Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold256
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: 1244454
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 3 of 8
Found at i:381003 original size:39 final size:38
Alignment explanation
Indices: 380950--381025 Score: 125
Period size: 39 Copynumber: 2.0 Consensus size: 38
380940 TGTTATTTTA
* *
380950 TGGATGATGTCATCCATGACATTAATAATTTTTAGAGT
1 TGGATGATGTCATCCATGACATCAACAATTTTTAGAGT
380988 TGGATTGATGTCATCCATGACATCAACAATTTTTAGAG
1 TGGA-TGATGTCATCCATGACATCAACAATTTTTAGAG
381026 AACTTTGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 4 0.11
39 31 0.89
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (38 bp):
TGGATGATGTCATCCATGACATCAACAATTTTTAGAGT
Found at i:386902 original size:31 final size:31
Alignment explanation
Indices: 386864--386953 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 31
386854 GCCTCAGAAT
*
386864 GTCAAAGCCCACACGAGTTGGTGACACCCCA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCCA
* * * * *
386895 GTCAAAGCCCGCACAAGTTGGCGGCACTCGA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCCA
* *
386926 GTCAAAGCCCATATGAGTTGGTGGCACC
1 GTCAAAGCCCACACGAGTTGGTGGCACC
386954 TAAGTTCGAG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.16
Consensus pattern (31 bp):
GTCAAAGCCCACACGAGTTGGTGGCACCCCA
Found at i:387051 original size:31 final size:31
Alignment explanation
Indices: 387013--387107 Score: 118
Period size: 31 Copynumber: 3.1 Consensus size: 31
387003 GCCTTAGAAT
* *
387013 GTCAAAGCCCACACGAGTTGGTGGTACCCTA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCAA
** * **
387044 GTCAAAGCCTGCACAAGTTGGCAGCACCCAA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCAA
*
387075 GTCAAAGCCCACACGAGTTGGTGGCACCTAA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCAA
387106 GT
1 GT
387108 TCGAGTCAAG
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.17
Consensus pattern (31 bp):
GTCAAAGCCCACACGAGTTGGTGGCACCCAA
Found at i:387101 original size:149 final size:149
Alignment explanation
Indices: 386831--387627 Score: 1247
Period size: 149 Copynumber: 5.4 Consensus size: 149
386821 CATGAGTAGG
* * * * *
386831 TGGCACTTGCCTAAGGAGGTTAAGCCTCAGAATGTCAAAGCCCACACGAGTTGGTGACACCCCAG
1 TGGCACCTGTCTAAGGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTGGTGGCACCCTAG
* * * *
386896 TCAAAGCCCGCACAAGTTGGCGGCACTCGAGTCAAAGCCCATATGAGTTGGTGGCACCTAAGTTC
66 TCAAAGCCTGCACAAGTTGGCAGCACCCGAGTCAAAGCCCACATGAGTTGGTGGCACCTAAGTTC
*
386961 GAGTCAAGTCCATATTAGT
131 GAGTCAAGTCCACATTAGT
*
386980 TGGCACCTGTCTAAGGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTGGTGGTACCCTAG
1 TGGCACCTGTCTAAGGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTGGTGGCACCCTAG
* *
387045 TCAAAGCCTGCACAAGTTGGCAGCACCCAAGTCAAAGCCCACACGAGTTGGTGGCACCTAAGTTC
66 TCAAAGCCTGCACAAGTTGGCAGCACCCGAGTCAAAGCCCACATGAGTTGGTGGCACCTAAGTTC
*
387110 GAGTCAAGTCCATATTAGT
131 GAGTCAAGTCCACATTAGT
*
387129 TGGCACCTGTCTAAGGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTGGTGGTACCCTAG
1 TGGCACCTGTCTAAGGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTGGTGGCACCCTAG
* * *
387194 TCAAAGCTTGCACAAGTTGGCAGCACCCAAGTCAAAGCCCACACGAGTTGGTGGCACCTAAGTTC
66 TCAAAGCCTGCACAAGTTGGCAGCACCCGAGTCAAAGCCCACATGAGTTGGTGGCACCTAAGTTC
387259 GAGTCAAGTCCACATTAGT
131 GAGTCAAGTCCACATTAGT
* * *
387278 TGGCAACTGTCTAAGGAGGTTAAGCCTTAAAATGTCAAAGCCCACACGAGTTGGTGGCACCCCAG
1 TGGCACCTGTCTAAGGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTGGTGGCACCCTAG
** * * * *
387343 TCAAAGCCTGCATGAGTTGGCGGCACCTGAGTCAAAGCCCACATGAGTTAGTGGCACCTAAGTTT
66 TCAAAGCCTGCACAAGTTGGCAGCACCCGAGTCAAAGCCCACATGAGTTGGTGGCACCTAAGTTC
387408 GAGTCAAGTCCACATTAGT
131 GAGTCAAGTCCACATTAGT
* * * * *
387427 TGGCACCTATCTGAGGAGGTTAAGCCATAGAATGTCAAAGCTCACACAAGTTGGTGGCACCCTAG
1 TGGCACCTGTCTAAGGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTGGTGGCACCCTAG
* * *
387492 TCAAAGCC--CACAGAGTTGGCAGCACCTGAGTCAAAGCCCACATGAGTTGATGGTACCTAAGTT
66 TCAAAGCCTGCACA-AGTTGGCAGCACCCGAGTCAAAGCCCACATGAGTTGGTGGCACCTAAGTT
*
387555 CGAGTTAAGTCCACATTAGT
130 CGAGTCAAGTCCACATTAGT
387575 TGGCACCTGTCTAAGGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTG
1 TGGCACCTGTCTAAGGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTG
387628 ATAGCACCTA
Statistics
Matches: 599, Mismatches: 48, Indels: 3
0.92 0.07 0.00
Matches are distributed among these distances:
147 2 0.00
148 112 0.19
149 485 0.81
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (149 bp):
TGGCACCTGTCTAAGGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTGGTGGCACCCTAG
TCAAAGCCTGCACAAGTTGGCAGCACCCGAGTCAAAGCCCACATGAGTTGGTGGCACCTAAGTTC
GAGTCAAGTCCACATTAGT
Found at i:387200 original size:31 final size:31
Alignment explanation
Indices: 387162--387256 Score: 109
Period size: 31 Copynumber: 3.1 Consensus size: 31
387152 GCCTTAGAAT
* *
387162 GTCAAAGCCCACACGAGTTGGTGGTACCCTA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCAA
*** * **
387193 GTCAAAGCTTGCACAAGTTGGCAGCACCCAA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCAA
*
387224 GTCAAAGCCCACACGAGTTGGTGGCACCTAA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCAA
387255 GT
1 GT
387257 TCGAGTCAAG
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.18
Consensus pattern (31 bp):
GTCAAAGCCCACACGAGTTGGTGGCACCCAA
Found at i:387401 original size:31 final size:31
Alignment explanation
Indices: 387311--387401 Score: 119
Period size: 31 Copynumber: 2.9 Consensus size: 31
387301 GCCTTAAAAT
* *
387311 GTCAAAGCCCACACGAGTTGGTGGCACCCCA
1 GTCAAAGCCCACATGAGTTGGTGGCACCTCA
** * *
387342 GTCAAAGCCTGCATGAGTTGGCGGCACCTGA
1 GTCAAAGCCCACATGAGTTGGTGGCACCTCA
*
387373 GTCAAAGCCCACATGAGTTAGTGGCACCT
1 GTCAAAGCCCACATGAGTTGGTGGCACCT
387402 AAGTTTGAGT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.18
Consensus pattern (31 bp):
GTCAAAGCCCACATGAGTTGGTGGCACCTCA
Found at i:387517 original size:30 final size:30
Alignment explanation
Indices: 387460--387540 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 30
387450 GCCATAGAAT
**
387460 GTCAAAGCTCACACA-AGTTGGTGGCACCCT-A
1 GTCAAAGC-C-CACAGAGTTGGCAGCA-CCTGA
387491 GTCAAAGCCCACAGAGTTGGCAGCACCTGA
1 GTCAAAGCCCACAGAGTTGGCAGCACCTGA
387521 GTCAAAGCCCACATGAGTTG
1 GTCAAAGCCCACA-GAGTTG
387541 ATGGTACCTA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
29 7 0.16
30 24 0.53
31 14 0.31
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (30 bp):
GTCAAAGCCCACAGAGTTGGCAGCACCTGA
Found at i:387667 original size:87 final size:87
Alignment explanation
Indices: 387521--387723 Score: 307
Period size: 87 Copynumber: 2.3 Consensus size: 87
387511 CAGCACCTGA
* * * *
387521 GTCAAAGCCCACATGAGTTGATGGTACCTAAGTTCGAGTTAAGTCCACATTAGTTGGCACCTGTC
1 GTCAAAGCCCACACGAGTTGATGGCACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTATC
**
387586 TAAGGAGGTTAAGCCTTAGAAT
66 TAAAAAGGTTAAGCCTTAGAAT
* *
387608 GTCAAAGCCCACACGAGTTGATAGCACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTATT
1 GTCAAAGCCCACACGAGTTGATGGCACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTATC
*
387673 TAAAAAGGTTAAGCTTTAGAAT
66 TAAAAAGGTTAAGCCTTAGAAT
* *
387695 GTCAGAGCCCACACGAGTTGGTGGCACCT
1 GTCAAAGCCCACACGAGTTGATGGCACCT
387724 CAATCAAAGC
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 104 1.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (87 bp):
GTCAAAGCCCACACGAGTTGATGGCACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTATC
TAAAAAGGTTAAGCCTTAGAAT
Found at i:387752 original size:31 final size:31
Alignment explanation
Indices: 387700--387789 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 31
387690 AGAATGTCAG
*
387700 AGCCCACACGAGTTGGTGGCACCTCAATCAA
1 AGCCCACACAAGTTGGTGGCACCTCAATCAA
** * * * *
387731 AGCCTGCACAAGTTGGCGGCACTTGAGTCAA
1 AGCCCACACAAGTTGGTGGCACCTCAATCAA
* *
387762 AGCCCACACGAGTTGATGGCACCTCAAT
1 AGCCCACACAAGTTGGTGGCACCTCAAT
387790 TTGAGTCAAG
Statistics
Matches: 44, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (31 bp):
AGCCCACACAAGTTGGTGGCACCTCAATCAA
Found at i:387855 original size:236 final size:236
Alignment explanation
Indices: 387373--387960 Score: 826
Period size: 236 Copynumber: 2.5 Consensus size: 236
387363 CGGCACCTGA
387373 GTCAAAGCCCACATGAGTT-AGTGGCACCTAAGTTTGAGTCAAGTCCACATTAGTTGGCACCTAT
1 GTCAAAGCCCACATGAGTTGA-TGGCACCTAAGTTTGAGTCAAGTCCACATTAGTTGGCACCTAT
* * * * *
387437 CTGAGGAGGTTAAGCCATAGAATGTCAAAGCTCACACAAGTTGGTGGCACC-CTAGTCAAAGCCC
65 CTAAGGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTGGTGGCACCTCTAATCAAAGCCC
* * *
387501 ACAGAGTTGGCAGCACCTGAGTCAAAGCCCACATGAGTTGATGGTACCTAAGTTCGAGTTAAGTC
130 ACAGAGTTGGCAGCACCTGAGTCAAAGCCCACACGAGTTGATGGCACCTAAGTTCGAGTCAAGTC
* * *
387566 CACATTAGTTGGCACCTGTCTAAGGAGGTTAAGCCTTAGAAT
195 CACATTAGTTAGCACCTGTCTAAAGAGGTTAAGCCTTAAAAT
* * * *
387608 GTCAAAGCCCACACGAGTTGATAGCACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTATT
1 GTCAAAGCCCACATGAGTTGATGGCACCTAAGTTTGAGTCAAGTCCACATTAGTTGGCACCTATC
** * *
387673 TAAAAAGGTTAAGCTTTAGAATGTCAGAGCCCACACGAGTTGGTGGCACCTC-AATCAAAGCCTG
66 TAAGGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTGGTGGCACCTCTAATCAAAGCC--
* * *
387737 CACA-AGTTGGCGGCACTTGAGTCAAAGCCCACACGAGTTGATGGCACCTCAA-TTTGAGTCAAG
