Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2053
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: 60693
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4548 original size:20 final size:20
Alignment explanation
Indices: 4523--4587 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
4513 TACAAGCCAA
4523 TGTATCGATACATTTTATGG
1 TGTATCGATACATTTTATGG
4543 TGTATCGATACA----A---
1 TGTATCGATACATTTTATGG
4556 TGTATCGATACATTTTATGG
1 TGTATCGATACATTTTATGG
4576 TGTATCGATACA
1 TGTATCGATACA
4588 ATGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 12 0.32
16 1 0.03
17 1 0.03
20 24 0.63
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.40
Consensus pattern (20 bp):
TGTATCGATACATTTTATGG
Found at i:4557 original size:33 final size:33
Alignment explanation
Indices: 4520--4620 Score: 168
Period size: 33 Copynumber: 3.1 Consensus size: 33
4510 CGTTACAAGC
4520 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATTTTATGGTGTATCGATA
4553 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATTTTATGGTGTATCGATA
** *
4586 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATTTTATGGTGTATCGATA
4618 CAA
1 CAA
4621 GTTTAACTAC
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 14 0.22
33 51 0.78
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATTTTATGGTGTATCGATA
Found at i:4561 original size:13 final size:13
Alignment explanation
Indices: 4543--4600 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
4533 CATTTTATGG
4543 TGTATCGATACAA
1 TGTATCGATACAA
4556 TGTATCGATACATTTTA
1 TGTATCGATACA----A
4573 TGGTGTATCGATACAA
1 ---TGTATCGATACAA
4589 TGTATCGATACA
1 TGTATCGATACA
4601 TACTGTGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 24 0.63
16 1 0.03
17 1 0.03
20 12 0.32
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:6076 original size:10 final size:10
Alignment explanation
Indices: 6057--6086 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
6047 TTTGAAAATA
*
6057 TAGCCATTAC
1 TAGCCGTTAC
6067 TAGCCGTTAC
1 TAGCCGTTAC
6077 TAGCCGTTAC
1 TAGCCGTTAC
6087 AAGCTAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (10 bp):
TAGCCGTTAC
Found at i:6171 original size:18 final size:20
Alignment explanation
Indices: 6148--6196 Score: 75
Period size: 18 Copynumber: 2.5 Consensus size: 20
6138 CCAATCACCT
6148 GTATCGATACATTT-G-CAA
1 GTATCGATACATTTGGTCAA
*
6166 GTATCGATACATTTGGTCAT
1 GTATCGATACATTTGGTCAA
6186 GTATCGATACA
1 GTATCGATACA
6197 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 14 0.50
19 1 0.04
20 13 0.46
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (20 bp):
GTATCGATACATTTGGTCAA
Found at i:6202 original size:13 final size:13
Alignment explanation
Indices: 6184--6208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6174 ACATTTGGTC
6184 ATGTATCGATACA
1 ATGTATCGATACA
6197 ATGTATCGATAC
1 ATGTATCGATAC
6209 TGTGCATTAT
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):
ATGTATCGATACA
Found at i:6891 original size:51 final size:51
Alignment explanation
Indices: 6829--6945 Score: 173
Period size: 51 Copynumber: 2.3 Consensus size: 51
6819 AATTAACTAG
* * * *
6829 ATGTATTGATACTTTGAAAAATGTATCGATACATTTAGGTAAAAAAATAGA
1 ATGTATCGATACATTGAAAAACGTATCGATACATCTAGGTAAAAAAATAGA
*
6880 ATGTATCGATACATTGAAAAACGTATCGATACATCTGGGTAAAAAAATAGA
1 ATGTATCGATACATTGAAAAACGTATCGATACATCTAGGTAAAAAAATAGA
*
6931 ATGTATCAAT-CATTG
1 ATGTATCGATACATTG
6946 TATTATTCAT
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 5 0.08
51 55 0.92
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAACGTATCGATACATCTAGGTAAAAAAATAGA
Found at i:7811 original size:11 final size:11
Alignment explanation
Indices: 7797--7830 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
7787 ATTTTCCCTA
7797 TTTTTTCTTTC
1 TTTTTTCTTTC
7808 TTTTTTCTTTCC
1 TTTTTTCTTT-C
7820 TTTTTT-TTTC
1 TTTTTTCTTTC
7830 T
1 T
7831 CTCTTTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.09
11 13 0.59
12 7 0.32
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:7818 original size:15 final size:14
Alignment explanation
Indices: 7800--7838 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
7790 TTCCCTATTT
7800 TTTCTTTCTTTTTTC
1 TTTCTTT-TTTTTTC
7815 TTTCCTTTTTTTTTC
1 TTT-CTTTTTTTTTC
*
7830 TCTCTTTTT
1 TTTCTTTTT
7839 GGTTGGAGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 6 0.27
15 12 0.55
16 4 0.18
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTCTTTTTTTTTC
Found at i:7818 original size:26 final size:26
Alignment explanation
Indices: 7789--7838 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
