Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008923.1 Hibiscus syriacus cultivar Beakdansim tig00112227_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: 468757
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 3 of 3
Found at i:441064 original size:20 final size:20
Alignment explanation
Indices: 441039--441150 Score: 75
Period size: 20 Copynumber: 5.5 Consensus size: 20
441029 TGGGAAAATT
* *
441039 GCAATGCGATACTGACTATC
1 GCAACGCGATAATGACTATC
* *
441059 GCAATGCGATAAT-ACAAAATC
1 GCAACGCGATAATGAC--TATC
* * *
441080 GCAACGAGATACTGACTTTC
1 GCAACGCGATAATGACTATC
** *
441100 GCAACGCGATTTTGACTTTC
1 GCAACGCGATAATGACTATC
441120 GCAACGCGATAAT-ACATAATC
1 GCAACGCGATAATGAC-T-ATC
*
441141 GCAATGCGAT
1 GCAACGCGAT
441151 TTTCAAAGCG
Statistics
Matches: 73, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
19 4 0.05
20 43 0.59
21 24 0.33
22 2 0.03
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (20 bp):
GCAACGCGATAATGACTATC
Found at i:441346 original size:22 final size:22
Alignment explanation
Indices: 441318--441361 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
441308 CACTCTCTCA
441318 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGGCGAAATCCGTC
441340 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGGCGAAATCCGTC
441362 TATCTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.45, G:0.18, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGGCGAAATCCGTC
Found at i:441678 original size:20 final size:20
Alignment explanation
Indices: 441624--441682 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
441614 GCGATTCTCT
**
441624 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
441644 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
441664 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
441683 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:441873 original size:25 final size:24
Alignment explanation
Indices: 441819--441873 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
441809 TGTTTATTAT
* *
441819 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
441843 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
441869 TGTTT
1 TGTTT
441874 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:443028 original size:18 final size:18
Alignment explanation
Indices: 443002--443046 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
442992 TCCACTTTGG
*
443002 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
443020 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
443038 GAGCCATCA
1 GAGCCATCA
443047 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:443578 original size:20 final size:20
Alignment explanation
Indices: 443528--443594 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
443518 TAGTTTACTT
*
443528 TCGCAACACGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
443548 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
443568 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
443587 TCGCAACG
1 TCGCAACG
443595 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 13 0.32
20 27 0.68
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:443601 original size:39 final size:34
Alignment explanation
Indices: 443566--443657 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 34
443556 CGAAAATGGC
443566 TATCGCAATGCGAAATGAAAATCGCAACGAC-AAA
1 TATCGCAATGCGAAATG-AAATCGCAACGACAAAA
443600 -ATCGCAATGCGAAATGAAATCGCAACGACAAAA
1 TATCGCAATGCGAAATGAAATCGCAACGACAAAA
*
443633 T-T-GCAACGCGAAATGAAAATCGCAA
1 TATCGCAATGCGAAATG-AAATCGCAA
443658 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
32 25 0.46
33 29 0.54
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.14
Consensus pattern (34 bp):
TATCGCAATGCGAAATGAAATCGCAACGACAAAA
Found at i:443602 original size:14 final size:14
Alignment explanation
Indices: 443583--443640 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
443573 ATGCGAAATG
443583 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
443597 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
443613 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
443629 AAAATTGCAACG
1 AAAATCGCAACG
443641 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:443625 original size:32 final size:33
Alignment explanation
Indices: 443567--443657 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
443557 GAAAATGGCT
443567 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
443600 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
443632 ATTGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
443658 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:443693 original size:14 final size:14
Alignment explanation
