Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004186.1 Hibiscus syriacus cultivar Beakdansim tig00009158_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: 72248
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:3624 original size:15 final size:15
Alignment explanation
Indices: 3594--3636 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3584 GGAGGTAGGG
* *
3594 AAAGCAAAAAAAGAA
1 AAAGCAAAAGAGGAA
3609 AAAG-AGAAAGAGGAA
1 AAAGCA-AAAGAGGAA
3624 AAAGCAAAAGAGG
1 AAAGCAAAAGAGG
3637 TCACTACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.70, C:0.05, G:0.26, T:0.00
Consensus pattern (15 bp):
AAAGCAAAAGAGGAA
Found at i:5948 original size:50 final size:50
Alignment explanation
Indices: 5843--5949 Score: 112
Period size: 50 Copynumber: 2.1 Consensus size: 50
5833 TCACACTCCA
* * * *
5843 ATTTTCCTTTTCATCGTGACTAGGAGGGTTGGTTAGAGCCATATTATCGT
1 ATTTTCCTTTTCATCGCGACTAGGAGGGTTGGATAGAGACATATCATCGT
* *
5893 GTTTTCCTTTTCATTGCGACTAGGAGGGATT-GATAG-GACATTATCCATCG-
1 ATTTTCCTTTTCATCGCGACTAGGAGGG-TTGGATAGAGACA-TAT-CATCGT
5943 ATTTTCC
1 ATTTTCC
5950 ATATATCCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
49 3 0.06
50 38 0.81
51 6 0.13
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (50 bp):
ATTTTCCTTTTCATCGCGACTAGGAGGGTTGGATAGAGACATATCATCGT
Found at i:7360 original size:15 final size:16
Alignment explanation
Indices: 7327--7384 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
7317 GGAAGATTAC
*
7327 TTGTCTCCACTTGGCT
1 TTGTCTCCACTTAGCT
7343 TTGTCTCCACTT-GCT
1 TTGTCTCCACTTAGCT
*
7358 TTGTCTTCACTTAGCT
1 TTGTCTCCACTTAGCT
7374 TTGTCTCCACT
1 TTGTCTCCACT
7385 AGACATCTCT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.36
16 25 0.64
ACGTcount: A:0.09, C:0.31, G:0.14, T:0.47
Consensus pattern (16 bp):
TTGTCTCCACTTAGCT
Found at i:7422 original size:44 final size:44
Alignment explanation
Indices: 7368--7455 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
7358 TTGTCTTCAC
7368 TTAGCTTTGTCTCCACTAGACATCTCTTGAAGGAATTCGACCAA
1 TTAGCTTTGTCTCCACTAGACATCTCTTGAAGGAATTCGACCAA
*
7412 TTAGCTTTGTCTCCACTAGACATCTCTTGAAGGAATTCGGCCAA
1 TTAGCTTTGTCTCCACTAGACATCTCTTGAAGGAATTCGACCAA
7456 GGAACTTCTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (44 bp):
TTAGCTTTGTCTCCACTAGACATCTCTTGAAGGAATTCGACCAA
Found at i:15707 original size:22 final size:22
Alignment explanation
Indices: 15673--15719 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
15663 ATTATTATGG
* *
15673 AACCTTCGGCCATGCAT-ATCTT
1 AACCTACGACCATGCATGAT-TT
15695 AACCTACGACCATGCATGATTT
1 AACCTACGACCATGCATGATTT
15717 AAC
1 AAC
15720 TCCTATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.28
Consensus pattern (22 bp):
AACCTACGACCATGCATGATTT
Found at i:23126 original size:21 final size:21
Alignment explanation
Indices: 23082--23122 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23072 TCTTTATTTC
* *
23082 ATTTCATTTATTATCTTTCTT
1 ATTTCATTGATTATCTTCCTT
23103 ATTTCATTGATT-TCTTCCTT
1 ATTTCATTGATTATCTTCCTT
23123 TATTAACCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.17, C:0.17, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTTCATTGATTATCTTCCTT
Found at i:28442 original size:91 final size:90
Alignment explanation
Indices: 28331--28650 Score: 419
Period size: 91 Copynumber: 3.5 Consensus size: 90
28321 TATTCTTTAT
* * **
28331 TTTCATTTATGTCATCCTTTCATGCCTATAATGCACTGTTATGCATTTTTCTTTATGGCATCCTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA-TTTTCTTTATGGCATCCTT
* * *
28396 TCATGCCGATAATGCACCATTGTGTG
65 TCATGCCGATAATGCACCGTTATGTA
* ** *
28422 TCTCATTTATGGCATCCTTTCATGTAGATAATGCACCGTTATGCA-TTTCATTTATGGCATCCTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTC-TTTATGGCATCCTT
* *
28486 TCATGCCTATAATGCACCGTTATGCATT
65 TCATGCCGATAATGCACCGTTATG--TA
* *
28514 TTTC-TTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTATTTATGGCATCATTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTCTTTATGGCATCCTTT
* *
28578 CATGTCGATAATGCACCGTTATGCA
66 CATGCCGATAATGCACCGTTATGTA
* *
28603 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCATTATGCATTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTT
28651 CATTTATTCA
Statistics
Matches: 202, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
89 8 0.04
90 76 0.38
91 111 0.55
92 7 0.03
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (90 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTCTTTATGGCATCCTTT
CATGCCGATAATGCACCGTTATGTA
Found at i:28452 original size:45 final size:45
Alignment explanation
Indices: 28331--28657 Score: 433
Period size: 45 Copynumber: 7.2 Consensus size: 45
28321 TATTCTTTAT
* * **
28331 TTTCATTTATGTCATCCTTTCATGCCTATAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* **
28376 TTTTTC-TTTATGGCATCCTTTCATGCCGATAATGCACCATTGTGTG
1 --TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* ** *
28422 TCTCATTTATGGCATCCTTTCATGTAGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* *
28467 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
