Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_157
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: 154975
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:643 original size:20 final size:20
Alignment explanation
Indices: 620--666 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
610 GGGTTAAGAT
*
620 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
640 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
660 TGAGCTG
1 TGAGCTG
667 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:3362 original size:30 final size:30
Alignment explanation
Indices: 3328--3424 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
3318 TAAACTAAAA
*
3328 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
3358 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
3388 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
3417 ATGAGCTA
1 -TGAGCTA
3425 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:5699 original size:6 final size:6
Alignment explanation
Indices: 5683--5732 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
5673 TTTCTTTTTA
*
5683 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
5732 T
1 T
5733 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:5715 original size:37 final size:37
Alignment explanation
Indices: 5672--5742 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
5662 CTTGCCTCTC
5672 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
5709 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
5743 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:5743 original size:16 final size:16
Alignment explanation
Indices: 5668--5728 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
5658 GCCTCTTGCC
*
5668 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
5684 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
5700 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
5716 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
5729 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:6669 original size:12 final size:12
Alignment explanation
Indices: 6644--6692 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
6634 TAAACTTGAT
6644 TTTTTTTTGCTCAC
1 TTTTTTTT--TCAC
*
6658 CTTTTTTTTCAC
1 TTTTTTTTTCAC
* *
6670 TTTTTTTTTGAA
1 TTTTTTTTTCAC
6682 TTTTTTTTTCA
1 TTTTTTTTTCA
6693 ATCAAATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 23 0.77
14 7 0.23
ACGTcount: A:0.10, C:0.14, G:0.04, T:0.71
Consensus pattern (12 bp):
TTTTTTTTTCAC
Found at i:6715 original size:12 final size:13
Alignment explanation
Indices: 6659--6719 Score: 61
Period size: 13 Copynumber: 4.5 Consensus size: 13
6649 TTTGCTCACC
*
6659 TTTTTTTTC-ACT
1 TTTTTTTTCAAAT
* *
6671 TTTTTTTTGAATT
1 TTTTTTTTCAAAT
6684 TTTTTTTCAATCAAAT
1 TTTTTTT---TCAAAT
6700 TTTTTTTTCAAAT
1 TTTTTTTTCAAAT
6713 TTTTTTT
1 TTTTTTT
6720 GATTTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
12 8 0.20
13 22 0.54
16 11 0.27
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.72
Consensus pattern (13 bp):
TTTTTTTTCAAAT
Found at i:8444 original size:30 final size:30
Alignment explanation
Indices: 8410--8506 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
8400 TAAACTAAAA
*
8410 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
8440 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
8470 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
8499 ATGAGCTA
1 -TGAGCTA
8507 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:9274 original size:48 final size:48
Alignment explanation
Indices: 9219--9324 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
9209 TTGTCTTTTC
*
9219 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTGTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
9267 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
*
9315 TTTTTTTTTC
1 TTTCTTTTTC
9325 CATGACACTC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
48 39 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.14, C:0.24, G:0.02, T:0.60
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:10366 original size:10 final size:9
Alignment explanation
Indices: 10353--10388 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 9
10343 TTTTCACTTT
10353 TTTTTTGTTC
1 TTTTTT-TTC
10363 TTTTTTTTAC
1 TTTTTTTT-C
10373 TTTTTTTTC
1 TTTTTTTTC
10382 TTTTTTT
1 TTTTTTT
10389 GCTCACTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.03, C:0.08, G:0.03, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:11958 original size:20 final size:20
Alignment explanation
Indices: 11935--11991 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
11925 GGGTTAAGAT
*
11935 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
11955 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
*
11975 TGAGCTGGAAATGAGCT
1 TGAGCT-GAATTGAGCT
11992 AAACGGAGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.25, C:0.12, G:0.35, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:13433 original size:30 final size:31
Alignment explanation
Indices: 13399--13495 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
13389 AGCTCACTCC
*
13399 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
13429 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
13459 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
13489 TAGCTCA
1 TAGCTCA
13496 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:20899 original size:19 final size:19
Alignment explanation
Indices: 20875--20914 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
20865 CGTGAGCTGA
*
20875 TAATGAGCTGGTCCCGAGC
1 TAATGAGCTAGTCCCGAGC
20894 TAATGAGCTAGTCCCGAGC
1 TAATGAGCTAGTCCCGAGC
20913 TA
1 TA
20915 CATGGGAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.23
Consensus pattern (19 bp):
TAATGAGCTAGTCCCGAGC
Found at i:27331 original size:23 final size:22
Alignment explanation
Indices: 27279--27331 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
27269 TCCACGTCTT
*
27279 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
27301 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
27324 TTTCTTTT
