Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1174
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1120009
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 47637 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:4756 original size:1 final size:1
Alignment explanation
Indices: 4750--4776 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
4740 TGTGTGTATA
4750 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
4777 ACGTTGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:10027 original size:15 final size:15
Alignment explanation
Indices: 10007--10036 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
9997 TTTTTGTTCT
*
10007 TGTTACACCAAGGAC
1 TGTTACACAAAGGAC
10022 TGTTACACAAAGGAC
1 TGTTACACAAAGGAC
10037 ATATTTATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (15 bp):
TGTTACACAAAGGAC
Found at i:10827 original size:44 final size:44
Alignment explanation
Indices: 10764--10940 Score: 354
Period size: 44 Copynumber: 4.0 Consensus size: 44
10754 TGACCCATAT
10764 AGATTAAATTCACACCTCTAGATACAAACAGTAAGAAACGGACA
1 AGATTAAATTCACACCTCTAGATACAAACAGTAAGAAACGGACA
10808 AGATTAAATTCACACCTCTAGATACAAACAGTAAGAAACGGACA
1 AGATTAAATTCACACCTCTAGATACAAACAGTAAGAAACGGACA
10852 AGATTAAATTCACACCTCTAGATACAAACAGTAAGAAACGGACA
1 AGATTAAATTCACACCTCTAGATACAAACAGTAAGAAACGGACA
10896 AGATTAAATTCACACCTCTAGATACAAACAGTAAGAAACGGACA
1 AGATTAAATTCACACCTCTAGATACAAACAGTAAGAAACGGACA
10940 A
1 A
10941 CAAACACCCA
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 133 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (44 bp):
AGATTAAATTCACACCTCTAGATACAAACAGTAAGAAACGGACA
Found at i:15916 original size:29 final size:29
Alignment explanation
Indices: 15844--15924 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
15834 TGCCACATAA
* *
15844 AAAGGACCAGGACTGAAATT-TCACAACAT
1 AAAGGACCAGAATTGAAATTGT-ACAACAT
*
15873 AAACGG-CCA-AGATTGGAATTGTACAACAT
1 AAA-GGACCAGA-ATTGAAATTGTACAACAT
15902 AAAGGACCAGAATTGAAATTGTA
1 AAAGGACCAGAATTGAAATTGTA
15925 AAAGAGATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
28 2 0.05
29 37 0.86
30 4 0.09
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (29 bp):
AAAGGACCAGAATTGAAATTGTACAACAT
Found at i:17962 original size:164 final size:165
Alignment explanation
Indices: 17544--18015 Score: 517
Period size: 164 Copynumber: 2.8 Consensus size: 165
17534 TGGCTTGGCA
* * * * *
17544 TAAACAAATAGTGTGTTG-CAATGTCAAGCATCTGCCATATATAGTTGCTAAGAAATCCTTGACG
1 TAAACAAATAGTGTG-TGAAAATTTCAAGCATCTGCCATAAATAGTTGCT-AGAAATCTTTGAAG
* ** ** * * * *
17608 AAAATTTG-TCAACAAATTTCA-GCTAAAAATAAACAAAAACGTCATTAAACAGGAAGTTGGCAT
64 AAATTTTGTTTGA-AAATTT-AGGCTAAAAATAAAC-AAGTCGTCATTTAACAGGAACTTGACGT
* * *
17671 CCAATTGATACAAAAATATATTCAGTACAATATGGAATGCC
126 CCGATTGGTACAAAAATATATTCAGTA-AATATGGAATACC
* *
17712 TAAACAAATAGTGTGTTAAAATTTCAAGCATCTAGCTGCCATAAATAGTTGCTAAAAATCTTTGA
1 TAAACAAATAGTGTGTGAAAATTTCAAGCA--T--CTGCCATAAATAGTTGCTAGAAATCTTTGA
* *
17777 AGAAATTTTGTTTGAAAATTTAGGCTAAAAATAAAC-AGTCATCATTTAACAGGCAA-TTGATGT
62 AGAAATTTTGTTTGAAAATTTAGGCTAAAAATAAACAAGTCGTCATTTAACAGG-AACTTGACGT
* * * * *
17840 CCGATTGGTTCAAAAATATATTACA-T-GATATTGCATACT
126 CCGATTGGTACAAAAATATATT-CAGTAAATATGGAATACC
17879 TAAACAAATAGTGTGTGAAAATTTCAAGCATCTGCCATAAATAGTTGCTGAGAAATCTTTGAAGA
1 TAAACAAATAGTGTGTGAAAATTTCAAGCATCTGCCATAAATAGTTGCT-AGAAATCTTTGAAGA
* *
17944 AATTTTGTTTGAAAATTTAGGCTAAAAATAAACAAAGTCGTCATTTAACAGGAACTTGAGGTCTG
65 AATTTTGTTTGAAAATTTAGGCTAAAAATAAAC-AAGTCGTCATTTAACAGGAACTTGACGTCCG
18009 ATTGGTA
129 ATTGGTA
18016 TTTATTAATA
Statistics
Matches: 260, Mismatches: 31, Indels: 28
0.82 0.10 0.09
Matches are distributed among these distances:
163 18 0.07
164 47 0.18
165 3 0.01
166 30 0.12
167 38 0.15
168 25 0.10
169 37 0.14
170 6 0.02
171 37 0.14
172 19 0.07
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (165 bp):
TAAACAAATAGTGTGTGAAAATTTCAAGCATCTGCCATAAATAGTTGCTAGAAATCTTTGAAGAA
ATTTTGTTTGAAAATTTAGGCTAAAAATAAACAAGTCGTCATTTAACAGGAACTTGACGTCCGAT
TGGTACAAAAATATATTCAGTAAATATGGAATACC
Found at i:19577 original size:127 final size:127
Alignment explanation
Indices: 19351--19604 Score: 352
Period size: 127 Copynumber: 2.0 Consensus size: 127
19341 CTTTGACAGT
* *
19351 AGTTCTTATGACATCACCGCTTTAGTATATATTGCGGATCACTTTCTGATTTTTCACATCAGTAG
1 AGTTCTTATGACATCACCGCTTTAGTATATATTGCGGATCACTTTATGATTTTTCAAATCAGTAG
* * * *
19416 CTAAATATACATGAAGGACAAAAATTTCCGACAAAAATAATAATTTTGATATTGATTCGATA
66 CTAAATATACACGAAGCACAAAAATTTCCGACAAAAATAATAATCTTAATATTGATTCGATA
* * * * *
19478 AGTTCTTATGACGTCACCGCTTTAGTGTATATTGCGGGTCACTTTTATGTTTTTTTCCAAATCGG
1 AGTTCTTATGACATCACCGCTTTAGTATATATTGCGGATCAC-TTTATG-ATTTTT-CAAATCAG
*
19543 TAGCTAAA-A-ACACGGAGCACAAAAA-TTCCGACAAAAATAATAATCTTAATATTGATTCGATA
63 TAGCTAAATATACACGAAGCACAAAAATTTCCGACAAAAATAATAATCTTAATATTGATTCGATA
19605 CACTTCAATC
Statistics
Matches: 112, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
127 74 0.66
128 18 0.16
129 6 0.05
130 14 0.12
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (127 bp):
AGTTCTTATGACATCACCGCTTTAGTATATATTGCGGATCACTTTATGATTTTTCAAATCAGTAG
CTAAATATACACGAAGCACAAAAATTTCCGACAAAAATAATAATCTTAATATTGATTCGATA
Found at i:33965 original size:51 final size:51
Alignment explanation
Indices: 33903--34005 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
33893 TGAAAAGAAA
33903 AATATTAGGTGTGATCCTTACAAATGTACTTTTAGAATGAAAAAAAAATAT
1 AATATTAGGTGTGATCCTTACAAATGTACTTTTAGAATGAAAAAAAAATAT
33954 AATATTAGGTGTGATCCTTACAAATGTACTTTTAGAATGAAAAAAAAATAT
1 AATATTAGGTGTGATCCTTACAAATGTACTTTTAGAATGAAAAAAAAATAT
34005 A
1 A
34006 GAGTCCATAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.33
Consensus pattern (51 bp):
AATATTAGGTGTGATCCTTACAAATGTACTTTTAGAATGAAAAAAAAATAT
Found at i:38506 original size:38 final size:37
Alignment explanation
Indices: 38433--38506 Score: 89
Period size: 38 Copynumber: 1.9 Consensus size: 37
38423 GAAATAATGT
*
38433 CAGCAATGTCTTTCAGCTATAATTGAAAACATGTACAC
1 CAGCAATGTCTTTCAGCTATAA-TAAAAACATGTACAC
38471 CAGCAATG-CATTTCAGCTATAA-AACAAACACTGTAC
1 CAGCAATGTC-TTTCAGCTATAATAA-AAACA-TGTAC
38507 TTCTTACCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
36 1 0.03
37 6 0.19
38 25 0.78
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (37 bp):
CAGCAATGTCTTTCAGCTATAATAAAAACATGTACAC
Found at i:39209 original size:20 final size:20
Alignment explanation
Indices: 39184--39221 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39174 ACAGCTGATG
39184 AATTATTCAACTTTCTAATT
1 AATTATTCAACTTTCTAATT
*
39204 AATTATTCTACTTTCTAA
1 AATTATTCAACTTTCTAA
39222 ATTTGTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTATTCAACTTTCTAATT
Found at i:42052 original size:18 final size:18
Alignment explanation
Indices: 42031--42082 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
42021 CAACACTGGC
*
42031 GATTTCATTGGGGAAGGT
1 GATTTCATTGGAGAAGGT
** *
42049 GATTTTGTCGGAGAAGGT
1 GATTTCATTGGAGAAGGT
42067 GATTTCATTGGAGAAG
1 GATTTCATTGGAGAAG
42083 ATGGCTCAGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.25, C:0.06, G:0.37, T:0.33
Consensus pattern (18 bp):
GATTTCATTGGAGAAGGT
Found at i:45241 original size:21 final size:21
Alignment explanation
Indices: 45215--45258 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
45205 TTTAATCTAG
45215 GATATCATTCTTTTGATCCTT
1 GATATCATTCTTTTGATCCTT
45236 GATATCATTCTTTTGATCCTT
1 GATATCATTCTTTTGATCCTT
45257 GA
1 GA
45259 AATATCAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.11, T:0.50
Consensus pattern (21 bp):
GATATCATTCTTTTGATCCTT
Found at i:56017 original size:12 final size:12
Alignment explanation
Indices: 56002--56028 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
55992 TATAATATAT
56002 ACAAGCATCTTG
1 ACAAGCATCTTG
56014 ACAAGCATCTTG
1 ACAAGCATCTTG
56026 ACA
1 ACA
56029 TTTTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (12 bp):
ACAAGCATCTTG
Found at i:65559 original size:36 final size:36
Alignment explanation
Indices: 65518--65597 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
65508 CTCATCGAGG
*
65518 CACAAGTCCTCACACAAGTC-ACCTCATAAATCGCCT
1 CACAAGTCATCACACAAGTCGACC-CATAAATCGCCT
* *
65554 CACAAGTCATCACACAAGTCGTCCCATAAGTCGCCT
1 CACAAGTCATCACACAAGTCGACCCATAAATCGCCT
65590 CACAAGTC
1 CACAAGTC
65598 GGACCACAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 38 0.95
37 2 0.05
ACGTcount: A:0.33, C:0.38, G:0.11, T:0.19
Consensus pattern (36 bp):
CACAAGTCATCACACAAGTCGACCCATAAATCGCCT
Found at i:65596 original size:12 final size:12
Alignment explanation
Indices: 65530--65598 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
65520 CAAGTCCTCA
*
65530 CACAAGTCACCT
1 CACAAGTCGCCT
* *
65542 CATAAATCGCCT
1 CACAAGTCGCCT
** *
65554 CACAAGTCATCA
1 CACAAGTCGCCT
65566 CACAAGTCGTCC-
1 CACAAGTCG-CCT
*
65578 CATAAGTCGCCT
1 CACAAGTCGCCT
65590 CACAAGTCG
1 CACAAGTCG
65599 GACCACAAAC
