Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001164.1 Hibiscus syriacus cultivar Beakdansim tig00002320_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: 67943
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:7542 original size:41 final size:43
Alignment explanation
Indices: 7454--7548 Score: 122
Period size: 43 Copynumber: 2.3 Consensus size: 43
7444 CGTTTTTTAT
** **
7454 AAAAACGCCGTAAAATATTATATATATTGCGGTGTTTATCTTA
1 AAAAACGCCACAAAATATTATATATATTGCGGCATTTATCTTA
* *
7497 AAAAATGCCACAAAATATTATATCTATTGCGGCATTTATC-T-
1 AAAAACGCCACAAAATATTATATATATTGCGGCATTTATCTTA
7538 AAAAACGCCAC
1 AAAAACGCCAC
7549 TAAGGGTACG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 10 0.22
42 1 0.02
43 34 0.76
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.32
Consensus pattern (43 bp):
AAAAACGCCACAAAATATTATATATATTGCGGCATTTATCTTA
Found at i:7565 original size:42 final size:41
Alignment explanation
Indices: 7519--7865 Score: 358
Period size: 41 Copynumber: 8.4 Consensus size: 41
7509 AAATATTATA
* * * *
7519 TCTATTGCGGCATTTATCTAAAAACGCCACTAAGGGTACGAG
1 TCTATAGCGGCGTTTATATAAAAACGCCACTAA-AGTACGAG
** * *
7561 TCTATAGCAACGTTTGTATAAAAACGCCACTAAAGTACTAG
1 TCTATAGCGGCGTTTATATAAAAACGCCACTAAAGTACGAG
*
7602 TCTATAGCGGCGTTTATATAAAAACGCTACTAAAGTACGAG
1 TCTATAGCGGCGTTTATATAAAAACGCCACTAAAGTACGAG
* * * *
7643 TCT-TAAGCGGCTTTTCAT-TCAAAACACCACTAAAGTACAAG
1 TCTAT-AGCGGCGTTT-ATATAAAAACGCCACTAAAGTACGAG
* * * * *
7684 TTTATAGCAGCGTTTAGATTCAAAACGCCACTAAAGTATGAG
1 TCTATAGCGGCGTTTATA-TAAAAACGCCACTAAAGTACGAG
* * * * *
7726 TATATAGCGGCGTTTGTATAGAAACACCACTAAAGTACTAG
1 TCTATAGCGGCGTTTATATAAAAACGCCACTAAAGTACGAG
* * * *
7767 TATATAGCGGCGTTTGTATAAAAACACCACTAAAGTACGAT
1 TCTATAGCGGCGTTTATATAAAAACGCCACTAAAGTACGAG
* *
7808 TCTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTACGTA-
1 TCTATAGCGGCGTTTATATAAAAACGCCACTAAAGTACG-AG
*
7849 CCTATAGCGGCGTTTAT
1 TCTATAGCGGCGTTTAT
7866 GGATACAAAC
Statistics
Matches: 257, Mismatches: 42, Indels: 13
0.82 0.13 0.04
Matches are distributed among these distances:
40 2 0.01
41 190 0.74
42 65 0.25
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (41 bp):
TCTATAGCGGCGTTTATATAAAAACGCCACTAAAGTACGAG
Found at i:7843 original size:165 final size:166
Alignment explanation
Indices: 7539--7845 Score: 424
Period size: 165 Copynumber: 1.9 Consensus size: 166
7529 CATTTATCTA
* * * *
7539 AAAACGCCACTAAGGGTACGAGTCTATAGCAACGTTTGTATAAAAACGCCACTAAAGTACTAGTC
1 AAAACGCCACTAAGAGTACGAGTATATAGCAACGTTTGTATAAAAACACCACTAAAGTACTAGTA
* * *
7604 TATAGCGGCGTTTATATAAAAACGCTACTAAAGTACGAGTCTTAAGCGGCTTTTCATTCAAAACA
66 TATAGCGGCGTTTATATAAAAACACCACTAAAGTACGAGTCTTAAGCGGCTTTTCATTAAAAACA
7669 CCACTAAAGTACAAGTTTATAGCAGCGTTTAGATTC
131 CCACTAAAGTACAAGTTTATAGCAGCGTTTAGATTC
* ** *
7705 AAAACGCCACTAA-AGTATGAGTATATAGCGGCGTTTGTATAGAAACACCACTAAAGTACTAGTA
1 AAAACGCCACTAAGAGTACGAGTATATAGCAACGTTTGTATAAAAACACCACTAAAGTACTAGTA
* *
7769 TATAGCGGCGTTTGTATAAAAACACCACTAAAGTACGATTC-TATAGCGGCGTTTGT-A-TAAAA
