Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3028
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: 91256
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:5634 original size:27 final size:27
Alignment explanation
Indices: 5604--5781 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
5594 ATATTAAGTC
* * *
5604 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
5631 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
5659 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
5686 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
5713 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
5740 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
5767 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
5782 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 105 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:5688 original size:55 final size:54
Alignment explanation
Indices: 5604--5781 Score: 232
Period size: 54 Copynumber: 3.3 Consensus size: 54
5594 ATATTAAGTC
* * *
5604 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAA-T
* * * *
5659 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* ** *
5713 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
5767 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
5782 GTACAATTTA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:5770 original size:81 final size:82
Alignment explanation
Indices: 5625--5780 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
5615 TGCTATATAA
* *
5625 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
5690 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
5707 TCAATTCGCACACTTAGTG-CATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
5770 ACACTTAGTGC
65 ACACTTAGTGC
5781 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 43 0.64
82 24 0.36
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Found at i:14900 original size:10 final size:10
Alignment explanation
Indices: 14873--14914 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
14863 TGTACTCAGG
14873 AGAG-CAAAA
1 AGAGCCAAAA
*
14882 AGAGTCAAAA
1 AGAGCCAAAA
*
14892 GGAGCCAAAA
1 AGAGCCAAAA
14902 ATGAGCCAAAA
1 A-GAGCCAAAA
14913 AG
1 AG
14915 GGGACAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 4 0.14
10 14 0.50
11 10 0.36
ACGTcount: A:0.57, C:0.14, G:0.24, T:0.05
Consensus pattern (10 bp):
AGAGCCAAAA
Found at i:17783 original size:79 final size:82
Alignment explanation
Indices: 17672--17856 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
17662 GCTACTCGTT
* *
17672 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
17735 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
17752 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* * *
17815 GATATGGTCACTTAGCG
66 GATATAGTAACTTAGCA
17832 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
17857 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 33 0.36
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:17856 original size:40 final size:40
Alignment explanation
Indices: 17653--17856 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
17643 CGGAATTTAA
** *
17653 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
17693 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
17733 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
17772 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * * *
17812 CCGGATATGGTCACTTAGCGCAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
17852 CCGGA
1 CCGGA
17857 CATCATTCAA
Statistics
Matches: 140, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.24
40 94 0.67
41 11 0.08
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:25687 original size:38 final size:39
Alignment explanation
Indices: 25577--25760 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 39
25567 GCTACTCGTT
*
25577 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTA-CCCGGATT-TAGTAACTCGCA
25617 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTT-ACCCGGATTTAGTAACTCGCA
* *
25657 CAAATGCCTTCGGG-CTTACCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTACCCGGATTTAGTAACTCGCA
* * * * *
25695 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTA-CCCGGATTTAGTAAC-TCGCA
