Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 123 of 182
Found at i:39426232 original size:10 final size:10
Alignment explanation
Indices: 39426212--39426252 Score: 66
Period size: 10 Copynumber: 4.1 Consensus size: 10
39426202 AACGATTTAT
39426212 TAAATAATTA
1 TAAATAATTA
39426222 TACAA-AATTA
1 TA-AATAATTA
39426232 TAAATAATTA
1 TAAATAATTA
39426242 TAAATAATTA
1 TAAATAATTA
39426252 T
1 T
39426253 TGAAATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 2 0.07
10 25 0.86
11 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (10 bp):
TAAATAATTA
Found at i:39426343 original size:28 final size:28
Alignment explanation
Indices: 39426310--39426367 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
39426300 ATATGTGTGC
*
39426310 AAATATT-TCAATTATAAGAAACTAATAA
1 AAATATTAACAATTATAAGAAA-TAATAA
*
39426338 AAATATTAAGAATTATAAGAAATAATAA
1 AAATATTAACAATTATAAGAAATAATAA
39426366 AA
1 AA
39426368 TAAGACTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.29
Consensus pattern (28 bp):
AAATATTAACAATTATAAGAAATAATAA
Found at i:39429399 original size:198 final size:198
Alignment explanation
Indices: 39428888--39429483 Score: 1086
Period size: 198 Copynumber: 3.0 Consensus size: 198
39428878 CCTGTTGCTA
* * *
39428888 TTGGAATAAAAGACTGCAATTTGTTTTCACAAGTTGCACCTTAGTGACAAAATCTTGTATCCATA
1 TTGGAATAAAAGGCTGCAATTTGTTTTCATAAGTTGCGCCTTAGTGACAAAATCTTGTATCCATA
* *
39428953 TTCCATCAAAATCGCAGTCTGCATACCTGATGATCTCTAACTGATAAGACCTCCGATATGTGAGC
66 TTCCATCAAAATCGGAGTCTGTATACCTGATGATCTCTAACTGATAAGACCTCCGATATGTGAGC
* *
39429018 ATGTAATATTTTTTCTTTGAAAATACCTTATAACCCTCTTAGATGCTATCCAATGGTCCAAACCA
131 ATGTAATCTTTGTTCTTTGAAAATACCTTATAACCCTCTTAGATGCTATCCAATGGTCCAAACCA
39429083 AGG
196 AGG
*
39429086 TTGGAATAAAAGGCTGC-ATTTGTTTTCATAAGTTGCGCCTTAGTGATAAAATCTTGTATCCATA
1 TTGGAATAAAAGGCTGCAATTTGTTTTCATAAGTTGCGCCTTAGTGACAAAATCTTGTATCCATA
* *
39429150 TTCCATCAAAATCGGAATCTGTATACCTGATGATCTCTAACTGATAAGACCTCTGATATGTGAGC
66 TTCCATCAAAATCGGAGTCTGTATACCTGATGATCTCTAACTGATAAGACCTCCGATATGTGAGC
39429215 ATGTAATCTTTGTTCTTTGAAAATACCTTATAACCCTCTTAGATGCTATCCAATGGTCCAAACCA
131 ATGTAATCTTTGTTCTTTGAAAATACCTTATAACCCTCTTAGATGCTATCCAATGGTCCAAACCA
39429280 AGG
196 AGG
39429283 TTGGAATAAAAGGCTGCAATTTGTTTTCATAAGTTGCGCCTTAGTGACAAAATCTTGTATCCATA
1 TTGGAATAAAAGGCTGCAATTTGTTTTCATAAGTTGCGCCTTAGTGACAAAATCTTGTATCCATA
*
39429348 TTCCATTAAAATCGGAGTCTGTATACCTGATGATCTCTAACTGATAAGACCTCCGATATGTGAGC
66 TTCCATCAAAATCGGAGTCTGTATACCTGATGATCTCTAACTGATAAGACCTCCGATATGTGAGC
39429413 ATGTAATCTTTGTTCTTTGAAAATACCTTATAACCCTCTTAGATGCTATCCAATGGTCCAAACCA
131 ATGTAATCTTTGTTCTTTGAAAATACCTTATAACCCTCTTAGATGCTATCCAATGGTCCAAACCA
39429478 AGG
196 AGG
39429481 TTG
1 TTG
39429484 CTTAAATATC
Statistics
Matches: 383, Mismatches: 14, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
197 188 0.49
198 195 0.51
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (198 bp):
TTGGAATAAAAGGCTGCAATTTGTTTTCATAAGTTGCGCCTTAGTGACAAAATCTTGTATCCATA
TTCCATCAAAATCGGAGTCTGTATACCTGATGATCTCTAACTGATAAGACCTCCGATATGTGAGC
ATGTAATCTTTGTTCTTTGAAAATACCTTATAACCCTCTTAGATGCTATCCAATGGTCCAAACCA
AGG
Found at i:39430062 original size:9 final size:9
Alignment explanation
Indices: 39430039--39430080 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
39430029 TTGTGTAAAA
*
39430039 AATTTAGAG
1 AATTTTGAG
39430048 AATTTTGA-
1 AATTTTGAG
39430056 AACTTTTGAG
1 AA-TTTTGAG
39430066 AATTTTGAG
1 AATTTTGAG
*
39430075 AGTTTT
1 AATTTT
39430081 AAAGAGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 2 0.07
9 25 0.86
10 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.45
Consensus pattern (9 bp):
AATTTTGAG
Found at i:39430096 original size:10 final size:10
Alignment explanation
Indices: 39430083--39430122 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
39430073 AGAGTTTTAA
39430083 AGAGAAATTG
1 AGAGAAATTG
*
39430093 AGAGAAATTT
1 AGAGAAATTG
*
39430103 ATAGAAAATTG
1 AGAG-AAATTG
39430114 AGAGAAATT
1 AGAGAAATT
39430123 TGAGTGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.25
Consensus pattern (10 bp):
AGAGAAATTG
Found at i:39430113 original size:21 final size:22
Alignment explanation
Indices: 39430078--39430123 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
39430068 TTTTGAGAGT
39430078 TTTAAAGAGAAATTGAGAGAAA
1 TTTAAAGAGAAATTGAGAGAAA
*
39430100 TTTATAGA-AAATTGAGAGAAA
1 TTTAAAGAGAAATTGAGAGAAA
39430121 TTT
1 TTT
39430124 GAGTGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (22 bp):
TTTAAAGAGAAATTGAGAGAAA
Found at i:39430119 original size:11 final size:11
Alignment explanation
Indices: 39430083--39430132 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
39430073 AGAGTTTTAA
39430083 AGAG-AAATTG
1 AGAGAAAATTG
*
39430093 AGAG-AAATTT
1 AGAGAAAATTG
*
39430103 ATAGAAAATTG
1 AGAGAAAATTG
*
39430114 AGAGAAATTTG
1 AGAGAAAATTG
*
39430125 AGTGAAAA
1 AGAGAAAA
39430133 ATAAAAGGGG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
10 12 0.38
11 20 0.62
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (11 bp):
AGAGAAAATTG
Found at i:39433087 original size:16 final size:16
Alignment explanation
Indices: 39433063--39433093 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39433053 ATTTATCTTG
39433063 TGGAACAATAAATCTA
1 TGGAACAATAAATCTA
*
39433079 TGGAGCAATAAATCT
1 TGGAACAATAAATCT
39433094 TTGAAGATTG
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:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (16 bp):
TGGAACAATAAATCTA
Found at i:39434150 original size:27 final size:27
Alignment explanation
Indices: 39434119--39434172 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
39434109 TTTCATTTTC
39434119 TTAGTGGTTATATATTTCTACTATTTG
1 TTAGTGGTTATATATTTCTACTATTTG
39434146 TTAGTGGTTATATATTTCTACTATTTG
1 TTAGTGGTTATATATTTCTACTATTTG
39434173 ATTTTGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.56
Consensus pattern (27 bp):
TTAGTGGTTATATATTTCTACTATTTG
Found at i:39436685 original size:29 final size:28
Alignment explanation
Indices: 39436653--39436976 Score: 170
Period size: 29 Copynumber: 11.2 Consensus size: 28
39436643 AAATGCTAAT
39436653 TTTTGGTGAAATCGAGGTTGAAAATGGAA
1 TTTTGGTGAAATCGAGGTT-AAAATGGAA
* * * *
39436682 TTTTAG-AAAATTTGAGGGTAAAATGGTAA
1 TTTTGGTGAAA-TCGAGGTTAAAATGG-AA
* * *
39436711 TTTTGGTGAAATTGGGGTTAAAAAAGGAA
1 TTTTGGTGAAATCGAGGTT-AAAATGGAA
*
39436740 TTTT-G-GAAAGTTC-AGGGGTAAAATGGTAA
1 TTTTGGTGAAA--TCGA-GGTTAAAATGG-AA
39436769 TTTTGGTGAAATCG-GGATTAAAAATGGAA
1 TTTTGGTGAAATCGAGG-TT-AAAATGGAA
* * *
39436798 TTTT-G-AAAAGTTCGGGGGTAAAATGGTAA
1 TTTTGGTGAAA--TCGAGGTTAAAATGG-AA
*
39436827 TTTTGGTGAAATCGAGATTAAAATGGAA
1 TTTTGGTGAAATCGAGGTTAAAATGGAA
*
39436855 TTTT-G-GAAAGTTCGAGGGTAAAATGGTAA
1 TTTTGGTGAAA--TCGAGGTTAAAATGG-AA
* *
39436884 TTTTTGGTAAAAT-TAGGGTTAAAAATGGAA
1 -TTTTGGTGAAATCGA-GGTT-AAAATGGAA
** *
39436914 TTTT-GT-AAAGTTTAGGGGTAAAATGGTAA
1 TTTTGGTGAAA-TCGA-GGTTAAAATGG-AA
* *
39436943 TTTTGGTGAAAT-AAGGTTAAAAATAGAA
1 TTTTGGTGAAATCGAGGTT-AAAATGGAA
39436971 TTTTGG
1 TTTTGG
39436977 AAAGTTCGGG
Statistics
Matches: 233, Mismatches: 29, Indels: 67
0.71 0.09 0.20
Matches are distributed among these distances:
26 4 0.02
27 11 0.05
28 67 0.29
29 97 0.42
30 33 0.14
31 18 0.08
32 3 0.01
ACGTcount: A:0.37, C:0.02, G:0.28, T:0.33
Consensus pattern (28 bp):
TTTTGGTGAAATCGAGGTTAAAATGGAA
Found at i:39436740 original size:58 final size:57
Alignment explanation
Indices: 39436642--39436975 Score: 381
Period size: 58 Copynumber: 5.8 Consensus size: 57
39436632 ACTCGGGGGC
* *
39436642 AAAATGCTAATTTTTGGTGAAATCGAGGTTGAAAATGGAATTTTAGAAAATTTGAGGGT
1 AAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAATGGAATTTT-GAAAATTTGAGGGT
* * * * * *
39436701 AAAATGGTAATTTTGGTGAAATTGGGGTTAAAAAAGGAATTTTGGAAAGTTCAGGGGT
1 AAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAATTTGA-GGGT
* *
39436759 AAAATGGTAATTTTGGTGAAATCG-GGATTAAAAATGGAATTTTGAAAAGTTCGGGGGT
1 AAAATGGTAATTTTGGTGAAATCGAGG-TTAAAAATGGAATTTTGAAAA-TTTGAGGGT
* * *
39436817 AAAATGGTAATTTTGGTGAAATCGAGATT-AAAATGGAATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTT-GAAAATTTGAGGGT
* * *
39436874 AAAATGGTAATTTTTGGTAAAAT-TAGGGTTAAAAATGGAATTTTGTAAAGTTT-AGGGGT
1 AAAATGGTAA-TTTTGGTGAAATCGA-GGTTAAAAATGGAATTTTG-AAAATTTGA-GGGT
* *
39436933 AAAATGGTAATTTTGGTGAAAT-AAGGTTAAAAATAGAATTTTG
1 AAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTG
39436976 GAAAGTTCGG
Statistics
Matches: 240, Mismatches: 25, Indels: 22
0.84 0.09 0.08
Matches are distributed among these distances:
57 59 0.25
58 137 0.57
59 44 0.18
ACGTcount: A:0.38, C:0.02, G:0.27, T:0.33
Consensus pattern (57 bp):
AAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAATTTGAGGGT
Found at i:39436796 original size:116 final size:114
Alignment explanation
Indices: 39436637--39436987 Score: 460
Period size: 116 Copynumber: 3.0 Consensus size: 114
39436627 TGGATACTCG
* * *
39436637 GGGGCAAAATGCTAATTTTTGGTGAAATCGAGGTTGAAAATGGAATTTTAGAAAATTTGAGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCG-GGTTAAAAATGGAATTTT-GAAAATTTGAGGGTA
*
39436702 AAATGGTAATTTTGGTGAAATTGGGGTTAAAAAAGGAATTTTGGAAAGTTC
64 AAATGGTAATTTTGGTGAAATTGAGGTTAAAAAAGGAATTTTGGAAAGTTC
* *
39436753 AGGGGTAAAATGGTAA-TTTTGGTGAAATCGGGATTAAAAATGGAATTTTGAAAAGTTCGGGGGT
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCGGG-TTAAAAATGGAATTTTGAAAA-TTTGAGGGT
* * *
39436817 AAAATGGTAATTTTGGTGAAATCGAGATT-AAAATGGAATTTTGGAAAGTTC
63 AAAATGGTAATTTTGGTGAAATTGAGGTTAAAAAAGGAATTTTGGAAAGTTC
* * *
39436868 GAGGGTAAAATGGTAATTTTTGGTAAAATTAGGGTTAAAAATGGAATTTTGTAAAGTTT-AGGGG
1 G-GGGTAAAATGGTAATTTTTGGTGAAA-TCGGGTTAAAAATGGAATTTTG-AAAATTTGA-GGG
*
39436932 TAAAATGGTAATTTTGGTGAAA-TAAGGTTAAAAATA-GAATTTTGGAAAGTTC
62 TAAAATGGTAATTTTGGTGAAATTGAGGTTAAAAA-AGGAATTTTGGAAAGTTC
39436984 GGGG
1 GGGG
39436988 ACCTATAAAC
Statistics
Matches: 207, Mismatches: 18, Indels: 20
0.84 0.07 0.08
Matches are distributed among these distances:
114 1 0.00
115 49 0.24
116 137 0.66
117 20 0.10
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.32
Consensus pattern (114 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGTTAAAAATGGAATTTTGAAAATTTGAGGGTAAA
ATGGTAATTTTGGTGAAATTGAGGTTAAAAAAGGAATTTTGGAAAGTTC
Found at i:39438845 original size:6 final size:6
Alignment explanation
Indices: 39438836--39438924 Score: 62
Period size: 6 Copynumber: 15.0 Consensus size: 6
39438826 TTAATATTAT
*
39438836 TTTAAA TTTAAA TTTAAA -ATAAA TTTAAATA TTTAAA TTTAAGA --TAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AA-A TTTAAA TTTAA-A TTTAAA
* * * *
39438884 TTTAAA TTCAAA -ATAAA TTTAAA ATT-AA TTTGAAC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
39438925 AAAAAAGAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 18
0.70 0.11 0.20
Matches are distributed among these distances:
4 1 0.02
5 14 0.22
6 36 0.56
7 9 0.14
8 4 0.06
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:39438856 original size:25 final size:25
Alignment explanation
Indices: 39438841--39438890 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
39438831 ATTATTTTAA
39438841 ATTTAAATTTAAAATAAATTTAAAT
1 ATTTAAATTTAAAATAAATTTAAAT
*
39438866 ATTTAAATTTAAGATAAATTTAAAT
1 ATTTAAATTTAAAATAAATTTAAAT
39438891 TCAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (25 bp):
ATTTAAATTTAAAATAAATTTAAAT
Found at i:39438858 original size:17 final size:17
Alignment explanation
Indices: 39438836--39438911 Score: 70
Period size: 17 Copynumber: 4.6 Consensus size: 17
39438826 TTAATATTAT
*
39438836 TTTAAATTTAAATTTAAA
1 TTTAAATTTAAA-ATAAA
*
39438854 -ATAAATTT-AAAT--A
1 TTTAAATTTAAAATAAA
*
39438867 TTTAAATTTAAGATAAA
1 TTTAAATTTAAAATAAA
*
39438884 TTTAAATTCAAAATAAA
1 TTTAAATTTAAAATAAA
*
39438901 TTTAAAATTAA
1 TTTAAATTTAA
39438912 TTTGAACTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
13 1 0.02
14 7 0.15
15 4 0.09
16 2 0.04
17 32 0.70
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:39438883 original size:11 final size:11
Alignment explanation
Indices: 39438844--39438889 Score: 56
Period size: 11 Copynumber: 3.9 Consensus size: 11
39438834 ATTTTAAATT
39438844 TAAATTTAAAA
1 TAAATTTAAAA
39438855 TAAATTTAAATA
1 TAAATTTAAA-A
*
39438867 TTTAAATTTAAGA
1 --TAAATTTAAAA
39438880 TAAATTTAAA
1 TAAATTTAAA
39438890 TTCAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 19 0.63
12 1 0.03
13 1 0.03
14 9 0.30
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:39438914 original size:11 final size:11
Alignment explanation
Indices: 39438819--39438914 Score: 54
Period size: 11 Copynumber: 8.7 Consensus size: 11
39438809 TTTTTTATTT
*
39438819 ATTAATTTTAAT
1 ATTAA-TTTAAA
*
39438831 ATTATTTTAAA
1 ATTAATTTAAA
*
39438842 TTTAAATTTAAA
1 ATT-AATTTAAA
*
39438854 ATAAATTT-AA
1 ATTAATTTAAA
39438864 A-T-ATTTAAA
1 ATTAATTTAAA
