Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168016.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_270, 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: 40915
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:3537 original size:22 final size:23
Alignment explanation
Indices: 3500--3553 Score: 92
Period size: 22 Copynumber: 2.3 Consensus size: 23
3490 TTTAATTTTT
3500 TATTTATATATATTTAAAAAATAA
1 TATTT-TATATATTTAAAAAATAA
3524 TATTTTATAT-TTTAAAAAATAA
1 TATTTTATATATTTAAAAAATAA
3546 TATTTTAT
1 TATTTTAT
3554 TAATTTCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 20 0.67
23 5 0.17
24 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTTTATATATTTAAAAAATAA
Found at i:7157 original size:15 final size:15
Alignment explanation
Indices: 7119--7150 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
7109 GAATCGAATT
*
7119 ATATATATATTTTTA
1 ATATATATATTTTAA
7134 ATATATATATTTTAA
1 ATATATATATTTTAA
7149 AT
1 AT
7151 TTTTATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATATATATTTTAA
Found at i:7211 original size:13 final size:13
Alignment explanation
Indices: 7193--7217 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7183 ATATATTTAA
7193 TTATATTAAAATT
1 TTATATTAAAATT
7206 TTATATTAAAAT
1 TTATATTAAAAT
7218 AACATAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTATATTAAAATT
Found at i:10127 original size:51 final size:51
Alignment explanation
Indices: 10072--10191 Score: 129
Period size: 50 Copynumber: 2.4 Consensus size: 51
10062 TTAAAATTGG
** *
10072 TTTTAGGATTATCTTGACTCTTTGACAAAATCTT-AAAATTTATTAAAC-AGA
1 TTTTAGGATTATCTCAACTCATTGACAAAATCTTAAAAATTT-TTAAACTA-A
* * *
10123 TTTTAAGATTATC-CAACTCATTGACGATATCTTAAAAATTTTTAAACTAA
1 TTTTAGGATTATCTCAACTCATTGACAAAATCTTAAAAATTTTTAAACTAA
* *
10173 TTTTAGGATCATCTAAACT
1 TTTTAGGATTATCTCAACT
10192 TTCTAATGAG
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
50 33 0.58
51 24 0.42
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (51 bp):
TTTTAGGATTATCTCAACTCATTGACAAAATCTTAAAAATTTTTAAACTAA
Found at i:12234 original size:34 final size:34
Alignment explanation
Indices: 12174--12252 Score: 81
Period size: 34 Copynumber: 2.4 Consensus size: 34
12164 TATGAAACTT
*
12174 TAAAA-TTTAAAAGGTTCCCCTAACCAGAAGCTA-
1 TAAAACTTTAAAAGGCTCCCCTAACCAGAAGC-AC
* * * *
12207 TAAAACTTTAAATGGCTCCTCTGACCAGAGGCAC
1 TAAAACTTTAAAAGGCTCCCCTAACCAGAAGCAC
*
12241 CAAAACTTTAAA
1 TAAAACTTTAAA
12253 GTTTAAAAGG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
33 6 0.16
34 32 0.84
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.24
Consensus pattern (34 bp):
TAAAACTTTAAAAGGCTCCCCTAACCAGAAGCAC
Found at i:12369 original size:40 final size:40
Alignment explanation
Indices: 12213--12381 Score: 124
Period size: 41 Copynumber: 4.2 Consensus size: 40
12203 GCTATAAAAC
* * * * **
12213 TTTAAATGGCTCCTCTGACCAGAGGCACCAAAACTTTAAA
1 TTTAAAAGGCTTCTATGACTAGAGGCAATAAAACTTTAAA
* * * *
12253 GTTTAAAAGGC-TCATTTGATTAGAGGCAATGAAAGTTTAGAA
1 -TTTAAAAGGCTTC-TATGACTAGAGGCAATAAAACTTTA-AA
* * * * * * * *
12295 TTTAAAAGACTTATCTGACCAAAGACTATGAAACTTTAAA
1 TTTAAAAGGCTTCTATGACTAGAGGCAATAAAACTTTAAA
*
12335 TTTAAAAGGCTTCTATAACTAGAGGCAATAAAACTTTAAA
1 TTTAAAAGGCTTCTATGACTAGAGGCAATAAAACTTTAAA
*
12375 TTAAAAA
1 TTTAAAA
12382 TATGAGAGGA
Statistics
Matches: 97, Mismatches: 28, Indels: 7
0.73 0.21 0.05
Matches are distributed among these distances:
