Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 142 of 150
Found at i:42837568 original size:20 final size:19
Alignment explanation
Indices: 42837543--42837581 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
42837533 CCAATTTTTT
42837543 TGAAAATTTTAATTATACCC
1 TGAAAATTTTAATTA-ACCC
42837563 TGAAAATTTTAATTAACCC
1 TGAAAATTTTAATTAACCC
42837582 CCTCCTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.38
Consensus pattern (19 bp):
TGAAAATTTTAATTAACCC
Found at i:42839489 original size:239 final size:230
Alignment explanation
Indices: 42838911--42839518 Score: 732
Period size: 239 Copynumber: 2.6 Consensus size: 230
42838901 CCAAAGTAAC
* * *
42838911 AAATAAAAAATGAACCCCATTATTATAAATCAAGTTATTAAATATTTCAAACAAATCTTGATATT
1 AAATAAAAAATGAACCTCATTATTATAAATCAAATTATTAAATATTTCAAACAAATCTTGAAATT
* * * * * *
42838976 CGAAACTTCCTATTATCTAATAAAAAACCTAAAATTTCTAATAATAAGCCAAAATCGCCTATAT-
66 TGAAACTTCCCATTATCCAAT-AAAAACCTAAGATTTCTAATAATAAACCAAAACCG-C-ATATC
* **** *
42839040 GATTAATTACAAATACTTTTTGACAAGTATTTACTGTTGGGAGTCATGTGAACCAAAAACCTATT
128 GATTAATTACAAATACTTTTTGACAAGCATTTACCACCGGGAGTCATGTGAACCAAAAACCTATC
* * * * * *
42839105 AATAAATAAGAATTCATTTCAGTAAAAAACTTATTAAC
193 AATAAATAAGAATACATTCCAATAAAAAACTAATAAAA
* * **
42839143 AAATAAAAACTGAACCTCAATATTATAAATCAAATTATTAAATATTTTGAACAAATCTTGAAATT
1 AAATAAAAAATGAACCTCATTATTATAAATCAAATTATTAAATATTTCAAACAAATCTTGAAATT
* * *
42839208 TGAAACTTCCCAGTATCCAATAAAAACTTAAGATTTCTAATAATAAACCGAAACCGCATATCGAA
66 TGAAACTTCCCATTATCCAATAAAAACCTAAGATTTCTAATAATAAACCAAAACCGCATATCG-A
* * * * *
42839273 TTAGTTACAAATACTTTTTGACAAGCGTTTGCCACCGTGAGTCTTGTGAACCAAAAACCTATCAA
130 TTAATTACAAATACTTTTTGACAAGCATTTACCACCGGGAGTCATGTGAACCAAAAACCTATCAA
42839338 TAAATAAGAATACATTCCAATAAAAACCTACTAACAAATAAAA
195 TAAATAAGAATACATTCCAATAAAAA---ACT----AATAAAA
* *
42839381 AAATAAAAAAATAAACCTCATTATTATGAATCAAATTATTAAATATTTCAAACAAATCTTGAAAT
1 AAAT-AAAAAATGAACCTCATTATTATAAATCAAATTATTAAATATTTCAAACAAATCTTGAAAT
* * * * *
42839446 TTAAAATTTCCCATTATCCAATAAAAACCTAAGATTCCTAATAATAACCCAAAACCGCCTATCTG
65 TTGAAACTTCCCATTATCCAATAAAAACCTAAGATTTCTAATAATAAACCAAAACCGCATATC-G
42839511 ATTAATTA
129 ATTAATTA
42839519 TATTTTTTTT
Statistics
Matches: 317, Mismatches: 48, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
229 4 0.01
230 2 0.01
231 108 0.34
232 75 0.24
234 3 0.01
238 8 0.03
239 116 0.37
240 1 0.00
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (230 bp):
AAATAAAAAATGAACCTCATTATTATAAATCAAATTATTAAATATTTCAAACAAATCTTGAAATT
TGAAACTTCCCATTATCCAATAAAAACCTAAGATTTCTAATAATAAACCAAAACCGCATATCGAT
TAATTACAAATACTTTTTGACAAGCATTTACCACCGGGAGTCATGTGAACCAAAAACCTATCAAT
AAATAAGAATACATTCCAATAAAAAACTAATAAAA
Found at i:42840291 original size:34 final size:35
Alignment explanation
Indices: 42840225--42840291 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
42840215 CAAACACTAG
*
42840225 AAAATATTTTCCAGTAAATTATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
42840260 AAAATATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
42840292 TATTTTAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:42844984 original size:51 final size:51
Alignment explanation
Indices: 42844907--42845016 Score: 132
Period size: 51 Copynumber: 2.2 Consensus size: 51
42844897 ATGCTACAGG
* * *
42844907 CTAAATTTGTTAAATTAAAATCAAATTAATA-GAATGTGTAAATGTTATGGA
1 CTAAATTTATTAAATTAAAATCAAATTAACACG-ATGTGTAAATCTTATGGA
* * * *
42844958 CTAAATTTATTAAATTAAAGTTAAATTGACACGATGTGTAAATCTTGTGGA
1 CTAAATTTATTAAATTAAAATCAAATTAACACGATGTGTAAATCTTATGGA
*
42845009 CTGAATTT
1 CTAAATTT
42845017 GTTATCATAC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
51 49 0.98
52 1 0.02
ACGTcount: A:0.41, C:0.06, G:0.15, T:0.38
Consensus pattern (51 bp):
CTAAATTTATTAAATTAAAATCAAATTAACACGATGTGTAAATCTTATGGA
Found at i:42848742 original size:21 final size:23
Alignment explanation
Indices: 42848706--42848748 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
42848696 TTTTGTTTTT
42848706 TTTTTATATATTTGAATGATTTC
1 TTTTTATATATTTGAATGATTTC
*
42848729 TTTTTAT-T-TTTGAATTATTT
1 TTTTTATATATTTGAATGATTT
42848749 TTGTATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.67
Consensus pattern (23 bp):
TTTTTATATATTTGAATGATTTC
Found at i:42852184 original size:11 final size:11
Alignment explanation
Indices: 42852151--42852198 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
42852141 TAACAACAAT
* *
42852151 AAAATAGTAAC
1 AAAATAATAGC
*
42852162 AATATAATAGC
1 AAAATAATAGC
*
42852173 AAAATGATAGC
1 AAAATAATAGC
*
42852184 AAAATAATAAC
1 AAAATAATAGC
42852195 AAAA
1 AAAA
42852199 CACAGCAGCA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (11 bp):
AAAATAATAGC
Found at i:42852250 original size:20 final size:20
Alignment explanation
Indices: 42852204--42852251 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
42852194 CAAAACACAG
42852204 CAGCAAAACAATAGAAACAA
1 CAGCAAAACAATAGAAACAA
* * *
42852224 CAACAAAACAGTGGAAACAA
1 CAGCAAAACAATAGAAACAA
*
42852244 TAGCAAAA
1 CAGCAAAA
42852252 TATAGCAGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.62, C:0.19, G:0.12, T:0.06
Consensus pattern (20 bp):
CAGCAAAACAATAGAAACAA
Found at i:42855778 original size:6 final size:6
Alignment explanation
Indices: 42855762--42855797 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
42855752 GTTAGACACA
42855762 ATTTATT ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
1 ATTT-TT ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
42855798 GTGATGGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:42858273 original size:60 final size:60
Alignment explanation
Indices: 42858200--42858333 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 60
42858190 TTAATATAAC
* * * *
42858200 ATTTTGTATCTAAACTTGACA-TTTTTTCTTAATTT-GATTACTAAACTTTTTTTGGGC-CTA
1 ATTTGGTACCTAAACTTGACATTTTTTTC-TAATTTAGA-AACTAAACTTTTTTTAGGCTC-A
* * *
42858260 ATTTGGTACCTAAACTTGACATTTTTTTCTATTTTAGAAACTAAGCTTTTTTTAGGTTCA
1 ATTTGGTACCTAAACTTGACATTTTTTTCTAATTTAGAAACTAAACTTTTTTTAGGCTCA
42858320 ATTTGGTACCTAAA
1 ATTTGGTACCTAAA
42858334 TTTATTAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
60 54 0.84
61 10 0.16
ACGTcount: A:0.27, C:0.13, G:0.11, T:0.49
Consensus pattern (60 bp):
ATTTGGTACCTAAACTTGACATTTTTTTCTAATTTAGAAACTAAACTTTTTTTAGGCTCA
Found at i:42858759 original size:31 final size:30
Alignment explanation
Indices: 42858724--42858850 Score: 94
Period size: 31 Copynumber: 4.2 Consensus size: 30
42858714 GATTAGGTAT
*
42858724 CAAATTAAGAAAAATAGTCAAGTTCATGTAC
1 CAAATTAAGAAAAATA-TCAAGTTCAAGTAC
* * *** ** *
42858755 CAAATT-GGACACCCAAAAAGTTTAAGTAC
1 CAAATTAAGAAAAATATCAAGTTCAAGTAC
* * * *
42858784 CAACTTAACAAAAAGTATCAAGTTTAGGTAC
1 CAAATTAAGAAAAA-TATCAAGTTCAAGTAC
*
42858815 CAAATTAAGAAAAAATGTCAAGTTCAAGTAC
1 CAAATTAAG-AAAAATATCAAGTTCAAGTAC
42858846 CAAAT
1 CAAAT
42858851 ATTATATTAA
Statistics
Matches: 69, Mismatches: 24, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
29 15 0.22
30 6 0.09
31 43 0.62
32 5 0.07
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.24
Consensus pattern (30 bp):
CAAATTAAGAAAAATATCAAGTTCAAGTAC
Found at i:42864206 original size:42 final size:42
Alignment explanation
Indices: 42864147--42864230 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
42864137 AACAGACGAG
42864147 GGATCAGATATCAGATCAGATATATATGACAAGCTCTACATT
1 GGATCAGATATCAGATCAGATATATATGACAAGCTCTACATT
42864189 GGATCAGATATCAGATCAGATATATATGACAAGCTCTACATT
1 GGATCAGATATCAGATCAGATATATATGACAAGCTCTACATT
42864231 CCTTATATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (42 bp):
GGATCAGATATCAGATCAGATATATATGACAAGCTCTACATT
Found at i:42865874 original size:175 final size:174
Alignment explanation
Indices: 42865572--42865973 Score: 628
Period size: 175 Copynumber: 2.3 Consensus size: 174
42865562 ACCTTGATTA
* * *
42865572 TTACCTGCATGCTGAA-GATGGTGGATCTCATAGTTGAACAGGTGGCAAAAGTGTTTCTCTTCCT