66 TATAGCGGCGTTTATATAAAAACACCACTAAAGTACGAGTCTTA-AGCGGC-TTT-TCATTAAAA
**
7831 ATGCCACTAAAGTAC
128 ACACCACTAAAGTAC
7846 GTACCTATAG
Statistics
Matches: 123, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
164 2 0.02
165 103 0.84
166 17 0.14
167 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (166 bp):
AAAACGCCACTAAGAGTACGAGTATATAGCAACGTTTGTATAAAAACACCACTAAAGTACTAGTA
TATAGCGGCGTTTATATAAAAACACCACTAAAGTACGAGTCTTAAGCGGCTTTTCATTAAAAACA
CCACTAAAGTACAAGTTTATAGCAGCGTTTAGATTC
Found at i:9216 original size:41 final size:41
Alignment explanation
Indices: 9108--9285 Score: 200
Period size: 41 Copynumber: 4.4 Consensus size: 41
9098 GACTATATAT
* * ** *
9108 TTAACA-TTTTGCGGCGTTTATATAAAAAAACCATTATTGA
1 TTAACACTATTGCGGCGTTTATTTAAAAACGCCACTATTGA
* * *
9148 TT-ACACTATTGTGGCGTTTGTTAAAAAACGCCACTATTGA
1 TTAACACTATTGCGGCGTTTATTTAAAAACGCCACTATTGA
* *
9188 TTAAAACTATTACGGCGTTT-TTCTAAAAACGCCACTATTGA
1 TTAACACTATTGCGGCGTTTATT-TAAAAACGCCACTATTGA
* *
9229 TTAACACTATTGCGGCGTTTATTTAAAAAGGCCACTATTTA
1 TTAACACTATTGCGGCGTTTATTTAAAAACGCCACTATTGA
* *
9270 TTATCATTATTGCGGC
1 TTAACACTATTGCGGC
9286 ATTTTAAGAA
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
39 3 0.03
40 32 0.28
41 79 0.68
42 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (41 bp):
TTAACACTATTGCGGCGTTTATTTAAAAACGCCACTATTGA
Found at i:9424 original size:41 final size:41
Alignment explanation
Indices: 9152--9446 Score: 171
Period size: 41 Copynumber: 7.1 Consensus size: 41
9142 TATTGATTAC
* * *
9152 ACTATTGTGGCGTTTGTT-AAAAAACGCCACTAT-TGATTAAA
1 ACTATTGCGGCGTTTTTTGTAAAAACGCCACTATATG-TT-AA
* *
9193 ACTATTACGGCG-TTTTTCTAAAAACGCCACTAT-TGATTAA
1 ACTATTGCGGCGTTTTTTGTAAAAACGCCACTATATG-TTAA
* * * * *
9233 CACTATTGCGGCGTTTATT-TAAAAAGGCCACTATTTATTATC
1 -ACTATTGCGGCGTTTTTTGTAAAAACGCCACTATATGTTA-A
* * ** *
9275 ATTATTGCGGCATTTTAAG-AATAAATGCCACTATATGTGGT-A
1 ACTATTGCGGCGTTTTTTGTAA-AAACGCCACTATATGT--TAA
* * * * *
9317 TCTATTACGGCGTTTGTGGTATAAACGCCACTA-AT-TTACCGA
1 ACTATTGCGGCGTTTTTTGTAAAAACGCCACTATATGTTA---A
* *
9359 TCTATTGCGGCG-TTTTAGCT-AAAACGCCACTATATGTTAA
1 ACTATTGCGGCGTTTTTTG-TAAAAACGCCACTATATGTTAA
* * *
9399 ACTATTGCGGCGTTTTTTGTAAAAACGCCGCTAAATGTCAA
1 ACTATTGCGGCGTTTTTTGTAAAAACGCCACTATATGTTAA
9440 ATCTATT
1 A-CTATT
9447 ACAACGTTTT
Statistics
Matches: 198, Mismatches: 36, Indels: 39
0.73 0.13 0.14
Matches are distributed among these distances:
38 1 0.01
40 20 0.10
41 112 0.57
42 60 0.30
43 4 0.02
44 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (41 bp):
ACTATTGCGGCGTTTTTTGTAAAAACGCCACTATATGTTAA
Found at i:13490 original size:40 final size:42
Alignment explanation
Indices: 13446--13848 Score: 180
Period size: 41 Copynumber: 9.8 Consensus size: 42
13436 TTTACACTTC
13446 AAACGCCACAA-A-A-TAGTAACTTTAGCGGCGTTTTTATACA
1 AAACGCCACAACAGAGTAGT-ACTTTAGCGGCGTTTTTATACA
* *
13486 AAACGCCGCAACAGAGTAGTACTTTAGTGGCGTTTTTATAC-
1 AAACGCCACAACAGAGTAGTACTTTAGCGGCGTTTTTATACA
** * ** * *
13527 AAACGCTGCAATAG-GT--TCATCCATAGTGGCGTTTTT-TAAA
1 AAACGCCACAACAGAGTAGT-A-CTTTAGCGGCGTTTTTATACA
