Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005806.1 Hibiscus syriacus cultivar Beakdansim tig00013614_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: 89155
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:5114 original size:24 final size:24
Alignment explanation
Indices: 5080--5174 Score: 102
Period size: 24 Copynumber: 4.0 Consensus size: 24
5070 AAATGGAGAT
*
5080 ATCAGAAATCAAAACAAAATTCAG
1 ATCAGAAATCAGAACAAAATTCAG
* * *
5104 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAAAATTCAG
*
5128 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAAAATTCAG
* * *
5152 GTAATG-TATCAGAACAAAATTCA
1 ATCA-GAAATCAGAACAAAATTCA
5175 AGTCGCAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 59 0.98
25 1 0.02
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAGAACAAAATTCAG
Found at i:5151 original size:12 final size:12
Alignment explanation
Indices: 5082--5151 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
5072 ATGGAGATAT
* *
5082 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
5094 CAAAATTCAGAT
1 CAGAATTCAGAA
5106 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
5118 CAGAATCCAGAT
1 CAGAATTCAGAA
*
5130 CAGAAATCAGAA
1 CAGAATTCAGAA
5142 CAGAATTCAG
1 CAGAATTCAG
5152 GTAATGTATC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.51, C:0.19, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:10611 original size:28 final size:27
Alignment explanation
Indices: 10579--10653 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 27
10569 TTTCTTTTTG
*
10579 ATTGTAATTTATAAAAAAATTGACGTT
1 ATTGTAATTTATAAAAAAATAGACGTT
* *
10606 AGTTGTAATTTATAGAAAGAAAATAGTCTTT
1 A-TTGTAATTTAT--AAA-AAAATAGACGTT
10637 ATTGTAATTTATAAAAA
1 ATTGTAATTTATAAAAA
10654 GTTGTATTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
27 3 0.07
28 14 0.34
30 14 0.34
31 10 0.24
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (27 bp):
ATTGTAATTTATAAAAAAATAGACGTT
Found at i:10644 original size:30 final size:29
Alignment explanation
Indices: 10579--10652 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 29
10569 TTTCTTTTTG
*
10579 ATTGTAATTTAT-AAA-AAAATTGACGTT
1 ATTGTAATTTATAAAAGAAAATAGACGTT
* *
10606 AGTTGTAATTTATAGAAAGAAAATAGTCTTT
1 A-TTGTAATTTATA-AAAGAAAATAGACGTT
10637 ATTGTAATTTATAAAA
1 ATTGTAATTTATAAAA
10653 AGTTGTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.03
28 11 0.28
29 3 0.08
30 15 0.38
31 10 0.25
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.41
Consensus pattern (29 bp):
ATTGTAATTTATAAAAGAAAATAGACGTT
Found at i:11895 original size:20 final size:20
Alignment explanation
Indices: 11870--11929 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
11860 GAATATTTTT
11870 TTAATTAAAAAAAATTATAA
1 TTAATTAAAAAAAATTATAA
* *
11890 TTAATT-TAAATAATATATAA
1 TTAATTAAAAAAAAT-TATAA
*
11910 TT-ATAAAATAAAAATT-TAA
1 TTAATTAAA-AAAAATTATAA
11929 T
1 T
11930 ATGAATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
19 12 0.38
20 15 0.47
21 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAATTAAAAAAAATTATAA
Found at i:12078 original size:9 final size:9
Alignment explanation
Indices: 12056--12089 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
12046 TATTTAAAAT
12056 TTAATTTCGG
1 TTAATTT-GG
12066 TTAATTTGG
1 TTAATTTGG
*
12075 TTAATTCGG
1 TTAATTTGG
12084 TTAATT
1 TTAATT
12090 AACCGATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 16 0.70
10 7 0.30
ACGTcount: A:0.24, C:0.06, G:0.18, T:0.53
Consensus pattern (9 bp):
TTAATTTGG
Found at i:17074 original size:14 final size:13
Alignment explanation
Indices: 17054--17095 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 13
17044 TTTATTATTA
17054 ATAATAATATAAT
1 ATAATAATATAAT
17067 ACTAATAATATAA-
1 A-TAATAATATAAT
17080 AT-ATAATATAAT
1 ATAATAATATAAT
