTCAAA
29798 GGACT-AAAAGGTCAA
1 GGACTAAAAAGGTCAA
29813 GTTCTAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.12, G:0.25, T:0.12
Consensus pattern (17 bp):
GGACTAAAAAGGTCAAA
Found at i:30166 original size:17 final size:16
Alignment explanation
Indices: 30139--30187 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
30129 TGAACCTAAT
30139 TAAAAAAATAAAACAA
1 TAAAAAAATAAAACAA
30155 TAAAATAAATAAAA-AA
1 TAAAA-AAATAAAACAA
* *
30171 CAAAAAACAAAAAACAA
1 TAAAAAA-ATAAAACAA
30188 CATAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 2 0.07
16 16 0.57
17 10 0.36
ACGTcount: A:0.82, C:0.08, G:0.00, T:0.10
Consensus pattern (16 bp):
TAAAAAAATAAAACAA
Found at i:30189 original size:17 final size:17
Alignment explanation
Indices: 30142--30205 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 17
30132 ACCTAATTAA
30142 AAAAATAAAACAATAAAAT
1 AAAAA-AAAACAA-AAAAT
*
30161 AAATAAAAAACAAAAAAC
1 AAA-AAAAAACAAAAAAT
* *
30179 AAAAAACAACATAAAAT
1 AAAAAAAAACAAAAAAT
30196 AAAAATAAAA
1 AAAAA-AAAA
30206 TAAACCTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
17 16 0.42
18 10 0.26
19 10 0.26
20 2 0.05
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAAAAAAACAAAAAAT
Found at i:32315 original size:39 final size:39
Alignment explanation
Indices: 32202--33008 Score: 1141
Period size: 39 Copynumber: 20.6 Consensus size: 39
32192 AGAAAAAATA
*
32202 ATCTCAAGTGAGAT-AAATCTTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
32240 ATCTCAAGCGAGATAAAAATATTCTGTTTTGAGTGAAACT
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACT
* * *
32280 ATCTCAAGCTAGATAAAATCTTATGTTTCGGGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
32319 ATCTCAAGCGAGATAAAAATCTTATGTTTCGAGTGAAAGT
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACT
* *
32359 ATCTCAAGCGAGATAAAATCTTTTGTTTCGAGTGAAAGT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* * * *
32398 ATCTAAAGCGAGATAAAATCTTCTGTTTTGACTGCAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
32437 ATCTCAAGCGAGATAAAAATATTTTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACT
*
32477 ATCTCAAGCGAGATAAAATCTTCTCTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
32516 ATCTCAAGAGAGATAAAAATCTTATGTTTCGAGTGAAACT
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACT
32556 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* * *
32595 ATCTCAAGCGGGATAAAATATTTTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* *
32634 ATCTCAAGCGAGATAAAAATCTTATGTTTCAAGTGAAACT
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACT
* * * *
32674 ATCTTAAGCAAGATAAAATCTTCTATTTCAAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
32713 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
*
32752 ATCTCAAGCGAGAT-AGATCTTCTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
* ** * *
32790 ATCTTAATTGAGATAAAAATCTTTTGTTTTGAGTGAAACT
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACT
* * *
32830 ATCTCAAGCGAGATAAAATCTTTTATTTCGAGTAAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
*
32869 ATCTCAAGCGAGATAAAAATCTTTTGTTTCGAGTGAAACT
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACT
* *
32909 ATCTCAAGCGAGATAAAATCTTCTGTTTTGAGTGAAATT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
** * *
32948 ATCTCAAGTAAGATAAAATCTTATGTTTCAAGTGAAACT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
32987 ATCTCAAGCGAGATAAAATCTT
1 ATCTCAAGCGAGATAAAATCTT
33009 GTTTTAAAAA
Statistics
Matches: 687, Mismatches: 73, Indels: 17
0.88 0.09 0.02
Matches are distributed among these distances:
38 47 0.07
39 395 0.57
40 245 0.36
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (39 bp):
ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACT
Found at i:32316 original size:79 final size:78
Alignment explanation
Indices: 32202--33008 Score: 1141
Period size: 79 Copynumber: 10.3 Consensus size: 78
32192 AGAAAAAATA
* *
32202 ATCTCAAGTGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAAATATTCTG
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTCTG
*
32266 TTTTGAGTGAAACT
65 TTTCGAGTGAAACT
* * * *
32280 ATCTCAAGCTAGATAAAATCTTATGTTTCGGGTGAAACTATCTCAAGCGAGATAAAAATCTTATG
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTCTG
*
32345 TTTCGAGTGAAAGT
65 TTTCGAGTGAAACT
* * *
32359 ATCTCAAGCGAGATAAAATCTTTTGTTTCGAGTGAAAGTATCTAAAGCGAGATAAAATCTTCTGT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
* * *
32424 TTTGACTGCAACT
66 TTCGAGTGAAACT
* * *
32437 ATCTCAAGCGAGATAAAAATATTTTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTC
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTG
32502 TTTCGAGTGAAACT
65 TTTCGAGTGAAACT
* *
32516 ATCTCAAGAGAGATAAAAATCTTATGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTG
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTG
32581 TTTCGAGTGAAACT
65 TTTCGAGTGAAACT
* * * *
32595 ATCTCAAGCGGGATAAAATATTTTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAAATCTTATG
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTCTG
*
32660 TTTCAAGTGAAACT
65 TTTCGAGTGAAACT
* * * *
32674 ATCTTAAGCAAGATAAAATCTTCTATTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
32739 TTCGAGTGAAACT
66 TTCGAGTGAAACT
* * ** *
32752 ATCTCAAGCGAGAT-AGATCTTCTGTTTCGAGTGAAACTATCTTAATTGAGATAAAAATCTTTTG
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTCTG
*
32816 TTTTGAGTGAAACT
65 TTTCGAGTGAAACT
* * * *
32830 ATCTCAAGCGAGATAAAATCTTTTATTTCGAGTAAAACTATCTCAAGCGAGATAAAAATCTTTTG
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTCTG
32895 TTTCGAGTGAAACT
65 TTTCGAGTGAAACT
* * ** *
32909 ATCTCAAGCGAGATAAAATCTTCTGTTTTGAGTGAAATTATCTCAAGTAAGATAAAATCTTATGT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
*
32974 TTCAAGTGAAACT
66 TTCGAGTGAAACT
32987 ATCTCAAGCGAGATAAAATCTT
1 ATCTCAAGCGAGATAAAATCTT
33009 GTTTTAAAAA
Statistics
Matches: 653, Mismatches: 71, Indels: 10
0.89 0.10 0.01
Matches are distributed among these distances:
77 32 0.05
78 200 0.31
79 421 0.64
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (78 bp):
ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
TTCGAGTGAAACT
Found at i:32362 original size:22 final size:22
Alignment explanation
Indices: 32337--32401 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
32327 CGAGATAAAA
32337 ATCTTATGTTTCGAGTGAAAGT
1 ATCTTATGTTTCGAGTGAAAGT
* *
32359 ATCTCAAG---CGAGAT-AAA--
1 ATCTTATGTTTCGAG-TGAAAGT
*
32376 ATCTTTTGTTTCGAGTGAAAGT
1 ATCTTATGTTTCGAGTGAAAGT
32398 ATCT
1 ATCT
32402 AAAGCGAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 14
0.62 0.10 0.28
Matches are distributed among these distances:
17 5 0.16
19 8 0.26
20 8 0.26
22 10 0.32
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (22 bp):
ATCTTATGTTTCGAGTGAAAGT
Found at i:32419 original size:118 final size:117
Alignment explanation
Indices: 32202--33008 Score: 1150
Period size: 118 Copynumber: 6.9 Consensus size: 117
32192 AGAAAAAATA
* *
32202 ATCTCAAGTGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAAATATTCTG
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTCTG
* * *
32266 TTTTGAGTGAAACTATCTCAAGCTAGATAAAATCTTATGTTTCGGGTGAAACT
65 TTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACT
* * *
32319 ATCTCAAGCGAGATAAAAATCTTATGTTTCGAGTGAAAGTATCTCAAGCGAGATAAAATCTTTTG
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTG
* * * * * *
32384 TTTCGAGTGAAAGTATCTAAAGCGAGATAAAATCTTCTGTTTTGACTGCAACT