40 40 0.41
41 54 0.56
42 3 0.03
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.29
Consensus pattern (40 bp):
TTTAAAAGGCTTCTATGACTAGAGGCAATAAAACTTTAAA
Found at i:12706 original size:33 final size:33
Alignment explanation
Indices: 12624--12707 Score: 80
Period size: 33 Copynumber: 2.5 Consensus size: 33
12614 AAAATATGAG
* ** *
12624 AGGCAATGGTATTTGAAAGATTTCTTTAAACAA
1 AGGCTATGGTATTTGAATCATTTCTCTAAACAA
* ** *
12657 AGGGTATGAAACTTGAATCATTTCTCTAAACATA
1 AGGCTATGGTATTTGAATCATTTCTCTAAACA-A
12691 A-GCTATGGTATTTGAAT
1 AGGCTATGGTATTTGAAT
12708 GATTCCGCTA
Statistics
Matches: 38, Mismatches: 12, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
33 36 0.95
34 2 0.05
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.35
Consensus pattern (33 bp):
AGGCTATGGTATTTGAATCATTTCTCTAAACAA
Found at i:12719 original size:33 final size:33
Alignment explanation
Indices: 12662--12758 Score: 86
Period size: 33 Copynumber: 2.9 Consensus size: 33
12652 AACAAAGGGT
* * * * * *
12662 ATGAAACTTGAATCATTTCTCTAAACATAAGCT
1 ATGAAATTTGAATGATTCCGCTAAACAGAAGCC
** * *
12695 ATGGTATTTGAATGATTCCGCTAAATAGAGGCC
1 ATGAAATTTGAATGATTCCGCTAAACAGAAGCC
**
12728 ATGAAATTTGAATGATTCCTTTAAACAGAAG
1 ATGAAATTTGAATGATTCCGCTAAACAGAAG
12759 GTTTACATCT
Statistics
Matches: 48, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (33 bp):
ATGAAATTTGAATGATTCCGCTAAACAGAAGCC
Found at i:18193 original size:59 final size:57
Alignment explanation
Indices: 18094--18316 Score: 281
Period size: 59 Copynumber: 3.7 Consensus size: 57
18084 TTTTTTTTAG
18094 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAATTTCGATTTTC-AA
1 GGAAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTGGAAATTT--ATTTTCTAA
*
18153 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCT-TTTTTTGAAAATTTA-TTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCC-CAAAAA---TATTTTTTGGAAATTTATTTTCTAA
18212 GGAAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTTGGAAATTTATTTTTCTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTGGAAATTTA-TTTTC---TAA
18274 GGAAAATTGATACTTTCAACTTTTCCCTAAAAAATATATTTTT
1 GGAAAATTGATACTTTCAACTTTTCCC--AAAAATAT-TTTTT
18317 TTTTGAAATT
Statistics
Matches: 148, Mismatches: 2, Indels: 23
0.86 0.01 0.13
Matches are distributed among these distances:
56 1 0.01
57 14 0.09
58 11 0.07
59 64 0.43
61 13 0.09
62 31 0.21
63 9 0.06
64 5 0.03
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGGAAATTTATTTTCTAA
Found at i:19368 original size:22 final size:24
Alignment explanation
Indices: 19317--19370 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
19307 ATATGATAGT
*
19317 ATAAAAATAAAAAAATAATATCAG
1 ATAAAATTAAAAAAATAATATCAG
*
19341 AT--AATTCAAAAAA-AA-ATCAG
1 ATAAAATTAAAAAAATAATATCAG
19361 ATAAAATTAA
1 ATAAAATTAA
19371 CAGATAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
20 7 0.28
21 2 0.08
22 14 0.56
24 2 0.08
ACGTcount: A:0.69, C:0.06, G:0.04, T:0.22
Consensus pattern (24 bp):
ATAAAATTAAAAAAATAATATCAG
Found at i:19767 original size:1 final size:1
Alignment explanation
Indices: 19763--19857 Score: 100
Period size: 1 Copynumber: 95.0 Consensus size: 1
19753 TTTTAAAAAA
* * * * * * *
19763 TTTTTGTTTTTTGTTTTTTGTTTTTTTGTTTTTTTTGTTTTTTTTGTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
19828 GTTTTTTTTTTGTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
