Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1324
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: 71275
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:6491 original size:51 final size:51
Alignment explanation
Indices: 6426--6700 Score: 279
Period size: 51 Copynumber: 5.3 Consensus size: 51
6416 GAAAATAATA
* *
6426 GGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTAGAAATAAGGCCG
1 GGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCG
*
6477 GGGTTGAAGTATCCCCGATTGTGAGAAATCAATA-TTTAGAAATAAAGCCG
1 GGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCG
*** * *** * **
6527 GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCTCAATGAAAT-AA--CG
1 GGGTTGGAGTAT-CCC-CGATTGTGA-GAAATCA-A-TAT--TTTA-GAAATAAAGCCG
* * *
6583 GGGTTGGAGTATCTCCGATTGTGAGAAATCAATATTTTAGAAATAAGGTCG
1 GGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCG
* * *
6634 GGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCTG
1 GGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCG
6685 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
6701 TCGGAAATAA
Statistics
Matches: 179, Mismatches: 33, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
48 5 0.03
49 3 0.02
50 26 0.15
51 100 0.56
52 6 0.03
53 6 0.03
54 6 0.03
55 4 0.02
56 14 0.08
58 4 0.02
59 5 0.03
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCG
Found at i:6559 original size:28 final size:28
Alignment explanation
Indices: 6525--6595 Score: 92
Period size: 28 Copynumber: 2.5 Consensus size: 28
6515 GAAATAAAGC
*
6525 CGGGGTTGGAGTATCCCCTCGA-AAATAA
1 CGGGGTTGGAGTAT-CCCTCAAGAAATAA
*
6553 CGGGGTTAGAGTAT-CCTCAATGAAATAA
1 CGGGGTTGGAGTATCCCTCAA-GAAATAA
6581 CGGGGTTGGAGTATC
1 CGGGGTTGGAGTATC
6596 TCCGATTGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.14
28 32 0.86
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCTCAAGAAATAA
Found at i:6715 original size:79 final size:79
Alignment explanation
Indices: 6632--6779 Score: 251
Period size: 79 Copynumber: 1.9 Consensus size: 79
6622 GAAATAAGGT
* * *
6632 CGGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCTGGGGTTGGAGTAT
1 CGGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGAAGTAT
6697 CCCCTCGGAAATAA
66 CCCCTCGGAAATAA
* *
6711 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGCCGGGGTTGAAGTAT
1 CGGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGAAGTAT
6776 CCCC
66 CCCC
6780 GATTGTGAGA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 64 1.00
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.26
Consensus pattern (79 bp):
CGGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTTGAAGTAT
CCCCTCGGAAATAA
Found at i:6777 original size:51 final size:51
Alignment explanation
Indices: 6711--6828 Score: 200
Period size: 51 Copynumber: 2.3 Consensus size: 51
6701 TCGGAAATAA
*
6711 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGC
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGC
* *
6762 CGGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGC
1 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGC
*
6813 CGGGATTGGAGTATCC
1 CGGGGTTGGAGTATCC
6829 TTTCGAAAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGC
Found at i:6787 original size:130 final size:130
Alignment explanation
Indices: 6574--6991 Score: 728
Period size: 130 Copynumber: 3.2 Consensus size: 130
6564 TATCCTCAAT
* *
6574 GAAATAACGGGGTTGGAGTATCTCCGATTGTGAGAAATCAATATTTTAGAAATAAGGTCGGGGTT
1 GAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGCCGGGGTT
*
6639 GAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCTGGGGTTGGAGTATCCCCTCG
66 GAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCG
6704 GAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGCCGGGGTT
1 GAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGCCGGGGTT
* **
