Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001256.1 Hibiscus syriacus cultivar Beakdansim tig00002467_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: 82059
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:5637 original size:24 final size:22
Alignment explanation
Indices: 5597--5659 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 22
5587 AAGCGACGGT
*
5597 GGGGGTGGGCGGAGGAGCGGGCGGA
1 GGGGGT-GG-GGAGGAGAGGG-GGA
*
5622 GGGGGTGGGGATGGAGATGGGGA
1 GGGGGTGGGGA-GGAGAGGGGGA
5645 GGGGGATGGGGAGGA
1 GGGGG-TGGGGAGGA
5660 ACATATTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 14 0.41
24 14 0.41
25 6 0.18
ACGTcount: A:0.16, C:0.05, G:0.71, T:0.08
Consensus pattern (22 bp):
GGGGGTGGGGAGGAGAGGGGGA
Found at i:9188 original size:24 final size:25
Alignment explanation
Indices: 9128--9188 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
9118 TCGGGCCGGG
9128 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
9151 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
9175 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
9189 ATATATATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:9525 original size:2 final size:2
Alignment explanation
Indices: 9518--9578 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
9508 AATATAAAGA
9518 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
9560 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
9579 GTTAGAAATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9864 original size:16 final size:16
Alignment explanation
Indices: 9832--9866 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9822 TAACGCCTTT
* *
9832 AATCATTAAACAGAGG
1 AATCATTAAAAAAAGG
9848 AATCATTAAAAAAAGG
1 AATCATTAAAAAAAGG
9864 AAT
1 AAT
9867 AATTTCGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.09, G:0.14, T:0.20
Consensus pattern (16 bp):
AATCATTAAAAAAAGG
Found at i:11148 original size:155 final size:155
Alignment explanation
Indices: 10866--11168 Score: 570
Period size: 155 Copynumber: 2.0 Consensus size: 155
10856 AACTTTTTGG
*
10866 TTTTACTATTACTTCTGATGAGTGTACAATGATGCTTCCCTCTTTCTTATTTTTTGAGGCTAGTG
1 TTTTACTATTACTTCTGATGAGTGTACAATGATGCTTCCCTCTTTCTTATTTTCTGAGGCTAGTG
*
10931 ATTTAATCATGTTGCGGTTTGACATTGCCATACTTGTCGAGGTCTCACTTGTGAATGAAAGTTGT
66 ATTTAATCATGTTGCAGTTTGACATTGCCATACTTGTCGAGGTCTCACTTGTGAATGAAAGTTGT
*
10996 ACATTCACCCTTACCAATATTACAT
131 ACATTAACCCTTACCAATATTACAT
11021 TTTTACTATTACTTCTGATGAGTGTACAATGATGCTTCCCTCTTTCTTATTTTCTGAGGCTAGTG
1 TTTTACTATTACTTCTGATGAGTGTACAATGATGCTTCCCTCTTTCTTATTTTCTGAGGCTAGTG
*
11086 ATTTAATCATGTTGCAGTTTGACATTGCCATACTTGTCGAGTTCTCACTTGTGAATGAAAGTTGT
66 ATTTAATCATGTTGCAGTTTGACATTGCCATACTTGTCGAGGTCTCACTTGTGAATGAAAGTTGT
11151 ACATTAACCCTTACCAAT
131 ACATTAACCCTTACCAAT
11169 GTTATATTAT
Statistics
Matches: 144, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
155 144 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (155 bp):
TTTTACTATTACTTCTGATGAGTGTACAATGATGCTTCCCTCTTTCTTATTTTCTGAGGCTAGTG
ATTTAATCATGTTGCAGTTTGACATTGCCATACTTGTCGAGGTCTCACTTGTGAATGAAAGTTGT
ACATTAACCCTTACCAATATTACAT
Found at i:13355 original size:23 final size:21
Alignment explanation
Indices: 13321--13369 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
13311 ATTATAATAA
*
13321 AATTTGAAAATTTAGTTATTT
1 AATTTGAAAATTTAATTATTT
*
13342 TATTTGACATAATTTAATTATTT
1 AATTTGA-A-AATTTAATTATTT
13365 AATTT
1 AATTT
13370 TATAATGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 6 0.26
22 1 0.04
23 16 0.70
