Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002843.1 Hibiscus syriacus cultivar Beakdansim tig00005854_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: 69030
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3257 original size:39 final size:39
Alignment explanation
Indices: 3203--3280 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
3193 ATTAACTGTA
* *
3203 GATAAACCAAGTAATGTAATTCAATTCACAAACTTTATT
1 GATAAACCAAGTAATGCAATTCAATCCACAAACTTTATT
*
3242 GATAAACCAAGTAATGCAATTCAATCCACGAACTTTATT
1 GATAAACCAAGTAATGCAATTCAATCCACAAACTTTATT
3281 CTGAATACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (39 bp):
GATAAACCAAGTAATGCAATTCAATCCACAAACTTTATT
Found at i:3853 original size:16 final size:16
Alignment explanation
Indices: 3834--3890 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
3824 TATTAACATG
*
3834 AATAGTAAATTTCGTG
1 AATAGTAAATTTCGTA
*
3850 AATAGTAAATTTTGTA
1 AATAGTAAATTTCGTA
3866 AATAGTAAATTTCGTA
1 AATAGTAAATTTCGTA
*
3882 AATAATAAA
1 AATAGTAAA
3891 AATTTTGTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.47, C:0.04, G:0.12, T:0.37
Consensus pattern (16 bp):
AATAGTAAATTTCGTA
Found at i:3875 original size:32 final size:33
Alignment explanation
Indices: 3834--3899 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
3824 TATTAACATG
* *
3834 AATAGTAAATTTCGTGAATAGT-AAATTTTGTA
1 AATAGTAAATTTCGTAAATAATAAAATTTTGTA
3866 AATAGTAAATTTCGTAAATAATAAAAATTTTGTA
1 AATAGTAAATTTCGTAAATAAT-AAAATTTTGTA
3900 TGCGATACGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 20 0.67
34 10 0.33
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.39
Consensus pattern (33 bp):
AATAGTAAATTTCGTAAATAATAAAATTTTGTA
Found at i:5278 original size:22 final size:22
Alignment explanation
Indices: 5253--5297 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5243 GCGAGAAAGG
5253 GATGAAGACACTTTTGTCAAAA
1 GATGAAGACACTTTTGTCAAAA
5275 GATGAAGACACTTTTGTCAAAA
1 GATGAAGACACTTTTGTCAAAA
5297 G
1 G
5298 GGAAGCTGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (22 bp):
GATGAAGACACTTTTGTCAAAA
Found at i:9584 original size:23 final size:24
Alignment explanation
Indices: 9551--9607 Score: 100
Period size: 23 Copynumber: 2.5 Consensus size: 24
9541 AAATAAGAGG
9551 ATAT-AAATAATGAGGTAAATAT-
1 ATATAAAATAATGAGGTAAATATA
9573 ATATAAAATAATGAGGTAAATATA
1 ATATAAAATAATGAGGTAAATATA
9597 ATATAAAATAA
1 ATATAAAATAA
9608 AAAAGAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 4 0.12
23 18 0.55
24 11 0.33
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.30
Consensus pattern (24 bp):
ATATAAAATAATGAGGTAAATATA
Found at i:9617 original size:26 final size:23
Alignment explanation
Indices: 9563--9620 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
9553 ATAAATAATG
**
9563 AGGTAAATATATATAAAATAATG
1 AGGTAAATATATATAAAATAAAA
9586 AGGTAAATATAATATAAAATAAAAA
1 AGGTAAATAT-ATATAAAAT-AAAA
9611 AGAGTAAATA
1 AG-GTAAATA
9621 AAATGGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 10 0.33
24 9 0.30
25 4 0.13