Indices: 443674--443713 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
443664 TTGTGTTTCG
443674 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
443688 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
443702 CATTGCGATTTT
1 CGTTGCGATTTT
443714 CATTTCGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.10, C:0.15, G:0.25, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:443748 original size:20 final size:19
Alignment explanation
Indices: 443714--443769 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
443704 TTGCGATTTT
*
443714 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
443733 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
443753 CATTTTCGTGTTGCGAT
1 CA-TTTCGCGTTGCGAT
443770 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:445657 original size:14 final size:14
Alignment explanation
Indices: 445638--445673 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
445628 ATTGTTTAAT
445638 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
445652 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
445666 TGATTTGT
1 TGATTTGT
445674 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:445781 original size:20 final size:20
Alignment explanation
Indices: 445756--445794 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
445746 ATGTTGAAGG
445756 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
445776 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
445795 GAGAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:445824 original size:19 final size:19
Alignment explanation
Indices: 445800--445864 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
445790 GCAACGAGAG
445800 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
445819 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
445838 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
445852 AATCGCAATGCGA
1 AATCGCAATGCGA
445865 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
19 27 0.63
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:445917 original size:19 final size:20
Alignment explanation
Indices: 445890--445976 Score: 142
Period size: 20 Copynumber: 4.5 Consensus size: 20
445880 GCGATTTTGT
*
445890 CGTTACGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
445909 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
445929 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
445949 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
*
445968 CATTGCGAT
1 CGTTGCGAT
445977 TTTGATGATG
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
19 26 0.40
20 39 0.60
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:445938 original size:39 final size:39
Alignment explanation
Indices: 445890--445976 Score: 140
Period size: 39 Copynumber: 2.2 Consensus size: 39
445880 GCGATTTTGT
*
445890 CGTTACGATAGCCA-TTTCGCGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCGCGTTGCGATAGCCA-TTTCG
445929 CGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTCG
1 CGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTCG
*
445968 CATTGCGAT
1 CGTTGCGAT
445977 TTTGATGATG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
39 26 0.58
40 19 0.42
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.33
Consensus pattern (39 bp):
CGTTGCGATAGCCATTTTCGCGTTGCGATAGCCATTTCG
Found at i:446174 original size:12 final size:12
Alignment explanation
Indices: 446157--446181 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
446147 ATATAATCTT
446157 GAAGAAGAAAAA
1 GAAGAAGAAAAA
446169 GAAGAAGAAAAA
1 GAAGAAGAAAAA
446181 G
1 G
446182 TCTCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:448495 original size:19 final size:19
Alignment explanation
Indices: 448473--448603 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
448463 GGAAATTACT
448473 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
448492 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
448506 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
448525 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
* *
448539 TTCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
**
448558 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
448572 ATCACAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
448591 ATCGCAACGCGAA
1 ATCGCAATGCGAA
448604 TTTAATTTCG
Statistics
Matches: 81, Mismatches: 16, Indels: 30
0.64 0.13 0.24
Matches are distributed among these distances:
14 25 0.31
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.47
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:448515 original size:33 final size:33
Alignment explanation
Indices: 448473--448599 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
448463 GGAAATTACT
448473 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
