Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009725.1 Corchorus olitorius cultivar O-4 contig09757, 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: 7847
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Found at i:1683 original size:5 final size:5
Alignment explanation
Indices: 1669--1706 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
1659 AATAAAACAC
* *
1669 CAAAA C-AAA CAAAA CAAAA CAAAC CAAAA CAACA CAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAA
1707 GCAACCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.74, C:0.26, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:2228 original size:40 final size:40
Alignment explanation
Indices: 2184--3047 Score: 404
Period size: 40 Copynumber: 21.0 Consensus size: 40
2174 ATGACGAGGA
*
2184 GGGAATAAGAACAACACCTTCCGATGAGGAAAGGCAAACT
1 GGGAATAAGAACAACACCTTCCGATGAGGAAGGGCAAACT
* * * *
2224 GGGAATTTAG-ACAACACCTTCCGGTGGGGAAGGGAAAACT
1 GGGAA-TAAGAACAACACCTTCCGATGAGGAAGGGCAAACT
* * * * *
2264 GGGAATTTA-AACAACACCTTCTGGTGGGGAAGGGCGAACT
1 GGGAA-TAAGAACAACACCTTCCGATGAGGAAGGGCAAACT
* * * * * *
2304 AGGAATTTA-AATAACACCTTCCGGTGGGGAAGGGCGAACT
1 GGGAA-TAAGAACAACACCTTCCGATGAGGAAGGGCAAACT
* * * * *
2344 AGGTATTTA-AACAACACCTTCCGGTGGGGAAGGGCAAACT
1 -GGGAATAAGAACAACACCTTCCGATGAGGAAGGGCAAACT
* * * * * * *
2384 GGGTATTTA-AAGAACAGCTTCTGGTGGGGAAGGGCAAACT
1 GGG-AATAAGAACAACACCTTCCGATGAGGAAGGGCAAACT
* * * *
2424 AGGTAAAGTAGACTTAGACAACACCTTCCGAT-AGGGAAGGGCGAATT
1 -GG-GAA-TA-A--GA-ACAACACCTTCCGATGA-GGAAGGGCAAACT
* * *
2471 GGGAATTTA-AACAAGACCTTCCGATGAGGAAGCGCAAACT
1 GGGAA-TAAGAACAACACCTTCCGATGAGGAAGGGCAAACT
* * ** * * *
2511 GGGAAATTA-AATAACACCTTCCGGCGGGGAAGGGCAGATT
1 GGG-AATAAGAACAACACCTTCCGATGAGGAAGGGCAAACT
* * *
2551 GGGTAAATTGGACAAAGGCAATAACACCTCCCGATGAGGAAGGGCAAATT
1 GGG--AA-T-----AA-G-AACAACACCTTCCGATGAGGAAGGGCAAACT
*
2601 GGGAATACTG-ACAACACCTTCCGATGAGGAAGGGCAAACT
1 GGGAATA-AGAACAACACCTTCCGATGAGGAAGGGCAAACT
* *
2641 -GGACA-AAGGCAACAACACCTCCCGATGAGGAAGGGCAAATT
1 GGGA-ATAA-G-AACAACACCTTCCGATGAGGAAGGGCAAACT
* *
2682 GGGAA-ATGCTGACAACACCTTCCGATGAGGAAGGGCAAACT
1 GGGAATAAG--AACAACACCTTCCGATGAGGAAGGGCAAACT
* * *
2723 -GGACA-AAGGCAACAACACCTCCCGATGAGGAAGGGTAAATT
1 GGGA-ATAA-G-AACAACACCTTCCGATGAGGAAGGGCAAACT
*
2764 GGGAATTTA-AACAACACCTTCCGATGAGGAAGGGCAAACT
1 GGGAA-TAAGAACAACACCTTCCGATGAGGAAGGGCAAACT
* * * *
2804 -GGACA-AAGACAACAACACCTCCCGATGAAGAAGGGTAAATT
1 GGGA-ATAAG--AACAACACCTTCCGATGAGGAAGGGCAAACT
* ** *
2845 AGGAATGCTG-ACAACACCTTCCGATGAGGAAGGGCAAATT
1 GGGAAT-AAGAACAACACCTTCCGATGAGGAAGGGCAAACT
* * ** * *
2885 GGTAA-ATGCTGGCAACACCTTCCGATGAGGAAAGGCAAATT
