Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001700.1 Hibiscus syriacus cultivar Beakdansim tig00003398_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: 2632955
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1301891 original size:19 final size:19
Alignment explanation
Indices: 1301867--1301904 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1301857 CTTTTTATTT
*
1301867 TATTTTAAATAGGTTTTAG
1 TATTTTAAATAAGTTTTAG
*
1301886 TATTTTAATTAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
1301905 GATATTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TATTTTAAATAAGTTTTAG
Found at i:1301922 original size:32 final size:32
Alignment explanation
Indices: 1301880--1301941 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1301870 TTTAAATAGG
1301880 TTTTAGTATTTTAATTAAGTTTTAGGATATTAA
1 TTTTAGTATTTTAATTAAGTTTTAGG-TATTAA
* **
1301913 TTTTA-TATTTTATTTTTGTTTTAGGTATT
1 TTTTAGTATTTTAATTAAGTTTTAGGTATT
1301942 TTAGTATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 4 0.15
32 17 0.65
33 5 0.19
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (32 bp):
TTTTAGTATTTTAATTAAGTTTTAGGTATTAA
Found at i:1302047 original size:74 final size:74
Alignment explanation
Indices: 1301825--1302053 Score: 264
Period size: 76 Copynumber: 3.1 Consensus size: 74
1301815 TAAACTCAAG
* * * *
1301825 TTTAGGATAATATTTTAAACATTA-TATTTTATCTTTTTATTTTATTTTAAATAGGTTTTAGTAT
1 TTTAGGATATTATTTTAAATATTATTATTTT-T-TATGTATTTTATTTTAAATAGGTTTTAGTAT
* *
1301889 TTTAATTAAGT
64 TTTAATTAGGA
* * * * * * *
1301900 TTTAGGATATTAATTTTATATTTTATTTTTGTTTTAGGTATTTTAGTATAAATATGTTTTAGTAT
1 TTTAGGATATT-ATTTTAAATATTATTATT-TTTTATGTATTTTATTTTAAATAGGTTTTAGTAT
1301965 TTTAATTAGGA
64 TTTAATTAGGA
* *
1301976 TTTAGAATATTATTTTAAATATTATTATTTTTTATGTATTTTATTTTAAATA-GTTTTAAGTGTT
1 TTTAGGATATTATTTTAAATATTATTATTTTTTATGTATTTTATTTTAAATAGGTTTT-AGTATT
1302040 TTAATTAGGA
65 TTAATTAGGA
1302050 TTTA
1 TTTA
1302054 AGATGTTTTA
Statistics
Matches: 129, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
73 5 0.04
74 39 0.30
75 25 0.19
76 54 0.42
77 4 0.03
78 2 0.02
ACGTcount: A:0.31, C:0.01, G:0.10, T:0.58
Consensus pattern (74 bp):
TTTAGGATATTATTTTAAATATTATTATTTTTTATGTATTTTATTTTAAATAGGTTTTAGTATTT
TAATTAGGA
Found at i:1302668 original size:14 final size:14
Alignment explanation
Indices: 1302636--1302678 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1302626 TCTCAATCTC
* *
1302636 TTTAATT-TGTTTA
1 TTTAATTATTTTTT
1302649 TTTAATTATTTTTT
1 TTTAATTATTTTTT
1302663 TTTAATTATTATTTT
1 TTTAATTATT-TTTT
1302678 T
1 T
1302679 ATTTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 7 0.27
14 14 0.54
15 5 0.19
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (14 bp):
TTTAATTATTTTTT
Found at i:1305599 original size:5 final size:5
Alignment explanation
Indices: 1305574--1305661 Score: 58
Period size: 5 Copynumber: 17.8 Consensus size: 5
1305564 ATATCTTTGT
* * ** * *
1305574 TTTTA TTTTCA TTTTAA TTTTG TTTTA -TTT- TTTTA GTGAA CTTTA TTTAA
1 TTTTA TTTT-A TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
*
1305624 TTATA -TTTA TTTTAA TTTTA -TTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTT
1305662 TTTCTCTGAA
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
4 13 0.21
5 35 0.56
6 15 0.24
ACGTcount: A:0.23, C:0.02, G:0.03, T:0.72
Consensus pattern (5 bp):
TTTTA
Found at i:1305639 original size:15 final size:15
Alignment explanation
Indices: 1305615--1305664 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
1305605 TTTAGTGAAC
*
1305615 TTTA-TTTAATTATA
1 TTTATTTTAATTTTA
1305629 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
1305644 TTTATTTT-ATTTTA
1 TTTATTTTAATTTTA
1305658 TTT-TTTT
1 TTTATTTT
1305665 CTCTGAACAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
13 4 0.12
14 13 0.38
15 17 0.50
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:1306490 original size:201 final size:202
Alignment explanation
Indices: 1306145--1306548 Score: 792
Period size: 201 Copynumber: 2.0 Consensus size: 202
1306135 AGATGAACTT
1306145 GACTCAATGCATATAAACTTTTATTGTGAGATTTGAGCCTAACGAGCATACATTTTCTTTCTTGC
1 GACTCAATGCATATAAACTTTTATTGTGAGATTTGAGCCTAACGAGCATACATTTTCTTTCTTGC
1306210 TCATTGTTTGACTTGTGTGTTCCAAACTAATTAGGATATTCTAGAACTTGTAATCATAATGCATA
66 TCATTGTTTGACTTGTGTGTTCCAAACTAATTAGGATATTCTAGAACTTGTAATCATAATGCATA
*
1306275 TCGAGACTACATGTTGAACGT-ATGTTTTAATGTGATAGGGGCACCTAGGATAACCCCACTTTTC
131 TCGAGACTACATGTTGAACGTAATGTTTTAATGTGATAGGGGCACCTAGGATAAACCCACTTTTC
1306339 CCAAAAA
196 CCAAAAA
1306346 GACTCAATGCATATAAACTTTTATTGTGAGATTTGAGCCTAACGAGCATACATTTTCTTTCTTGC
1 GACTCAATGCATATAAACTTTTATTGTGAGATTTGAGCCTAACGAGCATACATTTTCTTTCTTGC
1306411 TCATTGTTTGACTTGTGTGTTCCAAACTAATTAGGATATTCTAGAACTTGTAATCATAATGCATA
66 TCATTGTTTGACTTGTGTGTTCCAAACTAATTAGGATATTCTAGAACTTGTAATCATAATGCATA
1306476 TCGAGACTACATGTTGAACGTAATGTTTTAATGTGATAGGGGCACCTAGGATAAACCCACTTTTC
131 TCGAGACTACATGTTGAACGTAATGTTTTAATGTGATAGGGGCACCTAGGATAAACCCACTTTTC
1306541 CCAAAAA
196 CCAAAAA
1306548 G
1 G
1306549 CCTGCCCGTT
Statistics
Matches: 201, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
201 151 0.75
202 50 0.25
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (202 bp):
GACTCAATGCATATAAACTTTTATTGTGAGATTTGAGCCTAACGAGCATACATTTTCTTTCTTGC
TCATTGTTTGACTTGTGTGTTCCAAACTAATTAGGATATTCTAGAACTTGTAATCATAATGCATA
TCGAGACTACATGTTGAACGTAATGTTTTAATGTGATAGGGGCACCTAGGATAAACCCACTTTTC
CCAAAAA
Found at i:1307683 original size:76 final size:72
Alignment explanation
Indices: 1307566--1307797 Score: 270
Period size: 76 Copynumber: 3.1 Consensus size: 72
1307556 TAAACTCAAG
* * *
1307566 TTTAGGATAATATTTTAAATATTA-TATTTTATCTTTGTATTTTAGTTTAAATATGTTTTAGTAT
1 TTTAAGATATTATTTTAAATATTATTA-TTT-T-TATGTATTTTAGTTTAAATA-GTTTTAGTAT
* *
1307630 TTTAATTAAGT
62 TTTAATTAGGA
* * *
1307641 TTTAAGATATTATTTTTATATTTTATATTTGTTTTATGTATTTTAGTTTAAATAGGTTTTAGTAT
1 TTTAAGATATTA-TTTTAAATATTAT-TAT-TTTTATGTATTTTAGTTTAAATA-GTTTTAGTAT
1307706 TTTAATTAGGA
62 TTTAATTAGGA
* *
1307717 TTT-AGAATATTATTTTAAATATTATTATTTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTT
1 TTTAAG-ATATTATTTTAAATATTATTATTTTTATGTATTTTAGTTTAAATAGTTTT-AGTATTT
1307781 TAATTAGGA
64 TAATTAGGA
1307790 TTTAAGAT
1 TTTAAGAT
1307798 GTTTTAGCTT
Statistics
Matches: 136, Mismatches: 14, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
72 5 0.04
73 42 0.31
74 4 0.03
75 23 0.17
76 57 0.42
77 2 0.01
78 3 0.02
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (72 bp):
TTTAAGATATTATTTTAAATATTATTATTTTTATGTATTTTAGTTTAAATAGTTTTAGTATTTTA
ATTAGGA
Found at i:1310950 original size:48 final size:48
Alignment explanation
Indices: 1310838--1310960 Score: 156
Period size: 48 Copynumber: 2.6 Consensus size: 48
1310828 CCGAAGCATC
* * *
1310838 TGAAGATGCTCACTAGCCCACCAATGAAGATGCTCACTAGCCCGCCAA
1 TGAAGAGGCTCACTAGCCCGCCAATGAAGATGCTCACCAGCCCGCCAA
* *
1310886 TGAAGATGCTCACTAGCCCGCCAATGAAGTTGCTCACCAGCCCGCCAA
1 TGAAGAGGCTCACTAGCCCGCCAATGAAGATGCTCACCAGCCCGCCAA
* * * * *
1310934 TTAAGAGGTTCCCTAGCCAGCCGATGA
1 TGAAGAGGCTCACTAGCCCGCCAATGA
1310961 GGAAGAACCA
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.28, C:0.33, G:0.21, T:0.18
Consensus pattern (48 bp):
TGAAGAGGCTCACTAGCCCGCCAATGAAGATGCTCACCAGCCCGCCAA
Found at i:1310951 original size:24 final size:24
Alignment explanation
Indices: 1310838--1310939 Score: 168
Period size: 24 Copynumber: 4.2 Consensus size: 24
1310828 CCGAAGCATC
*
1310838 TGAAGATGCTCACTAGCCCACCAA
1 TGAAGATGCTCACTAGCCCGCCAA
1310862 TGAAGATGCTCACTAGCCCGCCAA
1 TGAAGATGCTCACTAGCCCGCCAA
1310886 TGAAGATGCTCACTAGCCCGCCAA
1 TGAAGATGCTCACTAGCCCGCCAA
* *
1310910 TGAAGTTGCTCACCAGCCCGCCAA
1 TGAAGATGCTCACTAGCCCGCCAA
*
1310934 TTAAGA
1 TGAAGA
1310940 GGTTCCCTAG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.30, C:0.32, G:0.20, T:0.18
Consensus pattern (24 bp):
TGAAGATGCTCACTAGCCCGCCAA
Found at i:1312785 original size:23 final size:24
Alignment explanation
Indices: 1312732--1312785 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
1312722 CAAGTACTCA
* * *
1312732 GCCAGCCACCCAGGCTGGATCAAT
1 GCCAGCTACCCAGGCGGGACCAAT
*
1312756 GCCAGCTACCCAGG-GGGACCACT
1 GCCAGCTACCCAGGCGGGACCAAT
1312779 GCCAGCT
1 GCCAGCT
1312786 CTGCCCGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.22, C:0.39, G:0.28, T:0.11
Consensus pattern (24 bp):
GCCAGCTACCCAGGCGGGACCAAT
Found at i:1316492 original size:30 final size:30
Alignment explanation
Indices: 1316456--1316515 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1316446 CTCGCTTGAG
1316456 ATAGTTTCACTCAAAACAAAAGATTTATCT
1 ATAGTTTCACTCAAAACAAAAGATTTATCT
*
1316486 ATAGTTTCACTCGAAACAAAAGATTTATCT
1 ATAGTTTCACTCAAAACAAAAGATTTATCT
1316516 CATTTGAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (30 bp):
ATAGTTTCACTCAAAACAAAAGATTTATCT
Found at i:1316645 original size:59 final size:59
Alignment explanation
Indices: 1316549--1316661 Score: 183
Period size: 59 Copynumber: 1.9 Consensus size: 59
1316539 ATGAACAACT
1316549 CCCCACCAGAGGGGTTAACATTTTCTTCACTCAATTCACGACATTTTGAATCAGTGATG
1 CCCCACCAGAGGGGTTAACATTTTCTTCACTCAATTCACGACATTTTGAATCAGTGATG
** *
1316608 CCCCACCAGAGGGGTTAAC-TTTTCCTTTGCTCGATTCACGACATTTTGAATCAG
1 CCCCACCAGAGGGGTTAACATTTT-CTTCACTCAATTCACGACATTTTGAATCAG
1316662 CGACACCTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
58 4 0.08
59 46 0.92
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.31
Consensus pattern (59 bp):
CCCCACCAGAGGGGTTAACATTTTCTTCACTCAATTCACGACATTTTGAATCAGTGATG
Found at i:1316773 original size:38 final size:39
Alignment explanation
Indices: 1316687--1316781 Score: 156
Period size: 39 Copynumber: 2.5 Consensus size: 39
1316677 GGGAAAAATG
*
1316687 TCTCACTTGAGATAGTTTCACTCAAAACAGAAGATTTTA
1 TCTCACTTGAGATAGTTTCACTCAAAACAAAAGATTTTA
*
1316726 TCTCGCTTGAGATAGTTTCACTCAAAACAAAAGA-TTTA
1 TCTCACTTGAGATAGTTTCACTCAAAACAAAAGATTTTA
*
1316764 TCTCACTTGAGATTGTTT
1 TCTCACTTGAGATAGTTT
1316782 TTTTAAACGA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 20 0.38
39 32 0.62
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.36
Consensus pattern (39 bp):
TCTCACTTGAGATAGTTTCACTCAAAACAAAAGATTTTA
Found at i:1316878 original size:43 final size:43
Alignment explanation
Indices: 1316807--1316891 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
1316797 GCCCCACCAT
*
1316807 AGGGGTTAACATTTTCTTCACTCAATTCATGGCATTTCGAATC
1 AGGGGTTAACATTTTCTTCACTCAATTCATGGAATTTCGAATC
* *
1316850 AGGGGTTAAC-TTTTCCTTTACTCGATTCATGGAATTTCGAAT
1 AGGGGTTAACATTTT-CTTCACTCAATTCATGGAATTTCGAAT
1316892 TAGTGACACC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 4 0.11
43 34 0.89
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.39
Consensus pattern (43 bp):
AGGGGTTAACATTTTCTTCACTCAATTCATGGAATTTCGAATC
Found at i:1316987 original size:39 final size:39
Alignment explanation
Indices: 1316919--1317171 Score: 332
Period size: 39 Copynumber: 6.5 Consensus size: 39
1316909 AGGGATCAAC
* *
1316919 ATCTCGCTTGAGATAGTTTTACTCTAAACAGAAAATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAAATTTT
* *
1316958 ATCACGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAA-AATTTT
* *
1316998 ATCTCGCTTGAGATAGTTTCACTCG--ACATAAATTTTTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAA--ATTTT
*
1317037 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAAATTTT
*
1317076 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAAATTTT
* * * *
1317115 GTCTCACTTGAGATAGTTTTACTCGAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAAATTTT
* *
1317153 ATCTCACTTGAGATTGTTT
1 ATCTCGCTTGAGATAGTTT
1317172 TTCTTAAAAC
Statistics
Matches: 195, Mismatches: 14, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
37 1 0.01
38 25 0.13
39 135 0.69
40 29 0.15
41 5 0.03
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (39 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAAATTTT
Found at i:1333339 original size:65 final size:66
Alignment explanation
Indices: 1333232--1333367 Score: 168
Period size: 65 Copynumber: 2.1 Consensus size: 66
1333222 CTTGGGGTAC
* * * * *
1333232 ATCGGCACACTAATTATATTCGATGTTTCAAAAGAGCCAGGAGTGCATCGATGCA-TCAGTTGTG
1 ATCGGCACACAAAATATATTCGATGTTTCAAAAGAACCAGGAGTGCATCGATGCATTCAATAGTG
1333296 T
66 T
* ** *
1333297 ATCGGCACACAAAATGTATTCGATGTTTCAATAA-AATTAGGAGTGTATCGATGCATTCAATAGT
1 ATCGGCACACAAAATATATTCGATGTTTCAA-AAGAACCAGGAGTGCATCGATGCATTCAATAGT
1333361 GT
65 GT
1333363 ATCGG
1 ATCGG