28512 TTTTTC-TTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
1 --TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* * * *
28558 TTTTATTTATGGCATCATTTCATGTCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* *
28603 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
28648 TTTCATTTAT
1 TTTCATTTAT
28658 TCATTCATTT
Statistics
Matches: 246, Mismatches: 30, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
44 6 0.02
45 161 0.65
46 71 0.29
47 8 0.03
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
Found at i:28535 original size:136 final size:136
Alignment explanation
Indices: 28331--28650 Score: 541
Period size: 136 Copynumber: 2.4 Consensus size: 136
28321 TATTCTTTAT
* *
28331 TTTCATTTATGTCATCCTTTCATGCCTATAATGCACTGTTATGCATTTTTCTTTATGGCATCCTT
1 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCATCCTT
* ** *
28396 TCATGCCGATAATGCACCATTGTGTGTCTCATTTATGGCATCCTTTCATGTAGATAATGCACCGT
66 TCATGCCGATAATGCACCATTATGCATCTCATTTATGGCATCATTTCATGTAGATAATGCACCGT
28461 TATGCA
131 TATGCA
*
28467 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCATCCTT
1 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCATCCTT
* * *
28532 TCATGCCGATAATGCACCATTATGCATTTTATTTATGGCATCATTTCATGTCGATAATGCACCGT
66 TCATGCCGATAATGCACCATTATGCATCTCATTTATGGCATCATTTCATGTAGATAATGCACCGT
28597 TATGCA
131 TATGCA
*
28603 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCATTATGCATTT
1 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCGTTATGCATTT
28651 CATTTATTCA
Statistics
Matches: 173, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
136 173 1.00
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (136 bp):
TTTCATTTATGACATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCATCCTT
TCATGCCGATAATGCACCATTATGCATCTCATTTATGGCATCATTTCATGTAGATAATGCACCGT
TATGCA
Found at i:29187 original size:45 final size:45
Alignment explanation
Indices: 29129--29336 Score: 240
Period size: 45 Copynumber: 4.6 Consensus size: 45
29119 TCAGTATCGG
* * * *
29129 TAATGCACTGTTATGTATTTCATTTATAGCATCATTTCATGCCTA
1 TAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTA
* * * *
29174 TAATGAACCGTTATGCATTTTTC-TTAATGGCATTCTTTCCTGCCTA
1 TAATGCACCGTTATGCA--TTTCATTTATGGCATCCTTTCATGCCTA
* *
29220 TAATGCACCATTATGCATTTCATTTATGGCATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTA
* *
29265 TAATGCACCGTTATGCA-TTCTAATTATGGAATCCTTTCATGCCTA
1 TAATGCACCGTTATGCATTTC-ATTTATGGCATCCTTTCATGCCTA
* * *
29310 TAATGCACCATTATACATTTAATTTAT
1 TAATGCACCGTTATGCATTTCATTTAT
29337 TCATTCATTT
Statistics
Matches: 136, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
44 7 0.05
45 90 0.66
46 35 0.26
47 4 0.03
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (45 bp):
TAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTA
Found at i:29865 original size:45 final size:45
Alignment explanation
Indices: 29806--30014 Score: 210
Period size: 45 Copynumber: 4.6 Consensus size: 45
29796 TTCAGTATCG
* * * * *
29806 ATAATGCACCGTTATGCATTTAATTCATGGCATCATTTCATACCT
1 ATAATGAACAGTTATGCATTTCATTTATGGCATCATTTCATGCCT
*
29851 ATAATGAACAGTTATGCATTTTTC-TTAATGGCATCCA-TTCATGCCT
1 ATAATGAACAGTTATGCA--TTTCATTTATGGCAT-CATTTCATGCCT
* * *
29897 ATAATGCACCA-TTATGCATTTCATTTATAGCATCATTTCATGCCA
1 ATAATG-AACAGTTATGCATTTCATTTATGGCATCATTTCATGCCT
* * * * *
29942 AAAATGCACGGTTATACATTTCATTTATGGCATCCTTTCATGCCT
1 ATAATGAACAGTTATGCATTTCATTTATGGCATCATTTCATGCCT
*
29987 ATAATGCACCA-TTATGCATTTCATTTAT
1 ATAATG-AACAGTTATGCATTTCATTTAT
30015 TCATTCATTT
Statistics
Matches: 134, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
44 7 0.05
45 88 0.66
46 31 0.23
47 8 0.06
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (45 bp):
ATAATGAACAGTTATGCATTTCATTTATGGCATCATTTCATGCCT
Found at i:30024 original size:90 final size:90
Alignment explanation
Indices: 29806--30014 Score: 285
Period size: 91 Copynumber: 2.3 Consensus size: 90
29796 TTCAGTATCG
* * * * * * *
29806 ATAATGCACCGTTATGCATTTAATTCATGGCATCATTTCATACCTATAATGAACAGTTATGCATT
1 ATAATGCACCATTATGCATTTCATTTATAGCATCATTTCATACCAAAAATGAACAGTTATACA-T
29871 TTTCTTAATGGCATCCATTCATGCCT
65 TTTCTTAATGGCATCCATTCATGCCT
* * *
29897 ATAATGCACCATTATGCATTTCATTTATAGCATCATTTCATGCCAAAAATGCACGGTTATACA-T
1 ATAATGCACCATTATGCATTTCATTTATAGCATCATTTCATACCAAAAATGAACAGTTATACATT
* *
29961 TTCATTTATGGCATCCTTTCATGCCT
66 TTC-TTAATGGCATCCATTCATGCCT
29987 ATAATGCACCATTATGCATTTCATTTAT
1 ATAATGCACCATTATGCATTTCATTTAT
30015 TCATTCATTT
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
89 4 0.04
90 48 0.46
91 53 0.50
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (90 bp):
ATAATGCACCATTATGCATTTCATTTATAGCATCATTTCATACCAAAAATGAACAGTTATACATT
TTCTTAATGGCATCCATTCATGCCT
Found at i:30389 original size:680 final size:679
Alignment explanation
Indices: 28448--30894 Score: 3860
Period size: 680 Copynumber: 3.6 Consensus size: 679
28438 CTTTCATGTA
* *
28448 GATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCAT
1 GATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCTATAATGAACCGTTATGCAT
* * *
28513 TTTTCTTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTATTTATGGCATCATTT
66 TTTTCTTAATGGCATCCTTTCATGCCTATAATGCACCATTATGCATTTCATTTATGGCATCATTT
* *
28578 CATGTCGATAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
131 CATGCCGAAAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
* * *
28643 ATGCATTTCATTTATTCATTCATTTTAGAGAAGTTCATACTCCAAAACTCATTCATAATATCCTT
196 ATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATCCTT
* * * * * * *
28708 TTCATATACAAAATGCAAATATATTAACTAATGTAAAACATACATAAAATCACAATATTCTAATA
261 TTCATAAACATAATGAAAATATATTAACTATTGTAAAACATACATTAAATCACAACATTCTAATT
*
28773 TGACTCATTGTC-AATCTTCCTCATCTCATATAAATACAATAAATGTACTCACATGATAATCCTC
326 TGACTCATTG-CGAATCTTCCTCATCTCATATAAATACAATAAATGTACTCACCTGATAATCCTC
* * *
28837 ACTAATAAGATATAATGATGTCCGGCTATTCAGCAACTTTATCTTTGCCCTTTTTCTTGCTAGAC
390 ACTAATAAGATGTAATGATGTCCGACTATTCAACAACTTTATCTTTGCCCTTTTTCTTGCTAGAC
*
28902 TCAGGAGCTTGGTTATGATCTACACAAACATCCATTAAAGACACATATCATACCAAATGTTAGTA
455 TCAGGAGCTTGGTTATGATCTATACAAACATCCATTAAAGACACATATCATACCAAATGTTAGTA
* * * *
28967 TATTCCATAACATTTATACCTTAATAAAACTCAAAAGTACAATTATTTCAATTTCTATAACAATT
520 TATTCCCTAACATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAATTTCTATAACAATT
** * * * *
29032 TCAACTTATCTTATAGTTACATGTTGAATAGTGTTGGTACGCTACCATGGTATCGATACTTCTAT
585 TCAACTTATCTTATAGTTACATACTCAATAGTATTGGTACCCTACCATGGTATAGATACTTCTAT
*
29097 ACAATGGTACCGATACTCATTTTCAGTATC
650 ACTATGGTACCGATACTCATTTTCAGTATC
* * * *
29127 GGTAATGCACTGTTATGTATTTCATTTATAGCATCATTTCATGCCTATAATGAACCGTTATGCAT
1 GATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCTATAATGAACCGTTATGCAT
* * *
29192 TTTTCTTAATGGCATTCTTTCCTGCCTATAATGCACCATTATGCATTTCATTTATGGCATCCTTT
66 TTTTCTTAATGGCATCCTTTCATGCCTATAATGCACCATTATGCATTTCATTTATGGCATCATTT
* *
29257 CATGCCGATAATGCACCGTTATGCA-TTCTAATTATGGA-ATCCTTTCATGCCTATAATGCACCA
131 CATGCCGAAAATGCACCGTTATGCATTTC-ATTTAT-GACATCCTTTCATGCCTATAATGCACCA
* * * *
29320 TTATACATTTAATTTATTCATTCATTTTACAGAAGTTCGTACTCTAAAACTCATTCATAATATCA
194 TTATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATCC
*
29385 TTTT-ATAAACATAATGAAAATATATTAACTATTGTAAAACATACATTAAATCACAACATTCTAG
259 TTTTCATAAACATAATGAAAATATATTAACTATTGTAAAACATACATTAAATCACAACATTCTAA
* *
29449 TTTGACTCATTGTGAATCTTCCTCATCTCATATAAATACAATGAATGTACTCACCTGATAATCCT
324 TTTGACTCATTGCGAATCTTCCTCATCTCATATAAATACAATAAATGTACTCACCTGATAATCCT
* * * *
29514 CACTAACAATATGTAATGATGTCCGACTATTCAACAACTTTATCTTTTCCCTTTTTCTTACTAGA
389 CACTAATAAGATGTAATGATGTCCGACTATTCAACAACTTTATCTTTGCCCTTTTTCTTGCTAGA
*
29579 CTCAGGAGCTTGGTTATGATCTATACAAACATCCATTAAAGACACATATCATACCAATTGTTAGT
454 CTCAGGAGCTTGGTTATGATCTATACAAACATCCATTAAAGACACATATCATACCAAATGTTAGT
* *
29644 ATATTCCCTAACATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAAATTCTGTAACAAT
519 ATATTCCCTAACATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAATTTCTATAACAAT
* * *
29709 TTCATCTAATTTTATAGTTACATACTCAATAGTATTGGTACCCTACCATGGTATAGATACTTCTA
584 TTCAACTTATCTTATAGTTACATACTCAATAGTATTGGTACCCTACCATGGTATAGATACTTCTA
* *
29774 TATTATGGTACCGATACTCCTTTTCAGTATC
649 TACTATGGTACCGATACTCATTTTCAGTATC
* * * *
29805 GATAATGCACCGTTATGCATTTAATTCATGGCATCATTTCATACCTATAATGAACAGTTATGCAT
1 GATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCTATAATGAACCGTTATGCAT
* *
29870 TTTTCTTAATGGCATCCATTCATGCCTATAATGCACCATTATGCATTTCATTTATAGCATCATTT
66 TTTTCTTAATGGCATCCTTTCATGCCTATAATGCACCATTATGCATTTCATTTATGGCATCATTT
* * * *
29935 CATGCCAAAAATGCACGGTTATACATTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATT
131 CATGCCGAAAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
*
30000 ATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATCTTT
196 ATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATCCTT
* * *
30065 TTCATAAACATAATGAAAAATATATTATCTACTGTAAAACATACAGTAAATCACAACATTCTAAT
261 TTCATAAACATAATG-AAAATATATTAACTATTGTAAAACATACATTAAATCACAACATTCTAAT
* * * * *
30130 TTGACTCATTGCAAATATTCCTCATCTCATATAAATACAATGAATGTGCTCACTTGATAATCCTC
325 TTGACTCATTGCGAATCTTCCTCATCTCATATAAATACAATAAATGTACTCACCTGATAATCCTC
*
30195 ACTAATAAGATGTAATGATGTCTGACTATTCAACAACTTTATCTTTGCCCTTTTTCTTGCTAGAC
390 ACTAATAAGATGTAATGATGTCCGACTATTCAACAACTTTATCTTTGCCCTTTTTCTTGCTAGAC
* * * *
30260 TTAGGTGCTTGGTTATGATCTATACAAGCATCCATTAAAGATACATATCATACCAAATGTTAGTA
455 TCAGGAGCTTGGTTATGATCTATACAAACATCCATTAAAGACACATATCATACCAAATGTTAGTA
*
30325 TATTCCCTAATATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAATTTCTATAACAATT
520 TATTCCCTAACATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAATTTCTATAACAATT
* * * *
30390 TCAACTTATCTTATAGTTACATTCTCAATAGTATCGGTTCCCTACCATGGTATAGATACTTATAT
585 TCAACTTATCTTATAGTTACATACTCAATAGTATTGGTACCCTACCATGGTATAGATACTTCTAT
30455 ACTATGGTACCGATACTCATTTTCAGTATC
650 ACTATGGTACCGATACTCATTTTCAGTATC
* * *
30485 GATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCAG
1 GATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCTATAATGAACCGTTATGCAT
* * * *
