Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003898.1 Hibiscus syriacus cultivar Beakdansim tig00008426_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: 77694
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:603 original size:21 final size:21
Alignment explanation
Indices: 573--630 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
563 AGAACCCCAG
573 GGGGGTATCGATTCCCCTACA
1 GGGGGTATCGATTCCCCTACA
* * *
594 GGGGGAATCGGTTCCCCTTCA
1 GGGGGTATCGATTCCCCTACA
*
615 AGGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
631 TCTGCACTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.17, C:0.28, G:0.31, T:0.24
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCTACA
Found at i:12255 original size:26 final size:27
Alignment explanation
Indices: 12226--12278 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
12216 GTTTTTAAAA
*
12226 TTTTGGCTTTTTTG-TTGTTGTTTTTT
1 TTTTGCCTTTTTTGTTTGTTGTTTTTT
*
12252 TTTTGCCTTTTTTGTTTTTTGTTTTTT
1 TTTTGCCTTTTTTGTTTGTTGTTTTTT
12279 GAAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.00, C:0.06, G:0.15, T:0.79
Consensus pattern (27 bp):
TTTTGCCTTTTTTGTTTGTTGTTTTTT
Found at i:12266 original size:23 final size:24
Alignment explanation
Indices: 12235--12279 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
12225 ATTTTGGCTT
12235 TTTTGTTGTTGTTTT-TTTTTTGCC
1 TTTTGTTGTT-TTTTGTTTTTTGCC
12259 TTTT-TTGTTTTTTGTTTTTTG
1 TTTTGTTGTTTTTTGTTTTTTG
12280 AAAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.00, C:0.04, G:0.16, T:0.80
Consensus pattern (24 bp):
TTTTGTTGTTTTTTGTTTTTTGCC
Found at i:18265 original size:2 final size:2
Alignment explanation
Indices: 18258--18283 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18248 ATCTTTCCTC
18258 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
18284 AAGCGCAATA
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):
TA
Found at i:40446 original size:16 final size:16
Alignment explanation
Indices: 40421--40451 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40411 TTTCTAAAAT
*
40421 TTTTTTAGTTCAAGTC
1 TTTTTGAGTTCAAGTC
40437 TTTTTGAGTTCAAGT
1 TTTTTGAGTTCAAGT
40452 TTCAATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.10, G:0.16, T:0.55
Consensus pattern (16 bp):
TTTTTGAGTTCAAGTC
Found at i:47759 original size:2 final size:2
Alignment explanation
Indices: 47752--47777 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47742 GATTGACCTC
47752 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
47778 CCAATATTTC
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:58170 original size:6 final size:6
Alignment explanation
Indices: 57738--58169 Score: 809
Period size: 6 Copynumber: 72.7 Consensus size: 6
57728 TAAGTGGGTA
57738 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
57786 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
57834 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
57882 TATATG TATATG TATATG TATA-- TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
57928 TATATG TATATG TATATG TATATG --TATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
57974 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
58022 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
58070 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* * *
58118 TATATG TATATG TATATG TATATG TATATG TATACG TATACG TATACG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
58166 TATA
1 TATA
58170 CATGAAGAAA
Statistics
Matches: 421, Mismatches: 1, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
4 8 0.02
6 413 0.98
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (6 bp):
TATATG
Found at i:62880 original size:19 final size:19
Alignment explanation
Indices: 62856--62892 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
62846 ATGATCAATA
62856 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
*
62875 AAATCGTAATGCGATCTC
1 AAATCGCAATGCGATCTC
62893 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (19 bp):
AAATCGCAATGCGATCTCT
Found at i:62967 original size:21 final size:21
Alignment explanation
Indices: 62938--62986 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
62928 ATTTTGACTA
*
62938 TCGCATTGCAATTTTCCAAAT
1 TCGCGTTGCAATTTTCCAAAT
*
62959 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCAATTTTCCAAAT
62980 TCGCGTT
1 TCGCGTT
62987 ACGATTTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCAATTTTCCAAAT
Found at i:62991 original size:21 final size:21
Alignment explanation
Indices: 62948--62994 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
62938 TCGCATTGCA
*
62948 ATTTTCCAAATTCGCGTTGCG
1 ATTTTCCAAATTCGCGTTACG
62969 ATTTTCCAAATTCGCGTTACG
1 ATTTTCCAAATTCGCGTTACG
62990 ATTTT
1 ATTTT
62995 AGAAAATCGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (21 bp):
ATTTTCCAAATTCGCGTTACG
Found at i:63004 original size:21 final size:21
Alignment explanation
Indices: 62948--63004 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
62938 TCGCATTGCA
* * *
62948 ATTTTCCAAATTCGCGTTGCG