1333368 TACATTCCTT
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
65 45 0.75
66 15 0.25
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (66 bp):
ATCGGCACACAAAATATATTCGATGTTTCAAAAGAACCAGGAGTGCATCGATGCATTCAATAGTG
T
Found at i:1337088 original size:23 final size:22
Alignment explanation
Indices: 1337061--1337140 Score: 72
Period size: 23 Copynumber: 3.6 Consensus size: 22
1337051 CATAGCAGAG
1337061 TGCATCAATGCACATTCAAGGAA
1 TGCATCAATGCACATTCAAGG-A
* * **
1337084 TGCATCAGTGCACCTTCGTGG-
1 TGCATCAATGCACATTCAAGGA
* *
1337105 TGTATCGATGCACATTCAAGGGA
1 TGCATCAATGCACATTCAA-GGA
*
1337128 TGCATCGATGCAC
1 TGCATCAATGCAC
1337141 TCTCTAGTGT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
21 13 0.30
22 2 0.05
23 29 0.66
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (22 bp):
TGCATCAATGCACATTCAAGGA
Found at i:1337117 original size:21 final size:21
Alignment explanation
Indices: 1337092--1337159 Score: 52
Period size: 23 Copynumber: 3.2 Consensus size: 21
1337082 AATGCATCAG
1337092 TGCACCTTCGTGGTGTATCGA
1 TGCACCTTCGTGGTGTATCGA
* *
1337113 TGCACATTCAAG-GGATGCATCGA
1 TGCACCTTC--GTGG-TGTATCGA
*
1337136 TGCA-CTCTC-TAGTGTATCGA
1 TGCACCT-TCGTGGTGTATCGA
1337156 TGCA
1 TGCA
1337160 TTATGCACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
20 11 0.30
21 9 0.24
22 3 0.08
23 14 0.38
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (21 bp):
TGCACCTTCGTGGTGTATCGA
Found at i:1337131 original size:44 final size:43
Alignment explanation
Indices: 1337059--1337159 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 43
1337049 TGCATAGCAG
* *
1337059 AGTGCATCAATGCACATTCAAGGAATGCATC-AGTGCAC-CTTCGT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGA-TGCACTC-TC-T
* *
1337103 GGTGTATCGATGCACATTCAAGGGATGCATCGATGCACTCTCT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGATGCACTCTCT
1337146 AGTGTATCGATGCA
1 AGTGTATCGATGCA
1337160 TTATGCACAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
43 14 0.28
44 34 0.68
45 2 0.04
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.27
Consensus pattern (43 bp):
AGTGTATCGATGCACATTCAAGGAATGCATCGATGCACTCTCT
Found at i:1341806 original size:10 final size:11
Alignment explanation
Indices: 1341793--1341831 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1341783 GTGCTTTAAC
1341793 TTTC-TTTCTT
1 TTTCTTTTCTT
*
1341803 TTTCTTTTTTAT
1 TTTCTTTTCT-T
1341815 TTTCTTTTCTT
1 TTTCTTTTCTT
1341826 TTTCTT
1 TTTCTT
1341832 CCTTTTTGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 4 0.16
11 11 0.44
12 10 0.40
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:1348682 original size:65 final size:65
Alignment explanation
Indices: 1348608--1348744 Score: 161
Period size: 65 Copynumber: 2.1 Consensus size: 65
1348598 ACACTAATTA
* * *
1348608 CATTTGATGTTTCAAACA-AGCCAGGAGTGCATCGATGCATGG-TCTACCCATCAGTACACAAAA
1 CATTCGATGTTACAAA-ATAGCCAAGAGTGCATCGATGCATGGCT-TACCCATCAGTACACAAAA
1348671 TG
64 TG
** *** *
1348673 CATTCGATGTTACAAAATATTCAAGAGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAATG
1 CATTCGATGTTACAAAATAGCCAAGAGTGCATCGATGCATGGCTTACCCATCAGTACACAAAATG
1348738 CATTCGA
1 CATTCGA
1348745 AATGGGTGTG
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
64 1 0.02
65 59 0.97
66 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (65 bp):
CATTCGATGTTACAAAATAGCCAAGAGTGCATCGATGCATGGCTTACCCATCAGTACACAAAATG
Found at i:1349547 original size:31 final size:31
Alignment explanation
Indices: 1349505--1349578 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
1349495 TAGTTACGTC
* *
1349505 AGGGACCATATTGCAAACGGACTAAATGTTG
1 AGGGACTATATTGCAAACGAACTAAATGTTG
*
1349536 AGGGACTATATTACAAACGAACTAAATGTTG
1 AGGGACTATATTGCAAACGAACTAAATGTTG
*
1349567 A-GGATTATATTG
1 AGGGACTATATTG
1349579 TAAGTTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 9 0.24
31 29 0.76
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (31 bp):
AGGGACTATATTGCAAACGAACTAAATGTTG
Found at i:1351383 original size:30 final size:31
Alignment explanation
Indices: 1351349--1351414 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
1351339 TAAAACTTAT
*
1351349 AATATAATCCC-CAATATTTAGTTCGTTTGC
1 AATATAATCCCTCAACATTTAGTTCGTTTGC
* *
1351379 AATATAGTCCCTCAACATTTAGTTCGTTTGT
1 AATATAATCCCTCAACATTTAGTTCGTTTGC
1351410 AATAT
1 AATAT
1351415 GATCTCTGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 10 0.31
31 22 0.69
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (31 bp):
AATATAATCCCTCAACATTTAGTTCGTTTGC
Found at i:1354667 original size:21 final size:21
Alignment explanation
Indices: 1354641--1354684 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1354631 GGAAGCCATT
1354641 GATGAAAGATTGAAACTTTGG
1 GATGAAAGATTGAAACTTTGG
*
1354662 GATGAAAGATTGGAACTTTGG
1 GATGAAAGATTGAAACTTTGG
1354683 GA
1 GA
1354685 AGATGAGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.32, T:0.27
Consensus pattern (21 bp):
GATGAAAGATTGAAACTTTGG
Found at i:1355200 original size:11 final size:12
Alignment explanation
Indices: 1355184--1355212 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1355174 GACACTTTAA
1355184 TATTAT-GATTT
1 TATTATGGATTT
1355195 TATTATGGATTT
1 TATTATGGATTT
1355207 TATTAT
1 TATTAT
1355213 TCTAGAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (12 bp):
TATTATGGATTT
Found at i:1355279 original size:75 final size:75
Alignment explanation
Indices: 1355156--1355329 Score: 201
Period size: 75 Copynumber: 2.3 Consensus size: 75
1355146 CTTGAAAAAT
* * * * * *
1355156 GTTTGAGTCTT-AAGATTTGACACTTTAATATTATGATTTTATTATGGATTTTATTATTCTAGAG
1 GTTTGAGTCTTGAA-ATTTGACATTTTAATATTATGATTTTATTATGGATTTTACTACTATAAAC
1355220 TTAATATTATG
65 TTAATATTATG
* *
1355231 GTTTGAATCTTGAAATTTGACATTTTAATATTGTTG-TTTGT-TTATGGATTTTACTACTATAAA
1 GTTTGAGTCTTGAAATTTGACATTTTAATATT-ATGATTT-TATTATGGATTTTACTACTATAAA
* *
1355294 CTTAATATTGTT
64 CTTAATATTATG
*
1355306 GTTTGAGTCTTGATATTTGACATT
1 GTTTGAGTCTTGAAATTTGACATT
1355330 ATTTATGATT
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
75 79 0.94
76 5 0.06
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (75 bp):
GTTTGAGTCTTGAAATTTGACATTTTAATATTATGATTTTATTATGGATTTTACTACTATAAACT
TAATATTATG
Found at i:1356636 original size:27 final size:28
Alignment explanation
Indices: 1356584--1356638 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
1356574 AGAAACTAGT
* * *
1356584 GTAAACACTAATAATCTTTGTTAACAAC
1 GTAAACAATAATAATCTATGTAAACAAC
1356612 GTAAACAATAAT-ATCTATGTAAACAAC
1 GTAAACAATAATAATCTATGTAAACAAC
1356639 ATAATTGATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.29
Consensus pattern (28 bp):
GTAAACAATAATAATCTATGTAAACAAC
Found at i:1356978 original size:38 final size:38
Alignment explanation
Indices: 1356936--1357051 Score: 133
Period size: 38 Copynumber: 3.1 Consensus size: 38
1356926 TCGTGCATGT
* *
1356936 AGTTACGGCAAGATAATGGCTCACCTTTTGCTTCTTTG
1 AGTTACGACAAGGTAATGGCTCACCTTTTGCTTCTTTG
** *
1356974 AGTTACGACAAGGTAATGATTCACCTTTTTCTTCTTTG
1 AGTTACGACAAGGTAATGGCTCACCTTTTGCTTCTTTG
* * * * * *
1357012 AGTCACGAAAAGGTAACGGCTCATCTTTTGATTATTTG
1 AGTTACGACAAGGTAATGGCTCACCTTTTGCTTCTTTG
1357050 AG
1 AG
1357052 AGGTAAATGT
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 64 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (38 bp):
AGTTACGACAAGGTAATGGCTCACCTTTTGCTTCTTTG
Found at i:1358185 original size:51 final size:50
Alignment explanation
Indices: 1358101--1358196 Score: 120
Period size: 51 Copynumber: 1.9 Consensus size: 50
1358091 AGTCATTTAA
* * *
1358101 TATAGATATATAAATTATTCTATAGATAATTCTAGACATGATACTAAATAT
1 TATAAATATATAAATTATTCTATAGACAATTCTAGAAAT-ATACTAAATAT
* * * *
1358152 TATAAATATATAGATTATTTTATATACATTTCTAGAAATATACTA
1 TATAAATATATAAATTATTCTATAGACAATTCTAGAAATATACTA
1358197 TTTTTATATT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 6 0.16
51 32 0.84
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (50 bp):
TATAAATATATAAATTATTCTATAGACAATTCTAGAAATATACTAAATAT
Found at i:1358765 original size:30 final size:29
Alignment explanation
Indices: 1358731--1358799 Score: 68
Period size: 30 Copynumber: 2.3 Consensus size: 29
1358721 ACTTTAGAGA
* *
1358731 AGTGTAGAA-CTCTCTAGAATCTTGTGGAAG
1 AGTGTAGAATC-CTCTAGAATATTCTGG-AG
* *
1358761 AGTGTGGAATCCTCTGGAATATTCTGGAG
1 AGTGTAGAATCCTCTAGAATATTCTGGAG
1358790 ATGTGTAGAA
1 A-GTGTAGAA
1358800 GCTTGTGGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
29 3 0.09
30 28 0.88
31 1 0.03
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.30
Consensus pattern (29 bp):
AGTGTAGAATCCTCTAGAATATTCTGGAG
Found at i:1358824 original size:50 final size:50
Alignment explanation
Indices: 1358745--1358868 Score: 194
Period size: 50 Copynumber: 2.5 Consensus size: 50
1358735 TAGAACTCTC
*
1358745 TAGAATCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTG
1 TAGAACCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTG
* *
1358795 TAGAAGCTTGTGGAAGAGTGTGGACTCCTCTGGAATATTCTGGAGATGTG
1 TAGAACCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTG
* * *
1358845 TGGAACCTTATGGAAGAGTATGGA
1 TAGAACCTTGTGGAAGAGTGTGGA
1358869 TGAATATGGA
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 68 1.00
ACGTcount: A:0.27, C:0.10, G:0.33, T:0.30
Consensus pattern (50 bp):
TAGAACCTTGTGGAAGAGTGTGGAATCCTCTGGAATATTCTGGAGATGTG
Found at i:1358879 original size:50 final size:50
Alignment explanation
Indices: 1358775--1358879 Score: 131
Period size: 50 Copynumber: 2.1 Consensus size: 50
1358765 TGGAATCCTC
* * * ** *
1358775 TGGAATATTCTGGAGATGTGTAGAAGCTTGTGGAAGAGTGTGGACTCCTC
1 TGGAATATTCTGGAGATGTGTAGAACCTTATGGAAGAGTATGGACTAATA
*
1358825 TGGAATATTCTGGAGATGTGTGGAACCTTATGGAAGAGTATGGA-TGAATA
1 TGGAATATTCTGGAGATGTGTAGAACCTTATGGAAGAGTATGGACT-AATA
1358875 TGGAA
1 TGGAA
1358880 GGGAGTGGAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
49 1 0.02
50 46 0.98
ACGTcount: A:0.29, C:0.09, G:0.33, T:0.30
Consensus pattern (50 bp):
TGGAATATTCTGGAGATGTGTAGAACCTTATGGAAGAGTATGGACTAATA
Found at i:1360784 original size:148 final size:150
Alignment explanation
Indices: 1360592--1360892 Score: 570
Period size: 148 Copynumber: 2.0 Consensus size: 150
1360582 AAGGAAGGGT
1360592 CATTGTTCGTGATGCAAGCTAAGCTCTGCAAATGAGAGGTAAACATCACCACTGAAGATGTGGAG
1 CATTGTTCGTGATGCAAGCTAAGCTCTGCAAATGAGAGGTAAACATCACCACTGAAGATGTGGAG
1360657 ATATGACATAAACGACTTGGGCACATCAGTGAGAAGGGTCTTCACATGCTCGCTCGGAAACAAC-
66 ATATGACATAAACGACTTGGGCACATCAGTGAGAAGGGTCTTCACATGCTCGCTCGGAAACAACT
1360721 CCTACCT-GTGAAAGGTAAA
131 CCTACCTAGTGAAAGGTAAA
1360740 CATTGTTCGTGATGCAAGCTAAGCTCTGCAAATGAGAGGTAAACATCACCACTGAAGATGTGGAG
1 CATTGTTCGTGATGCAAGCTAAGCTCTGCAAATGAGAGGTAAACATCACCACTGAAGATGTGGAG
1360805 ATATGACATAAACGACTTGGGCACATCAGTGAGAAGGGTCTTCACATGCTCGCTCGGAAACAACT
66 ATATGACATAAACGACTTGGGCACATCAGTGAGAAGGGTCTTCACATGCTCGCTCGGAAACAACT
1360870 CCTACCTGACGTGAAAGGTAAA
131 CCTACCT-A-GTGAAAGGTAAA
1360892 C
1 C
1360893 CACTTGATCT
Statistics
Matches: 149, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
148 129 0.87
149 7 0.05
152 13 0.09
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (150 bp):
CATTGTTCGTGATGCAAGCTAAGCTCTGCAAATGAGAGGTAAACATCACCACTGAAGATGTGGAG
ATATGACATAAACGACTTGGGCACATCAGTGAGAAGGGTCTTCACATGCTCGCTCGGAAACAACT
CCTACCTAGTGAAAGGTAAA
Found at i:1362475 original size:50 final size:50
Alignment explanation
Indices: 1362388--1362486 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
1362378 TACAACTCTC
** * **
1362388 TAGAAGCTTGTGGAAGAGTGTGGAATCCTTTGGAATATTCTAGAGATGTG
1 TAGAAGCTTGAAGAAGAGTGTGGAATCCTCTAAAATATTCTAGAGATGTG
* *
1362438 TAGAAGCTTGAAGAAGAGTGTGGATTCCTCTAAAATATTCTGGAGATGT
1 TAGAAGCTTGAAGAAGAGTGTGGAATCCTCTAAAATATTCTAGAGATGT
1362487 ATGGAACCTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.30, C:0.09, G:0.29, T:0.31
Consensus pattern (50 bp):
TAGAAGCTTGAAGAAGAGTGTGGAATCCTCTAAAATATTCTAGAGATGTG
Found at i:1362504 original size:50 final size:51
Alignment explanation
Indices: 1362388--1362506 Score: 127
Period size: 50 Copynumber: 2.4 Consensus size: 51
1362378 TACAACTCTC
* * ** *
1362388 TAGAAGCTTG-TGGAAGAGTGTGGAATCCTTTGGAATATTCTAGAGATGTG
1 TAGAACCTTGATGGAAGAGTGTGGAATCCTCTAAAATATTCTAGAGATGTA
* * * *
1362438 TAGAAGCTTGA-AGAAGAGTGTGGATTCCTCTAAAATATTCTGGAGATGTA
1 TAGAACCTTGATGGAAGAGTGTGGAATCCTCTAAAATATTCTAGAGATGTA
*
1362488 TGGAACCTT-ATGGAAGAGT
1 TAGAACCTTGATGGAAGAGT
1362507 ACAGAAGAAT
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
