Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005554.1 Hibiscus syriacus cultivar Beakdansim tig00012875_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: 72422
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:11424 original size:13 final size:13
Alignment explanation
Indices: 11386--11428 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
11376 ATAAAAATTA
11386 ATTATATAAATAAT
1 ATTATAT-AATAAT
*
11400 -TTAAATAATAAT
1 ATTATATAATAAT
*
11412 ATTATATATTAAT
1 ATTATATAATAAT
11425 ATTA
1 ATTA
11429 ACATGGACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 6 0.24
13 19 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTATATAATAAT
Found at i:13727 original size:2 final size:2
Alignment explanation
Indices: 13720--13754 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
13710 ATTAAGGTTG
13720 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13755 GAAGTTTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18324 original size:2 final size:2
Alignment explanation
Indices: 18317--18341 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18307 ATTAAAGTTG
18317 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 T
18342 GAAGTTTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25008 original size:67 final size:68
Alignment explanation
Indices: 24858--25050 Score: 221
Period size: 67 Copynumber: 2.9 Consensus size: 68
24848 GTGGTATATT
* * * * * *
24858 TTTGTGAGAACACTATACTTTGAAGTGACTAATGTTTGTGAGTGCACTTTACTTTAAAGGGGTGA
1 TTTGTGAGCACACTTTACTTCGAAGTGACTAATGTTTGTGAGCGCACTTTACTTTAAAGAGGTAA
24923 ATG
66 ATG
* *
24926 TTTGTGAGCATACTTTACTTCGAGGTGGA-TAATGTTTGTGAGCGCAC-TTACTTTGAAA-AGGT
1 TTTGTGAGCACACTTTACTTCGAAGT-GACTAATGTTTGTGAGCGCACTTTACTTT-AAAGAGGT
24988 AAATG
64 AAATG
** ** * *
24993 TTTGTGAGCACACTTTACTTTAAAGTGAAAAATATTTGTGAGTGCACTTTACTTTAAA
1 TTTGTGAGCACACTTTACTTCGAAGTGACTAATGTTTGTGAGCGCACTTTACTTTAAA
25051 ATGGTGAATA
Statistics
Matches: 106, Mismatches: 15, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
66 2 0.02
67 54 0.51
68 48 0.45
69 2 0.02
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.37
Consensus pattern (68 bp):
TTTGTGAGCACACTTTACTTCGAAGTGACTAATGTTTGTGAGCGCACTTTACTTTAAAGAGGTAA
ATG
Found at i:25063 original size:34 final size:34
Alignment explanation
Indices: 24846--25055 Score: 167
Period size: 34 Copynumber: 6.2 Consensus size: 34
24836 CTTTTGTTGG
* * ** * *
24846 AAGTGGTATATTTTTGTGAGAACACTATACTTTG
1 AAGTGGTAAATGTTTGTGAGCGCACTTTACTTTA
* *
24880 AAGTGACT-AATGTTTGTGAGTGCACTTTACTTTA
1 AAGTG-GTAAATGTTTGTGAGCGCACTTTACTTTA
* * ** **
24914 AAGGGGTGAATGTTTGTGAGCATACTTTACTTCG
1 AAGTGGTAAATGTTTGTGAGCGCACTTTACTTTA
*
24948 AGGTGG-ATAATGTTTGTGAGCGCAC-TTACTTTGA
1 AAGTGGTA-AATGTTTGTGAGCGCACTTTACTTT-A
* *
24982 AA-AGGTAAATGTTTGTGAGCACACTTTACTTTA
1 AAGTGGTAAATGTTTGTGAGCGCACTTTACTTTA
** * *
25015 AAGTGAAAAATATTTGTGAGTGCACTTTACTTTA
1 AAGTGGTAAATGTTTGTGAGCGCACTTTACTTTA
*
25049 AAATGGT
1 AAGTGGT
25056 GAATATTTAT
Statistics