19858 GCCGAAGTTC
Statistics
Matches: 74, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:19788 original size:9 final size:9
Alignment explanation
Indices: 19776--19854 Score: 117
Period size: 9 Copynumber: 8.7 Consensus size: 9
19766 TTGTTTTTTG
19776 TTTTTTG-T
1 TTTTTTGTT
19784 TTTTTTGTT
1 TTTTTTGTT
19793 TTTTTTGTT
1 TTTTTTGTT
19802 TTTTTTGTTT
1 TTTTTTG-TT
19812 TTTTTTGTTT
1 TTTTTTG-TT
19822 TTTTTTGTT
1 TTTTTTGTT
19831 TTTTTT-TT
1 TTTTTTGTT
19839 GTTTTTTGTT
1 -TTTTTTGTT
19849 TTTTTT
1 TTTTTT
19855 TTTGCCGAAG
Statistics
Matches: 67, Mismatches: 0, Indels: 7
0.91 0.00 0.09
Matches are distributed among these distances:
8 9 0.13
9 37 0.55
10 21 0.31
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:19807 original size:40 final size:38
Alignment explanation
Indices: 19763--19857 Score: 147
Period size: 38 Copynumber: 2.4 Consensus size: 38
19753 TTTTAAAAAA
19763 TTTTTGTTTTTTGTTTTTTGTTTTTTTGTTTTTTTTGTT-T
1 TTTTTGTTTTTT-TTTTTT-TTTTTTTGTTTTTTTT-TTGT
*
19803 TTTTTGTTTTTTTTTGTTTTTTTTTGTTTTTTTTTTGT
1 TTTTTGTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTGT
19841 TTTTTGTTTTTTTTTTT
1 TTTTTGTTTTTTTTTTT
19858 GCCGAAGTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
37 2 0.04
38 33 0.63
39 5 0.10
40 12 0.23
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (38 bp):
TTTTTGTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTGT
Found at i:19855 original size:18 final size:17
Alignment explanation
Indices: 19763--19857 Score: 113
Period size: 18 Copynumber: 5.4 Consensus size: 17
19753 TTTTAAAAAA
*
19763 TTTTTGTTTTTTGTTTT
1 TTTTTTTTTTTTGTTTT
19780 TTGTTTTTTTGTTT-TTTT
1 TT-TTTTTTT-TTTGTTTT
19798 TGTTTTTTTTGTTT-TTTT
1 T-TTTTTTTT-TTTGTTTT
*
19816 TTGTTTTTTTTTGTTTT
1 TTTTTTTTTTTTGTTTT
19833 TTTTTTGTTTTTTGTTTT
1 TTTTTT-TTTTTTGTTTT
19851 TTTTTTT
1 TTTTTTT
19858 GCCGAAGTTC
Statistics
Matches: 70, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
16 3 0.04
17 19 0.27
18 44 0.63
19 4 0.06
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (17 bp):
TTTTTTTTTTTTGTTTT
Found at i:19858 original size:40 final size:38
Alignment explanation
Indices: 19763--19858 Score: 133
Period size: 40 Copynumber: 2.5 Consensus size: 38
19753 TTTTAAAAAA
19763 TTTTTGTTTTTTGTTTTT-TGTTTTTTTGTTTTTTTTGT
1 TTTTTGTTTTTT-TTTTTGTGTTTTTTTGTTTTTTTTGT
*
19801 TTTTT-TTGTTTTTTTTTGTTTTTTTTTGTTTTTTTTTTGT
1 TTTTTGTT-TTTTTTTTTGTGTTTTTTTG--TTTTTTTTGT
19841 TTTTTGTTTTTTTTTTTG
1 TTTTTGTTTTTTTTTTTG
19859 CCGAAGTTCC
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
37 7 0.13
38 18 0.35
40 25 0.48
41 2 0.04
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (38 bp):
TTTTTGTTTTTTTTTTTGTGTTTTTTTGTTTTTTTTGT
Found at i:19967 original size:41 final size:41
Alignment explanation
Indices: 19910--20720 Score: 881
Period size: 41 Copynumber: 19.2 Consensus size: 41
19900 TAAATTGCTC
19910 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGA
1 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGA
* *
19951 AAAGTAAATTGCTCCTCTCAACAGAGGTACCACGACTTTGGA
1 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GA
19993 AAAGTAAATTGCTCCTCTAAACAGAGGCA--ACGAAACTTTGA
1 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACG--ACTTTGA
* *
20034 AAAATAAATTGCTCCTCTAAACAAAGGCA--ACGAACTTTGAA
1 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTG-A
20075 AAAGTAAATTGCTCCTCTAAACAGAGGCA--ACGAACTTTGA
