Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006479.1 Hibiscus syriacus cultivar Beakdansim tig00015704_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: 99910
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4591 original size:29 final size:29
Alignment explanation
Indices: 4545--4620 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
4535 GCGATCAACC
* *
4545 ATTTAC-ATAAATATCACCCTTTTTAAAAT
1 ATTTACGA-AAATAGCACCCTTTTAAAAAT
*
4574 ATTTATGAAAATAGCACCCTTTTAAAAAT
1 ATTTACGAAAATAGCACCCTTTTAAAAAT
*
4603 ATTTACGAAACTAGCACC
1 ATTTACGAAAATAGCACC
4621 AGATCAACGG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 40 0.98
30 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.34
Consensus pattern (29 bp):
ATTTACGAAAATAGCACCCTTTTAAAAAT
Found at i:4654 original size:21 final size:21
Alignment explanation
Indices: 4628--4689 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
4618 ACCAGATCAA
4628 CGGTCAACGGTCGGGTCGGGT
1 CGGTCAACGGTCGGGTCGGGT
* *
4649 CGGTCAATGGTCGAGTCGGGT
1 CGGTCAACGGTCGGGTCGGGT
* *
4670 CGGGTCAACAGACGGGTCGG
1 C-GGTCAACGGTCGGGTCGG
4690 ACATGTTCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.15, C:0.23, G:0.45, T:0.18
Consensus pattern (21 bp):
CGGTCAACGGTCGGGTCGGGT
Found at i:7988 original size:46 final size:47
Alignment explanation
Indices: 7925--8016 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 47
7915 TAGAACATCT
*
7925 TAACTTCATGTCATCTAGTTCGCATAC-TTACTCAAGAAATTAAACC
1 TAACTGCATGTCATCTAGTTCGCATACATTACTCAAGAAATTAAACC
* *
7971 TAACTGCATGATC-TCTAGTTCGCATACATTTATTCGAGAAATTAAA
1 TAACTGCATG-TCATCTAGTTCGCATACA-TTACTCAAGAAATTAAA
8017 ATTACACTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 23 0.57
47 2 0.05
48 15 0.38
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.34
Consensus pattern (47 bp):
TAACTGCATGTCATCTAGTTCGCATACATTACTCAAGAAATTAAACC
Found at i:10271 original size:10 final size:9
Alignment explanation
Indices: 10248--10287 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
10238 GCTGCTGGAA
10248 ACCGGTTTG
1 ACCGGTTTG
10257 ACCGGTTTCG
1 ACCGGTTT-G
10267 ACCGGTTTG
1 ACCGGTTTG
*
10276 ACCGGTCTG
1 ACCGGTTTG
10285 ACC
1 ACC
10288 CGACCCGACC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 20 0.69
10 9 0.31
ACGTcount: A:0.12, C:0.30, G:0.30, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:10310 original size:22 final size:22
Alignment explanation
Indices: 10284--10326 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
10274 TGACCGGTCT
10284 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
10306 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
10327 GTTGACCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:10328 original size:7 final size:7
Alignment explanation
Indices: 10316--10347 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
10306 GACCCGACCC
10316 GACCGTT
1 GACCGTT
10323 GACCGTT
1 GACCGTT
10330 GACCGTT
1 GACCGTT
10337 GACCGTT
1 GACCGTT
10344 GACC
1 GACC
10348 TTCTTTGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.16, C:0.31, G:0.28, T:0.25
Consensus pattern (7 bp):
GACCGTT
Found at i:17685 original size:22 final size:22
Alignment explanation
Indices: 17659--17703 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
