Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2077
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: 194399
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:4902 original size:20 final size:20
Alignment explanation
Indices: 4873--4923 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
4863 ATTCACTTGT
*
4873 TATATCGATACATAAGTGAA
1 TATATCGATACATAAGTAAA
*
4893 TATATTGATACATAAGTAAA
1 TATATCGATACATAAGTAAA
*
4913 TGTATCGATAC
1 TATATCGATAC
4924 TAGACTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (20 bp):
TATATCGATACATAAGTAAA
Found at i:5075 original size:52 final size:50
Alignment explanation
Indices: 4961--5097 Score: 170
Period size: 52 Copynumber: 2.7 Consensus size: 50
4951 TTTGAAAAGA
* * *
4961 AAATGTATCGATACATT-TTTATTATATCGATACATTCTGGGTTTGATCC
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTCTGGGTTTGACCC
* * * *
5010 AAATGTATTGATACATTCTTCATTGTATCTATACATTTTGGGTTTTTTACCC
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTCTGGG--TTTGACCC
5062 AAATGTATCGATACATTCTTTCA-TGTATCGATACAT
1 AAATGTATCGATACATTC-TTCATTGTATCGATACAT
5098 CCAGTTAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
49 16 0.21
50 20 0.27
52 35 0.47
53 4 0.05
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.44
Consensus pattern (50 bp):
AAATGTATCGATACATTCTTCATTGTATCGATACATTCTGGGTTTGACCC
Found at i:7591 original size:27 final size:26
Alignment explanation
Indices: 7553--7604 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
7543 ATCGTCATCA
*
7553 GAGATACTCTAACCCCATTCTTTCAAG
1 GAGACACTCTAACCCCATT-TTTCAAG
* *
7580 GAGACACTCTAATCCCGTTTTTCAA
1 GAGACACTCTAACCCCATTTTTCAA
7605 CCAAAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (26 bp):
GAGACACTCTAACCCCATTTTTCAAG
Found at i:13066 original size:36 final size:37
Alignment explanation
Indices: 13009--13082 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
12999 ATAACTTTTT
* * *
13009 TTTTCTTTTTATGTTTATTATTATAAGTTAAATAAAA
1 TTTTCTTTTAATGTTTATTATTACAAATTAAATAAAA
*
13046 TTTTC-TTTAATGTTTGTTATTACAAATTAAATAAAA
1 TTTTCTTTTAATGTTTATTATTACAAATTAAATAAAA
13082 T
1 T
13083 CTAAATTTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
36 28 0.85
37 5 0.15
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.54
Consensus pattern (37 bp):
TTTTCTTTTAATGTTTATTATTACAAATTAAATAAAA
Found at i:14436 original size:7 final size:7
Alignment explanation
Indices: 14426--14458 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
14416 TAAACAATAG
14426 AAGAAAA
1 AAGAAAA
14433 AAG-AAA
1 AAGAAAA
14439 AAG-AAA
1 AAGAAAA
14445 AAGAAAA
1 AAGAAAA
14452 AAGAAAA
1 AAGAAAA
14459 GAAAAATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:14441 original size:6 final size:6
Alignment explanation
Indices: 14430--14464 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
14420 CAATAGAAGA
14430 AAAAAG AAAAAG AAAAAG AAAAA- AGAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG A-AAAAG AAAAA
14465 TAAGCTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 1 0.04
6 25 0.93
7 1 0.04
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:15039 original size:18 final size:18
Alignment explanation
Indices: 15017--15054 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
15007 AAATGATCAA
15017 AAAAATATTTAATAAA-TTG
1 AAAAA-ATTT-ATAAAGTTG
15036 AAAAAATTTATAAAGTTG
1 AAAAAATTTATAAAGTTG
15054 A
1 A
15055 CAATTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.28
18 8 0.44
19 5 0.28
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (18 bp):
AAAAAATTTATAAAGTTG
Found at i:16260 original size:51 final size:51
Alignment explanation
Indices: 16100--16270 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
16090 GAAATAACGA
* * *
16100 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
16152 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
16205 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
16256 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
16271 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:16316 original size:27 final size:28
Alignment explanation
Indices: 16253--16328 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
16243 AAAATAAAGT
*
16253 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
16281 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
16308 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
16329 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:18807 original size:13 final size:13
Alignment explanation
Indices: 18789--18814 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18779 ACAAAGATCC
18789 ATGTATCGATACA
1 ATGTATCGATACA
18802 ATGTATCGATACA
1 ATGTATCGATACA
18815 CAGAAAAATG
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):
ATGTATCGATACA
Found at i:18810 original size:33 final size:33
Alignment explanation
Indices: 18768--18834 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
18758 AAAATTTCCA
***
18768 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
18801 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
18834 A
1 A
18835 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:18878 original size:19 final size:18
Alignment explanation
Indices: 18854--18921 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
18844 CAGTAGCTAA
18854 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
18873 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
18888 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
18905 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
18922 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:18894 original size:13 final size:13
Alignment explanation
Indices: 18876--18900 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18866 ACAATACTTA
18876 TGTATCGATACAT
1 TGTATCGATACAT
18889 TGTATCGATACA
1 TGTATCGATACA
18901 AAACTTATGT
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:18898 original size:32 final size:32
Alignment explanation
Indices: 18857--18919 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
18847 TAGCTAATTA
*
18857 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
18889 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
18920 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:19001 original size:21 final size:21
Alignment explanation
Indices: 18977--19033 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
18967 CATTTGTAGG
*
18977 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCAACAA
18998 ATGTATCGATACATTCAACAA
1 ATGTATCGATACATTCAACAA
19019 ATGTATCGATACATT
1 ATGTATCGATACATT
19034 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCAACAA
Found at i:19063 original size:15 final size:14
Alignment explanation
Indices: 19044--19071 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
19034 TAAATTTTTT
19044 TTTTTTTTTTCAAA
1 TTTTTTTTTTCAAA
19058 TTTTTTTTTTCAAA
1 TTTTTTTTTTCAAA
19072 CACTTTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTTTTTTTCAAA
Found at i:19748 original size:55 final size:55
Alignment explanation
Indices: 19653--20501 Score: 1122
Period size: 55 Copynumber: 15.3 Consensus size: 55
19643 ATAAAGTGAA
* * * * * * * * *
19653 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGATAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
19708 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* ** * *
19763 TCCTGCTCTTTGGGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
**
19818 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
19873 TCCTGCTCTTCGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* **
19928 TCCTGCTCTTTGAGGACT-AGAAGGCGCCACCAACTTGTGTGGGCTTTAA-AAATAAAAAG
1 TCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGT-----G
** * *
19987 CATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 --TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
** * *
20044 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
20099 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* * *
20154 TCCTGCTCTTCGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* * *
20209 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGGGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
20264 TCCTGCTCTTTGAGGACT-AGAAGGCGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
20319 TCCTACTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
20374 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
20429 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGACGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
20484 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
20502 AAAAAGCGGA
Statistics
Matches: 720, Mismatches: 52, Indels: 44
0.88 0.06 0.05
Matches are distributed among these distances:
54 15 0.02
55 644 0.89
56 12 0.02
57 2 0.00
59 1 0.00
61 43 0.06
62 3 0.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:20039 original size:27 final size:27
Alignment explanation
Indices: 20009--20094 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
19999 TGAGGACTGA
20009 AAAATGCCACCAACCTGTGTGGGCTTT
1 AAAATGCCACCAACCTGTGTGGGCTTT
* *** ** * * * **
20036 AAAAGGTGTCCTGCTCTTTGAGGACTGA
1 AAAATGCCACCAAC-CTGTGTGGGCTTT