17092 ATAA
1 ATAA
17096 ATTCGGATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 9 0.35
12 3 0.12
13 3 0.12
14 11 0.42
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATAATATAAT
Found at i:17391 original size:80 final size:79
Alignment explanation
Indices: 17298--17651 Score: 411
Period size: 80 Copynumber: 4.4 Consensus size: 79
17288 GGATGACGAG
* * * * * * * *
17298 TCTGCTCCTCTATTCATTCAGAGAAGATCAAACTTGATCCGTGCCATTTTTTCAGGTATTCATAT
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTGGATCTGTGCCACTTTTTC-GGTATTCAGAT
*
17363 CAACTTGAAGACTTA
65 CAACTTGAAGACATA
* * * * * *
17378 TTTTCTCCACTATTTATTCAGGGGAGATCAGACCGGATTTGTGCCACTTTTTTGTGTATTCAGAT
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTGGATCTGTGCCACTTTTTCG-GTATTCAGAT
17443 CAACTTGAAGACATA
65 CAACTTGAAGACATA
* * * * *
17458 TTTGATCCACTATTCATTCAGGGGAGATCAGACTAGATCTGTGTCACATTTTCGGGTATTCAGAT
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTGGATCTGTGCCACTTTTTC-GGTATTCAGAT
* * *
17523 AAATTTGAAGACTTA
65 CAACTTGAAGACATA
* * *
17538 TCTACTCCACTATTCATTCAAGGGAGATCAGACTGGATCTATGCCACTTTTTCTGGTATTCAGAT
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACTGGATCTGTGCCACTTTTTC-GGTATTCAGAT
* *
17603 CAACTTAAAGGCATA
65 CAACTTGAAGACATA
*
17618 TCTGCTCTACTATTCATTCAGGGGAGATCAGACT
1 TCTGCTCCACTATTCATTCAGGGGAGATCAGACT
17652 CATAAAATCT
Statistics
Matches: 228, Mismatches: 44, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
79 1 0.00
80 226 0.99
81 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (79 bp):
TCTGCTCCACTATTCATTCAGGGGAGATCAGACTGGATCTGTGCCACTTTTTCGGTATTCAGATC
AACTTGAAGACATA
Found at i:17648 original size:160 final size:160
Alignment explanation
Indices: 17298--17651 Score: 460
Period size: 160 Copynumber: 2.2 Consensus size: 160
17288 GGATGACGAG
* * * * ** *
17298 TCTGCTCCT-CTATTCATTCAGAGAAGATCAAACTTGATCCGTGCCATTTTTTCAGGTATTCATA
1 TCTGCT-CTACTATTCATTCAGGGGAGATCAGACTAGATCCGTGCCACATTTTCAGGTATTCAGA
* * * * * * *
17362 TCAACTTGAAGACTTATTTTCTCCACTATTTATTCAGGGGAGATCAGACCGGATTTGTGCCACTT
65 TAAACTTGAAGACTTATCTACTCCACTATTCATTCAAGGGAGATCAGACCGGATCTATGCCACTT
*
17427 TTTTGTGTATTCAGATCAACTTGAAGACATA
130 TTTTGTGTATTCAGATCAACTTAAAGACATA
* * * * * *
17458 TTTGATCCACTATTCATTCAGGGGAGATCAGACTAGATCTGTGTCACATTTTCGGGTATTCAGAT
1 TCTGCTCTACTATTCATTCAGGGGAGATCAGACTAGATCCGTGCCACATTTTCAGGTATTCAGAT
* *
17523 AAATTTGAAGACTTATCTACTCCACTATTCATTCAAGGGAGATCAGACTGGATCTATGCCACTTT
66 AAACTTGAAGACTTATCTACTCCACTATTCATTCAAGGGAGATCAGACCGGATCTATGCCACTTT
*
17588 TTCTG-GTATTCAGATCAACTTAAAGGCATA
131 TT-TGTGTATTCAGATCAACTTAAAGACATA
17618 TCTGCTCTACTATTCATTCAGGGGAGATCAGACT
1 TCTGCTCTACTATTCATTCAGGGGAGATCAGACT
17652 CATAAAATCT
Statistics
Matches: 165, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
159 1 0.01
160 162 0.98
161 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (160 bp):
TCTGCTCTACTATTCATTCAGGGGAGATCAGACTAGATCCGTGCCACATTTTCAGGTATTCAGAT
AAACTTGAAGACTTATCTACTCCACTATTCATTCAAGGGAGATCAGACCGGATCTATGCCACTTT
TTTGTGTATTCAGATCAACTTAAAGACATA
Found at i:30204 original size:14 final size:14
Alignment explanation
Indices: 30185--30229 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
30175 TTATTATTTA
30185 ATAATAATAATAAT
1 ATAATAATAATAAT
*
30199 ATAATACTAATAAT
1 ATAATAATAATAAT
30213 AT-A-AAT-ATAAT
1 ATAATAATAATAAT
30224 ATAATA
1 ATAATA
30230 TAAACTCGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 7 0.26
12 3 0.11
13 2 0.07
14 15 0.56
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:30845 original size:21 final size:21
Alignment explanation
Indices: 30821--30867 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
30811 AGTGGCCAAC
30821 AATAACAAAACCGGTAGAAAA
1 AATAACAAAACCGGTAGAAAA
*
30842 AATAACAAAACCGGTAGAAAT
1 AATAACAAAACCGGTAGAAAA
30863 AATAA
