Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000761.1 Hibiscus syriacus cultivar Beakdansim tig00001478_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: 5609167
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 23
Found at i:3935089 original size:1 final size:1
Alignment explanation
Indices: 3935079--3935144 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
3935069 TTGACCCTCC
* * ** * * * * *
3935079 TTTTTATTTTTTTTCTTGCTTTTTTTGTTTTTTTTTTTTTTTTTTTTATTTTCTTATTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3935144 T
1 T
3935145 CTTCATTTTC
Statistics
Matches: 48, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.05, C:0.06, G:0.03, T:0.86
Consensus pattern (1 bp):
T
Found at i:3935104 original size:14 final size:12
Alignment explanation
Indices: 3935079--3935147 Score: 61
Period size: 11 Copynumber: 5.7 Consensus size: 12
3935069 TTGACCCTCC
*
3935079 TTTTTATTTTTT
1 TTTTTCTTTTTT
*
3935091 TTCTTGCTTTTTT
1 TT-TTTCTTTTTT
*
3935104 TGTTT-TTTTTT
1 TTTTTCTTTTTT
3935115 TTTTT-TTTTTT
1 TTTTTCTTTTTT
*
3935126 ATTTTCTTATTTT
1 TTTTTCTT-TTTT
3935139 CTTTTTCTT
1 -TTTTTCTT
3935148 CATTTTCTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
11 20 0.43
12 6 0.13
13 13 0.28
14 7 0.15
ACGTcount: A:0.04, C:0.07, G:0.03, T:0.86
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:3935152 original size:15 final size:14
Alignment explanation
Indices: 3935127--3935157 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
3935117 TTTTTTTTTA
3935127 TTTTCTTATTTTCT
1 TTTTCTTATTTTCT
3935141 TTTTCTTCATTTTCT
1 TTTTCTT-ATTTTCT
3935156 TT
1 TT
3935158 GGCTTTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCTTATTTTCT
Found at i:3942980 original size:39 final size:38
Alignment explanation
Indices: 3942926--3943040 Score: 140
Period size: 39 Copynumber: 2.9 Consensus size: 38
3942916 CAGTCTCTTA
* *
3942926 GGCTTTGTGCTCAGGGTAAATCCTTACTGCAGGCTCCAC
1 GGCTTTGTGCTCAGGGTAAGTCCTTACT-CACGCTCCAC
* * **
3942965 GGCTTTGTGCTCAGGGTAAGTCCTTACATCATGTTCCTT
1 GGCTTTGTGCTCAGGGTAAGTCCTTAC-TCACGCTCCAC
*
3943004 GGCTTTGTGCTCAGGGTAAGTCATTACTACACGCTCC
1 GGCTTTGTGCTCAGGGTAAGTCCTTACT-CACGCTCC
3943041 TCTTCTTTGT
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.02
39 64 0.97
40 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.32
Consensus pattern (38 bp):
GGCTTTGTGCTCAGGGTAAGTCCTTACTCACGCTCCAC
Found at i:3943049 original size:39 final size:39
Alignment explanation
Indices: 3942927--3943068 Score: 126
Period size: 39 Copynumber: 3.6 Consensus size: 39
3942917 AGTCTCTTAG
* * * * * *
3942927 GCTTTGTGCTCAGGGTAAATCCTTACTGCAGGCTCCACG
1 GCTTTGTGCTCAGGGTAAGTCATTACTACACGCTCCTCT
* * *
3942966 GCTTTGTGCTCAGGGTAAGTCCTTAC-ATCATGTTCCT-T
1 GCTTTGTGCTCAGGGTAAGTCATTACTA-CACGCTCCTCT
3943004 GGCTTTGTGCTCAGGGTAAGTCATTACTACACGCTCCTCT
1 -GCTTTGTGCTCAGGGTAAGTCATTACTACACGCTCCTCT
* * * * *
3943044 TCTTTGTACACAGGATAAGACATTA
1 GCTTTGTGCTCAGGGTAAGTCATTA
3943069 TCGCAGGCTC
Statistics
Matches: 85, Mismatches: 14, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
39 83 0.98
40 2 0.02
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (39 bp):
GCTTTGTGCTCAGGGTAAGTCATTACTACACGCTCCTCT
Found at i:3946969 original size:16 final size:16
Alignment explanation
Indices: 3946944--3946975 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3946934 ATTAGTGATC
3946944 AAATTAAAAGATTTAA
1 AAATTAAAAGATTTAA
*
3946960 AAATTTAAAGATTTAA
1 AAATTAAAAGATTTAA
3946976 TTCTACAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (16 bp):
AAATTAAAAGATTTAA
Found at i:3947899 original size:12 final size:12
Alignment explanation
Indices: 3947882--3947907 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3947872 TTTATATGGA
3947882 TTGGTGATTGTT
1 TTGGTGATTGTT
3947894 TTGGTGATTGTT
1 TTGGTGATTGTT
3947906 TT
1 TT
3947908 ATGATCCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.31, T:0.62
Consensus pattern (12 bp):
TTGGTGATTGTT
Found at i:3948635 original size:14 final size:14
Alignment explanation
Indices: 3948616--3948644 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3948606 ATATTGGGCC
3948616 TACGTAAAAAACTA
1 TACGTAAAAAACTA
3948630 TACGTAAAAAACTA
1 TACGTAAAAAACTA
3948644 T
1 T
3948645 GTAAATGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24
Consensus pattern (14 bp):
TACGTAAAAAACTA
Found at i:3948794 original size:15 final size:15
Alignment explanation
Indices: 3948767--3948804 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3948757 TGAACTATGA
*
3948767 AATATACTAATTATTT
1 AATATA-TAATTATCT
3948783 AATATATAATTATCT
1 AATATATAATTATCT
3948798 AATATAT
1 AATATAT
3948805 GCAATGCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATATAATTATCT
Found at i:3948916 original size:23 final size:24
Alignment explanation
Indices: 3948883--3948930 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3948873 TAATATGTAC
* *
3948883 ATGCAATTA-TTATTTAATATGCT
1 ATGCAAATATTTACTTAATATGCT
3948906 ATGCAAATATTTACTTAATATGCT
1 ATGCAAATATTTACTTAATATGCT
3948930 A
1 A
3948931 ATTATATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (24 bp):
ATGCAAATATTTACTTAATATGCT
Found at i:3964791 original size:10 final size:10
Alignment explanation
Indices: 3964776--3964800 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3964766 CAACTATAAC
3964776 CTAAATGCAA
1 CTAAATGCAA
3964786 CTAAATGCAA
1 CTAAATGCAA
3964796 CTAAA
1 CTAAA
3964801 ACATTGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (10 bp):
CTAAATGCAA
Found at i:3973734 original size:147 final size:147
Alignment explanation
Indices: 3973467--3973760 Score: 579
Period size: 147 Copynumber: 2.0 Consensus size: 147
3973457 TGGGAACCGG
3973467 TAGAAAAATGTATGGTGCATATGAAATTAAGGGTAAGTATTCAGTAGTTGGTCAACTTTCTGCAA
1 TAGAAAAATGTATGGTGCATATGAAATTAAGGGTAAGTATTCAGTAGTTGGTCAACTTTCTGCAA
*
3973532 TAACTAATATGTTGAAAAATTTACAGCGTCCTTAAGAGGTGAGAGAAGTTAAAGCAACCAGTAAT
66 TAACTAATATGTTGAAAAATTTACAGCGTCCTAAAGAGGTGAGAGAAGTTAAAGCAACCAGTAAT
3973597 GCATGTATTTTATGCCA
131 GCATGTATTTTATGCCA
3973614 TAGAAAAATGTATGGTGCATATGAAATTAAGGGTAAGTATTCAGTAGTTGGTCAACTTTCTGCAA
1 TAGAAAAATGTATGGTGCATATGAAATTAAGGGTAAGTATTCAGTAGTTGGTCAACTTTCTGCAA
3973679 TAACTAATATGTTGAAAAATTTACAGCGTCCTAAAGAGGTGAGAGAAGTTAAAGCAACCAGTAAT
66 TAACTAATATGTTGAAAAATTTACAGCGTCCTAAAGAGGTGAGAGAAGTTAAAGCAACCAGTAAT
3973744 GCATGTATTTTATGCCA
131 GCATGTATTTTATGCCA
3973761 CGGCAACCAT
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 146 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (147 bp):
TAGAAAAATGTATGGTGCATATGAAATTAAGGGTAAGTATTCAGTAGTTGGTCAACTTTCTGCAA
TAACTAATATGTTGAAAAATTTACAGCGTCCTAAAGAGGTGAGAGAAGTTAAAGCAACCAGTAAT
GCATGTATTTTATGCCA
Found at i:3981652 original size:30 final size:34
Alignment explanation
Indices: 3981618--3981685 Score: 90
Period size: 32 Copynumber: 2.1 Consensus size: 34
3981608 CCTTACAAAC
*
3981618 TCCCTAG-TTTTTC-CGGGCTAAACTA-AA-CTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
*
3981648 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
3981682 TCCC
1 TCCC
3981686 CTTTACAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 7 0.22
31 5 0.16
32 11 0.34
33 2 0.06
34 7 0.22
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.32
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
Found at i:3981990 original size:21 final size:21
Alignment explanation
Indices: 3981964--3982005 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3981954 CCAGAATTGG
*
3981964 GGGAATCGGCACCCCTTCATA
1 GGGAATCGACACCCCTTCATA
*
3981985 GGGAATCGATACCCCTTCATA
1 GGGAATCGACACCCCTTCATA
3982006 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.31, G:0.21, T:0.21
Consensus pattern (21 bp):
GGGAATCGACACCCCTTCATA
Found at i:3982136 original size:19 final size:19
Alignment explanation
Indices: 3982112--3982153 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3982102 AGCCTCGGGG
* *
3982112 TACTGTTTAAACAGTGATT
1 TACTGTTAAAACAGTGAAT
*
3982131 TACTGTTAAAATAGTGAAT
1 TACTGTTAAAACAGTGAAT
3982150 TACT
1 TACT
3982154 ATTCATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (19 bp):
TACTGTTAAAACAGTGAAT
Found at i:3985370 original size:30 final size:31
Alignment explanation
Indices: 3985320--3985384 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 31
3985310 AGAAGTTTAG
*
3985320 TTTGAAAATTTCAATTAAGTCCAAATA-CAT
1 TTTGAAAATTTCAATTAAGTCCAAAAACCAT
*
3985350 TTTGTAAA-TTCAATTCAAGTCCAAAAACCAT
1 TTTGAAAATTTCAATT-AAGTCCAAAAACCAT
3985381 TTTG
1 TTTG
3985385 CCTTAAATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 7 0.23
30 17 0.55
31 7 0.23
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (31 bp):
TTTGAAAATTTCAATTAAGTCCAAAAACCAT
Found at i:3993242 original size:21 final size:20
Alignment explanation
Indices: 3993213--3993251 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3993203 TAAGGAATTA
*
3993213 AACATCATAAACAAAACAAAT
1 AACAACATAAA-AAAACAAAT
*
3993234 AACAACATACAAAAACAA
1 AACAACATAAAAAAACAA
3993252 CCATCCATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.69, C:0.21, G:0.00, T:0.10
Consensus pattern (20 bp):
AACAACATAAAAAAACAAAT
Found at i:3996598 original size:9 final size:9
Alignment explanation
Indices: 3996586--3996627 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
3996576 TTTTTTTAGA
*
3996586 TTTTTCTCC
1 TTTTTTTCC
*
3996595 TTTTTTGCC
1 TTTTTTTCC
3996604 TTTTTTTCC
1 TTTTTTTCC
3996613 TTTTTTTCC
1 TTTTTTTCC
3996622 TTTTTT
1 TTTTTT
3996628 ATTTTATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (9 bp):
TTTTTTTCC
Found at i:3998248 original size:14 final size:14
Alignment explanation
Indices: 3998229--3998256 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3998219 AGAGACTATA
3998229 GCATTAGTGATGTT
1 GCATTAGTGATGTT
3998243 GCATTAGTGATGTT
1 GCATTAGTGATGTT
3998257 TCCCTTTTGT
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:0.21, C:0.07, G:0.29, T:0.43
Consensus pattern (14 bp):
GCATTAGTGATGTT
Found at i:3999952 original size:37 final size:36
Alignment explanation
Indices: 3999877--3999952 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
3999867 TTTTTATATT
*
3999877 TTTAATTTTATAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTATAAAAAAATTATATAAATATTATCAA
* *
3999913 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTATAAA-AAAATTATATAAATATTAT-CAA
3999950 TTT
1 TTT
3999953 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (36 bp):
TTTAATTTTATAAAAAAATTATATAAATATTATCAA
Found at i:4000115 original size:18 final size:18
Alignment explanation
Indices: 4000092--4000136 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
4000082 CCAGTAATCC
4000092 TATTCCCTAGTAATCTTT
1 TATTCCCTAGTAATCTTT
*
4000110 TATTCCTACTGGTAATCTTT
1 TATTCC--CTAGTAATCTTT
4000130 TATTCCC
1 TATTCCC
4000137 ATTGATAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 7 0.29
20 17 0.71
ACGTcount: A:0.20, C:0.24, G:0.07, T:0.49
Consensus pattern (18 bp):
TATTCCCTAGTAATCTTT
Found at i:4000145 original size:20 final size:20
Alignment explanation
