Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005858.1 Hibiscus syriacus cultivar Beakdansim tig00013768_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: 68589
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:12396 original size:23 final size:23
Alignment explanation
Indices: 12339--12399 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
12329 CACCACAACT
* *
12339 CGTATAAATGCACCGAAGTGCCA
1 CGTATAGATGCACTGAAGTGCCA
*
12362 C--ATAGAATTGCACTGAAGTGCCG
1 CGTATAG-A-TGCACTGAAGTGCCA
12385 CGTATAGATGCACTG
1 CGTATAGATGCACTG
12400 TAGTACCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 3 0.10
22 1 0.03
23 22 0.71
24 1 0.03
25 4 0.13
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (23 bp):
CGTATAGATGCACTGAAGTGCCA
Found at i:13098 original size:14 final size:14
Alignment explanation
Indices: 13079--13111 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
13069 GATACCCAAA
13079 TTAAGTTTGAAATT
1 TTAAGTTTGAAATT
13093 TTAAGTTTGAAATT
1 TTAAGTTTGAAATT
13107 TTAAG
1 TTAAG
13112 GTATTGATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
TTAAGTTTGAAATT
Found at i:16358 original size:16 final size:16
Alignment explanation
Indices: 16337--16367 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16327 TTTCCATGTT
16337 TGATTTGATGAAAACG
1 TGATTTGATGAAAACG
*
16353 TGATTTGTTGAAAAC
1 TGATTTGATGAAAAC
16368 ATTTTGATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.35
Consensus pattern (16 bp):
TGATTTGATGAAAACG
Found at i:22270 original size:23 final size:21
Alignment explanation
Indices: 22204--22287 Score: 71
Period size: 23 Copynumber: 3.9 Consensus size: 21
22194 TTTAGTGCAG
* *
22204 AGGGAATCGATACCCCCTTGA
1 AGGGAACCGATTCCCCCTTGA
** *
22225 AGGGGAAATGATTCCCCATTTGA
1 A-GGGAACCGATTCCCC-CTTGA
22248 ATGGGAACCGATTCCCTCCTTG-
1 A-GGGAACCGATTCCC-CCTTGA
*
22270 AGGGAACCGATACCCCCT
1 AGGGAACCGATTCCCCCT
22288 ACGGGTTCTG
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
20 3 0.06
21 14 0.27
22 13 0.25
23 20 0.39
24 1 0.02
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (21 bp):
AGGGAACCGATTCCCCCTTGA
Found at i:41628 original size:23 final size:23
Alignment explanation
Indices: 41585--41629 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
41575 TTACCCTTTA
*
41585 TTTTAAATAATTTAATTTTAAAT
1 TTTTAAATAATTTAATATTAAAT
*
41608 TTTTAACTAATTT-ATAATTAAA
1 TTTTAAATAATTTAAT-ATTAAA
41630 CATTAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTTAAATAATTTAATATTAAAT
Found at i:48938 original size:6 final size:6
Alignment explanation
Indices: 48927--48959 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
48917 TCTACTATTT
48927 ATACAC ATACAC ATACAC ATACAC ATACAC ATA
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATA
48960 TAAAGTACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (6 bp):
ATACAC
Found at i:50136 original size:32 final size:32
Alignment explanation
Indices: 50065--50158 Score: 100
Period size: 32 Copynumber: 2.9 Consensus size: 32
50055 TTTAGCGAAA
** *
50065 TCGAAAGCAACCCGAACCGAATTTTAACCTGAC
1 TCGAAAGCAACCCGAA-TTAAATTTAACCTGAC
* * *
50098 TCGAAAGTAACCTGAATTGAATTTAATCC-GAC
