Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold576
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: 32462
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Found at i:2250 original size:52 final size:52
Alignment explanation
Indices: 2182--2322 Score: 221
Period size: 52 Copynumber: 2.7 Consensus size: 52
2172 TGAAAAGTTA
2182 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGAAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGAAAATTTGC
* * *
2234 CTGCATGTATCGATACATTTTATACTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGAAAATTTGC
**
2286 CTGCATGTATCGATACA-AAAATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
2323 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
51 2 0.02
52 79 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGAAAATTTGC
Found at i:2329 original size:13 final size:13
Alignment explanation
Indices: 2311--2335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2301 CAAAAATCAG
2311 TGTATCGATACAA
1 TGTATCGATACAA
2324 TGTATCGATACA
1 TGTATCGATACA
2336 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2420 original size:13 final size:13
Alignment explanation
Indices: 2402--2426 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2392 CAAAAAAATA
2402 TGTATCGATACAT
1 TGTATCGATACAT
2415 TGTATCGATACA
1 TGTATCGATACA
2427 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2422 original size:33 final size:33
Alignment explanation
Indices: 2380--2446 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2370 AGTAGCTTAA
2380 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2413 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2446 A
1 A
2447 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2525 original size:21 final size:21
Alignment explanation
Indices: 2484--2525 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2474 GTTGGGACCT
*
2484 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
2505 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
2526 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:3565 original size:49 final size:49
Alignment explanation
Indices: 3315--4123 Score: 1117
Period size: 49 Copynumber: 16.8 Consensus size: 49
3305 GATGTCAACG
* *
3315 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAATA
* *
3367 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
3410 TGCTGATTCAAGGCCAGCTACA-TGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * *
3458 TGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
*
3501 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * * *
3550 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG-AGGTGCTAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
*
3598 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * *
3647 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
*
3696 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * *
3745 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* *
3794 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * *
3843 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
*
3892 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * *
3941 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* *
3990 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * *
4039 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
*
4088 TGCTGAGTCAAGG-CAGCTACATTGGACTTAAAGATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
4124 GAAAAGGCCA
Statistics
Matches: 666, Mismatches: 77, Indels: 32
0.86 0.10 0.04
Matches are distributed among these distances:
42 7 0.01
43 64 0.10
44 4 0.01
45 2 0.00
46 2 0.00
47 2 0.00
48 94 0.14
49 460 0.69
50 1 0.00
51 2 0.00
52 28 0.04
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.24
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
Found at i:3756 original size:98 final size:98
Alignment explanation
Indices: 3247--4123 Score: 1424
Period size: 98 Copynumber: 9.0 Consensus size: 98
3237 AAAAGTGATA
* * * * * *
3247 AAGATGCCAATATGTTGATTTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGTCA
1 AAGATGCCAATATGCTGA-TTCAAGGCCAGCGATATTGGACTTAAAGAT--G---AAGG-TGCCA