30550 TTTTCTTAATGGCATCCTTTCATGCCTATAATTCACCATTATGCATTTCACTTGTGGTATCATTT
66 TTTTCTTAATGGCATCCTTTCATGCCTATAATGCACCATTATGCATTTCATTTATGGCATCATTT
*
30615 CATGCCGAAAATGCATCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
131 CATGCCGAAAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
* * *
30680 ATGTATTTCATTTATTCATTCATTGTATAGAAGTTCGTACTATAAAACTCATTCATAATATCCTT
196 ATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATCCTT
* *
30745 TTCATATAA-ATAATGAAAAAATGTTAACTATTGTAAAACATACATTAAATCACAACATTCTAAT
261 TTCATA-AACATAATGAAAATATATTAACTATTGTAAAACATACATTAAATCACAACATTCTAAT
* * *
30809 TTCACTCATTACGAATCTTCCTCATCTCATATAAACACAATAAATGTACTCACCTGATAATCCTC
325 TTGACTCATTGCGAATCTTCCTCATCTCATATAAATACAATAAATGTACTCACCTGATAATCCTC
30874 ACTAATAAGATGTAATGATGT
390 ACTAATAAGATGTAATGATGT
30895 TATTTGGTTT
Statistics
Matches: 1613, Mismatches: 147, Indels: 16
0.91 0.08 0.01
Matches are distributed among these distances:
677 1 0.00
678 613 0.38
679 372 0.23
680 625 0.39
681 2 0.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (679 bp):
GATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCTATAATGAACCGTTATGCAT
TTTTCTTAATGGCATCCTTTCATGCCTATAATGCACCATTATGCATTTCATTTATGGCATCATTT
CATGCCGAAAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
ATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATCCTT
TTCATAAACATAATGAAAATATATTAACTATTGTAAAACATACATTAAATCACAACATTCTAATT
TGACTCATTGCGAATCTTCCTCATCTCATATAAATACAATAAATGTACTCACCTGATAATCCTCA
CTAATAAGATGTAATGATGTCCGACTATTCAACAACTTTATCTTTGCCCTTTTTCTTGCTAGACT
CAGGAGCTTGGTTATGATCTATACAAACATCCATTAAAGACACATATCATACCAAATGTTAGTAT
ATTCCCTAACATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAATTTCTATAACAATTT
CAACTTATCTTATAGTTACATACTCAATAGTATTGGTACCCTACCATGGTATAGATACTTCTATA
CTATGGTACCGATACTCATTTTCAGTATC
Found at i:30540 original size:45 final size:45
Alignment explanation
Indices: 30486--30694 Score: 276
Period size: 45 Copynumber: 4.6 Consensus size: 45
30476 TTCAGTATCG
30486 ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCT
1 ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCT
*
30531 ATAATGCACCGTTATGCAGTTTTC-TTAATGGCATCCTTTCATGCCT
1 ATAATGCACCGTTATGCA--TTTCATTTATGGCATCCTTTCATGCCT
* * * * * * *
30577 ATAATTCACCATTATGCATTTCACTTGTGGTATCATTTCATGCCG
1 ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCT
* * *
30622 AAAATGCATCGTTATGCATTTCATTTATGACATCCTTTCATGCCT
1 ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCT
* *
30667 ATAATGCACCATTATGTATTTCATTTAT
1 ATAATGCACCGTTATGCATTTCATTTAT
30695 TCATTCATTG
Statistics
Matches: 138, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
44 4 0.03
45 93 0.67
46 37 0.27
47 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (45 bp):
ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCT
Found at i:33094 original size:45 final size:45
Alignment explanation
Indices: 32972--33236 Score: 365
Period size: 45 Copynumber: 5.9 Consensus size: 45
32962 TATTCTTTAT
*
32972 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
33017 TTTTTC-TTTATGGCAACCTTTCATGCCAATAATTCACCGTTATGCA
1 --TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
33063 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACCATTAT--A
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
33106 TATTCATTTATGGCATCCTTTCATGTCGATAATGCACCGTTATACA
1 T-TTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
33152 TTTCATTTATGACATCCTTTCATGCCGATAATGTACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
** *
33197 TTTCATTTATGGTGTCCTTTCATGCCTATAATGCACCGTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTT
33237 TTTAGAGTTC
Statistics
Matches: 196, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
43 2 0.01
44 44 0.22
45 107 0.55
46 39 0.20
47 4 0.02
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
Found at i:33154 original size:89 final size:89
Alignment explanation
Indices: 32972--33236 Score: 354
Period size: 89 Copynumber: 2.9 Consensus size: 89
32962 TATTCTTTAT
* *
32972 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTC-TTTATGGCAACCT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTAT-CA--TTTCATTTATGGCATCCT
* *
33036 TTCATGCCAATAATTCACCGTTATGCA
63 TTCATGCCAATAATGCACCGTTATACA
* *
33063 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACCATTAT-ATATTCATTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATCAT-TTCATTTATGGCATCCTTT
* *
33127 CATGTCGATAATGCACCGTTATACA
65 CATGCCAATAATGCACCGTTATACA
* * **
33152 TTTCATTTATGACATCCTTTCATGCCGATAATGTACCGTTATGCATTTCATTTATGGTGTCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTAT-CATTTCATTTATGGCATCCTTT
*
33217 CATGCCTATAATGCACCGTT
65 CATGCCAATAATGCACCGTT
33237 TTTAGAGTTC
Statistics
Matches: 154, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
87 1 0.01
88 3 0.02
89 74 0.48
90 35 0.23
91 41 0.27
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (89 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATCATTTCATTTATGGCATCCTTTC
ATGCCAATAATGCACCGTTATACA
Found at i:33215 original size:134 final size:134