1 TCGAAAGCAACCCGAATTAAATTTAA-CCTGAC
*
50130 TTGAAAGCAACCCGAATTAAATTTAACCT
1 TCGAAAGCAACCCGAATTAAATTTAACCT
50159 AAACCAAAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
31 2 0.04
32 31 0.63
33 16 0.33
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.24
Consensus pattern (32 bp):
TCGAAAGCAACCCGAATTAAATTTAACCTGAC
Found at i:50446 original size:22 final size:22
Alignment explanation
Indices: 50381--50456 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 22
50371 ATCTTACTTG
50381 TAAT-AAA-AATATTAGATTTA
1 TAATAAAATAATATTAGATTTA
* **
50401 TAATAAAATAATA-GA-AAATA
1 TAATAAAATAATATTAGATTTA
50421 -AATAAAATAATATTAGATTTA
1 TAATAAAATAATATTAGATTTA
50442 TAATAAAAATAATAT
1 TAAT-AAAATAATAT
50457 AAAATTTAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
19 12 0.27
20 8 0.18
21 7 0.16
22 7 0.16
23 10 0.23
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (22 bp):
TAATAAAATAATATTAGATTTA
Found at i:51035 original size:15 final size:15
Alignment explanation
Indices: 51015--51049 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
51005 TAATCTAAAC
51015 CTAAAATAACTCGAA
1 CTAAAATAACTCGAA
*
51030 CTAAAATAACTCGAC
1 CTAAAATAACTCGAA
51045 CTAAA
1 CTAAA
51050 CTCGATCCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.51, C:0.23, G:0.06, T:0.20
Consensus pattern (15 bp):
CTAAAATAACTCGAA
Found at i:53729 original size:21 final size:21
Alignment explanation
Indices: 53705--53754 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
53695 ATTTACATAC
*
53705 AAAATACAGAGAAAAACATGG
1 AAAATACAGAGAAAAACACGG
* *
53726 AAAATACAGAGGAAAGCACGG
1 AAAATACAGAGAAAAACACGG
53747 AAAATACA
1 AAAATACA
53755 AATGCAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.60, C:0.12, G:0.20, T:0.08
Consensus pattern (21 bp):
AAAATACAGAGAAAAACACGG
Found at i:54082 original size:8 final size:8
Alignment explanation
Indices: 54071--54178 Score: 56
Period size: 9 Copynumber: 12.2 Consensus size: 8
54061 ATATATTTAC
54071 TATTTTTT
1 TATTTTTT
54079 TA-TTTTT
1 TATTTTTT
54086 TATTTTTT
1 TATTTTTT
* *
54094 ATATATATATA
1 -TAT-T-TTTT
*
54105 CATTTTTAT
1 TATTTTT-T
54114 TATTTTATT
1 TATTTT-TT
54123 TATTTTATT
1 TATTTT-TT
* *
54132 TATTTATA
1 TATTTTTT
54140 TATTTTTTCT
1 TA-TTTTT-T
*
54150 TCTTTTCTT
1 TATTTT-TT
54159 TATTTTTT
1 TATTTTTT
54167 ATATTTATTT
1 -TATTT-TTT
54177 TA
1 TA
54179 CTTACTATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 21
0.70 0.11 0.19
Matches are distributed among these distances:
7 7 0.09
8 14 0.18
9 45 0.58
10 9 0.12
11 2 0.03
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (8 bp):
TATTTTTT
Found at i:54117 original size:35 final size:35
Alignment explanation
Indices: 54058--54170 Score: 106
Period size: 36 Copynumber: 3.1 Consensus size: 35
54048 TATATATATA
*
54058 TATATATATTTACTATTTTTTTATTT-TTTATTTTT
1 TATATATATATAC-ATTTTTTTATTTATTTATTTTT
54093 TATATATATATACATTTTTATTATTTTATTTATTTTAT
1 TATATATATATACATTTTT-TTA-TTTATTTATTTT-T
* * * *
54131 T-TATTTATATA-TTTTTTCTTCTTTTCTTTATTTTT
1 TATATATATATACATTTTT-TT-ATTTATTTATTTTT
54166 TATAT
1 TATAT
54171 TTATTTTACT
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
