Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001169.1 Hibiscus syriacus cultivar Beakdansim tig00002331_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: 60247
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2783 original size:22 final size:22
Alignment explanation
Indices: 2733--2816 Score: 123
Period size: 22 Copynumber: 3.8 Consensus size: 22
2723 CGATTCCCCT
*
2733 AGGGGAAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTC-A
2756 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGGTTCCCCTTCA
*
2778 AGGGGGTATCGGTTCCCCTTCA
1 AGGGGGAATCGGTTCCCCTTCA
* *
2800 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
2817 TCTGCCCTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
22 38 0.66
23 20 0.34
ACGTcount: A:0.19, C:0.26, G:0.31, T:0.24
Consensus pattern (22 bp):
AGGGGGAATCGGTTCCCCTTCA
Found at i:6533 original size:21 final size:22
Alignment explanation
Indices: 6509--6551 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
6499 TTTTCTTTTC
6509 TCATTTTTCA-ATTTT-GAAACA
1 TCATTTTT-ATATTTTAGAAACA
6530 TCATTTTTATATTTTAGAAACA
1 TCATTTTTATATTTTAGAAACA
6552 ATTTCTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.05
21 13 0.65
22 6 0.30
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.49
Consensus pattern (22 bp):
TCATTTTTATATTTTAGAAACA
Found at i:10112 original size:16 final size:16
Alignment explanation
Indices: 10088--10118 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10078 AAGAACTGTT
*
10088 ATTTTTTGTTTAATTG
1 ATTTGTTGTTTAATTG
10104 ATTTGTTGTTTAATT
1 ATTTGTTGTTTAATT
10119 TCAATCTGCA
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:0.19, C:0.00, G:0.13, T:0.68
Consensus pattern (16 bp):
ATTTGTTGTTTAATTG
Found at i:10461 original size:18 final size:18
Alignment explanation
Indices: 10438--10473 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
10428 AAGCCGGTTG
10438 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
10456 TGATTGTGATTTTGATTT
1 TGATTGAGATTTTGATTT
10474 CCTTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.58
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:13023 original size:19 final size:19
Alignment explanation
Indices: 12999--13050 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
12989 ATTGTTCAAT
*
12999 GTGTATCGATGCACAGGAA
1 GTGTATCGATGCACAAGAA
13018 GTGTATCGATGCACAAGAA
1 GTGTATCGATGCACAAGAA
13037 GTGTATCGATGCAC
1 GTGTATCGATGCAC
13051 CCCTTAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (19 bp):
GTGTATCGATGCACAAGAA
Found at i:16902 original size:24 final size:24
Alignment explanation
Indices: 16881--16961 Score: 116
Period size: 24 Copynumber: 3.5 Consensus size: 24
16871 GCATAAGGAG
16881 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCACATGTTAAGGGA
16905 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCACATGTTAAGGGA
* *
16929 TGCATCGATACAC-TG-T-A-GAA
1 TGCATCGATGCACATGTTAAGGGA
16949 TGCATCGATGCAC
1 TGCATCGATGCAC
16962 TTCAAGGGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
20 14 0.26
21 1 0.02
22 1 0.02
23 2 0.04
24 36 0.67
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (24 bp):
TGCATCGATGCACATGTTAAGGGA
Found at i:18054 original size:2 final size:2
Alignment explanation
Indices: 18047--18074 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18037 AGGAAAAATG
