Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006805.1 Hibiscus syriacus cultivar Beakdansim tig00017273_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: 95316
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:65 original size:23 final size:24
Alignment explanation
Indices: 5--73 Score: 88
Period size: 23 Copynumber: 2.9 Consensus size: 24
1 GAAA
**
5 TGTCTCGAAAGACTGCGTAGAATT
1 TGTCTCGAAAGACCACGTAGAATT
29 TGTC-CTGAAAGACCACGTAGAA-T
1 TGTCTC-GAAAGACCACGTAGAATT
*
52 TGTCTCGAAGGACCACGTAGAA
1 TGTCTCGAAAGACCACGTAGAA
74 CCCTCGACTC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
23 21 0.52
24 19 0.47
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (24 bp):
TGTCTCGAAAGACCACGTAGAATT
Found at i:6053 original size:23 final size:23
Alignment explanation
Indices: 5975--6037 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
5965 CACTGAAGTG
5975 CCATGTAGAAATGTCCCGAAGGA
1 CCATGTAGAAATGTCCCGAAGGA
*
5998 CCATGTAGAAATGTCTCGAAGGA
1 CCATGTAGAAATGTCCCGAAGGA
6021 CCATGTAGAAATGTCCC
1 CCATGTAGAAATGTCCC
6038 AGAGGACTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (23 bp):
CCATGTAGAAATGTCCCGAAGGA
Found at i:6066 original size:24 final size:24
Alignment explanation
Indices: 6040--6121 Score: 103
Period size: 24 Copynumber: 3.5 Consensus size: 24
6030 AATGTCCCAG
* *
6040 AGGACTGTGTAGAATTTATCCCGG
1 AGGACTGCGTAGAATTTATCCCGA
* *
6064 AGGACCGCGTAGAATTTATCCTGA
1 AGGACTGCGTAGAATTTATCCCGA
*
6088 AGGACTACGTAGAA-TTATCCCGA
1 AGGACTGCGTAGAATTTATCCCGA
*
6111 AGGACCGCGTA
1 AGGACTGCGTA
6122 TAACCTTCTA
Statistics
Matches: 49, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 17 0.35
24 32 0.65
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (24 bp):
AGGACTGCGTAGAATTTATCCCGA
Found at i:6112 original size:23 final size:23
Alignment explanation
Indices: 5975--6116 Score: 115
Period size: 23 Copynumber: 6.1 Consensus size: 23
5965 CACTGAAGTG
*
5975 CCATGTAGAAATGTCCCGAAGGA
1 CCATGTAGAAATATCCCGAAGGA
* *
5998 CCATGTAGAAATGTCTCGAAGGA
1 CCATGTAGAAATATCCCGAAGGA
*
6021 CCATGTAGAAATGTCCC-AGAGGA
1 CCATGTAGAAATATCCCGA-AGGA
** * *
6044 CTGTGTAGAATTTATCCCGGAGGA
1 CCATGTAGAA-ATATCCCGAAGGA
** * *
6068 CCGCGTAGAATTTATCCTGAAGGA
1 CCATGTAGAA-ATATCCCGAAGGA
* * *
6092 CTACGTAGAATTATCCCGAAGGA
1 CCATGTAGAAATATCCCGAAGGA
6115 CC
1 CC
6117 GCGTATAACC
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
22 1 0.01
23 63 0.62
24 37 0.37
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (23 bp):
CCATGTAGAAATATCCCGAAGGA
Found at i:6250 original size:15 final size:16
Alignment explanation
Indices: 6216--6252 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
6206 GCTTGTATCT
6216 CATAATCATATAATCA
1 CATAATCATATAATCA
6232 CATAGATCA-ATAA-CA
1 CATA-ATCATATAATCA
6247 CATAAT
1 CATAAT
6253 GTGAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.10
15 6 0.30
16 8 0.40
17 4 0.20
ACGTcount: A:0.51, C:0.19, G:0.03, T:0.27
Consensus pattern (16 bp):
CATAATCATATAATCA
Found at i:8240 original size:2 final size:2
Alignment explanation
Indices: 8233--8273 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
8223 CATAGGAAGA
8233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8274 GACTAGGGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:8679 original size:75 final size:75
Alignment explanation
Indices: 8554--8699 Score: 220
Period size: 75 Copynumber: 1.9 Consensus size: 75
8544 GTTGATCATA
* * * * * *
8554 AATAAAATTTCAGGGTGGGCACCATCAATAAAATATGTGATTGATCGAAGAGAATTTAAATTTCA
1 AATAAAATTTCAGGGTGGGCACCATCAATAAAATAGGTGACTAATAGAAGAAAATTCAAATTTCA
8619 GAGTGGGCAC
66 GAGTGGGCAC
*
8629 AATAAAATTTCAGGGTGGGCACCATCAATAAAATAGGTGACTAATAGAAGAAAATTCAGATTTCA
1 AATAAAATTTCAGGGTGGGCACCATCAATAAAATAGGTGACTAATAGAAGAAAATTCAAATTTCA
*
8694 GGGTGG
66 GAGTGG
8700 ACACTGAGTC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 63 1.00
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (75 bp):
AATAAAATTTCAGGGTGGGCACCATCAATAAAATAGGTGACTAATAGAAGAAAATTCAAATTTCA
GAGTGGGCAC
Found at i:9318 original size:32 final size:32
Alignment explanation
