Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006518.1 Hibiscus syriacus cultivar Beakdansim tig00015873_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: 61787
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Found at i:1298 original size:25 final size:25
Alignment explanation
Indices: 1269--1354 Score: 136
Period size: 25 Copynumber: 3.4 Consensus size: 25
1259 CGGGATAACA
*
1269 TTAAGACAATCAATCACAATATAAT
1 TTAAGACAATCAATTACAATATAAT
*
1294 TTAAGACAATCAATTACAGTATAAT
1 TTAAGACAATCAATTACAATATAAT
1319 TTAAGACAATCAATTACAATATAAT
1 TTAAGACAATCAATTACAATATAAT
*
1344 TCAAGAACAAT
1 TTAAG-ACAAT
1355 GTGGTTTAGA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
25 51 0.91
26 5 0.09
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (25 bp):
TTAAGACAATCAATTACAATATAAT
Found at i:1366 original size:40 final size:40
Alignment explanation
Indices: 1318--1433 Score: 191
Period size: 40 Copynumber: 2.9 Consensus size: 40
1308 TACAGTATAA
*
1318 TTTAAGACAATCAATTACAATATAATTCAAGAACAATGTGG
1 TTTAAGACAATCAATCACAATATAATTCAAGAACAATGT-G
1359 TTT-AGACAATCAATCACAATATAATTCAAGAACAATGTG
1 TTTAAGACAATCAATCACAATATAATTCAAGAACAATGTG
*
1398 TTTAAGACAATCAATCACAATATAATTTAAG-ACAAT
1 TTTAAGACAATCAATCACAATATAATTCAAGAACAAT
1434 TAATTACAGT
Statistics
Matches: 72, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
39 9 0.12
40 60 0.83
41 3 0.04
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.29
Consensus pattern (40 bp):
TTTAAGACAATCAATCACAATATAATTCAAGAACAATGTG
Found at i:4159 original size:2 final size:2
Alignment explanation
Indices: 4152--4186 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4142 TAATTCATAA
4152 AT AT 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 AT AT A
4187 ACTTTTTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17124 original size:20 final size:21
Alignment explanation
Indices: 17071--17124 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 21
17061 ATACCGAAGT
*
17071 GGGTATCGGTACCATAGAAGAG
1 GGGTATCGATACCATAG-AGAG
** *
17093 AAGTATCAATACCATAG-GAG
1 GGGTATCGATACCATAGAGAG
17113 GGGTATCGATAC
1 GGGTATCGATAC
17125 TATTCAGTCT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
20 12 0.48
22 13 0.52
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.20
Consensus pattern (21 bp):
GGGTATCGATACCATAGAGAG
Found at i:17503 original size:54 final size:54
Alignment explanation
Indices: 17421--17992 Score: 851
Period size: 54 Copynumber: 10.6 Consensus size: 54
17411 GTTTAATGTA
*
17421 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGACAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
* *
17475 TATGTGTGCAACCTACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGTAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
* * ***
17529 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCATACTAATAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
*
17583 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGTCAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
* *
17637 TATGTGTGCAACTCACGTAATTCATAATGAGTTTGTGAATTACAGTATTGGCAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
* * *
17691 TATGTGTGCAACCTACGTAATTCATAATGAATTTGTGAATTATCGTATTGGCAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
*
17745 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACAGTATTGGCAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
* * *
17799 TATGTGTGCAACTCACGTAATTCATAATGAGTTTGTTAATTATCGTATTGGCAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
* * * *
17853 TATGTGTGCAACCCACGTAATTAATAATTAGTTTTTGAATTA-CGTA-TGACAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
* * * * *
