Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2678
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: 53795
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:13406 original size:27 final size:27
Alignment explanation
Indices: 13368--13590 Score: 232
Period size: 27 Copynumber: 8.2 Consensus size: 27
13358 GGGACGAAAT
** *
13368 AATGACCGAAATACCCTTATAAGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* *
13395 AATGACCAAAATACCCCCATAGGGAAA
1 AATGACCGAAATACCCCCATAGGGTAA
* *
13422 AATGACTGAAATACCCCTATAGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* * *
13449 AATGACCAAAATACGCCCATGGGGTAA
1 AATGACCGAAATACCCCCATAGGGTAA
* *
13476 AATGACCGAAATACCCTCATAGGATAA
1 AATGACCGAAATACCCCCATAGGGTAA
*
13503 AATGACCGAAATACCCCCATAGGGGTCA
1 AATGACCGAAATACCCCCATA-GGGTAA
* * * *
13531 AATGACTGTAATACCCTCATAGGATAA
1 AATGACCGAAATACCCCCATAGGGTAA
* ** *
13558 AATGA-CTATAATACCCCTGTACGGTAA
1 AATGACCGA-AATACCCCCATAGGGTAA
13585 AATGAC
1 AATGAC
13591 TGTATTACCC
Statistics
Matches: 158, Mismatches: 35, Indels: 5
0.80 0.18 0.03
Matches are distributed among these distances:
27 136 0.86
28 22 0.14
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (27 bp):
AATGACCGAAATACCCCCATAGGGTAA
Found at i:13450 original size:54 final size:54
Alignment explanation
Indices: 13368--13601 Score: 274
Period size: 54 Copynumber: 4.3 Consensus size: 54
13358 GGGACGAAAT
* * *
13368 AATGACCGAAATACCCTTATAAGG-TAAAATGACCAAAATACCCCCATAGGGAAA
1 AATGACTGAAATACCCTCAT-AGGATAAAATGACCAAAATACCCCCATAGGGTAA
* * *
13422 AATGACTGAAATACCC-CTATAGGGTAAAATGACCAAAATACGCCCATGGGGTAA
1 AATGACTGAAATACCCTC-ATAGGATAAAATGACCAAAATACCCCCATAGGGTAA
* * *
13476 AATGACCGAAATACCCTCATAGGATAAAATGACCGAAATACCCCCATAGGGGTCA
1 AATGACTGAAATACCCTCATAGGATAAAATGACCAAAATACCCCCATA-GGGTAA
* * * ** *
13531 AATGACTGTAATACCCTCATAGGATAAAATGACTATAATACCCCTGTACGGTAA
1 AATGACTGAAATACCCTCATAGGATAAAATGACCAAAATACCCCCATAGGGTAA
* *
13585 AATGACTGTATTACCCT
1 AATGACTGAAATACCCT
13602 TGTAAGGCAA
Statistics
Matches: 155, Mismatches: 21, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
53 3 0.02
54 105 0.68
55 47 0.30
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.21
Consensus pattern (54 bp):
AATGACTGAAATACCCTCATAGGATAAAATGACCAAAATACCCCCATAGGGTAA
Found at i:13591 original size:27 final size:26
Alignment explanation
Indices: 13420--13616 Score: 103
Period size: 27 Copynumber: 7.3 Consensus size: 26
13410 CCCATAGGGA
* *
13420 AAAATGACTGAAATACCCCTATAGGGT
1 AAAATGACTGTAATACCCCTGTA-GGT
*** *
13447 AAAATGACCAAAATACGCCCATG-GGGT
1 AAAATGACTGTAATAC-CCC-TGTAGGT
* * *
13474 AAAATGACCGAAATA-CCCTCATAGGAT
1 AAAATGACTGTAATACCCCT-GTAGG-T
* * **
13501 AAAATGACCGAAATACCCCCATAGGGGT
1 AAAATGACTGTAATACCCCTGTA--GGT
* *
13529 CAAATGACTGTAATA-CCCTCATAGGAT
1 AAAATGACTGTAATACCCCT-GTAGG-T
*
13556 AAAATGACTATAATACCCCTGTACGGT
1 AAAATGACTGTAATACCCCTGTA-GGT
* * *
13583 AAAATGACTGTATTACCCTTGTAAGGC
1 AAAATGACTGTAATACCCCTGT-AGGT
13610 AAAATGA
1 AAAATGA
13617 TTGTTTTGCC
Statistics
Matches: 138, Mismatches: 19, Indels: 26
0.75 0.10 0.14
Matches are distributed among these distances:
24 1 0.01
25 3 0.02
26 4 0.03
27 98 0.71
28 29 0.21
29 3 0.02
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (26 bp):
AAAATGACTGTAATACCCCTGTAGGT
Found at i:13741 original size:27 final size:27
Alignment explanation
Indices: 13580--13742 Score: 139
Period size: 27 Copynumber: 6.0 Consensus size: 27