Indices: 4000102--4000148 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
4000092 TATTCCCTAG
* *
4000102 TAATCTTTTATTCCTACTGG
1 TAATCTTTTATTCCCACTGA
*
4000122 TAATCTTTTATTCCCATTGA
1 TAATCTTTTATTCCCACTGA
4000142 TAATCTT
1 TAATCTT
4000149 ACATTATGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.51
Consensus pattern (20 bp):
TAATCTTTTATTCCCACTGA
Found at i:4006401 original size:54 final size:54
Alignment explanation
Indices: 4006278--4006403 Score: 200
Period size: 54 Copynumber: 2.3 Consensus size: 54
4006268 ATTGAATGAT
* * * *
4006278 GGTATCAATATCCTTAAAACATCGAATGCAAGATTGTTATCGGTACCTTGAGGA
1 GGTATCGATACCCTTGAAACATCGAATGCAAGATTGGTATCGGTACCTTGAGGA
4006332 GGTATCGATACCCTTGAAACATCGAATGCCAA-ATTGGTATCGGTACCTTGAGGA
1 GGTATCGATACCCTTGAAACATCGAATG-CAAGATTGGTATCGGTACCTTGAGGA
4006386 GGTATCGATACCCTTGAA
1 GGTATCGATACCCTTGAA
4006404 GGGAAGTATC
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
54 64 0.96
55 3 0.04
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (54 bp):
GGTATCGATACCCTTGAAACATCGAATGCAAGATTGGTATCGGTACCTTGAGGA
Found at i:4006840 original size:21 final size:21
Alignment explanation
Indices: 4006785--4006844 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
4006775 TATGATCATA
* * *
4006785 TGAATATGGAAATATGAACTT
1 TGAATAAGTAAATGTGAACTT
4006806 TGAATAAGTAAATGTGAACTT
1 TGAATAAGTAAATGTGAACTT
* *
4006827 TGAATCAGTGAATGTGAA
1 TGAATAAGTAAATGTGAA
4006845 TAGATCCTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.42, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
TGAATAAGTAAATGTGAACTT
Found at i:4007034 original size:23 final size:23
Alignment explanation
Indices: 4007000--4007052 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
4006990 TCGGGACATA
* *
4007000 TATGTGGTACTTCAATGCAAACT
1 TATGTGGAACTTCAATGCAAACC
* *
4007023 TATGTGGAACTTTAGTGCAAACC
1 TATGTGGAACTTCAATGCAAACC
4007046 TATGTGG
1 TATGTGG
4007053 TCATTTGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (23 bp):
TATGTGGAACTTCAATGCAAACC
Found at i:4013268 original size:54 final size:54
Alignment explanation
Indices: 4013189--4013319 Score: 183
Period size: 54 Copynumber: 2.4 Consensus size: 54
4013179 TTATACCTAA
* * * **
4013189 AGGATGGTATTGATATCCTTAAAACA-CAGAATGCCAGATTGGTATCGGTACCTTG
1 AGGA-GGTATTGATACCCTTGAAACATC-GAATGCCAAATTGGTATCAATACCTTG
4013244 AGGAGGTATTGATACCCTTGAAACATCGAATGCCAAATTGGTATCAATACCTTG
1 AGGAGGTATTGATACCCTTGAAACATCGAATGCCAAATTGGTATCAATACCTTG
*
4013298 AGGAGGTATCGATACCCTTGAA
1 AGGAGGTATTGATACCCTTGAA
4013320 GGGAAGTATC
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
54 64 0.93
55 5 0.07
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (54 bp):
AGGAGGTATTGATACCCTTGAAACATCGAATGCCAAATTGGTATCAATACCTTG
Found at i:4013893 original size:21 final size:21
Alignment explanation
Indices: 4013867--4013923 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
4013857 TCGAGGGTCT
*
4013867 TATGTGGTCCTTCGGGATAAA
1 TATGTGGTCCTTCGGGAAAAA
*
4013888 TATGTGGTCCTTTGGGAAAAA
1 TATGTGGTCCTTCGGGAAAAA
4013909 TATGTGG-CACTTCGG
1 TATGTGGTC-CTTCGG
4013924 TGCAAACTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.33
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGAAAAA
Found at i:4015539 original size:16 final size:17
Alignment explanation
Indices: 4015501--4015571 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 17
4015491 AATTAAGAGT
* *
4015501 TAGTCTAATAAATGAAC
1 TAGTTTAATGAATGAAC
*
4015518 TAGTTTGATGAATGAA-
1 TAGTTTAATGAATGAAC
*
4015534 TAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
* * *
4015551 TAACTTTATTCAATGAAC
1 T-AGTTTAATGAATGAAC
4015569 TAG
1 TAG
4015572 ATGCATGAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
16 14 0.33
17 15 0.35
18 14 0.33
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:4017993 original size:8 final size:8
Alignment explanation
Indices: 4017982--4018044 Score: 56
Period size: 8 Copynumber: 7.5 Consensus size: 8
4017972 CTCTTTAAAA
4017982 TTTTCTCT
1 TTTTCTCT
*
4017990 TTTT-TCC
1 TTTTCTCT
*
4017997 TTTTCTTT
1 TTTTCTCT
4018005 TTTTCTCTT
1 TTTTCTC-T
4018014 TTTTCTCT
1 TTTTCTCT
*
4018022 TTTTTTGCT
1 TTTTCT-CT
4018031 TATTTCTTCT
1 T-TTTC-TCT
4018041 TTTT
1 TTTT
4018045 TGTTATTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
7 6 0.14
8 17 0.39
9 14 0.32
10 6 0.14
11 1 0.02
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTCTCT
Found at i:4018017 original size:9 final size:9
Alignment explanation
Indices: 4017982--4018045 Score: 66
Period size: 9 Copynumber: 7.4 Consensus size: 9
4017972 CTCTTTAAAA
4017982 TTTTCTCTT
1 TTTTCTCTT
4017991 TTTTC-C--
1 TTTTCTCTT
4017997 TTTTCT-TT
1 TTTTCTCTT
4018005 TTTTCTCTT
1 TTTTCTCTT
4018014 TTTTCTCTT
1 TTTTCTCTT
4018023 TTTT-TGCTT
1 TTTTCT-CTT
*
4018032 ATTTCTTCTT
1 TTTTC-TCTT
4018042 TTTT
1 TTTT
4018046 GTTATTTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
6 5 0.11
8 8 0.17
9 26 0.57
10 6 0.13
11 1 0.02
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (9 bp):
TTTTCTCTT
Found at i:4018024 original size:19 final size:19
Alignment explanation
Indices: 4017999--4018045 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
4017989 TTTTTTCCTT
* *
4017999 TTCTTTTTTTCTCTTTTTTC
1 TTCTTTTTTT-GCTTATTTC
4018019 -TCTTTTTTTGCTTATTTC
1 TTCTTTTTTTGCTTATTTC
4018037 TTCTTTTTT
1 TTCTTTTTT
4018046 GTTATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (19 bp):
TTCTTTTTTTGCTTATTTC
Found at i:4019496 original size:17 final size:17
Alignment explanation
Indices: 4019451--4019516 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
4019441 AGAGTTAGTC
* *
4019451 TAATAAATGAACTAGTT
1 TAATTAATGAACTAGAT
* * *
4019468 TGATGAAAGAACTAGAT
1 TAATTAATGAACTAGAT
4019485 TAATTAATGAACTA-ACT
1 TAATTAATGAACTAGA-T
*
4019502 TTATTCAATGAACTA
1 TAATT-AATGAACTA
4019517 CTTCCCTAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
16 1 0.03
17 29 0.74
18 9 0.23
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.33
Consensus pattern (17 bp):
TAATTAATGAACTAGAT
Found at i:4021149 original size:15 final size:15
Alignment explanation
Indices: 4021109--4021142 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
4021099 CACTTTCTTT
4021109 TTGTAGTTCTTGCAA
1 TTGTAGTTCTTGCAA
4021124 TTGTAGTTCTTGCAA
1 TTGTAGTTCTTGCAA
4021139 TTGT
1 TTGT
4021143 GATTCTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.12, G:0.21, T:0.50
Consensus pattern (15 bp):
TTGTAGTTCTTGCAA
Found at i:4023706 original size:15 final size:15
Alignment explanation
Indices: 4023670--4023699 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4023660 TTCTTTTTAC
4023670 AGTTCTTGCAATTGT
1 AGTTCTTGCAATTGT
4023685 AGTTCTTGCAATTGT
1 AGTTCTTGCAATTGT
4023700 GATTCTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (15 bp):
AGTTCTTGCAATTGT
Found at i:4027592 original size:60 final size:62
Alignment explanation
Indices: 4027528--4027658 Score: 178
Period size: 62 Copynumber: 2.1 Consensus size: 62
4027518 TTGTTTAATA
* *
4027528 TTCCAATTTTATCCTCAAACTATA-ACCT-TCATTCTAAAT-TGGTCCCCAAACTTTTGAATC
1 TTCCAATTTTATCCTCAAACTATATACATCTCATTCTAAATAAGG-CCCCAAACTTTTGAATC
* * * *
4027588 TTCCAAATTTATCCTTACACTATATACATCTCATTCTAAATAAGGCCTCAAACTTTTGAATC
1 TTCCAATTTTATCCTCAAACTATATACATCTCATTCTAAATAAGGCCCCAAACTTTTGAATC
4027650 TTCCAATTT
1 TTCCAATTT
4027659 CATTCCCAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
60 21 0.34
61 3 0.05
62 35 0.57
63 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (62 bp):
TTCCAATTTTATCCTCAAACTATATACATCTCATTCTAAATAAGGCCCCAAACTTTTGAATC
Found at i:4029537 original size:35 final size:34
Alignment explanation
Indices: 4029481--4029662 Score: 141
Period size: 35 Copynumber: 5.0 Consensus size: 34
4029471 AACAATATAT
* * *
4029481 ATAGTTTTTGAAGATACATAATATAGTTTTCGAAA
1 ATAGTTTTTAAAAATATATAATATAGTTTT-GAAA
*
4029516 ATAGTTTTTAAAAATATATAATATAGTTTTTAAAA
1 ATAGTTTTTAAAAATATATAATATAG-TTTTGAAA
* * *
4029551 ATTGTTTTGAAAACATATA-ATATATAGTTTTTAAA
1 ATAGTTTTTAAAA-ATATATA-ATATAGTTTTGAAA
* * *
4029586 ACTATTTTTTTAAAAACATATAATATATAGTTTTTAAA
1 A-TA-GTTTTTAAAAATATAT-A-ATATAGTTTTGAAA
* *
4029624 AGGAGATTTTTGAAAACGTATATAATATAGTTTTGAAA
1 A-TAG-TTTTT-AAAA-ATATATAATATAGTTTTGAAA
4029662 A
1 A
4029663 CATATATATA
Statistics
Matches: 120, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
35 46 0.38
36 20 0.17
37 8 0.07
38 37 0.31
39 5 0.04
40 4 0.03
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (34 bp):
ATAGTTTTTAAAAATATATAATATAGTTTTGAAA
Found at i:4029611 original size:38 final size:36
Alignment explanation
Indices: 4029501--4029624 Score: 153
Period size: 38 Copynumber: 3.4 Consensus size: 36
4029491 AAGATACATA
** * *
4029501 ATATAGTTTTCGAAAATAGTTTTTAAAAATATATAAT
1 ATATAGTTTTTAAAAAT-TTTTTTAAAAACATATAAT
* *
4029538 --ATAGTTTTTAAAAATTGTTTTGAAAACATATAAT
1 ATATAGTTTTTAAAAATTTTTTTAAAAACATATAAT
4029572 ATATAGTTTTTAAAACTATTTTTTTAAAAACATATAAT
1 ATATAGTTTTTAAAA--ATTTTTTTAAAAACATATAAT
4029610 ATATAGTTTTTAAAA
1 ATATAGTTTTTAAAA
4029625 GGAGATTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
34 15 0.20
35 13 0.17
36 13 0.17
38 34 0.45
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (36 bp):
ATATAGTTTTTAAAAATTTTTTTAAAAACATATAAT
Found at i:4029634 original size:38 final size:34
Alignment explanation
Indices: 4029501--4029662 Score: 137
Period size: 38 Copynumber: 4.4 Consensus size: 34
4029491 AAGATACATA
* * *
4029501 ATATAGTTTTCGAAAATAGTTTTTAAAAATATATA-
1 ATATAGTTTT-TAAAA-ATTTTTTAAAAACATATAT
*
4029536 ATATAGTTTTTAAAAATTGTTTTGAAAACATATAAT
1 ATATAGTTTTTAAAAATT-TTTTAAAAACATAT-AT
4029572 ATATAGTTTTTAAAACTATTTTTTTAAAAACATATAAT
1 ATATAGTTTTTAAAA--A-TTTTTTAAAAACATAT-AT
* * *
4029610 ATATAGTTTTTAAAAGGAGATTTTTGAAAACGTATAT
1 ATATAGTTTTTAAAA--A-TTTTTTAAAAACATATAT
*
4029647 AATATAGTTTTGAAAA
1 -ATATAGTTTTTAAAA
4029663 CATATATATA
Statistics
Matches: 108, Mismatches: 12, Indels: 11
0.82 0.09 0.08
Matches are distributed among these distances:
33 2 0.02
34 16 0.15
35 11 0.10
36 15 0.14
37 2 0.02
38 60 0.56
39 2 0.02
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.43
Consensus pattern (34 bp):
ATATAGTTTTTAAAAATTTTTTAAAAACATATAT
Found at i:4029647 original size:40 final size:38
Alignment explanation
Indices: 4029520--4029663 Score: 140
Period size: 38 Copynumber: 3.9 Consensus size: 38
4029510 TCGAAAATAG
*
4029520 TTTTT-AAAA-ATAT-ATAATATAGTTTTTAAAA--A-T
1 TTTTTGAAAACATATAAT-ATATAGTTTTTAAAACGAGA
* **
4029553 TGTTTTGAAAACATATAATATATAGTTTTTAAAACTATT
1 T-TTTTGAAAACATATAATATATAGTTTTTAAAACGAGA
* *
4029592 TTTTTAAAAACATATAATATATAGTTTTTAAAAGGAGA
1 TTTTTGAAAACATATAATATATAGTTTTTAAAACGAGA
* *
4029630 TTTTTGAAAACGTAT-ATAATATAGTTTTGAAAAC
1 TTTTTGAAAACATATAAT-ATATAGTTTTTAAAAC
4029664 ATATATATAG
Statistics
Matches: 94, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
33 1 0.01
34 4 0.04
35 4 0.04
36 19 0.20
37 4 0.04
38 60 0.64
39 2 0.02
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (38 bp):
TTTTTGAAAACATATAATATATAGTTTTTAAAACGAGA
Found at i:4029673 original size:20 final size:22