7779 TTCTACCTAT
*
7789 TTTCCCTATTTTTTCTTTCTTTTTTC
1 TTTCCCTATTTTTTCTCTCTTTTTTC
* *
7815 TTTCCTTTTTTTTTCTCTCTTTTT
1 TTTCCCTATTTTTTCTCTCTTTTT
7839 GGTTGGAGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTCCCTATTTTTTCTCTCTTTTTTC
Found at i:8910 original size:168 final size:165
Alignment explanation
Indices: 8473--9008 Score: 699
Period size: 167 Copynumber: 3.2 Consensus size: 165
8463 AACACCACAT
* * ** *
8473 TTTAGAAAAAGGGGAATTTCACGAAGAAAAATAAAAAACCCATAAAAATGAATTTGTTTTT-TAA
1 TTTAGAAAAAGGGGAATTTCAAGGA-AAAAATTCAAAACTCATAAAAATGAATTTGTTTTTCTAA
* * *
8537 AACTGAATTAATATGAAATAAATAATGATGTTTTATGAA-TTTAAAAATTAAAAACCAAG-AAAA
65 AAATGAATTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTTAAAACCAAGAAAAA
* ** *
8600 TTCCCTTGAAGAAATTTACA-GAGTAGAAAACATCGTA
130 TTCCCTCGAA-AAAAATCCAGGAGTAGAAAAC-TCGTA
* * * *
8637 CTTAGGAAAAAAGGGGAATTTTAAGGAAAAAATCCAAAACTCATGAAAATGAATTTGTTTTTC-A
1 TTTA-G-AAAAAGGGGAATTTCAAGGAAAAAATTCAAAACTCATAAAAATGAATTTGTTTTTCTA
*
8701 AAAATAAATTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTTAAAACCAAGAAAA
64 AAAATGAATTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTTAAAACCAAGAAAA
8766 ATTCCCTCGAAAAAAATCCATGGAGTAGAAAACTCTGTA
129 ATTCCCTCGAAAAAAATCCA-GGAGTAGAAAACTC-GTA
8805 TTTCAGAAAAAGGGGAATTTCAAGGAAAAAATTCAAAACTCATAAAAATGAATTTGTTTTTCTAA
1 TTT-AGAAAAAGGGGAATTTCAAGGAAAAAATTCAAAACTCATAAAAATGAATTTGTTTTTCTAA
* *
8870 AATTGAATTAATATAAAATAAATAATGATGTTTGATGAATTTTAAAAA-TTAAAACCAAGAAAAA
65 AAATGAATTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTTAAAACCAAGAAAAA
* *
8934 TACCCTCGAAAAAAATCCACGAAGTAGAAAACTCCGTA
130 TTCCCTCGAAAAAAATCCA-GGAGTAGAAAACT-CGTA
* * * *
8972 TTTTGAAGAAAGAGAAATTTC-AGGGAAAAATTCAAAA
1 TTTAGAA-AAAGGGGAATTTCAAGGAAAAAATTCAAAA
9009 ACTAATGAAA
Statistics
Matches: 330, Mismatches: 30, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
164 3 0.01
165 70 0.21
166 60 0.18
167 131 0.40
168 65 0.20
169 1 0.00
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.28
Consensus pattern (165 bp):
TTTAGAAAAAGGGGAATTTCAAGGAAAAAATTCAAAACTCATAAAAATGAATTTGTTTTTCTAAA
AATGAATTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTTAAAACCAAGAAAAAT
TCCCTCGAAAAAAATCCAGGAGTAGAAAACTCGTA
Found at i:9996 original size:42 final size:42
Alignment explanation
Indices: 9949--10039 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
9939 TTTCCCAAGG
*
9949 CTGAGCCGATGGGAAAAAG-ATGAAGAAGAAAGTCTCCCGAGT
1 CTGAGCCGATAGGAAAAAGAATGAAGAA-AAAGTCTCCCGAGT
* * * *
9991 CTGAGCCGATAGGCAAATGAATGATGGAAAAGTCTCCCGAGT
1 CTGAGCCGATAGGAAAAAGAATGAAGAAAAAGTCTCCCGAGT
*
10033 CTAAGCC
1 CTGAGCC
10040 AACGGGCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 36 0.86
43 6 0.14
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.16
Consensus pattern (42 bp):
CTGAGCCGATAGGAAAAAGAATGAAGAAAAAGTCTCCCGAGT
Found at i:10089 original size:42 final size:41
Alignment explanation
Indices: 9977--10195 Score: 133
Period size: 42 Copynumber: 5.2 Consensus size: 41
9967 GATGAAGAAG
* * *
9977 AAAGTCTCCCGAGTCTGAGCCGATAGGCAAATGAATGATGGA
1 AAAGTCTCCCGAGTCT-AACCGATGGGCAAATGAAAGATGGA
* *
10019 AAAGTCTCCCGAGTCTAAGCCAACGGGCAAATGAAAGAT-GA
1 AAAGTCTCCCGAGTCTAA-CCGATGGGCAAATGAAAGATGGA
* * *
10060 GCAAGTCTCCCAAGTCTCAACCGATGGGCAGATGATTGAAA-AAGG-
1 -AAAGTCTCCCGAGTCT-AACCGATGGGCA-A--A-TGAAAGATGGA
* * * * * * **
10105 -AAGTCTCCTGGGTCTGAGCTGACGGGCAGATGAAAGATTTA
1 AAAGTCTCCCGAGTCT-AACCGATGGGCAAATGAAAGATGGA
* * * *
10146 GAAGTCTCCCGAGTCTGAACTGATGGGC-AACGAAAGATGAA
1 AAAGTCTCCCGAGTCT-AACCGATGGGCAAATGAAAGATGGA
10187 AAAGTCTCC
1 AAAGTCTCC
10196 TAGGTCTAAG
Statistics
Matches: 136, Mismatches: 30, Indels: 23
0.72 0.16 0.12
Matches are distributed among these distances:
39 5 0.04
40 2 0.01
41 20 0.15
42 77 0.57
43 24 0.18
45 2 0.01
46 6 0.04
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (41 bp):
AAAGTCTCCCGAGTCTAACCGATGGGCAAATGAAAGATGGA
Found at i:10407 original size:43 final size:43
Alignment explanation
Indices: 10315--10532 Score: 170
Period size: 43 Copynumber: 5.1 Consensus size: 43
10305 AAGATGAAGA
* * * *
10315 AAGTTTCCTAGGTCAAAGCCGACGGGCTA-ATAGTTGATAAAGG
1 AAGTCTCCCAGGTCAAAGCCGATGGG-TAGACAGTTGATAAAGG
* * * *
10358 AAGTCTCCCGGGTCTAAGTCGATGGGTAAACAGTTGATAAAGG
1 AAGTCTCCCAGGTCAAAGCCGATGGGTAGACAGTTGATAAAGG
* * ** * * * *
10401 AAGTCTCCCAAGACTGAGCCGAGGGGTAGATAGTGGATGAA-G
1 AAGTCTCCCAGGTCAAAGCCGATGGGTAGACAGTTGATAAAGG
* * * ** * *
10443 AAGTCTCCCGGGTCAAAACCGATGGGTATACAGAAGATGAAGA
1 AAGTCTCCCAGGTCAAAGCCGATGGGTAGACAGTTGATAAAGG
* * * *
10486 AAGTCTCTCAGGTCAAAGACAATGGGTAGACAGTTGATAGAGG
1 AAGTCTCCCAGGTCAAAGCCGATGGGTAGACAGTTGATAAAGG
