Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold646
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: 66412
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:4427 original size:13 final size:13
Alignment explanation
Indices: 4409--4433 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4399 ACACAAAGTA
4409 TGTATCGATACAG
1 TGTATCGATACAG
4422 TGTATCGATACA
1 TGTATCGATACA
4434 CAAAAAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:4431 original size:32 final size:33
Alignment explanation
Indices: 4390--4453 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
4380 TAGCCAAACT
**
4390 TGTATCGATACACAAAGTA-TGTATCGATACAG
1 TGTATCGATACACAAAAAATTGTATCGATACAG
4422 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
4454 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAG
Found at i:7013 original size:20 final size:20
Alignment explanation
Indices: 6985--7059 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
6975 TCATACCCTG
6985 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
7005 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
7025 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
7045 ATGTATCGATACATT
1 ATGTATCGATACATT
7060 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:7052 original size:40 final size:39
Alignment explanation
Indices: 6985--7062 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
6975 TCATACCCTG
* *
6985 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
7025 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
7063 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:8013 original size:17 final size:19
Alignment explanation
Indices: 7980--8020 Score: 68
Period size: 17 Copynumber: 2.3 Consensus size: 19
7970 CATGCATTTT
7980 TTTTATTATGTTTCATGCA
1 TTTTATTATGTTTCATGCA
7999 TTTT-TTATG-TTCATGCA
1 TTTTATTATGTTTCATGCA
8016 TTTTA
1 TTTTA
8021 CATGTCCAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.57
18 5 0.24
19 4 0.19
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.61
Consensus pattern (19 bp):
TTTTATTATGTTTCATGCA
Found at i:8025 original size:17 final size:17
Alignment explanation
Indices: 7991--8025 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
7981 TTTATTATGT
**
7991 TTCATGCATTTTTTATG
1 TTCATGCATTTTACATG
8008 TTCATGCATTTTACATG
1 TTCATGCATTTTACATG
8025 T
1 T
8026 CCAGCATCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.14, G:0.11, T:0.54
Consensus pattern (17 bp):
TTCATGCATTTTACATG
Found at i:21099 original size:12 final size:11
Alignment explanation
Indices: 21080--21112 Score: 57
Period size: 12 Copynumber: 2.9 Consensus size: 11
21070 GTTACACCCA
21080 AAAAAAAAAAC
1 AAAAAAAAAAC
21091 AAAACAAAAAAC
1 AAAA-AAAAAAC
21103 AAAAAAAAAA
1 AAAAAAAAAA
21113 TAGCAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:21119 original size:21 final size:18
Alignment explanation
Indices: 21079--21122 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
21069 CGTTACACCC
*
21079 AAAAAAAAAAACAAAACA
1 AAAAAAAAAAAAAAAACA
21097 AAAAACAAAAAAAAAATAGCA
1 AAAAA-AAAAAAAAAA-A-CA
21118 AAAAA
1 AAAAA
21123 TAGAAGGGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 5 0.23
19 9 0.41
20 1 0.05
21 7 0.32
ACGTcount: A:0.86, C:0.09, G:0.02, T:0.02
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAACA
Found at i:22798 original size:32 final size:32
Alignment explanation
Indices: 22345--23627 Score: 1551
Period size: 32 Copynumber: 42.2 Consensus size: 32
22335 TGTTCATCCC
*
22345 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
* * *
22374 TTTCAAAGCCCACA-AA-TCAGTGGC-ACTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
22403 TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
22431 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
* ** * *
22460 TTTCAAAG-CC-TACAAGTTAGTGGC-ACTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
22489 TTTCAAAGCCCACA-AA-TCAGTGGC-ACTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
22518 TTTTAAAG-CC-CACAAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
*
22547 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
* * *
22576 TTTCAAAGCCCACA-AA-TCAGTGGC-ACTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
22605 TTTCAAAG-CC-CACAAGTCAGTGGC-ACCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* ** *