*** * *
13567 CAAACGCCGTGACATAGTAGTACTTTAGCGGCGTTTTAATA-A
1 -AAACGCCACAACAGAGTAGTACTTTAGCGGCGTTTTTATACA
* * * * * * *
13609 AAACGCCGCAATAGGGTTCA-TA-TATTA-TGGCATTTTCA-A-T
1 AAACGCCACAACAGAG-T-AGTACT-TTAGCGGCGTTTTTATACA
* *
13649 AAACGCCGCAACAGAGTAGTACTTTTGCGGCGTTTTTTATAC-
1 AAACGCCACAACAGAGTAGTACTTTAGCGGCG-TTTTTATACA
* * *
13691 AAACACCGCAAAAGAGTAGTACTTTAGCGGCGTTTTTATACA
1 AAACGCCACAACAGAGTAGTACTTTAGCGGCGTTTTTATACA
* * * * * *
13733 AAA-GCCGCTATAGA-CACGTACTTTAGTGGCGTTTTTATTC-
1 AAACGCCACAACAGAGTA-GTACTTTAGCGGCGTTTTTATACA
* * * * * *
13773 AAACGCCGCTATA-AATACGTTCTTTAGCGGCATTTTTATAC-
1 AAACGCCACAACAGAGTA-GTACTTTAGCGGCGTTTTTATACA
* * * * * *
13814 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTT
1 AAACGCCACAACAGAGTAGTACTTTAGCGGCGTTT
13849 GTGTTTACAA
Statistics
Matches: 288, Mismatches: 50, Indels: 49
0.74 0.13 0.13
Matches are distributed among these distances:
38 2 0.01
39 8 0.03
40 50 0.17
41 142 0.49
42 77 0.27
43 8 0.03
44 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (42 bp):
AAACGCCACAACAGAGTAGTACTTTAGCGGCGTTTTTATACA
Found at i:13562 original size:82 final size:82
Alignment explanation
Indices: 13472--13848 Score: 286
Period size: 82 Copynumber: 4.6 Consensus size: 82
13462 TAACTTTAGC
* *
13472 GGCGTTTTTATACAAAACGCCGCAACAGAGTAGTACTTTAGTGGCGTTTTTATACAAACGCTGCA
1 GGCGTTTTTATACAAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGCCGCA
*
13537 ATAGGTTCATCCATAGT
66 ATAGGTTCATCTATAGT
* ** * * *
13554 GGCGTTTTT-TAAACAAACGCCGTGACATAGTAGTACTTTAGCGGCGTTTTAATAAAAACGCCGC
1 GGCGTTTTTATACA-AAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGCCGC
*
13618 AATAGGGTTCATATATTA-T
65 AATA-GGTTCATCTA-TAGT
* * * * *
13637 GGCATTTTCA-A-TAAACGCCGCAACAGAGTAGTACTTTTGCGGCGTTTTTTATACAAACACCGC
1 GGCGTTTTTATACAAAACGCCGCAACAGAGTAGTACTTTAGCGGCG-TTTTTATACAAACGCCGC
* * *
13700 AAAAGAG-T-AGTACTTTAGC
65 AATAG-GTTCA-T-CTATAGT
* * * * *
13719 GGCGTTTTTATACAAAA-GCCGCTATAGA-CACGTACTTTAGTGGCGTTTTTATTCAAACGCCGC
1 GGCGTTTTTATACAAAACGCCGCAACAGAGTA-GTACTTTAGCGGCGTTTTTATACAAACGCCGC
* ** * * * *
13782 TATAAATACGTTCTTTAGC
65 AATAGGTTC-ATCTATAGT
* * * * * *
13801 GGCATTTTTATAC-AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTT
1 GGCGTTTTTATACAAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTT
13849 GTGTTTACAA
Statistics
Matches: 235, Mismatches: 43, Indels: 34
0.75 0.14 0.11
Matches are distributed among these distances:
80 1 0.00
81 39 0.17
82 150 0.64
83 40 0.17
84 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (82 bp):
GGCGTTTTTATACAAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGCCGCA
ATAGGTTCATCTATAGT
Found at i:13613 original size:41 final size:41
Alignment explanation
Indices: 13459--13616 Score: 96
Period size: 42 Copynumber: 3.8 Consensus size: 41
13449 CGCCACAAAA
* **
13459 TAGTAACTTTAGCGGCGTTTTTATACAAAACGCCGCAACAGAG
1 TAGTAACTTTAGCGGCGTTTTAATA-AAAACGCCGTGACA-AG
* * *
13502 TAGT-ACTTTAGTGGCGTTTTTATACAAACG-C-TG-CAA-
1 TAGTAACTTTAGCGGCGTTTTAATAAAAACGCCGTGACAAG
* ** * *
