Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013865.1 Corchorus capsularis cultivar CVL-1 contig13886, 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: 25859
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:2031 original size:22 final size:22
Alignment explanation
Indices: 2006--2479 Score: 154
Period size: 22 Copynumber: 21.7 Consensus size: 22
1996 ATGATCCCAT
2006 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* ** *
2028 TATGAAATTTTAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * **
2050 TATGGAATTTTGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
** *
2072 TAT-AAATTTTTTTTAACCTTCT
1 TATGAAA-TTTTGATAACCTTCC
* * * *
2094 TATAAAATTTGGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * * *
2116 TAAGGAATTTTGA-AGATC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
*
2138 TATGAAATTTTGATAACTTTCC
1 TATGAAATTTTGATAACCTTCC
* **
2160 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTTC-C
* * * **
2183 TATGATATGTTGATAACCATGT
1 TATGAAATTTTGATAACCTTCC
* * *
2205 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
2226 ATCTG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * * *
2249 TCTAAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
* *
2271 AATGAAATTGTGATAA-CTTCAC
1 TATGAAATTTTGATAACCTTC-C
* *
2293 TATGAAAATTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
* *
2316 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
2339 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
* *
2361 TATGAAATCTTAATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
2378 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** * *
2399 TATGATTTTTTGATAATC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * *
2421 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
2443 TATGAAATTTTGATCTA-CATAC
1 TATGAAATTTTGAT-AACCTTCC
2465 TATGAAATTTTGATA
1 TATGAAATTTTGATA
2480 TCCTCCCTGA
Statistics
Matches: 332, Mismatches: 95, Indels: 51
0.69 0.20 0.11
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
21 14 0.04
22 235 0.71
23 67 0.20
24 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:2301 original size:23 final size:22
Alignment explanation
Indices: 2275--2354 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 22
2265 TCACACAATG
*
2275 AAATTGTGAT-AACTTCACTATGA
1 AAATTTTGATAAACTTC-CTAT-A
2298 AAA-TTTGATAAATCTTCCTATA
1 AAATTTTGATAAA-CTTCCTATA
*
2320 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAA-CTTCCTATA
2343 AAATTTTGATAA
1 AAATTTTGATAA
2355 CTTTCTTATG
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
22 9 0.18
23 38 0.75
24 4 0.08
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAAACTTCCTATA
Found at i:2634 original size:22 final size:22
Alignment explanation
Indices: 2603--2656 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
2593 AATCACATTT
*
2603 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
2625 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
*
2647 TAAAATTTTG
1 TGAAATTTTG
2657 TTTGAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.44
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:2662 original size:56 final size:56