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.93
13 1 0.02
ACGTcount: A:0.32, C:0.36, G:0.13, T:0.19
Consensus pattern (12 bp):
CACAAGTCGCCT
Found at i:66693 original size:36 final size:36
Alignment explanation
Indices: 66653--66936 Score: 433
Period size: 36 Copynumber: 7.9 Consensus size: 36
66643 ATACGAGTAG
*
66653 TGAACGGGTATTTGAGTTACTCTGGTAACTTATTGC
1 TGAACGGGTATTTGAGTTACTCTAGTAACTTATTGC
* * *
66689 TGAACGGGTATTCGAGTTACTCTGGTAACTTAATGC
1 TGAACGGGTATTTGAGTTACTCTAGTAACTTATTGC
* * *
66725 TGAACGGGTATTCGAGTTACTCTGGTAACTTAATGC
1 TGAACGGGTATTTGAGTTACTCTAGTAACTTATTGC
66761 TGAACGGGTATTTGAGTTACTCTAGTAACTTATTGC
1 TGAACGGGTATTTGAGTTACTCTAGTAACTTATTGC
*
66797 TGAATGGGTATTTGAGTTACTCTAGTAACTTATTGC
1 TGAACGGGTATTTGAGTTACTCTAGTAACTTATTGC
*
66833 TGAATGGGTATTTGAGTTACTCTAGTAACTTATTGC
1 TGAACGGGTATTTGAGTTACTCTAGTAACTTATTGC
**
66869 TGAATTGGTATTTGAGTTACTCTAGTAACTTATTGC
1 TGAACGGGTATTTGAGTTACTCTAGTAACTTATTGC
** * *
66905 TGAATTGGTATTTGAGTTACCCTGGTAACTTA
1 TGAACGGGTATTTGAGTTACTCTAGTAACTTA
66937 CTGCCGTTGT
Statistics
Matches: 239, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 239 1.00
ACGTcount: A:0.25, C:0.13, G:0.23, T:0.39
Consensus pattern (36 bp):
TGAACGGGTATTTGAGTTACTCTAGTAACTTATTGC
Found at i:67390 original size:149 final size:148
Alignment explanation
Indices: 67120--67416 Score: 585
Period size: 149 Copynumber: 2.0 Consensus size: 148
67110 TGTCTTTTAA
67120 ATTTAGACCACGTGGTTTTATTTGATCCTTTCAGTTTGGCAGTAAAAATCATGCCTCGTGTTTAT
1 ATTTAGACCACGTGGTTTTATTTGATCCTTTCAGTTTGGCAGTAAAAATCATGCCTCGTGTTTAT
67185 AATCTATTTCCTAGAATCTAGGTACTTGTCATCAAATATAAAATCAAGACGTTTATTGTTTTTAA
66 AATCTATTTCCTAGAATCTAGGTACTTGTCATCAAATATAAAATCAAGACGTTTATTGTTTTTAA
67250 ACTTTATCTTTATTAATT
131 ACTTTATCTTTATTAATT
67268 NATTTAGACCACGTGGTTTTATTTGATCCTTTCAGTTTGGCAGTAAAAATCATGCCTCGTGTTTA
1 -ATTTAGACCACGTGGTTTTATTTGATCCTTTCAGTTTGGCAGTAAAAATCATGCCTCGTGTTTA
67333 TAATCTATTTCCTAGAATCTAGGTACTTGTCATCAAATATAAAATCAAGACGTTTATTGTTTTTA
65 TAATCTATTTCCTAGAATCTAGGTACTTGTCATCAAATATAAAATCAAGACGTTTATTGTTTTTA
67398 AACTTTATCTTTATTAATT
130 AACTTTATCTTTATTAATT
67417 GATGGATAAA
Statistics
Matches: 148, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 148 1.00
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (148 bp):
ATTTAGACCACGTGGTTTTATTTGATCCTTTCAGTTTGGCAGTAAAAATCATGCCTCGTGTTTAT
AATCTATTTCCTAGAATCTAGGTACTTGTCATCAAATATAAAATCAAGACGTTTATTGTTTTTAA
ACTTTATCTTTATTAATT
Found at i:85784 original size:21 final size:22
Alignment explanation
Indices: 85760--85801 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
85750 TCGCCTGGTA
*
85760 ACTATAGTTTACGAAT-TGCAG
1 ACTATAGTTAACGAATATGCAG
85781 ACTATAGTTAACGAATATGCA
1 ACTATAGTTAACGAATATGCA
85802 ATCGCAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (22 bp):
ACTATAGTTAACGAATATGCAG
Found at i:86284 original size:36 final size:36
Alignment explanation
Indices: 86244--86315 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
86234 TACATAGTAT
*
86244 CCAACACTATCCGATCACACGATAATAGTGCATCAC
1 CCAACACTATCCGATCACACGATAATAGCGCATCAC
86280 CCAACACTATCCGATCACACGATAATAGCGCATCAC
1 CCAACACTATCCGATCACACGATAATAGCGCATCAC
86316 AGAGGGAACG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.36, C:0.35, G:0.11, T:0.18
Consensus pattern (36 bp):
CCAACACTATCCGATCACACGATAATAGCGCATCAC
Found at i:86314 original size:18 final size:18
Alignment explanation
Indices: 86257--86316 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
86247 ACACTATCCG
*
86257 ATCACACGATAATAGTGC
1 ATCACACGATAATAGCGC
* * * * *
86275 ATCACCCAACACTATC-C
1 ATCACACGATAATAGCGC
86292 GATCACACGATAATAGCGC
1 -ATCACACGATAATAGCGC
86311 ATCACA
1 ATCACA
86317 GAGGGAACGA
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
17 1 0.03
18 27 0.93
19 1 0.03
ACGTcount: A:0.38, C:0.32, G:0.12, T:0.18
Consensus pattern (18 bp):
ATCACACGATAATAGCGC
Found at i:86603 original size:2 final size:2
Alignment explanation
Indices: 86530--86583 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
86520 ACCGGAAACA
86530 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
86572 AG AG AG AG AG AG
1 AG AG AG AG AG AG
86584 NNNNNNNNNG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:86604 original size:2 final size:2
Alignment explanation
Indices: 86593--86621 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
86583 GNNNNNNNNN
86593 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
86622 CGCTCAGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:93348 original size:24 final size:25
Alignment explanation
Indices: 93316--93363 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
93306 TGTTTGTTCG
93316 TTTCTGTCCG-TTTCCTTTCTTTTT
1 TTTCTGTCCGTTTTCCTTTCTTTTT
*
93340 TTTCTGTCCGTTTTCTTTTCTTTT
1 TTTCTGTCCGTTTTCCTTTCTTTT
93364 CTGTTCGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.00, C:0.23, G:0.08, T:0.69
Consensus pattern (25 bp):
TTTCTGTCCGTTTTCCTTTCTTTTT
Found at i:93375 original size:21 final size:20
Alignment explanation
Indices: 93331--93375 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
93321 GTCCGTTTCC
*
93331 TTTCTTTTTTTTCTGTCCGT
1 TTTCTTTTTTTTCTGTCCGA
*
93351 TTTCTTTTCTTTTCTGTTCGA
1 TTTCTTTT-TTTTCTGTCCGA
93372 TTTC
1 TTTC
93376 ACGACTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.02, C:0.20, G:0.09, T:0.69
Consensus pattern (20 bp):
TTTCTTTTTTTTCTGTCCGA
Found at i:93419 original size:11 final size:11
Alignment explanation
Indices: 93405--93474 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
93395 TTTCTTTCTT
93405 TTTTCTGTCCG
1 TTTTCTGTCCG
* *
93416 TTTTTTGTCGG
1 TTTTCTGTCCG
* *
93427 TTTCCT-ACC-
1 TTTTCTGTCCG
93436 TTTTCTGTCCG
1 TTTTCTGTCCG
*
93447 TTTTCT-TCCTT
1 TTTTCTGTCC-G
*
93458 TTTTCTGTTCG
1 TTTTCTGTCCG
93469 TTTTCT
1 TTTTCT
93475 TTCTTTTTTC
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
9 5 0.11
10 6 0.14
11 31 0.70
12 2 0.05
ACGTcount: A:0.01, C:0.24, G:0.13, T:0.61
Consensus pattern (11 bp):
TTTTCTGTCCG
Found at i:93444 original size:20 final size:20
Alignment explanation
Indices: 93416--93459 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
93406 TTTCTGTCCG
* *
93416 TTTTTTGTCGGTTTCCTACC
1 TTTTCTGTCCGTTTCCTACC
* *
93436 TTTTCTGTCCGTTTTCTTCC
1 TTTTCTGTCCGTTTCCTACC
93456 TTTT
1 TTTT
93460 TTCTGTTCGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.02, C:0.25, G:0.11, T:0.61
Consensus pattern (20 bp):
TTTTCTGTCCGTTTCCTACC
Found at i:93488 original size:22 final size:22
Alignment explanation
Indices: 93436--93489 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
93426 GTTTCCTACC
*
93436 TTTTCTGTCCGTTTTCTTCCTT
1 TTTTCTGTTCGTTTTCTTCCTT
*
93458 TTTTCTGTTCGTTTTCTTTCTT
1 TTTTCTGTTCGTTTTCTTCCTT
93480 TTTTCTGTTC
1 TTTTCTGTTC
93490 AACTTCACGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.00, C:0.22, G:0.09, T:0.69
Consensus pattern (22 bp):
TTTTCTGTTCGTTTTCTTCCTT
Found at i:98823 original size:1 final size:1
Alignment explanation
Indices: 98819--98858 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
98809 CTTTTTTTGT
** *
98819 AAAAAAAAAAAAAAAAAAAAAAAAAAGGAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
98859 GCAAAGAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:98868 original size:15 final size:14
Alignment explanation
Indices: 98819--98873 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
98809 CTTTTTTTGT
* **
98819 AAAAAAAAAAAAAA
1 AAAAAAAGAAAAGC
* *
98833 AAAAAAAAAAAAGG
1 AAAAAAAGAAAAGC
98847 AAAAAAAGAAAAGC
1 AAAAAAAGAAAAGC
98861 AAAGAAAAGAAAA
1 AAA-AAAAGAAAA
98874 TTGTATTAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
14 27 0.75
15 9 0.25
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAGC
Found at i:111668 original size:14 final size:14
Alignment explanation
Indices: 111646--111677 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
111636 AACAGAGTCT
111646 ATGAATAATCCATC
1 ATGAATAATCCATC
*
111660 ATGATTAATCCATC
1 ATGAATAATCCATC
111674 ATGA
1 ATGA
111678 CAAAGCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (14 bp):
ATGAATAATCCATC
Found at i:135506 original size:116 final size:118
Alignment explanation
Indices: 135296--135537 Score: 443
Period size: 117 Copynumber: 2.1 Consensus size: 118
135286 TGATTTTAAA
*
135296 AACATGTCCAAACATTGTTTAAAACCTCAAAAGTAACATACTAGAATTTTTTATGGAATAATTTA
1 AACATTTCCAAACATTGTTTAAAACCTCAAAAGTAACATACTAGAATTTTTTATGGAATAATTTA
135361 TTCAAGGTCTACTTGGTTATGAGCTCTTATTTTAT-AAAAAAAATTATTTGTC
66 TTCAAGGTCTACTTGGTTATGAGCTCTTATTTTATAAAAAAAAATTATTTGTC
* *
135413 AACATTTCCAAACATTGTTTTAAACCTCAAAAGTAACATACTAGGA-TTTTTATGGAATAATTTA
1 AACATTTCCAAACATTGTTTAAAACCTCAAAAGTAACATACTAGAATTTTTTATGGAATAATTTA
135477 TTCAAGGTCTACTTGGTTATGAGCTCTTATTTTATAAAAAAAAATTATTTGTC
66 TTCAAGGTCTACTTGGTTATGAGCTCTTATTTTATAAAAAAAAATTATTTGTC
135530 AACATTTC
1 AACATTTC
135538 ATTATCAAAT
