Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2099
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: 38480
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:68 original size:29 final size:28
Alignment explanation
Indices: 1--170 Score: 182
Period size: 29 Copynumber: 5.9 Consensus size: 28
1 AGCCCACAAGTCAGTGGCA-CCATTTCAA
1 AGCCCACAAGTCAGTGGCATCC-TTTCAA
*
29 AGCCCACAAGTTAGTGGCATTCCTTTCAA
1 AGCCCACAAGTCAGTGGCA-TCCTTTCAA
* *
58 AGCCCATAAGTCAGTGGCACCCTTTCAA
1 AGCCCACAAGTCAGTGGCATCCTTTCAA
*
86 AGCCCATAAGTCAGTGGCATTCCTTTCAA
1 AGCCCACAAGTCAGTGGCA-TCCTTTCAA
* * **
115 AGCCCACGAGTCGGTGGCAACTTTTTTCAA
1 AGCCCACAAGTCAGTGGC-A-TCCTTTCAA
*
145 AGCCTACACAAGTTAGTGGCA-CCTTT
1 AGCC--CACAAGTCAGTGGCATCCTTT
171 TTAAAAAAGC
Statistics
Matches: 120, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
28 45 0.38
29 49 0.41
30 14 0.12
31 1 0.01
32 11 0.09
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.25
Consensus pattern (28 bp):
AGCCCACAAGTCAGTGGCATCCTTTCAA
Found at i:89 original size:57 final size:57
Alignment explanation
Indices: 1--165 Score: 222
Period size: 57 Copynumber: 2.8 Consensus size: 57
1 AGCCCACAAGTCAGTGGCACCATTTCAAAGCCCACAAGTTAGTGGCATTCCTTTCAA
1 AGCCCACAAGTCAGTGGCACCATTTCAAAGCCCACAAGTTAGTGGCATTCCTTTCAA
* * * *
58 AGCCCATAAGTCAGTGGCACCCTTTCAAAGCCCATAAGTCAGTGGCATTCCTTTCAA
1 AGCCCACAAGTCAGTGGCACCATTTCAAAGCCCACAAGTTAGTGGCATTCCTTTCAA
* * **
115 AGCCCACGAGTCGGTGGCAACTTTTTTCAAAGCCTACACAAGTTAGTGGCA
1 AGCCCACAAGTCAGTGGC-AC-CATTTCAAAGCC--CACAAGTTAGTGGCA
166 CCTTTTTAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
57 68 0.73
58 2 0.02
59 10 0.11
61 13 0.14
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (57 bp):
AGCCCACAAGTCAGTGGCACCATTTCAAAGCCCACAAGTTAGTGGCATTCCTTTCAA
Found at i:4625 original size:14 final size:14
Alignment explanation
Indices: 4606--4986 Score: 224
Period size: 14 Copynumber: 27.5 Consensus size: 14
4596 CAAAGTTGTG
*
4606 TGTGCCAAAGTACT
1 TGTGCCAAAGTACC
*
4620 TGTGCCAAAATACC
1 TGTGCCAAAGTACC
* *
4634 TATGCCAAAGTGCC
1 TGTGCCAAAGTACC
4648 TGTGCC-AAGTACC
1 TGTGCCAAAGTACC
*
4661 TATGCCAAAGTACC
1 TGTGCCAAAGTACC
*
4675 TGTGCCAAAATACC
1 TGTGCCAAAGTACC
*
4689 TATGCC--AGCTACC
1 TGTGCCAAAG-TACC
* * *
4702 TATGCCAAAGCACA
1 TGTGCCAAAGTACC
*
4716 TGTGCTAAAGATACC
1 TGTGCCAAAG-TACC
* * *
4731 TATGCCAAAGTGCT
1 TGTGCCAAAGTACC
* *
4745 TGTGTC-AGGTACC
1 TGTGCCAAAGTACC
*
4758 TGTGCCAAAGTACT
1 TGTGCCAAAGTACC
* *
4772 TGTACCAAAATACC
1 TGTGCCAAAGTACC
* * *
4786 TGTACC-AGGTACT
1 TGTGCCAAAGTACC
4799 TGTGCCAAAGATACC
1 TGTGCCAAAG-TACC
* * *
4814 TATG-CTAGGTACC
1 TGTGCCAAAGTACC
** *
4827 TGTGCC-TGGTACT
1 TGTGCCAAAGTACC
*
4840 TGTGCCAAAGTACT
1 TGTGCCAAAGTACC
*
4854 TGTACCAAAGATACC
1 TGTGCCAAAG-TACC
* * * *
4869 TATGCCAAAATGCT
1 TGTGCCAAAGTACC
*
4883 TGTG-CTAAGTACC
1 TGTGCCAAAGTACC
*
4896 TGTGCCAAAATACC
1 TGTGCCAAAGTACC
* * * *
4910 TATACTAGA-TACC
1 TGTGCCAAAGTACC
4923 TGTGCCAAAGATACC
1 TGTGCCAAAG-TACC
* * *
4938 TATACCAAAGGTACT
