Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007720.1 Hibiscus syriacus cultivar Beakdansim tig00109952_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: 65998
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:3700 original size:3 final size:3
Alignment explanation
Indices: 3692--3761 Score: 106
Period size: 3 Copynumber: 23.7 Consensus size: 3
3682 ATTTATTTAA
* * *
3692 TAT TAT TAT TAC TA- TAT TAT TAT TAT TAT AAT TAT TAT TAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3739 TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
3762 AAAATATATA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:5831 original size:23 final size:21
Alignment explanation
Indices: 5803--5853 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
5793 TAATTTTTAA
*
5803 TTATTTTCTTTCAAATTATTTTT
1 TTATTTTATTT-AAA-TATTTTT
*
5826 TTATTTTATTTAGATATTTTT
1 TTATTTTATTTAAATATTTTT
5847 TTATTTT
1 TTATTTT
5854 TCTGTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 14 0.54
22 2 0.08
23 10 0.38
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (21 bp):
TTATTTTATTTAAATATTTTT
Found at i:9122 original size:15 final size:15
Alignment explanation
Indices: 9102--9133 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
9092 ATCAATACCT
9102 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
9117 TTTTGCATACATTCA
1 TTTTGCATACATGCA
9132 TT
1 TT
9134 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:16814 original size:15 final size:16
Alignment explanation
Indices: 16794--16827 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
16784 TTCTATCTAT
16794 TTTAAG-TTCAATTTA
1 TTTAAGATTCAATTTA
16809 TTTAAGATTCAATTTA
1 TTTAAGATTCAATTTA
16825 TTT
1 TTT
16828 TTGAAAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (16 bp):
TTTAAGATTCAATTTA
Found at i:17935 original size:82 final size:83
Alignment explanation
Indices: 17837--18146 Score: 451
Period size: 83 Copynumber: 3.6 Consensus size: 83
17827 AACAAATGTC
17837 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAGTC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAGTC
*
17902 ATT-AATTTTGAAGAGGA
66 ATTGAATTTGGAAGAGGA
* * *
17919 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAATCAATC
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAGTC
17984 ATTGAATTTGGAAGAGGA
66 ATTGAATTTGGAAGAGGA
18002 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACA
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-GAA-C-CA
*
18067 GAACCATTTATTGAATTTGGAAGAGGA
63 G------TCATTGAATTTGGAAGAGGA
* * * *
18094 ATGTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATTTGGTTTG
1 ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
18147 ATATAAAACC
Statistics
Matches: 206, Mismatches: 12, Indels: 10
0.90 0.05 0.04
Matches are distributed among these distances:
82 65 0.32
83 69 0.33
84 2 0.01
86 2 0.01
92 68 0.33
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (83 bp):
ATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAGTC
ATTGAATTTGGAAGAGGA
Found at i:18144 original size:92 final size:92
Alignment explanation
Indices: 17984--18164 Score: 292
Period size: 92 Copynumber: 2.0 Consensus size: 92
17974 AAAATCAATC
*
17984 ATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1 ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
* *
18049 GGTTTGGTAT-GAACCACAGAACCATTT
66 GGTTTGATATAAAACC-CAGAACCATTT
* * *
18076 ATTGAATTTGGAAGAGGAATGTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATTT
1 ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
