Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005246.1 Hibiscus syriacus cultivar Beakdansim tig00011869_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: 71552
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:6291 original size:16 final size:16
Alignment explanation
Indices: 6261--6303 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
6251 TAAATTATTT
*
6261 ATTAACATTATTTTAAA
1 ATTAA-ATTAATTTAAA
6278 ATTAAATTAATTTAAA
1 ATTAAATTAATTTAAA
*
6294 TTTAAATTAA
1 ATTAAATTAA
6304 ATTTTTCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 19 0.79
17 5 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTAAATTAATTTAAA
Found at i:14662 original size:47 final size:46
Alignment explanation
Indices: 14603--14700 Score: 133
Period size: 47 Copynumber: 2.1 Consensus size: 46
14593 AATATTTGTA
* * *
14603 TTAATATAAGAATATATTAATATAGTTTTCAATTTAGTATATGGTT
1 TTAATATAAGAATATATTAATATACTTTTCAATGTAGTATATGGCT
* * *
14649 TTAAGTATTAGAATATATTAGTATACTTTTCAATGTAGTGTATGGCT
1 TTAA-TATAAGAATATATTAATATACTTTTCAATGTAGTATATGGCT
14696 TTAAT
1 TTAAT
14701 TTTCAGATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 5 0.11
47 40 0.89
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (46 bp):
TTAATATAAGAATATATTAATATACTTTTCAATGTAGTATATGGCT
Found at i:16848 original size:2 final size:2
Alignment explanation
Indices: 16841--16872 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16831 TTGCATATTA
16841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16873 GTAGGTTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19263 original size:6 final size:6
Alignment explanation
Indices: 19249--19284 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
19239 TAAAACCTTG
* *
19249 TGCATT TGCACT TGCACT TGCATT TGCATT TGCATT
1 TGCATT TGCATT TGCATT TGCATT TGCATT TGCATT
19285 CTTTTTGCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (6 bp):
TGCATT
Found at i:25197 original size:13 final size:13
Alignment explanation
Indices: 25179--25203 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25169 TGAAGCAAAT
25179 CCATCAGTAAGTG
1 CCATCAGTAAGTG
25192 CCATCAGTAAGT
1 CCATCAGTAAGT
25204 CTTTCGAGCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:25332 original size:13 final size:13
Alignment explanation
Indices: 25314--25338 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25304 TTAAGCAAAT
25314 CCATCAGTAAGTG
1 CCATCAGTAAGTG
25327 CCATCAGTAAGT
1 CCATCAGTAAGT
25339 CTTTCGAGCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:25390 original size:135 final size:134
Alignment explanation
Indices: 25144--25490 Score: 536
Period size: 135 Copynumber: 2.6 Consensus size: 134
25134 AAGTGAATCC
* *
25144 ATTT-TAAGCTTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGTGCCATCAGTAAGTCTTT
1 ATTTGTAAGCTTTCACCAAAGAGTA-TTAAGCAAATCCATCAGTAAGTGCCATCAGTAAGTCTTT
* *
25208 CGAGCGTGATGATGAAGTACGTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTC
65 CGAGCGTGATGATGAAGTACGTCAGGCCAGCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC
25273 GGGTA
130 GGGTA
25278 ATTTGTAAGCTTTCACCAAAGAGTACTTAAGCAAATCCATCAGTAAGTGCCATCAGTAAGTCTTT
1 ATTTGTAAGCTTTCACCAAAGAGTA-TTAAGCAAATCCATCAGTAAGTGCCATCAGTAAGTCTTT
* *