129 CACAGAGTTGGCAGCACCTGAGTCAAAGCCCACACGAGTTGATGGCACCT-AAGTTCGAGTCAAG
*
387800 TCCACATTAGTTAGCACCTGTCTAAAGAGGTTTAGCCTTAAAAT
193 TCCACATTAGTTAGCACCTGTCTAAAGAGGTTAAGCCTTAAAAT
* * ** *
387844 GTCAAAGCCCACATGAGTTGGTGGCACCTAAGTTTGAGTCAAGGACCACATTAGTTGGTGCCTGT
1 GTCAAAGCCCACATGAGTTGATGGCACCTAAGTTTGAGTCAA-GTCCACATTAGTTGGCACCTAT
* *
387909 CTAAGGAGGTTAAGCCTTAAAATGTCAAAGTCCACACGAGTTGGTGGCACCT
65 CTAAGGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTGGTGGCACCT
387961 AAGTCCGAGT
Statistics
Matches: 309, Mismatches: 38, Indels: 10
0.87 0.11 0.03
Matches are distributed among these distances:
235 110 0.36
236 130 0.42
237 69 0.22
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (236 bp):
GTCAAAGCCCACATGAGTTGATGGCACCTAAGTTTGAGTCAAGTCCACATTAGTTGGCACCTATC
TAAGGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTGGTGGCACCTCTAATCAAAGCCCA
CAGAGTTGGCAGCACCTGAGTCAAAGCCCACACGAGTTGATGGCACCTAAGTTCGAGTCAAGTCC
ACATTAGTTAGCACCTGTCTAAAGAGGTTAAGCCTTAAAAT
Found at i:387932 original size:88 final size:87
Alignment explanation
Indices: 387757--388014 Score: 374
Period size: 88 Copynumber: 3.0 Consensus size: 87
387747 CGGCACTTGA
* *
387757 GTCAAAGCCCACACGAGTTGATGGCACCTCAA-TTTGAGTCAAGTCCACATTAGTTAGCACCTGT
1 GTCAAAGCCCACACGAGTTGGTGGCACCT-AAGTTTGAGTCAAGTCCACATTAGTTGGCACCTGT
* *
387821 CTAAAGAGGTTTAGCCTTAAAAT
65 CTAAGGAGGTTAAGCCTTAAAAT
* * **
387844 GTCAAAGCCCACATGAGTTGGTGGCACCTAAGTTTGAGTCAAGGACCACATTAGTTGGTGCCTGT
1 GTCAAAGCCCACACGAGTTGGTGGCACCTAAGTTTGAGTCAA-GTCCACATTAGTTGGCACCTGT
387909 CTAAGGAGGTTAAGCCTTAAAAT
65 CTAAGGAGGTTAAGCCTTAAAAT
* ** * *
387932 GTCAAAGTCCACACGAGTTGGTGGCACCTAAGTCCGAGTCAAGTCCATATTAGTTGGCACTTGTC
1 GTCAAAGCCCACACGAGTTGGTGGCACCTAAGTTTGAGTCAAGTCCACATTAGTTGGCACCTGTC
387997 TAAGGAGGTTAAGCCTTA
66 TAAGGAGGTTAAGCCTTA
388015 GAAAACCAAA
Statistics
Matches: 152, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
86 2 0.01
87 73 0.48
88 77 0.51
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (87 bp):
GTCAAAGCCCACACGAGTTGGTGGCACCTAAGTTTGAGTCAAGTCCACATTAGTTGGCACCTGTC
TAAGGAGGTTAAGCCTTAAAAT
Found at i:391665 original size:19 final size:20
Alignment explanation
Indices: 391621--391673 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
391611 CTGCCAGTTT
**
391621 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
391641 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
391660 CATGTATTGATACA
1 CATGTATCGATACA
391674 TTTATCGATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:391704 original size:32 final size:31
Alignment explanation
Indices: 391645--391706 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
391635 ATTGTCCATG
* *
391645 TATCGATACAATGAACATGTATTGATACATT
1 TATCGATACAAAGAACATGTATCGATACATT
391676 TATCGATACAAAGCATA-ATGTATCGATACAT
1 TATCGATACAAAG-A-ACATGTATCGATACAT
391707 CTGGGTGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 12 0.44
32 14 0.52
33 1 0.04
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (31 bp):
TATCGATACAAAGAACATGTATCGATACATT
Found at i:397470 original size:19 final size:18
Alignment explanation
Indices: 397446--397572 Score: 113
Period size: 19 Copynumber: 7.7 Consensus size: 18
397436 AAACAGTAAC
397446 TGTATCGATACATAGGTTT
1 TGTATCGATACATAGG-TT
397465 TGTATCGATACA-A----
1 TGTATCGATACATAGGTT
397478 TGTATCGATACATAGGCTT
1 TGTATCGATACATAGG-TT
397497 TGTATCGATACA-A----
1 TGTATCGATACATAGGTT
397510 TGTATCGATACATAGGCTT
1 TGTATCGATACATAGG-TT
397529 TGTATCGATACA-A----
1 TGTATCGATACATAGGTT
397542 TGTATCGATACATAGGCTT
1 TGTATCGATACATAGG-TT
397561 TGTATCGATACA
1 TGTATCGATACA
397573 ATGTATCGCT
Statistics
Matches: 90, Mismatches: 0, Indels: 36
0.71 0.00 0.29
Matches are distributed among these distances:
13 36 0.40
14 3 0.03
18 3 0.03
19 48 0.53
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (18 bp):
TGTATCGATACATAGGTT
Found at i:397482 original size:32 final size:32
Alignment explanation
Indices: 397446--397580 Score: 261
Period size: 32 Copynumber: 4.2 Consensus size: 32
397436 AAACAGTAAC
*
397446 TGTATCGATACATAGGTTTTGTATCGATACAA
1 TGTATCGATACATAGGCTTTGTATCGATACAA
397478 TGTATCGATACATAGGCTTTGTATCGATACAA
1 TGTATCGATACATAGGCTTTGTATCGATACAA
397510 TGTATCGATACATAGGCTTTGTATCGATACAA
1 TGTATCGATACATAGGCTTTGTATCGATACAA
397542 TGTATCGATACATAGGCTTTGTATCGATACAA
1 TGTATCGATACATAGGCTTTGTATCGATACAA
397574 TGTATCG
1 TGTATCG
397581 CTACGAAGCT
Statistics
Matches: 102, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 102 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAGGCTTTGTATCGATACAA
Found at i:397483 original size:13 final size:13
Alignment explanation
Indices: 397465--397553 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
397455 ACATAGGTTT
397465 TGTATCGATACAA
1 TGTATCGATACAA
397478 TGTATCGATACATA
1 TGTATCGATACA-A
397492 GGCTTTGTATCGATACAA
1 -----TGTATCGATACAA
397510 TGTATCGATACATA
1 TGTATCGATACA-A
397524 GGCTTTGTATCGATACAA
1 -----TGTATCGATACAA
397542 TGTATCGATACA
1 TGTATCGATACA
397554 TAGGCTTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 36 0.56
14 2 0.03
18 2 0.03
19 24 0.38
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:397622 original size:13 final size:13
Alignment explanation
Indices: 397604--397631 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
397594 GCCAAGGATA
397604 TGTATCGATACAT
1 TGTATCGATACAT
397617 TGTATCGATACAT
1 TGTATCGATACAT
397630 TG
1 TG
397632 ATCTTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:397693 original size:20 final size:21
Alignment explanation
Indices: 397660--397702 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
397650 TCTGAAAATT
397660 TTACCCAGATGTATCGATACA
1 TTACCCAGATGTATCGATACA
397681 TTACCCA-ATGTATCGATACA
1 TTACCCAGATGTATCGATACA
397701 TT
1 TT
397703 CAAGCATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (21 bp):
TTACCCAGATGTATCGATACA
Found at i:400078 original size:51 final size:49
Alignment explanation
Indices: 399998--400268 Score: 301
Period size: 51 Copynumber: 5.3 Consensus size: 49
399988 ATTTTTCATC
* * * **
399998 TCGGGGATACTCTAA-TCCCGGTTTCATTTCCAAAACATCAATTTCTCTTAA
1 TCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACA-CAATTT-TCACAA
* * *
400049 TCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACCCATTTTCCATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACA-CAATTTT-CACAA
* * *
400100 TCGTGGATATTCCAACTCTGATTTTATTTCCAAAACACTAATTTTTCACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC-AA-TTTTCACAA
* * *
400151 TTGGGGATACTCCAACTCCGATTGTATTTTCAAAACACTAATTTTTCACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC-AA-TTTTCACAA
*
400202 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTGACTTTTCACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC--AATTTTCACAA
400253 TCGGGGATACTCCAAC
1 TCGGGGATACTCCAAC
400269 CCCGTTATTT
Statistics
Matches: 191, Mismatches: 24, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
50 2 0.01
51 183 0.96
52 6 0.03
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (49 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACAATTTTCACAA
Found at i:400143 original size:102 final size:102
Alignment explanation
Indices: 399998--400268 Score: 334
Period size: 102 Copynumber: 2.7 Consensus size: 102
399988 ATTTTTCATC
* * * **
399998 TCGGGGATACTCTAA-TCCCGGTTTCATTTCCAAAACA-TCAATTTCTCTTAATCGGGGATACTC
1 TCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACACTCAATTT-TCACAATCGGGGATACTC
* * *
400061 CAACTCCGATTTTA-TTTCTAAAACACCCATTTTCCATAA
64 CAACTCCGATTGTATTTTC-AAAACACCAATTTTCCACAA
* * * *
400100 TCGTGGATATTCCAACTCTGATTTTATTTCCAAAACACT-AATTTTTCACAATTGGGGATACTCC
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTCAA-TTTTCACAATCGGGGATACTCC
* *
400164 AACTCCGATTGTATTTTCAAAACACTAATTTTTCACAA
65 AACTCCGATTGTATTTTCAAAACACCAATTTTCCACAA
* *
400202 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTGACTTTTCACAATCGGGGATACTCCA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTCAATTTTCACAATCGGGGATACTCCA
400267 AC
66 AC
400269 CCCGTTATTT
Statistics
Matches: 145, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
102 135 0.93
103 10 0.07
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (102 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTCAATTTTCACAATCGGGGATACTCCA
ACTCCGATTGTATTTTCAAAACACCAATTTTCCACAA
Found at i:400382 original size:51 final size:51
Alignment explanation
Indices: 400322--400452 Score: 165
Period size: 51 Copynumber: 2.5 Consensus size: 51
400312 AAAACACCAA
*
400322 TTCTCCACAATCAGGGATACTCCAACCCC-GAATTTATTTCCAAAATATTGAT
1 TTCT-CACAATCAGGGATACTCCAACCCCTG-ACTTATTTCCAAAATATTGAT
* * *
400374 TTCTCACAATCAGGGATACTTCAACCCCTGCCTTATTTCTAAAATATTGAT
1 TTCTCACAATCAGGGATACTCCAACCCCTGACTTATTTCCAAAATATTGAT
* ** *
400425 TTCTCATAATTGGGGATGCTCCAACCCC
1 TTCTCACAATCAGGGATACTCCAACCCC
400453 ATTATTTTCA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
51 64 0.93
52 5 0.07
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.32
Consensus pattern (51 bp):
TTCTCACAATCAGGGATACTCCAACCCCTGACTTATTTCCAAAATATTGAT
Found at i:400449 original size:181 final size:181
Alignment explanation
Indices: 400121--400459 Score: 414
Period size: 181 Copynumber: 1.9 Consensus size: 181
400111 CCAACTCTGA
* * * ** * *