65 TTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACT
* * *
32437 ATCTCAAGCGAGATAAAAATATTTTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTC
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTG
*
32502 TTTCGAGTGAAACTATCTCAAGAGAGATAAAAATCTTATGTTTCGAGTGAAACT
65 TTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTATGTTTCGAGTGAAACT
* * *
32556 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGGGATAAAATATTTTGT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
*
32621 TTCGAGTGAAACTATCTCAAGCGAGATAAAAATCTTATGTTTCAAGTGAAACT
66 TTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTATGTTTCGAGTGAAACT
* * * *
32674 ATCTTAAGCAAGATAAAATCTTCTATTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
* *
32739 TTCGAGTGAAACTATCTCAAGCGAGAT-AGATCTTCTGTTTCGAGTGAAACT
66 TTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACT
* ** * * * *
32790 ATCTTAATTGAGATAAAAATCTTTTGTTTTGAGTGAAACTATCTCAAGCGAGATAAAATCTTTTA
1 ATCTCAAGCGAGAT-AAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTG
* *
32855 TTTCGAGTAAAACTATCTCAAGCGAGATAAAAATCTTTTGTTTCGAGTGAAACT
65 TTTCGAGTGAAACTATCTCAAGCGAGAT-AAAATCTTATGTTTCGAGTGAAACT
* * ** *
32909 ATCTCAAGCGAGATAAAATCTTCTGTTTTGAGTGAAATTATCTCAAGTAAGATAAAATCTTATGT
1 ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
*
32974 TTCAAGTGAAACTATCTCAAGCGAGATAAAATCTT
66 TTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT
33009 GTTTTAAAAA
Statistics
Matches: 617, Mismatches: 67, Indels: 12
0.89 0.10 0.02
Matches are distributed among these distances:
116 32 0.05
117 92 0.15
118 389 0.63
119 104 0.17
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Consensus pattern (117 bp):
ATCTCAAGCGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGT
TTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGAGTGAAACT
Found at i:33107 original size:76 final size:76
Alignment explanation
Indices: 32982--33177 Score: 290
Period size: 76 Copynumber: 2.6 Consensus size: 76
32972 GTTTCAAGTG
* * *
32982 AAACTATCTCAAGCGAGATAAAATCTTGTTTT---AAAAACAATCTTGAGTGAAATGAAATGTCT
1 AAACTGTCTCAAGCGAGA-CAAATCTCGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCT
*
33044 TCTTTTGAGTAA
65 TCTTTCGAGTAA
*
33056 AAACTGTCTCAAGCGAGACAAATCTCGTTTTAAGAAAAACTATCTTGAGTGAAATGAAATGTCTT
1 AAACTGTCTCAAGCGAGACAAATCTCGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCTT
33121 CTTTCGAGTAA
66 CTTTCGAGTAA
* *
33132 AAACTGTCTCAAGTGAGACAAATCTGGTTTTAAAGAAAAACAATCT
1 AAACTGTCTCAAGCGAGACAAATCTCGTTTT-AAGAAAAACAATCT
33178 CAAGTAAGAT
Statistics
Matches: 110, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
73 11 0.10
74 17 0.15
76 69 0.63
77 13 0.12
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (76 bp):
AAACTGTCTCAAGCGAGACAAATCTCGTTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCTT
CTTTCGAGTAA
Found at i:33147 original size:40 final size:39
Alignment explanation
Indices: 33027--33147 Score: 122
Period size: 40 Copynumber: 3.1 Consensus size: 39
33017 AACAATCTTG
33027 AGTGAAATGAAATGTCTTCTTTTGAGTAAAAACTGTCTCA
1 AGTGAAATGAAATGTCTTC-TTTGAGTAAAAACTGTCTCA
* * * * * * * **
33067 AGCGAGA-CAAATCTCGT-TTTAAG-AAAAACTATCTTG
1 AGTGAAATGAAATGTCTTCTTTGAGTAAAAACTGTCTCA
33103 AGTGAAATGAAATGTCTTCTTTCGAGTAAAAACTGTCTCA
1 AGTGAAATGAAATGTCTTCTTT-GAGTAAAAACTGTCTCA
33143 AGTGA
1 AGTGA
33148 GACAAATCTG
Statistics
Matches: 59, Mismatches: 18, Indels: 8
0.69 0.21 0.09
Matches are distributed among these distances:
36 15 0.25
37 12 0.20
38 3 0.05
39 9 0.15
40 20 0.34
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (39 bp):
AGTGAAATGAAATGTCTTCTTTGAGTAAAAACTGTCTCA
Found at i:40786 original size:31 final size:32
Alignment explanation
