Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005220.1 Hibiscus syriacus cultivar Beakdansim tig00011820_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: 106090
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:7779 original size:20 final size:20
Alignment explanation
Indices: 7756--7809 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
7746 GCTAGGCCTA
*
7756 CTGTAAAGCTTCTAGACTTG
1 CTGTTAAGCTTCTAGACTTG
7776 CTGTTAAGCTTCTAGACTTG
1 CTGTTAAGCTTCTAGACTTG
*
7796 TTGTTAAGCTTCTA
1 CTGTTAAGCTTCTA
7810 CTTGCCGCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (20 bp):
CTGTTAAGCTTCTAGACTTG
Found at i:20331 original size:20 final size:21
Alignment explanation
Indices: 20308--20387 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 21
20298 TTGGTGCAGA
*
20308 GGGAATCGATACCCCCATGA-
1 GGGAACCGATACCCCCATGAG
* *
20328 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-ATG-AG
*
20351 GGGAACCGATTCCCCCCAT-AG
1 GGGAACCGA-TACCCCCATGAG
*
20372 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
20388 CTGGGGTTCT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 20 0.41
21 12 0.24
22 1 0.02
23 10 0.20
24 6 0.12
ACGTcount: A:0.25, C:0.34, G:0.25, T:0.16
Consensus pattern (21 bp):
GGGAACCGATACCCCCATGAG
Found at i:20375 original size:21 final size:21
Alignment explanation
Indices: 20319--20388 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
20309 GGAATCGATA
20319 CCCCCAT-GAGGGAACCGATTC
1 CCCCCATAG-GGGAACCGATTC
**
20340 CCCCTTTGAAGGGGAACCGATTC
1 CCCCCAT--AGGGGAACCGATTC
* *
20363 CCCCCATAGGGGAATCGATAC
1 CCCCCATAGGGGAACCGATTC
20384 CCCCC
1 CCCCC
20389 TGGGGTTCTG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
21 22 0.55
23 17 0.43
24 1 0.03
ACGTcount: A:0.23, C:0.39, G:0.23, T:0.16
Consensus pattern (21 bp):
CCCCCATAGGGGAACCGATTC
Found at i:23817 original size:33 final size:32
Alignment explanation
Indices: 23759--23843 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 32
23749 CTTTATTTTG
23759 TTTGGGTCGGGTCGGGTTTTTTAAGTGTGATA
1 TTTGGGTCGGGTCGGGTTTTTTAAGTGTGATA
*
23791 TTTGGGTCGGGTCAGGTTTTTTTAAGTGTGATA
1 TTTGGGTCGGGTC-GGGTTTTTTAAGTGTGATA
* *
23824 ATCGGGTCGGGTTCGGGTTT
1 TTTGGGTCGGG-TCGGGTTT
23844 AGGGTAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
32 13 0.28
33 32 0.68
34 2 0.04
ACGTcount: A:0.12, C:0.08, G:0.38, T:0.42
Consensus pattern (32 bp):
TTTGGGTCGGGTCGGGTTTTTTAAGTGTGATA
Found at i:24440 original size:16 final size:16
Alignment explanation
Indices: 24415--24477 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
24405 TATGGAATTG
* *
24415 GATTCTAATTCCTATA
1 GATTCCAATTCCTACA
24431 GATTCCAATTCCTACA
1 GATTCCAATTCCTACA
*
24447 TATTCCAATTCCTTCACA
1 GATTCCAATTCC-T-ACA
*
24465 GATTTCAATTCCT
1 GATTCCAATTCCT
24478 TCATAAACAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
16 25 0.62
17 2 0.05
18 13 0.32
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.40
Consensus pattern (16 bp):
GATTCCAATTCCTACA
Found at i:24475 original size:18 final size:18
Alignment explanation
Indices: 24430--24480 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
24420 TAATTCCTAT
24430 AGATTCCAATTCC-T-AC
1 AGATTCCAATTCCTTCAC
*
24446 ATATTCCAATTCCTTCAC
1 AGATTCCAATTCCTTCAC
*
24464 AGATTTCAATTCCTTCA
1 AGATTCCAATTCCTTCA
