Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold589
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: 93502
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1299 original size:19 final size:21
Alignment explanation
Indices: 1269--1307 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1259 ATTGGATTTT
1269 ATTTTGTTATTTT-GTTTTGC
1 ATTTTGTTATTTTAGTTTTGC
1289 ATTTT-TTATTTTAGTTTTG
1 ATTTTGTTATTTTAGTTTTG
1308 GTATGGGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.13, C:0.03, G:0.13, T:0.72
Consensus pattern (21 bp):
ATTTTGTTATTTTAGTTTTGC
Found at i:2157 original size:27 final size:30
Alignment explanation
Indices: 2104--2166 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
2094 TAACATCATT
* *
2104 TTATATTTATATATTATGTACACAAA-TAA
1 TTATATTTATATAATATATACACAAATTAA
2133 TTATATTTATATAATATATA-A-AAATTAA
1 TTATATTTATATAATATATACACAAATTAA
2161 -TATATT
1 TTATATT
2167 ATTTTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 9 0.29
28 4 0.13
29 18 0.58
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (30 bp):
TTATATTTATATAATATATACACAAATTAA
Found at i:5040 original size:6 final size:6
Alignment explanation
Indices: 5022--5058 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
5012 ATTTAAAATA
5022 ATAATT ATAAATT ATAATT AT-A-T ATAATT ATAATT AT
1 ATAATT AT-AATT ATAATT ATAATT ATAATT ATAATT AT
5059 CACAACTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
4 3 0.11
5 2 0.07
6 17 0.61
7 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
ATAATT
Found at i:5050 original size:16 final size:15
Alignment explanation
Indices: 5027--5058 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
5017 AAATAATAAT
5027 TATAAATTATAATTA
1 TATAAATTATAATTA
5042 TATATAATTATAATTA
1 TATA-AATTATAATTA
5058 T
1 T
5059 CACAACTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATAAATTATAATTA
Found at i:12184 original size:19 final size:20
Alignment explanation
Indices: 12154--12192 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
12144 GTTTTGTATC
*
12154 CATTTCATTCATTTGCATTA
1 CATTTCATTCATATGCATTA
12174 CATTTCA-TCATATGCATTA
1 CATTTCATTCATATGCATTA
12193 AGTTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.46
Consensus pattern (20 bp):
CATTTCATTCATATGCATTA
Found at i:21754 original size:44 final size:44
Alignment explanation
Indices: 21688--21799 Score: 138
Period size: 44 Copynumber: 2.5 Consensus size: 44
21678 GCTATGAATT
*
21688 ACAAACCTTATCTCCCTGAAGTTGCAGTGGAGC-AGATT-AGAGCG
1 ACAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAAG-TTGA-AGCG
* * **
21732 ACAAACCTTATCTCCCTAAAGTTTCAGTGTAGCAAGTTGAAGTT
1 ACAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAAGTTGAAGCG
*
21776 ACAAATCTTATCTCCCTAAAGTTG
1 ACAAACCTTATCTCCCTAAAGTTG
21800 TAATGCAGTA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
44 56 0.95
45 3 0.05
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (44 bp):
ACAAACCTTATCTCCCTAAAGTTGCAGTGGAGCAAGTTGAAGCG
Found at i:21990 original size:44 final size:44
Alignment explanation
Indices: 21897--21993 Score: 115
Period size: 44 Copynumber: 2.2 Consensus size: 44
21887 TAGAGTGGAG
* * * * *
21897 CAGTGGAGCAGATTGAAGCTACAAGTCTCATCTCCCTGAAGTTG
1 CAGTGGAGTAGATTGAAGCTACAAATCTCATCTCCCTAAAATTA
*
21941 CAGTGGAGTAGA-TGAAAGCTACAAATCTTATCTCCCTAAAATTA
1 CAGTGGAGTAGATTG-AAGCTACAAATCTCATCTCCCTAAAATTA
*
21985 TAGTGGAGT
1 CAGTGGAGT
21994 GGATCAAAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 2 0.04
44 43 0.96
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (44 bp):
CAGTGGAGTAGATTGAAGCTACAAATCTCATCTCCCTAAAATTA
