Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001306.1 Hibiscus syriacus cultivar Beakdansim tig00002547_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: 65608
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3654 original size:217 final size:217
Alignment explanation
Indices: 3270--3661 Score: 631
Period size: 217 Copynumber: 1.8 Consensus size: 217
3260 TTGAAATTTT
* *
3270 TGAAAAGTAAGAAAAATTTCTTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCCTTCGGGCCAT
1 TGAAAAGTAAGAAAAATTTCTTACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCAT
* * * * * * *
3335 CAGTAAGTCTTTCTAGCATGATGCTTAAATCCTTTGGGTCTTCTGTAAGTCTTTTAAGCAATATG
66 CAGTAAATCTTTCGAGCATGATACTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATG
* * *
3400 ATAAGTCTTTTGGGCCATCCGTAAGACCTTTGGGCAGGAGGTTTCTACATGTCTCTCGAAAAATG
131 ATAAGTCTTTTGGGCCATCCATAAAACCTTCGGGCAGGAGGTTTCTACATGTCTCTCGAAAAATG
3465 AGAAAGGTTTCTCATTGAAATC
196 AGAAAGGTTTCTCATTGAAATC
* *
3487 TGAAAAGTAAGAAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTTATAAGTCCTTCGGGCCAT
1 TGAAAAGTAAGAAAAATTTCTTACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCAT
*
3552 CAGTAAATCTTTCGAGCATGATACTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATG
66 CAGTAAATCTTTCGAGCATGATACTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATG
* *
3617 ATAAGTCTTTTGGGTCATCCATAAAACCTTCGGGCAGGAGTTTTC
131 ATAAGTCTTTTGGGCCATCCATAAAACCTTCGGGCAGGAGGTTTC
3662 GCATGATTTT
Statistics
Matches: 158, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
217 158 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (217 bp):
TGAAAAGTAAGAAAAATTTCTTACCTAGTAAACTATTTCCAAAATTGATAAGTCCTTCGGGCCAT
CAGTAAATCTTTCGAGCATGATACTTAAATCCTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATG
ATAAGTCTTTTGGGCCATCCATAAAACCTTCGGGCAGGAGGTTTCTACATGTCTCTCGAAAAATG
AGAAAGGTTTCTCATTGAAATC
Found at i:4918 original size:16 final size:16
Alignment explanation
Indices: 4897--4935 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
4887 TTTCTGAAGT
4897 AGAAAGGAAACAAAAG
1 AGAAAGGAAACAAAAG
4913 AGAAAGGAAACAAAAG
1 AGAAAGGAAACAAAAG
4929 AGAAAGG
1 AGAAAGG
4936 GTTGATTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.67, C:0.05, G:0.28, T:0.00
Consensus pattern (16 bp):
AGAAAGGAAACAAAAG
Found at i:6517 original size:131 final size:130
Alignment explanation
Indices: 6285--6648 Score: 308
Period size: 131 Copynumber: 2.8 Consensus size: 130
6275 CCGATATTGA
* * * * *
6285 GAAA-AGTAAAATCTTTTCATTTCGGTTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTTA
1 GAAATAGTAATATCTTTT-ATTTCGATTCGAGCAATAAATGATTGCTTTAAGGCATGAGAGGTCA
* * * *
6349 TTTATTCTCGATTGGAAATAATTTGATATTGATGTTTTCT-CTCGAATTAATATCGATTTTTAAG
65 TTTATTCTCGATTGGAAATAATTAGATATTCATGTTTT-TACTCGAATCAATATCGAATTTTAAG
*
6413 AT
129 AC
* * * *
6415 GGAATAGTGATATCTCTTTATTTCGATTCGAGCAATAAATGGA-TGCTTTAAGGTATGAGATGTC
1 GAAATAGTAATATCT-TTTATTTCGATTCGAGCAATAAAT-GATTGCTTTAAGGCATGAGAGGTC
* * * * * *
6479 ATTTATTCTCGATTGTAAATCATTAGTTA-TCATCGTTTTTACTTGAATCGATATTGAATTTTAA
64 ATTTATTCTCGATTGGAAATAATTAGATATTCAT-GTTTTTACTCGAATCAATATCGAATTTTAA
6543 GAC
128 GAC
* * * * * * ** ** * *
6546 GAAATAGTAATATCTTTTTATTTCAATT-GGGATAATAAATTACTGTTTTAATACACAAAAGATC
1 GAAATAGTAATATC-TTTTATTTCGATTCGAG-CAATAAATGATTGCTTTAAGGCATGAGAGGTC
* *
6610 ATTTATTCTTGATTGGAAATAAGTAGATATT-ATCGTTTT
64 ATTTATTCTCGATTGGAAATAATTAGATATTCAT-GTTTT
6649 CATTCTTAAA
Statistics
Matches: 185, Mismatches: 40, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
130 10 0.05
131 168 0.91
132 7 0.04
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.42
Consensus pattern (130 bp):
GAAATAGTAATATCTTTTATTTCGATTCGAGCAATAAATGATTGCTTTAAGGCATGAGAGGTCAT
TTATTCTCGATTGGAAATAATTAGATATTCATGTTTTTACTCGAATCAATATCGAATTTTAAGAC
Found at i:8064 original size:2 final size:2
Alignment explanation
Indices: 8057--8134 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
8047 TTGTTGTCTA
8057 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
8099 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
