Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017923.1 Corchorus olitorius cultivar O-4 contig17956, 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: 21429
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:636 original size:16 final size:15
Alignment explanation
Indices: 615--644 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
605 GTATGAATTC
615 AAATTGATTTCTTGAA
1 AAATTGATTT-TTGAA
631 AAATTGATTTTTGA
1 AAATTGATTTTTGA
645 TTAACTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (15 bp):
AAATTGATTTTTGAA
Found at i:7060 original size:2 final size:2
Alignment explanation
Indices: 7047--7078 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
7037 TGCTTTTCAG
*
7047 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7079 AGTCCTACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8180 original size:19 final size:17
Alignment explanation
Indices: 8156--8207 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 17
8146 AAGTGCACTA
8156 AAAAAAGAGAATAAGAAAG
1 AAAAAAGAGAA-AA-AAAG
*
8175 AAAAAAGAGAAGAAAAG
1 AAAAAAGAGAAAAAAAG
*
8192 AAAAAAAAGAAAAAAA
1 AAAAAAGAGAAAAAAA
8208 ACTAAAGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 18 0.60
18 1 0.03
19 11 0.37
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (17 bp):
AAAAAAGAGAAAAAAAG
Found at i:8192 original size:21 final size:19
Alignment explanation
Indices: 8155--8201 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
8145 CAAGTGCACT
8155 AAAAAAAGAGAATAAGAAA
1 AAAAAAAGAGAATAAGAAA
* *
8174 GAAAAAAGAGAAGAA-AAGA
1 AAAAAAAGAGAATAAGAA-A
8193 AAAAAAAGA
1 AAAAAAAGA
8202 AAAAAAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 2 0.08
19 22 0.92
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (19 bp):
AAAAAAAGAGAATAAGAAA
Found at i:8199 original size:9 final size:9
Alignment explanation
Indices: 8155--8208 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
8145 CAAGTGCACT
8155 AAAAAAAGAG
1 AAAAAAA-AG
*
8165 AATAAGAAAG
1 AA-AAAAAAG
*
8175 AAAAAAGAG
1 AAAAAAAAG
*
8184 -AAGAAAAG
1 AAAAAAAAG
8192 AAAAAAAAG
1 AAAAAAAAG
8201 AAAAAAAA
1 AAAAAAAA
8209 CTAAAGAAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
8 6 0.17
9 20 0.56
10 6 0.17
11 4 0.11
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:9366 original size:22 final size:22
Alignment explanation
Indices: 9331--9373 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
9321 ACCCAGGGTG
**
9331 GTCTATCTTTAGTTAATTTCAA
1 GTCTATCTACAGTTAATTTCAA
*
9353 GTCTATCTACAGTTTATTTCA
1 GTCTATCTACAGTTAATTTCA
9374 GTTGATCTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.16, G:0.09, T:0.49
Consensus pattern (22 bp):
GTCTATCTACAGTTAATTTCAA
Found at i:9408 original size:35 final size:35
Alignment explanation
Indices: 9353--10061 Score: 663
Period size: 35 Copynumber: 20.4 Consensus size: 35
9343 TTAATTTCAA
* * * *
9353 GTCTATCTACAGTTTATTTCAGTTGATCTAGGGCG
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
* * * *
9388 ATCTTTCTTCAGTTAATTTCAGTTGATCCAAGGCG
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
* *
9423 ATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
* * * * *
9458 ATCTTTTCTCCAATTTATTTCAGTTGATCTAGGGCG
1 GTC-TTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
* *
9494 ATCTTTCTTCAGTTTATTTCAGTTGACTCAGGGCG
