Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_375
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: 83997
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1777 original size:17 final size:19
Alignment explanation
Indices: 1745--1779 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1735 GGGGCTGTTC
1745 TGGGCCACGATGGGCCTGA
1 TGGGCCACGATGGGCCTGA
1764 TGGGCC-CG-TGGGCCTG
1 TGGGCCACGATGGGCCTG
1780 CCTGTGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.09, C:0.29, G:0.46, T:0.17
Consensus pattern (19 bp):
TGGGCCACGATGGGCCTGA
Found at i:2462 original size:22 final size:21
Alignment explanation
Indices: 2437--2510 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 21
2427 GGCCTTTAGC
2437 CGTCCTGTCTACGACGTTGAG
1 CGTCCTGTCTACGACGTTGAG
*
2458 TCGTCCTGTCTAC-AGCATTGAG
1 -CGTCCTGTCTACGA-CGTTGAG
* * *
2480 CCGTCTTGTCTATGGCGTTGAG
1 -CGTCCTGTCTACGACGTTGAG
2502 CTGTCCTGT
1 C-GTCCTGT
2511 TGACTTAGTG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
21 2 0.05
22 40 0.95
ACGTcount: A:0.12, C:0.27, G:0.27, T:0.34
Consensus pattern (21 bp):
CGTCCTGTCTACGACGTTGAG
Found at i:10891 original size:27 final size:26
Alignment explanation
Indices: 10853--10938 Score: 109
Period size: 27 Copynumber: 3.2 Consensus size: 26
10843 GGAGGAAGTA
10853 TTCTGGTGGCTCTGCCACAAATATCTG
1 TTCTGGTGGCTCTGCCAC-AATATCTG
10880 TTCTGGTGGCTCTGCCACAATATCTG
1 TTCTGGTGGCTCTGCCACAATATCTG
* * * * *
10906 TATCTGGTGACGCTGTCACAATGTCTA
1 T-TCTGGTGGCTCTGCCACAATATCTG
10933 TTCTGG
1 TTCTGG
10939 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
26 14 0.26
27 39 0.74
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.35
Consensus pattern (26 bp):
TTCTGGTGGCTCTGCCACAATATCTG
Found at i:16464 original size:16 final size:16
Alignment explanation
Indices: 16426--16464 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
16416 GAAAACCCCT
* *
16426 AAAAGGACCTTTTTAC
1 AAAAGGTCCTTTATAC
*
16442 AAAAGGTCCTTTATGC
1 AAAAGGTCCTTTATAC
16458 AAAAGGT
1 AAAAGGT
16465 GTAAAATATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (16 bp):
AAAAGGTCCTTTATAC
Found at i:22863 original size:23 final size:22
Alignment explanation
Indices: 22811--22863 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
22801 TCCACGTCTT
*
22811 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
22833 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
22856 TTTCTTTT
1 TTTCTTTT
22864 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:29214 original size:20 final size:20
Alignment explanation
Indices: 29189--29228 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
29179 TTCAGCTTGG
*
29189 AAGAAATCCTAGGTAATTCT
1 AAGAAATCCCAGGTAATTCT
29209 AAGAAATCCCAGGTAATTCT
1 AAGAAATCCCAGGTAATTCT
29229 TCTCTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (20 bp):
AAGAAATCCCAGGTAATTCT
Found at i:31359 original size:43 final size:42
Alignment explanation
Indices: 31299--31451 Score: 157
Period size: 43 Copynumber: 3.6 Consensus size: 42
31289 GTTCCAGATG
* *
31299 TGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACA
1 TGGTCTTACACGAAATCAAATATCGATGCCA-TGTCCCAGACA
* *
31342 AGGTCTTACACGAAATCAAATA-CAATGCCGATGTCCCAGACA
1 TGGTCTTACACGAAATCAAATATCGATGCC-ATGTCCCAGACA
* * * *
31384 TGGTCTTACACATAAATCATAA-GTCGATGCCAATGTCCTAGACG
1 TGGTCTTACAC-GAAATCA-AATATCGATGCC-ATGTCCCAGACA
* *
31428 TGGTCTTACATGAAATCATATATC
1 TGGTCTTACACGAAATCAAATATC
31452 AGAAATCCTA
Statistics
Matches: 90, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
42 28 0.31
43 34 0.38
44 28 0.31
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (42 bp):
TGGTCTTACACGAAATCAAATATCGATGCCATGTCCCAGACA
Found at i:32667 original size:27 final size:27
Alignment explanation
Indices: 32628--33048 Score: 560
Period size: 27 Copynumber: 15.7 Consensus size: 27
32618 CCCAAAACCA
*
32628 CTGTAGGGTAGAATTATCGAAATACCC
1 CTGTAGGGTAGAATTACCGAAATACCC
* *
32655 TTGTAGGGTAGAATTACCAAAATACCC
1 CTGTAGGGTAGAATTACCGAAATACCC
* *
32682 CTATAGGGTAGAATTATCGAAATACCC
1 CTGTAGGGTAGAATTACCGAAATACCC
* *
32709 CTGTAGGGTAGAATTATCGGAATACCC
1 CTGTAGGGTAGAATTACCGAAATACCC
*
32736 CTGTAGGGTAGAATTATCGAAATACCC
1 CTGTAGGGTAGAATTACCGAAATACCC
*
32763 CTGTAGGGTAGAATTACCGAAATACCA
1 CTGTAGGGTAGAATTACCGAAATACCC
32790 CTGTAGGGTAGAATTACC-AGAATACCC
1 CTGTAGGGTAGAATTACCGA-AATACCC
* * *
32817 CTGTAGGGTAGAATTATCGCAATTCCC
1 CTGTAGGGTAGAATTACCGAAATACCC
*
32844 TTGTAGGGTAGAATTACCGAAATACCC
1 CTGTAGGGTAGAATTACCGAAATACCC
*
32871 TTGTAGGGTAGAATTACCGAAATACCC
1 CTGTAGGGTAGAATTACCGAAATACCC
*
32898 CTGTAGGGTAAAATTACCG-AATACCC
1 CTGTAGGGTAGAATTACCGAAATACCC
* *
32924 CTGTAGGGTAGAATTATCGCAATACCC
1 CTGTAGGGTAGAATTACCGAAATACCC
* *
32951 CTATAGGGTAGAATTACCAAAATACCC
1 CTGTAGGGTAGAATTACCGAAATACCC
* * **
32978 CTATAAGGTAGAATTACTAAAATACCC
1 CTGTAGGGTAGAATTACCGAAATACCC
* *
33005 CTGTAGGGTGGAATTACCGAGATA-CC
1 CTGTAGGGTAGAATTACCGAAATACCC
* * *
33031 TTGTCGGGTAAAATTACC
1 CTGTAGGGTAGAATTACC
33049 ATTTTGCCCC
Statistics
Matches: 351, Mismatches: 40, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
26 41 0.12
27 310 0.88
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (27 bp):
CTGTAGGGTAGAATTACCGAAATACCC
Found at i:33526 original size:22 final size:23
Alignment explanation
Indices: 33477--33527 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
33467 AAGCCTTCTG
* *
33477 ATTATGGCTTTGTGTCAACCTAC
1 ATTATGGCTCTGTGCCAACCTAC
33500 A-TATGGCTCTGTGCCAACCTA-
1 ATTATGGCTCTGTGCCAACCTAC
33521 ATTATGG
1 ATTATGG
33528 TTGTATGCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (23 bp):
ATTATGGCTCTGTGCCAACCTAC
Found at i:33778 original size:27 final size:26
Alignment explanation
Indices: 33696--33797 Score: 114
Period size: 27 Copynumber: 3.8 Consensus size: 26
33686 ATTCTGTTAA
*
33696 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTTTGCCACAATATCTG-TTCTG
* *
33723 GCGGCTATGCCACAAATATCTGTTCTG
1 GTGGCTTTGCCAC-AATATCTGTTCTG
*
33750 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTTTGCCACAATATCTGT-TCTG
* * *
33777 GTGACTTTGTCACAACATCTG
1 GTGGCTTTGCCACAATATCTG
33798 ATAACTGAGT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
26 9 0.14
27 48 0.75
28 7 0.11
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.35