Matches: 136, Mismatches: 33, Indels: 14
0.74 0.18 0.08
Matches are distributed among these distances:
33 28 0.21
34 107 0.79
35 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (34 bp):
AAGTGGTAAATGTTTGTGAGCGCACTTTACTTTA
Found at i:25249 original size:63 final size:62
Alignment explanation
Indices: 25093--25392 Score: 278
Period size: 63 Copynumber: 4.9 Consensus size: 62
25083 TTTGAGTGTG
* * * * *
25093 CTTAACTTGGAAA-TGACTATTG-TTTGTGAGCATACTTTAATTTGTGAATATCTTTTAG--CG
1 CTTAACTT-GAAAGTGGCGATTGTTTTGTGAGCATACTTTAATTTGCGAGTAT-TTTTAGCACA
* * * *
25153 C---ACTTGGAAGTGGAGATTGTTTTGTGAGTATACTTTAATTTGCGAGTATTTCTTAGCTCA
1 CTTAACTTGAAAGTGGCGATTGTTTTGTGAGCATACTTTAATTTGCGAGTATTT-TTAGCACA
* * * *
25213 CTTAACTTGAAAGTGGTGATTGTTTTGTAAGCATACTTTAATTTGCAAGTATTTTTTAGCGCA
1 CTTAACTTGAAAGTGGCGATTGTTTTGTGAGCATACTTTAATTTGCGAGTA-TTTTTAGCACA
* * *
25276 CTTAACTTGGAAA-TGGCGGTTGTTTTATGAGCATACTTTAATTTTGAGAGTATATTTTAGCACA
1 CTTAACTT-GAAAGTGGCGATTGTTTTGTGAGCATACTTTAA-TTTGCGAGTAT-TTTTAGCACA
* * * * *
25340 CTTAACTTTAAAGTGGCGATT-CTTTGTGAGTACACTTTAATTTGTGAGT-TTTT
1 CTTAACTTGAAAGTGGCGATTGTTTTGTGAGCATACTTTAATTTGCGAGTATTTT
25393 ATCTTTGGAG
Statistics
Matches: 199, Mismatches: 28, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
56 3 0.02
57 12 0.06
58 30 0.15
60 6 0.03
61 1 0.01
62 8 0.04
63 100 0.50
64 39 0.20
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (62 bp):
CTTAACTTGAAAGTGGCGATTGTTTTGTGAGCATACTTTAATTTGCGAGTATTTTTAGCACA
Found at i:25366 original size:126 final size:121
Alignment explanation
Indices: 25093--25384 Score: 315
Period size: 126 Copynumber: 2.4 Consensus size: 121
25083 TTTGAGTGTG
* * *
25093 CTTAACTTGGAAA-TGACTATTG-TTTGTGAGCATACTTTAATTTGTGAATATCTTTTAGCGCAC
1 CTTAACTT-GAAAGTGGCGATTGCTTTGTGAGCATACTTTAATTTGTCAATATCTTTTAGCGCAC
* * * * *
25156 TTGGAAGTGGAGATTGTTTTGTGAGTATACTTTAATTTGCGAGTATTTCTTAGCTCA
65 TTGGAAATGGAGATTGTTTTATGAGCATACTTTAATTTGAGAGTATTTCTTAGCACA
* * * *
25213 CTTAACTTGAAAGTGGTGATTGTTTTGTAAGCATACTTTAATTTG-CAAGTATTTTTTAGCGCAC
1 CTTAACTTGAAAGTGGCGATTGCTTTGTGAGCATACTTTAATTTGTCAA-TATCTTTTAGCG--C
* *
25277 TTAACTTGGAAATGGCGGTTGTTTTATGAGCATACTTTAATTTTGAGAGTATATT-TTAGCACA
63 ---ACTTGGAAATGGAGATTGTTTTATGAGCATACTTTAA-TTTGAGAGTAT-TTCTTAGCACA
* * *
25340 CTTAACTTTAAAGTGGCGATT-CTTTGTGAGTACACTTTAATTTGT
1 CTTAACTTGAAAGTGGCGATTGCTTTGTGAGCATACTTTAATTTGT
25385 GAGTTTTTAT
Statistics
Matches: 142, Mismatches: 19, Indels: 15
0.81 0.11 0.09
Matches are distributed among these distances:
119 4 0.03
120 16 0.11
121 32 0.23
123 1 0.01
126 51 0.36
127 36 0.25
128 2 0.01
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (121 bp):
CTTAACTTGAAAGTGGCGATTGCTTTGTGAGCATACTTTAATTTGTCAATATCTTTTAGCGCACT
TGGAAATGGAGATTGTTTTATGAGCATACTTTAATTTGAGAGTATTTCTTAGCACA
Found at i:25599 original size:47 final size:47
Alignment explanation
Indices: 25396--25599 Score: 169
Period size: 47 Copynumber: 4.3 Consensus size: 47
25386 AGTTTTTATC
** * * *
25396 TTTGGAGGGTGAGCTCGTTTGGAAAAG-TCAAGCCCTTTGGATATTTA
