Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004506.1 Hibiscus syriacus cultivar Beakdansim tig00009940_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: 64418
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:144 original size:17 final size:19
Alignment explanation
Indices: 103--149 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
93 ACTTAAGGGG
*
103 GTGCATCGATACACTACTT
1 GTGCATCGATACACTACTA
122 GTGCATCGATACACT-C-A
1 GTGCATCGATACACTACTA
139 GTGCATTCGAT
1 GTGCA-TCGAT
150 GTTTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 5 0.19
18 6 0.23
19 15 0.58
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (19 bp):
GTGCATCGATACACTACTA
Found at i:2830 original size:488 final size:489
Alignment explanation
Indices: 1802--3258 Score: 2576
Period size: 488 Copynumber: 3.0 Consensus size: 489
1792 AGACACTATC
* * *
1802 GATATCGACACTCCTTGCAATCTAACTATTTCTTTTATAAATATCTCAGCATACTAATCCATTGG
1 GATATCGACACTCCATGCAATCTAACTATTTCTTTTATAAATATCTCAGCATACTTATCCATCGG
*
1867 GTAATCTACTCT-ACTGGAATAAAATA---ATTTTGGTCAATCGATCTATAATTACCCATATCGA
66 GTAATCTACTCTAACTGGAATAAAATAGCTGTTTTGGTCAATCGATCTATAATTACCCATATCGA
* * *
1928 GTCCTTTTTACCTAGTGACAAAGGTAGCCTCGAAACAAAATCCATTATAACTCGCTCCCACTTCC
131 GTCCTTTTTACCTGGTGACAAAGGTAGCCCCGAAACAAAATCCATTGTAACTCGCTCCCACTTCC
*
1993 ATTCAGGAATAGACATTGTTTGTAGTAGTCCAAAAGGTACTTGATGTTCAACTTTCACTTGCTGA
196 ATTCAGGAATAGACATTGTTTGTAGTAGTCCAGAAGGTACTTGATGTTCAACTTTCACTTGCTGA
* *
2058 CATGTCAAACATTTTGCAACAAACTCTGTTACAACTC-TTTCATACTCGACCACCAATAACGACT
261 CATGTCAAACATTTTGCAACAAACTCTGTTACAACTCTTTTCATACCCGGCCACCAATAACGACT
* * *
2122 CTTTAAGCCTTGATACATCTTATTTCCACCGGGATGCATCGTCAACAGACTGTAATACGCCTCGT
326 CTTTAAGTCTTGATACATCTTATTTCCACCGGGATGCATCGTCAACAGACTGTAATGCGCCTCGC
*
2187 AAAAAATTTCTTTCCTCATCCTCAAGAATACAAAGTCTTCCTCGATAATATAAACATCAATTATC
391 AAAAAATTTCTTTCCTCATCCTCAAGAATACAAAGTCTTCCTCGATAATATAAACATCCATTATC
2252 CCTTATTTCAAAATCTTTAATTTCTTCATTTTCA
456 CCTTATTTCAAAATCTTTAATTTCTTCATTTTCA
*
2286 GATATCGGCACTCCATGCAATCTAACTATTTCTTTTATAAATATCTCAGCATACTTATCCATCGG
1 GATATCGACACTCCATGCAATCTAACTATTTCTTTTATAAATATCTCAGCATACTTATCCATCGG
2351 GTAATCTACTCTAACTGGAATAAAATGAGCTGTTTTGGTCAATCGATCTAT-ATTACCCATATCG
66 GTAATCTACTCTAACTGGAATAAAAT-AGCTGTTTTGGTCAATCGATCTATAATTACCCATATCG
2415 AGTCCTTTTTACCTGGTGACAAAGGTAGCCCCGAAACAAAATCCATTGTAACTCGCTCCCACTTC
130 AGTCCTTTTTACCTGGTGACAAAGGTAGCCCCGAAACAAAATCCATTGTAACTCGCTCCCACTTC
*
2480 CATTCAGGAATAAACATTGTTTGTAGTAGTCCAGAAGGTACTTGATGTTCAACTTTCACTTGCTG
195 CATTCAGGAATAGACATTGTTTGTAGTAGTCCAGAAGGTACTTGATGTTCAACTTTCACTTGCTG
* * * *
2545 ACATGTCAAACATTTTGCAATAAACTCTATTATAACTCTTTTCATACCCGGCCACCTATAACGAC
260 ACATGTCAAACATTTTGCAACAAACTCTGTTACAACTCTTTTCATACCCGGCCACCAATAACGAC
*
2610 TCTTTAAGTCTTGATACATCTTATTTCCACCGGGATGCATCGTCAACAAACTGTAATGCGCCTCG
325 TCTTTAAGTCTTGATACATCTTATTTCCACCGGGATGCATCGTCAACAGACTGTAATGCGCCTCG