* **
39438873 TTTAAGATAAA
1 ATTAATTTAAA
* *
39438884 TTTAAATTCAAA
1 ATT-AATTTAAA
*
39438896 ATAAATTTAAA
1 ATTAATTTAAA
39438907 ATTAATTT
1 ATTAATTT
39438915 GAACTTTAAA
Statistics
Matches: 62, Mismatches: 17, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
8 4 0.06
9 2 0.03
10 4 0.06
11 34 0.55
12 18 0.29
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (11 bp):
ATTAATTTAAA
Found at i:39439504 original size:75 final size:76
Alignment explanation
Indices: 39439208--39439952 Score: 1129
Period size: 76 Copynumber: 9.8 Consensus size: 76
39439198 TGCTCTTCAG
* * * *
39439208 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
39439273 ACTTCAATTTC
66 ACTTCAATTTC
*
39439284 AGAGATAAAGACATGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
*
39439349 ACTTTAATTTC
66 ACTTCAATTTC
* ** *
39439360 GGAGATAAAGAGGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGA-CGTTGCTCT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATC-TTGCTCT
39439424 TACTTCAATTTC
65 TACTTCAATTTC
* *
39439436 AGAGGTAAAGACTTGTTATCCAACTGTACTTC-ATTTCAAGAGGATAGGAAATGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
39439500 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
39439511 AGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAATGATGTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
*
39439576 ACTTCAA-TTA
66 ACTTCAATTTC
* *
39439586 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATGTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
39439651 ACTTCAATTTC
66 ACTTCAATTTC
* *
39439662 AGAGATAAAGAC-TGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGAACTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
39439726 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
39439737 AGAGATAAAGACTTGATATCCATCTATACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
39439802 ACTTCAATTTC
66 ACTTCAATTTC
* * * * *
39439813 AGAGATAAAGACTTGATATCCATCTTTACTTCAATTTCAACAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
*
39439878 ACTTCAATTTTAG
66 ACTTCAA-TTT-C
* * *
39439891 AGAGATAATGACTTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGGAATGATCTTGCT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCT
39439953 GCGGTTTGAT
Statistics
Matches: 617, Mismatches: 45, Indels: 12
0.92 0.07 0.02
Matches are distributed among these distances:
75 210 0.34
76 348 0.56
77 3 0.00
78 56 0.09
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (76 bp):
AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTT
ACTTCAATTTC
Found at i:39439547 original size:151 final size:151
Alignment explanation
Indices: 39439208--39439952 Score: 1118
Period size: 151 Copynumber: 4.9 Consensus size: 151
39439198 TGCTCTTCAG
* * *
39439208 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAACGATCTTGCTCTT
1 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGA-CTTGCTCTT
*
39439273 ACTTCAATTTCAGAGATAAAGACATGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATG
65 ACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATG
*
39439338 ATCTTGCTCTTACTTTAATTTC
130 ATCTTGCTCTTACTTCAATTTC
* ** * * * *
39439360 GGAGATAAAGAGGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGACGTTGCTCTT
1 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGAC-TTGCTCTT
* *
39439425 ACTTCAATTTCAGAGGTAAAGACTTGTTATCCAACTGTACTTC-ATTTCAAGAGGATAGGAAATG
65 ACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATG
39439489 ATCTTGCTCTTACTTCAATTTC
130 ATCTTGCTCTTACTTCAATTTC
* * *
39439511 AGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAATGATGTTGCTCTT
1 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGA-CTTGCTCTT
* *
39439576 ACTTCAA-TTAAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATG
65 ACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATG
*
39439640 ATGTTGCTCTTACTTCAATTTC
130 ATCTTGCTCTTACTTCAATTTC
* *
39439662 AGAGATAAAGAC-TGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGAACTTGCTCTT
1 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAG-ACTTGCTCTT
* * * *
39439726 ACTTCAATTTCAGAGATAAAGACTTGATATCCATCTATACTTCAATTTCAAGAGGATAGGAAAAG
65 ACTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATG
39439791 ATCTTGCTCTTACTTCAATTTC
130 ATCTTGCTCTTACTTCAATTTC
* *
39439813 AGAGATAAAGACTTGATATCCATCTTTACTTCAATTTCAACAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGA-CTTGCTCTT
* * * *
39439878 ACTTCAATTTTAGAGAGATAATGACTTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGGAA
65 ACTTCAA-TTT-CAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAA
39439943 TGATCTTGCT
128 TGATCTTGCT
39439953 GCGGTTTGAT
Statistics
Matches: 537, Mismatches: 47, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
150 84 0.16
151 245 0.46
152 148 0.28
153 3 0.01
154 57 0.11
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (151 bp):
AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAAGACTTGCTCTTA
CTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGA
TCTTGCTCTTACTTCAATTTC
Found at i:39439867 original size:44 final size:45
Alignment explanation
Indices: 39439819--39439950 Score: 94
Period size: 38 Copynumber: 3.2 Consensus size: 45
39439809 TTTCAGAGAT
*
39439819 AAAGA-CTTGATATCCATCTTTACTTCAATTTCAACAGGATAGGA
1 AAAGATCTTGATATCCATCTTTACTTCAATTTCAAGAGGATAGGA
*
39439863 AAAGATCTTG-----C-TC-TTACTTCAATTT-TAGA-G--A-GA
1 AAAGATCTTGATATCCATCTTTACTTCAATTTCAAGAGGATAGGA
* * * *
39439896 TAATGA-CTTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGG
1 -AAAGATCTTGATATCCATCTTTACTTCAATTTCAAGAGGATAGGA
*
39439941 AATGATCTTG
1 AAAGATCTTG
39439951 CTGCGGTTTG
Statistics
Matches: 66, Mismatches: 7, Indels: 29
0.65 0.07 0.28
Matches are distributed among these distances:
33 6 0.09
34 5 0.08
36 1 0.02
37 2 0.03
38 13 0.20
39 3 0.05
40 12 0.18
41 3 0.05
42 1 0.02
44 11 0.17
45 9 0.14
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (45 bp):
AAAGATCTTGATATCCATCTTTACTTCAATTTCAAGAGGATAGGA
Found at i:39451063 original size:49 final size:49
Alignment explanation
Indices: 39450991--39451087 Score: 140
Period size: 49 Copynumber: 2.0 Consensus size: 49
39450981 ACTGCAAATT
* * * *
39450991 TGGTGGCTTGTCCACAACATTCTGTATCTGGTAGTATATTTGTATTATG
1 TGGTGGCTCGACCACAACATTCTGTATCTAGTAGTATATTTGCATTATG
* *
39451040 TGGTGGCTCGACCATAATATTCTGTATCTAGTAGTATATTTGCATTAT
1 TGGTGGCTCGACCACAACATTCTGTATCTAGTAGTATATTTGCATTAT
39451088 TTGTTGTGCC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (49 bp):
TGGTGGCTCGACCACAACATTCTGTATCTAGTAGTATATTTGCATTATG
Found at i:39467823 original size:19 final size:20
Alignment explanation
Indices: 39467796--39467836 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
39467786 AAGTTATTTG
*
39467796 TAAAAAATTTT-ATACGTTT
1 TAAAAAATTTTAATAAGTTT
*
39467815 TAAATAATTTTAATAAGTTT
1 TAAAAAATTTTAATAAGTTT
39467835 TA
1 TA
39467837 GTTTTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (20 bp):
TAAAAAATTTTAATAAGTTT
Found at i:39469783 original size:13 final size:13
Alignment explanation
Indices: 39469765--39469792 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
39469755 GTATAAGACT
39469765 ACAGTGATGGTGA
1 ACAGTGATGGTGA
39469778 ACAGTGATGGTGA
1 ACAGTGATGGTGA
39469791 AC
1 AC
39469793 TCCTAGTTGC
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:0.32, C:0.11, G:0.36, T:0.21
Consensus pattern (13 bp):
ACAGTGATGGTGA
Found at i:39477825 original size:30 final size:30
Alignment explanation
Indices: 39477750--39477856 Score: 171
Period size: 30 Copynumber: 3.6 Consensus size: 30
39477740 GGAGAATTTG
39477750 GGGTTAAAATGTAATTTTGGAAAAGTTTAA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAA
*
39477780 GGG-TGAAATGTAATTTTGGAAAAGTTTAA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAA
* *
39477809 GGGTTAAAATGCAATTTTAGAAAAGTTTAA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAA
*
39477839 GGGCTAAAATGTAATTTT
1 GGGTTAAAATGTAATTTT
39477857 TAAATAAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
29 28 0.40
30 42 0.60
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (30 bp):
GGGTTAAAATGTAATTTTGGAAAAGTTTAA
Found at i:39478562 original size:11 final size:11
Alignment explanation
Indices: 39478546--39478621 Score: 54
Period size: 11 Copynumber: 7.1 Consensus size: 11
39478536 TACCAAACCC
39478546 ATTTTAAATTT
1 ATTTTAAATTT
39478557 ATTTT-AA---
1 ATTTTAAATTT
*
39478564 AGTTTAAATTT
1 ATTTTAAATTT
39478575 ATTTTAAATTT
1 ATTTTAAATTT
*
39478586 AAATTT-AATTT
1 -ATTTTAAATTT
*
39478597 AAGTTTAAATTT
1 -ATTTTAAATTT
*
39478609 ATGTTCAAATTT
1 AT-TTTAAATTT
39478621 A
1 A
39478622 AAATTATTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
7 4 0.08
8 2 0.04
10 2 0.04
11 26 0.50
12 18 0.35
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:39478575 original size:6 final size:6
Alignment explanation
Indices: 39478548--39478623 Score: 68
Period size: 6 Copynumber: 13.0 Consensus size: 6
39478538 CCAAACCCAT
* *
39478548 TTTAAA TTT-AT TTTAAA GTTTAAA TTT-AT TTTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** *
39478594 TTTAAG TTTAAA TTTATG TTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
39478624 ATTATTATAA
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
5 13 0.24
6 35 0.65
7 6 0.11
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:39478587 original size:35 final size:36
Alignment explanation
Indices: 39478548--39478634 Score: 124
Period size: 35 Copynumber: 2.5 Consensus size: 36
39478538 CCAAACCCAT
*
39478548 TTTAAATTTATTTTAAAGTTTAAATTTAT-TTTAAA
1 TTTAAATTTATTTTAAAGTTTAAATTTATGTTCAAA
*
39478583 TTTAAATTTAATTT-AAGTTTAAATTTATGTTCAAA
1 TTTAAATTTATTTTAAAGTTTAAATTTATGTTCAAA
* *
39478618 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
39478635 TTCATACTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
34 14 0.31
35 29 0.64
36 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (36 bp):
TTTAAATTTATTTTAAAGTTTAAATTTATGTTCAAA
Found at i:39478588 original size:17 final size:17
Alignment explanation
Indices: 39478548--39478636 Score: 115
Period size: 17 Copynumber: 5.1 Consensus size: 17
39478538 CCAAACCCAT
39478548 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
39478565 GTTTAAATTTATTTTAAA
1 -TTTAAATTTATTTTAAA
* *
39478583 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
39478600 TTTAAATTTATGTTCAAA
1 TTTAAATTTAT-TTTAAA
* *
39478618 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
39478635 TT
1 TT
39478637 CATACTTAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
17 31 0.50
18 31 0.50
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:39485565 original size:18 final size:21
Alignment explanation
Indices: 39485542--39485584 Score: 65
Period size: 18 Copynumber: 2.2 Consensus size: 21
39485532 AAACCCAAAT
39485542 AAAAAGAG-AGAA-AA-AAGA
1 AAAAAGAGAAGAAGAAGAAGA
39485560 AAAAAGAGAAGAAGAAGAAGA
1 AAAAAGAGAAGAAGAAGAAGA
39485581 AAAA
1 AAAA
39485585 GTCAAGATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.36
19 4 0.18
20 2 0.09
21 8 0.36
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (21 bp):
AAAAAGAGAAGAAGAAGAAGA
Found at i:39486397 original size:6 final size:6
Alignment explanation
Indices: 39486386--39486420 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
39486376 TAAAAGAATA
39486386 AAAAAG AAAAAG AAAAAG AAAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG AAAA
39486421 GGAGAGGTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:39486408 original size:13 final size:13
Alignment explanation
Indices: 39486351--39486420 Score: 65
Period size: 13 Copynumber: 5.4 Consensus size: 13
39486341 TAGATTTGAT
39486351 GAAAAAAGAAAAA
1 GAAAAAAGAAAAA
* *
39486364 TAAATAAATAAATAA
1 GAAA-AAAGAAA-AA
*
39486379 -AAGAATA-AAAAA
1 GAA-AAAAGAAAAA
39486391 G-AAAAAGAAAAA
1 GAAAAAAGAAAAA
39486403 GAAAAAAGAAAAA
1 GAAAAAAGAAAAA
39486416 GAAAA
1 GAAAA
39486421 GGAGAGGTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
11 3 0.06
12 9 0.19
13 22 0.47
14 10 0.21
15 3 0.06
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.07
Consensus pattern (13 bp):
GAAAAAAGAAAAA
Found at i:39487656 original size:50 final size:49
Alignment explanation
Indices: 39487577--39487823 Score: 250
Period size: 50 Copynumber: 5.0 Consensus size: 49
39487567 CAGCACCATG
* *
39487577 AAACACGACGGGAAAGATCTAAAGTCGCAACGGCAGATCCAGTACCACGA
1 AAACACGACGGGAAAGATCT-AAGCCGCAACGGCGGATCCAGTACCACGA
* *
39487627 AAACACGACGGGAAAGATCTAAGGCCGCAACGGTGAATCCAGTACCACGA
1 AAACACGACGGGAAAGATCTAA-GCCGCAACGGCGGATCCAGTACCACGA
* * * * * *
39487677 AAACATGACGAGAAAGATTTAAGACCACAACGACGGATCCAGTACCGCGA
1 AAACACGACGGGAAAGATCTAAG-CCGCAACGGCGGATCCAGTACCACGA
* * * *
39487727 AGACAC-AAGGGAAAGATCTAAGCCG-AGACAGCGGATCCAGTACCATGA
1 AAACACGACGGGAAAGATCTAAGCCGCA-ACGGCGGATCCAGTACCACGA
* * * **
