Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005182.1 Hibiscus syriacus cultivar Beakdansim tig00011701_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: 61071
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3140 original size:40 final size:41
Alignment explanation
Indices: 3039--3141 Score: 113
Period size: 41 Copynumber: 2.5 Consensus size: 41
3029 CCCAAAATAG
* *
3039 TAAGTCCTT-GGGCCATCAGTAAGTCTTTCGAGCATGATGATT
1 TAAGTCCTTCGGGCCATCTGT-AGTCTTTCGAGCAAGATGA-T
* * *
3081 TAA-ACCTTCGGGTCATCTGTAGTCTTTTGAGCAAGATGA-
1 TAAGTCCTTCGGGCCATCTGTAGTCTTTCGAGCAAGATGAT
*
3120 TAAGTCCTTCGAGCCATCTGTA
1 TAAGTCCTTCGGGCCATCTGTA
3142 AGACCATCGG
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
39 3 0.06
40 15 0.29
41 21 0.41
42 12 0.24
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (41 bp):
TAAGTCCTTCGGGCCATCTGTAGTCTTTCGAGCAAGATGAT
Found at i:3600 original size:41 final size:41
Alignment explanation
Indices: 3546--3655 Score: 116
Period size: 41 Copynumber: 2.7 Consensus size: 41
3536 TATTTCCCAA
* *
3546 ATGGTAAGTCCTTCGGGCCATCAGTAAGTC-TTCGAGCATG
1 ATGGTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAG
* * **
3586 ATGATTAAATCCTTCGGG-TATTTTGTAAGTCTTTCGAGCAAG
1 ATG-GTAAATCCTTCGGGCCA-TCAGTAAGTCTTTCGAGCAAG
* *
3628 ATGGTAAGTCCTTCGGGCCATCCGTAAG
1 ATGGTAAATCCTTCGGGCCATCAGTAAG
3656 ACCTTCAAGT
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
40 4 0.07
41 38 0.69
42 13 0.24
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (41 bp):
ATGGTAAATCCTTCGGGCCATCAGTAAGTCTTTCGAGCAAG
Found at i:3670 original size:255 final size:258
Alignment explanation
Indices: 2917--3866 Score: 1323
Period size: 255 Copynumber: 3.7 Consensus size: 258
2907 TTAAGTTGAT
* * *
2917 TTTCAAAAAATGAG-AACCGATTTCCAAAGTTTTTCATTTAATCTTTTCTAAAAATGAAATTTTT
1 TTTCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATCTTTTCTAAAAATGAAATTTTT
* * *
2981 GAAAAGTAAGAAAGTGATTTCCAAAGTTTATTACCCAGTAAACTATTTCCCAAAATAGTAAGTCC
66 GAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTAGTAAGTCC
3046 TT-GGGCCATCAGTAAGTCTTTCGAGCATGATGATTTAAA-CCTTCGGGTCATCTGT-AGTCTTT
131 TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGA-TTAAATCCTTCGGGTCATCTGTAAGTCTTT
* * * * **
3108 TGAGCAAGATGATAAGTCCTTCGAGCCATCTGTAAGACCATCGGGTAGGATGTTTTCACATGAA
195 CGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCAAGTAGGATGTTTTCACATGAA
* * *
3172 TTTCGTAAAATGAGAAAGCGATTTCCAAAGTTTCTAATTTAATCTTTTCTGAAAATGAAATTTTT
1 TTTCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATCTTTTCTAAAAATGAAATTTTT
* * * *
3237 GAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCTAAATTGGTAAGTCA
66 GAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTAGTAAGTCC
* ** *
3302 TTCAGGCCATCAGTAAGTCTTTTAAGCATGATGATTAAATCCTTCGGATCATCTGTAAGTC-TTC
131 TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTC
* * * * * *
3366 GAGCAAGATGATTAGTCCTTTGGGCCATCCATAAGACCTTCATGTAGGATATTTTCACGTGAA
196 GAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCAAGTAGGATGTTTTCACATGAA
* * * *
3429 TTTTGAAAAATGAGAAAGTGATTTCCAAAGTTTATCATTTAATCTTTTTTAAAAATG-AATTTTT
1 TTTCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATCTTTTCTAAAAATGAAATTTTT
* * *
3493 TAAAAGTAAGAAAGCGATTTCTAAAGTTTCTTACCCAGTAAACTATTTCCCAAA-TGGTAAGTCC
66 GAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTAGTAAGTCC
*
3557 TTCGGGCCATCAGTAAGTC-TTCGAGCATGATGATTAAATCCTTCGGGT-ATTTTGTAAGTCTTT