*
2675 CAAAAAATTTCTTTCCTCATCCTCAAGAATACAAAGTCTTCCTCGATAATATAAATATCCATTAT
390 CAAAAAATTTCTTTCCTCATCCTCAAGAATACAAAGTCTTCCTCGATAATATAAACATCCATTAT
2740 CCCTTATTTCAAAATCTTTAATTTCTTCATTTTCA
455 CCCTTATTTCAAAATCTTTAATTTCTTCATTTTCA
*
2775 GATATCGACACTCCATGCAATCTAACTATTTCTTTTAT-AATATCTCAGTATACTTATCCATCGG
1 GATATCGACACTCCATGCAATCTAACTATTTCTTTTATAAATATCTCAGCATACTTATCCATCGG
2839 GTAATCTACTCTAACTGGAAT-AAATAAGCTGTTTTGGTCAATCGATCTATAATTACCCATATCG
66 GTAATCTACTCTAACTGGAATAAAAT-AGCTGTTTTGGTCAATCGATCTATAATTACCCATATCG
2903 AGTCCTTTTTACCTGGTGACAAAGGTAGCCCCGAAACAAAATCCATTGTAACTCGCTCCCACTTC
130 AGTCCTTTTTACCTGGTGACAAAGGTAGCCCCGAAACAAAATCCATTGTAACTCGCTCCCACTTC
2968 CATTCAGGAATAGACATTGTTTGTAGTAGTCCAGAAGGTACTTGATGTTCAACTTTCACTTGCTG
195 CATTCAGGAATAGACATTGTTTGTAGTAGTCCAGAAGGTACTTGATGTTCAACTTTCACTTGCTG
* *
3033 ACATGTCAAACATTTGGCAACAAACTCTGTTACATCTCTTTTCATACCCGGCCACCAATAACGAC
260 ACATGTCAAACATTTTGCAACAAACTCTGTTACAACTCTTTTCATACCCGGCCACCAATAACGAC
*
3098 TCTTTAAGTCTTGATACATCTTATTTCCACCGGGATGCATCGTCAACGGAC--TAATGCGCCTCG
325 TCTTTAAGTCTTGATACATCTTATTTCCACCGGGATGCATCGTCAACAGACTGTAATGCGCCTCG
3161 CAAAAAA-TTCTTTCCTCATCCTCAAGAATACAAAGTCTTCCTCGATAATATAAACATCCATTAT
390 CAAAAAATTTCTTTCCTCATCCTCAAGAATACAAAGTCTTCCTCGATAATATAAACATCCATTAT
*
3225 CCCTTATTTCAAAATTTTTAATTTCTTCATTTTC
455 CCCTTATTTCAAAATCTTTAATTTCTTCATTTTC
3259 GACTAGCTTC
Statistics
Matches: 930, Mismatches: 36, Indels: 13
0.95 0.04 0.01
Matches are distributed among these distances:
484 73 0.08
485 102 0.11
486 20 0.02
487 28 0.03
488 469 0.50
489 238 0.26
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (489 bp):
GATATCGACACTCCATGCAATCTAACTATTTCTTTTATAAATATCTCAGCATACTTATCCATCGG
GTAATCTACTCTAACTGGAATAAAATAGCTGTTTTGGTCAATCGATCTATAATTACCCATATCGA
GTCCTTTTTACCTGGTGACAAAGGTAGCCCCGAAACAAAATCCATTGTAACTCGCTCCCACTTCC
ATTCAGGAATAGACATTGTTTGTAGTAGTCCAGAAGGTACTTGATGTTCAACTTTCACTTGCTGA
CATGTCAAACATTTTGCAACAAACTCTGTTACAACTCTTTTCATACCCGGCCACCAATAACGACT
CTTTAAGTCTTGATACATCTTATTTCCACCGGGATGCATCGTCAACAGACTGTAATGCGCCTCGC
AAAAAATTTCTTTCCTCATCCTCAAGAATACAAAGTCTTCCTCGATAATATAAACATCCATTATC
CCTTATTTCAAAATCTTTAATTTCTTCATTTTCA
Found at i:3753 original size:31 final size:26
Alignment explanation
Indices: 3683--3747 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
3673 GTCTGGACGT
3683 ATAAGC-CACAACCTTTCCTTCTTGC
1 ATAAGCACACAACCTTTCCTTCTTGC
3708 ATAAGCACACAACCTTTCCTTCTTGC
1 ATAAGCACACAACCTTTCCTTCTTGC
3734 ATAAGCACACAACC
1 ATAAGCACACAACC
3748 CAACCTATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
25 6 0.15
26 33 0.85
ACGTcount: A:0.31, C:0.35, G:0.08, T:0.26
Consensus pattern (26 bp):
ATAAGCACACAACCTTTCCTTCTTGC
Found at i:5557 original size:28 final size:28
Alignment explanation
Indices: 5517--5576 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
5507 TTGCCACACG