17905 TATGTATGTAACCCACATAATTCATAATGAGTTTGTGAATTACCGTATCGGTAC
1 TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
* * *
17959 TATGTGTGCAAAACCACGGAATTTATAATGAGTT
1 TATGTGTGC-AACCCACGTAATTCATAATGAGTT
17993 GAAATAATCA
Statistics
Matches: 465, Mismatches: 50, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
52 41 0.09
53 8 0.02
54 396 0.85
55 20 0.04
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Consensus pattern (54 bp):
TATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAATTACCGTATTGGCAC
Found at i:20386 original size:26 final size:26
Alignment explanation
Indices: 20328--20380 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
20318 ATATTAATAC
* *
20328 TAAATAAT-TTTATATATTAATAAAT
1 TAAATAATAATTATATATCAATAAAT
*
20353 TAAATAATAATTATATATCATTAAAT
1 TAAATAATAATTATATATCAATAAAT
20379 TA
1 TA
20381 TTTAATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TAAATAATAATTATATATCAATAAAT
Found at i:21061 original size:17 final size:17
Alignment explanation
Indices: 21039--21091 Score: 106
Period size: 17 Copynumber: 3.1 Consensus size: 17
21029 TAGAGCCATA
21039 TATTATTAGATGATTGG
1 TATTATTAGATGATTGG
21056 TATTATTAGATGATTGG
1 TATTATTAGATGATTGG
21073 TATTATTAGATGATTGG
1 TATTATTAGATGATTGG
21090 TA
1 TA
21092 ACACTCTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (17 bp):
TATTATTAGATGATTGG
Found at i:24255 original size:22 final size:23
Alignment explanation
Indices: 24229--24282 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
24219 ATAAAAGAAT
*
24229 GTAAAAGATATTAATCT-AAGTAA
1 GTAAAAGATAGTAA-CTAAAGTAA
*
24252 -TAAAAGAAAGTAACTAAAGTAA
1 GTAAAAGATAGTAACTAAAGTAA
24274 GTAAAAGAT
1 GTAAAAGAT
24283 GAAAAGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 2 0.08
22 17 0.65
23 7 0.27
ACGTcount: A:0.57, C:0.04, G:0.15, T:0.24
Consensus pattern (23 bp):
GTAAAAGATAGTAACTAAAGTAA
Found at i:26067 original size:14 final size:14
Alignment explanation
Indices: 26034--26068 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
26024 TTGTTTCACT
*
26034 GAAAACGTTTTCCG
1 GAAAATGTTTTCCG
26048 GAAAATGTTTTCCG
1 GAAAATGTTTTCCG
*
26062 TAAAATG
1 GAAAATG
26069 AATTACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.31
Consensus pattern (14 bp):
GAAAATGTTTTCCG
Found at i:26250 original size:20 final size:20
Alignment explanation
Indices: 26227--26266 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
26217 TTTTTAAAAA
26227 TATTAAAATAATT-TTTTTAT
1 TATTAAAAT-ATTATTTTTAT
26247 TATTAAAATATTATTTTTAT
1 TATTAAAATATTATTTTTAT
26267 AATTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTAAAATATTATTTTTAT
Found at i:26409 original size:23 final size:23
Alignment explanation
Indices: 26360--26410 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
26350 GTGTTATATT
**
26360 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
26383 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
26406 ATATT
1 ATATT
26411 ATTAGTTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:26555 original size:23 final size:24
Alignment explanation
Indices: 26529--26580 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
26519 TTTATTATAT
26529 ATTATTA-AAATATAATATAATTG
1 ATTATTATAAATATAATATAATTG
* *
26552 ATTA-TATTATTATAATATAATTG
1 ATTATTATAAATATAATATAATTG
26575 ATTATT
1 ATTATT
26581 TTATTATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.08
23 22 0.88
24 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
ATTATTATAAATATAATATAATTG
Found at i:26584 original size:23 final size:23
Alignment explanation
Indices: 26539--26592 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
26529 ATTATTAAAA
26539 TATAATATAATTGATTATATTAT
1 TATAATATAATTGATTATATTAT
