Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006782.1 Hibiscus syriacus cultivar Beakdansim tig00017184_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: 84751
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:18020 original size:18 final size:18
Alignment explanation
Indices: 17999--18050 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
17989 GAAGCTGCAT
*
17999 AGCCCGTTGAACCTGAAG
1 AGCCCGATGAACCTGAAG
* * * *
18017 AGCCTGCTAAAGCTGAAG
1 AGCCCGATGAACCTGAAG
*
18035 AGCCCGATGACCCTGA
1 AGCCCGATGAACCTGA
18051 TCCCGTCCAT
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.15
Consensus pattern (18 bp):
AGCCCGATGAACCTGAAG
Found at i:18039 original size:36 final size:36
Alignment explanation
Indices: 17981--18050 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
17971 GATAGTCCCC
* * * *
17981 AGCCCGCTGAAGCTGCATAGCCCGTTGAACCTGAAG
1 AGCCCGCTAAAGCTGAAGAGCCCGATGAACCTGAAG
* *
18017 AGCCTGCTAAAGCTGAAGAGCCCGATGACCCTGA
1 AGCCCGCTAAAGCTGAAGAGCCCGATGAACCTGA
18051 TCCCGTCCAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (36 bp):
AGCCCGCTAAAGCTGAAGAGCCCGATGAACCTGAAG
Found at i:21559 original size:36 final size:36
Alignment explanation
Indices: 21512--21591 Score: 133
Period size: 36 Copynumber: 2.2 Consensus size: 36
21502 GACACATTAA
21512 GAGAATGATACACAGAAGTCAACGATATCAAACTAC
1 GAGAATGATACACAGAAGTCAACGATATCAAACTAC
* * *
21548 GAGAATGATACACAGAATTCATCGATATCAAGCTAC
1 GAGAATGATACACAGAAGTCAACGATATCAAACTAC
21584 GAGAATGA
1 GAGAATGA
21592 ATAAAGTCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.19
Consensus pattern (36 bp):
GAGAATGATACACAGAAGTCAACGATATCAAACTAC
Found at i:22525 original size:4 final size:4
Alignment explanation
Indices: 22518--25094 Score: 5019
Period size: 4 Copynumber: 648.8 Consensus size: 4
22508 TGTGTGTGTG
22518 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
22566 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
22614 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
22662 TGTA -GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
22709 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
22757 TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
22803 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
22851 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
22899 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
22947 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
22995 TGTA TGTA TGTA TGTA TGTA TG-A TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23042 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23090 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23138 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23186 TGTA TGTA TGTA --TA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23232 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23278 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23326 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23374 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23422 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23470 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23518 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23566 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23614 TGTA --TA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23660 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23708 TGTA TGTA TGTA TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23754 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23802 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23850 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23898 TGTA TGTA TGTA TGTA TGTA TGTA TG-A TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23945 TGTA TG-A TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
