Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003354.1 Hibiscus syriacus cultivar Beakdansim tig00007059_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: 52563
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:3235 original size:18 final size:20
Alignment explanation
Indices: 3212--3251 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3202 ATATTTGTCA
*
3212 TTTTAA-TAAAA-ATATTAT
1 TTTTAATTAAAACATAATAT
3230 TTTTAATTAAAACATAATAT
1 TTTTAATTAAAACATAATAT
3250 TT
1 TT
3252 AATTAAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 5 0.26
20 8 0.42
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTAATTAAAACATAATAT
Found at i:3294 original size:84 final size:84
Alignment explanation
Indices: 3159--3325 Score: 291
Period size: 84 Copynumber: 2.0 Consensus size: 84
3149 GAGTCGCCAC
*
3159 TAATATTTATTAAGGTGTGATTAGATATACCTAAAAAGTATTTATATTTGTCATTTTAATAAAAA
1 TAATATTTATTAAGGTGTGATTAGA-ACACCTAAAAAGTATTTATATTTGTCATTTTAATAAAAA
3224 TATTATTTTTAATTAAAACA
65 TATTATTTTTAATTAAAACA
*
3244 TAATATTTAATTAAGGTTTGATTAG-ACACCTAAAAAGTATTTATATTTGTCATTTTAATAAAAA
1 TAATATTT-ATTAAGGTGTGATTAGAACACCTAAAAAGTATTTATATTTGTCATTTTAATAAAAA
3308 TATTATTTTTAATTAAAA
65 TATTATTTTTAATTAAAA
3326 TAACAAATTT
Statistics
Matches: 79, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
84 56 0.71
85 8 0.10
86 15 0.19
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.45
Consensus pattern (84 bp):
TAATATTTATTAAGGTGTGATTAGAACACCTAAAAAGTATTTATATTTGTCATTTTAATAAAAAT
ATTATTTTTAATTAAAACA
Found at i:5106 original size:19 final size:19
Alignment explanation
Indices: 5079--5131 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
5069 GAATGCCATC
*
5079 AGTGTATCGATGCACAAGT
1 AGTGCATCGATGCACAAGT
*
5098 AGTGCATCGATGCAAAAGT
1 AGTGCATCGATGCACAAGT
5117 AGTGCATCGATGCAC
1 AGTGCATCGATGCAC
5132 CCCCTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (19 bp):
AGTGCATCGATGCACAAGT
Found at i:11420 original size:13 final size:13
Alignment explanation
Indices: 11402--11427 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11392 TCCAGACTTC
11402 TCTTCTTCTTCAT
1 TCTTCTTCTTCAT
11415 TCTTCTTCTTCAT
1 TCTTCTTCTTCAT
11428 CGTGAAGCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.62
Consensus pattern (13 bp):
TCTTCTTCTTCAT
Found at i:12285 original size:34 final size:33
Alignment explanation
Indices: 12224--12294 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 33
12214 ACCTTACAAC
* *
12224 TCCCTAGTTTTTCACGGGTTAAACTAGAACCTT
1 TCCCTAGTTTTACACGGGCTAAACTAGAACCTT
*
12257 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTACACGGGCTAAACTAGAACCTT
12291 TCCC
1 TCCC
12295 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 7 0.21
34 27 0.79
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (33 bp):
TCCCTAGTTTTACACGGGCTAAACTAGAACCTT
Found at i:12695 original size:21 final size:21
Alignment explanation
Indices: 12659--12726 Score: 120
Period size: 21 Copynumber: 3.3 Consensus size: 21
12649 TTGCAGCCTT
12659 GATGCATGGC-AGGATGCATC
1 GATGCATGGCAAGGATGCATC
*
12679 GATGCATGGCAAGGATGTATC
1 GATGCATGGCAAGGATGCATC
12700 GATGCATGGCAAGGATGCATC
1 GATGCATGGCAAGGATGCATC
12721 GATGCA
1 GATGCA
12727 CTAATTGCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 10 0.22
21 35 0.78
ACGTcount: A:0.28, C:0.18, G:0.34, T:0.21
Consensus pattern (21 bp):
GATGCATGGCAAGGATGCATC
Found at i:17858 original size:24 final size:22
Alignment explanation
Indices: 17830--17909 Score: 83
Period size: 24 Copynumber: 3.5 Consensus size: 22
17820 CACTTAACAA