17649 CCCAACTAGA
17659 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
17681 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
17703 C
1 C
17704 GTTGACCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.51, G:0.22, T:0.09
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:20119 original size:33 final size:33
Alignment explanation
Indices: 20077--20142 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
20067 CAGGAAAAAT
*
20077 CAAGTAATTTGCACACAAATCAATCAAATTTTA
1 CAAGTAATTTACACACAAATCAATCAAATTTTA
20110 CAAGTAATTTACACACAAATCAATCAAATTTTA
1 CAAGTAATTTACACACAAATCAATCAAATTTTA
20143 AGTCCAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.30
Consensus pattern (33 bp):
CAAGTAATTTACACACAAATCAATCAAATTTTA
Found at i:23849 original size:11 final size:11
Alignment explanation
Indices: 23833--23857 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
23823 AGGCAATCCA
23833 TTTCATTTTAT
1 TTTCATTTTAT
23844 TTTCATTTTAT
1 TTTCATTTTAT
23855 TTT
1 TTT
23858 TTAGCAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCATTTTAT
Found at i:30019 original size:9 final size:9
Alignment explanation
Indices: 29995--30027 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
29985 TGTGACATTA
*
29995 TAATAAATA
1 TAATAAATT
30004 TAA-AAATT
1 TAATAAATT
30012 TAATAAATT
1 TAATAAATT
30021 TAATAAA
1 TAATAAA
30028 CATTTTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TAATAAATT
Found at i:30032 original size:11 final size:10
Alignment explanation
Indices: 30006--30050 Score: 56
Period size: 11 Copynumber: 4.4 Consensus size: 10
29996 AATAAATATA
30006 AAAATTTAAT
1 AAAATTTAAT
30016 -AAATTTAAT
1 AAAATTTAAT
*
30025 AAACATTTTAT
1 AAA-ATTTAAT
30036 AAAATTTCAAT
1 AAAATTT-AAT
30047 AAAA
1 AAAA
30051 ATTTGATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 9 0.30
10 6 0.20
11 15 0.50
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATTTAAT
Found at i:41780 original size:17 final size:16
Alignment explanation
Indices: 41755--41797 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
41745 GTTTTCAAAC
*
41755 TCTAATTATTATTTTAT
1 TCTATTTATTATTTT-T
41772 TCTATTTATTATTTTT
1 TCTATTTATTATTTTT
41788 TCTACTTTAT
1 TCTA-TTTAT
41798 CTTTATCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (16 bp):
TCTATTTATTATTTTT
Found at i:43819 original size:23 final size:23
Alignment explanation
Indices: 43784--43827 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
43774 CAAACAACAG
* * *
43784 AAAATATGTCATAGAGGCAGAGA
1 AAAACATGCCATAAAGGCAGAGA
43807 AAAACATGCCATAAAGGCAGA
1 AAAACATGCCATAAAGGCAGA
43828 AGAATACGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.14, G:0.23, T:0.14
Consensus pattern (23 bp):
AAAACATGCCATAAAGGCAGAGA
Found at i:48699 original size:2 final size:2
Alignment explanation
Indices: 48692--48730 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
48682 CACACTCTGT
48692 TA TA 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 TA TA T
48731 CTGAAAAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52337 original size:2 final size:2
Alignment explanation
Indices: 52330--52441 Score: 115
Period size: 2 Copynumber: 56.5 Consensus size: 2
52320 TTAATTTTAT
52330 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