25343 CGAGCGTGATGATGAAGT-CTTTCGGGCCAGCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
65 CGAGCGTGATGATGAAGTAC-GTCAGGCCAGCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
25407 CGGGTA
129 CGGGTA
* * * * *
25413 ATTTGTAAGCCTTCACCAAGGAGTAGTAGAGAAAATCCATCAGTAAGTGCCATCATTAAGTCTTT
1 ATTTGTAAGCTTTCACCAAAGAGTATTA-AGCAAATCCATCAGTAAGTGCCATCAGTAAGTCTTT
*
25478 CGAGCGCGATGAT
65 CGAGCGTGATGAT
25491 TAAATCCTTA
Statistics
Matches: 197, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
134 7 0.04
135 190 0.96
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (134 bp):
ATTTGTAAGCTTTCACCAAAGAGTATTAAGCAAATCCATCAGTAAGTGCCATCAGTAAGTCTTTC
GAGCGTGATGATGAAGTACGTCAGGCCAGCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCG
GGTA
Found at i:25409 original size:42 final size:42
Alignment explanation
Indices: 25326--25410 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
25316 ATCAGTAAGT
* * * *
25326 GCCATCAGTAAGTCTTTCGAGCGTGATGATGAAGTCTTTCGG
1 GCCAGCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
*
25368 GCCAGCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGG
1 GCCAGCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
25410 G
1 G
25411 TAATTTGTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (42 bp):
GCCAGCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGG
Found at i:25542 original size:93 final size:93
Alignment explanation
Indices: 25368--25730 Score: 340
Period size: 93 Copynumber: 4.0 Consensus size: 93
25358 AGTCTTTCGG
* * * *
25368 GCCAGCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCAAG
1 GCCATCAGTAAGTCTTTCGAGCGTGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACCAAA
25433 GAGTAGTAGAGAAAATCCATCAGTAAGT
66 GAGTAGTAGAGAAAATCCATCAGTAAGT
* * *
25461 GCCATCATTAAGTCTTTCGAGCGCGATGATTAAATCCTTAGGGTAATTTGTAATCCTTCACCAAA
1 GCCATCAGTAAGTCTTTCGAGCGTGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACCAAA
* *
25526 GAGTAGT-GAAGCAAATCCATTAGTAAGT
66 GAGTAGTAG-AGAAAATCCATCAGTAAGT
* * * ** ** * *
25554 GCCTTCAGTAAGTCTTTCGAGCGTGATGATGAAGTCCTTCA-GGCCATCAGTAAGTCTTTCGAGC
1 GCCATCAGTAAGTCTTTCGAGCGTGATGATTAAATCCTT-AGGGTAATTTGTAAG-CCTTC-ACC
* * *
25618 -ATGA-T-G-AG-G-AAGTCCTTC-G---G-
63 AAAGAGTAGTAGAGAAAATCCATCAGTAAGT
* * * * *
25638 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGTCTGCACCGAA
1 GCCATCAGTAAGTCTTTCGAGCGTGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACCAAA
*
25703 GAGTAGT-GAAACAAATCCATCAGTAAGT
66 GAGTAGTAGAGA-AAATCCATCAGTAAGT
25731 CATTCGAGCA
Statistics
Matches: 210, Mismatches: 42, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
82 2 0.01
83 5 0.02
84 45 0.21
85 3 0.01
88 8 0.04
89 7 0.03
90 1 0.00
92 4 0.02
93 125 0.60
94 8 0.04
95 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (93 bp):
GCCATCAGTAAGTCTTTCGAGCGTGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACCAAA
GAGTAGTAGAGAAAATCCATCAGTAAGT
Found at i:25617 original size:42 final size:42
Alignment explanation
Indices: 25558--25798 Score: 204
Period size: 42 Copynumber: 5.8 Consensus size: 42
25548 GTAAGTGCCT
*
25558 TCAGTAAGTCTTTCGAGCGTGATGATGAAGTCCTTCAGGCCA
1 TCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCAGGCCA
* *
