Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold523
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: 19917
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Found at i:3268 original size:1 final size:1
Alignment explanation
Indices: 3258--3349 Score: 76
Period size: 1 Copynumber: 92.0 Consensus size: 1
3248 TGGCAATTGG
* * * ** * * * **
3258 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAAAACAAAACAAAAAAAAGGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
3323 AAAGAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
3350 GTGAAGATTT
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:3307 original size:34 final size:34
Alignment explanation
Indices: 3257--3349 Score: 170
Period size: 34 Copynumber: 2.7 Consensus size: 34
3247 ATGGCAATTG
3257 GAAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAA
1 GAAAAA-AAAAAAACAAAACAAAAAAAAGGAAAAA
3292 GAAAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
1 GAAAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
3326 GAAAAAAAAAAAACAAAA-AAAAAA
1 GAAAAAAAAAAAACAAAACAAAAAA
3350 GTGAAGATTT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
33 6 0.10
34 46 0.79
35 6 0.10
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (34 bp):
GAAAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
Found at i:3356 original size:29 final size:28
Alignment explanation
Indices: 3261--3356 Score: 86
Period size: 29 Copynumber: 3.1 Consensus size: 28
3251 CAATTGGAAA
* *
3261 AAGAAAAAAACAAAACAAAAAAAAGGAA-A
1 AAGAAAAAAAAAAAACAAAAAAAA--AAGG
3290 AAGAAAAAAAAAAAACAAAACAAAAAAAAGG
1 AAGAAAAAAAAAAAAC--AA-AAAAAAAAGG
3321 AAAAAGAAAAAAAAAAAACAAAAAAAAAAGTG
1 ---AAGAAAAAAAAAAAACAAAAAAAAAAG-G
3353 AAGA
1 AAGA
3357 TTTGTTCCTT
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
29 19 0.33
30 2 0.04
31 11 0.19
32 9 0.16
34 16 0.28
ACGTcount: A:0.83, C:0.05, G:0.10, T:0.01
Consensus pattern (28 bp):
AAGAAAAAAAAAAAACAAAAAAAAAAGG
Found at i:6231 original size:46 final size:46
Alignment explanation
Indices: 6178--6266 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
6168 TTACAAAACA
* *
6178 GTAAAACAGATGTGATAGAAAAATGACGAAAAAAAAGATTGGAGCT
1 GTAAAACAGATGTGATAAAAAAATGACAAAAAAAAAGATTGGAGCT
6224 GTAAAACAGATGTGATAAAAAAATGACAAAAAAAAAGATTGGA
1 GTAAAACAGATGTGATAAAAAAATGACAAAAAAAAAGATTGGA
6267 ACAGACCTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.56, C:0.06, G:0.21, T:0.17
Consensus pattern (46 bp):
GTAAAACAGATGTGATAAAAAAATGACAAAAAAAAAGATTGGAGCT
Found at i:6756 original size:15 final size:15
Alignment explanation
Indices: 6738--6778 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
6728 ACCACTTTTG
6738 CTAAAAGTACTTGTA
1 CTAAAAGTACTTGTA
*
6753 CT-AAAGCACTTGTA
1 CTAAAAGTACTTGTA
6767 -TCAAAAGTACTT
1 CT-AAAAGTACTT
6779 ATGTTAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 1 0.05
14 11 0.50
15 10 0.45
