Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010716.1 Corchorus olitorius cultivar O-4 contig10748, 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: 32990
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:1199 original size:16 final size:16
Alignment explanation
Indices: 1178--1208 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1168 CGGGTTTGAG
*
1178 GAAGAAGAAGGGAAAA
1 GAAGAAGAAGAGAAAA
1194 GAAGAAGAAGAGAAA
1 GAAGAAGAAGAGAAA
1209 GAGGGGTGCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (16 bp):
GAAGAAGAAGAGAAAA
Found at i:2756 original size:46 final size:46
Alignment explanation
Indices: 2639--2818 Score: 227
Period size: 46 Copynumber: 3.8 Consensus size: 46
2629 TCTTATCTCT
2639 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCAGTTTTCAATATCTCT-
1 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCAGTTTTC--T-T-T-TA
* * *
2689 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGATTTCTTTTA
1 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCAGTTTTCTTTTA
* * * *
2735 TTCCAAAAACGCCCCTTCCTGGTTGGAAGATCCCCGTTTTCTTTTA
1 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCAGTTTTCTTTTA
**
2781 TTCCAAAAATGCCCCTTCCCCGTCGGAAGGTCCCAGTT
1 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCAGTT
2819 GTCTATCTTT
Statistics
Matches: 116, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
45 1 0.01
46 75 0.65
47 1 0.01
48 1 0.01
50 38 0.33
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.32
Consensus pattern (46 bp):
TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCAGTTTTCTTTTA
Found at i:2828 original size:96 final size:95
Alignment explanation
Indices: 2639--2814 Score: 243
Period size: 96 Copynumber: 1.9 Consensus size: 95
2629 TCTTATCTCT
* *
2639 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCAGTTTTCAATATCTCTTTCCAAAAATGCCCC
1 TTCCAAAAACGCCCCTTCCTGGTCGGAAGATCCCAGTTTTC-ATATCTCTTTCCAAAAATGCCCC
** *
2704 TTCCTGGTTGGAAGGTCCCTGATTTCTTTTA
65 TTCCCCGTCGGAAGGTCCCTGATTTCTTTTA
* *
2735 TTCCAAAAACGCCCCTTCCTGGTTGGAAGATCCCCGTTTTC-T-T-T-TATTCCAAAAATGCCCC
1 TTCCAAAAACGCCCCTTCCTGGTCGGAAGATCCCAGTTTTCATATCTCT-TTCCAAAAATGCCCC
2796 TTCCCCGTCGGAAGGTCCC
65 TTCCCCGTCGGAAGGTCCC
2815 AGTTGTCTAT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
91 1 0.01
92 32 0.44
93 1 0.01
94 1 0.01
96 37 0.51
ACGTcount: A:0.20, C:0.31, G:0.16, T:0.32
Consensus pattern (95 bp):
TTCCAAAAACGCCCCTTCCTGGTCGGAAGATCCCAGTTTTCATATCTCTTTCCAAAAATGCCCCT
TCCCCGTCGGAAGGTCCCTGATTTCTTTTA
Found at i:2918 original size:41 final size:40
Alignment explanation
Indices: 2867--2982 Score: 146
Period size: 40 Copynumber: 2.9 Consensus size: 40
2857 ATTGTTTAAT
* *
2867 TTCCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGC-CTC
1 TTCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTT-CACTA
* * *
2907 TGTCCAATTTGCCCTTCCTCATTGGAAGGTCTTG-TCAGTA