1 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTGA
*
20115 AAAGTAAATCTGCTCCTCTACACAGAGGGCACC-CGACTTTGA
1 AAAGTAAAT-TGCTCCTCTAAACAGA-GGCACCACGACTTTGA
* *
20157 AAAGTAAAATTGCTCCTCTCAACAGAGGTAACCGCACGACTTTTGGA
1 AAAGT-AAATTGCTCCTCTAAACAGAGG-CA-C-CACGAC-TTT-GA
* *
20204 AAAGTAAATTGCTTCCCTCTCAACAGAGGCACCACGGACTTTGGG
1 AAAGTAAATTGC-T-CCTCTAAACAGAGGCACCAC-GACTTT-GA
* *
20249 AAAGTAAATTGCTCCTCTAAACAGAGGCA-AACGAAACTTTGG
1 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACG--ACTTTGA
* *
20291 AAAGTAAATTGCCTCCTCTCAACAGGAGGTC-TCACGACTTCTGGA
1 AAAGTAAATTG-CTCCTCTAAACA-GAGG-CACCACGACTT-T-GA
* * *
20336 AAA-AAAATTGCT-CTCTAAACAGGAGGTACCCACGTACTTTGG
1 AAAGTAAATTGCTCCTCTAAACA-GAGGCA-CCACG-ACTTTGA
* *
20378 AACGTAAATTGCCTCCTCTCAAACAGAGGTACCACGACTTTGGA
1 AAAGTAAATTG-CTCCTCT-AAACAGAGGCACCACGACTTT-GA
20422 AAAGTAAAATTGGCTCCT-TAAACAAGAGGCA--ACGGAACTTTGA
1 AAAGT-AAATT-GCTCCTCTAAAC-AGAGGCACCAC-G-ACTTTGA
*
20465 AAAATAAATTGGCTCCTCT-AACAGAGGGCA--ACGAACTTTGAA
1 AAAGTAAATT-GCTCCTCTAAACAGA-GGCACCACG-ACTTTG-A
20507 AAAGTAAATTGCTCCTCTTAAACCAGAGGCA--ACGACTTTGA
1 AAAGTAAATTGCTCCTC-TAAA-CAGAGGCACCACGACTTTGA
20548 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGA
1 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGA
*
20589 AAAGTAAATTGCTCCTCTAAACAGAGGTACCACGACTTTGGA
1 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTT-GA
*
20631 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGG
1 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGA
*
20672 AAAGTAAATTGCTCCTCTAAGCAGAGGCA--ACGAACTTTGA
1 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTGA
20712 AAAGTAAAT
1 AAAGTAAAT
20721 ACTCCTAGAC
Statistics
Matches: 685, Mismatches: 36, Indels: 99
0.84 0.04 0.12
Matches are distributed among these distances:
39 11 0.02
40 39 0.06
41 238 0.35
42 176 0.26
43 81 0.12
44 45 0.07
45 52 0.08
46 20 0.03
47 9 0.01
48 14 0.02
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (41 bp):
AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGA
Found at i:20049 original size:83 final size:82
Alignment explanation
Indices: 19910--20720 Score: 936
Period size: 83 Copynumber: 9.6 Consensus size: 82
19900 TAAATTGCTC
19910 AAAGTAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTTGAAAAGTAAATTGCTCCTCTCAACA
1 AAAGTAAATTGCTCCTCTAAACAGAGGCA--ACGAACTTTGAAAAGTAAATTGCTCCTCTCAACA
*
19974 GAGGTACCACGACTTTGGA
64 GAGGCACCACGACTTTGGA
* * *
19993 AAAGTAAATTGCTCCTCTAAACAGAGGCAACGAAACTTTGAAAAATAAATTGCTCCTCTAAACAA
1 AAAGTAAATTGCTCCTCTAAACAGAGGCAACG-AACTTTGAAAAGTAAATTGCTCCTCTCAACAG
*
20058 AGGCA--ACGAACTTTGAA
65 AGGCACCACG-ACTTTGGA
20075 AAAGTAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATCTGCTCCTCT-ACACA
1 AAAGTAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAAT-TGCTCCTCTCA-ACA
20139 GAGGGCACC-CGACTTT-GA
64 GA-GGCACCACGACTTTGGA
* *
20157 AAAGTAAAATTGCTCCTCTCAACAGAGGTAACCGCACGACTTTTGGAAAAGTAAATTGCTTCCCT
1 AAAGT-AAATTGCTCCTCTAAACAGAGGCAA-CG-A--AC-TTT-GAAAAGTAAATTGC-T-CCT
*
20222 CTCAACAGAGGCACCACGGACTTTGGG
57 CTCAACAGAGGCACCAC-GACTTTGGA
*
20249 AAAGTAAATTGCTCCTCTAAACAGAGGCAAACGAAACTTTGGAAAGTAAATTGCCTCCTCTCAAC
1 AAAGTAAATTGCTCCTCTAAACAGAGGC-AACG-AACTTTGAAAAGTAAATTG-CTCCTCTCAAC
*
20314 AGGAGGTC-TCACGACTTCTGGA
63 A-GAGG-CACCACGACTT-TGGA
* * * * *
20336 AAA-AAAATTGCT-CTCTAAACAGGAGGTACCCACGTACTTTGGAACGTAAATTGCCTCCTCTCA
