Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006086.1 Hibiscus syriacus cultivar Beakdansim tig00014429_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: 87874
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:29354 original size:33 final size:33
Alignment explanation
Indices: 29307--29383 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 33
29297 ACAAAGTTTA
*
29307 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
* *
29339 TGATAAATTTAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTGAAATACTTAAAAACTTCCAAGTT
29372 CGAT-AATTGAAA
1 CGATAAATTGAAA
29384 CAAAGTTTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 10 0.26
33 29 0.74
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (33 bp):
CGATAAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:35397 original size:40 final size:40
Alignment explanation
Indices: 35353--35474 Score: 96
Period size: 38 Copynumber: 3.1 Consensus size: 40
35343 CTAAAAAACA
35353 GGTTGCGATATGGAATGTTAATATCTTTATTAATAAAATG
1 GGTTGCGATATGGAATGTTAATATCTTTATTAATAAAATG
* * * * *
35393 GGTTGCG-TCCA-AGAAT-ATCATAT-TTCACTAATAAATAT-
1 GGTTGCGAT--ATGGAATGTTAATATCTTTATTAATAAA-ATG
* *
35431 -GTTGCGATCTGGAATGTTAATA-CTTTTATAAATAAAATG
1 GGTTGCGATATGGAATGTTAATATC-TTTATTAATAAAATG
35470 GGTTG
1 GGTTG
35475 TACCTAAGGA
Statistics
Matches: 60, Mismatches: 12, Indels: 20
0.65 0.13 0.22
Matches are distributed among these distances:
37 10 0.17
38 17 0.28
39 17 0.28
40 15 0.25
41 1 0.02
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (40 bp):
GGTTGCGATATGGAATGTTAATATCTTTATTAATAAAATG
Found at i:35420 original size:77 final size:79
Alignment explanation
Indices: 35316--35552 Score: 274
Period size: 77 Copynumber: 3.1 Consensus size: 79
35306 TAAGAAATAC
* * * * *
35316 GGTTGCG--CCTAAAAATGTCATGATTCACTAAAAAACAGGTTGCGATATGGAATGTTAATATCT
1 GGTTGCGTACCTAAGAATATCATGATTCACTAATAAATAGGTTGCGATCTGGAATGTTAATATCT
35379 TTATTAATAAAATG
66 TTATTAATAAAATG
*
35393 GGTTGCGT-CC-AAGAATATCAT-ATTTCACTAATAAATATGTTGCGATCTGGAATGTTAATA-C
1 GGTTGCGTACCTAAGAATATCATGA-TTCACTAATAAATAGGTTGCGATCTGGAATGTTAATATC
*
35454 TTTTATAAATAAAATG
65 -TTTATTAATAAAATG
* * * * * *
35470 GGTT--GTACCTAAGGATGTCATGATTCACTAATAAATAGGTTGCAATCTGAAATATTAATATTT
1 GGTTGCGTACCTAAGAATATCATGATTCACTAATAAATAGGTTGCGATCTGGAATGTTAATATCT
35533 TTATTAATAAAATG
66 TTATTAATAAAATG
*
35547 AGTTGC
1 GGTTGC
35553 ACATAATAAT
Statistics
Matches: 135, Mismatches: 16, Indels: 16
0.81 0.10 0.10
Matches are distributed among these distances:
75 2 0.01
76 4 0.03
77 126 0.93
78 3 0.02
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (79 bp):
GGTTGCGTACCTAAGAATATCATGATTCACTAATAAATAGGTTGCGATCTGGAATGTTAATATCT
TTATTAATAAAATG
Found at i:35975 original size:153 final size:153
Alignment explanation
Indices: 35673--35990 Score: 444
Period size: 153 Copynumber: 2.1 Consensus size: 153
35663 CGACTAAAAA
* ** * **
35673 AATT-GAAAGTATGGATACTTTTCTAAAAGTATCGATACTTTCAAATTTAAAGAAAAACGTGAAA
1 AATTCGAAAGTATCGATACAATTCCAAAAGTATCGATACTTTCAAATTTAAAGAAAAACACGAAA