6769 GAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCCGGGATTGGAGTATCCTTTCG
66 GAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCG
* *
6834 AAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAGGGCCGGGGTT
1 GAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGCCGGGGTT
* *
6899 GAAGTATCCCCAATTGTGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTTG
66 GAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCG
* *
6964 GAAATAATGGGGTTGGAGTATCCTCGAT
1 GAAATAACGGGGTTGGAGTATCCCCGAT
6992 GAAATATTGG
Statistics
Matches: 272, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 272 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (130 bp):
GAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAGGCCGGGGTT
GAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCCCCTCG
Found at i:6845 original size:79 final size:79
Alignment explanation
Indices: 6762--6907 Score: 238
Period size: 79 Copynumber: 1.8 Consensus size: 79
6752 GAAATAAGGC
* *
6762 CGGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGCCGGGATTGGAGTAT
1 CGGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGATTGAAGTAT
6827 CCTTTCGAAAATAA
66 CCTTTCGAAAATAA
* ** *
6841 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAGGGCCGGGGTTGAAGTAT
1 CGGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGATTGAAGTAT
6906 CC
66 CC
6908 CCAATTGTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 61 1.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.27
Consensus pattern (79 bp):
CGGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGATTGAAGTAT
CCTTTCGAAAATAA
Found at i:6908 original size:51 final size:51
Alignment explanation
Indices: 6841--6960 Score: 195
Period size: 51 Copynumber: 2.4 Consensus size: 51
6831 TCGAAAATAA
* **
6841 CGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAGGGC
1 CGGGGTTGGAGTATCCCCAATTGTGAGAAATCAATATTTTAGAAATAAAGC
* *
6892 CGGGGTTGAAGTATCCCCAATTGTGAGAAATCAATATTTTGGAAATAAAGC
1 CGGGGTTGGAGTATCCCCAATTGTGAGAAATCAATATTTTAGAAATAAAGC
6943 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
6961 TTGGAAATAA
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCAATTGTGAGAAATCAATATTTTAGAAATAAAGC
Found at i:7019 original size:28 final size:29
Alignment explanation
Indices: 6944--7019 Score: 102
Period size: 28 Copynumber: 2.7 Consensus size: 29
6934 AAATAAAGCC
*
6944 GGGGTTGGAGTATCCCC-TTGGAAATAAT
1 GGGGTTGGAGTATCCCCGATGGAAATAAT
* *
6972 GGGGTTGGAGTATCCTCGAT-GAAATATT
1 GGGGTTGGAGTATCCCCGATGGAAATAAT
*
7000 GGGGTTAGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
7020 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 41 0.98
29 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (29 bp):
GGGGTTGGAGTATCCCCGATGGAAATAAT
Found at i:7067 original size:51 final size:51
Alignment explanation
Indices: 7001--7118 Score: 184
Period size: 51 Copynumber: 2.3 Consensus size: 51
6991 TGAAATATTG
* *
7001 GGGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATC-
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAGAAATAAAATCA
* *
7051 GGAGTTGGAGTATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAATCA
1 GG-GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAGAAATAAAATCA
7103 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
7119 TCGGAAATAA
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
50 2 0.03
51 58 0.94
52 2 0.03
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.31
Consensus pattern (51 bp):
GGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAGAAATAAAATCA
Found at i:7138 original size:79 final size:79
Alignment explanation
Indices: 7054--7352 Score: 390
Period size: 79 Copynumber: 3.8 Consensus size: 79
7044 TAAAATCGGA
* * * *
7054 GTTGGAGTATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAATCAGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCAGGGTTGGAGTATCCCC
7119 TCGGAAATAACGGG
66 TCGGAAATAACGGG
* * *
7133 ATTGGAGTATCCCTGATTATGAAAAATTGATGTTTTAGAAATAAAATCAGGGTTGGAGTATCTCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCAGGGTTGGAGTATCCCC
7198 TCGGAAATAACGGG
66 TCGGAAATAACGGG
* * * * * ** *
7212 GTTTGAGTATCCCCGATTATGAGAAATTAATATTTTAAAAATAAAGCCGGGGTTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCAGGGTTGGAGTATCCCC
*
7277 TCGAAAATAACGGG
66 TCGGAAATAACGGG
* * *
7291 GTTGGAGTATCTCCG---ATGAAAAATTGATGTTTTGGAAATAAAA-CCGAGGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCAG-GGTTGGAGTATCCC
7352 C
65 C
7353 GAGATGAAAA
Statistics
Matches: 191, Mismatches: 28, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
75 2 0.01
76 37 0.19
79 152 0.80
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (79 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAATCAGGGTTGGAGTATCCCC
TCGGAAATAACGGG
Found at i:10123 original size:72 final size:72
Alignment explanation
Indices: 10006--10150 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
9996 CAAATACATC
10006 ATTATTTGTTTATAAGAATAAATATAAGCTTTATTGCTAACAAGATCTTTCAATTCATGCATCAG
1 ATTATTTGTTTATAAGAATAAATATAAGCTTTATTGCTAACAAGATCTTTCAATTCATGCATCAG
10071 CTAACTT
66 CTAACTT
10078 ATTATTTGTTTATAAGAATAAATATAAGCTTTATTGCTAACAAGATCTTTCAATTCATGCATCAG
1 ATTATTTGTTTATAAGAATAAATATAAGCTTTATTGCTAACAAGATCTTTCAATTCATGCATCAG
10143 CTAACTT
66 CTAACTT
10150 A
1 A
10151 ACAATACTTG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (72 bp):
ATTATTTGTTTATAAGAATAAATATAAGCTTTATTGCTAACAAGATCTTTCAATTCATGCATCAG
CTAACTT
Found at i:22879 original size:20 final size:19
Alignment explanation
Indices: 22828--22885 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
22818 TGTATTGATA
*
22828 CATTGTATCGATACATGCT
1 CATTGTATCGATACATACT
*
22847 CACTGTATCGATACATACT
1 CATTGTATCGATACATACT
*
22866 CAATTGTATTGATACATACT
1 C-ATTGTATCGATACATACT
22886 AACAATAGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATACT
Found at i:22946 original size:13 final size:13
Alignment explanation
Indices: 22925--22954 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
22915 CGATACGTGG
*
22925 TACATTGTATCGA
1 TACAATGTATCGA
22938 TACAATGTATCGA
1 TACAATGTATCGA
22951 TACA
1 TACA
22955 TGAAGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:22952 original size:33 final size:32
Alignment explanation
Indices: 22910--22974 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
22900 TATCATTGTT
*
22910 TGTATCGATACGTG-GTACATTGTATCGATACAA
1 TGTATCGATACATGAG-A-ATTGTATCGATACAA
22943 TGTATCGATACATGAAGAATTGTATCGATACA
1 TGTATCGATACATG-AGAATTGTATCGATACA
22975 TTATGCTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATGAGAATTGTATCGATACAA
Found at i:33948 original size:20 final size:20
Alignment explanation
Indices: 33904--33948 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
33894 CTATTATGCA
*
33904 AATTTTCCTTGCATTTAGGC
1 AATTTTCCTTGCATTTAAGC
33924 AATTTT-CTTGCATTTTAAGC
1 AATTTTCCTTGCA-TTTAAGC
*
33944 TATTT
1 AATTT
33949 AAAGGTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (20 bp):
AATTTTCCTTGCATTTAAGC
Found at i:40719 original size:106 final size:106
Alignment explanation
Indices: 40564--40774 Score: 282
Period size: 106 Copynumber: 2.0 Consensus size: 106
40554 AAAAATGACC
* * *
40564 TAAATGACATCAAAAGGCATGAAGTGATAATAAGTCCCTAAATCATGAAAAATGACCTAAATGGA
1 TAAATGACATCAAAAGGCATGAAATGATAATAAGTCCCTAAATCATGAAAAATAACCTAAATAGA
40629 ATTAAAATTCACAAAATTACATCCAAG-CCTTAGATCATGG
66 ATTAAAATTCACAAAATTACATCCAAGTCCTTAGATCATGG
* * * *
40669 TAAATGACATCAAAATGCATGAAATGACATAA-AAGTCTCTAGATCATGAAAAATAACTTAAATA
1 TAAATGACATCAAAAGGCATGAAATG--ATAATAAGTCCCTAAATCATGAAAAATAACCTAAATA
* * * * *
40733 GCATTAAAGTTCACATAATTGCATCCAAGTCCTTGGATCATG
64 GAATTAAAATTCACAAAATTACATCCAAGTCCTTAGATCATG
40775 ATGAATTACC