400121 TTTTATTTCCAAAACACTAATTTTTCACAATTGGGGATACTCCAACTCCGATTGTATTTTCAAAA
1 TTTTATTTCCAAAACACCAATTCTCCACAATCAGGGATACTCCAACCCCGATTGTATTTCCAAAA
* * * **
400186 CACTAATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTGACTTTTCAC
66 CACTAATTTCTCACAATCAGGGATACTCCAACCCCGACCTTATTTCCAAAACACTGACTTTTCAC
*
400251 AATCGGGGATACTCCAACCCCGTTATTTCCGAGAAGACACTTCAACCCCAG
131 AATCGGGGATACTCCAACCCCATTATTTCCGAGAAGACACTTCAACCCCAG
*
400302 TTTTATTTCTAAAACACCAATTCTCCACAATCAGGGATACTCCAACCCCGAATT-TATTTCCAAA
1 TTTTATTTCCAAAACACCAATTCTCCACAATCAGGGATACTCCAACCCCG-ATTGTATTTCCAAA
* * * * * * *
400366 ATATTGATTTCTCACAATCAGGGATACTTCAACCCCTG-CCTTATTTCTAAAATATTGA-TTTCT
65 ACACTAATTTCTCACAATCAGGGATACTCCAACCCC-GACCTTATTTCCAAAACACTGACTTT-T
* * *
400429 CATAATTGGGGATGCTCCAACCCCATTATTT
128 CACAATCGGGGATACTCCAACCCCATTATTT
400460 TCACGGGGAT
Statistics
Matches: 131, Mismatches: 24, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
180 3 0.02
181 124 0.95
182 4 0.03
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (181 bp):
TTTTATTTCCAAAACACCAATTCTCCACAATCAGGGATACTCCAACCCCGATTGTATTTCCAAAA
CACTAATTTCTCACAATCAGGGATACTCCAACCCCGACCTTATTTCCAAAACACTGACTTTTCAC
AATCGGGGATACTCCAACCCCATTATTTCCGAGAAGACACTTCAACCCCAG
Found at i:400469 original size:130 final size:131
Alignment explanation
Indices: 400335--400629 Score: 357
Period size: 130 Copynumber: 2.3 Consensus size: 131
400325 TCCACAATCA
* * *
400335 GGGATACTCCAACCCCGAATTTATTTCCAAAATAT-TGA-TTTCTCACAATCAGGGATACTTCAA
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACATCT-ATTTTCT-ACAATCAGGGACACTTCAA
** * * *
400398 CCCCTGCCTTATTTCTAAAAT-ATTGATTTCTCATAATTGGGGATGCTCCAACCCCATTA-TTTT
64 CCCCTGCCTTATTTCT-AAATCATCAATTTCTCACAATCGGGGATACTCCAACCCCATTATTTTT
400461 C-ACG
128 CGA-G
* *** * *
400465 GGGATACTCCAATCCCGATTTTATTTTTGAAACATCTATTTTCTATAATCGGGGACACTTCAACC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACATCTATTTTCTACAATCAGGGACACTTCAACC
* * *
400530 CTTGCCTTATTTCTAAATCATCAATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTTCGA
66 CCTGCCTTATTTCTAAATCATCAATTTCTCACAATCGGGGATACTCCAACCCCATTATTTTTCGA
400595 G
131 G
*
400596 GGGATACTCCAACCCCGATTTTACTTCCAAAACA
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACA
400630 CAGGTTTTTC
Statistics
Matches: 138, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
129 4 0.03
130 92 0.67
131 41 0.30
132 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.34
Consensus pattern (131 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAAACATCTATTTTCTACAATCAGGGACACTTCAACC
CCTGCCTTATTTCTAAATCATCAATTTCTCACAATCGGGGATACTCCAACCCCATTATTTTTCGA
G
Found at i:400489 original size:181 final size:180
Alignment explanation
Indices: 400110--400490 Score: 394
Period size: 181 Copynumber: 2.1 Consensus size: 180
400100 TCGTGGATAT
* * * * ** *
400110 TCCAACTCTGATTTTATTTCCAAAACACTAATTTTTCACAATTGGGGATACTCCAACTCCGATTG
1 TCCAAC-CCGATTTTATTTCCAAAACACCAATTCTCCACAATCAGGGATACTCCAACCCCGATTG
* * * * **
400175 TATTTTCAAAACACTAATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAC
65 TATTTCCAAAACACTAATTTCTCACAATCAGGGATACTCCAACCCCGACCTTATTTCCAAAACAC
*
400240 TGACTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGAAGACAC
130 TGACTTTTCACAATCGGGGATACTCCAACCCCATTATTTCCGAGAAGACAC
* * *
400291 TTCAACCCCAGTTTTATTTCTAAAACACCAATTCTCCACAATCAGGGATACTCCAACCCCGAATT
1 TCCAACCCGA-TTTTATTTCCAAAACACCAATTCTCCACAATCAGGGATACTCCAACCCCG-ATT
* * * * * *
400356 -TATTTCCAAAATATTGATTTCTCACAATCAGGGATACTTCAACCCCTG-CCTTATTTCTAAAAT
64 GTATTTCCAAAACACTAATTTCTCACAATCAGGGATACTCCAACCCC-GACCTTATTTCCAAAAC
* * * * * *
400419 ATTGA-TTTCTCATAATTGGGGATGCTCCAACCCCATTATTTTCACG-G-GGATAC
128 ACTGACTTT-TCACAATCGGGGATACTCCAACCCCATTA-TTTC-CGAGAAGACAC
400472 TCCAATCCCGATTTTATTT
1 TCCAA-CCCGATTTTATTT
400491 TTGAAACATC
Statistics
Matches: 162, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
180 5 0.03
181 142 0.88
182 13 0.08
183 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (180 bp):
TCCAACCCGATTTTATTTCCAAAACACCAATTCTCCACAATCAGGGATACTCCAACCCCGATTGT
ATTTCCAAAACACTAATTTCTCACAATCAGGGATACTCCAACCCCGACCTTATTTCCAAAACACT
GACTTTTCACAATCGGGGATACTCCAACCCCATTATTTCCGAGAAGACAC
Found at i:403262 original size:18 final size:18
Alignment explanation
Indices: 403241--403276 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
403231 CATCCGAGTC
403241 ACCATCATCATCATCATT
1 ACCATCATCATCATCATT
*
403259 ACCATCTTCATCATCATT
1 ACCATCATCATCATCATT
403277 TATGGTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (18 bp):
ACCATCATCATCATCATT
Found at i:404894 original size:20 final size:20
Alignment explanation
Indices: 404869--404915 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
404859 GCAATGTATT
*
404869 GATACAAT-TCACCATGCATC
1 GATACAATGT-ACCACGCATC
*
404889 GATACAATGTACCACGTATC
1 GATACAATGTACCACGCATC
404909 GATACAA
1 GATACAA
404916 ACAGTGGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (20 bp):
GATACAATGTACCACGCATC
Found at i:407208 original size:25 final size:22
Alignment explanation
Indices: 407174--407221 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 22
407164 GTGACCCAAT
407174 AATTAAAATATAATATATTATAAAA
1 AATTAAAATA-AATATA--ATAAAA
407199 AATTAAAATAAATATAATAAAA
1 AATTAAAATAAATATAATAAAA
407221 A
1 A
407222 TATAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.30
24 6 0.26
25 10 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AATTAAAATAAATATAATAAAA
Found at i:407228 original size:17 final size:17
Alignment explanation
Indices: 407206--407300 Score: 56
Period size: 16 Copynumber: 5.6 Consensus size: 17
407196 AAAAATTAAA
407206 ATAAATATAATAAAAAT
1 ATAAATATAATAAAAAT
* *
407223 ATAAAT-TTATTAAAAT
1 ATAAATATAATAAAAAT
* *
407239 -T-TATATAATATAAATT
1 ATAAATATAATA-AAAAT
407255 ATTAAATATTAA-AAAATAT
1 A-TAAATA-TAATAAAA-AT
* *
407274 ATAAATAT-ATAATATT
1 ATAAATATAATAAAAAT
*
407290 TTAAATATAAT
1 ATAAATATAAT
407301 TATAATATAT
Statistics
Matches: 58, Mismatches: 11, Indels: 18
0.67 0.13 0.21
Matches are distributed among these distances:
14 2 0.03
15 4 0.07
16 21 0.36
17 12 0.21
18 10 0.17
19 6 0.10
20 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAAATATAATAAAAAT
Found at i:407238 original size:31 final size:31
Alignment explanation
Indices: 407200--407307 Score: 86
Period size: 31 Copynumber: 3.6 Consensus size: 31
407190 ATTATAAAAA
407200 ATTAAAATAAATATAATAAAAATATAAATTT
1 ATTAAAATAAATATAATAAAAATATAAATTT
** *
407231 ATTAAAATTTATATAATATAAATTATTAAA--T
1 ATTAAAATAAATATAATA-AAAATA-TAAATTT
*
407262 ATT-AAA-AAATAT-ATAAATATAT-AATATT
1 ATTAAAATAAATATAATAAAAATATAAAT-TT
*
407290 -TTAAATATAATTATAATA
1 ATTAAA-ATAAATATAATA
407308 TATAAAATTA
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
25 2 0.03
26 1 0.02
27 6 0.10
28 6 0.10
29 5 0.08
30 8 0.13
31 23 0.38
32 5 0.08
33 4 0.07
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
ATTAAAATAAATATAATAAAAATATAAATTT
Found at i:415803 original size:153 final size:153
Alignment explanation
Indices: 415525--415833 Score: 600
Period size: 153 Copynumber: 2.0 Consensus size: 153
415515 ACCTTTTGTT
415525 TTTCAGGATGCCATAGCCTATAGCTAAATTCCTCATTTCGATATCCGACGAAGATACAAGGAATT
1 TTTCAGGATGCCATAGCCTATAGCTAAATTCCTCATTTCGATATCCGACGAAGATACAAGGAATT
*
415590 GCTTTGTCATCAAGCTTTGATCTTTGCTCCTTTGGTATATGCATAAAGCTTTGCGTCCAAACACT
66 GCTTTGTCATCAAGCTTTGATCTTTGCTCCTTTGGTATATGCATAAAGCTTTACGTCCAAACACT
415655 TTCAGGTGAGAGTATGAAATATC
131 TTCAGGTGAGAGTATGAAATATC
415678 TTTCAGGATGCCATAGCCTATAGCTAAATTCCTCATTTCGATATCCGACGAAGATACAAGGAATT
1 TTTCAGGATGCCATAGCCTATAGCTAAATTCCTCATTTCGATATCCGACGAAGATACAAGGAATT
*
415743 GCTTTGTCATCAAGCTTTGATCTTTGCTCCTTTGGTATATGCATAAAGCTTTATGTCCAAACACT
66 GCTTTGTCATCAAGCTTTGATCTTTGCTCCTTTGGTATATGCATAAAGCTTTACGTCCAAACACT
415808 TTCAGGTGAGAGTATGAAATATC
131 TTCAGGTGAGAGTATGAAATATC
415831 TTT
1 TTT
415834 TCCCCTCCAG
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 154 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (153 bp):
TTTCAGGATGCCATAGCCTATAGCTAAATTCCTCATTTCGATATCCGACGAAGATACAAGGAATT
GCTTTGTCATCAAGCTTTGATCTTTGCTCCTTTGGTATATGCATAAAGCTTTACGTCCAAACACT
TTCAGGTGAGAGTATGAAATATC
Found at i:416249 original size:12 final size:12
Alignment explanation
Indices: 416232--416258 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
416222 AAGGCATCAT
416232 CAATGAAGGTGA
1 CAATGAAGGTGA
416244 CAATGAAGGTGA
1 CAATGAAGGTGA
416256 CAA
1 CAA
416259 AGTATTTGTT
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:0.44, C:0.11, G:0.30, T:0.15
Consensus pattern (12 bp):
CAATGAAGGTGA
Found at i:417929 original size:37 final size:37
Alignment explanation
Indices: 417835--417919 Score: 170
Period size: 37 Copynumber: 2.3 Consensus size: 37
417825 GACAAGTAAT
417835 ATTTGGGTGGCTTGGCCAATCCACTATGATTGTTAGA
1 ATTTGGGTGGCTTGGCCAATCCACTATGATTGTTAGA
417872 ATTTGGGTGGCTTGGCCAATCCACTATGATTGTTAGA
1 ATTTGGGTGGCTTGGCCAATCCACTATGATTGTTAGA
417909 ATTTGGGTGGC
1 ATTTGGGTGGC
417920 AGTGCCAATC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.20, C:0.15, G:0.29, T:0.35
Consensus pattern (37 bp):
ATTTGGGTGGCTTGGCCAATCCACTATGATTGTTAGA
Found at i:422040 original size:20 final size:20
Alignment explanation
Indices: 422015--422067 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
