Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005385.1 Hibiscus syriacus cultivar Beakdansim tig00012334_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: 63538
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:913 original size:17 final size:17
Alignment explanation
Indices: 871--904 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
861 TAGCATTTTG
871 AAAATAAAG--CTTGAA
1 AAAATAAAGAACTTGAA
886 AAAATAAAGAACTTGAA
1 AAAATAAAGAACTTGAA
903 AA
1 AA
905 GAAAGAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (17 bp):
AAAATAAAGAACTTGAA
Found at i:3352 original size:11 final size:11
Alignment explanation
Indices: 3328--3369 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
3318 CTCATCCATC
3328 AGAGAAAAATAA
1 AGAGAAAAA-AA
3340 AGAGAAAAAAA
1 AGAGAAAAAAA
*
3351 AGAGAAAAAGA
1 AGAGAAAAAAA
3362 AGAAGAAA
1 AG-AGAAA
3370 GAGATTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
11 14 0.50
12 14 0.50
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (11 bp):
AGAGAAAAAAA
Found at i:4107 original size:15 final size:15
Alignment explanation
Indices: 4087--4115 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4077 TTCTTTCATT
4087 CTTCGATAAAGAAAG
1 CTTCGATAAAGAAAG
4102 CTTCGATAAAGAAA
1 CTTCGATAAAGAAA
4116 TGAGGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (15 bp):
CTTCGATAAAGAAAG
Found at i:5883 original size:56 final size:55
Alignment explanation
Indices: 5797--5952 Score: 237
Period size: 56 Copynumber: 2.9 Consensus size: 55
5787 CTGACGAGAA
5797 ATCTGTGCAGAAGCCACAGGAAAGAATGAATGTGTTGTCAAATGTTTTTACGAAAC
1 ATCTGTGCAGAAGCCACAGGAAAGAATGAATGTGTTGTCAAATGTTTTTACG-AAC
* * * *
5853 ATCTGGGCAGAAGCCACAGGAAAGAATGAATGTGTTCT-TAAT-ATTTTACGAAC
1 ATCTGTGCAGAAGCCACAGGAAAGAATGAATGTGTTGTCAAATGTTTTTACGAAC
*
5906 ATCTGTGCAGAAACCACAGGAAAG-ATGAATGTGTTGTCAAATGTTTT
1 ATCTGTGCAGAAGCCACAGGAAAGAATGAATGTGTTGTCAAATGTTTT
5953 ATAACCAGTG
Statistics
Matches: 89, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
52 12 0.13
53 28 0.31
54 10 0.11
55 3 0.03
56 36 0.40
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (55 bp):
ATCTGTGCAGAAGCCACAGGAAAGAATGAATGTGTTGTCAAATGTTTTTACGAAC
Found at i:7255 original size:73 final size:72
Alignment explanation
Indices: 7034--7293 Score: 423
Period size: 73 Copynumber: 3.6 Consensus size: 72
7024 AGATGTTTTC
* *
7034 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCCTTAAAACAAATGTTTCTCGCTGGAGAAATT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTT-CTTAAAACAAATGTTTCTCGCTAGAGAAAGT
7099 TTCACTTG
65 TTCACTTG
*
7107 AAATAGCAATTTATCTCACTTGAGATTG-TTTTCTTAAAACAAACTGTTTCTCGCTAGATAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-TGTTTCTCGCTAGAGAAAGT
7171 TTCACTTG
65 TTCACTTG
* *
7179 AAATAACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTTGCTAGAGAAAGT
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-TGTTTCTCGCTAGAGAAAGT
*
7244 TTCACTCG
65 TTCACTTG
*
7252 AAATAGCAATTTATCTCACTTGAGATTATTTTTCTTAAAACA
1 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
7294 TTTCAAGAAG
Statistics
Matches: 175, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
71 11 0.06
72 56 0.32
73 108 0.62
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (72 bp):
AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATGTTTCTCGCTAGAGAAAGTT
TCACTTG
Found at i:7357 original size:39 final size:39
Alignment explanation
Indices: 7298--7597 Score: 386
Period size: 39 Copynumber: 7.7 Consensus size: 39
7288 AAAACATTTC
* * *
7298 AAGAAGGAGTTCATAATCTGAAGAACTTGCCTGAAGAGG