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (21 bp):
AATTTGAAAATTTAATTATTT
Found at i:24962 original size:2 final size:2
Alignment explanation
Indices: 24920--24946 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24910 CCTTGTAGTT
24920 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
24947 TGCAGCAGGC
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:45789 original size:15 final size:15
Alignment explanation
Indices: 45745--45795 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
45735 GTCGTTCTGA
*
45745 TATAATTGTTTTTAT
1 TATAATTGATTTTAT
* ** *
45760 TATGACGGATCTTAT
1 TATAATTGATTTTAT
45775 TATAATTGATTTTAT
1 TATAATTGATTTTAT
45790 TATAAT
1 TATAAT
45796 CGTTCTGATA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.55
Consensus pattern (15 bp):
TATAATTGATTTTAT
Found at i:52766 original size:30 final size:30
Alignment explanation
Indices: 52698--52791 Score: 109
Period size: 30 Copynumber: 3.1 Consensus size: 30
52688 GAATGACCTA
* * *
52698 TCCAGAGGTCACAAAG-ACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCTCGGAAACTG
*
52727 TCCAGAGGTCATAAAGAACCTCGGAAACTG
1 TCCAGAGGTCACAAAGAACCTCGGAAACTG
* * *
52757 TCCATAGGTCCCAAAGAACCTAGGTAAACTG
1 TCCAGAGGTCACAAAGAACCTCGG-AAACTG
52788 TCCA
1 TCCA
52792 TATGTTCCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 15 0.27
30 30 0.55
31 10 0.18
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCTCGGAAACTG
Found at i:52789 original size:31 final size:31
Alignment explanation
Indices: 52739--52824 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 31
52729 CAGAGGTCAT
*
52739 AAAGAACCTCGG-AAACTGTCCATAGGTCCC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCCC
* *
52769 AAAGAACCTAGGTAAACTGTCCATATGTTCC
1 AAAGAACCTAGGTAAACTGTCCATAGGTCCC
** * *
52800 TTAGAACATAGGTATACTGTCCATA
1 AAAGAACCTAGGTAAACTGTCCATA
52825 TATCTCGAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 11 0.23
31 37 0.77
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (31 bp):
AAAGAACCTAGGTAAACTGTCCATAGGTCCC
Found at i:52825 original size:31 final size:31
Alignment explanation
Indices: 52751--52846 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
52741 AGAACCTCGG
* *
52751 AAACTGTCCATAGGTCCCAAAGAACCTAGGT
1 AAACTGTCCATATGTCCCAAAGAACATAGGT
* **
52782 AAACTGTCCATATGTTCCTTAGAACATAGGT
1 AAACTGTCCATATGTCCCAAAGAACATAGGT
* * *
52813 ATACTGTCCATATATCTCGAAAG-ACATAGGT
1 AAACTGTCCATATGTC-CCAAAGAACATAGGT
52844 AAA
1 AAA
52847 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (31 bp):
AAACTGTCCATATGTCCCAAAGAACATAGGT
Found at i:54150 original size:64 final size:62
Alignment explanation
Indices: 54017--54177 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 62
54007 TAATGAAGGT
* * *
54017 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATATAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTCTATATAAT-GGA
* * *
54082 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATAT-AATGGA
* *
54146 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
54178 CCTTAAACAA
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.69
65 22 0.26
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATATAATGGA
Found at i:55195 original size:20 final size:19
Alignment explanation
Indices: 55156--55197 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
55146 GTAACTTCAA
*
55156 TCCATTTTCATTTCTTTAT
1 TCCATTTTCATTTATTTAT
*
55175 TCCATTCTTCCTTTATTTAT
1 TCCATT-TTCATTTATTTAT
55195 TCC
1 TCC
55198 TTATGCACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.14, C:0.26, G:0.00, T:0.60