1 TTACCTGCATGCT-AAGGATGGTGGATCTCATAGTCGAACAGGAGGCATAAGTGTTTCTCTTCCT
* * * * *
42865636 ACTCTTGTCGGTCATGCCATAGGTGGCGGGATGACAACATTTATAGCATCCGACCTGATTCAGTA
65 ACCCTTGACGGTCATGCCATAGGTGGCGGGATGACAACATTGATAGCATCCAACCTAATTCAGTA
*
42865701 ACCTTAAGTGTAGTTTATCCTTTGAAATACCATGCTTGTCGGGTTC
130 ACCTTAAGTGTAGTTTATCCTTTGAAA-ACCATGCTTGTCGGCTTC
*
42865747 TTACCTGCATGCTAAGGATGGTGGATCTCATAGTCGAACAGGAGGCATAAGTGTTTCTCTTTCTA
1 TTACCTGCATGCTAAGGATGGTGGATCTCATAGTCGAACAGGAGGCATAAGTGTTTCTCTTCCTA
* *
42865812 CCCTTGACGGTTATGTCATAGGTGGCGGGATCG-CAACATTGATAGCATCCAACCTAATTCAGTA
66 CCCTTGACGGTCATGCCATAGGTGGCGGGAT-GACAACATTGATAGCATCCAACCTAATTCAGTA
* * *
42865876 ACCTTAAGTGTAGTTTATCCTTTGAAAACTATTCTTGTCGGCTTT
130 ACCTTAAGTGTAGTTTATCCTTTGAAAACCATGCTTGTCGGCTTC
42865921 TTACCTGCATGCTAAGGATGGTGGATCTCATAGTCGAACAGGAGGCATAAGTG
1 TTACCTGCATGCTAAGGATGGTGGATCTCATAGTCGAACAGGAGGCATAAGTG
42865974 GGGGGGGGGG
Statistics
Matches: 210, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
174 69 0.33
175 140 0.67
176 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (174 bp):
TTACCTGCATGCTAAGGATGGTGGATCTCATAGTCGAACAGGAGGCATAAGTGTTTCTCTTCCTA
CCCTTGACGGTCATGCCATAGGTGGCGGGATGACAACATTGATAGCATCCAACCTAATTCAGTAA
CCTTAAGTGTAGTTTATCCTTTGAAAACCATGCTTGTCGGCTTC
Found at i:42871913 original size:45 final size:45
Alignment explanation
Indices: 42871849--42871940 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
42871839 AATATAAACA
* * *
42871849 AGAGCTAACTCTTTAAAAGGAATGGTATGCCTTGTAAGCAATCAC
1 AGAGCTAACTCTGTAAAAGGAATGGCATACCTTGTAAGCAATCAC
42871894 AGAGCTAACTCTGTAAAAGGAATGGCATACCTTGTAAGCAATCAC
1 AGAGCTAACTCTGTAAAAGGAATGGCATACCTTGTAAGCAATCAC
42871939 AG
1 AG
42871941 TTCTCGGATT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (45 bp):
AGAGCTAACTCTGTAAAAGGAATGGCATACCTTGTAAGCAATCAC
Found at i:42877218 original size:8 final size:8
Alignment explanation
Indices: 42877205--42877229 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
42877195 CCTATAACCA
42877205 AAACCCAT
1 AAACCCAT
42877213 AAACCCAT
1 AAACCCAT
42877221 AAACCCAT
1 AAACCCAT
42877229 A
1 A
42877230 CCATGCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.36, G:0.00, T:0.12
Consensus pattern (8 bp):
AAACCCAT
Found at i:42884375 original size:13 final size:13
Alignment explanation
Indices: 42884357--42884381 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42884347 CGATGGTCCA
42884357 AGGTCCAAGGTTG
1 AGGTCCAAGGTTG
42884370 AGGTCCAAGGTT
1 AGGTCCAAGGTT
42884382 TAAGATTTAA
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:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (13 bp):
AGGTCCAAGGTTG
Found at i:42884697 original size:28 final size:28
Alignment explanation
Indices: 42884635--42884715 Score: 67
Period size: 28 Copynumber: 2.9 Consensus size: 28
42884625 ATCGAGAGTC
* ** * *
42884635 TAGGGTGTAAGGTTTGGGGTCCATAGTT
1 TAGGGTTTAAGGTTTAAGGTCCAGAATT
*
42884663 T-GAGGTTTAAGGTTTATGGTCCAGAATT
1 TAG-GGTTTAAGGTTTAAGGTCCAGAATT
*
42884691 TAGGGTTTGAA-GTTTAAGATCCAGA
1 TAGGGTTT-AAGGTTTAAGGTCCAGA
42884716 TTAAAAAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
27 1 0.02
28 39 0.91
29 3 0.07
ACGTcount: A:0.25, C:0.07, G:0.32, T:0.36
Consensus pattern (28 bp):
TAGGGTTTAAGGTTTAAGGTCCAGAATT
Found at i:42886867 original size:2 final size:2
Alignment explanation
Indices: 42886860--42886906 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
42886850 AATCACGCTT
42886860 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42886902 TA TA T
1 TA TA T
42886907 GTAATTAGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42887958 original size:2 final size:2
Alignment explanation
Indices: 42887951--42887985 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
42887941 ATAAATCTGA
42887951 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42887986 AATAGTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42894391 original size:21 final size:21
Alignment explanation
Indices: 42894365--42894404 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
42894355 NNNNNNNNAT
42894365 TCTATTTCTTTCTTG-ATTTGA
1 TCTA-TTCTTTCTTGTATTTGA
*
42894386 TCTATTCTTTTTTGTATTT
1 TCTATTCTTTCTTGTATTT
42894405 CTCTTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.12, C:0.12, G:0.07, T:0.68
Consensus pattern (21 bp):
TCTATTCTTTCTTGTATTTGA
Found at i:42898745 original size:13 final size:13
Alignment explanation
Indices: 42898710--42898747 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
42898700 GATATATTTG
*
42898710 TAATTTGAAAGCT
1 TAATTTGAAAACT
42898723 TAAGTTTGAAAACT
1 TAA-TTTGAAAACT
42898737 TAATTTGAAAA
1 TAATTTGAAAA
42898748 TTTGGAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:42898814 original size:12 final size:11
Alignment explanation
Indices: 42898786--42898818 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
42898776 AACTTAAAAG
42898786 TTTTGAGAAAC
1 TTTTGAGAAAC
42898797 -TTTGAGAAAC
1 TTTTGAGAAAC
42898807 TTTTTGAGAAAC
1 -TTTTGAGAAAC
42898819 AACTCAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.50
12 10 0.50
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (11 bp):
TTTTGAGAAAC
Found at i:42915881 original size:2 final size:2
Alignment explanation
Indices: 42915874--42915922 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
42915864 CCCTTAGAGA
*
42915874 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT 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
*
42915916 TT AT AT A
1 AT AT AT A
42915923 AAAAGCTCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:42920387 original size:26 final size:27
Alignment explanation
Indices: 42920358--42920416 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 27
42920348 AAGCCTATTT
* *
42920358 AGGCGTAAC-AACCTTATACTAATTGA
1 AGGCATAACAAACCTCATACTAATTGA
42920384 AGGCATAACGAAACCTCATACTAATTGA
1 AGGCATAAC-AAACCTCATACTAATTGA
42920412 AGGCA
1 AGGCA
42920417 ATAAGTTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 8 0.28
28 21 0.72
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (27 bp):
AGGCATAACAAACCTCATACTAATTGA
Found at i:42921901 original size:18 final size:19
Alignment explanation
Indices: 42921868--42921924 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
42921858 ATTAAATTTG
*
42921868 ATTAAGATAATATATTTTT-
1 ATTAAAATAAT-TATTTTTA
*
42921887 ATTAAAATAGTTATTTTTA
1 ATTAAAATAATTATTTTTA
42921906 ATTAAAATAATTCATTTTT
1 ATTAAAATAATT-ATTTTT
42921925 TAGCATTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.21
19 20 0.61
20 6 0.18
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (19 bp):
ATTAAAATAATTATTTTTA
Found at i:42940297 original size:2 final size:2
Alignment explanation
Indices: 42940290--42940532 Score: 256
Period size: 2 Copynumber: 121.0 Consensus size: 2
42940280 ATCTTTGATT
*
42940290 AG AG AG AG AG AG AG AG GG 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
* * * *
42940332 GG AG AG AG A- AG -G AA AG AG AG AG AG AG AG AG AG AG GG GG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * *
42940372 AG AG AG GG AG AG GG AG AG GG AG AG GG AG AG GG 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
* * * * *
42940414 TG AG AG AG AG AG GG AG GG AG AG AG AG AG GG AG AG AG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
** **
42940456 AG AG AG AG AG AG AG AG AG AG ATG TTT TT AG AG AG AG ATG AG AG
1 AG AG AG AG AG AG AG AG AG AG A-G -AG AG AG AG AG AG A-G AG AG
* *
42940499 AG AG AG AG GG AG AG AG AG AG AT AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
42940533 TAAAGTTCAA
Statistics
Matches: 200, Mismatches: 36, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
1 2 0.01
2 195 0.98
3 3 0.01
ACGTcount: A:0.43, C:0.00, G:0.53, T:0.04
Consensus pattern (2 bp):
AG
Found at i:42941852 original size:17 final size:18
Alignment explanation
Indices: 42941815--42941852 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