* * *
3312 ACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
59 ATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G
* *
3353 AAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTG
1 AAGA--TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
*
3412 CTGATTCAAGGCCAGCTACA-TGGACTTAAAGATG
64 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
3446 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
3505 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
*
3538 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG-AGGTGCTAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
3602 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
3635 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
3700 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
3733 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
3798 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
*
3831 GAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
3896 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
3929 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
3994 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
*
4027 GAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
4092 GAGTCAAGG-CAGCTACATTGGACTTAAAGATG
66 GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
4124 GAAAAGGCCA
Statistics
Matches: 743, Mismatches: 18, Indels: 29
0.94 0.02 0.04
Matches are distributed among these distances:
91 71 0.10
92 56 0.08
93 4 0.01
94 12 0.02
95 28 0.04
96 5 0.01
97 119 0.16
98 412 0.55
103 1 0.00
106 3 0.00
107 19 0.03
108 13 0.02
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.24
Consensus pattern (98 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
GAGTCAAGGCCAGCTACATTGGACTTAAAGATG
Found at i:4192 original size:33 final size:34
Alignment explanation
Indices: 4153--4217 Score: 123
Period size: 33 Copynumber: 1.9 Consensus size: 34
4143 GGCTTAGAGG
4153 GGTTGCCACCGACTTGTGTGGGCTTT-GGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAGAA
4186 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG
1 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG
4218 GAAAAAGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.17, C:0.18, G:0.37, T:0.28
Consensus pattern (34 bp):
GGTTGCCACCGACTTGTGTGGGCTTTAGGAAGAA
Found at i:4290 original size:34 final size:34
Alignment explanation
Indices: 4202--4721 Score: 463
Period size: 33 Copynumber: 15.3 Consensus size: 34
4192 CACCGACTTG
* *
4202 TGTGGGCTTTAGGAAGGAAAAAGA-TGCCACAGAGT
1 TGTGGGCTTTA--AAAGAAAAAGAGTGCCACGGAGT
* *
4237 TGTGGAC-TTAAAAGGGAAAAAGAGTGCCACAGAGT
1 TGTGGGCTTTAAAA--GAAAAAGAGTGCCACGGAGT
4272 TGTGGGCTTTAAAAGAAAAA-AGTGCCACGGAGT
1 TGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGT
4305 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAA--GAAAAAGAGTGCCACGGAGT
*
4342 TGTGGGCTTTTAAACGGAAAAAG-GTGCCACGGAGT
1 TGTGGGC-TTTAAA-AGAAAAAGAGTGCCACGGAGT
**
4377 TGTGGGCTTTGAAAAAGAAAAAAAGAGTGCCACAAAGT
1 TGTGGGCTTT--AAAAG--AAAAAGAGTGCCACGGAGT
* * *
4415 TGTGGGCTTTTAGAGAAGAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGT
* * * *
4448 TGTGGGCTTGAAAAGAAGAAG-GTTGCCACCGACTT
1 TGTGGGCTTTAAAAGAAAAAGAG-TGCCACGGA-GT
* *
4483 GTGTGGGCTTTAGGAAGGGAGAAAGA-TGCCACGGAGT
1 -TGTGGGCTTTA--AA-AGAAAAAGAGTGCCACGGAGT
* * *
4520 TGTGGAC-ATAAAAGGGAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAA-GAAAAAGAGTGCCACGGAGT
4554 TGTGGGCTTTAAAAGAAAAA-AGTGCCACGGAGT
1 TGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGT
4587 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTT-AAAAGAAAAAGAGTGCCACGGAGT
*
4621 TGTGGGC-TTAAACG-----G-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGT
* *
4648 TGTGGAC-TTAAAAGGAACAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAA-GAAAAAGAGTGCCACGGAGT
*
4681 TGTGGGCTTT-AAAGAAAAA-A-TGCCACTGAGT
1 TGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGT
* *
4712 CGTGGACTTT
1 TGTGGGCTTT
4722 GAGACAAAAT
Statistics
Matches: 410, Mismatches: 40, Indels: 74
0.78 0.08 0.14
Matches are distributed among these distances:
27 24 0.06
28 1 0.00
31 18 0.04
32 11 0.03
33 106 0.26
34 90 0.22
