Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002890.1 Hibiscus syriacus cultivar Beakdansim tig00005974_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5046466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 21
Found at i:1267676 original size:109 final size:109
Alignment explanation
Indices: 1267486--1267956 Score: 580
Period size: 109 Copynumber: 4.4 Consensus size: 109
1267476 AGCTAGAGTT
* * *
1267486 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGCCAAC-AACAATTTCCCAATTTCGGAACCGA
1 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCGA
* *
1267550 TTTCAACTCCATGACGGAGGATATCGTGCTAC-CAGAGATAACAC
66 TTTCAACTCCACGACGGAGGATATCGTGCTACTC-GAGACAACAC
*
1267594 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCGA
1 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCGA
*
1267659 TTTCAACTCCACGACGGAGGATATCGTGCTA-TCCGAGAAAACAC
66 TTTCAACTCCACGACGGAGGATATCGTGCTACT-CGAGACAACAC
* * ** * **
1267703 AAGTCCAACTTCACAACGAAGGGACGACTGGTTGTCAACGAACAACTTTTCAGTTTCA-TCCGCG
1 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAAC-CG
*
1267767 ATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACAC
65 ATTTCAACTCCACGACGGAGGATATCGTGCTACTCGAGACAACAC
* ** * ** * * * *
1267812 AAGTTCAACTTCACAATGAAGGGACAACTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCAA
1 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCGA
* * *
1267877 TTTCAACTTCAC-ATCGAAGGATAT--TG-GACTCGAGACAACAC
66 TTTCAACTCCACGA-CGGAGGATATCGTGCTACTCGAGACAACAC
* *
1267918 AAGTTCAACTTCACAACGAAGGGACGGATGATTGTCAAC
1 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC
1267957 AAGATTTCGT
Statistics
Matches: 320, Mismatches: 36, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
106 48 0.15
107 2 0.01
108 40 0.12
109 227 0.71
110 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (109 bp):
AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTTCAGAACCGA
TTTCAACTCCACGACGGAGGATATCGTGCTACTCGAGACAACAC
Found at i:1267953 original size:106 final size:104
Alignment explanation
Indices: 1267486--1268114 Score: 467
Period size: 109 Copynumber: 5.9 Consensus size: 104
1267476 AGCTAGAGTT
* * * * *
1267486 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGCCAACAACAATTTCCCAATTTCGGAACCGAT
1 AAGTTCAACTTCACAACGAAGGGACGGATGGTTGTCAACAAC-ATTTTCCAATTTCAGAACCAAT
* * * * *
1267551 TTCAACTCCATGACGGAGGATATCGTG-CTACCAGAGATAACAC
65 TTCAACTTCA-CACGAAGGATATTGTGACT--C-GAGACAACAC
* * * * *
1267594 AAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTCCCAATTCCAGAACCGA
1 AAGTTCAACTTCACAACGAAGGGACGGATGGTTGTCAAC-AAC-ATTTTCCAATTTCAGAACCAA
* * * *
1267659 TTTCAACTCCACGACGGAGGATATCGTG-CTATCCGAGAAAACAC
64 TTTCAACTTCAC-ACGAAGGATATTGTGAC--T-CGAGACAACAC
* * **
1267703 AAGTCCAACTTCACAACGAAGGGAC-GACTGGTTGTCAACGAACAACTTTT-CAGTTTCA-TCCG
1 AAGTTCAACTTCACAACGAAGGGACGGA-TGGTTGTCAAC-AAC-A-TTTTCCAATTTCAGAAC-
* * * *
1267765 CGATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACAC
61 CAATTTCAACTTCAC-ACGAAGGATATTGTG--ACTCGAGACAACAC
* * * *
1267812 AAGTTCAACTTCACAATGAAGGGAC-AACTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 AAGTTCAACTTCACAACGAAGGGACGGA-TGGTTGTCAAC-AACA-TTTTCCAATTTCAGAACCA
1267876 ATTTCAACTTCACATCGAAGGATATTG-GACTCGAGACAACAC
63 ATTTCAACTTCACA-CGAAGGATATTGTGACTCGAGACAACAC
* * * **
1267918 AAGTTCAACTTCACAACGAAGGGACGGATGATTGTCAACAAGA-TTT-C-GTTT-AGAGTCAATT
1 AAGTTCAACTTCACAACGAAGGGACGGATGGTTGTCAACAACATTTTCCAATTTCAGAACCAATT
* *
1267979 TCAACTTCACAGCGAAGGATATT-AGACTCGAGACAGCAC
66 TCAACTTCACA-CGAAGGATATTGTGACTCGAGACAACAC
* * * * *** * ***
1268018 AAGCTCAACTTCACAGCGAAGGGGCGGCTAACTGTCAACAAACAATTTCCCGGTTCTAGAACCAA
1 AAGTTCAACTTCACAACGAAGGGACGGATGGTTGTCAAC-AACATTTTCCAATTTC-AGAACCAA
1268083 TTTCAACTTCACA-GCAGAGGATATTG-GACTCG
64 TTTCAACTTCACACG-A-AGGATATTGTGACTCG
1268115 GAACAATATT
Statistics
Matches: 450, Mismatches: 47, Indels: 50
0.82 0.09 0.09
Matches are distributed among these distances:
100 78 0.17
101 6 0.01
102 3 0.01
103 4 0.01
104 4 0.01
105 4 0.01
106 81 0.18
107 1 0.00
108 47 0.10
109 214 0.48
110 6 0.01
111 1 0.00
112 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (104 bp):
AAGTTCAACTTCACAACGAAGGGACGGATGGTTGTCAACAACATTTTCCAATTTCAGAACCAATT
TCAACTTCACACGAAGGATATTGTGACTCGAGACAACAC
Found at i:1268673 original size:37 final size:36
Alignment explanation
Indices: 1268575--1268675 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 36
1268565 TTTCGTCCTA
1268575 CTAGGATTCAAACT-CTCAAAAATAGGATAGAATTCTG
1 CTAGGATT-AAACTCCT-AAAAATAGGATAGAATTCTG
* *
1268612 CTAGGATTCAACTCCTAAAAATAGGATAGAATTTTG
1 CTAGGATTAAACTCCTAAAAATAGGATAGAATTCTG
** *
1268648 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTAAACTCCTAAAAATAGGAT
1268676 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
36 26 0.46
37 30 0.54
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (36 bp):
CTAGGATTAAACTCCTAAAAATAGGATAGAATTCTG
Found at i:1280999 original size:5 final size:5
Alignment explanation
Indices: 1280989--1281019 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
1280979 CTTCAACTTC
1280989 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
1281020 CTTTTTGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:1281040 original size:28 final size:29
Alignment explanation
Indices: 1281009--1281072 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
1280999 TTTCTTTTCT
*
1281009 TTTCTTTTC-TTCTTTTTGAGTGCTGAAA
1 TTTCTTTTCTTTCTTTTGGAGTGCTGAAA
**
1281037 TTTC-TTTCTTTCTTTTGGAGTGCTTCAA
1 TTTCTTTTCTTTCTTTTGGAGTGCTGAAA
1281065 TTTCTTTT
1 TTTCTTTT
1281073 TCTGATTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 4 0.13
28 24 0.77
29 3 0.10
ACGTcount: A:0.11, C:0.16, G:0.12, T:0.61
Consensus pattern (29 bp):
TTTCTTTTCTTTCTTTTGGAGTGCTGAAA
Found at i:1282013 original size:91 final size:91
Alignment explanation
Indices: 1281835--1282015 Score: 272
Period size: 91 Copynumber: 2.0 Consensus size: 91
1281825 TAGTTGATGT
* *
1281835 TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGTGCCTAAATGAACCATATGCAAGGCACATGGG
1 TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATGGG
* *
1281900 GGCTTATCACATGCAAAACACATGGC
66 GGCTGATCACATACAAAACACATGGC
* *
1281926 TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGATCCACATGCAAGGCATATGGG
1 TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATGGG
* * **
1281991 GGCTGGTCATATACAAGGCACATGG
66 GGCTGATCACATACAAAACACATGG
1282016 GTGTTCTAGG
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 80 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (91 bp):
TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATGAACCACATGCAAGGCACATGGG
GGCTGATCACATACAAAACACATGGC
Found at i:1285436 original size:24 final size:23
Alignment explanation
Indices: 1285409--1285456 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 23
1285399 GCTCTGGGAT
1285409 TGAAAAACAAGCTGAAAAACAAGC
1 TGAAAAACAAGCTG-AAAACAAGC
*
1285433 TGAAAAACAAGCTGAAGACAAGC
1 TGAAAAACAAGCTGAAAACAAGC
1285456 T
1 T
1285457 TGGGAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.54, C:0.17, G:0.19, T:0.10
Consensus pattern (23 bp):
TGAAAAACAAGCTGAAAACAAGC
Found at i:1285456 original size:11 final size:12
Alignment explanation
Indices: 1285409--1285448 Score: 80
Period size: 12 Copynumber: 3.3 Consensus size: 12
1285399 GCTCTGGGAT
1285409 TGAAAAACAAGC
1 TGAAAAACAAGC
1285421 TGAAAAACAAGC
1 TGAAAAACAAGC
1285433 TGAAAAACAAGC
1 TGAAAAACAAGC
1285445 TGAA
1 TGAA
1285449 GACAAGCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.57, C:0.15, G:0.17, T:0.10
Consensus pattern (12 bp):
TGAAAAACAAGC
Found at i:1292013 original size:13 final size:13
Alignment explanation
Indices: 1291968--1292015 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
1291958 ATGCGCAATA
1291968 CGCGTCATAAATG
1 CGCGTCATAAATG
* *
1291981 CACATCATAAATG
1 CGCGTCATAAATG
* *
1291994 TGTGTCATAAATG
1 CGCGTCATAAATG
1292007 CGCGTCATA
1 CGCGTCATA
1292016 GATTTATGAC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (13 bp):
CGCGTCATAAATG
Found at i:1295945 original size:36 final size:36
Alignment explanation
Indices: 1295905--1295978 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
1295895 TTGAAGTCTC
*
1295905 TATAGGTTCAAC-TTCGATCAAACTGGTAATTCCTTA
1 TATAGGTTCAACATT-AATCAAACTGGTAATTCCTTA
**
1295941 TATAGGTTCAACATTAATCAAGTTGGTAATTCCTTA
1 TATAGGTTCAACATTAATCAAACTGGTAATTCCTTA
1295977 TA
1 TA
1295979 GAATAAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 32 0.94
37 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (36 bp):
TATAGGTTCAACATTAATCAAACTGGTAATTCCTTA
Found at i:1298870 original size:44 final size:47
Alignment explanation
Indices: 1298820--1298931 Score: 140
Period size: 44 Copynumber: 2.4 Consensus size: 47
1298810 GTAACCATGC
1298820 AAATAAGCTTATGAGCTTACGGAA-T-AATGGCAAGCATATTGG-AA
1 AAATAAGCTTATGAGCTTACGGAATTAAATGGCAAGCATATTGGTAA
* * * * *
1298864 AAATAAGCTTACGAGCTTATGGAATTTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTACGGAA--TTAAATGGCAAGCATATTGGTAA
1298913 AAATAAGCTTATGAGCTTA
1 AAATAAGCTTATGAGCTTA
1298932 TGGGATAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
44 22 0.39
47 1 0.02
48 14 0.25
49 20 0.35
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (47 bp):
AAATAAGCTTATGAGCTTACGGAATTAAATGGCAAGCATATTGGTAA
Found at i:1298922 original size:49 final size:44
Alignment explanation
Indices: 1298820--1298939 Score: 141
Period size: 49 Copynumber: 2.6 Consensus size: 44
1298810 GTAACCATGC
*
1298820 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGCATATTGGAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGCATATTGGAA
* * * *
1298864 AAATAAGCTTACGAGCTTATGGAATTTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA---T-AATGGCAAGCATATTGG-AA
*
1298913 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
1298940 AAGGTAAGAA
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
44 22 0.34
45 2 0.03
46 1 0.02
47 1 0.02
48 14 0.22
49 24 0.38
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGCATATTGGAA
Found at i:1302573 original size:20 final size:20
Alignment explanation
Indices: 1302550--1302587 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1302540 TAGAACCGAT
1302550 CTGAGTCAACCCAAACCATC
1 CTGAGTCAACCCAAACCATC
* *
1302570 CTGAGTTAACTCAAACCA
1 CTGAGTCAACCCAAACCA
1302588 ATCTGATCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.34, G:0.11, T:0.18
Consensus pattern (20 bp):
CTGAGTCAACCCAAACCATC
Found at i:1302593 original size:20 final size:19
Alignment explanation
Indices: 1302543--1302593 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
1302533 AACCCCCTAG
1302543 AACCGATCTGAGTCAACCCA
1 AACC-ATCTGAGTCAACCCA
* *
1302563 AACCATCCTGAGTTAACTCA
1 AACCAT-CTGAGTCAACCCA
1302583 AACCAATCTGA
1 AACC-ATCTGA
1302594 TCCATTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.37, C:0.31, G:0.12, T:0.20
Consensus pattern (19 bp):
AACCATCTGAGTCAACCCA
Found at i:1307240 original size:12 final size:13
Alignment explanation
Indices: 1307212--1307243 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1307202 ATACCTCTTC
1307212 AAAAAG-AGAGAG
1 AAAAAGAAGAGAG
1307224 AAAAAGAAGAGA-
1 AAAAAGAAGAGAG
1307236 AAAAAGAA
1 AAAAAGAA
1307244 AATACCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
AAAAAGAAGAGAG
Found at i:1313778 original size:4 final size:4
Alignment explanation
Indices: 1313769--1313799 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1313759 CAATAAGCTG
1313769 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1313800 AAGTAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1314605 original size:24 final size:23
Alignment explanation
Indices: 1314551--1314614 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 23
1314541 AATAGTAAAT
1314551 TTATAA-AAAAAATAAAAATTATA
1 TTATAATAAAAAATAAAAA-TATA
1314574 TTACTAATAAAAATATAAAAA-ATGA
1 TTA-TAATAAAAA-ATAAAAATAT-A
**
1314599 TTATAATTTAAAATAA
1 TTATAATAAAAAATAA
1314615 TTTAGAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
23 7 0.20
24 12 0.34
25 9 0.26
26 7 0.20
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
TTATAATAAAAAATAAAAATATA
Found at i:1316886 original size:48 final size:49
Alignment explanation
Indices: 1316817--1316923 Score: 148
Period size: 48 Copynumber: 2.2 Consensus size: 49
1316807 CATAATTCAC
*
1316817 GTCAAGTATCATATCAAAATCCAGGTCA-AGTATCAGATCAGAATCCA-A
1 GTCAAGTATCAGATCAAAATCCAGGTCAGA-TATCAGATCAGAATCCATA
* * *
1316865 GTCAAGTATCAGATCAGAATCCATGTCAGATATCATATCAGAATCCATA
1 GTCAAGTATCAGATCAAAATCCAGGTCAGATATCAGATCAGAATCCATA
1316914 -TCAAGTATCA
1 GTCAAGTATCA
1316924 TATCGTAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
48 51 0.96
49 2 0.04
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (49 bp):
GTCAAGTATCAGATCAAAATCCAGGTCAGATATCAGATCAGAATCCATA
Found at i:1316924 original size:24 final size:24
Alignment explanation
Indices: 1316818--1316927 Score: 134
Period size: 24 Copynumber: 4.6 Consensus size: 24
1316808 ATAATTCACG
* **
1316818 TCAAGTATCATATCAAAATCCAGG
1 TCAAGTATCATATCAGAATCCATA
*
1316842 TCAAGTATCAGATCAGAATCCA-A
1 TCAAGTATCATATCAGAATCCATA
* *
1316865 GTCAAGTATCAGATCAGAATCCATG
1 -TCAAGTATCATATCAGAATCCATA
1316890 TC-AGATATCATATCAGAATCCATA
1 TCAAG-TATCATATCAGAATCCATA
1316914 TCAAGTATCATATC
1 TCAAGTATCATATC
1316928 GTAAATCAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
23 2 0.03
24 72 0.95
25 2 0.03
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (24 bp):
TCAAGTATCATATCAGAATCCATA
Found at i:1322350 original size:60 final size:61
Alignment explanation
Indices: 1322237--1322368 Score: 137
Period size: 60 Copynumber: 2.2 Consensus size: 61
1322227 TAGTATAATG
* ** *
1322237 ATCATTTTATAACCTTTAATAATTAGAAGAATCAACAAAATATCCTCCTATAAT-ATAAAA
1 ATCATTTTATAACCTTTAATAATCAGAAGAATCAACAAAATATCCTCAAATAATCAGAAAA
** * *
1322297 ATCATTTTATAATTTTTAATAATCATAA-ATTCAACAAAATAAT-CTACAAATAATCAGAAAA
1 ATCATTTTATAACCTTTAATAATCAGAAGAATCAACAAAAT-ATCCT-CAAATAATCAGAAAA
1322358 A-CATTTATATA
1 ATCATTT-TATA
1322369 GCTTATCCTT
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
59 13 0.22
60 37 0.62
61 10 0.17
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (61 bp):
ATCATTTTATAACCTTTAATAATCAGAAGAATCAACAAAATATCCTCAAATAATCAGAAAA
Found at i:1325649 original size:3 final size:3
Alignment explanation
Indices: 1325629--1325675 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
1325619 ATCACCATTT
* *
1325629 TTA TT- TTA TTA GTA TTA TTA TTA TTA -TA TTA TTA GTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1325675 T
1 T
1325676 ATTGCAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1325658 original size:20 final size:20
Alignment explanation
Indices: 1325629--1325678 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1325619 ATCACCATTT
* *
1325629 TTATTTTATTAGTATTATTA
1 TTATTATATTAGTAGTATTA
*
1325649 TTATTATATTATTAGTATTA
1 TTATTATATTAGTAGTATTA
1325669 TTATTATATT
1 TTATTATATT
1325679 GCAAAAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (20 bp):
TTATTATATTAGTAGTATTA
Found at i:1325660 original size:23 final size:23
Alignment explanation
Indices: 1325629--1325675 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1325619 ATCACCATTT
*
1325629 TTATTTTATTAGTATTATTATTA
1 TTATATTATTAGTATTATTATTA
1325652 TTATATTATTAGTATTATTATTA
1 TTATATTATTAGTATTATTATTA
1325675 T
1 T
1325676 ATTGCAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (23 bp):
TTATATTATTAGTATTATTATTA
Found at i:1327926 original size:23 final size:23
Alignment explanation
Indices: 1327867--1327943 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 23
1327857 GAGAAAAAAG
*
1327867 AAAAGATAAAGAAAATTAAA-AATTA
1 AAAAGATAGAGAAAA-TAAAGAA--A
*
1327892 AAAAAATGAGAGAAAATAAAGAAA
1 AAAAGAT-AGAGAAAATAAAGAAA
* *
1327916 AAAAGATAGAGAAAAGAAAGCAA
1 AAAAGATAGAGAAAATAAAGAAA
1327939 AAAAG
1 AAAAG
1327944 GGGGAAGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
23 19 0.42
24 7 0.16
25 10 0.22
26 9 0.20
ACGTcount: A:0.73, C:0.01, G:0.16, T:0.10
Consensus pattern (23 bp):
AAAAGATAGAGAAAATAAAGAAA
Found at i:1330185 original size:57 final size:57
Alignment explanation
Indices: 1330097--1330268 Score: 247
Period size: 57 Copynumber: 3.0 Consensus size: 57
1330087 GTTACCCAAT
* * *
1330097 ATGATATTTTCAAATGAATTTTAAAAGAAGCTAAGTCTCATTTTTGGAAGTTTCTTG
1 ATGATATTTTCAAATGAATTTTCAAAGAAGCTAAGTCTGATTTTTAGAAGTTTCTTG
* * *
1330154 ATGATATTTTGAAATGAATTTTCAAAGAAGCTAAGTCTGATTTTCAGAAGTTTCTTA
1 ATGATATTTTCAAATGAATTTTCAAAGAAGCTAAGTCTGATTTTTAGAAGTTTCTTG
* * *
1330211 ATGAT-TTCTTCAAATGATTTTTCAAAGAAACTAAGTCTGATTTTTAGAGGTTTCTTG
1 ATGATATT-TTCAAATGAATTTTCAAAGAAGCTAAGTCTGATTTTTAGAAGTTTCTTG
1330268 A
1 A
1330269 GGATTACCCA
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
56 2 0.02
57 100 0.98
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (57 bp):
ATGATATTTTCAAATGAATTTTCAAAGAAGCTAAGTCTGATTTTTAGAAGTTTCTTG
Found at i:1330514 original size:56 final size:55
Alignment explanation
Indices: 1330412--1330637 Score: 211
Period size: 56 Copynumber: 4.0 Consensus size: 55
1330402 AACATGGTGT
* * *
1330412 TTCAAAAGATTTTTTAAAATAAACTAAGTCTAATTTTTAGAAGTTTCTTGATGATTTTC
1 TTCAAATGA-TTTTT-AAAGAAACTAAGTCTGA-TTTTAGAAGTTTCTTGATGA-TTTC
* * *
1330471 TT-AAATGATTTTTAAAGAAATTAAGTCTGATTTCTAGAGGTTTCTTGACATGATGTC
1 TTCAAATGATTTTTAAAGAAACTAAGTCTGATTT-TAGAAGTTTCTTG--ATGATTTC
* * * *
1330528 TTCAAATGAATTTTAAAGAAACTAAGTCCGATTTTCGCAAGTTTCTTTATGATTTC
1 TTCAAATGATTTTTAAAGAAACTAAGTCTGATTTTAG-AAGTTTCTTGATGATTTC
* * * * * * *
1330584 TTCAAATAAGTTTTTGAAGAAGCTAAATCTGATTTAAGAGGTTTCTTAATGATT
1 TTCAAATGA-TTTTTAAAGAAACTAAGTCTGATTTTAGAAGTTTCTTGATGATT
1330638 ACTCAACCAA
Statistics
Matches: 138, Mismatches: 23, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
55 3 0.02
56 55 0.40
57 33 0.24
58 45 0.33
59 2 0.01
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (55 bp):
TTCAAATGATTTTTAAAGAAACTAAGTCTGATTTTAGAAGTTTCTTGATGATTTC
Found at i:1330814 original size:41 final size:42
Alignment explanation
Indices: 1330708--1330814 Score: 101
Period size: 42 Copynumber: 2.6 Consensus size: 42
1330698 TCTTGATGAG
* * * * *
1330708 TAAGTCCCTCAGGCCAT-CAGCAAGTCTTTCGAGCATGATGCT
1 TAAGTCCTTCAGGCCATCCA-TAAGTCTTTCGAGCAAGACGCA
* ** * *
1330750 TAAATCCTTTGGGTCATCTATAAGTCTTTCGAGCAAGACG-A
1 TAAGTCCTTCAGGCCATCCATAAGTCTTTCGAGCAAGACGCA
1330791 TAAGTCCTTCAGGCCATCCATAAG
1 TAAGTCCTTCAGGCCATCCATAAG
1330815 ACCTTTGGGC
Statistics
Matches: 49, Mismatches: 15, Indels: 3
0.73 0.22 0.04
Matches are distributed among these distances:
41 19 0.39
42 29 0.59
43 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (42 bp):
TAAGTCCTTCAGGCCATCCATAAGTCTTTCGAGCAAGACGCA
Found at i:1331563 original size:31 final size:31
Alignment explanation
Indices: 1331525--1331613 Score: 160
Period size: 31 Copynumber: 2.9 Consensus size: 31
1331515 CCAACGAGGA
*
1331525 AGAAGAAGTTCATAATGAGAATAACTTATTT
1 AGAAGAAGTTCATAATGAGAATAACTTATTC
*
1331556 AGAAGAAGTTCATAATGAGAAGAACTTATTC
1 AGAAGAAGTTCATAATGAGAATAACTTATTC
1331587 AGAAGAAGTTCATAATGAGAATAACTT
1 AGAAGAAGTTCATAATGAGAATAACTT
1331614 GTTTGAAACT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.28
Consensus pattern (31 bp):
AGAAGAAGTTCATAATGAGAATAACTTATTC
Found at i:1331576 original size:17 final size:17
Alignment explanation
Indices: 1331525--1331607 Score: 79
Period size: 17 Copynumber: 5.2 Consensus size: 17
1331515 CCAACGAGGA
1331525 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
* * *
1331542 AGAATAACTT-AT--TT
1 AGAAGAAGTTCATAATG
1331556 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
* *
1331573 AGAAGAACTT-AT--TC
1 AGAAGAAGTTCATAATG
1331587 AGAAGAAGTTCATAATG
1 AGAAGAAGTTCATAATG
1331604 AGAA
1 AGAA
1331608 TAACTTGTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
14 19 0.38
15 4 0.08
16 4 0.08
17 23 0.46
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.27
Consensus pattern (17 bp):
AGAAGAAGTTCATAATG
Found at i:1331692 original size:178 final size:177
Alignment explanation