1 TGTGCCAAA-GTACC
4953 TGTGCCAAAGTACC
1 TGTGCCAAAGTACC
* * *
4967 TATGCC-AGGTATC
1 TGTGCCAAAGTACC
4980 TGTGCCA
1 TGTGCCA
4987 GGTGCCGGGT
Statistics
Matches: 272, Mismatches: 79, Indels: 32
0.71 0.21 0.08
Matches are distributed among these distances:
12 1 0.00
13 85 0.31
14 136 0.50
15 49 0.18
16 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.25
Consensus pattern (14 bp):
TGTGCCAAAGTACC
Found at i:4667 original size:41 final size:41
Alignment explanation
Indices: 4578--4710 Score: 133
Period size: 41 Copynumber: 3.2 Consensus size: 41
4568 AAGCCACCCT
* ** * *
4578 TGCCAAAAGTACTTATGCCAAAGTTGTGTGTGCCAAAGTACTTG
1 TGCCAAAA-TACCTATGCCAAAG-TGCCTGTGCC-AAGTACCTA
4622 TGCCAAAATACCTATGCCAAAGTGCCTGTGCCAAGTACCTA
1 TGCCAAAATACCTATGCCAAAGTGCCTGTGCCAAGTACCTA
* * * * *
4663 TGCCAAAGTACCTGTGCCAAAATACCTATGCC-AGCTACCTA
1 TGCCAAAATACCTATGCCAAAGTGCCTGTGCCAAG-TACCTA
4704 TGCCAAA
1 TGCCAAA
4711 GCACATGTGC
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
40 2 0.03
41 47 0.60
42 8 0.10
43 13 0.17
44 8 0.10
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (41 bp):
TGCCAAAATACCTATGCCAAAGTGCCTGTGCCAAGTACCTA
Found at i:4701 original size:27 final size:27
Alignment explanation
Indices: 4608--4986 Score: 138
Period size: 27 Copynumber: 13.7 Consensus size: 27
4598 AAGTTGTGTG
*
4608 TGCCAAAGTACTTGTGCCAAAATACCTA
1 TGCC-AAGTACCTGTGCCAAAATACCTA
* *
4636 TGCCAAAGTGCCTGTGCC-AAGTACCTA
1 TGCC-AAGTACCTGTGCCAAAATACCTA
4663 TGCCAAAGTACCTGTGCCAAAATACCTA
1 TGCC-AAGTACCTGTGCCAAAATACCTA
* ** * *
4691 TGCC-AGCTACCTATGCCAAAGCACATG
1 TGCCAAG-TACCTGTGCCAAAATACCTA
* * * * * *
4718 TGCTAAAGATACCTATGCCAAAGTGCTTG
1 TGC-CAAG-TACCTGTGCCAAAATACCTA
* * * * *
4747 TGTCAGGTACCTGTGCCAAAGTACTTG
1 TGCCAAGTACCTGTGCCAAAATACCTA
* * * ** * *
4774 TACCAAAATACCTGTACC-AGGTACTTG
1 TGCC-AAGTACCTGTGCCAAAATACCTA
* * ** *
4801 TGCCAAAGATACCTATG-CTAGGTACCTG
1 TGCC-AAG-TACCTGTGCCAAAATACCTA
** * * * *
4829 TGCCTGGTACTTGTGCCAAAGTACTTG
1 TGCCAAGTACCTGTGCCAAAATACCTA
* * * * *
4856 TACCAAAGATACCTATGCCAAAATGCTTG
1 TGCC-AAG-TACCTGTGCCAAAATACCTA
*
4885 TGCTAAGTACCTGTGCCAAAATACCTA
1 TGCCAAGTACCTGTGCCAAAATACCTA
* *
4912 T-ACTAGATACCTGTGCCAAAGATACCTA
1 TGCCAAG-TACCTGTGCCAAA-ATACCTA
* * *
4940 TACCAAAGGTACTTGTGCCAAAGTACCTA
1 TGCC-AA-GTACCTGTGCCAAAATACCTA
* *
4969 TGCCAGGTATCTGTGCCA
1 TGCCAAGTACCTGTGCCA
4987 GGTGCCGGGT
Statistics
Matches: 274, Mismatches: 62, Indels: 31
0.75 0.17 0.08
Matches are distributed among these distances:
26 10 0.04
27 130 0.47
28 71 0.26
29 49 0.18
30 13 0.05
31 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (27 bp):
TGCCAAGTACCTGTGCCAAAATACCTA
Found at i:4711 original size:41 final size:40
Alignment explanation
Indices: 4622--4737 Score: 133
Period size: 41 Copynumber: 2.8 Consensus size: 40
4612 AAAGTACTTG
* * * * *
4622 TGCCAAAATACCTATGCCAAAGTGCCTGTGCCAAGTACCTA
1 TGCCAAAGTACCTGTGCCAAAATACCTATGCC-AGTACCTA
4663 TGCCAAAGTACCTGTGCCAAAATACCTATGCCAGCTACCTA
