Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005174.1 Hibiscus syriacus cultivar Beakdansim tig00011675_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: 91287
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:4037 original size:11 final size:11
Alignment explanation
Indices: 4021--4052 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
4011 TAACCCTAAT
4021 TAAATTAAGGG
1 TAAATTAAGGG
4032 TAAATTAAGGG
1 TAAATTAAGGG
*
4043 TAGATTAAGG
1 TAAATTAAGG
4053 CTTTCTCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.28, T:0.28
Consensus pattern (11 bp):
TAAATTAAGGG
Found at i:4820 original size:26 final size:25
Alignment explanation
Indices: 4782--4841 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 25
4772 TTAGTCTTGC
* * *
4782 AAATTCAAATAAAAACAAATTAATT
1 AAATTAAAATAAAAACAAAATAAAT
*
4807 AAATTAAAATTAAAAATAAAATAAAT
1 AAATTAAAA-TAAAAACAAAATAAAT
*
4833 AAAATAAAA
1 AAATTAAAA
4842 GGTTAATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 8 0.28
26 21 0.72
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (25 bp):
AAATTAAAATAAAAACAAAATAAAT
Found at i:6473 original size:21 final size:21
Alignment explanation
Indices: 6404--6473 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
6394 CTCGAAAATG
*
6404 TTGACCCAACTCCTTATGTGA
1 TTGATCCAACTCCTTATGTGA
* * *
6425 TGGAAT-CAA-TCATAATGTTGA
1 TTG-ATCCAACTCCTTATG-TGA
6446 TGCTGATCCAACTCCTTATGTGA
1 T--TGATCCAACTCCTTATGTGA
6469 TTGAT
1 TTGAT
6474 GAGACAAGGT
Statistics
Matches: 36, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
20 6 0.17
21 13 0.36
22 3 0.08
23 8 0.22
24 6 0.17
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (21 bp):
TTGATCCAACTCCTTATGTGA
Found at i:7832 original size:29 final size:28
Alignment explanation
Indices: 7800--7895 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 28
7790 TTTTCCTTAT
*
7800 TTTTTCTTTTTCCTTTTTTCTCATTTCTCT
1 TTTTTCTTTTT-CTTTTTTCT-ATTTCTCA
*
7830 TTTTTCTTTTT-TCTTTTTCATTTTTCTCA
1 TTTTTCTTTTTCT-TTTTTC-TATTTCTCA
* *
7859 TTTTTCTTTTTTTTCTTTTCTTATTTTTC-
1 TTTTTCTTTTTCTT-TTTTC-TATTTCTCA
7888 TTTTTCTT
1 TTTTTCTT
7896 ATTAGCATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
28 1 0.02
29 32 0.56
30 24 0.42
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (28 bp):
TTTTTCTTTTTCTTTTTTCTATTTCTCA
Found at i:7862 original size:23 final size:23
Alignment explanation
Indices: 7800--7892 Score: 81
Period size: 23 Copynumber: 4.2 Consensus size: 23
7790 TTTTCCTTAT
*
7800 TTTTTCTTTTTC-CTTTTTTCTC
1 TTTTTCTTTTTCTCATTTTTCTC
*
7822 ATTTCTCTTTTT-TC-TTTTT-TC
1 -TTTTTCTTTTTCTCATTTTTCTC
7843 TTTTTCATTTTTCTCATTTTTCT-
1 TTTTTC-TTTTTCTCATTTTTCTC
* *
7866 TTTTTTTCTTTTCTTATTTTTCT-
1 TTTTTCT-TTTTCTCATTTTTCTC
7889 TTTT
1 TTTT
7893 CTTATTAGCA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
20 5 0.08
21 7 0.12
22 8 0.13
23 39 0.65
24 1 0.02
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTCTTTTTCTCATTTTTCTC
Found at i:7870 original size:7 final size:7
Alignment explanation
Indices: 7799--7892 Score: 84
Period size: 7 Copynumber: 12.7 Consensus size: 7
7789 CTTTTCCTTA
7799 TTTTTTC
1 TTTTTTC
*
7806 TTTTTCC
1 TTTTTTC
7813 TTTTTTC
1 TTTTTTC
*
7820 TCATTTCTC
1 T--TTTTTC
7829 TTTTTTC
1 TTTTTTC
7836 TTTTTTC
1 TTTTTTC
7843 -TTTTTC
1 TTTTTTC
7849 ATTTTTCTC
1 -TTTTT-TC
*
7858 ATTTTTC
1 TTTTTTC
7865 TTTTTT-
1 TTTTTTC
7871 TTCTTTTC
1 TT-TTTTC
7879 TTATTTTTC
1 -T-TTTTTC
7888 TTTTT
1 TTTTT
7893 CTTATTAGCA
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
6 8 0.11
7 40 0.56
8 9 0.12
9 14 0.19
10 1 0.01
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:10077 original size:23 final size:23
Alignment explanation