Consensus pattern (19 bp):
TCCATTTTCATTTATTTAT
Found at i:57303 original size:31 final size:31
Alignment explanation
Indices: 57265--57359 Score: 95
Period size: 31 Copynumber: 3.1 Consensus size: 31
57255 GAACCTCTGC
*
57265 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACCTAGGTA
* **
57296 AACTGTCCATATGTTCCTTAGAACAC-AGGTA
1 AACTGTCCATATGTCCCAAAGAAC-CTAGGTA
* * *
57327 TACTGTCCATATGTCTCAAA-AGACATAGGTA
1 AACTGTCCATATGTCCCAAAGA-ACCTAGGTA
57358 AA
1 AA
57360 ACCCTCGACT
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
30 1 0.02
31 48 0.96
32 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACCTAGGTA
Found at i:58621 original size:64 final size:62
Alignment explanation
Indices: 58488--58648 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 62
58478 TAATGAAGGT
* * *
58488 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* *
58553 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
58617 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
58649 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.68
65 23 0.27
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:60130 original size:22 final size:22
Alignment explanation
Indices: 60101--60153 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
60091 TTGCATTTCG
60101 CGTTGCGATAGTCTACAGTTAT
1 CGTTGCGATAGTCTACAGTTAT
* *
60123 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTAT
60145 CGTTGCGAT
1 CGTTGCGAT
60154 TTTCCAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTAT
Found at i:60775 original size:6 final size:6
Alignment explanation
Indices: 60759--60793 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
60749 GTCCGTCTCG
60759 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
60794 TGTAATACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.00, C:0.17, G:0.51, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:60901 original size:19 final size:19
Alignment explanation
Indices: 60877--60983 Score: 133
Period size: 19 Copynumber: 5.5 Consensus size: 19
60867 CAACGAATTT
*
60877 TCGCAACGAATTTGGGAAA
1 TCGCAACGAATTTGGAAAA
* * **
60896 TCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
60918 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
60937 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
60956 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
*
60975 TAGCAACGA
1 TCGCAACGA
60984 CAACTGTAGA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
19 59 0.79
20 2 0.03
21 2 0.03
22 12 0.16
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:60968 original size:38 final size:39
Alignment explanation
Indices: 60877--61024 Score: 147
Period size: 41 Copynumber: 3.7 Consensus size: 39
60867 CAACGAATTT
* **
60877 TCGCAACGAATTTGGGAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACG--AACTGTAGAAAA
* *
60918 TCGCAACGAATTTGGAAAATCGCAACGAA-TTTGGAAAA
1 TCGCAACGAATTTGGAAAATCGCAACGAACTGTAGAAAA
* **
60956 TCGCAACGAATTTGGAAAATAGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACG--AACTGTAGAAAA
*
60997 TCGCAACGCGAA-ATGGAAAATCGCAACG
1 TCGCAA--CGAATTTGGAAAATCGCAACG
61025 CGATTTTCAA
Statistics
Matches: 90, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
38 31 0.34
39 2 0.02
40 2 0.02
41 37 0.41
42 14 0.16
43 4 0.04
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (39 bp):
TCGCAACGAATTTGGAAAATCGCAACGAACTGTAGAAAA
Found at i:60992 original size:79 final size:79
Alignment explanation
Indices: 60877--61024 Score: 244