422005 GTTGGGCATA
*
422015 ATGTATCGATACAAT-TCTTC
1 ATGTATCGATACAATGTC-CC
422035 ATGTATCGATACAATGTCCC
1 ATGTATCGATACAATGTCCC
422055 ATGTATCGATACA
1 ATGTATCGATACA
422068 TTTCACTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATGTCCC
Found at i:422115 original size:13 final size:13
Alignment explanation
Indices: 422097--422123 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
422087 TGCCAGTTTC
422097 ATGTATCGATACA
1 ATGTATCGATACA
422110 ATGTATCGATACA
1 ATGTATCGATACA
422123 A
1 A
422124 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:424601 original size:13 final size:13
Alignment explanation
Indices: 424583--424608 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
424573 TAGTAACCTT
424583 TGTATCGATACAA
1 TGTATCGATACAA
424596 TGTATCGATACAA
1 TGTATCGATACAA
424609 AGATCCTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:427440 original size:13 final size:13
Alignment explanation
Indices: 427422--427447 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
427412 TACAGCAAGT
427422 ATGTATCGATACA
1 ATGTATCGATACA
427435 ATGTATCGATACA
1 ATGTATCGATACA
427448 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:429687 original size:21 final size:21
Alignment explanation
Indices: 429654--429698 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
429644 TTGCAAGTTG
*
429654 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
429676 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
429696 AAA
1 AAA
429699 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:433602 original size:33 final size:33
Alignment explanation
Indices: 433516--433624 Score: 114
Period size: 33 Copynumber: 3.3 Consensus size: 33
433506 TCCAAAATGT
* * *
433516 ATCGATACATGTTTCTGTGTATCGATACATCTGG
1 ATCGATACATTTTTCTTTGTATCGATACAT-TGC
* * *
433550 A--AATTCAATGTTTTCTTTGTATCTATACATTGC
1 ATCGATAC-AT-TTTTCTTTGTATCGATACATTGC
*
433583 ATCGATACATTTTTCTTTGTATCGATACATTGT
1 ATCGATACATTTTTCTTTGTATCGATACATTGC
433616 ATCGATACA
1 ATCGATACA
433625 GGGTGATTAT
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
32 3 0.05
33 35 0.57
34 20 0.33
35 3 0.05
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (33 bp):
ATCGATACATTTTTCTTTGTATCGATACATTGC
Found at i:433617 original size:13 final size:13
Alignment explanation
Indices: 433599--433624 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
433589 ACATTTTTCT
433599 TTGTATCGATACA
1 TTGTATCGATACA
433612 TTGTATCGATACA
1 TTGTATCGATACA
433625 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:436189 original size:13 final size:13
Alignment explanation
Indices: 436171--436196 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
436161 TACAGCAAGT
436171 ATGTATCGATACA
1 ATGTATCGATACA
436184 ATGTATCGATACA
1 ATGTATCGATACA
436197 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:441342 original size:167 final size:167
Alignment explanation
Indices: 441140--441443 Score: 461
Period size: 167 Copynumber: 1.8 Consensus size: 167
441130 TTTAGAATCC
* *
441140 CTCTTATTTTTGAAATAAGGAGTTTTCTACTCCGTAAATGTTTTTAGAGGA-ATTTTTCTTAGTT
1 CTCTTATTTGTGAAATAAGGAGTTTTCTACTCCGTAAATATTTTTAG-GGAGATTTTTCTTAGTT
* *
441204 TTTATTTTTTAAAATTCATCAAATATTATTAGTTAATTT-ATATTAAATCAATTTTCAAAAAATC
65 TTTAATTTTCAAAATTCATCAAATATTATTA-TTAATTTCATATTAAATCAATTTTCAAAAAATC
441268 ATTCATTTTCGTGTGTTTTTCATTTTTTTCCTTAAAATT
129 ATTCATTTTCGTGTGTTTTTCATTTTTTTCCTTAAAATT
* *
441307 CTCTTATTTGTGAAATACA-GAGTTTTCTACTCCGTAAATATTTTTAGGGAGTTTTTTCTTGGTT
1 CTCTTATTTGTGAAATA-AGGAGTTTTCTACTCCGTAAATATTTTTAGGGAGATTTTTCTTAGTT
* * * *
441371 TTTAATTTTCAAAATTCATCAAATATTATTATTTATTTCATATTAAATCAGTTTTTAAAAATTCA
65 TTTAATTTTCAAAATTCATCAAATATTATTATTAATTTCATATTAAATCAATTTTCAAAAAATCA
*
441436 TTTATTTT
130 TTCATTTT
441444 TATGAGTTTA
Statistics
Matches: 123, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
166 9 0.07
167 113 0.92
168 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (167 bp):
CTCTTATTTGTGAAATAAGGAGTTTTCTACTCCGTAAATATTTTTAGGGAGATTTTTCTTAGTTT
TTAATTTTCAAAATTCATCAAATATTATTATTAATTTCATATTAAATCAATTTTCAAAAAATCAT
TCATTTTCGTGTGTTTTTCATTTTTTTCCTTAAAATT
Found at i:441462 original size:167 final size:166
Alignment explanation
Indices: 441140--441480 Score: 447
Period size: 167 Copynumber: 2.1 Consensus size: 166
441130 TTTAGAATCC
* *
441140 CTCTTATTTTTGAAATAAGGAGTTTTCTACTCCGTAAATGTTTTTAGAGGAATTTTTCTTAGTTT
1 CTCTTATTTGTGAAATAAGGAGTTTTCTACTCCGTAAATATTTTTAGAGGAATTTTTCTTAGTTT
* *
441205 TTATTTTTTAAAATTCATCAAATATTATTAGTTAATTTATATTAAATCAATTTTCAAAAAATCAT
66 TTAATTTTCAAAATTCATCAAATATTATTAGTTAATTTATATTAAATCAATTTTCAAAAAATCAT
* * ** *
441270 TCATTTTCGTGTGTTTTTCATTTTTTTCCTTAAAATT
131 TCATTTTCATGAG-TTTAAAATTTTTTCCTTAAAATT
* *
441307 CTCTTATTTGTGAAATACA-GAGTTTTCTACTCCGTAAATATTTTTAG-GGAGTTTTTTCTTGGT
1 CTCTTATTTGTGAAATA-AGGAGTTTTCTACTCCGTAAATATTTTTAGAGGA-ATTTTTCTTAGT
* * * *
441370 TTTTAATTTTCAAAATTCATCAAATATTATTA-TTTATTTCATATTAAATCAGTTTTTAAAAATT
64 TTTTAATTTTCAAAATTCATCAAATATTATTAGTTAATTT-ATATTAAATCAATTTTCAAAAAAT
* * *
441434 CATTTATTTTTATGAGTTTAAAATTTTTTCTTTAAAATT
128 CATTCATTTTCATGAGTTTAAAATTTTTTCCTTAAAATT
*
441473 -TTTTATTT
1 CTCTTATTT
441481 CCGAAAAATC
Statistics
Matches: 152, Mismatches: 19, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
165 7 0.05
166 28 0.18
167 116 0.76
168 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.52
Consensus pattern (166 bp):
CTCTTATTTGTGAAATAAGGAGTTTTCTACTCCGTAAATATTTTTAGAGGAATTTTTCTTAGTTT
TTAATTTTCAAAATTCATCAAATATTATTAGTTAATTTATATTAAATCAATTTTCAAAAAATCAT
TCATTTTCATGAGTTTAAAATTTTTTCCTTAAAATT
Found at i:441467 original size:14 final size:14
Alignment explanation
Indices: 441450--441476 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
441440 TTTTTATGAG
441450 TTTAAAATTTTTTC
1 TTTAAAATTTTTTC
441464 TTTAAAATTTTTT
1 TTTAAAATTTTTT
441477 ATTTCCGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTAAAATTTTTTC
Found at i:444172 original size:15 final size:16
Alignment explanation
Indices: 444152--444181 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
444142 TTGTATTTCT
444152 ATCCTTAGAG-TTATC
1 ATCCTTAGAGCTTATC
444167 ATCCTTAGAGCTTAT
1 ATCCTTAGAGCTTAT
444182 ACTCTTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (16 bp):
ATCCTTAGAGCTTATC
Found at i:449513 original size:21 final size:20
Alignment explanation
Indices: 449489--449527 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
449479 AGGTCAAAAC
449489 CCTAGAAAGTATCGATACACA
1 CCTAG-AAGTATCGATACACA
*
449510 CCTAGATGTATCGATACA
1 CCTAGAAGTATCGATACA
449528 TATTGCTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (20 bp):
CCTAGAAGTATCGATACACA
Found at i:449555 original size:13 final size:13
Alignment explanation
Indices: 449537--449561 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
449527 ATATTGCTTA
449537 GTATCGATACATT
1 GTATCGATACATT
449550 GTATCGATACAT
1 GTATCGATACAT
449562 GTTCATAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:449576 original size:32 final size:33
Alignment explanation
Indices: 449516--449579 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
449506 CACACCTAGA
*
449516 TGTATCGATACATATTGCTTAGTATCGATACAT
1 TGTATCGATACATATTGCATAGTATCGATACAT
*
449549 TGTATCGATACATGTT-CATAGTATCGATACA
1 TGTATCGATACATATTGCATAGTATCGATACA
449580 CCTTGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (33 bp):
TGTATCGATACATATTGCATAGTATCGATACAT
Found at i:449803 original size:23 final size:20
Alignment explanation
Indices: 449777--449819 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
449767 ACAAGGTCCT
449777 AATAAGTCAAATATGTCATCCAA
1 AATAA-TCAAA-ATGTC-TCCAA
*
449800 AATAATCATAATGTCTCCAA
1 AATAATCAAAATGTCTCCAA
449820 CAGATACATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 5 0.26
22 4 0.21
23 5 0.26
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.28
Consensus pattern (20 bp):
AATAATCAAAATGTCTCCAA
Found at i:450158 original size:32 final size:32
Alignment explanation
Indices: 450117--450240 Score: 130
Period size: 32 Copynumber: 3.8 Consensus size: 32
450107 TGATTGAGAG
450117 GTTCTATCTTAGCCTTG-AAAGATAGGGATAAA
1 GTTCTATCTTAGCCTTGAAAAGATAGGGA-AAA
*
450149 GTTCTATCTTGGCCTTTGTAAAAGATAGGGAGAAA
1 GTTCTATCTTAGCC-TTG-AAAAGATAGGGA-AAA
* *
450184 GGTTCTATCTTAGCTCGTGAAAAGATAGGG--AG
1 -GTTCTATCTTAGC-CTTGAAAAGATAGGGAAAA
450216 GTTTCTATCTTAGCCTTG-AAAGATA
1 G-TTCTATCTTAGCCTTGAAAAGATA
450241 ATGTTGTAAG
Statistics
Matches: 80, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
30 7 0.09
31 4 0.05
32 26 0.32
33 3 0.04
35 25 0.31
36 14 0.17
37 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (32 bp):
GTTCTATCTTAGCCTTGAAAAGATAGGGAAAA
Found at i:450207 original size:35 final size:34
Alignment explanation
Indices: 450115--450240 Score: 147
Period size: 35 Copynumber: 3.8 Consensus size: 34
450105 AGTGATTGAG
*
450115 AGGTTCTATCTTAGCCTTG-AAAGATAGGGATAA
1 AGGTTCTATCTTAGCCTTGAAAAGATAGGGAGAA
*
450148 A-GTTCTATCTTGGCCTTTGTAAAAGATAGGGAGAA
1 AGGTTCTATCTTAGCC-TTG-AAAAGATAGGGAGAA
*
450183 AGGTTCTATCTTAGCTCGTGAAAAGATAGGGAG--
1 AGGTTCTATCTTAGC-CTTGAAAAGATAGGGAGAA
*
450216 -GTTTCTATCTTAGCCTTG-AAAGATA
1 AGGTTCTATCTTAGCCTTGAAAAGATA
450241 ATGTTGTAAG
Statistics
Matches: 82, Mismatches: 6, Indels: 13
0.81 0.06 0.13