* *
35737 AATGAAAAGGCTGCAAAGTATCGATAATTTTACAAAAGGATTGATACTTTAAAATTGAAAGTTAA
66 AATGAAAAGGCTGCAAAGTATCAATAATTTTACAAAAGGATCGATACTTTAAAATTGAAAGTTAA
35802 AATATCATTTTATATATTTTTTT
131 AATATCATTTTATATATTTTTTT
* *
35825 AATTCGAAAGTATCGATACAATTCCAAAAGTATCGATACTTTCGAATTTAAAGAAAAACACGGAA
1 AATTCGAAAGTATCGATACAATTCCAAAAGTATCGATACTTTCAAATTTAAAGAAAAACACGAAA
* * * * * *
35890 AATGAGAAGGCTGCAAAGTATCAATATTTTTCCAAAAGTATCGATACTTTTAACTTCGAAAGTTA
66 AATGAAAAGGCTGCAAAGTATCAATAATTTTACAAAAGGATCGATACTTTAAAATT-GAAAGTTA
35955 AAATATCATTTT-TCAT-TTTTTTT
130 AAATATCATTTTAT-ATATTTTTTT
*
35978 AATTCAAAAGTAT
1 AATTCGAAAGTAT
35991 TGGTAATTTT
Statistics
Matches: 146, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
152 4 0.03
153 120 0.82
154 22 0.15
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.35
Consensus pattern (153 bp):
AATTCGAAAGTATCGATACAATTCCAAAAGTATCGATACTTTCAAATTTAAAGAAAAACACGAAA
AATGAAAAGGCTGCAAAGTATCAATAATTTTACAAAAGGATCGATACTTTAAAATTGAAAGTTAA
AATATCATTTTATATATTTTTTT
Found at i:36758 original size:16 final size:16
Alignment explanation
Indices: 36739--36772 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
36729 CAATATACGA
36739 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
36755 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
36771 AT
1 AT
36773 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:36845 original size:16 final size:18
Alignment explanation
Indices: 36814--36846 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
36804 ATTAATGTAT
36814 GAATCATTTATATTTTTG
1 GAATCATTTATATTTTTG
36832 GAAT-ATTT-TATTTTT
1 GAATCATTTATATTTTT
36847 AATAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.27, C:0.03, G:0.09, T:0.61
Consensus pattern (18 bp):
GAATCATTTATATTTTTG
Found at i:37368 original size:23 final size:21
Alignment explanation
Indices: 37342--37388 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
37332 GTGTCACCAA
37342 TAACACATATCATGATCATGTGT
1 TAACACATATCA-GATCATG-GT
* *
37365 TAACACATGTCAGATCCTGGT
1 TAACACATATCAGATCATGGT
37386 TAA
1 TAA
37389 ATGATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (21 bp):
TAACACATATCAGATCATGGT
Found at i:37519 original size:130 final size:130
Alignment explanation
Indices: 37315--37562 Score: 442
Period size: 130 Copynumber: 1.9 Consensus size: 130
37305 AATTTTCTTC
*
37315 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
**
37380 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
37445 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
37510 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
37563 TATATAAATA
Statistics
Matches: 112, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 112 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:38009 original size:35 final size:35
Alignment explanation
Indices: 37962--38030 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
37952 TGAATTTAAT
* *
37962 TGAATTATTTTGGAATTTAGGGTTTAGAATGAAAA
1 TGAATTACTTTGGAAATTAGGGTTTAGAATGAAAA