20064 AAAATGCCACCAACCTGTGTGGGCTTT
1 AAAATGCCACCAACCTGTGTGGGCTTT
20091 AAAA
1 AAAA
20095 GGTGTCCTGC
Statistics
Matches: 36, Mismatches: 22, Indels: 2
0.60 0.37 0.03
Matches are distributed among these distances:
27 20 0.56
28 16 0.44
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (27 bp):
AAAATGCCACCAACCTGTGTGGGCTTT
Found at i:20234 original size:26 final size:26
Alignment explanation
Indices: 20204--20287 Score: 62
Period size: 26 Copynumber: 3.1 Consensus size: 26
20194 GGGCTTTGAG
*
20204 AGGTGTCCTGCTCTTTGAGGACTGGA
1 AGGTGTCCTGCTCTTTGAGGACTAGA
** * * * *
20230 AGGTG-CCACCAACTTGTGGGGGCTTTGA
1 AGGTGTCCTGC-TCTT-TGAGGAC-TAGA
20258 GAGGTGTCCTGCTCTTTGAGGACTAGA
1 -AGGTGTCCTGCTCTTTGAGGACTAGA
20285 AGG
1 AGG
20288 CGCCACCAAC
Statistics
Matches: 41, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
25 3 0.07
26 11 0.27
27 8 0.20
28 8 0.20
29 8 0.20
30 3 0.07
ACGTcount: A:0.18, C:0.19, G:0.36, T:0.27
Consensus pattern (26 bp):
AGGTGTCCTGCTCTTTGAGGACTAGA
Found at i:21487 original size:16 final size:16
Alignment explanation
Indices: 21466--21519 Score: 83
Period size: 15 Copynumber: 3.4 Consensus size: 16
21456 CTTAAGTAGG
*
21466 TTTTTTCTTTTCTCTT
1 TTTTTTTTTTTCTCTT
21482 TTTTTTTTTTTC-CTT
1 TTTTTTTTTTTCTCTT
21497 TTTTTTTTTTTGCTCTT
1 TTTTTTTTTTT-CTCTT
21514 TTTTTT
1 TTTTTT
21520 GAAGAGAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
15 14 0.40
16 12 0.34
17 9 0.26
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (16 bp):
TTTTTTTTTTTCTCTT
Found at i:21505 original size:14 final size:14
Alignment explanation
Indices: 21466--21506 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
21456 CTTAAGTAGG
* *
21466 TTTTTTCTTTTCTCT
1 TTTTTT-TTTTTTCC
21481 TTTTTTTTTTTTCC
1 TTTTTTTTTTTTCC
21495 TTTTTTTTTTTT
1 TTTTTTTTTTTT
21507 TGCTCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 18 0.75
15 6 0.25
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTTTCC
Found at i:22602 original size:21 final size:21
Alignment explanation
Indices: 22578--22634 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
22568 CATTTGTAGG
*
22578 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCAACAA
22599 ATGTATCGATACATTCAACAA
1 ATGTATCGATACATTCAACAA
22620 ATGTATCGATACATT
1 ATGTATCGATACATT
22635 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCAACAA
Found at i:22667 original size:16 final size:15
Alignment explanation
Indices: 22647--22676 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
22637 AATTTTTTTT
22647 TTTTTTTTTTTCAAA
1 TTTTTTTTTTTCAAA
22662 TTTTTTTTTTTCAAA
1 TTTTTTTTTTTCAAA
22677 CACTTTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTTTTTTCAAA
Found at i:25353 original size:393 final size:394
Alignment explanation
Indices: 24619--25408 Score: 1276
Period size: 393 Copynumber: 2.0 Consensus size: 394
24609 ACATTGAAAC
*
24619 ATAGGTATGCGAACCATTCACATAACTAAACCATTAAAACTTAAATGAGCTTAAGATAAAAGAGT
1 ATAGGTATGAGAACCATTCACATAACTAAACCATTAAAACTTAAATGAGCTTAAGATAAAAGAGT
* * *
24684 TTAATAATTAAATCATGGATGGGAACTGAATGACATCTAGTTTATTTGTTTCTTAACTATTTTGA
66 TTAATAATCAAATAATGGATGGGAACTAAATGACATCTAGTTTATTTGTTTCTTAACTATTTTGA
* * *
24749 ATTTAGTTCAACTATAATTTAATAGGGTTTTTTTAGGGTTATAATTAAAAGTTTTTTCTTACGTG
131 ATTTAGTTCAACTATAATTTAATAGGGTTTTTTTAGGGTTAGAACTAAAAGTTTTTTCTTACATG
* * **
24814 GAACCAAGATATGACCCTTTGGAATGGGGGTTTCTTTTTAAAGATATGTAGTTAAAATTATCGAC
196 GAACCAAGATATGACCATTTGGAATGGGGGTTTCTTTTTAAAGACATACAGTTAAAATTATCGAC
24879 CAAACTCAATTAAAATAATGCTCCATTTAAAAAGGTTTCAACCCTTAATCAGATCACCTAGCCAT
261 CAAACTCAATTAAAATAATGCTCCATTTAAAAAGGTTTCAACCCTTAATCAGATCACCTAGCCAT
*
24944 GTAAAGAGATTATTTACAAACAAGCTTGAATGAATTGTCAAGATATAGAGAAACTTCCACAGTGA
326 GTAAAGAGAATATTTACAAACAAGCTTGAATGAATTGTCAAGATATAGAGAAACTTCCACAGTGA
25009 TAAG
391 TAAG
* * * *
25013 ATAGGTATGAGAACCATTCACGTAACTAAGCCATTAAAATTTAAATGAGCTTAAGATAATAGAGT
1 ATAGGTATGAGAACCATTCACATAACTAAACCATTAAAACTTAAATGAGCTTAAGATAAAAGAGT
*
25078 TTAATAATCAAATAATGGATGGGAACTAAATGACATCTAGTTTATTTGTTTCTTGACTATTTTGA
66 TTAATAATCAAATAATGGATGGGAACTAAATGACATCTAGTTTATTTGTTTCTTAACTATTTTGA
*
25143 ATTTAGTTCAACTATAATTTAATA-GGTTTTTTTAGGGTTAGAGCTAAAAGTTTTTTCTTACATG
131 ATTTAGTTCAACTATAATTTAATAGGGTTTTTTTAGGGTTAGAACTAAAAGTTTTTTCTTACATG
* * * * *
25207 GAACCAAGATATGACCATTTGTAATGGGGGTTTCTTTTTAAGGGCATACAGTTAAGATTATTGAC
196 GAACCAAGATATGACCATTTGGAATGGGGGTTTCTTTTTAAAGACATACAGTTAAAATTATCGAC
** * * *
25272 CAAACTCAATTAAAATAATGCTTTATTTAAAAATGTTTCAACCTTTAATTAGATCACCTAGCCAT
261 CAAACTCAATTAAAATAATGCTCCATTTAAAAAGGTTTCAACCCTTAATCAGATCACCTAGCCAT
* * * * *
25337 TTAAAGAGAATATTTACAAACAAGCTTGGATGAGTTGTCAAGATGTGGAGAAACTTCCACAGTGA
326 GTAAAGAGAATATTTACAAACAAGCTTGAATGAATTGTCAAGATATAGAGAAACTTCCACAGTGA
25402 TAAG
391 TAAG
25406 ATA
1 ATA
25409 ATTGGCCAAT
Statistics
Matches: 363, Mismatches: 33, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
393 218 0.60
394 145 0.40
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Consensus pattern (394 bp):
ATAGGTATGAGAACCATTCACATAACTAAACCATTAAAACTTAAATGAGCTTAAGATAAAAGAGT
TTAATAATCAAATAATGGATGGGAACTAAATGACATCTAGTTTATTTGTTTCTTAACTATTTTGA
ATTTAGTTCAACTATAATTTAATAGGGTTTTTTTAGGGTTAGAACTAAAAGTTTTTTCTTACATG
GAACCAAGATATGACCATTTGGAATGGGGGTTTCTTTTTAAAGACATACAGTTAAAATTATCGAC
CAAACTCAATTAAAATAATGCTCCATTTAAAAAGGTTTCAACCCTTAATCAGATCACCTAGCCAT
GTAAAGAGAATATTTACAAACAAGCTTGAATGAATTGTCAAGATATAGAGAAACTTCCACAGTGA
TAAG
Found at i:25519 original size:23 final size:26
Alignment explanation
Indices: 25493--25544 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
25483 CTAAAGATCT
*
25493 AAAAAAGAAAAG-AAA-AATAGAGGA
1 AAAAAAGAAAAGAAAATAAGAGAGGA
*
25517 AAAAAACAAAAGAAAATAAGAGAGGA
1 AAAAAAGAAAAGAAAATAAGAGAGGA
25543 AA
1 AA
25545 GAAGAAGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 11 0.46
25 3 0.12
26 10 0.42
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (26 bp):
AAAAAAGAAAAGAAAATAAGAGAGGA
Found at i:26392 original size:57 final size:56
Alignment explanation
Indices: 26329--26566 Score: 189
Period size: 57 Copynumber: 4.2 Consensus size: 56
26319 GTGCATATTA
* * * *
26329 AATGTCATTTAGCTTATTTTCATAATTTAGGGACTTTTATACAATTTTATGAATTTT
1 AATGTCATTTAGCTCATTTTCATGATCTAGGAACTTTTATAC-ATTTTATGAATTTT
* * * * * * *
26386 GATGTCATTTAGGTCATTTCCATGATCCAGGAATTTTTATGCA-TTTATAAATTTT
1 AATGTCATTTAGCTCATTTTCATGATCTAGGAACTTTTATACATTTTATGAATTTT
* * * *
26441 AATGTCATTTA-ATCATTTTTTATGA-CTTAGGAACTTTTATATCTTTTTAT-ATATTTC
1 AATGTCATTTAGCTCA-TTTTCATGATC-TAGGAACTTTTATA-CATTTTATGA-ATTTT
* * *
26498 AATGTCATTTAGGTCATTTTTCATGATCTATGG-ACTTTAATATAGTTTTATGAATTTT
1 AATGTCATTTAGCTCA-TTTTCATGATCTA-GGAACTTTTATACA-TTTTATGAATTTT
* *
26556 GATATCATTTA
1 AATGTCATTTA
26567 AGTGATTTTC
Statistics
Matches: 143, Mismatches: 28, Indels: 19
0.75 0.15 0.10
Matches are distributed among these distances:
54 4 0.03
55 39 0.27
56 3 0.02
57 52 0.36
58 41 0.29
59 4 0.03
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.50
Consensus pattern (56 bp):
AATGTCATTTAGCTCATTTTCATGATCTAGGAACTTTTATACATTTTATGAATTTT
Found at i:27216 original size:36 final size:35
Alignment explanation
Indices: 27150--27217 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
27140 TAAAATGAAG
* *
27150 AAGAATAATATTAATTATAAAAAATTTTAAAAATT
1 AAGAATAATATTAAATATAAAAAATATTAAAAATT
*
27185 AAGAATTATAATTAAATATCAAAAAA-ATTAAAA
1 AAGAATAAT-ATTAAATAT-AAAAAATATTAAAA
27218 CCAATCATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
35 8 0.29
36 14 0.50
37 6 0.21
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (35 bp):
AAGAATAATATTAAATATAAAAAATATTAAAAATT
Found at i:27760 original size:18 final size:18
Alignment explanation
Indices: 27727--27771 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
27717 GAGAGATGAG
* *
27727 GAAAAA-AAAGAGAAAAT
1 GAAAAAGAAAGAAAAAAA
*
27744 GAAAGAGAAAGAAAAAAA
1 GAAAAAGAAAGAAAAAAA
27762 GAAAAAGAAA
1 GAAAAAGAAA
27772 AAAGACAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (18 bp):
GAAAAAGAAAGAAAAAAA
Found at i:27776 original size:13 final size:14
Alignment explanation
Indices: 27745--27774 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27735 AGAGAAAATG
*
27745 AAAGAGAAAGAAAA
1 AAAGAAAAAGAAAA
27759 AAAGAAAAAGAAAA
1 AAAGAAAAAGAAAA
27773 AA
1 AA
27775 GACAGCTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAGAAAA
Found at i:27905 original size:16 final size:16
Alignment explanation
Indices: 27886--27917 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27876 AAAGGGAAAG
27886 TAAAAAGAAAAATAAA
1 TAAAAAGAAAAATAAA
*
27902 TAAAAATAAAAATAAA
1 TAAAAAGAAAAATAAA
27918 AATTGAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (16 bp):
TAAAAAGAAAAATAAA
Found at i:37640 original size:18 final size:18
Alignment explanation
Indices: 37594--37647 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
37584 ATTTTTTTCA
37594 ATTAAAAAAATAATAAGTT
1 ATTAAAAAAAT-ATAAGTT
* *
37613 ATTTAGAAAATATAAG-T
1 ATTAAAAAAATATAAGTT
37630 ACTTAAAAAAATAGTAAG
1 A-TTAAAAAAATA-TAAG
37648 AGTTGTCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 14 0.48
19 13 0.45
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (18 bp):
ATTAAAAAAATATAAGTT