Matches are distributed among these distances:
30 7 0.09
31 3 0.04
32 26 0.32
33 4 0.05
35 27 0.33
36 14 0.17
37 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.32
Consensus pattern (34 bp):
AGGTTCTATCTTAGCCTTGAAAAGATAGGGAGAA
Found at i:451645 original size:50 final size:52
Alignment explanation
Indices: 451586--451704 Score: 172
Period size: 52 Copynumber: 2.3 Consensus size: 52
451576 CAAAACCCAG
*
451586 AATGTATCGATACATTT-GGGTC-AAAACC-AGAATGTATCCATACAATGAA
1 AATGTATCGATACATTTGGGGTCAAAAACCTAAAATGTATCCATACAATGAA
*
451635 TAATGTATCGATACATTTGGGGTCAAAAACCTAAAATGTATCGATACAATGAA
1 -AATGTATCGATACATTTGGGGTCAAAAACCTAAAATGTATCCATACAATGAA
* *
451688 AATGTATTGATAAATTT
1 AATGTATCGATACATTT
451705 TCTTTCTAGA
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
50 17 0.27
51 5 0.08
52 21 0.34
53 19 0.31
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (52 bp):
AATGTATCGATACATTTGGGGTCAAAAACCTAAAATGTATCCATACAATGAA
Found at i:455072 original size:21 final size:20
Alignment explanation
Indices: 455007--455079 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
454997 TTCTACAATT
*
455007 TGTATCGATACAATAAGTGAA
1 TGTATCGATAC-ATAAATGAA
*
455028 TGTATTGATACATAAATGAA
1 TGTATCGATACATAAATGAA
* *
455048 TGTATCGATACATGATTGAAA
1 TGTATCGATACATAAATG-AA
455069 TGTATCGATAC
1 TGTATCGATAC
455080 TGGACCATGT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 23 0.50
21 23 0.50
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATAAATGAA
Found at i:461191 original size:20 final size:19
Alignment explanation
Indices: 461166--461238 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
461156 ACCCTAGAAA
* *
461166 GTATCGATACATTATGCTTT
1 GTATCGATACATGAT-CATT
*
461186 GTATCGATACATGCTCATT
1 GTATCGATACATGATCATT
461205 GTATCGATACAT-ACTCAATT
1 GTATCGATACATGA-TC-ATT
*
461225 GTTTCGATACATGA
1 GTATCGATACATGA
461239 AACTGGTAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.38
20 27 0.60
21 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (19 bp):
GTATCGATACATGATCATT
Found at i:461208 original size:19 final size:20
Alignment explanation
Indices: 461184--461237 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
461174 ACATTATGCT
461184 TTGTATCGATACATGCTC-A
1 TTGTATCGATACATGCTCAA
*
461203 TTGTATCGATACATACTCAA
1 TTGTATCGATACATGCTCAA
*
461223 TTGTTTCGATACATG
1 TTGTATCGATACATG
461238 AAACTGGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGCTCAA
Found at i:468090 original size:113 final size:104
Alignment explanation
Indices: 467997--468338 Score: 241
Period size: 104 Copynumber: 3.2 Consensus size: 104
467987 GTAGAAAAGG
* *
467997 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGATACAAAGAATGTCAATGTGCTG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATACAAAGAATGTCAATGTGCTA
* *
468062 ATTCACGGCCAGTGACATTAGACTTGAAGATGAAAAGAA
66 ATTCAAGGCCAGCGACATTAGACTTGAAGATGAAAAGAA
* * ** * *
468101 TGCCAATGTGCTGATTCAAGGCCAGCGACATTTGGCTTAGAA-ATGTTAAAG-ATGCCAATATGC
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTA-AAGAT-ACAAAGAATGTCAATGTGC
* * * ** * * *
468164 TGATTCAAGGCCAACGATATCGGACTTAAAGATG--ATG-G
64 TAATTCAAGGCCAGCGACATTAGACTTGAAGATGAAAAGAA
* * * * *
468202 TGGCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAGGATGA-AAAGGATGATAAAGATGC
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGAT-ACAAA-GA--AT---G-T--
* * * * * *
468266 CAATATGCTAATCCAAGGCCAGCGACATT-GAGTTTAGGAATGTTAAAG-A
56 CAATGTGCTAATTCAAGGCCAGCGACATTAGACTTGAAG-ATG-AAAAGAA
468315 TGCCAATATGCTGATTCAAGGCCA
1 TGCCAATATGCTGATTCAAGGCCA
468339 ACGATATCAC
Statistics
Matches: 186, Mismatches: 35, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
100 4 0.02
101 39 0.21
102 2 0.01
104 77 0.41
105 6 0.03
107 1 0.01
109 6 0.03
110 27 0.15
113 24 0.13
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (104 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATACAAAGAATGTCAATGTGCTA
ATTCAAGGCCAGCGACATTAGACTTGAAGATGAAAAGAA
Found at i:468092 original size:52 final size:52
Alignment explanation
Indices: 467997--468251 Score: 243
Period size: 52 Copynumber: 5.0 Consensus size: 52
467987 GTAGAAAAGG
* * * *
467997 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGAT-ACAAAGAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGA-AAAGAA
* * * *
468049 TGTCAATGTGCTGATTCACGGCCAGTGACATTAGACTTGAAGATGAAAAGAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAAAAGAA
* * *
468101 TGCCAATGTGCTGATTCAAGGCCAGCGACATTTGGCTTAGAA-ATGTTAAAG-A
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTA-AAGATG-AAAAGAA
* * * ** * *
468153 TGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATG--ATG-G
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAAAAGAA
* * * *
468202 TGGCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAGGATGAAAAG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAAAAG
468252 GATGATAAAG
Statistics
Matches: 166, Mismatches: 31, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
49 40 0.24
51 4 0.02
52 115 0.69
53 7 0.04
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (52 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGAAAAGAA
Found at i:468540 original size:52 final size:52
Alignment explanation
Indices: 468455--468576 Score: 165
Period size: 52 Copynumber: 2.3 Consensus size: 52
468445 GGTGCGAATA
* * *
468455 TGCTGATTCAAGACCAGCGATATTAGGCATAAAGATGTGAAGAATGTCAATG
1 TGCTGATTCAAGGCCAGCGATATTAGGCATAAAGATGAGAAGAATGCCAATG
* * *
468507 TGCTGATTCAAGGCTAGCGATGTT-GGACTTAAAGATGAGAAGAATGCCAATG
1 TGCTGATTCAAGGCCAGCGATATTAGG-CATAAAGATGAGAAGAATGCCAATG
*
468559 TGTTGATTCAAGGCCAGC
1 TGCTGATTCAAGGCCAGC
468577 AACATTGGGC
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 2 0.03
52 59 0.97
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (52 bp):
TGCTGATTCAAGGCCAGCGATATTAGGCATAAAGATGAGAAGAATGCCAATG
Found at i:468649 original size:32 final size:33
Alignment explanation
Indices: 468613--468726 Score: 103
Period size: 32 Copynumber: 3.6 Consensus size: 33
468603 CCAATTTGTA
* *
468613 TGGGCTTTTGAA-AGGGTTGCCACTGA-CTTATG
1 TGGGCTTTTGAAGAAGGTTGCCAC-CACCTTATG
*
468645 TGGGC-TTTGAAGAAGGTTGCCACCACCTTGTG
1 TGGGCTTTTGAAGAAGGTTGCCACCACCTTATG
* * * **
468677 TGGGC-TTTAAAGAAAGTTGCCACCAACTCGTG
1 TGGGCTTTTGAAGAAGGTTGCCACCACCTTATG
*
468709 TGGGCTTTAG-AGAAGGTT
1 TGGGCTTTTGAAGAAGGTT
468727 CCTCTACTGG
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
31 7 0.10
32 60 0.87
33 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.30
Consensus pattern (33 bp):
TGGGCTTTTGAAGAAGGTTGCCACCACCTTATG
Found at i:468958 original size:28 final size:29
Alignment explanation
Indices: 468897--468970 Score: 93
Period size: 28 Copynumber: 2.7 Consensus size: 29
468887 TACATACAGC
468897 AAGTGCCACTGA-TTGTGGATTCTGAAAAG
1 AAGTGCCACTGACTTGTGGA-TCTGAAAAG
*
468926 -A-TGCCACTGACTTGTGGA-CTTAAAAG
1 AAGTGCCACTGACTTGTGGATCTGAAAAG
*
468952 AAGTGCCACTGACTAGTGG
1 AAGTGCCACTGACTTGTGG
468971 GCTTTGAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 7 0.17
27 10 0.25
28 23 0.57
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (29 bp):
AAGTGCCACTGACTTGTGGATCTGAAAAG
Found at i:468980 original size:28 final size:28
Alignment explanation
Indices: 468897--468980 Score: 84
Period size: 28 Copynumber: 3.0 Consensus size: 28
468887 TACATACAGC
*
468897 AAGTGCCACTGA-TTGT-GGATTCTGAA-
1 AAGTGCCACTGACTTGTGGGCTT-TGAAG
* **
468923 AAGATGCCACTGACTTGTGGACTTAAAAG
1 AAG-TGCCACTGACTTGTGGGCTTTGAAG
*
468952 AAGTGCCACTGACTAGTGGGCTTTGAAG
1 AAGTGCCACTGACTTGTGGGCTTTGAAG
468980 A
1 A
468981 GGGATTTGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
26 3 0.07
27 9 0.20
28 28 0.61
29 6 0.13
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (28 bp):
AAGTGCCACTGACTTGTGGGCTTTGAAG
Found at i:470321 original size:6 final size:6
Alignment explanation
Indices: 470306--470369 Score: 66
Period size: 6 Copynumber: 11.0 Consensus size: 6
470296 AGACCCTTTA
470306 TTTTTG -TTTTG TTTTTG TTTTT- TTTATGTG TTTGTT- TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTT-T-TG TTT-TTG TTTTTG TTTTTG
470354 TTTTT- TTTTT- TTTTTG
1 TTTTTG TTTTTG TTTTTG
470370 CAAAAGATGC
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
5 20 0.39
6 25 0.49
7 2 0.04
8 4 0.08
ACGTcount: A:0.02, C:0.00, G:0.14, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:470343 original size:14 final size:14
Alignment explanation
Indices: 470321--470358 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
470311 GTTTTGTTTT
470321 TGTTT-TTTTTATG
1 TGTTTGTTTTTATG
*
470334 TGTTTGTTTTTTTG
1 TGTTTGTTTTTATG
*
470348 TTTTTGTTTTT
1 TGTTTGTTTTT
470359 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.03, C:0.00, G:0.16, T:0.82
Consensus pattern (14 bp):
TGTTTGTTTTTATG
Found at i:472788 original size:32 final size:32
Alignment explanation
Indices: 472747--472811 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
472737 GGGATATGAA
472747 TCTGGAAATGTAGTTCAATCTCCCTAGAAAGC
1 TCTGGAAATGTAGTTCAATCTCCCTAGAAAGC
472779 TCTGGAAATGTAGTTCAATCTCCCTAGAAAGC
1 TCTGGAAATGTAGTTCAATCTCCCTAGAAAGC
472811 T
1 T
472812 TCTTACCTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (32 bp):
TCTGGAAATGTAGTTCAATCTCCCTAGAAAGC
Found at i:486531 original size:33 final size:33
