Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009226.1 Hibiscus syriacus cultivar Beakdansim tig00112828_pilon, whole genome shotgun sequence
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: 168013
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2667 original size:26 final size:26
Alignment explanation
Indices: 2634--2688 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 26
2624 AGTGGATATC
2634 TTTACAAAAGCTTTAGA-AAGGAAATA
1 TTTACAAAAGCTTTAGATAAGG-AATA
2660 TTTACAAAAGCTTTAGATAAGGAATA
1 TTTACAAAAGCTTTAGATAAGGAATA
2686 TTT
1 TTT
2689 TGGGCACTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 24 0.86
27 4 0.14
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (26 bp):
TTTACAAAAGCTTTAGATAAGGAATA
Found at i:3925 original size:20 final size:20
Alignment explanation
Indices: 3908--3960 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 20
3898 TTTACATACT
3908 TTTATATATGTATACATATA
1 TTTATATATGTATACATATA
* *
3928 TTTTTATATGTACA-AT-TA
1 TTTATATATGTATACATATA
* *
3946 TATATATATATATAC
1 TTTATATATGTATAC
3961 TTCTATATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 12 0.46
19 2 0.08
20 12 0.46
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTATATATGTATACATATA
Found at i:3959 original size:32 final size:32
Alignment explanation
Indices: 3912--4000 Score: 88
Period size: 32 Copynumber: 2.8 Consensus size: 32
3902 CATACTTTTA
* * *
3912 TATATGTATACATATATTTTTATATGTACAAT
1 TATATATATATATATATTTTTATATATACAAT
* * *
3944 TATATATATATATATACTTCTATATATACATT
1 TATATATATATATATATTTTTATATATACAAT
* * * *
3976 TATATTTATATTTACATATTTATAT
1 TATATATATATATATATTTTTATAT
4001 TTACCTTTTA
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (32 bp):
TATATATATATATATATTTTTATATATACAAT
Found at i:4001 original size:6 final size:6
Alignment explanation
Indices: 3943--4003 Score: 50
Period size: 6 Copynumber: 9.5 Consensus size: 6
3933 ATATGTACAA
* * * *
3943 TTATAT ATATAT ATATACT TCTATAT ATACAT TTATAT TTATAT TTACATAT
1 TTATAT TTATAT TTATA-T T-TATAT TTATAT TTATAT TTATAT TT--ATAT
3995 TTATAT TTA
1 TTATAT TTA
4004 CCTTTTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
6 33 0.73
7 2 0.04
8 10 0.22
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (6 bp):
TTATAT
Found at i:4014 original size:14 final size:14
Alignment explanation
Indices: 3977--4004 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3967 ATATACATTT
3977 ATATTTATATTTAC
1 ATATTTATATTTAC
3991 ATATTTATATTTAC
1 ATATTTATATTTAC
4005 CTTTTAATAT
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:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
ATATTTATATTTAC
Found at i:7941 original size:18 final size:18
Alignment explanation
Indices: 7918--7961 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
7908 AGCAAATTTC
7918 AGATATCATAGCCAACAA
1 AGATATCATAGCCAACAA
*
7936 AGATATAATAGCCAACAA
1 AGATATCATAGCCAACAA
*
7954 AGAGATCA
1 AGATATCA
7962 AGACAAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.52, C:0.18, G:0.14, T:0.16
Consensus pattern (18 bp):
AGATATCATAGCCAACAA
Found at i:15632 original size:23 final size:26
Alignment explanation
Indices: 15602--15652 Score: 72
Period size: 23 Copynumber: 2.1 Consensus size: 26
15592 TTATTTTTTG
*
15602 TAAATATAT-AT-TATAAAATA-TTT
1 TAAATATATGATACATAAAATAGTTT
15625 TAAATATATGATACATAAAATAGTTT
1 TAAATATATGATACATAAAATAGTTT
15651 TA
1 TA
15653 CAAAAAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 9 0.38
24 2 0.08
25 8 0.33
26 5 0.21
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (26 bp):
TAAATATATGATACATAAAATAGTTT
Found at i:16510 original size:21 final size:21
Alignment explanation
Indices: 16484--16528 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
16474 AACTGGTGAG
16484 GACAGGTGCATTTTTGGCAAA
1 GACAGGTGCATTTTTGGCAAA
*
16505 GACAGGTTCATTTTTGGCAAA
1 GACAGGTGCATTTTTGGCAAA
16526 GAC
1 GAC
16529 TTGAGGGGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (21 bp):
GACAGGTGCATTTTTGGCAAA
Found at i:20798 original size:31 final size:29
Alignment explanation
Indices: 20722--20801 Score: 124
Period size: 29 Copynumber: 2.7 Consensus size: 29
20712 TAAATTTATC
* *
20722 TTTTTGGTTAAAATATGTACTTAAAATAT
1 TTTTTGGTCAAAATAGGTACTTAAAATAT
20751 TTTTTGGTCAAAATAGGTACTTAAAATAT
1 TTTTTGGTCAAAATAGGTACTTAAAATAT
20780 TTTTTGGTCAAAAAATAGGTAC
1 TTTTTGGTC--AAAATAGGTAC
20802 CCAAAGTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 36 0.77
31 11 0.23
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (29 bp):
TTTTTGGTCAAAATAGGTACTTAAAATAT
Found at i:20927 original size:28 final size:29
Alignment explanation
Indices: 20894--20991 Score: 108
Period size: 29 Copynumber: 3.3 Consensus size: 29
20884 GAAAAAATTG
* *
20894 AATACTGTAGGTACTTATTTTGAT-TAAA
1 AATACTTTAGGTACTTATTTTGATAAAAA
*
20922 AATACTTTAGGTACCTATTTTGATAAAAA
1 AATACTTTAGGTACTTATTTTGATAAAAA
* * *
20951 AAAAGTTTACGTACTTATTTTGATCCAAAAA
1 AATACTTTAGGTACTTATTTTGAT--AAAAA
*
20982 AATATTTTAG
1 AATACTTTAG
20992 AAACTTAGAT
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
28 22 0.39
29 23 0.40
31 12 0.21
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (29 bp):
AATACTTTAGGTACTTATTTTGATAAAAA
Found at i:26699 original size:44 final size:44
Alignment explanation
Indices: 26646--26742 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
26636 CCATGATCGA
** * * * *
26646 TATCGATACTACTTTATATAGTAGTATCGATACTCCCTGGACGG
1 TATCGATACTACACTAAAAAGTAGTATCGATACTCCATGGACAG
*
26690 TATCGATACTACACTAAAAAGTAGTATCGATACTCCATGGCCAG
1 TATCGATACTACACTAAAAAGTAGTATCGATACTCCATGGACAG
26734 TATCGATAC
1 TATCGATAC
26743 CGTTGGATTG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (44 bp):
TATCGATACTACACTAAAAAGTAGTATCGATACTCCATGGACAG
Found at i:32510 original size:20 final size:20
Alignment explanation
Indices: 32472--32563 Score: 60
Period size: 21 Copynumber: 4.5 Consensus size: 20
32462 TCTTTCTAGA
**
32472 TATCGATACTACTAGAATAG
1 TATCGATACTACTTCAATAG
*
32492 TATCGATACTGCTTCAATAGG
1 TATCGATACTACTTCAATA-G
* ** *