49 1 0.02
50 56 0.98
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.30
Consensus pattern (51 bp):
TAGAACCTTGATGGAAGAGTGTGGAATCCTCTAAAATATTCTAGAGATGTA
Found at i:1362554 original size:17 final size:18
Alignment explanation
Indices: 1362535--1362570 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1362525 GAGTAGAAGA
*
1362535 GTGTAGAGCTTTCTAGAG
1 GTGTAGAGCATTCTAGAG
1362553 TGTGTAGAGCATTCTAGA
1 -GTGTAGAGCATTCTAGA
1362571 TAATTAATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.25, C:0.11, G:0.31, T:0.33
Consensus pattern (18 bp):
GTGTAGAGCATTCTAGAG
Found at i:1370325 original size:83 final size:83
Alignment explanation
Indices: 1370225--1370409 Score: 334
Period size: 83 Copynumber: 2.2 Consensus size: 83
1370215 AGGTCTTATG
* *
1370225 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACGGATGACCCCAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCAAAGGATTTAAGCATC
1370290 ATGCTCGAAAGACTTACT
66 ATGCTCGAAAGACTTACT
* *
1370308 GATGGCCCGAATGACTTATCATCTTGGTCTAAAGGCTTACAGATGACCCAAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCAAAGGATTTAAGCATC
1370373 ATGCTCGAAAGACTTACT
66 ATGCTCGAAAGACTTACT
1370391 GATGGCCCGAAGGACTTAT
1 GATGGCCCGAAGGACTTAT
1370410 AAATTGTGAA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 97 1.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (83 bp):
GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCAAAGGATTTAAGCATC
ATGCTCGAAAGACTTACT
Found at i:1370347 original size:41 final size:41
Alignment explanation
Indices: 1370225--1370409 Score: 190
Period size: 42 Copynumber: 4.5 Consensus size: 41
1370215 AGGTCTTATG
* * * *
1370225 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACG
1 GATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTTACT
* * * *
1370266 GATGACCCCAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGACTTACT
* * * * * *
1370308 GATGGCCCGAATGACTTATCATCTTGGTCTAAAGGCTTACA
1 GATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTTACT
* * * *
1370349 GATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-ATCATCATGCTCGAAAGACTTACT
1370391 GATGGCCCGAAGGACTTAT
1 GATGGCCCGAAGGACTTAT
1370410 AAATTGTGAA
Statistics
Matches: 110, Mismatches: 32, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
41 46 0.42
42 64 0.58
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTATCATCATGCTCGAAAGACTTACT
Found at i:1370577 original size:296 final size:297
Alignment explanation
Indices: 1370042--1370622 Score: 923
Period size: 296 Copynumber: 2.0 Consensus size: 297
1370032 CTCTTCTGTG
* * * * *
1370042 AAGGCTTAAAAATTACCCGAAGAATTTAATCATCACGCTCGGAAGACTTACAAATGACCTAAAGG
1 AAGGCTTAAAAATGACCCAAAGAATTTAAGCATCACGCTCGAAAGACTTACAAATGACCCAAAGG
* *
1370107 ATTTATAAATTGTGAAATTTTGAAACTCGCATTCTTCGTTTTCAAAAATTTCATCATCTTAAAAC
66 ACTTATAAATTGTGAAATTTTGAAACTCACATTCTTCGTTTTCAAAAATTTCATCATCTTAAAAC
* * *
1370172 ATCATTTTCTTATTTTCAGATTCAATGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAG
131 ATCATTTTCTCATTTTCAAATTCAATGAAAACATCCTACCCGAAGGTCTTACGGATGGCCCGAAG
*
1370237 GACTTATCATCTTGCTCTAAAGGCTTACGGATGACCCCAAGGATTTAAGCATCATGCTCGAAAGA
196 GACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCCAAGGATTTAAGCATCATGCTCGAAAGA
*
1370302 CTTACTGATGGCCCGAATGACTTATCATCTTGGTCTA
261 CTTACTGATGGCCCGAAAGACTTATCATCTTGGTCTA
* * * * ** * *
1370339 AAGGCTTACAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGG
1 AAGGCTTAAAAATGACCCAAAGAATTTAAGCATCACGCTCGAAAGACTTACAAATGACCCAAAGG
* *
1370404 ACTTATAAATTGTGAAATTTTGAAACTCACGTTCTTCGTTTTCAAAAATTTCATCTTCTTAAAAC
66 ACTTATAAATTGTGAAATTTTGAAACTCACATTCTTCGTTTTCAAAAATTTCATCATCTTAAAAC
*
1370469 ATCATTTT-TCATTTTCAAATTCATTTG-AAACATCCTACCCGAAGGTCTTACGGATGGCCCGAA
131 ATCATTTTCTCATTTTCAAATTCA-ATGAAAACATCCTACCCGAAGGTCTTACGGATGGCCCGAA
*
1370532 GGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAG
195 GGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCCAAGGATTTAAGCATCATGCTCGAAAG
1370597 ACTTACTGATGGCCCGAAAGACTTAT
260 ACTTACTGATGGCCCGAAAGACTTAT
1370623 AAATTGTGAA
Statistics
Matches: 259, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
296 136 0.53
297 123 0.47
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (297 bp):
AAGGCTTAAAAATGACCCAAAGAATTTAAGCATCACGCTCGAAAGACTTACAAATGACCCAAAGG
ACTTATAAATTGTGAAATTTTGAAACTCACATTCTTCGTTTTCAAAAATTTCATCATCTTAAAAC
ATCATTTTCTCATTTTCAAATTCAATGAAAACATCCTACCCGAAGGTCTTACGGATGGCCCGAAG
GACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCCAAGGATTTAAGCATCATGCTCGAAAGA
CTTACTGATGGCCCGAAAGACTTATCATCTTGGTCTA
Found at i:1370602 original size:42 final size:41
Alignment explanation
Indices: 1370515--1370621 Score: 124
Period size: 42 Copynumber: 2.6 Consensus size: 41
1370505 ACCCGAAGGT
* * * * *
1370515 CTTACGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGG
1 CTTACAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
* *
1370556 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTACAGATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGA
* *
1370598 CTTACTGATGGCCCGAAAGACTTA
1 CTTACAGATGGCCCGAAGGACTTA
1370622 TAAATTGTGA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 21 0.39
42 33 0.61
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (41 bp):
CTTACAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
Found at i:1370679 original size:213 final size:214
Alignment explanation
Indices: 1370302--1370739 Score: 743
Period size: 213 Copynumber: 2.1 Consensus size: 214
1370292 GCTCGAAAGA
* * *
1370302 CTTACTGATGGCCCGAATGACTTATCATCTTGGTCTAAAGGCTTACAGATGACCCAAAGGATTTA
1 CTTACGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCAAAGGATTTA
*
1370367 AGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTGTGAAATTTTGAAACTC
66 AGCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTATAAATTGTGAAATTTTGAAACTC
* * * *
1370432 ACGTTCTTCGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTTTCATTTTCAAATTCATTTG-
131 ACATTCTTCGTTTTCAAAAATTTCATCATCTTAAAACATCATTTTTCATTTCCAAATTCATGTGA
1370496 AAACATCCTACCCGAAGGT
196 AAACATCCTACCCGAAGGT
*
1370515 CTTACGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCGAAGGATTTA
1 CTTACGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCAAAGGATTTA
*
1370580 AGCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTATAAATTGTGAAATTTTGAAACTT
66 AGCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTATAAATTGTGAAATTTTGAAACTC
*
1370645 GCATTCTTCGTTTTCAAAAATTTCATCATCTTAAAACATCATTTTTCATTTCCAAATTCATGTGA
131 ACATTCTTCGTTTTCAAAAATTTCATCATCTTAAAACATCATTTTTCATTTCCAAATTCATGTGA
*
1370710 AAACATCCTACCTGAAGGT
196 AAACATCCTACCCGAAGGT
* *
1370729 TTTATGGATGG
1 CTTACGGATGG
1370740 ATTTGCTTCA
Statistics
Matches: 210, Mismatches: 14, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
213 183 0.87
214 27 0.13
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (214 bp):
CTTACGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACAGATGACCCAAAGGATTTA
AGCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTATAAATTGTGAAATTTTGAAACTC
ACATTCTTCGTTTTCAAAAATTTCATCATCTTAAAACATCATTTTTCATTTCCAAATTCATGTGA
AAACATCCTACCCGAAGGT
Found at i:1370827 original size:37 final size:35
Alignment explanation
Indices: 1370739--1371610 Score: 511
Period size: 34 Copynumber: 23.9 Consensus size: 35
1370729 TTTATGGATG
1370739 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
1 GATTTGCTTCACTACTC-TCGGTGAAGGCTTAAGAT
* * *
1370775 G--GTGCTTCACTATTCTCAAGTGAAGGCTTAAGAT
1 GATTTGCTTCACTACTCTC-GGTGAAGGCTTAAGAT
*
1370809 AGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATT
1 -GATTTGCTTCACTACTCTC-GGTGAAGGCTTAAGA-T
* ** * *
1370847 GCCCTGGGGACTT-AATCATCATGCTC-G-GAAGGCTTATTGAT
1 G--AT-TTG-CTTCACT-A-C-T-CTCGGTGAAGGCTTA-AGAT
* * *
1370888 GGATTTGCTTCACTACTCCTTGGTGAAAGCTTAAAATT
1 -GATTTGCTTCACTACT-CTCGGTGAAGGCTTAAGA-T
* *
1370926 GATTTGCTTCACTACTCTTTGGCGAAGGCTTAAGATT
1 GATTTGCTTCACTACTC-TCGGTGAAGGCTTAAGA-T
* *
1370963 GATTTGCTTCACTATTCTCAGGTGAAGGCTTTAAGACG
1 GATTTGCTTCACTACTCTC-GGTGAAGGC-TTAAGA-T
1371001 GA-TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATT
1 GATTTGCTTCACTACTC-TCGGTGAAGGCTTAAGA-T
* *
1371037 GATTTGCTTCACTATTCTCAGGTGAAGGCTTAACATT
1 GATTTGCTTCACTACTCTC-GGTGAAGGCTTAAGA-T
* ** * *
1371074 GCCCTGAGGACTT-AATCATCATGCTC-G-GAAGGCTTACTGAT
1 G--AT-TTG-CTTCACT-A-C-T-CTCGGTGAAGGCTTA-AGAT
1371115 GGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
1 -GATTTGCTTCACTACTC-TCGGTGAAGGCTTAAGAT
*
1371152 AGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATT
1 -GATTTGCTTCACTACTCTC-GGTGAAGGCTTAAGA-T
* ** * **
1371190 GCCCTGGGGACTT-AATCATCATGCTC-G-GAAGGCTTGTTGAT
1 G--AT-TTG-CTTCACT-A-C-T-CTCGGTGAAGGCTT-AAGAT
1371231 AGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
1 -GATTTGCTTCACTACTC-TCGGTGAAGGCTTAAGAT
* ** *
1371268 G--GTGCTTCACTACTCCTTTGTGAAGGATTAAGAT
1 GATTTGCTTCACTACT-CTCGGTGAAGGCTTAAGAT
* **
1371302 G--GTGCTTCACTACTCTTATGTGAAGGCTTAAGAT
1 GATTTGCTTCACTACTC-TCGGTGAAGGCTTAAGAT
* *
1371336 GGTTTGCTTCACTACTCCTTGGTGAAGGCTTAAGAT
1 GATTTGCTTCACTACT-CTCGGTGAAGGCTTAAGAT
** *
1371372 G--GGGCTTCACTACTCCTCTGTGAAGGCTTAAGAT
1 GATTTGCTTCACTACT-CTCGGTGAAGGCTTAAGAT
* **
1371406 G--GTGCTTCACTACTCTTCTATGAAGGCTTAAGAT
1 GATTTGCTTCACTACTC-TCGGTGAAGGCTTAAGAT
1371440 GA-TTGCTTCACT-CTTCTTCGGTGAAGGCTTAAGAT
1 GATTTGCTTCACTAC-TC-TCGGTGAAGGCTTAAGAT
*
1371475 GA-TTGCTTCACTACTCTTCGGTAAAGGCTTAAGAT
1 GATTTGCTTCACTACTC-TCGGTGAAGGCTTAAGAT
* *
1371510 G--GTGCTTCACTACTCCTCTGTGAAGGCTTAAGAT
1 GATTTGCTTCACTACT-CTCGGTGAAGGCTTAAGAT
* * *
1371544 G--GTGCTTCACTACTCTTCTGCGAAGGCTTAAGAT
1 GATTTGCTTCACTACTC-TCGGTGAAGGCTTAAGAT
* * *
1371578 GGTTTGCTTCACTCCTCTTTGGTGAAGGCTTAA
1 GATTTGCTTCACTACTC-TCGGTGAAGGCTTAA
1371611 CATTGACTTA
Statistics
Matches: 680, Mismatches: 88, Indels: 136
0.75 0.10 0.15
Matches are distributed among these distances:
33 5 0.01
34 206 0.30
35 66 0.10
36 80 0.12
37 185 0.27
38 50 0.07
39 12 0.02
40 12 0.02
41 41 0.06
42 11 0.02
43 3 0.00
44 9 0.01
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (35 bp):
GATTTGCTTCACTACTCTCGGTGAAGGCTTAAGAT
Found at i:1370987 original size:74 final size:73
Alignment explanation
Indices: 1370739--1371616 Score: 316
Period size: 70 Copynumber: 12.0 Consensus size: 73
1370729 TTTATGGATG
* * * * * *
1370739 GATTTGCTTCACTACTCTTC-GGTGAAGGCTTAAGA-TG-GTGCTTCACTATTC-TCAAGTGAAG
1 GATTTGCTTCACTATTC-TCAGGTGAAGGCTTAAAATTGATTGCTTCACTACTCTTC-GGCGAAG
*
1370800 GCTTAAGATA
64 GCTTAAGATT
* ** *** * * *
1370810 GATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTGCCCTG-GGGACTTAATCATCATGCTCG
1 GATTTGCTTCACTATTCTCAGGTGAAGGCTTAAAATTG-ATTGCTTCAC-TACTCTTC--G-GC-
* *
1370874 GAAGGCTTATTGATG
60 GAAGGCTTA-AGATT
* * * *
1370889 GATTTGCTTCACTACTC-CTTGGTGAAAGCTTAAAATTGATTTGCTTCACTACTCTTTGGCGAAG
1 GATTTGCTTCACTATTCTC-AGGTGAAGGCTTAAAATTGA-TTGCTTCACTACTCTTCGGCGAAG
1370953 GCTTAAGATT
64 GCTTAAGATT
* ** *
1370963 GATTTGCTTCACTATTCTCAGGTGAAGGCTTTAAGACGGATTGCTTCACTACTCTTCGGTGAAGG
1 GATTTGCTTCACTATTCTCAGGTGAAGGC-TTAAAATTGATTGCTTCACTACTCTTCGGCGAAGG
1371028 CTTAAGATT
65 CTTAAGATT
* ** *** * * *
1371037 GATTTGCTTCACTATTCTCAGGTGAAGGCTTAACATTGCCCTG-AGGACTTAATCATCATGCTCG
1 GATTTGCTTCACTATTCTCAGGTGAAGGCTTAAAATTG-ATTGCTTCAC-TACTCTTC--G-GC-
* *
1371101 GAAGGCTTACTGATG
60 GAAGGCTTA-AGATT
* * * * *
1371116 GATTTGCTTCACTACTCTTC-GGTGAAGGCTTAAGATAGATTTGCTTCACTATTC-TCAGGTGAA
1 GATTTGCTTCACTATTC-TCAGGTGAAGGCTTAAAATTGA-TTGCTTCACTACTCTTC-GGCGAA
1371179 GGCTTAAGATT
63 GGCTTAAGATT
*** *** * * *** *
1371190 GCCCTG-GGGACTTAATCATCATGCTCGGAAGGCTTGTTGATAGATTTGCTTCACTACTCTTCGG
1 GATTTGCTTCAC-TATTC-TCA-GGT--GAAGGCTT-AAAATTGA-TTGCTTCACTACTCTTCGG
*
1371254 TGAAGGCTTAAGA-T
59 CGAAGGCTTAAGATT
* * ** * * * ** *
1371268 G--GTGCTTCACTACTC-CTTTGTGAAGGATTAAGA-TG-GTGCTTCACTACTCTTATGTGAAGG
1 GATTTGCTTCACTATTCTC-AGGTGAAGGCTTAAAATTGATTGCTTCACTACTCTTCGGCGAAGG
1371328 CTTAAGA-T
65 CTTAAGATT
* * * * ** * * *
1371336 GGTTTGCTTCACTACTC-CTTGGTGAAGGCTTAAGA-TG-GGGCTTCACTACTCCTCTGTGAAGG
1 GATTTGCTTCACTATTCTC-AGGTGAAGGCTTAAAATTGATTGCTTCACTACTCTTCGGCGAAGG
1371398 CTTAAGA-T
65 CTTAAGATT
* * * *
1371406 G--GTGCTTCACTACTCTTCTA--TGAAGGCTTAAGA-TGATTGCTTCACT-CTTCTTCGGTGAA
1 GATTTGCTTCACTATTC-TC-AGGTGAAGGCTTAAAATTGATTGCTTCACTAC-TCTTCGGCGAA
1371465 GGCTTAAGA-T
63 GGCTTAAGATT
* * * * * * *
1371475 GA-TTGCTTCACTACTCTTC-GGTAAAGGCTTAAGA-TG-GTGCTTCACTACTCCTCTGTGAAGG
1 GATTTGCTTCACTATTC-TCAGGTGAAGGCTTAAAATTGATTGCTTCACTACTCTTCGGCGAAGG
1371536 CTTAAGA-T
65 CTTAAGATT
