Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000099.1 Hibiscus syriacus cultivar Beakdansim tig00000182_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: 100424
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5590 original size:114 final size:114
Alignment explanation
Indices: 5387--5612 Score: 398
Period size: 114 Copynumber: 2.0 Consensus size: 114
5377 AAGTGTCATG
*
5387 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
*
5452 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATT
* *
5501 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
* *
5566 TGGTTTGGTATGAACCCCAGAACCAATCATTGGAATTGAAAGGTGAA
66 TGGTTTGGTATGAACCCCAAAACCAATCATTGGAATTGAAAGATGAA
5613 CTGCATGATC
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 106 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATT
Found at i:9060 original size:76 final size:75
Alignment explanation
Indices: 8934--9126 Score: 302
Period size: 76 Copynumber: 2.6 Consensus size: 75
8924 ATTTCCCACG
8934 TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAG
1 TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA-
8999 CC-TCAGGGTCA
65 CCTTC-GGGTCA
* *
9010 TCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAAAC
1 TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAC
9075 CTTCGGGTCA
66 CTTCGGGTCA
* * *
9085 TCTGTAAGCCCTTCAGTGCATGATGTTTTC--AAAGCCTTCGGG
1 TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
9127 TCATCCGTAA
Statistics
Matches: 110, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
73 11 0.10
75 35 0.32
76 64 0.58
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (75 bp):
TCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAC
CTTCGGGTCA
Found at i:9131 original size:45 final size:45
Alignment explanation
Indices: 9061--9207 Score: 260
Period size: 45 Copynumber: 3.3 Consensus size: 45
9051 GGGAGCTTTT
*
9061 TGATGTTTTCAAA-CCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTTCAGTGCA
9105 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTTCAGTGCA
*
9150 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTGCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTTCAGTGCA
*
9195 GGATGTTTTCAAA
1 TGATGTTTTCAAA
9208 AAGCCTTCAA
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
44 13 0.13
45 86 0.87
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTTCAGTGCA
Found at i:9553 original size:75 final size:76
Alignment explanation
Indices: 9150--9656 Score: 786
Period size: 76 Copynumber: 6.7 Consensus size: 76
9140 CTTCAGTGCA
* * * * *
9150 TGATGTTTTCAAAGCCTTC-GGGTCATCCGTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCT
1 TGATGTTTTCAAAGCC-TCAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCT
**
9214 TCAAGAGCTTTT
65 TCGGGAGCTTTT
* * *
9226 TGATATTTTCAAAGCCTCAGGGTCGTTTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTCAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
9291 CGGGAGCTTTT
66 CGGGAGCTTTT
*
9302 TGATGTTTTCAAAGCCTCAGGGTCGTCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTCAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
9367 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
9378 TGATGTTCTCAAAGCCTCAGGGTCGTCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTCAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
9443 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
9454 TGATGTTTTCAAAGCCTCAGGGTCATCTGTAAGTCCTGCAGAGCATGATGTTTCC-AAAAGCCTT
1 TGATGTTTTCAAAGCCTCAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
*
9518 TGGGAGCTTTT
66 CGGGAGCTTTT
* *
9529 TGATGTTTTTAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTCAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
*
9594 CAGGAGCTTTT
66 CGGGAGCTTTT
* * *
9605 TGATGTTTTCAAA-CCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTT
1 TGATGTTTTCAAAGCCTCAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTT
9657 TCAACATTTC
Statistics
Matches: 402, Mismatches: 27, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
75 109 0.27
76 293 0.73
