Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007176.1 Hibiscus syriacus cultivar Beakdansim tig00018834_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: 51612
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:865 original size:21 final size:20
Alignment explanation
Indices: 828--883 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
818 CATATTGGAT
828 AATAAAATTAAAA-TTATATAA
1 AATAAAA-TAAAATTTATAT-A
*
849 AATAAAATAAAATTTATGTA
1 AATAAAATAAAATTTATATA
*
869 AATAACA-AAAATTTA
1 AATAAAATAAAATTTA
884 ATATTTAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.25
20 12 0.38
21 12 0.38
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
AATAAAATAAAATTTATATA
Found at i:10445 original size:32 final size:33
Alignment explanation
Indices: 10326--10464 Score: 244
Period size: 33 Copynumber: 4.2 Consensus size: 33
10316 GAAGAAAGAA
*
10326 AGAACGGGTGATCTAGTGCATTGCAAGGCGAGG
1 AGAACGGGTGATTTAGTGCATTGCAAGGCGAGG
10359 AGAACGGGTGATTTAGTGCATTGCAAGGCGAGG
1 AGAACGGGTGATTTAGTGCATTGCAAGGCGAGG
10392 AGAACGGGTGATTTAGTGCATTGCAAGGCGAGG
1 AGAACGGGTGATTTAGTGCATTGCAAGGCGAGG
*
10425 AGCACGGGTGA-TTAGTGCATTGCAAGGCGAGG
1 AGAACGGGTGATTTAGTGCATTGCAAGGCGAGG
*
10457 AGCACGGG
1 AGAACGGG
10465 GACGAACAGG
Statistics
Matches: 104, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
32 29 0.28
33 75 0.72
ACGTcount: A:0.27, C:0.14, G:0.40, T:0.19
Consensus pattern (33 bp):
AGAACGGGTGATTTAGTGCATTGCAAGGCGAGG
Found at i:13629 original size:21 final size:21
Alignment explanation
Indices: 13605--13648 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
13595 TAACAAACTT
*
13605 CTCTTAACTAACTAGTAACAA
1 CTCTTAACCAACTAGTAACAA
**
13626 CTCTTAACCAACTTTTAACAA
1 CTCTTAACCAACTAGTAACAA
13647 CT
1 CT
13649 TAGTTGAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.27, G:0.02, T:0.32
Consensus pattern (21 bp):
CTCTTAACCAACTAGTAACAA
Found at i:19186 original size:2 final size:2
Alignment explanation
Indices: 19179--19204 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19169 AGTAAAAATA
19179 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
19205 GAAAGTTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24584 original size:13 final size:13
Alignment explanation
Indices: 24566--24591 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24556 GCCCTCTCTC
24566 TCTCTCTCTCTTT
1 TCTCTCTCTCTTT
24579 TCTCTCTCTCTTT
1 TCTCTCTCTCTTT
24592 CCTTATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
TCTCTCTCTCTTT
Found at i:25636 original size:34 final size:34
Alignment explanation
Indices: 25598--25678 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 34
25588 CATAAGTCTC
*
25598 GTTCGTTCATTTACGTTC-GTGAACGTTCGGTTAT
1 GTTCGTTCATTTACGTTCGGT-AACGTTCGCTTAT
* * *
25632 GTTCGTTTATGTT-CGTTCGGTTATGTTCGCTTAT
1 GTTCGTTCAT-TTACGTTCGGTAACGTTCGCTTAT
*
25666 GTTCATTCATTTA
1 GTTCGTTCATTTA
25679 TGTTTAACCC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
33 2 0.05
34 32 0.84
35 4 0.11
ACGTcount: A:0.14, C:0.16, G:0.21, T:0.49
Consensus pattern (34 bp):
GTTCGTTCATTTACGTTCGGTAACGTTCGCTTAT
Found at i:25638 original size:24 final size:24
Alignment explanation
Indices: 25611--25660 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
25601 CGTTCATTTA
*
25611 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
* **
25635 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTCATGAACGTTCGGTTATGTT
25659 CG
1 CG
25661 CTTATGTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.10, C:0.16, G:0.28, T:0.46
Consensus pattern (24 bp):
CGTTCATGAACGTTCGGTTATGTT
Found at i:25649 original size:14 final size:14
Alignment explanation
Indices: 25621--25660 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
25611 CGTTCGTGAA
25621 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
25635 CG-T---TTATGTT
1 CGTTCGGTTATGTT
25645 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
25659 CG
1 CG
25661 CTTATGTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
10 9 0.41
11 1 0.05
13 1 0.05
14 11 0.50
ACGTcount: A:0.07, C:0.15, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:25665 original size:24 final size:24
Alignment explanation
Indices: 25621--25669 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
25611 CGTTCGTGAA
*
25621 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGCTTATGTT
25645 CGTTCGGTTATGTTCGCTTATGTT
1 CGTTCGGTTATGTTCGCTTATGTT
25669 C
1 C
