Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168303.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_529, 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: 23879
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Found at i:523 original size:18 final size:17
Alignment explanation
Indices: 451--524 Score: 50
Period size: 18 Copynumber: 4.5 Consensus size: 17
441 TTAATACATG
*
451 TATATATTTATTTAT-T
1 TATATATTTATGTATAT
* *
467 TATTTATTT-T-T-TGT
1 TATATATTTATGTATAT
*
481 TA-ATATTTATGTGTAT
1 TATATATTTATGTATAT
*
497 TTTATTATTTATGTATAT
1 TATA-TATTTATGTATAT
515 ATATATATTT
1 -TATATATTT
525 TTTTTATCTT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
13 6 0.13
14 5 0.11
15 2 0.04
16 11 0.24
17 1 0.02
18 17 0.38
19 3 0.07
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.66
Consensus pattern (17 bp):
TATATATTTATGTATAT
Found at i:1518 original size:12 final size:11
Alignment explanation
Indices: 1476--1544 Score: 54
Period size: 12 Copynumber: 6.2 Consensus size: 11
1466 CCGCTCCAGG
1476 TTTTTT-TTT-
1 TTTTTTATTTA
*
1485 TTTTTTCTTTGA
1 TTTTTTATTT-A
*
1497 ATTTTT-TTTA
1 TTTTTTATTTA
*
1507 TTTCTTTGTTTA
1 TTT-TTTATTTA
1519 TTTGTTTATTTTA
1 TTT-TTTA-TTTA
1532 TTTTTTATTTA
1 TTTTTTATTTA
1543 TT
1 TT
1545 AGATTAGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
9 6 0.12
10 6 0.12
11 12 0.24
12 19 0.38
13 7 0.14
ACGTcount: A:0.12, C:0.03, G:0.04, T:0.81
Consensus pattern (11 bp):
TTTTTTATTTA
Found at i:1821 original size:60 final size:60
Alignment explanation
Indices: 1604--1891 Score: 412
Period size: 60 Copynumber: 4.8 Consensus size: 60
1594 ATAAAAATAA
* *
1604 AAAATTCCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AGAAAT
1 AAAATTTC-AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAGAAAT
* * *
1664 -AAATTTC-CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTC-TCAGAAAT
1 AAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAGAAAT
*
1721 -AAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATT
1 AAAATTTC-AAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAGAAA-T
1781 AAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGA-AAAT
1 AAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAGAAAT
*
1840 CGAAATTTTC-AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 --AAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1892 CTACAAAAAA
Statistics
Matches: 210, Mismatches: 10, Indels: 16
0.89 0.04 0.07
Matches are distributed among these distances:
56 1 0.00
57 52 0.25
59 49 0.23
60 94 0.45
61 14 0.07
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (60 bp):
AAAATTTCAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAGAAAT
Found at i:9483 original size:58 final size:59
Alignment explanation
Indices: 9356--9694 Score: 323
Period size: 58 Copynumber: 5.7 Consensus size: 59
9346 TGTACAAGGG
* * * * *
9356 AAATTGATACTTTCAAATTTTCCTCAAAAAAAACCCTTTTTTTTAAAATTTTATTTTTAAGGA
1 AAATTGATACTTTCAACTTTT-CTCCAAAAAAA---TTTTTTTGAAAATTTTAATTTTAAGAA
* * **
9419 AAATTGATACTTTCAACTTTTCTCCAAAAATA-TTTTTTAAAAATTTTAATTTCGAGAA
