Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1118
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: 48467
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:3388 original size:40 final size:40
Alignment explanation
Indices: 3351--3575 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
3341 GCTACTCGTT
* *
3351 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
3391 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
3431 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
3471 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
3510 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
3551 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
3576 CATCATTCGA
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
38 2 0.01
39 32 0.19
40 118 0.72
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:3535 original size:119 final size:120
Alignment explanation
Indices: 3353--3575 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
3343 TACTCGTTCA
*
3353 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
3418 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
3473 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
3535 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
3576 CATCATTCGA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 4 0.04
119 66 0.73
120 20 0.22
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:4769 original size:56 final size:56
Alignment explanation
Indices: 4702--4821 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
4692 TATTAGTTTA
4702 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
4758 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
4814 TTGCCCAT
1 TTGCCCAT
4822 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:11394 original size:39 final size:40
Alignment explanation
Indices: 11288--11511 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
11278 GCTACTCGTT
*
11288 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
11328 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
11368 CAAATGCCTTC-GGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
11407 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
11446 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
11487 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
11512 CATCATTCGA
Statistics
Matches: 163, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
38 2 0.01
39 70 0.43
40 78 0.48
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:11400 original size:79 final size:79
Alignment explanation
Indices: 11288--11511 Score: 292
Period size: 79 Copynumber: 2.8 Consensus size: 79
11278 GCTACTCGTT
* *
11288 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTC-GGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
11352 GATTTAGTAACTCGCA
64 GAATTAGTAACTCGCA
* *
11368 CAAATGCCTTCGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
11432 ATTAGTATCTCGCA
66 ATTAGTAACTCGCA
* * * * *
11446 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
11510 GA
64 GA
11512 CATCATTCGA
Statistics
Matches: 127, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
78 36 0.28
79 60 0.47
80 31 0.24
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:12707 original size:56 final size:56
Alignment explanation
Indices: 12645--12754 Score: 211
Period size: 56 Copynumber: 2.0 Consensus size: 56
12635 TTATTGCCCA
12645 TGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTTTTGCCTG
1 TGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTTTTGCCTG
*
12701 TGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTTTTGCC
1 TGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTTTTGCC
12755 CATCATCCCT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.22, C:0.21, G:0.10, T:0.47
Consensus pattern (56 bp):
TGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTTTTGCCTG
Found at i:15292 original size:37 final size:37
Alignment explanation
Indices: 15233--15365 Score: 158