18047 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
18075 GAAGATGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18327 original size:23 final size:23
Alignment explanation
Indices: 18290--18352 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
18280 GTGACATAAT
*
18290 CTACGTG-CTATGTGAAAGTGAA
1 CTACGTGTATATGTGAAAGTGAA
*
18312 CTACGTGTTTATGTGAAAGTGAA
1 CTACGTGTATATGTGAAAGTGAA
18335 CTACGTGTATATGTGAAA
1 CTACGTGTATATGTGAAA
18353 ATGTGAAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 7 0.18
23 31 0.82
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (23 bp):
CTACGTGTATATGTGAAAGTGAA
Found at i:18599 original size:23 final size:23
Alignment explanation
Indices: 18566--18628 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
18556 AACCTTATAT
18566 GGCACTTCGGTGCATTTCTACAC
1 GGCACTTCGGTGCATTTCTACAC
* * ***
18589 GGCACTACGGTGCAATTCTATGT
1 GGCACTTCGGTGCATTTCTACAC
18612 GGCACTTCGGTGCATTT
1 GGCACTTCGGTGCATTT
18629 ATACGAGCTG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACAC
Found at i:22565 original size:23 final size:23
Alignment explanation
Indices: 22522--22565 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
22512 ATTTTATATT
*
22522 GCACTTCGGTGCAATTCTACGTG
1 GCACTTCGGTGCAATTATACGTG
*
22545 GCACTTCGGTGCATTTATACG
1 GCACTTCGGTGCAATTATACG
22566 AGTTGTGGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (23 bp):
GCACTTCGGTGCAATTATACGTG
Found at i:23945 original size:24 final size:24
Alignment explanation
Indices: 23894--23948 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
23884 AAAATCTGAG
**
23894 TATTGACCAAGATCAAAGTCCGGG
1 TATTGACCAAGATCAAAGTCCGAA
* * *
23918 TATTGACCAAGATTAAATTTCGAA
1 TATTGACCAAGATCAAAGTCCGAA
23942 TATTGAC
1 TATTGAC
23949 TAGTACTCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
TATTGACCAAGATCAAAGTCCGAA
Found at i:24912 original size:20 final size:20
Alignment explanation
Indices: 24889--24944 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
24879 TTAAAATTCG
*
24889 TGTTGAGATTTAGAAAATCT
1 TGTTGCGATTTAGAAAATCT
24909 TGTTGCGATTTAGAAAATCT
1 TGTTGCGATTTAGAAAATCT
*
24929 TGTTGCGATTCAGAAA
1 TGTTGCGATTTAGAAA
24945 TCGAGTTGCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (20 bp):
TGTTGCGATTTAGAAAATCT
Found at i:24974 original size:40 final size:40
Alignment explanation
Indices: 24870--24976 Score: 110
Period size: 40 Copynumber: 2.7 Consensus size: 40
24860 AATAAAAGTT
* * * * **
24870 GTTGCGAAATTAAAATTCGTGTTGAGATTTAGAAAATCTT
1 GTTGCGAATTTGAAATTCGTGTTGCGATTCAGAAAATCGA
* *
24910 GTTGCG-ATTTAGAAAATCTTGTTGCGATTCAG-AAATCGA
1 GTTGCGAATTT-GAAATTCGTGTTGCGATTCAGAAAATCGA
24949 GTTGCGAATTTGAAATTCCGTGTTGCGA
1 GTTGCGAATTTGAAATT-CGTGTTGCGA
24977 ATTTTGGAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
39 19 0.35
40 35 0.65
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (40 bp):
GTTGCGAATTTGAAATTCGTGTTGCGATTCAGAAAATCGA
Found at i:24999 original size:22 final size:22
Alignment explanation
Indices: 24949--25025 Score: 83
Period size: 21 Copynumber: 3.6 Consensus size: 22
24939 CAGAAATCGA
24949 GTTGCGAATTT-GAAATTCCGT
1 GTTGCGAATTTGGAAATTCCGT
24970 GTTGCGAATTTTGGAAATTCGCGT
1 GTTGCGAA-TTTGGAAATTC-CGT
*
24994 -TT-CGAATTTGGAAA--CTGT
1 GTTGCGAATTTGGAAATTCCGT
*
