Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168422.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_636, 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: 20948
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Found at i:2551 original size:57 final size:56
Alignment explanation
Indices: 2489--2765 Score: 281
Period size: 58 Copynumber: 4.7 Consensus size: 56
2479 CTTTTGTACA
* *
2489 AAGAAAATTGATACTTTCAACTTTTCCCCAAAATGTTTTTCT-G-AAACTTTAATTTC
1 AAGAAAATTGATACTTTCAACTTTTCCCCAAAATATTTTT-TAGAAAAC-TTATTTTC
* ** * *
2545 GAAGAAAATTGATACTTTCAATTTTTCCTAAAAAAAAAAAACCCTTTTTAGAAAA-TTATTTTC
1 -AAGAAAATTGATACTTTCAACTTTTCC-----CCAAAATA--TTTTTTAGAAAACTTATTTTC
* * *
2608 AAAGAAAATTAACACTTTCAATTTTTCCCCAAAATATTTTTTAGAAAACTTATTTTC
1 -AAGAAAATTGATACTTTCAACTTTTCCCCAAAATATTTTTTAGAAAACTTATTTTC
* *
2665 AAGGAAAATTAATACTTTCAACTTTTCCTCATAAATATTTTTTAGAAAACTTATTTTC
1 AA-GAAAATTGATACTTTCAACTTTTCCCCA-AAATATTTTTTAGAAAACTTATTTTC
*
2723 AAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
1 AAG-AAAATTGATACTTTCAACTTTTCC-CCAAAATATTTTTT
2766 TTGGAATTTT
Statistics
Matches: 186, Mismatches: 20, Indels: 27
0.80 0.09 0.12
Matches are distributed among these distances:
56 13 0.07
57 60 0.32
58 67 0.36
59 1 0.01
62 4 0.02
63 33 0.18
64 5 0.03
65 3 0.02
ACGTcount: A:0.39, C:0.15, G:0.05, T:0.40
Consensus pattern (56 bp):
AAGAAAATTGATACTTTCAACTTTTCCCCAAAATATTTTTTAGAAAACTTATTTTC
Found at i:2802 original size:5 final size:5
Alignment explanation
Indices: 2792--2859 Score: 73
Period size: 5 Copynumber: 12.6 Consensus size: 5
2782 AGAAAATCAA
* *
2792 AAAAT AAAAT AAAAC AAAATT AAAAT AAAAT AAAAAT AAAGGT AAAAAT
1 AAAAT AAAAT AAAAT AAAA-T AAAAT AAAAT -AAAAT AAA-AT -AAAAT
2841 AAAAAT AAAAT AAAAT AAA
1 -AAAAT AAAAT AAAAT AAA
2860 GAATACTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
5 35 0.64
6 17 0.31
7 3 0.05
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:2839 original size:12 final size:11
Alignment explanation
Indices: 2791--2864 Score: 80
Period size: 11 Copynumber: 6.6 Consensus size: 11
2781 AAGAAAATCA
2791 AAAAATAAAAT
1 AAAAATAAAAT
*
2802 -AAAACAAAAT
1 AAAAATAAAAT
*
2812 TAAAATAAAAT
1 AAAAATAAAAT
*
2823 AAAAATAAAGGT
1 AAAAATAAA-AT
2835 AAAAATAAAA-
1 AAAAATAAAAT
2845 ATAAAATAAAAT
1 A-AAAATAAAAT
2857 AAAGAATA
1 AAA-AATA
2865 CTAAATAATT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
10 10 0.19
11 28 0.53
12 15 0.28
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.18
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:2898 original size:3 final size:3
Alignment explanation
Indices: 2890--2924 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2880 CTAATCAATA
2890 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2925 ATAAGAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3430 original size:21 final size:21
Alignment explanation
