Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008498.1 Hibiscus syriacus cultivar Beakdansim tig00111343_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: 52382
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:11820 original size:2 final size:2
Alignment explanation
Indices: 11815--11855 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
11805 TAACAGTAAG
11815 TA TA TA TA TA TA 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 TA TA TA T
11856 CATTAAAAGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13973 original size:118 final size:118
Alignment explanation
Indices: 13760--13974 Score: 340
Period size: 118 Copynumber: 1.8 Consensus size: 118
13750 GAAAGTTGAT
*
13760 ACTTTGTGACCTCTAAGACCCTAAATAAGAATTAAATAAGCTTTGCTAGCTTTAGGGGAGTGAAT
1 ACTTTGTGACCTCTAAGACCCTAAATAAGAATTAAATAAGCTTTACTAGCTTTAGGGGAGTGAAT
* *
13825 GCTTGAGTTTTGGATGCATTTTTGTGCTCAAAATAGAGAACTTCACTCGATCA
66 GCATGAGTTTTGGATGCATTTTGGTGCTCAAAATAGAGAACTTCACTCGATCA
* * * * *
13878 ACTTTTTGACTTCTAAGACCCTAAATAATAATTAAATAAGTTTTACTAGCTTTAGGTGAGTGAAT
1 ACTTTGTGACCTCTAAGACCCTAAATAAGAATTAAATAAGCTTTACTAGCTTTAGGGGAGTGAAT
* *
13943 GGATGAGTTTTGGATGCATTTTGGTTCTCAAA
66 GCATGAGTTTTGGATGCATTTTGGTGCTCAAA
13975 TAAAGCACTT
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
118 87 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.36
Consensus pattern (118 bp):
ACTTTGTGACCTCTAAGACCCTAAATAAGAATTAAATAAGCTTTACTAGCTTTAGGGGAGTGAAT
GCATGAGTTTTGGATGCATTTTGGTGCTCAAAATAGAGAACTTCACTCGATCA
Found at i:14117 original size:20 final size:19
Alignment explanation
Indices: 14092--14143 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
14082 CCTCAAGGGG
*
14092 TATCGATACTA-TGGGTCCAA
1 TATCGATACTAGAGGGT--AA
14112 TATCGATACTCAGAGGGTAA
1 TATCGATACT-AGAGGGTAA
14132 TATCGATACTAG
1 TATCGATACTAG
14144 TGGAAAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.07
20 22 0.76
21 1 0.03
22 4 0.14
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (19 bp):
TATCGATACTAGAGGGTAA
Found at i:15988 original size:18 final size:18
Alignment explanation
Indices: 15965--16027 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
15955 TTCGTCTCGT
15965 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
15983 AGGACCACTGTATATGTCCCGT
1 AGGACCAC----TATGTCCCGA
*
16005 AGGACCACTATATCCCGA
1 AGGACCACTATGTCCCGA
16023 AGGAC
1 AGGAC
16028 TACTCCTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 21 0.55
22 17 0.45
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.19
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:17673 original size:64 final size:63
Alignment explanation
Indices: 17540--17700 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 63
17530 TAATGAAGGT
* *
17540 ATGCATCGATGCACTACACTATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATAGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATAGGA
* **
17605 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAA-ATTA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTTAATAGGA
* * *
17669 ATGCATCGATGCAGTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
17701 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 59 0.69
65 25 0.29
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATAGGA
Found at i:20999 original size:18 final size:18
Alignment explanation
Indices: 20976--21045 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
20966 TTTAGTATTC
*
20976 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
*
20994 GTCCCGAATGACCACTGTATAT
1 GTCCCGAAGGACCAC----TAT
*
21016 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
*
21034 ATCCCGAAGGAC
1 GTCCCGAAGGAC
21046 TACTCCTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
18 26 0.62
22 16 0.38
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.21
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAT
Found at i:22680 original size:65 final size:65
Alignment explanation
Indices: 22556--22680 Score: 198
Period size: 64 Copynumber: 1.9 Consensus size: 65
22546 TGATGAAGGT
*
22556 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGGG
** *
22621 ATGCATCGATGCACTAC-TTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAA
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTTAA
22681 ATTAATGCAT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
64 29 0.53
65 26 0.47
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (65 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGGG
Found at i:22689 original size:64 final size:64
Alignment explanation
Indices: 22556--22699 Score: 184
Period size: 64 Copynumber: 2.2 Consensus size: 64
22546 TGATGAAGGT
* *
22556 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
** * *
22621 ATGCATCGATGCACTAC-TTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-T
1 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGG
22684 A
64 A
*
22685 ATGCATCCATGCACT
1 ATGCATCGATGCACT
22700 GCATGTGTAT
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 43 0.61
65 24 0.34
66 3 0.04
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:22712 original size:64 final size:63
Alignment explanation
Indices: 22556--22716 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 63
22546 TGATGAAGGT
* * * *
22556 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCCATGCACTACA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* * * *
22621 ATGCATCGATGCACTACTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCCATGCACTACATATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* * *
22685 ATGCATCCATGCACTGCATGTGTATCGATGCA
1 ATGCATCCATGCACTACATATGCATCGATGCA
22717 CCTTAAACAA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 56 0.67
65 24 0.29
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (63 bp):
ATGCATCCATGCACTACATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:23869 original size:25 final size:25
Alignment explanation
Indices: 23840--23892 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
23830 GGTTCCATCT
23840 AAATAA-AATAATAAATAA-AAATTAA
1 AAATAAGAATAA-AAA-AATAAATTAA
*
23865 AAATAAGGATAAAAAAATAAATTAA
1 AAATAAGAATAAAAAAATAAATTAA
23890 AAA
1 AAA
23893 ATTTACTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 2 0.08
25 19 0.76
26 4 0.16
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (25 bp):
AAATAAGAATAAAAAAATAAATTAA
Found at i:23891 original size:12 final size:12
Alignment explanation
Indices: 23858--23919 Score: 54
Period size: 12 Copynumber: 5.0 Consensus size: 12
23848 TAATAAATAA
23858 AAATT-AAAAAT
1 AAATTAAAAAAT
*
23869 AAGGATAAAAAAAT
1 AA--ATTAAAAAAT
23883 AAATTAAAAAAT
1 AAATTAAAAAAT
** *
23895 TTACTAAAAAAT
1 AAATTAAAAAAT
23907 AAAGTTAAAAAAT
1 AAA-TTAAAAAAT
23920 TACCTTGCAG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
11 2 0.05
12 19 0.49
13 10 0.26
14 8 0.21
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (12 bp):
AAATTAAAAAAT
Found at i:27378 original size:22 final size:22
Alignment explanation
Indices: 27346--27402 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
27336 CCGGAAGGGG
* *
27346 GTATCAATACCATAGTATGGTA
1 GTATCAGTACCATACTATGGTA
27368 GTATCAGTACCATACTATGGTA
1 GTATCAGTACCATACTATGGTA
27390 GTATC-GATACCAT
1 GTATCAG-TACCAT
27403 GGTAGGGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 1 0.03
22 31 0.97
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (22 bp):
GTATCAGTACCATACTATGGTA
Found at i:27477 original size:117 final size:117
Alignment explanation
Indices: 27269--27535 Score: 338
Period size: 117 Copynumber: 2.3 Consensus size: 117
27259 ATACTAATGA
* * * *
27269 GGTAGTAACAATACCATGGTAAGGGTATCGATATCAAGCAACATCGAACCTAAAATTGGTATCGA
1 GGTAGTATCGATACCATGGTAGGGGTATCGATATCAAGCAACATCGAACCTAAAATTGGTATCAA
* * * *