5517 TCTGACAAAAAGGTTTTTCTCTATGAGC
1 TCTGACAAAAAGGTTTTTCTCTATGAGC
5545 TCTGACAAAAAGGTTTTTCTCTATGAGC
1 TCTGACAAAAAGGTTTTTCTCTATGAGC
5573 TCTG
1 TCTG
5577 CAGAATAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (28 bp):
TCTGACAAAAAGGTTTTTCTCTATGAGC
Found at i:7708 original size:59 final size:59
Alignment explanation
Indices: 7582--7709 Score: 147
Period size: 59 Copynumber: 2.2 Consensus size: 59
7572 CTTCCCATTT
* * **
7582 CATT-TAGCACA-CAAAGTGCCCTATTCGAATATCCATACCATTAGTAGGATTTTGTTAC
1 CATTGTAGCACATGAAA-TGCCCTATTCGAAAATCCATACCATTAGTAGGATTTCCTTAC
* *
7640 CATTTTAGCACATGAAATGCCCTATGT-GAAAATCCATACCATTAGTATGATTTCCTTATC
1 CATTGTAGCACATGAAATGCCCTAT-TCGAAAATCCATACCATTAGTAGGATTTCCTTA-C
7700 C-TTGTAGCAC
1 CATTGTAGCAC
7710 CCTTAGTGCT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
58 4 0.07
59 50 0.83
60 6 0.10
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (59 bp):
CATTGTAGCACATGAAATGCCCTATTCGAAAATCCATACCATTAGTAGGATTTCCTTAC
Found at i:7732 original size:59 final size:59
Alignment explanation
Indices: 7669--7953 Score: 285
Period size: 59 Copynumber: 4.8 Consensus size: 59
7659 CCCTATGTGA
* * * * *
7669 AAATCCATAC-CATTAGTATGATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTATCTGG
1 AAATCCATACAC-TTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCTTCATATGG
* * * * ** * * *
7728 AAATCCATACACTCAGTATGATTCCCTTACCATTTTAGTACA-TATAACGC-CCTATCTAG
1 AAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACT-TAGTGCTTC-ATATGG
* * * *
7787 AAATTCATATA-TTCAATATGATTTCCTTATCA-TTTAGCACACTCAGTGCTTCATATGG
1 AAATCCATACACTT-AGTATGATTTCCTTATCATTTTAGCACACTTAGTGCTTCATATGG
*
7845 AAATCCATACACTTAGTAGGATTTCCTTATCATTTTAGCACACTTAGTGCTTCATATGG
1 AAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCTTCATATGG
* * *
7904 AAATTCATACACTCAGTATGATTTCTTTATCATTTTAGCACA-TATAGTGC
1 AAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACT-TAGTGC
7954 CATTTGGTAA
Statistics
Matches: 183, Mismatches: 34, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
58 43 0.23
59 139 0.76
60 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (59 bp):
AAATCCATACACTTAGTATGATTTCCTTATCATTTTAGCACACTTAGTGCTTCATATGG
Found at i:7758 original size:118 final size:117
Alignment explanation
Indices: 7636--7886 Score: 310
Period size: 117 Copynumber: 2.1 Consensus size: 117
7626 TAGGATTTTG
* * *
7636 TTACCATTTTAGCACATGA-AATGCCCTATGT-GAAAATCCATACCATT-AGTATGATTTCCTTA
1 TTACCATTTTAGCACAT-ATAACGCCCTATCTAG-AAATCCATA-CATTCAATATGATTTCCTTA
* * * * * *
7698 TCCTTGTAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTCAGTATGATTCCC
63 TCATT-TAGCACACTCAGTGCTTCATATGGAAATCCATACACTCAGTAGGATTCCC
* * *
7754 TTACCATTTTAGTACATATAACGCCCTATCTAGAAATTCATATATTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATATAACGCCCTATCTAGAAATCCATACATTCAATATGATTTCCTTATCA
* *