Consensus pattern (26 bp):
GTGGCTTTGCCACAATATCTGTTCTG
Found at i:33966 original size:6 final size:6
Alignment explanation
Indices: 33934--34021 Score: 56
Period size: 6 Copynumber: 14.3 Consensus size: 6
33924 TTGCATTCAC
* * *
33934 ATTCTG ATTTTG ATTCTG -TTACTTG ATACTG ATTCTG ATTCTG ATTTTG
1 ATTCTG ATTCTG ATTCTG ATT-C-TG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
33983 -TCACCTA ATTCTG ATTCTA ATTCTG ATTCT- AGTTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
34022 AATGTTTCTT
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
5 4 0.06
6 51 0.82
7 5 0.08
8 2 0.03
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:33969 original size:31 final size:31
Alignment explanation
Indices: 33934--34012 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
33924 TTGCATTCAC
* * * *
33934 ATTCTGATTTTGATTCTGTTACTTGATACTG
1 ATTCTGATTCTGATTCTGTCACCTAATACTG
* *
33965 ATTCTGATTCTGATTTTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTCACCTAATACTG
*
33996 ATTCTAATTCTGATTCT
1 ATTCTGATTCTGATTCT
34013 AGTTCTGATA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.20, C:0.16, G:0.13, T:0.51
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTCACCTAATACTG
Found at i:36488 original size:40 final size:40
Alignment explanation
Indices: 36412--36707 Score: 348
Period size: 40 Copynumber: 7.5 Consensus size: 40
36402 AAATATAGTA
* * * * *
36412 CCAGCACGAAGCCTACGGATC-TTAAGTCTGGATACAATA
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
*
36451 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCAGATACAATT
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
* *
36491 CCAGCACGAAGCATGTGGGTCTTTAAGCCCGGATACAATTT
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAA-TT
* * * *
36532 CCAGCACGAAGCCTGC-AGACCTTAAGTCCGGATACAATT
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
* *
36571 CCAGCACAAAGCCTGCGGGTCTTTAAGCCCGGATATAATT
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
* *
36611 CCAGCA-TATAGCCTGCGGGTCTTTAAGCCCGGAGACAATT
1 CCAGCACGA-AGCCTGCGGGTCTTTAAGCCCGGATACAATT
* * * * * *
36651 CCAGCACGAAGCTTGC-GGACCTTAAGTCTGGATATAATT
1 CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
36690 CCAGCACGAAGCCTGCGG
1 CCAGCACGAAGCCTGCGG
36708 ACCTTAAGTC
Statistics
Matches: 218, Mismatches: 33, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
39 69 0.32
40 132 0.61
41 17 0.08
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (40 bp):
CCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACAATT
Found at i:36566 original size:120 final size:119
Alignment explanation
Indices: 36412--36707 Score: 441
Period size: 120 Copynumber: 2.5 Consensus size: 119
36402 AAATATAGTA
* * *
36412 CCAGCACGAAGCCTACGGATCTTAAGTCTGGATACAATACCAGCACGAAGCCTGCGGGTCTTTAA
1 CCAGCACGAAGCCTGCGGACCTTAAGTCTGGATACAATTCCAGCACGAAGCCTGCGGGTCTTTAA
* *
36477 GCCCAGATACAATTCCAGCACGA-AGCATGTGGGTCTTTAAGCCCGGATACAATTT
66 GCCCAGATACAATTCCAGCA-GATAGCATGCGGGTCTTTAAGCCCGGAGACAA-TT
* * *
36532 CCAGCACGAAGCCTGCAGACCTTAAGTCCGGATACAATTCCAGCACAAAGCCTGCGGGTCTTTAA
1 CCAGCACGAAGCCTGCGGACCTTAAGTCTGGATACAATTCCAGCACGAAGCCTGCGGGTCTTTAA
