Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008897.1 Hibiscus syriacus cultivar Beakdansim tig00112169_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: 67650
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:51 original size:2 final size:2
Alignment explanation
Indices: 44--103 Score: 106
Period size: 2 Copynumber: 31.0 Consensus size: 2
34 TATTTAAAAG
44 AT AT AT AT AT AT AT AT -T AT AT AT A- 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
84 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
104 GACTGATATA
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 54 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1351 original size:3 final size:3
Alignment explanation
Indices: 1345--1421 Score: 77
Period size: 3 Copynumber: 25.3 Consensus size: 3
1335 AATAATTATT
* *
1345 TAA TAA TAA T-A TAA TATA TATA TAA T-A TAA TAA TAAA TAT TTA TAA
1 TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA T-AA TAA TAA TAA
**
1391 TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1422 TTAAGTAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
2 4 0.06
3 48 0.77
4 10 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:1412 original size:21 final size:22
Alignment explanation
Indices: 1334--1421 Score: 107
Period size: 21 Copynumber: 4.2 Consensus size: 22
1324 TTTGGGCTTG
1334 TAATAAT-TA-TTTAATAATAA
1 TAATAATATATTTTAATAATAA
*
1354 T-ATAATATATATATAAT-ATAA
1 TAATAATATAT-TTTAATAATAA
1375 TAATAA-ATATTTATAATAATAA
1 TAATAATATATTT-TAATAATAA
1397 TAATAATA-ATTTTAATAATAA
1 TAATAATATATTTTAATAATAA
1418 TAAT
1 TAAT
1422 TTAAGTAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 13
0.80 0.03 0.18
Matches are distributed among these distances:
19 5 0.08
20 4 0.07
21 26 0.44
22 23 0.39
23 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATAATATATTTTAATAATAA
Found at i:2475 original size:36 final size:37
Alignment explanation
Indices: 2404--2488 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
2394 ATCCCATTAT
*
2404 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
2440 TATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
1 CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
2476 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
2489 TTGGTTACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 13 0.30
37 30 0.70
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (37 bp):
CATTTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:7033 original size:37 final size:36
Alignment explanation
Indices: 6970--7088 Score: 152
Period size: 35 Copynumber: 3.3 Consensus size: 36
6960 ATCCCATTAT
* * *
6970 CATTTTTC-AACAAACATCTACTAAACTTTGAAAAAC
1 CATTTTTCAAAAAAACATTTACCAAACTTTG-AAAAC
*
7006 TATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
**
7042 CA-TTTTCAAGGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
7077 CATTTTTTCAAA
1 CA-TTTTTCAAA
7089 GTTGGTTACC
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
35 33 0.46
36 13 0.18
37 26 0.36
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAAAAACATTTACCAAACTTTGAAAAC
Found at i:7045 original size:21 final size:21
Alignment explanation
Indices: 7016--7081 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 21
7006 TATTTTTCAA
*
7016 AAAAACATTTACCAAACTTTG
1 AAAACCATTTACCAAACTTTG
*
7037 AAAACCATTT-TC-AA----G
1 AAAACCATTTACCAAACTTTG
*
7052 GAAA-CATTTACCAAACTTTG
1 AAAACCATTTACCAAACTTTG
