Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2044
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: 81672
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:3311 original size:52 final size:52
Alignment explanation
Indices: 3233--3433 Score: 334
Period size: 52 Copynumber: 3.9 Consensus size: 52
3223 CGAAATATGA
*
3233 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
*
3285 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
3337 AAATTTGCCTGCATGTATCGATACAGTT-TATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGTATAGTGTATCGATACATCTGGGC
**
3389 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGTAT-AGTGTATCGATACA
3434 ATGTATCGAT
Statistics
Matches: 142, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
51 2 0.01
52 138 0.97
53 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.33
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
Found at i:3440 original size:13 final size:13
Alignment explanation
Indices: 3422--3446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3412 CAAAGATCAG
3422 TGTATCGATACAA
1 TGTATCGATACAA
3435 TGTATCGATACA
1 TGTATCGATACA
3447 TTTAAGTGAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3528 original size:13 final size:13
Alignment explanation
Indices: 3510--3534 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3500 AAAAAAAACA
3510 TGTATCGATACAT
1 TGTATCGATACAT
3523 TGTATCGATACA
1 TGTATCGATACA
3535 ACACTTTATG
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:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3633 original size:21 final size:21
Alignment explanation
Indices: 3592--3633 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3582 GTTGGGACCT
*
3592 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
3613 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
3634 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:6183 original size:37 final size:34
Alignment explanation
Indices: 6109--6176 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
6099 AATTGAGAAG
*
6109 TAAAAGAGTTAGAAATCATATAACAATAATGAAA
1 TAAAAGAGTTAGAAATCATATAACAACAATGAAA
* * *
6143 TAAAAGAGTTAGAAATTATATCATAACAATGAAA
1 TAAAAGAGTTAGAAATCATATAACAACAATGAAA
6177 AGATAAAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.57, C:0.06, G:0.12, T:0.25
Consensus pattern (34 bp):
TAAAAGAGTTAGAAATCATATAACAACAATGAAA
Found at i:6985 original size:20 final size:20
Alignment explanation
Indices: 6956--7114 Score: 153
Period size: 20 Copynumber: 7.8 Consensus size: 20
6946 TTTTACCTAG
*
6956 ATGTATCGATACCTTTTCCA
1 ATGTATCGATACATTTTCCA
* ** *
6976 ATGCATCGATACATTACCCTG
1 ATGTATCGATACATTTTCC-A
*
6997 ATGTATCGATACATCTTCCA
1 ATGTATCGATACATTTTCCA
**
7017 ATGTATCGATACATTACCCA
1 ATGTATCGATACATTTTCCA
7037 GATGTATCGATACATCTTT-CA
1 -ATGTATCGATACAT-TTTCCA
* *
7058 ATGTATCGATACATGTAT-GA
1 ATGTATCGATACAT-TTTCCA
*
7078 ATGTATAGATACATTCTT-CA
1 ATGTATCGATACATT-TTCCA
7098 ATGTATCGATACATTTT
1 ATGTATCGATACATTTT
7115 GTCCTTTTAC
Statistics
Matches: 113, Mismatches: 22, Indels: 9
0.78 0.15 0.06
Matches are distributed among these distances:
19 3 0.03
20 78 0.69
21 31 0.27
22 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTTTCCA
Found at i:7002 original size:41 final size:40
Alignment explanation
Indices: 6955--7112 Score: 196
Period size: 41 Copynumber: 3.9 Consensus size: 40
6945 TTTTTACCTA
* *
6955 GATGTATCGATACCTTTTCCAATGCATCGATACATTACCCT
1 GATGTATCGATACATTTT-CAATGTATCGATACATTACCCT
* *
6996 GATGTATCGATACATCTTCCAATGTATCGATACATTACCCA
1 GATGTATCGATACAT-TTTCAATGTATCGATACATTACCCT
7037 GATGTATCGATACATCTTTCAATGTATCGATACATGTA---T
1 GATGTATCGATACAT-TTTCAATGTATCGATACAT-TACCCT
*
7076 GAATGTATAGATACATTCTTCAATGTATCGATACATT
1 G-ATGTATCGATACATT-TTCAATGTATCGATACATT
7113 TTGTCCTTTT
Statistics
Matches: 106, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
39 3 0.03
40 31 0.29
41 68 0.64
42 4 0.04
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (40 bp):
GATGTATCGATACATTTTCAATGTATCGATACATTACCCT
Found at i:9451 original size:27 final size:27
Alignment explanation
Indices: 9415--9485 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
9405 TGTCATCATC
*
9415 GAGGACACTCCAACCCCATTCTTCCGA
1 GAGGATACTCCAACCCCATTCTTCCGA
*
9442 GAGGATACTCCAATCCCATTCTTCCGA
1 GAGGATACTCCAACCCCATTCTTCCGA
* *
9469 GGGGATACTCTAACCCC
1 GAGGATACTCCAACCCC
9486 GTTTTTTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.25, C:0.37, G:0.17, T:0.21
Consensus pattern (27 bp):
GAGGATACTCCAACCCCATTCTTCCGA
Found at i:15614 original size:27 final size:27
Alignment explanation
Indices: 15583--15854 Score: 307
Period size: 27 Copynumber: 10.0 Consensus size: 27
15573 AACCTCTTCA
*
15583 AAGTCCACAACTCCGTGGCAACCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
15610 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
15637 AAGTCCACAACTCTGTGGCATGCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
15664 AAGTCCATAACTCCGTGGCATCCTTTG
1 AAGTCCACAACTCCGTGGCATCCTTTT
* *
15691 AAGTCCACAACTCCGTGACATCCCTTTA
1 AAGTCCACAACTCCGTGGCAT-CCTTTT
* *
15719 AAGTCCACAACTCTGTGGCGTCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
15746 AAGTCCACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCCGTGGCATCCTTTT
*
15773 AAGTCCACAAGC-CGGTGGCA-CCTTTT
1 AAGTCCACAA-CTCCGTGGCATCCTTTT
* * * *
15799 CAAAGCCCATAAGC-CAGTGGCATCCTTTC
1 --AAGTCCACAA-CTCCGTGGCATCCTTTT
* * *
15828 AGAGCCCACAAGTCAGTGGCATCCTTT
1 A-AGTCCACAACTCCGTGGCATCCTTT
15855 CAAAGCCCAC
Statistics
