Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2208
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: 28295
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Found at i:306 original size:46 final size:46
Alignment explanation
Indices: 256--429 Score: 146
Period size: 47 Copynumber: 3.7 Consensus size: 46
246 TGGTTGAGCA
*
256 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCTATGATGGAATTG-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATGATGGAATCGC
* * *
302 TCCGAACTCGATTGAGTTGAGT-CGAAGTT--CTGA-GATGTAACTAGGC
1 TCCGAACTCG-TTGAGTTGAGTCCG-AGTTCACTTATGATGGAA-T-CGC
*
348 ATCCGAACTCGTTGAGTTTGAGTCCGAGTTCACTTTATGGTGCGAA-CGC
1 -TCCGAACTCGTTGAG-TTGAGTCCGAGTTCAC-TTATGATG-GAATCGC
* * *
397 CCCG-AGTCGTTGAGTTGAGTCCGAGTTCGCTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
430 GGGCGGGTTA
Statistics
Matches: 105, Mismatches: 10, Indels: 27
0.74 0.07 0.19
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 6 0.06
46 32 0.30
47 44 0.42
48 5 0.05
49 3 0.03
50 2 0.02
51 3 0.03
52 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGATGGAATCGC
Found at i:7884 original size:46 final size:46
Alignment explanation
Indices: 7834--8009 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
7824 TGGTTGAGCA
7834 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
7880 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
7925 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGGTGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
7973 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
8010 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:7990 original size:93 final size:93
Alignment explanation
Indices: 7831--8002 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
7821 GGATGGTTGA
* *
7831 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
7896 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
7924 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGGTGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
7989 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
8003 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:11103 original size:40 final size:40
Alignment explanation
Indices: 11048--11229 Score: 296
Period size: 40 Copynumber: 4.6 Consensus size: 40
11038 TATTCGAATG
11048 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
11088 ATATCCGGGCTAAGTCCCAAAGGCATTTGTGCTAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
11128 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
11168 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
11208 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
11230 TACTTGGGTT
Statistics
Matches: 133, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 14 0.11
40 117 0.88
41 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:13828 original size:6 final size:6
Alignment explanation
Indices: 13817--13908 Score: 80
Period size: 6 Copynumber: 14.8 Consensus size: 6
13807 TATCAAAACT
* *
13817 AGAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAATC
* * *
13866 AGTATC AGGTAAT- AGAATC AAAATC AGAATC AAAACTC AGAAT
1 AGAATC A-G-AATC AGAATC AGAATC AGAATC AGAA-TC AGAAT
13909 GTGAATGCAA
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
5 4 0.06
6 53 0.77
7 9 0.13
8 3 0.04
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:13852 original size:31 final size:31
Alignment explanation
Indices: 13817--13897 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
13807 TATCAAAACT
* *
13817 AGAATCAGAATCAGAATCAGAATTAGGTGAC
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
* *
13848 AGAATCAGAATCAGAATCAGTATCAGGTAAT
1 AGAATCAGAATCAGAATCAGAATCAGGTAAC
*
13879 AGAATCAAAATCAGAATCA
1 AGAATCAGAATCAGAATCA
13898 AAACTCAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.20