7072 AAAACCATTT
1 AAAACCATTT
7082 TTTCAAAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 14
0.63 0.10 0.27
Matches are distributed among these distances:
14 5 0.15
15 5 0.15
16 2 0.06
19 2 0.06
20 5 0.15
21 14 0.42
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (21 bp):
AAAACCATTTACCAAACTTTG
Found at i:16267 original size:19 final size:20
Alignment explanation
Indices: 16243--16296 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
16233 AGATATAGCA
*
16243 AAAAAAAGACATAAAAA-AG
1 AAAAAAAGACAGAAAAACAG
*
16262 AAAAAAA-ATAGAAAAACAG
1 AAAAAAAGACAGAAAAACAG
*
16281 AAAAAAAGAAAGAAAA
1 AAAAAAAGACAGAAAA
16297 TCAATCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.23
19 16 0.53
20 7 0.23
ACGTcount: A:0.81, C:0.04, G:0.11, T:0.04
Consensus pattern (20 bp):
AAAAAAAGACAGAAAAACAG
Found at i:16922 original size:15 final size:16
Alignment explanation
Indices: 16895--16927 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
16885 TTCTTCATCA
*
16895 AATCAATGAACACCAG
1 AATCAATGAACACAAG
16911 AATCAA-GAACACAAG
1 AATCAATGAACACAAG
16926 AA
1 AA
16928 GCCAACCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
AATCAATGAACACAAG
Found at i:19404 original size:42 final size:42
Alignment explanation
Indices: 19344--19445 Score: 186
Period size: 42 Copynumber: 2.4 Consensus size: 42
19334 TAATAGAGAG
*
19344 TTCATAATGAGAAGAACTCATCCAACGAGGGGGGAGAATAAA
1 TTCATAATGAGAAGAACTCATCCAACGAGGGGGGAGAAGAAA
*
19386 TTCATAATGAGAATAACTCATCCAACGAGGGGGGAGAAGAAA
1 TTCATAATGAGAAGAACTCATCCAACGAGGGGGGAGAAGAAA
19428 TTCATAATGAGAAGAACT
1 TTCATAATGAGAAGAACT
19446 TGTTCAACCT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.43, C:0.14, G:0.25, T:0.19
Consensus pattern (42 bp):
TTCATAATGAGAAGAACTCATCCAACGAGGGGGGAGAAGAAA
Found at i:19608 original size:92 final size:91
Alignment explanation
Indices: 19386--19641 Score: 404
Period size: 92 Copynumber: 2.8 Consensus size: 91
19376 GGAGAATAAA
*
19386 TTCATAATGAGAATAACTCATCCAACGAGGGGGGAGAAGAAATTCATAATGAGAAGAACTTGTTC
1 TTCATAATGAGAATAACTCATCCAACGA---GGGAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
19451 AACCTTGGCTCAACATTTCCAGTGGAGAG
63 AACCTTTGCTCAACATTTCCAGTGGAGAG
* *
19480 TTCATATTGAGAATAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAAAAGAACTTGTTCAAC
1 TTCATAATGAGAATAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* *
19545 CTTTTCTCAACATTTTTCAGTGGAGAG
66 CTTTGCTCAACA-TTTCCAGTGGAGAG
* *
19572 TTCATAATGAGAATAGCTCATACAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
1 TTCATAATGAGAATAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
19637 CTTTG
66 CTTTG
19642 TTCGATTCCA
Statistics
Matches: 150, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
91 45 0.30
92 78 0.52
94 27 0.18
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (91 bp):
TTCATAATGAGAATAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
CTTTGCTCAACATTTCCAGTGGAGAG
Found at i:19818 original size:118 final size:118
Alignment explanation
Indices: 19551--20134 Score: 823
Period size: 118 Copynumber: 5.0 Consensus size: 118
19541 CAACCTTTTC
* * *
19551 TCAACATTTTTCAGTGGAGAGTTCATAATGAGAATAGCTCATACAACGAGGGAGAAGAAGTTCAT
1 TCAACA-TTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCAACGAGGGAGAAGAAGTTCAT
*
19616 AATGAGAAGAACTTGTTCAACC-TTTGTTCGATTCCATCATA-AAAGGAGGTGGA
65 AATGAGAAGAACTTGTTCAACCTTTTGTTCGATTCCATCACAGAAA-GAGGTGGA
* *
