Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008784.1 Hibiscus syriacus cultivar Beakdansim tig00111915_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: 122791
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:7188 original size:134 final size:133
Alignment explanation
Indices: 7039--7381 Score: 440
Period size: 133 Copynumber: 2.6 Consensus size: 133
7029 TCTTTTAACA
* * ** *
7039 TTTGATCTTCCTGAAGAGCAGTGAAGCAAATTAAATTTGATTCAATCTTCTATGAAGAGCAGTGA
1 TTTG-TCTTCCTGAAGAGCAGTGAAGCAAATCAAGTTTGATTCAATCTTCCCTGAAGAGCAGCGA
* *
7104 AGTGGATCAAAATTTTCT-CAAGTCTGATCCCCCCTAAAGAGTAGTGGAGCATATTCTTATTCTT
65 AGTGGATCAAAA--TTCTACAAGTCTGATCCCCCCTAAAGAGTAGTGGAACATATCCTTATTCTT
7168 TCAGAT
128 TCAGAT
* * *
7174 TTTGTCTTCCTGAAGAGCAGTGAAGCAAATCAAGTTCGATTCAATCTTCCCTTAAGAGCAGCAAA
1 TTTGTCTTCCTGAAGAGCAGTGAAGCAAATCAAGTTTGATTCAATCTTCCCTGAAGAGCAGCGAA
** * * *
7239 GTGGATCACGATTCTACAAGTCTGATCTCCCCTAAAGAGTAGTGGAACATATCCTTTTTCTTTTA
66 GTGGATCAAAATTCTACAAGTCTGATCCCCCCTAAAGAGTAGTGGAACATATCCTTATTCTTTCA
7304 GAT
131 GAT
* * * * *
7307 TTGGTTTTACTGAATAGCAGTGAAGCAAATCAAGTTT-AGTTCAACCTTCCCTGAAGAGC-GACG
1 TTTGTCTTCCTGAAGAGCAGTGAAGCAAATCAAGTTTGA-TTCAATCTTCCCTGAAGAGCAG-CG
7370 AAGTGGATCAAA
64 AAGTGGATCAAA
7382 TCTTTCAGAT
Statistics
Matches: 180, Mismatches: 25, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
132 6 0.03
133 108 0.60
134 62 0.34
135 4 0.02
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (133 bp):
TTTGTCTTCCTGAAGAGCAGTGAAGCAAATCAAGTTTGATTCAATCTTCCCTGAAGAGCAGCGAA
GTGGATCAAAATTCTACAAGTCTGATCCCCCCTAAAGAGTAGTGGAACATATCCTTATTCTTTCA
GAT
Found at i:8257 original size:18 final size:19
Alignment explanation
Indices: 8222--8260 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
8212 TAATTCATGT
*
8222 AAAATAAATATTCATATTAA
1 AAAATAAAAATT-ATATTAA
8242 AAAATAAAAATT-TATTAA
1 AAAATAAAAATTATATTAA
8260 A
1 A
8261 TATTTAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAATAAAAATTATATTAA
Found at i:9130 original size:12 final size:12
Alignment explanation
Indices: 9115--9139 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9105 CCACCGTCAC
9115 CCTCATTATCTT
1 CCTCATTATCTT
9127 CCTCATTATCTT
1 CCTCATTATCTT
9139 C
1 C
9140 TCTTAAGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (12 bp):
CCTCATTATCTT
Found at i:29827 original size:15 final size:15
Alignment explanation
Indices: 29807--29961 Score: 175
Period size: 15 Copynumber: 10.1 Consensus size: 15
29797 GCAGAATCAC
* *
29807 TAATACAAGTAAAAT
1 TAATACAAGCAGAAT
* *
29822 TAATACGAGCATAATT
1 TAATACAAGCAGAA-T
*
29838 ATCAATTCAAGCAGAAT
1 -T-AATACAAGCAGAAT
29855 TAATACAAGCAGAAT
1 TAATACAAGCAGAAT
* *
29870 TATTACAGGCAGAAT
1 TAATACAAGCAGAAT
*
29885 TAATACGAGCAGAAT
1 TAATACAAGCAGAAT
*
29900 TATTACAAGCAGAAT
1 TAATACAAGCAGAAT
*
29915 TAATACGAGCAGAAT
1 TAATACAAGCAGAAT
*
29930 TATTACAAGCAGAAT
1 TAATACAAGCAGAAT
*
29945 TAATACGAGCAGAAT
1 TAATACAAGCAGAAT
29960 TA
1 TA
29962 GTAATACAAG
Statistics
Matches: 117, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
15 103 0.88
16 2 0.02
17 2 0.02
18 10 0.09
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.25
Consensus pattern (15 bp):
TAATACAAGCAGAAT
Found at i:29855 original size:18 final size:17
Alignment explanation
Indices: 29796--30067 Score: 145
Period size: 15 Copynumber: 16.5 Consensus size: 17
29786 AAAAATTATG
*
29796 AGCAGAATCACTAATACA
1 AGCAGAATTA-TAATACA
* * *
29814 AGTA-AAAT-TAATACG
1 AGCAGAATTATAATACA
* *
29829 AGCATAATTATCAATTCA
1 AGCAGAATTAT-AATACA
29847 AGCAGAA-T-TAATACA
1 AGCAGAATTATAATACA
29862 AGCAGAATTAT--TACA
1 AGCAGAATTATAATACA
* *
29877 GGCAGAA-T-TAATACG
1 AGCAGAATTATAATACA
29892 AGCAGAATTAT--TACA
1 AGCAGAATTATAATACA
*
29907 AGCAGAA-T-TAATACG
1 AGCAGAATTATAATACA
29922 AGCAGAATTAT--TACA
1 AGCAGAATTATAATACA
*
29937 AGCAGAA-T-TAATACG
1 AGCAGAATTATAATACA
29952 AGCAGAATTAGTAATACA
1 AGCAGAATTA-TAATACA
* * *
29970 AGCAAAATCATTA-ACA
1 AGCAGAATTATAATACA
29986 TGAGCAGAATTATTAATAGACA
1 --AGCAGAATTA-TAAT--ACA
30008 CTTGAGCAGAATTAT--TACA
1 ----AGCAGAATTATAATACA
*
30027 AGCAGAA-T-TAATACG
1 AGCAGAATTATAATACA
30042 AGCAGAATTAGTAATACA
1 AGCAGAATTA-TAATACA
*
30060 AGAAGAAT
1 AGCAGAAT
30068 CATTAACATG
Statistics
Matches: 196, Mismatches: 27, Indels: 62
0.69 0.09 0.22
Matches are distributed among these distances:
13 4 0.02
14 4 0.02
15 97 0.49
16 12 0.06
17 9 0.05
18 48 0.24
19 5 0.03
21 1 0.01
22 3 0.02
23 1 0.01
24 12 0.06
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.24
Consensus pattern (17 bp):
AGCAGAATTATAATACA
Found at i:29884 original size:30 final size:30
Alignment explanation
Indices: 29810--30051 Score: 246
Period size: 30 Copynumber: 8.0 Consensus size: 30
29800 GAATCACTAA
* * *
29810 TACAAGTAAAATTAATACGAGCATAATTAT
1 TACAAGCAGAATTAATACGAGCAGAATTAT
* *
29840 CAATTCAAGCAGAATTAATACAAGCAGAATTAT
1 ---TACAAGCAGAATTAATACGAGCAGAATTAT
*
29873 TACAGGCAGAATTAATACGAGCAGAATTAT
1 TACAAGCAGAATTAATACGAGCAGAATTAT
