Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007705.1 Hibiscus syriacus cultivar Beakdansim tig00109920_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: 62764
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2816 original size:29 final size:29
Alignment explanation
Indices: 2781--2862 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
2771 AAACTAAATT
*
2781 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
2810 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
2839 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
2863 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:9507 original size:30 final size:30
Alignment explanation
Indices: 9473--9538 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
9463 AACCGCTAAA
* *
9473 GAACCGGCTGAAAGCCGGGAAAACCGGGGT
1 GAACCGGCTGAAAACCGGCAAAACCGGGGT
* **
9503 GAACCGGCTGAAAACTGGCAAAACCGGTTT
1 GAACCGGCTGAAAACCGGCAAAACCGGGGT
9533 GAACCG
1 GAACCG
9539 CCGGTTCACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.24, G:0.33, T:0.11
Consensus pattern (30 bp):
GAACCGGCTGAAAACCGGCAAAACCGGGGT
Found at i:9792 original size:24 final size:24
Alignment explanation
Indices: 9762--9817 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
9752 TAGAAGTTCG
9762 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
9786 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
9810 ATTGAAGC
1 ATTGAAGC
9818 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:10429 original size:23 final size:24
Alignment explanation
Indices: 10399--10460 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 24
10389 GAAAACATTG
*
10399 TAAA-GAACATGTTTGTGAAC-CC
1 TAAATGAACATGTTTGTGAACACA
*
10421 TAAATGAACATGTTTGTGAACATA
1 TAAATGAACATGTTTGTGAACACA
*
10445 TAAATGAATATGTTTG
1 TAAATGAACATGTTTG
10461 CTAAAAGTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 4 0.11
23 16 0.46
24 15 0.43
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.34
Consensus pattern (24 bp):
TAAATGAACATGTTTGTGAACACA
Found at i:10502 original size:30 final size:32
Alignment explanation
Indices: 10463--10546 Score: 93
Period size: 30 Copynumber: 2.7 Consensus size: 32
10453 TATGTTTGCT
*
10463 AAAAGTAAATAAACGAACATGAACAC-AT-TC
1 AAAAATAAATAAACGAACATGAACACGATATC
** *
10493 AAAAATAAATAAATAAACATGAACACGATATT
1 AAAAATAAATAAACGAACATGAACACGATATC
* *
10525 AAAAA-AATTAAACGAAAATGAA
1 AAAAATAAATAAACGAACATGAA
10547 TTGAACGTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
30 23 0.52
31 15 0.34
32 6 0.14
ACGTcount: A:0.63, C:0.11, G:0.08, T:0.18
Consensus pattern (32 bp):
AAAAATAAATAAACGAACATGAACACGATATC
Found at i:10920 original size:43 final size:43
Alignment explanation
Indices: 10832--11140 Score: 286
Period size: 43 Copynumber: 7.2 Consensus size: 43
10822 TGTAAAATAA
* ** *
10832 AAACGCCGCAAAAAGTCAAGATCTATAGCCACGTTTTT-GACAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATAC
*
10875 AAACGCCGCAAAAGGTCGGATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* * * *