* * * *
36597 GCCCGGATATAATTCCAGCATATAGCCTGCGGGTCTTTAAGCCCGGAGACAATT
66 GCCCAGATACAATTCCAGCAGATAGCATGCGGGTCTTTAAGCCCGGAGACAATT
* *
36651 CCAGCACGAAGCTTGCGGACCTTAAGTCTGGATATAATTCCAGCACGAAGCCTGCGG
1 CCAGCACGAAGCCTGCGGACCTTAAGTCTGGATACAATTCCAGCACGAAGCCTGCGG
36708 ACCTTAAGTC
Statistics
Matches: 158, Mismatches: 17, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
119 55 0.35
120 103 0.65
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (119 bp):
CCAGCACGAAGCCTGCGGACCTTAAGTCTGGATACAATTCCAGCACGAAGCCTGCGGGTCTTTAA
GCCCAGATACAATTCCAGCAGATAGCATGCGGGTCTTTAAGCCCGGAGACAATT
Found at i:36725 original size:39 final size:39
Alignment explanation
Indices: 36380--36723 Score: 330
Period size: 40 Copynumber: 8.7 Consensus size: 39
36370 GTACCAGTAT
* ** * * *
36380 GAAGCCTGCGGACCTTAAGTTCAAATATAGTACCAGCAC
1 GAAGCCTGCGGACCTTAAGTCCGGATACAATTCCAGCAC
* * * *
36419 GAAGCCTACGGATCTTAAGTCTGGATACAATACCAGCAC
1 GAAGCCTGCGGACCTTAAGTCCGGATACAATTCCAGCAC
* * * *
36458 GAAGCCTGCGGGTCTTTAAGCCCAGATACAATTCCAGCAC
1 GAAGCCTGC-GGACCTTAAGTCCGGATACAATTCCAGCAC
* * * * *
36498 GAAGCATGTGGGTCTTTAAGCCCGGATACAATTTCCAGCAC
1 GAAGCCTG-CGGACCTTAAGTCCGGATACAA-TTCCAGCAC
*
36539 GAAGCCTGCAGACCTTAAGTCCGGATACAATTCCAGCAC
1 GAAGCCTGCGGACCTTAAGTCCGGATACAATTCCAGCAC
* * * * *
36578 AAAGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCA-
1 GAAGCCTGC-GGACCTTAAGTCCGGATACAATTCCAGCAC
* * * * *
36617 TATAGCCTGCGGGTCTTTAAGCCCGGAGACAATTCCAGCAC
1 GA-AGCCTGC-GGACCTTAAGTCCGGATACAATTCCAGCAC
* * *
36658 GAAGCTTGCGGACCTTAAGTCTGGATATAATTCCAGCAC
1 GAAGCCTGCGGACCTTAAGTCCGGATACAATTCCAGCAC
36697 GAAGCCTGCGGACCTTAAGTCCGGATA
1 GAAGCCTGCGGACCTTAAGTCCGGATA
36724 TACATCAAAT
Statistics
Matches: 255, Mismatches: 44, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
39 106 0.42
40 132 0.52
41 17 0.07
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.22
Consensus pattern (39 bp):
GAAGCCTGCGGACCTTAAGTCCGGATACAATTCCAGCAC
Found at i:39669 original size:2 final size:2
Alignment explanation
Indices: 39662--39687 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39652 GTATTAGCAT
39662 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
39688 TATATATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:42605 original size:39 final size:39
Alignment explanation
Indices: 42561--43062 Score: 164
Period size: 39 Copynumber: 12.9 Consensus size: 39
42551 CTAAGCTCGG
* **
42561 ATATAGTACCAGTACGAAGCCTGTGGACCTTAAGTCCGA
1 ATATAGTACCAGCACGAAGCCTACGGACCTTAAGTCCGA
* * *
42600 ATATAGTACCAGCACGAAGCCTACGGATCTTAAGTCTGG
1 ATATAGTACCAGCACGAAGCCTACGGACCTTAAGTCCGA
* * * * * * * *
42639 ATACAATTCCAACACGAAGCCTGCGGGTCTTTAAG-CCCA
1 ATATAGTACCAGCACGAAGCCTAC-GGACCTTAAGTCCGA
* * * * ** * *
42678 GATACAATTCCAGCACGAAACCTGTGCG-TCTTAAG-CCGG
1 -ATATAGTACCAGCACGAAGCCTACG-GACCTTAAGTCCGA
* * * *
42717 ATACAATTCCAGCACGAAGCCTACGGACCTTAAGTCCGG
1 ATATAGTACCAGCACGAAGCCTACGGACCTTAAGTCCGA
* * * * * * *
42756 ATACAATTCCAGCAC-AAGCCTGCGAGTCTTTAAG-CCGG
1 ATATAGTACCAGCACGAAGCCTACG-GACCTTAAGTCCGA
* * * * *** *
42794 ATATAATTCCAGCA-TATAGCCTGCGGGTTTTAAGCCCGA
1 ATATAGTACCAGCACGA-AGCCTACGGACCTTAAGTCCGA
