Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005695.1 Hibiscus syriacus cultivar Beakdansim tig00013321_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: 70450
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1658 original size:24 final size:24
Alignment explanation
Indices: 1631--1711 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
1621 ACACTTAACA
1631 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
1655 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
1677 -TGCACCGATGCA-CGCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
1699 GTGCATCGATGCA
1 GTGCATCGATGCA
1712 CATGGTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
20 3 0.07
21 11 0.24
22 1 0.02
23 14 0.31
24 16 0.36
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:1697 original size:44 final size:44
Alignment explanation
Indices: 1632--1734 Score: 138
Period size: 44 Copynumber: 2.3 Consensus size: 44
1622 CACTTAACAG
* * *
1632 TGCATCGATGCATCCCTTTGAATGTGCATCGATTCATCATGTTGA
1 TGCATCGATGCATCCCTTTGAATGTGCATCGATGCA-CATGGTCA
*
1677 TGCACCGATGCA-CGCC-TTGAATGTGCATCGATGCACATGGTCA
1 TGCATCGATGCATC-CCTTTGAATGTGCATCGATGCACATGGTCA
1720 TGCATCGATGCATCC
1 TGCATCGATGCATCC
1735 GTCGGGTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
43 18 0.35
44 20 0.39
45 13 0.25
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.29
Consensus pattern (44 bp):
TGCATCGATGCATCCCTTTGAATGTGCATCGATGCACATGGTCA
Found at i:2411 original size:21 final size:21
Alignment explanation
Indices: 2387--2439 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
2377 AAAATCGTCC
2387 TCCCGTTCCTCAACCTCCTAA
1 TCCCGTTCCTCAACCTCCTAA
2408 TCCCGTTCCTCAACCTCCTAA
1 TCCCGTTCCTCAACCTCCTAA
2429 TCCCGTTCCTC
1 TCCCGTTCCTC
2440 CTCTACCTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.15, C:0.49, G:0.06, T:0.30
Consensus pattern (21 bp):
TCCCGTTCCTCAACCTCCTAA
Found at i:4414 original size:65 final size:63
Alignment explanation
Indices: 4345--4504 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 63
4335 AATTAAATTG
* *
4345 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-
4409 A
63 A
* * * *
4410 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGA
* *
4474 AACATCGAATGCACTTGATACATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
4505 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
63 1 0.01
64 29 0.34
65 50 0.59
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:4504 original size:17 final size:18
Alignment explanation
Indices: 4470--4505 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4460 TCTGGCTATT
4470 TTGAAACATCGAATGCAC
1 TTGAAACATCGAATGCAC
*
4488 TTGATACATCG-ATGCAC