10918 AAATGCTGCAAAAGGTCGAGATTTATATCGGCGTTTTTGGA-AC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGATAC
* * *
10961 AAACACCGCAAAAGGTCAGATCTATAGCGGCATTTTT-GAAAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* * * * * *
11003 AAACACCACAAAAGGTTAGATCTATAGTGGCG--TTTGTATTC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* ** * *
11044 TAAAATGCCATAAAAGATCATATCTATAGCGGCGTTTTTGGATAC
1 --AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
* * ** *
11089 AAACGTCGCAAAAGGTCAGATTTATAGTAGCATTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
*
11132 AAATGCCGC
1 AAACGCCGC
11141 TAATTACCAT
Statistics
Matches: 214, Mismatches: 44, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
40 3 0.01
41 4 0.02
42 64 0.30
43 116 0.54
44 20 0.09
45 7 0.03
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
Found at i:13877 original size:40 final size:40
Alignment explanation
Indices: 13822--14003 Score: 133
Period size: 41 Copynumber: 4.5 Consensus size: 40
13812 TATTGCGGCA
13822 TTTTACATAAACGCCACTAAAGTACGCATTTTAGCAGCGT
1 TTTTACATAAACGCCACTAAAGTACGCATTTTAGCAGCGT
* * * * *
13862 TTTTATGA-AAACGCCACTATA-TAATCGGATATTA-C-TCGT
1 TTTTA-CATAAACGCCACTAAAGT-A-CGCATTTTAGCAGCGT
*
13901 TTTTACATAAACGCCACTAAAGTACGCATTTTTAGCAGTGT
1 TTTTACATAAACGCCACTAAAGTACGCA-TTTTAGCAGCGT
* * * * * * * *
13942 TTTCACAAAAATGCCGCTATATA-TTCGGATATT-GCGGCGTT
1 TTTTACATAAACGCCACTA-A-AGTACGCATTTTAGCAGCG-T
13983 TTTTACATAAACGCCACTAAA
1 TTTTACATAAACGCCACTAAA
14004 TTATGAGTTT
Statistics
Matches: 107, Mismatches: 24, Indels: 23
0.69 0.16 0.15
Matches are distributed among these distances:
38 4 0.04
39 27 0.25
40 26 0.24
41 44 0.41
42 5 0.05
43 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.33
Consensus pattern (40 bp):
TTTTACATAAACGCCACTAAAGTACGCATTTTAGCAGCGT
Found at i:13882 original size:80 final size:81
Alignment explanation
Indices: 13773--14065 Score: 292
Period size: 82 Copynumber: 3.6 Consensus size: 81
13763 CACAAGTTTA
* * ** *
13773 TAGCGGCGTTTTTGTAAAAATGCCGCTATATATCTAGTCTATTGCGGC-ATTTTACATAAACGCC
1 TAGCAGCGTTTTTATAAAAATGCCGCTATATATCT-GGATATTGCGGCGTTTTTACATAAACGCC
13837 ACTAAAGTACGCA-TTT
65 ACTAAAGTACGCATTTT
* * * * *
13853 TAGCAGCGTTTTTATGAAAACGCCACTATATAATC-GGATATTAC-TCGTTTTTACATAAACGCC
1 TAGCAGCGTTTTTATAAAAATGCCGCTATAT-ATCTGGATATTGCGGCGTTTTTACATAAACGCC
13916 ACTAAAGTACGCATTTT
65 ACTAAAGTACGCATTTT
* * *
13933 TAGCAGTGTTTTCACAAAAATGCCGCTATATAT-TCGGATATTGCGGCGTTTTTTACATAAACGC
1 TAGCAGCGTTTTTATAAAAATGCCGCTATATATCT-GGATATTGCGGCG-TTTTTACATAAACGC
* *
13997 CACTAAATTATG-AGTTTT
64 CACTAAAGTACGCA-TTTT
* ** * * * **
14015 TAGCGGCGTTTGCACAAAAATGCCACTATATATTTGGATATCACGGCGTTT
1 TAGCAGCGTTTTTATAAAAATGCCGCTATATATCTGGATATTGCGGCGTTT
14066 GTCCAAAAAT
Statistics
Matches: 178, Mismatches: 26, Indels: 17
0.81 0.12 0.08
Matches are distributed among these distances:
78 1 0.01
79 36 0.20
80 62 0.35
81 9 0.05
82 69 0.39
83 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (81 bp):
TAGCAGCGTTTTTATAAAAATGCCGCTATATATCTGGATATTGCGGCGTTTTTACATAAACGCCA
CTAAAGTACGCATTTT
Found at i:14015 original size:82 final size:81