39487775 AGATATC-A-GGGAAAGATCTAAGCCGCGACGGCGGATTTAGTACCACGA
1 AAACA-CGACGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGA
39487823 A
1 A
39487824 GATTTGAAGG
Statistics
Matches: 164, Mismatches: 28, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
47 1 0.01
48 58 0.35
49 18 0.11
50 87 0.53
ACGTcount: A:0.39, C:0.24, G:0.26, T:0.12
Consensus pattern (49 bp):
AAACACGACGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCACGA
Found at i:39488104 original size:92 final size:91
Alignment explanation
Indices: 39487954--39488634 Score: 1101
Period size: 92 Copynumber: 7.4 Consensus size: 91
39487944 ATAGCAAGTT
* * * *
39487954 TTTATCTCTCTAAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGA
1 TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGA
** * *
39488019 AGTTGCAGTAAAGTTGGATAGCAAGTC
66 AGTTATAGTAAAGTTGGATAACAA-CC
* * *
39488046 TTTATCCCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAATGTCAATTCTTATCCTCTTGA
1 TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGA
39488111 AGTTATAGTAAAGTTGGATAACAAACC
66 AGTTATAGTAAAGTTGGATAAC-AACC
*
39488138 TTTATCTCTCTGAAGTTATAGTAAAAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGA
1 TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGA
*
39488203 AGTTATAGTAAAGTTGGATAAGAACC
66 AGTTATAGTAAAGTTGGATAACAACC
*
39488229 TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCTTATCCTCTTGA
1 TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGA
39488294 AGTTATAGTAAAGTTGGATAACGAACC
66 AGTTATAGTAAAGTTGGATAAC-AACC
39488321 TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGA
1 TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGA
* *
39488386 AGTTCTTGTAAAGTTGGATAACGAACC
66 AGTTATAGTAAAGTTGGATAAC-AACC
*
39488413 TTTATCTCTCTGAAGTTATAGTAAGAGTAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGA
1 TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGA
*
39488478 AGTTATAGTAAAGTTAGATAACGAACC
66 AGTTATAGTAAAGTTGGATAAC-AACC
*
39488505 TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACTTCAATTCTTATCCTCTTGA
1 TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGA
*
39488570 AGTTATAGTAAAGTTGGATAACAAATC
66 AGTTATAGTAAAGTTGGATAAC-AACC
* * *
39488597 TTTATCTCTCCGAAGTTGTAGTAAGAGCAAGATAAAGC
1 TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGC
39488635 CTCGACATCA
Statistics
Matches: 555, Mismatches: 32, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
91 88 0.16
92 465 0.84
93 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (91 bp):
TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGA
AGTTATAGTAAAGTTGGATAACAACC
Found at i:39488645 original size:367 final size:367
Alignment explanation
Indices: 39487954--39488645 Score: 1138
Period size: 367 Copynumber: 1.9 Consensus size: 367
39487944 ATAGCAAGTT
*
39487954 TTTATCTCTCTAAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGA
1 TTTATCTCTCTAAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGA
* * *
39488019 AGTTGCAGTAAAGTTGGATAGCAAGTCTTTATCCCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
66 AGTTGCAGTAAAGTTGGATAACAAGCCTTTATCCCTCTGAAGTTATAGTAAGAGCAAGATGAAGC
* *
39488084 TTCAAATGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACAAACCTTTATCTCTCT
131 TTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTAGATAACAAACCTTTATCTCTCT
39488149 GAAGTTATAGTAAAAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAA
196 GAAGTTATAGTAAAAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAA
* * * *
39488214 AGTTGGATAAGAACCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATCAA
261 AGTTGGATAAAAACCTTTATCTCTCCGAAGTTATAGTAAGAGCAAGATAAAGCCTCAAACATCAA
39488279 TTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACC
326 TTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACC
* * *
39488321 TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGA
1 TTTATCTCTCTAAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGA
* * *
39488386 AGTT-CTTGTAAAGTTGGATAACGAA-CCTTTATCTCTCTGAAGTTATAGTAAGAGTAAGATGAA
66 AGTTGC-AGTAAAGTTGGATAAC-AAGCCTTTATCCCTCTGAAGTTATAGTAAGAGCAAGATGAA
*
39488449 GCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTAGATAACGAACCTTTATCTCT
129 GCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTAGATAACAAACCTTTATCTCT
* *
39488514 CTGAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACTTCAATTCTTATCCTCTTGAAGTTATAGT
194 CTGAAGTTATAGTAAAAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGT
* * *
39488579 AAAGTTGGATAACAAATCTTTATCTCTCCGAAGTTGTAGTAAGAGCAAGATAAAGCCTC-GACAT
259 AAAGTTGGATAA-AAACCTTTATCTCTCCGAAGTTATAGTAAGAGCAAGATAAAGCCTCAAACAT
39488643 CAA
323 CAA
39488646 ACCCTATTTT
Statistics
Matches: 300, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
366 1 0.00
367 257 0.86
368 42 0.14
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (367 bp):
TTTATCTCTCTAAAGTTATAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCTCTTGA
AGTTGCAGTAAAGTTGGATAACAAGCCTTTATCCCTCTGAAGTTATAGTAAGAGCAAGATGAAGC
TTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTAGATAACAAACCTTTATCTCTCT
GAAGTTATAGTAAAAGCAAGATGAAGCTTCAAACGTCAATTCTTATCCTCTTGAAGTTATAGTAA
AGTTGGATAAAAACCTTTATCTCTCCGAAGTTATAGTAAGAGCAAGATAAAGCCTCAAACATCAA
TTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAACC
Found at i:39488937 original size:6 final size:6
Alignment explanation
Indices: 39488919--39488977 Score: 57
Period size: 6 Copynumber: 9.8 Consensus size: 6
39488909 TTAAATTTGT
* ** *
39488919 TTTAAA GTTTAAA TTTAAA TTT-AA TTTAAG TTTAAA TTTATG TTCAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
39488967 TTTAAA ATTAA
1 TTTAAA TTTAA
39488978 TATAAATTCA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
5 5 0.12
6 31 0.74
7 6 0.14
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:39488952 original size:17 final size:17
Alignment explanation
Indices: 39488891--39488971 Score: 65
Period size: 17 Copynumber: 4.6 Consensus size: 17
39488881 CCAAACCCAT
*
39488891 TTTAAATTTATTTTAAG
1 TTTAAATTTAATTTAAG
* **
39488908 ATTAAATTTGTTTTAAAG
1 TTTAAATTTAATTT-AAG
39488926 TTTAAATTTAAATTTAA-
1 TTTAAATTT-AATTTAAG
* *
39488943 TTTAAGTTTAAATTTATG
1 TTTAAATTT-AATTTAAG
*
39488961 TTCAAATTTAA
1 TTTAAATTTAA
39488972 AATTAATATA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
17 29 0.56
18 20 0.38
19 3 0.06
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAATTTAAG
Found at i:39488953 original size:23 final size:24
Alignment explanation
Indices: 39488909--39488958 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
39488899 TATTTTAAGA
**
39488909 TTAAATTTGTTTTAAAGTTTAAAT
1 TTAAATTTAATTTAAAGTTTAAAT
39488933 TTAAATTTAATTT-AAGTTTAAAT
1 TTAAATTTAATTTAAAGTTTAAAT
39488956 TTA
1 TTA
39488959 TGTTCAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (24 bp):
TTAAATTTAATTTAAAGTTTAAAT
Found at i:39488956 original size:12 final size:12
Alignment explanation
Indices: 39488923--39488971 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
39488913 ATTTGTTTTA
39488923 AAGTTTAAATTT
1 AAGTTTAAATTT
*
39488935 AAATTT-AATTT
1 AAGTTTAAATTT
39488946 AAGTTTAAATTT
1 AAGTTTAAATTT
* *
39488958 ATGTTCAAATTT
1 AAGTTTAAATTT
39488970 AA
1 AA
39488972 AATTAATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (12 bp):
AAGTTTAAATTT
Found at i:39488971 original size:41 final size:41
Alignment explanation
Indices: 39488891--39488977 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
39488881 CCAAACCCAT
* * *
39488891 TTTAAATTTATTTTAAGATTAAATTTGTTTTAAAGTTTAAA
1 TTTAAATTTAATTTAAGATTAAATTTATTTCAAAGTTTAAA
*
39488932 TTTAAATTTAATTTAAGTTTAAATTTATGTTCAAA-TTTAAA
1 TTTAAATTTAATTTAAGATTAAATTTAT-TTCAAAGTTTAAA
*
39488973 ATTAA
1 TTTAA
39488978 TATAAATTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 35 0.88
42 5 0.12
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (41 bp):
TTTAAATTTAATTTAAGATTAAATTTATTTCAAAGTTTAAA
Found at i:39493405 original size:52 final size:52
Alignment explanation
Indices: 39493322--39493525 Score: 261
Period size: 52 Copynumber: 3.9 Consensus size: 52
39493312 ATTTCACTTC
* * *
39493322 ATTCATATACTCACGATGACACATAGCCATCGGACCT-TATAATCCATAAGGG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCT-TAATCCGTAAAGG
*
39493374 ATTCATATACTC-CTGATGACACAGT-GTCATCGGACTGTCTTAATCCGTAAAGG
1 ATTCATATACTCAC-GATGACACA-TAGTCATCGGAC-CTCTTAATCCGTAAAGG
* * *
39493427 ATTCATATACTCACGATGTCACTTAGTCATCGGACCTCTTAATCCGTAAAAG
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAAGG
* **
39493479 ATTCATATACTCACGATGACACTTAGTCATCAAACCTCTTAATCCGT
1 ATTCATATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGT
39493526 TTATGGCTCA
Statistics
Matches: 135, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
51 1 0.01
52 90 0.67
53 42 0.31
54 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAAGG
Found at i:39497111 original size:30 final size:30
Alignment explanation
Indices: 39497067--39497228 Score: 152
Period size: 30 Copynumber: 5.4 Consensus size: 30
39497057 ATTTGGGGTC
* * *
39497067 AAAATGTATTTTTTAAAAAAATTTAGGGGTT
1 AAAATGTA-ATTTTAGAAAAATTTAGAGGTT
* *
39497098 AAAATGTAATTTTAGGAAAGTTTA-AGGTT
1 AAAATGTAATTTTAGAAAAATTTAGAGGTT
* * *
39497127 AAAATGTGATTTTGGAAAAATTT-GAGGGTG
1 AAAATGTAATTTTAGAAAAATTTAGA-GGTT
* *
39497157 AAAATGTAATTTTGGAAAAGTTTA-AGGTT
1 AAAATGTAATTTTAGAAAAATTTAGAGGTT
* *
39497186 AAAATGTAATTTTA-ACAAAGTTCAGAGGTT
1 AAAATGTAATTTTAGA-AAAATTTAGAGGTT
*
39497216 AAAATATAATTTT
1 AAAATGTAATTTT
39497229 TGAATAAAAT
Statistics
Matches: 110, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
28 1 0.01
29 47 0.43
30 54 0.49
31 8 0.07
ACGTcount: A:0.42, C:0.01, G:0.19, T:0.38
Consensus pattern (30 bp):
AAAATGTAATTTTAGAAAAATTTAGAGGTT
Found at i:39497130 original size:29 final size:29
Alignment explanation
Indices: 39497094--39497228 Score: 157
Period size: 29 Copynumber: 4.6 Consensus size: 29
39497084 AAAATTTAGG
39497094 GGTTAAAATGTAATTTTAGG-AAAGTTTAA
1 GGTTAAAATGTAATTTT-GGAAAAGTTTAA
* * *
39497123 GGTTAAAATGTGATTTTGGAAAAATTTGAG
1 GGTTAAAATGTAATTTTGGAAAAGTTT-AA
*
39497153 GGTGAAAATGTAATTTTGGAAAAGTTTAA
1 GGTTAAAATGTAATTTTGGAAAAGTTTAA
* *
39497182 GGTTAAAATGTAATTTT-AACAAAGTTCAGA
1 GGTTAAAATGTAATTTTGGA-AAAGTTTA-A
*
39497212 GGTTAAAATATAATTTT
1 GGTTAAAATGTAATTTT
39497229 TGAATAAAAT
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
28 3 0.03
29 46 0.51
30 42 0.46
ACGTcount: A:0.41, C:0.01, G:0.21, T:0.37
Consensus pattern (29 bp):
GGTTAAAATGTAATTTTGGAAAAGTTTAA
Found at i:39497146 original size:59 final size:57
Alignment explanation
Indices: 39497083--39497228 Score: 179
Period size: 59 Copynumber: 2.5 Consensus size: 57
39497073 TATTTTTTAA
*
39497083 AAAAATTTAGGGGTTAAAATGTAATTTTAGG-AAAGTTTAAGGTTAAAATGTGATTTT
1 AAAAATTTAGGGGTTAAAATGTAATTTT-GGAAAAGTTTAAGGTTAAAATGTAATTTT
*
39497140 GGAAAAATTT-GAGGGTGAAAATGTAATTTTGGAAAAGTTTAAGGTTAAAATGTAATTTT
1 --AAAAATTTAG-GGGTTAAAATGTAATTTTGGAAAAGTTTAAGGTTAAAATGTAATTTT
* * *
39497199 AACAAAGTTCAGAGGTTAAAATATAATTTT
1 AA-AAA-TTTAGGGGTTAAAATGTAATTTT
39497229 TGAATAAAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
57 2 0.03
58 6 0.08
59 67 0.88
60 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.21, T:0.36
Consensus pattern (57 bp):
AAAAATTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGTTAAAATGTAATTTT
Found at i:39512422 original size:21 final size:21
Alignment explanation
Indices: 39512384--39512423 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
39512374 ATTTCTTAAA
*
39512384 ATAATACAAATGTGTTAATAT
1 ATAATACAAATATGTTAATAT
39512405 ATAATTACAAATAT-TTAAT
1 ATAA-TACAAATATGTTAAT
39512424 GGTTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (21 bp):
ATAATACAAATATGTTAATAT
Found at i:39517390 original size:23 final size:23
Alignment explanation
Indices: 39517364--39517408 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
39517354 TTAGGTAGGA
39517364 ACCTTAATCCTAGAAAAAAAAAT
1 ACCTTAATCCTAGAAAAAAAAAT
* *
39517387 ACCTTAATCGTTGAAAAAAAAA
1 ACCTTAATCCTAGAAAAAAAAA
39517409 ACTTTTTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.56, C:0.16, G:0.07, T:0.22
Consensus pattern (23 bp):
ACCTTAATCCTAGAAAAAAAAAT
Found at i:39525121 original size:34 final size:37
Alignment explanation
Indices: 39525041--39525130 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 37
39525031 TATAGAGGTA
*
39525041 AAGATAATTACATAAAAATTCAAATTACTAATTAGAAAAT
1 AAGATAA-TA-ATAATAATTCAAA-TACTAATTAGAAAAT
* *
39525081 AAGATAA-AATAATAATTCAAA-AC-AATTTGAAACT
1 AAGATAATAATAATAATTCAAATACTAATTAGAAAAT
*
39525115 AAGATAATGATAATAA
1 AAGATAATAATAATAA
39525131 ATAATTTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 16 0.36
35 9 0.20
37 12 0.27
38 1 0.02
40 7 0.16
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (37 bp):
AAGATAATAATAATAATTCAAATACTAATTAGAAAAT