13570 ACCCCTGTAC
* * * **
13580 GGTAAAATGACTGTATTACCCTTGTAA
1 GGTAAAATGACTGTTTTGCCCTTATGT
* * *
13607 GGCAAAATGATTGTTTTGCCCTTATAT
1 GGTAAAATGACTGTTTTGCCCTTATGT
** *
13634 ATTAAAATGAC-GATTTTGCCCTTATAT
1 GGTAAAATGACTG-TTTTGCCCTTATGT
* * *
13661 GGTAAAATGACAGTTTTGCGCTTATGA
1 GGTAAAATGACTGTTTTGCCCTTATGT
* *
13688 GGTAAAATAACTATTTTGCCCTTATGT
1 GGTAAAATGACTGTTTTGCCCTTATGT
** *
13715 GGTAGGATGACTGTTTTGCCCCTATGT
1 GGTAAAATGACTGTTTTGCCCTTATGT
13742 G
1 G
13743 ATGTATGTTT
Statistics
Matches: 109, Mismatches: 25, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
26 1 0.01
27 107 0.98
28 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (27 bp):
GGTAAAATGACTGTTTTGCCCTTATGT
Found at i:14037 original size:23 final size:23
Alignment explanation
Indices: 14007--14063 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
13997 ATATCTCCAC
*
14007 ATGGAGTGTAGGGTTGGACGGAG
1 ATGGAGTGTAGGGTTGGACAGAG
*
14030 ATGGAGTGTAAGGTTGGACAGAG
1 ATGGAGTGTAGGGTTGGACAGAG
14053 ATGGAGTGTAG
1 ATGGAGTGTAG
14064 AGGCTGGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.26, C:0.04, G:0.47, T:0.23
Consensus pattern (23 bp):
ATGGAGTGTAGGGTTGGACAGAG
Found at i:14253 original size:25 final size:25
Alignment explanation
Indices: 14219--14269 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
14209 CTTAGGCCCA
14219 GACTGTGTTTGTTGTCTGATTGATT
1 GACTGTGTTTGTTGTCTGATTGATT
14244 GACTGTGTTTGTTGTCTGATTGATT
1 GACTGTGTTTGTTGTCTGATTGATT
14269 G
1 G
14270 CTTATATGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.12, C:0.08, G:0.29, T:0.51
Consensus pattern (25 bp):
GACTGTGTTTGTTGTCTGATTGATT
Found at i:18309 original size:6 final size:6
Alignment explanation
Indices: 18279--18403 Score: 69
Period size: 6 Copynumber: 20.3 Consensus size: 6
18269 AAGAAACATT
* * *
18279 ATCAGA A-CTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * * * * *
18328 ATCAGA ATCAAA ATTAGGTG AT-AGA ATTAGA ATCAAA ATCAGA ATCAGT
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
*
18377 ATCAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCA-G-A ATCAGA ATCAGA ATCAGA AT
18404 GTGAATGCAA
Statistics
Matches: 90, Mismatches: 18, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
5 6 0.07
6 72 0.80
7 8 0.09
8 4 0.04
ACGTcount: A:0.50, C:0.13, G:0.18, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:18333 original size:25 final size:25
Alignment explanation
Indices: 18300--18369 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
18290 AATCAAAATG
*
18300 AGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAAAATCAGGTGAC
* *
18325 AGAATCAGAATCAAAATTAGGTGAT
1 AGAATCAGAATCAAAATCAGGTGAC
*
18350 AGAATTAGAATCAAAATCAG
1 AGAATCAGAATCAAAATCAG
18370 AATCAGTATC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (25 bp):
AGAATCAGAATCAAAATCAGGTGAC
Found at i:18337 original size:31 final size:31
Alignment explanation
Indices: 18302--18403 Score: 93
Period size: 31 Copynumber: 3.3 Consensus size: 31
18292 TCAAAATGAG
* *
18302 AATCAGAATCAGAATCAGGTGACAGAATCAG
1 AATCAGAATCAGAATCAGGTAACAGAATCAA
* * * *
18333 AATCAAAATTAGGTGAT-A-G-AATTAGAATCAA
1 AATCAGAATCA-G-AATCAGGTAA-CAGAATCAA
*
18364 AATCAGAATCAGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGAATCAGGTAACAGAATCAA
18395 AATCAGAAT
1 AATCAGAAT
18404 GTGAATGCAA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
29 2 0.04
30 3 0.05
31 44 0.80
32 4 0.07
33 2 0.04