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (76 bp):
TGATGTTTTCAAAGCCTCAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTT
Found at i:9798 original size:3 final size:3
Alignment explanation
Indices: 9790--9896 Score: 144
Period size: 3 Copynumber: 35.7 Consensus size: 3
9780 TCATTTAAAT
** *
9790 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
9838 TTA TAA TAA TAA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
9886 TTA TTA TTA TT
1 TTA TTA TTA TT
9897 TAATAAATAA
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
2 2 0.02
3 89 0.95
4 3 0.03
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:9909 original size:18 final size:19
Alignment explanation
Indices: 9792--9909 Score: 82
Period size: 18 Copynumber: 6.2 Consensus size: 19
9782 ATTTAAATTT
* *
9792 ATTATTATTATTA-AAATT
1 ATTATTATTATAATAAATA
* * *
9810 ATTATTATTATTATTAGTATT
1 ATTATTATTA-TAATA-AATA
9831 ATTATTATTATAAT-AATA
1 ATTATTATTATAATAAATA
* * *
9849 ATTATTATTATTAT-TATT
1 ATTATTATTATAATAAATA
* *
9867 ATTATTATTATATTATAT-
1 ATTATTATTATAATAAATA
9885 ATTATTATTATTTAATAAATA
1 ATTATTATTA--TAATAAATA
9906 ATTA
1 ATTA
9910 CAAAACTAGA
Statistics
Matches: 80, Mismatches: 13, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
18 49 0.61
19 4 0.05
20 10 0.12
21 17 0.21
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.58
Consensus pattern (19 bp):
ATTATTATTATAATAAATA
Found at i:10316 original size:29 final size:30
Alignment explanation
Indices: 10240--10317 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
10230 CGGATCTTGC
10240 AAAACAAAAAAAAGAGG-A-CGACGACAGAA
1 AAAAC-AAAAAAAGAGGAAGCGACGACAGAA
* *
10269 AAAAAAAGAAAAAGA-GAAGGGA-GACAGAA
1 AAAACAA-AAAAAGAGGAAGCGACGACAGAA
10298 AAAACAAAAAAAGAGGAAGC
1 AAAACAAAAAAAGAGGAAGC
10318 AACTAACGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 10 0.24
29 29 0.71
30 2 0.05
ACGTcount: A:0.68, C:0.09, G:0.23, T:0.00
Consensus pattern (30 bp):
AAAACAAAAAAAGAGGAAGCGACGACAGAA
Found at i:11008 original size:21 final size:19
Alignment explanation
Indices: 10982--11029 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
10972 TATTTAGTCC
*
10982 TTTAATTTTAATAATTAATAT
1 TTTAATTTGAATAA-T-ATAT
* *
11003 TTTAATCTGAATAATATGT
1 TTTAATTTGAATAATATAT
11022 TTTAATTT
1 TTTAATTT
11030 ATTTTAATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 10 0.43
20 1 0.04
21 12 0.52
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (19 bp):
TTTAATTTGAATAATATAT
Found at i:32213 original size:18 final size:19
Alignment explanation
Indices: 32178--32216 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
32168 TATATTAATG
*
32178 ATTCAAAATGGATAATTTT
1 ATTCAAAATAGATAATTTT
*
32197 ATTC-AAATAGATCATTTT
1 ATTCAAAATAGATAATTTT
32215 AT
1 AT
32217 ATATCAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (19 bp):
ATTCAAAATAGATAATTTT
Found at i:35271 original size:18 final size:18
Alignment explanation
Indices: 35248--35290 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
35238 TCTTAGATTA
35248 TTTATTTAATTATTT-TCT
1 TTTATTTAATT-TTTATCT
35266 TTTATTTAATTTTTATCT
1 TTTATTTAATTTTTATCT
35284 TTTATTT
1 TTTATTT
35291 TAAAATAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTTTTATCT
Found at i:35406 original size:36 final size:35
Alignment explanation
Indices: 35309--35411 Score: 106
Period size: 35 Copynumber: 2.9 Consensus size: 35
35299 CTTTTAAAAC
35309 CCCTTTTTATCTT-TACTATTA-TTATTTTATTA-TTT
1 CCCTTTTTAT-TTATA--ATTATTTATTTTATTATTTT
*
35344 CCCTTTTTATTTATTATTATTTATTTTATTATTTT
1 CCCTTTTTATTTATAATTATTTATTTTATTATTTT
**
35379 TTCTTTTTAAATTT-TAATTATTTATTTTATTAT
1 CCCTTTTT--ATTTATAATTATTTATTTTATTAT
35412 ATCTTTTCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
33 4 0.07
34 13 0.22
35 20 0.34
36 18 0.31
37 4 0.07
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (35 bp):
CCCTTTTTATTTATAATTATTTATTTTATTATTTT
Found at i:40844 original size:5 final size:5
Alignment explanation
Indices: 40818--40910 Score: 50
Period size: 5 Copynumber: 18.8 Consensus size: 5
40808 TCGTTCTATT
