Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003828.1 Hibiscus syriacus cultivar Beakdansim tig00008207_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: 152591
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5080 original size:8 final size:8
Alignment explanation
Indices: 5067--5094 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5057 AGATTCTCCC
5067 ATATGTAT
1 ATATGTAT
5075 ATATGTAT
1 ATATGTAT
5083 ATATGTAT
1 ATATGTAT
5091 ATAT
1 ATAT
5095 CTTCTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:8610 original size:8 final size:8
Alignment explanation
Indices: 8563--8612 Score: 61
Period size: 7 Copynumber: 6.5 Consensus size: 8
8553 AAAATGAGTG
8563 AAAATGAA
1 AAAATGAA
*
8571 AAAGT-AA
1 AAAATGAA
8578 AAAAT-AA
1 AAAATGAA
8585 AAAAT-AA
1 AAAATGAA
8592 AAAATGAA
1 AAAATGAA
8600 AAAATGGAA
1 AAAAT-GAA
8609 AAAA
1 AAAA
8613 AGAAGAAGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
7 20 0.53
8 11 0.29
9 7 0.18
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (8 bp):
AAAATGAA
Found at i:8610 original size:15 final size:15
Alignment explanation
Indices: 8563--8604 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
8553 AAAATGAGTG
*
8563 AAAATGAAAAAGTAA
1 AAAATGAAAAAATAA
8578 AAAAT-AAAAAATAA
1 AAAATGAAAAAATAA
8592 AAAATGAAAAAAT
1 AAAATGAAAAAAT
8605 GGAAAAAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAATGAAAAAATAA
Found at i:9607 original size:55 final size:55
Alignment explanation
Indices: 9538--10246 Score: 985
Period size: 55 Copynumber: 12.9 Consensus size: 55
9528 AGGTTTCCCA
9538 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
*
9593 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTC-GTAAGAAATAGGGAGCAAAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTG-AAGAAATAGGGAGCAGAC
* * *
9648 ACAATTGTTGAAGATTATTCGAGTCTCATACTCTTTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
*
9703 ACGATTGTTAAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
*
9758 ACAATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* *
9813 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAACAAATAGGGAACAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
9868 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * * *
9923 ACGATTGATGAAAATTGTTCGAGTCTTATACTCTCTGCATAAATAGGGAGCAAAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
9978 ACGACTGTTGAAGATTGTTCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * * *
10033 ACGATTGATGAAGATTTTTCAAGTCTTATACTCTCTGAAGGAATGGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * *
10088 ACGATTGATGAAGATTGTTCGGGTCTTATATTCTCTGAAGGAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
10143 AAGATTTGTTGAAGATTGTTTGGGTCTTATACTCTCTG-AGCAAATAGGGAGCAGAC
1 ACGA-TTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAG-AAATAGGGAGCAGAC
* * * * * *
10199 ACGATTGATGAAGATTCTTCAAGT-TCCTACTCCCT-AAGAAAGAGGGAG
1 ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAG
10247 TAAACTCGTT
Statistics
Matches: 591, Mismatches: 58, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
53 9 0.02
54 11 0.02
55 523 0.88
56 48 0.08
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (55 bp):
ACGATTGTTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:18064 original size:4 final size:4
Alignment explanation
Indices: 18055--18081 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
18045 TCCCCTTTCT
18055 CTTC CTTC CTTC CTTC CTTC CTTC CTT
1 CTTC CTTC CTTC CTTC CTTC CTTC CTT
18082 GTATTCTCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (4 bp):
CTTC