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.21
Consensus pattern (31 bp):
AATCAGAATCAGAATCAGGTAACAGAATCAA
Found at i:18674 original size:27 final size:26
Alignment explanation
Indices: 18626--18677 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
18616 GCGAGGCTAC
*
18626 CAGATATTGTGATGAAGTCACCAGAA
1 CAGATATTGTGATGAAGCCACCAGAA
* *
18652 CAGATATATGTGGTGAGGCCACCAGA
1 CAGATAT-TGTGATGAAGCCACCAGA
18678 TTACAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (26 bp):
CAGATATTGTGATGAAGCCACCAGAA
Found at i:18943 original size:27 final size:27
Alignment explanation
Indices: 18913--19231 Score: 390
Period size: 27 Copynumber: 11.8 Consensus size: 27
18903 AACACCCTAG
* * *
18913 GGGTAAAATAGAAATTTTATAAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
* *
18940 GGGTAAAATGGTAATTCTGTAAATTGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
* *
18967 GGGTAAAACAGTAATTTTGTAAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
* * *
18994 GGGTAAAACAGTAATTCTGTCAATCAA
1 GGGTAAAATAGTAATTCTGTAAATCGA
* * **
19021 AGGTAAAATGGTAATTCTAAAAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
* *
19048 GGGTAAAATAGTAATTTTGTAAATTGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
19075 GGGTAAAATAGTAATTCTGTAAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
* *
19102 GGGTAAAATAGTAATCCTGTCAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
*
19129 GGGTAAAACT-GTAATTTTGTAAATCGA
1 GGGTAAAA-TAGTAATTCTGTAAATCGA
*
19156 GGGTAAAAT-GATAATTTTGTAAATCGA
1 GGGTAAAATAG-TAATTCTGTAAATCGA
* *
19183 GGGTAAAACAGTAATTCTATAAATCGA
1 GGGTAAAATAGTAATTCTGTAAATCGA
* *
19210 GGGTAAAACAGTAATTTTGTAA
1 GGGTAAAATAGTAATTCTGTAA
19232 TTTAAGGATA
Statistics
Matches: 252, Mismatches: 37, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
26 2 0.01
27 248 0.98
28 2 0.01
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.30
Consensus pattern (27 bp):
GGGTAAAATAGTAATTCTGTAAATCGA
Found at i:19250 original size:81 final size:82
Alignment explanation
Indices: 18913--19231 Score: 430
Period size: 81 Copynumber: 3.9 Consensus size: 82
18903 AACACCCTAG
* * * * * *
18913 GGGTAAAAT-AGAAATTTTATAAATCGAGGGTAAAATGGTAATTCTGTAAATTGAGGGTAAAACA
1 GGGTAAAATGAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
18977 GTAATTTTGTAAATCGA
66 GTAATTTTGTAAATCGA
* * * * * * *
18994 GGGTAAAA-CAGTAATTCTGTCAATCAAAGGTAAAATGGTAATTCTAAAAATCGAGGGTAAAATA
1 GGGTAAAATGAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
*
19058 GTAATTTTGTAAATTGA
66 GTAATTTTGTAAATCGA
* * * *
19075 GGGTAAAAT-AGTAATTCTGTAAATCGAGGGTAAAATAGTAATCCTGTCAATCGAGGGTAAAACT
1 GGGTAAAATGAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
19139 GTAATTTTGTAAATCGA
66 GTAATTTTGTAAATCGA
* *
19156 GGGTAAAATGA-TAATTTTGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAACA
1 GGGTAAAATGAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
19220 GTAATTTTGTAA
66 GTAATTTTGTAA
19232 TTTAAGGATA
Statistics
Matches: 207, Mismatches: 28, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
81 206 1.00
82 1 0.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.30
Consensus pattern (82 bp):
GGGTAAAATGAGTAATTCTGTAAATCGAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACA
GTAATTTTGTAAATCGA
Found at i:19310 original size:54 final size:52
Alignment explanation
Indices: 19252--19387 Score: 119
Period size: 54 Copynumber: 2.5 Consensus size: 52
19242 CTTTGATAAC
* * * *