8135 GTTCCAGTGG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14789 original size:21 final size:24
Alignment explanation
Indices: 14747--14790 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
14737 ACCAGATAAC
14747 TAAAGATAATAATCAGCTCAAAAGA
1 TAAAGATAATAATCAGC-CAAAAGA
14772 TAAA-ATAA-AATCAG-CAAAA
1 TAAAGATAATAATCAGCCAAAA
14791 CTTAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.26
23 6 0.32
24 4 0.21
25 4 0.21
ACGTcount: A:0.61, C:0.11, G:0.09, T:0.18
Consensus pattern (24 bp):
TAAAGATAATAATCAGCCAAAAGA
Found at i:16410 original size:24 final size:24
Alignment explanation
Indices: 16381--16435 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
16371 TATCAGAGTG
* *
16381 AGCAATCCTTGGGAGATTGGGATC
1 AGCAATCCTTGGGAAATTAGGATC
* *
16405 ATCAATCTTTGGGAAATTAGGATC
1 AGCAATCCTTGGGAAATTAGGATC
16429 AGCAATC
1 AGCAATC
16436 ACGGGAGCTG
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:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (24 bp):
AGCAATCCTTGGGAAATTAGGATC
Found at i:23543 original size:31 final size:31
Alignment explanation
Indices: 23505--23563 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
23495 TAAGTCGGGG
*
23505 ACCATATTGCAAA-AGGACTAAATGTTGAAGA
1 ACCATATTGCAAACA-GAATAAATGTTGAAGA
23536 ACCATATTGCAAACAGAATAAATGTTGA
1 ACCATATTGCAAACAGAATAAATGTTGA
23564 GTGATTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.24
Consensus pattern (31 bp):
ACCATATTGCAAACAGAATAAATGTTGAAGA
Found at i:25845 original size:15 final size:15
Alignment explanation
Indices: 25825--25857 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
25815 GTAGGACTAT
25825 TACGTCCCGAAGGAC
1 TACGTCCCGAAGGAC
25840 TACGTCCCGAAGGAC
1 TACGTCCCGAAGGAC
25855 TAC
1 TAC
25858 AGAACCTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.33, G:0.24, T:0.15
Consensus pattern (15 bp):
TACGTCCCGAAGGAC
Found at i:26127 original size:20 final size:19
Alignment explanation
Indices: 26102--26144 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
26092 ATATCATGTA
26102 ACATTT-ATAATAATCTATAC
1 ACATTTCAT-ATAATC-ATAC
*
26122 ACATTTCATATATTCATAC
1 ACATTTCATATAATCATAC
26141 ACAT
1 ACAT
26145 ATAAAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 11 0.52
21 2 0.10
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.40
Consensus pattern (19 bp):
ACATTTCATATAATCATAC
Found at i:32693 original size:14 final size:15
Alignment explanation
Indices: 32668--32699 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
32658 GTAGGACCAT
32668 TACGTCCCGAAGGAC
1 TACGTCCCGAAGGAC
32683 TACGT-CCGAAGGAC
1 TACGTCCCGAAGGAC
32697 TAC
1 TAC
32700 AGAACCCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.28, C:0.31, G:0.25, T:0.16
Consensus pattern (15 bp):
TACGTCCCGAAGGAC
Found at i:34270 original size:31 final size:31
Alignment explanation
Indices: 34232--34293 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
34222 TCAAACGGGC
34232 GGGGACCATATTACAAACAGACTAAATGTTG
1 GGGGACCATATTACAAACAGACTAAATGTTG
* **
34263 GGGGACCATATTGCAAATGGACTAAATGTTG
1 GGGGACCATATTACAAACAGACTAAATGTTG
34294 AGAGATTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (31 bp):
GGGGACCATATTACAAACAGACTAAATGTTG
Found at i:38758 original size:2 final size:2
Alignment explanation
Indices: 38751--38785 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
38741 ATTGTCATTC
38751 AT AT 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 AT AT A
38786 AAATATTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39388 original size:19 final size:18
Alignment explanation
Indices: 39347--39398 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
39337 TTCTTTGCGT
* *
39347 TATATTATATATTTTCTA
1 TATATTATATATTATATA
39365 T-TATTATATATATATATA
1 TATATTATATAT-TATATA
39383 TATATTATATTATTAT
1 TATATTATA-TATTAT
39399 TTTTTATCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 10 0.34
18 6 0.21
19 10 0.34
20 3 0.10
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TATATTATATATTATATA