Alignment explanation
Indices: 4029631--4029682 Score: 72
Period size: 20 Copynumber: 2.4 Consensus size: 22
4029621 AAAAGGAGAT
4029631 TTTTGAAAACGTATATAATATAG
1 TTTTGAAAACG-ATATAATATAG
4029654 TTTTGAAAAC-ATAT-ATATAG
1 TTTTGAAAACGATATAATATAG
*
4029674 TTTTTAAAA
1 TTTTGAAAA
4029683 TAGTTTTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 14 0.50
21 4 0.14
23 10 0.36
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (22 bp):
TTTTGAAAACGATATAATATAG
Found at i:4029710 original size:58 final size:60
Alignment explanation
Indices: 4029608--4029747 Score: 162
Period size: 58 Copynumber: 2.3 Consensus size: 60
4029598 AAAACATATA
* * *
4029608 ATATATAGTTTTTAAAAGGAGATTTTTGAAAAC--GTATATAATATAGTT-TTGAAAACAT
1 ATATATAGTTTTTAAAA-TAGATTTTTGAAAACATATATATAATATAATTCTTGAAAACAT
*
4029666 ATATATAGTTTTTAAAATAG-TTTTTGAAAACATATATAATATATATAATTCTTGTAAACAT
1 ATATATAGTTTTTAAAATAGATTTTTGAAAACATATAT-ATA-ATATAATTCTTGAAAACAT
*
4029727 ATTATATACTTTTTGAAAATA
1 A-TATATAGTTTTT-AAAATA
4029748 TAATATATGT
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
56 11 0.16
57 2 0.03
58 20 0.29
59 3 0.04
60 7 0.10
61 10 0.14
62 11 0.16
63 6 0.09
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (60 bp):
ATATATAGTTTTTAAAATAGATTTTTGAAAACATATATATAATATAATTCTTGAAAACAT
Found at i:4029754 original size:22 final size:22
Alignment explanation
Indices: 4029706--4029755 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
4029696 CATATATAAT
*
4029706 ATATATAATTCTTGTAAACATA
1 ATATATAATTCTTGAAAACATA
* * * *
4029728 TTATATACTTTTTGAAAATATA
1 ATATATAATTCTTGAAAACATA
4029750 ATATAT
1 ATATAT
4029756 GTTATATAGT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (22 bp):
ATATATAATTCTTGAAAACATA
Found at i:4029785 original size:29 final size:29
Alignment explanation
Indices: 4029728--4029789 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
4029718 TGTAAACATA
*
4029728 TTATATACTTTTTGAAAATATAATATATG
1 TTATATACTTTTTAAAAATATAATATATG
*
4029757 TTATATAGTTTTTAAATAAT-T-ATATTATG
1 TTATATACTTTTTAAA-AATATAATA-TATG
4029786 TTAT
1 TTAT
4029790 GTTATGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 3 0.10
29 23 0.79
30 3 0.10
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (29 bp):
TTATATACTTTTTAAAAATATAATATATG
Found at i:4029789 original size:5 final size:5
Alignment explanation
Indices: 4029785--4030278 Score: 961
Period size: 5 Copynumber: 98.8 Consensus size: 5
4029775 ATTATATTAT
* * *
4029785 GTTAT GTTAT GTTAT GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
4029835 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
4029885 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
4029935 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
4029985 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
4030035 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
4030085 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
4030135 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
4030185 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC
4030235 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTA
1 GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTAC GTTA
4030279 TATTTATTAT
Statistics
Matches: 488, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 488 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (5 bp):
GTTAC
Found at i:4030337 original size:27 final size:23
Alignment explanation
Indices: 4030285--4030335 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 23
4030275 GTTATATTTA
4030285 TTATTTATTATTATTTTATTCGT
1 TTATTTATTATTATTTTATTCGT
*
4030308 TTATTTACTTAATTATATTTATTGGT
1 TTATTTA-TT-ATTAT-TTTATTCGT
4030334 TT
1 TT
4030336 TAGGTCCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 7 0.29
24 2 0.08
25 5 0.21
26 10 0.42
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.67
Consensus pattern (23 bp):
TTATTTATTATTATTTTATTCGT
Found at i:4031713 original size:5 final size:5
Alignment explanation
Indices: 4031698--4031727 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
4031688 TTTTTTGTGT
4031698 TTTTCC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTT-C TTTTC TTTTC TTTTC TTTTC TTTT
4031728 ATCTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:4041212 original size:23 final size:23
Alignment explanation
Indices: 4041194--4041254 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
4041184 CTCGTATAAA
*
4041194 TGCACCGAAGTGCCACGTAGATT
1 TGCACCGAAGTGCCACGTAGAAT
** *
4041217 TATACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
4041240 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
4041255 TATAAAGTGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:4053171 original size:19 final size:19
Alignment explanation
Indices: 4053144--4053186 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
4053134 ATACACGTGC
*
4053144 GTATCTTATTTATACATAT
1 GTATTTTATTTATACATAT
*
4053163 GTATTTTATTTGTACATAT
1 GTATTTTATTTATACATAT
4053182 GTATT
1 GTATT
4053187 ATTGATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.56
Consensus pattern (19 bp):
GTATTTTATTTATACATAT
Found at i:4058936 original size:134 final size:134
Alignment explanation
Indices: 4058717--4059392 Score: 952
Period size: 134 Copynumber: 5.1 Consensus size: 134
4058707 TTTCCAAGGT
* * * * **
4058717 AGATCAGA-TCGAGAAA-CGTTGATTCA-TTCCACTGTTCTTCAGGGAAGATTGAATCAGAATAA
1 AGATCAGACTCGAGAAATCTTTGATCCACTT-CACTGCTCTTCAGGGAAGATTGAATAAGAATCG
* * * * * *
4058779 ATTTACTTCATTGCTCTTTAGGAAGACCAAATCTGAAAGAAGAATAATCTTCCCCACTACTCTTT
65 ATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTACTCCACTACTCTTT
4058844 AGGGG
130 AGGGG
* * *
4058849 AGATCAGACTTGAGAAAAT-TTTGATCAACTTCACTACTCTTCAGGGAAGATTGAATAAGAATCG
1 AGATCAGACTCGAG-AAATCTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATAAGAATCG
* * * * *
4058913 ATTTGCTTCACTACTATTCAGGAAGACCAAATCTGAAAGAAGAAGAATATGCTCCATTACTCTTT
65 ATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTACTCCACTACTCTTT
4058978 AGGGG
130 AGGGG
*
4058983 AGATCAGACTCGAGAAATCTTTGGTCCACTTCACTGCTCTTCAGGGAAGATTGAATCAA-AATCG
1 AGATCAGACTCGAGAAATCTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAAT-AAGAATCG
* *
4059047 ATTTGCTTCACTGCTCTTTAGGAAGACC-AATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTT
65 ATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTACTCCACTACTCTTT
4059111 AGGGG
130 AGGGG
*
4059116 AGATCAGACTCGAGAAATCTTTGATCTACTTCACTGCTCTTCAGGGAAGATTGAATCAA-AATCG
1 AGATCAGACTCGAGAAATCTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAAT-AAGAATCG
* * *
4059180 ATTTGCATCACTGCTCTTCAGGAAGACCAAATCTGAAAGAATAAGAATCTACTCCACTACTTTTT
65 ATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTACTCCACTACTCTTT
4059245 AGGGG
130 AGGGG
* * * * *
4059250 AGGTCAGACTCGAGAAAACTTTGATCCACTTCACTGCTCTTTAGGGAAGATTGAATCAGAATCAA
1 AGATCAGACTCGAGAAATCTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATAAGAATCGA
* * *
4059315 TTTGCTTCACTACTTTTCAGGAAGACCAGATCTGAAAGAAGAAGAATCTACTCCACTACTCTTTA
66 TTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTACTCCACTACTCTTTA
4059380 GGGG
131 GGGG
4059384 AGATCAGAC
1 AGATCAGAC
4059393 CTTTCAAAGA
Statistics
Matches: 488, Mismatches: 48, Indels: 14
0.89 0.09 0.03
Matches are distributed among these distances:
132 8 0.02
133 136 0.28
134 340 0.70
135 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (134 bp):
AGATCAGACTCGAGAAATCTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATAAGAATCGA
TTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAGAATCTACTCCACTACTCTTTA
GGGG
Found at i:4059057 original size:41 final size:42
Alignment explanation
Indices: 4059011--4059205 Score: 132
Period size: 41 Copynumber: 4.5 Consensus size: 42
4059001 CTTTGGTCCA
*
4059011 CTTCACTGCTCTTCAGGGAAGAT-TGAATCAAAATCGATTTG
1 CTTCACTGCTCTTCAGGGAAGATCTGAATCAAAATCGATCTG
* **
4059052 CTTCACTGCTCTTTA-GGAAGACCAATCTGAAAGAAGAA--GAATCTG
1 CTTCACTGCTCTTCAGGGAAG----ATCTGAATCAA-AATCG-ATCTG
* * * * * * *
4059097 CTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAATCTTTGATCTA
1 CTTCACTGCTCTTCAGGGAAGATCTGAATC-A-AAATC---GATCTG
*
4059144 CTTCACTGCTCTTCAGGGAAGAT-TGAATCAAAATCGATTTG
1 CTTCACTGCTCTTCAGGGAAGATCTGAATCAAAATCGATCTG
*
4059185 CATCACTGCTCTTCA-GGAAGA
1 CTTCACTGCTCTTCAGGGAAGA
4059206 CCAAATCTGA
Statistics
Matches: 118, Mismatches: 21, Indels: 31
0.69 0.12 0.18
Matches are distributed among these distances:
40 11 0.09
41 32 0.27
42 5 0.04
43 3 0.03
44 9 0.08
45 24 0.20
46 10 0.08
47 23 0.19
48 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (42 bp):
CTTCACTGCTCTTCAGGGAAGATCTGAATCAAAATCGATCTG
Found at i:4059202 original size:267 final size:266
Alignment explanation
Indices: 4058717--4059392 Score: 1002
Period size: 267 Copynumber: 2.5 Consensus size: 266
4058707 TTTCCAAGGT
* * * *
4058717 AGATCAGA-TCGAGAAACGTTGATTCA-TTCCACTGTTCTTCAGGGAAGATTGAATCAGAATAAA
1 AGATCAGACTCGAGAAACTTTGATCCACTT-CACTGCTCTTCAGGGAAGATTGAATCAGAATCAA
* * * * *
4058780 TTTACTTCATTGCTCTTTAGGAAGACCAAATCTGAAAGAAGAATAATCTTCCCCACTACTCTTTA
65 TTTGCTTCACTGCTCTTTAGGAAGACC-AATCTGAAAGAAGAAGAATCTACTCCACTACTCTTTA
*
4058845 GGGGAGATCAGACTTGAGAAAATTTTGATCAACTTCACTACTCTTCAGGGAAGATTGAATAAGAA
129 GGGGAGATCAGACTCGAGAAAATTTTGATCAACTTCACTACTCTTCAGGGAAGATTGAATAAGAA
* * *
4058910 TCGATTTGCTTCACTACTATTCAGGAAGACCAAATCTGAAAGAAGAAGAATATGCTCCATTACTC
194 TCGATTTGCATCACTACTATTCAGGAAGACCAAATCTGAAAGAAGAAGAATATACTCCACTACTC
4058975 TTTAGGGG
259 TTTAGGGG
* * *
4058983 AGATCAGACTCGAGAAATCTTTGGTCCACTTCACTGCTCTTCAGGGAAGATTGAATCAAAATCGA
1 AGATCAGACTCGAGAAA-CTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCAGAATCAA
*
4059048 TTTGCTTCACTGCTCTTTAGGAAGACCAATCTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAG
65 TTTGCTTCACTGCTCTTTAGGAAGACCAATCTGAAAGAAGAAGAATCTACTCCACTACTCTTTAG
* *
4059113 GGGAGATCAGACTCGAG-AAATCTTTGATCTACTTCACTGCTCTTCAGGGAAGATTGAATCAA-A
130 GGGAGATCAGACTCGAGAAAAT-TTTGATCAACTTCACTACTCTTCAGGGAAGATTGAAT-AAGA
* * * *
4059176 ATCGATTTGCATCACTGCTCTTCAGGAAGACCAAATCTGAAAGAATAAGAATCTACTCCACTACT
193 ATCGATTTGCATCACTACTATTCAGGAAGACCAAATCTGAAAGAAGAAGAATATACTCCACTACT
*
4059241 TTTTAGGGG
258 CTTTAGGGG
* *
4059250 AGGTCAGACTCGAGAAAACTTTGATCCACTTCACTGCTCTTTAGGGAAGATTGAATCAGAATCAA
1 AGATCAGACTCGAG-AAACTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCAGAATCAA
*
4059315 TTTGCTTCACTACT-TTTCAGGAAGACCAGATCTGAAAGAAGAAGAATCTACTCCACTACTCTTT
65 TTTGCTTCACTGCTCTTT-AGGAAGACCA-ATCTGAAAGAAGAAGAATCTACTCCACTACTCTTT
4059379 AGGGGAGATCAGAC
128 AGGGGAGATCAGAC
4059393 CTTTCAAAGA
Statistics
Matches: 372, Mismatches: 30, Indels: 14
0.89 0.07 0.03
Matches are distributed among these distances:
266 15 0.04
267 240 0.65
268 115 0.31
269 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (266 bp):
AGATCAGACTCGAGAAACTTTGATCCACTTCACTGCTCTTCAGGGAAGATTGAATCAGAATCAAT
TTGCTTCACTGCTCTTTAGGAAGACCAATCTGAAAGAAGAAGAATCTACTCCACTACTCTTTAGG
GGAGATCAGACTCGAGAAAATTTTGATCAACTTCACTACTCTTCAGGGAAGATTGAATAAGAATC
GATTTGCATCACTACTATTCAGGAAGACCAAATCTGAAAGAAGAAGAATATACTCCACTACTCTT
TAGGGG