34 6 0.09
35 17 0.26
36 24 0.36
37 17 0.26
38 2 0.03
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (35 bp):
TATATATATATACATTTTTTTATTTATTTATTTTT
Found at i:56800 original size:26 final size:26
Alignment explanation
Indices: 56771--56844 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 26
56761 TTAATCAAAG
*
56771 CAAAAAGAGAAA-AAGAGAAAAAAAAA
1 CAAAAAGA-AAATAAAAGAAAAAAAAA
* *
56797 CAAAGAGAAAATAAAAGAGAAAAAAA
1 CAAAAAGAAAATAAAAGAAAAAAAAA
* **
56823 C-AAAGGAAAATTGAAGAAAAAA
1 CAAAAAGAAAATAAAAGAAAAAA
56845 GAAGACAAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
25 19 0.49
26 20 0.51
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (26 bp):
CAAAAAGAAAATAAAAGAAAAAAAAA
Found at i:56813 original size:28 final size:25
Alignment explanation
Indices: 56781--56833 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 25
56771 CAAAAAGAGA
56781 AAAAGAGAAAAAAAAACAAAGAGAAAAT
1 AAAAGAG--AAAAAAACAAAG-GAAAAT
56809 AAAAGAGAAAAAAACAAAGGAAAAT
1 AAAAGAGAAAAAAACAAAGGAAAAT
56834 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 12 0.48
28 7 0.28
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.04
Consensus pattern (25 bp):
AAAAGAGAAAAAAACAAAGGAAAAT
Found at i:56839 original size:25 final size:25
Alignment explanation
Indices: 56789--56844 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
56779 GAAAAAGAGA
56789 AAAAAAAACAAAGAGAAAATAAAAG
1 AAAAAAAACAAAGAGAAAATAAAAG
**
56814 AGAAAAAAACAAAG-GAAAATTGAAG
1 A-AAAAAAACAAAGAGAAAATAAAAG
56839 AAAAAA
1 AAAAAA
56845 GAAGACAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 5 0.18
25 11 0.39
26 12 0.43
ACGTcount: A:0.77, C:0.04, G:0.14, T:0.05
Consensus pattern (25 bp):
AAAAAAAACAAAGAGAAAATAAAAG
Found at i:57023 original size:69 final size:69
Alignment explanation
Indices: 56905--57039 Score: 198
Period size: 69 Copynumber: 2.0 Consensus size: 69
56895 GATTCAAACT
* * *
56905 ATGAGATTGATCAAGCACAATCATTTTTGAATCACTGAACCACTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATAAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
56970 TAAA
66 TAAA
* * * * *
56974 ATGAGATTGATAAAGCATAATCATTTCTGAATTACTGAATCACTCCACTCGAAGTTCATGGAGCA
1 ATGAGATTGATAAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
57039 T
66 T
57040 CAAGAGAGAG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (69 bp):
ATGAGATTGATAAAGCACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
TAAA
Found at i:58724 original size:106 final size:106
Alignment explanation
Indices: 58598--58920 Score: 414
Period size: 106 Copynumber: 3.0 Consensus size: 106
58588 GAATCGTGCC
* * * * *
58598 ACTCGAGACAACACAAGTTCAACTCCACAACGAATGGATGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAAAATTTCCT
* *
58663 AATTTCAGAGCCAATTTAAACTTCACAGCGAAGGATATTTG
66 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
* * * *
58704 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGACGGTTGGTTGTCATCAAATAATTTCCT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAAAATTTCCT
* * ** *
58769 AATTTCAGGGCTAATTTTAACTTCACAATGAATGATATTGG
66 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
