Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001376.1 Hibiscus syriacus cultivar Beakdansim tig00002688_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: 67224
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:21628 original size:9 final size:8
Alignment explanation
Indices: 21616--21737 Score: 88
Period size: 8 Copynumber: 14.4 Consensus size: 8
21606 AAAACATAGA
21616 AAAAAAAG
1 AAAAAAAG
*
21624 TAAAAACAGAA
1 -AAAAA-A-AG
21635 AAAAAAAG
1 AAAAAAAG
*
21643 AGAAAAAG
1 AAAAAAAG
21651 -AAAAAAG
1 AAAAAAAG
21658 AAAAAGAA-
1 AAAAA-AAG
21666 AAAAGGAGAGAG
1 AAAA--A-A-AG
21678 AAAAAGAAG
1 AAAAA-AAG
21687 AAAAGAAAG
1 AAAA-AAAG
* *
21696 AGAAAATG
1 AAAAAAAG
*
21704 AGAAAAAG
1 AAAAAAAG
21712 AAAAAAAG
1 AAAAAAAG
21720 AAAAAAAG
1 AAAAAAAG
21728 -AAAAAAG
1 AAAAAAAG
21735 AAA
1 AAA
21738 GAGGAAAATA
Statistics
Matches: 95, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
7 13 0.14
8 43 0.45
9 20 0.21
10 13 0.14
11 2 0.02
12 4 0.04
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:21630 original size:20 final size:19
Alignment explanation
Indices: 21605--21656 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
21595 GAGATATAGA
*
21605 AAAAACATAGAAAAAAAAGT
1 AAAAACAGA-AAAAAAAAGT
21625 AAAAACAGAAAAAAAAAG-
1 AAAAACAGAAAAAAAAAGT
21643 AGAAAA-AGAAAAAA
1 A-AAAACAGAAAAAA
21657 GAAAAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 9 0.30
19 13 0.43
20 8 0.27
ACGTcount: A:0.81, C:0.04, G:0.12, T:0.04
Consensus pattern (19 bp):
AAAAACAGAAAAAAAAAGT
Found at i:21641 original size:13 final size:13
Alignment explanation
Indices: 21618--21737 Score: 90
Period size: 13 Copynumber: 9.2 Consensus size: 13
21608 AACATAGAAA
21618 AAAAAGTAAAAACAG
1 AAAAAG-AAAAA-AG
*
21633 AAAAA-AAAAGAG
1 AAAAAGAAAAAAG
21645 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
21658 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
* *
21671 -GAGAGAGAAAAAG
1 AAAAAGA-AAAAAG
*
21684 AAGAAA-AGAAAGAG
1 AA-AAAGA-AAAAAG
*
21698 AAAATGAGAAAAAG
1 AAAAAGA-AAAAAG
*
21712 -AAAA-AAAGAA-
1 AAAAAGAAAAAAG
21722 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
21735 AAA
1 AAA
21738 GAGGAAAATA
Statistics
Matches: 85, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
11 8 0.09
12 17 0.20
13 37 0.44
14 16 0.19
15 7 0.08
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:21648 original size:8 final size:8
Alignment explanation
Indices: 21637--21735 Score: 75
Period size: 7 Copynumber: 12.9 Consensus size: 8
21627 AAACAGAAAA
21637 AAAAAGAG
1 AAAAAGAG
21645 -AAAA-AG
1 AAAAAGAG
21651 AAAAA-AG
1 AAAAAGAG
21658 AAAAAGA-
1 AAAAAGAG
21665 AAAAAG-G
1 AAAAAGAG
* * *
21672 AGAGAGAA
1 AAAAAGAG
*
21680 AAAGAAGAA
1 AAA-AAGAG
21689 AAGAAAGAG
1 AA-AAAGAG
*
21698 AAAATGAG
1 AAAAAGAG
*
21706 AAAAAGAA
1 AAAAAGAG
*
21714 AAAAAGAA
1 AAAAAGAG
21722 AAAAAGA-
1 AAAAAGAG
21729 AAAAAGA
1 AAAAAGA
21736 AAGAGGAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
6 2 0.03
7 32 0.42
8 29 0.38
9 12 0.16
10 1 0.01
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (8 bp):
AAAAAGAG
Found at i:21655 original size:33 final size:32
Alignment explanation
Indices: 21617--21745 Score: 122
Period size: 34 Copynumber: 4.0 Consensus size: 32
21607 AAACATAGAA
21617 AAAAAAGTAAAAACAGAAAAAA-AAAGAGAAAAAG
1 AAAAAAG--AAAA-AGAAAAAAGAAAGAGAAAAAG
*
21651 AAAAAAGAAAAAGAAAAAAGGAGAGAGAAAAAG
1 AAAAAAGAAAAAGAAAAAA-GAAAGAGAAAAAG
* * *
21684 AAGAAAAGAAAGAGAAAATGAGAAAAAG-AAAA-
1 AA-AAAAGAAAAAGAAAA-AAGAAAGAGAAAAAG
* *
21716 AAAGAA-AAAAAGAAAAAAGAAAGAGGAAAA
1 AAAAAAGAAAAAGAAAAAAGAAAGAGAAAAA
21746 TAGACAGATC
Statistics
Matches: 81, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
29 7 0.09
30 13 0.16