* * * * * * * * * *
1371544 G--GTGCTTCACTACTCTTC-TGCGAAGGCTTAAGATGGTTTGCTTCACTCCTCTTTGGTGAAGG
1 GATTTGCTTCACTATTC-TCAGGTGAAGGCTTAAAATTGATTGCTTCACTACTCTTCGGCGAAGG
*
1371606 CTTAACATT
65 CTTAAGATT
1371615 GA
1 GA
1371617 CTTACCCCAA
Statistics
Matches: 641, Mismatches: 118, Indels: 95
0.75 0.14 0.11
Matches are distributed among these distances:
68 88 0.14
69 58 0.09
70 124 0.19
71 35 0.05
72 9 0.01
73 12 0.02
74 116 0.18
75 28 0.04
76 10 0.02
77 4 0.01
78 31 0.05
79 118 0.18
80 8 0.01
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (73 bp):
GATTTGCTTCACTATTCTCAGGTGAAGGCTTAAAATTGATTGCTTCACTACTCTTCGGCGAAGGC
TTAAGATT
Found at i:1371131 original size:227 final size:224
Alignment explanation
Indices: 1370739--1371190 Score: 694
Period size: 227 Copynumber: 2.0 Consensus size: 224
1370729 TTTATGGATG
* *
1370739 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGTGCTTCACTATTCTCAAGTGAAGGCTT
1 GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGACGGTGCTTCACTACTCTCAAGTGAAGGCTT
* *
1370804 AAGATAGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTGCCCTGGGGACTTAATCATCAT
66 AAGATAGATTTGCTTCACTATTCTCAGGTGAAGGCTTAACATTGCCCTGAGGACTTAATCATCAT
* *
1370869 GCTCGGAAGGCTTATTGATGGATTTGCTTCACTACTCCTT-GGTGAAAGCTTAAAATTGATTTGC
131 GCTCGGAAGGCTTACTGATGGATTTGCTTCACTACT-CTTCGGTGAAAGCTTAAAATAGATTTGC
**
1370933 TTCACTACTCTTTGGCGAAGGCTTAAGATT
195 TTCACTACTCTCAGGCGAAGGCTTAAGATT
* *
1370963 GATTTGCTTCACTATTC-TCAGGTGAAGGCTTTAAGACGGATTGCTTCACTACTCTTC-GGTGAA
1 GATTTGCTTCACTACTCTTC-GGTGAAGGC-TTAAGACGG--TGCTTCACTACTC-TCAAGTGAA
*
1371026 GGCTTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAACATTGCCCTGAGGACTTAATC
61 GGCTTAAGATAGATTTGCTTCACTATTCTCAGGTGAAGGCTTAACATTGCCCTGAGGACTTAATC
* *
1371091 ATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGAT
126 ATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAAGCTTAAAATAGAT
* *
1371156 TTGCTTCACTATTCTCAGGTGAAGGCTTAAGATT
191 TTGCTTCACTACTCTCAGGCGAAGGCTTAAGATT
1371190 G
1 G
1371191 CCCTGGGGAC
Statistics
Matches: 207, Mismatches: 15, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
223 2 0.01
224 25 0.12
225 8 0.04
226 3 0.01
227 167 0.81
228 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (224 bp):
GATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGACGGTGCTTCACTACTCTCAAGTGAAGGCTT
AAGATAGATTTGCTTCACTATTCTCAGGTGAAGGCTTAACATTGCCCTGAGGACTTAATCATCAT
GCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAAGCTTAAAATAGATTTGCT
TCACTACTCTCAGGCGAAGGCTTAAGATT
Found at i:1371145 original size:116 final size:116
Alignment explanation
Indices: 1370777--1371267 Score: 658
Period size: 116 Copynumber: 4.3 Consensus size: 116
1370767 CTTAAGATGG
* *
1370777 TGCTTCACTATTC-TCAAGTGAAGGCTTAAGATAGATTTGCTTCACTATTCTCAGGTGAAGGCTT
1 TGCTTCACTACTCTTC-GGTGAAGGCTTAAGATAGATTTGCTTCACTATTCTCAGGTGAAGGCTT
1370841 AAGATTGCCCTGGGGACTTAATCATCATGCTCGGAAGGCTTATTGATGGATT
65 AAGATTGCCCTGGGGACTTAATCATCATGCTCGGAAGGCTTATTGATGGATT
* * * * ** *
1370893 TGCTTCACTACTCCTT-GGTGAAAGCTTAAAATTGATTTGCTTCACTACTCTTTGGCGAAGGCTT
1 TGCTTCACTACT-CTTCGGTGAAGGCTTAAGATAGATTTGCTTCACTATTCTCAGGTGAAGGCTT
*** *** * * * *
1370957 AAGATTGATTTGCTTCAC-TATTC-TCA-GGT--GAAGGCTT-TAAGACGGA-T
65 AAGATTGCCCTG-GGGACTTAATCATCATGCTCGGAAGGCTTAT-TGATGGATT
*
1371004 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTA
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGATTTGCTTCACTATTCTCAGGTGAAGGCTTA
* * *
1371069 ACATTGCCCTGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATT
66 AGATTGCCCTGGGGACTTAATCATCATGCTCGGAAGGCTTATTGATGGATT
1371120 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGATTTGCTTCACTATTCTCAGGTGAAGGCTTA
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGATTTGCTTCACTATTCTCAGGTGAAGGCTTA
* *
1371185 AGATTGCCCTGGGGACTTAATCATCATGCTCGGAAGGCTTGTTGATAGATT
66 AGATTGCCCTGGGGACTTAATCATCATGCTCGGAAGGCTTATTGATGGATT
1371236 TGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
1 TGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
1371268 GGTGCTTCAC
Statistics
Matches: 320, Mismatches: 43, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
110 5 0.02
111 68 0.21
112 16 0.05
113 2 0.01
114 2 0.01
115 16 0.05
116 207 0.65
117 3 0.01
118 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (116 bp):
TGCTTCACTACTCTTCGGTGAAGGCTTAAGATAGATTTGCTTCACTATTCTCAGGTGAAGGCTTA
AGATTGCCCTGGGGACTTAATCATCATGCTCGGAAGGCTTATTGATGGATT
Found at i:1371414 original size:104 final size:104
Alignment explanation
Indices: 1370743--1371610 Score: 551
Period size: 116 Copynumber: 8.0 Consensus size: 104
1370733 TGGATGGATT
* * *
1370743 TGCTTCACTACTCTTCGGTGAAGGCTTAAGATGG--TGCTTCACTATTC-TCAAGTGAAGGCTTA
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGTTTGCTTCACTACTCTTC-GGTGAAGGCTTA
* * * *
1370805 AGATAGATTTGCTTCACTA-TTCTCAGGTGAAGGCTTAAGATTG
65 AGAT-G--GTGCTTCACTACTCCTC-TGTGAAGGCTTAAGATGG
** ** * * *
1370848 CCCTGGGGACTTAATCATCATGCTCGGAAGGCTTATTGATGGATTTGCTTCACTACTCCTT-GGT
1 TGCT--TCAC-TACTCTTC-TG-T--GAAGGCTTA-AGATGG-TTTGCTTCACTACT-CTTCGGT
* * * * * *
1370912 GAAAGCTTAAAATTGATTTGCTTCACTACT-CTTTGGCGAAGGCTTAAGATTGATT
56 GAAGGCTTAAGA-TG--GTGCTTCACTACTCCTCT-GTGAAGGCTTAAGA-TG--G
* * * *
1370967 TGCTTCACTATTC-TCAGGTGAAGGCTTTAAGACGGATTGCTTCACTACTCTTCGGTGAAGGCTT
1 TGCTTCACTACTCTTC-TGTGAAGGC-TTAAGATGGTTTGCTTCACTACTCTTCGGTGAAGGCTT
* * * * *
1371031 AAGATTGATTTGCTTCACTA-TTCTCAGGTGAAGGCTTAACATTG
64 AAGA-TG--GTGCTTCACTACTCCTC-TGTGAAGGCTTAAGATGG
** ** * * *
1371075 CCCTGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTG
1 TGCT--TCAC-TACTCTTC-TG-T--GAAGGCTTA-AGATGG-TTTGCTTCACTACTCTTCGGTG
* * * *
1371140 AAGGCTTAAGATAGATTTGCTTCACTA-TTCTCAGGTGAAGGCTTAAGATTG
57 AAGGCTTAAGAT-G--GTGCTTCACTACTCCTC-TGTGAAGGCTTAAGATGG
** ** * * ** *
1371191 CCCTGGGGACTTAATCATCATGCTCGGAAGGCTTGTTGATAGATTTGCTTCACTACTCTTCGGTG
1 TGCT--TCAC-TACTCTTC-TG-T--GAAGGCTT-AAGAT-GGTTTGCTTCACTACTCTTCGGTG
* *
1371256 AAGGCTTAAGATGGTGCTTCACTACTCCTTTGTGAAGGATTAAGATGG
57 AAGGCTTAAGATGGTGCTTCACTACTCCTCTGTGAAGGCTTAAGATGG
*
1371304 TGCTTCACTACTCTTATGTGAAGGCTTAAGATGGTTTGCTTCACTACTCCTT-GGTGAAGGCTTA
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGTTTGCTTCACTACT-CTTCGGTGAAGGCTTA
*
1371368 AGATGGGGCTTCACTACTCCTCTGTGAAGGCTTAAGATGG
65 AGATGGTGCTTCACTACTCCTCTGTGAAGGCTTAAGATGG
* *
1371408 TGCTTCACTACTCTTCTATGAAGGCTTAAGAT-GATTGCTTCACT-CTTCTTCGGTGAAGGCTTA
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGTTTGCTTCACTAC-TCTTCGGTGAAGGCTTA
* * * *
1371471 AGATGATTGCTTCACTACTCTTCGGTAAAGGCTTAAGATGG
65 AGATG-GTGCTTCACTACTCCTCTGTGAAGGCTTAAGATGG
* * *
1371512 TGCTTCACTACTCCTCTGTGAAGGCTTAAGATGG--TGCTTCACTACTCTTCTGCGAAGGCTTAA
1 TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGTTTGCTTCACTACTCTTCGGTGAAGGCTTAA
* *
1371575 GATGGTTTGCTTCACTCCT-CTTTGGTGAAGGCTTAA
66 GATGG--TGCTTCACTACTCCTCT-GTGAAGGCTTAA
1371611 CATTGACTTA
Statistics
Matches: 634, Mismatches: 84, Indels: 91
0.78 0.10 0.11
Matches are distributed among these distances:
102 4 0.01
103 59 0.09
104 177 0.28
105 9 0.01
106 8 0.01
107 2 0.00
108 9 0.01
109 3 0.00
110 13 0.02
111 62 0.10
112 23 0.04
113 36 0.06
114 7 0.01
115 16 0.03
116 196 0.31
117 7 0.01
118 1 0.00
119 2 0.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (104 bp):
TGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGTTTGCTTCACTACTCTTCGGTGAAGGCTTAA
GATGGTGCTTCACTACTCCTCTGTGAAGGCTTAAGATGG
Found at i:1371485 original size:138 final size:137
Alignment explanation
Indices: 1371237--1371610 Score: 547
Period size: 138 Copynumber: 2.7 Consensus size: 137
1371227 TGATAGATTT
* * *
1371237 GCTTCACTACTCTTCGGTGAAGGCTTAAGATGGTGCTTCACTACTCCTT-TGTGAAGGATTAAGA
1 GCTTCACTACTCCTCTGTGAAGGCTTAAGATGGTGCTTCACTACT-CTTCTGTGAAGGCTTAAGA
* * * *
1371301 TGGTGCTTCACTACTCTTATGTGAAGGCTTAAGATGGTTTGCTTCACTACTCCTT-GGTGAAGGC
65 TGTTGCTTCACT-CTCTTAGGTGAAGGCTTAAGATGGATTGCTTCACTACT-CTTCGGTAAAGGC
1371365 TTAAGATGGG
128 TTAAGATGGG
*
1371375 GCTTCACTACTCCTCTGTGAAGGCTTAAGATGGTGCTTCACTACTCTTCTATGAAGGCTTAAGAT
1 GCTTCACTACTCCTCTGTGAAGGCTTAAGATGGTGCTTCACTACTCTTCTGTGAAGGCTTAAGAT
*
1371440 GATTGCTTCACTCTTCTTCGGTGAAGGCTTAAGAT-GATTGCTTCACTACTCTTCGGTAAAGGCT
66 G-TTGCTTCACTC-TCTTAGGTGAAGGCTTAAGATGGATTGCTTCACTACTCTTCGGTAAAGGCT
*
1371504 TAAGATGGT
129 TAAGATGGG
*
1371513 GCTTCACTACTCCTCTGTGAAGGCTTAAGATGGTGCTTCACTACTCTTCTGCGAAGGCTTAAGAT
1 GCTTCACTACTCCTCTGTGAAGGCTTAAGATGGTGCTTCACTACTCTTCTGTGAAGGCTTAAGAT
*
1371578 GGTTTGCTTCACTCCTCTTTGGTGAAGGCTTAA
66 -G-TTGCTTCACT-CTCTTAGGTGAAGGCTTAA
1371611 CATTGACTTA
Statistics
Matches: 216, Mismatches: 14, Indels: 11
0.90 0.06 0.05
Matches are distributed among these distances:
137 6 0.03
138 153 0.71
139 56 0.26
140 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (137 bp):
GCTTCACTACTCCTCTGTGAAGGCTTAAGATGGTGCTTCACTACTCTTCTGTGAAGGCTTAAGAT
GTTGCTTCACTCTCTTAGGTGAAGGCTTAAGATGGATTGCTTCACTACTCTTCGGTAAAGGCTTA
AGATGGG
Found at i:1373125 original size:125 final size:125
Alignment explanation
Indices: 1372898--1373158 Score: 407
Period size: 125 Copynumber: 2.1 Consensus size: 125
1372888 CTGAAACTAG
* *
1372898 TGCCGCAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCAACACCTTCGATTGTAAGGC
1 TGCCCCAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCAACACCTTCAATTGTAAGGC
* * * * * *
1372963 TCATTCTTCATGCCTCCTTGGTCTGAATCTTTTCATCTCTACATGATGTGGGTTTAGCCA
66 TCATTCTTAATGCCTCCTTGGTCTGAATATTATCATCTCAACATGAAGTGGGTTCAGCCA
*
1373023 TGCCCCAACATTATCTTATATTGGTACGGGCCTTCAAAATGCCCCAACACC-TCAAATTGTAAGG
1 TGCCCCAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCAACACCTTC-AATTGTAAGG
* *
1373087 CTCATTCTTAATGCCTCCTTGGTCTGAATATTATCATCTCAACATGAAGTGGGTTCAGTCG
65 CTCATTCTTAATGCCTCCTTGGTCTGAATATTATCATCTCAACATGAAGTGGGTTCAGCCA
1373148 TGCCCCAACAT
1 TGCCCCAACAT
1373159 ATCCTAACTC
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
124 2 0.02
125 122 0.98
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (125 bp):
TGCCCCAACATTATCTTATACTGGTACGGGCCTTCAAAATGCCCCAACACCTTCAATTGTAAGGC
TCATTCTTAATGCCTCCTTGGTCTGAATATTATCATCTCAACATGAAGTGGGTTCAGCCA
Found at i:1374416 original size:2 final size:2
Alignment explanation
Indices: 1374409--1374443 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1374399 TTGTATACAC
1374409 AT AT AT AT -T 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
1374444 TTTGTTGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1376282 original size:27 final size:27
Alignment explanation
Indices: 1376240--1376291 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1376230 CCAATATGAG
*
1376240 ATTGATTTCCTCTGTCTTCCATTTTCT
1 ATTGATTTCCTATGTCTTCCATTTTCT
1376267 ATTGATTTCCTATGTCTTCCATTTT
1 ATTGATTTCCTATGTCTTCCATTTT
1376292 GTCTTTACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.08, T:0.56
Consensus pattern (27 bp):
ATTGATTTCCTATGTCTTCCATTTTCT
Found at i:1376610 original size:7 final size:6
Alignment explanation
Indices: 1376578--1376620 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
1376568 AAATACATAC
*
1376578 ATGC-A ATGCAG ATGCAA ATGCAA ATGCCAA ATGCAA ATGCAA A
1 ATGCAA ATGCAA ATGCAA ATGCAA ATG-CAA ATGCAA ATGCAA A
1376621 AGGTGTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
5 4 0.12
6 24 0.71
7 6 0.18
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.16
Consensus pattern (6 bp):
ATGCAA
Found at i:1376610 original size:13 final size:13
Alignment explanation
Indices: 1376582--1376617 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1376572 ACATACATGC
*
1376582 AATGCAGATG-CA
1 AATGCAAATGCCA
1376594 AATGCAAATGCCA
1 AATGCAAATGCCA
1376607 AATGCAAATGC
1 AATGCAAATGC
1376618 AAAAGGTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 9 0.41
13 13 0.59
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.17
Consensus pattern (13 bp):
AATGCAAATGCCA
Found at i:1381868 original size:80 final size:80
Alignment explanation
Indices: 1381734--1382053 Score: 464
Period size: 80 Copynumber: 4.0 Consensus size: 80
1381724 AGTCCTTACG
*
1381734 GACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTAGTTCCCTTTGCTGTGTGCA
1 GACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCA
1381799 TAAGGTAACCCTACA
66 TAAGGTAACCCTACA
* *
1381814 GACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTTCCTTTGCTGTGTGCA
1 GACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCA
*
1381879 TAAGGTAACCCTACG
66 TAAGGTAACCCTACA
* * *
1381894 GACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTAGTTGTGTGCT
1 GACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCA
1381959 TAAGGTAACCCTACA
66 TAAGGTAACCCTACA
* * *** *
1381974 GATCTAAGGATGTCCTTGGGTA-AATCCAAGGTATATCCTTAGGTTGGCTT-CCTTTGTTGTGTG
1 GACCTAAGGATAT-CTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGG-TTCCCTTTGCTGTGTG
* *
1382037 CTTATGGTAAGCCCTAC
64 CATAAGGTAA-CCCTAC
1382054 GGACGCAGTT
Statistics
Matches: 220, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
80 204 0.93
81 16 0.07
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.33
Consensus pattern (80 bp):
GACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCA
TAAGGTAACCCTACA
Found at i:1382005 original size:160 final size:161
Alignment explanation
Indices: 1381721--1382057 Score: 525
Period size: 160 Copynumber: 2.1 Consensus size: 161
1381711 TGATTCGGCT
*
1381721 GTAAGTCCTTACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTAGTTCCC
1 GTAAG-CCCTACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTAGTTCCC
* **
1381786 TTTGCTGTGTGCATAAGGTAACCCTACAGACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATC
65 TTAGCTGTGTGCATAAGGTAACCCTACAGACCTAAGGATATCTTGGGTAAATCCCAAGGTATATC
*
1381851 CTTAGGTTGGTTTCCTTTGCTGTGTGCATAAG
130 CTTAGGTTGGCTTCCTTTGCTGTGTGCATAAG
*
1381883 GTAA-CCCTACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCT
1 GTAAGCCCTACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTAGTTCCCT
* * * *
1381947 TAGTTGTGTGCTTAAGGTAACCCTACAGATCTAAGGATGTCCTTGGGTAAAT-CCAAGGTATATC
66 TAGCTGTGTGCATAAGGTAACCCTACAGACCTAAGGATAT-CTTGGGTAAATCCCAAGGTATATC
* * *
1382011 CTTAGGTTGGCTTCCTTTGTTGTGTGCTTATG
130 CTTAGGTTGGCTTCCTTTGCTGTGTGCATAAG
1382043 GTAAGCCCTACGGAC
1 GTAAGCCCTACGGAC
1382058 GCAGTTCTGG
Statistics
Matches: 160, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
160 137 0.86
161 19 0.12
162 4 0.03
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (161 bp):
GTAAGCCCTACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTAGTTCCCT
TAGCTGTGTGCATAAGGTAACCCTACAGACCTAAGGATATCTTGGGTAAATCCCAAGGTATATCC
TTAGGTTGGCTTCCTTTGCTGTGTGCATAAG
Found at i:1387217 original size:82 final size:80
Alignment explanation
Indices: 1387042--1387355 Score: 357
Period size: 82 Copynumber: 4.0 Consensus size: 80
1387032 AGTCCTTACA
*
1387042 GACCTAAGGATATCTTGGGTAGGCCCCAAGGCATATCCTTAGGTTAGTTCCCTTTGCTGTGTGCA
1 GACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTAGTTCCCTTTGCTGTGTGCA
1387107 TAAGGTAACCCTACG
66 TAAGGTAACCCTACG
* * * *
1387122 GACCTAAGGATATCTTGGGTAGGTCCCAAGGTATATCCTTAGGTTGGTTTTTCCTTTGTTGTGTG
1 GACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTAG--TTCCCTTTGCTGTGTG
1387187 CATAAGGTAACCCTACG
64 CATAAGGTAACCCTACG
* *
1387204 GACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTA---TA---------GATGTGTGCT
1 GACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTAGTTCCCTTTGCTGTGTGCA
1387257 TAAGGTAACCCTACG
66 TAAGGTAACCCTACG
* * ** * * *
1387272 GATCTAAGGATGTCCTTGGGTA-GATCCAAGGTATATCCTTAGGTTGGCTCCCTTTGTTGTGTGC
1 GACCTAAGGATAT-CTTGGGTAGGCCCCAAGGTATATCCTTAGGTTAGTTCCCTTTGCTGTGTGC
* *
1387336 TTATGGTAAGCCCTACG
65 ATAAGGTAA-CCCTACG
1387353 GAC
1 GAC
1387356 GCAGTTCTAG
Statistics
Matches: 201, Mismatches: 17, Indels: 31
0.81 0.07 0.12
Matches are distributed among these distances:
68 51 0.25
69 8 0.04
71 1 0.00
79 1 0.00
80 60 0.30
81 9 0.04
82 71 0.35
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (80 bp):
GACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAGGTTAGTTCCCTTTGCTGTGTGCA
TAAGGTAACCCTACG
Found at i:1387301 original size:68 final size:68
Alignment explanation
Indices: 1387181--1387312 Score: 203
Period size: 68 Copynumber: 1.9 Consensus size: 68
1387171 TTTCCTTTGT
*
1387181 TGTGTGCATAAGGTAACCCTACGGACCTAAGGATATCTTGGGTAGGCCCCAAGGTATATCCTTAT
1 TGTGTGCATAAGGTAACCCTACGGACCTAAGGATATCTTGGGTAGGACCCAAGGTATATCCTTAT
1387246 AGA
66 AGA
* * * *
1387249 TGTGTGCTTAAGGTAACCCTACGGATCTAAGGATGTCCTTGGGTA-GATCCAAGGTATATCCTTA
1 TGTGTGCATAAGGTAACCCTACGGACCTAAGGATAT-CTTGGGTAGGACCCAAGGTATATCCTTA
1387313 GGTTGGCTCC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 50 0.86
69 8 0.14
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.29
Consensus pattern (68 bp):
TGTGTGCATAAGGTAACCCTACGGACCTAAGGATATCTTGGGTAGGACCCAAGGTATATCCTTAT
AGA
Found at i:1394884 original size:29 final size:29
Alignment explanation
Indices: 1394852--1394913 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
1394842 CCCTCGTTTA
1394852 AAAATGAATTATTGATGTCTAGTTGATAT
1 AAAATGAATTATTGATGTCTAGTTGATAT
* *
1394881 AAAATGTATTTTTGATGTCTAGTTGATAT
1 AAAATGAATTATTGATGTCTAGTTGATAT
1394910 AAAA
1 AAAA
1394914 GCCACTCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (29 bp):
AAAATGAATTATTGATGTCTAGTTGATAT
Found at i:1395210 original size:30 final size:30
Alignment explanation
Indices: 1395176--1395240 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
1395166 GGTCCTCGTT
1395176 TAAAAATGTATTATTGATGTCTAGTTGATA
1 TAAAAATGTATTATTGATGTCTAGTTGATA
*
1395206 TAAAAATGTATTTTTGATGTCTAGTTGATA
1 TAAAAATGTATTATTGATGTCTAGTTGATA
1395236 TAAAA
1 TAAAA
1395241 GCCACTCTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.43
Consensus pattern (30 bp):
TAAAAATGTATTATTGATGTCTAGTTGATA
Found at i:1397451 original size:7 final size:7
Alignment explanation
Indices: 1397441--1397466 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1397431 TTGTACTTTG
1397441 TTATTTA
1 TTATTTA
1397448 TTATTTA
1 TTATTTA
1397455 TTATTTA
1 TTATTTA
1397462 TTATT
1 TTATT
1397467 GTTTTATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTTA
Found at i:1399664 original size:65 final size:66
Alignment explanation
Indices: 1399555--1399690 Score: 168
Period size: 65 Copynumber: 2.1 Consensus size: 66
1399545 AAGGAATGTA
* * * * *
1399555 CCGATACACTATTGAATGCATCGATACACTCCTAATTTTATTGAAACATCGAATACATTTTGTGT
1 CCGATACACAACTGAATGCATCGATACACTCCTAATCTTATTGAAACATCGAATACAATTAGTGT
1399620 G
66 G
* ** *
1399621 CCGATACACAACTG-ATGCATCGATGCACTCCTGGCTCTT-TTGAAACATCGAATATAATTAGTG
1 CCGATACACAACTGAATGCATCGATACACTCCT-AATCTTATTGAAACATCGAATACAATTAGTG
1399684 TG
65 TG
1399686 CCGAT
1 CCGAT
1399691 GTACCCCAAG
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
65 45 0.75
66 15 0.25
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (66 bp):
CCGATACACAACTGAATGCATCGATACACTCCTAATCTTATTGAAACATCGAATACAATTAGTGT
G
Found at i:1405854 original size:21 final size:21
Alignment explanation
Indices: 1405830--1405869 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1405820 TTTGAAATAA
*
1405830 AAAAATTTTATTTTTGATTTT
1 AAAAATGTTATTTTTGATTTT
* *
1405851 AAAAGTGTTGTTTTTGATT
1 AAAAATGTTATTTTTGATT
1405870 GAATTATATT
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:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (21 bp):
AAAAATGTTATTTTTGATTTT
Found at i:1405937 original size:12 final size:12
Alignment explanation
Indices: 1405908--1405942 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
1405898 ATATTATGAT
*
1405908 TTTTCAAATATTG
1 TTTTCAAA-ATAG
1405921 TTTTCAAAATAG
1 TTTTCAAAATAG
1405933 TTTTCAAAAT
1 TTTTCAAAAT
1405943 TTTTCCCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.49
Consensus pattern (12 bp):
TTTTCAAAATAG
Found at i:1408110 original size:65 final size:66
Alignment explanation
Indices: 1407997--1408136 Score: 160
Period size: 65 Copynumber: 2.1 Consensus size: 66
1407987 TTCAAAGGAA
* * * * *
1407997 TGTACCGATACACTATTGAATGCATCGATACACTCCTAATTTTATTGAAACATTGAATGCATTTT
1 TGTACCGATACACTACTGAATGCATCGATACACTCCTAATCTTATTGAAACATCGAATGCAATTA
1408062 G
66 G
* ** *
1408063 TGTACCGATACAC-AGCTG-ATGCATCGATGCACTCCTGGCTCTT-TTGAAACATCGAATGTAAT
1 TGTACCGATACACTA-CTGAATGCATCGATACACTCCT-AATCTTATTGAAACATCGAATGCAAT
1408125 TAG
64 TAG
1408128 TGTACCGAT
1 TGTACCGAT
1408137 GCACCCCAAG
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
65 45 0.71
66 18 0.29
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (66 bp):
TGTACCGATACACTACTGAATGCATCGATACACTCCTAATCTTATTGAAACATCGAATGCAATTA
G
Found at i:1411188 original size:30 final size:30
Alignment explanation
Indices: 1411152--1411225 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
1411142 GATATAAGCG
1411152 TTGAGGGCTTAATTGATAAAAATGCAAGTA
1 TTGAGGGCTTAATTGATAAAAATGCAAGTA
1411182 TTGAGGGCTTAATTGATAAAAATGCAAGTA
1 TTGAGGGCTTAATTGATAAAAATGCAAGTA
*
1411212 TTGAGGGCTAAATT
1 TTGAGGGCTTAATT
1411226 AATGACTATG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (30 bp):
TTGAGGGCTTAATTGATAAAAATGCAAGTA
Found at i:1418386 original size:13 final size:13
Alignment explanation
Indices: 1418368--1418397 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1418358 GTAGCAGCGT
1418368 AAAAAAAAGAAGA
1 AAAAAAAAGAAGA
1418381 AAAAAAAAGAAGA
1 AAAAAAAAGAAGA
1418394 AAAA
1 AAAA
1418398 GAGAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAGA
Found at i:1422752 original size:44 final size:44
Alignment explanation
Indices: 1422697--1422826 Score: 179
Period size: 44 Copynumber: 3.0 Consensus size: 44
1422687 GACATGCATA
* *
1422697 TCCTTATCGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTTAG
1 TCCTTACCGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTGAG
** *
1422741 TCCTTACCGTTACCGTAGGCTCCTCTGCTATGTATAAGGGTGCG
1 TCCTTACCGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTGAG
* * * *
1422785 TCCTTACCGTTACTGCAGGATCCTCTGCTATGTGCAAAGGTG
1 TCCTTACCGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTG
1422827 TAACATCCTA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 75 1.00
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (44 bp):
TCCTTACCGTTACCGTAGGCTCCTCTGCTATGTGCAAGGGTGAG
Found at i:1426166 original size:21 final size:22
Alignment explanation
Indices: 1426132--1426172 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1426122 GAGAAATTGT
1426132 TTTTAAAATATAAAAAATGATA
1 TTTTAAAATATAAAAAATGATA
*
1426154 TTTTGAAAT-TAAAAAATGA
1 TTTTAAAATATAAAAAATGA
1426173 AAATCATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (22 bp):
TTTTAAAATATAAAAAATGATA
Found at i:1429994 original size:21 final size:21
Alignment explanation
Indices: 1429968--1430046 Score: 63
Period size: 21 Copynumber: 3.6 Consensus size: 21
1429958 TGTGCATAAG
1429968 GCATCGATACACTATGAAAGT
1 GCATCGATACACTATGAAAGT
* * *
1429989 GCATCGATGCATCCCTTTGAATGT
1 GCATCGAT--A-CACTATGAAAGT
1430013 GCATCGATACA-TCATG-AAGAT
1 GCATCGATACACT-ATGAAAG-T
*
1430034 GCATCGATGCACT
1 GCATCGATACACT
1430047 CCTTGAATGT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
20 3 0.07
21 22 0.49
22 2 0.04
23 1 0.02
24 17 0.38
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (21 bp):
GCATCGATACACTATGAAAGT
Found at i:1430059 original size:23 final size:22
Alignment explanation
Indices: 1429982--1430111 Score: 106
Period size: 23 Copynumber: 5.8 Consensus size: 22
1429972 CGATACACTA
*
1429982 TGAAAGTGCATCGATGCATCCCTT
1 TGAATGTGCATCGATGCAT-CC-T
* *
1430006 TGAATGTGCATCGATACAT-CA
1 TGAATGTGCATCGATGCATCCT
1430027 TGAA-GATGCATCGATGCACTCCT
1 TGAATG-TGCATCGATGCA-TCCT
* * *
1430050 TGAATGTGCATCGGTACAT-CA
1 TGAATGTGCATCGATGCATCCT
*
1430071 TGAA-GATGCACCGATGCACTCCT
1 TGAATG-TGCATCGATGCA-TCCT
*
1430094 TGAGTGTGCATCGATGCA
1 TGAATGTGCATCGATGCA
1430112 CTAGGCCATG
Statistics
Matches: 84, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
20 2 0.02
21 29 0.35
22 4 0.05
23 30 0.36
24 19 0.23
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (22 bp):
TGAATGTGCATCGATGCATCCT
Found at i:1430068 original size:44 final size:44
Alignment explanation
Indices: 1429968--1430108 Score: 198
Period size: 44 Copynumber: 3.2 Consensus size: 44
1429958 TGTGCATAAG
1429968 GCATCGATACA-CTATGAA-AGTGCATCGATGCA-TCCCTTTGAATGT
1 GCATCGATACATC-ATGAAGA-TGCATCGATGCACT-CC-TTGAATGT
1430013 GCATCGATACATCATGAAGATGCATCGATGCACTCCTTGAATGT
1 GCATCGATACATCATGAAGATGCATCGATGCACTCCTTGAATGT
* * *
1430057 GCATCGGTACATCATGAAGATGCACCGATGCACTCCTTGAGTGT
1 GCATCGATACATCATGAAGATGCATCGATGCACTCCTTGAATGT
1430101 GCATCGAT
1 GCATCGAT
1430109 GCACTAGGCC
Statistics
Matches: 89, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
44 56 0.63
45 30 0.34
46 3 0.03
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (44 bp):
GCATCGATACATCATGAAGATGCATCGATGCACTCCTTGAATGT
Found at i:1430080 original size:21 final size:21
Alignment explanation
Indices: 1430012--1430085 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 21