131 TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCA-TCTGTAAGTCTTT
*
3620 CGAGCAAGATGGTAAGTCCTTCGGGCCATCCGTAAGACCTTCAAGTAGGATGTTTTCACATGAA
195 CGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCAAGTAGGATGTTTTCACATGAA
* * * * * *
3684 CTTCGAAATATGAGAAAGTGATTTTCAAAGTTTCTCA-TTAATGTTTT-TAGAAAATGAAAATTT
1 TTTCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATCTTTTCTA-AAAATGAAATTTT
* *
3747 TGAAAAGTAAGAAAGCGATTTCCAAA-ATT-TTACCCAGTAAACTATTTCCAAAATTAGTAAGTC
65 TGAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTAGTAAGTC
* * * * *
3810 CTTCGGGCCATTAGTAAGTGTTTCGAGCATGATGATTAAATCTTTTGGGTTATCTGT
130 CTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGT
3867 CGGTCTCACT
Statistics
Matches: 615, Mismatches: 69, Indels: 22
0.87 0.10 0.03
Matches are distributed among these distances:
253 26 0.04
254 78 0.13
255 190 0.31
256 169 0.27
257 148 0.24
258 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (258 bp):
TTTCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATCTTTTCTAAAAATGAAATTTTT
GAAAAGTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCCAAATTAGTAAGTCC
TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTAAGTCTTTC
GAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAGACCTTCAAGTAGGATGTTTTCACATGAA
Found at i:3670 original size:512 final size:509
Alignment explanation
Indices: 2922--3851 Score: 1424
Period size: 512 Copynumber: 1.8 Consensus size: 509
2912 TTGATTTTCA
*
2922 AAAAATGAGAACCGATTTCCAAAGTTTTTCATTTAATCTTTTCTAAAAATGAAATTTTTGAAAAG
1 AAAAATGAGAACCGATTTCCAAAGTTTATCATTTAATCTTTTCTAAAAATGAAATTTTTGAAAAG
*
2987 TAAGAAAGTGATTTCCAAAGTTTATTACCCAGTAAACTATTTCCCAAAATAGTAAGTCCTTGGGC
66 TAAGAAAGCGATTTCCAAAGTTTATTACCCAGTAAACTATTTCCCAAAATAGTAAGTCCTTGGGC
*
3052 CATCAGTAAGTCTTTCGAGCATGATGATTTAAACCTTCGGGTCATCTGTAGTCTTTTGAGCAAGA
131 CATCAGTAAGTCTTTCGAGCATGATGATTTAAACCTTCGGGTCATCTGTAGTCTTTCGAGCAAGA
* ** *
3117 TGATAAGTCCTTCGAGCCATCTGTAAGACCATCGGGTAGGATGTTTTCACATGAATTTCGTAAA-
196 TGATAAGTCCTTCGAGCCATCCGTAAGACCATCAAGTAGGATGTTTTCACATGAACTTCG-AAAT
*
3181 ATGAGAAAGCGATTTCCAAAGTTTCTAATTTAATCTTTTCT-GAAAATGAAATTTTTGAAAAGTA
260 ATGAGAAAGCGATTTCCAAAGTTTCTAA-TTAATCTTTT-TAGAAAATGAAAATTTTGAAAAGTA
* * * *
3245 AGAAAGCGATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCTAAATTGGTAAGTCATTCAGGCC
323 AGAAAGCGATTTCCAAA-ATT-TTACCCAGTAAACTATTTCCAAAATTAGTAAGTCATTCAGGCC
*
3310 ATCAGTAAGTCTTTTAAGCATGATGATTAAATCCTTCGGATCATCTGTAAGTCTTCGAGCAAGAT
386 ATCAGTAAGTCTTTCAAGCATGATGATTAAATCCTTCGGATCATCTGTAAGTCTTCGAGCAAGAT
3375 GATTAGTCCTTTGGGCCATCCATAAGACCTTCATGTAGGATATTTTCACGTGAATTTTG
451 GATTAGTCCTTTGGGCCATCCATAAGACCTTCATGTAGGATATTTTCACGTGAATTTTG
** * *
3434 AAAAATGAGAAAGTGATTTCCAAAGTTTATCATTTAATCTTTTTTAAAAATG-AATTTTTTAAAA
1 AAAAATGAG-AACCGATTTCCAAAGTTTATCATTTAATCTTTTCTAAAAATGAAATTTTTGAAAA
* * *
3498 GTAAGAAAGCGATTTCTAAAGTTTCTTACCCAGTAAACTATTTCCC-AAATGGTAAGTCCTTCGG
65 GTAAGAAAGCGATTTCCAAAGTTTATTACCCAGTAAACTATTTCCCAAAATAGTAAGTCCTT-GG
*
3562 GCCATCAGTAAGTC-TTCGAGCATGATGA-TTAAATCCTTCGGGT-ATTTTGTAAGTCTTTCGAG
129 GCCATCAGTAAGTCTTTCGAGCATGATGATTTAAA-CCTTCGGGTCA-TCTGT-AGTCTTTCGAG
* * *
3624 CAAGATGGTAAGTCCTTCGGGCCATCCGTAAGACCTTCAAGTAGGATGTTTTCACATGAACTTCG
191 CAAGATGATAAGTCCTTCGAGCCATCCGTAAGACCATCAAGTAGGATGTTTTCACATGAACTTCG
* * * *
3689 AAATATGAGAAAGTGATTTTCAAAGTTTCTCATTAATGTTTTTAGAAAATGAAAATTTTGAAAAG
256 AAATATGAGAAAGCGATTTCCAAAGTTTCTAATTAATCTTTTTAGAAAATGAAAATTTTGAAAAG
* *
3754 TAAGAAAGCGATTTCCAAAATTTTACCCAGTAAACTATTTCCAAAATTAGTAAGTCCTTCGGGCC