Alignment explanation
Indices: 13822--14065 Score: 314
Period size: 82 Copynumber: 3.0 Consensus size: 81
13812 TATTGCGGCA
* ** * *
13822 TTTTACATAAACGCCACTAAAGTACGCA-TTTTAGCAGCGTTTTTATGAAAACGCCACTATATAA
1 TTTTACATAAACGCCACTAAAGTACGCATTTTTAGCAGCGTTTTCACAAAAATGCCACTATATAT
*
13886 TCGGATATTAC-TCGT
66 TCGGATATTACGGCGT
* *
13901 TTTTACATAAACGCCACTAAAGTACGCATTTTTAGCAGTGTTTTCACAAAAATGCCGCTATATAT
1 TTTTACATAAACGCCACTAAAGTACGCATTTTTAGCAGCGTTTTCACAAAAATGCCACTATATAT
*
13966 TCGGATATTGCGGCGTT
66 TCGGATATTACGGCG-T
* * * *
13983 TTTTACATAAACGCCACTAAATTATG-AGTTTTTAGCGGCGTTTGCACAAAAATGCCACTATATA
1 TTTTACATAAACGCCACTAAAGTACGCA-TTTTTAGCAGCGTTTTCACAAAAATGCCACTATATA
* *
14047 TTTGGATATCACGGCGT
65 TTCGGATATTACGGCGT
14064 TT
1 TT
14066 GTCCAAAAAT
Statistics
Matches: 143, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
79 28 0.20
80 39 0.27
81 6 0.04
82 70 0.49
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (81 bp):
TTTTACATAAACGCCACTAAAGTACGCATTTTTAGCAGCGTTTTCACAAAAATGCCACTATATAT
TCGGATATTACGGCGT
Found at i:17218 original size:73 final size:73
Alignment explanation
Indices: 17095--17241 Score: 233
Period size: 73 Copynumber: 2.0 Consensus size: 73
17085 CTTTACACCG
* * *
17095 AAAACACTTCAGTTGCTCCTGTTTGTTTACCCTCAGTTTTCCTACATGGTCCTTGGCTTTCGTAC
1 AAAACACTTCAGTTGATCCTGTTTGTTTACCCTCAGCTTTCCTACATGGTCCTTGGCTTTCGCAC
17160 CGAGCTTT
66 CGAGCTTT
* *
17168 AAAACAC-TCTAGTTGATCCTGTTTGTTTACCCTCGGCTTTCCTACTTGGTCCTTGGCTTTCGCA
1 AAAACACTTC-AGTTGATCCTGTTTGTTTACCCTCAGCTTTCCTACATGGTCCTTGGCTTTCGCA
17232 CCGAGCTTT
65 CCGAGCTTT
17241 A
1 A
17242 CTTGATTTGT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
72 2 0.03
73 66 0.97
ACGTcount: A:0.16, C:0.28, G:0.17, T:0.39
Consensus pattern (73 bp):
AAAACACTTCAGTTGATCCTGTTTGTTTACCCTCAGCTTTCCTACATGGTCCTTGGCTTTCGCAC
CGAGCTTT
Found at i:22190 original size:29 final size:29
Alignment explanation
Indices: 22134--22192 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
22124 TCCATTATTC
*
22134 TTTTACTCAACAATGTTTAACCGTTCATA
1 TTTTACTCAACAATGTTTAACCGCTCATA
**
22163 TTTTACTCAACAATGTTTAATTGCTCATA
1 TTTTACTCAACAATGTTTAACCGCTCATA
22192 T
1 T
22193 AACTGGCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.44
Consensus pattern (29 bp):
TTTTACTCAACAATGTTTAACCGCTCATA
Found at i:22656 original size:46 final size:46
Alignment explanation
Indices: 22601--22740 Score: 187
Period size: 46 Copynumber: 3.1 Consensus size: 46
22591 TAAATTTAAT
*
22601 TTTTATTTATGGCATTCTTTCATGCCTTAATTCATCCTTTCATGCA
1 TTTTATTTATGGCATTCTTTCATGCCTTAATGCATCCTTTCATGCA
* * *
22647 TTTTATTTATGGCATCCTTTCATGCCTTGATGCATCCTTTCATGCC
1 TTTTATTTATGGCATTCTTTCATGCCTTAATGCATCCTTTCATGCA
* *
22693 TTTTATTTATGGCA-TCATTTCATGCCAATAATGCA-CCTAT-ATGCA
1 TTTTATTTATGGCATTC-TTTCATGCC-TTAATGCATCCTTTCATGCA
22738 TTT
1 TTT
22741 CAGCTATGTC
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
45 8 0.10
46 69 0.83
47 6 0.07
ACGTcount: A:0.21, C:0.22, G:0.11, T:0.46
Consensus pattern (46 bp):
TTTTATTTATGGCATTCTTTCATGCCTTAATGCATCCTTTCATGCA
Found at i:22718 original size:26 final size:26