1 AAATTGATACTTTCAACTTTTCTCCAAAAAAATTTTTTTGAAAATTTTAATTTTAAGAA
* * ** * *
9477 AAATTGATACTTTCAAATTTTCTTCAAAAAAACCTTTTTGAAGA-TTT-ATTCTTAAGGA
1 AAATTGATACTTTCAACTTTTCTCCAAAAAAATTTTTTTGAAAATTTTAATT-TTAAGAA
* * * **
9535 AAATTGATACTTTCAACTTTTC-CTAAAAATATTTTTTTTTGAAATTTTTAATTTCGAGAA
1 AAATTGATACTTTCAACTTTTCTCCAAAAA-A-ATTTTTTTGAAAATTTTAATTTTAAGAA
*
9595 AAATTGATACTTTCAACTTTTCCTCAAAAAAAAAATTTTTTTGAAAA-TTT-ATTCTTAAGAA
1 AAATTGATACTTTCAACTTTT-CTC--CAAAAAAATTTTTTTGAAAATTTTAATT-TTAAGAA
*
9656 AAATTGATACTTTCAACTTTTC-CTCAAAAATATTTTTTT
1 AAATTGATACTTTCAACTTTTCTC-CAAAAAAATTTTTTT
9695 ATTTTTTTTA
Statistics
Matches: 229, Mismatches: 36, Indels: 27
0.78 0.12 0.09
Matches are distributed among these distances:
57 8 0.03
58 92 0.40
59 17 0.07
60 32 0.14
61 33 0.14
62 21 0.09
63 21 0.09
64 5 0.02
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (59 bp):
AAATTGATACTTTCAACTTTTCTCCAAAAAAATTTTTTTGAAAATTTTAATTTTAAGAA
Found at i:9504 original size:121 final size:118
Alignment explanation
Indices: 9356--9693 Score: 493
Period size: 121 Copynumber: 2.8 Consensus size: 118
9346 TGTACAAGGG
* *
9356 AAATTGATACTTTCAAATTTTCCTCAAAAAAAACCCTTTTTTTTAAAATTTTATTTTTAAGGAAA
1 AAATTGATACTTTCAAATTTTCCTCAAAAAAAA-CCTTTTTTTGAAAA-TTTATTCTTAAGGAAA
9421 ATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTAAAAATTTTAATTTCGAGAA
64 ATTGATACTTTCAACTTTTC-CCAAAAATATTTTTTAAAAATTTTAATTTCGAGAA
* *
9477 AAATTGATACTTTCAAATTTTCTTC-AAAAAAACC--TTTTTGAAGATTTATTCTTAAGGAAAAT
1 AAATTGATACTTTCAAATTTTCCTCAAAAAAAACCTTTTTTTGAAAATTTATTCTTAAGGAAAAT
* * *
9539 TGATACTTTCAACTTTTCCTAAAAATATTTTTTTTTGAAATTTTTAATTTCGAGAA
66 TGATACTTTCAACTTTTCCCAAAAATA---TTTTTTAAAAATTTTAATTTCGAGAA
* ** *
9595 AAATTGATACTTTCAACTTTTCCTCAAAAAAAAAATTTTTTTGAAAATTTATTCTTAAGAAAAAT
1 AAATTGATACTTTCAAATTTTCCTCAAAAAAAACCTTTTTTTGAAAATTTATTCTTAAGGAAAAT
9660 TGATACTTTCAACTTTTCCTCAAAAATATTTTTT
66 TGATACTTTCAACTTTTCC-CAAAAATATTTTTT
9694 TATTTTTTTT
Statistics
Matches: 196, Mismatches: 14, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
115 8 0.04
116 35 0.18
117 8 0.04
118 47 0.24
119 15 0.08
120 7 0.04
121 69 0.35
122 7 0.04
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (118 bp):
AAATTGATACTTTCAAATTTTCCTCAAAAAAAACCTTTTTTTGAAAATTTATTCTTAAGGAAAAT
TGATACTTTCAACTTTTCCCAAAAATATTTTTTAAAAATTTTAATTTCGAGAA
Found at i:10695 original size:22 final size:21
Alignment explanation
Indices: 10670--10807 Score: 61
Period size: 22 Copynumber: 6.2 Consensus size: 21
10660 AAATAAATAA
*
10670 AAAAATATTAATAGAT-AATT
1 AAAAATATTAATAGATAAATC
* *
10690 AGAAAAAAATAATAAGATAAATC
1 A-AAAATATTAAT-AGATAAATC
10713 AAAAATATTACA-AGATAAAT-
1 AAAAATATTA-ATAGATAAATC
*
10733 AAATAATAATAATAACAGATAAATC
1 AAA-AAT-AT--TAATAGATAAATC
* * *
10758 ATAATATATAAAT-GAATAAATA
1 A-AAAATATTAATAG-ATAAATC
10780 ATAATAATATATAACTAGATAAAT-
1 A-AA-AATAT-TAA-TAGATAAATC
10804 AAAA
1 AAAA
10808 TACATATATA
Statistics
Matches: 91, Mismatches: 11, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
20 4 0.04
21 21 0.23
22 26 0.29
23 12 0.13
24 15 0.16
25 10 0.11
26 3 0.03
ACGTcount: A:0.64, C:0.04, G:0.05, T:0.27
Consensus pattern (21 bp):