25012 GTTGCGAAATTGGA
1 GTTGCGAATTTGGA
25026 GTTCGCATTG
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.04
19 3 0.06
20 9 0.18
21 16 0.33
22 7 0.14
23 9 0.18
24 3 0.06
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.36
Consensus pattern (22 bp):
GTTGCGAATTTGGAAATTCCGT
Found at i:25024 original size:20 final size:21
Alignment explanation
Indices: 24869--25025 Score: 85
Period size: 20 Copynumber: 7.7 Consensus size: 21
24859 AAATAAAAGT
* * *
24869 TGTTGCGAAATT-AAAATTCG
1 TGTTGCGAATTTGGAAACTCG
* * * *
24889 TGTTGAG-ATTTAGAAAATCT
1 TGTTGCGAATTTGGAAACTCG
* * *
24909 TGTTGCG-ATTTAGAAAATCT
1 TGTTGCGAATTTGGAAACTCG
**
24929 TGTTGCG-ATTCAGAAA-TCG
1 TGTTGCGAATTTGGAAACTCG
* *
24948 AGTTGCGAATTT-GAAATTCCG
1 TGTTGCGAATTTGGAAACT-CG
*
24969 TGTTGCGAATTTTGGAAATTCG
1 TGTTGCGAA-TTTGGAAACTCG
* *
24991 CGTTTCGAATTTGGAAACT-G
1 TGTTGCGAATTTGGAAACTCG
*
25011 TGTTGCGAAATTGGA
1 TGTTGCGAATTTGGA
25026 GTTCGCATTG
Statistics
Matches: 114, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
19 15 0.13
20 62 0.54
21 19 0.17
22 12 0.11
23 6 0.05
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (21 bp):
TGTTGCGAATTTGGAAACTCG
Found at i:26386 original size:16 final size:16
Alignment explanation
Indices: 26365--26398 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
26355 TTACTATTCA
*
26365 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
26381 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
26397 CG
1 CG
26399 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:33754 original size:85 final size:85
Alignment explanation
Indices: 33601--33834 Score: 299
Period size: 85 Copynumber: 2.7 Consensus size: 85
33591 TAATATGTCT
* ** * * * *
33601 AGATCTATAGCGGCATTTGTTCCAA-AAACGCCGCAATATGTCGAGATCTCTAGCGGCATTTTTG
1 AGATATATAGCGGCATTT-TTGGAACAAACGCCGCAAAAGGTC-AGATCTATAGCGGCATTTTTA
33665 GAACAAACGCTGCAAAAGGTCG
64 GAACAAACGCTGCAAAAGGTCG
* * * * * *
33687 AGATCTATAGCGGCGTTTTTGGAGCAAACGTCGTAAAAGGTCAGATCTATAGCGGCGTTTTTAGA
1 AGATATATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTAGA
*
33752 ACAAACGCTGCAGAAGGTCG
66 ACAAACGCTGCAAAAGGTCG
**
33772 AGATATATAGCGGCATTTTTGGAACAAACGCCGCAAAATTTCAGATCTATAGCGGCATTTTTA
1 AGATATATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTA
33835 TATGCAAACG
Statistics
Matches: 127, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
85 97 0.76
86 30 0.24
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (85 bp):
AGATATATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCATTTTTAGA
ACAAACGCTGCAAAAGGTCG
Found at i:33842 original size:128 final size:128
Alignment explanation
Indices: 33601--33844 Score: 323
Period size: 128 Copynumber: 1.9 Consensus size: 128
33591 TAATATGTCT
* * * *
33601 AGATCTATAGCGGCATTTGTTCCAAAAACGCCGCAATATGTCGAGATCTCTAGCGGCATTTTTGG
1 AGATCTATAGCGGCATTTGTTACAAAAACGCCGCAATAGGTCGAGATATATAGCGGCATTTTTGG
* * *
33666 AACAAACGCTGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGAGCAAACGTCGTAAAAGGTC
66 AACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCATTTTTAGAGCAAACGTCGTAAAAGGTC
* * *
33729 AGATCTATAGCGGCGTTT-TTAGAACAAACGCTGCAGA-AGGTCGAGATATATAGCGGCATTTTT
1 AGATCTATAGCGGCATTTGTTACAA-AAACGCCGCA-ATAGGTCGAGATATATAGCGGCATTTTT
** *
33792 GGAACAAACGCCGCAAAATTTC-AGATCTATAGCGGCATTTTTATATGCAAACG