Found at i:4060155 original size:45 final size:45
Alignment explanation
Indices: 4060044--4060392 Score: 302
Period size: 45 Copynumber: 7.9 Consensus size: 45
4060034 GGATACTACT
* *
4060044 TAAAAG-TTGACTCCTCTTTACGAGAAAGTCAAG-ATGGAC-ACAA
1 TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAAT-GACAACAC
* * *
4060087 TAAAATATTGACTCATCTTCACTAGAAAGTCAAGAATGACAACAC
1 TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACAC
* * * * * * * *
4060132 TAAGATATTAACTCCTATTCACTAGAAAGTTAAGAAGGGCAACAC
1 TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACAC
* * * * * *
4060177 TAAAATATTAACTCCTCTTCGCGAGAAAGTCAATAATGAAAATAC
1 TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACAC
* * **
4060222 TGAGAGATTGACTTATCTTCACGAGAAAGTCAAGAAT---AACAC
1 TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACAC
* * * * *
4060264 TGAAAGATTGACTCCTCTTGACGAGAAAGTCCAGAATGACAATAT
1 TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACAC
* * *
4060309 TGAAAGATTGACTTCTCTTCACAAGAAAGTCAAGAAT---AACAC
1 TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACAC
* * ** *
4060351 TAAAAGATTAACTCCTCTTCATGAGGGAGTCAAGAATAACAA
1 TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAA
4060393 AGATCGACTT
Statistics
Matches: 246, Mismatches: 51, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
42 69 0.28
43 5 0.02
44 27 0.11
45 145 0.59
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (45 bp):
TAAAAGATTGACTCCTCTTCACGAGAAAGTCAAGAATGACAACAC
Found at i:4060196 original size:90 final size:87
Alignment explanation
Indices: 4060050--4060661 Score: 355
Period size: 76 Copynumber: 7.4 Consensus size: 87
4060040 TACTTAAAAG
* * * * * * * *
4060050 TTGACTCCTCTTTACGAGAAAGTCAAG-ATGGACACAATAAAATATTGACTCATCTTCACTAGAA
1 TTGACTTCTCTTCACAAGAAAGTCAAGAAT--A-ACACTAAAAGATTAACTCCTCTTCACGAGAA
* *
4060114 AGTCAAGAATGACAACACTAAGATA
63 AGTCAAGAATGACAATACTAAGAGA
* * * * * * * *
4060139 TTAACTCCTATTCACTAGAAAGTTAAGAAGGGCAACACTAAAATATTAACTCCTCTTCGCGAGAA
1 TTGACTTCTCTTCACAAGAAAGTCAAGAA---TAACACTAAAAGATTAACTCCTCTTCACGAGAA
* * *
4060204 AGTCAATAATGAAAATACTGAGAGA
63 AGTCAAGAATGACAATACTAAGAGA
* * * * *
4060229 TTGACTTATCTTCACGAGAAAGTCAAGAATAACACTGAAAGATTGACTCCTCTTGACGAGAAAGT
1 TTGACTTCTCTTCACAAGAAAGTCAAGAATAACACTAAAAGATTAACTCCTCTTCACGAGAAAGT
* *
4060294 CCAGAATGACAATATTGAA-AGA
66 CAAGAATGACAATACT-AAGAGA
* **
4060316 TTGACTTCTCTTCACAAGAAAGTCAAGAATAACACTAAAAGATTAACTCCTCTTCATGAGGGAGT
1 TTGACTTCTCTTCACAAGAAAGTCAAGAATAACACTAAAAGATTAACTCCTCTTCACGAGAAAGT
4060381 CAAGAAT----A-AC-AA-AGA
66 CAAGAATGACAATACTAAGAGA
* ** * * * * * * * **
4060396 TCGACTTCTCTTCATGAGGATGTCAAAAATAACATTGAAAGATTGACTCCTCTTCATGAGGGAGT
1 TTGACTTCTCTTCACAAGAAAGTCAAGAATAACACTAAAAGATTAACTCCTCTTCACGAGAAAGT
*
4060461 TAAG-A--A-AA-AC-AA-AGA
66 CAAGAATGACAATACTAAGAGA
* * * * * * *
4060476 TTAAATTCTCTTCACGAGGAAGTCAAGAA-AA-AC--AAAGATTGACTTCTCTTCACGAGGAAGT
1 TTGACTTCTCTTCACAAGAAAGTCAAGAATAACACTAAAAGATTAACTCCTCTTCACGAGAAAGT
4060537 CAAGAAT---AA-A--AA-AGA
66 CAAGAATGACAATACTAAGAGA
* * * *
4060552 TTGAATTCTCTTCACAAGGAAGTCAAGAAT-A-AC-AAAA-ATTGACTTCTCTTCACGAGAAAGT
1 TTGACTTCTCTTCACAAGAAAGTCAAGAATAACACTAAAAGATTAACTCCTCTTCACGAGAAAGT
* *
4060613 CATG--T-A-TA-AC-AAG-GA
66 CAAGAATGACAATACTAAGAGA
* * *
4060628 TTGACTTCTTTTCACGAGGAAGTCAAGAATAACA
1 TTGACTTCTCTTCACAAGAAAGTCAAGAATAACA
4060662 AAGTTCGACT
Statistics
Matches: 435, Mismatches: 72, Indels: 43
0.79 0.13 0.08
Matches are distributed among these distances:
74 1 0.00
75 2 0.00
76 120 0.28
77 8 0.02
78 2 0.00
79 3 0.01
80 95 0.22
82 1 0.00
83 1 0.00
87 108 0.25
88 1 0.00
89 22 0.05
90 70 0.16
91 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (87 bp):
TTGACTTCTCTTCACAAGAAAGTCAAGAATAACACTAAAAGATTAACTCCTCTTCACGAGAAAGT
CAAGAATGACAATACTAAGAGA
Found at i:4060302 original size:87 final size:87
Alignment explanation
Indices: 4060172--4060370 Score: 292
Period size: 87 Copynumber: 2.3 Consensus size: 87
4060162 TAAGAAGGGC
* * *
4060172 AACACTAAAATATTAACTCCTCTTCGCGAGAAAGTCAATAATGAAAATACTGAGAGATTGACTTA
1 AACACTAAAAGATTAACTCCTCTTCGCGAGAAAGTCAAGAATGAAAATACTGAAAGATTGACTTA
*
4060237 TCTTCACGAGAAAGTCAAGAAT
66 TCTTCACAAGAAAGTCAAGAAT
* * * * *
4060259 AACACTGAAAGATTGACTCCTCTT-GACGAGAAAGTCCAGAATGACAATATTGAAAGATTGACTT
1 AACACTAAAAGATTAACTCCTCTTCG-CGAGAAAGTCAAGAATGAAAATACTGAAAGATTGACTT
*
4060323 CTCTTCACAAGAAAGTCAAGAAT
65 ATCTTCACAAGAAAGTCAAGAAT
4060346 AACACTAAAAGATTAACTCCTCTTC
1 AACACTAAAAGATTAACTCCTCTTC
4060371 ATGAGGGAGT
Statistics
Matches: 98, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
86 1 0.01
87 97 0.99
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (87 bp):
AACACTAAAAGATTAACTCCTCTTCGCGAGAAAGTCAAGAATGAAAATACTGAAAGATTGACTTA
TCTTCACAAGAAAGTCAAGAAT
Found at i:4060387 original size:87 final size:82
Alignment explanation
Indices: 4060172--4061160 Score: 728
Period size: 76 Copynumber: 12.6 Consensus size: 82
4060162 TAAGAAGGGC
* * * * * * *
4060172 AACACTAAAATATTAACTCCTCTTCGCGAGAAAGTCAATAATGAAAATACTGAGAGATTGACTTA
1 AACACTAAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAAT--AAA-AC--AAAGATTGACTTC
*
4060237 TCTTCACGAGAAAGTCAAGAAT
61 TCTTCACGAGGAAGTCAAGAAT
* * * * *
4060259 AACACTGAAAGATTGACTCCTCTTGACGAGAAAGTCCAGAATGACAATATTGAAAGATTGACTTC
1 AACACTAAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAAT-A-AA-A--CAAAGATTGACTTC
* *
4060324 TCTTCACAAGAAAGTCAAGAAT
61 TCTTCACGAGGAAGTCAAGAAT
* * * *
4060346 AACACTAAAAGATTAACTCCTCTTCATGAGGGAGTCAAGAAT--AACAAAGATCGACTTCTCTTC
1 AACACTAAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAAACAAAGATTGACTTCTCTTC
* * *
4060409 ATGAGGATGTCAAAAAT
66 ACGAGGAAGTCAAGAAT
* * * * * * *
4060426 AACATTGAAAGATTGACTCCTCTTCATGAGGGAGTTAAG-A-AAAACAAAGATTAAATTCTCTTC
1 AACACTAAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAAACAAAGATTGACTTCTCTTC
4060489 ACGAGGAAGTCAAGAA-
66 ACGAGGAAGTCAAGAAT
* *
4060505 AA-AC--AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT-AAA-AAAGATTGAATTCTCTTC
1 AACACTAAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAAACAAAGATTGACTTCTCTTC
*
4060565 ACAAGGAAGTCAAGAAT
66 ACGAGGAAGTCAAGAAT
* * * * * *
4060582 -A-AC-AAAA-ATTGACTTCTCTTCACGAGAAAGTCATG--TATAACAAGGATTGACTTCTTTTC
1 AACACTAAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAAACAAAGATTGACTTCTCTTC
4060641 ACGAGGAAGTCAAGAAT
66 ACGAGGAAGTCAAGAAT
*
4060658 -A-AC--AAAG-TTCGACTTCTCTTCACGAGGAAGTCAAGAAT--AACAAAG-TTCGACTTCTCT
1 AACACTAAAAGATT-GACTCCTCTTCACGAGGAAGTCAAGAATAAAACAAAGATT-GACTTCTCT
*
4060715 TCATGAGGAAGTCAAGAAT
64 TCACGAGGAAGTCAAGAAT
* * * **
4060734 -A-AC--AAAGATCGACTTCTCTTCAAGAGGAAGTCAAGAAT-AAA-AAAGATAAACTTCTCTTC
1 AACACTAAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAAACAAAGATTGACTTCTCTTC
4060793 ACGAGGAAGTCAAGAAT
66 ACGAGGAAGTCAAGAAT
* * * * * *
4060810 -A-A--AAAAGATTGAATTCTATTCACGAGAAAGTCAATAAT--AACAATGATTGACTTCTCTTC
1 AACACTAAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAAACAAAGATTGACTTCTCTTC
* *
4060869 ACAAGGAAGTCAATAAT
66 ACGAGGAAGTCAAGAAT
* ** * *
4060886 -A-A-T-AAAGATTGACTTCTCTTTGCGAGGAATTCAAGAAT-AAA-AAAGATTGAATTCTCTTC
1 AACACTAAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAAACAAAGATTGACTTCTCTTC
*
4060945 ACGAGGAAGTTAAGAAT
66 ACGAGGAAGTCAAGAAT
* * * * *
4060962 -A-A--AAAAGATCGACTTCTCTTCA-TATGGAAGTCAAGAAT--AACAAAGATTGACTCCTTTT
1 AACACTAAAAGATTGACTCCTCTTCACGA-GGAAGTCAAGAATAAAACAAAGATTGACTTCTCTT
* * *
4061020 CGCGAGGGAGTCAGGAAT
65 CACGAGGAAGTCAAGAAT
* * * * *
4061038 -A-A--AAAAGATTGACTTCTCTTCAAGAGGAAGTCAAGAATAACAA-AGATAGATTGGCTCCTA
1 AACACTAAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAA-AACA-A-AGATTGACTTCTC
*
4061098 TTCACGAGGGAA-TTAAGAAT
63 TTCACGA-GGAAGTCAAGAAT
* *
4061118 -A-AC-AAAA-ATTGACTTCTCTTCACGAGAAAGTCAAGAATCAAAA
1 AACACTAAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAAT-AAAA
4061161 AGATAGATTA
Statistics
Matches: 762, Mismatches: 105, Indels: 77
0.81 0.11 0.08
Matches are distributed among these distances:
74 1 0.00
75 14 0.02
76 455 0.60
77 14 0.02
78 3 0.00
79 6 0.01
80 151 0.20
81 9 0.01
82 1 0.00
83 1 0.00
86 1 0.00
87 106 0.14
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.25
Consensus pattern (82 bp):
AACACTAAAAGATTGACTCCTCTTCACGAGGAAGTCAAGAATAAAACAAAGATTGACTTCTCTTC
ACGAGGAAGTCAAGAAT
Found at i:4060407 original size:38 final size:38
Alignment explanation
Indices: 4060311--4061164 Score: 946
Period size: 38 Copynumber: 22.2 Consensus size: 38
4060301 GACAATATTG
* *
4060311 AAAGATTGACTTCTCTTCACAAGAAAGTCAAGAATAACAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT-A-AC
* * * *
4060351 TAAAAGATTAACTCCTCTTCATGAGGGAGTCAAGAATAAC
1 --AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
4060391 AAAGATCGACTTCTCTTCATGAGGATGTCAAAAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * *
4060429 ATTGAAAGATTGACTCCTCTTCATGAGGGAGTTAAGAAAAAC
1 ----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
4060471 AAAGATTAAATTCTCTTCACGAGGAAGTCAAGAAAAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
4060509 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
4060547 AAAGATTGAATTCTCTTCACAAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
4060585 AAAAATTGACTTCTCTTCACGAGAAAGTCATGTATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
4060623 AAGGATTGACTTCTTTTCACGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
4060661 AAAG-TTCGACTTCTCTTCACGAGGAAGTCAAGAATAAC
1 AAAGATT-GACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
4060699 AAAG-TTCGACTTCTCTTCATGAGGAAGTCAAGAATAAC
1 AAAGATT-GACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
4060737 AAAGATCGACTTCTCTTCAAGAGGAAGTCAAGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
** *
4060775 AAAGATAAACTTCTCTTCACGAGGAAGTCAAGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
4060813 AAAGATTGAATTCTATTCACGAGAAAGTCAATAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * *
4060851 AATGATTGACTTCTCTTCACAAGGAAGTCAATAATAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
** * *
4060889 AAAGATTGACTTCTCTTTGCGAGGAATTCAAGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
4060927 AAAGATTGAATTCTCTTCACGAGGAAGTTAAGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
4060965 AAAGATCGACTTCTCTTCA-TATGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGA-GGAAGTCAAGAATAAC
* * * * * *
4061003 AAAGATTGACTCCTTTTCGCGAGGGAGTCAGGAATAAA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
*
4061041 AAAGATTGACTTCTCTTCAAGAGGAAGTCAAGAATAAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* *
4061079 AAAGATAGA-TTGGCTCCTATTCACGAGGGAA-TTAAGAATAAC
1 AAAGATTGACTT--CT-C--TTCACGA-GGAAGTCAAGAATAAC
* *
4061121 AAAAATTGACTTCTCTTCACGAGAAAGTCAAGAATCAA-
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAAT-AAC
4061159 AAAGAT
1 AAAGAT
4061165 AGATTAAATT
Statistics
Matches: 689, Mismatches: 106, Indels: 38
0.83 0.13 0.05
Matches are distributed among these distances:
37 8 0.01
38 579 0.84
39 6 0.01
40 4 0.01
41 3 0.00
42 83 0.12
43 6 0.01