Found at i:39624 original size:17 final size:18
Alignment explanation
Indices: 39587--39640 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
39577 TATATTATAC
*
39587 ATACTGTTTTATATTTTTTT
1 ATACT-TTTTAT-TTTATTT
39607 ATA-TTTTTATTTTATTT
1 ATACTTTTTATTTTATTT
*
39624 ATACTATTTA-TTTATTT
1 ATACTTTTTATTTTATTT
39641 TCATTATGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 16 0.52
18 11 0.35
19 1 0.03
20 3 0.10
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (18 bp):
ATACTTTTTATTTTATTT
Found at i:39723 original size:18 final size:19
Alignment explanation
Indices: 39700--39744 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
39690 TATATATATA
*
39700 TTTTTTCTTC-ATTT-ATT
1 TTTTTTATTCAATTTCATT
39717 TTATTTTATTCAATTTCATT
1 TT-TTTTATTCAATTTCATT
39737 TTTTTTAT
1 TTTTTTAT
39745 ATTTGTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 2 0.08
18 7 0.29
19 10 0.42
20 5 0.21
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTTATTCAATTTCATT
Found at i:40941 original size:19 final size:19
Alignment explanation
Indices: 40917--40953 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
40907 ACCTTACTAA
40917 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
40936 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
40954 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:45064 original size:22 final size:22
Alignment explanation
Indices: 45011--45065 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
45001 AGCACCCCAT
*
45011 CAAACCTTTAAGAATCAAATGC
1 CAAACCTTTGAGAATCAAATGC
*
45033 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGAATCAAATGC
45055 CAAACCTTTGA
1 CAAACCTTTGA
45066 CCAAACACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.25, G:0.11, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGAATCAAATGC
Found at i:45283 original size:24 final size:22
Alignment explanation
Indices: 45255--45314 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 22
45245 AGAGACAATA
45255 TTTTCAAAACTTTTGATTAAACAT
1 TTTTCAAAACTTTT-ATT-AACAT
* * *
45279 TTTTCGAAACTCTTTATTGATAT
1 TTTTCAAAACT-TTTATTAACAT
*
45302 TTTTCAGAACTTT
1 TTTTCAAAACTTT
45315 GAAAATAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 2 0.07
23 12 0.40
24 13 0.43
25 3 0.10
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (22 bp):
TTTTCAAAACTTTTATTAACAT
Found at i:46169 original size:106 final size:106
Alignment explanation
Indices: 45994--47827 Score: 2621
Period size: 106 Copynumber: 17.3 Consensus size: 106
45984 TGGCCATCCG
* * * * * * *
45994 CAATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACAACG
1 CAATTTCAACTTCACAACGAAGGATAT--TG-GACTCCAGACAACGCAAGTTCAACTTCACGACG
* * * *
46059 AAGGGA-TGACTGGTTTTCAACAAACAACTTCCCAAATTCATAGC
63 AAGGGACCG-CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* * * ** *
46103 CAATTTCAACTTCATAGCGAAGGATATTGGACTCCAGAAAATACAAGTTCAACTTCACGACAAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * * * *
46168 GGACCGCTGGTTCTCAATAAATAACTTCTCAATTTTAGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
*
46209 CAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * *
46274 GGACCGCTGGTTGTCAATAAATAATTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
*
46315 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGAAGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
46380 GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* * * *
46421 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGTCAACGCAAGTTCAACTTCACGAAGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
46486 GGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
46527 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * * *
46592 GGACTGCTGATTATCAATAAACAACTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* * *
46633 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAATGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
** * *
46698 GGATTGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* * *