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
116 53 0.44
117 68 0.56
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (118 bp):
AACATTTCCAAACATTGTTTAAAACCTCAAAAGTAACATACTAGAATTTTTTATGGAATAATTTA
TTCAAGGTCTACTTGGTTATGAGCTCTTATTTTATAAAAAAAAATTATTTGTC
Found at i:137060 original size:18 final size:18
Alignment explanation
Indices: 137037--137072 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
137027 CGGAAAGTCG
137037 TCCACGTATATATATATA
1 TCCACGTATATATATATA
137055 TCCACGTATATATATATA
1 TCCACGTATATATATATA
137073 GATAGAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (18 bp):
TCCACGTATATATATATA
Found at i:143022 original size:21 final size:21
Alignment explanation
Indices: 142997--143101 Score: 192
Period size: 21 Copynumber: 5.0 Consensus size: 21
142987 AATTGTGTAC
142997 TCAAAACAGCGATGTGGATAA
1 TCAAAACAGCGATGTGGATAA
*
143018 TCAAAACGGCGATGTGGATAA
1 TCAAAACAGCGATGTGGATAA
143039 TCAAAACAGCGATGTGGATAA
1 TCAAAACAGCGATGTGGATAA
143060 TCAAAACAGCGATGTGGATAA
1 TCAAAACAGCGATGTGGATAA
*
143081 TCAAAACGGCGATGTGGATAA
1 TCAAAACAGCGATGTGGATAA
143102 AGAGCATAAC
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 81 1.00
ACGTcount: A:0.41, C:0.14, G:0.26, T:0.19
Consensus pattern (21 bp):
TCAAAACAGCGATGTGGATAA
Found at i:145367 original size:17 final size:18
Alignment explanation
Indices: 145325--145367 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
145315 AATTCAAATC
* *
145325 AAAATATATATGCGATGT
1 AAAATATATATGAGAAGT
145343 AAACATATATAT-AGAAGT
1 AAA-ATATATATGAGAAGT
145361 AAAATAT
1 AAAATAT
145368 CATAAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 10 0.45
19 8 0.36
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30
Consensus pattern (18 bp):
AAAATATATATGAGAAGT
Found at i:150943 original size:28 final size:28
Alignment explanation
Indices: 150903--150960 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
150893 AATCCAAGAG
150903 AAGTAGCTCTTAAATGTGTCGTTTATTA
1 AAGTAGCTCTTAAATGTGTCGTTTATTA
150931 AAGTAGCTCTTAAATGTGTCGTTTATTA
1 AAGTAGCTCTTAAATGTGTCGTTTATTA
150959 AA
1 AA
150961 AACCAGTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (28 bp):
AAGTAGCTCTTAAATGTGTCGTTTATTA
Found at i:155338 original size:437 final size:436
Alignment explanation
Indices: 154524--155372 Score: 1106
Period size: 437 Copynumber: 1.9 Consensus size: 436
154514 ATAGCCCTCC
* * * *
154524 TGGCCCCTAATTTGAAGGGTCAGCCCCTTTTTCTTGATATCAAATTAAAGGTCTCGCAAATATAA
1 TGGCCCCTAATTTGAAGGGTCAGCCCCTTTTTCTTAATATCAAATAAAAGATCTCACAAATATAA
*
154589 ACATATTTTATTCAACAAGTGTTCACGAATTATTAACCGTTATAGAGATATCGGAACAACTGTGT
66 ACATATTTTATTCAACAAGTGTTCACGAATTATTAACCGTTATAGAGATATCGGAACAACAGTGT
* * * *
154654 TTTAGGGGCCGACCCTTCAACTCCTTACTGGGGCCACCAACGAAAAATGTTTAGGTATCACATTG
131 TTTAGGGGCCGACCCTTAAACTCCTTACTGGGGCCACAAACCAAAAATGTTAAGGTATCACATTG
*
154719 TTCACAACATTATTTTCAGCAACTTTTGTTATACAATGTTTTTCAAAATATTTCTCCTTTTCAAG
196 TTCACAACATTATTTTAAGCAACTTTTGTTATACAATGTTTTTCAAAATATTTCTCCTTTTCAAG
* * * *
154784 ATAATATTGATCAAAGTTTTGGACTTCTGGCCCCTTCAAACCCCTAATTATGTAACATATGACTT
261 ATAATAATGATCAAAGTGTTGGACTTCTGGCCCCTTCAAACCCCTAATTACGTAACAAATGA-TT
* * * *
154849 TAGTATGGTCCAGAATAGATGAACAGCTGTACAATGAACATTTTTGCTTCTATAAATAATAACAA
325 TAATAAGGTACAGAATAGATAAACAGCTGTACAATGAACATTTTTGCTTCTATAAATAATAACAA
**
154914 ATTATTTTTCAGTAAAGAGTTATTATATAAAGGTTTTAGAGCGCTCT
390 ATTATTGCTCAGTAAAGAGTTATTATATAAAGGTTTTAGAGCGCTCT
* * * * **
154961 TGGCCCCTAATTTG-AGGGGCTAGTCCCTTTTTCTTAATATTAAATAAAAGATCTTATTAATATA
1 TGGCCCCTAATTTGAAGGGTC-AGCCCCTTTTTCTTAATATCAAATAAAAGATCTCACAAATATA
* * * * * * *
155025 AACATATTTTGTTTAATAAGTGTTCA-GAAATTGTTGACCGATT-TGGAGATATCTTG-ACAACA
65 AACATATTTTATTCAACAAGTGTTCACG-AATTATTAACCG-TTATAGAGATATC-GGAACAACA
*
155087 GTGTTTTAGGGGCCGACCCTTAAACTCCTTACTGGGGCCACAAACCATAAAT-TTAAAGGTA-C-
127 GTGTTTTAGGGGCCGACCCTTAAACTCCTTACTGGGGCCACAAACCAAAAATGTT-AAGGTATCA
* *
155149 CA-TGTTCTAAAGAACATTATTTTAAGCAACTTTTGTTCA-ACATTGTTTTTCAAAATATTTCTC
191 CATTGTTC---ACAACATTATTTTAAGCAACTTTTGTT-ATACAATGTTTTTCAAAATATTTCTC
* * * *
155212 CTTTTTAAGATATTAATGATCAAAGTGTTGGTCTTCTGGCCCCTTGAAACCCCTAATTACGTAAC
252 CTTTTCAAGATAATAATGATCAAAGTGTTGGACTTCTGGCCCCTTCAAACCCCTAATTACGTAAC
* **
155277 AAATG-TTTAAAATAAGGTACTGTGTAGATAAACAGCTGTACAATGAACATTTTTGCTTCTATAA
317 AAATGATTT--AATAAGGTACAGAATAGATAAACAGCTGTACAATGAACATTTTTGCTTCTATAA
* * *
155341 TTAATGACAAATTATTGCTCAGTTAAGAGTTA
380 ATAATAACAAATTATTGCTCAGTAAAGAGTTA
155373 AAATTAAAAG
Statistics
Matches: 355, Mismatches: 46, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
434 5 0.01
435 5 0.01
436 9 0.03
437 332 0.94
438 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (436 bp):
TGGCCCCTAATTTGAAGGGTCAGCCCCTTTTTCTTAATATCAAATAAAAGATCTCACAAATATAA
ACATATTTTATTCAACAAGTGTTCACGAATTATTAACCGTTATAGAGATATCGGAACAACAGTGT
TTTAGGGGCCGACCCTTAAACTCCTTACTGGGGCCACAAACCAAAAATGTTAAGGTATCACATTG
TTCACAACATTATTTTAAGCAACTTTTGTTATACAATGTTTTTCAAAATATTTCTCCTTTTCAAG
ATAATAATGATCAAAGTGTTGGACTTCTGGCCCCTTCAAACCCCTAATTACGTAACAAATGATTT
AATAAGGTACAGAATAGATAAACAGCTGTACAATGAACATTTTTGCTTCTATAAATAATAACAAA
TTATTGCTCAGTAAAGAGTTATTATATAAAGGTTTTAGAGCGCTCT
Found at i:156022 original size:31 final size:31
Alignment explanation
Indices: 155987--156097 Score: 125
Period size: 31 Copynumber: 3.5 Consensus size: 31
155977 ATTATCCCTG
*
155987 GTACGACTTAACAAAATCCGAATGATTTTAA
1 GTACGACTTAACAAAATCCGAATGATTTCAA
* **
156018 GTACGACTTAACAAAAACCTTCATGATTTCAA
1 GTACGACTTAACAAAATCC-GAATGATTTCAA
*
156050 GAACGACTTAACAAAAAAATCCGAATG-TGTTCAA
1 GTACGACTTAAC---AAAATCCGAATGAT-TTCAA
156084 GTACGACTTAACAA
1 GTACGACTTAACAA
156098 TTTTTTTTGG
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
31 20 0.30
32 20 0.30
33 1 0.02
34 19 0.29
35 6 0.09
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (31 bp):
GTACGACTTAACAAAATCCGAATGATTTCAA
Found at i:156056 original size:32 final size:31
Alignment explanation
Indices: 155989--156097 Score: 112
Period size: 34 Copynumber: 3.4 Consensus size: 31
155979 TATCCCTGGT
* * *
155989 ACGACTTAACAAAATCCGAATGATTTTAAGT
1 ACGACTTAACAAAAACCGAATGATTTCAAGA
**
156020 ACGACTTAACAAAAACCTTCATGATTTCAAGA
1 ACGACTTAACAAAAACC-GAATGATTTCAAGA
*
156052 ACGACTTAACAAAAAAATCCGAATG-TGTTCAAGT
1 ACGACTTAAC--AAAAA-CCGAATGAT-TTCAAGA
156086 ACGACTTAACAA
1 ACGACTTAACAA
156098 TTTTTTTTGG
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
31 16 0.25
32 22 0.34
33 1 0.02
34 24 0.37
35 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (31 bp):
ACGACTTAACAAAAACCGAATGATTTCAAGA
Found at i:156083 original size:34 final size:34
Alignment explanation
Indices: 155987--156097 Score: 126
Period size: 32 Copynumber: 3.4 Consensus size: 34
155977 ATTATCCCTG
*
155987 GTACGACTTAAC---AAAATCCGAATGATTTTAA
1 GTACGACTTAACAAAAAAATCCGAATGATTTCAA
** *
156018 GTACGACTTAACAAAAACCTTC--ATGATTTCAA
1 GTACGACTTAACAAAAAAATCCGAATGATTTCAA
*
156050 GAACGACTTAACAAAAAAATCCGAATG-TGTTCAA
1 GTACGACTTAACAAAAAAATCCGAATGAT-TTCAA
156084 GTACGACTTAACAA
1 GTACGACTTAACAA
156098 TTTTTTTTGG
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
31 12 0.18
32 27 0.42
33 1 0.02
34 25 0.38
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (34 bp):
GTACGACTTAACAAAAAAATCCGAATGATTTCAA
Found at i:157552 original size:21 final size:21
Alignment explanation
Indices: 157526--157699 Score: 179
Period size: 21 Copynumber: 8.3 Consensus size: 21
157516 TTTTGCCACC
*
157526 ACTTGTCAGATAATTGTGTCG
1 ACTTGTCAGATAATTATGTCG
* *
157547 ACTTGTCAAAT-CTTAATGTCG
1 ACTTGTCAGATAATT-ATGTCG
**
157568 ACTTGTCAGATCGTTATGTCG
1 ACTTGTCAGATAATTATGTCG
* **
157589 ACTTGTCAGATAATGATGTTA
1 ACTTGTCAGATAATTATGTCG
* * **
157610 ACCTGTCAGATAATGATGTTA
1 ACTTGTCAGATAATTATGTCG
*
157631 ACTTGTCAGATAATTATGTTG
1 ACTTGTCAGATAATTATGTCG
**
157652 ACTTGTCAGATCTTTATGTCG
1 ACTTGTCAGATAATTATGTCG
* *
157673 ACTTGTCAGATAATGATGTCT
1 ACTTGTCAGATAATTATGTCG
157694 ACTTGT
1 ACTTGT
157700 TTTATCTTTA
Statistics
Matches: 130, Mismatches: 21, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
20 2 0.02
21 126 0.97
22 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (21 bp):
ACTTGTCAGATAATTATGTCG
Found at i:157635 original size:63 final size:63
Alignment explanation
Indices: 157526--157720 Score: 178
Period size: 63 Copynumber: 3.1 Consensus size: 63
157516 TTTTGCCACC
* * * ** * * *
157526 ACTTGTCAGATAATTG-TGTCGACTTGTCAAATCTTAATGTCGACTTGTCAGATCGTTATGTCG
1 ACTTGTCAGATAA-TGATGTCAACCTGTCAGATAATGATGTCTACTTGTCAGATCATTATGTCG
* * *
157589 ACTTGTCAGATAATGATGTTAACCTGTCAGATAATGATGT-TAACTTGTCAGATAATTATGTTG
1 ACTTGTCAGATAATGATGTCAACCTGTCAGATAATGATGTCT-ACTTGTCAGATCATTATGTCG
** * * * *** *
157652 ACTTGTCAGATCTTTATGTCGACTTGTCAGATAATGATGTCTACTTGTTTTATCTTTATGTCG
1 ACTTGTCAGATAATGATGTCAACCTGTCAGATAATGATGTCTACTTGTCAGATCATTATGTCG
157715 ACTTGT
1 ACTTGT
157721 TCACGTGTTT
Statistics
Matches: 106, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
62 2 0.02