25670 ATTCATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.16, G:0.24, T:0.51
Consensus pattern (24 bp):
CGTTCGGTTATGTTCGCTTATGTT
Found at i:25679 original size:24 final size:24
Alignment explanation
Indices: 25627--25682 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
25617 TGAACGTTCG
* * *
25627 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCGCTTATGTTCATTCA
25651 GTTATGTTCGCTTATGTTCATTCA
1 GTTATGTTCGCTTATGTTCATTCA
*
25675 TTTATGTT
1 GTTATGTT
25683 TAACCCAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.55
Consensus pattern (24 bp):
GTTATGTTCGCTTATGTTCATTCA
Found at i:26741 original size:16 final size:16
Alignment explanation
Indices: 26720--26786 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
26710 GTCTCCAGCG
26720 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
* *
26736 TTTATGTTTGTGTTCG
1 TTTATGTTCGTGTTCA
*
26752 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
26768 TTTATATTCGT-TT-A
1 TTTATGTTCGTGTTCA
26782 TTTAT
1 TTTAT
26787 TAAATGAACG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 39 0.85
ACGTcount: A:0.12, C:0.09, G:0.18, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:29258 original size:119 final size:119
Alignment explanation
Indices: 29116--29411 Score: 344
Period size: 119 Copynumber: 2.5 Consensus size: 119
29106 AAGTTTTGAA
** * * *
29116 AAAAAATGAAAGTTTAATTACTAAAACGGACTAAAATTGATAGTTTAGATACTAAGCACATTAAG
1 AAAAAATGAAAGTTTAGGTACTAAAACGGA-TAAAACTGATAGTTTAGGTACTAAACACATTAAG
* *
29181 TTTTTAACAAAATGGTACTAAAATGAAACAATAACTAAACATTAGGTAT-AATTT-
65 -TTTTAACAAAATGATACTAAAATGAAACAATAACTAAAAATTAGGTATGAATTTG
* * * **
29235 AAAAAATGAAAATTTAGGTACTAAAATGGATTAAAACTGATAGTTCAGGTACTAAACATGTTAAG
1 AAAAAATGAAAGTTTAGGTACTAAAACGGA-TAAAACTGATAGTTTAGGTACTAAACACATTAAG
*** * * *
29300 TTTTAACGGCATTATACTAAAATGAAACAATAACTAAAAATTAGTTATGATTTTG
65 TTTTAACAAAATGATACTAAAATGAAACAATAACTAAAAATTAGGTATGAATTTG
** *
29355 AAAATTTTGAAAGTTTAGGTATTAAAACGGATGAAAACTGATAGTTTAGGTACTAAA
1 AAAA-AATGAAAGTTTAGGTACTAAAACGGAT-AAAACTGATAGTTTAGGTACTAAA
29412 TGCATAGTTT
Statistics
Matches: 148, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
118 41 0.28
119 58 0.39
120 5 0.03
121 44 0.30
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (119 bp):
AAAAAATGAAAGTTTAGGTACTAAAACGGATAAAACTGATAGTTTAGGTACTAAACACATTAAGT
TTTAACAAAATGATACTAAAATGAAACAATAACTAAAAATTAGGTATGAATTTG
Found at i:31775 original size:31 final size:31
Alignment explanation
Indices: 31733--31792 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
31723 AATTTAAAAG
* * *
31733 AGTTTTGCAATATTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
31764 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
31793 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:31870 original size:54 final size:54
Alignment explanation
Indices: 31806--32492 Score: 603
Period size: 54 Copynumber: 12.6 Consensus size: 54
31796 ACAACTACAA
* *
31806 TAATAAATTATTTAAAATAGATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
31860 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* * * *
31914 TAATAAATTATTAAAAATAAATTAATACATATTTTAAAATAAATCAATACATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
** * **
31968 TAATAAATTATTTAAAATAAATCAATTTATACAACTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
** * ** * ** ** * *
32025 TTTTAAAATAAAT-CAATCCATACTAATAAAGTA-TTTAAAATAAATCAATTCATAT
1 TAATAAATTATTTAAAATAAAT-C-AATCCA-TATTTTAAAATAAATCAATCCATAC
32080 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* ** * ** * **
32134 TAATAAATTATTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATAAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATAC
** ** ** * **
32189 -AATCCA-TATTTTAAAATAAATCAATCCATACTAATAAAATATTTAAAATAAAT-C
1 TAATAAATTA-TTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATAC
** ** *
32243 -AATCCA-TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT-ATAT-CA-AT
1 TAATAAATTA-TTTAAAATAAATCAATCCATA-TTTTAAA--A--T-AAATCA-ATCCATAC
* * *
32300 TCATACAACTA--CAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATA-AATTATTTAA-AATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
32354 TAATCAAA-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAAT-AAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
32408 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
32462 TAATAAATTATTTAAAATATATCAATTCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
32493 CAACTACAAT
