Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005815.1 Hibiscus syriacus cultivar Beakdansim tig00013628_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: 55939
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:3692 original size:45 final size:45
Alignment explanation
Indices: 3586--3857 Score: 366
Period size: 45 Copynumber: 6.0 Consensus size: 45
3576 CTTTATTTTA
* ** * *
3586 ATTTATGGCATCCGTTCATGCTTATAATGCACCATTATGCATTTTC
1 ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTAAGCA-TTTC
*
3632 ATTTATGACATCCTTTCATGCCGATAATGCACCGTTAAGCATTTC
1 ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTAAGCATTTC
* * *
3677 ATTTATGGCATCCTTTCATTCTGATAATGCAACGTTAAGCATTTC
1 ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTAAGCATTTC
* * *
3722 ATTTATGGCATCATTTCATGCCGATAATGCACCATTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTAAGCATTTC
* *
3767 ATTTATAGCATCATTTCATGCCGATAATGCACCGTTATA-CATTTC
1 ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTA-AGCATTTC
* * *
3812 ATTTATGGCATCCTTTCATGCTGATAATGCACTGTTATGCATTTC
1 ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTAAGCATTTC
3857 A
1 A
3858 ATAATATATT
Statistics
Matches: 200, Mismatches: 24, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
45 165 0.82
46 35 0.17
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (45 bp):
ATTTATGGCATCCTTTCATGCCGATAATGCACCGTTAAGCATTTC
Found at i:3829 original size:135 final size:136
Alignment explanation
Indices: 3586--3857 Score: 426
Period size: 135 Copynumber: 2.0 Consensus size: 136
3576 CTTTATTTTA
* ** *
3586 ATTTATGGCATCCGTTCATGCTTATAATGCACCATTATGCATTTTCATTTATGACATCCTTTCAT
1 ATTTATGGCATCAGTTCATGCCGATAATGCACCATTATGCATTTTCATTTATGACATCATTTCAT
*
3651 GCCGATAATGCACCGTTAAGCATTTCATTTATGGCATCCTTTCATTCTGATAATGCAAC-GTTAA
66 GCCGATAATGCACCGTTAAGCATTTCATTTATGGCATCCTTTCATGCTGATAATGC-ACTGTTAA
3715 GCATTTC
130 GCATTTC
*
3722 ATTTATGGCATCATTTCATGCCGATAATGCACCATTATGCA-TTTCATTTAT-AGCATCATTTCA
1 ATTTATGGCATCAGTTCATGCCGATAATGCACCATTATGCATTTTCATTTATGA-CATCATTTCA
3785 TGCCGATAATGCACCGTTATA-CATTTCATTTATGGCATCCTTTCATGCTGATAATGCACTGTTA
65 TGCCGATAATGCACCGTTA-AGCATTTCATTTATGGCATCCTTTCATGCTGATAATGCACTGTTA
*
3849 TGCATTTC
129 AGCATTTC
3857 A
1 A
3858 ATAATATATT
Statistics
Matches: 126, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
134 3 0.02
135 85 0.67
136 38 0.30
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (136 bp):
ATTTATGGCATCAGTTCATGCCGATAATGCACCATTATGCATTTTCATTTATGACATCATTTCAT
GCCGATAATGCACCGTTAAGCATTTCATTTATGGCATCCTTTCATGCTGATAATGCACTGTTAAG
CATTTC
Found at i:10708 original size:45 final size:45
Alignment explanation
Indices: 10587--10910 Score: 400
Period size: 45 Copynumber: 7.2 Consensus size: 45
10577 TATTCTTTAT
* * **
10587 TTTCATTTATGGAATCCGTTCATGCTTATAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* * *
10632 TTTTAATTTATGGCATCCTTTCATGCCGATAATACACTATTATGCA
1 -TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* * * * *
10678 ATTCATTTATGGCTTCCTTTTATGCTGATAATGCACCATTTTGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
*
10723 TTTCATTTATGGCATCCTTTCATGCCGAT-ATGCACTATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* * * * *
10767 TTTCACTTATGGCATCCTTTCTTGCGGATAATGCACCGTTATACA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* **
10812 TTTCATTTATGGCATCCTTTCATGCTGATAATGTGCC-TTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* * * *