Indices: 9247--9319 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
9237 GTGGTAACAC
*
9247 ATCACATCACAGAAAATAATGATATGTTATATG
1 ATCACATCACAGAAAATAAT-ATATGTGATATG
9280 AT-ACATCACAGAAAATAAT-TATGTGATATG
1 ATCACATCACAGAAAATAATATATGTGATATG
*
9310 TTTCACATCA
1 -ATCACATCA
9320 ACAACATGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
30 10 0.28
31 1 0.03
32 23 0.64
33 2 0.06
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.32
Consensus pattern (32 bp):
ATCACATCACAGAAAATAATATATGTGATATG
Found at i:10325 original size:29 final size:29
Alignment explanation
Indices: 10275--10427 Score: 78
Period size: 29 Copynumber: 5.3 Consensus size: 29
10265 CTATGACCCT
* * * *
10275 CATTTTAAATTAGTCTTGAAACTTTTAAA
1 CATTCTAAATTAATCCTCAAACTTTTAAA
* **
10304 CATTCTAAATTAATCCTCAAACTATT-GT
1 CATTCTAAATTAATCCTCAAACTTTTAAA
* *
10332 CATTCTAAACTT-CTCCTTAAACTTTTGAAA
1 CATTCTAAA-TTAATCCTCAAACTTTT-AAA
* * * * * **
10362 -ATTCCAAATTCATCCCCAAACTATGACCT
1 CATTCTAAATTAATCCTCAAACTTTTA-AA
* * * *
10391 CATTCTAAATCAGTCCCCAAACTTTTGAA
1 CATTCTAAATTAATCCTCAAACTTTTAAA
10420 CATTCTAA
1 CATTCTAA
10428 TAACTTCCCC
Statistics
Matches: 89, Mismatches: 29, Indels: 12
0.68 0.22 0.09
Matches are distributed among these distances:
28 23 0.26
29 47 0.53
30 19 0.21
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.37
Consensus pattern (29 bp):
CATTCTAAATTAATCCTCAAACTTTTAAA
Found at i:10647 original size:2 final size:2
Alignment explanation
Indices: 10640--10666 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10630 TAAACTTAAT
10640 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
10667 GAACTGATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22579 original size:21 final size:21
Alignment explanation
Indices: 22541--22580 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
22531 TTTTGATTTT
*
22541 TTTAATTTAGTCCTATTTATG
1 TTTAATTTAGTCCCATTTATG
22562 TTTAATTT-GTTCCCATTTA
1 TTTAATTTAG-TCCCATTTA
22581 ATTTAGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.57
Consensus pattern (21 bp):
TTTAATTTAGTCCCATTTATG
Found at i:24809 original size:14 final size:15
Alignment explanation
Indices: 24792--24825 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
24782 ACTCTAGTTT
24792 ATTTTATCA-ATAAC
1 ATTTTATCACATAAC
*
24806 ATTTTATGACATAAC
1 ATTTTATCACATAAC
24821 ATTTT
1 ATTTT
24826 TATTATTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (15 bp):
ATTTTATCACATAAC
Found at i:29066 original size:25 final size:25
Alignment explanation
Indices: 29038--29098 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
29028 AAAACTCTAT
29038 TTGCAAGAAAGTCGAGTAACTTTGC
1 TTGCAAGAAAGTCGAGTAACTTTGC
* *
29063 TTGCAAGAATA-TCTAGTAATTTTGC
1 TTGCAAGAA-AGTCGAGTAACTTTGC
29088 TTGCAAGAAAG
1 TTGCAAGAAAG
29099 AAAGCCTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 1 0.03
25 30 0.94
26 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (25 bp):
TTGCAAGAAAGTCGAGTAACTTTGC
Found at i:31404 original size:2 final size:2
Alignment explanation
Indices: 31397--31449 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
31387 GATAGACATG
31397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31439 TA TA TA TA TA T
1 TA TA TA TA TA T
31450 TGTATTGATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32035 original size:28 final size:27
Alignment explanation
Indices: 31982--32038 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
31972 GTTGAAAAAA
*
31982 ATTGACAAAAAATTATTAAGGAACAAT
1 ATTGACAAAAAATTATTAAAGAACAAT
*
32009 ATTGACCAAAAAA-TATTATAAGTACAAT
1 ATTGA-CAAAAAATTATTA-AAGAACAAT
32037 AT
1 AT
32039 ATATAATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (27 bp):
ATTGACAAAAAATTATTAAAGAACAAT
Found at i:32896 original size:14 final size:15
Alignment explanation
Indices: 32863--32900 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
32853 TAATCAAAAT
32863 TTATAATTTTGAGTTG
1 TTATAATTTTGAG-TG
*
32879 TTATTATTTTGA-TG
1 TTATAATTTTGAGTG
32893 TTATAATT
1 TTATAATT
32901 AAATTCAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 9 0.45
16 11 0.55
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (15 bp):
