Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1673
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: 52640
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5592 original size:191 final size:191
Alignment explanation
Indices: 4994--5988 Score: 1593
Period size: 191 Copynumber: 5.2 Consensus size: 191
4984 CTTTCCAAGA
4994 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC-AGACACGTTGAGGTATTTTTAAAATTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTT-AAATTT
5058 TTTTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT
65 TTTT-AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTT
5123 AGTTTATGTTTTAAA-TGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTTTGTTTTT
128 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAA--TTTTTGTTTTT
5187 C
191 C
5188 AAAATCAAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAA-TT
1 AAAATC-AACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTT
* * *
5252 TTTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTCGGGGCACGCTGAGGTA-TTTTA
65 TTTTAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-GGGCACGCCGAGGTATTTTTA
5316 GTTTATG-TTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
129 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
5378 AAAATCAACT--TATTGCGAGAAATGAGTTGAGCC-CAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
5440 TTTAAAAAATCAACTCATATTGCCGAGAAGTGAGTTGAGCCTCGGGCACGCCGAGGGTATTTTTA
66 TTTAAAAAATCAACTCATATTG-CGAGAAGTGAGTTGAGCCTCGGGCACGCCGA-GGTATTTTTA
*
5505 GTTGATAGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAA-TTTTGTTTTTC
129 GTTTAT-GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
**
5568 AAAATCAACTCATATTGC-AGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTAA
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
*** *
5632 AAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGCATGCCGAAGGTATTTTTTA
66 TTTAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGCACGCCG-AGGTA-TTTTTA
*
5697 GTTTATGTTTTAAATTGACTCAT-GTGCGAGAGGTGAGTTAAGCCTTTTAA-TTTTGTTTTTC
129 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
5758 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAA-TTT
* *
5823 TTTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGACGCCGAGGTATTTTT
65 TTTT--AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGCACGCCGAGGTATTTTT
5888 AGTTTATGTTTT-AATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
128 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* * **
5951 AAAAATCAACTCATATTTCAAGAGGTGAGTTGAGCCTC
1 -AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
5989 GGCTCACATG
Statistics
Matches: 751, Mismatches: 29, Indels: 42
0.91 0.04 0.05
Matches are distributed among these distances:
186 25 0.03
187 57 0.08
188 23 0.03
189 14 0.02
190 95 0.13
191 167 0.22
192 157 0.21
193 69 0.09
194 90 0.12
195 34 0.05
196 20 0.03
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (191 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
TTTAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGCACGCCGAGGTATTTTTAGT
TTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:6039 original size:15 final size:16
Alignment explanation
Indices: 6007--6040 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5997 TGCTGAGGTA
*
6007 TTTTCAATTTATGTTT
1 TTTTCAATCTATGTTT
6023 TTTTCAATCTATGTTT
1 TTTTCAATCTATGTTT
6039 TT
1 TT
6041 CAAAAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.09, G:0.06, T:0.68
Consensus pattern (16 bp):
TTTTCAATCTATGTTT
Found at i:6241 original size:91 final size:87
Alignment explanation
Indices: 5933--6340 Score: 445