1 TGCCAAAGTACCTGTGCCAAAATACCTATGCCAG-TACCTA
* * *
4704 TGCCAAAGCACATGTGCTAAAGATACCTATGCCA
1 TGCCAAAGTACCTGTGCCAAA-ATACCTATGCCA
4738 AAGTGCTTGT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
40 2 0.03
41 51 0.78
42 12 0.18
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (40 bp):
TGCCAAAGTACCTGTGCCAAAATACCTATGCCAGTACCTA
Found at i:4780 original size:41 final size:41
Alignment explanation
Indices: 4735--4875 Score: 140
Period size: 41 Copynumber: 3.4 Consensus size: 41
4725 GATACCTATG
* * * *
4735 CCAAAGTGCTTGTGTCAGGTACCTGTGCCAAAGTACTTGTA
1 CCAAAGTACCTGTGCCAGGTACTTGTGCCAAAGTACTTGTA
* * * *
4776 CCAAAATACCTGTACCAGGTACTTGTGCCAAAGATACCTAT-
1 CCAAAGTACCTGTGCCAGGTACTTGTGCCAAAG-TACTTGTA
* * * *
4817 GCTAGGTACCTGTGCCTGGTACTTGTGCCAAAGTACTTGTA
1 CCAAAGTACCTGTGCCAGGTACTTGTGCCAAAGTACTTGTA
*
4858 CCAAAGATACCTATGCCA
1 CCAAAG-TACCTGTGCCA
4876 AAATGCTTGT
Statistics
Matches: 76, Mismatches: 21, Indels: 5
0.75 0.21 0.05
Matches are distributed among these distances:
40 5 0.07
41 57 0.75
42 14 0.18
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.27
Consensus pattern (41 bp):
CCAAAGTACCTGTGCCAGGTACTTGTGCCAAAGTACTTGTA
Found at i:4854 original size:82 final size:84
Alignment explanation
Indices: 4716--4869 Score: 222
Period size: 82 Copynumber: 1.9 Consensus size: 84
4706 CCAAAGCACA
* * * *
4716 TGTGCTAAAGATACCTATGCCAAAGTGCTTGTGTCAGGTACCTGTGCCAAAGTACTTGTACCAAA
1 TGTGCCAAAGATACCTATGCCAAAGTACCTGTGCCAGGTACCTGTGCCAAAGTACTTGTACCAAA
4781 -ATACCTGTACCAGGTACT
66 GATACCTGTACCAGGTACT
* * * *
4799 TGTGCCAAAGATACCTATG-CTAGGTACCTGTGCCTGGTACTTGTGCCAAAGTACTTGTACCAAA
1 TGTGCCAAAGATACCTATGCCAAAGTACCTGTGCCAGGTACCTGTGCCAAAGTACTTGTACCAAA
4863 GATACCT
66 GATACCT
4870 ATGCCAAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
82 38 0.61
83 24 0.39
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (84 bp):
TGTGCCAAAGATACCTATGCCAAAGTACCTGTGCCAGGTACCTGTGCCAAAGTACTTGTACCAAA
GATACCTGTACCAGGTACT
Found at i:5932 original size:135 final size:135
Alignment explanation
Indices: 5731--5990 Score: 287
Period size: 135 Copynumber: 1.9 Consensus size: 135
5721 CTACATTCAG
* * * *
5731 AGAACTTGTATATGTGGAGAATGATAGAAGTGGCGTATGAGACCACAAAGGTCAACTTCTCCATT
1 AGAACTTGTATATGAGGAGAATGATAAAAGTGGCGCATGAGACCACAAAGATCAACTTCTCCATT
* * * *
5796 AAGAGTACTT-GTAAATG-GAAAAGTGACGGGAGTGGCGCAT-G-AGACCACAATGGTTGACTTT
66 AAAAGTA-TTCATAAATGAG-AAAGTGACGGGAAT-G-GCATAGAAGACCACAATGGTCGACTTT
5857 TTCATTGGA
127 TTCATTGGA
* * * * ** * *
5866 AGAATTTGTATATGAGGAGAGTGATAAAAGTGTCGCATTGA-ACCACAACGATTGACTTTTCTAT
1 AGAACTTGTATATGAGGAGAATGATAAAAGTGGCGCA-TGAGACCACAAAGATCAACTTCTCCAT
*
5930 TAAAAGTATTCATAAATGAGAGAGTGACGGGAATGGCATAGAAGACCACAATGGTCGACTT
65 TAAAAGTATTCATAAATGAGAAAGTGACGGGAATGGCATAGAAGACCACAATGGTCGACTT
5991 CTCTATTAAT
Statistics
Matches: 103, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
133 4 0.04
134 4 0.04
135 91 0.88
136 4 0.04
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (135 bp):