Indices: 1331409--1331731 Score: 468
Period size: 178 Copynumber: 1.8 Consensus size: 177
1331399 CCAACGAGTA
*
1331409 AGAAGAAGTTCATAACGAGAAGAACTTGTTCGAAACTCAGCACATCCGTCACACATGGAGATGGA
1 AGAAGAAGTTCATAACGAGAAGAACTTGTTCGAAACTCAGCACATCCGTCACACAAGGAGATGGA
* *
1331474 TCAACATTTCAGAAGAAGGGTTCATAATGGGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATA
66 TCAACATTTCAGAAGAAGGGTTCATAATGAGAAGAACTCAT-CAACGAGGAAGAAGAAATTCATA
*
1331539 ATGAGAATAACTTATTTAGAAGAAGTTCATAATGAGAAGAACTTATTC
130 ATGAGAAGAACTTATTTAGAAGAAGTTCATAATGAGAAGAACTTATTC
* * * * * *
1331587 AGAAGAAGTTCATAATGAGAATAACTTGTTTGAAACTC-GACACATCTGTCACACAAGGATATTG
1 AGAAGAAGTTCATAACGAGAAGAACTTGTTCGAAACTCAG-CACATCCGTCACACAAGGAGATGG
* * * * ** *
1331651 ATCAATATTTGAGAATAGGGGTTTGTAATGAGAATAACTCATCAACGAGGAAGAAGAAATTCATA
65 ATCAACATTTCAGAAGAAGGGTTCATAATGAGAAGAACTCATCAACGAGGAAGAAGAAATTCATA
1331716 ATGAGAAGAACTTATT
130 ATGAGAAGAACTTATT
1331732 CGGAACTCGA
Statistics
Matches: 127, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
177 38 0.30
178 89 0.70
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (177 bp):
AGAAGAAGTTCATAACGAGAAGAACTTGTTCGAAACTCAGCACATCCGTCACACAAGGAGATGGA
TCAACATTTCAGAAGAAGGGTTCATAATGAGAAGAACTCATCAACGAGGAAGAAGAAATTCATAA
TGAGAAGAACTTATTTAGAAGAAGTTCATAATGAGAAGAACTTATTC
Found at i:1331863 original size:116 final size:115
Alignment explanation
Indices: 1331589--1331924 Score: 420
Period size: 116 Copynumber: 2.9 Consensus size: 115
1331579 ACTTATTCAG
* * *
1331589 AAGAAGTTCATAATGAGAATAACTTGTTTGAAACTCGACACATCTGTCACACAAGGATATTGATC
1 AAGAAGTTCATAATGAGAAGAACTTGTTTGAAACTCGACACATCTGTCACACAAGGAGATAGATC
* * * * ** * *
1331654 AATATTTGAGAATAGGGGTTTGTAATGAGAATAACTCATCAACGAGGAAG
66 AACATTTCAGAAGAAGGGTTCATAATGAGAAGAACTCATCAACGAGGAAC
* * * * * *
1331704 AAGAAATTCATAATGAGAAGAACTTATTCGGAACTCGACACATCCGTCACACAAGGAGATGGATC
1 AAGAAGTTCATAATGAGAAGAACTTGTTTGAAACTCGACACATCTGTCACACAAGGAGATAGATC
* ** *
1331769 AACATCTCTTAAGAAGGGTTCATAATGAGAAGAACTCAGTCAATGAGGAAC
66 AACATTTCAGAAGAAGGGTTCATAATGAGAAGAACTCA-TCAACGAGGAAC
* * * * *
1331820 AAGGAGTTCATAATGAGAAGAACTTGTTTAAAACTCGACACATCTATCACACAAGGAGATATACC
1 AAGAAGTTCATAATGAGAAGAACTTGTTTGAAACTCGACACATCTGTCACACAAGGAGATAGATC
*
1331885 AACATTTCAGAAGAAGAGTTCATAATGAGAAGAACTCATC
66 AACATTTCAGAAGAAGGGTTCATAATGAGAAGAACTCATC
1331925 CTATAAAGGG
Statistics
Matches: 185, Mismatches: 35, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
115 87 0.47
116 98 0.53
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (115 bp):
AAGAAGTTCATAATGAGAAGAACTTGTTTGAAACTCGACACATCTGTCACACAAGGAGATAGATC
AACATTTCAGAAGAAGGGTTCATAATGAGAAGAACTCATCAACGAGGAAC
Found at i:1331948 original size:32 final size:32
Alignment explanation
Indices: 1331902--1331962 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
1331892 CAGAAGAAGA
*
1331902 GTTCATAATGAGAAGAACTCATCCTATAAAGG
1 GTTCATAATGAGAAGAACTCATCCAATAAAGG
* *
1331934 GTTCGTAATGAGAAGCACTCATCCAATAA
1 GTTCATAATGAGAAGAACTCATCCAATAA
1331963 TGGAGAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (32 bp):
GTTCATAATGAGAAGAACTCATCCAATAAAGG
Found at i:1332303 original size:3 final size:3
Alignment explanation
Indices: 1332297--1332336 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
1332287 CATCATTTTT
*
1332297 TTA TTA TTA TTG TTA TTA -TA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1332337 CAAAAATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1332320 original size:17 final size:17
Alignment explanation
Indices: 1332298--1332336 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1332288 ATCATTTTTT
*
1332298 TATTATTATTGTTATTA
1 TATTATTATTATTATTA
1332315 TATTATTATTATTATTA
1 TATTATTATTATTATTA
1332332 TATTA
1 TATTA
1332337 CAAAAATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:1332373 original size:21 final size:22
Alignment explanation
Indices: 1332349--1332390 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1332339 AAAATACATA
*
1332349 AAAAGCCAAAAAA-ACAAAAGG
1 AAAAGACAAAAAATACAAAAGG
*
1332370 AAAATACAAAAAATACAAAAG
1 AAAAGACAAAAAATACAAAAG
1332391 AACGATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.74, C:0.12, G:0.10, T:0.05
Consensus pattern (22 bp):
AAAAGACAAAAAATACAAAAGG
Found at i:1332402 original size:22 final size:21
Alignment explanation
Indices: 1332356--1332403 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
1332346 ATAAAAAGCC
1332356 AAAAAAACAAAAGGAAAATACA
1 AAAAAAACAAAAGGAAAATA-A
* *
1332378 AAAAATACAAAA-GAACGATAA
1 AAAAAAACAAAAGGAA-AATAA
1332399 AAAAA
1 AAAAA
1332404 GAGAGAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.06
Consensus pattern (21 bp):
AAAAAAACAAAAGGAAAATAA
Found at i:1335518 original size:56 final size:56
Alignment explanation
Indices: 1335391--1335515 Score: 216
Period size: 55 Copynumber: 2.2 Consensus size: 56
1335381 CCCCATATAG
1335391 GGTACCGATACCCCTATGAACATTTTTAGTTCCGAGAAATAACAGAATGCTCGGAT
1 GGTACCGATACCCCTATGAACATTTTTAGTTCCGAGAAATAACAGAATGCTCGGAT
* *
1335447 GATACCGATACCCCTATGAATATTTTT-GTTCCGAGAAATAACAGAATGCTCGGAT
1 GGTACCGATACCCCTATGAACATTTTTAGTTCCGAGAAATAACAGAATGCTCGGAT
*
1335502 GGTACCGAAACCCC
1 GGTACCGATACCCC
1335516 CTAGTAGGTA
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
55 40 0.62
56 25 0.38
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (56 bp):
GGTACCGATACCCCTATGAACATTTTTAGTTCCGAGAAATAACAGAATGCTCGGAT
Found at i:1335570 original size:22 final size:20
Alignment explanation
Indices: 1335511--1335597 Score: 113
Period size: 20 Copynumber: 4.2 Consensus size: 20
1335501 TGGTACCGAA
1335511 ACCCCCTAGTAGGTATCGAT
1 ACCCCCTAGTAGGTATCGAT
1335531 ACCCCCTAGTAGGTATCGAT
1 ACCCCCTAGTAGGTATCGAT
1335551 ACCCCC-ATGATATGGTATCGAT
1 ACCCCCTA-G-TA-GGTATCGAT
* *
1335573 ACCCCCTACTTAGGTACCGAT
1 ACCCCCTA-GTAGGTATCGAT
1335594 ACCC
1 ACCC
1335598 TCAGGCATTT
Statistics
Matches: 60, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
19 1 0.02
20 27 0.45
21 14 0.23
22 17 0.28
23 1 0.02
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.24
Consensus pattern (20 bp):
ACCCCCTAGTAGGTATCGAT
Found at i:1341381 original size:21 final size:21
Alignment explanation
Indices: 1341314--1341395 Score: 94
Period size: 21 Copynumber: 3.8 Consensus size: 21
1341304 ATTTATGTGC
*
1341314 ATAGAGTATCGATACCC-CTGA
1 ATAG-GTATCGATACCCATTGA
* *
1341335 TACAGGTATTGATACCCACTTTGA
1 -ATAGGTATCGATACCCA--TTGA
1341359 ATAGGTATCGATACCCATTGA
1 ATAGGTATCGATACCCATTGA
1341380 ATAGGTATCGATACCC
1 ATAGGTATCGATACCC
1341396 TCTTTGAATG
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
21 31 0.60
22 3 0.06
23 15 0.29
24 3 0.06
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (21 bp):
ATAGGTATCGATACCCATTGA
Found at i:1341386 original size:44 final size:45
Alignment explanation
Indices: 1341314--1341419 Score: 137
Period size: 44 Copynumber: 2.4 Consensus size: 45
1341304 ATTTATGTGC
*
1341314 ATAGAGTATCGATACCCCTGATACAGGTATTGATACCCACTTTGA
1 ATAGAGTATCGATACCCCTGATACAGGTATCGATACCCACTTTGA
* * *
1341359 ATAG-GTATCGATACCCATTGA-ATAGGTATCGATACCCTCTTTGA
1 ATAGAGTATCGATACCC-CTGATACAGGTATCGATACCCACTTTGA
*
1341403 AT-GAGTAACGATACCCC
1 ATAGAGTATCGATACCCC
1341420 CTTATGGTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
43 1 0.02
44 45 0.85
45 7 0.13
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (45 bp):
ATAGAGTATCGATACCCCTGATACAGGTATCGATACCCACTTTGA
Found at i:1341435 original size:19 final size:19
Alignment explanation
Indices: 1341383--1341459 Score: 100
Period size: 19 Copynumber: 3.8 Consensus size: 19
1341373 CCATTGAATA
*
1341383 GGTATCGATACCCTCTTTGAAT
1 GGTATCGATACCC-CCTT--AT
*
1341405 GAGTAACGATACCCCCTTAT
1 G-GTATCGATACCCCCTTAT
1341425 GGTATCGATACCCCCTTAT
1 GGTATCGATACCCCCTTAT
1341444 GGTATCGATACCCCCT
1 GGTATCGATACCCCCT
1341460 GTTGGGTTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
19 33 0.65
20 3 0.06
22 4 0.08
23 11 0.22
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (19 bp):
GGTATCGATACCCCCTTAT
Found at i:1344223 original size:76 final size:77
Alignment explanation
Indices: 1344054--1344247 Score: 322
Period size: 77 Copynumber: 2.5 Consensus size: 77
1344044 TTTATTTAGT
* * *
1344054 ATGGTATCGATACCCCCATATAGGGTACCGATACCCCTATGAACATTTTTGGTTCCGAGAAATAA
1 ATGGTACCGATACCCCCCTATAGGGTATCGATACCCCTATGAACATTTTTGGTTCCGAGAAATAA
*
1344119 CAGAATGCTCGG
66 CAGAATCCTCGG
1344131 ATGGTACCGATACCCCCCTATAGGGTATCGATACCCCTATGAACATTTTT-GTTCCGAGAAATAA
1 ATGGTACCGATACCCCCCTATAGGGTATCGATACCCCTATGAACATTTTTGGTTCCGAGAAATAA
1344195 CAGAATCCTCGG
66 CAGAATCCTCGG
1344207 ATGGTACCGATA-CCCCCTAGTA-GGTATCGATACCCCTATGA
1 ATGGTACCGATACCCCCCTA-TAGGGTATCGATACCCCTATGA
1344248 TATGGTATCG
Statistics
Matches: 112, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
75 26 0.23
76 39 0.35
77 47 0.42
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (77 bp):
ATGGTACCGATACCCCCCTATAGGGTATCGATACCCCTATGAACATTTTTGGTTCCGAGAAATAA
CAGAATCCTCGG
Found at i:1344257 original size:22 final size:20
Alignment explanation
Indices: 1344207--1344264 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 20
1344197 GAATCCTCGG
*
1344207 ATGGTACCGATACCCCCTAGT
1 ATGGTATCGATA-CCCCTAGT
1344228 A-GGTATCGATACCCCTATGAT
1 ATGGTATCGATACCCCTA-G-T
1344249 ATGGTATCGATACCCC
1 ATGGTATCGATACCCC
1344265 CTACTTAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 6 0.18
20 10 0.30
21 3 0.09
22 14 0.42
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (20 bp):
ATGGTATCGATACCCCTAGT
Found at i:1345324 original size:22 final size:22
Alignment explanation
Indices: 1345284--1345327 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1345274 GTTGGGCTTC
*
1345284 TTGGGCCTTCGAGTTAGATCTG
1 TTGGGCCTTCGAGTCAGATCTG
1345306 TTGGGCCTTCG-GATCAGATCTG
1 TTGGGCCTTCGAG-TCAGATCTG
1345328 GATCTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.14, C:0.20, G:0.32, T:0.34
Consensus pattern (22 bp):
TTGGGCCTTCGAGTCAGATCTG
Found at i:1345419 original size:3 final size:3
Alignment explanation
Indices: 1345397--1345480 Score: 63
Period size: 3 Copynumber: 28.7 Consensus size: 3