1 TTTGGAGGGTGAGCTCACTTGGAAACGTTGAA-CCCTTTGGAGATTTA
* * * * *
25443 TTTCGAGGGTGAGCT-AGCTTGGAAGCATTGAATCCTTTGGAGATTTC
1 TTTGGAGGGTGAGCTCA-CTTGGAAACGTTGAACCCTTTGGAGATTTA
* * * ** ** * * *
25490 TTTGAAGGGTAAGCTCTCTTGGAAGTGCCGAATCATTTGGAGATTTC
1 TTTGGAGGGTGAGCTCACTTGGAAACGTTGAACCCTTTGGAGATTTA
** *
25537 TTTGGAGGGCAAGCTCACTTGGAAACGTTGAACCCTTTGGAGTTTTA
1 TTTGGAGGGTGAGCTCACTTGGAAACGTTGAACCCTTTGGAGATTTA
25584 TTTGGAGGGTGAGCTC
1 TTTGGAGGGTGAGCTC
25600 GCTAAAGAGC
Statistics
Matches: 122, Mismatches: 32, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
47 119 0.98
48 3 0.02
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (47 bp):
TTTGGAGGGTGAGCTCACTTGGAAACGTTGAACCCTTTGGAGATTTA
Found at i:25674 original size:141 final size:141
Alignment explanation
Indices: 25428--25699 Score: 307
Period size: 141 Copynumber: 1.9 Consensus size: 141
25418 AAAAGTCAAG
** * *
25428 CCCTTTGGATATTTATTTCGAGGGTGAGCTAGCTTGGAAGCATTGAATCCTTTGGAGATTTCTTT
1 CCCTTTGGATATTTATTTCGAGGGTGAGCTAGCTAAGAAGCATTGAACCCTTTGAAGATTTCTTT
* * * * * * *
25493 GAAGGGTAAGCTCTCTTGGAAGTGCCGAATCATTTGGAGATTTCTTTGGAGGGCAAGCTCACTTG
66 GAAGGGTAAGCTCACTTGGAAGAGCCGAACCATCTAGAGATTTCTTTAGAGAGCAAGCTCACTTG
25558 GAAACGTTGAA
131 GAAACGTTGAA
* *
25569 CCCTTTGGAGT-TTTATTTGGAGGGTGAGCTCGCTAA-AGAGCATTGAACCCTTTGAA-AGTTTC
1 CCCTTTGGA-TATTTATTTCGAGGGTGAGCTAGCTAAGA-AGCATTGAACCCTTTGAAGA-TTTC
* * * * * * * *
25631 TTTGTAGGTTGAGCTCACTTGGGAGAGTCGAACCCTCTAGAGATTTCTTTAGAGAGCGAGCTCGC
63 TTTGAAGGGTAAGCTCACTTGGAAGAGCCGAACCATCTAGAGATTTCTTTAGAGAGCAAGCTCAC
25696 TTGG
128 TTGG
25700 TAGCTTTAAA
Statistics
Matches: 107, Mismatches: 21, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
140 2 0.02
141 104 0.97
142 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (141 bp):
CCCTTTGGATATTTATTTCGAGGGTGAGCTAGCTAAGAAGCATTGAACCCTTTGAAGATTTCTTT
GAAGGGTAAGCTCACTTGGAAGAGCCGAACCATCTAGAGATTTCTTTAGAGAGCAAGCTCACTTG
GAAACGTTGAA
Found at i:25951 original size:47 final size:46
Alignment explanation
Indices: 25872--25965 Score: 118
Period size: 47 Copynumber: 2.0 Consensus size: 46
25862 TTTCTTTTAT
*
25872 GGTGAGCTTGCCTGGAAGCGTCAAACCATTTGGAAATTTGTTTGGAG
1 GGTGAGCTTGCCTGGAAGCATCAAACCATTTGGAAATTTG-TTGGAG
* * * *
25919 GGTGAGCTTGCTTCGG-AGCATCGAACCCTTTGGAAGTTTGTTGGAG
1 GGTGAGCTTGCCT-GGAAGCATCAAACCATTTGGAAATTTGTTGGAG
25965 G
1 G
25966 CTCTTGTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
46 7 0.17
47 32 0.78
48 2 0.05
ACGTcount: A:0.20, C:0.16, G:0.34, T:0.30
Consensus pattern (46 bp):
GGTGAGCTTGCCTGGAAGCATCAAACCATTTGGAAATTTGTTGGAG
Found at i:39253 original size:21 final size:19
Alignment explanation
Indices: 39225--39270 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
39215 TCATTGAATC
39225 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
39245 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
39264 ACTTAGT
1 A-TTAGT
39271 AGAATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:58902 original size:23 final size:23
Alignment explanation
