Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009179.1 Hibiscus syriacus cultivar Beakdansim tig00112746_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: 314897
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:189712 original size:3 final size:3
Alignment explanation
Indices: 189706--189751 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
189696 TAATATTTAT
189706 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
189750 TA
1 TA
189752 TTTAAATGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.10
3 34 0.85
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:191195 original size:34 final size:33
Alignment explanation
Indices: 191099--191196 Score: 80
Period size: 32 Copynumber: 3.0 Consensus size: 33
191089 GTTGGCATGG
191099 GTATGATCATGGGAGACATCTACTAGTGGCAAA
1 GTATGATCATGGGAGACATCTACTAGTGGCAAA
* * * *
191132 GTAATGGGTTAT-GGAG-C-TGCT--TGGTTGGCACGA
1 GT-AT-GATCATGGGAGACAT-CTACTAG-TGGCA-AA
191165 GTATGATCATGGGAGACATCTACTAGTGGCAA
1 GTATGATCATGGGAGACATCTACTAGTGGCAA
191197 GGTGATGTGG
Statistics
Matches: 47, Mismatches: 8, Indels: 20
0.63 0.11 0.27
Matches are distributed among these distances:
31 6 0.13
32 12 0.26
33 11 0.23
34 12 0.26
35 6 0.13
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.27
Consensus pattern (33 bp):
GTATGATCATGGGAGACATCTACTAGTGGCAAA
Found at i:193052 original size:87 final size:87
Alignment explanation
Indices: 192901--193079 Score: 349
Period size: 87 Copynumber: 2.1 Consensus size: 87
192891 TGTTGATATT
*
192901 TTCCGTAATTGCAACTGGAATTGTGAATAATGATAAGAAGAAAAGCGGTAGGTTGAATAAAACTG
1 TTCCATAATTGCAACTGGAATTGTGAATAATGATAAGAAGAAAAGCGGTAGGTTGAATAAAACTG
192966 ACAAGAATAAAGTTATTCACCC
66 ACAAGAATAAAGTTATTCACCC
192988 TTCCATAATTGCAACTGGAATTGTGAATAATGATAAGAAGAAAAGCGGTAGGTTGAATAAAACTG
1 TTCCATAATTGCAACTGGAATTGTGAATAATGATAAGAAGAAAAGCGGTAGGTTGAATAAAACTG
193053 ACAAGAATAAAGTTATTCACCC
66 ACAAGAATAAAGTTATTCACCC
193075 TTCCA
1 TTCCA
193080 ACAATAAGGT
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 91 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (87 bp):
TTCCATAATTGCAACTGGAATTGTGAATAATGATAAGAAGAAAAGCGGTAGGTTGAATAAAACTG
ACAAGAATAAAGTTATTCACCC
Found at i:195302 original size:13 final size:14
Alignment explanation
Indices: 195286--195320 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
195276 TTACATTAGT
195286 TTAATATTTATT-A
1 TTAATATTTATTAA
*
195299 TTAAGATTTATTAA
1 TTAATATTTATTAA
195313 TTAATATT
1 TTAATATT
195321 AAATATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
TTAATATTTATTAA
Found at i:195311 original size:28 final size:27
Alignment explanation
Indices: 195266--195320 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
195256 ACTTATACAC
*
195266 TATTATTAAATTACATTAGTTTAATATT
1 TATTATTAAATTACATTA-ATTAATATT
*
195294 TATTATTAAGATT-TATTAATTAATATT
1 TATTATTAA-ATTACATTAATTAATATT
195321 AAATATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.33
28 13 0.54
29 3 0.12
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (27 bp):
TATTATTAAATTACATTAATTAATATT
Found at i:196625 original size:29 final size:29
Alignment explanation
Indices: 196583--196671 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
196573 TACCGGGGGT
*
196583 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
***
196612 AGGTCGCCATGCACGCCCAGCGACCTGGT
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* *
196641 AGGTCGCCATGCATGCCCTGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
196670 AG
1 AG
196672 CCAACGACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.18, C:0.40, G:0.28, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:196701 original size:10 final size:10
Alignment explanation
Indices: 196686--196743 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
196676 CGACCTCCAT
196686 GCCCATGCAC
1 GCCCATGCAC
196696 GCCCATGCAC
1 GCCCATGCAC
*
196706 GCCCAT-CTC
1 GCCCATGCAC
* *
196715 GCCAAAGGAGCAC
1 GCC-CA--TGCAC
196728 GCCCATGCAC
1 GCCCATGCAC
196738 GCCCAT
1 GCCCAT
196744 CCATGCCCTG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 5 0.13
10 27 0.71
12 1 0.03
13 5 0.13
ACGTcount: A:0.22, C:0.47, G:0.21, T:0.10
Consensus pattern (10 bp):
GCCCATGCAC
Found at i:198664 original size:113 final size:114
Alignment explanation
Indices: 198530--198744 Score: 330
Period size: 113 Copynumber: 1.9 Consensus size: 114
198520 CATTTCAATA
* * *
198530 AAAAGATATTAATTTAATTTATGACGGGACAATGATTC-GATC-AGAAATTTTGTTTAACTTTAA
1 AAAAGATATCAATTTAATTTATGACGGGACAATAATTCTG-TCGA-AAATTTTGTTCAACTTTAA
*
198593 TTAAAATATATCAATTTAATTTGTAAT-GAAATAATCATTCCATCGGAAATT
64 TTAAAATATACCAATTTAATTTGTAATAG-AATAATCATTCCATCGGAAATT
198644 AAAA-ATATCAATTTAATTTATGACGGGACAATAATTCTGTCGAAAATTTTGTTCAACTTTAATT
1 AAAAGATATCAATTTAATTTATGACGGGACAATAATTCTGTCGAAAATTTTGTTCAACTTTAATT
*
198708 AAAATATACCAATTTAATTTGTGATAGAATAATCATT
66 AAAATATACCAATTTAATTTGTAATAGAATAATCATT
198745 ATGTAGAAAA
Statistics
Matches: 93, Mismatches: 5, Indels: 7
0.89 0.05 0.07
Matches are distributed among these distances:
113 86 0.92
114 7 0.08
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (114 bp):
AAAAGATATCAATTTAATTTATGACGGGACAATAATTCTGTCGAAAATTTTGTTCAACTTTAATT
AAAATATACCAATTTAATTTGTAATAGAATAATCATTCCATCGGAAATT
Found at i:205876 original size:22 final size:22
Alignment explanation
Indices: 205848--205934 Score: 119