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (15 bp):
CTAAAAGTACTTGTA
Found at i:6772 original size:29 final size:29
Alignment explanation
Indices: 6740--6863 Score: 122
Period size: 29 Copynumber: 4.2 Consensus size: 29
6730 CACTTTTGCT
* * * *
6740 AAAAGTACTTGTACTAAAGCACTTGTATC
1 AAAAGTACTTATGCTAAAGTACTTGTGTC
*
6769 AAAAGTACTTATGTTAAAGTACTTGTGTC
1 AAAAGTACTTATGCTAAAGTACTTGTGTC
* * *
6798 AAAGGTACCTATGCTAAAGTACTTGTGCC
1 AAAAGTACTTATGCTAAAGTACTTGTGTC
* * * * *
6827 AAAGGTACTTGTGCCAAAAATACTTGTGCC
1 AAAAGTACTTATG-CTAAAGTACTTGTGTC
6857 AAAAGTA
1 AAAAGTA
6864 TATGTGCCAA
Statistics
Matches: 80, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
29 60 0.75
30 20 0.25
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (29 bp):
AAAAGTACTTATGCTAAAGTACTTGTGTC
Found at i:6789 original size:14 final size:14
Alignment explanation
Indices: 6770--6821 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
6760 ACTTGTATCA
6770 AAAGTACTTATGTT
1 AAAGTACTTATGTT
* *
6784 AAAGTACTTGTGTC
1 AAAGTACTTATGTT
* *
6798 AAAGGTACCTATGCT
1 AAA-GTACTTATGTT
6813 AAAGTACTT
1 AAAGTACTT
6822 GTGCCAAAGG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 20 0.67
15 10 0.33
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (14 bp):
AAAGTACTTATGTT
Found at i:6850 original size:15 final size:15
Alignment explanation
Indices: 6740--6930 Score: 126
Period size: 15 Copynumber: 13.0 Consensus size: 15
6730 CACTTTTGCT
*
6740 AAAAGTACTTGT-AC
1 AAAAGTACTTGTGCC
* * **
6754 TAAAGCACTTGTATC
1 AAAAGTACTTGTGCC
* *
6769 AAAAGTACTTATG-T
1 AAAAGTACTTGTGCC
* *
6783 TAAAGTACTTGTGTC
1 AAAAGTACTTGTGCC
* * *
6798 AAAGGTACCTATG-C
1 AAAAGTACTTGTGCC
*
6812 TAAAGTACTTGTGCC
1 AAAAGTACTTGTGCC
*
6827 AAAGGTACTTGTGCC
1 AAAAGTACTTGTGCC
*
6842 AAAAATACTTGTGCC
1 AAAAGTACTTGTGCC
6857 AAAAGTA-TATGTGCC
1 AAAAGTACT-TGTGCC
6872 -AAAGTA-TCTGTGCC
1 AAAAGTACT-TGTGCC
* *
6886 GAAAGTAAC-TGTACC
1 AAAAGT-ACTTGTGCC
* * *
6901 AAAAATACTTATACC
1 AAAAGTACTTGTGCC
6916 AAAAGTACTTGTGCC
1 AAAAGTACTTGTGCC
6931 TAGGTACCTA
Statistics
Matches: 137, Mismatches: 32, Indels: 15
0.74 0.17 0.08
Matches are distributed among these distances:
14 47 0.34
15 89 0.65
16 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (15 bp):
AAAAGTACTTGTGCC
Found at i:7472 original size:66 final size:68
Alignment explanation
Indices: 7384--7724 Score: 204
Period size: 68 Copynumber: 5.1 Consensus size: 68
7374 TTTGAGAAAT
* * * * *
7384 TTGTATATATG-AGAATGGCAAAAGTGGTGCATAAGACTACAATGGTCGACTTTTTCATTAAGAA
1 TTGTATATAGGAAGAATGACAAAAGTGGTGCATAGGACCACAATGGTCGACTTTTCCATTAAGAA
7448 TAC
66 TAC
*** * **
7451 TTGTAT-TAGGAAGAAT-ACAAAAGTAACGCACAGGACCACAACAGTCGACTTTTCCATTGGAAG
1 TTGTATATAGGAAGAATGACAAAAGTGGTGCATAGGACCACAATGGTCGACTTTTCCATT--AAG
7514 -A-AC
64 AATAC
* * * * * *
7517 TTGTATATGGGGAGAATGACAAAAGTGGTGCATGGGACCACAATGATCAACTTCTCCATTAA-AA
1 TTGTATATAGGAAGAATGACAAAAGTGGTGCATAGGACCACAATGGTCGACTTTTCCATTAAGAA