Indices: 10033--10081 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
10023 ATAAAGAACC
*
10033 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
10056 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
10079 AAA
1 AAA
10082 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:11232 original size:7 final size:7
Alignment explanation
Indices: 11220--11254 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
11210 TAGTACACAT
11220 TTTTTTC
1 TTTTTTC
11227 TTTTTTC
1 TTTTTTC
*
11234 TTTTCTTT
1 TTTT-TTC
11242 TTTTTTC
1 TTTTTTC
11249 TTTTTT
1 TTTTTT
11255 TCACTTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:11239 original size:12 final size:11
Alignment explanation
Indices: 11219--11255 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
11209 TTAGTACACA
11219 TTTTTTTCTTT
1 TTTTTTTCTTT
11230 TTTCTTTTC-TT
1 TTT-TTTTCTTT
11241 TTTTTTTCTTT
1 TTTTTTTCTTT
11252 TTTT
1 TTTT
11256 CACTTTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.21
11 14 0.58
12 5 0.21
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:11253 original size:10 final size:10
Alignment explanation
Indices: 11219--11255 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
11209 TTAGTACACA
11219 TTTTTTTCTTT
1 TTTTTTTC-TT
11230 TTTCTTTTCTT
1 TTT-TTTTCTT
11241 TTTTTTTCTT
1 TTTTTTTCTT
11251 TTTTT
1 TTTTT
11256 CACTTTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 12 0.48
11 8 0.32
12 5 0.20
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:15724 original size:23 final size:23
Alignment explanation
Indices: 15680--15728 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
15670 ATAAAGAACC
*
15680 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
15703 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
15726 AAA
1 AAA
15729 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:18445 original size:47 final size:47
Alignment explanation
Indices: 18376--18469 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 47
18366 TAAAAAGAAA
*
18376 TATCCTCAAATTAACATCGAAATTAAATCATACAAATCCAAACAAAT
1 TATCCTCAAATTAACATCGAAATCAAATCATACAAATCCAAACAAAT
* * * *
18423 TATCCTCAAGA-TAACGTTGAAATCAAATCATACACATTCAAACAAAT
1 TATCCTCAA-ATTAACATCGAAATCAAATCATACAAATCCAAACAAAT
18470 CTTAGACAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
47 40 0.98
48 1 0.02
ACGTcount: A:0.49, C:0.21, G:0.04, T:0.26
Consensus pattern (47 bp):
TATCCTCAAATTAACATCGAAATCAAATCATACAAATCCAAACAAAT
Found at i:29299 original size:20 final size:22
Alignment explanation
Indices: 29274--29313 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
29264 AGAAATATAA
29274 ATAATATA-TATA-CATAAAAT
1 ATAATATACTATAGCATAAAAT
29294 ATAATATACTATAGCATAAA
1 ATAATATACTATAGCATAAA
29314 TAAATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (22 bp):
ATAATATACTATAGCATAAAAT
Found at i:29319 original size:20 final size:18
Alignment explanation
Indices: 29270--29319 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 18
29260 AAAAAGAAAT
29270 ATAAAT-AATATATATAC
1 ATAAATAAATATATATAC
29287 ATAAAATATAATATACTATAGC
1 AT-AAATA-AATATA-TATA-C
29309 ATAAATAAATA
1 ATAAATAAATA
29320 AATAAAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 2 0.07
18 4 0.14
20 10 0.36
21 9 0.32
22 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (18 bp):
ATAAATAAATATATATAC
Found at i:32362 original size:16 final size:13
Alignment explanation
Indices: 32331--32359 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
32321 ATCTTTATGG
32331 TCAATTTATTATA
1 TCAATTTATTATA
32344 TCAATTTATTATA
1 TCAATTTATTATA
32357 TCA
1 TCA
32360 TCACAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (13 bp):
TCAATTTATTATA