Alignment explanation
Indices: 2601--2711 Score: 222
Period size: 56 Copynumber: 2.0 Consensus size: 56
2591 GTAATCACAT
2601 TTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTTTATAAAATTTTG
1 TTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTTTATAAAATTTTG
2657 TTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTTTATAAAATTTT
1 TTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTTTATAAAATTTT
2712 ATTGACCCCT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (56 bp):
TTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACCTCTTTATAAAATTTTG
Found at i:2669 original size:34 final size:34
Alignment explanation
Indices: 2625--2690 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
2615 AACCTCTTTA
*
2625 TGAAATTTTGATAACCTCTTTATAAAATTTTGTT
1 TGAAAATTTGATAACCTCTTTATAAAATTTTGTT
*
2659 TGAAAATTTGATAACCTCTTTATGAAATTTTG
1 TGAAAATTTGATAACCTCTTTATAAAATTTTG
2691 ATAACCTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (34 bp):
TGAAAATTTGATAACCTCTTTATAAAATTTTGTT
Found at i:2888 original size:21 final size:22
Alignment explanation
Indices: 2659--2940 Score: 140
Period size: 22 Copynumber: 12.6 Consensus size: 22
2649 AAATTTTGTT
* *
2659 TGAAAATTTGATAA-CCTCTTTA
1 TGAAATTTTGATAATCCT-TCTA
*
2681 TGAAATTTTGATAA-CCTCTTTA
1 TGAAATTTTGATAATCCT-TCTA
* **
2703 TAAAATTTT-ATTGACCCCTT-TA
1 TGAAATTTTGA-T-AATCCTTCTA
* *
2725 TGAAATTCTGATAATCACAT-TA
1 TGAAATTTTGATAATC-CTTCTA
* * *
2747 TGTAATTTTGATAA-CCTCGCTT
1 TGAAATTTTGATAATCCT-TCTA
* *
2769 TGAAATTTTGATAATAAC-ACTA
1 TGAAATTTTGATAAT-CCTTCTA
2791 TGAAATTTTGATAATCCTTCTA
1 TGAAATTTTGATAATCCTTCTA
2813 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAATCC--T-TCTA
*
2837 TGAAATTTCGATAATCACTT-TA
1 TGAAATTTTGATAATC-CTTCTA
*
2859 TGAGA-TTTGATAA-CCTTCTA
1 TGAAATTTTGATAATCCTTCTA
* * * *
2879 TCAAATTTTGCTACTCCTTATGAAA
1 TGAAATTTTGATAATCCTTCT---A
*
2904 CTGAAAATTTT-ATAA-CTTTCATA
1 -TG-AAATTTTGATAATCCTTC-TA
2927 TGAAATTTTGATAA
1 TGAAATTTTGATAA
2941 CCACACTATA
Statistics
Matches: 203, Mismatches: 32, Indels: 50
0.71 0.11 0.18
Matches are distributed among these distances:
19 3 0.01
20 7 0.03
21 40 0.20
22 108 0.53
23 6 0.03
24 10 0.05
25 17 0.08
26 5 0.02
27 7 0.03
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAATCCTTCTA
Found at i:3145 original size:31 final size:32
Alignment explanation
Indices: 3109--3175 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 32
3099 TTTAGTAATG
* * *
3109 ACAATTTAGAAATATGTTTTTAGAA-AAGGGT
1 ACAATTTAGAAATATATTTTAAAAATAAGGGT
*
3140 ACAA-TTGGAAATATATTTTAAAAATAAGGGT
1 ACAATTTAGAAATATATTTTAAAAATAAGGGT
3171 ACAAT
1 ACAAT
3176 CGGAAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.46, C:0.04, G:0.16, T:0.33
Consensus pattern (32 bp):
ACAATTTAGAAATATATTTTAAAAATAAGGGT
Found at i:3152 original size:30 final size:31
Alignment explanation
Indices: 3117--3181 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
3107 TGACAATTTA
* * * *
3117 GAAATATGTTTTTAGAA-AAGGGTACAATTG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
3147 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
