Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004610.1 Hibiscus syriacus cultivar Beakdansim tig00010309_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: 55073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:64 original size:22 final size:23
Alignment explanation
Indices: 21--65 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
11 TCTTTTGTTC
21 CTTTTAAGTGCTTTCAATTTCTT
1 CTTTTAAGTGCTTTCAATTTCTT
* *
44 CTTTTGAGTGC-TTGAATTTCTT
1 CTTTTAAGTGCTTTCAATTTCTT
66 GCTGGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.56
Consensus pattern (23 bp):
CTTTTAAGTGCTTTCAATTTCTT
Found at i:6236 original size:244 final size:244
Alignment explanation
Indices: 5804--6536 Score: 1382
Period size: 244 Copynumber: 3.0 Consensus size: 244
5794 AACTCAGAAT
*
5804 ACTCAGAAAAACATTAGATTTCTTTCGATTCAAACAACATATATAGACACTTTATCACATAAAAG
1 ACTCAGAAAAACATTAGATTTCTTTCGATTCATACAACATATATAGACACTTTATCACATAAAAG
*
5869 GCATACAATGCCAAATCATAGCACTAGGCGAATTCTTTACTATCGTTTAATCAAATAACGTTTGA
66 GCATACAATGCCAAATCATAGCACTTGGCGAATTCTTTACTATCGTTTAATCAAATAACGTTTGA
*
5934 TGTTTACATATTCGTATCATATAACCTACACTTTTCAATTTCATATAAGTATAGCCCAATGTACA
131 TGTTTACATATTCATATCATATAACCTACACTTTTCAATTTCATATAAGTATAGCCCAATGTACA
5999 TTAGATGAGAATACAAGGTACGTGAATCAGATGAGTGTGCGCAATATAC
196 TTAGATGAGAATACAAGGTACGTGAATCAGATGAGTGTGCGCAATATAC
*
6048 ACTCAGAAAAACATTAGATTTCTTTCGATTCATACAACATATATAGATACTTTATCACATAAAAG
1 ACTCAGAAAAACATTAGATTTCTTTCGATTCATACAACATATATAGACACTTTATCACATAAAAG
6113 GCATACAATGCCAAATCATAGCACTTGGCGAATTCTTTACTATCGTTTAATCAAATAACGTTTGA
66 GCATACAATGCCAAATCATAGCACTTGGCGAATTCTTTACTATCGTTTAATCAAATAACGTTTGA
*
6178 TGTTTACATATTCATATCATATAACCTACACTTTTCAATTTCATATAAGTACAGCCCAATGTACA
131 TGTTTACATATTCATATCATATAACCTACACTTTTCAATTTCATATAAGTATAGCCCAATGTACA
6243 TTAGATGAGAATACAAGGTACGTGAATCAGATGAGTGTGCGCAATATAC
196 TTAGATGAGAATACAAGGTACGTGAATCAGATGAGTGTGCGCAATATAC
6292 ACTCAGAAAAACATTAGATTTCTTTCGATTCATACAAC--ATATAGACAC-TTATCACATAAAAG
1 ACTCAGAAAAACATTAGATTTCTTTCGATTCATACAACATATATAGACACTTTATCACATAAAAG
*
6354 GCATACAATGCCAAATCATAGCACTTGGCGAATTCATTACTATCGTTTAATCAAATAACGTTTGA
66 GCATACAATGCCAAATCATAGCACTTGGCGAATTCTTTACTATCGTTTAATCAAATAACGTTTGA
6419 TGTTTACATATTCATATCATATAACCTACACTTTTCAATTTCATATAAGTATAGCCCAATGTACA
131 TGTTTACATATTCATATCATATAACCTACACTTTTCAATTTCATATAAGTATAGCCCAATGTACA
*
6484 TTAGATGAGAATACAAGGTACGTGAATTAGATGAGTGTGCGCAATATAC
196 TTAGATGAGAATACAAGGTACGTGAATCAGATGAGTGTGCGCAATATAC
6533 ACTC
1 ACTC
6537 CAGGTGCCTC
Statistics
Matches: 480, Mismatches: 9, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
241 194 0.40
242 9 0.02
244 277 0.58
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.32
Consensus pattern (244 bp):
ACTCAGAAAAACATTAGATTTCTTTCGATTCATACAACATATATAGACACTTTATCACATAAAAG
GCATACAATGCCAAATCATAGCACTTGGCGAATTCTTTACTATCGTTTAATCAAATAACGTTTGA
TGTTTACATATTCATATCATATAACCTACACTTTTCAATTTCATATAAGTATAGCCCAATGTACA
TTAGATGAGAATACAAGGTACGTGAATCAGATGAGTGTGCGCAATATAC
Found at i:9201 original size:25 final size:24
Alignment explanation
Indices: 9173--9252 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 24
9163 GTATTATCCA
9173 GTATCAGTACCCTTTTCCACTGTTG
1 GTATCAGTACCCTTTTCCA-TGTTG
** **
9198 GTATTGGTACCCTTTTTTAT-TTCCG
1 GTATCAGTACCCTTTTCCATGTT--G
* *
9223 GTATCAATAACCTTTTCCAGTGTTG
1 GTATCAGTACCCTTTTCCA-TGTTG
9248 GTATC
1 GTATC
9253 TATACCATAT
