Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005808.1 Hibiscus syriacus cultivar Beakdansim tig00013618_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: 67879
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6152 original size:23 final size:23
Alignment explanation
Indices: 6122--6167 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
6112 GTGTCAACTC
*
6122 TGAAATTTTATTTATGCCTACCT
1 TGAAATTTTAATTATGCCTACCT
*
6145 TGAAATTTTAATTGTGCCTACCT
1 TGAAATTTTAATTATGCCTACCT
6168 CTTCAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (23 bp):
TGAAATTTTAATTATGCCTACCT
Found at i:6552 original size:23 final size:23
Alignment explanation
Indices: 6526--6583 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
6516 ATAAATGTAA
* *
6526 TATACAAATAAATTTATAATTAG
1 TATACAAATAAATTAATAATCAG
*
6549 TATATAAATAAATTAATAATCAG
1 TATACAAATAAATTAATAATCAG
* *
6572 AATACAATTAAA
1 TATACAAATAAA
6584 CATAAATTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.34
Consensus pattern (23 bp):
TATACAAATAAATTAATAATCAG
Found at i:7446 original size:21 final size:21
Alignment explanation
Indices: 7420--7464 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
7410 GATTTATGGG
* *
7420 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
7441 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
7462 CAA
1 CAA
7465 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:8483 original size:31 final size:31
Alignment explanation
Indices: 8445--8513 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
8435 AGAGTCGAGG
*
8445 GTTTACCTATGTCT-TTCGAGACATATGGACA
1 GTTTACCTAGGT-TATTCGAGACATATGGACA
* *
8476 GTTTACCTAGGTTATTCGGGACCTATGGACA
1 GTTTACCTAGGTTATTCGAGACATATGGACA
8507 GTTTACC
1 GTTTACC
8514 GAGGATCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 1 0.03
31 33 0.97
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTATTCGAGACATATGGACA
Found at i:8545 original size:30 final size:30
Alignment explanation
Indices: 8495--8594 Score: 139
Period size: 30 Copynumber: 3.3 Consensus size: 30
8485 GGTTATTCGG
*
8495 GACCTATGGACAGTTTACCGAGGATCTTTAT
1 GACCTCTGGACAG-TTACCGAGGATCTTTAT
8526 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
8556 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
8585 GATCTCTGGA
1 GACCTCTGGA
8595 TAGGTCCTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.27
30 35 0.55
31 12 0.19
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:10587 original size:324 final size:324
Alignment explanation
Indices: 9998--10645 Score: 1296
Period size: 324 Copynumber: 2.0 Consensus size: 324
9988 TGCAATGGAT
9998 CTGGATACAGTTGCATATTTGGATCATAATAATGTGGTATAGTAAAGGAAAAGGAAGTAAGAATT
1 CTGGATACAGTTGCATATTTGGATCATAATAATGTGGTATAGTAAAGGAAAAGGAAGTAAGAATT
10063 TGTATATTTAAGTAAAGCTGAGGATTGATAAGAAGAGTTTGAGAATGTGTATATCGATGATCAGA
66 TGTATATTTAAGTAAAGCTGAGGATTGATAAGAAGAGTTTGAGAATGTGTATATCGATGATCAGA
10128 TTATAGGACACAGGAAGTCAGAATGTTGAGTTTAAGCAAAAGAAATTTCAGGATGTGTGAGAATA
131 TTATAGGACACAGGAAGTCAGAATGTTGAGTTTAAGCAAAAGAAATTTCAGGATGTGTGAGAATA
10193 GAGGTGAAATTGATAAGTTGAGTAAGCGAATTTTAAGATAATTTCGATTTGAAAGGATGTATGTG
196 GAGGTGAAATTGATAAGTTGAGTAAGCGAATTTTAAGATAATTTCGATTTGAAAGGATGTATGTG
10258 TTTGGTTGATTAGGGTTTGTACCCTAGATTGAACATATGTTATTGACTACCTGTCAGAGTAAAG
261 TTTGGTTGATTAGGGTTTGTACCCTAGATTGAACATATGTTATTGACTACCTGTCAGAGTAAAG
10322 CTGGATACAGTTGCATATTTGGATCATAATAATGTGGTATAGTAAAGGAAAAGGAAGTAAGAATT