* * * * *
52372 TA T- TA GCA T- TG TA TA TA TA TA TA T- TCC TA T- TT TCC TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA T-A TA TA TA T-A TA TA
*
52411 TT 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 T
52442 GTGTTTTTCT
Statistics
Matches: 95, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
1 4 0.04
2 88 0.93
3 3 0.03
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55195 original size:2 final size:2
Alignment explanation
Indices: 55188--55220 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
55178 CAGTTGTTGG
55188 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 T
55221 TCCTAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60434 original size:2 final size:2
Alignment explanation
Indices: 60427--60463 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
60417 CAGTTGTTGG
60427 TA 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 TA T
60464 TCATACTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:64063 original size:61 final size:63
Alignment explanation
Indices: 63943--64064 Score: 153
Period size: 61 Copynumber: 2.0 Consensus size: 63
63933 CTAATGTGAC
* **
63943 TCTTAGGTAGGCTCTGTGGCCCTGAGATCATTCTCGGGTAGGCCTCGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCTCTGTGGCCCCGAGATCATTCTCGGGTAGGCCTCGAAGCCCTAAGATGTGT
* *
64006 TCTTAGGTAGGC-CTCGTGGCCCCGA-A-CTTTCTTGGGTAGGCTCTC-AAGCCCTAAGATGT
1 TCTTAGGTAGGCTCT-GTGGCCCCGAGATCATTCTCGGGTAGGC-CTCGAAGCCCTAAGATGT
64065 TCCCTTAGGT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
61 25 0.48
62 6 0.12
63 21 0.40
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.29
Consensus pattern (63 bp):
TCTTAGGTAGGCTCTGTGGCCCCGAGATCATTCTCGGGTAGGCCTCGAAGCCCTAAGATGTGT
Found at i:67166 original size:16 final size:15
Alignment explanation
Indices: 67102--67169 Score: 59
Period size: 16 Copynumber: 4.5 Consensus size: 15
67092 GTAAAAAAAG
*
67102 CAAAAAG-AAAGCAA
1 CAAAAAGAAAAGGAA
* *
67116 -AAAGAGAAACAAGAA
1 CAAAAAGAAA-AGGAA
67131 CAAAAAGAAAAGGAA
1 CAAAAAGAAAAGGAA
*
67146 TCAAAAAGAAAAAGGGA
1 -CAAAAAG-AAAAGGAA
67163 CAAAAAG
1 CAAAAAG
67170 CACATGCAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 5 0.12
14 2 0.05
15 7 0.16
16 22 0.51
17 7 0.16
ACGTcount: A:0.71, C:0.09, G:0.19, T:0.01
Consensus pattern (15 bp):
CAAAAAGAAAAGGAA
Found at i:67793 original size:22 final size:22
Alignment explanation
Indices: 67765--67819 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
67755 GCTACCCCAT
67765 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
67787 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
67809 CAAACCTTTGA
1 CAAACCTTTGA
67820 CCAAACACGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:68742 original size:13 final size:13
Alignment explanation
Indices: 68724--68798 Score: 87
Period size: 13 Copynumber: 5.3 Consensus size: 13
68714 AACCCCACCC
68724 GACCCGACCCGTT
1 GACCCGACCCGTT
68737 GACCCGACCCCGTT
1 GACCCGA-CCCGTT
*
68751 GACCCGACCAGTT
1 GACCCGACCCGTT
68764 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
68782 GACCCGACCCGTT
1 GACCCGACCCGTT
68795 GACC
1 GACC
68799 GTTGTCCCGC
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
13 29 0.54
14 13 0.24
18 12 0.22
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:68743 original size:18 final size:18