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
23 2 0.05
24 1 0.02
25 35 0.85
26 1 0.02
27 2 0.05
ACGTcount: A:0.17, C:0.23, G:0.16, T:0.44
Consensus pattern (24 bp):
GTATCAGTACCCTTTTCCATGTTG
Found at i:9357 original size:20 final size:20
Alignment explanation
Indices: 9332--9370 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9322 TTCATCCCAA
9332 TTCATCCAGTATCAATATTG
1 TTCATCCAGTATCAATATTG
* *
9352 TTCATCCATTATCGATATT
1 TTCATCCAGTATCAATATT
9371 TGAACCCACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.44
Consensus pattern (20 bp):
TTCATCCAGTATCAATATTG
Found at i:15041 original size:31 final size:31
Alignment explanation
Indices: 14968--15034 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
14958 TAGTTATGTC
14968 AGGGACCATATTGCAAACAGACTAAATGTTG
1 AGGGACCATATTGCAAACAGACTAAATGTTG
*
14999 AGGGACCATATTGCAAATAGACTAAATGTTG
1 AGGGACCATATTGCAAACAGACTAAATGTTG
*
15030 GGGGA
1 AGGGA
15035 TTATATTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.22
Consensus pattern (31 bp):
AGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:16999 original size:15 final size:15
Alignment explanation
Indices: 16979--17011 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
16969 CGTTGTTTTG
16979 CTGAATCAATCAGCA
1 CTGAATCAATCAGCA
*
16994 CTGAATCAGTCAGCA
1 CTGAATCAATCAGCA
17009 CTG
1 CTG
17012 TTAAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.21
Consensus pattern (15 bp):
CTGAATCAATCAGCA
Found at i:17650 original size:31 final size:31
Alignment explanation
Indices: 17612--17688 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
17602 AGTTACGTCG
*
17612 GGGACCATATTGCAAACGAACTAAATGTTGA
1 GGGACCATATTACAAACGAACTAAATGTTGA
*
17643 GGGACCATATTACAAATGAACTAAATGTTGA
1 GGGACCATATTACAAACGAACTAAATGTTGA
**
17674 GGGATTATATTACAA
1 GGGACCATATTACAA
17689 GTTTTAAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (31 bp):
GGGACCATATTACAAACGAACTAAATGTTGA
Found at i:20125 original size:31 final size:31
Alignment explanation
Indices: 20090--20157 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
20080 TCAATAAAGT
*
20090 TTAAAAAATTA-AAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAAATA-TTAATAAATTTA
* *
20121 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAAATATTAATAAATTTA
20152 TCTAAA
1 T-TAAA
20158 TACTATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 22 0.69
32 10 0.31
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (31 bp):
TTAAAAAATTATAAAAATATTAATAAATTTA
Found at i:20165 original size:31 final size:31
Alignment explanation
Indices: 20102--20173 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
20092 AAAAAATTAA
* * *
20102 AAAATACTTATTAAATTTATTAAAAGATTAT
1 AAAATAATTAATAAATTTATTAAAAGACTAT
* *
20133 AAAATTATTAATAAATTTATCT-AAATACTAT
1 AAAATAATTAATAAATTTAT-TAAAAGACTAT
20164 AAAATAATTA
1 AAAATAATTA
20174 TTATATTATC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (31 bp):
AAAATAATTAATAAATTTATTAAAAGACTAT
Found at i:26443 original size:15 final size:15
Alignment explanation
Indices: 26423--26458 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
26413 CCAAAGGATC
26423 GAGGCAGTCTGTTCG
1 GAGGCAGTCTGTTCG
26438 GAGGCAGTCTGTTCG
1 GAGGCAGTCTGTTCG
26453 GAGGCA
1 GAGGCA
26459 AGTATAGACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.17, C:0.19, G:0.42, T:0.22
Consensus pattern (15 bp):
GAGGCAGTCTGTTCG