Period size: 37 Copynumber: 3.6 Consensus size: 37
15223 CTTAGTGACA
* * *
15233 TGGCATGTTATCAGCTGGATTAGCTCTTGTGAGCATT
1 TGGCATGTTATCGGTTGGATTAGCTCTTATGAGCATT
* *
15270 TGGCATGTTATCGGTTGAATTAGATCTTATGAGCATT
1 TGGCATGTTATCGGTTGGATTAGCTCTTATGAGCATT
* * *
15307 TGGCGTGTTATCGATTGGATTAACTCTTATGAGCATT
1 TGGCATGTTATCGGTTGGATTAGCTCTTATGAGCATT
* * * *
15344 TTGTATGTTTTCAGTTGGATTA
1 TGGCATGTTATCGGTTGGATTA
15366 CTTATGTACT
Statistics
Matches: 80, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 80 1.00
ACGTcount: A:0.21, C:0.12, G:0.25, T:0.42
Consensus pattern (37 bp):
TGGCATGTTATCGGTTGGATTAGCTCTTATGAGCATT
Found at i:17121 original size:68 final size:69
Alignment explanation
Indices: 17049--17200 Score: 179
Period size: 67 Copynumber: 2.2 Consensus size: 69
17039 CATCATGTGT
* * *
17049 ACAAGAGAGCTACGAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTACGAGACA-TAT-ATGTAGCTAGGTCGCATGGGTGGATACAAGTGAAGGACACC
17111 ATGTAG
64 ATGTAG
* * * *
17117 ACAAGAGAGCTACG-G-GATATATGTAGCTAGGTCGCATGTGTGGTTCCAAGTGAAGGACACCAT
1 ACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCATGGGTGGATACAAGTGAAGGACACCAT
17180 GTAG
66 GTAG
*
17184 ACAAGAGAACTACGAGA
1 ACAAGAGAGCTACGAGA
17201 TAAACTGGCT
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
64 20 0.28
65 7 0.10
66 3 0.04
67 26 0.37
68 15 0.21
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (69 bp):
ACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCATGGGTGGATACAAGTGAAGGACACCAT
GTAG
Found at i:20772 original size:16 final size:16
Alignment explanation
Indices: 20747--20777 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20737 TTCCAACAGC
20747 AAAAAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
*
20763 AAAAAGAAAGAAAAA
1 AAAAAAAAAGAAAAA
20778 CAATTTATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:20937 original size:15 final size:15
Alignment explanation
Indices: 20917--20945 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20907 TTTAACCCTT
20917 TTAATTAAATTTATG
1 TTAATTAAATTTATG
20932 TTAATTAAATTTAT
1 TTAATTAAATTTAT
20946 AAAGGTTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTAATTAAATTTATG
Found at i:21491 original size:43 final size:43
Alignment explanation
Indices: 21431--21637 Score: 351
Period size: 43 Copynumber: 4.8 Consensus size: 43
21421 TTTATTGGAA
* *
21431 AAAAACGCCGCTAAAGGTTAAGGCTTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
*
21474 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTTTGGG
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
*
21517 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGT
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
* *
21560 AAAAGCGCCGCTATAGGTCAAGGCTTTTAGCGGCGTTTGTGGA
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
*
21603 AAAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCG
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCG
21638 CTTTTTTTAC
Statistics
Matches: 155, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 155 1.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
Found at i:21655 original size:43 final size:42
Alignment explanation
Indices: 21417--21660 Score: 319
Period size: 43 Copynumber: 5.6 Consensus size: 42
21407 AAAATTTTGT
* *
21417 GGCGTTTATTGGAAAAAAACGCCGCTAAAGGTTAAGGCTTTTAGC
1 GGCGTTT-TTGG--AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGC
*
21462 GGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAAGGCTTTTAGC
1 GGCGTTT-TTGGAAAAGCGCCGCTAAAGGTCAAGGCTTTTAGC
21505 GGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCAAGGCTTTTAGC
1 GGCGTTTTT-GGAAAAGCGCCGCTAAAGGTCAAGGCTTTTAGC
* *
21548 GGCGTTTGTGGTAAAAGCGCCGCTATAGGTCAAGGCTTTTAGC
1 GGCGTTTTTGG-AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGC
* *
21591 GGCGTTTGTGGAAAAAGCGCCGCTAAACGTCAAGGCTTTTAGC
1 GGCGTTTTTGG-AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGC
**
21634 GGCGCTTTTTTTACAAA-CGCCGCTAAA
1 GGCG-TTTTTGGA-AAAGCGCCGCTAAA
21661 TTTTGCAGAT
Statistics
Matches: 182, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
