Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013524.1 Kokia drynarioides strain JFW-HI SEQ_128550, whole genome shotgun sequence
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: 88695
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:14424 original size:22 final size:22
Alignment explanation
Indices: 14379--14424 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
14369 AATGTTAACT
*
14379 TTATTTTTTATAAATAATTTAA
1 TTATTTTTTATAAATAATTAAA
*
14401 TTATTTATTTATAAGT-ATTAAA
1 TTATTT-TTTATAAATAATTAAA
14423 TT
1 TT
14425 TAAATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TTATTTTTTATAAATAATTAAA
Found at i:22009 original size:18 final size:18
Alignment explanation
Indices: 21986--22030 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
21976 GCGTAGCCTG
21986 ACCAGATGCGATCATAGA
1 ACCAGATGCGATCATAGA
* * *
22004 ACCAGATACGGTCATATA
1 ACCAGATGCGATCATAGA
*
22022 ATCAGATGC
1 ACCAGATGC
22031 AACCATAAGC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (18 bp):
ACCAGATGCGATCATAGA
Found at i:29851 original size:20 final size:21
Alignment explanation
Indices: 29815--29853 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29805 ATTTTTGTTA
*
29815 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
29836 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
29854 AATTTCTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:32778 original size:25 final size:27
Alignment explanation
Indices: 32744--32794 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
32734 TCAGAAATGG
32744 AAAATGAGAAAA-AGAAAGAA-AAAAAT
1 AAAATGAGAAAAGA-AAAGAAGAAAAAT
32770 AAAA-GAGAAAAGAAAAGAAGAAAAA
1 AAAATGAGAAAAGAAAAGAAGAAAAA
32795 ATGTTTGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (27 bp):
AAAATGAGAAAAGAAAAGAAGAAAAAT
Found at i:32780 original size:12 final size:13
Alignment explanation
Indices: 32753--32793 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
32743 GAAAATGAGA
*
32753 AAAAG-AAAGAAA
1 AAAAGAAAAGAAG
*
32765 AAAATAAAAG-AG
1 AAAAGAAAAGAAG
32777 AAAAGAAAAGAAG
1 AAAAGAAAAGAAG
32790 AAAA
1 AAAA
32794 AATGTTTGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (13 bp):
AAAAGAAAAGAAG
Found at i:39388 original size:96 final size:96
Alignment explanation
Indices: 39221--39405 Score: 234
Period size: 96 Copynumber: 1.9 Consensus size: 96
39211 GAAAAAGATG
* ** *
39221 TTCGATTATCTCGATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGCGCAACATTTCAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAACATTTCAGAATCGA
*
39286 AGAT-AAAGAAACATTATCTCGATTGAGGGTA
66 AGATAAAAG-AACATTACCTCGATTGAGGGTA
**
39317 TTCGATTA-CTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTTTGAAACT
1 TTCGATTATC-TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAACATTTCAG-AA-T
*
39380 CGAA-ATAAAAGAATATTACCTCGATT
63 CGAAGATAAAAGAACATTACCTCGATT
39406 TGAAAGTCCT
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
95 6 0.08
96 62 0.81
97 9 0.12
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAACATTTCAGAATCGA
AGATAAAAGAACATTACCTCGATTGAGGGTA
Found at i:39876 original size:86 final size:87
Alignment explanation
Indices: 39762--39924 Score: 249
Period size: 86 Copynumber: 1.9 Consensus size: 87
39752 TTTGAGGGTA
* * * *
39762 AAAATGGAGATTTTAGAGGTTCGAGGGTAAAAATGTAATTTTTAGATG-TTTCGGGTTAAAAATG
1 AAAATGGAGATTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTCGGGTCAAAAATG
39826 GAATTTTTAGAATATTGGGGGG
66 GAATTTTTAGAATATTGGGGGG
* *
39848 AAAATGGA-ATTTTTGAAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAAT
1 AAAATGGAGATTTTAG-AAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTCGGGTCAAAAAT
39912 GGAATTTTTAGAA
65 GGAATTTTTAGAA
39925 ATTTAATGGT
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
85 6 0.09
86 37 0.54
87 26 0.38
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.34
Consensus pattern (87 bp):
AAAATGGAGATTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTCGGGTCAAAAATG
GAATTTTTAGAATATTGGGGGG
Found at i:39910 original size:30 final size:29
Alignment explanation
Indices: 39700--40038 Score: 235
Period size: 29 Copynumber: 11.6 Consensus size: 29
39690 GGTTTGAGGT
*
39700 TAAAAGATAGAATTTTTAG-A-TATTCGGGG
1 TAAAA-ATGGAATTTTTAGAAGT-TTCGGGG
** * *
39729 GCAAAATGGTAATTTTTAAAAGTTTTGAGGG
1 TAAAAATGG-AATTTTTAGAAGTTTCG-GGG
*
39760 TAAAAATGGAGA-TTTTAG-AGGTTCGAGGG
1 TAAAAATGGA-ATTTTTAGAAGTTTCG-GGG
* * *
39789 TAAAAATGTAATTTTTAGATGTTTCGGGT
1 TAAAAATGGAATTTTTAGAAGTTTCGGGG
39818 TAAAAATGGAATTTTTAGAA-TATT-GGGG
1 TAAAAATGGAATTTTTAGAAGT-TTCGGGG
**
39846 GGAAAATGGAATTTTT-GAAAG-TTCGAGGG
1 TAAAAATGGAATTTTTAG-AAGTTTCG-GGG
*
39875 TAAAAATGGAATTTTTAGAAGTTTTGGGG
1 TAAAAATGGAATTTTTAGAAGTTTCGGGG
* ***
39904 TCAAAAATGGAATTTTTAGAAATTTAATGG
1 T-AAAAATGGAATTTTTAGAAGTTTCGGGG
* * * * **
39934 TCAAGATGGAATTTTTGGAAATTTCAAGG
1 TAAAAATGGAATTTTTAGAAGTTTCGGGG
* * * **
39963 TCGAAAATGGAATTTTTGGAAATTTCAAGG
1 T-AAAAATGGAATTTTTAGAAGTTTCGGGG
* * *
39993 TCAAAAATGAAATTTTTGGAAGTTTAGGGG
1 T-AAAAATGGAATTTTTAGAAGTTTCGGGG
*
40023 TAAAAATGTAATTTTT
1 TAAAAATGGAATTTTT
40039 GGATAATTTA
Statistics
Matches: 254, Mismatches: 40, Indels: 32
0.78 0.12 0.10
Matches are distributed among these distances:
27 3 0.01
28 25 0.10
29 119 0.47
30 95 0.37
31 12 0.05
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (29 bp):
TAAAAATGGAATTTTTAGAAGTTTCGGGG
Found at i:39943 original size:29 final size:30
Alignment explanation
Indices: 39848--40009 Score: 179
Period size: 30 Copynumber: 5.5 Consensus size: 30
39838 TATTGGGGGG
* *
39848 AAAATGGAATTTTT-GAAAGTTCGAGGGT-A
1 AAAATGGAATTTTTAGAAATTTC-AAGGTCA
* ***
39877 AAAATGGAATTTTTAGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTAGAAATTTCAAGGTCA
39907 AAAATGGAATTTTTAGAAATTT-AATGGTC-
1 AAAATGGAATTTTTAGAAATTTCAA-GGTCA
* * *
39936 AAGATGGAATTTTTGGAAATTTCAAGGTCG
1 AAAATGGAATTTTTAGAAATTTCAAGGTCA
*
39966 AAAATGGAATTTTTGGAAATTTCAAGGTCA
1 AAAATGGAATTTTTAGAAATTTCAAGGTCA
*
39996 AAAATGAAATTTTT
1 AAAATGGAATTTTT
40010 GGAAGTTTAG
Statistics
Matches: 116, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
29 42 0.36
30 74 0.64
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.35
Consensus pattern (30 bp):
AAAATGGAATTTTTAGAAATTTCAAGGTCA
Found at i:39943 original size:59 final size:58
Alignment explanation
Indices: 39820--40050 Score: 218
Period size: 59 Copynumber: 3.9 Consensus size: 58
39810 TTTCGGGTTA
* ** * * *
39820 AAAATGGAATTTTTAGAA-TATTGGGG-GGAAAATGGAATTTTT-GAAAGTTCGAGGGTA
1 AAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAA-TT-TAAGGTC
*
39877 AAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTAGAAATTTAATGGTC
1 AAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAATTTAA-GGTC
* * * *** *
39936 AAGATGGAATTTTTGGAAATTTCAAGGTCGAAAATGGAATTTTTGGAAATTTCAAGGTC
1 AAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAATTT-AAGGTC
* * * *
39995 AAAAATGAAATTTTTGGAAGTTTAGGGGT-AAAAATGTAATTTTTGGATAATTTAAG
1 -AAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGA-AATTTAAG
40051 AACCTTCAAG
Statistics
Matches: 145, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
57 18 0.12
58 8 0.06
59 86 0.59
60 33 0.23
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (58 bp):
AAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAATTTAAGGTC
Found at i:41185 original size:27 final size:28
Alignment explanation
Indices: 41129--41189 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
41119 AAAAAAATGT
*
41129 TTATTATTATTAAATGTCATTAATATTA
1 TTATTATTATTAAATGTCATTAATACTA
*
41157 TTATTATTGTT-AATGTCATT-ATGACTA
1 TTATTATTATTAAATGTCATTAAT-ACTA
41184 TTATTA
1 TTATTA
41190 ATCCTGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
26 2 0.07
27 18 0.60
28 10 0.33
