Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002678.1 Hibiscus syriacus cultivar Beakdansim tig00005539_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: 51955
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2087 original size:7 final size:7
Alignment explanation
Indices: 2075--2105 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2065 GATTTTTTTA
2075 TGAATAG
1 TGAATAG
2082 TGAATAG
1 TGAATAG
2089 TGAATAG
1 TGAATAG
2096 TGAATAG
1 TGAATAG
2103 TGA
1 TGA
2106 GGGTATCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (7 bp):
TGAATAG
Found at i:2686 original size:24 final size:24
Alignment explanation
Indices: 2569--2686 Score: 63
Period size: 24 Copynumber: 5.2 Consensus size: 24
2559 CCATTTATTA
*
2569 ACCATAAGCTCGTAAGCTTATTTT
1 ACCATAAGCTAGTAAGCTTATTTT
* * * *
2593 ACCA-AA-ATAATTA-C-CATTTGT
1 ACCATAAGCTAGTAAGCTTATTT-T
*
2614 ACCATAAGCTTGTAAGCTTATTTT
1 ACCATAAGCTAGTAAGCTTATTTT
* * * *
2638 ACCA-AA-ATAATTA-C-CATTTGT
1 ACCATAAGCTAGTAAGCTTATTT-T
*
2659 ACCATAAGCTCGTAAGCTTATTTT
1 ACCATAAGCTAGTAAGCTTATTTT
2683 ACCA
1 ACCA
2687 ATATACTTAC
Statistics
Matches: 64, Mismatches: 20, Indels: 20
0.62 0.19 0.19
Matches are distributed among these distances:
20 8 0.12
21 12 0.19
22 10 0.16
23 10 0.16
24 16 0.25
25 8 0.12
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (24 bp):
ACCATAAGCTAGTAAGCTTATTTT
Found at i:2723 original size:44 final size:45
Alignment explanation
Indices: 2569--2725 Score: 264
Period size: 45 Copynumber: 3.5 Consensus size: 45
2559 CCATTTATTA
2569 ACCATAAGCTCGTAAGCTTATTTTACCAAAATAATTACCATTTGT
1 ACCATAAGCTCGTAAGCTTATTTTACCAAAATAATTACCATTTGT
*
2614 ACCATAAGCTTGTAAGCTTATTTTACCAAAATAATTACCATTTGT
1 ACCATAAGCTCGTAAGCTTATTTTACCAAAATAATTACCATTTGT
* *
2659 ACCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTAT-T
1 ACCATAAGCTCGTAAGCTTATTTTACCAAAATAATTACCATT-TGT
2704 -CCATAAGCTCGTAAGCTTATTT
1 ACCATAAGCTCGTAAGCTTATTT
2726 GTATGCTTAC
Statistics
Matches: 107, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
44 22 0.21
45 84 0.79
46 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (45 bp):
ACCATAAGCTCGTAAGCTTATTTTACCAAAATAATTACCATTTGT
Found at i:6227 original size:3 final size:3
Alignment explanation
Indices: 6219--6284 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
6209 TTCTATTTCT
* * *
6219 TTC TTC TTC TTC TCTC TTC TTC TTA TTC TTA TTC TTA TTC TTC TTC
1 TTC TTC TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
6265 TTC TTC GTT- TTC TTT TTC TT
1 TTC TTC -TTC TTC TTC TTC TT
6285 TTTTTTTCTT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
2 2 0.04
3 45 0.87
4 5 0.10
ACGTcount: A:0.05, C:0.26, G:0.02, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:6285 original size:6 final size:6
Alignment explanation
Indices: 6206--6304 Score: 76
Period size: 6 Copynumber: 16.0 Consensus size: 6
6196 TTTTTATTTA
* * * *
6206 TTTTTC TATTTC TTTCTTC TTCTTCTC TCTTCTTC TTATTC TTATTC TTATTC
1 TTTTTC TTTTTC TTT-TTC TT-TT-TC T-TT-TTC TTTTTC TTTTTC TTTTTC
* * *
6259 TTCTTC TTCTTC GTTTTC TTTTTC -TTTT- TTTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