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
* * *
9529 GTC-TTCCTAAGGTTTATTTCAGTTGACCCAGGGTG
1 GTCTTTCTTCA-GTTTATTTCAGTTGACCCAGGGCG
* * * * *
9564 GTCTTTCTTCAGTTCATTTCAGAATGATCGAGGGTG
1 GTCTTTCTTCAGTTTATTTCAG-TTGACCCAGGGCG
* * * * *
9600 GTCATTCTTCAGCTAATTTCAGTTGACCTAGGGTG
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
* *
9635 GTCTTCCTT-AGTTTATTTCAGTTGACCCAGGGTG
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
* * * * *
9669 GTCTTTCTTCAGTTTATTTCTGAATGATCGAGGGTG
1 GTCTTTCTTCAGTTTATTTCAG-TTGACCCAGGGCG
* *
9705 GTCGTTCTTCAGCTTATTTCAGTTGACCCAGGGCG
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
*
9740 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTG
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
* * *
9775 GTCTTTCTTCAGTTTATTCCAGTTGACCCAGGACA
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
* *
9810 ATCCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTG
1 GT-CTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
* * *
9846 GTCTTTCTTCAGTTTATTCCAGTTGACCCAGGACA
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
* * * *
9881 ATCCTTTCTTCAATTTATTTCTGTTGACCCAGGGTG
1 GT-CTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
**
9917 G----TC-T---TTT-TTT-AGTTGACCCAGGATG
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
* *
9942 GTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTG
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
** * * *
9977 GTCTTTTCTTCAGTTTAGGTCAGAATGATCGC-GGGTG
1 GTC-TTTCTTCAGTTTATTTCAG-TTGA-CCCAGGGCG
* *
10014 GTCGTTCTTCAGTTTA-TTCAGTTGACCCAGGGTG
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
10048 GTCCTTTCTTCAGT
1 GT-CTTTCTTCAGT
10062 ATATGTCGGA
Statistics
Matches: 562, Mismatches: 89, Indels: 46
0.81 0.13 0.07
Matches are distributed among these distances:
25 14 0.02
26 3 0.01
27 3 0.01
29 2 0.00
30 2 0.00
31 2 0.00
33 5 0.01
34 48 0.09
35 290 0.52
36 181 0.32
37 11 0.02
38 1 0.00
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (35 bp):
GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCG
Found at i:9502 original size:71 final size:70
Alignment explanation
Indices: 9353--10061 Score: 699
Period size: 71 Copynumber: 10.2 Consensus size: 70
9343 TTAATTTCAA
* * * * * *
9353 GTCTATCTACAGTTTATTTCAGTTGATCTAGGGCGATCTTTCTTCAGTTAATTTCAGTTGATCCA
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCCA
* *
9418 AGGCG
66 GGGTG
* * * * * *
9423 ATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTCCAATTTATTTCAGTTGATCT
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGATC-TTTCTTCAGTTTATTTCAGTTGACCC
*
9488 AGGGCG
65 AGGGTG
* * * * *
9494 ATCTTTCTTCAGTTTATTTCAGTTGACTCAGGGCGGTC-TTCCTAAGGTTTATTTCAGTTGACCC
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCTTTCTTCA-GTTTATTTCAGTTGACCC
9558 AGGGTG
65 AGGGTG
* * * * * * * * * *
9564 GTCTTTCTTCAGTTCATTTCAGAATGATCGAGGGTGGTCATTCTTCAGCTAATTTCAGTTGACCT
1 GTCTTTCTTCAGTTTATTTCAG-TTGACCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCC
9629 AGGGTG
65 AGGGTG
* * * * * * *
9635 GTCTTCCTT-AGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTATTTCTGAATGATCG
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCTTTCTTCAGTTTATTTCAG-TTGACCC
9699 AGGGTG
65 AGGGTG
* * *
9705 GTCGTTCTTCAGCTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCA
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCCA
9770 GGGTG
66 GGGTG
* * *
9775 GTCTTTCTTCAGTTTATTCCAGTTGACCCAGGACAATCCTTTCTTCAGTTTATTTCAGTTGACCC
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGAT-CTTTCTTCAGTTTATTTCAGTTGACCC
9840 AGGGTG
65 AGGGTG
* * * * *
9846 GTCTTTCTTCAGTTTATTCCAGTTGACCCAGGACAATCCTTTCTTCAATTTATTTCTGTTGACCC
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGAT-CTTTCTTCAGTTTATTTCAGTTGACCC
9911 AGGGTG
65 AGGGTG
** * *
9917 G----TC-T---TTT-TTT-AGTTGACCCAGGATGGTCTTTCTTCAGTTTATTTCAGTTGATCCA
1 GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCCA
9972 GGGTG
66 GGGTG
** * * * * *
9977 GTCTTTTCTTCAGTTTAGGTCAGAATGATCGC-GGGTGGTCGTTCTTCAGTTTA-TTCAGTTGAC
1 GTC-TTTCTTCAGTTTATTTCAG-TTGA-CCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGAC
10040 CCAGGGTG
63 CCAGGGTG
10048 GTCCTTTCTTCAGT
1 GT-CTTTCTTCAGT
10062 ATATGTCGGA
Statistics
Matches: 545, Mismatches: 73, Indels: 41
0.83 0.11 0.06
Matches are distributed among these distances:
60 31 0.06
61 14 0.03
62 2 0.00
63 3 0.01
65 2 0.00
66 2 0.00
67 2 0.00
69 35 0.06
70 144 0.26
71 280 0.51
72 28 0.05
73 2 0.00
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (70 bp):
GTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCCA
GGGTG
Found at i:9550 original size:106 final size:105
Alignment explanation
Indices: 9353--10061 Score: 706
Period size: 106 Copynumber: 6.8 Consensus size: 105
9343 TTAATTTCAA
* * * * *
9353 GTCTATCTACAGTTTATTTCAGTTGATCTAGGGCGATCTTTCTTCAGTTAATTTCAGTTGATCCA
1 GTCTTTCTTCAGTTTATTTCAGTTGATCGAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCCA
* * * *
9418 AGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG
66 GGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTG
* * * * *
9458 ATCTTTTCTCCAATTTATTTCAGTTGATCTAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACTC
1 GTC-TTTCTTCAGTTTATTTCAGTTGATCGAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCC
* *
9523 AGGGCGGTC-TTCCTAAGGTTTATTTCAGTTGACCCAGGGTG
65 AGGGCGGTCTTTCTTCA-GTTTATTTCAGTTGACCCAGGGTG
* * * * * * * *
9564 GTCTTTCTTCAGTTCATTTCAGAATGATCGAGGGTGGTCATTCTTCAGCTAATTTCAGTTGACCT
1 GTCTTTCTTCAGTTTATTTCAG-TTGATCGAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCC
* *
9629 AGGGTGGTCTTCCTT-AGTTTATTTCAGTTGACCCAGGGTG
65 AGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTG
* * * * * *
9669 GTCTTTCTTCAGTTTATTTCTGAATGATCGAGGGTGGTCGTTCTTCAGCTTATTTCAGTTGACCC
1 GTCTTTCTTCAGTTTATTTCAG-TTGATCGAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCC
9734 AGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTG
65 AGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTG
* * * * *
9775 GTCTTTCTTCAGTTTATTCCAGTTGACCCAGGACAATCCTTTCTTCAGTTTATTTCAGTTGACCC
1 GTCTTTCTTCAGTTTATTTCAGTTGATCGAGGGCGAT-CTTTCTTCAGTTTATTTCAGTTGACCC
* * ***
9840 AGGGTGGTCTTTCTTCAGTTTATTCCAGTTGACCCAGGACA
65 AGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTG
* * * * * **
9881 ATCCTTTCTTCAATTTATTTCTGTTGACCCA-GG-G-T-GGTC-T---TTT-TTT-AGTTGACCC
1 GT-CTTTCTTCAGTTTATTTCAGTTGATCGAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCC
** *
9936 AGGATGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTG
65 AGGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTG
** * * * * *
9977 GTCTTTTCTTCAGTTTAGGTCAGAATGATCGCGGGTGGTCGTTCTTCAGTTTA-TTCAGTTGACC
1 GTC-TTTCTTCAGTTTATTTCAG-TTGATCGAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACC
*
10041 CAGGGTGGTCCTTTCTTCAGT
64 CAGGGCGGT-CTTTCTTCAGT
10062 ATATGTCGGA
Statistics
Matches: 507, Mismatches: 77, Indels: 38
0.82 0.12 0.06
Matches are distributed among these distances:
95 1 0.00
96 60 0.12
97 7 0.01
98 5 0.01
99 1 0.00
100 1 0.00
101 4 0.01
102 3 0.01
104 1 0.00
105 133 0.26
106 252 0.50
107 39 0.08
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (105 bp):
GTCTTTCTTCAGTTTATTTCAGTTGATCGAGGGCGATCTTTCTTCAGTTTATTTCAGTTGACCCA
GGGCGGTCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTG
Found at i:9955 original size:25 final size:25
Alignment explanation
Indices: 9903--9955 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
9893 ATTTATTTCT
* * *
9903 GTTGACCCAGGGTGGTCTTTTTTTA
1 GTTGACCCAGGATGGTCTTTCTTCA
9928 GTTGACCCAGGATGGTCTTTCTTCA
1 GTTGACCCAGGATGGTCTTTCTTCA
9953 GTT
1 GTT
9956 TATTTCAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.13, C:0.19, G:0.26, T:0.42
Consensus pattern (25 bp):
GTTGACCCAGGATGGTCTTTCTTCA
Found at i:9960 original size:60 final size:61
Alignment explanation
Indices: 9866--9983 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 61
9856 AGTTTATTCC
*
9866 AGTTGACCCAGGACAATCCTTTCTTCAATTTATTTCTGTTGACCCAGGGTGGTCTTTTTTT
1 AGTTGACCCAGGACAATCCTTTCTTCAATTTATTTCAGTTGACCCAGGGTGGTCTTTTTTT
*** * *
9927 AGTTGACCCAGGATGGT-CTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGGTCTTTT
1 AGTTGACCCAGGACAATCCTTTCTTCAATTTATTTCAGTTGACCCAGGGTGGTCTTTT
9984 CTTCAGTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
60 37 0.73
61 14 0.27
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.42
Consensus pattern (61 bp):
AGTTGACCCAGGACAATCCTTTCTTCAATTTATTTCAGTTGACCCAGGGTGGTCTTTTTTT
Found at i:10038 original size:131 final size:132
Alignment explanation
Indices: 9795--10050 Score: 315
Period size: 131 Copynumber: 1.9 Consensus size: 132
9785 AGTTTATTCC
9795 AGTTGACCCAGGACAATCCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTT
1 AGTTGACCCAGGACAATCCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTT
* * * *
9860 TATTCCAGTTGACCCAGGACAATCCTTTCTTCAATTTATTTCTGTTGACCCAGGGTGGTCTTTTT
66 TAGTCCAGATGACCCAGGACAATCCGTTCTTCAATTTATTTCAGTTGACCCAGGGTGGTCTTTTT
9925 TT
131 TT
*** *
9927 AGTTGACCCAGGATGGT-CTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGGTCTTTTCTTCAGT
1 AGTTGACCCAGGACAATCCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTC-TTTCTTCAGT
* **** *
9991 TTAGGT-CAGAATGATCGC-GGGTGGT-CGTTCTTCAGTTTA-TTCAGTTGACCCAGGGTGGTC
65 TTA-GTCCAG-ATGA-CCCAGGACAATCCGTTCTTCAATTTATTTCAGTTGACCCAGGGTGGTC
10051 CTTTCTTCAG
Statistics
Matches: 106, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
131 55 0.52
132 42 0.40
133 7 0.07
134 2 0.02
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (132 bp):
AGTTGACCCAGGACAATCCTTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTT
TAGTCCAGATGACCCAGGACAATCCGTTCTTCAATTTATTTCAGTTGACCCAGGGTGGTCTTTTT
TT
Found at i:10087 original size:71 final size:71
Alignment explanation
Indices: 9938--10132 Score: 212
Period size: 71 Copynumber: 2.7 Consensus size: 71
9928 GTTGACCCAG
* * * * *
9938 GATGGTCTTTCTTCAGTTTATTTCAGTTGATCCAGGGTGGTCTTTTCTTCAGTTTAGGTCAGAAT