27334 TACCGGAAGGGGGTATCAATACCATAGTATGGTAGTATCAG-TACCATACTAT
66 TAACGGAAGGGGGTATCAATACCATAGTAGGGTACTAT-AGATACCATACTAG
* * * * *
27386 GGTAGTATCGATACCATGGTAGGGGTATTGATGTCAGGCCACATCGAATCTAAAATTGGTATCAA
1 GGTAGTATCGATACCATGGTAGGGGTATCGATATCAAGCAACATCGAACCTAAAATTGGTATCAA
* * * * *
27451 TAATGGAAGGGGGTATCGATATCATAGTAGGGTACTATTGATACCATAGTAG
66 TAACGGAAGGGGGTATCAATACCATAGTAGGGTACTATAGATACCATACTAG
* *
27503 GGTACTATCGATACCATGGTAGGGGTGTCGATA
1 GGTAGTATCGATACCATGGTAGGGGTATCGATA
27536 CTAAAGAGCC
Statistics
Matches: 127, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
116 1 0.01
117 126 0.99
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (117 bp):
GGTAGTATCGATACCATGGTAGGGGTATCGATATCAAGCAACATCGAACCTAAAATTGGTATCAA
TAACGGAAGGGGGTATCAATACCATAGTAGGGTACTATAGATACCATACTAG
Found at i:27498 original size:22 final size:22
Alignment explanation
Indices: 27464--27526 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
27454 TGGAAGGGGG
*
27464 TATCGATATCATAGTAGGGTAC
1 TATCGATACCATAGTAGGGTAC
*
27486 TATTGATACCATAGTAGGGTAC
1 TATCGATACCATAGTAGGGTAC
*
27508 TATCGATACCATGGTAGGG
1 TATCGATACCATAGTAGGG
27527 GTGTCGATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (22 bp):
TATCGATACCATAGTAGGGTAC
Found at i:28023 original size:59 final size:58
Alignment explanation
Indices: 27867--28045 Score: 268
Period size: 58 Copynumber: 3.1 Consensus size: 58
27857 ATGGCACTAA
* * * * *
27867 GTGTGTAAAATGCTAAGAAATTTATACTGAGTGTATGAATTTCCGTATTGGGCACTTC
1 GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
* *
27925 GTGTGCAAAATGTTAAGAATTTCATACTAAGTGTATGAATTTTCATATTGGGCACTTC
1 GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
* *
27983 GTGTGCAAAAATGTTAAGAAATTCATACCAAGTGTATGAATTTTCGTAATGGGCACTTC
1 GTGTGC-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
28042 GTGT
1 GTGT
28046 ATGAATTTCC
Statistics
Matches: 109, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
58 57 0.52
59 52 0.48
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (58 bp):
GTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTC
Found at i:28063 original size:28 final size:28
Alignment explanation
Indices: 28014--28069 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
28004 TTCATACCAA
* *
28014 GTGTATGAATTTTCGTAATGGGCACTTC
1 GTGTATGAATTTCCATAATGGGCACTTC
*
28042 GTGTATGAATTTCCATATTGGGCACTTC
1 GTGTATGAATTTCCATAATGGGCACTTC
28070 CTGTGAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.39
Consensus pattern (28 bp):
GTGTATGAATTTCCATAATGGGCACTTC
Found at i:28103 original size:87 final size:87
Alignment explanation
Indices: 27955--28132 Score: 302
Period size: 87 Copynumber: 2.0 Consensus size: 87
27945 TTCATACTAA
* * *
27955 GTGTATGAATTTTCATATTGGGCACTTCGTGTGCAAAAATGTTAAGAAATTCATACCAAGTGTAT
1 GTGTATGAATTTCCATATTGGGCACTTCCTGTGAAAAAATGTTAAGAAATTCATACCAAGTGTAT
28020 GAATTTTCGTAATGGGCACTTC
66 GAATTTTCGTAATGGGCACTTC
*
28042 GTGTATGAATTTCCATATTGGGCACTTCCTGTGAAAAAATGTTAAGAAATTCATACTAAGTGTAT
1 GTGTATGAATTTCCATATTGGGCACTTCCTGTGAAAAAATGTTAAGAAATTCATACCAAGTGTAT
* *
28107 GAATTTTCGTATTGGGCACTTT
66 GAATTTTCGTAATGGGCACTTC
28129 GTGT
1 GTGT
28133 GCAAAACCTT
Statistics
Matches: 85, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (87 bp):
GTGTATGAATTTCCATATTGGGCACTTCCTGTGAAAAAATGTTAAGAAATTCATACCAAGTGTAT
GAATTTTCGTAATGGGCACTTC
Found at i:28166 original size:58 final size:59
Alignment explanation
Indices: 28042--28176 Score: 182
Period size: 58 Copynumber: 2.3 Consensus size: 59
28032 TGGGCACTTC
**
28042 GTGTATGAATTTCCATATTGGGCACTTCCTGTGAAAAAATGTTAAGAAATTCATACTAA
1 GTGTATGAATTTCCATATTGGGCACTTCCTGTGAAAAAACCTTAAGAAATTCATACTAA
* * ** * * *
28101 GTGTATGAATTTTCGTATTGGGCACTTTGTGTG-CAAAACCTTAAGAGATTCATATTAA
1 GTGTATGAATTTCCATATTGGGCACTTCCTGTGAAAAAACCTTAAGAAATTCATACTAA
28159 GTGTATGAATTTCCATAT
1 GTGTATGAATTTCCATAT
28177 GGGAAATGTG
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