25736 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTA-CCCGGA
25761 CATCATTCAA
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
37 2 0.02
38 30 0.24
39 7 0.06
40 73 0.58
41 14 0.11
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTACCCGGATTTAGTAACTCGCA
Found at i:25703 original size:78 final size:82
Alignment explanation
Indices: 25577--25760 Score: 229
Period size: 78 Copynumber: 2.3 Consensus size: 82
25567 GCTACTCGTT
* *
25577 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
25640 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
25657 CAAATGCCTTCGGG-CTTA-CCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
25719 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
25736 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
25761 CATCATTCAA
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
77 3 0.03
78 51 0.57
79 16 0.18
80 20 0.22
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:28294 original size:31 final size:31
Alignment explanation
Indices: 28251--28458 Score: 364
Period size: 31 Copynumber: 6.7 Consensus size: 31
28241 TTAGTCTTGA
28251 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
28281 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
28312 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
28343 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
* * *
28374 CATTTCACTAGGCCGAAGCCTTTTCATAAGT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
28405 CATATCACTGGCCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
28436 CATATCATTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
28459 ACTGTAAATG
Statistics
Matches: 168, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 5 0.03
31 163 0.97
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:28699 original size:26 final size:26
Alignment explanation
Indices: 28661--28847 Score: 268
Period size: 26 Copynumber: 7.2 Consensus size: 26
28651 TATCTAGAGG
* *
28661 CCTTTTCAATAAACTAGGGCATAAGC
1 CCTTTTCGATAAACTGGGGCATAAGC
*
28687 CCTTTTCGGTAAACTGGGGCATAAGC
1 CCTTTTCGATAAACTGGGGCATAAGC
* *
28713 CCTTTTCAATAAACTGGGGCATAAAC
1 CCTTTTCGATAAACTGGGGCATAAGC
*
28739 CCTTTTCGGTAAACTGGGGCA-AAGC
1 CCTTTTCGATAAACTGGGGCATAAGC
* *
28764 CGTTTTCAATAAACTGGGGCATAAGC
1 CCTTTTCGATAAACTGGGGCATAAGC
* *
28790 CCTTTTCGGTAAACTAGGGCATAAGC
1 CCTTTTCGATAAACTGGGGCATAAGC
*
28816 CCTTTGCGATAAACTGGGGCATAAGC
1 CCTTTTCGATAAACTGGGGCATAAGC
28842 CCTTTT
1 CCTTTT
28848 GCACTTCCTC
Statistics
Matches: 140, Mismatches: 20, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
25 21 0.15
26 119 0.85
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (26 bp):
CCTTTTCGATAAACTGGGGCATAAGC
Found at i:28723 original size:52 final size:52
Alignment explanation
Indices: 28661--28847 Score: 313
Period size: 52 Copynumber: 3.6 Consensus size: 52
28651 TATCTAGAGG
*
28661 CCTTTTCAATAAACTAGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGC
1 CCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGC
*
28713 CCTTTTCAATAAACTGGGGCATAAACCCTTTTCGGTAAACTGGGGCA-AAGC
1 CCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGC
* *
28764 CGTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTAGGGCATAAGC
1 CCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGC
* *
28816 CCTTTGCGATAAACTGGGGCATAAGCCCTTTT
1 CCTTTTCAATAAACTGGGGCATAAGCCCTTTT
28848 GCACTTCCTC
Statistics
Matches: 126, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
51 48 0.38
52 78 0.62
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (52 bp):
CCTTTTCAATAAACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGC
Found at i:28922 original size:20 final size:20
Alignment explanation
Indices: 28897--29003 Score: 153
Period size: 20 Copynumber: 5.3 Consensus size: 20
28887 TTATGAATAC
28897 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
*
28917 ATCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACAT
*
28937 ATCATGCGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
* *
28957 TTCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACAT
*
28977 ATCATGTGCATATCATATCA-
1 ATCATGTGCATTTCATA-CAT
28997 ATCATGT
1 ATCATGT
29004 ATATCATATC
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
20 75 0.97
21 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAT
Found at i:28948 original size:40 final size:40
Alignment explanation
Indices: 28897--29003 Score: 171
Period size: 40 Copynumber: 2.7 Consensus size: 40
28887 TTATGAATAC
28897 ATCATGTGCATTTCATACATATCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACATATCATGTGCATTTTATACAT
* *
28937 ATCATGCGCATTTCATACATTTCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACATATCATGTGCATTTTATACAT
*
28977 ATCATGTGCATATCATATCA-ATCATGT
1 ATCATGTGCATTTCATA-CATATCATGT
29004 ATATCATATC
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 59 0.97
41 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (40 bp):
ATCATGTGCATTTCATACATATCATGTGCATTTTATACAT
Found at i:29957 original size:27 final size:27
Alignment explanation
Indices: 29805--30014 Score: 158
Period size: 27 Copynumber: 7.7 Consensus size: 27
29795 TTTCATCCTA
* * *
29805 CAAGGGTGTTTTGGTAAATCTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
** ** *
29832 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
** * *
29859 CAATAGTATGTTT-ATAATTTTTAGAAAGT
1 CAAGGGTAT-TTTGGTAA-TTTTACAAA-T
* * **
29888 CAAGGGTGTTTCT-ATAATTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTACAAAT
29915 CAAGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
29942 TAAGGGTATTTCGGTAATTTCACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
29968 CCAGTGGTATTTTGGTAATTTTACAAA-
1 CAAG-GGTATTTTGGTAATTTTACAAAT
29995 CTAAGGGTATTTTGGTAATT
1 C-AAGGGTATTTTGGTAATT
30015 CTATCCTACA
Statistics
Matches: 144, Mismatches: 32, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
26 3 0.02
27 110 0.76
28 20 0.14
29 11 0.08
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:30054 original size:27 final size:27
Alignment explanation
Indices: 29918--30054 Score: 102
Period size: 27 Copynumber: 5.1 Consensus size: 27
29908 TGTAAATCAA
* *
29918 GGGTATTTTGGTAATTTTACAAAT-TAA
1 GGGTATTTTGGTAATTTCAC-AATCTAG
* * *
29945 GGGTATTTCGGTAATTTCACAAACCAG
1 GGGTATTTTGGTAATTTCACAATCTAG
* * * *
29972 TGGTATTTTGGTAATTTTACAAACTAA
1 GGGTATTTTGGTAATTTCACAATCTAG
*
29999 GGGTATTTTGGTAA-TT--CTATCCTACAG
1 GGGTATTTTGGTAATTTCACAAT-CT--AG
* *
30026 GGGTATTTTAGTAATTTCACAATCGAG
1 GGGTATTTTGGTAATTTCACAATCTAG
30053 GG
1 GG
30055 TAAAACGATA
Statistics
Matches: 86, Mismatches: 17, Indels: 14
0.74 0.15 0.12
Matches are distributed among these distances:
24 2 0.02
25 2 0.02
26 4 0.05
27 72 0.84
28 2 0.02
29 1 0.01
30 3 0.03
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTCACAATCTAG
Found at i:30076 original size:27 final size:27
Alignment explanation
Indices: 30046--30189 Score: 164
Period size: 27 Copynumber: 5.3 Consensus size: 27
30036 GTAATTTCAC
*
30046 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGATAATTCTGTA
* * *
30073 AATCGAGGGTAAAATGGTAATTCTTTA
1 AATCGAGGGTAAAACGATAATTCTGTA
* *
30100 AATCGAGGATAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGATAATTCTGTA
* *
30127 AATCGAGGGTGAAAC-AGTAATTCTATA
1 AATCGAGGGTAAAACGA-TAATTCTGTA
* * **
30154 AATCGAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAACGATAATTCTGTA
30181 AATCGAGGG
1 AATCGAGGG
30190 CATTTCAGTA
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
27 100 1.00
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGATAATTCTGTA
Found at i:30121 original size:54 final size:54
Alignment explanation
Indices: 30046--30189 Score: 198
Period size: 54 Copynumber: 2.7 Consensus size: 54
30036 GTAATTTCAC
* * ** *
30046 AATCGAGGGTAAAACGATAATTTTGTAAATCGAGGGTAAAATGGTAATTCTTTA
1 AATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATA
* *
30100 AATCGAGGATAAAACGGTAATTCTGTAAATCGAGGGTGAAACAGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATA
* **
30154 AATCGAGGGTAAAATGGTAATTCTACAAATCGAGGG
1 AATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGG
30190 CATTTCAGTA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 79 1.00
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.27
Consensus pattern (54 bp):
AATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTATA
Found at i:32473 original size:31 final size:31
Alignment explanation
Indices: 32437--32608 Score: 290
Period size: 31 Copynumber: 5.5 Consensus size: 31
32427 TTTAACGGTT
32437 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
