Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_715
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: 49580
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7321 original size:47 final size:45
Alignment explanation
Indices: 7211--7378 Score: 160
Period size: 46 Copynumber: 3.6 Consensus size: 45
7201 ACTTGTGTGA
* *
7211 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTGTGA-GAG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGG---CATTGAGACTAG
* * *
7258 CCTA-TATAAGACCATGTTTGGGACATGGCATCGGCATTGAGACTAG
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGACTAG
* * * * *
7304 TGCTAGTGTAAGACATGTCTGGGACATGCTTCGACCTCGAGACATAA
1 -GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGAC-TAG
*
7351 GCCAGTGTAAGACATGTCTGGGACATGC
1 GCTAGTGTAAGACATGTCTGGGACATGC
7379 TGTGACAGCC
Statistics
Matches: 101, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
45 7 0.07
46 47 0.47
47 34 0.34
48 13 0.13
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (45 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACTAG
Found at i:9094 original size:27 final size:27
Alignment explanation
Indices: 9063--9240 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
9053 TAAATTGTAC
*
9063 AGCACTAAGTGTGCGATTTAACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
9090 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
9116 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
9144 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
9172 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
9199 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
9226 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
9241 GACTCAATAT
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 105 0.82
28 23 0.18
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:9180 original size:82 final size:81
Alignment explanation
Indices: 9064--9219 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
9054 AAATTGTACA
* *
9064 GCACTAAGTGTGCGATTTAACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
9128 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
9145 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
9210 TGCGAGTTGA
65 TGCGAATTGA
9220 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTAACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:9231 original size:82 final size:81
Alignment explanation
Indices: 9060--9240 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
9050 GATTAAATTG
* *
9060 TACAGCACTAAGTGTGCGATTTAACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
9125 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
9141 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTAACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
9205 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
9223 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
9241 GACTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTAACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:15882 original size:41 final size:41
Alignment explanation
Indices: 15638--15883 Score: 316
Period size: 41 Copynumber: 6.0 Consensus size: 41
15628 GTAAAACACA
* * *
15638 GAGCAATAGCGGCGTTTTTGGTAAAACGCCGCTAAAA-ACA
1 GAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCG
* * *
15678 GAGCAATAGCGGCGTTTTTTGGTAAAACGCCGCTAAAA-ACA
1 GAGCAATAGCGGCG-CTTTTGGTAAAACGCCGCTAAAAGTCG
* * *
15719 GAGCAATAGCGGCGTTTTTTTGTTAAAACGCCGCTAGAAGTCG
1 GAGCAATAGCGGCG--CTTTTGGTAAAACGCCGCTAAAAGTCG
* *
15762 GGGCAATAGCGGCACTTTTGGTAAAACGCCGCTAAAAGTCG
1 GAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCG
* * *
15803 GGGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTTG
1 GAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCG
*
15844 GAGCACTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTC
1 GAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTC
15884 ATATAACCCC
Statistics
Matches: 188, Mismatches: 15, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
40 14 0.07
41 139 0.74
42 22 0.12
43 13 0.07
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (41 bp):
GAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAGTCG
Found at i:15963 original size:37 final size:37
Alignment explanation
Indices: 15921--15992 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
15911 AAAAATCATG
* * *
15921 AACACTAATCTATAACTCCTAAAATACTAAACCCCTA
1 AACACTAAACCATAACTCCTAAAACACTAAACCCCTA
* *
15958 AACACTAAACCATAACTTCTAAAACCCTAAACCCC
1 AACACTAAACCATAACTCCTAAAACACTAAACCCC
15993 AAAAAACGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (37 bp):
AACACTAAACCATAACTCCTAAAACACTAAACCCCTA
Found at i:16115 original size:7 final size:7