24481 TAAACATTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 12 0.40
17 1 0.03
18 17 0.57
ACGTcount: A:0.29, C:0.29, G:0.04, T:0.37
Consensus pattern (18 bp):
AGATTCCAATTCCTTCAC
Found at i:24971 original size:23 final size:23
Alignment explanation
Indices: 24945--24990 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
24935 TTTATTACTG
*
24945 TCTTTATGACACGTTTATCTCTA
1 TCTTTATGACACATTTATCTCTA
* * *
24968 TCTTTGTGATACATTTTTCTCTA
1 TCTTTATGACACATTTATCTCTA
24991 GTTTTTTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.52
Consensus pattern (23 bp):
TCTTTATGACACATTTATCTCTA
Found at i:27714 original size:34 final size:34
Alignment explanation
Indices: 27673--27841 Score: 146
Period size: 34 Copynumber: 5.0 Consensus size: 34
27663 ACCAATTCAC
*
27673 CTCGATAATAAAAGAATTATTGTTATTCATTTAT
1 CTCGATAATAAAAGAATTATTGTTATTCCTTTAT
* **** *
27707 CTTGATAATAATTCTATTATTGTTATTCTTTTAT
1 CTCGATAATAAAAGAATTATTGTTATTCCTTTAT
**
27741 CTCGATGGTAAAAGAATTATTGTTATTCCTTAATAT
1 CTCGATAATAAAAGAATTATTGTTATTCCTT--TAT
* * ** * *
27777 C-CTA-AATTAATTAA-AATTGTTATTCTTTTAT
1 CTCGATAATAAAAGAATTATTGTTATTCCTTTAT
**
27808 CTCGATGGTAAAAGAATTATTGTTATTCCTTTAT
1 CTCGATAATAAAAGAATTATTGTTATTCCTTTAT
27842 ATCCTAAATT
Statistics
Matches: 100, Mismatches: 30, Indels: 10
0.71 0.21 0.07
Matches are distributed among these distances:
31 4 0.04
32 2 0.02
33 17 0.17
34 71 0.71
35 2 0.02
36 4 0.04
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (34 bp):
CTCGATAATAAAAGAATTATTGTTATTCCTTTAT
Found at i:27814 original size:67 final size:67
Alignment explanation
Indices: 27725--27859 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
27715 TAATTCTATT
27725 ATTGTTATTCTTTTATCTCGATGGTAAAAGAATTATTGTTATTCCTTAATATCCTAAATTAATTA
1 ATTGTTATTCTTTTATCTCGATGGTAAAAGAATTATTGTTATTCCTTAATATCCTAAATTAATTA
27790 AA
66 AA
*
27792 ATTGTTATTCTTTTATCTCGATGGTAAAAGAATTATTGTTATTCCTTTATATCCTAAATTAATTA
1 ATTGTTATTCTTTTATCTCGATGGTAAAAGAATTATTGTTATTCCTTAATATCCTAAATTAATTA
27857 AA
66 AA
27859 A
1 A
27860 AAAATTGCAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (67 bp):
ATTGTTATTCTTTTATCTCGATGGTAAAAGAATTATTGTTATTCCTTAATATCCTAAATTAATTA
AA
Found at i:30497 original size:51 final size:51
Alignment explanation
Indices: 30434--30560 Score: 130
Period size: 51 Copynumber: 2.5 Consensus size: 51
30424 GTAGCAATAA
* ** * **
30434 AACGCGCTCCCTGCCCCGCGCTATATGCTGATTTGGTGT-CACGTGGGGTAT
1 AACGCGCCCCCTGAACCGCGCTATACGCTGACATGGTGTACACGT-GGGTAT
* * *
30485 AGCGCGCCCCCTGTACCGCGCTATACGCTGACATGGTTTACACGTGGGTAT
1 AACGCGCCCCCTGAACCGCGCTATACGCTGACATGGTGTACACGTGGGTAT
* * *
30536 AACGCGGCCTCTGATCCGCGCTATA
1 AACGCGCCCCCTGAACCGCGCTATA
30561 GGCCACGTAG
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
51 57 0.92
52 5 0.08
ACGTcount: A:0.17, C:0.31, G:0.28, T:0.24
Consensus pattern (51 bp):
AACGCGCCCCCTGAACCGCGCTATACGCTGACATGGTGTACACGTGGGTAT
Found at i:30871 original size:15 final size:16
Alignment explanation
Indices: 30848--30895 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
30838 TCGTTATAAA
*
30848 TTTTGTTATAATT-TT
1 TTTTATTATAATTATT
*
30863 TTTTATTATACTTATT
1 TTTTATTATAATTATT
* *
30879 GTTTATTATGATTATT
1 TTTTATTATAATTATT
30895 T
1 T
30896 GAAAAAATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTTATTATAATTATT
Found at i:36336 original size:18 final size:17
Alignment explanation