10856 TTTCATTTATGGCATCCTTTTATACCGATAATGCACCTTTATACA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
10901 TTTCATTTAT
1 TTTCATTTAT
10911 ATATTCGTTT
Statistics
Matches: 237, Mismatches: 39, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
44 77 0.32
45 122 0.51
46 38 0.16
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
Found at i:10797 original size:89 final size:90
Alignment explanation
Indices: 10587--10910 Score: 420
Period size: 89 Copynumber: 3.6 Consensus size: 90
10577 TATTCTTTAT
* * * * * *
10587 TTTCATTTATGGAATCCGTTCATGCTTATAATGCACCATTATGCATTTTAATTTATGGCATCCTT
1 TTTCATTTATGGCATCCTTTTATGCTGATAATGCACCATTATACA-TTTCATTTATGGCATCCTT
*
10652 TCATGCCGATAATACACTATTATGCA
65 TCATGCCGATAATGCACTATTATGCA
* * * *
10678 ATTCATTTATGGCTTCCTTTTATGCTGATAATGCACCATTTTGCATTTCATTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTTATGCTGATAATGCACCATTATACATTTCATTTATGGCATCCTTT
10743 CATGCCGAT-ATGCACTATTATGCA
66 CATGCCGATAATGCACTATTATGCA
* * *
10767 TTTCACTTATGGCATCCTTTCT-TGCGGATAATGCACCGTTATACATTTCATTTATGGCATCCTT
1 TTTCATTTATGGCATCCTTT-TATGCTGATAATGCACCATTATACATTTCATTTATGGCATCCTT
* ** *
10831 TCATGCTGATAATGTGC-CTTATGCA
65 TCATGCCGATAATGCACTATTATGCA
* * *
10856 TTTCATTTATGGCATCCTTTTATACCGATAATGCACCTTTATACATTTCATTTAT
1 TTTCATTTATGGCATCCTTTTATGCTGATAATGCACCATTATACATTTCATTTAT
10911 ATATTCGTTT
Statistics
Matches: 206, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
88 1 0.00
89 134 0.65
90 33 0.16
91 38 0.18
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (90 bp):
TTTCATTTATGGCATCCTTTTATGCTGATAATGCACCATTATACATTTCATTTATGGCATCCTTT
CATGCCGATAATGCACTATTATGCA
Found at i:10817 original size:134 final size:134
Alignment explanation
Indices: 10587--10910 Score: 409
Period size: 134 Copynumber: 2.4 Consensus size: 134
10577 TATTCTTTAT
* * ** * *
10587 TTTCATTTATGGAATCCGTTCATGCTTATAATGCACCATTATGCATTTTAATTTATGGCATCCTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTATTATGCA-TTTCATTTATGGCATCCTT
* * * *
10652 TCATGCCGATAATACACTATTATGCAATTCATTTATGGCTTCCTTTTATGCTGATAATGCACCAT
65 TCATGCCGATAATACACCATTATACAATTCATTTATGGCATCCTTTCATGCTGATAATGCACC-T
*
10717 TTTGCA
129 TATGCA
*
10723 TTTCATTTATGGCATCCTTTCATGCCGAT-ATGCACTATTATGCATTTCACTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTATTATGCATTTCATTTATGGCATCCTTT
* * * * * **
10787 CTTGCGGATAATGCACCGTTATACATTTCATTTATGGCATCCTTTCATGCTGATAATGTGCCTTA
66 CATGCCGATAATACACCATTATACAATTCATTTATGGCATCCTTTCATGCTGATAATGCACCTTA
10852 TGCA
131 TGCA
* * *
10856 TTTCATTTATGGCATCCTTTTATACCGATAATGCACCT-TTATACATTTCATTTAT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCA-CTATTATGCATTTCATTTAT
10911 ATATTCGTTT
Statistics
Matches: 163, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
133 33 0.20
134 89 0.55
135 16 0.10
136 25 0.15
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (134 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACTATTATGCATTTCATTTATGGCATCCTTT
CATGCCGATAATACACCATTATACAATTCATTTATGGCATCCTTTCATGCTGATAATGCACCTTA
TGCA
Found at i:18267 original size:54 final size:54
Alignment explanation
Indices: 18202--18508 Score: 390
Period size: 54 Copynumber: 5.7 Consensus size: 54
18192 CATTGAAAAA
* *
18202 GGGTTTCACACATAGTGGTTATACGGTCGTTCATCAACATATGATGAATTTCGT
1 GGGTTGCACACATAGTGCTTATACGGTCGTTCATCAACATATGATGAATTTCGT
* * * * *
18256 GGATTACACACATAGTGCCTATACGGTCATTCATCAACAAATGATGAATTAT-GT
1 GGGTTGCACACATAGTGCTTATACGGTCGTTCATCAACATATGATGAATT-TCGT
* **
