Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_537
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: 61573
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3155 original size:24 final size:24
Alignment explanation
Indices: 3123--3183 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
3113 AACCGTATTT
* * *
3123 GCACACATAGTGCTA-ATTACACTC
1 GCACACATAGTGCCATAGTA-AATC
3147 GCACACATAGTGCCATAGTAAATC
1 GCACACATAGTGCCATAGTAAATC
3171 GCACACATAGTGC
1 GCACACATAGTGC
3184 ATTGGATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 30 0.91
25 3 0.09
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.21
Consensus pattern (24 bp):
GCACACATAGTGCCATAGTAAATC
Found at i:5474 original size:78 final size:78
Alignment explanation
Indices: 5341--5570 Score: 388
Period size: 78 Copynumber: 2.9 Consensus size: 78
5331 GAGTCACATC
* * * * *
5341 TCATGTAACTGTAGTGAATCAGGATTACCTTTTCAAGTCAGATCCTATCCACCTTAGGTTACCAT
1 TCATGTAACTGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCGCCTTAAGTTACCAT
*
5406 AATGAATCATATA
66 AGTGAATCATATA
5419 TCATGTAACTGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCGCCTTAAGTTACCAT
1 TCATGTAACTGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCGCCTTAAGTTACCAT
5484 AGTGAATCATATA
66 AGTGAATCATATA
* *
5497 TCATGTAATTGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCGCCTTAAGTTACTAT
1 TCATGTAACTGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCGCCTTAAGTTACCAT
5562 AGTGAATCA
66 AGTGAATCA
5571 GGAATAAATC
Statistics
Matches: 144, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 144 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (78 bp):
TCATGTAACTGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCGCCTTAAGTTACCAT
AGTGAATCATATA
Found at i:5583 original size:40 final size:40
Alignment explanation
Indices: 5535--5672 Score: 177
Period size: 40 Copynumber: 3.5 Consensus size: 40
5525 CTTTTCAGGT
* *
5535 CAAATCCTATCCGCCTTAAGTTACTATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAGTTACTATAGTGAATCAGGAA
* * * * *
5575 TAAATCCTATTCACTTTAAATTACCATAGTGAATTAGGAA
1 CAAATCCTATCCACTTTAAGTTACTATAGTGAATCAGGAA
* * *
5615 CAAATCCTATCCACTTTGAGGTATTATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAGTTACTATAGTGAATCAGGAA
*
5655 CGAATCCTATCCACTTTA
1 CAAATCCTATCCACTTTA
5673 TATTCTCGAG
Statistics
Matches: 81, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAGTTACTATAGTGAATCAGGAA
Found at i:12833 original size:27 final size:27
Alignment explanation
Indices: 12801--12977 Score: 194
Period size: 27 Copynumber: 6.5 Consensus size: 27
12791 TTAAATTGTA
12801 TAGCACTAAGTGTGCGATTTGACTATG
1 TAGCACTAAGTGTGCGATTTGACTATG
* ** *
12828 TTGCACTAAGTGTGCGAAATGAATATG
1 TAGCACTAAGTGTGCGATTTGACTATG
* *
12855 -ATGCACTAAGTGTGCGAATTGACCATG
1 TA-GCACTAAGTGTGCGATTTGACTATG
** *
12882 CGGCACTAAGTGTGCGAGTTTGAGTATG
1 TAGCACTAAGTGTGCGA-TTTGACTATG
* *
12910 TAGCACTAAGTGTGCGATTTGATTACG
1 TAGCACTAAGTGTGCGATTTGACTATG
* * *
12937 TAGCACTAAGTGTGCGAGTTGATTATA
1 TAGCACTAAGTGTGCGATTTGACTATG
*
12964 TAGCACTGAGTGTG
1 TAGCACTAAGTGTG
12978 TGGACTCAAT
Statistics
Matches: 127, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 105 0.83
28 22 0.17
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (27 bp):
TAGCACTAAGTGTGCGATTTGACTATG
Found at i:12916 original size:82 final size:81
Alignment explanation
Indices: 12803--12958 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
12793 AAATTGTATA
* *
12803 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
12867 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
12884 GCACTAAGTGTGCGAGTTTGAGTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
12949 TGCGAGTTGA
65 TGCGAATTGA
12959 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:12970 original size:82 final size:81
Alignment explanation
Indices: 12799--12977 Score: 216
Period size: 82 Copynumber: 2.2 Consensus size: 81
12789 GATTAAATTG
* *
12799 TATAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TATAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
12864 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
*** * ** *
12880 TGCGGCACTAAGTGTGCGAGTTTGAGTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TATAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
12944 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
*
12962 TATAGCACTGAGTGTG
1 TATAGCACTAAGTGTG
12978 TGGACTCAAT
Statistics
Matches: 80, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