29903 TACAAGCAGAATTAATACGAGCAGAATTAT
1 TACAAGCAGAATTAATACGAGCAGAATTAT
29933 TACAAGCAGAATTAATACGAGCAGAATTAGT
1 TACAAGCAGAATTAATACGAGCAGAATTA-T
* * *
29964 AATACAAGCAAAATCATTAACATGAGCAGAATTAT
1 --TACAAGC-AGA--ATTAATACGAGCAGAATTAT
* *
29999 TA-ATAG-A-CACT--T--GAGCAGAATTAT
1 TACA-AGCAGAATTAATACGAGCAGAATTAT
30023 TACAAGCAGAATTAATACGAGCAGAATTA
1 TACAAGCAGAATTAATACGAGCAGAATTA
30052 GTAATACAAG
Statistics
Matches: 178, Mismatches: 17, Indels: 31
0.79 0.08 0.14
Matches are distributed among these distances:
24 16 0.09
25 2 0.01
26 2 0.01
28 3 0.02
30 96 0.54
31 2 0.01
32 1 0.01
33 36 0.20
34 2 0.01
35 1 0.01
36 17 0.10
ACGTcount: A:0.47, C:0.13, G:0.15, T:0.24
Consensus pattern (30 bp):
TACAAGCAGAATTAATACGAGCAGAATTAT
Found at i:30015 original size:90 final size:90
Alignment explanation
Indices: 29921--30094 Score: 332
Period size: 90 Copynumber: 1.9 Consensus size: 90
29911 GAATTAATAC
29921 GAGCAGAATTATTACAAGCAGAATTAATACGAGCAGAATTAGTAATACAAGCAA-AATCATTAAC
1 GAGCAGAATTATTACAAGCAGAATTAATACGAGCAGAATTAGTAATACAAG-AAGAATCATTAAC
29985 ATGAGCAGAATTATTAATAGACACTT
65 ATGAGCAGAATTATTAATAGACACTT
30011 GAGCAGAATTATTACAAGCAGAATTAATACGAGCAGAATTAGTAATACAAGAAGAATCATTAACA
1 GAGCAGAATTATTACAAGCAGAATTAATACGAGCAGAATTAGTAATACAAGAAGAATCATTAACA
30076 TGAGCAGAATTATTAATAG
66 TGAGCAGAATTATTAATAG
30095 GCAGACAAGT
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
89 2 0.02
90 81 0.98
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24
Consensus pattern (90 bp):
GAGCAGAATTATTACAAGCAGAATTAATACGAGCAGAATTAGTAATACAAGAAGAATCATTAACA
TGAGCAGAATTATTAATAGACACTT
Found at i:30032 original size:15 final size:15
Alignment explanation
Indices: 30012--30090 Score: 68
Period size: 15 Copynumber: 4.9 Consensus size: 15
30002 TAGACACTTG
30012 AGCAGAATTATTACA
1 AGCAGAATTATTACA
* *
30027 AGCAGAATTAATACG
1 AGCAGAATTATTACA
30042 AGCAGAATTAGTAATACA
1 AGCAGAATTA-T--TACA
* *
30060 AGAAGAATCATTAACA
1 AGCAGAATTATT-ACA
30076 TGAGCAGAATTATTA
1 --AGCAGAATTATTA
30091 ATAGGCAGAC
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
15 24 0.48
16 3 0.06
17 2 0.04
18 21 0.42
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.24
Consensus pattern (15 bp):
AGCAGAATTATTACA
Found at i:32408 original size:18 final size:19
Alignment explanation
Indices: 32366--32409 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
32356 ATATTTGACT
* *
32366 TTATTTATAATTTTTTACA
1 TTATTTATAATTTTTAAAA
32385 TCTATTTATAA-TTTTAAAA
1 T-TATTTATAATTTTTAAAA
32404 TTATTT
1 TTATTT
32410 TATATGTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 9 0.41
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTTATAATTTTTAAAA
Found at i:32494 original size:12 final size:12
Alignment explanation
Indices: 32479--32504 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
32469 CCCCATCCCT
32479 GTCCCCGTATCC
1 GTCCCCGTATCC
32491 GTCCCCGTATCC
1 GTCCCCGTATCC
32503 GT
1 GT
32505 ATCGGTGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.46, G:0.19, T:0.27
Consensus pattern (12 bp):
GTCCCCGTATCC
Found at i:39801 original size:84 final size:84
Alignment explanation
Indices: 39623--39846 Score: 247
Period size: 84 Copynumber: 2.7 Consensus size: 84
39613 AGCTGTCAGG
* * * *
39623 GAACAAATCAGATGGTGCAGTTCAACCACCGAGGCTCTCGAAGG-CAAAATCAGATAGGGGAGTT
1 GAACAAATCAGATAGTGCATTTCAATCACCGAGGCTCTCGAAGGAC-AAACCAGATAGGGGAGTT
** * *
39687 ATATTTTCCGGGCCCCTGGT
65 ATATTCCCCAGGCCCCTAGT
* * * *
39707 GAACATATCAGAAAGTGCATTTCAATCACCAAGGCTCTTGAAGGACAAACCAGATAGGGGAGTTC
1 GAACAAATCAGATAGTGCATTTCAATCACCGAGGCTCTCGAAGGACAAACCAGATAGGGGAGTT-
*
39772 A-A-TCCCCAAGGCTCCTAGT
65 ATATTCCCC-AGGCCCCTAGT
* * * *
39791 GAGCAAATCAGATAGTGCATGTCGATCACCGAGGCTCTCGAAGGACAAACCTGATA
1 GAACAAATCAGATAGTGCATTTCAATCACCGAGGCTCTCGAAGGACAAACCAGATA
39847 CAGAATTTCA
Statistics
Matches: 116, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
83 3 0.03
84 111 0.96
85 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (84 bp):
GAACAAATCAGATAGTGCATTTCAATCACCGAGGCTCTCGAAGGACAAACCAGATAGGGGAGTTA
TATTCCCCAGGCCCCTAGT
Found at i:42864 original size:4 final size:4
Alignment explanation
Indices: 42855--42932 Score: 147
Period size: 4 Copynumber: 19.5 Consensus size: 4
42845 AATTCAATAT
*
42855 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
42903 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
42933 GTATACATAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 72 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:43080 original size:13 final size:13
Alignment explanation
Indices: 43062--43095 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
43052 AGCAGCTCTT
43062 TCATTTTTTAATC
1 TCATTTTTTAATC
43075 TCA-TTTTTAATC
1 TCATTTTTTAATC
43087 TCATTTTTT
1 TCATTTTTT
43096 GTCCTCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.65
Consensus pattern (13 bp):
TCATTTTTTAATC
Found at i:43987 original size:15 final size:15
Alignment explanation