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (38 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:4062963 original size:7 final size:7
Alignment explanation
Indices: 4062946--4063032 Score: 59
Period size: 7 Copynumber: 11.9 Consensus size: 7
4062936 TTCACTCTAT
4062946 TTTTTTC
1 TTTTTTC
4062953 -TTTTTC
1 TTTTTTC
*
4062959 TTTTTTTA
1 -TTTTTTC
4062967 TTTTTTC
1 TTTTTTC
*
4062974 TTATTTC
1 TTTTTTC
* *
4062981 TTTTCTA
1 TTTTTTC
*
4062988 TATTTTC
1 TTTTTTC
4062995 TATATTTTC
1 T-T-TTTTC
4063004 TCTTTTATC
1 T-TTTT-TC
4063013 TTTTTTC
1 TTTTTTC
* *
4063020 CTTGTTC
1 TTTTTTC
4063027 TTTTTT
1 TTTTTT
4063033 ATCTTCTCTC
Statistics
Matches: 60, Mismatches: 15, Indels: 10
0.71 0.18 0.12
Matches are distributed among these distances:
6 6 0.10
7 32 0.53
8 12 0.20
9 10 0.17
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.77
Consensus pattern (7 bp):
TTTTTTC
Found at i:4066873 original size:85 final size:83
Alignment explanation
Indices: 4066724--4066889 Score: 212
Period size: 85 Copynumber: 2.0 Consensus size: 83
4066714 TATGACTCAC
4066724 ATTTATGACACGCATTTATGACGCTCATTGCGTGTCATTGAAGCCTCCGTCATAAATGAAGATGA
1 ATTTATGACACGCATTTATGACGCTCATTGCGTGTCATTGAAGCCT-CGTCATAAA-GAAGATGA
*
4066789 CACACATTTGTGTGTCATAA
64 CACACATTCGTGTGTCATAA
* * *
4066809 ATTTATGACGCGCATTTATGAC-TTACATTGTGTGTCATTGAAGCACAT-GTCATTAAA-AATGA
1 ATTTATGACACGCATTTATGACGCT-CATTGCGTGTCATTGAAGC-C-TCGTCA-TAAAGAA-GA
4066871 TGACACACATTCGTGTGTC
61 TGACACACATTCGTGTGTC
4066890 GTGATTGTAT
Statistics
Matches: 72, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
84 3 0.04
85 63 0.88
86 5 0.07
87 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (83 bp):
ATTTATGACACGCATTTATGACGCTCATTGCGTGTCATTGAAGCCTCGTCATAAAGAAGATGACA
CACATTCGTGTGTCATAA
Found at i:4066916 original size:2 final size:2
Alignment explanation
Indices: 4066909--4066951 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
4066899 TGTCGTAAAT
4066909 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4066951 T
1 T
4066952 TGTATATTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4070901 original size:24 final size:25
Alignment explanation
Indices: 4070874--4070924 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
4070864 GCGATTTTAG
*
4070874 GGGAGGAGGAGGAGGAAGAGA-GGT
1 GGGAGGAGGAGAAGGAAGAGACGGT
* * *
4070898 GGGATGAGGCGAAGGGAGAGACGGT
1 GGGAGGAGGAGAAGGAAGAGACGGT
4070923 GG
1 GG
4070925 TGCGGTGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.29, C:0.04, G:0.61, T:0.06
Consensus pattern (25 bp):
GGGAGGAGGAGAAGGAAGAGACGGT
Found at i:4073905 original size:2 final size:2
Alignment explanation
Indices: 4073898--4073926 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4073888 TTCGAAATGA
4073898 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4073927 TGGTGTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4083480 original size:2 final size:2
Alignment explanation
Indices: 4083473--4083498 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4083463 GGACCTTTTC
4083473 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
4083499 TTACAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4083997 original size:2 final size:2
Alignment explanation
Indices: 4083990--4084017 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4083980 TTTCTATTTC
4083990 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
4084018 GTAAATTTTT
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:4084363 original size:81 final size:81
Alignment explanation
Indices: 4084276--4084551 Score: 238
Period size: 80 Copynumber: 3.4 Consensus size: 81
4084266 AAATGCCGAG
* * *
4084276 ACAGAGTTTTAGTTTAGCGACGTTTGTATAAAAACGTCGTAAAAGTGTCATCTATAGTGGCGTTT
1 ACAGAGTTTTACTTTAGCGGCGTTTGTATAAAAACGTCGCAAAAGTGTCATCTATAGTGGCGTTT
4084341 TTCAAAAAACGCCATA
66 TTCAAAAAACGCCATA
* * * * *
4084357 ATAGAGTTGTACTTTAGCGGCGTTT-TATACAAAA-GTCGCAATAG-GTTCATCCATAGTGGCAT
1 ACAGAGTTTTACTTTAGCGGCGTTTGTATA-AAAACGTCGCAAAAGTG-TCATCTATAGTGGCGT
* * * *
4084419 TTCTCAATAAACGCCGTG
64 TTTTCAAAAAACGCCATA
* ** ** * *
4084437 ACAGAGTATTACTTTAGCGGTATTTGTATAAAAACACCGCAATAGGTTTCGA-CTATAGTGGCGT
1 ACAGAGTTTTACTTTAGCGGCGTTTGTATAAAAACGTCGCAA-AAGTGTC-ATCTATAGTGGCGT
* **
4084501 TTTTCAACAAACGCCGCA
64 TTTTCAAAAAACGCCATA
* * * * *
4084519 AAAGACTATTAC-TTAGTGGCATTTGTATAAAAA
1 ACAGAGTTTTACTTTAGCGGCGTTTGTATAAAAA
4084552 TGCCGTAATA
Statistics
Matches: 156, Mismatches: 32, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
79 1 0.01
80 64 0.41
81 53 0.34
82 37 0.24
83 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.31
Consensus pattern (81 bp):
ACAGAGTTTTACTTTAGCGGCGTTTGTATAAAAACGTCGCAAAAGTGTCATCTATAGTGGCGTTT
TTCAAAAAACGCCATA
Found at i:4084585 original size:81 final size:81
Alignment explanation
Indices: 4084288--4084597 Score: 236
Period size: 81 Copynumber: 3.8 Consensus size: 81
4084278 AGAGTTTTAG
* * ** * * * *
4084288 TTTAGCGACGTTTGTATAAAAACGTCGTAA-AAGTGTCATCTATAGTGGCGTTTTTCAAAAAACG
1 TTTAGCGGCATTTGTATAAAAACACCGCAATAGGT-TCATCTATAGTGGCATTTTTCAACAAACG
** * *
4084352 CCATAATAGAGT-TGTAC
65 CCGCAAAAGACTAT-TAC
* ** * * *
4084369 TTTAGCGGCGTTT-TATACAAAA-GTCGCAATAGGTTCATCCATAGTGGCATTTCTCAATAAACG
1 TTTAGCGGCATTTGTATA-AAAACACCGCAATAGGTTCATCTATAGTGGCATTTTTCAACAAACG
** * *
4084432 CCGTGACAGAGTATTAC
65 CCGCAAAAGACTATTAC
* *
4084449 TTTAGCGGTATTTGTATAAAAACACCGCAATAGGTTTCGA-CTATAGTGGCGTTTTTCAACAAAC
1 TTTAGCGGCATTTGTATAAAAACACCGCAATAGG-TTC-ATCTATAGTGGCATTTTTCAACAAAC
4084513 GCCGCAAAAGACTATTAC
64 GCCGCAAAAGACTATTAC
* ** * * * *
4084531 -TTAGTGGCATTTGTATAAAAATGCCGTAATATGGTTCATATATAGTGGTATTTTTTCAACAGAC
1 TTTAGCGGCATTTGTATAAAAACACCGCAATA-GGTTCATCTATAGTGGCA-TTTTTCAACAAAC
4084595 GCC
64 GCC
4084598 ATAAAAACGC
Statistics
Matches: 188, Mismatches: 31, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
80 63 0.34
81 70 0.37
82 54 0.29
83 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (81 bp):
TTTAGCGGCATTTGTATAAAAACACCGCAATAGGTTCATCTATAGTGGCATTTTTCAACAAACGC
CGCAAAAGACTATTAC
Found at i:4084911 original size:21 final size:21
Alignment explanation
Indices: 4084837--4084917 Score: 85
Period size: 21 Copynumber: 3.9 Consensus size: 21
4084827 CAGCGCCCGG
*
4084837 TCACCATCGTCGT-GCCTCCGA
1 TCACCATCGTC-TCTCCTCCGA
* * *
4084858 TCACCATCGTCGCGCC-CTCGG
1 TCACCATCGTCTCTCCTC-CGA
4084879 TCACCATCGTCTCTCCTCCGA
1 TCACCATCGTCTCTCCTCCGA
*
4084900 TCACCATTGTCTCTCCTC
1 TCACCATCGTCTCTCCTC
4084918 AAGGCTCAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.02
21 49 0.96
22 1 0.02
ACGTcount: A:0.12, C:0.46, G:0.15, T:0.27
Consensus pattern (21 bp):
TCACCATCGTCTCTCCTCCGA
Found at i:4085077 original size:25 final size:25
Alignment explanation
Indices: 4085049--4085136 Score: 167
Period size: 25 Copynumber: 3.5 Consensus size: 25
4085039 GGTATTTAAC
*
4085049 GAGAGTAAGAAATGGTTATCAAATG
1 GAGAGTAAGAAATAGTTATCAAATG
4085074 GAGAGTAAGAAATAGTTATCAAATG
1 GAGAGTAAGAAATAGTTATCAAATG
4085099 GAGAGTAAGAAATAGTTATCAAATG
1 GAGAGTAAGAAATAGTTATCAAATG
4085124 GAGAGTAAGAAAT
1 GAGAGTAAGAAAT
4085137 CTCCCAACAT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 62 1.00
ACGTcount: A:0.48, C:0.03, G:0.26, T:0.23
Consensus pattern (25 bp):
GAGAGTAAGAAATAGTTATCAAATG
Found at i:4090679 original size:21 final size:21
Alignment explanation
Indices: 4090646--4090689 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4090636 ATATACTATA
* *
4090646 ATGGATTTGAAGTTGGTTGTT
1 ATGGAATTAAAGTTGGTTGTT
*
4090667 ATGGAATTAAAGTTTGTTGTT
1 ATGGAATTAAAGTTGGTTGTT
4090688 AT
1 AT
4090690 AGATGTCATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (21 bp):
ATGGAATTAAAGTTGGTTGTT
Found at i:4093883 original size:3 final size:3
Alignment explanation
Indices: 4093875--4093937 Score: 94
Period size: 3 Copynumber: 21.3 Consensus size: 3
4093865 CATTACCTTA
*
4093875 TAT TAT TAT TAG TAT CTA- TAT TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4093919 TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
4093938 TTAATATATA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 4 0.07
3 49 0.89
4 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:4093948 original size:2 final size:2
Alignment explanation
Indices: 4093941--4093971 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4093931 TATTATTTTA
4093941 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4093972 TTATTGCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4101280 original size:20 final size:18
Alignment explanation
Indices: 4101255--4101443 Score: 96
Period size: 20 Copynumber: 9.6 Consensus size: 18
4101245 TGAAGAGGAG
4101255 AAAAGAAAAAAAACAAAGTA
1 AAAAGAAAAAAAA-AAAG-A
4101275 AAAAGAGAAAAAAAAAGAGA
1 AAAAGA-AAAAAAAAA-AGA
*
4101295 AAGAGAAAAAAGAAAAAAGA
1 AAAAG-AAAAA-AAAAAAGA
4101315 AAAGAGAAAAGAGAAAAAATAGA
1 AAA-AG-AAA-A-AAAAAA-AGA
4101338 AAAA-AAAAAGAAAGGAAA-A
1 AAAAGAAAAA-AAA--AAAGA
**
4101357 AAAAGGAAAATAGAAAAATTA
1 AAAA-GAAAA-A-AAAAAAGA
* * *
4101378 GAAAGAAGAAAAAGAAGA
1 AAAAGAAAAAAAAAAAGA
*
4101396 AAAAGAAAAAAACCAAAGA
1 AAAAGAAAAAAA-AAAAGA
* *
4101415 AGAAA-AATAGAAGAAAAGA
1 A-AAAGAA-AAAAAAAAAGA
4101434 AAAAGAAAAA
1 AAAAGAAAAA
4101444 GGAAAAAATT
Statistics
Matches: 134, Mismatches: 16, Indels: 40
0.71 0.08 0.21
Matches are distributed among these distances:
18 21 0.16
19 25 0.19
20 38 0.28
21 31 0.23
22 12 0.09
23 7 0.05
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (18 bp):
AAAAGAAAAAAAAAAAGA
Found at i:4101332 original size:22 final size:22
Alignment explanation
Indices: 4101252--4101443 Score: 104
Period size: 22 Copynumber: 8.7 Consensus size: 22
4101242 TTTTGAAGAG
*
4101252 GAGAAAAGA-AAAAAAA-CAAA
1 GAGAAAAGAGAAAAAAAGAAAA
4101272 GTA-AAAAGAGAAAAAAAAAGAGAAA
1 G-AGAAAAGAG--AAAAAAAGA-AAA
*
4101297 GAGAAAAAAG-AAAAAAGAAAA
1 GAGAAAAGAGAAAAAAAGAAAA
4101318 GAGAAAAGAGAAAAAATAGAAAA
1 GAGAAAAGAGAAAAAA-AGAAAA
4101341 -A-AAAA-AGAAAGGAAAA-AAAA
1 GAGAAAAGAGAAA--AAAAGAAAA
* *
4101361 G-GAAAATAGAAAAATTAG-AAA
1 GAGAAAAGAGAAAAA-AAGAAAA
4101382 GAAGAAAA-AGAAGAAAAAGAAAA
1 G-AGAAAAGAGAA-AAAAAGAAAA
* *
4101405 -AAACCAAAGAAGAAAAATAGAAGAA
1 GAGA--AAAG-AGAAAAAAAGAA-AA
*
4101430 AAGAAAA-AGAAAAA
1 GAGAAAAGAGAAAAA
4101444 GGAAAAAATT
Statistics
Matches: 138, Mismatches: 8, Indels: 50
0.70 0.04 0.26
Matches are distributed among these distances:
20 18 0.13
21 29 0.21
22 35 0.25
23 27 0.20
24 11 0.08
25 16 0.12
26 2 0.01
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (22 bp):
GAGAAAAGAGAAAAAAAGAAAA
Found at i:4101340 original size:7 final size:7
Alignment explanation
Indices: 4101255--4101451 Score: 122
Period size: 7 Copynumber: 27.6 Consensus size: 7
4101245 TGAAGAGGAG
4101255 AAAAGAA
1 AAAAGAA
4101262 AAAA-AA
1 AAAAGAA
* *
4101268 CAAAGTA
1 AAAAGAA
4101275 AAAAG-A
1 AAAAGAA
*
4101281 GAAA-AA
1 AAAAGAA
4101287 AAAAGAGA
1 AAAAGA-A
*
4101295 AAGAGAA
1 AAAAGAA
4101302 AAAAGAA
1 AAAAGAA
4101309 AAAAGAA
1 AAAAGAA
*
4101316 AAGAGAA
1 AAAAGAA
*
4101323 AAGAGAA
1 AAAAGAA
* *
4101330 AAAATAG
1 AAAAGAA
4101337 AAAA-AA
1 AAAAGAA
4101343 AAAAGAA
1 AAAAGAA
4101350 AGGAAA-AA
1 A--AAAGAA
*
4101358 AAAGGAA
1 AAAAGAA
