Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168025.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_279, 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: 39404
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Found at i:10070 original size:15 final size:15
Alignment explanation
Indices: 10046--10117 Score: 53
Period size: 15 Copynumber: 4.9 Consensus size: 15
10036 TTATTAATAA
10046 AAAT-AAATAAAATC
1 AAATAAAATAAAATC
* * *
10060 CAGTAAAATAAAATG
1 AAATAAAATAAAATC
*
10075 AAATAAAATAAAAAC
1 AAATAAAATAAAATC
10090 TAAA-AATGAATAAAA--
1 -AAATAA--AATAAAATC
10105 AAATAAAATAAAA
1 AAATAAAATAAAA
10118 ATGAGAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
13 7 0.15
14 5 0.11
15 24 0.52
16 3 0.07
17 7 0.15
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.18
Consensus pattern (15 bp):
AAATAAAATAAAATC
Found at i:10107 original size:25 final size:24
Alignment explanation
Indices: 10063--10131 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 24
10053 TAAAATCCAG
*
10063 TAAAAT-AAAATGA-AATAAAATAA
1 TAAAATAAAAATGAGAA-AAAAAAA
* *
10086 -AAACTAAAAATGA-ATAAAAAAA
1 TAAAATAAAAATGAGAAAAAAAAA
10108 TAAAATAAAAATGAGAAAAAAAAA
1 TAAAATAAAAATGAGAAAAAAAAA
10132 ACCTGCAATC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
22 10 0.26
23 20 0.53
24 8 0.21
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.16
Consensus pattern (24 bp):
TAAAATAAAAATGAGAAAAAAAAA
Found at i:11055 original size:3 final size:3
Alignment explanation
Indices: 11047--11131 Score: 61
Period size: 3 Copynumber: 29.0 Consensus size: 3
11037 GTAAGATACT
* *
11047 ATA ATA AT- ATA GTA ACA -TA ATA ATA AT- ATA AT- ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
11091 CTA ATA TATT ATA TTA TATT ATA ATA ATA CTA ATA ATA ATA
1 ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
11132 CTATACTATT
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
2 7 0.11
3 52 0.84
4 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:11068 original size:16 final size:15
Alignment explanation
Indices: 11047--11087 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
11037 GTAAGATACT
11047 ATAATAATATAGTAAC
1 ATAATAATATA-TAAC
*
11063 ATAATAATAATATAAT
1 ATAATAAT-ATATAAC
11079 ATAATAATA
1 ATAATAATA
11088 ATACTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 1 0.04
16 19 0.83
17 3 0.13
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (15 bp):
ATAATAATATATAAC
Found at i:11071 original size:19 final size:19
Alignment explanation
Indices: 11047--11239 Score: 86
Period size: 22 Copynumber: 9.4 Consensus size: 19
11037 GTAAGATACT
*
11047 ATAATAATATAGTA-ACATA
1 ATAATAATATAATATA-ATA
11066 ATAATAATATAATATAATA
1 ATAATAATATAATATAATA
*
11085 ATAATACTAATATATTATATTATATT
1 AT-A-A-TAATATA--ATA-TA-ATA
11111 ATAATAATACTAATAATAATA
1 ATAATAATA-TAAT-ATAATA
* *
11132 CTATACTATTATAATAGTAATA
1 --ATAATAATATAATA-TAATA
* *
11154 ATACTATAATATACTATAGTA
1 ATA--ATAATATAATATAATA
* * *
11175 AT-ATACTGTATTATAATA
1 ATAATAATATAATATAATA
* *
11193 TATAATAACATACTATACTATA
1 -ATAATAATATAATATA--ATA
* *
11215 ACAATAATA-AAAATAATA