7819 TTTAGCACACTCAGTGCTTCATATGGAAATCCATACACTTAGTAGGATTTCC
66 TTTAGCACACTCAGTGCTTCATATGGAAATCCATACACTCAGTAGGATTCCC
*
7871 TTATCATTTTAGCACA
1 TTACCATTTTAGCACA
7887 CTTAGTGCTT
Statistics
Matches: 114, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
117 61 0.54
118 52 0.46
119 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (117 bp):
TTACCATTTTAGCACATATAACGCCCTATCTAGAAATCCATACATTCAATATGATTTCCTTATCA
TTTAGCACACTCAGTGCTTCATATGGAAATCCATACACTCAGTAGGATTCCC
Found at i:7873 original size:117 final size:118
Alignment explanation
Indices: 7612--7886 Score: 326
Period size: 118 Copynumber: 2.3 Consensus size: 118
7602 CTATTCGAAT
** * *
7612 ATCCATAC-CATTAGTAGGATTTTGTTACCATTTTAGCACATGAAATGCCCTATGTGAAAATCCA
1 ATCCATACAC-TTAGTAGGATTTCCTTACCATTTTAGCACATGAAACGCCCTATCTGAAAATCCA
* * * * * *
7676 TACCATTAGTATGATTTCCTTATCCTTGTAGCACCCTTAGTGCTTTATCTGGAA
65 TACCATTAATATGATTTCCTTATCATTGTAGCACACTCAGTGCTTCATATGGAA
* * * * *
7730 ATCCATACACTCAGTATGATTCCCTTACCATTTTAGTACAT-ATAACGCCCTATCT-AGAAATTC
1 ATCCATACACTTAGTAGGATTTCCTTACCATTTTAGCACATGA-AACGCCCTATCTGA-AAATCC
*
7793 ATA-TATTCAATATGATTTCCTTATCATT-TAGCACACTCAGTGCTTCATATGGAA
64 ATACCATT-AATATGATTTCCTTATCATTGTAGCACACTCAGTGCTTCATATGGAA
*
7847 ATCCATACACTTAGTAGGATTTCCTTATCATTTTAGCACA
1 ATCCATACACTTAGTAGGATTTCCTTACCATTTTAGCACA
7887 CTTAGTGCTT
Statistics
Matches: 132, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
117 62 0.47
118 69 0.52
119 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (118 bp):
ATCCATACACTTAGTAGGATTTCCTTACCATTTTAGCACATGAAACGCCCTATCTGAAAATCCAT
ACCATTAATATGATTTCCTTATCATTGTAGCACACTCAGTGCTTCATATGGAA
Found at i:7910 original size:117 final size:117
Alignment explanation
Indices: 7636--7945 Score: 306
Period size: 117 Copynumber: 2.6 Consensus size: 117
7626 TAGGATTTTG
* * * * *
7636 TTACCATTTTAGCACATGA-AATGCCCTATGT-GAAAATCCATAC-CATTAGTATGATTTCCTTA
1 TTACCATTTTAGCACAT-ATAACGCCCTATATAG-AAATTCATACAC-TCAATATGATTTCCTTA
* * * * * *
7698 TCCTTGTAGCACCCTTAGTGCTTTATCTGGAAATCCATACACTCAGTATGATTCCC
63 TCATT-TAGCACACTCAGTGCTTCATATGGAAATCCATACACTCAGTAGGATTCCC
* * * *
7754 TTACCATTTTAGTACATATAACGCCCTATCTAGAAATTCATATATTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATATAACGCCCTATATAGAAATTCATACACTCAATATGATTTCCTTATCA
* *
7819 TTTAGCACACTCAGTGCTTCATATGGAAATCCATACACTTAGTAGGATTTCC
66 TTTAGCACACTCAGTGCTTCATATGGAAATCCATACACTCAGTAGGATTCCC
* ** * * * *
7871 TTATCATTTTAGCACACT-TAGTG-CTTCATATGGAAATTCATACACTCAGTATGATTTCTTTAT
1 TTACCATTTTAGCACA-TATAACGCCCT-ATATAGAAATTCATACACTCAATATGATTTCCTTAT
7934 CATTTTAGCACA
64 CA-TTTAGCACA
7946 TATAGTGCCA
Statistics
Matches: 159, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
116 2 0.01
117 93 0.58
118 63 0.40
119 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (117 bp):
TTACCATTTTAGCACATATAACGCCCTATATAGAAATTCATACACTCAATATGATTTCCTTATCA