Alignment explanation
Indices: 16103--16166 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
16093 TTTATTTTTT
*
16103 GGTTTAC
1 GGTTTAA
16110 GGTTTAA
1 GGTTTAA
**
16117 TATTTAA
1 GGTTTAA
16124 GGTTTAA
1 GGTTTAA
* *
16131 GGTCTAT
1 GGTTTAA
*
16138 GGTTTAG
1 GGTTTAA
*
16145 GGTTTTAT
1 GG-TTTAA
16153 GGTTTAA
1 GGTTTAA
16160 GGTTTAA
1 GGTTTAA
16167 TGGCCATGGG
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
7 39 0.87
8 6 0.13
ACGTcount: A:0.23, C:0.03, G:0.27, T:0.47
Consensus pattern (7 bp):
GGTTTAA
Found at i:16155 original size:15 final size:15
Alignment explanation
Indices: 16119--16169 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
16109 CGGTTTAATA
*
16119 TTTAAGGTTTAAGG-
1 TTTATGGTTTAAGGT
* *
16133 TCTATGGTTTAGGGT
1 TTTATGGTTTAAGGT
16148 TTTATGGTTTAAGGT
1 TTTATGGTTTAAGGT
*
16163 TTAATGG
1 TTTATGG
16170 CCATGGGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (15 bp):
TTTATGGTTTAAGGT
Found at i:16772 original size:8 final size:8
Alignment explanation
Indices: 16759--16810 Score: 51
Period size: 8 Copynumber: 7.1 Consensus size: 8
16749 AAATAAACTC
16759 AAAATTTA
1 AAAATTTA
16767 AAAATTT-
1 AAAATTTA
*
16774 AAAAGTT-
1 AAAATTTA
16781 AAAATTTA
1 AAAATTTA
16789 AAAA---A
1 AAAATTTA
*
16794 AAAACTTA
1 AAAATTTA
16802 AAAATTTA
1 AAAATTTA
16810 A
1 A
16811 TATTTAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
5 5 0.14
7 12 0.32
8 20 0.54
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AAAATTTA
Found at i:19338 original size:40 final size:40
Alignment explanation
Indices: 19284--19508 Score: 238
Period size: 40 Copynumber: 5.6 Consensus size: 40
19274 CTTGCGCAAG
* * * *
19284 GCCTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
* *
19324 GCCTTCTGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
** * * *
19364 GCCTTCGGGTTTTAGCTCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
* * * * *
19404 GCCATCGGGTCTTAGCCCGAATATAG-CAACTCGCACGAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * *
19444 GCCTTC-GGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCA-CTAGCACAAAT
19485 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
19509 CATTCGAATA
Statistics
Matches: 151, Mismatches: 29, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
39 3 0.02
40 118 0.78
41 27 0.18
42 3 0.02
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:19397 original size:80 final size:80
Alignment explanation
Indices: 19248--19508 Score: 260
Period size: 80 Copynumber: 3.3 Consensus size: 80
19238 CTCAAGTAAT
* * * * * * * * *
19248 CTTCGGGATTTAG-CCGGATATAACTACTTGCGC-AAGGCCTTCGGGTCTTAGCCCGGATGTGGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCTCGGATATAGT
*
19311 CACTAGCATAAATGC
66 CACTAGCACAAATGC
* * * *
19326 CTTCTGGACTTAGCCCGGATATAGTC-GCTAGCACAAATGCCTTCGGGTTTTAGCTCGGATATAA
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTCGGGTCTTAGCTCGGATATAG
*
19390 TCGCTAGCACAAATGC
65 TCACTAGCACAAATGC
* * * * * * *
19406 CATCGGGTCTTAGCCCGAATATAGCAACTCGCACGAATGCCTTCGGATCTTAG-TCCGGTTATAG
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCT-CGGATATAG
*
19470 TCACCTAGCACAAAAGC
65 TCA-CTAGCACAAATGC
19487 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
19509 CATTCGAATA
Statistics
Matches: 147, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
78 11 0.07
79 16 0.11
80 89 0.61
81 31 0.21
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCTCGGATATAGT
CACTAGCACAAATGC
Found at i:27509 original size:40 final size:40
Alignment explanation
Indices: 27464--27685 Score: 254
Period size: 40 Copynumber: 5.6 Consensus size: 40
27454 CTTGCGCAAG
* * *
27464 GCCTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
27504 GCCTTCGGGACTTAGCCC-GATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
27543 GCCTTCGGGTTTTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
27583 GCCTTC-GGTCTTAGCCCGGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
27622 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
* *
27663 G-CTTCGGGACTTAGCCTGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
27686 CATTCGAATA
Statistics
Matches: 153, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.01
39 65 0.42
40 77 0.50
41 10 0.07
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:27547 original size:39 final size:40
Alignment explanation
Indices: 27429--27685 Score: 242
Period size: 40 Copynumber: 6.5 Consensus size: 40
27419 CTCAAGTAAT
* * * * *
27429 CTTCGGGATTTAG-CCGGATATAAT-ACTTGCGC-AAGGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * * *
27466 CTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
27506 CTTCGGGACTTAGCCC-GATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