1 GGGAATAAG--AACAACACCTTCCGATGAGGAAGGGCAAACT
* * * *
2926 GGTAA-ATGCTGACAACACCTTCCGATGAGGAAGGGCAAATT
1 GGGAATAAG--AACAACACCTTCCGATGAGGAAGGGCAAACT
* * * * * * **
2967 GGCAA-ATGCTGACAACACCTTCCAATAAGGAATGGCAAGTT
1 GGGAATAAG--AACAACACCTTCCGATGAGGAAGGGCAAACT
* * * *
3008 AGGAATTTA-AACAACACCTTCCGGTGGGGAAGGGCAAACT
1 GGGAA-TAAGAACAACACCTTCCGATGAGGAAGGGCAAACT
3048 AGGTATTGTT
Statistics
Matches: 668, Mismatches: 107, Indels: 98
0.77 0.12 0.11
Matches are distributed among these distances:
38 3 0.00
39 10 0.01
40 339 0.51
41 237 0.35
42 14 0.02
43 3 0.00
44 1 0.00
45 3 0.00
46 3 0.00
47 24 0.04
48 2 0.00
50 29 0.04
ACGTcount: A:0.36, C:0.20, G:0.28, T:0.17
Consensus pattern (40 bp):
GGGAATAAGAACAACACCTTCCGATGAGGAAGGGCAAACT
Found at i:2320 original size:80 final size:80
Alignment explanation
Indices: 2193--3047 Score: 437
Period size: 81 Copynumber: 10.4 Consensus size: 80
2183 AGGGAATAAG
* * * *
2193 AACAACACCTTCCGATGAGGAAAGGCAAACTGGGAATTTAGACAACACCTTCCGGTGGGGAAGGG
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
*
2258 AAAACTGGGAATTTA
66 CAAACTGGGAATTTA
* * * *
2273 AACAACACCTTCTGGTGGGGAAGGGCGAACTAGGAATTTAAATAACACCTTCCGGTGGGGAAGGG
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
* * *
2338 CGAACTAGGTATTTA
66 CAAACTGGGAATTTA
* * * *
2353 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGTATTTAAAGAACAGCTTCTGGTGGGGAAGGG
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
*
2418 CAAACTAGGTAAAGTAGACTTA
66 CAAACT-GG----G-A-ATTTA
* * * * * * * * *
2440 GACAACACCTTCCGATAGGGAAGGGCGAATTGGGAATTTAAACAAGACCTTCCGATGAGGAAGCG
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
*
2505 CAAACTGGGAAATTA
66 CAAACTGGGAATTTA
* * * * * * *
2520 AATAACACCTTCCGGCGGGGAAGGGCAGATTGGGTAAATTGGACAAAGGCAATAACACCTCCCGA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGG--AATT---TAAA--C---AACACCTTCCGG
* * *
2585 TGAGGAAGGGCAAATTGGGAATACT-
56 TGGGGAAGGGCAAACTGGGAAT-TTA
* * * * **** * * *
2610 GACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGG
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGG-GAATTTAAACAACACCTTCCGGTGGGGAAGG
* *
2675 GCAAATTGGGAAATGCT-
65 GCAAACTGGG-AAT-TTA
* * * * **** * * *
2692 GACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGG
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGG-GAATTTAAACAACACCTTCCGGTGGGGAAGG
* *
2757 GTAAATTGGGAATTTA
65 GCAAACTGGGAATTTA
* * *** * * **
2773 AACAACACCTTCCGATGAGGAAGGGCAAACT-GGACAAAGACAACAACACCTCCCGATGAAGAAG
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGA-ATTTA-AACAACACCTTCCGGTGGGGAAG
* * * *
2837 GGTAAATTAGGAATGCT-