TTATAATTTTGAGTG
Found at i:32998 original size:16 final size:16
Alignment explanation
Indices: 32977--33009 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
32967 TAATAAATAG
32977 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
32993 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
33009 A
1 A
33010 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:33090 original size:10 final size:10
Alignment explanation
Indices: 33075--33149 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
33065 CATTTAATAA
33075 ATAAACGAAC
1 ATAAACGAAC
33085 ATAAACGAAC
1 ATAAACGAAC
33095 ----ACGAAC
1 ATAAACGAAC
33101 ATAAACGAAC
1 ATAAACGAAC
** *
33111 ACGAAC-ATAA
1 ATAAACGA-AC
33121 ATGAACACGAAC
1 AT-AA-ACGAAC
33133 ATAAACGAAC
1 ATAAACGAAC
33143 ATAAACG
1 ATAAACG
33150 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:33100 original size:16 final size:16
Alignment explanation
Indices: 33079--33143 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
33069 TAATAAATAA
33079 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
33095 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
33111 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
33127 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
33143 A
1 A
33144 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:33913 original size:14 final size:14
Alignment explanation
Indices: 33896--33951 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
33886 AATGAACATA
33896 AACGAACATAATCG
1 AACGAACATAATCG
33910 AACGAACAT-A---
1 AACGAACATAATCG
* *
33920 AACAAACATAACCG
1 AACGAACATAATCG
*
33934 AACAAACATAATCG
1 AACGAACATAATCG
33948 AACG
1 AACG
33952 TTCACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.55, C:0.23, G:0.11, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:33916 original size:24 final size:24
Alignment explanation
Indices: 33876--33950 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
33866 GATTGAGTTA
*
33876 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
*
33900 AACATAATCGAACGAACATAAACA
1 AACATAATCGAACGAACATAAACG
* * *
33924 AACATAACCGAACAAACATAATCG
1 AACATAATCGAACGAACATAAACG
33948 AAC
1 AAC
33951 GTTCACGAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.57, C:0.20, G:0.09, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:36480 original size:20 final size:20
Alignment explanation
Indices: 36455--36510 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
36445 CATATTCCCT
*
36455 GGTAATCTTACATTCTCACC
1 GGTAATCTTACATTCCCACC
*
36475 GGTAATCTTACATTCCCACT
1 GGTAATCTTACATTCCCACC
36495 GGTAATCTTACATTCC
1 GGTAATCTTACATTCC
36511 GTAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.25, C:0.29, G:0.11, T:0.36
Consensus pattern (20 bp):
GGTAATCTTACATTCCCACC
Found at i:39089 original size:17 final size:18
Alignment explanation
Indices: 39063--39109 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
39053 TATGAAATTG
* *
39063 GATTTCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
*
39080 GATTCTAATTCCTTCACA
1 GATTCCAATTCCTTCACA
39098 GATTCCAATTCC
1 GATTCCAATTCC
39110 CTCAGAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:42084 original size:15 final size:15
Alignment explanation
Indices: 42050--42097 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
42040 ATAACTACTC
* *
42050 TGATGATGATGACGA
1 TGATGATGGTGATGA
*
42065 AGATGATGGTGATGA
1 TGATGATGGTGATGA
* *
42080 TGATGACGGTGGTGA
1 TGATGATGGTGATGA
42095 TGA
1 TGA
42098 CAACTAACAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.29, C:0.04, G:0.40, T:0.27
Consensus pattern (15 bp):
TGATGATGGTGATGA
Found at i:42612 original size:32 final size:28
Alignment explanation
Indices: 42540--42617 Score: 138
Period size: 28 Copynumber: 2.8 Consensus size: 28
42530 GCTGCTGAAT
42540 CATTTGTAAATTAATTACAGGACATGGA
1 CATTTGTAAATTAATTACAGGACATGGA
42568 CATTTGTAAATTAATTACAGGACATGGA
1 CATTTGTAAATTAATTACAGGACATGGA
* *
42596 CATTTGTAAACTAATTAAAGGA
1 CATTTGTAAATTAATTACAGGA
42618 GGCAAAATGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (28 bp):
CATTTGTAAATTAATTACAGGACATGGA