Period size: 91 Copynumber: 4.6 Consensus size: 87
5923 GAGTTAAGCC
* *
5933 TTTTAATTTTTGTTTTTCAAAAATCAACTCATATTTCAAGAGGTGAGTTGAGCCTC-GGCTCACA
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG---ACA
* * *
5997 TGCTGAGGTATTTTCAATTTATGTTT
63 CGCTGAGGTATTTTCAAATTCTG-TT
* * * *
6023 TTTTCAATCTATGTTTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG-CAC
1 TTTT-AATTTCTGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGACAC
*
6087 GCTGAGGT-TATTTCAATTTCTGCTT
64 GCTGAGGTAT-TTTCAAATTCTG-TT
** ** *
6112 TACTAA-TTCTACTTTTC--AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACAC
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG--ACAC
*
6174 GCTGAGGTCTTTTCAAATTCTG-T
64 GCTGAGGTATTTTCAAATTCTGTT
* *
6197 TTTTAATTTCTGTGTTTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGGCA
1 TTTTAATTTCTGTTTTTC---AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACA
**
6262 CGCTGAGGTATTTTC-AATTCTACT
63 CGCTGAGGTATTTTCAAATTCTGTT
* *
6286 TTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT
6341 TTTAATTCTA
Statistics
Matches: 273, Mismatches: 30, Indels: 34
0.81 0.09 0.10
Matches are distributed among these distances:
84 3 0.01
85 38 0.14
86 44 0.16
87 29 0.11
88 10 0.04
89 58 0.21
90 4 0.01
91 85 0.31
93 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (87 bp):
TTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTATTTTCAAATTCTGTT
Found at i:6247 original size:176 final size:175
Alignment explanation
Indices: 5946--6340 Score: 505
Period size: 176 Copynumber: 2.2 Consensus size: 175
5936 TAATTTTTGT
* *
5946 TTTTCAAAAATCAACTCATATTTCAAGAGGTGAGTTGAGCCTCGGCTCACATGCTGAGGTATTTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACACGCTGAGGTATTTT
* * * *
6011 CAATTTATGTTTTTTTCAATCTATGTTTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAG
65 CAAATTATG-TTTTTTCAATCTATGTGTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAG
*
6076 CCTCAAGGCACGCTGAGGT-TATTTCAATTTCTGCTTTACTAA-TTCTAC
129 CCTCAAGGCACGCTGAGGTAT-TTTCAA-TTCTACTTTAC-AATTTCTAC
* *
6124 TTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGC-CACACGCTGAGGTCTTTT
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACACGCTGAGGTATTTT
* * *
6187 CAAATTCTG-TTTTT-AATTTCTGTGTTTCAAAAAAAATCAACTCATATTGCAAGAGGTGAGTTG
65 CAAATTATGTTTTTTCAATCTATGTGTTTC---AAAAATCAACTCATATTGCAAGAGGTGAGTTG
* * **
6250 AGCCTCAGGGCACGCTGAGGTATTTTCAATTCTACTTTTCAATTTCTGT
127 AGCCTCAAGGCACGCTGAGGTATTTTCAATTCTACTTTACAATTTCTAC
*
6299 TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCT
6341 TTTAATTCTA
Statistics
Matches: 191, Mismatches: 18, Indels: 17
0.85 0.08 0.08
Matches are distributed among these distances:
173 11 0.06
174 7 0.04
175 18 0.09
176 113 0.59
177 37 0.19
178 5 0.03
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (175 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCGGCTCACACGCTGAGGTATTTTC
AAATTATGTTTTTTCAATCTATGTGTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCC
TCAAGGCACGCTGAGGTATTTTCAATTCTACTTTACAATTTCTAC
Found at i:6371 original size:52 final size:54
Alignment explanation
Indices: 6284--6500 Score: 320
Period size: 52 Copynumber: 4.1 Consensus size: 54
6274 TTCAATTCTA
*
6284 CTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAA-TTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
6339 CTTTT-AATTCTATTTTTC-AAAACCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
6391 CTTTT---TTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTCTATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
6443 CTTTTGCAAATTCT-GTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-C-AATTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