1 T-TCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTCACTA
2947 TTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTT
1 TT-CCAATTTGCCCTTCCTCATCGGAAGGTGTTGTT
2983 TAAATCCCAT
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
39 2 0.03
40 33 0.51
41 30 0.46
ACGTcount: A:0.14, C:0.28, G:0.21, T:0.38
Consensus pattern (40 bp):
TTCCAATTTGCCCTTCCTCATCGGAAGGTGTTGTTCACTA
Found at i:3025 original size:48 final size:47
Alignment explanation
Indices: 2954--3158 Score: 163
Period size: 40 Copynumber: 4.6 Consensus size: 47
2944 GTATTCCCAA
*
2954 TTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAA-TCCCATTCTTCCTAG
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAAAGT-CCATTCTTCC-AG
* * *
3002 TTTGCCCTTCCTCACCAGAAGGTGTTGTTT-AA---C-TT-GT-CGG
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAAAGTCCATTCTTCCAG
* * * *
3042 TTTGCCATT-TTCCATCGGAAGGTGTTGTTTAAAGTCCACTCTTCCCAG
1 TTTGCCCTTCCT-CACCGGAAGGTGTTGTTTAAAGTCCATTCTT-CCAG
*
3090 TTTGCCCTTCCTCACCGGAAGGTGTTGTCT-AA----ATTC--CCAG
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAAAGTCCATTCTTCCAG
* *
3130 TCTGCCCTTCCTCATCGGAAGGTGTTGTT
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTT
3159 CCTTTTCCTT
Statistics
Matches: 128, Mismatches: 19, Indels: 28
0.73 0.11 0.16
Matches are distributed among these distances:
39 1 0.01
40 55 0.43
41 3 0.02
42 1 0.01
43 5 0.04
44 2 0.02
45 1 0.01
46 1 0.01
47 4 0.03
48 54 0.42
49 1 0.01
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (47 bp):
TTTGCCCTTCCTCACCGGAAGGTGTTGTTTAAAGTCCATTCTTCCAG
Found at i:3146 original size:88 final size:88
Alignment explanation
Indices: 2914--3158 Score: 298
Period size: 88 Copynumber: 2.8 Consensus size: 88
2904 CTCTGTCCAA
** * * *
2914 TTTGCCCTTCCTCATTGGAAGGTCTTGTC-AGTATTCCCAATTTGCCCTTCCTCATCGGAAGGTG
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTCTA-AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTG
* *
2978 TTGTTTAAATCCCATTCTTCCTAG
65 TTGTTTAAATCCCACTCTTCCCAG
* * * ** * * *
3002 TTTGCCCTTCCTCACCAGAAGGTGTTGTTTAACTTGTCGGTTTGCCATT-TTCCATCGGAAGGTG
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTTCCT-CATCGGAAGGTG
3066 TTGTTTAAAGT-CCACTCTTCCCAG
65 TTGTTTAAA-TCCCACTCTTCCCAG
*
3090 TTTGCCCTTCCTCACCGGAAGGTGTTGTCTAAATTCCCAGTCTGCCCTTCCTCATCGGAAGGTGT
1 TTTGCCCTTCCTCACCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGT
3155 TGTT
66 TGTT
3159 CCTTTTCCTT
Statistics
Matches: 129, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
87 1 0.01
88 125 0.97
89 3 0.02
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (88 bp):
TTTGCCCTTCCTCACCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGT
TGTTTAAATCCCACTCTTCCCAG
Found at i:5079 original size:17 final size:16
Alignment explanation
Indices: 5059--5098 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
5049 ACCCAAGGAG
*