31 11 0.14
32 6 0.07
33 17 0.21
34 26 0.32
35 1 0.01
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.02
Consensus pattern (32 bp):
AAAAAAGAAAAAGAAAAAAGAAAGAGAAAAAG
Found at i:21744 original size:14 final size:14
Alignment explanation
Indices: 21633--21745 Score: 67
Period size: 14 Copynumber: 8.1 Consensus size: 14
21623 GTAAAAACAG
21633 AAAA-AAAAA-GAGA
1 AAAAGAAAAAGGA-A
*
21646 AAAAGAAAAAAG-A
1 AAAAGAAAAAGGAA
21659 AAAAGAAAAAAGG-A
1 AAAAG-AAAAAGGAA
* *
21673 GAGAGAAAAA-GAA
1 AAAAGAAAAAGGAA
*
21686 GAAAAGAAAGA-GAA
1 -AAAAGAAAAAGGAA
* *
21700 AATGAGAAAAAGAAA
1 AA-AAGAAAAAGGAA
*
21715 AAAAGAAAAAAAGAA
1 AAAAG-AAAAAGGAA
*
21730 AAAAGAAAGAGGAA
1 AAAAGAAAAAGGAA
21744 AA
1 AA
21746 TAGACAGATC
Statistics
Matches: 78, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
12 1 0.01
13 18 0.23
14 42 0.54
15 17 0.22
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (14 bp):
AAAAGAAAAAGGAA
Found at i:22418 original size:28 final size:28
Alignment explanation
Indices: 22378--22439 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
22368 GCGAGAAGAC
*
22378 ACCTGAAACACATTACCTCCCCAAATTA
1 ACCTGAAACACATTACCTCCCCAAATCA
* * *
22406 ACCTGAAACACATTATCTTCCCAAGTCA
1 ACCTGAAACACATTACCTCCCCAAATCA
22434 ACCTGA
1 ACCTGA
22440 GCCTTTTATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.37, C:0.34, G:0.06, T:0.23
Consensus pattern (28 bp):
ACCTGAAACACATTACCTCCCCAAATCA
Found at i:23807 original size:43 final size:42
Alignment explanation
Indices: 23754--24183 Score: 360
Period size: 43 Copynumber: 10.0 Consensus size: 42
23744 AGAAACGAGT
*
23754 TTGAGGGACCATCGTGATATGTAGGGGTTCCTTGAAGAAAAGC
1 TTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGAAAA-C
* * * * *
23797 TTGAGAGACCATCGTGATATGTAGGGGTTTCTCGA-GGACAC
1 TTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGAAAAC
* *
23838 GTTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATCACACAC
1 --TTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGA-AAAC
* * * * *
23883 TTGAGGGACCAACGAGATATGTAGGGGTTCTTTGGTGATAA-
1 TTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGAAAAC
* ** * * * * * *
23924 TTAAGAAACTAAGCTTGATTTTTAGGGGTTTCTTGATGAAAAGC
1 TTGAGGGAC-CATCGTGATATGTAGGGGTTCCTTGATGAAAA-C
** * * *
23968 TTGAGAAACCATCGTGATATGTAGGGGTTTCTTGAGGATAAC
1 TTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGAAAAC
* *
24010 TTTGAGGGACCATCGTGATATGTAGGGGTTCCTTAAAGAAAATC
1 -TTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGAAAA-C
* * * * **
24054 TTGAGAGACCATCGTGATATGTAGGGGGTTTCTTGAGGACGAGT
1 TTGAGGGACCATCGTGATATGTA-GGGGTTCCTTGATGA-AAAC
* * * *
24098 TTGAGGGACTATCATGATATGTAGGGGTTCATTGATGACATAC
1 TTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGA-AAAC
* * * *
24141 TTGAGGGACCAACGAGATATGTAGGGGTTCCTTGGTGACAAC
1 TTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGAAAAC
24183 T
1 T
24184 AAGAAACTGA
Statistics
Matches: 307, Mismatches: 69, Indels: 23
0.77 0.17 0.06
Matches are distributed among these distances:
41 7 0.02
42 30 0.10
43 224 0.73
44 41 0.13
45 5 0.02
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (42 bp):
TTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGAAAAC
Found at i:23902 original size:86 final size:85
Alignment explanation
Indices: 23751--24174 Score: 444
Period size: 86 Copynumber: 4.9 Consensus size: 85
23741 ATAAGAAACG
*
23751 AGTTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGAAGAAAAGCTTGAGAGACCATCGTGATA
1 AGTTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGAAAAGCTTGAGAGACCATCGTGATA
*
23816 TGTAGGGGTTTCTCGAGGAC
66 TGTAGGGGTTTCTTGAGGAC
* * * * *
23836 ACGTTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATCACACA-CTTGAGGGACCAACGAGA