25600 TCAGTAAGTCTTTCGAGCATGATGAGGAAGTCCTTCGGGCCA
1 TCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCAGGCCA
* * * **
25642 TCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAA
1 TCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCAGGCCA
** * * * * **** **
25684 TTTGTAAGTC-TGC-A-C-CGAAGA-GTAGTGAAACAAATCCA
1 TCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTC-AGGCCA
* * * *
25722 TCAGTAAGTCATTCGAGCATGATGATGAAATCCTTCGGGACA
1 TCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCAGGCCA
* *
25764 TCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
1 TCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTT
25799 TGGGTGTCAT
Statistics
Matches: 151, Mismatches: 42, Indels: 12
0.74 0.20 0.06
Matches are distributed among these distances:
37 3 0.02
38 13 0.09
39 3 0.02
40 2 0.01
41 3 0.02
42 123 0.81
43 4 0.03
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (42 bp):
TCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCAGGCCA
Found at i:25636 original size:22 final size:21
Alignment explanation
Indices: 25563--25666 Score: 61
Period size: 20 Copynumber: 4.9 Consensus size: 21
25553 TGCCTTCAGT
*
25563 AAGTCTTTCGAGCGTGATGATG
1 AAGTCTTTCGAGC-TGATGAGG
* * * *
25585 AAGTCCTTC-AGGC-CATCAGT
1 AAGTCTTTCGA-GCTGATGAGG
25605 AAGTCTTTCGAGCATGATGAGG
1 AAGTCTTTCGAGC-TGATGAGG
* * * * *
25627 AAGTCCTTCGGGC-CATCAGT
1 AAGTCTTTCGAGCTGATGAGG
25647 AAGTCTTTCGAGCATGATGA
1 AAGTCTTTCGAGC-TGATGA
25667 TTAAATCCTT
Statistics
Matches: 58, Mismatches: 18, Indels: 12
0.66 0.20 0.14
Matches are distributed among these distances:
20 28 0.48
21 2 0.03
22 28 0.48
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (21 bp):
AAGTCTTTCGAGCTGATGAGG
Found at i:25656 original size:20 final size:20
Alignment explanation
Indices: 25585--25656 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
25575 CGTGATGATG
*
25585 AAGTCCTTCAGGCCATCAGT
1 AAGTCCTTCGGGCCATCAGT
* * * * *
25605 AAGTCTTTCGAGCATGATGAGG
1 AAGTCCTTCGGGC--CATCAGT
25627 AAGTCCTTCGGGCCATCAGT
1 AAGTCCTTCGGGCCATCAGT
*
25647 AAGTCTTTCG
1 AAGTCCTTCG
25657 AGCATGATGA
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
20 23 0.61
22 15 0.39
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.28
Consensus pattern (20 bp):
AAGTCCTTCGGGCCATCAGT
Found at i:26430 original size:264 final size:264
Alignment explanation
Indices: 25959--26485 Score: 810
Period size: 264 Copynumber: 2.0 Consensus size: 264
25949 ATCAGATGTG
* *
25959 GAAGGAAATCGAATATTCTCGGGTACGAAGAAATAAAACAATCGATTAAAAAGGCTTGTGCACGT
1 GAAGGAAATCGAAGATTCTCAGGTACGAAGAAATAAAACAATCGATTAAAAAGGCTTGTGCACGT
* *
26024 GAAATGAAGGCGAAAGTCAAGAAAAAGATTGAAGAAAGGAAAAAGACATTGCAGTAAGACAAAAT
66 GAAA-GAAGGCGAAAGTCAAGAAAAAGACTGAAGAAAGGAAAAAGACATTACAGTAAGACAAAAT
* **
26089 TAGGTTAATTTTTATCTTTGCTACATTCTTGTGTTCACAACAACGTGCAAAGAGGGGCAGCTGTA
130 TAGGTTAATTTTTATCTTTGCTACATTCTTGTGTTCACAACAACGAGCAAAGAGGGGCAGCTACA
*
26154 ATTACCTAATTTTGTCCGGACCATTTAAATTCATTTGAAGATGATCGAGAATTAATTTGAAGATA
195 ATTACCTAATTTTGTCCGGACCATTTAAATTCATTTGAAGATAATCGAGAATTAATTTGAAGATA
26219 TTTGT
260 TTTGT
** * *
26224 GAAGGAAATCGAAGATTCTCAGGTACGAAGAAGA-GGAACAATCGATTAAAAGGGTTTGTGCACG
1 GAAGGAAATCGAAGATTCTCAGGTACGAAGAA-ATAAAACAATCGATTAAAAAGGCTTGTGCACG
