Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000829.1 Hibiscus syriacus cultivar Beakdansim tig00001604_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: 70012
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3523 original size:19 final size:20
Alignment explanation
Indices: 3499--3539 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3489 GTTTTCAACA
3499 ATACTA-CTAAAGAGTATCG
1 ATACTACCTAAAGAGTATCG
3518 ATACTACCTAAAGAGTATCG
1 ATACTACCTAAAGAGTATCG
3538 AT
1 AT
3540 CTCTTACCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (20 bp):
ATACTACCTAAAGAGTATCG
Found at i:6231 original size:34 final size:34
Alignment explanation
Indices: 6139--6232 Score: 115
Period size: 34 Copynumber: 2.8 Consensus size: 34
6129 TAAACGAATG
*
6139 TAAACGAACATAAATGAACAAAAC-AAATGGACA
1 TAAACGAACATAAATGAACAAAACAAAATGCACA
*
6172 TAAATGAACATAAACT-AA-AACAACAATAAT-CACA
1 TAAACGAACATAAA-TGAACAA-AACAA-AATGCACA
6206 TAAACGAACATAAATGAACAAAACAAA
1 TAAACGAACATAAATGAACAAAACAAA
6233 CGAGCATAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
32 2 0.04
33 20 0.38
34 25 0.48
35 5 0.10
ACGTcount: A:0.63, C:0.16, G:0.07, T:0.14
Consensus pattern (34 bp):
TAAACGAACATAAATGAACAAAACAAAATGCACA
Found at i:6234 original size:23 final size:23
Alignment explanation
Indices: 6140--6246 Score: 98
Period size: 23 Copynumber: 4.7 Consensus size: 23
6130 AAACGAATGT
6140 AAACGAACATAAATGAACAAAAC
1 AAACGAACATAAATGAACAAAAC
* *
6163 AAATGGACATAAATGAACATAAAC
1 AAACGAACATAAATGAACA-AAAC
* * *
6187 TAA--AACA-ACAAT-AATC-ACAT
1 AAACGAACATA-AATGAA-CAAAAC
6207 AAACGAACATAAATGAACAAAAC
1 AAACGAACATAAATGAACAAAAC
*
6230 AAACGAGCATAAATGAA
1 AAACGAACATAAATGAA
6247 TTTATTTTAC
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
20 4 0.06
21 3 0.05
22 15 0.23
23 38 0.58
24 6 0.09
ACGTcount: A:0.62, C:0.16, G:0.09, T:0.13
Consensus pattern (23 bp):
AAACGAACATAAATGAACAAAAC
Found at i:6532 original size:24 final size:24
Alignment explanation
Indices: 6505--6550 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
6495 TTTAAAATAT
*
6505 TAACGAACATAAATGAAGATAAAC
1 TAACGAACATAAACGAAGATAAAC
*
6529 TAACGAATATAAACGAAGATAA
1 TAACGAACATAAACGAAGATAA
6551 TACCGAACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.59, C:0.11, G:0.13, T:0.17
Consensus pattern (24 bp):
TAACGAACATAAACGAAGATAAAC
Found at i:7404 original size:14 final size:14
Alignment explanation
Indices: 7385--7423 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
7375 TAATTTACCC
7385 TTTATTTTAAATAA
1 TTTATTTTAAATAA
7399 TTTATTTTAAATAA
1 TTTATTTTAAATAA
7413 TTTATTTTAAA
1 TTTATTTTAAA
7424 ATTTTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTATTTTAAATAA
Found at i:7666 original size:29 final size:30
Alignment explanation
Indices: 7624--7680 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
7614 CAAATTTTTT
*
7624 TTGTTCATATTCGTTCA-TTAAAGAATAGC
1 TTGTTCATATTCGTCCATTTAAAGAATAGC
*
7653 TTGTTCATATTCGTCCATTTAAATAATA
1 TTGTTCATATTCGTCCATTTAAAGAATA
7681 AACGAACACG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (30 bp):
TTGTTCATATTCGTCCATTTAAAGAATAGC
Found at i:9159 original size:21 final size:21
Alignment explanation
Indices: 9147--9198 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
9137 TTTTAGTATT
9147 TTTAACTTCACTTTCGTTTTG
1 TTTAACTTCACTTTCGTTTTG
9168 TTTAACTTCACTTTCGTTTTG
1 TTTAACTTCACTTTCGTTTTG
9189 TTTAACTTCA
1 TTTAACTTCA
9199 TTATGTTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.17, C:0.19, G:0.08, T:0.56