*
4101365 AATAGAA
1 AAAAGAA
4101372 AAATTAGAA
1 AAA--AGAA
*
4101381 AGAAG-A
1 AAAAGAA
4101387 AAAAGAAGA
1 AAAAG-A-A
4101396 AAAAGAA
1 AAAAGAA
4101403 AAAA-ACCA
1 AAAAGA--A
4101411 AAGAAGAA
1 AA-AAGAA
4101419 AAATAGAA
1 AAA-AGAA
4101427 GAAAAG-A
1 -AAAAGAA
4101434 AAAAGAA
1 AAAAGAA
*
4101441 AAAGGAA
1 AAAAGAA
4101448 AAAA
1 AAAA
4101452 TTTTGAGGGT
Statistics
Matches: 150, Mismatches: 20, Indels: 40
0.71 0.10 0.19
Matches are distributed among these distances:
6 31 0.21
7 76 0.51
8 22 0.15
9 20 0.13
10 1 0.01
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.03
Consensus pattern (7 bp):
AAAAGAA
Found at i:4101359 original size:55 final size:53
Alignment explanation
Indices: 4101255--4101452 Score: 159
Period size: 55 Copynumber: 3.5 Consensus size: 53
4101245 TGAAGAGGAG
* * * *
4101255 AAAAGAAAAA-AAACAAAGTAAAAAGAGAAAAAAAAAGAGAAAGAGAAAAAAGAA
1 AAAAGAAAAAGAAA-AGAGAAAAAATAGAAAAAAAAA-AGAAAGAAAAAAAAGAA
4101309 AAAAGAAAAGAGAAAAGAGAAAAAATAGAAAAAAAAAAGAAAGGAAAAAAAAGGAA
1 AAAAGAAAA-AGAAAAGAGAAAAAATAGAAAAAAAAAAGAAA-GAAAAAAAA-GAA
* * *
4101365 AATAGAAAAATTAGAAAGAAGAAAAAGA-AGAAAAAGAAAAAAACCAAAGAAGAAAAATAGAA
1 AAAAGAAAAA-GA-AAAG-AGAAAAA-ATAG--AAA-AAAAAAA-GAAAGAA-AAAAA-AGAA
4101427 GAAAAGAAAAAGAAAA-AGGAAAAAAT
1 -AAAAGAAAAAGAAAAGA-GAAAAAAT
4101453 TTTGAGGGTT
Statistics
Matches: 118, Mismatches: 9, Indels: 28
0.76 0.06 0.18
Matches are distributed among these distances:
54 14 0.12
55 29 0.25
56 15 0.13
57 4 0.03
58 9 0.08
59 3 0.03
60 9 0.08
61 13 0.11
62 12 0.10
63 10 0.08
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (53 bp):
AAAAGAAAAAGAAAAGAGAAAAAATAGAAAAAAAAAAGAAAGAAAAAAAAGAA
Found at i:4101381 original size:31 final size:31
Alignment explanation
Indices: 4101301--4101437 Score: 92
Period size: 32 Copynumber: 4.4 Consensus size: 31
4101291 GAGAAAGAGA
4101301 AAAAAGAAAAA--AGAAA-AGAGAAAAGAGAA-
1 AAAAAGAAAAATTAGAAAGA-AGAAAA-AGAAG
* *
4101330 AAAATAGAAAAA--AAAAAGAAAGGAAAAAAAAGG
1 AAAA-AGAAAAATTAGAAAG-AA-GAAAAAGAA-G
4101363 AAAATAGAAAAATTAGAAAGAAGAAAAAGAAG
1 AAAA-AGAAAAATTAGAAAGAAGAAAAAGAAG
* *
4101395 AAAAAGAAAAA-AACCAAAGAAGAAAAATAGAAG
1 AAAAAGAAAAATTA-GAAAGAAG-AAAA-AGAAG
4101428 -AAAAGAAAAA
1 AAAAAGAAAAA
4101438 GAAAAAGGAA
Statistics
Matches: 91, Mismatches: 6, Indels: 19
0.78 0.05 0.16
Matches are distributed among these distances:
29 4 0.04
30 12 0.13
31 18 0.20
32 25 0.27
33 25 0.27
34 2 0.02
35 5 0.05
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (31 bp):
AAAAAGAAAAATTAGAAAGAAGAAAAAGAAG
Found at i:4101396 original size:47 final size:47
Alignment explanation
Indices: 4101335--4101451 Score: 127
Period size: 47 Copynumber: 2.5 Consensus size: 47
4101325 GAGAAAAAAT
* **
4101335 AGAA-AAAAAAAAGAAAGGAAAAAAAAGGAAA-ATAGAAAAATTAGAA-
1 AGAAGAAAAAGAAGAAAGGAAAAAAAACCAAAGA-AGAAAAA-TAGAAG
*
4101381 AGAAGAAAAAGAAGAAA-AAGAAAAAAACCAAAGAAGAAAAATAGAAG
1 AGAAGAAAAAGAAGAAAGGA-AAAAAAACCAAAGAAGAAAAATAGAAG
*
4101428 AAAAGAAAAAGAA-AAAGGAAAAAA
1 AGAAGAAAAAGAAGAAAGGAAAAAA
4101452 TTTTGAGGGT
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
46 18 0.30
47 41 0.68
48 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (47 bp):
AGAAGAAAAAGAAGAAAGGAAAAAAAACCAAAGAAGAAAAATAGAAG
Found at i:4103569 original size:17 final size:17
Alignment explanation
Indices: 4103547--4103585 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
4103537 CCAACAAAAG
4103547 GAGAAGAAGTTCATAAT
1 GAGAAGAAGTTCATAAT
*
4103564 GAGAAGAAGTTTATAAT
1 GAGAAGAAGTTCATAAT
4103581 GAGAA
1 GAGAA
4103586 TACCTTGTTT
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:0.03, G:0.26, T:0.23
Consensus pattern (17 bp):
GAGAAGAAGTTCATAAT
Found at i:4103819 original size:91 final size:91
Alignment explanation
Indices: 4103664--4104470 Score: 1283
Period size: 91 Copynumber: 8.9 Consensus size: 91
4103654 ATTTTCGATA
*
4103664 GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAAAAGTTCATAATGAGAAGAACTTGT
1 GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
*
4103729 TCAACCTTGGCTCAATATTTCCAGTG
66 TCAACCTTGGCTCAACATTTCCAGTG
*
4103755 GAGAGTTCATAATGAGAATAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
*
4103820 TCAATCTTGGCTCAACATTTCCAGTG
66 TCAACCTTGGCTCAACATTTCCAGTG
* * * *
4103846 AAGAGTTCATAAGGAGAATAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAATAACTTGT
1 GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
*
4103911 TCAACCTTGGCTCAACATTTCCAGCG
66 TCAACCTTGGCTCAACATTTCCAGTG
* * *
4103937 GATAGTTCATAATGAGAAGAACCCATCCAACGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
* *
4104002 TCAACCTTGGCTCAACATTACTAGTG
66 TCAACCTTGGCTCAACATTTCCAGTG
* *
4104028 GAGAGTTCATAATGAGAAGAACTCATCCAAGGAGGGAGAAGAAGTTCATAATGAGAATAACTTGT
1 GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
*
4104093 TCAACGTTGGCTCAACATTTCCAGTG
66 TCAACCTTGGCTCAACATTTCCAGTG
*
4104119 GATAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
1 GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
* *
4104184 TCAACCTTGGCTCAATATTACCAGTG
66 TCAACCTTGGCTCAACATTTCCAGTG
* ** *
4104210 GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAATAAGTTTGTAATGAGAAGAATTTGT
1 GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * *
4104275 TAAACTTTGGCTCAACATTTCTAGTA
66 TCAACCTTGGCTCAACATTTCCAGTG
* * *
4104301 GAGAGTTCATAATGAGAAGAGA-TCATCCAACGAGAGAGAAGAAGTTCATAATTACAAGAACTTG
1 GAGAGTTCATAATGAGAAGA-ACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTG
4104365 TTCAACCTTGGCTCAACATTTCCAGTG
65 TTCAACCTTGGCTCAACATTTCCAGTG
* * *
4104392 GAGAGTTCATAATGAGAAGAACTCATCCAATGAGGGAGAAAAAGTTCATAATGAGAATAACTTGT
1 GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
*
4104457 TCAACCTTAGCTCA
66 TCAACCTTGGCTCA
4104471 TCCATCACAT
Statistics
Matches: 652, Mismatches: 62, Indels: 4
0.91 0.09 0.01
Matches are distributed among these distances:
90 1 0.00
91 650 1.00
92 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (91 bp):
GAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTGGCTCAACATTTCCAGTG
Found at i:4104504 original size:40 final size:40
Alignment explanation
Indices: 4104460--4104546 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
4104450 AACTTGTTCA
*
4104460 ACCTTAGCTCAT-CCATCACATAAGGAGTTAGATCAACATC
1 ACCTTAGCTC-TCCCATCAAATAAGGAGTTAGATCAACATC
* * *
4104500 ACCTTGGCTCTCCCATCAAATAAGGAGTTGGATCAGCATC
1 ACCTTAGCTCTCCCATCAAATAAGGAGTTAGATCAACATC
4104540 ACCTTAG
1 ACCTTAG
4104547 GTCAACTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
39 1 0.02
40 40 0.98
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (40 bp):
ACCTTAGCTCTCCCATCAAATAAGGAGTTAGATCAACATC
Found at i:4104843 original size:8 final size:8
Alignment explanation
Indices: 4104816--4104883 Score: 54
Period size: 8 Copynumber: 8.2 Consensus size: 8
4104806 AATCATTACC
4104816 TTATATTA
1 TTATATTA
4104824 -T-TATTA
1 TTATATTA
4104830 TCTATATTA
1 T-TATATTA
4104839 TTATATTA
1 TTATATTA
4104847 TTATTATT-
1 TTA-TATTA
4104855 TTAATATATA
1 TT-ATAT-TA
4104865 TATATATATA
1 T-TATAT-TA
4104875 TTAT-TTA
1 TTATATTA
4104882 TT
1 TT
4104884 GCAACCCCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 17
0.75 0.00 0.25
Matches are distributed among these distances:
6 5 0.10
7 5 0.10
8 17 0.33
9 15 0.29
10 9 0.17
11 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (8 bp):
TTATATTA
Found at i:4104866 original size:23 final size:22
Alignment explanation
Indices: 4104816--4104880 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 22
4104806 AATCATTACC
* *
4104816 TTATATTATTATTATCTATATTA
1 TTATATTATTATTAT-TTTAATA
4104839 TTATATTATTATTATTTTAATA
1 TTATATTATTATTATTTTAATA
4104861 TATATATATATATATTATTT
1 T-TATAT-TAT-TATTATTT
4104881 ATTGCAACCC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.16
23 20 0.54
24 3 0.08
25 8 0.22
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATATTATTATTATTTTAATA
Found at i:4109074 original size:3 final size:3
Alignment explanation
Indices: 4109066--4109141 Score: 138
Period size: 3 Copynumber: 26.0 Consensus size: 3
4109056 TTTAATTAAT
4109066 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4109114 TAA TAA TAA TAA TAA T-A TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4109142 ATGGGCAAAA
Statistics
Matches: 71, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.06
3 67 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4109388 original size:39 final size:39
Alignment explanation
Indices: 4109345--4109539 Score: 250
Period size: 39 Copynumber: 5.0 Consensus size: 39
4109335 AAACTTCCTC
* ** * * *
4109345 TTCCTCTTTAGAAAAGTTTTTCATATTACGAACTCCTTT
1 TTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTT
* *
4109384 TTCCTCTTCAGACGAGTTCTTCAGATTATGAACACTTTT
1 TTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTT
* *
4109423 TTCCTATTCAGACGAGTTCTTTAGATTATGAACTCC-TT
1 TTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTT
* *
4109461 TTCCTCTTCAGATGAGTTCTTCAAATTATGAACT-CTGTT
1 TTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCT-TT
*
4109500 TTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCCTTT
1 TTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTT
4109539 T
1 T
4109540 GGAAATGTTT
Statistics
Matches: 136, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
37 1 0.01
38 32 0.24
39 101 0.74
40 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.44
Consensus pattern (39 bp):
TTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTT
Found at i:4109489 original size:77 final size:77
Alignment explanation
Indices: 4109359--4109539 Score: 263
Period size: 77 Copynumber: 2.3 Consensus size: 77
4109349 TCTTTAGAAA
* * * * *
4109359 AGTTTTTCATATTACGAACTCCTTTTTCCTCTTCAGACGAGTTCTTCAGATTATGAACACTTTTT
1 AGTTCTTCAGATTATGAACTCC-TTTTCCTCTTCAGACGAGTTCTTCAAATTATGAACACTGTTT
4109424 TCCTATTCAGACG
65 TCCTATTCAGACG
* * *
4109437 AGTTCTTTAGATTATGAACTCCTTTTCCTCTTCAGATGAGTTCTTCAAATTATGAACTCTGTTTT
1 AGTTCTTCAGATTATGAACTCCTTTTCCTCTTCAGACGAGTTCTTCAAATTATGAACACTGTTTT
* *
4109502 CCTCTTCAGATG
66 CCTATTCAGACG
4109514 AGTTCTTCAGATTATGAACTCCTTTT
1 AGTTCTTCAGATTATGAACTCCTTTT
4109540 GGAAATGTTT
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
77 74 0.80
78 18 0.20
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.44
Consensus pattern (77 bp):
AGTTCTTCAGATTATGAACTCCTTTTCCTCTTCAGACGAGTTCTTCAAATTATGAACACTGTTTT
CCTATTCAGACG
Found at i:4109757 original size:45 final size:45
Alignment explanation
Indices: 4109598--4110078 Score: 585
Period size: 45 Copynumber: 10.6 Consensus size: 45
4109588 AAAATATTCG
*
4109598 GCACTG-AAGGTCTTATGGATGACCCGAAGGCTTTTTAAAAACATCCT
1 GCACTGTAA-GTCTTATGGATGACCCGAAGG--TTTTGAAAACATCCT
* * * *
4109645 GTACTTTAGGTCTTATGGATGACCCGAAGGCTTTTGATAACATCCT
1 GCACTGTAAGTCTTATGGATGACCCGAAGG-TTTTGAAAACATCCT
* * ** *
4109691 GCACTATAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCCT
1 GCACTGTAAGTCTTATGGATGACCCGAAGGTTTTGAAAACATCCT
* *
4109736 GCACTGTAAGTTTTATGGATGACCCCAAGGTTTTGAAAACATCCT
1 GCACTGTAAGTCTTATGGATGACCCGAAGGTTTTGAAAACATCCT
* *