Indices: 43967--44002 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
43957 AAAGTTCGAT
*
43967 TAATTCGGTTAATGG
1 TAATTCGGTTAATAG
43982 TAATTCGGTTAATAG
1 TAATTCGGTTAATAG
43997 TAATTC
1 TAATTC
44003 AATTTTATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (15 bp):
TAATTCGGTTAATAG
Found at i:44252 original size:2 final size:2
Alignment explanation
Indices: 44245--44269 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44235 TCTTGATAGA
44245 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
44270 ATTCAAACCT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50012 original size:24 final size:24
Alignment explanation
Indices: 49983--50032 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
49973 TGGTGGTTGA
*
49983 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
50007 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
50031 TT
1 TT
50033 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:50538 original size:17 final size:16
Alignment explanation
Indices: 50507--50540 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
50497 CACGTGAGGA
50507 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
50523 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
50540 T
1 T
50541 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:53223 original size:19 final size:20
Alignment explanation
Indices: 53186--53225 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
53176 GGGTAATAAT
*
53186 ATAAGTAATGAAAATAAATA
1 ATAAGTAATGAAAAGAAATA
*
53206 ATAAG-AATGAAACGAAATA
1 ATAAGTAATGAAAAGAAATA
53225 A
1 A
53226 ATAAAAGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:53681 original size:19 final size:21
Alignment explanation
Indices: 53638--53689 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
53628 GAAACCCCTT
53638 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
53659 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
53678 TGAAGATACATG
1 TGAAAATACATG
53690 CTCTTGGACG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:57818 original size:19 final size:21
Alignment explanation
Indices: 57775--57826 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
57765 GAAACCCCTT
57775 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
57796 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
57815 TGAAGATACATG
1 TGAAAATACATG
57827 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:61353 original size:81 final size:81
Alignment explanation
Indices: 61251--61808 Score: 720
Period size: 81 Copynumber: 7.0 Consensus size: 81
61241 CACTTTCCTA
* ** * * * * * *
61251 TCAAATGCACAGCTAATCCATTATTCTCTTACTCAACAGTGTTTAATCGTACATCTAACTTGCAT
1 TCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCAT
61316 AATTGACACATTTCTG
66 AATTGACACATTTCTG
** * * *
61332 TCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACAATAGTTAACCTTTCATATAACTGGCAT
1 TCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCAT
* *
61397 AATTGACACTTTTATG
66 AATTGACACATTTCTG
* * *
61413 TCAAATGGACAATTAGGCCATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCAT
1 TCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCAT
* *
61478 AATTGACACCTTTCTA
66 AATTGACACATTTCTG
61494 TCAAATGCAC----A----ATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCAT
1 TCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCAT
*
61551 AATTGACACTTTTCTG
66 AATTGACACATTTCTG
* * *
61567 TCAATTGCACAGTTAGGCCATTATTATTTTACTCAACGGTATTTAACCGTTCATCTAACAGGCAT
1 TCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCAT
61632 AATTGACATC-TTTCTG
66 AATTGACA-CATTTCTG
* * * *
61648 TCAAATGCACAGTTAGGCCATTATTATTTTACTCAACGGTATTTAATCATTTATCTAACTGGCAT
1 TCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCAT
*
61713 AATTGACACATTTATG
66 AATTGACACATTTCTG
* * ** **
61729 TCAATTGCATAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAGTCGTTCATCTAACTTACAT
1 TCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCAT
61794 AATTGACACATTTCT
66 AATTGACACATTTCT
61809 TCCAATTACA
Statistics
Matches: 422, Mismatches: 45, Indels: 20
0.87 0.09 0.04
Matches are distributed among these distances:
73 68 0.16
77 2 0.00
80 1 0.00
81 350 0.83
82 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (81 bp):
TCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCAT
AATTGACACATTTCTG
Found at i:61681 original size:235 final size:239
Alignment explanation
Indices: 61270--61828 Score: 734
Period size: 235 Copynumber: 2.3 Consensus size: 239
61260 CAGCTAATCC
* * * *
61270 ATTATTCTCTTACTCAACAGTGTTTAATCGTACATCTAACTTGCATAATTGACACATTTCTGTCA
1 ATTATTCTTTTACTCAACGGTATTTAATCGTTCATCTAACTTGCATAATTGACACATTTCTGTCA
* * * *
61335 AATGCACAGTTAGGCCATTATTCTTTTACTCAACAATAGTTAACCTTTCATATAACTGGCATAAT
66 ATTGCACAGTTAGGCCATTATTATTTTACTCAACAATAGTTAACCGTTCATATAACAGGCATAAT
* * *
61400 TGACACTTTTATGTCAAATGGACAATTAGGCCATTATTCTTTTACTCAACAGTATTTAACCGTTC
131 TGACACTTTTATGTCAAATGCACAATTAGGCCATTATTATTTTACTCAACAGTATTTAACCATTC
* *