Matches: 214, Mismatches: 24, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
26 6 0.03
27 140 0.65
28 63 0.29
29 5 0.02
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCATCCTTTT
Found at i:15758 original size:82 final size:81
Alignment explanation
Indices: 15583--15854 Score: 332
Period size: 82 Copynumber: 3.3 Consensus size: 81
15573 AACCTCTTCA
* * *
15583 AAGTCCACAACTCCGTGGCAACCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAAC
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGACACCCTTTAAAGTCCACAAC
*
15648 TCTGTGGCATGCTTTT
66 TCTGTGGCATCCTTTT
* *
15664 AAGTCCATAACTCCGTGGCATCCTTTGAAGTCCACAACTCCGTGACATCCCTTTAAAGTCCACAA
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGACA-CCCTTTAAAGTCCACAA
*
15729 CTCTGTGGCGTCCTTTT
65 CTCTGTGGCATCCTTTT
* * * * *
15746 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAAGC-CGGTGGCACCTTTTCAAAGCCCATA
1 AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAA-CTCCGTGACACCCTTT-AAAGTCCACA
* *
15810 AGC-CAGTGGCATCCTTTC
64 A-CTCTGTGGCATCCTTTT
* * *
15828 AGAGCCCACAAGTCAGTGGCATCCTTT
1 A-AGTCCACAACTCCGTGGCATCCTTT
15855 CAAAGCCCAC
Statistics
Matches: 166, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
81 48 0.29
82 94 0.57
83 24 0.14
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (81 bp):
AAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGACACCCTTTAAAGTCCACAAC
TCTGTGGCATCCTTTT
Found at i:15818 original size:28 final size:28
Alignment explanation
Indices: 15750--16595 Score: 690
Period size: 28 Copynumber: 30.2 Consensus size: 28
15740 CCTTTTAAGT
* * *
15750 CCACAACTCCGTGGCATCCTTTT--AAGT
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* *
15777 CCACAAGCCGGTGGCACCTTTTCAAAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
* * *
15805 CCATAAGCCAGTGGCATCC-TTTCAGAGC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
15833 CCACAAGTCAGTGGCATCC-TTTCAAAGC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * *
15861 CCACGAA-CCAGCGGCACCCTTTCAAAGC
1 CCAC-AAGTCAGTGGCACCTTTTCAAAGC
* * *
15889 CCACGAA-CCAGTGGCATCTTTTCCAAGC
1 CCAC-AAGTCAGTGGCACCTTTTCAAAGC
* *
15917 CCACAAGTCAGTGGCATCTTTTCCAAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
* *
15945 CCACAAGTCAGTGACACCTTTTCATAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
* * * *
15973 CCATAAGTTAGTGGCACCTTTTCATAGT
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
*
16001 CCACAAGTTAGTGGCACCTTTTCAAAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
* * *
16029 CCACGAGTCAATGGCATCC-ATTCAAAGC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
*
16057 CCACGAGTCAGTGGCATCC-TTTCAAAGC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * * *
16085 CCACAAGTCGGTGACATCTCTTCAAAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
*
16113 CCACAAGTCAGTGGCATCC-TTCCAAAGC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * * * *
16141 CCACGAGTCATTTGCATC-TTTCAAAAC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
** *
16168 CCACAAGTCAGTGGCATATCTTCAAAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
*
16196 CCACGAA-TCAGTGGCACCCTTTCAAAGC
1 CCAC-AAGTCAGTGGCACCTTTTCAAAGC
* * *
16224 CCATAAGTCAGTGGCATCTTTTCCAAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
* * **
16252 CCACAAGTCCGTGTCATTTTTTTC-AAGC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* *
16280 CCACAAATCAGTGGCA-CTATTTCATAG-
1 CCACAAGTCAGTGGCACCT-TTTCAAAGC
16307 CCACAAGTCAGTGGCACCTTTTCAAAGC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
*
16335 CCACAAGTCAGTGGCATCCTTTT-AAAGT
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* ** * * *
16363 CCATAAGTCAACGGCATCTCTTCAAAGG
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
* * *
16391 CCACAAGTTAGTTGCATCC-TTCCAAAGC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* *
16419 CCACGAGTCAGTGGCATCC-TTCCAAAGC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* *
16447 CCACGAGTCAGTGGCATCC-TTCCAAAGC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
* * * *
16475 CCACGAGGT-AGTGGCATCTCTTCAAAGA
1 CCAC-AAGTCAGTGGCACCTTTTCAAAGC
* * * *
16503 CCACAAGTCCGAGGCACCTTCTCAAAAC
1 CCACAAGTCAGTGGCACCTTTTCAAAGC
16531 CCACAAGTCAGTGGCATCCTTTT-AAAGC
1 CCACAAGTCAGTGGCA-CCTTTTCAAAGC
*
16559 CTACACAAGTTC-GTGGCAACTTTCTCTAAAGC
1 C--CACAAG-TCAGTGGCACCTTT-TC-AAAGC
16591 CCACA
1 CCACA
16596 CAAGTTCGTG
Statistics
Matches: 676, Mismatches: 113, Indels: 57
0.80 0.13 0.07
Matches are distributed among these distances:
26 7 0.01
27 76 0.11
28 535 0.79
29 33 0.05
30 17 0.03
31 2 0.00
32 6 0.01
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.23
Consensus pattern (28 bp):
CCACAAGTCAGTGGCACCTTTTCAAAGC
Found at i:15847 original size:56 final size:56
Alignment explanation
Indices: 15574--16595 Score: 736
Period size: 56 Copynumber: 18.3 Consensus size: 56
15564 TAGTAATGTA
* * * * * * * * *
15574 ACCTCTTCAAAGTCCACAACTCCGTGGCAACCTTT-TAAGTCCACAACTCCGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGC
* * * * * * * * *
15629 ACCCTTTT--AAGTCCACAACTCTGTGGCATGCTTT-TAAGTCCATAACTCCGTGGC
1 A-CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGC
* * * * * * * *
15683 ATCC-TTT-GAAGTCCACAACTCCGTGACATCCCTTT-AAAGTCCACAACTCTGTGGC
1 A-CCTTTTCAAAGCCCACAAGTCAGTGGCAT-CCTTTCAAAGCCCACAAGTCAGTGGC
* * * * * * * *
15738 GTCCTTTT--AAGTCCACAACTCCGTGGCATCCTTT-TAAGTCCACAAGCCGGTGGC
1 -ACCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGC
* * *
15792 ACCTTTTCAAAGCCCATAAGCCAGTGGCATCCTTTCAGAGCCCACAAGTCAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGC
* * * *
15848 ATCC-TTTCAAAGCCCACGAA-CCAGCGGCACCCTTTCAAAGCCCACGAA-CCAGTGGC
1 A-CCTTTTCAAAGCCCAC-AAGTCAGTGGCATCCTTTCAAAGCCCAC-AAGTCAGTGGC
* * * * *
15904 ATCTTTTCCAAGCCCACAAGTCAGTGGCATCTTTTCCAAGCCCACAAGTCAGTGAC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGC
* * * * * *
15960 ACCTTTTCATAGCCCATAAGTTAGTGGCA-CCTTTTCATAGTCCACAAGTTAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGC
* * * *
16016 ACCTTTTCAAAGCCCACGAGTCAATGGCATCCATTCAAAGCCCACGAGTCAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGC
* *
16072 ATCC-TTTCAAAGCCCACAAGTCGGTGACAT-CTCTTCAAAGCCCACAAGTCAGTGGC
1 A-CCTTTTCAAAGCCCACAAGTCAGTGGCATCCT-TTCAAAGCCCACAAGTCAGTGGC
* * * * *
16128 ATCC-TTCCAAAGCCCACGAGTCATTTGCAT-CTTTCAAAACCCACAAGTCAGTGGC
1 A-CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGC
** * * *
16183 ATATCTTCAAAGCCCACGAA-TCAGTGGCACCCTTTCAAAGCCCATAAGTCAGTGGC
1 ACCTTTTCAAAGCCCAC-AAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGC
* * * * ** *
16239 ATCTTTTCCAAGCCCACAAGTCCGTGTCATTTTTTTC-AAGCCCACAAATCAGTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGC
*
16295 A-CTATTTCATAG-CCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGC
1 ACCT-TTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGC
* * ** * * *
16350 ATCCTTTT-AAAGTCCATAAGTCAACGGCAT-CTCTTCAAAGGCCACAAGTTAGTTGC
1 A-CCTTTTCAAAGCCCACAAGTCAGTGGCATCCT-TTCAAAGCCCACAAGTCAGTGGC
* * * *
16406 ATCC-TTCCAAAGCCCACGAGTCAGTGGCATCCTTCCAAAGCCCACGAGTCAGTGGC
1 A-CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGC
* * * * *
16462 ATCC-TTCCAAAGCCCACGAGGT-AGTGGCAT-CTCTTCAAAGACCACAAGTCCGAGGC
1 A-CCTTTTCAAAGCCCAC-AAGTCAGTGGCATCCT-TTCAAAGCCCACAAGTCAGTGGC
* * *
16518 ACCTTCTCAAAACCCACAAGTCAGTGGCATCCTTTTAAAGCCTACACAAGTTC-GTGGC
1 ACCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC--CACAAG-TCAGTGGC
*
16576 AACTTTCTCTAAAGCCCACA
1 ACCTTT-TC-AAAGCCCACA
16596 CAAGTTCGTG
Statistics
Matches: 785, Mismatches: 139, Indels: 81
0.78 0.14 0.08
Matches are distributed among these distances:
53 9 0.01
54 89 0.11
55 163 0.21
56 475 0.61
57 22 0.03
58 14 0.02
59 4 0.01
60 9 0.01
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (56 bp):
ACCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGC
Found at i:15891 original size:84 final size:84
Alignment explanation
Indices: 15579--16595 Score: 713
Period size: 84 Copynumber: 12.2 Consensus size: 84
15569 ATGTAACCTC
* * * * * * * * *
15579 TTCAAAGTCCACAACTCCGTGGCAACCTTT-TAAGTCCAC-AACTCCGTGGCACCCTTT-TAAGT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAA-TCAGTGGCACCCTTTCAAAGC
* * *
15641 CCACAACTCTGTGGCATGCT
65 CCACAAGTCAGTGGCATCCT
* * * * * * * * *
15661 TT-TAAGTCCATAACTCCGTGGCATCCTTT-GAAGTCCAC-AACTCCGTGACATCCCTTT-AAAG
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAA-TCAGTGGCA-CCCTTTCAAAG
* * * *
15722 TCCACAACTCTGTGGCGTCCT
64 CCCACAAGTCAGTGGCATCCT
* * * * * * * * *
15743 TT-TAAGTCCACAACTCCGTGGCATCCTTT-TAAGTCCAC-AAGCCGGTGGCACCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAA-TCAGTGGCACCCTTTCAAAGC
* *
15805 CCATAAGCCAGTGGCATCCT
65 CCACAAGTCAGTGGCATCCT
* * *
15825 TTCAGAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAACCAGCGGCACCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAATCAGTGGCACCCTTTCAAAGCC
* *
15890 CACGAA-CCAGTGGCATCTT
66 CAC-AAGTCAGTGGCATCCT
* * * * * *
15909 TTCCAAGCCCACAAGTCAGTGGCATCTTTTCCAAGCCCAC-AAGTCAGTGACACCTTTTCATAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAA-TCAGTGGCACCCTTTCAAAGC
* *
15973 CCATAAGTTAGTGGCA-CCTT
65 CCACAAGTCAGTGGCATCC-T
* * * * * * *
15993 TTCATAGTCCACAAGTTAGTGGCA-CCTTTTCAAAGCCCACGAGTCAATGGCATCCATTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACGAATCAGTGGCACCCTTTCAAAGC
*
16057 CCACGAGTCAGTGGCATCCT
65 CCACAAGTCAGTGGCATCCT
* * * *
16077 TTCAAAGCCCACAAGTCGGTGACAT-CTCTTCAAAGCCCAC-AAGTCAGTGGCATCCTTCCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCATCCT-TTCAAAGCCCACGAA-TCAGTGGCACCCTTTCAAAG
* * *
16140 CCCACGAGTCATTTGCAT-CT
64 CCCACAAGTCAGTGGCATCCT
* *
16160 TTCAAAACCCACAAGTCAGTGGCAT-ATCTTCAAAGCCCACGAATCAGTGGCACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCATCCT-TTCAAAGCCCACGAATCAGTGGCACCCTTTCAAAGC
* *
16224 CCATAAGTCAGTGGCATCTT
65 CCACAAGTCAGTGGCATCCT
* * * ** * ** *
16244 TTCCAAGCCCACAAGTCCGTGTCATTTTTTTC-AAGCCCACAAATCAGTGGCACTATTTCATAG-
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACGAATCAGTGGCACCCTTTCAAAGC
16307 CCACAAGTCAGTGGCA-CCTT
65 CCACAAGTCAGTGGCATCC-T
* * * ** *
16327 TTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGTCCA-TAAGTCAACGGCA-TCTCTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAA-TCAGTGGCACCCT-TTCAAAG
* * *
16390 GCCACAAGTTAGTTGCATCCT
64 CCCACAAGTCAGTGGCATCCT
* * * * * *
16411 TCCAAAGCCCACGAGTCAGTGGCATCCTTCCAAAGCCCACGAGTCAGTGGCATCCTTCCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAATCAGTGGCACCCTTTCAAAGCC
*
16476 CACGAGGT-AGTGGCAT-CT
66 CAC-AAGTCAGTGGCATCCT
* * * * * *
16494 CTTCAAAGACCACAAGTCCGAGGCA-CCTTCTCAAAACCCAC-AAGTCAGTGGCATCCTTTTAAA
1 -TTCAAAGCCCACAAGTCAGTGGCATCCTT-TCAAAGCCCACGAA-TCAGTGGCACCCTTTCAAA
* *
16557 GCCTACACAAGTTC-GTGGCAACTT
63 GCC--CACAAG-TCAGTGGCATCCT
16581 TCTCTAAAGCCCACA
1 T-TC-AAAGCCCACA
16596 CAAGTTCGTG
Statistics
Matches: 760, Mismatches: 137, Indels: 70
0.79 0.14 0.07
Matches are distributed among these distances:
81 48 0.06
82 104 0.14
83 163 0.21
84 400 0.53
85 21 0.03
86 12 0.02
87 3 0.00
88 9 0.01
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.24