Alignment explanation
Indices: 68720--68792 Score: 83
Period size: 18 Copynumber: 4.6 Consensus size: 18
68710 TCATAACCCC
68720 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
68738 ACCCGA--C--CCCGTTG
1 ACCCGACCCGACCCGTTG
68752 ACCCGA-CC-A---GTTG
1 ACCCGACCCGACCCGTTG
68765 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
68783 ACCCGACCCG
1 ACCCGACCCG
68793 TTGACCGTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
13 10 0.21
14 15 0.31
15 2 0.04
16 1 0.02
18 20 0.42
ACGTcount: A:0.18, C:0.49, G:0.22, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:68783 original size:31 final size:32
Alignment explanation
Indices: 68737--68798 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 32
68727 CCGACCCGTT
68737 GACCCGACCCCGTTGACCCGACCAGTTGACCC
1 GACCCGACCCCGTTGACCCGACCAGTTGACCC
*
68769 GACCCGA-CCCGTTGACCCGACCCGTTGACC
1 GACCCGACCCCGTTGACCCGACCAGTTGACC
68799 GTTGTCCCGC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 22 0.76
32 7 0.24
ACGTcount: A:0.18, C:0.47, G:0.23, T:0.13
Consensus pattern (32 bp):
GACCCGACCCCGTTGACCCGACCAGTTGACCC
Found at i:70119 original size:18 final size:18
Alignment explanation
Indices: 70093--70127 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
70083 TCGAAAGGAC
*
70093 TGAAATAAATGATAAGAT
1 TGAAATAAATAATAAGAT
*
70111 TGAATTAAATAATAAGA
1 TGAAATAAATAATAAGA
70128 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (18 bp):
TGAAATAAATAATAAGAT
Found at i:73288 original size:36 final size:36
Alignment explanation
Indices: 73193--73296 Score: 93
Period size: 36 Copynumber: 2.9 Consensus size: 36
73183 ATCACACTTG
* * **
73193 AGATTGTTTTTTTTAAAAC-AGACTTTGTCTCACTTG
1 AGATTGTTTTTCTTAAAACAAGA-TTTATCTCACTCA
* * ** * *
73229 AGACTGTTTTACTCGAAAGAAGATTTATTTCACTCA
1 AGATTGTTTTTCTTAAAACAAGATTTATCTCACTCA
73265 AGATTGTTTTTCTTAAAACAAGATTTTATCTC
1 AGATTGTTTTTCTTAAAACAAGA-TTTATCTC
73297 GCTTGAGATA
Statistics
Matches: 50, Mismatches: 16, Indels: 3
0.72 0.23 0.04
Matches are distributed among these distances:
36 40 0.80
37 10 0.20
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (36 bp):
AGATTGTTTTTCTTAAAACAAGATTTATCTCACTCA
Found at i:73317 original size:37 final size:37
Alignment explanation
Indices: 73276--73359 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 37
73266 GATTGTTTTT
* *
73276 CTTAAAACAAGATTTTATCTCGC-TTGAGATAGTTTCC
1 CTTAAAACAAAATTTTATCTC-CTTTGAGACAGTTTCC
* *
73313 CTTAAAACAAAATTTTGTCTCCTTTTGAGACAGTTTCT
1 CTTAAAACAAAATTTTATCTCC-TTTGAGACAGTTTCC
*
73351 CTTGAAACA
1 CTTAAAACA
73360 TAAACTTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
36 1 0.03
37 19 0.47
38 20 0.50
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (37 bp):
CTTAAAACAAAATTTTATCTCCTTTGAGACAGTTTCC
Found at i:73453 original size:36 final size:36
Alignment explanation
Indices: 73406--73528 Score: 185
Period size: 36 Copynumber: 3.4 Consensus size: 36
73396 TTGAATATGT
* *
73406 TTTCTCTTGAAATAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
73442 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
73478 TCTTC-CTTGAAACAAATTTTGTCTCCCTTGAGATAG
1 T-TTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
73514 TTTCTCTCGAAACAA
1 TTTCTCTTGAAACAA
73529 CACAATTTGC