1 CTGGATACAGTTGCATATTTGGATCATAATAATGTGGTATAGTAAAGGAAAAGGAAGTAAGAATT
10387 TGTATATTTAAGTAAAGCTGAGGATTGATAAGAAGAGTTTGAGAATGTGTATATCGATGATCAGA
66 TGTATATTTAAGTAAAGCTGAGGATTGATAAGAAGAGTTTGAGAATGTGTATATCGATGATCAGA
10452 TTATAGGACACAGGAAGTCAGAATGTTGAGTTTAAGCAAAAGAAATTTCAGGATGTGTGAGAATA
131 TTATAGGACACAGGAAGTCAGAATGTTGAGTTTAAGCAAAAGAAATTTCAGGATGTGTGAGAATA
10517 GAGGTGAAATTGATAAGTTGAGTAAGCGAATTTTAAGATAATTTCGATTTGAAAGGATGTATGTG
196 GAGGTGAAATTGATAAGTTGAGTAAGCGAATTTTAAGATAATTTCGATTTGAAAGGATGTATGTG
10582 TTTGGTTGATTAGGGTTTGTACCCTAGATTGAACATATGTTATTGACTACCTGTCAGAGTAAAG
261 TTTGGTTGATTAGGGTTTGTACCCTAGATTGAACATATGTTATTGACTACCTGTCAGAGTAAAG
10646 GTGATAGAGT
Statistics
Matches: 324, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
324 324 1.00
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.32
Consensus pattern (324 bp):
CTGGATACAGTTGCATATTTGGATCATAATAATGTGGTATAGTAAAGGAAAAGGAAGTAAGAATT
TGTATATTTAAGTAAAGCTGAGGATTGATAAGAAGAGTTTGAGAATGTGTATATCGATGATCAGA
TTATAGGACACAGGAAGTCAGAATGTTGAGTTTAAGCAAAAGAAATTTCAGGATGTGTGAGAATA
GAGGTGAAATTGATAAGTTGAGTAAGCGAATTTTAAGATAATTTCGATTTGAAAGGATGTATGTG
TTTGGTTGATTAGGGTTTGTACCCTAGATTGAACATATGTTATTGACTACCTGTCAGAGTAAAG
Found at i:12151 original size:21 final size:21
Alignment explanation
Indices: 12125--12169 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
12115 GATTTCTGGG
* *
12125 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
12146 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
12167 CAA
1 CAA
12170 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:12652 original size:2 final size:2
Alignment explanation
Indices: 12645--12673 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12635 CATGAGTTAG
12645 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
12674 GGATTTGTAT
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:13207 original size:31 final size:31
Alignment explanation
Indices: 13169--13246 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
13159 AGAGTCGAGG
*
13169 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
* *
13200 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGACA
* *
13231 GTTTACCGAGGATCTT
1 GTTTACCTAGGTTCTT
13247 TATGACCTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
31 39 0.95
32 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:13254 original size:31 final size:30
Alignment explanation
Indices: 13192--13306 Score: 124
Period size: 30 Copynumber: 3.8 Consensus size: 30
13182 TTTCGAGACA
* * ***
13192 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
13223 TATGGACAGTTTACCGAGGATCTTTATGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
*
13254 TCTGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* * *
13284 TCTGGATAGTTACCG-GGGTCTTT
1 TATGGACAGTTACCGAGGATCTTT
13307 GTGATCTCTG
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
29 7 0.09
30 35 0.46
31 34 0.45
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:13269 original size:30 final size:30
Alignment explanation
Indices: 13219--13318 Score: 139
Period size: 30 Copynumber: 3.3 Consensus size: 30
13209 GGTTCTTCGG
*
13219 GACCTATGGACAGTTTACCGAGGATCTTTAT
1 GACCTCTGGACAG-TTACCGAGGATCTTTAT
13250 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* * *
13280 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
13309 GATCTCTGGA
1 GACCTCTGGA