1 AATAA
30868 TATTTCCGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.13
Consensus pattern (21 bp):
AATAACAAAACCGGTAGAAAA
Found at i:32739 original size:23 final size:23
Alignment explanation
Indices: 32704--32751 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
32694 ATCAAGTACA
* **
32704 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAAAGCTTAT
*
32727 ATAATATAATAGGTAAAGCTTAT
1 ATAACATAATAGGTAAAGCTTAT
32750 AT
1 AT
32752 TGACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAAAGCTTAT
Found at i:32751 original size:87 final size:87
Alignment explanation
Indices: 32502--32738 Score: 438
Period size: 87 Copynumber: 2.7 Consensus size: 87
32492 TATGTTATAT
*
32502 TATTTAATGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
32567 AGCGCTTATATAATAAAACAGG
66 AGCGCTTATATAATAAAACAGG
32589 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
*
32654 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAACAGG
* *
32676 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAG
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAG
32739 GTAAAGCTTA
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 146 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.32
Consensus pattern (87 bp):
TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAACAGG
Found at i:36192 original size:200 final size:200
Alignment explanation
Indices: 35849--36560 Score: 1246
Period size: 200 Copynumber: 3.6 Consensus size: 200
35839 TGAAGGAAGA
* * *
35849 AAAACCGCGT-TACTTATACCGGTTAGATTGAAAAATTACCTAATACATTATACTTTTGGGTTTC
1 AAAACCG-GTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTC
* *
35913 GATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTGTTTGCCA
65 GATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCA
*
35978 TTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTAGACCTATTC
130 TTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTC
36043 TCTCAT
195 TCTCAT
*
36049 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACTTATTACATTATACTTATGGGTTTCG
1 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCG
* *
36114 ATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTTCCAA
66 ATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCAT
*
36179 TCATTCTGGACCAAAAATATCGACACATACTACAAAAGTGTCGATACATTATTTAGACCTATTCT
131 TCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCT
36244 CTCAT
196 CTCAT
*
36249 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTATGGGTTTCG
1 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCG
* *
36314 ATGTTTATCGGATCGACACTTTTTATATATGGATCAACACTTTATTGTTGCACCCTGTTTGCCAT
66 ATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCAT
*
36379 TCATTATGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCT
131 TCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCT
36444 CTCAT
196 CTCAT
* *
36449 AAAACCGGTATACTTGTACCGATTAGATTGAAAAATTACCTATTACATTATACTTTTGGGTTTCG
1 AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCG
*
36514 ATGTTTATGGGATCGACACTTTTTATATATAGATCGACACTTATATT
66 ATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTT-TATT
36561 TTACCTTCAA
Statistics
Matches: 487, Mismatches: 23, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
199 2 0.00
200 481 0.99
201 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
AAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCG
ATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCCTGTTTGCCAT
TCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGATACATTATTTAGACCTATTCT
CTCAT
Found at i:37203 original size:20 final size:19
Alignment explanation
Indices: 37157--37203 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
37147 TCCGGTAACG
37157 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