Found at i:39533122 original size:28 final size:27
Alignment explanation
Indices: 39533070--39533121 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
39533060 AGACTTTACC
* *
39533070 CTCCCTTTGTAATTCACCAAAAAAATA
1 CTCCCCTTGTAATTCACAAAAAAAATA
39533097 CTCCCCTTGTAATTCACAAAAAAAA
1 CTCCCCTTGTAATTCACAAAAAAAA
39533122 AAAATAAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.27, G:0.04, T:0.27
Consensus pattern (27 bp):
CTCCCCTTGTAATTCACAAAAAAAATA
Found at i:39533171 original size:14 final size:14
Alignment explanation
Indices: 39533152--39533185 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
39533142 AATCTAGACC
39533152 ATATAATTATATTA
1 ATATAATTATATTA
*
39533166 ATATAATTATATTT
1 ATATAATTATATTA
39533180 ATATAA
1 ATATAA
39533186 AATTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATAATTATATTA
Found at i:39533258 original size:29 final size:31
Alignment explanation
Indices: 39533173--39533262 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 31
39533163 TTAATATAAT
*
39533173 TATATTTATATAAAATTTAAATTTATTATTATATA
1 TATATTT-T-TAAAATTTAAA-TT-TTATTATAGA
*
39533208 TATATTTTTAAATATTT---GTTTATT-T-GA
1 TATATTTTTAAA-ATTTAAATTTTATTATAGA
39533235 TATATTTTTAAAATTTAAATTTTATTAT
1 TATATTTTTAAAATTTAAATTTTATTAT
39533263 TTCTTGTCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
26 4 0.09
27 13 0.28
28 1 0.02
29 11 0.23
30 2 0.04
33 4 0.09
34 5 0.11
35 7 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (31 bp):
TATATTTTTAAAATTTAAATTTTATTATAGA
Found at i:39533709 original size:21 final size:21
Alignment explanation
Indices: 39533685--39533730 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
39533675 AAAAATTACA
39533685 AAAAAATTAAAATAAATTTTC
1 AAAAAATTAAAATAAATTTTC
** * *
39533706 AAAATTTTAAAATAATTTTTT
1 AAAAAATTAAAATAAATTTTC
39533727 AAAA
1 AAAA
39533731 TTCAAAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAAATTAAAATAAATTTTC
Found at i:39533731 original size:21 final size:21
Alignment explanation
Indices: 39533691--39533732 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
39533681 TACAAAAAAA
39533691 TTAAAATAAATTTTCAAAATT
1 TTAAAATAAATTTTCAAAATT
* *
39533712 TTAAAATAATTTTTTAAAATT
1 TTAAAATAAATTTTCAAAATT
39533733 CAAAATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAAATAAATTTTCAAAATT
Found at i:39533737 original size:20 final size:20
Alignment explanation
Indices: 39533687--39533772 Score: 68
Period size: 19 Copynumber: 4.2 Consensus size: 20
39533677 AAATTACAAA
* *
39533687 AAAATT-AAAATAAATTTTC
1 AAAATTCAAAATAATTTTTT
*
39533706 AAAATTTTAAAATAATTTTTT
1 AAAA-TTCAAAATAATTTTTT
* *
39533727 AAAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTTTTT
39533746 AAAATTCCAAAATTTATATTTTTT
1 AAAATT-CAAAA--TA-ATTTTTT
39533770 AAA
1 AAA
39533773 TATAAAAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
19 15 0.28
20 14 0.26
21 15 0.28
22 1 0.02
24 8 0.15
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAATTCAAAATAATTTTTT
Found at i:39534573 original size:39 final size:39
Alignment explanation
Indices: 39534530--39534607 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
39534520 AATTTTTTTT
*
39534530 GAATATATTGGTGTAATTATATAATAGTATATATTCATA
1 GAATATATTGGTGTAATTACATAATAGTATATATTCATA
* **
39534569 GAATATATTGGTGTGATTACATGGTAGTATATATTCATA
1 GAATATATTGGTGTAATTACATAATAGTATATATTCATA
39534608 CTTTCTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.42
Consensus pattern (39 bp):
GAATATATTGGTGTAATTACATAATAGTATATATTCATA
Found at i:39534822 original size:8 final size:8
Alignment explanation
Indices: 39534809--39534839 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
39534799 ATAAATTAAA
39534809 TTGAAGAC
1 TTGAAGAC
39534817 TTGAAGAC
1 TTGAAGAC
39534825 TTGAAGAC
1 TTGAAGAC
39534833 TTGAAGA
1 TTGAAGA
39534840 TTAGTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.10, G:0.26, T:0.26
Consensus pattern (8 bp):
TTGAAGAC
Found at i:39535272 original size:19 final size:19
Alignment explanation
Indices: 39535231--39535272 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
39535221 TAAAATAAAA
*
39535231 ATAAAAAATATTAAAAGTT
1 ATAAAAAATATTAAAAGTG
*
39535250 ATAAAAGAATTTTAAAA-TG
1 ATAAAA-AATATTAAAAGTG
39535269 ATAA
1 ATAA
39535273 TTACTTAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (19 bp):
ATAAAAAATATTAAAAGTG
Found at i:39538956 original size:38 final size:39
Alignment explanation
Indices: 39538914--39539007 Score: 115
Period size: 38 Copynumber: 2.5 Consensus size: 39
39538904 GTTTTTATAA
39538914 ATATTTTATT-TTAATAA-TAATTATAATCTAAAATTTTG
1 ATATTTTATTGTTAATAATTAATT-TAATCTAAAATTTTG
* * *
39538952 ATATTTTATTGTTAATATATTGATTTAGTTTAAAATTTTG
1 ATATTTTATTGTTAATA-ATTAATTTAATCTAAAATTTTG
39538992 AT-TTTT-TTGTTAATAA
1 ATATTTTATTGTTAATAA
39539008 CATTATCTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
37 1 0.02
38 19 0.38
39 10 0.20
40 16 0.32
41 4 0.08
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.56
Consensus pattern (39 bp):
ATATTTTATTGTTAATAATTAATTTAATCTAAAATTTTG
Found at i:39539022 original size:38 final size:40
Alignment explanation
Indices: 39538937--39539023 Score: 108
Period size: 38 Copynumber: 2.2 Consensus size: 40
39538927 ATAATAATTA
* * *
39538937 TAATCTAAAATTTTGATATTTTATTGTTAATATATTGATT
1 TAATTTAAAATTTTGATATTTTATTGTTAATACATTGATC
*
39538977 TAGTTTAAAATTTTGAT-TTTT-TTGTTAATAACATT-ATC
1 TAATTTAAAATTTTGATATTTTATTGTTAAT-ACATTGATC
39539015 TAATTTAAA
1 TAATTTAAA
39539024 CTTTATGGGA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 18 0.44
39 8 0.20
40 15 0.37
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.54
Consensus pattern (40 bp):
TAATTTAAAATTTTGATATTTTATTGTTAATACATTGATC
Found at i:39541197 original size:2 final size:2
Alignment explanation
Indices: 39541190--39541214 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39541180 ACGTGGACAA
39541190 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 A
39541215 ACAATTAGAC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39541442 original size:20 final size:20
Alignment explanation
Indices: 39541403--39541450 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
39541393 TCATTAAATA
* *
39541403 ATTAAAAATATTTAATTAAT
1 ATTAAAATTAATTAATTAAT
39541423 -TTAAAATTAATTATATTAAT
1 ATTAAAATTAATTA-ATTAAT
39541443 ATTAAAAT
1 ATTAAAAT
39541451 AATATACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.46
20 6 0.25
21 7 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTAAAATTAATTAATTAAT
Found at i:39541453 original size:20 final size:18
Alignment explanation
Indices: 39541389--39541453 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
39541379 TTTTTTAAAA
* * *
39541389 AAAATCATTAAATAATTA
1 AAAATAATTAATTAATTT
*
39541407 AAAATATTTAATTAATTT
1 AAAATAATTAATTAATTT
39541425 AAAATTAATTATATTAATATT
1 AAAA-TAATTA-ATTAAT-TT
39541446 AAAATAAT
1 AAAATAAT
39541454 ATACAAATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 18 0.46
19 5 0.13
20 10 0.26
21 6 0.15
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAATAATTAATTAATTT
Found at i:39541496 original size:22 final size:21
Alignment explanation
Indices: 39541470--39541516 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
39541460 ATGTATCATG
*
39541470 ATTTAAATATTAATATATT-ATA
1 ATTTAAATACT-AT-TATTAATA
39541492 ATTTAAATACTATTATTAATA
1 ATTTAAATACTATTATTAATA
39541513 ATTT
1 ATTT
39541517 CTTACAGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 9 0.39
22 10 0.43
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTAAATACTATTATTAATA
Found at i:39542949 original size:29 final size:29
Alignment explanation
Indices: 39542917--39542978 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
39542907 AAACGGGACC
*
39542917 TTTGGA-TGCCCGAGGGT-GAAATGGTAATT
1 TTTGGACT-CCCGAGGGTAAAAAT-GTAATT
*
39542946 TTT-GACTTCCGAGGGTAAAAATGTAATT
1 TTTGGACTCCCGAGGGTAAAAATGTAATT
39542974 TTTGG
1 TTTGG
39542979 TGAAATTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.35
Consensus pattern (29 bp):
TTTGGACTCCCGAGGGTAAAAATGTAATT
Found at i:39543021 original size:59 final size:59
Alignment explanation
Indices: 39542958--39543427 Score: 470
Period size: 59 Copynumber: 8.1 Consensus size: 59
39542948 TGACTTCCGA
* ***
39542958 GGGTAAAAAT-GTAATTTTTGGTGAAAT-TAGGGTTAAAAATGGAATTTCAAAAAGTTTAG
1 GGGT-AAAATGGTAATTTTTGGTGAAATCGA-GGTTAAAAATGGAATTTTGGAAAGTTTAG
* * * *
39543017 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGCTAAAAATAGG-GTTTTAGAAA-ATTAG
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAT-GGAATTTTGGAAAGTTTAG
* * * *
39543075 AGGGTAAAATAGTAATTTTTGATGAAATTGGGGTT-AAAATGGAATTTTGGAAAGTTTTA-
1 -GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAG-TTTAG
* *
39543134 GGGTAAAATGATAATTTTTGATGAAATCGAGGTTAAAAAT-GAGATTTTGGAAAGTTT-G
1 GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGA-ATTTTGGAAAGTTTAG
**
39543192 AGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT--AAATGGAATTTTGGAAAGTTCGG
1 -GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
* *
39543250 GGGTAAAATGGTAATTTTTGGTGAAA-CTGGGGTCAAAAATGGAATTTTGGAAAGTTTAG
1 GGGTAAAATGGTAATTTTTGGTGAAATC-GAGGTTAAAAATGGAATTTTGGAAAGTTTAG
* * * * * *
39543309 GGGTAAAACGGTAATTTTT-G-GAAGTTTCAAGG-TCAAAATGGAATTTTGGGAAGTTTGG
1 GGGTAAAATGGTAATTTTTGGTGAA--ATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
* * *
39543367 GGGTAAAATGGTAATTTTT-G-GAAGTTTCGGGGTCAAAAATGGAATTTTGGAAAGTTT-G
1 GGGTAAAATGGTAATTTTTGGTGAA--ATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
39543425 GGG
1 GGG
39543428 ACCTACAAAA
Statistics
Matches: 352, Mismatches: 39, Indels: 41
0.81 0.09 0.09
Matches are distributed among these distances:
56 1 0.00
57 52 0.15
58 116 0.33
59 176 0.50
60 7 0.02
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAG
Found at i:39543149 original size:117 final size:116
Alignment explanation
Indices: 39542956--39543387 Score: 457
Period size: 117 Copynumber: 3.7 Consensus size: 116
39542946 TTTGACTTCC
* ***
39542956 GAGGGTAAAA-ATGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTCAAAAAGTTT-AGGG
1 GAGGGTAAAATA-GTAATTTTTGGTGAAATTAAGGTT-AAAATGGAATTTTGGAAAGTTTGA-GG
* *
39543019 GTAAAATGGTAATTTTTGGTGAAATCGAGGCTAAAAATAGGGTTTTAGAAAATTA
63 GTAAAATGGTAATTTTTGGTGAAATCGAGGCTAAAAAT-GGATTTTGGAAAATTA
* ** *
39543074 GAGGGTAAAATAGTAATTTTTGATGAAATTGGGGTTAAAATGGAATTTTGGAAAGTTTTAGGGTA
1 GAGGGTAAAATAGTAATTTTTGGTGAAATTAAGGTTAAAATGGAATTTTGGAAAGTTTGAGGGTA
* * * * *
39543139 AAATGATAATTTTTGATGAAATCGAGGTTAAAAATGAGATTTTGGAAAGTTT
66 AAATGGTAATTTTTGGTGAAATCGAGGCTAAAAATG-GATTTTGGAAAATTA
* ** * *
39543191 GAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTT-AAATGGAATTTTGGAAAGTTCGGGGGTA
1 GAGGGTAAAATAGTAATTTTTGGTGAAATTAAGGTTAAAATGGAATTTTGGAAAGTTTGAGGGTA
* *
39543255 AAATGGTAATTTTTGGTGAAA-CTG-GGGTCAAAAATGGAATTTTGGAAAGTTTA
66 AAATGGTAATTTTTGGTGAAATC-GAGGCT-AAAAATGG-ATTTTGGAAA-ATTA
** * * * *
39543308 G-GGGTAAAACGGTAATTTTT-G-GAAGTTTCAAGGTCAAAATGGAATTTTGGGAAGTTTGGGGG
1 GAGGGTAAAATAGTAATTTTTGGTGAA-ATT-AAGGTTAAAATGGAATTTTGGAAAGTTTGAGGG
39543370 TAAAATGGTAATTTTTGG
64 TAAAATGGTAATTTTTGG
39543388 AAGTTTCGGG
Statistics
Matches: 273, Mismatches: 31, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
114 3 0.01
115 7 0.03
116 85 0.31
117 144 0.53
118 33 0.12
119 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.34
Consensus pattern (116 bp):
GAGGGTAAAATAGTAATTTTTGGTGAAATTAAGGTTAAAATGGAATTTTGGAAAGTTTGAGGGTA
AAATGGTAATTTTTGGTGAAATCGAGGCTAAAAATGGATTTTGGAAAATTA
Found at i:39543316 original size:29 final size:27
Alignment explanation
Indices: 39543102--39543427 Score: 184
Period size: 29 Copynumber: 11.2 Consensus size: 27
39543092 TTTGATGAAA
39543102 TTGGGGTTAAAATGGAATTTTGGAAAGTT
1 TTGGGG-TAAAATGGAATTTTGGAAAG-T
* *
39543131 TTAGGGTAAAATGATAATTTTTGATGAAA--
1 TTGGGGTAAAATG-GAA-TTTTG--GAAAGT
* *
39543160 TCGAGGTTAAAAAT-GAGATTTTGGAAAGT
1 TTG-GGGT-AAAATGGA-ATTTTGGAAAGT
39543189 TTGAGGGTAAAATGGTAATTTTTGGTGAAA--
1 TTG-GGGTAAAATGG-AA-TTTT-G-GAAAGT
* * *
39543219 TCGAGGTTAAATGGAATTTTGGAAAGT
1 TTGGGGTAAAATGGAATTTTGGAAAGT
*
39543246 TCGGGGGTAAAATGGTAATTTTTGGTGAAA--
1 T-TGGGGTAAAATGG-AA-TTTT-G-GAAAGT
*
39543276 CTGGGGTCAAAAATGGAATTTTGGAAAGT
1 TTGGGGT--AAAATGGAATTTTGGAAAGT
*
39543305 TTAGGGGTAAAACGGTAATTTTTGG-AAGT
1 TT-GGGGTAAAATGG-AA-TTTTGGAAAGT
** *
39543334 TTCAAGGTCAAAATGGAATTTTGGGAAGT
1 TT-GGGGT-AAAATGGAATTTTGGAAAGT
39543363 TTGGGGGTAAAATGGTAATTTTTGG-AAGT
1 TT-GGGGTAAAATGG-AA-TTTTGGAAAGT
39543392 TTCGGGGTCAAAAATGGAATTTTGGAAAGT
1 TT-GGGGT--AAAATGGAATTTTGGAAAGT
39543422 TTGGGG
1 TTGGGG
39543428 ACCTACAAAA
Statistics
Matches: 236, Mismatches: 26, Indels: 70
0.71 0.08 0.21
Matches are distributed among these distances:
25 4 0.02
26 1 0.00
27 13 0.06
28 44 0.19
29 88 0.37
30 53 0.22
31 21 0.09
32 12 0.05