7581 GTAC
66 -TAC
* * *** ** * *
7585 TTGTA-A-ATGAGAGAGTGACGGGAGTGACGCAT-GAGACCACAATGATCGACTTCTCCATTGGA
1 TTGTATATAGGA-AGAATGACAAAAGTGGTGCATAG-GACCACAATGGTCGACTTTTCCATT--A
7647 AG-A-AC
62 AGAATAC
* * * * * * *
7652 TTGTACAT-GGATAGAGTGATAGAAGTGGCGCAT-GAGACCGCAATGGTCGACTTCTCCATTAAG
1 TTGTATATAGGA-AGAATGACAAAAGTGGTGCATAG-GACCACAATGGTCGACTTTTCCATTAAG
*
7715 ATTAC
64 AATAC
7720 TTGTA
1 TTGTA
7725 AATGAAAAAG
Statistics
Matches: 215, Mismatches: 42, Indels: 33
0.74 0.14 0.11
Matches are distributed among these distances:
66 51 0.24
67 67 0.31
68 94 0.44
69 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (68 bp):
TTGTATATAGGAAGAATGACAAAAGTGGTGCATAGGACCACAATGGTCGACTTTTCCATTAAGAA
TAC
Found at i:7555 original size:68 final size:67
Alignment explanation
Indices: 7394--7843 Score: 235
Period size: 67 Copynumber: 6.7 Consensus size: 67
7384 TTGTATATAT
* * * * * *
7394 GAGAATGGCAAAAGTGGTGCATAAGACTACAATGGTCGACTTTTTCATT--AAGAATACTTGTAT
1 GAGAATGACAAAAGTGGCGCATGAGACCACAA-GGTCGACTTCTCCATTGGAAG-A-ACTTGTAT
7457 -TAGGA
63 AT-GGA
** * * *
7462 -AGAAT-ACAAAAGTAACGCA-CAGGACCACAACAGTCGACTTTTCCATTGGAAGAACTTGTATA
1 GAGAATGACAAAAGTGGCGCATGA-GACCACAA-GGTCGACTTCTCCATTGGAAGAACTTGTATA
*
7524 TGGG
64 TGGA
* * * * ** * *
7528 GAGAATGACAAAAGTGGTGCATGGGACCACAATGATCAACTTCTCCATTAAAAGTACTTGTAAAT
1 GAGAATGACAAAAGTGGCGCATGAGACCACAA-GGTCGACTTCTCCATTGGAAGAACTTGTATAT
7593 -GA
65 GGA
* *** * * *
7595 GAGAGTGACGGGAGTGACGCATGAGACCACAATGATCGACTTCTCCATTGGAAGAACTTGTACAT
1 GAGAATGACAAAAGTGGCGCATGAGACCACAA-GGTCGACTTCTCCATTGGAAGAACTTGTATAT
7660 GGA
65 GGA
* * * * * *
7663 TAGAGTGATAGAAGTGGCGCATGAGACCGCAATGGTCGACTTCTCCATT--AAGATTACTTGTAA
1 GAGAATGACAAAAGTGGCGCATGAGACCACAA-GGTCGACTTCTCCATTGGAAGA--ACTTGTAT
7726 AT-GA
63 ATGGA
* * * * * * ** * **
7730 -AAAAGTGACAGAAGTGGCACATGAGACCACAACGGCCAACTTCTCTATTAAAAGTACTTACAT-
1 GAGAA-TGACAAAAGTGGCGCATGAGACCACAA-GGTCGACTTCTCCATTGGAAGAACTTGTATA
7793 TGG-
64 TGGA
* * *
7796 GAAGAGTGACGAAAA-TGACGCATGAGACCATAACGGTCGACTTCTCCA
1 G-AGAATGAC-AAAAGTGGCGCATGAGACCACAA-GGTCGACTTCTCCA
7844 CAATGTGAAA
Statistics
Matches: 298, Mismatches: 67, Indels: 35
0.75 0.17 0.09
Matches are distributed among these distances:
65 1 0.00
66 48 0.16
67 142 0.48
68 104 0.35
69 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (67 bp):
GAGAATGACAAAAGTGGCGCATGAGACCACAAGGTCGACTTCTCCATTGGAAGAACTTGTATATG
GA
Found at i:7627 original size:67 final size:67
Alignment explanation
Indices: 7533--7788 Score: 278
Period size: 67 Copynumber: 3.8 Consensus size: 67
7523 ATGGGGAGAA
* * * *
7533 TGACAAAAGTGGTGCATGGGACCACAATGATCAACTTCTCCATTAAAAGTACTTGTAAATGAGAG
1 TGACAGAAGTGGCGCATGAGACCACAATGATCAACTTCTCCATTAAAAGTACTTGTAAATGAAAG
7598 AG
66 AG
* * * * ** * * *
7600 TGACGGGAGTGACGCATGAGACCACAATGATCGACTTCTCCATTGGAAGAACTTGTACATGGATA
1 TGACAGAAGTGGCGCATGAGACCACAATGATCAACTTCTCCATTAAAAGTACTTGTAAAT-GAAA
7665 GAG