42941805 AATAAAAATT
*
42941815 TATTTTCTAATGAAATAA
1 TATTTTATAATGAAATAA
*
42941833 TATTTTATAAT-AATTAA
1 TATTTTATAATGAAATAA
42941850 TAT
1 TAT
42941853 CATATAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
TATTTTATAATGAAATAA
Found at i:42942094 original size:18 final size:20
Alignment explanation
Indices: 42942048--42942095 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
42942038 ATAATATTGG
*
42942048 AAATTATAATATTTGATATTA
1 AAATTTTAATATTTGATA-TA
*
42942069 ATATTTTAATATTT-ATA-A
1 AAATTTTAATATTTGATATA
42942087 AAATTTTAA
1 AAATTTTAA
42942096 AATATTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 9 0.38
20 3 0.12
21 12 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
AAATTTTAATATTTGATATA
Found at i:42942362 original size:17 final size:18
Alignment explanation
Indices: 42942340--42942374 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42942330 AACCCGCCGT
42942340 AATTT-GTAATTTTTATA
1 AATTTGGTAATTTTTATA
*
42942357 AATTTGGTGATTTTTATA
1 AATTTGGTAATTTTTATA
42942375 CTAAATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (18 bp):
AATTTGGTAATTTTTATA
Found at i:42952057 original size:30 final size:29
Alignment explanation
Indices: 42952023--42952081 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
42952013 AAATTGAGTC
* *
42952023 AAATCAAAATATTATGTATAAAATTACACA
1 AAATCAAAAT-TTATATACAAAATTACACA
*
42952053 AAATCAAAATTTATATACAAAGTTACACA
1 AAATCAAAATTTATATACAAAATTACACA
42952082 TCAGACCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.29
Consensus pattern (29 bp):
AAATCAAAATTTATATACAAAATTACACA
Found at i:42958569 original size:3 final size:3
Alignment explanation
Indices: 42958561--42958627 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
42958551 TCAGATAGTC
42958561 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
42958609 CCT CCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT C
42958628 TTGGATTCTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CCT
Found at i:42960200 original size:14 final size:14
Alignment explanation
Indices: 42960181--42960220 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42960171 TTGATTGTCA
42960181 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
42960195 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
42960209 GGAAAATGTTTT
1 GTAAAATGTTTT
42960221 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:42960229 original size:20 final size:20
Alignment explanation
Indices: 42960204--42960243 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
42960194 CGTAAAATGA
*
42960204 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
42960224 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
42960244 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:42960233 original size:34 final size:35
Alignment explanation
Indices: 42960189--42960255 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
42960179 CAGTAAAATG
*
42960189 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
42960223 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
42960256 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:42960259 original size:14 final size:15
Alignment explanation
Indices: 42960183--42960259 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
42960173 GATTGTCAGT
* *
42960183 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
42960197 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
42960211 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
42960231 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
42960246 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
42960260 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:42966501 original size:20 final size:21
Alignment explanation
Indices: 42966459--42966526 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
42966449 ATTAATTATT
42966459 TTTTAAAAA-A-AT-TTAAAA
1 TTTTAAAAATATATATTAAAA
*
42966477 TTTTTAAAAATATATA-TATAA
1 -TTTTAAAAATATATATTAAAA
* * *
42966498 TTTTTAAAATTTTTATTAAAA
1 TTTTAAAAATATATATTAAAA
42966519 TTTTAAAA
1 TTTTAAAA
42966527 TTTAATTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 9 0.23
20 13 0.33
21 17 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTAAAAATATATATTAAAA
Found at i:42966520 original size:21 final size:21
Alignment explanation
Indices: 42966471--42966535 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
42966461 TTAAAAAAAT
*
42966471 TTAAAATTTTTAAAA-ATATA
1 TTAAAATTTTTAAAATTTATA
* *
42966491 TATATAATTTTTAAAATTTTTA
1 T-TAAAATTTTTAAAATTTATA
42966513 TTAAAA-TTTTAAAATTTA-A
1 TTAAAATTTTTAAAATTTATA
42966532 TTAA
1 TTAA
42966536 TTCCTAACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
19 5 0.13
20 12 0.32
21 17 0.45
22 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAAAATTTTTAAAATTTATA
Found at i:42977286 original size:41 final size:39
Alignment explanation
Indices: 42977229--42977348 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 39
42977219 TGATCGAATG
*
42977229 TAATTCAGACTTATTGTCTAGCAGGCTAGATGCCGGTGATA
1 TAATTCAGAC-TATTGTCTAGCAGGCTA-ATGCCGGTGAAA
*
42977270 TAATTCAGACTCATTGTCTAGCAGGCTTAATGCCAGTGAAA
1 TAATTCAGACT-ATTGTCTAGCAGGC-TAATGCCGGTGAAA
* * * *
42977311 TTATTCGGACTATAAGTCTAGCAGGCTAAAAGCCGGTG
1 TAATTCAGACTAT-TGTCTAGCAGGCT-AATGCCGGTG
42977349 TATTAAATCA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
40 4 0.06
41 62 0.91
42 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.29
Consensus pattern (39 bp):
TAATTCAGACTATTGTCTAGCAGGCTAATGCCGGTGAAA
Found at i:42979806 original size:86 final size:85
Alignment explanation
Indices: 42979706--42979862 Score: 212
Period size: 86 Copynumber: 1.8 Consensus size: 85
42979696 TTCCGATATG
* * *
42979706 TGATTTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCAAT-TTTAGATTTACGTGTAAGGCCA
1 TGATTTCGTGTAAGACC-CTGTCTGAGACAG-TGGCATCAATATTT-GATTT-CATGTAAGACCA
42979768 TGTCTGGGACATTAGCATCGTATA
62 TGTCTGGGACATTAGCATCGTATA
* *
42979792 TGATTTCGTGTAAGACCCTGTCTGAGACAGTGTCATCGATATTTGATTTCATGTAAGACCATGTC
1 TGATTTCGTGTAAGACCCTGTCTGAGACAGTGGCATCAATATTTGATTTCATGTAAGACCATGTC
42979857 TGGGAC
66 TGGGAC
42979863 GTTGGCATTG
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
85 21 0.33
86 38 0.60
87 4 0.06
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (85 bp):
TGATTTCGTGTAAGACCCTGTCTGAGACAGTGGCATCAATATTTGATTTCATGTAAGACCATGTC
TGGGACATTAGCATCGTATA
Found at i:42979847 original size:43 final size:42
Alignment explanation
Indices: 42979699--42979862 Score: 172
Period size: 43 Copynumber: 3.8 Consensus size: 42
42979689 CATAGGATTC
* *
42979699 CGATATGTGATTTCGTGTAAGACCACGTCTGGGAC-GTTGGCAT
1 CGATATTTGATTTCGTGTAAGACCATGTCTGGGACAG-T-GCAT
* * *
42979742 CAAT-TTTAGATTTACGTGTAAGGCCATGTCTGGGACATTAGCAT
1 CGATATTT-GATTT-CGTGTAAGACCATGTCTGGGACAGT-GCAT
* * *
42979786 CG-TATATGATTTCGTGTAAGACCCTGTCTGAGACAGTGTCAT
1 CGATATTTGATTTCGTGTAAGACCATGTCTGGGACAGTG-CAT
*
42979828 CGATATTTGATTTCATGTAAGACCATGTCTGGGAC
1 CGATATTTGATTTCGTGTAAGACCATGTCTGGGAC
42979863 GTTGGCATTG
Statistics
Matches: 99, Mismatches: 16, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
41 1 0.01
42 28 0.28
43 42 0.42
44 28 0.28
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (42 bp):
CGATATTTGATTTCGTGTAAGACCATGTCTGGGACAGTGCAT
Found at i:42979885 original size:86 final size:86
Alignment explanation
Indices: 42979708--42979885 Score: 184
Period size: 86 Copynumber: 2.1 Consensus size: 86
42979698 CCGATATGTG
* * *
42979708 ATTTCGTGTAAGACCACGTCTGGGACGTTGGCATCAATTTTAGATTTACGTGTAAGGCCATGTCT
1 ATTTCGTGTAAGACCACGTCTGAGACGTTGGCATCAATTTTAGATTTACATGTAAGACCATGTCT
* * *
42979773 GGGACATTAGCATCGTATATG
66 GGGACATTAGCATCGAAAATC
* *
42979794 ATTTCGTGTAAGACC-CTGTCTGAGACAG-TGTCATCGATATTT-GATTT-CATGTAAGACCATG
1 ATTTCGTGTAAGACCAC-GTCTGAGAC-GTTGGCATCAAT-TTTAGATTTACATGTAAGACCATG
* * *
42979855 TCTGGGACGTTGGCATTGAACAATC
63 TCTGGGACATTAGCATCGAA-AATC