Found at i:39602 original size:14 final size:16
Alignment explanation
Indices: 39582--39620 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
39572 ATGTATATCA
39582 ATACATAAATTAT-CG
1 ATACATAAATTATACG
39597 -TACATAAA-TATACG
1 ATACATAAATTATACG
39611 ATACATAAAT
1 ATACATAAAT
39621 ACATTACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.14
14 10 0.48
15 8 0.38
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (16 bp):
ATACATAAATTATACG
Found at i:39617 original size:15 final size:16
Alignment explanation
Indices: 39575--39621 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 16
39565 ATAAATTATG
*
39575 TATATCAATACATAAA
1 TATATCGATACATAAA
39591 T-TATCG-TACATAAA
1 TATATCGATACATAAA
39605 TATA-CGATACATAAA
1 TATATCGATACATAAA
39620 TA
1 TA
39622 CATTACATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 11 0.39
15 16 0.57
16 1 0.04
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (16 bp):
TATATCGATACATAAA
Found at i:39887 original size:157 final size:157
Alignment explanation
Indices: 39586--39895 Score: 439
Period size: 157 Copynumber: 2.0 Consensus size: 157
39576 ATATCAATAC
* * *
39586 ATAAATTATCGTACATAAATATACGATACATAAATACATTACATGATTAATATCCATAATAAATG
1 ATAAATTATCGTACATAAATACACAATACATAAATACATTACACGATTAATATCCATAATAAATG
*
39651 AAAAATTTGTCTTATTATGCCCACTTAAAAAAGAAAAAAGTTTGGTTGTTAGTGTAAGGTGATAA
66 AAAAATTTGTCTCATTATGCCCACTTAAAAAAGAAAAAAGTTTGGTTGTTAGTGTAAGGTGATAA
* *
39716 GCAATTCCAGTGATGAAGTATGGACAT
131 ACAATTCCACTGATGAAGTATGGACAT
* * * *
39743 ATAAATTATCGTACGTAGATACACAATACATAAATACATTGCACGATTAATATCCATAATGAAT-
1 ATAAATTATCGTACATAAATACACAATACATAAATACATTACACGATTAATATCCATAATAAATG
** *
39807 AAGAAA-TTGATCTCATTATGTTCACTTAAAAAAGAAAAAAGTTTGGTTGTTAGTGTAAGATTG-
66 AA-AAATTTG-TCTCATTATGCCCACTTAAAAAAGAAAAAAGTTTGGTTGTTAGTGTAAG-GTGA
39870 TAAACAA-TCTCACTGATGAAGTATGG
128 TAAACAATTC-CACTGATGAAGTATGG
39896 GTTACTTCTG
Statistics
Matches: 136, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
156 7 0.05
157 127 0.93
158 2 0.01
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (157 bp):
ATAAATTATCGTACATAAATACACAATACATAAATACATTACACGATTAATATCCATAATAAATG
AAAAATTTGTCTCATTATGCCCACTTAAAAAAGAAAAAAGTTTGGTTGTTAGTGTAAGGTGATAA
ACAATTCCACTGATGAAGTATGGACAT
Found at i:39915 original size:2 final size:2
Alignment explanation
Indices: 39908--39949 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
39898 TACTTCTGTG
39908 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39950 TAATCAAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49289 original size:20 final size:20
Alignment explanation
Indices: 49248--49287 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
49238 AATTCTATTA
*
49248 AAAAAATTAAAACAAAATTT
1 AAAAAATAAAAACAAAATTT
*
49268 AAAAAATAAATAATAAAATT
1 AAAAAATAAA-AACAAAATT
49288 AATTTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAAAATAAAAACAAAATTT
Found at i:49306 original size:73 final size:72
Alignment explanation
Indices: 49217--49361 Score: 256
Period size: 73 Copynumber: 2.0 Consensus size: 72
49207 GTAATAATAT
49217 TTTTAATAATTTAACCATTCAAATTCTATTAAAAA-AATTAAAACAAAATTTAAAAAATAAATAA
1 TTTTAATAATTTAACCATTCAAATTCTATTAAAAAGAATTAAAACAAAATTT--AAAATAAATAA
49281 TAAAATTAA
64 TAAAATTAA
*
49290 TTTTAATAATTTAACCATTCAAATTCTATTAAAAAGAGTTAAAACAAAATTTAAAATAAATAATA
1 TTTTAATAATTTAACCATTCAAATTCTATTAAAAAGAATTAAAACAAAATTTAAAATAAATAATA
49355 AAATTAA
66 AAATTAA
49362 AATATGATAT
Statistics
Matches: 70, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
72 20 0.29
73 35 0.50
74 15 0.21
ACGTcount: A:0.57, C:0.07, G:0.01, T:0.34
Consensus pattern (72 bp):
TTTTAATAATTTAACCATTCAAATTCTATTAAAAAGAATTAAAACAAAATTTAAAATAAATAATA
AAATTAA
Found at i:49380 original size:19 final size:18
Alignment explanation
Indices: 49336--49390 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
49326 AGTTAAAACA
49336 AAATTTAAAATAAATAAT
1 AAATTTAAAATAAATAAT
* * *
49354 AAAATTAAAATATGATATT
1 AAATTTAAAATA-AATAAT
49373 AAATTTAATGAATAAATA
1 AAATTTAA--AATAAATA
49391 CTGAATTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 11 0.38
19 11 0.38
20 3 0.10
21 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
AAATTTAAAATAAATAAT
Found at i:50918 original size:34 final size:34
Alignment explanation
Indices: 50854--51036 Score: 251
Period size: 34 Copynumber: 5.4 Consensus size: 34
50844 TAAAACTTTG
* *
50854 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
50887 TGTTGACTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
50921 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
50955 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
50989 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
51023 TGTTGATTAAATGG
1 TGTTGATTAAATGG
51037 TGGTTTTTAC
Statistics
Matches: 130, Mismatches: 19, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
33 11 0.08
34 119 0.92
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:55517 original size:34 final size:34
Alignment explanation
Indices: 55451--55635 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
55441 AAGTGGGAGA
* *
55451 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
55484 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
55518 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
55552 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
55586 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
55620 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
55636 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:58830 original size:15 final size:15
Alignment explanation
Indices: 58812--58860 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
58802 AATTACAAAA
58812 AAATTAATTAGTAA-T
1 AAATT-ATTAGTAATT
58827 AAATT-TTA-TAATT
1 AAATTATTAGTAATT
*
58840 AAATTTTTAGTAATT
1 AAATTATTAGTAATT
*
58855 TAATTA
1 AAATTA
58861 ATTAATTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 3 0.10
13 9 0.31
14 3 0.10
15 14 0.48
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (15 bp):
AAATTATTAGTAATT
Found at i:58883 original size:20 final size:20
Alignment explanation
Indices: 58846--58884 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
58836 AATTAAATTT
* * *
58846 TTAGTAATTTAATTAATTAA
1 TTAGTAAATCAATAAATTAA
58866 TTAGTAAATCAATAAATTA
1 TTAGTAAATCAATAAATTA
58885 GCAACTTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (20 bp):
TTAGTAAATCAATAAATTAA
Found at i:59123 original size:43 final size:43
Alignment explanation
Indices: 59068--59284 Score: 138
Period size: 43 Copynumber: 4.9 Consensus size: 43
59058 CATTATTCTT
* *
59068 AATGAATCTATATATCTATATATCTATTAATTAATTTAAAGTC
1 AATGAATATATATATCTATATATCTATTAATTAATTTAAACTC
* * ***
59111 AATGAATATATATTTCTATACGAT-TAATTTAATATTATAAAAAAACTC
1 AATGAATATATATATCTATA-TATCT-A-TT-A-ATTA-ATTTAAACTC
* * ** *
59159 ATAATAAATAT-TAATAT-T-TATATCAAAAAAATTAA-TTAATACTT
1 --AATGAATATAT-ATATCTATATATC-TATTAATTAATTTAA-ACTC
* * *
59203 AATGAATCTATATATCTATATATCTATTAATTTATTTAAAATC
1 AATGAATATATATATCTATATATCTATTAATTAATTTAAACTC
* * *
59246 AATGAATATATATCTCTATACATCTATTGATTAATTTAA
1 AATGAATATATATATCTATATATCTATTAATTAATTTAA
59285 TATGATAAAA
Statistics
Matches: 129, Mismatches: 29, Indels: 32
0.68 0.15 0.17
Matches are distributed among these distances:
42 11 0.09
43 65 0.50
44 17 0.13
45 6 0.05
46 2 0.02
47 6 0.05
48 9 0.07
49 2 0.02
50 11 0.09
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (43 bp):
AATGAATATATATATCTATATATCTATTAATTAATTTAAACTC
Found at i:59334 original size:135 final size:131
Alignment explanation
Indices: 59065--59320 Score: 377
Period size: 135 Copynumber: 1.9 Consensus size: 131
59055 ATGCATTATT
* *
59065 CTTAATGAATCTATATATCTATATATCTATTAATTAATTTAAAGTCAATGAATATATATTTCTAT
1 CTTAATGAATCTATATATCTATATATCTATTAATTAATTTAAAATCAATGAATATATATCTCTAT
*
59130 ACGATTAATTTAATATTATAAAAAAACTCATAATAAATATTAATATTTATATCAAAAAAATTAAT
66 ACGATTAATTTAATATGATAAAAAAACTCATAATAAATATTAATATTTATAT----AAAATTAAT
59195 TAATA
127 TAATA
*
59200 CTTAATGAATCTATATATCTATATATCTATTAATTTATTTAAAATCAATGAATATATATCTCTAT
1 CTTAATGAATCTATATATCTATATATCTATTAATTAATTTAAAATCAATGAATATATATCTCTAT
59265 ACATCTATTGATTAATTTAATATGATAAAAAAACTCATAATAAATATTAATATTTA
66 --A-C----GATTAATTTAATATGATAAAAAAACTCATAATAAATATTAATATTTA
59321 ATTAATACTT
Statistics
Matches: 110, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
135 62 0.56
137 1 0.01
138 1 0.01
142 46 0.42
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (131 bp):
CTTAATGAATCTATATATCTATATATCTATTAATTAATTTAAAATCAATGAATATATATCTCTAT
ACGATTAATTTAATATGATAAAAAAACTCATAATAAATATTAATATTTATATAAAATTAATTAAT
A
Found at i:59544 original size:54 final size:53
Alignment explanation
Indices: 59448--59613 Score: 278
Period size: 54 Copynumber: 3.1 Consensus size: 53
59438 ATATATTCCC
*
59448 TATAAAAAGCTCATAATAAATATTAACATTTATATAAAAAAACTGTATTTTATA
1 TATAAAAA-CTCATAATAAATATTAACATTTATGTAAAAAAACTGTATTTTATA
*
59502 TATAAAAACTCATAATAAATATTAATATTTATGTAAAAAAAACTGTATTTTATA
1 TATAAAAACTCATAATAAATATTAACATTTATGT-AAAAAAACTGTATTTTATA
*
59556 TATAAAAACTCAAAATAAATATTAACATTTATGTTAAAAAAACTGTATTTTATA
1 TATAAAAACTCATAATAAATATTAACATTTATG-TAAAAAAACTGTATTTTATA
59610 TATA
1 TATA
59614 TTATATAGAA