65 GAG
* * * * * * *
7668 TGATAGAAGTGGCGCATGAGACCGCAATGGTCGACTTCTCCATTAAGATTACTTGTAAATGAAAA
1 TGACAGAAGTGGCGCATGAGACCACAATGATCAACTTCTCCATTAAAAGTACTTGTAAATGAAAG
7733 AG
66 AG
* * ** *
7735 TGACAGAAGTGGCACATGAGACCACAACGGCCAACTTCTCTATTAAAAGTACTT
1 TGACAGAAGTGGCGCATGAGACCACAATGATCAACTTCTCCATTAAAAGTACTT
7789 ACATTGGGAA
Statistics
Matches: 153, Mismatches: 35, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
67 99 0.65
68 54 0.35
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (67 bp):
TGACAGAAGTGGCGCATGAGACCACAATGATCAACTTCTCCATTAAAAGTACTTGTAAATGAAAG
AG
Found at i:7772 original size:135 final size:135
Alignment explanation
Indices: 7484--7774 Score: 357
Period size: 135 Copynumber: 2.2 Consensus size: 135
7474 TAACGCACAG
* * * * *
7484 GACCACAACAGTCGACTTTTCCATTGGAAGAACTTGTATATGGGGAGAATGACAAAAGTGGTGCA
1 GACCACAACGGTCGACTTCTCCATTGGAAGAACTTGTACATGGAGAGAATGACAAAAGTGGCGCA
* * * * * *
7549 TGGGACCACAATGATCAACTTCTCCATTAAAAGTACTTGTAAATGAGAGAGTGACGGGAGTGACG
66 TGAGACCACAATGATCAACTTCTCCATTAAAAGTACTTGTAAATGAAAAAGTGACAGAAGTGACA
7614 CATGA
131 CATGA
* * * * * *
7619 GACCACAATGATCGACTTCTCCATTGGAAGAACTTGTACATGGATAGAGTGATAGAAGTGGCGCA
1 GACCACAACGGTCGACTTCTCCATTGGAAGAACTTGTACATGGAGAGAATGACAAAAGTGGCGCA
* * * * * *
7684 TGAGACCGCAATGGTCGACTTCTCCATTAAGATTACTTGTAAATGAAAAAGTGACAGAAGTGGCA
66 TGAGACCACAATGATCAACTTCTCCATTAAAAGTACTTGTAAATGAAAAAGTGACAGAAGTGACA
7749 CATGA
131 CATGA
* *
7754 GACCACAACGGCCAACTTCTC
1 GACCACAACGGTCGACTTCTC
7775 TATTAAAAGT
Statistics
Matches: 129, Mismatches: 27, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
135 129 1.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (135 bp):
GACCACAACGGTCGACTTCTCCATTGGAAGAACTTGTACATGGAGAGAATGACAAAAGTGGCGCA
TGAGACCACAATGATCAACTTCTCCATTAAAAGTACTTGTAAATGAAAAAGTGACAGAAGTGACA
CATGA
Found at i:11963 original size:29 final size:29
Alignment explanation
Indices: 11929--11996 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
11919 CCAAAAAATG
*
11929 TTGTGCCAAACCACCTATGCTAAAAGTAC
1 TTGTGCCAAACCACCTATGCCAAAAGTAC
11958 TTGTGCCAAACCACCTATGCCAAAAGTAC
1 TTGTGCCAAACCACCTATGCCAAAAGTAC
*
11987 TTGTACCAAA
1 TTGTGCCAAA
11997 GATACCTGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (29 bp):
TTGTGCCAAACCACCTATGCCAAAAGTAC
Found at i:12055 original size:29 final size:31
Alignment explanation
Indices: 12007--12086 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 31
11997 GATACCTGTG
* *
12007 CTAAAGGTACCTGTGTCAAAAGTATTTATG-
1 CTAAAAGTACCTGTGCCAAAAGTATTTATGT
* *
12037 C-CAAAGTACCTGTGCC-AAAGTATTTGTGT
1 CTAAAAGTACCTGTGCCAAAAGTATTTATGT
*
12066 CTAAAAGTAACTGTGCCAAAA
1 CTAAAAGTACCTGTGCCAAAA
12087 TACCTTACCA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
28 11 0.27
29 13 0.32
30 14 0.34
31 3 0.07
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (31 bp):
CTAAAAGTACCTGTGCCAAAAGTATTTATGT
Found at i:12083 original size:44 final size:44