Period size: 22 Copynumber: 4.1 Consensus size: 22
205838 CATCCTGAAA
*
205848 GACCACTGTATACGTCCCGAAG
1 GACCACTGGATACGTCCCGAAG
*
205870 GACCACTGGATACGTCCCAAAG
1 GACCACTGGATACGTCCCGAAG
*
205892 GACCACT--AT--GTCCCGAAA
1 GACCACTGGATACGTCCCGAAG
205910 GACCACTGGATACGTCCCGAAG
1 GACCACTGGATACGTCCCGAAG
205932 GAC
1 GAC
205935 TAATATACCC
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
18 14 0.25
20 4 0.07
22 38 0.68
ACGTcount: A:0.30, C:0.32, G:0.23, T:0.15
Consensus pattern (22 bp):
GACCACTGGATACGTCCCGAAG
Found at i:210544 original size:22 final size:22
Alignment explanation
Indices: 210519--210636 Score: 181
Period size: 22 Copynumber: 5.5 Consensus size: 22
210509 GGACTGCTAT
*
210519 GTCCCGAAGGACCACTGTATAC
1 GTCCCGAAGGACCACTGGATAC
210541 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
210563 GTCCCGAAGGACCACT--AT--
1 GTCCCGAAGGACCACTGGATAC
210581 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
210603 GTCCCAAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
*
210625 ATCCCGAAGGAC
1 GTCCCGAAGGAC
210637 TAATATACCC
Statistics
Matches: 88, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.18
20 4 0.05
22 68 0.77
ACGTcount: A:0.29, C:0.32, G:0.25, T:0.14
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:210585 original size:40 final size:41
Alignment explanation
Indices: 210519--210636 Score: 157
Period size: 40 Copynumber: 2.8 Consensus size: 41
210509 GGACTGCTAT
210519 GTCCCGAAGGACCACTGTATACGTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCAC--TATA-GTCCCGAAGGACCACTGGATAC
210563 GTCCCGAAGGACCACTAT-GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTATAGTCCCGAAGGACCACTGGATAC
* *
210603 GTCCCAAAGGACCACTGGATACATCCCGAAGGAC
1 GTCCCGAAGGACCACT--ATA-GTCCCGAAGGAC
210637 TAATATACCC
Statistics
Matches: 68, Mismatches: 2, Indels: 8
0.87 0.03 0.10
Matches are distributed among these distances:
40 37 0.54
42 5 0.07
44 26 0.38
ACGTcount: A:0.29, C:0.32, G:0.25, T:0.14
Consensus pattern (41 bp):
GTCCCGAAGGACCACTATAGTCCCGAAGGACCACTGGATAC
Found at i:210597 original size:62 final size:62
Alignment explanation
Indices: 210500--210636 Score: 229
Period size: 62 Copynumber: 2.2 Consensus size: 62
210490 GTTTAGTATT
** * *
210500 CGTCCCGAAGGACTGCTATGTCCCGAAGGACCACTGTATACGTCCCGAAGGACCACTGGATA
1 CGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGGATACGTCCCAAAGGACCACTGGATA
210562 CGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGGATACGTCCCAAAGGACCACTGGATA
1 CGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGGATACGTCCCAAAGGACCACTGGATA
*
210624 CATCCCGAAGGAC
1 CGTCCCGAAGGAC
210637 TAATATACCC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 70 1.00
ACGTcount: A:0.28, C:0.32, G:0.25, T:0.15
Consensus pattern (62 bp):
CGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGGATACGTCCCAAAGGACCACTGGATA
Found at i:211062 original size:22 final size:24
Alignment explanation
Indices: 211019--211063 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
211009 CACTTATTTC
*
211019 ATATTAATTATATTCTAGTTTCAT
1 ATATTAATTATATTCTAATTTCAT
*
211043 ATATTACTTA-ATTC-AATTTCA
1 ATATTAATTATATTCTAATTTCA
211064 CATAGCTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 4 0.21
24 9 0.47
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (24 bp):
ATATTAATTATATTCTAATTTCAT
Found at i:214282 original size:54 final size:54
Alignment explanation
Indices: 214224--214404 Score: 238
Period size: 54 Copynumber: 3.4 Consensus size: 54
214214 TTTTTTGAGG
* **
214224 TGCACACGTAGTGCCGATACGGTTGTTCATAAACATATTATGAATTCTATGGGT
1 TGCACACTTAGTGCCGATACGGTTGTTCATAAACATATTATGAATTCCGTGGGT
** * *
214278 TGCACACTTAGTGTTGATATGGTCGTTCATAAACATATTATGAATTCCGTGGGT
1 TGCACACTTAGTGCCGATACGGTTGTTCATAAACATATTATGAATTCCGTGGGT
* * *
214332 TACACACTTATTGCCGATACAGTCT-TTCATAAACATATTATGAATTCCGTGGGT
1 TGCACACTTAGTGCCGATACGGT-TGTTCATAAACATATTATGAATTCCGTGGGT
* *
214386 TGCATACTCAGTGCCGATA
1 TGCACACTTAGTGCCGATA
214405 GTACACGTAG
Statistics
Matches: 108, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 108 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (54 bp):
TGCACACTTAGTGCCGATACGGTTGTTCATAAACATATTATGAATTCCGTGGGT
Found at i:215689 original size:3 final size:3
Alignment explanation
Indices: 215681--215757 Score: 127
Period size: 3 Copynumber: 25.7 Consensus size: 3
215671 TTCGTCCCGC
* * *
215681 TAT TAT TAT TAC TAC TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
215729 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
215758 GTAATAGTAG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:217889 original size:131 final size:131
Alignment explanation
Indices: 217741--218096 Score: 453
Period size: 131 Copynumber: 2.7 Consensus size: 131
217731 CGATATTAAG
* * *
217741 AATAGTAATATTTCTTCATTTTGGTTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATT
1 AATAGTGATATCTCTTCATTTTGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATT
* * * * *
217806 TATTCTCGATTGGAAAT-AGATCGATATTACCGTTTTCTCTCGAATCAATATTGATTTTTAAGAC
66 TATTCTCAATTGGAAATCA-ATAGATATTACCGTTTTCACTCAAATCAATATTGAATTTTAAGAC
*
217870 GA
130 AA
* * * *
217872 AATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGTATAAGAGGTCATA
1 AATAGTGATATCTCTTCATTTTGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATT
* * * *
217937 TATTCTCAATTGGAAATCATTAGATATTATCTTTTTCACTCAAATCAATATTTAATTTTAAGACA
