Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014059.1 Corchorus olitorius cultivar O-4 contig14092, 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: 2128
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Found at i:145 original size:48 final size:47
Alignment explanation
Indices: 85--1713 Score: 375
Period size: 48 Copynumber: 37.5 Consensus size: 47
75 CATTTTGGGA
*
85 CCCGACGCTCATGATATAACACCTTTGTCATTTTAGCCATTTTTTGCC
1 CCCGACGCTCATGATGTAACACCTTTG-CATTTTAGCCATTTTTTGCC
*
133 CCCGACGCTCATGATGTAACACCTAATGCATTTTAG-C-----TT---
1 CCCGACGCTCATGATGTAACACCT-TTGCATTTTAGCCATTTTTTGCC
* * * * *
172 -CCGATGCTCATGGTGTAACACCTTTAGCATTTTGGCCAGTTTTGGACC
1 CCCGACGCTCATGATGTAACACCTTT-GCATTTTAGCCATTTTTTG-CC
* * *
220 CCCGACGCTCATGCTGGTTA-ACCTTTGGCATTTTAGCCATTTTTTGTC
1 CCCGACGCTCATGAT-GTAACACCTTT-GCATTTTAGCCATTTTTTGCC
** *
268 CCCGACGCTGTTGATGTAACACC--T--A---T-GTCA-TTTTTG-C
1 CCCGACGCTCATGATGTAACACCTTTGCATTTTAGCCATTTTTTGCC
* *
305 CCCGACGCTTATGGTGTAACACCTTTGACATTTTAGCCATTTTTTGCC
1 CCCGACGCTCATGATGTAACACCTTTG-CATTTTAGCCATTTTTTGCC
* * * *
353 TCCGACGCTCATTATGTAACACC--TACA----A--CA-TTTTAGCC
1 CCCGACGCTCATGATGTAACACCTTTGCATTTTAGCCATTTTTTGCC
* * * * * * *
391 CCCGACGTTCATGGTGTATCAGCTTTAACATTTTGGCCAGTTTTTG-C
1 CCCGACGCTCATGATGTAACACCTTT-GCATTTTAGCCATTTTTTGCC
* * **
438 CCCGACGCTCATGCTGGTTA-ACCTTTGGCATTTTAGCCATACTTTG-C
1 CCCGACGCTCATGAT-GTAACACCTTT-GCATTTTAGCCATTTTTTGCC
* * * *
485 CCCGACGCTAATGATGTAACACC--T--A---T-GGCA-TTTTGGCA
1 CCCGACGCTCATGATGTAACACCTTTGCATTTTAGCCATTTTTTGCC
*
523 CCCGACGCTCATGATGTAACACC--TG-----T-GCCA--TTTTGGC
1 CCCGACGCTCATGATGTAACACCTTTGCATTTTAGCCATTTTTTGCC
* * * * * * *
560 ACCGACGCTCATGGTGTAACACCTTTAGCATTTTGGCAAATTTTGGCA
1 CCCGACGCTCATGATGTAACACCTTT-GCATTTTAGCCATTTTTTGCC
* * * * *
608 CCCGACGCTCATGCTAGTTA-ACCTTTGGTATTTTAGCCCTTTTTTGCA
1 CCCGACGCTCATGAT-GTAACACCTTT-GCATTTTAGCCATTTTTTGCC
* * * *
656 CCCGACGCTAATGATGTAACACC--T--A---T-GGCA-TTTTGGCA
1 CCCGACGCTCATGATGTAACACCTTTGCATTTTAGCCATTTTTTGCC
* * * * * *
694 CCCGACGATCATGATGTTACACCTTTGGCATATTGGCTATTTTTTGCT
1 CCCGACGCTCATGATGTAACACCTTT-GCATTTTAGCCATTTTTTGCC
* * *
742 CCCGACGCTCATTATTTAACACC--T--A---T-GCCA--TTTTGGC
1 CCCGACGCTCATGATGTAACACCTTTGCATTTTAGCCATTTTTTGCC
* * * * *
779 ACCGACGCTCAT-AGTGTAACACCTTTAGCATTTTGGCAAGTTTTGGCC
1 CCCGACGCTCATGA-TGTAACACCTTT-GCATTTTAGCCATTTTTTGCC
* * *
827 CCCGACGCTCATGCTAGTTA-ACCTTTGGCATTTTAGCCATTTTTTACC
1 CCCGACGCTCATGAT-GTAACACCTTT-GCATTTTAGCCATTTTTTGCC
** *
875 CCCGACGCAT-ATGATGTAACACC--T--A---T-GGTA-TTTTGGCC
1 CCCGACGC-TCATGATGTAACACCTTTGCATTTTAGCCATTTTTTGCC
* * * * *
913 CACGACGCTCATGGTGTAACACCTTTGGCATTTTGGCTATTTTTT-TC
1 CCCGACGCTCATGATGTAACACCTTT-GCATTTTAGCCATTTTTTGCC
* * * * *
960 CCCGACGCTCATTATGTAAAACC--T--A---T-GGCA-TTTTGGCG
1 CCCGACGCTCATGATGTAACACCTTTGCATTTTAGCCATTTTTTGCC
* * * *
998 CACGACGCTCATGATGTAACACC--T--A---T-GGCATTTTGT-CT
1 CCCGACGCTCATGATGTAACACCTTTGCATTTTAGCCATTTTTTGCC
* * * * *
1036 CCCGACGCTCATGGTGTAACTCCTTTGGCGTTTTGGTCATTTTTTGGCC
1 CCCGACGCTCATGATGTAACACCTTT-GCATTTTAGCCATTTTTT-GCC
*
1085 CCCGACG-TC--------AC-CTTTTGGCATTTTAAGCCCA-TTTTTGCC
1 CCCGACGCTCATGATGTAACACCTTT-GCATTTT-AG-CCATTTTTTGCC
* * *
1124 CCCAACGCTCATGATGTAACACC--T--A---T-GGCA-TTTTTGGC
1 CCCGACGCTCATGATGTAACACCTTTGCATTTTAGCCATTTTTTGCC
* * * * *
1162 CCCGACGCTTATGGTGTAACACCTTTGGCATTTTGGCTATTTTTTTCC
1 CCCGACGCTCATGATGTAACACCTTT-GCATTTTAGCCATTTTTTGCC
* * * * * *
1210 TCCGACGCTCATTACGTAACACC--T--A----CGACA-TTTTGGCC
1 CCCGACGCTCATGATGTAACACCTTTGCATTTTAGCCATTTTTTGCC
* * * * ** *
1248 CCCGACGCTCATGGTGTATCAGCTTTAGCATTTTGGCCCGTTTTGGCC
1 CCCGACGCTCATGATGTAACACCTTT-GCATTTTAGCCATTTTTTGCC
* * * *
1296 CCCGACGCTCATGCTGGTTA-ACCTTTGGCATTTTACCCATTCTTTGCC
1 CCCGACGCTCATGAT-GTAACACCTTT-GCATTTTAGCCATTTTTTGCC
* * *
1344 CCCGACGCTCATGATGTAACACC--T--A---T-GGCA-TTTTGGCA
1 CCCGACGCTCATGATGTAACACCTTTGCATTTTAGCCATTTTTTGCC
* * *
1382 CCCGACGCTCATGATGTAACACC--T--A---T-GGCA-TTTTGGCA
1 CCCGACGCTCATGATGTAACACCTTTGCATTTTAGCCATTTTTTGCC
* * * *
1420 CCCGACGCTCATGATGTAACACCTTTGGCATTTTGGCTATTTGTTGCT
1 CCCGACGCTCATGATGTAACACCTTT-GCATTTTAGCCATTTTTTGCC
* * * *
1468 CTCGACGCTCATTATGTAACACC--T--A---T-GGCA--TTTTGGC
1 CCCGACGCTCATGATGTAACACCTTTGCATTTTAGCCATTTTTTGCC
* * * * *
1505 ACCAACGCTCATGGTGTAACACCTTTTAGCATTTT-G-AACTGTTTTGGCC
1 CCCGACGCTCATGATGTAACACC-TTT-GCATTTTAGCCA-T-TTTTTGCC
* * * *
1554 CCCGACGCTCATGCTAGTTA-ACCTTTGGCATTTTCGCCACTTTTTGCC
1 CCCGACGCTCATGAT-GTAACACCTTT-GCATTTTAGCCATTTTTTGCC
* * *
1602 CCCGACGCTAATGATGTAACACCTATGGCATTTTAG---------G-A
1 CCCGACGCTCATGATGTAACACCT-TTGCATTTTAGCCATTTTTTGCC
* *
1640 CCCGACGCTCATGATATAACACCTTTGGCATTTTGGCCATTTTTTGCC
1 CCCGACGCTCATGATGTAACACCTTT-GCATTTTAGCCATTTTTTGCC
*