Alignment explanation
Indices: 486489--486552 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
486479 ATTCCCAGAT
486489 GTATCGATACAAAG-ATCAATGTATCGATACAAC
1 GTATCGATACAAAGAAT-AATGTATCGATACAAC
**
486522 GTATCGATACATTGAATAATGTATCGATACA
1 GTATCGATACAAAGAATAATGTATCGATACA
486553 TTTCCTTGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (33 bp):
GTATCGATACAAAGAATAATGTATCGATACAAC
Found at i:487964 original size:20 final size:21
Alignment explanation
Indices: 487939--487992 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
487929 TCCCATAGCC
487939 ATGTATCGATACAATT-CACA
1 ATGTATCGATACAATTGCACA
* *
487959 ATGTATCGATAC-ATTGTACC
1 ATGTATCGATACAATTGCACA
487979 ATGTATCGATACAA
1 ATGTATCGATACAA
487993 ATAGTGATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 3 0.10
20 26 0.87
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (21 bp):
ATGTATCGATACAATTGCACA
Found at i:488568 original size:21 final size:22
Alignment explanation
Indices: 488525--488569 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
488515 CCTCCTATAT
** *
488525 AAAAAAAATTTCTCATGCTTTA
1 AAAAAAAATTTCTCACCCCTTA
488547 AAAAAAAATTTCTC-CCCCTTA
1 AAAAAAAATTTCTCACCCCTTA
488568 AA
1 AA
488570 CGGTTATCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.47, C:0.20, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAAAAAATTTCTCACCCCTTA
Found at i:496655 original size:13 final size:13
Alignment explanation
Indices: 496610--496648 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
496600 CCGTTACAAG
496610 CAATGTATCGATA
1 CAATGTATCGATA
496623 CAATGTATCGATA
1 CAATGTATCGATA
496636 CAATGTATCGATA
1 CAATGTATCGATA
496649 TATTGTACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:496737 original size:13 final size:13
Alignment explanation
Indices: 496719--496745 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
496709 ATAAGTGTCC
496719 ATGTATCGATACA
1 ATGTATCGATACA
496732 ATGTATCGATACA
1 ATGTATCGATACA
496745 A
1 A
496746 AGCAAGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:497640 original size:21 final size:21
Alignment explanation
Indices: 497614--497678 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
497604 ATACATTAAA
*
497614 TAATGTATCCATACATTTGGG
1 TAATGTATCAATACATTTGGG
* **
497635 TAATGTATCAATTCA-TTGAA
1 TAATGTATCAATACATTTGGG
* * *
497655 TCATGTATCGATACATCTGGG
1 TAATGTATCAATACATTTGGG
497676 TAA
1 TAA
497679 ATACCTAGAT
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (21 bp):
TAATGTATCAATACATTTGGG
Found at i:497642 original size:41 final size:41
Alignment explanation
Indices: 497596--497678 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
497586 ATTTGCCTGC
* *
497596 ATGTATCTATACATTAAATAATGTATCCATACATTTGGGTA
1 ATGTATCAATACATTAAATAATGTATCCATACATCTGGGTA
* * * *
497637 ATGTATCAATTCATTGAATCATGTATCGATACATCTGGGTA
1 ATGTATCAATACATTAAATAATGTATCCATACATCTGGGTA
497678 A
1 A
497679 ATACCTAGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37
Consensus pattern (41 bp):
ATGTATCAATACATTAAATAATGTATCCATACATCTGGGTA
Found at i:500249 original size:13 final size:13
Alignment explanation
Indices: 500231--500256 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
500221 ACAAAGATCT
500231 TTGTATCGATACA
1 TTGTATCGATACA
500244 TTGTATCGATACA
1 TTGTATCGATACA
500257 GGGTTACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:502116 original size:41 final size:41
Alignment explanation
Indices: 502059--502201 Score: 241
Period size: 41 Copynumber: 3.5 Consensus size: 41
502049 GTTATAACAA
* *
502059 AAAGGGAGAGAAATTTTTTGAAAATAAATTTGAGTTTTGAC
1 AAAGGGGGAGAAATTTTTTGAAAATAAATTTGACTTTTGAC
*
502100 AAAGGGGGAGAAATTTTTTGAAAATAAATTTGACTTTTGAT
1 AAAGGGGGAGAAATTTTTTGAAAATAAATTTGACTTTTGAC
502141 AAAGGGGGAGAAATTTTTTGAAAATAAATTTGACTTTTGAC
1 AAAGGGGGAGAAATTTTTTGAAAATAAATTTGACTTTTGAC
*
502182 AAAGAGGGAGAAATTATTTT
1 AAAGGGGGAGAAATT-TTTT
502202 ATAGAAAGAA
Statistics
Matches: 96, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
41 92 0.96
42 4 0.04
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (41 bp):
AAAGGGGGAGAAATTTTTTGAAAATAAATTTGACTTTTGAC
Found at i:506299 original size:20 final size:20
Alignment explanation
Indices: 506276--506320 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
506266 TTCGGGATCA
506276 ATAC-TTTGAAGCATGTATCG
1 ATACTTTTGAA-CATGTATCG
*
506296 ATACTTTTTGGACATGTATCG
1 ATAC-TTTTGAACATGTATCG
506317 ATAC
1 ATAC
506321 ATTAACTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 4 0.18
21 13 0.59
22 5 0.23
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (20 bp):
ATACTTTTGAACATGTATCG
Found at i:506732 original size:20 final size:21
Alignment explanation
Indices: 506707--506761 Score: 87
Period size: 20 Copynumber: 2.7 Consensus size: 21
506697 TTTTCACAAT
506707 TTGTATCGATACATTGTT-CA
1 TTGTATCGATACATTGTTACA
*
506727 TTGTATCGATACATCGTT-CA
1 TTGTATCGATACATTGTTACA
506747 TTGTATCGATACATT
1 TTGTATCGATACATT
506762 CTGGGTTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (21 bp):
TTGTATCGATACATTGTTACA
Found at i:506802 original size:20 final size:19
Alignment explanation
Indices: 506777--506850 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
506767 TTTACCTAGA
506777 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
* *
506797 TGTATCAATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
*
506817 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
*
506837 TATATCGATACATT
1 TGTATCGATACATT
506851 CAGGCATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.96
21 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:509690 original size:79 final size:80
Alignment explanation
Indices: 509205--509688 Score: 603
Period size: 79 Copynumber: 6.2 Consensus size: 80
509195 TTTCTTAATC
* * * * *
509205 GGGGATACTCTAACTCCGATTTTATTTCCAAAA-CACCAACTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATCATCAATTTTTCACAATCGGGGATACTCCAA
*
509269 CCCCGTTATTTCTGA
66 CCCCGTTATTTCCGA
*
509284 GGGGACACTCCAACCCCGATTTTATTTCTAAAA-CATCAATTTTT--C-ATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATCATCAATTTTTCACAATCGGGGATACTCCAA
* * *
509345 TCCCGCTATTTTCGA
66 CCCCGTTATTTCCGA
* ** * * *
509360 GGGGATACCCCAACCCCGGCTTTATTTCTAAAAT-ATTAATTTCTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATCATCAATTTTTCACAATCGGGGATACTCCAA
509424 CCCCGTTA-TTCTCGA
66 CCCCGTTATTTC-CGA
* * * *
509439 GCGGATACTCCAACCCCGATTTTATTTCTAAAATC-TTAATTTCTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATCATCAATTTTTCACAATCGGGGATACTCCAA
509503 CCCCGTTATTTCCGA
66 CCCCGTTATTTCCGA
* * *
509518 GGGGATACTCCAACCCCGATTTTACTTCTAAAAT-ATCAATTTTTCATAGTCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATCATCAATTTTTCACAATCGGGGATACTCCAA
*
509582 CCCCGTTATTTCTGA
66 CCCCGTTATTTCCGA
* *
509597 GGGGATACTTCAATCCCGATTTTATTTCT-AAATCATCAATTTTTCACAAT-GGAGGATACTCCA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATCATCAATTTTTCACAATCGG-GGATACTCCA
* **
509660 ACCCTGTTATTTTTGA
65 ACCCCGTTATTTCCGA
*
509676 GAGGATACTCCAA
1 GGGGATACTCCAA
509689 TCTCGTTATT
Statistics
Matches: 356, Mismatches: 39, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
76 64 0.18
77 1 0.00
78 8 0.02
79 280 0.79
80 3 0.01
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.32
Consensus pattern (80 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAATCATCAATTTTTCACAATCGGGGATACTCCAA
CCCCGTTATTTCCGA
Found at i:511975 original size:26 final size:26
Alignment explanation
Indices: 511916--511968 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
511906 TTAATTTGAT
*
511916 CATAACACTTATATATTATGGCCAAA
1 CATAACACTTATATATTATGACCAAA
* *
511942 CATAACACTTATCTATTGTGACCAAA
1 CATAACACTTATATATTATGACCAAA
511968 C
1 C
511969 CTTACACATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.30
Consensus pattern (26 bp):
CATAACACTTATATATTATGACCAAA
Found at i:514090 original size:20 final size:21
Alignment explanation
Indices: 514065--514118 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
514055 GTTGCAAGCA
*
514065 ATGTATCGATACAATT-CATC
1 ATGTATCGATACAATTGCACC
*
514085 ATGTATCGATAC-ATTGTACC
1 ATGTATCGATACAATTGCACC
514105 ATGTATCGATACAA
1 ATGTATCGATACAA
514119 ACGGTGGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 3 0.10
20 26 0.87
21 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACAATTGCACC
Found at i:514186 original size:13 final size:13
Alignment explanation
Indices: 514168--514193 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
514158 ACAATTGTCC
514168 ATGTATCGATACA
1 ATGTATCGATACA
514181 ATGTATCGATACA
1 ATGTATCGATACA
514194 TTCAAAGCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:514807 original size:22 final size:22
Alignment explanation
Indices: 514745--514800 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
514735 AGTTTTCATT
* *
514745 TTTCTCCTCCTTAATTAAAGAA
1 TTTCTCCCCCTTAATCAAAGAA
*
514767 TTTCTCCCCCTTAATCAAAGCA
1 TTTCTCCCCCTTAATCAAAGAA
514789 TTTCTCCCCCTT
1 TTTCTCCCCCTT
514801 TGTCAAATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.23, C:0.34, G:0.04, T:0.39
Consensus pattern (22 bp):
TTTCTCCCCCTTAATCAAAGAA
Found at i:522761 original size:33 final size:33
Alignment explanation
Indices: 522721--522789 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