1 TTGAAACATCGAATGCAC
4505 T
1 T
4506 CTTAGTGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (18 bp):
TTGAAACATCGAATGCAC
Found at i:7194 original size:100 final size:100
Alignment explanation
Indices: 7001--7192 Score: 260
Period size: 100 Copynumber: 1.9 Consensus size: 100
6991 TTCAAACGGT
** ** * *
7001 TAAGTTGTAAATATTTTACCGTTTACATTTTTATTATACATTTAAACAAGTTGGTAAGTAGTTTA
1 TAAGTTGTAAATATTTTACCGTTTACATTAATATTATACATTTAAACAAACTGATAAGTAATTTA
*
7066 ACATAATAGGTATCACCTATTTTATTTTAACTGAA
66 ACATAATAGGTAGCACCTATTTTATTTTAACTGAA
* * *
7101 TAAGTTGTAAATATTTTATCGTTTACATTAATATTATACTTTTAAACAAACTGATAGGTAATTTA
1 TAAGTTGTAAATATTTTACCGTTTACATTAATATTATACATTTAAACAAACTGATAAGTAATTTA
** *
7166 ATGTAATAGGTAGC-GCTATTTTATTTT
66 ACATAATAGGTAGCACCTATTTTATTTT
7193 TACCGATTAC
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
99 12 0.15
100 67 0.85
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (100 bp):
TAAGTTGTAAATATTTTACCGTTTACATTAATATTATACATTTAAACAAACTGATAAGTAATTTA
ACATAATAGGTAGCACCTATTTTATTTTAACTGAA
Found at i:7232 original size:76 final size:77
Alignment explanation
Indices: 7114--7345 Score: 310
Period size: 76 Copynumber: 3.0 Consensus size: 77
7104 GTTGTAAATA
* * * *
7114 TTTTATCGTTTACATTAATATTATACTTTTAAACAAACTGATAGGTAATTTAATGTAATAGGTAG
1 TTTTACCGATTACATTATTATTATACCTTTAAACAAACTGATAGGTAATTTAATGTAATAGGTAG
7179 CGC-TATTTTAT
66 CGCTTATTTTAT
* *
7190 TTTTACCGATTACATTATTATTATACCTTTAAACAAACTGATATGTAATTTAACGTAATAGGTAG
1 TTTTACCGATTACATTATTATTATACCTTTAAACAAACTGATAGGTAATTTAATGTAATAGGTAG
**
7255 TACTTATTTTA-
66 CGCTTATTTTAT
* * * *
7266 TTTTACC-ATTTACATTATTATTGTATCTTTAAACAAA-TCGGTAGGTAGTTTAATGTAATAGGT
1 TTTTACCGA-TTACATTATTATTATACCTTTAAACAAACT-GATAGGTAATTTAATGTAATAGGT
7329 AGCGCTTATTTTAT
64 AGCGCTTATTTTAT
7343 TTT
1 TTT
7346 AACTGGTTAA
Statistics
Matches: 136, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
75 2 0.01
76 124 0.91
77 10 0.07
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (77 bp):
TTTTACCGATTACATTATTATTATACCTTTAAACAAACTGATAGGTAATTTAATGTAATAGGTAG
CGCTTATTTTAT
Found at i:7503 original size:177 final size:176
Alignment explanation
Indices: 7203--7523 Score: 486
Period size: 177 Copynumber: 1.8 Consensus size: 176
7193 TACCGATTAC
* * * *
7203 ATTATTATTATACCTTTAAACAAACTGATATGTAATTTAACGTAATAGGTAGTACTTATTTTATT
1 ATTAATATTATACCTTTAAACAAACAGATAGGTAATTTAACGTAATAGATAGTACTTATTTTATT
* * * *
7268 TTACCATTTACATTATTATTGTATCTTTAAACAAATCGGTAGGTAGTTTAATGTAATAGGTAGCG
66 TTAACATTTACATTATTATTATACCTTTAAACAAATCGGTAGGTAGTTTAACGTAATAGGTAGCG
*
7333 CTTATTTTATTTTAACTGGTTAAGTTGTAAATATTTTATTGTTTAT
131 CCTATTTTATTTTAACTGGTTAAGTTGTAAATATTTTATTGTTTAT
*
7379 ATTAATATTATACCTTTAAACAAATCAG-TAGGTAGTTTAACGTAATAGATAG--CGTCTATTTT