Alignment explanation
Indices: 22601--22718 Score: 107
Period size: 20 Copynumber: 5.0 Consensus size: 26
22591 TAAATTTAAT
*
22601 TTTTATTTATGGCATTCTTTCATGCC
1 TTTTATTTATGGCATCCTTTCATGCC
* *
22627 --TTA---AT-TCATCCTTTCATGCA
1 TTTTATTTATGGCATCCTTTCATGCC
22647 TTTTATTTATGGCATCCTTTCATGCC
1 TTTTATTTATGGCATCCTTTCATGCC
*
22673 -----TTGAT-GCATCCTTTCATGCC
1 TTTTATTTATGGCATCCTTTCATGCC
*
22693 TTTTATTTATGGCATCATTTCATGCC
1 TTTTATTTATGGCATCCTTTCATGCC
22719 AATAATGCAC
Statistics
Matches: 72, Mismatches: 8, Indels: 24
0.69 0.08 0.23
Matches are distributed among these distances:
20 27 0.38
21 6 0.08
22 3 0.04
24 3 0.04
25 6 0.08
26 27 0.38
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.48
Consensus pattern (26 bp):
TTTTATTTATGGCATCCTTTCATGCC
Found at i:29803 original size:44 final size:45
Alignment explanation
Indices: 29682--29805 Score: 223
Period size: 45 Copynumber: 2.8 Consensus size: 45
29672 TATAAAATCT
*
29682 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTATCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
29727 CTTATCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTATCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
29772 CTTATCA-TTATCCCATAAGCTCGTAAGCTTATTT
1 CTTATCATTTATCCCATAAGCTCGTAAGCTTATTT
29806 GAATGCTTAC
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
44 26 0.34
45 50 0.66
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTATCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:32635 original size:16 final size:16
Alignment explanation
Indices: 32611--32654 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
32601 ATCTATTTTA
*
32611 ATTACTATATTTATAT
1 ATTATTATATTTATAT
32627 ATTATTATATTT-TA-
1 ATTATTATATTTATAT
32641 ATTATT-TA-TTATAT
1 ATTATTATATTTATAT
32655 TTAATAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
12 2 0.08
13 4 0.16
14 6 0.24
15 2 0.08
16 11 0.44
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTATTATATTTATAT
Found at i:32791 original size:8 final size:9
Alignment explanation
Indices: 32774--32840 Score: 51
Period size: 9 Copynumber: 8.1 Consensus size: 9
32764 TCTATTTTAA
32774 TTATTATAT
1 TTATTATAT
32783 TTA-TATA-
1 TTATTATAT
32790 TTATTATAT
1 TTATTATAT
*
32799 TTCAAT-TAT
1 TT-ATTATAT
32808 TTA-T-TA-
1 TTATTATAT
32814 TTATTAGTA-
1 TTATTA-TAT
32823 TTATTATAT
1 TTATTATAT
32832 TTATT-TAT
1 TTATTATAT
32840 T
1 T
32841 ATAATATAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 15
0.76 0.02 0.23
Matches are distributed among these distances:
6 3 0.06
7 7 0.14
8 15 0.30
9 23 0.46
10 2 0.04
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (9 bp):
TTATTATAT
Found at i:32794 original size:16 final size:15
Alignment explanation
Indices: 32773--32843 Score: 67
Period size: 16 Copynumber: 4.6 Consensus size: 15
32763 CTCTATTTTA
32773 ATTATTATATTTATAT
1 ATTATTATATTTA-AT
32789 ATTATTATATTTCAATT
1 ATTATTATATTT-AA-T
*
32806 ATTTATTAT-TATTAGT
1 A-TTATTATAT-TTAAT
32822 ATTATTATATTT-AT
1 ATTATTATATTTAAT
32836 -TTATTATA
1 ATTATTATA