18141 GGTTTGATATAAAACCCAGAACCA
66 GGTTTGATATAAAACCCAGAACCA
18165 ATCATTGGAA
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
92 78 0.95
93 4 0.05
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (92 bp):
ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
GGTTTGATATAAAACCCAGAACCATTT
Found at i:18638 original size:94 final size:95
Alignment explanation
Indices: 18487--18671 Score: 354
Period size: 94 Copynumber: 2.0 Consensus size: 95
18477 GAATTAAAAT
*
18487 TCAAGATTTCTCGGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTGAAAGGTCACTTCAT
1 TCAAGATTTCTCAGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTGAAAGGTCACTTCAT
18552 AATCAGATGAGTTGTTATCAGAATCAGAAA
66 AATCAGATGAGTTGTTATCAGAATCAGAAA
18582 TCAAGATTTCTCAGT-TTAAAAGAACTATCGATATCTGTGAAATCATCTTGAAAGGTCACTTCAT
1 TCAAGATTTCTCAGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTGAAAGGTCACTTCAT
18646 AATCAGATGAGTTGTTATCAGAATCA
66 AATCAGATGAGTTGTTATCAGAATCA
18672 ACATGTTGCA
Statistics
Matches: 89, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
94 75 0.84
95 14 0.16
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.32
Consensus pattern (95 bp):
TCAAGATTTCTCAGTATTAAAAGAACTATCGATATCTGTGAAATCATCTTGAAAGGTCACTTCAT
AATCAGATGAGTTGTTATCAGAATCAGAAA
Found at i:19180 original size:113 final size:113
Alignment explanation
Indices: 18982--19195 Score: 351
Period size: 113 Copynumber: 1.9 Consensus size: 113
18972 CCATCATTCA
* *
18982 ATGGATCAGCATTGCTAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
19047 TCATAATGAGAAGAACTTGTTCAA-CTTTTTGCTCGAATTCATCTCTTG
66 TCATAATGAGAAGAACTTGTTCAATC-TTTTGCTCGAATTCATCTCTTG
*
19095 ATGGATCAACATTTGCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1 ATGGATCAACA-TTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
* *
19159 TTCATAATGAGAATAACTTGTTTAATCTTTTGCTCGA
65 TTCATAATGAGAAGAACTTGTTCAATCTTTTGCTCGA
19196 CGCTATCACA
Statistics
Matches: 94, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
113 86 0.91
114 8 0.09
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (113 bp):
ATGGATCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAACTTGTTCAATCTTTTGCTCGAATTCATCTCTTG
Found at i:19329 original size:123 final size:124
Alignment explanation
Indices: 19101--19516 Score: 479
Period size: 123 Copynumber: 3.4 Consensus size: 124
19091 CTTGATGGAT
** *
19101 CAACATTTGCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
1 CAACATTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAA
* * * * * * * *
19165 ATGAGAATAACTTGTTTAATCTTTTGC-TCGACGCTATCACAGAAGGAGATAGATCGGCAC
65 ATGAGAAGAGCTTATTCAACCTTTTGCAT-GACTCTATCACAGAAGGAGATAGATAGGCAA
* * *
19225 CAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCACAA
1 CAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAA
* * * * *
19289 TGAGAAGAGCTTCTTCAACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTA-GCAT
66 TGAGAAGAGCTTATTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGA-TAGGCAA
* *
19348 CAACCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCAAAA
1 CAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAA
* * *
19413 TAAGAAGAGCTTATTCAACCTTTGGAATGACTCTATCACAGAA-GA-A-A-ATAGGTCAA
66 TGAGAAGAGCTTATTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATAGG-CAA
* ** *
19469 CATCATCCCCAGCGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
1 CAACATTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
19517 AGAGAATAAT
Statistics
Matches: 252, Mismatches: 33, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