32513 TATCAATA-TTGTTCTTAACAG
1 TATCGATACTACTTC--AATAG
* *
32534 TACCGATACTACTTCAATGGG
1 TATCGATACTACTTCAAT-AG
32555 TATCGATAC
1 TATCGATAC
32564 CCTAGTATCG
Statistics
Matches: 53, Mismatches: 14, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
20 22 0.42
21 24 0.45
22 7 0.13
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (20 bp):
TATCGATACTACTTCAATAG
Found at i:34542 original size:16 final size:16
Alignment explanation
Indices: 34521--34555 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
34511 ATTTTGATAG
34521 ATTTGGTTATTTGAAT
1 ATTTGGTTATTTGAAT
* *
34537 ATTTGGTTGTTTGGAT
1 ATTTGGTTATTTGAAT
34553 ATT
1 ATT
34556 GGAGTGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (16 bp):
ATTTGGTTATTTGAAT
Found at i:34690 original size:13 final size:13
Alignment explanation
Indices: 34672--34696 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34662 TCCCTATTGC
34672 ATATTGATTATGA
1 ATATTGATTATGA
34685 ATATTGATTATG
1 ATATTGATTATG
34697 TCGACTAATG
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:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
ATATTGATTATGA
Found at i:35398 original size:44 final size:44
Alignment explanation
Indices: 35348--35448 Score: 141
Period size: 44 Copynumber: 2.3 Consensus size: 44
35338 ATACCATGAT
* *
35348 CGGTATCGATACTACT-TTACATAGTAGTATCGATACTCCCTGGA
1 CGGTATCGATACTA-TACTACAAAGTAGTATCGATACTCCCTGGA
*
35392 CGGTATCGATACTATACTACAAAGTAGTATCGATACTCCCTGGC
1 CGGTATCGATACTATACTACAAAGTAGTATCGATACTCCCTGGA
* *
35436 CAGTATTGATACT
1 CGGTATCGATACT
35449 GTTGGATTGC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 1 0.02
44 50 0.98
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (44 bp):
CGGTATCGATACTATACTACAAAGTAGTATCGATACTCCCTGGA
Found at i:36744 original size:18 final size:19
Alignment explanation
Indices: 36721--36756 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
36711 ATTTGGTAGT
*
36721 TTTTA-TAAAATAAAAATG
1 TTTTATTAAAAAAAAAATG
36739 TTTTATTAAAAAAAAAAT
1 TTTTATTAAAAAAAAAAT
36757 CTGATTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
TTTTATTAAAAAAAAAATG
Found at i:39701 original size:131 final size:131
Alignment explanation
Indices: 39420--39778 Score: 405
Period size: 131 Copynumber: 2.7 Consensus size: 131
39410 GTTCTAGTCG
* * * * * * *
39420 TCTAAGGGTGACAC-AGCTCCTACGTGATGAGGAGATTTGGCCGATGGATGACACAGTTCCTATA
1 TCTAGGGGTGACACGA-CTCCTACGTGATGAGGAGGTATGGTCGGTGGATGACACGGTTCCTATG
* * * * *** * *
39484 TGCTGTGGACGACAAACCATCTTTAGGGAGGGTGATAACATGGTTCCTACACGATGAGGATGTCT
65 TGATGAGGATGACATACCATCTTTAGGGA---TGATAACACAATTCCTACACGATGAGGACGACT
39549 GGTTA
127 GGTTA
* * *
39554 TCTAGGGGTGACACGACTCCTACGTGATGAGGTGGTCTGGTCGGTGGATGACACGGTTCTTATGT
1 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTATGGTCGGTGGATGACACGGTTCCTATGT
** * * *
39619 GATGAGGATGGTATATCATCTTTAGGGATGATAACACAATTCCTATATGATGAGGACGACTGGTT
66 GATGAGGATGACATACCATCTTTAGGGATGATAACACAATTCCTACACGATGAGGACGACTGGTT
39684 A
131 A
* * * * *
39685 TCTAGGGGTGACACGACTCCTATGTGATAAAGAGGTATGATCGGTGGATGACACGGTTCCTACGT
1 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTATGGTCGGTGGATGACACGGTTCCTATGT
*
39750 GATGAGGATGACATGCCATCTTTAGGGAT
66 GATGAGGATGACATACCATCTTTAGGGAT
39779 TTATTTCAAG
Statistics
Matches: 189, Mismatches: 35, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
131 113 0.60
134 75 0.40
135 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (131 bp):
TCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTATGGTCGGTGGATGACACGGTTCCTATGT
GATGAGGATGACATACCATCTTTAGGGATGATAACACAATTCCTACACGATGAGGACGACTGGTT
A
Found at i:39887 original size:68 final size:65
Alignment explanation
Indices: 39777--39992 Score: 261
Period size: 65 Copynumber: 3.3 Consensus size: 65
39767 ATCTTTAGGG
* *
39777 ATTTATTTCAAGGGAAACATACTCAAAGATGATTGTTTCAAGAGAAAACTGTCTCAAGAGAGACA
1 ATTTATTTCAAGGGAAA-AGACTCAAAGATGATTGTTTCAAGAG-AAACTGTCTCAAAAGAGACA
39842 AA
64 AA
* * * *
39844 ATTTTATTTCAAAGGAAATAGAATCAAAGATGATTGTTTCAAGAGAAACTATCTTAAAAGAGACA
1 A-TTTATTTCAAGGGAAA-AGACTCAAAGATGATTGTTTCAAGAGAAACTGTCTCAAAAGAGACA
39909 AA
64 AA
** * ** * *
39911 ATTCGTTTCAAGGGAAACGACTCAAAGATGGGTGTTTCAAGGGAAACTGTCTCAATAGAGACAAA
1 ATTTATTTCAAGGGAAAAGACTCAAAGATGATTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAA
* *
39976 ACTTGTTTCAAGGGAAA
1 ATTTATTTCAAGGGAAA
39993 CTATCTCAAG
Statistics
Matches: 128, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
65 55 0.43
66 13 0.10
67 21 0.16
68 39 0.30
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.26
Consensus pattern (65 bp):
ATTTATTTCAAGGGAAAAGACTCAAAGATGATTGTTTCAAGAGAAACTGTCTCAAAAGAGACAAA
Found at i:39928 original size:36 final size:36
Alignment explanation
Indices: 39877--40029 Score: 153
Period size: 36 Copynumber: 4.4 Consensus size: 36
39867 TCAAAGATGA
* *
39877 TTGTTTCAAGAGAAACTATCTTAAAAGAGACAAAA-
1 TTGTTTCAAGGGAAACTATCTCAAAAGAGACAAAAC
* *
39912 TTCGTTTCAAGGGAAACGA-CTC-AAAGATG------G
1 TT-GTTTCAAGGGAAACTATCTCAAAAGA-GACAAAAC
* * *
39942 GTGTTTCAAGGGAAACTGTCTCAATAGAGACAAAAC
1 TTGTTTCAAGGGAAACTATCTCAAAAGAGACAAAAC
*
39978 TTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAC
1 TTGTTTCAAGGGAAACTATCTCAAAAGAGACAAAAC
40014 TTGTTTCAAGGGAAAC
1 TTGTTTCAAGGGAAAC
40030 AAACTTAATG
Statistics
Matches: 96, Mismatches: 11, Indels: 21
0.75 0.09 0.16
Matches are distributed among these distances:
29 14 0.15
30 5 0.05
31 4 0.04
34 5 0.05
35 5 0.05
36 63 0.66
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (36 bp):
TTGTTTCAAGGGAAACTATCTCAAAAGAGACAAAAC
Found at i:40023 original size:21 final size:20
Alignment explanation
Indices: 39954--40014 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
39944 GTTTCAAGGG
*
39954 AAACTGTCTCAATAGAGACA
1 AAACTGTCTCAAGAGAGACA
*
39974 AAACTTGTTTCAAG-G-G---
1 AAAC-TGTCTCAAGAGAGACA
*
39990 AAACTATCTCAAGAGAGACA
1 AAACTGTCTCAAGAGAGACA
40010 AAACT
1 AAACT
40015 TGTTTCAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
15 7 0.23
16 5 0.16
17 1 0.03
19 1 0.03
20 10 0.32
21 7 0.23