Found at i:22033 original size:44 final size:44
Alignment explanation
Indices: 21926--22034 Score: 112
Period size: 44 Copynumber: 2.5 Consensus size: 44
21916 TACAAGTCTC
* * * * *
21926 ATCTCCCTGAAGTTGCAGTGGAGTAGATGAAAGCTACAAATCTT
1 ATCTCCCTGAAGTTGTAGTGGAGTAGATCAAAACAACAAATCCT
* * * * *
21970 ATCTCCCTAAAATTATAGTGGAGTGGATCAAAACAACAATTCCT
1 ATCTCCCTGAAGTTGTAGTGGAGTAGATCAAAACAACAAATCCT
22014 ATAC-CCCTGAAGTTGTAGTGG
1 AT-CTCCCTGAAGTTGTAGTGG
22035 GTTAGGACGA
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
44 50 0.98
45 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (44 bp):
ATCTCCCTGAAGTTGTAGTGGAGTAGATCAAAACAACAAATCCT
Found at i:22933 original size:16 final size:16
Alignment explanation
Indices: 22914--22951 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
22904 ACCGTATACG
22914 GTGGCCACCGACGCCA
1 GTGGCCACCGACGCCA
22930 GTGGCCACCGACGCCA
1 GTGGCCACCGACGCCA
22946 GTGGCC
1 GTGGCC
22952 GGCGGCCAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.16, C:0.42, G:0.34, T:0.08
Consensus pattern (16 bp):
GTGGCCACCGACGCCA
Found at i:25279 original size:27 final size:27
Alignment explanation
Indices: 25249--25304 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
25239 CAACTTATTG
*
25249 TTTTTTTTTTAATT-TTAATAGAACAAC
1 TTTTTTTTTT-ATTCCTAATAGAACAAC
25276 TTTTTTTTTTATTCCTAATAGAACAAC
1 TTTTTTTTTTATTCCTAATAGAACAAC
25303 TT
1 TT
25305 ATTGTTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.55
Consensus pattern (27 bp):
TTTTTTTTTTATTCCTAATAGAACAAC
Found at i:26753 original size:15 final size:16
Alignment explanation
Indices: 26733--26763 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
26723 TCTCAAAAAG
26733 ATATAAA-TTTCCAAA
1 ATATAAAGTTTCCAAA
26748 ATATAAAGTTTCCAAA
1 ATATAAAGTTTCCAAA
26764 TAATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.52, C:0.13, G:0.03, T:0.32
Consensus pattern (16 bp):
ATATAAAGTTTCCAAA
Found at i:27212 original size:22 final size:22
Alignment explanation
Indices: 27184--27229 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
27174 TGAACTCAAA
27184 AATTTATAAACGAATTTAGTTG
1 AATTTATAAACGAATTTAGTTG
27206 AATTTATAAACGAATTTAGTTG
1 AATTTATAAACGAATTTAGTTG
27228 AA
1 AA
27230 CTCAAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (22 bp):
AATTTATAAACGAATTTAGTTG
Found at i:29698 original size:4 final size:4
Alignment explanation
Indices: 29689--29722 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
29679 CATGAAAGTT
* *
29689 TTTA TTTA TTTA TTTG TTTA TTTA TTTA GTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
29723 CATTGATTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:29801 original size:3 final size:3
Alignment explanation
Indices: 29793--29833 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
29783 GCACATTTTG
* * *
29793 TTA TTA TTA TTA TTC TCA TTA TTA TTA TTG TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
29834 TATTTTTCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:32641 original size:35 final size:35
Alignment explanation
Indices: 32601--32672 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 35
32591 CTATTAAATA
*** *
32601 ATTTAATTTTTTGTTGACTCCGTTAAGAGAGAATG
1 ATTTAATTTTTTGCCAACTCCATTAAGAGAGAATG
*
32636 ATTTAATTTTTTGCCAACTCCATTAAGAGATAATG
1 ATTTAATTTTTTGCCAACTCCATTAAGAGAGAATG
32671 AT
1 AT
32673 GTGGCATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (35 bp):
ATTTAATTTTTTGCCAACTCCATTAAGAGAGAATG
Found at i:35152 original size:3 final size:3
Alignment explanation
Indices: 35144--35170 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
35134 ATTAAATGGA
