Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003894.1 Hibiscus syriacus cultivar Beakdansim tig00008416_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: 60729
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:95 original size:21 final size:21
Alignment explanation
Indices: 71--112 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
61 AACTACTTGT
* *
71 TTTCACATATATTTCATATCA
1 TTTCACATACACTTCATATCA
*
92 TTTCATATACACTTCATATCA
1 TTTCACATACACTTCATATCA
113 CATGCCATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTCACATACACTTCATATCA
Found at i:727 original size:21 final size:21
Alignment explanation
Indices: 697--741 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
687 ATTCTGTCGT
* *
697 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
718 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
739 TTG
1 TTG
742 CCCAGAATCA
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3693 original size:31 final size:31
Alignment explanation
Indices: 3655--3809 Score: 208
Period size: 31 Copynumber: 5.0 Consensus size: 31
3645 CCCGAAGGAC
* *
3655 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
3686 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
* *
3717 CAGTCCGTATGTTCCGAAGAACATAGGTAAT
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
3748 CA-TCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
3778 CAGTCCATATG-TCCAGAAGAACATAGGTAAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAAA
3809 C
1 C
3810 CCTCGACCCT
Statistics
Matches: 109, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
30 29 0.27
31 79 0.72
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:3777 original size:61 final size:62
Alignment explanation
Indices: 3655--3807 Score: 240
Period size: 61 Copynumber: 2.5 Consensus size: 62
3645 CCCGAAGGAC
* *
3655 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
*
3717 CAGTCCGTATGTTCCGAAGAACATAGGTAATCA-TCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
3778 CAGTCCATATG-TCCAGAAGAACATAGGTAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAA
3808 ACCCTCGACC
Statistics
Matches: 85, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
60 3 0.04
61 52 0.61
62 29 0.34
63 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (62 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:4640 original size:20 final size:20
Alignment explanation
Indices: 4612--4652 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4602 ATTCTGTCGT
* *
4612 TGAAGGGGTATCGGTTCCCC
1 TGAAGGGGTACCGATTCCCC
*
4632 TGAATGGGTACCGATTCCCC
1 TGAAGGGGTACCGATTCCCC
4652 T
1 T
4653 TGCCCAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (20 bp):
TGAAGGGGTACCGATTCCCC
Found at i:16771 original size:22 final size:22
Alignment explanation
Indices: 16729--16769 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
16719 ATTTTTACTA
*
16729 TTTTATTAACCATATAATTTAG
1 TTTTAGTAACCATATAATTTAG
*
16751 TTTTAGTAA-CATATTATTT
1 TTTTAGTAACCATATAATTT
16770 TAAAATTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (22 bp):
TTTTAGTAACCATATAATTTAG
Found at i:35567 original size:11 final size:11
Alignment explanation
Indices: 35551--35613 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
35541 AAAATTACAT
35551 TATTAAAAATA
1 TATTAAAAATA
35562 TATTAAAAATA
1 TATTAAAAATA
* ***
35573 CATTATTGATA
1 TATTAAAAATA
35584 -ATTATAAAAT-
1 TATTA-AAAATA
35594 T-TTAAAAATA
1 TATTAAAAATA
35604 TATTAAAAAT
1 TATTAAAAAT
35614 TCTATAATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:35747 original size:14 final size:14
Alignment explanation
Indices: 35725--35763 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
35715 TAATGAATCT
*
35725 TAAACCCTAAACTC
1 TAAACCCTAAACTA
*
35739 TAAATCCTAAACTA
1 TAAACCCTAAACTA
35753 TAAACCCTAAA
1 TAAACCCTAAA
35764 TCTGATTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:35749 original size:21 final size:21
Alignment explanation
Indices: 35720--35765 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
35710 ATTTGTAATG
* * *
35720 AATCTTAAACCCTAAACTCTA
1 AATCCTAAACCATAAACCCTA
*
35741 AATCCTAAACTATAAACCCTA
1 AATCCTAAACCATAAACCCTA
35762 AATC
1 AATC
35766 TGATTATGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (21 bp):