AAAAATATTAATAGATAAATC
Found at i:10716 original size:21 final size:20
Alignment explanation
Indices: 10656--10747 Score: 67
Period size: 21 Copynumber: 4.2 Consensus size: 20
10646 AAATCAGATA
*
10656 AATAAAATAAATAAAAAAAT
1 AATAAGATAAATAAAAAAAT
* *
10676 ATTAATAGATAATTAGAAAAAAAT
1 AAT-A-AGATAA--ATAAAAAAAT
*
10700 AATAAGATAAATCAAAAATAT
1 AATAAGATAAAT-AAAAAAAT
* *
10721 TACAAGATAAATAAATAATAAT
1 AATAAGATAAATAAA-AA-AAT
10743 AATAA
1 AATAA
10748 CAGATAAATC
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
20 6 0.11
21 20 0.37
22 16 0.30
23 1 0.02
24 11 0.20
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.25
Consensus pattern (20 bp):
AATAAGATAAATAAAAAAAT
Found at i:10730 original size:43 final size:43
Alignment explanation
Indices: 10656--10788 Score: 114
Period size: 43 Copynumber: 3.1 Consensus size: 43
10646 AAATCAGATA
* * *
10656 AATAAAATAAATAAAAAAATATTAATAGATAATTAGAA-AAAAAT
1 AATAAGATAAAT-CAAAAATATTAATAGATAAATA-AATAAAAAT
*
10700 AATAAGATAAATCAAAAATATTACA-AGATAAATAAATAATAAT
1 AATAAGATAAATCAAAAATATTA-ATAGATAAATAAATAAAAAT
* * * *
10743 AATAACAGATAAATC-ATAATA-T-ATAAATGAATAAATAATAAT
1 AAT-A-AGATAAATCAAAAATATTAATAGATAAATAAATAAAAAT
10785 AATA
1 AATA
10789 TATAACTAGA
Statistics
Matches: 77, Mismatches: 7, Indels: 13
0.79 0.07 0.13
Matches are distributed among these distances:
41 2 0.03
42 21 0.27
43 27 0.35
44 18 0.23
45 9 0.12
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (43 bp):
AATAAGATAAATCAAAAATATTAATAGATAAATAAATAAAAAT
Found at i:10789 original size:25 final size:24
Alignment explanation
Indices: 10758--10821 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 24
10748 CAGATAAATC
10758 ATAATATATAAAT-GAATAAATAATA
1 ATAATATATAAATAG-ATAAATAA-A
*
10783 ATAATATATAACTAGATAAATAAA
1 ATAATATATAAATAGATAAATAAA
10807 ATACATATATAAATA
1 ATA-ATATATAAATA
10822 TTAACAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 4 0.11
25 30 0.86
26 1 0.03
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (24 bp):
ATAATATATAAATAGATAAATAAA
Found at i:10809 original size:21 final size:21
Alignment explanation
Indices: 10666--10809 Score: 59
Period size: 21 Copynumber: 6.6 Consensus size: 21
10656 AATAAAATAA
10666 ATAAA-AAAATAT-TAA-TAG
1 ATAAATAAAATATATAACTAG
* * *
10684 ATAATTAGAAAAAAATAA-TAAG
1 ATAAATA-AAATATATAACT-AG
* *
10706 ATAAATCAAAA-ATATTACAAG
1 ATAAAT-AAAATATATAACTAG
10727 ATAAATAAATAATAATAATAAC-AG
1 ATAAAT-AA-AAT-AT-ATAACTAG
* *
10751 ATAAATCATAATATATAAAT-G
1 ATAAAT-AAAATATATAACTAG
10772 AATAAATAATAATAATATATAACTAG
1 -AT--A-AATAA-AATATATAACTAG
10798 ATAAATAAAATA
1 ATAAATAAAATA
10810 CATATATAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 31
0.68 0.10 0.22
Matches are distributed among these distances:
18 4 0.04
19 1 0.01
20 4 0.04
21 27 0.28
22 21 0.22
23 5 0.05
24 13 0.14
25 19 0.20
26 1 0.01
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (21 bp):
ATAAATAAAATATATAACTAG
Found at i:10949 original size:16 final size:15
Alignment explanation
Indices: 10924--10971 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 15
10914 GATACAAAGG