26 7 0.23
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (23 bp):
AGGTAAATATATATAAAATAAAA
Found at i:13653 original size:20 final size:20
Alignment explanation
Indices: 13628--13668 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
13618 TCATGTTAGG
*
13628 GCTGCTCCTGCCGTGAATTT
1 GCTGCTCCTACCGTGAATTT
*
13648 GCTGCTGCTACCGTGAATTT
1 GCTGCTCCTACCGTGAATTT
13668 G
1 G
13669 ATGTTGCTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.27, G:0.27, T:0.34
Consensus pattern (20 bp):
GCTGCTCCTACCGTGAATTT
Found at i:13676 original size:20 final size:20
Alignment explanation
Indices: 13638--13676 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13628 GCTGCTCCTG
*
13638 CCGTGAATTTGCTGCTGCTA
1 CCGTGAATTTGATGCTGCTA
*
13658 CCGTGAATTTGATGTTGCT
1 CCGTGAATTTGATGCTGCT
13677 GCCGCAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (20 bp):
CCGTGAATTTGATGCTGCTA
Found at i:14059 original size:8 final size:8
Alignment explanation
Indices: 14046--14074 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
14036 ATTTGAGGTT
14046 TTATTTAA
1 TTATTTAA
14054 TTATTTAA
1 TTATTTAA
14062 TTATTTAA
1 TTATTTAA
14070 TTATT
1 TTATT
14075 CTCTTCTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TTATTTAA
Found at i:14220 original size:20 final size:20
Alignment explanation
Indices: 14192--14249 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
14182 ATCTTGCCCA
*
14192 AAGGTCTTATAGATGACTCG
1 AAGGACTTATAGATGACTCG
**
14212 AAGGACTTATCATCTCG-CTCG
1 AAGGACTTAT-AGAT-GACTCG
*
14233 AAAGACTTATAGATGAC
1 AAGGACTTATAGATGAC
14250 CCACATGATT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
19 1 0.03
20 12 0.41
21 15 0.52
22 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
AAGGACTTATAGATGACTCG
Found at i:14457 original size:233 final size:231
Alignment explanation
Indices: 14175--15344 Score: 1287
Period size: 232 Copynumber: 5.0 Consensus size: 231
14165 ATATACCATA
* * * *
14175 TGAAAACATCTTGCCCAAAGGTCTTATAGA-TGACTCGAAGGACTTATCATCTCGCTCGAAAGAC
1 TGAAAACATCCTGCCCAAAGGTCTTATGGATTG-CCCGAA-GACTTATCATCTTGCTCGAAAGAC
* * * * *
14239 TTATAGATGACCCACATGATTTAATAATTATGCTTGAAAGACTTACTGATGGCCTGAAGGACTTA
64 TTACAGATGACCCA-ATGATTTAAGAATCATGCTCGAAAGACTTACTGATGGCCTGAAGAACTTA
*
14304 CCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAGTTTTCAG
128 CCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAG
* *
14369 ATTTAAATGGGAAACTTTTCTCATTTTTCGAGAGATATG
193 ATTTAAATGAGAAACTTTTCTCATTTTTCGAGAGACATG
* * *
14408 TGAAAACATCCTGCCCAAAGGTCGTATGGATGGCCCGAAGAACTTATCATCTTGCTCGTAAGACT
1 TGAAAACATCCTGCCCAAAGGTCTTATGGATTGCCCGAAG-ACTTATCATCTTGCTCGAAAGACT
* *
14473 TACAGATGACCCGAA-GATTTAAGCATCATGCTTGAAATACTTACCGATAGCCCGAAATACTTAC
65 TACAGATGACCC-AATGATTT----A--A-----G--A-A--T--C-AT-GCTCGAAAGACTTAC
* * * * *
14537 AGATGGCCCGAA-ATACTTACCAATTTTGGAAATGGTTTACTAAGTAAGAAACTTTTCTTGCTTT
109 TGATGGCCTGAAGA-ACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTAC-TT
* *
14601 TTCAAAAATTTCAATTTTCAAATTTAAATAAGAAA-TGTTTCTCATTTTT--AGAGACATG