13319 TAGGTCCTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.27
30 35 0.55
31 12 0.19
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:15216 original size:27 final size:27
Alignment explanation
Indices: 15186--15240 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
15176 ATTTTTTGTT
15186 AATTT-TTTACTCACTTAAAATTTTATA
1 AATTTATTT-CTCACTTAAAATTTTATA
15213 AATTTATTTCTCACTTAAAATTTTATA
1 AATTTATTTCTCACTTAAAATTTTATA
15240 A
1 A
15241 CTTCATCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 24 0.89
28 3 0.11
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (27 bp):
AATTTATTTCTCACTTAAAATTTTATA
Found at i:16651 original size:50 final size:50
Alignment explanation
Indices: 16538--16657 Score: 143
Period size: 50 Copynumber: 2.4 Consensus size: 50
16528 GTAAAGCGAG
*
16538 CCCCCTGAACCGCGCTATACGCTGATTTGGCACCACGTGGGTATAGCGCG
1 CCCCCTGAACCGCGCTATACGCTGATTTGGCACCACGTGGGTATAGCGCA
* *** * * *
16588 CCCCTTTCCCCGCGAC-ATACGGTGATTTGGCGCCACGTGGGTATAGTGCA
1 CCCCCTGAACCGCG-CTATACGCTGATTTGGCACCACGTGGGTATAGCGCA
*
16638 CCCCCTGATCCGCGCTATAC
1 CCCCCTGAACCGCGCTATAC
16658 CTGCGTATCT
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
49 1 0.02
50 54 0.96
51 1 0.02
ACGTcount: A:0.17, C:0.36, G:0.26, T:0.22
Consensus pattern (50 bp):
CCCCCTGAACCGCGCTATACGCTGATTTGGCACCACGTGGGTATAGCGCA
Found at i:16821 original size:12 final size:10
Alignment explanation
Indices: 16779--16819 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
16769 TTTATCACAC
16779 CAAATTCTCT
1 CAAATTCTCT
16789 CAAATTCTCT
1 CAAATTCTCT
16799 -AAATTTCTCT
1 CAAA-TTCTCT
*
16809 CAAATACTCT
1 CAAATTCTCT
16819 C
1 C
16820 TCTTTTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:17138 original size:111 final size:111
Alignment explanation
Indices: 16952--17276 Score: 596
Period size: 111 Copynumber: 2.9 Consensus size: 111
16942 ATATATCTAT
* * *
16952 ACACTTTGCTGATACGGTAACATTTTAACGTTTAAATTTAATTTAAATTATTAGTAATATTTAGT
1 ACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
*
17017 TGATTTATTTAATGCATGATTATTAGATTAATAATTAAATATCTCG
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
*
17063 ACATTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
17128 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
*
17174 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
17239 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
17277 TTTTTGTAAT
Statistics
Matches: 207, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 207 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (111 bp):
ACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
Found at i:22997 original size:51 final size:51
Alignment explanation
Indices: 22921--23046 Score: 141
Period size: 51 Copynumber: 2.5 Consensus size: 51
22911 CGGTATACCC
** * * * *
22921 ATAGCGCGGAGCAGGGGGCACGCTATACCCCATGTGTAAC-CC-AGTCAGCGT
1 ATAGCGCGGTTCAGGGGGCGCGCTATACCCCACGTG--ACGCCAAATCAGCAT
*
22972 ATAGCGCGGTAT-AGGGGGCGCGCTATACTCCACGTGACGCCAAATCAGCAT
1 ATAGCGCGGT-TCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCAGCAT
23023 ATAGCGCGGTTCAGGGGGCGCGCT
1 ATAGCGCGGTTCAGGGGGCGCGCT
23047 TTACTGCTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
49 2 0.03
50 3 0.05
51 59 0.92
ACGTcount: A:0.22, C:0.28, G:0.33, T:0.17
Consensus pattern (51 bp):
ATAGCGCGGTTCAGGGGGCGCGCTATACCCCACGTGACGCCAAATCAGCAT
Found at i:25111 original size:22 final size:22