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.21
Consensus pattern (20 bp):
AAACTGTCTCAAGAGAGACA
Found at i:40176 original size:36 final size:35
Alignment explanation
Indices: 40132--40242 Score: 123
Period size: 36 Copynumber: 3.1 Consensus size: 35
40122 ATCTCAGAGA
*
40132 AAAATTGTCTCTAGTGAGACAAAATTTGTTTTGAG
1 AAAATTGTCTCTAGCGAGACAAAATTTGTTTTGAG
* * * *
40167 AGAAATTGTCTCAAGCGAGATAAAATTTGTTTTTAC
1 A-AAATTGTCTCTAGCGAGACAAAATTTGTTTTGAG
* * * *
40203 ATAACTGTCTCTAGCAAGACAAAATTTTGTTTCGAG
1 AAAATTGTCTCTAGCGAGACAAAA-TTTGTTTTGAG
40239 AAAA
1 AAAA
40243 ACACCCTTAA
Statistics
Matches: 60, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
35 19 0.32
36 41 0.68
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (35 bp):
AAAATTGTCTCTAGCGAGACAAAATTTGTTTTGAG
Found at i:46734 original size:3 final size:3
Alignment explanation
Indices: 46721--46801 Score: 135
Period size: 3 Copynumber: 26.7 Consensus size: 3
46711 AAAAGATATG
* *
46721 TAA TAAA TAA TAA TGA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
46767 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
46802 TTGTTTTCGA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
3 70 0.96
4 3 0.04
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:49466 original size:12 final size:12
Alignment explanation
Indices: 49449--49473 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49439 GTTTCCCCCT
49449 AAAAATATTTTA
1 AAAAATATTTTA
49461 AAAAATATTTTA
1 AAAAATATTTTA
49473 A
1 A
49474 GGATTAAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAAATATTTTA
Found at i:63346 original size:6 final size:6
Alignment explanation
Indices: 63335--63380 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
63325 AATCTCTGTT
63335 GAAAAA GAAAAA GAAAAA -ATAGAAA GAAAAA -AGAAAA GAAAAA GAA
1 GAAAAA GAAAAA GAAAAA GA-A-AAA GAAAAA GA-AAAA GAAAAA GAA
63381 GTGAAGCCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
5 2 0.06
6 27 0.77
7 5 0.14
8 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:63360 original size:13 final size:12
Alignment explanation
Indices: 63336--63377 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 12
63326 ATCTCTGTTG
63336 AAAAAGAAAAAGA
1 AAAAAG-AAAAGA
*
63349 AAAAATAGAAAGA
1 AAAAAGA-AAAGA
63362 AAAAAGAAAAGA
1 AAAAAGAAAAGA
63374 AAAA
1 AAAA
63378 GAAGTGAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:65504 original size:16 final size:16
Alignment explanation
Indices: 65480--65510 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
65470 CAATAAATAA
65480 ATGAATCCATTTACAT
1 ATGAATCCATTTACAT
*
65496 ATGAGTCCATTTACA
1 ATGAATCCATTTACA
65511 AAATAAATAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (16 bp):
ATGAATCCATTTACAT
Found at i:73691 original size:24 final size:24
Alignment explanation
Indices: 73659--73728 Score: 140
Period size: 24 Copynumber: 2.9 Consensus size: 24
73649 TCTTCCAGAT
73659 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
73683 GATGTATAAAACATCTATGTACAC
1 GATGTATAAAACATCTATGTACAC
73707 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
73729 CATATCATGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:77160 original size:44 final size:44
Alignment explanation
Indices: 77018--77383 Score: 210
Period size: 44 Copynumber: 8.4 Consensus size: 44
77008 AGATTTGATA
* * * * * * *
77018 CCATCACAGAAGGAGGTGGATCAACAT-TCCTTTATTGCTCAATT
1 CCATCACATAAGAAGTTGGATCAACATCACCATT-TCGCTCGATT
* * * * *
77062 TCATCACATAAGAAGTTGGATCAACAT-TCCTTTATTGCTCAATT
1 CCATCACATAAGAAGTTGGATCAACATCACCATT-TCGCTCGATT
* *
77106 TCATCACATAAGAAGTTGGATCAACATCACCATTTCCCTCGATT
1 CCATCACATAAGAAGTTGGATCAACATCACCATTTCGCTCGATT
* * * * * * * *
77150 CCATCGCATAAGGAGTTGGAACAGCATCTCCATCTAGCTCGGTT
1 CCATCACATAAGAAGTTGGATCAACATCACCATTTCGCTCGATT
* * *
77194 CCATCATATAAGGAGTTGGATCAGCATCACCATTTTCGCTCGA-T
1 CCATCACATAAGAAGTTGGATCAACATCACCA-TTTCGCTCGATT
* * * * * *
77238 ---TC-CATAAGGAGTTGGATCGACATCATCATTTCTCTTGTTT
1 CCATCACATAAGAAGTTGGATCAACATCACCATTTCGCTCGATT
* * * * * * *
77278 CAATCACTTAAG-AGTTGGAGT-AGCGTCGACCTTTTTGCTAGATT
1 CCATCACATAAGAAGTTGGA-TCAACATC-ACCATTTCGCTCGATT
* * * * **
77322 CCATCACATAAGAAATTGGATTAGCATCACCATTTTGCTCTTTT
1 CCATCACATAAGAAGTTGGATCAACATCACCATTTCGCTCGATT
* *
77366 CTATCACATAAGGAGTTG
1 CCATCACATAAGAAGTTG
77384 AAATAATATC
Statistics
Matches: 257, Mismatches: 54, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
39 7 0.03
40 23 0.09
41 2 0.01
43 12 0.05
44 191 0.74
45 22 0.09
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (44 bp):
CCATCACATAAGAAGTTGGATCAACATCACCATTTCGCTCGATT
Found at i:79040 original size:15 final size:15
Alignment explanation
Indices: 79022--79060 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
79012 AATTGTGAAA
79022 TAAATATAAAAAAGT
1 TAAATATAAAAAAGT
*
79037 TAAAAATAAAAAAGT
1 TAAATATAAAAAAGT
*
79052 TGAATATAA
1 TAAATATAA
79061 CAATATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.26
Consensus pattern (15 bp):
TAAATATAAAAAAGT
Found at i:79206 original size:19 final size:20
Alignment explanation
Indices: 79170--79214 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
79160 AAAGAAATAA
*
79170 AAAATAGAAAAAATGTTAAG
1 AAAATAGAAAAAACGTTAAG
* *
79190 AAAA-AGAAAAAGCGTTAAT
1 AAAATAGAAAAAACGTTAAG
79209 AAAATA
1 AAAATA
79215 CTAAAACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.67, C:0.02, G:0.13, T:0.18
Consensus pattern (20 bp):
AAAATAGAAAAAACGTTAAG
Found at i:79995 original size:14 final size:14
Alignment explanation
Indices: 79976--80003 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
79966 TGCGCGTCGC
79976 TGCCAGTTGGTCCT
1 TGCCAGTTGGTCCT
79990 TGCCAGTTGGTCCT
1 TGCCAGTTGGTCCT
80004 CTTAGGGTTT
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:0.07, C:0.29, G:0.29, T:0.36
Consensus pattern (14 bp):
TGCCAGTTGGTCCT
Found at i:80298 original size:71 final size:71
Alignment explanation
Indices: 80208--80374 Score: 203
Period size: 72 Copynumber: 2.3 Consensus size: 71
80198 AACCATATAT
* * ** *