1 ATTAATATTATACCTTTAAACAAA-CAGATAGGTAATTTAACGTAATAGATAGTAC-T-TATTTT
*
7441 ATTTTAACGTGTTACATTATTATTATACCTTTAAACAAATCGGTAGGTAGTTTAACGTAATAGGT
63 ATTTTAACAT-TTACATTATTATTATACCTTTAAACAAATCGGTAGGTAGTTTAACGTAATAGGT
7506 AGCGCCTATTTTATTTTA
127 AGCGCCTATTTTATTTTA
7524 CCGTTTTCGT
Statistics
Matches: 130, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
174 1 0.01
175 1 0.01
176 58 0.45
177 70 0.54
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (176 bp):
ATTAATATTATACCTTTAAACAAACAGATAGGTAATTTAACGTAATAGATAGTACTTATTTTATT
TTAACATTTACATTATTATTATACCTTTAAACAAATCGGTAGGTAGTTTAACGTAATAGGTAGCG
CCTATTTTATTTTAACTGGTTAAGTTGTAAATATTTTATTGTTTAT
Found at i:7553 original size:253 final size:251
Alignment explanation
Indices: 7012--7856 Score: 1036
Period size: 253 Copynumber: 3.3 Consensus size: 251
7002 AAGTTGTAAA
* **** *
7012 TATTTTACCGTTTACATTTTTATTATACATTTAAACAAGTTGGTAAGTAGTTTAACATAATAGGT
1 TATTTTACCGTTTACATTATTATTATACATTTAAACAAACCAGTAAGTAGTTTAACGTAATAGGT
* ** *
7077 ATCACCTATTTTATTTTAACTGAATAAGTTGTAAATATTTTATCGTTTACATTAATATTATACTT
66 AGCACCTATTTTATTTTAACTGGTTAAGTTGTAAATATTTTATCGTTTACATTAATATTATACCT
* * * *
7142 TTAAACAAA-CTGATAGGTAATTTAATGTAATAGGTAGCG-CTATTTTATTTTTACCGATTACAT
131 TTAAACAAATCAG-TAGGTAGTTTAATGTAATA-GTAGCGTCTATTTTA-TTTTAACGGTTACAT
* * * * *
7205 TATTATTATACCTTTAAACAAACTGATATGTAATTTAACGTAATAGGTAGTACTTATTT
193 TATTATTATACCTTTAAACAAACTGGTAGGTAGTTTAACGTAATAGGTAGTGCCTATTT
* * * * * *
7264 TATTTTACCATTTACATTATTATTGTATC-TTTAAACAAATCGGTAGGTAGTTTAATGTAATAGG
1 TATTTTACCGTTTACATTATTATTATA-CATTTAAACAAACCAGTAAGTAGTTTAACGTAATAGG
* * * *
7328 TAGCGCTTATTTTATTTTAACTGGTTAAGTTGTAAATATTTTATTGTTTATATTAATATTATACC
65 TAGCACCTATTTTATTTTAACTGGTTAAGTTGTAAATATTTTATCGTTTACATTAATATTATACC
*
7393 TTTAAACAAATCAGTAGGTAGTTTAACGTAATAGATAGCGTCTATTTTATTTTAACGTGTTACAT
130 TTTAAACAAATCAGTAGGTAGTTTAATGTAATAG-TAGCGTCTATTTTATTTTAACG-GTTACAT
*
7458 TATTATTATACCTTTAAACAAA-TCGGTAGGTAGTTTAACGTAATAGGTAGCGCCTATTT
193 TATTATTATACCTTTAAACAAACT-GGTAGGTAGTTTAACGTAATAGGTAGTGCCTATTT
* * * * *
7517 TATTTTACCGTTTTCGTTATTATTATACATTTAAACAAACCAGTAGGTAGTTTAACGTAGTATGT
1 TATTTTACCGTTTACATTATTATTATACATTTAAACAAACCAGTAAGTAGTTTAACGTAATAGGT
* * * *
7582 AGCGCCTATTTTATTTTAACTTGTTAAGTTGTAAATATTTTACCGTTTACATTAATATTATGCCT
66 AGCACCTATTTTATTTTAACTGGTTAAGTTGTAAATATTTTATCGTTTACATTAATATTATACCT
* * *
7647 TCAAACAAATCGGTAAGTAGTTTAATGTAATATGTAGC-TCATATTTTATTTTAATCGGTTACAT
131 TTAAACAAATCAGTAGGTAGTTTAATGTAATA-GTAGCGTC-TATTTTATTTTAA-CGGTTACA-
* * * ** * *
7711 TGCTATTATAATAACTTTAAACAAACTGGTAGATAGTTT-ACGTAATAAATATTGTCTATTT
192 T--TATTATTATACCTTTAAACAAACTGGTAGGTAGTTTAACGTAATAGGTAGTGCCTATTT
* * * *