Consensus pattern (84 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAATCAGTGGCACCCTTTCAAAGCC
CACAAGTCAGTGGCATCCT
Found at i:20438 original size:51 final size:51
Alignment explanation
Indices: 20381--20516 Score: 236
Period size: 51 Copynumber: 2.7 Consensus size: 51
20371 TTTTAACTAG
* *
20381 ATGTATCGATACATTGAAAAATGTTTCGATACATCTGGGTAAAAAGATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
*
20432 ATGTATCGATACAATGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
*
20483 ATGTATCGATACATTGAAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACAT
20517 TCATACATGT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 80 1.00
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAGACAGA
Found at i:20505 original size:20 final size:20
Alignment explanation
Indices: 20480--20556 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
20470 GTAAAAAGAC
20480 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
20500 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*
20520 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
* *
20540 AAAAGGTATCGATACAT
1 AGAATGTATCGATACAT
20557 CTGGGTACTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:21278 original size:20 final size:19
Alignment explanation
Indices: 21214--21368 Score: 127
Period size: 21 Copynumber: 7.7 Consensus size: 19
21204 TTTTACCTAG
* *
21214 ATGTATCGATACATTTTCA
1 ATGTATCGATACACTTCCA
21233 ATGTATCGATACA-TTACCCAA
1 ATGTATCGATACACTT--CC-A
* *
21254 ATGTATCGATATAGCTTTCA
1 ATGTATCGATACA-CTTCCA
21274 ATGTATCGATACA-TTACCCAA
1 ATGTATCGATACACTT--CC-A
*
21295 ATGTATCGATATAGCTTCCA
1 ATGTATCGATACA-CTTCCA
21315 ATGTATCGATACA-TTACCTA
1 ATGTATCGATACACTT-CC-A
*
21335 GATGTATCGATACATCTTTCA
1 -ATGTATCGATACA-CTTCCA
21356 ATGTATCGATACA
1 ATGTATCGATACA
21369 TGTATGAATA
Statistics
Matches: 113, Mismatches: 8, Indels: 29
0.75 0.05 0.19
Matches are distributed among these distances:
18 6 0.05
19 15 0.13
20 42 0.37
21 43 0.38
22 1 0.01
23 6 0.05
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (19 bp):
ATGTATCGATACACTTCCA
Found at i:21284 original size:41 final size:41
Alignment explanation
Indices: 21214--21369 Score: 242
Period size: 41 Copynumber: 3.8 Consensus size: 41
21204 TTTTACCTAG
*
21214 ATGTATCGATACA-TTTTCAATGTATCGATACATTACCCAA
1 ATGTATCGATACAGCTTTCAATGTATCGATACATTACCCAA
*
21254 ATGTATCGATATAGCTTTCAATGTATCGATACATTACCCAA
1 ATGTATCGATACAGCTTTCAATGTATCGATACATTACCCAA
* * * *
21295 ATGTATCGATATAGCTTCCAATGTATCGATACATTACCTAG
1 ATGTATCGATACAGCTTTCAATGTATCGATACATTACCCAA
*
21336 ATGTATCGATACATCTTTCAATGTATCGATACAT
1 ATGTATCGATACAGCTTTCAATGTATCGATACAT
21370 GTATGAATAT
Statistics
Matches: 107, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 12 0.11
41 95 0.89
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (41 bp):
ATGTATCGATACAGCTTTCAATGTATCGATACATTACCCAA
Found at i:21449 original size:20 final size:20
Alignment explanation
Indices: 21214--21458 Score: 152
Period size: 20 Copynumber: 11.7 Consensus size: 20
21204 TTTTACCTAG
21214 ATGTATCGATACA-TTTTCA
1 ATGTATCGATACATTTTTCA
***
21233 ATGTATCGATACATTACCCAA
1 ATGTATCGATACATTTTTC-A
* **
21254 ATGTATCGATATAGCTTTCA
1 ATGTATCGATACATTTTTCA
***
21274 ATGTATCGATACATTACCCAA
1 ATGTATCGATACATTTTTC-A
* ** *
21295 ATGTATCGATATAGCTTCCA
1 ATGTATCGATACATTTTTCA
**
21315 ATGTATCGATACA-TTACCTA
1 ATGTATCGATACATTTTTC-A
*
21335 GATGTATCGATACATCTTTCA
1 -ATGTATCGATACATTTTTCA
* * *
21356 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
21376 ATATATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
* *
21396 ACGTATTGATACATTGTCCTTTTACCCAA
1 ATGTATCGATACA---T--TTTT---C-A
21425 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
21445 ATGTATCGATACAT
1 ATGTATCGATACAT
21459 CTAGTTAAAT
Statistics
Matches: 171, Mismatches: 40, Indels: 29
0.71 0.17 0.12
Matches are distributed among these distances:
19 16 0.09
20 87 0.51
21 44 0.26
22 2 0.01
23 1 0.01
24 4 0.02
25 3 0.02
26 1 0.01
28 1 0.01
29 12 0.07
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:23757 original size:27 final size:27
Alignment explanation
Indices: 23724--23792 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
23714 TCATCATCGA
23724 GGACACTCCAACCCCATTCTTCCGAGG
1 GGACACTCCAACCCCATTCTTCCGAGG
* *
23751 GGACACTCCAACTCTATTCTTCCGAGG
1 GGACACTCCAACCCCATTCTTCCGAGG
*
23778 GGATACTCCAACCCC
1 GGACACTCCAACCCC
23793 GTTTTTCAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.20
Consensus pattern (27 bp):
GGACACTCCAACCCCATTCTTCCGAGG
Found at i:25605 original size:3 final size:3
Alignment explanation
Indices: 25587--25643 Score: 75
Period size: 3 Copynumber: 19.7 Consensus size: 3
25577 ATATCATAAC
*
25587 ATA ATG ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A AT-
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25631 ATA ATA AT- ATA AT
1 ATA ATA ATA ATA AT
25644 TACACGATGA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 6 0.12
3 39 0.81
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25634 original size:28 final size:27
Alignment explanation
Indices: 25587--25643 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
25577 ATATCATAAC
*
25587 ATAATGATAATAAATAATAATAATAATA
1 ATAATAATAATAAATAATAATAAT-ATA
25615 ATAATAATAATAAA-ATATAATAATATA
1 ATAATAATAATAAATA-ATAATAATATA
25642 AT
1 AT
25644 TACACGATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (27 bp):
ATAATAATAATAAATAATAATAATATA
Found at i:31377 original size:79 final size:76