63 103 0.97
64 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (63 bp):
ACTTGTCAGATAATGATGTCAACCTGTCAGATAATGATGTCTACTTGTCAGATCATTATGTCG
Found at i:157685 original size:42 final size:42
Alignment explanation
Indices: 157526--157720 Score: 194
Period size: 42 Copynumber: 4.6 Consensus size: 42
157516 TTTTGCCACC
* * * ** * *
157526 ACTTGTCAGATAATTGTGTCGACTTGTCAAATCTTAATGTCG
1 ACTTGTCAGATCATTATGTCGACTTGTCAGATAATGATGTTG
* *
157568 ACTTGTCAGATCGTTATGTCGACTTGTCAGATAATGATGTTA
1 ACTTGTCAGATCATTATGTCGACTTGTCAGATAATGATGTTG
* * * ** *
157610 ACCTGTCAGATAATGATGTTAACTTGTCAGATAATTATGTTG
1 ACTTGTCAGATCATTATGTCGACTTGTCAGATAATGATGTTG
*
157652 ACTTGTCAGATCTTTATGTCGACTTGTCAGATAATGATGTCT-
1 ACTTGTCAGATCATTATGTCGACTTGTCAGATAATGATGT-TG
*** *
157694 ACTTGTTTTATCTTTATGTCGACTTGT
1 ACTTGTCAGATCATTATGTCGACTTGT
157721 TCACGTGTTT
Statistics
Matches: 125, Mismatches: 27, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
42 124 0.99
43 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (42 bp):
ACTTGTCAGATCATTATGTCGACTTGTCAGATAATGATGTTG
Found at i:157861 original size:21 final size:21
Alignment explanation
Indices: 157832--157897 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
157822 CTCATCTATA
157832 AAGTCGACATCTTTATTTGAC
1 AAGTCGACATCTTTATTTGAC
* *
157853 AAGTTGACA-CATTTATCTGAC
1 AAGTCGACATC-TTTATTTGAC
* ** *
157874 AAGTGGACATAATTATTTTAC
1 AAGTCGACATCTTTATTTGAC
157895 AAG
1 AAG
157898 ACGGCATAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
20 1 0.03
21 35 0.97
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (21 bp):
AAGTCGACATCTTTATTTGAC
Found at i:158385 original size:41 final size:39
Alignment explanation
Indices: 158303--158399 Score: 113
Period size: 41 Copynumber: 2.4 Consensus size: 39
158293 TACTCATTAT
* ** * *
158303 ACATTTACACATTACATTTATAAGATACATGAATACTTA
1 ACATTTACACATTACATTTACAAGATACACCAACACGTA
*
158342 ACATTCATACACATTACATTTACAAGATAGACCAACACGTA
1 ACATT--TACACATTACATTTACAAGATACACCAACACGTA
*
158383 ACATTTACACGTTACAT
1 ACATTTACACATTACAT
158400 ATTTTAGTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
39 16 0.33
41 33 0.67
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (39 bp):
ACATTTACACATTACATTTACAAGATACACCAACACGTA
Found at i:161127 original size:16 final size:16
Alignment explanation
Indices: 161106--161136 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
161096 AAACTGTCAT
161106 AATTTATAAGGATATA
1 AATTTATAAGGATATA
*
161122 AATTTATAAGTATAT
1 AATTTATAAGGATAT
161137 GTATTGCAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
AATTTATAAGGATATA
Found at i:170707 original size:16 final size:16
Alignment explanation
Indices: 170682--170712 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
170672 GAATTTCTTA
*
170682 TACGGTTATAACGAAT
1 TACGGATATAACGAAT
170698 TACGGATATAACGAA
1 TACGGATATAACGAA
170713 GTAATTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (16 bp):
TACGGATATAACGAAT
Found at i:176998 original size:4 final size:4
Alignment explanation
Indices: 176989--177081 Score: 186
Period size: 4 Copynumber: 23.2 Consensus size: 4
176979 GAATGTTTTA
176989 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
177037 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT A
177082 TTGTAGAATA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 89 1.00
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AGAT
Found at i:177761 original size:2 final size:2
Alignment explanation
Indices: 177756--177789 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
177746 TTATATCTTT
177756 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
177790 ACTTTACCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:180290 original size:2 final size:2
Alignment explanation
Indices: 180283--180319 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
180273 TGAATTCATC
*
180283 AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
180320 TTCATACTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:185135 original size:17 final size:17
Alignment explanation
Indices: 185115--185147 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
185105 TGTAGAATTT
185115 AATATATATATATATTA
1 AATATATATATATATTA
*
185132 AATATTTATATATATT
1 AATATATATATATATT
185148 TCAATACTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATATATATATATATTA
Found at i:185972 original size:2 final size:2
Alignment explanation
Indices: 185967--186024 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
185957 ATATCGCCCC
* *
185967 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT GT TT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
186009 CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT
186025 TATGTTGTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.52
Consensus pattern (2 bp):
CT
Found at i:187671 original size:166 final size:170
Alignment explanation
Indices: 187450--187851 Score: 605
Period size: 166 Copynumber: 2.3 Consensus size: 170
187440 TAATTAGATT
187450 AAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGT
1 AAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGT
* * * *
187515 ACGGACAACTCCTCCTACAG-T-T-GTTGTTCTTTTGCAGATGAATTTTACATATATTAGAGGTG
66 ACGGACAACTCCTCCTACAGTTATAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAAGTG
*
187577 TGCATATTGCTAGGATTTTGATTTATGATTATTT-ATGAA
131 TGCATATCGCTAGGATTTTGATTTATGATTATTTAATGAA
*
187616 AAAATACCAGCTTTTGAACTTAGTCATTTATTGGCAAAATATTGCATATAGGGTACCCTCATTGT
1 AAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGT
*
187681 ACGGAGAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATAT
66 ACGGACAACTCCTCCTACAG--TT----AT----AGTTGTTCTTTTGCAGATCAATTGTACATAT
* *
187746 ATCAGAAGTGTGTATATCGCTAGGATTTTGATTTATGATTATTTAATTAA
121 ATCAGAAGTGTGCATATCGCTAGGATTTTGATTTATGATTATTTAATGAA
187796 AAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTAC
1 AAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTAC
187852 ACCATTCACT
Statistics
Matches: 212, Mismatches: 10, Indels: 14
0.90 0.04 0.06
Matches are distributed among these distances:
166 83 0.39
169 1 0.00
174 1 0.00
179 68 0.32
180 59 0.28
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (170 bp):
AAAATACCAGCTTTTGAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGT
ACGGACAACTCCTCCTACAGTTATAGTTGTTCTTTTGCAGATCAATTGTACATATATCAGAAGTG
TGCATATCGCTAGGATTTTGATTTATGATTATTTAATGAA
Found at i:188027 original size:2 final size:2
Alignment explanation
Indices: 188020--188050 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
188010 TCTTCTATAT
*
188020 TC TC TC TC TC TC TC CC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
188051 TCATGCTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:189978 original size:2 final size:2
Alignment explanation
Indices: 189971--190037 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
189961 TTCTGATTAA
189971 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
190013 TC TC TC TC -C TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
190038 CTTCTCATGA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:190221 original size:2 final size:2
Alignment explanation
Indices: 190214--190246 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
190204 ATACATGTAA
*
190214 TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
190247 GTTTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:190928 original size:10 final size:10
Alignment explanation
Indices: 190913--190972 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
190903 CAAATTAATA
190913 GTACAGTGGG
1 GTACAGTGGG
*
190923 GTACAGTGATG
1 GTACAGTG-GG
*
190934 GT-CAGTGCCCG
1 GTACAGTG--GG
*
190945 GTACAGTGGC
1 GTACAGTGGG
190955 GTACAGTGGG
1 GTACAGTGGG
*
190965 ATACAGTG
1 GTACAGTG
190973 CTGGTCAATG
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
10 29 0.73
11 6 0.15
12 5 0.12
ACGTcount: A:0.22, C:0.17, G:0.40, T:0.22
Consensus pattern (10 bp):
GTACAGTGGG
Found at i:190972 original size:42 final size:42
Alignment explanation
Indices: 190913--191011 Score: 162
Period size: 42 Copynumber: 2.4 Consensus size: 42
190903 CAAATTAATA
*
190913 GTACAGTGGGGTACAGTGATGGTCAGTGCCCGGTACAGTGGC
1 GTACAGTGGGGTACAGTGATGGTCAATGCCCGGTACAGTGGC
* * *
190955 GTACAGTGGGATACAGTGCTGGTCAATGCCCTGTACAGTGGC
1 GTACAGTGGGGTACAGTGATGGTCAATGCCCGGTACAGTGGC
190997 GTACAGTGGGGTACA
1 GTACAGTGGGGTACA
191012 TTGGAAGTCA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.22
Consensus pattern (42 bp):
GTACAGTGGGGTACAGTGATGGTCAATGCCCGGTACAGTGGC
Found at i:191049 original size:43 final size:42
Alignment explanation
Indices: 190986--191131 Score: 161
Period size: 43 Copynumber: 3.4 Consensus size: 42
190976 GTCAATGCCC
* *
190986 TGTACAGTG-GCGTACAGTGGGGTACATTGGAAGTCAGTAGGAC
1 TGTACAGTGAG-GTACAGTGGGGTACATT-GAAGTCAGTAGAAA
* * * * **
191029 TGTACAGTGATGTACTGTGGGATACAGTGTTGTTCAGTAGAAA