Statistics
Matches: 106, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
53 24 0.23
54 81 0.76
55 1 0.01
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.38
Consensus pattern (53 bp):
TATAAAAACTCATAATAAATATTAACATTTATGTAAAAAAACTGTATTTTATA
Found at i:59650 original size:121 final size:115
Alignment explanation
Indices: 59497--59850 Score: 342
Period size: 121 Copynumber: 3.1 Consensus size: 115
59487 AAACTGTATT
* *
59497 TTATATA-TAAAAACTCATAATAAATATTAATATTTATGTAAAAAAAACTGTATTTTATATATAA
1 TTATATAGAAAAAACTCATAATAAATATTAATATTTATGTCAAAAAAACTGTATTTTATATATAA
59561 AAACTCAAAATAAATATTAACATTTATGTTAAAAAAACTGTATTTTATATATA
66 AAA-T-AAAATAAATATTAA-ATTTATGTTAAAAAAACTGTATTTTATATATA
*
59614 TTATATAGAAAAAGAAACTCATAATAAATATTAATATTTATGTCCAAAAAACTGTATTTTATATA
1 TTATATAG--AAA-AAACTCATAATAAATATTAATATTTATGTCAAAAAAACTGTATTTTATATA
**** *
59679 TTCTTTATAAAA-AAACTCATAATAAATATTAAGTT-AAAAAACTGTA---T-T-T-TA
63 -TAAAAATAAAATAAA-T-AT--TAAAT-TTATGTTAAAAAAACTGTATTTTATATATA
* *
59730 -TATAT---AAAAACTCATAATAAATATT-A-ATTTATGTCAAAAAAATTATATTTTATATATAA
1 TTATATAGAAAAAACTCATAATAAATATTAATATTTATGTCAAAAAAACTGTATTTTATATATAA
* * * *
59789 AAATTTATAATAAATATTAATATTTATGTAAAAAAAATTATATTTTATATATA
66 AAA--TAAAATAAATATTAA-ATTTATGTTAAAAAAACTGTATTTTATATATA
59842 TTATATAGA
1 TTATATAGA
59851 TTTGTTCTGA
Statistics
Matches: 192, Mismatches: 20, Indels: 51
0.73 0.08 0.19
Matches are distributed among these distances:
105 8 0.04
106 13 0.07
107 29 0.15
108 6 0.03
109 22 0.11
110 3 0.02
111 1 0.01
112 2 0.01
113 5 0.03
115 5 0.03
116 2 0.01
117 8 0.04
118 1 0.01
119 4 0.02
120 7 0.04
121 52 0.27
122 15 0.08
123 9 0.05
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (115 bp):
TTATATAGAAAAAACTCATAATAAATATTAATATTTATGTCAAAAAAACTGTATTTTATATATAA
AAATAAAATAAATATTAAATTTATGTTAAAAAAACTGTATTTTATATATA
Found at i:59709 original size:63 final size:65
Alignment explanation
Indices: 59547--59710 Score: 217
Period size: 67 Copynumber: 2.5 Consensus size: 65
59537 AAAAAAACTG
* * * *
59547 TATTTTATATATAAAAACTCAAAATAAATATTAACATTTATGTTAAAAAAACTGTATTTTATATA
1 TATTATATATAAAAAAACTCATAATAAATATTAACATTTATGTCAAAAAAACTGTATTTTATATA
* * *
59612 TATTATATAGAAAAAGAAACTCATAATAAATATTAATATTTATGTCCAAAAAACTGTATTTTATA
1 TATTATATA-TAAAA-AAACTCATAATAAATATTAACATTTATGTCAAAAAAACTGTATTTTATA
59677 TA
64 TA
59679 T-TCT-T-TATAAAAAAACTCATAATAAATATTAA
1 TAT-TATATATAAAAAAACTCATAATAAATATTAA
59711 GTTAAAAAAC
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
63 20 0.23
64 4 0.05
65 10 0.11
66 5 0.06
67 49 0.56
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (65 bp):
TATTATATATAAAAAAACTCATAATAAATATTAACATTTATGTCAAAAAAACTGTATTTTATATA
Found at i:59823 original size:54 final size:52
Alignment explanation
Indices: 59675--59841 Score: 195
Period size: 52 Copynumber: 3.3 Consensus size: 52
59665 CTGTATTTTA
* * *
59675 TATATTCTT-TATAAAAAAACTCATAATAAATATT-A---A-GT-TAAAAAAC
1 TATATT-TTATATATAAAAACTCATAATAAATATTAATTTATGTAAAAAAAAT
* *
59721 TGTATTTTATATATAAAAACTCATAATAAATATTAATTTATGTCAAAAAAAT
1 TATATTTTATATATAAAAACTCATAATAAATATTAATTTATGTAAAAAAAAT
* *
59773 TATATTTTATATATAAAAATTTATAATAAATATTAATATTTATGTAAAAAAAAT
1 TATATTTTATATATAAAAACTCATAATAAATATT-A-ATTTATGTAAAAAAAAT
59827 TATATTTTATATATA
1 TATATTTTATATATA
59842 TTATATAGAT
Statistics
Matches: 104, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
45 2 0.02
46 29 0.28
47 1 0.01
50 1 0.01
51 2 0.02
52 37 0.36
53 1 0.01
54 31 0.30
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.42
Consensus pattern (52 bp):
TATATTTTATATATAAAAACTCATAATAAATATTAATTTATGTAAAAAAAAT
Found at i:59835 original size:228 final size:234
Alignment explanation
Indices: 59387--59850 Score: 690
Period size: 228 Copynumber: 2.0 Consensus size: 234
59377 ATATCTCTAT
* *
59387 AAAAGAAATTCATAATAAATATTAACATTTATGTCAAAAAAATTGTATTTTATATATTCCCTATA
1 AAAAGAAACTCATAATAAATATTAACATTTATGTCAAAAAAACTGTATTTTATATATTCCCTATA
*
59452 AAAAGCTCATAATAAATATTAACATTTATATAAAAAAACTGTATTTTATATATAAAAACTCATAA
66 AAAAACTCATAATAAATATTAACA--TATATAAAAAAACTGTATTTTATATATAAAAACTCATAA
*
59517 TAAATATTAATATTTATGTAAAAAAAACTGTATTTTATATATAAAAACTCAAAATAAATATTAAC
129 TAAATATTAATATTTATGTAAAAAAAACTATATTTTATATATAAAAACTCAAAATAAATATTAAC
* *
59582 ATTTATGTTAAAAAAACTGTATTTTATATATATTATATAGA
194 ATTTATGTAAAAAAAACTATATTTTATATATATTATATAGA
* * **
59623 AAAAGAAACTCATAATAAATATTAATATTTATGTCCAAAAAACTGTATTTTATATATTCTTTATA
1 AAAAGAAACTCATAATAAATATTAACATTTATGTCAAAAAAACTGTATTTTATATATTCCCTAT-
*
59688 AAAAAACTCATAATAAATATT-A-A-GT-T-AAAAAACTGTATTTTATATATAAAAACTCATAAT
65 AAAAAACTCATAATAAATATTAACATATATAAAAAAACTGTATTTTATATATAAAAACTCATAAT
* * * * * *
59748 AAATATT-A-ATTTATGTCAAAAAAATTATATTTTATATATAAAAATTTATAATAAATATTAATA
130 AAATATTAATATTTATGTAAAAAAAACTATATTTTATATATAAAAACTCAAAATAAATATTAACA
*
59811 TTTATGTAAAAAAAATTATATTTTATATATATTATATAGA
195 TTTATGTAAAAAAAACTATATTTTATATATATTATATAGA
59851 TTTGTTCTGA
Statistics
Matches: 209, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
228 85 0.41
229 1 0.00
230 41 0.20
231 1 0.00
232 1 0.00
235 1 0.00
236 59 0.28
237 20 0.10
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (234 bp):
AAAAGAAACTCATAATAAATATTAACATTTATGTCAAAAAAACTGTATTTTATATATTCCCTATA
AAAAACTCATAATAAATATTAACATATATAAAAAAACTGTATTTTATATATAAAAACTCATAATA
AATATTAATATTTATGTAAAAAAAACTATATTTTATATATAAAAACTCAAAATAAATATTAACAT
TTATGTAAAAAAAACTATATTTTATATATATTATATAGA
Found at i:60025 original size:2 final size:2
Alignment explanation
Indices: 60018--60044 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
60008 TGATTTCTTG
60018 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
60045 TTTAATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61356 original size:28 final size:28
Alignment explanation
Indices: 61275--61356 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
61265 TTTTGGAGAT
*
61275 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
61303 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
61331 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
61357 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:61498 original size:51 final size:51
Alignment explanation
Indices: 61339--61509 Score: 189
Period size: 51 Copynumber: 3.3 Consensus size: 51
61329 GAAATAACGA
* * *
61339 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * * *
61391 AATTGGAGTATCACCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
61444 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
61495 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
61510 TCAGAAATAA
Statistics
Matches: 95, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
51 39 0.41
52 15 0.16
53 31 0.33
54 10 0.11
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:61555 original size:27 final size:28
Alignment explanation
Indices: 61492--61567 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
61482 AAAATAAAGT
*
61492 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
61520 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
61547 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
61568 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:64055 original size:13 final size:13
Alignment explanation
Indices: 64037--64062 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
64027 ACAAAGATCC
64037 ATGTATCGATACA
1 ATGTATCGATACA
64050 ATGTATCGATACA
1 ATGTATCGATACA
64063 TAGAAAAATG
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):
ATGTATCGATACA
Found at i:64058 original size:33 final size:33
Alignment explanation
Indices: 64016--64082 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
64006 AAAATTTCCA
***
64016 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
64049 AATGTATCGATACATAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
64082 A
1 A
64083 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:64126 original size:19 final size:18
Alignment explanation
Indices: 64102--64169 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
64092 CAGTAGCTAA
64102 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
64121 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
64136 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
64153 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
64170 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:64142 original size:13 final size:13
Alignment explanation
Indices: 64124--64148 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
64114 ACAATACTTA
64124 TGTATCGATACAT
1 TGTATCGATACAT
64137 TGTATCGATACA
1 TGTATCGATACA
64149 AAACTTATGT
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:64146 original size:32 final size:32
Alignment explanation
Indices: 64105--64167 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
64095 TAGCTAATTA
*
64105 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
64137 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
64168 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:64249 original size:21 final size:21
Alignment explanation
Indices: 64225--64281 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
64215 CATTTGTAGG
64225 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