10924 AAAAAATATAAAATA
1 AAAAAATATAAAATA
10939 AAAATAATATAAAAT-
1 AAAA-AATATAAAATA
** *
10954 GTAAAATACAAAATA
1 AAAAAATATAAAATA
10969 AAA
1 AAA
10972 GCAAAATTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
14 9 0.35
15 7 0.27
16 10 0.38
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (15 bp):
AAAAAATATAAAATA
Found at i:10950 original size:11 final size:12
Alignment explanation
Indices: 10926--10971 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
10916 TACAAAGGAA
10926 AAAATATAAAAT
1 AAAATATAAAAT
*
10938 AAAA-ATAATAT
1 AAAATATAAAAT
*
10949 AAAATGTAAAAT
1 AAAATATAAAAT
10961 ACAAA-ATAAAA
1 A-AAATATAAAA
10972 GCAAAATTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 10 0.36
12 15 0.54
13 3 0.11
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (12 bp):
AAAATATAAAAT
Found at i:12359 original size:29 final size:29
Alignment explanation
Indices: 12318--12376 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
12308 ACAAGAAATT
*
12318 ATTTCATATTACTTTAGTGAAGTTTTTAA
1 ATTTCATATTACTTCAGTGAAGTTTTTAA
12347 ATTTCAT-TCTACTTCAGTGAAGTTTTTAA
1 ATTTCATAT-TACTTCAGTGAAGTTTTTAA
12376 A
1 A
12377 ATTTACAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (29 bp):
ATTTCATATTACTTCAGTGAAGTTTTTAA
Found at i:12571 original size:42 final size:42
Alignment explanation
Indices: 12502--12587 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 42
12492 TTACTATTTG
*
12502 TGTATCGAAAGAAACTCCAAAAATATATTTCTCATCAAACATA
1 TGTATCGAAAGAAACT-CAAAAATATATTTCTCATCAAAAATA
* *
12545 TGTATTGAAAGCAAACT-AAAAATATATTTCTTATCAAAAATA
1 TGTATCGAAAG-AAACTCAAAAATATATTTCTCATCAAAAATA
12587 T
1 T
12588 AGGTTTTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
42 24 0.62
43 10 0.26
44 5 0.13
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (42 bp):
TGTATCGAAAGAAACTCAAAAATATATTTCTCATCAAAAATA
Found at i:13010 original size:21 final size:22
Alignment explanation
Indices: 12970--13012 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12960 CATATTTTTT
*
12970 ATTTTTATCAAATTTATAAATA
1 ATTTTTATAAAATTTATAAATA
*
12992 ATTTTTTTAAAATTT-TAAATA
1 ATTTTTATAAAATTTATAAATA
13013 TTATCATACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTTTATAAAATTTATAAATA
Found at i:13393 original size:17 final size:18
Alignment explanation
Indices: 13358--13395 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
13348 TTTTATGTCA
**
13358 AAAAATTTAAAAATCATG
1 AAAAATTTAAAAAAAATG
13376 AAAAA-TTAAAAAAAATG
1 AAAAATTTAAAAAAAATG
13393 AAA
1 AAA
13396 CATAGGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAAATTTAAAAAAAATG
Found at i:18959 original size:22 final size:22
Alignment explanation
Indices: 18934--19047 Score: 111
Period size: 22 Copynumber: 5.2 Consensus size: 22
18924 AATTTAGACA
* * *
18934 AAATCAATAATAACTTTATACT
1 AAATTAATAATAACTTAATAAT
* ** *
18956 AAATTAATGATAACTGCATAGT
1 AAATTAATAATAACTTAATAAT
* * *
18978 AAATTATTGATAACTTAATAGT
1 AAATTAATAATAACTTAATAAT
*
19000 AAAATAATAATAACTTAATAAT
1 AAATTAATAATAACTTAATAAT
* *
19022 AAATAAATAATAATTTAATAAT
1 AAATTAATAATAACTTAATAAT
19044 AAAT
1 AAAT