3178 GAAA
1 GAAA
3182 AAATAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 14 0.47
31 16 0.53
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATCG
Found at i:3852 original size:23 final size:24
Alignment explanation
Indices: 3826--3877 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
3816 TTTTATCTTT
*
3826 TATATTATAAGT-TTTTTAT-AATA
1 TATATTATAA-TATTATTATCAATA
*
3849 TATAATATAATATTATTATCAATA
1 TATATTATAATATTATTATCAATA
3873 TATAT
1 TATAT
3878 AAAGATTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 15 0.62
24 8 0.33
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
TATATTATAATATTATTATCAATA
Found at i:4807 original size:30 final size:31
Alignment explanation
Indices: 4758--4820 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
4748 ACTTTATGTT
* * *
4758 TTCCGATTGTACCCATTTTT-TAAAAATATA
1 TTCCAATTATACCCATTTTTAAAAAAATATA
*
4788 TTCCAATTATACCCTTTTTTAAAAAAATATA
1 TTCCAATTATACCCATTTTTAAAAAAATATA
4819 TT
1 TT
4821 TCTAAATTGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.44
Consensus pattern (31 bp):
TTCCAATTATACCCATTTTTAAAAAAATATA
Found at i:4820 original size:31 final size:30
Alignment explanation
Indices: 4758--4817 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
4748 ACTTTATGTT
* *
4758 TTCCGATTGTACCCATTTTTTAAAAATATA
1 TTCCAATTATACCCATTTTTTAAAAATATA
*
4788 TTCCAATTATACCC-TTTTTTAAAAAAATA
1 TTCCAATTATACCCATTTTTTAAAAATATA
4817 T
1 T
4818 ATTTCTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.37, C:0.17, G:0.03, T:0.43
Consensus pattern (30 bp):
TTCCAATTATACCCATTTTTTAAAAATATA
Found at i:7480 original size:2 final size:2
Alignment explanation
Indices: 7473--7512 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
7463 ACAAAAATAC
* *
7473 TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7513 CCAGTCCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:7748 original size:16 final size:16
Alignment explanation
Indices: 7704--7751 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
7694 CAACCTTATT
*
7704 TGAAACTGAAATGACC
1 TGAACCTGAAATGACC
* *
7720 TGAATCCT-CAATGATC
1 TGAA-CCTGAAATGACC
7736 TGAACCTGAAATGACC
1 TGAACCTGAAATGACC
7752 CGGACTCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
15 3 0.12
16 20 0.80
17 2 0.08
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (16 bp):
TGAACCTGAAATGACC
Found at i:8480 original size:27 final size:26
Alignment explanation
Indices: 8430--8485 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
8420 AAAAATAGTA
* *
8430 AAATAAAATGGTAAAAATAGAATTTT
1 AAATAAAATGGTAAAAAAAGAATTAT
* *
8456 AAATTAAATGGTAAAAAAAATAATTAT
1 AAATAAAATGGT-AAAAAAAGAATTAT
8483 AAA
1 AAA
8486 AATATTGAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (26 bp):
AAATAAAATGGTAAAAAAAGAATTAT
Found at i:8493 original size:153 final size:157
Alignment explanation
Indices: 8288--8587 Score: 473
Period size: 153 Copynumber: 1.9 Consensus size: 157
8278 GGTCAATCAC
8288 AATAAAATTTTAAATTAATAAATGGTAAAATAAAATAATTATAAAAACATTGAATTTAATTAAAT
1 AATAAAATTTTAAATT-ATAAATGGTAAAATAAAATAATTATAAAAACATTGAATTTAATTAAAT
* * * *
