Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005411.1 Hibiscus syriacus cultivar Beakdansim tig00012409_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: 70920
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4013 original size:24 final size:24
Alignment explanation
Indices: 3986--4037 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
3976 TATGGAAACA
* *
3986 CAAAGGTTTAGTGCTT-AGAACATT
1 CAAAGCTTTAGGGCTTGA-AACATT
*
4010 CAAAGCTTTGGGGCTTGAAACATT
1 CAAAGCTTTAGGGCTTGAAACATT
4034 CAAA
1 CAAA
4038 ATTCTGGGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (24 bp):
CAAAGCTTTAGGGCTTGAAACATT
Found at i:4931 original size:40 final size:41
Alignment explanation
Indices: 4885--4974 Score: 128
Period size: 40 Copynumber: 2.2 Consensus size: 41
4875 CTCGAATAAC
* *
4885 TCGTGTTTGTTTCATGTAATTTGTTTTTCGAAAAAT-TTTT
1 TCGTGTTTGTTTCACGTAATTTGTTTTTAGAAAAATGTTTT
* *
4925 TCGTGTTTGTTTTACGTAATTTGTTTTTAGGAAAATGTTTT
1 TCGTGTTTGTTTCACGTAATTTGTTTTTAGAAAAATGTTTT
*
4966 TAGTGTTTG
1 TCGTGTTTG
4975 ATTGGAGGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 32 0.73
41 12 0.27
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.57
Consensus pattern (41 bp):
TCGTGTTTGTTTCACGTAATTTGTTTTTAGAAAAATGTTTT
Found at i:5214 original size:21 final size:23
Alignment explanation
Indices: 5173--5230 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
5163 TTTTAATCAA
5173 AATATTAATTATTAAAATATT-TAA-
1 AATA-TAATTATT--AATATTCTAAT
*
5197 AATATATTTATTAATATTCTAAT
1 AATATAATTATTAATATTCTAAT
5220 AATATAATTAT
1 AATATAATTAT
5231 ATTTTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 6 0.20
22 3 0.10
23 17 0.57
24 4 0.13
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AATATAATTATTAATATTCTAAT
Found at i:5247 original size:28 final size:28
Alignment explanation
Indices: 5199--5277 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 28
5189 ATATTTAAAA
*
5199 TATATTTATTAATATTCTAATAATATAAT
1 TATATTT-TTAATATTATAATAATATAAT
*
5228 TATATTTTTAATATTATAATAAAATAAT
1 TATATTTTTAATATTATAATAATATAAT
*
5256 CA-A---TT-ATATTATAATAATATAA
1 TATATTTTTAATATTATAATAATATAA
5278 GATAATATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
23 16 0.35
24 2 0.04
27 1 0.02
28 20 0.43
29 7 0.15
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (28 bp):
TATATTTTTAATATTATAATAATATAAT
Found at i:5407 original size:26 final size:26
Alignment explanation
Indices: 5352--5407 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
5342 ATTTCATAGA
*
5352 AATAATATTATTAAATATTAATAATG
1 AATAATATTATTAAATATTAATAATC
*
5378 AATAATA-TATTTATATATTTAAT-ATC
1 AATAATATTA-TTAAATA-TTAATAATC
5404 AATA
1 AATA
5408 TAATAATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 2 0.08
26 19 0.73
27 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
AATAATATTATTAAATATTAATAATC
Found at i:5466 original size:22 final size:23
Alignment explanation
Indices: 5427--5473 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
5417 AATAATATTT
5427 TAATAAATATATTTAAAATATAA
1 TAATAAATATATTTAAAATATAA
*
5450 TAATTAATAT-TTTAAAATATAA
1 TAATAAATATATTTAAAATATAA
5472 TA
1 TA
5474 TAACATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAA
Found at i:5791 original size:15 final size:15
Alignment explanation
Indices: 5750--5818 Score: 52
Period size: 15 Copynumber: 4.7 Consensus size: 15
5740 TCTAGAAATG
* *
5750 TAATTC-ATTTTCTA
1 TAATTCAATTTCCAA
* *
5764 TAATTTAAATTCCAA
1 TAATTCAATTTCCAA
*
5779 TAATTCATTTTCCAA
1 TAATTCAATTTCCAA
*
5794 -AATTCAATTTCTAA
1 TAATTCAATTTCCAA
* *
5808 AAATTAAATTT
1 TAATTCAATTT
5819 AAGCCAAACA