1 ATAATAATATAATATAATA
11233 ATAATAA
1 ATAATAA
11240 CAAAAATATG
Statistics
Matches: 133, Mismatches: 22, Indels: 39
0.69 0.11 0.20
Matches are distributed among these distances:
18 21 0.16
19 20 0.15
20 18 0.14
21 17 0.13
22 31 0.23
23 13 0.10
24 6 0.05
25 3 0.02
26 4 0.03
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.37
Consensus pattern (19 bp):
ATAATAATATAATATAATA
Found at i:11079 original size:5 final size:5
Alignment explanation
Indices: 11063--11238 Score: 65
Period size: 5 Copynumber: 33.2 Consensus size: 5
11053 ATATAGTAAC
* * *
11063 ATAAT AATAAT ATAAT ATAAT AATAAT ACTAAT ATATT ATATT ATATT
1 ATAAT -ATAAT ATAAT ATAAT -ATAAT A-TAAT ATAAT ATAAT ATAAT
* *
11111 AT-A- ATAAT ACTAAT AATAAT ACT-AT ACTATT ATAAT AGTAAT AATACT
1 ATAAT ATAAT A-TAAT -ATAAT A-TAAT A-TAAT ATAAT A-TAAT -ATAAT
* * * * *
11159 ATAAT ATACTAT AGTAAT ATACT GTATT ATAAT AT-AT AATAAC ATACT
1 ATAAT ATA--AT A-TAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT
* * *
11207 ATACT ATAACA ATAAT A-AAA ATAAT AATAAT A
1 ATAAT ATAA-T ATAAT ATAAT ATAAT -ATAAT A
11239 ACAAAAATAT
Statistics
Matches: 133, Mismatches: 19, Indels: 37
0.70 0.10 0.20
Matches are distributed among these distances:
3 2 0.02
4 6 0.05
5 72 0.54
6 46 0.35
7 5 0.04
8 2 0.02
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (5 bp):
ATAAT
Found at i:11082 original size:32 final size:31
Alignment explanation
Indices: 11046--11238 Score: 86
Period size: 30 Copynumber: 6.3 Consensus size: 31
11036 CGTAAGATAC
*
11046 TATAATAATATAGTAACATAATAATAATATAA
1 TATAATAATATACTAACAT-ATAATAATATAA
* * * *
11078 TATAATAATAATACTAATATATTATATTATAT
1 TATAATAAT-ATACTAACATATAATAATATAA
* * *
11110 TATAAT-A-ATACTAATA-ATAATACTATAC
1 TATAATAATATACTAACATATAATAATATAA
* * *
11138 TATTATAATAGTAAT-A-ATACT-ATAATATAC
1 TATAATAATA-TACTAACATA-TAATAATATAA
* * *
11168 TATAGTAATATACTGTA-TTATAAT-ATATAA
1 TATAATAATATACT-AACATATAATAATATAA
*
11198 TA-ACATACTATACTATAACA-ATAATAA-A-AA
1 TATA-ATAATATAC--TAACATATAATAATATAA
11228 TAATAATAATA
1 T-ATAATAATA
11239 ACAAAAATAT
Statistics
Matches: 124, Mismatches: 21, Indels: 33
0.70 0.12 0.19
Matches are distributed among these distances:
28 14 0.11
29 15 0.12
30 37 0.30
31 23 0.19
32 27 0.22
33 8 0.06
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (31 bp):
TATAATAATATACTAACATATAATAATATAA
Found at i:11129 original size:76 final size:75
Alignment explanation
Indices: 11042--11238 Score: 205
Period size: 76 Copynumber: 2.7 Consensus size: 75
11032 GAAACGTAAG
*
11042 ATACT-ATAATAATA-TAGTAAC-ATAATAATAATATAATATAATAATAATACTAATA-TATTAT
1 ATACTAATAATAATACTA-T-ACTATAATAATAATATAATATAATAATAATACT-ATAGTAATAT
*
11103 ATTATATTATAAT
63 ACTATATTATAAT
* *
11116 AATACTAATAATAATACTATACTATTATAATAGTAATAATACT-ATAAT-ATACTATAGTAATAT
1 -ATACTAATAATAATACTATACTATAATAATAAT-ATAATA-TAATAATAATACTATAGTAATAT
*
11179 ACTGTATTATAAT
63 ACTATATTATAAT
* * *
11192 ATA-TAATAA-CATACTATACTATAACAATAATA-AAAATAATAATAATA
1 ATACTAATAATAATACTATACTATAATAATAATATAATATAATAATAATA
11239 ACAAAAATAT
Statistics
Matches: 104, Mismatches: 10, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