17830 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CC-TTGAATG
*
17854 TGCATCGATGCATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
* *
17874 ATACACCGATGCATGCCTTGAATG
1 -TGCATCGATGCAT-CCTTGAATG
17898 TGCATCGATGCA
1 TGCATCGATGCA
17910 CAAGACCATG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 11 0.24
22 2 0.04
23 12 0.26
24 17 0.37
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:20551 original size:19 final size:19
Alignment explanation
Indices: 20507--20558 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
20497 ATAAATTGAA
20507 ACATCGAATGCA-T-TCCAT
1 ACATCG-ATGCACTCTCCAT
* *
20525 GCACCGATGCACTCTCCAT
1 ACATCGATGCACTCTCCAT
20544 ACATCGATGCACTCT
1 ACATCGATGCACTCT
20559 GATTTAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 5 0.18
18 5 0.18
19 18 0.64
ACGTcount: A:0.27, C:0.35, G:0.13, T:0.25
Consensus pattern (19 bp):
ACATCGATGCACTCTCCAT
Found at i:20607 original size:64 final size:64
Alignment explanation
Indices: 20456--20612 Score: 190
Period size: 64 Copynumber: 2.4 Consensus size: 64
20446 TTTCAAAGGA
*
20456 ATGCACCGATGCATCAATACCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCATT
1 ATGCACCGATGCA-CAAT-CCATGCATCGATGCATC-ATGAATAAATTAAAACATCGAATGCATT
20521 CC
63 CC
** * * * **
20523 ATGCACCGATGCACTCTCCATACATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTTG
1 ATGCACCGATGCACAATCCATGCATCGATGCA-TCATGAATAAATTAAAACATCGAATGCATTCC
*
20587 ATGCATCGATGCACAATCCATGCATC
1 ATGCACCGATGCACAATCCATGCATC
20613 AGGCTGTTTT
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
64 46 0.60
65 14 0.18
66 4 0.05
67 13 0.17
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (64 bp):
ATGCACCGATGCACAATCCATGCATCGATGCATCATGAATAAATTAAAACATCGAATGCATTCC
Found at i:20655 original size:17 final size:19
Alignment explanation
Indices: 20627--20675 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
20617 TGTTTTCAAA
20627 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
20645 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
20664 CACCGATGCACT
1 CATCGATGCACT
20676 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:21745 original size:19 final size:20
Alignment explanation
Indices: 21721--21768 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
21711 AATGATTTTC
*
21721 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
21740 TTTTGAAATCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
21760 TTTTGAAAA
1 TTTTGAAAA
21769 AAGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.31
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:22939 original size:21 final size:21
Alignment explanation
Indices: 22913--22952 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
22903 CAACAATTGG
22913 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
*
22934 TAACAATTGATATCTTTTT
1 TAACAATTGATATCATTTT
22953 CATTAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:23133 original size:30 final size:30
Alignment explanation
Indices: 23062--23121 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
23052 ACAATTTAAG
23062 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
23092 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
23122 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:23229 original size:21 final size:21
Alignment explanation
Indices: 23203--23260 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
23193 AGGGTGTTAA
23203 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
23224 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
23245 AGTGCATCCATGCATC