23992 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24040 TGTA TGTA TGTA TGTA -GTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24087 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24135 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG-- TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24181 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24229 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24277 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24325 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24373 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24421 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24469 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24517 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24565 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24613 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24661 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24709 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24757 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24805 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24853 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24901 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA -GTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24948 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
24996 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
25044 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TATA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
25092 TGT
1 TGT
25095 TATTTTAAAT
Statistics
Matches: 2553, Mismatches: 2, Indels: 36
0.99 0.00 0.01
Matches are distributed among these distances:
2 12 0.00
3 18 0.01
4 2523 0.99
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:26630 original size:201 final size:201
Alignment explanation
Indices: 26285--26687 Score: 797
Period size: 201 Copynumber: 2.0 Consensus size: 201
26275 GTCACAACAC
26285 AAAAAAGTTCTCAGGTGGACTATGACAGACTTGAAGTGAATCAGTTCTACCATATGCATGGACAA
1 AAAAAAGTTCTCAGGTGGACTATGACAGACTTGAAGTGAATCAGTTCTACCATATGCATGGACAA
*
26350 GATCCAACTAGACGAGTTTCATAGCAATTCTGTGGAACCGTAAAAGAAACTTAATCCTATAATAA
66 AATCCAACTAGACGAGTTTCATAGCAATTCTGTGGAACCGTAAAAGAAACTTAATCCTATAATAA
26415 AAAAAGTGGTGATGAAGGAAGTCATAAAATGGCTCGATGCTGGGGTGATCTATCTTATATCCGAT
131 AAAAAGTGGTGATGAAGGAAGTCATAAAATGGCTCGATGCTGGGGTGATCTATCTTATATCCGAT
26480 AGCTCT
196 AGCTCT
26486 AAAAAAGTTCTCAGGTGGACTATGACAGACTTGAAGTGAATCAGTTCTACCATATGCATGGACAA
1 AAAAAAGTTCTCAGGTGGACTATGACAGACTTGAAGTGAATCAGTTCTACCATATGCATGGACAA
26551 AATCCAACTAGACGAGTTTCATAGCAATTCTGTGGAACCGTAAAAGAAACTTAATCCTATAATAA
66 AATCCAACTAGACGAGTTTCATAGCAATTCTGTGGAACCGTAAAAGAAACTTAATCCTATAATAA
26616 AAAAAGTGGTGATGAAGGAAGTCATAAAATGGCTCGATGCTGGGGTGATCTATCTTATATCCGAT
131 AAAAAGTGGTGATGAAGGAAGTCATAAAATGGCTCGATGCTGGGGTGATCTATCTTATATCCGAT
26681 AGCTCT
196 AGCTCT
26687 A
1 A
26688 GGGTTAGTTC
Statistics
Matches: 201, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 201 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.26
Consensus pattern (201 bp):
AAAAAAGTTCTCAGGTGGACTATGACAGACTTGAAGTGAATCAGTTCTACCATATGCATGGACAA
AATCCAACTAGACGAGTTTCATAGCAATTCTGTGGAACCGTAAAAGAAACTTAATCCTATAATAA
AAAAAGTGGTGATGAAGGAAGTCATAAAATGGCTCGATGCTGGGGTGATCTATCTTATATCCGAT
AGCTCT
Found at i:31802 original size:3 final size:3
Alignment explanation
Indices: 31794--31845 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
31784 TTACATTTCC
31794 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31842 TTA T
1 TTA T
31846 ATTGCCTCAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:33125 original size:23 final size:23
Alignment explanation
Indices: 33099--33167 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
33089 CACCACAGCT
* *
33099 CGTATAAATGCACCTAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
33122 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
33145 CATAGAATTGCACTGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
33168 TATAAAATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:40009 original size:23 final size:23
Alignment explanation
Indices: 39990--40081 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
39980 AAATGCACTT
*
39990 AAGTGCTGCGTAGAATTGCACCG
1 AAGTGCCGCGTAGAATTGCACCG
**
40013 AAGTATCGCGTAGAATTGCACCG
1 AAGTGCCGCGTAGAATTGCACCG
* *
40036 AAGTGCCACTTAGAATTGCACCG
1 AAGTGCCGCGTAGAATTGCACCG
* *
40059 AAGTGCCGCTTAGAATTACACCG
1 AAGTGCCGCGTAGAATTGCACCG
40082 TAATGCCATA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (23 bp):
AAGTGCCGCGTAGAATTGCACCG
Found at i:42693 original size:15 final size:15
Alignment explanation
Indices: 42673--42723 Score: 93
Period size: 15 Copynumber: 3.4 Consensus size: 15
42663 CGAAACTAAT
42673 GATGTCACTTGGCCA
1 GATGTCACTTGGCCA
42688 GATGTCACTTGGCCA
1 GATGTCACTTGGCCA
42703 GATGTCACTTGGCCA
1 GATGTCACTTGGCCA
*
42718 GCTGTC
1 GATGTC
42724 CAATTTACTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (15 bp):
GATGTCACTTGGCCA
Found at i:49191 original size:8 final size:8
Alignment explanation
Indices: 49178--49210 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
49168 ACAAACCTTG