Period size: 79 Copynumber: 1.9 Consensus size: 79
60867 CAACGAATTT
* * *
60877 TCGCAACGAATTTGGGAAATCGCAACGACAACTGTAGACTATCGCAA-CGAATTTGGAAAATCGC
1 TCGCAACGAATTTGGAAAATAGCAACGACAACTGTAGACTATCGCAACCGAA-ATGGAAAATCGC
60941 AACGAATTTGGAAAA
65 AACGAATTTGGAAAA
60956 TCGCAACGAATTTGGAAAATAGCAACGACAACTGTAGACTATCGCAACGCGAAATGGAAAATCGC
1 TCGCAACGAATTTGGAAAATAGCAACGACAACTGTAGACTATCGCAAC-CGAAATGGAAAATCGC
61021 AACG
65 AACG
61025 CGATTTTCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
79 45 0.70
80 15 0.23
81 4 0.06
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (79 bp):
TCGCAACGAATTTGGAAAATAGCAACGACAACTGTAGACTATCGCAACCGAAATGGAAAATCGCA
ACGAATTTGGAAAA
Found at i:61021 original size:20 final size:20
Alignment explanation
Indices: 60996--61092 Score: 122
Period size: 20 Copynumber: 4.8 Consensus size: 20
60986 ACTGTAGACT
60996 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
61016 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
61037 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
*
61057 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
61077 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
61093 CAACGCGAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 49 0.77
21 15 0.23
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:61024 original size:61 final size:61
Alignment explanation
Indices: 60930--61086 Score: 162
Period size: 61 Copynumber: 2.6 Consensus size: 61
60920 GCAACGAATT
* *
60930 TGGAAAATCGCAA--CGAATTTGGAAAATCGCAACG-AATTTGGAA-AATAGCAACGAC-AAC
1 TGGAAAATCGCAACGCGAA-ATGGAAAATCGCAACGCAATTTGCAACAATAGCAACG-CGAAC
** * * * *
60988 TGTAGACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAC
1 TG--GAAAATCGCAACGCGAAATGGAAAATCGCAACGCAATTTGCAACAATAGCAACGCGAAC
*
61051 TGGAAAATCGCAACGCGAAATGAAAAATCGCAACGC
1 TGGAAAATCGCAACGCGAAATGGAAAATCGCAACGC
61087 GAAATGCAAC
Statistics
Matches: 81, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
58 2 0.02
60 9 0.11
61 46 0.57
62 11 0.14
63 13 0.16
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.17
Consensus pattern (61 bp):
TGGAAAATCGCAACGCGAAATGGAAAATCGCAACGCAATTTGCAACAATAGCAACGCGAAC
Found at i:64511 original size:2 final size:2
Alignment explanation
Indices: 64504--64574 Score: 133
Period size: 2 Copynumber: 35.5 Consensus size: 2
64494 TCATAGTTTC
64504 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
*
64546 AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64575 CTTGTTCAGA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:64664 original size:2 final size:2
Alignment explanation
Indices: 64657--64696 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
64647 TTGTAATTCG
64657 TA TA 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 TA TA
64697 GAATTTGATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:70017 original size:53 final size:53
Alignment explanation
Indices: 69930--70098 Score: 241
Period size: 53 Copynumber: 3.2 Consensus size: 53
69920 CCTCTTCTTT
** * * *
69930 GAACAATCTTC-GATTAGCGGGTTCACTCCATCTTGCTTTAGGGAGTAGAACTC
1 GAACAATCTTCTGCCTA-CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
*
69983 GAACAGTCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
* * *
70036 GAACAATCTTCTGCCTACGAGTTCGCTCCCTCTTGCTTCAGGGAGTAAAACTA
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
70089 GAACAATCTT
1 GAACAATCTT
70099 ATGGTGTGAT
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
53 102 0.97
54 3 0.03
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (53 bp):
GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTC
Found at i:70539 original size:42 final size:41
Alignment explanation
Indices: 70458--70544 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 41
70448 TCCGAGAAGG
* * *
70458 CTTA-AAATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTACAAATGACCCGAAGGACTTATCATCATGCTCAAAAGA
*
70498 CTTACAAATGACCCGAAGGATTTCATCATCATGCTCAAAAGA
1 CTTACAAATGACCCGAAGGACTT-ATCATCATGCTCAAAAGA
70540 CTTAC
1 CTTAC
70545 TGATGGATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 4 0.10
41 16 0.39
42 21 0.51
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (41 bp):
CTTACAAATGACCCGAAGGACTTATCATCATGCTCAAAAGA
Found at i:70638 original size:42 final size:42
Alignment explanation
Indices: 70592--71160 Score: 210
Period size: 42 Copynumber: 13.0 Consensus size: 42
70582 CAAATTACCT
*
70592 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCC
1 GAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGCCC
*
70634 GAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG---
1 GAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGCCC
*** * * * * ** **
70673 GTTTG-CTTCA-CTACTCTTCCAT-G-AAGGCTTACAAATTACCC
1 GAAGGATTTCATC-A-TCATGC-TCGAAAGACTTACTGATGGCCC
* * *
70714 GAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGACACTTAC
1 GAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGC-C---C
* * * * * ** **
70760 TGATGGGTTTGCTTCA-CTACT-CTTCCGTGAAGGCTTACAAATTACCC
1 -GAAGGATTT-CATCATC-A-TGC-T-CG-AAAGACTTACTGATGGCCC
* * *
70807 TAAGGATTTAATCATCACGCTCGAAAGACTTACTGATGGCCC
1 GAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGCCC
*
70849 GAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCACTTAC
1 GAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGC-C---C
* * * * * ** **
70895 TGATGGGTTTGCTTCA-CTACT-CTTCCATGAAGGCTTACAAATAACCC
1 -GAAGGATTT-CATCATC-A-TGC-TCGA--AAGACTTACTGATGGCCC
*
70942 GAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCC
1 GAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGCCC
* * * *
70984 GAAAGACTTCATCATCATGCTCGTAAGACTTATTGATGGCACTTAC
1 GAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGC-C---C
* * * * * ** **
71030 TGATGGGTTTGCTTCA-CTACT-CTTCCGTGAAGGCTTACAAATTACCC
1 -GAAGGATTT-CATCATC-A-TGC-T-CG-AAAGACTTACTGATGGCCC
* * *
71077 TAAGAATTTAATCATCATGCTCGAAAGACTTACTGATGGCCC
1 GAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGCCC
* *
71119 GAATGACTTCATCATCATGCTCGAAAGACTTACTGATGGCCC
1 GAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGCCC
71161 TCGAAAGACT
Statistics
Matches: 374, Mismatches: 104, Indels: 98
0.65 0.18 0.17
Matches are distributed among these distances:
37 1 0.00
38 16 0.04
39 7 0.02
40 2 0.01
41 7 0.02
42 199 0.53
43 8 0.02
44 7 0.02
45 15 0.04
46 24 0.06
47 24 0.06
48 17 0.05
49 8 0.02
50 7 0.02
51 32 0.09
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (42 bp):
GAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGGCCC
Found at i:70647 original size:122 final size:122
Alignment explanation
Indices: 70454--70753 Score: 442
Period size: 122 Copynumber: 2.5 Consensus size: 122
70444 CTCTTCCGAG
** * * **
70454 AAGGCTTA-AAATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGACTTACAAATGACCCGAAGG
1 AAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGACCCGAAGG
* ***
70517 ATTTCATCATCATGCTCAAAAGACTTACTGATGGATTTGCTTCACTACTCTTTGGTA
66 ACTTCATCATCATGCTCAAAAGACTTACTGATGGATTTGCTTCACTACTCTTCCATA
* *
70574 AAGGCTTACAAATTACCTGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGACCCGAAGG
* * *
70639 ACTTCATCATCATGCTCGAAAGACTTACTGATGGGTTTGCTTCACTACTCTTCCATG
66 ACTTCATCATCATGCTCAAAAGACTTACTGATGGATTTGCTTCACTACTCTTCCATA
*
70696 AAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGAC
1 AAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGAC
70754 ACTTACTGAT
Statistics
Matches: 160, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
120 8 0.05
121 14 0.09
122 138 0.86
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (122 bp):
AAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGACCCGAAGG
ACTTCATCATCATGCTCAAAAGACTTACTGATGGATTTGCTTCACTACTCTTCCATA
Found at i:70663 original size:22 final size:21
Alignment explanation
Indices: 70602--70665 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
70592 GAAGGATTTA
70602 ATCATCATGCTCGAAAGACTT
1 ATCATCATGCTCGAAAGACTT
* * *
70623 A-C-TGATGGCCCGAAGGACTT
1 ATCATCAT-GCTCGAAAGACTT
70643 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
70665 A
1 A
70666 CTGATGGGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.09
20 12 0.36
21 3 0.09
22 12 0.36
23 3 0.09
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
ATCATCATGCTCGAAAGACTT
Found at i:70820 original size:93 final size:93
Alignment explanation
Indices: 70661--70844 Score: 332
Period size: 93 Copynumber: 2.0 Consensus size: 93
70651 TGCTCGAAAG
70661 ACTTACTGATGGGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATTACCCGAAGGATTTAAT
1 ACTTACTGATGGGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATTACCCGAAGGATTTAAT
* *
70726 CATCATGCTCGAAAGACTTATTGATGAC
66 CATCACGCTCGAAAGACTTACTGATGAC
* *
70754 ACTTACTGATGGGTTTGCTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCTAAGGATTTAAT
1 ACTTACTGATGGGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATTACCCGAAGGATTTAAT
70819 CATCACGCTCGAAAGACTTACTGATG
66 CATCACGCTCGAAAGACTTACTGATG
70845 GCCCGAAGGA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 87 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (93 bp):
ACTTACTGATGGGTTTGCTTCACTACTCTTCCATGAAGGCTTACAAATTACCCGAAGGATTTAAT
CATCACGCTCGAAAGACTTACTGATGAC
Found at i:70856 original size:20 final size:20
Alignment explanation
Indices: 70828--70888 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
70818 TCATCACGCT
70828 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTGATGGCC
* * *
70848 CGAAGGACTTCATCATCAT-GCT
1 CGAAAGACTT-A-C-TGATGGCC
70870 CGAAAGACTTACTGATGGC
1 CGAAAGACTTACTGATGGC
70889 ACTTACTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
19 3 0.09
20 12 0.38
21 2 0.06
22 12 0.38
23 3 0.09
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (20 bp):
CGAAAGACTTACTGATGGCC
Found at i:70867 original size:135 final size:135
Alignment explanation
Indices: 70711--71158 Score: 779
Period size: 135 Copynumber: 3.3 Consensus size: 135
70701 TTACAAATTA
* * * *
70711 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTATTGATGACACTTACTGATGGGTTTGCTTCA
1 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGGTTTGCTTCA
*
70776 CTACTCTTCCGTGAAGGCTTACAAATTACCCTAAGGATTTAATCATCACGCTCGAAAGACTTACT
66 CTACTCTTCCGTGAAGGCTTACAAATTACCCTAAGGATTTAATCATCATGCTCGAAAGACTTACT
70841 GATGG
131 GATGG
70846 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGGTTTGCTTCA
1 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGGTTTGCTTCA
* * *
70911 CTACTCTTCCATGAAGGCTTACAAATAACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACT
66 CTACTCTTCCGTGAAGGCTTACAAATTACCCTAAGGATTTAATCATCATGCTCGAAAGACTTACT
70976 GATGG
