Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008711.1 Hibiscus syriacus cultivar Beakdansim tig00111762_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: 31969
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Found at i:372 original size:1 final size:1
Alignment explanation
Indices: 366--408 Score: 59
Period size: 1 Copynumber: 43.0 Consensus size: 1
356 CCTTTATTTA
* **
366 TTTTTTTCTTTTTCATTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
409 AAGTGTAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.02, C:0.05, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:13636 original size:25 final size:25
Alignment explanation
Indices: 13602--13676 Score: 132
Period size: 25 Copynumber: 3.0 Consensus size: 25
13592 GAGTAGGGGA
* *
13602 TTAGGGTTTGAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGAT
13627 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
13652 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
13677 GGGTTGTTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:13708 original size:22 final size:22
Alignment explanation
Indices: 13683--13753 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
13673 TGATGGGTTG
13683 TTGGGCTCCGGGATTGGGCCAA
1 TTGGGCTCCGGGATTGGGCCAA
*
13705 TTGGGCTTCGGG-TT--G----
1 TTGGGCTCCGGGATTGGGCCAA
13720 TTGGGCTCCGGGATTGGGCCAA
1 TTGGGCTCCGGGATTGGGCCAA
*
13742 TTGGGCTTCGGG
1 TTGGGCTCCGGG
13754 TTGTTGGGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
15 11 0.28
16 2 0.05
18 1 0.03
19 1 0.03
21 2 0.05
22 22 0.56
ACGTcount: A:0.08, C:0.20, G:0.44, T:0.28
Consensus pattern (22 bp):
TTGGGCTCCGGGATTGGGCCAA
Found at i:13727 original size:37 final size:37
Alignment explanation
Indices: 13677--13776 Score: 200
Period size: 37 Copynumber: 2.7 Consensus size: 37
13667 CTAATCTGAT
13677 GGGTTGTTGGGCTCCGGGATTGGGCCAATTGGGCTTC
1 GGGTTGTTGGGCTCCGGGATTGGGCCAATTGGGCTTC
13714 GGGTTGTTGGGCTCCGGGATTGGGCCAATTGGGCTTC
1 GGGTTGTTGGGCTCCGGGATTGGGCCAATTGGGCTTC
13751 GGGTTGTTGGGCTCCGGGATTGGGCC
1 GGGTTGTTGGGCTCCGGGATTGGGCC
13777 TTTGTAATCT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 63 1.00
ACGTcount: A:0.07, C:0.19, G:0.45, T:0.29
Consensus pattern (37 bp):
GGGTTGTTGGGCTCCGGGATTGGGCCAATTGGGCTTC
Found at i:13824 original size:3 final size:3
Alignment explanation
Indices: 13818--13864 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
13808 AAAAAAAATG
13818 TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA TAA TAA -AA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
13862 TAA
1 TAA
13865 AAAAATAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:13863 original size:13 final size:14
Alignment explanation
Indices: 13818--13872 Score: 69
Period size: 13 Copynumber: 4.0 Consensus size: 14
13808 AAAAAAAATG
13818 TAATAATAATAATAA
1 TAATAATAA-AATAA
*
13833 TAATAAT-AATTAA
1 TAATAATAAAATAA
13846 TAATAATAAAATAA
1 TAATAATAAAATAA
*
13860 -AATAAAAAAATAA
1 TAATAATAAAATAA
13873 ATATAAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 23 0.64
14 6 0.17
15 7 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAATAATAAAATAA
Found at i:13873 original size:13 final size:13
Alignment explanation
Indices: 13847--13880 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
13837 AATAATTAAT
*
13847 AATAATAAAATAA
1 AATAAAAAAATAA
13860 AATAAAAAAATAA
1 AATAAAAAAATAA
13873 ATATAAAA
1 A-ATAAAA
13881 GACCCGGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AATAAAAAAATAA
Found at i:13942 original size:20 final size:20
Alignment explanation
Indices: 13917--13957 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
13907 CCATTAATTA
13917 AATATTTTATTA-AAAATATT
1 AATATTTT-TTATAAAATATT
13937 AATATTTTTTATAAAATATT
1 AATATTTTTTATAAAATATT
13957 A
1 A
13958 TTTAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATATTTTTTATAAAATATT
Found at i:13954 original size:14 final size:14
Alignment explanation
Indices: 13937--13986 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
13927 TAAAAATATT
13937 AATATTTTTTATAA
1 AATATTTTTTATAA
*
13951 AATATTATTTA-AA
1 AATATTTTTTATAA
13964 ATATATTTTTTACTAAA
1 A-ATATTTTTTA-T-AA
13981 AATATT
1 AATATT
13987 AATTTCGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 3 0.10
14 19 0.63
16 5 0.17
17 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
AATATTTTTTATAA
Found at i:23265 original size:5 final size:5
Alignment explanation
Indices: 23251--23305 Score: 51
Period size: 5 Copynumber: 11.2 Consensus size: 5
23241 TGGATGAAAC
* ** *