Found at i:36537 original size:22 final size:22
Alignment explanation
Indices: 36470--36538 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
36460 GAAGATCAAA
*
36470 AGTTGAATAATTAAAACCATAAT
1 AGTTGAATAATTAAAA-CAAAAT
* * *
36493 A-TTAGATATGATTTCAAATAAAAT
1 AGTT-GA-AT-AATTAAAACAAAAT
36517 AGTTGAATAATTAAAACAAAAT
1 AGTTGAATAATTAAAACAAAAT
36539 CACGAAAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 9
0.69 0.14 0.18
Matches are distributed among these distances:
22 13 0.37
23 5 0.14
24 9 0.26
25 8 0.23
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.32
Consensus pattern (22 bp):
AGTTGAATAATTAAAACAAAAT
Found at i:39547 original size:29 final size:29
Alignment explanation
Indices: 39505--39562 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
39495 TCAGCTTTTC
39505 TTATGGACTTGGATGTGGCCCTCAAGAAA
1 TTATGGACTTGGATGTGGCCCTCAAGAAA
*
39534 TTATGGGCTTGGATGTGGCCCTCAAGAAA
1 TTATGGACTTGGATGTGGCCCTCAAGAAA
39563 GAGTTGGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (29 bp):
TTATGGACTTGGATGTGGCCCTCAAGAAA
Found at i:43243 original size:20 final size:20
Alignment explanation
Indices: 43220--43267 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
43210 CTAGGGTATT
43220 GATACTACAACTAGAGTACC
1 GATACTACAACTAGAGTACC
*
43240 GATACTACAACTAGAGTATC
1 GATACTACAACTAGAGTACC
43260 GATACTAC
1 GATACTAC
43268 CCACCTCAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
GATACTACAACTAGAGTACC
Found at i:51373 original size:20 final size:20
Alignment explanation
Indices: 51345--51393 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
51335 TTTTTTGACT
51345 TTTTC-TTTTTC-CTTTTCA
1 TTTTCTTTTTTCACTTTTCA
* *
51363 TTTTCATTTTTTCATTTTTCT
1 TTTTC-TTTTTTCACTTTTCA
51384 TTTTCTTTTT
1 TTTTCTTTTT
51394 CCAATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 5 0.19
20 11 0.42
21 10 0.38
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTTTCACTTTTCA
Found at i:51392 original size:5 final size:6
Alignment explanation
Indices: 51343--51394 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
51333 ATTTTTTTGA
* *
51343 CTTTTT CTTTTT CCTTTT CATTTT CATTTTTT CATTTTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT C--TTTTT C-TTTTT CTTTTT CTTTTT
51394 C
1 C
51395 CAATAAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
6 29 0.73
7 6 0.15
8 5 0.12
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (6 bp):
CTTTTT
Found at i:54344 original size:21 final size:21
Alignment explanation
Indices: 54318--54373 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
54308 CTGACTATCA
*
54318 CATTGCGATTTTCCAAATTTG
1 CATTGCGATTTTCCAAATTCG
54339 CATTGCGATTTTCCAAATTCG
1 CATTGCGATTTTCCAAATTCG
*
54360 CGTTGCGATTTTCC
1 CATTGCGATTTTCC
54374 GACTATCGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (21 bp):
CATTGCGATTTTCCAAATTCG
Found at i:54421 original size:20 final size:19
Alignment explanation
Indices: 54374--54443 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
54364 GCGATTTTCC
54374 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCG-ATAT
*
54394 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGA-TAT
* *
54414 GACTATCGCAACGCGATCT
1 GACTATCGCAATGCGATAT
*
54433 GACTGTCGCAA
1 GACTATCGCAA
54444 CACTGAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
19 14 0.33
20 27 0.64
21 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.24
Consensus pattern (19 bp):
GACTATCGCAATGCGATAT
Found at i:55265 original size:24 final size:24
Alignment explanation
Indices: 55237--55286 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
55227 TACTAGTCGG
55237 TATTCGAAATTTGATCTTGGTCAA
1 TATTCGAAATTTGATCTTGGTCAA
* *
55261 TATTCGGACTTTGATCTTGGTCAA
1 TATTCGAAATTTGATCTTGGTCAA