49178 TCTCTTAT
1 TCTCTTAT
49186 TCTCTTAT
1 TCTCTTAT
*
49194 TCTCTTCT
1 TCTCTTAT
49202 TCTC-TAT
1 TCTCTTAT
49209 TC
1 TC
49211 ACTTCCTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 4 0.17
8 19 0.83
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (8 bp):
TCTCTTAT
Found at i:50149 original size:20 final size:21
Alignment explanation
Indices: 50126--50164 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
50116 CCAACATATG
50126 GGTATCGATACT-AAGGGTTT
1 GGTATCGATACTAAAGGGTTT
50146 GGTATCGATACTAAAGGGT
1 GGTATCGATACTAAAGGGT
50165 CAACATCGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.28, C:0.10, G:0.31, T:0.31
Consensus pattern (21 bp):
GGTATCGATACTAAAGGGTTT
Found at i:56250 original size:30 final size:31
Alignment explanation
Indices: 56198--56257 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
56188 CCAGGCAAAC
* * **
56198 GTGTAAGGATTAATTTTGTATTTT-TCTAAA
1 GTGTAAGGATAAAATTAATATTTTATCTAAA
56228 GTGTAAGGATAAAATTAATATTTTATCTAA
1 GTGTAAGGATAAAATTAATATTTTATCTAA
56258 GTCCAGGGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (31 bp):
GTGTAAGGATAAAATTAATATTTTATCTAAA
Found at i:58283 original size:29 final size:29
Alignment explanation
Indices: 58250--58305 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
58240 AAACGAAAAT
* *
58250 AAAATTTCATTATATTAACAAAGTAATTG
1 AAAATTTAATTATATGAACAAAGTAATTG
* *
58279 AAAATTTAATTGTATGAACAATGTAAT
1 AAAATTTAATTATATGAACAAAGTAAT
58306 ATCGAAAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (29 bp):
AAAATTTAATTATATGAACAAAGTAATTG
Found at i:59123 original size:13 final size:13
Alignment explanation
Indices: 59105--59131 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59095 TTCCCCTCTC
59105 GAGTTGGGATCAT
1 GAGTTGGGATCAT
59118 GAGTTGGGATCAT
1 GAGTTGGGATCAT
59131 G
1 G
59132 GCTCCGTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.41, T:0.30
Consensus pattern (13 bp):
GAGTTGGGATCAT
Found at i:65450 original size:29 final size:30
Alignment explanation
Indices: 65406--65485 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
65396 TCTATGGGTG
* *
65406 ATTGATTTTTTTTAAAAGATTT-AGGACTTA
1 ATTGATTCTTTTAAAAAG-TTTGAGGACTTA
*
65436 ATTGATTCTTTTAAAAAGTTTGAGGATTTA
1 ATTGATTCTTTTAAAAAGTTTGAGGACTTA
65466 ATTGATTCTTTTAAAAAGTT
1 ATTGATTCTTTTAAAAAGTT
65486 AGAACTCTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 3 0.07
30 43 0.93
ACGTcount: A:0.34, C:0.04, G:0.14, T:0.49
Consensus pattern (30 bp):
ATTGATTCTTTTAAAAAGTTTGAGGACTTA
Found at i:65937 original size:18 final size:19
Alignment explanation
Indices: 65910--65959 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 19
65900 GTTTTTTGTA
65910 ATTTTATAATA-TTTAATT
1 ATTTTATAATATTTTAATT
*
65928 ATTTTTTAATATTTTAATT
1 ATTTTATAATATTTTAATT
65947 -TTTTA-AATATTTT
1 ATTTTATAATATTTT
65960 TTTAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 8 0.28
18 14 0.48
19 7 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTTATAATATTTTAATT
Found at i:65970 original size:26 final size:26
Alignment explanation
Indices: 65901--65973 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 26
65891 TTTTCCAGTG
* * *
65901 TTTTTTGTAATTTTATAATATTTAATTA
1 TTTTTT-TAATTTTA-ATTTTTTAAATA
*
65929 TTTTTTAATATTTTAATTTTTTAAATA
1 TTTTTTTA-ATTTTAATTTTTTAAATA
65956 TTTTTTTAATTTTAATTT
1 TTTTTTTAATTTTAATTT
65974 GTTTGTACCA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 10 0.26
27 17 0.44
28 12 0.31
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (26 bp):
TTTTTTTAATTTTAATTTTTTAAATA
Found at i:69922 original size:7 final size:7
Alignment explanation
Indices: 69910--69955 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
69900 TAATACGTGG
69910 CATGACA
1 CATGACA
69917 CATGACA
1 CATGACA
69924 CCAGTGACA
1 -CA-TGACA
69933 CATGACA
1 CATGACA
69940 CCAGTGACA
1 -CA-TGACA
69949 CATGACA
1 CATGACA
69956 TCATTCAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 17 0.49
8 8 0.23
9 10 0.29
ACGTcount: A:0.39, C:0.30, G:0.17, T:0.13
Consensus pattern (7 bp):
CATGACA
Found at i:69933 original size:16 final size:16
Alignment explanation
Indices: 69912--69955 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
69902 ATACGTGGCA
69912 TGACACATGACACCAG
1 TGACACATGACACCAG
69928 TGACACATGACACCAG
1 TGACACATGACACCAG
69944 TGACACATGACA
1 TGACACATGACA
69956 TCATTCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.39, C:0.30, G:0.18, T:0.14
Consensus pattern (16 bp):
TGACACATGACACCAG
Found at i:70206 original size:3 final size:3
Alignment explanation