Found at i:44908 original size:5 final size:5
Alignment explanation
Indices: 44898--45183 Score: 515
Period size: 5 Copynumber: 57.0 Consensus size: 5
44888 AGTGAGACTC
44898 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
44948 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
44998 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
45048 ATATT ATATT ATA-T ATATT ATATT ATATT ATATT ATATT ATATT ATA-T
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
45096 -TATT ATATT ATATT ATATTAT ATATT ATATT ATATT ATATT ATATTAT
1 ATATT ATATT ATATT ATA-T-T ATATT ATATT ATATT ATATT ATA-T-T
45144 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
45184 TCAAATATCA
Statistics
Matches: 274, Mismatches: 0, Indels: 14
0.95 0.00 0.05
Matches are distributed among these distances:
3 2 0.01
4 6 0.02
5 254 0.93
6 4 0.01
7 8 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:48867 original size:27 final size:27
Alignment explanation
Indices: 48837--48888 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
48827 CATAAAAATA
*
48837 GGGGTCTTCAGAAAAAGTTAACAGGTC
1 GGGGTCTTAAGAAAAAGTTAACAGGTC
48864 GGGGTCTTAAGAAAAAGTTAACAGG
1 GGGGTCTTAAGAAAAAGTTAACAGG
48889 CCGAAGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.37, C:0.12, G:0.31, T:0.21
Consensus pattern (27 bp):
GGGGTCTTAAGAAAAAGTTAACAGGTC
Found at i:49415 original size:38 final size:36
Alignment explanation
Indices: 49333--49424 Score: 103
Period size: 37 Copynumber: 2.4 Consensus size: 36
49323 ATATATATTA
*
49333 ATATAGTATAATTTTTAGAAAACGGTTTGAAAAATAT
1 ATATA-TATAATTTTTAAAAAACGGTTTGAAAAATAT
*
49370 ATAATATATACTTTTTAAAAAATCGGTTTTTGAAAAAATAT
1 AT-ATATATAATTTTTAAAAAA-CGG--TTTG-AAAAATAT
49411 ATATATATATATTT
1 ATATATATA-ATTT
49425 ATTATATAGT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
37 16 0.35
38 6 0.13
40 11 0.24
41 13 0.28
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (36 bp):
ATATATATAATTTTTAAAAAACGGTTTGAAAAATAT
Found at i:53808 original size:104 final size:104
Alignment explanation
Indices: 53532--53828 Score: 435
Period size: 99 Copynumber: 2.9 Consensus size: 104
53522 CGTATACCCA
53532 GATTATAATATTATATGTATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCC
1 GATTATAATATTATATGTATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCC
* *
53597 TCGGCTTTATGGATAAGATTCAGCTAGCCTGATAAAGGT
66 CCGACTTTATGGATAAGATTCAGCTAGCCTGATAAAGGT
** *
53636 G-TT-T-ATA--ATACATACACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCC
1 GATTATAATATTATATGTATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCC
* * *
53696 CCGTCTTTATGGATAAGATTTAGCTAGCTTGATAAAGGT
66 CCGACTTTATGGATAAGATTCAGCTAGCCTGATAAAGGT
* * * *
53735 GATTATAATATTATATGTATACAATAAAG-TGTGAGTTTTCCCTCTAGAGCAATTAGTTAAACTC
1 GATTATAATATTATATGTATACAATAAAGCT-TGAGCTGTCCCTCTAGAGCAATTGGTTAAACGC
53799 CCCGACTTTATGGATAAGATTCAGCTAGCC
65 CCCGACTTTATGGATAAGATTCAGCTAGCC
53829 AGAAAATGGA
Statistics
Matches: 170, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
99 86 0.51
100 2 0.01
101 4 0.02
102 4 0.02
103 3 0.02
104 71 0.42
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (104 bp):
GATTATAATATTATATGTATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCC
CCGACTTTATGGATAAGATTCAGCTAGCCTGATAAAGGT
Found at i:55479 original size:186 final size:186
Alignment explanation
Indices: 55207--55761 Score: 823
Period size: 186 Copynumber: 3.0 Consensus size: 186
55197 ACTTATACAA
* *
55207 GATTGGATTTCAACTTTACAATGAAGGATATCCAACCCAAAGCCAA---GGCGAAGCACTATAAC
1 GATTGGATTTCAACTTCACAATGAAAGATATCCAACCCAAAGCCAATTTGGCGAAGCACTATAAC
*
55269 TCGAGATTGGATTTCAACTTCACAATGAAGGACATTCAATTCAAAGCTCAACTTCACAACGAAGG
66 TCGAGATTGGATTTCAACTTCACAATGAAGGACATCCAATTCAAAGCTCAACTTCACAACGAAGG
* *
55334 AGCCATCCATGATTTCAACTTCA-ACAAGAAGGATATTGTGCCCAAATAGATTGACT
131 AGCCATCCACGATTTCAACTTCACA-AAGAAGGATATCGTGCCCAAATAGATTGACT
* *
55390 GATTGGATTTCAACTTCACAATGAAAGATATCAAACCCAAAGCCAATTTGGCGAAGTACTATAAC
1 GATTGGATTTCAACTTCACAATGAAAGATATCCAACCCAAAGCCAATTTGGCGAAGCACTATAAC
* * *
55455 TCGAGATTGGATTTCAATTTCACAACGAAGGACATCCAATTCAAAGCTCAACTTCACAATGAAGG