** * *
27545 CTTCGGGTTTTAGCCCGGATATAATCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* * *
27585 CTTC-GGTCTTAGCCCGGATATAG-CAACTCGCACGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
27624 CTTC-GGATCTTAGTCCGGTTATAGTCACCTAGCACAAAAG-
1 CTTCGGGA-CTTAGCCCGGATATAGTCA-CTAGCACAAATGC
*
27664 CTTCGGGACTTAGCCTGGATAT
1 CTTCGGGACTTAGCCCGGATAT
27686 CATTCGAATA
Statistics
Matches: 180, Mismatches: 31, Indels: 15
0.80 0.14 0.07
Matches are distributed among these distances:
37 11 0.06
38 9 0.05
39 72 0.40
40 75 0.42
41 13 0.07
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:27563 original size:79 final size:80
Alignment explanation
Indices: 27464--27685 Score: 263
Period size: 79 Copynumber: 2.8 Consensus size: 80
27454 CTTGCGCAAG
* * *
27464 GCCTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAATGCCTTCGGGACTTAGCCC-GATATA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
*
27528 GTC-GCTAGCACAAAT
66 G-CAACTAGCACAAAT
* * * *
27543 GCCTTCGGGTTTTAGCCCGGATATAATCGCTAGCACAAATGCCTTC-GGTCTTAGCCCGGATATA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
* *
27607 GCAACTCGCACGAAT
66 GCAACTAGCACAAAT
* * * * *
27622 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAAG-CTTCGGGACTTAGCCTGGATAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
27686 CATTCGAATA
Statistics
Matches: 120, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
78 11 0.09
79 83 0.69
80 26 0.22
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (80 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATA
GCAACTAGCACAAAT
Found at i:30278 original size:49 final size:51
Alignment explanation
Indices: 30153--30287 Score: 159
Period size: 49 Copynumber: 2.7 Consensus size: 51
30143 TCTATTGTGA
* *
30153 GGTCGCATGTGTAGTACTAAGTGCA-GCTACTATGCATACCCTATAACTTC
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCACACCCGATAACTTC
* * * * ** *
30203 GATCACGTGAGTAGTACTAAGTGCAGGCTACTATGTGCACCGGATAA-TT-
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCACACCCGATAACTTC
*
30252 GGTCGCATGTGTAGTACTATGTGCAGGCTACTATGC
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGC
30288 GTACCAGATA
Statistics
Matches: 69, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
49 30 0.43
50 23 0.33
51 16 0.23
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (51 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCACACCCGATAACTTC
Found at i:36345 original size:19 final size:18
Alignment explanation
Indices: 36321--36362 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
36311 CACACGGCTA
*
36321 AGGCCAAATTTGGGCTTGT
1 AGGCC-AATATGGGCTTGT
36340 AGGCC-ATATGGGCTTGT
1 AGGCCAATATGGGCTTGT
*
36357 GGGCCA
1 AGGCCA
36363 CATGGGTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 15 0.75
19 5 0.25
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.26
Consensus pattern (18 bp):
AGGCCAATATGGGCTTGT
Found at i:36351 original size:17 final size:17
Alignment explanation
Indices: 36331--36387 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
36321 AGGCCAAATT
*
36331 TGGGCTTGTAGGCCATA
1 TGGGCTTGTAGGCCACA
*
36348 TGGGCTTGTGGGCCACA
1 TGGGCTTGTAGGCCACA
*
36365 TGGG-TGTGTGAGCCCACA
1 TGGGCT-TGT-AGGCCACA
36383 TGGGC
1 TGGGC
36388 CCGCATTATG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 1 0.03
17 22 0.67
18 10 0.30
ACGTcount: A:0.14, C:0.21, G:0.40, T:0.25
Consensus pattern (17 bp):
TGGGCTTGTAGGCCACA
Found at i:40410 original size:26 final size:26
Alignment explanation
Indices: 40353--40426 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 26
40343 CCAAAATTGA
* *
40353 TAAATGACTATTTTTCCCTTATGTGG
1 TAAATGACTATTTTGCCCTTCTGTGG
40379 TAAAATGACTATTTTGCCCTTCTAG-GG
1 T-AAATGACTATTTTGCCCTTCT-GTGG
* *
40406 TAAATGACTGTTTGGCCCTTC
1 TAAATGACTATTTTGCCCTTC
40427 AATGACTGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.45
27 22 0.52
28 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.41
Consensus pattern (26 bp):
TAAATGACTATTTTGCCCTTCTGTGG
Found at i:47128 original size:42 final size:43
Alignment explanation
Indices: 47022--47128 Score: 119
Period size: 43 Copynumber: 2.5 Consensus size: 43
47012 GATTAATGAG
* * *
47022 ATGTGATTATC-TGTAAGACCATGTCTGGGACATTGTCATTATT
1 ATGTGATTA-CGTGTAAGACCATGTCTGAGACATTGGCATTAGT
* *
47065 ATGTGATTACGTGTAAAACCATGTCTGAGACATTGGCA-TCGT
1 ATGTGATTACGTGTAAGACCATGTCTGAGACATTGGCATTAGT
* **
47107 ATTTGATTTTGTGTAAGACCAT
1 ATGTGATTACGTGTAAGACCAT
47129 AATTGGGCTA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
42 21 0.39
43 33 0.61
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.37
Consensus pattern (43 bp):
ATGTGATTACGTGTAAGACCATGTCTGAGACATTGGCATTAGT
Done.