Alignment explanation
Indices: 31260--31529 Score: 281
Period size: 79 Copynumber: 3.4 Consensus size: 76
31250 TTTCTAAAAT
* * *
31260 ATCAATTTTCCACCATCGGGGATACTCCAACCCCGTTATTTATGATGGGATACTCCAACTTCGGT
1 ATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTT-TGA-GGGATACTCCAAC-CCGGT
31325 TTTATTTTCAAACC
63 TTTATTTTCAAACC
* * * * * *
31339 ATCAATTTTTCATAATCGAGGATACTCTAACCCTGTTATTTTCGAGGGAAAACTCCAACCCTGAT
1 ATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTT-GAGGG-ATACTCCAACCC-GGT
*
31404 TTTATTTCCAAACC
63 TTTATTTTCAAACC
* * * ** *
31418 A-CTGATTTTTCACATTCGGGGATACTTCAACCCCGTTATTTCTGAAAAGATACTCTAACCCCGG
1 ATC-AATTTTTCACAATCGGGGATACTCCAACCCCGTTATTT-TG-AGGGATACTCCAA-CCCGG
*
31482 TTTTATTTTCAAAAC
62 TTTTATTTTCAAACC
*
31497 ATCAATTTTTCACCATCGGGGATACTCCAACCC
1 ATCAATTTTTCACAATCGGGGATACTCCAACCC
31530 TAGTTTTATT
Statistics
Matches: 155, Mismatches: 28, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
78 6 0.04
79 142 0.92
80 7 0.05
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.34
Consensus pattern (76 bp):
ATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTGAGGGATACTCCAACCCGGTTTT
ATTTTCAAACC
Found at i:31529 original size:51 final size:51
Alignment explanation
Indices: 31466--31582 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 51
31456 TTTCTGAAAA
* * * *
31466 GATACTCTAACCCCGGTTTTATTTTCAAAACATCAATTTTTCACCATCGGG
1 GATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTTCACAATCGGG
** * * *
31517 GATACTCCAACCCTAGTTTTATTTCCAAACCACCGATTTTTCATAATCGGG
1 GATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTTCACAATCGGG
31568 GATACTCCAACCCCG
1 GATACTCCAACCCCG
31583 TTATTTCCGA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.27, C:0.29, G:0.12, T:0.32
Consensus pattern (51 bp):
GATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTTCACAATCGGG
Found at i:31546 original size:130 final size:129
Alignment explanation
Indices: 31390--31789 Score: 496
Period size: 130 Copynumber: 3.1 Consensus size: 129
31380 TCGAGGGAAA
* *
31390 ACTCCAACCCTGATTTTATTTCCAAACCACTGATTTTTCACATTCGGGGATACTTCAACCCCGTT
1 ACTCCAACCCTG-TTTTATTTCCAAACCACCGATTTTTCACAATCGGGGATACTTCAACCCCGTT
* * * * *
31455 ATTTCTGAAAAGATACTCTAACCCCGGTTTTATTTTCAAAACATCAATTTTTCACCATCGGGGAT
65 ATTTCTGAAGAGATACTCTAACCTCGGTTTTATTTTTAAAACACCGATTTTTCACCATCGGGGAT
* *
31520 ACTCCAACCCTAGTTTTATTTCCAAACCACCGATTTTTCATAATCGGGGATACTCCAACCCCGTT
1 ACTCCAACCCT-GTTTTATTTCCAAACCACCGATTTTTCACAATCGGGGATACTTCAACCCCGTT
* * * * *
31585 ATTTCCGAAGAGATACTCTAACCTCAGTTTTATTTTTAAAACACCGATTCTCCACCATCGAGGAT
65 ATTTCTGAAGAGATACTCTAACCTCGGTTTTATTTTTAAAACACCGATTTTTCACCATCGGGGAT
* * * * * ** *
31650 ACTCCAACACCGGTTTTATTTCTAGAGCACCGATTTTTCACAATCGAGGATAC-TCTAACTTCAT
1 ACTCCAAC-CCTGTTTTATTTCCAAACCACCGATTTTTCACAATCGGGGATACTTC-AACCCCGT
* * * * * * *
31714 TATTTTTGAGGTGATACTCTAATCTCGATTTTATTTTTAAAGCACCGATTTTTCACCATCGGAGA
64 TATTTCTGAAGAGATACTCTAACCTCGGTTTTATTTTTAAAACACCGATTTTTCACCATCGGGGA
31779 T
129 T
31780 ACTCCAACCC
1 ACTCCAACCC
31790 CGTTATTTCC
Statistics
Matches: 231, Mismatches: 36, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
129 3 0.01
130 225 0.97
131 3 0.01
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (129 bp):
ACTCCAACCCTGTTTTATTTCCAAACCACCGATTTTTCACAATCGGGGATACTTCAACCCCGTTA
TTTCTGAAGAGATACTCTAACCTCGGTTTTATTTTTAAAACACCGATTTTTCACCATCGGGGAT
Found at i:31888 original size:158 final size:158
Alignment explanation
Indices: 31648--31984 Score: 423
Period size: 158 Copynumber: 2.1 Consensus size: 158
31638 ACCATCGAGG
* * *
31648 ATACTCCAACAC-CGGTTTTATTTCTAGAGCACCGATTTTTCACAATCGAGGATACTCTAACTTC
1 ATACTCCAAC-CTCGGTTTTATTTCTAAACCACCGATTTTTCACAATCGAGGATACTCTAACTCC
* * * * * *
31712 ATTATTTTTGAGGTGATACTCTAATCTCGATTTTATTTTTA-AAGCACCGATTTTTCACCATCG-
65 ATTATTTTTAAAGTGATACTCTAACCCCAATTTTATTTTTAGAA-CACCGATTTTTCACAATCGA
31775 GAGATACTCCAACCCCGTTATTTCCGAAGGA
129 G-GATACTCCAACCCCGTTATTTCCGAAGGA
* *
31806 ATACTCCAACCTCGGTTTTATTTCTAAACCACCGATTTTTCACAATTGGGGATACTAC-AACTCC
1 ATACTCCAACCTCGGTTTTATTTCTAAACCACCGATTTTTCACAATCGAGGATACT-CTAACTCC
* *
31870 GTTATTTTTAAAAG-GATACTCTAACCCCAATTTTATTTTTAGAATACCGATTTTTCACAATCGA
65 ATTATTTTT-AAAGTGATACTCTAACCCCAATTTTATTTTTAGAACACCGATTTTTCACAATCGA
** * *
31934 GGATACTCTTACCCCGTTATTTTCGAAGGG
129 GGATACTCCAACCCCGTTATTTCCGAAGGA
* *
31964 ATATTCCAACCTCGTTTTTAT
1 ATACTCCAACCTCGGTTTTAT
31985 CTCCAGAATA
Statistics
Matches: 155, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
157 1 0.01
158 148 0.95
159 6 0.04
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (158 bp):
ATACTCCAACCTCGGTTTTATTTCTAAACCACCGATTTTTCACAATCGAGGATACTCTAACTCCA
TTATTTTTAAAGTGATACTCTAACCCCAATTTTATTTTTAGAACACCGATTTTTCACAATCGAGG
ATACTCCAACCCCGTTATTTCCGAAGGA
Found at i:31994 original size:79 final size:79
Alignment explanation
Indices: 31646--31984 Score: 328
Period size: 79 Copynumber: 4.3 Consensus size: 79
31636 CCACCATCGA
* * * *
31646 GGATACTCCAACAC-CGGTTTTATTTCTAGAGCACCGATTTTTCACAATCGAGGATACTCTAACT
1 GGATACTCCAAC-CTCGATTTTATTTCTAAACCACCGATTTTTCACAATCGAGGATACTCTAACC
* * *
31710 TCATTATTTTTG-AG
65 CCGTTATTTTCGAAG
* * * * * *
31724 GTGATACTCTAATCTCGATTTTATTTTTAAAGCACCGATTTTTCACCATCG-GAGATACTCCAAC
1 G-GATACTCCAACCTCGATTTTATTTCTAAACCACCGATTTTTCACAATCGAG-GATACTCTAAC
*
31788 CCCGTTATTTCCGAAG
64 CCCGTTATTTTCGAAG
* * * * *
31804 GAATACTCCAACCTCGGTTTTATTTCTAAACCACCGATTTTTCACAATTGGGGATACTAC-AACT
1 GGATACTCCAACCTCGATTTTATTTCTAAACCACCGATTTTTCACAATCGAGGATACT-CTAACC
** *
31868 CCGTTATTTTTAAAA