6498 CTT
1 CTT
6501 GGCTCACGTG
Statistics
Matches: 150, Mismatches: 5, Indels: 14
0.89 0.03 0.08
Matches are distributed among these distances:
50 11 0.07
52 76 0.51
53 10 0.07
54 2 0.01
55 42 0.28
56 5 0.03
57 4 0.03
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37
Consensus pattern (54 bp):
CTTTTCAATTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:6806 original size:30 final size:31
Alignment explanation
Indices: 6772--6873 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
6762 TAAAAAATAA
*
6772 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
6802 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
6832 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
6862 AAATTTCATTTT
1 AAATTTCATTTT
6874 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:7153 original size:10 final size:10
Alignment explanation
Indices: 7134--7183 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
7124 TTTTTCGAAG
*
7134 GAAAAAAGAA
1 GAAAAGAGAA
7144 GAAAAGAGAA
1 GAAAAGAGAA
7154 GAAAAGAGAA
1 GAAAAGAGAA
* *
7164 -AGAGGAGAA
1 GAAAAGAGAA
7173 GAAAAGA-AA
1 GAAAAGAGAA
7182 GA
1 GA
7184 GTACCGGCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:7184 original size:17 final size:19
Alignment explanation
Indices: 7137--7179 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
7127 TTCGAAGGAA
7137 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
7155 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
7174 AAAAGA
1 AAAAGA
7180 AAGAGTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:7272 original size:10 final size:10
Alignment explanation
Indices: 7249--7281 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
7239 GTGTAGGAGG
7249 AGAAGAAG-A
1 AGAAGAAGAA
7258 AGAAGAAGAA
1 AGAAGAAGAA
7268 AGAAGAAGAA
1 AGAAGAAGAA
7278 AGAA
1 AGAA
7282 AAAAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
AGAAGAAGAA
Found at i:7422 original size:19 final size:18
Alignment explanation
Indices: 7395--7433 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
7385 AAAATTAATT
7395 AAAAAAAACAACACAAAA
1 AAAAAAAACAACACAAAA
* *
7413 AAAAACAAACAGCCCAAAA
1 AAAAA-AAACAACACAAAA
7432 AA
1 AA
7434 CCAAAGCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.77, C:0.21, G:0.03, T:0.00
Consensus pattern (18 bp):
AAAAAAAACAACACAAAA
Found at i:7610 original size:15 final size:15
Alignment explanation
Indices: 7590--7669 Score: 78
Period size: 15 Copynumber: 5.5 Consensus size: 15
7580 AGCAGGCCAG
*
7590 GAAAAAAGAGAGAAA
1 GAAAAAAGAGAAAAA
7605 G-AAAAA-AG-AAAA
1 GAAAAAAGAGAAAAA
*
7617 GAAAAAAGAAAAAAA
1 GAAAAAAGAGAAAAA
* *
7632 GAAAAGAGAAAAAAA
1 GAAAAAAGAGAAAAA
7647 GGAAAAAAG-GAAAAA
1 -GAAAAAAGAGAAAAA
7662 GAAGAAAA
1 GAA-AAAA
7670 AAAAAAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.07
13 7 0.13
14 9 0.16
15 28 0.51
16 7 0.13
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
GAAAAAAGAGAAAAA
Found at i:7614 original size:7 final size:7
Alignment explanation
Indices: 7590--7679 Score: 80
Period size: 7 Copynumber: 12.7 Consensus size: 7
7580 AGCAGGCCAG
7590 GAAAAAA
1 GAAAAAA
*
7597 GAGAGAAA
1 GA-AAAAA
7605 GAAAAAA
1 GAAAAAA
7612 G--AAAA
1 GAAAAAA
7617 GAAAAAA
1 GAAAAAA
7624 GAAAAAAA
1 G-AAAAAA
*
7632 GAAAAGA
1 GAAAAAA
7639 GAAAAAAA
1 G-AAAAAA
7647 GGAAAAAA
1 -GAAAAAA
*
7655 GGAAAAA
1 GAAAAAA
7662 GAAGAAAA
1 GAA-AAAA
7670 -AAAAAA
1 GAAAAAA
7676 -AAAA
1 GAAAA
7680 GAGTTTCAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
5 5 0.07
6 8 0.11
7 28 0.40
8 28 0.40
9 1 0.01
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:7631 original size:8 final size:8