AATCCTAAACCATAAACCCTA
Found at i:37914 original size:11 final size:11
Alignment explanation
Indices: 37898--37982 Score: 89
Period size: 11 Copynumber: 7.5 Consensus size: 11
37888 TTAAAACCCG
37898 TCGAGCTTGAA
1 TCGAGCTTGAA
**
37909 TCGAGCTCAAAA
1 TCGAGCT-TGAA
37921 TCGAGCTTGAA
1 TCGAGCTTGAA
**
37932 TCGAGCTCAAAA
1 TCGAGCT-TGAA
37944 TCGAGCTTGAA
1 TCGAGCTTGAA
*
37955 TCGAGCTTAAAA
1 TCGAGCTT-GAA
*
37967 TTGAGCTTGAA
1 TCGAGCTTGAA
37978 TCGAG
1 TCGAG
37983 TTTAAAATCG
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
11 32 0.54
12 27 0.46
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:37924 original size:12 final size:11
Alignment explanation
Indices: 37907--37994 Score: 68
Period size: 12 Copynumber: 7.6 Consensus size: 11
37897 GTCGAGCTTG
37907 AATCGAGCTCAA
1 AATCGAGCT-AA
**
37919 AATCGAGCTTG
1 AATCGAGCTAA
37930 AATCGAGCTCAA
1 AATCGAGCT-AA
**
37942 AATCGAGCTTG
1 AATCGAGCTAA
37953 AATCGAGCTTAA
1 AATCGAGC-TAA
* **
37965 AATTGAGCTTG
1 AATCGAGCTAA
*
37976 AATCGAGTTTAA
1 AATCGAG-CTAA
37988 AATCGAG
1 AATCGAG
37995 ATTCAGTCGA
Statistics
Matches: 58, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
11 24 0.41
12 34 0.59
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (11 bp):
AATCGAGCTAA
Found at i:38005 original size:46 final size:46
Alignment explanation
Indices: 37898--38005 Score: 135
Period size: 46 Copynumber: 2.3 Consensus size: 46
37888 TTAAAACCCG
* *
37898 TCGAGCTTGAATCGAGCTCAAAATCGAGCTTGAATCGAGCTCAAAA
1 TCGAGATTCAATCGAGCTCAAAATCGAGCTTGAATCGAGCTCAAAA
* * * * * *
37944 TCGAGCTTGAATCGAGCTTAAAATTGAGCTTGAATCGAGTTTAAAA
1 TCGAGATTCAATCGAGCTCAAAATCGAGCTTGAATCGAGCTCAAAA
*
37990 TCGAGATTCAGTCGAG
1 TCGAGATTCAATCGAG
38006 TTTGAGTCTC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (46 bp):
TCGAGATTCAATCGAGCTCAAAATCGAGCTTGAATCGAGCTCAAAA
Found at i:38008 original size:23 final size:23
Alignment explanation
Indices: 37898--37994 Score: 158
Period size: 23 Copynumber: 4.2 Consensus size: 23
37888 TTAAAACCCG
*
37898 TCGAGCTTGAATCGAGCTCAAAA
1 TCGAGCTTGAATCGAGCTTAAAA
*
37921 TCGAGCTTGAATCGAGCTCAAAA
1 TCGAGCTTGAATCGAGCTTAAAA
37944 TCGAGCTTGAATCGAGCTTAAAA
1 TCGAGCTTGAATCGAGCTTAAAA
* *
37967 TTGAGCTTGAATCGAGTTTAAAA
1 TCGAGCTTGAATCGAGCTTAAAA
37990 TCGAG
1 TCGAG
37995 ATTCAGTCGA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Consensus pattern (23 bp):
TCGAGCTTGAATCGAGCTTAAAA
Found at i:39017 original size:14 final size:15
Alignment explanation
Indices: 38984--39018 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
38974 CAACAAATAG
38984 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
38999 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
39014 -ATTTT
1 AATTTT
39019 GAATTTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:48707 original size:20 final size:20
Alignment explanation
Indices: 48682--48894 Score: 109
Period size: 20 Copynumber: 10.4 Consensus size: 20
48672 TTTTCCCAAT
48682 TCGCAATGCGAATTAGTAAA
1 TCGCAATGCGAATTAGTAAA
* * *
48702 TCGCAATGCAAATTTGAAAAA
1 TCGCAATGCGAATTAG-TAAA
* *
48723 TCGCAATGCG-A-TACTGACTA
1 TCGCAATGCGAATTAGT-A-AA
** *
48743 TCGCAATGC-AATTTTCCTAAT
1 TCGCAATGCGAA--TTAGTAAA
* * *
48764 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGAATTA-GTAAA
** * *
48784 TCGCGTTGCGATTTTCA-TAAT
1 TCGCAATGCGA-ATT-AGTAAA
48805 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTA-GTAAA
*
48825 TCGCAACGCG-ATTAAGTAAA
1 TCGCAATGCGAATT-AGTAAA
*
48845 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTA-GTAAA
48866 TCGCAATGCGAA-TACGTAAA
1 TCGCAATGCGAATTA-GTAAA
48886 TCGCAATGC
1 TCGCAATGC
48895 AAATCTGACT
Statistics
Matches: 150, Mismatches: 25, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
18 1 0.01
19 4 0.03
20 84 0.56
21 55 0.37
22 3 0.02
23 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (20 bp):
TCGCAATGCGAATTAGTAAA
Found at i:48777 original size:21 final size:21
Alignment explanation
Indices: 48640--48815 Score: 85
Period size: 21 Copynumber: 8.5 Consensus size: 21
48630 ATTATTACTA
*
48640 TCGCAATGCGATTTTCCA-ATT
1 TCGCAATGCGATTTT-CATAAT
** **
48661 TCGCGTTGCGATTTTCCCAAT
1 TCGCAATGCGATTTTCATAAT
* *
48682 TCGCAATGCGA-ATT-AGTAAA
1 TCGCAATGCGATTTTCA-TAAT
* * * * *