Indices: 58876--58924 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
58866 ATAAAAAACC
58876 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAATAT-CCATT
*
58899 AAAATAAAGTCTAAATATCCATT
1 AAAATAAACTCTAAATATCCATT
58922 AAA
1 AAA
58925 CCAACCACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAACTCTAAATATCCATT
Found at i:60656 original size:239 final size:240
Alignment explanation
Indices: 60189--60723 Score: 684
Period size: 239 Copynumber: 2.2 Consensus size: 240
60179 CCGAAGGTCT
*
60189 TACAGATGGCACGAAGGACTTACTAAGTAAGAAACTTTGGTAA-TCATTTTTTTACTCGTCAAGA
1 TACAGATGGCACGAAGGACTTACTAAGTAAGAAACTTTGG-AATTCATTTTCTTACTCGTCAAGA
* * * *
60253 AAACTCAATTTTTAGAAAAGATTCAAATGAGAAACTTTGAAATCGCTTTCTCATTTTTCGAAAAT
65 AAACTCAACTTTCAGAAAAGATTCAAACGAGAAACTTTGAAATCACTTTCTCATTTTTCGAAAAT
* * * ** * *
60318 CATGTGAAAACATCCTGCCCGAAGGTCTTCTGGATGGCCCGAAGGACTTATCATCTTCCTCTAAA
130 CATATGAAAACATCATGCCCGAAGGTCTTATGGATGAACCGAAAGACTTATCATCTTCCTCGAAA
* *
60383 GACTTATATATAACCCAAAGGTTTTATACATCATGCTCGAAAGACA
195 GACTTATAGATAACCCAAAGGATTTATACATCATGCTCGAAAGACA
* * * **
60429 TACAGATGGCCCGAAGGACTTACTATGTAAGAAACTTTGGAATTCGTTTTCTTACTTTTCAAGAA
1 TACAGATGGCACGAAGGACTTACTAAGTAAGAAACTTTGGAATTCATTTTCTTACTCGTCAAGAA
* *
60494 AATTCAACTTTCAGAAAAGATT-TAACGAGAAACTTTAGAAATCACTTTCTCATTTTT-GAAAAT
66 AACTCAACTTTCAGAAAAGATTCAAACGAGAAACTTT-GAAATCACTTTCTCATTTTTCGAAAAT
* **
60557 CATATGAAAACATCATGCCCGAAGGTCTTATGGATGAATCGAAAGACTTATCATCTTGTTCGAAA
130 CATATGAAAACATCATGCCCGAAGGTCTTATGGATGAACCGAAAGACTTATCATCTTCCTCGAAA
* ** *
60622 GACTTATAGATGACCTGAAGGATTTA-AGCATCATGCTCGAAAGACT
195 GACTTATAGATAACCCAAAGGATTTATA-CATCATGCTCGAAAGACA
** * * * * *
60668 TATTGATGGCTCGAAGAAATTAATAAGTAAGAAACTTTGAAAATT-ATTTTCTTACT
1 TACAGATGGCACGAAGGACTTACTAAGTAAGAAACTTTG-GAATTCATTTTCTTACT
60724 GTAGACACAT
Statistics
Matches: 254, Mismatches: 37, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
238 1 0.00
239 155 0.61
240 98 0.39
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (240 bp):
TACAGATGGCACGAAGGACTTACTAAGTAAGAAACTTTGGAATTCATTTTCTTACTCGTCAAGAA
AACTCAACTTTCAGAAAAGATTCAAACGAGAAACTTTGAAATCACTTTCTCATTTTTCGAAAATC
ATATGAAAACATCATGCCCGAAGGTCTTATGGATGAACCGAAAGACTTATCATCTTCCTCGAAAG
ACTTATAGATAACCCAAAGGATTTATACATCATGCTCGAAAGACA
Found at i:62276 original size:30 final size:29
Alignment explanation
Indices: 62242--62299 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
62232 TAGCCTTTTT
*
62242 AGTTTTTATTAATACCATTTTAGTTCCTTA
1 AGTTTCTATTAATACCATTTTAG-TCCTTA
** *
62272 AGTTTCTATTTTTTCCATTTTAGTCCTT
1 AGTTTCTATTAATACCATTTTAGTCCTT
62300 TAACTTTATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.21, C:0.16, G:0.07, T:0.57
Consensus pattern (29 bp):
AGTTTCTATTAATACCATTTTAGTCCTTA
Found at i:62351 original size:29 final size:28
Alignment explanation
Indices: 62258--62357 Score: 82
Period size: 29 Copynumber: 3.5 Consensus size: 28
62248 TATTAATACC
62258 ATTTTAGTTCC-TTAAGTTTCTATTTTTT
1 ATTTTAG-TCCTTTAAGTTTCTATTTTTT