*
26562 TATAATATAATTGATTATTTTAT
1 TATAATATAATTGATTATATTAT
26585 TATAATAT
1 TATAATAT
26593 TAAAAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
TATAATATAATTGATTATATTAT
Found at i:26610 original size:22 final size:23
Alignment explanation
Indices: 26582--26628 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
26572 TTGATTATTT
26582 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
26604 TATTATATTATTATAAATATTAA
1 TATTATAATATTAAAAATATTAA
26627 TA
1 TA
26629 AATATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:26633 original size:22 final size:23
Alignment explanation
Indices: 26590--26644 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
26580 TTTATTATAA
* *
26590 TATTAAAAATA-TAATATTATAT
1 TATTATAAATATTAATATAATAT
26612 TATTATAAATATTAATA-AATAT
1 TATTATAAATATTAATATAATAT
*
26634 T-TTTTAAATAT
1 TATTATAAATAT
26645 ATTAATAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.31
22 15 0.52
23 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTATAAATATTAATATAATAT
Found at i:26658 original size:53 final size:53
Alignment explanation
Indices: 26542--26697 Score: 144
Period size: 53 Copynumber: 2.9 Consensus size: 53
26532 ATTAAAATAT
* * *
26542 AATATAATTGATTATATTATTATAATATAATTGATTATTTTATTATAATATTAAA
1 AATATAA-T-ATTATATTATTATAATATAATTAAATATTTTATTAAAATATTAAA
*
26597 AATATAATATTATATTATTATAAATATTAA-TAAATATTTT-TTAAATATATTAAT
1 AATATAATATTATATTATTAT-AATA-TAATTAAATATTTTATTAAA-ATATTAAA
* *
26651 AAT-TAATATT-T-TGATTAAAATGAT-ATTAAAATATTTTATTAATAATA
1 AATATAATATTATATTATTATAAT-ATAATT-AAATATTTTATTAA-AATA
26698 AATTCATAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 19
0.78 0.05 0.17
Matches are distributed among these distances:
49 1 0.01
50 5 0.06
51 15 0.17
52 8 0.09
53 25 0.29
54 23 0.26
55 10 0.11
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (53 bp):
AATATAATATTATATTATTATAATATAATTAAATATTTTATTAAAATATTAAA
Found at i:27908 original size:22 final size:22
Alignment explanation
Indices: 27882--27959 Score: 147
Period size: 22 Copynumber: 3.5 Consensus size: 22
27872 AAACCATTCA
27882 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTACCCCCTTGG
27904 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTACCCCCTTGG
27926 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTACCCCCTTGG
*
27948 AGGGGAATCGGT
1 GGGGGAATCGGT
27960 TCCCTCTAGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.15, C:0.24, G:0.42, T:0.18
Consensus pattern (22 bp):
GGGGGAATCGGTACCCCCTTGG
Found at i:42532 original size:26 final size:26
Alignment explanation
Indices: 42503--42555 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
42493 TGGGAGCTTA
42503 TCAC-TGGTAACTCGCTT-AGAAACTTC
1 TCACATGG-AACTC-CTTGAGAAACTTC
*
42529 TCACATGGAACTCTTTGAGAAACTTC
1 TCACATGGAACTCCTTGAGAAACTTC
42555 T
1 T
42556 TTATGAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 2 0.08
26 19 0.79
27 3 0.12
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (26 bp):
TCACATGGAACTCCTTGAGAAACTTC
Found at i:46273 original size:61 final size:60
Alignment explanation
Indices: 46176--46331 Score: 154
Period size: 60 Copynumber: 2.6 Consensus size: 60
46166 GTGTGCTTGT
* * * * * *
46176 AGGTCCATAAGGACTTAAACTAA-GCACAAAGCAAATGAGACCAACTAAGGGGAGTGT-CCTC
1 AGGTCCATAAGGACTT-AACCAATGCAAAAAGCAAATGA-ACCAACGAAAGGAACT-TCCCTC
* * * * * *
46237 ATGTCCATAAGGACTTATCCAATGCATAAAGCAAATGATCCATCGAAAGGAACTTCCCTT
1 AGGTCCATAAGGACTTAACCAATGCAAAAAGCAAATGAACCAACGAAAGGAACTTCCCTC
*
46297 AGGTCCATAAGGACTTACCCAATGCAAAAAGCAAA
1 AGGTCCATAAGGACTTAACCAATGCAAAAAGCAAA
46332 AGAGCCACCC
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
59 1 0.01
60 49 0.62
61 29 0.37