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (27 bp):
TTGGGGTAAAATGGAATTTTGGAAAGT
Found at i:39544520 original size:9 final size:9
Alignment explanation
Indices: 39544508--39544541 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
39544498 TTTTTTTTGT
39544508 TTATTAATA
1 TTATTAATA
*
39544517 TTATTATTA
1 TTATTAATA
39544526 TTATTAATA
1 TTATTAATA
*
39544535 ATATTAA
1 TTATTAA
39544542 AAACAATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTATTAATA
Found at i:39545289 original size:14 final size:15
Alignment explanation
Indices: 39545262--39545293 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
39545252 CGATTGAGCC
39545262 TTTGTAATTTGGACA
1 TTTGTAATTTGGACA
39545277 TTTGTAA-TTGGACA
1 TTTGTAATTTGGACA
39545291 TTT
1 TTT
39545294 TATTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (15 bp):
TTTGTAATTTGGACA
Found at i:39545325 original size:17 final size:18
Alignment explanation
Indices: 39545305--39545381 Score: 79
Period size: 17 Copynumber: 4.4 Consensus size: 18
39545295 ATTTAATTTA
*
39545305 AAATTTAAA-TTTATAAT
1 AAATTTAAAGTTTAAAAT
* *
39545322 AAATTTAAAGTTT-ATAC
1 AAATTTAAAGTTTAAAAT
*
39545339 AAATTTAAA-TTCAAAAT
1 AAATTTAAAGTTTAAAAT
*
39545356 AAATTTAAATTTTAAAACT
1 AAATTTAAAGTTTAAAA-T
39545375 AAATTTA
1 AAATTTA
39545382 TTGGGCCCGG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
16 2 0.04
17 30 0.61
18 9 0.18
19 8 0.16
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (18 bp):
AAATTTAAAGTTTAAAAT
Found at i:39545348 original size:34 final size:34
Alignment explanation
Indices: 39545305--39545369 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
39545295 ATTTAATTTA
* *
39545305 AAATTTAAATTTATAATAAATTTAAAGTTTATAC
1 AAATTTAAATTCAAAATAAATTTAAAGTTTATAC
*
39545339 AAATTTAAATTCAAAATAAATTTAAATTTTA
1 AAATTTAAATTCAAAATAAATTTAAAGTTTA
39545370 AAACTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (34 bp):
AAATTTAAATTCAAAATAAATTTAAAGTTTATAC
Found at i:39545448 original size:30 final size:30
Alignment explanation
Indices: 39545414--39545539 Score: 180
Period size: 30 Copynumber: 4.2 Consensus size: 30
39545404 TCAACAATAT
*
39545414 ATATAGTAAGATTCTTGGCAAAATATATAC
1 ATATAGTAAGACTCTTGGCAAAATATATAC
39545444 ATATAGTAAGACTCTTGGCAAAATATATAC
1 ATATAGTAAGACTCTTGGCAAAATATATAC
* * *
39545474 ATATAGTAAAACTCTGGGTGAAAATATATAC
1 ATATAGTAAGACTCTTGG-CAAAATATATAC
* * *
39545505 ATATAGTAAGACTCTTGACAACATAGATAC
1 ATATAGTAAGACTCTTGGCAAAATATATAC
39545535 ATATA
1 ATATA
39545540 ATAACTCTGG
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
30 59 0.69
31 26 0.31
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.30
Consensus pattern (30 bp):
ATATAGTAAGACTCTTGGCAAAATATATAC
Found at i:39545570 original size:61 final size:60
Alignment explanation
Indices: 39545433--39545568 Score: 202
Period size: 61 Copynumber: 2.3 Consensus size: 60
39545423 GATTCTTGGC
* * *
39545433 AAAATATATACATATAGTAAGACTCTTGGCAAAATATATACATATAGTAAAACTCTGGGTG
1 AAAATATATACATATAGTAAGACTCTTGACAAAATAGATACATATAG-AAAACTCTGGGTA
* *
39545494 AAAATATATACATATAGTAAGACTCTTGACAACATAGATACATATA-ATAACTCTGGGTA
1 AAAATATATACATATAGTAAGACTCTTGACAAAATAGATACATATAGAAAACTCTGGGTA
*
39545553 AAAATATATATATATA
1 AAAATATATACATATA
39545569 TACATATAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
59 26 0.38
61 43 0.62
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (60 bp):
AAAATATATACATATAGTAAGACTCTTGACAAAATAGATACATATAGAAAACTCTGGGTA
Found at i:39545635 original size:33 final size:33
Alignment explanation
Indices: 39545590--39545740 Score: 169
Period size: 33 Copynumber: 4.6 Consensus size: 33
39545580 AGACTCCAAA
* * *
39545590 ATATACACATATACTAAGACCCTGGCTACAAAT
1 ATATATACATATAATAAGACCCTGGCTAAAAAT
* * * *
39545623 ATATATAAATATAGTAAAACTCC-GGATAAAAAT
1 ATATATACATATAATAAGAC-CCTGGCTAAAAAT
* *
39545656 ATATATACATATAATAAGACTCTTGCTAAAAAT
1 ATATATACATATAATAAGACCCTGGCTAAAAAT
* * * *
39545689 ATATATGCATATAGTAAGACTCTTGCTAAAAAT
1 ATATATACATATAATAAGACCCTGGCTAAAAAT
39545722 ATATATACATATAATAAGA
1 ATATATACATATAATAAGA
39545741 TTATAATTAT
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
32 1 0.01
33 97 0.97
34 2 0.02
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (33 bp):
ATATATACATATAATAAGACCCTGGCTAAAAAT
Found at i:39545674 original size:66 final size:66
Alignment explanation
Indices: 39545590--39545740 Score: 203
Period size: 66 Copynumber: 2.3 Consensus size: 66
39545580 AGACTCCAAA
* * *
39545590 ATATACACATATACTAAGACCCTGGCTACAAATATATATAAATATAGTAAAACTCCGGATAAAAA
1 ATATATACATATAATAAGACCCTGGCTAAAAATATATATAAATATAGTAAAACTCCGGATAAAAA
39545655 T
66 T
* * ** * ** *
39545656 ATATATACATATAATAAGACTCTTGCTAAAAATATATATGCATATAGTAAGACTCTTGCTAAAAA
1 ATATATACATATAATAAGACCCTGGCTAAAAATATATATAAATATAGTAAAACTCCGGATAAAAA
39545721 T
66 T
39545722 ATATATACATATAATAAGA
1 ATATATACATATAATAAGA
39545741 TTATAATTAT
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 74 1.00
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.30
Consensus pattern (66 bp):
ATATATACATATAATAAGACCCTGGCTAAAAATATATATAAATATAGTAAAACTCCGGATAAAAA
T
Found at i:39546971 original size:22 final size:21
Alignment explanation
Indices: 39546945--39546991 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
39546935 ATTTATCATG
*
39546945 ATTTAAATATTAATATATT-ATA
1 ATTTAAATACT-AT-TATTAATA
39546967 ATTTAAATACTATTATTAATA
1 ATTTAAATACTATTATTAATA
39546988 ATTT
1 ATTT
39546992 CTTACAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 9 0.39
22 10 0.43
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTAAATACTATTATTAATA
Found at i:39549594 original size:184 final size:182
Alignment explanation
Indices: 39549288--39549652 Score: 644
Period size: 184 Copynumber: 2.0 Consensus size: 182
39549278 CTAGGCAAAA
39549288 TTATAAAGATAAATTAAAAATAACAAAAATTTAATTGAAACAACTAAAAGAAAAAGGGGACTTAA
1 TTATAAAGATAAATTAAAAATAACAAAAATTTAATTGAAACAACTAAAAGAAAAAGGGGACTTAA
39549353 TGGGGAAATAACCCTATTTTAAAGAAAAGGACAAATACCCTTCCCCATGCCTGCCATTTCACGTG
66 TGGGGAAATAACCCTATTTTAAAGAAAAGGACAAATACCCTTCCCCATGCCTGCCATTTCACGTG
*
39549418 GGTGGCATCACTTTTCACCCA-TTTCCTTCTTTTTCAAATTAAAATTAATTC
131 GGTGGCATCACTTTTCAACCATTTTCCTTCTTTTTCAAATTAAAATTAATTC
*
39549469 TTATAAAGATAAATT-AAAATAACAAAAAAAAATTTAATTGAAACAACTAAAAGAAAAAGGTGAC
1 TTATAAAGATAAATTAAAAATAAC----AAAAATTTAATTGAAACAACTAAAAGAAAAAGGGGAC
* *
39549533 TTAATGGGGAAATAACCCTATTTTAAAGAAAAGGACAAATGCCCTTCCCCATGCTTGCCATTTCA
62 TTAATGGGGAAATAACCCTATTTTAAAGAAAAGGACAAATACCCTTCCCCATGCCTGCCATTTCA
39549598 CGTGGGTGGCATCACTTTTCAACCATTTTCCTTCTTTTTCAAATTAAAATTAATT
127 CGTGGGTGGCATCACTTTTCAACCATTTTCCTTCTTTTTCAAATTAAAATTAATT
39549653 TCTTCATTTT
Statistics
Matches: 175, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
180 8 0.05
181 15 0.09
184 123 0.70
185 29 0.17
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (182 bp):
TTATAAAGATAAATTAAAAATAACAAAAATTTAATTGAAACAACTAAAAGAAAAAGGGGACTTAA
TGGGGAAATAACCCTATTTTAAAGAAAAGGACAAATACCCTTCCCCATGCCTGCCATTTCACGTG
GGTGGCATCACTTTTCAACCATTTTCCTTCTTTTTCAAATTAAAATTAATTC
Found at i:39551237 original size:80 final size:80
Alignment explanation
Indices: 39550993--39551964 Score: 1637
Period size: 80 Copynumber: 12.3 Consensus size: 80
39550983 ATAACTTTAG
* * * * * *
39550993 GGGTAAAAGATTAGATTGT-TTCAATTTGCCTCATGGTCGAGGTAAAAGATCTGATGGTCTTCAA
1 GGGTAAAAGATTGGATT-TCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
*
39551057 --TTGCCTTCTGGTTA
65 TCTTGCCCTCTGGTTA
* * *
39551071 GGGTAAAAGATTTGATTTCTTTAATCTGCCCTATGATC-GGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
39551135 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* * *
39551150 GGGTAAAAGATTGGATTTATTCAATCTGCCCCATGATCGGGGTAAAAGATCAGATAGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
39551215 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* *
39551230 GGATAAAAGATTGGA-TTCTTCAATCTG-TCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
39551293 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* *
39551308 GGGTAAAAGATTGGATTTATTCAATCTGCCCCATGATCGGGGTAAAAGATCAGATGGTCTTC-AT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
39551372 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
*
39551387 GGGTAAAAGATTGGATTTCTTTAATCTGCCCCA-GATCGGGGTAAAAGATCGGATGGTCTT-AAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
39551450 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
*
39551465 GGGTAAAAGATTTGATTTCTTCAATCTGCCCCATGATCGGGGT-AAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
39551529 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
*
39551544 GGGTAAAAGATTGGATTTCTTCAATCTGTCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
39551609 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
39551624 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTT-AAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
39551688 CTTG-CCTTTGGTTA
66 CTTGCCCTCTGGTTA
*
39551702 GGGTAAAAGATTTGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
39551767 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
39551782 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
39551847 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
*
39551862 GGGTAAAAGATTGGATTTCCTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTT-AAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
39551926 CTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
39551941 GGGTAAAAGATTGGATTTCTTCAA
1 GGGTAAAAGATTGGATTTCTTCAA
39551965 AAAGATCGGA
Statistics
Matches: 844, Mismatches: 38, Indels: 23
0.93 0.04 0.03
Matches are distributed among these distances:
77 24 0.03
78 252 0.30
79 240 0.28
80 328 0.39
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (80 bp):
GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
CTTGCCCTCTGGTTA
Found at i:39551296 original size:158 final size:160
Alignment explanation
Indices: 39550993--39551964 Score: 1637
Period size: 158 Copynumber: 6.2 Consensus size: 160
39550983 ATAACTTTAG
* * * * * *
39550993 GGGTAAAAGATTAGATTGT-TTCAATTTGCCTCATGGTCGAGGTAAAAGATCTGATGGTCTTCAA
1 GGGTAAAAGATTGGATT-TCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
* * * *
39551057 --TTGCCTTCTGGTTAGGGTAAAAGATTTGATTTCTTTAATCTGCCCTATGATC-GGGTAAAAGA
65 TCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGA
39551119 TCGGATGGTCTTCAATCTTGCCCTCTGGTTA
130 TCGGATGGTCTTCAATCTTGCCCTCTGGTTA
* * *
39551150 GGGTAAAAGATTGGATTTATTCAATCTGCCCCATGATCGGGGTAAAAGATCAGATAGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* *
39551215 CTTGCCCTCTGGTTAGGATAAAAGATTGGA-TTCTTCAATCTG-TCCATGATCGGGGTAAAAGAT
66 CTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGAT
39551278 CGGATGGTCTTCAATCTTGCCCTCTGGTTA
131 CGGATGGTCTTCAATCTTGCCCTCTGGTTA
* *
39551308 GGGTAAAAGATTGGATTTATTCAATCTGCCCCATGATCGGGGTAAAAGATCAGATGGTCTTC-AT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
39551372 CTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTTAATCTGCCCCA-GATCGGGGTAAAAGAT
66 CTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGAT
39551436 CGGATGGTCTT-AATCTTGCCCTCTGGTTA
131 CGGATGGTCTTCAATCTTGCCCTCTGGTTA
*
39551465 GGGTAAAAGATTTGATTTCTTCAATCTGCCCCATGATCGGGGT-AAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
39551529 CTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAATCTGTCCCATGATCGGGGTAAAAGAT
66 CTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGAT
39551594 CGGATGGTCTTCAATCTTGCCCTCTGGTTA
131 CGGATGGTCTTCAATCTTGCCCTCTGGTTA
39551624 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTT-AAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* *
39551688 CTTG-CCTTTGGTTAGGGTAAAAGATTTGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGAT
66 CTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGAT
39551752 CGGATGGTCTTCAATCTTGCCCTCTGGTTA
131 CGGATGGTCTTCAATCTTGCCCTCTGGTTA
39551782 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
39551847 CTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCCTCAATCTGCCCCATGATCGGGGTAAAAGAT
66 CTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGAT
39551912 CGGATGGTCTT-AATCTTGCCCTCTGGTTA
131 CGGATGGTCTTCAATCTTGCCCTCTGGTTA
39551941 GGGTAAAAGATTGGATTTCTTCAA
1 GGGTAAAAGATTGGATTTCTTCAA
39551965 AAAGATCGGA
Statistics
Matches: 774, Mismatches: 29, Indels: 22
0.94 0.04 0.03
Matches are distributed among these distances:
156 18 0.02
157 200 0.26
158 326 0.42
159 145 0.19
160 85 0.11
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (160 bp):
GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
CTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGAT
CGGATGGTCTTCAATCTTGCCCTCTGGTTA
Found at i:39551983 original size:20 final size:19
Alignment explanation
Indices: 39551945--39551984 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39551935 TGGTTAGGGT
