Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005707.1 Hibiscus syriacus cultivar Beakdansim tig00013342_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: 91969
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:4654 original size:13 final size:13
Alignment explanation
Indices: 4636--4665 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
4626 CAAGGTTAAA
4636 CTACACTAATAGT
1 CTACACTAATAGT
4649 CTACACTAATAGT
1 CTACACTAATAGT
4662 CTAC
1 CTAC
4666 GAACTTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (13 bp):
CTACACTAATAGT
Found at i:6829 original size:31 final size:32
Alignment explanation
Indices: 6794--6861 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 32
6784 TTTTTATTAG
* *
6794 TTTAAAGATAATTTTGTAAT-AGTTTAAT-AAT
1 TTTAAACATAATTCTGTAATGA-TTTAATAAAT
* *
6825 TTTAAACATCATTCTGTAATGATTTGATAAAT
1 TTTAAACATAATTCTGTAATGATTTAATAAAT
6857 TTTAA
1 TTTAA
6862 TAATCGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (32 bp):
TTTAAACATAATTCTGTAATGATTTAATAAAT
Found at i:7716 original size:3 final size:3
Alignment explanation
Indices: 7708--7756 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
7698 AAAGATTCCG
* * * * *
7708 CTT CTT CTT CTT CTT CTT CTT CAT CAT CAT CAT CTT CGT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
7756 C
1 C
7757 AAAGCAAGCG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.08, C:0.35, G:0.02, T:0.55
Consensus pattern (3 bp):
CTT
Found at i:13774 original size:21 final size:21
Alignment explanation
Indices: 13750--13793 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
13740 CAAAGAATGG
*
13750 TAAGTTGAAGTTACCAAA-ATA
1 TAAGTTCAA-TTACCAAATATA
*
13771 TAAGTTCTATTACCAAATATA
1 TAAGTTCAATTACCAAATATA
13792 TA
1 TA
13794 CTACAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (21 bp):
TAAGTTCAATTACCAAATATA
Found at i:14025 original size:25 final size:25
Alignment explanation
Indices: 13997--14051 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
13987 AAAAAATAAT
**
13997 ATTTTAGATAGCGTTTAATATTAAC
1 ATTTTAGATAGCGCCTAATATTAAC
14022 ATTTTAGATAGCGCCTAATATTAAC
1 ATTTTAGATAGCGCCTAATATTAAC
14047 ATTTT
1 ATTTT
14052 CGGTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (25 bp):
ATTTTAGATAGCGCCTAATATTAAC
Found at i:18844 original size:19 final size:19
Alignment explanation
Indices: 18810--18846 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18800 ATGACCAACA
*
18810 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
18829 AAATCGCAACGTGATCTC
1 AAATCGCAACGCGATCTC
18847 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:18938 original size:21 final size:21
Alignment explanation
Indices: 18914--18985 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
18904 TATTTAAATT
18914 GCAACGCGATAATACATAATC
1 GCAACGCGATAATACATAATC
**
18935 GCAACGCGATTCTGAC-T-ATC
1 GCAACGCGATAAT-ACATAATC
*
18955 GCAACACGATAATACATAATC
1 GCAACGCGATAATACATAATC
18976 GCAACGCGAT
1 GCAACGCGAT
18986 TATGACTGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.05
20 14 0.33
21 24 0.57
22 2 0.05
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (21 bp):
GCAACGCGATAATACATAATC
Found at i:18959 original size:41 final size:41
Alignment explanation
Indices: 18914--19002 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
18904 TATTTAAATT
* *