321 TAAGAAAGCGATTTCCAAAATTTTACCCAGTAAACTATTTCCAAAATTAGTAAGTCATTCAGGCC
* * *
3819 ATTAGTAAGTGTTTCGAGCATGATGATTAAATC
386 ATCAGTAAGTCTTTCAAGCATGATGATTAAATC
3852 TTTTGGGTTA
Statistics
Matches: 378, Mismatches: 33, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
509 67 0.18
510 9 0.02
511 92 0.24
512 172 0.46
513 38 0.10
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (509 bp):
AAAAATGAGAACCGATTTCCAAAGTTTATCATTTAATCTTTTCTAAAAATGAAATTTTTGAAAAG
TAAGAAAGCGATTTCCAAAGTTTATTACCCAGTAAACTATTTCCCAAAATAGTAAGTCCTTGGGC
CATCAGTAAGTCTTTCGAGCATGATGATTTAAACCTTCGGGTCATCTGTAGTCTTTCGAGCAAGA
TGATAAGTCCTTCGAGCCATCCGTAAGACCATCAAGTAGGATGTTTTCACATGAACTTCGAAATA
TGAGAAAGCGATTTCCAAAGTTTCTAATTAATCTTTTTAGAAAATGAAAATTTTGAAAAGTAAGA
AAGCGATTTCCAAAATTTTACCCAGTAAACTATTTCCAAAATTAGTAAGTCATTCAGGCCATCAG
TAAGTCTTTCAAGCATGATGATTAAATCCTTCGGATCATCTGTAAGTCTTCGAGCAAGATGATTA
GTCCTTTGGGCCATCCATAAGACCTTCATGTAGGATATTTTCACGTGAATTTTG
Found at i:4014 original size:3 final size:3
Alignment explanation
Indices: 4008--4057 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
3998 TTAATAATAA
4008 TAT TAT TA- TAT TAT TAT TAT TAT TA- TAT T-T ATAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
4050 TAT T-T TAT
1 TAT TAT TAT
4058 GTAGGTCCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
2 9 0.22
3 31 0.76
4 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:4030 original size:17 final size:17
Alignment explanation
Indices: 4008--4057 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
3998 TTAATAATAA
4008 TATTATTATATTATTAT
1 TATTATTATATTATTAT
4025 TATTATTATA-T-TTA-
1 TATTATTATATTATTAT
*
4039 TATTATTTTATTATT-T
1 TATTATTATATTATTAT
4055 TAT
1 TAT
4058 GTAGGTCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 9 0.31
15 4 0.14
16 6 0.21
17 10 0.34
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTATTATATTATTAT
Found at i:4054 original size:8 final size:8
Alignment explanation
Indices: 4008--4057 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
3998 TTAATAATAA
*
4008 TATTATTA
1 TATTATTT
4016 TATTA--T
1 TATTATTT
4022 TATTATTAT
1 TATTATT-T
4031 TA-TATTT
1 TATTATTT
4038 ATATTATTT
1 -TATTATTT
4047 TATTATTT
1 TATTATTT
4055 TAT
1 TAT
4058 GTAGGTCCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
6 5 0.14
7 1 0.03
8 22 0.61
9 8 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (8 bp):
TATTATTT
Found at i:10571 original size:19 final size:18
Alignment explanation
Indices: 10530--10572 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 18
10520 TCAAAAAAAA
10530 TTAAAATATATATATATT
1 TTAAAATATATATATATT
10548 TTAAAATA-ATATTATATT
1 TTAAAATATATA-TATATT
10566 TATAAAA
1 T-TAAAA
10573 ATCTCTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.13
18 15 0.65
19 5 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAAAATATATATATATT
Found at i:10670 original size:25 final size:25
Alignment explanation
Indices: 10636--10692 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
10626 TAACTCACCG
10636 TCGTCGCCCTTTCTGACAACGATCA
1 TCGTCGCCCTTTCTGACAACGATCA
*
10661 TCGTCGCCCTTTCTGACCACGATCA
1 TCGTCGCCCTTTCTGACAACGATCA
10686 TCGTCGC
1 TCGTCGC
10693 TGACATAGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.16, C:0.39, G:0.18, T:0.28
Consensus pattern (25 bp):
TCGTCGCCCTTTCTGACAACGATCA
Found at i:11319 original size:26 final size:26
Alignment explanation
Indices: 11283--11344 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