35 51 0.12
36 41 0.10
37 30 0.07
38 33 0.08
39 5 0.01
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.21
Consensus pattern (34 bp):
TGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGT
Found at i:4646 original size:27 final size:27
Alignment explanation
Indices: 4608--4659 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
4598 AAAAGAAAAA
*
4608 GGTGCCACGGAGTTGTGGGCTTAAACG
1 GGTGCCACGGAGTTGTGGACTTAAACG
4635 GGTGCCACGGAGTTGTGGACTTAAA
1 GGTGCCACGGAGTTGTGGACTTAAA
4660 AGGAACAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.23
Consensus pattern (27 bp):
GGTGCCACGGAGTTGTGGACTTAAACG
Found at i:4732 original size:30 final size:31
Alignment explanation
Indices: 4637--4754 Score: 121
Period size: 30 Copynumber: 3.8 Consensus size: 31
4627 CTTAAACGGG
* * * **
4637 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGG
1 TGCCACTGAGTCGTGGACTTTAAA-GAA-AAAA
* * *
4670 TGCCACGGAGTTGTGGGCTTTAAAGAAAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAA
* *
4701 TGCCACTGAGTCGTGGACTTT-GAGACAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAA
4731 TGCCACTGAGTCGTGGACTTTAAA
1 TGCCACTGAGTCGTGGACTTTAAA
4755 AAGGTATTTG
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
30 28 0.38
31 21 0.28
32 3 0.04
33 22 0.30
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTAAAGAAAAAA
Found at i:5718 original size:17 final size:16
Alignment explanation
Indices: 5686--5716 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5676 TTTCCTCTCT
*
5686 TTTTTTTTCTTTTTTG
1 TTTTGTTTCTTTTTTG
5702 TTTTGTTTCTTTTTT
1 TTTTGTTTCTTTTTT
5717 TGGAAAAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.87
Consensus pattern (16 bp):
TTTTGTTTCTTTTTTG
Found at i:12985 original size:52 final size:52
Alignment explanation
Indices: 12917--13057 Score: 221
Period size: 52 Copynumber: 2.7 Consensus size: 52
12907 TGAAAAGTTA
12917 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGAAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGAAAATTTGC
* * *
12969 CTGCATGTATCGATACATTTTATACTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGAAAATTTGC
**
13021 CTGCATGTATCGATACA-AAAATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
13058 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
51 2 0.02
52 79 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGAAAATTTGC
Found at i:13064 original size:13 final size:13
Alignment explanation
Indices: 13046--13070 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13036 CAAAAATCAG
13046 TGTATCGATACAA
1 TGTATCGATACAA
13059 TGTATCGATACA
1 TGTATCGATACA
13071 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:13154 original size:13 final size:13
Alignment explanation
Indices: 13136--13160 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13126 CAAAAAAATA
13136 TGTATCGATACAT
1 TGTATCGATACAT
13149 TGTATCGATACA
1 TGTATCGATACA
13161 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:13156 original size:33 final size:33
Alignment explanation
Indices: 13114--13180 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
13104 AGTAGCTTAA
13114 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
13147 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
13180 A
1 A
13181 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:13259 original size:21 final size:21
Alignment explanation
Indices: 13218--13259 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
13208 GTTGGGACCT
*
13218 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
13239 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
13260 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:16019 original size:20 final size:19
Alignment explanation
Indices: 15994--16067 Score: 85
Period size: 20 Copynumber: 3.8 Consensus size: 19
15984 ACAAAAACAG
15994 AATGTATCGATACATTGACA
1 AATGTATCGATACATTGA-A
*
16014 AATGTATCGATACATTCATA
1 AATGTATCGATACATTGA-A
* * *
16034 CATTTATCGATGCATTGAA
1 AATGTATCGATACATTGAA
*
16053 AATGTATCAATACAT
1 AATGTATCGATACAT
16068 CTGGGTAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
19 12 0.27
20 32 0.73
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:19139 original size:20 final size:22