8353 TAAAATAGAGTTTTTAGTATAATAAAACTGTATATTAAA-TTTTTTTAATATATCCAAGTTTTTA
65 GAAAATAGAGTTTTAAGTAGAATAAAACTGTATAATAAATTTTTTTTAATATATCCAAGTTTTTA
8417 ATGAAAAATAGTAAAATAAAATGGTAAA
130 ATGAAAAATAGTAAAATAAAATGGTAAA
* *
8445 AATAGAATTTTAAA-T-TAAATGGTAAAA-AAAATAATTATAAAAATATTGAATTTAATTAAATG
1 AATAAAATTTTAAATTATAAATGGTAAAATAAAATAATTATAAAAACATTGAATTTAATTAAATG
* * *
8507 GAAATAGAGTTTTAAGTGGAATAAAACTGTATAATAAATTTTTTTTAATATATCCTAGTTTTTAA
66 AAAATAGAGTTTTAAGTAGAATAAAACTGTATAATAAATTTTTTTTAATATATCCAAGTTTTTAA
*
8572 TGAAAAATTGTAAAAT
131 TGAAAAATAGTAAAAT
8588 GGTAAAAATA
Statistics
Matches: 132, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
153 66 0.50
154 52 0.39
156 1 0.01
157 13 0.10
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (157 bp):
AATAAAATTTTAAATTATAAATGGTAAAATAAAATAATTATAAAAACATTGAATTTAATTAAATG
AAAATAGAGTTTTAAGTAGAATAAAACTGTATAATAAATTTTTTTTAATATATCCAAGTTTTTAA
TGAAAAATAGTAAAATAAAATGGTAAA
Found at i:8803 original size:16 final size:16
Alignment explanation
Indices: 8763--8805 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
8753 ATACAATATA
* *
8763 TATATTATAATATTTT
1 TATATTATATTATTAT
8779 TATA-T-TATTATTAT
1 TATATTATATTATTAT
8793 TATATTATATTAT
1 TATATTATATTAT
8806 ATAAGTCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 11 0.48
15 2 0.09
16 10 0.43
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATTATATTATTAT
Found at i:8944 original size:59 final size:57
Alignment explanation
Indices: 8851--8976 Score: 164
Period size: 59 Copynumber: 2.2 Consensus size: 57
8841 TCTAAATTAC
* * *
8851 CATTTGTAATTTTAAAATTGTAGTGTTCTTTTAAAGGATAAACATGTAATTTTTTATTT
1 CATTTATAATTTTAAAATTGTAGTGTTCTATTAAAAGATAAACATGT-A-TTTTTATTT
* * * *
8910 CATTTATAATTTTAAAATTTTATTGTTCTATTAAAAGTTAAATATGTATTTTTATTT
1 CATTTATAATTTTAAAATTGTAGTGTTCTATTAAAAGATAAACATGTATTTTTATTT
8967 CATTTA-AATT
1 CATTTATAATT
8977 AATTAATTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
56 4 0.07
57 15 0.25
58 1 0.02
59 40 0.67
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (57 bp):
CATTTATAATTTTAAAATTGTAGTGTTCTATTAAAAGATAAACATGTATTTTTATTT
Found at i:9965 original size:11 final size:11
Alignment explanation
Indices: 9949--9975 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
9939 TCGTCTTTCC
9949 AAATTCAGATT
1 AAATTCAGATT
9960 AAATTCAGATT
1 AAATTCAGATT
9971 AAATT
1 AAATT
9976 GTTCTGCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (11 bp):
AAATTCAGATT
Found at i:11024 original size:12 final size:12
Alignment explanation
Indices: 11007--11038 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
10997 GTAAAATGGA
11007 ATATGACATAGG
1 ATATGACATAGG
11019 ATATGACATAGG
1 ATATGACATAGG
11031 ATATGACA
1 ATATGACA
11039 GGGTCAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (12 bp):
ATATGACATAGG
Found at i:11099 original size:105 final size:105
Alignment explanation
Indices: 10917--11108 Score: 384
Period size: 105 Copynumber: 1.8 Consensus size: 105
10907 ACGATGGGGT
10917 TGACATAGGATATGACAGGGTCAAATGTCAGCTCCAAGGTCGTTCGAAAGAAAAAGAATACACTA
1 TGACATAGGATATGACAGGGTCAAATGTCAGCTCCAAGGTCGTTCGAAAGAAAAAGAATACACTA