19252 TTTACAAGTTGATGGTATTTCAGTAATTTTGCAAACTGAGGGTATTTTGGGAGT
1 TTTACAA-TTGA-GGTATTTCAGTAATTTTACAAACCGAGGGTACTTTGGGAAT
* ** * * *
19306 TTTACAAATCGAGGATATTTGGGTAATTTTATAAACCGGGGGTACTTTGGTAAT
1 TTTAC-AATTGAGG-TATTTCAGTAATTTTACAAACCGAGGGTACTTTGGGAAT
* *
19360 TTTACAACTGGGGGTATTTCAGTAATTT
1 TTTACAA-TTGAGGTATTTCAGTAATTT
19388 GGTAAACTAA
Statistics
Matches: 65, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
53 16 0.25
54 47 0.72
55 2 0.03
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (52 bp):
TTTACAATTGAGGTATTTCAGTAATTTTACAAACCGAGGGTACTTTGGGAAT
Found at i:19384 original size:26 final size:26
Alignment explanation
Indices: 19265--19387 Score: 86
Period size: 27 Copynumber: 4.6 Consensus size: 26
19255 ACAAGTTGAT
* *
19265 GGTATTTCAGTAATTTTGCAAACTGAG
1 GGTATTTCGGTAATTTTAC-AACTGAG
* * * *
19292 GGTATTTTGGGAGTTTTACAAATCGAG
1 GGTATTTCGGTAATTTTACAACT-GAG
* * * * *
19319 GATATTTGGGTAATTTTATAAACCGGG
1 GGTATTTCGGTAATTTTA-CAACTGAG
*
19346 GGTACTTT-GGTAATTTTACAACTGGG
1 GGTA-TTTCGGTAATTTTACAACTGAG
*
19372 GGTATTTCAGTAATTT
1 GGTATTTCGGTAATTT
19388 GGTAAACTAA
Statistics
Matches: 74, Mismatches: 18, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
25 3 0.04
26 20 0.27
27 46 0.62
28 5 0.07
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (26 bp):
GGTATTTCGGTAATTTTACAACTGAG
Found at i:21466 original size:31 final size:31
Alignment explanation
Indices: 21431--21503 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
21421 ATCAGGTGAC
* *
21431 AGAATCAGAATCAGAATTAGGTGACAGAATT
1 AGAATCAGAATCAGAATCAGGTAACAGAATT
*
21462 AGAATCAGAATCAGTATCAGGTAACAGAATT
1 AGAATCAGAATCAGAATCAGGTAACAGAATT
*
21493 AAAATCAGAAT
1 AGAATCAGAAT
21504 GTGAATGCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.48, C:0.11, G:0.19, T:0.22
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGGTAACAGAATT
Found at i:21491 original size:25 final size:25
Alignment explanation
Indices: 21408--21475 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 25
21398 TCAAAATGAA
*
21408 AATCAAAATCAGAATCAGGTGACAG
1 AATCAGAATCAGAATCAGGTGACAG
*
21433 AATCAGAATCAGAATTAGGTGACAG
1 AATCAGAATCAGAATCAGGTGACAG
*
21458 AATTAGAATCAGAATCAG
1 AATCAGAATCAGAATCAG
21476 TATCAGGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.19
Consensus pattern (25 bp):
AATCAGAATCAGAATCAGGTGACAG
Found at i:21669 original size:27 final size:26
Alignment explanation
Indices: 21621--21680 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
21611 GCGAGGCTGC
*
21621 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
21648 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
21674 CAAATAT
1 CAGATAT
21681 ATATATATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:21777 original size:27 final size:26
Alignment explanation
Indices: 21729--21780 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
21719 GCGAAGCTGC
*
21729 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
21755 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
21781 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:22047 original size:27 final size:27
Alignment explanation
Indices: 22017--22371 Score: 408
Period size: 27 Copynumber: 13.1 Consensus size: 27
22007 ACACCATAGC
** * *
22017 GGTAAAATGGTAATTTTATAAATCGAT
1 GGTAAAACAGTAATTTTGTAAATCGAG
* *
22044 GGTAAAACGGTAATTTTGTAAATAGAG
1 GGTAAAACAGTAATTTTGTAAATCGAG
* *
22071 GGTAAAATAATAATTTTGTAAATCGAG
1 GGTAAAACAGTAATTTTGTAAATCGAG
* *