Alignment explanation
Indices: 32973--33233 Score: 391
Period size: 134 Copynumber: 1.9 Consensus size: 134
32963 ATTCTTTATT
* * *
32973 TTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCAACCTTT
1 TTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATACA-TTTTCTTTATGACAACCTTT
*
33038 CATGCCAATAATTCACCGTTATGCATTTCATTTATGGCATCCTTTCATGTCGATAATGCACCATT
65 CATGCCAATAATTCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATT
33103 ATATA
130 ATATA
* *
33108 TTCATTTATGGCATCCTTTCATGTCGATAATGCACCGTTATACA-TTTCATTTATGACATCCTTT
1 TTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATACATTTTC-TTTATGACAACCTTT
* ** *
33172 CATGCCGATAATGT-ACCGTTATGCATTTCATTTATGGTGTCCTTTCATGCCTATAATGCACC
65 CATGCCAATAAT-TCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCGATAATGCACC
33234 GTTTTTAGAG
Statistics
Matches: 114, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
133 4 0.04
134 68 0.60
135 42 0.37
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.41
Consensus pattern (134 bp):
TTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATACATTTTCTTTATGACAACCTTTC
ATGCCAATAATTCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTA
TATA
Found at i:33787 original size:21 final size:19
Alignment explanation
Indices: 33761--33799 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
33751 CTCAAAGCAA
33761 TATCGATACTAATTGCATCAG
1 TATCGATACT-ATT-CATCAG
33782 TATCGATACTATTCATCA
1 TATCGATACTATTCATCA
33800 TAATTCTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 3 0.17
21 10 0.56
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (19 bp):
TATCGATACTATTCATCAG
Found at i:35835 original size:17 final size:17
Alignment explanation
Indices: 35815--35866 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
35805 TTTAGGGAAG
35815 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
35832 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
35849 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
35866 T
1 T
35867 GACTATTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:38949 original size:91 final size:90
Alignment explanation
Indices: 38838--39157 Score: 419
Period size: 91 Copynumber: 3.5 Consensus size: 90
38828 TATTCTTTAT
* * **
38838 TTTCATTTATGTCATCCTTTCATGCCTATAATGCACTGTTATGCATTTTTCTTTATGGCATCCTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA-TTTTCTTTATGGCATCCTT
* * *
38903 TCATGCCGATAATGCACCATTGTGTG
65 TCATGCCGATAATGCACCGTTATGTA
* ** *
38929 TCTCATTTATGGCATCCTTTCATGTAGATAATGCACCGTTATGCA-TTTCATTTATGGCATCCTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTC-TTTATGGCATCCTT
* *
38993 TCATGCCTATAATGCACCGTTATGCATT
65 TCATGCCGATAATGCACCGTTATG--TA
* *
39021 TTTC-TTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTATTTATGGCATCATTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTCTTTATGGCATCCTTT
* *
39085 CATGTCGATAATGCACCGTTATGCA
66 CATGCCGATAATGCACCGTTATGTA
* *
39110 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCATTATGCATTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTT
39158 CATTTATTCA
Statistics
Matches: 202, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
89 8 0.04
90 76 0.38
91 111 0.55
92 7 0.03
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (90 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTCTTTATGGCATCCTTT
CATGCCGATAATGCACCGTTATGTA
Found at i:38959 original size:45 final size:45
Alignment explanation
Indices: 38838--39164 Score: 433
Period size: 45 Copynumber: 7.2 Consensus size: 45
38828 TATTCTTTAT
* * **
38838 TTTCATTTATGTCATCCTTTCATGCCTATAATGCACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* **
38883 TTTTTC-TTTATGGCATCCTTTCATGCCGATAATGCACCATTGTGTG
1 --TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* ** *
38929 TCTCATTTATGGCATCCTTTCATGTAGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* *
38974 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
39019 TTTTTC-TTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
1 --TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* * * *
39065 TTTTATTTATGGCATCATTTCATGTCGATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
* *
39110 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
39155 TTTCATTTAT
1 TTTCATTTAT
39165 TCATTCATTT
Statistics
Matches: 246, Mismatches: 30, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
44 6 0.02
45 161 0.65
46 71 0.29
47 8 0.03
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCA
Found at i:39042 original size:136 final size:136
Alignment explanation
Indices: 38838--39157 Score: 541
Period size: 136 Copynumber: 2.4 Consensus size: 136
38828 TATTCTTTAT
* *
38838 TTTCATTTATGTCATCCTTTCATGCCTATAATGCACTGTTATGCATTTTTCTTTATGGCATCCTT
1 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCATCCTT
* ** *
38903 TCATGCCGATAATGCACCATTGTGTGTCTCATTTATGGCATCCTTTCATGTAGATAATGCACCGT
66 TCATGCCGATAATGCACCATTATGCATCTCATTTATGGCATCATTTCATGTAGATAATGCACCGT
38968 TATGCA
131 TATGCA
*