37176 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
37197 TTTTACC
1 TTTTACC
37204 TGGTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:37303 original size:181 final size:182
Alignment explanation
Indices: 37000--37415 Score: 629
Period size: 182 Copynumber: 2.3 Consensus size: 182
36990 TCCGGTATCG
* * * *
37000 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATA-TTTTTTTTAAAGTATTG
1 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCG
*
37064 ACACATTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-TAAAG
66 ACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAG
* * * **
37128 TATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGA
131 TACCGACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATTTCAA
*
37180 TACCGGTTTTATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCG
1 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCG
* ** * *
37245 ACACTTTATAGGATTTAAAACTGTTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATTAAAG
66 ACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAG
* *
37310 TACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAA
131 TACCGACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATTTCAA
* * *
37362 TACCGGTTTTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
1 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
37416 AATTTGGATC
Statistics
Matches: 212, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
180 45 0.21
181 67 0.32
182 100 0.47
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
TACCGGTTTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCG
ACACATTATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAG
TACCGACACTTTAAATATATCCGGTAACGCTTTACCGGTTTTATCATTTCAA
Found at i:41968 original size:18 final size:18
Alignment explanation
Indices: 41945--41979 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41935 ACTAATTATA
* *
41945 ATATTAGTATAATTTTAC
1 ATATTAGGATAACTTTAC
41963 ATATTAGGATAACTTTA
1 ATATTAGGATAACTTTA
41980 TAATATAGTT
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:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (18 bp):
ATATTAGGATAACTTTAC
Found at i:45639 original size:10 final size:9
Alignment explanation
Indices: 45616--45641 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
45606 TTAAATACAG
45616 ATTTTTGTA
1 ATTTTTGTA
45625 ATTTTTGTA
1 ATTTTTGTA
45634 ATTTTTGT
1 ATTTTTGT
45642 GCTTAATGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (9 bp):
ATTTTTGTA
Found at i:48449 original size:65 final size:63
Alignment explanation
Indices: 48376--48532 Score: 219
Period size: 65 Copynumber: 2.4 Consensus size: 63
48366 GAATAAATTG
*
48376 AACATCGAATGCATTATATGCATCGATGCACATA-CCATGCATCGATGCACTCAGG-TTTTTATG
1 AACATCGAATGCATT-TATGCATCGATGCACA-AGCCATGCATCGATGCACTCAGGCTTGTT-TG
48439 AA
63 -A
*
48441 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCGGGCTTGTTTGA
1 AACATCGAATGCATTT-ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTTGTTTGA
*
48505 AACATCGAATGCACTTCATGCATCGATG
1 AACATCGAATGCA-TTTATGCATCGATG
48533 GACTCTTAGT
Statistics
Matches: 85, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
64 27 0.32
65 54 0.64
66 4 0.05
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTTGTTTGA
Found at i:49864 original size:36 final size:36
Alignment explanation
Indices: 49824--49998 Score: 244
Period size: 36 Copynumber: 4.9 Consensus size: 36
49814 TTTTCAAGTC
*
49824 AATCAAGCCTTCACTAAAGAGTAGTGAAGCAATACG
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATACG
* *
49860 AATCAAGCCTTCCCAAAAGAGTAGTGAAGCTATACG
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATACG
* *
49896 AATCAAGCCTTCACAAAAGAGTAGTGAAGAAATACA
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATACG
* * * *
49932 AATCAAGCTTTCACAAAAGAGTAGTAAAGCGATGC-