1 AAAGTAAATTGCTCCTCTAAACA-GAGG---CAACGAACTTTGAAAAGTAAATTG-CTCCTCTC-
*
20399 AACAGAGGTACCACGACTTTGGA
60 AACAGAGGCACCACGACTTTGGA
*
20422 AAAGTAAAATTGGCTCCT-TAAACAAGAGGCAACGGAACTTTGAAAAATAAATTGGCTCCTCT-A
1 AAAGT-AAATT-GCTCCTCTAAAC-AGAGGCAAC-GAACTTTGAAAAGTAAATT-GCTCCTCTCA
*
20485 ACAGAGGGCA--ACGAACTTTGAA
61 ACAGA-GGCACCACG-ACTTTGGA
*
20507 AAAGTAAATTGCTCCTCTTAAACCAGAGGCAACG-ACTTTGAAAAGTAAATTGCTCCTCTAAACA
1 AAAGTAAATTGCTCCTC-TAAA-CAGAGGCAACGAACTTTGAAAAGTAAATTGCTCCTCTCAACA
20571 GAGGCACCACGACTTT-GA
64 GAGGCACCACGACTTTGGA
* *
20589 AAAGTAAATTGCTCCTCTAAACAGAGGTACCACG-ACTTTGGAAAAGTAAATTGCTCCTCTAAAC
1 AAAGTAAATTGCTCCTCTAAACAGAGG--CAACGAACTTT-GAAAAGTAAATTGCTCCTCTCAAC
20653 AGAGGCACCACGACTTTGG-
63 AGAGGCACCACGACTTTGGA
*
20672 AAAGTAAATTGCTCCTCTAAGCAGAGGCAACGAACTTTGAAAAGTAAAT
1 AAAGTAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAAT
20721 ACTCCTAGAC
Statistics
Matches: 640, Mismatches: 36, Indels: 106
0.82 0.05 0.14
Matches are distributed among these distances:
80 6 0.01
81 42 0.07
82 102 0.16
83 193 0.30
84 17 0.03
85 41 0.06
86 41 0.06
87 88 0.14
88 24 0.04
89 33 0.05
90 14 0.02
91 31 0.05
92 8 0.01
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (82 bp):
AAAGTAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATTGCTCCTCTCAACAGA
GGCACCACGACTTTGGA
Found at i:25921 original size:57 final size:55
Alignment explanation
Indices: 25826--26049 Score: 258
Period size: 57 Copynumber: 3.9 Consensus size: 55
25816 TTTTTTTTAG
25826 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGGAAATTTCGATTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGGAAATTT--ATTTCAA
* * *
25883 GGAAAATTGATACTTTCAACTTTTCTCAAAACCCT-TTTTTTGACAAATTTAATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCAAAA--ATATTTTTTG-GAAATTT-ATTTC-AA
*
25942 GGAAAA-TGATACTTTC-ACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTGGAAATTTA-TTTCAA
* *
25997 -GAAAATTGATACTTTCAACTTTTCCCTTAAAATATTTATTTATGAAATTTATT
1 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTT-TTT-GGAAATTTATT
26050 ATTAAGGTGA
Statistics
Matches: 145, Mismatches: 10, Indels: 24
0.81 0.06 0.13
Matches are distributed among these distances:
54 5 0.03
55 16 0.11
56 25 0.17
57 48 0.33
58 36 0.25
59 15 0.10
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (55 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGGAAATTTATTTCAA
Found at i:26127 original size:30 final size:33
Alignment explanation
Indices: 26075--26139 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 33
26065 TTTCCTAAAA
*
26075 TATTTTTTTTTGAATTTAATTGATATTCAATTTT
1 TATTTTTTTTT-AATTTAATTGATATTCAACTTT
*
26109 TATTTTTTTTT-A-TT-ATTGATCTTCAACTTT
1 TATTTTTTTTTAATTTAATTGATATTCAACTTT
26139 T
1 T
26140 CCCTAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 15 0.52
31 2 0.07
32 1 0.03
34 11 0.38
ACGTcount: A:0.23, C:0.06, G:0.05, T:0.66
Consensus pattern (33 bp):
TATTTTTTTTTAATTTAATTGATATTCAACTTT
Found at i:26644 original size:19 final size:20
Alignment explanation
Indices: 26599--26636 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
26589 GAACACCGGT
*
26599 GCCGGATTCTGGAAATTTTC
1 GCCGGAATCTGGAAATTTTC
26619 GCCGGAATCTGGAAATTT
1 GCCGGAATCTGGAAATTT
26637 CGTCGGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GCCGGAATCTGGAAATTTTC
Found at i:26737 original size:31 final size:31
Alignment explanation