1 AGTGCATCCATGCATC
23261 TGCACTAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:23346 original size:21 final size:21
Alignment explanation
Indices: 23320--23375 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
23310 ATGCAATTAG
23320 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
23341 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
*
23362 TGCATCCATGCATC
1 TGCATCGATGCATC
23376 AAGGCTGCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.34, G:0.18, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:24120 original size:63 final size:63
Alignment explanation
Indices: 24047--24168 Score: 160
Period size: 63 Copynumber: 1.9 Consensus size: 63
24037 AACTCAACAA
24047 AAATAAAAACATCGAAT-GCCA-TCAGTGTATCGATGCACAAG-TAGTGCATCGATGCACCCCCT
1 AAATAAAAACATCGAATAG-CATTCA-TGTATCGATGCA-AAGATAGTGCATCGATGCACCCCCT
24109 T
63 T
* * * *
24110 AAATACAAACATCGAATAGGATTTATGTATCGATGCATAGATAGTGCATCGATGCACCC
1 AAATAAAAACATCGAATAGCATTCATGTATCGATGCAAAGATAGTGCATCGATGCACCC
24169 GTCAAGGGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
62 2 0.04
63 47 0.90
64 3 0.06
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (63 bp):
AAATAAAAACATCGAATAGCATTCATGTATCGATGCAAAGATAGTGCATCGATGCACCCCCTT
Found at i:24903 original size:23 final size:23
Alignment explanation
Indices: 24812--24895 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
24802 CAATCTTATA
* *
24812 TGGCACTACGGTGCAATTTTACG
1 TGGCACTTCGGTGCAATTCTACG
*
24835 TGGCACTTCGGTGAAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
24858 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
24881 TGACACTTCGGTGCA
1 TGGCACTTCGGTGCA
24896 TTTATACGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:27321 original size:3 final size:3
Alignment explanation
Indices: 27313--27382 Score: 86
Period size: 3 Copynumber: 23.3 Consensus size: 3
27303 ACCTGAAAAT
* *
27313 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
27361 GTA GTA GTA ATA GTA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
27383 AAACCTGGGC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:27524 original size:18 final size:18
Alignment explanation
Indices: 27501--27591 Score: 86
Period size: 18 Copynumber: 5.4 Consensus size: 18
27491 GCGTTTTAAT
*
27501 TAATATTATTATGTTATA
1 TAATATAATTATGTTATA
*
27519 TAATATAATTACGTTAT-
1 TAATATAATTATGTTATA
*
27536 T-ACA-AATTATGTTATA
1 TAATATAATTATGTTATA
27552 TAATATAATTATG--ATA
1 TAATATAATTATGTTATA
* * *
27568 TTACA-AATTATATTATA
1 TAATATAATTATGTTATA
27585 TAATATA
1 TAATATA
27592 TATTTACATT
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
15 16 0.28
16 9 0.16
17 9 0.16
18 23 0.40
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.47
Consensus pattern (18 bp):
TAATATAATTATGTTATA
Found at i:27545 original size:33 final size:33
Alignment explanation
Indices: 27508--27591 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
27498 AATTAATATT
*
27508 ATTATGTTATATAATATAATTACGTTATTACAA
1 ATTATGTTATATAATATAATTACGATATTACAA
*
27541 ATTATGTTATATAATATAATTATGATATTACAA
1 ATTATGTTATATAATATAATTACGATATTACAA
*
27574 ATTATATTATATAATATA
1 ATTATGTTATATAATATA
27592 TATTTACATT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (33 bp):
ATTATGTTATATAATATAATTACGATATTACAA
Found at i:27549 original size:15 final size:15
Alignment explanation
Indices: 27525--27583 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
27515 TATATAATAT
*
27525 AATTACGTTATTACA
1 AATTATGTTATTACA
*
27540 AATTATGTTATATAATA
1 AATTATGTTAT-T-ACA
*
27557 TAATTATGATATTACA
1 -AATTATGTTATTACA