172 TTCAAAAATTTCAATTTTCAGATTTAAATGAGAAACT-TTTCTCATTTTTCGAGAGACATG
* * * *
14659 TGAAAACATCCTGCCTAAAGTTCATATGGATTGCCTGAAGGACTTATCATCTTGCTCGAAAGACT
1 TGAAAACATCCTGCCCAAAGGTCTTATGGATTGCCCGAA-GACTTATCATCTTGCTCGAAAGACT
* * * * * * *
14724 TACATATGACCGAAGGATTTAA-ACATCAAGCTCGAAAGACTTATTGATGGTCTGATGAACTTAC
65 TACAGATGACCCAATGATTTAAGA-ATCATGCTCGAAAGACTTACTGATGGCCTGAAGAACTTAC
* * * *
14788 TAATTTTGGAAATAGTTTACTAGCTAAGAAACTTTCCTTACTTCTCAAAAATTTCAATTTTCAGA
129 CAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGA
* * *
14853 TTTAAATGAGAAACATTTCTCATTTTTCGATAAACATG
194 TTTAAATGAGAAACTTTTCTCATTTTTCGAGAGACATG
* * * * *
14891 TAAAAACATCATGCTCGAATGTCTTATGGATTGCCCGAACGACTTATCATCTTGCTCGAAAGACT
1 TGAAAACATCCTGCCCAAAGGTCTTATGGATTGCCCGAA-GACTTATCATCTTGCTCGAAAGACT
* * * * *
14956 TACAGATGACCCGAATAATTTAAGCATCATGCTCGAAAGATTTACTGATGGTCT-AAGGGAC-TA
65 TACAGATGACCC-AATGATTTAAGAATCATGCTCGAAAGACTTACTGATGGCCTGAA-GAACTTA
* * ** * *
15019 CTAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTCCTTACTTTAAAAAAAATTCAATTTTCCG
128 CCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAG
*
15084 ATTTAAATGAGAAACTTTTCTCATTTTTCGAGAGTCATG
193 ATTTAAATGAGAAACTTTTCTCATTTTTCGAGAGACATG
* * * * * *
15123 TGAAAACATCCTGCCCGAATGTCTTATGGATTGCCTGAATGATTTATCATCTTGGTCAAAAGACT
1 TGAAAACATCCTGCCCAAAGGTCTTATGGATTGCCCGAA-GACTTATCATCTTGCTCGAAAGACT
** * * *
15188 TACAGATGATCTGAATGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAATAACTTAC
65 TACAGATGA-CCCAATGATTTAAGAATCATGCTCGAAAGACTTACTGATGGCCTGAAGAACTTAC
* * * *
15253 CAATTTTAGAAATAGTTTACTAGGTAAGAAACTTTTCTTAGTTTTCAAAAATTTTAATTTTTAGA
129 CAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGA
*
15318 TTTAAATGAGAAAATTTTCTCATTTTT
194 TTTAAATGAGAAACTTTTCTCATTTTT
15345 TAACTTATTA
Statistics
Matches: 789, Mismatches: 110, Indels: 76
0.81 0.11 0.08
Matches are distributed among these distances:
230 46 0.06
231 61 0.08
232 282 0.36
233 191 0.24
234 2 0.00
235 1 0.00
236 1 0.00
237 2 0.00
238 1 0.00
245 2 0.00
246 1 0.00
247 1 0.00
248 1 0.00
250 2 0.00
251 82 0.10
252 68 0.09
253 45 0.06
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (231 bp):
TGAAAACATCCTGCCCAAAGGTCTTATGGATTGCCCGAAGACTTATCATCTTGCTCGAAAGACTT
ACAGATGACCCAATGATTTAAGAATCATGCTCGAAAGACTTACTGATGGCCTGAAGAACTTACCA
ATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTTCAGATT
TAAATGAGAAACTTTTCTCATTTTTCGAGAGACATG
Found at i:14531 original size:20 final size:20
Alignment explanation
Indices: 14506--14557 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
14496 CATCATGCTT
14506 GAAATACTTACCGATAGCCC
1 GAAATACTTACCGATAGCCC
* *
14526 GAAATACTTACAGATGGCCC
1 GAAATACTTACCGATAGCCC
14546 GAAATACTTACC
1 GAAATACTTACC
14558 AATTTTGGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.21
Consensus pattern (20 bp):
GAAATACTTACCGATAGCCC
Found at i:27929 original size:20 final size:22
Alignment explanation
Indices: 27904--27952 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
27894 CAAAAAAATG
27904 TTATTAAT-TATATTAGTATT-