70 1 0.01
71 8 0.08
72 4 0.04
73 18 0.17
74 6 0.06
75 13 0.12
76 40 0.38
77 13 0.12
78 1 0.01
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.38
Consensus pattern (75 bp):
ATACTAATAATAATACTATACTATAATAATAATATAATATAATAATAATACTATAGTAATATACT
ATATTATAAT
Found at i:11158 original size:25 final size:24
Alignment explanation
Indices: 11124--11213 Score: 87
Period size: 25 Copynumber: 3.7 Consensus size: 24
11114 ATAATACTAA
11124 TAATAATACTATACTATTATAATAG
1 TAATAATACTATACTATTAT-ATAG
*
11149 TAATAATACTATAATA-TACTATAG
1 TAATAATACTATACTATTA-TATAG
* * *
11173 TAAT-ATACTGTATTATAATATA-
1 TAATAATACTATACTATTATATAG
11195 TAATAACATACTATACTAT
1 TAAT-A-ATACTATACTAT
11214 AACAATAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
22 4 0.07
23 13 0.24
24 11 0.20
25 26 0.48
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.40
Consensus pattern (24 bp):
TAATAATACTATACTATTATATAG
Found at i:11651 original size:16 final size:17
Alignment explanation
Indices: 11632--11665 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
11622 TAAACCCTTC
11632 AAATCCTAAAAT-CAAA
1 AAATCCTAAAATCCAAA
11648 AAATCCTAAAATCCAAA
1 AAATCCTAAAATCCAAA
11665 A
1 A
11666 TTGGAAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATCCTAAAATCCAAA
Found at i:11658 original size:8 final size:8
Alignment explanation
Indices: 11632--11719 Score: 51
Period size: 8 Copynumber: 11.6 Consensus size: 8
11622 TAAACCCTTC
11632 AAATCCTA
1 AAATCCTA
**
11640 AAATCAAA
1 AAATCCTA
11648 AAATCCTA
1 AAATCCTA
11656 AAATCC-A
1 AAATCCTA
***
11663 AAATTGGA
1 AAATCCTA
11671 AAA-CC-A
1 AAATCCTA
11677 AAATCCTA
1 AAATCCTA
*
11685 AAA-CCCA
1 AAATCCTA
*
11692 AAACCCTA
1 AAATCCTA
* *
11700 AACTTCT-
1 AAATCCTA
*
11707 AAACCCTA
1 AAATCCTA
11715 AAATC
1 AAATC
11720 AAAAACCCAA
Statistics
Matches: 58, Mismatches: 17, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
6 4 0.07
7 17 0.29
8 37 0.64
ACGTcount: A:0.53, C:0.26, G:0.02, T:0.18
Consensus pattern (8 bp):
AAATCCTA
Found at i:11692 original size:15 final size:15
Alignment explanation
Indices: 11632--11701 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 15
11622 TAAACCCTTC
**
11632 AAATCCTAAAATCAAA
1 AAATCCTAAAA-CCCA
*
11648 AAATCCTAAAATCCA
1 AAATCCTAAAACCCA
***
11663 AAATTGGAAAA-CCA
1 AAATCCTAAAACCCA
11677 AAATCCTAAAACCCA
1 AAATCCTAAAACCCA
*
11692 AAACCCTAAA
1 AAATCCTAAA
11702 CTTCTAAACC
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
14 11 0.26
15 21 0.49
16 11 0.26
ACGTcount: A:0.57, C:0.24, G:0.03, T:0.16
Consensus pattern (15 bp):
AAATCCTAAAACCCA
Found at i:11710 original size:15 final size:15
Alignment explanation
Indices: 11692--11746 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
11682 CTAAAACCCA
11692 AAACCCTAAACTTCT
1 AAACCCTAAACTTCT
* *
11707 AAACCCTAAA-ATCAA
1 AAACCCTAAACTTC-T
11722 AAACCC-AAACTTCT
1 AAACCCTAAACTTCT
*
11736 AAACCTTAAAC
1 AAACCCTAAAC
11747 CCTTGAAACC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
14 10 0.31
15 22 0.69
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (15 bp):
AAACCCTAAACTTCT
Found at i:11770 original size:25 final size:25