1 A-GTTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGA-AAAGCTTGAGAGACCATCGTGA
*
23900 TATGTAGGGG-TTCTTTG-GTGAT
64 TATGTAGGGGTTTC-TTGAG-GAC
* * ** * * * * * * *
23922 A-ATTAAGAAACTAAGCTTGATTTTTAGGGGTTTCTTGATGAAAAGCTTGAGAAACCATCGTGAT
1 AGTTTGAGGGAC-CATCGTGATATGTAGGGGTTCCTTGATGAAAAGCTTGAGAGACCATCGTGAT
*
23986 ATGTAGGGGTTTCTTGAGGATA
65 ATGTAGGGGTTTCTTGAGGA-C
* * * *
24008 ACTTTGAGGGACCATCGTGATATGTAGGGGTTCCTTAAAGAAAATCTTGAGAGACCATCGTGATA
1 AGTTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGAAAAGCTTGAGAGACCATCGTGATA
24073 TGTAGGGGGTTTCTTGAGGAC
66 TGTA-GGGGTTTCTTGAGGAC
* * * * * * *
24094 GAGTTTGAGGGACTATCATGATATGTAGGGGTTCATTGATGACATA-CTTGAGGGACCAACGAGA
1 -AGTTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGA-AAAGCTTGAGAGACCATCGTGA
*
24158 TATGTAGGGGTTCCTTG
64 TATGTAGGGGTTTCTTG
24175 GTGACAACTA
Statistics
Matches: 275, Mismatches: 51, Indels: 25
0.78 0.15 0.07
Matches are distributed among these distances:
84 8 0.03
85 56 0.20
86 130 0.47
87 79 0.29
88 2 0.01
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (85 bp):
AGTTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGAAAAGCTTGAGAGACCATCGTGATA
TGTAGGGGTTTCTTGAGGAC
Found at i:24215 original size:258 final size:257
Alignment explanation
Indices: 23753--24220 Score: 776
Period size: 258 Copynumber: 1.8 Consensus size: 257
23743 AAGAAACGAG
*
23753 TTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGAAGAAAAGCTTGAGAGACCATCGTGATATG
1 TTTGAGGGACCATCGTGATATGTAGGGGTTCCTTAAAGAAAAGCTTGAGAGACCATCGTGATATG
* *
23818 TAGGGGTTTCTCGAGGACACGTTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATCACACAC
66 TAGGGGTTTCTCGAGGACACGTTTGAGGGACCATCATGATATGTAGGGGTTCATTGATCACACAC
* * * *
23883 TTGAGGGACCAACGAGATATGTAGGGGTTCTTTGGTGATAATTAAGAAACTAAGCTTGATTTTTA
131 TTGAGGGACCAACGAGATATGTAGGGGTTCCTTGGTGACAACTAAGAAACTAAGCTTGATTTTCA
* *
23948 GGGGTTTCTTGATGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGAGGATAAC
196 AGAGTTTCTTGATGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGAGGATAAC
*
24010 TTTGAGGGACCATCGTGATATGTAGGGGTTCCTTAAAGAAAATCTTGAGAGACCATCGTGATATG
1 TTTGAGGGACCATCGTGATATGTAGGGGTTCCTTAAAGAAAAGCTTGAGAGACCATCGTGATATG
* * * *
24075 TAGGGGGTTTCTTGAGGACGA-GTTTGAGGGACTATCATGATATGTAGGGGTTCATTGATGACAT
66 TA-GGGGTTTCTCGAGGAC-ACGTTTGAGGGACCATCATGATATGTAGGGGTTCATTGATCACAC
*
24139 ACTTGAGGGACCAACGAGATATGTAGGGGTTCCTTGGTGACAACTAAGAAACTGAGCTTGATTTT
129 ACTTGAGGGACCAACGAGATATGTAGGGGTTCCTTGGTGACAACTAAGAAACTAAGCTTGATTTT
24204 CAAGAGTTTCTTGATGA
194 CAAGAGTTTCTTGATGA
24221 GTAAGTCATT
Statistics
Matches: 194, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
257 65 0.34
258 128 0.66
259 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.30
Consensus pattern (257 bp):
TTTGAGGGACCATCGTGATATGTAGGGGTTCCTTAAAGAAAAGCTTGAGAGACCATCGTGATATG
TAGGGGTTTCTCGAGGACACGTTTGAGGGACCATCATGATATGTAGGGGTTCATTGATCACACAC
TTGAGGGACCAACGAGATATGTAGGGGTTCCTTGGTGACAACTAAGAAACTAAGCTTGATTTTCA
AGAGTTTCTTGATGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGAGGATAAC
Found at i:24463 original size:90 final size:90
Alignment explanation
Indices: 24305--24644 Score: 601
Period size: 90 Copynumber: 3.8 Consensus size: 90
24295 AGCAAGATGA
*
24305 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGTGCATGATGTTTTCAAATGAGATTTTAGAAACT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGTGCAGGATGTTTTCAAATGAGATTTTAGAAACT
24370 AAGCCTTCGGGGGTTTCTTGATTTG
66 AAGCCTTCGGGGGTTTCTTGATTTG
*
24395 TAAGACCTTCGGGCCATCCATAAGACCTTCGGTGCAGGATGTTTTCAAATGAGATTTTAGAAACT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGTGCAGGATGTTTTCAAATGAGATTTTAGAAACT
*
24460 AAGCCTTCAGGGGTTTCTTGATTTG
66 AAGCCTTCGGGGGTTTCTTGATTTG