** * *
40818 TTTTA TTTT- TTTTA TTACA TTTTA TTTTCA TTTCA TTTTCA TTTTA -CTT-
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTT-A TTTTA TTTTA
* ** * *
40867 TTTTA GTAAA CTTTA TTTTCA TTCTA -TTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTT
40911 TCTTTGAACA
Statistics
Matches: 64, Mismatches: 17, Indels: 14
0.67 0.18 0.15
Matches are distributed among these distances:
4 11 0.17
5 40 0.62
6 13 0.20
ACGTcount: A:0.20, C:0.09, G:0.01, T:0.70
Consensus pattern (5 bp):
TTTTA
Found at i:40849 original size:11 final size:11
Alignment explanation
Indices: 40818--40868 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
40808 TCGTTCTATT
40818 TTTTATTTT--
1 TTTTATTTTCA
*
40827 TTTTA-TTACA
1 TTTTATTTTCA
40837 TTTTATTTTCA
1 TTTTATTTTCA
*
40848 TTTCATTTTCA
1 TTTTATTTTCA
40859 TTTTACTTTT
1 TTTTA-TTTT
40869 TTAGTAAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
8 2 0.06
9 5 0.15
10 5 0.15
11 18 0.53
12 4 0.12
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:42824 original size:75 final size:76
Alignment explanation
Indices: 42730--42904 Score: 223
Period size: 76 Copynumber: 2.3 Consensus size: 76
42720 TGAATTAATC
* *
42730 TTAAGTTTAGGATAATATTTTAAACATTATAT-TTTATCTTT-T-TATTTTAGTTTAAATATGTT
1 TTAAGTTTAGGATATTATTTTAAACATTATATCTTTAT-TTTATGTATTTTAGTTTAAATAGGTT
42792 TTAGTATTTTAA
65 TTAGTATTTTAA
* * * *
42804 TTAAGTTTTAGGATATTATTTT-TATATTTTATCTTTGTTTTATGTATTTTAGTTTAAATAGGTT
1 TTAAG-TTTAGGATATTATTTTAAACATTATATCTTTATTTTATGTATTTTAGTTTAAATAGGTT
42868 TTAGTATTTTAA
65 TTAGTATTTTAA
* *
42880 TTAGAATTTAGAATATTATTTTAAA
1 TTA-AGTTTAGGATATTATTTTAAA
42905 TAATATTTTG
Statistics
Matches: 86, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
74 15 0.17
75 20 0.23
76 49 0.57
77 2 0.02
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (76 bp):
TTAAGTTTAGGATATTATTTTAAACATTATATCTTTATTTTATGTATTTTAGTTTAAATAGGTTT
TAGTATTTTAA
Found at i:43558 original size:18 final size:18
Alignment explanation
Indices: 43535--43577 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
43525 TCTTGGATTA
43535 TTTATTTAATTACTT-TCT
1 TTTATTTAATT-CTTATCT
*
43553 TTTATTTAATTTTTATCT
1 TTTATTTAATTCTTATCT
43571 TTTATTT
1 TTTATTT
43578 TAAAAACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTCTTATCT
Found at i:43624 original size:3 final size:3
Alignment explanation
Indices: 43618--43712 Score: 56
Period size: 3 Copynumber: 31.0 Consensus size: 3
43608 TCTTTACTAC
*
43618 TAT TATT TAT TAT T-T TAT TAT T-T TCCAT TTT TATT TAT TAT TATT
1 TAT TA-T TAT TAT TAT TAT TAT TAT T--AT TAT TA-T TAT TAT TA-T
* * *
43663 TAT T-T TAT TAT TAT TATT TAA AAT TAT AAT TATT TAT T-T TAT T-T
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA-T TAT TAT TAT TAT
43707 TAT TAT
1 TAT TAT
43713 AGAAGAGCTA
Statistics
Matches: 72, Mismatches: 8, Indels: 24
0.69 0.08 0.23
Matches are distributed among these distances:
2 10 0.14
3 45 0.62
4 15 0.21
5 2 0.03
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:43633 original size:28 final size:28
Alignment explanation
Indices: 43601--43682 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
43591 TAAAAATTCT
*
43601 TTTTTTATCTTTACTACTATTATTTATTA
1 TTTTTTAT-TTTACTATTATTATTTATTA
* *
43630 TTTTATTATTTT-CCATTTTTATTTATTA
1 TTTT-TTATTTTACTATTATTATTTATTA
* *
43658 TTATTTATTTTATTATTATTATTTA
1 TTTTTTATTTTACTATTATTATTTA
43683 AAATTATAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
27 7 0.16
28 26 0.59
29 7 0.16
30 4 0.09
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTTTTATTTTACTATTATTATTTATTA
Found at i:60697 original size:12 final size:12
Alignment explanation
Indices: 60680--60706 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
60670 ATTCACACAG
60680 ACTGTTTGGTCT
1 ACTGTTTGGTCT
60692 ACTGTTTGGTCT
1 ACTGTTTGGTCT
60704 ACT
1 ACT
60707 TTTCATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (12 bp):
ACTGTTTGGTCT
Found at i:62326 original size:16 final size:16
Alignment explanation
Indices: 62305--62335 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
62295 TATCCATTTT
62305 TTTTAATACTATAATC