Alignment explanation
Indices: 11741--11789 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
11731 CTTCTAAACC
*
11741 TTAAACCCTTGAAACCCTAAAATCT
1 TTAAACCCTTAAAACCCTAAAATCT
*
11766 TTAAACCCTTAAAATCCTAAAATC
1 TTAAACCCTTAAAACCCTAAAATC
11790 CAAACTCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.29
Consensus pattern (25 bp):
TTAAACCCTTAAAACCCTAAAATCT
Found at i:11771 original size:16 final size:16
Alignment explanation
Indices: 11692--11781 Score: 57
Period size: 16 Copynumber: 5.8 Consensus size: 16
11682 CTAAAACCCA
11692 AAACCCT-AAA-CTTCT
1 AAACCCTAAAATCTT-T
**
11707 AAACCCTAAAATC-AA
1 AAACCCTAAAATCTTT
11722 AAACCC--AAA-CTTCT
1 AAACCCTAAAATCTT-T
* ** *
11736 AAACCTTAAACCCTTG
1 AAACCCTAAAATCTTT
11752 AAACCCTAAAATCTTT
1 AAACCCTAAAATCTTT
11768 AAACCCTTAAAATC
1 AAACCC-TAAAATC
11782 CTAAAATCCA
Statistics
Matches: 56, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
12 1 0.02
13 3 0.05
14 5 0.09
15 13 0.23
16 23 0.41
17 11 0.20
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.23
Consensus pattern (16 bp):
AAACCCTAAAATCTTT
Found at i:11786 original size:16 final size:16
Alignment explanation
Indices: 11692--11786 Score: 58
Period size: 15 Copynumber: 6.2 Consensus size: 16
11682 CTAAAACCCA
*
11692 AAACCCTAAACT-TCT
1 AAACCCTAAAATCTCT
**
11707 AAACCCTAAAATC-AA
1 AAACCCTAAAATCTCT
*
11722 AAACCC-AAACT-TCT
1 AAACCCTAAAATCTCT
* **
11736 AAACCTTAAACCCT-T
1 AAACCCTAAAATCTCT
*
11751 GAAACCCTAAAATCTTT
1 -AAACCCTAAAATCTCT
11768 AAACCCTTAAAATC-CT
1 AAACCC-TAAAATCTCT
11784 AAA
1 AAA
11787 ATCCAAACTC
Statistics
Matches: 61, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
14 9 0.15
15 22 0.36
16 22 0.36
17 8 0.13
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.23
Consensus pattern (16 bp):
AAACCCTAAAATCTCT
Found at i:12827 original size:22 final size:22
Alignment explanation
Indices: 12721--12829 Score: 80
Period size: 22 Copynumber: 4.9 Consensus size: 22
12711 AGTTTAGTTG
*
12721 GCACATAAGCCCA-ATTTAACT-
1 GCACATAAGCCTAGA-TTAACTA
* *
12742 GACACATAAGCTTAGATTAGCTA
1 G-CACATAAGCCTAGATTAACTA
* *
12765 GCACATAAGTCC-AGTTTAGCTA
1 GCACATAAG-CCTAGATTAACTA
* * *
12787 GCATAATATGCCTAAATTAACTA
1 GCA-CATAAGCCTAGATTAACTA
*
12810 GCACATAAGCCTGGATTAAC
1 GCACATAAGCCTAGATTAAC
12830 AAAAAATATA
Statistics
Matches: 68, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
21 1 0.01
22 50 0.74
23 17 0.25
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.26
Consensus pattern (22 bp):
GCACATAAGCCTAGATTAACTA
Found at i:13065 original size:33 final size:33
Alignment explanation
Indices: 13023--13135 Score: 127
Period size: 33 Copynumber: 3.4 Consensus size: 33
13013 GCACCTATTT
*
13023 TTAAGCCCAATTTATCTGGTCCTCAAGGAAATC
1 TTAAGCCCAATTTATCTGGCCCTCAAGGAAATC
* * *
13056 TTAAGCCCAATTTATCTAGCCCTTAAGAAAATC
1 TTAAGCCCAATTTATCTGGCCCTCAAGGAAATC
* * * * * * *
13089 TTAAACCCAGTTTATTTGACCCCCAATGAAATT
1 TTAAGCCCAATTTATCTGGCCCTCAAGGAAATC
13122 TTAAGCCCAATTTA
1 TTAAGCCCAATTTA
13136 GTTGGCACAA
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (33 bp):
