Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003070.1 Hibiscus syriacus cultivar Beakdansim tig00006399_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: 57130
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:9 original size:4 final size:4
Alignment explanation
Indices: 1--132 Score: 236
Period size: 4 Copynumber: 34.0 Consensus size: 4
1 GTAT GTAT GTA- GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
48 GTAT GTAT G-AT GTAT G-AT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
94 GTAT GTAT GTAT GTAT GTAT G-AT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
133 ATATAGTGTA
Statistics
Matches: 124, Mismatches: 0, Indels: 8
0.94 0.00 0.06
Matches are distributed among these distances:
3 12 0.10
4 112 0.90
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:178 original size:14 final size:14
Alignment explanation
Indices: 159--191 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
149 CATGAATAAG
159 GATATGAGTGGTAT
1 GATATGAGTGGTAT
173 GATATGAGTGGTAT
1 GATATGAGTGGTAT
187 GATAT
1 GATAT
192 AATAGTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (14 bp):
GATATGAGTGGTAT
Found at i:738 original size:30 final size:31
Alignment explanation
Indices: 704--766 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
694 TTTAAACAAC
*
704 TATAAAATAATTATT-AATATATTAAACTGT
1 TATAAAATAATTATTCAATATATCAAACTGT
* * *
734 TATAAAATGATTATTCAATTTATCAATCTGT
1 TATAAAATAATTATTCAATATATCAAACTGT
765 TA
1 TA
767 CATATTAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (31 bp):
TATAAAATAATTATTCAATATATCAAACTGT
Found at i:3826 original size:27 final size:28
Alignment explanation
Indices: 3772--3831 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
3762 AGTTTTTTCT
*
3772 CATTATTTTTAATTATATTCATTTTTTA
1 CATTATTTTTAATTATATTCATTATTTA
*
3800 CATTATTTTTAGA-TA-ATTGATTATTTA
1 CATTATTTTTA-ATTATATTCATTATTTA
*
3827 TATTA
1 CATTA
3832 AAAACATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 14 0.50
28 13 0.46
29 1 0.04
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (28 bp):
CATTATTTTTAATTATATTCATTATTTA
Found at i:7946 original size:32 final size:32
Alignment explanation
Indices: 7910--7990 Score: 128
Period size: 32 Copynumber: 2.5 Consensus size: 32
7900 GTTAAAACAG
*
7910 TCACTAGAAGGAACCTAGGCCTTTCAA-AGGAC
1 TCACTAGAAGGAACATAGGCCTTTCAAGA-GAC
7942 TCACTAGAAGGAACATAGGCCTTTCAAGAGAC
1 TCACTAGAAGGAACATAGGCCTTTCAAGAGAC
*
7974 TCACTTGAAGGAACATA
1 TCACTAGAAGGAACATA
7991 TTTTCTAGTG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 45 0.98
33 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.20
Consensus pattern (32 bp):
TCACTAGAAGGAACATAGGCCTTTCAAGAGAC
Found at i:13057 original size:22 final size:22
Alignment explanation
Indices: 13032--13075 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
13022 ATTTAAGATG
13032 ATTTTGTTCAACTTAAAATGTT
1 ATTTTGTTCAACTTAAAATGTT
* *
13054 ATTTTGTTGAATTTAAAATGTT
1 ATTTTGTTCAACTTAAAATGTT
13076 GTGAAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (22 bp):
ATTTTGTTCAACTTAAAATGTT
Found at i:13878 original size:25 final size:24
Alignment explanation
Indices: 13825--13878 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
13815 GAACTAAATG
13825 AATA-TTTTTCAAAATTTATATTT