Alignment explanation
Indices: 25089--25129 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
25079 TCATAATTAT
25089 TTAAAAA-ATTAAATAAAAATA
1 TTAAAAATATTAAATAAAAATA
*
25110 TTAAAAATATTTAATAAAAA
1 TTAAAAATATTAAATAAAAA
25130 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TTAAAAATATTAAATAAAAATA
Found at i:27924 original size:31 final size:31
Alignment explanation
Indices: 27862--27924 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
27852 TATAGTGACT
* *** *
27862 TATTTTTGAATTTTGGTTCAGGGTCTGAAAA
1 TATTTTTAAATTTTGGTTCAAACTCTAAAAA
*
27893 TATTTTTAAATTTTTGTTCAAACTCTAAAAA
1 TATTTTTAAATTTTGGTTCAAACTCTAAAAA
27924 T
1 T
27925 TAGTATATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.08, G:0.13, T:0.48
Consensus pattern (31 bp):
TATTTTTAAATTTTGGTTCAAACTCTAAAAA
Found at i:36617 original size:20 final size:20
Alignment explanation
Indices: 36594--36686 Score: 93
Period size: 20 Copynumber: 4.7 Consensus size: 20
36584 AATTCGCGTT
*
36594 GCGAAAGTCAAATTTGCAAC
1 GCGAAAGTCAAATTCGCAAC
*
36614 GCGAATTTGT-AAA-TCGCAAC
1 GCGAA--AGTCAAATTCGCAAC
*
36634 ACAGAAA-TCAAATTCGCAAC
1 GC-GAAAGTCAAATTCGCAAC
* *
36654 GCGATAGTCAAATTTGCAAC
1 GCGAAAGTCAAATTCGCAAC
36674 GCGAAAGTCAAAT
1 GCGAAAGTCAAAT
36687 GTTTTTACGC
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
18 1 0.02
19 6 0.10
20 44 0.75
21 6 0.10
22 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.20
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:37087 original size:13 final size:14
Alignment explanation
Indices: 37055--37084 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
37045 AGTATTTGTC
37055 TTTGTTTTGTCTTT
1 TTTGTTTTGTCTTT
37069 TTTGTTTTGTCTTT
1 TTTGTTTTGTCTTT
37083 TT
1 TT
37085 GTTGAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.13, T:0.80
Consensus pattern (14 bp):
TTTGTTTTGTCTTT
Found at i:38884 original size:21 final size:21
Alignment explanation
Indices: 38858--38907 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
38848 GTTAGGAGAG
* *
38858 TTACGTGATGAGGTCGGTGCT
1 TTACGTGATGAGGTCGATACT
*
38879 TTACGTCATGAGGTCGATACT
1 TTACGTGATGAGGTCGATACT
38900 TTACGTGA
1 TTACGTGA
38908 AGATAATAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCGATACT
Found at i:39326 original size:21 final size:21
Alignment explanation
Indices: 39301--39377 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
39291 TGCACCTATA
*
39301 ATCATTCAAGAGGCGCCTCCT
1 ATCATTCAAGAGGCCCCTCCT
39322 ATCATTCAAGAGGCCCCT-CT
1 ATCATTCAAGAGGCCCCTCCT
* *
39342 CATCA-TCGAAGAAGCCCCTCCC
1 -ATCATTC-AAGAGGCCCCTCCT
* *
39364 ACCGTTCAAGAGGC
1 ATCATTCAAGAGGC
39378 ACCTATCATC
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
20 4 0.09
21 39 0.85
22 3 0.07
ACGTcount: A:0.26, C:0.36, G:0.18, T:0.19
Consensus pattern (21 bp):
ATCATTCAAGAGGCCCCTCCT
Found at i:40905 original size:20 final size:20
Alignment explanation
Indices: 40882--40927 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
40872 AAATAAGCGT
40882 TGCGATAGTCAAATTCGCAA
1 TGCGATAGTCAAATTCGCAA
*
40902 TGCGAAAGTCAAATTCGCAA
1 TGCGATAGTCAAATTCGCAA
*
40922 CGCGAT
1 TGCGAT
40928 TTTCAGTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (20 bp):
TGCGATAGTCAAATTCGCAA
Found at i:40958 original size:20 final size:20
Alignment explanation
Indices: 40935--40973 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40925 GATTTTCAGT