23251 AAAA- AAAAT AAAAT AAAAT GAAAT TGAAT AAAAT AAAAT -AAAT GAAGAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT
23300 AAAAT A
1 AAAAT A
23306 TATATACAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
4 8 0.20
5 30 0.73
6 3 0.07
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:23305 original size:20 final size:20
Alignment explanation
Indices: 23257--23293 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
23247 AAACAAAAAA
23257 AATAAAATAAAATGAAATTG
1 AATAAAATAAAATGAAATTG
23277 AATAAAATAAAAT-AAAT
1 AATAAAATAAAATGAAAT
23294 GAAGATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (20 bp):
AATAAAATAAAATGAAATTG
Found at i:23409 original size:22 final size:21
Alignment explanation
Indices: 23383--23490 Score: 80
Period size: 22 Copynumber: 4.9 Consensus size: 21
23373 AAACTAAAAA
23383 TATAATGAAAATAAATAAATAG
1 TATAAT-AAAATAAATAAATAG
23405 TATAAATAAAAT-AATAATAATA-
1 TAT-AATAAAATAAAT-A-AATAG
* **
23427 TATATATAATATAAA-ATGTATG
1 TATA-ATAAAATAAATAAATA-G
23449 TATAATATAAAT-AATAAATAG
1 TATAATA-AAATAAATAAATAG
23470 TAATAATAATAATAAATAAAT
1 T-ATAATAA-AATAAATAAAT
23491 GAAAAATAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 23
0.70 0.06 0.24
Matches are distributed among these distances:
20 2 0.03
21 13 0.19
22 37 0.54
23 16 0.24
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (21 bp):
TATAATAAAATAAATAAATAG
Found at i:23681 original size:2 final size:2
Alignment explanation
Indices: 23634--23664 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23624 AAAAATAATA
23634 AT AT AT 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 AT AT AT A
23665 GGAAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24820 original size:106 final size:106
Alignment explanation
Indices: 24634--25789 Score: 1676
Period size: 106 Copynumber: 11.0 Consensus size: 106
24624 GCATTGTTCC
* * * * *
24634 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTAGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * * * *
24699 CCAATC-GTCCATTCGTTGTGAAGTTGAACTTGTGTTATCTC
66 CC-AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
24740 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
24805 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
24846 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
24911 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** *
24952 GAGTCCAATATCTTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGATAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
25017 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
25058 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
25123 CCAGCGGTCCCTTCTTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
25164 GAGTCC-A-ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGATTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
25227 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
25268 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
25333 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
25374 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
25439 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
25480 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
25545 CCAACGGTCCCTT-GTCGTGAAGTTGAA----C----T-TG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
25576 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGACTCTG-ATTTGAGAAGTTGTTTGTTGAAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
25640 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** * *
25681 GAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCCAAAATTGGAAAATTG-TTGTTGTCAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
25745 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
25786 GAGT
1 GAGT
25790 GACACGATAT
Statistics
Matches: 948, Mismatches: 88, Indels: 29
0.89 0.08 0.03
Matches are distributed among these distances:
95 31 0.03
96 51 0.05
97 1 0.00
100 1 0.00
101 1 0.00
104 97 0.10
105 103 0.11
106 663 0.70
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:25428 original size:422 final size:419
Alignment explanation
Indices: 24634--25789 Score: 1713
Period size: 422 Copynumber: 2.8 Consensus size: 419
24624 GCATTGTTCC
* * * *
24634 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTAGCTCTGGAATCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * *
24698 ACCAATC-GTCCATTCGTTGTGAAGTTGAACTTGTGTTATCTCGAGTCCAATATCCTTTGTTGTG
65 ACCAA-CGGTCCCTTCGTTGTGAAGTTGAACTTG-GTTGTCT-GAGTCC-A-ATCCTTCGTTGTG
*
24762 AAGTTGAAATTGGCTCCGAAATTGGGAAATT-ATTTGTTGACAACCAGCGGTCCCTTCGTCGTGA
