Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003969.1 Hibiscus syriacus cultivar Beakdansim tig00008602_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: 70445
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:12411 original size:2 final size:2
Alignment explanation
Indices: 12404--12444 Score: 64
Period size: 2 Copynumber: 19.5 Consensus size: 2
12394 AGAGCCAGAA
12404 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG ACG AG CAG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG -AG AG A
12445 TTCAAATCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 33 0.89
3 4 0.11
ACGTcount: A:0.49, C:0.05, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:15342 original size:12 final size:12
Alignment explanation
Indices: 15325--15356 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
15315 TTTTTAACAT
15325 GTTGATCTCGTC
1 GTTGATCTCGTC
15337 GTTGATCTCGTC
1 GTTGATCTCGTC
15349 GTTGATCT
1 GTTGATCT
15357 AGTACCCGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.22, G:0.25, T:0.44
Consensus pattern (12 bp):
GTTGATCTCGTC
Found at i:16992 original size:13 final size:13
Alignment explanation
Indices: 16974--16999 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16964 TGTTTTTCTT
16974 AAAATTAATGGAC
1 AAAATTAATGGAC
16987 AAAATTAATGGAC
1 AAAATTAATGGAC
17000 TGGAGTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (13 bp):
AAAATTAATGGAC
Found at i:17613 original size:133 final size:133
Alignment explanation
Indices: 17375--17640 Score: 487
Period size: 133 Copynumber: 2.0 Consensus size: 133
17365 TTTTGAAGCT
*
17375 CTGAAGAAAATGATTTGGAAACTTACCTTCACTAAACCGAAAATGAAGTGATGATCAACAAGTTT
1 CTGAAGAAAACGATTTGGAAACTTACCTTCACTAAACCGAAAATGAAGTGATGATCAACAAGTTT
17440 CTACCTTTAACTTGAGCCCAAGAAGAAAGATGAGATAGTTTAAAAGGAAGGAAGAAGACAATGGT
66 CTACCTTTAACTTGAGCCCAAGAAGAAAGATGAGATAGTTTAAAAGGAAGGAAGAAGACAATGGT
17505 GAA
131 GAA
* * *
17508 CTGAAGAAGACGATTTGGAAACTTACCTTCACTAAACCGAAAATGAAGTGTTGATCAACAGGTTT
1 CTGAAGAAAACGATTTGGAAACTTACCTTCACTAAACCGAAAATGAAGTGATGATCAACAAGTTT
*
17573 CTACCTTTAACTTGAGCCCAATAAGAAAGATGAGATAGTTTAAAAGGAAGGAAGAAGACAATGGT
66 CTACCTTTAACTTGAGCCCAAGAAGAAAGATGAGATAGTTTAAAAGGAAGGAAGAAGACAATGGT
17638 GAA
131 GAA
17641 GGAAAAGAGG
Statistics
Matches: 128, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
133 128 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (133 bp):
CTGAAGAAAACGATTTGGAAACTTACCTTCACTAAACCGAAAATGAAGTGATGATCAACAAGTTT
CTACCTTTAACTTGAGCCCAAGAAGAAAGATGAGATAGTTTAAAAGGAAGGAAGAAGACAATGGT
GAA
Found at i:18998 original size:19 final size:20
Alignment explanation
Indices: 18951--19001 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
18941 GAAACCCCTT
**
18951 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
18971 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
18990 TGAAGATACATG
1 TGAAAATACATG
19002 CTCTTGGCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:21046 original size:23 final size:23
Alignment explanation
Indices: 21020--21084 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
21010 CTCATATAAA
21020 TGCACCGTAGTGCCGTATAGAAT
1 TGCACCGTAGTGCCGTATAGAAT
21043 TGCACCGTAGTGCCGTATAGAAT
1 TGCACCGTAGTGCCGTATAGAAT
* *
21066 TGCAGCGTAGTGCCATATA
1 TGCACCGTAGTGCCGTATA
21085 ATAATGTCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (23 bp):
TGCACCGTAGTGCCGTATAGAAT
Found at i:21267 original size:103 final size:103
Alignment explanation
Indices: 21102--21313 Score: 361
Period size: 103 Copynumber: 2.1 Consensus size: 103
21092 CCATAAGAAG
* * *
21102 CACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACTTC
1 CACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTC
* *
21167 ATACATGTTCCAAAGAATACATATATGTCCCGAAAGAC
66 ACACATGTTCCAAACAATACATATATGTCCCGAAAGAC
*
21205 CACATATCATTCCTTAAAAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTC
1 CACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTC
*
21270 ACACATGTTCCAAACAATACATATATGTCCCGAAGGAC
66 ACACATGTTCCAAACAATACATATATGTCCCGAAAGAC
21308 CACATA
1 CACATA
21314 GACCCTCGAC
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (103 bp):
CACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTC
ACACATGTTCCAAACAATACATATATGTCCCGAAAGAC
Found at i:25544 original size:6 final size:6
Alignment explanation
Indices: 25521--25563 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
25511 GTTGTAGGAG
* *
25521 TCTTTT TCTTTC TCTTTT T-GTTT TCTTCTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCTTTT T
25564 GTTACTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 4 0.13
6 21 0.68
7 6 0.19
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (6 bp):
TCTTTT
Found at i:25562 original size:24 final size:23
Alignment explanation
Indices: 25521--25566 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
25511 GTTGTAGGAG
25521 TCTTTTTCTTTCTCTTTTTGTTT
1 TCTTTTTCTTTCTCTTTTTGTTT
*
25544 TCTTCTTTCTTTTTCTTTTTGTT
1 TCTT-TTTCTTTCTCTTTTTGTT
25567 ACTTTTGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.78
Consensus pattern (23 bp):
TCTTTTTCTTTCTCTTTTTGTTT
Found at i:25785 original size:18 final size:19
Alignment explanation
Indices: 25750--25788 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
25740 AGAAATGATT
25750 AAAATAGAATATGAAAGAA
1 AAAATAGAATATGAAAGAA
25769 AAAAT-GAA-ATGATAAGAA
1 AAAATAGAATATGA-AAGAA
25787 AA
1 AA
25789 TGAAATGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 10 0.53
19 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (19 bp):
AAAATAGAATATGAAAGAA
Found at i:26403 original size:19 final size:20
Alignment explanation
Indices: 26356--26406 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
26346 GAAACCCCTT
**
26356 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
26376 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
26395 TGAAGATACATG
1 TGAAAATACATG
26407 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:26730 original size:30 final size:31
Alignment explanation
Indices: 26657--26746 Score: 148
Period size: 31 Copynumber: 3.0 Consensus size: 31
26647 ATTTAAGGCA
*
26657 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAATGGTTTTTGGACTTTAATTGAATTTAC
26688 AAAATGGTTTTTGGACTTTAATTGAATTTAC
1 AAAATGGTTTTTGGACTTTAATTGAATTTAC
*
26719 AAAAT-GTTTTTGGAC-TTAATTGATTTTA
1 AAAATGGTTTTTGGACTTTAATTGAATTTA
26747 TTCAAAATTT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
29 12 0.21
30 10 0.18
31 35 0.61
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.46
Consensus pattern (31 bp):
AAAATGGTTTTTGGACTTTAATTGAATTTAC
Found at i:26838 original size:19 final size:19
Alignment explanation
Indices: 26811--26877 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
26801 AATGTTTTTA
* *
26811 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
26830 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
26849 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
26868 TGAACAGTAA
1 TGAACAGTAA
26878 CCCGAGGCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:27010 original size:21 final size:21
Alignment explanation
Indices: 26984--27025 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
26974 ATTTGAATAT
*
26984 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
27005 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
27026 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:27348 original size:34 final size:32