22633 TTTCAAAG-CC-CACAACTCATTGGC-ATCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
22661 TTTCAAAG-CC-CACAAGTCAGTGGC-ACTCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAAC-CCA
* * * *
22690 TTTCAAAG-CC-CACAAGCCAGTGGC-ACTCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* **
22719 TTTCAGAG-CC-CACAAGTTAGTGGC-ACCC-
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
22747 TTTCAGAG-CC-CACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
22777 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
22809 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
22841 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
22873 TTTCAAAGCCCACACAAGTCGGTGGCAA-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
22904 -TTC--AG--C-CACAAGTC-GT-GC-A-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
22926 -TTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
22957 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
22989 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
23021 TTCCAAAGCCCACACAAGTCGGTGGCAA-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
23052 -TTC-AAG-CC-CACAAGTCGGTGGCAA-CCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
23079 -TTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
23110 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
23142 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
23174 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
23206 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
23238 -TTCAAAGCCCACACAAGTCGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
23269 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
23301 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
23333 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
23365 TTCCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
23397 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
23429 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
23461 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
23493 TTTCAAAACCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* *
23525 TTCCAAAGCCCACACAAGTCGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
23557 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* ** * *
23589 TTTAAAAGCCCATGCAAGTCAGTGGCAACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
23621 TTTCAAA
1 TTTCAAA
23628 TCACCATATT
Statistics
Matches: 1166, Mismatches: 49, Indels: 75
0.90 0.04 0.06
Matches are distributed among these distances:
22 7 0.01
23 2 0.00
24 4 0.00
25 8 0.01
26 2 0.00
27 36 0.03
28 121 0.10
29 227 0.19
30 42 0.04
31 49 0.04
32 668 0.57
ACGTcount: A:0.30, C:0.34, G:0.18, T:0.17
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
Found at i:24183 original size:20 final size:20
Alignment explanation
Indices: 24155--24229 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
24145 TCATACCCTG
24155 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
24175 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
24195 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
24215 ATGTATCGATACATT
1 ATGTATCGATACATT
24230 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:24222 original size:40 final size:39
Alignment explanation
Indices: 24155--24232 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
24145 TCATACCCTG
* *
24155 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
24195 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
24233 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:29668 original size:21 final size:22
Alignment explanation
Indices: 29644--29693 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
29634 ATCAAATCTT
* *
29644 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
29665 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
29687 --TCAAAAT
1 CTTCAAAAT
29694 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:31471 original size:21 final size:23
Alignment explanation
Indices: 31431--31473 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
31421 TTTTAACCGA
*
31431 TTATCAAGGAGGAGAAATTTTTT
1 TTATCAAAGAGGAGAAATTTTTT
31454 TTATCAAAG-GGA-AAATTTTT
1 TTATCAAAGAGGAGAAATTTTT
31474 GACAAGAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
TTATCAAAGAGGAGAAATTTTTT
Found at i:32102 original size:20 final size:20