Indices: 36304--36349 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
36294 AAATTATATT
36304 AGTAAAATATTAAATAA
1 AGTAAAATATTAAATAA
36321 AGTAAAATACTTAAATAA
1 AGTAAAATA-TTAAATAA
*
36339 ATTAAATATAT
1 AGTAAA-ATAT
36350 AATATTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.35
18 14 0.54
19 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
AGTAAAATATTAAATAA
Found at i:36700 original size:29 final size:29
Alignment explanation
Indices: 36658--36736 Score: 131
Period size: 29 Copynumber: 2.7 Consensus size: 29
36648 TACTGCTACG
36658 GGTGTTAGATCGAGAAATATAATCTGACC
1 GGTGTTAGATCGAGAAATATAATCTGACC
36687 GGTGTTAGATCGAGAAATATAATCTGACC
1 GGTGTTAGATCGAGAAATATAATCTGACC
* * *
36716 GATGTTAAATCGATAAATATA
1 GGTGTTAGATCGAGAAATATA
36737 CCGGTCACCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (29 bp):
GGTGTTAGATCGAGAAATATAATCTGACC
Found at i:37878 original size:14 final size:14
Alignment explanation
Indices: 37861--37904 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
37851 GTTTGTGTTC
*
37861 ATTTACGTTCGTTT
1 ATTTATGTTCGTTT
37875 ATTTATGTTCGTTT
1 ATTTATGTTCGTTT
*
37889 ATTTATGTTCATTT
1 ATTTATGTTCGTTT
37903 AT
1 AT
37905 CATTTTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.18, C:0.09, G:0.11, T:0.61
Consensus pattern (14 bp):
ATTTATGTTCGTTT
Found at i:37883 original size:24 final size:24
Alignment explanation
Indices: 37838--37889 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
37828 ACTAATTAGT
* * *
37838 TTTATGTTCGTTCGTTTGTGTTCA
1 TTTACGTTCGTTCATTTATGTTCA
* *
37862 TTTACGTTCGTTTATTTATGTTCG
1 TTTACGTTCGTTCATTTATGTTCA
37886 TTTA
1 TTTA
37890 TTTATGTTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.17, T:0.60
Consensus pattern (24 bp):
TTTACGTTCGTTCATTTATGTTCA
Found at i:38337 original size:28 final size:25
Alignment explanation
Indices: 38227--38350 Score: 78
Period size: 26 Copynumber: 4.7 Consensus size: 25
38217 TTTTATTTTT
*
38227 AATATA-TATTATAAATATTCTTATAA
1 AATATATTATT-TTAATATT-TTATAA
38253 AA-ATAATATATTTTAAT-TTATGT-TAA
1 AATAT-AT-TATTTTAATATT-T-TATAA
38279 AATATATT-TTTATAATATTTTATAA
1 AATATATTATTT-TAATATTTTATAA
**
38304 TTTATATTATTTTGACATATTTTTATAA
1 AATATATTATTTT-A-ATA-TTTTATAA
38332 AATATAATTAATTTTAATA
1 AATAT-ATT-ATTTTAATA
38351 ATAAATTAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 26
0.71 0.05 0.24
Matches are distributed among these distances:
24 4 0.05
25 18 0.23
26 19 0.24
27 10 0.13
28 18 0.23
29 4 0.05
30 5 0.06
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
AATATATTATTTTAATATTTTATAA
Found at i:43215 original size:18 final size:18
Alignment explanation
Indices: 43194--43230 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
43184 TTTTAAGATT
43194 TATT-TTTCTATTAAATTA
1 TATTGTTTC-ATTAAATTA
43212 TATTGTTTCATTAAATTA
1 TATTGTTTCATTAAATTA
43230 T
1 T
43231 TATATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (18 bp):
TATTGTTTCATTAAATTA
Found at i:53758 original size:59 final size:59
Alignment explanation
Indices: 53692--53809 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
53682 TTCGGAATGT
*
53692 GGTGGTGTTCCTCGATATTAAAGTGCATTTCATCGGCCTCCATTTCTATTTTAGTCTAC
1 GGTGGTGTTCCTCGATATTAAAGTACATTTCATCGGCCTCCATTTCTATTTTAGTCTAC
53751 GGTGGTGTTCCTCGATATTAAAGTACATTTCATCGGCCTCCATTTCTATTTTAGTCTAC
