Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2643
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: 63841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:3211 original size:19 final size:19
Alignment explanation
Indices: 3167--3229 Score: 65
Period size: 20 Copynumber: 3.3 Consensus size: 19
3157 AGAAAAAATC
* *
3167 ATAAAAATAATAAATTTTA
1 ATAAAATTATTAAATTTTA
*
3186 GAAAAAATTATTAAATTTTA
1 -ATAAAATTATTAAATTTTA
*
3206 ATAAAATT-TAAAATTTTA
1 ATAAAATTATTAAATTTTA
*
3224 TTAAAA
1 ATAAAA
3230 ATTAGAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
18 14 0.38
19 7 0.19
20 16 0.43
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
ATAAAATTATTAAATTTTA
Found at i:3230 original size:19 final size:20
Alignment explanation
Indices: 3167--3233 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 20
3157 AGAAAAAATC
*
3167 ATAAAAATAAT-AAATTTTA
1 ATAAAAATTATAAAATTTTA
*
3186 GA-AAAAATTATTAAATTTTA
1 -ATAAAAATTATAAAATTTTA
3206 AT-AAAATT-TAAAATTTTA
1 ATAAAAATTATAAAATTTTA
*
3224 TTAAAAATTA
1 ATAAAAATTA
3234 GAATTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 10 0.25
19 21 0.52
20 9 0.22
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (20 bp):
ATAAAAATTATAAAATTTTA
Found at i:3241 original size:19 final size:18
Alignment explanation
Indices: 3167--3240 Score: 69
Period size: 18 Copynumber: 3.9 Consensus size: 18
3157 AGAAAAAATC
*
3167 ATAAAAATAATAAATTTTA
1 ATAAAAATTA-AAATTTTA
3186 GA-AAAAATTATTAAATTTTA
1 -ATAAAAATTA--AAATTTTA
*
3206 ATAAAATTTAAAATTTTA
1 ATAAAAATTAAAATTTTA
* *
3224 TTAAAAATTAGAATTTT
1 ATAAAAATTAAAATTTT
3241 TTTTAGAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
18 22 0.47
19 8 0.17
20 17 0.36
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
ATAAAAATTAAAATTTTA
Found at i:3576 original size:46 final size:48
Alignment explanation
Indices: 3487--3617 Score: 132
Period size: 46 Copynumber: 2.8 Consensus size: 48
3477 AATTAATTTC
* * *
3487 TTTAC-ATTTGTATA-ATTTCTT-ATAACTTTATAAAA-TTTTATAAATT
1 TTTACAATTT-TATATATTT-TTAATAAATTTTTAAAATTTTTATAAAAT
* *
3533 TTTA-TATTTCTATATA-TTTTAA-AATTTTTTAAAATTTTTATAAAAT
1 TTTACAATTT-TATATATTTTTAATAAATTTTTAAAATTTTTATAAAAT
*
3579 TTTACAATTTTATATATTTTTAATAAATTTTTAATATTT
1 TTTACAATTTTATATATTTTTAATAAATTTTTAAAATTT
3618 GATTTTTTAT
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
45 12 0.17
46 35 0.49
47 11 0.15
48 13 0.18
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (48 bp):
TTTACAATTTTATATATTTTTAATAAATTTTTAAAATTTTTATAAAAT
Found at i:3599 original size:10 final size:10
Alignment explanation
Indices: 3522--3617 Score: 53
Period size: 9 Copynumber: 10.2 Consensus size: 10
3512 CTTTATAAAA
*
3522 TTTTATA-AA
1 TTTTATATAT
3531 TTTT-TATAT
1 TTTTATATAT
*
3540 TTCTATATAT
1 TTTTATATAT
* *
3550 TTTAAAAT-T
1 TTTTATATAT
*
3559 TTTTA-AAAT
1 TTTTATATAT
* *
3568 TTTTATAAAA
1 TTTTATATAT
*
3578 TTTTACA-A-
1 TTTTATATAT
3586 TTTTATATAT
1 TTTTATATAT
*
3596 TTTTAATAAAT
1 TTTT-ATATAT
3607 TTTTA-ATAT
1 TTTTATATAT
