Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 91 of 145
Found at i:31281972 original size:47 final size:47
Alignment explanation
Indices: 31281919--31282014 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
31281909 TTTGGTCTTC
*
31281919 AAAAAATATTTTATATTACTTATATTGTATGATTGAAAATTATAATT
1 AAAAAATATTTTATATTACTTATATTGTATGATTAAAAATTATAATT
*
31281966 AAAAAATATTTTATATTACTTATATTGTTTGATTAAAAATTATAATT
1 AAAAAATATTTTATATTACTTATATTGTATGATTAAAAATTATAATT
31282013 AA
1 AA
31282015 CACTACAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (47 bp):
AAAAAATATTTTATATTACTTATATTGTATGATTAAAAATTATAATT
Found at i:31282996 original size:45 final size:44
Alignment explanation
Indices: 31282914--31283000 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 44
31282904 ACAACATCAT
31282914 TCCATTCAACCAAACACAATAATACTATTACAGCTCTATTCTGA
1 TCCATTCAACCAAACACAATAATACTATTACAGCTCTATTCTGA
*
31282958 TCCATTCAACCAAACA-ATTGAATTACTATTACAGCTCTATTCT
1 TCCATTCAACCAAACACAAT-AA-TACTATTACAGCTCTATTCT
31283001 ATTACAGTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
43 2 0.05
44 18 0.45
45 20 0.50
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (44 bp):
TCCATTCAACCAAACACAATAATACTATTACAGCTCTATTCTGA
Found at i:31284192 original size:9 final size:9
Alignment explanation
Indices: 31284178--31284214 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
31284168 TATAGTTTGA
31284178 TATTCGAAT
1 TATTCGAAT
31284187 TATTCGAAT
1 TATTCGAAT
*
31284196 TATTCGAGT
1 TATTCGAAT
31284205 TATTCGAAT
1 TATTCGAAT
31284214 T
1 T
31284215 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:31287087 original size:9 final size:9
Alignment explanation
Indices: 31287070--31287106 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
31287060 TGAGTTTTCG
31287070 AATTCGAAT
1 AATTCGAAT
*
31287079 AACTCGAAT
1 AATTCGAAT
31287088 AATTCGAAT
1 AATTCGAAT
31287097 AATTCGAAT
1 AATTCGAAT
31287106 A
1 A
31287107 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:31287840 original size:5 final size:5
Alignment explanation
Indices: 31287830--31287860 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
31287820 CTCGAAAATT
31287830 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
31287861 CGAATGCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:31314381 original size:27 final size:27
Alignment explanation
Indices: 31314351--31314480 Score: 172
Period size: 27 Copynumber: 4.9 Consensus size: 27
31314341 CCTTACAGGG
*
31314351 TTCACCATAAAGGCTACTATTTCATAT
1 TTCACCACAAAGGCTACTATTTCATAT
** *
31314378 TTCACCACAAAGGCTACTCGTTCTTAT
1 TTCACCACAAAGGCTACTATTTCATAT
** *
31314405 TTTTCCACAAAGGCTACTCTTTCATAT
1 TTCACCACAAAGGCTACTATTTCATAT
31314432 TTCACCACAAAGGCTACTATTTCATAT
1 TTCACCACAAAGGCTACTATTTCATAT
* *
31314459 TTCCCCA-AAAAGCTACTATTTC
1 TTCACCACAAAGGCTACTATTTC
31314481 TTGACATGTT
Statistics
Matches: 90, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
26 14 0.16
27 76 0.84
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.35
Consensus pattern (27 bp):
TTCACCACAAAGGCTACTATTTCATAT
Found at i:31315319 original size:25 final size:25
Alignment explanation
Indices: 31315291--31315340 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
31315281 TTCTTGAAGA
*
31315291 AGGAAAAAGAAAAACTTCCTCTTTC
1 AGGAAAAAGAAAAAATTCCTCTTTC
31315316 AGGAAAAAGAAAAAATTCCTCTTTC
1 AGGAAAAAGAAAAAATTCCTCTTTC
31315341 TTTAACTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (25 bp):
AGGAAAAAGAAAAAATTCCTCTTTC
Found at i:31319071 original size:40 final size:40
Alignment explanation
Indices: 31319008--31319093 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
31318998 CTTAATTTTG
* * *
31319008 ACCTGATAATATCTCGATCGAAGGTCAATTTTTTAAAACA
1 ACCTTATAATATCCCGATCGAAGGTCAATTTTTGAAAACA
*
31319048 ACCTTATAATATCCCGATTGAAGGTCAATTTTTGAAAACA
1 ACCTTATAATATCCCGATCGAAGGTCAATTTTTGAAAACA
31319088 ACCTTA
1 ACCTTA
31319094 CTCCCTCGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (40 bp):
ACCTTATAATATCCCGATCGAAGGTCAATTTTTGAAAACA
Found at i:31325060 original size:2 final size:2
Alignment explanation
Indices: 31325053--31325081 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31325043 CCAAGCTGAG
31325053 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31325082 CAGGCTACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31327548 original size:16 final size:18
Alignment explanation
Indices: 31327527--31327564 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
31327517 TTCTATAGGG
31327527 ATTTTACT-TT-TATTTT
1 ATTTTACTATTGTATTTT
31327543 ATTTTACTATTGTATTTT
1 ATTTTACTATTGTATTTT
31327561 ATTT
1 ATTT
31327565 AAATAAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (18 bp):
ATTTTACTATTGTATTTT
Found at i:31333433 original size:27 final size:26
Alignment explanation
Indices: 31333386--31333437 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
31333376 ATATGTTTAA
* *
31333386 AAATAACATATAATTATAATACATAAT
1 AAATAAAAAATAATTATAATA-ATAAT
31333413 AAATAAAAAATAATT-TGAATAATAA
1 AAATAAAAAATAATTAT-AATAATAA
31333438 CTCTCATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (26 bp):
AAATAAAAAATAATTATAATAATAAT
Found at i:31335371 original size:29 final size:29
Alignment explanation
Indices: 31335330--31335387 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
31335320 CAAGGTATGT
31335330 TGTTCTTCTCAGTCTAAGCGTTAAATCCA
1 TGTTCTTCTCAGTCTAAGCGTTAAATCCA
31335359 TGTTCTTCTCAGTCTAAGCGTTAAATCCA
1 TGTTCTTCTCAGTCTAAGCGTTAAATCCA
31335388 CCGTTCGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (29 bp):
TGTTCTTCTCAGTCTAAGCGTTAAATCCA
Found at i:31338669 original size:26 final size:26
Alignment explanation
Indices: 31338640--31338694 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
31338630 TAACTTTAAC
* *
31338640 AATTTCATTCGATTTGACTCAACTCG
1 AATTTCATTCCACTTGACTCAACTCG
* *
31338666 AATTTCATTCCACTTGATTCAATTCG
1 AATTTCATTCCACTTGACTCAACTCG
31338692 AAT
1 AAT
31338695 AAATTTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (26 bp):
AATTTCATTCCACTTGACTCAACTCG
Found at i:31340782 original size:60 final size:56
Alignment explanation
Indices: 31340680--31340804 Score: 151
Period size: 60 Copynumber: 2.1 Consensus size: 56
31340670 ATTCCTAAGA
* * * * *
31340680 AAAATAAATCAATTAAGCCCCTCAACTTACTTCACTCCCAATTGAATTTTTGTTGTTAATT
1 AAAA-AAATCAATTAAACCACTCAACTTAATTCACACCCAATTG-A--GTTGTTGTTAA-T
*
31340741 AAAAAAATCAATTAAACCACTCAACTTAATTCACACTCAATTGAGTTGTTGTTAAT
1 AAAAAAATCAATTAAACCACTCAACTTAATTCACACCCAATTGAGTTGTTGTTAAT
31340797 AAAAAAAT
1 AAAAAAAT
31340805 TTAATTAAGC
Statistics
Matches: 58, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
56 9 0.16
57 10 0.17
59 1 0.02
60 34 0.59
61 4 0.07
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.34
Consensus pattern (56 bp):
AAAAAAATCAATTAAACCACTCAACTTAATTCACACCCAATTGAGTTGTTGTTAAT
Found at i:31340968 original size:19 final size:19
Alignment explanation
Indices: 31340940--31341045 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 19
31340930 AAAATCATAA
*
31340940 ATAAATAATTATAAAACTT
1 ATAAAAAATTATAAAACTT
31340959 ATAAAAAATTCATAAAAGCTT
1 ATAAAAAATT-ATAAAA-CTT
** *
31340980 ATAAATAAACCATAAATA-AT
1 ATAAA-AAATTATAAA-ACTT
* *
31341000 ATTAAAAAA-TATATGAACCT
1 A-TAAAAAATTATA-AAACTT
*
31341020 AT-AAAACTTATAAAAACTT
1 ATAAAAAATTAT-AAAACTT
31341039 ATAAAAA
1 ATAAAAA
31341046 TTCACAAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
18 4 0.06
19 23 0.34
20 19 0.28
21 17 0.25
22 4 0.06
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.29
Consensus pattern (19 bp):
ATAAAAAATTATAAAACTT
Found at i:31340993 original size:21 final size:20
Alignment explanation
Indices: 31340950--31340995 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
31340940 ATAAATAATT
*
31340950 ATAAAACTTATAAAAAATTC
1 ATAAAACTTATAAAAAATCC
31340970 ATAAAAGCTTATAAATAAA-CC
1 ATAAAA-CTTATAAA-AAATCC
31340991 ATAAA
1 ATAAA
31340996 TAATATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.26
21 14 0.61
22 3 0.13
ACGTcount: A:0.61, C:0.11, G:0.02, T:0.26
Consensus pattern (20 bp):
ATAAAACTTATAAAAAATCC
Found at i:31341035 original size:10 final size:10
Alignment explanation
Indices: 31341022--31341065 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
31341012 ATGAACCTAT
31341022 AAAACTTATA
1 AAAACTTATA
31341032 AAAACTTATA
1 AAAACTTATA
*
31341042 AAAA-TTCACA
1 AAAACTT-ATA
*
31341052 AAAACCTATA
1 AAAACTTATA
31341062 AAAA
1 AAAA
31341066 TGTAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 2 0.07
10 26 0.90
11 1 0.03
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAACTTATA
Found at i:31341074 original size:20 final size:19
Alignment explanation
Indices: 31341015--31341075 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
31341005 AAAATATATG
* *
31341015 AACCTATAAAACTTATAAA
1 AACCTATAAAAATTAAAAA
* *
31341034 AACTTATAAAAATTCACAAA
1 AACCTATAAAAATT-AAAAA
31341054 AACCTATAAAAATGTAAAAA
1 AACCTATAAAAAT-TAAAAA
31341074 AA
1 AA
31341076 AATATAAAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 12 0.34
20 22 0.63
21 1 0.03
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.23
Consensus pattern (19 bp):
AACCTATAAAAATTAAAAA
Found at i:31341786 original size:10 final size:10
Alignment explanation
Indices: 31341773--31341855 Score: 66
Period size: 10 Copynumber: 8.4 Consensus size: 10
31341763 TATATTACAA
31341773 TTTTATAATT
1 TTTTATAATT
31341783 TTTTATAA--
1 TTTTATAATT
**
31341791 TTTTATAAGC
1 TTTTATAATT
31341801 TTTTAT-ATAT
1 TTTTATAAT-T
*
31341811 TCTTATAATT
1 TTTTATAATT
*
31341821 TTTTATAA-G
1 TTTTATAATT
31341830 TTTTATAAGTT
1 TTTTATAA-TT
*
31341841 TTTTAATGATT
1 TTTT-ATAATT
31341852 TTTT
1 TTTT
31341856 TTTATTTTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
8 8 0.14
9 9 0.15
10 27 0.46
11 12 0.20
12 3 0.05
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:31341853 original size:20 final size:18
Alignment explanation
Indices: 31341771--31341845 Score: 96
Period size: 20 Copynumber: 3.9 Consensus size: 18
31341761 AATATATTAC
31341771 AATTTTATAATTTTTTAT
1 AATTTTATAATTTTTTAT
**
31341789 AATTTTATAAGCTTTTAT
1 AATTTTATAATTTTTTAT
31341807 ATATTCTTATAATTTTTTAT