* * *
24485 TAAGTCCTTCGGGCCATCTATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTGTAGAAACT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGTGCAGGATGTTTTCAAATGAGATTTTAGAAACT
24550 AAGCCTTCGGGGGTTTCTTGATTTG
66 AAGCCTTCGGGGGTTTCTTGATTTG
* *
24575 TAAGTCCTTCGGGCCATCCATAAGACCTTCGG-GCAGGATGTTTTCAAATCAGTTTTTAGAAACT
1 TAAGTCCTTCGGGCCATCCATAAGACCTTCGGTGCAGGATGTTTTCAAATGAGATTTTAGAAACT
24639 AAGCCT
66 AAGCCT
24645 CATTTTCAGG
Statistics
Matches: 237, Mismatches: 13, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
89 35 0.15
90 202 0.85
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (90 bp):
TAAGTCCTTCGGGCCATCCATAAGACCTTCGGTGCAGGATGTTTTCAAATGAGATTTTAGAAACT
AAGCCTTCGGGGGTTTCTTGATTTG
Found at i:24828 original size:42 final size:42
Alignment explanation
Indices: 24763--24876 Score: 133
Period size: 42 Copynumber: 2.7 Consensus size: 42
24753 AAGGGTTTCT
24763 TGATGAGTAAGTCCTTCAAGCCA-TCAGTAAGTCTCTCGAGCA
1 TGATGAGTAAGTCCTTCAAGCCATTCA-TAAGTCTCTCGAGCA
* ** * *
24805 TGATGTGTAAGTCCTTCGGGCCATTTATAAGTCTTTCGAGCA
1 TGATGAGTAAGTCCTTCAAGCCATTCATAAGTCTCTCGAGCA
* * *
24847 AGATGA-TAAGTCATTCAAGCCATCCATAAG
1 TGATGAGTAAGTCCTTCAAGCCATTCATAAG
24877 ACCTTCGGGT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
41 19 0.32
42 38 0.64
43 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (42 bp):
TGATGAGTAAGTCCTTCAAGCCATTCATAAGTCTCTCGAGCA
Found at i:25081 original size:36 final size:36
Alignment explanation
Indices: 24997--25109 Score: 156
Period size: 36 Copynumber: 3.1 Consensus size: 36
24987 TTTTCCTAAG
* * ** *
24997 AACAAATTTTGTCTCACTTGAGACAATATTTACTTTA
1 AACAAATTTTGTCTCCCTTGAGACAGT-TTCCCTTGA
25034 AAC-AATCTTTGTCTCCCTTGAGACAGTTTCCCTTGA
1 AACAAAT-TTTGTCTCCCTTGAGACAGTTTCCCTTGA
25070 AACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGA
1 AACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGA
25106 AACA
1 AACA
25110 TCAATCTTTG
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
36 45 0.65
37 24 0.35
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.36
Consensus pattern (36 bp):
AACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGA
Found at i:30775 original size:13 final size:15
Alignment explanation
Indices: 30736--30789 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
30726 ATTTTAAAAG
30736 TAAATAAT-TAT-TT
1 TAAATAATATATGTT
*
30749 TATATATGATATATG-T
1 TA-A-ATAATATATGTT
30765 TAAA-AATATATGTT
1 TAAATAATATATGTT
30779 TAAATAATATA
1 TAAATAATATA
30790 CAAATTTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
13 9 0.27
14 7 0.21
15 11 0.33
16 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (15 bp):
TAAATAATATATGTT
Found at i:45039 original size:21 final size:21
Alignment explanation
Indices: 45015--45054 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
45005 ATCAATACTT
45015 ATTCATCAGGTATCGATATAC
1 ATTCATCAGGTATCGATATAC
**
45036 ATTCATTGGGTATCGATAT
1 ATTCATCAGGTATCGATAT
45055 TGTTAGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (21 bp):
ATTCATCAGGTATCGATATAC
Found at i:45553 original size:44 final size:44
Alignment explanation
Indices: 45473--45556 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 44
45463 TTTCTCCTAT
* * * * *
45473 TAGTGTTGAGGCACTTTAGTATTAGTGCAAATGCACTTCCATAC
1 TAGTGTCGAGGCACTTTAGAATCAATGCAAAGGCACTTCCATAC
**
45517 TAGTGTCGAGGCACTTTAGAATCAATGTTAAGGCACTTCC
1 TAGTGTCGAGGCACTTTAGAATCAATGCAAAGGCACTTCC
45557 GTTATTCGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
44 33 1.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (44 bp):
TAGTGTCGAGGCACTTTAGAATCAATGCAAAGGCACTTCCATAC
Found at i:48275 original size:18 final size:18
Alignment explanation