65 CCGTTATTTTCGAAG
* * * * * *
31883 GGATACTCTAACCCCAATTTTATTTTTAGAA-TACCGATTTTTCACAATCGAGGATACTCTTACC
1 GGATACTCCAACCTCGATTTTATTTCTA-AACCACCGATTTTTCACAATCGAGGATACTCTAACC
31947 CCGTTATTTTCGAAG
65 CCGTTATTTTCGAAG
* *
31962 GGATATTCCAACCTCGTTTTTAT
1 GGATACTCCAACCTCGATTTTAT
31985 CTCCAGAATA
Statistics
Matches: 209, Mismatches: 44, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
78 4 0.02
79 198 0.95
80 7 0.03
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.36
Consensus pattern (79 bp):
GGATACTCCAACCTCGATTTTATTTCTAAACCACCGATTTTTCACAATCGAGGATACTCTAACCC
CGTTATTTTCGAAG
Found at i:32246 original size:23 final size:22
Alignment explanation
Indices: 32215--32263 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
32205 CGTCCTTCCT
** *
32215 TTTTATGTATTTTTGTGTGTTTA
1 TTTTATGTAAATTTGTCTG-TTA
*
32238 TTTTGTGTAAATTTGTCTGTTA
1 TTTTATGTAAATTTGTCTGTTA
32260 TTTT
1 TTTT
32264 CTTTTTTACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.14, C:0.02, G:0.16, T:0.67
Consensus pattern (22 bp):
TTTTATGTAAATTTGTCTGTTA
Found at i:33742 original size:22 final size:21
Alignment explanation
Indices: 33689--33742 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
33679 AGATAATACG
* *
33689 AAAAACTAGT-TTCATTAATT
1 AAAAACTATTATTCATAAATT
33709 AAAAA-TATTTATTCCATAAATT
1 AAAAACTA-TTATT-CATAAATT
33731 AAAAACTATTAT
1 AAAAACTATTAT
33743 AATATAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 2 0.07
20 6 0.21
21 2 0.07
22 16 0.57
23 2 0.07
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAAACTATTATTCATAAATT
Found at i:34072 original size:18 final size:18
Alignment explanation
Indices: 34049--34083 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34039 TGGATGTACA
34049 ATAGTATTGATAT-TTATC
1 ATAGTATT-ATATATTATC
34067 ATAGTATTATATATTAT
1 ATAGTATTATATATTAT
34084 AAGAGGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (18 bp):
ATAGTATTATATATTATC
Found at i:35730 original size:45 final size:45
Alignment explanation
Indices: 35666--35753 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
35656 CTCTTTGTAT
35666 TTGATTTATGTTTATTCTTTCACAAACATCAACCTACTTAGAGGC
1 TTGATTTATGTTTATTCTTTCACAAACATCAACCTACTTAGAGGC
* * *
35711 TTGATTTGTGTTTATTCTTTCACAAACATCAGCCTATTTAGAG
1 TTGATTTATGTTTATTCTTTCACAAACATCAACCTACTTAGAG
35754 ATAATTTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (45 bp):
TTGATTTATGTTTATTCTTTCACAAACATCAACCTACTTAGAGGC
Found at i:36289 original size:61 final size:61
Alignment explanation
Indices: 36219--36340 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
36209 TTTAGTGGTA
36219 TATTATTTTAAAATCTAGAATAAGTTTATTCGGTAAACTATCTAATGGTAAACTTTGTATG
1 TATTATTTTAAAATCTAGAATAAGTTTATTCGGTAAACTATCTAATGGTAAACTTTGTATG
36280 TATTATTTTAAAATCTAGAATAAGTTTATTCGGTAAACTATCTAATGGTAAACTTTGTATG
1 TATTATTTTAAAATCTAGAATAAGTTTATTCGGTAAACTATCTAATGGTAAACTTTGTATG
36341 CCCAGGTTTG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (61 bp):
TATTATTTTAAAATCTAGAATAAGTTTATTCGGTAAACTATCTAATGGTAAACTTTGTATG
Found at i:38263 original size:2 final size:2
Alignment explanation
Indices: 38256--38300 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
38246 TAATGATTCA
*
38256 TC TC TC TC TC TC TC TC TC TA TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
38298 TC T
1 TC T
38301 ATATATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:40604 original size:17 final size:16
Alignment explanation
Indices: 40582--40628 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
40572 TTTTGAAATA
40582 TAAAAATAAATAATATT
1 TAAAAATAAATAAT-TT
*
40599 TAAAAATAAAAAATTT
1 TAAAAATAAATAATTT
40615 TAATAAAATAAATA
1 T-A-AAAATAAATA
40629 TCTATTTGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 3 0.12
17 14 0.54
18 9 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAAAATAAATAATTT
Found at i:48181 original size:33 final size:33
Alignment explanation
Indices: 48119--48182 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
48109 TCTTTGTGAC
* * ** *
48119 TAATCTTTTATCTCTTGTATATGTGAGATAAGA
1 TAATCTCTAATCTCTTGTATAAATAAGATAAGA
48152 TAATCTCTAATCTCTTGTATAAATAAGATAA
1 TAATCTCTAATCTCTTGTATAAATAAGATAA
48183 ACTAATTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (33 bp):
TAATCTCTAATCTCTTGTATAAATAAGATAAGA
Found at i:48742 original size:23 final size:21
Alignment explanation
Indices: 48709--48766 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
48699 CACAAGCTTC
*
48709 TGTATCAATACAAGTTCATGAGA
1 TGTATCGATACAAG-TCATGA-A
* *
48732 TGTATCGATACCCA-TCATGAT
1 TGTATCGATA-CAAGTCATGAA
48753 TGTATCGATACAAG
1 TGTATCGATACAAG
48767 CCTTAGCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 2 0.07
21 10 0.34
22 6 0.21
23 9 0.31
24 2 0.07
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (21 bp):
TGTATCGATACAAGTCATGAA
Found at i:48827 original size:114 final size:113
Alignment explanation
Indices: 48615--48854 Score: 277
Period size: 114 Copynumber: 2.1 Consensus size: 113
48605 AATTTTTATA
* * * * *
48615 AGATGTATCGATACCCATCATGATTGTATTAATAAAGACCTTGGCAGTTGCTATAGTTGTGACTG
1 AGATGTATCGATACCCATCATGATTGTATCAATAAAGACCTTAGCAATAGCTATAGTTGGGACTG
*
48680 CTAGCAGAATGTATCAATACACAAGCTTCTGTATCAATACAAGTTCATG
66 CTAGCAAAATGTATCAATACACAAGCTTCTGTATCAATACAAGTTCA-G
* * * *
48729 AGATGTATCGATACCCATCATGATTGTATCGATACAAG-CCTTAGCAATAGTTATGGTTGGGATT
1 AGATGTATCGATACCCATCATGATTGTATCAATA-AAGACCTTAGCAATAGCTATAGTTGGGACT
** * ** * * *
48793 TTTGGCAAAATGTATTGATACCCAAGTTTGTGTATCAATACAAGTTCAG
