Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000332.1 Hibiscus syriacus cultivar Beakdansim tig00000616_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: 47000
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:9 original size:4 final size:4
Alignment explanation
Indices: 1--220 Score: 353
Period size: 4 Copynumber: 56.2 Consensus size: 4
*
1 ACAT ACAT ACAT ACAT ACAT AACAT ACAT ACAT ACAT CCAT AC-T ACAT
1 ACAT ACAT ACAT ACAT ACAT -ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
49 ACAT ACAT CCAT AC-T ACAT ACAT AC-T ACAT ACA- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
94 ACAT -CAT ACAT ACAT ACAT ACAT ACA- GCAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
140 ACAT ACAT ACAT ACAT ACAT AAAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
188 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
221 ATGTCATCAT
Statistics
Matches: 201, Mismatches: 8, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
3 17 0.08
4 180 0.90
5 4 0.02
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:1182 original size:64 final size:64
Alignment explanation
Indices: 1114--1255 Score: 162
Period size: 64 Copynumber: 2.2 Consensus size: 64
1104 GCAGTACCCG
* * *
1114 TGCATCGATGCACAAATCACCTTCAATGTTTTCATTTTAAGGGGATGCATCG-ATGCA-TTCCTT
1 TGCATCGATGCACAAATCACATTCAATGTTTCCATTTTAAGAGG-TGCATCGTATGCACTTCCTT
* ** ** *
1177 ATGCATCGATGCACCAATTGCATTTGATGTTTCCATTTTAATAGGTGCATCGTATGCACTTCCTT
1 -TGCATCGATGCACAAATCACATTCAATGTTTCCATTTTAAGAGGTGCATCGTATGCACTTCCTT
*
1242 TGCATCGATACACA
1 TGCATCGATGCACA
1256 CTGAACAATT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 7 0.11
64 52 0.80
65 6 0.09
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (64 bp):
TGCATCGATGCACAAATCACATTCAATGTTTCCATTTTAAGAGGTGCATCGTATGCACTTCCTT
Found at i:5664 original size:3 final size:3
Alignment explanation
Indices: 5656--5680 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5646 GAGTGGTCCA
5656 CGC CGC CGC CGC CGC CGC CGC CGC C
1 CGC CGC CGC CGC CGC CGC CGC CGC C
5681 TCCCCACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.32, T:0.00
Consensus pattern (3 bp):
CGC
Found at i:8541 original size:39 final size:39
Alignment explanation
Indices: 8403--8533 Score: 165
Period size: 39 Copynumber: 3.4 Consensus size: 39
8393 CAGGGGGTGC
*
8403 ACCATTGGCCCCATCGATAGCA-ACAGTGGTAGGATCGGT
1 ACCATTGGCCCCATCGATAGCAGA-AGTGGTAGCATCGGT
* * * * *
8442 GCCATTGGCCCCAACAATAGCAGCAGTGGTAGCATCGGC
1 ACCATTGGCCCCATCGATAGCAGAAGTGGTAGCATCGGT
* *
8481 ACCATTGGCCCCATTGGTAGCAGAAGTGGTAGCATCGGT
1 ACCATTGGCCCCATCGATAGCAGAAGTGGTAGCATCGGT
*
8520 ACCACTGGCCCCAT
1 ACCATTGGCCCCAT
8534 TGGTAGCATT
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.19
Consensus pattern (39 bp):
ACCATTGGCCCCATCGATAGCAGAAGTGGTAGCATCGGT
Found at i:18173 original size:6 final size:6
Alignment explanation
Indices: 18162--18189 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
18152 TATCTCTTGA
18162 TTGCTT TTGCTT TTGCTT TTGCTT TTGC
1 TTGCTT TTGCTT TTGCTT TTGCTT TTGC
18190 AATGTCTAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.18, T:0.64
Consensus pattern (6 bp):
TTGCTT
Found at i:18479 original size:2 final size:2
Alignment explanation
Indices: 18474--18509 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
18464 CACGCGCGCG
18474 TA TA TA TA TA TA TA TA TA 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
18510 GAGAGAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18514 original size:2 final size:2
Alignment explanation
Indices: 18509--18536 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18499 ATATATATAT
18509 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
18537 TTGGTGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:19969 original size:17 final size:17
Alignment explanation
Indices: 19936--19974 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
19926 AAACGTCTTT
19936 CAAAATAATTTTTAAGA
1 CAAAATAATTTTTAAGA
*
19953 -AAAATCATTTTTAAAGA
1 CAAAATAATTTTT-AAGA
19970 CAAAA
1 CAAAA
19975 GGGGTCTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 11 0.58
17 4 0.21
18 4 0.21
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (17 bp):
CAAAATAATTTTTAAGA
Found at i:20434 original size:22 final size:22
Alignment explanation