32844 ATATAATTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
13 8 0.17
14 1 0.02
15 9 0.19
16 16 0.33
17 5 0.10
18 9 0.19
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (15 bp):
ATTATTATATTTAAT
Found at i:34045 original size:13 final size:13
Alignment explanation
Indices: 34027--34053 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
34017 CATAGTTGAA
34027 CAGTCTTCATATG
1 CAGTCTTCATATG
34040 CAGTCTTCATATG
1 CAGTCTTCATATG
34053 C
1 C
34054 GCGTCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:37480 original size:19 final size:20
Alignment explanation
Indices: 37456--37493 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
37446 TAACTCGAAA
37456 TTAATTCAAA-TTAAATTTT
1 TTAATTCAAATTTAAATTTT
37475 TTAATTCAAATTTAAATTT
1 TTAATTCAAATTTAAATTT
37494 ACCCGCCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAATTCAAATTTAAATTTT
Found at i:38425 original size:19 final size:18
Alignment explanation
Indices: 38389--38427 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
38379 GTTATAGTTA
*
38389 ATATAAATAAATATATAT
1 ATATAAATAAATAAATAT
38407 ATATAAATTAAATAAATAT
1 ATATAAA-TAAATAAATAT
38426 AT
1 AT
38428 CATATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATAAATAAATAAATAT
Found at i:38464 original size:37 final size:37
Alignment explanation
Indices: 38422--38591 Score: 96
Period size: 42 Copynumber: 4.3 Consensus size: 37
38412 AATTAAATAA
* *
38422 ATATATCATATTTTTAAAATATGTAG-TTT-ATA-TAT
1 ATATAT-ATATTTTTAAAATATATAGTTTTCAAATTAT
*
38457 ATATATATATTATATTGAAAATTTATAGTTTTCAAATTAT
1 ATATATATATT-T-TT-AAAATATATAGTTTTCAAATTAT
* * *
38497 ATATATTATATTTTTAAACATGTA-AATTTTAAAAATACATATT
1 ATATA-TATATTTTTAAA-ATATATAGTTTT-CAAAT---TA-T
* *
38540 ATATATATATATATTAAAAATATATAGTTTTTGATAATATAT
1 ATATATATAT-T-TTTAAAATATATAG-TTTTCA-AAT-TAT
38582 ATATATATAT
1 ATATATATAT
38592 ATATAATATT
Statistics
Matches: 107, Mismatches: 10, Indels: 29
0.73 0.07 0.20
Matches are distributed among these distances:
34 5 0.05
35 7 0.07
36 2 0.02
37 9 0.08
38 11 0.10
39 12 0.11
40 9 0.08
41 6 0.06
42 18 0.17
43 14 0.13
44 7 0.07
45 7 0.07
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (37 bp):
ATATATATATTTTTAAAATATATAGTTTTCAAATTAT
Found at i:38621 original size:38 final size:39
Alignment explanation
Indices: 38538--38626 Score: 101
Period size: 40 Copynumber: 2.3 Consensus size: 39
38528 AAAATACATA
*
38538 TTATATATATATATATTAAAAATATATAGTTTTTGATAAT
1 TTATATATATATATATTAAAAATATATAG-TTATGATAAT
* * * *
38578 ATATATATATATATATATAATATTATATA-TTAT-ATTAT
1 TTATATATATATATAT-TAAAAATATATAGTTATGATAAT
38616 TTATATATATA
1 TTATATATATA
38627 GTTATTCTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
38 14 0.33
39 3 0.07
40 15 0.36
41 10 0.24
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (39 bp):
TTATATATATATATATTAAAAATATATAGTTATGATAAT
Found at i:38642 original size:2 final size:2
Alignment explanation
Indices: 38535--38626 Score: 72
Period size: 2 Copynumber: 48.5 Consensus size: 2
38525 TTAAAAATAC
* * * *
38535 AT AT -T AT AT AT AT AT AT AT -T AA AA AT AT AT AGT TT TT GAT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT AT