10982 CTCCATATGTGTACAGTAAAATGGAATATGACATAGGATA
66 CTCCATATGTGTACAGTAAAATGGAATATGACATAGGATA
11022 TGACATAGGATATGACAGGGTCAAATGTCAGCTCCAAGGTCGTTCGAAAGAAAAAGAATACACTA
1 TGACATAGGATATGACAGGGTCAAATGTCAGCTCCAAGGTCGTTCGAAAGAAAAAGAATACACTA
11087 CTCCATATGTGTACAGTAAAAT
66 CTCCATATGTGTACAGTAAAAT
11109 ATTAAGATTA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 87 1.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (105 bp):
TGACATAGGATATGACAGGGTCAAATGTCAGCTCCAAGGTCGTTCGAAAGAAAAAGAATACACTA
CTCCATATGTGTACAGTAAAATGGAATATGACATAGGATA
Found at i:12081 original size:206 final size:206
Alignment explanation
Indices: 11727--12134 Score: 744
Period size: 206 Copynumber: 2.0 Consensus size: 206
11717 GGAGGCTGGA
*
11727 ACTAGGAGGTAGTTGGAGATAAAATCCCAACCTTTTCTCACGTGAGAGTGATAAACCATTTCCCA
1 ACTAGGAGGTAGTTGGAGATAAAATCCCAACATTTTCTCACGTGAGAGTGATAAACCATTTCCCA
11792 ACCTATTTTCCTTGATTATTTCCCTCTTAACATAATTCACGGGATTGACATCCTAAATCAATCTC
66 ACCTATTTTCCTTGATTATTTCCCTCTTAACATAATTCACGGGATTGACATCCTAAATCAATCTC
* *
11857 GTGAATCACTCGATTGAACCTATTTACTGTAATCCTTGATTGACATCCTAAATCAATCCTACCAT
131 ATGAATCACTCGATTGAACCTATTTACTGTAATCCTTGATTGACATCCTAAATCAATCATACCAT
11922 AAATTACAGGG
196 AAATTACAGGG
11933 ACTAGGAGGTAGTTGGAGATAAAATCCCAACATTTTCTCACGTGAGAGTGATAAACCATTTCCCA
1 ACTAGGAGGTAGTTGGAGATAAAATCCCAACATTTTCTCACGTGAGAGTGATAAACCATTTCCCA
*
11998 ACCTATTTTCCTTGATTATTTCCCTCTTACCATAATTCACGGGATTGACATCCTAAATCAATCTC
66 ACCTATTTTCCTTGATTATTTCCCTCTTAACATAATTCACGGGATTGACATCCTAAATCAATCTC
* * * *
12063 ATGAATCACTTGATTGAACCTATTTACTGTAATCGTTGATTGACATCCTAAATCAATCATATCGT
131 ATGAATCACTCGATTGAACCTATTTACTGTAATCCTTGATTGACATCCTAAATCAATCATACCAT
12128 AAATTAC
196 AAATTAC
12135 GACACATTAT
Statistics
Matches: 194, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
206 194 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (206 bp):
ACTAGGAGGTAGTTGGAGATAAAATCCCAACATTTTCTCACGTGAGAGTGATAAACCATTTCCCA
ACCTATTTTCCTTGATTATTTCCCTCTTAACATAATTCACGGGATTGACATCCTAAATCAATCTC
ATGAATCACTCGATTGAACCTATTTACTGTAATCCTTGATTGACATCCTAAATCAATCATACCAT
AAATTACAGGG
Found at i:13153 original size:74 final size:74
Alignment explanation
Indices: 12903--13194 Score: 353
Period size: 75 Copynumber: 3.9 Consensus size: 74
12893 CGACGTAAAG
* * *
12903 AAGATTCCATACTCAGCAAGGATTGTAGCCATAAGTGCCTTCCTTCTTTTTTTATGCTTCTGGCC
1 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGCC-T--TTC-CTTTTGATGCTTCTGGCC
*
12968 TATGTAGCCCATC
62 TATGTAGCCAATC
* * *
12981 GAGATTCCATACTCAGCAAGGATCGTAGCCATACGTGCCTTTCCTTTTTGATGCTTCTGGCTTAT
1 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGCCTTTCC-TTTTGATGCTTCTGGCCTAT
*
13046 GTAGCCAATT
65 GTAGCCAATC
* * * * *
13056 ATGA-T---T-C-CAGCAAGGATCGTAGCCATAAGTGCCTTTCCTTTTGTTGTTTATGGCTTATG
1 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGCCTTTCCTTTTGATGCTTCTGGCCTATG
13115 TAGCCAATC
66 TAGCCAATC
* *
13124 AAGATCCCATACTCAGCAAGGATCGTAGCCATAAGTGCCTTTCCTTGTTGATGATTCTGGCCTAT
1 AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGCCTTTCCTT-TTGATGCTTCTGGCCTAT
13189 GTAGCC
65 GTAGCC
13195 CATTAAAAAT
Statistics
Matches: 185, Mismatches: 21, Indels: 19