1 AATATTTTTTCAAAATTTATATTT
* *
13848 ACTATTTTTTCATAATTT-TAATTAT
1 AATATTTTTTCAAAATTTAT-ATT-T
13873 AATATT
1 AATATT
13879 ATTTATGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 4 0.16
24 15 0.60
25 6 0.24
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (24 bp):
AATATTTTTTCAAAATTTATATTT
Found at i:14991 original size:22 final size:20
Alignment explanation
Indices: 14948--14991 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
14938 ACGTTATAAG
* *
14948 TTTTATAAATTTAATGATAA
1 TTTTATAAATTCAATGAAAA
14968 TTTTATAACTATTCAATGAAAA
1 TTTTATAA--ATTCAATGAAAA
14990 TT
1 TT
14992 AATAATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
22 12 0.60
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (20 bp):
TTTTATAAATTCAATGAAAA
Found at i:28741 original size:51 final size:51
Alignment explanation
Indices: 28441--29085 Score: 654
Period size: 51 Copynumber: 12.3 Consensus size: 51
28431 AAGACTCGAA
** * * *
28441 CAATCTTCATA-AAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACT
1 CAATCTTCA-ACAAACTTGTCCGCTCCCTATCCATTCAGAGAGTATAGGACT
** * * * *
28492 CGAACAATCTTCATA-AAACGGGTCCGCTCCCTATCCGTTCAGGGAATATAGAACT
1 ----CAATCTTCA-ACAAACTTGTCCGCTCCCTATCCATTCAGAGAGTATAGGACT
** * *
28547 CGAACGATCTTCAACAAAACGGGTCCGCTCTCTATTCC-TTCAGAGAGTATAGAACT
1 C--A--ATCTTCAAC-AAACTTGTCCGCTCCCTA-TCCATTCAGAGAGTATAGGACT
** * * * *
28603 CGAACAATCTTCATA-AAACGGGTCCGCTCCTTATCCGTTCAGGGAGTATAGAACT
1 ----CAATCTTCA-ACAAACTTGTCCGCTCCCTATCCATTCAGAGAGTATAGGACT
** * * *
28658 CGAACAATCTTCATA-AAACGGGTCCGCTCCCTATCCGTTCAGGGAGTATAGAACT
1 ----CAATCTTCA-ACAAACTTGTCCGCTCCCTATCCATTCAGAGAGTATAGGACT
** * *
28713 CGTTCTTCAATAAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT
1 CAATCTTCAACAAACTTGTCCGCTCCCTATCCATTCAGAGAGTATAGGACT
* *
28764 CAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT
1 CAATCTTCAACAAACTTGTCCGCTCCCTATCCATTCAGAGAGTATAGGACT
* * *
28815 CAATCTTCAACAAACTTGTCCGCTCCCTATTCTTTCAGGGAGTATAGGACT
1 CAATCTTCAACAAACTTGTCCGCTCCCTATCCATTCAGAGAGTATAGGACT
*
28866 CAATCTTCAACAAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT
1 CAATCTTCAACAAACTTGTCCGCTCCCTATCCATTCAGAGAGTATAGGACT
* *
28917 CAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT
1 CAATCTTCAACAAACTTGTCCGCTCCCTATCCATTCAGAGAGTATAGGACT
* *
28968 CAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACT
1 CAATCTTCAACAAACTTGTCCGCTCCCTATCCATTCAGAGAGTATAGGACT
* *
29019 CAATCTTCAACGAACTTGTCCGCTCCCTATTCC-TTCAGAGATTATAGGACT
1 CAATCTTCAACAAACTTGTCCGCTCCCTA-TCCATTCAGAGAGTATAGGACT
*
29070 CAATCTTCAACGAACT
1 CAATCTTCAACAAACT
29086 AATTTGCTTC
Statistics
Matches: 547, Mismatches: 28, Indels: 34
0.90 0.05 0.06
Matches are distributed among these distances:
50 1 0.00
51 349 0.64
52 2 0.00
53 1 0.00
54 4 0.01
55 144 0.26
56 40 0.07
57 4 0.01
58 1 0.00
60 1 0.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (51 bp):
CAATCTTCAACAAACTTGTCCGCTCCCTATCCATTCAGAGAGTATAGGACT
Found at i:28856 original size:153 final size:154
Alignment explanation
Indices: 28458--29085 Score: 735
Period size: 153 Copynumber: 4.0 Consensus size: 154
28448 CATAAAACGG
* *
28458 GTCCGCTCCCTATCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCCC
1 GTCCGCTCCCTATCCATTCAGAGAGTATAGAACT---ACAATCTTCATAAAACGGGTCCGCTCCC