66 TCGAGATTGGATTTCAACTTCACAATGAAGGACATCCAATTCAAAGCTCAACTTCACAACGAAGG
* * * *
55520 AGCCATCCACGATTTCAACTTCACGAAGAAGGATATCGTGCCTAAATGGATTGATT
131 AGCCATCCACGATTTCAACTTCACAAAGAAGGATATCGTGCCCAAATAGATTGACT
* * * *
55576 GATTGGATTTCAACTTCACAACG-AAGAATATCCAACCCAAAGCCAATTTGGAGAAGCATTACAA
1 GATTGGATTTCAACTTCACAATGAAAG-ATATCCAACCCAAAGCCAATTTGGCGAAGCACTATAA
* * * *
55640 CTCGATATTGGATTTCAACTTCACAATGAAGGACATCCAATTCAATGCTTAACTTCACAACGAAA
65 CTCGAGATTGGATTTCAACTTCACAATGAAGGACATCCAATTCAAAGCTCAACTTCACAACGAAG
** * *
55705 GAGTTATCTACGATTTCAACTTCACAAAGAATGATATCGTGCCCAAATAGATTGACT
130 GAGCCATCCACGATTTCAACTTCACAAAGAAGGATATCGTGCCCAAATAGATTGACT
55762 TAAGTTTTAC
Statistics
Matches: 332, Mismatches: 35, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
183 43 0.13
185 3 0.01
186 286 0.86
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.25
Consensus pattern (186 bp):
GATTGGATTTCAACTTCACAATGAAAGATATCCAACCCAAAGCCAATTTGGCGAAGCACTATAAC
TCGAGATTGGATTTCAACTTCACAATGAAGGACATCCAATTCAAAGCTCAACTTCACAACGAAGG
AGCCATCCACGATTTCAACTTCACAAAGAAGGATATCGTGCCCAAATAGATTGACT
Found at i:56576 original size:36 final size:34
Alignment explanation
Indices: 56524--56778 Score: 132
Period size: 36 Copynumber: 6.8 Consensus size: 34
56514 ATTTTTGAAA
*
56524 AAAAAATATAATATATAGTTTTTAGAAAACGGTTTG
1 AAAATATATAATATATAG-TTTT-GAAAACGGTTTG
* * * *
56560 AAAACATATAATATATACTTTTTAAAAAAATTGGTTTTTG
1 AAAATATATAATATATA-GTTTT--GAAAA-CGG--TTTG
* * *
56600 AAAATATATATTATATAGTTTTGAAAATGATTTTTG
1 AAAATATATAATATATAGTTTTGAAAACG--GTTTG
* *
56636 AAAATATATATTATATAGTTTTGAAAACGATTTTTG
1 AAAATATATAATATATAGTTTTGAAAACG--GTTTG
***
56672 AATATATATATATATATTATATAGTTTTGAAAATAATTTTTG
1 -A-A-A-ATATATA-A-TATATAGTTTTG-AAA-ACGGTTTG
* **
56714 AAGATATATATATTATATAGTTTTGAAAACAATTTTTG
1 AA-A-ATATATAATATATAGTTTTGAAAAC--GGTTTG
* *
56752 AACATATATATTATATAGTTTTGAAAA
1 AAAATATATAATATATAGTTTTGAAAA
56779 TATATATAAT
Statistics
Matches: 185, Mismatches: 17, Indels: 34
0.78 0.07 0.14
Matches are distributed among these distances:
36 86 0.46
37 13 0.07
38 23 0.12
39 5 0.03
40 36 0.19
41 1 0.01
42 17 0.09
43 3 0.02
44 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (34 bp):
AAAATATATAATATATAGTTTTGAAAACGGTTTG
Found at i:56615 original size:40 final size:38
Alignment explanation
Indices: 56556--56778 Score: 156
Period size: 36 Copynumber: 5.8 Consensus size: 38
56546 TAGAAAACGG
* * *
56556 TTTGAAAACATATAATATATACTTTTTAAAAAAATTGGTT
1 TTTGAAAATATATATTATATA-TTTTTAAAAAAA-TGATT
* *
56596 TTTGAAAATATATATTATATAGTTTT--GAAAATGATT
1 TTTGAAAATATATATTATATATTTTTAAAAAAATGATT
* * *
56632 TTTGAAAATATATATTATATAGTTTT--GAAAACGATT
1 TTTGAAAATATATATTATATATTTTTAAAAAAATGATT
* *
56668 TTTGAATATATATATATATATTATATAGTTTT--GAAAATAATT
1 TTTGAA-A-ATATATAT-TA-TATAT--TTTTAAAAAAATGATT
* * *
56710 TTTGAAGATATATATATTATATAGTTTTGAAAACA--ATT
1 TTTGAA-A-ATATATATTATATATTTTTAAAAAAATGATT
* * *
56748 TTTGAACATATATATTATATAGTTTTGAAAA
1 TTTGAAAATATATATTATATATTTTTAAAAA
56779 TATATATAAT
Statistics
Matches: 161, Mismatches: 14, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
36 69 0.43
37 5 0.03
38 21 0.13
39 6 0.04
40 30 0.19
41 2 0.01
42 28 0.17
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (38 bp):
TTTGAAAATATATATTATATATTTTTAAAAAAATGATT
Found at i:56681 original size:38 final size:36
Alignment explanation
Indices: 56594--56778 Score: 253
Period size: 36 Copynumber: 4.9 Consensus size: 36
56584 AAAAAATTGG
**
56594 TTTTTGAAAATATATATTATATAGTTTTGAAAATGA
1 TTTTTGAAAATATATATTATATAGTTTTGAAAACAA
*
56630 TTTTTGAAAATATATATTATATAGTTTTGAAAACGA
1 TTTTTGAAAATATATATTATATAGTTTTGAAAACAA
*
56666 TTTTTGAATATATATATATATATTATATAGTTTTGAAAATAA
1 TTTTTG---A-A-A-ATATATATTATATAGTTTTGAAAACAA
56708 TTTTTGAAGATATATATATTATATAGTTTTGAAAACAA
1 TTTTTGAA-A-ATATATATTATATAGTTTTGAAAACAA
*
56746 TTTTTGAACATATATATTATATAGTTTTGAAAA
1 TTTTTGAAAATATATATTATATAGTTTTGAAAA
56779 TATATATAAT
Statistics
Matches: 137, Mismatches: 6, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
36 65 0.47
38 37 0.27
39 2 0.01
40 1 0.01
41 1 0.01
42 31 0.23
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.47