1345387 AATATTTGTA
* *
1345397 AAT AAA AAT -AT AAT -AT AAT AAT -AT ATAT AAAT ATGT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT -AAT A-AT AAT AAT AAT
*
1345441 AAT AAT AAC AAT AAT AAT AAT AAT -AT AAT -AT AATT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AA
1345481 CAAAAACTGA
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
2 12 0.18
3 43 0.66
4 9 0.14
5 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1345444 original size:15 final size:14
Alignment explanation
Indices: 1345397--1345479 Score: 80
Period size: 15 Copynumber: 5.7 Consensus size: 14
1345387 AATATTTGTA
*
1345397 AATAAAAATATAAT
1 AATAATAATATAAT
1345411 -ATAATAATATATAT
1 AATAATAATATA-AT
*
1345425 AAATATGTAATATAAT
1 -AATA-ATAATATAAT
*
1345441 AATAATAACAATAAT
1 AATAATAA-TATAAT
1345456 AATAATAATATAAT
1 AATAATAATATAAT
1345470 -ATAATTAATA
1 AATAA-TAATA
1345480 ACAAAAACTG
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
13 14 0.24
14 15 0.26
15 17 0.29
16 5 0.09
17 7 0.12
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (14 bp):
AATAATAATATAAT
Found at i:1345733 original size:41 final size:42
Alignment explanation
Indices: 1345653--1345775 Score: 115
Period size: 42 Copynumber: 3.0 Consensus size: 42
1345643 TTAAAGAGTG
* * * * * *
1345653 TAAACATCCTGCCCAAAGGTCTGACGGATGGCCCTAAGGACT
1 TAAACATCATGCTCAAAGGACTGACAGATGACCCAAAGGACT
* * *
1345695 T-ATCATCTTGCTCGAAA-GACTGACAGATGACCCAAAGGATT
1 TAAACATCATGCTC-AAAGGACTGACAGATGACCCAAAGGACT
* * *
1345736 TAAACATCATGCTCAAAGGGCTTACAGATGACCCGAAGGA
1 TAAACATCATGCTCAAAGGACTGACAGATGACCCAAAGGA
1345776 TTTACAAATT
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
41 32 0.49
42 33 0.51
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.20
Consensus pattern (42 bp):
TAAACATCATGCTCAAAGGACTGACAGATGACCCAAAGGACT
Found at i:1346609 original size:22 final size:22
Alignment explanation
Indices: 1346581--1346630 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
1346571 AAAGCTTTCT
1346581 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAAAGAGAATCTATCA
1346603 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAAAGAGAATCTATCA
1346625 TCTTTG
1 TCTTTG
1346631 TAGAATGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (22 bp):
TCTTTGAAAAGAGAATCTATCA
Found at i:1347435 original size:25 final size:26
Alignment explanation
Indices: 1347385--1347435 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1347375 CTTTCTGAAA
*
1347385 TGGGCCTTCATCATGCCCCCAACATT
1 TGGGCCTTCAGCATGCCCCCAACATT
1347411 TGGGCCTTCAGCATG-CCCCAACATT
1 TGGGCCTTCAGCATGCCCCCAACATT
1347436 CTAAGTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.20, C:0.37, G:0.18, T:0.25
Consensus pattern (26 bp):
TGGGCCTTCAGCATGCCCCCAACATT
Found at i:1353026 original size:12 final size:12
Alignment explanation
Indices: 1353011--1353040 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1353001 ATAAAAGTAT
1353011 ATTAATATTATA
1 ATTAATATTATA
1353023 ATTAATATTATA
1 ATTAATATTATA
1353035 A-TAATA
1 ATTAATA
1353041 AGTAGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTAATATTATA
Found at i:1354197 original size:22 final size:22
Alignment explanation
Indices: 1354172--1354214 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1354162 GTTGGGCTTC
1354172 TTGGGCCTTC-GAGTTGGATCTG
1 TTGGGCCTTCGGA-TTGGATCTG
1354194 TTGGGCCTTCGGATTGGATCT
1 TTGGGCCTTCGGATTGGATCT
1354215 TTAATTGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.09, C:0.19, G:0.35, T:0.37
Consensus pattern (22 bp):
TTGGGCCTTCGGATTGGATCTG
Found at i:1354301 original size:3 final size:3
Alignment explanation
Indices: 1354288--1354343 Score: 82
Period size: 3 Copynumber: 19.3 Consensus size: 3
1354278 AAATGCAAAT
1354288 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1354333 ATTA ATA ATA A
1 A-TA ATA ATA A
1354344 AAACAGACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.12
3 40 0.82
4 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:1354320 original size:29 final size:29
Alignment explanation
Indices: 1354288--1354343 Score: 96
Period size: 29 Copynumber: 1.9 Consensus size: 29
1354278 AAATGCAAAT
1354288 ATAATATAATAATAATAA-TAATAATAATA
1 ATAATATAATAAT-ATAATTAATAATAATA
1354317 ATAATATAATAATATAATTAATAATAA
1 ATAATATAATAATATAATTAATAATAA
1354344 AAACAGACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
ATAATATAATAATATAATTAATAATAATA
Found at i:1358194 original size:31 final size:30
Alignment explanation
Indices: 1358144--1358205 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
1358134 GGCACGCGTA
* *
1358144 TGAGTAAAAAAAATAGTTTAGGCTCTTATT
1 TGAGTAAAAAAAATAGTTTAGACACTTATT
1358174 TGAG-AAAAACAATATAGTTTAGACACTTATT
1 TGAGTAAAAA-AA-ATAGTTTAGACACTTATT
1358205 T
1 T
1358206 TGCTATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 5 0.18
30 6 0.21
31 17 0.61
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (30 bp):
TGAGTAAAAAAAATAGTTTAGACACTTATT
Found at i:1359366 original size:13 final size:13
Alignment explanation
Indices: 1359317--1359367 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
1359307 CTCTCGAGTC
*
1359317 TATATGATATATG
1 TATATTATATATG
*
1359330 TATATTACATATG
1 TATATTATATATG
* * *
1359343 AAGA-AATATATG
1 TATATTATATATG
1359355 TATATTATATATG
1 TATATTATATATG
1359368 GCTATATAAA
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
12 8 0.29
13 20 0.71
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (13 bp):
TATATTATATATG
Found at i:1367127 original size:85 final size:84
Alignment explanation
Indices: 1366911--1367208 Score: 447
Period size: 85 Copynumber: 3.5 Consensus size: 84
1366901 AATGATGTGT
* * * *
1366911 GCTTCAATGACACGCAATGTAAGTCATATATGCGTGTCATAAATTTATGACACGCAAATGTATGT
1 GCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
*
1366976 CAAGC--AGATTTATGACGGG
66 C-ATCTTA-ATTTATGACGGG
*
1366995 GCTTCAATGACACGCAATGTAAGTTATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
1 GCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
1367060 CATCTTAATTTATGACGGGG
66 CATCTTAATTTATGAC-GGG
* *
1367080 GCTTCAATGACGCACAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
1 GCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
*
1367145 CATCTTAATTTATGACATGG
66 CATCTTAATTTATGAC-GGG
* *
1367165 GCTTCAATGACGCGCAATGTAAGTCATACATGCGCGTCATAAAT
1 GCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAAT
1367209 GCGCGTCATA
Statistics
Matches: 198, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
83 2 0.01
84 70 0.35
85 126 0.64
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (84 bp):
GCTTCAATGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
CATCTTAATTTATGACGGG
Found at i:1367205 original size:13 final size:13
Alignment explanation
Indices: 1367187--1367218 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1367177 CGCAATGTAA
*
1367187 GTCATACATGCGC
1 GTCATAAATGCGC
1367200 GTCATAAATGCGC
1 GTCATAAATGCGC
1367213 GTCATA
1 GTCATA
1367219 GATTTATGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (13 bp):
GTCATAAATGCGC
Found at i:1369763 original size:23 final size:23
Alignment explanation
Indices: 1369737--1369782 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1369727 ATTTATCTTT
*
1369737 TAAATTTTATAAAAAATTATATA
1 TAAATTTTATAAAAAAGTATATA
*
1369760 TAAATTTTATTAAAAAGTATATA
1 TAAATTTTATAAAAAAGTATATA
1369783 AATTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TAAATTTTATAAAAAAGTATATA
Found at i:1370025 original size:20 final size:20
Alignment explanation
Indices: 1370000--1370057 Score: 116
Period size: 20 Copynumber: 2.9 Consensus size: 20
1369990 ATCCTATTCC
1370000 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
1370020 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
1370040 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1370058 GTGAACCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.36
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1370311 original size:13 final size:12
Alignment explanation
Indices: 1370294--1370342 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 12
1370284 ATTTATATAA
1370294 TTTTAATTAATT
1 TTTTAATTAATT
*
1370306 ATTTTATTTAATT
1 -TTTTAATTAATT
1370319 TGATTTAATTAATT
1 T--TTTAATTAATT
1370333 TTATTAATTA
1 TT-TTAATTA
1370343 CTCAAACAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 2 0.06
13 18 0.58
14 11 0.35
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (12 bp):
TTTTAATTAATT
Found at i:1370312 original size:23 final size:23
Alignment explanation
Indices: 1370285--1370341 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
1370275 CTTATATGTA
*
1370285 TTTATATAATTTTAATTAATT-AT
1 TTTAT-TAATTTGAATTAATTAAT
*
1370308 TTTATTTAATTTGATTTAATTAAT
1 TTTA-TTAATTTGAATTAATTAAT
1370332 TTTATTAATT
1 TTTATTAATT
1370342 ACTCAAACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 23 0.77
24 7 0.23
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTATTAATTTGAATTAATTAAT
Found at i:1372251 original size:25 final size:25
Alignment explanation
Indices: 1372219--1372283 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
1372209 ATCGAACTTA
1372219 TTATAAAATTTTAAGGAAGTTGAAC
1 TTATAAAATTTTAAGGAAGTTGAAC
1372244 TTATAAAATTTTAAGGAAGTTGAAC
1 TTATAAAATTTTAAGGAAGTTGAAC
*
1372269 TTATCAAATTTTAAG
1 TTATAAAATTTTAAG
1372284 AAAATAATCT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (25 bp):
TTATAAAATTTTAAGGAAGTTGAAC
Found at i:1373579 original size:22 final size:22
Alignment explanation
Indices: 1373551--1373599 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1373541 AATTCGGCTC
*
1373551 GTTTAACAAACGACGTCGTTTA
1 GTTTAACAAACGAAGTCGTTTA
*
1373573 GTTTAACAAACGAAGTCGTTTG
1 GTTTAACAAACGAAGTCGTTTA
1373595 GTTTA
1 GTTTA
1373600 TTTTTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (22 bp):
GTTTAACAAACGAAGTCGTTTA
Found at i:1375094 original size:2 final size:2
Alignment explanation
Indices: 1375089--1375115 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1375079 TTTTTTGAAT