1 A-ATT-TTATAATTTTTTAT
31341827 AAGTTTTATAAGTTTTTTA
1 AA-TTTTATAA-TTTTTTA
31341846 ATGATTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
18 17 0.35
19 10 0.20
20 22 0.45
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (18 bp):
AATTTTATAATTTTTTAT
Found at i:31344492 original size:16 final size:17
Alignment explanation
Indices: 31344471--31344502 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
31344461 GTTTGTAATC
31344471 TCATAAA-TGTTTGTTT
1 TCATAAATTGTTTGTTT
31344487 TCATAAATTGTTTGTT
1 TCATAAATTGTTTGTT
31344503 GAACGTCGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.56
Consensus pattern (17 bp):
TCATAAATTGTTTGTTT
Found at i:31363501 original size:21 final size:21
Alignment explanation
Indices: 31363471--31363543 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
31363461 GTTTGCGTGC
31363471 TGAAAAAGTCCCTTTACAGTT
1 TGAAAAAGTCCCTTTACAGTT
* *** * *
31363492 TGAAATAGTCACCAAGACTG-C
1 TGAAAAAGTC-CCTTTACAGTT
31363513 TGAAAAAGTCCCTTTACAGTT
1 TGAAAAAGTCCCTTTACAGTT
*
31363534 TGAAATAGTC
1 TGAAAAAGTC
31363544 ACCAAGACAG
Statistics
Matches: 37, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
20 5 0.14
21 27 0.73
22 5 0.14
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (21 bp):
TGAAAAAGTCCCTTTACAGTT
Found at i:31363527 original size:42 final size:42
Alignment explanation
Indices: 31363468--31363551 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
31363458 TATGTTTGCG
31363468 TGCTGAAAAAGTCCCTTTACAGTTTGAAATAGTCACCAAGAC
1 TGCTGAAAAAGTCCCTTTACAGTTTGAAATAGTCACCAAGAC
31363510 TGCTGAAAAAGTCCCTTTACAGTTTGAAATAGTCACCAAGAC
1 TGCTGAAAAAGTCCCTTTACAGTTTGAAATAGTCACCAAGAC
31363552 AGTGGTACAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (42 bp):
TGCTGAAAAAGTCCCTTTACAGTTTGAAATAGTCACCAAGAC
Found at i:31367720 original size:15 final size:14
Alignment explanation
Indices: 31367700--31367738 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
31367690 GAGATACCAA
*
31367700 CCTTTTCATTGATAT
1 CCTTTTCAAT-ATAT
31367715 CCTTTTCGAATATAT
1 CCTTTTC-AATATAT
31367730 CCTTTTCAA
1 CCTTTTCAA
31367739 CCTTATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.49
Consensus pattern (14 bp):
CCTTTTCAATATAT
Found at i:31368117 original size:76 final size:75
Alignment explanation
Indices: 31367953--31368117 Score: 177
Period size: 76 Copynumber: 2.2 Consensus size: 75
31367943 GTGCTAGTTA
* * * * * * *
31367953 GATAAATCGACGATGTCATATGTGTGTCGAGCATTAGTTAGATGTACCAACAATGAGTTGCGCCT
1 GATAAATCGACAATATCAAATGTGTGCCCAGCACTAGTTAGATGTACCAACAATGAGTTGCGCCC
*
31368018 AGTGCTAATC
66 AGCGCTAATC
* * * *
31368028 GAGTAAATTGACAATATCAAATGTGTGCCCAGCACTAGTTGGATGTACCAATAATGAGTTGTGCC
1 GA-TAAATCGACAATATCAAATGTGTGCCCAGCACTAGTTAGATGTACCAACAATGAGTTGCGCC
**
31368093 CAGCGCTTGTC
65 CAGCGCTAATC
*
31368104 GGATAAACCGACAA
1 -GATAAATCGACAA
31368118 ATACATACAT
Statistics
Matches: 72, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
75 2 0.03
76 68 0.94
77 2 0.03
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (75 bp):
GATAAATCGACAATATCAAATGTGTGCCCAGCACTAGTTAGATGTACCAACAATGAGTTGCGCCC
AGCGCTAATC
Found at i:31369459 original size:7 final size:7
Alignment explanation
Indices: 31369447--31369474 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
31369437 ATTTGACTCG
31369447 TAAATAT
1 TAAATAT
31369454 TAAATAT
1 TAAATAT
31369461 TAAATAT
1 TAAATAT
31369468 TAAATAT
1 TAAATAT
31369475 ATACGGACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TAAATAT
Found at i:31376077 original size:17 final size:17
Alignment explanation
Indices: 31376055--31376093 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
31376045 TTTAATTAAC
31376055 TAAATAAATTTCTCAAT
1 TAAATAAATTTCTCAAT
31376072 TAAATAAATTTCTCAAT
1 TAAATAAATTTCTCAAT
*
31376089 CAAAT
1 TAAAT
31376094 TTTAATTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATAAATTTCTCAAT
Found at i:31380310 original size:24 final size:23
Alignment explanation
Indices: 31380283--31380329 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
31380273 TGAATAGTGT
31380283 AAGAATATATATATACATAT-TATA
1 AAGAATATATA-A-ACATATATATA
*
31380307 AAGAATGTATAAACATATATATA
1 AAGAATATATAAACATATATATA
31380330 GATTATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 5 0.24
24 10 0.48
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (23 bp):
AAGAATATATAAACATATATATA
Found at i:31380425 original size:61 final size:63
Alignment explanation
Indices: 31380310--31380435 Score: 138
Period size: 61 Copynumber: 2.0 Consensus size: 63
31380300 TATTATAAAG
** *
31380310 AATGTATAAACATATATATAGATTATAAAATATGAAAAATGTATAGATATTATAA-AAT-ATA
1 AATGTATAAACATATATATAGATTATAAAATATGAAAAATAAATAGATAATATAATAATAATA
*
31380371 AATGTATATACATATATA-A-ATATATAAAAACTATG-AAAATAAAATA-ATAATATAATAATAA
1 AATGTATAAACATATATATAGAT-TAT-AAAA-TATGAAAAAT-AAATAGATAATATAATAATAA
31380432 TA
62 TA
31380434 AA
1 AA
31380436 AGATTTATAT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
59 2 0.04
60 4 0.07
61 34 0.62
62 10 0.18
63 5 0.09
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.33
Consensus pattern (63 bp):
AATGTATAAACATATATATAGATTATAAAATATGAAAAATAAATAGATAATATAATAATAATA
Found at i:31381755 original size:86 final size:83
Alignment explanation
Indices: 31381626--31381803 Score: 239
Period size: 86 Copynumber: 2.1 Consensus size: 83
31381616 CAAATTTAGA
* * *
31381626 GAGATAAGACTGGATGCGATCTGCTCTAATGCAACTTCAGAGAGATAAGATCTGTAATTTTTAAT
1 GAGATAAGACTAGATGCGATCTACTCTAATGCAACTTCAGAGAGATAAAATCTG--A-TTTTAAT
*
31381691 CCACCCCACTGCAACCTCAGG
63 CCACCCCACTGCAACCTCAAG
** *
31381712 GAGATAAGACTAGATGCGATCTACTCTTCTGCAACTTCAGAGAGATAAAATCTGATTTTAATCCG
1 GAGATAAGACTAGATGCGATCTACTCTAATGCAACTTCAGAGAGATAAAATCTGATTTTAATCCA
** *
31381777 CTTCACTGCAACTTCAAG
66 CCCCACTGCAACCTCAAG
31381795 GAGATAAGA
1 GAGATAAGA
31381804 TTGATTTCTT
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
83 32 0.39
84 1 0.01
86 49 0.60
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (83 bp):
GAGATAAGACTAGATGCGATCTACTCTAATGCAACTTCAGAGAGATAAAATCTGATTTTAATCCA
CCCCACTGCAACCTCAAG
Found at i:31381821 original size:86 final size:85
Alignment explanation
Indices: 31381655--31382102 Score: 364
Period size: 86 Copynumber: 5.3 Consensus size: 85
31381645 TCTGCTCTAA
* * *
31381655 TGCAACTTCAGAGAGATAAGATCTGTAATTTTTAATCCACCCCACTGCAACCTCAGGGAGATAAG
1 TGCAACTTCAGAGAGATAAGATCTG--A-TTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAG
* * * * *
31381720 ACTAGA-TGCGATCT-ACTCT--TC
63 A-TTGATTTC-TTCTGTCTCTCCAC
* * *
31381741 TGCAACTTCAGAGAGATAAAATCTGATTTTAATCCGCTTCACTGCAACTTCAAGGAGATAAGATT
1 TGCAACTTCAGAGAGATAAGATCTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATT
31381806 GATTTCTTCTGTCTACTCCAC
66 GATTTCTTCTGTCT-CTCCAC
* * * * ** *
31381827 TGCAACTTCAGGGAGATAAGA-CTGGA-TGTGATCTGCTCTTCTGCAACTTCAGAGAGATAAGAT
1 TGCAACTTCAGAGAGATAAGATCT-GATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGAT
* ** * *
31381890 CTAATTT-TAAT-CCGCTCCAC
65 -TGATTTCTTCTGTCTCTCCAC
* * ** *
31381910 TGCAACTTCAGGGAGATAGGAT-TGATTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAG
1 TGCAACTTCAGAGAGATAAGATCTGA-TT-TT-AATCCGCTCCACTGCAACTTCAGGGAGATAAG
* * *
31381974 ATTGGA-TGCGATCTG-CTCT--AT
63 ATT-GATTTC-TTCTGTCTCTCCAC
* * *
31381995 TGCAACTTTAGAAAGATAAGATCTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATT
1 TGCAACTTCAGAGAGATAAGATCTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATT
31382060 GATTTCTTCTGTCTGCTCCAC
66 GATTTCTTCTGTCT-CTCCAC
*
31382081 TGCAACTTCAGGGAGATAAGAT
1 TGCAACTTCAGAGAGATAAGAT
31382103 TGGATGCGAT
Statistics
Matches: 286, Mismatches: 54, Indels: 44
0.74 0.14 0.11
Matches are distributed among these distances:
82 14 0.05
83 98 0.34
84 9 0.03
85 57 0.20
86 104 0.36
87 4 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (85 bp):
TGCAACTTCAGAGAGATAAGATCTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATT
GATTTCTTCTGTCTCTCCAC
Found at i:31381834 original size:44 final size:44
Alignment explanation
Indices: 31381780--31382104 Score: 293
Period size: 44 Copynumber: 7.6 Consensus size: 44
31381770 TAATCCGCTT
* *
31381780 CACTGCAACTTCAAGGAGATAAGATTGATTTCTTCTGTCTACTC
1 CACTGCAACTTCAGGGAGATAAGATTGATTTCTTCTGTCTGCTC
* * **
31381824 CACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTG-CT-CT-
1 CACTGCAACTTCAGGGAGATAAGA-TTGATTTCTTCTGTCTGCTC
* * * ** *
31381866 -TCTGCAACTTCAGAGAGATAAGATCT-AATT-TT-AATCCGCTC
1 CACTGCAACTTCAGGGAGATAAGAT-TGATTTCTTCTGTCTGCTC
*
31381907 CACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCTC
1 CACTGCAACTTCAGGGAGATAAGATTGATTTCTTCTGTCTGCTC
*
31381951 CACTGCAACTTCAGGGAGATAAGATTGGA----TGC-GATCTGCTC
1 CACTGCAACTTCAGGGAGATAAGATT-GATTTCTTCTG-TCTGCTC
* * * ** ** *
31381992 TATTGCAACTTTAGAAAGATAAGATCTGA-TT-TT-AATCCGCTC
1 CACTGCAACTTCAGGGAGATAAGAT-TGATTTCTTCTGTCTGCTC
*
31382034 CACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCTC
1 CACTGCAACTTCAGGGAGATAAGATTGATTTCTTCTGTCTGCTC
31382078 CACTGCAACTTCAGGGAGATAAGATTG
1 CACTGCAACTTCAGGGAGATAAGATTG
31382105 GATGCGATCT
Statistics
Matches: 222, Mismatches: 41, Indels: 36
0.74 0.14 0.12
Matches are distributed among these distances:
39 2 0.01
40 6 0.03
41 56 0.25
42 52 0.23
43 7 0.03
44 88 0.40
45 11 0.05
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (44 bp):
CACTGCAACTTCAGGGAGATAAGATTGATTTCTTCTGTCTGCTC
Found at i:31382133 original size:127 final size:127
Alignment explanation
Indices: 31381696--31382129 Score: 710
Period size: 127 Copynumber: 3.4 Consensus size: 127
31381686 TTAATCCACC
* * * *
31381696 CCACTGCAACCTCAGGGAGATAAGACTAGATGCGATCTACTCTTCTGCAACTTCAGAGAGATAAA
1 CCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTTCTGCAACTTCAGAGAGATAAG
* * * *
31381761 ATCTGATTTTAATCCGCTTCACTGCAACTTCAAGGAGATAAGATTGATTTCTTCTGTCTACT
66 ATCTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCT
*
31381823 CCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTTCTGCAACTTCAGAGAGATAAG
1 CCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTTCTGCAACTTCAGAGAGATAAG
*
31381888 ATCTAATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCT
66 ATCTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCT
* * *