11273 TATACCGTGC
11283 TCGACGAGCAGCGATAAACACCACTA
1 TCGACGAGCAGCGATAAACACCACTA
*
11309 TCGACGAGCAGCGATAAACATCACTA
1 TCGACGAGCAGCGATAAACACCACTA
*
11335 ACGACGAGCA
1 TCGACGAGCA
11345 TCATTAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.39, C:0.29, G:0.21, T:0.11
Consensus pattern (26 bp):
TCGACGAGCAGCGATAAACACCACTA
Found at i:12649 original size:21 final size:21
Alignment explanation
Indices: 12621--12662 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
12611 ATAGTTTACA
12621 CTTTA-TTTTAAATAATTTAT
1 CTTTATTTTTAAATAATTTAT
*
12641 CTTTAATTTTTAACTAATTTAT
1 CTTT-ATTTTTAAATAATTTAT
12663 AATTATACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 1 0.05
22 14 0.74
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (21 bp):
CTTTATTTTTAAATAATTTAT
Found at i:12879 original size:22 final size:22
Alignment explanation
Indices: 12854--12910 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
12844 TGATAAAAAT
*
12854 ATTATTACAAACATCAATAGTA
1 ATTATAACAAACATCAATAGTA
12876 ATTATAACAAACATCAATAGTA
1 ATTATAACAAACATCAATAGTA
12898 ATTATAACAAACA
1 ATTATAACAAACA
12911 AATTGAAGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.54, C:0.14, G:0.04, T:0.28
Consensus pattern (22 bp):
ATTATAACAAACATCAATAGTA
Found at i:13954 original size:13 final size:13
Alignment explanation
Indices: 13936--13968 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
13926 TATATATAAT
13936 AAAATAGTTTTT-A
1 AAAATA-TTTTTGA
13949 AAAATATTTTTGA
1 AAAATATTTTTGA
13962 AAAATAT
1 AAAATAT
13969 ATATAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (13 bp):
AAAATATTTTTGA
Found at i:13986 original size:68 final size:67
Alignment explanation
Indices: 13914--14153 Score: 195
Period size: 72 Copynumber: 3.4 Consensus size: 67
13904 TAAAAAGCAG
*
13914 TTTTTGAAAATA-TAT-ATATA-ATA-AAATAGTTTTTAAAAATATTTTTGAAAAATATATATAA
1 TTTTTGAAAATATTATAATATATATATAAATAG-TTTT-AAAACA-TTTTGAAAAAT-TATATAA
13975 TATATAA
62 TATAT-A
* * *
13982 TTTTT-AAAATATTTTGAATATATATATATATAGTTTTAAAACATTTTGAAAACTTATATAATAT
1 TTTTTGAAAATATTAT-AATATATATATAAATAGTTTTAAAACATTTTGAAAAATTATATAATAT
14046 ATA
65 ATA
* * * *
14049 GTTTTGAAAACATTTTGAAAAAATATATATAATATATAGTTTTAAAAACATTTTGAAAAAATATA
1 TTTTTG-AAA-ATATT---ATAATATATAT-ATAAATAGTTTT-AAAACATTTTG-AAAAAT-TA
14114 TATAATATATAA
57 TATAATATAT-A
* *
14126 TTTTT-AAAACATTTTGAATATATATATA
1 TTTTTGAAAATATTAT-AATATATATATA
14154 TATATATATA
Statistics
Matches: 141, Mismatches: 14, Indels: 31
0.76 0.08 0.17
Matches are distributed among these distances:
67 11 0.08
68 19 0.13
69 13 0.09
70 14 0.10
71 10 0.07
72 23 0.16
73 12 0.09
74 14 0.10
75 8 0.06
76 12 0.09
77 5 0.04
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (67 bp):
TTTTTGAAAATATTATAATATATATATAAATAGTTTTAAAACATTTTGAAAAATTATATAATATA
TA
Found at i:13991 original size:38 final size:37
Alignment explanation
Indices: 13915--14249 Score: 321
Period size: 38 Copynumber: 8.8 Consensus size: 37
13905 AAAAAGCAGT
* * *
13915 TTTTGAAAATATATATATAATAAAATAGTTTTTAAAAATA
1 TTTTGAAAA-ATATATATAAT-ATATAATTTTT-AAAACA
*
13955 TTTTTGAAAAATATATATAATATATAATTTTTAAAATA
1 -TTTTGAAAAATATATATAATATATAATTTTTAAAACA
*
13993 TTTTG---AATATATAT-ATATAT-AGTTTTAAAACA
1 TTTTGAAAAATATATATAATATATAATTTTTAAAACA
* * *
14025 TTTTGAAAACT-TATATAATATATAGTTTTGAAAACA
1 TTTTGAAAAATATATATAATATATAATTTTTAAAACA
* *
14061 TTTTGAAAAAATATATATAATATATAGTTTTAAAAACA
1 TTTTG-AAAAATATATATAATATATAATTTTTAAAACA