Alignment explanation
Indices: 32056--32114 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
32046 TTGTATTGAT
*
32056 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGA
*
32075 TC-ATTGTATCGATACATGA
1 ACAATTGTATCGATACATGA
*
32094 ACAATTGTATTGATACATGA
1 ACAATTGTATCGATACATGA
32114 A
1 A
32115 ACTGGCAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 17 0.50
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (20 bp):
ACAATTGTATCGATACATGA
Found at i:33012 original size:36 final size:36
Alignment explanation
Indices: 32971--33118 Score: 98
Period size: 36 Copynumber: 3.6 Consensus size: 36
32961 AGAAAAAAAT
32971 TATTGTACATGTATTATTTTTATTAAAATTAATTAA
1 TATTGTACATGTATTATTTTTATTAAAATTAATTAA
* *
33007 TATTGTGCATGCATTATTACTTTTTATCTATAAATTATTTTTAA
1 TATTGTACATG---TATTA-TTTTTAT-TA-AAATTA--ATTAA
* * *
33051 TTTATTTATAAATTATACAAATTTATTTTTATTAAAATTAATTAA
1 --TA-TTGTACA-TGT----A-TTATTTTTATTAAAATTAATTAA
33096 TATTGTACATGTATTATTTTTAT
1 TATTGTACATGTATTATTTTTAT
33119 AATAAATAGA
Statistics
Matches: 85, Mismatches: 10, Indels: 34
0.66 0.08 0.26
Matches are distributed among these distances:
36 20 0.24
37 1 0.01
39 5 0.06
40 7 0.08
41 4 0.05
42 11 0.13
43 2 0.02
44 4 0.05
45 5 0.06
46 2 0.02
47 10 0.12
48 3 0.04
49 8 0.09
50 3 0.04
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.55
Consensus pattern (36 bp):
TATTGTACATGTATTATTTTTATTAAAATTAATTAA
Found at i:36566 original size:94 final size:92
Alignment explanation
Indices: 36036--37135 Score: 1113
Period size: 94 Copynumber: 12.1 Consensus size: 92
36026 ACTGTGATAG
*** * * *
36036 TTACAATCAATCAACTTT-TTAACTTTTCTATCAAAAGGAATCTGATTCTCAAATATAATTTATG
1 TTACAATCAATCAACTTTCTTTTTTTTTCTAT-AAAAAGAATCTGATTCTCAGATATAATTCATG
** * * * * *
36100 CATTAGTCTAATATTTGCAGTGTCATAC
65 CATTAGTCTAATCCTTACAGTCTGACAT
* * * * * *
36128 TTATAATTAACCAACTTTTCTTCTTTTTTTACCA-AAAAA-AATCCGATTCTCATG-TACAATTC
1 TTACAATCAATCAAC-TTTCTT-TTTTTTT-CTATAAAAAGAATCTGATTCTCA-GATATAATTC
* * *
36190 ATGCATTAGTCTAATCATTGCAGTTTGACAT
62 ATGCATTAGTCTAATCCTTACAGTCTGACAT
* *
36221 TTACAATCAGTCAA----CTTTTTTTTTCTATAAAAAAGAATCTGATTCTTAGATATAATTCATG
1 TTACAATCAATCAACTTTCTTTTTTTTTCTAT-AAAAAGAATCTGATTCTCAGATATAATTCATG
*
36282 TATTAGTCTAATCCTTACAGTCTGACAT
65 CATTAGTCTAATCCTTACAGTCTGACAT
* * * *
36310 TTACAGTCAGTCAA----C-TTTTTTTTCTATAAAAAAGAAT-TCGATTTTCATATATAATTCAT
1 TTACAATCAATCAACTTTCTTTTTTTTTCTAT-AAAAAGAATCT-GATTCTCAGATATAATTCAT
* ** *
36369 ACATTAGTCTAATCCTTGTAGTCTAACAT
64 GCATTAGTCTAATCCTTACAGTCTGACAT
* * *
36398 TTACAATCAATCAACTTT-TCTTTTTTTCTATAAAAAAAAT-TAATTCTCAGATATAATTCATGC
1 TTACAATCAATCAACTTTCTTTTTTTTTCTATAAAAAGAATCTGATTCTCAGATATAATTCATGC
* *
36461 ATTAGTCTAATCCTTACTGTCTGATAT
66 ATTAGTCTAATCCTTACAGTCTGACAT
36488 TTACAATCAATCAATCTTTCTTTTTTTTTCTATAAAAGAGAATCTGATTCTCAGATATAATTCAT
1 TTACAATCAATCAA-CTTTCTTTTTTTTTCTATAAAA-AGAATCTGATTCTCAGATATAATTCAT
* * * ** **
36553 GTATTAGTTTAATCTTTACAACCTGATGT
64 GCATTAGTCTAATCCTTACAGTCTGACAT
* *
36582 TTACAATCAGTCAACTTTTCTTTTTTTTTCTATAAAAAAGAATAC-GATTCTCAAATATAATTCA
1 TTACAATCAATCAAC-TTTCTTTTTTTTTCTAT-AAAAAGAAT-CTGATTCTCAGATATAATTCA
* *
36646 TGCATTAGTCTAATCCTTGCAGTTTGACAT
63 TGCATTAGTCTAATCCTTACAGTCTGACAT
* * * *
36676 TTATAATCAATCAACTTT-TCTTTTTTTCTATGAAAAAGAAT-TGATTCTCAAATATAATTTATG
1 TTACAATCAATCAACTTTCTTTTTTTTTCTAT-AAAAAGAATCTGATTCTCAGATATAATTCATG
* *
36739 CATTAGTCTAATTCTTACAGTCTGATAT
65 CATTAGTCTAATCCTTACAGTCTGACAT
* * * ** *
36767 TTACAATCATTCAAATTTTCTTTTTTTTTATA-AAAAAGAATCCAATTCTCAAATATAATTCATG
1 TTACAATCAATC-AACTTTCTTTTTTTTTCTATAAAAAGAATCTGATTCTCAGATATAATTCATG
*
36831 CATTAGTCTAATCCTTGCAGTCTGACAT
65 CATTAGTCTAATCCTTACAGTCTGACAT
* * * *
36859 TTATAATCAATCAA----CTTTTTTTTTCTATAAAAAAAAT-TGATTCTCAGATATAATTTATGT
1 TTACAATCAATCAACTTTCTTTTTTTTTCTATAAAAAGAATCTGATTCTCAGATATAATTCATGC
* *
36919 ATTGGTCTAATCCTTGCAGTCTGACAT
66 ATTAGTCTAATCCTTACAGTCTGACAT
* * * * *
36946 TTACAATTAGTCAAC-TT-TTTTTTTTTGTA-AAAAAGAATCTGATTTTCAGATATAATTCATGT
1 TTACAATCAATCAACTTTCTTTTTTTTTCTATAAAAAGAATCTGATTCTCAGATATAATTCATGC
* * *
37008 ATTAGTTTAATCTTTATAGTCTGACAT
66 ATTAGTCTAATCCTTACAGTCTGACAT
* * * *
37035 TTACAATCAGTCAACTTTTCTTTTTTTTTTCTATAAAAAAAATCCGATTCTTAGATATAATTCAT
1 TTACAATCAATCAAC-TTTC-TTTTTTTTTCTATAAAAAGAATCTGATTCTCAGATATAATTCAT
* *
37100 GTATTAGTCTATTCCTTACAGTCTGACAT
64 GCATTAGTCTAATCCTTACAGTCTGACAT
37129 TTACAAT
1 TTACAAT