119 2 0.01
120 2 0.01
121 11 0.04
122 35 0.14
123 111 0.44
124 91 0.36
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (124 bp):
CAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAAAA
TGAGAAGAGCTTATTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATAGGCAA
Found at i:19681 original size:3 final size:3
Alignment explanation
Indices: 19673--19744 Score: 108
Period size: 3 Copynumber: 24.0 Consensus size: 3
19663 TTAAATTTAT
* * *
19673 TTA TTA TTA TTA TTA CTA TAA TTA TTA TTA TTA TAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
19721 TAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
19745 AATATATATA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:22726 original size:15 final size:16
Alignment explanation
Indices: 22701--22735 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
22691 GGTAAAACTC
*
22701 TCTTCTTTGTTTTGTT
1 TCTTCTTTGTTTTGGT
22717 TCTT-TTTGTTTTGGT
1 TCTTCTTTGTTTTGGT
22732 TCTT
1 TCTT
22736 AGGTCCTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.00, C:0.11, G:0.14, T:0.74
Consensus pattern (16 bp):
TCTTCTTTGTTTTGGT
Found at i:24164 original size:54 final size:54
Alignment explanation
Indices: 24101--24745 Score: 808
Period size: 54 Copynumber: 11.9 Consensus size: 54
24091 TTACCAAATA
* * *
24101 GGCACTAAGTGTGCATTTCATGGAATTCATCATATGTTGATGAATGACCATTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * * *
24155 GGCACTAAGTGTGCATTTAACAGAATTCAGCATATGTTGATGAATTATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
*** **
24209 GGCACTAAGTGTGCATTTCATAAAATTCATCATATGTTGATGAATGACTATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* *
24263 GGTACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * *
24317 GACACTAAGTGTGCATTTCACGAAATTCATCATATGTTGATGAATGACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
*
24371 GGCACTAAGTGTGTC-TTTCACGGAACTCATCATATGTTGATGAATGACCGTTTC
1 GGCACTAAGTGTG-CATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* ** **
24425 GGCACTAAGTGTGTC-TTTCATGGAATTCATCATAAATTGATGAATGACCAATTC
1 GGCACTAAGTGTG-CATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * * * *
24479 AGCACTATGTGTGTATTTCATGGAATTCATCATATGTTGATGAATTATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * * * **
24533 GGCAGTCAGTGTTCATTTCACGGAATTCATTATATATTGATGAATGACCAATTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * ** *
24587 AGCACTAAGTTTGCATTTCACATAATTCATCATATGTTGATGAATGATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * *
24641 GGCACTAAGTGTGCATTTCAAGGAATTCATCATATGTTGATGAATGACCCTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
* * * * *
24695 GGCACTAAGTGTTCATTTCATGGAATTCATAATATGTTTATGAATAACCGT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGT
24746 ATGGGTACTA
Statistics
Matches: 503, Mismatches: 86, Indels: 4
0.85 0.15 0.01
Matches are distributed among these distances:
54 502 1.00
55 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
Found at i:31678 original size:54 final size:54
Alignment explanation
Indices: 31338--31656 Score: 485
Period size: 54 Copynumber: 5.9 Consensus size: 54
31328 TTACCAAATA
* * *
31338 GGCACTAAGTGTGCATTTCACAGAATTCATCATATGTTGATGAATGATCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCATTTC
* * * * *
31392 GGCACTAAATGTGAATTTAACAGAATTCATCATATATTGATGAATGACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCATTTC
*
31446 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCATTTC
*
