Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003177.1 Hibiscus syriacus cultivar Beakdansim tig00006686_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: 54149
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4181 original size:33 final size:34
Alignment explanation
Indices: 4137--4206 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 34
4127 GAGACAATTA
4137 AAAAAATTAGTATAATTAGGGCGCGGGTCCTTGT
1 AAAAAATTAGTATAATTAGGGCGCGGGTCCTTGT
* * *
4171 AAAAAA-TAGTATAATTAGGGCGTGTGTTCTTGT
1 AAAAAATTAGTATAATTAGGGCGCGGGTCCTTGT
4204 AAA
1 AAA
4207 GTTATGTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 27 0.82
34 6 0.18
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (34 bp):
AAAAAATTAGTATAATTAGGGCGCGGGTCCTTGT
Found at i:5222 original size:2 final size:2
Alignment explanation
Indices: 5215--5248 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5205 AATCATATTT
5215 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
5249 GAAAAATTCT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5510 original size:2 final size:2
Alignment explanation
Indices: 5503--5541 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5493 TAAAAATAAA
5503 AT AT 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 AT AT A
5542 ATAAACAGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6214 original size:37 final size:37
Alignment explanation
Indices: 6141--6215 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
6131 GTTGAAAAAT
* *
6141 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
6178 ATTTATATAATTGTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATT-TTCTTTAAAAAATTGAAAATCATAAA
6215 A
1 A
6216 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 17 0.52
39 2 0.06
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:9088 original size:10 final size:10
Alignment explanation
Indices: 9073--9112 Score: 62
Period size: 10 Copynumber: 3.8 Consensus size: 10
9063 AAAACCAATA
9073 AAATATAATT
1 AAATATAATT
9083 AAATATAAATAT
1 AAATAT-AAT-T
9095 AAATATAATT
1 AAATATAATT
9105 AAATATAA
1 AAATATAA
9113 ATCTAAAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 15 0.54
11 6 0.21
12 7 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAATATAATT
Found at i:9093 original size:6 final size:6
Alignment explanation
Indices: 9069--9119 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
9059 TTTTAAAACC
9069 AATA-A AATAT- AAT-TA AATATA AATATA AATAT- AAT-TA AATATA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATATA
*
9112 AATCTA AA
1 AATATA AA
9120 GTTCACAGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
4 2 0.05
5 16 0.40
6 22 0.55
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:9094 original size:16 final size:16
Alignment explanation
Indices: 9069--9114 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
9059 TTTTAAAACC
*
9069 AATA-AAATATAATTA
1 AATATAAATATAAATA
9084 AATATAAATATAAATA
1 AATATAAATATAAATA
9100 TAAT-TAAATATAAAT
1 -AATATAAATATAAAT
9115 CTAAAGTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 4 0.14
16 21 0.75
17 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATATAAATATAAATA
Found at i:9098 original size:22 final size:22
Alignment explanation
Indices: 9069--9119 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
9059 TTTTAAAACC
9069 AATA-AAATATAATTAAATATA
1 AATATAAATATAATTAAATATA
9090 AATATAAATATAATTAAATATA
1 AATATAAATATAATTAAATATA
*
9112 AATCTAAA
1 AATATAAA
9120 GTTCACAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 4 0.14
22 24 0.86
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
AATATAAATATAATTAAATATA
Found at i:12491 original size:53 final size:53
Alignment explanation
Indices: 12409--12517 Score: 157
Period size: 53 Copynumber: 2.1 Consensus size: 53
12399 AGAAGATAAG
* * *