37136 TTATACATTA
Statistics
Matches: 847, Mismatches: 125, Indels: 70
0.81 0.12 0.07
Matches are distributed among these distances:
86 2 0.00
87 75 0.09
88 100 0.12
89 127 0.15
90 54 0.06
91 80 0.09
92 119 0.14
93 85 0.10
94 194 0.23
95 9 0.01
96 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (92 bp):
TTACAATCAATCAACTTTCTTTTTTTTTCTATAAAAAGAATCTGATTCTCAGATATAATTCATGC
ATTAGTCTAATCCTTACAGTCTGACAT
Found at i:36839 original size:183 final size:183
Alignment explanation
Indices: 36059--37135 Score: 1111
Period size: 183 Copynumber: 5.9 Consensus size: 183
36049 ACTTTTTAAC
* * * * ** * * *
36059 TTTTCTATCAAAAGGAATCTGATTCTCAAATATAATTTATGCATTAGTCTAATATTTGCAGTGTC
1 TTTTTTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTACAGTCTG
* * * * * * * * *
36124 ATACTTATAATTAACCAACTTTTCTTCTTTTTTTACCAAAAAAAATCCGATTCTCATG-TACAAT
66 ACATTTACAATCAATCAACTTTTCTT-TTTTTCTA-TAAAAAAAATCTGATTCTCA-GATATAAT
* * *
36188 TCATGCATTAGTCTAA-TCATTGCAGTTTGACATTTACAATCAGTC-AA-CTT-TTT
128 TCATGCATTAGTCTAATTC-TTACAGTCTGACATTTACAATCAGTCAAATTTTCTTT
* * * *
36241 TTTTCTATAAAAAAGAATCTGATTCTTAGATATAATTCATGTATTAGTCTAATCCTTACAGTCTG
1 TTTTTTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTACAGTCTG
* * * *
36306 ACATTTACAGTCAGTCAAC---T-TTTTTTTCTATAAAAAAGAAT-TCGATTTTCATATATAATT
66 ACATTTACAATCAATCAACTTTTCTTTTTTTCTATAAAAAA-AATCT-GATTCTCAGATATAATT
* * ** * * *
36366 CATACATTAGTCTAATCCTTGTAGTCTAACATTTACAATCAATCAACTTTTCTTT
129 CATGCATTAGTCTAATTCTTACAGTCTGACATTTACAATCAGTCAAATTTTCTTT
* * * *
36421 TTTTCTATAAAAAA-AAT-TAATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACTGTCTG
1 TTTTTTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTACAGTCTG
* * *
36484 ATATTTACAATCAATCAATCTTTCTTTTTTTTTCTATAAAAGAGAATCTGATTCTCAGATATAAT
66 ACATTTACAATCAATCAA-CTTT-TCTTTTTTTCTATAAAA-AAAATCTGATTCTCAGATATAAT
* * ** ** *
36549 TCATGTATTAGTTTAA-TCTTTACAACCTGATGTTTACAATCAGTCAACTTTTCTTTT
128 TCATGCATTAGTCTAATTC-TTACAGTCTGACATTTACAATCAGTCAAATTTTC-TTT
* *
36606 TTTTTCTATAAAAAAGAATAC-GATTCTCAAATATAATTCATGCATTAGTCTAATCCTTGCAGTT
1 TTTTT-TATAAAAAAGAAT-CTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTACAGTC
* * *
36670 TGACATTTATAATCAATCAACTTTTCTTTTTTTCTATGAAAAAGAAT-TGATTCTCAAATATAAT
64 TGACATTTACAATCAATCAACTTTTCTTTTTTTCTAT-AAAAAAAATCTGATTCTCAGATATAAT
* * *
36734 TTATGCATTAGTCTAATTCTTACAGTCTGATATTTACAATCATTCAAATTTTCTTT
128 TCATGCATTAGTCTAATTCTTACAGTCTGACATTTACAATCAGTCAAATTTTCTTT
** *
36790 TTTTTTATAAAAAAGAATCCAATTCTCAAATATAATTCATGCATTAGTCTAATCCTTGCAGTCTG
1 TTTTTTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTACAGTCTG
* *
36855 ACATTTATAATCAATCAAC--TT-TTTTTTTCTATAAAAAAAAT-TGATTCTCAGATATAATTTA
66 ACATTTACAATCAATCAACTTTTCTTTTTTTCTATAAAAAAAATCTGATTCTCAGATATAATTCA
* * * * * *
36916 TGTATTGGTCTAATCCTTGCAGTCTGACATTTACAATTAGTC-AA-CTT-TTT
131 TGCATTAGTCTAATTCTTACAGTCTGACATTTACAATCAGTCAAATTTTCTTT
* * * * * * *
36966 TTTTTTGTAAAAAAGAATCTGATTTTCAGATATAATTCATGTATTAGTTTAATCTTTATAGTCTG
1 TTTTTTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTACAGTCTG
* * *
37031 ACATTTACAATCAGTCAACTTTTCTTTTTTTTTTCTATAAAAAAAATCCGATTCTTAGATATAAT
66 ACATTTACAATCAATCAACTTTTC---TTTTTTTCTATAAAAAAAATCTGATTCTCAGATATAAT
*
37096 TCATGTATTAGTCT-ATTCCTTACAGTCTGACATTTACAAT
128 TCATGCATTAGTCTAATT-CTTACAGTCTGACATTTACAAT
37136 TTATACATTA
Statistics
Matches: 761, Mismatches: 102, Indels: 63
0.82 0.11 0.07
Matches are distributed among these distances:
176 81 0.11
177 61 0.08
178 65 0.09
179 69 0.09
180 28 0.04
181 2 0.00
182 89 0.12
183 125 0.16
184 79 0.10
185 67 0.09
186 28 0.04
187 11 0.01
188 56 0.07
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (183 bp):
TTTTTTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTACAGTCTG
ACATTTACAATCAATCAACTTTTCTTTTTTTCTATAAAAAAAATCTGATTCTCAGATATAATTCA
TGCATTAGTCTAATTCTTACAGTCTGACATTTACAATCAGTCAAATTTTCTTT
Found at i:37063 original size:270 final size:272
Alignment explanation
Indices: 36036--37135 Score: 1276
Period size: 270 Copynumber: 4.0 Consensus size: 272
36026 ACTGTGATAG
* * * *
36036 TTACAATCAATCAACTTTTTAACTTTTCTATCAAAAGGAATCTGATTCTCAAATATAATTTATGC
1 TTACAATCAATCAACTTTTT---TTTTCTATAAAAAAGAATATGATTCTCAAATATAATTCATGC
** * * * * * * * *
36101 ATTAGTCTAATATTTGCAGTGTCATACTTATAATTAACCAACTTTTCTTCTTTTTTTACCAAAAA
63 ATTAGTCTAATCCTTGCAGTCTGACATTTACAATCAATCAACTTTTCTT-TTTTTCTA-CAAAAA
* * * * *