5059 AAAAGAAACAAAAGAAA
1 AAAAAAAACAAAA-AAA
5076 AAAAAAAACAAAAAAA
1 AAAAAAAACAAAAAAA
5092 AAGAAAA
1 AA-AAAA
5099 GCGCATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (16 bp):
AAAAAAAACAAAAAAA
Found at i:5970 original size:46 final size:46
Alignment explanation
Indices: 5871--6116 Score: 374
Period size: 46 Copynumber: 5.4 Consensus size: 46
5861 AATATTTTTT
* * *
5871 TTAT-TATTTATTCACTATTTATCTATTTATATATT--TTTAACTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTAATTTAACTA
5914 TTATCTATTTATTTACTATTTATCTTTTTATTTATTAATTTAACTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTAATTTAACTA
* *
5960 TTATCTATTTAGTTACTATTTATCTTTTTATTTATTAATTTAATTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTAATTTAACTA
*
6006 TTATCTATTTATTTACTATTTATCTTTTTATTTATTAATTTAATTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTAATTTAACTA
* *
6052 TTATCTATTTATTTACTATTTAT-TTTTTATTTATTCATTTAGCTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTAATTTAACTA
* *
6097 TTATTTATTTATTTATTATT
1 TTATCTATTTATTTACTATT
6117 ATTATTTTTT
Statistics
Matches: 189, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
43 4 0.02
44 28 0.15
45 37 0.20
46 120 0.63
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (46 bp):
TTATCTATTTATTTACTATTTATCTTTTTATTTATTAATTTAACTA
Found at i:6038 original size:19 final size:19
Alignment explanation
Indices: 5886--6084 Score: 76
Period size: 19 Copynumber: 10.3 Consensus size: 19
5876 ATTTATTCAC
* *
5886 TATTTATCTATTTATATATT
1 TATTTA-CTATTTATCTTTT
* *
5906 T-TTAACTA-TTATCTATT
1 TATTTACTATTTATCTTTT
5923 TATTTACTATTTATCTTTT
1 TATTTACTATTTATCTTTT
* *
5942 TATTTATTAATTTAACTATTAT
1 TATTTACT-ATTTATCT-TT-T
5964 CTATTTAGTTACTATTTATCTTTT
1 -TA--T--TTACTATTTATCTTTT
* * *
5988 TATTTATTAATTTA-ATTAT
1 TATTTACT-ATTTATCTTTT
**
6007 TA--T-CTATTTAT-TTAC
1 TATTTACTATTTATCTTTT
*
6022 TATTTATCTTTTTAT-TTATT
1 TATTTA-CTATTTATCTT-TT
* * *
6042 AATTTAAT-TATTATCTATT
1 TATTTACTAT-TTATCTTTT
6061 TATTTACTATTTAT-TTTT
1 TATTTACTATTTATCTTTT
6079 TATTTA
1 TATTTA
6085 TTCATTTAGC
Statistics
Matches: 137, Mismatches: 22, Indels: 42
0.68 0.11 0.21
Matches are distributed among these distances:
15 10 0.07
16 1 0.01
17 11 0.08
18 19 0.14
19 53 0.39
20 20 0.15
21 3 0.02
22 1 0.01
23 4 0.03
24 1 0.01
25 3 0.02
26 7 0.05
27 4 0.03
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (19 bp):
TATTTACTATTTATCTTTT
Found at i:6091 original size:19 final size:19
Alignment explanation
Indices: 5921--6123 Score: 84
Period size: 23 Copynumber: 9.4 Consensus size: 19
5911 CTATTATCTA
*
5921 TTTATTTACT-ATTTATCTT
1 TTTATTTATTCATTTAT-TT
*
5940 TTTATTTATTAATTTAACTATT
1 TTTATTTATTCATTT-A-T-TT
*
5962 ATCTATTTAGTTACTATTTATCTT
1 -TTTATTTA-TT-C-ATTTAT-TT
*
5986 TTTATTTATTAATTTAATTAT
1 TTTATTTATTCATTT-ATT-T
6007 TATCTATTTATTTACTATTTATCTT
1 T-T-TATTTA-TT-C-ATTTAT-TT
*
6032 TTTATTTATTAATTTAATTAT