3616 TT
1 TT
3618 GATTTTTTAT
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
8 9 0.13
9 26 0.38
10 24 0.35
11 9 0.13
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
TTTTATATAT
Found at i:3614 original size:11 final size:10
Alignment explanation
Indices: 3513--3611 Score: 77
Period size: 10 Copynumber: 10.4 Consensus size: 10
3503 TTCTTATAAC
*
3513 TTTATAAAAT
1 TTTATAAATT
3523 TTTATAAATT
1 TTTATAAATT
3533 TTTAT--ATT
1 TTTATAAATT
* *
3541 TCTATATA-T
1 TTTATAAATT
3550 TTTA-AAATT
1 TTTATAAATT
3559 TTT-TAAAATT
1 TTTAT-AAATT
*
3569 TTTATAAAAT
1 TTTATAAATT
*
3579 TTTA-CAA-T
1 TTTATAAATT
*
3587 TTTATATATT
1 TTTATAAATT
3597 TTTAATAAATT
1 TTT-ATAAATT
3608 TTTA
1 TTTA
3612 ATATTTGATT
Statistics
Matches: 71, Mismatches: 9, Indels: 18
0.72 0.09 0.18
Matches are distributed among these distances:
8 14 0.20
9 11 0.15
10 36 0.51
11 10 0.14
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTATAAATT
Found at i:3651 original size:29 final size:28
Alignment explanation
Indices: 3567--3651 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 28
3557 TTTTTTAAAA
* * *
3567 TTTTTATAAAATTTTACAATTTTATATAT
1 TTTTTATAAAA-TTTATAATATTATAGAT
* *
3596 TTTTAAT-AAATTTTTAATATT-T-GAT
1 TTTTTATAAAATTTATAATATTATAGAT
3621 TTTTTATTAAAATTTATAATATTATAGAT
1 TTTTTA-TAAAATTTATAATATTATAGAT
3650 TT
1 TT
3652 ATTGATTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
25 7 0.16
26 2 0.04
27 21 0.47
28 4 0.09
29 11 0.24
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (28 bp):
TTTTTATAAAATTTATAATATTATAGAT
Found at i:6334 original size:54 final size:54
Alignment explanation
Indices: 6275--6384 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 54
6265 ATATATATAT
* * *
6275 ATATAAAAGAAAACACATTTTTATGAAATATAAGATTTTGTTAAAAGAAAGAGC
1 ATATAAAAGAAAACACATTTTTATGAAATACAAGATTTTGCTAAAAGAAAAAGC
* * *
6329 ATATAAAAGCATACACGTTTTTATGAAATACAAGATTTTGCTAAAAGAAAAAGC
1 ATATAAAAGAAAACACATTTTTATGAAATACAAGATTTTGCTAAAAGAAAAAGC
6383 AT
1 AT
6385 CCAATTTTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.29
Consensus pattern (54 bp):
ATATAAAAGAAAACACATTTTTATGAAATACAAGATTTTGCTAAAAGAAAAAGC
Found at i:10486 original size:84 final size:85
Alignment explanation
Indices: 10355--10611 Score: 248
Period size: 87 Copynumber: 3.0 Consensus size: 85
10345 ATTTAAGTCC
* * * * * * * * * *
10355 TTTTTTTCTACTCAATTGAGCACTTAAACTTTTAAAATGTATCAAAAATCTTTACA-CTTCTTCA
1 TTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAACCTTAAATCTTCTTCA
10419 AAAAAAGCAATTAAACCCCT-
66 AAAAAA-CAATTAAACCCCTA
* * * *
10439 TTTTTTTCCGCTCAATTGGGTACTTGAACTTTCATAATGCATAAAAAAACCTTAAATTTTTTTTC
1 TTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAACCTTAAA-TCTTCTTC
* * *
10504 AAAGAAACAATTAAGCCTCTA
65 AAAAAAACAATTAAACCCCTA
* * * * *
10525 TTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAGGCCTTTATTTTTTTT
1 TTTTTTT-CCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAA-ACCTTAAATCTTCTT
* *
10590 CAAAAAAGCAATTAAGCCCCTA
64 CAAAAAAACAATTAAACCCCTA