Indices: 48254--48307 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
48244 CTTTCATCAA
*
48254 CATTTTTTAAAATTCTTT
1 CATTTTTAAAAATTCTTT
48272 CA---TTAAAAATTCTTT
1 CATTTTTAAAAATTCTTT
*
48287 CATTTTTCAAAATTCTTT
1 CATTTTTAAAAATTCTTT
48305 CAT
1 CAT
48308 CAAACATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 14 0.45
18 17 0.55
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (18 bp):
CATTTTTAAAAATTCTTT
Found at i:48282 original size:15 final size:15
Alignment explanation
Indices: 48262--48290 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
48252 AACATTTTTT
48262 AAAATTCTTTCATTA
1 AAAATTCTTTCATTA
48277 AAAATTCTTTCATT
1 AAAATTCTTTCATT
48291 TTTCAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATTCTTTCATTA
Found at i:48322 original size:24 final size:25
Alignment explanation
Indices: 48287--48335 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
48277 AAAATTCTTT
*
48287 CATTTTTCAAAATTCT-TTCATCAAA
1 CATTTTTCAAAA-CCTATTCATCAAA
48312 CATTTTT-AAAACCTATTCATCAAA
1 CATTTTTCAAAACCTATTCATCAAA
48336 TTTTTCTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 2 0.09
24 13 0.59
25 7 0.32
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (25 bp):
CATTTTTCAAAACCTATTCATCAAA
Found at i:49557 original size:40 final size:40
Alignment explanation
Indices: 49341--49557 Score: 104
Period size: 40 Copynumber: 5.3 Consensus size: 40
49331 ATTAGGACTT
* * * *
49341 AACGTCCTTCAGAGGAATGAGTGAGATCATC-CCGTGACTC
1 AACGTCCTTCAGAGAAAAGAGTGAGATCATCACC-AGATTC
* * * * *
49381 AATGTCTTTTAGA-AGAAAGAGTGAAATCATCACCAGATTT
1 AACGTCCTTCAGAGA-AAAGAGTGAGATCATCACCAGATTC
* * *
49421 AACATCCTTCAGCA-AAAGGAGTG-GATCACCTACCA-ATTATGAC
1 AACGTCCTTCAG-AGAAAAGAGTGAGATCATC-ACCAGA-T-T--C
* * * * * * *
49464 TTAACATCCTTAAGAGGAAGGAGTAAGATCGTC-CCACGACTC
1 --AACGTCCTTCAGAGAAAAGAGTGAGATCATCACCA-GATTC
* *
49506 AGCGTCTTTCAGAGAAAAGAGTGAGATCATCACCAGATTC
1 AACGTCCTTCAGAGAAAAGAGTGAGATCATCACCAGATTC
49546 AACGTCCTTCAG
1 AACGTCCTTCAG
49558 TAAGAGGAGT
Statistics
Matches: 128, Mismatches: 34, Indels: 30
0.67 0.18 0.16
Matches are distributed among these distances:
39 6 0.05
40 84 0.66
41 8 0.06
42 1 0.01
44 5 0.04
45 18 0.14
46 6 0.05
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (40 bp):
AACGTCCTTCAGAGAAAAGAGTGAGATCATCACCAGATTC
Found at i:49566 original size:125 final size:125
Alignment explanation
Indices: 49331--49841 Score: 515
Period size: 125 Copynumber: 4.0 Consensus size: 125
49321 TTGACCCTAG
* * * * * * * *
49331 ATTAGGACTTAACGTCCTTCAGAGGAATGAGTGAGATCATCCCGTGACTCAATGTCTTTTAGA-A
1 ATTATGACTTAACATCCTTAAGAGGAAGGAGTAAGATCGTCCCATGACTCAACGTCTTTTAGAGA
* *
49395 GAAAGAGTGAAATCATCACCAGATTTAACATCCTTCAGCAAAAGGAGTGGATCACCTACCA
66 -AAAGAGTGAGATCATCACCAGATTCAACATCCTTCAGCAAAAGGAGTGGATCACCTACCA
* * *
49456 ATTATGACTTAACATCCTTAAGAGGAAGGAGTAAGATCGTCCCACGACTCAGCGTCTTTCAGAGA
1 ATTATGACTTAACATCCTTAAGAGGAAGGAGTAAGATCGTCCCATGACTCAACGTCTTTTAGAGA
* * * *
49521 AAAGAGTGAGATCATCACCAGATTCAACGTCCTTCAGTAAGAGGAGTGGGTCACCTACCA
66 AAAGAGTGAGATCATCACCAGATTCAACATCCTTCAGCAAAAGGAGTGGATCACCTACCA
* * * * * *
49581 ATTATGACTTACAACTTAGCGTCATTCAGATGAAGGAGTAAGATCGTTCCATAACTTAACGTCTT
1 ATTATGACTT--AAC--A---TCCTTAAGAGGAAGGAGTAAGATCGTCCCATGACTCAACGTCTT
* * * * * *
49646 TTAGAGGAAATAGTGAGATCGTCACCAGATTCAACATCCTTCAACAAAAGGAGT-AAGTTACCTA
59 TTAGAGAAAAGAGTGAGATCATCACCAGATTCAACATCCTTCAGCAAAAGGAGTGGA-TCACCTA
49710 CCA
123 CCA
* * ** *
49713 ATTACGACTTAGA-GTCCTTAAGAGGAAGGAGTAAGATTTTCCCATGACTTAACGTCTTTTAGAG
1 ATTATGACTTA-ACATCCTTAAGAGGAAGGAGTAAGATCGTCCCATGACTCAACGTCTTTTAGAG
* * * * * * * ** *
49777 AAAATAGTGAGATCATCACCAAATTCATCGTACTTCAGCAAGAGGAATACATTACCTACCA
65 AAAAGAGTGAGATCATCACCAGATTCAACATCCTTCAGCAAAAGGAGTGGATCACCTACCA
