Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002114.1 Hibiscus syriacus cultivar Beakdansim tig00004337_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: 76732
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:7200 original size:21 final size:21
Alignment explanation
Indices: 7176--7347 Score: 143
Period size: 21 Copynumber: 8.3 Consensus size: 21
7166 GCATTTTGCA
* *
7176 TTGCGATAGTTGGAGATCGCG
1 TTGCGATAGTTGAAAATCGCG
* *
7197 TTGCGATAGTTGGAGATCGCG
1 TTGCGATAGTTGAAAATCGCG
* ** **
7218 TTGCGAT-TTTCCATTTCGCG
1 TTGCGATAGTTGAAAATCGCG
7238 TTGCGATAGTTGAAAATCGCG
1 TTGCGATAGTTGAAAATCGCG
* ** **
7259 TTGCGAT-TTTCCATTTCGCG
1 TTGCGATAGTTGAAAATCGCG
*
7279 TTGCGATAGTTGAAAATCACG
1 TTGCGATAGTTGAAAATCGCG
* ** **
7300 TTGCGAT-TTTCCATTTCGCG
1 TTGCGATAGTTGAAAATCGCG
7320 TTGCGATAGTTGAAAATCGCG
1 TTGCGATAGTTGAAAATCGCG
7341 TTGCGAT
1 TTGCGAT
7348 TTTCCATTTC
Statistics
Matches: 116, Mismatches: 32, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
20 44 0.38
21 72 0.62
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (21 bp):
TTGCGATAGTTGAAAATCGCG
Found at i:7238 original size:20 final size:20
Alignment explanation
Indices: 7213--7367 Score: 139
Period size: 20 Copynumber: 7.6 Consensus size: 20
7203 TAGTTGGAGA
7213 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
7233 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
7254 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
7274 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
7295 TCACGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
7315 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
7336 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
7356 TCGCGTTGCGAT
1 TCGCGTTGCGAT
7368 AGTTAAAAAA
Statistics
Matches: 100, Mismatches: 32, Indels: 6
0.72 0.23 0.04
Matches are distributed among these distances:
20 56 0.56
21 44 0.44
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:7239 original size:41 final size:41
Alignment explanation
Indices: 7192--7376 Score: 334
Period size: 41 Copynumber: 4.5 Consensus size: 41
7182 TAGTTGGAGA
* *
7192 TCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
7233 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
*
7274 TCGCGTTGCGATAGTTGAAAATCACGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
7315 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
*
7356 TCGCGTTGCGATAGTTAAAAA
1 TCGCGTTGCGATAGTTGAAAA
7377 AAAGATTTTG
Statistics
Matches: 139, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 139 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (41 bp):
TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
Found at i:7494 original size:40 final size:40
Alignment explanation
Indices: 7439--7523 Score: 170
Period size: 40 Copynumber: 2.1 Consensus size: 40
7429 GTTGAAACAC
7439 TATTGGGAACAAGTGTTGGTAATGCTCAAATCCCACATAG
1 TATTGGGAACAAGTGTTGGTAATGCTCAAATCCCACATAG
7479 TATTGGGAACAAGTGTTGGTAATGCTCAAATCCCACATAG
1 TATTGGGAACAAGTGTTGGTAATGCTCAAATCCCACATAG
7519 TATTG
1 TATTG
7524 AAAACACTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.29
Consensus pattern (40 bp):
TATTGGGAACAAGTGTTGGTAATGCTCAAATCCCACATAG
Found at i:7659 original size:6 final size:6
Alignment explanation
Indices: 7633--7701 Score: 117
Period size: 6 Copynumber: 12.0 Consensus size: 6
7623 TCTCGTCTCG
7633 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
7678 GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT
7702 ACGTGTCTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.24
6 48 0.76
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:7821 original size:19 final size:19
Alignment explanation
Indices: 7793--7850 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
7783 AACGAATTTG
7793 GAAAATCGCAATGACAACT
1 GAAAATCGCAATGACAACT
* * **
7812 GAATATCGCAACGA-ATTT
1 GAAAATCGCAATGACAACT
7830 GGAAAATCGCAATGACAACT