Consensus pattern (36 bp):
TTTTTGAAAATATATATTATATAGTTTTGAAAACAA
Found at i:56792 original size:61 final size:60
Alignment explanation
Indices: 56709--56828 Score: 188
Period size: 61 Copynumber: 2.0 Consensus size: 60
56699 TGAAAATAAT
* *
56709 TTTTGAAGATATATATATTATATAGTTTTGAAAACAATTTTTGAACATATATAT-TATATAG
1 TTTTGAAAATATATATAATATATAGTTTTGAAAA-AATTTTTGAA-ATATATATATATATAG
*
56770 TTTTGAAAATATATATAATATATAGTTTTGAAAATATTTTTGAAATATATATATATATA
1 TTTTGAAAATATATATAATATATAGTTTTGAAAAAATTTTTGAAATATATATATATATA
56829 TATATATTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
59 8 0.15
60 15 0.27
61 32 0.58
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (60 bp):
TTTTGAAAATATATATAATATATAGTTTTGAAAAAATTTTTGAAATATATATATATATAG
Found at i:56819 original size:27 final size:25
Alignment explanation
Indices: 56747--56806 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
56737 TGAAAACAAT
*
56747 TTTTGAACATATATAT--TATATAG
1 TTTTGAAAATATATATAATATATAG
56770 TTTTGAAAATATATATAATATATAG
1 TTTTGAAAATATATATAATATATAG
56795 TTTTGAAAATAT
1 TTTTGAAAATAT
56807 TTTTGAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 15 0.44
25 19 0.56
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (25 bp):
TTTTGAAAATATATATAATATATAG
Found at i:56849 original size:23 final size:24
Alignment explanation
Indices: 56747--56846 Score: 66
Period size: 25 Copynumber: 4.2 Consensus size: 24
56737 TGAAAACAAT
*
56747 TTTTGA-ACATATATATTATATAG
1 TTTTGATATATATATATTATATAG
* *
56770 TTTTGAAAATATATATAATATATAG
1 TTTTG-ATATATATATATTATATAG
* *
56795 TTTTGA-AAATAT-TTTTGAAATATA-
1 TTTTGATATATATATATT---ATATAG
*
56819 TATAT-ATATATATATATTATATAG
1 T-TTTGATATATATATATTATATAG
56843 TTTT
1 TTTT
56847 ATAACATTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
22 2 0.03
23 17 0.29
24 5 0.08
25 32 0.54
26 3 0.05
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.50
Consensus pattern (24 bp):
TTTTGATATATATATATTATATAG
Found at i:67820 original size:16 final size:17
Alignment explanation
Indices: 67787--67824 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
67777 GGATAAATTT
*
67787 ATAAAATTTTATAAAAA
1 ATAAAAATTTATAAAAA
67804 ATAAAAATTTA-AAAAA
1 ATAAAAATTTATAAAAA
67820 ATAAA
1 ATAAA
67825 GTGCGTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAAATTTATAAAAA
Found at i:70097 original size:23 final size:23
Alignment explanation
Indices: 70067--70115 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
70057 ATTATATTAC
*
70067 ATTTTAAAAATATTAATTAATAT
1 ATTTTAAAAATATTAATTAAAAT
* * *
70090 ATTTTAAATATCTTTATTAAAAT
1 ATTTTAAAAATATTAATTAAAAT
70113 ATT
1 ATT
70116 ATTAGATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTTAAAAATATTAATTAAAAT
Found at i:70117 original size:11 final size:11
Alignment explanation
Indices: 70073--70132 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
70063 TTACATTTTA
70073 AAAATATTAATT
1 AAAATATT-ATT
*
70085 AATATATT-TT
1 AAAATATTATT
*
70095 AAATATCTTTATT
1 AAA-AT-ATTATT
70108 AAAATATTATT
1 AAAATATTATT
* *
70119 AGATTATTATT
1 AAAATATTATT
70130 AAA
1 AAA
70133 CACATAAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
10 4 0.11
11 18 0.47
12 11 0.29
13 5 0.13
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (11 bp):
AAAATATTATT
Found at i:70174 original size:27 final size:25
Alignment explanation
Indices: 70139--70231 Score: 89
Period size: 27 Copynumber: 3.5 Consensus size: 25
70129 TAAACACATA
70139 AATAATATTATTCATTATTAATAATTT
1 AATAATATTATT--TTATTAATAATTT
* *
70166 AATAATATTATTTCTATGAAATTAA-TA
1 AATAATATTATTT-TAT-TAA-TAATTT
70193 AATAATATTAATTTTATTAATAATTT
1 AATAATATT-ATTTTATTAATAATTT
*
70219 ATTATATATTATT
1 AATA-ATATTATT
70232 AAAATAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
25 4 0.07
26 12 0.22
27 32 0.58
28 7 0.13
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (25 bp):
AATAATATTATTTTATTAATAATTT
Found at i:70247 original size:54 final size:53
Alignment explanation
Indices: 70136--70271 Score: 129
Period size: 54 Copynumber: 2.6 Consensus size: 53
70126 TATTAAACAC
*** * **
70136 ATAAATAATATTATTCATTATTAATAATTTAATAATATTATTTCTATGAAATTA