18310 GGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATGCCGT
1 GGGTTGCACACATAGTGCTTATACGGTCGTTCATCAACATATGATGAATTTCGT
* * * * *
18364 GGGTTACATACATAGTGCATATACGGTCGTTCATCAAAATATGATAAATTAT-GT
1 GGGTTGCACACATAGTGCTTATACGGTCGTTCATCAACATATGATGAATT-TCGT
* *
18418 GGGTTGCACA-TTAGTGCTTATACGGTGGTTCATCAACATATGATG-ATTTCTGT
1 GGGTTGCACACATAGTGCTTATACGGTCGTTCATCAACATATGATGAATTTC-GT
18471 GGGTTGCACACATAGTG-TATATACGGTCGTTCATCAAC
1 GGGTTGCACACATAGTGCT-TATACGGTCGTTCATCAAC
18509 GTATATATTT
Statistics
Matches: 218, Mismatches: 28, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
51 1 0.00
52 3 0.01
53 43 0.20
54 170 0.78
55 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (54 bp):
GGGTTGCACACATAGTGCTTATACGGTCGTTCATCAACATATGATGAATTTCGT
Found at i:18391 original size:108 final size:109
Alignment explanation
Indices: 18202--18508 Score: 449
Period size: 108 Copynumber: 2.8 Consensus size: 109
18192 CATTGAAAAA
* * * *
18202 GGGTTTCACACATAGTGGTTATACGGTCGTTCATCAACATATGATGAATTTCGTGGATTACACAC
1 GGGTTGCACACATAGTGCTTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTACACAC
* * *
18267 ATAGTGCCTATACGGTCATTCATCAACAA-ATGATGAATTATGT
66 ATAGTGCATATACGGTCGTTCATCAACAATATGATAAATTATGT
* * *
18310 GGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATGCCGTGGGTTACATAC
1 GGGTTGCACACATAGTGCTTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTACACAC
18375 ATAGTGCATATACGGTCGTTCATCAA-AATATGATAAATTATGT
66 ATAGTGCATATACGGTCGTTCATCAACAATATGATAAATTATGT
* * * * *
18418 GGGTTGCACA-TTAGTGCTTATACGGTGGTTCATCAACATATGATGATTTCTGTGGGTTGCACAC
1 GGGTTGCACACATAGTGCTTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTACACAC
*
18482 ATAGTGTATATACGGTCGTTCATCAAC
66 ATAGTGCATATACGGTCGTTCATCAAC
18509 GTATATATTT
Statistics
Matches: 178, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
107 73 0.41
108 105 0.59
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (109 bp):
GGGTTGCACACATAGTGCTTATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTACACAC
ATAGTGCATATACGGTCGTTCATCAACAATATGATAAATTATGT
Found at i:18477 original size:161 final size:162
Alignment explanation
Indices: 18202--18508 Score: 438
Period size: 161 Copynumber: 1.9 Consensus size: 162
18192 CATTGAAAAA
* ** * *
18202 GGGTTTCACACATAGTGGTTATACGGTCGTTCATCAACATATGATGAATTTCGTGGATTACACAC
1 GGGTTACACACATAGTGCATATACGGTCGTTCATCAAAATATGATAAATTTCGTGGATTACACAC
*
18267 ATAGTGCCTATACGGTCATTCATCAACAAATGATGAATTATGTGGGTTGCACACATAGTGCCTAT
66 ATAGTGCCTATACGGTCATTCATCAACAAATGATGAATTATGTGGGTTGCACACATAGTGCATAT
18332 ACGGTCGTTCATCAACATATGATGAATGCCGT
131 ACGGTCGTTCATCAACATATGATGAATGCCGT
* * *
18364 GGGTTACATACATAGTGCATATACGGTCGTTCATCAAAATATGATAAATTAT-GTGGGTTGCACA
1 GGGTTACACACATAGTGCATATACGGTCGTTCATCAAAATATGATAAATT-TCGTGGATTACACA
* * ** * * * *
18428 -TTAGTGCTTATACGGTGGTTCATCAACATATGATGATTTCTGTGGGTTGCACACATAGTGTATA
65 CATAGTGCCTATACGGTCATTCATCAACAAATGATGAATTATGTGGGTTGCACACATAGTGCATA
18492 TACGGTCGTTCATCAAC
130 TACGGTCGTTCATCAAC
18509 GTATATATTT
Statistics
Matches: 127, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
161 72 0.57
162 54 0.43
163 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (162 bp):
GGGTTACACACATAGTGCATATACGGTCGTTCATCAAAATATGATAAATTTCGTGGATTACACAC
ATAGTGCCTATACGGTCATTCATCAACAAATGATGAATTATGTGGGTTGCACACATAGTGCATAT
ACGGTCGTTCATCAACATATGATGAATGCCGT
Found at i:23479 original size:54 final size:54
Alignment explanation
Indices: 23421--23786 Score: 511