12409 ATAGTTTGTGAGTTATAACCATCTCTTGATATAGT-TTTCTATTGATATTGTAA
1 ATAGTTTGTAAGTTATAACCATATCTTGATATAGTCTTT-TATTAATATTGTAA
* *
12462 ATAGTTTGTAAGTTATAACCGTATTTTGATATAGTCTTTTATTAATATTGTAA
1 ATAGTTTGTAAGTTATAACCATATCTTGATATAGTCTTTTATTAATATTGTAA
12515 ATA
1 ATA
12518 TTAATATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
53 47 0.94
54 3 0.06
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.48
Consensus pattern (53 bp):
ATAGTTTGTAAGTTATAACCATATCTTGATATAGTCTTTTATTAATATTGTAA
Found at i:12632 original size:24 final size:24
Alignment explanation
Indices: 12585--12634 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
12575 TTTAGTTAGG
* **
12585 ACTCTTAGATCAACTAGATCTCTA
1 ACTCATAGATCAACTAGAAATCTA
12609 ACTCATAGATCAACTAGAAATCTA
1 ACTCATAGATCAACTAGAAATCTA
12633 AC
1 AC
12635 ACCTTTTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (24 bp):
ACTCATAGATCAACTAGAAATCTA
Found at i:18753 original size:23 final size:24
Alignment explanation
Indices: 18703--18756 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
18693 CTAACTCATT
*
18703 TCACAATCCAACTGCTCCAACAAT
1 TCACAATCCAACTGCTCCAACAAA
18727 TCACAATCCAACTGCT-CAACAAA
1 TCACAATCCAACTGCTCCAACAAA
18750 TCACAAT
1 TCACAAT
18757 AAAATAGAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 13 0.45
24 16 0.55
ACGTcount: A:0.41, C:0.35, G:0.04, T:0.20
Consensus pattern (24 bp):
TCACAATCCAACTGCTCCAACAAA
Found at i:19213 original size:21 final size:21
Alignment explanation
Indices: 19162--19215 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
19152 AAGACGAAAT
*
19162 AACCAAAGGATAATATATTCA
1 AACCAAAGGCTAATATATTCA
19183 AACCAAAGGCTAATATATTCA
1 AACCAAAGGCTAATATATTCA
19204 AACCAAAGGCTA
1 AACCAAAGGCTA
19216 TTTTTTTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.50, C:0.19, G:0.11, T:0.20
Consensus pattern (21 bp):
AACCAAAGGCTAATATATTCA
Found at i:22527 original size:11 final size:11
Alignment explanation
Indices: 22507--22545 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
22497 GAGTACCTAC
22507 AAAA-TCAAGA
1 AAAATTCAAGA
22517 AAAATTCAAGA
1 AAAATTCAAGA
22528 ATTAAATTCAAGA
1 A--AAATTCAAGA
22541 AAAAT
1 AAAAT
22546 AAAATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 4 0.15
11 11 0.42
13 11 0.42
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.21
Consensus pattern (11 bp):
AAAATTCAAGA
Found at i:22554 original size:24 final size:24
Alignment explanation
Indices: 22511--22557 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
22501 ACCTACAAAA
**
22511 TCAAGAAAAATTCAAGAATTAAAT
1 TCAAGAAAAATAAAAGAATTAAAT
*
22535 TCAAGAAAAATAAAATAATTAAA
1 TCAAGAAAAATAAAAGAATTAAA
22558 ATCGAAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.23
Consensus pattern (24 bp):
TCAAGAAAAATAAAAGAATTAAAT
Found at i:23704 original size:24 final size:24
Alignment explanation
Indices: 23672--23719 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
23662 ATTTACCTGA
23672 AATTTTGGGATTTGGCACTTCTTC
1 AATTTTGGGATTTGGCACTTCTTC
23696 AATTTTGGGATTTGGCACTTCTTC
1 AATTTTGGGATTTGGCACTTCTTC
23720 CTCCTTGTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.46
Consensus pattern (24 bp):
AATTTTGGGATTTGGCACTTCTTC
Found at i:25439 original size:36 final size:34
Alignment explanation
Indices: 25399--25466 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 34
25389 AATAAATTAC
*
25399 AAAAGATAAATCCTAAATTTTTTTGAATTT-AATTCT
1 AAAAGATAAAT-CT-AA-TTTCTTGAATTTGAATTCT
25435 AAAAGATAAATCTAATTTCTTGAATTTGAATT
1 AAAAGATAAATCTAATTTCTTGAATTTGAATT
25467 GCTCAGCCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 11 0.37
34 6 0.20
35 2 0.07
36 11 0.37
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (34 bp):
AAAAGATAAATCTAATTTCTTGAATTTGAATTCT
Found at i:38020 original size:21 final size:21
Alignment explanation