64 GGCAAACTGGGAAT-TTA
* * * * * * ** * * *
2854 GACAACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCT-GGCAACACCTTCCGATGAGGAAA
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGG-GAAT-TTAAACAACACCTTCCGGTGGGGAAG
* * *
2918 GGCAAATTGGTAAATGCT-
64 GGCAAACTGG-GAAT-TTA
* * * * * * * ** ** *
2936 GACAACACCTTCCGATGAGGAAGGGCAAATTGGCAAATGCT-GACAACACCTTCCAATAAGGAAT
1 AACAACACCTTCCGGTGGGGAAGGGCAAACTGG-GAAT-TTAAACAACACCTTCCGGTGGGGAAG
** *
3000 GGCAAGTTAGGAATTTA
64 GGCAAACTGGGAATTTA
3017 AACAACACCTTCCGGTGGGGAAGGGCAAACT
1 AACAACACCTTCCGGTGGGGAAGGGCAAACT
3048 AGGTATTGTT
Statistics
Matches: 646, Mismatches: 100, Indels: 57
0.80 0.12 0.07
Matches are distributed among these distances:
79 1 0.00
80 168 0.26
81 186 0.29
82 160 0.25
83 1 0.00
84 1 0.00
85 4 0.01
86 4 0.01
87 63 0.10
89 2 0.00
90 55 0.09
91 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.28, T:0.17
Consensus pattern (80 bp):
AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
CAAACTGGGAATTTA
Found at i:2405 original size:120 final size:123
Alignment explanation
Indices: 2193--2803 Score: 444
Period size: 127 Copynumber: 4.9 Consensus size: 123
2183 AGGGAATAAG
* * * *
2193 AACAACACCTTCCGATGAGGAAAGGCAAACTGGGAATTTAGACAACACCTTCCGGTGGGGAAGGG
1 AACAACACCTTCCGATGGGGAAGGGCGAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
* *
2258 AAAACTGGGAATTTAAACAACACCTTCTGGTGGGGAAGGGCGAACTAGG-AA-T-TTA
66 CAAACTGGGAATTTAAACAACACCTTCTGGTGGGGAAGGGCAAACTAGGAAAGTATTA
* * * *
2313 AATAACACCTTCCGGTGGGGAAGGGCGAACTAGGTATTTAAACAACACCTTCCGGTGGGGAAGGG
1 AACAACACCTTCCGATGGGGAAGGGCGAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
* * *
2378 CAAACTGGGTATTTAAAGAACAGCTTCTGGTGGGGAAGGGCAAACTAGGTAAAGTAGACTTA
66 CAAACTGGGAATTTAAACAACACCTTCTGGTGGGGAAGGGCAAACTAGG-AAAGT--A-TTA
* * * * * * *
2440 GACAACACCTTCCGATAGGGAAGGGCGAATTGGGAATTTAAACAAGACCTTCCGATGAGGAAGCG
1 AACAACACCTTCCGATGGGGAAGGGCGAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
* * * * * * * * *
2505 CAAACTGGGAAATTAAATAACACCTTCCGGCGGGGAAGGGCAGATTGGGTAAATTGGA-CA
66 CAAACTGGGAATTTAAACAACACCTTCTGGTGGGGAAGGGCAAACTAGG-AAA--GTATTA
* * * * * * * *
2565 AAGGCAATAACACCTCCCGATGAGGAAGGGCAAATTGGGAATACT-GACAACACCTTCCGATGAG
1 AA--C---AACACCTTCCGATGGGGAAGGGCGAACTGGGAAT-TTAAACAACACCTTCCGGTGGG
* **** * * * * * * **
2629 GAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGGAAA-TGCT-
60 GAAGGGCAAACTGG-GAATTTAAACAACACCTTCTGGTGGGGAAGGGCAAACTAGGAAAGTATTA
* * * * **** * * *
2692 GACAACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGG
1 AACAACACCTTCCGATGGGGAAGGGCGAACTGG-GAATTTAAACAACACCTTCCGGTGGGGAAGG