Found at i:22423 original size:14 final size:14
Alignment explanation
Indices: 22404--22436 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
22394 TAAATAATTT
22404 ATATTACATATTAA
1 ATATTACATATTAA
22418 ATATTACATATTAA
1 ATATTACATATTAA
22432 ATATT
1 ATATT
22437 TTGATTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATTACATATTAA
Found at i:22866 original size:14 final size:14
Alignment explanation
Indices: 22830--22871 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
22820 TATGATCACT
22830 AATTAATGAAGTGA
1 AATTAATGAAGTGA
*
22844 AAATAATGAAGTGA
1 AATTAATGAAGTGA
* *
22858 AATTGATGACGTGA
1 AATTAATGAAGTGA
22872 GTGTGAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.24, T:0.26
Consensus pattern (14 bp):
AATTAATGAAGTGA
Found at i:36796 original size:15 final size:16
Alignment explanation
Indices: 36772--36812 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
36762 TATGTTTTTA
36772 TTTT-ATTTTTATT-T
1 TTTTCATTTTTATTAT
36786 TTTTCATTTTTATTAT
1 TTTTCATTTTTATTAT
36802 TTTTC-TTTTTA
1 TTTTCATTTTTA
36813 CTAAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.16
15 15 0.60
16 6 0.24
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTCATTTTTATTAT
Found at i:40990 original size:24 final size:23
Alignment explanation
Indices: 40963--41011 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
40953 CCACTAGGGG
* *
40963 CTATGAATTTATCCCGAAGGACCA
1 CTATGAA-ATATCCCGAAAGACCA
*
40987 CTATGAAATGTCCCGAAAGACCA
1 CTATGAAATATCCCGAAAGACCA
41010 CT
1 CT
41012 GTATGTCCCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (23 bp):
CTATGAAATATCCCGAAAGACCA
Found at i:49931 original size:59 final size:59
Alignment explanation
Indices: 49838--50019 Score: 190
Period size: 60 Copynumber: 3.1 Consensus size: 59
49828 CATATGCCCC
* * * * *
49838 AAACTATAACTCTCATTTTAAATTGGTCCTTAAACTTTTGAATATTTCAATTCCATCCCT
1 AAACTATGACTCT-ATTCTAAATTAGTCTTTAAACTTTTGAATATTTCAATTTCATCCCT
* * * *
49898 AAACTATGACTCTATTCTAAATTAGTCTTTAAACTTTTTAACA-TTCTAATTTTAACCCT
1 AAACTATGACTCTATTCTAAATTAGTCTTTAAACTTTTGAATATTTC-AATTTCATCCCT
* * *
49957 AAATTGTGACCCTCT-TTCTAAATTAGT-TCTCAAACTTTTGAATATTTCAATTTCATCCCT
1 AAACTATGA--CTCTATTCTAAATTAGTCT-TTAAACTTTTGAATATTTCAATTTCATCCCT
50017 AAA
1 AAA
50020 TTCATCCAAA
Statistics
Matches: 101, Mismatches: 16, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
58 3 0.03
59 42 0.42
60 49 0.49
61 7 0.07
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.42
Consensus pattern (59 bp):
AAACTATGACTCTATTCTAAATTAGTCTTTAAACTTTTGAATATTTCAATTTCATCCCT
Found at i:50309 original size:60 final size:59
Alignment explanation
Indices: 50173--50322 Score: 176
Period size: 60 Copynumber: 2.5 Consensus size: 59
50163 ATGTCCAAAA
*
50173 AGGACCAATTTAGAATGAATATCATAGTTTGGGGATGAAATTAAAATGTTTAAAAGTTTG
1 AGGACCAATTTAGAATG-ATATCATAGTTTAGGGATGAAATTAAAATGTTTAAAAGTTTG
** * * * *
50233 AGGATTAATTTTGAATGATGGTCATAGTTTAGGGATGAAATTAGAATTTTTAAAAGTTT-
1 AGGACCAATTTAGAATGAT-ATCATAGTTTAGGGATGAAATTAAAATGTTTAAAAGTTTG
* * *
50292 AGGGACCAGTTTAGAATGAGATCATACTTTA
1 A-GGACCAATTTAGAATGATATCATAGTTTA
50323 AGGAAATGTG
Statistics
Matches: 74, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
59 12 0.16
60 62 0.84
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.35
Consensus pattern (59 bp):
AGGACCAATTTAGAATGATATCATAGTTTAGGGATGAAATTAAAATGTTTAAAAGTTTG
Found at i:52209 original size:16 final size:16
Alignment explanation
Indices: 52184--52217 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
52174 TTAATGATAA
52184 TAATTCTAATAAAATT
1 TAATTCTAATAAAATT
* *