Indices: 26697--26767 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
26687 ACTGGGCTGG
*
26697 TCGCCGGAAACTTC-AATGTTCGCCGGAATTGT
1 TCGCCGGAAAATTCAAAT-TTCGCCGGAATT-T
*
26729 T-GCCGGAAAATTCAAATTTCGTCGGAATTT
1 TCGCCGGAAAATTCAAATTTCGCCGGAATTT
26759 TCGCCGGAA
1 TCGCCGGAA
26768 TCTGGAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 2 0.06
31 29 0.83
32 4 0.11
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (31 bp):
TCGCCGGAAAATTCAAATTTCGCCGGAATTT
Found at i:27261 original size:16 final size:14
Alignment explanation
Indices: 27209--27264 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 14
27199 AATCTAATCT
27209 AATAAAAATAAT-A
1 AATAAAAATAATAA
*
27222 AATAAATATATATAA
1 AATAAAAATA-ATAA
27237 TAATAAAAATACATAA
1 -AATAAAAATA-ATAA
27253 AATACAAAATAA
1 AATA-AAAATAA
27265 AATACAGGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
13 9 0.25
14 2 0.06
15 6 0.17
16 19 0.53
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (14 bp):
AATAAAAATAATAA
Found at i:28219 original size:21 final size:21
Alignment explanation
Indices: 28185--28235 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
28175 TATATATTTA
*
28185 AATA-TTTGTATTTAAAAAAT
1 AATATTTTATATTTAAAAAAT
*
28205 AATATTTTATATTTAACAAAT
1 AATATTTTATATTTAAAAAAT
28226 AATATTTTAT
1 AATATTTTAT
28236 TAATTTCAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AATATTTTATATTTAAAAAAT
Found at i:28306 original size:16 final size:16
Alignment explanation
Indices: 28285--28328 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
28275 AAACCCTTAT
28285 TGACCCAACCTGTTGC
1 TGACCCAACCTGTTGC
28301 TGACCCAACCTGTTGC
1 TGACCCAACCTGTTGC
* *
28317 TAACCCTACCTG
1 TGACCCAACCTG
28329 CATTGCTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.20, C:0.39, G:0.16, T:0.25
Consensus pattern (16 bp):
TGACCCAACCTGTTGC
Found at i:29901 original size:575 final size:571
Alignment explanation
Indices: 28553--30122 Score: 2309
Period size: 575 Copynumber: 2.7 Consensus size: 571
28543 ATAAAAAATA
* **
28553 ATATTTATTTTGACTAAATTAGGTATATTTATTTTCTTAT-AATATTAAATATTATTGTCTTTTA
1 ATATTTATTTTGACTAAATTAGGTATATTTATTTTCTTATAAATATAAAATATTATTACCTTTTA
*
28617 TAATTACATTACAATTCAATTATCTTAAATCACTTT-TAATAAATTCAAATT-TTAATTTTAAAC
66 TAATTACATTACAATTCAATTATCTTAAATCACTTTCAAATAAATTC-AATTCTTAATTTTAAAC
* *
28680 ACTAAGCATGAACACTATAAATAAGAAATATACTTTAAAAAAACA-TGACTATTTGATATCCATA
130 ACTAAACATGAACACTATAAATAAGAAATATACTTT--AAAAGCATTGACTATTTGATATCCATA
* * *
28744 GTTTTAGTATTTAAATTAAAAAATAATTTAATGTAATGAATATATTAATCATATAATACTAAAGA
193 ATTTTAGTATTT-AATTAAAAAATAATTT-ATGTAATGAATATA-TAGTCATATAATGCT-AAGA
* * * *
28809 ATTCAAATCTAAAATAAAAGGCCTAATTGATTGCACAAATATATTTTTTATCTTCTTTCTAATTA
254 ATTCAAATCTAAAATAAAAAGCCTAATTAATT-CACAAACATATTTTTTATCTTCTTTAT-A-TA
* * *
28874 AAT-TTAATTACAATCACACATATTTA-TGAATATAATTTACTATTTCAAAATATATTCTCTAAT
316 AATATTAATTACAATCACACATATTTACT-AACATAATTTACTATTTCAAAATGTATTATCTAAT
* *
28937 AACCCATTATAATTACTTTACATAAATTACTCTCAATTAATCTTATATAAATATATAAAAGCCAA
380 AACCCATTATAATTACTATACATAAATTACTTTCAATTAATCTTATATAAATATATAAAAGCCAA
* * * *
29002 AACTTAAAAAAAAAAATCTAATGTGAAATTATCTATTTTTTTTACACTTAGACGGTCTTGAACAA
445 AACTTAAAAAAAAAAATCCAATGTGAAATGATCTATTCTTTTGACACTTAGACGGTCTTGAACAA
29067 TCCCTATATGTCCTACATTATTATTTTGATTTGTTTTCATATAAATTTTATTAATTTAAAAG
510 TCCCTATATGTCCTACATTATTATTTTGATTTGTTTTCATATAAATTTTATTAATTTAAAAG
*
29129 ATATTTATTTTGACTAAATTAGATATATTTATTTTCTTATAAATATAAAATATTATTACCTTTTA