22098 GGTAAAATAATAATTTTGTAAATCGAG
1 GGTAAAACAGTAATTTTGTAAATCGAG
* * * *
22125 GGTAAAATAGTAATTCTGTCAACCGAG
1 GGTAAAACAGTAATTTTGTAAATCGAG
*
22152 GGTAAAAC-GATAATTCTGTAAATCGAG
1 GGTAAAACAG-TAATTTTGTAAATCGAG
* * *
22179 GGTAAAATAATAATTTTGTAAATTGAG
1 GGTAAAACAGTAATTTTGTAAATCGAG
* *
22206 GGTAAAACAGTAATTCTATAAATCGAG
1 GGTAAAACAGTAATTTTGTAAATCGAG
* * * *
22233 GGTAAAAAAGTAATTCTGTCAATCGTG
1 GGTAAAACAGTAATTTTGTAAATCGAG
** *
22260 GGTAAAATGGTAATTTTGTAAATCAAG
1 GGTAAAACAGTAATTTTGTAAATCGAG
22287 GGTAAAAC-GATAATTTTGTAAATCGAG
1 GGTAAAACAG-TAATTTTGTAAATCGAG
*
22314 GGTAAAACAGTAATTCTGTAAATCGAG
1 GGTAAAACAGTAATTTTGTAAATCGAG
* *
22341 GGTAAAACAGTAATTTTGTAATTTGAG
1 GGTAAAACAGTAATTTTGTAAATCGAG
22368 GGTA
1 GGTA
22372 CTTTGATAAT
Statistics
Matches: 284, Mismatches: 40, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
26 2 0.01
27 281 0.99
28 1 0.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (27 bp):
GGTAAAACAGTAATTTTGTAAATCGAG
Found at i:22153 original size:81 final size:81
Alignment explanation
Indices: 22017--22371 Score: 453
Period size: 81 Copynumber: 4.4 Consensus size: 81
22007 ACACCATAGC
* * * * * * *
22017 GGTAAAATGGTAATTTTATAAATCGATGGTAAAACGGTAATTTTGTAAATAGAGGGTAAAATAAT
1 GGTAAAATAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAACAAT
*
22082 AATTTTGTAAATCGAG
66 AATTCTGTAAATCGAG
* * * * *
22098 GGTAAAATAATAATTTTGTAAATCGAGGGTAAAATAGTAATTCTGTCAACCGAGGGTAAAACGAT
1 GGTAAAATAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAACAAT
22163 AATTCTGTAAATCGAG
66 AATTCTGTAAATCGAG
* * *
22179 GGTAAAATAATAATTTTGTAAATTGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAA-AAG
1 GGTAAAATAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAACAA-
* *
22243 TAATTCTGTCAATCGTG
65 TAATTCTGTAAATCGAG
* * * *
22260 GGTAAAATGGTAATTTTGTAAATCAAGGGTAAAAC-GATAATTTTGTAAATCGAGGGTAAAACAG
1 GGTAAAATAGTAATTTTGTAAATCGAGGGTAAAACAG-TAATTCTGTAAATCGAGGGTAAAACAA
22324 TAATTCTGTAAATCGAG
65 TAATTCTGTAAATCGAG
* * *
22341 GGTAAAACAGTAATTTTGTAATTTGAGGGTA
1 GGTAAAATAGTAATTTTGTAAATCGAGGGTA
22372 CTTTGATAAT
Statistics
Matches: 236, Mismatches: 35, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
80 2 0.01
81 233 0.99
82 1 0.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (81 bp):
GGTAAAATAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAACAAT
AATTCTGTAAATCGAG
Found at i:22406 original size:54 final size:53
Alignment explanation
Indices: 22348--22525 Score: 169
Period size: 54 Copynumber: 3.3 Consensus size: 53
22338 GAGGGTAAAA
** * *
22348 CAGTAATTTTGTAATTTGAGGGTACTTTGATAATTTTACAAGTCGATGGTATTT
1 CAGTAATTTTGTAAACTGAGGGTACTTTGGTAATTTTACAAATCGA-GGTATTT
* * * *
22402 CAGTAATTTTGCAAACTGATGCTA-TTTCGGTAGTTTTACAAATCGAGGATATTT
1 CAGTAATTTTGTAAACTGAGGGTACTTT-GGTAATTTTACAAATCGAGG-TATTT
** * * * * * *
22456 GGGTAATTTTATAAACCGGGGGTACTTTGGTAATTTTACAACTGGGGGTATTT
1 CAGTAATTTTGTAAACTGAGGGTACTTTGGTAATTTTACAAATCGAGGTATTT
*
22509 CAGTAATTTGGTAAACT
1 CAGTAATTTTGTAAACT
22526 AAAGTATTCT
Statistics
Matches: 96, Mismatches: 25, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
53 22 0.23
54 71 0.74
55 3 0.03
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (53 bp):
CAGTAATTTTGTAAACTGAGGGTACTTTGGTAATTTTACAAATCGAGGTATTT
Found at i:22514 original size:26 final size:26
Alignment explanation
Indices: 22364--22517 Score: 96
Period size: 27 Copynumber: 5.8 Consensus size: 26
22354 TTTTGTAATT
* *
22364 TGAGGGTACTTT-GATAATTTTACAAG