52200 TAATTTTAATAAAGTT
1 TAATTCTAATAAAATT
52216 TA
1 TA
52218 TTAAAAATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
TAATTCTAATAAAATT
Found at i:60516 original size:2 final size:2
Alignment explanation
Indices: 60509--60537 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
60499 AATTTAGTAT
60509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60538 TCTTTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64723 original size:24 final size:25
Alignment explanation
Indices: 64694--64753 Score: 68
Period size: 30 Copynumber: 2.2 Consensus size: 25
64684 GAGTCCTGCC
64694 TAACTTC-TCCTAAGAATAATAAAG
1 TAACTTCATCCTAAGAATAATAAAG
64718 TAACTTATACTCATCCTAAGAATAATAAAG
1 TAAC---T--TCATCCTAAGAATAATAAAG
64748 TAACTT
1 TAACTT
64754 ATTTTATAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
24 4 0.13
25 1 0.03
27 2 0.07
29 2 0.07
30 21 0.70
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.32
Consensus pattern (25 bp):
TAACTTCATCCTAAGAATAATAAAG
Found at i:64968 original size:2 final size:2
Alignment explanation
Indices: 64961--64993 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
64951 CACTCTCATT
64961 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
64994 TTGATAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:65283 original size:19 final size:19
Alignment explanation
Indices: 65259--65300 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
65249 TTCCCTAATA
65259 AGCTAGAACACTATCAACT
1 AGCTAGAACACTATCAACT
65278 AGCTAGAACACTATCAACT
1 AGCTAGAACACTATCAACT
65297 AGCT
1 AGCT
65301 TTTGGTGTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.21
Consensus pattern (19 bp):
AGCTAGAACACTATCAACT
Found at i:73449 original size:17 final size:17
Alignment explanation
Indices: 73427--73470 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
73417 ATGTAAAAAT
73427 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
73444 AAATATAAAAATTTATT
1 AAATATTTAAATTTAAA
73461 AAATATTTAA
1 AAATATTTAA
73471 TCAAGTAGGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:77292 original size:29 final size:28
Alignment explanation
Indices: 77258--77428 Score: 154
Period size: 29 Copynumber: 6.0 Consensus size: 28
77248 CGTTGATCGG
77258 GTGATATTTTAGTAATTATTTTGAAAATA
1 GTGATATTTTAGTAATTATTTTGAAAA-A
* * *
77287 TTGATATTTTGGTAATTATTTTGAAAAT
1 GTGATATTTTAGTAATTATTTTGAAAAA
* *
77315 GATGCTATTTTCA-TAA--ATTTTTAAAAA
1 G-TGATATTTT-AGTAATTATTTTGAAAAA
* * *
77342 GTGATAAATTT-GTAATTTTTTTTTAAAAA
1 GTGAT-ATTTTAGTAA-TTATTTTGAAAAA
77371 GTGATATTTTAGTAATTATTTTGAAAAA
1 GTGATATTTTAGTAATTATTTTGAAAAA
* *
77399 TGTGATATCTTT-GTAATTTTTTTTAAAAA
1 -GTGATAT-TTTAGTAATTATTTTGAAAAA
77428 G
1 G
77429 GGTGATAAAT
Statistics
Matches: 116, Mismatches: 16, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
26 6 0.05
27 14 0.12
28 16 0.14
29 77 0.66
30 3 0.03
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (28 bp):
GTGATATTTTAGTAATTATTTTGAAAAA
Found at i:79133 original size:31 final size:31
Alignment explanation
Indices: 79097--79209 Score: 102
Period size: 31 Copynumber: 3.6 Consensus size: 31
79087 ATTTTAATTG
* * *
79097 AATTTAAGAGTTAATTTGATATTTTATTTAA
1 AATTTAAGAATTAAATTAATATTTTATTTAA
* * * *
79128 AATTTAAAAATAAAAATAATATTTTATCT-A
1 AATTTAAGAATTAAATTAATATTTTATTTAA
*
79158 AAGTTAAGATATTAAATTAATATTTTATTTAA
1 AATTTAAGA-ATTAAATTAATATTTTATTTAA
* * *
79190 AAATTAGGAGTTAAAATTAA
1 AATTTAAGAATT-AAATTAA
79210 AAATTAATTT
Statistics
Matches: 64, Mismatches: 15, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
30 8 0.12
31 41 0.64
32 15 0.23