19048 AATTGATAAA
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 77 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.35
Consensus pattern (22 bp):
AAATTAATAATAACTTAATAAT
Found at i:19018 original size:11 final size:11
Alignment explanation
Indices: 18934--19047 Score: 75
Period size: 11 Copynumber: 10.4 Consensus size: 11
18924 AATTTAGACA
*
18934 AAATCAATAAT
1 AAATTAATAAT
* * *
18945 AACTTTATACT
1 AAATTAATAAT
*
18956 AAATTAATGAT
1 AAATTAATAAT
* ** *
18967 AACTGCATAGT
1 AAATTAATAAT
* *
18978 AAATTATTGAT
1 AAATTAATAAT
* *
18989 AACTTAATAGT
1 AAATTAATAAT
*
19000 AAAATAATAAT
1 AAATTAATAAT
*
19011 AACTTAATAAT
1 AAATTAATAAT
*
19022 AAATAAATAAT
1 AAATTAATAAT
*
19033 AATTTAATAAT
1 AAATTAATAAT
19044 AAAT
1 AAAT
19048 AATTGATAAA
Statistics
Matches: 70, Mismatches: 33, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
11 70 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.35
Consensus pattern (11 bp):
AAATTAATAAT
Found at i:19090 original size:11 final size:10
Alignment explanation
Indices: 19001--19093 Score: 60
Period size: 11 Copynumber: 8.2 Consensus size: 10
18991 CTTAATAGTA
19001 AAATAATAAT
1 AAATAATAAT
*
19011 AACTTAATAAT
1 AA-ATAATAAT
19022 AAATAAATAAT
1 AAAT-AATAAT
*
19033 AATTTAATAAT
1 AA-ATAATAAT
*
19044 AAATAATTGAT
1 AAATAA-TAAT
19055 AAAATAGCATATGAT
1 -AAATA--ATA--AT
19070 AACATAATAAT
1 AA-ATAATAAT
19081 AAATACATAAT
1 AAATA-ATAAT
19092 AA
1 AA
19094 CGTAGTAGGA
Statistics
Matches: 66, Mismatches: 6, Indels: 21
0.71 0.06 0.23
Matches are distributed among these distances:
10 9 0.14
11 39 0.59
12 6 0.09
13 4 0.06
14 3 0.05
15 5 0.08
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.31
Consensus pattern (10 bp):
AAATAATAAT
Found at i:19221 original size:22 final size:22
Alignment explanation
Indices: 19163--19258 Score: 79
Period size: 22 Copynumber: 4.4 Consensus size: 22
19153 TAACACATAT
* *
19163 TAGTAAATTAAAGATAACTTAA
1 TAGTAAATCAATGATAACTTAA
*
19185 TA-AAAAGT-AAGTGATAACTTAA
1 TAGTAAA-TCAA-TGATAACTTAA
* * * * *
19207 TAGTTAATTATTGATAATTTAG
1 TAGTAAATCAATGATAACTTAA
*
19229 TAATAAATCAATGATAACTTAA
1 TAGTAAATCAATGATAACTTAA
19251 TAGTAAAT
1 TAGTAAAT
19259 AAAACTCAGT
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
21 5 0.09
22 48 0.86
23 3 0.05
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.35
Consensus pattern (22 bp):
TAGTAAATCAATGATAACTTAA
Found at i:19704 original size:21 final size:20
Alignment explanation
Indices: 19649--19704 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 20
19639 ATTAAAATTA
19649 AATCAAT-ATAACTTAATAGT
1 AATCAATAATAA-TTAATAGT
19669 AATC-ATAAGTAAATTAATAGTT
1 AATCAATAA-T-AATTAATAG-T
19691 AATCAATAATAATT
1 AATCAATAATAATT
19705 TAGTATAGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
19 2 0.06
20 5 0.16
21 12 0.39
22 8 0.26
23 4 0.13
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (20 bp):
AATCAATAATAATTAATAGT
Found at i:19829 original size:22 final size:22
Alignment explanation
Indices: 19804--19861 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
19794 ACTTAATAAT
*
19804 AAATCAATTATAACATAATTGC