10612 CTCTTATTAA
Statistics
Matches: 143, Mismatches: 25, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
84 44 0.31
85 11 0.08
86 18 0.13
87 65 0.45
88 5 0.03
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (85 bp):
TTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAACCTTAAATCTTCTTCA
AAAAAACAATTAAACCCCTA
Found at i:10546 original size:87 final size:85
Alignment explanation
Indices: 10419--10610 Score: 280
Period size: 87 Copynumber: 2.2 Consensus size: 85
10409 CACTTCTTCA
* *
10419 AAAAAAGCAATTAAACCCCTTTTTTTTCCGCTCAATTGGGTACTTGAACTTTCATAATGCAT-AA
1 AAAAAAGCAATTAAGCCCCTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAA
10483 AAAAACCTTAAATTTTTTTTC
66 AAAAACCTT-AATTTTTTTTC
*
10504 AAAGAAA-CAATTAAGCCTCTATTTTTTTCCCACTCAATTGGGTACTTGAACTTTCATAATGCAT
1 AAA-AAAGCAATTAAGCCCCT-TTTTTTT-CCACTCAATTGGGTACTTGAACTTTCATAATGCAT
** *
10568 CAAAAAGGCCTTTATTTTTTTTC
63 CAAAAAAACCTTAATTTTTTTTC
10591 AAAAAAGCAATTAAGCCCCT
1 AAAAAAGCAATTAAGCCCCT
10611 ACTCTTATTA
Statistics
Matches: 95, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
85 14 0.15
86 13 0.14
87 59 0.62
88 9 0.09
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (85 bp):
AAAAAAGCAATTAAGCCCCTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAA
AAAAACCTTAATTTTTTTTC
Found at i:12450 original size:50 final size:50
Alignment explanation
Indices: 12381--12501 Score: 172
Period size: 50 Copynumber: 2.4 Consensus size: 50
12371 GCAAGTGTGA
* ** *
12381 AGTCAATAGACAACTGATAGTCTTAGTCTTTTTTTGTCGAGTT-AAAGTGT
1 AGTCAATAGACAATTGATAGTCTTAG-CCCTTTTTGTCGAGTTAAAAGTAT
*
12431 AGTCAATAGACAATTGATAGTCTTAGCCCTTTTTGTGGAGTTAAAAGTAT
1 AGTCAATAGACAATTGATAGTCTTAGCCCTTTTTGTCGAGTTAAAAGTAT
*
12481 AGTCAATAAACAATTGATAGT
1 AGTCAATAGACAATTGATAGT
12502 TAAATTTGTA
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 13 0.20
50 51 0.80
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (50 bp):
AGTCAATAGACAATTGATAGTCTTAGCCCTTTTTGTCGAGTTAAAAGTAT
Found at i:16228 original size:61 final size:61
Alignment explanation
Indices: 16154--16272 Score: 150
Period size: 61 Copynumber: 2.0 Consensus size: 61
16144 TTTGTTTTTT
* * *
16154 CCTTTAAAATTTTTAGAAAATTTCAATTAGGCCCTC-AAAATTTTTGAAAATTTTCATTATA
1 CCTTTAAAATTTTTAGAAAATTTCAATTAAGCACTCTAAAA-TTTTGAAAATTCTCATTATA
* * * * *
16215 CCTTTTAATTTTTTTGAAAATTTTAATTAAGCACTCTTAAATTTTGAAAATTCTCATT
1 CCTTTAAAATTTTTAGAAAATTTCAATTAAGCACTCTAAAATTTTGAAAATTCTCATT
16273 GATCTCACAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
61 46 0.94
62 3 0.06
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (61 bp):
CCTTTAAAATTTTTAGAAAATTTCAATTAAGCACTCTAAAATTTTGAAAATTCTCATTATA
Found at i:21164 original size:30 final size:31
Alignment explanation
Indices: 21105--21164 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
21095 TTGGGATAGA
*
21105 TGGGAGGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAGGGGAATAAAAATTTTAGGGGAAAAG
*
21136 TGGGA-GGGAGTAAAAATTTT-GGGAGAAAA
1 TGGGAGGGGAATAAAAATTTTAGGG-GAAAA