1 GGTGGTGTTCCTCGATATTAAAGTACATTTCATCGGCCTCCATTTCTATTTTAGTCTAC
53810 AGGTCACCAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (59 bp):
GGTGGTGTTCCTCGATATTAAAGTACATTTCATCGGCCTCCATTTCTATTTTAGTCTAC
Found at i:54196 original size:20 final size:20
Alignment explanation
Indices: 54171--54261 Score: 65
Period size: 20 Copynumber: 5.0 Consensus size: 20
54161 TAAATTAAAT
54171 ATTAGATA-AGATCAGTTTTA
1 ATTAGATAGA-ATCAGTTTTA
*
54191 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
54211 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
54223 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
54243 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
54262 TTATTCTATT
Statistics
Matches: 54, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 37 0.69
21 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:54289 original size:53 final size:52
Alignment explanation
Indices: 54170--54319 Score: 257
Period size: 53 Copynumber: 2.9 Consensus size: 52
54160 CTAAATTAAA
*
54170 TATTAGATAAGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAAGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
*
54222 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAAGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
*
54275 TATTAGATATGATCATTTTTAATTAGATAGAATCA-TTTTTATTCT
1 TATTAGATAAGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
54320 GTTGCTAATT
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 10 0.11
52 34 0.36
53 50 0.53
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (52 bp):
TATTAGATAAGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:54301 original size:20 final size:20
Alignment explanation
Indices: 54276--54315 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
54266 TCTATTAGTT
54276 ATTAGATATG-ATCATTTTTA
1 ATTAGATA-GAATCATTTTTA
54296 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
54316 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:66277 original size:23 final size:23
Alignment explanation
Indices: 66247--66301 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
66237 ATGGACTTTA
66247 CGTTGAACGGTTCACGAATGATT
1 CGTTGAACGGTTCACGAATGATT
66270 CGTTGAACGGTTCACGAATGATT
1 CGTTGAACGGTTCACGAATGATT
66293 CGTTGAACG
1 CGTTGAACG
66302 TTTGATTCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (23 bp):
CGTTGAACGGTTCACGAATGATT
Found at i:72877 original size:3 final size:3
Alignment explanation
Indices: 72871--72947 Score: 73
Period size: 3 Copynumber: 25.7 Consensus size: 3
72861 ATGAGTTGGG
* * * * *
72871 GGT GGT GGT GGT GGT GAT AGT GAT GGT GGT GGT GGT GGT GGT GGA GTT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
* * * *
72919 GGT TGT GGT GGC GGT GGC GGT GGC GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
72948 AGGAGTTGAG
Statistics
Matches: 56, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.05, C:0.04, G:0.61, T:0.30
Consensus pattern (3 bp):
GGT
Found at i:75173 original size:23 final size:22
Alignment explanation
Indices: 75125--75180 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
75115 AAAAAATAGT
**
75125 AAAGAAAAA-AAATGAATACGA
1 AAAGAAAAATAAATGAATAAAA
*
75146 TAAGAAAAATAAATTGAATAAAA
1 AAAGAAAAATAAA-TGAATAAAA
*
75169 AAAGAATAATAA
1 AAAGAAAAATAA
75181 TATATACATA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 8 0.29
22 3 0.11