1 AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATACG
*
49967 ACATCCAGCCTTCACAAAAGAGTAGTGAAGCA
1 A-ATCAAGCCTTCACAAAAGAGTAGTGAAGCA
49999 GGAACAAATC
Statistics
Matches: 122, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
35 1 0.01
36 121 0.99
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.18
Consensus pattern (36 bp):
AATCAAGCCTTCACAAAAGAGTAGTGAAGCAATACG
Found at i:52123 original size:17 final size:18
Alignment explanation
Indices: 52088--52128 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
52078 TTTTAAAAAA
*
52088 TATTTATTAGATTATTAT
1 TATTTATTAGATAATTAT
52106 T-TTTATT-GATAATATAT
1 TATTTATTAGATAAT-TAT
52123 TATTTA
1 TATTTA
52129 ATAAAAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 5 0.25
17 10 0.50
18 5 0.25
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
TATTTATTAGATAATTAT
Found at i:53283 original size:3 final size:3
Alignment explanation
Indices: 53275--53379 Score: 201
Period size: 3 Copynumber: 35.0 Consensus size: 3
53265 ACCGACATGT
53275 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
53323 GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
53371 GAA GAA GAA
1 GAA GAA GAA
53380 ACAGCAGCTT
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 100 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:56671 original size:18 final size:18
Alignment explanation
Indices: 56643--56684 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
56633 AAGCTTTGTT
56643 GAAGA-ATCATCACAGGC
1 GAAGACATCATCACAGGC
56660 GAAGACATCATCACAGGC
1 GAAGACATCATCACAGGC
56678 GAAGACA
1 GAAGACA
56685 GGCTTCTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.43, C:0.24, G:0.24, T:0.10
Consensus pattern (18 bp):
GAAGACATCATCACAGGC
Found at i:59786 original size:22 final size:22
Alignment explanation
Indices: 59760--59804 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
59750 TGAAGGCTTC
*
59760 AAAACTTAATCGAAGGAGAAAG
1 AAAACTAAATCGAAGGAGAAAG
59782 AAAACTAAATCGAAGGAGAAAG
1 AAAACTAAATCGAAGGAGAAAG
59804 A
1 A
59805 CCCGATCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.58, C:0.09, G:0.22, T:0.11
Consensus pattern (22 bp):
AAAACTAAATCGAAGGAGAAAG
Found at i:64555 original size:13 final size:13
Alignment explanation
Indices: 64537--64575 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
64527 AAAACTATAC
64537 ATATTATTTTCAA
1 ATATTATTTTCAA
64550 ATATTATTTTCAA
1 ATATTATTTTCAA
*
64563 ATAAT-TTTTCAA
1 ATATTATTTTCAA
64575 A
1 A
64576 ACATTGCCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATTATTTTCAA
Found at i:65630 original size:21 final size:21
Alignment explanation
Indices: 65588--65631 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
65578 ACTCTGGGAG
* *
65588 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
65609 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
65630 CT
1 CT
65632 CATCCTCTGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:66823 original size:65 final size:65
Alignment explanation
Indices: 66704--66915 Score: 213
Period size: 65 Copynumber: 3.3 Consensus size: 65
66694 TTTTTCAGAG
* * * *
66704 TGATGCACCGATGCAC-CAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATG
1 TGATGCATCGATGCACTC-AGCCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATG
66765 CATT
62 CATT
* * *
66769 TCATGCATCGATGCACTTA-CCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCA
66832 TT
64 TT
** * * *
66834 TGATGCATCGATGCAC-CAGCCATGCATTGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
66898 TGATGCATCGATGCACTC
1 TGATGCATCGATGCACTC
66916 TTAGTGCACC
Statistics
Matches: 124, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 47 0.38
65 71 0.57
66 3 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.27
Consensus pattern (65 bp):
TGATGCATCGATGCACTCAGCCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:66913 original size:17 final size:19
Alignment explanation
Indices: 66885--66933 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
66875 TATTTTGAAA
66885 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
66903 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
66922 CACCGATGCACT
1 CATCGATGCACT
66934 AAGGGTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:69283 original size:46 final size:45
Alignment explanation
Indices: 69211--69323 Score: 190
Period size: 46 Copynumber: 2.5 Consensus size: 45
69201 ATACTGGTTA
*
69211 ACATGTTCATCATATATACATTCACAATCAGTTCTTGTTTGTACAT
1 ACATGTTCATCATATAT-CCTTCACAATCAGTTCTTGTTTGTACAT
*
69257 ACATGTTCATCATATATCCTTCCACAATCTGTTCTTGTTTGTACAT
1 ACATGTTCATCATATATCCTT-CACAATCAGTTCTTGTTTGTACAT
69303 ACATGTTCATCATATATCCTT
1 ACATGTTCATCATATATCCTT
69324 GTTGTGATTC
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
45 3 0.05
46 61 0.95
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.42
Consensus pattern (45 bp):
ACATGTTCATCATATATCCTTCACAATCAGTTCTTGTTTGTACAT
Found at i:70899 original size:10 final size:10
Alignment explanation
Indices: 70884--70910 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
70874 TGAGATTTAA
70884 ATATAATCAC
1 ATATAATCAC
70894 ATATAATCAC
1 ATATAATCAC
70904 ATATAAT
1 ATATAAT
70911 ATAGAGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (10 bp):
ATATAATCAC
Found at i:71508 original size:3 final size:3
Alignment explanation
Indices: 71500--71585 Score: 163
Period size: 3 Copynumber: 28.3 Consensus size: 3
71490 CGGTAAAATG
71500 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
71548 AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT A
71586 CATTTATTTA
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 79 0.96
4 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:77357 original size:14 final size:14
Alignment explanation
Indices: 77340--77389 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
77330 AAAATGCAAT
77340 AATTAAAGGACTAA
1 AATTAAAGGACTAA
*
77354 AATTAAAGTACTAAA
1 AATTAAAGGACT-AA
* * *
77369 AAATAAAGGGCAAA
1 AATTAAAGGACTAA
77383 AATTAAA
1 AATTAAA
77390 AATAAAAGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.20
Consensus pattern (14 bp):
AATTAAAGGACTAA
Found at i:79123 original size:25 final size:22
Alignment explanation
Indices: 79073--79125 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
79063 CTTTATGAAT
79073 TTCTTCTCACTCCTCAAAGAAG
1 TTCTTCTCACTCCTCAAAGAAG
79095 TTCTTCTCACTCCTCAAATG-AG
1 TTCTTCTCACTCCTCAAA-GAAG
79117 TTCTTCTCA
1 TTCTTCTCA
79126 TTCTGAACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.23, C:0.32, G:0.08, T:0.38
Consensus pattern (22 bp):
TTCTTCTCACTCCTCAAAGAAG
Found at i:79448 original size:66 final size:66
Alignment explanation
Indices: 79302--79628 Score: 393
Period size: 66 Copynumber: 4.9 Consensus size: 66
79292 GAAAGAAATT
* * * * * * *
79302 TGTTTTAAGAGAAGCTATCTCATGTGAGATAAAATTTTGTTTCGAGTGAAACAATATCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGA-AAAAATTTGTTTCGAGAGAAACAATATCAAAGGTT
79367 TA
65 TA
* * *** * * * *
79369 TGTTTCAAGAGAAACCGTCTCAAGTGAGATGCAATTTATTTTGAGAGAAAAAATCTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGAAAAAATTTGTTTCGAGAGAAACAATATCAAAGGTTT
79434 A
66 A
* * * *
79435 TATTTCAAGAGAAATTGTCTCAAGCGAGACAAAACTTTGTTTCGAGAGAAATAATATCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGA-AAAAATTTGTTTCGAGAGAAACAATATCAAAGGTT
79500 TA
65 TA
79502 TGTTTCAAGAGAAACTGTCTCAAGCGAGAAAAAATTTGTTTCGAGAGAAACAATATCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGAAAAAATTTGTTTCGAGAGAAACAATATCAAAGGTTT
79567 A
66 A
* * * * * * *
79568 TGTTTCAAGTGAAATTGTCTCAAGCCAGACAAAATTTGTTTCAAGAGAAATAATCTCAAAG