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGAATCAGGTAAC
Found at i:14082 original size:27 final size:25
Alignment explanation
Indices: 14040--14141 Score: 105
Period size: 27 Copynumber: 3.8 Consensus size: 25
14030 GCTCAGTTAT
*
14040 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTG-CAGAGCCACCAGA-A
14067 CAGATATTGTAGCAGAGCCACCAGAA
1 CAGATATTGT-GCAGAGCCACCAGAA
*
14093 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGT-GCAGAGCCACCAG-AA
* *
14121 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGT-GCAGAGCCAC
14142 TTAACAGAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
26 7 0.10
27 51 0.76
28 9 0.13
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.19
Consensus pattern (25 bp):
CAGATATTGTGCAGAGCCACCAGAA
Found at i:14124 original size:54 final size:53
Alignment explanation
Indices: 14040--14141 Score: 132
Period size: 54 Copynumber: 1.9 Consensus size: 53
14030 GCTCAGTTAT
* * * *
14040 CAGATATTGTGACAGAGTCACCAGATACAGATATTGTAGCAGAGCCACCAGAA
1 CAGATATTGTGACAGAGCCACCAGAAACAGATAATGTAGCAAAGCCACCAGAA
* * *
14093 CAGATATTTGTGGCATAGCCACCAGAAACAGATAATGTGGCAAAGCCAC
1 CAGATA-TTGTGACAGAGCCACCAGAAACAGATAATGTAGCAAAGCCAC
14142 TTAACAGAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 6 0.15
54 35 0.85
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.19
Consensus pattern (53 bp):
CAGATATTGTGACAGAGCCACCAGAAACAGATAATGTAGCAAAGCCACCAGAA
Found at i:14328 original size:22 final size:22
Alignment explanation
Indices: 14300--14364 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
14290 GCAAATACAT
*
14300 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
14322 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
14344 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
14365 AAGGCTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:14873 original size:27 final size:27
Alignment explanation
Indices: 14818--14957 Score: 160
Period size: 27 Copynumber: 5.2 Consensus size: 27
14808 AGGTATCTTG
* * * *
14818 GTAATTCCACCCTACA-GGGTTTTTTA
1 GTAATTCTACCCTAAAGGGGTATTTCA
14844 GTAATTCTACCCTAAAGGGGTATTTCA
1 GTAATTCTACCCTAAAGGGGTATTTCA
* * *
14871 GTAATTTTACCCTATAGGGGTATTTCG
1 GTAATTCTACCCTAAAGGGGTATTTCA
*
14898 GTAATTCTACCCTACAGGGGTATTT-A
1 GTAATTCTACCCTAAAGGGGTATTTCA
*
14924 TGTATTTCTACCCTACAA-GGGTATTTCA
1 -GTAATTCTACCCTA-AAGGGGTATTTCA
14952 GTAATT
1 GTAATT
14958 TTGTAAATCG
Statistics
Matches: 97, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
26 14 0.14
27 81 0.84
28 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (27 bp):
GTAATTCTACCCTAAAGGGGTATTTCA
Found at i:14973 original size:81 final size:80
Alignment explanation
Indices: 14809--14959 Score: 207
Period size: 81 Copynumber: 1.9 Consensus size: 80
14799 TACCCCACAA
* *
14809 GGTATCTTGGTAATTCCACCCTACAGGGTTTTTTAGTAATTCTACCCTAAAGGGGTATTTCAGTA
1 GGTATCTTGGTAATTCCACCCTACAGGGGTATTTAGTAATTCTACCCTAAAGGGGTATTTCAGTA
**
14874 ATTTTACCCTATAGG
66 ATTTTACCAAATAGG
* *
14889 GGTAT-TTCGGTAATTCTACCCTACAGGGGTATTTATGTATTTCTACCCTACAA-GGGTATTTCA
1 GGTATCTT-GGTAATTCCACCCTACAGGGGTATTTA-GTAATTCTACCCTA-AAGGGGTATTTCA
14952 GTAATTTT
63 GTAATTTT
14960 GTAAATCGAG
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
79 2 0.03
80 29 0.45
81 31 0.48
82 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.39
Consensus pattern (80 bp):
GGTATCTTGGTAATTCCACCCTACAGGGGTATTTAGTAATTCTACCCTAAAGGGGTATTTCAGTA
ATTTTACCAAATAGG
Found at i:15159 original size:108 final size:108
Alignment explanation
Indices: 14941--15284 Score: 309
Period size: 108 Copynumber: 3.2 Consensus size: 108
14931 CTACCCTACA
** * * *
14941 AGGGTATTTCAGTAATTTTGTAAATCGAGGGTAAAATGGTAATTTTGTAAATCAAGGGTACTTTG
1 AGGGTATTTCAGTAATTTTACAAATCGAGGATAAAATGGTAATTTTATAAATCAAGGGTAATTTG
* *
15006 GTAATTTTACAAGTCGAGGGTATTTTAATAATTTTGCAAACTG
66 GTAATTTTACAAGTCGAGGGTATTTCAATAATTTTACAAACTG