64246 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
64267 ATGTATCGATACATT
1 ATGTATCGATACATT
64282 TGGATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:64327 original size:13 final size:14
Alignment explanation
Indices: 64287--64324 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
64277 ACATTTGGAT
64287 TTTTTTTTTTTCAA
1 TTTTTTTTTTTCAA
64301 TTTTTTTTTTTCAA
1 TTTTTTTTTTTCAA
64315 TTTTTTTTTT
1 TTTTTTTTTT
64325 CAAACACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTTTTTTCAA
Found at i:69088 original size:38 final size:38
Alignment explanation
Indices: 69031--69106 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
69021 AATAAATCCG
* *
69031 ATAGTTGTCGTTATGGAAAGTTCAAGGCCAAAAGCTAC
1 ATAGTTGTCGCTATAGAAAGTTCAAGGCCAAAAGCTAC
*
69069 ATAGTTGTCGCTATAGAAAGTTCAAGGCTAAAAGCTAC
1 ATAGTTGTCGCTATAGAAAGTTCAAGGCCAAAAGCTAC
69107 CTATCCCGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (38 bp):
ATAGTTGTCGCTATAGAAAGTTCAAGGCCAAAAGCTAC
Found at i:71717 original size:28 final size:31
Alignment explanation
Indices: 71685--71741 Score: 84
Period size: 28 Copynumber: 1.9 Consensus size: 31
71675 TTATTTCAAA
71685 ATTTTAAAAAATAA-TA-TTA-AAATTAATC
1 ATTTTAAAAAATAAGTATTTATAAATTAATC
*
71713 ATTTTATAAAATAAGTATTTATAAATTAA
1 ATTTTAAAAAATAAGTATTTATAAATTAA
71742 ACAATCATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 13 0.52
29 2 0.08
30 3 0.12
31 7 0.28
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (31 bp):
ATTTTAAAAAATAAGTATTTATAAATTAATC
Found at i:76564 original size:14 final size:14
Alignment explanation
Indices: 76547--76573 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
76537 TTATTTTTTT
76547 AATTTTAAAAATAA
1 AATTTTAAAAATAA
76561 AATTTTAAAAATA
1 AATTTTAAAAATA
76574 TATTAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTTTAAAAATAA
Found at i:76872 original size:14 final size:14
Alignment explanation
Indices: 76853--76879 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
76843 GTTTTTTTTG
76853 TCTTAACAAATAAA
1 TCTTAACAAATAAA
76867 TCTTAACAAATAA
1 TCTTAACAAATAA
76880 CGAATCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (14 bp):
TCTTAACAAATAAA
Found at i:77504 original size:22 final size:22
Alignment explanation
Indices: 77461--77505 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
77451 TAGAATAACA
* * *
77461 TTATTCATCTATCTTAAGAATT
1 TTATTCATCTAGCTAAAAAATT
*
77483 TTATTCCTCTAGCTAAAAAATT
1 TTATTCATCTAGCTAAAAAATT
77505 T
1 T
77506 AACTCAAGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.47
Consensus pattern (22 bp):
TTATTCATCTAGCTAAAAAATT
Found at i:79463 original size:28 final size:28
Alignment explanation
Indices: 79378--79444 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
79368 TCACATCAAT
** *
79378 ATTTTTAAAA-AAAATTATTTATGATGAAA
1 ATTTTTAAAATAAAA-TA-TTATTTTTAAA
79407 ATTTTTAAAATAAAATATTATTTTTAAA
1 ATTTTTAAAATAAAATATTATTTTTAAA
79435 ATTTATTAAA
1 ATTT-TTAAA
79445 TTTAAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 12 0.36
29 17 0.52
30 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (28 bp):
ATTTTTAAAATAAAATATTATTTTTAAA
Found at i:82765 original size:2 final size:2
Alignment explanation
Indices: 82758--82786 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
82748 ATCTAAGAAC
82758 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
82787 GATAGATAAA
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:83377 original size:38 final size:35
Alignment explanation
Indices: 83335--83427 Score: 89
Period size: 38 Copynumber: 2.5 Consensus size: 35
83325 ATAATTTGTG
* *
83335 TATTATATATTTTTTAT-AAATTATAATTATAATTATGA
1 TATTATATATATTATATAAAATT-TAA-TAT-ATTAT-A
*
83373 TATTAAATATATTATATAAAATTTAATATATTATA
1 TATTATATATATTATATAAAATTTAATATATTATA
83408 TAATTATATTATAATTATAT
1 T-ATTATA-TAT-ATTATAT
83428 TATTATTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
35 2 0.04
36 10 0.21
37 6 0.13
38 24 0.51
39 5 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (35 bp):
TATTATATATATTATATAAAATTTAATATATTATA
Found at i:83389 original size:14 final size:14
Alignment explanation
Indices: 83354--83435 Score: 60
Period size: 14 Copynumber: 5.6 Consensus size: 14
83344 TTTTTTATAA
83354 ATTATAATTATAAT-T
1 ATTAT-ATTA-AATAT
*
83369 ATGATATTAAATAT
1 ATTATATTAAATAT
* *
83383 ATTATATAAAATTT
1 ATTATATTAAATAT
* *
83397 AATATATTATATA-
1 ATTATATTAAATAT
83410 ATTATATTATAATTAT
1 ATTATATTA-AA-TAT
83426 ATTATTATTA
1 ATTA-TATTA
83436 TTATAATCAT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
13 11 0.21
14 26 0.50
15 6 0.12
16 4 0.08
17 5 0.10
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (14 bp):
ATTATATTAAATAT
Found at i:83422 original size:11 final size:11
Alignment explanation
Indices: 83335--83450 Score: 66
Period size: 11 Copynumber: 10.5 Consensus size: 11
83325 ATAATTTGTG
83335 TATTATATATT-
1 TATTATA-ATTA
*
83346 TTTTATAAATTA
1 TATTAT-AATTA
83358 TAATTATAATTA
1 T-ATTATAATTA
*
83370 TGA-TATTAAATA
1 T-ATTA-TAATTA
*
83382 TATTAT-ATAA
1 TATTATAATTA
*
83392 AATT-TAA-TA
1 TATTATAATTA
83401 TATTATATAATTA
1 TA-T-TATAATTA
83414 TATTATAATTA
1 TATTATAATTA
*
83425 TATTATTA-T-
1 TATTATAATTA
*
83434 TATTATAATCA
1 TATTATAATTA
83445 TATTAT
1 TATTAT
83451 TTTTATCGTA
Statistics
Matches: 81, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
9 10 0.12
10 8 0.10
11 34 0.42
12 21 0.26
13 8 0.10
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (11 bp):
TATTATAATTA
Found at i:83424 original size:19 final size:19
Alignment explanation
Indices: 83348--83447 Score: 77
Period size: 19 Copynumber: 5.3 Consensus size: 19
83338 TATATATTTT
83348 TTATA-AATTATAATTATAA
1 TTATATAATTAT-ATTATAA
*
83367 TTATGAT-ATTA-AATAT-A
1 TTAT-ATAATTATATTATAA
*
83384 TTATATAA-AAT-TTAATATA
1 TTATATAATTATATT-ATA-A
83403 TTATATAATTATATTATAA
1 TTATATAATTATATTATAA
*
83422 TTATATTATTATTATTATAA
1 TTATATAATTA-TATTATAA
*
83442 TCATAT
1 TTATAT
83448 TATTTTTATC
Statistics
Matches: 65, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
16 4 0.06
17 8 0.12
18 4 0.06
19 24 0.37
20 23 0.35
21 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (19 bp):
TTATATAATTATATTATAA
Found at i:83434 original size:17 final size:17
Alignment explanation
Indices: 83354--83456 Score: 62
Period size: 17 Copynumber: 6.3 Consensus size: 17
83344 TTTTTTATAA
83354 ATTATAATTATAATTATGAT
1 ATTATAATTAT-ATTAT--T
83374 ATTA-AA-TATATTA-T
1 ATTATAATTATATTATT
*
83388 A-TAAAATT-TAATATATT
1 ATTATAATTAT-AT-TATT
*
83405 A-TATAATTATATTATA
1 ATTATAATTATATTATT
83421 ATTAT-A-T-TATTATT
1 ATTATAATTATATTATT
*
83435 ATTATAATCATATTATT
1 ATTATAATTATATTATT
*
83452 TTTAT
1 ATTAT
83457 CGTATTGTCT
Statistics
Matches: 68, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
13 2 0.03
14 16 0.24
15 5 0.07
16 7 0.10
17 28 0.41
18 4 0.06
19 2 0.03
20 4 0.06
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (17 bp):
ATTATAATTATATTATT
Found at i:87057 original size:17 final size:20
Alignment explanation
Indices: 87023--87064 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
87013 ATCTTGTCGT
87023 ATTATTTTTTTATAATAATC
1 ATTATTTTTTTATAATAATC
87043 ATTATTTTTTTATAATAATC
1 ATTATTTTTTTATAATAATC
87063 AT
1 AT
87065 ATTAAAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTATTTTTTTATAATAATC
Found at i:87430 original size:25 final size:25
Alignment explanation
Indices: 87401--87449 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
87391 GTTTGTATAA
* *
87401 ATATGTCATGTTTTTATTATTTTTC
1 ATATGTCATATTTTAATTATTTTTC
*
87426 ATATGTTATATTTTAATTATTTTT
1 ATATGTCATATTTTAATTATTTTT
87450 ATGTTCGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.65
Consensus pattern (25 bp):
ATATGTCATATTTTAATTATTTTTC
Found at i:87889 original size:16 final size:17
Alignment explanation
Indices: 87863--87895 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
87853 TAAATCTTAT
87863 TATATTATTTTTTAAAA
1 TATATTATTTTTTAAAA
87880 TATA-TATTTTTTAAAA
1 TATATTATTTTTTAAAA
87896 ATTTAATCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTATTTTTTAAAA
Found at i:88030 original size:23 final size:24
Alignment explanation
Indices: 88004--88050 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
87994 TCTTTATATG
88004 ATAAAATT-ATTTA-ATGTATAAAA
1 ATAAAATTAATTTATAT-TATAAAA
*
88027 ATAAAGTTAATTTATATTATAAAA
1 ATAAAATTAATTTATATTATAAAA
88051 TTGTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
24 12 0.57
25 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
ATAAAATTAATTTATATTATAAAA
Found at i:88307 original size:2 final size:2
Alignment explanation
Indices: 88300--88345 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
88290 AACTATACAA
88300 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
88342 -T AT A
1 AT AT A
88346 GGTTGCGTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90178 original size:23 final size:25
Alignment explanation
Indices: 90147--90197 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
90137 AAATTTTAAA
* *
90147 AATATATAA-ATAATTTTATTT-TT
1 AATAAATAATATAATTTGATTTATT
*
90170 AATAAATAATATTATTTGATTTATT
1 AATAAATAATATAATTTGATTTATT
90195 AAT