13538 TAGGTTCATCCATAGTGGCGTTTTTTAA-ACAAACGCCGTGACATAG
1 TA-G-T-AACTTTAGCGGCG--TTTTAATAAAAACGCCGTGACA-AG
13584 TAGT-ACTTTAGCGGCGTTTTAATAAAAACGCCG
1 TAGTAACTTTAGCGGCGTTTTAATAAAAACGCCG
13617 CAATAGGGTT
Statistics
Matches: 90, Mismatches: 13, Indels: 26
0.70 0.10 0.20
Matches are distributed among these distances:
36 2 0.02
37 2 0.02
38 3 0.03
40 16 0.18
41 21 0.23
42 33 0.37
43 6 0.07
44 3 0.03
45 2 0.02
46 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (41 bp):
TAGTAACTTTAGCGGCGTTTTAATAAAAACGCCGTGACAAG
Found at i:13754 original size:41 final size:41
Alignment explanation
Indices: 13667--13848 Score: 197
Period size: 41 Copynumber: 4.4 Consensus size: 41
13657 CAACAGAGTA
* * * *
13667 GTACTTTTGCGGCGTTTTTTATACAAACA-CCGCAAAAGAGTA-
1 GTACTTTAGCGGCG-TTTTTATACAAA-AGCCGCTATAGA-CAC
13709 GTACTTTAGCGGCGTTTTTATACAAAAGCCGCTATAGACAC
1 GTACTTTAGCGGCGTTTTTATACAAAAGCCGCTATAGACAC
* * * * *
13750 GTACTTTAGTGGCGTTTTTATTCAAACGCCGCTATAAATAC
1 GTACTTTAGCGGCGTTTTTATACAAAAGCCGCTATAGACAC
* * * *
13791 GTTCTTTAGCGGCATTTTTATACAAACGCCGCTATAGACTC
1 GTACTTTAGCGGCGTTTTTATACAAAAGCCGCTATAGACAC
*
13832 GTACTTTAGTGGCGTTT
1 GTACTTTAGCGGCGTTT
13849 GTGTTTACAA
Statistics
Matches: 119, Mismatches: 19, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
40 2 0.02
41 104 0.87
42 13 0.11
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (41 bp):
GTACTTTAGCGGCGTTTTTATACAAAAGCCGCTATAGACAC
Found at i:13809 original size:123 final size:125
Alignment explanation
Indices: 13445--13848 Score: 362
Period size: 123 Copynumber: 3.3 Consensus size: 125
13435 GTTTACACTT
* * *
13445 CAAACGCCACAAAATAGTA--ACTTTAGCGGCGTTTTTATACAAAACGCCGCAACAGAGTA-GTA
1 CAAACGCCGCAAAAGAGTAGTACTTTAGCGGCGTTTTTATACAAAACGCCGCAATAGA-TACGTA
* * * * * ** * *
13507 CTTTAGTGGCGTTTTTATACAAACGCTGCAATAGGTTC-ATCCATAGTGGCGTTTTTTAAA
65 CTTTAGTGGCGTTTTTATTCAAACGCCGCAATAAGTACGTTCTTTAGCGGCGTTTTTTATA
** * * * * * *
13567 CAAACGCCGTGACATAGTAGTACTTTAGCGGCGTTTTAATA-AAAACGCCGCAATAGGGTTCATA
1 CAAACGCCGCAAAAGAGTAGTACTTTAGCGGCGTTTTTATACAAAACGCCGCAATA-GATACGTA
* * * * * *
13631 -TATTA-TGGCATTTTCAAT-AAACGCCGCAACAGAGTA-GTACTTTTGCGGCGTTTTTTATA
65 CT-TTAGTGGCGTTTTTATTCAAACGCCGCAATA-AGTACGTTCTTTAGCGGCGTTTTTTATA
* * *
13690 CAAACACCGCAAAAGAGTAGTACTTTAGCGGCGTTTTTATACAAAA-GCCGCTATAGACACGTAC
1 CAAACGCCGCAAAAGAGTAGTACTTTAGCGGCGTTTTTATACAAAACGCCGCAATAGATACGTAC
* * *
13754 TTTAGTGGCGTTTTTATTCAAACGCCGCTATAAATACGTTCTTTAGCGGC-ATTTTTATA
66 TTTAGTGGCGTTTTTATTCAAACGCCGCAATAAGTACGTTCTTTAGCGGCGTTTTTTATA
* * * * *
13813 CAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTT
1 CAAACGCCGCAAAAGAGTAGTACTTTAGCGGCGTTT
13849 GTGTTTACAA
Statistics
Matches: 220, Mismatches: 50, Indels: 23
0.75 0.17 0.08
Matches are distributed among these distances:
122 33 0.15
123 136 0.62
124 51 0.23
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (125 bp):
CAAACGCCGCAAAAGAGTAGTACTTTAGCGGCGTTTTTATACAAAACGCCGCAATAGATACGTAC
TTTAGTGGCGTTTTTATTCAAACGCCGCAATAAGTACGTTCTTTAGCGGCGTTTTTTATA