19669 TCAATATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCAACGAGGGAGAAGAAGTTCATA
* *
19734 ATGAGGAGAACTTGTTCAACATTTTGTTCGATTCCATCACA-AAAGGAGGTGGA
66 ATGAGAAGAACTTGTTCAACCTTTTGTTCGATTCCATCACAGAAA-GAGGTGGA
* *
19787 TCAATATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
19852 ATGAGGAGAACTTGTTCAACCTTTTGTTCGATTCCATCACAGAAAGAGGTGGA
66 ATGAGAAGAACTTGTTCAACCTTTTGTTCGATTCCATCACAGAAAGAGGTGGA
* * **
19905 TCAACATTTCCAGTGGAAAGTTCATAAT--GAATAACTCATTCGGCGAGGGA-AA-AAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCAACGAGGGAGAAGAAGTTCATA
19966 ATGAGAAGAACTTGTTGTTCAACCTTTTGTTCGATTCCATCACAGAAAGAGGTGGA
66 ATGAGAAGAAC---TTGTTCAACCTTTTGTTCGATTCCATCACAGAAAGAGGTGGA
* * **
20022 TCAACATTTCCAGTGGAAAGTTCATAATGAGAATAACTCATTCGGCGAGGGA-AA-AAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCAACGAGGGAGAAGAAGTTCATA
* * * *
20085 ATGAGAAGAACTTGTACAACC--TTGGT-GATTCCATCACAGAATGAAGTGGA
66 ATGAGAAGAACTTGTTCAACCTTTTGTTCGATTCCATCACAGAAAGAGGTGGA
20135 CTGACATCGC
Statistics
Matches: 439, Mismatches: 20, Indels: 19
0.92 0.04 0.04
Matches are distributed among these distances:
113 22 0.05
114 23 0.05
115 2 0.00
116 27 0.06
117 144 0.33
118 174 0.40
119 47 0.11
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (118 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCAACGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGTTCGATTCCATCACAGAAAGAGGTGGA
Found at i:19986 original size:235 final size:234
Alignment explanation
Indices: 19551--20134 Score: 826
Period size: 235 Copynumber: 2.5 Consensus size: 234
19541 CAACCTTTTC
* *
19551 TCAACATTTTTCAGTGGAGAGTTCATAATGAGAATAGCTCATACAACGAGGGAGAAGAAGTTCAT
1 TCAACA-TTTCCAGTGGAGAGTTCATAATGAGAATAACTCATACAACGAGGGAGAAGAAGTTCAT
* *
19616 AATGAGAAGAACTTGTTCAACCTTTGTTCGATTCCATCATA-AAAGGAGGTGGATCAATATTTCC
65 AATGAGAAGAACTTGTTCAACCTTTGTTCGATTCCATCACAGAAA-GAGGTGGATCAACATTTCC
* *
19680 AGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGGAGAAC
129 AGTGGAAAGTTCATAAT-AGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAAC
19745 TTGTTCAACATTTTGTTCGATTCCATCACA-AAAGGAGGTGGA
193 TTGTTCAACATTTTGTTCGATTCCATCACAGAAA-GAGGTGGA
* * *
19787 TCAATATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATACAACGAGGGAGAAGAAGTTCATA
*
19852 ATGAGGAGAACTTGTTCAACCTTTTGTTCGATTCCATCACAGAAAGAGGTGGATCAACATTTCCA
66 ATGAGAAGAACTTGTTCAACC-TTTGTTCGATTCCATCACAGAAAGAGGTGGATCAACATTTCCA
* * **
19917 GTGGAAAGTTCATAAT-GAATAACTCATTCGGCGAGGGA-AA-AAGTTCATAATGAGAAGAACTT
130 GTGGAAAGTTCATAATAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAAC--
*
19979 GTTGTTCAACCTTTTGTTCGATTCCATCACAGAAAGAGGTGGA
193 -TTGTTCAACATTTTGTTCGATTCCATCACAGAAAGAGGTGGA
* * **
20022 TCAACATTTCCAGTGGAAAGTTCATAATGAGAATAACTCATTCGGCGAGGGA-AA-AAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATACAACGAGGGAGAAGAAGTTCATA
* * * *
20085 ATGAGAAGAACTTGTACAACC-TTGGT-GATTCCATCACAGAATGAAGTGGA
66 ATGAGAAGAACTTGTTCAACCTTTGTTCGATTCCATCACAGAAAGAGGTGGA
20135 CTGACATCGC
Statistics
Matches: 316, Mismatches: 26, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
230 22 0.07
231 4 0.01
232 19 0.06
233 30 0.09
234 20 0.06
235 158 0.50
236 60 0.19
237 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (234 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATACAACGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTGTTCGATTCCATCACAGAAAGAGGTGGATCAACATTTCCAG
TGGAAAGTTCATAATAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
TTCAACATTTTGTTCGATTCCATCACAGAAAGAGGTGGA