18914 GCAACGCGATAATACATAATCGCAACGCGATTCTGACTATC
1 GCAACACGATAATACATAATCGCAACGCGATTATGACTATC
*
18955 GCAACACGATAATACATAATCGCAACGCGATTATGACTGTC
1 GCAACACGATAATACATAATCGCAACGCGATTATGACTATC
*
18996 ACAACAC
1 GCAACAC
19003 TGAATTTCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.37, C:0.27, G:0.16, T:0.20
Consensus pattern (41 bp):
GCAACACGATAATACATAATCGCAACGCGATTATGACTATC
Found at i:19847 original size:24 final size:24
Alignment explanation
Indices: 19820--19873 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
19810 GTATTCGAAA
19820 TTTGATCTCAGTCAATACCCGGAC
1 TTTGATCTCAGTCAATACCCGGAC
** * *
19844 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTCAGTCAATACCCGGAC
19868 TTTGAT
1 TTTGAT
19874 GATGTTTCAG
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:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATCTCAGTCAATACCCGGAC
Found at i:21106 original size:23 final size:22
Alignment explanation
Indices: 21080--21143 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
21070 CAGCTCATAT
21080 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
21103 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
21126 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
21144 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:27855 original size:23 final size:22
Alignment explanation
Indices: 27829--27890 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
27819 CAGCTCATAT
27829 AATTACACCTAAGTGCCACGTAG
1 AATTACACCT-AGTGCCACGTAG
* * *
27852 AATTACACC-GGAGCCGCGTAG
1 AATTACACCTAGTGCCACGTAG
*
27873 AATTGCACCTTAGTGCCA
1 AATTACACC-TAGTGCCA
27891 TATAATAATG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
21 17 0.57
23 13 0.43
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (22 bp):
AATTACACCTAGTGCCACGTAG
Found at i:30770 original size:22 final size:22
Alignment explanation
Indices: 30733--30787 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
30723 TCTGAGAGAT
*
30733 GGAGAT-A-GACGGATTTCGTC
1 GGAGATGAGGACGAATTTCGTC
*
30753 GGAGATGGGGACGAATTTCGTC
1 GGAGATGAGGACGAATTTCGTC
30775 GGAGATGAGGACG
1 GGAGATGAGGACG
30788 GATGTCGCCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 6 0.20
22 24 0.80
ACGTcount: A:0.25, C:0.13, G:0.42, T:0.20
Consensus pattern (22 bp):
GGAGATGAGGACGAATTTCGTC
Found at i:30981 original size:20 final size:20
Alignment explanation
Indices: 30934--31088 Score: 93
Period size: 20 Copynumber: 7.7 Consensus size: 20
30924 GCGCTTTGAA
*
30934 AATCGCATTGCGATATTGT-AT
1 AATCGCGTTGCGATA--GTCAT
* *
30955 TATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAT
30975 AATCGCGTTGCGATTATGT-AT
1 AATCGCGTTGCGA-TA-GTCAT
* * *
30996 TATCACGTTGCGAT-TTACAT
1 AATCGCGTTGCGATAGT-CAT
* * * *
31016 ATTCGCATTGCGATAGTTAA
1 AATCGCGTTGCGATAGTCAT
*
31036 AATCGCGTTGCGAT-TTACAT
1 AATCGCGTTGCGATAGT-CAT
* * *
31056 ATTCGCATTGCGATAGTCAA
1 AATCGCGTTGCGATAGTCAT
*
31076 AATCACGTTGCGA
1 AATCGCGTTGCGA
31089 ATCTGGAAAC
Statistics
Matches: 99, Mismatches: 27, Indels: 17
0.69 0.19 0.12
Matches are distributed among these distances:
18 1 0.01
19 3 0.03
20 64 0.65
21 29 0.29
22 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAT
Found at i:31010 original size:21 final size:20
Alignment explanation
Indices: 30935--31009 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
30925 CGCTTTGAAA
*
30935 ATCGCATTGCGATATTGTATT