36166 AAATCCGATTCTCATG-TACAATTCATGCATTAGTCTAATCATTGCAGTTTGACATTTACAATCA
126 AAAT-TGATTCTCA-GATATAATTCATGCATTAGTCTAATCTTTACAGTCTGACATTTACAATCA
* *
36230 GTCAA----CTTTTTTTTTCTATAAAAAAGAATCTGATTCTTAGATATAATTCATGTATTAGTCT
189 GTCAATTTTCTTTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTCATGTATTAGTCT
36291 AATCCTTACAGTCTGACAT
254 AATCCTTACAGTCTGACAT
* * * * *
36310 TTACAGTCAGTCAAC-TTTTTTTTCTATAAAAAAGAAT-TCGATTTTCATATATAATTCATACAT
1 TTACAATCAATCAACTTTTTTTTTCTATAAAAAAGAATAT-GATTCTCAAATATAATTCATGCAT
* * *
36373 TAGTCTAATCCTTGTAGTCTAACATTTACAATCAATCAACTTTTCTTTTTTTCTATAAAAAAAAT
65 TAGTCTAATCCTTGCAGTCTGACATTTACAATCAATCAACTTTTCTTTTTTTCTACAAAAAAAAT
* * * * *
36438 TAATTCTCAGATATAATTCATGCATTAGTCTAATCCTTACTGTCTGATATTTACAATCAATCAAT
130 TGATTCTCAGATATAATTCATGCATTAGTCTAATCTTTACAGTCTGACATTTACAATCAGTCAAT
* * * *
36503 CTTTCTTTTTTTTTCTATAAAAGAGAATCTGATTCTCAGATATAATTCATGTATTAGTTTAATCT
195 -TTTCTTTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTCATGTATTAGTCTAATCC
** **
36568 TTACAACCTGATGT
259 TTACAGTCTGACAT
* *
36582 TTACAATCAGTCAACTTTTCTTTTTTTTTCTATAAAAAAGAATACGATTCTCAAATATAATTCAT
1 TTACAATCAATCAA-----CTTTTTTTTTCTATAAAAAAGAATATGATTCTCAAATATAATTCAT
* * *
36647 GCATTAGTCTAATCCTTGCAGTTTGACATTTATAATCAATCAACTTTTCTTTTTTTCTATGAAAA
61 GCATTAGTCTAATCCTTGCAGTCTGACATTTACAATCAATCAACTTTTCTTTTTTTCTA-CAAAA
* * * *
36712 AGAATTGATTCTCAAATATAATTTATGCATTAGTCTAAT-TCTTACAGTCTGATATTTACAATCA
125 AAAATTGATTCTCAGATATAATTCATGCATTAGTCTAATCT-TTACAGTCTGACATTTACAATCA
* * * *
36776 TTCAAATTTTC-TTTTTTTT-TATAAAAAAGAATCCAATTCTCAAATATAATTCATGCATTAGTC
189 GTC-AATTTTCTTTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTCATGTATTAGTC
*
36839 TAATCCTTGCAGTCTGACAT
253 TAATCCTTACAGTCTGACAT
* * * *
36859 TTATAATCAATCAACTTTTTTTTTCTATAAAAAA-AAT-TGATTCTCAGATATAATTTATGTATT
1 TTACAATCAATCAACTTTTTTTTTCTATAAAAAAGAATATGATTCTCAAATATAATTCATGCATT
* * * * *
36922 GGTCTAATCCTTGCAGTCTGACATTTACAATTAGTCAACTTTT-TTTTTTTGTA-AAAAAGAATC
66 AGTCTAATCCTTGCAGTCTGACATTTACAATCAATCAACTTTTCTTTTTTTCTACAAAAAAAAT-
* * * *
36985 TGATTTTCAGATATAATTCATGTATTAGTTTAATCTTTATAGTCTGACATTTACAATCAGTCAAC
130 TGATTCTCAGATATAATTCATGCATTAGTCTAATCTTTACAGTCTGACATTTACAATCAGTCAA-
* *
37050 TTTTCTTTTTTTTTTCTATAAAAAA-AATCCGATTCTTAGATATAATTCATGTATTAGTCTATTC
194 TTTTC-TTTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTCATGTATTAGTCTAATC
37114 CTTACAGTCTGACAT
258 CTTACAGTCTGACAT
37129 TTACAAT
1 TTACAAT
37136 TTATACATTA
Statistics
Matches: 710, Mismatches: 93, Indels: 50
0.83 0.11 0.06
Matches are distributed among these distances:
266 1 0.00
267 64 0.09
268 66 0.09
269 18 0.03
270 195 0.27
271 12 0.02
272 100 0.14
273 4 0.01
274 13 0.02
277 65 0.09
278 102 0.14
279 67 0.09
280 3 0.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (272 bp):
TTACAATCAATCAACTTTTTTTTTCTATAAAAAAGAATATGATTCTCAAATATAATTCATGCATT
AGTCTAATCCTTGCAGTCTGACATTTACAATCAATCAACTTTTCTTTTTTTCTACAAAAAAAATT
GATTCTCAGATATAATTCATGCATTAGTCTAATCTTTACAGTCTGACATTTACAATCAGTCAATT
TTCTTTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTCATGTATTAGTCTAATCCTT
ACAGTCTGACAT
Found at i:37644 original size:27 final size:26
Alignment explanation
Indices: 37597--37673 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 26
37587 ATTTAAAAGA
*
37597 TTTAATAAATAATAATGTATTAATTATTAT
1 TTTAATAAA-AATAA--TATTAATTA-AAT
37627 TTTAATAAAAATAATATTTAATTAAAT
1 TTTAATAAAAATAATA-TTAATTAAAT
*
37654 TTTAA-AAAAATTTATATTAA
1 TTTAATAAAAA-TAATATTAA
37674 AAAATTAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 9 0.21
27 13 0.30
28 7 0.16
29 5 0.12
30 9 0.21
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (26 bp):
TTTAATAAAAATAATATTAATTAAAT
Found at i:37830 original size:126 final size:123
Alignment explanation
Indices: 37632--37973 Score: 417
Period size: 123 Copynumber: 2.7 Consensus size: 123
37622 ATTATTTTAA
* * *
37632 TAAAAATAATATTTAATTAAATTTTAAAAAAATTTATATTAAAAAATTAAAATATTAATT-TT-T
1 TAAAAATAATATTTAATT-AAGTTT-AAAAAA-TTACATTAACAAATTAAAATATTAATTATTAT
*** *
37695 -TTAAAATAAAAAAATTTAAA-TAAAAATAAAAAATGATTTATTATTATTATTTTTTAATAAAAT
63 GTTTTTATAAAAAAATTTAAATTAAAAAT-AAAAATG-TTT-TTATTA-TAATTTTTAATAAAAT
*
37758 TAAAAATAATATTTAATTAGGTTTAAAAAATTACATTAACAAATTAAAATATTAATTATTATGTT
1 TAAAAATAATATTTAATTAAGTTTAAAAAATTACATTAACAAATTAAAATATTAATTATTATGTT
* *
37823 TTTATAAAAATAA--AAAATTTTAAAATAAAAATGTTTTTATTATAATTTTTAATAAAAT