* * * * *
2757 GTAAATTGGGAATTTAAACAACACCTTCCGATGAGGAAGGGCAAACT
65 GCAAACTGGGAATTTAAACAACACCTTCTGGTGGGGAAGGGCAAACT
2804 GGACAAAGAC
Statistics
Matches: 397, Mismatches: 75, Indels: 36
0.78 0.15 0.07
Matches are distributed among these distances:
120 101 0.25
122 61 0.15
123 32 0.08
125 3 0.01
127 104 0.26
129 1 0.00
130 63 0.16
131 32 0.08
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.17
Consensus pattern (123 bp):
AACAACACCTTCCGATGGGGAAGGGCGAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGG
CAAACTGGGAATTTAAACAACACCTTCTGGTGGGGAAGGGCAAACTAGGAAAGTATTA
Found at i:2666 original size:41 final size:41
Alignment explanation
Indices: 2573--3004 Score: 495
Period size: 41 Copynumber: 10.6 Consensus size: 41
2563 CAAAGGCAAT
* * *
2573 AACACCTCCCGATGAGGAAGGGCAAATTGG-GAATACTGAC
1 AACACCTTCCGATGAGGAAGGGCAAATTGGCAAATGCTGAC
* * *
2613 AACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGC-AAC
1 AACACCTTCCGATGAGGAAGGGCAAATTGG-CAAATGCTGAC
* *
2654 AACACCTCCCGATGAGGAAGGGCAAATTGGGAAATGCTGAC
1 AACACCTTCCGATGAGGAAGGGCAAATTGGCAAATGCTGAC
* * *
2695 AACACCTTCCGATGAGGAAGGGCAAACTGGACAAAGGC-AAC
1 AACACCTTCCGATGAGGAAGGGCAAATTGG-CAAATGCTGAC
* * * * *
2736 AACACCTCCCGATGAGGAAGGGTAAATTGG-GAAT-TTAAAC
1 AACACCTTCCGATGAGGAAGGGCAAATTGGCAAATGCT-GAC
* *
2776 AACACCTTCCGATGAGGAAGGGCAAACTGGACAAA-GAC-AAC
1 AACACCTTCCGATGAGGAAGGGCAAATTGG-CAAATG-CTGAC
* * *
2817 AACACCTCCCGATGAAGAAGGGTAAATTAGG--AATGCTGAC
1 AACACCTTCCGATGAGGAAGGGCAAATT-GGCAAATGCTGAC
* *
2857 AACACCTTCCGATGAGGAAGGGCAAATTGGTAAATGCTGGC
1 AACACCTTCCGATGAGGAAGGGCAAATTGGCAAATGCTGAC
* *
2898 AACACCTTCCGATGAGGAAAGGCAAATTGGTAAATGCTGAC
1 AACACCTTCCGATGAGGAAGGGCAAATTGGCAAATGCTGAC
2939 AACACCTTCCGATGAGGAAGGGCAAATTGGCAAATGCTGAC
1 AACACCTTCCGATGAGGAAGGGCAAATTGGCAAATGCTGAC
* * *
2980 AACACCTTCCAATAAGGAATGGCAA
1 AACACCTTCCGATGAGGAAGGGCAA
3005 GTTAGGAATT
Statistics
Matches: 334, Mismatches: 43, Indels: 29
0.82 0.11 0.07
Matches are distributed among these distances:
39 7 0.02
40 91 0.27
41 224 0.67
42 12 0.04
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (41 bp):
AACACCTTCCGATGAGGAAGGGCAAATTGGCAAATGCTGAC
Found at i:2746 original size:163 final size:161
Alignment explanation
Indices: 2559--3047 Score: 633
Period size: 163 Copynumber: 3.0 Consensus size: 161
2549 TTGGGTAAAT
*
2559 TGGACAAAGGCAATAACACCTCCCGATGAGGAAGGGCAAATTGGGAATACTGACAACACCTTCCG
1 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGGAAT-CTGACAACACCTTCCG
*
2624 ATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGGAAAT
65 ATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTAGG-AAT