* ** *
26288 TGAGAA-AAGGC-AGAAGTCAAGAAAAAGACTGAAGAAAGGAAAAAGACGTTATGGTCAGACAAA
65 TGA-AAGAAGGCGA-AAGTCAAGAAAAAGACTGAAGAAAGGAAAAAGACATTACAGTAAGACAAA
* * *
26351 ATTAGGTTATTTTTTGTCTTTGCTACATTCTTGTGTTCACAACAATGAGCAAAGAGGGGCAGCTA
128 ATTAGGTTAATTTTTATCTTTGCTACATTCTTGTGTTCACAACAACGAGCAAAGAGGGGCAGCTA
26416 CAA-TACCCTAATTTTGTCCGGACCATTTAAATTCATTTGAAGATAATCGAGAATTAATTTGAAG
193 CAATTA-CCTAATTTTGTCCGGACCATTTAAATTCATTTGAAGATAATCGAGAATTAATTTGAAG
26480 ATATTT
257 ATATTT
26486 ATGCTCGATG
Statistics
Matches: 239, Mismatches: 19, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
263 3 0.01
264 174 0.73
265 59 0.25
266 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.27
Consensus pattern (264 bp):
GAAGGAAATCGAAGATTCTCAGGTACGAAGAAATAAAACAATCGATTAAAAAGGCTTGTGCACGT
GAAAGAAGGCGAAAGTCAAGAAAAAGACTGAAGAAAGGAAAAAGACATTACAGTAAGACAAAATT
AGGTTAATTTTTATCTTTGCTACATTCTTGTGTTCACAACAACGAGCAAAGAGGGGCAGCTACAA
TTACCTAATTTTGTCCGGACCATTTAAATTCATTTGAAGATAATCGAGAATTAATTTGAAGATAT
TTGT
Found at i:26840 original size:28 final size:29
Alignment explanation
Indices: 26809--26864 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
26799 ATGAATACAT
* *
26809 CATCTGTCCATGCT-CCACAACGCCCAAG
1 CATCTGCCCATGCTACCACAACACCCAAG
*
26837 CATCTGCCCATGCTAGCACAACACCCAA
1 CATCTGCCCATGCTACCACAACACCCAA
26865 CAGCCCGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.29, C:0.43, G:0.12, T:0.16
Consensus pattern (29 bp):
CATCTGCCCATGCTACCACAACACCCAAG
Found at i:28331 original size:17 final size:17
Alignment explanation
Indices: 28309--28349 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
28299 GTAGGTTATA
28309 ATGTATAGTTATAAAAG
1 ATGTATAGTTATAAAAG
28326 ATGTATAGTTATAAAAG
1 ATGTATAGTTATAAAAG
28343 ATGTATA
1 ATGTATA
28350 TGATTTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (17 bp):
ATGTATAGTTATAAAAG
Found at i:37814 original size:29 final size:29
Alignment explanation
Indices: 37777--37850 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 29
37767 TAAAATTATT
*
37777 AAATTTATTTTATTCTTT-TCT-TAACCTAA
1 AAATATATTTTATTCTTTAT-TATAA-CTAA
*
37806 AAATATATTTTATT-TTTATTATAACTTA
1 AAATATATTTTATTCTTTATTATAACTAA
*
37834 AAATATATTTTAATCTT
1 AAATATATTTTATTCTT
37851 ATTTTTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
28 20 0.51
29 19 0.49
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.55
Consensus pattern (29 bp):
AAATATATTTTATTCTTTATTATAACTAA
Found at i:37845 original size:28 final size:27
Alignment explanation
Indices: 37743--37845 Score: 88
Period size: 29 Copynumber: 3.7 Consensus size: 27
37733 ATTCAGATAT
37743 TAACATTAAAATAT-TTTTA-TTTTTTA
1 TAAC-TTAAAATATATTTTATTTTTTTA
* *
37769 -AAATTATTAAATTTATTTTATTCTTTTCT-
1 TAACTTA--AAATATATTTTATT-TTTT-TA
*
37798 TAACCTAAAAATATATTTTATTTTTATTA
1 TAA-CTTAAAATATATTTTATTTTT-TTA
37827 TAACTTAAAATATATTTTA
1 TAACTTAAAATATATTTTA
37846 ATCTTATTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
24 3 0.05
25 2 0.03
26 5 0.08
27 5 0.08
28 20 0.33
29 21 0.34
30 3 0.05
31 2 0.03
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (27 bp):
TAACTTAAAATATATTTTATTTTTTTA
Found at i:37906 original size:29 final size:30
Alignment explanation