6305 CTATAATATT
Statistics
Matches: 79, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
5 8 0.10
6 54 0.68
7 7 0.09
8 8 0.10
9 2 0.03
ACGTcount: A:0.04, C:0.22, G:0.01, T:0.73
Consensus pattern (6 bp):
TTTTTC
Found at i:6293 original size:16 final size:16
Alignment explanation
Indices: 6272--6303 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6262 TTCTTCTTCG
6272 TTTTCTTTTTCTTTTT
1 TTTTCTTTTTCTTTTT
6288 TTTTCTTTTTCTTTTT
1 TTTTCTTTTTCTTTTT
6304 CCTATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTCTTTTTCTTTTT
Found at i:16978 original size:17 final size:17
Alignment explanation
Indices: 16958--16992 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
16948 GAAAGTCAAC
*
16958 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
*
16975 GGTCAACAGTTGGGTCG
1 GGTCAACAGTCGGGTCG
16992 G
1 G
16993 TCGGGTCGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.20, G:0.46, T:0.20
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:23476 original size:5 final size:5
Alignment explanation
Indices: 23466--23523 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
23456 AACGGTCAAC
** *
23466 GTCGG GTCGG GTCGG GTCAACA GTCGG GTC-G GTCGG GTCGG GTC-A GTCGG
1 GTCGG GTCGG GTCGG GTC--GG GTCGG GTCGG GTCGG GTCGG GTCGG GTCGG
23516 GTCGG GTC
1 GTCGG GTC
23524 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
4 7 0.16
5 33 0.77
7 3 0.07
ACGTcount: A:0.07, C:0.22, G:0.50, T:0.21
Consensus pattern (5 bp):
GTCGG
Found at i:23485 original size:21 final size:21
Alignment explanation
Indices: 23459--23504 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
23449 AACGGTCAAC
23459 GGTCAAC-GTCGGGTCGGGTCG
1 GGTCAACAGTCGGGTC-GGTCG
23480 GGTCAACAGTCGGGTCGGTCG
1 GGTCAACAGTCGGGTCGGTCG
23501 GGTC
1 GGTC
23505 GGGTCAGTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.11, C:0.24, G:0.46, T:0.20
Consensus pattern (21 bp):
GGTCAACAGTCGGGTCGGTCG
Found at i:23507 original size:14 final size:14
Alignment explanation
Indices: 23471--23525 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
23461 TCAACGTCGG
23471 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
* * *
23485 -AC-AGTCGGGTCG
1 GTCGGGTCGGGTCA
23497 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
23511 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
23525 G
1 G
23526 ACCGGTCAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
12 8 0.24
13 2 0.06
14 23 0.70
ACGTcount: A:0.09, C:0.22, G:0.49, T:0.20
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:24724 original size:60 final size:60
Alignment explanation
Indices: 24658--24776 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
24648 TCCTCTGACT
* * * * *
24658 ATAGGGTGATGTTTTGTTGAGTCCCTCAACTATTAAAAGTTACAAAATGATCATTCGACA
1 ATAGGGTGATGCTTTGTTAAGTCCATCAACTATTAAAAGTTACAAAATAATCACTCGACA
* * *
24718 ATAGGGTGTTGCTTTGTTAAGTTCATCGACTATTAAAAGTTACAAAATAATCACTCGAC
1 ATAGGGTGATGCTTTGTTAAGTCCATCAACTATTAAAAGTTACAAAATAATCACTCGAC
24777 TATTTAGTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Consensus pattern (60 bp):
ATAGGGTGATGCTTTGTTAAGTCCATCAACTATTAAAAGTTACAAAATAATCACTCGACA