Indices: 3393--3437 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
3383 AATTTTCCAG
3393 AAAAAAACTTCAAAAATT-CT
1 AAAAAAACTTCAAAAATTCCT
* *
3413 AAAAAAATTCTCACAAATTCCT
1 AAAAAAACT-TCAAAAATTCCT
3435 AAA
1 AAA
3438 GCTGTATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 8 0.38
22 5 0.24
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAAACTTCAAAAATTCCT
Found at i:3783 original size:48 final size:46
Alignment explanation
Indices: 3677--3833 Score: 153
Period size: 48 Copynumber: 3.4 Consensus size: 46
3667 AAAAAATAAA
* * * * * *
3677 AATAGATAAATAATAA-ATAAATAAATATATATACTAATAGATA-AAT
1 AATAGATAAATAATAATATATATTAATAGATA-A-AAATATATACATT
3723 AATAGATAAATAATAGATA-ATAGTTAATA-ATAAAAATTTATATACATT
1 AATAGATAAATAATA-ATATATA-TTAATAGATAAAAA--TATATACATT
*
3771 AATAGATAAATAATAATATATATTAATAGATAAAAATATATATATT
1 AATAGATAAATAATAATATATATTAATAGATAAAAATATATACATT
*
3817 AATAAAT-AATAATAATA
1 AATAGATAAATAATAATA
3834 GCAATAAATA
Statistics
Matches: 96, Mismatches: 7, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
45 12 0.12
46 31 0.32
47 20 0.21
48 33 0.34
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (46 bp):
AATAGATAAATAATAATATATATTAATAGATAAAAATATATACATT
Found at i:3815 original size:24 final size:25
Alignment explanation
Indices: 3722--3830 Score: 117
Period size: 24 Copynumber: 4.6 Consensus size: 25
3712 AATAGATAAA
*
3722 TAATAGATAAATAATAGATA-ATAGT
1 TAATAGATAAATAATATATATATA-T
* *
3747 TAATA-ATAAA-AATTTATATACAT
1 TAATAGATAAATAATATATATATAT
3770 TAATAGATAAATAATA-ATATATAT
1 TAATAGATAAATAATATATATATAT
3794 TAATAGAT-AA-AA-ATATATATAT
1 TAATAGATAAATAATATATATATAT
*
3816 TAATAAAT-AATAATA
1 TAATAGATAAATAATA
3831 ATAGCAATAA
Statistics
Matches: 72, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
21 1 0.01
22 19 0.26
23 16 0.22
24 28 0.39
25 8 0.11
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.36
Consensus pattern (25 bp):
TAATAGATAAATAATATATATATAT
Found at i:3831 original size:10 final size:10
Alignment explanation
Indices: 3671--3844 Score: 84
Period size: 11 Copynumber: 15.9 Consensus size: 10
3661 AGCCAAAAAA
3671 AATAAA-AAT
1 AATAAATAAT
3680 AGATAAATAAT
1 A-ATAAATAAT
3691 AAATAAATAAAT
1 -AATAAAT-AAT
*
3703 ATATATACTAAT
1 A-ATA-AATAAT
3715 AGATAAATAAT
1 A-ATAAATAAT
3726 AGATAAATAAT
1 A-ATAAATAAT
3737 AGATAATAGTTAAT
1 A-ATAA-A--TAAT
3751 AATAAA-AATTT
1 AATAAATAA--T
*
3762 ATATACATTAAT
1 A-ATA-AATAAT
3774 AGATAAATAAT
1 A-ATAAATAAT
* *
3785 AATATATATT
1 AATAAATAAT
* *
3795 AATAGATAAA
1 AATAAATAAT
*
3805 AATATATATATT
1 AATA-A-ATAAT
3817 AATAAATAAT
1 AATAAATAAT
**
3827 AAT-AATAGC
1 AATAAATAAT
3836 AATAAATAA
1 AATAAATAA
3845 ATAAGATACA
Statistics
Matches: 130, Mismatches: 18, Indels: 33
0.72 0.10 0.18
Matches are distributed among these distances:
9 10 0.08
10 34 0.26
11 41 0.32
12 31 0.24
13 7 0.05
14 7 0.05