32468 ACTGGGTCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
32499 ACTGGGCCGAAGCCTTTTCATAAATCATTTC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* * *
32530 ACTAGGTCGAAGACTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
32561 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
32592 ATTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
32609 ATTGTAAATG
Statistics
Matches: 130, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 130 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:32897 original size:26 final size:26
Alignment explanation
Indices: 32826--33051 Score: 278
Period size: 26 Copynumber: 8.8 Consensus size: 26
32816 CCTCTTTAAT
* *
32826 AACTGGGGCA-AAGCCCTTTTTAGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
32851 AACTGGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
* **
32876 AACTAGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
32902 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
* *
32928 AACTGGGGCATAAACCCTTTTCGATA
1 AACTGGGGCATAAGCCCTTTTCAATA
* *
32954 AACTGGGGTA-AAGCCGTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
** **
32979 AACTGGGGCATATTCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
** *
33005 AACTAAGGCATAAGCCCTTTTCGATA
1 AACTGGGGCATAAGCCCTTTTCAATA
*
33031 AACTGGGGCATATGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
33052 GCACTTCCTC
Statistics
Matches: 171, Mismatches: 28, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
25 53 0.31
26 118 0.69
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAATA
Found at i:32930 original size:77 final size:78
Alignment explanation
Indices: 32826--33051 Score: 296
Period size: 77 Copynumber: 2.9 Consensus size: 78
32816 CCTCTTTAAT
* * *
32826 AACTGGGGCA-AAGCCCTTTTTAGTAAACTGGGGCA-AAGCCCTTTTCAATAAACTAGGGCATAA
1 AACTGGGGCATAAGCCCTTTTCAGTAAACTGGGGCATAAGCCCTTTTCGATAAACTGGGGCATAA
**
32889 GCCCTTTTCGGTA
66 GCCCTTTTCAATA
* * *
32902 AACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAACCCTTTTCGATAAACTGGGGTA-AA
1 AACTGGGGCATAAGCCCTTTTCAGTAAACTGGGGCATAAGCCCTTTTCGATAAACTGGGGCATAA
*
32966 GCCGTTTTCAATA
66 GCCCTTTTCAATA
** * ** *
32979 AACTGGGGCATATTCCCTTTTCGGTAAACTAAGGCATAAGCCCTTTTCGATAAACTGGGGCATAT
1 AACTGGGGCATAAGCCCTTTTCAGTAAACTGGGGCATAAGCCCTTTTCGATAAACTGGGGCATAA
33044 GCCCTTTT
66 GCCCTTTT
33052 GCACTTCCTC
Statistics
Matches: 128, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
76 10 0.08
77 89 0.70
78 29 0.23
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.28
Consensus pattern (78 bp):
AACTGGGGCATAAGCCCTTTTCAGTAAACTGGGGCATAAGCCCTTTTCGATAAACTGGGGCATAA
GCCCTTTTCAATA
Found at i:32967 original size:103 final size:103
Alignment explanation
Indices: 32826--33052 Score: 332
Period size: 103 Copynumber: 2.2 Consensus size: 103
32816 CCTCTTTAAT
*
32826 AACTGGGGCA-AAGCCCTTTTTAGTAAACTGGGGCAAAGCCCTTTTCAATAAACTAGGGCATAAG
1 AACTGGGGCATAAGCCCTTTTGAGTAAACTGGGGCAAAGCCCTTTTCAATAAACTAGGGCATAAG
**
32890 CCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
66 CCCTTTTCGGTAAACTAAGGCATAAGCCCTTTTCAATA
* * * * *
32928 AACTGGGGCATAAACCCTTTTCGA-TAAACTGGGGTAAAGCCGTTTTCAATAAACTGGGGCATAT
1 AACTGGGGCATAAGCCCTTTT-GAGTAAACTGGGGCAAAGCCCTTTTCAATAAACTAGGGCATAA
* *
32992 TCCCTTTTCGGTAAACTAAGGCATAAGCCCTTTTCGATA
65 GCCCTTTTCGGTAAACTAAGGCATAAGCCCTTTTCAATA
*
33031 AACTGGGGCATATGCCCTTTTG
1 AACTGGGGCATAAGCCCTTTTG
33053 CACTTCCTCC
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
102 11 0.10
103 99 0.89
104 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (103 bp):
AACTGGGGCATAAGCCCTTTTGAGTAAACTGGGGCAAAGCCCTTTTCAATAAACTAGGGCATAAG
CCCTTTTCGGTAAACTAAGGCATAAGCCCTTTTCAATA
Found at i:33130 original size:20 final size:20
Alignment explanation
Indices: 33101--33208 Score: 155
Period size: 20 Copynumber: 5.4 Consensus size: 20
33091 TTATGAATAC
33101 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
* *
33121 ATCGTGTGCATTTTATACAT
1 ATCATGTGCATTTCATACAT
33141 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
* *
33161 TTCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACAT
*
33181 ATCATGTGCATATCATATCA-
1 ATCATGTGCATTTCATA-CAT
33201 ATCATGTG
1 ATCATGTG
33209 TATCATATCC
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
20 76 0.97