Found at i:25049 original size:60 final size:60
Alignment explanation
Indices: 24985--25122 Score: 201
Period size: 60 Copynumber: 2.3 Consensus size: 60
24975 AATAGTTGGG
24985 TGACTATTTTGTAACTTTTAATAGTCG-GGGGACTCAACAAAGCAACATCC-TATAGTCGAA
1 TGACTATTTTGTAACTTTTAATAGTCGAGGGG-CTCAACAAAGCAACA-CCATATAGTCGAA
* *
25045 TGACTATTTTGTAACTTTTAATAGTCGAGGGGCTCAACAAAGCATCACCATATAGTCGAG
1 TGACTATTTTGTAACTTTTAATAGTCGAGGGGCTCAACAAAGCAACACCATATAGTCGAA
*
25105 GGACTATTTGTGT-ACTTT
1 TGACTATTT-TGTAACTTT
25123 ACTCTTAAAT
Statistics
Matches: 72, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
59 2 0.03
60 63 0.88
61 7 0.10
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (60 bp):
TGACTATTTTGTAACTTTTAATAGTCGAGGGGCTCAACAAAGCAACACCATATAGTCGAA
Found at i:25865 original size:15 final size:15
Alignment explanation
Indices: 25842--25882 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
25832 ATAAATAAAC
25842 TTATTTAAATGCAAA
1 TTATTTAAATGCAAA
* **
25857 TTATATAAACACAAA
1 TTATTTAAATGCAAA
25872 TTATTTAAATG
1 TTATTTAAATG
25883 AATTAATATT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (15 bp):
TTATTTAAATGCAAA
Found at i:26564 original size:4 final size:4
Alignment explanation
Indices: 26555--26581 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
26545 TTCAACTATG
26555 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
26582 ACATGCATGT
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:30103 original size:21 final size:20
Alignment explanation
Indices: 30077--30120 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
30067 GATTTCTGGG
* *
30077 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCC-TT
30098 CAAGGGGAACCGATACCCTT
1 CAAGGGGAACCGATACCCTT
30118 CAA
1 CAA
30121 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (20 bp):
CAAGGGGAACCGATACCCTT
Found at i:31138 original size:2 final size:2
Alignment explanation
Indices: 31131--31162 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31121 GAACATGTGA
31131 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
31163 GTTTAAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31864 original size:23 final size:22
Alignment explanation
Indices: 31805--31871 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
31795 TATGGACATC
*
31805 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
31827 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
31849 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
31872 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:35030 original size:21 final size:20
Alignment explanation
Indices: 35004--35047 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
34994 TGATTCTGGG
* *
35004 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCC-TT
35025 CAAGGGGAACCGATACCCTT
1 CAAGGGGAACCGATACCCTT
35045 CAA
1 CAA
35048 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (20 bp):
CAAGGGGAACCGATACCCTT
Found at i:36063 original size:2 final size:2
Alignment explanation
Indices: 36056--36143 Score: 176
Period size: 2 Copynumber: 44.0 Consensus size: 2
36046 GAACATGTGA
36056 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