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (10 bp):
AATAAATAAT
Found at i:7380 original size:15 final size:15
Alignment explanation
Indices: 7355--7443 Score: 65
Period size: 15 Copynumber: 5.8 Consensus size: 15
7345 ACTTGGCTCG
7355 AATTCATATATATAAA
1 AATT-ATATATATAAA
**
7371 AATTATATATATATG
1 AATTATATATATAAA
*
7386 AATTATATATA-AATT
1 AATTATATATATAA-A
* *
7401 AATTCACATGTATATAA
1 AATT-ATATATATA-AA
* *
7418 AATTTTA-AAATAAA
1 AATTATATATATAAA
7432 AATTATATATAT
1 AATTATATATAT
7444 TTTATTCAAC
Statistics
Matches: 55, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
14 9 0.16
15 30 0.55
16 10 0.18
17 5 0.09
18 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (15 bp):
AATTATATATATAAA
Found at i:8843 original size:13 final size:13
Alignment explanation
Indices: 8825--8871 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
8815 TTTATATAAA
8825 TTTTATTTTTAAT
1 TTTTATTTTTAAT
* *
8838 TTTTATACATATAAT
1 TTTTAT--TTTTAAT
8853 TTTTATTTTTAAT
1 TTTTATTTTTAAT
8866 TTTTAT
1 TTTTAT
8872 ATATATGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 17 0.61
15 11 0.39
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTATTTTTAAT
Found at i:8844 original size:22 final size:22
Alignment explanation
Indices: 8808--8863 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
8798 TAAACTCAAA
* * *
8808 TTTTACTTTTATATAAATTTTAT
1 TTTTAATTTT-TATAAATATAAT
*
8831 TTTTAATTTTTATACATATAAT
1 TTTTAATTTTTATAAATATAAT
8853 TTTT-ATTTTTA
1 TTTTAATTTTTA
8864 ATTTTTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 7 0.24
22 13 0.45
23 9 0.31
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTAATTTTTATAAATATAAT
Found at i:8851 original size:28 final size:28
Alignment explanation
Indices: 8818--8877 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
8808 TTTTACTTTT
8818 ATATAAATTTTATTTTTAATTTTTATAC
1 ATATAAATTTTATTTTTAATTTTTATAC
* *
8846 ATATAATTTTTATTTTTAATTTTTATAT
1 ATATAAATTTTATTTTTAATTTTTATAC
8874 ATAT
1 ATAT
8878 GTGAATTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (28 bp):
ATATAAATTTTATTTTTAATTTTTATAC
Found at i:10775 original size:57 final size:56
Alignment explanation
Indices: 10713--10822 Score: 150
Period size: 56 Copynumber: 1.9 Consensus size: 56
10703 ATCAAAATTT
* * *
10713 ATTTTTATTTTTATTTTA-TTTTATTTCTAAAATTTTCACCATTTGGGTCTATTTTAA
1 ATTTTTATTTTTA--TAAGTTTTATTTCTAAAATTTTAACCATTTAGGTCTATTTTAA
* *
10770 ATTTTTCTTTTTATAAGTTTTATTTCTAAAATTTTAACTATTTAGGTCTATTT
1 ATTTTTATTTTTATAAGTTTTATTTCTAAAATTTTAACCATTTAGGTCTATTT
10823 AGAAAAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
55 2 0.04
56 33 0.70
57 12 0.26
ACGTcount: A:0.25, C:0.08, G:0.05, T:0.61
Consensus pattern (56 bp):
ATTTTTATTTTTATAAGTTTTATTTCTAAAATTTTAACCATTTAGGTCTATTTTAA
Found at i:10821 original size:28 final size:27
Alignment explanation
Indices: 10734--10822 Score: 65