1 ATAAATAATATTATT-ATTATTAATAATTTAATAATATTATTAAAATAAAAAAA
*
70190 ATAAATAATATTAATT-TTATTAATAATTTATTATATATTATTAAAATAAAAAAA
1 ATAAATAATATT-ATTATTATTAATAATTTAATA-ATATTATTAAAATAAAAAAA
* *
70244 AT-AAT-ATCTTA-TATTATT-ATAATATAAT
1 ATAAATAATATTATTATTATTAATAATTTAAT
70272 TGAGTATTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
50 9 0.13
51 6 0.09
52 4 0.06
53 19 0.28
54 28 0.41
55 3 0.04
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (53 bp):
ATAAATAATATTATTATTATTAATAATTTAATAATATTATTAAAATAAAAAAA
Found at i:70311 original size:8 final size:8
Alignment explanation
Indices: 70298--70351 Score: 58
Period size: 8 Copynumber: 6.9 Consensus size: 8
70288 ATATTTAAAA
70298 AATATTAT
1 AATATTAT
*
70306 ATTATTAT
1 AATATTAT
70314 AATATTA-
1 AATATTAT
*
70321 AA-AATAT
1 AATATTAT
70328 AATATTAT
1 AATATTAT
*
70336 ATTATTAT
1 AATATTAT
70344 AAATATTA
1 -AATATTA
70352 ATAAATATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
6 3 0.08
7 4 0.11
8 24 0.65
9 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATATTAT
Found at i:70333 original size:22 final size:23
Alignment explanation
Indices: 70281--70354 Score: 87
Period size: 22 Copynumber: 3.1 Consensus size: 23
70271 TTGAGTATTT
70281 TATTATAATATTTAAAAAATATTATA
1 TATTATAATA-TT-AAAAATATTA-A
70307 TTATTATAATATTAAAAATA-TAA
1 -TATTATAATATTAAAAATATTAA
* *
70330 TATTATATTATTATAAATATTAA
1 TATTATAATATTAAAAATATTAA
70353 TA
1 TA
70355 AATATATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
22 17 0.39
23 6 0.14
24 2 0.05
25 7 0.16
26 2 0.05
27 10 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:70334 original size:30 final size:30
Alignment explanation
Indices: 70280--70360 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 30
70270 ATTGAGTATT
*
70280 TTATTATAATATT-TAAA-A-AATATTATA
1 TTATTATAATATTAAAAATATAATATTATA
70307 TTATTATAATATTAAAAATATAATATTATA
1 TTATTATAATATTAAAAATATAATATTATA
70337 TTATTATAAATATTAATAAATATA
1 TTATTAT-AATATTAA-AAATATA
70361 TTTTAAATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
27 13 0.27
28 3 0.06
29 1 0.02
30 16 0.33
31 8 0.17
32 7 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TTATTATAATATTAAAAATATAATATTATA
Found at i:78610 original size:18 final size:18
Alignment explanation
Indices: 78587--78622 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
78577 GATACTAAGG
* *
78587 TGATGGGGTATCGCTACT
1 TGATGGAGTATCGATACT
78605 TGATGGAGTATCGATACT
1 TGATGGAGTATCGATACT
78623 AATTTTTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (18 bp):
TGATGGAGTATCGATACT
Found at i:79953 original size:41 final size:41
Alignment explanation
Indices: 79894--80028 Score: 146
Period size: 41 Copynumber: 3.3 Consensus size: 41
79884 CTTTTTAAGG
* *
79894 TTAGGTTTTAGGACTTAGGATTTGAGATTTAACTTTAGGAT
1 TTAGGGTTTAGAACTTAGGATTTGAGATTTAACTTTAGGAT
* * * * *
79935 TTAGGGTTTATAATTTAGGATTAGAGATTTAAGGTTTTGG-T
1 TTAGGGTTTAGAACTTAGGATTTGAGATTTAA-CTTTAGGAT
** * *
79976 TTAAAGTTTAGAACTTAGGGTTTGAGATTTAAACTTTAGAAT
1 TTAGGGTTTAGAACTTAGGATTTGAGATTT-AACTTTAGGAT
80018 TTAGGGTTTAG
1 TTAGGGTTTAG
80029 GTTTAAAGTT
Statistics
Matches: 73, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
41 56 0.77
42 17 0.23
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.44
Consensus pattern (41 bp):
TTAGGGTTTAGAACTTAGGATTTGAGATTTAACTTTAGGAT
Found at i:79986 original size:28 final size:27
Alignment explanation
Indices: 79955--80039 Score: 91
Period size: 28 Copynumber: 3.1 Consensus size: 27
79945 TAATTTAGGA
79955 TTAGAGATTTAAGGTTTTGGTTTAAAGT
1 TTAGA-ATTTAAGGTTTTGGTTTAAAGT
* * *
79983 TTAGAACTT-AGGGTTTGAGATTTAAACT
1 TTAGAATTTAAGGTTTTG-G-TTTAAAGT
* *
80011 TTAGAATTTAGGGTTTAGGTTTAAAGT
1 TTAGAATTTAAGGTTTTGGTTTAAAGT
80038 TT
1 TT
80040 GATATTGGAG
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
26 7 0.15
27 13 0.28
28 21 0.46
29 5 0.11
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.45
Consensus pattern (27 bp):
TTAGAATTTAAGGTTTTGGTTTAAAGT
Found at i:80027 original size:14 final size:14
Alignment explanation
Indices: 79927--80028 Score: 57
Period size: 14 Copynumber: 7.4 Consensus size: 14