14099 TTTTGAAAAAATATATATAATATATAATTTTTAAAACA
1 TTTTG-AAAAATATATATAATATATAATTTTTAAAACA
14137 TTTTGAATATATATATATATATATATATATATATATATATATAAACA
1 TTTTGAA-A-A-ATATATATA-ATATATA-AT-T-T-T-TA-AAACA
* * *
14184 TTTTGGAAACT-TATATAATATAT-AGTTTTAAAACA
1 TTTTGAAAAATATATATAATATATAATTTTTAAAACA
14219 TTTTTGAAAACATATATA-AA-ATATAATTTTT
1 -TTTTGAAAA-ATATATATAATATATAATTTTT
14250 TTTTAAAAAC
Statistics
Matches: 255, Mismatches: 18, Indels: 46
0.80 0.06 0.14
Matches are distributed among these distances:
32 15 0.06
33 6 0.02
34 14 0.05
35 13 0.05
36 28 0.11
37 21 0.08
38 77 0.30
39 11 0.04
40 21 0.08
41 16 0.06
42 8 0.03
43 7 0.03
44 2 0.01
45 2 0.01
46 3 0.01
47 11 0.04
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (37 bp):
TTTTGAAAAATATATATAATATATAATTTTTAAAACA
Found at i:14150 original size:2 final size:2
Alignment explanation
Indices: 14143--14179 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
14133 AACATTTTGA
14143 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 A
14180 AACATTTTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14218 original size:35 final size:36
Alignment explanation
Indices: 14179--14248 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
14169 ATATATATAT
* * * *
14179 AAACA-TTTTGGAAACTTATATAATATATAGTTTTA
1 AAACATTTTTGAAAACATATATAAAATATAATTTTA
14214 AAACATTTTTGAAAACATATATAAAATATAATTTT
1 AAACATTTTTGAAAACATATATAAAATATAATTTT
14249 TTTTTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 5 0.17
36 25 0.83
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (36 bp):
AAACATTTTTGAAAACATATATAAAATATAATTTTA
Found at i:14346 original size:13 final size:12
Alignment explanation
Indices: 14328--14390 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 12
14318 CATTTTTTCC
14328 TTTTATTTATTA
1 TTTTATTTATTA
14340 TTATTA-TTATTA
1 TT-TTATTTATTA
14352 -TTTATTT-TCTA
1 TTTTATTTAT-TA
14363 TTTTTATTTATTA
1 -TTTTATTTATTA
*
14376 TCTTAATTTATTA
1 T-TTTATTTATTA
14389 TT
1 TT
14391 ATTTTTTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
10 4 0.09
11 5 0.12
12 10 0.23
13 23 0.53
14 1 0.02
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:14389 original size:20 final size:18
Alignment explanation
Indices: 14330--14390 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
14320 TTTTTTCCTT
14330 TTATTTATTAT-TATTATTA
1 TTATTTATTATCTA-T-TTA
*
14349 TTATTTATTTTCTATTT-
1 TTATTTATTATCTATTTA
14366 TTATTTATTATCTTAATTTA
1 TTATTTATTATC-T-ATTTA
14386 TTATT
1 TTATT
14391 ATTTTTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
17 11 0.31
18 3 0.08
19 15 0.42
20 7 0.19
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATTTATTATCTATTTA
Found at i:15527 original size:53 final size:51
Alignment explanation
Indices: 15463--15569 Score: 160
Period size: 52 Copynumber: 2.1 Consensus size: 51
15453 TCTTTAAATT
*
15463 TTTAGTTATTCATTTTCTTCTCCTTTTTAATTTTAACATTCTTTTTATTATTA
1 TTTAGTTATTCATTTTCTTCTCC-TTTTAATTTTAACATACTTTTTATT-TTA
* * *
15516 TTTAGTTATTCATTTTTTTCTCCTTTTAATTTTAGCATACTTTTTGTTTTA
1 TTTAGTTATTCATTTTCTTCTCCTTTTAATTTTAACATACTTTTTATTTTA
15567 TTT
1 TTT
15570 TATTATTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
51 6 0.12
52 22 0.44
53 22 0.44
ACGTcount: A:0.19, C:0.12, G:0.04, T:0.65
Consensus pattern (51 bp):
TTTAGTTATTCATTTTCTTCTCCTTTTAATTTTAACATACTTTTTATTTTA
Found at i:15543 original size:24 final size:24
Alignment explanation
Indices: 15462--15543 Score: 58
Period size: 25 Copynumber: 3.2 Consensus size: 24