1 TTTCTTTT
27332 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:33008 original size:11 final size:10
Alignment explanation
Indices: 32983--33043 Score: 59
Period size: 10 Copynumber: 5.7 Consensus size: 10
32973 CATAAATCAC
32983 TTTTTTTTTCGA
1 TTTTTTTTT--A
32995 TTTTATTTTTA
1 TTTT-TTTTTA
**
33006 TTTTTTTCGA
1 TTTTTTTTTA
*
33016 TTTTTTTTGAA
1 TTTTTTTT-TA
33027 TTTTTTTTTA
1 TTTTTTTTTA
33037 TTTTTTT
1 TTTTTTT
33044 AACTTGTATA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
10 19 0.45
11 14 0.33
12 4 0.10
13 5 0.12
ACGTcount: A:0.11, C:0.03, G:0.05, T:0.80
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:33011 original size:21 final size:21
Alignment explanation
Indices: 32985--33043 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
32975 TAAATCACTT
*
32985 TTTTTTTCGATTTTATTTT-TA
1 TTTTTTTCGATTTT-TTTTGAA
33006 TTTTTTTCGATTTTTTTTGAA
1 TTTTTTTCGATTTTTTTTGAA
**
33027 TTTTTTTTTATTTTTTT
1 TTTTTTTCGATTTTTTT
33044 AACTTGTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 4 0.12
21 30 0.88
ACGTcount: A:0.12, C:0.03, G:0.05, T:0.80
Consensus pattern (21 bp):
TTTTTTTCGATTTTTTTTGAA
Found at i:33035 original size:31 final size:32
Alignment explanation
Indices: 32984--33043 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
32974 ATAAATCACT
32984 TTTTTTTTCGATTTTATTTTTATTTTTTTCGA
1 TTTTTTTTCGATTTTATTTTTATTTTTTTCGA
33016 TTTTTTTT-GAATTTT-TTTTTATTTTTTT
1 TTTTTTTTCG-ATTTTATTTTTATTTTTTT
33044 AACTTGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
31 14 0.52
32 13 0.48
ACGTcount: A:0.12, C:0.03, G:0.05, T:0.80
Consensus pattern (32 bp):
TTTTTTTTCGATTTTATTTTTATTTTTTTCGA
Found at i:35806 original size:19 final size:19
Alignment explanation
Indices: 35761--35806 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
35751 ATTAACACAC
*
35761 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
35780 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
35798 AATTAATAA
1 AATTAATAA
35807 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:37643 original size:18 final size:19
Alignment explanation
Indices: 37620--37658 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
37610 ATTATCTCAA
*
37620 TTTCTTTTTC-CACTCTTT
1 TTTCTTGTTCACACTCTTT
*
37638 TTTCTTGTTCACATTCTTT
1 TTTCTTGTTCACACTCTTT
37657 TT
1 TT
37659 CTCTCTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.08, C:0.23, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTCTTGTTCACACTCTTT
Found at i:37688 original size:48 final size:48
Alignment explanation
Indices: 37622--37724 Score: 111
Period size: 48 Copynumber: 2.1 Consensus size: 48
37612 TATCTCAATT
* * *
37622 TCTTTTTCCACTCTTTTTTC-TTGTTCACATTCTTTTTCTCTCTCAAAC
1 TCTTTTTCCACTCTTTTTTCAAT-CTCACATTCTTTTTCACTCTCAAAC
* ** *
37670 TCTTTTT-CATTCTCTTTTTCAATCTCATTTTCTTTTTCACTCTCAATC
1 TCTTTTTCCACTCT-TTTTTCAATCTCACATTCTTTTTCACTCTCAAAC
37718 TCTTTTT
1 TCTTTTT
37725 TCTTTTTCTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
47 5 0.11
48 40 0.87
49 1 0.02
ACGTcount: A:0.13, C:0.27, G:0.01, T:0.59
Consensus pattern (48 bp):
TCTTTTTCCACTCTTTTTTCAATCTCACATTCTTTTTCACTCTCAAAC
Found at i:37697 original size:18 final size:18
Alignment explanation
Indices: 37676--37724 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
37666 AAACTCTTTT
37676 TCATTCTCTTTTTCAATC
1 TCATTCTCTTTTTCAATC
* *
37694 TCATTTTCTTTTTCACTC
1 TCATTCTCTTTTTCAATC
*
37712 TCAATCTCTTTTT
1 TCATTCTCTTTTT
37725 TCTTTTTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.14, C:0.27, G:0.00, T:0.59
Consensus pattern (18 bp):
TCATTCTCTTTTTCAATC
Found at i:37715 original size:24 final size:24
Alignment explanation
Indices: 37651--37733 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
37641 CTTGTTCACA
*
37651 TTCTTTTTCTCTCTCAAACTCTTT
1 TTCTTTTTCTCTCTCAATCTCTTT
* * * * *
37675 TTCATTCTCTTTTTCAATCTCATT
1 TTCTTTTTCTCTCTCAATCTCTTT
*
37699 TTCTTTTTCACTCTCAATCTCTTTT
1 TTCTTTTTCTCTCTCAATCTC-TTT
37724 TTCTTTTTCT
1 TTCTTTTTCT
37734 TTCATTTCTT
Statistics
Matches: 45, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
24 34 0.76
25 11 0.24
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (24 bp):
TTCTTTTTCTCTCTCAATCTCTTT
Found at i:37793 original size:42 final size:42
Alignment explanation
Indices: 37730--37826 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
37720 TTTTTTCTTT
* * *
37730 TTCTTTCA-TTTCTTTGTTTCTTTTCTCGATTTCATTCAAGA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
37771 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
1 TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
*
37813 TCCTCTCATTTTCT
1 TTCTCTCATTTTCT
37827 CTCATAATCT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 7 0.14
42 44 0.86
ACGTcount: A:0.14, C:0.24, G:0.05, T:0.57
Consensus pattern (42 bp):
TTCTCTCATTTTCTTTGTTTCTTCTCTCGATTTCATTCAAAA
Found at i:37804 original size:21 final size:21
Alignment explanation
Indices: 37737--37804 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
37727 TTTTTCTTTC
*
37737 ATTTCTTTGTTTCTTTTCTCG
1 ATTTCTTTGTTTCTTCTCTCG
* *****
37758 ATTTCATTCAAGATTCTCTC-
1 ATTTCTTTGTTTCTTCTCTCG
37778 ATTTTCTTTGTTTCTTCTCTCG
1 A-TTTCTTTGTTTCTTCTCTCG
37800 ATTTC
1 ATTTC
37805 ATTCAAAATC
Statistics
Matches: 32, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.12, C:0.22, G:0.07, T:0.59
Consensus pattern (21 bp):
ATTTCTTTGTTTCTTCTCTCG
Found at i:37874 original size:17 final size:17
Alignment explanation
Indices: 37845--37891 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
37835 CTTTTCTTGC
*
37845 CTCTCTTTTCTTTTGAT
1 CTCTCTTTTCTTTTCAT
37862 CTCT-TTTTGCTTTTCAT
1 CTCTCTTTT-CTTTTCAT
37879 CTTCTTCTTTTCT
1 C-TC-TCTTTTCT
37892 CGCTTACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 4 0.16
17 12 0.48
18 2 0.08
19 3 0.12
20 4 0.16
ACGTcount: A:0.04, C:0.26, G:0.04, T:0.66
Consensus pattern (17 bp):
CTCTCTTTTCTTTTCAT
Found at i:39944 original size:29 final size:29
Alignment explanation
Indices: 39911--39970 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
39901 ATAACCAAAC
* *
39911 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