TTTAGCACACTCAGTGCTTCATATGGAAATCCATACACTCAGTAGGATTCCC
Found at i:12893 original size:2 final size:2
Alignment explanation
Indices: 12884--12926 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
12874 ATATAAACTC
12884 AT AT -T 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
12925 AT
1 AT
12927 GTATGTATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:14701 original size:13 final size:13
Alignment explanation
Indices: 14685--14711 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
14675 AAATCAGCAT
14685 AAAAATAAAATAA
1 AAAAATAAAATAA
14698 AAAAATAAAATAA
1 AAAAATAAAATAA
14711 A
1 A
14712 TGTTACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:16199 original size:14 final size:13
Alignment explanation
Indices: 16170--16210 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
16160 TAAAAGTAAG
*
16170 ATAATA-ATAATA
1 ATAATATATACTA
16182 ATAATATCATACTA
1 ATAATAT-ATACTA
16196 ATAATATATAC-A
1 ATAATATATACTA
16208 ATA
1 ATA
16211 TGGGCTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 10 0.38
13 4 0.15
14 12 0.46
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAATATATACTA
Found at i:16252 original size:17 final size:18
Alignment explanation
Indices: 16218--16256 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
16208 ATATGGGCTA
*
16218 ATATATTTTACTATATAAT
1 ATATATTTTAC-AAATAAT
16237 ATATATTTTA-AAATAAT
1 ATATATTTTACAAATAAT
16254 ATA
1 ATA
16257 CTTACTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
19 10 0.53
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATATTTTACAAATAAT
Found at i:16334 original size:32 final size:34
Alignment explanation
Indices: 16235--16339 Score: 119
Period size: 31 Copynumber: 3.1 Consensus size: 34
16225 TTACTATATA
* *
16235 ATATATATTTTAAAATAATATACT-TACTATTATACT
1 ATATATATTTTAAAA-ACTATA-TATA-TAATATACT
*
16271 ATATATATTTTTAAAAACTATACATAT-ATATA-T
1 ATATATA-TTTTAAAAACTATATATATAATATACT
16304 A-ATATATTTTAAAAACTATATATATAATATACT
1 ATATATATTTTAAAAACTATATATATAATATACT
16337 ATA
1 ATA
16340 AGATTAAAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
31 18 0.30
32 10 0.17
33 4 0.07
34 5 0.08
35 1 0.02
36 14 0.23
37 8 0.13
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.45
Consensus pattern (34 bp):
ATATATATTTTAAAAACTATATATATAATATACT
Found at i:16350 original size:30 final size:31
Alignment explanation
Indices: 16281--16348 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
16271 ATATATATTT
**
16281 TTAAAAACTATACATATATATATAATATATT
1 TTAAAAACTATACATATATATATAATATAGA
* *
16312 TTAAAAACTATATATATA-ATATACTATAAGA
1 TTAAAAACTATACATATATATATAATAT-AGA
16343 TTAAAA
1 TTAAAA
16349 CTTGAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 8 0.25
31 24 0.75
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.38
Consensus pattern (31 bp):
TTAAAAACTATACATATATATATAATATAGA