66 TATTCTCAATTGGAAATCAATAGATATTACCGTTTTCACTCAAATCAATATTGAATTTTAAGACA
218002 A
131 A
* * * * * * *
218003 AATAATGATATCTCTTAATTTTAATTGGAGTAATAAATGATTGTTTTAAGGCATGAAAGATCATT
1 AATAGTGATATCTCTTCATTTTGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATT
* * *
218068 CATTCTCAATCGGAAATCATTAGATATTA
66 TATTCTCAATTGGAAATCAATAGATATTA
218097 TCATTTTCTC
Statistics
Matches: 194, Mismatches: 30, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
131 193 0.99
132 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.39
Consensus pattern (131 bp):
AATAGTGATATCTCTTCATTTTGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATT
TATTCTCAATTGGAAATCAATAGATATTACCGTTTTCACTCAAATCAATATTGAATTTTAAGACA
A
Found at i:223424 original size:18 final size:19
Alignment explanation
Indices: 223403--223441 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
223393 ATAAAAAGAG
*
223403 AAAAAGTCAAAAAATT-AA
1 AAAAAATCAAAAAATTGAA
*
223421 AAAAAATCAAGAAATTGAA
1 AAAAAATCAAAAAATTGAA
223440 AA
1 AA
223442 CGAAGGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.72, C:0.05, G:0.08, T:0.15
Consensus pattern (19 bp):
AAAAAATCAAAAAATTGAA
Found at i:224549 original size:14 final size:14
Alignment explanation
Indices: 224542--224570 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
224532 ATTTCCTTTG
224542 ATTAATTTCCAATA
1 ATTAATTTCCAATA
224556 ATTAATTTCCAATA
1 ATTAATTTCCAATA
224570 A
1 A
224571 CCCTAAATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTAATTTCCAATA
Found at i:226102 original size:54 final size:54
Alignment explanation
Indices: 226044--226222 Score: 234
Period size: 54 Copynumber: 3.3 Consensus size: 54
226034 TTTTGAGGTA
* *
226044 CACACGTAGTGCCGATACGGTTGTTCATAAACATATTATGAATTCTATGGGTTG
1 CACACTTAGTGCCGATACGGTTGTTCATAAACATATTATGAATTCTGTGGGTTG
** * * *
226098 CACACTTAGTGTTGATATGGTCGTTCATAAACATATTATGAATTCTGTGGGTTA
1 CACACTTAGTGCCGATACGGTTGTTCATAAACATATTATGAATTCTGTGGGTTG
* * *
226152 CACACTTATTGCCGATACAGTCT-TTCATAAACATATTATGAATTCCGTGGGTTG
1 CACACTTAGTGCCGATACGGT-TGTTCATAAACATATTATGAATTCTGTGGGTTG
* *
226206 CATACTCAGTGCCGATA
1 CACACTTAGTGCCGATA
226223 GTACACGTAG
Statistics
Matches: 106, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
54 106 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (54 bp):
CACACTTAGTGCCGATACGGTTGTTCATAAACATATTATGAATTCTGTGGGTTG
Found at i:226328 original size:13 final size:15
Alignment explanation
Indices: 226300--226331 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
226290 TACATAACAA
226300 ATGCACTCACCTAGT
1 ATGCACTCACCTAGT
226315 ATGC-CTCA-CTAGT
1 ATGCACTCACCTAGT
226328 ATGC
1 ATGC
226332 TGCAAATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 4 0.24
15 4 0.24
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.28
Consensus pattern (15 bp):
ATGCACTCACCTAGT
Found at i:229674 original size:131 final size:131
Alignment explanation
Indices: 229525--229880 Score: 473
Period size: 131 Copynumber: 2.7 Consensus size: 131
229515 CGATATTAAG
* * *
229525 AATAGTAATATTTCTTCATTTTGGTTGGAGTAATAAATGACTGCTTTAAGGCATGAAAGGTCATT
1 AATAGTGATATCTCTTCATTTTGATTGGAGTAATAAATGACTGCTTTAAGGCATGAAAGGTCATT
* * * * *
229590 TATTCTCGATTGGAAAT-AGATCGATATTACCGTTTTCTCTCGAATCAATATTGATTTTTAAGAC
66 TATTCTCAATTGGAAATCA-ATAGATATTACCGTTTTCACTCAAATCAATATTGAATTTTAAGAC
*
229654 GA
130 AA
*
229656 AATAGTGATATCTCTTCATTTTGATTGGAGTAATAAATGACTGCTTTAAGGTAT-AAGAGGTCAT
1 AATAGTGATATCTCTTCATTTTGATTGGAGTAATAAATGACTGCTTTAAGGCATGAA-AGGTCAT
* * * *
229720 ATATTCTCAATTTGAAATCATTAGATATTATCGTTTTCACTCAAATCAATATTGAATTTTAAGAC
65 TTATTCTCAATTGGAAATCAATAGATATTACCGTTTTCACTCAAATCAATATTGAATTTTAAGAC
229785 AA
130 AA
* * * * * * *
229787 AATAATGATATCTCTTAATTTTAATTTGAATAATAAATGACTGTTTTAAGGCATGAAAGATCATT
1 AATAGTGATATCTCTTCATTTTGATTGGAGTAATAAATGACTGCTTTAAGGCATGAAAGGTCATT
* *
229852 TATTCTCAATCGGAAATCATTAGATATTA
66 TATTCTCAATTGGAAATCAATAGATATTA
229881 TCATTTTCTC
Statistics
Matches: 197, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
130 2 0.01
131 192 0.97
132 3 0.02
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (131 bp):
AATAGTGATATCTCTTCATTTTGATTGGAGTAATAAATGACTGCTTTAAGGCATGAAAGGTCATT
TATTCTCAATTGGAAATCAATAGATATTACCGTTTTCACTCAAATCAATATTGAATTTTAAGACA
A
Found at i:235235 original size:18 final size:18
Alignment explanation
Indices: 235188--235235 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
235178 AGCAATGCAT
* *
235188 AAAAAGAGAAAAAAGTCA
1 AAAAATAGAAAAAAATCA
*
235206 AAAAATAAAAAAAAATCA
1 AAAAATAGAAAAAAATCA
* *
235224 AGAAATTGAAAA
1 AAAAATAGAAAA
235236 CGAAGGAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.75, C:0.04, G:0.10, T:0.10
Consensus pattern (18 bp):
AAAAATAGAAAAAAATCA
Found at i:240777 original size:7 final size:7
Alignment explanation
Indices: 240767--240823 Score: 50
Period size: 7 Copynumber: 8.7 Consensus size: 7
240757 AAAAAGAGAA
240767 AAAAATG
1 AAAAATG
240774 -AAAA-G
1 AAAAATG
*
240779 AAATATG
1 AAAAATG
*
240786 AAATATG
1 AAAAATG
*
240793 AAAAAAG
1 AAAAATG
*
240800 AAAGA--
1 AAAAATG
240805 AAAAATG
1 AAAAATG
240812 AAAAATG
1 AAAAATG
240819 AAAAA
1 AAAAA
240824 GAGAATAAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
5 5 0.12
6 7 0.17
7 29 0.71
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:240812 original size:19 final size:18
Alignment explanation