522711 CCGTTACAAG
522721 CAATGTATCGATACAATTCAT-CATGTATCGATA
1 CAATGTATCGATAC-ATTCATCCATGTATCGATA
* **
522754 CAATGTATTGATACATTGTTCCATGTATCGATA
1 CAATGTATCGATACATTCATCCATGTATCGATA
522787 CAA
1 CAA
522790 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 4 0.12
33 28 0.88
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATTCATCCATGTATCGATA
Found at i:522843 original size:20 final size:20
Alignment explanation
Indices: 522818--522875 Score: 84
Period size: 19 Copynumber: 3.0 Consensus size: 20
522808 CTGCCAATTT
*
522818 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTA
*
522838 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTA
522857 CATGTATCGATAC-ATTGTA
1 CATGTATCGATACAATTGTA
522876 TCGATACAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.03
19 18 0.53
20 15 0.44
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:522877 original size:13 final size:13
Alignment explanation
Indices: 522859--522883 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
522849 ACAATGAACA
522859 TGTATCGATACAT
1 TGTATCGATACAT
522872 TGTATCGATACA
1 TGTATCGATACA
522884 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:522900 original size:33 final size:32
Alignment explanation
Indices: 522840--522904 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
522830 CAATTGTCCA
*
522840 TGTATCGATACAATGAACATGTATCGATACAT
1 TGTATCGATACAAAGAACATGTATCGATACAT
522872 TGTATCGATACAAAGCATA-ATGTATCGATACAT
1 TGTATCGATACAAAG-A-ACATGTATCGATACAT
522905 CTTCAATCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.47
33 15 0.50
34 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATGTATCGATACAT
Found at i:525895 original size:121 final size:121
Alignment explanation
Indices: 525740--525974 Score: 407
Period size: 121 Copynumber: 1.9 Consensus size: 121
525730 CAAGTTAGTT
*
525740 CTTAAATATAAATATTGACAAAAATAAAACTTTAAACATAAAATGATAATCTAAAACAAGTATTA
1 CTTAAATATAAATATTGACAAAAATAAAACTTTAAACATAAAAAGATAATCTAAAACAAGTATTA
*
525805 TTATTCACACTACAACTTGCAAAATAAAGTAAAAAGTTTGAAATTGTTCTTTCGTG
66 TTATTCACACTACAACTTGCAAAATAAAGTAAAAAGGTTGAAATTGTTCTTTCGTG
* * *
525861 CTTAAATATAAATATTTATAAAAATAAAACTTTAAACATAAAAAGATAATCTAAAACATGTATTA
1 CTTAAATATAAATATTGACAAAAATAAAACTTTAAACATAAAAAGATAATCTAAAACAAGTATTA
* *
525926 TTATTTACATTACAACTTGCAAAATAAAGTAAAAAGGTTGAAATTGTTC
66 TTATTCACACTACAACTTGCAAAATAAAGTAAAAAGGTTGAAATTGTTC
525975 CTTCACGTGT
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 107 1.00
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (121 bp):
CTTAAATATAAATATTGACAAAAATAAAACTTTAAACATAAAAAGATAATCTAAAACAAGTATTA
TTATTCACACTACAACTTGCAAAATAAAGTAAAAAGGTTGAAATTGTTCTTTCGTG
Found at i:527750 original size:16 final size:15
Alignment explanation
Indices: 527731--527774 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
527721 TTTTTTTGGA
*
527731 TTTCTATATTTTTGTT
1 TTTCTAT-TTTTTATT
*
527747 TTTCTTTTTTTTATT
1 TTTCTATTTTTTATT
527762 TCTTCTATTTTTT
1 T-TTCTATTTTTT
527775 TCATTTTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTCTATTTTTTATT
Found at i:528793 original size:26 final size:28
Alignment explanation
Indices: 528764--528823 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
528754 ACTTGGGATG
*
528764 ATTAA-AT-TTTTTTTCTTTCTTCACGT
1 ATTAATATCTTTTTTTCTTTCGTCACGT
*
528790 ATTAAATATCTTTTTTTCTTTCGTCATGT
1 ATT-AATATCTTTTTTTCTTTCGTCACGT
528819 ATTAA
1 ATTAA
528824 GACGAGGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 3 0.10
27 2 0.07
28 4 0.14
29 20 0.69
ACGTcount: A:0.23, C:0.13, G:0.05, T:0.58
Consensus pattern (28 bp):
ATTAATATCTTTTTTTCTTTCGTCACGT
Found at i:529966 original size:13 final size:13
Alignment explanation
Indices: 529926--529972 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
529916 CCGTTACAAG
529926 CAATGTATCGATA
1 CAATGTATCGATA
529939 CAA--T-TC-AT-
1 CAATGTATCGATA
529947 C-ATGTATCGATA
1 CAATGTATCGATA
529959 CAATGTATCGATA
1 CAATGTATCGATA
529972 C
1 C
529973 TCACCCAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
7 1 0.04
8 1 0.04
9 3 0.11
10 4 0.14
11 3 0.11
12 1 0.04
13 15 0.54
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:530971 original size:78 final size:78
Alignment explanation
Indices: 530833--530991 Score: 185
Period size: 78 Copynumber: 2.0 Consensus size: 78
530823 TTCAACCCAC
* * * * * ** *
530833 ATAAGCCTAATAGACATCTATTGACATAAAGGTTCCACATGATCGTACTAGACTTGGTTTTAACA
1 ATAACCCTAAAAGACATCTATTGACATAAAAGTTCCACATGATCCTACGAGACTCAGTTTTAAAA
* *
530898 TAGTATTATCTAA
66 TAATATTACCTAA
* * *
530911 ATAACCCTAAAAGACATGTTTTGACATAAAAGTTCTCACATGATCCTA-GGGACTCAGTTTTAAA
1 ATAACCCTAAAAGACATCTATTGACATAAAAGTTC-CACATGATCCTACGAGACTCAGTTTTAAA
530975 ATAATATTACCTAA
65 ATAATATTACCTAA
530989 ATA
1 ATA
530992 CATTTAATGG
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
78 56 0.84
79 11 0.16
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (78 bp):
ATAACCCTAAAAGACATCTATTGACATAAAAGTTCCACATGATCCTACGAGACTCAGTTTTAAAA
TAATATTACCTAA
Found at i:531329 original size:58 final size:59
Alignment explanation
Indices: 531208--531331 Score: 153
Period size: 58 Copynumber: 2.1 Consensus size: 59
531198 CTCAATGGCT
* * * *
531208 TTAAAATGCAAGAAATTGTAAAATAGTCCCTTAATCATGAAAAATGACTAAAATGAGCC
1 TTAAAATGCAAGAAATTGCAAAATAGTCCCTAAATCATGAAAAATAACTAAAATGAACC
* * * * *
531267 -TAAAATGCATGAAATTGCATAGTGGTCCCTAAATCATGAAAAATAACTAGAAT-AACC
1 TTAAAATGCAAGAAATTGCAAAATAGTCCCTAAATCATGAAAAATAACTAAAATGAACC
531324 TTAAAATG
1 TTAAAATG
531332 TATGCATTTG
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
57 3 0.05
58 52 0.95
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.26
Consensus pattern (59 bp):
TTAAAATGCAAGAAATTGCAAAATAGTCCCTAAATCATGAAAAATAACTAAAATGAACC
Found at i:535075 original size:21 final size:20
Alignment explanation
Indices: 535028--535081 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
535018 CATTTGAGAC
* *
535028 ATGTATTGATACATTCACTT
1 ATGTATCGATACATTCACTA
535048 ATGTATCGATACATTCACTA
1 ATGTATCGATACATTCACTA
535068 ATTGTATCGATACA
1 A-TGTATCGATACA
535082 AATTGTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:536583 original size:20 final size:20
Alignment explanation
Indices: 536526--536583 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
536516 AAAATACACA
*
536526 ACATTTATTGATACAAAGGC
1 ACATTTATTGATACAATGGC
536546 ACATTTTATTGATACAATGG-
1 ACA-TTTATTGATACAATGGC
*
536566 GCATTGTATTGATACAAT
1 ACATT-TATTGATACAAT
536584 ATTGTACTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.06
20 17 0.50
21 15 0.44
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (20 bp):
ACATTTATTGATACAATGGC
Found at i:537121 original size:20 final size:20
Alignment explanation
Indices: 537080--537134 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
537070 ATACACAACA
*
537080 TTTATTGATACAAAGGCACAT
1 TTTATTGATACAATGG-ACAT
537101 TTTATTGATACAAT-GAGCAT
1 TTTATTGATACAATGGA-CAT
*
537121 TGTATTGATACAAT
1 TTTATTGATACAAT
537135 ATTGCACGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 1 0.03
20 17 0.55
21 13 0.42
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (20 bp):
TTTATTGATACAATGGACAT
Found at i:537653 original size:46 final size:46
Alignment explanation
Indices: 537586--537673 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
537576 TGATTGATAC
* * *
537586 ATTTTCAAATTTAGAGACTAATATAAAATTTATCCTAAAATTTAAG
1 ATTTTAAAATTTAAAAACTAATATAAAATTTATCCTAAAATTTAAG
537632 ATTTTAAAATTTAAAAACTAATATAAAATTTATCCTAAAATT
1 ATTTTAAAATTTAAAAACTAATATAAAATTTATCCTAAAATT
537674 AAGGACCATG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.40
Consensus pattern (46 bp):
ATTTTAAAATTTAAAAACTAATATAAAATTTATCCTAAAATTTAAG
Found at i:538611 original size:19 final size:21
Alignment explanation
Indices: 538573--538611 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
538563 TGAGTTTTAT
*
538573 GATAAAATATAATATTAAATA
1 GATAAAATAAAATATTAAATA
538594 GATAAAA-AAAAT-TTAAAT
1 GATAAAATAAAATATTAAAT
538612 TTTACTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (21 bp):
GATAAAATAAAATATTAAATA
Found at i:541447 original size:93 final size:93
Alignment explanation
Indices: 541288--541474 Score: 329
Period size: 93 Copynumber: 2.0 Consensus size: 93
541278 TTTATATGCA
* ** *
541288 TAAAGAAATTCAAAGTGTGAGATTGTGTGTGTTGCAAGAATTGGACTCACAGAAGCATGCCAATA
1 TAAAGAAATTCAAAGTGTGAGACTGTGTACGTAGCAAGAATTGGACTCACAGAAGCATGCCAATA
541353 TTAATTATTATGGCAGTAGACCAAGACT
66 TTAATTATTATGGCAGTAGACCAAGACT
*
541381 TAAAGAAATTCAAAGTGTGAGACTGTGTACGTAGCAAGAATTGGACTCACAGAAGCATGCCGATA
1 TAAAGAAATTCAAAGTGTGAGACTGTGTACGTAGCAAGAATTGGACTCACAGAAGCATGCCAATA
541446 TTAATTATTATGGCAGTAGACCAAGACT
66 TTAATTATTATGGCAGTAGACCAAGACT
541474 T
1 T
541475 TTTTCTTTTT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (93 bp):
TAAAGAAATTCAAAGTGTGAGACTGTGTACGTAGCAAGAATTGGACTCACAGAAGCATGCCAATA
TTAATTATTATGGCAGTAGACCAAGACT
Found at i:541548 original size:9 final size:9
Alignment explanation
Indices: 541534--541562 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
541524 TGTTACATAG
541534 TACATTGCA
1 TACATTGCA
541543 TACATTGCA
1 TACATTGCA
541552 TACATTGCA
1 TACATTGCA
541561 TA
1 TA
541563 AGCAAATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (9 bp):