1 TTTATTTATTCATTT-ATT-T
6053 TATCTATTTATTTACTATTTATTT
1 T-T-TATTTA-TT-C-ATTTATTT
**
6077 TTTATTTATTCATTTAGCT
1 TTTATTTATTCATTTATTT
* *
6096 ATTATTTATTTATTTATTAT
1 TTTATTTATTCATTTATT-T
6116 TATTATTT
1 T-TTATTT
6124 TTTTAGCTAC
Statistics
Matches: 143, Mismatches: 17, Indels: 46
0.69 0.08 0.22
Matches are distributed among these distances:
19 29 0.20
20 16 0.11
21 17 0.12
22 15 0.10
23 33 0.23
24 12 0.08
25 8 0.06
26 13 0.09
ACGTcount: A:0.27, C:0.06, G:0.01, T:0.66
Consensus pattern (19 bp):
TTTATTTATTCATTTATTT
Found at i:6158 original size:24 final size:24
Alignment explanation
Indices: 6131--6189 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
6121 TTTTTTTAGC
*
6131 TACCTATTTATCTA-TTATTCTCTG
1 TACCTATTTATCTATTTA-TCTCTA
6155 TACCTATTTATCTATTTATCTCTA
1 TACCTATTTATCTATTTATCTCTA
6179 TACCTATTTAT
1 TACCTATTTAT
6190 TTTTTTATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
24 30 0.91
25 3 0.09
ACGTcount: A:0.24, C:0.20, G:0.02, T:0.54
Consensus pattern (24 bp):
TACCTATTTATCTATTTATCTCTA
Found at i:6196 original size:24 final size:24
Alignment explanation
Indices: 6131--6197 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
6121 TTTTTTTAGC
* * *
6131 TACCTATTTA-TCTATTATTCTCTG
1 TACCTATTTATTTTTTTA-TCTCTA
* *
6155 TACCTATTTATCTATTTATCTCTA
1 TACCTATTTATTTTTTTATCTCTA
6179 TACCTATTTATTTTTTTAT
1 TACCTATTTATTTTTTTAT
6198 TATTTTATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
24 32 0.91
25 3 0.09
ACGTcount: A:0.22, C:0.18, G:0.01, T:0.58
Consensus pattern (24 bp):
TACCTATTTATTTTTTTATCTCTA
Found at i:10840 original size:21 final size:21
Alignment explanation
Indices: 10811--10860 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
10801 GGAATGGCGA
* **
10811 TGGCTCGGGCATGGCCGGTGG
1 TGGCACGGGCATAACCGGTGG
*
10832 TGGCACGGGCTTAACCGGTGG
1 TGGCACGGGCATAACCGGTGG
10853 TGGCACGG
1 TGGCACGG
10861 TGAATGGGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.10, C:0.24, G:0.48, T:0.18
Consensus pattern (21 bp):
TGGCACGGGCATAACCGGTGG
Found at i:14125 original size:23 final size:23
Alignment explanation
Indices: 14095--14138 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
14085 TTTCCAAAAA
*
14095 AAAAAACGCAAACACAAAAAATT
1 AAAAAACGCAAAAACAAAAAATT
*
14118 AAAAAACGCAAAAATAAAAAA
1 AAAAAACGCAAAAACAAAAAA
14139 AAATTTCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.75, C:0.14, G:0.05, T:0.07
Consensus pattern (23 bp):
AAAAAACGCAAAAACAAAAAATT
Found at i:17745 original size:70 final size:70
Alignment explanation
Indices: 17655--17804 Score: 223
Period size: 70 Copynumber: 2.1 Consensus size: 70
17645 CGATTGCTTT
* * *
17655 GGCTTTTCCACAAGCCAAACTCGTTTCCATATG-AGCTAGTTCAAGCTTTGGTTCCATCCAAGCA
1 GGCTTTTCCACAAGCCAAACTCGTTTCAATACGAAGCAAG-TCAAGCTTTGGTTCCATCCAAGCA
17719 ATC-GAG
65 ATCAG-G
* *
17725 GGCTTTTCCACAAGCCAAACTCGTTTCAATACGAAGCAAGTCAAGCTTTGGTTCCATCCGAGCAT