38576 AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT AT AT -T AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
38614 AT TT AT AT AT AT A
1 AT AT AT AT AT AT A
38627 GTTATTCTAA
Statistics
Matches: 75, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
1 7 0.09
2 66 0.88
3 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:42548 original size:19 final size:20
Alignment explanation
Indices: 42524--42562 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
42514 CTTTGTATTT
*
42524 TATTTTAAA-TACGTTTTAG
1 TATTTTAAATTAAGTTTTAG
42543 TATTTTAAATTAAGTTTTAG
1 TATTTTAAATTAAGTTTTAG
42563 GATATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (20 bp):
TATTTTAAATTAAGTTTTAG
Found at i:42562 original size:76 final size:75
Alignment explanation
Indices: 42482--42717 Score: 211
Period size: 76 Copynumber: 3.2 Consensus size: 75
42472 TAAACTCAAG
* *
42482 TTTAGGATAATATTTTAAACATTATATTTTATCTTT-G-TATTTTATTTTAAATACGTTTTAGTA
1 TTTAGGATAAT-TTTTAAATATTATATTTTAT-TTTAGATATTTTAGTTTAAATACGTTTTAGTA
*
42545 TTTTAAATTAAGT
64 TTTT-AATTAAGA
** * * *
42558 TTTAGGAT-ATTTTTTTATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATAGGTTTTAGTAT
1 TTTAGGATAATTTTTAAATATTATAT-TTTATTTTAGATATTTTAGTTTAAATACGTTTTAGTAT
*
42622 TTTAATTAGGA
65 TTTAATTAAGA
* * *
42633 TTTAGAATATTGTTTTAAATA-T-TA--TT-TTTTAGGTATTTTAGTTTAAATA-GTTTTTAAGT
1 TTTAGGATAAT-TTTTAAATATTATATTTTATTTTAGATATTTTAGTTTAAATACG-TTTT-AGT
*
42692 ATTTTAATTAGGA
63 ATTTTAATTAAGA
* *
42705 TTTAAGATGATTT
1 TTTAGGATAATTT
42718 AGCTTATTTT
Statistics
Matches: 135, Mismatches: 18, Indels: 19
0.78 0.10 0.11
Matches are distributed among these distances:
70 1 0.01
71 28 0.21
72 25 0.19
74 14 0.10
75 22 0.16
76 38 0.28
77 7 0.05
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (75 bp):
TTTAGGATAATTTTTAAATATTATATTTTATTTTAGATATTTTAGTTTAAATACGTTTTAGTATT
TTAATTAAGA
Found at i:42682 original size:71 final size:73
Alignment explanation
Indices: 42518--42708 Score: 242
Period size: 76 Copynumber: 2.6 Consensus size: 73
42508 TTTTATCTTT
* * * * * * * *
42518 GTATTTTATTTTAAATACGTTTTAGTATTTTAAATTAAGTTTTAGGATATTTTTTTATATTTTAT
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTT-AATTAGGATTTAGAATATTGTTTTAAATATTA-
42583 CTTTGTTTTAG
64 -TTTGTTTTAG
*
42594 ATATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTGTTTTAAATATTA-T
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTGTTTTAAATATTATT
42658 T-TTTTAG
66 TGTTTTAG
*
42665 GTATTTTAGTTTAAATAGTTTTTAAGTATTTTAATTAGGATTTA
1 GTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTA
42709 AGATGATTTA
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
71 27 0.26
72 22 0.21
75 26 0.25
76 28 0.27
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.57
Consensus pattern (73 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTGTTTTAAATATTATT
TGTTTTAG
Found at i:43338 original size:17 final size:16
Alignment explanation
Indices: 43298--43341 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