81 17 0.21
82 63 0.79
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (81 bp):
TATAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:20981 original size:27 final size:27
Alignment explanation
Indices: 20949--21126 Score: 198
Period size: 27 Copynumber: 6.6 Consensus size: 27
20939 TTAAATTGTA
20949 TAGCACTAAGTGTGCGATTTGACTATG
1 TAGCACTAAGTGTGCGATTTGACTATG
* ** *
20976 TTGCACTAAGTGTGC-AAATGAATATG
1 TAGCACTAAGTGTGCGATTTGACTATG
* *
21002 -ATGCACTAAGTGTGCGAATTGACCATG
1 TA-GCACTAAGTGTGCGATTTGACTATG
**
21029 CGGCACTAAGTGTGCGAGTTTGACTATG
1 TAGCACTAAGTGTGCGA-TTTGACTATG
* *
21057 TAGCACTAAGTGTGCGATTTGATTACG
1 TAGCACTAAGTGTGCGATTTGACTATG
* * *
21084 TAGCACTAAGTGTGCGAGTTGATTATA
1 TAGCACTAAGTGTGCGATTTGACTATG
*
21111 TAGCACTGAGTGTGCG
1 TAGCACTAAGTGTGCG
21127 GACTCAATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
26 21 0.16
27 84 0.66
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
TAGCACTAAGTGTGCGATTTGACTATG
Found at i:21090 original size:55 final size:54
Alignment explanation
Indices: 20949--21126 Score: 207
Period size: 55 Copynumber: 3.3 Consensus size: 54
20939 TTAAATTGTA
* **
20949 TAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGC-AAATGAATATG
1 TAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATG
* * ** *
21002 -ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATG
1 TA-GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAG-TTGAATATG
* * * *
21057 TAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTATA
1 TAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATG
*
21111 TAGCACTGAGTGTGCG
1 TAGCACTAAGTGTGCG
21127 GACTCAATAT
Statistics
Matches: 105, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
52 1 0.01
53 36 0.34
54 23 0.22
55 44 0.42
56 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (54 bp):
TAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAGTTGAATATG
Found at i:27892 original size:31 final size:31
Alignment explanation
Indices: 27849--27963 Score: 196
Period size: 31 Copynumber: 3.7 Consensus size: 31
27839 TTAGTCTTGA
27849 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
27879 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
**
27910 CATATCACTGGGCCGAAGCCTTTTTGTAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
27941 CATTTCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
27964 ACTGTAAACG
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
30 5 0.06
31 76 0.94
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:28038 original size:42 final size:42
Alignment explanation
Indices: 27987--28078 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
27977 TGGCCCATAG
* ** * *
27987 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGTAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
* *
28029 GCCTATTTCAATATCATATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
28071 GCCCATTT
1 GCCCATTT
28079 GGGGAGACTA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:28252 original size:25 final size:26
Alignment explanation
Indices: 28224--28371 Score: 221
Period size: 25 Copynumber: 5.8 Consensus size: 26
28214 CTCTTTTAAT
28224 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
28249 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* **
28274 AACTGGGGCA-AAGCCCTTTCCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
28299 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCGGTA
* **
28325 AACTGGGGCATAAGCCCTATTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTA
28351 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
28372 GCACTTCCTC
Statistics
Matches: 112, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
25 57 0.51
26 55 0.49
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGGTA
Found at i:28362 original size:52 final size:50
Alignment explanation
Indices: 28224--28371 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 50
28214 CTCTTTTAAT
**
28224 AACTGGGGCAAAGCCCTTTTCGGTAAACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCC-TTTCAATAAACTGGGGCATAAGCCCTTTTCGGTA
28274 AACTGGGGCAAAGCCCTTTCCAATAAACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTT-CAATAAACTGGGGCATAAGCCCTTTTCGGTA
28325 AACTGGGGCATAAGCCCTATTCAATAAACTGGGGCATAAGCCCTTTT
1 AACTGGGGCA-AAGCCCT-TTCAATAAACTGGGGCATAAGCCCTTTT
28372 GCACTTCCTC
Statistics
Matches: 92, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
49 3 0.03
50 29 0.32
51 25 0.27
52 33 0.36
53 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (50 bp):
AACTGGGGCAAAGCCCTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTA
Found at i:28446 original size:20 final size:20
Alignment explanation
Indices: 28421--28487 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
28411 TTATGAATAC
28421 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
*
28441 ATCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACAT
*
28461 ATCATGTGCATATCATATCA-
1 ATCATGTGCATTTCATA-CAT
28481 ATCATGT
1 ATCATGT
28488 ATATCATATC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.40
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAT
Found at i:28550 original size:25 final size:25
Alignment explanation
Indices: 28522--28596 Score: 96
Period size: 25 Copynumber: 3.0 Consensus size: 25
28512 ATAATTAAAC
* * * *
28522 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATAGTCATTTTCA
* *
28547 CCTAGAGGCAAAACAGTCATTTTCA
1 CCTAGGGGCAAAATAGTCATTTTCA
28572 CCTAGGGGCAAAATAGTCATTTTCA
1 CCTAGGGGCAAAATAGTCATTTTCA
28597 TACTATAAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (25 bp):
CCTAGGGGCAAAATAGTCATTTTCA
Found at i:29277 original size:27 final size:27
Alignment explanation
Indices: 29218--29279 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
29208 CGTATTCATA
*
29218 ATTTTACCATACAAGGGTATTACAGTC
1 ATTTTACCATACAAGGGCATTACAGTC
* * * *
29245 ACTTTACCCTACAGGGGCATTACGGTC
1 ATTTTACCATACAAGGGCATTACAGTC
*
29272 TTTTTACC
1 ATTTTACC
29280 TATTAGGGGT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (27 bp):
ATTTTACCATACAAGGGCATTACAGTC
Found at i:29389 original size:27 final size:27
Alignment explanation
Indices: 29313--29462 Score: 142
Period size: 27 Copynumber: 5.6 Consensus size: 27
29303 CATCCTACAA
* * * * *
29313 GGGTGTTTTGGTAAATCTACAAATCAA
1 GGGTATTTTGGTAATTTTACAAATTAG
**
29340 GGGTATTTT-GTAATTTTGTAAATTAG
1 GGGTATTTTGGTAATTTTACAAATTAG
29366 GGGTATTTTGGTAATTTTACAAATT-G
1 GGGTATTTTGGTAATTTTACAAATTAG
* * **
29392 AGGATATTTTGGTAATTTCACAAACCAG
1 -GGGTATTTTGGTAATTTTACAAATTAG
* * *
29420 TGGTATTTTGATAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAATTAG
*
29447 GGGTGTTTTGGTAATT
1 GGGTATTTTGGTAATT
29463 CTACCCTATA
Statistics
Matches: 99, Mismatches: 21, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
26 21 0.21
27 77 0.78
28 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATTAG
Found at i:29623 original size:55 final size:55
Alignment explanation
Indices: 29562--29690 Score: 138
Period size: 55 Copynumber: 2.3 Consensus size: 55
29552 GAGGGTAAAA
* * * *
29562 CAGTAATTCTATAAATCGAT-GGTACTTTGGTAATTTTTACAAGTCGAGG-GTATTT
1 CAGTAATTTTATAAATCGATGGGTACTTTAGTAA-TTTTACAA-ACCAGGAGTATTT
* *
29617 CAGTAATTTTACAAATC-ATGGGGTATTTTAGTAATTTTACAAACCAGGAGTATTT
1 CAGTAATTTTATAAATCGAT-GGGTACTTTAGTAATTTTACAAACCAGGAGTATTT
* *
29672 TAGTAATTTTGTAAATCGA
1 CAGTAATTTTATAAATCGA
29691 GGATAAAACG
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
54 6 0.10
55 43 0.70
56 12 0.20
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.40
Consensus pattern (55 bp):
CAGTAATTTTATAAATCGATGGGTACTTTAGTAATTTTACAAACCAGGAGTATTT
Found at i:29787 original size:27 final size:27
Alignment explanation
Indices: 29494--29776 Score: 144
Period size: 27 Copynumber: 10.4 Consensus size: 27
29484 GTAAATTTAC
* * *
29494 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTCTATA
* *
29521 AATC-AGGGGTAAAATAGTAATTCTGTA
1 AATCGA-GGGTAAAATGGTAATTCTATA
**
29548 AATCGAGGGTAAAACAGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTATA
* *** *
29575 AATCGATGGTACTTTGGTAATT-TTTA
1 AATCGAGGGTAAAATGGTAATTCTATA
** * * *
29601 CAAGTCGAGGGT-ATTTCAGTAATTTTACA
1 -AA-TCGAGGGTAAAAT-GGTAATTCTATA
*** * * *
29630 AATC-ATGGGGTATTTTAGTAATTTTACA
1 AATCGA--GGGTAAAATGGTAATTCTATA
* *** * * *
29658 AA-CCAGGAGTATTTTAGTAATTTTGTA
1 AATCGAGG-GTAAAATGGTAATTCTATA
* *
29685 AATCGAGGATAAAACGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTATA
29712 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTCTATA
* * *
29739 AATCGAGGGTAGAACGGTAATTCTGTA
1 AATCGAGGGTAAAATGGTAATTCTATA
*
29766 AATCGGGGGTA
1 AATCGAGGGTA
29777 CTTTGGTAAT
Statistics
Matches: 209, Mismatches: 35, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
26 7 0.03
27 158 0.76
28 39 0.19
29 5 0.02
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTCTATA
Found at i:33440 original size:22 final size:22
Alignment explanation
Indices: 33415--33458 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
33405 CACAGACATG