1 TGAGGGTA-TTTCGGTAATTTTACAAC
* * *
22390 TCGATGGTATTTCAGTAATTTTGCAAAC
1 T-GAGGGTATTTCGGTAATTTTAC-AAC
* * * *
22418 TGATGCTATTTCGGTAGTTTTACAAA
1 TGAGGGTATTTCGGTAATTTTACAAC
* * *
22444 TCGAGGATATTTGGGTAATTTTATAAAC
1 T-GAGGGTATTTCGGTAATTTTA-CAAC
* *
22472 CGGGGGTACTTT-GGTAATTTTACAAC
1 TGAGGGTA-TTTCGGTAATTTTACAAC
* *
22498 TGGGGGTATTTCAGTAATTT
1 TGAGGGTATTTCGGTAATTT
22518 GGTAAACTAA
Statistics
Matches: 99, Mismatches: 22, Indels: 14
0.73 0.16 0.10
Matches are distributed among these distances:
25 3 0.03
26 24 0.24
27 64 0.65
28 8 0.08
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (26 bp):
TGAGGGTATTTCGGTAATTTTACAAC
Found at i:24831 original size:43 final size:43
Alignment explanation
Indices: 24782--24937 Score: 192
Period size: 43 Copynumber: 3.7 Consensus size: 43
24772 ATGTGTTCTC
* *
24782 GTGTAAGACCACGTCTGGGACGTTGGCATCGATGTGTGATTAT
1 GTGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTAT
* * * * *
24825 GTGTAAGACCATGTCTAGGACATCGGCATC-ATATTTGATTCT
1 GTGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTAT
* *
24867 -TGTAAGACC-CTGTCTGGGACAGTGGCATCGATATGTGATTAC
1 GTGTAAGACCAC-GTCTGGGACATTGGCATCGATATGTGATTAT
*
24909 ATGTAAGACCACGTCTGGGACATTGGCAT
1 GTGTAAGACCACGTCTGGGACATTGGCAT
24938 TGTATGATAT
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
41 24 0.26
42 18 0.19
43 51 0.54
44 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (43 bp):
GTGTAAGACCACGTCTGGGACATTGGCATCGATATGTGATTAT
Found at i:24930 original size:84 final size:84
Alignment explanation
Indices: 24783--24937 Score: 224
Period size: 84 Copynumber: 1.8 Consensus size: 84
24773 TGTGTTCTCG
* ** *
24783 TGTAAGACCACGTCTGGGACGTTGGCATCGATGTGTGATTATGTGTAAGACCATGTCTAGGACAT
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACATGTAAGACCACGTCTAGGACAT
24848 CGGCATCATATTTGATTCT
66 CGGCATCATATTTGATTCT
*
24867 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATGTGATTACATGTAAGACCACGTCTGGGAC
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATGTGATTACATGTAAGACCACGTCTAGGAC
*
24930 ATTGGCAT
64 ATCGGCAT
24938 TGTATGATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
83 1 0.02
84 61 0.97
85 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (84 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTACATGTAAGACCACGTCTAGGACAT
CGGCATCATATTTGATTCT
Found at i:33169 original size:27 final size:27
Alignment explanation
Indices: 33139--33414 Score: 300
Period size: 27 Copynumber: 10.2 Consensus size: 27
33129 ATTACCAAAG
*
33139 TACCCTCGATTTAAAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACCATTT
* * *
33166 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAAAATTACCATTT
* * *
33193 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACCATTT
* * *
33220 TGCCCTCAATTTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACCATTT
* * *
33247 TACCCTCAATTTACAAATTTACCGTTT
1 TACCCTCGATTTACAAAATTACCATTT
*
33274 TACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACCATTT
* * *
33301 TACCCTCGATTTATAGAATTAACATTT
1 TACCCTCGATTTACAAAATTACCATTT
** ***
33328 TACCCTCGATTTACTGAATTATTGTTT
1 TACCCTCGATTTACAAAATTACCATTT
* * *
33355 TACCCTCGATTTAAAAAATTATCGTTT
1 TACCCTCGATTTACAAAATTACCATTT
* *
33382 TACCCTCAATTTATAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACCATTT
*
33409 TTCCCT
1 TACCCT
33415 TAGAGTGTTA
Statistics
Matches: 209, Mismatches: 40, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 209 1.00