21165 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAGGGGAATAAAAATTTTAGGGGAAAAG
Found at i:21392 original size:9 final size:9
Alignment explanation
Indices: 21378--21414 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
21368 TATAGTTTGA
21378 TATTCGAAT
1 TATTCGAAT
21387 TATTCGAAT
1 TATTCGAAT
*
21396 TATTCGAGT
1 TATTCGAAT
21405 TATTCGAAT
1 TATTCGAAT
21414 T
1 T
21415 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:21658 original size:29 final size:28
Alignment explanation
Indices: 21602--21748 Score: 125
Period size: 30 Copynumber: 5.0 Consensus size: 28
21592 TAAATGTAGC
* * *
21602 AAAAGTTTTGGGGCAAAAATGTAATTTTGA
1 AAAAGTTTAGGGTC-AAAATATAATTTT-A
*
21632 GAAAGTTTAGGGTCAAAATATAATTTTA
1 AAAAGTTTAGGGTCAAAATATAATTTTA
* *
21660 AAAAATATTAAGGGTTAAAATATAATTTTA
1 AAAAGT-TT-AGGGTCAAAATATAATTTTA
*
21690 TAAAAATTTAAGGGTCAAAATGA-AATTTTA
1 -AAAAGTTT-AGGGTCAAAAT-ATAATTTTA
* *
21720 GAAAAGTTCAGAGGTCAAAATACAATTTT
1 -AAAAGTTTAG-GGTCAAAATATAATTTT
21749 TAAATTTTTT
Statistics
Matches: 100, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
28 5 0.05
29 17 0.17
30 71 0.71
31 7 0.07
ACGTcount: A:0.46, C:0.04, G:0.16, T:0.33
Consensus pattern (28 bp):
AAAAGTTTAGGGTCAAAATATAATTTTA
Found at i:21674 original size:30 final size:29
Alignment explanation
Indices: 21617--21748 Score: 133
Period size: 30 Copynumber: 4.4 Consensus size: 29
21607 TTTTGGGGCA
* * *
21617 AAAATGTAATTTTGAGAAAGTTT-AGGGTC
1 AAAATATAATTTT-AAAAAATTTAAGGGTC
*
21646 AAAATATAATTTTAAAAAATATTAAGGGTT
1 AAAATATAATTTTAAAAAAT-TTAAGGGTC
21676 AAAATATAATTTTATAAAAATTTAAGGGTC
1 AAAATATAATTTTA-AAAAATTTAAGGGTC
* * *
21706 AAAATGA-AATTTTAGAAAAGTTCAGAGGTC
1 AAAAT-ATAATTTTAAAAAATTTAAG-GGTC
*
21736 AAAATACAATTTT
1 AAAATATAATTTT
21749 TAAATTTTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 11
0.82 0.07 0.10
Matches are distributed among these distances:
28 5 0.06
29 23 0.26
30 54 0.61
31 7 0.08
ACGTcount: A:0.48, C:0.04, G:0.14, T:0.34
Consensus pattern (29 bp):
AAAATATAATTTTAAAAAATTTAAGGGTC
Found at i:25802 original size:3 final size:3
Alignment explanation
Indices: 25794--25820 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
25784 GAAGTGGTGT
25794 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
25821 CAACAACAAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:29113 original size:5 final size:6
Alignment explanation
Indices: 29099--29123 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29089 TAAAAGAGGC
29099 AAAAGA AAAAGA AAAAGA AAAAGA A
1 AAAAGA AAAAGA AAAAGA AAAAGA A
29124 GCTAAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:31203 original size:36 final size:36
Alignment explanation
Indices: 31097--31209 Score: 95
Period size: 36 Copynumber: 3.1 Consensus size: 36
31087 ACTTGTCGGT
*
31097 GAACCAATTGAGTGGACAAATTCCAAGATCATTGGG
1 GAACCAATTGAGCGGACAAATTCCAAGATCATTGGG
** * ** ** * * *
31133 GAACCTCTTGCAACTCACTCATT--TAGACTTATTGGT
1 GAACCAATTG-AGCGGACAAATTCCAAGA-TCATTGGG
31169 GAACCAATTGAGCGGACAAATTCCAAGATCATTGGG