Found at i:16837 original size:40 final size:40
Alignment explanation
Indices: 16777--16865 Score: 151
Period size: 40 Copynumber: 2.2 Consensus size: 40
16767 TCTTTCTGAT
* *
16777 GGATGCTAAATCAGGGGACGATCTTACTCATTCCTTTGAA
1 GGATGCTAAATCAGGAGACGATCTCACTCATTCCTTTGAA
*
16817 GGATGCTAAATCAGGAGACGATCTCACTTATTCCTTTGAA
1 GGATGCTAAATCAGGAGACGATCTCACTCATTCCTTTGAA
16857 GGATGCTAA
1 GGATGCTAA
16866 GTTGTAGGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (40 bp):
GGATGCTAAATCAGGAGACGATCTCACTCATTCCTTTGAA
Found at i:21759 original size:2 final size:2
Alignment explanation
Indices: 21752--21780 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
21742 AAGTAAAGGA
21752 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21781 CTCACACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22933 original size:20 final size:21
Alignment explanation
Indices: 22905--22959 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
22895 GAGATTTGTA
* *
22905 GTATCGATACCCA-ATGCTCG
1 GTATTGATACCCAGATACTCG
*
22925 GTATTGATA-CTAGATACTCG
1 GTATTGATACCCAGATACTCG
22945 GTATTGATA-CCAGAT
1 GTATTGATACCCAGAT
22960 GCTTGTTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (21 bp):
GTATTGATACCCAGATACTCG
Found at i:30271 original size:21 final size:22
Alignment explanation
Indices: 30248--30323 Score: 83
Period size: 21 Copynumber: 3.7 Consensus size: 22
30238 TTTTTTTAAT
*
30248 TTAATTATATATTTAATTTTT-
1 TTAATTTTATATTTAATTTTTA
30269 TT-A--TTA-ATTTAATTTTTA
1 TTAATTTTATATTTAATTTTTA
*
30287 GTAATTTTATATTT-ATTTTTA
1 TTAATTTTATATTTAATTTTTA
*
30308 TTAATTTTAAATTTAA
1 TTAATTTTATATTTAA
30324 AAGATTTGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
17 11 0.24
18 3 0.07
19 1 0.02
20 1 0.02
21 24 0.53
22 5 0.11
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (22 bp):
TTAATTTTATATTTAATTTTTA
Found at i:30294 original size:26 final size:26
Alignment explanation
Indices: 30224--30304 Score: 65
Period size: 26 Copynumber: 3.0 Consensus size: 26
30214 ATTTATTTTA
*
30224 AATTTTTAATAGTATTTTT-TTAATTT
1 AATTTTTAATAAT-TTTTTATTAATTT
* *
30250 AATTATATATTTAATTTTTTTATTAATTT
1 AATT-TTTA-ATAA-TTTTTTATTAATTT
* * *
30279 AATTTTTAGTAATTTTATATTTATTT
1 AATTTTTAATAATTTTTTATTAATTT
30305 TTATTAATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
26 16 0.36
27 6 0.14
28 10 0.23
29 12 0.27
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
AATTTTTAATAATTTTTTATTAATTT
Found at i:30316 original size:15 final size:15
Alignment explanation
Indices: 30237--30303 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 15
30227 TTTTAATAGT
30237 ATTTTT-TTAATTTA
1 ATTTTTATTAATTTA
*
30251 A-TTATA-T-ATTTA
1 ATTTTTATTAATTTA
30263 ATTTTTTTATTAATTTA
1 A--TTTTTATTAATTTA
* *
30280 ATTTTTAGTAATTTT
1 ATTTTTATTAATTTA
*
30295 ATATTTATT
1 ATTTTTATT
30304 TTTATTAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