1688 CCCGACGCTAATGAGTGTAACGACCT
1 CCCGACGCTCATGA-TGTAAC-ACCT
1714 ATGAAATTTT
Statistics
Matches: 1165, Mismatches: 238, Indels: 354
0.66 0.14 0.20
Matches are distributed among these distances:
36 1 0.00
37 102 0.09
38 339 0.29
39 49 0.04
40 25 0.02
41 7 0.01
42 6 0.01
43 13 0.01
44 2 0.00
45 8 0.01
46 27 0.02
47 115 0.10
48 379 0.33
49 81 0.07
50 11 0.01
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (47 bp):
CCCGACGCTCATGATGTAACACCTTTGCATTTTAGCCATTTTTTGCC
Found at i:182 original size:86 final size:85
Alignment explanation
Indices: 20--256 Score: 221
Period size: 86 Copynumber: 2.8 Consensus size: 85
10 ATGCTAGTTT
* * * * * *
20 ACCTTTGGCATTTTCGCCACTTTTTG-CCCCGGCGCTAATTATGTAAATCCTATGGCATTTTGGG
1 ACCTTT-GCATTTTAGCCACTTTTTGCCCCCGACGCTCATGATGTAAATCCTATGGCATTTTAGC
84 ACCCGACGCTCATGATATAAC
65 ACCCGACGCTCATGATATAAC
*
105 ACCTTTGTCATTTTAGCCATTTTTTGCCCCCGACGCTCATGATGTAACA-CCTAAT-GCATTTTA
1 ACCTTTG-CATTTTAGCCACTTTTTGCCCCCGACGCTCATGATGTAA-ATCCT-ATGGCATTTTA
** * * *
168 GCTTCCGATGCTCATGGTGTAAC
63 GCACCCGACGCTCATGATATAAC
* * * * * *
191 ACCTTTAGCATTTTGGCCAGTTTTGGACCCCCGACGCTCATGCTGGTTAA-CCTTTGGCATTTTA
1 ACCTTT-GCATTTTAGCCACTTTTTG-CCCCCGACGCTCATGAT-GTAAATCCTATGGCATTTTA
255 GC
63 GC
257 CATTTTTTGT
Statistics
Matches: 126, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
84 1 0.01
85 22 0.17
86 66 0.52
87 34 0.27
88 3 0.02
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.35
Consensus pattern (85 bp):
ACCTTTGCATTTTAGCCACTTTTTGCCCCCGACGCTCATGATGTAAATCCTATGGCATTTTAGCA
CCCGACGCTCATGATATAAC
Found at i:252 original size:135 final size:133
Alignment explanation
Indices: 105--753 Score: 402
Period size: 134 Copynumber: 4.9 Consensus size: 133
95 ATGATATAAC
*
105 ACCTTTGTCATTTTAGCCATTTTTTGCCCCCGACGCTCATGATGTAACACCTAATG-CATTTTAG
1 ACCTTTGGCATTTTAGCCATTTTTTGCCCCCGACGCTCATGATGTAACACCT-ATGTCATTTTAG
* * *
169 CTTCCGATGCTCATGGTGTAACACCTTT-AGCATTTTGGCCAGTTTTGGACCCCCGACGCTCATG
65 C-CCCGACGCTCATGGTGTAACACCTTTGA-CATTTTAGCCAGTTTTGG-CCCCCGACGCTCATG
233 CTGGTTA
127 CTGGTTA
* ** *
240 ACCTTTGGCATTTTAGCCATTTTTTGTCCCCGACGCTGTTGATGTAACACCTATGTCATTTTTGC
1 ACCTTTGGCATTTTAGCCATTTTTTGCCCCCGACGCTCATGATGTAACACCTATGTCATTTTAGC
* * * * **
305 CCCGACGCTTATGGTGTAACACCTTTGACATTTTAGCCATTTTTTGCCTCCGACGCTCATTAT-G
66 CCCGACGCTCATGGTGTAACACCTTTGACATTTTAGCCAGTTTTGGCCCCCGACGCTCATGCTGG
369 -TA
131 TTA
* * * * * * *
371 ACAC-CT-ACA----A--CA-TTTTAGCCCCCGACGTTCATGGTGTATCAGCTTTAACATTTTGG
1 AC-CTTTGGCATTTTAGCCATTTTTTGCCCCCGACGCTCATGATGTA--A-C----AC-CTAT-G
* * * * *
427 CCAGTTTTTGCCCCGACGCTCATGCTGGTTA-ACCTTTGGCATTTTAGCCA-TACTTT-G-CCCC
56 TCA-TTTTAGCCCCGACGCTCATGGT-GTAACACCTTTGACATTTTAGCCAGT--TTTGGCCCCC
* * *
488 GACGCTAATGAT-GTAA
117 GACGCTCATGCTGGTTA
* * * * *
504 CACCTATGGCATTTT-G---------GCACCCGACGCTCATGATGTAACACCTGTGCCATTTTGG
1 -ACCTTTGGCATTTTAGCCATTTTTTGCCCCCGACGCTCATGATGTAACACCTATGTCATTTTAG
* * * * *
559 CACCGACGCTCATGGTGTAACACCTTT-AGCATTTTGGCAAATTTTGGCACCCGACGCTCATGCT
65 CCCCGACGCTCATGGTGTAACACCTTTGA-CATTTTAGCCAGTTTTGGCCCCCGACGCTCATGCT
*
623 AGTTA
129 GGTTA
* * * * * *
628 ACCTTTGGTATTTTAGCCCTTTTTTGCACCCGACGCTAATGATGTAACACCTATGGCATTTTGGC
1 ACCTTTGGCATTTTAGCCATTTTTTGCCCCCGACGCTCATGATGTAACACCTATGTCATTTTAGC
* * * * * * * * * *
693 ACCCGACGATCATGATGTTACACCTTTGGCATATTGGCTATTTTTTGCTCCCGACGCTCAT
66 -CCCGACGCTCATGGTGTAACACCTTTGACATTTTAGCCAGTTTTGGCCCCCGACGCTCAT
754 TATTTAACAC
Statistics
Matches: 405, Mismatches: 66, Indels: 87
0.73 0.12 0.16
Matches are distributed among these distances:
121 6 0.01
122 35 0.09
123 50 0.12
124 8 0.02
125 3 0.01
126 2 0.00
129 1 0.00
130 5 0.01
131 7 0.02
132 38 0.09
133 92 0.23
134 99 0.24
135 59 0.15
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.34
Consensus pattern (133 bp):
ACCTTTGGCATTTTAGCCATTTTTTGCCCCCGACGCTCATGATGTAACACCTATGTCATTTTAGC
CCCGACGCTCATGGTGTAACACCTTTGACATTTTAGCCAGTTTTGGCCCCCGACGCTCATGCTGG
TTA
Found at i:310 original size:37 final size:38
Alignment explanation
Indices: 260--338 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 38
250 TTTTAGCCAT
*
260 TTTTTGTCCCCGACGCTGT-TGATGTAACACCTATGTCA
1 TTTTTGTCCCCGACGCT-TATGATGTAACACCTATGACA
* *
298 TTTTTG-CCCCGACGCTTATGGTGTAACACCTTTGACA
1 TTTTTGTCCCCGACGCTTATGATGTAACACCTATGACA
335 TTTT
1 TTTT
339 AGCCATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 1 0.03
37 30 0.81
38 6 0.16
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (38 bp):
TTTTTGTCCCCGACGCTTATGATGTAACACCTATGACA
Found at i:330 original size:85 final size:85
Alignment explanation
Indices: 218--449 Score: 265
Period size: 85 Copynumber: 2.7 Consensus size: 85
208 CAGTTTTGGA
* * * * *
218 CCCCCGACGCTCATGCTGGTTA-ACCTTTGGCATTTTAGCCATTTTTTGTCCCCGACGCT-GTTG