1 GAACCAATTGAGCGGACAAATTCCAAGATCATTGGG
31205 GAACC
1 GAACC
31210 TCTTGCAACT
Statistics
Matches: 52, Mismatches: 21, Indels: 8
0.64 0.26 0.10
Matches are distributed among these distances:
35 10 0.19
36 33 0.63
37 9 0.17
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (36 bp):
GAACCAATTGAGCGGACAAATTCCAAGATCATTGGG
Found at i:31354 original size:72 final size:72
Alignment explanation
Indices: 30750--31337 Score: 878
Period size: 72 Copynumber: 8.1 Consensus size: 72
30740 TCAGGACCGG
* **
30750 TTCCAAGATCACT-GGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGCAGAACCAATTGAGT
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAACCAATTGAGT
30814 GGACAAA
66 GGACAAA
* *
30821 TTCCAAGATTATTGGGGAACCTCTTTCAACTCACTCATTTAGACTTGTC-GTGGAACCAATTGAG
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGT-GAACCAATTGAG
30885 TGGACAAA
65 TGGACAAA
* *
30893 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGATTTGTCGATGAACCAATTGAGT
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAACCAATTGAGT
30958 GGACAAA
66 GGACAAA
*
30965 TTCCAAGATCATTGGGGATCATTGGGGAACATCTTGCAACTCACTCATTT--ACTTGTCGGTGAA
1 TTCC---A--A-----GATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAA
31028 CCAATTGAGTGGACAAA
56 CCAATTGAGTGGACAAA
31045 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAACCAATTGAGT
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAACCAATTGAGT
31110 GGACAAA
66 GGACAAA
* * *
31117 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTATTGGTGAACCAATTGAGC
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAACCAATTGAGT
31182 GGACAAA
66 GGACAAA
* * *
31189 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTACAGTTGCCGGTGAACCAATTGAGT
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAACCAATTGAGT
*
31254 GGAAAAA
66 GGACAAA
* * * *
31261 TTCCAAGATCATTGGGGAACCTCTTGCATCTCACTCATTTACACTTGCCGATGAACCAATTGAGT
1 TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAACCAATTGAGT
31326 GGACAAA
66 GGACAAA
31333 TTCCA
1 TTCCA
31338 TTGTCAATTC
Statistics
Matches: 475, Mismatches: 27, Indels: 29
0.89 0.05 0.05
Matches are distributed among these distances:
70 33 0.07
71 11 0.02
72 361 0.76
73 1 0.00
75 2 0.00
77 2 0.00
80 32 0.07
82 33 0.07
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (72 bp):
TTCCAAGATCATTGGGGAACCTCTTGCAACTCACTCATTTAGACTTGTCGGTGAACCAATTGAGT
GGACAAA
Found at i:36174 original size:28 final size:29
Alignment explanation
Indices: 36141--36202 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
36131 TACAAAATTC
36141 TAAAAATTAAAAAT-TAAATGAAAGT-AGA
1 TAAAAATTAAAAATATAAAT-AAAGTGAGA
**
36169 TAAAAATTTCAAATATAAATAAAGTGAGA
1 TAAAAATTAAAAATATAAATAAAGTGAGA
*
36198 GAAAA
1 TAAAA
36203 TGAGGGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.63, C:0.02, G:0.11, T:0.24
Consensus pattern (29 bp):
TAAAAATTAAAAATATAAATAAAGTGAGA
Found at i:37643 original size:23 final size:25
Alignment explanation
Indices: 37607--37655 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