125 AAGTTGAAATTGGCTCTGAAATTGGGAAATTGA-TTGTTGACAACCAGCGGTCCCTTCGTCGTGA
* *
24826 AGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT
189 AGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATT
*
24891 GGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTAGAGT
254 -GGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGT
* * *
24956 CCAATATCTTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGATAAGTTGTTTGTTGACAACCAG
318 CCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAG
25021 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
383 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
25058 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
25123 CCAGCGGTCCCTTCTTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATCCTTCGTTGTGAAGT
66 CCAACGGTCCCTTCGTTGTGAAGTTGAACTTG-GTTGTCT-GAGTCCAATCCTTCGTTGTGAAGT
*
25188 TGAAATTGGCTCTGAAATTGGGAAATTGATTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
129 TGAAATTGGCTCTGAAATTGGGAAATTGATTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
*
25253 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAA
194 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTG-GAA
* *
25318 GTTGTTTGTTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
258 GTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAAT
* *
25383 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTC
323 ATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTC
*
25448 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
388 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
25480 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * * *
25545 CCAACGGTCCCTT-GTCGTGAAGTTGAACTTGG-AGTC-CAAT---ATCCTTCGTTGTAAAGTTG
66 CCAACGGTCCCTTCGTTGTGAAGTTGAACTTGGTTGTCTGAGTCCAATCCTTCGTTGTGAAGTTG
* * * * * *
25604 AAATTGACTCTG-ATTTGAGAAGTTGTTTGTTGAAAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 AAATTGGCTCTGAAATTGGGAAATTGATTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
* * *
25668 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCCAAAATTGGAAAAT
196 CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGG-AAGT
* * * * *
25733 TG-TTGTTGTCAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
260 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGT
25790 GACACGATAT
Statistics
Matches: 672, Mismatches: 55, Indels: 22
0.90 0.07 0.03
Matches are distributed among these distances:
412 50 0.07
413 107 0.16
414 29 0.04
417 2 0.00
419 3 0.00
420 1 0.00
421 17 0.03
422 363 0.54
423 3 0.00
424 96 0.14
425 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (419 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAACGGTCCCTTCGTTGTGAAGTTGAACTTGGTTGTCTGAGTCCAATCCTTCGTTGTGAAGTTG
AAATTGGCTCTGAAATTGGGAAATTGATTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
CTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGAAGTT
GTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAATATC
CTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCT
TCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:25658 original size:96 final size:96
Alignment explanation
Indices: 25480--25776 Score: 285
Period size: 105 Copynumber: 3.0 Consensus size: 96
25470 GCGTTGTCTT
* * * *
25480 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTAAAGTTGAAATTGACTCTAAAATTGAGAAATTATTTGTTGAAAA
25545 CCAACGGTCCCTTGTCGTGAAGTTGAACTTG
66 CCAACGGTCCCTTGTCGTGAAGTTGAACTTG
* * * * *
25576 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGACTCT-GATTTGAGAAGTTGTTTGTTGAAAA
1 GAGTCCAATATCCTTCGCTGTAAAGTTGAAATTGACTCTAAAATTGAGAAATTATTTGTTGAAAA
*
25640 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAACGGTCCCTT-GTCGTGAAGTTGAA----C----T-TG
* * * * * **
25681 GAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCCAAAATTG-GAAAATT-GTTGTTGTCA
1 GAGTCCAATATCCTTCGCTGTAAAGTTGAAATTGACTCTAAAATTGAG-AAATTATTTGTTGAAA
* * *
25744 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
65 ACCAACGGTCCCTT-GTCGTGAAGTTGAACTTG
25777 TGTTGTCTTG
Statistics
Matches: 166, Mismatches: 23, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
95 31 0.19
96 52 0.31
97 1 0.01
100 1 0.01
101 1 0.01
104 1 0.01
105 71 0.43
106 8 0.05
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (96 bp):
GAGTCCAATATCCTTCGCTGTAAAGTTGAAATTGACTCTAAAATTGAGAAATTATTTGTTGAAAA
CCAACGGTCCCTTGTCGTGAAGTTGAACTTG
Found at i:26194 original size:18 final size:19
Alignment explanation
Indices: 26165--26201 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
26155 TATTGAATCC
26165 CCAAATAATGCCCCAATAT
1 CCAAATAATGCCCCAATAT
*