12 6 0.15
13 4 0.10
14 1 0.02
15 23 0.56
16 1 0.02
17 6 0.15
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (15 bp):
ATTTTTATTAATTTA
Found at i:30323 original size:12 final size:12
Alignment explanation
Indices: 30241--30323 Score: 52
Period size: 10 Copynumber: 7.0 Consensus size: 12
30231 AATAGTATTT
30241 TTTTA-ATTTAA
1 TTTTATATTTAA
*
30252 TTATATATTTAA
1 TTTTATATTTAA
30264 TTTTTTTATTAATTTAA
1 ---TTTTA-T-ATTTAA
*
30281 TTTT-TA-GTAA
1 TTTTATATTTAA
30291 TTTTATATTT-A
1 TTTTATATTTAA
30302 TTTT-TA-TTAA
1 TTTTATATTTAA
*
30312 TTTTAAATTTAA
1 TTTTATATTTAA
30324 AAGATTTGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 21
0.68 0.06 0.26
Matches are distributed among these distances:
9 2 0.04
10 14 0.25
11 13 0.23
12 12 0.21
14 4 0.07
15 4 0.07
16 1 0.02
17 6 0.11
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:30538 original size:24 final size:24
Alignment explanation
Indices: 30506--30553 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
30496 TTGGGTTATT
30506 CTACAAGACTTAATTCAAATGTTG
1 CTACAAGACTTAATTCAAATGTTG
30530 CTACAAGACTTAATTCAAATGTTG
1 CTACAAGACTTAATTCAAATGTTG
30554 TTCTTCACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (24 bp):
CTACAAGACTTAATTCAAATGTTG
Found at i:33672 original size:29 final size:29
Alignment explanation
Indices: 33633--33716 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
33623 TTAGAGTAAG
* *
33633 GACGGGGATATAATCCCATGCAGAATCAA
1 GACGGGAATATAATCCCATGCAAAATCAA
* *
33662 GATGGGAATATAATCTCC-TGCAAAATTAA
1 GACGGGAATATAATC-CCATGCAAAATCAA
*
33691 GACGGGGATATAATCCCATGCAAAAT
1 GACGGGAATATAATCCCATGCAAAAT
33717 AAAAAATGCA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.04
29 43 0.91
30 2 0.04
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (29 bp):
GACGGGAATATAATCCCATGCAAAATCAA
Found at i:37101 original size:11 final size:11
Alignment explanation
Indices: 37085--37111 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
37075 TTTTTTTTTC
37085 AAAAAAACAAA
1 AAAAAAACAAA
37096 AAAAAAACAAA
1 AAAAAAACAAA
37107 AAAAA
1 AAAAA
37112 GGAAAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:37132 original size:20 final size:20
Alignment explanation
Indices: 37085--37149 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
37075 TTTTTTTTTC
**
37085 AAAAAAA-CAAAAAAAAAACA
1 AAAAAAAGC-AAAAAAAGCCA
* *
37105 AAAAAAAGGAAAAAAAGGCA
1 AAAAAAAGCAAAAAAAGCCA
*
37125 AAAAAAAGCCAAAAAAGCCA
1 AAAAAAAGCAAAAAAAGCCA
37145 AAAAA
1 AAAAA
37150 GCCAAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (20 bp):
AAAAAAAGCAAAAAAAGCCA
Found at i:37137 original size:11 final size:11
Alignment explanation
Indices: 37092--37149 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
37082 TTCAAAAAAA
**
37092 CAAAAAAAAAA
1 CAAAAAAAAGC
37103 CAAAAAAAAG-
1 CAAAAAAAAGC
* *
37113 -GAAAAAAAGG