* *
62286 CCATTTTAGTCCTTTAA-CTT-TATGTGTTT
1 --ATTTTAGTCCTTTAAGTTTCTAT-TTTTT
62315 ACTATTTAGTCCTTTAAGTTTCTATTTTTT
1 A-T-TTTAGTCCTTTAAGTTTCTATTTTTT
*
62345 TTGTTTAG-CCTTT
1 AT-TTTAGTCCTTT
62358 TAAATTTATG
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
27 1 0.02
28 9 0.16
29 28 0.48
30 17 0.29
31 3 0.05
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (28 bp):
ATTTTAGTCCTTTAAGTTTCTATTTTTT
Found at i:62352 original size:58 final size:58
Alignment explanation
Indices: 62260--62379 Score: 149
Period size: 58 Copynumber: 2.1 Consensus size: 58
62250 TTAATACCAT
*
62260 TTTAGTTCCTTAAGTTTCTATTTTTTCCATTTTAGTCC-TTTAACTTTATGTGTTTA-CTA
1 TTTAGTTCCTTAAGTTTCTATTTTTT-CATTTTAG-CCTTTTAAATTTATGT-TTTAGCTA
*
62319 TTTAG-TCCTTTAAGTTTCTATTTTTT-TTGTTTAGCCTTTTAAATTTATGTTTTAGCTA
1 TTTAGTTCC-TTAAGTTTCTATTTTTTCAT-TTTAGCCTTTTAAATTTATGTTTTAGCTA
62377 TTT
1 TTT
62380 TAGCCCTTCA
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
57 7 0.13
58 26 0.47
59 22 0.40
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.60
Consensus pattern (58 bp):
TTTAGTTCCTTAAGTTTCTATTTTTTCATTTTAGCCTTTTAAATTTATGTTTTAGCTA
Found at i:62382 original size:59 final size:59
Alignment explanation
Indices: 62258--62387 Score: 153
Period size: 59 Copynumber: 2.2 Consensus size: 59
62248 TATTAATACC
*
62258 ATTTTAGTTCC-TTAAGTTTCTATTTTTTCCATTTTAGTCCTTTAACTTTATGTGTTTACT
1 ATTTTAG-TCCTTTAAGTTTCTATTTTTT-CATTTTAGTCCTTTAAATTTATGTGTTTACT
*
62318 A-TTTAGTCCTTTAAGTTTCTATTTTTT-TTGTTTAG-CCTTTTAAATTTATGT-TTTAGCT
1 ATTTTAGTCCTTTAAGTTTCTATTTTTTCAT-TTTAGTCC-TTTAAATTTATGTGTTTA-CT
*
62376 ATTTTAGCCCTT
1 ATTTTAGTCCTT
62388 CAAGCTTTGT
Statistics
Matches: 62, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
57 7 0.11
58 23 0.37
59 31 0.50
60 1 0.02
ACGTcount: A:0.18, C:0.14, G:0.09, T:0.58
Consensus pattern (59 bp):
ATTTTAGTCCTTTAAGTTTCTATTTTTTCATTTTAGTCCTTTAAATTTATGTGTTTACT
Found at i:67221 original size:18 final size:17
Alignment explanation
Indices: 67195--67251 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
67185 AGAAAAAGAA
*
67195 AAAGGGCAAAATAAAAAT
1 AAAGAGCAAAA-AAAAAT
*
67213 AAAGAGCAAAGAAAAAAC
1 AAAGAGCAAA-AAAAAAT
67231 AAAGAG-AAAAGAGAAAAT
1 AAAGAGCAAAA-A-AAAAT
67249 AAA
1 AAA
67252 CAAAAAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 1 0.03
17 4 0.12
18 27 0.82
19 1 0.03
ACGTcount: A:0.72, C:0.05, G:0.18, T:0.05
Consensus pattern (17 bp):
AAAGAGCAAAAAAAAAT
Found at i:69250 original size:3 final size:3
Alignment explanation
Indices: 69242--69313 Score: 53
Period size: 3 Copynumber: 24.7 Consensus size: 3
69232 TCAACCAAAA
* * *
69242 TAT TAT TA- TAT TA- TATT TATT TAT TAT TAT TAT TAT TAC TAC TAC
1 TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT
* *
69287 TAT TAC TAC TAT TA- TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
69314 ACAAAAATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
2 8 0.13
3 46 0.77
4 6 0.10
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:70674 original size:29 final size:30