* * * * *
58810 ACTCGAAACAGCACAAGCTCAACTTCACAGCGAAGGGACGGCTGGTTGTCAACAAAAAATTTCTT
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAAAATTTCCT
* * *
58875 AGTTCCAGAGCCAATTTTAACTTCACGGC-AGAGGATATTGG
66 AATTTCAGAGCCAATTTTAACTTCACAGCGA-AGGATATTGG
58916 ACTCG
1 ACTCG
58921 GAACAATACA
Statistics
Matches: 184, Mismatches: 32, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
105 1 0.01
106 183 0.99
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAAAAATTTCCT
AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
Found at i:59286 original size:86 final size:87
Alignment explanation
Indices: 59173--59434 Score: 415
Period size: 86 Copynumber: 3.1 Consensus size: 87
59163 GACAGTTTCT
59173 CTTGAAACATAAACATTG-AAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
59237 CTTGAAACGAAATTTTGTCTCC
66 CTTGAAACGAAATTTTGTCTCC
* * *
59259 CTTGAAACAT-AACATTGAAAACCTTTCCCTTGAAACGAATTTTATCTCGATTGAGATAGTTTCT
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
* *
59323 CTTGAAACGGAATTTTGTCTAC
66 CTTGAAACGAAATTTTGTCTCC
* * *
59345 CTTGAAACATAAACATTGAAAACATTT-CCTTGAAAT-AATTTTATCTCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
*
59408 CTTGAAACTAAATTTTGTCTCC
66 CTTGAAACGAAATTTTGTCTCC
59430 CTTGA
1 CTTGA
59435 GACAATTTCT
Statistics
Matches: 160, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
85 54 0.34
86 91 0.57
87 15 0.09
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (87 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
CTTGAAACGAAATTTTGTCTCC
Found at i:59590 original size:86 final size:85
Alignment explanation
Indices: 59445--59620 Score: 257
Period size: 86 Copynumber: 2.1 Consensus size: 85
59435 GACAATTTCT
* *
59445 CTTGAAACATAAACATTGAAACATTCCCTTAAAATGAATTTTATCTCGATTGAGATAGTTTCCCT
1 CTTGAAACATAAACATTGAAACATTCCCTTAAAATAAATTTTATCTCGATTGAGATAGTTTCCAT
*
59510 TG-AACGAAATTTTGTCTCC
66 TGAAACAAAATTTTGTCTCC
* * *
59529 CTTGAAACATAAACATTGAAAACATTTCCCTTTAAATAAATTTTATCTC-ACTTGGGGTAGTTTC
1 CTTGAAACATAAACATTG-AAACA-TTCCCTTAAAATAAATTTTATCTCGA-TTGAGATAGTTTC
59593 CATTGAAACAAAATTTTGTCTCC
63 CATTGAAACAAAATTTTGTCTCC
59616 CTTGA
1 CTTGA
59621 GACAGTTTCT
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
84 18 0.22
85 6 0.07
86 37 0.45
87 21 0.26
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (85 bp):
CTTGAAACATAAACATTGAAACATTCCCTTAAAATAAATTTTATCTCGATTGAGATAGTTTCCAT
TGAAACAAAATTTTGTCTCC
Found at i:59592 original size:271 final size:280
Alignment explanation
Indices: 59141--59753 Score: 854
Period size: 271 Copynumber: 2.2 Consensus size: 280
59131 TTTCTTTTGG
*
59141 AACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAACATTTCCCTTGA
1 AACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAACATTTCCCTTAA
59206 AATGAATTTTATCTCGATTGAGATAGTTTCCCTTGAAACGAAATTTTGTCTCCCTTGAAACATAA
66 AATGAATTTTATCTCGATTGAGATAGTTTCCCTTGAAACGAAATTTTGTCTCCCTTGAAACATAA
* * **
59271 CATTGAAAACCTTTCCCTTGAAACGAATTTTATCTCGATTGAGATAGTTTCTC-TTGAAACGGAA
131 CATTGAAAACATTTCCCTTGAAACAAATTTTATCTCGATTGAGATAGTTTC-CATTGAAACAAAA
*
59335 TTTTG-T-C-T-A-C-CTTGAAACATAAACATTGAAAACATTTCC-TTGAAA-TAATTTTATCTC