46739 CAATTTCAACTTCACAACGAAAGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
46804 GGACCGCTGGTTGTCAACAAACAAATTCCCAATTTCGGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* * *
46845 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * *
46910 GGACCGTTGGTTGTCAACAAATAACTTCTCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* * *
46951 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGTCAACGCAAGTTCAACTTCACGAAGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
47016 GGACCGCTGGTTGTCAACAAATAACTTCTCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
*
47057 CAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * *
47122 GGACCGCTGGTTATCAATAAACAACTTCCCAATTTTAGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* * * * *
47163 CAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAATGCAAGTTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
** * **
47228 GGATTGCTGGTTGTCAACAAACAA-TTTCCAATTTTGGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* *
47268 CAATTTCAACTTCACAACGAAAGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
47333 GGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* * *
47374 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * * *
47439 GGACCGTTGGTTGTCAACAAATAACTTCTCAATTTCAGATC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* *
47480 CAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
*
47545 GGACCGCTGGTTATCAACAAACAACTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* * * * *
47586 CAATTTCAATTTCACAGCGAAGGATTTTGGACTCGAGACAACGCAAGTTCAACTTCACGATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
47651 GGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* * ** * * *
47692 CAATTTCAACTTCACAACAAAGGATATTGGACTCGAGACAACATATGTTCAACTTCACAATGAAG
1 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * * * *
47757 GGACGGCTGGTTGTCAACAAACAATTTCCCGATTCCAAAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
*
47798 CAATTTCAACTTCACGACGGAA-GATATTGG
1 CAATTTCAACTTCACAAC-GAAGGATATTGG
47828 GCTCGAAACA
Statistics
Matches: 1569, Mismatches: 153, Indels: 9
0.91 0.09 0.01
Matches are distributed among these distances:
105 95 0.06
106 1447 0.92
107 5 0.00
109 22 0.01
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
Found at i:48634 original size:37 final size:37
Alignment explanation
Indices: 48577--48681 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
48567 CCTTTTTGTC
*
48577 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
48614 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
48651 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
48682 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:49425 original size:9 final size:9
Alignment explanation
Indices: 49392--49441 Score: 52
Period size: 8 Copynumber: 5.9 Consensus size: 9
49382 TTTTTTATAT
*
49392 TTTTATATA
1 TTTTATTTA
49401 TTTT-TTTA
1 TTTTATTTA
49409 TTTT-TTTA
1 TTTTATTTA
49417 TTTTATTTA
1 TTTTATTTA
**
49426 TACTATTTA
1 TTTTATTTA
49435 -TTTATTT
1 TTTTATTT
49442 TCATTATGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
8 20 0.57
9 15 0.43
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTATTTA
Found at i:49429 original size:47 final size:47
Alignment explanation
Indices: 49360--49455 Score: 106
Period size: 47 Copynumber: 2.0 Consensus size: 47
49350 TACTATTTAG
* *
49360 TATTTTATTATATTATACATACT-TTT-TTATATTTTTATATATTTTTT
1 TATTTTATTATATTATACATACTATTTATT-TATTTTCAT-TATGTTTT
* * **
49407 TATTTTTTTATTTTATTTATACTATTTATTTATTTTCATTATGTTTT
1 TATTTTATTATATTATACATACTATTTATTTATTTTCATTATGTTTT
49454 TA
1 TA
49456 GTTTCTTTGC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
47 28 0.68
48 11 0.27
49 2 0.05
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (47 bp):
TATTTTATTATATTATACATACTATTTATTTATTTTCATTATGTTTT
Found at i:49556 original size:18 final size:19
Alignment explanation
Indices: 49534--49577 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
49524 TATATATATA
*
49534 TTTTTCTTC-ATTT-ATTT
1 TTTTTATTCAATTTCATTT
49551 TATTTTATTCAATTTCATTT