* * * * * *
42833 ATACAAT-CCAGCAAGAAGCTTGCGGACCTTAAGTCCGG
1 ATATAGTACCAGCACGAAGCCTACGGACCTTAAGTCCGA
* * * * *
42871 ATACAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCGG
1 ATATAGTACCAGCACGAAGCCTACGGACCTTAAGTCCGA
* * * * * *
42910 ATACAATTCCAGCAC-AACGCCTACAGGTCTTTAAGCCCGA
1 ATATAGTACCAGCACGAA-GCCTAC-GGACCTTAAGTCCGA
* * * * * * *
42950 ATATAAT-CCAGCA-TATAACCTGCGGTCTTTAAG-CTCGG
1 ATATAGTACCAGCACGA-AGCCTACGGACCTTAAGTC-CGA
* * * * *
42988 ATACAATTCCAGCACGAAGCTTGCGGACCTTAAGTCC-A
1 ATATAGTACCAGCACGAAGCCTACGGACCTTAAGTCCGA
* * * *
43026 GATACAATTCCAGCACGAAGCCTGCGGACCTTAAGTC
1 -ATATAGTACCAGCACGAAGCCTACGGACCTTAAGTC
43063 TTAATATACA
Statistics
Matches: 381, Mismatches: 62, Indels: 40
0.79 0.13 0.08
Matches are distributed among these distances:
37 2 0.01
38 110 0.29
39 220 0.58
40 49 0.13
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.22
Consensus pattern (39 bp):
ATATAGTACCAGCACGAAGCCTACGGACCTTAAGTCCGA
Found at i:42761 original size:117 final size:115
Alignment explanation
Indices: 42569--43049 Score: 490
Period size: 117 Copynumber: 4.1 Consensus size: 115
42559 GGATATAGTA
* * * * * * *
42569 CCAGTACGAAGCCTGTGGACCTTAAGTCCGAATATAGTACCAGCACGAAGCCTACGGATCTTAAG
1 CCAGCACGAAGCCTGAGG-TCTTAAGCCCGAATACAAT-CCAGCACGAAGCCTACGGACCTTAAG
* * * * *
42634 TCTGGATACAATTCCAACACGAAGCCTGCGGGTCTTTAAGCCCAGATACAATT
64 TCCGGATACAATTCCAGCACGAAGCCTGC-GGACCTTAAGTCCAGATACAATT
* * *
42687 CCAGCACGAAACCTGTGCGTCTTAAG-CCGGATACAATTCCAGCACGAAGCCTACGGACCTTAAG
1 CCAGCACGAAGCCTGAG-GTCTTAAGCCCGAATACAA-TCCAGCACGAAGCCTACGGACCTTAAG
* * * *
42751 TCCGGATACAATTCCAGCAC-AAGCCTGCGAGTCTTTAAG-CCGGATATAATT
64 TCCGGATACAATTCCAGCACGAAGCCTGCG-GACCTTAAGTCCAGATACAATT
* * * * * *
42802 CCAGCA-TATAGCCTGCGGGTTTTAAGCCCGAATACAATCCAGCAAGAAGCTTGCGGACCTTAAG
1 CCAGCACGA-AGCCTG-AGGTCTTAAGCCCGAATACAATCCAGCACGAAGCCTACGGACCTTAAG
*
42866 TCCGGATACAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCGGATACAATT
64 TCCGGATACAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCAGATACAATT
* * * * * * *
42918 CCAGCAC-AACGCCTACAGGTCTTTAAGCCCGAATATAATCCAGCA-TATAACCTGCGGTCTTTA
1 CCAGCACGAA-GCCT-GAGGTC-TTAAGCCCGAATACAATCCAGCACGA-AGCCTACGGACCTTA
*
42981 AG-CTCGGATACAATTCCAGCACGAAGCTTGCGGACCTTAAGTCCAGATACAATT
62 AGTC-CGGATACAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCAGATACAATT
43035 CCAGCACGAAGCCTG
1 CCAGCACGAAGCCTG
43050 CGGACCTTAA
Statistics
Matches: 314, Mismatches: 34, Indels: 32
0.83 0.09 0.08
Matches are distributed among these distances:
114 1 0.00
115 81 0.26
116 63 0.20
117 144 0.46
118 24 0.08
119 1 0.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (115 bp):
CCAGCACGAAGCCTGAGGTCTTAAGCCCGAATACAATCCAGCACGAAGCCTACGGACCTTAAGTC
CGGATACAATTCCAGCACGAAGCCTGCGGACCTTAAGTCCAGATACAATT
Found at i:47340 original size:15 final size:15
Alignment explanation
Indices: 47300--47341 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 15
47290 GAGACTCTCC
47300 AGAAATGCTTGTAAA
1 AGAAATGCTTGTAAA
*
47315 AG--AT-ATTGTAAA
1 AGAAATGCTTGTAAA
47327 AGAAATGCTTGTAAA
1 AGAAATGCTTGTAAA