7772 TATTTTACCGTATATATTATTATTATACCTTTAAACAAACCAGTAAGTAGTTTAACGTAATAAGT
1 TATTTTACCGTTTACATTATTATTATACATTTAAACAAACCAGTAAGTAGTTTAACGTAATAGGT
*
7837 AACACCTATTTTATTTTAAC
66 AGCACCTATTTTATTTTAAC
7857 CGATTACATT
Statistics
Matches: 515, Mismatches: 64, Indels: 25
0.85 0.11 0.04
Matches are distributed among these distances:
251 1 0.00
252 154 0.30
253 232 0.45
254 4 0.01
255 92 0.18
256 31 0.06
257 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.43
Consensus pattern (251 bp):
TATTTTACCGTTTACATTATTATTATACATTTAAACAAACCAGTAAGTAGTTTAACGTAATAGGT
AGCACCTATTTTATTTTAACTGGTTAAGTTGTAAATATTTTATCGTTTACATTAATATTATACCT
TTAAACAAATCAGTAGGTAGTTTAATGTAATAGTAGCGTCTATTTTATTTTAACGGTTACATTAT
TATTATACCTTTAAACAAACTGGTAGGTAGTTTAACGTAATAGGTAGTGCCTATTT
Found at i:7575 original size:76 final size:77
Alignment explanation
Indices: 7379--7607 Score: 343
Period size: 77 Copynumber: 3.0 Consensus size: 77
7369 TATTGTTTAT
* * *
7379 ATTAATATTATACCTTTAAACAAATCAGTAGGTAGTTTAACGTAATAGATAGCGTCTATTTTATT
1 ATTATTATTATACCTTTAAACAAATCAGTAGGTAGTTTAACGTAATAGGTAGCGCCTATTTTATT
7444 TTAACGTGTTAC
66 TTAACGTGTTAC
*
7456 ATTATTATTATACCTTTAAACAAATCGGTAGGTAGTTTAACGTAATAGGTAGCGCCTATTTTATT
1 ATTATTATTATACCTTTAAACAAATCAGTAGGTAGTTTAACGTAATAGGTAGCGCCTATTTTATT
* *
7521 TTACCGT-TTTC
66 TTAACGTGTTAC
* * * * *
7532 GTTATTATTATACATTTAAACAAACCAGTAGGTAGTTTAACGTAGTATGTAGCGCCTATTTTATT
1 ATTATTATTATACCTTTAAACAAATCAGTAGGTAGTTTAACGTAATAGGTAGCGCCTATTTTATT
*
7597 TTAACTTGTTA
66 TTAACGTGTTA
7608 AGTTGTAAAT
Statistics
Matches: 136, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
76 67 0.49
77 69 0.51
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (77 bp):
ATTATTATTATACCTTTAAACAAATCAGTAGGTAGTTTAACGTAATAGGTAGCGCCTATTTTATT
TTAACGTGTTAC
Found at i:7642 original size:100 final size:100
Alignment explanation
Indices: 7517--7700 Score: 251
Period size: 100 Copynumber: 1.8 Consensus size: 100
7507 GCGCCTATTT
* * * * * *
7517 TATTTTACCGTTTTCGTTATTATTATACATTTAAACAAACCAGTAGGTAGTTTAACGTAGTATGT
1 TATTTTACCGTTTACATTAATATTATACATTCAAACAAACCAGTAAGTAGTTTAACGTAATATGT
*
7582 AGCGCCTATTTTATTTTAACTTGTTAAGTTGTAAA
66 AGCGCATATTTTATTTTAACTTGTTAAGTTGTAAA
* * * * *
7617 TATTTTACCGTTTACATTAATATTATGCCTTCAAACAAATCGGTAAGTAGTTTAATGTAATATGT
1 TATTTTACCGTTTACATTAATATTATACATTCAAACAAACCAGTAAGTAGTTTAACGTAATATGT
*
7682 AGCTCATATTTTATTTTAA
66 AGCGCATATTTTATTTTAA
7701 TCGGTTACAT
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
100 71 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (100 bp):
TATTTTACCGTTTACATTAATATTATACATTCAAACAAACCAGTAAGTAGTTTAACGTAATATGT
AGCGCATATTTTATTTTAACTTGTTAAGTTGTAAA
Found at i:7819 original size:155 final size:154