23 17 0.61
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.16
Consensus pattern (22 bp):
AAAGAAAAATAAATGAATAAAA
Found at i:76097 original size:37 final size:37
Alignment explanation
Indices: 76047--76117 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
76037 TTATGGATCA
76047 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCT
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCT
* *
76084 TATTTTTAGGAGTTTGAGTCCTAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
76118 ACGTTATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.42
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCT
Found at i:76748 original size:84 final size:84
Alignment explanation
Indices: 76660--76913 Score: 297
Period size: 84 Copynumber: 3.1 Consensus size: 84
76650 AAATTTGGTT
76660 TGCCTCT-GAGCTGAGTGTAATCGAACTCGAAGGTCTTCGGTTGGCAGATAGCCCTTCTCGACTT
1 TGCCTCTCGAGCTGAGTGTAATCGAACTCGAAGGTCTT-GGTTGGCAGATAGCCCTTCTCGACTT
76724 AAGCTATACTGCAAATGATG
65 AAGCTATACTGCAAATGATG
* * * * * * *
76744 TGCCT-TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCT
1 TGCCTCTCGAGCTGAGTGTAATCGAACTCGAAGGTC--TTGGTTGGCAGATAGCCCTTCTCGACT
* * *
76807 TGAGCTATGCTGTAAATGATG
64 TAAGCTATACTGCAAATGATG
* *
76828 TGCC-CTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-T--TTGGCAGATAGCCATTCTCGACTT
1 TGCCTCTCG-AGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGGCAGATAGCCCTTCTCGACTT
*
76889 AAGCTATACTACAAATGATG
65 AAGCTATACTGCAAATGATG
*
76909 CGCCT
1 TGCCT
76914 TGGATTTGTT
Statistics
Matches: 140, Mismatches: 23, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
81 37 0.26
82 1 0.01
83 1 0.01
84 73 0.52
85 26 0.19
86 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.28
Consensus pattern (84 bp):
TGCCTCTCGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGGCAGATAGCCCTTCTCGACTTA
AGCTATACTGCAAATGATG
Found at i:80825 original size:29 final size:30
Alignment explanation
Indices: 80791--80856 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
80781 AATAAACTAG
80791 TAAATAAAA-AAAT-AACAAGAAAATAAAAA
1 TAAATAAAACAAATGAA-AAGAAAATAAAAA
* *
80820 TAAATAAAACAAATGTAAAGAAGATAAAAA
1 TAAATAAAACAAATGAAAAGAAAATAAAAA
80850 -AAATAAA
1 TAAATAAA
80857 GATAAGGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 16 0.48
30 16 0.48
31 1 0.03
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (30 bp):
TAAATAAAACAAATGAAAAGAAAATAAAAA
Found at i:80928 original size:3 final size:3
Alignment explanation
Indices: 80920--80945 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
80910 AATAAAATAG
80920 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
80946 AAGTAGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:81685 original size:37 final size:37
Alignment explanation
Indices: 81634--81742 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
81624 CTTATGGATT
*
81634 ATATTTTTAGGAGTTTGAATCTTAGTAAAACTCTATC
1 ATATTTTTAGGAGTTTGAATCATAGTAAAACTCTATC
*
81671 CTATTTTTAGGAGTTTGAATCATAGTAAAACTCTATC
1 ATATTTTTAGGAGTTTGAATCATAGTAAAACTCTATC
*
81708 ATATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
1 ATATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
81743 ACGTTATGTT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (37 bp):
ATATTTTTAGGAGTTTGAATCATAGTAAAACTCTATC
Found at i:85129 original size:113 final size:113