*
27573 AATTATATTAT
1 AATTATGTTAT
27584 ATAATATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 19 0.54
16 3 0.09
17 3 0.09
18 10 0.29
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (15 bp):
AATTATGTTATTACA
Found at i:28828 original size:2 final size:2
Alignment explanation
Indices: 28815--28847 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28805 ATTTTATTTT
*
28815 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28848 TTCTTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28859 original size:3 final size:3
Alignment explanation
Indices: 28851--28936 Score: 63
Period size: 3 Copynumber: 28.7 Consensus size: 3
28841 TATATATTTC
* * * *
28851 TTA TTA TTA TTA TTA TTA TT- TCTCC TTT TTA TTT TTA -TA TTA -AA
1 TTA TTA TTA TTA TTA TTA TTA T-T-A TTA TTA TTA TTA TTA TTA TTA
*
28895 TT- TTA TTA TACA TGTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TT
28937 CTTTTCTTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
2 6 0.09
3 55 0.82
4 5 0.07
5 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:29036 original size:15 final size:15
Alignment explanation
Indices: 28997--29043 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
28987 TTTCTCATTA
*
28997 TTTTATTT-TATGTT
1 TTTTATTTATTTGTT
*
29011 TTTTAGGTTATTTGTT
1 TTTTA-TTTATTTGTT
*
29027 TTTTATTTATTTATT
1 TTTTATTTATTTGTT
29042 TT
1 TT
29044 ATTACCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 5 0.19
15 12 0.44
16 10 0.37
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.77
Consensus pattern (15 bp):
TTTTATTTATTTGTT
Found at i:29039 original size:24 final size:24
Alignment explanation
Indices: 28994--29039 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
28984 TTTTTTCTCA
*
28994 TTATTTTATTTTATGTTTTTTAGG
1 TTATTTTATTTTATGTTATTTAGG
*
29018 TTATTTGTTTTTTAT-TTATTTA
1 TTATTT-TATTTTATGTTATTTA
29040 TTTTATTACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (24 bp):
TTATTTTATTTTATGTTATTTAGG
Found at i:29093 original size:14 final size:14
Alignment explanation
Indices: 29074--29104 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29064 GCATTCAGTT
*
29074 TTTTTATTTATTTA
1 TTTTTATTTACTTA
29088 TTTTTATTTACTTA
1 TTTTTATTTACTTA
29102 TTT
1 TTT
29105 CGTTGGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTATTTACTTA
Found at i:29186 original size:26 final size:26
Alignment explanation
Indices: 29123--29188 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
29113 TTTCTATGTT
* *
29123 TTTTTATTTTTTTCATTTTCATTTAC
1 TTTTTATTTTTTTCATTGTCAATTAC
* *
29149 TTTTTATATTTTTTCCTTGT-AATTAG
1 TTTTTAT-TTTTTTCATTGTCAATTAC
29175 TGTTTTATTTTTTT
1 T-TTTTATTTTTTT
29189 TTTAACTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 18 0.53
27 16 0.47
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.73
Consensus pattern (26 bp):
TTTTTATTTTTTTCATTGTCAATTAC
Found at i:32299 original size:99 final size:99
Alignment explanation
Indices: 32111--32317 Score: 281
Period size: 99 Copynumber: 2.1 Consensus size: 99
32101 ATATTATAAT
32111 ATTAT-ATATATATACAATAAACCTTGAACTGTACCTCTAAAGAAATTGGTTAAACGCCCCGGCT
1 ATTATAATATATATACAATAAACCTTGAACTGTACCTCTAAAGAAATTGGTTAAACGCCCCGGCT
* ** * *
32175 TTATGGATAAGATTCAGTTAGCCTGATAAATGCG
66 CTATGGATAAGATTCAACTAACCTGATAAAGGCG
* * ** * * *
32209 ATTATAATATCTATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCT
1 ATTATAATATATATACAATAAACCTTGAACTGTACCTCTAAAGAAATTGGTTAAACGCCCCGGCT
*
32274 CTATGGATAAGATTCAACTAACCTGATAAAGGTG
66 CTATGGATAAGATTCAACTAACCTGATAAAGGCG
*
32308 ATCATAATAT
1 ATTATAATAT
32318 TGAGATGTCC