31381950 CCACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTAT-TGCAACTTTAGAAAGATAA
1 CCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCT-TCTGCAACTTCAGAGAGATAA
31382014 GATCTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCT
65 GATCTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCT
*
31382077 CCACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTAT-TGCAACTT
1 CCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCT-TCTGCAACTT
31382130 TAGATGATTT
Statistics
Matches: 291, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
127 290 1.00
128 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (127 bp):
CCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTTCTGCAACTTCAGAGAGATAAG
ATCTGATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTGCT
Found at i:31382181 original size:74 final size:75
Alignment explanation
Indices: 31382059--31382203 Score: 240
Period size: 74 Copynumber: 1.9 Consensus size: 75
31382049 GAGATAGGAT
* *
31382059 TGATTTCTTCTGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGATGCGATCTGCTCTAT-T
1 TGATTTCTTCTGTCTACTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCT-TCT
31382123 GCAACTTTAGA
65 GCAACTTTAGA
*
31382134 TGATTTCTTC-GTCTACTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTGCTCTTCTG
1 TGATTTCTTCTGTCTACTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTTCTG
31382198 CAACTT
66 CAACTT
31382204 CAGAGAGATA
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
73 1 0.02
74 55 0.83
75 10 0.15
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (75 bp):
TGATTTCTTCTGTCTACTCCACTGCAACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTTCTG
CAACTTTAGA
Found at i:31382254 original size:42 final size:41
Alignment explanation
Indices: 31382149--31382255 Score: 126
Period size: 42 Copynumber: 2.6 Consensus size: 41
31382139 TCTTCGTCTA
* * *
31382149 CTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTGAATGTAATCCG
** * *
31382190 CTCTTCTGCAACTTCAGAGAGATAAGATCT-AATTTTAATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CTGAA-TGTAATCCG
31382232 CTCCACTGCAACTTCAGGGAGATA
1 CTCCACTGCAACTTCAGGGAGATA
31382256 GGATTGATTT
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 25 0.46
42 29 0.54
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (41 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTGAATGTAATCCG
Found at i:31386973 original size:16 final size:16
Alignment explanation
Indices: 31386952--31386986 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
31386942 TTCTATAATG
31386952 AAATGTCATGCAGTCA
1 AAATGTCATGCAGTCA
31386968 AAATGTCATGCAGTCA
1 AAATGTCATGCAGTCA
31386984 AAA
1 AAA
31386987 CAAAACACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (16 bp):
AAATGTCATGCAGTCA
Found at i:31387934 original size:2 final size:2
Alignment explanation
Indices: 31387927--31387952 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31387917 GCTTTTATTT
31387927 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
31387953 AAATCTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31390053 original size:3 final size:3
Alignment explanation
Indices: 31390045--31390078 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
31390035 ATACGTAAGT
*
31390045 ATA ATA ATA ATA ATGA ATA ATA ATG ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
31390079 GTGTAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:31392836 original size:16 final size:16
Alignment explanation
Indices: 31392814--31392852 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
31392804 GTTTGGTTCA
31392814 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
*
31392830 GTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
31392846 CTGTAAT
1 CTGTAAT
31392853 AGTAATTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.05, G:0.31, T:0.28
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:31393098 original size:24 final size:23
Alignment explanation
Indices: 31393071--31393133 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 23
31393061 ATATTTTAAC
31393071 ATAAATATTATTAAATATAATTTA
1 ATAAA-ATTATTAAATATAATTTA
*
31393095 ATAAAA--A--ATATATAATTTA
1 ATAAAATTATTAAATATAATTTA
*
31393114 ATAAAATTCTT-AATATAATT
1 ATAAAATTATTAAATATAATT
31393134 ATTCTTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
19 17 0.53
21 1 0.03
22 8 0.25
23 1 0.03
24 5 0.16
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAAAATTATTAAATATAATTTA
Found at i:31397466 original size:17 final size:18
Alignment explanation
Indices: 31397436--31397470 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
31397426 TCTTAAGACC
31397436 GTTTTTAATAATTTTTAT
1 GTTTTTAATAATTTTTAT
*
31397454 GTTTTTGAT-ATTTTTAT
1 GTTTTTAATAATTTTTAT
31397471 AGCTTAATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (18 bp):
GTTTTTAATAATTTTTAT
Found at i:31403430 original size:79 final size:80
Alignment explanation
Indices: 31403276--31403430 Score: 244
Period size: 81 Copynumber: 1.9 Consensus size: 80
31403266 TACTTGCTCA
*
31403276 TCAATCAAGAAGTTTTTTGTGTCCTTCAACTTTTATTTTTTTTAGTAACTTACACAACTTAAAAA
1 TCAATCAAGAAGTTTTTTGTGTCCTTCAACTTTTATTTTCTTTAGTAACTTACACAACTTAAAAA
*
31403341 TGGCACTTCTAGTCT
66 TGGAACTTCTAGTCT
*
31403356 TCAATCAAGGAGTTTTTTTGTGT-CTGTCAACTTTTATTTTCTTTAGTAAC-T-CACAACTTAAA
1 TCAATCAAGAAG-TTTTTTGTGTCCT-TCAACTTTTATTTTCTTTAGTAACTTACACAACTTAAA
31403418 AATGGAACTTCTA
64 AATGGAACTTCTA
31403431 AACATTCTTA
Statistics
Matches: 70, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
79 23 0.33
80 14 0.20
81 33 0.47
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (80 bp):
TCAATCAAGAAGTTTTTTGTGTCCTTCAACTTTTATTTTCTTTAGTAACTTACACAACTTAAAAA
TGGAACTTCTAGTCT
Found at i:31417163 original size:6 final size:7
Alignment explanation
Indices: 31417153--31417184 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
31417143 TTTTTTCGTT
31417153 TTTTTCA
1 TTTTTCA
31417160 TTTTTCA
1 TTTTTCA
31417167 TTTTTCA
1 TTTTTCA
31417174 TTTTT-A
1 TTTTTCA
31417180 TTTTT
1 TTTTT
31417185 TTATTATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTCA
Found at i:31417267 original size:17 final size:19
Alignment explanation
Indices: 31417235--31417281 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
31417225 AATTCTTACG
31417235 TATATTTTTAATATATACA
1 TATATTTTTAATATATACA
31417254 TATATTTTTAATATATACA
1 TATATTTTTAATATATACA
31417273 TAT-TTTTTA
1 TATATTTTTA
31417282 TAACTATGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATTTTTAATATATACA
Found at i:31418908 original size:21 final size:21
Alignment explanation
Indices: 31418860--31418966 Score: 108
Period size: 21 Copynumber: 5.1 Consensus size: 21
31418850 CGTGTTTACT
* *
31418860 TTTC-GTTTAACTCTCACGAG
1 TTTCTGTTTAACTCTTATGAG
* *
31418880 CTTCTGTTTAACTCATATGAG
1 TTTCTGTTTAACTCTTATGAG
* * *
31418901 TTTATGTTTAACCCTTATGGG
1 TTTCTGTTTAACTCTTATGAG
* *
31418922 TTTCTGTTTAGCTCTTTTGAG
1 TTTCTGTTTAACTCTTATGAG
* *
31418943 TTTCTGTTTAACCCTTATGGG
1 TTTCTGTTTAACTCTTATGAG
31418964 TTT
1 TTT
31418967 TCGTTCAGCT
Statistics
Matches: 68, Mismatches: 18, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
20 3 0.04
21 65 0.96
ACGTcount: A:0.17, C:0.18, G:0.17, T:0.49
Consensus pattern (21 bp):
TTTCTGTTTAACTCTTATGAG
Found at i:31418977 original size:42 final size:43
Alignment explanation
Indices: 31418881--31419036 Score: 147
Period size: 42 Copynumber: 3.7 Consensus size: 43
31418871 TCTCACGAGC
* * * *
31418881 TTCTGTTTAACTCATATGAGTTTATGTTTAACCCTTATGGG-T
1 TTCTGTTCAGCTCTTATGAGTTTCTGTTTAACCCTTATGGGTT
* *
31418923 TTCTGTTTAGCTCTTTTGAGTTTCTGTTTAACCCTTATGGGTT
1 TTCTGTTCAGCTCTTATGAGTTTCTGTTTAACCCTTATGGGTT
** * * *
31418966 TTC-GTTCAGCTCTTACAAGCTTCTATTCAACCCTTATGGG-T
1 TTCTGTTCAGCTCTTATGAGTTTCTGTTTAACCCTTATGGGTT
* * * * *
31419007 TTCTATTTAGCACTTATGTGCTTCTGTTTA
1 TTCTGTTCAGCTCTTATGAGTTTCTGTTTA
31419037 GCCTTCGGGC
Statistics
Matches: 93, Mismatches: 19, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
41 4 0.04
42 85 0.91
43 4 0.04
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.48
Consensus pattern (43 bp):
TTCTGTTCAGCTCTTATGAGTTTCTGTTTAACCCTTATGGGTT
Found at i:31419013 original size:21 final size:21
Alignment explanation
Indices: 31418881--31419010 Score: 73
Period size: 21 Copynumber: 6.2 Consensus size: 21
31418871 TCTCACGAGC
* * * *
31418881 TTCTGTTTAACTCATATGAGT
1 TTCTGTTCAACCCTTATGGGT
* *
31418902 TTATGTTTAACCCTTATGGGT
1 TTCTGTTCAACCCTTATGGGT
* * * * *
31418923 TTCTGTTTAGCTCTTTTGAGT
1 TTCTGTTCAACCCTTATGGGT
*
31418944 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTCAACCCTTATGGGT
* * *** *
31418965 TT-TCGTTCAGCTCTTACAAGC
1 TTCT-GTTCAACCCTTATGGGT
*
31418986 TTCTATTCAACCCTTATGGGT
1 TTCTGTTCAACCCTTATGGGT
31419007 TTCT
1 TTCT
31419011 ATTTAGCACT
Statistics
Matches: 80, Mismatches: 27, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
20 1 0.01
21 78 0.98
22 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.48
Consensus pattern (21 bp):
TTCTGTTCAACCCTTATGGGT
Found at i:31419022 original size:21 final size:21
Alignment explanation
Indices: 31418984--31419038 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
31418974 GCTCTTACAA
* * *
31418984 GCTTCTATTCAACCCTTATGG
1 GCTTCTATTTAGCACTTATGG
* *
31419005 GTTTCTATTTAGCACTTATGT
1 GCTTCTATTTAGCACTTATGG
*
31419026 GCTTCTGTTTAGC
1 GCTTCTATTTAGC
31419039 CTTCGGGCTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.45
Consensus pattern (21 bp):
GCTTCTATTTAGCACTTATGG
Found at i:31428283 original size:7 final size:7
Alignment explanation
Indices: 31428273--31428298 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31428263 TTATATACAT
31428273 AATACTA
1 AATACTA
31428280 AATACTA
1 AATACTA
31428287 AATACTA
1 AATACTA
31428294 AATAC
1 AATAC
31428299 CAATCGACTA
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:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:31428505 original size:20 final size:20
Alignment explanation
Indices: 31428468--31428505 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31428458 TTTATTTTTA
*
31428468 AAAATCTACATAATAATTAT
1 AAAATCTACATAAAAATTAT
31428488 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