1 GGCTTTTCCACAAGCCAAACTCGTTTCAATACGAAGCAAGTCAAGCTTTGGTTCCATCCAAGCAA
17790 TCAGG
66 TCAGG
17795 GGCTTTTCCA
1 GGCTTTTCCA
17805 TAAGTGAAGT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
70 67 0.92
71 6 0.08
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.28
Consensus pattern (70 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCAATACGAAGCAAGTCAAGCTTTGGTTCCATCCAAGCAA
TCAGG
Found at i:19888 original size:16 final size:16
Alignment explanation
Indices: 19867--19899 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
19857 GGGTTTGAGG
*
19867 AAGAAGAAGAAGGGAA
1 AAGAAGAAGAAGAGAA
19883 AAGAAGAAGAAGAGAA
1 AAGAAGAAGAAGAGAA
19899 A
1 A
19900 GAGGGGTGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
AAGAAGAAGAAGAGAA
Found at i:21448 original size:46 final size:46
Alignment explanation
Indices: 21329--21508 Score: 236
Period size: 46 Copynumber: 3.8 Consensus size: 46
21319 TCTTATCTCT
* *
21329 TTCCAAAAATGCCCCTTCCTTGTAGGAAGGTCCCAGTTTTCAATATCTCT-
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTC--T-T-T-TA
*
21379 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCTTTTA
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTCTTTTA
* * *
21425 TTCCAAAAACGCCCCTTCATGGTTGGAAGGTCCCCGTTTTCTTTTA
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTCTTTTA
* *
21471 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTT
1 TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTT
21509 GTCTATCTTT
Statistics
Matches: 118, Mismatches: 11, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
45 1 0.01
46 77 0.65
47 1 0.01
48 1 0.01
50 38 0.32
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (46 bp):
TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTCTTTTA
Found at i:21503 original size:92 final size:95
Alignment explanation
Indices: 21329--21504 Score: 243
Period size: 96 Copynumber: 1.9 Consensus size: 95
21319 TCTTATCTCT
* * *
21329 TTCCAAAAATGCCCCTTCCTTGTAGGAAGGTCCCAGTTTTCAATATCTCTTTCCAAAAATGCCCC
1 TTCCAAAAACGCCCCTTCATGGTAGGAAGGTCCCAGTTTTC-ATATCTCTTTCCAAAAATGCCCC
* *
21394 TTCCTGGTTGGAAGGTCCCTGTTTTCTTTTA
65 TTCCCGGTCGGAAGGTCCCTGTTTTCTTTTA
* *
21425 TTCCAAAAACGCCCCTTCATGGTTGGAAGGTCCCCGTTTTC-T-T-T-TATTCCAAAAATGCCCC
1 TTCCAAAAACGCCCCTTCATGGTAGGAAGGTCCCAGTTTTCATATCTCT-TTCCAAAAATGCCCC
21486 TTCCCGGTCGGAAGGTCCC
65 TTCCCGGTCGGAAGGTCCC
21505 AGTTGTCTAT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
91 1 0.01
92 33 0.46
93 1 0.01
94 1 0.01
96 36 0.50
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (95 bp):
TTCCAAAAACGCCCCTTCATGGTAGGAAGGTCCCAGTTTTCATATCTCTTTCCAAAAATGCCCCT
TCCCGGTCGGAAGGTCCCTGTTTTCTTTTA
Found at i:21612 original size:41 final size:41
Alignment explanation
Indices: 21558--21769 Score: 234
Period size: 41 Copynumber: 5.2 Consensus size: 41
21548 TTGTTTAATT
**
21558 TCCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGCCCCTA
1 TCCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGCCTTTA
* * * *
21599 TCCAATTTTCCCTTCCTCATCGGAAGGTATTG-T-CAGTATT-
1 TCCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGC-CT-TTA
* * *
21639 CCCAATTTGCCCTTCCTCATCGGGAGGTGTTTTTGCCTTTG
1 TCCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGCCTTTA
* * * * *
21680 TCCAATTTGCCCTTTCTCATTGGAAGGTGTTGTCAGCATTTA
1 TCCAATTTGCCCTTCCTCATCGGGAGGTGTTGT-TGCCTTTA
*
21722 -CCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGCCTTTG
1 TCCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGCCTTTA
21762 TCCAATTT
1 TCCAATTT
21770 ACCCAATCTG
Statistics
Matches: 138, Mismatches: 26, Indels: 14
0.78 0.15 0.08
Matches are distributed among these distances:
39 1 0.01
40 35 0.25
41 96 0.70
42 6 0.04
ACGTcount: A:0.15, C:0.27, G:0.20, T:0.39
Consensus pattern (41 bp):
TCCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGCCTTTA
Found at i:21654 original size:40 final size:40
Alignment explanation
Indices: 21559--21969 Score: 212
Period size: 41 Copynumber: 9.8 Consensus size: 40
21549 TGTTTAATTT
* **
21559 CCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGCCCCTA-T-
1 CCAATTTGCCCTTCCTCATCGGAAGGTGTTG-T--CAGTATTC
* *
21600 CCAATTTTCCCTTCCTCATCGGAAGGTATTGTCAGTATTC
1 CCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGTATTC
* * * *
21640 CCAATTTGCCCTTCCTCATCGGGAGGTGTTTTTGC-CT-TTGT
1 CCAATTTGCCCTTCCTCATCGGAAGGTG-TTGT-CAGTATT-C
* * * *
21681 CCAATTTGCCCTTTCTCATTGGAAGGTGTTGTCAGCATTTA
1 CCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGTA-TTC
* *
21722 CCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGCCTTTGTCCAATTTAC
1 CCAATTTGCCCTTCCTCATCGGAAGGTGTTG-T--C--AGT---A-TT-C
* * * *
21772 CCAATCTGCCCTTCCCCACCGGAAGGTGTTGT--TTAACTTC
1 CCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGT-A-TTC
* *
21812 CCAATTTGCCCTTCCTCATCGGAAGGTGATAT-TTA-AATT-
1 CCAATTTGCCCTTCCTCATCGGAAGGTG-T-TGTCAGTATTC
* *
21851 CCAGTTCGCCCTTCCTCATCGGAAGGTGTTGTCTAAGGTTACTTTTC
1 CCAATTTGCCCTTCCTCATCGGAAGGTGTTGTC--A-G-TA---TTC
** * * * *
21898 CCAGCTTGCCCTCCCCCACCGGAAGGTGTTGTTTAG-ATTC
1 CCAATTTGCCCTTCCTCATCGGAAGGTGTTG-TCAGTATTC
* *
21938 CCAGTTTGACCTTCCTCATCGGAAGGTGTTGT
1 CCAATTTGCCCTTCCTCATCGGAAGGTGTTGT
21970 TTAAAGCCCA
Statistics
Matches: 289, Mismatches: 49, Indels: 66
0.72 0.12 0.16
Matches are distributed among these distances:
37 1 0.00
38 5 0.02
39 29 0.10
40 89 0.31
41 92 0.32
42 5 0.02
43 3 0.01
44 1 0.00
45 1 0.00
46 4 0.01
47 26 0.09
48 1 0.00
49 5 0.02
50 27 0.09
ACGTcount: A:0.16, C:0.28, G:0.20, T:0.36
Consensus pattern (40 bp):
CCAATTTGCCCTTCCTCATCGGAAGGTGTTGTCAGTATTC
Found at i:21660 original size:81 final size:82
Alignment explanation
Indices: 21555--21757 Score: 302
Period size: 81 Copynumber: 2.5 Consensus size: 82
21545 ATATTGTTTA
*