21 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.42
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAT
Found at i:33147 original size:40 final size:40
Alignment explanation
Indices: 33101--33208 Score: 173
Period size: 40 Copynumber: 2.7 Consensus size: 40
33091 TTATGAATAC
*
33101 ATCATGTGCATTTCATACATATCGTGTGCATTTTATACAT
1 ATCATGTGCATTTCATACATATCATGTGCATTTTATACAT
*
33141 ATCATGTGCATTTCATACATTTCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACATATCATGTGCATTTTATACAT
*
33181 ATCATGTGCATATCATATCA-ATCATGTG
1 ATCATGTGCATTTCATA-CATATCATGTG
33209 TATCATATCC
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 61 0.97
41 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.42
Consensus pattern (40 bp):
ATCATGTGCATTTCATACATATCATGTGCATTTTATACAT
Found at i:33214 original size:18 final size:19
Alignment explanation
Indices: 33181--33217 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
33171 TTTTATACAT
33181 ATCATGTGCATATCATATCA
1 ATCATGTG-ATATCATATCA
33201 ATCATGTG-TATCATATC
1 ATCATGTGATATCATATC
33218 CCACGTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (19 bp):
ATCATGTGATATCATATCA
Found at i:34790 original size:46 final size:46
Alignment explanation
Indices: 34740--34915 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
34730 TGGTTGAGCA
*
34740 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * *
34786 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* *
34831 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * *
34879 -CCGGAGCTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
34916 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
43 6 0.06
45 6 0.06
46 58 0.54
47 29 0.27
48 4 0.04
50 5 0.05
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:34896 original size:93 final size:93
Alignment explanation
Indices: 34737--34908 Score: 283
Period size: 93 Copynumber: 1.8 Consensus size: 93
34727 GGATGGTTGA
* *
34737 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGTCCGAACTCGTTGAGT
34802 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
34830 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAATG-CCGGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGTCC-GAACTCGTTGAG
*
34894 TTGAGTCTGAGTTCG
65 TTGAGTCCGAGTTCG
34909 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 71 0.97
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41930 original size:27 final size:27
Alignment explanation
Indices: 41900--41964 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
41890 GGGCATATTC
41900 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACG
* * * *
41927 GTCACTTTACCCTATAGGGGCTTTACG
1 GTCATTTTACCATACAAGGGCTTTACG
*
41954 GTCTTTTTACC
1 GTCATTTTACC
41965 TATTAGGGGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
27 30 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACG
Found at i:41966 original size:26 final size:28
Alignment explanation
Indices: 41922--41973 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
41912 TACAAGGGTA
41922 TTACGGTCACTTTACCCTA-TAGGGGCT
1 TTACGGTCACTTTACCCTATTAGGGGCT
**
41949 TTACGGTCTTTTTA-CCTATTAGGGG
1 TTACGGTCACTTTACCCTATTAGGGG
41974 TATTTTAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.38
Consensus pattern (28 bp):
TTACGGTCACTTTACCCTATTAGGGGCT
Found at i:42114 original size:56 final size:54
Alignment explanation
Indices: 42015--42196 Score: 159
Period size: 54 Copynumber: 3.3 Consensus size: 54
42005 TTGGTAAATC
* * *
42015 TACAAATTAAGGGTATTTCAATAATTTTGTAAACCAATAGTATTTTTATAATTTT
1 TACAAATTAAGGGTATTTCAGTAATTTTGTAAACCAAGAGTATTTTGATAA-TTT
* * * * * *
42070 TAGAAAGTTAAGGGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTT
1 TACAAA-TTAAGGGTATTTCAGTAATTTTGTAAACCAAGAGTATTTTGATAATTT
** * *** * *
42125 TACAAATTGGGGGTATTTCGGTAATTTCACAAACC-AGTGGTATTTTGGTAATTT
1 TACAAATTAAGGGTATTTCAGTAATTTTGTAAACCAAG-AGTATTTTGATAATTT
* *
42179 TACAAACTAGGGGTATTT
1 TACAAATTAAGGGTATTT
42197 TGGTAATTCT
Statistics
Matches: 105, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
53 1 0.01
54 54 0.51
55 13 0.12
56 37 0.35
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.42
Consensus pattern (54 bp):
TACAAATTAAGGGTATTTCAGTAATTTTGTAAACCAAGAGTATTTTGATAATTT
Found at i:42121 original size:27 final size:27
Alignment explanation