31500 GGCACTAAGTGTGTATTTCACGGAATTCATCATATGTTGATGAATGACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCATTTC
** *
31554 GATACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGCCCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCATTTC
* * * *
31608 GGCACTAAGTGTGCATTTCACGGAATCCGTAATATGTTTATGAATGACC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACC
31657 GTATGGGCAC
Statistics
Matches: 240, Mismatches: 25, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 240 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCATATGTTGATGAATGACCATTTC
Found at i:32440 original size:24 final size:24
Alignment explanation
Indices: 32411--32464 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
32401 GGACCTGCAA
**
32411 AATAAAATAAAATG-TTTTAATAAT
1 AATAAAAT-AAATGATAATAATAAT
32435 AATAAAATAAATGATAATAATAAT
1 AATAAAATAAATGATAATAATAAT
32459 AATAAA
1 AATAAA
32465 TAGATTGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (24 bp):
AATAAAATAAATGATAATAATAAT
Found at i:35923 original size:21 final size:21
Alignment explanation
Indices: 35867--35923 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
35857 TTTTCGTAAG
*
35867 AGTACTTTGTGTAATTGGAGT
1 AGTACTTTGTGTACTTGGAGT
*
35888 AGTACTTTGTATACTTGGAGT
1 AGTACTTTGTGTACTTGGAGT
35909 AGTACTTTGTGTACT
1 AGTACTTTGTGTACT
35924 ATGGCACTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.44
Consensus pattern (21 bp):
AGTACTTTGTGTACTTGGAGT
Found at i:36507 original size:2 final size:2
Alignment explanation
Indices: 36500--36969 Score: 741
Period size: 2 Copynumber: 233.5 Consensus size: 2
36490 TATGTATGTA
36500 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
36542 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
36584 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
** * ** * * * *
36626 TG TG TG TG T- TCG AAC T- TAA AC TAC TG TT TG ATG -G AT- TT TAA
1 TG TG TG TG TG T-G -TG TG T-G TG T-G TG TG TG -TG TG -TG TG T-G
* * *
36667 TA TA TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
36709 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
36751 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
36793 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
36835 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
36877 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
36919 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
36961 TG TG TG TG T
1 TG TG TG TG T
36970 ATTTGAAGAA
Statistics
Matches: 444, Mismatches: 13, Indels: 22
0.93 0.03 0.05
Matches are distributed among these distances:
1 4 0.01
2 435 0.98
3 5 0.01
ACGTcount: A:0.03, C:0.01, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:37165 original size:30 final size:30
Alignment explanation
Indices: 37129--37199 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
37119 CCTTACTTCT
37129 TGTACTATTTAACATTGGTGGCCAAGTCCC
1 TGTACTATTTAACATTGGTGGCCAAGTCCC
* *
37159 TGTACTATTTAACCTTGGTGGTCAAGTCCC
1 TGTACTATTTAACATTGGTGGCCAAGTCCC
*
37189 TATACTATTTA
1 TGTACTATTTA
37200 GTTCTTAGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (30 bp):
TGTACTATTTAACATTGGTGGCCAAGTCCC
Found at i:37587 original size:25 final size:25
Alignment explanation
Indices: 37534--37598 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
37524 TTTCGAAAGG
*
37534 TGAAAATGTTTGA-GAAATAAGTTT
1 TGAAAATGTTTGATGAAAGAAGTTT
*
37558 TGAAAATGTTTTATGAAAGAA-TTT
1 TGAAAATGTTTGATGAAAGAAGTTT
*
37582 TGGAAAATATTTGATGA
1 T-GAAAATGTTTGATGA
37599 TGTTTTGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 16 0.46
25 19 0.54