** * **
15049 AGGGTATTTCAGTAATTTTACAAATCGAGGAT-ATTTGGGTAGTTTTATAAATCGGGGGTAATTT
1 AGGGTATTTCAGTAATTTTACAAATCGAGGATAAAAT-GGTAATTTTATAAATCAAGGGTAATTT
***
15113 GGTAATTTTACAAGTCGAGGGTATTTCAATAATTTTACAGGTTG
65 GGTAATTTTACAAGTCGAGGGTATTTCAATAATTTTACAAACTG
* * * * * *** * *
15157 AGGGTATTTTAGTAACTTCACAAAT-TAGGGGTATTTTGGTAATTTTACAAA-CTAAGGGTATTT
1 AGGGTATTTCAGTAATTTTACAAATCGA-GGATAAAATGGTAATTTTATAAATC-AAGGGTAATT
* * * *** **
15220 TGATAATTTTACAA-ACTAGGGGTATTTTGGTAATTTTACAAACCA
64 TGGTAATTTTACAAGTCGA-GGGTATTTCAATAATTTTACAAACTG
**
15265 AGGGTATTTTGGTAATTTTA
1 AGGGTATTTCAGTAATTTTA
15285 TAAACAAAAG
Statistics
Matches: 191, Mismatches: 40, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
107 6 0.03
108 182 0.95
109 3 0.02
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (108 bp):
AGGGTATTTCAGTAATTTTACAAATCGAGGATAAAATGGTAATTTTATAAATCAAGGGTAATTTG
GTAATTTTACAAGTCGAGGGTATTTCAATAATTTTACAAACTG
Found at i:15343 original size:27 final size:27
Alignment explanation
Indices: 14977--15336 Score: 270
Period size: 27 Copynumber: 13.3 Consensus size: 27
14967 GAGGGTAAAA
** * *
14977 TGGTAATTTTGTAAATCAAGGGTACTT
1 TGGTAATTTTACAAACCAAGGGTATTT
** *
15004 TGGTAATTTTACAAGTCGAGGGTATTT
1 TGGTAATTTTACAAACCAAGGGTATTT
** * **
15031 TAATAATTTTGCAAACTGAGGGTATTT
1 TGGTAATTTTACAAACCAAGGGTATTT
** * * *
15058 CAGTAATTTTACAAATCGAGGATATTT
1 TGGTAATTTTACAAACCAAGGGTATTT
* * * * ** *
15085 GGGTAGTTTTATAAATCGGGGGTAATT
1 TGGTAATTTTACAAACCAAGGGTATTT
** *
15112 TGGTAATTTTACAAGTCGAGGGTATTT
1 TGGTAATTTTACAAACCAAGGGTATTT
*** *****
15139 CAATAATTTTACAGGTTGAGGGTATTT
1 TGGTAATTTTACAAACCAAGGGTATTT
* * * ** *
15166 TAGTAACTTCACAAATTAGGGGTATTT
1 TGGTAATTTTACAAACCAAGGGTATTT
*
15193 TGGTAATTTTACAAACTAAGGGTATTT
1 TGGTAATTTTACAAACCAAGGGTATTT
* * *
15220 TGATAATTTTACAAACTAGGGGTATTT
1 TGGTAATTTTACAAACCAAGGGTATTT
15247 TGGTAATTTTACAAACCAAGGGTATTT
1 TGGTAATTTTACAAACCAAGGGTATTT
* * *
15274 TGGTAATTTTATAAACAAAAGGTATTT
1 TGGTAATTTTACAAACCAAGGGTATTT
* *
15301 TAGTAATTTTACAAACCAGGGGTATTT
1 TGGTAATTTTACAAACCAAGGGTATTT
15328 TGGTAATTT
1 TGGTAATTT
15337 GGTAAACTAA
Statistics
Matches: 271, Mismatches: 62, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 271 1.00
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.40
Consensus pattern (27 bp):
TGGTAATTTTACAAACCAAGGGTATTT
Found at i:15560 original size:28 final size:28
Alignment explanation
Indices: 15520--15584 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
15510 TGGGCTCGTA
*
15520 GGCCCATTGGGCCTACATGGCCCCTTTC
1 GGCCCATTGGGCCCACATGGCCCCTTTC
15548 GGCCCATTGGGCCCACATGGCCCCTTTC
1 GGCCCATTGGGCCCACATGGCCCCTTTC
15576 GGCCCATTG
1 GGCCCATTG
15585 TGGCTCGAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.11, C:0.40, G:0.26, T:0.23
Consensus pattern (28 bp):
GGCCCATTGGGCCCACATGGCCCCTTTC
Found at i:16520 original size:42 final size:44
Alignment explanation
Indices: 16428--16588 Score: 190
Period size: 43 Copynumber: 3.8 Consensus size: 44
16418 AATGACAACA
* * *
16428 TCCCAGAC-GTGGTCTTACATGTAATCAAATATCGATGCCACTG
1 TCCCAGACAGTGGTCTTACACGAAATCAAATATCGATGCCAATG
16471 TCCCAGACAG-GGTCTTACACGAAATCAAATAT-GATGCCAATG
1 TCCCAGACAGTGGTCTTACACGAAATCAAATATCGATGCCAATG
* *
16513 TCCCAGACA-TAGTCTTACACGTAAATCACAA-ATCGATGTCAATG
1 TCCCAGACAGTGGTCTTACACG-AAATCA-AATATCGATGCCAATG
* * *
16557 TCCCAGA-TGTGGTCTTACACGATATCACATAT
1 TCCCAGACAGTGGTCTTACACGAAATCAAATAT
16589 TGAAATCCTA
Statistics
Matches: 102, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
42 29 0.28
43 43 0.42
44 30 0.29
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (44 bp):
TCCCAGACAGTGGTCTTACACGAAATCAAATATCGATGCCAATG
Found at i:18132 original size:26 final size:26
Alignment explanation
Indices: 18097--18148 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
18087 AATGTGAAAG
*
18097 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