1 TTATTAATATATATTAGTATTA
*
27924 TTATT-ATATATATTATTATTA
1 TTATTAATATATATTAGTATTA
27945 TTATTAAT
1 TTATTAAT
27953 CTTATTACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 16 0.64
21 5 0.20
22 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTATTAATATATATTAGTATTA
Found at i:32129 original size:6 final size:6
Alignment explanation
Indices: 32118--32152 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
32108 ATCGATACCT
32118 TTTGCA TTTGCA TTTGCA TTTGCA TCTTTGCA TTT
1 TTTGCA TTTGCA TTTGCA TTTGCA --TTTGCA TTT
32153 TACGTTTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 21 0.78
8 6 0.22
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.54
Consensus pattern (6 bp):
TTTGCA
Found at i:37270 original size:38 final size:37
Alignment explanation
Indices: 37209--37433 Score: 258
Period size: 38 Copynumber: 6.2 Consensus size: 37
37199 TTTAATACAG
37209 AAGATTTTATC-ACTCAAGATTGTTTTTCCTTGAACA
1 AAGATTTTATCTACTCAAGATTGTTTTTCCTTGAACA
*
37245 AAGATTTTATCTAATTCAAGATTGTTTTTCCTTGAA-A
1 AAGATTTTATCT-ACTCAAGATTGTTTTTCCTTGAACA
*
37282 CAGAATTTTATCTCACTCAAGATTG----T--TTGAAACA
1 AAG-ATTTTATCT-ACTCAAGATTGTTTTTCCTTG-AACA
37316 GAAGATTTTATCT-CTTCAAGATTGTTTTTCCTTGGAACA
1 -AAGATTTTATCTAC-TCAAGATTGTTTTTCCTT-GAACA
37355 AAGATTTTATCTGACTCAAGATTGTTTTTCCTTGAACA
1 AAGATTTTATCT-ACTCAAGATTGTTTTTCCTTGAACA
*
37393 GAAGATTTTATCT-CTC-A-ATTGTTTTTCCTTGAAAA
1 -AAGATTTTATCTACTCAAGATTGTTTTTCCTTGAACA
37428 AAGATT
1 AAGATT
37434 ATTCTGAAAC
Statistics
Matches: 166, Mismatches: 6, Indels: 36
0.80 0.03 0.17
Matches are distributed among these distances:
32 4 0.02
33 11 0.07
34 17 0.10
35 19 0.11
36 12 0.07
37 7 0.04
38 58 0.35
39 36 0.22
40 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (37 bp):
AAGATTTTATCTACTCAAGATTGTTTTTCCTTGAACA
Found at i:37312 original size:32 final size:33
Alignment explanation
Indices: 37276--37342 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
37266 TTGTTTTTCC
37276 TTGAAACAG-A-ATTTTATCTCACTCAAGATTGT
1 TTGAAACAGAAGATTTTATCTC-CTCAAGATTGT
*
37308 TTGAAACAGAAGATTTTATCTCTTCAAGATTGT
1 TTGAAACAGAAGATTTTATCTCCTCAAGATTGT
37341 TT
1 TT
37343 TTCCTTGGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 9 0.28
33 13 0.41
34 10 0.31
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (33 bp):
TTGAAACAGAAGATTTTATCTCCTCAAGATTGT
Found at i:37374 original size:110 final size:109
Alignment explanation
Indices: 37205--37406 Score: 336
Period size: 110 Copynumber: 1.8 Consensus size: 109
37195 CTCATTTAAT
*
37205 ACAGAAGATTTTATCACTCAAGATTGTTTTTCCTTGAACAAAGATTTTATCTAATTCAAGATTGT
1 ACAGAAGATTTTATCACTCAAGATTGTTTTTCCTTGAACAAAGATTTTATCTAACTCAAGATTGT
37270 TTTTCCTTGAAACAG-A-ATTTTATCTCACTCAAGATTGTTTGAA
66 TTTTCCTTG-AACAGAAGATTTTATCTCACTCAAGATTGTTTGAA
* *
37313 ACAGAAGATTTTATCTCTTCAAGATTGTTTTTCCTTGGAACAAAGATTTTATCTGACTCAAGATT
1 ACAGAAGATTTTATCAC-TCAAGATTGTTTTTCCTT-GAACAAAGATTTTATCTAACTCAAGATT
37378 GTTTTTCCTTGAACAGAAGATTTTATCTC
64 GTTTTTCCTTGAACAGAAGATTTTATCTC
37407 TCAATTGTTT
Statistics