Period size: 54 Copynumber: 6.8 Consensus size: 54
23411 CATTGAAAAA
* * * * * **
23421 GGGTTGCACACTTAGTCCCTATATGATTGTTCATCAACATATGATGAATTCCAT
1 GGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGT
* * * *
23475 GGGTTGTACACATAGTGCCTATACAGTCGTTCATCAACATGTGATGAATTTTGT
1 GGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGT
* *
23529 GGGTTGCACACATAGTGCCTATACGGTTGTTCATCAACATATGATAAATTCTGT
1 GGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGT
23583 GGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCT-T
1 GGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAA-TTCTGT
* **
23637 GGG-TACACACATAGTGGTTATACGGTCGTTCATCAACATATGATGAATTCTGT
1 GGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGT
* * *
23690 GGGTTGCACACATAGTGCCTATATGGTCGTTCACCAACATATGATGAATTATGT
1 GGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGT
* * *
23744 GGCTTGCACACATATTGCCTATACGGTCATTCATCAACATATG
1 GGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATG
23787 CATTTAACTA
Statistics
Matches: 276, Mismatches: 33, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
52 4 0.01
53 45 0.16
54 223 0.81
55 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (54 bp):
GGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCTGT
Found at i:23693 original size:161 final size:162
Alignment explanation
Indices: 23421--23786 Score: 527
Period size: 161 Copynumber: 2.3 Consensus size: 162
23411 CATTGAAAAA
* * * * * **
23421 GGGTTGCACACTTAGTCCCTATATGATTGTTCATCAACATATGATGAATTCCATGGGTTGTACAC
1 GGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCATGGGTTACACAC
* *
23486 ATAGTGCCTATACAGTCGTTCATCAACATGTGATGAATTTTGTGGGTTGCACACATAGTGCCTAT
66 ATAGTGCCTATACAGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACATAGTGCCTAT
* * *
23551 ACGGTTGTTCATCAACATATGATAAATTCTGT
131 ACGGTCGTTCACCAACATATGATAAATTATGT
* *
23583 GGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCTTGGG-TACACAC
1 GGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCATGGGTTACACAC
** *
23647 ATAGTGGTTATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACATAGTGCCTAT
66 ATAGTGCCTATACAGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACATAGTGCCTAT
* *
23712 ATGGTCGTTCACCAACATATGATGAATTATGT
131 ACGGTCGTTCACCAACATATGATAAATTATGT
* * *
23744 GGCTTGCACACATATTGCCTATACGGTCATTCATCAACATATG
1 GGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATG
23787 CATTTAACTA
Statistics
Matches: 182, Mismatches: 22, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
161 132 0.73
162 50 0.27
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (162 bp):
GGGTTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCATGGGTTACACAC
ATAGTGCCTATACAGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACATAGTGCCTAT
ACGGTCGTTCACCAACATATGATAAATTATGT
Found at i:26376 original size:42 final size:42
Alignment explanation
Indices: 26289--26382 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 42
26279 GGGCTATCAG
* * ** * * *
26289 TAAGTCTTTCGAGCATGATTCTTAAATCCTTCATGTCATCTA
1 TAAGCCTTTCGAACATGATGATTAAATCCTTCAGGCCATCCA
26331 TAAGCCTTTCGAACATGATGATTAAATCCTT-AGGGCCATCCA
1 TAAGCCTTTCGAACATGATGATTAAATCCTTCA-GGCCATCCA
26373 TAAGACCTTT
1 TAAG-CCTTT
26383 GGGTAGGCTG
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.02
42 37 0.86
43 5 0.12
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (42 bp):
TAAGCCTTTCGAACATGATGATTAAATCCTTCAGGCCATCCA