*
37997 TGAATTACTTTGGAAATTGGGGTTTAGAATGAAA
1 TGAATTACTTTGGAAATTAGGGTTTAGAATGAAA
38031 TTGAGGATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.38
Consensus pattern (35 bp):
TGAATTACTTTGGAAATTAGGGTTTAGAATGAAAA
Found at i:39741 original size:48 final size:48
Alignment explanation
Indices: 39670--39766 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
39660 ACGATATCAA
39670 ACTACTAACCATTTGAACCAACCTCTATCAGTTAACGTATCGTATTTG
1 ACTACTAACCATTTGAACCAACCTCTATCAGTTAACGTATCGTATTTG
39718 ACTACTAACCATTTGAACCAACCTCTATCAGTTAACGTATCGTATTTG
1 ACTACTAACCATTTGAACCAACCTCTATCAGTTAACGTATCGTATTTG
39766 A
1 A
39767 TATACCGTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.33
Consensus pattern (48 bp):
ACTACTAACCATTTGAACCAACCTCTATCAGTTAACGTATCGTATTTG
Found at i:41816 original size:13 final size:13
Alignment explanation
Indices: 41800--41855 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
41790 GAGTTTAATA
41800 TTTAATGTTAAAT
1 TTTAATGTTAAAT
*
41813 TTTAATTTTAAAT
1 TTTAATGTTAAAT
*
41826 TAT-AT-TTAAAT
1 TTTAATGTTAAAT
41837 ATTTAATGTTAGAAT
1 -TTTAATGTTA-AAT
41852 TTTA
1 TTTA
41856 TTTTATCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
11 6 0.17
12 4 0.11
13 16 0.44
14 7 0.19
15 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (13 bp):
TTTAATGTTAAAT
Found at i:41838 original size:38 final size:38
Alignment explanation
Indices: 41783--41860 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
41773 GTAGTGCGGG
41783 TAAATTAGAGTTTAATATTTAATGTTA-AATTTTAATTT
1 TAAATTAGAGTTTAATATTTAATGTTAGAATTTT-ATTT
*
41821 TAAATTATA-TTTAAATATTTAATGTTAGAATTTTATTT
1 TAAATTAGAGTTT-AATATTTAATGTTAGAATTTTATTT
41859 TA
1 TA
41861 TCTTAATACT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
37 3 0.08
38 28 0.76
39 6 0.16
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (38 bp):
TAAATTAGAGTTTAATATTTAATGTTAGAATTTTATTT
Found at i:53858 original size:50 final size:50
Alignment explanation
Indices: 53801--53916 Score: 198
Period size: 50 Copynumber: 2.3 Consensus size: 50
53791 AAGTTATATA
* *
53801 TCGGGTCGAGGTCGGGTCGGATCTCGGGTGGAGACTCCCTTGTTCTCGGG
1 TCGGGTCGAGGTCGGGTCGGATCTCGAGTGAAGACTCCCTTGTTCTCGGG
*
53851 TCGGGTCGAGGTCGGGTCGGATCTCGAGTGAAGACTCCCTTGTTCTTGGG
1 TCGGGTCGAGGTCGGGTCGGATCTCGAGTGAAGACTCCCTTGTTCTCGGG
53901 TCGGGTCG-GGTCGGGT
1 TCGGGTCGAGGTCGGGT
53917 GGACAAAAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
49 8 0.13
50 55 0.87
ACGTcount: A:0.09, C:0.22, G:0.42, T:0.27
Consensus pattern (50 bp):
TCGGGTCGAGGTCGGGTCGGATCTCGAGTGAAGACTCCCTTGTTCTCGGG
Found at i:54666 original size:14 final size:15
Alignment explanation
Indices: 54643--54675 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
54633 TCCTTTGATA
54643 TAATAATTTA-ATTT
1 TAATAATTTATATTT
*
54657 TAATATTTTATATTT
1 TAATAATTTATATTT
54672 TAAT
1 TAAT
54676 CTTATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TAATAATTTATATTT
Found at i:55391 original size:29 final size:30
Alignment explanation