35144 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
35171 GATGCTGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:36917 original size:2 final size:2
Alignment explanation
Indices: 36910--36938 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36900 AACTGAGAAA
36910 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
36939 TTAATGGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42532 original size:16 final size:17
Alignment explanation
Indices: 42500--42533 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42490 TCATGTTAAA
42500 AAATTATAAACATTTAT
1 AAATTATAAACATTTAT
*
42517 AAATTTTAAA-ATTTAT
1 AAATTATAAACATTTAT
42533 A
1 A
42534 TTGATTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTATAAACATTTAT
Found at i:45281 original size:34 final size:34
Alignment explanation
Indices: 45243--45311 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
45233 ATTTGGCCAC
45243 TAAGCGCGCCTTATACTTGTCAACTTCTCCATTT
1 TAAGCGCGCCTTATACTTGTCAACTTCTCCATTT
*
45277 TAAGCGCGCCTTATACTTGTCAACTTCTCTATTT
1 TAAGCGCGCCTTATACTTGTCAACTTCTCCATTT
45311 T
1 T
45312 CCTTCGACTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.20, C:0.28, G:0.12, T:0.41
Consensus pattern (34 bp):
TAAGCGCGCCTTATACTTGTCAACTTCTCCATTT
Found at i:48039 original size:13 final size:13
Alignment explanation
Indices: 48023--48053 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
48013 GCACATGGGT
48023 GTGTCACACGAGC
1 GTGTCACACGAGC
48036 GTGTCACACGAGC
1 GTGTCACACGAGC
*
48049 ATGTC
1 GTGTC
48054 CCTACCGAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.29, G:0.29, T:0.19
Consensus pattern (13 bp):
GTGTCACACGAGC
Found at i:48420 original size:32 final size:32
Alignment explanation
Indices: 48384--48449 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
48374 TTGTTATTAT
48384 TTTCTGAATCGTATGATAAATATTTAAACTTG
1 TTTCTGAATCGTATGATAAATATTTAAACTTG
48416 TTTCTGAATCGTATGATAAATATTTAAACTTG
1 TTTCTGAATCGTATGATAAATATTTAAACTTG
48448 TT
1 TT
48450 CTTAATTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (32 bp):
TTTCTGAATCGTATGATAAATATTTAAACTTG
Found at i:50200 original size:62 final size:62
Alignment explanation
Indices: 50116--50315 Score: 256
Period size: 62 Copynumber: 3.2 Consensus size: 62
50106 GCCCAGACTG
* * * * *
50116 TGTAACTCACTGTTCATGGTATAAAACCACATAGCCAGGAACATAGGCTTGTGCCCAAGCCA
1 TGTAACTCACTGTTCATGGTATAAAACCACACAGCCAGGGACACAGGCGTGTGCCCAGGCCA
* * * * * * *
50178 TGCAACTTACTGTTCATGGTATAAAACTACACAGTCAGGGACACGGGCGTGTGCCTAGGCCG
1 TGTAACTCACTGTTCATGGTATAAAACCACACAGCCAGGGACACAGGCGTGTGCCCAGGCCA
* *
50240 TGTAACTCACTGTTCATAGTATAAAACCACACGGCCAGGGACACAGGCGTGTGCCCAGGCCA
1 TGTAACTCACTGTTCATGGTATAAAACCACACAGCCAGGGACACAGGCGTGTGCCCAGGCCA
* *
50302 TGTGACTTACTGTT
1 TGTAACTCACTGTT
50316 GATACTTAAA
Statistics
Matches: 115, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
62 115 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (62 bp):
TGTAACTCACTGTTCATGGTATAAAACCACACAGCCAGGGACACAGGCGTGTGCCCAGGCCA
Found at i:50270 original size:124 final size:125
Alignment explanation
Indices: 50093--50359 Score: 340
Period size: 124 Copynumber: 2.1 Consensus size: 125
50083 GGTATAAACC
* * * * *
50093 CACACGGGCATGTGCCCAGACTGTGTAACTCACTGTTCATGGTATAAAACCACATAGCCAGGAAC
1 CACACGGGCGTGTGCCTAGACCGTGTAACTCACTGTTCATAGTATAAAACCACACAGCCAGGAAC
* * **
50158 ATAGGCTTGTGCCCAAGCCATGCAACTTACTGTTCATGGTATAAAA-CTACACAGTC-AGG
66 ACAGGCGTGTGCCCAAGCCATGCAACTTACTGTTCATACT-TAAAATCTACACAGTCAAGG
* * * *
50217 GACACGGGCGTGTGCCTAGGCCGTGTAACTCACTGTTCATAGTATAAAACCACACGGCCAGGGAC
1 CACACGGGCGTGTGCCTAGACCGTGTAACTCACTGTTCATAGTATAAAACCACACAGCCAGGAAC