64 GGAACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCATTTTTAGA-GCAAACG
33845 CCGCTAATTA
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
127 24 0.24
128 75 0.75
129 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (128 bp):
AGATCTATAGCGGCATTTGTTACAAAAACGCCGCAATAGGTCGAGATATATAGCGGCATTTTTGG
AACAAACGCCGCAAAAGGTCGAGATCTATAGCGGCATTTTTAGAGCAAACGTCGTAAAAGGTC
Found at i:33844 original size:43 final size:43
Alignment explanation
Indices: 33601--33833 Score: 283
Period size: 43 Copynumber: 5.5 Consensus size: 43
33591 TAATATGTCT
** * *
33601 AGATCTATAGCGGCATTTGTTCCAA-AAACGCCGCAATATGTCG
1 AGATCTATAGCGGCATTT-TTGGAACAAACGCCGCAAAAGGTCG
* *
33644 AGATCTCTAGCGGCATTTTTGGAACAAACGCTGCAAAAGGTCG
1 AGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTCG
* * * *
33687 AGATCTATAGCGGCGTTTTTGGAGCAAACGTCGTAAAAGGTC-
1 AGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTCG
* * * *
33729 AGATCTATAGCGGCGTTTTTAGAACAAACGCTGCAGAAGGTCG
1 AGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTCG
* **
33772 AGATATATAGCGGCATTTTTGGAACAAACGCCGCAAAATTTC-
1 AGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTCG
33814 AGATCTATAGCGGCATTTTT
1 AGATCTATAGCGGCATTTTT
33834 ATATGCAAAC
Statistics
Matches: 162, Mismatches: 26, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
42 59 0.36
43 103 0.64
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.26
Consensus pattern (43 bp):
AGATCTATAGCGGCATTTTTGGAACAAACGCCGCAAAAGGTCG
Found at i:38053 original size:74 final size:73
Alignment explanation
Indices: 37932--38079 Score: 217
Period size: 74 Copynumber: 2.0 Consensus size: 73
37922 TGTTACCAAA
* *
37932 ACGCCGCTAAAGTTATAATTTGTTGTGGTGTTTATTAAAAAACGCCACTATAGATAAACTCTATT
1 ACGCCGCTAAAGTTATAATCTGTTGTGGTGTTTATTAAAAAACGCCACTATAGATAAAC-CTAGT
37997 GCGGCGTTT
65 GCGGCGTTT
* * *
38006 ACGCCGCTAAAG-TACTAATCTGTTGTGTTGTTTATTGAAAAACGCCACTATAGATAGACCTAGT
1 ACGCCGCTAAAGTTA-TAATCTGTTGTGGTGTTTATTAAAAAACGCCACTATAGATAAACCTAGT
*
38070 GTGGCGTTT
65 GCGGCGTTT
38079 A
1 A
38080 TTGAAAAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
73 15 0.22
74 52 0.78
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (73 bp):
ACGCCGCTAAAGTTATAATCTGTTGTGGTGTTTATTAAAAAACGCCACTATAGATAAACCTAGTG
CGGCGTTT
Found at i:40165 original size:27 final size:27
Alignment explanation
Indices: 40127--40195 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
40117 TAACTATCTG
40127 TCAATATTTGTCAATTTTTTATAGAAA
1 TCAATATTTGTCAATTTTTTATAGAAA
*
40154 TCAATATTTGTCATTTTTTTATAGAAA
1 TCAATATTTGTCAATTTTTTATAGAAA
40181 TCAATATTTGT-AATT
1 TCAATATTTGTCAATT
40196 GATGCGACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 3 0.08
27 37 0.93
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (27 bp):
TCAATATTTGTCAATTTTTTATAGAAA
Found at i:41359 original size:21 final size:22
Alignment explanation
Indices: 41318--41359 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
41308 GTGATTTGAT
41318 TGATATCATTAAAATAATTAAG
1 TGATATCATTAAAATAATTAAG
*
41340 TGATATGATTAAAA-AATTAA
1 TGATATCATTAAAATAATTAA
41360 AATATTAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (22 bp):
TGATATCATTAAAATAATTAAG
Found at i:49985 original size:44 final size:44
Alignment explanation
Indices: 49930--50048 Score: 229
Period size: 44 Copynumber: 2.7 Consensus size: 44