43288 TCTCTTTAGA
43298 TTATTTATTTAATTAT
1 TTATTTATTTAATTAT
* *
43314 TTCTTTTATTTAATTCT
1 TT-ATTTATTTAATTAT
43331 TATATTTATTT
1 T-TATTTATTT
43342 TAAAAACAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 2 0.09
17 20 0.87
18 1 0.04
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTATTTAATTAT
Found at i:43413 original size:20 final size:20
Alignment explanation
Indices: 43388--43437 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
43378 CTATTATTTA
* *
43388 TTATTTTATTATTTTCCCTT
1 TTATTTTATTATTATCCATT
*
43408 TTA-TTTATTATTATCTATT
1 TTATTTTATTATTATCCATT
43427 TTATTTTATTA
1 TTATTTTATTA
43438 AATATTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTTTATTATTATCCATT
Found at i:43428 original size:19 final size:19
Alignment explanation
Indices: 43379--43437 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
43369 ATTTTACTAC
* *
43379 TATTATTTATTAT-TTTAT
1 TATTATCTATTTTATTTAT
* **
43397 TATTTTCCCTTTTATTTAT
1 TATTATCTATTTTATTTAT
43416 TATTATCTATTTTATTTTAT
1 TATTATCTATTTTA-TTTAT
43436 TA
1 TA
43438 AATATTTTCA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
18 8 0.26
19 16 0.52
20 7 0.23
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTATCTATTTTATTTAT
Found at i:45092 original size:20 final size:20
Alignment explanation
Indices: 45067--45104 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
45057 CACATATTAA
*
45067 AGAATGCATCGACGCACTGT
1 AGAATGCACCGACGCACTGT
*
45087 AGAATGCACCGATGCACT
1 AGAATGCACCGACGCACT
45105 TCAAGGGGAA
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:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (20 bp):
AGAATGCACCGACGCACTGT
Found at i:49496 original size:20 final size:20
Alignment explanation
Indices: 49471--49508 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
49461 CACATATTAA
*
49471 AGAATGCATCGATGCACTGT
1 AGAATGCACCGATGCACTGT
49491 AGAATGCACCGATGCACT
1 AGAATGCACCGATGCACT
49509 TCAAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.21
Consensus pattern (20 bp):
AGAATGCACCGATGCACTGT
Found at i:50612 original size:23 final size:23
Alignment explanation
Indices: 50556--50612 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
50546 AATCTTACAT
* * *
50556 GCACTCCGGTGCATTTCTAGGCG
1 GCACTTCGGTGCAATTCTACGCG
*
50579 GCACTAT-GGTGCAATTCTACGTG
1 GCACT-TCGGTGCAATTCTACGCG
50602 GCACTTCGGTG
1 GCACTTCGGTG
50613 TATTTATATG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 1 0.04
23 27 0.96
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCG
Found at i:60049 original size:19 final size:19
Alignment explanation
Indices: 60006--60049 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
59996 AAATAACCAA
* *
60006 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACACGAACT
*
60025 CAAATTCGCAACATGAACT
1 CAAATTCGCAACACGAACT
*
60044 CCAATT
1 CAAATT
60050 TCACAAATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.30, G:0.11, T:0.23
Consensus pattern (19 bp):
CAAATTCGCAACACGAACT
Found at i:60679 original size:20 final size:20
Alignment explanation