15452 TTCTTTAAAT
*
15462 TTTTAGTTATTCATTTTCTTCTCC
1 TTTTAGTTATTCATTTTTTTCTCC
* * **
15486 TTTTTAATT-TTAACATTCTTTTTATTAT
1 -TTTTAGTTATT--CATT-TTTTT-CTCC
15514 TATTTAGTTATTCATTTTTTTCTCC
1 T-TTTAGTTATTCATTTTTTTCTCC
15539 TTTTA
1 TTTTA
15544 ATTTTAGCAT
Statistics
Matches: 42, Mismatches: 9, Indels: 13
0.66 0.14 0.20
Matches are distributed among these distances:
24 6 0.14
25 9 0.21
26 9 0.21
27 9 0.21
28 7 0.17
29 2 0.05
ACGTcount: A:0.18, C:0.13, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTAGTTATTCATTTTTTTCTCC
Found at i:15636 original size:15 final size:14
Alignment explanation
Indices: 15562--15637 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 14
15552 ATACTTTTTG
15562 TTTTATTTTATTA-
1 TTTTATTTTATTAT
**
15575 TTTT-TTAAATTATT
1 TTTTATTTTATTA-T
*
15589 TTTTGTTTTA-TATT
1 TTTTATTTTATTA-T
*
15603 TTTTACTTCTTCTTAT
1 TTTTA-TT-TTATTAT
*
15619 TTTTATTTTATTAC
1 TTTTATTTTATTAT
15633 TTTTA
1 TTTTA
15638 AAATTTAACA
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
12 6 0.12
13 4 0.08
14 22 0.45
15 7 0.14
16 8 0.16
17 2 0.04
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.74
Consensus pattern (14 bp):
TTTTATTTTATTAT
Found at i:22289 original size:38 final size:38
Alignment explanation
Indices: 22205--22578 Score: 498
Period size: 38 Copynumber: 9.9 Consensus size: 38
22195 AAAAATCGAT
* * *
22205 TTTTGAAAAAATATATATAATATAAAGTTTTCAAAAACA
1 TTTTGAAAATATATATATAATATATAGTTTT-TAAAACA
22244 TTTTGAATATATATATATATAATATA-A-TTTTTAAAACA
1 TTTTGAA-A-ATATATATATAATATATAGTTTTTAAAACA
*
22282 TTTTGAATATATATATAT-ATAATATAGTTTTTAAAACA
1 TTTTGAAAATATATATATAAT-ATATAGTTTTTAAAACA
* * * *
22320 TTTTGAAAA-CT-TATATAATATATAGTTATGAAAATA
1 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
**
22356 TTTTGAAAAATATATATATAATATATAGTTTCGAAAACA
1 TTTTG-AAAATATATATATAATATATAGTTTTTAAAACA
22395 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
22433 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
*
22471 TTTTGATAATATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
*
22509 TTTTGAAAA-CT-TATATAATATATA-TTTTTAAAACA
1 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
* *
22544 TTTTTGAAAACATATATA-AA-ATATAATTTTTAAAA
1 -TTTTGAAAATATATATATAATATATAGTTTTTAAAA
22579 AAAACTTATT
Statistics
Matches: 304, Mismatches: 18, Indels: 28
0.87 0.05 0.08
Matches are distributed among these distances:
35 13 0.04
36 64 0.21
37 21 0.07
38 151 0.50
39 38 0.12
40 2 0.01
41 15 0.05
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (38 bp):
TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
Found at i:22463 original size:27 final size:27
Alignment explanation
Indices: 22433--22485 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
22423 TTTTAAAACA
*
22433 TTTTGAAAATATATAT-ATAATATATAG
1 TTTTGAAAACAT-TATGATAATATATAG
* *
22460 TTTTTAAAACATTTTGATAATATATA
1 TTTTGAAAACATTATGATAATATATA
22486 TATAATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (27 bp):
TTTTGAAAACATTATGATAATATATAG
Found at i:22671 original size:13 final size:13
Alignment explanation
Indices: 22655--22717 Score: 53
Period size: 13 Copynumber: 4.9 Consensus size: 13
22645 TTTTTCCCTT
22655 TTATTTATTATTA
1 TTATTTATTATTA
22668 TTATTTA-T-TTA
1 TTATTTATTATTA
*
22679 TTTATTT-TCTATTT
1 -TTATTTAT-TATTA
22693 TTATTTATTATCT-
1 TTATTTATTAT-TA
*
22706 TTATTTTTTATT
1 TTATTTATTATT
22718 TTCTGTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