39940 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
39969 CT
1 CT
39971 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:39963 original size:15 final size:15
Alignment explanation
Indices: 39917--39964 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
39907 AAACCTACAA
*
39917 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
39932 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
39946 AAACTTCATATCCAT
1 AAACTTCATATCCAT
39961 AAAC
1 AAAC
39965 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:44148 original size:19 final size:19
Alignment explanation
Indices: 44103--44148 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
44093 TTTAACACAC
*
44103 AATTAATTAAAATATAACT
1 AATTAATAAAAATATAACT
*
44122 -ATTCATAAAAATCATAA-T
1 AATTAATAAAAAT-ATAACT
44140 AATTAATAA
1 AATTAATAA
44149 TTAAACAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AATTAATAAAAATATAACT
Found at i:44375 original size:10 final size:10
Alignment explanation
Indices: 44362--44396 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
44352 AAGCTCGGTT
44362 GAGCTCAAAC
1 GAGCTCAAAC
*
44372 GAGCTGAAAC
1 GAGCTCAAAC
*
44382 GAGCTCAAAT
1 GAGCTCAAAC
44392 GAGCT
1 GAGCT
44397 GAGTTGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.37, C:0.23, G:0.26, T:0.14
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:44405 original size:20 final size:20
Alignment explanation
Indices: 44359--44406 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
44349 AGTAAGCTCG
44359 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
*** *
44379 AACGAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
44399 GTTGAGCT
1 GTTGAGCT
44407 GGACGGAGCT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:44920 original size:30 final size:31
Alignment explanation
Indices: 44886--44982 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
44876 AGCTCACTCC
*
44886 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
44916 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
44946 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
44976 TAGCTCA
1 TAGCTCA
44983 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:45872 original size:22 final size:20
Alignment explanation
Indices: 45840--45888 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
45830 GCCGAATTTA
45840 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
45863 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
45883 TGAACA
1 TGAACA
45889 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:48186 original size:30 final size:30
Alignment explanation
Indices: 48152--48248 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
48142 AGCTCACTCC
48152 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
48182 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
48212 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
48242 TAGCTCA
1 TAGCTCA
48249 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:49988 original size:15 final size:14
Alignment explanation
Indices: 49968--49997 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
49958 AAAGGAGAAG
49968 AAATTCAGAAAAAAA
1 AAATTCA-AAAAAAA
49983 AAATTCAAAAAAAA
1 AAATTCAAAAAAAA
49997 A
1 A
49998 TCGAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (14 bp):
AAATTCAAAAAAAA
Found at i:49994 original size:12 final size:12
Alignment explanation
Indices: 49977--50035 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 12
49967 GAAATTCAGA
49977 AAAAAAAAATTC-
1 AAAAAAAAA-TCG
49989 AAAAAAAAATCG
1 AAAAAAAAATCG
*
50001 -AAAAAAAA-GG
1 AAAAAAAAATCG
*
50011 AAAAAAAAGT-G
1 AAAAAAAAATCG
50022 ACAAAAAAAATCG
1 A-AAAAAAAATCG
50035 A
1 A
50036 GTTAAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 1 0.03
11 19 0.49
12 17 0.44
13 2 0.05
ACGTcount: A:0.75, C:0.07, G:0.10, T:0.08
Consensus pattern (12 bp):
AAAAAAAAATCG
Found at i:50999 original size:37 final size:37
Alignment explanation
Indices: 50948--51018 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
50938 CATTCTTGTA
50948 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
50985 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
51019 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:51018 original size:6 final size:6
Alignment explanation
Indices: 50958--51007 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
50948 AAGAGAAAAC
*
50958 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
51007 A
1 A
51008 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:51100 original size:11 final size:12
Alignment explanation
Indices: 51068--51098 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
51058 TTGAGAGAAC
51068 TTGAAAAAGCCT
1 TTGAAAAAGCCT
51080 TTGAAAAAGCCT
1 TTGAAAAAGCCT
51092 TTGAAAA
1 TTGAAAA
51099 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:53312 original size:30 final size:30
Alignment explanation
Indices: 53278--53374 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
53268 AGCTCACTCC
53278 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
53308 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
53338 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
53368 TAGCTCA
1 TAGCTCA
53375 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:57524 original size:21 final size:21
Alignment explanation
Indices: 57475--57541 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
57465 CCTCTTTGAA
* * *
57475 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
57498 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
57519 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
57540 CC
1 CC
57542 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:57867 original size:12 final size:12
Alignment explanation
Indices: 57840--57888 Score: 80
Period size: 12 Copynumber: 4.0 Consensus size: 12
57830 ATAGGTGCGT
*
57840 AAAAAAAAGTTCG
1 AAAAAAAAATT-G
57853 AAAAAAAAATTG
1 AAAAAAAAATTG
57865 AAAAAAAAATTG
1 AAAAAAAAATTG
57877 AAAAAAAAATTG
1 AAAAAAAAATTG
57889 CATACGGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
12 25 0.71
13 10 0.29