195 TTTTGCTCCTTAATCTCTTGAAACATAAACATTGAAAACATTTCCTTTGAAATTAACTTTATCTC
* *
59392 GCTTGGGGTAGTTTCCCTTGA
260 GCTTGAGATAGTTTCCCTTGA
*
59413 AACTAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTGAAACA-TTCCCTTAA
1 AACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAACATTTCCCTTAA
59477 AATGAATTTTATCTCGATTGAGATAGTTTCCCTTG-AACGAAATTTTGTCTCCCTTGAAACATAA
66 AATGAATTTTATCTCGATTGAGATAGTTTCCCTTGAAACGAAATTTTGTCTCCCTTGAAACAT-A
* * * *
59541 ACATTGAAAACATTTCCCTTTAAATAAATTTTATCTC-ACTTGGGGTAGTTTCCATTGAAACAAA
130 ACATTGAAAACATTTCCCTTGAAACAAATTTTATCTCGA-TTGAGATAGTTTCCATTGAAACAAA
59605 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCTTTGAAATTA
194 ATTTTG-CT-CCTT---A-A---TCTCTTGAAACATAAACATTGAAAACATTTCCTTTGAAATTA
* *
59670 ACTTTGTCTCTCTTGAGATAGTTTCCCTTGA
250 ACTTTATCTCGCTTGAGATAGTTTCCCTTGA
* * * * *
59701 AACAAAATTTTATCTCCCTTGATATAGTTTCTCTTGAAACATAAACCTTGAAA
1 AACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAA
59754 ATGTTTCCCT
Statistics
Matches: 300, Mismatches: 21, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
270 29 0.10
271 102 0.34
272 54 0.18
273 1 0.00
275 1 0.00
276 1 0.00
281 1 0.00
285 1 0.00
286 29 0.10
287 6 0.02
288 75 0.25
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (280 bp):
AACTAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAACATTTCCCTTAA
AATGAATTTTATCTCGATTGAGATAGTTTCCCTTGAAACGAAATTTTGTCTCCCTTGAAACATAA
CATTGAAAACATTTCCCTTGAAACAAATTTTATCTCGATTGAGATAGTTTCCATTGAAACAAAAT
TTTGCTCCTTAATCTCTTGAAACATAAACATTGAAAACATTTCCTTTGAAATTAACTTTATCTCG
CTTGAGATAGTTTCCCTTGA
Found at i:59601 original size:186 final size:186
Alignment explanation
Indices: 59259--59722 Score: 700
Period size: 186 Copynumber: 2.5 Consensus size: 186
59249 TTTTGTCTCC
* * *
59259 CTTGAAACAT-AACATTGAAAACCTTTCCCTTGAAACGAATTTTATCTCGATTGAGATAGTTTCT
1 CTTGAAACATAAACATTGAAAA-CATTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
* *
59323 CTTGAAACGGAATTTTGTCTACCTTGAAACATAAACATTGAAAACATTTCCTTGAAATAATTTTA
65 CTTGAAACGAAATTTTGTCTCCCTTGAAACATAAACATTGAAAACATTTCCTTGAAATAATTTTA
* * *
59388 TCTCGCTTGGGGTAGTTTCCCTTGAAACTAAATTTTGTCTCCCTTGAGACAATTTCT
130 TCTCACTTGGGGTAGTTTCCATTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCT
*
59445 CTTGAAACATAAACATTG-AAACATTCCCTTAAAATGAATTTTATCTCGATTGAGATAGTTTCCC
1 CTTGAAACATAAACATTGAAAACATTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCCC
*
59509 TTG-AACGAAATTTTGTCTCCCTTGAAACATAAACATTGAAAACATTTCCCTTTAAATAAATTTT
66 TTGAAACGAAATTTTGTCTCCCTTGAAACATAAACATTGAAAACATTT-CCTTGAAAT-AATTTT
*
59573 ATCTCACTTGGGGTAGTTTCCATTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
129 ATCTCACTTGGGGTAGTTTCCATTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCT
* * * * **
59631 CTTGAAACATAAACATTGAAAACATTTCCTTTGAAATTAACTTTGTCTCTCTTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACA-TTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
* *
59696 CTTGAAACAAAATTTTATCTCCCTTGA
65 CTTGAAACGAAATTTTGTCTCCCTTGA
59723 TATAGTTTCT
Statistics
Matches: 252, Mismatches: 20, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
184 42 0.17
185 50 0.20
186 91 0.36
187 12 0.05