1 ATATTTATTTTGACTAAATTAGGTATATTTATTTTCTTATAAATATAAAATATTATTACCTTTTA
* * * *
29194 TAATTACGTTGCAAATTTAATTATCTTAAATCACTTTCAAATAAATTCAATTCTTAATTTTAAGC
66 TAATTACATTAC-AATTCAATTATCTTAAATCACTTTCAAATAAATTCAATTCTTAATTTTAAAC
* * *
29259 ATTAAACATGAACACTATAAATAAGAAATATACTTTAAAAGCATTGACTATTTGATTTCCGTAAT
130 ACTAAACATGAACACTATAAATAAGAAATATACTTTAAAAGCATTGACTATTTGATATCCATAAT
29324 TTTAGTATTTAATTAAAAAATAATTTATGTAATGAATATAT-GTCATATAATGCTAAGAATTCAA
195 TTTAGTATTTAATTAAAAAATAATTTATGTAATGAATATATAGTCATATAATGCTAAGAATTCAA
* * *
29388 ATCTAAAATAAAATGCCTAATTAATT-ACAAACATATATATT-TCTT-TTTATATAAATATTAAT
260 ATCTAAAATAAAAAGCCTAATTAATTCACAAACATATTTTTTATCTTCTTTATATAAATATTAAT
*
29450 TACAATCACACATATTTACTAACATAATTTACTATTTCAAAATGTATTTTCTAATAACCCATTAT
325 TACAATCACACATATTTACTAACATAATTTACTATTTCAAAATGTATTATCTAATAACCCATTAT
* *
29515 AATTACTCTACATAAATTACTTTCAATTAATCTTATATAAATATATAAAAGCCAAAGCTTTTAAC
390 AATTACTATACATAAATTACTTTCAATTAATCTTATATAAATATATAAAAGCCAAAAC--TT---
* *
29580 AAAAAAGGGAAAAATCCAATGT-AAATGATCTATTCTTTTGACA-TGTGGATGGTCTTGAACAAT
450 AAAAAA---AAAAATCCAATGTGAAATGATCTATTCTTTTGACACT-TAGACGGTCTTGAACAAT
**
29643 CGTTATATGTCCTACATTAATTATTTTGATTTGTTTTCATATAAATTTTATTAATTTAAAAG
511 CCCTATATGTCCTACATT-ATTATTTTGATTTGTTTTCATATAAATTTTATTAATTTAAAAG
* * * *
29705 ATATTTATCTTGACAAAATTAGGTATATTTATTTTCTTATAAATATCAAATATTATTACCTTCTA
1 ATATTTATTTTGACTAAATTAGGTATATTTATTTTCTTATAAATATAAAATATTATTACCTTTTA
29770 TAATTACATTACAATTCAATTATCTTAAATCACTTTCAAATAAATTCAATTCTTAATTTTAAACA
66 TAATTACATTACAATTCAATTATCTTAAATCACTTTCAAATAAATTCAATTCTTAATTTTAAACA
* ** * * *
29835 CTAAACATGAATACTATATCTAGGAAATATACTTTAAAAGCATTGACTATTTAATACCCATAATT
131 CTAAACATGAACACTATAAATAAGAAATATACTTTAAAAGCATTGACTATTTGATATCCATAATT
*
29900 TTAGTATTTAATTAAAAAATAATTTATGTAATGAATATATAAGTCATATAACGCTAAGAATTCAA
196 TTAGTATTTAATTAAAAAATAATTTATGTAATGAATATAT-AGTCATATAATGCTAAGAATTCAA
* *
29965 AACTAAAATAAAAAGCCTAATTAATTGCACAAACATATTTTTTTATCTTTCTTTATGTATAAGTA
260 ATCTAAAATAAAAAGCCTAATTAATT-CACAAACATA-TTTTTTATC-TTCTTTA--TATAAATA
*
30030 TTAATTACAATAACACATATTTACTAACATAATTTACTATTTCAAAATGTATTATCTAATAACCC
320 TTAATTACAATCACACATATTTACTAACATAATTTACTATTTCAAAATGTATTATCTAATAACCC
*
30095 ATTATAATTACTATGCATAAATTACTTT
385 ATTATAATTACTATACATAAATTACTTT
30123 TTATTCATTT
Statistics
Matches: 902, Mismatches: 65, Indels: 45
0.89 0.06 0.04
Matches are distributed among these distances:
567 5 0.01
568 121 0.13
569 5 0.01
570 6 0.01
571 12 0.01
573 40 0.04
574 12 0.01
575 198 0.22
576 178 0.20
577 99 0.11
578 55 0.06
579 63 0.07
580 4 0.00
581 2 0.00
582 2 0.00
583 4 0.00
585 96 0.11
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.41
Consensus pattern (571 bp):
ATATTTATTTTGACTAAATTAGGTATATTTATTTTCTTATAAATATAAAATATTATTACCTTTTA
TAATTACATTACAATTCAATTATCTTAAATCACTTTCAAATAAATTCAATTCTTAATTTTAAACA
CTAAACATGAACACTATAAATAAGAAATATACTTTAAAAGCATTGACTATTTGATATCCATAATT
TTAGTATTTAATTAAAAAATAATTTATGTAATGAATATATAGTCATATAATGCTAAGAATTCAAA
TCTAAAATAAAAAGCCTAATTAATTCACAAACATATTTTTTATCTTCTTTATATAAATATTAATT
ACAATCACACATATTTACTAACATAATTTACTATTTCAAAATGTATTATCTAATAACCCATTATA
ATTACTATACATAAATTACTTTCAATTAATCTTATATAAATATATAAAAGCCAAAACTTAAAAAA
AAAAATCCAATGTGAAATGATCTATTCTTTTGACACTTAGACGGTCTTGAACAATCCCTATATGT
CCTACATTATTATTTTGATTTGTTTTCATATAAATTTTATTAATTTAAAAG
Found at i:30761 original size:15 final size:15
Alignment explanation