Statistics
Matches: 94, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
98 5 0.05
99 89 0.95
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (99 bp):
ATTATAATATATATACAATAAACCTTGAACTGTACCTCTAAAGAAATTGGTTAAACGCCCCGGCT
CTATGGATAAGATTCAACTAACCTGATAAAGGCG
Found at i:34150 original size:156 final size:156
Alignment explanation
Indices: 33634--34568 Score: 1345
Period size: 156 Copynumber: 6.0 Consensus size: 156
33624 CACAACTTAA
* * *
33634 GTCTGTCAACAAAAAACTTTCCAGTTTCATTCAGAGTCAATATCAATTTCACATCGAAGGATATT
1 GTCTGTCAGCAAAAAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATT
** * *
33699 GGACTCGAAACAATGCCACTTACACAAGATTGGATTTCAACTTCACAATGAATGATATCCAATTC
66 GGACTCGAAACAACCCCACTTACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAATTC
* *
33764 AAAGCT-ACACTTCACAGTGAAGGAGA
131 AAAGCTCA-ACTTCACAGCGAAGGAGC
** * *
33790 AACTGTCAGCAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTTACAGT-GAAGGATAT
1 GTCTGTCAGCAAAAAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACA-TCGAAGGATAT
* * * * * *
33854 TGGACTTGAAACAACGCCACTTACACAATATTGGATTTCAAATTCAC-ACGAATGATATCTAATT
65 TGGACTCGAAACAACCCCACTTACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAATT
**
33918 CAAAGCTCAACTTCACAGCGAATAAGC
130 CAAAGCTCAACTTCACAGCGAAGGAGC
33945 GTCTGTCAGCAAAAAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATT
1 GTCTGTCAGCAAAAAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATT
*
34010 GGACTCGAAACAACCCCACTTACACAAGATTGGATTTCAACTTCACAACGAATGATATCCAATTC
66 GGACTCGAAACAACCCCACTTACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAATTC
* *
34075 AAAGCTCAACTTTACAGCGAATGAGC
131 AAAGCTCAACTTCACAGCGAAGGAGC
* * * *
34101 GTCTGTCAGCAAAAAACTTTCCAGTTTTATTCAGAGTCAATTTCGACTTCACAACGAATGATATT
1 GTCTGTCAGCAAAAAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATT
* *
34166 GGACTCAAAACAACCCCACTTACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAATTT
66 GGACTCGAAACAACCCCACTTACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAATTC
* *
34231 AAAGCTCAACTTAACACCGAAGGAGC
131 AAAGCTCAACTTCACAGCGAAGGAGC
* * * * *
34257 GTCTGTCAGCAAACAACTTTCCAGTTTCGTTCAGAGTCAATTTCAACTTCACAGCAAATGATATT
1 GTCTGTCAGCAAAAAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATT
* *
34322 GGACTCGAAACAACCCCACTTACACAAGATTGAATTTCAACTTCACAATGAAGGATATCCAATTC
66 GGACTCGAAACAACCCCACTTACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAATTC
*
34387 AAAGCTCAACTTCACAACGAAGGAGC
131 AAAGCTCAACTTCACAGCGAAGGAGC
* * * * *
34413 GTTTGTCAGCAAATAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAATGATATT
1 GTCTGTCAGCAAAAAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATT
* * * * * *
34478 GGACTCGAAGCAACACAACTTATACAAGATTGGATTTCAACATCACAACAAAGGATATCCAATTC
66 GGACTCGAAACAACCCCACTTACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAATTC
* **
34543 AAATCTCAACTTCGTAGCGAAGGAGC
131 AAAGCTCAACTTCACAGCGAAGGAGC
34569 CAGCCACGAT
Statistics
Matches: 708, Mismatches: 67, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
154 1 0.00
155 137 0.19
156 569 0.80
157 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (156 bp):
GTCTGTCAGCAAAAAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACATCGAAGGATATT
GGACTCGAAACAACCCCACTTACACAAGATTGGATTTCAACTTCACAACGAAGGATATCCAATTC
AAAGCTCAACTTCACAGCGAAGGAGC
Found at i:34821 original size:85 final size:85
Alignment explanation
Indices: 34724--34973 Score: 331
Period size: 85 Copynumber: 2.9 Consensus size: 85
34714 TTAAAGATAA
* *
34724 TCGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTATAGCATAGATCAAGGCGAGAAGGG