11 3 0.07
12 8 0.19
13 27 0.64
14 4 0.10
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:22674 original size:17 final size:18
Alignment explanation
Indices: 22655--22717 Score: 73
Period size: 17 Copynumber: 3.7 Consensus size: 18
22645 TTTTTCCCTT
22655 TTATTTA-TTATTAT-TA
1 TTATTTATTTATTATCTA
*
22671 TTTATTTATTTATTTTCTA
1 -TTATTTATTTATTATCTA
22690 TT-TTTATTTATTATCT-
1 TTATTTATTTATTATCTA
22706 TTATTT-TTTATT
1 TTATTTATTTATT
22718 TTCTGTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
16 8 0.20
17 23 0.56
18 8 0.20
19 2 0.05
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
TTATTTATTTATTATCTA
Found at i:22678 original size:21 final size:19
Alignment explanation
Indices: 22654--22718 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 19
22644 ATTTTTCCCT
22654 TTTATTTATTATTATTATTTA
1 TTTATTTATT-TTATT-TTTA
22675 TTTATTTATTTTCTATTTTTA
1 TTTATTTA-TTT-TATTTTTA
22696 TTTA-TTATCTTTATTTTTTA
1 TTTATTTAT-TTTA-TTTTTA
22716 TTT
1 TTT
22719 TCTGTTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
19 3 0.08
20 14 0.35
21 17 0.43
22 6 0.15
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTATTTATTTTATTTTTA
Found at i:22719 original size:7 final size:7
Alignment explanation
Indices: 22665--22729 Score: 53
Period size: 7 Copynumber: 9.4 Consensus size: 7
22655 TTATTTATTA
*
22665 TTATTAT
1 TTATTTT
22672 TTATTTAT
1 TTATTT-T
22680 TTATTTT
1 TTATTTT
*
22687 CTA-TTT
1 TTATTTT
*
22693 TTATTTA
1 TTATTTT
*
22700 TTA-TCT
1 TTATTTT
22706 TTATTTT
1 TTATTTT
22713 TTATTTT
1 TTATTTT
* *
22720 CTGTTTT
1 TTATTTT
22727 TTA
1 TTA
22730 AGGGTCTAAG
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
6 9 0.20
7 28 0.64
8 7 0.16
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (7 bp):
TTATTTT
Found at i:22729 original size:34 final size:34
Alignment explanation
Indices: 22658--22727 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
22648 TTCCCTTTTA
22658 TTTATTATTATTATTTATTTATTTATTTTCTATT
1 TTTATTATTATTATTTATTTATTTATTTTCTATT
* *
22692 TTTATTTATTA-TCTTTATTT-TTTATTTTCTGTT
1 TTTA-TTATTATTATTTATTTATTTATTTTCTATT
22725 TTT
1 TTT
22728 TAAGGGTCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 15 0.45
34 12 0.36
35 6 0.18
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.76
Consensus pattern (34 bp):
TTTATTATTATTATTTATTTATTTATTTTCTATT
Found at i:23107 original size:29 final size:30
Alignment explanation
Indices: 23070--23130 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
23060 CATCGAACTA
23070 CACCAGTACAACACACACAAAA-AACCAAC
1 CACCAGTACAACACACACAAAATAACCAAC
* *
23099 CACCAGTACAACACACAGAAAATAAGCAAC
1 CACCAGTACAACACACACAAAATAACCAAC
23129 CA
1 CA
23131 TAAACGCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.54, C:0.34, G:0.07, T:0.05
Consensus pattern (30 bp):
CACCAGTACAACACACACAAAATAACCAAC
Found at i:23795 original size:51 final size:52
Alignment explanation
Indices: 23694--23794 Score: 159
Period size: 52 Copynumber: 1.9 Consensus size: 52
23684 AAATTTCCAG
*
23694 TTATTCATTTTTCCTCCTTTTTAATTTTAGCATTCTTTTTATTATTTTTTAT
1 TTATTCATTTTTCCTCCTTATTAATTTTAGCATTCTTTTTATTATTTTTTAT
* *
23746 TTATTCATTTTTTCTCC-TATTAATTTTAGCATTTTATTTTATTATTTTT
1 TTATTCATTTTTCCTCCTTATTAATTTTAGCATTCT-TTTTATTATTTTT
23795 AAATTATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 16 0.36
52 29 0.64
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.67
Consensus pattern (52 bp):
TTATTCATTTTTCCTCCTTATTAATTTTAGCATTCTTTTTATTATTTTTTAT