Found at i:26661 original size:241 final size:241
Alignment explanation
Indices: 26233--26694 Score: 694
Period size: 241 Copynumber: 1.9 Consensus size: 241
26223 TTATAAGTTA
*
26233 AAAAGTATGAAAACGATTTCCAAAGTTCTTAATTAGTAAGTCCTTCGGGCTATCAGTAAGTCTTT
1 AAAAGTAAGAAAACGATTTCCAAAGTTCTTAATTAGTAAGTCCTTCGGGCTATCAGTAAGTCTTT
* * *
26298 CGAGCATGATTCTTAAATCCTTCATGTCATCTATAAGCCTTTCGAACATGATGATTAAATCCTTA
66 CGAGCATGATGCTTAAATCCTTCAGGTCATCTATAAGCCTTTCGAACAAGATGATTAAATCCTTA
* * * *
26363 GGGCCATCCATAAGACCTTTGGGTAGGCTGATTTAACATGATTTTCAAAAGATGAGAAAACGATT
131 GGGCCATCCATAAGACCTTCGGGTAGGATGATTTAACATGATTTGCAAAAAATGAGAAAACGATT
*
26428 TCCAAAGTTTCTCATTTAAATCTTTTCTGAAAATTGAAATTTTTTG
196 TCCAAAGTTTCTCATTAAAATCTTTTCTGAAAATTGAAATTTTTTG
* *
26474 AAAAGTAAGAAAACGATTTCCAAAGTTTCTT-ATGTAGTAAGTCCTTTGGGCTATCAGTAAGTTT
1 AAAAGTAAGAAAACGATTTCCAAAG-TTCTTAAT-TAGTAAGTCCTTCGGGCTATCAGTAAGTCT
* * * * * *
26538 TTCTAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTTGAGCAAGATGA-TAAGTCCT
64 TTCGAGCATGATGCTTAAATCCTTCAGGTCATCTATAAGCCTTTCGAACAAGATGATTAAATCCT
* * * * *
26602 TCGGGCCATCCATAAGACCTTCGGGTGGGATGTTTTCACATGATTTGCAAAAAATGAGAAAATGA
129 TAGGGCCATCCATAAGACCTTCGGGTAGGATGATTTAACATGATTTGCAAAAAATGAGAAAACGA
26667 TTTCCAAAGTTTCTCATTAAAATCTTTT
194 TTTCCAAAGTTTCTCATTAAAATCTTTT
26695 TTTGAAAAGT
Statistics
Matches: 197, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
241 116 0.59
242 81 0.41
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (241 bp):
AAAAGTAAGAAAACGATTTCCAAAGTTCTTAATTAGTAAGTCCTTCGGGCTATCAGTAAGTCTTT
CGAGCATGATGCTTAAATCCTTCAGGTCATCTATAAGCCTTTCGAACAAGATGATTAAATCCTTA
GGGCCATCCATAAGACCTTCGGGTAGGATGATTTAACATGATTTGCAAAAAATGAGAAAACGATT
TCCAAAGTTTCTCATTAAAATCTTTTCTGAAAATTGAAATTTTTTG
Found at i:26830 original size:41 final size:42
Alignment explanation
Indices: 26732--26844 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
26722 TCTTACTTAG
* * * * *
26732 TAAGTCCTTTGAGTCGTCAATAAGTCTTTCGAGCATGATGCT
1 TAAGTCCTTTGGGTCATCAATAAGCCTTTCGAGCAAGATGCA
* * * *
26774 TAAATTCTTTGGGTCATCTATAAGCCTTTTGAGCAAGATG-A
1 TAAGTCCTTTGGGTCATCAATAAGCCTTTCGAGCAAGATGCA
*
26815 TAAGTCCTTTGGGTCATCCATAAGACCTTT
1 TAAGTCCTTTGGGTCATCAATAAG-CCTTT
26845 GGACAGGTTG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
41 21 0.36
42 37 0.64
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (42 bp):
TAAGTCCTTTGGGTCATCAATAAGCCTTTCGAGCAAGATGCA
Found at i:26882 original size:221 final size:224
Alignment explanation
Indices: 26467--26915 Score: 665
Period size: 221 Copynumber: 2.0 Consensus size: 224
26457 AAAATTGAAA
*
26467 TTTTTTGAAAAGTAAGAAAACGATTTCCAAAGTTTCTTATGTAGTAAGTCCTTTGGGCTATCAGT
1 TTTTTTGAAAAGTAAGAAAAC-ATTTCCAAAGTTTCTTATGTAGTAAGTCCTTTGGGCTATCAAT
* * *
26532 AAGTTTTTCTAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTTGAGCAAGATGATAA
65 AAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTTGAGCAAGATGATAA
*** *
26597 GTCCTTCGGGCCATCCATAAGACCTTCGGGTGGGATGTTTTCACATGATTTGCAAAAAATGAGAA
130 GTCCTTCGGGCCATCCATAAGACCTTCGGACAGGATGATTTCACATGATTTGCAAAAAATGAGAA
26662 AATGATTTCCAAAGTTTCTCATTAAAATCT
195 AATGATTTCCAAAGTTTCTCATTAAAATCT
* *
26692 TTTTTTGAAAAGTAAG-AAA-A-TTCCAAAGTTTCTTACT-TAGTAAGTCCTTTGAG-TCGTCAA
1 TTTTTTGAAAAGTAAGAAAACATTTCCAAAGTTTCTTA-TGTAGTAAGTCCTTTGGGCT-ATCAA
* *
26752 TAAGTCTTTCGAGCATGATGCTTAAATTCTTTGGGTCATCTATAAGCCTTTTGAGCAAGATGATA
64 TAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTTGAGCAAGATGATA
* * * * * *