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.43
Consensus pattern (31 bp):
AATTTAAGAATTAAATTAATATTTTATTTAA
Found at i:80151 original size:26 final size:26
Alignment explanation
Indices: 80115--80188 Score: 139
Period size: 26 Copynumber: 2.8 Consensus size: 26
80105 AAGAAGGTTT
80115 TTAGTCGGCAGATTGATTCGACTATC
1 TTAGTCGGCAGATTGATTCGACTATC
*
80141 TTAGTTGGCAGATTGATTCGACTATC
1 TTAGTCGGCAGATTGATTCGACTATC
80167 TTAGTCGGCAGATTGATTCGAC
1 TTAGTCGGCAGATTGATTCGAC
80189 ATGGATATGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (26 bp):
TTAGTCGGCAGATTGATTCGACTATC
Found at i:83754 original size:63 final size:63
Alignment explanation
Indices: 83655--83778 Score: 212
Period size: 63 Copynumber: 2.0 Consensus size: 63
83645 GTGACGATGG
* * *
83655 TGGTGGAGGACATGGTGCTGACAATGATGGTGAAGGTGGCGGTGGAGGTGTAGATGGCGGCAT
1 TGGTGGAGGAAATGGTGCTGACAATGATGGTGAAGGTGACGGTGGAGGTGCAGATGGCGGCAT
*
83718 TGGTGTAGGAAATGGTGCTGACAATGATGGTGAAGGTGACGGTGGAGGTGCAGATGGCGGC
1 TGGTGGAGGAAATGGTGCTGACAATGATGGTGAAGGTGACGGTGGAGGTGCAGATGGCGGC
83779 GGCGGTGGAG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.22, C:0.10, G:0.47, T:0.22
Consensus pattern (63 bp):
TGGTGGAGGAAATGGTGCTGACAATGATGGTGAAGGTGACGGTGGAGGTGCAGATGGCGGCAT
Found at i:84715 original size:24 final size:24
Alignment explanation
Indices: 84675--84727 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
84665 TAGTGGTAGT
* *
84675 GGTGGAGGTGAAGGTGGCGGTGGC
1 GGTGGAGATGAAGGTGGCGGTGGA
*
84699 GGTGGAGATGATA-GTGGTGGTGGA
1 GGTGGAGATGA-AGGTGGCGGTGGA
84723 GGTGG
1 GGTGG
84728 CGGAGGTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.15, C:0.04, G:0.60, T:0.21
Consensus pattern (24 bp):
GGTGGAGATGAAGGTGGCGGTGGA
Found at i:91726 original size:18 final size:18
Alignment explanation
Indices: 91703--91737 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
91693 TTCCATCCGG
*
91703 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
91721 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
91738 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:93053 original size:18 final size:18
Alignment explanation
Indices: 93030--93070 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
93020 AACGGGTCAA
*
93030 CGGGTCGAGTTAACGGGT
1 CGGGTCGAGTAAACGGGT
*
93048 CGGGTCGGGTAAACGGGT
1 CGGGTCGAGTAAACGGGT
*
93066 TGGGT
1 CGGGT
93071 AAACGGGTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.49, T:0.22
Consensus pattern (18 bp):
CGGGTCGAGTAAACGGGT
Found at i:93057 original size:31 final size:31
Alignment explanation
Indices: 93022--93089 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
93012 TAGTGGTCAA
*
93022 CGGGTCAACGGGTCGAGTTAACGGGTCGGGT
1 CGGGTCAACGGGTCGAGTAAACGGGTCGGGT
* * *
93053 CGGGTAAACGGGTTGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGAGTAAACGGGTCGGGT
93084 CGGGTC
1 CGGGTC
93090 GGGTTGTGAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.16, C:0.18, G:0.47, T:0.19
Consensus pattern (31 bp):
CGGGTCAACGGGTCGAGTAAACGGGTCGGGT
Found at i:93064 original size:13 final size:13
Alignment explanation
Indices: 93048--93083 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
93038 GTTAACGGGT
93048 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
*
93061 CGGGTTGGGTAAA
1 CGGGTCGGGTAAA
93074 CGGGTCGGGT
1 CGGGTCGGGT
93084 CGGGTCGGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.17, C:0.14, G:0.50, T:0.19
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:96885 original size:18 final size:18
Alignment explanation
Indices: 96862--96896 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