1 CCCCCGACGTTCATGGT-GTAACACCTTTGACATTTTAGCCATTTTTTG-CCCCGACGCTCATT-
*** *
281 ATGTAACACCTATGTCATTTTTG
63 ATGTAACACCTACAACATTTTAG
304 -CCCCGACGCTT-ATGGTGTAACACCTTTGACATTTTAGCCATTTTTTGCCTCCGACGCTCATTA
1 CCCCCGACG-TTCATGGTGTAACACCTTTGACATTTTAGCCATTTTTTGCC-CCGACGCTCATTA
367 TGTAACACCTACAACATTTTAG
64 TGTAACACCTACAACATTTTAG
* * * * *
389 CCCCCGACGTTCATGGTGTATCAGCTTTAACATTTTGGCCAGTTTTTGCCCCGACGCTCAT
1 CCCCCGACGTTCATGGTGTAACACCTTTGACATTTTAGCCATTTTTTGCCCCGACGCTCAT
450 GCTGGTTAAC
Statistics
Matches: 126, Mismatches: 14, Indels: 13
0.82 0.09 0.08
Matches are distributed among these distances:
84 5 0.04
85 77 0.61
86 44 0.35
ACGTcount: A:0.19, C:0.29, G:0.17, T:0.35
Consensus pattern (85 bp):
CCCCCGACGTTCATGGTGTAACACCTTTGACATTTTAGCCATTTTTTGCCCCGACGCTCATTATG
TAACACCTACAACATTTTAG
Found at i:387 original size:220 final size:217
Alignment explanation
Indices: 1--556 Score: 758
Period size: 220 Copynumber: 2.5 Consensus size: 217
* * * * *
1 CCGACGCTCATGCTAGTTTACCTTTGGCATTTTCGCCACTTTTTGCCCCGGCGCTAATT-ATGTA
1 CCGACGCTCATGCTGGTTAACCTTTGGCATTTTAGCCATTTTTTGCCCCGACGCT-ATTGATGTA
* * *
65 A-ATCCTATGGCATTTTGGGACCCGACGCTCATGATATAACACCTTTGTCATTTTAGCCATTTTT
65 ACA-CCTATGGCATTTT-GGCCCCGACGCTCATGATGTAACACCTTTGACATTTTAGCCATTTTT
* ** *
129 TGCCCCCGACGCTCATGATGTAACACCTAATGCATTTTAGCTTCCGATGCTCATGGTGTAACACC
128 TGCCCCCGACGCTCATGATGTAACACCTAATACATTTTAGCCCCCGACGCTCATGGTGTAACACC
*
194 TTTAGCATTTTGGCCAGTTTTGGACCC
193 TTTAACATTTTGGCCAGTTTTGG--CC
*
221 CCGACGCTCATGCTGGTTAACCTTTGGCATTTTAGCCATTTTTTGTCCCCGACGCTGTTGATGTA
1 CCGACGCTCATGCTGGTTAACCTTTGGCATTTTAGCCATTTTTTG-CCCCGACGCTATTGATGTA
* * * *
286 ACACCTATGTCATTTTTGCCCCGACGCTTATGGTGTAACACCTTTGACATTTTAGCCATTTTTTG
65 ACACCTATGGCATTTTGGCCCCGACGCTCATGATGTAACACCTTTGACATTTTAGCCATTTTTTG
* * * * *
351 CCTCCGACGCTCATTATGTAACACCTACA-ACATTTTAGCCCCCGACGTTCATGGTGTATCAGCT
130 CCCCCGACGCTCATGATGTAACACCTA-ATACATTTTAGCCCCCGACGCTCATGGTGTAACACCT
*
415 TTAACATTTTGGCCAGTTTTTGCC
194 TTAACATTTTGGCCAGTTTTGGCC
** *
439 CCGACGCTCATGCTGGTTAACCTTTGGCATTTTAGCCATACTTTGCCCCGACGCTAATGATGTAA
1 CCGACGCTCATGCTGGTTAACCTTTGGCATTTTAGCCATTTTTTGCCCCGACGCTATTGATGTAA
* *
504 CACCTATGGCATTTTGGCACCCGACGCTCATGATGTAACACCTGTGCCATTTT
66 CACCTATGGCATTTTGGC-CCCGACGCTCATGATGTAACACCTTTGACATTTT
557 GGCACCGACG
Statistics
Matches: 297, Mismatches: 34, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
217 34 0.11
218 75 0.25
220 159 0.54
221 28 0.09
222 1 0.00
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (217 bp):
CCGACGCTCATGCTGGTTAACCTTTGGCATTTTAGCCATTTTTTGCCCCGACGCTATTGATGTAA
CACCTATGGCATTTTGGCCCCGACGCTCATGATGTAACACCTTTGACATTTTAGCCATTTTTTGC
CCCCGACGCTCATGATGTAACACCTAATACATTTTAGCCCCCGACGCTCATGGTGTAACACCTTT
AACATTTTGGCCAGTTTTGGCC
Found at i:470 original size:47 final size:47
Alignment explanation
Indices: 419--521 Score: 120
Period size: 47 Copynumber: 2.2 Consensus size: 47
409 TCAGCTTTAA
* * * * *
419 CATTTTGGCCAGT-TTTTGCCCCGACGCTCATGCTGGTTA-ACCTTTGG
1 CATTTTGGCCA-TACTTTGCCCCGACGCTAATGAT-GTAACACCTATGG
*
466 CATTTTAGCCATACTTTGCCCCGACGCTAATGATGTAACACCTATGG
1 CATTTTGGCCATACTTTGCCCCGACGCTAATGATGTAACACCTATGG
513 CATTTTGGC
1 CATTTTGGC
522 ACCCGACGCT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
46 4 0.09
47 43 0.91
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.34
Consensus pattern (47 bp):
CATTTTGGCCATACTTTGCCCCGACGCTAATGATGTAACACCTATGG
Found at i:537 original size:38 final size:38
Alignment explanation
Indices: 485--1528 Score: 319
Period size: 38 Copynumber: 24.6 Consensus size: 38
475 CATACTTTGC
*
485 CCCGACGCTAATGATGTAACACCTATGGCATTTTGGCA
1 CCCGACGCTCATGATGTAACACCTATGGCATTTTGGCA
* *
523 CCCGACGCTCATGATGTAACACCTGTGCCATTTTGGCA
1 CCCGACGCTCATGATGTAACACCTATGGCATTTTGGCA
*
561 -CCGACGCTCATGGTGTAACACCTTTAGCATTTTGGCAAATTTTGGCA
1 CCCGACGCTCATGATGTAACACC--T---A---TGGC--ATTTTGGCA
* * * *
608 CCCGACGCTCATGCTAGTTA-ACCTTTGGTATTTTAGCCCTTTTTTGCA
1 CCCGACGCTCATGAT-GTAACACCTATGGCATTTT-G---------GCA
*
656 CCCGACGCTAATGATGTAACACCTATGGCATTTTGGCA
1 CCCGACGCTCATGATGTAACACCTATGGCATTTTGGCA
* * * *
694 CCCGACGATCATGATGTTACACCTTTGGCATATTGGCTATTTTTTGCT
1 CCCGACGCTCATGATGTAACA-C-----C-TA-TGGC-A-TTTTGGCA
* * *
742 CCCGACGCTCATTATTTAACACCTATGCCATTTTGGCA
1 CCCGACGCTCATGATGTAACACCTATGGCATTTTGGCA
*
780 -CCGACGCTCAT-AGTGTAACACCTTTAGCATTTTGGCAAGTTTTGGCC
1 CCCGACGCTCATGA-TGTAACACC--T---A---TGGC-A-TTTTGGCA
* * * *
827 CCCGACGCTCATGCTAGTTA-ACCTTTGGCATTTTAGCCATTTTTTA
1 CCCGACGCTCATGAT-GTAACACCTATGGCATTTT-GGC-------A
*
873 CCCCCGACGCAT-ATGATGTAACACCTATGGTATTTTGGC-
1 --CCCGACGC-TCATGATGTAACACCTATGGCATTTTGGCA
* *
912 CCACGACGCTCATGGTGTAACACCTTTGGCATTTTGGCTA
1 CC-CGACGCTCATGATGTAACACCTATGGCATTTTGGC-A
* * *