188 37 0.15
189 20 0.08
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (186 bp):
CTTGAAACATAAACATTGAAAACATTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCCC
TTGAAACGAAATTTTGTCTCCCTTGAAACATAAACATTGAAAACATTTCCTTGAAATAATTTTAT
CTCACTTGGGGTAGTTTCCATTGAAACAAAATTTTGTCTCCCTTGAGACAATTTCT
Found at i:59692 original size:102 final size:102
Alignment explanation
Indices: 59529--59768 Score: 338
Period size: 102 Copynumber: 2.4 Consensus size: 102
59519 TTTTGTCTCC
* * *
59529 CTTGAAACATAAACATTGAAAACATTTCCCTTT-AAATAAATTTTATCTCACTTGGGGTAGTTTC
1 CTTGAAACATAAACATTGAAAACATTT-CCTTTGAAATAAACTTTATCTCACTTGAGATAGTTTC
*
59593 CATTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
65 CATTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCT
* * *
59631 CTTGAAACATAAACATTGAAAACATTTCCTTTGAAATTAACTTTGTCTCTCTTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCTTTGAAATAAACTTTATCTCACTTGAGATAGTTTCC
* * *
59696 CTTGAAACAAAATTTTATCTCCCTTGATATAGTTTCT
66 ATTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCT
* ** *
59733 CTTGAAACATAAACCTTGAAAATGTTTCCCTTGAAA
1 CTTGAAACATAAACATTGAAAACATTTCCTTTGAAA
59769 CACAAAATAT
Statistics
Matches: 123, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
101 5 0.04
102 118 0.96
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (102 bp):
CTTGAAACATAAACATTGAAAACATTTCCTTTGAAATAAACTTTATCTCACTTGAGATAGTTTCC
ATTGAAACAAAATTTTATCTCCCTTGAGACAGTTTCT
Found at i:59702 original size:36 final size:37
Alignment explanation
Indices: 59669--59746 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
59659 CTTTGAAATT
* *
59669 AACTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAA
1 AACTTTATCTCCCTTGAGATAGTTTCCCTTGAAACAA
* * *
59706 AATTTTATCTCCCTTGATATAGTTTCTCTTGAAACATA
1 AACTTTATCTCCCTTGAGATAGTTTCCCTTGAAACA-A
59744 AAC
1 AAC
59747 CTTGAAAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
37 31 0.91
38 3 0.09
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (37 bp):
AACTTTATCTCCCTTGAGATAGTTTCCCTTGAAACAA
Found at i:59989 original size:35 final size:35
Alignment explanation
Indices: 59881--60002 Score: 147
Period size: 35 Copynumber: 3.4 Consensus size: 35
59871 TTGAATATCT
* *
59881 TTTCCTTGAAACAAATTTCGTCTC-CTTGAGACAG
1 TTTCTTTGAAACAAATTTTGTCTCTCTTGAGACAG
* * *
59915 TTTCTTTTAGAACTAAGTTTTGTCTCTCTAGAGACAG
1 TTTCTTTGA-AAC-AAATTTTGTCTCTCTTGAGACAG
* *
59952 TTTCTTTGAAACAAATTTTGTCCCTCTTGAGAAAG
1 TTTCTTTGAAACAAATTTTGTCTCTCTTGAGACAG
59987 TTTCTCTTGAAACAAA
1 TTTCT-TTGAAACAAA
60003 AAAAACCCTC
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
34 7 0.09
35 27 0.36
36 23 0.31
37 17 0.23
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (35 bp):
TTTCTTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:61048 original size:37 final size:36
Alignment explanation
Indices: 60944--61108 Score: 134
Period size: 37 Copynumber: 4.6 Consensus size: 36
60934 TTTACTTTAG
* * *
60944 TATATATTTTTATTT-TT-TTAGATTATATATATATA
1 TATATTTTTTTATTTATTATT-TATTATATATATATT
*
60979 TATTTTTTTTATCAATTTTATTAATTTA-TATATATATATT
1 TATATTTTTT-T--A-TTTATT-ATTTATTATATATATATT
*
61019 TACTATTTTTTTATTTATTATTTATTATATATATATA