1430002 CCTTTGAATG
1430012 TGCATCGATACATCATGAAGA
1 TGCATCGATACATCATGAAGA
* *
1430033 TGCATCGATGCACTCCTTGAATG-
1 TGCATCGATACA-T-CATGAA-GA
*
1430056 TGCATCGGTACATCATGAAGA
1 TGCATCGATACATCATGAAGA
*
1430077 TGCACCGAT
1 TGCATCGAT
1430086 GCACTCCTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
20 1 0.02
21 23 0.55
22 2 0.05
23 15 0.36
24 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26
Consensus pattern (21 bp):
TGCATCGATACATCATGAAGA
Found at i:1441859 original size:33 final size:33
Alignment explanation
Indices: 1441816--1441878 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
1441806 CTTTGTACAG
1441816 ATGGTAGACACGACCTTATCTGTCATACGGATT
1 ATGGTAGACACGACCTTATCTGTCATACGGATT
*
1441849 ATGGTGGACACGACCTTATCTGTCATACGG
1 ATGGTAGACACGACCTTATCTGTCATACGG
1441879 GATAGCACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (33 bp):
ATGGTAGACACGACCTTATCTGTCATACGGATT
Found at i:1448258 original size:30 final size:29
Alignment explanation
Indices: 1448223--1448300 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
1448213 AGTATGCTAC
*
1448223 AAGTTTTAGAAAATTTGAGGATCATTTTGT
1 AAGTTTTAGAAAA-TTGAGGATCAATTTGT
*
1448253 AAGTTTT-GAAAAGTTG-GAGATTAATTTGT
1 AAGTTTTAGAAAA-TTGAG-GATCAATTTGT
* *
1448282 AAATTCTAGAAAATTGAGG
1 AAGTTTTAGAAAATTGAGG
1448301 GATTGTTGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
28 1 0.03
29 26 0.65
30 13 0.32
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (29 bp):
AAGTTTTAGAAAATTGAGGATCAATTTGT
Found at i:1448667 original size:38 final size:37
Alignment explanation
Indices: 1448616--1448698 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 37
1448606 ATATTTTGGA
* *
1448616 AAATTATAAAGTGTCAAGGTGGGTGCAATACATGCATG
1 AAATTATAAAGTGTCAAGGTGAGTGCAATACA-ACATG
1448654 AAATTATAAAGTGTCAAGGTGAGTGCAATACAACATG
1 AAATTATAAAGTGTCAAGGTGAGTGCAATACAACATG
*
1448691 ATATTATA
1 AAATTATA
1448699 TCATATTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 11 0.26
38 31 0.74
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.28
Consensus pattern (37 bp):
AAATTATAAAGTGTCAAGGTGAGTGCAATACAACATG
Found at i:1449066 original size:33 final size:33
Alignment explanation
Indices: 1449024--1449086 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
1449014 CTTAGTACAG
* *
1449024 ATGGTGGACACGACCTTATGTGTCATACGGATT
1 ATGGTGGACACGAACTTATCTGTCATACGGATT
1449057 ATGGTGGACACGAACTTATCTGTCATACGG
1 ATGGTGGACACGAACTTATCTGTCATACGG
1449087 GATAGCACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (33 bp):
ATGGTGGACACGAACTTATCTGTCATACGGATT
Found at i:1454653 original size:60 final size:60
Alignment explanation
Indices: 1454560--1454674 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
1454550 GTCGAATAAT
* ** * *
1454560 CATTTTGTAACTTTTAATAGTCAGGAAACTCAACAAAACAACACCCTATAGTTGAATGAC
1 CATTTTATAACTTTTAATAACCAGGAAACTCAACAAAACAAAACCCTATAATTGAATGAC
* **
1454620 CATTTTATAACTTTTAATAACCGAGG-GACTCAACAAAGTAAAACCCTATAATTGA
1 CATTTTATAACTTTTAATAACC-AGGAAACTCAACAAAACAAAACCCTATAATTGA
1454675 GGGACAATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 43 0.93
61 3 0.07
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (60 bp):
CATTTTATAACTTTTAATAACCAGGAAACTCAACAAAACAAAACCCTATAATTGAATGAC
Found at i:1457931 original size:25 final size:25
Alignment explanation
Indices: 1457883--1457931 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1457873 AAATTTATAA
*
1457883 AATTTTAGAGAAAATAAACTTAAAG
1 AATTTTAGAGAAAATAAACATAAAG
*
1457908 AATTTTATAGAAAAATAAA-ATAAA
1 AATTTTAGAG-AAAATAAACATAAA
1457932 TTACCTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (25 bp):
AATTTTAGAGAAAATAAACATAAAG
Found at i:1469312 original size:3 final size:3
Alignment explanation
Indices: 1469304--1469366 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
1469294 TTCACTATCA
1469304 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1469352 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
1469367 ATATATATAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1474696 original size:27 final size:27
Alignment explanation
Indices: 1474665--1474759 Score: 176
Period size: 27 Copynumber: 3.6 Consensus size: 27
1474655 TCTATTTACA
1474665 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
1474692 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
1474719 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
1474746 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
1474760 ATTCCTACAC
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
25 9 0.13
27 59 0.87
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:1478369 original size:27 final size:27
Alignment explanation
Indices: 1478338--1478405 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
1478328 TCTATTTACA
1478338 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
1478365 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
1478392 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
1478406 ATTCCTACAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:1480389 original size:26 final size:26
Alignment explanation
Indices: 1480350--1480412 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
1480340 ATAATAGAAT
* * *
1480350 AAAA-TAAAATAAAATAAATCTTAAA
1 AAAATTAAATTAAAAGAAATATTAAA
1480375 AAAATTAAATTAAAAGAAATATTAAA
1 AAAATTAAATTAAAAGAAATATTAAA
*
1480401 AAGGATTAAATT
1 AA-AATTAAATT
1480413 GGAAAACATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 4 0.12
26 20 0.62
27 8 0.25
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (26 bp):
AAAATTAAATTAAAAGAAATATTAAA
Found at i:1481448 original size:6 final size:5
Alignment explanation
Indices: 1481439--1481618 Score: 72
Period size: 5 Copynumber: 37.2 Consensus size: 5
1481429 AAAAAAAGAA
*
1481439 AATATT AATAT -A-AT AATAAT AATAT AA-AT GATAT -ATAT -ATAT AAGTAT
1 AATA-T AATAT AATAT AAT-AT AATAT AATAT AATAT AATAT AATAT AA-TAT
* *
1481487 -A-AG AATAT ACAT-T AATAT ACA-AT AATAT -ATAAT AATAAT ACTAT
1 AATAT AATAT A-ATAT AATAT A-ATAT AATAT AAT-AT AAT-AT AATAT
*
1481531 AATA- ATTAT AATAT -ATAT AATAT -ATA- ATATAT AATAT -ATAAT AATAAT
1 AATAT AATAT AATAT AATAT AATAT AATAT A-ATAT AATAT AAT-AT AAT-AT
* *
1481579 AATA- ATATAT AATA- CA-AT AATAT AATAT ATAGAT AATAT A
1 AATAT A-ATAT AATAT AATAT AATAT AATAT A-ATAT AATAT A
1481619 TACTACTATA
Statistics
Matches: 137, Mismatches: 11, Indels: 53
0.68 0.05 0.26
Matches are distributed among these distances:
3 4 0.03
4 34 0.25
5 63 0.46
6 36 0.26
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:1481518 original size:7 final size:7
Alignment explanation
Indices: 1481508--1481646 Score: 146
Period size: 7 Copynumber: 19.7 Consensus size: 7
1481498 TTAATATACA
1481508 ATAATAT
1 ATAATAT
1481515 ATAATA-
1 ATAATAT
1481521 ATAATACT
1 ATAATA-T
1481529 ATAATA-
1 ATAATAT
*
1481535 ATTATA-
1 ATAATAT
1481541 AT-ATAT
1 ATAATAT
1481547 ATAATAT
1 ATAATAT
1481554 ATAATAT
1 ATAATAT
1481561 ATAATAT
1 ATAATAT
1481568 ATAATA-
1 ATAATAT
1481574 ATAATA-
1 ATAATAT
1481580 ATAATAT
1 ATAATAT
*
1481587 ATAATACA
1 ATAATA-T
1481595 ATAATAT
1 ATAATAT
*
1481602 AATATATAG
1 -ATA-ATAT
1481611 ATAATAT
1 ATAATAT
1481618 ATACTACTAT
1 ATA--A-TAT
1481628 ATAATAT
1 ATAATAT
1481635 ATAATAT
1 ATAATAT
1481642 ATAAT
1 ATAAT
1481647 TGTAGTCACT
Statistics
Matches: 116, Mismatches: 5, Indels: 22
0.81 0.03 0.15
Matches are distributed among these distances:
5 3 0.03
6 27 0.23
7 57 0.49
8 19 0.16
9 4 0.03
10 6 0.05
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.40
Consensus pattern (7 bp):
ATAATAT
Found at i:1481541 original size:53 final size:55
Alignment explanation
Indices: 1481446--1481646 Score: 159
Period size: 57 Copynumber: 3.7 Consensus size: 55
1481436 GAAAATATTA
* *
1481446 ATATAATA-ATAATAATATA-AATGAT-ATATATATATAAGTATAAGA-ATAT-AC
1 ATATAATATACAATAATATATAATAATAATATATA-ATAAGTATAAGATATATAAC
* * *
1481497 AT-TAATATACAATAATATATAATAATAATACTATAATAATTATAATATATATAAT
1 ATATAATATACAATAATATATAATAATAATA-TATAATAAGTATAAGATATATAAC
* * *
1481552 ATATAATATATAATATATAATAATAATAATAATATATAATACA--ATAATATA-ATATAT
1 ATATAATATACAATA-AT-AT-ATAATAATAATATATAATA-AGTATAAGATATATA-AC
* * * *
1481609 AGATAATATATACTACTATATAATATATAATATATAAT
1 ATATAATATACAATAATATATAATA-ATAATATATAAT
1481647 TGTAGTCACT
Statistics
Matches: 128, Mismatches: 9, Indels: 22
0.81 0.06 0.14
Matches are distributed among these distances:
50 5 0.04
51 12 0.09
52 5 0.04
53 13 0.10
54 14 0.11
55 17 0.13
56 15 0.12
57 25 0.20
58 9 0.07
59 13 0.10
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (55 bp):
ATATAATATACAATAATATATAATAATAATATATAATAAGTATAAGATATATAAC
Found at i:1481550 original size:26 final size:24
Alignment explanation
Indices: 1481446--1481644 Score: 157
Period size: 24 Copynumber: 8.1 Consensus size: 24
1481436 GAAAATATTA
1481446 ATATAATA-ATAATAATATAA-AT
1 ATATAATATATAATAATATAATAT
*
1481468 GATATATATATATAAGT-ATAAGAATAT
1 -ATATA-ATATATAA-TAAT-ATAATAT
* *
1481495 ACATTAATATACAATAATAT-ATA-
1 ATA-TAATATATAATAATATAATAT
1481518 ATAATAATACTATAATAATTATAATAT
1 AT-ATAATA-TATAATAA-TATAATAT
1481545 ATATAATATATAAT-ATATAATAT
1 ATATAATATATAATAATATAATAT
1481568 ATAATAATA-ATAATAATAT-ATA-
1 AT-ATAATATATAATAATATAATAT
*
1481590 ATACAATAATATAATATATAGATAATAT
1 ATATAAT-ATATAATA-AT--ATAATAT
*
1481618 ATACTACTATATAAT-ATATAATAT
1 ATA-TAATATATAATAATATAATAT
1481642 ATA
1 ATA
1481645 ATTGTAGTCA
Statistics
Matches: 145, Mismatches: 9, Indels: 43
0.74 0.05 0.22
Matches are distributed among these distances:
21 4 0.03
22 3 0.02
23 35 0.24
24 37 0.26
25 17 0.12
26 28 0.19
27 9 0.06
28 10 0.07
29 2 0.01
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (24 bp):
ATATAATATATAATAATATAATAT
Found at i:1481626 original size:97 final size:96
Alignment explanation
Indices: 1481439--1481644 Score: 241
Period size: 97 Copynumber: 2.2 Consensus size: 96
1481429 AAAAAAAGAA
*
1481439 AATAT-TAATATA-ATAATAATAATATAAATGATATATATATATAAGTATAAGAATATACATTAA
1 AATATATAATATATATAATAATAATATAAATGATATATATATATAAGTATAAGAATATACAATAA
*
1481502 TATACAATAATATATAATAATAATACTATAAT
66 TATACAATAATAGATAATAATAATACTAT-AT
*
1481534 AAT-TATAATATATATAATATATAATATATAAT-ATATA-ATA-ATAA-TAATAATATATAATAC
1 AATATATAATATATATAATA-ATAATATA-AATGATATATATATATAAGT-ATAAGA-AT-ATAC
*
1481594 AATAATAT--AATATATAGATAATATATACTACTATAT
61 AATAATATACAATA-ATAGATAATA-ATAATACTATAT
1481630 AATATATAATATATA
1 AATATATAATATATA
1481645 ATTGTAGTCA
Statistics
Matches: 97, Mismatches: 4, Indels: 18
0.82 0.03 0.15
Matches are distributed among these distances:
94 2 0.02
95 23 0.24
96 25 0.26
97 44 0.45
98 3 0.03
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (96 bp):
AATATATAATATATATAATAATAATATAAATGATATATATATATAAGTATAAGAATATACAATAA
TATACAATAATAGATAATAATAATACTATAT
Found at i:1481768 original size:38 final size:38
Alignment explanation
Indices: 1481698--1481940 Score: 169
Period size: 39 Copynumber: 6.2 Consensus size: 38
1481688 AATAATATAG
* *
1481698 TATAGTTTCT-GAAAATA-TTTTTGAAAAACATATAATA
1 TATAGTTTTTAGAAAATAGTTTTT-AAAAGCATATAATA
*
1481735 TATAGTTTTTAGAAAATGGTTTTTAAAAGCATATAATA
1 TATAGTTTTTAGAAAATAGTTTTTAAAAGCATATAATA
* * *
1481773 TATAGTTTTTTAAAAAATAGTTTTT-GAAGATATATATATA
1 TATAG-TTTTTAGAAAATAGTTTTTAAAAG-CATATA-ATA
* *
1481813 TATAGTATGGTTTTGAAAACACGTTTTTGAAAATG--TATAATA
1 TATAGT-T--TTTAGAAAATA-GTTTTT-AAAA-GCATATAATA
* * * *
1481855 TATAGTTTTGA-AAACATATTTTTGTAAACGTATATAATA
1 TATAGTTTTTAGAAA-ATAGTTTT-TAAAAGCATATAATA
* * *
1481894 TATAGTTTTTA-AAAATTGGTTTTGGAAAA-AATATAATA
1 TATAGTTTTTAGAAAA-TAGTTTT-TAAAAGCATATAATA
1481932 TATAGTTTT
1 TATAGTTTT
1481941 GAAAACATAT
Statistics
Matches: 167, Mismatches: 22, Indels: 33
0.75 0.10 0.15
Matches are distributed among these distances:
37 10 0.06
38 55 0.33
39 62 0.37
40 9 0.05
41 1 0.01
42 17 0.10
43 10 0.06
45 2 0.01
46 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.44
Consensus pattern (38 bp):
TATAGTTTTTAGAAAATAGTTTTTAAAAGCATATAATA
Found at i:1481819 original size:120 final size:119
Alignment explanation
Indices: 1481681--1481937 Score: 297
Period size: 120 Copynumber: 2.1 Consensus size: 119
1481671 CCTTAGTTAG
* *
1481681 TATATATAATAATATAGTATAGTTTCTGAAAATA-TTTTTGAAAAACATATAATATATAGTTTTT
1 TATATAT-AT-ATATAGTATAGTTT-TGAAAACACTTTTTG-AAAACATATAATATATAGTTTTG
* * *
1481745 AGAAA-ATGGTTTT-TAAAAGCATATAATATATAGTTTTTTAAAAAATAGTTTTTGAAGA
62 A-AAACATAGTTTTGTAAAAGCATATAATATATAG-TTTTTAAAAAATAGTTTTGGAAAA
* **