96852 TTCCATCCGG
*
96862 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
96880 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
96897 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:98205 original size:13 final size:13
Alignment explanation
Indices: 98187--98215 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
98177 GTCAACGACG
98187 GTCAACGGGTCGA
1 GTCAACGGGTCGA
98200 GTCAACGGGTCGA
1 GTCAACGGGTCGA
98213 GTC
1 GTC
98216 GGGTTGTGAC
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:0.21, C:0.24, G:0.38, T:0.17
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:115004 original size:59 final size:59
Alignment explanation
Indices: 114873--115009 Score: 150
Period size: 59 Copynumber: 2.3 Consensus size: 59
114863 AACATAATAA
* *
114873 ATAGTCGAGTGACCATTTTATAACTTTTAATAGTCAAAGGACTCAACAAAGCAACATCCC
1 ATAGTCAAGGGACCATTTTATAACTTTTAATAGTC-AAGGACTCAACAAAGCAACATCCC
* * * * ** * *
114933 ATAGTCAGGGGACTATTTTCTAACTTTTAATAGTC-TGGATCTCAACAAAGCATTATTCT
1 ATAGTCAAGGGACCATTTTATAACTTTTAATAGTCAAGGA-CTCAACAAAGCAACATCCC
*
114992 ATAGTTAAGGGACCATTT
1 ATAGTCAAGGGACCATTT
115010 GTGAACTTTA
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
58 3 0.05
59 30 0.48
60 30 0.48
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (59 bp):
ATAGTCAAGGGACCATTTTATAACTTTTAATAGTCAAGGACTCAACAAAGCAACATCCC
Found at i:115249 original size:14 final size:15
Alignment explanation
Indices: 115212--115249 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
115202 TCAATAAATA
*
115212 AAAT-AAAAATGATT
1 AAATAAAAAATGAAT
115226 AAATAAAAAAT-AAT
1 AAATAAAAAATGAAT
115240 AAATAAAAAA
1 AAATAAAAAA
115250 ATGCATTCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAATAAAAAATGAAT
Found at i:117331 original size:77 final size:77
Alignment explanation
Indices: 117204--117492 Score: 328
Period size: 77 Copynumber: 3.6 Consensus size: 77
117194 TATGTTATAT
* *
117204 CATTTAAACGAAAATATTATTAAGTACAATAACATATTAGGTAGCGCTAATAGGTTGCGCTTATA
1 CATTTAAACGAAAATATTATCAAATACAATAACATATTAGGTAGCGCTAATAGGTTGCGCTTATA
*
117269 TAATAAAATTGG
66 TAATAAAATTGA
* *
117281 CATTTAAACGAAAATATTATCAAATACAATAACATGTTAGGTAGCGCTAATAGGTAT-TGCTTAT
1 CATTTAAACGAAAATATTATCAAATACAATAACATATTAGGTAGCGCTAATAGGT-TGCGCTTAT
117345 ATAATAAAATTGA
65 ATAATAAAATTGA
* * * *
117358 TATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTACCGCTTATATAATGTAATAGGT
1 CATTTAAACGAAAATATTATCAAATACAATAACATATTAGGTAGCGC----------TAATAGGT
* *
117423 AGCGCTTATATAATAAAATAGA
56 TGCGCTTATATAATAAAATTGA
* ** * *
117445 TATTTAGTCGGAAATATTATCAAATACAATAACATATTATGTAGCGCT
1 CATTTAAACGAAAATATTATCAAATACAATAACATATTAGGTAGCGCT
117493 TATATTAGAT
Statistics
Matches: 181, Mismatches: 19, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
77 113 0.62
78 1 0.01
87 67 0.37
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (77 bp):
CATTTAAACGAAAATATTATCAAATACAATAACATATTAGGTAGCGCTAATAGGTTGCGCTTATA
TAATAAAATTGA
Found at i:117442 original size:23 final size:23
Alignment explanation
Indices: 117395--117443 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
117385 AATAACATAT
**
117395 TAGGTACCGCTTATATAATGTAA
1 TAGGTACCGCTTATATAATAAAA
*
117418 TAGGTAGCGCTTATATAATAAAA
1 TAGGTACCGCTTATATAATAAAA
117441 TAG
1 TAG
117444 ATATTTAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (23 bp):
TAGGTACCGCTTATATAATAAAA
Found at i:117474 original size:87 final size:87
Alignment explanation
Indices: 117328--117497 Score: 259
Period size: 87 Copynumber: 2.0 Consensus size: 87
117318 TAGGTAGCGC