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
35 3 0.04
36 74 0.93
37 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:73506 original size:21 final size:21
Alignment explanation
Indices: 73447--73508 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
73437 GACAGTTTCT
*
73447 CTTGAAACAAATTTTGTCTCT
1 CTTGAAACAAATTTTGTCTCC
* *
73468 CTTGAGAC--A----GTCTTC
1 CTTGAAACAAATTTTGTCTCC
73483 CTTGAAACAAATTTTGTCTCC
1 CTTGAAACAAATTTTGTCTCC
73504 CTTGA
1 CTTGA
73509 GATAGTTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 12
0.64 0.11 0.26
Matches are distributed among these distances:
15 11 0.37
17 1 0.03
19 1 0.03
21 17 0.57
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.39
Consensus pattern (21 bp):
CTTGAAACAAATTTTGTCTCC
Found at i:73920 original size:162 final size:165
Alignment explanation
Indices: 73733--74046 Score: 375
Period size: 174 Copynumber: 1.9 Consensus size: 165
73723 GGCCATCCGC
* **
73733 GATTTCAACTCCACGACGGAGGATAT-TGT-G-C-CACTTGAGACAACACAAGTTCAACTTCACA
1 GATTTCAACTCCACGACGAAGGATATAT-TAGCCACACTCAAGACAACACAAGTTCAACTTCACA
* * * * *
73794 GCGAAGGGATAGCTGGTTGTAAACAAACAATTTCCCAGTTCCAAAACCAATTTCAACTTCACGGC
65 ACGAAGGGACAGCTGGTTGTAAACAAACAACTTCCCAATTCCAAAACCAATTTCAACTTCACAGC
73859 GAAGGATATTGGACTCGGAGCAATACAACTTACTTA
130 GAAGGATATTGGACTCGGAGCAATACAACTTACTTA
*
73895 GATTTCAACTTCACGACGAAGGATATCCAATTACCAGGCTCAACACTCAAGACAACACAAGTTCA
1 GATTTCAACTCCACGACGAAGGATAT---ATT---A-GC-C-ACACTCAAGACAACACAAGTTCA
* * * * * *
73960 ACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAACTTCCCAATTTCAGAGCCAATTTCAAC
57 ACTTCACAACGAAGGGACAGCTGGTTGTAAACAAACAACTTCCCAATTCCAAAACCAATTTCAAC
74025 TTCACAGCGAAGGATATTGGAC
122 TTCACAGCGAAGGATATTGGAC
74047 GCGAGACAAC
Statistics
Matches: 124, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
162 24 0.19
165 1 0.01
166 1 0.01
170 1 0.01
172 1 0.01
174 96 0.77
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.23
Consensus pattern (165 bp):
GATTTCAACTCCACGACGAAGGATATATTAGCCACACTCAAGACAACACAAGTTCAACTTCACAA
CGAAGGGACAGCTGGTTGTAAACAAACAACTTCCCAATTCCAAAACCAATTTCAACTTCACAGCG
AAGGATATTGGACTCGGAGCAATACAACTTACTTA
Found at i:74071 original size:106 final size:106
Alignment explanation
Indices: 73944--74166 Score: 347
Period size: 106 Copynumber: 2.1 Consensus size: 106
73934 TCAACACTCA
* *
73944 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTC
*
74009 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACGCG
66 CAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACGCG
* * *
74050 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAAACAATTTCCCAGTTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTC
* * *
74115 CAGAACCAATTTCAACTTCACGGCGGAGGATATTGGACTCG
66 CAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACGCG
* *
74156 AAACAATACAA
1 AGACAACACAA
74167 CTTACTTGGA
Statistics
Matches: 106, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (106 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAATTC
CAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACGCG
Found at i:80792 original size:33 final size:33
Alignment explanation
Indices: 80750--80815 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
80740 CAGGAAAAAT
*
80750 CAAGTAATTTGCACACAAATCAATCAAATTTTA