26817 AGTCCTTTGGGTCATCCATAAGACCTTTGGACAGGTTGATTTCACATGATTTTCAAAAGATGAGA
129 AGTCCTTCGGGCCATCCATAAGACCTTCGGACAGGATGATTTCACATGATTTGCAAAAAATGAGA
*
26882 AAATGATTTCCAAAGTTTCTCATTTAAATCT
194 AAATGATTTCCAAAGTTTCTCATTAAAATCT
26913 TTT
1 TTT
26916 CAGAATATTG
Statistics
Matches: 203, Mismatches: 19, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
220 1 0.00
221 181 0.89
222 2 0.01
224 3 0.01
225 16 0.08
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (224 bp):
TTTTTTGAAAAGTAAGAAAACATTTCCAAAGTTTCTTATGTAGTAAGTCCTTTGGGCTATCAATA
AGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTTGAGCAAGATGATAAG
TCCTTCGGGCCATCCATAAGACCTTCGGACAGGATGATTTCACATGATTTGCAAAAAATGAGAAA
ATGATTTCCAAAGTTTCTCATTAAAATCT
Found at i:27017 original size:20 final size:20
Alignment explanation
Indices: 26992--27043 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
26982 TACAAAATTC
26992 GTAAGTCCTTCGGGTCATCA
1 GTAAGTCCTTCGGGTCATCA
*
27012 GTAAGTCCTTAGGGTCATCA
1 GTAAGTCCTTCGGGTCATCA
*
27032 GTAAGTCTTTCG
1 GTAAGTCCTTCG
27044 AGCATGATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (20 bp):
GTAAGTCCTTCGGGTCATCA
Found at i:27463 original size:197 final size:196
Alignment explanation
Indices: 27212--27581 Score: 546
Period size: 197 Copynumber: 1.9 Consensus size: 196
27202 AAAGTTTCTT
* *
27212 AATTAATAAGTCCTTCGGGCCATCAGTGAGTCTTTCGAGCATGATACTTAAATCCTTCAGGTCAT
1 AATTAATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATACTTAAATCCTTCAGGTAAT
* * * * * *
27277 CTATAAGCCTTTCGAGCAATATGATAAGTC-CTTCGGGCCATTCATAAGACCTTTGGGAAGGATG
66 CTATAAGCCTTTCGAGCAAGAAGACAAGTCAC-TCGGGCCATCCATAAGACCCTCGGGAAGGAT-
* *
27341 ATT-TCACATGATTTTCAAAAGATGAGAAAACGATTTCCAAAGTTTCTTACCTAGTAAACTATTT
129 ATTCTCACATGATTTTCAAAAAATAAGAAAACGATTTCC-AAGTTTCTTACCTAGTAAACTATTT
27405 TTAA
193 TTAA
* * *
27409 AATTAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGATGCTTAAATCCTTCAGGTAAT
1 AATTAATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATACTTAAATCCTTCAGGTAAT
* * *
27474 CTATAAGTCTTTCGAGCAAGAAGACAAGTCACTCGGGTCATCCATAAGACCCTCGGGCAGGATAT
66 CTATAAGCCTTTCGAGCAAGAAGACAAGTCACTCGGGCCATCCATAAGACCCTCGGGAAGGATAT
*
27539 TCTCACATGATTTTCAAAAAATAAGAAAACGATTTTCAAGTTT
131 TCTCACATGATTTTCAAAAAATAAGAAAACGATTTCCAAGTTT
27582 TCTCATTTAA
Statistics
Matches: 154, Mismatches: 17, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
196 9 0.06
197 144 0.94
198 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (196 bp):
AATTAATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATACTTAAATCCTTCAGGTAAT
CTATAAGCCTTTCGAGCAAGAAGACAAGTCACTCGGGCCATCCATAAGACCCTCGGGAAGGATAT
TCTCACATGATTTTCAAAAAATAAGAAAACGATTTCCAAGTTTCTTACCTAGTAAACTATTTTTA
A
Found at i:31885 original size:44 final size:44
Alignment explanation
Indices: 31835--32140 Score: 423
Period size: 44 Copynumber: 7.0 Consensus size: 44
31825 TGTTACCAAA
* * * * *
31835 ATAAATGAAAATGCATAATGTTACATTATTGGTAGAAAGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGAAGAAAGGTGCC
* * * * * *
31879 ATAAATGAAAATGTATAATGGTGCATTATTAGCATAAAGGTGCA
1 ATAAATGAAAATGCATAACGGTGCATTATTGGAAGAAAGGTGCC
* *
31923 ATAAATGAAAATGCATAACGGTGCATTACTAGAAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGAAGAAAGGTGCC
* *
31967 ATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGAAGAAAGGTGCC
* * **
32011 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGACGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGAAGAAAGGTGCC
*