* ** * *
28523 TATCCGTTCAGGGAATATAGAACTCGAACGATCTTCAACAAAACGGGTCCGCTCTCTATTCCTTC
63 TATCCGTTCAGGGAGTATAGAACTC--A--ATCTTCAAC-AAACTTGTCCGCTCCCTATTCATTC
* * **
28588 AGAGAGTATAGAACTCGAACAATCTTCATA-AAACGG
123 AGAGAGTATAGGACT----CAATCTTCA-ACGAACTT
* * *
28624 GTCCGCTCCTTATCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCCC
1 GTCCGCTCCCTATCCATTCAGAGAGTATAGAACT---ACAATCTTCATAAAACGGGTCCGCTCCC
** *
28689 TATCCGTTCAGGGAGTATAGAACTCGTTCTTCAATAAACTTGTCCGCTCCCTATTCATTCAGAGA
63 TATCCGTTCAGGGAGTATAGAACTCAATCTTCAACAAACTTGTCCGCTCCCTATTCATTCAGAGA
28754 GTATAGGACTCAATCTTCAACGAACTT
128 GTATAGGACTCAATCTTCAACGAACTT
* * **
28781 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACT-CAATCTTCA-ACAAACTTGTCCGCTCCCTA
1 GTCCGCTCCCTATCCATTCAGAGAGTATAGAACTACAATCTTCATA-AAACGGGTCCGCTCCCTA
* * *
28844 TTCTTTCAGGGAGTATAGGACTCAATCTTCAACAAACTTGTCCGCTCCCTATTCATTCAGAGAGT
65 TCCGTTCAGGGAGTATAGAACTCAATCTTCAACAAACTTGTCCGCTCCCTATTCATTCAGAGAGT
28909 ATAGGACTCAATCTTCAACGAACTT
130 ATAGGACTCAATCTTCAACGAACTT
* * * **
28934 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACT-CAATCTTCA-ACGAACTTGTCCGCTCCCTA
1 GTCCGCTCCCTATCCATTCAGAGAGTATAGAACTACAATCTTCATA-AAACGGGTCCGCTCCCTA
* * * * * * *
28997 TTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTATTCCTTCAGAGATT
65 TCCGTTCAGGGAGTATAGAACTCAATCTTCAACAAACTTGTCCGCTCCCTATTCATTCAGAGAGT
29062 ATAGGACTCAATCTTCAACGAACT
130 ATAGGACTCAATCTTCAACGAACT
29086 AATTTGCTTC
Statistics
Matches: 428, Mismatches: 32, Indels: 17
0.90 0.07 0.04
Matches are distributed among these distances:
152 1 0.00
153 255 0.60
156 1 0.00
157 41 0.10
161 35 0.08
162 7 0.02
166 88 0.21
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (154 bp):
GTCCGCTCCCTATCCATTCAGAGAGTATAGAACTACAATCTTCATAAAACGGGTCCGCTCCCTAT
CCGTTCAGGGAGTATAGAACTCAATCTTCAACAAACTTGTCCGCTCCCTATTCATTCAGAGAGTA
TAGGACTCAATCTTCAACGAACTT
Found at i:30427 original size:15 final size:14
Alignment explanation
Indices: 30396--30434 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
30386 TGAACCCTCC
* *
30396 TTTTATTTCTCTTT
1 TTTTATTTTTCTCT
30410 TTTTCATTTTTCTCT
1 TTTT-ATTTTTCTCT
30425 TTTTATTTTT
1 TTTTATTTTT
30435 TTTTCATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTATTTTTCTCT
Found at i:30436 original size:17 final size:16
Alignment explanation
Indices: 30396--30466 Score: 56
Period size: 17 Copynumber: 4.4 Consensus size: 16
30386 TGAACCCTCC
*
30396 TTTTATTTCTCTTTTT
1 TTTTTTTTCTCTTTTT
*
30412 TTCATTTTTCTCTTTTT
1 TT-TTTTTTCTCTTTTT
*
30429 ATTTTTTTT-TCATTTT
1 -TTTTTTTTCTCTTTTT
* *
30445 TTTCTCTTCT-TTTTT
1 TTTTTTTTCTCTTTTT
30460 TTATTTT
1 TT-TTTT
30467 ATTTTTCGTT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
15 12 0.29
16 11 0.26
17 17 0.40
18 2 0.05
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTTTCTCTTTTT
Found at i:30446 original size:27 final size:27
Alignment explanation
Indices: 30407--30472 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
30397 TTTATTTCTC
30407 TTTTTTTCA--TTTTTCTCTT-TTTATT
1 TTTTTTTCATTTTTTTCTCTTCTTT-TT
30432 TTTTTTTCATTTTTTTCTCTTCTTTTT
1 TTTTTTTCATTTTTTTCTCTTCTTTTT
30459 TTTATTTT-ATTTTT
1 TTT-TTTTCATTTTT
30473 CGTTTTTTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
25 9 0.24
27 21 0.57