Alignment explanation
Indices: 70635--70705 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
70625 TTTTTATTAA
*
70635 TACCATTTTAGTCCCT-TAATTTTCTATTTT
1 TACCA-TTTAGTCCCTGTAACTTTCTATTTT
*
70665 TTCCATTTAGT-CCTGTAACTTTCTATTTT
1 TACCATTTAGTCCCTGTAACTTTCTATTTT
*
70694 TACTATTTAGTC
1 TACCATTTAGTC
70706 ATTTAAGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 3 0.09
29 28 0.80
30 4 0.11
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.55
Consensus pattern (30 bp):
TACCATTTAGTCCCTGTAACTTTCTATTTT
Found at i:71659 original size:42 final size:41
Alignment explanation
Indices: 71587--71701 Score: 158
Period size: 42 Copynumber: 2.7 Consensus size: 41
71577 CTTATCATTT
* * * *
71587 TGCTCGAAAGACTTATAGATGACCCGAAGGATTTAAGCATCA
1 TGCTTGAAAGATTTAT-GATGGCCCGAAGGATTTAAGCAGCA
*
71629 TGCTTGAAAGATTTACTGATGGCCCAAAGGATTTAAGCAGCA
1 TGCTTGAAAGATTTA-TGATGGCCCGAAGGATTTAAGCAGCA
71671 TGCTTGAAAGATTTATTGATGGCCCGAAGGA
1 TGCTTGAAAGATTTA-TGATGGCCCGAAGGA
71702 CTTACTCATC
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 64 0.98
43 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (41 bp):
TGCTTGAAAGATTTATGATGGCCCGAAGGATTTAAGCAGCA
Found at i:71683 original size:22 final size:22
Alignment explanation
Indices: 71616--71685 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
71606 TGACCCGAAG
*
71616 GATTTAAGCATCATGCTTGAAA
1 GATTTAAGCAGCATGCTTGAAA
* **
71638 GATTT-A-CTG-ATGGC-CCAAA
1 GATTTAAGCAGCAT-GCTTGAAA
71657 GGATTTAAGCAGCATGCTTGAAA
1 -GATTTAAGCAGCATGCTTGAAA
71680 GATTTA
1 GATTTA
71686 TTGATGGCCC
Statistics
Matches: 35, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
19 5 0.14
20 8 0.23
21 2 0.06
22 15 0.43
23 5 0.14
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.30
Consensus pattern (22 bp):
GATTTAAGCAGCATGCTTGAAA
Found at i:71839 original size:54 final size:54
Alignment explanation
Indices: 71768--71955 Score: 236
Period size: 54 Copynumber: 3.5 Consensus size: 54
71758 CAATTATCAC
*
71768 CAAGAAACCCCTAAAAATTAGGCTTCGCTTCTTTAAAAATTTATTTGAAAACAT
1 CAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTTATTTGAAAACAT
* * * *
71822 CAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAACTTAGTTGAAAACAT
1 CAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTTATTTGAAAACAT
* ** ** * *
71876 CAAGAAACTCCT-AAAATTCACACTTAGCTT-TTTTCAAATTCATTTAAAAACAT
1 CAAGAAACCCCTAAAAATT-AGGCTTAGCTTCTTTAAAAATTTATTTGAAAACAT
*
71929 CAAGAAACCTCTAAAAATTAGGCTTAG
1 CAAGAAACCCCTAAAAATTAGGCTTAG
71956 AAATTCATTT
Statistics
Matches: 113, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
53 38 0.34
54 75 0.66
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (54 bp):
CAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAATTTATTTGAAAACAT
Found at i:71932 original size:53 final size:51
Alignment explanation
Indices: 71768--72164 Score: 265
Period size: 53 Copynumber: 7.5 Consensus size: 51
71758 CAATTATCAC
* * * ** *
71768 CAAGAAACCCCTAAAAATTAGGCTTCGCTTCTTTAAAAATTTATTTGAAAACAT