Alignment explanation
Indices: 7617--8061 Score: 501
Period size: 155 Copynumber: 2.9 Consensus size: 154
7607 AAGTTGTAAA
* * * *
7617 TATTTTACCGTTTACATTAATATTATGCCTTCAAACAAATCGGTAAGTAGTTTAATGTAATATGT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAAGTAGTTTAATGTAATA-GT
* * * *
7682 AGCTCATATTTTATTTTAATCGGTTACATTGCTATTATAATAACTTTAAACAAACTGGTAGATAG
65 AACACATATTTTATTTTAATCGATTACA-T--TATTATTATAACTTTAAACAAACTGGTAGATAG
*
7747 TTT-ACGTAATAAATATTG-TC-TATTT
127 TTTAACGTAATAAATATTGCGCATATTT
* * * *
7772 TATTTTACCGTATATATTATTATTATACCTTTAAACAAACCAGTAAGTAGTTTAACGTAATAAGT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAAGTAGTTTAATGTAAT-AGT
* * * * *
7837 AACACCTATTTTATTTTAACCGATTACATTATTATTATACCTTTAAACAAACTTGTAGCTAGTTT
65 AACACATATTTTATTTTAATCGATTACATTATTATTATAACTTTAAACAAACTGGTAGATAGTTT
*
7902 AACGTAAT--ATGTTGCGCATATTT
130 AACGTAATAAATATTGCGCATATTT
* * * *
7925 TATTTTACCGTTTACATTATTATTATACCATTAACCAAACCGGTAGGTTGTTTAATGTAATAGAT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAAGTAGTTTAATGTAATAG-T
* * * * * * *
7990 ATCGCATA-TTT-TTTTACT-GTTTATATTATTATTATATCTTTAAACAAACTGGTAGTTAGTTT
65 AACACATATTTTATTTTAATCGATTACATTATTATTATAACTTTAAACAAACTGGTAGATAGTTT
*
8052 AACATAATAA
130 AACGTAATAA
8062 GTTGCATTTA
Statistics
Matches: 245, Mismatches: 38, Indels: 17
0.82 0.13 0.06
Matches are distributed among these distances:
150 46 0.19
151 10 0.04
152 38 0.16
153 71 0.29
154 1 0.00
155 78 0.32
156 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (154 bp):
TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACCGGTAAGTAGTTTAATGTAATAGTA
ACACATATTTTATTTTAATCGATTACATTATTATTATAACTTTAAACAAACTGGTAGATAGTTTA
ACGTAATAAATATTGCGCATATTT
Found at i:7944 original size:76 final size:75
Alignment explanation
Indices: 7617--8081 Score: 406
Period size: 76 Copynumber: 6.1 Consensus size: 75
7607 AAGTTGTAAA
* * * *
7617 TATTTTACCGTTTACATTAATATTATGCCTTCAAACAAA-TCGGTAAGTAGTTTAATGTAATATG
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACT-GGT-AGTAGTTTAACGTAATATG
* *
7681 TAGCTCATATTT
64 TTGCACATATTT
* * * *
7693 TATTTTAATCGGTTACATTGCTATTATAATAACTTTAAACAAACTGGTAGATAGTTT-ACGTAAT
1 TATTTT-ACCGTTTACA-T--TATTATTATACCTTTAAACAAACTGGTAG-TAGTTTAACGTAAT
* *
7757 AAATATTG-TC-TATTT
61 --ATGTTGCACATATTT
* * ** *
7772 TATTTTACCGTATATATTATTATTATACCTTTAAACAAACCAGTAAGTAGTTTAACGTAATAAGT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACTGGT-AGTAGTTTAACGTAATATGT
** *
7837 AACACCTATTT
65 TGCACATATTT
* *
7848 TATTTTAACCGATTACATTATTATTATACCTTTAAACAAACTTGTAGCTAGTTTAACGTAATATG
1 TATTTT-ACCGTTTACATTATTATTATACCTTTAAACAAACTGGTAG-TAGTTTAACGTAATATG
*
7913 TTGCGCATATTT
64 TTGCACATATTT
* * * * *