Statistics
Matches: 535, Mismatches: 67, Indels: 62
0.81 0.10 0.09
Matches are distributed among these distances:
52 6 0.01
53 13 0.02
54 406 0.76
55 25 0.05
56 17 0.03
57 22 0.04
58 40 0.07
59 4 0.01
60 2 0.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:31876 original size:32 final size:31
Alignment explanation
Indices: 31838--31993 Score: 141
Period size: 32 Copynumber: 5.5 Consensus size: 31
31828 CAATCCATAT
31838 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATC-ATACTAATAAATTA
31870 TTTAAAATAAATCAATC---C--AT--A-T-
1 TTTAAAATAAATCAATCATACTAATAAATTA
31892 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAAT-CATACTAATAAATTA
* *
31924 TTAAAAATAAAT---TAATAC--AT--A-T-
1 TTTAAAATAAATCAATCATACTAATAAATTA
31946 TTTAAAATAAATCAATACATACTAATAAATTA
1 TTTAAAATAAATCAAT-CATACTAATAAATTA
31978 TTTAAAATAAATCAAT
1 TTTAAAATAAATCAAT
31994 TTATACAACT
Statistics
Matches: 100, Mismatches: 4, Indels: 40
0.69 0.03 0.28
Matches are distributed among these distances:
22 27 0.27
23 3 0.03
24 2 0.02
25 1 0.01
26 9 0.09
28 9 0.09
29 1 0.01
30 2 0.02
31 2 0.02
32 44 0.44
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (31 bp):
TTTAAAATAAATCAATCATACTAATAAATTA
Found at i:31896 original size:22 final size:22
Alignment explanation
Indices: 31870--31912 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
31860 TAATAAATTA
31870 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
31892 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
31913 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:31921 original size:22 final size:22
Alignment explanation
Indices: 31872--31920 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
31862 ATAAATTATT
**
31872 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
31894 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
31917 TAAA
1 TAAA
31921 TTATTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:31975 original size:22 final size:22
Alignment explanation
Indices: 31927--31974 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
31917 TAAATTATTA
* **
31927 AAAATAAATTAATACATATTTT
1 AAAATAAATCAATACATATAAT
31949 AAAATAAATCAATACATACTAAT
1 AAAATAAATCAATACATA-TAAT
31972 AAA
1 AAA
31975 TTATTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATAAATCAATACATATAAT
Found at i:32052 original size:18 final size:19
Alignment explanation
Indices: 32008--32054 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
31998 ACAACTACAA
*
32008 TAATAAATCAATCCATATTT
1 TAATAAATCAATCCATA-TC
32028 TAAAATAAATCAATCCATA-C
1 T--AATAAATCAATCCATATC
32048 TAATAAA
1 TAATAAA
32055 GTATTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 6 0.25
20 2 0.08
22 16 0.67
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (19 bp):
TAATAAATCAATCCATATC
Found at i:32065 original size:32 final size:31
Alignment explanation
Indices: 32026--32594 Score: 372
Period size: 32 Copynumber: 20.4 Consensus size: 31
32016 CAATCCATAT
32026 TTTAAAATAAATCAATCCATACTAATAAAGTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
* *
32058 TTTAAAATAAATCAATTCATATTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
32090 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
32112 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
*
32144 TTTAAAATAAATAAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
32176 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
32198 TTTAAAATAAATCAATCCATACTAATAAAATA
1 TTTAAAATAAATCAATCCATACTAAT-AAATA
32230 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
32252 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
* * *
32284 TTTAAAATATATCAATTCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
32314 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
32332 TTTAAAATAAATCAATCCATACTAATCAAATA
1 TTTAAAATAAATCAATCCATACTAAT-AAATA
32364 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
32386 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
32418 TTTAAAATAAATCAAT-C---C--AT--AT-
1 TTTAAAATAAATCAATCCATACTAATAAATA
32440 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
* * *
32472 TTTAAAATATATCAATTCATAC-AACTACA-A
1 TTTAAAATAAATCAATCCATACTAA-TAAATA
32502 --T--AATAAATCAATCC--A-T-AT-----
1 TTTAAAATAAATCAATCCATACTAATAAATA
*
32520 TTTAAAATAAATCATTCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA
* * *
32552 TTTAAAATAAATCAATTCATATTCAA-AATTA
1 TTTAAAATAAATCAATCCATACT-AATAAATA
32583 TTTAAAATAAAT