Indices: 42081--42237 Score: 149
Period size: 27 Copynumber: 5.8 Consensus size: 27
42071 AGAAAGTTAA
**
42081 GGGTATTTCT-GTAATTTTGTAAATCAG
1 GGGTATTT-TGGTAATTTTACAAATCAG
**
42108 GGGTATTTTGGTAATTTTACAAATTGG
1 GGGTATTTTGGTAATTTTACAAATCAG
* * *
42135 GGGTATTTCGGTAATTTCACAAACCAG
1 GGGTATTTTGGTAATTTTACAAATCAG
*
42162 TGGTATTTTGGTAATTTTACAAA-CTAG
1 GGGTATTTTGGTAATTTTACAAATC-AG
* **
42189 GGGTATTTTGGTAATTCTATCCTAT-AG
1 GGGTATTTTGGTAATTTTA-CAAATCAG
* *
42216 GGGTATTTTAGTAATTTCACAA
1 GGGTATTTTGGTAATTTTACAA
42238 TCGAGGGTAA
Statistics
Matches: 105, Mismatches: 21, Indels: 9
0.78 0.16 0.07
Matches are distributed among these distances:
26 3 0.03
27 100 0.95
28 2 0.02
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAATCAG
Found at i:42232 original size:54 final size:54
Alignment explanation
Indices: 42081--42204 Score: 167
Period size: 54 Copynumber: 2.3 Consensus size: 54
42071 AGAAAGTTAA
* *** * * *
42081 GGGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTGG
1 GGGTATTTCGGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACTAG
*
42135 GGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTCGGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACTAG
*
42189 GGGTATTTTGGTAATT
1 GGGTATTTCGGTAATT
42205 CTATCCTATA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (54 bp):
GGGTATTTCGGTAATTTCACAAACCAGGGGTATTTTGGTAATTTTACAAACTAG
Found at i:42266 original size:27 final size:27
Alignment explanation
Indices: 42236--42381 Score: 186
Period size: 27 Copynumber: 5.4 Consensus size: 27
42226 GTAATTTCAC
* * *
42236 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAATGATAATTCTATA
42263 AATCGAGGGTAAAATTG-TAATTCTATA
1 AATCGAGGGTAAAA-TGATAATTCTATA
* *
42290 AATCGAGGGTAAAATGGTAATTCTGTA
1 AATCGAGGGTAAAATGATAATTCTATA
* *
42317 AATCGAGGGTGAAACGATAATTCTATA
1 AATCGAGGGTAAAATGATAATTCTATA
* * *
42344 AATCGAGGGTAAAATGGTAATTTTACA
1 AATCGAGGGTAAAATGATAATTCTATA
42371 AATCGAGGGTA
1 AATCGAGGGTA
42382 TTTCAGTAAT
Statistics
Matches: 104, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
26 2 0.02
27 101 0.97
28 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (27 bp):
AATCGAGGGTAAAATGATAATTCTATA
Found at i:42311 original size:54 final size:54
Alignment explanation
Indices: 42236--42381 Score: 213
Period size: 54 Copynumber: 2.7 Consensus size: 54
42226 GTAATTTCAC
* * *
42236 AATCGAGGGTAAAACGATAATTTTGTAAATCGAGGGTAAAATTG-TAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAA-CGATAATTCTATA
* *
42290 AATCGAGGGTAAAATGGTAATTCTGTAAATCGAGGGTGAAACGATAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTATA
**
42344 AATCGAGGGTAAAATGGTAATTTTACAAATCGAGGGTA
1 AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTA
42382 TTTCAGTAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
53 1 0.01
54 81 0.99
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (54 bp):
AATCGAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAACGATAATTCTATA
Found at i:53536 original size:21 final size:20
Alignment explanation
Indices: 53504--53545 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
53494 GCCGTTTAGC
*
53504 CATGTACAATAATACACGGG
1 CATGTACAATAACACACGGG
*
53524 CATGCTACCATAACACACGGG
1 CATG-TACAATAACACACGGG
53545 C
1 C
53546 GTGGGAGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.36, C:0.29, G:0.19, T:0.17
Consensus pattern (20 bp):
CATGTACAATAACACACGGG
Found at i:60567 original size:49 final size:49
Alignment explanation
Indices: 60514--61016 Score: 765
Period size: 49 Copynumber: 10.4 Consensus size: 49
60504 TTGTGACGTG
* *
60514 AGTGTATATATATGTGATAAGGCCTAATGGCTGATGTGATGAATTTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
60563 AGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
60610 AGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
60659 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGGGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
60708 AGTGTATATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTG--TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
60759 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
60808 AGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
60855 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