58 36 0.55
59 29 0.45
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37
Consensus pattern (59 bp):
GTGTATGAATTTCCATATTGGGCACTTCCTGTGAAAAAACCTTAAGAAATTCATACTAA
Found at i:33976 original size:12 final size:12
Alignment explanation
Indices: 33959--33988 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
33949 GACAAGGACT
33959 TAATTATTAGTA
1 TAATTATTAGTA
*
33971 TAATTATTAGTT
1 TAATTATTAGTA
33983 TAATTA
1 TAATTA
33989 AACTAGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (12 bp):
TAATTATTAGTA
Found at i:36902 original size:6 final size:6
Alignment explanation
Indices: 36885--36928 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
36875 TAATATATAT
* * * *
36885 TAATAA TAATTA TTATTA TAATTA TAATAA TAATTA TTATTA TA
1 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TA
36929 TAAATAACAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATTA
Found at i:36907 original size:12 final size:12
Alignment explanation
Indices: 36890--36928 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
36880 TATATTAATA
36890 ATAATTATTATT
1 ATAATTATTATT
* *
36902 ATAATTATAATA
1 ATAATTATTATT
36914 ATAATTATTATT
1 ATAATTATTATT
36926 ATA
1 ATA
36929 TAAATAACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATAATTATTATT
Found at i:36911 original size:21 final size:23
Alignment explanation
Indices: 36878--36935 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 23
36868 TATTAAATAA
*
36878 TATATATTAATAATAATTATTAT
1 TATATATTAATAATAATAATTAT
36901 TATA-ATT-ATAATAATAATTAT
1 TATATATTAATAATAATAATTAT
*
36922 TATTATATAAATAA
1 TA-TATATTAATAA
36936 CATTAAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 15 0.50
22 5 0.17
23 6 0.20
24 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATATTAATAATAATAATTAT
Found at i:37384 original size:40 final size:39
Alignment explanation
Indices: 37284--37412 Score: 184
Period size: 40 Copynumber: 3.5 Consensus size: 39
37274 GTTGAACAAA
37284 TTCTTCTCATTATGAA--T-TTCTTC-T-TTCAGATGAG
1 TTCTTCTCATTATGAACTTATTCTTCTTCTTCAGATGAG
37318 TTCTTCTCATTATGAA---ATTCTTCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTATTCTTCTTCTTCAGATGAG
*
37354 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTATTCTT-CTTCTTCAGATGAG
37394 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
37413 TCTCTGGAAA
Statistics
Matches: 87, Mismatches: 1, Indels: 8
0.91 0.01 0.08
Matches are distributed among these distances:
34 22 0.25
35 1 0.01
36 26 0.30
39 5 0.06
40 33 0.38
ACGTcount: A:0.20, C:0.21, G:0.10, T:0.49
Consensus pattern (39 bp):
TTCTTCTCATTATGAACTTATTCTTCTTCTTCAGATGAG
Found at i:37415 original size:182 final size:184
Alignment explanation
Indices: 37177--37527 Score: 507
Period size: 182 Copynumber: 1.9 Consensus size: 184
37167 TTGAATAAGC
* * *
37177 TCTTCTTATTATGAACTTTCTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGTAAAG
1 TCTTCTCATTATGAACTTTCTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAA
* * *
37242 GTTGATCCATTAAGTGATGAATTTGAAC-AAAGGTTGAACAAATTCTTCTCATTATGAA-T-TTC
66 GCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTGAACAAACTCTTCTCATTATGAACTCTTC
37304 TT-C-T-TTCAGATGAGTTCTTCTCATTATGAAATTCTTCTTCTTCAGATGAGT
131 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAAATTCTTCTTCTTCAGATGAGT
37355 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAAC-T-TTC-T-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* * * *
37420 AAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACT
62 AAAAGCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTGAACAAACTCTTCTCATTATGAAC-
* *
37485 TCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCT
126 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAATTCT
37528 CTGGAAAAGC
Statistics
Matches: 150, Mismatches: 12, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
178 15 0.10
179 1 0.01
180 3 0.02
181 1 0.01