1 ATCGCGTTGCGATA-TGTATT
**
30956 ATCGCGTTGCGATA-GTCAGA
1 ATCGCGTTGCGATATGT-ATT
30976 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGA-TATGTATT
*
30997 ATCACGTTGCGAT
1 ATCGCGTTGCGAT
31010 TTACATATTC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
19 2 0.04
20 14 0.31
21 27 0.60
22 2 0.04
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (20 bp):
ATCGCGTTGCGATATGTATT
Found at i:31027 original size:41 final size:40
Alignment explanation
Indices: 30936--31070 Score: 157
Period size: 41 Copynumber: 3.3 Consensus size: 40
30926 GCTTTGAAAA
* * *
30936 TCGCATTGCGATATTGTATTATCGCGTTGCGATAGT-CAGAA
1 TCGCATTGCGATA-TGTATTATCGCGTTGCGAT-TTACATAT
* *
30977 TCGCGTTGCGATTATGTATTATCACGTTGCGATTTACATAT
1 TCGCATTGCGA-TATGTATTATCGCGTTGCGATTTACATAT
**
31018 TCGCATTGCGATA-GTTAAAATCGCGTTGCGATTTACATAT
1 TCGCATTGCGATATG-TATTATCGCGTTGCGATTTACATAT
31058 TCGCATTGCGATA
1 TCGCATTGCGATA
31071 GTCAAAATCA
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
39 1 0.01
40 38 0.46
41 41 0.50
42 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (40 bp):
TCGCATTGCGATATGTATTATCGCGTTGCGATTTACATAT
Found at i:31050 original size:40 final size:40
Alignment explanation
Indices: 30997--31088 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 40
30987 ATTATGTATT
*
30997 ATCACGTTGCGATTTACATATTCGCATTGCGATAGTTAAA
1 ATCACGTTGCGATTTACATATTCGCATTGCGATAGTCAAA
*
31037 ATCGCGTTGCGATTTACATATTCGCATTGCGATAGTCAAA
1 ATCACGTTGCGATTTACATATTCGCATTGCGATAGTCAAA
31077 ATCACGTTGCGA
1 ATCACGTTGCGA
31089 ATCTGGAAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (40 bp):
ATCACGTTGCGATTTACATATTCGCATTGCGATAGTCAAA
Found at i:45892 original size:48 final size:48
Alignment explanation
Indices: 45821--45914 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
45811 TCGCTTCATT
* * * *
45821 GATTCAGCCTTTGGGACTGATGGGGTACTGGCAACCTCCTGCTTTACC
1 GATTCAACCTTTGAGACTGATGGGATACTAGCAACCTCCTGCTTTACC
*
45869 GATTCAACCTTTGAGACTGATGGGATACTAGTAACCTCCTGCTTTA
1 GATTCAACCTTTGAGACTGATGGGATACTAGCAACCTCCTGCTTTA
45915 TAGATTCAGC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.31
Consensus pattern (48 bp):
GATTCAACCTTTGAGACTGATGGGATACTAGCAACCTCCTGCTTTACC
Found at i:48446 original size:7 final size:7
Alignment explanation
Indices: 48434--48499 Score: 123
Period size: 7 Copynumber: 9.4 Consensus size: 7
48424 TGTCTTTGGT
48434 TGGAGGC
1 TGGAGGC
48441 TGGAGGC
1 TGGAGGC
48448 TGGAGGC
1 TGGAGGC
48455 TGGAGGC
1 TGGAGGC
48462 TGGAGGC
1 TGGAGGC
48469 TGGAGGC
1 TGGAGGC
48476 TGGAGGC
1 TGGAGGC
48483 TGGAGGC
1 TGGAGGC
*
48490 TGGATGC
1 TGGAGGC
48497 TGG
1 TGG
48500 CTGGCGTGTC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 58 1.00
ACGTcount: A:0.14, C:0.14, G:0.56, T:0.17
Consensus pattern (7 bp):
TGGAGGC
Found at i:50542 original size:22 final size:22
Alignment explanation
Indices: 50514--50574 Score: 122
Period size: 22 Copynumber: 2.8 Consensus size: 22
50504 TCCTATTGAC
50514 ACGTTTTCAAAGTATAAATCAA
1 ACGTTTTCAAAGTATAAATCAA
50536 ACGTTTTCAAAGTATAAATCAA
1 ACGTTTTCAAAGTATAAATCAA
50558 ACGTTTTCAAAGTATAA
1 ACGTTTTCAAAGTATAA
50575 TAATTGCAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.33
Consensus pattern (22 bp):
ACGTTTTCAAAGTATAAATCAA
Found at i:62346 original size:21 final size:21
Alignment explanation
Indices: 62322--62416 Score: 102