*
42979880 TTTTCG
1 ATTTCG
42979886 AGCTATCTAA
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
85 29 0.38
86 43 0.57
87 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (86 bp):
ATTTCGTGTAAGACCACGTCTGAGACGTTGGCATCAATTTTAGATTTACATGTAAGACCATGTCT
GGGACATTAGCATCGAAAATC
Found at i:42982395 original size:11 final size:10
Alignment explanation
Indices: 42982374--42982467 Score: 57
Period size: 11 Copynumber: 8.5 Consensus size: 10
42982364 TTTAAAATTA
42982374 AAAAGTATTTT
1 AAAA-TATTTT
42982385 AACAATATTTT
1 AA-AATATTTT
42982396 AAAAT-TATTT
1 AAAATAT-TTT
42982406 AAAATATTTAAATT
1 AAAATA-TT---TT
*
42982420 AAAA-ATTTAA
1 AAAATATTT-T
42982430 AAAAGTATTTT
1 AAAA-TATTTT
42982441 AAAAATATTTT
1 -AAAATATTTT
*
42982452 AAAATTTATTT
1 AAAATAT-TTT
42982463 AAAAT
1 AAAAT
42982468 TAAAAAATAT
Statistics
Matches: 68, Mismatches: 3, Indels: 24
0.72 0.03 0.25
Matches are distributed among these distances:
9 2 0.03
10 21 0.31
11 25 0.37
12 13 0.19
13 1 0.01
14 6 0.09
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (10 bp):
AAAATATTTT
Found at i:42982404 original size:22 final size:21
Alignment explanation
Indices: 42982371--42982466 Score: 77
Period size: 22 Copynumber: 4.3 Consensus size: 21
42982361 AATTTTAAAA
42982371 TTAAAAAGTATTTTAACAATATT
1 TTAAAAA-TATTTTAA-AATATT
*
42982394 TTAAAATTA-TTTAAAATATT
1 TTAAAAATATTTTAAAATATT
* * *
42982414 TAAATTAAAAATTTAAAAAAGTATT
1 TTAA--AAATATTT-TAAAA-TATT
*
42982439 TTAAAAATATTTTAAAATTTAT
1 TTAAAAATATTTTAAAATAT-T
42982461 TTAAAA
1 TTAAAA
42982467 TTAAAAAATA
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
20 9 0.16
21 7 0.12
22 16 0.28
23 15 0.26
24 4 0.07
25 7 0.12
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (21 bp):
TTAAAAATATTTTAAAATATT
Found at i:42982414 original size:56 final size:57
Alignment explanation
Indices: 42982357--42982467 Score: 174
Period size: 56 Copynumber: 2.0 Consensus size: 57
42982347 CCATTTTTAT
* *
42982357 TTTAAATTTTAAAA-TT-AAAAAGTATTTTAACAATATTTTAAAA-TTATTTAAAATA
1 TTTAAA-TTAAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTTATTTAAAATA
42982412 TTTAAATTAAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTTATTTAAAAT
1 TTTAAATTAAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTTATTTAAAAT
42982468 TAAAAAATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
54 6 0.12
55 8 0.16
56 26 0.51
57 11 0.22
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (57 bp):
TTTAAATTAAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTTATTTAAAATA
Found at i:42987234 original size:6 final size:6
Alignment explanation
Indices: 42987223--42987266 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
42987213 ATATAAAACA
42987223 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AA
1 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AA
42987267 CGTGAGCTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (6 bp):
AATGAT
Found at i:42994599 original size:30 final size:30
Alignment explanation
Indices: 42994565--42994624 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
42994555 CTGCTTGGAG
*
42994565 GAAAAATTGTCATTAGATATACATAAGCTT
1 GAAAAATTGTCAATAGATATACATAAGCTT
42994595 GAAAAATTGTCAATAGATATACATAAGCTT
1 GAAAAATTGTCAATAGATATACATAAGCTT
42994625 CATCCTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (30 bp):
GAAAAATTGTCAATAGATATACATAAGCTT
Found at i:42996413 original size:3 final size:3
Alignment explanation
Indices: 42996405--42996454 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
42996395 CACCTACAGA
*
42996405 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42996453 AA
1 AA
42996455 AACAGCACAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:43007869 original size:6 final size:6
Alignment explanation
Indices: 43007858--43007891 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
43007848 AAAGAGGGAT
43007858 TAAATC TAAATC TAAATC TAAATC TAAAT- TAAAT
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAAT
43007892 AATAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:43007897 original size:18 final size:18
Alignment explanation
Indices: 43007858--43007897 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
43007848 AAAGAGGGAT
*
43007858 TAAATCTAAATCTAAATC
1 TAAATCTAAATCTAAATA
43007876 TAAATCTAAAT-TAAATAA
1 TAAATCTAAATCTAAAT-A
43007894 TAAA
1 TAAA
43007898 AATTAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAATCTAAATCTAAATA
Found at i:43007911 original size:25 final size:25
Alignment explanation
Indices: 43007887--43007939 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
43007877 AAATCTAAAT
*
43007887 TAAATAATA-AAAATTAAATAAAAA
1 TAAATAAAACAAAATTAAATAAAAA
* **
43007911 TAAGTAAAACAAAATTAAATCTAAA
1 TAAATAAAACAAAATTAAATAAAAA
43007936 TAAA
1 TAAA
43007940 ACAAATAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (25 bp):
TAAATAAAACAAAATTAAATAAAAA
Found at i:43007929 original size:21 final size:21
Alignment explanation
Indices: 43007905--43007944 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
43007895 AAAAATTAAA
*
43007905 TAAAAATAAGTAAAACAAAAT
1 TAAAAATAAATAAAACAAAAT
**
43007926 TAAATCTAAATAAAACAAA
1 TAAAAATAAATAAAACAAA
43007945 TAAATGAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (21 bp):
TAAAAATAAATAAAACAAAAT
Found at i:43008206 original size:14 final size:14
Alignment explanation
Indices: 43008166--43008231 Score: 52
Period size: 14 Copynumber: 4.9 Consensus size: 14
43008156 TCAAAATCTA
43008166 AAATAAATAAT-AT-
1 AAATAAA-AATAATG
43008179 AAATTAAATAATAATG
1 AAA-TAAA-AATAATG
43008195 AAATAAAAATAA-G
1 AAATAAAAATAATG
* *
43008208 TAA-AACAA-AATG
1 AAATAAAAATAATG
43008220 AAATAAAAATAA
1 AAATAAAAATAA
43008232 GTAAAACAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
11 2 0.05
12 7 0.16
13 10 0.23
14 15 0.35
15 6 0.14
16 3 0.07
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.23
Consensus pattern (14 bp):
AAATAAAAATAATG
Found at i:43008256 original size:25 final size:25
Alignment explanation
Indices: 43008191--43008248 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
43008181 ATTAAATAAT
43008191 AATGAAATAAAAATAAGTAAAACAA
1 AATGAAATAAAAATAAGTAAAACAA
43008216 AATGAAATAAAAATAAGTAAAACAA
1 AATGAAATAAAAATAAGTAAAACAA
*
43008241 AATTAAAT
1 AATGAAAT
43008249 CTAAATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (25 bp):
AATGAAATAAAAATAAGTAAAACAA
Found at i:43011076 original size:16 final size:16
Alignment explanation
Indices: 43011051--43011085 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
43011041 TTTCTATTGA
*
43011051 TCTGTTCTTCCAATTT
1 TCTGTCCTTCCAATTT
*
43011067 TCTGTCCTTCCTATTT
1 TCTGTCCTTCCAATTT
43011083 TCT
1 TCT
43011086 TTTCACTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.09, C:0.29, G:0.06, T:0.57
Consensus pattern (16 bp):
TCTGTCCTTCCAATTT
Found at i:43013866 original size:6 final size:6
Alignment explanation
Indices: 43013855--43013879 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43013845 TATTGATAAA
43013855 CACACG CACACG CACACG CACACG C
1 CACACG CACACG CACACG CACACG C
43013880 TTCTTACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
CACACG
Found at i:43023056 original size:22 final size:22
Alignment explanation
Indices: 43023016--43023066 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
43023006 TTAGCATCTG
*
43023016 GTGCTCTCTGCTTGACACTTCA
1 GTGCTCTCTGCTTGACACTACA
*
43023038 GTGCTCTCTG-TTTAGCACTACA
1 GTGCTCTCTGCTTGA-CACTACA
*
43023060 ATGCTCT
1 GTGCTCT
43023067 TTGGTGTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37
Consensus pattern (22 bp):
GTGCTCTCTGCTTGACACTACA
Found at i:43024103 original size:15 final size:16
Alignment explanation
Indices: 43024080--43024135 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
43024070 TTTTTATGTT
*
43024080 TTATATATATTATTCTA
1 TTATATATA-TATTATA
*
43024097 TTATATAATATAATATA
1 TTATAT-ATATATTATA