1 AAT
90198 TATATATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 8 0.35
24 10 0.43
25 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
AATAAATAATATAATTTGATTTATT
Found at i:90206 original size:28 final size:25
Alignment explanation
Indices: 90139--90208 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 25
90129 TATTTAAAAA
* * *
90139 ATTTTAAAAATATATAAATAATTTT
1 ATTTTTAATATATATAAATAATTTG
*
90164 ATTTTTAATA-A-ATAATATTATTTG
1 ATTTTTAATATATATAA-ATAATTTG
90188 ATTTATTAATTATATATAAAT
1 ATTT-TTAA-TATATATAAAT
90209 TTATAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
23 4 0.11
24 11 0.31
25 12 0.33
26 2 0.06
27 3 0.08
28 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (25 bp):
ATTTTTAATATATATAAATAATTTG
Found at i:98791 original size:25 final size:25
Alignment explanation
Indices: 98757--98805 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
98747 AAAAAAATAA
*
98757 ATTTCAAATTTATAAATATATAAAT
1 ATTTCAAATTCATAAATATATAAAT
* *
98782 ATTTCAAATTCATCATTATATAAA
1 ATTTCAAATTCATAAATATATAAA
98806 GATTCAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (25 bp):
ATTTCAAATTCATAAATATATAAAT
Found at i:104803 original size:284 final size:284
Alignment explanation
Indices: 104288--104807 Score: 636
Period size: 284 Copynumber: 1.8 Consensus size: 284
104278 TATACGGCCT
* * *** * *
104288 CAATCATTGCAAGTATCATCGCTTGATTAGCCACTTTCTAGAAAAGTCTTTGTTTTGAAAAACAA
1 CAATCATTGCAAGGATCATCGCTTGATTAACCACACCCTAGAAAAGTCTTTGCTTCGAAAAACAA
** * * ***
104353 AATCATGCAACTTTATAAGGATGGGAAAATGGATTTTGAAGAAAAAATGGTGTCATCAAATATGG
66 AATCATGCAACTTTATAAGGATGGGAAAATCAAGTTTAAAGAAAAAATGGTGTCATCAAATACAA
* * * *
104418 CATCAATCAATATAGTTTTTCAATCCAGTATGTTGGATAAAATCATAAAATCTAACTCTTTTGAT
131 CATCAATCAATATAGTTTCTCAATCCAATATGTTAGATAAAACCATAAAATCTAACTCTTTTGAT
* *
104483 CTTTACATATTAACATCAAGCAAAAGTACGATGGTAGATCTTCAAGCAAATAAGGATAACTATTT
196 CTTTACATATTAACACCAAGCAAAAGTACAATGGTAGATCTTCAAGCAAATAAGGATAACTATTT
104548 GGAAGCTGATAAAGTAGATGATTC
261 GGAAGCTGATAAAGTAGATGATTC
* * * *
104572 CAATTATTGCAAGGATCATCGCTTGCTTAACCACACCCTTGAGAAA-TCTTTGCTTCGAAAGACA
1 CAATCATTGCAAGGATCATCGCTTGATTAACCACACCCTAGA-AAAGTCTTTGCTTCGAAAAACA
* * * * * *
104636 AAATCTTGCAACTTTATGATGATGGGAAAATCAAGTTTAAAGAAGAAATGTTGTCATCAAATCCA
65 AAATCATGCAACTTTATAAGGATGGGAAAATCAAGTTTAAAGAAAAAATGGTGTCATCAAATACA
* * *
104701 ACATCAATCATTATAGTTTCTCAATCTAATATGTTAGATAGAACCATAAAAT-TAAACT-TATTT
130 ACATCAATCAATATAGTTTCTCAATCCAATATGTTAGATAAAACCATAAAATCT-AACTCT-TTT
* **
104764 GATC-TTATCATATTGATGCCAAG-AATAAGTACAATGGTAGATCT
193 GATCTTTA-CATATTAACACCAAGCAA-AAGTACAATGGTAGATCT
104808 CCGAGGGAAT
Statistics
Matches: 195, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
283 7 0.04
284 185 0.95
285 3 0.02
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (284 bp):
CAATCATTGCAAGGATCATCGCTTGATTAACCACACCCTAGAAAAGTCTTTGCTTCGAAAAACAA
AATCATGCAACTTTATAAGGATGGGAAAATCAAGTTTAAAGAAAAAATGGTGTCATCAAATACAA
CATCAATCAATATAGTTTCTCAATCCAATATGTTAGATAAAACCATAAAATCTAACTCTTTTGAT
CTTTACATATTAACACCAAGCAAAAGTACAATGGTAGATCTTCAAGCAAATAAGGATAACTATTT
GGAAGCTGATAAAGTAGATGATTC
Found at i:105388 original size:31 final size:31
Alignment explanation
Indices: 105352--105439 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 31
105342 CTTAAAAAAA
* *
105352 ATGATGCTCTTAACCAAAAACTTAAATTGTT
1 ATGATGCTCTTAAACAAAAACTTAAATTATT
* * * *
105383 ATGATGTTCCTAAATAAAAGCTTAAATTATT
1 ATGATGCTCTTAAACAAAAACTTAAATTATT
* * *
105414 AT-ATTACTCTTAAGCACAAACTTAAA
1 ATGA-TGCTCTTAAACAAAAACTTAAA
105440 CTGCTCATTA
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
30 1 0.02
31 42 0.98
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (31 bp):
ATGATGCTCTTAAACAAAAACTTAAATTATT
Found at i:118826 original size:6 final size:6
Alignment explanation
Indices: 118805--118924 Score: 110
Period size: 6 Copynumber: 20.5 Consensus size: 6
118795 TTCGTAAAAG
* *
118805 AAACAA ACAA-AA AAACAA AAACAA CAA-AA AAAC-A ACACAA AAACAA
1 AAACAA A-AACAA AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA
*
118851 AAACAA AAACAA AGACAA AAAC-A AAAC-A AAAC-A AAACAAA ACAACAA
1 AAACAA AAACAA AAACAA AAACAA AAACAA AAACAA AAAC-AA A-AACAA
* *
118898 AAACAA GAATAA ATAA-AA AAACAA AAA
1 AAACAA AAACAA A-AACAA AAACAA AAA
118925 GGGGGTTCGG
Statistics
Matches: 96, Mismatches: 9, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
5 27 0.28
6 57 0.59
7 9 0.09
8 3 0.03
ACGTcount: A:0.80, C:0.17, G:0.02, T:0.02
Consensus pattern (6 bp):
AAACAA
Found at i:118849 original size:40 final size:39
Alignment explanation
Indices: 118805--118923 Score: 136
Period size: 40 Copynumber: 2.9 Consensus size: 39
118795 TTCGTAAAAG
*
118805 AAACAAACAA-AAAAACAAAAACAACAAAAAAACAACACAA
1 AAACAAACAACAAAAACAAAAACAA-AAAAAAACAAAAC-A
*
118845 AAACAAA-AACAAAAACAAAGACAAAAACAAAACAAAACA
1 AAACAAACAACAAAAACAAAAACAAAAA-AAAACAAAACA
118884 AAACAAAACAACAAAAACAAGAATA-AATAAAAAAACAAAA
1 AAAC-AAACAACAAAAACAA-AA-ACAA-AAAAAAACAAAA
118924 AGGGGGTTCG
Statistics
Matches: 69, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
39 10 0.14
40 32 0.46
41 11 0.16
42 12 0.17
43 4 0.06
ACGTcount: A:0.80, C:0.17, G:0.02, T:0.02
Consensus pattern (39 bp):
AAACAAACAACAAAAACAAAAACAAAAAAAAACAAAACA
Found at i:120571 original size:65 final size:65
Alignment explanation
Indices: 120477--120616 Score: 174
Period size: 65 Copynumber: 2.2 Consensus size: 65
120467 TTATCCTTTT
* * * *
120477 AAGCCCACACAAGTTGGCGGTAATCTTCCTCCAAGCTCACACAAGTTGGTGGCAACCTTTTTTCA
1 AAGCCCACACAAGTCGGCGGCAATCTTCCTCAAAGCCCACACAAGTTGGTGGCAACCTTTTTTCA
* * * * ** *
120542 AAGCCCACATAAGTCGGTGGCAATTTTCCTCAAAGCCCACAGAAGTTGGTGGCAACC-TCCTTAA
1 AAGCCCACACAAGTCGGCGGCAATCTTCCTCAAAGCCCACACAAGTTGGTGGCAACCTTTTTTCA
120606 AAGCCCACACA
1 AAGCCCACACA
120617 CGTTGGTGGC
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
64 14 0.22
65 49 0.78
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (65 bp):
AAGCCCACACAAGTCGGCGGCAATCTTCCTCAAAGCCCACACAAGTTGGTGGCAACCTTTTTTCA
Found at i:120578 original size:32 final size:32
Alignment explanation
Indices: 120477--120627 Score: 144
Period size: 32 Copynumber: 4.7 Consensus size: 32
120467 TTATCCTTTT
* * * *
120477 AAGCCCACACAAGTTGGCGGTAATCTTCCTCC
1 AAGCCCACACAAGTTGGTGGCAATTTTCCTCA
* *
120509 AAGCTCACACAAGTTGGTGGCAACCTTTT-TTCA
1 AAGCCCACACAAGTTGGTGGCAA--TTTTCCTCA
* *
120542 AAGCCCACATAAGTCGGTGGCAATTTTCCTCA
1 AAGCCCACACAAGTTGGTGGCAATTTTCCTCA
* ** *
120574 AAGCCCACAGAAGTTGGTGGCAA-CCTCCTTAA
1 AAGCCCACACAAGTTGGTGGCAATTTTCC-TCA
*
120606 AAGCCCACACACGTTGGTGGCA
1 AAGCCCACACAAGTTGGTGGCA
120628 TCCCTTTCCA
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
31 7 0.07
32 66 0.67
33 22 0.22
34 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.23
Consensus pattern (32 bp):
AAGCCCACACAAGTTGGTGGCAATTTTCCTCA
Found at i:120927 original size:52 final size:52
Alignment explanation
Indices: 120849--120995 Score: 163
Period size: 52 Copynumber: 2.8 Consensus size: 52
120839 TGGGACCTTT
** * *
120849 TTTAAGTCCAATATCACTGGTCTTGAATTAGCATATTGGC-CTTTTTGTCATC
1 TTTAAGTCCAATATCACTGACCTTGAATTAGCATATTGGCACCTCTT-TCATC
* * * * * *
120901 TTTAAGTCCAATGTCGCTGACCTTGAATCAGCATATTAGCACCTCTTTCTTT
1 TTTAAGTCCAATATCACTGACCTTGAATTAGCATATTGGCACCTCTTTCATC
*
120953 TTTAAGTCTAATATCACT-AGCCTTGAATTAGCATATTGGCACC
1 TTTAAGTCCAATATCACTGA-CCTTGAATTAGCATATTGGCACC
120996 CATGTCATCT
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
51 1 0.01
52 73 0.94
53 4 0.05
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (52 bp):
TTTAAGTCCAATATCACTGACCTTGAATTAGCATATTGGCACCTCTTTCATC
Found at i:126195 original size:17 final size:17
Alignment explanation
Indices: 126173--126209 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
126163 CTAGCAATAA
126173 TGAATGTTCTGCTTCTT
1 TGAATGTTCTGCTTCTT
126190 TGAATGTTCTGCTTCTT
1 TGAATGTTCTGCTTCTT
126207 TGA
1 TGA
126210 TTTTTTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.51
Consensus pattern (17 bp):
TGAATGTTCTGCTTCTT
Found at i:126590 original size:17 final size:17
Alignment explanation
Indices: 126569--126628 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 17
126559 TTTATTCGAT
126569 ATAAAATAT-TATAATA
1 ATAAAATATATATAATA
126585 AGTAAAAAATATATATAATA
1 A-T--AAAATATATATAATA
* *
126605 ATAAAA-ATAAAAAATA
1 ATAAAATATATATAATA
*
126621 AAAAAATA
1 ATAAAATA
126629 AACTACAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
16 14 0.39
17 6 0.17
19 8 0.22
20 8 0.22
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
ATAAAATATATATAATA
Found at i:126613 original size:18 final size:19
Alignment explanation
Indices: 126571--126611 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
126561 TATTCGATAT
126571 AAAATATTATAATAAGTAA
1 AAAATATTATAATAAGTAA
126590 AAAATATATATAATAA-TAA
1 AAAATAT-TATAATAAGTAA
126609 AAA
1 AAA
126612 TAAAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAATATTATAATAAGTAA
Found at i:126732 original size:5 final size:5
Alignment explanation
Indices: 126694--126728 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
126684 GACTTAGGTG
*
126694 GCATT GCATT GCATT GCATT GCATT GCATT ACATT
1 GCATT GCATT GCATT GCATT GCATT GCATT GCATT