448506 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
448538 TTTCGCAATGCGAAATAAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
448572 ATCACAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
448600 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 80 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:448580 original size:66 final size:66
Alignment explanation
Indices: 448474--448606 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
448464 GAAATTACTA
* * *
448474 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
448539 T
66 T
*
448540 TCGCAATGCGAAATAAAAATCGCAACGAGGGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
448605 T
66 T
448606 T
1 T
448607 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCACAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:448652 original size:19 final size:19
Alignment explanation
Indices: 448628--448664 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
448618 GCGATTCTCT
448628 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
448647 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
448665 TAATTGCGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.49
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:448671 original size:19 final size:19
Alignment explanation
Indices: 448630--448674 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
448620 GATTCTCTCG
**
448630 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGAA
*
448649 TTGCGATTTTCATTTCTAA
1 TTGCGATTTTCATTTCGAA
448668 TTGCGAT
1 TTGCGAT
448675 AGTACTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGAA
Found at i:448800 original size:14 final size:14
Alignment explanation
Indices: 448781--448817 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
448771 CATCAATTAA
448781 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
448795 ACAAATCACCTTTT
1 ACAAATCAACTTTT
448809 ACAAATCAA
1 ACAAATCAA
448818 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:450232 original size:42 final size:41
Alignment explanation
Indices: 450173--450378 Score: 155
Period size: 42 Copynumber: 4.9 Consensus size: 41
450163 GTGAATCGGG
* * *
450173 CTCTTGAATGGTGGGAGGTACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
450215 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
450257 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * *
450299 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
450341 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
450379 GCGAGTCGGG
Statistics
Matches: 125, Mismatches: 31, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
41 9 0.07
42 106 0.85
43 10 0.08
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:450314 original size:84 final size:84
Alignment explanation
Indices: 450203--450378 Score: 343
Period size: 84 Copynumber: 2.1 Consensus size: 84
450193 CCTCTTCAAC
*
450203 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
450268 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
450287 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
450352 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
450371 GATGACAG
1 GATGACAG
450379 GCGAGTCGGG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:450772 original size:91 final size:90
Alignment explanation
Indices: 450595--450781 Score: 304
Period size: 91 Copynumber: 2.0 Consensus size: 90
450585 ATATTTCAAA
*
450595 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTA
450660 GCAGAATTGGCAGCAACCGAATAAATTT
63 GCAGAATTGGCAGCAACCGAATAAATTT
450688 ACTTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 ACTTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAG
*
450752 CAGTATTGGCAGCAACCGAATAAATTT
64 CAGAATTGGCAGCAACCGAATAAATTT
450779 ACT
1 ACT
450782 AAGCAATCTA
Statistics
Matches: 90, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 42 0.47
93 21 0.23
95 27 0.30
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.21
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
GAATTGGCAGCAACCGAATAAATTT
Found at i:450984 original size:63 final size:63
Alignment explanation
Indices: 450925--451066 Score: 142
Period size: 63 Copynumber: 2.3 Consensus size: 63
450915 CTTAGAGCGG
* * *
450925 CAACCTCAC-CACGTAAAGTAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 CAACCTC-CTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* * * *** * *
450988 CGATCTCCTCACGCAAGGCATTGACCTCTACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 CAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* * *
451051 CGATCTCCTCATGCAA
1 CAACCTCCTCACGCAA
451067 GGCATTGACC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 1 0.01
63 67 0.99
ACGTcount: A:0.27, C:0.36, G:0.17, T:0.20