** * *
117328 TAATAGGTATTGCTTATATAATAAAATTGATATTTAACCGAAAATATTATCAAGTACAATAACAT
1 TAATAGGTAGCGCTTATATAATAAAATAGATATTTAACCGAAAATATTATCAAATACAATAACAT
117393 ATTAGGTACCGCTTATATAATG
66 ATTAGGTACCGCTTATATAATG
** *
117415 TAATAGGTAGCGCTTATATAATAAAATAGATATTTAGTCGGAAATATTATCAAATACAATAACAT
1 TAATAGGTAGCGCTTATATAATAAAATAGATATTTAACCGAAAATATTATCAAATACAATAACAT
* *
117480 ATTATGTAGCGCTTATAT
66 ATTAGGTACCGCTTATAT
117498 TAGATAGCGC
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 74 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (87 bp):
TAATAGGTAGCGCTTATATAATAAAATAGATATTTAACCGAAAATATTATCAAATACAATAACAT
ATTAGGTACCGCTTATATAATG
Found at i:117753 original size:21 final size:21
Alignment explanation
Indices: 117714--117754 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
117704 CGGTAAAAAT
* *
117714 TACCTAAAACATTATTATTTC
1 TACCTAAAACATCAATATTTC
117735 TACCTAAAACATCAATATTT
1 TACCTAAAACATCAATATTT
117755 TGTAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (21 bp):
TACCTAAAACATCAATATTTC
Found at i:118074 original size:125 final size:125
Alignment explanation
Indices: 117801--118066 Score: 399
Period size: 125 Copynumber: 2.1 Consensus size: 125
117791 ATCGGTAAAA
* * * *
117801 AATAACAAAACCGGTAACGCTTTTATCGGTTTTGTTAAGAAACCCGGTAAAATGTCAAAATAATA
1 AATAACAAAACCGGTAACGTTTTTACCAGTTTTGTTAAGAAACCCGGTAAAATATCAAAATAATA
* * * *
117866 ATAAAACCAATAGAAATAATGATGTTTTCGATATTTTTTACCAGTTTTGTTATGCACAAC
66 ATAAAACCAATAAAAATAATGATGTTTACGATAATTTTTACCAGTTTTATTATGCACAAC
*
117926 AATAACAAAACCGGTAACGTTTTTACCAGTTTTGTTAAGAAACCTGGTAAAATATCAAAATAATA
1 AATAACAAAACCGGTAACGTTTTTACCAGTTTTGTTAAGAAACCCGGTAAAATATCAAAATAATA
* * *
117991 ATAAAACTAATAAAAATAATGATGTTTACGATAATTTTTATC-GATTTTATTATGCATAAC
66 ATAAAACCAATAAAAATAATGATGTTTACGATAATTTTTACCAG-TTTTATTATGCACAAC
*
118051 AATAACAAAATCGGTA
1 AATAACAAAACCGGTA
118067 CCATTTTTTT
Statistics
Matches: 127, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
124 1 0.01
125 126 0.99
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (125 bp):
AATAACAAAACCGGTAACGTTTTTACCAGTTTTGTTAAGAAACCCGGTAAAATATCAAAATAATA
ATAAAACCAATAAAAATAATGATGTTTACGATAATTTTTACCAGTTTTATTATGCACAAC
Found at i:122216 original size:17 final size:16
Alignment explanation
Indices: 122176--122218 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
122166 AGGTAATTTA
*
122176 ATGATAATTTTTTATT
1 ATGATTATTTTTTATT
122192 AT-ATTTATTGTTTTATT
1 ATGA-TTATT-TTTTATT
122209 ATGATTATTT
1 ATGATTATTT
122219 GAAAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
15 1 0.04
16 7 0.30
17 14 0.61
18 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (16 bp):
ATGATTATTTTTTATT
Found at i:125640 original size:35 final size:34
Alignment explanation
Indices: 125555--125641 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
125545 AAAATAATTT
*
125555 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
125589 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
125627 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
125642 AATGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:129516 original size:24 final size:24
Alignment explanation
Indices: 129489--129569 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
129479 TTTATATTTT
129489 ATATTTTAGATGCTTTTAAGAATG
1 ATATTTTAGATGCTTTTAAGAATG
* * * * * *
129513 ATATTTTATAGTAC-GTAAATATATTTT
1 ATATTTTAGA-TGCTTTTAAGA-A--TG
129540 ATATTTTAGATGCTTTTAAGAATG
1 ATATTTTAGATGCTTTTAAGAATG
129564 ATATTT
1 ATATTT
129570 ATAAATCATT
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
24 20 0.50
25 3 0.08
26 3 0.08
27 14 0.35