Found at i:18703 original size:43 final size:43
Alignment explanation
Indices: 18515--18798 Score: 269
Period size: 42 Copynumber: 6.7 Consensus size: 43
18505 ACGATAATTA
* ** *
18515 GCGGCGTTTGCATCCAAAAACGCCGCTATAGATCTAAAAAT-TT
1 GCGGCGTTTTC-TCCAAAAACGCCGCTATAGATCTCGACATATT
* * *
18558 ACGGCGTTTAT-TCCAAAAACGCCGCTATAAATCT-GACATTTT
1 GCGGCGTTT-TCTCCAAAAACGCCGCTATAGATCTCGACATATT
* * *
18600 GCAGCGTTTTCTCCAAAAACGCCGCTATAGATCT-AACATTTT
1 GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCTCGACATATT
* *
18642 GCGGCGTTTTCAT--AGAAAACGCCGTTATAGATCTCGACCTATT
1 GCGGCGTTTTC-TCCA-AAAACGCCGCTATAGATCTCGACATATT
* * *
18685 GCGGCGTTTTCTCCGAAAACGCCGCTATAGAGCTCGACTTATT
1 GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCTCGACATATT
* * * *
18728 GCGGCGTTTGT-TCCGAAAAACGCCACTATAGAGC-CGACCTGTT
1 GCGGCGTTT-TCTCC-AAAAACGCCGCTATAGATCTCGACATATT
**
18771 GCGGCGTTTTCTAAAAAAACGCCGCTAT
1 GCGGCGTTTTCTCCAAAAACGCCGCTAT
18799 CGATTTAGAT
Statistics
Matches: 205, Mismatches: 25, Indels: 23
0.81 0.10 0.09
Matches are distributed among these distances:
41 5 0.02
42 103 0.50
43 79 0.39
44 18 0.09
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (43 bp):
GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCTCGACATATT
Found at i:18773 original size:86 final size:82
Alignment explanation
Indices: 18515--18798 Score: 291
Period size: 85 Copynumber: 3.3 Consensus size: 82
18505 ACGATAATTA
* ** *
18515 GCGGCGTTTGCATCCAAAAACGCCGCTATAGATCTAAAAATTTACGGCGTTTATTCCAAAAACGC
1 GCGGCGTTTTC-TCCAAAAACGCCGCTATAGATCT-AACTTTTGCGGCGTTT-TTCCAAAAACGC
* * * *
18580 CGCTATAAATCTGACATTTT
63 CGCTATAGATCCGACCTATT
* *
18600 GCAGCGTTTTCTCCAAAAACGCCGCTATAGATCTAACATTTTGCGGCG-TTTTCATAGAAAACGC
1 GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCTAAC-TTTTGCGGCGTTTTTC-CA-AAAACGC
*
18664 CGTTATAGATCTCGACCTATT
63 CGCTATAGATC-CGACCTATT
* * *
18685 GCGGCGTTTTCTCCGAAAACGCCGCTATAGAGCTCGACTTATTGCGGCGTTTGTTCCGAAAAACG
1 GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCT-AACTT-TTGCGGCGTTT-TTCC-AAAAACG
* * *
18750 CCACTATAGAGCCGACCTGTT
62 CCGCTATAGATCCGACCTATT
**
18771 GCGGCGTTTTCTAAAAAAACGCCGCTAT
1 GCGGCGTTTTCTCCAAAAACGCCGCTAT
18799 CGATTTAGAT
Statistics
Matches: 167, Mismatches: 23, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
82 3 0.02
83 5 0.03
84 47 0.28
85 48 0.29
86 43 0.26
87 17 0.10
88 4 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (82 bp):
GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCTAACTTTTGCGGCGTTTTTCCAAAAACGCCGC
TATAGATCCGACCTATT
Found at i:18815 original size:86 final size:82
Alignment explanation
Indices: 18515--18842 Score: 282
Period size: 86 Copynumber: 3.8 Consensus size: 82
18505 ACGATAATTA
* * * *
18515 GCGGCGTTTGCATCCAAAAACGCCGCTATAGATCTAAAAATTTACGGCGTTTATTCCAAAAACGC
1 GCGGCGTTTTC-TCCAAAAACGCCGCTATAGATCTAGACA-TTGCGGCGTTT-TTCCAAAAACGC
* * * *
18580 CGCTATAAATCTGACATTTT
63 CGCTATAGATCCGACCTATT
* *
18600 GCAGCGTTTTCTCCAAAAACGCCGCTATAGATCTA-ACATTTTGCGGCG-TTTTCATAGAAAACG
