Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4545.1
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: 54717
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 906 characters in sequence are not A, C, G, or T
Found at i:3083 original size:15 final size:16
Alignment explanation
Indices: 3063--3095 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3053 ATTAAAACTT
*
3063 TGAAGA-ATTTTTAAA
1 TGAAGACATTTTAAAA
3078 TGAAGACATTTTAAAA
1 TGAAGACATTTTAAAA
3094 TG
1 TG
3096 CATCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.36
Consensus pattern (16 bp):
TGAAGACATTTTAAAA
Found at i:14192 original size:31 final size:32
Alignment explanation
Indices: 14151--14210 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
14141 AATATTACTA
14151 TAGTGACAGCAATGAAGGCTGAAACAGGACTG
1 TAGTGACAGCAATGAAGGCTGAAACAGGACTG
* *
14183 TAGTG-CAGCAATGAAGGTTGAAATAGGA
1 TAGTGACAGCAATGAAGGCTGAAACAGGA
14211 GGGAAAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 21 0.81
32 5 0.19
ACGTcount: A:0.38, C:0.12, G:0.32, T:0.18
Consensus pattern (32 bp):
TAGTGACAGCAATGAAGGCTGAAACAGGACTG
Found at i:16688 original size:20 final size:20
Alignment explanation
Indices: 16663--16701 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
16653 TGTGAAGTTT
*
16663 ATTGATGAGTATTTTATATA
1 ATTGATGAATATTTTATATA
16683 ATTGATGAATATTTTATAT
1 ATTGATGAATATTTTATAT
16702 TAGAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (20 bp):
ATTGATGAATATTTTATATA
Found at i:23139 original size:21 final size:22
Alignment explanation
Indices: 23106--23146 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
23096 TTCATTTATG
*
23106 TTTCATTGGCACATA-ATCATA
1 TTTCATTGCCACATACATCATA
*
23127 TTTCATTTCCACATACATCA
1 TTTCATTGCCACATACATCA
23147 CAATACATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (22 bp):
TTTCATTGCCACATACATCATA
Found at i:23849 original size:18 final size:19
Alignment explanation
Indices: 23836--23873 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
23826 TCCTTGATTT
23836 TCCA-CCCGATCTTGATCA
1 TCCATCCCGATCTTGATCA
*
23854 TGCATCCCGATCTTGATCA
1 TCCATCCCGATCTTGATCA
23873 T
1 T
23874 GCATTAGCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (19 bp):
TCCATCCCGATCTTGATCA
Found at i:23864 original size:19 final size:19
Alignment explanation
Indices: 23840--23877 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
23830 TGATTTTCCA
23840 CCCGATCTTGATCATGCAT
1 CCCGATCTTGATCATGCAT
23859 CCCGATCTTGATCATGCAT
1 CCCGATCTTGATCATGCAT
23878 TAGCTGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.32, G:0.16, T:0.32
Consensus pattern (19 bp):
CCCGATCTTGATCATGCAT
Found at i:25734 original size:3 final size:3
Alignment explanation
Indices: 25720--25768 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
25710 CGATAATATA
* ** *
25720 AAT AAC AAT AAT AAT AAT AGC AAT AAT AAC AAT AAT AAT AAT GAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
25766 AAT
1 AAT
25769 CTGAATTTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:25949 original size:12 final size:12
Alignment explanation
Indices: 25934--25966 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
25924 AATAAATAAA
25934 TAAATAAAATAT
1 TAAATAAAATAT
*
25946 TAAATGAAATAT
1 TAAATAAAATAT
25958 TAAATAAAA
1 TAAATAAAA
25967 AAGTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (12 bp):