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
14 17 0.40
15 26 0.60
ACGTcount: A:0.41, C:0.13, G:0.00, T:0.46
Consensus pattern (15 bp):
TAATTCAATTTCCAA
Found at i:5812 original size:29 final size:29
Alignment explanation
Indices: 5751--5812 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
5741 CTAGAAATGT
* * * *
5751 AATTCATTTTCTATAATTTAAATTCCAAT
1 AATTCATTTTCCAAAATTCAAATTCCAAA
* *
5780 AATTCATTTTCCAAAATTCAATTTCTAAA
1 AATTCATTTTCCAAAATTCAAATTCCAAA
5809 AATT
1 AATT
5813 AAATTTAAGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (29 bp):
AATTCATTTTCCAAAATTCAAATTCCAAA
Found at i:6636 original size:20 final size:19
Alignment explanation
Indices: 6588--6638 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
6578 AAATGACCAA
* *
6588 CAAATTCGTAACGCGATCT
1 CAAATTCGCAACGCGAACT
6607 CAAATTCGCAACGCGAACT
1 CAAATTCGCAACGCGAACT
*
6626 CCAATTTCGCAAC
1 -CAAATTCGCAAC
6639 ACATGTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (19 bp):
CAAATTCGCAACGCGAACT
Found at i:6672 original size:20 final size:20
Alignment explanation
Indices: 6649--6695 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 20
6639 ACATGTTTCA
6649 AAATCGCAACGCGAATAAGT
1 AAATCGCAACGCGAATAAGT
* *
6669 AAAT--C-ACGTGAATATGT
1 AAATCGCAACGCGAATAAGT
6686 AAATCGCAAC
1 AAATCGCAAC
6696 ACAGAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
17 14 0.64
18 1 0.05
19 1 0.05
20 6 0.27
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATAAGT
Found at i:7052 original size:146 final size:146
Alignment explanation
Indices: 6796--7059 Score: 422
Period size: 146 Copynumber: 1.8 Consensus size: 146
6786 ATCGCAATGT
*
6796 GAATTTCATTTCCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGAGAAATTCGAGTTGCGA
1 GAATTTCATTTCCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGAGAAATTCAAGTTGCGA
* *
6861 ATTTGGAGAATTCGCGTTGTGATTTACATATTATCGTTGCAATTTAACTATTCACGTTGCGAATT
66 ATTTGGAGAATTCGCGTTGCGATTTACATATGATCGTTGCAATTTAACTATTCACGTTGCGAATT
6926 TGGAAAATCGCTACGC
131 TGGAAAATCGCTACGC
* * * *
6942 GAATTTCGTTTTCGCAACGCTAATTACCTATATCGGTAATT-GTCTTTGCGAAATTCAAGTTGCG
1 GAATTTCATTTCCGCAACGCTAATTACCTATATCGGTAATTAG-CGTTGAGAAATTCAAGTTGCG
** *
7006 AATTTGGAGAATTCGCGTTGCGATTTACATATGATCGTTGTGATTTACCTATTC
65 AATTTGGAGAATTCGCGTTGCGATTTACATATGATCGTTGCAATTTAACTATTC
7060 GCAACGCTAA
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
145 1 0.01
146 106 0.99
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (146 bp):
GAATTTCATTTCCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGAGAAATTCAAGTTGCGA
ATTTGGAGAATTCGCGTTGCGATTTACATATGATCGTTGCAATTTAACTATTCACGTTGCGAATT
TGGAAAATCGCTACGC
Found at i:7192 original size:104 final size:104
Alignment explanation
Indices: 6929--7217 Score: 295
Period size: 104 Copynumber: 2.8 Consensus size: 104
6919 GCGAATTTGG
* * *
6929 AAAATCGCTACGCGAATTTCGTTTTCGCAACGCTAATTACCTATATCGGTAATT-GTCTTTGCGA
1 AAAATCGCAACGCGAATTTCGTTTTCGCAACGCTAATTACCAATATCGGTAATTAG-CGTTGCGA
*** * **
6993 AATTCAAGTTGCGAATTTGGAGAATTCGCGTTGCGATTTAC
65 AATTCAAGTTGCGAA-TAACAAAATTCGCAATGCGATTTAC
* * * * * *
7034 -ATAT-G-ATCGTTGTGATTTACCTATTCGCAACGCTAATTACCGAAGTA--GGTAATTAGCGTT
1 AAAATCGCAACG-CG-AATTT-CGTTTTCGCAACGCTAATTACC-AA-TATCGGTAATTAGCGTT
*
7094 GCGAAATTCAAGTTGCGAA-AACAAAATTCGCAATGCGATTCTCC
61 GCGAAATTCAAGTTGCGAATAACAAAATTCGCAATGCGATT-TAC
*
7138 AAAATCGCAACGCGAATTTCGTTTTCGCAACACTAATTACCAATATCGGTAATTAGCGTTGCGAA
1 AAAATCGCAACGCGAATTTCGTTTTCGCAACGCTAATTACCAATATCGGTAATTAGCGTTGCGAA
*
7203 ATTCGAGTTGCGAAT
66 ATTCAAGTTGCGAAT
7218 TTGGAAAATT
Statistics
Matches: 147, Mismatches: 24, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