1375089 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1375116 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1379445 original size:20 final size:21
Alignment explanation
Indices: 1379420--1379471 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
1379410 GATTAAAGTA
* *
1379420 GTATCGATACTGATGTGT-AG
1 GTATCGATACTGAAGGGTAAG
*
1379440 GTATCGATAC-CAAGGGTAAG
1 GTATCGATACTGAAGGGTAAG
1379460 GTATCGATACTG
1 GTATCGATACTG
1379472 TAATTAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (21 bp):
GTATCGATACTGAAGGGTAAG
Found at i:1386736 original size:24 final size:25
Alignment explanation
Indices: 1386693--1386741 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
1386683 CAACTTTCTG
1386693 CGTGGTCCTTCGGGACAAAT-TATA
1 CGTGGTCCTTCGGGACAAATCTATA
1386717 CGTGGTCCTTCGGGTA-AAATCTATA
1 CGTGGTCCTTCGGG-ACAAATCTATA
1386742 TGGCACTTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (25 bp):
CGTGGTCCTTCGGGACAAATCTATA
Found at i:1387761 original size:15 final size:14
Alignment explanation
Indices: 1387741--1387846 Score: 69
Period size: 15 Copynumber: 7.7 Consensus size: 14
1387731 AAAAATACAA
1387741 AATAAATTATTACGT
1 AATAAATTATTAC-T
*
1387756 AATAAATTATTA-A
1 AATAAATTATTACT
*
1387769 AAT-ATTTATTAC-
1 AATAAATTATTACT
*
1387781 AATAAATTATTAAAT
1 AATAAATTATT-ACT
**
1387796 AATAAATTATTTTT
1 AATAAATTATTACT
* *
1387810 AAT-GATT-TTAAT
1 AATAAATTATTACT
* *
1387822 ATTAAATTATTAAGT
1 AATAAATTATT-ACT
1387837 AATAAATTAT
1 AATAAATTAT
1387847 ATTAAATATA
Statistics
Matches: 71, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
12 15 0.21
13 15 0.21
14 7 0.10
15 34 0.48
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (14 bp):
AATAAATTATTACT
Found at i:1387788 original size:40 final size:39
Alignment explanation
Indices: 1387741--1387855 Score: 131
Period size: 41 Copynumber: 2.8 Consensus size: 39
1387731 AAAAATACAA
* * *
1387741 AATAAATTATTACGTAATAAATTATTAAAATATTTATTAC
1 AATAAATTATTAAGTAATAAATTATTTAAATATTT-TAAC
* * *
1387781 AATAAATTATTAAATAATAAATTATTTTTAATGATTTTAAT
1 AATAAATTATTAAGTAATAAATTA-TTTAAAT-ATTTTAAC
*
1387822 ATTAAATTATTAAGTAATAAATTATATTAAATAT
1 AATAAATTATTAAGTAATAAATTAT-TTAAATAT
1387856 AGAATTTAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
40 25 0.40
41 34 0.54
42 4 0.06
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (39 bp):
AATAAATTATTAAGTAATAAATTATTTAAATATTTTAAC
Found at i:1387804 original size:25 final size:25
Alignment explanation
Indices: 1387756--1387804 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1387746 ATTATTACGT
**
1387756 AATAAATTATTAAAATATTTATTAC
1 AATAAATTATTAAAATATAAATTAC
1387781 AATAAATTATT-AAATAATAAATTA
1 AATAAATTATTAAAAT-ATAAATTA
1387805 TTTTTAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
AATAAATTATTAAAATATAAATTAC
Found at i:1387876 original size:44 final size:41
Alignment explanation
Indices: 1387743--1387868 Score: 107
Period size: 41 Copynumber: 3.0 Consensus size: 41
1387733 AAATACAAAA
** * *
1387743 TAAATTATTACGTAATAAATTA-TTAAAAT--ATTTATTACAA
1 TAAATTATTAAATAATAAATTATTTAAAATGAATTTA--ATAT
** *
1387783 TAAATTATTAAATAATAAATTATTTTTAATGATTTTAATAT
1 TAAATTATTAAATAATAAATTATTTAAAATGAATTTAATAT
*
1387824 TAAATTATTAAGTAATAAATTATATTAAATATAGAATTTAA-AT
1 TAAATTATTAAATAATAAATTAT-TTAAA-AT-GAATTTAATAT
1387867 TA
1 TA
1387869 TATTTATTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
40 20 0.29
41 29 0.42
42 3 0.04
43 10 0.14
44 7 0.10
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (41 bp):
TAAATTATTAAATAATAAATTATTTAAAATGAATTTAATAT
Found at i:1393239 original size:13 final size:12
Alignment explanation
Indices: 1393223--1393269 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 12
1393213 TCTTTTTAAC
1393223 TTTTTTTTTCTGA
1 TTTTTTTTTCT-A
1393236 TTTTTTTCTTCTA
1 TTTTTTT-TTCTA
1393249 TTTTTCTTTTCT-
1 TTTTT-TTTTCTA
1393261 TTTCTTTTT
1 TTT-TTTTT
1393270 ATACTCCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.19
13 19 0.61
14 6 0.19
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTCTA
Found at i:1393263 original size:11 final size:10
Alignment explanation
Indices: 1393222--1393269 Score: 51
Period size: 11 Copynumber: 4.6 Consensus size: 10
1393212 TTCTTTTTAA
1393222 CTTTTTTTTT
1 CTTTTTTTTT
*
1393232 CTGATTTTTTT
1 CT-TTTTTTTT
*
1393243 CTTCTATTTTT
1 CTT-TTTTTTT
*
1393254 CTTTTCTTTT
1 CTTTTTTTTT
1393264 CTTTTT
1 CTTTTT
1393270 ATACTCCAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
10 12 0.40
11 18 0.60
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:1400784 original size:20 final size:20
Alignment explanation
Indices: 1400755--1400810 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 20
1400745 CCCCTTGATA
1400755 TGTATCGATACACTATGAATG
1 TGTATCGATACACT-TGAATG
1400776 TGT-TCGATACATTCCTTGAATG
1 TGTATCGATACA---CTTGAATG
1400798 TGTATCGATACAC
1 TGTATCGATACAC
1400811 CCCGAGGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
20 9 0.29
21 3 0.10
22 9 0.29
23 10 0.32
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (20 bp):
TGTATCGATACACTTGAATG
Found at i:1400809 original size:23 final size:21
Alignment explanation
Indices: 1400733--1400811 Score: 74
Period size: 21 Copynumber: 3.7 Consensus size: 21
1400723 TTTGTGCAAA
* *
1400733 GTGTATCAATACCCCCTTG-AT
1 GTGTATCGATA-CACCTTGAAT
*
1400754 ATGTATCGATACA-CTATGAAT
1 GTGTATCGATACACCT-TGAAT
1400775 GTGT-TCGATACATTCCTTGAAT
1 GTGTATCGATACA--CCTTGAAT
1400797 GTGTATCGATACACC
1 GTGTATCGATACACC
1400812 CCGAGGTGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
19 2 0.04
20 11 0.23
21 16 0.33
22 9 0.19
23 10 0.21
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (21 bp):
GTGTATCGATACACCTTGAAT
Found at i:1402257 original size:18 final size:17
Alignment explanation
Indices: 1402234--1402280 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
1402224 TGTTTATGAG
1402234 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
*
1402252 GGAATTGGAATCTGTCA
1 GGAATTGGAATCTGTAA
*
1402269 GCAATTGGAATC
1 GGAATTGGAATC
1402281 CAATTCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.32, C:0.11, G:0.30, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:1402914 original size:37 final size:38
Alignment explanation
Indices: 1402828--1402917 Score: 137
Period size: 38 Copynumber: 2.4 Consensus size: 38
1402818 TTTTTACCCT
1402828 AAACCCGAACCCGACCCGACATGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCCGACATGAATATCACACTTAAAA
** *
1402867 AAACCCGACCCGACTTGACCTGAATATCACACTT-AAA
1 AAACCCGACCCGACCCGACATGAATATCACACTTAAAA
1402904 AAACCCGACCCGAC
1 AAACCCGACCCGAC
1402918 ACAAACAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
37 17 0.35
38 24 0.50
39 7 0.15
ACGTcount: A:0.40, C:0.36, G:0.11, T:0.13
Consensus pattern (38 bp):
AAACCCGACCCGACCCGACATGAATATCACACTTAAAA
Found at i:1408516 original size:46 final size:46
Alignment explanation
Indices: 1408441--1408737 Score: 389
Period size: 46 Copynumber: 6.5 Consensus size: 46
1408431 GTCGTTACTA
** * * * *
1408441 CACCGTTATATATTTTCATTTGTGGCATCCTTTCATGCCGATTATG
1 CACCGTTATGCATTTTCATTTATGACATCCTTTCATGCCTATAATG
* *
1408487 CACCGTTATGGATTTTCATTTATGACATCCTTTCATG-CTGATTATG
1 CACCGTTATGCATTTTCATTTATGACATCCTTTCATGCCT-ATAATG
*
1408533 CACCGTTATACATTTTCATTTATGACATCCTTTCATGCCTATAATG
1 CACCGTTATGCATTTTCATTTATGACATCCTTTCATGCCTATAATG
* *
1408579 CACCATTATGCATTTTCATTTATGGCATCCTTTCATGCCTATAATG
1 CACCGTTATGCATTTTCATTTATGACATCCTTTCATGCCTATAATG
* * * * * *
1408625 TACCATTATGTATTTTCATTTATGACATCCTTTCACGTCTATAATC
1 CACCGTTATGCATTTTCATTTATGACATCCTTTCATGCCTATAATG
** *
1408671 CACCGTTATGCATTTTCATTTATGGTATCCTTTCATTCCTATAATG
1 CACCGTTATGCATTTTCATTTATGACATCCTTTCATGCCTATAATG
*
1408717 CACCGTTATTCATTTTCATTT
1 CACCGTTATGCATTTTCATTT
1408738 TTCATCTAAC
Statistics
Matches: 222, Mismatches: 27, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
45 1 0.00
46 219 0.99
47 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (46 bp):
CACCGTTATGCATTTTCATTTATGACATCCTTTCATGCCTATAATG
Found at i:1409207 original size:20 final size:21
Alignment explanation
Indices: 1409179--1409232 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
1409169 AGGCTTAATA
*
1409179 GTATTGATACTCT-TACCATG
1 GTATCGATACTCTATACCATG
*
1409199 GTATCGATACTTCTATACTATG
1 GTATCGATAC-TCTATACCATG
*
1409221 GTACCGATACTC
1 GTATCGATACTC
1409233 CCTTTCAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.31
21 5 0.17
22 15 0.52
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (21 bp):
GTATCGATACTCTATACCATG
Found at i:1412732 original size:19 final size:18
Alignment explanation
Indices: 1412708--1412795 Score: 71
Period size: 19 Copynumber: 5.0 Consensus size: 18
1412698 TGAATGTTAA
1412708 TATCTTTTATTTTTAAGTG
1 TATCTTTTATTTTTAAG-G
1412727 TATCTTTTATTTTTCAAGG
1 TATCTTTTATTTTT-AAGG
* * *
1412746 -A-C--TGAATGTTAA--
1 TATCTTTTATTTTTAAGG
1412758 TATCTTTTATTTTTAAGTG
1 TATCTTTTATTTTTAAG-G
1412777 TATCTTTTATTTTTCAAGG
1 TATCTTTTATTTTT-AAGG
1412796 ACTGAATGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
13 1 0.02
14 3 0.06
15 5 0.09
16 7 0.13
17 1 0.02
18 1 0.02
19 30 0.56
20 6 0.11
ACGTcount: A:0.24, C:0.08, G:0.11, T:0.57
Consensus pattern (18 bp):
TATCTTTTATTTTTAAGG
Found at i:1412761 original size:50 final size:50
Alignment explanation
Indices: 1412686--1412818 Score: 257
Period size: 50 Copynumber: 2.7 Consensus size: 50
1412676 TTAATCGTTG
*
1412686 TTTTTCGAGGACTGAATGTTAATATCTTTTATTTTTAAGTGTATCTTTTA
1 TTTTTCAAGGACTGAATGTTAATATCTTTTATTTTTAAGTGTATCTTTTA
1412736 TTTTTCAAGGACTGAATGTTAATATCTTTTATTTTTAAGTGTATCTTTTA
1 TTTTTCAAGGACTGAATGTTAATATCTTTTATTTTTAAGTGTATCTTTTA
1412786 TTTTTCAAGGACTGAATGTTAATATCTTTTATT
1 TTTTTCAAGGACTGAATGTTAATATCTTTTATT
1412819 ACAATGTCGC
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 82 1.00
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (50 bp):
TTTTTCAAGGACTGAATGTTAATATCTTTTATTTTTAAGTGTATCTTTTA
Found at i:1414284 original size:20 final size:20
Alignment explanation