Consensus pattern (63 bp):
CAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
Found at i:451067 original size:63 final size:63
Alignment explanation
Indices: 450948--451078 Score: 244
Period size: 63 Copynumber: 2.1 Consensus size: 63
450938 TAAAGTAGAC
450948 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
* *
451011 ACCTCTACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCATGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
451074 ACCTC
1 ACCTC
451079 ATCACGTAAC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:452601 original size:33 final size:33
Alignment explanation
Indices: 452559--452621 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
452549 ACAAGATAAT
**
452559 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
452592 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
452622 TGCGAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:452678 original size:19 final size:19
Alignment explanation
Indices: 452534--452678 Score: 103
Period size: 19 Copynumber: 8.1 Consensus size: 19
452524 TCTTTTGGTT
***
452534 GAAATGAAAATCGCAACAA
1 GAAATGAAAATCGCAATGC
* *
452553 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAATGC
**
452573 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAATGC
* *
452590 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAATGC
452606 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
452625 GAAATGAAAATCGCAAT--
1 GAAATGAAAATCGCAATGC
* *
452642 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAATGC
*
452658 GAAATGAAAATCGTAATGC
1 GAAATGAAAATCGCAATGC
452677 GA
1 GA
452679 TTTTGGTTTC
Statistics
Matches: 101, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
14 19 0.19
15 2 0.02
16 3 0.03
17 3 0.03
18 2 0.02
19 56 0.55
20 16 0.16
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:452691 original size:52 final size:52
Alignment explanation
Indices: 452542--452678 Score: 193
Period size: 52 Copynumber: 2.6 Consensus size: 52
452532 TTGAAATGAA
** * * **
452542 AATCGCAACAAGATAATGAGAATCGCAACGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
452595 AATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
452647 AATCGCAACGCGAAATGAAAATCGTAATGCGA
1 AATCGCAACGCGAAATGAAAATCGCAATGCGA
452679 TTTTGGTTTC
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
52 65 0.86
53 11 0.14
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.14
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:453354 original size:20 final size:20
Alignment explanation
Indices: 453269--453398 Score: 136
Period size: 20 Copynumber: 6.5 Consensus size: 20
453259 CGCTATGTAA
* * *
453269 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
453289 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
453309 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
453330 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
453350 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
*
453370 ATCGCATTGCAATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
453390 ATCGCATTG
1 ATCGCATTG
453399 TGATTTTCCC
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.03
20 79 0.82
21 12 0.12
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:458122 original size:22 final size:22
Alignment explanation
Indices: 458094--458138 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
458084 AAGTAATTAA
*
458094 TTATTTTA-TTTTTTATTTTATT
1 TTATTTTAGTTTTTT-TATTATT
458116 TTATTTTAGTTTTTTTATTATT
1 TTATTTTAGTTTTTTTATTATT
458138 T
1 T
458139 AATTGTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (22 bp):
TTATTTTAGTTTTTTTATTATT
Found at i:458136 original size:17 final size:16
Alignment explanation
Indices: 458097--458138 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
458087 TAATTAATTA
458097 TTTTATT-TTTTATTT
1 TTTTATTATTTTATTT
*
458112 TATT-TTATTTTAGTTT
1 TTTTATTATTTTA-TTT
458128 TTTTATTATTT
1 TTTTATTATTT
458139 AATTGTAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.09
15 8 0.36
16 6 0.27
17 6 0.27
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.81
Consensus pattern (16 bp):
TTTTATTATTTTATTT
Found at i:461697 original size:17 final size:17
Alignment explanation
Indices: 461664--461696 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
461654 ATAGAAAATA
461664 TAATTTTTTATTATTTT
1 TAATTTTTTATTATTTT
461681 TAA--TTTTATTATTTT
1 TAATTTTTTATTATTTT
461696 T
1 T
461697 TAATAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.81
17 3 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TAATTTTTTATTATTTT
Found at i:461820 original size:49 final size:49
Alignment explanation
Indices: 461747--461868 Score: 156
Period size: 49 Copynumber: 2.4 Consensus size: 49
461737 AGATGCACGT
* * *