21555 ATTT-CCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGCCCCTATCCAATTTTCCCTTCCTCAT
1 ATTTACCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGCCCCTATCCAATTTGCCCTTCCTCAT
*
21619 CGGAAGGTATTGTCAGT
66 CGGAAGGTATTGTCAGC
* * ** * *
21636 A-TTCCCAATTTGCCCTTCCTCATCGGGAGGTGTTTTTGCCTTTGTCCAATTTGCCCTTTCTCAT
1 ATTTACCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGCCCCTATCCAATTTGCCCTTCCTCAT
* *
21700 TGGAAGGTGTTGTCAGC
66 CGGAAGGTATTGTCAGC
21717 ATTTACCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGCC
1 ATTTACCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGCC
21758 TTTGTCCAAT
Statistics
Matches: 109, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
80 2 0.02
81 70 0.64
82 37 0.34
ACGTcount: A:0.15, C:0.27, G:0.20, T:0.38
Consensus pattern (82 bp):
ATTTACCAATTTGCCCTTCCTCATCGGGAGGTGTTGTTGCCCCTATCCAATTTGCCCTTCCTCAT
CGGAAGGTATTGTCAGC
Found at i:21970 original size:40 final size:41
Alignment explanation
Indices: 21778--22185 Score: 280
Period size: 40 Copynumber: 9.7 Consensus size: 41
21768 TTACCCAATC
* * *
21778 TGCCCTTCCCCACCGGAAGGTGTTGTTTA-ACTTCCCAATT
1 TGCCCTTCCTCATCGGAAGGTGTTGTTTAGACTTCCCAGTT
* * *
21818 TGCCCTTCCTCATCGGAAGGTGATATTTA-AATT-CCAGTT
1 TGCCCTTCCTCATCGGAAGGTGTTGTTTAGACTTCCCAGTT
* * *
21857 CGCCCTTCCTCATCGGAAGGTGTTGTCTAAGGTTACTTTTCCCAGCT
1 TGCCCTTCCTCATCGGAAGGTGTTGT-TTA-G--AC--TTCCCAGTT
* * *
21904 TGCCCTCCCCCACCGGAAGGTGTTGTTTAGA-TTCCCAGTT
1 TGCCCTTCCTCATCGGAAGGTGTTGTTTAGACTTCCCAGTT
*
21944 TGACCTTCCTCATCGGAAGGTGTTGTTTAAAGCCCATTCTTCCCAGTT
1 TGCCCTTCCTCATCGGAAGGTGTTGTTT--AG---A--CTTCCCAGTT
* *
21992 TGCCCTTCAC-CA-CTGGAAGGTTGTTGTTTA-ACTTCTCGGTT
1 TGCCCTTC-CTCATC-GGAAGG-TGTTGTTTAGACTTCCCAGTT
**
22033 TGCCCTTTTTCATC-GAAGGTGTTGTTTAAAGTCCACTCTTCCCAGTT
1 TGCCCTTCCTCATCGGAAGGTGTTGTTT--AG---A--CTTCCCAGTT
* * * * * *
22080 TGCCCTTTCTCACCAGAAGGTGTTGTCTA-AATTCCCAGTC
1 TGCCCTTCCTCATCGGAAGGTGTTGTTTAGACTTCCCAGTT
* * * * *
22120 TGCCCTTCCTCATTGGAAGGTATTGTCTATA-TT-CCAGTC
1 TGCCCTTCCTCATCGGAAGGTGTTGTTTAGACTTCCCAGTT
22159 TGCCCTTCCTCATCGGAAGGTGTTGTT
1 TGCCCTTCCTCATCGGAAGGTGTTGTT
22186 CCTTTTCCCT
Statistics
Matches: 295, Mismatches: 42, Indels: 63
0.74 0.10 0.16
Matches are distributed among these distances:
39 66 0.22
40 101 0.34
41 19 0.06
42 4 0.01
43 2 0.01
44 1 0.00
45 3 0.01
46 5 0.02
47 49 0.17
48 36 0.12
49 9 0.03
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.36
Consensus pattern (41 bp):
TGCCCTTCCTCATCGGAAGGTGTTGTTTAGACTTCCCAGTT
Found at i:22010 original size:48 final size:45
Alignment explanation
Indices: 21935--22086 Score: 129
Period size: 48 Copynumber: 3.4 Consensus size: 45
21925 GTTGTTTAGA
*
21935 TTCCCAGTTTGACCTTCCTCATCGGAAGGTGTTGTTTAAAGCCCATTC
1 TTCCCAGTTTGCCCTTCC-CAT-GGAAGGTGTTGTTTAAAG-CCATTC
21983 TTCCCAGTTTGCCCTTCACCACTGGAAGGTTGTTGTTT-AA--C-TTC
1 TTCCCAGTTTGCCCTTC-CCA-TGGAAGG-TGTTGTTTAAAGCCATTC
* ** * *