55285 TA
1 TA
55287 CTCGGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (24 bp):
TATTCGAAATTTGATCTTGGTCAA
Found at i:55291 original size:24 final size:24
Alignment explanation
Indices: 55246--55299 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
55236 GTATTCGAAA
*
55246 TTTGATCTTGGTCAATATTCGGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
55270 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
55294 TTTGAT
1 TTTGAT
55300 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.44
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:55518 original size:14 final size:14
Alignment explanation
Indices: 55489--55526 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
55479 AGAAAAAGAA
*
55489 GAAGAAGAAATCCCC
1 GAAGAA-AATTCCCC
55504 GAAGAAAATTCCCC
1 GAAGAAAATTCCCC
55518 GAAGAAAAT
1 GAAGAAAAT
55527 GCCACGGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.11
Consensus pattern (14 bp):
GAAGAAAATTCCCC
Found at i:57585 original size:18 final size:18
Alignment explanation
Indices: 57562--57596 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
57552 AGAAAAAGGC
*
57562 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
57580 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
57597 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:57908 original size:140 final size:140
Alignment explanation
Indices: 57656--57925 Score: 504
Period size: 140 Copynumber: 1.9 Consensus size: 140
57646 AAACGTTGTA
* *
57656 TTATGTGTAAACTTTTAACATTTTTAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGCAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
57721 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTTACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACAAATTCATTTGAATATCGCAACGCGAATTTGACTAT
57786 TATGTGTATT
131 TATGTGTATT
57796 TTATGTGCAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGCAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
57861 TGATATGTTCAGTTGTTATCACTTATTACAAATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACAAATTCATTTGAATATCGCAACGCGAATTTGACTAT
57926 CGTAATGCAA
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 126 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TTATGTGCAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACAAATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:57921 original size:20 final size:20
Alignment explanation
Indices: 57896--58218 Score: 212
Period size: 20 Copynumber: 17.4 Consensus size: 20
57886 TTACAAATTC
*
57896 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
57916 ATTTGACTATCGTAATGCAA
1 ATTTGACTATCGCAACGCGA
* *
57936 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
57955 A----A-AATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
*
57970 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
57990 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
58009 A----A-AATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
*
58024 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
58044 ATTTGATTATCGCAACG-GCT
1 ATTTGACTATCGCAACGCG-A
*
58064 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
58084 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
58098 ATTTGACTATCGCAATGAGA
1 ATTTGACTATCGCAACGCGA
* *
58118 ATTTGAGTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
58138 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
*
58158 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
58178 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
58192 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
58212 A-TTGACT
1 ATTTGACT
58219 TTCGTGTTGC
Statistics
Matches: 232, Mismatches: 45, Indels: 53