1 TGTACAGTGAGGTACAGTGGGGTACATTGAAG-TCAGTAGAAA
*
191072 TGTACAGTGGGGTACAGTGGGGTACAGTTGAAGTCAGT-GAAA
1 TGTACAGTGAGGTACAGTGGGGTACA-TTGAAGTCAGTAGAAA
191114 TGTACAGTGAGGTACAGT
1 TGTACAGTGAGGTACAGT
191132 CAATGTACAG
Statistics
Matches: 84, Mismatches: 16, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
42 23 0.27
43 58 0.69
44 3 0.04
ACGTcount: A:0.27, C:0.11, G:0.35, T:0.27
Consensus pattern (42 bp):
TGTACAGTGAGGTACAGTGGGGTACATTGAAGTCAGTAGAAA
Found at i:191088 original size:10 final size:10
Alignment explanation
Indices: 191073--191099 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
191063 CAGTAGAAAT
191073 GTACAGTGGG
1 GTACAGTGGG
191083 GTACAGTGGG
1 GTACAGTGGG
191093 GTACAGT
1 GTACAGT
191100 TGAAGTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.11, G:0.44, T:0.22
Consensus pattern (10 bp):
GTACAGTGGG
Found at i:191119 original size:22 final size:21
Alignment explanation
Indices: 191093--191151 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
191083 GTACAGTGGG
191093 GTACAGTTGAAGTCAGTGAAAT
1 GTACAGTTGAAGTCAGT-AAAT
* *
191115 GTACAG-TGAGGTACAGTCAAT
1 GTACAGTTGAAGT-CAGTAAAT
* *
191136 GTACAGTGGATGTCAG
1 GTACAGTTGAAGTCAG
191152 ACAATGTCGG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.32, C:0.12, G:0.31, T:0.25
Consensus pattern (21 bp):
GTACAGTTGAAGTCAGTAAAT
Found at i:191156 original size:21 final size:21
Alignment explanation
Indices: 191112--191158 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
191102 AAGTCAGTGA
*
191112 AATGTACAGTGAGGTACAGTC
1 AATGTACAGTGAGGTACAGAC
*
191133 AATGTACAGTGGATGT-CAGAC
1 AATGTACAGT-GAGGTACAGAC
191154 AATGT
1 AATGT
191159 CGGAATATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.26
Consensus pattern (21 bp):
AATGTACAGTGAGGTACAGAC
Found at i:199493 original size:16 final size:16
Alignment explanation
Indices: 199472--199506 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
199462 GAACTACTAG
199472 TATGTTTCATTTAACT
1 TATGTTTCATTTAACT
199488 TATGTTTCATTTAACT
1 TATGTTTCATTTAACT
199504 TAT
1 TAT
199507 TCTGAACAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (16 bp):
TATGTTTCATTTAACT
Found at i:207081 original size:16 final size:17
Alignment explanation
Indices: 207060--207092 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
207050 CTATGATTTC
207060 AAAAAATCAA-AAATCG
1 AAAAAATCAATAAATCG
207076 AAAAAATCAATAAATCG
1 AAAAAATCAATAAATCG
207093 CAACCTCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.67, C:0.12, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAAAATCAATAAATCG
Found at i:212283 original size:14 final size:15
Alignment explanation
Indices: 212264--212292 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
212254 ATTTCATTTG
212264 GAAT-AAAAGAGATA
1 GAATAAAAAGAGATA
212278 GAATAAAAAGAGATA
1 GAATAAAAAGAGATA
212293 CTGTAATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.14
Consensus pattern (15 bp):
GAATAAAAAGAGATA
Found at i:217385 original size:21 final size:21
Alignment explanation
Indices: 217359--217399 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
217349 TCTATTATTG
* *
217359 GGGTTCTTATGAGTATCCTTC
1 GGGTTCCTAGGAGTATCCTTC
*
217380 GGGTTCCTAGGGGTATCCTT
1 GGGTTCCTAGGAGTATCCTT
217400 GGGATACTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.20, G:0.29, T:0.39
Consensus pattern (21 bp):
GGGTTCCTAGGAGTATCCTTC
Found at i:217683 original size:11 final size:10
Alignment explanation
Indices: 217659--217726 Score: 109
Period size: 10 Copynumber: 6.6 Consensus size: 10
217649 TTCAATCATC
217659 GGGGTTCCTT
1 GGGGTTCCTT
*
217669 GGGGTTTCGTT
1 GGGG-TTCCTT
217680 GGGGTTTCCTT
1 GGGG-TTCCTT
217691 GGGGTTCCTT
1 GGGGTTCCTT
217701 GGGGTTCCTT
1 GGGGTTCCTT
217711 GGGGTTCCTT
1 GGGGTTCCTT
217721 GGGGTT
1 GGGGTT
217727 AAAAGACGCA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
10 36 0.65
11 19 0.35
ACGTcount: A:0.00, C:0.16, G:0.43, T:0.41
Consensus pattern (10 bp):
GGGGTTCCTT
Found at i:217906 original size:2 final size:2
Alignment explanation
Indices: 217893--217937 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
217883 AAAAATGCAC
*
217893 CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
217935 CT C
1 CT C
217938 AACCGATTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:235390 original size:22 final size:22
Alignment explanation
Indices: 235362--235422 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
235352 AATATTGACT
*
235362 TAAAGGCCACTTAAAGACAGTG
1 TAAAGGCCACTTAAAGACAGCG
* *
235384 TAAAGG-CAGTGTAAAGAGAGCG
1 TAAAGGCCACT-TAAAGACAGCG
*
235406 TAAATGCCACTTAAAGA
1 TAAAGGCCACTTAAAGA
235423 TGCTTAAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 3 0.09
22 26 0.81
23 3 0.09
ACGTcount: A:0.43, C:0.15, G:0.25, T:0.18
Consensus pattern (22 bp):
TAAAGGCCACTTAAAGACAGCG
Found at i:235438 original size:11 final size:11
Alignment explanation
Indices: 235415--235464 Score: 75
Period size: 11 Copynumber: 4.6 Consensus size: 11
235405 GTAAATGCCA
*
235415 CTTAAAGAT-G
1 CTTAAAGGTGG
235425 CTTAAAGGTGG
1 CTTAAAGGTGG
235436 CTTAAAGGTGG
1 CTTAAAGGTGG
*
235447 CTTAAAGGTAG
1 CTTAAAGGTGG
235458 CTTAAAG
1 CTTAAAG
235465 AAGTTTGGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
10 8 0.22
11 29 0.78
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:235550 original size:10 final size:11
Alignment explanation
Indices: 235535--235574 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
235525 GGTTGTATAG
*
235535 CCTTTAAG-CT
1 CCTTTAAGCCA
*
235545 CCTTTAAGTCA
1 CCTTTAAGCCA
235556 CCTTTAAGCCA
1 CCTTTAAGCCA
235567 CCTTTAAG
1 CCTTTAAG
235575 GACTTGCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.25, C:0.30, G:0.10, T:0.35
Consensus pattern (11 bp):
CCTTTAAGCCA
Found at i:236500 original size:128 final size:128
Alignment explanation
Indices: 236272--236503 Score: 358
Period size: 128 Copynumber: 1.8 Consensus size: 128
236262 ATGAAATTTG
236272 GTATACAGGTTTATCATGATAATATCTAGATCAAATTCGATATTGGGTACAATTAAGCAATTTTC
1 GTATACAGGTTTATCATGATAATATCTAGATCAAATTCGATATTGGGTACAATTAAGCAATTTTC
** * *
236337 GACAGGGCTATGGCCCTTGGACGTAGAAAAATTCCAGTTATTTTCAGTTTCCGCTCATTTTCT
66 GACAGGGCTATACCCCTTGAACATAGAAAAATTCCAGTTATTTTCAGTTTCCGCTCATTTTCT
* * ** *
236400 GTATACAGGTTTATCATGATAGTATCTAGGTCACGTTCGATATTGGGTACAATTGAGCAATTTTC
1 GTATACAGGTTTATCATGATAATATCTAGATCAAATTCGATATTGGGTACAATTAAGCAATTTTC
*
236465 GAC-GGAGTTATACCCCTTGAACATAGAAAAATTCCAGTT
66 GACAGG-GCTATACCCCTTGAACATAGAAAAATTCCAGTT
236504 GTTTGTAGTT
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
127 2 0.02
128 91 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (128 bp):
GTATACAGGTTTATCATGATAATATCTAGATCAAATTCGATATTGGGTACAATTAAGCAATTTTC
GACAGGGCTATACCCCTTGAACATAGAAAAATTCCAGTTATTTTCAGTTTCCGCTCATTTTCT
Found at i:237805 original size:15 final size:16
Alignment explanation
Indices: 237776--237809 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
237766 TAAAGGTGGT
237776 CTCATAAAGGTGATGC
1 CTCATAAAGGTGATGC
237792 CTCATAAA-GTGATGC
1 CTCATAAAGGTGATGC
237807 CTC
1 CTC
237810 GTCTCGGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (16 bp):
CTCATAAAGGTGATGC
Found at i:242940 original size:37 final size:37
Alignment explanation
Indices: 242890--242960 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
242880 CATTTTACCA
242890 TTGATTATCATTTTAATATCTTATGTCAATTAAAATG
1 TTGATTATCATTTTAATATCTTATGTCAATTAAAATG
* *
242927 TTGATTATTATTTTAATATCTTATGTCATTTAAA
1 TTGATTATCATTTTAATATCTTATGTCAATTAAA
242961 CATTAGTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (37 bp):
TTGATTATCATTTTAATATCTTATGTCAATTAAAATG
Found at i:243847 original size:2 final size:2
Alignment explanation
Indices: 243840--243872 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
243830 ATATTTAAGA
*
243840 TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
243873 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
TC
Found at i:243877 original size:2 final size:2
Alignment explanation
Indices: 243872--243904 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
243862 TCTCTCTCTC
243872 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
243905 TTGTTTTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:244731 original size:26 final size:26
Alignment explanation
Indices: 244678--244727 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
244668 TGTTATGTAC
* **
244678 AATGAAATAATAAAATGATAATTTAT
1 AATGAAATAAAAAAATGATAATAAAT
244704 AATGAAATAAAAAAAT-ATAATAAA
1 AATGAAATAAAAAAATGATAATAAA
244728 ATAAATCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (26 bp):
AATGAAATAAAAAAATGATAATAAAT
Found at i:257392 original size:4 final size:4
Alignment explanation
Indices: 257383--257438 Score: 78
Period size: 4 Copynumber: 13.5 Consensus size: 4
257373 TGTGCGTTGT
257383 TTTG TTTG TTTG TTTG TTTG TTTTG TTTG TTTGGG TTT- TTTG TTTG TTTG