65 GCTAGCAAAATGTATCAATACACAAGCTTCTGTATCAATACAAGTTCAG
*
48842 -GAAGTATCGATAC
1 AGATGTATCGATAC
48855 ATACTTCAAA
Statistics
Matches: 106, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
112 12 0.11
113 1 0.01
114 90 0.85
115 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (113 bp):
AGATGTATCGATACCCATCATGATTGTATCAATAAAGACCTTAGCAATAGCTATAGTTGGGACTG
CTAGCAAAATGTATCAATACACAAGCTTCTGTATCAATACAAGTTCAG
Found at i:49314 original size:11 final size:10
Alignment explanation
Indices: 49294--49341 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
49284 GAGCTCAGCT
*
49294 AAAAAGGGGA
1 AAAAAAGGGA
49304 GAAAAAAGGGA
1 -AAAAAAGGGA
**
49315 AAAAAAGAAAA
1 AAAAAAG-GGA
49326 AAAAAAGGGA
1 AAAAAAGGGA
49336 AAAAAA
1 AAAAAA
49342 TAGATTTCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
10 14 0.45
11 17 0.55
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (10 bp):
AAAAAAGGGA
Found at i:51374 original size:100 final size:103
Alignment explanation
Indices: 51217--51425 Score: 228
Period size: 100 Copynumber: 2.0 Consensus size: 103
51207 TATAATTTTA
** * * * **
51217 TTGGGAAAACTCTAACCTTACTATTCTGAAGGGATACTCTAACCTCATT-TTTCAAAAAA-AAA-
1 TTGGGAAAACTCTAACCCCACTACTCCGAAGGGATACTCCAACCTCATTCTTAAAAAAAACAAAT
* * *
51279 TTACTCTTTGTTCCTAAATATTTTTATAATTTTTGACT
66 TTACTCTTTCTTCCTAAATATTTTCATAATCTTTGACT
* * *
51317 TTGGGAAAACTCTGACCCCATTACTCCGAAGGGATACTCCAATCCT-GTTCTTAAAAAAAAACTC
1 TTGGGAAAACTCTAACCCCACTACTCCGAAGGGATACTCCAA-CCTCATTCTT-AAAAAAAA--C
*
51381 AAATTTACTTTTTCTTCCTAAATATTTTCATAATCTTTGACT
62 AAATTTACTCTTTCTTCCTAAATATTTTCATAATCTTTGACT
51423 TTG
1 TTG
51426 AGGATACTCC
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
100 37 0.42
101 5 0.06
102 6 0.07
105 3 0.03
106 37 0.42
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (103 bp):
TTGGGAAAACTCTAACCCCACTACTCCGAAGGGATACTCCAACCTCATTCTTAAAAAAAACAAAT
TTACTCTTTCTTCCTAAATATTTTCATAATCTTTGACT
Found at i:51482 original size:80 final size:80
Alignment explanation
Indices: 51371--51528 Score: 214
Period size: 80 Copynumber: 2.0 Consensus size: 80
51361 CTGTTCTTAA
* *
51371 AAAAAAACTCAAATTTACTTTTTCTTCCTAAATATTTTCATAATCTTTGA-CTTTGAGG-ATACT
1 AAAAAAACTCAAATTTACTCTTTATTCCTAAATATTTTCATAAT-TTT-ATCTTT-AGGAATACT
*
51434 CCAACCTCA-TTCTCCAC
63 CCAACCCCACTTCTCCAC
* * *
51451 AAAAAAACTCAAATTTTCTCTTTATTTCTAAATATTTTTATAATTTTATCTTTAGGAATACTCCA
1 AAAAAAACTCAAATTTACTCTTTATTCCTAAATATTTTCATAATTTTATCTTTAGGAATACTCCA
51516 ACCCCACTTCTCC
66 ACCCCACTTCTCC
51529 GAGGGAAACT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
78 4 0.06
79 20 0.29
80 45 0.65
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.41
Consensus pattern (80 bp):
AAAAAAACTCAAATTTACTCTTTATTCCTAAATATTTTCATAATTTTATCTTTAGGAATACTCCA
ACCCCACTTCTCCAC
Found at i:52273 original size:52 final size:52
Alignment explanation
Indices: 52147--52273 Score: 218
Period size: 52 Copynumber: 2.4 Consensus size: 52
52137 CTAGTTTTTG
* * *
52147 TATCGATACATGCAGACAAATTCGCCCAGATGTATCGATACACTATGAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATA
*
52199 TATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATA
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATA
52251 TATCGATACATGCAGGCAAATTT
1 TATCGATACATGCAGGCAAATTT
52274 TCATATTTTA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (52 bp):
TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATA
Found at i:61376 original size:150 final size:150
Alignment explanation
Indices: 61186--61482 Score: 540
Period size: 150 Copynumber: 2.0 Consensus size: 150
61176 CTAAATGCAC
* *
61186 ACCTTTGGCATAAAAATATCCCGTGATTACTTAGAACTCGGCTTTAGAAAAAATACTAAAATACC
1 ACCTTTGGCATAAAAATATCCCGTGACTACTTAGAACTCGGCGTTAGAAAAAATACTAAAATACC
*
61251 TTTAAGGTATACTTTTGACGTGAAAGTATCTCGGCAACCCTAAAGAACATGAAAATGGTATAAAA
66 TTTAAGGTATACTTTTGACGTGAAAGTATCTCGACAACCCTAAAGAACATGAAAATGGTATAAAA
61316 TGACATTTTTACCCTAAAAT
131 TGACATTTTTACCCTAAAAT
* *
61336 ACCTTTGGCATAAAAATATCCCGTGACTACTTAGAACTCGGCGTTAGAAAAATTACTAAAATGCC
1 ACCTTTGGCATAAAAATATCCCGTGACTACTTAGAACTCGGCGTTAGAAAAAATACTAAAATACC
*
61401 TTTAAGGTATACTTTTGACGTGAAAGTATCTCGACAACCCTAAAGAACATGAAAATGGTATAATA
66 TTTAAGGTATACTTTTGACGTGAAAGTATCTCGACAACCCTAAAGAACATGAAAATGGTATAAAA
61466 TGACATTTTTACCCTAA
131 TGACATTTTTACCCTAA
61483 CTAGGTAGTT
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
150 141 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.29
Consensus pattern (150 bp):
ACCTTTGGCATAAAAATATCCCGTGACTACTTAGAACTCGGCGTTAGAAAAAATACTAAAATACC
TTTAAGGTATACTTTTGACGTGAAAGTATCTCGACAACCCTAAAGAACATGAAAATGGTATAAAA
TGACATTTTTACCCTAAAAT
Found at i:63308 original size:20 final size:19
Alignment explanation
Indices: 63243--63315 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
63233 CTGCCAGTTT
* *
63243 TATGTATCGATACAATTCAG
1 TATGTATCGATACAA-GCAA
*
63263 TGTGTATCGATACCAAG--A
1 TATGTATCGATA-CAAGCAA
63281 TCATGTATCGATACTAAGCAA
1 T-ATGTATCGATAC-AAGCAA
*
63302 TATGTATCAATACA
1 TATGTATCGATACA
63316 TCTGGGTGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
18 2 0.05
19 14 0.33
20 22 0.51
21 5 0.12
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (19 bp):
TATGTATCGATACAAGCAA
Found at i:65138 original size:26 final size:26
Alignment explanation
Indices: 65108--65158 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
65098 CATTGTCATT
65108 ATGCTCAAAATGAGCATTGCTAAGAA
1 ATGCTCAAAATGAGCATTGCTAAGAA
65134 ATGCTCAAAATGAGCATTGCTAAGA
1 ATGCTCAAAATGAGCATTGCTAAGA
65159 CAAGGTTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (26 bp):