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (28 bp):
TTATTATTATTAAATGTCATTAATACTA
Found at i:41862 original size:14 final size:15
Alignment explanation
Indices: 41839--41868 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
41829 AATTTGGACA
41839 TGTAATTTGGACTTT
1 TGTAATTTGGACTTT
41854 TGTAA-TTGGACTTT
1 TGTAATTTGGACTTT
41868 T
1 T
41869 AATTTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (15 bp):
TGTAATTTGGACTTT
Found at i:41923 original size:17 final size:17
Alignment explanation
Indices: 41866--41936 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 17
41856 TAATTGGACT
* *
41866 TTTAATTTTGAAATTAAA
1 TTTAAATTT-AAAATAAA
** *
41884 TTTAAATTTACGATTAA
1 TTTAAATTTAAAATAAA
41901 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
41918 TATAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
41935 TT
1 TT
41937 AAAAAAAGGG
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
17 35 0.81
18 8 0.19
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:42356 original size:37 final size:37
Alignment explanation
Indices: 42306--42376 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
42296 CATATCACTT
* *
42306 GTTTTGATCCACTT-CTCTGTGTTTCATCAGGAAGATG
1 GTTTTGATCCACTTCCCCT-TATTTCATCAGGAAGATG
* *
42343 GTTTTGGTTCACTTCCCCTTATTTCATCAGGAAG
1 GTTTTGATCCACTTCCCCTTATTTCATCAGGAAG
42377 CTAACCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 26 0.90
38 3 0.10
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (37 bp):
GTTTTGATCCACTTCCCCTTATTTCATCAGGAAGATG
Found at i:42622 original size:205 final size:205
Alignment explanation
Indices: 42260--42863 Score: 796
Period size: 205 Copynumber: 2.9 Consensus size: 205
42250 TTTCATTAAC
* * ** ** * *
42260 TTGGCCTTCTTCTCAGTATCTCATCAGGAAGACGACCATATCACTTGTTTTGATCCACTTCTCTG
1 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCGATTCACTTCTCTG
* * ** * * ** *
42325 TGTTTCATCAGGAAGATGGTTTTGGTTCACTTCCCCTTATTTCATCAGGAAGCTAACCTTTTATT
66 TATTTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATT
* * * * * * * *
42390 GCTTCGACCTGCTTCTCGGTGTCTCATCAAGAAGCTGGGGTTCAAAAATTTGCTCATAACGAGCA
131 GCTTCGACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACAACGAGCA
42455 TGAGTTTGAT
196 TGAGTTTGAT
* * * *
42465 TTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATTTACTTCTCTG
1 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCGATTCACTTCTCTG
*
42530 TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATT
66 TATTTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATT
* ** * *
42595 GCTTCGACCCGCTTCTCAGTATCTCATCAGGAAGCTGGAATTCGAAGATTCACTCACATCGAGCG
131 GCTTCGACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACAACGAGCA
*
42660 TGGGTTTGAT
196 TGAGTTTGAT
* * * *
42670 TTGGTCTTCTTCTCAGTACCTTATCAGGAAGATGACCGCATCGTTCGTTTCGATTCGCTTCTCTG
1 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCGATTCACTTCTCTG
* *
42735 TATTTCATCAAGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGCTAACCTTTTATT
66 TATTTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATT
* *
42800 GCTTCG-CCCTGCTTCTTAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGC
131 GCTTCGACCC-GCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACAACGAGC
42864 CTTGAGTTGG
Statistics
Matches: 347, Mismatches: 51, Indels: 2
0.87 0.13 0.00
Matches are distributed among these distances:
204 3 0.01
205 344 0.99
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (205 bp):
TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCGATTCACTTCTCTG
TATTTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATT
GCTTCGACCCGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACAACGAGCA
TGAGTTTGAT
Found at i:42980 original size:115 final size:114
Alignment explanation
Indices: 42763--42969 Score: 326
Period size: 115 Copynumber: 1.8 Consensus size: 114
42753 AATTTGGTCC
* * *