1 TTTG TTTG TTTG TTTG TTTG -TTTG TTTG TTT--G TTTG TTTG TTTG TTTG
257433 TTTG TT
1 TTTG TT
257439 AGTTGGGGGG
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.06
4 37 0.77
5 4 0.08
6 4 0.08
ACGTcount: A:0.00, C:0.00, G:0.25, T:0.75
Consensus pattern (4 bp):
TTTG
Found at i:257405 original size:21 final size:20
Alignment explanation
Indices: 257379--257438 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 20
257369 TAGGTGTGCG
257379 TTGTTTTGTTTGTTTGTTTGT
1 TTGTTTTGTTTGTTTGTTT-T
257400 TTGTTTTGTTTGTTTGGGTTTT
1 TTGTTTTGTTTGTTT--GTTTT
257422 TTG-TTTGTTTGTTTGTT
1 TTGTTTTGTTTGTTTGTT
257439 AGTTGGGGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.08
21 26 0.70
22 4 0.11
23 4 0.11
ACGTcount: A:0.00, C:0.00, G:0.25, T:0.75
Consensus pattern (20 bp):
TTGTTTTGTTTGTTTGTTTT
Found at i:258181 original size:2 final size:2
Alignment explanation
Indices: 258174--258224 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
258164 AAATATTGTC
258174 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
258216 CT CT CT CT C
1 CT CT CT CT C
258225 ACACACACAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:258750 original size:2 final size:2
Alignment explanation
Indices: 258743--258795 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
258733 TTGCTTAACA
258743 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
258785 AG AG AG AG AG A
1 AG AG AG AG AG A
258796 AGAATCGTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:259367 original size:12 final size:12
Alignment explanation
Indices: 259350--259378 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
259340 TTTGATCAGT
259350 ATCTGTATTATA
1 ATCTGTATTATA
259362 ATCTGTATTATA
1 ATCTGTATTATA
259374 ATCTG
1 ATCTG
259379 GTTCCCGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.48
Consensus pattern (12 bp):
ATCTGTATTATA
Found at i:261578 original size:18 final size:18
Alignment explanation
Indices: 261557--261593 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
261547 CCTGTAGGAA
261557 AATTATTTCTCCTATGGG
1 AATTATTTCTCCTATGGG
*
261575 AATTATTTTTCCTATGGG
1 AATTATTTCTCCTATGGG
261593 A
1 A
261594 TATTTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (18 bp):
AATTATTTCTCCTATGGG
Found at i:272959 original size:2 final size:2
Alignment explanation
Indices: 272952--273010 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
272942 ATTTACATGA
272952 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
272994 CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT C
273011 CAATTCGTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:274109 original size:16 final size:16
Alignment explanation
Indices: 274088--274134 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
274078 GTGGTCCGAT
274088 TTTGCTTTTTAGATTA
1 TTTGCTTTTTAGATTA
274104 TTTGCTTTTTAGATTA
1 TTTGCTTTTTAGATTA
**
274120 TTTGGATTTTAGATT
1 TTTGCTTTTTAGATT
274135 CTCATTTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.19, C:0.04, G:0.15, T:0.62
Consensus pattern (16 bp):
TTTGCTTTTTAGATTA
Found at i:275971 original size:3 final size:3
Alignment explanation
Indices: 275963--275988 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
275953 AAAATTATGA
275963 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
275989 TTTCCTCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:278516 original size:2 final size:2
Alignment explanation
Indices: 278509--278571 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
278499 ATCCAAAGAT
278509 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
278551 AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG A
278572 AAAGAAATCA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:281625 original size:2 final size:2
Alignment explanation
Indices: 281620--281662 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
281610 TTTTTTATAT
281620 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
281662 G
1 G
281663 TTTTCTATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:284278 original size:2 final size:2
Alignment explanation
Indices: 284271--284320 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
284261 AGTACACAAA
284271 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
284313 TC TC TC TC
1 TC TC TC TC
284321 ATTGTGTAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:289177 original size:13 final size:13
Alignment explanation
Indices: 289156--289186 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
289146 TTTAATTTAA
289156 AAAAAAAACCCAC
1 AAAAAAAACCCAC
*
289169 AAAATAAACCCAC
1 AAAAAAAACCCAC
289182 AAAAA
1 AAAAA
289187 GCAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.71, C:0.26, G:0.00, T:0.03
Consensus pattern (13 bp):
AAAAAAAACCCAC
Found at i:296167 original size:2 final size:2
Alignment explanation
Indices: 296160--296204 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
296150 GCTTGGTATA
296160 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
296202 AG A
1 AG A
296205 ATTTTCAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:312215 original size:2 final size:2
Alignment explanation
Indices: 312208--312255 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
312198 AGTCTACACC
312208 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
312250 CT CT CT
1 CT CT CT
312256 AATATGCAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:324430 original size:139 final size:140
Alignment explanation
Indices: 324167--324444 Score: 531
Period size: 139 Copynumber: 2.0 Consensus size: 140
324157 AACAAAATGC
*
324167 AAATGTTTACTGGGAAATTTTAAATCAATTGCCTTATATTTGTGACAAAGATAAATGATATATAT
1 AAATGTTTACTCGGAAATTTTAAATCAATTGCCTTATATTTGTGACAAAGATAAATGA-ATATAT
324232 ATATTTGCCAAGCTATATTTATTATAGAAACATGATCAAAGTGCAAAAACAAAATTACAAAATGA
65 ATATTTGCCAAGCTATATTTATTATAGAAACATGATCAAAGTGCAAAAACAAAATTACAAAATGA
324297 AATTATTTGTT
130 AATTATTTGTT
324308 AAATGTTTACTCGGAAATTTTAAATCAATTGCCTTATATTTGTGACAAAGATAAATG-ATATATA
1 AAATGTTTACTCGGAAATTTTAAATCAATTGCCTTATATTTGTGACAAAGATAAATGAATATATA
324372 TATTTGCCAAGCTATATTTATTATAGAAACATGATCAAAGTGCAAAAACAAAATTACAAAATGAA
66 TATTTGCCAAGCTATATTTATTATAGAAACATGATCAAAGTGCAAAAACAAAATTACAAAATGAA
324437 ATTATTTG
131 ATTATTTG
324445 GGTTTTTCTT
Statistics
Matches: 136, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
139 80 0.59
141 56 0.41
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.35
Consensus pattern (140 bp):
AAATGTTTACTCGGAAATTTTAAATCAATTGCCTTATATTTGTGACAAAGATAAATGAATATATA
TATTTGCCAAGCTATATTTATTATAGAAACATGATCAAAGTGCAAAAACAAAATTACAAAATGAA
ATTATTTGTT
Found at i:331747 original size:2 final size:2
Alignment explanation
Indices: 331740--331783 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
331730 GACCCACTCA
331740 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
331782 CT
1 CT
331784 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:345163 original size:68 final size:68
Alignment explanation
Indices: 345085--345354 Score: 531
Period size: 68 Copynumber: 4.0 Consensus size: 68
345075 TATTTGATAC
345085 ATAAATATGTTTCCTAATTATAAGAATAGAATAGCGAAAACGTTTATTCTGTGTGAACTTTTTAA
1 ATAAATATGTTTCCTAATTATAAGAATAGAATAGCGAAAACGTTTATTCTGTGTGAACTTTTTAA
345150 TAA
66 TAA
345153 ATAAATATGTTTCCTAATTATAAGAATAGAATAGCGAAAACGTTTATTCTGTGTGAACTTTTTAA
1 ATAAATATGTTTCCTAATTATAAGAATAGAATAGCGAAAACGTTTATTCTGTGTGAACTTTTTAA
345218 TAA
66 TAA
345221 ATAAATATGTTTCCTAATTATAAGAATAGAATAGCGAAAACGTTTATTCTGTGTGAACTTTTTAA
1 ATAAATATGTTTCCTAATTATAAGAATAGAATAGCGAAAACGTTTATTCTGTGTGAACTTTTTAA
345286 TAA
66 TAA
*
345289 TTAAATATGTTTCCTAATTATAAGAATAGAATAGCGAAAACGTTTATTCTGTGTGAACTTTTTAA
1 ATAAATATGTTTCCTAATTATAAGAATAGAATAGCGAAAACGTTTATTCTGTGTGAACTTTTTAA
345354 T
66 T
345355 GACGTCACAT
Statistics
Matches: 201, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 201 1.00
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (68 bp):
ATAAATATGTTTCCTAATTATAAGAATAGAATAGCGAAAACGTTTATTCTGTGTGAACTTTTTAA
TAA
Found at i:345850 original size:3 final size:3
Alignment explanation
Indices: 345844--345886 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
345834 TTTATGTTGT
*
345844 TGA TGA TAA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
345887 CCGTACGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.35, C:0.00, G:0.30, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:347411 original size:2 final size:2
Alignment explanation
Indices: 347404--347460 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
347394 TTTACCTACT
347404 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
347446 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
347461 TGTCACTCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:347938 original size:31 final size:31
Alignment explanation
Indices: 347797--347938 Score: 97
Period size: 31 Copynumber: 4.3 Consensus size: 31