Found at i:21512 original size:22 final size:22
Alignment explanation
Indices: 21469--21526 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
21459 AATTAGGTCC
* *
21469 TTATTTTATGTTTATTTCATTT
1 TTATTCTATGTTTATTACATTT
21491 TTATTCTATGTTT-TTACTATTT
1 TTATTCTATGTTTATTAC-ATTT
21513 TT-TT-TAT-TTTATTA
1 TTATTCTATGTTTATTA
21527 TTTGTTAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 3 0.09
20 6 0.19
21 5 0.16
22 18 0.56
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.72
Consensus pattern (22 bp):
TTATTCTATGTTTATTACATTT
Found at i:24488 original size:23 final size:23
Alignment explanation
Indices: 24457--24522 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
24447 TGTACTTTTG
*
24457 TGCTGAATCATTCAACACTGTTT
1 TGCTTAATCATTCAACACTGTTT
24480 TGCTTAATCATTCAACACTGTTT
1 TGCTTAATCATTCAACACTGTTT
*
24503 TGCTTAATCATTCAGCACTG
1 TGCTTAATCATTCAACACTG
24523 AATCATTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (23 bp):
TGCTTAATCATTCAACACTGTTT
Found at i:26857 original size:41 final size:41
Alignment explanation
Indices: 26807--26916 Score: 129
Period size: 40 Copynumber: 2.7 Consensus size: 41
26797 TATTTTTAAA
*
26807 AATAATTAAAATAATATATTTCTAAT-TA-TTTATTATATTT
1 AATAATTAAAATAATATATTT-TAATATATTTTATTATATGT
* * *
26847 AA-ACGATTAAATTAATCTATTTTATTATATTTTATTATATGT
1 AATA--ATTAAAATAATATATTTTAATATATTTTATTATATGT
26889 AATAATT-AAATAATATATTTTAATATAT
1 AATAATTAAAATAATATATTTTAATATAT
26917 ACATATAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
39 1 0.02
40 23 0.40
41 20 0.34
42 13 0.22
43 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.51
Consensus pattern (41 bp):
AATAATTAAAATAATATATTTTAATATATTTTATTATATGT
Found at i:26937 original size:40 final size:37
Alignment explanation
Indices: 26896--26970 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 37
26886 TGTAATAATT
*
26896 AAATAATATATTTTAATATATACATATAATAAAAATTATTA
1 AAATAATA-ATTATAATATAT--ATA-AATAAAAATTATTA
*
26937 AAATATTAATTATAATATATATAAATAAAAATTA
1 AAATAATAATTATAATATATATAAATAAAAATTA
26971 ACCGAATTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 11 0.34
38 3 0.09
40 11 0.34
41 7 0.22
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (37 bp):
AAATAATAATTATAATATATATAAATAAAAATTATTA
Found at i:38414 original size:18 final size:18
Alignment explanation
Indices: 38391--38433 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
38381 GATCCCTGAT
* *
38391 CGGTCAGTCTTGGGGACG
1 CGGTCAGTCTAGAGGACG
38409 CGGTCAGTCTAGAGGACG
1 CGGTCAGTCTAGAGGACG
*
38427 GGGTCAG
1 CGGTCAG
38434 AGTTCAAATC
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:0.16, C:0.21, G:0.44, T:0.19
Consensus pattern (18 bp):
CGGTCAGTCTAGAGGACG
Found at i:41411 original size:18 final size:19
Alignment explanation
Indices: 41388--41423 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
41378 ATTCAACCTT
*
41388 ATAAAATCTCTAA-AAAAA
1 ATAAAATCCCTAACAAAAA
41406 ATAAAATCCCTAACAAAA
1 ATAAAATCCCTAACAAAA
41424 TTTCATCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.64, C:0.17, G:0.00, T:0.19
Consensus pattern (19 bp):
ATAAAATCCCTAACAAAAA
Found at i:48942 original size:2 final size:2
Alignment explanation
Indices: 48935--48985 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
48925 TTAAATTCAA
48935 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
48977 AT AT AT AT A
1 AT AT AT AT A
48986 ACTTTCATTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50261 original size:32 final size:32