Indices: 240756--240823 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 18
240746 TCAAAGAAGA
*
240756 AAAAAAGAGAAAAAAATG
1 AAAAAAGAAAAAAAAATG
*
240774 --AAAAGAAATATGAAATATG
1 AAAAAAGAAA-A--AAAAATG
240793 AAAAAAGAAAGAAAAAATG
1 AAAAAAGAAA-AAAAAATG
*
240812 AAAAATGAAAAA
1 AAAAAAGAAAAA
240824 GAGAATAAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
16 7 0.17
17 1 0.03
18 2 0.05
19 21 0.52
21 9 0.22
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (18 bp):
AAAAAAGAAAAAAAAATG
Found at i:240812 original size:26 final size:26
Alignment explanation
Indices: 240766--240828 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 26
240756 AAAAAAGAGA
* *
240766 AAAAAATGAAAAGAAATATGAAATATG
1 AAAAAA-GAAAAGAAAAATGAAAAATG
240793 AAAAAAG-AAAGAAAAAATGAAAAATG
1 AAAAAAGAAAAG-AAAAATGAAAAATG
240819 AAAAAGAGAA
1 AAAAA-AGAA
240829 TAAGGAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 4 0.13
26 18 0.58
27 8 0.26
28 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (26 bp):
AAAAAAGAAAAGAAAAATGAAAAATG
Found at i:240858 original size:41 final size:40
Alignment explanation
Indices: 240751--240858 Score: 100
Period size: 41 Copynumber: 2.6 Consensus size: 40
240741 TCGCATCAAA
* *
240751 GAAGAAAAAAAGAGAAAAAAATGAAAA-GAAATATGAAATAT
1 GAAGAAAAAAAGAG--AAAAATGAAAATGAAATAAGAAATAG
240792 GAA-AAAAGAAAGA-AAAAATGAAAAATGAAA-AAGAGAATAAG
1 GAAGAAAA-AAAGAGAAAAATG-AAAATGAAATAAGA-AAT-AG
240833 GAAGAAAAAAAGAGAATAAAT-AAAAT
1 GAAGAAAAAAAGAGAA-AAATGAAAAT
240859 AGGGGTTCAA
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
38 7 0.12
39 7 0.12
40 11 0.19
41 22 0.39
42 6 0.11
43 4 0.07
ACGTcount: A:0.72, C:0.00, G:0.18, T:0.10
Consensus pattern (40 bp):
GAAGAAAAAAAGAGAAAAATGAAAATGAAATAAGAAATAG
Found at i:242400 original size:93 final size:94
Alignment explanation
Indices: 242237--242429 Score: 230
Period size: 93 Copynumber: 2.1 Consensus size: 94
242227 CATGATTCAA
* * *
242237 TCTTCTCTGAAGAACAATGGAATGAATCAATGTCCCTAAATATAATTTTATCTAAAGAAAAAGTG
1 TCTTCCCTGAAGAACAATGGAATGAATCAACGTCCCTAAATATAATTTTATCTAAAGAAAAAGTC
*
242302 AAACAAAT-CCCTCTTTTTCTAGATCTGG
66 AAACAAATCCCCTCTATTTCTAGATCTGG
* * * * * * *
242330 TCTTCCCTTAAGAACAATGGAATGAATCAACGTCCCTAGATTTGATTTT-CCTTGAAGAAACAG-
1 TCTTCCCTGAAGAACAATGGAATGAATCAACGTCCCTAAATATAATTTTATC-TAAAGAAAAAGT
*
242393 CATAACAAATCCCCTCTATTTCTAGATTTGG
65 CA-AACAAATCCCCTCTATTTCTAGATCTGG
*
242424 TTTTCC
1 TCTTCC
242430 TTGAGTAGCA
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
92 2 0.02
93 59 0.70
94 23 0.27
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (94 bp):
TCTTCCCTGAAGAACAATGGAATGAATCAACGTCCCTAAATATAATTTTATCTAAAGAAAAAGTC
AAACAAATCCCCTCTATTTCTAGATCTGG
Found at i:242729 original size:133 final size:133
Alignment explanation
Indices: 242330--242765 Score: 475
Period size: 135 Copynumber: 3.2 Consensus size: 133
242320 CTAGATCTGG
* * *
242330 TCTTCCCTTAAGAACAATGGAATGAATCAACGTC-CCTAGATTTGATTTTCCTTGAAGAAACAGC
1 TCTTCCCTGAAGAACAATGGAATGAATCAACATCTCC-AGATTTGATTTTCCCTGAAGAAACAGC
* * * * *
242394 -ATAACAAATCCCCTCTATTTCTAGATTTGGTTTTCCTTGAGTAGCAGTGGAACAAGTCTGCATC
65 GA-AATAAATCCCCTC--TTTCTAGATTTGATCTTCCTTGAGTAGAAGTGGAACAAGTCTGCCTC
242458 GA-TCTAA
127 GATTC-AA
* * * * * *
242465 CCTTCCCTGAGGAACAATGGAATGAATCAACGT-TCCCAAATTTGATTTTCCCTTAAGAAACATC
1 TCTTCCCTGAAGAACAATGGAATGAATCAACATCT-CCAGATTTGATTTTCCCTGAAGAAACAGC
* * * * *
242529 GAAATATATCCAATCTCTTTCCAGATTTGATCTTCCTTGAGTAGAAGTGGAACAAGCCTGCCACG
65 GAAATAAATCC--CCTCTTTCTAGATTTGATCTTCCTTGAGTAGAAGTGGAACAAGTCTGCCTCG
242594 ATTCAA
128 ATTCAA
* * * * * *
242600 TCTTCCCTGAAGAATAGTGGAATGAATCAACATCTCCAGATATGATTTCCCCCGAAGAAGCAGCG
1 TCTTCCCTGAAGAACAATGGAATGAATCAACATCTCCAGATTTGATTTTCCCTGAAGAAACAGCG
* * * *
242665 AAATAGATCCCCTCTTTCTAGATTTGATCTTCCATGAGCAGTAGTGGAACAAGTCTGCCTCGATT
66 AAATAAATCCCCTCTTTCTAGATTTGATCTTCCTTGAGTAGAAGTGGAACAAGTCTGCCTCGATT
242730 CAA
131 CAA
* * * *
242733 TCTCCCCTGAAGAATATTGGAATTAATCAACAT
1 TCTTCCCTGAAGAACAATGGAATGAATCAACAT
242766 TTCTTGATCT
Statistics
Matches: 254, Mismatches: 40, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
133 81 0.32
135 164 0.65
136 6 0.02
137 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (133 bp):
TCTTCCCTGAAGAACAATGGAATGAATCAACATCTCCAGATTTGATTTTCCCTGAAGAAACAGCG
AAATAAATCCCCTCTTTCTAGATTTGATCTTCCTTGAGTAGAAGTGGAACAAGTCTGCCTCGATT
CAA
Found at i:242790 original size:133 final size:133
Alignment explanation
Indices: 242543--242795 Score: 335
Period size: 133 Copynumber: 1.9 Consensus size: 133
242533 TATATCCAAT
* * *
242543 CTCTTTCCAGATTTGATCTTCCTTGAGTAGAAGTGGAACAAGCCTGCCACGATTCAATCTTCCCT
1 CTCTTTCCAGATTTGATCTTCCATGAGCAGAAGTGGAACAAGCCTGCCACGATTCAATCTCCCCT
* ** *
242608 GAAGAATAGTGGAATGAATCAACATCTCCAGATATGATTTCCCCCGAAGAAGCAGCGAAATAGAT
66 GAAGAATAGTGGAATGAATCAACATCTCCAGATATGATCTAACACGAAGAAGCAGCGAAATAGAT
242673 CCC
131 CCC
* * * *
242676 CTCTTTCTAGATTTGATCTTCCATGAGCAGTAGTGGAACAAGTCTGCCTCGATTCAATCTCCCCT
1 CTCTTTCCAGATTTGATCTTCCATGAGCAGAAGTGGAACAAGCCTGCCACGATTCAATCTCCCCT
* * * ** * * *
242741 GAAGAATATTGGAATTAATCAACATTTCTTGATCTGATCTAATATGAAGAAGCAG
66 GAAGAATAGTGGAATGAATCAACATCTCCAGATATGATCTAACACGAAGAAGCAG
242796 TGGAGCAGAT
Statistics
Matches: 101, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
133 101 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (133 bp):