1 GATGGTCGTTCTTCAGTTTA-TTCAGTTGACCCAGGGTGGTCCTTTCTTCAGTATAGGTCAGAAA
**
10003 GATCGCG
65 GATCGAA
* * *
10010 GGTGGTCGTTCTTCAGTTTATTCAGTTGACCCAGGGTGGTCCTTTCTTCAGTATATGTCGGAAAG
1 GATGGTCGTTCTTCAGTTTATTCAGTTGACCCAGGGTGGTCCTTTCTTCAGTATAGGTCAGAAAG
*
10075 ATTGAA
66 ATCGAA
* * * ** *
10081 GATGGTCGCTCTTCAGTTTAACTCAGTTCACCCATAGTGGT-CTTTCATCAGT
1 GATGGTCGTTCTTCAGTTT-ATTCAGTTGACCCAGGGTGGTCCTTTCTTCAGT
10133 TTGCTCGATT
Statistics
Matches: 104, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
71 69 0.66
72 35 0.34
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.38
Consensus pattern (71 bp):
GATGGTCGTTCTTCAGTTTATTCAGTTGACCCAGGGTGGTCCTTTCTTCAGTATAGGTCAGAAAG
ATCGAA
Found at i:10672 original size:40 final size:40
Alignment explanation
Indices: 10612--11035 Score: 238
Period size: 40 Copynumber: 10.6 Consensus size: 40
10602 CGATTTGACA
* * *
10612 CTTCTGATGAGGAAGGGCAAATTGGTAAACTCGACAACAC
1 CTTCCGATGAGGAAGGGCAAACTGGTAAACTCAACAACAC
* * * * *
10652 CTTCCGATGAAGAAGGGCAAAGTGATAAGCTCAACTACAC
1 CTTCCGATGAGGAAGGGCAAACTGGTAAACTCAACAACAC
*
10692 CTTCCGATGAGGAAGGGCAAACTGGGAAACTCAACAACAC
1 CTTCCGATGAGGAAGGGCAAACTGGTAAACTCAACAACAC
* * * * * *
10732 CTCCCGATGAGGAAGGG-TAACTCGCAATCTTAAACAACAC
1 CTTCCGATGAGGAAGGGCAAACTGGTAAAC-TCAACAACAC
* * * * * * *
10772 CTTCCGGTGGGGAAAGGC-AACTCGCAATCTTAAACAACAC
1 CTTCCGATGAGGAAGGGCAAACTGGTAAAC-TCAACAACAC
* * * * *
10812 CTTTCGGTGGGGAAGGGCAAATTGGTGAA-TGCAGACAACAC
1 CTTCCGATGAGGAAGGGCAAACTGGTAAACT-CA-ACAACAC
* * ** * *
10853 CTTCCGCTGGGGAAGGGCAAACTAAGG-ATGCT-GACAATAC
1 CTTCCGATGAGGAAGGGCAAACT--GGTAAACTCAACAACAC
* * * ** *
10893 CTTCCGATGGGGAAGGGCAAACTAG-ATA-TTGACGACAC
1 CTTCCGATGAGGAAGGGCAAACTGGTAAACTCAACAACAC
* * * ** *
10931 CTTCCGGTGGGGAAGGGCAAACTGAGGATGCT-GACAACAC
1 CTTCCGATGAGGAAGGGCAAACTG-GTAAACTCAACAACAC
* * * * **
10971 CTTCTGAAGAGGAAGGGTAAACTGGACAAAGGCAACAACAC
1 CTTCCGATGAGGAAGGGCAAACTGG-TAAACTCAACAACAC
11012 C-TCCAGATGAGGAAGGG-AAACTGG
1 CTTCC-GATGAGGAAGGGCAAACTGG
11036 GAAAAGAAGA
Statistics
Matches: 308, Mismatches: 61, Indels: 30
0.77 0.15 0.08
Matches are distributed among these distances:
37 1 0.00
38 31 0.10
39 11 0.04
40 210 0.68
41 52 0.17
43 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.28, T:0.17
Consensus pattern (40 bp):
CTTCCGATGAGGAAGGGCAAACTGGTAAACTCAACAACAC
Found at i:10951 original size:78 final size:78
Alignment explanation
Indices: 10849--10993 Score: 227
Period size: 78 Copynumber: 1.9 Consensus size: 78
10839 AATGCAGACA
* * *
10849 ACACCTTCCGCTGGGGAAGGGCAAACTAAGGATGCTGACAATACCTTCCGATGGGGAAGGGCAAA
1 ACACCTTCCGCTGGGGAAGGGCAAACTAAGGATGCTGACAACACCTTCCGAAGAGGAAGGGCAAA
10914 CTAGATATTGACG
66 CTAGATATTGACG
* * * *
10927 ACACCTTCCGGTGGGGAAGGGCAAACTGAGGATGCTGACAACACCTTCTGAAGAGGAAGGGTAAA
1 ACACCTTCCGCTGGGGAAGGGCAAACTAAGGATGCTGACAACACCTTCCGAAGAGGAAGGGCAAA
10992 CT
66 CT
10994 GGACAAAGGC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 60 1.00
ACGTcount: A:0.31, C:0.21, G:0.30, T:0.17
Consensus pattern (78 bp):
ACACCTTCCGCTGGGGAAGGGCAAACTAAGGATGCTGACAACACCTTCCGAAGAGGAAGGGCAAA
CTAGATATTGACG
Found at i:11049 original size:40 final size:42
Alignment explanation
Indices: 10963--11055 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 42
10953 TGAGGATGCT
* * *