42 3 0.02
43 162 0.89
44 7 0.04
45 10 0.05
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (42 bp):
GGCGTTTTTGGAAAAGCGCCGCTAAAGGTCAAGGCTTTTAGC
Found at i:21746 original size:31 final size:31
Alignment explanation
Indices: 21711--21791 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
21701 CTTCCTGCAT
* *
21711 TAAAATCCAACCAAATACAACAAATATAATA
1 TAAAATCCAACCAAAAACAACAAATATAACA
* * *
21742 TAAAATGCAGCCAAAAACAACAAATTTAACA
1 TAAAATCCAACCAAAAACAACAAATATAACA
*
21773 TAAAAAATACAACCAAAAA
1 T--AAAATCCAACCAAAAA
21792 TATTAATTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 27 0.66
33 14 0.34
ACGTcount: A:0.63, C:0.19, G:0.02, T:0.16
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAACA
Found at i:27727 original size:9 final size:9
Alignment explanation
Indices: 27713--27936 Score: 143
Period size: 9 Copynumber: 24.6 Consensus size: 9
27703 TATTTAAGTA
27713 TTATGTAAG
1 TTATGTAAG
*
27722 TTATGTAAT
1 TTATGTAAG
*
27731 TTATGATATG
1 TTATG-TAAG
* * *
27741 ATATAT-AT
1 TTATGTAAG
*
27749 TTATGTAAA
1 TTATGTAAG
* *
27758 TTATAT-AT
1 TTATGTAAG
*
27766 TTATCTAAG
1 TTATGTAAG
*
27775 TTATATAAG
1 TTATGTAAG
27784 TTATGTAAG
1 TTATGTAAG
*
27793 TTATGTAAA
1 TTATGTAAG
*
27802 TTATGATATAAAA
1 TTATG---T-AAG
*
27815 TATATTTAAG
1 T-TATGTAAG
27825 TATTATGTAAG
1 --TTATGTAAG
27836 TTATGTAAG
1 TTATGTAAG
*
27845 TTAT-T-AT
1 TTATGTAAG
*
27852 TTATCTAAG
1 TTATGTAAG
*
27861 TTATATAAG
1 TTATGTAAG
*
27870 TTATATAAG
1 TTATGTAAG
27879 TTATGT-AG
1 TTATGTAAG
*
27887 TTATATAAG
1 TTATGTAAG
27896 TTATGTAAG
1 TTATGTAAG
* *
27905 TTATATATG
1 TTATGTAAG
*
27914 TTATATAAG
1 TTATGTAAG
*
27923 TTATGTAAA
1 TTATGTAAG
27932 TTATG
1 TTATG
27937 ATATCAAATA
Statistics
Matches: 171, Mismatches: 31, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
7 5 0.03
8 19 0.11
9 123 0.72
10 7 0.04
11 8 0.05
12 2 0.01
13 4 0.02
14 3 0.02
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:27792 original size:18 final size:18
Alignment explanation
Indices: 27713--27936 Score: 161
Period size: 18 Copynumber: 12.3 Consensus size: 18
27703 TATTTAAGTA
* *
27713 TTATGTAAGTTATGTAAT
1 TTATGTAAGTTATATAAG
* * *
27731 TTATGATATGATATAT-AT
1 TTATG-TAAGTTATATAAG
* *
27749 TTATGTAAATTATAT-AT
1 TTATGTAAGTTATATAAG
*
27766 TTATCTAAGTTATATAAG
1 TTATGTAAGTTATATAAG
* *
27784 TTATGTAAGTTATGTAAA
1 TTATGTAAGTTATATAAG
* *
27802 TTATGATATAAAATATATTTAAG
1 TTATG---T-AAGT-TATATAAG
*
27825 TATTATGTAAGTTATGTAAG
1 --TTATGTAAGTTATATAAG
* *
27845 TTAT-T-ATTTATCTAAG
1 TTATGTAAGTTATATAAG
*
27861 TTATATAAGTTATATAAG
1 TTATGTAAGTTATATAAG
27879 TTATGT-AGTTATATAAG
1 TTATGTAAGTTATATAAG
*
27896 TTATGTAAGTTATATATG
1 TTATGTAAGTTATATAAG
* * *
27914 TTATATAAGTTATGTAAA
1 TTATGTAAGTTATATAAG
27932 TTATG
1 TTATG
27937 ATATCAAATA
Statistics
Matches: 166, Mismatches: 28, Indels: 24
0.76 0.13 0.11
Matches are distributed among these distances:
16 13 0.08
17 41 0.25
18 79 0.48
19 7 0.04
20 7 0.04
21 4 0.02
22 4 0.02
23 6 0.04
25 5 0.03
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.48
Consensus pattern (18 bp):
TTATGTAAGTTATATAAG
Found at i:27823 original size:114 final size:112
Alignment explanation
Indices: 27689--27908 Score: 307
Period size: 114 Copynumber: 1.9 Consensus size: 112
27679 ACTAGTTATG
* * * * *
27689 TATGATATGATATATATTTAAGTATTATGTAAGTTATGTAATTTATGATATGATATATATTTATG
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGAT-TGATATA-AGTTATA
*
27754 TAAATTATAT-ATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
64 TAAATTATATAAGTTATCT-AGTTATATAAGTTATGTAAGTTATGTAAAT
* * *
27803 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATTATTTATCTAAGTTATATA
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATTGATATAAGTTATATA
* *
27868 AGTTATATAAGTTATGTAGTTATATAAGTTATGTAAGTTAT
66 AATTATATAAGTTATCTAGTTATATAAGTTATGTAAGTTAT
27909 ATATGTTATA
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
112 38 0.40
113 11 0.12
114 45 0.48
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.48