37597 AGAATAAAAA
*
37607 AATAACATCTTAATTT-AAATAATT
1 AATAACATCTTAATTTGAAAAAATT
*
37631 AATAA-ATTTTAATTTGAAAAAATT
1 AATAACATCTTAATTTGAAAAAATT
37655 A
1 A
37656 TTTTGAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (25 bp):
AATAACATCTTAATTTGAAAAAATT
Found at i:40568 original size:29 final size:29
Alignment explanation
Indices: 40526--40595 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
40516 GGCAGTAGTA
*
40526 ACTTGGGAAAAAAAAGT-AGTTTATGTACC
1 ACTTGGGAAAAAAAA-TAAGTTTAGGTACC
* *
40555 ACTTGTGACAAAAAATAAGTTTAGGTACC
1 ACTTGGGAAAAAAAATAAGTTTAGGTACC
*
40584 AACATGGGAAAA
1 -ACTTGGGAAAA
40596 TGAGTATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
28 1 0.03
29 24 0.73
30 8 0.24
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.24
Consensus pattern (29 bp):
ACTTGGGAAAAAAAATAAGTTTAGGTACC
Found at i:45089 original size:89 final size:86
Alignment explanation
Indices: 44950--45177 Score: 224
Period size: 89 Copynumber: 2.6 Consensus size: 86
44940 CTTTTTTTTT
* * * * * * * * *
44950 CTTTTTTTTTACACTCAATTGAGCACTTAAACTTTTAAAATGTATCAAAAATATCTTTA-CACTT
1 CTTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAA-ACCTTAATCACTT
45014 CTTCAAAAAAAGCAATTAAACCCCC
65 CTTCAAAAAAA-CAATT-AA-CCCC
* *** *
45039 CTTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATAAAAAAACCTTAATTTTTTT
1 CTTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAACCTTAATCACTTC
* * *
45104 TTCAAAGAAACAATTAAGCCT
66 TTCAAAAAAACAATTAACCCC
**
45125 CTATTTTTTCCCCACTCAATTTGGGTACTTGAACTTTCATAATGCATCAAAAA
1 CT-TTTTTTTTCCACTCAA-TTGGGTACTTGAACTTTCATAATGCATCAAAAA
45178 GGCCTTAAAT
Statistics
Matches: 116, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
86 4 0.03
87 16 0.14
88 42 0.36
89 54 0.47
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (86 bp):
CTTTTTTTTTCCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAACCTTAATCACTTC
TTCAAAAAAACAATTAACCCC
Found at i:45149 original size:88 final size:87
Alignment explanation
Indices: 45049--45211 Score: 258
Period size: 88 Copynumber: 1.9 Consensus size: 87
45039 CTTTTTTTTT
*
45049 CCACTCAATTGGGTACTTGAACTTTCATAATGCAT-AAAAAAACCTTAATTTTTTTTTCAAAGAA
1 CCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAAACCTTAA-ATTTTTTTCAAA-AA
45113 A-CAATTAAGCCTCTATTTTTTCC
64 AGCAATTAAGCCTCTATTTTTTCC
**
45136 CCACTCAATTTGGGTACTTGAACTTTCATAATGCATCAAAAAGGCCTTAAATTTTTTTCAAAAAA
1 CCACTCAA-TTGGGTACTTGAACTTTCATAATGCATCAAAAAAACCTTAAATTTTTTTCAAAAAA
45201 GCAATTAAGCC
65 GCAATTAAGCC
45212 CCTACTCTTA
Statistics
Matches: 70, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
87 11 0.16
88 48 0.69
89 11 0.16
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.35
Consensus pattern (87 bp):
CCACTCAATTGGGTACTTGAACTTTCATAATGCATCAAAAAAACCTTAAATTTTTTTCAAAAAAG
CAATTAAGCCTCTATTTTTTCC
Found at i:45288 original size:20 final size:21
Alignment explanation
Indices: 45243--45291 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
45233 AAAAAGAATC