Indices: 37863--37926 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
37853 TTTTATTTTT
*
37863 AAAATATATTCTATTTTATCTTAAC-TA-TTA
1 AAAATATATTATATTTT-T-TTAACTTATTTA
37893 AAAATATA-TATATTTTTTTAACTTATTTA
1 AAAATATATTATATTTTTTTAACTTATTTA
37922 AAAAT
1 AAAAT
37927 TTATCCTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 5 0.16
28 3 0.10
29 15 0.48
30 8 0.26
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (30 bp):
AAAATATATTATATTTTTTTAACTTATTTA
Found at i:37963 original size:5 final size:5
Alignment explanation
Indices: 37955--37979 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
37945 AATTATATAT
37955 TTTAA TTTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA
37980 AAATATATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:37995 original size:33 final size:34
Alignment explanation
Indices: 37935--38005 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 34
37925 ATTTATCCTT
* ** *
37935 ATTTAACTTAAATTATATATTTTAATTTAATTTA
1 ATTTAACTTAAATAATATATTCCAATTTAATGTA
* *
37969 ATTTAATTTAAA-AATATATTCCAATTTTATGTA
1 ATTTAACTTAAATAATATATTCCAATTTAATGTA
38002 ATTT
1 ATTT
38006 TAAAATATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
33 20 0.65
34 11 0.35
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (34 bp):
ATTTAACTTAAATAATATATTCCAATTTAATGTA
Found at i:38047 original size:20 final size:22
Alignment explanation
Indices: 38007--38054 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
37997 ATGTAATTTT
38007 AAAATATTATAAGAATAAAATA
1 AAAATATTATAAGAATAAAATA
* *
38029 TAAATATT-TAAG-TTAAAATA
1 AAAATATTATAAGAATAAAATA
38049 AAAATA
1 AAAATA
38055 AAATATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 12 0.52
21 4 0.17
22 7 0.30
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (22 bp):
AAAATATTATAAGAATAAAATA
Found at i:38055 original size:31 final size:32
Alignment explanation
Indices: 38015--38096 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 32
38005 TTAAAATATT
*
38015 ATAAGAATAAAATATAAATATTTAAGTTAA-A
1 ATAAAAATAAAATATAAATATTTAAGTTAAGA
* *
38046 ATAAAAATAAAATAT--ATTTTTAGGTTAAGA
1 ATAAAAATAAAATATAAATATTTAAGTTAAGA
*
38076 A-AAAAATAAAA-AAAAATATTT
1 ATAAAAATAAAATATAAATATTT
38097 TAACGTTAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 1 0.02
29 21 0.49
30 7 0.16
31 14 0.33
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (32 bp):
ATAAAAATAAAATATAAATATTTAAGTTAAGA
Found at i:39442 original size:147 final size:147
Alignment explanation
Indices: 39187--39486 Score: 573
Period size: 147 Copynumber: 2.0 Consensus size: 147
39177 AACAAATCAA
39187 CAAACTAACAACTAATTACAACTTATTTCTAACATTCTCCCTACTTTCTCAACCTTCTTGATCTT
1 CAAACTAACAACTAATTACAACTTATTTCTAACATTCTCCCTACTTTCTCAACCTTCTTGATCTT
*
39252 CAGAACTTGACTCGTTCACGAGTAAATTACAATTCATTTATGACATTCTCCACTTGGCTAGTTCA
66 CAAAACTTGACTCGTTCACGAGTAAATTACAATTCATTTATGACATTCTCCACTTGGCTAGTTCA
39317 CGATCAAAACTAGCCTC
131 CGATCAAAACTAGCCTC
*
39334 CAAACTAACAACTAATTACAACTTATTTCTAACATTCTCCCTATTTTCTCAACCTTCTTGATCTT
1 CAAACTAACAACTAATTACAACTTATTTCTAACATTCTCCCTACTTTCTCAACCTTCTTGATCTT
*
39399 CAAAACTTGACTCGTTCACGATTAAATTACAATTCATTTATGACATTCTCCACTTGGCTAGTTCA
66 CAAAACTTGACTCGTTCACGAGTAAATTACAATTCATTTATGACATTCTCCACTTGGCTAGTTCA