48702 TCGCAATGCAAATTTGAAAAA
1 TCGCAATGCGATTTTCATAAT
** *
48723 TCGCAATGCGATACTGACT-A-
1 TCGCAATGCGATTTTCA-TAAT
* *
48743 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
48764 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
48784 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
48805 TCGCAATGCGA
1 TCGCAATGCGA
48816 ATACGTAAAT
Statistics
Matches: 115, Mismatches: 32, Indels: 16
0.71 0.20 0.10
Matches are distributed among these distances:
19 1 0.01
20 45 0.39
21 68 0.59
22 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:48836 original size:41 final size:41
Alignment explanation
Indices: 48667--48876 Score: 144
Period size: 41 Copynumber: 5.1 Consensus size: 41
48657 AATTTCGCGT
**
48667 TGCGATTTTCCCAATTCGCAATGCGAATTA-GTAAATCGCAA
1 TGCGATTTTCATAATTCGCAATGCGAA-TACGTAAATCGCAA
* * * * * *
48708 TGCAAATTTGAAAAATCGCAATGCG-ATAC-TGACTATCGCAA
1 TGCGATTTTCATAATTCGCAATGCGAATACGT-A-AATCGCAA
* * * * * **
48749 TGCAATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCATAATTCGCAATGCGA-ATACGTAAATCGCAA
48790 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
* * * * *
48831 CGCGA--TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCA-TAATTCGCAATGCGAA-TACGTAAATCGCAA
48872 TGCGA
1 TGCGA
48877 ATACGTAAAT
Statistics
Matches: 129, Mismatches: 31, Indels: 18
0.72 0.17 0.10
Matches are distributed among these distances:
39 6 0.05
40 22 0.17
41 97 0.75
43 3 0.02
44 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.29
Consensus pattern (41 bp):
TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
Found at i:48885 original size:41 final size:40
Alignment explanation
Indices: 48805--48894 Score: 126
Period size: 41 Copynumber: 2.2 Consensus size: 40
48795 TTTTCATAAT
* *
48805 TCGCAATGCGAATACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGAAAATCGCAACGCGAATAAGTAAA
* * *
48845 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAA-TACGAAAATCGCAACGCGAATAAGTAAA
48886 TCGCAATGC
1 TCGCAATGC
48895 AAATCTGACT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 12 0.27
41 32 0.73
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGAATACGAAAATCGCAACGCGAATAAGTAAA
Found at i:49508 original size:14 final size:14
Alignment explanation
Indices: 49491--49546 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
49481 AATCGCAACG
49491 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
49505 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
49524 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
49538 CGTTGCGAT
1 CGTTGCGAT
49547 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:49531 original size:33 final size:33
Alignment explanation
Indices: 49489--49595 Score: 133
Period size: 33 Copynumber: 3.0 Consensus size: 33
49479 ATAATCGCAA
49489 CGCGTTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGCGTTGCGATTCTCTCGTTGCGATTTTCATTT
**
49522 CGCGTTGCGATTCTCTCGTTGCGATAGTCATTT
1 CGCGTTGCGATTCTCTCGTTGCGATTTTCATTT
49555 CCGCGTTGCGATTTTCATTCTCTCGTTGCGATTTTCATTT
1 -CGCGTTGCG------ATTCTCTCGTTGCGATTTTCATTT
49595 C
1 C
49596 AACCAAAAGA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
33 31 0.49
34 9 0.14
39 1 0.02
40 22 0.35
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (33 bp):
CGCGTTGCGATTCTCTCGTTGCGATTTTCATTT
Found at i:49572 original size:20 final size:20
Alignment explanation
Indices: 49505--49595 Score: 81
Period size: 20 Copynumber: 4.9 Consensus size: 20
49495 GCGATTCTCT
49505 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATTTTCATTTCCG
*
49524 CGTTGCGA--TTC---T-CT
1 CGTTGCGATTTTCATTTCCG
**
49538 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCCG
*
49558 CGTTGCGATTTTCA-TTCTCT
1 CGTTGCGATTTTCATTTC-CG
49578 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
49596 AACCAAAAGA
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
14 10 0.17
16 2 0.03
17 3 0.05
19 12 0.21
20 28 0.48
21 3 0.05
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCG
Found at i:51465 original size:94 final size:94
Alignment explanation
Indices: 51274--51578 Score: 467
Period size: 94 Copynumber: 3.3 Consensus size: 94
51264 TAGATTGCTT
* * * * * *
51274 AGTAAATTTATTTGATTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTATAAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
51335 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
51364 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
51429 ATTTGTCTTTCTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
51458 AGTAAATTTGTTCGGTTGCTGCCGATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
51523 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
51552 AGTAAATTTGTTCGTTTGCTGCCAATT
1 AGTAAATTTATTCGGTTGCTGCCAATT
51579 GAAACTATTC
Statistics
Matches: 198, Mismatches: 12, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
90 33 0.17
92 3 0.02
93 21 0.11
94 141 0.71
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:53459 original size:14 final size:14
Alignment explanation
Indices: 53440--53475 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
53430 ATTGTTTAAT
53440 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
53454 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
53468 TGATTTGT
1 TGATTTGT
53476 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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:53604 original size:19 final size:19
Alignment explanation
Indices: 53582--53642 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
53572 AAAAATGACT
53582 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
53601 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
* *
53615 ATCACAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
53634 ATCGCAATG
1 ATCGCAATG
53643 ACAAAATCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
14 9 0.28
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.53
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:53632 original size:33 final size:33
Alignment explanation
Indices: 53590--53661 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
53580 CTATCGCAAT
* *
53590 GCGAAATGAAAATCGCAACGAGAGAATCACAAC
1 GCGAAATGAAAATCGCAACGACAAAATCACAAC
* *
53623 GCGAAATGAAAATCGCAATGACAAAATCGCAAC
1 GCGAAATGAAAATCGCAACGACAAAATCACAAC
53656 GCGAAA
1 GCGAAA
53662 CTAAATTCGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.49, C:0.21, G:0.21, T:0.10
Consensus pattern (33 bp):
GCGAAATGAAAATCGCAACGACAAAATCACAAC
Found at i:53689 original size:19 final size:19
Alignment explanation
Indices: 53667--53817 Score: 62
Period size: 19 Copynumber: 8.7 Consensus size: 19
53657 CGAAACTAAA
53667 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
53686 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* * **
53701 -CCTCGTTATGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
53719 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
53734 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
53752 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
53767 -TCTCGTTGTGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
53785 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
*
53804 TTCCGCGATGCGAT
1 TT-CGCGTTGCGAT
53818 AGACATTAAG
Statistics
Matches: 91, Mismatches: 25, Indels: 31
0.62 0.17 0.21
Matches are distributed among these distances:
14 23 0.25
16 9 0.10
17 9 0.10
19 41 0.45
20 9 0.10
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:53719 original size:33 final size:33
Alignment explanation
Indices: 53671--53797 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
53661 ACTAAATTCG
* * *
53671 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGTGATTTTCATTTCGCATTGCGATTCTCT
*
53704 CGTTATGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGTGATTTTCATTTCGCATTGCGATTCTCT
*
53737 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGTGATTTTCATTTCGCATTGCGATTCTCT
53770 CGTTGTGATTTTCATTTCGCATTGCGAT
1 CGTTGTGATTTTCATTTCGCATTGCGAT
53798 AGTCATTTCC
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGTGATTTTCATTTCGCATTGCGATTCTCT
Found at i:53863 original size:20 final size:20
Alignment explanation
Indices: 53791--53863 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
53781 TCATTTCGCA
*
53791 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGTG
* * **
53811 ATGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCCG-TG
53831 ATTGCGA-ACGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCCGTG
53852 TTGCGATAGTCA