* *
39551945 AAAAGATTGGATTTCTTCA
1 AAAAGATCGGATGTCTTCA
39551964 AAAAGATCGGATGGTCTTCA
1 AAAAGATCGGAT-GTCTTCA
39551984 A
1 A
39551985 TCTTGCCCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (19 bp):
AAAAGATCGGATGTCTTCA
Found at i:39552009 original size:59 final size:59
Alignment explanation
Indices: 39551905--39552023 Score: 222
Period size: 59 Copynumber: 2.0 Consensus size: 59
39551895 TGATCGGGGT
39551905 AAAAGATCGGATGGTCTTAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCA
1 AAAAGATCGGATGGTCTTAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCA
39551964 AAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGT-AAAGATTGGATTTCTTCA
1 AAAAGATCGGATGGTCTT-AATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCA
39552023 A
1 A
39552024 TCTGCCCCAT
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 37 0.63
60 22 0.37
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (59 bp):
AAAAGATCGGATGGTCTTAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCA
Found at i:39552022 original size:39 final size:39
Alignment explanation
Indices: 39551964--39552110 Score: 172
Period size: 40 Copynumber: 3.7 Consensus size: 39
39551954 GATTTCTTCA
* *
39551964 AAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGT
1 AAAAGATTGGAT-TTCTTCAATC-TGCCCTCTGGTTAGGGT
* **
39552005 -AAAGATTGGATTTCTTCAATCTGCCC-CATGATCGGGGT
1 AAAAGATTGGATTTCTTCAATCTGCCCTC-TGGTTAGGGT
*
39552043 AAAAGATTGGATGATCTTCAATCTTGCCCTCTGGTTAGGGT
1 AAAAGATTGGAT-TTCTTCAATC-TGCCCTCTGGTTAGGGT
*
39552084 AAAAGATTAGATTTCTTCAATCTGCCC
1 AAAAGATTGGATTTCTTCAATCTGCCC
39552111 ATGATCGAGG
Statistics
Matches: 90, Mismatches: 11, Indels: 12
0.80 0.10 0.11
Matches are distributed among these distances:
37 1 0.01
38 12 0.13
39 25 0.28
40 28 0.31
41 23 0.26
42 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (39 bp):
AAAAGATTGGATTTCTTCAATCTGCCCTCTGGTTAGGGT
Found at i:39552075 original size:139 final size:139
Alignment explanation
Indices: 39551825--39552103 Score: 506
Period size: 139 Copynumber: 2.0 Consensus size: 139
39551815 TGATCGGGGT
39551825 AAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCCTCAATCTG
1 AAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCCTCAATCTG
* *
39551890 CCCCATGATCGGGGTAAAAGATCGGATGGTCTTAATCTTGCCCTCTGGTTAGGGTAAAAGATTGG
66 CCCCATGATCGGGGTAAAAGATCGGATGATCTTAATCTTGCCCTCTGGTTAGGGTAAAAGATTAG
39551955 ATTTCTTCA
131 ATTTCTTCA
*
39551964 AAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGT-AAAGATTGGATTTCTTCAATCTG
1 AAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCCTCAATCTG
*
39552028 CCCCATGATCGGGGTAAAAGATTGGATGATCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTA
66 CCCCATGATCGGGGTAAAAGATCGGATGATCTT-AATCTTGCCCTCTGGTTAGGGTAAAAGATTA
39552093 GATTTCTTCA
130 GATTTCTTCA
39552103 A
1 A
39552104 TCTGCCCATG
Statistics
Matches: 135, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
138 53 0.39
139 82 0.61
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (139 bp):
AAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCCTCAATCTG
CCCCATGATCGGGGTAAAAGATCGGATGATCTTAATCTTGCCCTCTGGTTAGGGTAAAAGATTAG
ATTTCTTCA
Found at i:39552112 original size:79 final size:79
Alignment explanation
Indices: 39551964--39552132 Score: 286
Period size: 79 Copynumber: 2.1 Consensus size: 79
39551954 GATTTCTTCA
* * *
39551964 AAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAGATTGGATTTCTTCAATCTGC
1 AAAAGATTGGATGATCTTCAATCTTGCCCTCTGGTTAGGGTAAAGATTAGATTTCTTCAATCTGC
*
39552029 CCCATGATCGGGGT
66 CCCATGATCGAGGT
39552043 AAAAGATTGGATGATCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTAGATTTCTTCAATCTG
1 AAAAGATTGGATGATCTTCAATCTTGCCCTCTGGTTAGGGT-AAAGATTAGATTTCTTCAATCTG
39552108 -CCCATGATCGAGGT
65 CCCCATGATCGAGGT
39552122 AAAAGATTGGA
1 AAAAGATTGGA
39552133 GGTTGTAACT
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
79 63 0.74
80 22 0.26
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (79 bp):
AAAAGATTGGATGATCTTCAATCTTGCCCTCTGGTTAGGGTAAAGATTAGATTTCTTCAATCTGC
CCCATGATCGAGGT
Found at i:39564414 original size:186 final size:185
Alignment explanation
Indices: 39564102--39564473 Score: 660
Period size: 186 Copynumber: 2.0 Consensus size: 185
39564092 CTAGGCAAAA
39564102 TTATAAAGATAAATTAAAAATAACAAAAAATTTAATTGAAACAACTAAAAGAAAAAGGGGACTTA
1 TTATAAAGATAAATTAAAAATAACAAAAAATTTAATTGAAACAACTAAAAGAAAAAGGGGACTTA
39564167 ATGGGGAAATACCCTATTTTAAAGAAAAGGACAAATGCCCTTCCCCATGCCTGCCATTTCACGTG
66 ATGGGGAAATACCCTATTTTAAAGAAAAGGACAAATGCCCTTCCCCATGCCTGCCATTTCACGTG
*
39564232 GGTGGCATCACTTT-TCAC-CCATTTTCCTTCTTTTTCAAATT-AAATTAATTTT
131 GGTGGCATCACTTTAACACACCATTTTCCTTCTTTTTCAAATTAAAATTAATTTT
39564284 TTATAAAGATAAATTAAAAATAACAAAAAAAAATTTAATTGAAACAACTAAAAGAAAAAGGGGAC
1 TTATAAAGATAAATTAAAAATAAC---AAAAAATTTAATTGAAACAACTAAAAGAAAAAGGGGAC
39564349 TTAATGGGGAAATAACCCTATTTTAAAGAAAAGGACAAATGCCCTTCCCCATGCCTGCCATTTCA
63 TTAATGGGGAAAT-ACCCTATTTTAAAGAAAAGGACAAATGCCCTTCCCCATGCCTGCCATTTCA
39564414 CGTGGGTGGCATCACTTTCAACACAACCATTTTCCTTCTTTTTCAAATTAAAATTAATTT
127 CGTGGGTGGCATCACTTT-AACAC-ACCATTTTCCTTCTTTTTCAAATTAAAATTAATTT
39564474 CTTCATTTCC
Statistics
Matches: 180, Mismatches: 1, Indels: 9
0.95 0.01 0.05
Matches are distributed among these distances:
182 24 0.13
185 51 0.28
186 69 0.38
188 3 0.02
190 23 0.13
191 10 0.06
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (185 bp):
TTATAAAGATAAATTAAAAATAACAAAAAATTTAATTGAAACAACTAAAAGAAAAAGGGGACTTA
ATGGGGAAATACCCTATTTTAAAGAAAAGGACAAATGCCCTTCCCCATGCCTGCCATTTCACGTG
GGTGGCATCACTTTAACACACCATTTTCCTTCTTTTTCAAATTAAAATTAATTTT
Found at i:39568600 original size:43 final size:41
Alignment explanation
Indices: 39568454--39568707 Score: 256
Period size: 41 Copynumber: 6.1 Consensus size: 41
39568444 ACGGAGGAAG
* * * * *
39568454 AGTGGCAGTTTATCTGCAAATATGCTGTGCATCCATAGCCC
1 AGTGGTAGTTTATCTGCAAATATGTTGTGCATCCACAACCT
* *
39568495 AGTGGTAGTTTATCTTCAAATATGTTATGCATCCACAACCT
1 AGTGGTAGTTTATCTGCAAATATGTTGTGCATCCACAACCT
* * * * *
39568536 AGTGGCAATTTATTTGCAAATATGGTGTGCACCCACAACCT
1 AGTGGTAGTTTATCTGCAAATATGTTGTGCATCCACAACCT
* * **
39568577 AATGGTAGTTTTTATCTGCAAATATGTTGTGCATACACAATTT
1 AGTGGTAG--TTTATCTGCAAATATGTTGTGCATCCACAACCT
* * * * *
39568620 AATGGTAGTTTTTATCTTCAAATATATTGTGCATCCATAACCC
1 AGTGGTAG--TTTATCTGCAAATATGTTGTGCATCCACAACCT
* * *
39568663 AGTGGCAGTTTATCAGCAAATATGTTGTGCATCCACAACCC
1 AGTGGTAGTTTATCTGCAAATATGTTGTGCATCCACAACCT
39568704 AGTG
1 AGTG
39568708 AGGTGTGTAT
Statistics
Matches: 175, Mismatches: 36, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
41 106 0.61
43 69 0.39
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (41 bp):
AGTGGTAGTTTATCTGCAAATATGTTGTGCATCCACAACCT
Found at i:39570765 original size:45 final size:45
Alignment explanation
Indices: 39570715--39570816 Score: 150
Period size: 45 Copynumber: 2.3 Consensus size: 45
39570705 TTGGCTTTTG
* * *
39570715 TGGCATTCTGTTCTCCATTGTGGTGTATTTTTTATGTTACCTTTA
1 TGGCATTCTGTTCGCCATTGTAGTGTATTTTGTATGTTACCTTTA
* * *
39570760 TGGCATTCTGTTCGCCGTTGTAGTGTATTTTGTATGTTGCCTTTG
1 TGGCATTCTGTTCGCCATTGTAGTGTATTTTGTATGTTACCTTTA
39570805 TGGCATTCTGTT
1 TGGCATTCTGTT
39570817 TGGCCTTTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.51
Consensus pattern (45 bp):
TGGCATTCTGTTCGCCATTGTAGTGTATTTTGTATGTTACCTTTA
Found at i:39570822 original size:21 final size:21
Alignment explanation
Indices: 39570798--39570890 Score: 64
Period size: 21 Copynumber: 4.3 Consensus size: 21
39570788 TTTGTATGTT
39570798 GCCTTTGTGGCATTCTGTTTG
1 GCCTTTGTGGCATTCTGTTTG
* * *
39570819 GCCTTT-TCGACGTTATGTTT-
1 GCCTTTGT-GGCATTCTGTTTG
* * *
39570839 GCCATTGTGATGTATTCTGTATGTT
1 GCCTTTGTG--GCATTCTGT-T-TG
*
39570864 GCCTTTGTGGTATTCTGTTTG
1 GCCTTTGTGGCATTCTGTTTG
39570885 GCCTTT
1 GCCTTT
39570891 TCGACATTAT
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
20 7 0.13
21 23 0.42
22 6 0.11
23 10 0.18
24 1 0.02
25 8 0.15
ACGTcount: A:0.09, C:0.17, G:0.25, T:0.49
Consensus pattern (21 bp):
GCCTTTGTGGCATTCTGTTTG
Found at i:39570860 original size:66 final size:66
Alignment explanation
Indices: 39570783--39570955 Score: 283
Period size: 66 Copynumber: 2.6 Consensus size: 66
39570773 GCCGTTGTAG
* *
39570783 TGTATTTTGTATGTTGCCTTTGTGGCATTCTGTTTGGCCTTTTCGACGTTATGTTTGCCATTGTG
1 TGTATTCTGTATGTTGCCTTTGTGGCATTCTGTTTGGCCTTTTCGACATTATGTTTGCCATTGTG
39570848 A
66 A
*
39570849 TGTATTCTGTATGTTGCCTTTGTGGTATTCTGTTTGGCCTTTTCGACATTATGTTTGCCATTGTG
1 TGTATTCTGTATGTTGCCTTTGTGGCATTCTGTTTGGCCTTTTCGACATTATGTTTGCCATTGTG
39570914 A
66 A
* *
39570915 TGTATTCTGTATGTTGACTTTGTGGCGTATTTTGTTTGGCC
1 TGTATTCTGTATGTTGCCTTTGTGGC--ATTCTGTTTGGCC
39570956 CTTATGGTGT
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
66 87 0.88
68 12 0.12
ACGTcount: A:0.11, C:0.14, G:0.24, T:0.50
Consensus pattern (66 bp):
TGTATTCTGTATGTTGCCTTTGTGGCATTCTGTTTGGCCTTTTCGACATTATGTTTGCCATTGTG
A
Found at i:39570871 original size:25 final size:24
Alignment explanation
Indices: 39570832--39570938 Score: 68
Period size: 25 Copynumber: 4.6 Consensus size: 24
39570822 TTTTCGACGT
*
39570832 TATGTTTGCCATTGTGATGTATTCTG
1 TATG-TTGCCTTTGTGA-GTATTCTG
39570858 TATGTTGCCTTTGTG-GTATTCTG
1 TATGTTGCCTTTGTGAGTATTCTG
* * *
39570881 T-T-TGGCCTTT-TCGA-CATTATG
1 TATGTTGCCTTTGT-GAGTATTCTG
*
39570902 --T-TTGCCATTGTGATGTATTCTG
1 TATGTTGCCTTTGTGA-GTATTCTG
*
39570924 TATGTTGACTTTGTG
1 TATGTTGCCTTTGTG
39570939 GCGTATTTTG
Statistics
Matches: 63, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
20 10 0.16
21 14 0.22
22 6 0.10
23 9 0.14
24 1 0.02
25 19 0.30
26 4 0.06
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.50
Consensus pattern (24 bp):
TATGTTGCCTTTGTGAGTATTCTG
Found at i:39572522 original size:30 final size:30
Alignment explanation
Indices: 39572486--39572553 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
39572476 GACAGCTACG
* *
39572486 AAGGCGTCCATACATCATTAGATAGCCACA
1 AAGGCGTCCACACATCACTAGATAGCCACA
** *
39572516 AAGGCGTCCACACATTGCTAGATAGCCACG
1 AAGGCGTCCACACATCACTAGATAGCCACA
*
39572546 GAGGCGTC
1 AAGGCGTC
39572554 TAGACACATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.28, G:0.24, T:0.18
Consensus pattern (30 bp):
AAGGCGTCCACACATCACTAGATAGCCACA
Found at i:39582479 original size:51 final size:51
Alignment explanation
Indices: 39582403--39582687 Score: 356
Period size: 51 Copynumber: 5.5 Consensus size: 51
39582393 CAAAAGTGTT
*
39582403 CGATGACTAAGTGTCATTGTGAGTAAATGAATCCCTTACGGATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACGGATTAAAGGTC
*
39582454 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCATC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACGGATTAAAGG---TC
*
39582508 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACGGATTAAAGGTC
* * * * * *
39582559 CGATGACTAAGTGTTATCATGAGTAAATGAATCCATGATGAATTAAAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACGGATTAAAGGTC
* * * * * * **
39582610 CGATGACTCAGTGTGATCGTGAGCACATGAATTCCTATACAGAACAAGAGGTC
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCCT-TACGGATTAA-AGGTC
39582663 CGATGACTATA-TGTCATCGTGAGTA
1 CGATGACTA-AGTGTCATCGTGAGTA
39582688 TTAAATGAAA
Statistics
Matches: 204, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
51 123 0.60
52 4 0.02
53 25 0.12
54 52 0.25
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.28
Consensus pattern (51 bp):
CGATGACTAAGTGTCATCGTGAGTAAATGAATCCCTTACGGATTAAAGGTC
Found at i:39582585 original size:105 final size:102
Alignment explanation
Indices: 39582403--39582687 Score: 356
Period size: 105 Copynumber: 2.7 Consensus size: 102
39582393 CAAAAGTGTT
* *
39582403 CGATGACTAAGTGTCATTGTGAGTAAATGAATCCCTTACGGATTAAAGGTCCGATGACTAAGTGT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAAGTGT
* * * *
39582468 CATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCATC
66 CATCATGAGTAAATGAATCCATGACGAATTAAAGG---TC
39582508 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAAGTGT
1 CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAAGTGT
* *
39582573 TATCATGAGTAAATGAATCCATGATGAATTAAAGGTC
66 CATCATGAGTAAATGAATCCATGACGAATTAAAGGTC
* * * * * * **
39582610 CGATGACTCAGTGTGATCGTGAGCACATGAATTCCTATACAGAACAAGAGGTCCGATGACTATA-
1 CGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATTAA-AGGTCCGATGACTA-AG
*
39582674 TGTCATCGTGAGTA
63 TGTCATCATGAGTA
39582688 TTAAATGAAA
Statistics
Matches: 159, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
102 29 0.18
103 11 0.07
104 26 0.16
105 93 0.58
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.28
Consensus pattern (102 bp):
CGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAAGTGT
CATCATGAGTAAATGAATCCATGACGAATTAAAGGTC
Found at i:39587579 original size:21 final size:22
Alignment explanation
Indices: 39587555--39587614 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