Matches: 87, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
108 16 0.18
109 23 0.26
110 38 0.44
111 10 0.11
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (109 bp):
ACAGAAGATTTTATCACTCAAGATTGTTTTTCCTTGAACAAAGATTTTATCTAACTCAAGATTGT
TTTTCCTTGAACAGAAGATTTTATCTCACTCAAGATTGTTTGAA
Found at i:37397 original size:22 final size:21
Alignment explanation
Indices: 37333--37399 Score: 54
Period size: 22 Copynumber: 3.3 Consensus size: 21
37323 TTATCTCTTC
37333 AAGATTGTTTTTCCTTGGAACA
1 AAGATTGTTTTTCCTT-GAACA
* *
37355 AAGA-T-TTTAT-C-TG-ACTC
1 AAGATTGTTTTTCCTTGAAC-A
37372 AAGATTGTTTTTCCTTGAACA
1 AAGATTGTTTTTCCTTGAACA
37393 GAAGATT
1 -AAGATT
37400 TTATCTCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
16 2 0.06
17 5 0.15
18 2 0.06
19 5 0.15
20 5 0.15
21 3 0.09
22 12 0.35
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.40
Consensus pattern (21 bp):
AAGATTGTTTTTCCTTGAACA
Found at i:37440 original size:72 final size:75
Alignment explanation
Indices: 37209--37433 Score: 276
Period size: 72 Copynumber: 3.1 Consensus size: 75
37199 TTTAATACAG
*
37209 AAGATTTTATC--ACTCAAGATTGTTTTTCCTTGAACA-AAGATTTTATCTAATTCAAGATTGTT
1 AAGATTTTATCTGACTCAAGATTGTTTTTCCTTGAACAGAAGATTTTATCT--CTCAAGATTGTT
37271 TTTCCTTG-AAA
64 TTTCCTTGAAAA
* *
37282 CAGAATTTTATCTCACTCAAGATTG----T--TTGAAACAGAAGATTTTATCTCTTCAAGATTGT
1 AAG-ATTTTATCTGACTCAAGATTGTTTTTCCTTG-AACAGAAGATTTTATCTC-TCAAGATTGT
*
37341 TTTTCCTTGGAACA
63 TTTTCCTT-GAAAA
37355 AAGATTTTATCTGACTCAAGATTGTTTTTCCTTGAACAGAAGATTTTATCTCTC-A-ATTGTTTT
1 AAGATTTTATCTGACTCAAGATTGTTTTTCCTTGAACAGAAGATTTTATCTCTCAAGATTGTTTT
37418 TCCTTGAAAA
66 TCCTTGAAAA
37428 AAGATT
1 AAGATT
37434 ATTCTGAAAC
Statistics
Matches: 132, Mismatches: 6, Indels: 28
0.80 0.04 0.17
Matches are distributed among these distances:
70 3 0.02
71 22 0.17
72 34 0.26
73 16 0.12
74 21 0.16
75 1 0.01
76 14 0.11
77 18 0.14
78 3 0.02
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (75 bp):
AAGATTTTATCTGACTCAAGATTGTTTTTCCTTGAACAGAAGATTTTATCTCTCAAGATTGTTTT
TCCTTGAAAA
Found at i:37504 original size:36 final size:36
Alignment explanation
Indices: 37456--37625 Score: 188
Period size: 36 Copynumber: 4.9 Consensus size: 36
37446 AAGATTTTCG
*
37456 CTTGAGATAGTTTCCCTTGAAACAAATTTTTTCTCT
1 CTTGAGACAGTTTCCCTTGAAACAAATTTTTTCTCT
* * * *
37492 CTTGATACAGTTTCCCTCG-AACAAGTTTTGTCTCT
1 CTTGAGACAGTTTCCCTTGAAACAAATTTTTTCTCT
* * *
37527 CTTAAGATAGTTTCCCTTGAAACAAA---TTT-TAT
1 CTTGAGACAGTTTCCCTTGAAACAAATTTTTTCTCT
* *
37559 CTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTTGAAACAAATTTTTTCTCT
* * *
37595 CTTGAGATAGTTTCTCTTGAAACAAGTTTTT
1 CTTGAGACAGTTTCCCTTGAAACAAATTTTT
37626 GATACAGTTT
Statistics
Matches: 108, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
32 26 0.24
33 2 0.02
35 31 0.29
36 49 0.45
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
CTTGAGACAGTTTCCCTTGAAACAAATTTTTTCTCT
Found at i:37614 original size:68 final size:67
Alignment explanation
Indices: 37456--37667 Score: 261