31428506 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTAT
Found at i:31429438 original size:11 final size:11
Alignment explanation
Indices: 31429424--31429475 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
31429414 TGGAAGGAGT
*
31429424 TTGAGAGCAAA
1 TTGAGAGGAAA
31429435 TTGAGAGGAAA
1 TTGAGAGGAAA
*
31429446 TTTAGAGGAAA
1 TTGAGAGGAAA
31429457 TTGAGAGGAAA
1 TTGAGAGGAAA
31429468 TTTGAGAG
1 -TTGAGAG
31429476 AGGATTAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
11 30 0.81
12 7 0.19
ACGTcount: A:0.42, C:0.02, G:0.33, T:0.23
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:31429443 original size:22 final size:23
Alignment explanation
Indices: 31429423--31429475 Score: 90
Period size: 22 Copynumber: 2.3 Consensus size: 23
31429413 TTGGAAGGAG
31429423 TTTGAGAGCAAATTGAGAGGAAA
1 TTTGAGAGCAAATTGAGAGGAAA
*
31429446 TTT-AGAGGAAATTGAGAGGAAA
1 TTTGAGAGCAAATTGAGAGGAAA
31429468 TTTGAGAG
1 TTTGAGAG
31429476 AGGATTAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 21 0.75
23 7 0.25
ACGTcount: A:0.42, C:0.02, G:0.32, T:0.25
Consensus pattern (23 bp):
TTTGAGAGCAAATTGAGAGGAAA
Found at i:31431897 original size:92 final size:92
Alignment explanation
Indices: 31431739--31431925 Score: 347
Period size: 92 Copynumber: 2.0 Consensus size: 92
31431729 TCAGCTTGAG
31431739 ACACAATAATCCTTATCCAAGCTCGACCTAAGTTGGGTCGAGCCTATCAGGTCAAGCGAACAACC
1 ACACAATAATCCTTATCCAAGCTCGACCTAAGTTGGGTCGAGCCTATCAGGTCAAGCGAACAACC
31431804 CGATTTTTGGATAGGTCTAAGCCCAAT
66 CGATTTTTGGATAGGTCTAAGCCCAAT
* * *
31431831 ACACAATAATCCTTATCCAAGCTCGACCTAAGTTGGGTCGAGCGTATCAGGTCAAGCGGACTACC
1 ACACAATAATCCTTATCCAAGCTCGACCTAAGTTGGGTCGAGCCTATCAGGTCAAGCGAACAACC
31431896 CGATTTTTGGATAGGTCTAAGCCCAAT
66 CGATTTTTGGATAGGTCTAAGCCCAAT
31431923 ACA
1 ACA
31431926 GCCTAATAAA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (92 bp):
ACACAATAATCCTTATCCAAGCTCGACCTAAGTTGGGTCGAGCCTATCAGGTCAAGCGAACAACC
CGATTTTTGGATAGGTCTAAGCCCAAT
Found at i:31432515 original size:128 final size:128
Alignment explanation
Indices: 31432358--31432613 Score: 467
Period size: 128 Copynumber: 2.0 Consensus size: 128
31432348 AATAATATTT
* *
31432358 TTAGCAGAACACTTGTTATTTCAGAAATTACGCACAGAGCTTATTTATTTTACATAATAGTTCTT
1 TTAGCAGAACACTTGTTATTTCAAAAATTACGCACAGAGCTTATTTATTTTACATAATAGCTCTT
* *
31432423 AACTTGATCTTGTTTGAAAACTTTTGATTTCAGTGAGTGTTTGGAAAATATAAATATGAAAAA
66 AACTTGATCTCGTTTGAAAACTTCTGATTTCAGTGAGTGTTTGGAAAATATAAATATGAAAAA
*
31432486 TTAGCAGAACACTTGTTATTTCAAAAATTACGCATAGAGCTTATTTATTTTACATAATAGCTCTT
1 TTAGCAGAACACTTGTTATTTCAAAAATTACGCACAGAGCTTATTTATTTTACATAATAGCTCTT
31432551 AACTTGATCTCGTTTGAAAACTTCTGATTTCAGTGAGTGTTTGGAAAATATAAATATGAAAAA
66 AACTTGATCTCGTTTGAAAACTTCTGATTTCAGTGAGTGTTTGGAAAATATAAATATGAAAAA
31432614 CATTCGTTAG
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 123 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (128 bp):
TTAGCAGAACACTTGTTATTTCAAAAATTACGCACAGAGCTTATTTATTTTACATAATAGCTCTT
AACTTGATCTCGTTTGAAAACTTCTGATTTCAGTGAGTGTTTGGAAAATATAAATATGAAAAA
Found at i:31435139 original size:42 final size:41
Alignment explanation
Indices: 31435086--31435209 Score: 160
Period size: 42 Copynumber: 3.0 Consensus size: 41
31435076 ATGCTATCAT
31435086 ATATCGATGCTAATAG-CCTAGCTATGGTCTTACACGAATCTC
1 ATATCGATGCTAAT-GTCCTAGC-ATGGTCTTACACGAATCTC
* *
31435128 ATATCGATGCTAATGTCCCAAACATGGTCTTACACGAATCTC
1 ATATCGATGCTAATGT-CCTAGCATGGTCTTACACGAATCTC
* * *
31435170 ATATCGATGCCAATGTTCTAGACATGGTCTTACACAAATC
1 ATATCGATGCTAATGTCCTAG-CATGGTCTTACACGAATC
31435210 ACATCTCAGT
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
41 3 0.04
42 65 0.90
43 4 0.06
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (41 bp):
ATATCGATGCTAATGTCCTAGCATGGTCTTACACGAATCTC
Found at i:31438634 original size:19 final size:19
Alignment explanation
Indices: 31438610--31438665 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
31438600 AATTAAACCA
31438610 TTAAAATTTTGATTACATG
1 TTAAAATTTTGATTACATG
* * *
31438629 TTAAAATTCATAATTTATATG
1 TTAAAATT-TTGA-TTACATG
*
31438650 TGAAAATTTTGATTAC
1 TTAAAATTTTGATTAC
31438666 TTGGAATACA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
19 11 0.39
20 4 0.14
21 13 0.46
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.46
Consensus pattern (19 bp):
TTAAAATTTTGATTACATG
Found at i:31441545 original size:49 final size:49
Alignment explanation
Indices: 31441481--31441583 Score: 206
Period size: 49 Copynumber: 2.1 Consensus size: 49
31441471 TTCTCTCTTT
31441481 TATCAAGTTCTTTCAAGGTATCATTCGCCATTTGATTCTGGATTTTGTC
1 TATCAAGTTCTTTCAAGGTATCATTCGCCATTTGATTCTGGATTTTGTC
31441530 TATCAAGTTCTTTCAAGGTATCATTCGCCATTTGATTCTGGATTTTGTC
1 TATCAAGTTCTTTCAAGGTATCATTCGCCATTTGATTCTGGATTTTGTC
31441579 TATCA
1 TATCA
31441584 TGGCTTCCGC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 54 1.00
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (49 bp):
TATCAAGTTCTTTCAAGGTATCATTCGCCATTTGATTCTGGATTTTGTC
Found at i:31449556 original size:16 final size:17
Alignment explanation
Indices: 31449535--31449567 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31449525 ATAATTTTAC
*
31449535 TTTAAAT-TTTAATTAT
1 TTTAAATATATAATTAT
31449551 TTTAAATATATAATTAT
1 TTTAAATATATAATTAT
31449568 CACAAAATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAAATATATAATTAT
Found at i:31449585 original size:43 final size:44
Alignment explanation
Indices: 31449536--31449632 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
31449526 TAATTTTACT
*
31449536 TTAAATTTTAATTA-TTTTAAATATATAATTATCACAAAATCTA
1 TTAAATTTTAATCATTTTTAAATATATAATTATCACAAAATCTA
* * **
31449579 TTAAATTTTAATCATTTTTAAATGTATAATTATGACAACTTCTA
1 TTAAATTTTAATCATTTTTAAATATATAATTATCACAAAATCTA
*
31449623 TTATATTTTA
1 TTAAATTTTA
31449633 TTTTTAACTA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 13 0.28
44 34 0.72
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.49
Consensus pattern (44 bp):
TTAAATTTTAATCATTTTTAAATATATAATTATCACAAAATCTA
Found at i:31449658 original size:21 final size:21
Alignment explanation
Indices: 31449632--31449676 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
31449622 ATTATATTTT
31449632 ATTTTTA-ACTAATAATTTTAA
1 ATTTTTATA-TAATAATTTTAA
*
31449653 ATTTTTATTATAATTATTTTAA
1 ATTTTTA-TATAATAATTTTAA
31449675 AT
1 AT
31449677 ATGAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 13 0.62
23 1 0.05
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATTTTTATATAATAATTTTAA
Found at i:31449938 original size:21 final size:21
Alignment explanation
Indices: 31449914--31449953 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31449904 TATAACACGG
31449914 TATTAA-AATATGATTAAAAAA
1 TATTAATAA-ATGATTAAAAAA
*
31449935 TATTAATAAATGGTTAAAA
1 TATTAATAAATGATTAAAA
31449954 TGAGTGATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (21 bp):
TATTAATAAATGATTAAAAAA
Found at i:31450096 original size:2 final size:2
Alignment explanation
Indices: 31450089--31450117 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31450079 AGACATTTGC
31450089 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 A
31450118 ATTTTCGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31450469 original size:4 final size:4
Alignment explanation
Indices: 31450460--31450488 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
31450450 AGGCTCTTGT
31450460 AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA A
31450489 GAATAATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:31450673 original size:5 final size:5
Alignment explanation
Indices: 31450663--31450688 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31450653 TGAGCATTCG
31450663 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
31450689 GATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:31451519 original size:9 final size:9
Alignment explanation
Indices: 31451505--31451541 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
31451495 TATAGTTTGA
31451505 TATTCGAAT
1 TATTCGAAT
31451514 TATTCGAAT
1 TATTCGAAT
*
31451523 TATTCGAGT
1 TATTCGAAT
31451532 TATTCGAAT
1 TATTCGAAT
31451541 T
1 T
31451542 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:31451614 original size:9 final size:9
Alignment explanation
Indices: 31451597--31451627 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
31451587 TCGAGTTGAT
31451597 TCGAATAAC
1 TCGAATAAC
*
31451606 TCGATTAAC
1 TCGAATAAC
31451615 TCGAATAAC
1 TCGAATAAC
31451624 TCGA
1 TCGA
31451628 TTAGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:31454858 original size:28 final size:27
Alignment explanation
Indices: 31454824--31454921 Score: 144
Period size: 27 Copynumber: 3.6 Consensus size: 27
31454814 GGGGTATAAC
31454824 AGTCATTTTACCCTATGGGGGATATTTT
1 AGTCATTTTACCCTATGGGGG-TATTTT
*
31454852 AGTCATTTTACCCTAT-GGGGTATTTC
1 AGTCATTTTACCCTATGGGGGTATTTT
* *
31454878 AGTTATTTTACTCTATGGGGGTATTTT
1 AGTCATTTTACCCTATGGGGGTATTTT
*
31454905 GGTCATTTTACCCTATG
1 AGTCATTTTACCCTATG
31454922 AAGTATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
26 19 0.31
27 27 0.44
28 16 0.26
ACGTcount: A:0.19, C:0.15, G:0.20, T:0.45
Consensus pattern (27 bp):
AGTCATTTTACCCTATGGGGGTATTTT
Found at i:31454885 original size:26 final size:26
Alignment explanation
Indices: 31454796--31454930 Score: 128
Period size: 27 Copynumber: 5.0 Consensus size: 26
31454786 ATGGCCATAA
* **
31454796 CAGTCATTTCATCTCCTA-GGGGTATAA
1 CAGTCATTTTA-C-CCTATGGGGTATTT
31454823 CAGTCATTTTACCCTATGGGGGATATTT
1 CAGTCATTTTACCCTAT-GGGG-TATTT
*
31454851 TAGTCATTTTACCCTATGGGGTATTT
1 CAGTCATTTTACCCTATGGGGTATTT
* *
31454877 CAGTTATTTTACTCTATGGGGGTATTT
1 CAGTCATTTTACCCTAT-GGGGTATTT
** **
31454904 TGGTCATTTTACCCTATGAAGTATTT
1 CAGTCATTTTACCCTATGGGGTATTT
31454930 C
1 C
31454931 GGTCTATAAC
Statistics
Matches: 90, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
25 4 0.04
26 27 0.30
27 40 0.44
28 19 0.21
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.42
Consensus pattern (26 bp):
CAGTCATTTTACCCTATGGGGTATTT
Found at i:31454928 original size:53 final size:54
Alignment explanation
Indices: 31454823--31454930 Score: 164
Period size: 53 Copynumber: 2.0 Consensus size: 54