80208 TATGTTTCCAAAAATACCTTTTTAGAAAATTATAT-TATATACGTTTTT-AAAATTATTTTAAAA
1 TATGTTTAC-AAAA-ACCTTTTTA-AAAATTATATAT-TATACATTTTTAAAAAAAATTTAAAAA
80271 CTATATACTA
62 CTATATACTA
80281 TATGTTTACAAAAACCTTCTTTAAAAATTATATATTATACATTTTTAAAAAAAATTTAAAAACTA
1 TATGTTTACAAAAACCTT-TTTAAAAATTATATATTATACATTTTTAAAAAAAATTTAAAAACTA
80346 TATACTA
65 TATACTA
* *
80353 TATATTTTCAAAAACCATTTTT
1 TATGTTTACAAAAACC-TTTTT
80375 TTTAAAACTA
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
71 25 0.30
72 48 0.58
73 10 0.12
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (71 bp):
TATGTTTACAAAAACCTTTTTAAAAATTATATATTATACATTTTTAAAAAAAATTTAAAAACTAT
ATACTA
Found at i:80331 original size:37 final size:36
Alignment explanation
Indices: 80218--80331 Score: 92
Period size: 37 Copynumber: 3.1 Consensus size: 36
80208 TATGTTTCCA
80218 AAAATACCTTTTTAGAAAATTATAT-TATATACGTTTTT
1 AAAA-ACCTTTTTA-AAAATTATATAT-TATACGTTTTT
* * * * **
80256 -AAAA--TTATTTTAAAACTATATACTATATGTTTAC
1 AAAAACCTT-TTTAAAAATTATATATTATACGTTTTT
*
80290 AAAAACCTTCTTTAAAAATTATATATTATACATTTTT
1 AAAAACCTT-TTTAAAAATTATATATTATACGTTTTT
80327 AAAAA
1 AAAAA
80332 AAATTTAAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
34 19 0.33
35 7 0.12
36 1 0.02
37 30 0.53
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (36 bp):
AAAAACCTTTTTAAAAATTATATATTATACGTTTTT
Found at i:80348 original size:35 final size:35
Alignment explanation
Indices: 80300--80366 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
80290 AAAAACCTTC
* * *
80300 TTTAAAAATTATATATTATACATTTTTAAAAAAAA
1 TTTAAAAACTATATACTATACATTTTCAAAAAAAA
*
80335 TTTAAAAACTATATACTATATATTTTCAAAAA
1 TTTAAAAACTATATACTATACATTTTCAAAAA
80367 CCATTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (35 bp):
TTTAAAAACTATATACTATACATTTTCAAAAAAAA
Found at i:80417 original size:18 final size:18
Alignment explanation
Indices: 80373--80417 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
80363 AAAACCATTT
*
80373 TTTTTAAAACTATATACG
1 TTTTTAAAACTATATACA
** *
80391 TTTCAAAAACTATATATA
1 TTTTTAAAACTATATACA
80409 TTTTTAAAA
1 TTTTTAAAA
80418 TGTTTTCAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTTTAAAACTATATACA
Found at i:80454 original size:36 final size:36
Alignment explanation
Indices: 80391--80519 Score: 139
Period size: 36 Copynumber: 3.7 Consensus size: 36
80381 ACTATATACG
80391 TTTCAAAAACTATATA-TAT---TTTT--AAAATGT
1 TTTCAAAAACTATATATTATACGTTTTCAAAAATGT
*
80421 TTTCAAAAACTATATATTATACGTTTTCAAAAATCAT
1 TTTCAAAAACTATATATTATACGTTTTCAAAAAT-GT
*
80458 TTT-TAAAACTATATATTATACGTTTTCAAAAATGTGT
1 TTTCAAAAACTATATATTATACGTTTTCAAAAA--TGT
* *
80495 TTTC-AAAACTATATAGTATATGTTT
1 TTTCAAAAACTATATATTATACGTTT
80520 AAAAACGTAT
Statistics
Matches: 84, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
30 16 0.19
31 3 0.04
34 4 0.05
36 33 0.39
37 27 0.32
38 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.45
Consensus pattern (36 bp):
TTTCAAAAACTATATATTATACGTTTTCAAAAATGT
Found at i:81304 original size:201 final size:202
Alignment explanation
Indices: 80972--81334 Score: 489
Period size: 201 Copynumber: 1.8 Consensus size: 202
80962 AAATAGTAGT
* * * *
80972 CAACCTTGGTCTTCTTCTCGGATTAAAGACCTCGGTATGAAAAGTCTACCGAAAAGTAGTTTTTT
1 CAACCTAGGTCTTCTTCTCGGATTAAAGACCTCGATATGAAAAGTCTACCGAAAAGTAGTTTCTC
* * ** * * * *
81037 GCTGCTACTATGCGGTTGATATGCCTTCGAGCTGAATGGAATCGAACTCGAAAGTTTTCATTGAC
66 GCTGCTACCATGCAGTTGATACACCCTAGAGATGAATGGAATCAAACTCGAAAGTTTTCATTGAC
* *
81102 AGATAACCCTTATCGCCTTGAGCTATGTTGTAGATTAGGCTATGAGATATTTCTTTGTTGCTAAA
131 AGATAACCATTATCACCTTGAGCTATGTTGTAGATTAGGCTATGAGATATTTCTTTGTTGCTAAA
81167 TCGCAAC
196 TCGCAAC
* * **
81174 CAACCTAGGTCTTCTTCT-TGATTTAAAGACCTCGAT-TTAAACTTCTACC-AGAAAGTAGTTTC
1 CAACCTAGGTCTTCTTCTCGGA-TTAAAGACCTCGATATGAAAAGTCTACCGA-AAAGTAGTTTC
**
81236 TCGCTGCTACCATGCAGTTGATACACCCTAGAGATGAATGGAATCAAACTCGAAAGTTTTTGTTG
64 TCGCTGCTACCATGCAGTTGATACACCCTAGAGATGAATGGAATCAAACTCGAAAGTTTTCATTG
* *
81301 ACAGATAGCCATTCTCACCTTGAGCTATGTTGTA
129 ACAGATAACCATTATCACCTTGAGCTATGTTGTA
81335 AATGGTTCCT
Statistics
Matches: 137, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
200 1 0.01
201 106 0.77
202 30 0.22
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (202 bp):
CAACCTAGGTCTTCTTCTCGGATTAAAGACCTCGATATGAAAAGTCTACCGAAAAGTAGTTTCTC
GCTGCTACCATGCAGTTGATACACCCTAGAGATGAATGGAATCAAACTCGAAAGTTTTCATTGAC
AGATAACCATTATCACCTTGAGCTATGTTGTAGATTAGGCTATGAGATATTTCTTTGTTGCTAAA
TCGCAAC
Found at i:88075 original size:15 final size:15
Alignment explanation
Indices: 88057--88092 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
88047 AATTGTGAAA
88057 TAAATATAAAAAAGT
1 TAAATATAAAAAAGT
*
88072 TAAAAATAAAAAAGT
1 TAAATATAAAAAAGT
*
88087 TGAATA
1 TAAATA
88093 GAACAATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (15 bp):
TAAATATAAAAAAGT
Found at i:89956 original size:107 final size:107
Alignment explanation
Indices: 89768--89977 Score: 393
Period size: 107 Copynumber: 2.0 Consensus size: 107
89758 TTCATTTAAT
*
89768 TTTATATTAGATTAAATTATTTGACGTTAGATTTTTCACACTTCAGTCTATGAACATCTTAATTT
1 TTTATATTAGATTAAATTATTTGACGTTAGATTTTTCACACTTCAATCTATGAACATCTTAATTT
*
89833 AAGGAATAATTTAATTTGACTATCGCATTAAAATGCACAAGG
66 AAGGAATAATTCAATTTGACTATCGCATTAAAATGCACAAGG
89875 TTTATATTAGATTAAATTATTTGACGTTAGATTTTTCACACTTCAATCTATGAACATCTTAATTT
1 TTTATATTAGATTAAATTATTTGACGTTAGATTTTTCACACTTCAATCTATGAACATCTTAATTT
*
89940 AAGGAATAATTCAATTTGACTCTCGCATTAAAATGCAC
66 AAGGAATAATTCAATTTGACTATCGCATTAAAATGCAC
89978 GAGGATCCAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 100 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.40
Consensus pattern (107 bp):
TTTATATTAGATTAAATTATTTGACGTTAGATTTTTCACACTTCAATCTATGAACATCTTAATTT
AAGGAATAATTCAATTTGACTATCGCATTAAAATGCACAAGG
Found at i:90115 original size:141 final size:141
Alignment explanation
Indices: 89932--90191 Score: 376
Period size: 141 Copynumber: 1.8 Consensus size: 141
89922 CTATGAACAT
* *
89932 CTTAATTTAAGGAATAATTCAATTTGACTCTCGCATTAAAATGCACGAGGATCCATTTTGATTAT