Indices: 55358--55418 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
55348 TAAATTACGA
55358 TGTTAG-TTAATATCTAAACTATTAATTTT
1 TGTTAGTTTAATATCTAAACTATTAATTTT
* * *
55387 TGTTAGTTTTAGTATCTAAACTTTTATTTTT
1 TGTTAG-TTTAATATCTAAACTATTAATTTT
55418 T
1 T
55419 AAAAAAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 6 0.22
31 21 0.78
ACGTcount: A:0.28, C:0.07, G:0.08, T:0.57
Consensus pattern (30 bp):
TGTTAGTTTAATATCTAAACTATTAATTTT
Found at i:57900 original size:6 final size:6
Alignment explanation
Indices: 57889--57919 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
57879 AAGGCACCAA
57889 CCACTG CCACTG CCACTG CCACTG CCACTG C
1 CCACTG CCACTG CCACTG CCACTG CCACTG C
57920 TTCCTCCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.52, G:0.16, T:0.16
Consensus pattern (6 bp):
CCACTG
Found at i:66170 original size:450 final size:449
Alignment explanation
Indices: 65295--66633 Score: 1567
Period size: 456 Copynumber: 3.0 Consensus size: 449
65285 AGTTGCCCCA
* * * * *
65295 GAGATTTCCACTTTC--GAAGCAGTTCTGCCTTTTGGTTTGGGAGCGGGATGCGGCTTTACATTC
1 GAGATTTCCACTTTCAAGAAGCAGTACTGCCTTTTGGTTTGGCAGCAGGATGTGGCATTACATTC
65358 TCCTTTTCATATTTCGTCTCCTCAACATTCTTCCGGACACTACTATTTTCCCCAACCAAATCATT
66 TCCTTTTCAT-TTTCGTCTCCTCAACATTCTTCCGGACACTACTATTTTCCCCAACCAAATCATT
* * * *
65423 TTTGGAATTAGAAGGATCAGCCTTCATCATGGCTCTACTGGAAGGCTGTTTCTCCCTTTTGCTTG
130 TTTGGAATTAGAAGGATCAGCCTTCATCATGGCTCTACTGGAAAGTTGTTTCTTCCTTTTTCTTG
* * * * *
65488 CTTTCTTTTTCAAG---C-TACCAC-AC-TT-GAC-ATCAAAGTCAGAATTATTACTACCAACTG
195 CTTTCTTTTTCAAGCCACATACCTCAACGTTGGTCTACCAAAGTCAGAATTCTTGCTACCAACTG
* * *
65545 TCTTCTCAGGATCAGTTTCATTTGTTCTATTGTCCAATGCAATTGGACTCCCATGTTGAATGGAA
260 CCTTCTCAGGATCAGTTTCATTTGTTCTATTCTCCAAGGCAATTGGACTCCCATGTTGAATGGAA
*
65610 TCATGGCTGACATGTTCCACTTCTACAAATGTTTCTGTTTTATGAGTCAATTCAATCAACTCAGG
325 TCATGGCTGACATGTTCCACTTCTACAAATGTTTCTGCTTTATGAGTCAATTCAATCAACTC-GG
* ** *
65675 -CTTCTCATTTTCAGCTGTCTTCTTACCATAATT-TTCATCTTCCTCATCTGGAGCAGC-G-
389 ACTTCTCTTTTTCAGCTGTCTTCTTAGGATCATTGTT-ATCTTCCTCATCTGGAGCAGCTGC
* * *
65733 GAGATTTCCACTTTCGAAGAAGCAGTACTGCCTTTTGGTTTGGCAGCAGGAAGTAGCATGACATT
1 GAGATTTCCACTTTC-AAGAAGCAGTACTGCCTTTTGGTTTGGCAGCAGGATGTGGCATTACATT
* * * * *
65798 CTTCGTTTCATTTTCTGTCTCCTCAACATTCATCCGGATACTACTATCTTCCCCAACCAAATCAT
65 CTCCTTTTCATTTTC-GTCTCCTCAACATTCTTCCGGACACTACTATTTTCCCCAACCAAATCAT
* * * *
65863 TTTTAGAACTAGAAGGATCAGCCTTCATCATGACTCTACTGGAAAGTTGTTTCTTCGTTTTTCTT
129 TTTTGGAATTAGAAGGATCAGCCTTCATCATGGCTCTACTGGAAAGTTGTTTCTTCCTTTTTCTT
* * *
65928 GCTTTCTTTTTCAAGCCACAAAACCTCAACGTTGGTCTACCAAAGTCGGAGTTCTTGCTACCAAC
194 GCTTTCTTTTTCAAGCCAC-ATACCTCAACGTTGGTCTACCAAAGTCAGAATTCTTGCTACCAAC
* **
65993 TGCCTTCTCAGGATCAGTTACATTCATTCTATTCTCCAAGGCAATTGGACTCCCATGTTGAATGG
258 TGCCTTCTCAGGATCAGTTTCATTTGTTCTATTCTCCAAGGCAATTGGACTCCCATGTTGAATGG
* * * * **
66058 AATCGTGGCCGACATGTTCCACATCTACAAATGTTTCTGCTTTACGAGTCAACCCAATCAACTCG
323 AATCATGGCTGACATGTTCCACTTCTACAAATGTTTCTGCTTTATGAGTCAATTCAATCAACTCG
* * *