10529 AAGT
1 AAGT
10533 TTCTCAAGTC
Statistics
Matches: 133, Mismatches: 40, Indels: 4
0.75 0.23 0.02
Matches are distributed among these distances:
42 33 0.25
43 100 0.75
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.20
Consensus pattern (43 bp):
AAGTCTCCCAGGTCAAAGCCGATGGGTAGACAGTTGATAAAGG
Found at i:10490 original size:85 final size:86
Alignment explanation
Indices: 10331--10492 Score: 202
Period size: 85 Copynumber: 1.9 Consensus size: 86
10321 CCTAGGTCAA
* * ** **
10331 AGCCGACGGGCTAATAGTTGATAAAGGAAGTCTCCCGGGTCTAAGTCGATGGGTAAACAGTTGAT
1 AGCCGACGGGCTAATAGTGGATAAAGGAAGTCTCCCGGGTCAAAACCGATGGGTAAACAGAAGAT
*
10396 AAAGGAAGTCTCCCAAGACTG
66 AAAGAAAGTCTCCCAAGACTG
* * *
10417 AGCCGA-GGGGTAGATAGTGGATGAA-GAAGTCTCCCGGGTCAAAACCGATGGGTATACAGAAGA
1 AGCCGACGGGCTA-ATAGTGGATAAAGGAAGTCTCCCGGGTCAAAACCGATGGGTAAACAGAAGA
*
10480 TGAAGAAAGTCTC
65 TAAAGAAAGTCTC
10493 TCAGGTCAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
85 48 0.75
86 16 0.25
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.19
Consensus pattern (86 bp):
AGCCGACGGGCTAATAGTGGATAAAGGAAGTCTCCCGGGTCAAAACCGATGGGTAAACAGAAGAT
AAAGAAAGTCTCCCAAGACTG
Found at i:10917 original size:42 final size:42
Alignment explanation
Indices: 10807--10919 Score: 102
Period size: 42 Copynumber: 2.7 Consensus size: 42
10797 TTAAGCAGAC
* * **
10807 GATGGATGAAGAAGTCACCCGGGTCTAAGCCAAGGGGAAGAT
1 GATGGATGAAGAAGTCTCCTGGGTCTAAGCCAACAGGAAGAT
** * * ** * *
10849 GAAAGATGAAAAAGTCTCTTATGTCTAAGCCGACAGGTAGAT
1 GATGGATGAAGAAGTCTCCTGGGTCTAAGCCAACAGGAAGAT
10891 -AGTGGATGAAGAAGTCTCCTGGGTCTAAG
1 GA-TGGATGAAGAAGTCTCCTGGGTCTAAG
10920 TTGACGACGG
Statistics
Matches: 52, Mismatches: 18, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
41 1 0.02
42 51 0.98
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.20
Consensus pattern (42 bp):
GATGGATGAAGAAGTCTCCTGGGTCTAAGCCAACAGGAAGAT
Found at i:11021 original size:43 final size:43
Alignment explanation
Indices: 10952--11137 Score: 151
Period size: 43 Copynumber: 4.3 Consensus size: 43
10942 TGGAAAACAA
* * *
10952 TCTATGGTCAAAGCTGACAGGCAGACTTAAGGAG-GAAGAAGTC
1 TCTAGGGTCAAAGCCGATAGGCAGACTTAAGG-GCGAAGAAGTC
* * *
10995 TCTAGGGTCAAAGCCGATAGGTAGACTTTAGGGCAAAGAAGTC
1 TCTAGGGTCAAAGCCGATAGGCAGACTTAAGGGCGAAGAAGTC
* * * * * *
11038 TCCACGGTTAAAGCCAATAGGCAGACTTAAGGGTGAGGAAGTC
1 TCTAGGGTCAAAGCCGATAGGCAGACTTAAGGGCGAAGAAGTC
* * * * * * * *
11081 TCTGGGGTTAAAGCCAACACGCAGGCTTAAGGGTGAATAAGTC
1 TCTAGGGTCAAAGCCGATAGGCAGACTTAAGGGCGAAGAAGTC
*
11124 TGC-AAGGTCAAAGC
1 T-CTAGGGTCAAAGC
11138 TGACGGGTAG
Statistics
Matches: 115, Mismatches: 26, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
42 1 0.01
43 113 0.98
44 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.30, T:0.19
Consensus pattern (43 bp):
TCTAGGGTCAAAGCCGATAGGCAGACTTAAGGGCGAAGAAGTC
Found at i:11137 original size:86 final size:86
Alignment explanation
Indices: 10970--11137 Score: 185
Period size: 86 Copynumber: 2.0 Consensus size: 86
10960 CAAAGCTGAC
* * * * *
10970 AGGCAGACTTAAGGAGGAAGAAGTCTCTAGGGTCAAAGCCGATAGGTAGACTTTAGGGCAAAGAA
1 AGGCAGACTTAAGGAGGAAGAAGTCTCTAGGGTCAAAGCCAACACGCAGACTTAAGGGCAAAGAA
* *
11035 GTCTCCACGGTTAAAGCCAAT
66 GTCTCCAAGGTCAAAGCCAAT
* * * * ** *
11056 AGGCAGACTTAAGG-GTGAGGAAGTCTCTGGGGTTAAAGCCAACACGCAGGCTTAAGGGTGAATA
1 AGGCAGACTTAAGGAG-GAAGAAGTCTCTAGGGTCAAAGCCAACACGCAGACTTAAGGGCAAAGA
*
11120 AGTCTGCAAGGTCAAAGC
65 AGTCTCCAAGGTCAAAGC
11138 TGACGGGTAG
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
85 1 0.02
86 65 0.98
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.18
Consensus pattern (86 bp):
AGGCAGACTTAAGGAGGAAGAAGTCTCTAGGGTCAAAGCCAACACGCAGACTTAAGGGCAAAGAA
GTCTCCAAGGTCAAAGCCAAT
Found at i:11287 original size:44 final size:44
Alignment explanation
Indices: 11232--11372 Score: 135
Period size: 44 Copynumber: 3.2 Consensus size: 44
11222 ATGCGAATCG
* *
11232 TTTGACCAGGGTGGTAGCCATATGTCAAATAGGAATGAGGCAAA
1 TTTGACTAGGGTGGTAACCATATGTCAAATAGGAATGAGGCAAA
* * * **
11276 TTTGACTAGGGTGG-AACCATACGTCAAATCGAAATGAGAAAAA
1 TTTGACTAGGGTGGTAACCATATGTCAAATAGGAATGAGGCAAA
* * * * *
11319 TCTGACCT-GGGTGGTAACCATATGTCAGACAGGAGA-GAGGCGAC
1 TTTGA-CTAGGGTGGTAACCATATGTCAAATAGGA-ATGAGGCAAA
11363 TTTGACTAGG
1 TTTGACTAGG
11373 CCCTAACACC
Statistics
Matches: 75, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
43 35 0.47
44 39 0.52
45 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (44 bp):
TTTGACTAGGGTGGTAACCATATGTCAAATAGGAATGAGGCAAA
Found at i:11312 original size:43 final size:44
Alignment explanation
Indices: 11232--11345 Score: 133