Alignment explanation
Indices: 84968--85193 Score: 425
Period size: 113 Copynumber: 2.0 Consensus size: 113
84958 AGTCATGGAG
*
84968 GGCCTATCCGGAAAGTGTCTTTATTAAGGACATTCCATCGTATATATTAGTGTCGTATCTAGTTG
1 GGCCTATCCGGAAAGTGTCTTTATTAAGGACATTCCATCATATATATTAGTGTCGTATCTAGTTG
85033 AGTTTTTTTATTACGAGGAGTGACTCTGTATTAGATTTTTACCATCCC
66 AGTTTTTTTATTACGAGGAGTGACTCTGTATTAGATTTTTACCATCCC
*
85081 GGCCTATCTGGAAAGTGTCTTTATTAAGGACATTCCATCATATATATTAGTGTCGTATCTAGTTG
1 GGCCTATCCGGAAAGTGTCTTTATTAAGGACATTCCATCATATATATTAGTGTCGTATCTAGTTG
*
85146 AGTTTTTTTTTTACGAGGAGTGACTCTGTATTAGATTTTTACCATCCC
66 AGTTTTTTTATTACGAGGAGTGACTCTGTATTAGATTTTTACCATCCC
85194 ATCACTTTGA
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 110 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (113 bp):
GGCCTATCCGGAAAGTGTCTTTATTAAGGACATTCCATCATATATATTAGTGTCGTATCTAGTTG
AGTTTTTTTATTACGAGGAGTGACTCTGTATTAGATTTTTACCATCCC
Found at i:86379 original size:15 final size:16
Alignment explanation
Indices: 86359--86388 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
86349 ATGGCCGGTT
86359 TTCTCATT-TCTCTCA
1 TTCTCATTCTCTCTCA
86374 TTCTCATTCTCTCTC
1 TTCTCATTCTCTCTC
86389 GCTTCCCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.37, G:0.00, T:0.53
Consensus pattern (16 bp):
TTCTCATTCTCTCTCA
Found at i:87224 original size:18 final size:19
Alignment explanation
Indices: 87203--87253 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 19
87193 ATTAATAATA
87203 ATAAGAATAAGAATAT-TT
1 ATAAGAATAAGAATATATT
* *
87221 ATAATAATAATAAT-TATT
1 ATAAGAATAAGAATATATT
87239 ATAAGAATAAGAATA
1 ATAAGAATAAGAATA
87254 AAAAATCGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (19 bp):
ATAAGAATAAGAATATATT
Found at i:87226 original size:15 final size:15
Alignment explanation
Indices: 87208--87248 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
87198 TAATAATAAG
*
87208 AATAAGAATATTTAT
1 AATAAGAATAATTAT
*
87223 AATAATAATAATTAT
1 AATAAGAATAATTAT
*
87238 TATAAGAATAA
1 AATAAGAATAA
87249 GAATAAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (15 bp):
AATAAGAATAATTAT
Found at i:87789 original size:12 final size:12
Alignment explanation
Indices: 87772--87807 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
87762 CTATGAAAAG
87772 ATGCAAATGTAA
1 ATGCAAATGTAA
87784 ATGCAAATGT-A
1 ATGCAAATGTAA
87795 ATG-AAATG-AA
1 ATGCAAATGTAA
87805 ATG
1 ATG
87808 TAAAAATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 9 0.39
11 4 0.17
12 10 0.43
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (12 bp):
ATGCAAATGTAA
Found at i:87998 original size:43 final size:43
Alignment explanation
Indices: 87913--87998 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
87903 CGGTACATCA
* * *
87913 AACAAAACTTTACATATAGGGGATAACTTTCCCTCCTGACTTC
1 AACAAAACTTTACATATAGGGGATAACTTTCACTCATAACTTC
*
87956 AACAAAACTTTACATATATGGGATAACTTTCACTCATAACTTC
1 AACAAAACTTTACATATAGGGGATAACTTTCACTCATAACTTC
87999 TCTAAAGCCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.31
Consensus pattern (43 bp):
AACAAAACTTTACATATAGGGGATAACTTTCACTCATAACTTC
Found at i:90315 original size:2 final size:2
Alignment explanation
Indices: 90308--90345 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
90298 TTAATCTTTC
* *