42763 ACTTCTTAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGCCCTGCTTCTTAGTATCTCATC
1 ACTTCTTAGTATCTCATCAGGAAGCTAACCTTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
42828 AGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCCTTGAGTTGGTAT
66 AGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCCTTGAGTTGGTAT
* * * *
42877 ACTTCTCT-GTATCTCATCAGGGAGCTATCCATTTTATTACTTCGATCTTCTTCTCAGTATCTCA
1 ACTTCT-TAGTATCTCATCAGGAAGCTAACC-TTTTATTACTTCGACCTGCTTCTCAGTATCTCA
42941 TCAGGAAGCTGGGATTCGAAGATTTGCTC
64 TCAGGAAGCTGGGATTCGAAGATTTGCTC
42970 GCTTTGAGCC
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
114 26 0.31
115 58 0.69
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (114 bp):
ACTTCTTAGTATCTCATCAGGAAGCTAACCTTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
AGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCCTTGAGTTGGTAT
Found at i:52729 original size:25 final size:21
Alignment explanation
Indices: 52679--52719 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
52669 GTGGTGTATT
52679 CTTCTATCGTCGGTGTCATGA
1 CTTCTATCGTCGGTGTCATGA
52700 CTTCTATCGTCGGTGTCATG
1 CTTCTATCGTCGGTGTCATG
52720 TCTGTATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.39
Consensus pattern (21 bp):
CTTCTATCGTCGGTGTCATGA
Found at i:54264 original size:96 final size:96
Alignment explanation
Indices: 54097--54281 Score: 218
Period size: 96 Copynumber: 1.9 Consensus size: 96
54087 GAAAAGGATG
* * ** * *
54097 TTCGATTATCTCGATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGCGCAACATTTCAGAATTAA
1 TTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAACATTTCAGAATCAA
54162 AGAT-AAAGAAACATTACCTCGATTGAGGGTA
66 AGATAAAAG-AACATTACCTCGATTGAGGGTA
54193 TTCGATTA-CTTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTTC-GAAAC
1 TTCGATTATC-TCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAACA-TTTCAG-AA-
* *
54255 TCGAA-ATAAAAGAATATTACCTCGATT
62 TCAAAGATAAAAGAACATTACCTCGATT
54282 TGAAATTCTT
Statistics
Matches: 76, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
95 3 0.04
96 66 0.87
97 7 0.09
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (96 bp):
TTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAACATTTCAGAATCAA
AGATAAAAGAACATTACCTCGATTGAGGGTA
Found at i:54588 original size:29 final size:30
Alignment explanation
Indices: 54554--54709 Score: 96
Period size: 29 Copynumber: 5.4 Consensus size: 30
54544 AGGCAAGATG
*
54554 GAATTTTTAGACATTCGGGGGTAAAAATGA
1 GAATTTTTGGACATTCGGGGGTAAAAATGA
*
54584 -AA-TTTTGGAGC-TTC-GGGGTCGAAAAT-A
1 GAATTTTTGGA-CATTCGGGGGT-AAAAATGA
* *
54611 GAGTTTTTGGACATTCGGGGG-AAAAACGA
1 GAATTTTTGGACATTCGGGGGTAAAAATGA
* * ** * *
54640 TAATTTTTGAATGTTTTGGGGGCAAAAATG-
1 GAATTTTTGGA-CATTCGGGGGTAAAAATGA
** *
54670 GAGA-TTTTGGAGGTTCGAGGGTAAAAATG-
1 GA-ATTTTTGGACATTCGGGGGTAAAAATGA
54699 GAATTTTTGGA
1 GAATTTTTGGA
54710 AGTTTAAGGA
Statistics
Matches: 97, Mismatches: 18, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
27 6 0.06
28 21 0.22
29 45 0.46
30 18 0.19
31 7 0.07
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.31
Consensus pattern (30 bp):
GAATTTTTGGACATTCGGGGGTAAAAATGA
Found at i:54723 original size:29 final size:29
Alignment explanation
Indices: 54663--54768 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 29
54653 TTTTGGGGGC
* * *
54663 AAAAATGGAGA-TTTTGGAGGTTCGAGGGT
1 AAAAATGGA-ATTTTTGGAAGTTTGAGGAT
*
54692 AAAAATGGAATTTTTGGAAGTTTAAGGAT
1 AAAAATGGAATTTTTGGAAGTTTGAGGAT
* ** * *
54721 AAAACTGGAATTTTTAAAAGTTTTGGGGTT
1 AAAAATGGAATTTTTGGAAG-TTTGAGGAT
*
54751 AAAAATAGAATTTTTGGA
1 AAAAATGGAATTTTTGGA
54769 GGTCAAGATG
Statistics
Matches: 61, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
28 1 0.02
29 40 0.66
30 20 0.33
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.34
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTGAGGAT
Found at i:55966 original size:3 final size:3