66123 GACTTCTCTTTTTCAGCTGTTTTCTTGGGATCATTGTTATCTTCCTCATCTGGAGCTGCTGCTCC
388 GACTTCTCTTTTTCAGCTGTCTTCTTAGGATCATTGTTATCTTCCTCATCTGGAGCAGCTG---C
* * * * * *
66188 AGAGATTTCAACTTCCACAAAAGCAGTACTGCCTTTCGGTTTGGCAACAGGATGTGGCATTACAC
1 -GAGATTTCCACTTTCA-AGAAGCAGTACTGCCTTTTGGTTTGGCAGCAGGATGTGGCATTACAT
* * ** *
66253 TCTCCTTTTCATTTTCCATCTCATCAACATTCTTTGGGACACTACTATTTTCACCAACCAAATCA
64 TCTCCTTTTCATTTT-CGTCTCCTCAACATTCTTCCGGACACTACTATTTTCCCCAACCAAATCA
* * * * * * *
66318 TTTTTGGAGTTGGAAGGATCGGCCTTCATCACGGTTATACTGTAAAGTTGTTTCTTCCTTTTGT-
128 TTTTTGGAATTAGAAGGATCAGCCTTCATCATGGCTCTACTGGAAAGTTGTTTCTTCCTTTT-TC
* * * * *
66382 TTGCTTTCTTTTTCAAGCCACCATGCTTCAACGTTGGT-TCACCGAAGTCAGAATCCTTGCTAAC
192 TTGCTTTCTTTTTCAAGCCA-CATACCTCAACGTTGGTCT-ACCAAAGTCAGAATTCTTGCTACC
* * * * * ** *
66446 AACTGCCCTCTCAAGATCTGTTTCATTTGTTATTTTCTCTGAGGCAATTGGACTCCCATGTTGAG
255 AACTGCCTTCTCAGGATCAGTTTCATTTGTTCTATTCTCCAAGGCAATTGGACTCCCATGTTGAA
* * * * * ** * * *
66511 TGAAATCATGGCTGGCGTGTTCCACTTCTACAAATATATCAACTTTATGACTCAATTCAACCATC
320 TGGAATCATGGCTGACATGTTCCACTTCTACAAATGTTTCTGCTTTATGAGTCAATTCAATCAAC
* * * * * *
66576 TCAGACTTCTCTATTTCAGATGTCTTCTTAGGATCATAGTCATCTTCCTCGTCTGGAG
385 TCGGACTTCTCTTTTTCAGCTGTCTTCTTAGGATCATTGTTATCTTCCTCATCTGGAG
66634 ATTGAGTTTC
Statistics
Matches: 753, Mismatches: 122, Indels: 34
0.83 0.13 0.04
Matches are distributed among these distances:
438 15 0.02
440 4 0.01
441 166 0.22
444 1 0.00
446 4 0.01
447 2 0.00
448 2 0.00
449 4 0.01
450 185 0.25
451 3 0.00
455 2 0.00
456 362 0.48
457 3 0.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (449 bp):
GAGATTTCCACTTTCAAGAAGCAGTACTGCCTTTTGGTTTGGCAGCAGGATGTGGCATTACATTC
TCCTTTTCATTTTCGTCTCCTCAACATTCTTCCGGACACTACTATTTTCCCCAACCAAATCATTT
TTGGAATTAGAAGGATCAGCCTTCATCATGGCTCTACTGGAAAGTTGTTTCTTCCTTTTTCTTGC
TTTCTTTTTCAAGCCACATACCTCAACGTTGGTCTACCAAAGTCAGAATTCTTGCTACCAACTGC
CTTCTCAGGATCAGTTTCATTTGTTCTATTCTCCAAGGCAATTGGACTCCCATGTTGAATGGAAT
CATGGCTGACATGTTCCACTTCTACAAATGTTTCTGCTTTATGAGTCAATTCAATCAACTCGGAC
TTCTCTTTTTCAGCTGTCTTCTTAGGATCATTGTTATCTTCCTCATCTGGAGCAGCTGC
Found at i:67407 original size:279 final size:278
Alignment explanation
Indices: 66905--67467 Score: 677
Period size: 279 Copynumber: 2.0 Consensus size: 278
66895 TCACAAGCTT
* * * * *
66905 CTTGCTAACTGGTTTTGTTACCAACTTACCATTTCCCCCTTCAAGCAAATCGATGTTAGAAGGAC
1 CTTGCTAACTAGTTTTGTCAACAACTTACCATTTCCCCCTCCAAGCAAATCGAAGTTAGAAGGAC
* * * * * *
66970 TATGGGAATTTTCATTCCCCAGATTTTTTTCATCATGTGAAGGAACCTCAACATCTTGCTGCTTA
66 TATGGGAATTTTCATTCACAAGATTTCTATAATCAAGTGAAGGAACCTCAACATCTTGCTGCTTA
* * * * *
67035 TTCTGCAGCTCACCTGGCTCTTCGACAACGCGTAGTGGTTCTAAGCCATACTCTCCGATATTTGA
131 TTCAGCAGCTCACCTGGCTCTCCAACAACGCGTAGTCGTTCTAAGCCATACTCT-CGATATTCGA
* * * *
67100 TTTGCTTGCAGAGGTGGACTCTCTTAATCCCTTGAA-GA-ATGCTTGGGGTGACTTCTCATAAGC
195 TCTGCTAGCAGAGGTGGACTCCCTTAATCCCTTGAAGGACAT--TTGGGGTGACTTCACATAAGC
* *
67163 ATTCTCGTTTTGCATATCTGG
258 AATCTCATTTTGCATATCTGG
* *
67184 CTTGCTAACTAGTTTTGTCAACAACTTATCATTTCCTCCTCCAAGCAAATTC-AAGTTAGAAGGA