Consensus pattern (112 bp):
TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATTGATATAAGTTATATA
AATTATATAAGTTATCTAGTTATATAAGTTATGTAAGTTATGTAAAT
Found at i:27839 original size:43 final size:43
Alignment explanation
Indices: 27784--27967 Score: 121
Period size: 43 Copynumber: 4.3 Consensus size: 43
27774 GTTATATAAG
27784 TTATGTAAGTTATGTAAATTATGATATAAAATATATTTAAGTA
1 TTATGTAAGTTATGTAAATTATGATATAAAATATATTTAAGTA
* * * * *
27827 TTATGTAAGTTATGTAAGTTATTATTTATCTAAGT-TATATAAG--
1 TTATGTAAGTTATGTAAATTATGA--TAT-AAAATATATTTAAGTA
* * ** * *
27870 TTATATAAGTTATGT-AGTTAT-ATA-AGTTATGTAAGTTATATA-TG
1 TTATGTAAGTTATGTAAATTATGATATA-AAATAT-A-TT-TA-AGTA
* * *
27914 TTATATAAGTTATGTAAATTATGATATCAAATATATTTATGTA
1 TTATGTAAGTTATGTAAATTATGATATAAAATATATTTAAGTA
27957 TTATGTAAGTT
1 TTATGTAAGTT
27968 TTTTATTTCA
Statistics
Matches: 107, Mismatches: 19, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
38 1 0.01
39 3 0.03
40 1 0.01
41 2 0.02
42 8 0.07
43 50 0.47
44 17 0.16
45 16 0.15
46 9 0.08
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (43 bp):
TTATGTAAGTTATGTAAATTATGATATAAAATATATTTAAGTA
Found at i:28060 original size:15 final size:15
Alignment explanation
Indices: 28040--28095 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
28030 TAAGTAGCGG
28040 AATTAAATAATATTT
1 AATTAAATAATATTT
28055 AATTAAATAATATTT
1 AATTAAATAATATTT
28070 -A-TAAA-AATTATTTT
1 AATTAAATAA-TA-TTT
28084 AATTAAATAATA
1 AATTAAATAATA
28096 GACATGTCGT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.44
16 6 0.17
17 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTAAATAATATTT
Found at i:28300 original size:24 final size:24
Alignment explanation
Indices: 28272--28339 Score: 102
Period size: 24 Copynumber: 2.8 Consensus size: 24
28262 ACTTAAATGG
28272 TAAAACGGACGATAATATTTGTAA
1 TAAAACGGACGATAATATTTGTAA
*
28296 TAAAACGGA-GAATAATATTTGTGA
1 TAAAACGGACG-ATAATATTTGTAA
*
28320 TAAAACGGACGAGAATATTT
1 TAAAACGGACGATAATATTT
28340 CAATAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.03
24 38 0.95
25 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (24 bp):
TAAAACGGACGATAATATTTGTAA
Found at i:29278 original size:373 final size:372
Alignment explanation
Indices: 28427--29340 Score: 1783
Period size: 373 Copynumber: 2.5 Consensus size: 372
28417 AATTGAAACA
28427 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
1 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
28492 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
66 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
*
28557 AATAAGGTTGGAGAGAAGGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
131 AATAAGGTTGGAGAGAAAGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
28622 GAAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATAAAAAATAGTAATTTGAATAT
196 GAAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATAAAAAATAGTAATTTGAATAT
28687 AATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGGTTATA
261 AATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGGTTATA
*
28752 TAAATATTCAATAGTAAATGAGCTCGATAGAACTTTTTTCAAGTTTT
326 TAAATATTCAATAGTAAATGAGCTCGATAGAACTTTTTTCAAGTCTT
28799 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
1 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
28864 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
66 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
*
28929 AATAAGGTTGGAGAGAAAGTCAGTTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
131 AATAAGGTTGGAGAGAAAGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
28994 GAAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATAAAAAAATAGTAATTTGAATA
196 GAAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATAT-AAAAAATAGTAATTTGAATA
29059 TAATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGGTTAT
260 TAATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGGTTAT
29124 ATAAATATTCAATAGTAAATGAGCTCGATAGAACTTTTTTCAAGTCTT
325 ATAAATATTCAATAGTAAATGAGCTCGATAGAACTTTTTTCAAGTCTT