* ** *
50282 ACAGGCGTGTGCCCAGGCCATGTGACTTACTGTTGATACTTAAAATCTACACAGTCAAGG
66 ACAGGCGTGTGCCCAAGCCATGCAACTTACTGTTCATACTTAAAATCTACACAGTCAAGG
* *
50342 CACATGGGTGTGTGCCTA
1 CACACGGGCGTGTGCCTA
50360 AGTCATGTGG
Statistics
Matches: 121, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
123 5 0.04
124 98 0.81
125 18 0.15
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.22
Consensus pattern (125 bp):
CACACGGGCGTGTGCCTAGACCGTGTAACTCACTGTTCATAGTATAAAACCACACAGCCAGGAAC
ACAGGCGTGTGCCCAAGCCATGCAACTTACTGTTCATACTTAAAATCTACACAGTCAAGG
Found at i:54661 original size:17 final size:17
Alignment explanation
Indices: 54632--54669 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
54622 AAATAAGGAA
54632 AACAATCCAATTTTATT
1 AACAATCCAATTTTATT
54649 AACAA-CCAGATTTTATT
1 AACAATCCA-ATTTTATT
54666 AACA
1 AACA
54670 TAGGCATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (17 bp):
AACAATCCAATTTTATT
Found at i:55174 original size:7 final size:7
Alignment explanation
Indices: 55164--55206 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
55154 CCCAATACCC
55164 AAAACAA
1 AAAACAA
55171 AAAACAA
1 AAAACAA
55178 AAAACAA
1 AAAACAA
55185 AAAA-AA
1 AAAACAA
*
55191 AAGA-AA
1 AAAACAA
*
55197 AAAAGAA
1 AAAACAA
55204 AAA
1 AAA
55207 GAAACCCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 10 0.30
7 23 0.70
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (7 bp):
AAAACAA
Found at i:55206 original size:18 final size:18
Alignment explanation
Indices: 55163--55199 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
55153 GCCCAATACC
55163 CAAAACAAAAAACAAAAAA
1 CAAAA-AAAAAACAAAAAA
*
55182 CAAAAAAAAAAGAAAAAA
1 CAAAAAAAAAACAAAAAA
55200 AGAAAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (18 bp):
CAAAAAAAAAACAAAAAA
Found at i:55207 original size:14 final size:13
Alignment explanation
Indices: 55164--55210 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
55154 CCCAATACCC
* *
55164 AAAACAAAAAACA
1 AAAAGAAAAAAAA
*
55177 AAAA-ACAAAAAA
1 AAAAGAAAAAAAA
55189 AAAAGAAAAAAAGA
1 AAAAGAAAAAAA-A
55203 AAAAGAAA
1 AAAAGAAA
55211 CCCTTAATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 10 0.34
13 10 0.34
14 9 0.31
ACGTcount: A:0.87, C:0.06, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAA
Found at i:55467 original size:24 final size:25
Alignment explanation
Indices: 55440--55492 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
55430 TATTTTGGAG
55440 AGAAAAGA-TTTTTTTTGAGATTCA
1 AGAAAAGATTTTTTTTTGAGATTCA
*
55464 AGAAGAGATTTTTTTTTTGAGATTCA
1 AGAAAAGA-TTTTTTTTTGAGATTCA
55490 AGA
1 AGA
55493 GGGGATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 7 0.27
26 19 0.73
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.42
Consensus pattern (25 bp):
AGAAAAGATTTTTTTTTGAGATTCA
Found at i:55484 original size:26 final size:26
Alignment explanation
Indices: 55448--55508 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
55438 AGAGAAAAGA
55448 TTTTTTTTGAGATTCAAGAAGAGATT
1 TTTTTTTTGAGATTCAAGAAGAGATT
* *
55474 TTTTTTTTGAGATTCAAGAGGGGATT
1 TTTTTTTTGAGATTCAAGAAGAGATT
55500 TTTCTTTTT
1 TTT-TTTTT
55509 TTTTTGAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 27 0.84
27 5 0.16
ACGTcount: A:0.23, C:0.05, G:0.20, T:0.52
Consensus pattern (26 bp):
TTTTTTTTGAGATTCAAGAAGAGATT
Found at i:56243 original size:16 final size:15
Alignment explanation
Indices: 56212--56254 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
56202 CCTTCATTCC
*
56212 ATTATTATTATTACT
1 ATTATTATTTTTACT
56227 ATTATTATATTTTACT
1 ATTATTAT-TTTTACT
*
56243 ATCATTATTTTT