0.82 0.09 0.08
Matches are distributed among these distances:
68 29 0.16
69 30 0.16
70 1 0.01
71 1 0.01
72 1 0.01
73 1 0.01
74 34 0.18
75 51 0.28
77 1 0.01
78 36 0.19
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (74 bp):
AAGATTCCATACTCAGCAAGGATCGTAGCCATAAGTGCCTTTCCTTTTGATGCTTCTGGCCTATG
TAGCCAATC
Found at i:13182 original size:143 final size:146
Alignment explanation
Indices: 12916--13199 Score: 412
Period size: 143 Copynumber: 2.0 Consensus size: 146
12906 ATTCCATACT
* * * * *
12916 CAGCAAGGATTGTAGCCATAAGTGCCTTCCTTCTTTTTTTATGCTTCTGGCCTATGTAGCCCATC
1 CAGCAAGGATCGTAGCCATAAGTGCCTT-CTTCCTTTTGTATGCTTATGGCCTATGTAGCCAATC
* * * * * *
12981 GAGATTCCATACTCAGCAAGGATCGTAGCCATACGTGCCTTTCCTTTTTGATGCTTCTGGCTTAT
65 AAGATCCCATACTCAGCAAGGATCGTAGCCATAAGTGCCTTTCCTTGTTGATGATTCTGGCCTAT
13046 GTAGCCAATTATGATTC
130 GTAGCCAATTATGATTC
* *
13063 CAGCAAGGATCGTAGCCATAAGTGCC-T-TTCCTTTTGT-TGTTTATGGCTTATGTAGCCAATCA
1 CAGCAAGGATCGTAGCCATAAGTGCCTTCTTCCTTTTGTATGCTTATGGCCTATGTAGCCAATCA
13125 AGATCCCATACTCAGCAAGGATCGTAGCCATAAGTGCCTTTCCTTGTTGATGATTCTGGCCTATG
66 AGATCCCATACTCAGCAAGGATCGTAGCCATAAGTGCCTTTCCTTGTTGATGATTCTGGCCTATG
*
13190 TAGCCCATTA
131 TAGCCAATTA
13200 AAAATATCTA
Statistics
Matches: 123, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
143 89 0.72
144 8 0.07
146 1 0.01
147 25 0.20
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.35
Consensus pattern (146 bp):
CAGCAAGGATCGTAGCCATAAGTGCCTTCTTCCTTTTGTATGCTTATGGCCTATGTAGCCAATCA
AGATCCCATACTCAGCAAGGATCGTAGCCATAAGTGCCTTTCCTTGTTGATGATTCTGGCCTATG
TAGCCAATTATGATTC
Found at i:13359 original size:109 final size:109
Alignment explanation
Indices: 13157--13519 Score: 582
Period size: 109 Copynumber: 3.3 Consensus size: 109
13147 CGTAGCCATA
*
13157 AGTGCCTTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAATATCTATATTTTGACTTG
1 AGTGCCCTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAA-ATCTATATTTTGACTTG
* * *
13222 GAGTGAGTGTACCCTTAGGAGTGCTGCACTAGTTGCGCCTCAAGG
65 GAGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
*
13267 AGTGCCCTTCCTTGTTGATGATTCGGGCCTATGTAGCCCATTAAAAAATCTATATTTTGACTTGG
1 AGTGCCCTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAAATCTATATTTTGACTTGG
*
13332 AGTGAGTGCACCCTTAGGAGTGCTGCACTGGTTGCACCTCCAGG
66 AGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
* **
13376 AGTGCCCTTCCTTGTTGATGATTCTAGCCTATGTAGCCCATTAAAAAATCTATATTTCAACTTGG
1 AGTGCCCTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAAATCTATATTTTGACTTGG
* *
13441 AATGAGTGCACCCTTAGAAGTGCTGCACTAGTTGCACCTCCAGG
66 AGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
* * * *
13485 AGTGCTCTTCCTTGTTGATGCTTTTAGCCTATGTA
1 AGTGCCCTTCCTTGTTGATGATTCTGGCCTATGTA
13520 TCTTAAAAGA
Statistics
Matches: 237, Mismatches: 16, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
109 192 0.81
110 45 0.19
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (109 bp):
AGTGCCCTTCCTTGTTGATGATTCTGGCCTATGTAGCCCATTAAAAAATCTATATTTTGACTTGG
AGTGAGTGCACCCTTAGGAGTGCTGCACTAGTTGCACCTCCAGG
Found at i:14779 original size:45 final size:45
Alignment explanation
Indices: 14728--14921 Score: 254