1 CTTGCTAACTAGTTTTGTCAACAACTTACCATTTCCCCCTCCAAGCAAA-TCGAAGTTAGAAGGA
* *
67248 CTATGGGAATTTTCATTCAGAAGCTTTCTATAATCAAGTGAAGGAACCTCAACATCTTGCTGCTT
65 CTATGGGAATTTTCATTCACAAGATTTCTATAATCAAGTGAAGGAACCTCAACATCTTGCTGCTT
* * ** * ** *
67313 ATTCAGCAGCTCATCTGGCTCTCCAACCACTTGTATTCGTTCTGGGTTGCA-AGCTCT-GATATT
130 ATTCAGCAGCTCACCTGGCTCTCCAACAACGCGTAGTCGTTCTAAG--CCATA-CTCTCGATATT
* * * *
67376 CGATCTGCTAGCTGAGGTGGACTCCCTTAATCCCTTTAAGGACATTTTGGGTGACTTCACATGAG
192 CGATCTGCTAGCAGAGGTGGACTCCCTTAATCCCTTGAAGGACATTTGGGGTGACTTCACATAAG
*
67441 CAATCTCATTTTGCATATTTGG
257 CAATCTCATTTTGCATATCTGG
67463 CTTGC
1 CTTGC
67468 CTGCCAAGGT
Statistics
Matches: 239, Mismatches: 39, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
279 226 0.95
280 5 0.02
281 8 0.03
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.34
Consensus pattern (278 bp):
CTTGCTAACTAGTTTTGTCAACAACTTACCATTTCCCCCTCCAAGCAAATCGAAGTTAGAAGGAC
TATGGGAATTTTCATTCACAAGATTTCTATAATCAAGTGAAGGAACCTCAACATCTTGCTGCTTA
TTCAGCAGCTCACCTGGCTCTCCAACAACGCGTAGTCGTTCTAAGCCATACTCTCGATATTCGAT
CTGCTAGCAGAGGTGGACTCCCTTAATCCCTTGAAGGACATTTGGGGTGACTTCACATAAGCAAT
CTCATTTTGCATATCTGG
Found at i:72251 original size:18 final size:17
Alignment explanation
Indices: 72197--72245 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
72187 TTGGACCCTT
* *
72197 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
72215 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
72233 AGTGCATTCGATG
1 AGTGCA-TCGATG
72246 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:72303 original size:64 final size:63
Alignment explanation
Indices: 72197--72380 Score: 221
Period size: 64 Copynumber: 2.9 Consensus size: 63
72187 TTGGACCCTT
* * * *
72197 AGTGCATCGGTGCACT-AAGAGTGCATCGATGCATCAAGTGCATTCGATGTTTCAA-AATAGCCC
1 AGTGCATCGATGCA-TGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATAA-A-CCA
72260 G
63 G
** * *
72261 AGTGCATCGATGCATGGCTAGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAG
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAA-TAAACCAG
*
72325 AGTGCATCGATGCATGGAGAGTGCATCGGTGCAT-AGAATGCATTCGATGTTTCAAT
1 AGTGCATCGATGCATGGAGAGTGCATCGATGCATCA-AATGCATTCGATGTTTCAAT
72381 TTATCCATTG
Statistics
Matches: 104, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
63 3 0.03
64 98 0.94
65 1 0.01
66 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (63 bp):
AGTGCATCGATGCATGGAGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAATAAACCAG
Found at i:76442 original size:21 final size:21
Alignment explanation
Indices: 76418--76573 Score: 93
Period size: 21 Copynumber: 7.6 Consensus size: 21
76408 GCGTTGCATT
76418 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
76439 TCGCGTTGCGAT-TTTTCATT
1 TCGCGTTGCGATAGTTGAAAA
*
76459 TCGTGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
76480 TCGCGTTGCGCT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
76500 TAGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
76521 TCACGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