1 TTTTAATACTATAATC
62321 TTTTAATACTATAAT
1 TTTTAATACTATAAT
62336 TTCCATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTAATACTATAATC
Found at i:66274 original size:45 final size:46
Alignment explanation
Indices: 66189--66276 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
66179 AAATAGCCTG
* *
66189 AGTGCATCAATGCATGGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCATCAATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
*
66235 AGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATCAATGCATGGTCATGTGCATCGATGCATAAAATGCA
66277 TTCGATGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.56
46 17 0.44
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (46 bp):
AGTGCATCAATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
Found at i:71298 original size:45 final size:46
Alignment explanation
Indices: 71213--71300 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
71203 AAATAGCCTG
* * *
71213 AGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACTA
1 AGTGCATCGATGCATGGTCATGTGCATCAATGCATAAAATGCACTA
*
71259 AGTGCATCGATGCATGGT-ATGTGCATTAATGCATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCAATGCATAAAATGCA
71301 TTCGATGTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 20 0.53
46 18 0.47
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCAATGCATAAAATGCACTA
Found at i:72357 original size:3 final size:3
Alignment explanation
Indices: 72351--72391 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
72341 AATAATATTT
72351 TAA TAA TAA TAA TAA TAA TATA TAA TAA T-A TAAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA T-AA TAA TAA T
72392 CAAATGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 2 0.06
3 28 0.80
4 5 0.14
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:72916 original size:113 final size:112
Alignment explanation
Indices: 72713--73174 Score: 541
Period size: 113 Copynumber: 4.0 Consensus size: 112
72703 TGTGATAGAA
* * *
72713 TCAAAC-AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTCTTCAGATAAGTTCTT
1 TCAAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTT
*
72777 CTCATTACGAACTTTCTCTGGAAAAGTTGATCCATTGAGTAATGAAT
66 CTCATTATGAACTTTCTCTGGAAAAGTTGATCCATTGAGTAATGAAT
* *
72824 TCAAACAAAAGGTTAAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCT
*
72889 TCTCATTATGAACTTTCTTTGGAAAAGTTGATCCATTGAGTAATGAAT
65 TCTCATTATGAACTTTCTCTGGAAAAGTTGATCCATTGAGTAATGAAT
* * * *
72937 TCAAACAAAAGGTTAAACGAGTTCTTCTCATTATGAACTTCTTCTTCATTCTACAGATGAGTTCT
1 TCAAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATAAGTTCT
* * * ** * *
73002 TCCCATTATGAACTTTCTCTGTTAAAGTTGATGTTGATCTATCTCCTTCTGTGAT-AGAG
65 TCTCATTATGAACTTTCTCTG-GAAA----A-GTTG----ATC-CATTGAGTAATGA-AT
** * * *
73061 TCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTTTT
1 TCAAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTT
* * * *
73126 CTCATTATGGACTTTCTCTGGAAAAGTTGATCTATTGAGTGATGGAT
66 CTCATTATGAACTTTCTCTGGAAAAGTTGATCCATTGAGTAATGAAT
73173 TC
1 TC
73175 GAATATTTGC
Statistics
Matches: 298, Mismatches: 37, Indels: 31
0.81 0.10 0.08
Matches are distributed among these distances:
111 6 0.02
112 47 0.16
113 143 0.48
114 3 0.01
117 4 0.01
118 2 0.01
119 4 0.01
122 3 0.01
123 36 0.12
124 50 0.17
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (112 bp):
TCAAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTT
CTCATTATGAACTTTCTCTGGAAAAGTTGATCCATTGAGTAATGAAT
Found at i:79611 original size:46 final size:46
Alignment explanation
Indices: 79551--79643 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
79541 TATTTTCTGC
79551 ATCATACTGTCTTGTGAATTTGCAATGTTGGATTCAATCTTTTCTA
1 ATCATACTGTCTTGTGAATTTGCAATGTTGGATTCAATCTTTTCTA
*
79597 ATCATACTGTCTTGTGAATTTGCAATTTTGGATTCAATCTTTTCTA
1 ATCATACTGTCTTGTGAATTTGCAATGTTGGATTCAATCTTTTCTA
79643 A
1 A
79644 CATCAATCTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (46 bp):
ATCATACTGTCTTGTGAATTTGCAATGTTGGATTCAATCTTTTCTA
Found at i:85517 original size:3 final size:3
Alignment explanation
Indices: 85511--85563 Score: 72