4109781 GCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCAT
1 GCACTGTAAGTCTTATGGATGACCCGAAGGTTTTGAAAACATCCT
* *
4109826 GCACTG-AAGGTCTTATAGATGACCCGAAGGTTTTGAAAACATCAT
1 GCACTGTAA-GTCTTATGGATGACCCGAAGGTTTTGAAAACATCCT
* **
4109871 GCGCTG-AAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCCT
1 GCACTGTAA-GTCTTATGGATGACCCGAAGGTTTTGAAAACATCCT
* * *
4109916 GCATTGTAGGTCTTATGGATGACTCGAAGGTTTTGAAAACATCCT
1 GCACTGTAAGTCTTATGGATGACCCGAAGGTTTTGAAAACATCCT
* *
4109961 GCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCAT
1 GCACTGTAAGTCTTATGGATGACCCGAAGGTTTTGAAAACATCCT
** * *
4110006 GCACTG-AAGGTCTTACAGATGACCTGAAGGTTTTGAAAACATCAT
1 GCACTGTAA-GTCTTATGGATGACCCGAAGGTTTTGAAAACATCCT
**
4110051 GCACTG-AAGGTCTTACAGATGACCCGAA
1 GCACTGTAA-GTCTTATGGATGACCCGAA
4110079 ATAGTTTACT
Statistics
Matches: 388, Mismatches: 42, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
44 2 0.01
45 320 0.82
46 40 0.10
47 25 0.06
48 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (45 bp):
GCACTGTAAGTCTTATGGATGACCCGAAGGTTTTGAAAACATCCT
Found at i:4109850 original size:135 final size:135
Alignment explanation
Indices: 4109598--4110078 Score: 687
Period size: 135 Copynumber: 3.5 Consensus size: 135
4109588 AAAATATTCG
** * * *
4109598 GCACTGAAGGTCTTATGGATGACCCGAAGGCTTTTTAAAAACATCCTGTACTTTAGGTCTTATGG
1 GCACTGAAGGTCTTACAGATGACCCGAAGG--TTTTGAAAACATCCTGCACTGTAGGTCTTATGG
* * *
4109663 ATGACCCGAAGGCTTTTGATAACATCCTGCACT-ATAGGTCTTACAGATGACCCGAAGGCTTTGA
64 ATGACCCGAAGG-TTTTGAAAACATCCTGCACTGA-AGGTCTTATAGATGACCCGAAGGTTTTGA
*
4109727 AAACATCCT
127 AAACATCAT
* ** *
4109736 GCACTGTAA-GTTTTATGGATGACCCCAAGGTTTTGAAAACATCCTGCACTGTAGGTCTTATGGA
1 GCACTG-AAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCCTGCACTGTAGGTCTTATGGA
*
4109800 TGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGTCTTATAGATGACCCGAAGGTTTTGAAAA
65 TGACCCGAAGGTTTTGAAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGTTTTGAAAA
4109865 CATCAT
130 CATCAT
* *
4109871 GCGCTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCCTGCATTGTAGGTCTTATGGAT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCCTGCACTGTAGGTCTTATGGAT
* * *
4109936 GACTCGAAGGTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
66 GACCCGAAGGTTTTGAAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGTTTTGAAAAC
4110001 ATCAT
131 ATCAT
* * * **
4110006 GCACTGAAGGTCTTACAGATGACCTGAAGGTTTTGAAAACATCATGCACTGAAGGTCTTACAGAT
1 GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCCTGCACTGTAGGTCTTATGGAT
4110071 GACCCGAA
66 GACCCGAA
4110079 ATAGTTTACT
Statistics
Matches: 312, Mismatches: 28, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
134 2 0.01
135 240 0.77
136 43 0.14
138 25 0.08
139 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (135 bp):
GCACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCCTGCACTGTAGGTCTTATGGAT
GACCCGAAGGTTTTGAAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGTTTTGAAAAC
ATCAT
Found at i:4110763 original size:22 final size:22
Alignment explanation
Indices: 4110738--4110811 Score: 114
Period size: 22 Copynumber: 3.4 Consensus size: 22
4110728 AATAAAGCTT
4110738 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
4110760 TCATATTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
4110782 TCATCTTTGAAGAA-TGAATCTA
1 TCATCTTTGAA-AAGAGAATCTA
4110804 TCATCTTT
1 TCATCTTT
4110812 AAAGAATGTA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
22 46 0.96
23 2 0.04
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:4110816 original size:22 final size:22
Alignment explanation
Indices: 4110753--4110819 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
4110743 TTTGAAAAGA
*
4110753 GAATCTATCATATTTGAAA-AGA-
1 GAATCTATCATCTTT-AAAGA-AT
*
4110775 GAATCTATCATCTTTGAAGAAT
1 GAATCTATCATCTTTAAAGAAT
4110797 GAATCTATCATCTTTAAAGAAT
1 GAATCTATCATCTTTAAAGAAT
4110819 G
1 G
4110820 TAGATGTAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
21 3 0.08
22 37 0.93
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (22 bp):
GAATCTATCATCTTTAAAGAAT
Found at i:4111264 original size:54 final size:54
Alignment explanation
Indices: 4111182--4111289 Score: 180
Period size: 54 Copynumber: 2.0 Consensus size: 54
4111172 ATAATCACTG
* *
4111182 GTTCGTAGAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCATATGGCTTCTGCACAGAT
* *
4111236 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTATGGCTTCTGCCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCATATGGCTTCTGCACAGAT
4111290 TTCTTGCCAG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCATATGGCTTCTGCACAGAT
Found at i:4115791 original size:42 final size:42
Alignment explanation
Indices: 4115731--4115814 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
4115721 TTAGTTTTGT
* * * * *
4115731 CATTTGCTCTTTTGAATCATC-TTGGAATTTTTTTGCTTGATC
1 CATTTGCTCATTTAAATCA-CACTGGAACTTTTTTACTTGATC
*
4115773 CATTTGTTCATTTAAATCACACTGGAACTTTTTTACTTGATC
1 CATTTGCTCATTTAAATCACACTGGAACTTTTTTACTTGATC
4115815 AATCATCTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.49
Consensus pattern (42 bp):
CATTTGCTCATTTAAATCACACTGGAACTTTTTTACTTGATC
Found at i:4122913 original size:21 final size:18
Alignment explanation
Indices: 4122872--4122910 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
4122862 CTTTTTGTCC
4122872 ATTTATGAAAACTTTTCA
1 ATTTATGAAAACTTTTCA
*
4122890 ATTTGATGAACACTCTTTCA
1 ATTT-ATGAAAACT-TTTCA
4122910 A
1 A
4122911 ATTAACACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (18 bp):
ATTTATGAAAACTTTTCA
Found at i:4123129 original size:46 final size:49
Alignment explanation
Indices: 4123062--4123152 Score: 116
Period size: 46 Copynumber: 1.9 Consensus size: 49
4123052 TGGTATAAAT
* * * * *
4123062 CCTAACCTCATGCTTTCTAGTT-TCATGC-TTTGTTT-GGAAAAACTAA
1 CCTAACCGCATGATTACTAGTTCGCATGCATTTATTTAGGAAAAACTAA
4123108 CCTAACCGCATGATTACTAGTTCGCATGCATTTATTTAGGAAAAA
1 CCTAACCGCATGATTACTAGTTCGCATGCATTTATTTAGGAAAAA
4123153 GAAAAATGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
46 19 0.51
47 5 0.14
48 6 0.16
49 7 0.19
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (49 bp):
CCTAACCGCATGATTACTAGTTCGCATGCATTTATTTAGGAAAAACTAA
Found at i:4124251 original size:10 final size:10
Alignment explanation
Indices: 4124236--4124260 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4124226 CTTTAATATT
4124236 AAAAAAATAA
1 AAAAAAATAA
4124246 AAAAAAATAA
1 AAAAAAATAA
4124256 AAAAA
1 AAAAA
4124261 TATATGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:4125852 original size:3 final size:3
Alignment explanation
Indices: 4125844--4125910 Score: 75
Period size: 3 Copynumber: 23.0 Consensus size: 3
4125834 TATTTGTAAT
* * * *
4125844 TAA TAA TAA TAA GAA TAA TAA GAA TAA TAA TAT TAA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
4125892 TAA T-A TTA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
4125911 ATGGGAAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
2 4 0.08
3 49 0.92
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:4128523 original size:23 final size:23
Alignment explanation
Indices: 4128492--4128570 Score: 131
Period size: 23 Copynumber: 3.4 Consensus size: 23
4128482 TGCATTTCCA
*
4128492 GCAGCATAACCCTATGAAACAAC
1 GCAGAATAACCCTATGAAACAAC
4128515 GCAGAATAACCCTATGAAACAAC
1 GCAGAATAACCCTATGAAACAAC
* *
4128538 GCAGATTAACCCTATGAAACAAT
1 GCAGAATAACCCTATGAAACAAC
4128561 GCAGAATAAC
1 GCAGAATAAC
4128571 AAATATAAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.46, C:0.25, G:0.14, T:0.15
Consensus pattern (23 bp):
GCAGAATAACCCTATGAAACAAC
Found at i:4132668 original size:35 final size:36
Alignment explanation
Indices: 4132616--4132703 Score: 133
Period size: 35 Copynumber: 2.5 Consensus size: 36
4132606 GTGGCATGTG
* * *
4132616 CACATTGCTCAAAGTGTGTTTAATGTAAAC-AAAAC
1 CACATTGCTCCATGTGTGGTTAATGTAAACAAAAAC
4132651 CACATTGCTCCATGTGTGGTTAATGTAAACAAAAAC
1 CACATTGCTCCATGTGTGGTTAATGTAAACAAAAAC
*
4132687 CACACTGCTCCATGTGT
1 CACATTGCTCCATGTGT
4132704 CTAGTGTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
35 27 0.56
36 21 0.44
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (36 bp):
CACATTGCTCCATGTGTGGTTAATGTAAACAAAAAC
Found at i:4132717 original size:34 final size:34
Alignment explanation
Indices: 4132630--4132717 Score: 124
Period size: 36 Copynumber: 2.6 Consensus size: 34
4132620 TTGCTCAAAG
*
4132630 TGTGTTTAATGTAAAC-AAAACCACATTGCTCCA
1 TGTGTTTAATGTAAACAAAAACCACACTGCTCCA
4132663 TGTGTGGTTAATGTAAACAAAAACCACACTGCTCCA
1 TGTGT--TTAATGTAAACAAAAACCACACTGCTCCA
* *
4132699 TGTGTCTAGTGTAAACAAA
1 TGTGTTTAATGTAAACAAA
4132718 CCAAAATATT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
33 5 0.10
34 12 0.24
35 11 0.22
36 21 0.43
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (34 bp):
TGTGTTTAATGTAAACAAAAACCACACTGCTCCA
Found at i:4133715 original size:88 final size:88
Alignment explanation
Indices: 4133563--4133738 Score: 334
Period size: 88 Copynumber: 2.0 Consensus size: 88
4133553 CAGAAATTTG
* *
4133563 ATGATTAATCTTACAGAGTAAGGTCAACTGCATTGAAATCAAATGATCCATGATAGTAATAAGAG
1 ATGATTAATCTTACAGAATAAGGTCAACTGCATTGAAATCAAATGATCCATGATAGTAACAAGAG
4133628 TGATAAAGCCAAAGAAAAAACAC
66 TGATAAAGCCAAAGAAAAAACAC
4133651 ATGATTAATCTTACAGAATAAGGTCAACTGCATTGAAATCAAATGATCCATGATAGTAACAAGAG
1 ATGATTAATCTTACAGAATAAGGTCAACTGCATTGAAATCAAATGATCCATGATAGTAACAAGAG
4133716 TGATAAAGCCAAAGAAAAAACAC
66 TGATAAAGCCAAAGAAAAAACAC
4133739 GGTTCACACA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.22
Consensus pattern (88 bp):
ATGATTAATCTTACAGAATAAGGTCAACTGCATTGAAATCAAATGATCCATGATAGTAACAAGAG
TGATAAAGCCAAAGAAAAAACAC
Found at i:4138623 original size:17 final size:16
Alignment explanation
Indices: 4138592--4138625 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4138582 CACGTGAGGA
4138592 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
4138608 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
4138625 T
1 T
4138626 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:4145017 original size:19 final size:21
Alignment explanation
Indices: 4144980--4145022 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
4144970 TAACTTTTTC
4144980 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
4145000 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
4145020 TTT
1 TTT
4145023 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:4145028 original size:19 final size:20
Alignment explanation
Indices: 4144979--4145028 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
4144969 TTAACTTTTT
*
4144979 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
4144999 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
4145018 CTTTTACCTTT
1 CTTTTACCTTT
4145029 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:4148884 original size:17 final size:16
Alignment explanation
Indices: 4148853--4148886 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4148843 CACGTGAAGA
4148853 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
4148869 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