Indices: 37991--38069 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 21
37981 ATATGCAAAA
*
37991 AAATTAATTAAATAAAATATT
1 AAATAAATTAAATAAAATATT
*
38012 AAATAAATTAAAT---A-CTT
1 AAATAAATTAAATAAAATATT
38029 AAATAAATTAAATACAAAATATT
1 AAATAAATTAAAT--AAAATATT
38052 -AA-AAA-TATAATAAAATAT
1 AAATAAATTA-AATAAAATAT
38070 ACCTTAGACA
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
17 15 0.31
18 1 0.02
19 7 0.15
20 2 0.04
21 18 0.38
22 3 0.06
23 2 0.04
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATAAATTAAATAAAATATT
Found at i:38021 original size:9 final size:9
Alignment explanation
Indices: 37991--38042 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
37981 ATATGCAAAA
*
37991 AAATTAATT
1 AAATTAAAT
38000 AAA-TAAA-
1 AAATTAAAT
*
38007 ATATTAAAT
1 AAATTAAAT
38016 AAATTAAAT
1 AAATTAAAT
*
38025 -ACTTAAAT
1 AAATTAAAT
38033 AAATTAAAT
1 AAATTAAAT
38042 A
1 A
38043 CAAAATATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 2 0.06
8 14 0.40
9 19 0.54
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AAATTAAAT
Found at i:38023 original size:17 final size:17
Alignment explanation
Indices: 37988--38040 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
37978 TATATATGCA
* *
37988 AAAAAATTAATTAAA-T
1 AAAATATTAAATAAATT
38004 AAAATATTAAATAAATT
1 AAAATATTAAATAAATT
38021 -AAATACTTAAATAAATT
1 AAAATA-TTAAATAAATT
38038 AAA
1 AAA
38041 TACAAAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 18 0.56
17 12 0.38
18 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATATTAAATAAATT
Found at i:38041 original size:17 final size:17
Alignment explanation
Indices: 37994--38043 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
37984 TGCAAAAAAA
* *
37994 TTAATTAAATAAAATA-
1 TTAAATAAATTAAATAC
38010 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
38027 TTAAATAAATTAAATAC
1 TTAAATAAATTAAATAC
38044 AAAATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAATAAATTAAATAC
Found at i:39051 original size:31 final size:31
Alignment explanation
Indices: 39015--39074 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
39005 AACTTAAAAA
* * *
39015 AGTTTTGCAATATTGATATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
39046 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
39075 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:39654 original size:31 final size:31
Alignment explanation
Indices: 39619--39715 Score: 85
Period size: 31 Copynumber: 3.1 Consensus size: 31
39609 ATCTATAATC
39619 TAATATTAAATATTTAATTTATTTAAAAAAT
1 TAATATTAAATATTTAATTTATTTAAAAAAT
* * * *
39650 TAATATTAAA-A-TTAATATCTATAATATATAT
1 TAATATTAAATATTTAATTTATTTAA-A-AAAT
*
39681 TAAAAAATT-AATATTTAA-TTATTTAAAAAAT
1 T--AATATTAAATATTTAATTTATTTAAAAAAT
39712 TAAT
1 TAAT
39716 TAATATTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 14
0.68 0.14 0.19
Matches are distributed among these distances:
29 12 0.24
30 2 0.04
31 18 0.36
32 3 0.06
33 11 0.22
34 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (31 bp):
TAATATTAAATATTTAATTTATTTAAAAAAT
Found at i:39662 original size:12 final size:12
Alignment explanation
Indices: 39645--39745 Score: 51
Period size: 12 Copynumber: 8.9 Consensus size: 12
39635 ATTTATTTAA
39645 AAAATTAATATT
1 AAAATTAATATT
39657 AAAATTAATATCT
1 AAAATTAATAT-T
*
39670 ATAA-TATATATT
1 AAAATTA-ATATT
39682 AAAAAATTAATATT
1 --AAAATTAATATT
*
39696 -TAATT-AT-TT
1 AAAATTAATATT
39705 -AAA--AA-ATT
1 AAAATTAATATT
39713 --AATTAATATT
1 AAAATTAATATT
* *
39723 AAAATTAAAATC
1 AAAATTAATATT
*
39735 AAATTTAATAT
1 AAAATTAATAT
39746 AAATTAAATA
Statistics
Matches: 69, Mismatches: 8, Indels: 24
0.68 0.08 0.24
Matches are distributed among these distances:
7 2 0.03
8 3 0.04
9 6 0.09
10 5 0.07
11 4 0.06
12 31 0.45
13 8 0.12
14 8 0.12
15 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:39710 original size:23 final size:27