Alignment explanation
Indices: 55960--56003 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
55950 AAAAAACTGT
* * *
55960 TTA TTA TTA TTA ATG TCA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
56004 GTTAATGTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:55986 original size:21 final size:21
Alignment explanation
Indices: 55960--56030 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 21
55950 AAAAAACTGT
55960 TTATTATTATTAATGTC---A
1 TTATTATTATTAATGTCATTA
55978 TTATTATTATT-AT-T-ATTA
1 TTATTATTATTAATGTCATTA
*
55996 TTATTATTGTTAATGTCATTA
1 TTATTATTATTAATGTCATTA
* *
56017 TGACTATTATTAAT
1 TTATTATTATTAAT
56031 CCTGATTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
16 1 0.02
17 2 0.05
18 22 0.51
19 2 0.05
20 1 0.02
21 15 0.35
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (21 bp):
TTATTATTATTAATGTCATTA
Found at i:56009 original size:36 final size:36
Alignment explanation
Indices: 55960--56028 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
55950 AAAAAACTGT
* *
55960 TTATTATTATTAATGTCATTATTATTATTATTATTA
1 TTATTATTATTAATGTCATTATGACTATTATTATTA
*
55996 TTATTATTGTTAATGTCATTATGACTATTATTA
1 TTATTATTATTAATGTCATTATGACTATTATTA
56029 ATCCTGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.58
Consensus pattern (36 bp):
TTATTATTATTAATGTCATTATGACTATTATTATTA
Found at i:56721 original size:12 final size:11
Alignment explanation
Indices: 56715--56778 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
56705 TTTAATTTTG
56715 AAATTAAATTT
1 AAATTAAATTT
56726 AAATTTAAGA-TT
1 AAA-TTAA-ATTT
*
56738 AATTTAAATTT
1 AAATTAAATTT
* *
56749 AAAATAAATCT
1 AAATTAAATTT
*
56760 AAATTTAAA-AT
1 AAA-TTAAATTT
56771 AAATTAAA
1 AAATTAAA
56779 AAAAAAGGGG
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
10 6 0.14
11 24 0.56
12 12 0.28
13 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:56743 original size:17 final size:17
Alignment explanation
Indices: 56705--56775 Score: 88
Period size: 17 Copynumber: 4.1 Consensus size: 17
56695 TAATTGGATT
* *
56705 TTTAATTTTGAAATTAAA
1 TTTAAATTT-AAAATAAA
* *
56723 TTTAAATTTAAGATTAA
1 TTTAAATTTAAAATAAA
56740 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
56757 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
56774 TT
1 TT
56776 AAAAAAAAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 37 0.82
18 8 0.18
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:56770 original size:7 final size:6
Alignment explanation
Indices: 56705--56768 Score: 55
Period size: 6 Copynumber: 11.0 Consensus size: 6
56695 TAATTGGATT
*
56705 TTTAAT TTTGAAA -TTAAA TTTAAA TTTAAGA -TT-AA TTTAAA TTTAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA
* *
56752 -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA
56769 ATAAATTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
4 1 0.02
5 10 0.21
6 34 0.71
7 3 0.06
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:57414 original size:9 final size:8
Alignment explanation
Indices: 57402--57458 Score: 53
Period size: 9 Copynumber: 6.8 Consensus size: 8
57392 TGAGGGTATT
57402 GAAGCAAAA
1 GAAG-AAAA
*
57411 GAAGAGAA
1 GAAGAAAA
57419 -AAGAAAA
1 GAAGAAAA
57426 GAAGTAAAA
1 GAAG-AAAA
57435 GAAGAGAAA
1 GAAGA-AAA
*
57444 TAAGAAGAA
1 GAAGAA-AA
57453 GAAGAA
1 GAAGAA
57459 GACGTTGCCC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
7 6 0.15
8 8 0.20
9 26 0.65
ACGTcount: A:0.68, C:0.02, G:0.26, T:0.04
Consensus pattern (8 bp):
GAAGAAAA
Found at i:57903 original size:17 final size:17
Alignment explanation
Indices: 57851--57893 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
57841 ATATATTTTC
* *
57851 TTTAGTTGTCATTACAT
1 TTTAATTGTCACTACAT
*
57868 TTTAATTGTCACTGCAT
1 TTTAATTGTCACTACAT
57885 TTTAATTGT
1 TTTAATTGT
57894 TCTCACATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (17 bp):
TTTAATTGTCACTACAT