Alignment explanation
Indices: 27309--27378 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
27299 TTTGTAAAGG
*
27309 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
27343 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
27375 GGGA
1 GGGA
27379 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:30844 original size:18 final size:18
Alignment explanation
Indices: 30821--30855 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30811 ACTGAATATT
*
30821 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
30839 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
30856 GATAATCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:39003 original size:2 final size:2
Alignment explanation
Indices: 38991--39035 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
38981 ACAATCAGAG
38991 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
39033 AT A
1 AT A
39036 AGATATGGTG
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39364 original size:47 final size:47
Alignment explanation
Indices: 39290--39382 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 47
39280 ATCAAAATCA
*
39290 ATATGTCATACCAATCCATGAAGAAAATAGCAGAACCCACATGTTCG
1 ATATGTCATACCAATCCATGAAGAAAATAACAGAACCCACATGTTCG
* * *
39337 ATATGTCATACGAGTCCATGAATAAAATAACAGAACCCACATGTTC
1 ATATGTCATACCAATCCATGAAGAAAATAACAGAACCCACATGTTC
39383 ACTTCTATTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.23
Consensus pattern (47 bp):
ATATGTCATACCAATCCATGAAGAAAATAACAGAACCCACATGTTCG
Found at i:40391 original size:6 final size:6
Alignment explanation
Indices: 40382--40409 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
40372 CATCGAAGCA
40382 GAAGAT GAAGAT GAAGAT GAAGAT GAAG
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAG
40410 CTGGAGCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.36, T:0.14
Consensus pattern (6 bp):
GAAGAT
Found at i:41352 original size:29 final size:29
Alignment explanation
Indices: 41310--41375 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
41300 ATATCCTCTA
41310 GATAATTATAATTGTTAAATTGATTATAT
1 GATAATTATAATTGTTAAATTGATTATAT
41339 GATAATTATAATTGTTAAATTGATTATAT
1 GATAATTATAATTGTTAAATTGATTATAT
*
41368 GACAATTA
1 GATAATTA
41376 AGTTTATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (29 bp):
GATAATTATAATTGTTAAATTGATTATAT
Found at i:43122 original size:13 final size:13
Alignment explanation
Indices: 43104--43136 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
43094 TATGTGACAA
43104 ATTTTTATAATAT
1 ATTTTTATAATAT
43117 ATTTTTATAATAT
1 ATTTTTATAATAT
43130 ATTTTTA
1 ATTTTTA
43137 GAAGAAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATTTTTATAATAT
Found at i:47409 original size:12 final size:12
Alignment explanation
Indices: 47392--47417 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
47382 GAATTTCACA
47392 CAAAGTTTAGCT
1 CAAAGTTTAGCT
47404 CAAAGTTTAGCT
1 CAAAGTTTAGCT
47416 CA
1 CA
47418 GTAACTGTGG
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:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (12 bp):
CAAAGTTTAGCT
Found at i:49904 original size:2 final size:2
Alignment explanation
Indices: 49897--49931 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
49887 AATATGTTCA
49897 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49932 GATGAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53225 original size:20 final size:20
Alignment explanation
Indices: 53200--53237 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
53190 TCTAGGTTCG
53200 AATATCGATATTGGATGAAC
1 AATATCGATATTGGATGAAC
53220 AATATCGATATTGGATGA
1 AATATCGATATTGGATGA