90308 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90346 TAATATGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:90558 original size:3 final size:3
Alignment explanation
Indices: 90550--90586 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
90540 ATAAAATTTT
90550 ATA ATA ATA A-A ATA ATA ATA A-A ATA ATA ATTA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA AT
90587 TTGAACATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 24 0.77
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:90565 original size:8 final size:9
Alignment explanation
Indices: 90550--90586 Score: 51
Period size: 8 Copynumber: 4.2 Consensus size: 9
90540 ATAAAATTTT
90550 ATAATAATA
1 ATAATAATA
90559 A-AATAATA
1 ATAATAATA
90567 ATAA-AATA
1 ATAATAATA
90575 ATAATTAATA
1 ATAA-TAATA
90585 AT
1 AT
90587 TTGAACATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 16 0.64
9 3 0.12
10 6 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
ATAATAATA
Found at i:90566 original size:11 final size:11
Alignment explanation
Indices: 90550--90579 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
90540 ATAAAATTTT
90550 ATAATAATAAA
1 ATAATAATAAA
90561 ATAATAATAAA
1 ATAATAATAAA
90572 ATAATAAT
1 ATAATAAT
90580 TAATAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
ATAATAATAAA
Found at i:95515 original size:2 final size:2
Alignment explanation
Indices: 95508--95534 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
95498 TGCTGGTGAA
95508 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 A
95535 CACACACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:96348 original size:144 final size:143
Alignment explanation
Indices: 96087--96512 Score: 512
Period size: 144 Copynumber: 2.9 Consensus size: 143
96077 TGAATACTCG
* * * * * * * * * *
96087 TTATTTTTAAGAAAATAATATTTAAATTTTGGACCCTCATTCTTAAATTTGTTAGGAAGAGATTG
1 TTATTTTAAAGAAAAGAATATTAAAATTTTGGA-TCTCGTTCTTAAATCTGCTAGAAAGGGATTA
* * *
96152 GGATTGGCTTCTCTTGTTTGCTTTGTTCCTGGATTTTGGTTCTCTCGGTGATTTTTTTGGGGATC
65 GGATTGGATTCTCTTGTTTGCTTTGTTCCTGGATTTTGGTTCCCTTGGTGATTTTTTT-GGGATC
*
96217 TTTTCTGTATACCTA
129 TTTTCTGTATACCCA
* * *
96232 TTATTTTAAAGAGAAGAATATTAAAATTTTGTAT-TCCGTTCTTAAATCTGCTAGAAATGGATTA
1 TTATTTTAAAGAAAAGAATATTAAAATTTTGGATCT-CGTTCTTAAATCTGCTAGAAAGGGATTA
* *
96296 GGATTGGATTCTCTTGTTTGCTTTGCTCCTGGATTTTGGTTCCCTTGATGATTTGTTTTGGGATC
65 GGATTGGATTCTCTTGTTTGCTTTGTTCCTGGATTTTGGTTCCCTTGGTGATTT-TTTTGGGATC
*
96361 TTTTATGTATACCCA
129 TTTTCTGTATACCCA
* * *
96376 TTATTTTTAAGAAAAGAATATTAAAATTTTGGATCTCGTTCTTAAATCTGCTGGGAAGGGATTAG
1 TTATTTTAAAGAAAAGAATATTAAAATTTTGGATCTCGTTCTTAAATCTGCTAGAAAGGGATTAG
* * * * * * *
96441 GATCGAATTCTCTTGTTTCCTTTGTTCCTGGGTTTAGGGTTCCCTTCGGTGACCTGTTTTGGGAT
66 GATTGGATTCTCTTGTTTGCTTTGTTCCTGGATTT-TGGTTCCCTT-GGTGA-TTTTTTTGGGAT
96506 CTTTTCT
128 CTTTTCT
96513 TATTTATCTG
Statistics
Matches: 239, Mismatches: 36, Indels: 11
0.84 0.13 0.04
Matches are distributed among these distances:
143 1 0.00
144 176 0.74
145 42 0.18
146 19 0.08
147 1 0.00
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.45
Consensus pattern (143 bp):
TTATTTTAAAGAAAAGAATATTAAAATTTTGGATCTCGTTCTTAAATCTGCTAGAAAGGGATTAG
GATTGGATTCTCTTGTTTGCTTTGTTCCTGGATTTTGGTTCCCTTGGTGATTTTTTTGGGATCTT
TTCTGTATACCCA
Found at i:97333 original size:75 final size:74
Alignment explanation
Indices: 97204--97353 Score: 171
Period size: 75 Copynumber: 2.0 Consensus size: 74