49838 ATTA
1 ATTA
49842 CAACCTAGCG
Statistics
Matches: 320, Mismatches: 55, Indels: 22
0.81 0.14 0.06
Matches are distributed among these distances:
125 212 0.66
126 2 0.01
127 3 0.01
129 1 0.00
130 1 0.00
131 1 0.00
132 100 0.31
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (125 bp):
ATTATGACTTAACATCCTTAAGAGGAAGGAGTAAGATCGTCCCATGACTCAACGTCTTTTAGAGA
AAAGAGTGAGATCATCACCAGATTCAACATCCTTCAGCAAAAGGAGTGGATCACCTACCA
Found at i:50506 original size:3 final size:3
Alignment explanation
Indices: 50480--50543 Score: 55
Period size: 3 Copynumber: 21.7 Consensus size: 3
50470 TTCGTCTGGT
*
50480 TTA TTT TTA TTA TT- TT- TTA TTTA TTA TTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA
*
50525 ATA TTTA TT- TTA TT- TTA TT
1 TTA -TTA TTA TTA TTA TTA TT
50544 TTTTCTTTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
2 8 0.16
3 35 0.69
4 8 0.16
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:50523 original size:23 final size:23
Alignment explanation
Indices: 50480--50523 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
50470 TTCGTCTGGT
* * *
50480 TTATTTTTATTATTTTTTATTTA
1 TTATTATTATTATTATATATTTA
50503 TTATTATTATTATTATATATT
1 TTATTATTATTATTATATATT
50524 AATATTTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (23 bp):
TTATTATTATTATTATATATTTA
Found at i:50537 original size:19 final size:18
Alignment explanation
Indices: 50490--50537 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
50480 TTATTTTTAT
* *
50490 TATT-TTTTATTTATTAT
1 TATTATTTTATATATTAA
50507 TATTATTATTATATATTAA
1 TATTATT-TTATATATTAA
50526 TATTTATTTTAT
1 TA-TTATTTTAT
50538 TTTATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
18 2 0.08
19 15 0.58
20 5 0.19
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTATTTTATATATTAA
Found at i:55889 original size:18 final size:19
Alignment explanation
Indices: 55866--55907 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
55856 ACATAAGCAT
55866 AAATAACCAAAAT-AT-CCA
1 AAATAACC-AAATCATCCCA
*
55884 AAATAATCAAATCATCCCA
1 AAATAACCAAATCATCCCA
55903 AAATA
1 AAATA
55908 TGAAATCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 9 0.43
19 8 0.38
ACGTcount: A:0.60, C:0.21, G:0.00, T:0.19
Consensus pattern (19 bp):
AAATAACCAAATCATCCCA
Found at i:55889 original size:28 final size:29
Alignment explanation
Indices: 55835--55889 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
55825 TATATCCATT
* *
55835 ATAAGTAACCAAAAATATCCAACATAAGC
1 ATAAATAACCAAAAATATCCAAAATAAGC
55864 ATAAATAACC-AAAATATCCAAAATAA
1 ATAAATAACCAAAAATATCCAAAATAA
55890 TCAAATCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.60, C:0.18, G:0.04, T:0.18
Consensus pattern (29 bp):
ATAAATAACCAAAAATATCCAAAATAAGC
Found at i:58535 original size:15 final size:15
Alignment explanation
Indices: 58517--58569 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
58507 CAAATGCTAG
58517 AAATTTAAAGGA-AA
1 AAATTTAAAGGACAA
* * *
58531 AAAATTAAAGTACAT
1 AAATTTAAAGGACAA
*
58546 AAATTTAAAAGACAA
1 AAATTTAAAGGACAA
*
58561 AAATGTAAA
1 AAATTTAAA
58570 TAGAAGAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
14 10 0.33
15 20 0.67
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.23
Consensus pattern (15 bp):
AAATTTAAAGGACAA
Found at i:58661 original size:33 final size:33
Alignment explanation
Indices: 58623--58700 Score: 88
Period size: 31 Copynumber: 2.4 Consensus size: 33
58613 AGAACAAAAA
58623 TAAAATAAAATAAAAAGGGGAAAATATAAATAAC
1 TAAAAT-AAATAAAAAGGGGAAAATATAAATAAC
* * * *
58657 -AAAATAAAT-AAAATGTGTAAATGTAAATAAC
1 TAAAATAAATAAAAAGGGGAAAATATAAATAAC
58688 TAAAATTAAATAA
1 TAAAA-TAAATAA
58701 TGAAAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
