Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168203.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_439, 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: 26814
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:664 original size:12 final size:12
Alignment explanation
Indices: 647--671 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
637 ATTGATTAGG
647 AGTTTCTGATCA
1 AGTTTCTGATCA
659 AGTTTCTGATCA
1 AGTTTCTGATCA
671 A
1 A
672 TCTCAATTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AGTTTCTGATCA
Found at i:867 original size:11 final size:11
Alignment explanation
Indices: 835--876 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
825 ATAATTACAT
835 AAATAATAACAA
1 AAATAATAA-AA
*
847 AAA-AAAAAAA
1 AAATAATAAAA
857 AAATAATAAAA
1 AAATAATAAAA
*
868 TAATAATAA
1 AAATAATAA
877 TAATAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 5 0.19
11 18 0.69
12 3 0.12
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (11 bp):
AAATAATAAAA
Found at i:975 original size:47 final size:46
Alignment explanation
Indices: 924--1053 Score: 122
Period size: 47 Copynumber: 2.8 Consensus size: 46
914 AATGCCTAAA
*
924 AAATAATAATAAAAGAAAGAAAAGAAATATATATAC-ATATATAAAAT
1 AAATAATAATAAAAGAAAGAAAA-AAATATATATACAAAATA-AAAAT
* ** * *
971 AAATAATAAATAAATA-AAATAAAAATGTAAAAATACAAAATAAAAAT
1 AAATAAT-AATAAA-AGAAAGAAAAAAATATATATACAAAATAAAAAT
* *
1018 AAATAAAAATAAAATG-AAGAGAAAAATATATATACA
1 AAATAATAATAAAA-GAAAGAAAAAAATATATATACA
1054 GACTTACCCA
Statistics
Matches: 65, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
45 1 0.02
46 20 0.31
47 26 0.40
48 17 0.26
49 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (46 bp):
AAATAATAATAAAAGAAAGAAAAAAATATATATACAAAATAAAAAT
Found at i:1031 original size:21 final size:21
Alignment explanation
Indices: 964--1032 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
954 ATATACATAT
964 ATAAAATAAATAATAAAT--AA
1 ATAAAATAAA-AATAAATAAAA
*
984 ATAAAATAAAAAT--GTAAAA
1 ATAAAATAAAAATAAATAAAA
1003 ATACAAAATAAAAATAAATAAAA
1 AT--AAAATAAAAATAAATAAAA
1026 ATAAAAT
1 ATAAAAT
1033 GAAGAGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
17 1 0.02
19 7 0.17
20 10 0.24
21 16 0.39
23 7 0.17
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (21 bp):
ATAAAATAAAAATAAATAAAA
Found at i:1360 original size:41 final size:42
Alignment explanation
Indices: 1225--1438 Score: 292
Period size: 42 Copynumber: 5.1 Consensus size: 42
1215 TTTGATCAAA
* * * * * *
1225 GCTCCTCTGAACAGAGGCTCAACAACTTTGAAAAAATAAACT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
*
1267 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
* *
1309 GCTTCTCTAAACAGAGGCACCACGACTTTG-GAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
*
1350 GCTCCTCTAAACAGAGACACCACGACTTTG-AAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
1391 GCTCCTCTAAACAGAGGCA--ACGAAACTTTGAAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACG--ACTTTGAAAAAGTAAATT
1433 GCTCCT
1 GCTCCT
1439 TGACAATCAT
Statistics