26184 CCAAA-AATGCCCCCATAT
1 CCAAATAATGCCCCAATAT
26202 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.41, C:0.35, G:0.05, T:0.19
Consensus pattern (19 bp):
CCAAATAATGCCCCAATAT
Found at i:26647 original size:21 final size:22
Alignment explanation
Indices: 26614--26666 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
26604 TTGTGTTTGG
*
26614 TCAAAGG-TTGGCA-TTGATGC
1 TCAAAGGTTTGGCATTTAATGC
26634 TCAAAGGTTTGGCATTTAATGC
1 TCAAAGGTTTGGCATTTAATGC
26656 TCAAAGGTTTG
1 TCAAAGGTTTG
26667 ATGGGGTAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.34
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTAATGC
Found at i:27300 original size:16 final size:16
Alignment explanation
Indices: 27281--27316 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
27271 TTTTTGTTTA
27281 TTTTTGTTT-TCTTCT
1 TTTTTGTTTCTCTTCT
*
27296 TTTTTGTTTCTTTTCT
1 TTTTTGTTTCTCTTCT
27312 TTTTT
1 TTTTT
27317 ATTTTTGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTTGTTTCTCTTCT
Found at i:27314 original size:14 final size:15
Alignment explanation
Indices: 27281--27321 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
27271 TTTTTGTTTA
27281 TTTTTGTTTTCTTCT
1 TTTTTGTTTTCTTCT
*
27296 TTTTTGTTTCTTTTCT
1 TTTTTGTTT-TCTTCT
*
27312 TTTTTATTTT
1 TTTTTGTTTT
27322 TGGCCTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.02, C:0.10, G:0.05, T:0.83
Consensus pattern (15 bp):
TTTTTGTTTTCTTCT
Found at i:31576 original size:18 final size:18
Alignment explanation
Indices: 31553--31595 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
31543 ATGCCCTTAA
**
31553 AAAATAAGATGTTAAAAG
1 AAAATAAGATAATAAAAG
*
31571 AAAATAATATAATAAAAG
1 AAAATAAGATAATAAAAG
31589 AAAATAA
1 AAAATAA
31596 CAAAATAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAAATAAGATAATAAAAG
Found at i:31602 original size:18 final size:18
Alignment explanation
Indices: 31565--31604 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
31555 AATAAGATGT
* *
31565 TAAAAGAAAATAATATAA
1 TAAAAGAAAATAACAAAA
31583 TAAAAGAAAATAACAAAA
1 TAAAAGAAAATAACAAAA
31601 TAAA
1 TAAA
31605 GAGTAAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (18 bp):
TAAAAGAAAATAACAAAA
Found at i:31690 original size:20 final size:20
Alignment explanation
Indices: 31667--31707 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
31657 GGATGAAACA
31667 AAAAAAAATGAA-ATTAAAAT
1 AAAAAAAATGAAGA-TAAAAT
*
31687 AAAATAAATGAAGATAAAAT
1 AAAAAAAATGAAGATAAAAT
31707 A
1 A
31708 TATACAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (20 bp):
AAAAAAAATGAAGATAAAAT
Found at i:31804 original size:13 final size:12
Alignment explanation
Indices: 31788--31904 Score: 56
Period size: 12 Copynumber: 10.1 Consensus size: 12
31778 TATAATGAAA
31788 ATAAATAAATAGT
1 ATAAATAAATA-T
31801 ATAAATAAATA-
1 ATAAATAAATAT
31812 AT-AAT-AATAT
1 ATAAATAAATAT
* *
31822 ATATATATATAT
1 ATAAATAAATAT
*
31834 A-AATATAAATGT
1 ATAA-ATAAATAT
**
31846 ATGTAT-AATAT
1 ATAAATAAATAT
31857 AATAAAT-AATA-
1 -ATAAATAAATAT
31868 AT-AAT-AATAAT
1 ATAAATAAAT-AT
31879 AATAAATAAATGA-
1 -ATAAATAAAT-AT
*
31892 AAAAATAAATAT
1 ATAAATAAATAT
31904 A
1 A
31905 CATATAATAT
Statistics
Matches: 80, Mismatches: 12, Indels: 25
0.68 0.10 0.21
Matches are distributed among these distances:
9 10 0.12
10 8 0.10
11 10 0.12
12 34 0.43
13 14 0.17
14 4 0.05
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (12 bp):
ATAAATAAATAT
Found at i:31865 original size:12 final size:12
Alignment explanation
Indices: 31776--31902 Score: 64
Period size: 13 Copynumber: 10.1 Consensus size: 12
31766 AAGAAACTAA
*
31776 AATATAATGAA-
1 AATATAATAAAT
31787 AATA-AATAAAT
1 AATATAATAAAT
*
31798 AGTATAAATAAAT
1 AATAT-AATAAAT
*
31811 AATAATAATATAT
1 AAT-ATAATAAAT
31824 ATATATATATAAAT
1 A-ATATA-ATAAAT
* * **
31838 ATAAATGTATGTAT
1 A-ATAT-AATAAAT
31852 AATATAATAAAT
1 AATATAATAAAT
31864 AATAATAAT-AAT
1 AAT-ATAATAAAT
31876 AATAATAAATAAAT
1 AAT-AT-AATAAAT
*
31890 GAA-AAAATAAAT
1 -AATATAATAAAT
31902 A
1 A
31903 TACATATAAT
Statistics
Matches: 91, Mismatches: 14, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
10 5 0.05
11 8 0.09
12 23 0.25
13 31 0.34
14 22 0.24
15 2 0.02
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (12 bp):
AATATAATAAAT
Found at i:31867 original size:3 final size:3
Alignment explanation
Indices: 31850--31883 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
31840 AAATGTATGT
31850 ATA AT- ATA ATAA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA A
31884 ATAAATGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Done.