1 AAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGAGG
* * * *
7337 AATAAGAAGTTCATAGTCTGAAGAACTCATCTAAAGAGG
1 AAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGAGG
* *
7376 AAGAAGGAGTTCATAATCTGAAGAACTCGTCT-AACGAGA
1 AAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAA-GAGG
* *
7415 AAGAAAAAGTTCATAGTCTGAAGAACTCGTCTGAAGAGG
1 AAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGAGG
* * *
7454 AAAAAGGAGTTCATAATCTGAAGAACTCGTCTCAAGAGG
1 AAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGAGG
* ** *
7493 AAGAAGAAGTTCATAGTCTGAAGAACTTATATGAAGAGG
1 AAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGAGG
* *
7532 AAGAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGG
1 AAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGAGG
* *
7571 AATAAGAAGTTCATAGTCTGAAGAACT
1 AAGAAGAAGTTCATAATCTGAAGAACT
7598 TATTCAACCT
Statistics
Matches: 224, Mismatches: 35, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
38 2 0.01
39 220 0.98
40 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.22
Consensus pattern (39 bp):
AAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGAGG
Found at i:7600 original size:78 final size:78
Alignment explanation
Indices: 7298--7597 Score: 467
Period size: 78 Copynumber: 3.8 Consensus size: 78
7288 AAAACATTTC
* * *
7298 AAGAAGGAGTTCATAATCTGAAGAACTTGCCTGAAGAGGAATAAGAAGTTCATAGTCTGAAGAAC
1 AAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAAC
*
7363 TCATCTAAAGAGG
66 TCATCTGAAGAGG
* *
7376 AAGAAGGAGTTCATAATCTGAAGAACTCGTCT-AACGAGAAAGAAAAAGTTCATAGTCTGAAGAA
1 AAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAA-GAGGAAGAAGAAGTTCATAGTCTGAAGAA
*
7440 CTCGTCTGAAGAGG
65 CTCATCTGAAGAGG
* *
7454 AAAAAGGAGTTCATAATCTGAAGAACTCGTCTCAAGAGGAAGAAGAAGTTCATAGTCTGAAGAAC
1 AAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAAC
* *
7519 TTATATGAAGAGG
66 TCATCTGAAGAGG
* *
7532 AAGAAGGAGTTCATAATCTGAAGAACTCATCTGAAGAGGAATAAGAAGTTCATAGTCTGAAGAAC
1 AAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAAC
7597 T
66 T
7598 TATTCAACCT
Statistics
Matches: 203, Mismatches: 17, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
77 2 0.01
78 199 0.98
79 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.22
Consensus pattern (78 bp):
AAGAAGGAGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAAC
TCATCTGAAGAGG
Found at i:9124 original size:27 final size:29
Alignment explanation
Indices: 9063--9125 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 29
9053 TTATTTAGTC
9063 ATATTAATATATATTTTGATTAATTTTATA
1 ATATTAATATATATTTT-ATTAATTTTATA
*
9093 A-ATTAATA-ATA-TTTATTTATTTT-TAA
1 ATATTAATATATATTTTATTAATTTTAT-A
9119 ATATTAA
1 ATATTAA
9126 GAAGGGTGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
25 1 0.03
26 10 0.33
27 8 0.27
28 3 0.10
29 7 0.23
30 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (29 bp):
ATATTAATATATATTTTATTAATTTTATA
Found at i:9196 original size:2 final size:2
Alignment explanation
Indices: 9189--9217 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9179 ATACCTTACT
9189 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9218 TTGTTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9251 original size:20 final size:18
Alignment explanation
Indices: 9215--9265 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
9205 TATATATATA
9215 TATTTGTTTTAAT-TTTAT
1 TATTT-TTTTAATATTTAT
9233 TCAATTTTTTTAATATTTAT
1 T--ATTTTTTTAATATTTAT
9253 TA-TTTTTTAATAT
1 TATTTTTTTAATAT
9266 CGAAGAAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 11 0.37