Consensus pattern (21 bp):
TTTAACTTCACTTTCGTTTTG
Found at i:13945 original size:13 final size:13
Alignment explanation
Indices: 13927--13956 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
13917 AATCTTAGAA
*
13927 ACAACTTTGAGAG
1 ACAACTTTGAGAC
13940 ACAACTTTGAGAC
1 ACAACTTTGAGAC
13953 ACAA
1 ACAA
13957 TTCACAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (13 bp):
ACAACTTTGAGAC
Found at i:16276 original size:36 final size:36
Alignment explanation
Indices: 16227--16362 Score: 175
Period size: 36 Copynumber: 3.8 Consensus size: 36
16217 TGATTTCATA
* *
16227 GGCACTTCCGATTCAAGTCGAACGGAAGGAAACAAC
1 GGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATC
* * *
16263 GTCACTTTCGATTCAAGTCGAACGGAAGGAAGTATC
1 GGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATC
* *
16299 GGCACTTCCTATTCAAGTCGAACGGAAAGAAGCATC
1 GGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATC
**
16335 GGCACTTTTGATTCAAGAT-GAACGGAAG
1 GGCACTTCCGATTCAAG-TCGAACGGAAG
16363 AAGGTGTTGC
Statistics
Matches: 85, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
36 84 0.99
37 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (36 bp):
GGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATC
Found at i:16348 original size:72 final size:72
Alignment explanation
Indices: 16227--16387 Score: 202
Period size: 72 Copynumber: 2.2 Consensus size: 72
16217 TGATTTCATA
* *
16227 GGCACTTCCGATTCAAGTCGAACGGAAGGAAACAACGTCACTTTCGATTCAAG-TCGAACGGAAG
1 GGCACTTCCGATTCAAGTCGAACGGAAAGAAACAACGGCACTTTCGATTCAAGAT-GAACGGAAG
16291 GAAGTATC
65 GAAGTATC
* * * *
16299 GGCACTTCCTATTCAAGTCGAACGGAAAGAAGCATCGGCACTTTTGATTCAAGATGAACGGAA-G
1 GGCACTTCCGATTCAAGTCGAACGGAAAGAAACAACGGCACTTTCGATTCAAGATGAACGGAAGG
*
16363 AAGGTGT-
66 AA-GTATC
* *
16370 TGCACTTTCGATTCAAGT
1 GGCACTTCCGATTCAAGT
16388 GTTCATCTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
71 18 0.23
72 58 0.75
73 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (72 bp):
GGCACTTCCGATTCAAGTCGAACGGAAAGAAACAACGGCACTTTCGATTCAAGATGAACGGAAGG
AAGTATC
Found at i:19400 original size:13 final size:13
Alignment explanation
Indices: 19382--19411 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19372 AATCTTAGAA
*
19382 ACAACTTTGAGAG
1 ACAACTTTGAGAC
19395 ACAACTTTGAGAC
1 ACAACTTTGAGAC
19408 ACAA
1 ACAA
19412 TTCACAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (13 bp):
ACAACTTTGAGAC
Found at i:26752 original size:2 final size:2
Alignment explanation
Indices: 26745--26772 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26735 TAAGCTAATA
26745 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
26773 CAAACAAATA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28440 original size:75 final size:76
Alignment explanation
Indices: 28316--28467 Score: 297
Period size: 75 Copynumber: 2.0 Consensus size: 76
28306 TCATCGACAT
28316 CATTTTTCATTTTTTTTTATTCATCATTTTCCTCCAATGATGAAAGTTCTACACTTTGATTGTTA
1 CATTTTTCATTTTTTTTTATTCATCATTTTCCTCCAATGATGAAAGTTCTACACTTTGATTGTTA
28381 TGCCATGCTAG
66 TGCCATGCTAG
28392 CATTTTTCA-TTTTTTTTATTCATCATTTTCCTCCAATGATGAAAGTTCTACACTTTGATTGTTA
1 CATTTTTCATTTTTTTTTATTCATCATTTTCCTCCAATGATGAAAGTTCTACACTTTGATTGTTA
28456 TGCCATGCTAG
66 TGCCATGCTAG
28467 C
1 C
28468 GTTGCAATTA
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
75 67 0.88
76 9 0.12
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.48
Consensus pattern (76 bp):
CATTTTTCATTTTTTTTTATTCATCATTTTCCTCCAATGATGAAAGTTCTACACTTTGATTGTTA
TGCCATGCTAG