Indices: 40751--40812 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
40741 TTTAATATTT
* * *
40751 AAATT-AAATTTATATTTATTTTGACTATTAC
1 AAATTAAAATATATATTTAATTTGAATATTAC
*
40782 AAATTAAAATATATTTTTAATTTGAATATTA
1 AAATTAAAATATATATTTAATTTGAATATTA
40813 TTAGGATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 5 0.19
32 21 0.81
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (32 bp):
AAATTAAAATATATATTTAATTTGAATATTAC
Found at i:40938 original size:61 final size:63
Alignment explanation
Indices: 40863--40979 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 63
40853 ATTTATTATA
* *
40863 TATTTAAGTTTGAATATTAAA-GATAATATATA-C-TTTGAATATTTCAAATTAAAATAATATC
1 TATTTAAGTTTGAATAGTAAATG-TAATATATATCTTTTAAATATTTCAAATTAAAATAATATC
** *
40924 TATTTAAGTTTGAATAGTAAATGTTGTCTATATCTTTTAAATATTTCAAATTAAAA
1 TATTTAAGTTTGAATAGTAAATGTAATATATATCTTTTAAATATTTCAAATTAAAA
40980 GATATTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
61 26 0.54
62 2 0.04
63 20 0.42
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (63 bp):
TATTTAAGTTTGAATAGTAAATGTAATATATATCTTTTAAATATTTCAAATTAAAATAATATC
Found at i:49961 original size:19 final size:20
Alignment explanation
Indices: 49922--49962 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
49912 TAGAAGAATG
*
49922 GGCAGAGTTTGATTCGTGGA
1 GGCAGAGTTTGATTCGAGGA
*
49942 GGCA-AGTTTGATTTGAGGA
1 GGCAGAGTTTGATTCGAGGA
49961 GG
1 GG
49963 AGGCCATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.22, C:0.07, G:0.41, T:0.29
Consensus pattern (20 bp):
GGCAGAGTTTGATTCGAGGA
Found at i:50456 original size:13 final size:13
Alignment explanation
Indices: 50440--50468 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
50430 TGTTTGTGTT
50440 TTTTTTTTCTTTA
1 TTTTTTTTCTTTA
50453 TTTTTTTTCTTTA
1 TTTTTTTTCTTTA
50466 TTT
1 TTT
50469 ACTTTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTCTTTA
Found at i:50460 original size:17 final size:18
Alignment explanation
Indices: 50438--50474 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
50428 AGTGTTTGTG
*
50438 TTTTTTT-TTTCTTTA-T
1 TTTTTTTCTTTATTTACT
50454 TTTTTTTCTTTATTTACT
1 TTTTTTTCTTTATTTACT
50472 TTT
1 TTT
50475 AATATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 7 0.39
18 4 0.22
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTTCTTTATTTACT
Found at i:55324 original size:55 final size:55
Alignment explanation
Indices: 55253--55805 Score: 732
Period size: 55 Copynumber: 10.1 Consensus size: 55
55243 TATATGTTGC
**
55253 AATTTTTGTATTGGCACTATGTACGCAACCCCACGAAATTCATAATGAGTTTATG
1 AATTTTTGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* * *
55308 AATTTTTGTATTGGCACTATGTGTGCAACACCATGAAATTCATAAAGAGTTTATG
1 AATTTTTGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
** * * *
55363 AATTTCCGTATTGGCACTATGTGTGCAACCCCACAAAATTTATAATGATTTTATG
1 AATTTTTGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
***
55418 AATTTCCATATTGGCACTATGTGTGCAA-CCCACGAAATTCATAATGAGTTTATG
1 AATTTTTGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* * * * *
55472 AAATTTCGTATTGGCACTATGTGTGCAACCCCATGAAATTCATAATGCGTTTATC
1 AATTTTTGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* * * * * *
55527 AATTTTTGTATTGGCACTATATGCGTAACCCCATGAAATTCATAACGAGTTTAAG
1 AATTTTTGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
*
55582 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
1 AATTTTTGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* * * **
55637 AATTTTTCATATTCGCACTAGGTGTGCAACCCCAAAAAATTCATAATGAGTTTATG
1 AATTTTT-GTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* * *
55693 AATTTTTTTATTGGCACTATGTGTGCAACCCCATGAAATGCATAATGAGTTTATG
1 AATTTTTGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