0.70 0.14 0.16
Matches are distributed among these distances:
14 40 0.17
15 6 0.03
16 2 0.01
18 2 0.01
19 11 0.05
20 170 0.73
21 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:58001 original size:54 final size:54
Alignment explanation
Indices: 57904--58214 Score: 217
Period size: 54 Copynumber: 5.6 Consensus size: 54
57894 TCATTTGAAT
* * * * *
57904 ATCGCAACGCGAATTTGACTATCGTAATGCAAATTTGATTATCGCAACTCAAAA
1 ATCGCAACGAGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCAAAA
* * *
57958 ATCGCAACGAGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAA
1 ATCGCAACGAGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCAAAA
* **
58012 ATCGCAACGCA-AATTTGTCTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACT
1 ATCGCAACG-AGAATTTGACTATCGCAACGCGAATTTGATTATCGCAAC-GC-A----AAA
* *
58072 ATCGCAACGAGAA----A--ATCGCAACGCGAATTTGACTATCGCAATG-AGAATTTGA
1 ATCGCAACGAGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCA-AA----A
* * * * * *
58124 GTATCACAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACG-AGAAA
1 --ATCGCAACGAGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCA-AAA
* * * *
58180 ATCGCAAAGCGTATTAGACTATCGCAACGCGAATT
1 ATCGCAACGAGAATTTGACTATCGCAACGCGAATT
58215 GACTTTCGTG
Statistics
Matches: 206, Mismatches: 31, Indels: 40
0.74 0.11 0.14
Matches are distributed among these distances:
48 2 0.01
51 1 0.00
53 1 0.00
54 153 0.74
55 3 0.01
56 2 0.01
58 1 0.00
59 1 0.00
60 42 0.20
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (54 bp):
ATCGCAACGAGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGCAAAA
Found at i:58017 original size:14 final size:14
Alignment explanation
Indices: 57998--58024 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
57988 GAATATGACT
57998 ATCGCAACGCAAAA
1 ATCGCAACGCAAAA
58012 ATCGCAACGCAAA
1 ATCGCAACGCAAA
58025 TTTGTCTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
ATCGCAACGCAAAA
Found at i:58036 original size:74 final size:73
Alignment explanation
Indices: 57958--58154 Score: 252
Period size: 74 Copynumber: 2.7 Consensus size: 73
57948 CAACTCAAAA
*
57958 ATCGCAACGAGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCA-AAAATCGCAACGC
1 ATCGCAACGAGAATTTGACTATCGCAAC-CGAATTTGACTATCGCAACG-AGAAAATCGCAACGC
*
58022 AAATTTGTCT
64 AAATTTGACT
* * * * *
58032 ATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGCAACGAGAAAATCGCAACGCG
1 ATCGCAACGAGAATTTGACTATCGCAACCG-AATTTGACTATCGCAACGAGAAAATCGCAACGCA
58097 AATTTGACT
65 AATTTGACT
* * * *
58106 ATCGCAATGAGAATTTGAGTATCACAACGCGAATTTGATTATCGCAACG
1 ATCGCAACGAGAATTTGACTATCGCAAC-CGAATTTGACTATCGCAACG
58155 GGTATTTGAC
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
73 2 0.02
74 103 0.97
75 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (73 bp):
ATCGCAACGAGAATTTGACTATCGCAACCGAATTTGACTATCGCAACGAGAAAATCGCAACGCAA
ATTTGACT
Found at i:58068 original size:94 final size:94
Alignment explanation
Indices: 57970--58186 Score: 253
Period size: 94 Copynumber: 2.3 Consensus size: 94
57960 CGCAACGAGA
* * *
57970 ATTTGACTATCGCAAC-ACGAATAT-GACTATCGC-AACGCAAAAATCGCAACGCA-AATTTGTC
1 ATTTGACTATCGCAACGA-GAAAATCG-C-AACGCGAACGCAAAAATCGCAACG-AGAATTTGAC
*
58031 TATCGCAACGCGAATTTGATTATCGCAACGGCT
62 TATCACAACGCGAATTTGATTATCGCAACGGCT
**** ** * *
58064 ATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACTATCGCAATGAGAATTTGAGTATC
1 ATTTGACTATCGCAACGAGAAAATCGCAACGCGAACGCAAAAATCGCAACGAGAATTTGACTATC
*
58129 ACAACGCGAATTTGATTATCGCAACGGGT
66 ACAACGCGAATTTGATTATCGCAACGGCT
58158 ATTTGACTATCGCAACGAGAAAATCGCAA
1 ATTTGACTATCGCAACGAGAAAATCGCAA
58187 AGCGTATTAG
Statistics
Matches: 106, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
93 5 0.05