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.16
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:64438 original size:21 final size:21
Alignment explanation
Indices: 64389--64455 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
64379 CCTCTTTGAA
* * *
64389 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
64412 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
64433 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
64454 CC
1 CC
64456 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:70500 original size:23 final size:22
Alignment explanation
Indices: 70449--70500 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
70439 CCTCGTCTTT
*
70449 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
70471 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
70494 TTCTTTT
1 TTCTTTT
70501 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:70515 original size:18 final size:18
Alignment explanation
Indices: 70494--70532 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
70484 TTTCTTCAAC
* *
70494 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
70512 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
70530 TTC
1 TTC
70533 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:73471 original size:13 final size:13
Alignment explanation
Indices: 73453--73478 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
73443 TGGCTAACCT
73453 ACATAATTAAATA
1 ACATAATTAAATA
73466 ACATAATTAAATA
1 ACATAATTAAATA
73479 TGTAATAGCC
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:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
ACATAATTAAATA
Found at i:75199 original size:67 final size:66
Alignment explanation
Indices: 75119--75247 Score: 181
Period size: 67 Copynumber: 1.9 Consensus size: 66
75109 TACTATGTGT
* * *
75119 ACACCATGTAGACAAGAGAGCTAC-AGGATATA-TGTAGCTAGGTCGCATGCGTGGTTCTAAGTG
1 ACACCATGTAGACAAGAGAGCTACGA-GATAAACTG--GCTAGGTCACATGCGTGGTACTAAGTG
75182 AAGG
63 AAGG
*
75186 ACACCATGTAGACAAGAGAGCTACGAGATAAACTGGCTAGGTCACATGGGTGGTACTAAGTG
1 ACACCATGTAGACAAGAGAGCTACGAGATAAACTGGCTAGGTCACATGCGTGGTACTAAGTG
75248 TTCACCATGT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
66 24 0.43
67 29 0.52
68 3 0.05
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (66 bp):
ACACCATGTAGACAAGAGAGCTACGAGATAAACTGGCTAGGTCACATGCGTGGTACTAAGTGAAG
G
Found at i:77311 original size:10 final size:10
Alignment explanation
Indices: 77278--77346 Score: 77
Period size: 10 Copynumber: 6.8 Consensus size: 10
77268 AAAAAGGAAT
*
77278 GAGCTGAAAC
1 GAGCTCAAAC
77288 GAGCT-AAATTC
1 GAGCTCAAA--C
77299 GAGCTCAAAC
1 GAGCTCAAAC
*
77309 GAGCTAAAAC
1 GAGCTCAAAC
77319 GAGCTCAAAC
1 GAGCTCAAAC
*
77329 GAGCTAAAAC
1 GAGCTCAAAC
*
77339 AAGCTCAA
1 GAGCTCAA
77347 GTGAGCTGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
9 3 0.06
10 39 0.76
11 6 0.12
12 3 0.06
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.13
Consensus pattern (10 bp):
GAGCTCAAAC
Found at i:77323 original size:20 final size:20
Alignment explanation
Indices: 77278--77346 Score: 102
Period size: 20 Copynumber: 3.4 Consensus size: 20
77268 AAAAAGGAAT
* *
77278 GAGCTGAAACGAGCTAAATTC
1 GAGCTCAAACGAGCTAAA-AC
77299 GAGCTCAAACGAGCTAAAAC
1 GAGCTCAAACGAGCTAAAAC
77319 GAGCTCAAACGAGCTAAAAC
1 GAGCTCAAACGAGCTAAAAC
*
77339 AAGCTCAA
1 GAGCTCAA
77347 GTGAGCTGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 28 0.62
21 17 0.38
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.13
Consensus pattern (20 bp):
GAGCTCAAACGAGCTAAAAC
Found at i:82291 original size:22 final size:22
Alignment explanation
Indices: 82261--82304 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
82251 TTTGGTATTT
82261 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
82283 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
82305 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:84827 original size:20 final size:20
Alignment explanation
Indices: 84780--84827 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
84770 AGTAAGCTCG
84780 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
84800 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
84820 GTTGAGCT
1 GTTGAGCT
84828 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:86499 original size:11 final size:12
Alignment explanation
Indices: 86469--86500 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
86459 TTTCACTCTT
86469 CTCTTTTTCAAA
1 CTCTTTTTCAAA
86481 CTCTTTTTCAAA
1 CTCTTTTTCAAA
*
86493 TTCTTTTT
1 CTCTTTTT
86501 TCGCTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.59
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:86512 original size:27 final size:27
Alignment explanation
Indices: 86482--86543 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
86472 TTTTTCAAAC
*
86482 TCTTTTTCAAATTCTT-TTTTC-GCTTTT
1 TCTTTTTC-AATT-TTCTTTTCTGCATTT
*
86509 TCTTTTTCAATTTTCTTTTCTTCATTT
1 TCTTTTTCAATTTTCTTTTCTGCATTT
86536 TCTTTTTC
1 TCTTTTTC
86544 TCTCACTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 2 0.06
26 9 0.29
27 20 0.65
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (27 bp):
TCTTTTTCAATTTTCTTTTCTGCATTT
Found at i:86522 original size:13 final size:12
Alignment explanation
Indices: 86506--86614 Score: 57
Period size: 12 Copynumber: 9.0 Consensus size: 12
86496 TTTTTTCGCT
86506 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
86519 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
86533 TTTTCTTTTTC-
1 TTTTCTTTTTCA
** *
86544 TCTCACTTTTTTGA
1 T-TTTC-TTTTTCA
86558 -TTTCTTTTTC-
1 TTTTCTTTTTCA
** *
86568 TTTTGCAATTTCT
1 TTTT-CTTTTTCA
*
86581 TTTTCTTTTTCG
1 TTTTCTTTTTCA
86593 TTTTC--TTTCA
1 TTTTCTTTTTCA
*
86603 ATTTCTTTTTCA
1 TTTTCTTTTTCA
86615 ATCTCTTTCT
Statistics
Matches: 73, Mismatches: 13, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
10 8 0.11
11 9 0.12
12 27 0.37
13 17 0.23
14 9 0.12
15 3 0.04
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:86535 original size:14 final size:14
Alignment explanation
Indices: 86484--86542 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