36098 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
36140 AT AT
1 AT AT
36144 GTTTAAGAGA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36845 original size:23 final size:22
Alignment explanation
Indices: 36786--36852 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
36776 TATGGACATC
*
36786 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
36808 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
36830 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
36853 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:40373 original size:27 final size:27
Alignment explanation
Indices: 40315--40366 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
40305 GGATATAGTC
40315 CTTGTAAATTTCCACAACAAAATCTTA
1 CTTGTAAATTTCCACAACAAAATCTTA
40342 CTTGTAAATTTCCACAAC-AAATCTT
1 CTTGTAAATTTCCACAACAAAATCTT
40367 GTCTTGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (27 bp):
CTTGTAAATTTCCACAACAAAATCTTA
Found at i:40565 original size:2 final size:2
Alignment explanation
Indices: 40558--40584 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40548 TGACCACGTT
40558 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 T
40585 CATTTCCCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40681 original size:32 final size:32
Alignment explanation
Indices: 40644--40712 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
40634 TATGTATATG
**
40644 TGATTTTTTAATATTAGCTTATTAAATTTAGC
1 TGATTTTTTAATATTAGCAGATTAAATTTAGC
* *
40676 TGATTTTTTAATATTAGCAGATTAAGTTTAGT
1 TGATTTTTTAATATTAGCAGATTAAATTTAGC
40708 TGATT
1 TGATT
40713 AAAAAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.30, C:0.04, G:0.13, T:0.52
Consensus pattern (32 bp):
TGATTTTTTAATATTAGCAGATTAAATTTAGC
Found at i:40692 original size:18 final size:18
Alignment explanation
Indices: 40644--40698 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
40634 TATGTATATG
40644 TGATTTTTTAATATTAGC
1 TGATTTTTTAATATTAGC
* *
40662 ---TTATTAAAT-TTAGC
1 TGATTTTTTAATATTAGC
40676 TGATTTTTTAATATTAGC
1 TGATTTTTTAATATTAGC
*
40694 AGATT
1 TGATT
40699 AAGTTTAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
14 5 0.18
15 7 0.25
17 7 0.25
18 9 0.32
ACGTcount: A:0.31, C:0.05, G:0.11, T:0.53
Consensus pattern (18 bp):
TGATTTTTTAATATTAGC
Found at i:41618 original size:69 final size:69
Alignment explanation
Indices: 41508--42197 Score: 669
Period size: 69 Copynumber: 9.9 Consensus size: 69
41498 GCCGATAAAT
* * * *
41508 CTTTTCTCAAGGA-TTTGACCCGAATA-GTCTCTAGTACCATTATCTATCTCAGGAGGCAATGAA
1 CTTTTCTCAAGGATTTTGACCCCAA-ACGTCCCCAGTACCATTATCTATCTCAGGAGGCCATGAA
*
41571 GAATG
65 GAACG
* * * *
41576 CTTTTCTCAAGGACTTTGACCCCAAACGTCCCCAGTATCATTATATATCTCAGGAGGCCACGAAG
1 CTTTTCTCAAGGATTTTGACCCCAAACGTCCCCAGTACCATTATCTATCTCAGGAGGCCATGAAG
41641 AACG
66 AACG
* * * *
41645 CTTTTCTCAAGGATTTTAACCCCAACCGTCCCCAGTACCATTATCTATCTAAGGAGGCCACGAAG
1 CTTTTCTCAAGGATTTTGACCCCAAACGTCCCCAGTACCATTATCTATCTCAGGAGGCCATGAAG
41710 AACG
66 AACG
* * * *
41714 CTTTTCTCAAGGA-TTTGACCCCAATCGTGCCCAGTACCATTATCTATCTAAGGAGACCATGAAG
1 CTTTTCTCAAGGATTTTGACCCCAAACGTCCCCAGTACCATTATCTATCTCAGGAGGCCATGAAG