Period size: 21 Copynumber: 4.6 Consensus size: 21
62312 TATCGCAAAT
* *
62322 TCGCGTTGCGATAATTGGAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
62343 TCGCGTTGCGAT-TTTTCATT
1 TCGCGTTGCGATAGTTGAAAA
62363 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
62384 TCACGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
*
62405 TCGCATTGCGAT
1 TCGCGTTGCGAT
62417 TTTCCATTTT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 15 0.25
21 45 0.75
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:62491 original size:19 final size:19
Alignment explanation
Indices: 62469--62508 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
62459 TTTCAAATTC
* *
62469 GTTGCGATAGTCTACGGTT
1 GTTGCGAAAGTCTACAGTT
62488 GTTGCGAAAGTCTACAGTT
1 GTTGCGAAAGTCTACAGTT
62507 GT
1 GT
62509 CGTTGCGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.35
Consensus pattern (19 bp):
GTTGCGAAAGTCTACAGTT
Found at i:62516 original size:22 final size:19
Alignment explanation
Indices: 62467--62516 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
62457 TTTTTCAAAT
*
62467 TCGTTGCGATAGTCTACGG
1 TCGTTGCGAAAGTCTACGG
*
62486 TTGTTGCGAAAGTCTACAGTTG
1 TCGTTGCGAAAGTCTAC-G--G
62508 TCGTTGCGA
1 TCGTTGCGA
62517 TTTTCCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 15 0.60
20 1 0.04
22 9 0.36
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.34
Consensus pattern (19 bp):
TCGTTGCGAAAGTCTACGG
Found at i:62645 original size:10 final size:11
Alignment explanation
Indices: 62616--62649 Score: 52
Period size: 10 Copynumber: 3.1 Consensus size: 11
62606 GACACGTATT
62616 ACCACGACCACG
1 ACCACGA-CACG
62628 ACCACGACACG
1 ACCACGACACG
62639 A-CACGACACG
1 ACCACGACACG
62649 A
1 A
62650 TACAACCCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.45
11 5 0.23
12 7 0.32
ACGTcount: A:0.38, C:0.44, G:0.18, T:0.00
Consensus pattern (11 bp):
ACCACGACACG
Found at i:63155 original size:6 final size:6
Alignment explanation
Indices: 63146--63200 Score: 110
Period size: 6 Copynumber: 9.2 Consensus size: 6
63136 GCCGTCCGTC
63146 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
63194 TCGTGG T
1 TCGTGG T
63201 AATACGTGTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:63339 original size:41 final size:41
Alignment explanation
Indices: 63294--63383 Score: 153
Period size: 41 Copynumber: 2.2 Consensus size: 41
63284 CAACGAATTT
* *
63294 TCGCAACGAATTTGGAAAATCACAACGATAACTGTAGACTA
1 TCGCAACGAATTTGAAAAATCACAACGACAACTGTAGACTA
*
63335 TCGCAACGAATTTGAAAAATCGCAACGACAACTGTAGACTA
1 TCGCAACGAATTTGAAAAATCACAACGACAACTGTAGACTA
63376 TCGCAACG
1 TCGCAACG
63384 CGATTTTCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (41 bp):
TCGCAACGAATTTGAAAAATCACAACGACAACTGTAGACTA
Found at i:63420 original size:41 final size:40
Alignment explanation
Indices: 63375--63549 Score: 133
Period size: 41 Copynumber: 4.3 Consensus size: 40
63365 ACTGTAGACT
* *
63375 ATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGACTTT-AACTATCGCAACGCGAATTGGAAA
** * **
63416 ATCGCAACGCGAAATGAAAAATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGACTTTAACTATCGCAACGCGAA-TTGGAAA
* *
63455 ATCGCAACGACAACTGTAGACTATCGCAA--CGAATTTGGAAA
1 ATCGCAACG-CGACTTTA-ACTATCGCAACGCGAA-TTGGAAA
* * * * *
63496 ATCGCAACGACAACTGTAGACTATCGCAACGTGAACTCGAAA
1 ATCGCAACG-CGACTTTA-ACTATCGCAACGCGAATTGGAAA
63538 ATCGCAACGCGA