1 ATTATTATTTTT
56255 CATACGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTTTTACT
Found at i:56378 original size:16 final size:16
Alignment explanation
Indices: 56357--56388 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
56347 CTATTGTTAC
56357 TGTTATTATCATCACT
1 TGTTATTATCATCACT
*
56373 TGTTATTCTCATCACT
1 TGTTATTATCATCACT
56389 ATTATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.22, G:0.06, T:0.50
Consensus pattern (16 bp):
TGTTATTATCATCACT
Found at i:56396 original size:3 final size:3
Alignment explanation
Indices: 56388--56498 Score: 50
Period size: 3 Copynumber: 36.7 Consensus size: 3
56378 TTCTCATCAC
* * * *
56388 TAT TAT TAT AATT TAT CAT TGT TACT TAT TAT T-T TAC TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
56434 CTAA TA- TAT CAT CAT TAT CAT TAT T-T TCAT TAT AACT TAA TA- GAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA-T TAT TAT TAT
56479 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
56499 GCACTACTTT
Statistics
Matches: 81, Mismatches: 18, Indels: 18
0.69 0.15 0.15
Matches are distributed among these distances:
2 7 0.09
3 63 0.78
4 11 0.14
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:56542 original size:12 final size:13
Alignment explanation
Indices: 56507--56544 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
56497 TAGCACTACT
56507 TTTATTACTATTA
1 TTTATTACTATTA
*
56520 TTTAATA-TATTA
1 TTTATTACTATTA
56532 TTT-TTACTATTA
1 TTTATTACTATTA
56544 T
1 T
56545 CGTCATATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 2 0.09
12 14 0.64
13 6 0.27
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTATTACTATTA
Found at i:56620 original size:22 final size:22
Alignment explanation
Indices: 56590--56650 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
56580 TTATTATATC
*
56590 TTTTACTATTATTATTGTTGTA
1 TTTTACTATTATTATTGTTATA
* * *
56612 TTTTTCTATTATTGTTATTATA
1 TTTTACTATTATTATTGTTATA
* *
56634 TTTTCCT-TTATTTTTGT
1 TTTTACTATTATTATTGT
56651 ATTTACTTAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 8 0.25
22 24 0.75
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.69
Consensus pattern (22 bp):
TTTTACTATTATTATTGTTATA
Found at i:60643 original size:47 final size:47
Alignment explanation
Indices: 60584--60960 Score: 619
Period size: 47 Copynumber: 7.9 Consensus size: 47
60574 TAGTATGGCG
*
60584 TAATGACCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
*
60631 TAATGGCCGATGTGATGAATATGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
60678 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
*
60725 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
60774 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCC
60823 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
* *
60870 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCC
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
* * * * * *
60917 GAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
60961 TCCCGAAGGG
Statistics
Matches: 313, Mismatches: 15, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 219 0.70
49 94 0.30
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
TAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCC
Found at i:60941 original size:192 final size:188
Alignment explanation
Indices: 60584--60958 Score: 633
Period size: 192 Copynumber: 2.0 Consensus size: 188
60574 TAGTATGGCG
60584 TAATGACCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 TAATGACCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
60649 ATATGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