461747 ATGTAAGTATATATTTATTGTTAGGTTGGGAGATGTACATACTTACACC-
1 ATGTAAGTATGT-TTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
* *
461796 ATGTAAGTATGTGTTTATTTTTAGGCTGAGAGATGTATATACTTACACCG
1 ATGTAAGTATGT-TTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
*
461846 ATATAAGTATGTTTTAATTGTTA
1 ATGTAAGTATGTTTT-ATTGTTA
461869 CACTTTTTTA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
49 46 0.73
50 17 0.27
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (49 bp):
ATGTAAGTATGTTTTATTGTTAGGCTGAGAGATGTACATACTTACACCG
Found at i:463031 original size:2 final size:2
Alignment explanation
Indices: 463024--463064 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
463014 AAAAATATTA
463024 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
463065 GGGTTTTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:463468 original size:19 final size:18
Alignment explanation
Indices: 463432--463469 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
463422 CCTTTCTTAA
463432 TATTTAAAAAATAAATAT
1 TATTTAAAAAATAAATAT
*
463450 TATTTAAACAAATATATAT
1 TATTTAAA-AAATAAATAT
463469 T
1 T
463470 TATATGACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TATTTAAAAAATAAATAT
Found at i:464946 original size:3 final size:3
Alignment explanation
Indices: 464933--465031 Score: 111
Period size: 3 Copynumber: 34.0 Consensus size: 3
464923 GGCCTGTTTG
* *
464933 TAA TGA TAA TAA TAT TAA TAA TAAA TAA T-A TAA T-A TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
464976 TATA TAA TAA TAA TAA TAA TAA TAAA TAA -AA TAA TAA -AA TAA TAA
1 TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
465021 TAA TAA -AA TAA
1 TAA TAA TAA TAA
465032 AAAAACAAAA
Statistics
Matches: 83, Mismatches: 4, Indels: 18
0.79 0.04 0.17
Matches are distributed among these distances:
2 12 0.14
3 62 0.75
4 9 0.11
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:464972 original size:26 final size:25
Alignment explanation
Indices: 464938--465032 Score: 106
Period size: 26 Copynumber: 3.7 Consensus size: 25
464928 GTTTGTAATG
464938 ATAATAATATTAATAATAAATAATATA
1 ATAATAATA-TAAT-ATAAATAATATA
464965 AT-ATAATATAATATATAATAATAATA
1 ATAATAATATAATATA-AATAAT-ATA
*
464991 ATAATAATA-AATA-AAATAATAAA
1 ATAATAATATAATATAAATAATATA
*
465014 ATAATAATAATAAAATAAA
1 ATAATAAT-ATAATATAAA
465033 AAAACAAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 13
0.80 0.03 0.17
Matches are distributed among these distances:
23 10 0.17
24 10 0.17
25 14 0.23
26 18 0.30
27 8 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
ATAATAATATAATATAAATAATATA
Found at i:464982 original size:29 final size:30
Alignment explanation
Indices: 464941--465030 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 30
464931 TGTAATGATA
464941 ATAATATTAATAATAAATAAT-ATAATATAAT
1 ATAATA-T-ATAATAAATAATAATAATATAAT
464972 ATAATATATAAT-AATAATAATAATAATAA-
1 ATAATATATAATAAATAATAATAAT-ATAAT
*
465001 ATAA-A-ATAATAAAATAATAATAATAAAAT
1 ATAATATATAAT-AAATAATAATAATATAAT
465030 A
1 A
465031 AAAAAACAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
27 5 0.09
28 10 0.19
29 27 0.51
30 5 0.09
31 6 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (30 bp):
ATAATATATAATAAATAATAATAATATAAT
Found at i:465000 original size:44 final size:41
Alignment explanation
Indices: 464933--465031 Score: 137
Period size: 44 Copynumber: 2.4 Consensus size: 41
464923 GGCCTGTTTG
* * *
464933 TAATGATAATAATATTAATAATAAATAATATAATATAATATAA
1 TAATAATAATAATAATAATAATAAATAAAATAATA-AA-ATAA
464976 TATATAATAATAATAATAATAATAAATAAAATAATAAAATAA
1 TA-ATAATAATAATAATAATAATAAATAAAATAATAAAATAA
465018 TAATAATAA-AATAA
1 TAATAATAATAATAA
465032 AAAAACAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
40 5 0.10
41 7 0.13
42 6 0.12
43 4 0.08
44 30 0.58
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (41 bp):
TAATAATAATAATAATAATAATAAATAAAATAATAAAATAA
Found at i:465047 original size:14 final size:13
Alignment explanation
Indices: 464999--465051 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
464989 TAATAATAAT
* *
464999 AAATAAAATAATA
1 AAATAAAAAAACA
* *
465012 AAATAATAATAATA
1 AAATAA-AAAAACA
465026 AAATAAAAAAACA
1 AAATAAAAAAACA
465039 AAATGAAAAAAAC
1 AAAT-AAAAAAAC
465052 TAGTGTCTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
13 15 0.42
14 21 0.58
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (13 bp):
AAATAAAAAAACA
Found at i:465363 original size:18 final size:20
Alignment explanation
Indices: 465332--465368 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
465322 GAGCTTTATA
465332 ATATATTTTCATATATCATC
1 ATATATTTTCATATATCATC
465352 ATATA-TTT-ATATATCAT
1 ATATATTTTCATATATCAT
465369 TCTCTCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATATTTTCATATATCATC
Done.