86474 TTTCAAACTC
*
86484 TTTTTCAA-ATTCT
1 TTTTTCAATTTTCT
**
86497 TTTTTCGCTTTT-T
1 TTTTTCAATTTTCT
86510 CTTTTTCAATTTTCT
1 -TTTTTCAATTTTCT
86525 TTTCTTC-ATTTTCT
1 TTT-TTCAATTTTCT
86539 TTTT
1 TTTT
86543 CTCTCACTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
13 8 0.22
14 25 0.68
15 4 0.11
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTCAATTTTCT
Found at i:86570 original size:18 final size:18
Alignment explanation
Indices: 86549--86600 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
86539 TTTTCTCTCA
*
86549 CTTTTTTGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
86567 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
86585 CTTTTTCGTTTTCTTT
1 CTTTTTCGATTTCTTT
86601 CAATTTCTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.73
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:86613 original size:6 final size:6
Alignment explanation
Indices: 86504--86600 Score: 61
Period size: 6 Copynumber: 15.7 Consensus size: 6
86494 TCTTTTTTCG
* * * **
86504 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
* * ** *
86555 -TGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTT
1 CT-TTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
86601 CAATTTCTTT
Statistics
Matches: 66, Mismatches: 21, Indels: 8
0.69 0.22 0.08
Matches are distributed among these distances:
5 1 0.02
6 52 0.79
7 10 0.15
8 3 0.05
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:86621 original size:22 final size:22
Alignment explanation
Indices: 86582--86623 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
86572 GCAATTTCTT
** *
86582 TTTCTTTTTCGTTTTCTTTCAA
1 TTTCTTTTTCAATCTCTTTCAA
86604 TTTCTTTTTCAATCTCTTTC
1 TTTCTTTTTCAATCTCTTTC
86624 TCCTTTTCTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.10, C:0.21, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTCTTTTTCAATCTCTTTCAA
Found at i:87676 original size:13 final size:12
Alignment explanation
Indices: 87633--87690 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 12
87623 TTTCAACTCG
*
87633 ATTTTTTTTTCA
1 ATTTTTTTTTGA
* *
87645 CTTCTTTATTTTTA
1 ATT-TTT-TTTTGA
87659 ATTTTTTTTTCGA
1 ATTTTTTTTT-GA
87672 ATTTTTTTTTG-
1 ATTTTTTTTTGA
87683 ATTTTTTT
1 ATTTTTTT
87691 GTTACTCCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 8 0.21
12 7 0.18
13 17 0.44
14 7 0.18
ACGTcount: A:0.14, C:0.07, G:0.03, T:0.76
Consensus pattern (12 bp):
ATTTTTTTTTGA
Found at i:89241 original size:20 final size:20
Alignment explanation
Indices: 89194--89241 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
89184 AGTAAGCTCG
89194 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
89214 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
89234 GTTGAGCT
1 GTTGAGCT
89242 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:90134 original size:24 final size:24
Alignment explanation
Indices: 90107--90156 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
90097 TTTTTCTCTC
* *
90107 TCAAACTCTTTTTCATTCTCTTTT
1 TCAAACTCATTTTCATTCTCATTT
* *
90131 TCAATCTCATTTTCATTTTCATTT
1 TCAAACTCATTTTCATTCTCATTT
90155 TC
1 TC
90157 TTTTTTTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.58
Consensus pattern (24 bp):
TCAAACTCATTTTCATTCTCATTT
Found at i:90143 original size:13 final size:12
Alignment explanation
Indices: 90107--90145 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
90097 TTTTTCTCTC
*
90107 TCAAACTCTTTT
1 TCAATCTCTTTT
*
90119 TCATTCTCTTTT
1 TCAATCTCTTTT
*
90131 TCAATCTCATTT
1 TCAATCTCTTTT
90143 TCA
1 TCA
90146 TTTTCATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.26, G:0.00, T:0.54
Consensus pattern (12 bp):
TCAATCTCTTTT
Found at i:90152 original size:12 final size:12
Alignment explanation
Indices: 90116--90156 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
90106 CTCAAACTCT
*
90116 TTTTCATTCTCT
1 TTTTCATTCTCA
*
90128 TTTTCAATCTCA
1 TTTTCATTCTCA
*
90140 TTTTCATTTTCA
1 TTTTCATTCTCA
90152 TTTTC
1 TTTTC
90157 TTTTTTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTTCATTCTCA
Found at i:90161 original size:12 final size:12
Alignment explanation
Indices: 90112--90147 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
90102 CTCTCTCAAA
90112 CTCTTTTTCATT
1 CTCTTTTTCATT
*
90124 CTCTTTTTCAAT
1 CTCTTTTTCATT
*
90136 CTCATTTTCATT
1 CTCTTTTTCATT
90148 TTCATTTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (12 bp):
CTCTTTTTCATT
Found at i:98271 original size:23 final size:24
Alignment explanation
Indices: 98238--98289 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
98228 ACAAATTCTT
* *
98238 TTTTTCATTTT-CATCACTCATTTC
1 TTTTTCATTTTGAATCACTC-TCTC
98262 TTTTTC-TTTTGAATCACTCTCTC
1 TTTTTCATTTTGAATCACTCTCTC
98285 TTTTT
1 TTTTT
98290 TTATCACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.13, C:0.23, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTTTCATTTTGAATCACTCTCTC
Found at i:106928 original size:30 final size:30
Alignment explanation
Indices: 106894--106990 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
106884 AGCTCACTCC
106894 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
106924 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
106954 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
106984 TAGCTCA
1 TAGCTCA
106991 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:107920 original size:22 final size:20
Alignment explanation
Indices: 107888--107936 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 20
107878 GCCGAATTTA
107888 TGAACTATTTTAATACATTAGTG
1 TGAAC-ATTTTAAT-CATT-GTG
* *
107911 TGAACATTTTTATTATTGTG
1 TGAACATTTTAATCATTGTG
107931 TGAACA
1 TGAACA
107937 CCTAGATGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 3 0.12
22 7 0.29
23 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGAACATTTTAATCATTGTG
Found at i:108641 original size:11 final size:10
Alignment explanation
Indices: 108605--108647 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 10
108595 GTTCGTAACG
108605 AAAAAAAATA
1 AAAAAAAATA
108615 AAAAAAGGAAGTA
1 AAAAAA--AA-TA
108628 AAAAAAAATCA
1 AAAAAAAAT-A
108639 AAAAAAAAT
1 AAAAAAAAT