31454813 AGGGGTATAA
**
31454823 CAGTCATTTTACCCTATGGGGGATATTTTAGTCATTTTACCCTATGGGGTATTT
1 CAGTCATTTTACCCTATGGGGGATATTTTAGTCATTTTACCCTATGAAGTATTT
* * *
31454877 CAGTTATTTTACTCTATGGGGG-TATTTTGGTCATTTTACCCTATGAAGTATTT
1 CAGTCATTTTACCCTATGGGGGATATTTTAGTCATTTTACCCTATGAAGTATTT
31454930 C
1 C
31454931 GGTCTATAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 29 0.59
54 20 0.41
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.44
Consensus pattern (54 bp):
CAGTCATTTTACCCTATGGGGGATATTTTAGTCATTTTACCCTATGAAGTATTT
Found at i:31457742 original size:26 final size:27
Alignment explanation
Indices: 31457690--31457744 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
31457680 CTATTACACG
31457690 GTCATTTTACCCTGTGGGGGTATTTCA
1 GTCATTTTACCCTGTGGGGGTATTTCA
* *
31457717 GTCATTTTATCTTGT-GGGGTATTTCA
1 GTCATTTTACCCTGTGGGGGTATTTCA
31457743 GT
1 GT
31457745 GCAGATATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.45
Consensus pattern (27 bp):
GTCATTTTACCCTGTGGGGGTATTTCA
Found at i:31462178 original size:41 final size:43
Alignment explanation
Indices: 31462133--31462296 Score: 158
Period size: 44 Copynumber: 3.9 Consensus size: 43
31462123 AAGTCTCGTA
*
31462133 TATCACATA-CAATGCCATATCCCAGATATGGTCTTACATA-T
1 TATCACATATCAATGCCATATCCCAGATATGGTCTTACATACG
* *
31462174 TATCACATATCGATGCCAATAGCCCAGCA-ATGGTC-T-CATACG
1 TATCACATATCAATGCC-ATATCCCAG-ATATGGTCTTACATACG
* * * *
31462216 AATCATATATCAATGCCATATCCCAGATATGGTCTTACACAAAG
1 TATCACATATCAATGCCATATCCCAGATATGGTCTTACA-TACG
* * * * *
31462260 TCTCATATATCGATGCCATAGCCCAGCTATGGTCTTA
1 TATCACATATCAATGCCATATCCCAGATATGGTCTTA
31462297 TATGAAATCA
Statistics
Matches: 101, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
40 1 0.01
41 27 0.27
42 22 0.22
43 16 0.16
44 35 0.35
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (43 bp):
TATCACATATCAATGCCATATCCCAGATATGGTCTTACATACG
Found at i:31462243 original size:84 final size:83
Alignment explanation
Indices: 31462134--31462294 Score: 234
Period size: 84 Copynumber: 1.9 Consensus size: 83
31462124 AGTCTCGTAT
* *
31462134 ATCACATACAATGCCATATCCCAGATATGGTCTT-ACATATTATCACATATCGATGCCAATAGCC
1 ATCACATACAATGCCATATCCCAGATATGGTCTTAACAAAGTATCACATATCGATGCC-ATAGCC
31462198 CAGCAATGGTCTCATACGA
65 CAGCAATGGTCTCATACGA
* * *
31462217 ATCATATATCAATGCCATATCCCAGATATGGTCTTACACAAAGTCTCATATATCGATGCCATAGC
1 ATCACATA-CAATGCCATATCCCAGATATGGTCTTA-ACAAAGTATCACATATCGATGCCATAGC
*
31462282 CCAGCTATGGTCT
64 CCAGCAATGGTCT
31462295 TATATGAAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
83 7 0.10
84 26 0.38
85 17 0.25
86 19 0.28
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (83 bp):
ATCACATACAATGCCATATCCCAGATATGGTCTTAACAAAGTATCACATATCGATGCCATAGCCC
AGCAATGGTCTCATACGA
Found at i:31464349 original size:43 final size:43
Alignment explanation
Indices: 31464288--31464402 Score: 158
Period size: 43 Copynumber: 2.7 Consensus size: 43
31464278 GTGTCCGCCT
* * *
31464288 GTGTGAATATTTGAAATAGGGCCACATGGTCATGTGCCAAACC
1 GTGTGTATATTCGAAATAGGGCCACACGGTCATGTGCCAAACC
*
31464331 GTGTGTATATTCGAAATAGGGCCACACGGTCGTGTGCCAAACC
1 GTGTGTATATTCGAAATAGGGCCACACGGTCATGTGCCAAACC
* * * *
31464374 ATGTGTATATTCGAATTATGGACACACGG
1 GTGTGTATATTCGAAATAGGGCCACACGG
31464403 CCGTGTTGTA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (43 bp):
GTGTGTATATTCGAAATAGGGCCACACGGTCATGTGCCAAACC
Found at i:31472261 original size:6 final size:6
Alignment explanation
Indices: 31472250--31472276 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31472240 ATTAGAGAAC
31472250 AAATAT AAATAT AAATAT AAATAT AAA
1 AAATAT AAATAT AAATAT AAATAT AAA
31472277 ATTTATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATAT
Found at i:31473183 original size:2 final size:2
Alignment explanation
Indices: 31473176--31473204 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31473166 TTTGTATACT
31473176 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31473205 TAAAATACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31473631 original size:19 final size:19
Alignment explanation
Indices: 31473607--31473648 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
31473597 ATGATTTATT
31473607 CAACTATTATTATATTTGC
1 CAACTATTATTATATTTGC
31473626 CAACTATTATTATATTTGC
1 CAACTATTATTATATTTGC
31473645 CAAC
1 CAAC
31473649 ATCATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (19 bp):
CAACTATTATTATATTTGC
Found at i:31492487 original size:18 final size:18
Alignment explanation
Indices: 31492453--31492489 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31492443 TTCAGAATTA
* *
31492453 TGGGCCCACATGCCCGTG
1 TGGGCCCACACGACCGTG
31492471 TGGGCCCACACGACCGTG
1 TGGGCCCACACGACCGTG
31492489 T
1 T
31492490 CACCTACACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.38, G:0.32, T:0.16
Consensus pattern (18 bp):
TGGGCCCACACGACCGTG
Found at i:31492550 original size:21 final size:21
Alignment explanation
Indices: 31492524--31492571 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
31492514 GCCCGTGTGG
*
31492524 CCCACACGGCTTGGCCCAAAA
1 CCCACACGACTTGGCCCAAAA
*
31492545 CTCACACGACTTGGCCCAAAA
1 CCCACACGACTTGGCCCAAAA
31492566 CCCACA
1 CCCACA
31492572 TGCCCGTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.44, G:0.15, T:0.10
Consensus pattern (21 bp):
CCCACACGACTTGGCCCAAAA
Found at i:31494581 original size:40 final size:40
Alignment explanation
Indices: 31494526--31494607 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
31494516 ATTTTGCCCA
* *
31494526 GGCCCGGCCCTGG-AAAAAATAATAAGCCCGAGCCCGACCC
1 GGCCCAGCCCGGGAAAAAAATAATAAGCCCG-GCCCGACCC
*
31494566 GGCCCAGCCCGGGAAAAAAATAATAAGCCCGGCCCGGCCC
1 GGCCCAGCCCGGGAAAAAAATAATAAGCCCGGCCCGACCC
31494606 GG
1 GG
31494608 TTTTTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 21 0.55
41 17 0.45
ACGTcount: A:0.29, C:0.37, G:0.28, T:0.06
Consensus pattern (40 bp):
GGCCCAGCCCGGGAAAAAAATAATAAGCCCGGCCCGACCC
Found at i:31496643 original size:18 final size:18
Alignment explanation
Indices: 31496597--31496652 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
31496587 GGAAACCCTC
*
31496597 ATTTTTGGTAAACTTTC-C
1 ATTTTTGG-AAACTTTCTT
**
31496615 ATTTTAAGAAACTTTCTT
1 ATTTTTGGAAACTTTCTT
*
31496633 ATTTTTGGAAA-TTTATT
1 ATTTTTGGAAACTTTCTT
31496650 ATT
1 ATT
31496653 ATTATAGTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.54
Consensus pattern (18 bp):
ATTTTTGGAAACTTTCTT
Found at i:31519938 original size:18 final size:19
Alignment explanation
Indices: 31519917--31519953 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
31519907 AAAGAAAGAC
31519917 AGAAAAAGA-AATCAAAAA
1 AGAAAAAGAGAATCAAAAA
*
31519935 AGAAAAAGAGAATGAAAAA
1 AGAAAAAGAGAATCAAAAA
31519954 GAGCAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (19 bp):
AGAAAAAGAGAATCAAAAA
Found at i:31523473 original size:42 final size:42
Alignment explanation
Indices: 31523417--31523625 Score: 260
Period size: 42 Copynumber: 5.0 Consensus size: 42
31523407 CAGCGTTTAC
* * * *
31523417 AGAAAAAACA-CCGCTAAAGGTCATGTTCTTTAGCGGTGTTT
1 AGAAAAAAAAGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
* *
31523458 AGAAAAAAAAGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTT
1 AGAAAAAAAAGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
* *
31523500 A-AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGGGGCGCAT
1 AGAAAAAAAA-GCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
* * * * *
31523542 GGAGAAAAACGCCACTAAAGATCATGTTCTTTAGTGGCGCTT
1 AGAAAAAAAAGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
* *
31523584 AGAGAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
1 AGAAAAAAAAGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
31523626 TCTTCACAAA
Statistics
Matches: 150, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
41 17 0.11
42 127 0.85
43 6 0.04
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (42 bp):
AGAAAAAAAAGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT
Found at i:31524081 original size:21 final size:21
Alignment explanation
Indices: 31524057--31524124 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
31524047 TTCTTTTGAA
*
31524057 CCTCTGCTTCTCTCGTTGCAG
1 CCTCTGCTTCTCTCGCTGCAG
31524078 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCTCTCGCTGCAG
* * *
31524099 CCTCTGATTCCCTCGCTGCCG
1 CCTCTGCTTCTCTCGCTGCAG
31524120 CCTCT
1 CCTCT
31524125 TCTTTAAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.04, C:0.44, G:0.18, T:0.34
Consensus pattern (21 bp):
CCTCTGCTTCTCTCGCTGCAG
Found at i:31529919 original size:20 final size:19
Alignment explanation
Indices: 31529882--31529921 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
31529872 GTTATGTAGG
* *
31529882 TTATGTATTATGTTAGTTA
1 TTATGTATTATATAAGTTA
31529901 TTATGTTATTATATAAGTTA
1 TTATG-TATTATATAAGTTA
31529921 T
1 T
31529922 GCAAGTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (19 bp):
TTATGTATTATATAAGTTA
Found at i:31529990 original size:25 final size:25
Alignment explanation
Indices: 31529837--31530274 Score: 107
Period size: 25 Copynumber: 17.9 Consensus size: 25
31529827 NTTATTTAAG
* *
31529837 TTATGTAAGTTATTTAATTTATGTAA
1 TTATGTAAGTTATGTAAGTTATGT-A
*
31529863 GTTATGTAAGTTATGTAGGTTATGTA
1 -TTATGTAAGTTATGTAAGTTATGTA
* *
31529889 TTATGTTAGTTAT-TATGTTAT-TA
1 TTATGTAAGTTATGTAAGTTATGTA
* *
31529912 -TA--TAAGTTATGCAAGTTATATAA
1 TTATGTAAGTTATGTAAGTTATGT-A
* ** *
31529935 GTTATTTAAGTCGTGTAAATGT-TGTA
1 -TTATGTAAGTTATGTAAGT-TATGTA
31529961 TTATGTAAGTTATGT-A-TTATGTAA
1 TTATGTAAGTTATGTAAGTTATGT-A
* **
31529985 GATATGTAAG-T-TGTATTTTATGTAA
1 -TTATGTAAGTTATGTAAGTTATGT-A
* * *
31530010 GT-TCTATA-TTATGTATGTTATGTAA
1 TTATGTA-AGTTATGTAAGTTATGT-A
* * *
31530035 GTTGTGT-AG-AATGTAAGCTATGTAA
1 -TTATGTAAGTTATGTAAGTTATGT-A
**
31530060 GTTATGTAAGTGGTGT-A-TTATGTAA
1 -TTATGTAAGTTATGTAAGTTATGT-A
*
31530085 CTTGTGTAAGTTATGTAAG---T-TA
1 -TTATGTAAGTTATGTAAGTTATGTA
*
31530107 TTATGTAAGTTATGCAAGCTTA--TA
1 TTATGTAAGTTATGTAAG-TTATGTA
* *
31530131 -TA--TAAGTTATGTATTATGTAATTTA
1 TTATGTAAGTTATGTA--A-GTTATGTA
* * * *
31530156 TTATATTATTATATATAAGTTATGTAA
1 TTATGTAAGT-TATGTAAGTTATGT-A
* *
31530183 GTTAT-TATGTTAT-T-A-TATAT-AA