41778 AACG
66 AACG
* * * * * *
41782 CTTTTCTCAAGGATTTTGA--CCAATGATTTTGATCTCAACC-GTCCCCAGTACCATTATCTAAT
1 CTTTTCTCAAGGATTTTGACCCCAA--A---CG-TC-C--CCAGT-ACCATTATC--TATCTCAG
* * *
41844 GAGACCATGAATAACT
54 GAGGCCATGAAGAACG
** * * * *
41860 CTTTTCTCTGGGATTTTGACCCCAATCGTGCCCAATACCATTATCCATCTCAGGAGGCCATGAA-
1 CTTTTCTCAAGGATTTTGACCCCAAACGTCCCCAGTACCATTATCTATCTCAGGAGGCCATGAAG
41924 AAC-
66 AACG
* * * * *
41927 CTTTTCTCAAGGATTTTGACCCCAACCATCCCCAGTAGCATTATCTATCTCAAGAGGCAATGAAG
1 CTTTTCTCAAGGATTTTGACCCCAAACGTCCCCAGTACCATTATCTATCTCAGGAGGCCATGAAG
*
41992 AATG
66 AACG
* *** *
41996 CTTTTCTCAACGATTTTGATATC-AACTGTCCCCAGTACCATTATCTATCTCAGGAGGCTATGAA
1 CTTTTCTCAAGGATTTTGACCCCAAAC-GTCCCCAGTACCATTATCTATCTCAGGAGGCCATGAA
42060 GAACG
65 GAACG
* * *
42065 CTTTTCTCAAAGATTTTGACCCCAACCGTCCCCAGTACCATTATCTATCTCAAGAGGCCATGAAG
1 CTTTTCTCAAGGATTTTGACCCCAAACGTCCCCAGTACCATTATCTATCTCAGGAGGCCATGAAG
*
42130 AATG
66 AACG
* * * * * * * * * **
42134 TTTTTCTCAAAGATTTCGACCCGAACCGTCCTCAATACCACTACCTATCTCAAAAGGCCATGAA
1 CTTTTCTCAAGGATTTTGACCCCAAACGTCCCCAGTACCATTATCTATCTCAGGAGGCCATGAA
42198 CTCTTTGAAG
Statistics
Matches: 522, Mismatches: 78, Indels: 43
0.81 0.12 0.07
Matches are distributed among these distances:
67 58 0.11
68 84 0.16
69 311 0.60
70 2 0.00
71 8 0.02
72 2 0.00
73 2 0.00
74 2 0.00
75 3 0.01
76 8 0.02
78 38 0.07
80 4 0.01
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (69 bp):
CTTTTCTCAAGGATTTTGACCCCAAACGTCCCCAGTACCATTATCTATCTCAGGAGGCCATGAAG
AACG
Found at i:42115 original size:138 final size:138
Alignment explanation
Indices: 41508--42197 Score: 745
Period size: 138 Copynumber: 5.0 Consensus size: 138
41498 GCCGATAAAT
* ** * * * *
41508 CTTTTCTCAAGGA-TTTGACCCGAATAGTCTCTAGTACCATTATCTATCTCAGGAGGCAATGAAG
1 CTTTTCTCAAGGATTTTGACCCCAACCGTCCCCAGTACCATTATCTATCTCAAGAGGCCATGAAG
* * * * *
41572 AATGCTTTTCTCAAGGACTTTGACCCCAAACGTCCCCAGTATCATTATATATCTCAGGAGGCCAC
66 AATGCTTTTCTCAAGGATTTTGACCCCAATCGTCCCCAGTACCATTATCTATCTCAGGAGGCCAT
41637 GAAGAACG
131 GAAGAACG
* *
41645 CTTTTCTCAAGGATTTTAACCCCAACCGTCCCCAGTACCATTATCTATCT-AAGGAGGCCACGAA
1 CTTTTCTCAAGGATTTTGACCCCAACCGTCCCCAGTACCATTATCTATCTCAA-GAGGCCATGAA
* * * *
41709 GAACGCTTTTCTCAAGGA-TTTGACCCCAATCGTGCCCAGTACCATTATCTATCTAAGGAGACCA
65 GAATGCTTTTCTCAAGGATTTTGACCCCAATCGTCCCCAGTACCATTATCTATCTCAGGAGGCCA
41773 TGAAGAACG
130 TGAAGAACG
41782 CTTTTCTCAAGGATTTTGACCAATGATTTTGATCTCAACCGTCCCCAGTACCATTATCTA----A
1 CTTTTCTCAAGGATTTTGACC------------C-CAACCGTCCCCAGTACCATTATCTATCTCA
* * * ** * * *
41843 TGAGACCATGAATAACT-CTTTTCTCTGGGATTTTGACCCCAATCGTGCCCAATACCATTATCCA
53 AGAGGCCATGAAGAA-TGCTTTTCTCAAGGATTTTGACCCCAATCGTCCCCAGTACCATTATCTA
41907 TCTCAGGAGGCCATGAA-AAC-
117 TCTCAGGAGGCCATGAAGAACG
* * *
41927 CTTTTCTCAAGGATTTTGACCCCAACCATCCCCAGTAGCATTATCTATCTCAAGAGGCAATGAAG
1 CTTTTCTCAAGGATTTTGACCCCAACCGTCCCCAGTACCATTATCTATCTCAAGAGGCCATGAAG
* *** *
41992 AATGCTTTTCTCAACGATTTTGATATCAA-CTGTCCCCAGTACCATTATCTATCTCAGGAGGCTA
66 AATGCTTTTCTCAAGGATTTTGACCCCAATC-GTCCCCAGTACCATTATCTATCTCAGGAGGCCA
42056 TGAAGAACG
130 TGAAGAACG
*
42065 CTTTTCTCAAAGATTTTGACCCCAACCGTCCCCAGTACCATTATCTATCTCAAGAGGCCATGAAG