76541 TCGCGGTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* *
76562 GCGGGTTGCGAT
1 TCGCGTTGCGAT
76574 TTTTATTTCG
Statistics
Matches: 90, Mismatches: 42, Indels: 6
0.65 0.30 0.04
Matches are distributed among these distances:
20 40 0.44
21 50 0.56
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:76471 original size:41 final size:41
Alignment explanation
Indices: 76414--76592 Score: 270
Period size: 41 Copynumber: 4.4 Consensus size: 41
76404 CTTCGCGTTG
*
76414 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
76455 CATTTCGTGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
76496 CATTTAGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* * *
76537 CATTTCGCGGTGCGATAGTTGAAAAGCGGGTTGCGATTTT-
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
*
76577 TATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
76593 TTTCCATTTC
Statistics
Matches: 124, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 14 0.11
41 110 0.89
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:76590 original size:19 final size:20
Alignment explanation
Indices: 76566--76608 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
76556 TGAAAAGCGG
*
76566 GTTGCGATTTT-TATTTCGC
1 GTTGCGATTTTCCATTTCGC
76585 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
76605 GTTG
1 GTTG
76609 TGATATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.09, C:0.19, G:0.23, T:0.49
Consensus pattern (20 bp):
GTTGCGATTTTCCATTTCGC
Found at i:76606 original size:20 final size:20
Alignment explanation
Indices: 76439--76608 Score: 90
Period size: 20 Copynumber: 8.4 Consensus size: 20
76429 TAGTTGAAAA
*
76439 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
76459 TCGTGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
76480 TCGCGTTGCGCTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
76500 TAGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
76521 TCACGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
76541 TCGCGGTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
* * *
76562 GCGGGTTGCGATTTT-TATT
1 TCGCGTTGCGATTTTCCATT
76581 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
76601 TCGCGTTG
1 TCGCGTTG
76609 TGATATTCTA
Statistics
Matches: 102, Mismatches: 44, Indels: 8
0.66 0.29 0.05
Matches are distributed among these distances:
19 14 0.14
20 50 0.49
21 38 0.37
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:76649 original size:19 final size:19
Alignment explanation
Indices: 76625--76690 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
76615 TCTACAGTTG
*
76625 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTACAAAT
* **
76644 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTACAAAT
*
76665 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTACAAAT
76685 TCGTTG
1 TCGTTG
76691 TGATAGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTACAAAT
Found at i:76661 original size:41 final size:41
Alignment explanation
Indices: 76584--76697 Score: 167
Period size: 41 Copynumber: 2.8 Consensus size: 41