47342 TGTTAGTGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
12 9 0.41
13 2 0.09
14 2 0.09
15 9 0.41
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.29
Consensus pattern (15 bp):
AGAAATGCTTGTAAA
Found at i:49540 original size:20 final size:21
Alignment explanation
Indices: 49501--49540 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
49491 GTAGGATATG
*
49501 TGTATCGAAGAATTTAGAACT
1 TGTATAGAAGAATTTAGAACT
*
49522 TGTATAGAAG-ATTTTGAAC
1 TGTATAGAAGAATTTAGAAC
49541 AAAGCTGTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (21 bp):
TGTATAGAAGAATTTAGAACT
Found at i:55164 original size:23 final size:24
Alignment explanation
Indices: 55135--55201 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
55125 GAACTTTGTA
55135 AGCTTCCTGATA-GGCTCTACGTG
1 AGCTTCCTGATATGGCTCTACGTG
* * **
55158 AGCTTCCCGATATGGTTCTTTGTG
1 AGCTTCCTGATATGGCTCTACGTG
*
55182 AACTTCCTGATTATGGCTCT
1 AGCTTCCTGA-TATGGCTCT
55202 TATGAGCTTC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
23 11 0.31
24 16 0.46
25 8 0.23
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.37
Consensus pattern (24 bp):
AGCTTCCTGATATGGCTCTACGTG
Found at i:55211 original size:24 final size:23
Alignment explanation
Indices: 55135--55212 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 23
55125 GAACTTTGTA
55135 AGCTTCCTGATA-GGCTC-TACGTG
1 AGCTTCCTGATATGGCTCTTA--TG
* * *
55158 AGCTTCCCGATATGGTTCTTTGTG
1 AGCTTCCTGATATGGCTC-TTATG
*
55182 AACTTCCTGATTATGGCTCTTATG
1 AGCTTCCTGA-TATGGCTCTTATG
55206 AGCTTCC
1 AGCTTCC
55213 CATCTATAGC
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
23 11 0.26
24 24 0.56
25 7 0.16
26 1 0.02
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (23 bp):
AGCTTCCTGATATGGCTCTTATG
Found at i:55278 original size:24 final size:24
Alignment explanation
Indices: 55233--55284 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
55223 CTGGATAAGC
*
55233 TTCCTGAAAGGCTCTTTATGAG-T
1 TTCCTGAAAGGCTCTGTATGAGCT
* *
55256 TTCCTGAAATTGCTCTGTGTGAGCT
1 TTCCTGAAA-GGCTCTGTATGAGCT
55281 TTCC
1 TTCC
55285 ATTACAAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.38
24 10 0.42
25 5 0.21
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.40
Consensus pattern (24 bp):
TTCCTGAAAGGCTCTGTATGAGCT
Found at i:56119 original size:19 final size:19
Alignment explanation
Indices: 56082--56121 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
56072 AAATATTGGC
* *
56082 TTGATTTAAATGTCTTTAT
1 TTGATTTAAATGGCCTTAT
56101 TTGATTTAAATGGCCTTAT
1 TTGATTTAAATGGCCTTAT
56120 TT
1 TT
56122 TGTCCATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.55
Consensus pattern (19 bp):
TTGATTTAAATGGCCTTAT
Found at i:64378 original size:47 final size:47
Alignment explanation
Indices: 64324--64417 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
64314 GTAAGCCATA
64324 TACAAATAAACTTAACAAATAACATCAATTCATTCATAAAATTTAAG
1 TACAAATAAACTTAACAAATAACATCAATTCATTCATAAAATTTAAG
64371 TACAAATAAACTTAACAAATAACATCAATTCATTCATAAAATTTAAG
1 TACAAATAAACTTAACAAATAACATCAATTCATTCATAAAATTTAAG
64418 GCAAAATACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.53, C:0.15, G:0.02, T:0.30