Matches: 157, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
39 3 0.02
41 71 0.45
42 83 0.53
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.22
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATT
Found at i:1363 original size:83 final size:82
Alignment explanation
Indices: 1225--1438 Score: 288
Period size: 83 Copynumber: 2.6 Consensus size: 82
1215 TTTGATCAAA
* * * * * *
1225 GCTCCTCTGAACAGAGGCTCAACAACTTTGAAAAAATAAACTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCAC-ACGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGACACCAC
1290 GACTTTGAAAAAATAAATT
65 GACTTTG-AAAAATAAATT
* *
1309 GCTTCTCTAAACAGAGGCACCACGACTTTG-GAAAGTAAATTGCTCCTCTAAACAGAGACACCAC
1 GCTCCTCTAAACAGAGGCA-CACGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGACACCAC
*
1373 GACTTTGAAAAGTAAATT
65 GACTTTGAAAAATAAATT
1391 GCTCCTCTAAACAGAGGCA-ACGAAACTTTGAAAAAGTAAATTGCTCCT
1 GCTCCTCTAAACAGAGGCACACG--ACTTTGAAAAAGTAAATTGCTCCT
1439 TGACAATCAT
Statistics
Matches: 115, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
80 3 0.03
82 34 0.30
83 53 0.46
84 24 0.21
85 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.22
Consensus pattern (82 bp):
GCTCCTCTAAACAGAGGCACACGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGACACCACG
ACTTTGAAAAATAAATT
Found at i:2750 original size:21 final size:21
Alignment explanation
Indices: 2707--2746 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
2697 TTCATTCTTT
*
2707 TTTTTTCTTTTTTTTTCATCA
1 TTTTTTCTTTTATTTTCATCA
2728 TTTTTT-TTTTATTTTCATC
1 TTTTTTCTTTTATTTTCATC
2747 CATTGTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTTCTTTTATTTTCATCA
Found at i:6768 original size:58 final size:58
Alignment explanation
Indices: 6651--6986 Score: 455
Period size: 59 Copynumber: 5.7 Consensus size: 58
6641 TTGTGTAGGA
* *
6651 AAAATTGATACTTTCAACTTTTTCTCCAAAAATA-TTTTTTGAAACTTTTATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTTC-CCAAAAATATTTTTTTGAAA-ATTTATTTTTAAGG
6710 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAATTTATTTTTAAGG
* *
6768 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATA-TTTTTTTGAAAATTTATTTTTAAGG
* * * * *
6827 AAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTGATTTTCAAGA
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAATTT-ATTTTTAAGG
* * * *
6886 AAAATTGATATTTTCAACTTTTTCTCAAAAACCCT-TTTTTTTAAAAATTT-TTTTTAAGA
1 AAAATTGATACTTTCAACTTTTTCCCAAAAA---TATTTTTTTGAAAATTTATTTTTAAGG
6945 AAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTTTGA
1 AAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTTGA
6987 TTTTTATTTA
Statistics
Matches: 250, Mismatches: 19, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
56 1 0.00
57 8 0.03
58 70 0.28
59 158 0.63
61 12 0.05
62 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.46
Consensus pattern (58 bp):
AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAATTTATTTTTAAGG
Found at i:6924 original size:118 final size:113
Alignment explanation
Indices: 6649--6983 Score: 429
Period size: 117 Copynumber: 2.8 Consensus size: 113