2689 GCTGACAACACCTTCCGATGAGGAAGGGCAAAC
129 GCTGACAACACCTTCCGATGAGGAAGGGCAAAC
* * *
2722 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGTAAATTGGGAATTTAAACAACACCTTCCG
1 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGGAATCT-GACAACACCTTCCG
* * *
2787 ATGAGGAAGGGCAAACTGGACAAAGACAACAACACCTCCCGATGAAGAAGGGTAAATTAGGAATG
65 ATGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTAGGAATG
*
2852 CTGACAACACCTTCCGATGAGGAAGGGCAAAT
130 CTGACAACACCTTCCGATGAGGAAGGGCAAAC
* * ** * * *
2884 TGG-TAAATGCTGGCAACACCTTCCGATGAGGAAAGGCAAATTGGTAAATGCTGACAACACCTTC
1 TGGACAAAGGC-AACAACACCTCCCGATGAGGAAGGGCAAATTGG-GAAT-CTGACAACACCTTC
* * * * * * * *
2948 CGATGAGGAAGGGCAAATTGG-CAAATGCTGACAACACCTTCCAATAAGGAATGGCAAGTTAGGA
63 CGATGAGGAAGGGCAAACTGGACAAAGGC-AACAACACCTCCCGATGAGGAAGGGCAAATTAGGA
* * * *
3012 AT-TTAAACAACACCTTCCGGTGGGGAAGGGCAAAC
127 ATGCT-GACAACACCTTCCGATGAGGAAGGGCAAAC
3047 T
1 T
3048 AGGTATTGTT
Statistics
Matches: 285, Mismatches: 35, Indels: 12
0.86 0.11 0.04
Matches are distributed among these distances:
161 5 0.02
162 73 0.26
163 206 0.72
164 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (161 bp):
TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGGAATCTGACAACACCTTCCGA
TGAGGAAGGGCAAACTGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTAGGAATGC
TGACAACACCTTCCGATGAGGAAGGGCAAAC
Found at i:2828 original size:81 final size:81
Alignment explanation
Indices: 2559--3047 Score: 626
Period size: 81 Copynumber: 6.0 Consensus size: 81
2549 TTGGGTAAAT
* *
2559 TGGACAAAGGCAATAACACCTCCCGATGAGGAAGGGCAAATTGGGAATACTGACAACACCTTCCG
1 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGGAATGCTGACAACACCTTCCG
2624 ATGAGGAAGGGCAAAC
66 ATGAGGAAGGGCAAAC
2640 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGGAAATGCTGACAACACCTTCC
1 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGG-AATGCTGACAACACCTTCC
2705 GATGAGGAAGGGCAAAC
65 GATGAGGAAGGGCAAAC
* * *
2722 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGTAAATTGGGAAT-TTAAACAACACCTTCC
1 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGGAATGCT-GACAACACCTTCC
2786 GATGAGGAAGGGCAAAC
65 GATGAGGAAGGGCAAAC
* * * *
2803 TGGACAAAGACAACAACACCTCCCGATGAAGAAGGGTAAATTAGGAATGCTGACAACACCTTCCG
1 TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGGAATGCTGACAACACCTTCCG
*
2868 ATGAGGAAGGGCAAAT
66 ATGAGGAAGGGCAAAC
* * ** * * *
2884 TGG-TAAATGCTGGCAACACCTTCCGATGAGGAAAGGCAAATTGGTAAATGCTGACAACACCTTC
1 TGGACAAAGGC-AACAACACCTCCCGATGAGGAAGGGCAAATTGG-GAATGCTGACAACACCTTC
*
2948 CGATGAGGAAGGGCAAAT
64 CGATGAGGAAGGGCAAAC
* * * * * * * * * *