40935 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
*
40955 TTGCGAATTTTACTTTCGC
1 TTGCGAATTTGACTTTCGC
40974 ATTGATCGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.44
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:41033 original size:18 final size:18
Alignment explanation
Indices: 41010--41046 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
41000 TTAAATTGAT
41010 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
41028 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
41046 A
1 A
41047 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:41065 original size:24 final size:24
Alignment explanation
Indices: 41002--41054 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
40992 CATCAAGGTT
*
41002 AAATTGATATTGAAATTCAAACTC
1 AAATTGAAATTGAAATTCAAACTC
*
41026 AAATTGAAATTTAAATTCAAACTC
1 AAATTGAAATTGAAATTCAAACTC
*
41050 CAATT
1 AAATT
41055 ACATATGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (24 bp):
AAATTGAAATTGAAATTCAAACTC
Found at i:41466 original size:25 final size:25
Alignment explanation
Indices: 41432--41481 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
41422 ATTATTTTTC
*
41432 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
41457 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
41482 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:41612 original size:20 final size:20
Alignment explanation
Indices: 41587--41633 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
41577 CGTGAAATAA
*
41587 GCGTTGCAAATTTGACTTTT
1 GCGTTGCAAATTTGACTTTC
*
41607 GCGTTGCGAATTTGACTTTC
1 GCGTTGCAAATTTGACTTTC
41627 GCGTTGC
1 GCGTTGC
41634 TCGTAACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.19, G:0.26, T:0.40
Consensus pattern (20 bp):
GCGTTGCAAATTTGACTTTC
Found at i:41934 original size:6 final size:6
Alignment explanation
Indices: 41925--41959 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
41915 TTGTGATTGG
**
41925 GATTTT GATTTT GATTGC GATTTT GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
41960 CCTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:41941 original size:18 final size:18
Alignment explanation
Indices: 41918--41958 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
41908 AAGCCAGTTG
*
41918 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
41936 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
41954 TGATT
1 TGATT
41959 TCCTTTTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.02, G:0.24, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:45179 original size:20 final size:20
Alignment explanation
Indices: 45143--45314 Score: 92
Period size: 20 Copynumber: 8.6 Consensus size: 20
45133 ACTAAAACCT
*
45143 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
45162 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
* *
45181 GTTGCG-ATTTACAAATTCAC
1 GTTGCGAATTT-GAAATTCGC
45201 GTTGCGAATTTGGGAAA-TCGC
1 GTTGCGAATTT--GAAATTCGC
**
45222 AATGCG-ATTT-ACATATTCGC
1 GTTGCGAATTTGA-A-ATTCGC
*
45242 GTTGCGAATTTGGAAAATCGC
1 GTTGCGAATTT-GAAATTCGC
**
45263 AATGCG-ATTT-ACATATTCGC
1 GTTGCGAATTTGA-A-ATTCGC
* * *
45283 TTTGCGAAATTGGAGA-TCGC
1 GTTGCG-AATTTGAAATTCGC
45303 GTTGCGAATTTG
1 GTTGCGAATTTG
45315 TTGGTCATTT
Statistics
Matches: 116, Mismatches: 21, Indels: 32
0.69 0.12 0.19
Matches are distributed among these distances:
17 1 0.01
18 6 0.05
19 29 0.25
20 46 0.40