1 ATCGCAACGCGA
63550 AATGGAAAAT
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
38 4 0.04
39 15 0.13
40 12 0.11
41 64 0.57
42 14 0.12
43 3 0.03
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (40 bp):
ATCGCAACGCGACTTTAACTATCGCAACGCGAATTGGAAA
Found at i:63421 original size:20 final size:20
Alignment explanation
Indices: 63396--63569 Score: 135
Period size: 20 Copynumber: 8.6 Consensus size: 20
63386 ATTTTCAACT
63396 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAACTGGAAA
* *
63416 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAACTGGAAA
*
63436 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-CTGGAAA
**
63455 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTG--GAAA
*
63477 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAA-CTGGAAA
**
63496 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTG--GAAA
* *
63518 ATCGCAACGTGAACTCGAAA
1 ATCGCAACGCGAACTGGAAA
*
63538 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAACTGGAAA
63558 ATCGCAACGCGA
1 ATCGCAACGCGA
63570 TTTTCAACTA
Statistics
Matches: 120, Mismatches: 20, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
18 4 0.03
19 22 0.18
20 62 0.52
21 6 0.05
22 26 0.22
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAACTGGAAA
Found at i:63456 original size:102 final size:102
Alignment explanation
Indices: 63334--63612 Score: 311
Period size: 102 Copynumber: 2.7 Consensus size: 102
63324 ACTGTAGACT
*
63334 ATCGCAACGAATTTGAAAAATCGCAACGACAACTGTAGACTATCGCAACGCGATTTTCAACTATC
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGATTTTCAA-TATC
63399 GCAACGCGAACTG-GAAAATCGCAACGCGAAAT-GAAAA
65 GCAACGCGAACTGAGAAAATCGCAACGCGAAATCG-AAA
* ** *
63436 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACG-AATTTGGAAAATCG
1 ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGATTTTCAATATCG
** * *
63500 CAACGAC-AACTGTAGACTATCGCAACGTGAACTCGAAA
66 CAACG-CGAACTG-AGAAAATCGCAACGCGAAATCGAAA
* * * * *
63538 ATCGCAACGCGAA-ATGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAATGCGATTTTCAATT
1 ATCGCAA--CGAATTTGGAAAATCGCAACGACAACTGT-AGACTATCGCAACGCGATTTTCAA-T
63600 ATCGCAACGCGAA
62 ATCGCAACGCGAA
63613 ATGCAACGCG
Statistics
Matches: 149, Mismatches: 18, Indels: 18
0.81 0.10 0.10
Matches are distributed among these distances:
100 14 0.09
101 7 0.05
102 89 0.60
103 24 0.16
104 15 0.10
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (102 bp):
ATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGATTTTCAATATCG
CAACGCGAACTGAGAAAATCGCAACGCGAAATCGAAA
Found at i:63457 original size:19 final size:19
Alignment explanation
Indices: 63410--63505 Score: 86
Period size: 19 Copynumber: 4.8 Consensus size: 19
63400 CAACGCGAAC
*
63410 TGGAAAATCGCAACGCGAA-A
1 TGGAAAATCGCAA--CGAATT
*
63430 TGAAAAATCGCAACGAATT
1 TGGAAAATCGCAACGAATT
*
63449 TGGAAAATCGCAACGACAACTG
1 TGGAAAATCGCAACG--AA-TT
* **
63471 TAGACTATCGCAACGAATT
1 TGGAAAATCGCAACGAATT
63490 TGGAAAATCGCAACGA
1 TGGAAAATCGCAACGA
63506 CAACTGTAGA
Statistics
Matches: 61, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
18 4 0.07
19 28 0.46
20 14 0.23
21 2 0.03
22 13 0.21
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.17
Consensus pattern (19 bp):
TGGAAAATCGCAACGAATT
Found at i:63532 original size:22 final size:22
Alignment explanation
Indices: 63316--63526 Score: 87