Alignment explanation
Indices: 7590--7681 Score: 84
Period size: 8 Copynumber: 11.2 Consensus size: 8
7580 AGCAGGCCAG
7590 GAAAAAAGA
1 GAAAAAA-A
7599 GAGAAAGAAA
1 GA-AAA-AAA
7609 -AAAGAAAA
1 GAAA-AAAA
7617 G-AAAAAA
1 GAAAAAAA
7624 GAAAAAAA
1 GAAAAAAA
*
7632 G-AAAAGA
1 GAAAAAAA
7639 GAAAAAAA
1 GAAAAAAA
*
7647 GGAAAAAAG
1 -GAAAAAAA
7656 GAAAAAGAA
1 GAAAAA-AA
7665 GAAAAAAA
1 GAAAAAAA
7673 -AAAAAAA
1 GAAAAAAA
7680 GA
1 GA
7682 GTTTCAATTC
Statistics
Matches: 70, Mismatches: 4, Indels: 19
0.75 0.04 0.20
Matches are distributed among these distances:
7 18 0.26
8 28 0.40
9 18 0.26
10 4 0.06
11 2 0.03
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:7681 original size:15 final size:15
Alignment explanation
Indices: 7600--7681 Score: 83
Period size: 15 Copynumber: 5.2 Consensus size: 15
7590 GAAAAAAGAG
*
7600 AGAAAGAAAAAAGAAA
1 AGAAA-AAAAAAAAAA
*
7616 AGAAAAAAGAAAAAA
1 AGAAAAAAAAAAAAA
*
7631 AGAAAAGAGAAAAAAA
1 AGAAAA-AAAAAAAAA
* *
7647 GGAAAAAAGGAAAAAGA
1 AGAAAAAA--AAAAAAA
7664 AGAAAAAAAAAAAAA
1 AGAAAAAAAAAAAAA
7679 AGA
1 AGA
7682 GTTTCAATTC
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
15 24 0.44
16 17 0.31
17 13 0.24
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAAAAAAA
Found at i:8263 original size:20 final size:22
Alignment explanation
Indices: 8222--8264 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
8212 AATTTTGTGT
*
8222 AAAAAAATCCAGTGTTTTCAAA
1 AAAAAAATCCAGTGTTTCCAAA
8244 AAAAAAATCCA-T-TTTCCAAA
1 AAAAAAATCCAGTGTTTCCAAA
8264 A
1 A
8265 TTTTTAGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 11 0.55
ACGTcount: A:0.53, C:0.16, G:0.05, T:0.26
Consensus pattern (22 bp):
AAAAAAATCCAGTGTTTCCAAA
Found at i:8334 original size:18 final size:17
Alignment explanation
Indices: 8260--8422 Score: 159
Period size: 17 Copynumber: 9.4 Consensus size: 17
8250 ATCCATTTTC
* *
8260 CAAAATTTTTAGTGTCTT
1 CAAAAATTTTCGTGT-TT
*
8278 CTAAAAATTTTTGTGTTT
1 C-AAAAATTTTCGTGTTT
8296 CAAAAATTTTCGT-TTT
1 CAAAAATTTTCGTGTTT
*
8312 CAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTT
8329 CAAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
* *
8347 CAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTT
** *
8364 CAAAAATCCTCTTGTTTT
1 CAAAAATTTTCGTG-TTT
8382 CAAAAA-TTTCGGTGTTT
1 CAAAAATTTTC-GTGTTT
**
8399 TGAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
8417 CAAAAA
1 CAAAAA
8423 AAAATCTCGT
Statistics
Matches: 119, Mismatches: 19, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
16 15 0.13
17 51 0.43
18 41 0.34
19 12 0.10
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (17 bp):
CAAAAATTTTCGTGTTT
Found at i:8422 original size:35 final size:34
Alignment explanation
Indices: 8260--8422 Score: 168
Period size: 35 Copynumber: 4.7 Consensus size: 34
8250 ATCCATTTTC
* * * *
8260 CAAAATTTTTAGTGTCTTCTAAAAATTTTTGTGTTT
1 CAAAAATTTTCGTGTTTTC-AAAAA-TTTCGTGTTT
8296 CAAAAATTTTC--GTTTTCAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTT-CGTGTTT
* *
8329 CAAAAATTTTCGTGTTTTCAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTTTCAAAA-ATTTCGTGTTT
** *
8364 CAAAAATCCTCTTGTTTTCAAAAATTTCGGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTC-GTGTTT
**
8399 TGAAAATTTTCGTGTTTTCAAAAA
1 CAAAAATTTTCGTGTTTTCAAAAA
8423 AAAATCTCGT
Statistics
Matches: 106, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
32 3 0.03
33 22 0.21
34 9 0.08
35 60 0.57
36 12 0.11
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (34 bp):
CAAAAATTTTCGTGTTTTCAAAAATTTCGTGTTT
Found at i:14243 original size:40 final size:41
Alignment explanation