Found at i:30970 original size:13 final size:13
Alignment explanation
Indices: 30944--30978 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
30934 CAATCCTGGC
30944 GACATACG-GGGT
1 GACATACGAGGGT
30956 GACATACGAGGGT
1 GACATACGAGGGT
30969 GACATACGAG
1 GACATACGAG
30979 CCATATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.31, C:0.17, G:0.37, T:0.14
Consensus pattern (13 bp):
GACATACGAGGGT
Found at i:30988 original size:11 final size:11
Alignment explanation
Indices: 30972--31005 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
30962 CGAGGGTGAC
30972 ATACGAGCCAT
1 ATACGAGCCAT
30983 ATACGAGCCAT
1 ATACGAGCCAT
*
30994 ATACGAGTCAT
1 ATACGAGCCAT
31005 A
1 A
31006 CGAGCCAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (11 bp):
ATACGAGCCAT
Found at i:31036 original size:22 final size:22
Alignment explanation
Indices: 31005--31084 Score: 79
Period size: 22 Copynumber: 3.4 Consensus size: 22
30995 TACGAGTCAT
*
31005 ACGAGCCAATGGGGAGGATGCA
1 ACGAGCCAATGGGGAGCATGCA
*
31027 ACGAGTCAATGGGGAGCATGCAGGAA
1 ACGAGCCAATGGGGAGCATGC----A
*
31053 TAGAGAGCCAATGGGGAGCATGCA
1 -A-CGAGCCAATGGGGAGCATGCA
31077 ACGAGCCA
1 ACGAGCCA
31085 TATACGAGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
22 25 0.53
23 1 0.02
24 1 0.02
26 1 0.02
27 1 0.02
28 18 0.38
ACGTcount: A:0.34, C:0.19, G:0.38, T:0.10
Consensus pattern (22 bp):
ACGAGCCAATGGGGAGCATGCA
Found at i:31065 original size:28 final size:28
Alignment explanation
Indices: 31033--31198 Score: 188
Period size: 28 Copynumber: 5.6 Consensus size: 28
31023 TGCAACGAGT
31033 CAATGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
* *
31061 CAATGGGGAGCATGCAACGAGCCATATACGAGC
1 CAATGGGGAGCATGC-A-G-G-AATAGA-GAGC
* *
31094 CCACGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
* *
31122 CAATGGGGAGCATGCAACGAGCCATATACGAGC
1 CAATGGGGAGCATGC-A-G-G-AATAGA-GAGC
31155 CAATGGGGAGCATGCAGGAATAGAGAGC
1 CAATGGGGAGCATGCAGGAATAGAGAGC
31183 CAATGGGGAGCATGCA
1 CAATGGGGAGCATGCA
31199 ACGAGCCATA
Statistics
Matches: 116, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
28 52 0.45
29 10 0.09
30 4 0.03
31 4 0.03
32 10 0.09
33 36 0.31
ACGTcount: A:0.34, C:0.20, G:0.36, T:0.11
Consensus pattern (28 bp):
CAATGGGGAGCATGCAGGAATAGAGAGC
Found at i:31066 original size:50 final size:53
Alignment explanation
Indices: 31007--31203 Score: 211
Period size: 61 Copynumber: 3.5 Consensus size: 53
30997 CGAGTCATAC
*
31007 GAGCCAATGGGGAGGATGCAACGAG-T-CA-ATGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAGATACACATGGGGAGCATGCAGGAATAGA
*
31057 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCCACGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAG----ATAC-A---CATGGGGAGCATGCAGGAATAGA
31118 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCAATGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAG----ATAC-A--C-ATGGGGAGCATGCAGGAATAGA
31179 GAGCCAATGGGGAGCATGCAACGAG
1 GAGCCAATGGGGAGCATGCAACGAG
31204 CCATATACGA
Statistics
Matches: 131, Mismatches: 4, Indels: 13
0.89 0.03 0.09
Matches are distributed among these distances:
50 24 0.18
55 1 0.01
56 1 0.01
57 1 0.01
60 2 0.02
61 102 0.78
ACGTcount: A:0.34, C:0.19, G:0.37, T:0.11
Consensus pattern (53 bp):
GAGCCAATGGGGAGCATGCAACGAGATACACATGGGGAGCATGCAGGAATAGA
Found at i:31122 original size:61 final size:61
Alignment explanation
Indices: 31027--31217 Score: 346