6639 TCTTGTGTAG
*
6649 GAAAAATTGATACTTTCAACTTTTTCTCCAAAAATATTTTTTGAAACTTTTATTTTCAAGGAAAA
1 GAAAAATTGATACTTTCAACTTTTTCT-CAAAAAT-TTTTTTGAAA--TTTATTTTTAAGGAAAA
* * *
6714 TTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAAATTTATTTTTAA
62 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAAATTTATTTTCAA
* * *
6766 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTATTTTTAAGGAAAA
1 GAAAAATTGATACTTTCAACTTTTTCTC-AAAA-A-TTTTTTT-GAAATTTATTTTTAAGGAAAA
*
6831 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACTTTGATTTTCAA
62 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAAATTT-ATTTTCAA
* * *
6884 GAAAAATTGATATTTTCAACTTTTTCTCAAAAACCCTTTTTTTTAAAAATTT-TTTTTAAGAAAA
1 GAAAAATTGATACTTTCAACTTTTTCTCAAAAA----TTTTTTT-GAAATTTATTTTTAAGGAAA
*
6948 ATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
61 ATTGATACTTTCAACTTTTCCCCAAAAATATTTTTT
6984 TGATTTTTAT
Statistics
Matches: 194, Mismatches: 16, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
116 2 0.01
117 89 0.46
118 84 0.43
119 19 0.10
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (113 bp):
GAAAAATTGATACTTTCAACTTTTTCTCAAAAATTTTTTTGAAATTTATTTTTAAGGAAAATTGA
TACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAAATTTATTTTCAA
Found at i:7046 original size:6 final size:6
Alignment explanation
Indices: 7018--7094 Score: 56
Period size: 6 Copynumber: 13.7 Consensus size: 6
7008 ATAATGAAAC
* * * * *
7018 AAAATA AAAGTG AAAAT- -AAATA AAAATA AAAA-A TAAAGA AAAGT-
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* *
7062 AAAACA AAAATA AAAAT- AAAATA AAGATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
7095 GAATATTAAA
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
4 4 0.07
5 12 0.22
6 38 0.70
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:7132 original size:4 final size:4
Alignment explanation
Indices: 7117--7166 Score: 84
Period size: 4 Copynumber: 12.8 Consensus size: 4
7107 AACCTACTCT
*
7117 AATA AA-A AATA AATA AATA AATA AATA AATA AACA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
7164 AAT
1 AAT
7167 TCAAAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 3 0.07
4 40 0.93
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (4 bp):
AATA
Found at i:7718 original size:24 final size:24
Alignment explanation
Indices: 7685--7740 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
7675 ATATGGAAAT
*
7685 TTTCCAAAAATTTCTAGAAAAATT-
1 TTTCCAAAAATCTCTA-AAAAATTA
7709 TTTGCCAAAAATCTCTAAAAAATTA
1 TTT-CCAAAAATCTCTAAAAAATTA
7734 TTTCCAA
1 TTTCCAA
7741 TTCCCACAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 14 0.48
25 15 0.52
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.36
Consensus pattern (24 bp):
TTTCCAAAAATCTCTAAAAAATTA
Found at i:7720 original size:25 final size:23
Alignment explanation
Indices: 7684--7740 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 23
7674 AATATGGAAA
*
7684 TTTTCCAAAAATTTCTAGAAAAAT
1 TTTTCCAAAAATCTCTA-AAAAAT
7708 TTTTGCCAAAAATCTCTAAAAAAT
1 TTTT-CCAAAAATCTCTAAAAAAT