1 -GAAAATCGCAATGACAACT
7850 G
1 G
7851 TAGAAAATCG
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
18 2 0.07
19 25 0.86
20 2 0.07
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (19 bp):
GAAAATCGCAATGACAACT
Found at i:7825 original size:38 final size:38
Alignment explanation
Indices: 7777--7850 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
7767 TTTTTTTAAC
7777 TATCACAACGAATTTGGAAAATCGCAATGACAACTGAA
1 TATCACAACGAATTTGGAAAATCGCAATGACAACTGAA
*
7815 TATCGCAACGAATTTGGAAAATCGCAATGACAACTG
1 TATCACAACGAATTTGGAAAATCGCAATGACAACTG
7851 TAGAAAATCG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.22
Consensus pattern (38 bp):
TATCACAACGAATTTGGAAAATCGCAATGACAACTGAA
Found at i:9306 original size:27 final size:26
Alignment explanation
Indices: 9276--9339 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 26
9266 TATTTGACAC
*
9276 TTTATATATA-AATAAGTTCATTATATT
1 TTTATATATATAAT-A-TTCATTAAATT
*
9303 TTTATGATATATAATATTGATTAAATT
1 TTTAT-ATATATAATATTCATTAAATT
9330 TTTATA-ATAT
1 TTTATATATAT
9340 TTTAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 4 0.12
26 1 0.03
27 19 0.58
28 6 0.18
29 3 0.09
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (26 bp):
TTTATATATATAATATTCATTAAATT
Found at i:11077 original size:20 final size:20
Alignment explanation
Indices: 11054--11091 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11044 CAATTAAAAT
11054 TATAAATCT-TAAATTCTATA
1 TATAAA-CTATAAATTCTATA
11074 TATAAACTATAAATTCTA
1 TATAAACTATAAATTCTA
11092 AACTCTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (20 bp):
TATAAACTATAAATTCTATA
Found at i:11594 original size:26 final size:28
Alignment explanation
Indices: 11564--11619 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
11554 ATGTTATGGT
*
11564 AATTTAAAAA-AATTAT-TTTTTAAAAA
1 AATTTAAAAATAATTATATTTATAAAAA
*
11590 AATTTAAAAATTATTATATTTATAAAAA
1 AATTTAAAAATAATTATATTTATAAAAA
11618 AA
1 AA
11620 AATCCTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 10 0.38
27 5 0.19
28 11 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
AATTTAAAAATAATTATATTTATAAAAA
Found at i:17679 original size:102 final size:103
Alignment explanation
Indices: 17493--17754 Score: 316
Period size: 102 Copynumber: 2.5 Consensus size: 103
17483 ATGTGCCAAC
* * * *
17493 AATATCGATACTA-ATCCTTGGGTATCGATACTCAAGC-TGAGTATTAATACAAAAAATAACTTC
1 AATATCAATACTATACCCTT-GGTATCGATACTC--CCTTGAGTATCAATACAAAAAATAACTTC
17556 AATGTTTTGAAAAAAAACTCAGTATCGATACACC-TATGGGG
63 AATGTTTTGAAAAAAAACTCAGTATCGATAC-CCATATGGGG
* * *
17597 AATATCAATACTATACCCTTGGTATCGATACTCCCTTGAGTATCAGTAC-AAAAATAGCTTCGAT
1 AATATCAATACTATACCCTTGGTATCGATACTCCCTTGAGTATCAATACAAAAAATAACTTCAAT
* *
17661 GTTTTGAAAAATACCTCAGTATCGATACCCATATGGGG
66 GTTTTGAAAAAAAACTCAGTATCGATACCCATATGGGG
* * * * * * *
17699 AGTATCAATACTCTACCCTTGGTTTCAATACTCCATTGAGTATCCATACCAAAAAT
1 AATATCAATACTATACCCTTGGTATCGATACTCCCTTGAGTATCAATACAAAAAAT
17755 GGCTACTAGA
Statistics
Matches: 138, Mismatches: 16, Indels: 9
0.85 0.10 0.06
Matches are distributed among these distances:
101 2 0.01
102 89 0.64
103 17 0.12
104 25 0.18
105 5 0.04
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (103 bp):
AATATCAATACTATACCCTTGGTATCGATACTCCCTTGAGTATCAATACAAAAAATAACTTCAAT
GTTTTGAAAAAAAACTCAGTATCGATACCCATATGGGG
Found at i:18535 original size:20 final size:22
Alignment explanation
Indices: 18501--18540 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
18491 CTCTCAACCA
*
18501 CTTTAGGTATTGATA-TCAAGC
1 CTTTAGGTATGGATACTCAAGC
18522 CTTT-GGTATGGATACTCAA
1 CTTTAGGTATGGATACTCAA
18541 TCTTCGGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.38
Consensus pattern (22 bp):
CTTTAGGTATGGATACTCAAGC
Found at i:18580 original size:20 final size:20
Alignment explanation
Indices: 18566--18618 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
18556 TCAGTCCTCC
*