1 CTTAATTTAAGGAATAATTCAATTTGACTCCCGCATTAAAATGCACGAGGATCCATTTTGATTAC
* * * *
89997 TCAATTCAATAATTGGATAAAATAAATTATGATTGATATTAGAGCCTCCATTTTAGATTCATTTT
66 TCAACTCAATAATAGGATAAAATAAATTATGATTAATATTAAAGCCTCCATTTTAGATTCATTTT
90062 CATTTTAGTCC
131 CATTTTAGTCC
* ** * * * *
90073 CTTAATTTAGGGAATAATTTGATTTGGCTCCCGCATTTAAATGCATGAGGATCTATTTTGATTAC
1 CTTAATTTAAGGAATAATTCAATTTGACTCCCGCATTAAAATGCACGAGGATCCATTTTGATTAC
* * *
90138 TCGACTCAATAATAGGTTAAAATAAATTATGATTAATATTAAATCCTCCATTTT
66 TCAACTCAATAATAGGATAAAATAAATTATGATTAATATTAAAGCCTCCATTTT
90192 TAGGTTTAGT
Statistics
Matches: 103, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
141 103 1.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.40
Consensus pattern (141 bp):
CTTAATTTAAGGAATAATTCAATTTGACTCCCGCATTAAAATGCACGAGGATCCATTTTGATTAC
TCAACTCAATAATAGGATAAAATAAATTATGATTAATATTAAAGCCTCCATTTTAGATTCATTTT
CATTTTAGTCC
Found at i:97729 original size:20 final size:20
Alignment explanation
Indices: 97704--97757 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
97694 TGAAATATGG
*
97704 GTGTATCAGTACATACA-AGA
1 GTGTATCGGTACATACATA-A
97724 GTGTATCGGTACATACATAA
1 GTGTATCGGTACATACATAA
97744 GTGTATCGGTACAT
1 GTGTATCGGTACAT
97758 CCCTTTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (20 bp):
GTGTATCGGTACATACATAA
Found at i:98323 original size:17 final size:18
Alignment explanation
Indices: 98301--98337 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
98291 GCAAAAATTA
98301 ATGAAG-TC-AATATAAAT
1 ATGAAGTTCAAAT-TAAAT
98318 ATGAAGTTCAAATTAAAT
1 ATGAAGTTCAAATTAAAT
98336 AT
1 AT
98338 TCAAACCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 9 0.50
19 3 0.17
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (18 bp):
ATGAAGTTCAAATTAAAT
Found at i:98738 original size:17 final size:18
Alignment explanation
Indices: 98716--98752 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
98706 GCAAAAATTA
98716 ATGAAG-TC-AATATAAAT
1 ATGAAGTTCAAAT-TAAAT
98733 ATGAAGTTCAAATTAAAT
1 ATGAAGTTCAAATTAAAT
98751 AT
1 AT
98753 TCAAACCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 9 0.50
19 3 0.17
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.32
Consensus pattern (18 bp):
ATGAAGTTCAAATTAAAT
Found at i:99440 original size:410 final size:415
Alignment explanation
Indices: 98067--99732 Score: 3038
Period size: 415 Copynumber: 4.0 Consensus size: 415
98057 TCAATTTTGA
98067 AAAATTACTCCCTTACTTTATTCTCCCCCTTTTTGTTAAATCAAAAAGACTCTAGAAAATGTTTA
1 AAAATTACTCCCTTACTTTATTCTCCCCCTTTTTGTTAAATCAAAAAGACTCTAGAAAATGTTTA
*
98132 AAGAAGATTTTTAAGAAAATAGCCAATTGTTATAAATAGATATAGATGTAGCTGCTAAGATCACA
66 AAGAAGATTTTTAAGAAAATAGCCAATTGATATAAATAGATATAGATGTAGCTGCTAAGATCACA
*
98197 ATCAAGAGAAAGATTAGTCATTAGTCCATAACCAATATTCATAAACAATATGTAAATTGGTAATT
131 ATCAAGAGAAAGATTAGTCATTAGTCCATAACCAATATTCATAAACAATATGTAAATTGGGAATT
98262 GGTCATATGAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTC
196 GGTCATATGAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTC
*
98327 AAATTAAATATTCAAACCATTCAAAAAAATATATCCAAACATCCAAAAACACACAAATCTAAAAC
261 AAATTAAATATTCAAACCATTCAAACAAATATATCCAAACATCCAAAAACACACAAATCTAAAAC
98392 ATTCAAAATGTTTTAACAATAAGTTCAAATTCAATCCAAGAAAACTAAGCAAGAAAAGGTCTAAT
326 ATTCAAAATGTTTTAACAATAAGTTCAAATTCAATCCAAGAAAACTAAGCAAGAAAAGGTCTAAT
98457 TATCCATAGGTGGATCGGGAGGAGG
391 TATCCATAGGTGGATCGGGAGGAGG
* *
98482 AAAATTACTCCCTTACTTTATTATCCCCCTTTTTGTTAAAACAAAAAGACTCTAGAAAATGTTTA
1 AAAATTACTCCCTTACTTTATTCTCCCCCTTTTTGTTAAATCAAAAAGACTCTAGAAAATGTTTA
*
98547 AAGAAGATTTTTAAGAAAATAGCTAATTGATATAAATAGATATAGATGTAGCTGCTAAGATCACA
66 AAGAAGATTTTTAAGAAAATAGCCAATTGATATAAATAGATATAGATGTAGCTGCTAAGATCACA
*
98612 ATCAAAAGAAAGATTAGTCATTAGTCCATAACCAATATTCATAAACAATATGTAAATTGGGAATT
131 ATCAAGAGAAAGATTAGTCATTAGTCCATAACCAATATTCATAAACAATATGTAAATTGGGAATT
*
98677 GGTCATATAAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTC
196 GGTCATATGAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTC
* *
98742 AAATTAAATATTCAAACCATTCATACAAATATATCCAAACATCCAAAAACAAACAAATCTAAAAC
261 AAATTAAATATTCAAACCATTCAAACAAATATATCCAAACATCCAAAAACACACAAATCTAAAAC
*
98807 ATTCAAAATGTTTTAACAATAAGTTCAAATTCAATCCAAGAAAACTAAACAAGAAAAGGTCTAAT
326 ATTCAAAATGTTTTAACAATAAGTTCAAATTCAATCCAAGAAAACTAAGCAAGAAAAGGTCTAAT
98872 TATCCATAGGTGGATCGGGAGGAGG
391 TATCCATAGGTGGATCGGGAGGAGG
*
98897 AAAATTACTCCTTTACTTTATTCTCCCCCTTTTTGTTAAATCAAAAAGACTCTAGAAAATGTTTA
1 AAAATTACTCCCTTACTTTATTCTCCCCCTTTTTGTTAAATCAAAAAGACTCTAGAAAATGTTTA
* * *
98962 AAGAAGGTTTTTAAGAAAATAGTCAATTGATATAAATAGATATAGATGTAGCTACTAAGATCACA
66 AAGAAGATTTTTAAGAAAATAGCCAATTGATATAAATAGATATAGATGTAGCTGCTAAGATCACA
99027 ATCAAGAGAAAGATTAGTCATTAGTCCATAACCAATATTCATAAACAATATGTAAATTGGGAATT
131 ATCAAGAGAAAGATTAGTCATTAGTCCATAACCAATATTCATAAACAATATGTAAATTGGGAATT
99092 GGTCATATGAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTC
196 GGTCATATGAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTC
99157 AAATT-AATATTCAAACCATTCAAAC-AA-ATATCCAAACATCCAAAAACACACAAATCTAAAAC
261 AAATTAAATATTCAAACCATTCAAACAAATATATCCAAACATCCAAAAACACACAAATCTAAAAC
99219 ATTC-AAATGTTTTAACAATAAGTTCAAATTCAATCCAAGAAAACTAAGCAAGAAAAGGTCTAAT
326 ATTCAAAATGTTTTAACAATAAGTTCAAATTCAATCCAAGAAAACTAAGCAAGAAAAGGTCTAAT
99283 TATCCATA-GTGGATCGGGAGGAGG
391 TATCCATAGGTGGATCGGGAGGAGG
99307 AAAATTACTCCCTTACTTTATTCTCCCCCTTTTTGTTAAATCAAAAAGACTCTAGAAAATGTTTA
1 AAAATTACTCCCTTACTTTATTCTCCCCCTTTTTGTTAAATCAAAAAGACTCTAGAAAATGTTTA
99372 AAGAAGATTTTTAAGAAAATAGCCAATTGATATAAATAGATATAGATGTAGCTGCTAAGATCACA
66 AAGAAGATTTTTAAGAAAATAGCCAATTGATATAAATAGATATAGATGTAGCTGCTAAGATCACA
*
99437 ATCAAGAGAAAGATTAGTCATTAGTCTATAACCAATATTCATAAACAATATGTAAATTGGGAATT
131 ATCAAGAGAAAGATTAGTCATTAGTCCATAACCAATATTCATAAACAATATGTAAATTGGGAATT
*
99502 GGTCATATGAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTA
196 GGTCATATGAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTC
99567 AAATTAAATATTCAAACCATTCAAACAAATATATCCAAACATCCAAAAACACACAAATCT-AAAC
261 AAATTAAATATTCAAACCATTCAAACAAATATATCCAAACATCCAAAAACACACAAATCTAAAAC
*
99631 ATTCAAATGTTTTAACATGTTTTAACAATAAGTTCAAATTCAATCCAAGAAAACTATGCAAGAAA