Period size: 3 Copynumber: 17.3 Consensus size: 3
85501 AATAATATTT
*
85511 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CATA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA T-AA
85557 TAA TAA T
1 TAA TAA T
85564 CAAATGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.87
4 4 0.09
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:86950 original size:20 final size:20
Alignment explanation
Indices: 86922--86962 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
86912 AATTTCACGA
*
86922 GGAATAAAGGTATAAATCGT
1 GGAACAAAGGTATAAATCGT
86942 GGAACAAAGGTATAAATCGT
1 GGAACAAAGGTATAAATCGT
86962 G
1 G
86963 ATGTCATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.07, G:0.27, T:0.22
Consensus pattern (20 bp):
GGAACAAAGGTATAAATCGT
Found at i:87251 original size:20 final size:20
Alignment explanation
Indices: 87222--87259 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
87212 TTAATTTAAG
87222 AAAAATTAAT-TTTTTAAAT
1 AAAAATTAATATTTTTAAAT
87241 AAAATATTAATATTTTTAA
1 AAAA-ATTAATATTTTTAA
87260 GTTTTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 6 0.35
21 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAAATTAATATTTTTAAAT
Found at i:87743 original size:21 final size:20
Alignment explanation
Indices: 87702--87743 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
87692 AAACAAAAAA
*
87702 AAAATTAACGTTTTTTTAAT
1 AAAATTAACGTTTTTTAAAT
87722 AAAATTAACGTTTTTTCAAAT
1 AAAATTAACGTTTTTT-AAAT
87743 A
1 A
87744 CTAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (20 bp):
AAAATTAACGTTTTTTAAAT
Found at i:90026 original size:46 final size:46
Alignment explanation
Indices: 89960--90051 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 46
89950 CCTCAAAAAC
* * *
89960 CCTAAAAATCTAAAAGATAATTCTTAA-AACATTGC-AAAGATAATT
1 CCTAAAAATCCAAAAGATAATTCCTAATAA-ATTACAAAAGATAATT
90005 CCTAAAAATCACAAAAGATAATTCCTAATAAATTACAAAAGATAATT
1 CCTAAAAATC-CAAAAGATAATTCCTAATAAATTACAAAAGATAATT
90052 TTCATAATTG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
45 10 0.24
46 19 0.46
47 12 0.29
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.27
Consensus pattern (46 bp):
CCTAAAAATCCAAAAGATAATTCCTAATAAATTACAAAAGATAATT
Found at i:90042 original size:24 final size:23
Alignment explanation
Indices: 89971--90051 Score: 110
Period size: 23 Copynumber: 3.5 Consensus size: 23
89961 CTAAAAATCT
* *
89971 AAAAGATAATTCTTAAAACATTGC
1 AAAAGATAATTCCTAAAA-ATTAC
*
89995 -AAAGATAATTCCTAAAAATCAC
1 AAAAGATAATTCCTAAAAATTAC
90017 AAAAGATAATTCCTAATAAATTAC
1 AAAAGATAATTCCTAA-AAATTAC
90041 AAAAGATAATT
1 AAAAGATAATT
90052 TTCATAATTG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.06
23 31 0.61
24 17 0.33
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.27
Consensus pattern (23 bp):
AAAAGATAATTCCTAAAAATTAC
Found at i:92958 original size:44 final size:45
Alignment explanation
Indices: 92903--93005 Score: 111
Period size: 45 Copynumber: 2.3 Consensus size: 45
92893 CACATTCAAT
* * * *
92903 GTGCGTCGATGCA-CTCTTTAAAGAAG-AAACATCGAATGCAATTG
1 GTGCATCGATGCATCCCCTTAAA-AAGAAAACATCGAAGGCAATTG
* * *
92947 GTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTAATTT
1 GTGCATCGATGCATCCCCTTAAAAAGAAAACATCGAAGGCAATTG
*
92992 GTGTATCGATGCAT
1 GTGCATCGATGCAT
93006 GGGTAGTGCA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
44 14 0.29
45 35 0.71
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (45 bp):
GTGCATCGATGCATCCCCTTAAAAAGAAAACATCGAAGGCAATTG
Found at i:93876 original size:18 final size:18
Alignment explanation
Indices: 93853--93922 Score: 113
Period size: 18 Copynumber: 3.9 Consensus size: 18
93843 GAGGGTCTAC
*
93853 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACACA
93871 GTGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACACA
*
93889 GTGGTCCTTTGGGACACA
1 GTGGTCCTTCGGGACACA
*
93907 GTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACA
93923 AATTCTGCGC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.17, C:0.24, G:0.34, T:0.24
Consensus pattern (18 bp):
GTGGTCCTTCGGGACACA
Done.