1 CTTTTCTCAAGGATTTTGACCCCAACCGTCCCCAGTACCATTATCTATCTCAAGAGGCCATGAAG
* * * * * * * * * **
42130 AATGTTTTTCTCAAAGATTTCGACCCGAACCGTCCTCAATACCACTACCTATCTCAAAAGGCCAT
66 AATGCTTTTCTCAAGGATTTTGACCCCAATCGTCCCCAGTACCATTATCTATCTCAGGAGGCCAT
42195 GAA
131 GAA
42198 CTCTTTGAAG
Statistics
Matches: 464, Mismatches: 63, Indels: 51
0.80 0.11 0.09
Matches are distributed among these distances:
132 23 0.05
133 1 0.00
135 2 0.00
136 64 0.14
137 85 0.18
138 169 0.36
139 1 0.00
145 21 0.05
146 25 0.05
147 47 0.10
149 1 0.00
150 25 0.05
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (138 bp):
CTTTTCTCAAGGATTTTGACCCCAACCGTCCCCAGTACCATTATCTATCTCAAGAGGCCATGAAG
AATGCTTTTCTCAAGGATTTTGACCCCAATCGTCCCCAGTACCATTATCTATCTCAGGAGGCCAT
GAAGAACG
Found at i:43166 original size:3 final size:3
Alignment explanation
Indices: 43158--43192 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
43148 GAATATTTCG
43158 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
43193 TAATTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:43229 original size:6 final size:6
Alignment explanation
Indices: 43209--43241 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
43199 TTAATTTTTA
*
43209 TATATT TAT-TT TATATT TATACT TATATT TATA
1 TATATT TATATT TATATT TATATT TATATT TATA
43242 CTTCTTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:43236 original size:12 final size:12
Alignment explanation
Indices: 43209--43244 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
43199 TTAATTTTTA
*
43209 TATATTTAT-TT
1 TATATTTATACT
43220 TATATTTATACT
1 TATATTTATACT
43232 TATATTTATACT
1 TATATTTATACT
43244 T
1 T
43245 CTTTCTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (12 bp):
TATATTTATACT
Found at i:46452 original size:32 final size:33
Alignment explanation
Indices: 46412--46486 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
46402 AAAATTTCTG
46412 TTAAAACACATAAAA-CATAAAACAATTTATAA
1 TTAAAACACATAAAATCATAAAACAATTTATAA
*
46444 TTAAAACACATAAAATCATAAAATAATTTATAA
1 TTAAAACACATAAAATCATAAAACAATTTATAA
*
46477 GTAAAACACA
1 TTAAAACACA
46487 AGTTCATAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 15 0.38
33 25 0.62
ACGTcount: A:0.61, C:0.12, G:0.01, T:0.25
Consensus pattern (33 bp):
TTAAAACACATAAAATCATAAAACAATTTATAA
Found at i:48571 original size:68 final size:68
Alignment explanation
Indices: 48364--48591 Score: 314
Period size: 68 Copynumber: 3.4 Consensus size: 68
48354 GCTAAAATGG
* *
48364 GATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCTAG
1 GATGAAAGGCTAAGTACCTTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAG
48429 TTA
66 TTA
* * *
48432 GATAAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGTC-TTTGAAAGAAAGGTGTCAATCATGCCA
1 GATGAAAGGCTAAGTACCTTTGAGGCCTAACTGTG-CATTTGACAGAAAGGTGTCAATCATGCCA
*
48496 GTCA
65 GTTA
* ** * *
48500 GATGAAAGACTAAGTACCTTTGAGGCCTAACTGTGCATTTGACAGAAAAATGACAATCTTGCCAG
1 GATGAAAGGCTAAGTACCTTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAG
48565 TTA
66 TTA
* * *
48568 GATGAAATGTTAAGTACATTTGAG
1 GATGAAAGGCTAAGTACCTTTGAG
48592 TAAAATATTA
Statistics
Matches: 141, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