Found at i:29403 original size:57 final size:57
Alignment explanation
Indices: 29316--29429 Score: 183
Period size: 57 Copynumber: 2.0 Consensus size: 57
29306 CAACGGTGCC
** *
29316 ATATATAATGTACACGAATGTATTATAACTTAACCTAACTTGAGCTTTATTCAACTT
1 ATATATAATGTACACGAATGTACCATAACTTAACCTAACTTGAGCTTTACTCAACTT
* *
29373 ATATATAATGTACATGAATGTACCATAACTTAACTTAACTTGAGCTTTACTCAACTT
1 ATATATAATGTACACGAATGTACCATAACTTAACCTAACTTGAGCTTTACTCAACTT
29430 CCTGACATGC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.38
Consensus pattern (57 bp):
ATATATAATGTACACGAATGTACCATAACTTAACCTAACTTGAGCTTTACTCAACTT
Found at i:35425 original size:21 final size:21
Alignment explanation
Indices: 35399--35443 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35389 GATTTCTGGG
* *
35399 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
35420 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
35441 CAA
1 CAA
35444 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:37193 original size:23 final size:22
Alignment explanation
Indices: 37134--37200 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
37124 TATGGACATC
*
37134 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
37156 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
37178 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
37201 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:40364 original size:21 final size:21
Alignment explanation
Indices: 40338--40382 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40328 GATTTCTGGG
* *
40338 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
40359 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
40380 CAA
1 CAA
40383 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:42138 original size:23 final size:22
Alignment explanation
Indices: 42079--42145 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
42069 TATGGACATC
*
42079 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
42101 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
42123 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
42146 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:44575 original size:20 final size:20
Alignment explanation
Indices: 44550--44587 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44540 TTTTGGTGCA
*
44550 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
44570 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
44588 TTTGAAGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:55310 original size:72 final size:69
Alignment explanation
Indices: 55176--55311 Score: 152
Period size: 72 Copynumber: 1.9 Consensus size: 69
55166 CACGTGTCTT
* * * **
55176 TCTTGAAATATAATTTTTTTATTAGTTATTTATTTTATTGATGATATTCATACTTATTTTTTATA
1 TCTTGAAATATAATTTTTTTATTAATTACTTATTTTATCGATGATATTCATACTTAAATTTTATA
55241 TTTA
66 TTTA
55245 TCTTGAAAT-TAAAGTTTTCTTTAATTAATTACTTATTTTA-CGAATGATATTCAT-CTTAAAAT
1 TCTTGAAATAT-AA-TTTT-TTT-ATTAATTACTTATTTTATCG-ATGATATTCATACTT-AAAT
55307 TTTAT
60 TTTAT
55312 TTGTACCAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
68 1 0.02
69 11 0.20
70 4 0.07
71 7 0.12
72 33 0.59
ACGTcount: A:0.32, C:0.07, G:0.06, T:0.56
Consensus pattern (69 bp):
TCTTGAAATATAATTTTTTTATTAATTACTTATTTTATCGATGATATTCATACTTAAATTTTATA
TTTA
Found at i:56791 original size:20 final size:20
Alignment explanation
Indices: 56766--56817 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
56756 TAGTTGAAAA
56766 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