Period size: 43 Copynumber: 2.6 Consensus size: 44
11222 ATGCGAATCG
* * * **
11232 TTTGACCAGGGTGGTAGCCATATGTCAAATAGGAATGAGGCAAA
1 TTTGACTAGGGTGGTAACCATATGTCAAATAGAAATGAGAAAAA
* *
11276 TTTGACTAGGGTGG-AACCATACGTCAAATCGAAATGAGAAAAA
1 TTTGACTAGGGTGGTAACCATATGTCAAATAGAAATGAGAAAAA
*
11319 TCTGACCT-GGGTGGTAACCATATGTCA
1 TTTGA-CTAGGGTGGTAACCATATGTCA
11346 GACAGGAGAG
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
43 33 0.56
44 26 0.44
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (44 bp):
TTTGACTAGGGTGGTAACCATATGTCAAATAGAAATGAGAAAAA
Found at i:11441 original size:48 final size:48
Alignment explanation
Indices: 11363--11688 Score: 350
Period size: 48 Copynumber: 6.8 Consensus size: 48
11353 GAGAGGCGAC
* *
11363 TTTGACTAGGCCCTAACACCAATACAGTCAAATGAAGGATGAAAAGAG
1 TTTGACCAGGCCCTAACACCAATACAGTCAAATGAGGGATGAAAAGAG
* ** * *
11411 TTCGACCAGGCCCTAACACTGATGA-AGTCAAATAAGAGATGAAAAGAG
1 TTTGACCAGGCCCTAACACCAAT-ACAGTCAAATGAGGGATGAAAAGAG
* * * * ** * *
11459 TTTGACCAAGTCTTAAAACCAATACAAACAAATG-GGGGTGGAAAGAG
1 TTTGACCAGGCCCTAACACCAATACAGTCAAATGAGGGATGAAAAGAG
* * * **
11506 TTTGACCAGGCCCTAACACTAATACAATTAAATGAGGGATGAAAATTG
1 TTTGACCAGGCCCTAACACCAATACAGTCAAATGAGGGATGAAAAGAG
* * *
11554 TTTGACCAAGCCTTAACACCAATACAGTTAAATGAGGGATGAAAAGAG
1 TTTGACCAGGCCCTAACACCAATACAGTCAAATGAGGGATGAAAAGAG
* * * ***
11602 TTTGACCAGGCCCTAACACCAATACAGTCAAACGAAGGAAGATTTGAG
1 TTTGACCAGGCCCTAACACCAATACAGTCAAATGAGGGATGAAAAGAG
* *
11650 TTTGACCAGGCCTTAACACCAATATAGTCAAATGAGGGA
1 TTTGACCAGGCCCTAACACCAATACAGTCAAATGAGGGA
11689 AGATTTGAGT
Statistics
Matches: 225, Mismatches: 50, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
47 38 0.17
48 186 0.83
49 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.20
Consensus pattern (48 bp):
TTTGACCAGGCCCTAACACCAATACAGTCAAATGAGGGATGAAAAGAG
Found at i:11623 original size:143 final size:143
Alignment explanation
Indices: 11363--11627 Score: 343
Period size: 143 Copynumber: 1.9 Consensus size: 143
11353 GAGAGGCGAC
* * *
11363 TTTGACTAGGCCCTAACACCAATACAGTCAAATGAAGGATGAAAAGAGTTCGACCAGGCCCTAAC
1 TTTGACCAGGCCCTAACACCAATACAATCAAATGAAGGATGAAAAGAGTTCGACCAAGCCCTAAC
** * *
11428 ACTGATGAAGTCAAATAAGAGATGAAAAGAGTTTGACCAAGTCTTAAAACCAATACAAACAAATG
66 ACCAATGAAGTCAAATAAGAGATGAAAAGAGTTTGACCAAGCCCTAAAACCAATACAAACAAATG
11493 GGGGTGGAAAGAG
131 GGGGTGGAAAGAG
* * * ** * *
11506 TTTGACCAGGCCCTAACACTAATACAATTAAATGAGGGATGAAAATTGTTTGACCAAGCCTTAAC
1 TTTGACCAGGCCCTAACACCAATACAATCAAATGAAGGATGAAAAGAGTTCGACCAAGCCCTAAC
* * * * *
11571 ACCAAT-ACAGTTAAATGAGGGATGAAAAGAGTTTGACCAGGCCCTAACACCAATACA
66 ACCAATGA-AGTCAAATAAGAGATGAAAAGAGTTTGACCAAGCCCTAAAACCAATACA
11628 GTCAAACGAA
Statistics
Matches: 102, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
142 1 0.01
143 101 0.99
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (143 bp):
TTTGACCAGGCCCTAACACCAATACAATCAAATGAAGGATGAAAAGAGTTCGACCAAGCCCTAAC
ACCAATGAAGTCAAATAAGAGATGAAAAGAGTTTGACCAAGCCCTAAAACCAATACAAACAAATG
GGGGTGGAAAGAG
Found at i:12748 original size:89 final size:88
Alignment explanation
Indices: 12646--12839 Score: 212
Period size: 88 Copynumber: 2.2 Consensus size: 88
12636 GAAATGACAT
* * * *
12646 AAATACAAGCATCAGTAAAATGGCAAAAATAGAT-GAGATAATGCAAAT-ACTAAGCGTCATCTA
1 AAATGCAAGCATCAATAAAAGGGCAAAAACAGATGGA-ATAATGCAAATAAC-AA-CGTCATCTA
* * *
12709 AAGTGTAGATATATGTGAAATAATGC
63 AAATGCAGATATAGGTGAAATAATGC
* * ** * * *
12735 AAATGCAAACATCAATAGAAGGGCAAATGCATATGGAATAATGCAAATAACAATGTTATCTAAAA
1 AAATGCAAGCATCAATAAAAGGGCAAAAACAGATGGAATAATGCAAATAACAACGTCATCTAAAA
*
12800 TGCAGATGTAGGTGAAATAATGC
66 TGCAGATATAGGTGAAATAATGC
12823 AAATGCAAGCATCAATA
1 AAATGCAAGCATCAATA
12840 GGAAGGCAAA
Statistics
Matches: 87, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
88 45 0.52
89 38 0.44
90 4 0.05
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (88 bp):
AAATGCAAGCATCAATAAAAGGGCAAAAACAGATGGAATAATGCAAATAACAACGTCATCTAAAA
TGCAGATATAGGTGAAATAATGC
Found at i:12826 original size:88 final size:88
Alignment explanation
Indices: 12704--12870 Score: 239
Period size: 88 Copynumber: 1.9 Consensus size: 88
12694 ACTAAGCGTC
* * * *
12704 ATCTAAAGTGTAGATATATGTGAAATAATGCAAATGCAAACATCAATA-GAAGGGCAAATGCATA
1 ATCTAAAATGCAGATATAGGTGAAATAATGCAAATGCAAACATCAATAGGAA-GGCAAAAGCATA
*
12768 TGGAATA-ATGCAAATAACAATGTT
65 T-GAAAAGATGCAAATAACAATGTT
* *
12792 ATCTAAAATGCAGATGTAGGTGAAATAATGCAAATGCAAGCATCAATAGGAAGGCAAAAGCATAT
1 ATCTAAAATGCAGATATAGGTGAAATAATGCAAATGCAAACATCAATAGGAAGGCAAAAGCATAT
12857 GAAAAGATGCAAAT
66 GAAAAGATGCAAAT
12871 GCTGATGCAA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