28 7 0.19
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.82
Consensus pattern (27 bp):
TTTTTTTCATTTTTTTCTCTTCTTTTT
Found at i:30461 original size:15 final size:15
Alignment explanation
Indices: 30396--30461 Score: 50
Period size: 15 Copynumber: 4.5 Consensus size: 15
30386 TGAACCCTCC
* *
30396 TTTTATTTCTCTTTT
1 TTTTTTTTCTCTTCT
30411 TTTCATTTTTCTCTT-T
1 TTT--TTTTTCTCTTCT
30427 TTATTTTTT-T-TTC-
1 TT-TTTTTTCTCTTCT
*
30440 ATTTTTTTCTCTTCT
1 TTTTTTTTCTCTTCT
30455 TTTTTTT
1 TTTTTTT
30462 ATTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
12 6 0.15
13 4 0.10
14 4 0.10
15 14 0.34
16 3 0.07
17 10 0.24
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTTTCTCTTCT
Found at i:30494 original size:34 final size:33
Alignment explanation
Indices: 30424--30510 Score: 88
Period size: 34 Copynumber: 2.6 Consensus size: 33
30414 CATTTTTCTC
* * *
30424 TTTTTATTTTTTTTTCATTTTTTTCTCTTCTTT
1 TTTTTATTTTTTTTTCATTTTTTCCTCATCTAT
*
30457 TTTTTATTTTATTTTTCGTTTTTTCCATCATC-AT
1 TTTTTATTTT-TTTTTCATTTTTTCC-TCATCTAT
* *
30491 TTTTTCTTTTTTCTT-ATTTT
1 TTTTTATTTTTTTTTCATTTT
30511 CTCTTTTATT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
32 4 0.09
33 14 0.31
34 23 0.51
35 4 0.09
ACGTcount: A:0.09, C:0.13, G:0.01, T:0.77
Consensus pattern (33 bp):
TTTTTATTTTTTTTTCATTTTTTCCTCATCTAT
Found at i:44294 original size:44 final size:47
Alignment explanation
Indices: 44228--44325 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 47
44218 TTTCGTTTTT
*
44228 TTTTTCGAATAAATGCATGCGAACTAGGTATCATGCGGTTAGG-TTTA
1 TTTTT-GAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
* *
44275 TTTTTGAAT-AA-GCATGCGAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
44320 TTTTTG
1 TTTTTG
44326 TGGATAACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
44 27 0.57
45 11 0.23
46 4 0.09
47 5 0.11
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (47 bp):
TTTTTGAATAAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:53933 original size:15 final size:14
Alignment explanation
Indices: 53913--53969 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 14
53903 TTGCTTGAAG
*
53913 AAGAAATAAAGAGAA
1 AAGAAA-AAAAAGAA
53928 AAGAAAAAAAAGAAA
1 AAGAAAAAAAAG-AA
53943 AAGAAGAAAAAAGAGA
1 AAGAA-AAAAAAGA-A
53959 AA-AAAGAAAAA
1 AAGAAA-AAAAA
53970 TGATGGAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 6 0.16
15 21 0.57
16 10 0.27
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.02
Consensus pattern (14 bp):
AAGAAAAAAAAGAA
Found at i:53940 original size:9 final size:9
Alignment explanation
Indices: 53926--53963 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
53916 AAATAAAGAG
53926 AAAAGAAAA
1 AAAAGAAAA
53935 AAAAGAAAA
1 AAAAGAAAA
*
53944 AGAAGAAAA
1 AAAAGAAAA
*
53953 AAGAGAAAA
1 AAAAGAAAA
53962 AA
1 AA
53964 GAAAAATGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:53952 original size:16 final size:17
Alignment explanation
Indices: 53910--53969 Score: 90
Period size: 16 Copynumber: 3.6 Consensus size: 17
53900 TATTTGCTTG
53910 AAGAAGAAATAAAGAGAA
1 AAGAAGAAA-AAAGAGAA
53928 AAGAA-AAAAAAGA-AA
1 AAGAAGAAAAAAGAGAA
53943 AAGAAGAAAAAAGAGAA
1 AAGAAGAAAAAAGAGAA
53960 AA-AAGAAAAA
1 AAGAAGAAAAA
53970 TGATGGAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.17