39587545 TAGTTGCATG
39587555 ACTTGTATCGGTAGAAATTA-T
1 ACTTGTATCGGTAGAAATTAGT
**
39587576 ACTTGTATAAGTAG-AATTAGT
1 ACTTGTATCGGTAGAAATTAGT
**
39587597 AAATGTATCGGTAGAAAT
1 ACTTGTATCGGTAGAAAT
39587615 CTGCACAGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 5 0.16
21 23 0.74
22 3 0.10
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (22 bp):
ACTTGTATCGGTAGAAATTAGT
Found at i:39589987 original size:30 final size:29
Alignment explanation
Indices: 39589946--39590147 Score: 176
Period size: 30 Copynumber: 6.8 Consensus size: 29
39589936 TTTCGAAGAA
* *
39589946 TTTGGGGTCAAAATGTAATTTTGGAAAAA
1 TTTGGAGTCAAAATGTAATTTTGGAAAAG
* *
39589975 TTTAAGAGTCAAAATGTATTTTTAGGAAAAG
1 TTT-GGAGTCAAAATGTAATTTT-GGAAAAG
* * *
39590006 TTTGGGGTCAAAATATGATTTTGG-AAAG
1 TTTGGAGTCAAAATGTAATTTTGGAAAAG
* *
39590034 ATTTGGTAGTCAAAATGTGATTTTGGGAAAG
1 -TTTGG-AGTCAAAATGTAATTTTGGAAAAG
* *
39590065 CTTTGGGGTTAAAATGTAATTTTGGAAAAG
1 -TTTGGAGTCAAAATGTAATTTTGGAAAAG
*
39590095 TTTTAGG-GTTAAAATGTAAATTTT-GAAAAG
1 -TTT-GGAGTCAAAATGT-AATTTTGGAAAAG
* *
39590125 TTTGGGAGTCAGAATGCAATTTT
1 TTT-GGAGTCAAAATGTAATTTT
39590148 TTAGTAAATA
Statistics
Matches: 144, Mismatches: 21, Indels: 16
0.80 0.12 0.09
Matches are distributed among these distances:
28 4 0.03
29 21 0.15
30 93 0.65
31 26 0.18
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (29 bp):
TTTGGAGTCAAAATGTAATTTTGGAAAAG
Found at i:39590016 original size:60 final size:58
Alignment explanation
Indices: 39589946--39590147 Score: 217
Period size: 60 Copynumber: 3.4 Consensus size: 58
39589936 TTTCGAAGAA
*
39589946 TTTGGGGTCAAAATGTAATTTTGGAAAAATTTAAGAGTCAAAATGTATTTTTAGGAAAAG
1 TTTGGGGTCAAAATGTAATTTTGGAAAAATTT-AGAGTCAAAATGTAATTTT-GGAAAAG
* * * * * *
39590006 TTTGGGGTCAAAATATGATTTTGGAAAGATTTGGTAGTCAAAATGTGATTTTGGGAAAG
1 TTTGGGGTCAAAATGTAATTTTGGAAAAATTTAG-AGTCAAAATGTAATTTTGGAAAAG
* * * *
39590065 CTTTGGGGTTAAAATGTAATTTTGGAAAAGTTTTAGGGTTAAAATGTAAATTTT-GAAAAG
1 -TTTGGGGTCAAAATGTAATTTTGGAAAA-ATTTAGAGTCAAAATGT-AATTTTGGAAAAG
* *
39590125 TTTGGGAGTCAGAATGCAATTTT
1 TTTGGG-GTCAAAATGTAATTTT
39590148 TTAGTAAATA
Statistics
Matches: 117, Mismatches: 20, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
59 13 0.11
60 95 0.81
61 9 0.08
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (58 bp):
TTTGGGGTCAAAATGTAATTTTGGAAAAATTTAGAGTCAAAATGTAATTTTGGAAAAG
Found at i:39591194 original size:11 final size:11
Alignment explanation
Indices: 39591171--39591202 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
39591161 ACTTCCCTTA
39591171 TTATTAT-TAT
1 TTATTATATAT
39591181 TTATTATATAT
1 TTATTATATAT
39591192 TTATTATATAT
1 TTATTATATAT
39591203 CGTTTTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATTATATAT
Found at i:39592429 original size:48 final size:47
Alignment explanation
Indices: 39592371--39592547 Score: 140
Period size: 48 Copynumber: 3.9 Consensus size: 47
39592361 TTGAGCTTCG
* * *
39592371 CTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCA
1 CTTCACTGATTTGATCCACTTCTCTGTATCTCATCAAGAAGATGA-CA
**
39592419 CTTCACTGATTCAATCCACTTCTCTGTATCTCATC-AGAA-A-G---
1 CTTCACTGATTTGATCCACTTCTCTGTATCTCATCAAGAAGATGACA
* * * * *
39592460 ----GCTGATTTGGTCCACTTCTCTATATCTCACCAGGAAGATGACCA
1 CTTCACTGATTTGATCCACTTCTCTGTATCTCATCAAGAAGATGA-CA
* * * *
39592504 CTTTATTGCTTTGACCCACTTCTCTGTATCTCATCAAGAAGATG
1 CTTCACTGATTTGATCCACTTCTCTGTATCTCATCAAGAAGATG
39592548 GGTTTGAAGT
Statistics
Matches: 98, Mismatches: 20, Indels: 22
0.70 0.14 0.16
Matches are distributed among these distances:
37 25 0.26
38 3 0.03
39 1 0.01
40 1 0.01
45 1 0.01
46 1 0.01
47 4 0.04
48 62 0.63
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (47 bp):
CTTCACTGATTTGATCCACTTCTCTGTATCTCATCAAGAAGATGACA
Found at i:39592523 original size:85 final size:85
Alignment explanation
Indices: 39592377--39592539 Score: 227
Period size: 85 Copynumber: 1.9 Consensus size: 85
39592367 TTCGCTTCAT
* * * * *
39592377 TGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCACTTCACTGATTCAATCCACTTCT
1 TGATTTGGTCCACTTCTCTATATCTCACCAAGAAGATGACCACTTCACTGATTCAACCCACTTCT
39592442 CTGTATCTCATCAGAAAGGC
66 CTGTATCTCATCAGAAAGGC
* * * * **
39592462 TGATTTGGTCCACTTCTCTATATCTCACCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCT
1 TGATTTGGTCCACTTCTCTATATCTCACCAAGAAGATGACCACTTCACTGATTCAACCCACTTCT
39592527 CTGTATCTCATCA
66 CTGTATCTCATCA
39592540 AGAAGATGGG
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 67 1.00
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.36
Consensus pattern (85 bp):
TGATTTGGTCCACTTCTCTATATCTCACCAAGAAGATGACCACTTCACTGATTCAACCCACTTCT
CTGTATCTCATCAGAAAGGC
Found at i:39592622 original size:207 final size:208
Alignment explanation
Indices: 39592258--39592662 Score: 625
Period size: 207 Copynumber: 2.0 Consensus size: 208
39592248 GCTTCATTTC
* * * * *
39592258 TTGGTCTACTTCTCTACATCTCATCAGGAAGATGATCGCTTTATTACTTCGACCTACTTCTCTGC
1 TTGGTCCACTTCTCTACATCTCACCAGGAAGATGACCACTTTATTACTTCGACCCACTTCTCTGC
*
39592323 ATCTCATCAGGAAGATAGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCT
66 ATCTCATCAAGAAGATAGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCT
* *
39592388 ACTTCTCTGTATCTCATCAAGAAGATGATCACTTCACTGATTCAATCCACTTCTCTGTATCTCAT
131 ACTTCTCTGTATCTCATCAAGAAGATGACCACATCACTGATTCAATCCACTTCTCTGTATCTCAT
39592453 CAGAAAGGCTGAT
196 CAGAAAGGCTGAT
* * * *
39592466 TTGGTCCACTTCTCTATATCTCACCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTGT
1 TTGGTCCACTTCTCTACATCTCACCAGGAAGATGACCACTTTATTACTTCGACCCACTTCTCTGC
* *
39592531 ATCTCATCAAGAAGAT-GGGTTTGAAGTCTCATTTGTATTGAGCTTTGCTTCATTGATTTGGTCT
66 ATCTCATCAAGAAGATAGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCT
* * * *
39592595 ACTTCTCTGTATCTCATC-AGAAAGATGACCGCATCATTGATTTAATCCACTTCTCTGTATCTTA
131 ACTTCTCTGTATCTCATCAAG-AAGATGACCACATCACTGATTCAATCCACTTCTCTGTATCTCA
39592659 TCAG
195 TCAG
39592663 GAAGATAACC
Statistics
Matches: 178, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
206 2 0.01
207 105 0.59
208 71 0.40
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (208 bp):
TTGGTCCACTTCTCTACATCTCACCAGGAAGATGACCACTTTATTACTTCGACCCACTTCTCTGC
ATCTCATCAAGAAGATAGGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCATTGATTTGGTCT
ACTTCTCTGTATCTCATCAAGAAGATGACCACATCACTGATTCAATCCACTTCTCTGTATCTCAT
CAGAAAGGCTGAT
Found at i:39592635 original size:48 final size:48
Alignment explanation
Indices: 39592580--39592709 Score: 152
Period size: 48 Copynumber: 2.7 Consensus size: 48
39592570 GAGCTTTGCT
* * * *
39592580 TCATTGATTTGGTCTACTTCTCTGTATCTCATCAGAAAGATGACCGCA
1 TCATTGATTTGATCCACTTCTCTGTATCTCATCAGAAAGATAACCACA
* * * *
39592628 TCATTGATTTAATCCACTTCTCTGTATCTTATCAGGAAGATAACCACT
1 TCATTGATTTGATCCACTTCTCTGTATCTCATCAGAAAGATAACCACA
* * * *
39592676 TTATTGCTTTGACCCACTTCTCTATATCTCATCA
1 TCATTGATTTGATCCACTTCTCTGTATCTCATCA
39592710 AGAAGATTGG
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 68 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (48 bp):
TCATTGATTTGATCCACTTCTCTGTATCTCATCAGAAAGATAACCACA
Found at i:39592804 original size:171 final size:170
Alignment explanation
Indices: 39592470--39592835 Score: 554
Period size: 171 Copynumber: 2.1 Consensus size: 170
39592460 GCTGATTTGG
* * * *
39592470 TCCACTTCTCTATATCTCACCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTGTATCT
1 TCCACTTCTCTGTATCTCATCAGGAAGATAACCACTTTATTGCTTTGACCCACTTCTCTATATCT
* ** * * *
39592535 CATCAAGAAGATGGGTTTGAAGTCTCATTTGTATTGAGCTTTGCTTCATTGATTTGGTCTACTTC
66 CATCAAGAAGATGGATTTGAAGTCTCATTCATATTGAGCTTCGCTTCATTAATTTGGTATACTTC
*
39592600 TCTGTATCTCATCAGAAAGATGACCGCATCATTGATTTAA
131 TATGTATCTCATCAGAAAGATGACCGCATCATTGATTTAA
*
39592640 TCCACTTCTCTGTATCTTATCAGGAAGATAACCACTTTATTGCTTTGACCCACTTCTCTATATCT
1 TCCACTTCTCTGTATCTCATCAGGAAGATAACCACTTTATTGCTTTGACCCACTTCTCTATATCT
*
39592705 CATCAAGAAGATTGGATTTGAAGTCTTATTCATATTGAGCTTCGCTTCATTAATTTGGTATACTT
66 CATCAAGAAGA-TGGATTTGAAGTCTCATTCATATTGAGCTTCGCTTCATTAATTTGGTATACTT
* *
39592770 CTATGTATCTCATCA-AGAAGATGATCGTATCATTGATTTAA
130 CTATGTATCTCATCAGA-AAGATGACCGCATCATTGATTTAA
* *
39592811 TCCATTTCTTTGTATCTCATCAGGA
1 TCCACTTCTCTGTATCTCATCAGGA
39592836 TGACGAATTT
Statistics
Matches: 176, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
170 72 0.41
171 104 0.59
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (170 bp):
TCCACTTCTCTGTATCTCATCAGGAAGATAACCACTTTATTGCTTTGACCCACTTCTCTATATCT
CATCAAGAAGATGGATTTGAAGTCTCATTCATATTGAGCTTCGCTTCATTAATTTGGTATACTTC
TATGTATCTCATCAGAAAGATGACCGCATCATTGATTTAA
Found at i:39592881 original size:210 final size:210
Alignment explanation
Indices: 39592658--39593045 Score: 587
Period size: 210 Copynumber: 1.8 Consensus size: 210
39592648 TCTGTATCTT
*
39592658 ATCAGGAAGATAACCACTTTATTGCTTTGACCCACTTCTCTATATCTCATCAAGAAGATTGGATT
1 ATCAGGAAGATAACCACTTTATTGCTTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGATT
* *
39592723 TGAAGTCTTATTCATATTGAGCTTCGCTTCATTAATTTGGTATACTTCTATGTATCTCATCAAGA
66 TGAAGTCTTATTCATATTAAGCTTCACTTCATTAATTTGGTATACTTCTATGTATCTCATCAAGA
* * *
39592788 AGATGATCGTATCATTGATTTAATCCATTTCTTTGTATCTCATCAGGATGACGAATTTGGTCTAC
131 AGATGATCGCATCATTGATTTAATCCACTTCTCTGTATCTCATCAGGATGACGAATTTGGTCTAC
39592853 TTCTCTCTGTATTAC
196 TTCTCTCTGTATTAC
* * * * * * * *
39592868 ATCAGGAAGATAACCGCTTTCTTGCTTTGAGCTACTTCTTTGTATCTCATCAGGAAGATGGGGTT
1 ATCAGGAAGATAACCACTTTATTGCTTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGATT
* * * * *
39592933 TGAAGTCTTATTCGTATTAAGCTTCACTTCATTGATTTGGTCTACTTCTCTGTATCTTATCAAGA
66 TGAAGTCTTATTCATATTAAGCTTCACTTCATTAATTTGGTATACTTCTATGTATCTCATCAAGA
* *
39592998 AGATGATCGCATCATTGGTTTAATCCACTTCTCTGTATCTTATCAGGA
131 AGATGATCGCATCATTGATTTAATCCACTTCTCTGTATCTCATCAGGA
39593046 AGATGGATTT
Statistics
Matches: 157, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
210 157 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (210 bp):
ATCAGGAAGATAACCACTTTATTGCTTTGACCCACTTCTCTATATCTCATCAAGAAGATGGGATT
TGAAGTCTTATTCATATTAAGCTTCACTTCATTAATTTGGTATACTTCTATGTATCTCATCAAGA
AGATGATCGCATCATTGATTTAATCCACTTCTCTGTATCTCATCAGGATGACGAATTTGGTCTAC
TTCTCTCTGTATTAC
Found at i:39593177 original size:45 final size:44
Alignment explanation
Indices: 39593060--39593194 Score: 123
Period size: 46 Copynumber: 3.0 Consensus size: 44
39593050 GGATTTGATT
* * * *
39593060 TGCCCCTCTTGACTAGGGGTAAAAGATCAGAATG-TGACTTCAATT
1 TGCCCCTCTTGATTAGGGGTAAAAGATTAGAA-GATGGC-TCAATC
* * * *
39593105 TTCTCCTATTGACTTAAGGGTAAAAGATTAGAAGATGGCTGCAATC
1 TGCCCCTCTTGA-TTAGGGGTAAAAGATTAGAAGATGGCT-CAATC
* *
39593151 TGCCCCTCTTGGTTAGGGGTAAAAGATT-GGA-ATGGCTCAATC
1 TGCCCCTCTTGATTAGGGGTAAAAGATTAGAAGATGGCTCAATC
39593193 TG
1 TG
39593195 TCCTATGATC
Statistics
Matches: 73, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
42 7 0.10
43 6 0.08
44 2 0.03
45 26 0.36
46 32 0.44
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (44 bp):
TGCCCCTCTTGATTAGGGGTAAAAGATTAGAAGATGGCTCAATC
Found at i:39593430 original size:96 final size:98
Alignment explanation
Indices: 39593230--39593485 Score: 300
Period size: 96 Copynumber: 2.6 Consensus size: 98
39593220 TGTGTCTTCA
* * *
39593230 ATCTTTCTAAAGGTACCGGGTTTGCCGTTGCGGCCTAAACCTTTCCCTTCATATCTTCATGGTAC
1 ATCTTT-T-AAGGTACCGGGTTCGCCGTTGCGGCCTAAACCTTTCACTT-ATATCCTCATGGTAC
* * * *
39593295 CGGATTCACAGTCGCGGCTTCAATCCTTCCCGTCTC
63 CAGATCCACAGTCGCGGCTTCAATCCTTCCCATCAC
* *
39593331 ATCTTTTAAGGTACCAGGTTCGCCGTTGCGGCCTAAACCTTTCACTT-TTTCCT-ATGGTACCAG
1 ATCTTTTAAGGTACCGGGTTCGCCGTTGCGGCCTAAACCTTTCACTTATATCCTCATGGTACCAG
* * * *
39593394 ATCCGCCGTTGCGGCTTCGATCCTTCCCATCAC
66 ATCCACAGTCGCGGCTTCAATCCTTCCCATCAC
* * * * *
39593427 ATCTTCTAAGATACCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATG
1 ATCTTTTAAGGTACCGGGTTCGCCGTTGCGGCCTAAACCTTTCACTT-ATATCCTCATG
39593486 TTTTCTTGGT
Statistics
Matches: 132, Mismatches: 20, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
96 77 0.58
97 4 0.03
98 4 0.03
99 40 0.30
100 1 0.01
101 6 0.05
ACGTcount: A:0.17, C:0.32, G:0.18, T:0.33
Consensus pattern (98 bp):
ATCTTTTAAGGTACCGGGTTCGCCGTTGCGGCCTAAACCTTTCACTTATATCCTCATGGTACCAG
ATCCACAGTCGCGGCTTCAATCCTTCCCATCAC
Found at i:39593481 original size:50 final size:50
Alignment explanation
Indices: 39593225--39593482 Score: 201
Period size: 50 Copynumber: 5.2 Consensus size: 50
39593215 ATTGGTGTGT
* *
39593225 CTTCA-ATCTTTCTAAAGGTACCGGGTTTGCCGTTGCGGCCTAAACCTTTCC
1 CTTCATATC-TTCT-AAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
* * * * * *
39593276 CTTCATATCTTC-ATGGTACCGGATTCACAGTCGCGGCTTCAATCC-TTCC
1 CTTCATATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAA-CCTTTCC
* * * * *
39593325 CGTC-TCATCTTTTAAGGTACCAGGTTCGCCGTTGCGGCCTAAACCTTTCA
1 CTTCAT-ATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
* * * * * * *