1 GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCTAGACA--TTGCGGCGTTTTTC-CA-AAAACG
*
18663 CCGTTATAGATCTCGACCTATT
62 CCGCTATAGATC-CGACCTATT
* * *
18685 GCGGCGTTTTCTCCGAAAACGCCGCTATAGAGCTCGACTTATTGCGGCGTTTGTTCCGAAAAACG
1 GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCTAGAC--ATTGCGGCGTTT-TTCC-AAAAACG
* * *
18750 CCACTATAGAGCCGACCTGTT
62 CCGCTATAGATCCGACCTATT
** * * * *
18771 GCGGCGTTTTCTAAAAAAACGCCGCTATCGATTTAGATCGATTGCGGCATTTTTTTTCCACAAAC
1 GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCTAGA-C-ATTGCGGC---GTTTTTCCAAAAAC
18836 GCCGCTA
61 GCCGCTA
18843 ACTTTAGCGA
Statistics
Matches: 199, Mismatches: 30, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
82 3 0.02
83 5 0.03
84 48 0.24
85 46 0.23
86 56 0.28
87 29 0.15
88 9 0.05
89 3 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (82 bp):
GCGGCGTTTTCTCCAAAAACGCCGCTATAGATCTAGACATTGCGGCGTTTTTCCAAAAACGCCGC
TATAGATCCGACCTATT
Found at i:22907 original size:26 final size:26
Alignment explanation
Indices: 22878--22930 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
22868 TGAGGCCACT
22878 TGTCTTCTCCAATCGATTCTTATTTC
1 TGTCTTCTCCAATCGATTCTTATTTC
22904 TGTCTTCTCCAATCGATTCTTATTTC
1 TGTCTTCTCCAATCGATTCTTATTTC
22930 T
1 T
22931 TGGCAAGTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.15, C:0.26, G:0.08, T:0.51
Consensus pattern (26 bp):
TGTCTTCTCCAATCGATTCTTATTTC
Found at i:27103 original size:7 final size:7
Alignment explanation
Indices: 27091--27115 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
27081 ACCAAATTTT
27091 ACTATTC
1 ACTATTC
27098 ACTATTC
1 ACTATTC
27105 ACTATTC
1 ACTATTC
27112 ACTA
1 ACTA
27116 AATAGTAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.28, G:0.00, T:0.40
Consensus pattern (7 bp):
ACTATTC
Found at i:40061 original size:41 final size:41
Alignment explanation
Indices: 40024--40349 Score: 562
Period size: 41 Copynumber: 7.9 Consensus size: 41
40014 ACGCGATAGT
* * * *
40024 CGAAGTTCACGTTGCGATTCATTCCAAATCGTTGCGATAGG
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
*
40065 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
*
40106 AGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
40147 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
*
40188 CGAAGTTCGCGTTGCGATTCATTCCAAATTCGTTGCGACAGG
1 CGAAGTTCGCATTGCGATTCATTCC-AATTCGTTGCGACAGG
40230 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
40271 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
*
40312 CGAAGTTCGCGTTGCGATTCATTCCAAATTCGTTGCGA
1 CGAAGTTCGCATTGCGATTCATTCC-AATTCGTTGCGA
40350 TTGTCCAAAT
Statistics
Matches: 274, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
41 222 0.81
42 52 0.19
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (41 bp):
CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
Found at i:40277 original size:124 final size:124
Alignment explanation
Indices: 40024--40349 Score: 600
Period size: 124 Copynumber: 2.6 Consensus size: 124
40014 ACGCGATAGT
* * * *
40024 CGAAGTTCACGTTGCGATTCATTCCAAATCGTTGCGATAGGCGAAGTTCGCGTTGCGATTCATTC