66 TTTATAAAAA-AATTTAAA-TTAAAAATAAAAATGTTTTTATTATAATTTTTAATAAAAT
* *
37881 AAAAAATAATATTTAATTAAGTTTAAAAATTTACATTAACAAATTAAAATATTAATTATTATGTT
1 TAAAAATAATATTTAATTAAGTTTAAAAAATTACATTAACAAATTAAAATATTAATTATTATG-T
*
37946 TTTTAAAATAAAAATTTTAAATTAAAAA
65 TTTTATAA-AAAAA-TTTAAATTAAAAA
37974 AAGTTTTTTA
Statistics
Matches: 189, Mismatches: 16, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
123 100 0.53
124 24 0.13
125 14 0.07
126 40 0.21
127 11 0.06
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (123 bp):
TAAAAATAATATTTAATTAAGTTTAAAAAATTACATTAACAAATTAAAATATTAATTATTATGTT
TTTATAAAAAAATTTAAATTAAAAATAAAAATGTTTTTATTATAATTTTTAATAAAAT
Found at i:38605 original size:118 final size:117
Alignment explanation
Indices: 38383--38607 Score: 291
Period size: 117 Copynumber: 1.9 Consensus size: 117
38373 TTTTTATAAA
* * *
38383 AAAATAATAGTTAATATTTTAATTTGTTAATATAATTTTTTTAAACTTAATTAAATATTATTTTT
1 AAAATAATAATTAATATTTTAATTTATTAATATAATTTTTTTAAACTTAATTAAATATTACTTTT
*
38448 AATTTTATTAAAAATAATAATAATAAATCCTTTTTAATTTAATTTTTTATTTTT
66 AA-TTTA-TAAAAATAATAATAATAAATCATTTTTAATTTAATTTTTTATTTTT
* *
38502 AAAA-AATAATTAATATTTTAATTTATTAATGTAA-TTTTTTAAAGTTAATTAAATATTACTTTT
1 AAAATAATAATTAATATTTTAATTTATTAATATAATTTTTTTAAACTTAATTAAATATTACTTTT
* * *
38565 -A-TTA-AAAAATAATAATTAATACATTATTATTT-ATTAAATTTTT
66 AATTTATAAAAATAATAA-TAATAAATCATT-TTTAATTTAATTTTT
38608 AAATTTAATT
Statistics
Matches: 95, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
112 11 0.12
113 19 0.20
114 6 0.06
116 1 0.01
117 27 0.28
118 27 0.28
119 4 0.04
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (117 bp):
AAAATAATAATTAATATTTTAATTTATTAATATAATTTTTTTAAACTTAATTAAATATTACTTTT
AATTTATAAAAATAATAATAATAAATCATTTTTAATTTAATTTTTTATTTTT
Found at i:38749 original size:15 final size:15
Alignment explanation
Indices: 38729--38777 Score: 59
Period size: 14 Copynumber: 3.3 Consensus size: 15
38719 AGTATTCATA
38729 AAAAAAACTTATTTT
1 AAAAAAACTTATTTT
38744 -AAAAAA--TATTTT
1 AAAAAAACTTATTTT
38756 ATAAAAAACTTATTTAT
1 A-AAAAAACTTATTT-T
38773 AAAAA
1 AAAAA
38778 TAAAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 6 0.21
14 12 0.41
16 9 0.31
17 2 0.07
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAAAAACTTATTTT
Found at i:39100 original size:14 final size:15
Alignment explanation
Indices: 39077--39115 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
39067 GTATTATGTT
39077 TAAATT-ATTTTTTA
1 TAAATTAATTTTTTA
39091 -AAATTAATTTTTTA
1 TAAATTAATTTTTTA
*
39105 TATATTAATTT
1 TAAATTAATTT
39116 ATTTTATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 5 0.23
14 8 0.36
15 9 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TAAATTAATTTTTTA
Found at i:39111 original size:15 final size:15
Alignment explanation
Indices: 39083--39124 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
39073 TGTTTAAATT
*
39083 ATTTTTTA-AAATTA
1 ATTTTTTATATATTA
39097 ATTTTTTATATATTA
1 ATTTTTTATATATTA
39112 ATTTATTT-TATAT
1 ATTT-TTTATATAT
39125 CTTACATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 8 0.32
15 14 0.56
16 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTTTTATATATTA
Found at i:39518 original size:20 final size:19
Alignment explanation
Indices: 39471--39522 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
39461 ATAAATTATT
*
39471 AATATATAAAAATTTAAATA
1 AATATAT-AATATTTAAATA
39491 AATATATAATATTTAAAATA
1 AATATATAATATTT-AAATA
39511 AA-ATTATAATAT
1 AATA-TATAATAT
39523 ATTTTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATATATAATATTTAAATA
Found at i:40960 original size:3 final size:3
Alignment explanation
Indices: 40952--40976 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40942 ATACCGTTCT
40952 CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC C
40977 GCCGCTGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:41639 original size:24 final size:24
Alignment explanation
Indices: 41612--41676 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
41602 AACATTTTTA
* *
41612 ATTTAATAATTTAATATACGGTAT
1 ATTTAATAATTAAATATACGATAT
*
41636 ATTTAATAATTAAATATATGATAT
1 ATTTAATAATTAAATATACGATAT
41660 ATTT--TAATGTAAATATA
1 ATTTAATAAT-TAAATATA
41677 TTTTTAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.11
23 8 0.22
24 25 0.68
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (24 bp):