Period size: 28 Copynumber: 3.2 Consensus size: 27
10724 TATTTTATTT
* *
10734 TATTTCTAAAATTTTCACCATTTGGGTC
1 TATTTCTAAAATTTT-ACTATTTAGGTC
* * * *
10762 TATTT-T-AAATTTTTCTTTTTATAAGTTT
1 TATTTCTAAAATTTTAC-TATT-T-AGGTC
10790 TATTTCTAAAATTTTAACTATTTAGGTC
1 TATTTCTAAAATTTT-ACTATTTAGGTC
10818 TATTT
1 TATTT
10823 AGAAAAAAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
25 1 0.02
26 9 0.20
27 2 0.04
28 20 0.44
29 2 0.04
30 10 0.22
31 1 0.02
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.56
Consensus pattern (27 bp):
TATTTCTAAAATTTTACTATTTAGGTC
Found at i:12453 original size:44 final size:43
Alignment explanation
Indices: 12392--12735 Score: 251
Period size: 44 Copynumber: 8.0 Consensus size: 43
12382 ACATTAAAAA
* *
12392 CTCCTCTAAACAAAGGCTTCACAACTTTTGAGAAATAAATAAAG
1 CTCCTCTAAACAGAGGCTTCACAACTTTTGA-AAATAAATAAGG
* * * *
12436 CTCCTATAAGCAGAGGC-TCAACCACTTCTGAAACATAAATAAGG
1 CTCCTCTAAACAGAGGCTTC-ACAACTTTTGAAA-ATAAATAAGG
* * *
12480 CTCATCTAAATAGAAG-TTCAACAAC-TTTGAAAAATAAATAAGG
1 CTCCTCTAAACAGAGGCTTC-ACAACTTTTG-AAAATAAATAAGG
* * * * *
12523 CTCATTTAAACAAAGGCTT-ACGAC-TTTGAGAAATAAATATGG
1 CTCCTCTAAACAGAGGCTTCACAACTTTTGA-AAATAAATAAGG
* *
12565 CTCCTCTAAACAAAGAC-TCA-ATGACTTTTGAAAAGTAAATAAGG
1 CTCCTCTAAACAGAGGCTTCACA--ACTTTTGAAAA-TAAATAAGG
* *
12609 CTCCTCTAAACAGAGGCTTAATAA-TTTTGAAAAGTAAAT-AGG
1 CTCCTCTAAACAGAGGCTTCACAACTTTTGAAAA-TAAATAAGG
* * * * * **
12651 GTCCTTTAAACAGATGC-TCAACTACCTTTGAAAAATAAATAAAA
1 CTCCTCTAAACAGAGGCTTC-ACAACTTTTG-AAAATAAATAAGG
* *
12695 CTCCTCTAAACAAAGGCTTAACAAC-TTTGAAAAGTAAATAA
1 CTCCTCTAAACAGAGGCTTCACAACTTTTGAAAA-TAAATAA
12736 AGTTGCTCGA
Statistics
Matches: 239, Mismatches: 42, Indels: 39
0.75 0.13 0.12
Matches are distributed among these distances:
41 3 0.01
42 57 0.24
43 69 0.29
44 106 0.44
45 3 0.01
46 1 0.00
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (43 bp):
CTCCTCTAAACAGAGGCTTCACAACTTTTGAAAATAAATAAGG
Found at i:12585 original size:129 final size:127
Alignment explanation
Indices: 12398--12735 Score: 356
Period size: 129 Copynumber: 2.6 Consensus size: 127
12388 AAAACTCCTC
* * * *
12398 TAAACAAAGGCTTCACAACTTTTGAGAAATAAATAAAGCTCCTATAAGCAGAGGCTCAACCACTT
1 TAAACAAAGGCTT-ACAAC-TTTGAGAAATAAATAAAGCTCCTCTAAACAAAGGCTCAACAACTT
*
12463 CTGAAACA-TAAATAAGGCTCATCTAAATAGAAG-TTCAACAACTTTGAAAAATAAATAAGGCTC
64 -TGAAA-AGTAAATAAGGCTCATCTAAACAGAAGCTT-AACAACTTTGAAAAATAAAT-AGGCTC
12526 ATT
125 ATT
* ** * **
12529 TAAACAAAGGCTTACGACTTTGAGAAATAAATATGGCTCCTCTAAACAAAGACTCAATGACTTTT
1 TAAACAAAGGCTTACAACTTTGAGAAATAAATAAAGCTCCTCTAAACAAAGGCTCAACAAC-TTT
* * * * * * *
12594 GAAAAGTAAATAAGGCTCCTCTAAACAGAGGCTTAATAATTTTGAAAAGTAAATAGGGTCCTT
65 GAAAAGTAAATAAGGCTCATCTAAACAGAAGCTTAACAACTTTGAAAAATAAATAGGCTCATT
* * * * * * *
12657 TAAACAGATGCTCAACTACCTTTGAAAAATAAATAAAACTCCTCTAAACAAAGGCTTAACAACTT
1 TAAACAAAGGCT-TAC-AACTTTGAGAAATAAATAAAGCTCCTCTAAACAAAGGCTCAACAACTT