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGGCGAAGTTCGCGTTGCGATTCATTC
40089 C-AATTCGTTGCGACAGGAGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
66 CAAATTCGTTGCGACAGGAGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
40147 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGGCGAAGTTCGCGTTGCGATTCATTC
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGGCGAAGTTCGCGTTGCGATTCATTC
*
40212 CAAATTCGTTGCGACAGGCGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
66 CAAATTCGTTGCGACAGGAGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
40271 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGGCGAAGTTCGCGTTGCGATTCATTC
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGGCGAAGTTCGCGTTGCGATTCATTC
40336 CAAATTCGTTGCGA
66 CAAATTCGTTGCGA
40350 TTGTCCAAAT
Statistics
Matches: 197, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
123 62 0.31
124 135 0.69
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (124 bp):
CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGGCGAAGTTCGCGTTGCGATTCATTC
CAAATTCGTTGCGACAGGAGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
Found at i:41141 original size:6 final size:6
Alignment explanation
Indices: 41130--41156 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41120 TCTCGGGCCG
41130 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
41157 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:41302 original size:20 final size:20
Alignment explanation
Indices: 41236--41305 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
41226 TATTTAGACT
*
41236 ATCGCAACGATTCGGAATGA
1 ATCGCAACGATTTGGAATGA
*
41256 ATCACAAAGCGAACTTT-GAAT--
1 ATCGC-AA-CG-A-TTTGGAATGA
41277 ATCGCAACGATTTGGAATGA
1 ATCGCAACGATTTGGAATGA
41297 ATCGCAACG
1 ATCGCAACG
41306 CGAACTCCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
17 3 0.08
18 5 0.12
19 2 0.05
20 15 0.38
21 6 0.15
22 2 0.05
23 5 0.12
24 2 0.05
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (20 bp):
ATCGCAACGATTTGGAATGA
Found at i:41321 original size:41 final size:41
Alignment explanation
Indices: 41232--41364 Score: 158
Period size: 41 Copynumber: 3.2 Consensus size: 41
41222 GTAATATTTA
* * *
41232 GACTATCGCAACGATTCGGAATGAATCACAAAGCGAACTTT
1 GACTATCGCAACGATTTGGAATGAATCGCAAAGCGAACTTC
* * *
41273 GAATATCGCAACGATTTGGAATGAATCGCAACGCGAACTCC
1 GACTATCGCAACGATTTGGAATGAATCGCAAAGCGAACTTC
* * ** *
41314 GCCTATCGCAACGAATTTGGAATAAAAAGCAATGCGAACTTC
1 GACTATCGCAACG-ATTTGGAATGAATCGCAAAGCGAACTTC
41356 GACTATCGC
1 GACTATCGC
41365 GTTGCGAATC
Statistics
Matches: 77, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
41 46 0.60
42 31 0.40
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (41 bp):
GACTATCGCAACGATTTGGAATGAATCGCAAAGCGAACTTC
Found at i:41713 original size:21 final size:21
Alignment explanation
Indices: 41674--41712 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41664 AATTTTAAGA
41674 ATAAACGATAAAAATAAAAGT
1 ATAAACGATAAAAATAAAAGT
*
41695 ATAAA-GATTAAAATAAAA