1 -TTATGTAAGTTATGTAAGT-TATGTA
**
31530205 GTTATGTAAGTTATGTAAGTGGTGTA
1 -TTATGTAAGTTATGTAAGTTATGTA
31530231 TTATGTAAGTTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTA
*
31530256 --A-GTTA-TTATGTAAGTTATG
1 TTATGTAAGTTATGTAAGTTATG
31530275 CAAGCTTATA
Statistics
Matches: 313, Mismatches: 54, Indels: 94
0.68 0.12 0.20
Matches are distributed among these distances:
20 7 0.02
21 46 0.15
22 14 0.04
23 28 0.09
24 22 0.07
25 122 0.39
26 19 0.06
27 42 0.13
28 8 0.03
29 5 0.02
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.48
Consensus pattern (25 bp):
TTATGTAAGTTATGTAAGTTATGTA
Found at i:31530006 original size:41 final size:41
Alignment explanation
Indices: 31529961--31530039 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
31529951 AAATGTTGTA
*
31529961 TTATGTAAGTTATGTATTATGTAAGATATGTAAGTTGTATT
1 TTATGTAAGTTATATATTATGTAAGATATGTAAGTTGTATT
* * *
31530002 TTATGTAAGTTCTATATTATGTATGTTATGTAAGTTGT
1 TTATGTAAGTTATATATTATGTAAGATATGTAAGTTGT
31530040 GTAGAATGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.19, T:0.51
Consensus pattern (41 bp):
TTATGTAAGTTATATATTATGTAAGATATGTAAGTTGTATT
Found at i:31530049 original size:41 final size:41
Alignment explanation
Indices: 31529963--31530069 Score: 106
Period size: 41 Copynumber: 2.6 Consensus size: 41
31529953 ATGTTGTATT
* ***
31529963 ATGTAAGTTATGTATTATGTAAGATATGTAAGTTGTATTTT
1 ATGTAAGTTATATATTATGTAAGATATGTAAGTTGTATAGA
* * * *
31530004 ATGTAAGTTCTATATTATGTATGTTATGTAAGTTGTGTAGA
1 ATGTAAGTTATATATTATGTAAGATATGTAAGTTGTATAGA
* *
31530045 ATGTAAGCTATGTAAGTTATGTAAG
1 ATGTAAGTTATAT-A-TTATGTAAG
31530070 TGGTGTATTA
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 43 0.83
42 1 0.02
43 8 0.15
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (41 bp):
ATGTAAGTTATATATTATGTAAGATATGTAAGTTGTATAGA
Found at i:31530112 original size:12 final size:12
Alignment explanation
Indices: 31530095--31530273 Score: 58
Period size: 12 Copynumber: 16.1 Consensus size: 12
31530085 CTTGTGTAAG
31530095 TTATGTAAGTTA
1 TTATGTAAGTTA
31530107 TTATGTAAG---
1 TTATGTAAGTTA
*
31530116 TTATGCAAGCTTA
1 TTATGTAAG-TTA
*
31530129 -TATATAAGTTATGTA
1 TTATGTAAG---T-TA
*
31530144 TTATGTAATTTA
1 TTATGTAAGTTA
* *
31530156 TTATATTA-TTA
1 TTATGTAAGTTA
*
31530167 -TATATAAG-T-
1 TTATGTAAGTTA
31530176 T-ATGTAAGTTA
1 TTATGTAAGTTA
*
31530187 TTATGTTA-TTA
1 TTATGTAAGTTA
*
31530198 -TATATAAG---
1 TTATGTAAGTTA
31530206 TTATGTAAGTTA
1 TTATGTAAGTTA
* *
31530218 TGTAAGT-GGTGTA
1 T-TATGTAAGT-TA
31530231 TTATGTAAG---
1 TTATGTAAGTTA
31530240 TTATGTAAG---
1 TTATGTAAGTTA
31530249 TTATGTAAGTTA
1 TTATGTAAGTTA
31530261 TTATGTAAGTTA
1 TTATGTAAGTTA
31530273 T
1 T
31530274 GCAAGCTTAT
Statistics
Matches: 125, Mismatches: 18, Indels: 48
0.65 0.09 0.25
Matches are distributed among these distances:
9 39 0.31
10 13 0.10
11 7 0.06
12 48 0.38
13 9 0.07
14 1 0.01
15 2 0.02
16 6 0.05
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:31530180 original size:31 final size:31
Alignment explanation
Indices: 31530144--31530218 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
31530134 AAGTTATGTA
*
31530144 TTATGTAATTTATTATATTATTATATATAAG
1 TTATGTAAGTTATTATATTATTATATATAAG
*
31530175 TTATGTAAGTTATTATGTTATTATATATAAG
1 TTATGTAAGTTATTATATTATTATATATAAG
31530206 TTATGTAAGTTAT
1 TTATGTAAGTTAT
31530219 GTAAGTGGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (31 bp):
TTATGTAAGTTATTATATTATTATATATAAG
Found at i:31530245 original size:34 final size:31
Alignment explanation
Indices: 31530018--31530283 Score: 185
Period size: 34 Copynumber: 8.4 Consensus size: 31
31530008 AAGTTCTATA
* **
31530018 TTATGTATGTTATGTAAGTTGTGTAGAATGTAAG
1 TTATGTAAGTTATGTAA--TGT-TATTATGTAAG
* *
31530052 CTATGTAAGTTATGTAAGTGGTGTATTATGTAAC
1 TTATGTAAGTTATGTAA-T-GT-TATTATGTAAG
*
31530086 TTGTGTAAGTTATGTAA-GTTATTATGTAAG
1 TTATGTAAGTTATGTAATGTTATTATGTAAG
* * *
31530116 TTATGCAAGCTTA--T-ATATAAGTTATGT-A-
1 TTATGTAAG-TTATGTAATGTTA-TTATGTAAG
* * *
31530144 TTATGTAATTTAT-T-ATATTATTATATATAAG
1 TTATGTAAGTTATGTAATGTTA-T-TATGTAAG
*
31530175 TTATGTAAGTTAT-T-ATGTTATTATATATAAG
1 TTATGTAAGTTATGTAATGTTA-T-TATGTAAG
31530206 TTATGTAAGTTATGTAAGTGGTGTATTATGTAAG
1 TTATGTAAGTTATGTAA-T-GT-TATTATGTAAG
31530240 TTATGTAAGTTATGTAA-GTTATTATGTAAG
1 TTATGTAAGTTATGTAATGTTATTATGTAAG
*
31530270 TTATGCAAGCTTAT
1 TTATGTAAG-TTAT
31530284 ATATAAGTTA
Statistics
Matches: 196, Mismatches: 22, Indels: 31
0.79 0.09 0.12
Matches are distributed among these distances:
27 3 0.02
28 15 0.08
29 8 0.04
30 43 0.22
31 53 0.27
32 1 0.01
33 2 0.01
34 66 0.34
35 3 0.02
36 2 0.01
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.46
Consensus pattern (31 bp):
TTATGTAAGTTATGTAATGTTATTATGTAAG
Found at i:31530274 original size:9 final size:9
Alignment explanation
Indices: 31529828--31530261 Score: 246
Period size: 9 Copynumber: 50.4 Consensus size: 9
31529818 NNNNNNNNNN
*
31529828 TTATTTAAG
1 TTATGTAAG
31529837 TTATGTAAG
1 TTATGTAAG
* *
31529846 TTATTTAAT
1 TTATGTAAG
31529855 TTATGTAAG
1 TTATGTAAG
31529864 TTATGTAAG
1 TTATGTAAG
*
31529873 TTATGTAGG
1 TTATGTAAG
31529882 TTATGT-A-
1 TTATGTAAG
*
31529889 TTATGTTAG
1 TTATGTAAG
*
31529898 TTAT-TATG
1 TTATGTAAG
*
31529906 TTATTATATAAG
1 ---TTATGTAAG
*
31529918 TTATGCAAG
1 TTATGTAAG
*
31529927 TTATATAAG
1 TTATGTAAG
*
31529936 TTATTTAAG
1 TTATGTAAG
** *
31529945 TCGTGTAAA
1 TTATGTAAG
31529954 TGT-TGT-A-
1 T-TATGTAAG
31529961 TTATGTAAG
1 TTATGTAAG
31529970 TTATGT-A-
1 TTATGTAAG
31529977 TTATGTAAG
1 TTATGTAAG
*
31529986 ATATGTAAG
1 TTATGTAAG
**
31529995 -T-TGTATT
1 TTATGTAAG
31530002 TTATGTAAG
1 TTATGTAAG
* *
31530011 TTCTAT-A-
1 TTATGTAAG
*
31530018 TTATGTATG
1 TTATGTAAG
31530027 TTATGTAAG
1 TTATGTAAG
*
31530036 TTGTGT-AG
1 TTATGTAAG
*
31530044 -AATGTAAG
1 TTATGTAAG
*
31530052 CTATGTAAG
1 TTATGTAAG
31530061 TTATGTAAG
1 TTATGTAAG
**
31530070 TGGTGT-A-
1 TTATGTAAG
*
31530077 TTATGTAAC
1 TTATGTAAG
*
31530086 TTGTGTAAG
1 TTATGTAAG
31530095 TTATGTAAG
1 TTATGTAAG
31530104 TTATTATGTAAG
1 ---TTATGTAAG
*
31530116 TTATGCAAG
1 TTATGTAAG
*
31530125 CTTATATATAAG
1 --T-TATGTAAG
31530137 TTATGT-A-
1 TTATGTAAG
*
31530144 TTATGTAAT
1 TTATGTAAG
31530153 TTAT-TATA-
1 TTATGTA-AG
31530161 TTAT-T-A-
1 TTATGTAAG
*
31530167 -TATATAAG
1 TTATGTAAG
31530175 TTATGTAAG
1 TTATGTAAG
*
31530184 TTAT-TATG
1 TTATGTAAG
31530192 TTAT-T-A-
1 TTATGTAAG
*
31530198 -TATATAAG
1 TTATGTAAG
31530206 TTATGTAAG
1 TTATGTAAG
31530215 TTATGTAAG
1 TTATGTAAG
**
31530224 TGGTGT-A-
1 TTATGTAAG
31530231 TTATGTAAG
1 TTATGTAAG
31530240 TTATGTAAG
1 TTATGTAAG
31530249 TTATGTAAG
1 TTATGTAAG
31530258 TTAT
1 TTAT
31530262 TATGTAAGTT
Statistics
Matches: 331, Mismatches: 55, Indels: 78
0.71 0.12 0.17
Matches are distributed among these distances:
5 6 0.02
6 4 0.01
7 43 0.13
8 35 0.11
9 219 0.66
10 1 0.00
11 5 0.02
12 18 0.05
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:31530290 original size:21 final size:21
Alignment explanation
Indices: 31530240--31530293 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
31530230 ATTATGTAAG
* *
31530240 TTATGTAAGTTATGTAAGTTA
1 TTATATAAGTTATGCAAGTTA
*
31530261 TTATGTAAGTTATGCAAGCTTA
1 TTATATAAGTTATGCAAG-TTA
31530283 -TATATAAGTTA
1 TTATATAAGTTA
31530294 ATATATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (21 bp):
TTATATAAGTTATGCAAGTTA
Found at i:31532012 original size:14 final size:14
Alignment explanation
Indices: 31531993--31532020 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31531983 TAGGAAATGG
31531993 GAAATTGGGGAAAT
1 GAAATTGGGGAAAT
31532007 GAAATTGGGGAAAT
1 GAAATTGGGGAAAT
31532021 CAGAGTGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.36, T:0.21
Consensus pattern (14 bp):
GAAATTGGGGAAAT
Found at i:31532017 original size:23 final size:24
Alignment explanation
Indices: 31531952--31532020 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 24
31531942 AAAGGATTTG
* *
31531952 GGGGGAAATGAAATCGGGGAAGTT
1 GGGGGAAATGAAATTGGGGAAATT
* *
31531976 GGGGGCATAGGAAA-T-GGGAAATT
1 GGGGG-AAATGAAATTGGGGAAATT
31531999 -GGGGAAATGAAATTGGGGAAAT
1 GGGGGAAATGAAATTGGGGAAAT
31532021 CAGAGTGGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
21 6 0.17
22 5 0.14
23 14 0.39
24 5 0.14
25 6 0.17
ACGTcount: A:0.36, C:0.03, G:0.43, T:0.17
Consensus pattern (24 bp):
GGGGGAAATGAAATTGGGGAAATT
Found at i:31532358 original size:115 final size:113
Alignment explanation
Indices: 31532135--31532594 Score: 370
Period size: 115 Copynumber: 4.0 Consensus size: 113
31532125 AAAAAATCCC
* * *
31532135 AGATAGAAAACGACAACGTTTAGCAAACACTTAAAACATAATAGCGGCGTTTATAATAAAAATGC
1 AGATA-AAAACGAAAACGTTTAGC-AACACTTATAACATAATTGCGGC-TTT-TAATAAAAATGC
* * *
31532200 CACTAAAACATATCCTTTACCGGCATTTTAGTACAAACGCCACTAAAAACGT
62 CACTAACACATATCCTTTAGCGGCATTTTAGTAAAAACGCCACTAAAAACGT
* *
31532252 AGATAAAAACGAAAACGTTTAGCGAACACTTATAACATAATTGCGGCATTTTTATAAAAACGCCA
1 AGATAAAAACGAAAACGTTTAGC-AACACTTATAACATAATTGCGGC-TTTTAATAAAAATGCCA
* * * * * * *
31532317 CTACCACATAACCTTTAGCAGCATTTTTGTAAAAATGCCACTAATAATGT
64 CTAACACATATCCTTTAGCGGCATTTTAGTAAAAACGCCACTAAAAACGT
* * * * * *
31532367 AGATAAAAAC-AACAATGTTTA-CAAAAGGTTAATAACATAATTGCGGC-GTTACCTGAAAATGC
1 AGATAAAAACGAA-AACGTTTAGCAACA-CTT-ATAACATAATTGCGGCTTTTA-ATAAAAATGC
* * * * * *
31532429 CACTAACACATATCATTTTGCGGCGTTTTGGAAAAAACGCCACTGAAAACGT
62 CACTAACACATATCCTTTAGCGGCATTTTAGTAAAAACGCCACTAAAAACGT
* * * * ** * * ** * *
31532481 AGATAAAAATGACAACGTTTAACAAAGACAAAAAACATAATTGCGGTGTTTTTCGTAGAAACGCC
1 AGATAAAAACGAAAACGTTTAGC-AACACTTATAACATAATTGC-G-GCTTTTAATAAAAATGCC
* * * *
31532546 ACTAATATA-ACTCCTTTTGCGGCATTTTAGAAAAAAACGCCACTAAAAA
63 ACTAACACATA-TCCTTTAGCGGCATTTTAG-TAAAAACGCCACTAAAAA
31532595 ATCAGACAAA
Statistics
Matches: 273, Mismatches: 58, Indels: 24
0.77 0.16 0.07
Matches are distributed among these distances:
113 5 0.02
114 80 0.29
115 89 0.33
116 75 0.27
117 24 0.09
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (113 bp):
AGATAAAAACGAAAACGTTTAGCAACACTTATAACATAATTGCGGCTTTTAATAAAAATGCCACT
AACACATATCCTTTAGCGGCATTTTAGTAAAAACGCCACTAAAAACGT
Found at i:31533019 original size:14 final size:14
Alignment explanation
Indices: 31532900--31533049 Score: 92