TAAATAAAATAT
Found at i:29938 original size:17 final size:17
Alignment explanation
Indices: 29916--29989 Score: 76
Period size: 17 Copynumber: 4.1 Consensus size: 17
29906 ACTAAACCGA
29916 CCACTAACTCCATCACC
1 CCACTAACTCCATCACC
29933 CCACTAACTCCATCACCC
1 CCACTAACTCCATCA-CC
*
29951 TTTGCCACTAATTCCATCACC
1 ----CCACTAACTCCATCACC
* *
29972 CCACTAACCCCATTACC
1 CCACTAACTCCATCACC
29989 C
1 C
29990 TACTTGCCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
17 30 0.62
18 2 0.04
21 2 0.04
22 14 0.29
ACGTcount: A:0.27, C:0.50, G:0.01, T:0.22
Consensus pattern (17 bp):
CCACTAACTCCATCACC
Found at i:29959 original size:39 final size:39
Alignment explanation
Indices: 29916--29990 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
29906 ACTAAACCGA
*
29916 CCACTAACTCCATCACCCCACTAACTCCATCACCCTTTG
1 CCACTAACTCCATCACCCCACTAACCCCATCACCCTTTG
* *
29955 CCACTAATTCCATCACCCCACTAACCCCATTACCCT
1 CCACTAACTCCATCACCCCACTAACCCCATCACCCT
29991 ACTTGCCTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.27, C:0.49, G:0.01, T:0.23
Consensus pattern (39 bp):
CCACTAACTCCATCACCCCACTAACCCCATCACCCTTTG
Found at i:30552 original size:21 final size:22
Alignment explanation
Indices: 30507--30549 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
30497 TTTTATAAAC
30507 ATTTTTTAAATATTATATTATT
1 ATTTTTTAAATATTATATTATT
*
30529 ATTTTTATATATATTAT-TTAT
1 ATTTTT-TAAATATTATATTAT
30550 ATTAAGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTTTTAAATATTATATTATT
Found at i:30679 original size:25 final size:25
Alignment explanation
Indices: 30646--30696 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
30636 TTCTTGCACT
30646 TATATATATGTAAATGCTTCCTATA
1 TATATATATGTAAATGCTTCCTATA
*
30671 TATATATATGTAAATGTTTCCTATA
1 TATATATATGTAAATGCTTCCTATA
30696 T
1 T
30697 CATCAGCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (25 bp):
TATATATATGTAAATGCTTCCTATA
Found at i:31974 original size:26 final size:26
Alignment explanation
Indices: 31944--32002 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
31934 AATCAATCTC
31944 CATTTTCAAAATAAAAATAGTTTCGA
1 CATTTTCAAAATAAAAATAGTTTCGA
31970 CATTTTCAAAATAAAAATAGTTTCGA
1 CATTTTCAAAATAAAAATAGTTTCGA
31996 CATTTTC
1 CATTTTC
32003 TTTTTCCTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (26 bp):
CATTTTCAAAATAAAAATAGTTTCGA
Found at i:34333 original size:45 final size:45
Alignment explanation
Indices: 34278--34364 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 45
34268 CAAATTTTAA
* *
34278 GAATTATTGACATTATTATCCATATAATA-TCATTTTATGTTTCAG
1 GAATTATTGACACTATTATCCACATAATACT-ATTTTATGTTTCAG
* *
34323 GAATTTTTGACACTATTATCCACGTAATACTATTTTATGTTT
1 GAATTATTGACACTATTATCCACATAATACTATTTTATGTTT
34365 GCATATCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 36 0.97
46 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (45 bp):
GAATTATTGACACTATTATCCACATAATACTATTTTATGTTTCAG
Found at i:40883 original size:43 final size:43
Alignment explanation
Indices: 40818--40981 Score: 292
Period size: 43 Copynumber: 3.8 Consensus size: 43
40808 GTTTATTGGA
* *
40818 AAAAACGCCACTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
* *
40861 AAAAGCGACGCTAAAGGTCAAGGCTTTTAGCGGCGTTTTTGGG
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
40904 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