952 TTTTTTTCCCCGACGCTCATTATGTAAAACCTATGGCATTTTGGCG
1 --------CCCGACGCTCATGATGTAACACCTATGGCATTTTGGCA
* * *
998 CACGACGCTCATGATGTAACACCTATGGCATTTTGTCT
1 CCCGACGCTCATGATGTAACACCTATGGCATTTTGGCA
* * * *
1036 CCCGACGCTCATGGTGTAACTCCTTTGGCGTTTTGGTCATTTTTTGGCC
1 CCCGACGCTCATGATGTAAC-AC-----C--TATGG-CA--TTTTGGCA
*** * ** ** * * * *
1085 CCCGACG-TCACCTTTTGGCATTTTAAGCCCATTTTTGCC
1 CCCGACGCTCATGATGTAACA-CCTATG-GCATTTTGGCA
*
1124 CCCAACGCTCATGATGTAACACCTATGGCATTTTTGGC-
1 CCCGACGCTCATGATGTAACACCTATGGCA-TTTTGGCA
* * *
1162 CCCGACGCTTATGGTGTAACACCTTTGGCATTTTGGCTA
1 CCCGACGCTCATGATGTAACACCTATGGCATTTTGGC-A
* * * * *
1201 TTTTTTTCCTCCGACGCTCATTACGTAACACCTACGACATTTTGGCC
1 --------C-CCGACGCTCATGATGTAACACCTATGGCATTTTGGCA
* * * * *
1248 CCCGACGCTCATGGTGTATCAGCTTTAGCATTTTGGCCCGTTTTGGCC
1 CCCGACGCTCATGATGTA--A-C---A-C-CTATGG--CATTTTGGCA
* * * * *
1296 CCCGACGCTCATGCTGGTTA-ACCTTTGGCATTTTACCCATTCTTTGCC
1 CCCGACGCTCATGAT-GTAACACCTATGG---------CATT-TTGGCA
1344 CCCGACGCTCATGATGTAACACCTATGGCATTTTGGCA
1 CCCGACGCTCATGATGTAACACCTATGGCATTTTGGCA
1382 CCCGACGCTCATGATGTAACACCTATGGCATTTTGGCA
1 CCCGACGCTCATGATGTAACACCTATGGCATTTTGGCA
*
1420 CCCGACGCTCATGATGTAACACCTTTGGCATTTTGGCTA
1 CCCGACGCTCATGATGTAACACCTATGGCATTTTGGC-A
*
1459 TTTGTTGCTCTCGACGCTCATTATGTAACACCTATGGCATTTTGGCA
1 -------C-C-CGACGCTCATGATGTAACACCTATGGCATTTTGGCA
* *
1506 -CCAACGCTCATGGTGTAACACCT
1 CCCGACGCTCATGATGTAACACCT
1529 TTTAGCATTT
Statistics
Matches: 759, Mismatches: 120, Indels: 255
0.67 0.11 0.22
Matches are distributed among these distances:
36 1 0.00
37 69 0.09
38 273 0.36
39 37 0.05
40 23 0.03
41 8 0.01
42 3 0.00
44 3 0.00
45 9 0.01
46 14 0.02
47 72 0.09
48 225 0.30
49 22 0.03
ACGTcount: A:0.20, C:0.28, G:0.19, T:0.33
Consensus pattern (38 bp):
CCCGACGCTCATGATGTAACACCTATGGCATTTTGGCA
Found at i:555 original size:85 final size:86
Alignment explanation
Indices: 438--835 Score: 333
Period size: 85 Copynumber: 4.7 Consensus size: 86
428 CAGTTTTTGC
* **
438 CCCGACGCTCATGCTGGTTA-ACCTTTGGCATTTTAGCCATACTTTGC-CCCGACGCTAATGATG
1 CCCGACGCTCATGAT-GTTACACCTTTGGCATTTTAGCCATTTTTTGCACCCGACGCTAATGATG
501 TAACACCTATGGCATTTTGGCA
65 TAACACCTATGGCATTTTGGCA
* * * *
523 CCCGACGCTCATGATGTAACACC--T-G-----T-GCCA-TTTTGGCA-CCGACGCTCATGGTGT
1 CCCGACGCTCATGATGTTACACCTTTGGCATTTTAGCCATTTTTTGCACCCGACGCTAATGATGT
577 AACACCTTTAGCATTTTGGCAAATTTTGGCA
66 AACACC--T---A---TGGC--ATTTTGGCA
* * *
608 CCCGACGCTCATGCTAGTTA-ACCTTTGGTATTTTAGCCCTTTTTTGCACCCGACGCTAATGATG
1 CCCGACGCTCATGAT-GTTACACCTTTGGCATTTTAGCCATTTTTTGCACCCGACGCTAATGATG
672 TAACACCTATGGCATTTTGGCA
65 TAACACCTATGGCATTTTGGCA
* * * * * * * *
694 CCCGACGATCATGATGTTACACCTTTGGCATATTGGCTATTTTTTGCTCCCGACGCTCATTATTT
1 CCCGACGCTCATGATGTTACACCTTTGGCATTTTAGCCATTTTTTGCACCCGACGCTAATGATGT
*
759 AACACCTATGCCATTTTGGCA
66 AACACCTATGGCATTTTGGCA
* * * * * * *
780 -CCGACGCTCAT-AGTGTAACACCTTTAGCATTTTGGCAAGTTTTGGCCCCCGACGCT
1 CCCGACGCTCATGA-TGTTACACCTTTGGCATTTTAGCCATTTTTTGCACCCGACGCT
836 CATGCTAGTT
Statistics
Matches: 254, Mismatches: 33, Indels: 52
0.75 0.10 0.15
Matches are distributed among these distances:
75 24 0.09
76 4 0.02
77 2 0.01
80 1 0.00
82 1 0.00
83 5 0.02
84 4 0.02
85 93 0.37
86 81 0.32
87 1 0.00
88 5 0.02
91 1 0.00
93 1 0.00
94 4 0.02
95 7 0.03
96 20 0.08
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (86 bp):
CCCGACGCTCATGATGTTACACCTTTGGCATTTTAGCCATTTTTTGCACCCGACGCTAATGATGT
AACACCTATGGCATTTTGGCA
Found at i:708 original size:171 final size:169
Alignment explanation
Indices: 392--717 Score: 508
Period size: 171 Copynumber: 1.9 Consensus size: 169
382 ATTTTAGCCC
* * * * * * *
392 CCGACGTTCATGGTGTATCAGCTTTAACATTTTGGCCAGTTTTTGCCCCGACGCTCATGCTGGTT
1 CCGACGCTCATGGTGTAACACCTTTAACATTTTGGCAAATTTTGGCCCCGACGCTCATGCTAGTT
457 AACCTTTGGCATTTTAGCCATACTTTGCCCCGACGCTAATGATGTAACACCTATGGCATTTTGGC
66 AACCTTTGGCATTTTAGCCATACTTTGCCCCGACGCTAATGATGTAACACCTATGGCATTTTGGC
*
522 ACCCGACGCTCATGATGTAACACCTGTGCCATTTTGGCA
131 ACCCGACGATCATGATGTAACACCTGTGCCATTTTGGCA
*
561 CCGACGCTCATGGTGTAACACCTTTAGCATTTTGGCAAATTTTGGCACCCGACGCTCATGCTAGT
1 CCGACGCTCATGGTGTAACACCTTTAACATTTTGGCAAATTTTGGC-CCCGACGCTCATGCTAGT
* * **
626 TAACCTTTGGTATTTTAGCCCTTTTTTGCACCCGACGCTAATGATGTAACACCTATGGCATTTTG
65 TAACCTTTGGCATTTTAGCCATACTTTGC-CCCGACGCTAATGATGTAACACCTATGGCATTTTG
*
691 GCACCCGACGATCATGATGTTACACCT
129 GCACCCGACGATCATGATGTAACACCT
718 TTGGCATATT
Statistics
Matches: 141, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
169 39 0.28
170 42 0.30
171 60 0.43
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.32
Consensus pattern (169 bp):
CCGACGCTCATGGTGTAACACCTTTAACATTTTGGCAAATTTTGGCCCCGACGCTCATGCTAGTT
AACCTTTGGCATTTTAGCCATACTTTGCCCCGACGCTAATGATGTAACACCTATGGCATTTTGGC