Period size: 14 Copynumber: 10.9 Consensus size: 14
31532890 CCATAAATCG
* *
31532900 TAAACACTAAACTC
1 TAAACCCTAAACTA
* * *
31532914 TTAACACTAAACCA
1 TAAACCCTAAACTA
* *
31532928 TAAACCTTAAACTT
1 TAAACCCTAAACTA
*
31532942 TATACCCTAAAC-A
1 TAAACCCTAAACTA
** *
31532955 TGCACCCTAAGCTA
1 TAAACCCTAAACTA
31532969 TAAACCCTAAA-T-
1 TAAACCCTAAACTA
**
31532981 T-AACCCTAAAACCG
1 TAAACCCT-AAACTA
* * *
31532995 TAAATCATAAATTA
1 TAAACCCTAAACTA
*
31533009 TAAACCCTAAACCA
1 TAAACCCTAAACTA
*
31533023 TAAACCCTAAACTC
1 TAAACCCTAAACTA
31533037 TAAACCACTAAAC
1 TAAACC-CTAAAC
31533050 CCCGTAAACC
Statistics
Matches: 101, Mismatches: 29, Indels: 11
0.72 0.21 0.08
Matches are distributed among these distances:
11 6 0.06
12 4 0.04
13 10 0.10
14 71 0.70
15 10 0.10
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:31533059 original size:17 final size:17
Alignment explanation
Indices: 31533037--31533069 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
31533027 CCCTAAACTC
31533037 TAAACCACTAAACCCCG
1 TAAACCACTAAACCCCG
*
31533054 TAAACCCCTAAACCCC
1 TAAACCACTAAACCCC
31533070 TAACCTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.45, G:0.03, T:0.12
Consensus pattern (17 bp):
TAAACCACTAAACCCCG
Found at i:31533088 original size:8 final size:7
Alignment explanation
Indices: 31533009--31533144 Score: 85
Period size: 7 Copynumber: 18.3 Consensus size: 7
31532999 TCATAAATTA
31533009 TAAACCC
1 TAAACCC
*
31533016 TAAACCA
1 TAAACCC
31533023 TAAACCC
1 TAAACCC
*
31533030 TAAACTC
1 TAAACCC
31533037 TAAACCAC
1 TAAACC-C
31533045 TAAACCCC
1 TAAA-CCC
31533053 GTAAACCCC
1 -TAAA-CCC
31533062 TAAACCCC
1 TAAA-CCC
*
31533070 T-AACCTA
1 TAAACC-C
31533077 TAAACCC
1 TAAACCC
*
31533084 TTAAACTC
1 -TAAACCC
*
31533092 AAAACCC
1 TAAACCC
*
31533099 TAAGCCAC
1 TAAACC-C
**
31533107 TACTCCC
1 TAAACCC
*
31533114 TAGACCC
1 TAAACCC
*
31533121 TAAGCCC
1 TAAACCC
*
31533128 ATAACCCC
1 -TAAACCC
31533136 TAAACCC
1 TAAACCC
31533143 TA
1 TA
31533145 TGCTCATAAC
Statistics
Matches: 102, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
6 2 0.02
7 54 0.53
8 36 0.35
9 10 0.10
ACGTcount: A:0.40, C:0.40, G:0.03, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:31533136 original size:22 final size:22
Alignment explanation
Indices: 31533093--31533155 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
31533083 CTTAAACTCA
31533093 AAACCCTAAG-CCACT-ACTCCCT
1 AAACCCTAAGCCCA-TAAC-CCCT
*
31533115 AGACCCTAAGCCCATAACCCCT
1 AAACCCTAAGCCCATAACCCCT
* *
31533137 AAACCCTATGCTCATAACC
1 AAACCCTAAGCCCATAACC
31533156 ACAAAACCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 30 0.86
23 5 0.14
ACGTcount: A:0.33, C:0.43, G:0.06, T:0.17
Consensus pattern (22 bp):
AAACCCTAAGCCCATAACCCCT
Found at i:31533162 original size:22 final size:22
Alignment explanation
Indices: 31533117--31533163 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
31533107 TACTCCCTAG
* *
31533117 ACCCTAAGCCCATAACCCCTAA
1 ACCCTAAGCCCATAACCACAAA
* *
31533139 ACCCTATGCTCATAACCACAAA
1 ACCCTAAGCCCATAACCACAAA
31533161 ACC
1 ACC
31533164 ATAAACCACG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.43, G:0.04, T:0.15
Consensus pattern (22 bp):
ACCCTAAGCCCATAACCACAAA
Found at i:31533274 original size:21 final size:22
Alignment explanation
Indices: 31533244--31533298 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
31533234 ATAAATCCTA
*
31533244 AAACCCTAAACTA-TAAA-AATT
1 AAACCTTAAA-TACTAAACAATT
*
31533265 AAACCTTAAATACTAAACACTT
1 AAACCTTAAATACTAAACAATT
*
31533287 AAACCTAAAATA
1 AAACCTTAAATA
31533299 AATTTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.07
21 13 0.45
22 14 0.48
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (22 bp):
AAACCTTAAATACTAAACAATT
Found at i:31538911 original size:25 final size:25
Alignment explanation
Indices: 31538883--31538935 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
31538873 CTGTTTTTGA
*
31538883 TAGTATATCCTGAAACTACTATAGG
1 TAGTATATACTGAAACTACTATAGG
* *
31538908 TAGTATATATTGAGACTACTATAGG
1 TAGTATATACTGAAACTACTATAGG
31538933 TAG
1 TAG
31538936 ACTGTACTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (25 bp):
TAGTATATACTGAAACTACTATAGG
Found at i:31551925 original size:24 final size:24
Alignment explanation
Indices: 31551893--31551949 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
31551883 GGTTGAACTT
31551893 TCATCAAAAACACCTACAAAGGTC
1 TCATCAAAAACACCTACAAAGGTC
*
31551917 TCATCAAAAACACCTACAAAGTTC
1 TCATCAAAAACACCTACAAAGGTC
31551941 TCATCAAAA
1 TCATCAAAA
31551950 CAGTAATAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.47, C:0.28, G:0.05, T:0.19
Consensus pattern (24 bp):
TCATCAAAAACACCTACAAAGGTC
Found at i:31556399 original size:20 final size:19
Alignment explanation
Indices: 31556374--31556418 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
31556364 TTTCGTTTGG
*
31556374 CTTTTTCTGTTT-CTTTCCTT
1 CTTTTTCTATTTCCTTT--TT
31556394 CTTTTTCTATTTCCTTTTT
1 CTTTTTCTATTTCCTTTTT
31556413 CTTTTT
1 CTTTTT
31556419 ATTTATTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 11 0.48
21 4 0.17
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.73
Consensus pattern (19 bp):
CTTTTTCTATTTCCTTTTT
Found at i:31556470 original size:25 final size:24
Alignment explanation
Indices: 31556430--31556480 Score: 93
Period size: 25 Copynumber: 2.1 Consensus size: 24
31556420 TTTATTTGTT
31556430 TTATTATAATAATAATATAATATA
1 TTATTATAATAATAATATAATATA
31556454 TTATTATATATAATAATATAATATA
1 TTATTATA-ATAATAATATAATATA
31556479 TT
1 TT
31556481 TACTTAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTATTATAATAATAATATAATATA
Found at i:31557168 original size:49 final size:49
Alignment explanation
Indices: 31557111--31557209 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
31557101 TCACCGGTTT
31557111 GATTTTTAATTCAGCCAATAAGCTTCAATCGTCATTAATACTGAGCTGA
1 GATTTTTAATTCAGCCAATAAGCTTCAATCGTCATTAATACTGAGCTGA
31557160 GATTTTTAATTCAGCCAATAAGCTTCAATCGTCATTAATACTGAGCTGA
1 GATTTTTAATTCAGCCAATAAGCTTCAATCGTCATTAATACTGAGCTGA
31557209 G
1 G
31557210 CAAACATCGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (49 bp):
GATTTTTAATTCAGCCAATAAGCTTCAATCGTCATTAATACTGAGCTGA
Found at i:31560365 original size:2 final size:2
Alignment explanation
Indices: 31560358--31560385 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31560348 ATAACAACAA
31560358 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31560386 CAGCATCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31561917 original size:40 final size:39
Alignment explanation
Indices: 31561812--31561919 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 39
31561802 CAGATAATTT
* *
31561812 GAAGTAATAATTTGACACCCAGTGTCTCATCGGCTAAACC
1 GAAGT-ATAAATTGACACCCAGTGTCTCATCGACTAAACC
* * * *
31561852 GAAG--TAAATTCACATCCAGTGTCTCATCGAATTAATCC
1 GAAGTATAAATTGACACCCAGTGTCTCATCG-ACTAAACC
31561890 GAAGTACTAAATTGACA-CCAGTGTCTCATC
1 GAAGTA-TAAATTGACACCCAGTGTCTCATC
31561920 AACAAAAAGT
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
37 22 0.39
38 9 0.16
40 17 0.30
41 9 0.16
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (39 bp):
GAAGTATAAATTGACACCCAGTGTCTCATCGACTAAACC
Found at i:31564862 original size:40 final size:40
Alignment explanation
Indices: 31564802--31564950 Score: 172
Period size: 40 Copynumber: 3.7 Consensus size: 40
31564792 TACTAGCAGG
*
31564802 TTGTCTGCAATTCTGGTGGCTTGTCCACATTACTGGCAAC
1 TTGTTTGCAATTCTGGTGGCTTGTCCACATTACTGGCAAC
* * * * *
31564842 TTGTTTGCAATTTTAGTGGCTTGTCCACAATACTAGCAAT
1 TTGTTTGCAATTCTGGTGGCTTGTCCACATTACTGGCAAC
* * **
31564882 TTGTTTGCAATTCTGGTGGCTTGTCCATATTACTGACAGT
1 TTGTTTGCAATTCTGGTGGCTTGTCCACATTACTGGCAAC
* * * *
31564922 TTATATGTAATACTGGTGGCTTGTCCACA
1 TTGTTTGCAATTCTGGTGGCTTGTCCACA
31564951 AACTGGTGTG
Statistics
Matches: 91, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 91 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (40 bp):
TTGTTTGCAATTCTGGTGGCTTGTCCACATTACTGGCAAC
Found at i:31564941 original size:80 final size:80
Alignment explanation
Indices: 31564792--31564951 Score: 203
Period size: 80 Copynumber: 2.0 Consensus size: 80
31564782 AAGGAGGAAG
* * * * **
31564792 TACTAGCAGGTTGTCTGCAATTCTGGTGGCTTGTCCACATTACTGGCAACTTGTTTGCAATTTTA
1 TACTAGCAAGTTGTCTGCAATTCTGGTGGCTTGTCCACATTACTGACAACTTATATGCAATACTA
31564857 GTGGCTTGTCCACAA
66 GTGGCTTGTCCACAA
* * * ** * *
31564872 TACTAGCAATTTGTTTGCAATTCTGGTGGCTTGTCCATATTACTGACAGTTTATATGTAATACTG
1 TACTAGCAAGTTGTCTGCAATTCTGGTGGCTTGTCCACATTACTGACAACTTATATGCAATACTA
31564937 GTGGCTTGTCCACAA
66 GTGGCTTGTCCACAA
31564952 ACTGGTGTGT
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
80 67 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (80 bp):
TACTAGCAAGTTGTCTGCAATTCTGGTGGCTTGTCCACATTACTGACAACTTATATGCAATACTA
GTGGCTTGTCCACAA
Found at i:31568485 original size:31 final size:29
Alignment explanation
Indices: 31568448--31568508 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 29
31568438 TTATCCGAAA
*
31568448 ATATATAACTTAAACATTCAAATATATATAT
1 ATATATAACTTAAA-ATTCAAA-AAATATAT
*
31568479 ATATATAATTTAAAATTCAAAAAATATAT
1 ATATATAACTTAAAATTCAAAAAATATAT
31568508 A
1 A
31568509 AAGTTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 8 0.29
30 7 0.25
31 13 0.46
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (29 bp):
ATATATAACTTAAAATTCAAAAAATATAT
Found at i:31568522 original size:29 final size:28
Alignment explanation
Indices: 31568490--31568546 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
31568480 TATATAATTT
31568490 AAAAT-TCAAAAAATATATAAAGTTTAAAA
1 AAAATCTC-AAAAATATATAAA-TTTAAAA
* *
31568519 AAAATCTCAAAATTATATATATTTAAAA
1 AAAATCTCAAAAATATATAAATTTAAAA
31568547 TCATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.28
29 16 0.64
30 2 0.08
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (28 bp):
AAAATCTCAAAAATATATAAATTTAAAA
Found at i:31569263 original size:27 final size:28
Alignment explanation
Indices: 31569233--31569291 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
31569223 TATAGATTCC
* *
31569233 TTTTGAAT-TTTTTTTTATTTTCTAA-AA
1 TTTT-AATATTTTTTTAATTTTCAAACAA
*
31569260 TTTTTATATTTTTTTAATTTTCAAACAA