76574 TTTTATTTCG
* *
76584 CGTTGCGATTTTCC-ATTTCGCGTTGTGATATTCTACAGTTGT
1 CGTTGCGATTTTCCAAATT--CGTTGTGATAGTCTACAGTTGT
* *
76626 CGTTGCGATTTTTCAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGTGATAGTCTACAGTTGT
76667 CGTTGCGATTTTCCAAATTCGTTGTGATAGT
1 CGTTGCGATTTTCCAAATTCGTTGTGATAGT
76698 TAAAAAAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
41 49 0.75
42 13 0.20
43 3 0.05
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.43
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGTGATAGTCTACAGTTGT
Found at i:76672 original size:22 final size:21
Alignment explanation
Indices: 76604--76675 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
76594 TTCCATTTCG
*
76604 CGTTGTGATATTCTACAGTTGT
1 CGTTGCGATA-TCTACAGTTGT
* * **
76626 CGTTGCGAT-TTTTCAAAT-T
1 CGTTGCGATATCTACAGTTGT
76645 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATA-TCTACAGTTGT
76667 CGTTGCGAT
1 CGTTGCGAT
76676 TTTCCAAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 18 0.47
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.42
Consensus pattern (21 bp):
CGTTGCGATATCTACAGTTGT
Found at i:77480 original size:21 final size:21
Alignment explanation
Indices: 77442--77505 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
77432 ATAACTTGAT
* **
77442 ATATTATAATATAAAAATATA
1 ATATTATATTATTTAAATATA
77463 ATATTATATTATTTAAATTATTA
1 ATATTATATTATTTAAA-TA-TA
*
77486 ATAAATATATT-TTTAAATAT
1 AT-ATTATATTATTTAAATAT
77506 TTTAATAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 15 0.42
22 4 0.11
23 10 0.28
24 7 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATTATATTATTTAAATATA
Found at i:77510 original size:24 final size:23
Alignment explanation
Indices: 77467--77525 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 23
77457 AATATAATAT
77467 TATATTATTTAAATTATTAATAAA
1 TATATT-TTTAAATTATTAATAAA
* *
77491 TATATTTTTAAATATTTTAATAAT
1 TATATTTTTAAAT-TATTAATAAA
77515 TAATATTTTTA
1 T-ATATTTTTA
77526 TTAAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
23 7 0.23
24 15 0.48
25 9 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATATTTTTAAATTATTAATAAA
Found at i:83862 original size:22 final size:21
Alignment explanation
Indices: 83820--83870 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
83810 GGTCACTAGT
83820 ATAATTTACTCTTTATTTTAA
1 ATAATTTACTCTTTATTTTAA
83841 ATAATTTA-TCTTTAAATTTTAA
1 ATAATTTACTCTTT--ATTTTAA
*
83863 CTAATTTA
1 ATAATTTA
83871 ATTATATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 5 0.19
21 8 0.30
22 14 0.52
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (21 bp):
ATAATTTACTCTTTATTTTAA
Found at i:85021 original size:18 final size:18
Alignment explanation
Indices: 84998--85033 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
84988 TGTTTTATTC
84998 CCCGAAACATGGTACTGG
1 CCCGAAACATGGTACTGG
85016 CCCGAAACATGGTACTGG
1 CCCGAAACATGGTACTGG
85034 GAACTTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (18 bp):
CCCGAAACATGGTACTGG
Done.