21 25 0.22
22 7 0.06
23 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:45184 original size:19 final size:19
Alignment explanation
Indices: 45143--45212 Score: 72
Period size: 19 Copynumber: 3.6 Consensus size: 19
45133 ACTAAAACCT
* *
45143 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTC-A
45162 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
45181 GTTGCG-ATTTACAAATTCA
1 GTTGCGAATTT-GAAATTCA
45200 CGTTGCGAATTTG
1 -GTTGCGAATTTG
45213 GGAAATCGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
18 4 0.09
19 23 0.53
20 12 0.28
21 4 0.09
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:45227 original size:21 final size:21
Alignment explanation
Indices: 45203--45269 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
45193 AAATTCACGT
*
45203 TGCGAATTTGGGAAATCGCAA
1 TGCGAATTTGGAAAATCGCAA
** * * **
45224 TGCG-ATTTACATATTCGCGT
1 TGCGAATTTGGAAAATCGCAA
45244 TGCGAATTTGGAAAATCGCAA
1 TGCGAATTTGGAAAATCGCAA
45265 TGCGA
1 TGCGA
45270 TTTACATATT
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.28
Consensus pattern (21 bp):
TGCGAATTTGGAAAATCGCAA
Found at i:45296 original size:41 final size:41
Alignment explanation
Indices: 45156--45296 Score: 189
Period size: 41 Copynumber: 3.5 Consensus size: 41
45146 GCGAAATTAA
* * *
45156 ATTCGCGTTGCGAATTT-G-AAAT-TCAGTTGCGATTTACAA
1 ATTCGCGTTGCGAATTTGGAAAATCGCA-ATGCGATTTACAT
* *
45195 ATTCACGTTGCGAATTTGGGAAATCGCAATGCGATTTACAT
1 ATTCGCGTTGCGAATTTGGAAAATCGCAATGCGATTTACAT
45236 ATTCGCGTTGCGAATTTGGAAAATCGCAATGCGATTTACAT
1 ATTCGCGTTGCGAATTTGGAAAATCGCAATGCGATTTACAT
* *
45277 ATTCGCTTTGCGAAATTGGA
1 ATTCGCGTTGCGAATTTGGA
45297 GATCGCGTTG
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
39 16 0.18
40 1 0.01
41 72 0.79
42 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.33
Consensus pattern (41 bp):
ATTCGCGTTGCGAATTTGGAAAATCGCAATGCGATTTACAT
Found at i:50957 original size:13 final size:13
Alignment explanation
Indices: 50935--51013 Score: 51
Period size: 13 Copynumber: 6.5 Consensus size: 13
50925 ACGTTGAAAT
*
50935 TAAATGAATATAA
1 TAAATAAATATAA
50948 TAAATAAATATAA
1 TAAATAAATATAA
*
50961 T-AAT--AT-TAC
1 TAAATAAATATAA
* *
50970 TTATTAAATATAA
1 TAAATAAATATAA
* *
50983 TAAATAATTAAAA
1 TAAATAAATATAA
* *
50996 CATATAAATAT-A
1 TAAATAAATATAA
51008 TAAATA
1 TAAATA
51014 TAGTAATTAA
Statistics
Matches: 48, Mismatches: 14, Indels: 9
0.68 0.20 0.13
Matches are distributed among these distances:
9 3 0.06
10 4 0.08
12 10 0.21
13 31 0.65
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (13 bp):
TAAATAAATATAA
Found at i:57873 original size:22 final size:23
Alignment explanation
Indices: 57813--57866 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
57803 AGAACCCCAT
57813 GGGGGTATCGGTTCCCCTACAAA
1 GGGGGTATCGGTTCCCCTACAAA
* *
57836 GGGGGAATCGGTTCCCCTTC-AA
1 GGGGGTATCGGTTCCCCTACAAA
57858 GGGGGTATC
1 GGGGGTATC
57867 AATTCCCTCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.22
Consensus pattern (23 bp):
GGGGGTATCGGTTCCCCTACAAA
Found at i:67232 original size:20 final size:20
Alignment explanation
Indices: 67209--67248 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
67199 ATTTTGTTGC
67209 TAGAATTCACATTTATGGCA
1 TAGAATTCACATTTATGGCA
67229 TAGAATTCACATTTATGGCA
1 TAGAATTCACATTTATGGCA
67249 ATACCACGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (20 bp):
TAGAATTCACATTTATGGCA
Done.