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (25 bp):
TGAAAATGTTTGATGAAAGAAGTTT
Found at i:38103 original size:5 final size:5
Alignment explanation
Indices: 38081--38151 Score: 128
Period size: 5 Copynumber: 14.6 Consensus size: 5
38071 ACTGAAACTC
38081 TTTAA TTT-A TTTAA -TTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
38129 TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTT
38152 TCCTTTGTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.12
5 56 0.88
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:44590 original size:2 final size:2
Alignment explanation
Indices: 44583--44671 Score: 96
Period size: 2 Copynumber: 45.5 Consensus size: 2
44573 ATGGATTGCT
* * *
44583 TA TA TA TA TA TGA TA TA TA TT TA TA T- TA TGA T- TA AA TT TA -A
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
*
44624 TG TA T- 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
44665 TA TA TA T
1 TA TA TA T
44672 TACGAAATAC
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
1 4 0.05
2 65 0.89
3 4 0.05
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44846 original size:13 final size:13
Alignment explanation
Indices: 44825--44889 Score: 94
Period size: 13 Copynumber: 5.0 Consensus size: 13
44815 AATGACGCTC
44825 AATGCGCGTCATA
1 AATGCGCGTCATA
*
44838 AATGAGCGTCATA
1 AATGCGCGTCATA
* *
44851 AATGTGTGTCATA
1 AATGCGCGTCATA
*
44864 AATGCGTGTCATA
1 AATGCGCGTCATA
44877 AATGCGCGTCATA
1 AATGCGCGTCATA
44890 GATTTATGAC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:47587 original size:3 final size:3
Alignment explanation
Indices: 47572--47616 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
47562 TAAAATGTAT
*
47572 TAA TAA TAT TAA TAA TAA TAA -AA TAAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
47617 AGAGACCAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:49054 original size:36 final size:36
Alignment explanation
Indices: 48883--49178 Score: 296
Period size: 36 Copynumber: 8.2 Consensus size: 36
48873 AGATCATTCC
** * * * *
48883 TATAATCATTATTCTCAATCACATGAATACCATCCA
1 TATAATCATTATTAGCAAGCACATGTATATCATGCA
** * *
48919 TATAATCATTAGCAACAAGCACATGCATATCATGCA
1 TATAATCATTATTAGCAAGCACATGTATATCATGCA
* * * * *
48955 TGTAACCATCAGTAGCAAGCGCATGTATATCATGCA
1 TATAATCATTATTAGCAAGCACATGTATATCATGCA
* *
48991 TAT-ATCATTATTAG-AAGGCGCGTGTATATCATGCA
1 TATAATCATTATTAGCAA-GCACATGTATATCATGCA
* * *
49026 TATAATGATTATTAGCAAGCACAAGTATACCATGCA
1 TATAATCATTATTAGCAAGCACATGTATATCATGCA
*
49062 TATAATCATTATTAGC-AGACACATGTATATCATACA
1 TATAATCATTATTAGCAAG-CACATGTATATCATGCA
* *
49098 TATGATCATTATTAG-AAGGCACATGTATATCAAGCA
1 TATAATCATTATTAGCAA-GCACATGTATATCATGCA
* *
49134 TATAATCATTATTAGAAAGCGA-ATATATATCATGCA
1 TATAATCATTATTAGCAAGC-ACATGTATATCATGCA
49170 TATAATCAT
1 TATAATCAT
49179 CAACAACTAG
Statistics
Matches: 217, Mismatches: 35, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
34 2 0.01
35 30 0.14
36 179 0.82
37 6 0.03
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (36 bp):
TATAATCATTATTAGCAAGCACATGTATATCATGCA
Found at i:50070 original size:38 final size:38
Alignment explanation
Indices: 50010--50253 Score: 240
Period size: 38 Copynumber: 6.4 Consensus size: 38
50000 AAAGATATGG
* * * * *
50010 TTTCCAACCTAAAATATCG-TTTCCAACCTGAAATTTGA
1 TTTCCAACCTGAAATCT-GATTTCTAACCTAAAATCTGA
* * * * *
50048 TTTCCAACCTGAAATCTGGTTTCCAACTTGAAATCTAA
1 TTTCCAACCTGAAATCTGATTTCTAACCTAAAATCTGA
* *
50086 TTTCCAACTTGAAAT-TCGATTTCTAACCTAAAATCTGG
1 TTTCCAACCTGAAATCT-GATTTCTAACCTAAAATCTGA