40947 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCG
1 AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCG
40982 CTTTTTTTGC
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 115 1.00
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
Found at i:40927 original size:86 final size:86
Alignment explanation
Indices: 40805--40987 Score: 312
Period size: 86 Copynumber: 2.1 Consensus size: 86
40795 AAAAATTTGT
40805 GGCGTTTATTGGAAAAAACGCCACTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGAC
1 GGCGTTT-TTGGAAAAAACGCCACTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGAC
40870 GCTAAAGGTCAAGGCTTTTAGC
65 GCTAAAGGTCAAGGCTTTTAGC
* * * *
40892 GGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGCCG
1 GGCGTTTTTGGAAAAAACGCCACTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGACG
40957 CTAAAGGTCAAGGCTTTTAGC
66 CTAAAGGTCAAGGCTTTTAGC
40978 GGCGCTTTTT
1 GGCG-TTTTT
40988 TTGCAAGCAC
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
86 79 0.87
87 12 0.13
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.26
Consensus pattern (86 bp):
GGCGTTTTTGGAAAAAACGCCACTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGGAAAAGCGACG
CTAAAGGTCAAGGCTTTTAGC
Found at i:46875 original size:9 final size:9
Alignment explanation
Indices: 46861--47011 Score: 169
Period size: 9 Copynumber: 16.9 Consensus size: 9
46851 TGACAACATA
46861 TAAGTTATG
1 TAAGTTATG
*
46870 TAAGTTATA
1 TAAGTTATG
46879 TAAGTTATG
1 TAAGTTATG
46888 TAAGTTATG
1 TAAGTTATG
46897 TAAGTTATG
1 TAAGTTATG
**
46906 TAAGTTACA
1 TAAGTTATG
*
46915 TAACTTATG
1 TAAGTTATG
46924 TAAGTTATG
1 TAAGTTATG
* *
46933 TATGTTATA
1 TAAGTTATG
*
46942 TGAGTTATG
1 TAAGTTATG
*
46951 TAAGTTATA
1 TAAGTTATG
*
46960 TAAGTTATA
1 TAAGTTATG
* *
46969 T-ATTTATC
1 TAAGTTATG
*
46977 TAAGTTATA
1 TAAGTTATG
46986 TAAGTTATG
1 TAAGTTATG
* *
46995 TACGTTTTG
1 TAAGTTATG
47004 TAAGTTAT
1 TAAGTTAT
47012 ATAAATTATA
Statistics
Matches: 117, Mismatches: 24, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
8 6 0.05
9 111 0.95
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:46892 original size:27 final size:27
Alignment explanation
Indices: 46862--47021 Score: 196
Period size: 27 Copynumber: 6.0 Consensus size: 27
46852 GACAACATAT
*
46862 AAGTTATGTAAGTTATATAAGTTATGT
1 AAGTTATGTAAGTTATATAAGTTATAT
* *
46889 AAGTTATGTAAGTTATGTAAGTTACAT
1 AAGTTATGTAAGTTATATAAGTTATAT
* * *
46916 AACTTATGTAAGTTATGTATGTTATAT
1 AAGTTATGTAAGTTATATAAGTTATAT
*
46943 GAGTTATGTAAGTTATATAAGTTATAT
1 AAGTTATGTAAGTTATATAAGTTATAT
* * *
46970 -ATTTATCTAAGTTATATAAGTTATGT
1 AAGTTATGTAAGTTATATAAGTTATAT
* * *
46996 ACGTTTTGTAAGTTATATAAATTATA
1 AAGTTATGTAAGTTATATAAGTTATA
47022 ATATCAAATA
Statistics
Matches: 113, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
26 23 0.20
27 90 0.80
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.46
Consensus pattern (27 bp):
AAGTTATGTAAGTTATATAAGTTATAT
Found at i:47146 original size:15 final size:15
Alignment explanation
Indices: 47126--47181 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
47116 AAGTAGCGGG
47126 ATTAAATAATATTTA
1 ATTAAATAATATTTA
47141 ATTAAATAATATTT-
1 ATTAAATAATATTTA
47155 A-TAAA-AATTATTTTA
1 ATTAAATAA-TA-TTTA
*
47170 ATTAAGTAATAT
1 ATTAAATAATAT
47182 ACATGTCATT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.46