10963 GACAACACCTTCTGAAGAGGAAGGGTAAACTGGACAAAGGCA
1 GACAACACCTCCAGAAGAGGAAGGGTAAACTGGACAAAGGAA
*
11005 -ACAACACCTCCAGATGAGGAAGGG-AAACTGGGA-AAA-GAA
1 GACAACACCTCCAGAAGAGGAAGGGTAAACT-GGACAAAGGAA
11044 GACAACACCTCC
1 GACAACACCTCC
11056 CGACCGGGGA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
39 2 0.04
40 19 0.42
41 24 0.53
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.10
Consensus pattern (42 bp):
GACAACACCTCCAGAAGAGGAAGGGTAAACTGGACAAAGGAA
Found at i:11239 original size:43 final size:43
Alignment explanation
Indices: 11095--11391 Score: 373
Period size: 43 Copynumber: 6.7 Consensus size: 43
11085 AAGAAAATTG
* * * **
11095 GGACCTTCCGACCGGGAAGGGGCATTTTTGGTAATGAAGAAGACGG
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATG-A-AA-ACAA
11141 GGACCTTCCAACCAGGAA-GGGCATTTTTGGAAATAAAGAAAACAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAT---GAAAACAA
11186 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
* *
11229 GGACCTTCCAACCAGGAAGGGGCATTTTTGCAAATGAAAATAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
* * *
11272 GGACCCTCCAACCAGGAAGGGGTATTTTTGGAAATAAAGAATACAA
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAT---GAAAACAA
* *
11318 AGACCTTCCAACCAGTAAGGGGCATTTTTGGAAATGAAAAC-A
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
*
11360 GAGACCTTCCAACCAGGAAGGGGAATTTTTGG
1 G-GACCTTCCAACCAGGAAGGGGCATTTTTGG
11392 TATAAAAGAA
Statistics
Matches: 223, Mismatches: 20, Indels: 19
0.85 0.08 0.07
Matches are distributed among these distances:
42 1 0.00
43 114 0.51
45 35 0.16
46 71 0.32
47 1 0.00
48 1 0.00
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (43 bp):
GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAACAA
Found at i:11338 original size:132 final size:132
Alignment explanation
Indices: 11095--11390 Score: 434
Period size: 132 Copynumber: 2.2 Consensus size: 132
11085 AAGAAAATTG
* * ** * *
11095 GGACCTTCCGACCGGGAAGGGGCATTTTTGGTAATGAAGAAGACGGGGACCTTCCAACCAGGAAG
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGCAAATGAAGAAGAC-AGGACCCTCCAACCAGGAAG
*
11160 GGCATTTTTGGAAATAAAGAAAACAAGGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAA
65 GGCATTTTTGGAAATAAAGAAAACAAAGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAA
11225 ACAA
130 AC-A
*
11229 GGACCTTCCAACCAGGAAGGGGCATTTTTGCAAATGAA-AATA-AGGACCCTCCAACCAGGAAGG
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGCAAATGAAGAAGACAGGACCCTCCAACCAGGAA-G
* * *
11292 GGTATTTTTGGAAATAAAGAATACAAAGACCTTCCAACCAGTAAGGGGCATTTTTGGAAATGAAA
65 GGCATTTTTGGAAATAAAGAAAACAAAGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAA
11357 ACA
130 ACA
*
11360 GAGACCTTCCAACCAGGAAGGGGAATTTTTG
1 G-GACCTTCCAACCAGGAAGGGGCATTTTTG
11391 GTATAAAAGA
Statistics
Matches: 148, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
131 19 0.13
132 92 0.62
133 3 0.02
134 34 0.23
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (132 bp):
GGACCTTCCAACCAGGAAGGGGCATTTTTGCAAATGAAGAAGACAGGACCCTCCAACCAGGAAGG
GCATTTTTGGAAATAAAGAAAACAAAGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATGAAAA
CA
Found at i:11341 original size:89 final size:87
Alignment explanation
Indices: 11095--11404 Score: 376
Period size: 89 Copynumber: 3.5 Consensus size: 87
11085 AAGAAAATTG
* * * * **