Found at i:59797 original size:16 final size:16
Alignment explanation
Indices: 59776--59808 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
59766 GATAAACCAC
*
59776 AAATATTTTTAGATAA
1 AAATATTTGTAGATAA
59792 AAATATTTGTAGATAA
1 AAATATTTGTAGATAA
59808 A
1 A
59809 CTGTCATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (16 bp):
AAATATTTGTAGATAA
Found at i:60413 original size:90 final size:90
Alignment explanation
Indices: 60260--60440 Score: 344
Period size: 90 Copynumber: 2.0 Consensus size: 90
60250 AATACTAAGC
*
60260 AGTATTACGTGGTCGGATCGTAGTACGGAAAGACTGCTTATGTTAGTAGATGAATCTAAACATGT
1 AGTATTACGTGGTCGGATCGTAGTACGGAAAGACTACTTATGTTAGTAGATGAATCTAAACATGT
60325 CCTTAGTCTAATTAAAAATGAGCAA
66 CCTTAGTCTAATTAAAAATGAGCAA
*
60350 AGTATTACGTGGTCGGATCGTAGTACGGAAAGACTACTTGTGTTAGTAGATGAATCTAAACATGT
1 AGTATTACGTGGTCGGATCGTAGTACGGAAAGACTACTTATGTTAGTAGATGAATCTAAACATGT
60415 CCTTAGTCTAATTAAAAATGAGCAA
66 CCTTAGTCTAATTAAAAATGAGCAA
60440 A
1 A
60441 CCGATTAAAA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (90 bp):
AGTATTACGTGGTCGGATCGTAGTACGGAAAGACTACTTATGTTAGTAGATGAATCTAAACATGT
CCTTAGTCTAATTAAAAATGAGCAA
Found at i:63080 original size:26 final size:26
Alignment explanation
Indices: 63044--63101 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
63034 ACATATTTTC
* **
63044 TCAAAATTTTACCAAGGGTAAAATCG
1 TCAAAAGTTTACCAACAGTAAAATCG
63070 TCAAAAGTTTACCAACAGTAAAATCG
1 TCAAAAGTTTACCAACAGTAAAATCG
63096 TCAAAA
1 TCAAAA
63102 TTTTGTTGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.24
Consensus pattern (26 bp):
TCAAAAGTTTACCAACAGTAAAATCG
Found at i:68202 original size:3 final size:3
Alignment explanation
Indices: 68196--68230 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
68186 CTACTACTAC
68196 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
68231 CATTAAGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:68485 original size:26 final size:26
Alignment explanation
Indices: 68447--68514 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
68437 TAACCATGTA
*
68447 TGCTCACACGAGCTGTAAAATGGGTC
1 TGCTCACACGAGCTATAAAATGGGTC
* *
68473 TGCTCACATGAGCTATGAAATGGGTC
1 TGCTCACACGAGCTATAAAATGGGTC
*
68499 TACTCACACGAGCTAT
1 TGCTCACACGAGCTAT
68515 GGATCGAGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (26 bp):
TGCTCACACGAGCTATAAAATGGGTC
Found at i:68943 original size:15 final size:15
Alignment explanation
Indices: 68925--68996 Score: 71
Period size: 15 Copynumber: 4.9 Consensus size: 15
68915 TTTCATTGAT
*
68925 TATCATTTCGGATAA
1 TATCCTTTCGGATAA
*
68940 TATCCTTTTC-AATAA
1 TATCC-TTTCGGATAA
68955 TATCCTTTCGGAT-A
1 TATCCTTTCGGATAA
*
68969 TA-CCTTTTC-AATAA
1 TATCC-TTTCGGATAA
68983 TATCCTTTCGGATA
1 TATCCTTTCGGATA
68997 TAACCTTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
13 4 0.09
14 18 0.39
15 20 0.43
16 4 0.09
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.43
Consensus pattern (15 bp):
TATCCTTTCGGATAA
Found at i:68949 original size:40 final size:40
Alignment explanation
Indices: 68863--68951 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
68853 AATAATTTTA
* * * * *
68863 CCTTTTCAATCTTTTCATTTAGTATCCTTTTGGATAACGT
1 CCTTTTCAACCTTTTCATTGAGTATCATTTCGGATAACAT
* * *
68903 CTTTTTCAACCTTTTCATTGATTATCATTTCGGATAATAT
1 CCTTTTCAACCTTTTCATTGAGTATCATTTCGGATAACAT
68943 CCTTTTCAA
1 CCTTTTCAA
68952 TAATATCCTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.22, C:0.20, G:0.08, T:0.49
Consensus pattern (40 bp):
CCTTTTCAACCTTTTCATTGAGTATCATTTCGGATAACAT
Found at i:68979 original size:28 final size:28
Alignment explanation
Indices: 68911--69008 Score: 133
Period size: 28 Copynumber: 3.4 Consensus size: 28
68901 GTCTTTTTCA
* * *
68911 ACCTTTTCATTGATTATCATTTCGGATAAT
1 ACCTTTTCAAT-AATATCCTTTCGGAT-AT
68941 ATCCTTTTCAATAATATCCTTTCGGATAT
1 A-CCTTTTCAATAATATCCTTTCGGATAT
68970 ACCTTTTCAATAATATCCTTTCGGATAT