60904 AGTG--TATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
60951 AGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
60998 AGTGTATA-A-ATGTGATAAG
1 AGTGTATATATATGTGATAAG
61017 TCCCGAAGGG
Statistics
Matches: 423, Mismatches: 23, Indels: 18
0.91 0.05 0.04
Matches are distributed among these distances:
47 181 0.43
48 1 0.00
49 193 0.46
51 48 0.11
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (49 bp):
AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:60639 original size:96 final size:97
Alignment explanation
Indices: 60514--61016 Score: 752
Period size: 96 Copynumber: 5.2 Consensus size: 97
60504 TTGTGACGTG
* *
60514 AGTGTATATATATGTGATAAGGCCTAATGGCTGATGTGATGAATTTGAAAGTG-TATATATGTGA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGA
* *
60578 TAAGGCCGAATGGCCAATGTGATGAATGTGAA
66 TAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
60610 AGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTG
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTG
*
60675 ATAAGGCCTAATGGCCGATGGGATGAATGTGAA
65 ATAAGGCCTAATGGCCGATGTGATGAATGTGAA
60708 AGTGTATATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG
1 AGTG--TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATG
60773 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
63 TGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
60808 AGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTG
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATATGTG
60871 ATAAGGCCTAATGGCCGATGTGATGAATGTGAA
65 ATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
60904 AGTG--TATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATATGTGA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGA
* * * * * * *
60966 CAGGGCCGAGTGGCCAACGTGATGGATGTGAA
66 TAAGGCCTAATGGCCGATGTGATGAATGTGAA
60998 AGTGTATA-A-ATGTGATAAG
1 AGTGTATATATATGTGATAAG
61017 TCCCGAAGGG
Statistics
Matches: 378, Mismatches: 23, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
94 49 0.13
95 1 0.00
96 189 0.50
98 44 0.12
100 95 0.25
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (97 bp):
AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGTGA
TAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:63305 original size:40 final size:40
Alignment explanation
Indices: 63240--63466 Score: 298
Period size: 40 Copynumber: 5.7 Consensus size: 40
63230 AGGTCTCGAC
* *
63240 GATG-ATCCGGGCTAAGTCCCAAAGAGCATTCATGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
63279 GATGTACCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
*
63319 GATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * *
63359 GATGTATCCGGGCTAAGTTCCAAAGAGCATTTGTGCTAGT
1 GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
* * * * *
63399 AATATATCCGTGCTAA-ACCTCGAAGAGCATTCGTGCTGGT
1 GATGTATCCGGGCTAAGTCC-CGAAGAGCATTCGTGCTAGT
* *
63439 GTTATATCCGGGCT-AGTCCCGAAGAGCA
1 GATGTATCCGGGCTAAGTCCCGAAGAGCA
63467 ATCATGCTGG
Statistics
Matches: 164, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
39 15 0.09
40 149 0.91
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
GATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGT
Found at i:63741 original size:58 final size:57
Alignment explanation
Indices: 63672--63780 Score: 155
Period size: 57 Copynumber: 1.9 Consensus size: 57
63662 CGAATGATTA
* * *
63672 GAGGCACTGTGTGTGCAAATTCTTTTATCCGAGCACTATGTGTGCGAAATCGGTAATT
1 GAGGCACTGTGTGTGCAAATTC-TTCAACCAAGCACTATGTGTGCGAAATCGGTAATT
* * *
63730 GAGGCACTGTGTGTGCGAGTTCTTCAACCAAGCACTATGTGTGCGAGATCG
1 GAGGCACTGTGTGTGCAAATTCTTCAACCAAGCACTATGTGTGCGAAATCG
63781 ATCAGTGGGC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
57 25 0.56
58 20 0.44
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.29
Consensus pattern (57 bp):
GAGGCACTGTGTGTGCAAATTCTTCAACCAAGCACTATGTGTGCGAAATCGGTAATT
Found at i:67297 original size:49 final size:49
Alignment explanation
Indices: 67244--67793 Score: 836
Period size: 47 Copynumber: 11.4 Consensus size: 49
67234 TTGTGATGTG
67244 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
67293 AGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * *
67340 AGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATTTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