Period size: 45 Copynumber: 4.4 Consensus size: 45
14718 CAAAGGGTAC
* * * *
14728 ACCCTTTTCCAACATGGTGGTGGTGTTTTCAATGACAAAAATTAT
1 ACCCTCTTCCAACATGGTGGTGGCGCTTCCAATGACAAAAATTAT
* *
14773 ACCCTTTTCCAACATGGTGGTGGCGCTTCCAATGACAAAATTTAT
1 ACCCTCTTCCAACATGGTGGTGGCGCTTCCAATGACAAAAATTAT
*
14818 ACCCTCTTCCAACATGGTGGTGGCG----C-ATGACAAGAATTAT
1 ACCCTCTTCCAACATGGTGGTGGCGCTTCCAATGACAAAAATTAT
* * *
14858 ATCCTCTTCCAACATGGTGGTGGCGCTTCCAAAGACAAGAATTAT
1 ACCCTCTTCCAACATGGTGGTGGCGCTTCCAATGACAAAAATTAT
*
14903 ACCCTCTTCCAATATGGTG
1 ACCCTCTTCCAACATGGTG
14922 AAGGCGATTA
Statistics
Matches: 133, Mismatches: 11, Indels: 10
0.86 0.07 0.06
Matches are distributed among these distances:
40 36 0.27
41 1 0.01
44 1 0.01
45 95 0.71
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (45 bp):
ACCCTCTTCCAACATGGTGGTGGCGCTTCCAATGACAAAAATTAT
Found at i:14879 original size:85 final size:85
Alignment explanation
Indices: 14759--14921 Score: 265
Period size: 85 Copynumber: 1.9 Consensus size: 85
14749 GGTGTTTTCA
* *
14759 ATGACAAAAATTATACCCTTTTCCAACATGGTGGTGGCGCTTCCAATGACAA-AATTTATACCCT
1 ATGACAAAAATTATACCCTCTTCCAACATGGTGGTGGCGCTTCCAAAGACAAGAA-TTATACCCT
14823 CTTCCAACATGGTGGTGGCGC
65 CTTCCAACATGGTGGTGGCGC
* *
14844 ATGACAAGAATTATATCCTCTTCCAACATGGTGGTGGCGCTTCCAAAGACAAGAATTATACCCTC
1 ATGACAAAAATTATACCCTCTTCCAACATGGTGGTGGCGCTTCCAAAGACAAGAATTATACCCTC
*
14909 TTCCAATATGGTG
66 TTCCAACATGGTG
14922 AAGGCGATTA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
85 70 0.97
86 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (85 bp):
ATGACAAAAATTATACCCTCTTCCAACATGGTGGTGGCGCTTCCAAAGACAAGAATTATACCCTC
TTCCAACATGGTGGTGGCGC
Found at i:14970 original size:56 final size:56
Alignment explanation
Indices: 14882--15032 Score: 203
Period size: 56 Copynumber: 2.7 Consensus size: 56
14872 TGGTGGTGGC
* * * *
14882 GCTTCCAAAGACAAGAATTATACCCTCTTCCAATATGGTGAAGGCGATTATCACTT
1 GCTTCCAATGACAAGAATTACACCCTCTTCCAATATGGTGAAGCCGAATATCACTT
* **
14938 GTTTCCAATGACAAGAATTACACCCTCTTCCAATATGGTGTTGCCGAATATCACTT
1 GCTTCCAATGACAAGAATTACACCCTCTTCCAATATGGTGAAGCCGAATATCACTT
* * * *
14994 GCTTCCAATGACAAGAATCACACCATCTTCGAACATGGT
1 GCTTCCAATGACAAGAATTACACCCTCTTCCAATATGGT
15033 AGCAGTGATC
Statistics
Matches: 83, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 83 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (56 bp):
GCTTCCAATGACAAGAATTACACCCTCTTCCAATATGGTGAAGCCGAATATCACTT
Found at i:15047 original size:56 final size:53
Alignment explanation
Indices: 14882--15063 Score: 168
Period size: 56 Copynumber: 3.3 Consensus size: 53
14872 TGGTGGTGGC
* * *
14882 GCTTCCAAAGACAAGAATTATACCCTCTTCCAATATGGTGAAGGCGATTATCACTT
1 GCTTCCAATGACAAGAATTACACCCTCTTCCAATATGGTGCA-G-GA-TATCACTT
* * *
14938 GTTTCCAATGACAAGAATTACACCCTCTTCCAATATGGTGTTGCCGAATATCACTT
1 GCTTCCAATGACAAGAATTACACCCTCTTCCAATAT-G-G-TGCAGGATATCACTT
* * * *
14994 GCTTCCAATGACAAGAATCACACCATCTTCGAACATGGTAGCAGTGATCATCACCTT
1 GCTTCCAATGACAAGAATTACACCCTCTTCCAATATGGT-GCAG-GAT-ATCA-CTT
*
15051 -CTTCCAACGACAA
1 GCTTCCAATGACAA
15064 ATAACTACAC
Statistics
Matches: 105, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