61465 ATCTAACTGGCATAATTGACACCTTTCTATCAA-AT-G-CA-CA
196 ATCTAACTGGCATAATTGACACATTTATATCAATATAGTCAGCA
* * *
61505 ATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACTTTTCTGTCA
1 ATTATTCTTTTACTCAACGGTATTTAATCGTTCATCTAACTTGCATAATTGACACATTTCTGTCA
** * *
61570 ATTGCACAGTTAGGCCATTATTATTTTACTCAACGGTATTTAACCGTTCATCTAACAGGCATAAT
66 ATTGCACAGTTAGGCCATTATTATTTTACTCAACAATAGTTAACCGTTCATATAACAGGCATAAT
* * * *
61635 TGACA-TCTTTCTGTCAAATGCACAGTTAGGCCATTATTATTTTACTCAACGGTATTTAATCATT
131 TGACACT-TTTATGTCAAATGCACAATTAGGCCATTATTATTTTACTCAACAGTATTTAACCATT
* * * *
61699 TATCTAACTGGCATAATTGACACATTTATGTCAATTGCATAGTTAGGCC
195 CATCTAACTGGCATAATTGACACATTTATATCAA-T--ATAGTCA-GCA
* *
61748 ATTATTCTTTTACTCAACGGTATTTAGTCGTTCATCTAACTTACATAATTGACACATTTCT-TCC
1 ATTATTCTTTTACTCAACGGTATTTAATCGTTCATCTAACTTGCATAATTGACACATTTCTGT-C
* *
61812 AATTACATAGTTAGGCC
65 AATTGCACAGTTAGGCC
61829 TCAAAGGGAC
Statistics
Matches: 279, Mismatches: 35, Indels: 12
0.86 0.11 0.04
Matches are distributed among these distances:
234 1 0.00
235 200 0.72
239 2 0.01
240 1 0.00
241 1 0.00
242 1 0.00
243 73 0.26
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (239 bp):
ATTATTCTTTTACTCAACGGTATTTAATCGTTCATCTAACTTGCATAATTGACACATTTCTGTCA
ATTGCACAGTTAGGCCATTATTATTTTACTCAACAATAGTTAACCGTTCATATAACAGGCATAAT
TGACACTTTTATGTCAAATGCACAATTAGGCCATTATTATTTTACTCAACAGTATTTAACCATTC
ATCTAACTGGCATAATTGACACATTTATATCAATATAGTCAGCA
Found at i:61871 original size:68 final size:67
Alignment explanation
Indices: 61778--62033 Score: 302
Period size: 68 Copynumber: 3.8 Consensus size: 67
61768 TATTTAGTCG
* * * * *
61778 TTCATCTAACT-TACATAATTGACACATTTCTTCCAATTACATAGTTAGGCCTCAAAGGGACTTA
1 TTCATCTAACTGGA-ATAAATGACACATTTCTT-CAATTGCACAGTTAGGCCTCAAAGGCACTTA
61842 GCCT
64 GCCT
61846 TTCATCTAACTGGAATAAATGACACATTTCTTTC-ATATGCACAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGAATAAATGACACATTTC-TTCAAT-TGCACAGTTAGGCCTCAAAGGCACTTA
61910 GCCT
64 GCCT
*** * * * *
61914 TTCATCTAACTACCATAAATGACACCTTTCTGTCATTTGCACAGTTAGACCTCATAGGCACTTAG
1 TTCATCTAACTGGAATAAATGACACATTTCT-TCAATTGCACAGTTAGGCCTCAAAGGCACTTAG
61979 CCT
65 CCT
* *
61982 TTCATCTAACTGGCATAAATGACATC-TTTCTATCATTTGCACAGTTAGGCCT
1 TTCATCTAACTGGAATAAATGACA-CATTTCT-TCAATTGCACAGTTAGGCCT
62034 ATAATCGTTT
Statistics
Matches: 166, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
67 3 0.02
68 158 0.95
69 5 0.03
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (67 bp):
TTCATCTAACTGGAATAAATGACACATTTCTTCAATTGCACAGTTAGGCCTCAAAGGCACTTAGC
CT
Found at i:62004 original size:136 final size:136
Alignment explanation
Indices: 61778--62033 Score: 365
Period size: 136 Copynumber: 1.9 Consensus size: 136
61768 TATTTAGTCG
* * * *
61778 TTCATCTAACTTACATAATTGACACATTTCTTCCAATTACATAGTTAGGCCTCAAAGGGACTTAG
1 TTCATCTAACTTACATAAATGACACATTTCTTCCAATTACACAGTTAGACCTCAAAGGCACTTAG
*
61843 CCTTTCATCTAACTGGAATAAATGACA-CATTTCTTTCATATGCACAGTTAGGCCTCAAAGGCAC
66 CCTTTCATCTAACTGGAATAAATGACATC-TTTCTATCATATGCACAGTTAGGCCTCAAAGGCAC
61907 TTAGCCT
130 TTAGCCT
* * * *
61914 TTCATCTAAC-TACCATAAATGACACCTTTCTGT-CATTTGCACAGTTAGACCTCATAGGCACTT
1 TTCATCTAACTTA-CATAAATGACACATTTCT-TCCAATTACACAGTTAGACCTCAAAGGCACTT
* *
61977 AGCCTTTCATCTAACTGGCATAAATGACATCTTTCTATCATTTGCACAGTTAGGCCT
64 AGCCTTTCATCTAACTGGAATAAATGACATCTTTCTATCATATGCACAGTTAGGCCT
62034 ATAATCGTTT
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
135 2 0.02
136 102 0.96
137 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (136 bp):
TTCATCTAACTTACATAAATGACACATTTCTTCCAATTACACAGTTAGACCTCAAAGGCACTTAG
CCTTTCATCTAACTGGAATAAATGACATCTTTCTATCATATGCACAGTTAGGCCTCAAAGGCACT
TAGCCT
Found at i:62798 original size:20 final size:21
Alignment explanation
Indices: 62773--62817 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
62763 ATGTTGCCTA
*
62773 GTATCGATACT-CTTACTATG
1 GTATCGATACTACATACTATG
62793 GTATCGATACTACCATACTATG
1 GTATCGATACTA-CATACTATG
62815 GTA
1 GTA
62818 CCAATATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.50
22 11 0.50
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (21 bp):
GTATCGATACTACATACTATG
Found at i:66313 original size:31 final size:31
Alignment explanation
Indices: 66270--66334 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
66260 GTCCCGAATG
*
66270 ACCTATCCATATGTCCTGAAGGACATACGTA
1 ACCTATCCATATGTCCCGAAGGACATACGTA
* *
66301 ACCTGTCCATATGTCCCGAAGGACATAGGTA
1 ACCTATCCATATGTCCCGAAGGACATACGTA
66332 ACC
1 ACC
66335 CTCGACTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (31 bp):
ACCTATCCATATGTCCCGAAGGACATACGTA
Found at i:69428 original size:81 final size:81
Alignment explanation
Indices: 69209--69817 Score: 767
Period size: 81 Copynumber: 7.5 Consensus size: 81
69199 GTTTTTCACT
* * * * * ** * *
69209 TAACTTGCATATTTGACA-ATTTCCTGTCAAATGTAAAGCTAATCCATTATTCTCTTACTCAACA
1 TAACTGGCATAATTGACACATTT-CTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACG
* * *
69273 GTGTTTAACCGTACATC
65 GTATTTAACCATTCATC
* * *