AGAACTTGTATATGAGGAGAATGATAAAAGTGGCGCATGAGACCACAAAGATCAACTTCTCCATT
AAAAGTATTCATAAATGAGAAAGTGACGGGAATGGCATAGAAGACCACAATGGTCGACTTTTTCA
TTGGA
Found at i:6304 original size:271 final size:271
Alignment explanation
Indices: 5828--6353 Score: 686
Period size: 271 Copynumber: 1.9 Consensus size: 271
5818 GTGACGGGAG
* * * *
5828 TGGCGCATGAGACCACAATGGTTGACTTTTTCATTGGAAGAATTTGTATATGAGGAGAGTGATAA
1 TGGCGCATGAGACCACAATGGTCGACTTCTCCATTGAAAGAATTTGTATATGAGGAGAGTGATAA
* * * *
5893 AAGTGTCGCATTGAACCACAACGATTGACTTTTCTATTAAAAGTATTCATAAATGAGAGAGTGAC
66 AAGTGGCGCATTGAACCACAACGATTGACTTCTCTATTAAAAGTATTCATAAATGAAAGAGGGAC
* *
5958 GGGAATGGCATAGAAGACCACAATGGTCGACTTCTCTATTAATAATACTTACATTAAGAAGAGTG
131 GGGAATGGCATAGAAGACCACAACGGTCGACTTCTCTATTAATAATACTTACATTAAGAAAAGTG
* *
6023 AAAGAAATGGTGCATGGGACCATAACAGTCGATTTCTCCACAATGTGAGAATTTGTAAAAGAGAA
196 AAAGAAATGGTGCATGGGACCACAACAGTCGACTTCTCCACAATGTGAGAATTTGTAAAAGAGAA
6088 AGTAACGGAAA
261 AGTAACGGAAA
*
6099 TGGCGCAT-AGGACTACAATGGTCGACTTCTCCATTGAAAGAATTTGTATAT-AGGGAGAGTGAT
1 TGGCGCATGA-GACCACAATGGTCGACTTCTCCATTGAAAGAATTTGTATATGA-GGAGAGTGAT
* * * * * *
6162 AGAAGTGGCGCA-TGAGACTACAATGGTTGACTTCTCTATTAAGAG--TTCGTGTAAATGAAAGA
64 AAAAGTGGCGCATTGA-ACCACAACGATTGACTTCTCTATTAAAAGTATTC--ATAAATGAAAGA
* * * * * * **
6224 GGGATGGGAGTGGCGTAGGAGACCATAACGGTCGACTTCTCTATTAATAATACTTGCATTTGGAA
126 GGGACGGGAATGGCATAGAAGACCACAACGGTCGACTTCTCTATTAATAATACTTACATTAAGAA
* **
6289 AAGTG-ACGAAAATGGTGCATGGGACCACAATGGTCGACTTCTCCACAATGTGAGAATTTGTAAA
191 AAGTGAAAG-AAATGGTGCATGGGACCACAACAGTCGACTTCTCCACAATGTGAGAATTTGTAAA
6353 A
255 A
6354 AAAAAAAAAA
Statistics
Matches: 219, Mismatches: 30, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
269 3 0.01
270 7 0.03
271 209 0.95
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (271 bp):
TGGCGCATGAGACCACAATGGTCGACTTCTCCATTGAAAGAATTTGTATATGAGGAGAGTGATAA
AAGTGGCGCATTGAACCACAACGATTGACTTCTCTATTAAAAGTATTCATAAATGAAAGAGGGAC
GGGAATGGCATAGAAGACCACAACGGTCGACTTCTCTATTAATAATACTTACATTAAGAAAAGTG
AAAGAAATGGTGCATGGGACCACAACAGTCGACTTCTCCACAATGTGAGAATTTGTAAAAGAGAA
AGTAACGGAAA
Found at i:7771 original size:20 final size:20
Alignment explanation
Indices: 7724--7777 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
7714 AAATAACCTA
7724 TATATATCGATACATTGAAG
1 TATATATCGATACATTGAAG
* * * **
7744 AATGTATCGATACATTTACT
1 TATATATCGATACATTGAAG
7764 TATATATCGATACA
1 TATATATCGATACA
7778 ATTTTTCACC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (20 bp):
TATATATCGATACATTGAAG
Found at i:7853 original size:20 final size:20
Alignment explanation
Indices: 7828--7877 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
7818 TTGAGACATG
* *
7828 TATCGATACATTCACTTATC
1 TATCGATACATGCACTAATC
*
7848 TATCGATACATGCACTAATT
1 TATCGATACATGCACTAATC
7868 TATCGATACA
1 TATCGATACA
7878 AATTGTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (20 bp):
TATCGATACATGCACTAATC
Found at i:8886 original size:20 final size:21
Alignment explanation