31 18 0.49
32 8 0.22
33 10 0.27
34 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.09, T:0.23
Consensus pattern (33 bp):
TAAAATAAATAAAAAGGGGAAAATATAAATAAC
Found at i:58687 original size:84 final size:83
Alignment explanation
Indices: 58559--58806 Score: 257
Period size: 85 Copynumber: 2.9 Consensus size: 83
58549 TTTAAAAGAC
* * * ** **
58559 AAAAATGTAAATAGA-AGAAAAATAAAGTGCTTAAATGTAAATAACAAAACTAAAAGAACAAAAA
1 AAAAATATAAATA-ACAAAAAAATAAAATGAGTAAATGTAAATAACAAAA-TAAAAGAATGAAAA
58623 TAAAATAAAATAAAAAGGGG
64 TAAAATAAAATAAAAAGGGG
* * *
58643 -AAAATATAAATAACAAAATAAATAAAATGTGTAAATGTAAATAACTAAAATTAAATAATGAAAA
1 AAAAATATAAATAACAAAA-AAATAAAATGAGTAAATGTAAATAAC-AAAATAAAAGAATGAAAA
*
58707 TAAAATAAAGTAAAAAGGGG
64 TAAAATAAAATAAAAAGGGG
* * * * * * * *
58727 CAAAAATGTAATTAACAAAAAATTAAAGTGAGTAAATATAAAGAACAAAAATGAAAGAGTGAAAA
1 -AAAAATATAAATAACAAAAAAATAAAATGAGTAAATGTAAATAAC-AAAATAAAAGAATGAAAA
58792 TAAAATAAAATAAAA
64 TAAAATAAAATAAAA
58807 TAAAAAAGGA
Statistics
Matches: 137, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
82 1 0.01
83 14 0.10
84 52 0.38
85 54 0.39
86 16 0.12
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.19
Consensus pattern (83 bp):
AAAAATATAAATAACAAAAAAATAAAATGAGTAAATGTAAATAACAAAATAAAAGAATGAAAATA
AAATAAAATAAAAAGGGG
Found at i:58797 original size:85 final size:84
Alignment explanation
Indices: 58558--58806 Score: 279
Period size: 84 Copynumber: 2.9 Consensus size: 84
58548 ATTTAAAAGA
** * **
58558 CAAAAATGTAAATAGA-AGAAAAATAAAGTGCTTAAATGTAAATAACAAAACTAAAAGAACAAAA
1 CAAAAATGTAAATA-ACA-AAAAATAAAGTGAGTAAATGTAAATAACAAAAATAAAAGAATGAAA
58622 ATAAAATAAAATAAAAAGGGG
64 ATAAAATAAAATAAAAAGGGG
* * * * * *
58643 --AAAATATAAATAACAAAATAAATAAAATGTGTAAATGTAAATAACTAAAATTAAATAATGAAA
1 CAAAAATGTAAATAAC-AAA-AAATAAAGTGAGTAAATGTAAATAACAAAAATAAAAGAATGAAA
*
58706 ATAAAATAAAGTAAAAAGGGG
64 ATAAAATAAAATAAAAAGGGG
* * * * *
58727 CAAAAATGTAATTAACAAAAAATTAAAGTGAGTAAATATAAAGAACAAAAATGAAAGAGTGAAAA
1 CAAAAATGTAAATAACAAAAAA-TAAAGTGAGTAAATGTAAATAACAAAAATAAAAGAATGAAAA
58792 TAAAATAAAATAAAA
65 TAAAATAAAATAAAA
58807 TAAAAAAGGA
Statistics
Matches: 136, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
82 1 0.01
83 13 0.10
84 59 0.43
85 51 0.38
86 12 0.09
ACGTcount: A:0.65, C:0.04, G:0.12, T:0.19
Consensus pattern (84 bp):
CAAAAATGTAAATAACAAAAAATAAAGTGAGTAAATGTAAATAACAAAAATAAAAGAATGAAAAT
AAAATAAAATAAAAAGGGG
Found at i:58850 original size:85 final size:87
Alignment explanation
Indices: 58703--58864 Score: 195
Period size: 90 Copynumber: 1.9 Consensus size: 87
58693 TTAAATAATG
* ** *
58703 AAAATAAAATAAAGTAAAAAGGGGCAAAAATGTAATTAACAAAAAATTAAAGTGAGTAAATATAA
1 AAAATAAAATAAAATAAAAAGGAACAAAAATGTAAATAACAAAAAATT--AGT-AGTAAATATAA
58768 AGAACAAAAATGAAAGAGTGAAAAT
63 AGAACAAAAATGAAAGAGTGAAAAT
* * *
58793 AAAATAAAATAAAATAAAAAAGGAACATAAATGTAAATAAC-AAAAATT-GT-GTCAATATAAAT
1 AAAATAAAATAAAAT-AAAAAGGAACAAAAATGTAAATAACAAAAAATTAGTAGTAAATATAAAG
*
58855 AACAGAAATG
65 AACAAAAATG
58865 TAAATCGAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
85 19 0.30
87 2 0.03
90 21 0.33
91 21 0.33
ACGTcount: A:0.64, C:0.04, G:0.13, T:0.19
Consensus pattern (87 bp):
AAAATAAAATAAAATAAAAAGGAACAAAAATGTAAATAACAAAAAATTAGTAGTAAATATAAAGA
ACAAAAATGAAAGAGTGAAAAT
Found at i:60564 original size:44 final size:44
Alignment explanation
Indices: 60502--60650 Score: 126
Period size: 44 Copynumber: 3.4 Consensus size: 44
60492 GCTGATTTAG
* * *
60502 CTCCTTCTATGATAGAATCTAGTAAAAGGTAAATGTTGATCCAA
1 CTCCTTATATGATGGAATCTAGAAAAAGGTAAATGTTGATCCAA
* * * *
60546 CTCCTTATGTGATGGAATCTAGCAAAAAGGGAAA-ATTGATCCAC
1 CTCCTTATATGATGGAATCTAG-AAAAAGGTAAATGTTGATCCAA
* * * * * *
60590 CTCATTCTATGATGGAATC-A-AACAAAAGT-GATGCTGATCTAA