1481803 TATATATATATATAGTATGGTTTTGAAAACACGTTTTTGAAAATGTATAATATATAGTTTTGAAA
1 TATATATATATATAGTATAGTTTTGAAAACAC-TTTTTGAAAACATATAATATATAGTTTTGAAA
* * * * *
1481868 ACATATTTTTGTAAACGTATATAATATATAGTTTTTAAAAATTGGTTTTGGAAAA
65 ACATAGTTTTGTAAAAGCATATAATATATAGTTTTTAAAAAATAGTTTTGGAAAA
*
1481923 AATATA-ATATATAGT
1 TATATATATATATAGT
1481938 TTTGAAAACA
Statistics
Matches: 117, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
119 19 0.16
120 65 0.56
121 26 0.22
122 7 0.06
ACGTcount: A:0.43, C:0.03, G:0.12, T:0.43
Consensus pattern (119 bp):
TATATATATATATAGTATAGTTTTGAAAACACTTTTTGAAAACATATAATATATAGTTTTGAAAA
CATAGTTTTGTAAAAGCATATAATATATAGTTTTTAAAAAATAGTTTTGGAAAA
Found at i:1481955 original size:21 final size:24
Alignment explanation
Indices: 1481912--1481963 Score: 88
Period size: 23 Copynumber: 2.2 Consensus size: 24
1481902 TTAAAAATTG
1481912 GTTTTGGAAAAAATATAATATATA
1 GTTTTGGAAAAAATATAATATATA
*
1481936 GTTTT-GAAAACATATAATATATA
1 GTTTTGGAAAAAATATAATATATA
1481959 GTTTT
1 GTTTT
1481964 TAAAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (24 bp):
GTTTTGGAAAAAATATAATATATA
Found at i:1481971 original size:21 final size:22
Alignment explanation
Indices: 1481920--1481968 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
1481910 TGGTTTTGGA
1481920 AAAAATATAATATATAGTTTTG
1 AAAAATATAATATATAGTTTTG
*
1481942 AAAACATATAATATATAGTTTTT
1 AAAA-ATATAATATATAGTTTTG
1481965 AAAA
1 AAAA
1481969 TATTTATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (22 bp):
AAAAATATAATATATAGTTTTG
Found at i:1482051 original size:36 final size:36
Alignment explanation
Indices: 1481937--1482102 Score: 165
Period size: 36 Copynumber: 4.4 Consensus size: 36
1481927 TAATATATAG
1481937 TTTTGAAAACATATAATATATAG-TTTTTAAAATAT
1 TTTTGAAAACATATAATATATAGATTTTTAAAATAT
* * ** *
1481972 TTATGAATATGTATATATAATATAGATTTTGAGAACATAT
1 TTTTGAAAACATATA-AT-ATATAGATTTTTA-AA-ATAT
* *
1482012 TTTTGAAAACATATAGTATATAG-TTTTTAAAATGTT
1 TTTTGAAAACATATAATATATAGATTTTTAAAAT-AT
*
1482048 TTTTGAAAACATATAATATATAGTTTTTTAAAAACTAGT
1 TTTTGAAAACATATAATATATAGATTTTT-AAAA-TA-T
1482087 TTTTGGAAAACATATA
1 TTTT-GAAAACATATA
1482103 GTTTCGAAAT
Statistics
Matches: 106, Mismatches: 14, Indels: 17
0.77 0.10 0.12
Matches are distributed among these distances:
35 13 0.12
36 27 0.25
37 16 0.15
38 15 0.14
39 9 0.08
40 26 0.25
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.44
Consensus pattern (36 bp):
TTTTGAAAACATATAATATATAGATTTTTAAAATAT
Found at i:1482090 original size:75 final size:75
Alignment explanation
Indices: 1481937--1482104 Score: 198
Period size: 75 Copynumber: 2.2 Consensus size: 75
1481927 TAATATATAG
* * **
1481937 TTTTGAAAACATATAATATATAGTTTTTAAAATATTTATGAATATGTATATATAATATAGATTTT
1 TTTTGAAAACATATAGTATATAGTTTTTAAAATATTTATGAAAACATATATATAATATAGATTTT
* *
1482002 GAGAACATAT
66 AAAAACATAT
* * *
1482012 TTTTGAAAACATATAGTATATAGTTTTTAAAATGTTTTTTGAAAACATATA-AT-ATATAGTTTT
1 TTTTGAAAACATATAGTATATAGTTTTTAAAAT-ATTTATGAAAACATATATATAATATAG-ATT
1482075 TTAAAAAC-TAGT
64 TTAAAAACATA-T
1482087 TTTTGGAAAACATATAGT
1 TTTT-GAAAACATATAGT
1482105 TTCGAAATAT
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
74 8 0.10
75 47 0.59
76 25 0.31
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (75 bp):
TTTTGAAAACATATAGTATATAGTTTTTAAAATATTTATGAAAACATATATATAATATAGATTTT
AAAAACATAT
Found at i:1482136 original size:8 final size:7
Alignment explanation
Indices: 1482125--1482201 Score: 57
Period size: 8 Copynumber: 10.1 Consensus size: 7
1482115 ATACATATTA
1482125 TTATTATT
1 TTATT-TT
1482133 TTATTTT
1 TTATTTT
*
1482140 CTATTTT
1 TTATTTT
*
1482147 TAATTTT
1 TTATTTT
*
1482154 ATT-TTGT
1 -TTATTTT
1482161 TTATTTATT
1 TTA-TT-TT
1482170 TTATTTT
1 TTATTTT
1482177 ATTATTTAT
1 -TTATTT-T
1482186 TTATTTT
1 TTATTTT
1482193 CTTATTTT
1 -TTATTTT
1482201 T
1 T
1482202 CGGTCCAATC
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
6 2 0.04
7 20 0.36
8 29 0.52
9 5 0.09
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.77
Consensus pattern (7 bp):
TTATTTT
Found at i:1482138 original size:5 final size:5
Alignment explanation
Indices: 1482122--1482192 Score: 51
Period size: 5 Copynumber: 14.4 Consensus size: 5
1482112 TATATACATA
* * * *
1482122 TTATT ATTATT TTATT TTCTA TT-TT TAATT TTATT TT-GT TTA-T TTATT
1 TTATT -TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
1482170 TTATT TTATT ATT-TAT TTATT TT
1 TTATT TTATT -TTAT-T TTATT TT
1482193 CTTATTTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
4 9 0.17
5 35 0.66
6 9 0.17
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:1482146 original size:7 final size:6
Alignment explanation
Indices: 1482122--1482201 Score: 53
Period size: 6 Copynumber: 13.3 Consensus size: 6
1482112 TATATACATA
* *
1482122 TTATTA TTA-TT TTATTT TCTATTT TTAATT TTATTT TGT-TTAT TTA-TT
1 TTATTT TTATTT TTATTT T-TATTT TTATTT TTATTT T-TATT-T TTATTT
*
1482170 TTA-TT TTATTAT TTATTT ATT-TTC TTATTT TT
1 TTATTT TTATT-T TTATTT -TTATTT TTATTT TT
1482202 CGGTCCAATC
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
5 15 0.25
6 28 0.47
7 17 0.28
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (6 bp):
TTATTT
Found at i:1482165 original size:9 final size:8
Alignment explanation
Indices: 1482150--1482201 Score: 59
Period size: 8 Copynumber: 6.2 Consensus size: 8
1482140 CTATTTTTAA
1482150 TTTTATTT
1 TTTTATTT
1482158 TGTTTATTT
1 T-TTTATTT
1482167 ATTTTATTT
1 -TTTTATTT
*
1482176 TATTATTT
1 TTTTATTT
*
1482184 ATTTATTT
1 TTTTATTT
*
1482192 TCTTATTT
1 TTTTATTT
1482200 TT
1 TT
1482202 CGGTCCAATC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
8 21 0.58
9 14 0.39
10 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (8 bp):
TTTTATTT
Found at i:1485920 original size:24 final size:24
Alignment explanation
Indices: 1485893--1485968 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
1485883 TATATCAAAA
1485893 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* *
1485917 ATCATATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
1485941 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
1485965 ATCA
1 ATCA
1485969 GATCAGAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.09
24 42 0.91
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:1485969 original size:24 final size:24
Alignment explanation
Indices: 1485910--1486021 Score: 163
Period size: 24 Copynumber: 4.7 Consensus size: 24
1485900 CATAAATCAG
* * *
1485910 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
1485934 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
1485958 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
1485982 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
1486006 GTCAAGTATCAGATCA
1 GTCAAGTATCAGATCA
1486022 TAATTCAAAT
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 2 0.03
24 76 0.95
25 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:1486041 original size:48 final size:48
Alignment explanation
Indices: 1485941--1486043 Score: 136
Period size: 48 Copynumber: 2.1 Consensus size: 48
1485931 CAGGTCAAGT
** * *
1485941 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTATGTCAGAT
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAAAA
* *
1485989 ATCAGATCAGAATCCATGTCAAGTATCAGATCATAAT-TCAAATCAAAA
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCT-AAATCAAAA
1486037 ATCAGAT
1 ATCAGAT
1486044 AAAATATTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
47 1 0.02
48 47 0.98
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (48 bp):
ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAAAA
Found at i:1488508 original size:18 final size:18
Alignment explanation
Indices: 1488482--1488530 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
1488472 GTCAACGGTC
1488482 AACGGGTCGGGTAGGGTA
1 AACGGGTCGGGTAGGGTA
* * *
1488500 AACGAGTCGGGTTGGGTC
1 AACGGGTCGGGTAGGGTA
1488518 AACGGGTCGGGTA
1 AACGGGTCGGGTA
1488531 AATGGGTCGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.20, C:0.14, G:0.47, T:0.18
Consensus pattern (18 bp):
AACGGGTCGGGTAGGGTA
Found at i:1488524 original size:31 final size:31
Alignment explanation
Indices: 1488489--1488547 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1488479 GTCAACGGGT
*
1488489 CGGGTAGGGTAAACGAGTCGGGTTGGGTCAA
1 CGGGTAGGGTAAACGAGTCGGGTCGGGTCAA
* * *
1488520 CGGGTCGGGTAAATGGGTCGGGTCGGGT
1 CGGGTAGGGTAAACGAGTCGGGTCGGGT
1488548 AATGACCGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.17, C:0.14, G:0.49, T:0.20
Consensus pattern (31 bp):
CGGGTAGGGTAAACGAGTCGGGTCGGGTCAA
Found at i:1489791 original size:14 final size:13
Alignment explanation
Indices: 1489772--1489847 Score: 55
Period size: 14 Copynumber: 5.3 Consensus size: 13
1489762 TAAATAAGAG
1489772 AATAAAATAAATAA
1 AATAAAATAAA-AA
1489786 AATAAAAATGAAAAA
1 AAT-AAAAT-AAAAA
1489801 TAA-AAAATAAAAA
1 -AATAAAATAAAAA
*
1489814 ATAAAAAATATAAAA
1 A-ATAAAATA-AAAA
*
1489829 AATTAAATTAAAAGA
1 AA-TAAAATAAAA-A
1489844 AATA
1 AATA
1489848 TTAAAGAAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
12 1 0.02
13 6 0.12
14 20 0.38
15 20 0.38
16 5 0.10
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AATAAAATAAAAA
Found at i:1489801 original size:7 final size:7
Alignment explanation
Indices: 1489775--1489829 Score: 67
Period size: 7 Copynumber: 7.6 Consensus size: 7
1489765 ATAAGAGAAT
1489775 AAAATAA
1 AAAATAA
1489782 ATAAA-ATA
1 A-AAATA-A
*
1489790 AAAATGA
1 AAAATAA
1489797 AAAATAA
1 AAAATAA
1489804 AAAATAA
1 AAAATAA
1489811 AAAATAA
1 AAAATAA
1489818 AAAATATA
1 AAAATA-A
1489826 AAAA
1 AAAA
1489830 ATTAAATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
7 32 0.76
8 10 0.24
ACGTcount: A:0.82, C:0.00, G:0.02, T:0.16
Consensus pattern (7 bp):
AAAATAA
Found at i:1491030 original size:17 final size:19
Alignment explanation
Indices: 1490997--1491126 Score: 79
Period size: 20 Copynumber: 6.4 Consensus size: 19
1490987 AAGAAAATAT
1490997 TAATATAATAATAATATAAA
1 TAATATAATAAT-ATATAAA
* *
1491017 TTATAT-AT-ATATATATA
1 TAATATAATAATATATAAA
1491034 TAATATAATAATATATAACAA
1 TAATATAATAATATAT-A-AA
1491055 TAATATTACTATAATATTACTAAA
1 TAATA-TA--ATAATA-TA-TAAA
*
1491079 -ATATATTATAATATAT-AA
1 TA-ATATAATAATATATAAA
*
1491097 TAATAATTTATAATACTATAATA
1 TAAT-A-TAATAATA-TATAA-A
1491120 TAATATA
1 TAATATA
1491127 TTTAATATAC
Statistics
Matches: 88, Mismatches: 6, Indels: 31
0.70 0.05 0.25
Matches are distributed among these distances:
17 11 0.12
18 8 0.09
19 11 0.12
20 16 0.18
21 16 0.18
22 4 0.05
23 7 0.08
24 11 0.12
25 3 0.03
26 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATATAATAATATATAAA
Found at i:1491039 original size:13 final size:13
Alignment explanation
Indices: 1490993--1491135 Score: 79
Period size: 13 Copynumber: 10.9 Consensus size: 13
1490983 CAAAAAGAAA
1490993 ATAT-TAATATA-
1 ATATATAATATAT
*
1491004 ATA-ATAATATAA
1 ATATATAATATAT
1491016 AT-TATATATATAT
1 ATATATA-ATATAT
1491029 ATATATAATATAAT
1 ATATATAATAT-AT
*
1491043 AATATATAACA-AT
1 -ATATATAATATAT
*
1491056 A-ATATTACTATA-
1 ATATA-TAATATAT
*
1491068 ATATTACTAAAATAT
1 ATA-TA-TAATATAT
1491083 AT-TATAATATAT
1 ATATATAATATAT
*
1491095 A-ATAATAATTTAT
1 ATAT-ATAATATAT
1491108 AATACTATAATATAAT
1 -ATA-TATAATAT-AT
*
1491124 ATATTTAATATA
1 ATATATAATATA
1491136 CACTAATATT
Statistics
Matches: 103, Mismatches: 11, Indels: 34
0.70 0.07 0.23
Matches are distributed among these distances:
11 13 0.13
12 19 0.18
13 26 0.25
14 21 0.20
15 21 0.20
16 3 0.03
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATATAATATAT
Found at i:1491068 original size:32 final size:36
Alignment explanation
Indices: 1490993--1491127 Score: 98
Period size: 33 Copynumber: 4.0 Consensus size: 36
1490983 CAAAAAGAAA
1490993 ATAT-TAATATAATAATAATATAAATTATATATATAT
1 ATATATAATATAATAATAATATAAA-TATATATATAT
1491029 ATATATAATATAATAAT-ATATAACA-ATA-ATAT-T
1 ATATATAATATAATAATAATATAA-ATATATATATAT
* * *
1491062 A-CTATAATATTACTAA-AATAT-ATTATA-ATATAT
1 ATATATAATA-TAATAATAATATAAATATATATATAT
* *
1491095 A-ATAATAAT-TTATAATACTAT-AATATA-ATATAT
1 ATAT-ATAATATAATAATAATATAAATATATATATAT
1491128 TTAATATACA
Statistics
Matches: 83, Mismatches: 8, Indels: 19
0.75 0.07 0.17
Matches are distributed among these distances:
32 19 0.23
33 29 0.35
34 9 0.11
35 3 0.04
36 10 0.12
37 13 0.16
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (36 bp):
ATATATAATATAATAATAATATAAATATATATATAT
Found at i:1491090 original size:45 final size:43