87 4 0.06
88 63 0.90
89 3 0.04
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (88 bp):
ATCTAAAATGCAGATATAGGTGAAATAATGCAAATGCAAACATCAATAGGAAGGCAAAAGCATAT
GAAAAGATGCAAATAACAATGTT
Found at i:12860 original size:44 final size:43
Alignment explanation
Indices: 12724--12872 Score: 124
Period size: 44 Copynumber: 3.4 Consensus size: 43
12714 TAGATATATG
*
12724 TGAAATAATGCAAATGCAAACATCAATAGAAGGGCAAATGCATA
1 TGAAATAATGCAAATGCAAGCATCAATAGAA-GGCAAATGCATA
* * * * * * * **
12768 TGGAATAATGCAAATAACAATGTTATC--TAAAATGCAGATGTAGG
1 TGAAATAATGCAAAT-GCAA-G-CATCAATAGAAGGCAAATGCATA
*
12812 TGAAATAATGCAAATGCAAGCATCAATAGGAAGGCAAAAGCATA
1 TGAAATAATGCAAATGCAAGCATCAATA-GAAGGCAAATGCATA
12856 TGAAA-AGATGCAAATGC
1 TGAAATA-ATGCAAATGC
12873 TGATGCAATC
Statistics
Matches: 78, Mismatches: 20, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
41 3 0.04
42 1 0.01
43 6 0.08
44 58 0.74
45 7 0.09
47 3 0.04
ACGTcount: A:0.48, C:0.12, G:0.20, T:0.20
Consensus pattern (43 bp):
TGAAATAATGCAAATGCAAGCATCAATAGAAGGCAAATGCATA
Found at i:14738 original size:30 final size:31
Alignment explanation
Indices: 14697--14772 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
14687 TGAATAGTAC
*
14697 ATGTATTGATACATTCT-TTTTTTTACCCAG
1 ATGTATCGATACATTCTGTTTTTTTACCCAG
*
14727 ATGTATCGATACATTTTGTTTTTTTACCCAG
1 ATGTATCGATACATTCTGTTTTTTTACCCAG
14758 ATGTATCGATACATT
1 ATGTATCGATACATT
14773 AAAAAAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
30 15 0.35
31 28 0.65
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (31 bp):
ATGTATCGATACATTCTGTTTTTTTACCCAG
Found at i:21199 original size:20 final size:19
Alignment explanation
Indices: 21173--21229 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
21163 TATTACCGTT
*
21173 TCATGTATTGATATAATTG-
1 TCATGTATTGATACAA-TGA
*
21192 TGCATGTATCGATACAATGA
1 T-CATGTATTGATACAATGA
21212 TCATGTATTGATACAATG
1 TCATGTATTGATACAATG
21230 TATTGATGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.39
Consensus pattern (19 bp):
TCATGTATTGATACAATGA
Found at i:23003 original size:21 final size:21
Alignment explanation
Indices: 22970--23010 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
22960 CTAAGTAAAA
22970 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
22991 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
23011 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:23075 original size:20 final size:19
Alignment explanation
Indices: 23050--23120 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
23040 ACCCTGAAAA
23050 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
23070 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
23089 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
23110 GTATCGATACA
1 GTATCGATACA
23121 GGTCATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:23216 original size:10 final size:10
Alignment explanation
Indices: 23197--23227 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
23187 AATCTCATTT
23197 TCACTGTTCA
1 TCACTGTTCA
*
23207 TCACTATTCA
1 TCACTGTTCA
23217 TCACTGTTCA
1 TCACTGTTCA
23227 T
1 T
23228 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:23249 original size:21 final size:22
Alignment explanation
Indices: 23215--23270 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
23205 CATCACTATT
23215 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
23237 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
23258 CATCACTGTTCAT
1 CATCACTGTTCAT
23271 AGGTCACTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:23371 original size:13 final size:13
Alignment explanation
Indices: 23353--23378 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23343 ACATATTTGT
23353 GTGTATCGATACA
1 GTGTATCGATACA
23366 GTGTATCGATACA
1 GTGTATCGATACA
23379 TCATAAATAG
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:23920 original size:34 final size:35
Alignment explanation
Indices: 23857--23923 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
23847 CTAAGTGATT
23857 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
23893 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
23924 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:27029 original size:13 final size:13
Alignment explanation
Indices: 27011--27035 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27001 TTTTCCAGAT
27011 TATATCGATACAA
1 TATATCGATACAA
27024 TATATCGATACA
1 TATATCGATACA
27036 TTGCTTCAGT
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
TATATCGATACAA
Found at i:28711 original size:21 final size:21
Alignment explanation