Indices: 14199--14292 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
14189 TTTGGCATCT
* * * *
14199 AGTGCCTCATCGGA-TAATTCGAAGTAATAAATTGACACTC
1 AGTGCCTCATCGAATTAATCCAAAGTAATAAATTGACACCC
*
14239 AGTGCCTCATCGAATTAATCCAAAGTAGTAAATTGACACCC
1 AGTGCCTCATCGAATTAATCCAAAGTAATAAATTGACACCC
*
14280 AGTGTCTCATCGA
1 AGTGCCTCATCGA
14293 CTCGAAGTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 13 0.28
41 34 0.72
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (41 bp):
AGTGCCTCATCGAATTAATCCAAAGTAATAAATTGACACCC
Found at i:15143 original size:10 final size:10
Alignment explanation
Indices: 15128--15195 Score: 57
Period size: 10 Copynumber: 6.3 Consensus size: 10
15118 CTTTCTCCCT
15128 TTTCTTTTTC
1 TTTCTTTTTC
15138 TTTCTTTTTTC
1 TTTC-TTTTTC
*
15149 TTTCTGTTTC
1 TTTCTTTTTC
15159 GTTTCGTTTCTATC
1 -TTTC-TTT-T-TC
15173 TTTCTTTCTT-
1 TTTCTTT-TTC
*
15183 TTTCTATTTC
1 TTTCTTTTTC
15193 TTT
1 TTT
15196 TTATTACTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
9 2 0.04
10 18 0.37
11 15 0.31
12 7 0.14
13 5 0.10
14 2 0.04
ACGTcount: A:0.03, C:0.19, G:0.04, T:0.74
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:15146 original size:11 final size:11
Alignment explanation
Indices: 15128--15197 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 11
15118 CTTTCTCCCT
15128 TTTC-TTTTTC
1 TTTCTTTTTTC
15138 TTTCTTTTTTC
1 TTTCTTTTTTC
15149 TTTCTGTTTCGTTTC
1 TTTC--TTT--TTTC
*
15164 GTTTCTATCTTTC
1 -TTTCT-TTTTTC
*
15177 TTTCTTTTTCTA
1 TTTCTTTTT-TC
15189 TTTCTTTTT
1 TTTCTTTTT
15198 ATTACTTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
10 4 0.08
11 13 0.27
12 15 0.31
13 7 0.14
14 1 0.02
15 5 0.10
16 4 0.08
ACGTcount: A:0.03, C:0.19, G:0.04, T:0.74
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:15912 original size:21 final size:21
Alignment explanation
Indices: 15888--15977 Score: 110
Period size: 21 Copynumber: 4.3 Consensus size: 21
15878 TAAAAAAAGT
* *
15888 TTAATAAATAAAAATAAAAAA
1 TTAATAAATATAAATTAAAAA
*
15909 TTAATAAATATAAATTCAAAA
1 TTAATAAATATAAATTAAAAA
15930 TTAATAAATATAAATTAAAAA
1 TTAATAAATATAAATTAAAAA
* **
15951 TAATATAAATATATTTTAAAAA
1 TTA-ATAAATATAAATTAAAAA
15973 -TAATA
1 TTAATA
15978 CGGGTGGGTC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
20 3 0.05
21 41 0.68
22 16 0.27
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (21 bp):
TTAATAAATATAAATTAAAAA
Found at i:16378 original size:24 final size:24
Alignment explanation
Indices: 16351--16408 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
16341 ATTTTTAAAA
16351 ATATTTAAAAATTATTAAA-ATATT
1 ATATTTAAAAATTATTAAACATA-T
* *
16375 ATATTTTTCAATATTATTAAACATAT
1 ATA--TTTAAAAATTATTAAACATAT
16401 ATATTTAA
1 ATATTTAA
16409 TTATTTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 7 0.25
26 18 0.64
27 3 0.11
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATTTAAAAATTATTAAACATAT
Found at i:16447 original size:16 final size:16
Alignment explanation
Indices: 16426--16465 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 16
16416 TATTTAGTCA
16426 TATAATAAATTATTAT
1 TATAATAAATTATTAT
16442 TATAAT---TTATTAT
1 TATAATAAATTATTAT
*
16455 TTTAATAAATT
1 TATAATAAATT
16466 GTTTAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 6
0.74 0.04 0.22
Matches are distributed among these distances:
13 12 0.60
16 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATAATAAATTATTAT
Found at i:16524 original size:16 final size:15
Alignment explanation
Indices: 16484--16524 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
16474 TTTTAATTTT
16484 ATTTT-AATAATAAA
1 ATTTTAAATAATAAA