Indices: 20391--20434 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
20381 AAATTTACAT
*
20391 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
20413 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
20435 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:22517 original size:3 final size:3
Alignment explanation
Indices: 22504--22565 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
22494 GTAATATGTA
** *
22504 AAT AA- AAT AAT AAT AAT AAT GCT AAT AAT AAT AATT AA- AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
22548 GAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT A-AT AA
22566 AAAAGACCCG
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
3 37 0.79
4 6 0.13
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:22566 original size:24 final size:23
Alignment explanation
Indices: 22504--22567 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
22494 GTAATATGTA
* *
22504 AATAA-AATAATAATAATAATGCT
1 AATAATAATAATAA-AATAACGAT
22527 AATAATAATAATTAAAATAACGAT
1 AATAATAATAA-TAAAATAACGAT
22551 AATAATAATATATAAAA
1 AATAATAATA-ATAAAA
22568 AAGACCCGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
23 5 0.14
24 27 0.75
25 4 0.11
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (23 bp):
AATAATAATAATAAAATAACGAT
Found at i:22832 original size:40 final size:42
Alignment explanation
Indices: 22718--22961 Score: 104
Period size: 40 Copynumber: 5.7 Consensus size: 42
22708 TGTTGGGGAC
* * ***
22718 GACACTGCTCATACGTGATGAAGAGTTCGGGTCGTTTTAAGGTT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGTCGTGGGAA-G-T
* * * * **
22762 AACACGGTTCCTACGTGATGAGGAAATCTGGTCG-GGGAA-T
1 GACACGGCTCATACGTGATGAAGAGTTCTGGTCGTGGGAAGT
* * ***
22802 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGTCGTGGGAA-GT
* * * * ** ** *
22845 GATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTAT-CTATGGTT
1 G---ACACGGCTCATACGTGATGAAGA-GTTCTGGTCGTGGGA-AG-T
* * *
22891 GACACGGCTCCTACGTGATGAGGAGATCTGGTC-TGGGAA-T
1 GACACGGCTCATACGTGATGAAGAGTTCTGGTCGTGGGAAGT
*
22931 GACATGGCTCATACGTGATGAAGAGTTCTGG
1 GACACGGCTCATACGTGATGAAGAGTTCTGG
22962 CCATCTAAAG
Statistics
Matches: 148, Mismatches: 41, Indels: 26
0.69 0.19 0.12
Matches are distributed among these distances:
40 55 0.37
41 2 0.01
42 2 0.01
43 32 0.22
44 26 0.18
45 2 0.01
46 28 0.19
47 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (42 bp):
GACACGGCTCATACGTGATGAAGAGTTCTGGTCGTGGGAAGT
Found at i:22885 original size:46 final size:45
Alignment explanation
Indices: 22800--23051 Score: 168
Period size: 46 Copynumber: 5.8 Consensus size: 45
22790 TGGTCGGGGA
* * ** **
22800 ATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTG
1 ATGACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCT-AAGGTG
* * *
22846 ATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT-
1 ATGACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTAAGGTG
*
22890 -TGACACGGCTCCTACGTGATGAGGAGATCTGG---TCT--GG-G
1 ATGACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTAAGGTG
* * * ** **
22928 AATGACATGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTG
1 -ATGACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCT-AAGGTG
* * * *
22975 ATAACACGGTTCCTACGTGATGAGGACG-GTTGGTTATCTATGGT-
1 ATGACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTAAGGTG
* *
23019 -TGACATGGCTCCTACGTGATGAGGAGATCTGGT
1 ATGACACGGCTCCTACGTGATGAGGAGAGCTGGT
23052 CTGGGGATGA
Statistics
Matches: 162, Mismatches: 30, Indels: 31
0.73 0.13 0.14
Matches are distributed among these distances:
38 2 0.01
40 31 0.19
42 2 0.01
43 56 0.35
45 8 0.05
46 60 0.37
47 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (45 bp):
ATGACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTAAGGTG
Found at i:22907 original size:43 final size:43
Alignment explanation
Indices: 22849--23051 Score: 157
Period size: 43 Copynumber: 4.7 Consensus size: 43
22839 AAAGGTGATA
*
22849 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTATGGTTG
* * *
22892 ACACGGCTCCTACGTGATGAGGAGATCTGG---TCT-GGGAATG
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTATGG-TTG
* * * ** ** * *
22932 ACATGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCT-ATGGT--TG
* *
22978 ACACGGTTCCTACGTGATGAGGACG-GTTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTATGGTTG
* *
23021 ACATGGCTCCTACGTGATGAGGAGATCTGGT
1 ACACGGCTCCTACGTGATGAGGAGAGCTGGT
23052 CTGGGGATGA
Statistics
Matches: 124, Mismatches: 25, Indels: 22
0.73 0.15 0.13
Matches are distributed among these distances:
39 2 0.02
40 31 0.25
42 2 0.02
43 55 0.44
45 6 0.05
46 27 0.22
47 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.28
Consensus pattern (43 bp):
ACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTATGGTTG
Found at i:22993 original size:129 final size:129
Alignment explanation
Indices: 22758--23080 Score: 547
Period size: 129 Copynumber: 2.5 Consensus size: 129
22748 GTCGTTTTAA
* * * *
22758 GGTTAACACGGTTCCTACGTGATGAGGAAATCTGGTCGGGGAATGACACGGCTCATACGTGATGA
1 GGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGA
22823 AGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAT
66 AGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAT
*
22887 GGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGAATGACATGGCTCATACGTGATGA
1 GGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGA
*
22952 AGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGTTGGTTATCTAT
66 AGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAT
* * * * *
23016 GGTTGACATGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGA
1 GGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGA
23081 GACGGCTGGC
Statistics
Matches: 182, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 182 1.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.26
Consensus pattern (129 bp):
GGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGA
AGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAT
Found at i:23079 original size:40 final size:41
Alignment explanation
Indices: 22763--23081 Score: 200
Period size: 40 Copynumber: 7.5 Consensus size: 41
22753 TTTAAGGTTA
* *
22763 ACACGGTTCCTACGTGATGAGGAAATCTGG-TC-GGGGAATG
1 ACACGGCTCCTACGTGATGAGGAGATCTGGATCTGGGG-ATG
* * * * *
22803 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGATCTGG--ATCT---GGGGATG
* * ** *
22849 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GATCTGG--ATCTGGGGATG
*
22892 ACACGGCTCCTACGTGATGAGGAGATCTGG-TCTGGGAATG
1 ACACGGCTCCTACGTGATGAGGAGATCTGGATCTGGGGATG
* * * * * *
22932 ACATGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGATCTGG--ATCT---GGGGATG
* * ** *
22978 ACACGGTTCCTACGTGATGAGGACGGT-TGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GATCTGG--ATCTGGGGATG
*
23021 ACATGGCTCCTACGTGATGAGGAGATCTGG-TCTGGGGATG
1 ACACGGCTCCTACGTGATGAGGAGATCTGGATCTGGGGATG
* *
23061 ACACGGTTCCTACATGATGAG
1 ACACGGCTCCTACGTGATGAG
23082 ACGGCTGGCC
Statistics
Matches: 210, Mismatches: 52, Indels: 34
0.71 0.18 0.11
Matches are distributed among these distances:
40 82 0.39
42 3 0.01
43 59 0.28
46 60 0.29
47 6 0.03
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.26
Consensus pattern (41 bp):
ACACGGCTCCTACGTGATGAGGAGATCTGGATCTGGGGATG
Found at i:23148 original size:28 final size:28
Alignment explanation
Indices: 23108--23204 Score: 83
Period size: 28 Copynumber: 3.4 Consensus size: 28
23098 AGGAGTTATG
* *
23108 GTTTCAAGAGAAACCA-AATTAAAGATTT
1 GTTTCAAAAGAAA-CAGAATCAAAGATTT
*
23136 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGAATCAAAGATTT
*
23164 GTTTCAAGAA-AAACA-AGCTCAAAGATAATGT
1 GTTTCAA-AAGAAACAGA-ATCAAAGAT--T-T
23195 GTTTCAAAAG
1 GTTTCAAAAG
23205 CAACTGTCTC
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
27 3 0.05
28 43 0.73
29 2 0.03
30 3 0.05
31 8 0.14
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.26
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGAATCAAAGATTT
Found at i:23201 original size:31 final size:28
Alignment explanation
Indices: 23128--23204 Score: 95
Period size: 28 Copynumber: 2.6 Consensus size: 28
23118 AAACCAAATT
23128 AAAGATTTGTTTCAAAAGAAACAGACTC
1 AAAGATTTGTTTCAAAAGAAACAGACTC
23156 AAAGATTTGTTTCAAGAA-AAACA-AGCTC
1 AAAGATTTGTTTCAA-AAGAAACAGA-CTC
23184 AAAGATAATGTGTTTCAAAAG
1 AAAGAT--T-TGTTTCAAAAG
23205 CAACTGTCTC
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
27 1 0.02
28 29 0.67
29 2 0.05
30 3 0.07
31 8 0.19
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.26
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAGACTC
Found at i:23395 original size:66 final size:64