Indices: 8848--8886 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
8838 ATATCTTCGA
8848 TAAATATTGACAAAAAATAGT
1 TAAATATTGACAAAAAATAGT
8869 TAAA-ATTG-CAAAATAATA
1 TAAATATTGACAAAA-AATA
8887 ACTGTAACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (21 bp):
TAAATATTGACAAAAAATAGT
Found at i:13033 original size:13 final size:13
Alignment explanation
Indices: 13014--13053 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
13004 ATAGTAACCC
13014 ATGTATCGATACA
1 ATGTATCGATACA
*
13027 TTGTATCGATACA
1 ATGTATCGATACA
*
13040 ATGTATCAATACA
1 ATGTATCGATACA
13053 A
1 A
13054 AGAACATTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:16010 original size:26 final size:26
Alignment explanation
Indices: 15981--16041 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 26
15971 TATGCTTACC
15981 CTTAAT-ACATGCATCACATACTTTAT
1 CTTAATCA-ATGCATCACATACTTTAT
16007 CTTAATCAATGCATCACATACTTTAT
1 CTTAATCAATGCATCACATACTTTAT
16033 CTTAATCAA
1 CTTAATCAA
16042 ATTTAACCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 33 0.97
27 1 0.03
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (26 bp):
CTTAATCAATGCATCACATACTTTAT
Found at i:19249 original size:20 final size:20
Alignment explanation
Indices: 19224--19289 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
19214 GTTTAAAGCA
19224 ATGTATCGATACAATTTATC
1 ATGTATCGATACAATTTATC
19244 ATGTATCGATAC-----AT-
1 ATGTATCGATACAATTTATC
19258 -TGTATCGATACAATTTATC
1 ATGTATCGATACAATTTATC
19277 ATGTATCGATACA
1 ATGTATCGATACA
19290 TTGTATCGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
18 2 0.05
20 24 0.62
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACAATTTATC
Found at i:19261 original size:13 final size:13
Alignment explanation
Indices: 19245--19302 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 13
19235 CAATTTATCA
19245 TGTATCGATACAT
1 TGTATCGATACAT
*
19258 TGTATCGATACAA
1 TGTATCGATACAT
19271 T-T-T--AT-CA-
1 TGTATCGATACAT
19278 TGTATCGATACAT
1 TGTATCGATACAT
19291 TGTATCGATACA
1 TGTATCGATACA
19303 ATGTGCCATG
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
7 1 0.03
8 3 0.08
9 3 0.08
11 3 0.08
12 3 0.08
13 25 0.66
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:19267 original size:33 final size:33
Alignment explanation
Indices: 19225--19322 Score: 169
Period size: 33 Copynumber: 3.0 Consensus size: 33
19215 TTTAAAGCAA
19225 TGTATCGATACAATTTATCATGTATCGATACAT
1 TGTATCGATACAATTTATCATGTATCGATACAT
19258 TGTATCGATACAATTTATCATGTATCGATACAT
1 TGTATCGATACAATTTATCATGTATCGATACAT
* **
19291 TGTATCGATACAATGTGCCATGTATCGATACA
1 TGTATCGATACAATTTATCATGTATCGATACA
19323 AATAGTGGTA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (33 bp):
TGTATCGATACAATTTATCATGTATCGATACAT
Found at i:19396 original size:19 final size:19
Alignment explanation
Indices: 19352--19424 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
19342 CTTCCAGTTT
* **
19352 CATGTATCAATACAATTGTG
1 CATGTATCGATACAA-TGAA