ACCCGACGATCATGATGTAACACCTGTGCCATTTTGGCA
Found at i:773 original size:219 final size:218
Alignment explanation
Indices: 523--1032 Score: 772
Period size: 219 Copynumber: 2.3 Consensus size: 218
513 CATTTTGGCA
* *
523 CCCGACGCTCATGATGTAACACCTGTGCCATTTTGGCACCGACGCTCATGGTGTAACACCTTTAG
1 CCCGACGCTCATTATGTAACACCTATGCCATTTTGGCACCGACGCTCATGGTGTAACACCTTTAG
* *
588 CATTTTGGCAAATTTTGGCACCCGACGCTCATGCTAGTTAACCTTTGGTATTTTAGCCCTTTTTT
66 CATTTTGGCAAATTTTGGCACCCGACGCTCATGCTAGTTAACCTTTGGCATTTTAGCCATTTTTT
* *
653 GCACCCGACGC-TAATGATGTAACACCTATGGCATTTTGGCACC-CGACGATCATGATGTTACAC
131 ACACCCGACGCAT-ATGATGTAACACCTATGGCATTTTGGC-CCACGACGATCATGATGTAACAC
716 CTTTGGCATATTGGCTATTTTTTGC
194 CTTTGGCATATTGGCTATTTTTTGC
* *
741 TCCCGACGCTCATTATTTAACACCTATGCCATTTTGGCACCGACGCTCATAGTGTAACACCTTTA
1 -CCCGACGCTCATTATGTAACACCTATGCCATTTTGGCACCGACGCTCATGGTGTAACACCTTTA
* *
806 GCATTTTGGCAAGTTTTGGCCCCCGACGCTCATGCTAGTTAACCTTTGGCATTTTAGCCATTTTT
65 GCATTTTGGCAAATTTTGGCACCCGACGCTCATGCTAGTTAACCTTTGGCATTTTAGCCATTTTT
* * * *
871 TACCCCCGACGCATATGATGTAACACCTATGGTATTTTGGCCCACGACGCTCATGGTGTAACACC
130 TACACCCGACGCATATGATGTAACACCTATGGCATTTTGGCCCACGACGATCATGATGTAACACC
* *
936 TTTGGCATTTTGGCTATTTTTTTC
195 TTTGGCATATTGGCTATTTTTTGC
* * * * * *
960 CCCGACGCTCATTATGTAAAACCTATGGCATTTTGGCGCACGACGCTCATGATGTAACACCTATG
1 CCCGACGCTCATTATGTAACACCTATGCCATTTTGGCAC-CGACGCTCATGGTGTAACACCTTTA
1025 GCATTTTG
65 GCATTTTG
1033 TCTCCCGACG
Statistics
Matches: 264, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
218 37 0.14
219 226 0.86
220 1 0.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.33
Consensus pattern (218 bp):
CCCGACGCTCATTATGTAACACCTATGCCATTTTGGCACCGACGCTCATGGTGTAACACCTTTAG
CATTTTGGCAAATTTTGGCACCCGACGCTCATGCTAGTTAACCTTTGGCATTTTAGCCATTTTTT
ACACCCGACGCATATGATGTAACACCTATGGCATTTTGGCCCACGACGATCATGATGTAACACCT
TTGGCATATTGGCTATTTTTTGC
Found at i:784 original size:37 final size:37
Alignment explanation
Indices: 743--816 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
733 TTTTTTGCTC
*
743 CCGACGCTCATTA-TTTAACACCTAT-GCCATTTTGGCA
1 CCGACGCTCA-TAGTGTAACACCTATAG-CATTTTGGCA
*
780 CCGACGCTCATAGTGTAACACCTTTAGCATTTTGGCA
1 CCGACGCTCATAGTGTAACACCTATAGCATTTTGGCA
817 AGTTTTGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 2 0.06
37 30 0.91
38 1 0.03
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.31
Consensus pattern (37 bp):
CCGACGCTCATAGTGTAACACCTATAGCATTTTGGCA
Found at i:852 original size:133 final size:133
Alignment explanation
Indices: 681--990 Score: 358
Period size: 133 Copynumber: 2.3 Consensus size: 133
671 GTAACACCTA
* * * * * *
681 TGGC-ATTTTGGCACCCGACGATCATGATGTTACACCTTTGGCATATTGGCTATTTTTTGCTCCC
1 TGGCAATTTTGGCCCCCGACGCTCATGATGTTACACCTTTGGCATATTAGCCATTTTTTACCCCC
* *
745 GACGC-TCATTATTTAACACCTATGCCATTTTGGCAC-CGACGCTCATAGTGTAACACCTTTAGC
66 GACGCAT-ATGATGTAACACCTATGCCATTTTGGCACACGACGCTCATAGTGTAACACCTTTAGC
808 ATTT
130 ATTT
* *
812 TGGCAAGTTTTGGCCCCCGACGCTCATGCTAGTTA-ACCTTTGGCATTTTAGCCATTTTTTACCC
1 TGGCAA-TTTTGGCCCCCGACGCTCATGAT-GTTACACCTTTGGCATATTAGCCATTTTTTACCC
** * * *
876 CCGACGCATATGATGTAACACCTATGGTATTTTGGCCCACGACGCTCATGGTGTAACACCTTTGG
64 CCGACGCATATGATGTAACACCTATGCCATTTTGGCACACGACGCTCATAGTGTAACACCTTTAG
941 CATTT
129 CATTT
* *** * * * *
946 TGGCTATTTTTTTCCCCGACGCTCATTATGTAAAACCTATGGCAT
1 TGGCAATTTTGGCCCCCGACGCTCATGATGTTACACCTTTGGCAT
991 TTTGGCGCAC
Statistics
Matches: 150, Mismatches: 23, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
131 4 0.03
132 4 0.03
133 103 0.69
134 39 0.26
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (133 bp):
TGGCAATTTTGGCCCCCGACGCTCATGATGTTACACCTTTGGCATATTAGCCATTTTTTACCCCC
GACGCATATGATGTAACACCTATGCCATTTTGGCACACGACGCTCATAGTGTAACACCTTTAGCA
TTT
Found at i:859 original size:85 final size:86
Alignment explanation
Indices: 672--860 Score: 224
Period size: 85 Copynumber: 2.2 Consensus size: 86
662 GCTAATGATG
* * * *
672 TAACACCTATGGCATTTTGGCACCCGACGATCATGATGTTACACCTTTGGCATATTGGCTATTTT
1 TAACACCTATGGCATTTTGGCACCCGACGATCATGATGTAACACCTTTAGCATATTGGCAAGTTT
* * *
737 TTGCTCCCGACGCTCATTATT
66 TGGCCCCCGACGCTCATTAGT
* * *
758 TAACACCTATGCCATTTTGGCA-CCGACGCTCAT-AGTGTAACACCTTTAGCATTTTGGCAAGTT
1 TAACACCTATGGCATTTTGGCACCCGACGATCATGA-TGTAACACCTTTAGCATATTGGCAAGTT
821 TTGGCCCCCGACGCTCATGCTAGT
65 TTGGCCCCCGACGCTCAT--TAGT
*
845 T-A-ACCTTTGGCATTTT
1 TAACACCTATGGCATTTT
861 AGCCATTTTT
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
84 1 0.01
85 61 0.69
86 22 0.25
87 4 0.05
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (86 bp):
TAACACCTATGGCATTTTGGCACCCGACGATCATGATGTAACACCTTTAGCATATTGGCAAGTTT
TGGCCCCCGACGCTCATTAGT
Found at i:1229 original size:86 final size:84
Alignment explanation