69290 TAACTGGCATAATTGACAC-TTTCTGTTAAATGCACAGTTAGACCATTATCCTTTTACTCAACGG
1 TAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGG
**
69354 TATTTAACTGTTCATC
66 TATTTAACCATTCATC
* * *
69370 TAACTAGCATAATTGACATATTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGT
1 TAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGG
69435 TATTTAACCATTCATC
66 TATTTAACCATTCATC
* * * * * *
69451 TAACTGGCATAATTGACACTTTTTCTATTAAATACACAATTAGGCCATTATTCTTTTACTCAATG
1 TAACTGGCATAATTGACAC-ATTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACG
* *
69516 GTATTTAGCCTTTCATC
65 GTATTTAACCATTCATC
* * * *
69533 TAACTGGCATAATTGACACTTTTCTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTTAATGG
1 TAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGG
*
69598 TATTTATCCATTCATC
66 TATTTAACCATTCATC
* * * *
69614 TAACAGGCATAATTGACACATTTATGTCAAATGCATAGTTAGGCCATTATTCTTTTGCTCAACGG
1 TAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGG
*
69679 TATTTAACTATTCATC
66 TATTTAACCATTCATC
* *
69695 TAACTGGCATAATTGACACATTTCTGT-AAATTGCACAGTTAGGTCATTATTCTTTTACTCAATG
1 TAACTGGCATAATTGACACATTTCTGTCAAA-TGCACAGTTAGGCCATTATTCTTTTACTCAACG
* *
69759 GTGTTTAGCCATTCATC
65 GTATTTAACCATTCATC
*
69776 TAACTGGCATAATTGACACATTTCT-TCCAATTGCACAGTTAG
1 TAACTGGCATAATTGACACATTTCTGT-CAAATGCACAGTTAG
69818 ACCTCAAAGG
Statistics
Matches: 461, Mismatches: 61, Indels: 12
0.86 0.11 0.02
Matches are distributed among these distances:
80 67 0.15
81 320 0.69
82 74 0.16
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (81 bp):
TAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCATTATTCTTTTACTCAACGG
TATTTAACCATTCATC
Found at i:70090 original size:68 final size:68
Alignment explanation
Indices: 69763--70093 Score: 493
Period size: 68 Copynumber: 4.9 Consensus size: 68
69753 TCAATGGTGT
* * * *
69763 TTAGCCATTCATCTAACTGGCATAATTGACACATTTCT-TCCAATTGCACAGTTAGACCTCAAAG
1 TTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGT-CATTTGCACAGTTAGGCCTCAAAG
69827 GCAC
65 GCAC
* * *
69831 TTAGCCTTTCATCTAACTGGCATAAATAATACATTTCTGTCATTTGCACAGTTAAGCCTCAAAGG
1 TTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGG
69896 CAC
66 CAC
* * * * * *
69899 CTAGCCTTTCATCTAACTGGCATAAATGATACTTTTCTATCATTTGCACAGTTCGGCCTTAAAGG
1 TTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGG
69964 CAC
66 CAC
* * *
69967 TTAGCCTTTTATCTAACTGGCATGAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGG
1 TTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGG
70032 CAC
66 CAC
*
70035 TTAGCCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCT
1 TTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCT
70094 ATAATCGTTT
Statistics
Matches: 238, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
68 237 1.00
69 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (68 bp):
TTAGCCTTTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCACAGTTAGGCCTCAAAGG
CAC
Found at i:70947 original size:94 final size:95
Alignment explanation
Indices: 70771--70950 Score: 247
Period size: 94 Copynumber: 1.9 Consensus size: 95
70761 TGATACTTCT
* * * *
70771 ATACTATGGTATCGATACTCCCTTCTGGTATCGATACTGATTTTAGGTTTGATGTTGCCTAGTAT
1 ATACTATGGTATCGATACCCCCTTCAGGTATCGATACTGATTTTAGATTCGATGTTGCCTAGTAT
* *
70836 CGATACTCTTACTATGGTATCAAAACTATC
66 CGATACCCTAACTATGGTATCAAAACTATC
* * * *
70866 ATACTATGGTATCGATACCCCCTT-AGGTATCGATACTGGTTTTTGATTCGATGTTGCTTGGTAT
1 ATACTATGGTATCGATACCCCCTTCAGGTATCGATACTGATTTTAGATTCGATGTTGCCTAGTAT
70930 CGATACCCTAA-TCATGGTATC
66 CGATACCCTAACT-ATGGTATC
70951 GATACTACCT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
93 1 0.01
94 50 0.68
95 23 0.31
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.38
Consensus pattern (95 bp):
ATACTATGGTATCGATACCCCCTTCAGGTATCGATACTGATTTTAGATTCGATGTTGCCTAGTAT
CGATACCCTAACTATGGTATCAAAACTATC
Found at i:73766 original size:15 final size:15
Alignment explanation
Indices: 73748--73816 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
73738 CTAATATTGA
73748 AATTTATGTTATTTT
1 AATTTATGTTATTTT
* * *
73763 AATTTTTGGTATTAT
1 AATTTATGTTATTTT
*
73778 -ATTTATTGTTATGTT
1 AATTTA-TGTTATTTT
* *
73793 ATTTTATGTTCTTTT
1 AATTTATGTTATTTT
73808 AATTCTATG
1 AATT-TATG
73817 ACTAGGATTT
Statistics
Matches: 40, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
14 4 0.10
15 28 0.70
16 8 0.20
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.64
Consensus pattern (15 bp):
AATTTATGTTATTTT
Found at i:75258 original size:24 final size:24
Alignment explanation
Indices: 75231--75329 Score: 65
Period size: 24 Copynumber: 4.2 Consensus size: 24
75221 TATATCAAAA
*
75231 ATCAAAACATAATTCAAGTCAAGT
1 ATCAAAACAGAATTCAAGTCAAGT
* * * *
75255 ATCAGATCAGAATTCAGGTCATGT
1 ATCAAAACAGAATTCAAGTCAAGT
* * * *
75279 ATCAGATCAGAATCCATGTCAA-T
1 ATCAAAACAGAATTCAAGTCAAGT
* * * * *
75302 ATCAGATCAGAATCCAGGTCAGGT
1 ATCAAAACAGAATTCAAGTCAAGT
75326 ATCA
1 ATCA
75330 TAGCAAAATT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
23 21 0.33