19372 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
19391 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
19412 -ATGTATCGATACA
1 CATGTATCGATACA
19425 TTTGGATGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 18 0.38
20 28 0.60
21 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:24937 original size:16 final size:16
Alignment explanation
Indices: 24903--24963 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
24893 GTCATTTCGG
*
24903 GTTCAGATCACTTT-GA
1 GTTCAGATCA-TTTCAA
24919 GTTCAGATCATTTCAA
1 GTTCAGATCATTTCAA
*
24935 GTTCGGATCATTTCAA
1 GTTCAGATCATTTCAA
24951 GTTC-GAATCATTT
1 GTTCAG-ATCATTT
24964 TGGGTTTGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.10
16 37 0.90
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (16 bp):
GTTCAGATCATTTCAA
Found at i:28094 original size:11 final size:12
Alignment explanation
Indices: 28070--28099 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
28060 TTTTTATCTC
28070 TTTATTTTTAAT
1 TTTATTTTTAAT
28082 TTTATTTTT-AT
1 TTTATTTTTAAT
28093 TTTATTT
1 TTTATTT
28100 CGATGAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTATTTTTAAT
Found at i:36858 original size:19 final size:20
Alignment explanation
Indices: 36834--36884 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
36824 CGATACATTA
36834 TATCGATACAATACT-TATG
1 TATCGATACAATACTGTATG
* *
36853 TATCGATACATTTACTGTTTG
1 TATCGATACA-ATACTGTATG
36874 TATCGATACAA
1 TATCGATACAA
36885 ATTGTTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 10 0.37
20 4 0.15
21 13 0.48
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (20 bp):
TATCGATACAATACTGTATG
Found at i:37147 original size:26 final size:24
Alignment explanation
Indices: 37101--37158 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
37091 CAGGAGAAGA
*
37101 GGGGAAAGGGAAGAGGGGGGGGAGG
1 GGGGAAAGGGAAGAGGAGGGGG-GG
*
37126 GGGGAAAAGGGAAG-GGA-AGGGGG
1 GGGG-AAAGGGAAGAGGAGGGGGGG
37149 GGGGAAAGGG
1 GGGGAAAGGG
37159 GGAGGGAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 6 0.20
23 6 0.20
24 3 0.10
25 6 0.20
26 9 0.30
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (24 bp):
GGGGAAAGGGAAGAGGAGGGGGGG
Found at i:37154 original size:23 final size:23
Alignment explanation
Indices: 37124--37167 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
37114 AGGGGGGGGA
37124 GGGGGGAAAAGGGAAGGGAAGGG
1 GGGGGGAAAAGGGAAGGGAAGGG
* *
37147 GGGGGGAAAGGGGGAGGGAAG
1 GGGGGGAAAAGGGAAGGGAAG
37168 AAGGAGGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (23 bp):
GGGGGGAAAAGGGAAGGGAAGGG
Found at i:37176 original size:23 final size:23
Alignment explanation
Indices: 37127--37179 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
37117 GGGGGGAGGG
* ** *
37127 GGGAAAAGGGAAGGGAAGGGGGG
1 GGGAAAGGGGAAGGGAAGAAGGA
*
37150 GGGAAAGGGGGAGGGAAGAAGGA
1 GGGAAAGGGGAAGGGAAGAAGGA
37173 GGGAAAG
1 GGGAAAG
37180 AAGAGGGGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (23 bp):
GGGAAAGGGGAAGGGAAGAAGGA
Done.