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.49
Consensus pattern (24 bp):
ATATTTTAGATGCTTTTAAGAATG
Found at i:131294 original size:16 final size:16
Alignment explanation
Indices: 131273--131303 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
131263 ATAAATAAAT
131273 GAACATAAACGAACAC
1 GAACATAAACGAACAC
131289 GAACATAAACGAACA
1 GAACATAAACGAACA
131304 AATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:131385 original size:10 final size:10
Alignment explanation
Indices: 131370--131444 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
131360 CATTTAATAA
131370 ATAAACGAAC
1 ATAAACGAAC
131380 ATAAACGAAC
1 ATAAACGAAC
*
131390 ----GCGAAC
1 ATAAACGAAC
131396 ATAAACGAAC
1 ATAAACGAAC
** *
131406 ACGAAC-ATAA
1 ATAAACGA-AC
131416 ATGAACACGAAC
1 AT-AA-ACGAAC
131428 ATAAACGAAC
1 ATAAACGAAC
131438 ATAAACG
1 ATAAACG
131445 TTGGAGACCC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 5 0.10
9 1 0.02
10 34 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.56, C:0.21, G:0.13, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:131396 original size:16 final size:16
Alignment explanation
Indices: 131374--131438 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
131364 TAATAAATAA
131374 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
131390 GCGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
131406 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
131422 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
131438 A
1 A
131439 TAAACGTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.55, C:0.23, G:0.14, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:134865 original size:13 final size:14
Alignment explanation
Indices: 134847--134875 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
134837 TTGTCGAATT
134847 CGGATTTTTT-TAC
1 CGGATTTTTTCTAC
134860 CGGATTTTTTCTAC
1 CGGATTTTTTCTAC
134874 CG
1 CG
134876 TGTTTACCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (14 bp):
CGGATTTTTTCTAC
Found at i:144382 original size:21 final size:22
Alignment explanation
Indices: 144352--144397 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
144342 ACAAGCATCG
*
144352 TAATTGTCAAAT-AAATAAACA
1 TAATTCTCAAATCAAATAAACA
* *
144373 TAATTCTCAATTCAAATAAATA
1 TAATTCTCAAATCAAATAAACA
144395 TAA
1 TAA
144398 AATAAATAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (22 bp):
TAATTCTCAAATCAAATAAACA
Found at i:146262 original size:17 final size:18
Alignment explanation
Indices: 146240--146277 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
146230 TAATTTGTTT
146240 GATTTAATTACTCTTT-G
1 GATTTAATTACTCTTTAG
146257 GATTTAATTACTCTTTAG
1 GATTTAATTACTCTTTAG
146275 GAT
1 GAT
146278 CTTTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (18 bp):
GATTTAATTACTCTTTAG
Found at i:147482 original size:19 final size:19
Alignment explanation
Indices: 147458--147503 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
147448 TAAAAACACA
147458 TTAAATA-GTAGAATACTAT
1 TTAAATATGTAGAATA-TAT
* *
147477 TTAAATATGTATAATATTT
1 TTAAATATGTAGAATATAT
147496 TTAAATAT
1 TTAAATAT
147504 TAAACTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (19 bp):
TTAAATATGTAGAATATAT
Found at i:150109 original size:16 final size:16
Alignment explanation
Indices: 150088--150121 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
150078 TTTTCACCTC
*
150088 TTGTATTATAATCACT
1 TTGTATTACAATCACT
150104 TTGTATTACAATCACT
1 TTGTATTACAATCACT
150120 TT
1 TT
150122 TTCACCACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (16 bp):
TTGTATTACAATCACT
Done.