67389 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGGGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
67438 AGTGTATATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTG--TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
67489 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
67538 AGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
67585 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
67634 AGTG--TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
67681 AGTG--TATATATGTGATGAGGCCTAATGGCCGATGTGATGGATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
67728 AGTG--TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
67775 AGTGTATA-A-ATGTGATAAG
1 AGTGTATATATATGTGATAAG
67794 TCCCGAAGGG
Statistics
Matches: 468, Mismatches: 25, Indels: 18
0.92 0.05 0.04
Matches are distributed among these distances:
47 228 0.49
48 1 0.00
49 191 0.41
51 48 0.10
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (49 bp):
AGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Found at i:67369 original size:96 final size:95
Alignment explanation
Indices: 67250--67793 Score: 815
Period size: 96 Copynumber: 5.7 Consensus size: 95
67240 TGTGAGTGTA
* *
67250 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGC
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGATATATATGTGATAAGGC
* *
67314 CGAATGGCCAATGTGATGAATGTGAAAGTG
66 CTAATGGCCGATGTGATGAATGTGAAAGTG
*
67344 TATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATTTGAAAGTGTATATATATGTGATAA
1 --TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG-ATATATATGTGATAA
*
67409 GGCCTAATGGCCGATGGGATGAATGTGAAAGTG
63 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* *
67442 TATATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAT
1 ----TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG-ATATATATGTGAT
67507 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
61 AAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
67542 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGG
67607 CCTAATGGCCGATGTGATGAATGTGAAAGTG
65 CCTAATGGCCGATGTGATGAATGTGAAAGTG
* * * *
67638 TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG-TATATATGTGATGAGGC
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGATATATATGTGATAAGGC
*
67702 CTAATGGCCGATGTGATGGATGTGAAAGTG
66 CTAATGGCCGATGTGATGAATGTGAAAGTG
* * * * * *
67732 TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTG-TATAAATGTGATAAG
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGATATATATGTGATAAG
67794 TCCCGAAGGG
Statistics
Matches: 417, Mismatches: 27, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
94 97 0.23
96 182 0.44
98 44 0.11
100 94 0.23
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (95 bp):
TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGATATATATGTGATAAGGC
CTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:79087 original size:9 final size:9
Alignment explanation
Indices: 79073--79101 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
79063 CCAAATAAAC
79073 TTCAAAAGG
1 TTCAAAAGG
79082 TTCAAAAGG
1 TTCAAAAGG
79091 TTCAAAAGG
1 TTCAAAAGG
79100 TT
1 TT
79102 GAGGCTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (9 bp):
TTCAAAAGG
Found at i:80628 original size:14 final size:16
Alignment explanation
Indices: 80600--80633 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
80590 TGAAAATCGT
80600 AAAAACAAAATTAAAG
1 AAAAACAAAATTAAAG
80616 AAAAAC-AAA-TAAAG
1 AAAAACAAAATTAAAG
80630 AAAA
1 AAAA
80634 TAAAGGCAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 3 0.17
16 6 0.33
ACGTcount: A:0.79, C:0.06, G:0.06, T:0.09
Consensus pattern (16 bp):
AAAAACAAAATTAAAG
Found at i:84345 original size:40 final size:40
Alignment explanation
Indices: 84290--84428 Score: 228
Period size: 40 Copynumber: 3.5 Consensus size: 40
84280 TATTCGAATG
84290 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
84330 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
84370 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
84410 ATATCC-GGCTAAATCCCGA
1 ATATCCGGGCTAAGTCCCGA
84429 TGGTACTTGG
Statistics
Matches: 94, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
39 11 0.12
40 81 0.86
41 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Done.