108648 TTTGAGTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.24
11 12 0.41
12 2 0.07
13 8 0.28
ACGTcount: A:0.81, C:0.02, G:0.07, T:0.09
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:108744 original size:13 final size:13
Alignment explanation
Indices: 108726--108764 Score: 57
Period size: 11 Copynumber: 3.2 Consensus size: 13
108716 AAAGGAGAAG
108726 AAATTCAGAAAAA
1 AAATTCAGAAAAA
108739 AAATTCA-AAAAA
1 AAATTCAGAAAAA
108751 AAA-TC-GAAAAA
1 AAATTCAGAAAAA
108762 AAA
1 AAA
108765 AGGAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.40
12 8 0.32
13 7 0.28
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (13 bp):
AAATTCAGAAAAA
Found at i:108748 original size:11 final size:12
Alignment explanation
Indices: 108733--108776 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
108723 AAGAAATTCA
*
108733 GAAAAAAAATTC
1 GAAAAAAAAATC
108745 -AAAAAAAAATC
1 GAAAAAAAAATC
*
108756 GAAAAAAAAA-G
1 GAAAAAAAAATC
108767 GAAAAAAAAA
1 GAAAAAAAAA
108777 AGTGACAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.80, C:0.05, G:0.09, T:0.07
Consensus pattern (12 bp):
GAAAAAAAAATC
Found at i:108751 original size:12 final size:12
Alignment explanation
Indices: 108726--108765 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
108716 AAAGGAGAAG
108726 AAATTCAGAAAAA
1 AAATTCA-AAAAA
108739 AAATTCAAAAAA
1 AAATTCAAAAAA
108751 AAA-TCGAAAAAA
1 AAATTC-AAAAAA
108763 AAA
1 AAA
108766 GGAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 2 0.08
12 17 0.65
13 7 0.27
ACGTcount: A:0.75, C:0.07, G:0.05, T:0.12
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:108771 original size:23 final size:24
Alignment explanation
Indices: 108711--108776 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
108701 TATTGGATTT
* * *
108711 AAAAAAAAGGAGAAGAAATTCAGA
1 AAAAAAAAGGAAAAAAAAATCAGA
***
108735 AAAAAAATTCAAAAAAAAATC-GA
1 AAAAAAAAGGAAAAAAAAATCAGA
108758 AAAAAAAAGGAAAAAAAAA
1 AAAAAAAAGGAAAAAAAAA
108777 AGTGACAAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 18 0.55
24 15 0.45
ACGTcount: A:0.76, C:0.05, G:0.12, T:0.08
Consensus pattern (24 bp):
AAAAAAAAGGAAAAAAAAATCAGA
Found at i:108772 original size:12 final size:14
Alignment explanation
Indices: 108757--108789 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
108747 AAAAAAATCG
108757 AAAAAAAAAG-GA-
1 AAAAAAAAAGTGAC
108769 AAAAAAAAAGTGAC
1 AAAAAAAAAGTGAC
108783 AAAAAAA
1 AAAAAAA
108790 TCGAGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.53
13 2 0.11
14 7 0.37
ACGTcount: A:0.82, C:0.03, G:0.12, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAGTGAC
Found at i:108786 original size:13 final size:13
Alignment explanation
Indices: 108744--108789 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
108734 AAAAAAAATT
*
108744 CAAAAAAAAATCGA
1 CAAAAAAAAGT-GA
108758 -AAAAAAAAG-GA
1 CAAAAAAAAGTGA
*
108769 AAAAAAAAAGTGA
1 CAAAAAAAAGTGA
108782 CAAAAAAA
1 CAAAAAAA
108790 TCGAGTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 2 0.07
12 9 0.32
13 17 0.61
ACGTcount: A:0.78, C:0.07, G:0.11, T:0.04
Consensus pattern (13 bp):
CAAAAAAAAGTGA
Found at i:109749 original size:6 final size:6
Alignment explanation
Indices: 109729--109778 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
109719 AAGAGAAAAC
*
109729 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
109778 A
1 A
109779 TAAAAGAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:109759 original size:21 final size:21
Alignment explanation
Indices: 109729--109788 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
109719 AAGAGAAAAC
109729 AAAGAAAAGAAAAGAAAAAGAA
1 AAAG-AAAGAAAAGAAAAAGAA
* *
109751 AAAGCAAGAGAAGAAAAAGAA
1 AAAGAAAGAAAAGAAAAAGAA
* *
109772 AATGAAATAAAAGAAAA
1 AAAGAAAGAAAAGAAAA
109789 GAGAGGCAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (21 bp):
AAAGAAAGAAAAGAAAAAGAA
Found at i:109759 original size:26 final size:25
Alignment explanation
Indices: 109729--109790 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
109719 AAGAGAAAAC
109729 AAAGAAAAGAAAAGAAAAAGAAA-A
1 AAAGAAAAGAAAAGAAAAAGAAATA
* *
109753 AGCAAGAGAAGAAAAAGAAAATGAAATA
1 A--AAGAAAAG-AAAAGAAAAAGAAATA
109781 AAAGAAAAGA
1 AAAGAAAAGA
109791 GAGGCAACAG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 1 0.03
25 1 0.03
26 14 0.45
27 13 0.42
28 2 0.06
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (25 bp):
AAAGAAAAGAAAAGAAAAAGAAATA
Found at i:113405 original size:40 final size:40
Alignment explanation
Indices: 113361--113544 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 40
113351 AAGTGAATAT
* * *
113361 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGATACTAA
* **
113401 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAA
**
113441 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGA-ATTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGA-TACTAA
* * * *
113481 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACGAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAA
* *
113520 ATCCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATT
113545 TGAACGAGGA
Statistics
Matches: 127, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
39 33 0.26
40 94 0.74
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAA
Found at i:113564 original size:79 final size:80
Alignment explanation
Indices: 113397--113579 Score: 208
Period size: 79 Copynumber: 2.3 Consensus size: 80
113387 GTGCGAGATA
*** *
113397 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACGAAATCCGGGCTAAGTCCCGAAGG
** **
113462 CATTCGTGCGAATTG
66 CATTCGAACGAAGAG
* * * *
113477 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACGAAATCCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACGAAATCCGGGCTAAGTCCCGAAGG
* *
113541 CATTTGAACGAGGAG
66 CATTCGAACGAAGAG
* *
113556 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
113580 TACGTGATTT
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 14 0.16
79 44 0.52
80 27 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACGAAATCCGGGCTAAGTCCCGAAGG
CATTCGAACGAAGAG
Found at i:121311 original size:40 final size:40