18566 GGTATGGAGACCAGTCTTTT
1 GGTATGGAGACCAGTCCTTT
* *
18586 GGTATGAAGACTAGTCCTTT
1 GGTATGGAGACCAGTCCTTT
*
18606 GTTATGGAGACCA
1 GGTATGGAGACCA
18619 ATTTTTTAGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (20 bp):
GGTATGGAGACCAGTCCTTT
Found at i:23780 original size:16 final size:16
Alignment explanation
Indices: 23759--23792 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
23749 TTACTATTCA
*
23759 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
23775 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
23791 CG
1 CG
23793 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:30067 original size:20 final size:19
Alignment explanation
Indices: 30026--30068 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
30016 ACACATAAAA
*
30026 ATATAATTTTAATCCAATT
1 ATATAATTTTAATCAAATT
30045 ATATACATTTTAAT-AAA-T
1 ATATA-ATTTTAATCAAATT
30063 ATATAA
1 ATATAA
30069 GCTTCCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 6 0.27
19 7 0.32
20 8 0.36
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATAATTTTAATCAAATT
Found at i:31544 original size:20 final size:20
Alignment explanation
Indices: 31521--31569 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
31511 TTGGGTAGGA
* *
31521 TATCGATACTGATCAGA-GAG
1 TATCGATACTG-TAAGACCAG
*
31541 TATCAATACTGTAAGACCAG
1 TATCGATACTGTAAGACCAG
31561 TATCGATAC
1 TATCGATAC
31570 CAAGGTTAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (20 bp):
TATCGATACTGTAAGACCAG
Found at i:32924 original size:16 final size:16
Alignment explanation
Indices: 32882--32925 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
32872 TTTTAAGGTC
*
32882 TTTTCACTTAAGTTAT
1 TTTTCACTTAAGATAT
***
32898 TTTTTGTTTAAGATAT
1 TTTTCACTTAAGATAT
32914 TTTTCACTTAAG
1 TTTTCACTTAAG
32926 TTAATGATTT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.57
Consensus pattern (16 bp):
TTTTCACTTAAGATAT
Found at i:35352 original size:20 final size:20
Alignment explanation
Indices: 35327--35369 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
35317 TAAGGGTGTT
35327 CAAACGGTTAATTCGATCAC
1 CAAACGGTTAATTCGATCAC
* *
35347 CAAACGGTTAATTTGGTCAC
1 CAAACGGTTAATTCGATCAC
35367 CAA
1 CAA
35370 CTGAAGCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (20 bp):
CAAACGGTTAATTCGATCAC
Found at i:41502 original size:25 final size:25
Alignment explanation
Indices: 41468--41523 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
41458 ATTTTTACAA
* * *
41468 TTTAGATTATAAAAAAAATAGTTGT
1 TTTAAATTATAAAAAAAATAGTCGC
41493 TTTAAATTATAAAAAAAATAGTCGC
1 TTTAAATTATAAAAAAAATAGTCGC
41518 TTTAAA
1 TTTAAA
41524 GCTAGAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.38
Consensus pattern (25 bp):
TTTAAATTATAAAAAAAATAGTCGC
Found at i:41685 original size:41 final size:41
Alignment explanation
Indices: 41640--41726 Score: 158
Period size: 41 Copynumber: 2.1 Consensus size: 41
41630 TAGTTCATAT
41640 AAAATTATATGTTCTATCAGGGTTGAATAAA-TGTCATTCCC
1 AAAATTATATGTTCTATCAGGGTTGAA-AAATTGTCATTCCC
41681 AAAATTATATGTTCTATCAGGGTTGAAAAATTGTCATTCCC
1 AAAATTATATGTTCTATCAGGGTTGAAAAATTGTCATTCCC
41722 AAAAT
1 AAAAT
41727 GTCAAACATG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 3 0.07
41 42 0.93
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Consensus pattern (41 bp):
AAAATTATATGTTCTATCAGGGTTGAAAAATTGTCATTCCC
Found at i:48692 original size:2 final size:2
Alignment explanation
Indices: 48687--48711 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48677 GTTATTAACA
48687 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 A
48712 CTTAACTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51518 original size:29 final size:29
Alignment explanation
Indices: 51485--51564 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
51475 AAATTAAGTT
* *
51485 GATGTCATTGCTTACATCGATTAGGATAA
1 GATGTCATTGCTTACATCAATTAGGAGAA
51514 GATGTCATTGCTTACATCAATTAGGAGAA