1 TCGAGTTCGATTACATTCAGCTCAAAGGTATATCAAATTTATAGTATAGATCAAGGCGAGAAGGG
*
34789 CTATCTGTTAACAAAGACCT
66 CTATCTGTCAACAAAGACCT
* *
34809 TCGAGTTCGATTACATTCAGCTCAAAGGTATATCAAATTTACAGTATAGCTCAAGGCGAGAAGGG
1 TCGAGTTCGATTACATTCAGCTCAAAGGTATATCAAATTTATAGTATAGATCAAGGCGAGAAGGG
* * *
34874 CTAACTATCAATAAAGACCT
66 CTATCTGTCAACAAAGACCT
* * * * * * * *
34894 TCGAATTCGATTACATTCAGCTTAAACGTACATCAAATTTTTAGTATA-ATTCAATGTGAGAAGA
1 TCGAGTTCGATTACATTCAGCTCAAAGGTATATCAAATTTATAGTATAGA-TCAAGGCGAGAAGG
*
34958 GTTATCTGTCAACAAA
65 GCTATCTGTCAACAAA
34974 CCATGTCGAG
Statistics
Matches: 142, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
85 142 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (85 bp):
TCGAGTTCGATTACATTCAGCTCAAAGGTATATCAAATTTATAGTATAGATCAAGGCGAGAAGGG
CTATCTGTCAACAAAGACCT
Found at i:36709 original size:2 final size:2
Alignment explanation
Indices: 36702--36734 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
36692 TATGTTTTAT
36702 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36735 TGTTTTTATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:36793 original size:18 final size:18
Alignment explanation
Indices: 36757--36792 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
36747 TTTTTTCTTA
36757 TATTTTTTCTTATATTTT
1 TATTTTTTCTTATATTTT
*
36775 TATTTTTT-TTGTATTTT
1 TATTTTTTCTTATATTTT
36792 T
1 T
36793 TGCTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.14, C:0.03, G:0.03, T:0.81
Consensus pattern (18 bp):
TATTTTTTCTTATATTTT
Found at i:36878 original size:3 final size:3
Alignment explanation
Indices: 36872--36906 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
36862 CTTCTTCTTC
*
36872 TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
36907 TCTCCTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:38598 original size:11 final size:10
Alignment explanation
Indices: 38576--38638 Score: 58
Period size: 11 Copynumber: 6.1 Consensus size: 10
38566 TTCACTTTTT
38576 TAAAAA-TAA
1 TAAAAATTAA
38585 TAAAAATGTAA
1 TAAAAAT-TAA
*
38596 TAAAAATAAA
1 TAAAAATTAA
*
38606 TTAAAAATGAA
1 -TAAAAATTAA
38617 T-AAAATTCAA
1 TAAAAATT-AA
38627 TAAAAATATAA
1 TAAAAAT-TAA
38638 T
1 T
38639 GTAAATTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
9 11 0.24
10 6 0.13
11 27 0.60
12 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (10 bp):
TAAAAATTAA
Found at i:38610 original size:31 final size:32
Alignment explanation
Indices: 38575--38643 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
38565 ATTCACTTTT
38575 TTAAAAAT-AATAAAAATGT-AATAAAAATA-AA
1 TTAAAAATGAAT-AAAAT-TCAATAAAAATATAA
38606 TTAAAAATGAATAAAATTCAATAAAAATATAA
1 TTAAAAATGAATAAAATTCAATAAAAATATAA
38638 TGTAAA
1 T-TAAA
38644 TTTAAAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
30 1 0.03
31 23 0.68
32 6 0.18
33 4 0.12
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (32 bp):
TTAAAAATGAATAAAATTCAATAAAAATATAA
Found at i:38611 original size:21 final size:20
Alignment explanation
Indices: 38576--38632 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
38566 TTCACTTTTT
38576 TAAAAATAAT-AAAAATGTAA
1 TAAAAATAATAAAAAATG-AA
*
38596 TAAAAATAAATTAAAAATGAA
1 TAAAAAT-AATAAAAAATGAA
*
38617 TAAAATTCAATAAAAA
1 TAAAAAT-AATAAAAA
38633 TATAATGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.22
21 18 0.56
22 7 0.22
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (20 bp):
TAAAAATAATAAAAAATGAA
Found at i:39296 original size:26 final size:27
Alignment explanation
Indices: 39266--39318 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