22027 -T--CGGTTTGCCCTTTTTCATCGAAGGTGTTGTTTAAAGTCCACTC
1 TTCCCAGTTTGCCC-TTCCCATGGAAGGTGTTGTTTAAAG-CCATTC
22071 TTCCCAGTTTGCCCTT
1 TTCCCAGTTTGCCCTT
22087 TCTCACCAGA
Statistics
Matches: 85, Mismatches: 7, Indels: 26
0.72 0.06 0.22
Matches are distributed among these distances:
39 8 0.09
40 8 0.09
41 11 0.13
42 2 0.02
43 2 0.02
44 5 0.06
45 2 0.02
46 2 0.02
47 9 0.11
48 26 0.31
49 10 0.12
ACGTcount: A:0.16, C:0.27, G:0.18, T:0.39
Consensus pattern (45 bp):
TTCCCAGTTTGCCCTTCCCATGGAAGGTGTTGTTTAAAGCCATTC
Found at i:22051 original size:88 final size:88
Alignment explanation
Indices: 21808--22145 Score: 319
Period size: 88 Copynumber: 3.9 Consensus size: 88
21798 TGTTGTTTAA
* * * * * * *
21808 CTTCCCAATTTGCCCTTC-CTCATCGGAAGGTGATATTTAAATT-CCAGTTCGCCCTTCCTCATC
1 CTTCCCAGTTTGCCCTTCAC-CACCGGAAGGTGTTGTTTAGATTCCCAGTTTGACCTTCCTCATC
* ***
21871 GGAAGGTGTTGTCT-AAGGTTACT
65 GGAAGGTGTTGTTTAAAGCCCACT
* * * *
21894 TTTCCCAGCTTGCCCTCCCCCACCGGAAGGTGTTGTTTAGATTCCCAGTTTGACCTTCCTCATCG
1 CTTCCCAGTTTGCCCTTCACCACCGGAAGGTGTTGTTTAGATTCCCAGTTTGACCTTCCTCATCG
*
21959 GAAGGTGTTGTTTAAAGCCCATT
66 GAAGGTGTTGTTTAAAGCCCACT
* * * * **
21982 CTTCCCAGTTTGCCCTTCACCACTGGAAGGTTGTTGTTTA-ACTTCTCGGTTTGCCCTTTTTCAT
1 CTTCCCAGTTTGCCCTTCACCACCGGAAGG-TGTTGTTTAGA-TTCCCAGTTTGACCTTCCTCAT
*
22046 C-GAAGGTGTTGTTTAAAGTCCACT
64 CGGAAGGTGTTGTTTAAAGCCCACT
* * * * * * *
22070 CTTCCCAGTTTGCCCTTTC-TCACCAGAAGGTGTTGTCTAAATTCCCAGTCTGCCCTTCCTCATT
1 CTTCCCAGTTTGCCC-TTCACCACCGGAAGGTGTTGTTTAGATTCCCAGTTTGACCTTCCTCATC
*
22134 GGAAGGTATTGT
65 GGAAGGTGTTGT
22146 CTATATTCCA
Statistics
Matches: 206, Mismatches: 38, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
86 33 0.16
87 57 0.28
88 86 0.42
89 30 0.15
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (88 bp):
CTTCCCAGTTTGCCCTTCACCACCGGAAGGTGTTGTTTAGATTCCCAGTTTGACCTTCCTCATCG
GAAGGTGTTGTTTAAAGCCCACT
Found at i:27153 original size:30 final size:31
Alignment explanation
Indices: 27086--27167 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 31
27076 TTAAGTAAAT
*
27086 CCAAAAGAAGATTTTGGAAAATAAGGTAACTC
1 CCAAAAGAAGATTTTGGAAAATAAGATAAC-C
27118 CCAAAAGAAGATTTTGGAAAATAAAGAT-A-C
1 CCAAAAGAAGATTTTGGAAAAT-AAGATAACC
27148 CCAAAAGAAGATTTTGGAAA
1 CCAAAAGAAGATTTTGGAAA
27168 TTAATAAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
30 21 0.44
32 23 0.48
33 4 0.08
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (31 bp):
CCAAAAGAAGATTTTGGAAAATAAGATAACC
Found at i:28997 original size:14 final size:16
Alignment explanation
Indices: 28967--29001 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
28957 GGAAAAAGAA
28967 GATGAGATTTGTGATG
1 GATGAGATTTGTGATG
28983 GATGAG-TTT-TGATG
1 GATGAGATTTGTGATG
28997 GATGA
1 GATGA
29002 AACTTGATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
15 3 0.16
16 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (16 bp):
GATGAGATTTGTGATG
Done.