67 1 0.01
68 139 0.99
69 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (68 bp):
GATGAAAGGCTAAGTACCTTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAG
TTA
Found at i:48658 original size:81 final size:81
Alignment explanation
Indices: 48524--48922 Score: 489
Period size: 81 Copynumber: 4.9 Consensus size: 81
48514 TACCTTTGAG
* * ** * * * *
48524 GCCTAACTGTGCATTTGACAGAAAAATGACAATCT-TGCCAGTTAGATGAAATGTTAAGTACATT
1 GCCTAGCTGTGCATTTGACTGAAAGGTGTCAAT-TATGTCAGTTAGATGAAATGTTAAATACCTT
* *
48588 TGAGTAAAATATTAATG
65 TGAGTAAAAGATTAATA
*
48605 GCCTAGCTGTGTATTTGACTGAAAGGTGTCAATTATGTCAGTTAGATGAAATGTTAAATACCTTT
1 GCCTAGCTGTGCATTTGACTGAAAGGTGTCAATTATGTCAGTTAGATGAAATGTTAAATACCTTT
48670 GAGTAAAAGATTAATA
66 GAGTAAAAGATTAATA
* * * *
48686 GCCTAACTGTGCATTTGA-TAAAAATGTGTCAATTATGCCAGTTAGATGAAATGTTAAATACCTT
1 GCCTAGCTGTGCATTTGACT-GAAAGGTGTCAATTATGTCAGTTAGATGAAATGTTAAATACCTT
*
48750 TGAGTAAAAGATTAATG
65 TGAGTAAAAGATTAATA
* * * * *
48767 GCCTAGCTGTGCATTTAACGGAAAGGTGTCAATTATGTCAGCTAGATGAAAGGTTAACTACCTTT
1 GCCTAGCTGTGCATTTGACTGAAAGGTGTCAATTATGTCAGTTAGATGAAATGTTAAATACCTTT
48832 GAGTAAAAGATTAATA
66 GAGTAAAAGATTAATA
* * * * * **
48848 GCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATG-CAAGTTAGATAAAAGGCTAAATGTCTT
1 GCCTAGCTGTGCATTTGACTGAAAGGTGTCAATTATGTC-AGTTAGATGAAATGTTAAATACCTT
*
48912 TGGGTAAAAGA
65 TGAGTAAAAGA
48923 CTAAAGGAAA
Statistics
Matches: 277, Mismatches: 37, Indels: 8
0.86 0.11 0.02
Matches are distributed among these distances:
80 3 0.01
81 274 0.99
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (81 bp):
GCCTAGCTGTGCATTTGACTGAAAGGTGTCAATTATGTCAGTTAGATGAAATGTTAAATACCTTT
GAGTAAAAGATTAATA
Found at i:48727 original size:162 final size:161
Alignment explanation
Indices: 48524--48894 Score: 555
Period size: 162 Copynumber: 2.3 Consensus size: 161
48514 TACCTTTGAG
* * *
48524 GCCTAACTGTGCATTTGACAGAAAAATGACAATCT-TGCCAGTTAGATGAAATGTTAAGTACATT
1 GCCTAACTGTGCATTTGACA-AAAAGTGTCAAT-TATGCCAGTTAGATGAAATGTTAAATACATT
* * * * *
48588 TGAGTAAAATATTAATGGCCTAGCTGTGTATTTGACTGAAAGGTGTCAATTATGTCAGTTAGATG
64 TGAGTAAAAGATTAATGGCCTAGCTGTGCATTTAACGGAAAGGTGTCAATTATGTCAGCTAGATG
*
48653 AAATGTTAAATACCTTTGAGTAAAAGATTAATA
129 AAAGGTTAAATACCTTTGAGTAAAAGATTAATA
* *
48686 GCCTAACTGTGCATTTGATAAAAATGTGTCAATTATGCCAGTTAGATGAAATGTTAAATACCTTT
1 GCCTAACTGTGCATTTGACAAAAA-GTGTCAATTATGCCAGTTAGATGAAATGTTAAATACATTT
48751 GAGTAAAAGATTAATGGCCTAGCTGTGCATTTAACGGAAAGGTGTCAATTATGTCAGCTAGATGA
65 GAGTAAAAGATTAATGGCCTAGCTGTGCATTTAACGGAAAGGTGTCAATTATGTCAGCTAGATGA
*
48816 AAGGTTAACTACCTTTGAGTAAAAGATTAATA
130 AAGGTTAAATACCTTTGAGTAAAAGATTAATA
* * * *
48848 GCCTAGCTGTGCATTTGACAGAAAGGTGTCAATCATGCAAGTTAGAT
1 GCCTAACTGTGCATTTGACA-AAAAGTGTCAATTATGCCAGTTAGAT
48895 AAAAGGCTAA
Statistics
Matches: 189, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
161 5 0.03
162 181 0.96
163 3 0.02
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (161 bp):
GCCTAACTGTGCATTTGACAAAAAGTGTCAATTATGCCAGTTAGATGAAATGTTAAATACATTTG
AGTAAAAGATTAATGGCCTAGCTGTGCATTTAACGGAAAGGTGTCAATTATGTCAGCTAGATGAA
AGGTTAAATACCTTTGAGTAAAAGATTAATA
Done.