Indices: 1128--1540 Score: 342
Period size: 86 Copynumber: 4.8 Consensus size: 84
1118 TTTGCCCCCA
* *
1128 ACGCTCATGATGTAACACCTATGGCATTTTTGGCCCCGACGCTTATGGTGTAACACCTTTGGCAT
1 ACGCTCATTATGTAACACCTATGGCA-TTTTGGCCCCGACGCTCATGGTGTAACACCTTTGGCAT
1193 TTTGGCTATTTTTTTCCTCCG
65 TTTGGCTA-TTTTTTCCTCCG
* * * * * *
1214 ACGCTCATTACGTAACACCTACGACATTTTGGCCCCCGACGCTCATGGTGTATCAGCTTTAGCAT
1 ACGCTCATTATGTAACACCTATGGCATTTTGG-CCCCGACGCTCATGGTGTAACACCTTTGGCAT
** ** *
1279 TTTGGCCCGTTTTGGCCCCCG
65 TTTGG-CTATTTTTTCCTCCG
** * * * *
1300 ACGCTCATGCTGGTTA-ACCTTTGGCATTTTACCCATTCTTTGCCCCCGACGCTCATGATGTAAC
1 ACGCTCATTAT-GTAACACCTATGG---------CA-T-TTTGGCCCCGACGCTCATGGTGTAAC
*
1364 ACCTATGGCATTTTGGC-A-------C-CCG
54 ACCTTTGGCATTTTGGCTATTTTTTCCTCCG
* *
1386 ACGCTCATGATGTAACACCTATGGCATTTTGGCACCCGACGCTCATGATGTAACACCTTTGGCAT
1 ACGCTCATTATGTAACACCTATGGCATTTTGGC-CCCGACGCTCATGGTGTAACACCTTTGGCAT
* *
1451 TTTGGCTATTTGTTGCTCTCG
65 TTTGGCTATTTTTTCCTC-CG
* * *
1472 ACGCTCATTATGTAACACCTATGGCATTTTGGCACCAACGCTCATGGTGTAACACCTTTTAGCAT
1 ACGCTCATTATGTAACACCTATGGCATTTTGGCCCCGACGCTCATGGTGTAACACC-TTTGGCAT
1537 TTTG
65 TTTG
1541 AACTGTTTTG
Statistics
Matches: 263, Mismatches: 37, Indels: 54
0.74 0.10 0.15
Matches are distributed among these distances:
75 5 0.02
76 37 0.14
77 3 0.01
84 1 0.00
85 30 0.11
86 142 0.54
87 5 0.02
95 3 0.01
96 33 0.13
97 4 0.02
ACGTcount: A:0.19, C:0.28, G:0.20, T:0.33
Consensus pattern (84 bp):
ACGCTCATTATGTAACACCTATGGCATTTTGGCCCCGACGCTCATGGTGTAACACCTTTGGCATT
TTGGCTATTTTTTCCTCCG
Found at i:1321 original size:134 final size:133
Alignment explanation
Indices: 1155--1931 Score: 604
Period size: 134 Copynumber: 6.0 Consensus size: 133
1145 CCTATGGCAT
* * * * *
1155 TTTTGG-CCCCGACGCTTATGGTGTAACACCTTTGGCATTTTGGCTATTTTTTTCCTCCGACGCT
1 TTTTGGCCCCCGACGCTCATGCTGTAACACCTTTGGCATTTTGGCCATTTTTTGCCCCCGACGCT
* * * * * * * *
1219 CATTACGTAACACCTACGACATTTTGGCCCCCGACGCTCATGGTGTATCAGCTTTAGCATTTTGG
66 CATGATGTAACACCTATGGCATTTTGG-ACCCGACGCTCATGATGTAACACCTTTAGCATTTTGG
1284 CCCG
130 CCCG
* ** *
1288 TTTTGGCCCCCGACGCTCATGCTGGTTA-ACCTTTGGCATTTTACCCATTCTTTGCCCCCGACGC
1 TTTTGGCCCCCGACGCTCATGCT-GTAACACCTTTGGCATTTTGGCCATTTTTTGCCCCCGACGC
1352 TCATGATGTAACACCTATGGCATTTTGGCACCCGACGCTCATGATGTAACACC--T---A---TG
65 TCATGATGTAACACCTATGGCATTTTGG-ACCCGACGCTCATGATGTAACACCTTTAGCATTTTG
*
1409 G--CA
129 GCCCG
* * * * * *
1412 TTTTGGCACCCGACGCTCATGATGTAACACCTTTGGCATTTTGGCTATTTGTTGCTCTCGACGCT
1 TTTTGGCCCCCGACGCTCATGCTGTAACACCTTTGGCATTTTGGCCATTTTTTGCCCCCGACGCT
* * *
1477 CATTATGTAACACCTATGGCATTTTGG-CACCAACGCTCATGGTGTAACACCTTTTAGCATTTTG
66 CATGATGTAACACCTATGGCATTTTGGAC-CCGACGCTCATGATGTAACACC-TTTAGCATTTTG
** *
1541 AACTG
129 GCCCG
* * *
1546 TTTTGGCCCCCGACGCTCATGCTAGTTA-ACCTTTGGCATTTTCGCCACTTTTTGCCCCCGACGC
1 TTTTGGCCCCCGACGCTCATGCT-GTAACACCTTTGGCATTTTGGCCATTTTTTGCCCCCGACGC
* * *
1610 TAATGATGTAACACCTATGGCATTTTAGGACCCGACGCTCATGATATAACACCTTTGGCATTTTG
65 TCATGATGTAACACCTATGGCATTTT-GGACCCGACGCTCATGATGTAACACCTTTAGCATTTTG
**
1675 GCCAT
129 GCCCG
* * * * ** *
1680 TTTTTGCCCCCGACGCTAATGAGTGTAACGACCTATGAAATTTTGGCC-----TT-----CGATG
1 TTTTGGCCCCCGACGCTCATG-CTGTAAC-ACCTTTGGCATTTTGGCCATTTTTTGCCCCCGACG
* ** * * **
1735 CTCATGATGTAAAACCTATGGCATTTTAGTTCCTGATGCTCATGAT-T---ACCTTCGGCATTTT
64 CTCATGATGTAACACCTATGGCATTTT-GGACCCGACGCTCATGATGTAACACCTTTAGCATTTT
* **
1796 AGCCTTT
128 GGCC-CG
* * * * * * * *
1803 TTTTTGCCCCCGAGGCTTATGATGTATCACCTTTGACATTTTGGTCATTTTATT-CCCCCGACAC
1 TTTTGGCCCCCGACGCTCATGCTGTAACACCTTTGGCATTTTGGCCATTTT-TTGCCCCCGACGC
* * * * * * *
1867 TCATGATGTAATACTTATGGCATTTTGGCCCCCGACACTAATGATGTAACACCTATGGCATTTTG
65 TCATGATGTAACACCTATGGCATTTTGG-ACCCGACGCTCATGATGTAACACCTTTAGCATTTTG
1932 TCTCCCGACG
Statistics
Matches: 516, Mismatches: 91, Indels: 72
0.76 0.13 0.11
Matches are distributed among these distances:
121 15 0.03
122 22 0.04
123 43 0.08
124 78 0.15
125 1 0.00
126 48 0.09
127 2 0.00
129 2 0.00
130 1 0.00
131 41 0.08
132 4 0.01
133 6 0.01
134 198 0.38
135 40 0.08
136 15 0.03
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (133 bp):
TTTTGGCCCCCGACGCTCATGCTGTAACACCTTTGGCATTTTGGCCATTTTTTGCCCCCGACGCT
CATGATGTAACACCTATGGCATTTTGGACCCGACGCTCATGATGTAACACCTTTAGCATTTTGGC
CCG
Found at i:1440 original size:258 final size:251
Alignment explanation
Indices: 875--1979 Score: 912
Period size: 258 Copynumber: 4.3 Consensus size: 251
865 ATTTTTTACC
*
875 CCCGACGCAT-ATGATGTAACACCTATGGTATTTTGGCCCACGACGCTCATGGTGTAACACCTTT
1 CCCGACGC-TCATGATGTAACACCTATGGCATTTTGGCCC-CGACGCTCATGGTGTAACACCTTT
* * *
939 GGCATTTTGGCTATTTTTTTCC-CCGACGCTCATTATGTAAAACCTATGGCATTTTGGCGCACGA
64 GGCATTTTGGCTATTTTTTTCCTCCGACGCTCATTATGTAACACCTATGGCATTTTGGCCCCCGA