126729 ACATGCTGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (5 bp):
GCATT
Found at i:126894 original size:19 final size:18
Alignment explanation
Indices: 126863--126912 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
126853 ACTTAAGAAA
*
126863 CATTTGATGCATTGCATT
1 CATTTCATGCATTGCATT
*
126881 CATTTCATTGCATTGCTTT
1 CATTTCA-TGCATTGCATT
126900 CATTTCATGCATT
1 CATTTCATGCATT
126913 CATACGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 12 0.41
19 17 0.59
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.48
Consensus pattern (18 bp):
CATTTCATGCATTGCATT
Found at i:127204 original size:16 final size:16
Alignment explanation
Indices: 127166--127204 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
127156 TGGAGAAACG
*
127166 CATGAAACATGCAGCA
1 CATGAAGCATGCAGCA
127182 CATGAAGCATGCAGCA
1 CATGAAGCATGCAGCA
*
127198 TATGAAG
1 CATGAAG
127205 TGCTAAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (16 bp):
CATGAAGCATGCAGCA
Found at i:127504 original size:30 final size:30
Alignment explanation
Indices: 127470--127614 Score: 175
Period size: 30 Copynumber: 4.9 Consensus size: 30
127460 CTTCCACAAT
*
127470 AGCAACAACAACAGCTCCAACAAGCACGAC
1 AGCAACAACAGCAGCTCCAACAAGCACGAC
* *
127500 AGCAATAACAGCAGCTCCAACAAGC-CGGC
1 AGCAACAACAGCAGCTCCAACAAGCACGAC
* * **
127529 AGTAGCAACAGCAGCTCCAACAAGCACGGT
1 AGCAACAACAGCAGCTCCAACAAGCACGAC
* *
127559 AGCAACAATAGCAGCTCCAACAAGCATGAC
1 AGCAACAACAGCAGCTCCAACAAGCACGAC
* * *
127589 AGTAGCAACAGCAGCTCTAACAAGCA
1 AGCAACAACAGCAGCTCCAACAAGCA
127615 GGCAAGCACG
Statistics
Matches: 97, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
29 25 0.26
30 72 0.74
ACGTcount: A:0.41, C:0.32, G:0.19, T:0.08
Consensus pattern (30 bp):
AGCAACAACAGCAGCTCCAACAAGCACGAC
Found at i:127544 original size:59 final size:60
Alignment explanation
Indices: 127475--127614 Score: 201
Period size: 59 Copynumber: 2.4 Consensus size: 60
127465 ACAATAGCAA
* * *
127475 CAACAACAGCTCCAACAAGCACGACAGCAATAACAGCAGCTCCAACAAGC-CGGCAGTAG
1 CAACAGCAGCTCCAACAAGCACGACAGCAACAACAGCAGCTCCAACAAGCACGACAGTAG
** * *
127534 CAACAGCAGCTCCAACAAGCACGGTAGCAACAATAGCAGCTCCAACAAGCATGACAGTAG
1 CAACAGCAGCTCCAACAAGCACGACAGCAACAACAGCAGCTCCAACAAGCACGACAGTAG
*
127594 CAACAGCAGCTCTAACAAGCA
1 CAACAGCAGCTCCAACAAGCA
127615 GGCAAGCACG
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
59 45 0.62
60 27 0.38
ACGTcount: A:0.41, C:0.32, G:0.19, T:0.09
Consensus pattern (60 bp):
CAACAGCAGCTCCAACAAGCACGACAGCAACAACAGCAGCTCCAACAAGCACGACAGTAG
Found at i:127640 original size:89 final size:91
Alignment explanation
Indices: 127469--127675 Score: 244
Period size: 89 Copynumber: 2.3 Consensus size: 91
127459 TCTTCCACAA
* * * *
127469 TAGCAACAACAACAGCTCCAACAAGCACGACAGCAATAACAGCAGCTCCAACAAGCCGGCAGTAG
1 TAGCAACAACAGCAGCTCCAACAAGCACGACAGCAACAACAGCAGCTCCAACAAGCAGGCAGCAG
*
127534 CAACAGCAGCTC---CAACAAGCACGG
66 CAACAGCAACTCAAACAACAA-CACGG
* * * * *
127558 TAGCAACAATAGCAGCTCCAACAAGCATGACAGTAGCAACAGCAGCTCTAACAAGCAGGCAAGCA
1 TAGCAACAACAGCAGCTCCAACAAGCACGACAGCAACAACAGCAGCTCCAACAAGCAGGC-AGCA
*
127623 -CGAATAGCAAC-CAAACAACAACACGG
65 GC-AACAGCAACTCAAACAACAACACGG
*
127649 TAGCAGCAACAGCAGCTCCAACAAGCA
1 TAGCAACAACAGCAGCTCCAACAAGCA
127676 GGCAAACATG
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
89 54 0.54
90 10 0.10
91 30 0.30
92 6 0.06
ACGTcount: A:0.42, C:0.31, G:0.19, T:0.08
Consensus pattern (91 bp):
TAGCAACAACAGCAGCTCCAACAAGCACGACAGCAACAACAGCAGCTCCAACAAGCAGGCAGCAG
CAACAGCAACTCAAACAACAACACGG
Found at i:132983 original size:20 final size:20
Alignment explanation
Indices: 132958--133016 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 20
132948 GTAAAAAAAC
*
132958 AGAATGTATTGATACATTGA
1 AGAATGTATTGATACATTAA
132978 AGAATGTATATCGATACATTAA
1 AGAATGTAT-T-GATACATTAA
* *
133000 AAAATGTATCGATACAT
1 AGAATGTATTGATACAT
133017 CTGGATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 16 0.47
21 1 0.03
22 17 0.50
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.32
Consensus pattern (20 bp):
AGAATGTATTGATACATTAA
Found at i:132996 original size:22 final size:22
Alignment explanation
Indices: 132958--133016 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 22
132948 GTAAAAAAAC
*
132958 AGAATGTAT-T-GATACATTGA
1 AGAATGTATATCGATACATTAA
132978 AGAATGTATATCGATACATTAA
1 AGAATGTATATCGATACATTAA
*
133000 AAAATG--TATCGATACAT
1 AGAATGTATATCGATACAT
133017 CTGGATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 20 0.57
21 1 0.03
22 14 0.40
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.32
Consensus pattern (22 bp):
AGAATGTATATCGATACATTAA
Found at i:133876 original size:28 final size:27
Alignment explanation
Indices: 133828--134121 Score: 311
Period size: 28 Copynumber: 10.5 Consensus size: 27
133818 CACCGATTTG
* *
133828 TGTGGGCTTTAAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGG-TGCCACTGACT
* *
133856 TGTGGGTTTTGAGAAGGTGCCTCTGACT
1 TGTGGGCTTTGA-AAGGTGCCACTGACT
*
133884 TGTGGGCTTTGAAGAGATGCCACTGACT
1 TGTGGGCTTTGAA-AGGTGCCACTGACT
* *
133912 TATGAGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGG-TGCCACTGACT
* * *
133940 CGTGGGCTTTGGAATA-ATGCCACTAACT
1 TGTGGGCTTT-GAA-AGGTGCCACTGACT
* * *
133968 TGTGGGCTTTGAAGAGATGTCATTGACT
1 TGTGGGCTTTGAA-AGGTGCCACTGACT
133996 TGTGGGCTTTGAAAAGGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGTGCCACTGACT
*
134024 TGTGGGCTTTGAAAGAATGCCACTGACT
1 TGTGGGCTTTGAAAG-GTGCCACTGACT
* *
134052 AGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGG-TGCCACTGACT
* *
134080 CGTGGGTTTTGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTG-AAA-GGTGCCACTGACT
134109 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
134122 GAGATGAGCA
Statistics
Matches: 223, Mismatches: 32, Indels: 22
0.81 0.12 0.08
Matches are distributed among these distances:
27 11 0.05
28 178 0.80
29 31 0.14
30 3 0.01
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (27 bp):
TGTGGGCTTTGAAAGGTGCCACTGACT
Found at i:133945 original size:84 final size:85
Alignment explanation
Indices: 133828--134120 Score: 373
Period size: 84 Copynumber: 3.5 Consensus size: 85
133818 CACCGATTTG
* * * *
133828 TGTGGGCTTT-AAAAGGATGCCACTAACTTGTGGGTTTTGAGAAGGTGCCTCTGACTTGTGGGCT
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAGAAGATGCCACTGACTTGTGGGCT
133892 TTGAAGAGATGCCACTGACT
66 TTGAAGAGATGCCACTGACT
* * * * *
133912 TATGAGCTTTG-AAAGGATGCCACTGACTCGTGGGCTTTG-GAATAATGCCACTAACTTGTGGGC
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAGAA-GATGCCACTGACTTGTGGGC
* *
133975 TTTGAAGAGATGTCATTGACT
65 TTTGAAGAGATGCCACTGACT
*
133996 TGTGGGCTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTGA-AAGAATGCCACTGACTAGTGGGC
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAGAAG-ATGCCACTGACTTGTGGGC
*
134059 TTTGAA-AGGATGCCACTAACT
65 TTTGAAGA-GATGCCACTGACT
* * *
134080 CGTGGGTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGA
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGA
134121 AGAGATGAGC
Statistics
Matches: 180, Mismatches: 22, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
83 4 0.02
84 148 0.82
85 28 0.16
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (85 bp):
TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAGAAGATGCCACTGACTTGTGGGCT
TTGAAGAGATGCCACTGACT
Found at i:135379 original size:1 final size:1
Alignment explanation
Indices: 135369--135449 Score: 54
Period size: 1 Copynumber: 81.0 Consensus size: 1
135359 TTTGGATCCC
* * * * * * * * * *
135369 TTTTTGTTTTTTTTTTTTGTTTGTGTTTTTTTGTTTGTTTTTGTTTGTTTTTTTATTTTTTTATT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
135434 TTTTCTTGTTTTTTTT
1 TTTTTTTTTTTTTTTT
135450 GGTACGAAGG
Statistics
Matches: 56, Mismatches: 24, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.02, C:0.01, G:0.11, T:0.85
Consensus pattern (1 bp):
T
Found at i:135397 original size:14 final size:13
Alignment explanation
Indices: 135369--135449 Score: 87
Period size: 13 Copynumber: 6.2 Consensus size: 13
135359 TTTGGATCCC
*
135369 TTTTTGTTTTTTT
1 TTTTTGTTTGTTT
135382 TTTTTGTTTGTGTT
1 TTTTTGTTTGT-TT
135396 TTTTTGTTTGTTT
1 TTTTTGTTTGTTT
135409 TTGTTTGTTT-TTT
1 TT-TTTGTTTGTTT
*
135422 TATTTT-TTTATTT
1 T-TTTTGTTTGTTT
135435 TTTCTTGTTT-TTT
1 TTT-TTGTTTGTTT
135448 TT
1 TT
135450 GGTACGAAGG
Statistics
Matches: 61, Mismatches: 1, Indels: 12
0.82 0.01 0.16
Matches are distributed among these distances:
12 5 0.08
13 32 0.52
14 24 0.39
ACGTcount: A:0.02, C:0.01, G:0.11, T:0.85
Consensus pattern (13 bp):
TTTTTGTTTGTTT
Found at i:135401 original size:10 final size:9
Alignment explanation
Indices: 135369--135450 Score: 85
Period size: 10 Copynumber: 8.7 Consensus size: 9
135359 TTTGGATCCC
135369 TTTTTGTTT
1 TTTTTGTTT
135378 TTTTT-TTT
1 TTTTTGTTT
*
135386 TGTTTGTGTT
1 TTTTTGT-TT
135396 TTTTTGTTT
1 TTTTTGTTT
135405 GTTTTTGTTT
1 -TTTTTGTTT
*
135415 GTTTTTTTATT
1 -TTTTTGT-TT
*
135426 TTTTTATTT
1 TTTTTGTTT
135435 TTTCTTGTTT
1 TTT-TTGTTT
135445 TTTTTG
1 TTTTTG
135451 GTACGAAGGA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
8 7 0.11
9 16 0.25
10 38 0.60
11 2 0.03
ACGTcount: A:0.02, C:0.01, G:0.12, T:0.84