7925 TATTTTACCGTTTACATTATTATTATACCATTAACCAAACCGGTAGGTTGTTTAATGTAATA-GA
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACTGGTA-GTAGTTTAACGTAATATG-
*
7989 TAT-CGCATA-TT
64 T-TGCACATATTT
* * * * *
8000 T-TTTTACTGTTTATATTATTATTATATCTTTAAACAAACTGGTAGTTAGTTTAACATAATAAGT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACTGGTAG-TAGTTTAACGTAATATGT
**
8064 TGCATTTATTT
65 TGCACATATTT
8075 TATTTTA
1 TATTTTA
8082 ACTGGTTAAG
Statistics
Matches: 315, Mismatches: 52, Indels: 44
0.77 0.13 0.11
Matches are distributed among these distances:
73 2 0.01
74 55 0.17
75 38 0.12
76 87 0.28
77 74 0.23
78 7 0.02
79 19 0.06
80 28 0.09
81 5 0.02
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (75 bp):
TATTTTACCGTTTACATTATTATTATACCTTTAAACAAACTGGTAGTAGTTTAACGTAATATGTT
GCACATATTT
Found at i:8153 original size:100 final size:101
Alignment explanation
Indices: 8016--8207 Score: 253
Period size: 100 Copynumber: 1.9 Consensus size: 101
8006 CTGTTTATAT
* ** * * *
8016 TATTATTATATCTTTAAACAAACTGGTAGTTAGTTTAACATAATA-AGTTGCATTTATTTTATTT
1 TATTATTATACCTTTAAACAAACCAGTAGATAATTTAACATAATAGA-TTGCATCTATTTTATTT
*
8080 TAACTGGTTAAGTTATAAATATT-TTACCGATTAAAA
65 TAACAGGTTAAGTTATAAATATTATTACCGATTAAAA
* * *
8116 TATTATTATACCTTTAAATAAACCAGTAGATAATTTAACGTAATAGATTGTATCTATTTTATTTT
1 TATTATTATACCTTTAAACAAACCAGTAGATAATTTAACATAATAGATTGCATCTATTTTATTTT
* *
8181 AACAGGTTAAGTTGTAATTATTATTAC
66 AACAGGTTAAGTTATAAATATTATTAC
8208 ATTATCTATA
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
100 73 0.94
101 5 0.06
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (101 bp):
TATTATTATACCTTTAAACAAACCAGTAGATAATTTAACATAATAGATTGCATCTATTTTATTTT
AACAGGTTAAGTTATAAATATTATTACCGATTAAAA
Found at i:17596 original size:12 final size:12
Alignment explanation
Indices: 17579--17609 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
17569 TTTGTTTACT
17579 AAATCTAAATCC
1 AAATCTAAATCC
17591 AAATCTAAATCC
1 AAATCTAAATCC
17603 AACATCT
1 AA-ATCT
17610 CTCTACTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (12 bp):
AAATCTAAATCC
Found at i:19621 original size:19 final size:18
Alignment explanation
Indices: 19597--19665 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 18
19587 AACTATTTGT
19597 AAAATTATTAAAATAAATA
1 AAAATTA-TAAAATAAATA
* *
19616 AAAATTAAGAAAATAAGTA
1 AAAATT-ATAAAATAAATA
19635 AAAATTA-AAAAT--ATA
1 AAAATTATAAAATAAATA
19650 AGAAATTATAAAATAA
1 A-AAATTATAAAATAA
19666 CAAATATTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
15 3 0.07
16 6 0.14
17 10 0.24
18 1 0.02
19 21 0.50
20 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (18 bp):
AAAATTATAAAATAAATA
Found at i:32364 original size:109 final size:107
Alignment explanation