1 CAAGAAACTCCT-AAAA-TAGACTTAGCTT-TTTTCAAATTCATTTGAAAACAT
* * ** *
71822 CAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAACTT-AGTTGAAAACAT
1 CAAGAAACTCCT-AAAAT-AGACTTAGCTT-TTTTCAAA-TTCATTTGAAAACAT
* *
71876 CAAGAAACTCCTAAAATTCACACTTAGCTTTTTTCAAATTCATTTAAAAACAT
1 CAAGAAACTCCTAAAA-T-AGACTTAGCTTTTTTCAAATTCATTTGAAAACAT
**
71929 CAAGAAAC-CTCT-AAA-A-A-TTAGGC---TTAGAAATTCATTTGAAAACAT
1 CAAGAAACTC-CTAAAATAGACTTA-GCTTTTTTCAAATTCATTTGAAAACAT
* * *
71974 CAAGAAACTCCTAAAATTAGGCTTAGCTTCTTTCAAATTCATCTGAAAAAACAT
1 CAAGAAACTCCTAAAA-TAGACTTAGCTTTTTTCAAATTCATTTG--AAAACAT
* * * * *
72028 GAAAAAAAAC-CCTAAAAATTAGGCTTAGCTTCTTTAAAATTCATTTGAAAACAT
1 --CAAGAAACTCCT-AAAA-TAGACTTAGCTTTTTTCAAATTCATTTGAAAACAT
* * *
72082 CAAGACACTCATGAAAATCAGACTTACCTTTTTTCAAATTCATTTGAAAACAT
1 CAAGAAACTCCT-AAAAT-AGACTTAGCTTTTTTCAAATTCATTTGAAAACAT
* * *
72135 CAATAAACCCCTAAAAATTAGGCTTAGCTT
1 CAAGAAACTCCT-AAAA-TAGACTTAGCTT
72165 CTTCATTTGA
Statistics
Matches: 283, Mismatches: 37, Indels: 47
0.77 0.10 0.13
Matches are distributed among these distances:
45 29 0.10
46 4 0.01
47 3 0.01
48 4 0.01
49 3 0.01
50 3 0.01
52 24 0.08
53 88 0.31
54 83 0.29
55 5 0.02
56 37 0.13
ACGTcount: A:0.42, C:0.19, G:0.09, T:0.30
Consensus pattern (51 bp):
CAAGAAACTCCTAAAATAGACTTAGCTTTTTTCAAATTCATTTGAAAACAT
Found at i:71975 original size:45 final size:44
Alignment explanation
Indices: 71911--71999 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 44
71901 AGCTTTTTTC
71911 AAATTCATTTAAAAACATCAAGAAAC-CTCTAAAAATTAGGCTTAG
1 AAATTCATTTAAAAACATCAAGAAACTC-CT-AAAATTAGGCTTAG
*
71956 AAATTCATTTGAAAACATCAAGAAACTCCTAAAATTAGGCTTAG
1 AAATTCATTTAAAAACATCAAGAAACTCCTAAAATTAGGCTTAG
72000 CTTCTTTCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
44 14 0.33
45 27 0.64
46 1 0.02
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (44 bp):
AAATTCATTTAAAAACATCAAGAAACTCCTAAAATTAGGCTTAG
Found at i:72080 original size:108 final size:106
Alignment explanation
Indices: 71956--72167 Score: 300
Period size: 106 Copynumber: 2.0 Consensus size: 106
71946 TTAGGCTTAG
* * * *
71956 AAATTCATTTGAAAACATCAAGAAACTCCT-AAAATTAGGCTTAGCTTCTTTCAAATTCATCTGA
1 AAATTCATTTGAAAACATCAAGAAACTCATGAAAATCAGACTTACCTTCTTTCAAATTCATCTG-
72020 AAAAACATGAAAAAAAACCCTAAAAATTAGGCTTAGCTTCTTTA
65 -AAAACAT-AAAAAAAACCCTAAAAATTAGGCTTAGCTTCTTTA
* * *
72064 AAATTCATTTGAAAACATCAAGACACTCATGAAAATCAGACTTACCTTTTTTCAAATTCATTTGA
1 AAATTCATTTGAAAACATCAAGAAACTCATGAAAATCAGACTTACCTTCTTTCAAATTCATCTGA
* * *
72129 AAACATCAATAAACCCCTAAAAATTAGGCTTAGCTTCTT
66 AAACATAAAAAAAACCCTAAAAATTAGGCTTAGCTTCTT
72168 CATTTGAAAC
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
106 30 0.32
107 7 0.08
108 28 0.30
109 28 0.30
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (106 bp):
AAATTCATTTGAAAACATCAAGAAACTCATGAAAATCAGACTTACCTTCTTTCAAATTCATCTGA
AAACATAAAAAAAACCCTAAAAATTAGGCTTAGCTTCTTTA
Found at i:72122 original size:206 final size:205
Alignment explanation
Indices: 71768--72216 Score: 586