39464 CGATCAAAACTAGCCTC
131 CGATCAAAACTAGCCTC
39481 CAAACT
1 CAAACT
39487 GGTTGAAGTT
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
147 150 1.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.34
Consensus pattern (147 bp):
CAAACTAACAACTAATTACAACTTATTTCTAACATTCTCCCTACTTTCTCAACCTTCTTGATCTT
CAAAACTTGACTCGTTCACGAGTAAATTACAATTCATTTATGACATTCTCCACTTGGCTAGTTCA
CGATCAAAACTAGCCTC
Found at i:39621 original size:35 final size:35
Alignment explanation
Indices: 39570--39651 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 35
39560 CTGTCAATGA
* *
39570 GAATCAAAAGTACTATGCCTCATTTCGTTCAACTT
1 GAATCGAAAGTGCTATGCCTCATTTCGTTCAACTT
* *
39605 GAATCGAAAGTGCTATGCCTCCTTTCGTTCTACTT
1 GAATCGAAAGTGCTATGCCTCATTTCGTTCAACTT
39640 GAATCGAAAGTG
1 GAATCGAAAGTG
39652 TGATGATTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (35 bp):
GAATCGAAAGTGCTATGCCTCATTTCGTTCAACTT
Found at i:39669 original size:35 final size:35
Alignment explanation
Indices: 39570--39750 Score: 120
Period size: 35 Copynumber: 5.0 Consensus size: 35
39560 CTGTCAATGA
* * * * * *
39570 GAATCAAAAGTACTATGCCTCATTTCGTTCAACTT
1 GAATCGAAAGTGCTATGACTCCTTCCGTTCTACTT
* *
39605 GAATCGAAAGTGCTATGCCTCCTTTCGTTCTACTT
1 GAATCGAAAGTGCTATGACTCCTTCCGTTCTACTT
* *
39640 GAATCGAAAGTG-TGATGATTTCTTCCGTTCTACTTT
1 GAATCGAAAGTGCT-ATGACTCCTTCCGTTCTAC-TT
*
39676 AGAGGAGAATC-AAAGTGCTATGCCTCCTTTCC-TTCTTA-TT
1 ------GAATCGAAAGTGCTATGACTCC-TTCCGTTC-TACTT
*
39716 GAATCGAAAGTGCGATG-CTTCCTTCCGTTCTACTT
1 GAATCGAAAGTGCTATGAC-TCCTTCCGTTCTACTT
39751 TATACAAGAA
Statistics
Matches: 119, Mismatches: 12, Indels: 30
0.74 0.07 0.19
Matches are distributed among these distances:
34 13 0.11
35 76 0.64
36 2 0.02
40 2 0.02
41 14 0.12
42 12 0.10
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (35 bp):
GAATCGAAAGTGCTATGACTCCTTCCGTTCTACTT
Found at i:39701 original size:76 final size:77
Alignment explanation
Indices: 39605--39809 Score: 288
Period size: 76 Copynumber: 2.7 Consensus size: 77
39595 CGTTCAACTT
* *
39605 GAATCGAAAGTGCTATGCCTCCTTTCGTTCTACTTGAATCGAAAGTGTGATGATTTCTTCCGTTC
1 GAATCAAAAGTGCTATGCCTCCTTTCGTTCTACTTGAATCGAAAGTGTGATGATTCCTTCCGTTC
**
39670 TACTTTAGAGGA
66 TACTTTAGACAA
* * *
39682 GAATC-AAAGTGCTATGCCTCCTTTCCTTCTTA-TTGAATCGAAAGTGCGATGCTTCCTTCCGTT
1 GAATCAAAAGTGCTATGCCTCCTTTCGTTC-TACTTGAATCGAAAGTGTGATGATTCCTTCCGTT
*
39745 CTACTTTATACAA
65 CTACTTTAGACAA
* **
39758 GAATCAAAAATGCTATGCCTCCTTTCGTTAAACTTGAATCGAAAGTGTGATG
1 GAATCAAAAGTGCTATGCCTCCTTTCGTTCTACTTGAATCGAAAGTGTGATG
39810 CTTCATTTCA
Statistics
Matches: 113, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
76 67 0.59
77 46 0.41
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (77 bp):
GAATCAAAAGTGCTATGCCTCCTTTCGTTCTACTTGAATCGAAAGTGTGATGATTCCTTCCGTTC
TACTTTAGACAA
Found at i:44669 original size:2 final size:2
Alignment explanation
Indices: 44662--44711 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
44652 AAAGTATAAC
44662 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44704 AT AT AT AT
1 AT AT AT AT
44712 GAAATTTTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48090 original size:17 final size:17
Alignment explanation
Indices: 48068--48120 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