53 1 0.01
54 4 0.04
55 3 0.03
56 88 0.84
57 5 0.05
58 2 0.02
59 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.27
Consensus pattern (53 bp):
GCTTCCAATGACAAGAATTACACCCTCTTCCAATATGGTGCAGGATATCACTT
Found at i:15155 original size:44 final size:44
Alignment explanation
Indices: 15092--15186 Score: 156
Period size: 44 Copynumber: 2.2 Consensus size: 44
15082 ATTGGCGACC
* *
15092 ATCACCCTATTTCAATGTCAAAAGCATATGGTGTTCACGAAACT
1 ATCACCCTACTTCAATGTCAAAAGCACATGGTGTTCACGAAACT
15136 ATCACCCT-CTTCAAATGTCAAAAGCACATGGTGTTCACGAAACT
1 ATCACCCTACTTC-AATGTCAAAAGCACATGGTGTTCACGAAACT
15180 ATCACCC
1 ATCACCC
15187 GCCTTCAACT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 3 0.06
44 45 0.94
ACGTcount: A:0.34, C:0.27, G:0.13, T:0.26
Consensus pattern (44 bp):
ATCACCCTACTTCAATGTCAAAAGCACATGGTGTTCACGAAACT
Found at i:22283 original size:12 final size:12
Alignment explanation
Indices: 22266--22290 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
22256 TGTCGTGAAT
22266 GCAAGCTTGGAG
1 GCAAGCTTGGAG
22278 GCAAGCTTGGAG
1 GCAAGCTTGGAG
22290 G
1 G
22291 AGCATGAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.44, T:0.16
Consensus pattern (12 bp):
GCAAGCTTGGAG
Found at i:22435 original size:30 final size:30
Alignment explanation
Indices: 22399--22464 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
22389 CCATCGCAAG
*
22399 GGCCATCGGATGGAG-CAACCGGCCACAACC
1 GGCCATCGCATGG-GCCAACCGGCCACAACC
* *
22429 GGCCATCGCATGGGCCATCCGGGCACAACC
1 GGCCATCGCATGGGCCAACCGGCCACAACC
22459 GGCCAT
1 GGCCAT
22465 TTGACCCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.23, C:0.38, G:0.30, T:0.09
Consensus pattern (30 bp):
GGCCATCGCATGGGCCAACCGGCCACAACC
Found at i:23418 original size:36 final size:36
Alignment explanation
Indices: 23323--23406 Score: 123
Period size: 36 Copynumber: 2.3 Consensus size: 36
23313 TCACTCTGTC
* *
23323 TTTGGCTATAATGTCGATGGCCTAAGTCACCTAATA
1 TTTGGCTATAATGTCGATGGCCTTAGTCACCCAATA
* **
23359 CTTGGCTATAATGTCGATGGCCTTAGTGGCCCAATA
1 TTTGGCTATAATGTCGATGGCCTTAGTCACCCAATA
23395 TTTGGCTATAAT
1 TTTGGCTATAAT
23407 ACCGTTGGCC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (36 bp):
TTTGGCTATAATGTCGATGGCCTTAGTCACCCAATA
Found at i:23635 original size:46 final size:46
Alignment explanation
Indices: 23563--23653 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
23553 GAGATGCATT
*
23563 TTATGTGAGCACCATTCTTCATAAAGAATACTCTACACGGTAGCTC
1 TTATGTGAGCACCATTCTTCAGAAAGAATACTCTACACGGTAGCTC
* *
23609 TTATGTGAGCACCCA-TCTTCAGAAAGAATTCTCTATACGGTAGCT
1 TTATGTGAGCA-CCATTCTTCAGAAAGAATACTCTACACGGTAGCT
23654 TCTTGCAAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
46 38 0.93
47 3 0.07
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (46 bp):
TTATGTGAGCACCATTCTTCAGAAAGAATACTCTACACGGTAGCTC
Found at i:23810 original size:2 final size:2
Alignment explanation
Indices: 23803--23834 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
23793 CATGTTTACC
23803 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23835 GCTACTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.