Alignment explanation
Indices: 11951--12123 Score: 122
Period size: 44 Copynumber: 4.0 Consensus size: 44
11941 ACCTATGCTA
* ** * * *
11951 AAAGTACTTGTGCCAAA-CCACCTATGCCAAAAGT-ACTTGTACC
1 AAAGTACCTGTGCCAAAGGTACCTGTGTCAAAAGTAAC-TGTGCC
* ** *
11994 AAAGATACCTGTGCTAAAGGTACCTGTGTCAAAAGTATTTATGCC
1 AAAG-TACCTGTGCCAAAGGTACCTGTGTCAAAAGTAACTGTGCC
**
12039 AAAGTACCTGTGCCAAA-GTATTTGTGTCTAAAAGTAACTGTGCC
1 AAAGTACCTGTGCCAAAGGTACCTGTGTC-AAAAGTAACTGTGCC
* * * * * *
12083 AAAATACCT-TACCAAAAGTACATGTG-CCAAAGTACCTGTGC
1 AAAGTACCTGTGCCAAAGGTACCTGTGTCAAAAGTAACTGTGC
12124 TAAAAATACT
Statistics
Matches: 103, Mismatches: 22, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
42 12 0.12
43 20 0.19
44 50 0.49
45 21 0.20
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (44 bp):
AAAGTACCTGTGCCAAAGGTACCTGTGTCAAAAGTAACTGTGCC
Found at i:12116 original size:14 final size:14
Alignment explanation
Indices: 11951--12123 Score: 114
Period size: 14 Copynumber: 11.9 Consensus size: 14
11941 ACCTATGCTA
*
11951 AAAGTACTTGTGCC
1 AAAGTACCTGTGCC
** *
11965 AAACCACCTATGCC
1 AAAGTACCTGTGCC
* *
11979 AAAAGTACTTGTACC
1 -AAAGTACCTGTGCC
*
11994 AAAGATACCTGTGCT
1 AAAG-TACCTGTGCC
*
12009 AAAGGTACCTGTGTCA
1 AAA-GTACCTGTG-CC
** *
12025 AAAGTATTTATGCC
1 AAAGTACCTGTGCC
12039 AAAGTACCTGTGCC
1 AAAGTACCTGTGCC
** *
12053 AAAGTATTTGTGTCTA
1 AAAGTACCTGTG-C-C
*
12069 AAAGTAACTGTGCC
1 AAAGTACCTGTGCC
* *
12083 AAAATACCT-TACC
1 AAAGTACCTGTGCC
*
12096 AAAAGTACATGTGCC
1 -AAAGTACCTGTGCC
12111 AAAGTACCTGTGC
1 AAAGTACCTGTGC
12124 TAAAAATACT
Statistics
Matches: 118, Mismatches: 33, Indels: 16
0.71 0.20 0.10
Matches are distributed among these distances:
13 3 0.03
14 62 0.53
15 38 0.32
16 15 0.13
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (14 bp):
AAAGTACCTGTGCC
Found at i:14283 original size:16 final size:15
Alignment explanation
Indices: 14264--14308 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 15
14254 AAAATATCTT
14264 AAATTTTATATAATA
1 AAATTTTATATAATA
14279 CAAATTATTAATATAATA
1 -AAATT-TT-ATATAATA
14297 AAA-TTTATATAA
1 AAATTTTATATAA
14309 ATATAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.22
15 2 0.07
16 6 0.22
17 5 0.19
18 8 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATTTTATATAATA
Found at i:14294 original size:18 final size:17
Alignment explanation
Indices: 14271--14360 Score: 77
Period size: 17 Copynumber: 5.5 Consensus size: 17
14261 CTTAAATTTT
14271 ATATAATACAAATTATTA
1 ATATAATA-AAATTATTA
14289 ATATAATAAAATTTATATA
1 ATATAATAAAA-TTAT-TA
14308 A-AT-ATAAAATATATTA
1 ATATAATAAAAT-TATTA
14324 AT-T-AT--AATTA-TA
1 ATATAATAAAATTATTA
* *
14336 ATATGATAAAAATATTA
1 ATATAATAAAATTATTA
14353 ATATAATA
1 ATATAATA
14361 TACATATATG
Statistics
Matches: 61, Mismatches: 2, Indels: 19
0.74 0.02 0.23
Matches are distributed among these distances:
12 4 0.07
13 3 0.05
14 5 0.08
16 11 0.18