ATTTAATAATTAAATATACGATAT
Found at i:42520 original size:21 final size:21
Alignment explanation
Indices: 42473--42542 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 21
42463 TACTGTATTT
* *
42473 TTTTATTATAATTTTATTTAAA
1 TTTT-TTATAAATTTATATAAA
*
42495 -ATTTTATAAATTTATATAAA
1 TTTTTTATAAATTTATATAAA
42515 TTTTTTATAAA-TTA-AT-AA
1 TTTTTTATAAATTTATATAAA
42533 TTTATTTATA
1 TTT-TTTATA
42543 TTAATTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 5 0.12
19 8 0.19
20 18 0.43
21 11 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTTTATAAATTTATATAAA
Found at i:42549 original size:14 final size:14
Alignment explanation
Indices: 42530--42581 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
42520 TATAAATTAA
42530 TAATTTATTTATAT
1 TAATTTATTTATAT
*
42544 TAATTTAATTATAT
1 TAATTTATTTATAT
* * *
42558 TTATATGTTTATAT
1 TAATTTATTTATAT
42572 TATATTTATT
1 TA-ATTTATT
42582 AAAATTTAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 24 0.83
15 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
TAATTTATTTATAT
Found at i:42964 original size:31 final size:31
Alignment explanation
Indices: 42937--43001 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
42927 TATTTATTTA
*
42937 TTTATTTA-TACTATATTATATTTTTTATAT
1 TTTAATTATTACTATATTATATTTTTTATAT
**
42967 TTTAATTATTTTTATATTATATTATTTTATAT
1 TTTAATTATTACTATATTATATT-TTTTATAT
42999 TTT
1 TTT
43002 TTAATTAGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 7 0.23
31 12 0.40
32 11 0.37
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (31 bp):
TTTAATTATTACTATATTATATTTTTTATAT
Found at i:42966 original size:9 final size:9
Alignment explanation
Indices: 42952--43004 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 9
42942 TTATACTATA
42952 TTATATTTT
1 TTATATTTT
42961 TTATATTTT
1 TTATATTTT
*
42970 AATTATTTTTAT
1 --TTATATTT-T
42982 ATTATATTATT
1 -TTATATT-TT
42993 TTATATTTT
1 TTATATTTT
43002 TTA
1 TTA
43005 ATTAGTGTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 14 0.37
10 7 0.18
11 15 0.39
12 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTATATTTT
Found at i:42980 original size:17 final size:17
Alignment explanation
Indices: 42958--43008 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
42948 TATATTATAT
42958 TTTTTATATTTTAATTA
1 TTTTTATATTTTAATTA
*
42975 TTTTTATATTAT-ATTA
1 TTTTTATATTTTAATTA
*
42991 TTTTATATTTTTTAATTA
1 TTTT-TATATTTTAATTA
43009 GTGTATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 8 0.28
17 17 0.59
18 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTATATTTTAATTA
Found at i:43233 original size:2 final size:2
Alignment explanation
Indices: 43228--43256 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43218 TCACACACAC
43228 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
43257 AAAAGAAAAA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45245 original size:24 final size:22
Alignment explanation
Indices: 45218--45277 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 22
45208 AAAATTAAAA
45218 TAATAAATTATATTAAAAATATT
1 TAATAAATTATATTAAAAA-ATT
** *
45241 CTAATAAAAAATATTTAAAAATT
1 -TAATAAATTATATTAAAAAATT
45264 TAATAAATTATATT
1 TAATAAATTATATT
45278 TTAAAATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 12 0.39
23 3 0.10
24 16 0.52
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TAATAAATTATATTAAAAAATT
Found at i:45270 original size:22 final size:23
Alignment explanation
Indices: 45218--45284 Score: 82
Period size: 22 Copynumber: 2.9 Consensus size: 23
45208 AAAATTAAAA
*
45218 TAATAAATTATATTAAAAATATTC
1 TAATAAATTATATTTAAAA-ATTC
**
45242 TAATAAAAAATATTTAAAAATT-
1 TAATAAATTATATTTAAAAATTC
*
45264 TAATAAATTATATTTTAAAAT
1 TAATAAATTATATTTAAAAAT
45285 AAAATTTAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
22 18 0.49
23 3 0.08
24 16 0.43
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATAAATTATATTTAAAAATTC
Found at i:45320 original size:13 final size:13
Alignment explanation
Indices: 45302--45344 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
45292 AGATATATTG
45302 AAAATAAGATTTA
1 AAAATAAGATTTA
**
45315 AAAATATTATTTA
1 AAAATAAGATTTA
45328 AAAAT-AGCATTTA
1 AAAATAAG-ATTTA
45341 AAAA
1 AAAA
45345 ATATTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (13 bp):
AAAATAAGATTTA
Found at i:45321 original size:22 final size:22