Indices: 32164--32380 Score: 398
Period size: 109 Copynumber: 2.0 Consensus size: 107
32154 AAGTACTCTA
*
32164 ATGTTCATTCCATTAAGCAGATTCCACCAGCTTATTAACACTGTAAATCAATGGCAGACATGTCC
1 ATGTTCATTCCATTAAGCAGATTCCACCAGCTTATTAACACTGTAAATCAATGGCAGACATGCCC
32229 AAAAAAACACAACCAGAATGTAACAAAACATTCAGTAATACC
66 AAAAAAACACAACCAGAATGTAACAAAACATTCAGTAATACC
32271 ATGTTCATTCCATTAAGCAGATTCCACCAGCTTATTAACACTGTGTAAATCAATGGCAGACATGC
1 ATGTTCATTCCATTAAGCAGATTCCACCAGCTTATTAACAC--TGTAAATCAATGGCAGACATGC
*
32336 CCAAAAATACACAACCAGAATGTAACAAAACATTCAGTAATACC
64 CCAAAAAAACACAACCAGAATGTAACAAAACATTCAGTAATACC
32380 A
1 A
32381 AGTTTCTTCT
Statistics
Matches: 106, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
107 41 0.39
109 65 0.61
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (107 bp):
ATGTTCATTCCATTAAGCAGATTCCACCAGCTTATTAACACTGTAAATCAATGGCAGACATGCCC
AAAAAAACACAACCAGAATGTAACAAAACATTCAGTAATACC
Found at i:38262 original size:19 final size:20
Alignment explanation
Indices: 38215--38263 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
38205 AATCCGAGAT
38215 TAGAAAGATGTCAATAAAACA
1 TAGAAA-ATGTCAATAAAACA
*
38236 TGAGAAAAT-TCAATAAAACC
1 T-AGAAAATGTCAATAAAACA
38256 TAGAAAAT
1 TAGAAAAT
38264 ATGGACCTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 7 0.27
20 11 0.42
21 3 0.12
22 5 0.19
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.20
Consensus pattern (20 bp):
TAGAAAATGTCAATAAAACA
Found at i:49142 original size:15 final size:15
Alignment explanation
Indices: 49118--49147 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
49108 ATGGGTAGAT
*
49118 CTGAGGAGGTTGGGC
1 CTGAGCAGGTTGGGC
49133 CTGAGCAGGTTGGGC
1 CTGAGCAGGTTGGGC
49148 ATGTTTCTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.17, G:0.50, T:0.20
Consensus pattern (15 bp):
CTGAGCAGGTTGGGC
Found at i:49641 original size:15 final size:15
Alignment explanation
Indices: 49621--49650 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
49611 ACATTAGTAG
49621 CAGTTGTTCTCCAAT
1 CAGTTGTTCTCCAAT
49636 CAGTTGTTCTCCAAT
1 CAGTTGTTCTCCAAT
49651 GCAGAAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (15 bp):
CAGTTGTTCTCCAAT
Found at i:55974 original size:23 final size:23
Alignment explanation
Indices: 55946--55996 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
55936 CCAACTGGAC
55946 TACAACAGAGCCCAACTAAAACT
1 TACAACAGAGCCCAACTAAAACT
* * * *
55969 TACAACGGAGCCTAATTAATACT
1 TACAACAGAGCCCAACTAAAACT
55992 TACAA
1 TACAA
55997 TGGAGCCGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.25, G:0.10, T:0.20
Consensus pattern (23 bp):
TACAACAGAGCCCAACTAAAACT
Found at i:56930 original size:87 final size:87
Alignment explanation