56786 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
56806 TCGCGTTGCGAT
1 TCGCGTTGCGAT
56818 AGTCTACAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:56854 original size:61 final size:60
Alignment explanation
Indices: 56741--56857 Score: 148
Period size: 61 Copynumber: 1.9 Consensus size: 60
56731 ATTCGCGTTG
*
56741 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC-CGTTGCGATTTTC
* * *
56802 CATTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT-CGTTGCGA
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATTCCGTTGCGA
56858 AAATTCGTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
61 31 0.63
62 15 0.31
63 3 0.06
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (60 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTCCGTTGCGATTTTC
Found at i:56963 original size:6 final size:6
Alignment explanation
Indices: 56952--56976 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
56942 GACACGTATT
56952 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
56977 GACGAGACGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:57644 original size:22 final size:22
Alignment explanation
Indices: 57616--57794 Score: 244
Period size: 22 Copynumber: 8.4 Consensus size: 22
57606 AATTTGGAAA
57616 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
57638 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
** **
57660 ATCGCAACGA-ATTTG-A-AAA
1 ATCGCAACGACAACTGTAGACT
*
57679 ATCGCAACGAAAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
57701 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
57723 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* **
57745 ATCGCAACG--AACT-TGGAAA
1 ATCGCAACGACAACTGTAGACT
57764 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
57786 ATCGCAACG
1 ATCGCAACG
57795 CGAAATGGAA
Statistics
Matches: 136, Mismatches: 15, Indels: 12
0.83 0.09 0.07
Matches are distributed among these distances:
19 23 0.17
20 8 0.06
21 8 0.06
22 97 0.71
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:57670 original size:63 final size:62
Alignment explanation
Indices: 57598--57814 Score: 269
Period size: 63 Copynumber: 3.4 Consensus size: 62
57588 CAACGAATTT
57598 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACGA-AACTGTAGACTATCGCAACGACAACTGTAGACTA
*
57661 TCGCAACGAATTTGAAAAATCGCAACGAAAACTGTAGACTATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGGAAAATCGCAACG-AAACTGTAGACTATCGCAACGACAACTGTAGACTA
* * ** * **
57724 TCGCAACGACAACTGTAGACTATCGCAACG-AACT-TGGAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAATCGCAACGAAACTGTAGACTATCGCAACGACAACTGTAGACTA
*
57787 TCGCAACGCGAA-ATGGAAAATCGCAACG
1 TCGCAA--CGAATTTGGAAAATCGCAACG
57815 CGATTTTCAA
Statistics
Matches: 135, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
61 12 0.09
63 102 0.76
64 5 0.04
65 4 0.03
66 12 0.09
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (62 bp):
TCGCAACGAATTTGGAAAATCGCAACGAAACTGTAGACTATCGCAACGACAACTGTAGACTA
Found at i:57738 original size:85 final size:85
Alignment explanation
Indices: 57616--57794 Score: 331
Period size: 85 Copynumber: 2.1 Consensus size: 85
57606 AATTTGGAAA
*
57616 ATCGCAACGACAACTGTAGACTATCGCAACGACAACTGTAGACTATCGCAACGAATTTGAAAAAT
1 ATCGCAACGACAACTGTAGACTATCGCAACGACAACTGTAGACTATCGCAACGAACTTGAAAAAT
57681 CGCAACGAAAACTGTAGACT
66 CGCAACGAAAACTGTAGACT
*
57701 ATCGCAACGACAACTGTAGACTATCGCAACGACAACTGTAGACTATCGCAACGAACTTGGAAAAT
1 ATCGCAACGACAACTGTAGACTATCGCAACGACAACTGTAGACTATCGCAACGAACTTGAAAAAT
*
57766 CGCAACGACAACTGTAGACT