16 21 0.52
17 7 0.17
18 5 0.12
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (17 bp):
AAGAAGAAAAAAGAGAA
Found at i:53955 original size:25 final size:25
Alignment explanation
Indices: 53913--54002 Score: 80
Period size: 25 Copynumber: 3.7 Consensus size: 25
53903 TTGCTTGAAG
* *
53913 AAGAAATA-AAGAGAAAAGAAAAAA
1 AAGAAAAAGAAGAAAAAAGAAAAAA
*
53937 AAGAAAAAGAAGAAAAAAGAGAAAA
1 AAGAAAAAGAAGAAAAAAGAAAAAA
* * *
53962 AAGAAAAATGATGGAAAAACG-AAAAG
1 AAGAAAAA-GA-AGAAAAAAGAAAAAA
53988 AA-AAAAAG-AGAAAAA
1 AAGAAAAAGAAGAAAAA
54003 TGGAAAAAGG
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
22 6 0.11
24 8 0.15
25 27 0.49
26 7 0.13
27 7 0.13
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (25 bp):
AAGAAAAAGAAGAAAAAAGAAAAAA
Found at i:53964 original size:9 final size:9
Alignment explanation
Indices: 53914--53969 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
53904 TGCTTGAAGA
53914 AGAAATAAAG
1 AGAAA-AAAG
53924 AG--AAAAG
1 AGAAAAAAG
53931 A-AAAAAA-
1 AGAAAAAAG
53938 AG-AAAAAG
1 AGAAAAAAG
53946 AAGAAAAAAG
1 -AGAAAAAAG
53956 AGAAAAAAG
1 AGAAAAAAG
53965 A-AAAA
1 AGAAAA
53970 TGATGGAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
7 11 0.28
8 9 0.22
9 12 0.30
10 8 0.20
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (9 bp):
AGAAAAAAG
Found at i:54001 original size:15 final size:15
Alignment explanation
Indices: 53913--53961 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 15
53903 TTGCTTGAAG
*
53913 AAGAAATAAAGAGAA
1 AAGAAAAAAAGAGAA
53928 AAGAAAAAAA-AGAAA
1 AAGAAAAAAAGAG-AA
53943 AAGAAGAAAAAAGAGAA
1 AAG-A-AAAAAAGAGAA
53960 AA
1 AA
53962 AAGAAAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 2 0.07
15 14 0.48
16 1 0.03
17 10 0.34
18 2 0.07
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (15 bp):
AAGAAAAAAAGAGAA
Found at i:54033 original size:40 final size:38
Alignment explanation
Indices: 53946--54045 Score: 112
Period size: 40 Copynumber: 2.5 Consensus size: 38
53936 AAAGAAAAAG
* *
53946 AAGAAAAAAGAGAAAAAAGAAAAATGATGGAAAAACGAA
1 AAGAAAAAAGAGAAAAAAGAAAAAGGAAGGAAAAAC-AA
*
53985 AAGAAAAAAAGAGAAAAATGGAAAAAGGAAGGAAAAGA-AA
1 AAG-AAAAAAGAGAAAAA-AGAAAAAGGAAGGAAAA-ACAA
54025 AATGAAAAAAGAGAATAAAAG
1 AA-GAAAAAAGAGAA-AAAAG
54046 GAGGTTCAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
39 3 0.06
40 30 0.58
41 18 0.35
42 1 0.02
ACGTcount: A:0.72, C:0.01, G:0.22, T:0.05
Consensus pattern (38 bp):
AAGAAAAAAGAGAAAAAAGAAAAAGGAAGGAAAAACAA
Found at i:54039 original size:16 final size:15
Alignment explanation
Indices: 53913--54039 Score: 73
Period size: 16 Copynumber: 7.9 Consensus size: 15
53903 TTGCTTGAAG
53913 AAGAAATAAAGAGAAA
1 AAGAAA-AAAGAGAAA
* *
53929 AGAAAAAAAAGAAAAA
1 A-AGAAAAAAGAGAAA
53945 GAAGAAAAAAGAGAAAA
1 -AAGAAAAAAGAG-AAA
*
53962 AAGAAAAATGATGGAAA
1 AAGAAAAAAGA--GAAA
53979 AACGAAAAGAA-A-AAA
1 AA-GAAAA-AAGAGAAA
*
53994 AGAGAAAAATG-GAAA
1 A-AGAAAAAAGAGAAA
54009 AAGGAAGGAAAAGA-AAA
1 AA-GAA--AAAAGAGAAA
*
54026 ATGAAAAAAGAGAA
1 AAGAAAAAAGAGAA
54040 TAAAAGGAGG
Statistics
Matches: 87, Mismatches: 9, Indels: 31
0.69 0.07 0.24
Matches are distributed among these distances:
14 8 0.09
15 18 0.21
16 32 0.37
17 21 0.24
18 7 0.08
19 1 0.01
ACGTcount: A:0.74, C:0.01, G:0.21, T:0.04