* * * * * * *
1003 CGCTCATGATGTA-AC---A-C-CTATGG-CATTTTGTCTCCCGACGCTCATGGTG-TAACTCCT
129 CGCTCATGGTGTACACTTTAGCATTTTGGCCGTTTTGGCCCCCGACGCTCATGCTGTTAA--CCT
* ** *** * ** ** * * * *
1060 TTGGCGTTTTGGTCATTTTTTGGCCCCCGACG-TCACCTTTTGGCATTTTAAGCCCATTTTTGCC
192 TTGGCATTTT-CCCA-TTTTT-GCCCCCGACGCTCATGATGTAACA-CCTATG-GCATTTTGGCA
* *
1124 CCCAACGCTCATGATGTAACACCTATGGCATTTTTGGCCCCGACGCTTATGGTGTAACACCTTTG
1 CCCGACGCTCATGATGTAACACCTATGGCA-TTTTGGCCCCGACGCTCATGGTGTAACACCTTTG
* * *
1189 GCATTTTGGCTATTTTTTTCCTCCGACGCTCATTACGTAACACCTACGACATTTTGGCCCCCGAC
65 GCATTTTGGCTATTTTTTTCCTCCGACGCTCATTATGTAACACCTATGGCATTTTGGCCCCCGAC
1254 GCTCATGGTGTATCAGCTTTAGCATTTTGGCCCGTTTTGGCCCCCGACGCTCATGCTGGTTAACC
130 GCTCATGGTGTA-CA-CTTTAGCATTTTGG-CCGTTTTGGCCCCCGACGCTCATGCT-GTTAACC
1319 TTTGGCATTTTACCCATTCTTTGCCCCCGACGCTCATGATGTAACACCTATGGCATTTTGGCA
191 TTTGGCATTTT-CCCATT-TTTGCCCCCGACGCTCATGATGTAACACCTATGGCATTTTGGCA
*
1382 CCCGACGCTCATGATGTAACACCTATGGCATTTTGGCACCCGACGCTCATGATGTAACACCTTTG
1 CCCGACGCTCATGATGTAACACCTATGGCATTTTGGC-CCCGACGCTCATGGTGTAACACCTTTG
* * * *
1447 GCATTTTGGCTA-TTTGTTGCTCTCGACGCTCATTATGTAACACCTATGGCATTTTGG-CACCAA
65 GCATTTTGGCTATTTTTTTCCTC-CGACGCTCATTATGTAACACCTATGGCATTTTGGCCCCCGA
* *
1510 CGCTCATGGTGTAACACCTTTTAGCATTTTGAACTGTTTTGGCCCCCGACGCTCATGCTAGTTAA
129 CGCTCATGGTGT-ACA-C-TTTAGCATTTTG-GCCGTTTTGGCCCCCGACGCTCATGCT-GTTAA
*
1575 CCTTTGGCATTTTCGCCACTTTTTGCCCCCGACGCTAATGATGTAACACCTATGGCATTTTAGG-
189 CCTTTGGCATTTTC-CCA-TTTTTGCCCCCGACGCTCATGATGTAACACCTATGGCATTTT-GGC
1639 A
251 A
* * *
1640 CCCGACGCTCATGATATAACACCTTTGGCATTTTGGCCATTTTTTGCCCCCGACGCTAATGAGTG
1 CCCGACGCTCATGATGTAACACC--T---A---TGG-CA--TTTTGGCCCCGACGCTCATG-GTG
* ** * * * *
1705 TAACGACCTATGAAATTTTGG----------CCTTCGATGCTCATGATGTAAAACCTATGGCATT
54 TAAC-ACCTTTGGCATTTTGGCTATTTTTTTCCTCCGACGCTCATTATGTAACACCTATGGCATT
* ** * * * ** * * * * *
1760 TTAGTTCCTGATGCTCATGAT-TAC-CTTCGGCATTTTAGCCTTTTTTTTGCCCCCGAGGCTTAT
118 TTGGCCCCCGACGCTCATGGTGTACACTTTAGCATTTTGGCC--GTTTTGGCCCCCGACGCTCAT
* * * ** * * * *
1823 GATGTATCACCTTTGACATTTTGGTCATTTTATTCCCCCGACACTCATGATGTAATACTTATGGC
181 GCTGT-TAACCTTTGGCATTTT-CCCATTTT-TGCCCCCGACGCTCATGATGTAACACCTATGGC
*
1888 ATTTTGGCC
243 ATTTTGGCA
* * * *
1897 CCCGACACTAATGATGTAACACCTATGGCATTTTGTCTCCCGACGCTTATGGTGTAACACCTTTT
1 CCCGACGCTCATGATGTAACACCTATGGCATTTTGGC-CCCGACGCTCATGGTGTAACACC-TTT
* *
1962 GGAATTTTGGCCATTTTT
64 GGCATTTTGGCTATTTTT
1980 AGCCCCCGAA
Statistics
Matches: 708, Mismatches: 93, Indels: 105
0.78 0.10 0.12
Matches are distributed among these distances:
245 3 0.00
246 24 0.03
247 12 0.02
248 3 0.00
249 74 0.10
250 57 0.08
252 2 0.00
253 1 0.00
255 2 0.00
256 18 0.03
257 125 0.18
258 230 0.32
259 21 0.03
260 77 0.11
261 13 0.02
262 3 0.00
263 1 0.00
266 3 0.00
267 2 0.00
268 12 0.02
269 12 0.02
270 13 0.02
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (251 bp):
CCCGACGCTCATGATGTAACACCTATGGCATTTTGGCCCCGACGCTCATGGTGTAACACCTTTGG
CATTTTGGCTATTTTTTTCCTCCGACGCTCATTATGTAACACCTATGGCATTTTGGCCCCCGACG
CTCATGGTGTACACTTTAGCATTTTGGCCGTTTTGGCCCCCGACGCTCATGCTGTTAACCTTTGG
CATTTTCCCATTTTTGCCCCCGACGCTCATGATGTAACACCTATGGCATTTTGGCA
Found at i:1583 original size:86 final size:85
Alignment explanation
Indices: 1373--1587 Score: 249
Period size: 86 Copynumber: 2.5 Consensus size: 85
1363 CACCTATGGC
*
1373 ATTTTGGCACCCGACGCTCATG-ATGTAACACCTATGGCATTTTGGCACCCGACGCTCATGATGT
1 ATTTTGGCACCCGACGCTCATGTA-GTAACACCTATGGCATTTTGGCACCCAACGCTCATGATGT
* *
1437 AACACCTTTGGCATTTTGGCT
65 AACACCTTTAGCATTTTGACT
* * * *
1458 ATTTGTTGCTCTCGACGCTCAT-TATGTAACACCTATGGCATTTTGGCA-CCAACGCTCATGGTG
1 ATTT-TGGCACCCGACGCTCATGTA-GTAACACCTATGGCATTTTGGCACCCAACGCTCATGATG
1521 TAACACCTTTTAGCATTTTGAACT
64 TAACACC-TTTAGCATTTTG-ACT
* * * *
1545 GTTTTGGCCCCCGACGCTCATGCTAGTTA-ACCTTTGGCATTTT
1 ATTTTGGCACCCGACGCTCATG-TAGTAACACCTATGGCATTTT
1588 CGCCACTTTT
Statistics
Matches: 111, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
85 24 0.22
86 77 0.69
87 8 0.07
88 2 0.02
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (85 bp):
ATTTTGGCACCCGACGCTCATGTAGTAACACCTATGGCATTTTGGCACCCAACGCTCATGATGTA
ACACCTTTAGCATTTTGACT
Found at i:1759 original size:88 final size:86
Alignment explanation
Indices: 1554--1761 Score: 260
Period size: 86 Copynumber: 2.4 Consensus size: 86
1544 TGTTTTGGCC
* *
1554 CCCGACGCTCATGCTAGT-TAACCTTTGGCATTTTCGCCACTTTTTGCCCCCGACGCTAATGATG
1 CCCGACGCTCATGATA-TAAAACCTTTGGCATTTTCGCCACTTTTTGCCCCCGACGCTAATGATG
**
1618 TAACACCTATGGCATTTTAGGA
65 TAACACCTATGAAATTTTAGGA
* * *
1640 CCCGACGCTCATGATATAACACCTTTGGCATTTTGGCCATTTTTTGCCCCCGACGCTAATGAGTG
1 CCCGACGCTCATGATATAAAACCTTTGGCATTTTCGCCACTTTTTGCCCCCGACGCTAATGA-TG
1705 TAACGACCTATGAAATTTT-GG-