38974 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCATCCTT
1 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCATCCTT
* * *
39039 TCATGCCGATAATGCACCATTATGCATTTTATTTATGGCATCATTTCATGTCGATAATGCACCGT
66 TCATGCCGATAATGCACCATTATGCATCTCATTTATGGCATCATTTCATGTAGATAATGCACCGT
39104 TATGCA
131 TATGCA
*
39110 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCATTATGCATTT
1 TTTCATTTATGACATCCTTTCATGCCTATAATGCACCGTTATGCATTT
39158 CATTTATTCA
Statistics
Matches: 173, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
136 173 1.00
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (136 bp):
TTTCATTTATGACATCCTTTCATGCCTATAATGCACCGTTATGCATTTTTCTTTATGGCATCCTT
TCATGCCGATAATGCACCATTATGCATCTCATTTATGGCATCATTTCATGTAGATAATGCACCGT
TATGCA
Found at i:39694 original size:45 final size:45
Alignment explanation
Indices: 39636--39843 Score: 240
Period size: 45 Copynumber: 4.6 Consensus size: 45
39626 TCAGTATCGG
* * * *
39636 TAATGCACTGTTATGTATTTCATTTATAGCATCATTTCATGCCTA
1 TAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTA
* * * *
39681 TAATGAACCGTTATGCATTTTTC-TTAATGGCATTCTTTCCTGCCTA
1 TAATGCACCGTTATGCA--TTTCATTTATGGCATCCTTTCATGCCTA
* *
39727 TAATGCACCATTATGCATTTCATTTATGGCATCCTTTCATGCCGA
1 TAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTA
* *
39772 TAATGCACCGTTATGCA-TTCTAATTATGGAATCCTTTCATGCCTA
1 TAATGCACCGTTATGCATTTC-ATTTATGGCATCCTTTCATGCCTA
* * *
39817 TAATGCACCATTATACATTTAATTTAT
1 TAATGCACCGTTATGCATTTCATTTAT
39844 TCATTCATTT
Statistics
Matches: 136, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
44 7 0.05
45 90 0.66
46 35 0.26
47 4 0.03
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (45 bp):
TAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTA
Found at i:40372 original size:45 final size:45
Alignment explanation
Indices: 40313--40521 Score: 210
Period size: 45 Copynumber: 4.6 Consensus size: 45
40303 TTCAGTATCG
* * * * *
40313 ATAATGCACCGTTATGCATTTAATTCATGGCATCATTTCATACCT
1 ATAATGAACAGTTATGCATTTCATTTATGGCATCATTTCATGCCT
*
40358 ATAATGAACAGTTATGCATTTTTC-TTAATGGCATCCA-TTCATGCCT
1 ATAATGAACAGTTATGCA--TTTCATTTATGGCAT-CATTTCATGCCT
* * *
40404 ATAATGCACCA-TTATGCATTTCATTTATAGCATCATTTCATGCCA
1 ATAATG-AACAGTTATGCATTTCATTTATGGCATCATTTCATGCCT
* * * * *
40449 AAAATGCACGGTTATACATTTCATTTATGGCATCCTTTCATGCCT
1 ATAATGAACAGTTATGCATTTCATTTATGGCATCATTTCATGCCT
*
40494 ATAATGCACCA-TTATGCATTTCATTTAT
1 ATAATG-AACAGTTATGCATTTCATTTAT
40522 TCATTCATTT
Statistics
Matches: 134, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
44 7 0.05
45 88 0.66
46 31 0.23
47 8 0.06
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (45 bp):
ATAATGAACAGTTATGCATTTCATTTATGGCATCATTTCATGCCT
Found at i:40531 original size:90 final size:90
Alignment explanation
Indices: 40313--40521 Score: 285
Period size: 91 Copynumber: 2.3 Consensus size: 90
40303 TTCAGTATCG
* * * * * * *
40313 ATAATGCACCGTTATGCATTTAATTCATGGCATCATTTCATACCTATAATGAACAGTTATGCATT
1 ATAATGCACCATTATGCATTTCATTTATAGCATCATTTCATACCAAAAATGAACAGTTATACA-T
40378 TTTCTTAATGGCATCCATTCATGCCT
65 TTTCTTAATGGCATCCATTCATGCCT
* * *
40404 ATAATGCACCATTATGCATTTCATTTATAGCATCATTTCATGCCAAAAATGCACGGTTATACA-T
1 ATAATGCACCATTATGCATTTCATTTATAGCATCATTTCATACCAAAAATGAACAGTTATACATT
* *
40468 TTCATTTATGGCATCCTTTCATGCCT
66 TTC-TTAATGGCATCCATTCATGCCT
40494 ATAATGCACCATTATGCATTTCATTTAT
1 ATAATGCACCATTATGCATTTCATTTAT
40522 TCATTCATTT
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
89 4 0.04
90 48 0.46
91 53 0.50
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (90 bp):
ATAATGCACCATTATGCATTTCATTTATAGCATCATTTCATACCAAAAATGAACAGTTATACATT
TTCTTAATGGCATCCATTCATGCCT
Found at i:40895 original size:680 final size:679
Alignment explanation
Indices: 38955--41401 Score: 3869
Period size: 680 Copynumber: 3.6 Consensus size: 679
38945 CTTTCATGTA
* *
38955 GATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCAT
1 GATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCTATAATGAACCGTTATGCAT
* * *
39020 TTTTCTTTATGGCATCCTTTCATGCCGATAATGCACCATTATGCATTTTATTTATGGCATCATTT
66 TTTTCTTAATGGCATCCTTTCATGCCTATAATGCACCATTATGCATTTCATTTATGGCATCATTT
* *
39085 CATGTCGATAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
131 CATGCCGAAAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
* * *
39150 ATGCATTTCATTTATTCATTCATTTTAGAGAAGTTCATACTCCAAAACTCATTCATAATATCCTT
196 ATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATCCTT
* * * * * *
39215 TTCATATACAAAATGCAAATATATTAACTAATGTAAAACATACATAAAATCACAACATTCTAATA
261 TTCATAAACATAATGAAAATATATTAACTATTGTAAAACATACATTAAATCACAACATTCTAATT
*
39280 TGACTCATTGTC-AATCTTCCTCATCTCATATAAATACAATAAATGTACTCACATGATAATCCTC
326 TGACTCATTG-CGAATCTTCCTCATCTCATATAAATACAATAAATGTACTCACCTGATAATCCTC
* * *
39344 ACTAATAAGATATAATGATGTCCGGCTATTCAGCAACTTTATCTTTGCCCTTTTTCTTGCTAGAC
390 ACTAATAAGATGTAATGATGTCCGACTATTCAACAACTTTATCTTTGCCCTTTTTCTTGCTAGAC
*
39409 TCAGGAGCTTGGTTATGATCTACACAAACATCCATTAAAGACACATATCATACCAAATGTTAGTA
455 TCAGGAGCTTGGTTATGATCTATACAAACATCCATTAAAGACACATATCATACCAAATGTTAGTA