Indices: 28678--28718 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28668 CTAAGTAAAA
28678 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
28699 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
28719 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:28783 original size:20 final size:19
Alignment explanation
Indices: 28758--28828 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
28748 ACCCTGAAAA
28758 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
28778 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
28797 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
28818 GTATCGATACA
1 GTATCGATACA
28829 GGTCATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:28924 original size:10 final size:10
Alignment explanation
Indices: 28905--28935 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
28895 AATCTCATTT
28905 TCACTGTTCA
1 TCACTGTTCA
*
28915 TCACTATTCA
1 TCACTGTTCA
28925 TCACTGTTCA
1 TCACTGTTCA
28935 T
1 T
28936 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:28957 original size:21 final size:22
Alignment explanation
Indices: 28923--28978 Score: 105
Period size: 21 Copynumber: 2.6 Consensus size: 22
28913 CATCACTATT
28923 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
28945 CATCACT-TTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
28966 CATCACTGTTCAT
1 CATCACTGTTCAT
28979 AGGTCACTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.64
22 12 0.36
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:29079 original size:13 final size:13
Alignment explanation
Indices: 29061--29086 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29051 ACATATTTGT
29061 GTGTATCGATACA
1 GTGTATCGATACA
29074 GTGTATCGATACA
1 GTGTATCGATACA
29087 TCATAAATAG
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GTGTATCGATACA
Found at i:29629 original size:34 final size:35
Alignment explanation
Indices: 29566--29632 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
29556 CTAAGTGATT
29566 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
29602 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
29633 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:36837 original size:271 final size:268
Alignment explanation
Indices: 36323--36857 Score: 729
Period size: 271 Copynumber: 2.0 Consensus size: 268
36313 ACCAATTGTA
* *
36323 AGCTCAAGGAATAATGAACCAAGAGGGGGCGAATTGGTTCTTTTCGAATTTTGAGTGTTTTGAAA
1 AGCTCAAGGAATAATAAACCAAGAGGGGGCGAATTGGTTCTTTTCGAATTTTCAGTGTTTTGAAA
* * * * *
36388 GATTTGATGCAAAACAATTCAAAAGATAAAAACATTGAGGAAGAAAAGCTCAACATAAGAGTTTA
66 GATTTGATACAAAACAATTCAAAAGATAAAAACATTAAGGAAGAAAAGCTCAACACAAAAGATTA
* * * * *
36453 TAGAAGTTCGGTCCAATTTGGTACCTACGTCTTTTCTCCTCGACACTTCCTTGTTGAGTGGTTGT
131 TAGAAGTTCGGTCCAACTTCGTACCTACGTCCTCTCTCCTCGACACTTCCTTGTTGAGTGGTTAT
* * * *
36518 CCAATTCACTACAAGAATTGATTACTTTTAAGGCAAGGGTAGAACCTTACAAAACCTTATCTTTT
196 CCAATTCACTACAAGAATTGATTACCTTTAAGGCAAAGATAGAACCTTAC-AAACCGTATCTTTT
36583 AAAGGTGAG
260 AAAGGTGAG
* * * *
36592 AGCTCAAGGAATGATAAACCAAGAGGGGGGGTGAATTGGTTCTTTTCTAATTTTCTG-GTTTTGA
1 AGCTCAAGGAATAATAAACCAAGA--GGGGGCGAATTGGTTCTTTTCGAATTTTCAGTGTTTTGA
* * *
36656 AGGATTTTGA-ACAAAACAATTCGAAAGATAAAAAGGATTAAGGAAGAAAAGCT-AGACACAAAA
64 AAGA-TTTGATACAAAACAATTCAAAAGATAAAAA-CATTAAGGAAGAAAAGCTCA-ACACAAAA
*
36719 GATTATA-AAGGTTCGGTCTAACTTCGTACCTACGTCCTCTCTCCTCGACACTTCCTTGTTGAGT
126 GATTATAGAA-GTTCGGTCCAACTTCGTACCTACGTCCTCTCTCCTCGACACTTCCTTGTTGAGT
* *
36783 GGTTATCCAATTCACTACTAA-AATTGATTACCTTTAAGGCAAAGATATAACCTTACAAATCGTA
190 GGTTATCCAATTCACTAC-AAGAATTGATTACCTTTAAGGCAAAGATAGAACCTTACAAACCGTA
36847 TCTTTTAAAGG
254 TCTTTTAAAGG
36858 CTTAGATACC
Statistics
Matches: 233, Mismatches: 26, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
269 22 0.09
270 52 0.22
271 157 0.67
272 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (268 bp):
AGCTCAAGGAATAATAAACCAAGAGGGGGCGAATTGGTTCTTTTCGAATTTTCAGTGTTTTGAAA
GATTTGATACAAAACAATTCAAAAGATAAAAACATTAAGGAAGAAAAGCTCAACACAAAAGATTA
TAGAAGTTCGGTCCAACTTCGTACCTACGTCCTCTCTCCTCGACACTTCCTTGTTGAGTGGTTAT
CCAATTCACTACAAGAATTGATTACCTTTAAGGCAAAGATAGAACCTTACAAACCGTATCTTTTA
AAGGTGAG
Found at i:37372 original size:19 final size:20
Alignment explanation
Indices: 37327--37378 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
37317 TTACAAGCCA
*
37327 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATATTGGG
*
37347 ATGTATCGATACATATTGTG
1 ATGTATCGATACATATTGGG
37367 -TGTATCGATACA
1 ATGTATCGATACA
37379 AACAGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATATTGGG
Found at i:37467 original size:20 final size:21
Alignment explanation
Indices: 37420--37472 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
37410 GCCAATCACC
*
37420 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
37441 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
37461 TGTATCGATACA
1 TGTATCGATACA
37473 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:38099 original size:17 final size:16
Alignment explanation
Indices: 38067--38098 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38057 CCTTAATAAA
*
38067 GCAATTTAACAATTTT
1 GCAAATTAACAATTTT
38083 GCAAATTAACAATTTT
1 GCAAATTAACAATTTT
38099 TTTCCCCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (16 bp):
GCAAATTAACAATTTT
Found at i:40179 original size:8 final size:8
Alignment explanation
Indices: 40161--40191 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
40151 TTTTCAACAT
40161 CAAACATCA
1 CAAA-ATCA
40170 CAAAATCA
1 CAAAATCA
40178 CAAAATCA
1 CAAAATCA
40186 CAAAAT
1 CAAAAT
40192 TTAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (8 bp):
CAAAATCA
Found at i:44437 original size:3 final size:3
Alignment explanation
Indices: 44424--44468 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
44414 TCTTCATCTG
* *
44424 ATC ACC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC TTC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
44469 CTTGATGGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:46092 original size:33 final size:32
Alignment explanation
Indices: 46048--46115 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
46038 CGTTACAAGC
* *
46048 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCAATA
* *
46081 CAATGTGTCGATACATATTGTGTGTATCAATA
1 CAATGTATCGATACATATTGGGTGTATCAATA
46113 CAA
1 CAA
46116 ACAGTTAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCAATA
Found at i:46192 original size:20 final size:21
Alignment explanation
Indices: 46145--46196 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
46135 GCCAATCACC
*
46145 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
46166 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
46186 TGTATCGATAC
1 TGTATCGATAC
46197 TGTGCATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 13 0.48
21 14 0.52
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:47005 original size:33 final size:33
Alignment explanation
Indices: 46963--47027 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
46953 TTTGGGACAA
46963 TGTATCGATACAAT-T-CTTCATGTATTGATACAT
1 TGTATCGATACAATGTGC--CATGTATTGATACAT
46996 TGTATCGATACAATGTGCCATGTATTGATACA
1 TGTATCGATACAATGTGCCATGTATTGATACA
47028 AACAGTGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATTGATACAT
Found at i:47101 original size:19 final size:19
Alignment explanation
Indices: 47051--47107 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 19
47041 TAGCAATTGC
47051 CAATT-TCATGTATCGATA
1 CAATTGTCATGTATCGATA
47069 CAATTGTGCATGTATCGATA
1 CAATTGT-CATGTATCGATA
47089 CAA-TGATCATGTATCGATA
1 CAATTG-TCATGTATCGATA
47108 ACATGTATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.14
19 15 0.42
20 16 0.44
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
CAATTGTCATGTATCGATA
Found at i:47121 original size:32 final size:33
Alignment explanation
Indices: 47077--47140 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
47067 TACAATTGTG
* *
47077 CATGTATCGATACAATG-ATCATGTATCGATAA
1 CATGTATCGATACAAAGCATAATGTATCGATAA
*
47109 CATGTATTGATACAAAGCATAATGTATCGATA
1 CATGTATCGATACAAAGCATAATGTATCGATA
47141 CATCTGGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (33 bp):
CATGTATCGATACAAAGCATAATGTATCGATAA
Found at i:52380 original size:3 final size:3
Alignment explanation
Indices: 52372--52402 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
52362 TCTGAGTCAC
*
52372 CAT CAT CAT CAT CAT CAT CAT CAT CTT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
52403 GTCCTTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:54014 original size:13 final size:13
Alignment explanation
Indices: 53996--54021 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53986 ACATTTTGGG
53996 ATGTATCGATACA
1 ATGTATCGATACA
54009 ATGTATCGATACA
1 ATGTATCGATACA
54022 TATTTGTGTG
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:54016 original size:33 final size:33
Alignment explanation
Indices: 53974--54042 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
53964 CGTTACAAGC
53974 CAATGTATCGATACAT-TTTGGGATGTATCGATA
1 CAATGTATCGATACATATTTGGG-TGTATCGATA
*
54007 CAATGTATCGATACATATTTGTGTGTATCGATA
1 CAATGTATCGATACATATTTGGGTGTATCGATA