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
105 24 0.26
106 52 0.57
107 15 0.16
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.26
Consensus pattern (106 bp):
TAAATGACATCAAAAGGCATGAAATGATAATAAGTCCCTAAATCATGAAAAATAACCTAAATAGA
ATTAAAATTCACAAAATTACATCCAAGTCCTTAGATCATGG
Found at i:41753 original size:20 final size:19
Alignment explanation
Indices: 41723--41767 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
41713 ACTCTATTTC
41723 TCTTTTTTTTTAATTTTTT
1 TCTTTTTTTTTAATTTTTT
*
41742 TCTTTATTTTTTACTTTTTT
1 TCTTT-TTTTTTAATTTTTT
41762 TGCTTT
1 T-CTTT
41768 CTAGTTTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 14 0.61
21 4 0.17
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.80
Consensus pattern (19 bp):
TCTTTTTTTTTAATTTTTT
Found at i:47613 original size:17 final size:18
Alignment explanation
Indices: 47591--47625 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
47581 CTACTACTAG
47591 TTTTAT-CTATCAATACA
1 TTTTATGCTATCAATACA
*
47608 TTTTATGGTATCAATACA
1 TTTTATGCTATCAATACA
47626 AAAAACATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (18 bp):
TTTTATGCTATCAATACA
Found at i:47643 original size:19 final size:19
Alignment explanation
Indices: 47615--47664 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
47605 ACATTTTATG
*
47615 GTATCAATACAAAAAACAT
1 GTATCGATACAAAAAACAT
** *
47634 GTATCGATACTAAGCAATAT
1 GTATCGATAC-AAAAAACAT
47654 GTATCGATACA
1 GTATCGATACA
47665 TCTGGATGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.46, C:0.16, G:0.12, T:0.26
Consensus pattern (19 bp):
GTATCGATACAAAAAACAT
Found at i:50257 original size:19 final size:19
Alignment explanation
Indices: 50233--50297 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
50223 ATATAGTTGA
50233 AATGTATCGATACAATTTT
1 AATGTATCGATACAATTTT
*
50252 AATGTATAGATAC-A---T
1 AATGTATCGATACAATTTT
50267 --TGTATCGATACAATTTT
1 AATGTATCGATACAATTTT
*
50284 AATATATCGATACA
1 AATGTATCGATACA
50298 TTGTATCAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
13 10 0.27
14 1 0.03
15 1 0.03
17 1 0.03
18 1 0.03
19 23 0.62
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (19 bp):
AATGTATCGATACAATTTT
Found at i:50260 original size:32 final size:32
Alignment explanation
Indices: 50233--50304 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
50223 ATATAGTTGA
50233 AATGTATCGATACAATTTTAATGTATAGATAC
1 AATGTATCGATACAATTTTAATGTATAGATAC
* * *
50265 ATTGTATCGATACAATTTTAATATATCGATAC
1 AATGTATCGATACAATTTTAATGTATAGATAC
*
50297 ATTGTATC
1 AATGTATC
50305 AATAGATCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (32 bp):
AATGTATCGATACAATTTTAATGTATAGATAC
Found at i:57067 original size:48 final size:48
Alignment explanation
Indices: 56993--57106 Score: 183
Period size: 48 Copynumber: 2.4 Consensus size: 48
56983 TTCTTCTCCT
* * *
56993 TACTATTAGAAGTCACCATCTCTGTCATATCCTAGTCCCCCATCATTA
1 TACTACTACAAGTCACCATCTCTGTCATATCCTAGTCCCCCACCATTA
* *
57041 TAGTACTACAAGTCACCATCTCTGTCATCTCCTAGTCCCCCACCATTA
1 TACTACTACAAGTCACCATCTCTGTCATATCCTAGTCCCCCACCATTA
57089 TACTACTACAAGTCACCA
1 TACTACTACAAGTCACCA
57107 CCCTTTTATC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 60 1.00
ACGTcount: A:0.28, C:0.34, G:0.08, T:0.30
Consensus pattern (48 bp):
TACTACTACAAGTCACCATCTCTGTCATATCCTAGTCCCCCACCATTA
Found at i:58767 original size:20 final size:20
Alignment explanation
Indices: 58744--58820 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
58734 AAGTACCCAG
* *
58744 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
* *
58764 ATGTATCGATACA-TGTACGA
1 ATGTATCGATACATTCTTC-A
58784 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
*
58804 ATGTATTGATACATTCT
1 ATGTATCGATACATTCT
58821 ATCTTTTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.06
20 43 0.88
21 3 0.06
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Done.