12722 TGAAAAGTAAATAA
64 TGAAAAGTAAATAA
12736 AGTTGCTCGA
Statistics
Matches: 172, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
128 18 0.10
129 97 0.56
130 44 0.26
131 13 0.08
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (127 bp):
TAAACAAAGGCTTACAACTTTGAGAAATAAATAAAGCTCCTCTAAACAAAGGCTCAACAACTTTG
AAAAGTAAATAAGGCTCATCTAAACAGAAGCTTAACAACTTTGAAAAATAAATAGGCTCATT
Found at i:12619 original size:86 final size:85
Alignment explanation
Indices: 12392--12734 Score: 313
Period size: 86 Copynumber: 4.0 Consensus size: 85
12382 ACATTAAAAA
* * * * *
12392 CTCCTCTAAACA-AAGGCTTCACA-ACTTTTGAGAAATAAATAAAGCTCCTATAAGCAGAGGCTC
1 CTCCTCTAAACAGAA-GC-TCA-ATACTTTTGAAAAATAAATAAAGCTCCTCTAAACAAAGGCTT
*
12455 AACCACTTCTGAAACA-TAAATAAGG
63 AACAACTT-TGAAA-AGTAAAT-AGG
* * * * * * *
12480 CTCATCTAAATAGAAGTTCAACAAC-TTTGAAAAATAAATAAGGCTCATTTAAACAAAGGCTT-A
1 CTCCTCTAAACAGAAGCTCAA-TACTTTTGAAAAATAAATAAAGCTCCTCTAAACAAAGGCTTAA
*
12543 CGACTTTGAGAAA-TAAATATGG
65 CAACTTTGA-AAAGTAAATA-GG
* * *
12565 CTCCTCTAAACA-AAGACTCAATGACTTTTGAAAAGTAAATAAGGCTCCTCTAAACAGAGGCTTA
1 CTCCTCTAAACAGAAG-CTCAAT-ACTTTTGAAAAATAAATAAAGCTCCTCTAAACAAAGGCTTA
* *
12629 ATAATTTTGAAAAGTAAATAGG
64 ACAACTTTGAAAAGTAAATAGG
* * * * *
12651 GTCCTTTAAACAGATGCTCAACTACCTTTGAAAAATAAATAAAACTCCTCTAAACAAAGGCTTAA
1 CTCCTCTAAACAGAAGCTCAA-TACTTTTGAAAAATAAATAAAGCTCCTCTAAACAAAGGCTTAA
12716 CAACTTTGAAAAGTAAATA
65 CAACTTTGAAAAGTAAATA
12735 AAGTTGCTCG
Statistics
Matches: 211, Mismatches: 32, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
84 4 0.02
85 27 0.13
86 116 0.55
87 49 0.23
88 13 0.06
89 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (85 bp):
CTCCTCTAAACAGAAGCTCAATACTTTTGAAAAATAAATAAAGCTCCTCTAAACAAAGGCTTAAC
AACTTTGAAAAGTAAATAGG
Found at i:15441 original size:23 final size:22
Alignment explanation
Indices: 15415--15459 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
15405 AAAAAATGGT
15415 TAAT-TTAGTATTTTCAAATAAAA
1 TAATATTAG-ATTTTC-AATAAAA
*
15438 TAATATTTGATTTTCAATAAAA
1 TAATATTAGATTTTCAATAAAA
15460 CCAAAACACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 10 0.50
24 3 0.15
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (22 bp):
TAATATTAGATTTTCAATAAAA
Found at i:16185 original size:145 final size:149
Alignment explanation
Indices: 15918--16214 Score: 516
Period size: 145 Copynumber: 2.0 Consensus size: 149
15908 TAACAAACAC
*
15918 AAACAATGTGTATCTTAATTATTTACTATTATTTAAAAATATTTTTAACTGCATTTTATTTTTAG
1 AAACAATGTGAATCTTAATTATTTACTATTATTTAAAAATATTTTTAACTGCATTTTATTTTTAG
*
15983 ATAACTCAAAATTTCATTCTCATTACTTGGACTAAAAAAGGTTAATTGGTTCTTTACAAGAAGAA
66 ATAACTCAAAATTTCATTCTCATTACTTGGACTAAAAAAAGTTAATTGGTTCTTTACAAGAAGAA
16048 ATGAATGCTAATAAATAAA
131 ATGAATGCTAATAAATAAA
16067 AAACAATGTGAATCTTAATTATTTA-TA-TA-TT-AAAA-ATTTTTAACT-CATTTTTTATTTTT
1 AAACAATGTGAATCTTAATTATTTACTATTATTTAAAAATATTTTTAACTGCA--TTTTATTTTT