32055 ATAAATGAAAATGCATAACGGTGTATTATTGGAAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGAAGAAAGGTGCC
*
32099 ACAAATGAAAATGCATAACGGTGCATTATTGGAAGAAAGGTG
1 ATAAATGAAAATGCATAACGGTGCATTATTGGAAGAAAGGTG
32141 ACACTCATGG
Statistics
Matches: 233, Mismatches: 29, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 233 1.00
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.24
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGAAGAAAGGTGCC
Found at i:33687 original size:6 final size:6
Alignment explanation
Indices: 33678--33730 Score: 61
Period size: 7 Copynumber: 8.2 Consensus size: 6
33668 ACTTGGACCT
*
33678 AAATAA AAATAA AAATAA ATAATAA ATAAAAA TAAATAA TAAATAA AAATAA
1 AAATAA AAATAA AAATAA A-AATAA A-AATAA -AAATAA -AAATAA AAATAA
33730 A
1 A
33731 CAAACAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
6 20 0.47
7 22 0.51
8 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
AAATAA
Found at i:33697 original size:4 final size:4
Alignment explanation
Indices: 33677--33753 Score: 60
Period size: 4 Copynumber: 20.8 Consensus size: 4
33667 GACTTGGACC
*
33677 TAAA TAAA -AATA AAAA TAAA T-AA TAAA T-AA -AAA TAAA T-AA TAAA
1 TAAA TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * *
33721 T-AA -AAA TAAA CAAA CAAA TAAT TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
33754 GCATAAAATA
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
3 16 0.27
4 42 0.70
5 2 0.03
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (4 bp):
TAAA
Found at i:33706 original size:17 final size:17
Alignment explanation
Indices: 33677--33753 Score: 102
Period size: 17 Copynumber: 4.4 Consensus size: 17
33667 GACTTGGACC
33677 TAAATAA-AAATAAAAA
1 TAAATAATAAATAAAAA
33693 TAAATAATAAATAAAAA
1 TAAATAATAAATAAAAA
33710 TAAATAATAAATAAAAA
1 TAAATAATAAATAAAAA
* *
33727 TAAACAAACAAATAATTAAA
1 TAAA-TAATAAATAA--AAA
33747 TAAATAA
1 TAAATAA
33754 GCATAAAATA
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
16 7 0.13
17 30 0.56
18 8 0.15
19 2 0.04
20 7 0.13
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (17 bp):
TAAATAATAAATAAAAA
Found at i:34783 original size:201 final size:200
Alignment explanation
Indices: 34302--34783 Score: 511
Period size: 200 Copynumber: 2.4 Consensus size: 200
34292 CTACTATGCG
* * * * * * * **
34302 GTTGATATGCCTTCGAGCTGAATGAAATTGAAGTCAAAAGTTTTTTGTTAACATATAGCCCTTCT
1 GTTGATATGCCATCGAGCTGAATGGAATAGAACTCGAAAG-TTTTTGTTGACAGATAGCCCTTAA
* * * * * * **
34367 TGCCTTGAGCTATGCTGTAAATTCGGTTGGGAGATAGTTCTTTGTTTCTAGATCGCAGCCGACCT
65 CGCCTTGAGCTATGCTATAAATTCGGTTGGAAGATAGTTCTTTGTTGCTAAATCACAGCAAACCT
* * * * *
34432 AGGTCTTCTTCTAGGCTCAAAGAACTTGGCTTAAAATTCAATTGGAATGTAGTCCTTACTACTAC
130 AGGTCTTCTTCTAGACTCAAAGAACTTAGCTTAAAATTCAACTGGAAAGTAGTCCTCACTACTAC
***
34497 CATGTG
195 CATACA
* **
34503 GTTGATATGCCATCGAGCTGAATGGAATCGAACTCGAAAGTTTTTGTTGACAGATAGCCCTTCTC
1 GTTGATATGCCATCGAGCTGAATGGAATAGAACTCGAAAGTTTTTGTTGACAGATAGCCCTTAAC
* * *
34568 ACCTTGAGCTATGCTATAAATTTGGTTGGAAGATAGTTCTTTGTTGCTAAATCACCGCAAACCTA
66 GCCTTGAGCTATGCTATAAATTCGGTTGGAAGATAGTTCTTTGTTGCTAAATCACAGCAAACCTA
* * * * * * * *
34633 GGTCTTCTTCTTGACTTAAAGACCTTAGTTTAAACTTCAACCT-GAAAGTAGTTTCTCGCTGCTA
131 GGTCTTCTTCTAGACTCAAAGAACTTAGCTTAAAATTCAA-CTGGAAAGTAG-TCCTCACTACTA
34697 CCATACA
194 CCATACA
* * *
34704 GTTGATGCAT-CC-TCGAGCTGAATGGAATATAACTCGAAAGTTTTTGTTGATAGGTAGCCCTTA
1 GTTGAT--ATGCCATCGAGCTGAATGGAATAGAACTCGAAAGTTTTTGTTGACAGATAGCCCTTA
*
34767 ACGCCTTGAACTATGCT