1 AAATCAATAATAACATAATTGC
* *
19826 AAATGC-ATAATAACATAGTTGT
1 AAAT-CAATAATAACATAATTGC
*
19848 AAATTAATAATAAC
1 AAATCAATAATAAC
19862 TTCATAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (22 bp):
AAATCAATAATAACATAATTGC
Found at i:19954 original size:22 final size:22
Alignment explanation
Indices: 19907--19959 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
19897 GATAATTTAG
* *
19907 TAGTAAATTAATGAAAACTTAG
1 TAGTAAATTAATGAAAACATAA
* *
19929 TAGTAAATTAATGATAGCATAA
1 TAGTAAATTAATGAAAACATAA
19951 TAGTAAATT
1 TAGTAAATT
19960 TATTTTAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.34
Consensus pattern (22 bp):
TAGTAAATTAATGAAAACATAA
Found at i:20132 original size:22 final size:22
Alignment explanation
Indices: 20106--20221 Score: 88
Period size: 22 Copynumber: 5.3 Consensus size: 22
20096 ATAGTATAGA
*
20106 GTAAATCATTAATAATTTAGTT
1 GTAAATCATTGATAATTTAGTT
* * *
20128 GTAAATTATCGATAATTTAGTA
1 GTAAATCATTGATAATTTAGTT
* * ** * *
20150 GTAAATCACTAATAACGTAATA
1 GTAAATCATTGATAATTTAGTT
* *
20172 GTAAAACATTGATAATTTATTT
1 GTAAATCATTGATAATTTAGTT
* * *
20194 ATAAATTAATGATAATTTAGTT
1 GTAAATCATTGATAATTTAGTT
*
20216 ATAAAT
1 GTAAAT
20222 TAGTTAATTA
Statistics
Matches: 71, Mismatches: 23, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 71 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (22 bp):
GTAAATCATTGATAATTTAGTT
Found at i:20303 original size:11 final size:10
Alignment explanation
Indices: 20263--20342 Score: 61
Period size: 11 Copynumber: 7.4 Consensus size: 10
20253 ATCAATAACT
*
20263 TTATAGTAAA
1 TTATAATAAA
20273 TTAGTAATAACA
1 TTA-TAATAA-A
*
20285 TTAAAATAAA
1 TTATAATAAA
*
20295 TTACTAATAAC
1 TTA-TAATAAA
*
20306 TTAATAGTAAA
1 TT-ATAATAAA
*
20317 TTATCAATAAC
1 TTAT-AATAAA
20328 TTAGTAATAAA
1 TTA-TAATAAA
20339 TTAT
1 TTAT
20343 TTATAACTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
10 10 0.18
11 39 0.71
12 6 0.11
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (10 bp):
TTATAATAAA
Found at i:20349 original size:66 final size:65
Alignment explanation
Indices: 20227--20353 Score: 175
Period size: 66 Copynumber: 1.9 Consensus size: 65
20217 TAAATTAGTT
* * *
20227 AATTATTAATAACTTTATAGTAAATCATCAATAACTTTATAGTAAATTAGTAATAACATTAAAAT
1 AATTACTAATAACTTAATAGTAAATCATCAATAACTTTATAATAAATTAGTAATAAC-TTAAAAT
20292 A
65 A
* * *
20293 AATTACTAATAACTTAATAGTAAATTATCAATAAC-TTAGTAATAAATTATTTATAACTTAA
1 AATTACTAATAACTTAATAGTAAATCATCAATAACTTTA-TAATAAATTAGTAATAACTTAA
20354 TAGTAAATCA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
65 7 0.13
66 47 0.87
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.39
Consensus pattern (65 bp):
AATTACTAATAACTTAATAGTAAATCATCAATAACTTTATAATAAATTAGTAATAACTTAAAATA
Found at i:20374 original size:22 final size:22
Alignment explanation
Indices: 20222--20374 Score: 150
Period size: 22 Copynumber: 7.0 Consensus size: 22
20212 AGTTATAAAT
* * *
20222 TAGTTAATTATTAATAACTTTA
1 TAGTAAATTATCAATAACTTAA
* *
20244 TAGTAAATCATCAATAACTTTA
1 TAGTAAATTATCAATAACTTAA
20266 TAGTAAATTAGT-AATAACATTAA
1 TAGTAAATTA-TCAATAAC-TTAA
*