Period size: 61 Copynumber: 3.1 Consensus size: 61
31017 GGAGGATGCA
* *
31027 ACGAGTCAATGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
*
31088 ACGAGCCCACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
*
31149 ACGAGCCAATGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
1 ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
31210 ACGAGCCA
1 ACGAGCCA
31218 TGCAGGAATA
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 125 1.00
ACGTcount: A:0.34, C:0.21, G:0.34, T:0.11
Consensus pattern (61 bp):
ACGAGCCAACGGGGAGCATGCAGGAATAGAGAGCCAATGGGGAGCATGCAACGAGCCATAT
Found at i:31281 original size:29 final size:29
Alignment explanation
Indices: 31231--31339 Score: 184
Period size: 29 Copynumber: 3.8 Consensus size: 29
31221 AGGAATAGAG
* *
31231 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
31260 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
31289 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
31318 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
31340 CCATTCCATC
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
29 75 0.97
30 2 0.03
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:31457 original size:36 final size:37
Alignment explanation
Indices: 31389--31462 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
31379 CATAGATTCC
31389 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
31426 TTCACGTGCTCCCCGCTGCA-TGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
31462 T
1 T
31463 GCATGCATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 17 0.46
37 20 0.54
ACGTcount: A:0.16, C:0.46, G:0.14, T:0.24
Consensus pattern (37 bp):
TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
Found at i:31490 original size:18 final size:18
Alignment explanation
Indices: 31467--31501 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
31457 CCCAATGCAT
31467 GCATGTGAACCATTTGAG
1 GCATGTGAACCATTTGAG
31485 GCATGTGAACCATTTGA
1 GCATGTGAACCATTTGA
31502 TTATTGGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (18 bp):
GCATGTGAACCATTTGAG
Found at i:31619 original size:23 final size:23
Alignment explanation
Indices: 31591--31636 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
31581 AAAAGAAAGA
31591 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
31614 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
31637 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:31651 original size:25 final size:23
Alignment explanation
Indices: 31591--31651 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
31581 AAAAGAAAGA
**
31591 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
31614 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
31637 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
31652 AGAAAGGGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:31675 original size:21 final size:21
Alignment explanation
Indices: 31639--31697 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
31629 GATTGCAGCC
31639 GAGAAA-GAAAGAAAGAAAGG
1 GAGAAAGGAAAGAAAGAAAGG
*
31659 GAGAAAGGAAAGGAAGAAAGG
1 GAGAAAGGAAAGAAAGAAAGG
*
31680 GAGAAAGGAAAGTAAGAA
1 GAGAAAGGAAAGAAAGAA
31698 GAAGAAAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 6 0.17
21 30 0.83
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (21 bp):
GAGAAAGGAAAGAAAGAAAGG
Found at i:31965 original size:46 final size:48