16498 A-TTTAAA-AATAATA
1 ATTTTAAATAATAA-A
16512 ATTTTAAATAATA
1 ATTTTAAATAATA
16525 TTCTTCACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 8 0.35
14 5 0.22
15 6 0.26
16 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTTTAAATAATAAA
Found at i:16964 original size:20 final size:19
Alignment explanation
Indices: 16941--16981 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
16931 CAAACACCAG
*
16941 AAAATATTAACTTTTTCAAA
1 AAAATAATAA-TTTTTCAAA
*
16961 AAAATAATCATTTTTCAAA
1 AAAATAATAATTTTTCAAA
16980 AA
1 AA
16982 CTATTTTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATAATAATTTTTCAAA
Found at i:23511 original size:16 final size:16
Alignment explanation
Indices: 23490--23531 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
23480 ATTTTATGAG
*
23490 TTATTTTAATTTTGAA
1 TTATTTTAAATTTGAA
23506 TTATTTTAAATTTGAA
1 TTATTTTAAATTTGAA
*
23522 TCA-TTTAAAT
1 TTATTTTAAAT
23532 AATTATTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (16 bp):
TTATTTTAAATTTGAA
Found at i:32834 original size:31 final size:32
Alignment explanation
Indices: 32770--32844 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 32
32760 TCTGAACTTG
*
32770 AAATTGACCCAAACCTGAATGACCCGGAGTCA
1 AAATTGACCCAAACCTGAATGACCCAGAGTCA
32802 AAATTGACCCAAA-CTGAAGTGACCCAGA-TCA
1 AAATTGACCCAAACCTGAA-TGACCCAGAGTCA
*
32833 AAACTTAACCCA
1 AAA-TTGACCCA
32845 TCCCGCTCGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
31 11 0.28
32 28 0.72
ACGTcount: A:0.41, C:0.28, G:0.15, T:0.16
Consensus pattern (32 bp):
AAATTGACCCAAACCTGAATGACCCAGAGTCA
Found at i:37443 original size:19 final size:18
Alignment explanation
Indices: 37402--37445 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
37392 TTCAAATTTT
* *
37402 AAAAATATTTTAAAGATA
1 AAAAATAATTTAAAAATA
37420 AAAAATAATTTAAAAAGTA
1 AAAAATAATTTAAAAA-TA
37439 TAAAAAT
1 -AAAAAT
37446 TGTAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 14 0.64
19 2 0.09
20 6 0.27
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
AAAAATAATTTAAAAATA
Found at i:38396 original size:20 final size:20
Alignment explanation
Indices: 38354--38396 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
38344 CTTAATTTTA
* *
38354 AATCTCGATCTTCGAATCTT
1 AATCTCGATCTTCGAACCCT
38374 AATCTCGAATCTT-GAACCCT
1 AATCTCG-ATCTTCGAACCCT
38394 AAT
1 AAT
38397 ATTAAATCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (20 bp):
AATCTCGATCTTCGAACCCT
Found at i:41663 original size:43 final size:43
Alignment explanation
Indices: 41554--41714 Score: 238
Period size: 43 Copynumber: 3.8 Consensus size: 43
41544 TAAAGAAAAT
41554 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAA-A
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAGA
* *
41596 AAATGCCGCTAAAGATCATATTCTTTAGCGGCGCTTAGGAAGA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAGA
* *
41639 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTGGGAGGA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAGA
*
41682 AAACACCGCTAAA-AGT-AGTGTTCTTTAGCGGCG
1 AAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCG
41715 TTTATTTCAC
Statistics
Matches: 109, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
42 41 0.38
43 68 0.62
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAGA
Found at i:43179 original size:16 final size:16
Alignment explanation
Indices: 43151--43183 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
43141 TACACTCATG
43151 TATATGTTTTATATTT
1 TATATGTTTTATATTT
43167 TATA-GTTTATATATTT
1 TATATGTTT-TATATTT
43183 T
1 T
43184 CTTTGTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
TATATGTTTTATATTT
Done.