Consensus pattern (47 bp):
TACAAATAAACTTAACAAATAACATCAATTCATTCATAAAATTTAAG
Found at i:64830 original size:44 final size:42
Alignment explanation
Indices: 64685--64841 Score: 149
Period size: 43 Copynumber: 3.7 Consensus size: 42
64675 ATCTCATACA
* * *
64685 ATGCCAACATCCAAGACGTGGTCTTACATGT-ACTCAAATATCG
1 ATGCCAACATCCCAGACATGGTCTTACATGTAAATC-AA-ATCG
* *
64728 ATGCC-ACTATCCCAGACAGGGTCTTACACG-AAATCAAATACG
1 ATGCCAAC-ATCCCAGACATGGTCTTACATGTAAATCAAAT-CG
* * *
64770 ATTCCAACGTCTCAGACATGGTCTTACATGTAAATCATAAGTCG
1 ATGCCAACATCCCAGACATGGTCTTACATGTAAATCA-AA-TCG
* *
64814 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAACATCCCAGACATGGTCTTACA
64842 CGATGACACA
Statistics
Matches: 94, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
41 2 0.02
42 28 0.30
43 34 0.36
44 29 0.31
45 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (42 bp):
ATGCCAACATCCCAGACATGGTCTTACATGTAAATCAAATCG
Found at i:68759 original size:43 final size:43
Alignment explanation
Indices: 68704--68789 Score: 108
Period size: 43 Copynumber: 2.0 Consensus size: 43
68694 ATATCGTATA
68704 ATGCCAACGTCCCAGAC-GTGGTCTTACAT-GT-AGCCACATATCG
1 ATGCCAACGTCCCAGACAG-GGTCTTAC-TCGTAAG-CACATATCG
68747 ATGCC-ACTGTCCCAGACAGGGTCTTACTCGTAAGCACATATCG
1 ATGCCAAC-GTCCCAGACAGGGTCTTACTCGTAAGCACATATCG
68790 GAGTCACAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
42 3 0.08
43 33 0.85
44 3 0.08
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACAGGGTCTTACTCGTAAGCACATATCG
Found at i:76707 original size:40 final size:40
Alignment explanation
Indices: 76630--76846 Score: 314
Period size: 40 Copynumber: 5.5 Consensus size: 40
76620 AAACCAAGTA
* * *
76630 CCTTCGGGAATTAG-CCGGATATAGCT-ACTCACTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
76669 CCTTCGGGATTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
76709 CCTTCGGGAATTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
76749 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATA
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
76789 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATA
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
76829 CCTTC-AGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
76847 TTATCATCCG
Statistics
Matches: 166, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
39 26 0.16
40 140 0.84
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:80088 original size:40 final size:40
Alignment explanation
Indices: 80026--80201 Score: 223
Period size: 40 Copynumber: 4.4 Consensus size: 40
80016 CAACCAAGTA
* * * *
80026 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
**
80065 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
80105 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
80145 CCTTCGGGACTTAGCCCGGA-ATTACTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
80185 CCTTTGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
80202 TGTTATCATC
Statistics
Matches: 122, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
39 14 0.11
40 108 0.89
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Done.