Alignment explanation
Indices: 31900--31991 Score: 127
Period size: 46 Copynumber: 2.0 Consensus size: 48
31890 TTATATAGTT
31900 AAAAAATAATTAATCAGTTTGTATT-GTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATCAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
* * *
31945 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATCAGTTTGTATTAGTTAAATAGTTAAGTTATAT
31992 TGTTTGTTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
45 6 0.15
46 16 0.40
47 3 0.08
48 7 0.17
49 8 0.20
ACGTcount: A:0.42, C:0.01, G:0.12, T:0.45
Consensus pattern (48 bp):
AAAAAATAATTAATCAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
Found at i:34388 original size:14 final size:13
Alignment explanation
Indices: 34369--34411 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
34359 AAATCATTAC
34369 TAGTATCAAATAAT
1 TAGTAT-AAATAAT
*
34383 TAGTATTAAATCAT
1 TAGTA-TAAATAAT
*
34397 TATTATAAATAAT
1 TAGTATAAATAAT
34410 TA
1 TA
34412 CTAAATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 9 0.36
14 15 0.60
15 1 0.04
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (13 bp):
TAGTATAAATAAT
Found at i:34401 original size:17 final size:17
Alignment explanation
Indices: 34351--34401 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
34341 ACAATGATTT
34351 TTAGTATCAAATCATTA
1 TTAGTATCAAATCATTA
*
34368 CTAGTATCAAAT-A--A
1 TTAGTATCAAATCATTA
*
34382 TTAGTATTAAATCATTA
1 TTAGTATCAAATCATTA
34399 TTA
1 TTA
34402 TAAATAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 11 0.39
15 1 0.04
16 1 0.04
17 15 0.54
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (17 bp):
TTAGTATCAAATCATTA
Found at i:34453 original size:26 final size:25
Alignment explanation
Indices: 34377--34693 Score: 157
Period size: 26 Copynumber: 12.8 Consensus size: 25
34367 ACTAGTATCA
*
34377 AATAATTAGTATTAAATCATTATTAT
1 AATAATTATTA-TAAATCATTATTAT
* * **
34403 AAATAATTA--CTAAAT-AATAACAT
1 -AATAATTATTATAAATCATTATTAT
34426 AATAATTATTATAAAATCATTATTAT
1 AATAATTATTAT-AAATCATTATTAT
* *
34452 AATGATTATTATCAAATCATTACTA-
1 AATAATTATTAT-AAATCATTATTAT
* * *
34477 AATCATCAAATCATTAAAT-A-T-TTA-
1 AATAAT--TATTA-TAAATCATTATTAT
* *
34501 AATCATTA-T-TAAATCATTTTTAT
1 AATAATTATTATAAATCATTATTAT
* *
34524 AATGATTATTACTAAATCATTACTAT
1 AATAATTATTA-TAAATCATTATTAT
* *
34550 AATGATTATTATCAAATCATTA--CT
1 AATAATTATTAT-AAATCATTATTAT
* * *
34574 -A-AATCA-T-CAAATCATTAATAT
1 AATAATTATTATAAATCATTATTAT
* *
34595 -TTAAATCATTATTAAATCATT-TTAT
1 AAT-AATTATTA-TAAATCATTATTAT
*
34620 AATGATTATTACTAAATCATTATTAT
1 AATAATTATTA-TAAATCATTATTAT
* *
34646 AATGATTATTATCAAATCATTACTAT
1 AATAATTATTAT-AAATCATTATTAT
*
34672 AATGATTATTATCAAATCATTA
1 AATAATTATTAT-AAATCATTA
34694 CTAAATCATC
Statistics
Matches: 232, Mismatches: 33, Indels: 51
0.73 0.10 0.16
Matches are distributed among these distances:
19 14 0.06
20 1 0.00
21 3 0.01
22 15 0.06
23 18 0.08
24 17 0.07
25 30 0.13
26 118 0.51
27 15 0.06
28 1 0.00
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (25 bp):
AATAATTATTATAAATCATTATTAT
Found at i:34461 original size:12 final size:12
Alignment explanation
Indices: 34386--34463 Score: 54
Period size: 11 Copynumber: 6.5 Consensus size: 12
34376 AAATAATTAG
*
34386 TATTA-AATCAT
1 TATTATAATAAT
34397 TATTATAAATAAT
1 TATTAT-AATAAT
*
34410 TACTA-AATAA-
1 TATTATAATAAT
**
34420 TAACATAATAAT
1 TATTATAATAAT
*
34432 TATTATAAAATCAT