TTAAGCCCAATTTATCTGGCCCTCAAGGAAATC
Found at i:13645 original size:32 final size:32
Alignment explanation
Indices: 13598--13703 Score: 115
Period size: 32 Copynumber: 3.3 Consensus size: 32
13588 GGCACCTATT
*
13598 TTTAAGCCTAGTTTACCTAACACCAGTGAAAG
1 TTTAAGCCTAATTTACCTAACACCAGTGAAAG
* * *
13630 TTTAAACCTAATTTACCTTACACCTAATGAAAAG
1 TTTAAGCCTAATTTACCTAACACC-AGTG-AAAG
* * * *
13664 TTTAAGCCTAATTTAGCTAGCACTAGAGAAAG
1 TTTAAGCCTAATTTACCTAACACCAGTGAAAG
13696 -TTAAGCCT
1 TTTAAGCCT
13704 GGTTTATTTG
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
31 8 0.13
32 25 0.41
33 5 0.08
34 23 0.38
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (32 bp):
TTTAAGCCTAATTTACCTAACACCAGTGAAAG
Found at i:14098 original size:27 final size:28
Alignment explanation
Indices: 14046--14100 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
14036 CGAAGAAAAA
* *
14046 TTTAAGCCCAGTTTAGCTGGCACTCAAT
1 TTTAAGCCCAATTTAGCTGACACTCAAT
*
14074 TTTAAGCCCAATTTATCTGAC-CTCAAT
1 TTTAAGCCCAATTTAGCTGACACTCAAT
14101 GAAATTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (28 bp):
TTTAAGCCCAATTTAGCTGACACTCAAT
Found at i:14343 original size:12 final size:11
Alignment explanation
Indices: 14326--14387 Score: 54
Period size: 12 Copynumber: 5.3 Consensus size: 11
14316 CCCAAACCTT
14326 AAAAAACAAAA
1 AAAAAACAAAA
14337 CAAAAAACAAAA
1 -AAAAAACAAAA
14349 AGAAAAA-AAAA
1 A-AAAAACAAAA
*
14360 ACACAAACCAAAA
1 A-A-AAAACAAAA
*
14373 AACAAACCAAAA
1 AA-AAAACAAAA
14385 AAA
1 AAA
14388 GAAAAAAACT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
11 8 0.18
12 32 0.71
13 5 0.11
ACGTcount: A:0.82, C:0.16, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:14354 original size:24 final size:24
Alignment explanation
Indices: 14326--14373 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
14316 CCCAAACCTT
14326 AAAAAACAAAACAAAAAACAAAAAG
1 AAAAAA-AAAACAAAAAACAAAAAG
* *
14351 AAAAAAAAAACACAAACCAAAAA
1 AAAAAAAAAACAAAAAACAAAAA
14374 ACAAACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAACAAAAAACAAAAAG
Found at i:16574 original size:8 final size:8
Alignment explanation
Indices: 16563--16692 Score: 66
Period size: 8 Copynumber: 17.4 Consensus size: 8
16553 TTAAAAAACC
16563 AAAACTCT
1 AAAACTCT
16571 AAAAC-CT
1 AAAACTCT
*
16578 AAAACCCT
1 AAAACTCT
16586 AAAA-TC-
1 AAAACTCT
16592 AAAACTCT
1 AAAACTCT
**
16600 AAGCCTCT
1 AAAACTCT
*
16608 AAACCT-T
1 AAAACTCT
16615 AAAAC-C-
1 AAAACTCT
16621 AAAACTCT
1 AAAACTCT
16629 AAAA-TC-
1 AAAACTCT
*
16635 AAAACACT
1 AAAACTCT
*
16643 -AAACTTT
1 AAAACTCT
* *
16650 TAAACCCT
1 AAAACTCT
16658 AAAA-TCTT
1 AAAACTC-T
* *
16666 CAAACCCTT
1 AAAACTC-T
*
16675 AAAACCCT
1 AAAACTCT
16683 AAAA-TCT
1 AAAACTCT
16690 AAA
1 AAA
16693 CCCTCAAAAC
Statistics
Matches: 95, Mismatches: 16, Indels: 23
0.71 0.12 0.17
Matches are distributed among these distances:
6 13 0.14
7 30 0.32
8 43 0.45
9 9 0.09
ACGTcount: A:0.51, C:0.27, G:0.01, T:0.22
Consensus pattern (8 bp):
AAAACTCT
Found at i:16574 original size:14 final size:14
Alignment explanation
Indices: 16557--16645 Score: 81
Period size: 14 Copynumber: 6.2 Consensus size: 14