65 TAAC-ACCTATGAAATTTTAGGA
* * *
1726 CCTTCGATGCTCATGATGTAAAACCTATGGCATTTT
1 CC--CGACGCTCATGATATAAAACCTTTGGCATTTT
1762 AGTTCCTGAT
Statistics
Matches: 106, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
85 1 0.01
86 57 0.54
87 8 0.08
88 40 0.38
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (86 bp):
CCCGACGCTCATGATATAAAACCTTTGGCATTTTCGCCACTTTTTGCCCCCGACGCTAATGATGT
AACACCTATGAAATTTTAGGA
Found at i:1778 original size:126 final size:121
Alignment explanation
Indices: 1612--1846 Score: 292
Period size: 126 Copynumber: 1.9 Consensus size: 121
1602 CCCGACGCTA
* * *
1612 ATGATGTAACACCTATGGCATTTTAGGACCCGACGCTCATGATATAACACCTTTGGCATTTTGGC
1 ATGATGTAAAACCTATGGCATTTTAGGACCCGACGCTCATGAT-T---ACCTTCGGCATTTTAGC
1677 C-ATTTTTTGCCCCCGACGCTAATGAGTGTAACGACCTATGAAATTTTGGCCTTCGATGCTC
62 CTATTTTTTGCCCCCGACGCTAATGA-TGTAAC-ACCTATGAAATTTTGGCCTTCGATGCTC
** * * *
1738 ATGATGTAAAACCTATGGCATTTTAGTTCCTGATGCTCATGATTACCTTCGGCATTTTAGCCTTT
1 ATGATGTAAAACCTATGGCATTTTAGGACCCGACGCTCATGATTACCTTCGGCATTTTAGCCTAT
* * * * *
1803 TTTTTGCCCCCGAGGCTTATGATGTATCACCTTTGACATTTTGG
66 TTTTTGCCCCCGACGCTAATGATGTAACACCTATGAAATTTTGG
1847 TCATTTTATT
Statistics
Matches: 95, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
121 14 0.15
122 21 0.22
123 21 0.22
125 1 0.01
126 38 0.40
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (121 bp):
ATGATGTAAAACCTATGGCATTTTAGGACCCGACGCTCATGATTACCTTCGGCATTTTAGCCTAT
TTTTTGCCCCCGACGCTAATGATGTAACACCTATGAAATTTTGGCCTTCGATGCTC
Found at i:1900 original size:38 final size:38
Alignment explanation
Indices: 1857--1973 Score: 135
Period size: 38 Copynumber: 3.1 Consensus size: 38
1847 TCATTTTATT
* *
1857 CCCCCGACACTCATGATGTAATACTTATGGCATTTTGG
1 CCCCCGACACTAATGATGTAACACTTATGGCATTTTGG
* *
1895 CCCCCGACACTAATGATGTAACACCTATGGCATTTTGT
1 CCCCCGACACTAATGATGTAACACTTATGGCATTTTGG
* * * * * *
1933 CTCCCGACGCTTATGGTGTAACACCTTTTGGAATTTTGG
1 CCCCCGACACTAATGATGTAACA-CTTATGGCATTTTGG
1972 CC
1 CC
1974 ATTTTTAGCC
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
38 53 0.82
39 12 0.18
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.32
Consensus pattern (38 bp):
CCCCCGACACTAATGATGTAACACTTATGGCATTTTGG
Found at i:1998 original size:49 final size:50
Alignment explanation
Indices: 1935--2056 Score: 142
Period size: 49 Copynumber: 2.5 Consensus size: 50
1925 CATTTTGTCT
* *
1935 CCCGACGCTTATGGTGTAACACCTTTTGGAATTTTGGCCA-TTTTTAGCC
1 CCCGACGCTCATGGTGTAACACCTTTTGGAATTTTAGCCATTTTTTAGCC
* * * *
1984 CCCGAAGCTCATGGTGGTTA-ACC-TTTGGCATTTTAGCCATTTTTTTGCC
1 CCCGACGCTCATGGT-GTAACACCTTTTGGAATTTTAGCCATTTTTTAGCC
* *
2033 CCCGACGCTCAAGATGTAACACCT
1 CCCGACGCTCATGGTGTAACACCT
2057 ACGACATTAT
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
48 17 0.29
49 39 0.66
50 3 0.05
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.34
Consensus pattern (50 bp):
CCCGACGCTCATGGTGTAACACCTTTTGGAATTTTAGCCATTTTTTAGCC
Found at i:2073 original size:174 final size:170
Alignment explanation
Indices: 1640--2104 Score: 449
Period size: 174 Copynumber: 2.7 Consensus size: 170
1630 CATTTTAGGA
* *
1640 CCCGACGCTCATGATATA-ACACCTTTGGCATTTTGGCCA-TTTTTTGCCCCCGACGCT-AATGA
1 CCCGAAGCTCATGATGTATA-ACCTTTGGCATTTTGGCCATTTTTTTGCCCCCGACGCTCAA-GA
* ** ** *
1702 GTGTAACGACCTATGAAATTTTGGCCTTCGATGCTCATGATGTAAAACCTATGGCATTTTAGTTC
64 -TGTAAC-ACCTATGACATTTTGGCCCCCGACACTCATGATGTAACACCTATGGCATTTTAGTTC
* * * * *
1767 CTGATGCTCATGATTACCTTCGGCATTTTAGCCTTTTTTTTGCC
127 CCGACGCTCATGATTACCTTCGGAATTTTAGCCTATTTTTAGCC
* * * * * * * *
1811 CCCGAGGCTTATGATGTATCACCTTTGACATTTTGGTCATTTTATT-CCCCCGACACTCATGATG
1 CCCGAAGCTCATGATGTATAACCTTTGGCATTTTGGCCATTTTTTTGCCCCCGACGCTCAAGATG
* * * *
1875 TAATACTTATGGCATTTTGGCCCCCGACACTAATGATGTAACACCTATGGCATTTT-GTCTCCCG
66 TAACACCTATGACATTTTGGCCCCCGACACTCATGATGTAACACCTATGGCATTTTAGT-TCCCG
* * * *
1939 ACGCTTATGGTGTAACACCTTTTGGAATTTTGGCC-ATTTTTAGCC
130 ACGCTCATGAT-T---ACC-TTCGGAATTTTAGCCTATTTTTAGCC
* *
1984 CCCGAAGCTCATGGTGGT-TAACCTTTGGCATTTTAGCCATTTTTTTGCCCCCGACGCTCAAGAT
1 CCCGAAGCTCATGAT-GTATAACCTTTGGCATTTTGGCCATTTTTTTGCCCCCGACGCTCAAGAT
* * * * * *
2048 GTAACACCTACGACATTATGGCCCCCGACACTCATGGTTTAACACCTTTAGCATTTT
65 GTAACACCTATGACATTTTGGCCCCCGACACTCATGATGTAACACCTATGGCATTTT
2105 TGGCCATTTT
Statistics
Matches: 235, Mismatches: 48, Indels: 19
0.78 0.16 0.06
Matches are distributed among these distances:
168 2 0.01
169 55 0.23
170 6 0.03
171 44 0.19
172 6 0.03
173 46 0.20
174 76 0.32
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.35
Consensus pattern (170 bp):
CCCGAAGCTCATGATGTATAACCTTTGGCATTTTGGCCATTTTTTTGCCCCCGACGCTCAAGATG
TAACACCTATGACATTTTGGCCCCCGACACTCATGATGTAACACCTATGGCATTTTAGTTCCCGA
CGCTCATGATTACCTTCGGAATTTTAGCCTATTTTTAGCC
Done.