Indices: 56836--57012 Score: 338
Period size: 87 Copynumber: 2.0 Consensus size: 87
56826 ATAAACGCTA
56836 AAAGTTAAATACCATAAAAATGTAAAAAAAAACATTTATAACTTGTA-TGACACTCTCATTTAAT
1 AAAGTTAAATACCATAAAAATGTAAAAAAAAACATTTATAACTTGTACT-ACACTCTCATTTAAT
56900 AAAGCAACAATATCATCCAAGTT
65 AAAGCAACAATATCATCCAAGTT
56923 AAAGTTAAATACCATAAAAATGTAAAAAAAAACATTTATAACTTGTACTACACTCTCATTTAATA
1 AAAGTTAAATACCATAAAAATGTAAAAAAAAACATTTATAACTTGTACTACACTCTCATTTAATA
56988 AAGCAACAATATCATCCAAGTT
66 AAGCAACAATATCATCCAAGTT
57010 AAA
1 AAA
57013 AGAAATAAGT
Statistics
Matches: 89, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
87 88 0.99
88 1 0.01
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.28
Consensus pattern (87 bp):
AAAGTTAAATACCATAAAAATGTAAAAAAAAACATTTATAACTTGTACTACACTCTCATTTAATA
AAGCAACAATATCATCCAAGTT
Found at i:67104 original size:30 final size:30
Alignment explanation
Indices: 67063--67153 Score: 130
Period size: 30 Copynumber: 3.0 Consensus size: 30
67053 ATATATCTCC
*
67063 TAAATTTTAGATAGAATATTAATTTGATCT
1 TAAATTTTAGATAAAATATTAATTTGATCT
*
67093 TGAAA-TTTAGATAAAATATTAATTTAATCCT
1 T-AAATTTTAGATAAAATATTAATTTGAT-CT
*
67124 TAAATTTTAGATAAAATATAAATTTGATCT
1 TAAATTTTAGATAAAATATTAATTTGATCT
67154 ATTAATACGG
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
30 27 0.50
31 27 0.50
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (30 bp):
TAAATTTTAGATAAAATATTAATTTGATCT
Found at i:67637 original size:21 final size:20
Alignment explanation
Indices: 67588--67638 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
67578 TTCATGTGTA
*
67588 ATTTTTTAT-TAAATTAAAT
1 ATTTATTATATAAATTAAAT
**
67607 ATAAATTTATATAAATTAAATT
1 ATTTA-TTATATAAATTAAA-T
67629 ATTTATTATA
1 ATTTATTATA
67639 ATTTGTATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
19 2 0.08
20 4 0.17
21 14 0.58
22 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTATTATATAAATTAAAT
Found at i:69484 original size:21 final size:21
Alignment explanation
Indices: 69460--69500 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
69450 CTTCCTGCAC
69460 TACTTATCTA-ATATCCTTTTA
1 TACTTATCTATATA-CCTTTTA
69481 TACTTATCTATATACCTTTT
1 TACTTATCTATATACCTTTT
69501 CCTTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.54
Consensus pattern (21 bp):
TACTTATCTATATACCTTTTA
Found at i:69988 original size:20 final size:20
Alignment explanation
Indices: 69952--69989 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
69942 ATCGAGTACC
*
69952 ACATATATGTTCCAAGAATT
1 ACATATATGTCCCAAGAATT
69972 ACATATAT-TCCCGAAGAA
1 ACATATATGTCCC-AAGAA
69990 CCACGTAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (20 bp):
ACATATATGTCCCAAGAATT
Done.