1 TTGCGATAGTCA
53864 AATGATTGCC
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
19 3 0.08
20 22 0.56
21 11 0.28
22 3 0.08
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGTG
Found at i:56088 original size:12 final size:12
Alignment explanation
Indices: 56071--56095 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56061 TCTTCGGGGA
56071 CTTTTTCTTCTT
1 CTTTTTCTTCTT
56083 CTTTTTCTTCTT
1 CTTTTTCTTCTT
56095 C
1 C
56096 AGGATTTTAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:56304 original size:24 final size:24
Alignment explanation
Indices: 56270--56323 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
56260 CTGAAACATC
* *
56270 ATCAAAATCCGAGTATTGACTAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
56294 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
56318 ATCAAA
1 ATCAAA
56324 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:0.19, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:57087 original size:20 final size:20
Alignment explanation
Indices: 57062--57114 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
57052 ATTCTGTATT
57062 ATCTCGTTGCGATAGTCAGA
1 ATCTCGTTGCGATAGTCAGA
*
57082 ATCTCGTTGCGAAAGTCAGA
1 ATCTCGTTGCGATAGTCAGA
*
57102 ATCGCGTTGCGAT
1 ATCTCGTTGCGAT
57115 TTGTATTATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.28
Consensus pattern (20 bp):
ATCTCGTTGCGATAGTCAGA
Found at i:57125 original size:20 final size:21
Alignment explanation
Indices: 57096--57239 Score: 88
Period size: 21 Copynumber: 7.0 Consensus size: 21
57086 CGTTGCGAAA
* *
57096 GTCAGAATCGCGTTGCGATTT
1 GTCAGTATCGCATTGCGATTT
* * *
57117 GT-ATTATCGCGTTGCGA-TA
1 GTCAGTATCGCATTGCGATTT
*
57136 GTCAGTATCGCATTGCAATTT
1 GTCAGTATCGCATTGCGATTT
*
57157 -TCCA-AATTCGCATTGCGATTTT
1 GT-CAGTA-TCGCATTGCGA-TTT
* * *
57179 GT-ATTATCGCGTTGCGA-TA
1 GTCAGTATCGCATTGCGATTT
57198 GTCAGTATCGCATTGCGATTT
1 GTCAGTATCGCATTGCGATTT
*
57219 -TCCA-AATTCGCATTGCGATTT
1 GT-CAGTA-TCGCATTGCGATTT
57240 ACTTATTCGC
Statistics
Matches: 96, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
19 6 0.06
20 42 0.44
21 43 0.45
22 4 0.04
23 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (21 bp):
GTCAGTATCGCATTGCGATTT
Found at i:57190 original size:62 final size:62
Alignment explanation
Indices: 57042--57239 Score: 269
Period size: 62 Copynumber: 3.2 Consensus size: 62
57032 ACTTTGAAAA
* * * * * **
57042 TCGCATTGCGATTCTGTATTATCTCGTTGCGATAGTCAGAATCTCGTTGCGAA-AGT-CAGAA-
1 TCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGC-AATTTTCCA-AAT
*
57103 TCGCGTTGCGA-TTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCCAAAT
1 TCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCCAAAT
*
57164 TCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCCAAAT
57226 TCGCATTGCGATTT
1 TCGCATTGCGATTT
57240 ACTTATTCGC
Statistics
Matches: 123, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
59 2 0.02
60 36 0.29
61 22 0.18
62 63 0.51
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (62 bp):
TCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCCAAAT
Found at i:57231 original size:21 final size:20
Alignment explanation
Indices: 57143--57256 Score: 86
Period size: 21 Copynumber: 5.5 Consensus size: 20
57133 ATAGTCAGTA
*
57143 TCGCATTGCAATTTTCCAAAT
1 TCGCATTGCGATTTT-CAAAT
** *
57164 TCGCATTGCGATTTTGTATT
1 TCGCATTGCGATTTTCAAAT
* ** *
57184 ATCGCGTTGCGATAGTC-AGT
1 -TCGCATTGCGATTTTCAAAT
57204 ATCGCATTGCGATTTTCCAAAT
1 -TCGCATTGCGATTTT-CAAAT
* **
57226 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTTCAAAT
57246 TCGCATTGCGA
1 TCGCATTGCGA
57257 ATTGGGAAAT
Statistics
Matches: 74, Mismatches: 16, Indels: 7
0.76 0.16 0.07
Matches are distributed among these distances:
20 31 0.42
21 41 0.55
22 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTTCAAAT
Found at i:57270 original size:21 final size:20
Alignment explanation
Indices: 57244--57298 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
57234 CGATTTACTT
57244 ATTCGCATTGCGAATTGGGAA
1 ATTCGCATTGCGAATT-GGAA
**
57265 ATTCGCAACGCGAAATTGGAA
1 ATTCGCATTGCG-AATTGGAA
*
57286 AATCGCATTGCGA
1 ATTCGCATTGCGA
57299 TAGTAATAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (20 bp):
ATTCGCATTGCGAATTGGAA
Done.