326 ATTC--A------AA-ATGTTTTAACAATAAGTTCAAATTCAATCCAAGAAAACTAAGCAAGAAA
*
99696 AGGTCTAATTATCCATAGGTGGATCAGGAGGAGG
382 AGGTCTAATTATCCATAGGTGGATCGGGAGGAGG
99730 AAA
1 AAA
99733 TGTGCTCGCA
Statistics
Matches: 1206, Mismatches: 31, Indels: 20
0.96 0.02 0.02
Matches are distributed among these distances:
410 275 0.23
411 87 0.07
412 48 0.04
413 32 0.03
414 19 0.02
415 660 0.55
421 2 0.00
422 65 0.05
423 18 0.01
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (415 bp):
AAAATTACTCCCTTACTTTATTCTCCCCCTTTTTGTTAAATCAAAAAGACTCTAGAAAATGTTTA
AAGAAGATTTTTAAGAAAATAGCCAATTGATATAAATAGATATAGATGTAGCTGCTAAGATCACA
ATCAAGAGAAAGATTAGTCATTAGTCCATAACCAATATTCATAAACAATATGTAAATTGGGAATT
GGTCATATGAAATCTAATATACAGATGATGCAAAAATTAATGAAGTCAATATAAATATGAAGTTC
AAATTAAATATTCAAACCATTCAAACAAATATATCCAAACATCCAAAAACACACAAATCTAAAAC
ATTCAAAATGTTTTAACAATAAGTTCAAATTCAATCCAAGAAAACTAAGCAAGAAAAGGTCTAAT
TATCCATAGGTGGATCGGGAGGAGG
Found at i:101068 original size:13 final size:13
Alignment explanation
Indices: 101050--101083 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
101040 ATGGGAAAAA
* *
101050 TTTGAAAACTATT
1 TTTGAAAACAATG
101063 TTTGAAAACAATG
1 TTTGAAAACAATG
101076 TTTGAAAA
1 TTTGAAAA
101084 ATCATAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:101613 original size:21 final size:21
Alignment explanation
Indices: 101543--101619 Score: 86
Period size: 23 Copynumber: 3.6 Consensus size: 21
101533 AACCCGACGG
* **
101543 GTGTATCGGTACAC-TTGTTA
1 GTGTATCGATACACATTCATA
101563 GTGTATCGATACACATTCA-A
1 GTGTATCGATACACATTCATA
101583 GGAATGTATCGATACACATTCATA
1 -G--TGTATCGATACACATTCATA
101607 GTGTATCGATACA
1 GTGTATCGATACA
101620 TAGCGAGGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
20 14 0.29
21 15 0.31
23 19 0.39
24 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (21 bp):
GTGTATCGATACACATTCATA
Found at i:117320 original size:32 final size:32
Alignment explanation
Indices: 117274--117346 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
117264 CTACACAACC
*
117274 CAAACAACATATGTATTGGATAACCCTGCCAG
1 CAAACAACAAATGTATTGGATAACCCTGCCAG
117306 CAAACAACAAATGTATTGGATAACCCTGCCAG
1 CAAACAACAAATGTATTGGATAACCCTGCCAG
117338 CAAACAACA
1 CAAACAACA
117347 TATAACATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.18
Consensus pattern (32 bp):
CAAACAACAAATGTATTGGATAACCCTGCCAG
Found at i:122171 original size:2 final size:2
Alignment explanation
Indices: 122164--122201 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
122154 TATACCCATA
122164 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
122202 GCATATGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123746 original size:102 final size:99
Alignment explanation
Indices: 123598--123998 Score: 277
Period size: 102 Copynumber: 3.9 Consensus size: 99
123588 TAAGACATGA
* * *
123598 ACATTTGATATTGTTTTTCCTCAAAACAAACTTCGTCTCTCTTGAGACAGTTTCCTTCTAAAAAC
1 ACATTTGATATTGTTTTT-CTCAAAACAAATTTCGTCTCGC-TGAGACAATTTCCTTC-AAAAAC
*
123663 AAATTTTGAAATTGTTTCACTTGAAACAAAATTGATG
63 AAATTTTGAAATTGTTTCACTTGAAACAAAATTGATC
* * * * * ** * *
123700 ACATTTGATATTGTTTTTACTCGAAGCAAATTTCATCTCGCATGAGATAATTCCCTTGGAACATA
1 ACATTTGATATTGTTTTT-CTCAAAACAAATTTCGTCTCGC-TGAGACAATTTCCTTCAAAAACA
* * *
123765 AATTTT-AAAGTTATTTTACTTGAAACAAAATTAATC
64 AATTTTGAAA-TTGTTTCACTTGAAACAAAATTGATC
* * * * *
123801 TCACTTGATATTGTTTCTT-TCAAAACAAATTTTGTCTCGCTAGAAACGATTTTTCC-TCAAAAT
1 ACATTTGATATTGTTT-TTCTCAAAACAAATTTCGTCTCGCT-GAGAC-A-ATTTCCTTCAAAA-
* * *
123864 ACAAAATTTGGAAATTGTTTCACTTGAAACATAATTGAAAC
61 AC-AAATTTTGAAATTGTTTCACTTGAAACAAAATTG-ATC
* ** * * * * *
123905 ACAAATCTTTGAGATTGTTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCATGAAA
1 AC--A--TTTGATATTGTTTTTCTCAAAACAAATTTCGTCTCGC-TGAGACAATTTC-CTTCAAA
* * * * *
123970 CATAAACTTTGAGATTGTTTCTCTTGAAA
60 AACAAATTTTGAAATTGTTTCACTTGAAA
123999 TAAATTTTGT
Statistics
Matches: 229, Mismatches: 53, Indels: 30
0.73 0.17 0.10
Matches are distributed among these distances:
99 1 0.00
100 23 0.10
101 50 0.22
102 54 0.24
103 25 0.11
104 6 0.03
106 27 0.12
107 5 0.02
108 37 0.16
109 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (99 bp):
ACATTTGATATTGTTTTTCTCAAAACAAATTTCGTCTCGCTGAGACAATTTCCTTCAAAAACAAA
TTTTGAAATTGTTTCACTTGAAACAAAATTGATC
Found at i:123982 original size:65 final size:66
Alignment explanation
Indices: 123898--124168 Score: 384
Period size: 67 Copynumber: 4.1 Consensus size: 66
123888 TGAAACATAA
* * *
123898 TTGAAACACAAATCTTTGAGATTGTTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
1 TTGAAACATAAAACTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
123963 C
66 C
* * * *
123964 ATGAAACAT-AAACTTTGAGATTGTTTCTCTTGAAATAAATTTTGTTTCTCTTGAGACAATTTCT
1 TTGAAACATAAAACTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
124028 C
66 C
* * * *
124029 TTGAAACATAAAAACATTGAGAATGTTTATCTTGAAACAAATTTTGTCTCTCTTTAGACAGTTTC
1 TTGAAACAT-AAAACTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
124094 TC
65 TC
* * *
124096 TTGAAACATAAAAATATTGAGATTGTTTCCCTTGAAACAAA-TTTGTCTCTCTTGAGATAGTTTC
1 TTGAAACATAAAACT-TTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
124160 TC
65 TC
124162 TTGAAAC
1 TTGAAAC
124169 TTTATCCCTA
Statistics
Matches: 180, Mismatches: 22, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
65 59 0.33
66 41 0.23
67 80 0.44
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (66 bp):
TTGAAACATAAAACTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT
C
Found at i:124416 original size:137 final size:137
Alignment explanation
Indices: 124168--124579 Score: 574
Period size: 137 Copynumber: 3.0 Consensus size: 137
124158 TCTCTTGAAA
* *
124168 CTTTATCCCTAAAGATGGTCAGACATCCTCATCACATAGGAATTGTGTCATCCACCGACCAGATC
1 CTTTATCCCTAAAGATGGTCAGACGTCCTCATCACATAGGAATAGTGTCATCCACCGACCAGATC
* * * *
124233 TCCTCATCACGTAGGAGTAGTGTCAACCTTAGATAACCAGACTTCCTCATCATGTAGGAATCGTG
66 TCCTCATCACGTAGGAGCAGCGTCAACCTTAGATAACCAGACTTCCTCATCACGTAGGAATCATG
124298 TTATCTC
131 TTATCTC
* * ** **