24 43 0.67
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.25
Consensus pattern (24 bp):
ATCAAAACAGAATTCAAGTCAAGT
Found at i:75308 original size:23 final size:23
Alignment explanation
Indices: 75248--75322 Score: 105
Period size: 24 Copynumber: 3.2 Consensus size: 23
75238 CATAATTCAA
*
75248 GTCAAGTATCAGATCAGAATTCAG
1 GTCAA-TATCAGATCAGAATCCAG
* *
75272 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAG
75296 GTCAATATCAGATCAGAATCCAG
1 GTCAATATCAGATCAGAATCCAG
75319 GTCA
1 GTCA
75323 GGTATCATAG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.47
24 24 0.53
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAG
Found at i:76941 original size:17 final size:18
Alignment explanation
Indices: 76910--76945 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
76900 AAACTAACAT
76910 TTTTTATGCACATCAATA
1 TTTTTATGCACATCAATA
*
76928 TTTTTAT-CAGATCAATA
1 TTTTTATGCACATCAATA
76945 T
1 T
76946 GTATGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (18 bp):
TTTTTATGCACATCAATA
Found at i:83370 original size:35 final size:35
Alignment explanation
Indices: 83329--83397 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
83319 ATCAATTATA
*
83329 TTAAACCCCAAAATCCAAAAAT-TTTCAATTACATT
1 TTAAACCCC-AAATCCAAAAATACTTCAATTACATT
* * *
83364 TTAAACCTCAAATTCTAAAATACTTCAATTACAT
1 TTAAACCCCAAATCCAAAAATACTTCAATTACAT
83398 ACCCAACCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 10 0.34
35 19 0.66
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (35 bp):
TTAAACCCCAAATCCAAAAATACTTCAATTACATT
Found at i:83766 original size:142 final size:147
Alignment explanation
Indices: 83567--83854 Score: 433
Period size: 147 Copynumber: 2.0 Consensus size: 147
83557 AAATACTCAA
* * * *
83567 TTCAGTTTATAAAAATAGTTGACTCGAATTTTTTTTGATTTGATTTTATAAAATTTAAATC-A-A
1 TTCAGTTTATAAAAATAATTGACTCGAATATTTTTCGATTTGAGTTTATAAAATTTAAATCAAGA
* *
83630 G-TCGAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTATAATATT
66 GATCGAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATT
*
83694 ATTTGATTCTAATTCAG
131 ATTTGATTATAATTCAG
83711 TTCAGTTTAT-AAAATAATTGACTCGAA-ATTTTTCGATTTGAGTTTATAAAATTTAAATCAAGT
1 TTCAGTTTATAAAAATAATTGACTCGAATATTTTTCGATTTGAGTTTATAAAATTTAAATCAAG-
* * *
83774 AGAATTGAATTGAATTTTCAAGTTTTTGTTTAAATTTAATTATCAATATTTATAATACTATAATA
65 AG-ATCGAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATA
83839 TTATTTGATTATAATT
129 TTATTTGATTATAATT
83855 TAAATAGTTT
Statistics
Matches: 129, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
142 29 0.22
143 17 0.13
144 10 0.08
145 2 0.02
147 71 0.55
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (147 bp):
TTCAGTTTATAAAAATAATTGACTCGAATATTTTTCGATTTGAGTTTATAAAATTTAAATCAAGA
GATCGAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATT
ATTTGATTATAATTCAG
Found at i:84353 original size:6 final size:6
Alignment explanation
Indices: 84342--84368 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
84332 AATTATGAAT
84342 TTGGGG TTGGGG TTGGGG TTGGGG TTG
1 TTGGGG TTGGGG TTGGGG TTGGGG TTG
84369 TAACTGAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.63, T:0.37
Consensus pattern (6 bp):
TTGGGG
Found at i:84418 original size:35 final size:35
Alignment explanation
Indices: 84367--84445 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
84357 GGGTTGGGGT
* *
84367 TGTAACTGAAGTATTTTGAAATTTGA-GGTTTAGAA
1 TGTAATTGAAGCATTTTG-AATTTGAGGGTTTAGAA
* *
84402 TGTAATTGAAGCATTTTGGATTTTAGGGTTTAGAA
1 TGTAATTGAAGCATTTTGAATTTGAGGGTTTAGAA
84437 TGTAATTGA
1 TGTAATTGA
84446 TGATTGTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 5 0.13
35 34 0.87
ACGTcount: A:0.32, C:0.03, G:0.24, T:0.42
Consensus pattern (35 bp):
TGTAATTGAAGCATTTTGAATTTGAGGGTTTAGAA
Found at i:87362 original size:3 final size:3
Alignment explanation
Indices: 87354--87394 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
87344 CAATGGTACT
87354 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
87395 TCTTTTGATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:91351 original size:3 final size:3
Alignment explanation
Indices: 91330--91374 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
91320 TAATTAATTT
* **
91330 ATA ATA AAA ATA ACG ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
91375 CGGAAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:91607 original size:43 final size:43
Alignment explanation
Indices: 91559--91792 Score: 153
Period size: 43 Copynumber: 5.2 Consensus size: 43
91549 AATGAAGAGG
* *
91559 TCTGGTCGTCTAAGGGTGACACGGCTCCTACGTGATGAGGAAA
1 TCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAGGACA
* * *
91602 TCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGAGGACG
1 TCTGGTCATC--T---AAGGGTG---ACACGGCTCCTACGTGATGAGGACA
* * * * * * *
91653 GCTGGTTATCCTAATGTTGACACGGCTCTTACGTGATGAAGAGA
1 TCTGGTCAT-CTAAGGGTGACACGGCTCCTACGTGATGAGGACA
* * * *
91697 TCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG
1 TCTGGTCATCT-AAGG-G-TGACACGGCTCCTACGTGATGAGGACA
* * * * * * *
91743 GCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGA
1 TCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAGGACA
91786 TCTGGTC
1 TCTGGTC
91793 TGGGGATGAC
Statistics
Matches: 140, Mismatches: 39, Indels: 24
0.69 0.19 0.12
Matches are distributed among these distances:
43 37 0.26
44 28 0.20
45 4 0.03
46 29 0.21
47 5 0.04
48 7 0.05
50 1 0.01
51 28 0.20
52 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (43 bp):
TCTGGTCATCTAAGGGTGACACGGCTCCTACGTGATGAGGACA
Found at i:91743 original size:90 final size:92
Alignment explanation
Indices: 91575--91790 Score: 314
Period size: 90 Copynumber: 2.3 Consensus size: 92
91565 CGTCTAAGGG
* * * * *
91575 TGACACGGCTCCTACGTGATGAGGAAATCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATC-TTA-GAAGGGTGATAACACGGTTCCTA
91640 CGTGATGAGGACGGCTGGTTATCCTAAT-GT
64 CGTGATGAGGACGGCTGGTTAT-CT-ATGGT
*
91670 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATC-TA-AA-GGTGATAACACGGTTCCTACG
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACG
91732 TGATGAGGACGGCTGGTTATCTATGGT
66 TGATGAGGACGGCTGGTTATCTATGGT
91759 TGACACGGCTCATACGTGATGAAGAGATCTGG
1 TGACACGGCTCATACGTGATGAAGAGATCTGG
91791 TCTGGGGATG
Statistics
Matches: 114, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
88 2 0.02
89 35 0.31
90 40 0.35
91 2 0.02
93 2 0.02
95 33 0.29
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (92 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACG
TGATGAGGACGGCTGGTTATCTATGGT
Found at i:91754 original size:46 final size:46
Alignment explanation
Indices: 91621--91754 Score: 141
Period size: 46 Copynumber: 3.0 Consensus size: 46
91611 CTTTAGGAAG
*
91621 GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGTTATCCT-AA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTAT-CTAAA
* * * * * * **
91667 --TGTTGACACGGCTCTTACGTGATGAAGA-GATCTGGCCATCTAAA
1 GGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAAA
91711 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
1 GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTA
91755 TGGTTGACAC
Statistics
Matches: 66, Mismatches: 17, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
43 3 0.05
44 30 0.45
46 32 0.48
47 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (46 bp):
GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAA
Found at i:108445 original size:103 final size:100
Alignment explanation
Indices: 108266--108455 Score: 258
Period size: 103 Copynumber: 1.9 Consensus size: 100
108256 TCTGTTGACG
* *
108266 TTCAATCTAAAGTTTGATCTTGAGTGGATTTTTTTGCTGTTTTACTCTGGTTTGAGCTTAGAGAT
1 TTCAATCTAAAGTTTGATCTTGAGT-GATTTTTTTGCTGTTTTACTCTGGTTTGAGCTTAAAAAT
108331 CGATTCTTTGATTCAGTTTGTGATGCCCATTTGAACA
65 CGATTCTTTGA-TCAGTTTGTGATGCCCATTTGAACA
*
108368 TTCAATCTAAAGTTTTGATCTTGAGT-ATATTTTTTGCTGTTTTTAGTCTGGTTTGAGCTTAAAA
1 TTCAATCTAAAG-TTTGATCTTGAGTGAT-TTTTTTGCTG-TTTTACTCTGGTTTGAGCTTAAAA
* * *
108432 ATTGGTT-TGTTGATCATTTTGTGA
63 ATCGATTCT-TTGATCAGTTTGTGA
108456 ACACCCTACT
Statistics
Matches: 78, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
101 2 0.03
102 33 0.42
103 43 0.55
ACGTcount: A:0.21, C:0.11, G:0.20, T:0.48
Consensus pattern (100 bp):
TTCAATCTAAAGTTTGATCTTGAGTGATTTTTTTGCTGTTTTACTCTGGTTTGAGCTTAAAAATC
GATTCTTTGATCAGTTTGTGATGCCCATTTGAACA
Found at i:111974 original size:56 final size:56
Alignment explanation
Indices: 111888--112002 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
111878 CCACGCTTGA
111888 AACCGAGAGCGGCAAGAACTAGTGCGGCTTCTTCGGGTGTCAATGGGCATCTTCCC
1 AACCGAGAGCGGCAAGAACTAGTGCGGCTTCTTCGGGTGTCAATGGGCATCTTCCC
111944 AACCGAGAGCGGCAAGAACTAGTGCGGCTTCTTCGGGTGTCAATGGGCATCTTCCC
1 AACCGAGAGCGGCAAGAACTAGTGCGGCTTCTTCGGGTGTCAATGGGCATCTTCCC
112000 AAC
1 AAC
112003 TTCCGCAACT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.23, C:0.27, G:0.30, T:0.21
Consensus pattern (56 bp):
AACCGAGAGCGGCAAGAACTAGTGCGGCTTCTTCGGGTGTCAATGGGCATCTTCCC
Found at i:112130 original size:25 final size:26
Alignment explanation
Indices: 112087--112148 Score: 99
Period size: 25 Copynumber: 2.4 Consensus size: 26
112077 TTCGACTCAA
112087 ACTCGAAAACTTTCAAAGCCAGCTCG
1 ACTCGAAAACTTTCAAAGCCAGCTCG
*
112113 ACTCGAAAA-TTTCAAAGCCAGCTTG
1 ACTCGAAAACTTTCAAAGCCAGCTCG
*
112138 AGTCGAAAACT
1 ACTCGAAAACT
112149 CGCGAGCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 23 0.70
26 10 0.30
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (26 bp):
ACTCGAAAACTTTCAAAGCCAGCTCG
Found at i:112305 original size:23 final size:23
Alignment explanation
Indices: 112278--112404 Score: 182
Period size: 23 Copynumber: 5.5 Consensus size: 23
112268 GATTGAAACT
* **
112278 ATTGAAGCTCTATTCCGAGAGCG
1 ATTGAAGCTCGATTCCGAGCTCG
112301 ATTGAAGCTCGATTCCGAGCTCG
1 ATTGAAGCTCGATTCCGAGCTCG
*
112324 ATTGAAGCTCAATTCCGAGCTCG
1 ATTGAAGCTCGATTCCGAGCTCG
* *
112347 ATTGAAGCTCGATTCCAAACTCG
1 ATTGAAGCTCGATTCCGAGCTCG
* *
112370 ATTAAAGCTCGATTCCGAGCTCA