66 ATATGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
* * * *
60714 GTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAGGGCC
131 GTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATA-A-ATGTGATAGGGCC
*
60774 TAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 TAATGACCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
*
60839 GAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
64 GAATATGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
* * *
60904 ATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATA
129 ATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGATA
60959 AGTCCCGAAG
Statistics
Matches: 174, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
190 36 0.21
191 1 0.01
192 137 0.79
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (188 bp):
TAATGACCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
ATATGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
GTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGATAGGGCC
Found at i:61136 original size:37 final size:37
Alignment explanation
Indices: 61079--61157 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
61069 CTGAGCTCTA
* * * *
61079 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
**
61116 AAGACCCGATAACTTTGTGTGGAGATTATGTCCAGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
61153 AAGAC
1 AAGAC
61158 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCAGGT
Found at i:64153 original size:15 final size:15
Alignment explanation
Indices: 64133--64163 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
64123 TTTACTTTCC
64133 AGAGAGGTAGAAAAG
1 AGAGAGGTAGAAAAG
64148 AGAGAGGTAGAAAAG
1 AGAGAGGTAGAAAAG
64163 A
1 A
64164 AAATCTGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.39, T:0.06
Consensus pattern (15 bp):
AGAGAGGTAGAAAAG
Found at i:67921 original size:31 final size:30
Alignment explanation
Indices: 67881--67957 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
67871 TTGTTTGATT
*
67881 TATAACTAAAATT-TTAATATTCAAAAAATA
1 TATAACTAAAATTGATAA-ATTCAAAAAATA
*
67911 TATAGACTAAAATTGATAAATTCAAATAATA
1 TATA-ACTAAAATTGATAAATTCAAAAAATA
* *
67942 TAAATATTAAAATTGA
1 TATA-ACTAAAATTGA
67958 CCAAAATTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
30 4 0.10
31 33 0.82
32 3 0.08
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (30 bp):
TATAACTAAAATTGATAAATTCAAAAAATA
Found at i:70310 original size:29 final size:27
Alignment explanation
Indices: 70278--70341 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
70268 TCTTAAATGA
*
70278 TTTAATTTTACTACTAAACTTTAAACTTT
1 TTTAATTTTACAACT-AAC-TTAAACTTT
* * *
70307 TTTAAATTTTGCAACTAACTTCAATTTT
1 TTT-AATTTTACAACTAACTTAAACTTT
70335 TTTAATT
1 TTTAATT
70342 AACGTTTACG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 4 0.13
28 10 0.33
29 6 0.20
30 10 0.33
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (27 bp):
TTTAATTTTACAACTAACTTAAACTTT
Found at i:75592 original size:21 final size:21
Alignment explanation
Indices: 75568--75609 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
75558 TCATTTTACT
75568 TTAAAAAAGGG-TCAAAAAGGG
1 TTAAAAAAGGGCT-AAAAAGGG
*
75589 TTAAAAAATGGCTAAAAAGGG
1 TTAAAAAAGGGCTAAAAAGGG
75610 CTTCTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.52, C:0.05, G:0.26, T:0.17
Consensus pattern (21 bp):
TTAAAAAAGGGCTAAAAAGGG
Found at i:79063 original size:13 final size:14
Alignment explanation
Indices: 79032--79063 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
79022 TATTTCTATT
*
79032 TTTTTTCCTTTTAA
1 TTTTTTCCTTGTAA
79046 TTTTTTCCTTGTAA
1 TTTTTTCCTTGTAA