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCATTT
Found at i:33186 original size:54 final size:54
Alignment explanation
Indices: 33139--33414 Score: 345
Period size: 54 Copynumber: 5.1 Consensus size: 54
33129 ATTACCAAAG
* * *
33139 TACCCTCGATTTAAAAAATTACCATTTTACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTAAAAAATTACCGTTTTACCCTCGATTTACAAAATTACTATTT
* * * *
33193 TACCCTCGATTTATAGAATTACCGTTTTGCCCTCAATTTACAAAATTACTATTT
1 TACCCTCGATTTAAAAAATTACCGTTTTACCCTCGATTTACAAAATTACTATTT
* * *
33247 TACCCTCAATTTACAAATTTACCGTTTTACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTAAAAAATTACCGTTTTACCCTCGATTTACAAAATTACTATTT
* * * * ** * *
33301 TACCCTCGATTTATAGAATTAACATTTTACCCTCGATTTACTGAATTATTGTTT
1 TACCCTCGATTTAAAAAATTACCGTTTTACCCTCGATTTACAAAATTACTATTT
* * * *
33355 TACCCTCGATTTAAAAAATTATCGTTTTACCCTCAATTTATAAAATTACCATTT
1 TACCCTCGATTTAAAAAATTACCGTTTTACCCTCGATTTACAAAATTACTATTT
*
33409 TTCCCT
1 TACCCT
33415 TAGAGTGTTA
Statistics
Matches: 187, Mismatches: 35, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 187 1.00
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (54 bp):
TACCCTCGATTTAAAAAATTACCGTTTTACCCTCGATTTACAAAATTACTATTT
Found at i:33198 original size:81 final size:81
Alignment explanation
Indices: 33125--33414 Score: 339
Period size: 81 Copynumber: 3.6 Consensus size: 81
33115 CCTCAACTTG
*** * * * *
33125 TAAAATTACCAAAGTACCCTCGATTTAAAAAATTACCATTTTACCCTTGATTTACAGAATTACTA
1 TAAAATTACCATTTTACCCTCAATTTATAAAATTACCATTTTACCCTCGATTTACAGAATTACTG
33190 TTTTACCCTCGATTTA
66 TTTTACCCTCGATTTA
* * * * * * *
33206 TAGAATTACCGTTTTGCCCTCAATTTACAAAATTACTATTTTACCCTCAATTTACA-AATTTACC
1 TAAAATTACCATTTTACCCTCAATTTATAAAATTACCATTTTACCCTCGATTTACAGAA-TTACT
33270 GTTTTACCCTCGATTTA
65 GTTTTACCCTCGATTTA
* * * * * * *
33287 CAAAATTACTATTTTACCCTCGATTTATAGAATTAACATTTTACCCTCGATTTACTGAATTATTG
1 TAAAATTACCATTTTACCCTCAATTTATAAAATTACCATTTTACCCTCGATTTACAGAATTACTG
33352 TTTTACCCTCGATTTA
66 TTTTACCCTCGATTTA
* * * *
33368 AAAAATTATCGTTTTACCCTCAATTTATAAAATTACCATTTTTCCCT
1 TAAAATTACCATTTTACCCTCAATTTATAAAATTACCATTTTACCCT
33415 TAGAGTGTTA
Statistics
Matches: 172, Mismatches: 35, Indels: 4
0.82 0.17 0.02
Matches are distributed among these distances:
80 2 0.01
81 168 0.98
82 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (81 bp):
TAAAATTACCATTTTACCCTCAATTTATAAAATTACCATTTTACCCTCGATTTACAGAATTACTG
TTTTACCCTCGATTTA
Found at i:33765 original size:33 final size:32
Alignment explanation
Indices: 33716--33779 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
33706 CTCGCTGTAA
* *
33716 TCTGGTGGCTTCGCCACATATATATATATCTGT
1 TCTGGTGGCCTAGCCACA-ATATATATATCTGT
* *
33749 TCTGGTGGCCTAGCCACAATATCTGTATCTG
1 TCTGGTGGCCTAGCCACAATATATATATCTG
33780 GTGACTTCGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.36
Consensus pattern (32 bp):
TCTGGTGGCCTAGCCACAATATATATATCTGT
Found at i:33793 original size:27 final size:26
Alignment explanation
Indices: 33741--33800 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
33731 ACATATATAT
*
33741 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
33767 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
33794 ATATCTG
1 ATATCTG
33801 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:33956 original size:6 final size:6
Alignment explanation
Indices: 33947--34024 Score: 61
Period size: 6 Copynumber: 12.8 Consensus size: 6
33937 TTACCTGAAA