1 ATTTTACAAAATCGCGTTACG
* *
62969 ATTTTCCAAATTCGCGTTACG
1 ATTTTACAAAATCGCGTTACG
*
62990 ATTTTAGAAAATCGC
1 ATTTTACAAAATCGC
63005 AATGCGAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (21 bp):
ATTTTACAAAATCGCGTTACG
Found at i:63066 original size:21 final size:21
Alignment explanation
Indices: 63018--63073 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
63008 GCGAATATGT
*
63018 AAATCGCAACGCGATTCTGAC
1 AAATCGCAACGCGATACTGAC
*
63039 -TATCGCAACGCGATACT-AC
1 AAATCGCAACGCGATACTGAC
*
63058 AAAATCGCAATGCGAT
1 -AAATCGCAACGCGAT
63074 TTCCAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 15 0.52
21 12 0.41
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.20
Consensus pattern (21 bp):
AAATCGCAACGCGATACTGAC
Found at i:63125 original size:21 final size:21
Alignment explanation
Indices: 63099--63189 Score: 105
Period size: 21 Copynumber: 4.4 Consensus size: 21
63089 AGTCCAAATT
* *
63099 CGTTGCGATAGTCCAAGTTCA
1 CGTTGCGATAGTCCAAGATCG
*
63120 CGTTGCGATAGTCGAAGATCG
1 CGTTGCGATAGTCCAAGATCG
** *
63141 CGTTGCGATTTTCCAA-AT-T
1 CGTTGCGATAGTCCAAGATCG
*
63160 CGTTGCGATAGTCGAAGATCG
1 CGTTGCGATAGTCCAAGATCG
63181 CGTTGCGAT
1 CGTTGCGAT
63190 TTTCCAAAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
19 13 0.23
20 4 0.07
21 40 0.70
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGATCG
Found at i:63164 original size:40 final size:40
Alignment explanation
Indices: 63120--63197 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
63110 TCCAAGTTCA
63120 CGTTGCGATAGTCGAAGATCGCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCGAAGATCGCGTTGCGATTTTCCAAATT
63160 CGTTGCGATAGTCGAAGATCGCGTTGCGATTTTCCAAA
1 CGTTGCGATAGTCGAAGATCGCGTTGCGATTTTCCAAA
63198 ATCGCAACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.31
Consensus pattern (40 bp):
CGTTGCGATAGTCGAAGATCGCGTTGCGATTTTCCAAATT
Found at i:63201 original size:21 final size:21
Alignment explanation
Indices: 63137--63202 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
63127 ATAGTCGAAG
63137 ATCGCGTTGCGATTTTCC-AA
1 ATCGCGTTGCGATTTTCCAAA
* ** * *
63157 AT-TCGTTGCGATAGTCGAAG
1 ATCGCGTTGCGATTTTCCAAA
63177 ATCGCGTTGCGATTTTCCAAA
1 ATCGCGTTGCGATTTTCCAAA
63198 ATCGC
1 ATCGC
63203 AACAACTGGT
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
19 11 0.32
20 5 0.15
21 18 0.53
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTCCAAA
Found at i:63548 original size:19 final size:19
Alignment explanation
Indices: 63524--63632 Score: 101
Period size: 19 Copynumber: 5.4 Consensus size: 19
63514 TTATTTTGGA
63524 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
63543 TTTTTCACTATCGCAACAACAC
1 TTTTTCACTATCG---CAACAC
*
63565 GTTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* *
63587 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
* * *
63606 ATTTTAACTGTCGCAACAC
1 TTTTTCACTATCGCAACAC
63625 ATTTTTCA
1 -TTTTTCA
63633 AAATCGCGTT
Statistics
Matches: 76, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
19 43 0.57
20 5 0.07
21 4 0.05
22 12 0.16
23 6 0.08
25 6 0.08
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.35
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:63685 original size:21 final size:20
Alignment explanation
Indices: 63634--63689 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
63624 CATTTTTCAA
63634 AATCGCGTTGCGAATCTTAC
1 AATCGCGTTGCGAATCTTAC
* *
63654 AATCCCGTTGCGAATC-TAG
1 AATCGCGTTGCGAATCTTAC
63673 ATATTCGCGTTGCGAAT
1 A-A-TCGCGTTGCGAAT
63690 TTGGAAACTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.10
20 16 0.52
21 12 0.39
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (20 bp):
AATCGCGTTGCGAATCTTAC
Found at i:67080 original size:20 final size:21
Alignment explanation
Indices: 67055--67106 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
67045 TTTTCCCAAT
*
67055 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
67075 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
67096 TCGCAATGCGA
1 TCGCAATGCGA
67107 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:67120 original size:20 final size:20
Alignment explanation
Indices: 67095--67208 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
67085 AATTGGGAAA
*
67095 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
67115 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
67135 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
67156 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* **
67176 TTCGCAACGCGATTTTGACT
1 ATCGCAACGCGATACTGACT
*
67196 TTCGCAACGCGAT
1 ATCGCAACGCGAT
67209 TTACATAGCG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:67201 original size:61 final size:61
Alignment explanation
Indices: 67092--67208 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 61
67082 GCGAATTGGG
* * * *
67092 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTTACTATCGCAACGCGATAATAC
* * *
67153 AAAATCGCAACGAGATACTGACTTTCGCAACGCGAT-TTTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTT-ACTATCGCAACGCGAT
67209 TTACATAGCG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 2 0.04