17 21 0.34
18 14 0.23
19 3 0.05
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (17 bp):
ATATAATAAAATTATTA
Found at i:14301 original size:33 final size:36
Alignment explanation
Indices: 14263--14331 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 36
14253 AAAAATATCT
* *
14263 TAAATTTTATAT-AATA-CAAAT-TATTAA-TATAA
1 TAAAATTTATATAAATATAAAATATATTAATTATAA
14295 TAAAATTTATATAAATATAAAATATATTAATTATAA
1 TAAAATTTATATAAATATAAAATATATTAATTATAA
14331 T
1 T
14332 TATAATATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 11 0.35
33 4 0.13
34 4 0.13
35 6 0.19
36 6 0.19
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (36 bp):
TAAAATTTATATAAATATAAAATATATTAATTATAA
Found at i:14311 original size:20 final size:18
Alignment explanation
Indices: 14271--14331 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
14261 CTTAAATTTT
14271 ATATAATACAAATTATTA
1 ATATAATACAAATTATTA
14289 ATATAATA-AAATTTATATA
1 ATATAATACAAA-TTAT-TA
14308 A-AT-ATA-AAATATATTA
1 ATATAATACAAAT-TATTA
14324 ATTATAAT
1 A-TATAAT
14332 TATAATATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 4 0.11
17 12 0.32
18 16 0.43
19 5 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAATACAAATTATTA
Found at i:15515 original size:5 final size:5
Alignment explanation
Indices: 15505--15531 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
15495 AAAGAAATGA
15505 TATAT TATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TATAT TATAT TA
15532 CTCTAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:15994 original size:13 final size:13
Alignment explanation
Indices: 15967--16005 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
15957 TTTGAAAGTT
15967 AAAATTAAAAA-A
1 AAAATTAAAAATA
15979 AAAATTAAAAATA
1 AAAATTAAAAATA
* *
15992 AAAAATAATAATA
1 AAAATTAAAAATA
16005 A
1 A
16006 GAGTATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAATTAAAAATA
Found at i:19778 original size:30 final size:31
Alignment explanation
Indices: 19744--19806 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
19734 TCAGATTAAT
19744 TTAAAAATT-TATTTTTATTATTTAAAATTA
1 TTAAAAATTATATTTTTATTATTTAAAATTA
* *
19774 TTAAAAATTAAATATTTTTATTTTTTATAATTA
1 TTAAAAATT--ATATTTTTATTATTTAAAATTA
19807 AATTTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 9 0.32
33 19 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
TTAAAAATTATATTTTTATTATTTAAAATTA
Found at i:19843 original size:29 final size:28
Alignment explanation
Indices: 19793--19850 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 28
19783 AAATATTTTT
* *
19793 ATTTTTTATAATTAAATTTAAA-TAAAA
1 ATTTTTTATAAATAAATATAAATTAAAA
19820 ATTTTTTATTAAATAAATAATAAATTAAAA
1 ATTTTTTA-TAAATAAAT-ATAAATTAAAA
19850 A
1 A
19851 ATTAAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 8 0.31
28 8 0.31
29 4 0.15
30 6 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTTTTTATAAATAAATATAAATTAAAA
Done.