Period size: 22 Copynumber: 10.2 Consensus size: 22
63306 TGGAAAATCA
*
63316 CAACGATAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
** **
63338 CAACGA-ATTTG-A-AAAATCG
1 CAACGACAACTGTAGACTATCG
63357 CAACGACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
* * *
63379 CAACG-CGATTTTCA-ACTATCG
1 CAACGACAACTGT-AGACTATCG
**
63400 CAACG-CGAACTG--GAAAATCG
1 CAACGAC-AACTGTAGACTATCG
* **
63420 CAACG-CGAAATG-A-AAAATCG
1 CAACGAC-AACTGTAGACTATCG
* * **
63440 CAACG--AA-TTTGGAAAATCG
1 CAACGACAACTGTAGACTATCG
63459 CAACGACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
* * **
63481 CAACG--AA-TTTGGAAAATCG
1 CAACGACAACTGTAGACTATCG
63500 CAACGACAACTGTAGACTATCG
1 CAACGACAACTGTAGACTATCG
63522 CAACG
1 CAACG
63527 TGAACTCGAA
Statistics
Matches: 143, Mismatches: 31, Indels: 30
0.70 0.15 0.15
Matches are distributed among these distances:
17 1 0.01
18 2 0.01
19 36 0.25
20 34 0.24
21 25 0.17
22 45 0.31
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.18
Consensus pattern (22 bp):
CAACGACAACTGTAGACTATCG
Found at i:63584 original size:21 final size:21
Alignment explanation
Indices: 63558--63611 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
63548 GAAATGGAAA
63558 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* *
63579 ATCGCAATGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
63600 ATCGCAACGCGA
1 ATCGCAACGCGA
63612 AATGCAACGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:63585 original size:143 final size:143
Alignment explanation
Indices: 63294--63569 Score: 448
Period size: 143 Copynumber: 1.9 Consensus size: 143
63284 CAACGAATTT
*
63294 TCGCAACGAATTTGGAAAATCACAACGATAACTGTAGACTATCGCAACGAATTTGAAAAATCGCA
1 TCGCAACGAATTTGGAAAATCACAACGACAACTGTAGACTATCGCAACGAATTTGAAAAATCGCA
** * *
63359 ACGACAACTGTAGACTATCGCAACGCGATTTTCAACTATCGCAACGCGAACTGGAAAATCGCAAC
66 ACGACAACTGTAGACTATCGCAACGCGATACTCAACAATCGCAACGCGAAATGGAAAATCGCAAC
*
63424 GCGAAATGAAAAA
131 GCGAAATCAAAAA
* *
63437 TCGCAACGAATTTGGAAAATCGCAACGACAACTGTAGACTATCGCAACGAATTTGGAAAATCGCA
1 TCGCAACGAATTTGGAAAATCACAACGACAACTGTAGACTATCGCAACGAATTTGAAAAATCGCA
*
63502 ACGACAACTGTAGACTATCGCAACGTGA-ACTCGAA-AATCGCAACGCGAAATGGAAAATCGCAA
66 ACGACAACTGTAGACTATCGCAACGCGATACTC-AACAATCGCAACGCGAAATGGAAAATCGCAA
63565 CGCGA
130 CGCGA
63570 TTTTCAACTA
Statistics
Matches: 124, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
142 33 0.27
143 91 0.73
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.18
Consensus pattern (143 bp):
TCGCAACGAATTTGGAAAATCACAACGACAACTGTAGACTATCGCAACGAATTTGAAAAATCGCA
ACGACAACTGTAGACTATCGCAACGCGATACTCAACAATCGCAACGCGAAATGGAAAATCGCAAC
GCGAAATCAAAAA
Found at i:69769 original size:2 final size:2
Alignment explanation
Indices: 69758--69791 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
69748 ACAATGGTGG
69758 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
69792 GGATGACAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:71937 original size:18 final size:18
Alignment explanation
Indices: 71916--71951 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
71906 TTCTGGGTCC
*
71916 GGTTCTGCTTCGGGTTCT
1 GGTTCTGCTTCAGGTTCT
*
71934 GGTTCTGTTTCAGGTTCT
1 GGTTCTGCTTCAGGTTCT
71952 TGTATTAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.19, G:0.31, T:0.47
Consensus pattern (18 bp):
GGTTCTGCTTCAGGTTCT
Done.