16547 CCAAAATTAA
16557 AAAACCAAAACTCT
1 AAAACCAAAACTCT
*
16571 AAAACCTAAAACCCT
1 AAAACC-AAAACTCT
*
16586 AAAATCAAAACTCT
1 AAAACCAAAACTCT
** *
16600 AAGCCTCTAAAC-CTT
1 AAAAC-CAAAACTC-T
16615 AAAACCAAAACTCT
1 AAAACCAAAACTCT
* *
16629 AAAATCAAAACACT
1 AAAACCAAAACTCT
16643 AAA
1 AAA
16646 CTTTTAAACC
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
14 37 0.63
15 22 0.37
ACGTcount: A:0.55, C:0.27, G:0.01, T:0.17
Consensus pattern (14 bp):
AAAACCAAAACTCT
Found at i:16589 original size:29 final size:29
Alignment explanation
Indices: 16557--16645 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 29
16547 CCAAAATTAA
16557 AAAACCAAAACTCTAAAACCTAAAACCCT
1 AAAACCAAAACTCTAAAACCTAAAACCCT
* * * *
16586 AAAATCAAAACTCT-AAGCCTCTAAACCTT
1 AAAACCAAAACTCTAAAACCT-AAAACCCT
* *
16615 AAAACCAAAACTCTAAAATC-AAAACACT
1 AAAACCAAAACTCTAAAACCTAAAACCCT
16643 AAA
1 AAA
16646 CTTTTAAACC
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
28 13 0.27
29 32 0.67
30 3 0.06
ACGTcount: A:0.55, C:0.27, G:0.01, T:0.17
Consensus pattern (29 bp):
AAAACCAAAACTCTAAAACCTAAAACCCT
Found at i:16654 original size:43 final size:44
Alignment explanation
Indices: 16564--16724 Score: 138
Period size: 43 Copynumber: 3.7 Consensus size: 44
16554 TAAAAAACCA
* * *
16564 AAACTCTAAAACCTAAAACCCTAAAATCAAAACTCTAAGCCTCT
1 AAACCCTAAAACCTAAAACCCTAAAATCAAAACACTAAACCTCT
* * * *
16608 AAACCTTAAAACC-AAAACTCTAAAATCAAAACACTAAACTTTT
1 AAACCCTAAAACCTAAAACCCTAAAATCAAAACACTAAACCTCT
* * * *
16651 AAACCCTAAAATCTTCAAACCCT----T-AAAACCCTAAA-ATCT
1 AAACCCTAAAA-CCTAAAACCCTAAAATCAAAACACTAAACCTCT
16690 AAACCCTCAAAACCTTCAAAACCCTAAAATCAAAA
1 AAACCCT-AAAACC-T-AAAACCCTAAAATCAAAA
16725 TCCAAATCCT
Statistics
Matches: 91, Mismatches: 16, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
39 10 0.11
40 15 0.16
41 8 0.09
43 35 0.38
44 12 0.13
45 7 0.08
46 4 0.04
ACGTcount: A:0.50, C:0.29, G:0.01, T:0.20
Consensus pattern (44 bp):
AAACCCTAAAACCTAAAACCCTAAAATCAAAACACTAAACCTCT
Found at i:16681 original size:9 final size:8
Alignment explanation
Indices: 16651--16718 Score: 50
Period size: 9 Copynumber: 8.4 Consensus size: 8
16641 CTAAACTTTT
16651 AAACCCTA
1 AAACCCTA
* * *
16659 AAATCTTC
1 AAACCCTA
16667 AAACCCTTA
1 AAACCC-TA
16676 AAACCCTA
1 AAACCCTA
*
16684 AAA-TCT-
1 AAACCCTA
16690 AAACCCTCA
1 AAACCCT-A
*
16699 AAACCTTCA
1 AAACCCT-A
16708 AAACCCTA
1 AAACCCTA
16716 AAA
1 AAA
16719 TCAAAATCCA
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
6 3 0.07
7 4 0.09
8 18 0.39
9 21 0.46
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.19
Consensus pattern (8 bp):
AAACCCTA
Found at i:16684 original size:25 final size:23
Alignment explanation
Indices: 16651--16703 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 23
16641 CTAAACTTTT
*
16651 AAACCCTAAAATCTTCAAACCCTTA
1 AAACCCTAAAATC-T-AAACCCTCA
16676 AAACCCTAAAATCTAAACCCTCA
1 AAACCCTAAAATCTAAACCCTCA
16699 AAACC
1 AAACC
16704 TTCAAAACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 13 0.48
24 1 0.04
25 13 0.48
ACGTcount: A:0.47, C:0.34, G:0.00, T:0.19
Consensus pattern (23 bp):
AAACCCTAAAATCTAAACCCTCA