Alignment explanation
Indices: 19116--19169 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
19106 ACAATTCAAA
*
19116 GTATCGATACATTG-CA-ACAT
1 GTATCGATACATTGAAAGACAT
*
19136 GTATCGATACA-TGAAAGAGAT
1 GTATCGATACATTGAAAGACAT
19157 GTATCGATACATT
1 GTATCGATACATT
19170 TCTTGGCAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 2 0.07
20 12 0.41
21 14 0.48
22 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (22 bp):
GTATCGATACATTGAAAGACAT
Found at i:19225 original size:13 final size:13
Alignment explanation
Indices: 19207--19232 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19197 TACACCAAGT
19207 ATGTATCGATACA
1 ATGTATCGATACA
19220 ATGTATCGATACA
1 ATGTATCGATACA
19233 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:21684 original size:19 final size:20
Alignment explanation
Indices: 21641--21691 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
21631 CACACCCAGA
* *
21641 TGTATCGATACTTATTGCTT
1 TGTATCGATACATATTGCAT
*
21661 TGTATCGATACATGTT-CAT
1 TGTATCGATACATATTGCAT
21680 TGTATCGATACA
1 TGTATCGATACA
21692 CACTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATATTGCAT
Found at i:23398 original size:12 final size:12
Alignment explanation
Indices: 23383--23407 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23373 TCAACCATCA
23383 AAGATGATGATG
1 AAGATGATGATG
23395 AAGATGATGATG
1 AAGATGATGATG
23407 A
1 A
23408 CGAAGTTGAC
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:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (12 bp):
AAGATGATGATG
Found at i:30528 original size:13 final size:13
Alignment explanation
Indices: 30510--30536 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
30500 ACATAGGTAT
30510 TTGTATCGATACA
1 TTGTATCGATACA
30523 TTGTATCGATACA
1 TTGTATCGATACA
30536 T
1 T
30537 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:30650 original size:20 final size:20
Alignment explanation
Indices: 30603--30655 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
30593 AAACTCACAT
*
30603 TGTATCGATACATGAAGGAT
1 TGTATCGATACATGAAGGAA
* *
30623 TGTGTCGATACATG-GGGAAA
1 TGTATCGATACATGAAGG-AA
30643 TGTATCGATACAT
1 TGTATCGATACAT
30656 TGAGCCCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATGAAGGAA
Found at i:31757 original size:156 final size:153
Alignment explanation
Indices: 31469--31992 Score: 559
Period size: 156 Copynumber: 3.4 Consensus size: 153
31459 GTTGGTTCTA
* * * * *
31469 AGGGATACTTTCGACGTAAAAGTACTCGATACCCCTAAACGACTTAAAAAGGATTTTAAAAAGGG
1 AGGGATACCTTCGACGTAAAAGTGCCCGATACCCCTAAAAGACTTAAAAAGGATTAT-AAAAGGG
*
31534 ATGAACCTATCCTAAATATCTACCTTCGGCATAAAAGCTGATCTAGTGATGACATAGGAGTTGGT
65 ATGAACCTATCCTAAATATCTACCTTCGGCATAAAAGCTGACCTAGTGATGACATAGGA-TTGGT
*
31599 TCTAAAAAATTACAAAAATGCCTCT
129 TCTAAAAAATTACAAAAATACCTCT
* * *
31624 AGGAGATACCTTCGACGTAAAAGTGCCCGATACCCCTAAAAGTCCTAAAAAGGATTACAAAATGG
1 AGG-GATACCTTCGACGTAAAAGTGCCCGATACCCCTAAAAGACTTAAAAAGGATTATAAAA-GG
* * * *
31689 GATGAACATATCCTAAATAT-TAACCTTCGGCATAAGAA-CTGACCTAGTGATGACCTATGACTC
64 GATGAACCTATCCTAAATATCT-ACCTTCGGCATAA-AAGCTGACCTAGTGATGACATAGGA-TT
* * *
31752 AGTTCTAAAAAATTACCAAAATACACCTAT
126 GGTTCTAAAAAATTA-CAAAA-ATACCTCT
* * * * * * * * *
31782 AGGTATACCTTCGACATGAAAGTATCCCGATATCCCTAAAGGACTTAAAAATGATTATAGAAGAG
1 AGGGATACCTTCGACGTAAAAGT-GCCCGATACCCCTAAAAGACTTAAAAAGGATTATAAAAGGG
* * ** * * *
31847 ATGAACCTATCCAAAATATCTACCTTTGGCATAAAAGCAAACC-CGACGATGACGTAGGATTGGT
65 ATGAACCTATCCTAAATATCTACCTTCGGCATAAAAGCTGACCTAG-TGATGACATAGGATTGGT
*
31911 TCTAAAAAAATTACGAAAATACCTCT
129 TCT-AAAAAATTACAAAAATACCTCT
** * * *
31937 AAGGGATACCTTCGACGTAAAAGTGCTTGATACCTCTCAAAGACTTAAAAGGGATT
1 -AGGGATACCTTCGACGTAAAAGTGCCCGATACCCCTAAAAGACTTAAAAAGGATT
31993 TATAGATGTG
Statistics
Matches: 301, Mismatches: 56, Indels: 24
0.79 0.15 0.06
Matches are distributed among these distances:
155 37 0.12
156 147 0.49
157 78 0.26
158 39 0.13
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (153 bp):
AGGGATACCTTCGACGTAAAAGTGCCCGATACCCCTAAAAGACTTAAAAAGGATTATAAAAGGGA
TGAACCTATCCTAAATATCTACCTTCGGCATAAAAGCTGACCTAGTGATGACATAGGATTGGTTC
TAAAAAATTACAAAAATACCTCT
Done.