Period size: 68 Copynumber: 3.1 Consensus size: 67
37446 AAGATTTTCG
* *
37456 CTTGAGATAGTTTCCCTTGAAACAAATTTTTTCTCTCTTGATACAGTTTCCCTCG-AACAAGTTT
1 CTTGAGATAGTTTCCCTTGAAACAAA---TTT-T-TCTTGATACAGTTTCCCTTGAAACAAATTT
*
37520 TGTCTCT
61 TGTCTCC
* *
37527 CTTAAGATAGTTTCCCTTGAAACAAATTTTATCTTGAGACAGTTTCCCTTGAAACAAATTTTGTC
1 CTTGAGATAGTTTCCCTTGAAACAAATTTT-TCTTGATACAGTTTCCCTTGAAACAAATTTTGTC
37592 TCC
65 TCC
* * *
37595 CTTGAGATAGTTTCTCTTGAAAC-AA-GTTT-TTGATACAGTTTCTCTTGAAACAAAGTTTTGTC
1 CTTGAGATAGTTTCCCTTGAAACAAATTTTTCTTGATACAGTTTCCCTTGAAACAAA-TTTTGTC
37657 TCC
65 TCC
37660 CTTGAGAT
1 CTTGAGAT
37668 GGGTTTTCTT
Statistics
Matches: 128, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
64 23 0.18
65 19 0.15
66 2 0.02
67 21 0.16
68 38 0.30
71 25 0.20
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (67 bp):
CTTGAGATAGTTTCCCTTGAAACAAATTTTTCTTGATACAGTTTCCCTTGAAACAAATTTTGTCT
CC
Found at i:37773 original size:73 final size:71
Alignment explanation
Indices: 37624--37885 Score: 272
Period size: 73 Copynumber: 3.6 Consensus size: 71
37614 AAACAAGTTT
* * * * * * * * *
37624 TTGATACAGTTTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGATGGGTTTTCTTAAAACCAAGTT
1 TTGAGACAATTTCCCTTGAAACAAA-ATTTATCTCACTTGAGAT-GGTTTTTTTAAAACCTACTT
*
37689 CGTCTCAC
64 CGTCTCGC
* **
37697 TTGAGGCAACTTTCCCTTGAAACAAAATGAATCTCACTTGAGATGGTTTTTTTAAAACCTACTTC
1 TTGAGACAA-TTTCCCTTGAAACAAAATTTATCTCACTTGAGATGGTTTTTTTAAAACCTACTTC
* *
37762 ATCTGGGC
65 GTCT-CGC
* *
37770 TTGAGACAGTTTTCCTTTGAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCTACTT
1 TTGAGACA-ATTTCCCTTGAAACAAAATTTATCTCACTTGAGATGGTTTTT-TTAAAACCTACTT
*
37835 CGTCTTGC
64 CGTCTCGC
** *
37843 TTGAGACAATTTTACTTCGGAACAAAATTTATCTCACTTGAGA
1 TTGAGACAATTTCCCTT-GAAACAAAATTTATCTCACTTGAGA
37886 GTGCTTCTCT
Statistics
Matches: 157, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
72 26 0.17
73 99 0.63
74 32 0.20
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (71 bp):
TTGAGACAATTTCCCTTGAAACAAAATTTATCTCACTTGAGATGGTTTTTTTAAAACCTACTTCG
TCTCGC
Found at i:37811 original size:37 final size:37
Alignment explanation
Indices: 37769--37885 Score: 92
Period size: 37 Copynumber: 3.2 Consensus size: 37
37759 TTCATCTGGG
*
37769 CTTGAGACAGTTTTCCTTTGAAACAAAATTTATCTCA
1 CTTGAGACAGTTTTACTTTGAAACAAAATTTATCTCA
** * * ** * ** **
37806 CTTGAGATGGTTTTTC-TTAAAACCTACTTCGTCTTG
1 CTTGAGACAGTTTTACTTTGAAACAAAATTTATCTCA
* * *
37842 CTTGAGACAATTTTACTTCGGAACAAAATTTATCTCA
1 CTTGAGACAGTTTTACTTTGAAACAAAATTTATCTCA
37879 CTTGAGA
1 CTTGAGA
37886 GTGCTTCTCT
Statistics
Matches: 54, Mismatches: 25, Indels: 2
0.67 0.31 0.02
Matches are distributed among these distances:
36 24 0.44
37 30 0.56
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (37 bp):
CTTGAGACAGTTTTACTTTGAAACAAAATTTATCTCA
Found at i:38567 original size:20 final size:20
Alignment explanation
Indices: 38503--38568 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
38493 TTTCAGTGGA
38503 TTGTTCATAATGAGAAGAAC
1 TTGTTCATAATGAGAAGAAC