Consensus pattern (15 bp):
AAGAAAAAAGAGAAA
Found at i:54044 original size:24 final size:24
Alignment explanation
Indices: 53914--54045 Score: 78
Period size: 24 Copynumber: 5.4 Consensus size: 24
53904 TGCTTGAAGA
* *
53914 AGAAATAAAGAGAAAA-GAAAAAAA
1 AGAAAAAAAGA-AAAATGAAAAAAG
*
53938 AGAAAAAGAAGAAAAAAGAGAAAAA-
1 AGAAAAA-AAGAAAAATGA-AAAAAG
* *
53963 AGAAAAATGATGGAAAAACG--AAAAG
1 AGAAAAA--A-AGAAAAATGAAAAAAG
*
53988 A-AAAAAAGAGAAAAATGGAAAAAG
1 AGAAAAAA-AGAAAAATGAAAAAAG
*
54012 -GAAGGAAAAGAAAAATGAAAAAAG
1 AGAA-AAAAAGAAAAATGAAAAAAG
*
54036 AGAATAAAAG
1 AGAAAAAAAG
54046 GAGGTTCAAG
Statistics
Matches: 88, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
22 8 0.09
24 46 0.52
25 20 0.23
26 7 0.08
27 7 0.08
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.05
Consensus pattern (24 bp):
AGAAAAAAAGAAAAATGAAAAAAG
Found at i:55406 original size:50 final size:51
Alignment explanation
Indices: 55329--55779 Score: 745
Period size: 50 Copynumber: 9.0 Consensus size: 51
55319 GAAGCAAATT
55329 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
55380 AGTTCGTTGAAGA-TGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
55430 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAA-GAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
55480 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATA-GGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
*
55530 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
* * *
55581 AGTTTGTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
55632 AGTT-GTTGAA-ATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
55681 A-TTCGTTGAAGATTGAGTCCTATACTCTCTGAA-GAATAGGGAGCGGACA
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
** ** * * * *
55730 AGTTTATTGAAGAACGAGTTCTATACTCCCTGAACGGATAGGGAGCGGAC
1 AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
55780 CCGTTTTATG
Statistics
Matches: 381, Mismatches: 12, Indels: 14
0.94 0.03 0.03
Matches are distributed among these distances:
48 2 0.01
49 61 0.16
50 203 0.53
51 115 0.30
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.26
Consensus pattern (51 bp):
AGTTCGTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
Found at i:55833 original size:52 final size:54
Alignment explanation
Indices: 55545--55901 Score: 231
Period size: 49 Copynumber: 6.9 Consensus size: 54
55535 GTTGAAGATT
* * * * **
55545 GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACAAGTTTGT-TGAAGA-T-T-
1 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTT-TATGAAGATTGTC
* * * ** *
55596 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACAAGTTGT-TGAA-A-T-T-
1 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTC
* * * * ** *
55645 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGA-CAATTCGT-TGAAGA-T-T-
1 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTT-TTATGAAGATTGTC
* * * ** *
55695 GAGTCCTATACTCTCTGAA-GAATAGGGAGCGGACAAG-TTTATTGAAGA---AC
1 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTA-TGAAGATTGTC
55745 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATG-A-ATTGTTC
1 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTG-TC
55798 GAGTTCTATACTCCCTGAACGGATA-GGAGCGGACCCGTTTTATGAAGATTGTC