Alignment explanation
Indices: 50223--50378 Score: 118
Period size: 32 Copynumber: 4.9 Consensus size: 32
50213 TAGCTCTGTT
*
50223 TATGCATTATCTAAATACAATATTGACTTTAC
1 TATGCATTATCTAAATGCAATATTGACTTTAC
* * *
50255 TATGCATTATATAAATGCAATACTGA-TTCTGC
1 TATGCATTATCTAAATGCAATATTGACTT-TAC
* * * * * * *
50287 AATGTATTATTTGAATGCTATATTGACTCTGC
1 TATGCATTATCTAAATGCAATATTGACTTTAC
* * *
50319 TATGCATTACCTGAAA-GGAATATTGACTGTAC
1 TATGCATTATCT-AAATGCAATATTGACTTTAC
* * * *
50351 TGTGCATTATTTGAATGCAATACTGACT
1 TATGCATTATCTAAATGCAATATTGACT
50379 CTATTGTGTA
Statistics
Matches: 94, Mismatches: 26, Indels: 8
0.73 0.20 0.06
Matches are distributed among these distances:
31 4 0.04
32 87 0.93
33 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (32 bp):
TATGCATTATCTAAATGCAATATTGACTTTAC
Found at i:51452 original size:21 final size:21
Alignment explanation
Indices: 51426--51480 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
51416 ATCTACTAGT
* * *
51426 AGTATCGATACTTTGGGGTTA
1 AGTATCGATACTCTAGGGTCA
51447 AGTATCGATACTCTAGGGTCA
1 AGTATCGATACTCTAGGGTCA
*
51468 AGTATTGATACTC
1 AGTATCGATACTC
51481 CTATGAGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (21 bp):
AGTATCGATACTCTAGGGTCA
Found at i:55362 original size:10 final size:11
Alignment explanation
Indices: 55342--55397 Score: 78
Period size: 12 Copynumber: 5.0 Consensus size: 11
55332 AACCTACATT
*
55342 TATAAATTATA
1 TATATATTATA
55353 T-TATATTATA
1 TATATATTATA
55363 TATATATATATA
1 TATATAT-TATA
55375 TATATATATATA
1 TATATAT-TATA
55387 TATATATTATA
1 TATATATTATA
55398 AGTATTATTA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
10 9 0.21
11 10 0.24
12 23 0.55
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TATATATTATA
Found at i:55366 original size:2 final size:2
Alignment explanation
Indices: 55349--55397 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
55339 ATTTATAAAT
55349 TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55389 TA TA T- TA TA
1 TA TA TA TA TA
55398 AGTATTATTA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:56595 original size:12 final size:11
Alignment explanation
Indices: 56578--56617 Score: 53
Period size: 12 Copynumber: 3.4 Consensus size: 11
56568 TATATACGTG
56578 TATTATTATTAT
1 TATTATTATT-T
56590 TATTATTATTT
1 TATTATTATTT
56601 TATTTATTTATTT
1 TA-TTA-TTATTT
56614 TATT
1 TATT
56618 TATATGCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.12
12 15 0.58
13 8 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTATTATTT
Found at i:56613 original size:13 final size:13
Alignment explanation
Indices: 56583--56620 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
56573 ACGTGTATTA
56583 TTATTATTA-TTA-
1 TTATT-TTATTTAT
56595 TTATTTTATTTAT
1 TTATTTTATTTAT
56608 TTATTTTATTTAT
1 TTATTTTATTTAT
56621 ATGCTATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 3 0.12
12 8 0.33
13 13 0.54
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTTTATTTAT
Found at i:65166 original size:21 final size:20
Alignment explanation
Indices: 65142--65180 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
65132 ATTCCCCTGT
*
65142 GGGGGGAATCGGTTCCCTCAA
1 GGGGGG-ATCGATTCCCTCAA
65163 GGGGGGATCGATTCCCTC
1 GGGGGGATCGATTCCCTC
65181 TGCACCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.15, C:0.26, G:0.38, T:0.21
Consensus pattern (20 bp):
GGGGGGATCGATTCCCTCAA
Done.