1 TA-TATTTTTTTATTTATTATTTATTATATATATATT
61056 TATATTATTTTTACTTTATTA-TTATTAT-T-T-T-TT
1 TATATT-TTTTTA-TTTATTATTTATTATATATATATT
61089 TAT-TTTTTTTATTTA-TATTT
1 TATATTTTTTTATTTATTATTT
61109 TTTCTTCTTT
Statistics
Matches: 111, Mismatches: 7, Indels: 29
0.76 0.05 0.20
Matches are distributed among these distances:
29 2 0.02
30 6 0.05
31 6 0.05
32 2 0.02
33 4 0.04
34 1 0.01
35 9 0.08
36 11 0.10
37 32 0.29
38 9 0.08
39 3 0.03
40 16 0.14
41 8 0.07
42 2 0.02
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.68
Consensus pattern (36 bp):
TATATTTTTTTATTTATTATTTATTATATATATATT
Found at i:61095 original size:9 final size:9
Alignment explanation
Indices: 61060--61151 Score: 59
Period size: 9 Copynumber: 10.3 Consensus size: 9
61050 TATATATATA
61060 TTATTTTTACT
1 TTATTTTT--T
* *
61071 TTATTATTA
1 TTATTTTTT
61080 TTA-TTTTT
1 TTATTTTTT
61088 TTATTTTTT
1 TTATTTTTT
61097 TTA---TTT
1 TTATTTTTT
*
61103 ATATTTTTT
1 TTATTTTTT
*
61112 CTTCTTTTTCT
1 -TTATTTTT-T
61123 TTA-TTTTT
1 TTATTTTTT
61131 TTATTTTTT
1 TTATTTTTT
* *
61140 ATATTTATT
1 TTATTTTTT
61149 TTA
1 TTA
61152 CTTGCTATTT
Statistics
Matches: 63, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
6 5 0.08
8 10 0.16
9 32 0.51
10 8 0.13
11 8 0.13
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.78
Consensus pattern (9 bp):
TTATTTTTT
Found at i:61103 original size:4 final size:4
Alignment explanation
Indices: 60995--61149 Score: 50
Period size: 4 Copynumber: 37.8 Consensus size: 4
60985 TTTTATCAAT
* * * *
60995 TTTA TTAA TTTA TATATA TATA TTTA -CTA TTTT TTTA TTTA -TTA TTTA
1 TTTA TTTA TTTA T-T-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * *
61043 TTATA TATA TATA TATA TTATT TTTA CTTTA -TTA -TTA -TTA TTTT TTTA
1 TT-TA TTTA TTTA TTTA TT-TA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA
* * * * * * *
61091 TTTTT TTTA TTTA TATTT TTTC TTCTT TTTC TTTA TTTT TTTA TTTT TTATA
1 -TTTA TTTA TTTA T-TTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TT-TA
61143 TTTA TTT
1 TTTA TTT
61150 TACTTGCTAT
Statistics
Matches: 114, Mismatches: 25, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
3 14 0.12
4 74 0.65
5 23 0.20
6 3 0.03
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:61127 original size:43 final size:44
Alignment explanation
Indices: 61080--61206 Score: 136
Period size: 43 Copynumber: 2.9 Consensus size: 44
61070 TTTATTATTA
*
61080 TTATTTTTTTATTTTTTTTATTTATATTT-TTTCTTCTTTTTCT
1 TTATTTTTTTATTTTTTTTATTTATATTTATTTCTTCTTTATCT
* *
61123 TTATTTTTTTATTTTTTATATTTAT-TTTACTTGCTAT-TTTATCT
1 TTATTTTTTTATTTTTTTTATTTATATTTA-TTTCT-TCTTTATCT
* * *
61167 TTATTTTCTTTATCTTCTTTTATTTA-ATTTGTTTTTTCTT
1 TTATTTT-TTTAT-TTTTTTTATTTATATTTATTTCTTCTT
61207 CATTTTAATT
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
42 3 0.04
43 24 0.35
44 18 0.26
45 11 0.16
46 13 0.19
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (44 bp):
TTATTTTTTTATTTTTTTTATTTATATTTATTTCTTCTTTATCT
Found at i:61178 original size:9 final size:9
Alignment explanation
Indices: 61080--61191 Score: 60
Period size: 9 Copynumber: 12.7 Consensus size: 9
61070 TTTATTATTA