1 TTTAAAATAAAT
32595 TATTTTAAAA
Statistics
Matches: 433, Mismatches: 21, Indels: 167
0.70 0.03 0.27
Matches are distributed among these distances:
20 2 0.00
22 107 0.25
23 14 0.03
24 7 0.02
25 2 0.00
26 41 0.09
28 16 0.04
30 6 0.01
31 29 0.07
32 207 0.48
33 2 0.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (31 bp):
TTTAAAATAAATCAATCCATACTAATAAATA
Found at i:32116 original size:22 final size:22
Alignment explanation
Indices: 32090--32132 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
32080 TAATAAATTA
32090 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
32112 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
32133 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:32141 original size:22 final size:22
Alignment explanation
Indices: 32092--32140 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
32082 ATAAATTATT
**
32092 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
32114 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
32137 TAAA
1 TAAA
32141 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:32202 original size:22 final size:22
Alignment explanation
Indices: 32176--32218 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
32166 TAATAAATTA
32176 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
32198 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
32219 CTAATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:32257 original size:22 final size:22
Alignment explanation
Indices: 32230--32272 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
32220 TAATAAAATA
32230 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
32252 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
32273 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:32281 original size:22 final size:22
Alignment explanation
Indices: 32232--32280 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
32222 ATAAAATATT
**
32232 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
32254 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
32277 TAAA
1 TAAA
32281 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:32378 original size:18 final size:20
Alignment explanation
Indices: 32355--32400 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
32345 AATCCATACT
32355 AATCAA-ATA-TTTAAAATA
1 AATCAACATATTTTAAAATA
32373 AATCAATCCATATTTTAAAATA
1 AATCAA--CATATTTTAAAATA
32395 AATCAA
1 AATCAA
32401 TCCATACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.25
21 3 0.12
22 15 0.62
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.33
Consensus pattern (20 bp):
AATCAACATATTTTAAAATA
Found at i:32387 original size:188 final size:188
Alignment explanation
Indices: 31929--32574 Score: 834
Period size: 188 Copynumber: 3.4 Consensus size: 188
31919 AATTATTAAA
* * *
31929 AATAAATTAATACATATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
** * ** ** ** * ** **
31994 TTATACAACTACAATAATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATACTAATAAAGT
66 CCAT---ATTTTAA-AATAAATCAATCCATACTAATAAAATATTTAAAATAAAT-C-AATCCA-T
* * * * *** *
32057 A-TTTAAAATAAATCAATTCATATTAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAAT
124 ATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATATATCAATTCATACAACTACAAT
* * * *
32120 AAATCAATCCATACTAATAAATTATTTAAAATAAATAAATCCATACTAATAAATTATTTAAAATA
1 -AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
32185 AATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAAATATTTAAAATAAATCAATCCAT
59 AATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAAATATTTAAAATAAATCAATCCAT
32250 ATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATATATCAATTCATACAACTACAAT
124 ATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATATATCAATTCATACAACTACAAT
32315 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATCAAA-TATTTAAAATAAATCAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT-AAATTATTTAAAATAAATCAA
*
32379 TCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTA
65 TCCATATTTTAAAATAAATCAATCCATACTAATAAAATATTTAAAATAAATCAATCCATATTTTA
32444 AAATAAATCAATCCATACTAATAAATTATTTAAAATATATCAATTCATACAACTACAAT
130 AAATAAATCAATCCATACTAATAAATTATTTAAAATATATCAATTCATACAACTACAAT
*
32503 AATAAATCAATCCATATTTTAAAATAAATCATTCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
32568 TCATATT
66 CCATATT
32575 CAAAATTATT
Statistics
Matches: 406, Mismatches: 36, Indels: 28
0.86 0.08 0.06