131 GATGG
* * *
70981 CCCGAAAGACTTCATCATCATGCTCGTAAGACTTATTGATGGCACTTACTGATGGGTTTGCTTCA
1 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGGTTTGCTTCA
*
71046 CTACTCTTCCGTGAAGGCTTACAAATTACCCTAAGAATTTAATCATCATGCTCGAAAGACTTACT
66 CTACTCTTCCGTGAAGGCTTACAAATTACCCTAAGGATTTAATCATCATGCTCGAAAGACTTACT
71111 GATGG
131 GATGG
*
71116 CCCGAATGACTTCATCATCATGCTCGAAAGACTTACTGATGGC
1 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGC
71159 CCTCGAAAGA
Statistics
Matches: 295, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
135 295 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (135 bp):
CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGGTTTGCTTCA
CTACTCTTCCGTGAAGGCTTACAAATTACCCTAAGGATTTAATCATCATGCTCGAAAGACTTACT
GATGG
Found at i:70878 original size:22 final size:21
Alignment explanation
Indices: 70817--70880 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 21
70807 TAAGGATTTA
*
70817 ATCATCACGCTCGAAAGACTT
1 ATCATCATGCTCGAAAGACTT
* * *
70838 A-C-TGATGGCCCGAAGGACTT
1 ATCATCAT-GCTCGAAAGACTT
70858 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
70880 A
1 A
70881 CTGATGGCAC
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
19 2 0.06
20 12 0.38
21 3 0.09
22 12 0.38
23 3 0.09
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (21 bp):
ATCATCATGCTCGAAAGACTT
Found at i:70894 original size:13 final size:13
Alignment explanation
Indices: 70876--70900 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
70866 TGCTCGAAAG
70876 ACTTACTGATGGC
1 ACTTACTGATGGC
70889 ACTTACTGATGG
1 ACTTACTGATGG
70901 GTTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:71148 original size:22 final size:21
Alignment explanation
Indices: 71087--71150 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 21
71077 TAAGAATTTA
71087 ATCATCATGCTCGAAAGACTT
1 ATCATCATGCTCGAAAGACTT
* * *
71108 A-C-TGATGGCCCGAATGACTT
1 ATCATCAT-GCTCGAAAGACTT
71128 CATCATCATGCTCGAAAGACTT
1 -ATCATCATGCTCGAAAGACTT
71150 A
1 A
71151 CTGATGGCCC
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.09
20 12 0.36
21 3 0.09
22 12 0.36
23 3 0.09
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (21 bp):
ATCATCATGCTCGAAAGACTT
Found at i:71163 original size:22 final size:21
Alignment explanation
Indices: 71096--71194 Score: 107
Period size: 22 Copynumber: 4.7 Consensus size: 21
71086 AATCATCATG
71096 CTCGAAAGACTTACTGATGGC
1 CTCGAAAGACTTACTGATGGC
* *
71117 C-CGAATGACTTCATCATCAT-G-
1 CTCGAAAGACTT-A-C-TGATGGC
71138 CTCGAAAGACTTACTGATGGCC
1 CTCGAAAGACTTACTGATGG-C
*
71160 CTCGAAAGACTTATTGATGGC
1 CTCGAAAGACTTACTGATGGC
71181 C-CGAAAGACTTACT
1 CTCGAAAGACTTACT
71195 AAGTGGGGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
19 3 0.05
20 23 0.35
21 6 0.09
22 30 0.46
23 3 0.05
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
CTCGAAAGACTTACTGATGGC
Found at i:71186 original size:42 final size:41
Alignment explanation
Indices: 71090--71194 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 41
71080 GAATTTAATC
* *
71090 ATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTCAT
1 ATCATGCCCGAAAGACTTACTGATGGCCCGAAAGACTTCAT
*
71131 CATCATGCTCGAAAGACTTACTGATGGCCCTCGAAAGACTT-AT
1 -ATCATGCCCGAAAGACTTACTGATGG-CC-CGAAAGACTTCAT
*
71174 -TGATGGCCCGAAAGACTTACT
1 ATCAT-GCCCGAAAGACTTACT
71195 AAGTGGGGAA
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
41 3 0.05
42 41 0.72
43 4 0.07
44 9 0.16
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (41 bp):
ATCATGCCCGAAAGACTTACTGATGGCCCGAAAGACTTCAT
Done.