1 ACCTTTTCAATAATATCCTTTCGGATAT
68998 AACCTTTTCAA
1 -ACCTTTTCAA
69009 ATATTTTAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
28 27 0.43
29 13 0.21
30 14 0.22
31 9 0.14
ACGTcount: A:0.29, C:0.20, G:0.07, T:0.44
Consensus pattern (28 bp):
ACCTTTTCAATAATATCCTTTCGGATAT
Found at i:69006 original size:15 final size:16
Alignment explanation
Indices: 68930--69006 Score: 78
Period size: 14 Copynumber: 5.2 Consensus size: 16
68920 TTGATTATCA
68930 TTTCGGATAATATCCT
1 TTTCGGATAATATCCT
*
68946 TTTC-AATAATATCC-
1 TTTCGGATAATATCCT
68960 TTTCGGAT-ATA-CCT
1 TTTCGGATAATATCCT
*
68974 TTTC-AATAATATCC-
1 TTTCGGATAATATCCT
*
68988 TTTCGGAT-ATAACCT
1 TTTCGGATAATATCCT
69003 TTTC
1 TTTC
69007 AAATATTTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
13 4 0.08
14 23 0.46
15 19 0.38
16 4 0.08
ACGTcount: A:0.27, C:0.21, G:0.08, T:0.44
Consensus pattern (16 bp):
TTTCGGATAATATCCT
Found at i:69552 original size:20 final size:21
Alignment explanation
Indices: 69527--69565 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
69517 TTTCATAGCT
*
69527 TCAAAA-TCTAACAATTTCTA
1 TCAAAACTCAAACAATTTCTA
69547 TCAAAACTCAAACAATTTC
1 TCAAAACTCAAACAATTTC
69566 ACTCCAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (21 bp):
TCAAAACTCAAACAATTTCTA
Found at i:71514 original size:6 final size:6
Alignment explanation
Indices: 71503--71555 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
71493 TTAAACAATT
* * *
71503 AAAGTC AAAGTC AAAGCC AATGGTC AAAGTC AAAATC AACAGTC AAAGGTC
1 AAAGTC AAAGTC AAAGTC AA-AGTC AAAGTC AAAGTC AA-AGTC AAA-GTC
71554 AA
1 AA
71556 CAGGTCGAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
6 24 0.63
7 14 0.37
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.15
Consensus pattern (6 bp):
AAAGTC
Found at i:71547 original size:19 final size:19
Alignment explanation
Indices: 71505--71555 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
71495 AAACAATTAA
* *
71505 AGTCAAAGTCAAAGCCAAT
1 AGTCAAAGTCAAAACCAAC
* *
71524 GGTCAAAGTCAAAATCAAC
1 AGTCAAAGTCAAAACCAAC
71543 AGTCAAAGGTCAA
1 AGTCAAA-GTCAA
71556 CAGGTCGAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.47, C:0.20, G:0.18, T:0.16
Consensus pattern (19 bp):
AGTCAAAGTCAAAACCAAC
Found at i:73250 original size:25 final size:26
Alignment explanation
Indices: 73216--73283 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 26
73206 AGTCAGACAA
*
73216 ATCGCTCTTACGAGCCAAATAGAATT
1 ATCGCTCTTACGAGCCAAATAGAATC
* *
73242 AT-GCTCTTATGAGCCAGATAGAATC
1 ATCGCTCTTACGAGCCAAATAGAATC
73267 ATCGCTCTTACGAGCCA
1 ATCGCTCTTACGAGCCA
73284 GACAGAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
25 22 0.59
26 15 0.41
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (26 bp):
ATCGCTCTTACGAGCCAAATAGAATC
Found at i:81741 original size:28 final size:27
Alignment explanation
Indices: 81702--81754 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
81692 GAATTTGATA
*
81702 TTTTTTTTCTAATTTGGTACTTAAACC
1 TTTTTTTTCTAATTTGATACTTAAACC
81729 TTTTTTTATCTAATTTGATACTTAAA
1 TTTTTTT-TCTAATTTGATACTTAAA
81755 TTTGACATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (27 bp):
TTTTTTTTCTAATTTGATACTTAAACC
Found at i:82136 original size:58 final size:56
Alignment explanation
Indices: 82043--82207 Score: 206
Period size: 57 Copynumber: 2.9 Consensus size: 56
82033 ATTGAATCTA
* * * *
82043 AAAAAAGCTTAGGTACCAAATTAGAAAAAAAGTCAAGTTCAGATACTAAATTGGGTT
1 AAAAAAGTTTAGGTACCAAATTAGAAAAAATGTCAAGTTCAGATACCAAATTAGG-T
** *
82100 AAAAAAGTTTAGGTACCAAATTAAGAAAATGTGTCAAATTCA-AGTACCAAATTAGGT
1 AAAAAAGTTTAGGTACCAAATT-AGAAAAAATGTCAAGTTCAGA-TACCAAATTAGGT
* * *
82157 AAAAAAATTTAAGTACCAAATTAGAAAAAATGTAAAGTTCAGATACCAAAT
1 AAAAAAGTTTAGGTACCAAATTAGAAAAAATGTCAAGTTCAGATACCAAAT
82208 ATCATATTAA
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
56 23 0.25
57 44 0.48
58 25 0.27