182 65 0.43
183 28 0.19
185 1 0.01
186 5 0.03
187 1 0.01
188 1 0.01
189 29 0.19
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (184 bp):
TCTTCTCATTATGAACTTTCTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAA
GCTGATCCATCAAGTGATGAATTTGAACAAAAGGTTGAACAAACTCTTCTCATTATGAACTCTTC
TTCCTTCTTCAGATGAGTTCTTCTCATTATGAAATTCTTCTTCTTCAGATGAGT
Found at i:37490 original size:113 final size:113
Alignment explanation
Indices: 37355--38014 Score: 1015
Period size: 113 Copynumber: 5.8 Consensus size: 113
37345 TCAGATGAGT
37355 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
*
37420 AAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
*
37468 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
37532 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
66 AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
*
37580 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAA-TTTCTTCTG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC-TCTG
37644 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
65 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
* *
37693 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTTCTG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC-TCTG
* **
37757 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCATAAGGTTGAACAAAT
65 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
* * *
37806 TCTTCTCATTATGAATTTCTTCTTCCTCCTTCAAGTAATGAGTTCTTCTCATTATGAACTCTAC-
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTC-AG--ATGAGTTCTTCTCATTATGAACT-TTCT
*** * * ** * * **
37870 CTGGAAATTTTAATCCATCACA-TGATGAATTCAAACAAAAGGTTAAACAAAT
62 CTGGAAAAGCTGATCCATCA-AGTGATGGATTTGAGCAAAAGGTTGAACAAGC
37922 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
*
37987 AAAAGTTGATCCATCAAGTGATGGATTT
66 AAAAGCTGATCCATCAAGTGATGGATTT
38015 AAATCTTTGC
Statistics
Matches: 507, Mismatches: 29, Indels: 22
0.91 0.05 0.04
Matches are distributed among these distances:
112 116 0.23
113 293 0.58
114 2 0.00
115 2 0.00
116 91 0.18
117 1 0.00
118 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (113 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGC
Found at i:37601 original size:225 final size:224
Alignment explanation
Indices: 37355--38014 Score: 1018
Period size: 225 Copynumber: 2.9 Consensus size: 224
37345 TCAGATGAGT
37355 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
37420 AAAAGCTGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACT
66 AAAAGCTGATCCATC-AGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACT
37485 TCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAGCTGATCCATCAAG
130 TCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAGCTGATCCATCAAG
*
37550 TGATGGATTTGAGCAAAAGGTTGAACAAGC
195 TGATGGATTTGAGCAAAAGGTTGAACAAAC
*
37580 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAA-TTTCTTCTG
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTC-TCTG
37644 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
65 GAAAAGCTGATCCATC-AGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
*
37709 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTTCTGGAAAAGCTGATCCATCA
129 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTC-TCTGGAAAAGCTGATCCATCA
* *
37774 AGTGATGGATTTGAGCATAAGGTTGAACAAAT
193 AGTGATGGATTTGAGCAAAAGGTTGAACAAAC
* * *
37806 TCTTCTCATTATGAATTTCTTCTTCCTCCTTCAAGTAATGAGTTCTTCTCATTATGAACTCTAC-
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTTC-AG--ATGAGTTCTTCTCATTATGAACT-TTCT
*** * * * ** * * **
37870 CTGGAAATTTTAATCCATCACATGATGAATTCAAACAAAAGGTTAAACAAATTCTTCTCATTATG
62 CTGGAAAAGCTGATCCATCA-GTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATG
* *
37935 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATCCA
126 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC-TTCTCTGGAAAAGCTGATCCA
38000 TCAAGTGATGGATTT
190 TCAAGTGATGGATTT