39593375 CTT--T-T-TCCTATGGTACCAGATCCGCCGTTGCGGCTTCGATCC-TTCC
1 CTTCATATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTC-AACCTTTCC
* * *
39593421 CATCACATCTTCTAAGATACCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
1 CTTCATATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
39593471 CTTCATATCTTC
1 CTTCATATCTTC
39593483 ATGTTTTCTT
Statistics
Matches: 155, Mismatches: 41, Indels: 23
0.71 0.19 0.11
Matches are distributed among these distances:
46 30 0.19
47 4 0.03
48 1 0.01
49 41 0.26
50 68 0.44
51 8 0.05
52 3 0.02
ACGTcount: A:0.17, C:0.33, G:0.18, T:0.33
Consensus pattern (50 bp):
CTTCATATCTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTTCC
Found at i:39600158 original size:30 final size:29
Alignment explanation
Indices: 39599915--39600228 Score: 209
Period size: 30 Copynumber: 10.6 Consensus size: 29
39599905 GAAGAATTTT
* * * *
39599915 GGGTTAAAATGTAATTTTAGAAAAATTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTG
** * * *
39599944 GGGTCAAAACATAAATTTAGGAAATGTTTA
1 GGGTCAAAATGT-AATTTTGGAAAAGTTTG
* *
39599974 GGGTCAAATATG--ATTTTGGAGAGGTTTG
1 GGGTCAAA-ATGTAATTTTGGAAAAGTTTG
* *
39600002 GGAGTCAAAATGTGATTTTGGAAAGGTTTG
1 GG-GTCAAAATGTAATTTTGGAAAAGTTTG
* * *
39600032 GGAGTCAAAATGTGATTTTGGGAATGTTTAG
1 GG-GTCAAAATGTAATTTTGGAAAAGTTT-G
* * ** *
39600063 CGGTTAAAATGTGCTTTTGGGAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTT-G
* *
39600093 GGGTCAAAATGTAATTTTAGAAAAATTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTT-G
*
39600123 GGGTTAAAATGTAATTTTGGAAAAGTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTG
* * * *
39600152 GAGGTTAAAATATAATTTTGAAAAAGTTTA
1 G-GGTCAAAATGTAATTTTGGAAAAGTTTG
* * * * * * *
39600182 GGATTAAAATGCAATTTTTGAAAGGTCTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTG
* *
39600211 GGATCAGAATGTAATTTT
1 GGGTCAAAATGTAATTTT
39600229 TAAGTAAAAT
Statistics
Matches: 235, Mismatches: 43, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
28 17 0.07
29 53 0.23
30 162 0.69
31 3 0.01
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTG
Found at i:39600171 original size:90 final size:89
Alignment explanation
Indices: 39599915--39600183 Score: 260
Period size: 90 Copynumber: 3.0 Consensus size: 89
39599905 GAAGAATTTT
* ** * *
39599915 GGGTTAAAATGTAATTTTAGAAAAATTTA-GGGTCAAAACATAAATTTAGGAAATGTTT-AGGGT
1 GGGTCAAAATGTAATTTTAGAAAAATTTAGGGGTCAAAATGT-AATTTTGGAAATGTTTGAGGTT
* *
39599978 CAAATATGATTTT-GGAGAGGTTT-G
65 AAAATATGATTTTGGGA-AAGTTTAG
* * ** * * *
39600002 GGAGTCAAAATGTGATTTTGGAAAGGTTT-GGGAGTCAAAATGTGATTTTGGGAATGTTTAGCGG
1 GG-GTCAAAATGTAATTTTAGAAAAATTTAGGG-GTCAAAATGTAATTTTGGAAATGTTT-GAGG
* *
39600066 TTAAAATGTGCTTTTGGGAAAGTTTAG
63 TTAAAATATGATTTTGGGAAAGTTTAG
* *
39600093 GGGTCAAAATGTAATTTTAGAAAAATTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTGGAGGTT
1 GGGTCAAAATGTAATTTTAGAAAAATTTAGGGGTCAAAATGTAATTTTGGAAATGTTT-GAGGTT
* **
39600158 AAAATATAATTTTGAAAAAGTTTAG
65 AAAATATGATTTTGGGAAAGTTTAG
39600183 G
1 G
39600184 ATTAAAATGC
Statistics
Matches: 143, Mismatches: 31, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
87 2 0.01
88 36 0.25
89 8 0.06
90 88 0.62
91 9 0.06
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (89 bp):
GGGTCAAAATGTAATTTTAGAAAAATTTAGGGGTCAAAATGTAATTTTGGAAATGTTTGAGGTTA
AAATATGATTTTGGGAAAGTTTAG
Found at i:39601267 original size:7 final size:7
Alignment explanation
Indices: 39601248--39601280 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
39601238 GACTGCCCTT
39601248 TTTATTA
1 TTTATTA
39601255 -TTATTA
1 TTTATTA
39601261 TTTATTA
1 TTTATTA
39601268 TTTATTA
1 TTTATTA
*
39601275 TATATT
1 TTTATT
39601281 TATTATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTATTA
Found at i:39601295 original size:14 final size:11
Alignment explanation
Indices: 39601248--39601287 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
39601238 GACTGCCCTT
39601248 TTTATTAT-TA
1 TTTATTATATA
39601258 -TTATT-TATTA
1 TTTATTATA-TA
39601268 TTTATTATATA
1 TTTATTATATA
39601279 TTTATTATA
1 TTTATTATA
39601288 AATCATTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
8 1 0.04
9 5 0.19
10 2 0.08
11 16 0.62
12 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATTATATA
Found at i:39601539 original size:28 final size:27
Alignment explanation
Indices: 39601481--39601549 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 27
39601471 TTCATATTTC
*** *
39601481 TATTGATTTCGAATATTTTTGTCTTTA
1 TATTGATTTCGAATAAACTTGTCTGTA
*
39601508 TATTGATTTCGAAATAAACTTGTCTGTG
1 TATTGATTTCG-AATAAACTTGTCTGTA
* *
39601536 TATTGGTTTTGAAT
1 TATTGATTTCGAAT
39601550 GCTAGAAGGT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
27 14 0.41
28 20 0.59
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.52
Consensus pattern (27 bp):
TATTGATTTCGAATAAACTTGTCTGTA
Found at i:39602825 original size:13 final size:14
Alignment explanation
Indices: 39602802--39602831 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
39602792 ATCATTACAC
39602802 AACCTCAAGATTCA
1 AACCTCAAGATTCA
39602816 AACC-CAAGATTCA
1 AACCTCAAGATTCA
39602829 AAC
1 AAC
39602832 TTTCATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.47, C:0.30, G:0.07, T:0.17
Consensus pattern (14 bp):
AACCTCAAGATTCA
Found at i:39603696 original size:21 final size:21
Alignment explanation
Indices: 39603672--39603711 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39603662 GTTTATTTCC
*
39603672 TTGTATTTAAAAGTTAGTTAG
1 TTGTAGTTAAAAGTTAGTTAG
**
39603693 TTGTAGTTATTAGTTAGTT
1 TTGTAGTTAAAAGTTAGTT
39603712 TTTTTAGCTG
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:0.28, C:0.00, G:0.20, T:0.53
Consensus pattern (21 bp):
TTGTAGTTAAAAGTTAGTTAG
Found at i:39611643 original size:36 final size:36
Alignment explanation
Indices: 39611598--39611690 Score: 132
Period size: 36 Copynumber: 2.6 Consensus size: 36
39611588 ATGATTGATG
* * *
39611598 AACTTACCAATATTGGTGAACACCCTCAGAATGGCA
1 AACTCACCAATATTGGTGAACACCCCCAGAATAGCA
*
39611634 AACTCACCAATATTGGTGAACTCCCCCAGAATAGCA
1 AACTCACCAATATTGGTGAACACCCCCAGAATAGCA
* *
39611670 AACACACCAATATTGATGAAC
1 AACTCACCAATATTGGTGAAC
39611691 CCTCTAAGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.20
Consensus pattern (36 bp):
AACTCACCAATATTGGTGAACACCCCCAGAATAGCA
Found at i:39615915 original size:24 final size:24
Alignment explanation
Indices: 39615884--39615942 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
39615874 GAAGAAGGTT
*
39615884 AACT-GGTTCATAATATCATGGTG
1 AACTAGGTTCATAATATCATGGCG
*
39615907 AACTAGGTTCACAATATCATGGCG
1 AACTAGGTTCATAATATCATGGCG
* *
39615931 AGCAAGGTTCAT
1 AACTAGGTTCAT
39615943 TGAGACATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 4 0.13
24 26 0.87
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (24 bp):
AACTAGGTTCATAATATCATGGCG
Found at i:39620612 original size:21 final size:22
Alignment explanation
Indices: 39620583--39620625 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
39620573 ATAACAACAA
*
39620583 CAAACATAAAAT-AAAAATGTT
1 CAAAAATAAAATAAAAAATGTT
*
39620604 CAAAAATAAATTAAAAAATGTT
1 CAAAAATAAAATAAAAAATGTT
39620626 TAATAGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.26
Consensus pattern (22 bp):
CAAAAATAAAATAAAAAATGTT
Found at i:39638567 original size:13 final size:15
Alignment explanation
Indices: 39638548--39638583 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
39638538 TGCCATCGTA
39638548 GTAATTGTACC-TCT
1 GTAATTGTACCATCT
39638562 -TAATTG-ACCATCT
1 GTAATTGTACCATCT
39638575 GTAATTGTA
1 GTAATTGTA
39638584 ATCGTTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 3 0.16
13 9 0.47
14 6 0.32
15 1 0.05
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.42
Consensus pattern (15 bp):
GTAATTGTACCATCT
Found at i:39638700 original size:3 final size:3
Alignment explanation
Indices: 39638685--39638720 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
39638675 CTATAGCCTA
*
39638685 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
39638721 GAAAATGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39643655 original size:53 final size:53
Alignment explanation
Indices: 39643597--39643940 Score: 393
Period size: 53 Copynumber: 6.6 Consensus size: 53
39643587 TCACATTTGA
* *
39643597 AACTCACGATGACACAGAATCATCGGACCTTTAATCCATGATAGGATTCTTGT
1 AACTCACGATGACACAGAATCATCGGACCTTTAATCCATGATAGGATTCATAT
* *
39643650 AACTCACGATGACACA-AAGTCATCGGACCCTTAATCCGT-AGTAGGATTCATAT
1 AACTCACGATGACACAGAA-TCATCGGACCTTTAATCCATGA-TAGGATTCATAT
* * * * *
39643703 AACTCACGAT-A-ACATAGTCATCAGACCTTTAAT-CAGTAATAGGATTCGTAT
1 AACTCACGATGACACAGAATCATCGGACCTTTAATCCA-TGATAGGATTCATAT
* * * *
39643754 AACTCACGATGACATAGAGTCATCGGACCTTTAATCCGTGATAGGATTCGTAT
1 AACTCACGATGACACAGAATCATCGGACCTTTAATCCATGATAGGATTCATAT
39643807 AACTCACGATGACACAGAATCATCGGACCTTTAAT-CAGTGATAGGATTCATAT
1 AACTCACGATGACACAGAATCATCGGACCTTTAATCCA-TGATAGGATTCATAT
* * * * *
39643860 -ACTCACGATGATATATAATCATCGGACC--TCATCCATAATAGGATTCATAT
1 AACTCACGATGACACAGAATCATCGGACCTTTAATCCATGATAGGATTCATAT
* * *
39643910 -ACTTACGATGATACATAATCATCGGACCTTT
1 AACTCACGATGACACAGAATCATCGGACCTTT
39643941 TTGCATTTTC
Statistics
Matches: 254, Mismatches: 25, Indels: 25
0.84 0.08 0.08
Matches are distributed among these distances:
50 44 0.17
51 41 0.16
52 34 0.13
53 134 0.53
54 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (53 bp):
AACTCACGATGACACAGAATCATCGGACCTTTAATCCATGATAGGATTCATAT
Found at i:39643757 original size:104 final size:106
Alignment explanation
Indices: 39643597--39643940 Score: 436
Period size: 104 Copynumber: 3.3 Consensus size: 106
39643587 TCACATTTGA
* *
39643597 AACTCACGATGACACAGAATCATCGGACCTTTAATCCA-TGATAGGATTCTTGTAACTCACGATG
1 AACTCACGATGACACAGAATCATCGGACCTTTAAT-CAGTGATAGGATTCATATAACTCACGATG
*
39643661 ACACAAAGTCATCGGACCCTTAATCCGTAGTAGGATTCATAT
65 ACATAAAGTCATCGGACCCTTAATCCGTAGTAGGATTCATAT
* * * * *
39643703 AACTCACGAT-A-ACATAGTCATCAGACCTTTAATCAGTAATAGGATTCGTATAACTCACGATGA
1 AACTCACGATGACACAGAATCATCGGACCTTTAATCAGTGATAGGATTCATATAACTCACGATGA
* * *
39643766 CATAGAGTCATCGGACCTTTAATCCGT-GATAGGATTCGTAT
66 CATAAAGTCATCGGACCCTTAATCCGTAG-TAGGATTCATAT
39643807 AACTCACGATGACACAGAATCATCGGACCTTTAATCAGTGATAGGATTCATAT-ACTCACGATGA
1 AACTCACGATGACACAGAATCATCGGACCTTTAATCAGTGATAGGATTCATATAACTCACGATGA
* * * *
39643871 TATATAA-TCATCGGA-CC-TCATCCATAATAGGATTCATAT
66 CATA-AAGTCATCGGACCCTTAATCCGTAGTAGGATTCATAT
* * *
39643910 -ACTTACGATGATACATAATCATCGGACCTTT
1 AACTCACGATGACACAGAATCATCGGACCTTT
39643941 TTGCATTTTC
Statistics
Matches: 207, Mismatches: 25, Indels: 16
0.83 0.10 0.06
Matches are distributed among these distances:
102 28 0.14
103 20 0.10
104 89 0.43
105 24 0.12
106 46 0.22
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (106 bp):
AACTCACGATGACACAGAATCATCGGACCTTTAATCAGTGATAGGATTCATATAACTCACGATGA
CATAAAGTCATCGGACCCTTAATCCGTAGTAGGATTCATAT
Found at i:39643926 original size:157 final size:154
Alignment explanation
Indices: 39643597--39643940 Score: 430
Period size: 157 Copynumber: 2.2 Consensus size: 154
39643587 TCACATTTGA
* * *
39643597 AACTCACGATGACACAGAATCATCGGACCTTTAATCCATGATAGGATTCTTGTAACTCACGATGA
1 AACTCACGATG--ACATAATCATCGGACCTTTAATCCATGATAGGATTCGTATAACTCACGATGA
* *
39643662 CACAAAGTCATCGGACCCTTAATCCGTAGTAGGATTCATATAACTCACGATAACATAGTCATCAG
64 CACAAAGTCATCGGACCCTTAATCAGTAGTAGGATTCATATAACTCACGATAACATAATCATCAG
*
39643727 ACCTTTAATCAGTAATAGGATTCGTAT
129 ACC-TTAATCAGTAATAGGATTCATAT
*
39643754 AACTCACGATGACATAGAGTCATCGGACCTTTAATCCGTGATAGGATTCGTATAACTCACGATGA
1 AACTCACGATGACATA-A-TCATCGGACCTTTAATCCATGATAGGATTCGTATAACTCACGATGA
* *
39643819 CACAGAA-TCATCGGACCTTTAATCAGT-GATAGGATTCATAT-ACTCACGATGATATATAATCA
64 CACA-AAGTCATCGGACCCTTAATCAGTAG-TAGGATTCATATAACTCACGAT-A-ACATAATCA
* *
39643881 TCGGACC-TCATCCA-TAATAGGATTCATAT
125 TCAGACCTTAAT-CAGTAATAGGATTCATAT
*
39643910 -ACTTACGATGATACATAATCATCGGACCTTT
1 AACTCACGATG--ACATAATCATCGGACCTTT
39643941 TTGCATTTTC
Statistics
Matches: 166, Mismatches: 12, Indels: 20
0.84 0.06 0.10
Matches are distributed among these distances:
155 26 0.16
156 29 0.17
157 96 0.58
158 15 0.09
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (154 bp):
AACTCACGATGACATAATCATCGGACCTTTAATCCATGATAGGATTCGTATAACTCACGATGACA
CAAAGTCATCGGACCCTTAATCAGTAGTAGGATTCATATAACTCACGATAACATAATCATCAGAC
CTTAATCAGTAATAGGATTCATAT
Found at i:39645737 original size:10 final size:10
Alignment explanation
Indices: 39645724--39645757 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
39645714 GAAAAAGTGC
39645724 AAAGAAAACT
1 AAAGAAAACT
39645734 AAAGAAAACTT
1 AAAGAAAAC-T
*
39645745 AGAGAAAACT
1 AAAGAAAACT
39645755 AAA
1 AAA
39645758 CCTAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.68, C:0.09, G:0.12, T:0.12
Consensus pattern (10 bp):
AAAGAAAACT
Done.