Indices: 1414261--1414304 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1414251 TTTTCAACAT
1414261 TTTTCCATTTTTCTATTTTC
1 TTTTCCATTTTTCTATTTTC
**
1414281 TTTTTGATTTTTCTATTTTC
1 TTTTCCATTTTTCTATTTTC
1414301 TTTT
1 TTTT
1414305 TGATGTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTCCATTTTTCTATTTTC
Found at i:1414305 original size:20 final size:20
Alignment explanation
Indices: 1414267--1414308 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1414257 ACATTTTTCC
1414267 ATTTTTCTATTTTCTTTTTG
1 ATTTTTCTATTTTCTTTTTG
1414287 ATTTTTCTATTTTCTTTTTG
1 ATTTTTCTATTTTCTTTTTG
1414307 AT
1 AT
1414309 GTAAAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.12, C:0.10, G:0.05, T:0.74
Consensus pattern (20 bp):
ATTTTTCTATTTTCTTTTTG
Found at i:1416736 original size:30 final size:28
Alignment explanation
Indices: 1416702--1416803 Score: 78
Period size: 31 Copynumber: 3.4 Consensus size: 28
1416692 GCGACCCCTA
1416702 GGTAGGCTCTGTGCCCTAAGATCTTTCTTG
1 GGTAGGCTCTG-GCCCT-AGATCTTTCTTG
* *
1416732 GGTAGGCCCTGCGGCCCGTAGATTTTTCTTG
1 GGTAGGCTCT--GGCCC-TAGATCTTTCTTG
* * *
1416763 GGCAGGCCTCCTGGCCTCGAGAACTTTCTTG
1 GGTAGG-CT-CTGGCC-CTAGATCTTTCTTG
*
1416794 GGTAGACTCT
1 GGTAGGCTCT
1416804 CAGGCCCCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 13
0.72 0.11 0.16
Matches are distributed among these distances:
29 2 0.04
30 11 0.19
31 38 0.67
32 4 0.07
33 2 0.04
ACGTcount: A:0.13, C:0.26, G:0.29, T:0.31
Consensus pattern (28 bp):
GGTAGGCTCTGGCCCTAGATCTTTCTTG
Found at i:1429478 original size:2 final size:2
Alignment explanation
Indices: 1429471--1429496 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1429461 AAAGTAATGG
1429471 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1429497 TATTTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1432684 original size:2 final size:2
Alignment explanation
Indices: 1432677--1432712 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1432667 CCTTTCTGTT
1432677 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1432713 ACACACACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1440732 original size:75 final size:77
Alignment explanation
Indices: 1440644--1440803 Score: 216
Period size: 82 Copynumber: 2.0 Consensus size: 77
1440634 TGTACACATA
* * * *
1440644 ATGATTTTGATAAACATAAATGTGCTAGTG-A-AATAAATAATAGGTACATGTATAATTCATAAA
1 ATGATTTTCATAAAAATAAATATGCTAGTGAATAATAAATAATAGGAACATGTATAATTCATAAA
*
1440707 TTCAAGCGTTAC
66 TTCAAGCGCTAC
1440719 ATGATTTTCATAAAAATAAATATGCTAGTGAAATAAATAATAAATAATAGGAACATGTATAATTC
1 ATGATTTTCATAAAAATAAATATGCTAGTG-----AATAATAAATAATAGGAACATGTATAATTC
1440784 ATAAATTCAAGCGCTAC
61 ATAAATTCAAGCGCTAC
1440801 ATG
1 ATG
1440804 CTTAAGTTTA
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
75 27 0.37
81 1 0.01
82 45 0.62
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (77 bp):
ATGATTTTCATAAAAATAAATATGCTAGTGAATAATAAATAATAGGAACATGTATAATTCATAAA
TTCAAGCGCTAC
Found at i:1445833 original size:29 final size:29
Alignment explanation
Indices: 1445791--1445846 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
1445781 GAACTATACC
1445791 AAATTCTCAGTTTCATACATAATGTTTAA
1 AAATTCTCAGTTTCATACATAATGTTTAA
*
1445820 AAATTCTC-GATTTCATACATGATGTTT
1 AAATTCTCAG-TTTCATACATAATGTTT
1445847 TTTTGCCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (29 bp):
AAATTCTCAGTTTCATACATAATGTTTAA
Found at i:1450020 original size:90 final size:90
Alignment explanation
Indices: 1449886--1450054 Score: 248
Period size: 90 Copynumber: 1.9 Consensus size: 90
1449876 AGGATATCCA
* * *
1449886 GGCAGTGTGAGTTATACTAGATATACTCCTAGAAGTATTGTCAGGTTTATCACCTGACCGTGAAT
1 GGCAGTGTGAGTTATACTAGATATACTCATAGAAGAATTGTCAGGTTTACCACCTGACCGTGAAT
1449951 TAAAGTTTGATATTAAAGTAATCTG
66 TAAAGTTTGATATTAAAGTAATCTG
* * * * * *
1449976 GGCAGTGTGAGTTTTACTCGATGTGCTCATAGAAGAATTTTCAGGTTTACCACCTGAGCGTGAAT
1 GGCAGTGTGAGTTATACTAGATATACTCATAGAAGAATTGTCAGGTTTACCACCTGACCGTGAAT
*
1450041 TAGAGTTTGATATT
66 TAAAGTTTGATATT
1450055 GAAGGAGTTA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 69 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (90 bp):
GGCAGTGTGAGTTATACTAGATATACTCATAGAAGAATTGTCAGGTTTACCACCTGACCGTGAAT
TAAAGTTTGATATTAAAGTAATCTG
Found at i:1459509 original size:75 final size:77
Alignment explanation
Indices: 1459421--1459580 Score: 216
Period size: 82 Copynumber: 2.0 Consensus size: 77
1459411 TGTACACATA
* * * *
1459421 ATGATTTTGATAAACATAAATGTGCTAGTG-A-AATAAATAATAGGTACATGTATAATTCATAAA
1 ATGATTTTCATAAAAATAAATATGCTAGTGAATAATAAATAATAGGAACATGTATAATTCATAAA
*
1459484 TTCAAGCGTTAC
66 TTCAAGCGCTAC
1459496 ATGATTTTCATAAAAATAAATATGCTAGTGAAATAAATAATAAATAATAGGAACATGTATAATTC
1 ATGATTTTCATAAAAATAAATATGCTAGTG-----AATAATAAATAATAGGAACATGTATAATTC
1459561 ATAAATTCAAGCGCTAC
61 ATAAATTCAAGCGCTAC
1459578 ATG
1 ATG
1459581 CTTAAGTTTA
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
75 27 0.37
81 1 0.01
82 45 0.62
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (77 bp):
ATGATTTTCATAAAAATAAATATGCTAGTGAATAATAAATAATAGGAACATGTATAATTCATAAA
TTCAAGCGCTAC
Found at i:1464654 original size:29 final size:29
Alignment explanation
Indices: 1464612--1464667 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
1464602 GAACTATACC
1464612 AAATTCTCAGTTTCATACATAATGTTTAA
1 AAATTCTCAGTTTCATACATAATGTTTAA
*
1464641 AAATTCTC-GATTTCATACATGATGTTT
1 AAATTCTCAG-TTTCATACATAATGTTT
1464668 TTTTGCCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 1 0.04
29 24 0.96
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (29 bp):
AAATTCTCAGTTTCATACATAATGTTTAA
Found at i:1468883 original size:90 final size:90
Alignment explanation
Indices: 1468749--1468917 Score: 248
Period size: 90 Copynumber: 1.9 Consensus size: 90
1468739 AGGATATCCA
* * *
1468749 GGCAGTGTGAGTTATACTAGATATACTCCTAGAAGTATTGTCAGGTTTATCACCTGACCGTGAAT
1 GGCAGTGTGAGTTATACTAGATATACTCATAGAAGAATTGTCAGGTTTACCACCTGACCGTGAAT
1468814 TAAAGTTTGATATTAAAGTAATCTG
66 TAAAGTTTGATATTAAAGTAATCTG
* * * * * *
1468839 GGCAGTGTGAGTTTTACTCGATGTGCTCATAGAAGAATTTTCAGGTTTACCACCTGAGCGTGAAT
1 GGCAGTGTGAGTTATACTAGATATACTCATAGAAGAATTGTCAGGTTTACCACCTGACCGTGAAT
*
1468904 TAGAGTTTGATATT
66 TAAAGTTTGATATT
1468918 GAAGGAGTTA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 69 1.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (90 bp):
GGCAGTGTGAGTTATACTAGATATACTCATAGAAGAATTGTCAGGTTTACCACCTGACCGTGAAT
TAAAGTTTGATATTAAAGTAATCTG
Found at i:1477939 original size:38 final size:37
Alignment explanation
Indices: 1477809--1477984 Score: 172
Period size: 39 Copynumber: 4.5 Consensus size: 37
1477799 CGAGTCAAAT
* * *
1477809 ATATGCACCATAGTGCTTAAACATAAGGTAGTGCCCAAC
1 ATATGCACCAAAGTGCTTAAACATAAGGT-GT-ACCACC
* *
1477848 ATATGCACCGAAGTGCTTACACATAAGGTTGTACCCACC
1 ATATGCACCAAAGTGCTTAAACATAAGG-TGTA-CCACC
* *
1477887 ATATGCACCGAAGTGCATTACACATAAGGTGTACCACC
1 ATATGCACCAAAGTGC-TTAAACATAAGGTGTACCACC
* * * *
1477925 ATATGCACAAAAGTGCATTAAACATAAGGTCATGCTCAAC
1 ATATGCACCAAAGTGC-TTAAACATAAGGT-GTAC-CACC
*
1477965 ATATTCACCAAAGTGCTTAA
1 ATATGCACCAAAGTGCTTAA
1477985 TCGATATGCA
Statistics
Matches: 119, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
38 32 0.27
39 57 0.48
40 30 0.25
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.23
Consensus pattern (37 bp):
ATATGCACCAAAGTGCTTAAACATAAGGTGTACCACC
Found at i:1477950 original size:78 final size:78
Alignment explanation
Indices: 1477809--1477954 Score: 190
Period size: 78 Copynumber: 1.9 Consensus size: 78
1477799 CGAGTCAAAT
* ** *
1477809 ATATGCACCATAGTGCTTAAACATAAGGTAGTGCCCAACATATGCACCGAAGTGCTTACACATAA
1 ATATGCACCATAGTGCTTAAACATAAGGTAGTGACCAACATATGCACAAAAGTGCTTAAACATAA
1477874 GGTTGTACCCACC
66 GGTTGTACCCACC
* *
1477887 ATATGCACCGA-AGTGCATTACACATAAGGT-GT-ACCACCATATGCACAAAAGTGCATTAAACA
1 ATATGCACC-ATAGTGC-TTAAACATAAGGTAGTGACCAACATATGCACAAAAGTGC-TTAAACA
1477949 TAAGGT
63 TAAGGT
1477955 CATGCTCAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
77 18 0.31
78 28 0.47
79 13 0.22
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (78 bp):
ATATGCACCATAGTGCTTAAACATAAGGTAGTGACCAACATATGCACAAAAGTGCTTAAACATAA
GGTTGTACCCACC
Found at i:1479313 original size:70 final size:70
Alignment explanation
Indices: 1479221--1479356 Score: 236
Period size: 70 Copynumber: 1.9 Consensus size: 70
1479211 CCTAACAATT
1479221 TTTCGGATGCTTATTCGATACAATTTCAAAGTCACAACATAAATGTTGACCTTAATACTTCTAAT
1 TTTCGGATGCTTATTCGATACAATTTCAAAGTCACAACATAAATGTTGACCTTAATACTTCTAAT
1479286 TGAAC
66 TGAAC
* * * *
1479291 TTTCTGATGCTTATTCGATACAATTTCCATGTTACAACATAAATGTTGACCTTAATACTTCTAAT
1 TTTCGGATGCTTATTCGATACAATTTCAAAGTCACAACATAAATGTTGACCTTAATACTTCTAAT
1479356 T
66 T
1479357 AAACACTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.39
Consensus pattern (70 bp):
TTTCGGATGCTTATTCGATACAATTTCAAAGTCACAACATAAATGTTGACCTTAATACTTCTAAT
TGAAC
Found at i:1489912 original size:23 final size:23
Alignment explanation
Indices: 1489886--1489930 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1489876 CCTTAGGAAC
* *
1489886 AATTCTATATGGCACTACGGTGT
1 AATTCTACACGGCACTACGGTGT
*
1489909 AATTCTACGCGGCACTACGGTG
1 AATTCTACACGGCACTACGGTG
1489931 CATTTATACG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (23 bp):
AATTCTACACGGCACTACGGTGT
Found at i:1489940 original size:23 final size:23
Alignment explanation
Indices: 1489896--1489940 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1489886 AATTCTATAT
* *
1489896 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
1489919 GGCACTACGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1489941 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1490053 original size:2 final size:2
Alignment explanation
Indices: 1490046--1490153 Score: 207
Period size: 2 Copynumber: 54.0 Consensus size: 2
1490036 ACAACGTATG
1490046 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1490088 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1490130 TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