97194 AGGTGGGCAC
* * *
97204 GTGCCTATCCTGAAATCTAATTTTTCTTTGTTTAATCACTTATTTTATTAATGGTGTCCATCATG
1 GTGCCTACCCTGAAATCTAATTTTTCTTTATTTAATCAC-TATTTTATTAATGGTGTCCACCATG
97269 AAATTTTATT
65 AAATTTTATT
* * *
97279 GTGCCTACCCTGAAATCTGAA-TTTTCTTCTATTAATAATC-C-ATTTTGTTGATGGTTTCCACC
1 GTGCCTACCCTGAAATCT-AATTTTTCTT-TATT--TAATCACTATTTTATTAATGGTGTCCACC
*
97341 GTGAAATTTTATT
62 ATGAAATTTTATT
97354 TATGCTTACC
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
75 53 0.83
76 5 0.08
77 1 0.02
78 5 0.08
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.47
Consensus pattern (74 bp):
GTGCCTACCCTGAAATCTAATTTTTCTTTATTTAATCACTATTTTATTAATGGTGTCCACCATGA
AATTTTATT
Found at i:103913 original size:21 final size:21
Alignment explanation
Indices: 103884--103936 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
103874 ATTCTGACTA
*
103884 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGACTTTCCAAAT
* *
103905 TCGCGTTGCGACTTTCCTAAT
1 TCGCATTGCGACTTTCCAAAT
*
103926 TCGCAATGCGA
1 TCGCATTGCGA
103937 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGACTTTCCAAAT
Found at i:103951 original size:20 final size:20
Alignment explanation
Indices: 103926--103978 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
103916 CTTTCCTAAT
103926 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
103946 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
103966 TCGCAACGCGAAT
1 TCGCAATGCGAAT
103979 CTGACTATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:104207 original size:22 final size:22
Alignment explanation
Indices: 104181--104241 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
104171 CATCCGTTCT
104181 CATCTCCGACGAAATCAGTCCC
1 CATCTCCGACGAAATCAGTCCC
* *
104203 CATCTCCGACGATATCAGTCTC
1 CATCTCCGACGAAATCAGTCCC
*
104225 CATCTCCGGCGAAATCA
1 CATCTCCGACGAAATCA
104242 TTCACGGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.21
Consensus pattern (22 bp):
CATCTCCGACGAAATCAGTCCC
Found at i:104618 original size:20 final size:20
Alignment explanation
Indices: 104593--104630 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
104583 CGATTTTCAT
104593 TTCACGTTGCGATAGTCAAA
1 TTCACGTTGCGATAGTCAAA
104613 TTCACGTTGCGATAGTCA
1 TTCACGTTGCGATAGTCA
104631 TTTTCGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (20 bp):
TTCACGTTGCGATAGTCAAA
Found at i:104641 original size:20 final size:20
Alignment explanation
Indices: 104598--104665 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
104588 TTCATTTCAC
** **
104598 GTTGCGATAGTCAAATTCAC
1 GTTGCGATAGTCATTTTCGT
104618 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
104638 GTTGCGATTTTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
*
104658 GCTGCGAT
1 GTTGCGAT
104666 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.41
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:104675 original size:20 final size:20
Alignment explanation
Indices: 104632--104675 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
104622 CGATAGTCAT
* * *
104632 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGCTGCGATTTTAAG
104652 TTTCGTGCTGCGATTTTAAG
1 TTTCGTGCTGCGATTTTAAG
104672 TTTC
1 TTTC
104676 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.16, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGCTGCGATTTTAAG
Done.