7732 TATTTCCAA
1 T-TTTCCAA
7741 TTCCCACAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 15 0.50
25 15 0.50
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.37
Consensus pattern (23 bp):
TTTTCCAAAAATCTCTAAAAAAT
Found at i:8095 original size:3 final size:3
Alignment explanation
Indices: 8089--8238 Score: 68
Period size: 3 Copynumber: 49.7 Consensus size: 3
8079 AAAAGAAAAA
8089 AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AGAT ATAT ACAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT A-AT
* ** * *
8137 ATT AAT AAAT ACAT AAAT CCTT AA- AAA AAT AAT AAT AAT AA- AAG AA-
1 AAT AAT -AAT A-AT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
8183 AAG AA- AA- AAT -AT ATAT ACAT ATAT AA- AAT AAT AAT AAT AAA AAT
1 AAT AAT AAT AAT AAT A-AT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT
8227 AA- AAT AA- AAT AA
1 AAT AAT AAT AAT AA
8239 AAATGTAAAA
Statistics
Matches: 118, Mismatches: 14, Indels: 30
0.73 0.09 0.19
Matches are distributed among these distances:
2 19 0.16
3 71 0.60
4 27 0.23
5 1 0.01
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:8241 original size:6 final size:6
Alignment explanation
Indices: 8212--8277 Score: 68
Period size: 6 Copynumber: 11.2 Consensus size: 6
8202 TATATAAAAT
*
8212 AATAAT AATAAA AAT-AA AAT-AA AATAAA AATGTAAA AATACAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AA--TAAA AATA-AA AATAAA
8261 AAT--A AATAAA AATAAA A
1 AATAAA AATAAA AATAAA A
8278 TGAAGAGAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
4 4 0.08
5 10 0.19
6 27 0.51
7 6 0.11
8 6 0.11
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (6 bp):
AATAAA
Found at i:8241 original size:51 final size:49
Alignment explanation
Indices: 8161--8298 Score: 156
Period size: 51 Copynumber: 2.8 Consensus size: 49
8151 AAATCCTTAA
* * *
8161 AAAAATAATAATAATAAAAGAAAAGAAAAAATATATATACATATATAAAAT
1 AAAAATAATAAAAATAAAATAAAAGAAAAAATATATATA-A-ATACAAAAT
* * *
8212 AATAATAATAAAAATAAAATAAAA-TAAAAATGTA-A-AAATACAAAAT
1 AAAAATAATAAAAATAAAATAAAAGAAAAAATATATATAAATACAAAAT
*
8258 AAAAATAAATAAAAATAAAATGAAGAGAAAAAATATATATA
1 AAAAAT-AATAAAAATAAAAT-AAAAGAAAAAATATATATA
8299 TACAGACTTA
Statistics
Matches: 72, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
46 13 0.18
47 15 0.21
48 4 0.06
49 9 0.12
50 9 0.12
51 22 0.31
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.22
Consensus pattern (49 bp):
AAAAATAATAAAAATAAAATAAAAGAAAAAATATATATAAATACAAAAT
Found at i:8288 original size:104 final size:100
Alignment explanation
Indices: 8075--8275 Score: 225
Period size: 104 Copynumber: 2.0 Consensus size: 100
8065 ATATTAACAG
* * * *
8075 AAAA-AAAAGAAAAAAATAATAAATAATAATAATAATAATAATAATAATAAAGATATATACATAT
1 AAAAGAAAAGAAAAAAATAATAAATAATAATAATAATAATAATAAAAATAAAGATAAATAAAAAT
* *
8139 TAATAAATACATAAATCCTTAAAAAAATAATAATAAT
66 TAATAAATACATAAA--CTAAAAAAAATAAAAATAAT
*
8176 AAAAGAAAAGAAAAAATATATATACATATATAA-AATAATAATAATAAAAATAAA-ATAAAATAA
1 AAAAGAAAAGAAAAAA-ATA-ATAAATA-ATAATAATAATAATAATAAAAATAAAGAT-AAATAA