102 4 0.03
103 19 0.13
104 59 0.40
105 56 0.38
106 4 0.03
107 5 0.03
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (104 bp):
AAAATCGCAACGCGAATTTCGTTTTCGCAACGCTAATTACCAATATCGGTAATTAGCGTTGCGAA
ATTCAAGTTGCGAATAACAAAATTCGCAATGCGATTTAC
Found at i:7455 original size:20 final size:20
Alignment explanation
Indices: 7430--7494 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
7420 TTGTGTTGTT
*
7430 ATTTACATATTATCATTGCG
1 ATTTACATATTATCGTTGCG
* **
7450 ATTTACTTATTCGCGTTGCG
1 ATTTACATATTATCGTTGCG
* *
7470 AATTACATATTATCGTTGTG
1 ATTTACATATTATCGTTGCG
7490 ATTTA
1 ATTTA
7495 ACTATTCACG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (20 bp):
ATTTACATATTATCGTTGCG
Found at i:7477 original size:40 final size:40
Alignment explanation
Indices: 7432--7513 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
7422 GTGTTGTTAT
* *
7432 TTACATATTATCATTGCGATTT-ACTTATTCGCGTTGCGAA
1 TTACATATTATCATTGCGATTTAAC-TATTCACGTTGCAAA
* *
7472 TTACATATTATCGTTGTGATTTAACTATTCACGTTGCAAA
1 TTACATATTATCATTGCGATTTAACTATTCACGTTGCAAA
7512 TT
1 TT
7514 TTACTTTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 35 0.95
41 2 0.05
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (40 bp):
TTACATATTATCATTGCGATTTAACTATTCACGTTGCAAA
Found at i:7547 original size:60 final size:59
Alignment explanation
Indices: 7483--7613 Score: 140
Period size: 60 Copynumber: 2.2 Consensus size: 59
7473 TACATATTAT
* *
7483 CGTTGTGATTTAACTATTC-ACGTTGCAAATTTT-ACTTTTGCATTGCGATTTTGAATTTCG
1 CGTTGTGATTTAACT-TTCGA-GTTGC-AATTTTGACTTTCGCATTGCGAATTTGAATTTCG
* * * * *
7543 CGTTGCTGTTTTGACTTTCGAGTTGCGATTTTGACTTTCGCGTTGCGAATTTGATTTTCG
1 CGTTG-TGATTTAACTTTCGAGTTGCAATTTTGACTTTCGCATTGCGAATTTGAATTTCG
*
7603 CGTTGCGATTT
1 CGTTGTGATTT
7614 TGGAACCTGT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
59 9 0.15
60 41 0.69
61 9 0.15
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (59 bp):
CGTTGTGATTTAACTTTCGAGTTGCAATTTTGACTTTCGCATTGCGAATTTGAATTTCG
Found at i:7554 original size:20 final size:20
Alignment explanation
Indices: 7511--7615 Score: 133
Period size: 20 Copynumber: 5.3 Consensus size: 20
7501 CACGTTGCAA
* *
7511 ATTTT-ACTTTTGCATTGCG
1 ATTTTGACTTTCGCGTTGCG
*
7530 ATTTTGAATTTCGCGTTGCTG
1 ATTTTGACTTTCGCGTTGC-G
*
7551 -TTTTGACTTTCGAGTTGCG
1 ATTTTGACTTTCGCGTTGCG
7570 ATTTTGACTTTCGCGTTGCG
1 ATTTTGACTTTCGCGTTGCG
* *
7590 AATTTGATTTTCGCGTTGCG
1 ATTTTGACTTTCGCGTTGCG
7610 ATTTTG
1 ATTTTG
7616 GAACCTGTGT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
19 6 0.08
20 67 0.91
21 1 0.01
ACGTcount: A:0.13, C:0.15, G:0.23, T:0.49
Consensus pattern (20 bp):
ATTTTGACTTTCGCGTTGCG
Found at i:9351 original size:22 final size:22
Alignment explanation
Indices: 9323--9377 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
9313 GCATGTGAAC
9323 TTTGTCCCGAAAGACCTATGTA
1 TTTGTCCCGAAAGACCTATGTA
* * * *
9345 TTTGTCCTGAAGGACTTCTGTA
1 TTTGTCCCGAAAGACCTATGTA
*
9367 TATGTCCCGAA
1 TTTGTCCCGAA
9378 TGACTGCGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (22 bp):
TTTGTCCCGAAAGACCTATGTA
Found at i:23274 original size:13 final size:12
Alignment explanation
Indices: 23246--23293 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
23236 ATTTTGTGTT
*
23246 TAAACTATTTTTA
1 TAAA-TATTTTAA
23259 TAAATATTTTACA
1 TAAATATTTTA-A
23272 TAAACTATTTTAA
1 TAAA-TATTTTAA
23285 -AAATATTTT
1 TAAATATTTT
23294 CTTCACATGC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
11 6 0.19
12 9 0.28
13 10 0.31
14 7 0.22
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAATATTTTAA
Found at i:23976 original size:20 final size:21
Alignment explanation
Indices: 23940--23978 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
23930 ATTAAAGCAG
*
23940 ATTAAAATTGATAGTTTAATC
1 ATTAAAATAGATAGTTTAATC
23961 ATTAAAATAG-TAGTTTAA
1 ATTAAAATAGATAGTTTAA
23979 CCAATAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (21 bp):
ATTAAAATAGATAGTTTAATC
Found at i:36244 original size:78 final size:78
Alignment explanation
Indices: 36144--36300 Score: 255
Period size: 78 Copynumber: 2.0 Consensus size: 78
36134 TCTACTTTTG
* *
36144 ACGTTTGTGAATGGAGTAAATTGGGTTGGAAGGATCGTTC-TAGCCTCTGTATTATCCGATCTAA
1 ACGTTTGTGAATGGAGTAAATTGGATTGGAAGGATC-ATCATAGCCTCTGTATTATCCGATCTAA
36208 A-TCAATCGATTAAT
65 ACT-AATCGATTAAT
*
36222 ACGTTTGTGAATGGAGTAAATTGGATTGGAAGGATCATCATCGCCTCTGTATTATCCGATCTAAA
1 ACGTTTGTGAATGGAGTAAATTGGATTGGAAGGATCATCATAGCCTCTGTATTATCCGATCTAAA
36287 CTAATCGATTAAT
66 CTAATCGATTAAT
36300 A
1 A
36301 AATCAAATAT
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
77 2 0.03
78 71 0.96
79 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.34
Consensus pattern (78 bp):
ACGTTTGTGAATGGAGTAAATTGGATTGGAAGGATCATCATAGCCTCTGTATTATCCGATCTAAA
CTAATCGATTAAT
Found at i:36795 original size:23 final size:22
Alignment explanation
Indices: 36758--36803 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
36748 GTGTCATCAT
** *
36758 AAAATAATATCATATTATCATTA
1 AAAATAATAAAATATCA-CATTA
36781 AAAATAATAAAATATCACATTA
1 AAAATAATAAAATATCACATTA
36803 A
1 A
36804 TAGTTTTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAATAATAAAATATCACATTA
Found at i:41887 original size:21 final size:21
Alignment explanation
Indices: 41863--41907 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
41853 TATAATTTTT
*
41863 AATATTTGAATGTTAATAAAA
1 AATAGTTGAATGTTAATAAAA
*
41884 AATAGTTGAATGTTGATAAAA
1 AATAGTTGAATGTTAATAAAA
41905 AAT
1 AAT
41908 TATAATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (21 bp):
AATAGTTGAATGTTAATAAAA
Found at i:42010 original size:18 final size:20
Alignment explanation
Indices: 41987--42025 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
41977 TGAATGAGTC
*
41987 AATTAAATAAT-A-TTATAT
1 AATTAAAGAATCATTTATAT
42005 AATTAAAGAATCATTTATAT
1 AATTAAAGAATCATTTATAT
42025 A
1 A
42026 TTTTATCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 1 0.06
20 7 0.39
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
AATTAAAGAATCATTTATAT
Found at i:43290 original size:23 final size:23
Alignment explanation
Indices: 43264--43307 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
43254 AAGGTAGAAA
*
43264 AAAATGTGTCATA-AAGACATATG
1 AAAACGTGTCATACAA-ACATATG
43287 AAAACGTGTCATACAAACATA
1 AAAACGTGTCATACAAACATA
43308 CTTATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.23
Consensus pattern (23 bp):
AAAACGTGTCATACAAACATATG
Found at i:54679 original size:24 final size:23
Alignment explanation
Indices: 54634--54684 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
54624 GTTGGAAGCT
*
54634 ATAAAATACTTTATAATTTATTC
1 ATAAAATACTTTATAAATTATTC
* *
54657 ATAAACATATTTTTTAAATTATTC
1 ATAAA-ATACTTTATAAATTATTC
54681 ATAA
1 ATAA
54685 TTTATAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAAAATACTTTATAAATTATTC
Found at i:54698 original size:2 final size:2
Alignment explanation
Indices: 54687--54740 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
54677 ATTCATAATT
54687 TA TA -A TA TA TA 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
54728 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
54741 TTTACAAAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.