Alignment explanation
Indices: 39657--39715 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 27
39647 AATTAATATT
39657 AAAATTAATATCTATAATATATATTAA
1 AAAATTAATATCTATAATATATATTAA
39684 AAAATTAATAT-T-TAAT-TAT-TTAA
1 AAAATTAATATCTATAATATATATTAA
39707 AAAATTAAT
1 AAAATTAAT
39716 TAATATTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 13 0.41
24 3 0.09
25 4 0.12
26 1 0.03
27 11 0.34
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
AAAATTAATATCTATAATATATATTAA
Found at i:39756 original size:62 final size:66
Alignment explanation
Indices: 39614--39756 Score: 167
Period size: 62 Copynumber: 2.3 Consensus size: 66
39604 TAAATATCTA
* * * *
39614 TAATCTAATATTAAATATTTAATTTATTTAAAAAATTAATATTAAAATTAATATCTATAATATAT
1 TAATATAA-ATTAAATATTTAATTTATTTAAAAAATTAATATTAAAATTAAAATCTAAAATAAAT
39679 AT
65 AT
*
39681 TAA-A-AAATT-AATATTTAA-TTATTTAAAAAATT-A-ATTAATATTAAAAT-TAAAATCAAAT
1 TAATATAAATTAAATATTTAATTTATTTAAAAAATTAATATTAAAATTAAAATCTAAAAT-AAAT
39739 -T
65 AT
39740 TAATATAAATTAAATAT
1 TAATATAAATTAAATAT
39757 AAAACCTCTT
Statistics
Matches: 67, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
59 9 0.13
60 16 0.24
61 6 0.09
62 19 0.28
63 9 0.13
64 3 0.04
65 2 0.03
67 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (66 bp):
TAATATAAATTAAATATTTAATTTATTTAAAAAATTAATATTAAAATTAAAATCTAAAATAAATA
T
Found at i:40092 original size:2 final size:2
Alignment explanation
Indices: 40085--40142 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
40075 CTTAATTGAA
40085 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
40127 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
40143 GTATTATTGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44014 original size:3 final size:3
Alignment explanation
Indices: 44000--44030 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
43990 GCATGTTTAG
*
44000 TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
44031 GGAAAACCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:45911 original size:31 final size:31
Alignment explanation
Indices: 45849--45911 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
45839 ATTTGATCGT
** *
45849 TTTCGTTTTTATTTAACTAAAATTTGGTCAC
1 TTTCGTTTTTATTTAACTAAAATACGATCAC
* *
45880 TTTCGTTTTTATTTAATTAAGATACGATCAC
1 TTTCGTTTTTATTTAACTAAAATACGATCAC
45911 T
1 T
45912 AAGGGTTAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.51
Consensus pattern (31 bp):
TTTCGTTTTTATTTAACTAAAATACGATCAC
Found at i:47141 original size:22 final size:23
Alignment explanation
Indices: 47103--47154 Score: 97
Period size: 22 Copynumber: 2.3 Consensus size: 23
47093 AATTGATATT
47103 TTATGTTAGAAATTATGAGAATA
1 TTATGTTAGAAATTATGAGAATA
47126 TTATGTTAG-AATTATGAGAATA
1 TTATGTTAGAAATTATGAGAATA
47148 TTATGTT
1 TTATGTT
47155 GTACGTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.44
Consensus pattern (23 bp):
TTATGTTAGAAATTATGAGAATA
Found at i:48197 original size:26 final size:26
Alignment explanation
Indices: 48168--48221 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
48158 ACTTAATGCA
*
48168 TATGGTGGGCACGACCTTATGAGTAT
1 TATGGTGAGCACGACCTTATGAGTAT
* *
48194 TATGGTGAGCATGACCTTATGTGTAT
1 TATGGTGAGCACGACCTTATGAGTAT
48220 TA
1 TA
48222 GCACTTCGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.13, G:0.28, T:0.35
Consensus pattern (26 bp):
TATGGTGAGCACGACCTTATGAGTAT
Found at i:50068 original size:23 final size:24
Alignment explanation
Indices: 50035--50080 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
50025 ATTATACATG
50035 CCTATAGAATGGTT-TCCCTTTTC
1 CCTATAGAATGGTTGTCCCTTTTC
*
50058 CCTATATAATGGTTGTCCCTTTT
1 CCTATAGAATGGTTGTCCCTTTT
50081 GAGGTTGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.17, C:0.24, G:0.13, T:0.46
Consensus pattern (24 bp):
CCTATAGAATGGTTGTCCCTTTTC
Done.