61 46 0.96
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTTACTATCGCAACGCGATAATAC
Found at i:67766 original size:19 final size:19
Alignment explanation
Indices: 67728--67794 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
67718 TTCGAGAATG
67728 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
67748 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
67767 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
67786 AAAATCGCA
1 AAAATCGCA
67795 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:67836 original size:20 final size:19
Alignment explanation
Indices: 67790--67955 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
67780 GAAACCAAAA
*
67790 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
67809 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
67828 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
67848 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
67864 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
67881 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
67895 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
67914 TCGGCGTTGCGATTCTCATT
1 TC-GCGTTGCGATTTTCATT
*
67934 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
67954 TC
1 TC
67956 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 42 0.35
20 47 0.39
21 2 0.02
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:67871 original size:39 final size:39
Alignment explanation
Indices: 67795--67871 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
67785 CAAAATCGCA
* **
67795 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
67834 TTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
67872 ATAGTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.26, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCGG
Found at i:67880 original size:33 final size:33
Alignment explanation
Indices: 67843--67930 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
67833 GTTGCGATTT
* *
67843 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
67876 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
67909 TCATTTCGGCGTTGCGATTCTC
1 TCATTTC-GCGTTGCGATTCTC
67931 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 37 0.73
34 14 0.27
ACGTcount: A:0.11, C:0.24, G:0.26, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:70036 original size:42 final size:42
Alignment explanation
Indices: 69956--70048 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
69946 GCCCGACTCG
* *
69956 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCTACCGTTCAAGAGGCC
* * *
69998 CCTATCATTCCTCGAGAGTCCCCTTCC-ACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCAC-TCCTACCGTTCAAGAGGCC
* *
70040 ACTGTCATC
1 CCTATCATC
70049 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.25
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCTACCGTTCAAGAGGCC
Found at i:71457 original size:14 final size:14
Alignment explanation
Indices: 71438--71473 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
71428 ATTGTTTAAT
71438 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
71452 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
71466 TGATTTGT
1 TGATTTGT
71474 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:71698 original size:33 final size:32
Alignment explanation
Indices: 71656--71782 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
71646 ATTAAATTCG
*
71656 CGTTGCGATTTTCATTTCACATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
71689 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
71722 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
71755 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
71783 AGTAATTTCC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:71745 original size:66 final size:66
Alignment explanation
Indices: 71649--71781 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
71639 ACGCGAAATT
*
71649 AAATTCGCGTTGCGATTTTCATTTCACATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCACATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
71714 G
66 G
* *
71715 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCACATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
71780 G
66 G
71781 A
1 A
71782 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCACATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:74300 original size:24 final size:24
Alignment explanation
Indices: 74266--74319 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
74256 CTGAAACATC
* * *
74266 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATAGACCAAG
*
74290 ATCAAAGTCCGGGTATAGACCAAG
1 ATCAAAATCCGGGTATAGACCAAG
74314 ATCAAA
1 ATCAAA
74320 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGGGTATAGACCAAG
Found at i:75284 original size:20 final size:20
Alignment explanation
Indices: 75259--75316 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
75249 AATCATTTGA
75259 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
75279 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