61080 TTATTTT-T
1 TTATTTTCT
*
61088 TTATTTTTT
1 TTATTTTCT
*
61097 TTATTTAT-A
1 TTATTT-TCT
61106 TT-TTTTCT
1 TTATTTTCT
61114 TCT-TTTTCT
1 T-TATTTTCT
61123 TTATTTT-T
1 TTATTTTCT
61131 TTATTTT-T
1 TTATTTTCT
61139 TATATTTAT-T
1 T-TATTT-TCT
* *
61149 TTACTTGCT
1 TTATTTTCT
*
61158 ATT-TTATCT
1 -TTATTTTCT
61167 TTATTTTCT
1 TTATTTTCT
*
61176 TTATCTTCTT
1 TTATTTTC-T
61186 TTATTT
1 TTATTT
61192 AATTTGTTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
7 1 0.01
8 24 0.29
9 46 0.55
10 12 0.14
ACGTcount: A:0.14, C:0.08, G:0.01, T:0.77
Consensus pattern (9 bp):
TTATTTTCT
Found at i:61179 original size:53 final size:51
Alignment explanation
Indices: 61022--61191 Score: 150
Period size: 53 Copynumber: 3.3 Consensus size: 51
61012 ATATATTTAC
* * * * *
61022 TATTTTTTTA-TTTATTATTTATTATA-T-ATATATATATATTATTTTTACTT
1 TATTTTTTTATTTTTTTATTTATTTTATTGATAT-TTTATCTTCTTTTT-CTT
* * * *
61072 TATTATTATTATTTTTTTATTTTTTTTATTTATATTTTTTCTTCTTTTTCTT
1 TATT-TTTTTATTTTTTTATTTATTTTATTGATATTTTATCTTCTTTTTCTT
*
61124 TATTTTTTTATTTTTTATATTTATTTTACTTGCTATTTTATCTT-TATTTTCTT
1 TATTTTTTTATTTTTT-TATTTATTTTA-TTGATATTTTATCTTCT-TTTTCTT
61177 TATCTTCTTTTATTT
1 TAT-TT-TTTTATTT
61192 AATTTGTTTT
Statistics
Matches: 98, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
50 4 0.04
51 16 0.16
52 31 0.32
53 33 0.34
54 6 0.06
55 8 0.08
ACGTcount: A:0.20, C:0.06, G:0.01, T:0.74
Consensus pattern (51 bp):
TATTTTTTTATTTTTTTATTTATTTTATTGATATTTTATCTTCTTTTTCTT
Found at i:61221 original size:26 final size:25
Alignment explanation
Indices: 61179--61233 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
61169 ATTTTCTTTA
*
61179 TCTTCTTTTATTTAATTTGTTT-TT
1 TCTTCTTTTATTTAATTTATTTATT
61203 TCTTCATTTTAATTTAATTTATTTATT
1 TCTTC-TTTT-ATTTAATTTATTTATT
61230 TCTT
1 TCTT
61234 ACCTTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 4 0.15
26 12 0.44
27 6 0.22
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.71
Consensus pattern (25 bp):
TCTTCTTTTATTTAATTTATTTATT
Found at i:63482 original size:20 final size:21
Alignment explanation
Indices: 63449--63491 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
63439 TTTGAAGTCT
*
63449 TTATACTATCTGAAAAGTTCA
1 TTATACTATATGAAAAGTTCA
63470 TTATA-TATATGAAAAGTTCA
1 TTATACTATATGAAAAGTTCA
63490 TT
1 TT
63492 TGGTAGTCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (21 bp):
TTATACTATATGAAAAGTTCA
Found at i:64170 original size:17 final size:17
Alignment explanation
Indices: 64148--64186 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
64138 ACTCATCAAT
64148 AATATTTTTATAA-ATAA
1 AATATTTTTATAAGA-AA
*
64165 AATATTTTTTTAAGAAA
1 AATATTTTTATAAGAAA
64182 AATAT
1 AATAT
64187 ATTATCAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 19 0.95
18 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
AATATTTTTATAAGAAA
Found at i:66624 original size:2 final size:2
Alignment explanation
Indices: 66617--66659 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
66607 GATTATTTAA
66617 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66659 A
1 A
66660 AGTTAGATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.