CTCTTTCCAGATTTGATCTTCCATGAGCAGAAGTGGAACAAGCCTGCCACGATTCAATCTCCCCT
GAAGAATAGTGGAATGAATCAACATCTCCAGATATGATCTAACACGAAGAAGCAGCGAAATAGAT
CCC
Found at i:246929 original size:28 final size:29
Alignment explanation
Indices: 246890--246954 Score: 123
Period size: 28 Copynumber: 2.3 Consensus size: 29
246880 CCTCAATAGC
246890 AATAATCTTATTTTGGACTAGTTTGATT-
1 AATAATCTTATTTTGGACTAGTTTGATTA
246918 AATAATCTTATTTTGGACTAGTTTGATTA
1 AATAATCTTATTTTGGACTAGTTTGATTA
246947 AATAATCT
1 AATAATCT
246955 CATCTTTGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 28 0.78
29 8 0.22
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (29 bp):
AATAATCTTATTTTGGACTAGTTTGATTA
Found at i:250982 original size:5 final size:5
Alignment explanation
Indices: 250972--250998 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
250962 CCAGCCCCCG
250972 GAGAT GAGAT GAGAT GAGAT GAGAT GA
1 GAGAT GAGAT GAGAT GAGAT GAGAT GA
250999 TGGAAGGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.19
Consensus pattern (5 bp):
GAGAT
Found at i:258899 original size:2 final size:2
Alignment explanation
Indices: 258892--258921 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
258882 ATAATTTTTA
258892 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
258922 TACATGGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:261831 original size:131 final size:131
Alignment explanation
Indices: 261466--261824 Score: 459
Period size: 131 Copynumber: 2.7 Consensus size: 131
261456 ATCGATATTG
* * * * ** *
261466 AGAATAATAATATATTTTCATTTCGATTGGAGTAATAAATGACTGCTTGAAGGCGTGAGAGGTCA
1 AGAATAATGATATCTTTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGTATGAGAGGTCG
* ** * * *
261531 TTTATTCTCGATTAGAAATAATTTGATATCGTCGTTTTCTCTCGGATTAATATTGATTTTTAGGA
66 TTTATTCTCGATTAGAAATAATTAGATATTATCGTTTTCACTCGGATCAATATTGAATTTTAGGA
*
261596 T
131 C
* * * * * *
261597 GGAATAGTGATATCTCTTCATTTCGATTGGAGCAATAAATGTATGCTTTAAGGTATGAGAAGTCA
1 AGAATAATGATATCTTTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGTATGAGAGGTC-
* * *
261662 G-TTATTATCGATTAGAAATTATTAGATATTATCGTTTTCACTCGGATCAGTATTGAATTTTAGG
65 GTTTATTCTCGATTAGAAATAATTAGATATTATCGTTTTCACTCGGATCAATATTGAATTTTAGG
261726 AC
130 AC
* * *
261728 AGAATAATGACATCTTTTCATTTTGATTGGAGTAATAAATGAATGTTTTAAGGTATGAGAGGTCG
1 AGAATAATGATATCTTTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGTATGAGAGGTCG
*
261793 TTTATTCTCGATTGGAAATAATTAGATATTAT
66 TTTATTCTCGATTAGAAATAATTAGATATTAT
261825 TATTTTCTCT
Statistics
Matches: 191, Mismatches: 35, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
130 1 0.01
131 190 0.99
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (131 bp):
AGAATAATGATATCTTTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGTATGAGAGGTCG
TTTATTCTCGATTAGAAATAATTAGATATTATCGTTTTCACTCGGATCAATATTGAATTTTAGGA
C
Found at i:265521 original size:11 final size:11
Alignment explanation
Indices: 265505--265538 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
265495 CAACACCATT
265505 CATTGCATTTA
1 CATTGCATTTA
*
265516 CATTGCATCTA
1 CATTGCATTTA
265527 CATTGCATTTA
1 CATTGCATTTA
265538 C
1 C
265539 TTTTCGCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (11 bp):
CATTGCATTTA
Found at i:269835 original size:93 final size:93
Alignment explanation
Indices: 269730--269926 Score: 265
Period size: 93 Copynumber: 2.1 Consensus size: 93
269720 TTCCTTGAAG
* * *
269730 AACAGTGAAATGAATCAACATACCCAAATCAGATTTTCCCTCAAGAAGAAG-AGGAACATAT-CA
1 AACAGTGGAATGAATCAACATACCCAAATCAGATTTTCCCTCAACAAAAAGCA-GAACATATCCA
269793 T-TCTTCTTCAAGATTTGATATTCCCTGAGT
65 TCTC-T-TTCAAGATTTGATATTCCCTGAGT
* * * * *
269823 AACAGTGGAATGAATCTACGTCCCCAAATCTGATTTTCCCTCAACAAAAAGCATAACATATCCAT
1 AACAGTGGAATGAATCAACATACCCAAATCAGATTTTCCCTCAACAAAAAGCAGAACATATCCAT
*
269888 CTCTTTCAAGATTTGATATTCCCTGGGT
66 CTCTTTCAAGATTTGATATTCCCTGAGT
269916 AACAGTGGAAT
1 AACAGTGGAAT
269927 AATTATGCTT
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
93 85 0.92
94 5 0.05
95 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (93 bp):
AACAGTGGAATGAATCAACATACCCAAATCAGATTTTCCCTCAACAAAAAGCAGAACATATCCAT
CTCTTTCAAGATTTGATATTCCCTGAGT
Found at i:269951 original size:134 final size:134
Alignment explanation
Indices: 269813--270059 Score: 395
Period size: 134 Copynumber: 1.8 Consensus size: 134
269803 AGATTTGATA
* * *
269813 TTCCCTGAGTAACAGTGGAATGAATCTACGTCCCCAAATCTGATTTTCCCTCAACAAAAAGCATA
1 TTCCCTGAGTAACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTCCCTAAAAAAAAAGCATA
* * ** *
269878 ACATATCCATCTCTTTCAAGATTTGATATTCCCTGGGTAACAGTGGAATAATTATGCTTTTATTC
66 ACAGATCAATCTCTTTCAAGATTTGATATTCCCTAAGTAACAATGGAATAATTATGCTTTTATTC
269943 AATC
131 AATC
* *
269947 TTCCCTGAGTAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTAAAAAAAAAGTATA
1 TTCCCTGAGTAACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTCCCTAAAAAAAAAGCATA
*
270012 ATAGATCAATCTCTTTCAAGATTTGATATTCCCTAAGTAACAATGGAA
66 ACAGATCAATCTCTTTCAAGATTTGATATTCCCTAAGTAACAATGGAA
270060 CAAGTCTACC
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
134 102 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (134 bp):
TTCCCTGAGTAACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTCCCTAAAAAAAAAGCATA
ACAGATCAATCTCTTTCAAGATTTGATATTCCCTAAGTAACAATGGAATAATTATGCTTTTATTC
AATC
Found at i:270085 original size:134 final size:134
Alignment explanation
Indices: 269804--270086 Score: 377