Alignment explanation
Indices: 23206--23395 Score: 159
Period size: 66 Copynumber: 2.9 Consensus size: 64
23196 TTTCAAAAGC
** * *
23206 AACTGTCTCGAAAGAGACAAAATTCATTTCAAATGAAAC-AACTCAAAAGATG-ACGTTTAAAGG
1 AACTGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACGATCTC-AAAGATGTATGTTTAAAGG
23269 G
64 G
* * ** * * * * * * *
23270 AATTGTCTCAAGCGAGACAAAATTTGTTTTTAAGGGAAACGTTCTCAAATATCTGTGTTTCATGG
1 AACTGTCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACGATCTCAAAGATGTATGTTTAAAGG
23335 G
64 G
* *
23336 AAACTGTCTCAAATGAGACAAAATTCATTTCGAGGGAAACGATCTCAAAGATGTTTGTTT
1 -AACTGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGTATGTTT
23396 TGTTTCAAGG
Statistics
Matches: 95, Mismatches: 25, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
63 2 0.02
64 17 0.18
65 17 0.18
66 40 0.42
67 19 0.20
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (64 bp):
AACTGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGTATGTTTAAAGGG
Found at i:23622 original size:26 final size:27
Alignment explanation
Indices: 23593--23645 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
23583 TATCTTAGTG
*
23593 AGAC-AAAATTTTGT-TTCCAAAGAAAC
1 AGACTAAAATTTT-TCTTCAAAAGAAAC
*
23619 AGACTCAAATTTTTCTTCAAAAGAAAC
1 AGACTAAAATTTTTCTTCAAAAGAAAC
23646 TGTTTTAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.28
Consensus pattern (27 bp):
AGACTAAAATTTTTCTTCAAAAGAAAC
Found at i:24347 original size:36 final size:36
Alignment explanation
Indices: 24263--24366 Score: 133
Period size: 36 Copynumber: 3.0 Consensus size: 36
24253 GAGAAAATGA
* *
24263 TGTCTCAAGCGAGACAAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
24297 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
24333 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
24367 ACGATCTCAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 20 0.34
35 10 0.17
36 29 0.49
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:24394 original size:36 final size:36
Alignment explanation
Indices: 24264--24382 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 36
24254 AGAAAATGAT
* * *
24264 GTCTCAAGCGAGACAAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGA-AAAC
* **
24298 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
24334 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
24369 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
24383 TCAACTTTGT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
34 20 0.29
35 12 0.17
36 38 0.54
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:24513 original size:105 final size:101
Alignment explanation
Indices: 24334--24566 Score: 292
Period size: 105 Copynumber: 2.3 Consensus size: 101
24324 TAGAGAAATT
*
24334 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAAT
* *
24398 GTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
64 GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
24436 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * *
24500 TAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
60 TAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
24541 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
24567 AAAATTCTCA
Statistics
Matches: 115, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 5 0.04
104 4 0.03
105 78 0.68
106 5 0.04
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:30425 original size:22 final size:22
Alignment explanation
Indices: 30382--30425 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
30372 AAATTTACAT
*
30382 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
30404 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
30426 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:32497 original size:3 final size:3
Alignment explanation
Indices: 32484--32548 Score: 62
Period size: 3 Copynumber: 21.7 Consensus size: 3
32474 GTAATATGTA
**
32484 AAT AA- AAT AAT AAT AAT AAT AAT GCT AAT AAT AAT AATT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
* *
32528 AAC GAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT AAT A-AT AA
32549 AAAAGACCCG
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 4 0.08
3 40 0.80
4 6 0.12
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:32521 original size:24 final size:23