94 99 0.93
95 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (94 bp):
ATTTGACTATCGCAACGAGAAAATCGCAACGCGAACGCAAAAATCGCAACGAGAATTTGACTATC
ACAACGCGAATTTGATTATCGCAACGGCT
Found at i:58118 original size:34 final size:34
Alignment explanation
Indices: 57978--58154 Score: 133
Period size: 34 Copynumber: 4.9 Consensus size: 34
57968 GAATTTGACT
* *
57978 ATCGCAACACGAATATGACTATCGCAACGCA-AAA
1 ATCGCAACGCGAATTTGACTATCGCAACG-AGAAA
* * *
58012 ATCGCAACGCAAATTTGTCTATCGCAACGCGAATTTGA
1 ATCGCAACGCGAATTTGACTATCGCAACGAGAA----A
*
58050 TTATCGCAACG-GCTATTTGACTATCGCAACGAGAAA
1 --ATCGCAACGCG-AATTTGACTATCGCAACGAGAAA
*
58086 ATCGCAACGCGAATTTGACTATCGCAATGAGAATTTGA
1 ATCGCAACGCGAATTTGACTATCGCAACGAGAA----A
* *
58124 GTATCACAACGCGAATTTGATTATCGCAACG
1 --ATCGCAACGCGAATTTGACTATCGCAACG
58155 GGTATTTGAC
Statistics
Matches: 114, Mismatches: 14, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
34 56 0.49
35 1 0.01
36 1 0.01
38 2 0.02
40 54 0.47
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGAGAAA
Found at i:58214 original size:94 final size:94
Alignment explanation
Indices: 58012--58218 Score: 317
Period size: 94 Copynumber: 2.2 Consensus size: 94
58002 CAACGCAAAA
* * *
58012 ATCGCAACGCAAATTTGTCTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGC
* *
58077 AACGAGAAAATCGCAACGCGAATTTGACT
66 AACGAGAAAATCGCAAAGCGAATTAGACT
* * * *
58106 ATCGCAATGAGAATTTGAGTATCACAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGC
1 ATCGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGC
*
58171 AACGAGAAAATCGCAAAGCGTATTAGACT
66 AACGAGAAAATCGCAAAGCGAATTAGACT
58200 ATCGCAACGCGAA-TTGACT
1 ATCGCAACGCGAATTTGACT
58219 TTCGTGTTGC
Statistics
Matches: 100, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
93 5 0.05
94 95 0.95
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.25
Consensus pattern (94 bp):
ATCGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGCAACGGCTATTTGACTATCGC
AACGAGAAAATCGCAAAGCGAATTAGACT
Found at i:58429 original size:14 final size:14
Alignment explanation
Indices: 58369--58430 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
58359 CACAAATAAG
*
58369 AATTATTTACACATC
1 AATT-TTTACAAATC
**
58384 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
58399 AACTTTTACAAATC
1 AATTTTTACAAATC
*
58413 AATTTTTATAAATC
1 AATTTTTACAAATC
58427 AATT
1 AATT
58431 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:59908 original size:21 final size:20
Alignment explanation
Indices: 59826--59925 Score: 58
Period size: 21 Copynumber: 4.8 Consensus size: 20
59816 AGAATGTTGG
* *
59826 GAGGGACCTCTTCAACGATGA
1 GAGGGGCCTCTTGAACGAT-A
* * *
59847 CAGTGGCCTCTTGAATTG-TA
1 GAGGGGCCTCTTGAA-CGATA
* **
59867 GGAGGGGACTCTTGAGGGATAA
1 -GAGGGGCCTCTTGAACGAT-A
*
59889 TAGGGGCCTCTTGAACGATA
1 GAGGGGCCTCTTGAACGATA
*
59909 GGGGAGGCCTCTTGAAC
1 GAGG-GGCCTCTTGAAC
59926 AATGACATGT
Statistics
Matches: 58, Mismatches: 16, Indels: 10
0.69 0.19 0.12
Matches are distributed among these distances:
20 5 0.09
21 51 0.88
22 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.23
Consensus pattern (20 bp):
GAGGGGCCTCTTGAACGATA
Found at i:60472 original size:20 final size:20
Alignment explanation
Indices: 60447--60492 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
60437 GTGATTCTTT
60447 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAATCATTTTCG
*
60467 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAATCATTTTCG
*
60487 AGTTGC
1 CGTTGC
60493 AAAAGTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAATCATTTTCG
Found at i:62424 original size:20 final size:20
Alignment explanation
Indices: 62401--62439 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