1 T-TTTTATTCAATTTCATTT
49571 TTTTTAT
1 TTTTTAT
49578 ATTTGTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 7 0.30
19 10 0.43
20 5 0.22
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTATTCAATTTCATTT
Found at i:51172 original size:46 final size:46
Alignment explanation
Indices: 51119--51209 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
51109 TCAGTGCCAC
* *
51119 ACTAATAATTGTATTATACTACATTCATTCACGAAAACATATTCTA
1 ACTAATAACTGTACTATACTACATTCATTCACGAAAACATATTCTA
51165 ACTAATAACTGTACTATACTACATTCATTCACGAAAACATATTCT
1 ACTAATAACTGTACTATACTACATTCATTCACGAAAACATATTCT
51210 GAACGCTGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.41, C:0.20, G:0.04, T:0.35
Consensus pattern (46 bp):
ACTAATAACTGTACTATACTACATTCATTCACGAAAACATATTCTA
Found at i:51288 original size:74 final size:74
Alignment explanation
Indices: 51165--51332 Score: 291
Period size: 74 Copynumber: 2.3 Consensus size: 74
51155 ACATATTCTA
*
51165 ACTAATAACTGTACTATACTACATTCATTCACGAAAACATATTCTGAACGCTGAGCTTAAGAGCT
1 ACTAATAACTGTACTATACTACATTCATTCACGAAAACATATTCCGAACGCTGAGCTTAAGAGCT
*
51230 CAGTGTCAC
66 CAGTGACAC
* *
51239 ACTAATAACTATATTATACTACATTCATTCACGAAAACATATTCCGAACGCTGAGCTTAAGAGCT
1 ACTAATAACTGTACTATACTACATTCATTCACGAAAACATATTCCGAACGCTGAGCTTAAGAGCT
*
51304 CAGTGACAT
66 CAGTGACAC
51313 ACTAATAACTGTACTATACT
1 ACTAATAACTGTACTATACT
51333 GATATAAAGT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 87 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (74 bp):
ACTAATAACTGTACTATACTACATTCATTCACGAAAACATATTCCGAACGCTGAGCTTAAGAGCT
CAGTGACAC
Found at i:56022 original size:17 final size:16
Alignment explanation
Indices: 55985--56020 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
55975 AATAAGTCCT
*
55985 ATTTATTTTATAAATG
1 ATTTAATTTATAAATG
56001 ATTTAATTTATAAATG
1 ATTTAATTTATAAATG
56017 ATTT
1 ATTT
56021 TATATGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
ATTTAATTTATAAATG
Found at i:56041 original size:166 final size:164
Alignment explanation
Indices: 55863--56168 Score: 540
Period size: 166 Copynumber: 1.9 Consensus size: 164
55853 TGCAGGTTTG
55863 ATTTTTATATTTTACAGTAAAGTTCTATTTACAAAGTTTGATTTAATACAACGTGATTTATAGAC
1 ATTTTTATATTTTACAGTAAAGTTCTATTTACAAAGTTTGATTTAATACAACGTGATTTATAGAC
* * *
55928 TAAAGATTAAAAAGTTAATTGCATATGAAATATATGAAAATGATTTTAATAAGTCCTATTTATTT
66 GAAAGATT--AAAGTTAATCGCATATGAAATATATGAAAATGATTTTAACAAGTCCTATTTATTT
55993 TATAAATGATTTAATTTATAAATGATTTTATATGAT
129 TATAAATGATTTAATTTATAAATGATTTTATATGAT
*
56029 ATTTTTATATTTTATAGTAAAGTTCTATTTACAAAGTTTGATTTAATACAACGTGATTTATAGAC
1 ATTTTTATATTTTACAGTAAAGTTCTATTTACAAAGTTTGATTTAATACAACGTGATTTATAGAC
* *
56094 GAAATATTAAAGTTAATCGTATATGAAATATATGAAAATGATTTTAACAAGTCCTATTTATTTTA
66 GAAAGATTAAAGTTAATCGCATATGAAATATATGAAAATGATTTTAACAAGTCCTATTTATTTTA
56159 TAAATGATTT
131 TAAATGATTT
56169 TATATGATAT
Statistics
Matches: 134, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
164 64 0.48
166 70 0.52
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (164 bp):
ATTTTTATATTTTACAGTAAAGTTCTATTTACAAAGTTTGATTTAATACAACGTGATTTATAGAC
GAAAGATTAAAGTTAATCGCATATGAAATATATGAAAATGATTTTAACAAGTCCTATTTATTTTA
TAAATGATTTAATTTATAAATGATTTTATATGAT
Found at i:63491 original size:85 final size:84
Alignment explanation
Indices: 63351--63510 Score: 248
Period size: 85 Copynumber: 1.9 Consensus size: 84
63341 TTAATTGTGG
* ** * *
63351 TTTTTTACAGGCGTGGGAAAATCATGTTGCTCTTGCAGTTTATTGACAAGAGATTCCAATCGGTT
1 TTTTTTACAGGCGTGGAAAAATCATGTTGCTCTTGCAGTTTACCGACAAGAGATTCCAACCGATT
*
63416 CATGATTTAATCGGCGAGT
66 CAAGATTTAATCGGCGAGT
*
63435 TTTTTTACAGGCGTGGAAAAATCATGTTTGCTCTTGCATTTTACCGACAAGAGATTCCAACCGAT
1 TTTTTTACAGGCGTGGAAAAATCATG-TTGCTCTTGCAGTTTACCGACAAGAGATTCCAACCGAT
63500 TCAAGATTTAA
65 TCAAGATTTAA
63511 CCATCGGTGT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
84 25 0.37
85 43 0.63
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (84 bp):
TTTTTTACAGGCGTGGAAAAATCATGTTGCTCTTGCAGTTTACCGACAAGAGATTCCAACCGATT
CAAGATTTAATCGGCGAGT
Done.