48058 AATTAAGCGT
48068 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
48085 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
48102 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
48119 TA
1 TA
48121 ACTTTATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:48133 original size:18 final size:18
Alignment explanation
Indices: 48071--48138 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 18
48061 TAAGCGTTAG
* *
48071 TTTAATAAATGAACT-AG
1 TTTAATTAATGAACTAAC
* * *
48088 TTTGATGAATGAACT-AG
1 TTTAATTAATGAACTAAC
48105 TTTAATTAATGAACTAAC
1 TTTAATTAATGAACTAAC
48123 TTT-ATTCAATGAACTA
1 TTTAATT-AATGAACTA
48139 TATGCATGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
17 31 0.70
18 13 0.30
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (18 bp):
TTTAATTAATGAACTAAC
Found at i:50662 original size:14 final size:14
Alignment explanation
Indices: 50645--50674 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
50635 TAACAAGATT
50645 TAAATTCTCACCAA
1 TAAATTCTCACCAA
50659 TAAATTCTCACCAA
1 TAAATTCTCACCAA
50673 TA
1 TA
50675 CACTCAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAATTCTCACCAA
Found at i:51056 original size:28 final size:28
Alignment explanation
Indices: 51003--51060 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
50993 CCCTCTTTAA
**
51003 ACTTTTTATTTCTTTTTTTTGATTTTTT
1 ACTTTTTATTTCTTTTTTTCAATTTTTT
51031 ACTTTTTATTTC-TTTTTTCAATTTTTT
1 ACTTTTTATTTCTTTTTTTCAATTTTTT
51058 ACT
1 ACT
51061 AACCCGTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 16 0.57
28 12 0.43
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.74
Consensus pattern (28 bp):
ACTTTTTATTTCTTTTTTTCAATTTTTT
Found at i:54886 original size:87 final size:86
Alignment explanation
Indices: 54818--55026 Score: 227
Period size: 87 Copynumber: 2.4 Consensus size: 86
54808 TTAAATTATT
* * *
54818 AAATTTATTTTATTCTTT-TCTTAAC-TTAGAAATATATTTTATTTTTATTTTAACTAAAAAAAT
1 AAATATATTTTATT-TTTATCTTAACTTTAAAAATATATCTTATTTTTATTTTAACTAAAAAAAT
54881 ATTTTAATCTTATTTTAATTTA
65 ATTTTAATCTTATTTTAATTTA
*
54903 AAATATATTTTATTTTTATCTTAACTTTTAAAAATATATCTTATTTTTATTTTAACTTATATAAA
1 AAATATATTTTATTTTTATCTTAAC-TTTAAAAATATATCTTATTTTTATTTTAAC-TA-AAAAA
**
54968 A-A--TTAATCATTA-TTTAACATA
63 ATATTTTAATC-TTATTTTAATTTA
* *
54989 AAATATATATTT-TATTTTAT-TTTATTTTAAAAATATAT
1 AAATATAT-TTTAT-TTTTATCTTAACTTTAAAAATATAT
55027 TCCACTTTTA
Statistics
Matches: 108, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
84 3 0.03
85 33 0.31
86 25 0.23
87 39 0.36
88 3 0.03
89 5 0.05
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (86 bp):
AAATATATTTTATTTTTATCTTAACTTTAAAAATATATCTTATTTTTATTTTAACTAAAAAAATA
TTTTAATCTTATTTTAATTTA
Found at i:54893 original size:28 final size:28
Alignment explanation
Indices: 54818--55027 Score: 140
Period size: 28 Copynumber: 7.3 Consensus size: 28
54808 TTAAATTATT
* *
54818 AAATTTATTTTATTCTT-TTCTTAACTTAG
1 AAATATATTTTATTCTTATT-TTAAC-TAA
*
54847 AAATATATTTTATTTTTATTTTAACTAA
1 AAATATATTTTATTCTTATTTTAACTAA
* * * *
54875 AAAAATATTTTAATCTTATTTTAATTTA
1 AAATATATTTTATTCTTATTTTAACTAA
* *
54903 AAATATATTTTATTTTTATCTTAACTTTTAA
1 AAATATATTTTATTCTTATTTTAAC---TAA
* * *