124305 CTTTATCCTTAAAGATGGTCAGACGTTCTCATCATGTAGGAACCGTGTCATCCACCGACCAGATC
1 CTTTATCCCTAAAGATGGTCAGACGTCCTCATCACATAGGAATAGTGTCATCCACCGACCAGATC
* * * * *
124370 TCCTCATCGCGTAGGAGCAGCGTTAACCTTAGATAGCCAGAATTCCTCATCGCGTAGGAATCATG
66 TCCTCATCACGTAGGAGCAGCGTCAACCTTAGATAACCAGACTTCCTCATCACGTAGGAATCATG
124435 TTATCTC
131 TTATCTC
* * * * *
124442 CATTTATCCCTAAAGATGGGCAGTCGTCCTCATCACCTAGGAATAGTGTCATCCACTGACTAGAT
1 C-TTTATCCCTAAAGATGGTCAGACGTCCTCATCACATAGGAATAGTGTCATCCACCGACCAGAT
* * * *
124507 CTCCTCATCACGTAGGA-CCGCGTCACCCTTAGATAACCAGACTTCCTCATCACGTATGAACCAT
65 CTCCTCATCACGTAGGAGCAGCGTCAACCTTAGATAACCAGACTTCCTCATCACGTAGGAATCAT
124571 GTTATCTC
130 GTTATCTC
124579 C
1 C
124580 AAATTTACCT
Statistics
Matches: 239, Mismatches: 35, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
137 170 0.71
138 69 0.29
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (137 bp):
CTTTATCCCTAAAGATGGTCAGACGTCCTCATCACATAGGAATAGTGTCATCCACCGACCAGATC
TCCTCATCACGTAGGAGCAGCGTCAACCTTAGATAACCAGACTTCCTCATCACGTAGGAATCATG
TTATCTC
Found at i:124773 original size:3 final size:3
Alignment explanation
Indices: 124765--124808 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
124755 CGGGTCATAA
*
124765 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
124809 ATTTATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:125509 original size:25 final size:26
Alignment explanation
Indices: 125480--125530 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
125470 AAATGAAAAA
125480 AAGAAAAGA-AAGAGAGAGAAA-ATAC
1 AAGAAAAGAGAAG-GAGAGAAACATAC
*
125505 AAGAAAATAGAAGGAGAGAAACATAC
1 AAGAAAAGAGAAGGAGAGAAACATAC
125531 CTTGGTCGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.65, C:0.06, G:0.24, T:0.06
Consensus pattern (26 bp):
AAGAAAAGAGAAGGAGAGAAACATAC
Found at i:126458 original size:15 final size:16
Alignment explanation
Indices: 126429--126458 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
126419 ATTTCACATA
126429 TTTCCATTCGCATTTG
1 TTTCCATTCGCATTTG
126445 TTTCCATT-GCATTT
1 TTTCCATTCGCATTT
126459 CTTTATCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.23, G:0.10, T:0.53
Consensus pattern (16 bp):
TTTCCATTCGCATTTG
Found at i:131292 original size:28 final size:27
Alignment explanation
Indices: 131256--131319 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
131246 AAAAAGTTTG
* * *
131256 AATAGTTTAGTTACCTATTTTGGCATAA
1 AATATTTTAGGTACCTATTTTAGCA-AA
* *
131284 AATATTTTAGGTACTTATTTTATCAAA
1 AATATTTTAGGTACCTATTTTAGCAAA
131311 AATATTTTA
1 AATATTTTA
131320 AATACTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
27 11 0.35
28 20 0.65
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (27 bp):
AATATTTTAGGTACCTATTTTAGCAAA
Found at i:132177 original size:124 final size:121
Alignment explanation
Indices: 131922--132180 Score: 302
Period size: 124 Copynumber: 2.1 Consensus size: 121
131912 TCATATATAG
* * * *
131922 TGGCGTTTATTCAAAAAACGCCACAACAGAGTAGTACTTTAGCGGCGTTGTTAGACAAACGTTGC
1 TGGCATTTTTTCAAAAAACGCCACAACAGAGTAGTACTTTAGCGGCGTAGTTAGACAAACGCTGC
* * * * * *
131987 GATAGGTTTCATATATAGTGGCGTTTCTATACAAACGCCGCAATAAGATTAATTTA
66 AATAGGTTTCATATATAGCGGCGTTTCTAGACAAACGACGCAATAACATTAATTAA
* *
132043 TAGAGCCATTTTTTCAACAAACGCCACAACATAGTAGTACTTTAGCGGCGTAGTTAGACAAACGC
1 T-G-G-CATTTTTTCAAAAAACGCCACAACAGAGTAGTACTTTAGCGGCGTAGTTAGACAAACGC
* * * * **
132108 TGCAATAGGTTTCATATTTAGCGGTGTTTTTAGACAAACGACGCTATTCCCATGTAATGTAA
63 TGCAATAGGTTTCATATATAGCGGCGTTTCTAGACAAACGACGC-AATAACAT-TAAT-TAA
132170 TGGCATTTTTT
1 TGGCATTTTTT
132181 GTAATAAACG
Statistics
Matches: 114, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
121 1 0.01
122 1 0.01
123 1 0.01
124 98 0.86
125 5 0.04
126 5 0.04
127 3 0.03
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (121 bp):
TGGCATTTTTTCAAAAAACGCCACAACAGAGTAGTACTTTAGCGGCGTAGTTAGACAAACGCTGC
AATAGGTTTCATATATAGCGGCGTTTCTAGACAAACGACGCAATAACATTAATTAA
Found at i:132205 original size:43 final size:42
Alignment explanation
Indices: 132158--132248 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 42
132148 ACGCTATTCC
132158 CATGTAATGTAATGGCATTTTT-TGTAATAAACGCCGCAATAGT
1 CATGTAATGTAATGGCATTTTTAT-T-ATAAACGCCGCAATAGT
* * * * *
132201 CATGTACTTTAGTGGTATTTTTATTATAAATGCCGCAATAGT
1 CATGTAATGTAATGGCATTTTTATTATAAACGCCGCAATAGT
132243 CATGTA
1 CATGTA
132249 TGCTTCCTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 22 0.52
43 19 0.45
44 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (42 bp):
CATGTAATGTAATGGCATTTTTATTATAAACGCCGCAATAGT
Found at i:137635 original size:22 final size:22
Alignment explanation
Indices: 137610--137667 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
137600 AAAATATAGT
*
137610 AAAGTATATAGTAAAAATATTA
1 AAAGTATATAGTAAAAATAATA
* *
137632 AAAGTACATA-TAGATAATAATA
1 AAAGTATATAGTA-AAAATAATA
137654 AAA-TATAGTAGTAA
1 AAAGTATA-TAGTAA
137668 TATAGAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 5 0.17
22 22 0.76
23 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.29
Consensus pattern (22 bp):
AAAGTATATAGTAAAAATAATA
Found at i:139455 original size:105 final size:104
Alignment explanation
Indices: 139233--139756 Score: 509
Period size: 105 Copynumber: 5.0 Consensus size: 104
139223 AGTATTGTTC
* * * *
139233 TGAGTCCAATATCC-TCTGCTGTGAAGTTGAGATTGGTTCTGGAACCGGGAAATTGTTTATTGAC
1 TGAGTCCAATATCCTTC-GCTGTGAAGTTGAAATTGG-CCTGGAACTGGGAAATTG-TTGTTGAC
** * * * * *
139297 AGTCAGCCGCCCCTTCGCTGCGAAGTTGAGCTTGTGCTGTCT
63 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
139339 TGGGTCCAATATCCTTCGCTGTGAAGTTGAAACTGGCCCTGGAACTGGGAAATTGTTGTTGACAA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG-CCTGGAACTGGGAAATTGTTGTTGACAA
*
139404 CCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * *
139444 TGAGTCCAATATCCTTCGTTGTGAAGTTGAGATTGG-CT----C--CGAAATTGTTTGTTGACAG
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCTGGAACTGGGAAATTG-TTGTTGACAA
* * * * *
139502 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
65 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