Indices: 70194--70223 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
70184 AATCTGAGAC
70194 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
70224 ATATTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:73044 original size:19 final size:20
Alignment explanation
Indices: 73020--73059 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
73010 AAAATAAAAG
*
73020 TAAATTTAA-TATTTTATTT
1 TAAATTAAATTATTTTATTT
73039 TAAATTAAATTATTTTATTT
1 TAAATTAAATTATTTTATTT
73059 T
1 T
73060 GTGATTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TAAATTAAATTATTTTATTT
Found at i:73101 original size:18 final size:19
Alignment explanation
Indices: 73080--73119 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
73070 TTCTCTAAAT
73080 TATTTTAATATAATTT-TA
1 TATTTTAATATAATTTATA
*
73098 TA-TTTAATATACTTTATA
1 TATTTTAATATAATTTATA
73116 TATT
1 TATT
73120 ATTATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 12 0.63
18 6 0.32
19 1 0.05
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTTTAATATAATTTATA
Found at i:73113 original size:16 final size:17
Alignment explanation
Indices: 73079--73116 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
73069 ATTCTCTAAA
*
73079 TTAT-TTTAATATAATT
1 TTATATTTAATATAACT
73095 TTATATTTAATAT-ACT
1 TTATATTTAATATAACT
73111 TTATAT
1 TTATAT
73117 ATTATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATTTAATATAACT
Found at i:75127 original size:21 final size:21
Alignment explanation
Indices: 75094--75135 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
75084 TTTTAAAAAT
75094 ATTGAAAGGTTAGATACTAAA
1 ATTGAAAGGTTAGATACTAAA
* * *
75115 ATTGAGAGTTTAGGTACTAAA
1 ATTGAAAGGTTAGATACTAAA
75136 TACATAGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.31
Consensus pattern (21 bp):
ATTGAAAGGTTAGATACTAAA
Found at i:75399 original size:31 final size:30
Alignment explanation
Indices: 75364--75450 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 30
75354 AGAATAAAGG
* * *
75364 GTTAAATTGATATTTTATCTGAAATTTATAA
1 GTTAAATTAATATTTAATCTAAAATTTA-AA
*
75395 GTTAAATTAACATTTAATCTAAAATTTAAA
1 GTTAAATTAATATTTAATCTAAAATTTAAA
* *
75425 ATTAAAATTAATATTTCATCTAAAAT
1 GTT-AAATTAATATTTAATCTAAAAT
75451 CTAGAAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 4 0.08
31 44 0.92
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.44
Consensus pattern (30 bp):
GTTAAATTAATATTTAATCTAAAATTTAAA
Found at i:76139 original size:31 final size:30
Alignment explanation
Indices: 76104--76189 Score: 84
Period size: 33 Copynumber: 2.7 Consensus size: 30
76094 GTTTAGGGGA
*
76104 TTAAAATAAAGGTTTTTAAAATATTATATT-T
1 TTAAAATAAA-ATTTTTAAAATATT-TATTAT
*
76135 TTAAAAATATAATATTTTTAAATATATTTTTTAT
1 TT-AAAATA-AA-ATTTTTAAA-ATATTTATTAT
*
76169 TTTAAATAAAATTTTTAAAAT
1 TTAAAATAAAATTTTTAAAAT
76190 TACTAGAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
30 2 0.04
31 11 0.23
32 8 0.17
33 18 0.38
34 8 0.17
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
TTAAAATAAAATTTTTAAAATATTTATTAT
Found at i:76141 original size:17 final size:17
Alignment explanation
Indices: 76116--76162 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
76106 AAAATAAAGG
76116 TTTTT-AAAATATTATA
1 TTTTTAAAAATATTATA
*
76132 TTTTTAAAAATATAATA
1 TTTTTAAAAATATTATA
*
76149 TTTTTAAATATATT
1 TTTTTAAAAATATT
76163 TTTTATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTTAAAAATATTATA
Found at i:76183 original size:18 final size:18
Alignment explanation
Indices: 76150--76185 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
76140 AATATAATAT
* *
76150 TTTTAAATATATTTTTTA
1 TTTTAAATAAAATTTTTA
76168 TTTTAAATAAAATTTTTA
1 TTTTAAATAAAATTTTTA
76186 AAATTACTAG
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTAAATAAAATTTTTA
Found at i:80715 original size:22 final size:21
Alignment explanation
Indices: 80677--80724 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
80667 CCCTATTTAT
*
80677 AAATATAAACTTTAAAACACTA
1 AAATATAAACTTAAAAAC-CTA
*
80699 AAATATTAAAC-TAAAAACCTT
1 AAATA-TAAACTTAAAAACCTA
80720 AAATA
1 AAATA
80725 ACATAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 7 0.30
22 11 0.48
23 5 0.22
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATATAAACTTAAAAACCTA
Found at i:81101 original size:2 final size:2
Alignment explanation
Indices: 81094--81126 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
81084 CGTTGAATGA
81094 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 A
81127 CACACACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.