54040 CAA
1 CAA
54043 ACAGTTAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 29 0.85
34 5 0.15
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (33 bp):
CAATGTATCGATACATATTTGGGTGTATCGATA
Found at i:54130 original size:20 final size:21
Alignment explanation
Indices: 54083--54135 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
54073 GCCAATCACC
*
54083 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
54104 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
54124 TGTATCGATACA
1 TGTATCGATACA
54136 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:54141 original size:13 final size:13
Alignment explanation
Indices: 54123--54147 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54113 ACATTTGGTC
54123 ATGTATCGATACA
1 ATGTATCGATACA
54136 ATGTATCGATAC
1 ATGTATCGATAC
54148 TGTGCATTAT
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):
ATGTATCGATACA
Found at i:56202 original size:149 final size:150
Alignment explanation
Indices: 56051--56317 Score: 346
Period size: 148 Copynumber: 1.8 Consensus size: 150
56041 ATTTTCTTAA
* * * *
56051 AAAAATCATTTCGTACCTTGATGAAAATCTGCCAAA-ATATGAAAA-ATTTTGAAATAT-TTTAA
1 AAAAATCATTTCGTACCTTAATGAAAAGCCG-AAAAGATATGAAAAGATTTTGAAA-ATCTTTAA
* *
56113 TACCCCTACAGATACCCATAGGAATATAAAAGA-TTGAAAATGATTAATATTTATTTTAGTAAGG
64 TACCCCTACAGATACCCATAAGAATATAAAAGACTTGAAAATAATTAATATTTATTTTAGTAAGG
56177 AGGATTAATTTAATTATTTC-T
129 AGGATTAATTTAATTATTTCTT
* * * * * * *
56198 AAAAATGATTTTGTACCTTAATGGATAGCCGAAAAGATGTGAAAAGTTTTTGAAAATCTTTTATA
1 AAAAATCATTTCGTACCTTAATGAAAAGCCGAAAAGATATGAAAAGATTTTGAAAATCTTTAATA
* *
56263 CCCCTACGGATACCCATAAGAATATAAAAGACTTGAAAATAATTGATATTTATTT
66 CCCCTACAGATACCCATAAGAATATAAAAGACTTGAAAATAATTAATATTTATTT
56318 GTGTTTTGAA
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
146 3 0.03
147 34 0.34
148 43 0.43
149 21 0.21
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (150 bp):
AAAAATCATTTCGTACCTTAATGAAAAGCCGAAAAGATATGAAAAGATTTTGAAAATCTTTAATA
CCCCTACAGATACCCATAAGAATATAAAAGACTTGAAAATAATTAATATTTATTTTAGTAAGGAG
GATTAATTTAATTATTTCTT
Found at i:57464 original size:11 final size:11
Alignment explanation
Indices: 57425--57465 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
57415 ATTTTCCCTA
57425 TTTTTCTTTCT
1 TTTTTCTTTCT
*
57436 CTTTTCGTTTCTT
1 TTTTTC-TTTC-T
57449 TTTTTCTTTCT
1 TTTTTCTTTCT
57460 TTTTTC
1 TTTTTC
57466 AGCTGGAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 12 0.46
12 8 0.31
13 6 0.23
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:58525 original size:167 final size:166
Alignment explanation
Indices: 58110--58655 Score: 660
Period size: 167 Copynumber: 3.3 Consensus size: 166
58100 AAAACACTGC
**
58110 ATTTT-GAAAAAAGGGGAATTTTGAGGAGAAAAA-TCAAAAACCTCATGAAAATG-A-TTTTTTT
1 ATTTTAGAAAAAA-GGGAATTTCAAGGA-AAAAATTCAAAAA-CTCATGAAAATGAATTTTTTTT
*
58171 TTAAAAATGAATTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTAAAAACCAAGA
63 TTAAAACTGAATTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATT-AAAACCAAGA
* *
58236 AAAATCCCCTCAAAGAAAAT-TTACGGAGTAGAAAA-TACCGT
127 AAAATCTCCTCAAA-AAAATCTAAC-GAGTAGAAAACT-CCGT
*
58277 A-TTTAGGAAAAAAGGG-A----AA--AAAAAATTC-AAAACTCATGAAAATGAATTTTGGTTTT
1 ATTTTA-GAAAAAAGGGAATTTCAAGGAAAAAATTCAAAAACTCATGAAAATGAATTTT-TTTTT
* **
58333 TAAAACTGAATTAATATGAAATAAATAATGATATTTGATGAATTTTAAAAATTAAAACTTAG-AA
64 TAAAACTGAATTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTAAAACCAAGAAA
* *
58397 AATCTCCTCGAAAAAAATCTAACGAGAAGAAAACTCCAT
129 AATCTCCTC-AAAAAAATCTAACGAGTAGAAAACTCCGT
58436 ATTTTAGAAAAAAGGGAATTTCAAGGAAAAAATTCAAAAACTCATGAAAATGAATTTATTTTTTT
1 ATTTTAGAAAAAAGGGAATTTCAAGGAAAAAATTCAAAAACTCATGAAAATGAATTT-TTTTTTT
* * *
58501 AAAACTGAA-TACATATGAAATAAATAATGTTGTTTGAAGAATTTTAACAATTAAAACCAAGAAA
65 AAAACTGAATTA-ATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTAAAACCAAGAAA
* *
58565 AATCTCCTCAAAAAAAATC-CACGAAGTAGAAAACTCTGT
129 AATCTCCTC-AAAAAAATCTAACG-AGTAGAAAACTCCGT
* * *
58604 ATTTCAAAAAAAAGAGGAATTTCAAGGAAAAAATTCAAAAACTAATGAAAAT
1 ATTTTAGAAAAAAG-GGAATTTCAAGGAAAAAATTCAAAAACTCATGAAAAT
58656 AAAAAAATTT
Statistics
Matches: 331, Mismatches: 25, Indels: 44
0.83 0.06 0.11
Matches are distributed among these distances:
158 12 0.04
159 48 0.15
160 25 0.08
161 55 0.17
162 1 0.00
164 2 0.01
166 15 0.05
167 85 0.26
168 52 0.16
169 36 0.11
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (166 bp):
ATTTTAGAAAAAAGGGAATTTCAAGGAAAAAATTCAAAAACTCATGAAAATGAATTTTTTTTTTA
AAACTGAATTAATATGAAATAAATAATGATGTTTGATGAATTTTAAAAATTAAAACCAAGAAAAA
TCTCCTCAAAAAAATCTAACGAGTAGAAAACTCCGT
Done.