1490154 ATGTGTAATA
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 104 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1490172 original size:12 final size:13
Alignment explanation
Indices: 1490043--1490178 Score: 51
Period size: 14 Copynumber: 9.9 Consensus size: 13
1490033 AATACAACGT
*
1490043 ATGTATATATATA
1 ATGTGTATATATA
* *
1490056 TATATATATATATA
1 -ATGTGTATATATA
* *
1490070 TATATATATATATA
1 -ATGTGTATATATA
* *
1490084 TATATATATATATA
1 -ATGTGTATATATA
* *
1490098 TATATATATATATA
1 -ATGTGTATATATA
* *
1490112 TATATATATATATA
1 -ATGTGTATATATA
* *
1490126 TATATATATATATA
1 -ATGTGTATATATA
*
1490140 TATATGTATATATA
1 -ATGTGTATATATA
1490154 ATGTGTA-ATATGA
1 ATGTGTATATAT-A
1490167 AT-TGTATGATAT
1 ATGTGTAT-ATAT
1490179 GATATATGTG
Statistics
Matches: 116, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
12 8 0.07
13 9 0.08
14 99 0.85
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (13 bp):
ATGTGTATATATA
Found at i:1493673 original size:24 final size:24
Alignment explanation
Indices: 1493646--1493702 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
1493636 GCATGGGTAG
1493646 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCACATGTTAAGGGA
*
1493670 TGCATCGATGCACATGTTATGGGA
1 TGCATCGATGCACATGTTAAGGGA
1493694 TGCATCGAT
1 TGCATCGAT
1493703 ACACTGTAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (24 bp):
TGCATCGATGCACATGTTAAGGGA
Found at i:1494414 original size:22 final size:21
Alignment explanation
Indices: 1494389--1494441 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
1494379 TGTGATAATG
1494389 TTATAGGAATTAAAAATATAAA
1 TTATAGGAATT-AAAATATAAA
* ** *
1494411 TTATATGACATTAATGTATCAA
1 TTATAGGA-ATTAAAATATAAA
1494433 TTATAGGAA
1 TTATAGGAA
1494442 AAGAAGTACA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.04
22 21 0.84
23 3 0.12
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (21 bp):
TTATAGGAATTAAAATATAAA
Found at i:1495157 original size:23 final size:23
Alignment explanation
Indices: 1495083--1495149 Score: 109
Period size: 23 Copynumber: 2.9 Consensus size: 23
1495073 AATCTTATAT
*
1495083 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
1495106 GGCACTACGGTGC-ATATCTACGC
1 GGCACTACGGTGCAAT-TCTACGC
1495129 GGCACTACGGTGCAATTCTAC
1 GGCACTACGGTGCAATTCTAC
1495150 ATGTCACTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
22 2 0.05
23 37 0.90
24 2 0.05
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1500325 original size:23 final size:23
Alignment explanation
Indices: 1500235--1500317 Score: 130
Period size: 23 Copynumber: 3.6 Consensus size: 23
1500225 AATCTTATAT
1500235 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
1500258 GACACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1500281 GGCGCTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
1500304 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
1500318 TTTATACGAG
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.20, C:0.29, G:0.28, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1500440 original size:2 final size:2
Alignment explanation
Indices: 1500433--1500470 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1500423 AATGTATGCA
*
1500433 AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1500471 GATGTGTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1503273 original size:12 final size:12
Alignment explanation
Indices: 1503243--1503276 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1503233 AATGCAGAAA
*
1503243 TTACTGCAGCAG
1 TTACTGTAGCAG
1503255 TTACTGTAGCAG
1 TTACTGTAGCAG
1503267 TTACTGTAGC
1 TTACTGTAGC
1503277 GTATCAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (12 bp):
TTACTGTAGCAG
Found at i:1504605 original size:21 final size:21
Alignment explanation
Indices: 1504581--1504622 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1504571 AATCCTCAAT
1504581 TAAAAAGAATGAATAATAAAA
1 TAAAAAGAATGAATAATAAAA
* * *
1504602 TAAAGAGTATGAATACTAAAA
1 TAAAAAGAATGAATAATAAAA
1504623 AAAGAAAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.64, C:0.02, G:0.12, T:0.21
Consensus pattern (21 bp):
TAAAAAGAATGAATAATAAAA
Found at i:1507726 original size:2 final size:2
Alignment explanation
Indices: 1507721--1507745 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1507711 AAAACTAATA
1507721 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
1507746 CATACATACA
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:1508260 original size:123 final size:123
Alignment explanation
Indices: 1508008--1508248 Score: 305
Period size: 123 Copynumber: 2.0 Consensus size: 123
1507998 TGCTTCACTT
1508008 CTCTTCAGGAAGACCAAATCTAAAAGAAGAAAAATATGCTCCACTACATTTTAGGAGAGATCAAT
1 CTCTTCAGGAAGACCAAATCTAAAAGAAGAAAAATATGCTCCACTACATTTTAGGAGAGATCAAT
* * * *
1508073 CTCGAGAACATTTTAATTAACTTCACTGCTCTTTAGGGAAGATTGAATCGAATAATCA
66 CTCAAGAACATTTTAATTAACCTCACTGCTCTTCAGGGAAGATTAAATCGAATAATCA
* *
1508131 CTCTTCAGGAAGACCAAATCTGAAATA-AAG-AGAATATGCTCCACTAC-TCTTTACGG-GAGGT
1 CTCTTCAGGAAGACCAAATCT-AAA-AGAAGAAAAATATGCTCCACTACAT-TTTA-GGAGAGAT
* * * *
1508192 C-ATACTCAAGAA-ATTTTTATTAACCTCGCTTCTCTTCAGGGAAGTTTAAATCGAATA
62 CAAT-CTCAAGAACATTTTAATTAACCTCACTGCTCTTCAGGGAAGATTAAATCGAATA
1508249 TGATTTGCTT
Statistics
Matches: 103, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
122 41 0.40
123 53 0.51
124 8 0.08
125 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (123 bp):
CTCTTCAGGAAGACCAAATCTAAAAGAAGAAAAATATGCTCCACTACATTTTAGGAGAGATCAAT
CTCAAGAACATTTTAATTAACCTCACTGCTCTTCAGGGAAGATTAAATCGAATAATCA
Found at i:1508410 original size:134 final size:133
Alignment explanation
Indices: 1508131--1508797 Score: 635
Period size: 134 Copynumber: 5.0 Consensus size: 133
1508121 CGAATAATCA
* * * * * *
1508131 CTCTTCAGGAAGACCAAATCTGAAATAAAGAGAATATGCTCCACTACTCTTTACGGGAGGTCATA
1 CTCTTCAGGAAGACCAAATCTGAAAGAAAAAGAATCTGTTCCACTACTCTTTAGGGGAGGTCAGA
* * * * * * * *
1508196 CTCAAG-AAATTTTTATTAACCTCGCTTCTCTTCAGGGAAGTTTAAATCGAATATGATTTGCTTC
66 CTCGAGAAAATTTTGATTCACTTCGCTACTCTTCAGGGAAGATTGAATCGACT-TGATTTGCTTC
*
1508260 ATTG
130 ACTG
* * * ** * **
1508264 CTCTTCGGGAAGATCAAGTCTGAAAGAAGGAGAATATGTTATACTACTCTTTAGGGGAGGTCAGA
1 CTCTTCAGGAAGACCAAATCTGAAAGAAAAAGAATCTGTTCCACTACTCTTTAGGGGAGGTCAGA
* * * * * *
1508329 CTCGAGAAACTTTTGATTCACCTCACTACTCTTTAGGGAAGATTGAATCGACTGTGATTTTCTTT
66 CTCGAGAAAATTTTGATTCACTTCGCTACTCTTCAGGGAAGATTGAATCGACT-TGATTTGCTTC
*
1508394 ACTC
130 ACTG
* * * *
1508398 CTCTTCAGGAAGATCAAATCTAAAAGAAAAAGAATCT-TCTCCACTATTCTTTAGGGGAGGTTAG
1 CTCTTCAGGAAGACCAAATCTGAAAGAAAAAGAATCTGT-TCCACTACTCTTTAGGGGAGGTCAG
* * *
1508462 ACTCGAGAAAACTTTGATTCACTTTGC-AGCTCTTCAGGGAAGGTTGAATCGGACTTGATTTGCT
65 ACTCGAGAAAATTTTGATTCACTTCGCTA-CTCTTCAGGGAAGATTGAATC-GACTTGATTTGCT
1508526 TCACTG
128 TCACTG
* * ** * * *
1508532 CTCTTCAGGAAGACTAAATCTGAATGAAGAAAGAATCTACTCCGCTACTCTTTAGGGAAGGACAG
1 CTCTTCAGGAAGACCAAATCTGAAAGAA-AAAGAATCTGTTCCACTACTCTTTAGGGGAGGTCAG
* * * * *
1508597 ACTCGAGAAAAAAATTTCATTCACTTCGTTGA-TCTTCAAGGAAGATTGAATCGGATTTGATTTG
65 ACTCGAG--AAAATTTTGATTCACTTCGCT-ACTCTTCAGGGAAGATTGAATC-GACTTGATTTG
1508661 CTTCACTG
126 CTTCACTG
* ** * *
1508669 CTCTTCAGGAAGACCAAATTTGAAAGAAAAAGAATCTGCTT-TGCTACTTTTTAGGGGAGGTCAT
1 CTCTTCAGGAAGACCAAATCTGAAAGAAAAAGAATCTG-TTCCACTACTCTTTAGGGGAGGTCAG
* ** * * *
1508733 ACTGGAGAAAATTTTGATTCACTTTACTTCTC-TCTAGGGAAGATTGAATCGTACATGATTGGCT
65 ACTCGAGAAAATTTTGATTCACTTCGCTACTCTTC-AGGGAAGATTGAATCG-ACTTGATTTGCT
1508797 T
128 T
1508798 TGAAGATCGA
Statistics
Matches: 437, Mismatches: 83, Indels: 27
0.80 0.15 0.05
Matches are distributed among these distances:
133 65 0.15
134 219 0.50
135 40 0.09
136 33 0.08
137 79 0.18
139 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (133 bp):
CTCTTCAGGAAGACCAAATCTGAAAGAAAAAGAATCTGTTCCACTACTCTTTAGGGGAGGTCAGA
CTCGAGAAAATTTTGATTCACTTCGCTACTCTTCAGGGAAGATTGAATCGACTTGATTTGCTTCA
CTG
Found at i:1508697 original size:271 final size:268
Alignment explanation
Indices: 1508131--1508797 Score: 700
Period size: 271 Copynumber: 2.5 Consensus size: 268
1508121 CGAATAATCA
* * * * *
1508131 CTCTTCAGGAAGACCAAATCTGAAATAAAGAGAATATGCTCCACTACTCTTTACGGGAGGTCATA
1 CTCTTCAGGAAGACCAAATCTGAAAGAAAAAGAATCTGCTCCACTATTCTTTAGGGGAGGTCATA
* * * * * * * *
1508196 CTCAAG-AAATTTTTATTAACCTCGCTTCTCTTCAGGGAAGTTTAAATC-GAATATGATTTGCTT
66 CTCGAGAAAATTTTGATTCACTTTGCTTCTCTTCAGGGAAGATTGAATCGGACT-TGATTTGCTT
* * * * ** * *
1508259 CATTGCTCTTCGGGAAGATCAAGTCTGAAAGAAGGAGAATATGTTATACTACTCTTTAGGGGAGG
130 CACTGCTCTTCAGGAAGATCAAATCTGAAAGAAGAAGAATATACTACACTACTCTTTAGGGAAGG
* ** * * *
1508324 TCAGACTCGAGAAACTTTTGATTCACCTCACTACTCTTTAGGGAAGATTGAATCGACTGTGATTT
195 ACAGACTCGAGAAAAATTTCATTCACCTCACTACTCTTCAAGGAAGATTGAATCGACTGTGATTT
* *
1508389 TCTTTACTC
260 GCTTCACTC
* * * * *
1508398 CTCTTCAGGAAGATCAAATCTAAAAGAAAAAGAATCTTCTCCACTATTCTTTAGGGGAGGTTAGA
1 CTCTTCAGGAAGACCAAATCTGAAAGAAAAAGAATCTGCTCCACTATTCTTTAGGGGAGGTCATA
* ** *
1508463 CTCGAGAAAACTTTGATTCACTTTGCAGCTCTTCAGGGAAGGTTGAATCGGACTTGATTTGCTTC
66 CTCGAGAAAATTTTGATTCACTTTGCTTCTCTTCAGGGAAGATTGAATCGGACTTGATTTGCTTC
* * * *
1508528 ACTGCTCTTCAGGAAGA-CTAAATCTGAATGAAGAAAGAATCTACTCCGCTACTCTTTAGGGAAG
131 ACTGCTCTTCAGGAAGATC-AAATCTGAAAGAAG-AAGAATATACTACACTACTCTTTAGGGAAG
* ** *
1508592 GACAGACTCGAGAAAAAAATTTCATTCACTTCGTTGA-TCTTCAAGGAAGATTGAATCGGA-TTT
194 GACAGACTCGAG--AAAAATTTCATTCACCTCACT-ACTCTTCAAGGAAGATTGAATC-GACTGT
*
1508655 GATTTGCTTCACTG
255 GATTTGCTTCACTC
* ***
1508669 CTCTTCAGGAAGACCAAATTTGAAAGAAAAAGAATCTGCTTTGCTACTT-TTTAGGGGAGGTCAT
1 CTCTTCAGGAAGACCAAATCTGAAAGAAAAAGAATCTGCTCCACTA-TTCTTTAGGGGAGGTCAT
* * * * *
1508733 ACTGGAGAAAATTTTGATTCACTTTACTTCTC-TCTAGGGAAGATTGAATCGTACATGATTGGCT
65 ACTCGAGAAAATTTTGATTCACTTTGCTTCTCTTC-AGGGAAGATTGAATCGGACTTGATTTGCT
1508797 T
129 T
1508798 TGAAGATCGA
Statistics
Matches: 326, Mismatches: 64, Indels: 16
0.80 0.16 0.04
Matches are distributed among these distances:
267 61 0.19
268 71 0.22
269 36 0.11
270 2 0.01
271 151 0.46
272 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (268 bp):