Matches are distributed among these distances:
187 3 0.01
188 231 0.57
189 4 0.01
190 1 0.00
192 10 0.02
193 3 0.01
194 80 0.20
195 19 0.05
196 6 0.01
197 1 0.00
198 48 0.12
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (188 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATATTTTAAAATAAATCAATCCATACTAATAAAATATTTAAAATAAATCAATCCATATTTTAA
AATAAATCAATCCATACTAATAAATTATTTAAAATATATCAATTCATACAACTACAAT
Found at i:32389 original size:22 final size:22
Alignment explanation
Indices: 32364--32406 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
32354 TAATCAAATA
32364 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
32386 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
32407 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:32415 original size:22 final size:22
Alignment explanation
Indices: 32366--32414 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
32356 ATCAAATATT
**
32366 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
32388 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
32411 TAAA
1 TAAA
32415 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:32424 original size:306 final size:296
Alignment explanation
Indices: 31807--32492 Score: 1004
Period size: 306 Copynumber: 2.3 Consensus size: 296
31797 CAACTACAAT
* *
31807 AATAAAT-TATTTAAAATAGATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTAT
1 AATAAATAT-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
*
31871 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTAAAAATAAAT
65 TTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAAATATTAAAAATAAAT
* *
31936 TAATACATATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATTTATACA
130 CAATACATATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATTCATACA
32001 ACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAAGTATTTAAAAT
195 ACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAAGTATTTAAAAT
* * **
32066 AAATCAATTCATATTAATAAATTATTTAAAATAAATC
260 AAATCAATCCATATTAATAAAATAAATAAAATAAATC
** *
32103 AATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATAAATCCATACTA
1 AATAAATATTTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATACTA
*
32168 ATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAAATATTT
56 ATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAAATATTA
* * *
32233 AAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATATATCA
121 AAAATAAATCAATACATATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCA
32298 ATTCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATCAAA-
186 ATTCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT-AAAG
* * **
32362 TATTTAAAATAAATCAATCCATATT-TTAAAATAAAT-CAATCCATAC
250 TATTTAAAATAAATCAATCCATATTAATAAAATAAATAAAATAAAT-C
32408 TAATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
1 -AATAAATAT-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
* *
32472 TTTAAAATATATCAATTCATA
64 TTTAAAATAAATCAATCCATA
32493 CAACTACAAT
Statistics
Matches: 350, Mismatches: 25, Indels: 30
0.86 0.06 0.07
Matches are distributed among these distances:
296 70 0.20
297 3 0.01
298 1 0.00
300 3 0.01
302 3 0.01
304 6 0.02
305 11 0.03
306 250 0.71
307 3 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (296 bp):
AATAAATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATT
TAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAAATATTAAAAATAAATC
AATACATATTTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATTCATACAA
CTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAAGTATTTAAAATA
AATCAATCCATATTAATAAAATAAATAAAATAAATC
Found at i:32444 original size:22 final size:22
Alignment explanation
Indices: 32418--32460 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
32408 TAATAAATTA
32418 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
32440 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
32461 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:32469 original size:22 final size:22
Alignment explanation
Indices: 32420--32468 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
32410 ATAAATTATT
**
32420 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
32442 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
32465 TAAA
1 TAAA
32469 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:32603 original size:15 final size:15
Alignment explanation
Indices: 32577--32701 Score: 112
Period size: 15 Copynumber: 8.1 Consensus size: 15