Alignment explanation
Indices: 121228--121450 Score: 213
Period size: 40 Copynumber: 5.6 Consensus size: 40
121218 TTGAATGCTG
* * * * *
121228 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGA-T-ACTAAA
* * *
121268 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGATACTAAA
* **
121308 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
**
121348 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGA-ATTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGA-TACTAAA
* * *
121388 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
* *
121427 TCCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
121451 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
39 34 0.21
40 114 0.72
41 10 0.06
42 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGATACTAAA
Found at i:121365 original size:80 final size:79
Alignment explanation
Indices: 121228--121452 Score: 242
Period size: 80 Copynumber: 2.8 Consensus size: 79
121218 TTGAATGCTG
* * * * * *
121228 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAG-TGAATATATCCGGATTAAGAT-CCGAAGGCCT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTG-ATAAATCCGGGTTAAG-TCCCGAAGGCAT
121291 TTGTGCGAGA-TACTAAA
63 TTGTGCGA-ATTACTAAA
* *
121308 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTGATAAATCCGGGTTAAGTCCCGAAGGCATTT
**
121373 GTGCGAATTGTTAAA
65 GTGCGAATTACTAAA
* * * *
121388 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTT-ACTAAATCCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTGA-TAAATCCGGGTTAAGTCCCGAAGGCATTT
121452 G
65 G
121453 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
79 37 0.30
80 81 0.65
81 6 0.05
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTGATAAATCCGGGTTAAGTCCCGAAGGCATTTG
TGCGAATTACTAAA
Found at i:121470 original size:79 final size:80
Alignment explanation
Indices: 121303--121485 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 80
121293 GTGCGAGATA
** *
121303 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGG
** **
121368 CATTCGTGCGAATTG
66 CATTCGAACGAAGAG
* * * *
121383 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGG
* *
121447 CATTTGAACGAGGAG
66 CATTCGAACGAAGAG
* *
121462 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
121486 TACGTGATTT
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 14 0.16
79 45 0.52
80 27 0.31
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGG
CATTCGAACGAAGAG
Found at i:121470 original size:119 final size:120
Alignment explanation
Indices: 121228--121485 Score: 281
Period size: 119 Copynumber: 2.2 Consensus size: 120
121218 TTGAATGCTG
* * * * *
121228 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTTT
1 TCCGGGTTAAGTCCCGAAGGCTTCGTGCGAAGTGAATAAATCCGGATTAAGATCCGAAGGCCATT
* ** ** *
121293 GTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
66 GTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTAAA
* * * *
121348 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAATTG-TTAAATCCGGGTTATG-TCCCGAAGG-CA
1 TCCGGGTTAAGTCCCGAAGGC-TTCGTGCGAAGTGAATAAATCCGGATTAAGAT-CCGAAGGCCA
* * * * *
121410 TTGTGTGAGTTACTAAATCCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTATA
64 TTGTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTAAA
*
121467 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
121486 TACGTGATTT
Statistics
Matches: 115, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
118 15 0.13
119 51 0.44
120 39 0.34
121 10 0.09
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (120 bp):
TCCGGGTTAAGTCCCGAAGGCTTCGTGCGAAGTGAATAAATCCGGATTAAGATCCGAAGGCCATT
GTGCGAGATACTAAATCCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTAAA
Found at i:123080 original size:30 final size:30
Alignment explanation
Indices: 123046--123142 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
123036 AGCTCACTCC
123046 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
123076 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
123106 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
123136 TAGCTCA
1 TAGCTCA
123143 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:126930 original size:14 final size:14
Alignment explanation
Indices: 126911--126943 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
126901 TATACAAAAA
126911 TTTTTGTTTGTTTT
1 TTTTTGTTTGTTTT
126925 TTTTTGTTTGTTTT
1 TTTTTGTTTGTTTT
126939 TTTTT
1 TTTTT
126944 CTGACCCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (14 bp):
TTTTTGTTTGTTTT
Found at i:128390 original size:10 final size:10
Alignment explanation
Indices: 128375--128401 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
128365 TAAGTTGAAG
128375 TTGAGCTGAT
1 TTGAGCTGAT
128385 TTGAGCTGAT
1 TTGAGCTGAT
128395 TTGAGCT
1 TTGAGCT
128402 TGAAGGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (10 bp):
TTGAGCTGAT
Found at i:128967 original size:14 final size:14
Alignment explanation
Indices: 128920--128967 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
128910 GTACGAATGG
*
128920 AATGGTAGGAACGA
1 AATGGTAGGAACAA
*
128934 AAGGGTAGGAACAA
1 AATGGTAGGAACAA
*
128948 AATGGTATGAACAA
1 AATGGTAGGAACAA
*
128962 ATTGGT
1 AATGGT
128968 CGGTTTAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGGTAGGAACAA
Found at i:130593 original size:30 final size:31
Alignment explanation
Indices: 130559--130654 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 31
130549 GCTCACTCCT
*
130559 AGCTC-ACTTTCAACTCACGAGCTAAACCTC
1 AGCTCAACTTTCAGCTCACGAGCTAAACCTC
* * * * *
130589 AGCTCAAC-TTCAGCTTAGGAGTTTAGCCTC
1 AGCTCAACTTTCAGCTCACGAGCTAAACCTC
* *
130619 AGCTCAACTTT-AGCTCACGAGCTAAAGCTT
1 AGCTCAACTTTCAGCTCACGAGCTAAACCTC
130649 AGCTCA
1 AGCTCA
130655 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (31 bp):
AGCTCAACTTTCAGCTCACGAGCTAAACCTC
Found at i:134412 original size:30 final size:29
Alignment explanation
Indices: 134372--134474 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 29
134362 CGAGTTTAAA
*
134372 CTAAAATGAGCTAAGCTTTAGCTCGTGAG
1 CTAAAGTGAGCTAAGCTTTAGCTCGTGAG
* * * * *
134401 CTAAAGCTGAGCTGAGGC-TAAACTCCTAAG