62391 TCTGAAACTT
*
62401 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
*
62421 AAAATCGTAACACGAAAAT
1 AAAATCGCAACACGAAAAT
62440 TCACAGGGTT
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:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:63071 original size:20 final size:20
Alignment explanation
Indices: 63041--63154 Score: 138
Period size: 20 Copynumber: 5.7 Consensus size: 20
63031 GCGCTTTGAA
*
63041 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
63061 CATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
63081 AATCGCGTTACGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
63101 AATCTCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
** *
63121 AATTACGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* *
63141 ACTCGCATTGCGAT
1 AATCGCGTTGCGAT
63155 TTACATATTC
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.27
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:64008 original size:51 final size:50
Alignment explanation
Indices: 63933--64032 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 50
63923 GATTGTTGAA
*
63933 CATCTAACATAGTTAGGTTGCATGAGGTATGTGTTGTTTTAAGTATTGTG
1 CATCTAACATAGTTAGGTTACATGAGGTATGTGTTGTTTTAAGTATTGTG
* * *
63983 CATCTTAACGTAGTTGGGTTACATGAGGTATGTGTTGTTTTAATTATTGT
1 CATC-TAACATAGTTAGGTTACATGAGGTATGTGTTGTTTTAAGTATTGT
64033 ACATTATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 4 0.09
51 41 0.91
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.44
Consensus pattern (50 bp):
CATCTAACATAGTTAGGTTACATGAGGTATGTGTTGTTTTAAGTATTGTG
Found at i:64140 original size:2 final size:2
Alignment explanation
Indices: 64135--64178 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
64125 TATATCGTTA
64135 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
64177 AT
1 AT
64179 TATTCTTGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64775 original size:67 final size:66
Alignment explanation
Indices: 64668--64798 Score: 208
Period size: 67 Copynumber: 2.0 Consensus size: 66
64658 TTAGGTTAAC
64668 CGACCTCACTGACAATAAAAATTTTAGGTCAACATCAAATGATCAATATATTAAAAAAAAAAATA
1 CGACCTCACTGACAATAAAAATTTTAGGTCAACATCAAATGATCAATATATTAAAAAAAAAAATA
64733 A
66 A
* * * * *
64734 CGACCTCACGTGATAATACAAATTTTAGGTCAACATCAAATGATCGATTTATTATAAAAAAAAAT
1 CGACCTCAC-TGACAATAAAAATTTTAGGTCAACATCAAATGATCAATATATTAAAAAAAAAAAT
64799 TAACCAATTG
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
66 9 0.15
67 50 0.85
ACGTcount: A:0.49, C:0.15, G:0.09, T:0.27
Consensus pattern (66 bp):
CGACCTCACTGACAATAAAAATTTTAGGTCAACATCAAATGATCAATATATTAAAAAAAAAAATA
A
Found at i:65138 original size:2 final size:2
Alignment explanation
Indices: 65131--65158 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
65121 CAAGATTCTA
65131 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
65159 CTTTTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76847 original size:20 final size:20
Alignment explanation
Indices: 76822--76879 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
76812 TATTTCCAAT
76822 CATCATCGTTCATCTCCGAC
1 CATCATCGTTCATCTCCGAC
76842 CATCATCGTTCATCTCCGAC
1 CATCATCGTTCATCTCCGAC
*
76862 CATCATCG-TCATCACCGA
1 CATCATCGTTCATCTCCGA
76880 ACGGTCACCC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 9 0.24
20 28 0.76
ACGTcount: A:0.22, C:0.40, G:0.10, T:0.28
Consensus pattern (20 bp):
CATCATCGTTCATCTCCGAC
Found at i:80836 original size:2 final size:2
Alignment explanation
Indices: 80829--80862 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
80819 TTTACCAATT
80829 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
80863 CCTGATCAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Done.