64 ACGCCTTGAGCTATGCT
34784 GAGAACAGTT
Statistics
Matches: 235, Mismatches: 42, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
200 117 0.50
201 114 0.49
202 2 0.01
203 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (200 bp):
GTTGATATGCCATCGAGCTGAATGGAATAGAACTCGAAAGTTTTTGTTGACAGATAGCCCTTAAC
GCCTTGAGCTATGCTATAAATTCGGTTGGAAGATAGTTCTTTGTTGCTAAATCACAGCAAACCTA
GGTCTTCTTCTAGACTCAAAGAACTTAGCTTAAAATTCAACTGGAAAGTAGTCCTCACTACTACC
ATACA
Found at i:36373 original size:23 final size:23
Alignment explanation
Indices: 36343--36393 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
36333 TATAGTCATT
36343 TGACAAGTGTCAAGATCTATGGG
1 TGACAAGTGTCAAGATCTATGGG
*
36366 TGACAAGTGTCAAGTTCTATGGG
1 TGACAAGTGTCAAGATCTATGGG
36389 TGACA
1 TGACA
36394 TGAGAAGGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.27
Consensus pattern (23 bp):
TGACAAGTGTCAAGATCTATGGG
Found at i:42639 original size:2 final size:2
Alignment explanation
Indices: 42634--42659 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42624 TATACTAAGC
42634 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
42660 TAGTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44234 original size:10 final size:10
Alignment explanation
Indices: 44219--44247 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
44209 TTTAGGTGCT
44219 AAAACAAATC
1 AAAACAAATC
44229 AAAACAAATC
1 AAAACAAATC
44239 AAAACAAAT
1 AAAACAAAT
44248 AATTTAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.72, C:0.17, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAACAAATC
Found at i:44611 original size:18 final size:19
Alignment explanation
Indices: 44577--44614 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
44567 TTTTTGGTAC
*
44577 GTTTTTCTTTGTCTTTTAT
1 GTTTTTCTCTGTCTTTTAT
44596 GTTTTTCTCTGT-TTTTAT
1 GTTTTTCTCTGTCTTTTAT
44614 G
1 G
44615 GCACATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.05, C:0.11, G:0.13, T:0.71
Consensus pattern (19 bp):
GTTTTTCTCTGTCTTTTAT
Found at i:47277 original size:16 final size:17
Alignment explanation
Indices: 47252--47285 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
47242 GTTCCAATTG
47252 TATAACAAGTT-GATTA
1 TATAACAAGTTGGATTA
*
47268 TATAAGAAGTTGGATTA
1 TATAACAAGTTGGATTA
47285 T
1 T
47286 GCGCAAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.03, G:0.18, T:0.38
Consensus pattern (17 bp):
TATAACAAGTTGGATTA
Found at i:50207 original size:112 final size:111
Alignment explanation
Indices: 50008--50236 Score: 352
Period size: 112 Copynumber: 2.1 Consensus size: 111
49998 CCAAAGTGCT
* * *
50008 GAAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCGAAAATGCACTGTT
1 GAAATGGTAATTCACCTCATTATGAATACCATGGGCGACACCTTTTATGCCGAAAATGCAATGTT
* * * *
50073 ATGCATTAAGCAAAATCTATCGATAACTTTCATACACGAAGTATGTC
66 ATACATTAAGCAAAATCGATCGAT-ACTATCATACACAAAGTATGTC
*
50120 GAAATGGTAATTCACCTCGTTATGAATACCATGGGCGACACCTTTTATGCCGAAAATGCAATGTT
1 GAAATGGTAATTCACCTCATTATGAATACCATGGGCGACACCTTTTATGCCGAAAATGCAATGTT
*
50185 ATACATTATA-CAAAATCGATCGATACTATCATACACAAAGTATGTT
66 ATACATTA-AGCAAAATCGATCGATACTATCATACACAAAGTATGTC
50231 GAAATG
1 GAAATG
50237 CACCTATAAC
Statistics
Matches: 107, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
111 25 0.23
112 81 0.76
113 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (111 bp):
GAAATGGTAATTCACCTCATTATGAATACCATGGGCGACACCTTTTATGCCGAAAATGCAATGTT
ATACATTAAGCAAAATCGATCGATACTATCATACACAAAGTATGTC
Done.