54934 AAATATATCTTATTTTTATTTTAACT-T
1 AAATATATTTTATTCTTATTTTAACTAA
* * ** *
54961 ATATAAAAATTAATCATTA-TTTAACATAA
1 AAATATATTTTATTC-TTATTTTAAC-TAA
**
54990 AATATATATTTTATT-TTATTTTATTTTAA
1 AA-ATATATTTTATTCTTATTTTA-ACTAA
55019 AAATATATT
1 AAATATATT
55028 CCACTTTTAT
Statistics
Matches: 140, Mismatches: 31, Indels: 21
0.73 0.16 0.11
Matches are distributed among these distances:
27 15 0.11
28 60 0.43
29 30 0.21
30 10 0.07
31 25 0.18
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (28 bp):
AAATATATTTTATTCTTATTTTAACTAA
Found at i:56838 original size:29 final size:29
Alignment explanation
Indices: 56777--56852 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
56767 GTAAAAAGAC
* *
56777 AAAACTTTACATAAATTAAAATTAAGG-CC
1 AAAACTTT-TATAAATTAAAATTAAGGACA
*
56806 AAAACATTTTATAAATTAAAATTAAGGATA
1 AAAAC-TTTTATAAATTAAAATTAAGGACA
56836 AAAACTTTTATAAATTA
1 AAAACTTTTATAAATTA
56853 TAATAGAGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 34 0.81
30 8 0.19
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (29 bp):
AAAACTTTTATAAATTAAAATTAAGGACA
Found at i:61301 original size:26 final size:26
Alignment explanation
Indices: 61269--61329 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
61259 GAATGTTGAG
61269 GCCTTGTGCCATAGTTAGTCTTAAGT
1 GCCTTGTGCCATAGTTAGTCTTAAGT
*
61295 GTCTTGTGCCATAGTTAGTCTTAAGT
1 GCCTTGTGCCATAGTTAGTCTTAAGT
61321 GCCTTGTGC
1 GCCTTGTGC
61330 ACTACATAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.39
Consensus pattern (26 bp):
GCCTTGTGCCATAGTTAGTCTTAAGT
Found at i:66741 original size:2 final size:2
Alignment explanation
Indices: 66734--66815 Score: 136
Period size: 2 Copynumber: 43.0 Consensus size: 2
66724 GCGCTTCAAA
66734 AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66774 AT AT AT AT AT AT -T AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66814 AT
1 AT
66816 GAATTGTGAT
Statistics
Matches: 76, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
1 4 0.05
2 72 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:66757 original size:15 final size:14
Alignment explanation
Indices: 66734--66815 Score: 136
Period size: 13 Copynumber: 6.1 Consensus size: 14
66724 GCGCTTCAAA
66734 ATATATATATATAT
1 ATATATATATATAT
66748 ATAT-TATATATAT
1 ATATATATATATAT
66761 ATATATAT-TATAT
1 ATATATATATATAT
66774 ATATATATATAT-T
1 ATATATATATATAT
66787 ATATATATATAT-T
1 ATATATATATATAT
66800 ATATATATATATAT
1 ATATATATATATAT
66814 AT
1 AT
66816 GAATTGTGAT
Statistics
Matches: 65, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
13 52 0.80
14 13 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATATATATATAT
Found at i:66757 original size:17 final size:17
Alignment explanation
Indices: 66735--66815 Score: 148
Period size: 17 Copynumber: 4.9 Consensus size: 17
66725 CGCTTCAAAA
66735 TATATATATATATATAT
1 TATATATATATATATAT
66752 TATATATATATATATAT
1 TATATATATATATATAT
66769 TATATATATATATATAT
1 TATATATATATATATAT
66786 TATATATATATAT-TA-
1 TATATATATATATATAT
66801 TATATATATATATAT
1 TATATATATATATAT
66816 GAATTGTGAT
Statistics
Matches: 63, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.21
16 3 0.05
17 47 0.75
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Done.