2966 TGG-CAAATGCTGACAACACCTTCCAATAAGGAATGGCAAGTTAGGAAT-TTAAACAACACCTTC
1 TGGACAAAGGC-AACAACACCTCCCGATGAGGAAGGGCAAATTGGGAATGCT-GACAACACCTTC
* *
3029 CGGTGGGGAAGGGCAAAC
64 CGATGAGGAAGGGCAAAC
3047 T
1 T
3048 AGGTATTGTT
Statistics
Matches: 367, Mismatches: 35, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
80 6 0.02
81 208 0.57
82 153 0.42
ACGTcount: A:0.37, C:0.21, G:0.26, T:0.16
Consensus pattern (81 bp):
TGGACAAAGGCAACAACACCTCCCGATGAGGAAGGGCAAATTGGGAATGCTGACAACACCTTCCG
ATGAGGAAGGGCAAAC
Found at i:4202 original size:50 final size:50
Alignment explanation
Indices: 4103--4235 Score: 189
Period size: 50 Copynumber: 2.7 Consensus size: 50
4093 AAGATTACAC
* * * * * * *
4103 TTTTATTTACAAATT-ACTTAAAA-ACAATTTCTAACTCAAAGGTGGCAT
1 TTTTATTTACAAATTGCCTCAAAATTCAATTTTTTACCCAAAGGTGACAT
4151 TTTTATTTACAAATTGCCTCAAAATTCAATTTTTTACCCAAAGGTGACAT
1 TTTTATTTACAAATTGCCTCAAAATTCAATTTTTTACCCAAAGGTGACAT
4201 TTTTATTTACAAATTGCCTCAAAATTCAATTTTTT
1 TTTTATTTACAAATTGCCTCAAAATTCAATTTTTT
4236 TAACATAAAG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
48 15 0.20
49 6 0.08
50 55 0.72
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (50 bp):
TTTTATTTACAAATTGCCTCAAAATTCAATTTTTTACCCAAAGGTGACAT
Found at i:5180 original size:41 final size:41
Alignment explanation
Indices: 5099--5182 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
5089 GCCTCTTATC
5099 TCACGGTCCTCCCCTTTTCTAATTTTGGTTACCTTTAATTT
1 TCACGGTCCTCCCCTTTTCTAATTTTGGTTACCTTTAATTT
5140 TCACGGTCCTCCCCTTTTCTAATTTTGGTTACCTTTAATTT
1 TCACGGTCCTCCCCTTTTCTAATTTTGGTTACCTTTAATTT
5181 TC
1 TC
5183 TAACAAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.14, C:0.27, G:0.10, T:0.49
Consensus pattern (41 bp):
TCACGGTCCTCCCCTTTTCTAATTTTGGTTACCTTTAATTT
Found at i:6266 original size:20 final size:20
Alignment explanation
Indices: 6241--6280 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6231 AAAGAGCATT
6241 AATTTGCAAATCAAAGGCCC
1 AATTTGCAAATCAAAGGCCC
* *
6261 AATTTGTAAATCAAATGCCC
1 AATTTGCAAATCAAAGGCCC
6281 TTGTATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (20 bp):
AATTTGCAAATCAAAGGCCC
Found at i:7041 original size:26 final size:25
Alignment explanation
Indices: 7012--7093 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 25
7002 CTGGCGCGCG
7012 GCCCAGGCTGCGCTGCCTGCTGGGTA
1 GCCCAGGCTGCGCTGCCTGCTGGG-A
* *
7038 GCCCAGCACTTG-G--GCCTGGCATGCG-
1 GCCCAG-GC-TGCGCTGCCT-GC-TGGGA
7063 GCCCAGGCTGCGCTGCCTGCTGGGCA
1 GCCCAGGCTGCGCTGCCTGCTGGG-A
7089 GCCCA
1 GCCCA
7094 ACGCTTGGGC
Statistics
Matches: 43, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
23 2 0.05