1 ATAAACGATAAAAATAAAA
41713 AAATAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (21 bp):
ATAAACGATAAAAATAAAAGT
Found at i:41718 original size:20 final size:21
Alignment explanation
Indices: 41673--41718 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
41663 TAATTTTAAG
*
41673 AATAAACGATAAAAATAAAAG
1 AATAAACGATAAAAATAAAAA
* *
41694 TATAAA-GATTAAAATAAAAA
1 AATAAACGATAAAAATAAAAA
41714 AATAA
1 AATAA
41719 TATTTTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.20
Consensus pattern (21 bp):
AATAAACGATAAAAATAAAAA
Found at i:43030 original size:2 final size:2
Alignment explanation
Indices: 43023--43047 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43013 ATCTTATTTC
43023 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 A
43048 ACATATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52782 original size:21 final size:21
Alignment explanation
Indices: 52743--52781 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
52733 AATTTTAAGA
52743 ATAAACGATAAAAATAAAAGT
1 ATAAACGATAAAAATAAAAGT
*
52764 ATAAA-GATTAAAATAAAA
1 ATAAACGATAAAAATAAAA
52782 AAATAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (21 bp):
ATAAACGATAAAAATAAAAGT
Found at i:52787 original size:20 final size:21
Alignment explanation
Indices: 52742--52787 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
52732 TAATTTTAAG
*
52742 AATAAACGATAAAAATAAAAG
1 AATAAACGATAAAAATAAAAA
* *
52763 TATAAA-GATTAAAATAAAAA
1 AATAAACGATAAAAATAAAAA
52783 AATAA
1 AATAA
52788 TATTTTTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.72, C:0.02, G:0.07, T:0.20
Consensus pattern (21 bp):
AATAAACGATAAAAATAAAAA
Found at i:53011 original size:18 final size:20
Alignment explanation
Indices: 52988--53032 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
52978 AAAGAACAAT
52988 AAATTACAATAATA-A-A-AA
1 AAATTACAA-AATATATATAA
53006 AAATTA-AAAATATATATAA
1 AAATTACAAAATATATATAA
53025 AAATTACA
1 AAATTACA
53033 TGTATTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.17
17 3 0.13
18 7 0.30
19 8 0.35
20 1 0.04
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATTACAAAATATATATAA
Found at i:54079 original size:2 final size:2
Alignment explanation
Indices: 54072--54111 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
54062 TAATCTTATT
54072 TA TA TA TA TA TA TA -A TA TA TA -A 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
54112 ACATATGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:56367 original size:37 final size:37
Alignment explanation
Indices: 56297--56371 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 37
56287 CATTAAAACT
*
56297 TTTTATATTTTAAATTTTGTAAAAAAAATTATATAAA
1 TTTTATAATTTAAATTTTGTAAAAAAAATTATATAAA
* *
56334 TTTTATGAATTTAAATTTTTTAAAGAAAA-TATATAAA
1 TTTTAT-AATTTAAATTTTGTAAAAAAAATTATATAAA
56371 T
1 T
56372 ATTTTCCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 15 0.44
38 19 0.56
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTTATAATTTAAATTTTGTAAAAAAAATTATATAAA
Done.