Indices: 60624--60680 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
60614 TCTTGAACTT
* *
60624 AAATTTGCAACTCAAAAATG
1 AAATTCGCAACTCGAAAATG
60644 AAATTCGCAACTCGAAAATG
1 AAATTCGCAACTCGAAAATG
*
60664 AAATTCGCAACACGAAA
1 AAATTCGCAACTCGAAA
60681 TTCGTAATGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.49, C:0.19, G:0.12, T:0.19
Consensus pattern (20 bp):
AAATTCGCAACTCGAAAATG
Found at i:60703 original size:20 final size:21
Alignment explanation
Indices: 60678--60722 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
60668 TCGCAACACG
60678 AAATTCGTAATGCGAAAA-TA
1 AAATTCGTAATGCGAAAACTA
60698 AAATTCGTAATGCGAAAACTA
1 AAATTCGTAATGCGAAAACTA
60719 AAAT
1 AAAT
60723 CGTGTTGCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.24
Consensus pattern (21 bp):
AAATTCGTAATGCGAAAACTA
Found at i:60763 original size:20 final size:20
Alignment explanation
Indices: 60722--60763 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
60712 AAAACTAAAA
* *
60722 TCGTGTTGCGAATTTCATTT
1 TCGTGTTGCGAATTTAAGTT
60742 TCGTGTTGCGAATTTAAGTT
1 TCGTGTTGCGAATTTAAGTT
60762 TC
1 TC
60764 AAAAACTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (20 bp):
TCGTGTTGCGAATTTAAGTT
Found at i:61263 original size:25 final size:25
Alignment explanation
Indices: 61226--61273 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
61216 ATTTGTGTTG
* * * *
61226 CGAATTAATATTCGTGTTTCGAATT
1 CGAAATAAAATTCGCGTTGCGAATT
61251 CGAAATAAAATTCGCGTTGCGAA
1 CGAAATAAAATTCGCGTTGCGAA
61274 AGTAAATGCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (25 bp):
CGAAATAAAATTCGCGTTGCGAATT
Found at i:61407 original size:20 final size:20
Alignment explanation
Indices: 61364--61435 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
61354 AGAAATTCGA
* *
61364 GTTGCGAATTT-CAAAACTGA
1 GTTGCGAATTTGGAAAA-TGT
61384 GTTGCGAATTTGGAAAATGT
1 GTTGCGAATTTGGAAAATGT
* **
61404 GTTGCGAAATTGG-AGTTCGT
1 GTTGCGAATTTGGAAAAT-GT
61424 GTTGCGAATTTG
1 GTTGCGAATTTG
61436 AGATCGCGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
19 2 0.05
20 38 0.86
21 4 0.09
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTTGGAAAATGT
Found at i:61446 original size:19 final size:19
Alignment explanation
Indices: 61404--61454 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
61394 TGGAAAATGT
* * *
61404 GTTGCGAAATTGGAGTTCGT
1 GTTGCG-AATTTGAGATCGC
61424 GTTGCGAATTTGAGATCGC
1 GTTGCGAATTTGAGATCGC
*
61443 GTTGTGAATTTG
1 GTTGCGAATTTG
61455 TTGGTTCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 21 0.78
20 6 0.22
ACGTcount: A:0.20, C:0.10, G:0.33, T:0.37
Consensus pattern (19 bp):
GTTGCGAATTTGAGATCGC
Found at i:61599 original size:15 final size:15
Alignment explanation
Indices: 61563--61600 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
61553 ATAAACAACT
61563 AAATAATATTAGAATA
1 AAATAA-ATTAGAATA
61579 AAATAAATTA-AATAA
1 AAATAAATTAGAAT-A
61594 AAATAAA
1 AAATAAA
61601 ATAATCAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 12 0.57
16 6 0.29
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AAATAAATTAGAATA
Done.