Found at i:23805 original size:25 final size:25
Alignment explanation
Indices: 23777--23847 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
23767 AATTTTAGCA
*
23777 TTTTATTTTATTATTTTTAAATTAT
1 TTTTATTTTTTTATTTTTAAATTAT
* *
23802 TTTTGTTTTTTTTACTTCTT--ATTAT
1 TTTT-ATTTTTTTA-TTTTTAAATTAT
*
23827 TTTTATTTTTTTACTTTTAAA
1 TTTTATTTTTTTATTTTTAAA
23848 GTTTAACATT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
23 3 0.08
24 8 0.22
25 14 0.39
26 7 0.19
27 4 0.11
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.73
Consensus pattern (25 bp):
TTTTATTTTTTTATTTTTAAATTAT
Found at i:23907 original size:11 final size:11
Alignment explanation
Indices: 23891--23916 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
23881 TTTCCCTTTG
23891 ATTTATTTATT
1 ATTTATTTATT
23902 ATTTATTTATT
1 ATTTATTTATT
23913 ATTT
1 ATTT
23917 GTTATCTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTATTTATT
Found at i:24657 original size:34 final size:32
Alignment explanation
Indices: 24595--24657 Score: 74
Period size: 33 Copynumber: 1.9 Consensus size: 32
24585 TATGTCTACA
*
24595 ATTTTATAAATAAAAAATATTAAGATTATTAT
1 ATTTTATAAATAAAAAATATTAAAATTATTAT
*
24627 ATTTTATTAAA-ATAAAATTATTATAAATTAT
1 ATTTTA-TAAATA-AAAAATATTA-AAATTAT
24658 ATGATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
32 7 0.27
33 13 0.50
34 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (32 bp):
ATTTTATAAATAAAAAATATTAAAATTATTAT
Found at i:26970 original size:21 final size:21
Alignment explanation
Indices: 26944--26983 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
26934 ATATATTTGT
*
26944 GTTTGAATCTAGGGTTTTAGG
1 GTTTGAATCTAGGGATTTAGG
*
26965 GTTTGAATTTAGGGATTTA
1 GTTTGAATCTAGGGATTTA
26984 AAAGTTTAAA
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:0.23, C:0.03, G:0.30, T:0.45
Consensus pattern (21 bp):
GTTTGAATCTAGGGATTTAGG
Found at i:43523 original size:5 final size:5
Alignment explanation
Indices: 43503--43541 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
43493 GTCCGTCCGT
* * *
43503 CTCGT CTCGT CTCGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
43542 TGGTCGTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.03, C:0.41, G:0.33, T:0.23
Consensus pattern (5 bp):
CTCGG
Found at i:43848 original size:22 final size:22
Alignment explanation
Indices: 43818--43872 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
43808 TCAGGAGTTA
* *
43818 CAGGAGTTATTTGATTTAATTT
1 CAGGAGTTATATGATATAATTT
*
43840 CATGG-GTTACATGATATAATTT
1 CA-GGAGTTATATGATATAATTT
43862 CAGGAGTTATA
1 CAGGAGTTATA
43873 ACAGCTGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 2 0.07
22 23 0.85
23 2 0.07
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTT
Found at i:55891 original size:3 final size:3
Alignment explanation
Indices: 55883--55909 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
55873 GAAAGTAAAA
55883 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
55910 GCATTAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:60602 original size:22 final size:22
Alignment explanation
Indices: 60574--60619 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
60564 CGTACCGAAT
*
60574 CGCGATTTTAAAATGACTGGAA
1 CGCGATTTTAAAACGACTGGAA
*
60596 CGCGATTTTGAAACGACTGGAA
1 CGCGATTTTAAAACGACTGGAA
60618 CG
1 CG
60620 TTTGTACTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (22 bp):
CGCGATTTTAAAACGACTGGAA
Done.