1 CTCCTTATATGATGGAATCTAGAA-AAAGGTAAATGTTGATCCAA
*
60632 CTCCTTATGTGATGGAATC
1 CTCCTTATATGATGGAATC
60651 GAGCAAATAA
Statistics
Matches: 82, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
41 3 0.04
42 26 0.32
43 1 0.01
44 43 0.52
45 9 0.11
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (44 bp):
CTCCTTATATGATGGAATCTAGAAAAAGGTAAATGTTGATCCAA
Found at i:60922 original size:110 final size:110
Alignment explanation
Indices: 60777--61079 Score: 312
Period size: 110 Copynumber: 2.7 Consensus size: 110
60767 AAAGATCCAA
* * *** *
60777 AGTCGAACAAGTTCTTCTCATTGGGAACTTCTTCTCCCTAATTGGACGAGTTCTTCTCATTATGA
1 AGTCGAACAAGCTCTTCTCATTAGGAACTTCTTCTCCCTAATCAAACAAGTTCTTCTCATTATGA
*
60842 ACCCTTCCACTGGAAATACTGATCCAACTCC-TTCTCTGATGAACG
66 ACCCTTCCACTGGAAATACTGATCCAAC-CCTTTCTATGATGAACG
* * * *
60887 AGTCGAACAAGCTCTTCTCATTAGGAA-TTGGTTCTCTCTCATCAAACAAGTTCTTGTCATTATG
1 AGTCGAACAAGCTCTTCTCATTAGGAACTT-CTTCTCCCTAATCAAACAAGTTCTTCTCATTATG
* ** * *
60951 AATCCTTCCACTGGAAATGTTGATCCAACCCTTTCTATGATGGATG
65 AACCCTTCCACTGGAAATACTGATCCAACCCTTTCTATGATGAACG
* * * *
60997 AGCCAAGGGAATAAG--CTTCTCATTAGGAACTTC-TCTCCCTCATCAAACACGTTCTTCTCATT
1 AGTC----GAACAAGCTCTTCTCATTAGGAACTTCTTCTCCCTAATCAAACAAGTTCTTCTCATT
*
61059 AGGAACCCTTCC-CTTGGAAAT
62 ATGAACCCTTCCAC-TGGAAAT
61080 GTTGATAGGA
Statistics
Matches: 161, Mismatches: 24, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
109 4 0.02
110 92 0.57
111 43 0.27
112 14 0.09
113 2 0.01
114 6 0.04
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (110 bp):
AGTCGAACAAGCTCTTCTCATTAGGAACTTCTTCTCCCTAATCAAACAAGTTCTTCTCATTATGA
ACCCTTCCACTGGAAATACTGATCCAACCCTTTCTATGATGAACG
Found at i:62669 original size:12 final size:12
Alignment explanation
Indices: 62643--62695 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 12
62633 GTATCTGAAA
62643 GAAAA-GAATAT
1 GAAAATGAATAT
*
62654 GAAAATGAATAC
1 GAAAATGAATAT
*
62666 GAAAGTGAAATAT
1 GAAAATG-AATAT
*
62679 GAAAATAAAATAT
1 GAAAAT-GAATAT
62692 GAAA
1 GAAA
62696 TGTTTAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
11 5 0.15
12 11 0.32
13 18 0.53
ACGTcount: A:0.62, C:0.02, G:0.17, T:0.19
Consensus pattern (12 bp):
GAAAATGAATAT
Found at i:62682 original size:13 final size:13
Alignment explanation
Indices: 62649--62695 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
62639 GAAAGAAAAG
62649 AATATGAAAATG-
1 AATATGAAAATGA
* *
62661 AATACGAAAGTGA
1 AATATGAAAATGA
*
62674 AATATGAAAATAA
1 AATATGAAAATGA
62687 AATATGAAA
1 AATATGAAA
62696 TGTTTAGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.62, C:0.02, G:0.15, T:0.21
Consensus pattern (13 bp):
AATATGAAAATGA
Found at i:63182 original size:23 final size:23
Alignment explanation
Indices: 63139--63184 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
63129 TGTGTTTTTG
*
63139 ATAAAAAAATATATTTTATTAGA
1 ATAAAAAAATATATTTAATTAGA
*
63162 ATAAAGAAATAT-TTTAAATTAGA
1 ATAAAAAAATATATTT-AATTAGA
63185 CAGTTATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (23 bp):
ATAAAAAAATATATTTAATTAGA
Found at i:66057 original size:50 final size:48
Alignment explanation
Indices: 65982--66080 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 48
65972 AAGTTTCCCC
65982 CAACCCACGTGAAAATCAGCTAAAAATCGTCTCAAATCAGCCATGTTTTT
1 CAACCCACGTGAAAATCAGCTAAAAATC-TCTCAAATCAG-CATGTTTTT
66032 CAACCCACGTGAAAATCAGCTAAAAATCTCTCAAATCAGCATGTTTTT
1 CAACCCACGTGAAAATCAGCTAAAAATCTCTCAAATCAGCATGTTTTT
66080 C
1 C
66081 TTTAATGGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 10 0.20
49 11 0.22
50 28 0.57
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.26
Consensus pattern (48 bp):
CAACCCACGTGAAAATCAGCTAAAAATCTCTCAAATCAGCATGTTTTT
Done.