** * *
38523 -TCATC-CAATGAGGAAGAAG
1 TTGTTCATAATGA-GAAGAAC
**
38542 AAGTTCATAATGAGAAGAAC
1 TTGTTCATAATGAGAAGAAC
38562 TTGTTCA
1 TTGTTCA
38569 ACCTTTGTTC
Statistics
Matches: 32, Mismatches: 11, Indels: 6
0.65 0.22 0.12
Matches are distributed among these distances:
18 5 0.16
19 9 0.28
20 13 0.41
21 5 0.16
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (20 bp):
TTGTTCATAATGAGAAGAAC
Found at i:38640 original size:115 final size:106
Alignment explanation
Indices: 38287--38674 Score: 389
Period size: 112 Copynumber: 3.6 Consensus size: 106
38277 ACATTTCCAA
38287 TGAAGAGTTTCATAATG-GAAGAACTCATCC--TAAAGGAAAAGTTCATAATGAGAAGAACTTGT
1 TGAAGAG-TTCATAATGAGAAGAACTCATCCAATAAA-GAAAAGTTCATAATGAGAAGAACTTGT
* * * * *
38349 TCCTTTCAATTCACCACAGAAGAAGGTGAACCAATATTTTCC-
64 TCCTTTCATTTCATCACAGAAGGAGGTGAATCAACATTTTCCG
* * *
38391 AGAAGAGTTTATAATGAGAAGAACTCGTCC--TAAAGGAGAAAGTTCATAATGAGAAGAACTTGT
1 TGAAGAGTTCATAATGAGAAGAACTCATCCAATAAA-GA-AAAGTTCATAATGAGAAGAACTTGT
* * * *
38454 TCCTTTCAAGTTCCATCACAGAAAGAGGTGGATCAACATTTTCAG
64 TCCTTTC-A-TTTCATCACAGAAGGAGGTGAATCAACATTTTCCG
* **
38499 TGGATTGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
1 TGAAGAGTTCATAATGAGAAGAACTCATCCAAT-A--AAGAA-AAGTTCATAATGAGAAGAACTT
38564 GTTCAACCTTTGTTCGATTTCATCACAGAAGGAGGTGAATC-ACA-TTTCCG
62 GTT---CC--T-TTC-ATTTCATCACAGAAGGAGGTGAATCAACATTTTCCG
* *
38614 TGAAGAGTTCATAATGAGAAGAACTCATCTAACGAAA-AAGAAGTTCATAATGAGAAGAACT
1 TGAAGAGTTCATAATGAGAAGAACTCATCCAA-TAAAGAA-AAGTTCATAATGAGAAGAACT
38675 CATTCAACCT
Statistics
Matches: 238, Mismatches: 28, Indels: 28
0.81 0.10 0.10
Matches are distributed among these distances:
103 8 0.03
104 25 0.11
105 32 0.13
106 1 0.00
107 25 0.11
108 24 0.10
110 1 0.00
111 2 0.01
112 51 0.21
113 4 0.02
115 36 0.15
116 3 0.01
117 22 0.09
118 4 0.02
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (106 bp):
TGAAGAGTTCATAATGAGAAGAACTCATCCAATAAAGAAAAGTTCATAATGAGAAGAACTTGTTC
CTTTCATTTCATCACAGAAGGAGGTGAATCAACATTTTCCG
Found at i:42564 original size:17 final size:17
Alignment explanation
Indices: 42542--42582 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
42532 CAAATCTACT
42542 CAAACCCTCTTAAAGCC
1 CAAACCCTCTTAAAGCC
* *
42559 CAAACCCTCTTAATGCT
1 CAAACCCTCTTAAAGCC
42576 CAAACCC
1 CAAACCC
42583 GTTCAAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.34, C:0.41, G:0.05, T:0.20
Consensus pattern (17 bp):
CAAACCCTCTTAAAGCC
Found at i:44683 original size:3 final size:3
Alignment explanation
Indices: 44675--44731 Score: 69
Period size: 3 Copynumber: 19.0 Consensus size: 3
44665 TATCTACTCC
* * * * *
44675 TGA TGA TGA TGA TGA TGA TGA TGA TGG TGG TGG TGG TGA TGG TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
44723 TGA TGA TGA
1 TGA TGA TGA
44732 GAGTGAGGAG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:47287 original size:60 final size:60
Alignment explanation
Indices: 47193--47306 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
47183 CCATGCTGTC
* * * * * * *
47193 GACATTTAGGTCGAAAAAGCTGGTAGTTGCATGCCTTCTCCTTGAACTTGAAGGAATCTT