347787 CTTTTTTAAA
*
347797 ACAAAGTAATGGTAATGGTAATGCATTACTTT
1 ACAATGTAATGGTAAT-GTAATGCATTACTTT
* *
347829 ACTCATGTAATGGTAATGTAATGCATTACTTCAAG
1 AC-AATGTAATGGTAATGTAATGCATTACTT---T
* * *** * *
347864 AAAATCAAGTAATGGTAATTTAATGCCCAAATTC
1 ACAAT---GTAATGGTAATGTAATGCATTACTTT
*
347898 ATGAA-GTAATGGTAATGTAATGCATTACTTT
1 A-CAATGTAATGGTAATGTAATGCATTACTTT
347929 ACAATGTAAT
1 ACAATGTAAT
347939 TCGCCAAGCC
Statistics
Matches: 82, Mismatches: 19, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
30 2 0.02
31 26 0.32
32 16 0.20
33 12 0.15
34 3 0.04
35 3 0.04
37 20 0.24
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (31 bp):
ACAATGTAATGGTAATGTAATGCATTACTTT
Found at i:348423 original size:165 final size:164
Alignment explanation
Indices: 348074--348526 Score: 568
Period size: 165 Copynumber: 2.7 Consensus size: 164
348064 CCTACGACCT
* * * * **
348074 GAACGCCTGACCCAGGGGCCATGAATTTCACAATTCAAGTAAAGGAGTTTGTGGACATCATAACC
1 GAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGA-GAGTCAGTGGACATCATAACC
* * * * * *
348139 ATGCATTCAGTTTTTTCCCCACATGTGTGGGAGTTAAGAAGAAGATTTCCTAAGACTTAATACAT
65 ATGAACTCAGTTTTTTCCACACATGTGTGGGAG-T-AG-AGAAGATTTTCTAAAATTTAATACAT
* *
348204 TTTCACTATATGGCAAAAGTGGACCCACCCTAGAGCCT
127 TTTCACTACATGGCAAAAGTGGACCCACCCTAGAGCCA
*
348242 GAACCCCTGACCCAGGGGCCAAGAATTTCACAATTTAGGTAGATGAGTCAGTGGACATCATAACC
1 GAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGA-GAGTCAGTGGACATCATAACC
* * * * * *
348307 ATGAACTCAGTTTTATACAAATATATATGGGAGTAGAGAAGATTTTCTAAAATTTAATACATTTT
65 ATGAACTCAGTTTTTTCCACACATGTGTGGGAGTAGAGAAGATTTTCTAAAATTTAATACATTTT
* *
348372 CACTACATGGCCAAAGTGGCCCCACCCTAGAGCCA
130 CACTACATGGCAAAAGTGGACCCACCCTAGAGCCA
* * * *
348407 GAACCCCTGTCCCAGGGGCCATGAATTTCACAATTTTGGTAGAGGGCTTCA-TGGAGATCATAAC
1 GAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGAG--TCAGTGGACATCATAAC
*
348471 CATGAACTCAGTTTTTTCCTCACATGTGTGGGAGTAGAGAAGATTTT-TGAAAATTT
64 CATGAACTCAGTTTTTTCCACACATGTGTGGGAGTAGAGAAGATTTTCT-AAAATTT
348527 GGCTTTTTTT
Statistics
Matches: 246, Mismatches: 36, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
164 3 0.01
165 156 0.63
166 5 0.02
167 1 0.00
168 81 0.33
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (164 bp):
GAACCCCTGACCCAGGGGCCATGAATTTCACAATTTAGGTAGAGAGTCAGTGGACATCATAACCA
TGAACTCAGTTTTTTCCACACATGTGTGGGAGTAGAGAAGATTTTCTAAAATTTAATACATTTTC
ACTACATGGCAAAAGTGGACCCACCCTAGAGCCA
Found at i:351556 original size:29 final size:29
Alignment explanation
Indices: 351523--351606 Score: 132
Period size: 31 Copynumber: 2.8 Consensus size: 29
351513 CTGAAAAATG
351523 GGTCAAGGTAAAAAAAATCAAAATAATTA
1 GGTCAAGGTAAAAAAAATCAAAATAATTA
351552 GGTCAAGGTAAAAAAAAAATCAAAATAATTA
1 GGTCAAGGT--AAAAAAAATCAAAATAATTA
* *
351583 GGTCAATGTAAAAAACATCAAAAT
1 GGTCAAGGTAAAAAAAATCAAAAT
351607 TCCGAAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
29 23 0.45
31 28 0.55
ACGTcount: A:0.58, C:0.08, G:0.13, T:0.20
Consensus pattern (29 bp):
GGTCAAGGTAAAAAAAATCAAAATAATTA
Found at i:356711 original size:38 final size:38
Alignment explanation
Indices: 356659--356854 Score: 338
Period size: 38 Copynumber: 5.1 Consensus size: 38
356649 TCCAAAACAT
* *
356659 TGTGTGTGCTGTGTTTATCTACTAGCATTTGATATCTG
1 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTG
356697 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTG
1 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATC--TG
356737 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTG
1 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTG
356775 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTG
1 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATC--TG
356815 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTG
1 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTG
356853 TG
1 TG
356855 CTGCACTCTC
Statistics
Matches: 152, Mismatches: 2, Indels: 8
0.94 0.01 0.05
Matches are distributed among these distances:
38 76 0.50
40 76 0.50
ACGTcount: A:0.17, C:0.11, G:0.24, T:0.47
Consensus pattern (38 bp):
TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTG
Found at i:356739 original size:40 final size:40
Alignment explanation
Indices: 356659--356854 Score: 346
Period size: 40 Copynumber: 5.0 Consensus size: 40
356649 TCCAAAACAT
* *
356659 TGTGTGTGCTGTGTTTATCTACTAGCATTTGATATC--TG
1 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTG
356697 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTG
1 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTG
356737 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATC--TG
1 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTG
356775 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTG
1 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTG
356815 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTG
1 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTG
356855 CTGCACTCTC
Statistics
Matches: 152, Mismatches: 2, Indels: 6
0.95 0.01 0.04
Matches are distributed among these distances:
38 72 0.47
40 80 0.53
ACGTcount: A:0.17, C:0.11, G:0.24, T:0.47
Consensus pattern (40 bp):
TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTG
Found at i:356745 original size:78 final size:78
Alignment explanation
Indices: 356659--356854 Score: 374
Period size: 78 Copynumber: 2.5 Consensus size: 78
356649 TCCAAAACAT
* *
356659 TGTGTGTGCTGTGTTTATCTACTAGCATTTGATATCTGTGTGTGTGCAGTGTTTATTTACTAGCA
1 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTGTGTGTGCAGTGTTTATTTACTAGCA
356724 TTTGATATCTGTG
66 TTTGATATCTGTG
356737 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTGTGTGTGCAGTGTTTATTTACTAGCA
1 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTGTGTGTGCAGTGTTTATTTACTAGCA
356802 TTTGATATCTGTG
66 TTTGATATCTGTG
356815 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTG
1 TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTG
356855 CTGCACTCTC
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 116 1.00
ACGTcount: A:0.17, C:0.11, G:0.24, T:0.47
Consensus pattern (78 bp):
TGTGTGTGCAGTGTTTATTTACTAGCATTTGATATCTGTGTGTGTGCAGTGTTTATTTACTAGCA
TTTGATATCTGTG
Found at i:357191 original size:94 final size:97
Alignment explanation
Indices: 357072--357317 Score: 234
Period size: 98 Copynumber: 2.5 Consensus size: 97
357062 CTATTTGCAC
* * * * * *
357072 TGAGATGCACAGTTTGATGGAATAAG-TATGCGTTTTATTTGTG-TTAA-AGC-ACATACCGTCA
1 TGAGATGCACAGTTTAATGGAATAAGCT-TGCATTATATTTGTGCTGAAGAACAACATACCCTCA
* *
357133 CGATTTGTGTGTGCTGTCTTGATGTGCTTTCTT
65 CAATTTATGTGTGCTGTCTTGATGTGCTTTCTT
* * * * *
357166 TGAGGTGCACAGTTTAATTGTATAAGCTTGCATTATATTTTTGCTGAAGAACATACATACCCTGA
1 TGAGATGCACAGTTTAATGGAATAAGCTTGCATTATATTTGTGCTGAAGAACA-ACATACCCTCA
*
357231 CAATTTATGTGTGCTGTCTTGGTGTGCTTTCTT
65 CAATTTATGTGTGCTGTCTTGATGTGCTTTCTT
*
357264 TGCACTGAGGTGCACAGTTTGATGGTAAT-AG-TGTGCATTATATTTGTGCTGAAG
1 TG-A--GA--TGCACAGTTTAATGG-AATAAGCT-TGCATTATATTTGTGCTGAAG
357318 TACGTACCCT
Statistics
Matches: 121, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
94 34 0.28
95 4 0.03
96 2 0.02
98 41 0.34
99 1 0.01
101 1 0.01
102 1 0.01
103 35 0.29
104 2 0.02
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.39
Consensus pattern (97 bp):
TGAGATGCACAGTTTAATGGAATAAGCTTGCATTATATTTGTGCTGAAGAACAACATACCCTCAC
AATTTATGTGTGCTGTCTTGATGTGCTTTCTT
Found at i:357316 original size:103 final size:101
Alignment explanation
Indices: 357054--357347 Score: 306
Period size: 103 Copynumber: 3.0 Consensus size: 101
357044 TGACAAACTG
* * * * * * *
357054 GGTGTGCTCTATTTGCACTGAGATGCACAGTTTGATGG-AATAAGTATGCGTTTTATTTGTGTTA
1 GGTGTGCTTTCTTTGCACTGAGGTGCACAGTTTGATGGTAATAAGT-TGCATTATATTTGTGCTG
* * *
357118 AAG-C-ACATACCGTCACGATTTGTGTGTGCTGTCTT
65 AAGACTACATACCCTGACAATTTGTGTGTGCTGTCTT
* * * *
357153 GATGTGCTTTC-TT----TGAGGTGCACAGTTTAATTGT-ATAAGCTTGCATTATATTTTTGCTG
1 GGTGTGCTTTCTTTGCACTGAGGTGCACAGTTTGATGGTAATAAG-TTGCATTATATTTGTGCTG
*
357212 AAGAACATACATACCCTGACAATTTATGTGTGCTGTCTT
65 AAG-AC-TACATACCCTGACAATTTGTGTGTGCTGTCTT
357251 GGTGTGCTTTCTTTGCACTGAGGTGCACAGTTTGATGGTAAT-AGTGTGCATTATATTTGTGCTG
1 GGTGTGCTTTCTTTGCACTGAGGTGCACAGTTTGATGGTAATAAGT-TGCATTATATTTGTGCTG
* *
357315 AAG--TACGTACCCTGACAATTTGTGTGTGTTGTC
65 AAGACTACATACCCTGACAATTTGTGTGTGCTGTC
357348 GTTCCACAGC
Statistics
Matches: 160, Mismatches: 22, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
94 38 0.24
95 1 0.01
96 1 0.01
98 39 0.24
99 37 0.23
102 1 0.01
103 41 0.26
104 2 0.01
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.39
Consensus pattern (101 bp):
GGTGTGCTTTCTTTGCACTGAGGTGCACAGTTTGATGGTAATAAGTTGCATTATATTTGTGCTGA
AGACTACATACCCTGACAATTTGTGTGTGCTGTCTT
Found at i:360464 original size:16 final size:16
Alignment explanation
Indices: 360443--360476 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
360433 TCATTCAGCA
*