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:135445 original size:18 final size:16
Alignment explanation
Indices: 135375--135449 Score: 78
Period size: 18 Copynumber: 4.3 Consensus size: 16
135365 TCCCTTTTTG
135375 TTTTTTTTTTTTGTTT
1 TTTTTTTTTTTTGTTT
*
135391 GTGTTTTTTTGTTTGTTT
1 -T-TTTTTTTTTTTGTTT
*
135409 TTGTTTGTTTTTTTATTT
1 TT-TTT-TTTTTTTGTTT
135427 TTTTATTTTTTCTTGTTT
1 TTTT-TTTTTT-TTGTTT
135445 TTTTT
1 TTTTT
135450 GGTACGAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
16 1 0.02
17 13 0.27
18 35 0.71
ACGTcount: A:0.03, C:0.01, G:0.11, T:0.85
Consensus pattern (16 bp):
TTTTTTTTTTTTGTTT
Found at i:146754 original size:52 final size:52
Alignment explanation
Indices: 146606--146734 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
146596 CGAAATATGA
146606 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
146658 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
146710 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
146735 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:146761 original size:13 final size:13
Alignment explanation
Indices: 146743--146767 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
146733 CAAAGATCAG
146743 TGTATCGATACAA
1 TGTATCGATACAA
146756 TGTATCGATACA
1 TGTATCGATACA
146768 TTTAAGTAAT
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:146834 original size:19 final size:18
Alignment explanation
Indices: 146810--146907 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
146800 TAGCTTACAT
146810 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
146829 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
146842 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
146861 TGTATCAATAC--A--T-
1 TGTATCGATACAAACTTA
146874 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
146894 TGTATCGATACAAA
1 TGTATCGATACAAA
146908 TCGTTGAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 23 0.36
20 13 0.20
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:146846 original size:32 final size:32
Alignment explanation
Indices: 146805--146905 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
146795 GGCAGTAGCT
*
146805 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAACACTTATGTATCGA
*
146837 TACATTGTATCGATACAACACTTATGTATCAA
1 TACATTGTATCGATACAACACTTATGTATCGA
146869 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAACAC-TTATGTATCGA
146902 TACA
1 TACA
146906 AATCGTTGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 51 0.78
33 14 0.22
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (32 bp):
TACATTGTATCGATACAACACTTATGTATCGA
Found at i:146847 original size:13 final size:13
Alignment explanation
Indices: 146829--146885 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
146819 ACAAAACTTA
146829 TGTATCGATACAT
1 TGTATCGATACAT
146842 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
*
146860 ATGTATCAATACAT
1 -TGTATCGATACAT
146874 TGTATCGATACA
1 TGTATCGATACA
146886 ACACTTTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 20 0.56
14 1 0.03
16 6 0.17
18 1 0.03
19 8 0.22
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:149968 original size:13 final size:13
Alignment explanation
Indices: 149950--149977 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
149940 CATTATTCAA
149950 TGTATCGATACAT
1 TGTATCGATACAT
149963 TGTATCGATACAT
1 TGTATCGATACAT
149976 TG
1 TG
149978 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:149973 original size:33 final size:33
Alignment explanation
Indices: 149930--149995 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
149920 TCCAAGGAAA
*
149930 TGTATTGATACATT-ATTCAATGTATCGATACAT
1 TGTATCGATACATTGA-TCAATGTATCGATACAT
**
149963 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCAATGTATCGATACAT
149996 CTGGGAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTGATCAATGTATCGATACAT
Found at i:150845 original size:20 final size:20
Alignment explanation
Indices: 150820--150873 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
150810 TACCCAGATG
*
150820 TATCGATACATTTTTCAATA
1 TATCGATACATTCTTCAATA
*
150840 TATCGATACATTCTTCAATG
1 TATCGATACATTCTTCAATA
150860 TATCGATACATTCT
1 TATCGATACATTCT
150874 GTCTTTTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (20 bp):
TATCGATACATTCTTCAATA
Found at i:150913 original size:20 final size:20
Alignment explanation
Indices: 150888--150941 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
150878 TTTTACCTAG
150888 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
*
150908 ATGTATCGATACATTTAATA
1 ATGTATCGATACATTGAATA
150928 ATGTATCGATACAT
1 ATGTATCGATACAT
150942 CTAGTTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:150922 original size:71 final size:70
Alignment explanation
Indices: 150806--150941 Score: 186
Period size: 71 Copynumber: 1.9 Consensus size: 70
150796 AAAAGTCACA
**
150806 TTTTTACCCAGATGTATCGATACATTTTTCAATATATCGATACATTCT-TCAATGTATCGATACA
1 TTTTTACCCAGATGTATCGATACATTAATCAATATATCGATACATT-TAT-AATGTATCGATACA
150870 TTCTGTC
64 TTCTGTC
* *
150877 TTTTTACCTAGATGTATCGATACATTGAAT-AATGTATCGATACATTTAATAATGTATCGATACA
1 TTTTTACCCAGATGTATCGATACATT-AATCAATATATCGATACATTT-ATAATGTATCGATACA
150941 T
64 T
150942 CTAGTTAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
70 1 0.02
71 55 0.95
72 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (70 bp):
TTTTTACCCAGATGTATCGATACATTAATCAATATATCGATACATTTATAATGTATCGATACATT
CTGTC
Found at i:151680 original size:37 final size:37
Alignment explanation
Indices: 151638--151714 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
151628 CACTTGCTGT
*
151638 TTTTATTTTTCTCATCATTTTAGTGCGCTTATCATGC
1 TTTTATTTTTCTCATCATTTTAGTGCACTTATCATGC
151675 TTTTATTTTTCTCATCATTTTAGTGCACTTATCATGC
1 TTTTATTTTTCTCATCATTTTAGTGCACTTATCATGC
151712 TTT
1 TTT
151715 CATGACCCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.17, C:0.18, G:0.09, T:0.56
Consensus pattern (37 bp):
TTTTATTTTTCTCATCATTTTAGTGCACTTATCATGC
Found at i:162687 original size:15 final size:16
Alignment explanation
Indices: 162667--162696 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
162657 TCTGTCAAAC
162667 CCGCCAGTG-TTGGTA
1 CCGCCAGTGCTTGGTA
162682 CCGCCAGTGCTTGGT
1 CCGCCAGTGCTTGGT
162697 CGTCCTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.10, C:0.30, G:0.33, T:0.27
Consensus pattern (16 bp):
CCGCCAGTGCTTGGTA
Found at i:164945 original size:8 final size:8
Alignment explanation
Indices: 164932--164986 Score: 60
Period size: 8 Copynumber: 7.1 Consensus size: 8
164922 TTACACCCCA
164932 AAAAAAAC
1 AAAAAAAC
164940 AAAAAAAC
1 AAAAAAAC
164948 -AAAAAAC
1 AAAAAAAC
164955 AAAAAAAC
1 AAAAAAAC
* *
164963 CAAGAAA-
1 AAAAAAAC
* *
164970 AAAATAGC
1 AAAAAAAC
164978 AAAAAAAC
1 AAAAAAAC
164986 A
1 A
164987 GAAAGGGGTC
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
7 10 0.27
8 27 0.73
ACGTcount: A:0.82, C:0.13, G:0.04, T:0.02
Consensus pattern (8 bp):
AAAAAAAC
Found at i:164961 original size:23 final size:22
Alignment explanation
Indices: 164932--164986 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
164922 TTACACCCCA
164932 AAAAAAACAAAAAAACAAAAAAC
1 AAAAAAACAAAAAAA-AAAAAAC
* * *
164955 AAAAAAACCAAGAAAAAAATAGC
1 AAAAAAA-CAAAAAAAAAAAAAC
164978 AAAAAAACA
1 AAAAAAACA
164987 GAAAGGGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.07
23 19 0.68
24 7 0.25
ACGTcount: A:0.82, C:0.13, G:0.04, T:0.02
Consensus pattern (22 bp):
AAAAAAACAAAAAAAAAAAAAC
Found at i:164973 original size:15 final size:15
Alignment explanation
Indices: 164933--164962 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
164923 TACACCCCAA
164933 AAAAAACAAAAAAAC
1 AAAAAACAAAAAAAC
164948 AAAAAACAAAAAAAC
1 AAAAAACAAAAAAAC
164963 CAAGAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAACAAAAAAAC
Found at i:166294 original size:57 final size:57
Alignment explanation
Indices: 166206--166651 Score: 583
Period size: 57 Copynumber: 7.7 Consensus size: 57
166196 CGTTCATCTC
* * * *
166206 TTCAAAGCCCACAAGTTAATGGCACTCTTTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * *
166263 TTCAAAGCCCACAAGTCAGTGACACCCTTTCAAA-CACCACAAAATCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC-CCAC-AAGTCAGTGGCACTCTT
* * * * *
166320 TTCAAACCCCACAAAATCAGTGGCATCTTTTCAAAGCCCACAAATCAGTGGCACTCTT
1 TTCAAAGCCCAC-AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * *
166378 TTCAAAGCCCACAAGTCAGAGGCACCCTTTTAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * *
166435 TTCAAAGCCCACAAGTTAGTGGCATCTTTTCAAAGCCCACAAGTCAATGGCAC-CTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
*
166491 TTCAAAGCCCACGCAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
*
166550 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
166607 TTCAAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACA
1 TTCAAAGCCCACA--AGTCAGTGGC-AC-CCTTTCAAAGCCCACA
166652 CAAGTTAGTG
Statistics
Matches: 339, Mismatches: 38, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
56 15 0.04
57 201 0.59
58 83 0.24
59 23 0.07
60 2 0.01
61 15 0.04
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (57 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
Done.