20289 -AATAAATTA-CTAATAACTTAA
1 TAGTAAATTATC-AATAACTTAA
*
20310 TAGTAAATTATCAATAACTTAG
1 TAGTAAATTATCAATAACTTAA
* **
20332 TAATAAATTATTTATAACTTAA
1 TAGTAAATTATCAATAACTTAA
* *
20354 TAGTAAATCATCTATAACTTA
1 TAGTAAATTATCAATAACTTA
20375 GTGATAAATC
Statistics
Matches: 110, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
21 4 0.04
22 101 0.92
23 5 0.05
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (22 bp):
TAGTAAATTATCAATAACTTAA
Found at i:20382 original size:22 final size:21
Alignment explanation
Indices: 20301--20386 Score: 82
Period size: 22 Copynumber: 3.9 Consensus size: 21
20291 TAAATTACTA
* * *
20301 ATAACTTAATAGTAAATTATCA
1 ATAACTTAGTA-TAAATCATCT
* *
20323 ATAACTTAGTAATAAATTATTT
1 ATAACTTAGT-ATAAATCATCT
*
20345 ATAACTTAATAGTAAATCATCT
1 ATAACTTAGTA-TAAATCATCT
20367 ATAACTTAGTGATAAATCAT
1 ATAACTTAGT-ATAAATCAT
20387 GATAATTTAG
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
21 1 0.02
22 51 0.94
23 2 0.04
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (21 bp):
ATAACTTAGTATAAATCATCT
Found at i:20383 original size:66 final size:66
Alignment explanation
Indices: 20233--20374 Score: 173
Period size: 66 Copynumber: 2.2 Consensus size: 66
20223 AGTTAATTAT
* * *
20233 TAATAACTTTATAGTAAATCATCAATAACTTTATAGTAAATTAGTAATAACATTAAAATAAATTA
1 TAATAACTTAATAGTAAATCATCAATAACTTTATAATAAATTAGTAATAACATTAAAATAAATCA
20298 C
66 C
* * * *
20299 TAATAACTTAATAGTAAATTATCAATAAC-TTAGTAATAAATTATTTATAAC-TTAATAGTAAAT
1 TAATAACTTAATAGTAAATCATCAATAACTTTA-TAATAAATTAGTAATAACATTAA-AATAAAT
20362 CATC
64 CA-C
20366 T-ATAACTTA
1 TAATAACTTA
20375 GTGATAAATC
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
65 7 0.11
66 57 0.86
67 2 0.03
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (66 bp):
TAATAACTTAATAGTAAATCATCAATAACTTTATAATAAATTAGTAATAACATTAAAATAAATCA
C
Found at i:20690 original size:22 final size:22
Alignment explanation
Indices: 20665--20716 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
20655 TATATCATAA
* *
20665 ATAACTTAGTAGTAATTTAA-TG
1 ATAACTTAGTAATAA-ATAATTG
*
20687 ATAATTTAGTAATAAATAATTG
1 ATAACTTAGTAATAAATAATTG
20709 ATAACTTA
1 ATAACTTA
20717 ATAGCTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (22 bp):
ATAACTTAGTAATAAATAATTG
Found at i:21311 original size:19 final size:21
Alignment explanation
Indices: 21287--21327 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
21277 TTTTATAGTC
21287 GAAAAAAT-TAAAAAAA-GAA
1 GAAAAAATATAAAAAAATGAA
21306 G-AAAAATATAAAAAAATGAA
1 GAAAAAATATAAAAAAATGAA
21326 GA
1 GA
21328 TGATGACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.32
19 9 0.47
20 4 0.21
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (21 bp):
GAAAAAATATAAAAAAATGAA
Found at i:21319 original size:20 final size:19
Alignment explanation
Indices: 21287--21327 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
21277 TTTTATAGTC
*
21287 GAAAAAATTAAAAAAAGAA
1 GAAAAAATAAAAAAAAGAA
*
21306 GAAAAATATAAAAAAATGAA
1 GAAAAA-ATAAAAAAAAGAA
21326 GA
1 GA
21328 TGATGACTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (19 bp):
GAAAAAATAAAAAAAAGAA
Done.