79917 GAGATTTAAC
* *
79927 TTTAGGATTTAGGG
1 TTTAGAATTTAAGG
*
79941 TTTATAATTT-AGG
1 TTTAGAATTTAAGG
*
79954 ATTAGAGATTTAAGG
1 TTTAGA-ATTTAAGG
* * *
79969 TTTTG-GTTTAAAG
1 TTTAGAATTTAAGG
* *
79982 TTTAGAACTTAGGG
1 TTTAGAATTTAAGG
**
79996 TTT-GAGATTTAAAC
1 TTTAGA-ATTTAAGG
*
80010 TTTAGAATTTAGGG
1 TTTAGAATTTAAGG
80024 TTTAG
1 TTTAG
80029 GTTTAAAGTT
Statistics
Matches: 62, Mismatches: 21, Indels: 10
0.67 0.23 0.11
Matches are distributed among these distances:
13 18 0.29
14 36 0.58
15 8 0.13
ACGTcount: A:0.29, C:0.02, G:0.25, T:0.44
Consensus pattern (14 bp):
TTTAGAATTTAAGG
Found at i:81419 original size:30 final size:30
Alignment explanation
Indices: 81329--81434 Score: 83
Period size: 30 Copynumber: 3.6 Consensus size: 30
81319 GACTATGCTT
* *
81329 GTGTTCGTTTCTTTA-TTTTTAAGGTGTTT
1 GTGTTCGTTTGTTTATTTTTTAAGGTGTTC
* ** ** *
81358 ATGTTC-TTT-TAAATTTTTAATATTGTATTC
1 GTGTTCGTTTGTTTATTTTT--TAAGGTGTTC
81388 GTGTTCGTTTGTTTATTTTTTAAGGTGTTC
1 GTGTTCGTTTGTTTATTTTTTAAGGTGTTC
* *
81418 GTTTTCGTTCGTTTATT
1 GTGTTCGTTTGTTTATT
81435 GCTTGAAAAC
Statistics
Matches: 57, Mismatches: 15, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
27 2 0.04
28 7 0.12
29 5 0.09
30 33 0.58
31 3 0.05
32 7 0.12
ACGTcount: A:0.14, C:0.08, G:0.17, T:0.61
Consensus pattern (30 bp):
GTGTTCGTTTGTTTATTTTTTAAGGTGTTC
Found at i:83744 original size:78 final size:78
Alignment explanation
Indices: 83646--83794 Score: 176
Period size: 77 Copynumber: 1.9 Consensus size: 78
83636 ATATAGTAAG
** * *
83646 TAAACATTAAAAGAATGTAATTTTGATTACAACTCTTTTAATCGATATTTAATTCGGAAT-AATT
1 TAAACATTAAAAGAATGTAATTCAGATTACAACTC-TTTAATCGATATCTAATT-GAAATAAATT
83710 AAATAAGAGTTTAAA
64 AAATAAGAGTTTAAA
* * * * * *
83725 TAAACGTT-AAAGATTGTAATTCAGATTATAAGTCTTTAATGGATATCTAATTTAAATAAATTAA
1 TAAACATTAAAAGAATGTAATTCAGATTACAACTCTTTAATCGATATCTAATTGAAATAAATTAA
83789 ATAAGA
66 ATAAGA
83795 TTTTTATTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
76 3 0.05
77 28 0.47
78 21 0.36
79 7 0.12
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.38
Consensus pattern (78 bp):
TAAACATTAAAAGAATGTAATTCAGATTACAACTCTTTAATCGATATCTAATTGAAATAAATTAA
ATAAGAGTTTAAA
Found at i:84357 original size:2 final size:2
Alignment explanation
Indices: 84350--84535 Score: 72
Period size: 2 Copynumber: 96.5 Consensus size: 2
84340 TTTATTTTAA
* *
84350 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT CA- AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A-T AT
* * * * *
84393 AT AG GT -T TT A- AA AA AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * *
84432 TT A- AA ACT AT AT AT AA AA AT AT -T AC AT AT AT AT -T TT CA- AA
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
* * * * *
84472 AC A- AT AT AT AT AT AT AT GT -T TT CA- AA AC A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
84511 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
84536 AAAAACCATA
Statistics
Matches: 147, Mismatches: 20, Indels: 34
0.73 0.10 0.17
Matches are distributed among these distances:
1 12 0.08
2 133 0.90
3 2 0.01
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:84504 original size:24 final size:26
Alignment explanation
Indices: 84449--84516 Score: 111
Period size: 26 Copynumber: 2.7 Consensus size: 26
84439 TATATATAAA
*
84449 AATAT-TACATATATATTTTCAAAAC
1 AATATATATATATATATTTTCAAAAC
*
84474 AATATATATATATATGTTTTCAAAAC
1 AATATATATATATATATTTTCAAAAC
84500 AATATATATATATATAT
1 AATATATATATATATAT
84517 ATATATATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 5 0.13
26 34 0.87
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (26 bp):
AATATATATATATATATTTTCAAAAC
Found at i:94113 original size:20 final size:20
Alignment explanation
Indices: 94088--94138 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
94078 CTTTATATAA
94088 CTTGAATCCACTAAAATGAG
1 CTTGAATCCACTAAAATGAG
94108 CTTGAATCCACTAAAATGAG
1 CTTGAATCCACTAAAATGAG
*
94128 CTAGAATCCAC
1 CTTGAATCCAC
94139 AATTTTCTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.24, G:0.14, T:0.24
Consensus pattern (20 bp):
CTTGAATCCACTAAAATGAG
Done.