16 5 0.14
17 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:47906 original size:290 final size:290
Alignment explanation
Indices: 47386--48393 Score: 2016
Period size: 290 Copynumber: 3.5 Consensus size: 290
47376 TTGTGATAAA
47386 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGGGTTGTTACACCTAGGGAGGATCCATTA
1 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGGGTTGTTACACCTAGGGAGGATCCATTA
47451 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
66 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
47516 TATTTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATAATATCA
131 TATTTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATAATATCA
47581 AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAATGTTATATAAATATTCA
196 AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAATGTTATATAAATATTCA
47646 ATAGTAAATGAGCTCGATAGAACTTTTTTC
261 ATAGTAAATGAGCTCGATAGAACTTTTTTC
47676 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGGGTTGTTACACCTAGGGAGGATCCATTA
1 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGGGTTGTTACACCTAGGGAGGATCCATTA
47741 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
66 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
47806 TATTTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATAATATCA
131 TATTTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATAATATCA
47871 AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAATGTTATATAAATATTCA
196 AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAATGTTATATAAATATTCA
47936 ATAGTAAATGAGCTCGATAGAACTTTTTTC
261 ATAGTAAATGAGCTCGATAGAACTTTTTTC
47966 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGGGTTGTTACACCTAGGGAGGATCCATTA
1 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGGGTTGTTACACCTAGGGAGGATCCATTA
48031 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
66 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
48096 TATTTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATAATATCA
131 TATTTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATAATATCA
48161 AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAATGTTATATAAATATTCA
196 AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAATGTTATATAAATATTCA
48226 ATAGTAAATGAGCTCGATAGAACTTTTTTC
261 ATAGTAAATGAGCTCGATAGAACTTTTTTC
48256 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGGGTTGTTACACCTAGGGAGGATCCATTA
1 AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGGGTTGTTACACCTAGGGAGGATCCATTA
48321 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
66 TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
48386 TATTTAAA
131 TATTTAAA
48394 ATAAGGTTGG
Statistics
Matches: 718, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
290 718 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.37
Consensus pattern (290 bp):
AAGTCTTTTTGAATTTTTTAAGATTCATCATACGTGGGGTTGTTACACCTAGGGAGGATCCATTA
TATCTTGCAGCTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAA
TATTTAAATATTAAAATCAAACATTATTAATATAAAAAAATAGTAATTTGAATATAATAATATCA
AAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATTAATGTTATATAAATATTCA
ATAGTAAATGAGCTCGATAGAACTTTTTTC
Found at i:50497 original size:62 final size:61
Alignment explanation
Indices: 50339--50519 Score: 353
Period size: 61 Copynumber: 3.0 Consensus size: 61
50329 ACAAACTAGT