1 TATTAT--AATAAT
*
34446 TATTATAATGAT
1 TATTATAATAAT
34458 TATTAT
1 TATTAT
34464 CAAATCATTA
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
10 3 0.06
11 15 0.28
12 15 0.28
13 9 0.17
14 11 0.21
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (12 bp):
TATTATAATAAT
Found at i:34611 original size:11 final size:11
Alignment explanation
Indices: 34595--34756 Score: 64
Period size: 11 Copynumber: 13.5 Consensus size: 11
34585 TCATTAATAT
34595 TTAAATCATTA
1 TTAAATCATTA
34606 TTAAATCATT-
1 TTAAATCATTA
*
34616 TTATAATGATTA
1 TTA-AATCATTA
34628 TTACTAAATCATTA
1 -T--TAAATCATTA
*
34642 TTATAATGATTA
1 TTA-AATCATTA
34654 TTATCAAATCATTA
1 -T-T-AAATCATTA
*
34668 CTATAATGATTATTA
1 -T-TAA--ATCATTA
*
34683 TCAAATCATTA
1 TTAAATCATTA
*
34694 CTAAATCATCAAATCA
1 TTAAATCAT----T-A
34710 TTAAAT-A-T-
1 TTAAATCATTA
34718 TTAAATCATTA
1 TTAAATCATTA
34729 TTAAATCATT-
1 TTAAATCATTA
*
34739 TTATAATGATTA
1 TTA-AATCATTA
*
34751 ATAAAT
1 TTAAAT
34757 ACATAGAAAT
Statistics
Matches: 117, Mismatches: 13, Indels: 42
0.68 0.08 0.24
Matches are distributed among these distances:
8 6 0.05
9 1 0.01
10 8 0.07
11 50 0.43
12 9 0.08
13 7 0.06
14 19 0.16
15 11 0.09
16 6 0.05
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (11 bp):
TTAAATCATTA
Found at i:34664 original size:122 final size:123
Alignment explanation
Indices: 34505--34750 Score: 451
Period size: 122 Copynumber: 2.0 Consensus size: 123
34495 TATTTAAATC
* *
34505 ATTATTAAATCATTTTTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCAT
1 ATTACTAAATCATTATTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCAT
34570 TACTAAATCATCAAATCATT-AATATTTAAATCATTATTAAATCATTTTATAATGATT
66 TACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTATAATGATT
34627 ATTACTAAATCATTATTATAATGATTATTA-TCAAATCATTACTATAATGATTATTATCAAATCA
1 ATTACTAAATCATTATTATAATGATTATTACT-AAATCATTACTATAATGATTATTATCAAATCA
34691 TTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTATAATGATT
65 TTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTATAATGATT
34750 A
1 A
34751 ATAAATACAT
Statistics
Matches: 120, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
121 1 0.01
122 81 0.68
123 38 0.32
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.44
Consensus pattern (123 bp):
ATTACTAAATCATTATTATAATGATTATTACTAAATCATTACTATAATGATTATTATCAAATCAT
TACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAATCATTTTATAATGATT
Found at i:37627 original size:26 final size:24
Alignment explanation
Indices: 37569--37627 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
37559 CTAATAAACC
*
37569 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
37593 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
37621 TAATAAT
1 TAATAAT
37628 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:38477 original size:28 final size:30
Alignment explanation
Indices: 38429--38491 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
38419 AATTTTTATA
*
38429 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
38459 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
38487 TAATA
1 TAATA
38492 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:38498 original size:28 final size:28
Alignment explanation
Indices: 38433--38498 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
38423 TTTATATAAT
*
38433 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