360443 GAGAGAGAATGAGAGG
1 GAGAGAGAAAGAGAGG
360459 GAGAGAGAAAGAGAGG
1 GAGAGAGAAAGAGAGG
360475 GA
1 GA
360477 AAAAATATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (16 bp):
GAGAGAGAAAGAGAGG
Found at i:364088 original size:2 final size:2
Alignment explanation
Indices: 364081--364134 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
364071 AGGACAGTGT
364081 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
364123 TC TC TC TC TC TC
1 TC TC TC TC TC TC
364135 CACACCCTGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:364205 original size:2 final size:2
Alignment explanation
Indices: 364186--364241 Score: 85
Period size: 2 Copynumber: 27.0 Consensus size: 2
364176 GGTTTCAACC
*
364186 CT CT CC CT CT CT CAT CT CT CT CAT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT C-T CT CT CT C-T CT CT CT CT CT CT CT CT CT CT
364230 CT CT CT CT CT CT
1 CT CT CT CT CT CT
364242 TTTCCTCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 46 0.92
3 4 0.08
ACGTcount: A:0.04, C:0.50, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:365833 original size:12 final size:12
Alignment explanation
Indices: 365816--365842 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
365806 AAGCTGCTTT
365816 AAAAGTTGTTTC
1 AAAAGTTGTTTC
365828 AAAAGTTGTTTC
1 AAAAGTTGTTTC
365840 AAA
1 AAA
365843 TGCAATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (12 bp):
AAAAGTTGTTTC
Found at i:366674 original size:17 final size:16
Alignment explanation
Indices: 366652--366685 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
366642 ATTTTCGATT
366652 AAAATTTAAATAAAAAA
1 AAAATTT-AATAAAAAA
*
366669 AAAATTTGATAAAAAA
1 AAAATTTAATAAAAAA
366685 A
1 A
366686 TGAAGATCGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAATTTAATAAAAAA
Found at i:367557 original size:14 final size:14
Alignment explanation
Indices: 367546--367576 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
367536 ACATATGTGT
367546 ATCAAAATATGTCC
1 ATCAAAATATGTCC
367560 ATCAAAATATGTCC
1 ATCAAAATATGTCC
367574 ATC
1 ATC
367577 TTAATTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.06, T:0.29
Consensus pattern (14 bp):
ATCAAAATATGTCC
Found at i:367739 original size:35 final size:35
Alignment explanation
Indices: 367693--367759 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
367683 AAAACTTTTA
367693 CATTTAATCTTTGAATTACTGGTTAAAGAAAAGCC
1 CATTTAATCTTTGAATTACTGGTTAAAGAAAAGCC
367728 CATTTAATCTTTGAATTACTGGTTAAAGAAAA
1 CATTTAATCTTTGAATTACTGGTTAAAGAAAA
367760 AACCCCTCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (35 bp):
CATTTAATCTTTGAATTACTGGTTAAAGAAAAGCC
Found at i:368840 original size:200 final size:200
Alignment explanation
Indices: 368497--368896 Score: 800
Period size: 200 Copynumber: 2.0 Consensus size: 200
368487 AAGATTTCAG
368497 TTCTATTCTTATCCACAACAACCACTGAGAGAAGTTTAAAACTGCATGATAATATCCTGGAAAGG
1 TTCTATTCTTATCCACAACAACCACTGAGAGAAGTTTAAAACTGCATGATAATATCCTGGAAAGG
368562 GCTTGTCAGCCACAGTCGTTAGTGTAAATACAGACTACCCCATCCTATTAGCGAATTGCGTAAAA
66 GCTTGTCAGCCACAGTCGTTAGTGTAAATACAGACTACCCCATCCTATTAGCGAATTGCGTAAAA
368627 AAGTAGGGAAAACTGAGGTTTTAATTATGCGGCATACAAGTTTTTTGTTGTTATTTCTAACTTGC
131 AAGTAGGGAAAACTGAGGTTTTAATTATGCGGCATACAAGTTTTTTGTTGTTATTTCTAACTTGC
368692 AAACA
196 AAACA
368697 TTCTATTCTTATCCACAACAACCACTGAGAGAAGTTTAAAACTGCATGATAATATCCTGGAAAGG
1 TTCTATTCTTATCCACAACAACCACTGAGAGAAGTTTAAAACTGCATGATAATATCCTGGAAAGG
368762 GCTTGTCAGCCACAGTCGTTAGTGTAAATACAGACTACCCCATCCTATTAGCGAATTGCGTAAAA
66 GCTTGTCAGCCACAGTCGTTAGTGTAAATACAGACTACCCCATCCTATTAGCGAATTGCGTAAAA
368827 AAGTAGGGAAAACTGAGGTTTTAATTATGCGGCATACAAGTTTTTTGTTGTTATTTCTAACTTGC
131 AAGTAGGGAAAACTGAGGTTTTAATTATGCGGCATACAAGTTTTTTGTTGTTATTTCTAACTTGC
368892 AAACA
196 AAACA
368897 CATAACATGT
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 200 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (200 bp):
TTCTATTCTTATCCACAACAACCACTGAGAGAAGTTTAAAACTGCATGATAATATCCTGGAAAGG
GCTTGTCAGCCACAGTCGTTAGTGTAAATACAGACTACCCCATCCTATTAGCGAATTGCGTAAAA
AAGTAGGGAAAACTGAGGTTTTAATTATGCGGCATACAAGTTTTTTGTTGTTATTTCTAACTTGC
AAACA
Found at i:374838 original size:102 final size:101
Alignment explanation
Indices: 374628--374816 Score: 269
Period size: 102 Copynumber: 1.9 Consensus size: 101
374618 TTTCTAAAGT
* *
374628 TTACAACTTTTTAACATTTCCTTACTGAAATCATATCAATATGTAACACATCCCCTCCCCTCCAT
1 TTACAACTTTTTAAAATTTCCTTACTGAAATCATATCAATATGTAACACA-CCCCTCCCCTCCAA
* **
374693 GTCCTCTTAAAGTGTGTGAAAATTCTTATTCTATAGT
65 GTCCTCTTAAAGTGTGTGAAAATACTTATTCTATACA
374730 TTACAACTTTTTAAAATTTCCTTACTGAAATCATATCAATATGT-A-ACA-CCC-CCCCTCCAAG
1 TTACAACTTTTTAAAATTTCCTTACTGAAATCATATCAATATGTAACACACCCCTCCCCTCCAAG
* *
374791 TCTTCTTGAAGTGTGTGAACAATACT
66 TCCTCTTAAAGTGTGTGAA-AATACT
374817 GTTGTGTAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
97 26 0.32
98 8 0.10
100 3 0.04
101 1 0.01
102 43 0.53
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (101 bp):
TTACAACTTTTTAAAATTTCCTTACTGAAATCATATCAATATGTAACACACCCCTCCCCTCCAAG
TCCTCTTAAAGTGTGTGAAAATACTTATTCTATACA
Found at i:375129 original size:2 final size:2
Alignment explanation
Indices: 375122--375177 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
375112 GTCTTCCAGA
375122 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
375164 TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC
375178 AAAATTAACA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:375893 original size:2 final size:2
Alignment explanation
Indices: 375886--375921 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
375876 AGGGAACAAT
375886 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
375922 TTGCCTTCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:379889 original size:8 final size:8
Alignment explanation
Indices: 379889--379923 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
379879 CAGACGGACA
379889 GACAGACG
1 GACAGACG
379897 GACAGACG
1 GACAGACG
379905 GACAGACG
1 GACAGACG
379913 GAC-GACG
1 GACAGACG
379920 GACA
1 GACA
379924 AAATGTGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.27
8 19 0.73
ACGTcount: A:0.37, C:0.26, G:0.37, T:0.00
Consensus pattern (8 bp):
GACAGACG
Found at i:379895 original size:12 final size:12
Alignment explanation
Indices: 379878--379923 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
379868 TAAAAAGTTT
379878 ACAGACGGACAG
1 ACAGACGGACAG
379890 ACAGACGGACAG
1 ACAGACGGACAG
* * *
379902 ACGGACAGACGG
1 ACAGACGGACAG
379914 AC-GACGGACA
1 ACAGACGGACA
379924 AAATGTGATC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 6 0.21
12 23 0.79
ACGTcount: A:0.39, C:0.26, G:0.35, T:0.00
Consensus pattern (12 bp):
ACAGACGGACAG
Found at i:379910 original size:16 final size:15
Alignment explanation
Indices: 379878--379923 Score: 62
Period size: 16 Copynumber: 3.2 Consensus size: 15
379868 TAAAAAGTTT
379878 ACAGACGGAC-A--G
1 ACAGACGGACGACGG
379890 ACAGACGGACAGACGG
1 ACAGACGGAC-GACGG
379906 ACAGACGGACGACGG
1 ACAGACGGACGACGG
379921 ACA
1 ACA
379924 AAATGTGATC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.33
14 1 0.03
15 8 0.27
16 11 0.37
ACGTcount: A:0.39, C:0.26, G:0.35, T:0.00
Consensus pattern (15 bp):
ACAGACGGACGACGG
Found at i:393077 original size:10 final size:10
Alignment explanation
Indices: 393062--393155 Score: 125
Period size: 10 Copynumber: 9.0 Consensus size: 10
393052 GCGTCGATTT
393062 ACCCAAATGG
1 ACCCAAATGG
*
393072 ACCCAAATGA
1 ACCCAAATGG
393082 ACCCAAATGG
1 ACCCAAATGG
*
393092 ACCCAAATGA
1 ACCCAAATGG
*
393102 ACCCAAATGA
1 ACCCAAATGG
393112 ACCCAAATGGCG
1 ACCCAAAT-G-G
393124 ACCCAAATGG
1 ACCCAAATGG
393134 ACCCAAATGGCG
1 ACCCAAAT-G-G
393146 ACCCAAATGG
1 ACCCAAATGG
393156 CGATTAAAGT
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
10 55 0.72
11 4 0.05
12 17 0.22
ACGTcount: A:0.41, C:0.31, G:0.18, T:0.10
Consensus pattern (10 bp):
ACCCAAATGG
Found at i:393098 original size:30 final size:32
Alignment explanation
Indices: 393062--393158 Score: 144
Period size: 30 Copynumber: 3.0 Consensus size: 32
393052 GCGTCGATTT
393062 ACCCAAATGGACCCAAATGAACCCAAAT-G-G
1 ACCCAAATGGACCCAAATGAACCCAAATGGCG
*
393092 ACCCAAATGAACCCAAATGAACCCAAATGGCG
1 ACCCAAATGGACCCAAATGAACCCAAATGGCG
*
393124 ACCCAAATGGACCCAAATGGCGACCCAAATGGCG
1 ACCCAAATGGACCCAAAT-G-AACCCAAATGGCG
393158 A
1 A
393159 TTAAAGTGGA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
30 27 0.45
31 1 0.02
32 18 0.30
33 1 0.02
34 13 0.22
ACGTcount: A:0.41, C:0.31, G:0.19, T:0.09
Consensus pattern (32 bp):
ACCCAAATGGACCCAAATGAACCCAAATGGCG
Found at i:393899 original size:2 final size:2
Alignment explanation
Indices: 393894--393937 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
393884 ACACACCGGG
*
393894 CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
393936 CT
1 CT
393938 TGGGGTAGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Done.