8239 AAATGTAA-AAATACA-AAA-TAAAAATAAATAAAAATAA
62 AAAT-TAATAAATACATAAACTAAAAA-AAATAAAAATAA
8276 AATGAAGAGA
Statistics
Matches: 86, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
100 5 0.06
101 15 0.17
102 11 0.13
103 8 0.09
104 40 0.47
105 7 0.08
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (100 bp):
AAAAGAAAAGAAAAAAATAATAAATAATAATAATAATAATAATAAAAATAAAGATAAATAAAAAT
TAATAAATACATAAACTAAAAAAAATAAAAATAAT
Found at i:11418 original size:16 final size:16
Alignment explanation
Indices: 11397--11453 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
11387 TAATAGAAAA
11397 AAAAAAGGAAAAGAAG
1 AAAAAAGGAAAAGAAG
*
11413 AAAAAA-GATAAAGATAA
1 AAAAAAGGA-AAAGA-AG
*
11430 AAAAAGAGGAAAAAAATG
1 AAAAA-AGGAAAAGAA-G
11448 AAAAAA
1 AAAAAA
11454 ATAAAGGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
15 2 0.06
16 11 0.33
17 8 0.24
18 10 0.30
19 2 0.06
ACGTcount: A:0.77, C:0.00, G:0.18, T:0.05
Consensus pattern (16 bp):
AAAAAAGGAAAAGAAG
Found at i:11440 original size:34 final size:34
Alignment explanation
Indices: 11394--11459 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
11384 CATTAATAGA
*
11394 AAAAAAAAAGGAAAAGAA-GAAAAAAGATAAAGAT
1 AAAAAAAAAGGAAAAAAATGAAAAAA-ATAAAGAT
*
11428 AAAAAAAGAGGAAAAAAATGAAAAAAATAAAG
1 AAAAAAAAAGGAAAAAAATGAAAAAAATAAAG
11460 GAATGGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 22 0.76
35 7 0.24
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (34 bp):
AAAAAAAAAGGAAAAAAATGAAAAAAATAAAGAT
Found at i:12232 original size:63 final size:63
Alignment explanation
Indices: 12079--12232 Score: 177
Period size: 63 Copynumber: 2.4 Consensus size: 63
12069 ATAGATTAGT
* * * * * * * *
12079 GGATGAAATTTGTTCTAAAATGGTTAGTGTTGAGAAATCTATAAGTGGTGACCTAGTGTTGGA
1 GGATGAAATTTGTTCTGAGATGGCTAGTATTGAGAAACCTATAAGTGGTGACCAAGTGATAGA
** *
12142 GGATGAAATTTGTTCTG-GAATAACTAGTATTGAGAAACCTATGAGTGGTGACCAAGTGATAGA
1 GGATGAAATTTGTTCTGAG-ATGGCTAGTATTGAGAAACCTATAAGTGGTGACCAAGTGATAGA
12205 GGAT-ATAATTTGTTCTGAGATGGCTAGT
1 GGATGA-AATTTGTTCTGAGATGGCTAGT
12233 GCTATGAAGC
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
62 1 0.01
63 73 0.97
64 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.33
Consensus pattern (63 bp):
GGATGAAATTTGTTCTGAGATGGCTAGTATTGAGAAACCTATAAGTGGTGACCAAGTGATAGA
Found at i:13215 original size:41 final size:41
Alignment explanation
Indices: 13059--13337 Score: 283
Period size: 41 Copynumber: 6.6 Consensus size: 41
13049 ATGATTGTCA
*
13059 AGGAGCCTTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTAG
1 AGGAGCCTTTTATTTTTCAAAGTTGTGGTGCCTCTATTTAG
* *
13100 AGGAGCATTTTACTTTTTCAAAGTTATGGTGCCTCTATTTAG
1 AGGAGCCTTTTA-TTTTTCAAAGTTGTGGTGCCTCTATTTAG
* *
13142 AGGAG--TATTTATTTTTCAAAGTTGTGGAGCCTCTGTTTAG
1 AGGAGCCT-TTTATTTTTCAAAGTTGTGGTGCCTCTATTTAG
* * *
13182 AGGAGCCTTTCATTTTTCAAAGTTATTGTGCCTCTATTTAG
1 AGGAGCCTTTTATTTTTCAAAGTTGTGGTGCCTCTATTTAG
* * * * *
13223 AGAAACTTTTTAACTTTTTATTTTTCAAAGTCGTTGAGCCTCTATTTAG
1 AGGAGC-------C-TTTTATTTTTCAAAGTTGTGGTGCCTCTATTTAG
* * * *