Alignment explanation
Indices: 1490990--1491135 Score: 117
Period size: 43 Copynumber: 3.4 Consensus size: 43
1490980 CCACAAAAAG
* * *
1490990 AAAATATTAATATAATA-ATAA-TATAAATTAT-ATATATATATAT
1 AAAATA-TATTATAATATATAACAATAATTTATAATA-ATATA-AT
* *
1491033 ATAATATA--ATAATATATAACAATAATATTACT-ATAATATTACT
1 AAAATATATTATAATATATAACAATAAT-TTA-TAATAATA-TAAT
* *
1491076 AAAATATATTATAATATATAATAATAATTTATAATACTATAAT
1 AAAATATATTATAATATATAACAATAATTTATAATAATATAAT
*
1491119 ATAATATATT-TAATATA
1 AAAATATATTATAATATA
1491136 CACTAATATT
Statistics
Matches: 86, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
40 6 0.07
41 4 0.05
42 13 0.15
43 32 0.37
44 14 0.16
45 17 0.20
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (43 bp):
AAAATATATTATAATATATAACAATAATTTATAATAATATAAT
Found at i:1491136 original size:24 final size:24
Alignment explanation
Indices: 1491096--1491153 Score: 59
Period size: 24 Copynumber: 2.4 Consensus size: 24
1491086 ATAATATATA
1491096 ATAATA-ATTTATAATACTA-TAAT
1 ATAATATATTTATAATAC-ACTAAT
1491119 ATAATATATTTA-ATATACACTAAT
1 ATAATATATTTATA-ATACACTAAT
1491143 ATTTAATATAT
1 A--TAATATAT
1491154 AATTATAGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 8 0.27
24 14 0.47
26 8 0.27
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (24 bp):
ATAATATATTTATAATACACTAAT
Found at i:1491252 original size:37 final size:36
Alignment explanation
Indices: 1491208--1491285 Score: 111
Period size: 38 Copynumber: 2.1 Consensus size: 36
1491198 AATAATATAG
1491208 TATAGTTTTTGAAAATATTTTTGAGAAACATATAATA
1 TATAGTTTTTGAAAATATTTTTGA-AAACATATAATA
* *
1491245 TATAGTTTTTAGAAAACAGTTTTTGAAAGCATATAATA
1 TATAGTTTTT-GAAAATA-TTTTTGAAAACATATAATA
1491283 TAT
1 TAT
1491286 TATTTTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 10 0.27
38 20 0.54
39 7 0.19
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (36 bp):
TATAGTTTTTGAAAATATTTTTGAAAACATATAATA
Found at i:1491325 original size:2 final size:2
Alignment explanation
Indices: 1491313--1491349 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1491303 GTTTTTGAAG
*
1491313 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1491350 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1491424 original size:37 final size:37
Alignment explanation
Indices: 1491369--1491663 Score: 201
Period size: 37 Copynumber: 7.9 Consensus size: 37
1491359 AGAGAGTATG
** *
1491369 GTTTTGAAAACACGTTTTTGAAAACGTAAAATATACA
1 GTTTTGAAAACATATTTTTGAAAACGTAAAATATATA
*
1491406 GTTTGGAAAACATATTTTTGAAAACGTATATAATATTTATA
1 GTTTTGAAAACATATTTTTGAAAACGTA-A-AATA--TATA
* * * * *
1491447 TTTTTTAAAA-ATCAGTTTTGAAAAACATATAATATATA
1 GTTTTGAAAACAT-ATTTTTG-AAAACGTAAAATATATA
*
1491485 GTTTTGAAAACAT-TTTTT-AAAACAT-AAATATATA
1 GTTTTGAAAACATATTTTTGAAAACGTAAAATATATA
* *
1491519 GTTTT-TAAA-ATATTTTTGAAAACGTATATATAATATA
1 GTTTTGAAAACATATTTTTGAAAACGTA-AAAT-ATATA
** ** *
1491556 GTTTTTGAAAATGTATTTTTGAAAAAAATATAATA-ATA
1 G-TTTTGAAAACATATTTTTG-AAAACGTAAAATATATA
* * * * *
1491594 GTTTTTAAAAAATATTTTTGAAAACTTATAGTATATA
1 GTTTTGAAAACATATTTTTGAAAACGTAAAATATATA
* ** * *
1491631 GTTTTTAAAATGT-TTTTTGAAAACATATAATAT
1 GTTTTGAAAACATATTTTTGAAAACGTAAAATAT
1491664 GTAATTTTTT
Statistics
Matches: 208, Mismatches: 33, Indels: 35
0.75 0.12 0.13
Matches are distributed among these distances:
32 2 0.01
33 8 0.04
34 19 0.09
35 7 0.03
36 31 0.15
37 65 0.31
38 21 0.10
39 10 0.05
40 16 0.08
41 22 0.11
42 7 0.03
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.42
Consensus pattern (37 bp):
GTTTTGAAAACATATTTTTGAAAACGTAAAATATATA
Found at i:1491743 original size:14 final size:14
Alignment explanation
Indices: 1491720--1491774 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
1491710 GATATACTTA
1491720 TTATTAATTTATTT
1 TTATTAATTTATTT
*
1491734 TTATTTATTTA-TT
1 TTATTAATTTATTT
* *
1491747 TTCTTAA-TT-TTA
1 TTATTAATTTATTT
*
1491759 TTATAAATTTATTT
1 TTATTAATTTATTT
1491773 TT
1 TT
1491775 CTTATTTTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
12 8 0.26
13 9 0.29
14 14 0.45
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTAATTTATTT
Found at i:1492664 original size:11 final size:11
Alignment explanation
Indices: 1492648--1492675 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1492638 TAGGCTGGTT
1492648 GAGAGAGTTTA
1 GAGAGAGTTTA
1492659 GAGAGAGTTTA
1 GAGAGAGTTTA
1492670 GAGAGA
1 GAGAGA
1492676 AGGGAAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.21
Consensus pattern (11 bp):
GAGAGAGTTTA
Found at i:1494058 original size:13 final size:13
Alignment explanation
Indices: 1494035--1494071 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1494025 ATGGGGTAGG
*
1494035 AATTTTTATTTTT
1 AATTATTATTTTT
*
1494048 TATTATTATTTTT
1 AATTATTATTTTT
1494061 AATTATTATTT
1 AATTATTATTT
1494072 CTAGTTTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
AATTATTATTTTT
Found at i:1500345 original size:201 final size:201
Alignment explanation
Indices: 1499997--1500363 Score: 495
Period size: 201 Copynumber: 1.8 Consensus size: 201
1499987 TAAGCAAAGA
** ** *
1499997 AGAAGAACTAGGTTGGCTACAATTTAGAAACAAGGATTTATCTCTTAACAGAATTTACAGCATAG
1 AGAAGAACTAGGTTGGCTACAATTTAGAAACAAGGAACTATCTCCCAACAGAATTTACAACATAG
* *
1500062 CTCAAGGCGAGAAGGGCTATCTGTCAACGAAAACTTTCGAGTTTGATTTCATTTAGCTTAAGGGC
66 CTCAAGGCGAGAAGAGCTATCTGTCAACGAAAACTTTCGAGTTTGATTTCATTCAGCTTAAGGGC
* * * *
1500127 GTATCAACCATATGGTAGTAGTGAGGAACTACTTTTTGGTTGATGTTTAAACTGATGATTGTAAG
131 GTATCAACCACATGGTAGAAGCGAGGAACTAATTTTTGGTTGATGTTTAAACTGATGATTGTAAG
1500192 TCAAGT
196 TCAAGT
* * *
1500198 AGAAGACCTAGGTTGGCCT-CAATTTAGGAACAAGGAACTATCTCCCAACATAATTTACAACATA
1 AGAAGAACTAGGTTGG-CTACAATTTAGAAACAAGGAACTATCTCCCAACAGAATTTACAACATA
* * * * * *
1500262 GCTTAAGTCGACGAA-AGCTGTCTGTCAACGAAAACTTTTGAGTTTGATTTTATTCAGCTTGAGG
65 GCTCAAGGCGA-GAAGAGCTATCTGTCAACGAAAACTTTCGAGTTTGATTTCATTCAGCTTAAGG
***
1500326 GCGTATCAATTGCATGGTAGAAGCGAGGAACTAATTTT
129 GCGTATCAACCACATGGTAGAAGCGAGGAACTAATTTT
1500364 CAGTTGAACT
Statistics
Matches: 141, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
201 136 0.96
202 5 0.04
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (201 bp):
AGAAGAACTAGGTTGGCTACAATTTAGAAACAAGGAACTATCTCCCAACAGAATTTACAACATAG
CTCAAGGCGAGAAGAGCTATCTGTCAACGAAAACTTTCGAGTTTGATTTCATTCAGCTTAAGGGC
GTATCAACCACATGGTAGAAGCGAGGAACTAATTTTTGGTTGATGTTTAAACTGATGATTGTAAG
TCAAGT
Found at i:1501210 original size:38 final size:37
Alignment explanation
Indices: 1501150--1501568 Score: 285
Period size: 37 Copynumber: 11.3 Consensus size: 37
1501140 AATAATATAG
*
1501150 TATAGTTTTTGAAAAT-ATTTTTTAAAAACATATAATA
1 TATAGTTTTTGAAAATGA-TTTTTGAAAACATATAATA
*
1501187 TATAGTTTTTAGAAAATGATTTTTGAAAGCATAATATATA
1 TATAGTTTTT-GAAAATGATTTTTGAAAACAT-ATA-ATA
** ** ***
1501227 TATA-TATTTAAAAAAATTGGGTTTTGAAGTTATAT-ATA
1 TATAGT-TTT-TGAAAA-TGATTTTTGAAAACATATAATA
* * *
1501265 GTAT-GGTTTTGAAAATTCG-TTTTTGAAAACGTAAAATA
1 -TATAGTTTTTGAAAA-T-GATTTTTGAAAACATATAATA
* *
1501303 TATAG-TTTAGAAAATATATTTTTGAAAACATATATAATA
1 TATAGTTTTTGAAAAT-GATTTTTGAAAAC--ATATAATA
* * * *
1501342 TATAATTTTTAAAAATAGGTTTTGGAAAACATATAATA
1 TATAGTTTTTGAAAAT-GATTTTTGAAAACATATAATA
* * *
1501380 TAT-GGTTTTGAAAA-CATTTTTGAAAACAAATAATA
1 TATAGTTTTTGAAAATGATTTTTGAAAACATATAATA
* **
1501415 TATTGTTTTT-AAAAT-ATTTTTGAAAATGTATATATAA
1 TATAGTTTTTGAAAATGATTTTTGAAAACATATA-AT-A
* * *
1501452 TATAGTTATTGAAAACGTATTTTTGAAAATATATAATA
1 TATAGTTTTTGAAAATG-ATTTTTGAAAACATATAATA
* *
1501490 TATAGTTTTTTAAAAAT-ATTTTTGAAAA-ATATAGTA
1 TATAG-TTTTTGAAAATGATTTTTGAAAACATATAATA
* *
1501526 TATA-ATTTT--AAAT-TTTTTTGAAAACATATAATA
1 TATAGTTTTTGAAAATGATTTTTGAAAACATATAATA
1501559 TATAGTTTTT
1 TATAGTTTTT
1501569 TTAAAAAAGA
Statistics
Matches: 304, Mismatches: 52, Indels: 55
0.74 0.13 0.13
Matches are distributed among these distances:
32 14 0.05
33 11 0.04
34 8 0.03
35 38 0.12
36 19 0.06
37 75 0.25
38 49 0.16
39 28 0.09
40 51 0.17
41 11 0.04
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.44
Consensus pattern (37 bp):
TATAGTTTTTGAAAATGATTTTTGAAAACATATAATA
Found at i:1501384 original size:114 final size:113
Alignment explanation
Indices: 1501144--1501455 Score: 284
Period size: 114 Copynumber: 2.7 Consensus size: 113
1501134 ATATATAATA
* * * *
1501144 ATATAGTATAGTTTTTGAAAATAT-TTTTTAAAAACATATAATATATAGTTTTTAGAAAAT-GAT
1 ATATAGTAT-GGTTTTGAAAAT-TCTTTTTGAAAAC-TAAAATATATAG--TTTAGAAAATATAT
* * ***
1501207 TTTTGAAAGCATA-ATATATATATATATTTAAAAAAATTGGGTTTTGAAGTTAT
61 TTTTGAAAACATATATA-ATATATATATTTAAAAAAATTAGGTTTTGAAAACAT
1501260 ATATAGTATGGTTTTGAAAATTCGTTTTTGAAAACGTAAAATATATAGTTTAGAAAATATATTTT
1 ATATAGTATGGTTTTGAAAATTC-TTTTTGAAAAC-TAAAATATATAGTTTAGAAAATATATTTT
**
1501325 TGAAAACATATATAATATATA-ATTTTTAAAAA-TAGGTTTTGGAAAACAT
64 TGAAAACATATATAATATATATATTTAAAAAAATTAGGTTTT-GAAAACAT
* * **
1501374 ATAATA-TATGGTTTTGAAAA--CATTTTTGAAAACAAATAATATATTGTTT-TTAAA-ATATTT
1 AT-ATAGTATGGTTTTGAAAATTC-TTTTTGAAAACTAA-AATATATAGTTTAGAAAATATATTT
*
1501434 TTGAAAATGTATATATAATATA
63 TTGAAAA--CATATATAATATA
1501456 GTTATTGAAA
Statistics
Matches: 169, Mismatches: 18, Indels: 22
0.81 0.09 0.11
Matches are distributed among these distances:
110 13 0.08
111 5 0.03
112 35 0.21
113 7 0.04
114 41 0.24
115 35 0.21
116 33 0.20
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.43
Consensus pattern (113 bp):
ATATAGTATGGTTTTGAAAATTCTTTTTGAAAACTAAAATATATAGTTTAGAAAATATATTTTTG
AAAACATATATAATATATATATTTAAAAAAATTAGGTTTTGAAAACAT
Found at i:1501431 original size:112 final size:109
Alignment explanation
Indices: 1501156--1501568 Score: 324
Period size: 110 Copynumber: 3.7 Consensus size: 109
1501146 ATAGTATAGT
* * * *
1501156 TTTTGAAAATATTTTTTAAAAACATATAATATATAGTTTTTAGAAAATGATTTTTGAAAGCATA-
1 TTTTGAAAACA-TTTTTGAAAACAAATAATATATAGTTTTT--AAAAT-ATTTTTGAAAACATAT
** * **
1501220 ATATATATATATATTTAAAAAAATTGGGTTTTGAAGTTATAT-ATAGTATGG
62 ATA-ATATATA-ATTTTTAAAAA-TAGGTTTTGAAAATATATAATA-TATGG
* * **
1501271 TTTTGAAAATTCGTTTTTGAAAACGTAA-AATATATAGTTTAGAAAATATATTTTTGAAAACATA
1 TTTTGAAAA--CATTTTTGAAAAC-AAATAATATATAGTTT-TTAAA-ATATTTTTGAAAACATA
*
1501335 TATAATATATAATTTTTAAAAATAGGTTTTGGAAAACATATAATATATGG
61 TATAATATATAATTTTTAAAAATAGGTTTT-GAAAATATATAATATATGG
* **
1501385 TTTTGAAAACATTTTTGAAAACAAATAATATATTGTTTTTAAAATATTTTTGAAAATGTATAT-A
1 TTTTGAAAACATTTTTGAAAACAAATAATATATAGTTTTTAAAATATTTTTGAAAACATATATAA
* * * * *
1501449 TAATATAGTTATTGAAAACGTA-TTTTTGAAAATATATAATATATAGTT
66 T-ATATAATT-TTTAAAA-ATAGGTTTTGAAAATATATAATATAT-G-G
* * * * * *
1501497 TTTTAAAAATATTTTTGAAAA-ATATAGTATATA-ATTTT-AAATTTTTTTGAAAAC--ATATAA
1 TTTTGAAAACATTTTTGAAAACAAATAATATATAGTTTTTAAAATATTTTTGAAAACATATATAA
*
1501557 TATATAGTTTTT
66 TATATAATTTTT
1501569 TTAAAAAAGA
Statistics
Matches: 247, Mismatches: 36, Indels: 39
0.77 0.11 0.12
Matches are distributed among these distances:
106 2 0.01
107 12 0.05
108 2 0.01
109 16 0.06
110 45 0.18
111 25 0.10
112 44 0.18
113 7 0.03
114 30 0.12
115 36 0.15
116 27 0.11
117 1 0.00
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (109 bp):
TTTTGAAAACATTTTTGAAAACAAATAATATATAGTTTTTAAAATATTTTTGAAAACATATATAA
TATATAATTTTTAAAAATAGGTTTTGAAAATATATAATATATGG
Found at i:1501585 original size:110 final size:110
Alignment explanation
Indices: 1501318--1501597 Score: 270
Period size: 110 Copynumber: 2.5 Consensus size: 110
1501308 TTTAGAAAAT
* *
1501318 ATATTTTTGAAAACATAT-ATAATATA-TAATTTTTAAAAATAG-GTTTTGGAAAACATATAATA
1 ATATTTTTGAAAACATATAATAATATAGT--TTTTTAAAAA-AGTATTTTTGAAAACATATAATA
* **
1501380 TATGGTTTTGAAAACATTTTTGAAAACAAATAATATATTGTTTTTAAA
63 TATGGTTTTAAAAACATTTTTGAAAACAAATAATATATTAATTTTAAA
** * * * *
1501428 ATATTTTTGAAAATGTATATATAATATAG-TTATTGAAAACGTATTTTTGAAAATATATAATATA
1 ATATTTTTGAAAACATATA-ATAATATAGTTTTTTAAAAAAGTATTTTTGAAAACATATAATATA
* * * *
1501492 TAGTTTTTTAAAAATATTTTTGAAAA-ATATAGTATA-TAATTTT-AA
65 T-G-GTTTTAAAAACATTTTTGAAAACAAATAATATATTAATTTTAAA
* *
1501537 ATTTTTTTGAAAACATATAAT-ATATAGTTTTTTTAAAAAAGATTTTTTTGGAAAACATATA
1 ATATTTTTGAAAACATATAATAATATAG-TTTTTTAAAAAAG-TATTTTT-GAAAACATATA
1501598 GTTTCAAAAT
Statistics
Matches: 137, Mismatches: 23, Indels: 19
0.77 0.13 0.11
Matches are distributed among these distances:
107 6 0.04
108 2 0.01
109 28 0.20
110 55 0.40
111 19 0.14
112 27 0.20
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.44
Consensus pattern (110 bp):
ATATTTTTGAAAACATATAATAATATAGTTTTTTAAAAAAGTATTTTTGAAAACATATAATATAT
GGTTTTAAAAACATTTTTGAAAACAAATAATATATTAATTTTAAA
Done.