29172 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
1 TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
*
29237 CAGCTCGATATAAGGCAACCCGTTAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
66 CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
29302 AATAAGGTTGGAGAGAAAGTCAGCTATTGTTGTAATTTT
131 AATAAGGTTGGAGAGAAAGTCAGCTATTGTTGTAATTTT
29341 AATGGACAAG
Statistics
Matches: 536, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
372 237 0.44
373 299 0.56
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (372 bp):
TTTGAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTG
CAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAA
AATAAGGTTGGAGAGAAAGTCAGCTATTGTTGTAATTTTGATAAAAAGTAGTTATAACTTTTAAA
GAAATTTAAAAATATTAAATATTAAAATAAAACATTATTAATATAAAAAATAGTAATTTGAATAT
AATAATATCAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAAGGTTATA
TAAATATTCAATAGTAAATGAGCTCGATAGAACTTTTTTCAAGTCTT
Found at i:32576 original size:134 final size:133
Alignment explanation
Indices: 32406--32658 Score: 479
Period size: 134 Copynumber: 1.9 Consensus size: 133
32396 GAATTCAACA
32406 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
32471 TAAGTTGGATAGAAACATGAAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTT
66 TAAGTTGGATAGAAACATG-AAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTT
32536 TATT
130 TATT
*
32540 ATATAAAACGTGGGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
*
32605 TAAGTTGGATAGAAACATGAAAACAGACCAAAATAACATCTAAATAACCAAAAT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAAT
32659 GGAATCACCA
Statistics
Matches: 117, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
133 34 0.29
134 83 0.71
ACGTcount: A:0.51, C:0.19, G:0.10, T:0.20
Consensus pattern (133 bp):
ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
ATT
Found at i:33250 original size:19 final size:19
Alignment explanation
Indices: 33226--33286 Score: 95
Period size: 19 Copynumber: 3.2 Consensus size: 19
33216 AGGACTGGGC
33226 CTGGGCATTTCCACACGGG
1 CTGGGCATTTCCACACGGG
* *
33245 CTGGGCATTTCCACATGGC
1 CTGGGCATTTCCACACGGG
*
33264 CTGGGCATTTTCACACGGG
1 CTGGGCATTTCCACACGGG
33283 CTGG
1 CTGG
33287 CCATACGCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.15, C:0.30, G:0.31, T:0.25
Consensus pattern (19 bp):
CTGGGCATTTCCACACGGG
Found at i:34467 original size:35 final size:35
Alignment explanation
Indices: 34428--34573 Score: 222
Period size: 35 Copynumber: 4.2 Consensus size: 35
34418 GTTAGACTAA
*
34428 CTCTTATTAGCATTGGTGTGTTTTGGAGGGATTAG
1 CTCTTATAAGCATTGGTGTGTTTTGGAGGGATTAG
34463 CTCTTATAAGCATTGGTGTGTTTTGGAGGGATTAG
1 CTCTTATAAGCATTGGTGTGTTTTGGAGGGATTAG
* *
34498 CTCTTATTAGCATTGGTGTGTTTTAGAGGGATTAG
1 CTCTTATAAGCATTGGTGTGTTTTGGAGGGATTAG
* * *
34533 CTCTTATAAGAATTGGTGTGTTTCGG-GTGGATTGG
1 CTCTTATAAGCATTGGTGTGTTTTGGAG-GGATTAG
34568 CTCTTA
1 CTCTTA
34574 CGTGCATCTA
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
34 1 0.01
35 101 0.99
ACGTcount: A:0.18, C:0.10, G:0.30, T:0.42
Consensus pattern (35 bp):
CTCTTATAAGCATTGGTGTGTTTTGGAGGGATTAG
Found at i:34482 original size:70 final size:70
Alignment explanation
Indices: 34406--34556 Score: 221
Period size: 70 Copynumber: 2.2 Consensus size: 70
34396 TATAATTTTG
** *
34406 TGGTGTGTTTCAGTTAGACTAACTCTTATTAGCATTGGTGTGTTTTGGAGGGATTAGCTCTTATA
1 TGGTGTGTTTCAGAGAGACTAACTCTTATTAGCATTGGTGTGTTTTAGAGGGATTAGCTCTTATA
*
34471 AGCAT
66 AGAAT
** * * *
34476 TGGTGTGTTTTGGAGGGATTAGCTCTTATTAGCATTGGTGTGTTTTAGAGGGATTAGCTCTTATA
1 TGGTGTGTTTCAGAGAGACTAACTCTTATTAGCATTGGTGTGTTTTAGAGGGATTAGCTCTTATA
34541 AGAAT
66 AGAAT
34546 TGGTGTGTTTC
1 TGGTGTGTTTC
34557 GGGTGGATTG
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.20, C:0.09, G:0.28, T:0.42
Consensus pattern (70 bp):
TGGTGTGTTTCAGAGAGACTAACTCTTATTAGCATTGGTGTGTTTTAGAGGGATTAGCTCTTATA
AGAAT
Found at i:38836 original size:40 final size:40
Alignment explanation
Indices: 38799--39023 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
38789 GCTACTCGTT
* *
38799 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