13272 AGGGGCTTTTTATTTTTCAAAGTTGTTGTGCCTCTATTTAA
1 AGGAGCCTTTTATTTTTCAAAGTTGTGGTGCCTCTATTTAG
*
13313 AGGAGCCTTTTTATTTTTGAAAGTT
1 AGGAGCC-TTTTATTTTTCAAAGTT
13338 ACGGAGCCTC
Statistics
Matches: 198, Mismatches: 27, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
40 32 0.16
41 83 0.42
42 49 0.25
48 1 0.01
49 33 0.17
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.45
Consensus pattern (41 bp):
AGGAGCCTTTTATTTTTCAAAGTTGTGGTGCCTCTATTTAG
Found at i:13347 original size:42 final size:40
Alignment explanation
Indices: 13236--13355 Score: 127
Period size: 41 Copynumber: 2.9 Consensus size: 40
13226 AACTTTTTAA
* *
13236 CTTTTTATTTTTCAAAG-TCGTTGAGCCTCTATTTAGAGGGG
1 CTTTTTATTTTTCAAAGTTCG--GAGCCTCTATTTAAAGGGC
*
13277 CTTTTTATTTTTCAAAGTT-GTTGTGCCTCTATTTAAAGGAGC
1 CTTTTTATTTTTCAAAGTTCG--GAGCCTCTATTTAAAGG-GC
* *
13319 CTTTTTATTTTTGAAAGTTACGGAGCCTCTGTTTAAA
1 CTTTTTATTTTTCAAAGTT-CGGAGCCTCTATTTAAA
13356 AGAGTTTTTC
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
41 35 0.51
42 33 0.48
44 1 0.01
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (40 bp):
CTTTTTATTTTTCAAAGTTCGGAGCCTCTATTTAAAGGGC
Found at i:13364 original size:131 final size:131
Alignment explanation
Indices: 13107--13353 Score: 325
Period size: 131 Copynumber: 1.9 Consensus size: 131
13097 TAGAGGAGCA
* *
13107 TTTTACTTTTTCAAAGTTATGGTGCCTCTATTTAGAGGAGTATTTATTTTTCAAAGTTGTGGAGC
1 TTTTACTTTTTCAAAGTCATGGAGCCTCTATTTAGAGGAGTATTTATTTTTCAAAGTTGTGGAGC
* * ** *
13172 CTCTGTTTAGAGGAGCCTTTCATTTTTCAAAGTTATTGTGCCTCTATTTAGAGAAACTTTTTAAC
66 CTCTATTTAAAGGAGCCTTTCATTTTTCAAAGTTACGGAGCCTCTATTTAGAGAAACTTTTTAAC
13237 T
131 T
* * * * * *
13238 TTTTA-TTTTTCAAAGTCGTTGAGCCTCTATTTAGAGGGGCTTTTTATTTTTCAAAGTTGTTGTG
1 TTTTACTTTTTCAAAGTCATGGAGCCTCTATTTAGAGGAG-TATTTATTTTTCAAAGTTGTGGAG
* * *
13302 CCTCTATTTAAAGGAGCCTTTTTATTTTTGAAAGTTACGGAGCCTCTGTTTA
65 CCTCTATTTAAAGGAGCC-TTTCATTTTTCAAAGTTACGGAGCCTCTATTTA
13354 AAAGAGTTTT
Statistics
Matches: 98, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
130 29 0.30
131 42 0.43
132 27 0.28
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (131 bp):
TTTTACTTTTTCAAAGTCATGGAGCCTCTATTTAGAGGAGTATTTATTTTTCAAAGTTGTGGAGC
CTCTATTTAAAGGAGCCTTTCATTTTTCAAAGTTACGGAGCCTCTATTTAGAGAAACTTTTTAAC
T
Found at i:14070 original size:24 final size:24
Alignment explanation
Indices: 14043--14118 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 24
14033 ATAATAATTA
14043 TTCAATGATGAAATTTATATAAAT
1 TTCAATGATGAAATTTATATAAAT
*
14067 TTCAAATGAT-AAATTTCTATAAAAT
1 TTC-AATGATGAAATTTATAT-AAAT
* *
14092 TCTTAGATGA-GAAATTTATCTAAAT
1 T-TCA-ATGATGAAATTTATATAAAT
14117 TT
1 TT
14119 GTCTCAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
24 13 0.30
25 17 0.40
26 13 0.30
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (24 bp):
TTCAATGATGAAATTTATATAAAT
Found at i:18653 original size:128 final size:128
Alignment explanation
Indices: 18386--18745 Score: 618
Period size: 128 Copynumber: 2.8 Consensus size: 128
18376 TACTTCTTTC
* *
18386 AAAATAAGAAAAAGTTAATTAAATTCAATAAATAGCTAGCTAAGAAATTACCAGCAAATTATAAG