1 CAAGTAATTTACACACAAATCAATCAAATTTTA
*
80783 CAAGTAATTTACACACAAATCAATTAAATTTTA
1 CAAGTAATTTACACACAAATCAATCAAATTTTA
80816 AGTCCAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.32
Consensus pattern (33 bp):
CAAGTAATTTACACACAAATCAATCAAATTTTA
Found at i:82883 original size:42 final size:42
Alignment explanation
Indices: 82749--82891 Score: 141
Period size: 41 Copynumber: 3.5 Consensus size: 42
82739 AGGTCTTATG
* * *
82749 GATGGCCCAAAGGACATAT-CATCTTGCTCTA-AAGACTTACA
1 GATGGCCCAAAGGACTTATGCATCATGCTC-AGAAGACTTACT
* * *
82790 GA-GGACCCAAAGGATTTATGCATCATACTTAGAA-ACTTACT
1 GATGG-CCCAAAGGACTTATGCATCATGCTCAGAAGACTTACT
* * * *
82831 GATGACCCGAAGGATTTATGCATCATGCTCGGAAGACTTACT
1 GATGGCCCAAAGGACTTATGCATCATGCTCAGAAGACTTACT
*
82873 GATGGCCCGAAGGACTTAT
1 GATGGCCCAAAGGACTTAT
82892 AAATTTTGGA
Statistics
Matches: 84, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
40 2 0.02
41 48 0.57
42 34 0.40
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (42 bp):
GATGGCCCAAAGGACTTATGCATCATGCTCAGAAGACTTACT
Found at i:83198 original size:231 final size:231
Alignment explanation
Indices: 82824--83537 Score: 1248
Period size: 231 Copynumber: 3.1 Consensus size: 231
82814 ATACTTAGAA
* * *
82824 ACTTACTGATGACCCGAAGGATTTATGCATCATGCTCGGAAGACTTACTGATGGCCCGAAGGACT
1 ACTTACAGATGACCCGAAGGATTTATGCATCACGCTAGGAAGACTTACTGATGGCCCGAAGGACT
82889 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAATAATTTCAATTTCA
66 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAATAATTTCAATTTCA
*
82954 GATTTAAATGAGAAACCTTTCTCATTTCATGATAGACATTTGAAAACATCCTACCAAATGTCTTA
131 GATTTAAATGAGAAACCTTTCTCATTTCATGATAGACATTTGAAAACATCCTACCAAAGGTCTTA
83019 TGGATGGCCCAAAGGACTAATCATCTTGCTCGAAAG
196 TGGATGGCCCAAAGGACTAATCATCTTGCTCGAAAG
** *
83055 ACTTACAGATGACCCGAAGGATTTATGCATCACAATAGGAAGACTTACTGATGGCCTGAAGGACT
1 ACTTACAGATGACCCGAAGGATTTATGCATCACGCTAGGAAGACTTACTGATGGCCCGAAGGACT
83120 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAATAATTTCAATTTCA
66 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAATAATTTCAATTTCA
*
83185 GATTTAAATGAGAAACCTTTCTCATTTCATGATAGACATTTGAAAACATCATACCAAAGGTCTTA
131 GATTTAAATGAGAAACCTTTCTCATTTCATGATAGACATTTGAAAACATCCTACCAAAGGTCTTA
83250 TGGATGGCCCAAAGGACTAATCATCTTGCTCGAAAG
196 TGGATGGCCCAAAGGACTAATCATCTTGCTCGAAAG
83286 ACTTACAGATGACCCGAAGGATTTATGCATCACGCTAGGAAGACTTACTGATGGCCCGAAGGACT
1 ACTTACAGATGACCCGAAGGATTTATGCATCACGCTAGGAAGACTTACTGATGGCCCGAAGGACT
* * * *
83351 TATAAATTTTTGAAATAATTTACAAGGTAAGAAACCTTTCTTATTTTTCAATAATTTCAATTTCA
66 TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAATAATTTCAATTTCA
* * *
83416 TACTTAAATGAGAAACCTTTCTCATTTCATGATAGGCATTTGAAAACATCCTACCAAAGGTCTTA
131 GATTTAAATGAGAAACCTTTCTCATTTCATGATAGACATTTGAAAACATCCTACCAAAGGTCTTA
* * *
83481 TGGATGGCCCAAACGACTTATCATCTTGCTCGGAAG
196 TGGATGGCCCAAAGGACTAATCATCTTGCTCGAAAG
* *
83517 ACTTACTGATGGCCCGAAGGA
1 ACTTACAGATGACCCGAAGGA
83538 CATATAAATT
Statistics
Matches: 459, Mismatches: 24, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
231 459 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (231 bp):
ACTTACAGATGACCCGAAGGATTTATGCATCACGCTAGGAAGACTTACTGATGGCCCGAAGGACT
TATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAATAATTTCAATTTCA
GATTTAAATGAGAAACCTTTCTCATTTCATGATAGACATTTGAAAACATCCTACCAAAGGTCTTA
TGGATGGCCCAAAGGACTAATCATCTTGCTCGAAAG
Found at i:86968 original size:29 final size:29
Alignment explanation
Indices: 86908--87006 Score: 135
Period size: 29 Copynumber: 3.4 Consensus size: 29
86898 CATTTTACAC
**
86908 AAATATCACCCTTTTAAAAAATATTTGGGA
1 AAATATCACCCTTTT-AAAAATATTTACGA
*
86938 AAATAACACCCTTTTAAAAATATTTACGA
1 AAATATCACCCTTTTAAAAATATTTACGA
*
86967 AAATATCACCCTTTTAAAAATATTTATGA
1 AAATATCACCCTTTTAAAAATATTTACGA
* *
86996 AACTAGCACCC
1 AAATATCACCC
87007 GATCAACGGT
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
29 48 0.77
30 14 0.23
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.31
Consensus pattern (29 bp):
AAATATCACCCTTTTAAAAATATTTACGA
Found at i:94091 original size:29 final size:30
Alignment explanation
Indices: 94037--94105 Score: 104
Period size: 29 Copynumber: 2.3 Consensus size: 30
94027 CATTTTACAT
* *
94037 AAATATCACCCTTTTTAAAAATATTTATGA
1 AAATAGCACCCTTTTTAAAAATATTTACGA
94067 AAATAGCACCC-TTTTAAAAATATTTACGA
1 AAATAGCACCCTTTTTAAAAATATTTACGA
*
94096 AACTAGCACC
1 AAATAGCACC
94106 AGATCAACGG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 26 0.72
30 10 0.28
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (30 bp):
AAATAGCACCCTTTTTAAAAATATTTACGA
Found at i:94139 original size:21 final size:21
Alignment explanation
Indices: 94113--94174 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
94103 ACCAGATCAA
94113 CGGTCAACGGTCGGGTCGGGT
1 CGGTCAACGGTCGGGTCGGGT
* *
94134 CGGTCAATGGTCGAGTCGGGT
1 CGGTCAACGGTCGGGTCGGGT
* *
94155 CGGGTCAACAGACGGGTCGG
1 C-GGTCAACGGTCGGGTCGG
94175 ACATGTTCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.15, C:0.23, G:0.45, T:0.18
Consensus pattern (21 bp):
CGGTCAACGGTCGGGTCGGGT
Found at i:97476 original size:46 final size:47
Alignment explanation
Indices: 97413--97504 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 47
97403 TAGAACATCT
*
97413 TAACTTCATGTCATCTAGTTCGCATAC-TTACTCAAGAAATTAAACC
1 TAACTGCATGTCATCTAGTTCGCATACATTACTCAAGAAATTAAACC
* *
97459 TAACTGCATGATC-TCTAGTTCGCATACATTTATTCGAGAAATTAAA
1 TAACTGCATG-TCATCTAGTTCGCATACA-TTACTCAAGAAATTAAA
97505 ATTACACTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 23 0.57
47 2 0.05
48 15 0.38
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.34
Consensus pattern (47 bp):
TAACTGCATGTCATCTAGTTCGCATACATTACTCAAGAAATTAAACC
Found at i:99778 original size:21 final size:21
Alignment explanation
Indices: 99753--99793 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
99743 GACCCGTCTG
99753 ACCCGACCCGACCGTTGACCC
1 ACCCGACCCGACCGTTGACCC
99774 ACCCGACCCGACCGTTGACC
1 ACCCGACCCGACCGTTGACC
99794 ATTGACCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.51, G:0.20, T:0.10
Consensus pattern (21 bp):
ACCCGACCCGACCGTTGACCC
Found at i:99779 original size:16 final size:18
Alignment explanation
Indices: 99746--99781 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
99736 CGGTTTCGAC
99746 CCGTCTGACCCGACCCGA
1 CCGTCTGACCCGACCCGA
99764 CCGT-TGACCC-ACCCGA
1 CCGTCTGACCCGACCCGA
99780 CC
1 CC
99782 CGACCGTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 6 0.33
18 4 0.22
ACGTcount: A:0.17, C:0.53, G:0.19, T:0.11
Consensus pattern (18 bp):
CCGTCTGACCCGACCCGA
Done.