11095 GGACCTTCCGACCGGGAAGGGGCATTTTTGGTAATGAAGAAGACGGGGACCTTCCAACCAGGAA-
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAT-AAGAAAACAAGGACCTTCCAACCAGGAAG
11159 GGGCATTTTTGGAAATAAAGAAAACAA
65 GGGCATTTTTGGAAAT---GAAAA-AA
11186 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAT--GAAAACAAGGACCTTCCAACCAGGAAGG
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATAAGAAAACAAGGACCTTCCAACCAGGAAGG
*
11249 GGCATTTTTGCAAATGAAAATAA
66 GGCATTTTTGGAAATGAAAA-AA
* * * * *
11272 GGACCCTCCAACCAGGAAGGGGTATTTTTGGAAATAAAGAATACAAAGACCTTCCAACCAGTAAG
1 GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAAT-AAGAAAACAAGGACCTTCCAACCAGGAAG
*
11337 GGGCATTTTTGGAAATGAAAACA
65 GGGCATTTTTGGAAATGAAAAAA
*
11360 GAGACCTTCCAACCAGGAAGGGGAATTTTTGGTATAA-AAGAAAAC
1 G-GACCTTCCAACCAGGAAGGGGCATTTTTGG-A-AATAAGAAAAC
11405 GGTTCTTTTG
Statistics
Matches: 194, Mismatches: 18, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
86 40 0.21
88 25 0.13
89 94 0.48
90 1 0.01
91 34 0.18
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (87 bp):
GGACCTTCCAACCAGGAAGGGGCATTTTTGGAAATAAGAAAACAAGGACCTTCCAACCAGGAAGG
GGCATTTTTGGAAATGAAAAAA
Found at i:14625 original size:84 final size:84
Alignment explanation
Indices: 14530--14688 Score: 282
Period size: 84 Copynumber: 1.9 Consensus size: 84
14520 AATATATTTA
* *
14530 GAAAAATTCTAATATATCTAAGTTTTGCAATTAAATTAGTAAAATGGTAAAAATAAAATAGTTAT
1 GAAAAATTCTAATATATCTAAGTTTTGCAATTAAAATAGTAAAATGGTAAAAATAAAATACTTAT
14595 AAAGAGATTAGATTTAATT
66 AAAGAGATTAGATTTAATT
**
14614 GAAAAATTCTAATATATCTAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATACTTAT
1 GAAAAATTCTAATATATCTAAGTTTTGCAATTAAAATAGTAAAATGGTAAAAATAAAATACTTAT
14679 AAAGAGATTA
66 AAAGAGATTA
14689 AAAAGTCTCC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 71 1.00
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.35
Consensus pattern (84 bp):
GAAAAATTCTAATATATCTAAGTTTTGCAATTAAAATAGTAAAATGGTAAAAATAAAATACTTAT
AAAGAGATTAGATTTAATT
Found at i:14916 original size:88 final size:88
Alignment explanation
Indices: 14809--14996 Score: 240
Period size: 88 Copynumber: 2.1 Consensus size: 88
14799 TAAAAAAATA
* **
14809 AATTTAAAAAATTCTAATATAT-TTAAG-TTTTGT-AATTAAAA-TAGTAAAAATGGTAAAAATA
1 AATTAAAAAAATTCTAATATATCAAAAGTTTTTGTAAATTAAAATTA--AAAAATGGTAAAAATA
14870 AAATAGTTATATAAAGAGATTAGATTT
64 AAATAG-T-TATAAAGAGATTAGATTT
* * *
14897 AATTAAAAAAATTCTAATATATCAAAAGTTTTTTTAAATTAAAATTAAAAAATGTTAAAGATAAA
1 AATTAAAAAAATTCTAATATATCAAAAGTTTTTGTAAATTAAAATTAAAAAATGGTAAAAATAAA
*
14962 ATAGTTATAAAGAGATTTGATTT
66 ATAGTTATAAAGAGATTAGATTT
14985 AATTAAATAAAA
1 AATTAAA-AAAA
14997 ATAGAATTTT
Statistics
Matches: 88, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
88 45 0.51
89 8 0.09
90 25 0.28
91 8 0.09
92 2 0.02
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.37
Consensus pattern (88 bp):
AATTAAAAAAATTCTAATATATCAAAAGTTTTTGTAAATTAAAATTAAAAAATGGTAAAAATAAA
ATAGTTATAAAGAGATTAGATTT
Found at i:15374 original size:17 final size:17
Alignment explanation
Indices: 15348--15380 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
15338 GAATCAATGC
*
15348 CCCCGGGTGTTTGTAAA
1 CCCCGAGTGTTTGTAAA
15365 CCCCGAGTGTTTGTAA
1 CCCCGAGTGTTTGTAA
15381 TACGGACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.30
Consensus pattern (17 bp):
CCCCGAGTGTTTGTAAA
Done.