*
43024114 TTATAT-TGTATTATA
1 TTATATATATATTATA
43024129 TTATATA
1 TTATATA
43024136 AATTAAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
15 13 0.39
17 17 0.52
18 3 0.09
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
TTATATATATATTATA
Found at i:43024115 original size:17 final size:17
Alignment explanation
Indices: 43024095--43024136 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
43024085 TATATTATTC
43024095 TATTATATAATATAATA
1 TATTATATAATATAATA
* *
43024112 TATTATAT--TGTATTA
1 TATTATATAATATAATA
43024127 TATTATATAA
1 TATTATATAA
43024137 ATTAAATAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 13 0.62
17 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TATTATATAATATAATA
Found at i:43024120 original size:27 final size:29
Alignment explanation
Indices: 43024081--43024136 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
43024071 TTTTATGTTT
43024081 TATATATATTATTCTATTATATAATATAA
1 TATATATATTATTCTATTATATAATATAA
* *
43024110 TATAT-TA-TATTGTATTATATTATATAA
1 TATATATATTATTCTATTATATAATATAA
43024137 ATTAAATAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 18 0.72
28 2 0.08
29 5 0.20
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (29 bp):
TATATATATTATTCTATTATATAATATAA
Found at i:43030025 original size:20 final size:20
Alignment explanation
Indices: 43029991--43030032 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
43029981 AACTATTTAA
** *
43029991 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
43030011 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
43030031 AT
1 AT
43030033 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:43035100 original size:20 final size:20
Alignment explanation
Indices: 43035066--43035107 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
43035056 AACTATTTAA
** *
43035066 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
43035086 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
43035106 AT
1 AT
43035108 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:43037815 original size:14 final size:15
Alignment explanation
Indices: 43037787--43037817 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
43037777 CGAATATCAA
43037787 ATTTCTATGTATTTC
1 ATTTCTATGTATTTC
43037802 ATTTCTAT-TATTTC
1 ATTTCTATGTATTTC
43037816 AT
1 AT
43037818 CTACATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.61
Consensus pattern (15 bp):
ATTTCTATGTATTTC
Found at i:43039154 original size:31 final size:31
Alignment explanation
Indices: 43039116--43039174 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
43039106 CATTTGAGTT
*
43039116 AATTAAGTTATTCGGATAAACTCGAATAAAA
1 AATTAAGTTATTCAGATAAACTCGAATAAAA
* * *
43039147 AATTAAGTTTTTCAGCTTAACTCGAATA
1 AATTAAGTTATTCAGATAAACTCGAATA
43039175 TGAATTACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (31 bp):
AATTAAGTTATTCAGATAAACTCGAATAAAA
Found at i:43040276 original size:2 final size:2
Alignment explanation
Indices: 43040271--43040295 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43040261 TCTTAAAAAA
43040271 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
43040296 AAAGATGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:43043400 original size:15 final size:13
Alignment explanation
Indices: 43043358--43043391 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
43043348 AGCTTTTTTT
*
43043358 TATTTTTAATTAA
1 TATTTATAATTAA
43043371 TATTTATAATTAA
1 TATTTATAATTAA
*
43043384 TATATATA
1 TATTTATA
43043392 TTATTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTATAATTAA
Found at i:43043483 original size:16 final size:17
Alignment explanation
Indices: 43043462--43043496 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
43043452 TATCAACTAA
43043462 TTCTTTAGATAT-ATAT
1 TTCTTTAGATATAATAT
*
43043478 TTCTTTATATATAATAT
1 TTCTTTAGATATAATAT
43043495 TT
1 TT
43043497 ATATGTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (17 bp):
TTCTTTAGATATAATAT
Found at i:43061830 original size:33 final size:33
Alignment explanation
Indices: 43061783--43061852 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
43061773 CCATAAAGAG
* **
43061783 TCATACAAAGTCATTTTGGTTACTTTAGAAAAA
1 TCATACAAAATCATTAGGGTTACTTTAGAAAAA
*
43061816 TCATACAAAATCATTAGGGTTACTTTAGATAAA
1 TCATACAAAATCATTAGGGTTACTTTAGAAAAA
43061849 -CATA
1 TCATA
43061853 AACATTTGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 4 0.12
33 29 0.88
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.34
Consensus pattern (33 bp):
TCATACAAAATCATTAGGGTTACTTTAGAAAAA
Found at i:43071232 original size:7 final size:7
Alignment explanation
Indices: 43071220--43071248 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
43071210 TACCCTACTA
43071220 CTTAATG
1 CTTAATG
43071227 CTTAATG
1 CTTAATG
43071234 CTTAATG
1 CTTAATG
43071241 CTTAATG
1 CTTAATG
43071248 C
1 C
43071249 CATTCCCTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (7 bp):
CTTAATG
Found at i:43082454 original size:13 final size:13
Alignment explanation
Indices: 43082436--43082499 Score: 92
Period size: 13 Copynumber: 4.9 Consensus size: 13
43082426 AGTTCTTCAT
43082436 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
43082449 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
43082462 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
* *
43082475 TGCTTTTCAGAAG
1 TGCTTTTGAAAAG
43082488 TGCTTTTGAAAA
1 TGCTTTTGAAAA
43082500 ATTTGGTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:43095492 original size:32 final size:32
Alignment explanation
Indices: 43095441--43095520 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
43095431 ATCATACATT
* * * *
43095441 TTAAATAAACATAATTATTCAAGTAATATATC
1 TTAAATAAATATAACTATTCAAATAACATATC
* *
43095473 TTAAATAGATATAACTATTCAAATAACATTTC
1 TTAAATAAATATAACTATTCAAATAACATATC
*
43095505 ATAAATAAATATAACT
1 TTAAATAAATATAACT
43095521 CCAAGTAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (32 bp):
TTAAATAAATATAACTATTCAAATAACATATC
Found at i:43097801 original size:43 final size:42
Alignment explanation
Indices: 43097747--43097871 Score: 126
Period size: 42 Copynumber: 3.0 Consensus size: 42
43097737 TGTATCATCA
43097747 GATAAAGCGAAGTAAATACACTAGCACACATAA-TGCATCATTG
1 GATAAAGCGAAGTAAATACACTA--ACACATAAGTGCATCATTG
* * * *
43097790 GATAAATCGAAGTAAATATACTAACACATAAGTGTATCATTC
1 GATAAAGCGAAGTAAATACACTAACACATAAGTGCATCATTG
* * * * * * *
43097832 GATGAACCAAAGCAAATATATTAGCACATAAGTGCATCAT
1 GATAAAGCGAAGTAAATACACTAACACATAAGTGCATCAT
43097872 CAGATAAACT
Statistics
Matches: 70, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 8 0.11
42 41 0.59
43 21 0.30
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (42 bp):
GATAAAGCGAAGTAAATACACTAACACATAAGTGCATCATTG
Found at i:43099217 original size:6 final size:6
Alignment explanation
Indices: 43099206--43099234 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
43099196 AAAATTAAAT
43099206 TTACAG TTACAG TTACAG TTACAG TTACA
1 TTACAG TTACAG TTACAG TTACAG TTACA
43099235 TATTATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (6 bp):
TTACAG
Found at i:43109233 original size:14 final size:13
Alignment explanation
Indices: 43109210--43109253 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
43109200 TTTTAGTTTT
43109210 TTTTTTATTTTAGA
1 TTTTTTATTTTA-A
*
43109224 TTTTTAATTTTAA
1 TTTTTTATTTTAA
43109237 TTTTTTATTTT-A
1 TTTTTTATTTTAA
43109249 TTTTT
1 TTTTT
43109254 AAGACGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 6 0.21
13 11 0.39
14 11 0.39
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTTTATTTTAA
Found at i:43115210 original size:21 final size:19
Alignment explanation
Indices: 43115182--43115221 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
43115172 GGCAAGCACT
43115182 AATATTAAAATAAAAATAAA
1 AATATTAAAAT-AAAATAAA
*
43115202 AATACTTAAAATTAAATAAA
1 AATA-TTAAAATAAAATAAA