16126 AGATAACTCAAAATTTCATTCTCATTACTTGGACTAAAAAAAGTTAATTGGTTCTTTACAAGAAG
64 AGATAACTCAAAATTTCATTCTCATTACTTGGACTAAAAAAAGTTAATTGGTTCTTTACAAGAAG
16191 AAATGAATGCTAATAAATAAA
129 AAATGAATGCTAATAAATAAA
16212 AAA
1 AAA
16215 ACCTCAGATC
Statistics
Matches: 144, Mismatches: 2, Indels: 8
0.94 0.01 0.05
Matches are distributed among these distances:
143 2 0.01
144 10 0.07
145 102 0.71
146 2 0.01
147 2 0.01
148 2 0.01
149 24 0.17
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.40
Consensus pattern (149 bp):
AAACAATGTGAATCTTAATTATTTACTATTATTTAAAAATATTTTTAACTGCATTTTATTTTTAG
ATAACTCAAAATTTCATTCTCATTACTTGGACTAAAAAAAGTTAATTGGTTCTTTACAAGAAGAA
ATGAATGCTAATAAATAAA
Found at i:17237 original size:3 final size:3
Alignment explanation
Indices: 17224--17260 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
17214 TAAATAGCTC
17224 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17261 TTTTGTTCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:17515 original size:5 final size:5
Alignment explanation
Indices: 17499--17538 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
17489 GTAATAAGTC
* *
17499 AAATC AAATT AATTT AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT AAATT AAATT
17539 GTTTTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:18329 original size:24 final size:24
Alignment explanation
Indices: 18282--18362 Score: 103
Period size: 26 Copynumber: 3.4 Consensus size: 24
18272 ATTATATATA
* *
18282 TTTTAT-TAAACTTAATTTTT-AT
1 TTTTATATAAATTTTATTTTTAAT
18304 TTTTATATAAATTTTATTTTTAAT
1 TTTTATATAAATTTTATTTTTAAT
*
18328 TTATATATATAACTTTTATTTTTAAT
1 TT-T-TATATAAATTTTATTTTTAAT
18354 TTTTATATA
1 TTTTATATA
18363 TTTATGAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
22 6 0.12
23 12 0.23
24 10 0.19
25 2 0.04
26 22 0.42
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTATATAAATTTTATTTTTAAT
Found at i:19814 original size:52 final size:52
Alignment explanation
Indices: 19729--19881 Score: 184
Period size: 52 Copynumber: 2.9 Consensus size: 52
19719 ATAACCATAT
* * * *
19729 AAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATCCCTTCTC-TGTAAGTC
1 AAACTTGCCTATTAAGAATCTCTTTCTTCTTAGAAT-CCTTCTCTTGCAAGTC
* *
19781 AAACTTGCCTATTAAGAATCTCTTTCTTTTTAGAATTCTTCTCTTGCAAGTC
1 AAACTTGCCTATTAAGAATCTCTTTCTTCTTAGAATCCTTCTCTTGCAAGTC
* * * *
19833 AAACTTACCTATTAAGAATTCTCTTTC-TCTTATAATTCTTCTTTTGCAA
1 AAACTTGCCTATTAAGAA-TCTCTTTCTTCTTAGAATCCTTCTCTTGCAA
19882 TTCTTCTTAT
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 6 0.07
52 75 0.84
53 8 0.09
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (52 bp):
AAACTTGCCTATTAAGAATCTCTTTCTTCTTAGAATCCTTCTCTTGCAAGTC
Found at i:19925 original size:11 final size:11
Alignment explanation
Indices: 19909--19948 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
19899 GCAATATCTG
19909 ACAAATCCCAA