49920 ATGATATTTG
*
49930 GTGTAATTGATTTAATTTGTATGGTGTTGAAATCTATCGTGAAT
1 GTGTAAATGATTTAATTTGTATGGTGTTGAAATCTATCGTGAAT
49974 GTGTAAATGATTTAATTTGTATGGTGTTGAAATCTATCGTGAAT
1 GTGTAAATGATTTAATTTGTATGGTGTTGAAATCTATCGTGAAT
50018 GTGTAAATGATTTAATTTGTATGGTGTTGAA
1 GTGTAAATGATTTAATTTGTATGGTGTTGAA
50049 TATATTGAGT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 74 1.00
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.45
Consensus pattern (44 bp):
GTGTAAATGATTTAATTTGTATGGTGTTGAAATCTATCGTGAAT
Found at i:50234 original size:30 final size:31
Alignment explanation
Indices: 50200--50276 Score: 147
Period size: 30 Copynumber: 2.5 Consensus size: 31
50190 AATTATTTTC
50200 TTACTTCTATTTTGGTTATTAAAA-TTTAAA
1 TTACTTCTATTTTGGTTATTAAAATTTTAAA
50230 TTACTTCTATTTTGGTTATTAAAATTTTAAA
1 TTACTTCTATTTTGGTTATTAAAATTTTAAA
50261 TTACTTCTATTTTGGT
1 TTACTTCTATTTTGGT
50277 CACTATAAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 24 0.52
31 22 0.48
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.56
Consensus pattern (31 bp):
TTACTTCTATTTTGGTTATTAAAATTTTAAA
Found at i:52357 original size:39 final size:39
Alignment explanation
Indices: 52303--52393 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 39
52293 TAAGGACTGT
*
52303 GGTAAGGACTAACCCTGAGCACAAAGCAGAGGAGTCTGC
1 GGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGTCTGC
* * * *
52342 GGTAAGGACTTACCCTGATCATAAAGTATAGGAGTCTGC
1 GGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGTCTGC
* *
52381 AGTAAGGTCTTAC
1 GGTAAGGACTTAC
52394 AAGTCATAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (39 bp):
GGTAAGGACTTACCCTGAGCACAAAGCAGAGGAGTCTGC
Found at i:54874 original size:12 final size:12
Alignment explanation
Indices: 54856--54910 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
54846 AACGACGGTA
54856 ACGATGGCAGTG
1 ACGATGGCAGTG
*
54868 GCGATGGCAGTG
1 ACGATGGCAGTG
** *
54880 GTGATGGCAGTA
1 ACGATGGCAGTG
*
54892 ACGATAGCAGTG
1 ACGATGGCAGTG
54904 ACGATGG
1 ACGATGG
54911 TAATGGTGAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.25, C:0.15, G:0.42, T:0.18
Consensus pattern (12 bp):
ACGATGGCAGTG
Found at i:55054 original size:16 final size:17
Alignment explanation
Indices: 55021--55056 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
55011 TAAAATAAGA
55021 TTATAAAAATTAATATT
1 TTATAAAAATTAATATT
*
55038 TTATAAATATT-ATATT
1 TTATAAAAATTAATATT
55054 TTA
1 TTA
55057 AGTAAATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATAAAAATTAATATT
Found at i:55115 original size:15 final size:15
Alignment explanation
Indices: 55097--55132 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
55087 TACTTATACG
55097 TTTAATACTTTATAA
1 TTTAATACTTTATAA
*
55112 TTTAATATTTTATAA
1 TTTAATACTTTATAA
*
55127 ATTAAT
1 TTTAAT
55133 TTAATAGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTAATACTTTATAA
Found at i:55382 original size:15 final size:17
Alignment explanation
Indices: 55358--55398 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
55348 TAGATAAATT
* *
55358 TTAATTTAATT-ATTTT
1 TTAATATAATTAATTTA
55374 TTAA-ATAATTAATTTA
1 TTAATATAATTAATTTA
55390 TTAATATAA
1 TTAATATAA
55399 AATTATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 12 0.57
17 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATATAATTAATTTA
Done.