18123 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
18149 TTCATTGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:18267 original size:104 final size:103
Alignment explanation
Indices: 18019--18387 Score: 634
Period size: 103 Copynumber: 3.6 Consensus size: 103
18009 TTGTATATAA
** *
18019 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTT
18084 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
18122 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCT-AGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTT
18186 TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTG-AAAGGGGGTTGCTATGTGCTGATT-CCCCG
*
18226 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCG-TGATCCACCATATCT
18290 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
** *
18329 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGCGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCA
18388 ATAACGGTTA
Statistics
Matches: 253, Mismatches: 8, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
102 30 0.12
103 123 0.49
104 70 0.28
105 29 0.11
106 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:18339 original size:26 final size:26
Alignment explanation
Indices: 18304--18355 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
18294 AATGTGAAAG
*
18304 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
18330 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
18356 TTCAGCGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:25704 original size:26 final size:26
Alignment explanation
Indices: 25668--25720 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
25658 TGAAATGTAA
*
25668 AGGGGTTGCTATGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
25694 AGGGGTTGCTAAGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
25720 A
1 A
25721 TTCATTGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.23, G:0.34, T:0.28
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCTGATTCCCCG
Found at i:25800 original size:101 final size:101
Alignment explanation
Indices: 25595--25954 Score: 563
Period size: 101 Copynumber: 3.6 Consensus size: 101
25585 GTTGTATAAA
**
25595 AGGGGTTGCTGTGTGCTGATTCCCCGATT-ATGGTGGTGCTATGTGCGTGATCCACCATATCTTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTA-GTGCGTGATCCACCATATCTTT
25659 GAAATGT-AAA-GGGGTTGCTATGTGCTGATTCCCCG
65 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
25694 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCT-GTGCGTGATCCACCATATCTTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCA-TGGTGGTGCTAGTGCGTGATCCACCATATCTTT
25758 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
65 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
*
25795 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCA-TGGTGGTGCT-AGTGCG-TGATCCACCATATCT
25859 TTGAAA--TGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
63 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATT-CCCCG
* *
25897 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCT-AGTGCGTGATCCACCA
25955 ATAACGGTTA
Statistics
Matches: 246, Mismatches: 6, Indels: 16
0.92 0.02 0.06
Matches are distributed among these distances:
99 56 0.23
100 4 0.02
101 126 0.51
102 35 0.14
103 24 0.10
104 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.31
Consensus pattern (101 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAGTGCGTGATCCACCATATCTTTG
AAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:25805 original size:26 final size:26
Alignment explanation
Indices: 25770--25820 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
25760 AATGTGAAAG
*
25770 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
25796 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
25821 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Done.