TACATTGCA
Found at i:542125 original size:2 final size:2
Alignment explanation
Indices: 542118--542150 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
542108 GTTGAATCGT
542118 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
542151 GTTTCCTTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:542560 original size:2 final size:2
Alignment explanation
Indices: 542555--542599 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
542545 TTTTAGGATG
* *
542555 AT AT AT AT TT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
542597 AT A
1 AT A
542600 ATTTTCTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:544224 original size:25 final size:25
Alignment explanation
Indices: 544196--544248 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
544186 AATTTTTAAA
544196 TATTAAAAATTTATTTAATAAAATT
1 TATTAAAAATTTATTTAATAAAATT
* ** * *
544221 TATTTATTATTTATTTATTTAAATT
1 TATTAAAAATTTATTTAATAAAATT
544246 TAT
1 TAT
544249 ATTAAATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTAAAAATTTATTTAATAAAATT
Found at i:544248 original size:14 final size:13
Alignment explanation
Indices: 544202--544258 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 13
544192 TAAATATTAA
*
544202 AAATTTATTTAATA
1 AAATTTATTT-ATT
544216 AAATTTATTTATT
1 AAATTTATTTATT
544229 --ATTTATTTATTT
1 AAATTTATTTA-TT
544241 AAATTTA--TATT
1 AAATTTATTTATT
544252 AAATTTA
1 AAATTTA
544259 AAAAGTAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
11 18 0.46
12 4 0.10
13 2 0.05
14 15 0.38
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
AAATTTATTTATT
Found at i:544257 original size:25 final size:24
Alignment explanation
Indices: 544202--544258 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
544192 TAAATATTAA
544202 AAATTTATTTAATAAAATTTATTT
1 AAATTTATTTAATAAAATTTATTT
* * *
544226 ATTATTTATTTATTTAAATTTATATT
1 A-AATTTATTTAATAAAATTTAT-TT
544252 AAATTTA
1 AAATTTA
544259 AAAAGTAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 23 0.85
26 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
AAATTTATTTAATAAAATTTATTT
Found at i:544298 original size:17 final size:17
Alignment explanation
Indices: 544276--544308 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
544266 ATATTCATTT
544276 AATATTAAAATTTATTA
1 AATATTAAAATTTATTA
*
544293 AATATTTAAATTTATT
1 AATATTAAAATTTATT
544309 GAATTAATTT
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):
AATATTAAAATTTATTA
Found at i:546018 original size:23 final size:24
Alignment explanation
Indices: 545967--546019 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
545957 GTTCATCAGT
* *
545967 TGTTCACATATCACTGTTTATTAC
1 TGTTCACATATCACTATTCATTAC
*
545991 TGTTCACGTATCACTATTCA-TAC
1 TGTTCACATATCACTATTCATTAC
546014 TGTTCA
1 TGTTCA
546020 TCGTTGTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.43
Consensus pattern (24 bp):
TGTTCACATATCACTATTCATTAC
Found at i:546028 original size:33 final size:34
Alignment explanation
Indices: 545991--546055 Score: 114
Period size: 33 Copynumber: 1.9 Consensus size: 34
545981 TGTTTATTAC
*
545991 TGTTCACGTATCACTATTCA-TACTGTTCATCGT
1 TGTTCACATATCACTATTCATTACTGTTCATCGT
546024 TGTTCACATATCACTATTCATTACTGTTCATC
1 TGTTCACATATCACTATTCATTACTGTTCATC
546056 ACTGTTCCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 19 0.63
34 11 0.37
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.43
Consensus pattern (34 bp):
TGTTCACATATCACTATTCATTACTGTTCATCGT
Found at i:546086 original size:13 final size:13
Alignment explanation
Indices: 546064--546105 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
546054 TCACTGTTCC
546064 TGTATCGATACAT
1 TGTATCGATACAT
* *
546077 TGTATTGATACAC
1 TGTATCGATACAT
*
546090 TATATCGATACAT
1 TGTATCGATACAT
546103 TGT
1 TGT
546106 GAATAGTATC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:547104 original size:14 final size:14
Alignment explanation
Indices: 547085--547112 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
547075 TTTGAAAACA
547085 TAATTTATTTAGCC
1 TAATTTATTTAGCC
547099 TAATTTATTTAGCC
1 TAATTTATTTAGCC
547113 ATGACATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
TAATTTATTTAGCC
Found at i:556640 original size:34 final size:35
Alignment explanation
Indices: 556602--556668 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
556592 CCTTACAACA
556602 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
556636 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
556669 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:557144 original size:13 final size:13
Alignment explanation
Indices: 557126--557151 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
557116 CAATTTTTTG
557126 TGTATCGATACAT
1 TGTATCGATACAT
557139 TGTATCGATACAT
1 TGTATCGATACAT
557152 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:557216 original size:21 final size:21
Alignment explanation
Indices: 557190--557265 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
557180 CTGCCAAGAA
557190 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
557211 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
557231 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
557252 ATGTATCGATACAT
1 ATGTATCGATACAT
557266 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:557235 original size:20 final size:20
Alignment explanation
Indices: 557210--557283 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
557200 ACATCTTTTT
557210 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
557230 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
557251 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
557271 CATGTATCGATAC
1 CATGTATCGATAC
557284 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:557247 original size:41 final size:41
Alignment explanation
Indices: 557190--557283 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
557180 CTGCCAAGAA
557190 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
557231 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
557272 ATGTATCGATAC
1 ATGTATCGATAC
557284 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:557972 original size:32 final size:32
Alignment explanation
Indices: 557902--557963 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
557892 TCCCCCGTTT
557902 AAAAAATCTCCCCCTTAATCAAGTAATTCAAA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCAAA
557934 AAAAAATCTCCCCCTTAATCAAGTAATTCA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCA
557964 TATCAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.45, C:0.26, G:0.03, T:0.26
Consensus pattern (32 bp):
AAAAAATCTCCCCCTTAATCAAGTAATTCAAA
Found at i:559151 original size:13 final size:13
Alignment explanation
Indices: 559133--559157 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
559123 ACTGAAGCAA
559133 TGTATCGATACAT
1 TGTATCGATACAT
559146 TGTATCGATACA
1 TGTATCGATACA
559158 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:561983 original size:34 final size:35
Alignment explanation
Indices: 561945--562011 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
561935 CCTTACAACA
561945 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
561979 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
562012 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:562487 original size:13 final size:13
Alignment explanation
Indices: 562469--562494 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
562459 CAATTTTTTG
562469 TGTATCGATACAT
1 TGTATCGATACAT
562482 TGTATCGATACAT
1 TGTATCGATACAT
562495 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:562559 original size:21 final size:21
Alignment explanation
Indices: 562533--562608 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
562523 CTGCCAAGAA
562533 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
562554 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
562574 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
562595 ATGTATCGATACAT
1 ATGTATCGATACAT
562609 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:562578 original size:20 final size:20
Alignment explanation
Indices: 562553--562626 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
562543 ACATCTTTTT
562553 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
562573 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
562594 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
562614 CATGTATCGATAC
1 CATGTATCGATAC
562627 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:562590 original size:41 final size:41
Alignment explanation
Indices: 562533--562626 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
562523 CTGCCAAGAA
562533 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
562574 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
562615 ATGTATCGATAC
1 ATGTATCGATAC
562627 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:564131 original size:13 final size:13
Alignment explanation
Indices: 564113--564137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
564103 ATATTACTTA
564113 GTATCGATACATT
1 GTATCGATACATT
564126 GTATCGATACAT
1 GTATCGATACAT
564138 GTCCATAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Done.