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (60 bp):
AGGTCCATAAGGACTTAACCAATGCAAAAAGCAAATGAACCAACGAAAGGAACTTCCCTC
Found at i:47293 original size:8 final size:8
Alignment explanation
Indices: 47280--47310 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
47270 AAGCATCCTT
47280 TAATATTG
1 TAATATTG
47288 TAATATTG
1 TAATATTG
47296 TAATATTG
1 TAATATTG
47304 TAATATT
1 TAATATT
47311 TATTTCTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (8 bp):
TAATATTG
Found at i:47464 original size:26 final size:26
Alignment explanation
Indices: 47414--47479 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
47404 ACATTATGTT
*
47414 ATTTTAGTCA-TTAGGTCTTTGAGGGC
1 ATTTTAGTCATTTAGGTC-TTAAGGGC
*
47440 ATTTTAGTCATTTAGGATC-TAAGGGT
1 ATTTTAGTCATTTAGG-TCTTAAGGGC
*
47466 ATTTTGGTCATTTA
1 ATTTTAGTCATTTA
47480 AAATTTTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 28 0.80
27 5 0.14
28 2 0.06
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (26 bp):
ATTTTAGTCATTTAGGTCTTAAGGGC
Found at i:48711 original size:16 final size:16
Alignment explanation
Indices: 48690--48720 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48680 ATAAATAAAT
48690 GAACATAAACAAACAC
1 GAACATAAACAAACAC
*
48706 GAACATAAACGAACA
1 GAACATAAACAAACA
48721 AATTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.23, G:0.10, T:0.06
Consensus pattern (16 bp):
GAACATAAACAAACAC
Found at i:48811 original size:16 final size:16
Alignment explanation
Indices: 48790--48850 Score: 86
Period size: 16 Copynumber: 3.8 Consensus size: 16
48780 TAATAAATAA
*
48790 ACGAACATAAACAAAC
1 ACGAACATAAACGAAC
* *
48806 ACGAACAGAAATGAAC
1 ACGAACATAAACGAAC
*
48822 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
48838 ACGAACATAAACG
1 ACGAACATAAACG
48851 TTGGAGACCC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.57, C:0.21, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:51094 original size:36 final size:33
Alignment explanation
Indices: 51045--51166 Score: 135
Period size: 31 Copynumber: 3.7 Consensus size: 33
51035 ATGTTTTAAT
*
51045 GAACACATTTTAATTAAAACGAAACGAAACGAAAGA
1 GAACACATCTTAATTAAAACGAAACGAAA--AAA-A
51081 GAACACATCTTAATTAAAACGAAACG--AAAAA
1 GAACACATCTTAATTAAAACGAAACGAAAAAAA
* * **
51112 GATCACATCTTAATTAAAACGAAATG--AAAGT
1 GAACACATCTTAATTAAAACGAAACGAAAAAAA
*
51143 GATCACATCTTAATTAAAACGAAA
1 GAACACATCTTAATTAAAACGAAA
51167 TGCAAATAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
31 52 0.64
32 3 0.04
34 1 0.01
36 25 0.31
ACGTcount: A:0.53, C:0.15, G:0.11, T:0.20
Consensus pattern (33 bp):
GAACACATCTTAATTAAAACGAAACGAAAAAAA
Found at i:51168 original size:31 final size:31
Alignment explanation
Indices: 51066--51166 Score: 166
Period size: 31 Copynumber: 3.3 Consensus size: 31
51056 AATTAAAACG
*
51066 AAACGAAACGAAAGAGAACACATCTTAATTA
1 AAACGAAACGAAAGAGATCACATCTTAATTA
*
51097 AAACGAAACGAAAAAGATCACATCTTAATTA
1 AAACGAAACGAAAGAGATCACATCTTAATTA
* *
51128 AAACGAAATGAAAGTGATCACATCTTAATTA
1 AAACGAAACGAAAGAGATCACATCTTAATTA
51159 AAACGAAA
1 AAACGAAA
51167 TGCAAATAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.19
Consensus pattern (31 bp):
AAACGAAACGAAAGAGATCACATCTTAATTA
Found at i:53722 original size:35 final size:35
Alignment explanation
Indices: 53676--53751 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
53666 AAAACAGTTC
* *
53676 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
53711 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
53746 TCAATT
1 TCAATT
53752 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:54288 original size:130 final size:130
Alignment explanation
Indices: 54147--54391 Score: 436