53238 TTGGGACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (20 bp):
AATATCGATATTGGATGAAC
Found at i:55512 original size:194 final size:192
Alignment explanation
Indices: 55170--55643 Score: 506
Period size: 194 Copynumber: 2.5 Consensus size: 192
55160 AATTTCATTG
* * * * * * *
55170 TATACGTGACGAAA-AGAAAATTGTCACATTGTTAGTAACGTAGTATATCGTCACCTAATAAT-T
1 TATATGTGACGAAAGAG-ATATTGTCA-ATTTTTAGTGACATAATATATCGTTACCTAATAATAT
* * ** * * * * * ** ** *
55233 GCATGGATGAC-ATTTATATATAATGTCACTATATAATTAATATTCAATGACAACTAATTATGTC
64 -TATGAATGACGA-TTATGCATAACGCCACTTTATAATTTATATTCTATGACAGTTGGTTACGTC
* ** * ***
55297 ACTAGATTATGTAAAATTTCGTTATTGATGATTTAAATCATCACGGATAATACATTAAAATCAAC
127 ACTAAATTAAATAAAATTTCGTTATTGATAATTTAAATCATCAAAAATAATACATTAAAATCAAC
55362 C
192 C
*
55363 TATATGTGACGAAAGAGATATTGTCAAATTTTTAGTGATATAATATAAAT-GTTACCTAATAATA
1 TATATGTGACGAAAGAGATATTGTC-AATTTTTAGTGACATAATAT--ATCGTTACCTAATAATA
*
55427 TTATGAATGACGTTTATGCATAACGCCACTTTATAATTTATATTCTATGACAGTTGGTTACGTCA
63 TTATGAATGACGATTATGCATAACGCCACTTTATAATTTATATTCTATGACAGTTGGTTACGTCA
* * ** * *
55492 CTAAATTAAATAAGATTTCGTTATTGATAATTTATATTGTCAAAAATAATGCATTAAAATCAACT
128 CTAAATTAAATAAAATTTCGTTATTGATAATTTAAATCATCAAAAATAATACATTAAAATCAACC
* *
55557 TATATGTGACGAAAGAGATATTGTCACTTTTTAGTGACATAATATATCGTTGCCTAATAATATTA
1 TATATGTGACGAAAGAGATATTGTCAATTTTTAGTGACATAATATATCGTTACCTAATAATATTA
*
55622 TGAATGATGATTATGCATAACG
66 TGAATGACGATTATGCATAACG
55644 TCACCATATA
Statistics
Matches: 233, Mismatches: 41, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
191 2 0.01
192 36 0.15
193 52 0.22
194 140 0.60
195 3 0.01
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (192 bp):
TATATGTGACGAAAGAGATATTGTCAATTTTTAGTGACATAATATATCGTTACCTAATAATATTA
TGAATGACGATTATGCATAACGCCACTTTATAATTTATATTCTATGACAGTTGGTTACGTCACTA
AATTAAATAAAATTTCGTTATTGATAATTTAAATCATCAAAAATAATACATTAAAATCAACC
Found at i:55661 original size:15 final size:15
Alignment explanation
Indices: 55638--55713 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
55628 ATGATTATGC
*
55638 ATAACGTCACCATAT
1 ATAATGTCACCATAT
55653 ATAATGTCACCA-AT
1 ATAATGTCACCATAT
* * **
55667 ATAGTGGCAAAAT-T
1 ATAATGTCACCATAT
*
55681 AAAAATTGTCACCATAT
1 -ATAA-TGTCACCATAT
55698 ATAATGTCACCA-AT
1 ATAATGTCACCATAT
55712 AT
1 AT
55714 CGTTTTGTTC
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
14 15 0.33
15 21 0.46
16 9 0.20
17 1 0.02
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.29
Consensus pattern (15 bp):
ATAATGTCACCATAT
Found at i:62041 original size:26 final size:23
Alignment explanation
Indices: 61995--62039 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
61985 AGACTTAAGG
*
61995 AAAAAAAATAAAGGACATAATAT
1 AAAAAAAATAAAGAACATAATAT
62018 AAAAAAAATAAGAGAAC-TAATA
1 AAAAAAAATAA-AGAACATAATA
62040 ATCCCGACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.71, C:0.04, G:0.09, T:0.16
Consensus pattern (23 bp):
AAAAAAAATAAAGAACATAATAT
Found at i:67498 original size:2 final size:2
Alignment explanation
Indices: 67491--67542 Score: 95
Period size: 2 Copynumber: 25.5 Consensus size: 2
67481 TTAATCATTA
67491 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
67533 AT AT GAT AT A
1 AT AT -AT AT A
67543 ATTACTTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:67580 original size:30 final size:30
Alignment explanation
Indices: 67546--67602 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
67536 TGATATAATT
67546 ACTTA-AACTCAAATT-AAAAAAATAATATTC
1 ACTTATAAC-CAAATTGAAAAAAA-AATATTC
*
67576 ACTTATCACCAAATTGAAAAAAAAATA
1 ACTTATAACCAAATTGAAAAAAAAATA
67603 AAACAATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (30 bp):
ACTTATAACCAAATTGAAAAAAAAATATTC
Done.