* * *
50124 TTTCCAACCTGAAATATGATTTCTAACCTGAAATCATCA
1 TTTCCAACCTGAAATCTGATTTCTAACCTAAAATC-TGA
* * *
50163 TATCCAATCTGAAATCTGATTTCTAACCTAAAATCTGG
1 TTTCCAACCTGAAATCTGATTTCTAACCTAAAATCTGA
* * * *
50201 TTTTCAACCTAAAATCTGATTTTTAACCTAAAATATGA
1 TTTCCAACCTGAAATCTGATTTCTAACCTAAAATCTGA
*
50239 TTTCCAACCAGAAAT
1 TTTCCAACCTGAAAT
50254 ATGTTTTCAT
Statistics
Matches: 170, Mismatches: 32, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
37 2 0.01
38 135 0.79
39 33 0.19
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (38 bp):
TTTCCAACCTGAAATCTGATTTCTAACCTAAAATCTGA
Found at i:50261 original size:19 final size:19
Alignment explanation
Indices: 50004--50261 Score: 205
Period size: 19 Copynumber: 13.5 Consensus size: 19
49994 ACCCTTAAAG
* *
50004 ATATGGTTTCCAACCTAAA
1 ATATGATTTCCAACCTGAA
50023 ATATCG-TTTCCAACCTGAA
1 ATAT-GATTTCCAACCTGAA
*
50042 ATTTGATTTCCAACCTGAA
1 ATATGATTTCCAACCTGAA
* * *
50061 ATCTGGTTTCCAACTTGAA
1 ATATGATTTCCAACCTGAA
* * *
50080 ATCTAATTTCCAACTTGAA
1 ATATGATTTCCAACCTGAA
* *
50099 AT-TCGATTTCTAACCTAAA
1 ATAT-GATTTCCAACCTGAA
* *
50118 ATCTGGTTTCCAACCTGAA
1 ATATGATTTCCAACCTGAA
*
50137 ATATGATTTCTAACCTGAA
1 ATATGATTTCCAACCTGAA
* * *
50156 ATCATCATATCCAATCTGAA
1 AT-ATGATTTCCAACCTGAA
* * *
50176 ATCTGATTTCTAACCTAAA
1 ATATGATTTCCAACCTGAA
* * * *
50195 ATCTGGTTTTCAACCTAAA
1 ATATGATTTCCAACCTGAA
* ** *
50214 ATCTGATTTTTAACCTAAA
1 ATATGATTTCCAACCTGAA
*
50233 ATATGATTTCCAACCAGAA
1 ATATGATTTCCAACCTGAA
*
50252 ATATGTTTTC
1 ATATGATTTC
50262 ATTCGAAATC
Statistics
Matches: 196, Mismatches: 38, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
18 2 0.01
19 177 0.90
20 17 0.09
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (19 bp):
ATATGATTTCCAACCTGAA
Found at i:51790 original size:56 final size:56
Alignment explanation
Indices: 51704--51815 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
51694 TCTTTTGTTC
*
51704 TTAGAAGATAAACCTTTGTATATCTGTGTGAACATATACAAAGGTGATATAATAGT
1 TTAGAAGATAAACCTTTGTATATATGTGTGAACATATACAAAGGTGATATAATAGT
*
51760 TTAGAAGATAAACCTTTGTATATATGTGTGATCATATACAAAGGTGATATAATAGT
1 TTAGAAGATAAACCTTTGTATATATGTGTGAACATATACAAAGGTGATATAATAGT
51816 GTTTTCCTCC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (56 bp):
TTAGAAGATAAACCTTTGTATATATGTGTGAACATATACAAAGGTGATATAATAGT
Found at i:61295 original size:12 final size:12
Alignment explanation
Indices: 61278--61303 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
61268 TAGGTAAGGG
61278 TGATCTTCAATT
1 TGATCTTCAATT
61290 TGATCTTCAATT
1 TGATCTTCAATT
61302 TG
1 TG
61304 GTATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (12 bp):
TGATCTTCAATT
Found at i:61815 original size:21 final size:21
Alignment explanation
Indices: 61791--61831 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
61781 CAATTATGGG
* *
61791 TATTTAATGTTGAATTTTAAT
1 TATTGAATGTTGAAGTTTAAT
61812 TATTGAATGTTGAAGTTTAA
1 TATTGAATGTTGAAGTTTAA
61832 GTTGGAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (21 bp):
TATTGAATGTTGAAGTTTAAT
Found at i:64346 original size:25 final size:23
Alignment explanation
Indices: 64309--64359 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 23
64299 CAATTGAGAG
64309 AAAATATTCGTTTCACACACTTTGA
1 AAAATATTCGTTT-ACACAC-TTGA
*
64334 AAAATA-TCAGTTTTCACACTTGA
1 AAAATATTC-GTTTACACACTTGA
64357 AAA
1 AAA
64360 TGTGTTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 7 0.29
24 7 0.29
25 10 0.42
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (23 bp):
AAAATATTCGTTTACACACTTGA
Done.