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGAAAAAATTTGTTTCGAGAGAAACAATATCAAAG
79629 CATGCAGACA
Statistics
Matches: 222, Mismatches: 37, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
66 142 0.64
67 80 0.36
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.31
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGAAAAAATTTGTTTCGAGAGAAACAATATCAAAGGTTT
A
Found at i:79548 original size:133 final size:132
Alignment explanation
Indices: 79327--79628 Score: 433
Period size: 133 Copynumber: 2.3 Consensus size: 132
79317 TATCTCATGT
* * *
79327 GAGATAAAATTTTGTTTCGAGTGAAACAATATCAAAGGTTTATGTTTCAAGAGAAACCGTCTCAA
1 GAGACAAAA-TTTGTTTCGAGAGAAATAATATCAAAGGTTTATGTTTCAAGAGAAACCGTCTCAA
* *** * *
79392 GTGAGATGCAATTTATTTTGAGAGAAAAAATCTCAAAGGTTTATATTTCAAGAGAAATTGTCTCA
65 GCGAGAAAAAATTTATTTCGAGAGAAAAAATATCAAAGGTTTATATTTCAAGAGAAATTGTCTCA
79457 AGC
130 AGC
*
79460 GAGACAAAACTTTGTTTCGAGAGAAATAATATCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAA
1 GAGACAAAA-TTTGTTTCGAGAGAAATAATATCAAAGGTTTATGTTTCAAGAGAAACCGTCTCAA
* * * *
79525 GCGAGAAAAAATTTGTTTCGAGAGAAACAATATCAAAGGTTTATGTTTCAAGTGAAATTGTCTCA
65 GCGAGAAAAAATTTATTTCGAGAGAAAAAATATCAAAGGTTTATATTTCAAGAGAAATTGTCTCA
79590 AGC
130 AGC
* * *
79593 CAGACAAAATTTGTTTCAAGAGAAATAATCTCAAAG
1 GAGACAAAATTTGTTTCGAGAGAAATAATATCAAAG
79629 CATGCAGACA
Statistics
Matches: 151, Mismatches: 18, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
132 25 0.17
133 126 0.83
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (132 bp):
GAGACAAAATTTGTTTCGAGAGAAATAATATCAAAGGTTTATGTTTCAAGAGAAACCGTCTCAAG
CGAGAAAAAATTTATTTCGAGAGAAAAAATATCAAAGGTTTATATTTCAAGAGAAATTGTCTCAA
GC
Found at i:85106 original size:14 final size:15
Alignment explanation
Indices: 85089--85126 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
85079 AAAATGCAAT
85089 AATTAAAGGACT-AA
1 AATTAAAGGACTGAA
*
85103 AATTAAAGCACTGAA
1 AATTAAAGGACTGAA
*
85118 AAATAAAGG
1 AATTAAAGG
85127 GAAAAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.58, C:0.08, G:0.16, T:0.18
Consensus pattern (15 bp):
AATTAAAGGACTGAA
Found at i:85243 original size:19 final size:20
Alignment explanation
Indices: 85219--85259 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
85209 TTAAATGTGC
* *
85219 ATAAAATTG-AATAATAAAA
1 ATAAAATAGCAATAAAAAAA
85238 ATAAAATAGCAATAAAAAAA
1 ATAAAATAGCAATAAAAAAA
85258 AT
1 AT
85260 GTTAATGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (20 bp):
ATAAAATAGCAATAAAAAAA
Found at i:85832 original size:17 final size:17
Alignment explanation
Indices: 85812--85844 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
85802 TATTTTCAAG
*
85812 TTTTAATTTTTATTTTA
1 TTTTAAGTTTTATTTTA
85829 TTTTAAGTTTTATTTT
1 TTTTAAGTTTTATTTT
85845 TAAACATGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTTAAGTTTTATTTTA
Found at i:85836 original size:24 final size:24
Alignment explanation
Indices: 85800--85846 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
85790 TCTTCTTTTC
85800 TTTATTTTCAAGTTTTAATTTTTAT
1 TTTATTTTCAAGTTTT-ATTTTTAT
85825 TTTATTTT-AAGTTTTATTTTTA
1 TTTATTTTCAAGTTTTATTTTTA
85847 AACATGCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 7 0.32
24 7 0.32
25 8 0.36
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTATTTTCAAGTTTTATTTTTAT
Found at i:85839 original size:12 final size:12
Alignment explanation
Indices: 85800--85844 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
85790 TCTTCTTTTC
85800 TTTATTTTCAAGT
1 TTTATTTT-AAGT
*
85813 TTTAATTTTTA-T
1 TTT-ATTTTAAGT
85825 TTTATTTTAAGT
1 TTTATTTTAAGT
85837 TTTATTTT
1 TTTATTTT
85845 TAAACATGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 6 0.21
12 13 0.46
13 4 0.14
14 5 0.18
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.71
Consensus pattern (12 bp):
TTTATTTTAAGT
Done.