Period size: 130 Copynumber: 1.9 Consensus size: 130
54137 TTATATAATA
*
54147 AATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTAACATGTGTTA
1 AATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTAACATGTGTTA
*
54212 GCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATC
66 ACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATC
*
54277 AATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTA
1 AATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTAACATGTGTTA
* * *
54342 ACACATGATCATGATATGTGTTATTGGTGACACATGTCACCACCTAATTA
66 ACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTA
54392 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
AATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTAACATGTGTTA
ACACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATC
Found at i:54422 original size:130 final size:129
Alignment explanation
Indices: 54158--54422 Score: 327
Period size: 130 Copynumber: 2.0 Consensus size: 129
54148 ATTTGGTCCT
* *
54158 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTAACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTAACATGTGTTAACACATGATCA
*** * * **** *
54223 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
54288 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTAACATGTGTTAACACATGATCA
* * * *
54353 TGATATGTGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
54417 -A
128 CA
54418 AAATT
1 AAATT
54423 TGGGTCTTGG
Statistics
Matches: 115, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
130 102 0.89
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTAACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:54745 original size:28 final size:27
Alignment explanation
Indices: 54714--54776 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
54704 AGTTGATACA
*
54714 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
54742 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
54770 ATATTTT
1 ATATTTT
54777 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:54877 original size:16 final size:18
Alignment explanation
Indices: 54856--54889 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
54846 ATTTCTTATT
54856 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
54872 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
54890 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:54940 original size:16 final size:16
Alignment explanation
Indices: 54919--54953 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
54909 ATATTTTATT
54919 TATACATCTAAATAAA
1 TATACATCTAAATAAA
* *
54935 TATACATTTATATAAA
1 TATACATCTAAATAAA
54951 TAT
1 TAT
54954 TTTTATTCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (16 bp):
TATACATCTAAATAAA
Found at i:59904 original size:27 final size:27
Alignment explanation
Indices: 59867--59925 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
59857 CCACCACCAT
59867 CATCACTTTGAACTTGAAACTCCA-TAG
1 CATCACTTTGAACTTGAAACTCCACT-G
*
59894 CATCACTTTGAACTTGAAAGTCCACTG
1 CATCACTTTGAACTTGAAACTCCACTG
59921 CATCA
1 CATCA
59926 AGATATTCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 29 0.97
28 1 0.03
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.29
Consensus pattern (27 bp):
CATCACTTTGAACTTGAAACTCCACTG
Found at i:60646 original size:28 final size:28
Alignment explanation
Indices: 60614--60673 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
60604 ATACCCTCTC
60614 ACATTTTGTTGACACTTATACTTTATGG
1 ACATTTTGTTGACACTTATACTTTATGG
60642 ACATTTTGTTGACACTTATACTTTATGG
1 ACATTTTGTTGACACTTATACTTTATGG
60670 ACAT
1 ACAT
60674 CAAAGAAGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (28 bp):
ACATTTTGTTGACACTTATACTTTATGG
Done.