43115222 TAAAGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
AATATTAAAATAAAATAAA
Found at i:43115737 original size:19 final size:20
Alignment explanation
Indices: 43115715--43115754 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
43115705 TAGTTTAAAG
43115715 TTTA-TTTTATTTTTAAATA
1 TTTATTTTTATTTTTAAATA
43115734 TTTATTTTTTATTTTTAAATA
1 TTTA-TTTTTATTTTTAAATA
43115755 AAATATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
21 15 0.79
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTATTTTTATTTTTAAATA
Found at i:43117912 original size:14 final size:15
Alignment explanation
Indices: 43117890--43117966 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
43117880 CAATCAAACA
43117890 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
43117904 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
43117919 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
43117939 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
43117953 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
43117967 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:43117931 original size:20 final size:20
Alignment explanation
Indices: 43117906--43117945 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43117896 AATATTTTCC
*
43117906 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
43117926 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
43117946 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:43117951 original size:34 final size:35
Alignment explanation
Indices: 43117894--43117960 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
43117884 CAAACACCAG
*
43117894 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
43117929 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
43117961 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:43117967 original size:14 final size:14
Alignment explanation
Indices: 43117929--43117968 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
43117919 ACAGAAAAGT
*
43117929 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
43117943 AAATCATTTTACGG
1 AAAACATTTTACAG
43117957 AAAACATTTTAC
1 AAAACATTTTAC
43117969 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:43120688 original size:2 final size:2
Alignment explanation
Indices: 43120681--43120716 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
43120671 ATTGAAACCA
43120681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43120717 GGGAAAGCAC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43135423 original size:15 final size:16
Alignment explanation
Indices: 43135401--43135431 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43135391 AATTTTTATT
*
43135401 AAATTTTTTTAAAATA
1 AAATTTTTATAAAATA
43135417 AAATTTTTATAAAAT
1 AAATTTTTATAAAAT
43135432 TTGATTGCAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTTTTATAAAATA
Found at i:43136286 original size:11 final size:11
Alignment explanation
Indices: 43136272--43136301 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
43136262 TTTATTTTTT
43136272 TATTTTTAAAA
1 TATTTTTAAAA
43136283 TATTTTTAAAA
1 TATTTTTAAAA
43136294 TACTTTTT
1 TA-TTTTT
43136302 TTATTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:43138577 original size:33 final size:32
Alignment explanation
Indices: 43138521--43138681 Score: 97
Period size: 33 Copynumber: 4.8 Consensus size: 32
43138511 ACATTTGTAG
* * * *
43138521 TGTCATAACCTAGTTATGATCTTATCATCAAAA
1 TGTCATAGCCCAGCTATGGTCTTA-CATCAAAA
*
43138554 TGTCATAGCCCAGCTATGGTCTTACATATAAACA
1 TGTCATAGCCCAGCTATGGTCTTACAT-CAAA-A
* * * * * * * *
43138588 CTGCCATGGTCCAACCATGGTCTTACGTTCATAG
1 -TGTCATAGCCCAGCTATGGTCTTAC-ATCAAAA
* ** * *
43138622 TGTCATAACCCAATTATGGTCTTATTATCAGAA
1 TGTCATAGCCCAGCTATGGTCTTA-CATCAAAA
*
43138655 TATCATAGCCCAGCTATGGTCTTACAT
1 TGTCATAGCCCAGCTATGGTCTTACAT
43138682 ATATTCATAG
Statistics
Matches: 94, Mismatches: 29, Indels: 11
0.70 0.22 0.08
Matches are distributed among these distances:
32 5 0.05
33 65 0.69
34 1 0.01
35 22 0.23
36 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (32 bp):
TGTCATAGCCCAGCTATGGTCTTACATCAAAA
Found at i:43138611 original size:101 final size:101
Alignment explanation
Indices: 43138501--43138684 Score: 287
Period size: 101 Copynumber: 1.8 Consensus size: 101
43138491 CATGGCCCTG
** * * *
43138501 CCATGGTCTTACATTTGTAGTGTCATAACCTAGTTATGATCTTATCATCAAAATGTCATAGCCCA
1 CCATGGTCTTACATTCATAGTGTCATAACCCAATTATGATCTTATCATCAAAATATCATAGCCCA
43138566 GCTATGGTCTTACATATAAACACTGCCATGGTCCAA
66 GCTATGGTCTTACATATAAACACTGCCATGGTCCAA
* * * *
43138602 CCATGGTCTTACGTTCATAGTGTCATAACCCAATTATGGTCTTATTATCAGAATATCATAGCCCA
1 CCATGGTCTTACATTCATAGTGTCATAACCCAATTATGATCTTATCATCAAAATATCATAGCCCA
43138667 GCTATGGTCTTACATATA
66 GCTATGGTCTTACATATA
43138685 TTCATAGTGC
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 74 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (101 bp):
CCATGGTCTTACATTCATAGTGTCATAACCCAATTATGATCTTATCATCAAAATATCATAGCCCA
GCTATGGTCTTACATATAAACACTGCCATGGTCCAA
Found at i:43147443 original size:17 final size:17
Alignment explanation
Indices: 43147414--43147462 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
43147404 TAAATTTTAC
43147414 TAAAAATTTTTAAAATAT
1 TAAAAA-TTTTAAAATAT
* * *
43147432 TAGAAATTTTAACATTT
1 TAAAAATTTTAAAATAT
43147449 TAAAAATTTCTAAA
1 TAAAAATTT-TAAA
43147463 TCACCATCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAAAATTTTAAAATAT
Found at i:43148543 original size:2 final size:2
Alignment explanation
Indices: 43148538--43148578 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
43148528 TGACTTCTTT
43148538 TA TA TA TA 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 TA TA TA TA T
43148579 TTAGACTTCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43150832 original size:101 final size:102
Alignment explanation
Indices: 43150611--43150843 Score: 290
Period size: 103 Copynumber: 2.3 Consensus size: 102
43150601 TTTACATTTG
* * * *
43150611 TAGTGTCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCTCAGCTAAGGTCTTACATAT
1 TAGTGACATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTAAGGTATTACATAT
* *
43150676 GAACGTAAGACCATGGTCCAACCATGGTCTTACGTTCA
66 AAACG-AAGACCATGGTCCAACCATGGTCCTACGTTCA
* * * * *
43150714 TAGTGATATAACTCAGTTATAGTCTTATCATCAGAATGTCATAGCCCAACTATGGTATTACATAT
1 TAGTGACATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTAAGGTATTACATAT
* * *
43150779 AAAC-ACTG-TCGTGGTCCAACCATGGTCCTACGTTCA
66 AAACGA-AGACCATGGTCCAACCATGGTCCTACGTTCA
**
43150815 TAGTTCCATAACCCAGTTATGGTCTTATC
1 TAGTGACATAACCCAGTTATGGTCTTATC
43150844 CGTCAATTCA
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
101 50 0.45
102 1 0.01
103 59 0.54
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (102 bp):
TAGTGACATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAACTAAGGTATTACATAT
AAACGAAGACCATGGTCCAACCATGGTCCTACGTTCA
Found at i:43154341 original size:17 final size:17
Alignment explanation
Indices: 43154319--43154352 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
43154309 TCCAAGTACC
*
43154319 AAAATTAAATGAAAAAA
1 AAAATTAAAAGAAAAAA
43154336 AAAATTAAAAGAAAAAA
1 AAAATTAAAAGAAAAAA
43154353 GCAATGATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAATTAAAAGAAAAAA
Found at i:43170840 original size:24 final size:26
Alignment explanation
Indices: 43170798--43170848 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
43170788 AAGCGTTAAA
* *
43170798 ATTAAGTTATATATTTTTATCATTTT
1 ATTAAGTTATATATATTTATAATTTT
43170824 ATTAA-TT-TATATATTTATAATTTT
1 ATTAAGTTATATATATTTATAATTTT
43170848 A
1 A
43170849 AAAAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 2 0.09
26 5 0.22
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
ATTAAGTTATATATATTTATAATTTT
Found at i:43171494 original size:6 final size:6
Alignment explanation
Indices: 43171483--43171507 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43171473 AACAAAATAA