* * * *
33947 CTGATT CTGATT CTAATT CTG-TCAC CTAATT CTGATT CTAATT CTGATT
1 CTGATT CTGATT CTGATT CTGAT--T CTGATT CTGATT CTGATT CTGATT
* *
33996 CTGATT CTCATT TTGATT CT-AGTT CTGAT
1 CTGATT CTGATT CTGATT CTGA-TT CTGAT
34025 AATGTTTCTT
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
5 2 0.04
6 49 0.89
7 3 0.05
8 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.49
Consensus pattern (6 bp):
CTGATT
Found at i:39806 original size:34 final size:33
Alignment explanation
Indices: 39750--39820 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 33
39740 TTTATGCATT
39750 ACTGATACTGTACTGAGTTGGGC-TAAGGCCCAC
1 ACTGATACTGTACTGAGTTGGGCTTAA-GCCCAC
* *
39783 ACTGATATTGCTACTGA-TATGGGCTTAAGCCCAG
1 ACTGATACTG-TACTGAGT-TGGGCTTAAGCCCAC
39817 ACTG
1 ACTG
39821 TTCAACACTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
33 10 0.30
34 20 0.61
35 3 0.09
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (33 bp):
ACTGATACTGTACTGAGTTGGGCTTAAGCCCAC
Found at i:45462 original size:29 final size:29
Alignment explanation
Indices: 45428--45501 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
45418 TAATCAACCA
*
45428 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
45457 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
45486 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
45502 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:48406 original size:26 final size:26
Alignment explanation
Indices: 48361--48432 Score: 96
Period size: 26 Copynumber: 2.8 Consensus size: 26
48351 GAGGAAGTGC
*
48361 AAAAGGGC-TTTG-CCTCAGTTTAC-CG
1 AAAAGGGCTTTTGCCCT-AGTTT-CTCA
48386 AAAAGGGCTTTTGCCCTAGTTTCTCA
1 AAAAGGGCTTTTGCCCTAGTTTCTCA
48412 AAAAGGGCTTTTGCCCTAGTT
1 AAAAGGGCTTTTGCCCTAGTT
48433 ATTAAAAGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 9 0.21
26 31 0.72
27 3 0.07
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (26 bp):
AAAAGGGCTTTTGCCCTAGTTTCTCA
Found at i:48445 original size:25 final size:26
Alignment explanation
Indices: 48386--48445 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
48376 CAGTTTACCG
48386 AAAAG-GGCTTTTGCCCTAGTTTCTC
1 AAAAGAGGCTTTTGCCCTAGTTTCTC
48411 AAAA-AGGGCTTTTGCCCTAGTTAT-T-
1 AAAAGA-GGCTTTTGCCCTAGTT-TCTC
48436 AAAAGAGGCT
1 AAAAGAGGCT
48446 AGGCCTCCAG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
25 12 0.39
26 18 0.58
27 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (26 bp):
AAAAGAGGCTTTTGCCCTAGTTTCTC
Found at i:48690 original size:31 final size:31
Alignment explanation
Indices: 48652--48735 Score: 109
Period size: 31 Copynumber: 2.7 Consensus size: 31
48642 TTTTTATAGT
*
48652 AAAGGCTTCAGCCCGGTGATATGAATAATGA
1 AAAGGCTTCAGCCCAGTGATATGAATAATGA
* * *
48683 AAAGGCTTCGGCCTAGTGATATGAATAATGT
1 AAAGGCTTCAGCCCAGTGATATGAATAATGA
48714 AAAGGCTT-AGGCCCAGT-ATATG
1 AAAGGCTTCA-GCCCAGTGATATG
48736 CTGAGATTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 5 0.11
31 41 0.89
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCAGCCCAGTGATATGAATAATGA
Found at i:52526 original size:13 final size:13
Alignment explanation
Indices: 52508--52538 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
52498 TCGGAGCGGA
*
52508 CTCCCCCCCTCCC
1 CTCCCCCCCCCCC
52521 CTCCCCCCCCCCC
1 CTCCCCCCCCCCC
52534 CTCCC
1 CTCCC
52539 TCAAGGCGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.87, G:0.00, T:0.13
Consensus pattern (13 bp):
CTCCCCCCCCCCC
Done.