18 2 0.07
19 7 0.23
20 10 0.33
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (18 bp):
TATTTTTTTAATATTTAT
Found at i:9259 original size:19 final size:18
Alignment explanation
Indices: 9215--9260 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
9205 TATATATATA
*
9215 TATTTGTTTTAATTTTAT
1 TATTTTTTTTAATTTTAT
*
9233 TCAATTTTTTTAATATTTAT
1 T-ATTTTTTTTAAT-TTTAT
9253 TATTTTTT
1 TATTTTTT
9261 AATATCGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 16 0.70
20 6 0.26
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
TATTTTTTTTAATTTTAT
Found at i:11951 original size:30 final size:30
Alignment explanation
Indices: 11863--11954 Score: 132
Period size: 30 Copynumber: 3.1 Consensus size: 30
11853 CACATGGATT
* *
11863 GATCGAAAAATAGTTTATGTATCTAAATAA
1 GATCAAAAAATAGTTTATGTATCTAAATGA
*
11893 GAT-AGAAAAATAGTTTATGAATCTAAATGA
1 GATCA-AAAAATAGTTTATGTATCTAAATGA
*
11923 GATCAAAAAATAGTTTATGTATCAAAATGA
1 GATCAAAAAATAGTTTATGTATCTAAATGA
11953 GA
1 GA
11955 AAAGCGGTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
30 54 0.98
31 1 0.02
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.30
Consensus pattern (30 bp):
GATCAAAAAATAGTTTATGTATCTAAATGA
Found at i:15393 original size:24 final size:24
Alignment explanation
Indices: 15366--15453 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 24
15356 TTCTATTATA
*
15366 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
* *
15390 ATACTTGACCTGGATTCTGATTGA
1 ATACTTGACCTGGATTCTGATCGG
* * *
15414 ATACTTGACATGGATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
*
15438 ATACTTGAACTGGATT
1 ATACTTGACCTGGATT
15454 ATGTTATATT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:17951 original size:97 final size:87
Alignment explanation
Indices: 17773--17955 Score: 240
Period size: 97 Copynumber: 2.0 Consensus size: 87
17763 TCCCTGTAGC
*
17773 TATCATGTTGTATTAGAAGAAGAAGAAAAAGAAAAAGAAGACATTTTTTTAGTTTTTTAATTATC
1 TATCATGTTGTATTAGAAGAAGAAGAAAAAGAAAAAAAAGACATTTTTTTAGTTTTTTAATTATC
17838 AACTCATACTTCCGTTAATGGA
66 AACTCATACTTCCGTTAATGGA
*
17860 TATCATGTTGTATTAGAAGAAGAAGAAAAAGAACAATAAAAAGACATGCATTTTTTTTAAATTTT
1 TATCATGTTGTATTAGAAGAAGAAGAAAAAG-A-AA-AAAAAG--A--CA-TTTTTTT--AGTTT
* *
17925 TTTAATTATCAACTCGTACTTTCGTTAATGG
56 TTTAATTATCAACTCATACTTCCGTTAATGG
17956 GTTAACAAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 10
0.85 0.04 0.10
Matches are distributed among these distances:
87 31 0.38
88 1 0.01
89 2 0.02
90 5 0.06
92 1 0.01
94 2 0.02
95 7 0.09
97 33 0.40
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (87 bp):
TATCATGTTGTATTAGAAGAAGAAGAAAAAGAAAAAAAAGACATTTTTTTAGTTTTTTAATTATC
AACTCATACTTCCGTTAATGGA
Found at i:25697 original size:2 final size:2
Alignment explanation
Indices: 25692--25722 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25682 TTTTTTTGTA
25692 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
25723 CATACGGCTT
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:25947 original size:1 final size:1
Alignment explanation
Indices: 25943--25973 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
25933 AAAAAACTCT
25943 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
25974 ATTGTCTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:26946 original size:27 final size:27
Alignment explanation
Indices: 26912--26963 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
26902 ATTACTACTT
* *
26912 TATAAAATTATGTTTATTGAATTTTAA
1 TATAAAATTACGTTAATTGAATTTTAA
26939 TATAAAATTACGTTAATTGAATTTT