79060 TTTT
1 TTTT
79064 ACTTTCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTTTTCCTTGTAA
Found at i:79447 original size:27 final size:24
Alignment explanation
Indices: 79394--79463 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 24
79384 ATATTTTTCA
79394 TATT-TTTCATTTTATTATTATTAT
1 TATTATTTCATTTT-TTATTATTAT
79418 TATTATTTCATTTTTTATCTATTCATT
1 TATTATTTCATTTTTTAT-TATT-A-T
*
79445 TATCTATCT-ATTTTTTATT
1 TAT-TATTTCATTTTTTATT
79464 TTTTATATAC
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
24 8 0.20
25 13 0.32
26 2 0.05
27 13 0.32
28 4 0.10
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.69
Consensus pattern (24 bp):
TATTATTTCATTTTTTATTATTAT
Found at i:81319 original size:79 final size:82
Alignment explanation
Indices: 81208--81392 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
81198 GCTACTCGTT
* *
81208 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
81271 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
81288 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
81351 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
81368 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
81393 CATCATTCGA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:81392 original size:40 final size:40
Alignment explanation
Indices: 81189--81392 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
81179 CGGAATTTAA
** *
81189 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
81229 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
81269 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
81308 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
81348 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
81388 CCGGA
1 CCGGA
81393 CATCATTCGA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:82586 original size:56 final size:56
Alignment explanation
Indices: 82519--82638 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
82509 TATTAGTTTA
82519 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
82575 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
82631 TTGCCCAT
1 TTGCCCAT
82639 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:89122 original size:40 final size:40
Alignment explanation
Indices: 89085--89266 Score: 217
Period size: 40 Copynumber: 4.5 Consensus size: 40
89075 GCTACTCGTT
*
89085 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
89125 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
89165 CAAATGCCTGCGGGACTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
89205 CAAATGCCTT-TGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
89246 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
89267 GGACATCATT
Statistics
Matches: 121, Mismatches: 17, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
39 3 0.02
40 105 0.87
41 13 0.11
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:90459 original size:54 final size:55
Alignment explanation
Indices: 90395--90511 Score: 202
Period size: 55 Copynumber: 2.1 Consensus size: 55
90385 TATTAGTTTA
90395 TTGCCCATGCTTCTTATTTTATTCTTCCATT-A-ACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTA-TTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
90449 TTGCCCATGCTTCTTATTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
90504 TTGCCCAT
1 TTGCCCAT
90512 CATCCCTTGT
Statistics
Matches: 60, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
53 13 0.22
54 17 0.28
55 30 0.50
ACGTcount: A:0.22, C:0.23, G:0.09, T:0.45
Consensus pattern (55 bp):
TTGCCCATGCTTCTTATTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Done.