CTCTTCAGGAAGACCAAATCTGAAAGAAAAAGAATCTGCTCCACTATTCTTTAGGGGAGGTCATA
CTCGAGAAAATTTTGATTCACTTTGCTTCTCTTCAGGGAAGATTGAATCGGACTTGATTTGCTTC
ACTGCTCTTCAGGAAGATCAAATCTGAAAGAAGAAGAATATACTACACTACTCTTTAGGGAAGGA
CAGACTCGAGAAAAATTTCATTCACCTCACTACTCTTCAAGGAAGATTGAATCGACTGTGATTTG
CTTCACTC
Found at i:1510125 original size:7 final size:7
Alignment explanation
Indices: 1510115--1510158 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
1510105 CTTTTTGTTT
1510115 ATTTTTC
1 ATTTTTC
1510122 ATTTTT-
1 ATTTTTC
1510128 A-TTTTC
1 ATTTTTC
*
1510134 ATTTTTT
1 ATTTTTC
1510141 ATTTTTC
1 ATTTTTC
1510148 ATTTTT-
1 ATTTTTC
1510154 ATTTT
1 ATTTT
1510159 CTCTTCAGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 4 0.12
6 7 0.21
7 22 0.67
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (7 bp):
ATTTTTC
Found at i:1510126 original size:26 final size:26
Alignment explanation
Indices: 1510074--1510159 Score: 106
Period size: 26 Copynumber: 3.3 Consensus size: 26
1510064 CCCCATTTTA
* *
1510074 TTTATTTTCCTTTTCT-TTTTTC-TT
1 TTTATTTTCATTTTTTATTTTTCATT
*
1510098 TTT-TTTTCTTTTTGTTTATTTTTCATT
1 TTTATTTTC-ATTT-TTTATTTTTCATT
1510125 TTTATTTTCATTTTTTATTTTTCATT
1 TTTATTTTCATTTTTTATTTTTCATT
1510151 TTTATTTTC
1 TTTATTTTC
1510160 TCTTCAGGCA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
23 5 0.09
24 6 0.11
25 2 0.04
26 28 0.52
27 8 0.15
28 5 0.09
ACGTcount: A:0.09, C:0.10, G:0.01, T:0.79
Consensus pattern (26 bp):
TTTATTTTCATTTTTTATTTTTCATT
Found at i:1511877 original size:225 final size:225
Alignment explanation
Indices: 1511486--1511940 Score: 901
Period size: 225 Copynumber: 2.0 Consensus size: 225
1511476 GTGAGATATA
1511486 ATATAGTAAATAACATTAAAGAATACATAAATATCTCATAGTTATTTAACTTCAAAAGAAGTTAT
1 ATATAGTAAATAACATTAAAGAATACATAAATATCTCATAGTTATTTAACTTCAAAAGAAGTTAT
1511551 ATCATCCATAAGAATTTGTTAAGTCATTCGTTTTATATTCAAACCTTGGTTATATTATCCATAAT
66 ATCATCCATAAGAATTTGTTAAGTCATTCGTTTTATATTCAAACCTTGGTTATATTATCCATAAT
1511616 ATCATCTTTAGTATGTCCAACATACTTCTCTTTAGATCATTAACCTCATTTATGTCTATTTTAAT
131 ATCATCTTTAGTATGTCCAACATACTTCTCTTTAGATCATTAACCTCATTTATGTCTATTTTAAT
*
1511681 GTATTAACACATCCATTTATGCATTTTAAT
196 GTATTAACACATCCATTTATACATTTTAAT
1511711 ATATAGTAAATAACATTAAAGAATACATAAATATCTCATAGTTATTTAACTTCAAAAGAAGTTAT
1 ATATAGTAAATAACATTAAAGAATACATAAATATCTCATAGTTATTTAACTTCAAAAGAAGTTAT
1511776 ATCATCCATAAGAATTTGTTAAGTCATTCGTTTTATATTCAAACCTTGGTTATATTATCCATAAT
66 ATCATCCATAAGAATTTGTTAAGTCATTCGTTTTATATTCAAACCTTGGTTATATTATCCATAAT
1511841 ATCATCTTTAGTATGTCCAACATACTTCTCTTTAGATCATTAACCTCATTTATGTCTATTTTAAT
131 ATCATCTTTAGTATGTCCAACATACTTCTCTTTAGATCATTAACCTCATTTATGTCTATTTTAAT
1511906 GTATTAACACATCCATTTATACATTTTAAT
196 GTATTAACACATCCATTTATACATTTTAAT
1511936 ATATA
1 ATATA
1511941 TATGGTATCC
Statistics
Matches: 229, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
225 229 1.00
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.41
Consensus pattern (225 bp):
ATATAGTAAATAACATTAAAGAATACATAAATATCTCATAGTTATTTAACTTCAAAAGAAGTTAT
ATCATCCATAAGAATTTGTTAAGTCATTCGTTTTATATTCAAACCTTGGTTATATTATCCATAAT
ATCATCTTTAGTATGTCCAACATACTTCTCTTTAGATCATTAACCTCATTTATGTCTATTTTAAT
GTATTAACACATCCATTTATACATTTTAAT
Found at i:1512003 original size:47 final size:47
Alignment explanation
Indices: 1511941--1512099 Score: 246
Period size: 47 Copynumber: 3.4 Consensus size: 47
1511931 TTAATATATA
* * * *
1511941 TATGGTATCCTTTCATGCCTTAATACATCATTTCATGCATTTTTAAT
1 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAAAT
* * * *
1511988 TATGGCATCTTTTCATGCCTTTATGCATCCTTTAATGCATTTTCAAT
1 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAAAT
1512035 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAAAT
1 TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAAAT
1512082 TATGGCATCCTTTCATGC
1 TATGGCATCCTTTCATGC
1512100 ATTTTTAATT
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 101 1.00
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.45
Consensus pattern (47 bp):
TATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAAAT
Found at i:1512004 original size:27 final size:27
Alignment explanation
Indices: 1511966--1512113 Score: 135
Period size: 27 Copynumber: 6.0 Consensus size: 27
1511956 TGCCTTAATA
*
1511966 CATCATTTCATGCATTTTTAATTATGG
1 CATCCTTTCATGCATTTTTAATTATGG
* *
1511993 CATCTTTTCATGC----CT--TTAT-G
1 CATCCTTTCATGCATTTTTAATTATGG
* *
1512013 CATCCTTTAATGCATTTTCAATTATGG
1 CATCCTTTCATGCATTTTTAATTATGG
*
1512040 CATCCTTTCATGC---CTT-A--AT-G
1 CATCCTTTCATGCATTTTTAATTATGG
*
1512060 CATCCTTTCATGCATTTTAAATTATGG
1 CATCCTTTCATGCATTTTTAATTATGG
1512087 CATCCTTTCATGCATTTTTAATTATGG
1 CATCCTTTCATGCATTTTTAATTATGG
1512114 ATTCGATTTA
Statistics
Matches: 95, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
20 26 0.27
21 6 0.06
23 3 0.03
24 2 0.02
26 6 0.06
27 52 0.55
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (27 bp):
CATCCTTTCATGCATTTTTAATTATGG
Found at i:1512025 original size:20 final size:21
Alignment explanation
Indices: 1511987--1512025 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1511977 GCATTTTTAA
* *
1511987 TTATGGCATCTTTTCATGCCT
1 TTATGGCATCCTTTAATGCCT
1512008 TTAT-GCATCCTTTAATGC
1 TTATGGCATCCTTTAATGC
1512026 ATTTTCAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.18, C:0.23, G:0.13, T:0.46
Consensus pattern (21 bp):
TTATGGCATCCTTTAATGCCT
Found at i:1512667 original size:95 final size:95
Alignment explanation
Indices: 1512529--1512724 Score: 277
Period size: 95 Copynumber: 2.1 Consensus size: 95
1512519 CTAGTACCGT
* * * *
1512529 TACTTCTATACTATGGTACCGATACCCCCTTCCGGTATCGATACTAAAATTA-ACTTCGATGTTT
1 TACTACTATACTACGGTACCAATACCCCCTTCCGGTATCGATACCAAAATTATA-TTCGATGTTT
*
1512593 CCTGGCATCAATACCCTTACCATGGTATCAA
65 ACTGGCATCAATACCCTTACCATGGTATCAA
* *
1512624 TACTACTATACTACGGTACCAATACCCCTTTCTGGTATCGATACCAAAATTATATTCGATGTTTA
1 TACTACTATACTACGGTACCAATACCCCCTTCCGGTATCGATACCAAAATTATATTCGATGTTTA
* * * *
1512689 CTGGTATCGATACCCTTACCTTGGTATCGA
66 CTGGCATCAATACCCTTACCATGGTATCAA
1512719 TACTAC
1 TACTAC
1512725 CTCATTGGTA
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
95 88 0.99
96 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.34
Consensus pattern (95 bp):
TACTACTATACTACGGTACCAATACCCCCTTCCGGTATCGATACCAAAATTATATTCGATGTTTA
CTGGCATCAATACCCTTACCATGGTATCAA
Found at i:1516210 original size:21 final size:21
Alignment explanation
Indices: 1516185--1516243 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
1516175 CGTGAACAGT
1516185 GGGGAATCGGTTCCCTATATG
1 GGGGAATCGGTTCCCTATATG
1516206 GGGGAATCGGTTCCCTATATG
1 GGGGAATCGGTTCCCTATATG
*
1516227 GGGGAATCGGTACCCTA
1 GGGGAATCGGTTCCCTA
1516244 AATGCATTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.25
Consensus pattern (21 bp):
GGGGAATCGGTTCCCTATATG
Found at i:1516743 original size:89 final size:89
Alignment explanation
Indices: 1516628--1516824 Score: 260
Period size: 89 Copynumber: 2.2 Consensus size: 89
1516618 TGCATATCCA
1516628 ATATTTTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTATCC
1 ATATTTTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCA-TTATCC
1516693 CATAAGCCCGTAACCTTCTTTTACC
65 CATAAGCCCGTAACCTTCTTTTACC
* * * *
1516718 ATATTCTTGCCATTTA-T-ACCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCATTATTC
1 ATATT-TTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTATCC
* * * *
1516781 CATAAGCTCGTAAGCTT-ATTT-GC
65 CATAAGCCCGTAACCTTCTTTTACC
*
1516804 ATA-CTTACCATTTATTAACCA
1 ATATTTTACCATTTATTAACCA
1516825 ATAAACCATA
Statistics
Matches: 94, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
84 9 0.10
85 1 0.01
86 8 0.09
87 3 0.03
88 20 0.21
89 38 0.40
90 6 0.06
91 9 0.10
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (89 bp):
ATATTTTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTATCCC
ATAAGCCCGTAACCTTCTTTTACC
Found at i:1516749 original size:44 final size:45
Alignment explanation
Indices: 1516625--1516801 Score: 225
Period size: 44 Copynumber: 4.0 Consensus size: 45
1516615 ATTTGCATAT
*
1516625 CCAATAT-TTTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTA-T-ACCATAAGCTCGTAAGCTTATTTTA
* * * * *
1516671 CCAAAATACTTACCATTTATCCCATAAGCCCGTAACCTTCTTTTA
1 CCAATATACTTACCATTTATACCATAAGCTCGTAAGCTTATTTTA
* *
1516716 CC-ATATTCTTGCCATTTATACCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTATACCATAAGCTCGTAAGCTTATTTTA
* *
1516760 CCAATATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 CCAATATACTTACCATTTATACCATAAGCTCGTAAGCTTATTT
1516802 GCATACTTAC
Statistics
Matches: 114, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
44 63 0.55
45 34 0.30
46 7 0.06
47 10 0.09
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.38
Consensus pattern (45 bp):
CCAATATACTTACCATTTATACCATAAGCTCGTAAGCTTATTTTA
Found at i:1530584 original size:140 final size:140
Alignment explanation
Indices: 1530393--1530676 Score: 426
Period size: 140 Copynumber: 2.0 Consensus size: 140
1530383 TTTCTTATGC
* * * *
1530393 TAGTATGATACTATCATATGATTTGAAATGAATGTATTGTGAATGTGATCTCTGTTTAGATAATC
1 TAGTATGATACTAACATATCATTTGAAATGAATGTATAGTGAATGTAATCTCTGTTTAGATAATC
* * ** * *
1530458 CATAAAAGCGTGATGAAATCAAATCAAAGGTTAAAGAAAAAGTACCTGAGTAAGGAATATTGAAG
66 CACAAAAGCGTGATCAAATCAAATCAAA-GTTAAAGAAAAAACACATGAGTAAGGAATATCGAAG
1530523 TAAAGGTGTGT
130 TAAAGGTGTGT
*
1530534 TAGTATGATACTAACATA-CATTTGAAATGAATGTATAGTGAATGTAATCTCTGTTTAGATACTC
1 TAGTATGATACTAACATATCATTTGAAATGAATGTATAGTGAATGTAATCTCTGTTTAGATAATC
* *
1530598 CACAAAAGTGTGATCAAATCAAATCAAAGTTTAAGAAAAAACACATGAGTAAGGAATATCGAAGT
66 CACAAAAGCGTGATCAAATCAAATCAAAGTTAAAGAAAAAACACATGAGTAAGGAATATCGAAGT
*
1530663 AAAGGTTTGT
131 AAAGGTGTGT
1530673 TAGT
1 TAGT
1530677 GAGGCATATA
Statistics
Matches: 129, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
139 45 0.35
140 67 0.52
141 17 0.13
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (140 bp):
TAGTATGATACTAACATATCATTTGAAATGAATGTATAGTGAATGTAATCTCTGTTTAGATAATC
CACAAAAGCGTGATCAAATCAAATCAAAGTTAAAGAAAAAACACATGAGTAAGGAATATCGAAGT
AAAGGTGTGT
Done.