45243 ATAAAAA-TAATAAATTTTAG
1 ATAAAAATTAATAAATTTTAG
* *
45263 AAAAAAATTATTAAATTTTA-
1 ATAAAAATTAATAAATTTTAG
45283 ATAAAAATT
1 ATAAAAATT
45292 TAAAAACTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAAAAATTAATAAATTTTAG
Found at i:45675 original size:55 final size:55
Alignment explanation
Indices: 45615--45757 Score: 166
Period size: 55 Copynumber: 2.6 Consensus size: 55
45605 TTCTTATGAC
* *
45615 TTTATAAAATTTTATAATTTTT-TATATTTCTAT-ATATTTTTTAAATTTTTAAATT
1 TTTATAAAATTTTATAATTTTTATATATTT-TATAATAATTTTT-AATATTTAAATT
* * *
45670 TTTATAAAATTTTACAATTTTTATATATTTTTTAATAATTTTTAATATTTGAATT
1 TTTATAAAATTTTATAATTTTTATATATTTTATAATAATTTTTAATATTTAAATT
* * *
45725 TTTATTAAAATTTAATAA-TATTATAGATTTTAT
1 TTTA-TAAAATTTTATAATTTTTATATATTTTAT
45758 TGATTTTAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
55 49 0.65
56 26 0.35
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (55 bp):
TTTATAAAATTTTATAATTTTTATATATTTTATAATAATTTTTAATATTTAAATT
Found at i:45679 original size:19 final size:19
Alignment explanation
Indices: 45615--45704 Score: 66
Period size: 19 Copynumber: 4.8 Consensus size: 19
45605 TTCTTATGAC
45615 TTTATAAAA-TTTTATAATT
1 TTTATAAAATTTTTA-AATT
* *
45634 TTT-T-ATATTTCTATATATT
1 TTTATAAAATTT-T-TAAATT
45653 TTT-T-AAATTTTTAAATT
1 TTTATAAAATTTTTAAATT
45670 TTTATAAAA-TTTTACAATT
1 TTTATAAAATTTTTA-AATT
* *
45689 TTTATATATTTTTTAA
1 TTTATAAAATTTTTAA
45705 TAATTTTTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
17 10 0.17
18 10 0.17
19 31 0.53
20 7 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATAAAATTTTTAAATT
Found at i:45699 original size:10 final size:10
Alignment explanation
Indices: 45624--45719 Score: 73
Period size: 9 Copynumber: 10.2 Consensus size: 10
45614 CTTTATAAAA
45624 TTTTATA-AT
1 TTTTATATAT
45633 TTTT-TATAT
1 TTTTATATAT
*
45642 TTCTATATAT
1 TTTTATATAT
*
45652 TTTT-TAAAT
1 TTTTATATAT
45661 TTTTA-A-AT
1 TTTTATATAT
* *
45669 TTTTATAAAA
1 TTTTATATAT
*
45679 TTTTACA-AT
1 TTTTATATAT
45688 TTTTATATAT
1 TTTTATATAT
45698 TTTT-TAATAAT
1 TTTTAT-AT-AT
45709 TTTTA-ATAT
1 TTTTATATAT
45718 TT
1 TT
45720 GAATTTTTAT
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
8 9 0.13
9 31 0.44
10 25 0.35
11 6 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTATATAT
Found at i:45701 original size:11 final size:10
Alignment explanation
Indices: 45631--45719 Score: 57
Period size: 10 Copynumber: 9.4 Consensus size: 10
45621 AAATTTTATA
45631 ATTTTTT-AT
1 ATTTTTTAAT
*
45640 A-TTTCTATAT
1 ATTTTTTA-AT
45650 ATTTTTTAA-
1 ATTTTTTAAT
45659 A-TTTTTAA-
1 ATTTTTTAAT
*
45667 ATTTTTATAAA
1 ATTTTT-TAAT
**
45678 ATTTTACAAT
1 ATTTTTTAAT
*
45688 -TTTTAT-AT
1 ATTTTTTAAT
45696 ATTTTTTAAT
1 ATTTTTTAAT
*
45706 AATTTTTAAT
1 ATTTTTTAAT
45716 ATTT
1 ATTT
45720 GAATTTTTAT
Statistics
Matches: 63, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
8 14 0.22
9 16 0.25
10 23 0.37
11 10 0.16
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTTTAAT
Found at i:45744 original size:28 final size:27