Indices: 30741--30770 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30731 AGAGAATTAA
30741 AATCATGATCACATT
1 AATCATGATCACATT
*
30756 AATCATGGTCACATT
1 AATCATGATCACATT
30771 TAATAATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.10, T:0.33
Consensus pattern (15 bp):
AATCATGATCACATT
Found at i:35113 original size:20 final size:20
Alignment explanation
Indices: 35069--35113 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
35059 CTACCTGTAC
* *
35069 CACACAGTAAAATGTCTGCA
1 CACATAGTAAAATGTCTACA
*
35089 CACATAGTAAAATGTTTACA
1 CACATAGTAAAATGTCTACA
*
35109 TACAT
1 CACAT
35114 GGTATGATGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (20 bp):
CACATAGTAAAATGTCTACA
Found at i:36781 original size:2 final size:2
Alignment explanation
Indices: 36774--36809 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
36764 CTTTGGCTTT
* *
36774 TA TA TA TA TA TA TA TA TA TC TA TA TA TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36810 AGATACACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:37814 original size:247 final size:244
Alignment explanation
Indices: 37349--37841 Score: 729
Period size: 247 Copynumber: 2.0 Consensus size: 244
37339 TAACAGACAA
* * *
37349 AACCAAGTCACTTACATCCAACCTTATTCCATTCTCAGGCTTAACACAGAAATGGCCACTTTGAA
1 AACCAAGTCACTTACATCCAACCTTATTCCATTCTCAAGCTCAACACAGAAATGGCCAATTTGAA
* *
37414 CAATCCCAGAAATACAAAGACAAAATATTACGAACATAACCAAATATTCAACAACACTTCAAATA
66 CAATCCCAGAAATACAAAGACAAAATATTACAAACACAACCAAATATTCAACAACACTTCAAATA
**
37479 AAATAAAAAAATTTGATCAAACATTTAAAAACTAAAAAACCAATCAGATTTAGAATTCAAACCAA
131 AAATAAAAAAATTCAATCAAACATTTAAAAACTAAAAAACCAATCAGATTTAGAATTCAAACCAA
37544 CTTCGAATACAATTACGAAAATAACTTGAACACTCATTGTAAGAAAATG
196 CTTCGAATACAATTACGAAAATAACTTGAACACTCATTGTAAGAAAATG
* * * * * *
37593 AACCAAGTCACTTATATCTAACCTTGTTTCATTTTCAAGCTCAACATAGAAATGGCCAATTTGAA
1 AACCAAGTCACTTACATCCAACCTTATTCCATTCTCAAGCTCAACACAGAAATGGCCAATTTGAA
* * * *
37658 CAATCCTAGCAATACAAAATAGAAAATATTACAAACACAACCAAATATTCAACAACAACCTT-AA
66 CAATCCCAGAAATAC-AAAGACAAAATATTACAAACACAACCAAATATTCAACAAC-A-CTTCAA
*
37722 ATAAAAT-AAAAAATCTCAATCAAACATTTAAAAACTAAAATAACCAATCAGATTTAGTATTCAA
128 ATAAAATAAAAAAAT-TCAATCAAACATTTAAAAACTAAAA-AACCAATCAGATTTAGAATTCAA
*** *
37786 ACCAACTTCGAATACAATTGTTAAAATAACTTGAACACTCCTTGTAAGAAAATG
191 ACCAACTTCGAATACAATTACGAAAATAACTTGAACACTCATTGTAAGAAAATG
37840 AA
1 AA
37842 AAATCAAGTA
Statistics
Matches: 222, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
244 69 0.31
245 43 0.19
246 33 0.15
247 77 0.35
ACGTcount: A:0.48, C:0.20, G:0.07, T:0.25
Consensus pattern (244 bp):
AACCAAGTCACTTACATCCAACCTTATTCCATTCTCAAGCTCAACACAGAAATGGCCAATTTGAA
CAATCCCAGAAATACAAAGACAAAATATTACAAACACAACCAAATATTCAACAACACTTCAAATA
AAATAAAAAAATTCAATCAAACATTTAAAAACTAAAAAACCAATCAGATTTAGAATTCAAACCAA
CTTCGAATACAATTACGAAAATAACTTGAACACTCATTGTAAGAAAATG
Found at i:38692 original size:20 final size:21
Alignment explanation
Indices: 38647--38694 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
38637 TTTGATTGGT
38647 AGAGAAGAAAAAGAGAAGCAA
1 AGAGAAGAAAAAGAGAAGCAA
*
38668 A-AGAAGGAAAA-AGAAG-ATA
1 AGAGAAGAAAAAGAGAAGCA-A
38687 AGAGAAGA
1 AGAGAAGA
38695 GGAAGGAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 1 0.04
19 7 0.30
20 14 0.61
21 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.29, T:0.02
Consensus pattern (21 bp):
AGAGAAGAAAAAGAGAAGCAA
Done.