66 CGCAACGAAAACTGTAGACT
57786 ATCGCAACG
1 ATCGCAACG
57795 CGAAATGGAA
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 91 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (85 bp):
ATCGCAACGACAACTGTAGACTATCGCAACGACAACTGTAGACTATCGCAACGAACTTGAAAAAT
CGCAACGAAAACTGTAGACT
Found at i:57811 original size:20 final size:20
Alignment explanation
Indices: 57786--57858 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
57776 ACTGTAGACT
57786 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
57806 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
57827 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
57847 ATCGCAACGCGA
1 ATCGCAACGCGA
57859 TTTTCAACTA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:57887 original size:21 final size:21
Alignment explanation
Indices: 57783--57887 Score: 106
Period size: 21 Copynumber: 5.1 Consensus size: 21
57773 ACAACTGTAG
*
57783 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
57804 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
57824 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
57845 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
57865 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
57886 AC
1 AC
57888 GCGAATTTGC
Statistics
Matches: 63, Mismatches: 19, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 30 0.48
21 33 0.52
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:57900 original size:41 final size:41
Alignment explanation
Indices: 57783--57883 Score: 202
Period size: 41 Copynumber: 2.5 Consensus size: 41
57773 ACAACTGTAG
57783 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
57824 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
57865 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
57884 CAACGCGAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:60985 original size:23 final size:22
Alignment explanation
Indices: 60937--60985 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
60927 ACAGAATGTC
60937 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
60958 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
60981 AAGGA
1 AAGGA
60986 AAATTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:62671 original size:103 final size:102
Alignment explanation
Indices: 62448--62663 Score: 362
Period size: 103 Copynumber: 2.1 Consensus size: 102
62438 GTCGAGGGTC
* *
62448 TATGTGGTCCTTCGGA-ACATGTGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
1 TATGTGGTCCTTCGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
* * *
62512 TGATCCTTGGCATTTGTATATGATTCTTAAGGAATGA
66 TGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
62549 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTC-GGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
62614 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
65 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
62652 TATGTGGTCCTT
1 TATGTGGTCCTT
62664 ATGGACATTA
Statistics
Matches: 107, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
101 13 0.12
102 3 0.03
103 91 0.85
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (102 bp):
TATGTGGTCCTTCGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
TGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:62709 original size:23 final size:23
Alignment explanation
Indices: 62679--62737 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
62669 CATTATTATA
62679 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
62702 TGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