Period size: 206 Copynumber: 2.2 Consensus size: 205
71758 CAATTATCAC
* * * * * * *
71768 CAAGAAACCCCTAAAAATTAGGCTTCGCTTCTTTAAAAATTTATTTGAAAACATCAAGAAACCCC
1 CAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTT-CAAATTCATCTGAAAACATAAAAAAAACCC
* *
71833 TGAAAATCAGGCTTAGCTTCTTTAAAAACTTAGTTGAAAACATCAAGAAACTCCTAAAATTCACA
65 TAAAAATCAGGCTTAGCTTCTTTAAAAACTTAGTTGAAAACATCAAGAAACTCATAAAATTCACA
* *
71898 CTTAGCTTTTTTCAAATTCATTTAAAAACATCAAGAAACCTCTAAAAATTAGGCTTAG-AAATTC
130 CTTACCTTTTTTCAAATTCATTTAAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGCAAATTC
71962 ATTTGAAAACAT
195 ATTTG-AAACAT
*
71974 CAAGAAACTCCT-AAAATTAGGCTTAGCTTCTTTCAAATTCATCTGAAAAAACATGAAAAAAAAC
1 CAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATCTG--AAAACAT-AAAAAAAAC
* * *
72038 CCTAAAAATTAGGCTTAGCTTCTTT-AAAA-TTCATTTGAAAACATCAAGACACTCATGAAAA-T
63 CCTAAAAATCAGGCTTAGCTTCTTTAAAAACTT-AGTTGAAAACATCAAGAAACTCAT-AAAATT
* * * **
72100 CAGACTTACCTTTTTTCAAATTCATTTGAAAACATCAATAAACCCCTAAAAATTAGGCTTAGCTT
126 CACACTTACCTTTTTTCAAATTCATTTAAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGCAA
*
72165 CTTCATTTGAAACAT
191 ATTCATTTGAAACAT
* *
72180 CAAG-AACCCCTAAAAATCAGGCTTAGCTTATTTCAAA
1 CAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAA
72217 AATTCATCAT
Statistics
Matches: 212, Mismatches: 24, Indels: 14
0.85 0.10 0.06
Matches are distributed among these distances:
204 9 0.04
205 28 0.13
206 134 0.63
207 41 0.19
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.30
Consensus pattern (205 bp):
CAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTCAAATTCATCTGAAAACATAAAAAAAACCCT
AAAAATCAGGCTTAGCTTCTTTAAAAACTTAGTTGAAAACATCAAGAAACTCATAAAATTCACAC
TTACCTTTTTTCAAATTCATTTAAAAACATCAAGAAACCCCTAAAAATTAGGCTTAGCAAATTCA
TTTGAAACAT
Found at i:72194 original size:44 final size:46
Alignment explanation
Indices: 72120--72208 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 46
72110 TTTTTTCAAA
*
72120 TTCATTTGAAAACATCAATAAACCCCTAAAAATTAGGCTTAGCTTC
1 TTCATTTGAAAACATCAATAAACCCCTAAAAATCAGGCTTAGCTTC
*
72166 TTCATTTG-AAACATCAA-GAACCCCTAAAAATCAGGCTTAGCTT
1 TTCATTTGAAAACATCAATAAACCCCTAAAAATCAGGCTTAGCTT
72209 ATTTCAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 24 0.59
45 9 0.22
46 8 0.20
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.29
Consensus pattern (46 bp):
TTCATTTGAAAACATCAATAAACCCCTAAAAATCAGGCTTAGCTTC
Found at i:72352 original size:54 final size:54
Alignment explanation
Indices: 72304--72422 Score: 157
Period size: 54 Copynumber: 2.2 Consensus size: 54
72294 AAAATCGAAT
* ** *
72304 TTAGTTTCTTTAAAAGCTCATTTAAAATTGTCAAGAAACTTCTGAAAATCATAC
1 TTAGTTTCTTTAAAAACTCATTTAAAATCATCAAGAAACTTCTGAAAATCAGAC
* * * * *
72358 TCAATTTCTTTAAAAATTCATTTAAAATCATCAAGAAACGTCTGAAAAGCAGAC
1 TTAGTTTCTTTAAAAACTCATTTAAAATCATCAAGAAACTTCTGAAAATCAGAC
72412 TTAGTTTCTTT
1 TTAGTTTCTTT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (54 bp):
TTAGTTTCTTTAAAAACTCATTTAAAATCATCAAGAAACTTCTGAAAATCAGAC
Done.