1 ATTGAAGCTCGATTCCGAGCTCG
112393 ATTGAAGCTCGA
1 ATTGAAGCTCGA
112405 CATTGCCCAA
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 92 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (23 bp):
ATTGAAGCTCGATTCCGAGCTCG
Found at i:112323 original size:12 final size:12
Alignment explanation
Indices: 112306--112391 Score: 74
Period size: 12 Copynumber: 7.4 Consensus size: 12
112296 GAGCGATTGA
112306 AGCTCGATTCCG
1 AGCTCGATTCCG
112318 AGCTCGATT--G
1 AGCTCGATTCCG
*
112328 AAGCTCAATTCCG
1 -AGCTCGATTCCG
112341 AGCTCGATT--G
1 AGCTCGATTCCG
*
112351 AAGCTCGATTCCA
1 -AGCTCGATTCCG
* **
112364 AACTCGATT-AA
1 AGCTCGATTCCG
112375 AGCTCGATTCCG
1 AGCTCGATTCCG
112387 AGCTC
1 AGCTC
112392 AATTGAAGCT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
10 2 0.03
11 26 0.44
12 30 0.51
13 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (12 bp):
AGCTCGATTCCG
Found at i:113564 original size:14 final size:14
Alignment explanation
Indices: 113545--113633 Score: 74
Period size: 14 Copynumber: 6.4 Consensus size: 14
113535 TCAATTGAGA
113545 GTTTAGAGTTTAGG
1 GTTTAGAGTTTAGG
*
113559 GTTTAGAATTTAGG
1 GTTTAGAGTTTAGG
*
113573 GTTTA-AGGTTTAAG
1 GTTTAGA-GTTTAGG
* *
113587 GTTTATG-CTTTAAG
1 GTTTA-GAGTTTAGG
* *
113601 GTTTATAGTTGAGG
1 GTTTAGAGTTTAGG
* *
113615 GTTTATAGATTAGG
1 GTTTAGAGTTTAGG
113629 GTTTA
1 GTTTA
113634 TAGATTAAGA
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
13 1 0.02
14 60 0.98
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.45
Consensus pattern (14 bp):
GTTTAGAGTTTAGG
Found at i:113582 original size:7 final size:7
Alignment explanation
Indices: 113567--113605 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
113557 GGGTTTAGAA
*
113567 TTTAGGG
1 TTTAAGG
113574 TTTAAGG
1 TTTAAGG
113581 TTTAAGG
1 TTTAAGG
* *
113588 TTTATGC
1 TTTAAGG
113595 TTTAAGG
1 TTTAAGG
113602 TTTA
1 TTTA
113606 TAGTTGAGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.23, C:0.03, G:0.26, T:0.49
Consensus pattern (7 bp):
TTTAAGG
Found at i:113591 original size:21 final size:21
Alignment explanation
Indices: 113542--113619 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
113532 TCCTCAATTG
* *
113542 AGAGTTTAGAGTTTAGGGTTT
1 AGAGTTTAGGGTTTAAGGTTT
*
113563 AGAATTTAGGGTTTAAGGTTT
1 AGAGTTTAGGGTTTAAGGTTT
* *
113584 A-AGGTTTATGCTTTAAGGTTT
1 AGA-GTTTAGGGTTTAAGGTTT
* *
113605 ATAGTTGAGGGTTTA
1 AGAGTTTAGGGTTTA
113620 TAGATTAGGG
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 1 0.02
21 44 0.96
22 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.29, T:0.44
Consensus pattern (21 bp):
AGAGTTTAGGGTTTAAGGTTT
Found at i:113634 original size:14 final size:14
Alignment explanation
Indices: 113600--113640 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
113590 TATGCTTTAA
113600 GGTTTATAG-TTGAG
1 GGTTTATAGATT-AG
113614 GGTTTATAGATTAG
1 GGTTTATAGATTAG
113628 GGTTTATAGATTA
1 GGTTTATAGATTA
113641 AGATTTAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 24 0.92
15 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.44
Consensus pattern (14 bp):
GGTTTATAGATTAG
Found at i:116638 original size:20 final size:20
Alignment explanation
Indices: 116615--116669 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
116605 AGATTCGCAA
*
116615 TGCGATTTTGAAAAATGTGT
1 TGCGATATTGAAAAATGTGT
116635 TGCGATAGTT--AAAATGTGT
1 TGCGATA-TTGAAAAATGTGT
*
116654 TGCGATAGTGAAAAAT
1 TGCGATATTGAAAAAT
116670 CCAAAATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 16 0.53
20 11 0.37
21 2 0.07
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (20 bp):
TGCGATATTGAAAAATGTGT
Found at i:116650 original size:19 final size:19
Alignment explanation
Indices: 116626--116667 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
116616 GCGATTTTGA
*
116626 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
116645 AAAATGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTG
116664 AAAA
1 AAAA
116668 ATCCAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:117010 original size:24 final size:24
Alignment explanation
Indices: 116982--117038 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
116972 GAGTCGGGGT
* *
116982 GGGGTCGTGATCGTAGTCGTGGCC
1 GGGGTCGTGACCGTAGCCGTGGCC
* *
117006 GGGGTCATGACCGTGGCCGTGGCC
1 GGGGTCGTGACCGTAGCCGTGGCC
117030 GGGGTCGTG
1 GGGGTCGTG
117039 GCTTTTTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.07, C:0.23, G:0.49, T:0.21
Consensus pattern (24 bp):
GGGGTCGTGACCGTAGCCGTGGCC
Found at i:117040 original size:12 final size:12
Alignment explanation
Indices: 116997--117040 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
116987 CGTGATCGTA
116997 GTCGTGGCCGGG
1 GTCGTGGCCGGG
* * *
117009 GTCATGACCGTG
1 GTCGTGGCCGGG
*
117021 GCCGTGGCCGGG
1 GTCGTGGCCGGG
117033 GTCGTGGC
1 GTCGTGGC
117041 TTTTTTTAGT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.05, C:0.27, G:0.50, T:0.18
Consensus pattern (12 bp):
GTCGTGGCCGGG
Done.