1 GATGTCATTGCTTACATCAATTAGGAGAA
51543 GATGTCATTGCTTACATCAATT
1 GATGTCATTGCTTACATCAATT
51565 TAGTTAGGTG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (29 bp):
GATGTCATTGCTTACATCAATTAGGAGAA
Found at i:54829 original size:18 final size:18
Alignment explanation
Indices: 54806--54933 Score: 139
Period size: 18 Copynumber: 6.9 Consensus size: 18
54796 AGGGATTATC
54806 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
54824 AGTGGTCCTTCAGGATAT
1 AGTGGTCCTTCGGGACAT
54842 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
54860 AGTGGTCCTTCAGGATAT
1 AGTGGTCCTTCGGGACAT
* * *
54878 AGTGGTCATTTGGGATATATT
1 AGTGGTCCTTCGGG--ACA-T
*
54899 AGTGGTCATTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
54917 AGTGGTCATTCGAGACA
1 AGTGGTCCTTCGGGACA
54934 AATATTCAGT
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
18 76 0.80
19 2 0.02
20 3 0.03
21 14 0.15
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:54853 original size:36 final size:36
Alignment explanation
Indices: 54806--54884 Score: 158
Period size: 36 Copynumber: 2.2 Consensus size: 36
54796 AGGGATTATC
54806 AGTGGTCCTTCGGGACATAGTGGTCCTTCAGGATAT
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCAGGATAT
54842 AGTGGTCCTTCGGGACATAGTGGTCCTTCAGGATAT
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCAGGATAT
54878 AGTGGTC
1 AGTGGTC
54885 ATTTGGGATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (36 bp):
AGTGGTCCTTCGGGACATAGTGGTCCTTCAGGATAT
Found at i:54894 original size:54 final size:56
Alignment explanation
Indices: 54806--54923 Score: 159
Period size: 54 Copynumber: 2.1 Consensus size: 56
54796 AGGGATTATC
* * *
54806 AGTGGTCCTTCGGGACATAGTGGTCCTTCAGG-ATA-TAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCAGGACATAGTGGTCATTCAGGAATATTAGTGGTCATTCGGGACAT
* **
54860 AGTGGTCCTTCAGGATATAGTGGTCATTTGGGATATATTAGTGGTCATTCGGGACAT
1 AGTGGTCCTTCAGGACATAGTGGTCATTCAGGA-ATATTAGTGGTCATTCGGGACAT
54917 AGTGGTC
1 AGTGGTC
54924 ATTCGAGACA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
54 27 0.49
56 3 0.05
57 25 0.45
ACGTcount: A:0.20, C:0.16, G:0.31, T:0.32
Consensus pattern (56 bp):
AGTGGTCCTTCAGGACATAGTGGTCATTCAGGAATATTAGTGGTCATTCGGGACAT
Found at i:61217 original size:23 final size:24
Alignment explanation
Indices: 61182--61226 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
61172 TCTAGTCATT
*
61182 GAGTCAACTCGTTGACA-TTGATC
1 GAGTCAACCCGTTGACAGTTGATC
*
61205 GAGTTAACCCGTTGACAGTTGA
1 GAGTCAACCCGTTGACAGTTGA
61227 CTTTGATCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (24 bp):
GAGTCAACCCGTTGACAGTTGATC
Found at i:62352 original size:15 final size:15
Alignment explanation
Indices: 62332--62362 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
62322 GGAATTAAGT
62332 GAATAACTTAGATAA
1 GAATAACTTAGATAA
*
62347 GAATAACTTGGATAA
1 GAATAACTTAGATAA
62362 G
1 G
62363 TCTGGAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.26
Consensus pattern (15 bp):
GAATAACTTAGATAA
Found at i:63285 original size:30 final size:32
Alignment explanation
Indices: 63245--63328 Score: 84
Period size: 30 Copynumber: 2.7 Consensus size: 32
63235 TAAGGCGACC
* *
63245 CTTGGATAGGCTCTGCGGTCCCGAG-AT-TTT
1 CTTGGGTAGGCTCTGCGGCCCCGAGAATCTTT
* * *
63275 CTTGGGTAGGCCCCGTGGCCCCGAGAATCTTT
1 CTTGGGTAGGCTCTGCGGCCCCGAGAATCTTT
*
63307 CTTGGGTAGACTCT-CAGGCCCC
1 CTTGGGTAGGCTCTGC-GGCCCC
63329 AATGTGCTCC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
30 20 0.48
31 2 0.05
32 20 0.48
ACGTcount: A:0.13, C:0.30, G:0.30, T:0.27
Consensus pattern (32 bp):
CTTGGGTAGGCTCTGCGGCCCCGAGAATCTTT
Found at i:71040 original size:2 final size:2
Alignment explanation
Indices: 71033--71059 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
71023 ATCAGGCATC
71033 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
71060 TCTACCTGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Done.