* * * * *
55748 AATTTTTCGTATTGGCACTATGTGTGCAA-CCTACGTAATTCACAAAGAGTTTGTG
1 AATTTTT-GTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
55803 AAT
1 AAT
55806 GACCATATGG
Statistics
Matches: 436, Mismatches: 59, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
54 48 0.11
55 318 0.73
56 70 0.16
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (55 bp):
AATTTTTGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
Found at i:55540 original size:164 final size:165
Alignment explanation
Indices: 55253--55805 Score: 768
Period size: 164 Copynumber: 3.4 Consensus size: 165
55243 TATATGTTGC
* ** *
55253 AATTTTTGTATTGGCACTATGTACGCAACCCCACGAAATTCATAATGAGTTTATGAATTTTTGTA
1 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTA
* * **
55318 TTGGCACTATGTGTGCAACACCATGAAATTCATAAAGAGTTTATGAATTTCCGTATTGGCACTAT
66 TTGGCACTATGTGTGCAACCCCATGAAATTCATAATGAGTTTATGAATTTTTGTATTGGCACTAT
** * *
55383 GTGTGCAACCCCACAAAATTTATAATGATTTTATG
131 GTGTGCAACCCCATGAAATTCATAATGAGTTTATG
* * *
55418 AATTTCCATATTGGCACTATGTGTGCAA-CCCACGAAATTCATAATGAGTTTATGAAATTTCGTA
1 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTA
* *
55482 TTGGCACTATGTGTGCAACCCCATGAAATTCATAATGCGTTTATCAATTTTTGTATTGGCACTAT
66 TTGGCACTATGTGTGCAACCCCATGAAATTCATAATGAGTTTATGAATTTTTGTATTGGCACTAT
* * * * *
55547 ATGCGTAACCCCATGAAATTCATAACGAGTTTAAG
131 GTGTGCAACCCCATGAAATTCATAATGAGTTTATG
*
55582 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAATTTTTCAT
1 AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAA-TTTTCGT
* * ** *
55647 ATTCGCACTAGGTGTGCAACCCCAAAAAATTCATAATGAGTTTATGAATTTTTTTATTGGCACTA
65 ATTGGCACTATGTGTGCAACCCCATGAAATTCATAATGAGTTTATGAATTTTTGTATTGGCACTA
*
55712 TGTGTGCAACCCCATGAAATGCATAATGAGTTTATG
130 TGTGTGCAACCCCATGAAATTCATAATGAGTTTATG
* * * * *
55748 AATTTTTCGTATTGGCACTATGTGTGCAA-CCTACGTAATTCACAAAGAGTTTGTGAAT
1 AA-TTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAAT
55806 GACCATATGG
Statistics
Matches: 341, Mismatches: 44, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
164 145 0.43
165 52 0.15
166 118 0.35
167 26 0.08
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (165 bp):
AATTTTCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAATTTTCGTA
TTGGCACTATGTGTGCAACCCCATGAAATTCATAATGAGTTTATGAATTTTTGTATTGGCACTAT
GTGTGCAACCCCATGAAATTCATAATGAGTTTATG
Found at i:56408 original size:2 final size:2
Alignment explanation
Indices: 56401--56519 Score: 238
Period size: 2 Copynumber: 59.5 Consensus size: 2
56391 GACGTGTTTA
56401 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56443 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56485 AT AT 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 AT AT A
56520 ATGGTTTTAT
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 117 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60539 original size:55 final size:55
Alignment explanation
Indices: 60470--60794 Score: 463
Period size: 55 Copynumber: 5.9 Consensus size: 55
60460 TGCAATTTCT
* *
60470 GTATTGGCACTATGTGTGTAACCCCACAAAATTCATAATGAGTTTATGAATTTAC
1 GTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAATTTAC
* * *
60525 GTATTGGCATTATGTGTGCAACCCCACAAAATTCATAATGAGTTTATGAATTTCC
1 GTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAATTTAC
* * * * * *
60580 ATATTGGCACTATGTATGTAACCCCACGAAATTCCTAATGAGTTTATGAATATCC
1 GTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAATTTAC
* *
60635 ATATTGGCACTATGTGTGCAACCCCACGAAATTTATAATGAGTTTATGAATTTAC
1 GTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAATTTAC
* **
60690 GTATTGGCACTATGTGTGCAACCCCATGAAATTCATAATGAGTTTATGAATTTTT
1 GTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAATTTAC
* * * *
60745 GTATTGGCACTATGTGTGCAA-CCTACGTAATTCACAATGAGTTTGTGAAT
1 GTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAAT
60795 GACTGTATCG
Statistics
Matches: 244, Mismatches: 26, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
54 24 0.10
55 220 0.90
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (55 bp):
GTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATGAATTTAC
Found at i:65240 original size:13 final size:13
Alignment explanation
Indices: 65210--65254 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
65200 CATGATTTTA
*
65210 TTATATGT-GATG
1 TTATATGTATATG
*
65222 TGATATGTATATG
1 TTATATGTATATG
*
65235 TTATATATATATG
1 TTATATGTATATG
65248 TTATATG
1 TTATATG
65255 ATGATGATCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 7 0.26
13 20 0.74
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (13 bp):
TTATATGTATATG
Found at i:65651 original size:48 final size:48
Alignment explanation
Indices: 65589--65694 Score: 133
Period size: 48 Copynumber: 2.2 Consensus size: 48
65579 GAGTCGAGGG
* * * *
65589 TTCTACGCGATCCTTCGGGGACAAA-TCTATACGGTCCTTCGAGATAAA
1 TTCTACGTGGTCCTTC-GGGACAAATTCTACACGGTCCTTCGAGACAAA
* * *
65637 TTCTATGTGGTCCTTCGGGATAAATTCTACGCGGTCCTTCGAGACAAA
1 TTCTACGTGGTCCTTCGGGACAAATTCTACACGGTCCTTCGAGACAAA
65685 TTCTACGTGG
1 TTCTACGTGG
65695 CACTTTGGTG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
47 7 0.14
48 42 0.86
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.30
Consensus pattern (48 bp):
TTCTACGTGGTCCTTCGGGACAAATTCTACACGGTCCTTCGAGACAAA
Found at i:65690 original size:24 final size:24
Alignment explanation
Indices: 65589--65691 Score: 109
Period size: 24 Copynumber: 4.3 Consensus size: 24
65579 GAGTCGAGGG
* *
65589 TTCTACGCGATCCTTCGGGGACAAA
1 TTCTACGCGGTCCTTC-GAGACAAA
** *
65614 -TCTATACGGTCCTTCGAGATAAA
1 TTCTACGCGGTCCTTCGAGACAAA
* * * *
65637 TTCTATGTGGTCCTTCGGGATAAA
1 TTCTACGCGGTCCTTCGAGACAAA
65661 TTCTACGCGGTCCTTCGAGACAAA
1 TTCTACGCGGTCCTTCGAGACAAA
65685 TTCTACG
1 TTCTACG
65692 TGGCACTTTG
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
23 6 0.09
24 59 0.91
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.30
Consensus pattern (24 bp):
TTCTACGCGGTCCTTCGAGACAAA
Found at i:66881 original size:50 final size:50
Alignment explanation
Indices: 66806--66905 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
66796 TGGGGACCTT
*
66806 CACCTCTCAATTCAAACGGTAGGAAGGTTTAAAGCACCACCGGGAACGTC
1 CACCTCTCAATTCAAACGATAGGAAGGTTTAAAGCACCACCGGGAACGTC
66856 CACCTCTCAATTCAAACGATAGGAAGGTTTAAAGCACCACCGGGAACGTC
1 CACCTCTCAATTCAAACGATAGGAAGGTTTAAAGCACCACCGGGAACGTC
66906 ATACCTCAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (50 bp):
CACCTCTCAATTCAAACGATAGGAAGGTTTAAAGCACCACCGGGAACGTC
Found at i:67803 original size:22 final size:22
Alignment explanation
Indices: 67774--67821 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
67764 ATTCTTCTTA
* *
67774 TTTAATTTACTAACTTTGTTTAT
1 TTTATTTTACTAA-TTTATTTAT
*
67797 TTTATTTTCCTAATTTATTTAT
1 TTTATTTTACTAATTTATTTAT
67819 TTT
1 TTT
67822 CCCTTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTATTTTACTAATTTATTTAT
Found at i:68750 original size:18 final size:18
Alignment explanation
Indices: 68721--68785 Score: 112
Period size: 18 Copynumber: 3.6 Consensus size: 18
68711 CTTTGCATCC
68721 ATAATGATTTCTAAATTAA
1 ATAAT-ATTTCTAAATTAA
68740 ATAATATTTCTAAATTAA
1 ATAATATTTCTAAATTAA
*
68758 ATAATATTTCGAAATTAA
1 ATAATATTTCTAAATTAA
68776 ATAATATTTC
1 ATAATATTTC
68786 AAACTCCAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 40 0.89
19 5 0.11
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
ATAATATTTCTAAATTAA
Done.