1 TATAAAATTACGTTAATTGAATTTT
26964 TAAAAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (27 bp):
TATAAAATTACGTTAATTGAATTTTAA
Found at i:26977 original size:23 final size:26
Alignment explanation
Indices: 26915--26972 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
26905 ACTACTTTAT
* * *
26915 AAAATTATGTTTATTGAATTTTAATAT
1 AAAATTACGTTAATTGAATTTT-ATAA
26942 AAAATTACGTTAATTGAATTTT-TAA
1 AAAATTACGTTAATTGAATTTTATAA
26967 AAAATT
1 AAAATT
26973 CTTAAAGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 8 0.29
27 20 0.71
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (26 bp):
AAAATTACGTTAATTGAATTTTATAA
Found at i:27047 original size:29 final size:29
Alignment explanation
Indices: 27007--27062 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
26997 TCATAATATG
*
27007 TTATTAACGAAGTTGGTTAAAGTGGTATA
1 TTATTAACGAAGTTGATTAAAGTGGTATA
27036 TTATTAACGAAGTTGATTAAAGTGGTA
1 TTATTAACGAAGTTGATTAAAGTGGTA
27063 AGCAGTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.38
Consensus pattern (29 bp):
TTATTAACGAAGTTGATTAAAGTGGTATA
Found at i:27230 original size:2 final size:2
Alignment explanation
Indices: 27225--27272 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
27215 AACATTCATA
27225 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
27267 AT AT AT
1 AT AT AT
27273 TGAAAACTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29259 original size:22 final size:22
Alignment explanation
Indices: 29233--29277 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
29223 GTCGCATTGA
29233 TTGAGATGATAAGGGACCCATG
1 TTGAGATGATAAGGGACCCATG
29255 TTGAGATGATAAGGGACCCATG
1 TTGAGATGATAAGGGACCCATG
29277 T
1 T
29278 GCCCCAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.24
Consensus pattern (22 bp):
TTGAGATGATAAGGGACCCATG
Found at i:36150 original size:43 final size:43
Alignment explanation
Indices: 36102--36350 Score: 301
Period size: 43 Copynumber: 5.8 Consensus size: 43
36092 AAGTCTTATA
* *
36102 CTTGCACATAGCAAAAGAGCCTGGGGAAACAGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAGCCTGGGGGAACAGTAAGGCTTACC
* * *
36145 CTTGCACACAGCAAAGGAACCT-GGGAAACTA-TAAGGCTTACC
1 CTTGCACACAGCAAAAGAGCCTGGGGGAAC-AGTAAGGCTTACC
* * *
36187 CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAGCCTGGGGGAACAGTAAGGCTTACC
* *
36230 CTTGCACACAG-GAAAGGGACCTGGGGGAACAGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAG-CCTGGGGGAACAGTAAGGCTTACC
* *
36273 CTTGCACACAGC-AAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAAGAG-CCTGGGGGAACAGTAAGGCTTACC
* *
36316 CTTGCACACAGC-AAAGGGACCTGGGGGAACTGTAA
1 CTTGCACACAGCAAAAGAG-CCTGGGGGAACAGTAA
36351 CGGTAATTAA
Statistics
Matches: 190, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
42 43 0.23
43 147 0.77
ACGTcount: A:0.32, C:0.24, G:0.28, T:0.16
Consensus pattern (43 bp):
CTTGCACACAGCAAAAGAGCCTGGGGGAACAGTAAGGCTTACC
Found at i:36287 original size:86 final size:86
Alignment explanation
Indices: 36102--36350 Score: 385
Period size: 86 Copynumber: 2.9 Consensus size: 86
36092 AAGTCTTATA
* * * * * *
36102 CTTGCACATAGCAAAAGAGCCTGGGGAAACAGTAAGGCTTACCCTTGCACACAGCAAAGGAACCT
1 CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
*
36167 -GGGAAACTA-TAAGGCTTACC
66 GGGGGAAC-AGTAAGGCTTACC
*
36187 CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGGAAAGGGACCT
1 CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
36252 GGGGGAACAGTAAGGCTTACC
66 GGGGGAACAGTAAGGCTTACC
*
36273 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
1 CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