32567 TTCATATTCA
32577 AAATTA-TTTAAAAT
1 AAATTATTTTAAAAT
32591 AAATTATTTTAAAAT
1 AAATTATTTTAAAAT
*
32606 AAATCAATCCATATTTTATAAT
1 --A--AAT---TATTTTAAAAT
* *
32628 AATTTATTTTAATAT
1 AAATTATTTTAAAAT
*
32643 AAA-T-TTTTATAAT
1 AAATTATTTTAAAAT
*
32656 AAATTTTTTTAAAAT
1 AAATTATTTTAAAAT
*
32671 AAATTATTTTATAAT
1 AAATTATTTTAAAAT
32686 AAATTATTTTAAAAT
1 AAATTATTTTAAAAT
32701 A
1 A
32702 TATAACCTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
13 10 0.11
14 8 0.09
15 55 0.61
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.11
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
AAATTATTTTAAAAT
Found at i:32657 original size:28 final size:30
Alignment explanation
Indices: 32617--32701 Score: 122
Period size: 28 Copynumber: 2.9 Consensus size: 30
32607 AATCAATCCA
*
32617 TATTTTATAATAATTTATTTTAATATAAA-
1 TATTTTATAATAATTTATTTTAAAATAAAT
32646 T-TTTTATAATAAATTT-TTTTAAAATAAAT
1 TATTTTATAAT-AATTTATTTTAAAATAAAT
*
32675 TATTTTATAATAAATTATTTTAAAATA
1 TATTTTATAATAATTTATTTTAAAATA
32702 TATAACCTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
28 20 0.40
29 11 0.22
30 19 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
TATTTTATAATAATTTATTTTAAAATAAAT
Found at i:32659 original size:50 final size:49
Alignment explanation
Indices: 32503--32659 Score: 135
Period size: 46 Copynumber: 3.1 Consensus size: 49
32493 CAACTACAAT
* * *
32503 AATAAATCAATCCATATTTTAAAATAAATCATTCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAAT-AATTATT--TTAAT-ATAAATT-TTTAA
* * *
32557 AATAAATCAATTCATA--TT-CAA-AATTA-TTTAAAATAAATTATTTTAA
1 AATAAATCAATCCATATTTTAAAATAATTATTTTAATATAAA-T-TTTTAA
* *
32603 AATAAATCAATCCATATTTTATAATAATTTATTTTAATATAAATTTTTAT
1 AATAAATCAATCCATATTTTAAAATAA-TTATTTTAATATAAATTTTTAA
32653 AATAAAT
1 AATAAAT
32660 TTTTTTAAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
45 5 0.06
46 23 0.27
47 1 0.01
48 3 0.04
49 6 0.07
50 14 0.16
51 6 0.07
52 12 0.14
54 15 0.18
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (49 bp):
AATAAATCAATCCATATTTTAAAATAATTATTTTAATATAAATTTTTAA
Found at i:32717 original size:58 final size:56
Alignment explanation
Indices: 32617--32727 Score: 127
Period size: 58 Copynumber: 1.9 Consensus size: 56
32607 AATCAATCCA
* ** *
32617 TATTTTATAATAATTTATTTTAATATAAATTTTTATAATAAATTTTTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAATATAAATCCTTAT-ATAAA-TTATTTAAAATAAAT
32675 TATTTTATAATAAATTATTTTAAAATATATAA-CCTTAT-TAAATTATTTAAAAT
1 TATTTTATAATAAATTATTTT--AATATA-AATCCTTATATAAATTATTTAAAAT
32728 TATTTTAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
57 10 0.22
58 24 0.52
60 10 0.22
61 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (56 bp):
TATTTTATAATAAATTATTTTAATATAAATCCTTATATAAATTATTTAAAATAAAT
Found at i:37365 original size:31 final size:31
Alignment explanation
Indices: 37329--37391 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
37319 CGATTGAGAA
* *
37329 ATTAAAATCGAA-CGCATCGATAATGTTAGGG
1 ATTAAAATCAAATCG-ATCAATAATGTTAGGG
*
37360 ATTAAAATCAAATCGGTCAATAATGTTAGGG
1 ATTAAAATCAAATCGATCAATAATGTTAGGG
37391 A
1 A
37392 CCGTTCCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (31 bp):
ATTAAAATCAAATCGATCAATAATGTTAGGG
Found at i:44324 original size:22 final size:22
Alignment explanation
Indices: 44282--44330 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
44272 AAATATTAAA
* *
44282 TTTAAAAATATATATTCATTTT
1 TTTAAAAATATATACTAATTTT
44304 TTTAAAAATAT-TCACTAATTTT
1 TTTAAAAATATAT-ACTAATTTT
*
44326 CTTAA
1 TTTAA
44331 GGAATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAAAAATATATACTAATTTT
Found at i:45210 original size:3 final size:3
Alignment explanation
Indices: 45202--45235 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
45192 ACGGATTCTC
45202 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
45236 AGACTCCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:45759 original size:38 final size:39
Alignment explanation
Indices: 45706--45782 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 39
45696 GGTGTGTTCG
* **
45706 GTTCGTTTATATTCATAAACAAGTTTGTTTATCT-ATTC
1 GTTCATTTATATTCATAAACAAACTTGTTTATCTGATTC
* * *
45744 GTTCATTTATGTTCATGATCAAACTTGTTTATCTGATTC
1 GTTCATTTATATTCATAAACAAACTTGTTTATCTGATTC
45783 TCTTTTTCTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
38 28 0.88
39 4 0.12
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (39 bp):
GTTCATTTATATTCATAAACAAACTTGTTTATCTGATTC
Done.