43171483 ACTCTC ACTCTC ACTCTC ACTCTC A
1 ACTCTC ACTCTC ACTCTC ACTCTC A
43171508 TACAAAAACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.48, G:0.00, T:0.32
Consensus pattern (6 bp):
ACTCTC
Found at i:43183421 original size:15 final size:15
Alignment explanation
Indices: 43183398--43183427 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43183388 TATGAAATGA
43183398 TTTAATCTTCTTCTT
1 TTTAATCTTCTTCTT
*
43183413 TTTAGTCTTCTTCTT
1 TTTAATCTTCTTCTT
43183428 CCCTCTTTCA
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:0.10, C:0.20, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTAATCTTCTTCTT
Found at i:43195281 original size:31 final size:30
Alignment explanation
Indices: 43195246--43195305 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
43195236 GGAGGTGGGA
*
43195246 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
43195277 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
43195306 TAAAAAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:43195534 original size:9 final size:9
Alignment explanation
Indices: 43195520--43195556 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
43195510 TATAGTTTGA
43195520 TATTCGAAT
1 TATTCGAAT
43195529 TATTCGAAT
1 TATTCGAAT
*
43195538 TATTCGAGT
1 TATTCGAAT
43195547 TATTCGAAT
1 TATTCGAAT
43195556 T
1 T
43195557 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:43195628 original size:9 final size:9
Alignment explanation
Indices: 43195611--43195641 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
43195601 TCGAGTTGAT
43195611 TCGAATAAC
1 TCGAATAAC
*
43195620 TCGATTAAC
1 TCGAATAAC
43195629 TCGAATAAC
1 TCGAATAAC
43195638 TCGA
1 TCGA
43195642 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:43195953 original size:8 final size:8
Alignment explanation
Indices: 43195940--43195973 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
43195930 TTTCTATAAC
43195940 ACATTATT
1 ACATTATT
43195948 ACATTATT
1 ACATTATT
43195956 ACATTATT
1 ACATTATT
43195964 ACATTATT
1 ACATTATT
43195972 AC
1 AC
43195974 CCTTTCAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (8 bp):
ACATTATT
Found at i:43196283 original size:2 final size:2
Alignment explanation
Indices: 43196276--43196303 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43196266 TGAAAGCTTT
43196276 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43196304 GATCCAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43197221 original size:40 final size:42
Alignment explanation
Indices: 43197173--43197250 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 42
43197163 ATTTAAAAAT
*
43197173 TATTTTAAAAATAAATAAA-AAA-CTAAAAATAT-TTTTAAAG
1 TATTTTAAAAATAAA-AAATAAATATAAAAATATATTTTAAAG
*
43197213 TATTTTAAAATTAAAAAATAAATATAAAAATATATTTT
1 TATTTTAAAAATAAAAAATAAATATAAAAATATATTTT
43197251 TATTAAATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 3 0.09
40 17 0.52
41 9 0.27
42 4 0.12
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (42 bp):
TATTTTAAAAATAAAAAATAAATATAAAAATATATTTTAAAG
Found at i:43202939 original size:16 final size:17
Alignment explanation
Indices: 43202909--43202942 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
43202899 CAATGAATAA
43202909 AATAATAATAAAATTTT
1 AATAATAATAAAATTTT
*
43202926 AATAA-AATATAATTTT
1 AATAATAATAAAATTTT
43202942 A
1 A
43202943 TATTTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATAATAATAAAATTTT
Found at i:43203265 original size:19 final size:19
Alignment explanation
Indices: 43203218--43203274 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
43203208 TTTAAATTTT
* * *
43203218 TTGTAGGAATATTATAATTT
1 TTGTATGAATATTGTAA-TG
*
43203238 TTTTATGAATATTGTAATG
1 TTGTATGAATATTGTAATG
43203257 TTGTATGAATATTGTAAT
1 TTGTATGAATATTGTAAT
43203275 TATTTTATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (19 bp):
TTGTATGAATATTGTAATG
Found at i:43203360 original size:41 final size:40
Alignment explanation
Indices: 43203194--43203453 Score: 170
Period size: 41 Copynumber: 6.0 Consensus size: 40
43203184 TAGATTAGAA
* *
43203194 TTTTGTATGAATATTTTAAATTTTTTGTAGGAATATTATAATT
1 TTTTGTATGAATATTGT-AA--TTTTGTATGAATATTATAATT
* *
43203237 TTTT-TATGAATATTGTAATGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTATAATT
* * * *
43203276 ATTTTATAATTAA-ATTTGT-ATTTATAGTTTTG--GATTAGTAATT
1 -TTTTGT-ATGAATA-TTGTAATTT-T-G-TATGAATATTA-TAATT
43203319 TTTTGTATGAATATTGTAATTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTGTAATTTTGTATGAATATTAT-AATT
**
43203360 TTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTGCAATTT
1 TTTTGTATGAATATTG------TA-A-TTTTGTATGAATATTATAA-TT
* *
43203409 TTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAA---TTTTGTATGAATATTATAATT
43203452 TT
1 TT
43203454 GTAATTTTGT
Statistics
Matches: 175, Mismatches: 18, Indels: 48
0.73 0.07 0.20
Matches are distributed among these distances:
39 21 0.12
40 6 0.03
41 40 0.23
42 34 0.19
43 15 0.09
44 21 0.12
47 2 0.01
48 3 0.02
49 33 0.19
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (40 bp):
TTTTGTATGAATATTGTAATTTTGTATGAATATTATAATT
Found at i:43203381 original size:49 final size:49
Alignment explanation
Indices: 43203328--43203424 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
43203318 TTTTTGTATG
* *
43203328 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATATTATAATTTTGTATGAATATTACAAATTTTTTGTATGAATATTGT
* * *
43203377 AATATTATAGTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTG
1 AATATTATAATTTTGTATGAATATTACAAATTTTTTGTATGAATATTG
43203425 CAATTTTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (49 bp):
AATATTATAATTTTGTATGAATATTACAAATTTTTTGTATGAATATTGT
Found at i:43203462 original size:49 final size:50
Alignment explanation
Indices: 43203409--43203565 Score: 246
Period size: 49 Copynumber: 3.2 Consensus size: 50
43203399 ATTGCAATTT
* *
43203409 TTTTGTATGAATATTGCAATTT-TTTTGTATGAATATTGTAATTTTGTAA
1 TTTTGTATGAATATTGTAATTTATTTTGTATGAATATTGTAATATTGTAA
* * * *
43203458 TTTTGTATGAATATTATATTTTATTTTGAATGAATATTGTAATATTATAA
1 TTTTGTATGAATATTGTAATTTATTTTGTATGAATATTGTAATATTGTAA
43203508 TTTTGTATGAATATTGTAATTT-TTTTGTATGAATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATTTATTTTGTATGAATATTGTAATATTGTAA
43203557 TTTTGTATG
1 TTTTGTATG
43203566 CGGCTCCACA
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
49 53 0.55
50 44 0.45
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.55
Consensus pattern (50 bp):
TTTTGTATGAATATTGTAATTTATTTTGTATGAATATTGTAATATTGTAA
Found at i:43203522 original size:19 final size:19
Alignment explanation
Indices: 43203498--43203555 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 19
43203488 TGAATATTGT
*
43203498 AATATTATAATTTTGTATG
1 AATATTGTAATTTTGTATG
43203517 AATATTGTAATTTTTTTGTATG
1 AATATTGTAA---TTTTGTATG
*
43203539 AATATTGTAATATTGTA
1 AATATTGTAATTTTGTA
43203556 ATTTTGTATG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 15 0.44
22 19 0.56
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (19 bp):
AATATTGTAATTTTGTATG
Found at i:43203549 original size:22 final size:22
Alignment explanation
Indices: 43203194--43203549 Score: 272
Period size: 22 Copynumber: 15.9 Consensus size: 22
43203184 TAGATTAGAA
* *
43203194 TTTTGTATGAATATTTTAAATT
1 TTTTGTATGAATATTGTAATTT
* *
43203216 TTTTGTAGGAATATTATAA-TT
1 TTTTGTATGAATATTGTAATTT
43203237 TTTT-TATGAATATTGTAA---
1 TTTTGTATGAATATTGTAATTT
* *
43203255 TGTTGTATGAATATTGTAATTA
1 TTTTGTATGAATATTGTAATTT
* *
43203277 TTTTATAATTAA-ATTTGT-ATTT
1 TTTTGT-ATGAATA-TTGTAATTT
* * *
43203299 ATAGTT-T-TGGAT-TAGTAA-TT
1 -T-TTTGTATGAATATTGTAATTT
43203319 TTTTGTATGAATATTGTAA---
1 TTTTGTATGAATATTGTAATTT
* *
43203338 TTTTGTATGAATATTATAAATT
1 TTTTGTATGAATATTGTAATTT
43203360 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-ATT-T
*
43203385 AGTTTTGTATGAATATTGCAATTT
1 --TTTTGTATGAATATTGTAATTT
*