** *
33415 CCCTAGGGTCACATGGGCGTGT
1 CCCTAGGACCACACGGGCGTGT
*
33437 CCCTTGGACCACACGGGCGTGT
1 CCCTAGGACCACACGGGCGTGT
33459 GAGCCCTGCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.32, G:0.34, T:0.20
Consensus pattern (22 bp):
CCCTAGGACCACACGGGCGTGT
Found at i:38230 original size:39 final size:40
Alignment explanation
Indices: 38135--38436 Score: 372
Period size: 39 Copynumber: 7.7 Consensus size: 40
38125 TTGAATGATG
*
38135 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
38173 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
38214 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
38253 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
38292 TCCGGGCTAAG-CCCGAAGGCATTTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* * *
38331 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
38371 TCCGGGTTAAGTCCCAAAGGCATTTGTGCGA-ATGACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGAT-ACTAAT
* *
38410 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
38437 AACGAGGAGC
Statistics
Matches: 239, Mismatches: 15, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
39 132 0.55
40 95 0.40
41 11 0.05
42 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:46557 original size:40 final size:40
Alignment explanation
Indices: 46281--46543 Score: 324
Period size: 40 Copynumber: 6.7 Consensus size: 40
46271 TTGAATGATG
* * *
46281 TCCGGGCTAAGTCCTGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
* * *
46320 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
46360 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
46399 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
46438 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
46478 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
46519 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
46544 AACGAGGAGC
Statistics
Matches: 202, Mismatches: 15, Indels: 13
0.88 0.07 0.06
Matches are distributed among these distances:
39 89 0.44
40 103 0.51
41 10 0.05
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:50622 original size:26 final size:26
Alignment explanation
Indices: 50593--50652 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
50583 TTACCCCCAG
* *
50593 TAAAATTTTGATGATTTTACATCTAA
1 TAAAATTTTGACGATTTTACACCTAA
* * *
50619 TAAAATTTTGGCGATTTTACCCCTAG
1 TAAAATTTTGACGATTTTACACCTAA
50645 TAAAATTT
1 TAAAATTT
50653 GAGAAAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (26 bp):
TAAAATTTTGACGATTTTACACCTAA
Found at i:50906 original size:10 final size:10
Alignment explanation
Indices: 50882--50910 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
50872 TTATTTCTCC
50882 TTTCTATTC-
1 TTTCTATTCA
50891 TTTCTATTCA
1 TTTCTATTCA
50901 TTTCTATTCA
1 TTTCTATTCA
50911 AACATGCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.17, C:0.21, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:53305 original size:48 final size:48
Alignment explanation
Indices: 53228--53363 Score: 121
Period size: 48 Copynumber: 2.8 Consensus size: 48
53218 CACAGGTGAA
* * ** * **
53228 AATAATAGTGCTTGGTTACCCGTTTGGGTTAAACCTATATGAATAATG
1 AATAATAGTCCATGGTTACCCGTCAGGGTTAAACCTACACAAATAATG
* *
53276 AATAATAGTCCATGGTTACCTGTCAGGGTTAAACGTACACAAATAATG
1 AATAATAGTCCATGGTTACCCGTCAGGGTTAAACCTACACAAATAATG
* * * * * *
53324 AGTAATAGTGTC-TGGATACTCGTTAGGGTTGAACCTACAC
1 AATAATAGT-CCATGGTTACCCGTCAGGGTTAAACCTACAC
53364 GATAAATAGC
Statistics
Matches: 70, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
48 69 0.99
49 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (48 bp):
AATAATAGTCCATGGTTACCCGTCAGGGTTAAACCTACACAAATAATG
Found at i:58403 original size:47 final size:48
Alignment explanation
Indices: 58275--58437 Score: 213
Period size: 48 Copynumber: 3.4 Consensus size: 48
58265 TAGACTAGCT
*** * * * * *
58275 ATGGTCTTACATGATTTCTCATATCGATGCTAATGCCATATCCCAAAT
1 ATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGTCCCAGAC
* * *
58323 ATGGTATTACATGGTATCAAATATCGATG-CAATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGTCCCAGAC
58370 AT-GTCTTACATGGGATCACATATCGATGCCAATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGTCCCAGAC
58417 ATGGTCTTACATGGGATCACA
1 ATGGTCTTACATGGGATCACA
58438 CATAACCCTA
Statistics
Matches: 101, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
46 23 0.23
47 36 0.36
48 42 0.42
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (48 bp):
ATGGTCTTACATGGGATCACATATCGATGCCAATGCCATGTCCCAGAC
Done.