1 GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTC
* * * *
55851 GAGTTCTTATACTCCTTGAA-AGAAAGGGAGCAGACCCGTTATT-TGAAGATT
1 GAGTTC-TATACTCCCTGAACGGATAGGGAGCGGACCCGTT-TTATGAAGATT
55902 TTTCAAGTAT
Statistics
Matches: 269, Mismatches: 20, Indels: 31
0.84 0.06 0.10
Matches are distributed among these distances:
48 4 0.01
49 57 0.21
50 52 0.19
51 56 0.21
52 23 0.09
53 38 0.14
54 37 0.14
55 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.27
Consensus pattern (54 bp):
GAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTC
Found at i:55844 original size:103 final size:104
Alignment explanation
Indices: 55394--55890 Score: 310
Period size: 100 Copynumber: 4.9 Consensus size: 104
55384 CGTTGAAGAT
* ** * *
55394 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCGTTGAAGAT-TGAG-TCCTATACT
1 GAGTCCTATACTCCCTGAA-GAATAGGGAGCGGACAAGTTTATTGAAGATACGAGTTCTTATACT
* * ** *
55457 CTCTG-AAGAATAGGGAGCGGACAAGTTCGT-TGAA--GATT-
65 CCCTGAAAGAA-AGGGAGCAGACCCGTT-TTATGAATTG-TTC
* ** * *
55495 GAGTCCTATACTCTCTGAATGAATA-GGAGCGGACAAGTTCGTTGAAGAT-TGAG-TCCTATACT
1 GAGTCCTATACTCCCTGAA-GAATAGGGAGCGGACAAGTTTATTGAAGATACGAGTTCTTATACT
* * **
55557 CTCTGAAAGAATAGGGAGCGGACAAGTTTGT-TGAA--GATT-
65 CCCTGAAAGAA-AGGGAGCAGACCCGTTT-TATGAATTG-TTC
* * *
55596 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACAAG-TTGTTGAA-AT-TGAG-TCCTATACT
1 GAGTCCTATACTCCCTG-AAGAATAGGGAGCGGACAAGTTTATTGAAGATACGAGTTCTTATACT
* * * ** *
55657 CTCTGAATGAATAGGGAGCGGA-CAATTCGT-TGAA--GATT-
65 CCCTGAAAGAA-AGGGAGCAGACCCGTT-TTATGAATTG-TTC
*
55695 GAGTCCTATACTCTCTGAAGAATAGGGAGCGGACAAGTTTATTGAAGA-ACGAGTTC-TATACTC
1 GAGTCCTATACTCCCTGAAGAATAGGGAGCGGACAAGTTTATTGAAGATACGAGTTCTTATACTC
* * *
55758 CCTGAACGGATAGGGAGCGGACCCGTTTTATGAATTGTTC
66 CCTGAA-AGAAAGGGAGCAGACCCGTTTTATGAATTGTTC
* * ** *
55798 GAGTTCTATACTCCCTGAACGGATA-GGAGCGGACCCGTTT-TATGAAGATTGTCGAGTTCTTAT
1 GAGTCCTATACTCCCTGAA-GAATAGGGAGCGGACAAGTTTAT-TGAAGA-T-ACGAGTTCTTAT
*
55861 ACTCCTTGAAAGAAAGGGAGCAGACCCGTT
62 ACTCCCTGAAAGAAAGGGAGCAGACCCGTT
55891 ATTTGAAGAT
Statistics
Matches: 349, Mismatches: 26, Indels: 37
0.85 0.06 0.09
Matches are distributed among these distances:
98 20 0.06
99 35 0.10
100 105 0.30
101 95 0.27
102 17 0.05
103 37 0.11
104 4 0.01
106 24 0.07
107 12 0.03
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (104 bp):
GAGTCCTATACTCCCTGAAGAATAGGGAGCGGACAAGTTTATTGAAGATACGAGTTCTTATACTC
CCTGAAAGAAAGGGAGCAGACCCGTTTTATGAATTGTTC
Found at i:55881 original size:54 final size:55
Alignment explanation
Indices: 55744--55901 Score: 220
Period size: 53 Copynumber: 2.9 Consensus size: 55
55734 TATTGAAGAA
55744 CGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATG-A-ATTGTT
1 CGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTT
55797 CGAGTTCTATACTCCCTGAACGGATA-GGAGCGGACCCGTTTTATGAAGATTG-T
1 CGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTT
* * * *
55850 CGAGTTCTTATACTCCTTGAA-AGAAAGGGAGCAGACCCGTTATT-TGAAGATT
1 CGAGTTC-TATACTCCCTGAACGGATAGGGAGCGGACCCGTT-TTATGAAGATT
55902 TTTCAAGTAT
Statistics
Matches: 96, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
52 19 0.20
53 38 0.40
54 37 0.39
55 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (55 bp):
CGAGTTCTATACTCCCTGAACGGATAGGGAGCGGACCCGTTTTATGAAGATTGTT
Done.