50339 TTTTCCATTTCAGAACAAAAAATCCAAACAACAGACATAAAACTGACAAAAAAGAAATGAA
1 TTTTCCATTTCAGAACAAAAAATCCAAACAACAGACATAAAACTGACAAAAAAGAAATGAA
50400 TTTTCCATTTCAGAACAAAAAATCCAAACAACAGACATAAAACTGACAAAAAAGAAATGAA
1 TTTTCCATTTCAGAACAAAAAATCCAAACAACAGACATAAAACTGACAAAAAAGAAATGAA
50461 TTTTCCATTTCAGAACAAAAATATCCAAACAACAGACATAAAACTGACAAAAAAGAAAT
1 TTTTCCATTTCAGAACAAAAA-ATCCAAACAACAGACATAAAACTGACAAAAAAGAAAT
50520 CAAATTTTGG
Statistics
Matches: 119, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
61 82 0.69
62 37 0.31
ACGTcount: A:0.55, C:0.18, G:0.08, T:0.19
Consensus pattern (61 bp):
TTTTCCATTTCAGAACAAAAAATCCAAACAACAGACATAAAACTGACAAAAAAGAAATGAA
Found at i:52884 original size:26 final size:25
Alignment explanation
Indices: 52855--52904 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
52845 GAATTAATCA
52855 TAAACCTTCAAATAC-TAGTTAACTCC
1 TAAACCTT-AAA-ACATAGTTAACTCC
*
52881 TAAACCTTAAACCATAGTTAACTC
1 TAAACCTTAAAACATAGTTAACTC
52905 ATAATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 13 0.59
26 8 0.36
ACGTcount: A:0.40, C:0.26, G:0.04, T:0.30
Consensus pattern (25 bp):
TAAACCTTAAAACATAGTTAACTCC
Found at i:52939 original size:14 final size:14
Alignment explanation
Indices: 52922--52961 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
52912 ATTAAACATG
* *
52922 CTTAAACCATATAT
1 CTTAAACCATAAAC
52936 CTTAAACCATAAAC
1 CTTAAACCATAAAC
*
52950 CTTAAACTATAA
1 CTTAAACCATAA
52962 TGATAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (14 bp):
CTTAAACCATAAAC
Found at i:53174 original size:41 final size:41
Alignment explanation
Indices: 53117--53295 Score: 254
Period size: 41 Copynumber: 4.4 Consensus size: 41
53107 GGTTATGAGA
53117 TTTTTAGCGGCGTTTTACGAAAAGCGCAGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTTACGAAAAGCGCAGCTAATGCTCTGG
* * *
53158 TTTTTTGCGGCATTTTAGGAAAAGCG-ACGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTTACGAAAAGCGCA-GCTAATGCTCTGG
* *
53199 TTTTTAGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTAG
1 TTTTTAGCGGCGTTTTACGAAAAGCGCAGCTAATGCTCTGG
* * *
53240 TTTTTTGCGGCGTTTTAGGAAAAGCGCCGCTAATGCTCTGG
1 TTTTTAGCGGCGTTTTACGAAAAGCGCAGCTAATGCTCTGG
*
53281 -TTTTAGCGGCATTTT
1 TTTTTAGCGGCGTTTT
53296 TTTAGAACGC
Statistics
Matches: 123, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
40 14 0.11
41 109 0.89
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (41 bp):
TTTTTAGCGGCGTTTTACGAAAAGCGCAGCTAATGCTCTGG
Found at i:53211 original size:82 final size:82
Alignment explanation
Indices: 53117--53295 Score: 306
Period size: 82 Copynumber: 2.2 Consensus size: 82
53107 GGTTATGAGA
*
53117 TTTTTAGCGGCGTTTTACGAAAAGCGCAGCTAATGCTCTGGTTTTTTGCGGCATTTTAGGAAAAG
1 TTTTTAGCGGCGTTTTACGAAAAGCGCAGCTAATGCTCTAGTTTTTTGCGGCATTTTAGGAAAAG
53182 CGACGCTAATGCTCTGG
66 CGACGCTAATGCTCTGG
* *
53199 TTTTTAGCGGCGTTTTACGAAAAGCGCCGCTAATGCTCTAGTTTTTTGCGGCGTTTTAGGAAAAG
1 TTTTTAGCGGCGTTTTACGAAAAGCGCAGCTAATGCTCTAGTTTTTTGCGGCATTTTAGGAAAAG
*
53264 CGCCGCTAATGCTCTGG
66 CGACGCTAATGCTCTGG
*
53281 -TTTTAGCGGCATTTT
1 TTTTTAGCGGCGTTTT
53296 TTTAGAACGC
Statistics
Matches: 92, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
81 14 0.15
82 78 0.85
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (82 bp):
TTTTTAGCGGCGTTTTACGAAAAGCGCAGCTAATGCTCTAGTTTTTTGCGGCATTTTAGGAAAAG
CGACGCTAATGCTCTGG
Done.