Alignment explanation
Indices: 45666--45746 Score: 69
Period size: 28 Copynumber: 2.9 Consensus size: 27
45656 TAAATTTTTA
* *
45666 AATTTTTA-TAAAATTTTACAAT-TTTT
1 AATTTTTATTAAAA-TTTATAATATTTG
*
45692 ATATATTTT-TTAATAATTTTTAATATTTG
1 A-AT-TTTTATTAA-AATTTATAATATTTG
45721 AATTTTTATTAAAATTTAATAATATT
1 AATTTTTATTAAAATTT-ATAATATT
45747 ATAGATTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
26 1 0.02
27 11 0.25
28 26 0.59
29 6 0.14
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (27 bp):
AATTTTTATTAAAATTTATAATATTTG
Found at i:47454 original size:28 final size:29
Alignment explanation
Indices: 47421--47482 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
47411 TACAAAATTC
47421 TAAAAATTAAAAAT-TAAATGAAAGT-AGA
1 TAAAAATTAAAAATATAAAT-AAAGTGAGA
**
47449 TAAAAATTTCAAATATAAATAAAGTGAGA
1 TAAAAATTAAAAATATAAATAAAGTGAGA
*
47478 GAAAA
1 TAAAA
47483 TGAGGAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.63, C:0.02, G:0.11, T:0.24
Consensus pattern (29 bp):
TAAAAATTAAAAATATAAATAAAGTGAGA
Found at i:49401 original size:62 final size:61
Alignment explanation
Indices: 49326--49450 Score: 189
Period size: 62 Copynumber: 2.0 Consensus size: 61
49316 AAATGTTTAG
*
49326 TGGTACAAGTACTTTGAAAATATATAATGTGGTACCTGAACTATCAATATG-TGTTATTATTA
1 TGGTACAAGTACTTTGAAAATATATAATGTGGTACCTAAACTATCAATA-GATGTT-TTATTA
* * *
49388 TGGTACATGTACTTTGAAAATGTTTAATGTGGTACCTAAACTATCAATAGATGTTTTATTA
1 TGGTACAAGTACTTTGAAAATATATAATGTGGTACCTAAACTATCAATAGATGTTTTATTA
49449 TG
1 TG
49451 ATACTTGGTA
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
61 9 0.16
62 49 0.84
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.40
Consensus pattern (61 bp):
TGGTACAAGTACTTTGAAAATATATAATGTGGTACCTAAACTATCAATAGATGTTTTATTA
Found at i:58868 original size:15 final size:16
Alignment explanation
Indices: 58837--58869 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58827 GACAAAACCT
58837 AAAATAAAATCAAATC
1 AAAATAAAATCAAATC
*
58853 AAAATTAAAT-AAATC
1 AAAATAAAATCAAATC
58868 AA
1 AA
58870 TTAAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATAAAATCAAATC
Found at i:58873 original size:13 final size:14
Alignment explanation
Indices: 58841--58892 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 14
58831 AAACCTAAAA
58841 TAAAATCAAATCAAAAT
1 TAAAAT-AAATC--AAT
58858 T-AAATAAATCAAT
1 TAAAATAAATCAAT
*
58871 TAAAATAAAT-AAC
1 TAAAATAAATCAAT
58884 TAAAATAAA
1 TAAAATAAA
58893 AAATAAATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 15 0.45
14 8 0.24
15 5 0.15
16 4 0.12
17 1 0.03
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAAATAAATCAAT
Found at i:61809 original size:15 final size:15
Alignment explanation
Indices: 61789--61824 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
61779 ACCCATAGAA
* *
61789 TATTTTTTTATTTTT
1 TATTTTTTCATATTT
61804 TATTTTTTCATATTT
1 TATTTTTTCATATTT
61819 TATTTT
1 TATTTT
61825 ATTTTTTCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (15 bp):
TATTTTTTCATATTT
Done.