Alignment explanation
Indices: 45280--45322 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
45270 ATTATATTTT
* *
45280 AAAATAAAATTTAGATATATTG
1 AAAATAAAATTTAAAAATATTG
*
45302 AAAATAAGATTTAAAAATATT
1 AAAATAAAATTTAAAAATATT
45323 ATTTAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (22 bp):
AAAATAAAATTTAAAAATATTG
Found at i:45339 original size:26 final size:26
Alignment explanation
Indices: 45302--45367 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
45292 AGATATATTG
45302 AAAATAAGATTT-AAAAATATTATTTA
1 AAAATAAGATTTAAAAAATATT-TTTA
45328 AAAAT-AGCATTTAAAAAATATTTTTA
1 AAAATAAG-ATTTAAAAAATATTTTTA
* * *
45354 TATATAATATTTAA
1 AAAATAAGATTTAA
45368 TACTAAAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 2 0.06
26 22 0.65
27 10 0.29
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (26 bp):
AAAATAAGATTTAAAAAATATTTTTA
Found at i:45475 original size:12 final size:12
Alignment explanation
Indices: 45458--45496 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
45448 AAATAATAAT
45458 TTATATTTAAAA
1 TTATATTTAAAA
45470 TTATA-TTAAAA
1 TTATATTTAAAA
*
45481 TTATATATAAATA
1 TTATATTTAAA-A
45494 TTA
1 TTA
45497 AGTTTTACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 11 0.46
12 9 0.38
13 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TTATATTTAAAA
Found at i:50312 original size:18 final size:18
Alignment explanation
Indices: 50298--50337 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
50288 CAAAAAAGAA
*
50298 AAAGGAAAAACAAAAAAT
1 AAAGAAAAAACAAAAAAT
50316 AAAGAAAAAACAAAAAAT
1 AAAGAAAAAACAAAAAAT
50334 AAAG
1 AAAG
50338 TAAGAAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.80, C:0.05, G:0.10, T:0.05
Consensus pattern (18 bp):
AAAGAAAAAACAAAAAAT
Found at i:51375 original size:48 final size:49
Alignment explanation
Indices: 51317--51416 Score: 121
Period size: 49 Copynumber: 2.1 Consensus size: 49
51307 TCAAATAGAC
** * *
51317 CAAAATTAAGTCTTTTGGGGTTAA-CTCATGCTTTCAGTCAAAATTGAT
1 CAAAATTAAGTCTTTTAAGGTAAATCTCATGCTTTCAGTCAAAACTGAT
* * * *
51365 CAAAATTAAGTTTTTTAAGGTAAATTTTATGCTTTCTGTCAAAACTGAT
1 CAAAATTAAGTCTTTTAAGGTAAATCTCATGCTTTCAGTCAAAACTGAT
51414 CAA
1 CAA
51417 GAATCTAGTC
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
48 20 0.47
49 23 0.53
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (49 bp):
CAAAATTAAGTCTTTTAAGGTAAATCTCATGCTTTCAGTCAAAACTGAT
Found at i:51488 original size:50 final size:50
Alignment explanation
Indices: 51348--51492 Score: 134
Period size: 50 Copynumber: 2.9 Consensus size: 50
51338 TAACTCATGC
* * * * *
51348 TTTCAGTCAAAATTGATCAAAATTAAGTTTTTTAAGGTAAATTTTATGCTT
1 TTTCA-TCAAAATTGATCAAAATCAAGTCTTTTAAGGTTAGTTTTATGATT
* * * * *
51399 TCT-GTCAAAACTGATCAAGAATCTAGTCTCTT-AGAGTTAGTTTT-TGTATT
1 TTTCATCAAAATTGATCAA-AATCAAGTCTTTTAAG-GTTAGTTTTATG-ATT
*
51449 TTTCATCGAAATTGATCAAAATCAAGTCTTTTAAGGTTAGTTTT
1 TTTCATCAAAATTGATCAAAATCAAGTCTTTTAAGGTTAGTTTT
51493 GCACTTACTA
Statistics
Matches: 73, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
49 17 0.23
50 40 0.55
51 16 0.22
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (50 bp):
TTTCATCAAAATTGATCAAAATCAAGTCTTTTAAGGTTAGTTTTATGATT
Found at i:61268 original size:13 final size:13
Alignment explanation
Indices: 61250--61276 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
61240 ACATTATGCT
61250 TTGTATCGATACA
1 TTGTATCGATACA
61263 TTGTATCGATACA
1 TTGTATCGATACA
61276 T
1 T
61277 AATTTATACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:62818 original size:20 final size:21
Alignment explanation
Indices: 62793--62844 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
62783 AGGCCAAATG
*
62793 TATCGATACAATTCAAGC-TA
1 TATCGATACAATTCAAACATA
* * *
62813 TATCGATAAAATTTAAACATT
1 TATCGATACAATTCAAACATA
62834 TATCGATACAA
1 TATCGATACAA
62845 ACACAGGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (21 bp):
TATCGATACAATTCAAACATA
Found at i:62956 original size:33 final size:33
Alignment explanation
Indices: 62914--62978 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
62904 AATTTCATAG
62914 TGTATCGATACAAAGCAATTTGTATCGATACAA
1 TGTATCGATACAAAGCAATTTGTATCGATACAA
** *
62947 TGTATCGATACTTAGTAATTTGTATCGATACA
1 TGTATCGATACAAAGCAATTTGTATCGATACA
62979 TCCATATGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAAAGCAATTTGTATCGATACAA
Done.