1 ACAAATCCCAA
* *
19920 ACAAATCTCTA
1 ACAAATCCCAA
19931 ACAAATCCCAA
1 ACAAATCCCAA
*
19942 ATAAATC
1 ACAAATC
19949 TCTTATGAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.53, C:0.30, G:0.00, T:0.17
Consensus pattern (11 bp):
ACAAATCCCAA
Found at i:19934 original size:22 final size:22
Alignment explanation
Indices: 19909--19951 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
19899 GCAATATCTG
19909 ACAAATCCCAAACAAATCTCTA
1 ACAAATCCCAAACAAATCTCTA
*
19931 ACAAATCCCAAATAAATCTCT
1 ACAAATCCCAAACAAATCTCT
19952 TATGAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (22 bp):
ACAAATCCCAAACAAATCTCTA
Found at i:20208 original size:23 final size:25
Alignment explanation
Indices: 20169--20233 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
20159 GAACTTGTTT
**
20169 CTTCCCATGTCTCAAACC-AT-GCA
1 CTTCCCACATCTCAAACCTATAGCA
* * *
20192 CTTCCCACATCTTAAACCTTTAGCT
1 CTTCCCACATCTCAAACCTATAGCA
20217 CTTCCCACATCTCAAAC
1 CTTCCCACATCTCAAAC
20234 TTTTAGCTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 15 0.44
24 1 0.03
25 18 0.53
ACGTcount: A:0.26, C:0.40, G:0.05, T:0.29
Consensus pattern (25 bp):
CTTCCCACATCTCAAACCTATAGCA
Found at i:20221 original size:25 final size:25
Alignment explanation
Indices: 20192--20241 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
20182 AAACCATGCA
*
20192 CTTCCCACATCTTAAACCTTTAGCT
1 CTTCCCACATCTCAAACCTTTAGCT
*
20217 CTTCCCACATCTCAAACTTTTAGCT
1 CTTCCCACATCTCAAACCTTTAGCT
20242 TTTTCACGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.36, G:0.04, T:0.36
Consensus pattern (25 bp):
CTTCCCACATCTCAAACCTTTAGCT
Found at i:20266 original size:24 final size:24
Alignment explanation
Indices: 20238--20315 Score: 75
Period size: 25 Copynumber: 3.2 Consensus size: 24
20228 TCAAACTTTT
20238 AGCTTTTTCACGTCTCGAACCTTC
1 AGCTTTTTCACGTCTCGAACCTTC
* * * *
20262 GGCTTTTTCCACATCTTGAATCTTC
1 AGCTTTTT-CACGTCTCGAACCTTC
* * *
20287 AACTCTTCTCACGTTTCGAACCTTC
1 AGCT-TTTTCACGTCTCGAACCTTC
20312 AGCT
1 AGCT
20316 CTGATACCAC
Statistics
Matches: 40, Mismatches: 12, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
24 7 0.17
25 30 0.75
26 3 0.08
ACGTcount: A:0.18, C:0.32, G:0.12, T:0.38
Consensus pattern (24 bp):
AGCTTTTTCACGTCTCGAACCTTC
Found at i:20911 original size:51 final size:51
Alignment explanation
Indices: 20846--20945 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 51
20836 TTCTTCTCTC
* *
20846 TTAGAATTCTTCTC-TGTAAGTCAAACTTGCCTATTAAGAATCC-CTTTCTTT
1 TTAGAATTCTTCTCTTGCAA-TCAAACTTACCTATTAA-AATCCTCTTTCTTT
20897 TTAGAATTCTTCTCTTGCAATCAAACTTACCTATTAAAATCCTCTTTCT
1 TTAGAATTCTTCTCTTGCAATCAAACTTACCTATTAAAATCCTCTTTCT
20946 CTT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
50 5 0.11
51 36 0.80
52 4 0.09
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (51 bp):
TTAGAATTCTTCTCTTGCAATCAAACTTACCTATTAAAATCCTCTTTCTTT
Done.