*
36338 GGGGGAACTGTAA
66 GGGGGAACAGTAA
36351 CGGTAATTAA
Statistics
Matches: 151, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
85 59 0.39
86 92 0.61
ACGTcount: A:0.32, C:0.24, G:0.28, T:0.16
Consensus pattern (86 bp):
CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
GGGGGAACAGTAAGGCTTACC
Found at i:41351 original size:43 final size:43
Alignment explanation
Indices: 41218--41466 Score: 347
Period size: 43 Copynumber: 5.8 Consensus size: 43
41208 AAGTCTTATA
* * * *
41218 CTTGCACATAGCAAAAGAGCCTGGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACC
* * *
41261 CTTGCACACAGTAAAGGAA-CTTGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACC
*
41303 CTTGCACACAACAAAGGAACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACC
* * * *
41346 TTTGCACAGAGCAAAGGGACCTGGGGGAACTGTAAGGCATACC
1 CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACC
*
41389 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACC
* * *
41432 CTTGCAAACAACAAAGGGACCTGGGGGAACTGTAA
1 CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAA
41467 CGGTAATTAA
Statistics
Matches: 186, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
42 39 0.21
43 147 0.79
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.17
Consensus pattern (43 bp):
CTTGCACACAGCAAAGGAACCTGGGGGAACTGTAAGGCTTACC
Found at i:50714 original size:16 final size:17
Alignment explanation
Indices: 50689--50724 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
50679 CCGAGGTGTC
50689 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
50705 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
50722 ACA
1 ACA
50725 ACTAAAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:54602 original size:21 final size:21
Alignment explanation
Indices: 54565--54604 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
54555 GAAAGGTTGT
*
54565 GGTGCCATTTAATACGACTTC
1 GGTGCCATTGAATACGACTTC
54586 GGTGCCATCTGAA-ACGACT
1 GGTGCCAT-TGAATACGACT
54605 GCGAAATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (21 bp):
GGTGCCATTGAATACGACTTC
Found at i:57008 original size:59 final size:59
Alignment explanation
Indices: 56910--57023 Score: 185
Period size: 59 Copynumber: 1.9 Consensus size: 59
56900 GGGTTTGTTG
*
56910 GAGCCATATTATCGAGTTGTCCTTTTCATTACGACTAGGAGGTTTCAATAGGACACTTA
1 GAGCCATATTATCGAGTTGTCCTTTTCATTACGACTAGGAGGGTTCAATAGGACACTTA
* *
56969 GAGCCATATTATCGAGTT-TGCCTTTTCATTGCGATTAGGAGGGTTCAATAGGACA
1 GAGCCATATTATCGAGTTGT-CCTTTTCATTACGACTAGGAGGGTTCAATAGGACA
57024 TTTATCCATC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
58 1 0.02
59 50 0.98
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (59 bp):
GAGCCATATTATCGAGTTGTCCTTTTCATTACGACTAGGAGGGTTCAATAGGACACTTA
Found at i:59189 original size:19 final size:18
Alignment explanation
Indices: 59165--59204 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
59155 ATATTTAAGT
59165 ATTAATAATAA-TTATATTA
1 ATTAATAA-AATTTA-ATTA
59184 ATTAATAAAATTTAATTA
1 ATTAATAAAATTTAATTA
59202 ATT
1 ATT
59205 TTTATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTAATAAAATTTAATTA
Found at i:62004 original size:16 final size:17
Alignment explanation
Indices: 61954--62005 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
61944 AAAAAAAATA
61954 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
61971 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
61986 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
62002 AATT
1 AATT
62006 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Done.