39256 AATGATGATG
39266 ATAAATATTT-TATA-ATTTAAAAAATT
1 ATAAAT-TTTATATATATTTAAAAAATT
*
39292 ATAAATTTTATATATTTTTAAAAAATT
1 ATAAATTTTATATATATTTAAAAAATT
39319 TATTGACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 3 0.12
26 10 0.42
27 11 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
ATAAATTTTATATATATTTAAAAAATT
Found at i:39874 original size:21 final size:21
Alignment explanation
Indices: 39849--39897 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
39839 TTTACATTAT
*
39849 ATTTTT-ATTGAATTTTATTC
1 ATTTTTAATTCAATTTTATTC
* *
39869 ATTTTTAATTCATTTTTATTT
1 ATTTTTAATTCAATTTTATTC
39890 ATTTTTAA
1 ATTTTTAA
39898 AAAATGAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTTTTAATTCAATTTTATTC
Found at i:39879 original size:11 final size:10
Alignment explanation
Indices: 39849--39896 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
39839 TTTACATTAT
*
39849 ATTTTTATTG
1 ATTTTTATTC
*
39859 AATTTTATTC
1 ATTTTTATTC
39869 ATTTTTAATTC
1 ATTTTT-ATTC
*
39880 ATTTTTATTT
1 ATTTTTATTC
39890 ATTTTTA
1 ATTTTTA
39897 AAAAATGAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 23 0.70
11 10 0.30
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (10 bp):
ATTTTTATTC
Found at i:48489 original size:71 final size:70
Alignment explanation
Indices: 48367--48502 Score: 211
Period size: 71 Copynumber: 1.9 Consensus size: 70
48357 CGAGAGACTT
* *
48367 AACAAAATAACTCCCTATAATCGGAGGACTATTATGTATGTTACCCTTAAATGTACATAGTGTTA
1 AACAAAACAACTCCCTATAATCGGAGGACCATTATGTATGTTACCCTTAAATGTACATAGTGTTA
48432 GACCC
66 GACCC
* *
48437 AACAAAACAACTCCTTATAATCGGGGGACCATTCATGTACT-TTACCCTTAAATGTACATAGTGT
1 AACAAAACAACTCCCTATAATCGGAGGACCATT-ATGTA-TGTTACCCTTAAATGTACATAGTGT
48501 TA
64 TA
48503 ATCTACTTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
70 29 0.48
71 30 0.50
72 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (70 bp):
AACAAAACAACTCCCTATAATCGGAGGACCATTATGTATGTTACCCTTAAATGTACATAGTGTTA
GACCC
Found at i:49021 original size:19 final size:20
Alignment explanation
Indices: 48997--49036 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
48987 AAAAATTTTT
*
48997 TATGAATAGTA-CTATAATG
1 TATGAATAGTATCGATAATG
49016 TATGAATAGTATCGATAATG
1 TATGAATAGTATCGATAATG
49036 T
1 T
49037 GCAAATAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (20 bp):
TATGAATAGTATCGATAATG
Found at i:49117 original size:21 final size:21
Alignment explanation
Indices: 49079--49119 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
49069 CCATGGGCAG
**
49079 TGCTACACTGTAGTGATGCAT
1 TGCTACACTGTACCGATGCAT
*
49100 TGCTACAGTGTACCGATGCA
1 TGCTACACTGTACCGATGCA
49120 CAAAAACATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCTACACTGTACCGATGCAT
Found at i:49167 original size:21 final size:21
Alignment explanation
Indices: 49141--49184 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
49131 AAAATAAATT
*
49141 GTGTATCGATGTACTGCTACA
1 GTGTATCGATGCACTGCTACA
49162 GTGTATCGATGCACTGCTACA
1 GTGTATCGATGCACTGCTACA
49183 GT
1 GT
49185 AACTTCAGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (21 bp):
GTGTATCGATGCACTGCTACA
Found at i:49946 original size:23 final size:23
Alignment explanation
Indices: 49903--49946 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
49893 AATACATATA
* *
49903 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCAAAGGACCACATAGAAT
*
49926 TGTCCCAAAGGACCGCATAGA
1 TGTCCCAAAGGACCACATAGA
49947 CCCTCTACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (23 bp):
TGTCCCAAAGGACCACATAGAAT
Done.