*
62725 TGGCACTTCGGTG
1 TGGCACTACGGTG
62738 TATTTATATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.29
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:62747 original size:23 final size:23
Alignment explanation
Indices: 62670--62747 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
62660 CCTTATGGAC
*
62670 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* *
62694 ATTCTACGTGGCACTACGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* * *
62717 ATTCTATGTGGCACTTCGGTGTA
1 ATTATATGTGGCACTACGGTGCA
*
62740 TTTATATG
1 ATTATATG
62748 AGCTGTGGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
23 43 0.93
24 3 0.07
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:63841 original size:20 final size:20
Alignment explanation
Indices: 63800--63837 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
63790 ACTTAACCTT
*
63800 TGGTATCGATACCCACCTAC
1 TGGTATCGATACCCACATAC
63820 TGGTATCGATACCC-CATA
1 TGGTATCGATACCCACATA
63838 ACTGATGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (20 bp):
TGGTATCGATACCCACATAC
Found at i:65287 original size:359 final size:359
Alignment explanation
Indices: 64628--65346 Score: 1267
Period size: 359 Copynumber: 2.0 Consensus size: 359
64618 TAACTTCTCT
64628 TGGTAACAACTGAAATCTATAAAGGTTCTACCTTTAAGTTTGGCTTAAAGAAAGATAGGTTGAAG
1 TGGTAACAACTGAAATCTATAAAGGTTCTACCTTTAAGTTTGGCTTAAAGAAAGATAGGTTGAAG
*
64693 AGAGGAGAAGAGTAGAAGACAATAGTTGTGGAGAAAAAGAGGGACTTGTACAGATGTAAGATCAC
66 AGAGGAGAAGAGTAGAAGACAATAGTTGTGGAGAAAAAGAGGGACTTGTACAGACGTAAGATCAC
* * *
64758 CAAATTTTAATTGTATTCAACATTTATTTTGAATAGTGATCTAATTACACTCTGGGTCTTTCTTA
131 CAAATTTTAATGGTATTCAACATTTATTTTGAAAAGTGATCTAATTACACTCTGGGTCCTTCTTA
* *
64823 TTTTAGCTACAACTGAAAACATCCCTTTTTACTCTCTATTGGGCTTAACTCAAGCCTAAATTCAC
196 TTTTAGCTACAACTGAAAACACCCCTTTTTACTCTCTATTGGGCTTAACTCAAGCCCAAATTCAC
* * * *
64888 CTCAAATTAGGTCAAAGCTTCGTACAAGCTAGATAATTAATCTAAGACCTATCTCGGTTTATCCT
261 CTCAAATTAGGTCAAAGCTTCATACAAGCTAGAGAATTAATCTAAGACCTATATCAGTTTATCCT
*
64953 AAAACTCCTAACCTGGGATTTGAGGAGTTACAAC
326 AAAACTCCTAACCTGGGATTCGAGGAGTTACAAC
64987 TGGTAACAACTGAAATCTATAAAGGTTCTACCTTTAAGTTTGGCTTAAAGAAAGATAGGTTGAAG
1 TGGTAACAACTGAAATCTATAAAGGTTCTACCTTTAAGTTTGGCTTAAAGAAAGATAGGTTGAAG
* *
65052 AGATGAGAAGAGTAGAAGATAATAGTTGTGGAGAAAAAGAGGGACTTGTACAGACGTAAGATCAC
66 AGAGGAGAAGAGTAGAAGACAATAGTTGTGGAGAAAAAGAGGGACTTGTACAGACGTAAGATCAC
*
65117 CAAATTTTAATGGTATTCATCATTTATTTTGAAAAGTGATCTAATTACACTCTGGGTCCTTCTTA
131 CAAATTTTAATGGTATTCAACATTTATTTTGAAAAGTGATCTAATTACACTCTGGGTCCTTCTTA
*
65182 TTTTAGCTACAGCTGAAAACACCCCTTTTTACTCTCTATTGGGCTTAACTCAAGCCCAAATTCAC
196 TTTTAGCTACAACTGAAAACACCCCTTTTTACTCTCTATTGGGCTTAACTCAAGCCCAAATTCAC
* * *
65247 CTCAAATTGGGTCAAATCTTCATACAAGCTAGAGAATTAATCTAAGGCCTATATCAGTTTATCCT
261 CTCAAATTAGGTCAAAGCTTCATACAAGCTAGAGAATTAATCTAAGACCTATATCAGTTTATCCT
*
65312 AAAACTCCTAACCTGGGATTCGATGAGTTACAAC
326 AAAACTCCTAACCTGGGATTCGAGGAGTTACAAC
65346 T
1 T
65347 CTCCCCTAAT
Statistics
Matches: 341, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
359 341 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (359 bp):
TGGTAACAACTGAAATCTATAAAGGTTCTACCTTTAAGTTTGGCTTAAAGAAAGATAGGTTGAAG
AGAGGAGAAGAGTAGAAGACAATAGTTGTGGAGAAAAAGAGGGACTTGTACAGACGTAAGATCAC
CAAATTTTAATGGTATTCAACATTTATTTTGAAAAGTGATCTAATTACACTCTGGGTCCTTCTTA
TTTTAGCTACAACTGAAAACACCCCTTTTTACTCTCTATTGGGCTTAACTCAAGCCCAAATTCAC
CTCAAATTAGGTCAAAGCTTCATACAAGCTAGAGAATTAATCTAAGACCTATATCAGTTTATCCT
AAAACTCCTAACCTGGGATTCGAGGAGTTACAAC
Done.