Alignment explanation
Indices: 32485--32550 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
32475 TAATATGTAA
*
32485 ATAA-AATAATAATAATAATAATG
1 ATAATAATAATAATAA-AATAACG
*
32508 CTAATAATAATAATTAAAATAACG
1 ATAATAATAATAA-TAAAATAACG
32532 ATAATAATAATATATAAAA
1 ATAATAATAATA-ATAAAA
32551 AAGACCCGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 3 0.08
24 30 0.81
25 4 0.11
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (23 bp):
ATAATAATAATAATAAAATAACG
Found at i:36400 original size:15 final size:15
Alignment explanation
Indices: 36382--36411 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
36372 GGCCAAACAT
36382 TAAAAGAGAGTAACC
1 TAAAAGAGAGTAACC
36397 TAAAAGAGAGTAACC
1 TAAAAGAGAGTAACC
36412 GTTGGGGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.20, T:0.13
Consensus pattern (15 bp):
TAAAAGAGAGTAACC
Found at i:37129 original size:16 final size:16
Alignment explanation
Indices: 37110--37167 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
37100 TATACCTTTT
37110 ATATATACTATAGTTA
1 ATATATACTATAGTTA
*
37126 ATATATACTA-A-TGA
1 ATATATACTATAGTTA
*
37140 CTATATATA-TATAGTTT
1 --ATATATACTATAGTTA
37157 ATATATACTAT
1 ATATATACTAT
37168 TTAGTTAGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 2 0.06
15 10 0.29
16 21 0.62
17 1 0.03
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (16 bp):
ATATATACTATAGTTA
Found at i:38910 original size:31 final size:30
Alignment explanation
Indices: 38849--38909 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
38839 GACTAAAATG
38849 ACAAAAAACTTAGGGACTAAAATAGTAAAA
1 ACAAAAAACTTAGGGACTAAAATAGTAAAA
* *
38879 ACAAAAAAC-TAGAGGATTAAAATGGTAAAA
1 ACAAAAAACTTAG-GGACTAAAATAGTAAAA
38909 A
1 A
38910 ATAGAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 3 0.11
30 25 0.89
ACGTcount: A:0.61, C:0.08, G:0.15, T:0.16
Consensus pattern (30 bp):
ACAAAAAACTTAGGGACTAAAATAGTAAAA
Found at i:39008 original size:30 final size:29
Alignment explanation
Indices: 38956--39034 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 29
38946 TTAAAGGGCT
* *
38956 AAAATAGA-AGAAAGAAAATTTAGGGACC
1 AAAATAGAGAAAAAGAAACTTTAGGGACC
38984 AAAATAGAGAAAATAGAAACTTTAGGGACC
1 AAAATAGAGAAAA-AGAAACTTTAGGGACC
*
39014 AAAATAGATGAAACAGAAACT
1 AAAATAGA-GAAAAAGAAACT
39035 AAAGGGAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 8 0.18
29 3 0.07
30 30 0.67
31 4 0.09
ACGTcount: A:0.57, C:0.09, G:0.19, T:0.15
Consensus pattern (29 bp):
AAAATAGAGAAAAAGAAACTTTAGGGACC
Found at i:39041 original size:30 final size:30
Alignment explanation
Indices: 38977--39064 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 30
38967 AAGAAAATTT
* **
38977 AGGGACCAAAATAGA-GAAAATAGAAACTTT
1 AGGGACCAAAATAGATG-AAACAGAAACTAA
39007 AGGGACCAAAATAGATGAAACAGAAACTAA
1 AGGGACCAAAATAGATGAAACAGAAACTAA
** * * *
39037 AGGGAATAAAATGGATAAAACATAAACT
1 AGGGACCAAAATAGATGAAACAGAAACT
39065 TAGGGGGCTA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
30 48 0.98
31 1 0.02
ACGTcount: A:0.56, C:0.10, G:0.19, T:0.15
Consensus pattern (30 bp):
AGGGACCAAAATAGATGAAACAGAAACTAA
Found at i:39953 original size:25 final size:24
Alignment explanation
Indices: 39907--39956 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
39897 TGGTGGTTGG
39907 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
* *
39931 TTTAATGGTATGTTTTAAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
39956 T
1 T
39957 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:43158 original size:13 final size:13
Alignment explanation
Indices: 43140--43177 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
43130 TTCATGAGTG
43140 TTTGTTTGT-TTTC
1 TTTGTTT-TATTTC
43153 TTTGTTTTATTTC
1 TTTGTTTTATTTC
*
43166 TTTATTTTATTT
1 TTTGTTTTATTT
43178 TTAATATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 1 0.04
13 22 0.96
ACGTcount: A:0.08, C:0.05, G:0.08, T:0.79
Consensus pattern (13 bp):
TTTGTTTTATTTC
Found at i:45472 original size:24 final size:24
Alignment explanation
Indices: 45427--45476 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
45417 TGGTGGTTGG
45427 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
45451 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
45475 TT
1 TT
45477 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Done.