* * * *
39474 TATTCCATAACATTTATACCTTAATAAAACTCAAAAGTACAATTATTTCAATTTCTATAACAATT
520 TATTCCCTAACATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAATTTCTATAACAATT
** * * * * *
39539 TCAACTTATCTTATAGTTACATGTTGAATAGTGTTGGTACGCTACCATGGTATCGATACTTCTAT
585 TCAACTTATCTTATAGTTACATACTCAATAGTATCGGTACCCTACCATGGTATAGATACTTCTAT
*
39604 ACAATGGTACCGATACTCATTTTCAGTATC
650 ACTATGGTACCGATACTCATTTTCAGTATC
* * * *
39634 GGTAATGCACTGTTATGTATTTCATTTATAGCATCATTTCATGCCTATAATGAACCGTTATGCAT
1 GATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCTATAATGAACCGTTATGCAT
* * *
39699 TTTTCTTAATGGCATTCTTTCCTGCCTATAATGCACCATTATGCATTTCATTTATGGCATCCTTT
66 TTTTCTTAATGGCATCCTTTCATGCCTATAATGCACCATTATGCATTTCATTTATGGCATCATTT
* *
39764 CATGCCGATAATGCACCGTTATGCA-TTCTAATTATGGA-ATCCTTTCATGCCTATAATGCACCA
131 CATGCCGAAAATGCACCGTTATGCATTTC-ATTTAT-GACATCCTTTCATGCCTATAATGCACCA
* * * *
39827 TTATACATTTAATTTATTCATTCATTTTACAGAAGTTCGTACTCTAAAACTCATTCATAATATCA
194 TTATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATCC
*
39892 TTTT-ATAAACATAATGAAAATATATTAACTATTGTAAAACATACATTAAATCACAACATTCTAG
259 TTTTCATAAACATAATGAAAATATATTAACTATTGTAAAACATACATTAAATCACAACATTCTAA
* *
39956 TTTGACTCATTGTGAATCTTCCTCATCTCATATAAATACAATGAATGTACTCACCTGATAATCCT
324 TTTGACTCATTGCGAATCTTCCTCATCTCATATAAATACAATAAATGTACTCACCTGATAATCCT
* * * *
40021 CACTAACAATATGTAATGATGTCCGACTATTCAACAACTTTATCTTTTCCCTTTTTCTTACTAGA
389 CACTAATAAGATGTAATGATGTCCGACTATTCAACAACTTTATCTTTGCCCTTTTTCTTGCTAGA
*
40086 CTCAGGAGCTTGGTTATGATCTATACAAACATCCATTAAAGACACATATCATACCAATTGTTAGT
454 CTCAGGAGCTTGGTTATGATCTATACAAACATCCATTAAAGACACATATCATACCAAATGTTAGT
* *
40151 ATATTCCCTAACATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAAATTCTGTAACAAT
519 ATATTCCCTAACATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAATTTCTATAACAAT
* * *
40216 TTCATCTAATTTTATAGTTACATACTCAATAGTATCGGTACCCTACCATGGTATAGATACTTCTA
584 TTCAACTTATCTTATAGTTACATACTCAATAGTATCGGTACCCTACCATGGTATAGATACTTCTA
* *
40281 TATTATGGTACCGATACTCCTTTTCAGTATC
649 TACTATGGTACCGATACTCATTTTCAGTATC
* * * *
40312 GATAATGCACCGTTATGCATTTAATTCATGGCATCATTTCATACCTATAATGAACAGTTATGCAT
1 GATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCTATAATGAACCGTTATGCAT
* *
40377 TTTTCTTAATGGCATCCATTCATGCCTATAATGCACCATTATGCATTTCATTTATAGCATCATTT
66 TTTTCTTAATGGCATCCTTTCATGCCTATAATGCACCATTATGCATTTCATTTATGGCATCATTT
* * * *
40442 CATGCCAAAAATGCACGGTTATACATTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATT
131 CATGCCGAAAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
*
40507 ATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATCTTT
196 ATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATCCTT
* * *
40572 TTCATAAACATAATGAAAAATATATTATCTACTGTAAAACATACAGTAAATCACAACATTCTAAT
261 TTCATAAACATAATG-AAAATATATTAACTATTGTAAAACATACATTAAATCACAACATTCTAAT
* * * * *
40637 TTGACTCATTGCAAATATTCCTCATCTCATATAAATACAATGAATGTGCTCACTTGATAATCCTC
325 TTGACTCATTGCGAATCTTCCTCATCTCATATAAATACAATAAATGTACTCACCTGATAATCCTC
*
40702 ACTAATAAGATGTAATGATGTCTGACTATTCAACAACTTTATCTTTGCCCTTTTTCTTGCTAGAC
390 ACTAATAAGATGTAATGATGTCCGACTATTCAACAACTTTATCTTTGCCCTTTTTCTTGCTAGAC
* * * *
40767 TTAGGTGCTTGGTTATGATCTATACAAGCATCCATTAAAGATACATATCATACCAAATGTTAGTA
455 TCAGGAGCTTGGTTATGATCTATACAAACATCCATTAAAGACACATATCATACCAAATGTTAGTA
*
40832 TATTCCCTAATATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAATTTCTATAACAATT
520 TATTCCCTAACATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAATTTCTATAACAATT
* * *
40897 TCAACTTATCTTATAGTTACATTCTCAATAGTATCGGTTCCCTACCATGGTATAGATACTTATAT
585 TCAACTTATCTTATAGTTACATACTCAATAGTATCGGTACCCTACCATGGTATAGATACTTCTAT
40962 ACTATGGTACCGATACTCATTTTCAGTATC
650 ACTATGGTACCGATACTCATTTTCAGTATC
* * *
40992 GATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCAG
1 GATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCTATAATGAACCGTTATGCAT
* * * *
41057 TTTTCTTAATGGCATCCTTTCATGCCTATAATTCACCATTATGCATTTCACTTGTGGTATCATTT
66 TTTTCTTAATGGCATCCTTTCATGCCTATAATGCACCATTATGCATTTCATTTATGGCATCATTT
*
41122 CATGCCGAAAATGCATCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
131 CATGCCGAAAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
* * *
41187 ATGTATTTCATTTATTCATTCATTGTATAGAAGTTCGTACTATAAAACTCATTCATAATATCCTT
196 ATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATCCTT
* *
41252 TTCATATAA-ATAATGAAAAAATGTTAACTATTGTAAAACATACATTAAATCACAACATTCTAAT
261 TTCATA-AACATAATGAAAATATATTAACTATTGTAAAACATACATTAAATCACAACATTCTAAT
* * *
41316 TTCACTCATTACGAATCTTCCTCATCTCATATAAACACAATAAATGTACTCACCTGATAATCCTC
325 TTGACTCATTGCGAATCTTCCTCATCTCATATAAATACAATAAATGTACTCACCTGATAATCCTC
41381 ACTAATAAGATGTAATGATGT
390 ACTAATAAGATGTAATGATGT
41402 TATTTGGTTT
Statistics
Matches: 1614, Mismatches: 146, Indels: 16
0.91 0.08 0.01
Matches are distributed among these distances:
677 1 0.00
678 613 0.38
679 372 0.23
680 626 0.39
681 2 0.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (679 bp):
GATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCTATAATGAACCGTTATGCAT
TTTTCTTAATGGCATCCTTTCATGCCTATAATGCACCATTATGCATTTCATTTATGGCATCATTT
CATGCCGAAAATGCACCGTTATGCATTTCATTTATGACATCCTTTCATGCCTATAATGCACCATT
ATGCATTTCATTTATTCATTCATTTTATAGAAGTTCGTACTCTAAAACTCATTCATAATATCCTT
TTCATAAACATAATGAAAATATATTAACTATTGTAAAACATACATTAAATCACAACATTCTAATT
TGACTCATTGCGAATCTTCCTCATCTCATATAAATACAATAAATGTACTCACCTGATAATCCTCA
CTAATAAGATGTAATGATGTCCGACTATTCAACAACTTTATCTTTGCCCTTTTTCTTGCTAGACT
CAGGAGCTTGGTTATGATCTATACAAACATCCATTAAAGACACATATCATACCAAATGTTAGTAT
ATTCCCTAACATTTATACTTTAATAATACTCAAAAGTACTATTATTTCAATTTCTATAACAATTT
CAACTTATCTTATAGTTACATACTCAATAGTATCGGTACCCTACCATGGTATAGATACTTCTATA
CTATGGTACCGATACTCATTTTCAGTATC
Found at i:41047 original size:45 final size:45
Alignment explanation
Indices: 40993--41201 Score: 276
Period size: 45 Copynumber: 4.6 Consensus size: 45
40983 TTCAGTATCG
40993 ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCT
1 ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCT
*
41038 ATAATGCACCGTTATGCAGTTTTC-TTAATGGCATCCTTTCATGCCT
1 ATAATGCACCGTTATGCA--TTTCATTTATGGCATCCTTTCATGCCT
* * * * * * *
41084 ATAATTCACCATTATGCATTTCACTTGTGGTATCATTTCATGCCG
1 ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCT
* * *
41129 AAAATGCATCGTTATGCATTTCATTTATGACATCCTTTCATGCCT
1 ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCT
* *
41174 ATAATGCACCATTATGTATTTCATTTAT
1 ATAATGCACCGTTATGCATTTCATTTAT
41202 TCATTCATTG
Statistics
Matches: 138, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
44 4 0.03
45 93 0.67
46 37 0.27
47 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (45 bp):
ATAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGCCT
Found at i:43602 original size:45 final size:45
Alignment explanation
Indices: 43480--43745 Score: 381
Period size: 45 Copynumber: 5.9 Consensus size: 45
43470 TATTCTTTAT
*
43480 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * *
43525 TTTTTC-TTTATGGCAACCTTTCATGCCAATAATTCACCGTTATGCA
1 --TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* * **
43571 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACCATTATATA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
43616 TTTCATTTATGGCATCCTTTCATGTCGATAATGCACCGTTATACA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
43661 TTTCATTTATGACATCCTTTCATGCCGATAATGTACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
* *
43706 TTTCATTTATGGTATCCTTTCATGCCTATAATGCACCGTT
1 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTT
43746 TTTAGAGTTC
Statistics
Matches: 198, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
44 4 0.02
45 153 0.77
46 37 0.19
47 4 0.02
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATGCA
Found at i:44296 original size:21 final size:19
Alignment explanation
Indices: 44270--44308 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
44260 CTCAAAGCAA
44270 TATCGATACTAATTGCATCAG
1 TATCGATACT-ATT-CATCAG
44291 TATCGATACTATTCATCA
1 TATCGATACTATTCATCA
44309 TAATTCTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 3 0.17
21 10 0.56
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (19 bp):
TATCGATACTATTCATCAG
Found at i:46343 original size:17 final size:17
Alignment explanation
Indices: 46323--46374 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
46313 TTTAGGGAAG
46323 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
46340 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
46357 TAGTTCATTTATTAAAC
1 TAGTTCATTAATTAAAC
46374 T
1 T
46375 GACTATTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:50671 original size:26 final size:24
Alignment explanation
Indices: 50637--50689 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
50627 TATTCCATCT
*
50637 TTATTTCATTTCATTTTTTATCTTTA
1 TTATTTCA-TTCATTTCTT-TCTTTA
*
50663 TTATTTCATTGATTTCTTTCTTTA
1 TTATTTCATTCATTTCTTTCTTTA
50687 TTA
1 TTA
50690 ACCATATTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.36
25 8 0.32
26 8 0.32
ACGTcount: A:0.19, C:0.11, G:0.02, T:0.68
Consensus pattern (24 bp):
TTATTTCATTCATTTCTTTCTTTA
Found at i:52393 original size:21 final size:21
Alignment explanation
Indices: 52369--52417 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
52359 ATCGAGGAAA
*
52369 AGACATCCCTGAACGATCAAG
1 AGACATCCCTGAACGATAAAG
52390 AGACATCCCTGAACGATAAAG
1 AGACATCCCTGAACGATAAAG
52411 AGACATC
1 AGACATC
52418 ATAACAAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.27, G:0.18, T:0.14
Consensus pattern (21 bp):
AGACATCCCTGAACGATAAAG
Found at i:68262 original size:26 final size:27
Alignment explanation
Indices: 68215--68271 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
68205 ATGAATAACA
* * *
68215 TATGTTTCCACATCTTTCTTAGCTTTAT
1 TATGTTT-CACATATTTCTTAGATTCAT
*
68243 TATGTTT-ACATATTTTTTAGATTCAT
1 TATGTTTCACATATTTCTTAGATTCAT
68269 TAT
1 TAT
68272 TATGTTTGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 18 0.72
28 7 0.28
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (27 bp):
TATGTTTCACATATTTCTTAGATTCAT
Done.