24 5 0.12
25 12 0.28
26 17 0.40
27 5 0.12
28 2 0.05
ACGTcount: A:0.10, C:0.38, G:0.37, T:0.16
Consensus pattern (25 bp):
GCCCAGGCTGCGCTGCCTGCTGGGA
Found at i:7064 original size:51 final size:51
Alignment explanation
Indices: 7000--7121 Score: 181
Period size: 51 Copynumber: 2.4 Consensus size: 51
6990 CTGGCGTTGT
* * *
7000 GCCTGGCGCGCGGCCCAGGCTGCGCTGCCTGCTGGGTAGCCCAGCACTTGG
1 GCCTGGCACGCGGCCCAGGCTGCGCTGCCTGCTGGGCAGCCCAACACTTGG
* *
7051 GCCTGGCATGCGGCCCAGGCTGCGCTGCCTGCTGGGCAGCCCAACGCTTGG
1 GCCTGGCACGCGGCCCAGGCTGCGCTGCCTGCTGGGCAGCCCAACACTTGG
* *
7102 GCCTGGCGCACGGCCCAGGC
1 GCCTGGCACGCGGCCCAGGC
7122 CGCTTGGCCT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.09, C:0.39, G:0.39, T:0.14
Consensus pattern (51 bp):
GCCTGGCACGCGGCCCAGGCTGCGCTGCCTGCTGGGCAGCCCAACACTTGG
Found at i:7192 original size:6 final size:6
Alignment explanation
Indices: 7176--7251 Score: 70
Period size: 6 Copynumber: 12.8 Consensus size: 6
7166 CCAAACCAAA
* *
7176 AAAAAG TAAAAA- AAAAAG AAAAAG AAAAAG -AAAAG -AGAAG GAAAAG
1 AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
*
7222 AAATAAA AAAAAG AAGAAAG -AAAAG AAAAA
1 AAA-AAG AAAAAG AA-AAAG AAAAAG AAAAA
7252 TAGGAGAACA
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
5 18 0.31
6 27 0.46
7 14 0.24
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:7259 original size:20 final size:20
Alignment explanation
Indices: 7185--7272 Score: 81
Period size: 21 Copynumber: 4.2 Consensus size: 20
7175 AAAAAAGTAA
* *
7185 AAAAAAAAGAAAAAGAAAAAG
1 AAAAAAAGGAGAAAG-AAAAG
7206 AAAAGAGAAGGA-AAAGAAATA-
1 AAAA-A-AAGGAGAAAGAAA-AG
*
7227 AAAAAAAGAAGAAAGAAAAG
1 AAAAAAAGGAGAAAGAAAAG
*
7247 AAAAATAGGAGAACAGAAAAG
1 AAAAAAAGGAGAA-AGAAAAG
7268 AAAAA
1 AAAAA
7273 GGAAAGTAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
19 5 0.09
20 19 0.33
21 23 0.40
22 6 0.11
23 4 0.07
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.02
Consensus pattern (20 bp):
AAAAAAAGGAGAAAGAAAAG
Found at i:7264 original size:21 final size:20
Alignment explanation
Indices: 7186--7272 Score: 81
Period size: 20 Copynumber: 4.2 Consensus size: 20
7176 AAAAAGTAAA
7186 AAAAAAAGAA-AAAGAAAA-
1 AAAAAAAGAAGAAAGAAAAG
*
7204 AGAAAAGAGAAGGAAAAGAAATA-
1 A-AAAAAAGAA-G-AAAGAAA-AG
7227 AAAAAAAGAAGAAAGAAAAG
1 AAAAAAAGAAGAAAGAAAAG
* *
7247 AAAAATAGGAGAACAGAAAAG
1 AAAAAAAGAAGAA-AGAAAAG
7268 AAAAA
1 AAAAA
7273 GGAAAGTAAG
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
18 1 0.02
19 9 0.16
20 18 0.31
21 13 0.22
22 15 0.26
23 2 0.03
ACGTcount: A:0.77, C:0.01, G:0.20, T:0.02
Consensus pattern (20 bp):
AAAAAAAGAAGAAAGAAAAG
Done.