Period size: 134 Copynumber: 2.1 Consensus size: 134
269794 TCTTCTTCAA
* * * *
269804 GATTTGATATTCCCTGAGTAACAGTGGAATGAATCTACGTCCCCAAATCTGATTTTCCCTCAACA
1 GATTTAATATTCCCTGAGTAACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTCCCTAAAAA
* * ** * * * *
269869 AAAAGCATAACATATCCATCTCTTTCAAGATTTGATATTCCCTGGGTAACAGTGGAATAATTATG
66 AAAAGCATAACAGATCAATCTCTTTCAAGATTTGATATTCCCTAAGTAACAATGGAACAAGTATA
* *
269934 CTTT
131 CCTC
* * * *
269938 TATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTAAAAA
1 GATTTAATATTCCCTGAGTAACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTCCCTAAAAA
* * *
270003 AAAAGTATAATAGATCAATCTCTTTCAAGATTTGATATTCCCTAAGTAACAATGGAACAAGTCTA
66 AAAAGCATAACAGATCAATCTCTTTCAAGATTTGATATTCCCTAAGTAACAATGGAACAAGTATA
270068 CCTC
131 CCTC
270072 GATTTAATATTCCCT
1 GATTTAATATTCCCT
270087 AAAGAACAAT
Statistics
Matches: 125, Mismatches: 24, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
134 125 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.32
Consensus pattern (134 bp):
GATTTAATATTCCCTGAGTAACAGTGGAATGAATCAACGTCCCCAAATCTGATTTTCCCTAAAAA
AAAAGCATAACAGATCAATCTCTTTCAAGATTTGATATTCCCTAAGTAACAATGGAACAAGTATA
CCTC
Found at i:270307 original size:3 final size:3
Alignment explanation
Indices: 270299--270395 Score: 180
Period size: 3 Copynumber: 33.0 Consensus size: 3
270289 ATTGTATTAA
270299 ATT ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
270345 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
270393 ATT
1 ATT
270396 CAGGGCTAAT
Statistics
Matches: 92, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
2 4 0.04
3 88 0.96
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:270989 original size:197 final size:197
Alignment explanation
Indices: 270654--271010 Score: 714
Period size: 197 Copynumber: 1.8 Consensus size: 197
270644 TAGGATTTAA
270654 CCCTTAGCTCCAGTTTCCACTCATCTCAGCCACACGAACTGGACCCATCCAAAGGTCCAAATCGA
1 CCCTTAGCTCCAGTTTCCACTCATCTCAGCCACACGAACTGGACCCATCCAAAGGTCCAAATCGA
270719 GCCTCTGCTGTCGCCTATCTCCACTAGTCGGTTGCCACCGTCGCTGCCACAAACTGAAGCTCCTG
66 GCCTCTGCTGTCGCCTATCTCCACTAGTCGGTTGCCACCGTCGCTGCCACAAACTGAAGCTCCTG
270784 TAGTGTCAGAGATCCCAAATCAACACACAACTAAATTCAAACTTAAACATGGCATTTTGTAATGA
131 TAGTGTCAGAGATCCCAAATCAACACACAACTAAATTCAAACTTAAACATGGCATTTTGTAATGA
270849 TT
196 TT
270851 CCCTTAGCTCCAGTTTCCACTCATCTCAGCCACACGAACTGGACCCATCCAAAGGTCCAAATCGA
1 CCCTTAGCTCCAGTTTCCACTCATCTCAGCCACACGAACTGGACCCATCCAAAGGTCCAAATCGA
270916 GCCTCTGCTGTCGCCTATCTCCACTAGTCGGTTGCCACCGTCGCTGCCACAAACTGAAGCTCCTG
66 GCCTCTGCTGTCGCCTATCTCCACTAGTCGGTTGCCACCGTCGCTGCCACAAACTGAAGCTCCTG
270981 TAGTGTCAGAGATCCCAAATCAACACACAA
131 TAGTGTCAGAGATCCCAAATCAACACACAA
271011 TAAGCAGAGA
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
197 160 1.00
ACGTcount: A:0.27, C:0.34, G:0.16, T:0.23
Consensus pattern (197 bp):
CCCTTAGCTCCAGTTTCCACTCATCTCAGCCACACGAACTGGACCCATCCAAAGGTCCAAATCGA
GCCTCTGCTGTCGCCTATCTCCACTAGTCGGTTGCCACCGTCGCTGCCACAAACTGAAGCTCCTG
TAGTGTCAGAGATCCCAAATCAACACACAACTAAATTCAAACTTAAACATGGCATTTTGTAATGA
TT
Found at i:273744 original size:13 final size:13
Alignment explanation
Indices: 273726--273751 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
273716 TATTCCATGT
273726 TTCCTTTCAACTC
1 TTCCTTTCAACTC
273739 TTCCTTTCAACTC
1 TTCCTTTCAACTC
273752 CCATCTTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.00, T:0.46
Consensus pattern (13 bp):
TTCCTTTCAACTC
Found at i:275225 original size:85 final size:85
Alignment explanation
Indices: 275077--275242 Score: 212
Period size: 85 Copynumber: 2.0 Consensus size: 85
275067 ATACAATTAC
* * *
275077 GACACACGAATGTGTGTCATCATTTTTAATGACGTGTGCTTCAATGACACGCAATGTAAGTCATA
1 GACACACAAATGTGTGTCATCATTTTTAATGACGTGGGCTTCAATGACACGCAATGCAAGTCATA
275142 CA-TGTGTGTCATAAATTTAT
66 -ATTGTGTGTCATAAATTTAT
* * **
275162 GACACACAAATGTGTGTCATC-TTCATTT-ATGACGTGGGCTTCAATGACGCTCAATGCGCGTCA
1 GACACACAAATGTGTGTCATCATT--TTTAATGACGTGGGCTTCAATGACACGCAATGCAAGTCA
*
275225 TAATTGTGTGTTATAAAT
64 TAATTGTGTGTCATAAAT
275243 GCGTGTCATT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
84 3 0.04
85 64 0.91
86 3 0.04
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (85 bp):
GACACACAAATGTGTGTCATCATTTTTAATGACGTGGGCTTCAATGACACGCAATGCAAGTCATA
ATTGTGTGTCATAAATTTAT
Found at i:275248 original size:13 final size:13
Alignment explanation
Indices: 275214--275265 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
275204 AATGACGCTC
*
275214 AATGCGCGTCATA
1 AATGCGTGTCATA
* * *
275227 ATTGTGTGTTATA
1 AATGCGTGTCATA
*
275240 AATGCGTGTCATT
1 AATGCGTGTCATA
*
275253 AATGCGCGTCATA
1 AATGCGTGTCATA
275266 GATTTATGAC
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (13 bp):
AATGCGTGTCATA
Found at i:278241 original size:131 final size:131
Alignment explanation
Indices: 277875--278241 Score: 414
Period size: 131 Copynumber: 2.8 Consensus size: 131
277865 ATAGATATTG
* * * * * *
277875 AGAATAGTAATATCTTTTTATTTCGGTTGGAGTAATAAATGACTGCTTTAAGGCATGACAAGTCA
1 AGAATAATGATATCTTTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
* * * ** * * *
277940 TTTATTCTCGATT-GAATTTTTTTTTGATATCGTTGTTTTCTCTCGAATTACTATCGATTTTTAG
66 TTTATTCTCGATTGGAA--ATTATTAGATATTATTGTTTTCACTCGAATTACTATCGAATTTTAA
**
278004 GTT
129 GAC
* * * * * *
278007 AGAATAGTGAGATCTCTTCATTTTGATTGGAGCAATAAATGACTGCTTTAAGGTATGAGAGGTCA
1 AGAATAATGATATCTTTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
* * *
278072 TTTATTCTCGATTGGAAATTATTAGATATTATCGTTTTCACTCGGATTGA-TATTGAATTTTAAG
66 TTTATTCTCGATTGGAAATTATTAGATATTATTGTTTTCACTCGAATT-ACTATCGAATTTTAAG
278136 AC
130 AC
* * * *
278138 AGAATAATGTTATCTTTTCATTTCGATTGGAGTAATAAATGATTGTTTTAATGCATGAGAGGTCA
1 AGAATAATGATATCTTTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
* *
278203 TTTATTCTCGATTGGAAATAATTAGATATTATTATTTTC
66 TTTATTCTCGATTGGAAATTATTAGATATTATTGTTTTC
278242 TCTCTTAAAA
Statistics
Matches: 197, Mismatches: 36, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
131 125 0.63
132 69 0.35
133 3 0.02
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (131 bp):
AGAATAATGATATCTTTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
TTTATTCTCGATTGGAAATTATTAGATATTATTGTTTTCACTCGAATTACTATCGAATTTTAAGA
C
Found at i:282972 original size:35 final size:35
Alignment explanation
Indices: 282926--282992 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
282916 AGTTCATGCA
* **
282926 ATCCAACATAATGTCACTTATTATTTAAGTTGCGT
1 ATCCAACATAATCTCACTTACGATTTAAGTTGCGT
282961 ATCCAACATAATCTCACTTACGATTTAAGTTG
1 ATCCAACATAATCTCACTTACGATTTAAGTTG
282993 TGTTTGCTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.37
Consensus pattern (35 bp):
ATCCAACATAATCTCACTTACGATTTAAGTTGCGT
Found at i:284448 original size:18 final size:19
Alignment explanation
Indices: 284415--284450 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
284405 TTTTCATTTG
*
284415 CCTTTATGACATTTTTTTA
1 CCTTTATGACACTTTTTTA
284434 CCTTT-TGACACTTTTTT
1 CCTTTATGACACTTTTTT
284451 CGGTTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.17, C:0.19, G:0.06, T:0.58
Consensus pattern (19 bp):
CCTTTATGACACTTTTTTA
Found at i:284767 original size:19 final size:19
Alignment explanation
Indices: 284745--284845 Score: 66
Period size: 19 Copynumber: 5.3 Consensus size: 19
284735 TATTTCAATG
284745 ATTATAGGATATTGTTCTA
1 ATTATAGGATATTGTTCTA
* * * *
284764 ATTATA--TTCTTAAGTTATG
1 ATTATAGGATATT--GTTCTA
284783 ATTATAGGATATTGTTCTA
1 ATTATAGGATATTGTTCTA
* * * *
284802 ATTATA--TTCTTAAGTTATG
1 ATTATAGGATATT--GTTCTA
284821 ATTATAGGATATTGTTCTA
1 ATTATAGGATATTGTTCTA
284840 ATTATA
1 ATTATA
284846 TTCTTAAGTT
Statistics
Matches: 58, Mismatches: 16, Indels: 16
0.64 0.18 0.18
Matches are distributed among these distances:
17 6 0.10
19 46 0.79
21 6 0.10
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.50
Consensus pattern (19 bp):
ATTATAGGATATTGTTCTA
Found at i:284793 original size:38 final size:38
Alignment explanation
Indices: 284742--284863 Score: 244
Period size: 38 Copynumber: 3.2 Consensus size: 38
284732 TTTTATTTCA
284742 ATGATTATAGGATATTGTTCTAATTATATTCTTAAGTT
1 ATGATTATAGGATATTGTTCTAATTATATTCTTAAGTT
284780 ATGATTATAGGATATTGTTCTAATTATATTCTTAAGTT
1 ATGATTATAGGATATTGTTCTAATTATATTCTTAAGTT
284818 ATGATTATAGGATATTGTTCTAATTATATTCTTAAGTT
1 ATGATTATAGGATATTGTTCTAATTATATTCTTAAGTT
284856 ATGATTAT
1 ATGATTAT
284864 GATTATAAAT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 84 1.00
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.50
Consensus pattern (38 bp):
ATGATTATAGGATATTGTTCTAATTATATTCTTAAGTT
Found at i:284862 original size:19 final size:19
Alignment explanation
Indices: 284764--284863 Score: 64
Period size: 19 Copynumber: 5.3 Consensus size: 19
284754 TATTGTTCTA
284764 ATTATATTCTTAAGTTATG
1 ATTATATTCTTAAGTTATG
* * * *
284783 ATTATAGGATATT--GTTCTA
1 ATTATA--TTCTTAAGTTATG
284802 ATTATATTCTTAAGTTATG
1 ATTATATTCTTAAGTTATG
* * * *
284821 ATTATAGGATATT--GTTCTA
1 ATTATA--TTCTTAAGTTATG
284840 ATTATATTCTTAAGTTATG
1 ATTATATTCTTAAGTTATG
284859 ATTAT
1 ATTAT
284864 GATTATAAAT
Statistics
Matches: 57, Mismatches: 16, Indels: 16
0.64 0.18 0.18
Matches are distributed among these distances:
17 6 0.11
19 45 0.79
21 6 0.11
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.51
Consensus pattern (19 bp):
ATTATATTCTTAAGTTATG
Found at i:285332 original size:13 final size:13
Alignment explanation
Indices: 285290--285332 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
285280 CTATGATGCG
*
285290 CATTTATGACACA
1 CATTTATGACATA
* *
285303 CATTTATGACGTG
1 CATTTATGACATA
*
285316 CATTTATGACATT
1 CATTTATGACATA
285329 CATT
1 CATT
285333 GAGCGTCATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (13 bp):
CATTTATGACATA
Found at i:285552 original size:85 final size:84
Alignment explanation
Indices: 285304--285554 Score: 256
Period size: 85 Copynumber: 3.0 Consensus size: 84
285294 TATGACACAC
** * * *
285304 ATTTATGACGTGCATTTATGACATTCATTGAGCGTCATTGAAGCCCCCGTCATAAATAAAGATGA
1 ATTTATGACACGCATGTATGAC-TTCATTGCGTGTCATTGAAGCCCCCGTCATAAATAAAGATGA
* *
285369 TACACATTTATGTGTCATAA
65 CACACATTTGTGTGTCATAA
* * * ** **
285389 ATTTATGACTCCCATGTATGACTTCCATTGAAC-T-TCATTGAAACCCCCGTCATAAATCTACTT
1 ATTTATGACACGCATGTATGACTT-CATTG--CGTGTCATTGAAGCCCCCGTCATAAATAAAGAT
*
285452 GACATACATTTGTGTGTCATAA
63 GACACACATTTGTGTGTCATAA
* * *
285474 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCACACGTCATTAAA-AAAGATA
1 ATTTATGACACGCATGTATGACTT-CATTGCGTGTCATTGAAGCCCCCGTCA-TAAATAAAGATG
*
285538 ACACACATTCGTGTGTC
64 ACACACATTTGTGTGTC
285555 GTGATTGTAT
Statistics
Matches: 133, Mismatches: 27, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
83 1 0.01
84 3 0.02
85 125 0.94
86 4 0.03