1 TTTTAATATTTTTTTAATTTTCAAACAA
31569288 TTTT
1 TTTT
31569292 TTTAGATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 2 0.07
27 19 0.70
28 6 0.22
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (28 bp):
TTTTAATATTTTTTTAATTTTCAAACAA
Found at i:31570358 original size:19 final size:18
Alignment explanation
Indices: 31570330--31570365 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
31570320 AATATATATA
31570330 TAAATTTAAATTCATGAT
1 TAAATTTAAATTCATGAT
*
31570348 TAAATTTTAAATTTATGA
1 TAAA-TTTAAATTCATGA
31570366 ATAAGTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (18 bp):
TAAATTTAAATTCATGAT
Found at i:31570662 original size:3 final size:3
Alignment explanation
Indices: 31570654--31570689 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
31570644 TTACTCTTTA
31570654 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
31570690 TGTTGGAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:31576918 original size:18 final size:17
Alignment explanation
Indices: 31576895--31576937 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
31576885 GAATCCAAGT
31576895 TAAATAAAAAAATTAAAA
1 TAAATAAAAAAA-TAAAA
*
31576913 TAAATAACTAAAATAAAA
1 TAAATAA-AAAAATAAAA
31576931 T-AATAAA
1 TAAATAAA
31576938 TCAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 5 0.23
18 13 0.59
19 4 0.18
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (17 bp):
TAAATAAAAAAATAAAA
Found at i:31576937 original size:13 final size:14
Alignment explanation
Indices: 31576896--31576937 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
31576886 AATCCAAGTT
* *
31576896 AAATAAAAAAATTA
1 AAATAAAATAACTA
31576910 AAAT-AAATAACTA
1 AAATAAAATAACTA
31576923 AAATAAAATAA-TA
1 AAATAAAATAACTA
31576936 AA
1 AA
31576938 TCAAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAATAACTA
Found at i:31580908 original size:851 final size:851
Alignment explanation
Indices: 31578900--31581456 Score: 4443
Period size: 851 Copynumber: 3.0 Consensus size: 851
31578890 TTCCTTGAAA
31578900 GATGTAGAAGAATGTTTTGTAGGAGCTCCACTTTTCCACTCAAAAGGTTTAGTCTCAGCATGTTT
1 GATGTAGAAGAATGTTTTGTAGGAGCTCCACTTTTCCACTCAAAAGGTTTAGTCTCAGCATGTTT
31578965 TGGAAATAACTTATTAATAGCATAAGAAGGTTTCAAATTGTTGAAAGTAGAATTAGAACTTGTAC
66 TGGAAATAACTTATTAATAGCATAAGAAGGTTTCAAATTGTTGAAAGTAGAATTAGAACTTGTAC
31579030 CTTGAAAATAGTGTGATGCGCCAAATGGACGAGATTGATGCTGCTGAAATTGTTGCTCAATCTCA
131 CTTGAAAATAGTGTGATGCGCCAAATGGACGAGATTGATGCTGCTGAAATTGTTGCTCAATCTCA
31579095 ATTGTCTTGTGTACCATCTCCTCAAGATCAATATAGGTTTGAAGATTAAGAGCATTGGCTATCGA
196 ATTGTCTTGTGTACCATCTCCTCAAGATCAATATAGGTTTGAAGATTAAGAGCATTGGCTATCGA
* * * *
31579160 AACGTTCAAGCCATCTACAAATTGTACCACGCTAGTTTCTTCACCCTCTCGTATATTTGCCCTTT
261 AACGTTCAAGCCATCTACAAATTGCACCATGCTAGTTTCTTCATCCTCTCGTATATTTGCTCTTT
* * *
31579225 GCGTAAGCATCTTTATGTCTTTAAAGTACTCATCAACAGATCGATTACCTTGAACAAGGTGTTGA
326 GCATAAGCATCTTTATCTCCTTAAAGTACTCATCAACAGATCGATTACCTTGAACAAGGTGTTGA
31579290 AGTCTCGTTGAGACCTCTCTATAGTAATGAGAAGGAACGTAACGCTTTCGTATCACTTGCTTCAA
391 AGTCTCGTTGAGACCTCTCTATAGTAATGAGAAGGAACGTAACGCTTTCGTATCACTTGCTTCAA
* * * *
31579355 CTTGTCCCATGTTTCAATTACCCTTTAGCGGTTTCTTTGATGATCAATTCCAAGTTAAACCCACC
456 CTTGTCCCATGTTTCAATTACCCTTTCGCGGTTTCTTTGACGATCAATTCCAAGTTGAATCCACC
* * *
31579420 AACTCAATGCATGATCTTAAAATCCAAGGGTCGCCAATTGGACTTTCTCCTCTTCCCAAAATTTA
521 AACTCAATGCATAATCTTAAAATCCAAGGGTCGCCAATTGGACTTTTTCCTCTTCCCGAAATTTA
* *
31579485 TAGTAATGAAACATAAGTTCAATTTTCTATTCCCACTCACAATATGCTTTGGGATCATACTTTCC
586 TAGTAACGAAACATAAGTTCAATTTTCTATTCCCACTCACAATATGCTTTGGGATCATACTTCCC
* * *
31579550 TCGAAATGGTGGATTGTTGAACTTTAGTTTAGCTAAAAAAATATTGTATACAGTCATTAATAACC
651 TCGAAATGGTGGATTGTTGAACTTTGGTTTAGCT-AAAAAATGTTGCATACAGTCATTAATAACC
31579615 AAAGTCTCATCATTTGCACGAGACACACGTTGAGCATTATTTACATGAAGAC-ACGGCTGATCAA
715 AAAGTCTCATCATTTGCACGAGACACACGTTGAGCATTATTTACATGAAGACGA-GGCTGATCAA
31579679 CCTTATTGTAACACCCCAAAACCCAACCTAGAAGTTTCAGTCGGATCTCAAAGGTTACATTGACC
779 CCTTATTGTAACACCCCAAAACCCAACCTAGAAGTTTCAGTCGGATCTCAAAGGTTACATTGACC
31579744 ACTAAAGT
844 ACTAAAGT
31579752 GATGTAGAAGAATGTTTTGTAGGAGCTCCACTTTTCCACTCAAAAGGTTTAGTCTCAGCATGTTT
1 GATGTAGAAGAATGTTTTGTAGGAGCTCCACTTTTCCACTCAAAAGGTTTAGTCTCAGCATGTTT
*
31579817 TGGAAATAACTTATTAATAGCATAAGAAGGTTTCAAACTGTTGAAAGTAGAATTAGAACTTGTAC
66 TGGAAATAACTTATTAATAGCATAAGAAGGTTTCAAATTGTTGAAAGTAGAATTAGAACTTGTAC
*
31579882 CTTGAAAATAGTGTGATGCGCCAAATGGACGAGATTGATGCTACTGAAATTGTTGCTCAATCTCA
131 CTTGAAAATAGTGTGATGCGCCAAATGGACGAGATTGATGCTGCTGAAATTGTTGCTCAATCTCA
31579947 ATTGTCTTGTGTACCATCTCCTCAAGATCAATATAGGTTTGAAGATTAAGAGCATTGGCTATCGA
196 ATTGTCTTGTGTACCATCTCCTCAAGATCAATATAGGTTTGAAGATTAAGAGCATTGGCTATCGA
* *
31580012 AACGTTCAAGCCATCTACAAATTGCACCATGCTAGTTTATTCATCCTCTCATATATTTGCTCTTT
261 AACGTTCAAGCCATCTACAAATTGCACCATGCTAGTTTCTTCATCCTCTCGTATATTTGCTCTTT
* * * * *
31580077 GCATAAGCATTTTTATCTCCTTAAAGTACTCATCAATAGATCGATTATCTTGAACAAGGTGGTGC
326 GCATAAGCATCTTTATCTCCTTAAAGTACTCATCAACAGATCGATTACCTTGAACAAGGTGTTGA
* * *
31580142 AGTCTCATTGAGACCTCTCTATAGTAATAAGAAGGAACGTAACACTTTCGTATCACTTGCTTCAA
391 AGTCTCGTTGAGACCTCTCTATAGTAATGAGAAGGAACGTAACGCTTTCGTATCACTTGCTTCAA
* * * * *
31580207 CTTGTCCCATGTTTCAATTACCCTTTCGCGATTTCTTTTACAACCAATTCCAAGTTGAATCCACT
456 CTTGTCCCATGTTTCAATTACCCTTTCGCGGTTTCTTTGACGATCAATTCCAAGTTGAATCCACC
*
31580272 AACTCAATGCATAATCTTAACATCCAAGGGTCGCCAATTGGACTTTTTCCTCTTCCCGAAATTTA
521 AACTCAATGCATAATCTTAAAATCCAAGGGTCGCCAATTGGACTTTTTCCTCTTCCCGAAATTTA
* *
31580337 TAGTAACAAAACATAAGTTCAATTTTTTATTCCCACTCACAATATGCTTTGGGATCATACTTCCC
586 TAGTAACGAAACATAAGTTCAATTTTCTATTCCCACTCACAATATGCTTTGGGATCATACTTCCC
*
31580402 TCGAAATGGTGGATTATTGAACTTTGGTTTAGCTAAAAAATGTTGCATACAGTCATTAATAACCA
651 TCGAAATGGTGGATTGTTGAACTTTGGTTTAGCTAAAAAATGTTGCATACAGTCATTAATAACCA
* * *
31580467 AAGTCTTATCATTTGCTCGAGACACACATTGAGCATTATTTACATGAAGACGAGGCTGATCAACC
716 AAGTCTCATCATTTGCACGAGACACACGTTGAGCATTATTTACATGAAGACGAGGCTGATCAACC
31580532 TTATTGTAACACCCCAAAACCCAACCTAGAAGTTTCAGTCGGATCTCAAAGGTTACATTGACCAC
781 TTATTGTAACACCCCAAAACCCAACCTAGAAGTTTCAGTCGGATCTCAAAGGTTACATTGACCAC
31580597 TAAAGT
846 TAAAGT
* *
31580603 GATGTAGAAGAATGTTTTGTAGGAGCTACACTTTTCCACTCAAAAGGTTTAGTCTCAACATGTTT
1 GATGTAGAAGAATGTTTTGTAGGAGCTCCACTTTTCCACTCAAAAGGTTTAGTCTCAGCATGTTT
*
31580668 TGGAAATAACTTATTAATAGCATAAGAAGGTTTCAAATTGTTGAAATTAGAATTAGAACTTGTAC
66 TGGAAATAACTTATTAATAGCATAAGAAGGTTTCAAATTGTTGAAAGTAGAATTAGAACTTGTAC
* * * *
31580733 CTCGATAATAGTGTGATGCGCCAAATGGACGAGATTAATGTTGCTGAAATTGTTGCTCAATCTCA
131 CTTGAAAATAGTGTGATGCGCCAAATGGACGAGATTGATGCTGCTGAAATTGTTGCTCAATCTCA
*
31580798 ATTGTCTTGTGTACCATCTCCTCAAGATCAATATAGGTTTGAAGATTAAAAGCATTGGCTATCGA
196 ATTGTCTTGTGTACCATCTCCTCAAGATCAATATAGGTTTGAAGATTAAGAGCATTGGCTATCGA
* * * * *
31580863 AACATTCAAGCCATCTATAAATTACACGATGGTAGTTTCTTCATCCTCTCGTATATTTGCTCTTT
261 AACGTTCAAGCCATCTACAAATTGCACCATGCTAGTTTCTTCATCCTCTCGTATATTTGCTCTTT
* * * *
31580928 TCACAAGCATCTTTATCTCCTTAAGGTACTCATCAAGAGATCGATTACCTTGAACAAGGTGTTGA
326 GCATAAGCATCTTTATCTCCTTAAAGTACTCATCAACAGATCGATTACCTTGAACAAGGTGTTGA
*
31580993 AGTCTCGTTGAGACCTCTCTATAGTAATGAGAAGGAACGTAACGCTTTCATATCACTTGCTTCAA
391 AGTCTCGTTGAGACCTCTCTATAGTAATGAGAAGGAACGTAACGCTTTCGTATCACTTGCTTCAA
*
31581058 CTTGTCCCATGTTTCAATTACCCTTTCGTGGTTTCTTTGACGATCAATTCCAAGTTGAATCCACC
456 CTTGTCCCATGTTTCAATTACCCTTTCGCGGTTTCTTTGACGATCAATTCCAAGTTGAATCCACC
* *
31581123 AACTCAATGCATAATCCTAAAATCCAAGGGTCGCCAATTGGACTTTTTCCTCTTCCTGAAATTTA
521 AACTCAATGCATAATCTTAAAATCCAAGGGTCGCCAATTGGACTTTTTCCTCTTCCCGAAATTTA
*
31581188 TAGTAACGAAACATAAGTTCAATTTTCCATTCCCACTCACAATATGCTTTGGGATCATACTTCCC
586 TAGTAACGAAACATAAGTTCAATTTTCTATTCCCACTCACAATATGCTTTGGGATCATACTTCCC
31581253 TCGAAATGGTGGATTGTTGAACTTTGGTTTAGCTAAAAAATGTTGCATACAGTCATTAATAACCA
651 TCGAAATGGTGGATTGTTGAACTTTGGTTTAGCTAAAAAATGTTGCATACAGTCATTAATAACCA
31581318 AAGTCTCATCATTTGCACGAGACACACGTTGAGCATTATTTACATGAAGACGAGGCTGATCAACC
716 AAGTCTCATCATTTGCACGAGACACACGTTGAGCATTATTTACATGAAGACGAGGCTGATCAACC
* * * *
31581383 TTATTATAGCACCCCAAAACCCAACCTAGAAGTTTTAG-CTGGATCTCAGAGGTTACATTGACCA
781 TTATTGTAACACCCCAAAACCCAACCTAGAAGTTTCAGTC-GGATCTCAAAGGTTACATTGACCA
*
31581447 CTGAAGT
845 CTAAAGT
31581454 GAT
1 GAT
31581457 CCTAAAATGA
Statistics
Matches: 1610, Mismatches: 93, Indels: 5
0.94 0.05 0.00
Matches are distributed among these distances:
850 1 0.00
851 962 0.60
852 647 0.40
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (851 bp):
GATGTAGAAGAATGTTTTGTAGGAGCTCCACTTTTCCACTCAAAAGGTTTAGTCTCAGCATGTTT
TGGAAATAACTTATTAATAGCATAAGAAGGTTTCAAATTGTTGAAAGTAGAATTAGAACTTGTAC
CTTGAAAATAGTGTGATGCGCCAAATGGACGAGATTGATGCTGCTGAAATTGTTGCTCAATCTCA
ATTGTCTTGTGTACCATCTCCTCAAGATCAATATAGGTTTGAAGATTAAGAGCATTGGCTATCGA
AACGTTCAAGCCATCTACAAATTGCACCATGCTAGTTTCTTCATCCTCTCGTATATTTGCTCTTT
GCATAAGCATCTTTATCTCCTTAAAGTACTCATCAACAGATCGATTACCTTGAACAAGGTGTTGA
AGTCTCGTTGAGACCTCTCTATAGTAATGAGAAGGAACGTAACGCTTTCGTATCACTTGCTTCAA
CTTGTCCCATGTTTCAATTACCCTTTCGCGGTTTCTTTGACGATCAATTCCAAGTTGAATCCACC
AACTCAATGCATAATCTTAAAATCCAAGGGTCGCCAATTGGACTTTTTCCTCTTCCCGAAATTTA
TAGTAACGAAACATAAGTTCAATTTTCTATTCCCACTCACAATATGCTTTGGGATCATACTTCCC
TCGAAATGGTGGATTGTTGAACTTTGGTTTAGCTAAAAAATGTTGCATACAGTCATTAATAACCA
AAGTCTCATCATTTGCACGAGACACACGTTGAGCATTATTTACATGAAGACGAGGCTGATCAACC
TTATTGTAACACCCCAAAACCCAACCTAGAAGTTTCAGTCGGATCTCAAAGGTTACATTGACCAC
TAAAGT
Found at i:31582798 original size:21 final size:21
Alignment explanation
Indices: 31582759--31582798 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31582749 TACAGAGTAG
**
31582759 ACACGACCGTGTGGGAATCTC
1 ACACGACCGTGTGCAAATCTC
*
31582780 ACACGCCCGTGTGCAAATC
1 ACACGACCGTGTGCAAATC
31582799 AATAAAAATC
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:0.25, C:0.33, G:0.25, T:0.17
Consensus pattern (21 bp):
ACACGACCGTGTGCAAATCTC
Found at i:31583243 original size:21 final size:21
Alignment explanation
Indices: 31583219--31583266 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
31583209 AAAAATGGAG
*
31583219 CAAAAGAAGAA-AATTGATGAA
1 CAAAAGAA-AAGAATTGATAAA
31583240 CAAAAGAAAAGAATTGATAAA
1 CAAAAGAAAAGAATTGATAAA
*
31583261 CGAAAG
1 CAAAAG
31583267 TGACAATTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.62, C:0.06, G:0.19, T:0.12
Consensus pattern (21 bp):
CAAAAGAAAAGAATTGATAAA
Done.