1 AAAATAAGAAAAAGTTAATGAAATTCAATAACTAGCTAGCTAAGAAATTACCAGCAAATTATAAG
*
18451 GAAAAGTAAACTTGGA-TTCTCGGCGCCGGAAAATTTCGGCCCTCAATCAAACAACCATTGGA
66 GAAAAGTAAACTTGGATTTCTCGGCGCTGGAAAATTTCGGCCCTCAATCAAACAACCATTGGA
*
18513 AAAATAAGAAAAAGTTAATGAAATTCAATAACTAGCTGGCTAAG-AA-TACCAGCAAATTATAAG
1 AAAATAAGAAAAAGTTAATGAAATTCAATAACTAGCTAGCTAAGAAATTACCAGCAAATTATAAG
18576 GAAAAGTAAACTTGGATTTCTCAGGCGCTTGGAAAATTTCGGCCCTCAATCAAACAACCATTGGA
66 GAAAAGTAAACTTGGATTTCTC-GGCGC-TGGAAAATTTCGGCCCTCAATCAAACAACCATTGGA
18641 AAAATAAGAAAAAGTTAATGAAATTCAATAACTAGCTAGCTAAGAAATTACCAGCAAATTATAAG
1 AAAATAAGAAAAAGTTAATGAAATTCAATAACTAGCTAGCTAAGAAATTACCAGCAAATTATAAG
*
18706 GAAAAGCAAACTTGGATTTCTCGGGGCGCTGGAAAATTTC
66 GAAAAGTAAACTTGGATTTCTC--GGCGCTGGAAAATTTC
18746 ATCCGATCAA
Statistics
Matches: 220, Mismatches: 7, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
125 33 0.15
126 7 0.03
127 46 0.21
128 78 0.35
129 2 0.01
130 49 0.22
131 5 0.02
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (128 bp):
AAAATAAGAAAAAGTTAATGAAATTCAATAACTAGCTAGCTAAGAAATTACCAGCAAATTATAAG
GAAAAGTAAACTTGGATTTCTCGGCGCTGGAAAATTTCGGCCCTCAATCAAACAACCATTGGA
Found at i:20002 original size:19 final size:19
Alignment explanation
Indices: 19967--20004 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
19957 AGATTAAACA
*
19967 AAAACTAAAATTGAAAAAT
1 AAAACTAAAAATGAAAAAT
19986 AAAACTAAATAAT-AAAAAT
1 AAAACTAAA-AATGAAAAAT
20005 TGATTAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (19 bp):
AAAACTAAAAATGAAAAAT
Found at i:20445 original size:27 final size:26
Alignment explanation
Indices: 20415--20494 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 26
20405 ATATTTATAT
20415 ATAATTAGTAAATATATTTTTTATTAA
1 ATAATTAGTAAAT-TATTTTTTATTAA
20442 ATAA-TA-TAAATTATTATTTTA--AA
1 ATAATTAGTAAATTATT-TTTTATTAA
* *
20465 TTAATTAGAATTAATGTATTTTTTATTAA
1 ATAATTAG--TAAAT-TATTTTTTATTAA
20494 A
1 A
20495 AATATATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
23 5 0.12
24 6 0.14
25 10 0.24
26 2 0.05
27 13 0.31
28 4 0.10
29 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (26 bp):
ATAATTAGTAAATTATTTTTTATTAA
Found at i:20476 original size:23 final size:24
Alignment explanation
Indices: 20438--20486 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
20428 ATATTTTTTA
20438 TTAAATAATATAAATT-AT-TATT
1 TTAAATAATATAAATTAATGTATT
20460 TTAAATTAAT-TAGAATTAATGTATT
1 TTAAA-TAATATA-AATTAATGTATT
20485 TT
1 TT
20487 TTATTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 7 0.30
23 8 0.35
24 2 0.09
25 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
TTAAATAATATAAATTAATGTATT
Found at i:23476 original size:21 final size:21
Alignment explanation
Indices: 23450--23492 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
23440 CCATAGTACA
23450 TAGGAATTGAAAGCTCCTAAG
1 TAGGAATTGAAAGCTCCTAAG
23471 TAGGAATTGAAAGCTCCTAAG
1 TAGGAATTGAAAGCTCCTAAG
23492 T
1 T
23493 CATGCTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (21 bp):
TAGGAATTGAAAGCTCCTAAG
Done.