38461 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
38489 ATAATTTATA
1 ATAATATATA
38499 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:38501 original size:21 final size:21
Alignment explanation
Indices: 38468--38516 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
38458 CTAATATAAT
38468 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
38489 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
38510 ATTAACT
1 A-TAACT
38517 AGATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:39061 original size:25 final size:25
Alignment explanation
Indices: 39007--39064 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
38997 GTTCCCACGT
* *
39007 CCCATGCACAGCATGCATCTGCATG
1 CCCATGCACAGCATGCATCTCCATC
* *
39032 ACCATGCACAGCATGCATC-CCCTCC
1 CCCATGCACAGCATGCATCTCCAT-C
39057 CCCATGCA
1 CCCATGCA
39065 TTCCCACGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.24, C:0.43, G:0.16, T:0.17
Consensus pattern (25 bp):
CCCATGCACAGCATGCATCTCCATC
Found at i:39154 original size:29 final size:29
Alignment explanation
Indices: 39122--39201 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
39112 TATACCTTGG
*
39122 AGGTCGCCCGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
39151 AGGTCGCCTGGATTGCATGGCGACCTCCA
1 AGGTCGCCTGGATTGCATGGCGACCTCCA
39180 AGGTCGCCTGGATTGCATGGCG
1 AGGTCGCCTGGATTGCATGGCG
39202 TCCTATGGCG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.16, C:0.30, G:0.34, T:0.20
Consensus pattern (29 bp):
AGGTCGCCTGGATTGCATGGCGACCTCCA
Found at i:42836 original size:12 final size:12
Alignment explanation
Indices: 42819--42848 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
42809 ATTCACCTTG
42819 AGTTTCTTCACC
1 AGTTTCTTCACC
42831 AGTTTCTTCACC
1 AGTTTCTTCACC
42843 AGTTTC
1 AGTTTC
42849 ATTAAGTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.17, C:0.30, G:0.10, T:0.43
Consensus pattern (12 bp):
AGTTTCTTCACC
Found at i:43856 original size:16 final size:16
Alignment explanation
Indices: 43835--43876 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
43825 TGAGAAAATT
43835 TTAATTTAAATTTAAA
1 TTAATTTAAATTTAAA
*
43851 TTAATTTAATTTTAAA
1 TTAATTTAAATTTAAA
*
43867 ATAATGTTAA
1 TTAAT-TTAA
43877 TAAATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTAATTTAAATTTAAA
Found at i:46757 original size:5 final size:5
Alignment explanation
Indices: 46719--46755 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
46709 CGAGCCGAGT
* *
46719 CGTGC CGTGC CGTGC CGTGC CGTGT CGTGC CGAGC CG
1 CGTGC CGTGC CGTGC CGTGC CGTGC CGTGC CGTGC CG
46756 AGACGGACGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.03, C:0.38, G:0.41, T:0.19
Consensus pattern (5 bp):
CGTGC
Found at i:47125 original size:2 final size:2
Alignment explanation
Indices: 47118--47142 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47108 GATGTATAAG
47118 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
47143 CAAAAGTATG
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:52620 original size:12 final size:12
Alignment explanation
Indices: 52603--52632 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
52593 ATACCCATTC
52603 CCAATAGTATTT
1 CCAATAGTATTT
52615 CCAATAGTATTT
1 CCAATAGTATTT
*
52627 TCAATA
1 CCAATA
52633 ATATGTGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.40
Consensus pattern (12 bp):
CCAATAGTATTT
Done.