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (56 bp):
AAAAAAGTTTAGGTACCAAATTAGAAAAAATGTCAAGTTCAGATACCAAATTAGGT
Found at i:82186 original size:26 final size:26
Alignment explanation
Indices: 82135--82186 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
82125 AAAATGTGTC
**
82135 AAATTCAAGTACCAAATTAGGTAAAA
1 AAATTCAAGTACCAAATTAGAAAAAA
*
82161 AAATTTAAGTACCAAATTAGAAAAAA
1 AAATTCAAGTACCAAATTAGAAAAAA
82187 TGTAAAGTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.58, C:0.10, G:0.10, T:0.23
Consensus pattern (26 bp):
AAATTCAAGTACCAAATTAGAAAAAA
Found at i:82847 original size:21 final size:21
Alignment explanation
Indices: 82823--82864 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
82813 TGGAATAAAG
82823 AAAGAAAGATGGGTTTCTTAT
1 AAAGAAAGATGGGTTTCTTAT
*
82844 AAAGAAAGATGGGTTTTTTAT
1 AAAGAAAGATGGGTTTCTTAT
82865 CTAAGTAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (21 bp):
AAAGAAAGATGGGTTTCTTAT
Found at i:83451 original size:117 final size:119
Alignment explanation
Indices: 83276--83540 Score: 319
Period size: 117 Copynumber: 2.2 Consensus size: 119
83266 CGGCCACATT
* * * *
83276 TTTATTTGATAAAAAAATTAAATTTTTTGGTGTTGGCAATTGCATGGCAGACAGCACCTTTTTGT
1 TTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGGCAATTGCATGGCAGACACCACCTTTTTAT
* *
83341 CAGAT-AAAAAAT-ATTTTTTTGGTGTTGGTCA-TGCCATGACCGACAACC-CTTA
66 CAGATAAAAAAATAATTTTTTTGGTGTCGGCCACTG-CATGACCGAC-ACCACTTA
*
83393 TTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGGTC-A-TGCAATGGCCGACACCACCTTTTT
1 TTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGG-CAATTGC-ATGGCAGACACCACCTTTTT
** * *
83456 ATTTGATAAAAAAAATCAATTTTTTTGGTGTCGGCCACTGCATGATCGACACCACTTT
64 ATCAGAT-AAAAAAAT-AATTTTTTTGGTGTCGGCCACTGCATGACCGACACCACTTA
83514 TTTATCTGATAAAAAAAATC-AATTTTT
1 TTTATCTGAT-AAAAAAATCAAATTTTT
83541 GCAATGGCCA
Statistics
Matches: 128, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
116 3 0.02
117 57 0.45
118 1 0.01
119 7 0.05
120 3 0.02
121 46 0.36
122 11 0.09
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (119 bp):
TTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGGCAATTGCATGGCAGACACCACCTTTTTAT
CAGATAAAAAAATAATTTTTTTGGTGTCGGCCACTGCATGACCGACACCACTTA
Found at i:83480 original size:61 final size:60
Alignment explanation
Indices: 83269--83540 Score: 279
Period size: 61 Copynumber: 4.5 Consensus size: 60
83259 TTGGTGTCGG
* * * * * * *
83269 CCACATTTTTATTTGATAAAAAAATTAAATTTTTTGGTGTTGG-CAATTGCATGGCAGACA
1 CCACCTTTTTATCTGATAAAAAAATCAATTTTTTTGGTGTTGGTC-ACTGCATGACCGACA
* * *
83329 GCACCTTTTTGTCAGAT-AAAAAAT--ATTTTTTTGGTGTTGGTCA-TGCCATGACCGACA
1 CCACCTTTTTATCTGATAAAAAAATCAATTTTTTTGGTGTTGGTCACTG-CATGACCGACA
* * *
83386 AC-CCTTATTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGGTCA-TGCAATGGCCGACA
1 CCACCTT-TTTATCTGATAAAAAAATCAATTTTTTTGGTGTTGGTCACTGC-ATGACCGACA
* * * *
83446 CCACCTTTTTATTTGATAAAAAAAATCAATTTTTTTGGTGTCGGCCACTGCATGATCGACA
1 CCACCTTTTTATCTGAT-AAAAAAATCAATTTTTTTGGTGTTGGTCACTGCATGACCGACA
*
83507 CCACTTTTTTATCTGATAAAAAAAATCAATTTTT
1 CCACCTTTTTATCTGAT-AAAAAAATCAATTTTT
83541 GCAATGGCCA
Statistics
Matches: 180, Mismatches: 22, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
56 6 0.03
57 34 0.19
58 8 0.04
59 8 0.04
60 51 0.28
61 70 0.39
62 3 0.02
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (60 bp):
CCACCTTTTTATCTGATAAAAAAATCAATTTTTTTGGTGTTGGTCACTGCATGACCGACA
Found at i:88162 original size:20 final size:20
Alignment explanation
Indices: 88137--88190 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
88127 CTCTAGTGAG
* *
88137 ATTTCTACCGGTAGAACTCC
1 ATTTCTACCGATACAACTCC
*
88157 ATTTCTACCAATACAACTCC
1 ATTTCTACCGATACAACTCC
*
88177 ACTTCTACCGATAC
1 ATTTCTACCGATAC
88191 CTTGCAGACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.30, C:0.33, G:0.07, T:0.30
Consensus pattern (20 bp):
ATTTCTACCGATACAACTCC
Done.