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (84 bp):
ATTTATGACACGCATGTATGACTTCATTGCGTGTCATTGAAGCCCCCGTCATAAATAAAGATGAC
ACACATTTGTGTGTCATAA
Found at i:285581 original size:2 final size:2
Alignment explanation
Indices: 285574--285608 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
285564 TTTCGTAAAT
285574 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
285609 GATTGACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:290583 original size:21 final size:22
Alignment explanation
Indices: 290559--290599 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
290549 GCGATTTTAG
*
290559 GGGAGGAGGAGGA-GGAGAGGT
1 GGGACGAGGAGGAGGGAGAGGT
*
290580 GGGACGAGGCGGAGGGAGAG
1 GGGACGAGGAGGAGGGAGAG
290600 ACGGTGGCGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.27, C:0.05, G:0.66, T:0.02
Consensus pattern (22 bp):
GGGACGAGGAGGAGGGAGAGGT
Found at i:291509 original size:14 final size:16
Alignment explanation
Indices: 291490--291521 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
291480 GAGATTAATC
291490 TAAATAT-TATT-TTT
1 TAAATATATATTATTT
291504 TAAATATATATTATTT
1 TAAATATATATTATTT
291520 TA
1 TA
291522 TTTTTTAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 4 0.25
16 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TAAATATATATTATTT
Found at i:298751 original size:60 final size:60
Alignment explanation
Indices: 298649--298768 Score: 177
Period size: 60 Copynumber: 2.0 Consensus size: 60
298639 CATATTCGGG
** * *
298649 AATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGTCACATTCAGGA
1 AATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTCACATTCAGGA
* * *
298709 AATATACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTCATATTCAGGA
1 AATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTCACATTCAGGA
298769 TTGCACTACG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.28
Consensus pattern (60 bp):
AATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGTCACATTCAGGA
Found at i:298871 original size:20 final size:20
Alignment explanation
Indices: 298830--298872 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
298820 TATATTGGGC
* * *
298830 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATAGT
298850 TATTGTCTATGGTATATAGT
1 TATTGTCTATGGTATATAGT
298870 TAT
1 TAT
298873 GGAATAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.19, T:0.56
Consensus pattern (20 bp):
TATTGTCTATGGTATATAGT
Found at i:298989 original size:46 final size:44
Alignment explanation
Indices: 298869--299018 Score: 187
Period size: 45 Copynumber: 3.3 Consensus size: 44
298859 TGGTATATAG
* *
298869 TTATGGA-ATAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGATA-AATGGAAAGTATATTGGTAAAATAAGCTTACGAGC
* * *
298913 TTATAGAACAAAT-GATAAGTATATTGGTAAAATAAGGTTACGAGC
1 TTAT-GGATAAATGGA-AAGTATATTGGTAAAATAAGCTTACGAGC
298958 TTATGGTATTAAATGGAAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGG-A-TAAATGGAAAGTATATTGGTAAAATAAGCTTACGAGC
299004 TTATGGGATAAATGG
1 TTAT-GGATAAATGG
299019 TAAGAGATTT
Statistics
Matches: 92, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
44 6 0.07
45 44 0.48
46 38 0.41
47 4 0.04
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.31
Consensus pattern (44 bp):
TTATGGATAAATGGAAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:300997 original size:16 final size:16
Alignment explanation
Indices: 300976--301007 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
300966 ATTGATGAAA
300976 AAGTGAAATCATCAAT
1 AAGTGAAATCATCAAT
*
300992 AAGTGATATCATCAAT
1 AAGTGAAATCATCAAT
301008 GGTTGCGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (16 bp):
AAGTGAAATCATCAAT
Found at i:310643 original size:64 final size:64
Alignment explanation
Indices: 310575--310755 Score: 231
Period size: 66 Copynumber: 2.8 Consensus size: 64
310565 TTGGACTCTC
* * * * *
310575 AGTGCATCGGTGCACTAAGA-GTGCATCGATACATAAAATGCATTCGATGTTTTGA-AAAAGCTT
1 AGTGCATCGATGCA-T-AGATGTGCATCGATGCATCAAATGCATTCGATGTTTTGATAAAACCCT
310638 G
64 G
* *
310639 AGTGCATCGATGCATGGTATGTGCATCGATGCATCAAATGCATTCGATGTTTTTTATAAAACCCT
1 AGTGCATCGATGCATAG-ATGTGCATCGATGCATCAAATGCATTCGATG-TTTTGATAAAACCCT
310704 G
64 G
*
310705 AGTGCATCGATGCATGATATGTGCATCGATGCATCAAATGCATTCGATGTT
1 AGTGCATCGATGCAT-AGATGTGCATCGATGCATCAAATGCATTCGATGTT
310756 CAATTAAATC
Statistics
Matches: 103, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 40 0.39
65 7 0.07
66 53 0.51
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (64 bp):
AGTGCATCGATGCATAGATGTGCATCGATGCATCAAATGCATTCGATGTTTTGATAAAACCCTG
Found at i:310731 original size:66 final size:65
Alignment explanation
Indices: 310595--310755 Score: 252
Period size: 66 Copynumber: 2.5 Consensus size: 65
310585 TGCACTAAGA
* * * * *
310595 GTGCATCGATACATAAAATGCATTCGATG-TTTTGAAAAAGCTTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTTGAAAAACCCTGAGTGCATCGATGCATGATAT
*
310659 GTGCATCGATGCATCAAATGCATTCGATGTTTTTTATAAAACCCTGAGTGCATCGATGCATGATA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTTGA-AAAACCCTGAGTGCATCGATGCATGATA
310724 T
65 T
310725 GTGCATCGATGCATCAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
310756 CAATTAAATC
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
64 27 0.30
65 5 0.06
66 57 0.64
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTTGAAAAACCCTGAGTGCATCGATGCATGATAT
Done.