1 GACATTGAGGTCGAAAAAGCTCGCAGTTGAATGCCTCCCCCTGGAACTTGAAGGAATCTT
* * *
47253 GACATTGAGGTCGAAGAATCTCGCAGTTGAATGCCTCCCCCTGGATCTTGAAGG
1 GACATTGAGGTCGAAAAAGCTCGCAGTTGAATGCCTCCCCCTGGAACTTGAAGG
47307 CATCGTGTCA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.28
Consensus pattern (60 bp):
GACATTGAGGTCGAAAAAGCTCGCAGTTGAATGCCTCCCCCTGGAACTTGAAGGAATCTT
Found at i:50094 original size:25 final size:24
Alignment explanation
Indices: 50024--50153 Score: 106
Period size: 25 Copynumber: 5.3 Consensus size: 24
50014 TTTTCAAAAC
* *
50024 TTCATCAAACATTTTTTTAAAATTAT
1 TTCAT-AAA-ATTTCTTCAAAATTAT
* *
50050 TTGATCAACA-TTCTTCAAAATTAT
1 TTCAT-AAAATTTCTTCAAAATTAT
50074 TTCATAAAATGTTCTTCAAAATTAT
1 TTCATAAAAT-TTCTTCAAAATTAT
* *
50099 TTCAT-CAATTTC-TCAAAATTCT
1 TTCATAAAATTTCTTCAAAATTAT
* *
50121 TTTATCAAAAATTT-TTCAAAATTCT
1 TTCAT--AAAATTTCTTCAAAATTAT
50146 TTCATAAA
1 TTCATAAA
50154 TATTGTCAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
22 13 0.15
23 9 0.10
24 19 0.22
25 39 0.45
26 7 0.08
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.45
Consensus pattern (24 bp):
TTCATAAAATTTCTTCAAAATTAT
Found at i:50139 original size:47 final size:49
Alignment explanation
Indices: 50024--50150 Score: 136
Period size: 47 Copynumber: 2.6 Consensus size: 49
50014 TTTTCAAAAC
* * *
50024 TTCATCAAACATTTTTTTAAAATTATTTGATCAACATTCTTCAAAATTAT
1 TTCATCAAA-AATTTTTCAAAATTATTTCATCAACATTCTTCAAAATTAT
* *
50074 TTCAT--AAAATGTTCTTCAAAATTATTTCATCAA-TTTC-TCAAAATTCT
1 TTCATCAAAAAT-TT-TTCAAAATTATTTCATCAACATTCTTCAAAATTAT
* *
50121 TTTATCAAAAATTTTTCAAAATTCTTTCAT
1 TTCATCAAAAATTTTTCAAAATTATTTCAT
50151 AAATATTGTC
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
47 30 0.45
48 9 0.14
49 22 0.33
50 5 0.08
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (49 bp):
TTCATCAAAAATTTTTCAAAATTATTTCATCAACATTCTTCAAAATTAT
Found at i:57969 original size:15 final size:15
Alignment explanation
Indices: 57948--57986 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
57938 GTATTTATTT
57948 ATCTTTATTATCTT-
1 ATCTTTATTATCTTG
*
57962 AGTCTTTATTGTCTTG
1 A-TCTTTATTATCTTG
57978 ATCTTTATT
1 ATCTTTATT
57987 TTTGATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.18, C:0.13, G:0.08, T:0.62
Consensus pattern (15 bp):
ATCTTTATTATCTTG
Found at i:66446 original size:3 final size:3
Alignment explanation
Indices: 66438--66472 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
66428 CATTAGACGA
66438 TTC TTC TTC TTC -TC TTC TTC TTTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TT
66473 TTTTTTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:68811 original size:20 final size:20
Alignment explanation
Indices: 68786--68826 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
68776 AATATGAGAT
*
68786 TATTTGAGACATAGCACAAA
1 TATTTGAGACATAGAACAAA
*
68806 TATTTGAGAGATAGAACAAA
1 TATTTGAGACATAGAACAAA
68826 T
1 T
68827 GCAAAATAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (20 bp):
TATTTGAGACATAGAACAAA
Done.