38015 AAATCTTTGC
Statistics
Matches: 401, Mismatches: 25, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
224 4 0.01
225 164 0.41
226 80 0.20
227 2 0.00
228 1 0.00
229 144 0.36
230 4 0.01
231 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (224 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAAAGCTGATCCATCAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTT
CTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTCTCTGGAAAAGCTGATCCATCAAGT
GATGGATTTGAGCAAAAGGTTGAACAAAC
Found at i:38390 original size:52 final size:52
Alignment explanation
Indices: 38312--38416 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
38302 CAACATGTTA
38312 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
1 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
*
38364 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGTTTTCAC
1 ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
38416 A
1 A
38417 GATATCGATA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37
Consensus pattern (52 bp):
ATTCTGATAACAACTCATCTGATTATGAAGTGATCTTTCAAGATGATTTCAC
Found at i:39020 original size:83 final size:83
Alignment explanation
Indices: 38881--39102 Score: 390
Period size: 83 Copynumber: 2.7 Consensus size: 83
38871 CTGTGGTTCA
*
38881 TACCAAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCC
1 TACCAAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCC
38946 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
* * * *
38964 TACCAAATCAGATCAGATAACTCAAAGAACACTTCTAGAAGATTCTATGAGCACATTATTCTTCC
1 TACCAAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCC
39029 AAATTCAATGATTGATTT
66 AAATTCAATGATTGATTT
*
39047 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
1 TACCAAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACAT
39103 GGCATTTGTT
Statistics
Matches: 131, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 131 1.00
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (83 bp):
TACCAAAACAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTACTCTTCC
AAATTCAATGATTGATTT
Found at i:40483 original size:4 final size:4
Alignment explanation
Indices: 40474--40518 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
40464 TTTTTTCCTT
40474 TTTC TTTC TTT- TTTC TTTTC TTT- TTT- TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
40519 TTCTCTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 9 0.24
4 25 0.66
5 4 0.11
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (4 bp):
TTTC
Found at i:40503 original size:22 final size:23
Alignment explanation
Indices: 40462--40522 Score: 83
Period size: 22 Copynumber: 2.7 Consensus size: 23
40452 CCTTGACCCC
40462 CTTT-TTTTCCTTTTTCTTTCTTT
1 CTTTCTTTT-CTTTTTCTTTCTTT
*
40485 -TTTCTTTTCTTTTTTTTTCTTT
1 CTTTCTTTTCTTTTTCTTTCTTT
40507 CTTTC-TTTCTTTTTCT
1 CTTTCTTTTCTTTTTCT
40523 CTTCAAGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 26 0.76
23 8 0.24
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (23 bp):
CTTTCTTTTCTTTTTCTTTCTTT
Found at i:40521 original size:18 final size:17
Alignment explanation
Indices: 40465--40522 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 17
40455 TGACCCCCTT
*
40465 TTTTTCCTTTTTCTTTC
1 TTTTTCTTTTTTCTTTC
* *
40482 TTTTT-TCTTTTCTTTT
1 TTTTTCTTTTTTCTTTC
40498 TTTTTCTTTCTTTCTTTC
1 TTTTTCTTT-TTTCTTTC
40516 TTTTTCT
1 TTTTTCT
40523 CTTCAAGCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
16 13 0.38
17 7 0.21
18 14 0.41
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTCTTTTTTCTTTC
Found at i:47806 original size:15 final size:15
Alignment explanation
Indices: 47783--47814 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
47773 TGAAATGAAT
47783 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
47798 AATGCATGTATGCAA
1 AATGAATGTATGCAA
47813 AA
1 AA
47815 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Done.