4148886 T
1 T
4148887 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:4152361 original size:16 final size:16
Alignment explanation
Indices: 4152340--4152376 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
4152330 CTACGAGACG
4152340 CAAGCTCCAAGTGCTA
1 CAAGCTCCAAGTGCTA
4152356 CAAGCTCCAAGTGCTA
1 CAAGCTCCAAGTGCTA
4152372 CAAGC
1 CAAGC
4152377 AACTACCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.16
Consensus pattern (16 bp):
CAAGCTCCAAGTGCTA
Found at i:4158483 original size:13 final size:13
Alignment explanation
Indices: 4158465--4158532 Score: 109
Period size: 13 Copynumber: 5.2 Consensus size: 13
4158455 TGCGTCATAA
4158465 ATTTATGACGCGC
1 ATTTATGACGCGC
*
4158478 ATTTATGACACGC
1 ATTTATGACGCGC
*
4158491 ATTTATGACACGC
1 ATTTATGACGCGC
4158504 ATTTATGACGCGC
1 ATTTATGACGCGC
*
4158517 ATTTATGACGCTC
1 ATTTATGACGCGC
4158530 ATT
1 ATT
4158533 GCGCGTCATT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 52 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:4158640 original size:85 final size:85
Alignment explanation
Indices: 4158504--4158669 Score: 203
Period size: 85 Copynumber: 2.0 Consensus size: 85
4158494 TATGACACGC
* * ***
4158504 ATTTATGACGCGCATTTATGACGCTCATTGCGCGTCATTGAAGCCCCCATCA-TA-AATGAAGAC
1 ATTTATGACACGCATTTATGACGCTCATTGCACGTCATTGAAGCAAACATCATTAGAA--AAGAC
*
4158567 GACACACATTTGTGTGTCATAA
64 GACACACATTCGTGTGTCATAA
* * *
4158589 ATTTATGACACGCATTTATGAC-TTACATTGCATGTCATTGAAGCAAACATCATTAGAAAAGATG
1 ATTTATGACACGCATTTATGACGCT-CATTGCACGTCATTGAAGCAAACATCATTAGAAAAGACG
4158653 ACACACATTCGTGTGTC
65 ACACACATTCGTGTGTC
4158670 GTGATTATAT
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
84 1 0.01
85 64 0.93
86 2 0.03
87 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (85 bp):
ATTTATGACACGCATTTATGACGCTCATTGCACGTCATTGAAGCAAACATCATTAGAAAAGACGA
CACACATTCGTGTGTCATAA
Found at i:4166174 original size:26 final size:26
Alignment explanation
Indices: 4166133--4166186 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
4166123 ACTAAGTGCA
* *
4166133 TATGGTGGGCATGACCTTATGTGTAT
1 TATGGTGGGAACGACCTTATGTGTAT
4166159 TATGGTGGGAACGACCTTATGTGTAT
1 TATGGTGGGAACGACCTTATGTGTAT
4166185 TA
1 TA
4166187 GCACTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.11, G:0.30, T:0.37
Consensus pattern (26 bp):
TATGGTGGGAACGACCTTATGTGTAT
Found at i:4184681 original size:26 final size:26
Alignment explanation
Indices: 4184650--4184699 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
4184640 AGTGCATAAA
4184650 GTGGGCACGAACTTAAGTGTATTATG
1 GTGGGCACGAACTTAAGTGTATTATG
* * *
4184676 GTGGGCATGACCTTATGTGTATTA
1 GTGGGCACGAACTTAAGTGTATTA
4184700 GCACTTCGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.24, C:0.12, G:0.30, T:0.34
Consensus pattern (26 bp):
GTGGGCACGAACTTAAGTGTATTATG
Found at i:4191577 original size:21 final size:21
Alignment explanation
Indices: 4191552--4191601 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 21
4191542 AGAGCTTAGT
4191552 GATTTTAAAGAGTTGATTAAG
1 GATTTTAAAGAGTTGATTAAG
4191573 GATTTTAAAGAGTTGATTAAG
1 GATTTTAAAGAGTTGATTAAG
4191594 GAATTTTA
1 G-ATTTTA
4191602 TGTTTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.22, T:0.40
Consensus pattern (21 bp):
GATTTTAAAGAGTTGATTAAG
Found at i:4202483 original size:59 final size:59
Alignment explanation
Indices: 4202375--4202579 Score: 319
Period size: 59 Copynumber: 3.5 Consensus size: 59
4202365 AATTTACCTG
* * * *
4202375 TTCATTGCGACTAGAAGGGTTGGTTA-GA-A--TAGAGTCATATTATCGAGTTTGCCTT
1 TTCATTGCGACTAGAAGGGTTCGATAGGACACTTAGAGTAATATTATCGAGTTTCCCTT
*
4202430 TTCATTGCAACTAGAAGGGTTCGATAGGACACTTAGAGTAATATTATCGAGTTTCCCTT
1 TTCATTGCGACTAGAAGGGTTCGATAGGACACTTAGAGTAATATTATCGAGTTTCCCTT
4202489 TTCATTGCGACTAGAAGGGTTCGATAGGACACTTAGAGTAATATTATCGAGTTTCCCTT
1 TTCATTGCGACTAGAAGGGTTCGATAGGACACTTAGAGTAATATTATCGAGTTTCCCTT
* *
4202548 TTCATTGCGACTAGGAGGGTTCTATAGGACAC
1 TTCATTGCGACTAGAAGGGTTCGATAGGACAC
4202580 ATATCTATCT
Statistics
Matches: 138, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
55 23 0.17
56 2 0.01
57 1 0.01
59 112 0.81
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (59 bp):
TTCATTGCGACTAGAAGGGTTCGATAGGACACTTAGAGTAATATTATCGAGTTTCCCTT
Found at i:4206642 original size:20 final size:20
Alignment explanation
Indices: 4206617--4206658 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4206607 TAATTTAATA
4206617 TAGGATTATGAATTA-TATTT
1 TAGGATTAT-AATTACTATTT
*
4206637 TAGGATTATATTTACTATTT
1 TAGGATTATAATTACTATTT
4206657 TA
1 TA
4206659 TTAGAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (20 bp):
TAGGATTATAATTACTATTT
Found at i:4207052 original size:59 final size:60
Alignment explanation
Indices: 4206980--4207101 Score: 201
Period size: 60 Copynumber: 2.0 Consensus size: 60
4206970 GGAGGGTTGG
* * *
4206980 TTAGAGTCATATTATCGAGTTTTC-CTTTTCATTGTGACTAGGAGGGTTCGATAGGACAC
1 TTAGAGTCATATTATCAAGTTTTCACTTTTCATTGAGACTAAGAGGGTTCGATAGGACAC
*
4207039 TTAGAGTCATATTATCAAGTTTTCATTTTTCATTGAGACTAAGAGGGTTCGATAGGACAC
1 TTAGAGTCATATTATCAAGTTTTCACTTTTCATTGAGACTAAGAGGGTTCGATAGGACAC
4207099 TTA
1 TTA
4207102 TCTATCTATT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
59 23 0.40
60 35 0.60
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (60 bp):
TTAGAGTCATATTATCAAGTTTTCACTTTTCATTGAGACTAAGAGGGTTCGATAGGACAC
Found at i:4207883 original size:19 final size:19
Alignment explanation
Indices: 4207853--4207897 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
4207843 AGATCTCTTT
4207853 CTTTTCAACTTATTTGTATC
1 CTTTT-AACTTATTTGTATC
4207873 CTTTTAACTTATTTGTATC
1 CTTTTAACTTATTTGTATC
*
4207892 TTTTTA
1 CTTTTA
4207898 CAAATCTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.20, C:0.16, G:0.04, T:0.60
Consensus pattern (19 bp):
CTTTTAACTTATTTGTATC
Found at i:4210629 original size:21 final size:21
Alignment explanation
Indices: 4210603--4210642 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4210593 AAATCCTAAA
4210603 GATAATTCCCAAAAGATAAGG
1 GATAATTCCCAAAAGATAAGG
**
4210624 GATAATTCTTAAAAGATAA
1 GATAATTCCCAAAAGATAA
4210643 AAAGAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (21 bp):
GATAATTCCCAAAAGATAAGG
Found at i:4210663 original size:12 final size:13
Alignment explanation
Indices: 4210642--4210674 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
4210632 TTAAAAGATA
4210642 AAAAGA-AAA-TT
1 AAAAGATAAATTT
4210653 AAAAGATAAATTT
1 AAAAGATAAATTT
4210666 AAAAGATAA
1 AAAAGATAA
4210675 TCCTAATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 6 0.30
12 3 0.15
13 11 0.55
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (13 bp):
AAAAGATAAATTT
Found at i:4213258 original size:23 final size:24
Alignment explanation
Indices: 4213213--4213258 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
4213203 TGACTAAAAT
* *
4213213 AAATATAAATAAAATTCAGACATC
1 AAATATAAATAAAATTAAAACATC
*
4213237 AAAT-TAAATTAAATTAAAACAT
1 AAATATAAATAAAATTAAAACAT
4213259 GCTATTCGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28
Consensus pattern (24 bp):
AAATATAAATAAAATTAAAACATC
Found at i:4214414 original size:3 final size:3
Alignment explanation
Indices: 4214406--4214464 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
4214396 TAAAATTATT
* * *
4214406 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TTA TAA TAA TAT TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4214453 TAA TAA TAA TAA
1 TAA TAA TAA TAA
4214465 AACAGGGATA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:4214957 original size:122 final size:121
Alignment explanation
Indices: 4214827--4215384 Score: 809
Period size: 122 Copynumber: 4.6 Consensus size: 121
4214817 GAATTAAGGC
* * *
4214827 AAGGTTGAACAAATTCTTCTTATTATGAACTTATTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
* * *
4214891 TGAACTCTTC-CGGAAATGTTGATGCGGATCTATCTCCTTCTGCGATAGAGTCATGCAA
65 TGAACT-TTCTCGGAAAAGTTGATGCTGATCTATCTCCTTCTGCGATAGAATCATGC-A
*
4214949 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA-GAAGTTTTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG-AGTTCTTCTCATTA
*
4215013 TGAACTTTCTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCATGCA
65 TGAACTTTCTC-GGAAAAGTTGATGCTGATCTATCTCCTTCTGCGATAGAATCATGCA
* *
4215071 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAAATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * *
4215136 GAACTTTCTTTGGAAAAGTTGATGATGATCCATCTCCTTCTGTGATAGAATCATGCA
66 GAACTTTC-TCGGAAAAGTTGATGCTGATCTATCTCCTTCTGCGATAGAATCATGCA
*
4215193 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * * * *
4215258 GAATTTTCTCTGGAAAAGTTGATGTTGATCTATCTCCTTATACGATAGAGT-AGAGCAA
66 GAACTTTCTC-GGAAAAGTTGATGCTGATCTATCTCCTTCTGCGATAGAATCA-TGC-A
*
4215316 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCCTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
4215381 GAAC
66 GAAC
4215385 ACTTCTAGAA
Statistics
Matches: 400, Mismatches: 27, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
121 6 0.01
122 282 0.70
123 112 0.28
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (121 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTTTCTCGGAAAAGTTGATGCTGATCTATCTCCTTCTGCGATAGAATCATGCA
Found at i:4215836 original size:22 final size:22
Alignment explanation
Indices: 4215784--4215837 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
4215774 AAATATTTCT
*
4215784 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAGAGAGAATCTATCA
4215806 TCTTTGAAGAGAGAATCTATCA
1 TCTTTGAAGAGAGAATCTATCA
4215828 TCTTTGAAGA
1 TCTTTGAAGA
4215838 ATGTAGATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (22 bp):
TCTTTGAAGAGAGAATCTATCA
Found at i:4216268 original size:54 final size:54
Alignment explanation
Indices: 4216204--4216382 Score: 200
Period size: 54 Copynumber: 3.3 Consensus size: 54
4216194 TAACTGGTTC
* ** * *
4216204 GTAAAACATTTGACAACATATTCATCATCTCATGTGGTTTCTGCTCAGATGCTA
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGACTTCTACCCAGATGCTA
* * * *
4216258 GTAAAACATTTGATAACACATTCATCATTTCCTGTGACTTCTACCCATATGCTA
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGACTTCTACCCAGATGCTA
** * * *
4216312 GTAAAACATTTGACAACACATTCATC-T-AGATGTGGCTTCTACCCAGATGTTTC
1 GTAAAACATTTGACAACACATTCATCATCTCATGTGACTTCTACCCAGATG-CTA
*
4216365 GTAAAACTTTTGACAACA
1 GTAAAACATTTGACAACA
4216383 TTCATTCTTT
Statistics
Matches: 106, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
52 17 0.16
53 19 0.18
54 70 0.66
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.34
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCATCTCATGTGACTTCTACCCAGATGCTA
Found at i:4220637 original size:6 final size:7
Alignment explanation
Indices: 4220620--4220645 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
4220610 CTTGATTCAA
4220620 TTTTTCC
1 TTTTTCC
4220627 TTTTTCC
1 TTTTTCC
4220634 TTTTTCC
1 TTTTTCC
4220641 TTTTT
1 TTTTT
4220646 TTTTATGAGT
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:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCC
Done.