75299 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
75317 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:75383 original size:19 final size:19
Alignment explanation
Indices: 75353--75400 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
75343 CGATTTCTCG
75353 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
75371 TTTCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
75390 TTGCGATTTTC
1 TTGCGATTTTC
75401 TCGTTGCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.50
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:77417 original size:19 final size:19
Alignment explanation
Indices: 77393--77459 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
77383 GAAACTTAAA
77393 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
* *
77412 ATCGCAACACGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
77432 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
77451 ATCGCAACG
1 ATCGCAACG
77460 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 23 0.59
20 16 0.41
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:77417 original size:39 final size:37
Alignment explanation
Indices: 77374--77510 Score: 107
Period size: 39 Copynumber: 3.9 Consensus size: 37
77364 TAGTTTACTT
*
77374 TCGCAACAGGAAACTTAAAATCGCAACGCGAAATGACTA
1 TCGCAACAGGAAAC-TAAAATCGCAACGCGAAATGA-AA
*** *
77413 TCGCAACACGGAAA-TGGCTATCGCAATGCGAAATGAAAA
1 TCGCAACA-GGAAACT-AAAATCGCAACGCGAAATG-AAA
77452 TCGCAAC--G--AC-AAAATCGCAACGCGAAATGAAA
1 TCGCAACAGGAAACTAAAATCGCAACGCGAAATGAAA
77484 TCGCAAC--G--AC-AAAATCGCAACGCGAAA
1 TCGCAACAGGAAACTAAAATCGCAACGCGAAA
77511 CACAAATCGC
Statistics
Matches: 85, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
32 30 0.35
33 15 0.18
34 1 0.01
36 1 0.01
38 1 0.01
39 31 0.36
40 6 0.07
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.12
Consensus pattern (37 bp):
TCGCAACAGGAAACTAAAATCGCAACGCGAAATGAAA
Found at i:77467 original size:14 final size:14
Alignment explanation
Indices: 77448--77505 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
77438 ATGCGAAATG
77448 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
77462 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
77478 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
77494 AAAATCGCAACG
1 AAAATCGCAACG
77506 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:77490 original size:32 final size:33
Alignment explanation
Indices: 77432--77510 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
77422 GGAAATGGCT
*
77432 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
77465 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
77497 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
77511 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:77543 original size:18 final size:18
Alignment explanation
Indices: 77517--77648 Score: 100
Period size: 18 Copynumber: 7.6 Consensus size: 18
77507 GAAACACAAA
*
77517 TCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
*
77535 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
77551 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
*
77567 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
*
77583 T--CGTTGCGATTTTATT
1 TCGCGTTGCGATTTCATT
* **
77599 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGAT-TTCATT
*
77618 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGAT-TTCATT
*
77638 TCGTGTTGCGA
1 TCGCGTTGCGA
77649 AAGTAAACTA
Statistics
Matches: 92, Mismatches: 12, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
14 22 0.24
16 8 0.09
18 32 0.35
19 13 0.14
20 17 0.18
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.42
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:77557 original size:14 final size:14
Alignment explanation
Indices: 77538--77595 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
77528 TTTCATTTCG
77538 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
77552 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
77568 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
77584 CGTTGCGATTTT
1 CGTTGCGATTTT
77596 ATTTCGCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:77563 original size:32 final size:32
Alignment explanation
Indices: 77522--77610 Score: 160
Period size: 32 Copynumber: 2.8 Consensus size: 32
77512 ACAAATCGCA
77522 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
77554 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
* *
77586 TTGCGATTTTATTTCGCATTGCGAT
1 TTGCGATTTCATTTCGCGTTGCGAT
77611 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
Found at i:77629 original size:20 final size:19
Alignment explanation
Indices: 77596--77648 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
77586 TTGCGATTTT
*
77596 ATTTCGCATTGCGATAGCC
1 ATTTCGCGTTGCGATAGCC
*
77615 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGATAGCC
*
77635 ATTTCGTGTTGCGA
1 ATTTCGCGTTGCGA
77649 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.36
Consensus pattern (19 bp):
ATTTCGCGTTGCGATAGCC
Done.