ATGCTCAAAATGAGCATTGCTAAGAA
Found at i:66897 original size:13 final size:13
Alignment explanation
Indices: 66879--66904 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
66869 CAATTTTTTG
66879 TGTATCGATACAA
1 TGTATCGATACAA
66892 TGTATCGATACAA
1 TGTATCGATACAA
66905 ACTTTGGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:66898 original size:33 final size:33
Alignment explanation
Indices: 66856--66924 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
66846 CGTTACAAGC
** *
66856 CAATGTATCGATACAATTTTTTGTGTATCGATA
1 CAATGTATCGATACAAACTTTGGTGTATCGATA
66889 CAATGTATCGATACAAACTTTGGTGTATCGATA
1 CAATGTATCGATACAAACTTTGGTGTATCGATA
66922 CAA
1 CAA
66925 GTTTGGCTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (33 bp):
CAATGTATCGATACAAACTTTGGTGTATCGATA
Found at i:67028 original size:20 final size:20
Alignment explanation
Indices: 66976--67030 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
66966 CATATTTTTG
*
66976 ATGTATCGATACATTGCAAC
1 ATGTATCGATACTTTGCAAC
*
66996 ATGTATCGATACTTTG-AATT
1 ATGTATCGATACTTTGCAA-C
67016 ATGTATCGATACTTT
1 ATGTATCGATACTTT
67031 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACTTTGCAAC
Found at i:69484 original size:13 final size:13
Alignment explanation
Indices: 69466--69504 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
69456 ATAATCCCCT
* *
69466 TGTATCGATATAG
1 TGTATCGATACAA
69479 TGTATCGATACAA
1 TGTATCGATACAA
69492 TGTATCGATACAA
1 TGTATCGATACAA
69505 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:75777 original size:20 final size:20
Alignment explanation
Indices: 75725--75779 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
75715 CATATTTTTG
*
75725 ATGTATCGATACATTGCAAC
1 ATGTATCGATACTTTGCAAC
*
75745 ATGTATCGATACTTTG-AATT
1 ATGTATCGATACTTTGCAA-C
75765 ATGTATCGATACTTT
1 ATGTATCGATACTTT
75780 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACTTTGCAAC
Found at i:76912 original size:4 final size:4
Alignment explanation
Indices: 76905--76954 Score: 55
Period size: 4 Copynumber: 11.5 Consensus size: 4
76895 AAAAGAAATA
*
76905 AATT AATT AATT AAATAT AATT AATAT AATT AATT GATTT AATT AATT
1 AATT AATT AATT -AAT-T AATT AAT-T AATT AATT -AATT AATT AATT
76953 AA
1 AA
76955 AAAATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 26 0.65
5 13 0.32
6 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:76932 original size:9 final size:9
Alignment explanation
Indices: 76901--76938 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
76891 GTGGAAAAGA
76901 AATA-AATT
1 AATATAATT
76909 AAT-TAATT
1 AATATAATT
76917 AAATATAATT
1 -AATATAATT
76927 AATATAATT
1 AATATAATT
76936 AAT
1 AAT
76939 TGATTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 7 0.26
9 15 0.56
10 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATATAATT
Found at i:76938 original size:13 final size:13
Alignment explanation
Indices: 76901--76954 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
76891 GTGGAAAAGA
76901 AATA-AATTAATT
1 AATATAATTAATT
76913 AAT-TAAATATAATT
1 AATAT-AAT-TAATT
76927 AATATAATTAATT
1 AATATAATTAATT
* *
76940 GATTTAATTAATT
1 AATATAATTAATT
76953 AA
1 AA
76955 AAAATATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
12 3 0.09
13 20 0.57
14 11 0.31
15 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
AATATAATTAATT
Found at i:77651 original size:20 final size:21
Alignment explanation
Indices: 77613--77652 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
77603 AGAAAATTTT
* *
77613 AAAAATAATTCTAATTTTAAG
1 AAAAATAAGTCTAAATTTAAG
77634 AAAAATAAGT-TAAATTTAA
1 AAAAATAAGTCTAAATTTAA
77653 TATTTTACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAATAAGTCTAAATTTAAG
Found at i:78451 original size:13 final size:13
Alignment explanation
Indices: 78433--78458 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
78423 TTTTTAGTGT
78433 AAAAACTTTAAAA
1 AAAAACTTTAAAA
78446 AAAAACTTTAAAA
1 AAAAACTTTAAAA
78459 GATCAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAACTTTAAAA
Found at i:78731 original size:16 final size:16
Alignment explanation
Indices: 78703--78733 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
78693 CGAAATAACC
78703 CGAACCCAAAATGACT
1 CGAACCCAAAATGACT
78719 CGAACCCAAAATGAC
1 CGAACCCAAAATGAC
78734 CTAAATCCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.32, G:0.13, T:0.10
Consensus pattern (16 bp):
CGAACCCAAAATGACT
Found at i:78760 original size:16 final size:16
Alignment explanation
Indices: 78689--78772 Score: 55
Period size: 16 Copynumber: 5.2 Consensus size: 16
78679 ACTAACCCAA
* *
78689 AACTCGAAATAACCCG
1 AACTCGAAATGACCTG
* *
78705 AACCCAAAATGA-CTCG
1 AACTCGAAATGACCT-G
* *
78721 AACCCAAAATGACCT-
1 AACTCGAAATGACCTG
* * *
78736 AAATCCGAAATTATCTG
1 AACT-CGAAATGACCTG
78753 AACTCGAAATGACCTG
1 AACTCGAAATGACCTG
78769 AACT
1 AACT
78773 TAAATTAAGT
Statistics
Matches: 52, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
15 3 0.06
16 44 0.85
17 5 0.10
ACGTcount: A:0.43, C:0.27, G:0.12, T:0.18
Consensus pattern (16 bp):
AACTCGAAATGACCTG
Found at i:81001 original size:21 final size:20
Alignment explanation
Indices: 80977--81021 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
80967 ATATTCAATA
*
80977 TATAAAATAAATAATTTTTTT
1 TATAAAATAAAT-ATTTTTAT
**
80998 TATAACGTAAATATTTTTAT
1 TATAAAATAAATATTTTTAT
81018 TATA
1 TATA
81022 TTATAAGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TATAAAATAAATATTTTTAT
Done.