43203409 TTTTGTATGAATATTGCAATTT
1 TTTTGTATGAATATTGTAATTT
43203431 TTTTGTATGAATATTGTAATTTTGT
1 TTTTGTATGAATATTGTAA--TT-T
* *
43203456 AATTTTGTATGAATATTATATTTT
1 --TTTTGTATGAATATTGTAATTT
*
43203480 ATTTTGAATGAATATTGTAATATTAT
1 -TTTTGTATGAATATTGT-A-ATT-T
43203506 AATTTTGTATGAATATTGTAATTT
1 --TTTTGTATGAATATTGTAATTT
43203530 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
43203550 ATTGTAATTT
Statistics
Matches: 277, Mismatches: 27, Indels: 60
0.76 0.07 0.16
Matches are distributed among these distances:
18 5 0.02
19 34 0.12
20 21 0.08
21 14 0.05
22 101 0.36
23 27 0.10
24 10 0.04
25 12 0.04
26 3 0.01
27 50 0.18
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.55
Consensus pattern (22 bp):
TTTTGTATGAATATTGTAATTT
Found at i:43203795 original size:27 final size:27
Alignment explanation
Indices: 43203764--43203842 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
43203754 ATATTTTGTT
43203764 CACCATTGGCGCCTCCCAAATAGGCAC
1 CACCATTGGCGCCTCCCAAATAGGCAC
43203791 CACCATTGGCGCCTCCCAAATAGGCAC
1 CACCATTGGCGCCTCCCAAATAGGCAC
* *
43203818 CACCATTGGCGCCTTCCAGATAGGC
1 CACCATTGGCGCCTCCCAAATAGGC
43203843 GCCAATACTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.24, C:0.39, G:0.20, T:0.16
Consensus pattern (27 bp):
CACCATTGGCGCCTCCCAAATAGGCAC
Found at i:43204880 original size:16 final size:16
Alignment explanation
Indices: 43204859--43204900 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
43204849 TTCGCTGTAT
43204859 TGGAATAGAGACGTAA
1 TGGAATAGAGACGTAA
**
43204875 TGGAATAGAGGTGTAA
1 TGGAATAGAGACGTAA
*
43204891 TGAAATAGAG
1 TGGAATAGAG
43204901 GTGTAATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.33, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGACGTAA
Found at i:43204901 original size:16 final size:16
Alignment explanation
Indices: 43204871--43204907 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
43204861 GAATAGAGAC
*
43204871 GTAATGGAATAGAGGT
1 GTAATGAAATAGAGGT
43204887 GTAATGAAATAGAGGT
1 GTAATGAAATAGAGGT
43204903 GTAAT
1 GTAAT
43204908 AGTAAATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.32, T:0.27
Consensus pattern (16 bp):
GTAATGAAATAGAGGT
Found at i:43205158 original size:16 final size:16
Alignment explanation
Indices: 43205121--43205162 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
43205111 TTAATCATAT
*
43205121 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
43205137 TT-AAATATATTATAA
1 TTAAAATATATTATAA
43205152 TTAAAATATAT
1 TTAAAATATAT
43205163 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:43205169 original size:14 final size:15
Alignment explanation
Indices: 43205130--43205171 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
43205120 TTTAAACATA
*
43205130 ATTATTATTAAATAT
1 ATTATAATTAAATAT
43205145 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
43205159 A-TATAATTTAATA
1 ATTATAATTAAATA
43205172 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:43205499 original size:16 final size:17
Alignment explanation
Indices: 43205473--43205510 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
43205463 AGTAAATGAT
43205473 ATATAAGATAAATTAAC
1 ATATAAGATAAATTAAC
*
43205490 ATATAA-ATAATTTAAC
1 ATATAAGATAAATTAAC
*
43205506 TTATA
1 ATATA
43205511 TAATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (17 bp):
ATATAAGATAAATTAAC
Found at i:43208687 original size:6 final size:6
Alignment explanation
Indices: 43208668--43208707 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
43208658 CAGAGAAGAG
*
43208668 AAAAGC AAAA-C AAAATC AAAATC AAAATC AAAATC AAAAT
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT
43208708 TGATTTTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.70, C:0.15, G:0.03, T:0.12
Consensus pattern (6 bp):
AAAATC
Found at i:43208791 original size:14 final size:14
Alignment explanation
Indices: 43208772--43208799 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
43208762 AGCAGAAATC
43208772 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
43208786 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
43208800 GAAATGTGAG
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:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:43208797 original size:19 final size:18
Alignment explanation
Indices: 43208775--43208819 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
43208765 AGAAATCTGG
43208775 AGAAAAGAAAATG-GAGAAA
1 AGAAAAGAAAATGTGAG--A
43208794 AGAAAAG-AAATGTGAGA
1 AGAAAAGAAAATGTGAGA
43208811 AGAAAAGAA
1 AGAAAAGAA
43208820 GCGTACCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (18 bp):
AGAAAAGAAAATGTGAGA
Found at i:43213470 original size:27 final size:27
Alignment explanation
Indices: 43213440--43213502 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
43213430 CAAGCCTTAT
* *
43213440 TCCAGGCTCTACAACTC-TGAGTTTTTC
1 TCCAGGCACTACAAC-CATGAGCTTTTC
43213467 TCCAGGCACTACAACCATGAGCTTTTC
1 TCCAGGCACTACAACCATGAGCTTTTC
43213494 TCCAGGCAC
1 TCCAGGCAC
43213503 CACAGCTGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 1 0.03
27 32 0.97
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.29
Consensus pattern (27 bp):
TCCAGGCACTACAACCATGAGCTTTTC
Found at i:43214772 original size:24 final size:24
Alignment explanation
Indices: 43214738--43214784 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
43214728 TGCAGAATTT
*
43214738 GACCTTGTTTCGAGTATTTGAGTA
1 GACCTTATTTCGAGTATTTGAGTA
43214762 GACCTTATTTCGAGTATTTGAGT
1 GACCTTATTTCGAGTATTTGAGT
43214785 GGCATGTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (24 bp):
GACCTTATTTCGAGTATTTGAGTA
Found at i:43218823 original size:6 final size:6
Alignment explanation
Indices: 43218812--43218847 Score: 63
Period size: 6 Copynumber: 5.8 Consensus size: 6
43218802 AAGATATTAT
43218812 AAAATA AAAATA AAAATA AAAATA AAAATA AGAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAATA A-AAAT
43218848 TCTATTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:43221645 original size:3 final size:3
Alignment explanation
Indices: 43221637--43221672 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
43221627 TTTTCATTGG
43221637 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
43221673 GTATTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:43226155 original size:23 final size:23
Alignment explanation
Indices: 43226104--43226160 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
43226094 AGCTGCTCAA
* *
43226104 ATGTTATATATCTGATTTTAAAT
1 ATGTTATATATCTGATTCTAAAC
* * *
43226127 AAGTTATATATTTTATTCTAAAC
1 ATGTTATATATCTGATTCTAAAC
43226150 ATGTTA-ATATC
1 ATGTTATATATC
43226161 CATTCAAATT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (23 bp):
ATGTTATATATCTGATTCTAAAC
Found at i:43230607 original size:18 final size:18
Alignment explanation
Indices: 43230584--43230626 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
43230574 ACGTGTACTT
43230584 TATTTTAATTTCTATGAA
1 TATTTTAATTTCTATGAA
* * *
43230602 TATTTTTATTTTTTTTGAA
1 TA-TTTTAATTTCTATGAA
43230621 TATTTT
1 TATTTT
43230627 TATAATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (18 bp):
TATTTTAATTTCTATGAA
Found at i:43230635 original size:19 final size:19
Alignment explanation
Indices: 43230598--43230635 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
43230588 TTAATTTCTA
**
43230598 TGAATATTTTTATTTTTTT
1 TGAATATTTTTATAATTTT
43230617 TGAATATTTTTATAATTTT
1 TGAATATTTTTATAATTTT
43230636 AAAATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (19 bp):
TGAATATTTTTATAATTTT
Found at i:43250364 original size:12 final size:12
Alignment explanation
Indices: 43250347--43250371 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43250337 CGATCAGTCC
43250347 ACGTGCAGTTTG
1 ACGTGCAGTTTG
43250359 ACGTGCAGTTTG
1 ACGTGCAGTTTG
43250371 A
1 A
43250372 AGCATAGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (12 bp):
ACGTGCAGTTTG
Done.