38839 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
38879 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
38919 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
38958 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
38999 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
39024 CATCATTCGA
Statistics
Matches: 165, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
38 2 0.01
39 32 0.19
40 118 0.72
41 13 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:39007 original size:119 final size:120
Alignment explanation
Indices: 38801--39023 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
38791 TACTCGTTCA
*
38801 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
* *
38866 TTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
38921 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* * *
38983 ATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
64 ATATAGTAAC-TAGCACAAATGCCTTCGGGACTTAACCCGGA
39024 CATCATTCGA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 4 0.04
119 66 0.73
120 20 0.22
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
ATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:40218 original size:56 final size:56
Alignment explanation
Indices: 40151--40270 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
40141 TATTAGTTTA
40151 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
40207 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
40263 TTGCCCAT
1 TTGCCCAT
40271 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:46935 original size:115 final size:117
Alignment explanation
Indices: 46697--46943 Score: 283
Period size: 115 Copynumber: 2.1 Consensus size: 117
46687 AAATCACGTA
* *
46697 CCTTCGGAATTTAACCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGT
1 CCTTCGG-ACTTAACCGGATATAGCTACTCG-TCAAATGCCTTCGGGACATAGCCCGGATATAGT
* *
46762 AACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATG
64 AACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAATG
*
46816 CCTTCGGACTTAACCGGAT-TAG-TAACTCG-CACAATGCCTTCGGG-CTTAGCCCGGA-ATTAG
1 CCTTCGGACTTAACCGGATATAGCT-ACTCGTCA-AATGCCTTCGGGACATAGCCCGGATA-TAG
* ** * *
46876 TATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-G
63 TAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACAAATG
46931 CCTTCGGGACTTA
1 CCTTC-GGACTTA
46944 GCCCGGACAT
Statistics
Matches: 112, Mismatches: 10, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
114 4 0.04
115 54 0.48
116 28 0.25
117 8 0.07
118 11 0.10
119 7 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (117 bp):
CCTTCGGACTTAACCGGATATAGCTACTCGTCAAATGCCTTCGGGACATAGCCCGGATATAGTAA
CTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAATG
Found at i:46950 original size:40 final size:40
Alignment explanation
Indices: 46711--46950 Score: 273
Period size: 40 Copynumber: 6.1 Consensus size: 40
46701 CGGAATTTAA
** *
46711 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
46751 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
46791 CCGGATTTAGTAACTCGCACAAATGCCTTC-GGACTTA-A
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
46829 CCGGAT-TAGTAACTCGCAC-AATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
46866 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
46906 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
46946 CCGGA
1 CCGGA
46951 CATCATTCGA
Statistics
Matches: 173, Mismatches: 16, Indels: 22
0.82 0.08 0.10
Matches are distributed among these distances:
36 13 0.08
37 20 0.12
38 20 0.12
39 17 0.10
40 91 0.53
41 12 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:48145 original size:56 final size:56
Alignment explanation
Indices: 48078--48197 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
48068 TATTAGTTTA
48078 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
48134 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
48190 TTGCCCAT
1 TTGCCCAT
48198 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Done.