1 CTAAAG-TGAGCT-AAGCTTTAGCTCGTGAG
*
134431 CTAAAGTTGAGCTAAGGTTTAGCTCGTGAG
1 CTAAAG-TGAGCTAAGCTTTAGCTCGTGAG
*
134461 TTGAAAGTGAGCTA
1 CT-AAAGTGAGCTA
134475 GGAGTGAGCT
Statistics
Matches: 56, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
29 7 0.12
30 42 0.75
31 7 0.12
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (29 bp):
CTAAAGTGAGCTAAGCTTTAGCTCGTGAG
Found at i:136417 original size:11 final size:12
Alignment explanation
Indices: 136385--136417 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
136375 GAGCTGTAGC
136385 AAACTTAATTAT
1 AAACTTAATTAT
*
136397 AAACTGAATTA-
1 AAACTTAATTAT
136408 AAACTTAATT
1 AAACTTAATT
136418 TATTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
AAACTTAATTAT
Found at i:138249 original size:56 final size:56
Alignment explanation
Indices: 138144--138250 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
138134 ATTAATGTCG
* * * * *
138144 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGCCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
138200 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
138251 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
Found at i:138899 original size:20 final size:20
Alignment explanation
Indices: 138874--138928 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
138864 ACGAGTTAAA
*
138874 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTTGAATGAGCTAAC
*
138894 TTGAGCATGAATGAGCTAAC
1 TTGAGCTTGAATGAGCTAAC
*
138914 TTGAGCTCGAATGAG
1 TTGAGCTTGAATGAG
138929 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (20 bp):
TTGAGCTTGAATGAGCTAAC
Found at i:139843 original size:16 final size:15
Alignment explanation
Indices: 139817--139846 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
139807 TTTCAATCCA
139817 TCATCCCAATCAAAG
1 TCATCCCAATCAAAG
139832 TCATCACCAATCAAA
1 TCATC-CCAATCAAA
139847 AATTGATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
TCATCCCAATCAAAG
Found at i:141389 original size:16 final size:16
Alignment explanation
Indices: 141368--141404 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
141358 TGAATACAAA
141368 TTTTTTTTTTGAATTT
1 TTTTTTTTTTGAATTT
141384 TTTTTTTTTTGAATTT
1 TTTTTTTTTTGAATTT
141400 TTTTT
1 TTTTT
141405 CCTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.11, C:0.00, G:0.05, T:0.84
Consensus pattern (16 bp):
TTTTTTTTTTGAATTT
Found at i:141410 original size:17 final size:16
Alignment explanation
Indices: 141368--141410 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
141358 TGAATACAAA
141368 TTTTTT-TTTTGAATT
1 TTTTTTCTTTTGAATT
*
141383 TTTTTTTTTTTGAATT
1 TTTTTTCTTTTGAATT
141399 TTTTTTCCTTTT
1 TTTTTT-CTTTT
141411 TTTTACAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 6 0.24
16 15 0.60
17 4 0.16
ACGTcount: A:0.09, C:0.05, G:0.05, T:0.81
Consensus pattern (16 bp):
TTTTTTCTTTTGAATT
Found at i:142576 original size:56 final size:55
Alignment explanation
Indices: 142460--142577 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
142450 TGCATGCTTT
* * * *
142460 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
142514 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
142570 CATTAAAT
1 CATTAAAT
142578 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:143215 original size:20 final size:20
Alignment explanation
Indices: 143184--143255 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
143174 AGCTAATAAC
* *
143184 GAGCTC-AATGAGTTAAATT
1 GAGCTCGAATGAGCTAACTT
* *
143203 GAGCTTGAATGAGCTGACTT
1 GAGCTCGAATGAGCTAACTT
* *
143223 GAGCACAAATGAGCTAACTT
1 GAGCTCGAATGAGCTAACTT
143243 GAGCTCGAATGAG
1 GAGCTCGAATGAG
143256 TTGAACCACA
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
19 5 0.12
20 37 0.88
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.25
Consensus pattern (20 bp):
GAGCTCGAATGAGCTAACTT
Found at i:143754 original size:21 final size:21
Alignment explanation
Indices: 143707--143758 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
143697 CTCTTTTTCT
* **
143707 TTTCTCTTTCAATTTCTTTTC
1 TTTCTTTTTCAATTTCTTGCC
* *
143728 TCTCTTTTTCATTTTCTTGCC
1 TTTCTTTTTCAATTTCTTGCC
143749 TTTCTTTTTC
1 TTTCTTTTTC
143759 CACTCTCATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.06, C:0.25, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTCTTTTTCAATTTCTTGCC
Found at i:146048 original size:22 final size:21
Alignment explanation
Indices: 146017--146067 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
146007 ACCTCTTTGA
146017 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCAATTCGTACC-AAT
*
146040 ACCATACCATTTCGTACCAAT
1 ACCATACCAATTCGTACCAAT
*
146061 TCCATAC
1 ACCATAC
146068 TATTTTGAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 13 0.50
23 4 0.15
ACGTcount: A:0.35, C:0.33, G:0.04, T:0.27
Consensus pattern (21 bp):
ACCATACCAATTCGTACCAAT
Found at i:146067 original size:21 final size:21
Alignment explanation
Indices: 146022--146084 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
146012 TTTGAACCAT
* *
146022 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
146044 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* * *
146065 TACTATTTTGAACCAATTCC
1 TACCATTTCGTACCAATTCC
146085 CAAATACCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 23 0.64
22 13 0.36
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.32
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:150102 original size:11 final size:11
Alignment explanation
Indices: 150086--150110 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
150076 TTCGTTCCAT
150086 AATAATTTTCA
1 AATAATTTTCA
150097 AATAATTTTCA
1 AATAATTTTCA
150108 AAT
1 AAT
150111 CCTCACCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (11 bp):
AATAATTTTCA
Found at i:153426 original size:11 final size:12
Alignment explanation
Indices: 153394--153426 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
153384 GAGCTGTAGC
153394 AAACTTAATTAT
1 AAACTTAATTAT
*
153406 AAACTGAATTA-
1 AAACTTAATTAT
153417 AAACTTAATT
1 AAACTTAATT
153427 TATTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (12 bp):
AAACTTAATTAT
Done.