1 CAAAAAAAAGC
37123 CAAAAAAAAGC
1 CAAAAAAAAGC
37134 C--AAAAAAGC
1 CAAAAAAAAGC
37143 CAAAAAA
1 CAAAAAA
37150 GCCAAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 17 0.44
11 22 0.56
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAGC
Found at i:37138 original size:9 final size:9
Alignment explanation
Indices: 37126--37156 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
37116 AAAAAGGCAA
37126 AAAAAAGCC
1 AAAAAAGCC
37135 AAAAAAGCC
1 AAAAAAGCC
37144 AAAAAAGCC
1 AAAAAAGCC
37153 AAAA
1 AAAA
37157 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.71, C:0.19, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAGCC
Found at i:37166 original size:18 final size:18
Alignment explanation
Indices: 37105--37156 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
37095 AAAAAAAACA
**
37105 AAAAAAAGGAAAAAAAGGC
1 AAAAAAAGCCAAAAAA-GC
37124 AAAAAAAAGCCAAAAAAGC
1 -AAAAAAAGCCAAAAAAGC
*
37143 CAAAAAAGCCAAAA
1 AAAAAAAGCCAAAA
37157 TTTCAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 13 0.45
19 2 0.07
20 14 0.48
ACGTcount: A:0.73, C:0.13, G:0.13, T:0.00
Consensus pattern (18 bp):
AAAAAAAGCCAAAAAAGC
Found at i:42014 original size:20 final size:19
Alignment explanation
Indices: 41975--42017 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
41965 GAGCATGATA
**
41975 TTCATTAAAATCATGTATT
1 TTCATTAAAATCATACATT
41994 TTCATTAAAAATCATACATT
1 TTCATT-AAAATCATACATT
42014 TTCA
1 TTCA
42018 AAGGGGTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.44
Consensus pattern (19 bp):
TTCATTAAAATCATACATT
Found at i:42785 original size:6 final size:6
Alignment explanation
Indices: 42774--42813 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
42764 GTGTTGTAAC
*
42774 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG -AAAAG AAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAA
42814 GAACTCCTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
6 19 0.63
7 6 0.20
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:46154 original size:19 final size:20
Alignment explanation
Indices: 46127--46182 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
46117 CCATTCGGCC
* *
46127 AAAAGCATGTATCTTCATT-
1 AAAACCATGTATTTTCATTA
*
46146 AAAATCATGTATTTTCATTA
1 AAAACCATGTATTTTCATTA
46166 AAAACCATGTATTTTCA
1 AAAACCATGTATTTTCA
46183 AAGGGGTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.39
Consensus pattern (20 bp):
AAAACCATGTATTTTCATTA
Found at i:64183 original size:20 final size:20
Alignment explanation
Indices: 64160--64197 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
64150 TAATTTTTGC
64160 ATATGATGTTATCATGAAAT
1 ATATGATGTTATCATGAAAT
*
64180 ATATGATTTTATCATGAA
1 ATATGATGTTATCATGAA
64198 TGTTATTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.42
Consensus pattern (20 bp):
ATATGATGTTATCATGAAAT
Done.