139542 TGGGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTGTTGTTGACAA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG-CCTGGAACTGGGAAATTGTTGTTGACAA
139607 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * ** * * * *
139647 T-AGGTAGCATGATATCCTCCG-TCGTG--G--AAAATCAGCTTTGAAATTGGAAAGTTGTTCGT
1 TGA-GT-CCA--ATATCCTTCGCT-GTGAAGTTGAAATTGGCCTGGAACTGGGAAA-TTGTT-GT
*
139706 TGACAACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
59 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
139752 TGAGT
1 TGAGT
139757 GGCACGATAT
Statistics
Matches: 351, Mismatches: 49, Indels: 37
0.80 0.11 0.08
Matches are distributed among these distances:
97 7 0.02
98 75 0.21
99 1 0.00
100 2 0.01
103 12 0.03
104 11 0.03
105 170 0.48
106 57 0.16
107 3 0.01
108 13 0.04
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (104 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCTGGAACTGGGAAATTGTTGTTGACAAC
CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:139527 original size:203 final size:203
Alignment explanation
Indices: 139281--139647 Score: 680
Period size: 203 Copynumber: 1.8 Consensus size: 203
139271 CTGGAACCGG
139281 GAAATTGTTTATTGACAGTCAGCCGCCCCTTCGCTGCGAAGTTGAGCTTGTGCTGTCTTGGGTCC
1 GAAATTGTTTATTGACAGTCAGCCGCCCCTTCGCTGCGAAGTTGAGCTTGTGCTGTCTTGGGTCC
* *
139346 AATATCCTTCGCTGTGAAGTTGAAACTGGCCCTGGAACTGGGAAATTGTTGTTGACAACCAACCG
66 AATATCCTCCGCTGTGAAGTTGAAACTGGCCCTGAAACTGGGAAATTGTTGTTGACAACCAACCG
139411 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAGA
131 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAGA
139476 TTGGCTCC
196 TTGGCTCC
* *
139484 GAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCC
1 GAAATTGTTTATTGACAGTCAGCCGCCCCTTCGCTGCGAAGTTGAGCTTGTGCTGTCTTGGGTCC
* *
139549 AATATCCTCCGCTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTGTTGTTGACAACCAGCCG
66 AATATCCTCCGCTGTGAAGTTGAAACTGGCCCTGAAACTGGGAAATTGTTGTTGACAACCAACCG
139614 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
131 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
139648 AGGTAGCATG
Statistics
Matches: 158, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
203 158 1.00
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (203 bp):
GAAATTGTTTATTGACAGTCAGCCGCCCCTTCGCTGCGAAGTTGAGCTTGTGCTGTCTTGGGTCC
AATATCCTCCGCTGTGAAGTTGAAACTGGCCCTGAAACTGGGAAATTGTTGTTGACAACCAACCG
TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAGA
TTGGCTCC
Found at i:139542 original size:98 final size:97
Alignment explanation
Indices: 139387--139647 Score: 297
Period size: 98 Copynumber: 2.6 Consensus size: 97
139377 CTGGAACTGG
* * *
139387 GAAATTGTTGTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCA
1 GAAATTGTTGTTGACAACCAACCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTTGAGTCCA
* * *
139452 ATATCCTTCGTTGTGAAGTTGAGATTGGCTCC
66 ATATCCTCCGCTGTGAAGTTGAAATTGGCTCC
** * * *
139484 GAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCC
1 GAAATTG-TTGTTGACAACCAACCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTTGAGTCC
*
139549 AATATCCTCCGCTGTGAAGTTGAAATTGGCCCTGAAACTGG
65 AATATCCTCCGCTGTGAAGTTGAAATTGG--CT----C--C
* * * *
139590 GAAATTGTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
1 GAAATTGTTGTTGACAACCAACCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTT
139648 AGGTAGCATG
Statistics
Matches: 137, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
97 7 0.05
98 75 0.55
100 2 0.01
104 1 0.01
105 45 0.33
106 7 0.05
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (97 bp):
GAAATTGTTGTTGACAACCAACCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTTGAGTCCA
ATATCCTCCGCTGTGAAGTTGAAATTGGCTCC
Found at i:140509 original size:12 final size:11
Alignment explanation
Indices: 140487--140525 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
140477 TGAACCCACC
*
140487 TTTTTGTTCTT
1 TTTTTTTTCTT
140498 TTTTTTTCTCTT
1 TTTTTTT-TCTT
140510 GTTTTTTTTCTT
1 -TTTTTTTTCTT
140522 TTTT
1 TTTT
140526 CGATTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 10 0.40
12 8 0.32
13 7 0.28
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:140599 original size:49 final size:51
Alignment explanation
Indices: 140521--140618 Score: 137
Period size: 49 Copynumber: 1.9 Consensus size: 51
140511 TTTTTTTTCT
* * *
140521 TTTTTCGATTTTTTTCAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACG
1 TTTTTCGATTTTTTT-AACTTAGGACGCCCCTTCGGGTTTTCACCCTAAACG
*
140573 TTTTTC-ATTTTTTT-ACTTAGGACGCCCCTTCGGGTTTTCATCCTAA
1 TTTTTCGATTTTTTTAACTTAGGACGCCCCTTCGGGTTTTCACCCTAA
140619 GCGAAGTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
49 28 0.67
51 8 0.19
52 6 0.14
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (51 bp):
TTTTTCGATTTTTTTAACTTAGGACGCCCCTTCGGGTTTTCACCCTAAACG
Found at i:151285 original size:24 final size:22
Alignment explanation
Indices: 151258--151350 Score: 64
Period size: 24 Copynumber: 3.9 Consensus size: 22
151248 ACAAATAACT
151258 AAAGTATATAGTAATAAAATATTA
1 AAAGTATATA-TAATAAAATA-TA
* *
151282 AAAGTACATATAGATAATA-ATA
1 AAAGTATATATA-ATAAAATATA
151304 AAA-TATAGTAGTAATATAGAATATA
1 AAAGTATA-TA-TAATA-A-AATATA
*
151329 AACATGTATATATATTAAAATA
1 AA-A-GTATATATAATAAAATA
151351 CCGAATGGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
21 3 0.05
22 10 0.18
23 6 0.11
24 19 0.35
25 6 0.11
26 5 0.09
27 2 0.04
28 4 0.07
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (22 bp):
AAAGTATATATAATAAAATATA
Found at i:167410 original size:21 final size:22
Alignment explanation
Indices: 167384--167450 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 22
167374 TGTAAATTTG
167384 CACCGAAGTGCCACATAATTGT
1 CACCGAAGTGCCACATAATTGT
**
167406 C-CCGAAGAACCACATAGATT-T
1 CACCGAAGTGCCACATA-ATTGT
* *
167427 GCACCAAAGTGCCACATATTTGT
1 -CACCGAAGTGCCACATAATTGT
167450 C
1 C
167451 TCGGAGGACA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
21 14 0.40
22 8 0.23
23 13 0.37
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.22
Consensus pattern (22 bp):
CACCGAAGTGCCACATAATTGT
Done.