Found at i:16692 original size:32 final size:33
Alignment explanation
Indices: 16656--16727 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 33
16646 CTTTTAAACC
* *
16656 CTAAAATCTTCAAACCCTT-AAAACCCTAAAAT
1 CTAAAATCCTCAAAACCTTCAAAACCCTAAAAT
*
16688 CT-AAACCCTCAAAACCTTCAAAACCCTAAAAT
1 CTAAAATCCTCAAAACCTTCAAAACCCTAAAAT
16720 C-AAAATCC
1 CTAAAATCC
16728 AAATCCTAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
31 13 0.38
32 21 0.62
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (33 bp):
CTAAAATCCTCAAAACCTTCAAAACCCTAAAAT
Found at i:16724 original size:14 final size:14
Alignment explanation
Indices: 16557--16724 Score: 76
Period size: 14 Copynumber: 11.7 Consensus size: 14
16547 CCAAAATTAA
* *
16557 AAAACCAAAACTCT
1 AAAATCAAAACCCT
*
16571 AAAACCTAAAACCCT
1 AAAATC-AAAACCCT
*
16586 AAAATCAAAACTCT
1 AAAATCAAAACCCT
** * *
16600 AAGCCTCTAAACCTT
1 AA-AATCAAAACCCT
* *
16615 AAAACCAAAACTCT
1 AAAATCAAAACCCT
*
16629 AAAATCAAAACACT
1 AAAATCAAAACCCT
* **
16643 AAACTTTTAAACCCT
1 AAA-ATCAAAACCCT
*
16658 AAAATCTTCAAACCCT
1 AAAATC--AAAACCCT
16674 ----T-AAAACCCT
1 AAAATCAAAACCCT
*
16683 AAAATCTAAACCCT
1 AAAATCAAAACCCT
16697 CAAAACCTTCAAAACCCT
1 -AAAA---TCAAAACCCT
16715 AAAATCAAAA
1 AAAATCAAAA
16725 TCCAAATCCT
Statistics
Matches: 114, Mismatches: 26, Indels: 28
0.68 0.15 0.17
Matches are distributed among these distances:
9 7 0.06
12 1 0.01
13 1 0.01
14 50 0.44
15 35 0.31
16 7 0.06
17 4 0.04
18 9 0.08
ACGTcount: A:0.51, C:0.29, G:0.01, T:0.20
Consensus pattern (14 bp):
AAAATCAAAACCCT
Found at i:16768 original size:22 final size:22
Alignment explanation
Indices: 16743--16797 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
16733 CTAGACCCTC
16743 AAAACTCAAAACCTGAA-ACCTT
1 AAAACTCAAAACCT-AAGACCTT
*
16765 AAAA-TCCAAACCCTAAGACCTT
1 AAAACT-CAAAACCTAAGACCTT
16787 AAAACCTCAAA
1 AAAA-CTCAAA
16798 CGAGGCCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 3 0.11
22 20 0.71
23 4 0.14
24 1 0.04
ACGTcount: A:0.51, C:0.29, G:0.04, T:0.16
Consensus pattern (22 bp):
AAAACTCAAAACCTAAGACCTT
Found at i:19871 original size:14 final size:14
Alignment explanation
Indices: 19852--19881 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19842 TATTATTACG
*
19852 TAGTAAATTATGAA
1 TAGTAAATTAAGAA
19866 TAGTAAATTAAGAA
1 TAGTAAATTAAGAA
19880 TA
1 TA
19882 TTTACTCATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (14 bp):
TAGTAAATTAAGAA
Found at i:20054 original size:22 final size:21
Alignment explanation
Indices: 20027--20085 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
20017 GATAACTAAT
20027 AACTTAGTAATTAATCATTGAA
1 AACTTAGTAATTAATCATT-AA
* *
20049 AACTTA--AATGTAATCAATAT
1 AACTTAGTAAT-TAATCATTAA
20069 AACTTAGTAA-TAATCAT
1 AACTTAGTAATTAATCAT
20086 CAGTAACTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 16 0.52
21 7 0.23
22 8 0.26
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (21 bp):
AACTTAGTAATTAATCATTAA
Found at i:20135 original size:22 final size:22
Alignment explanation
Indices: 20100--20161 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
20090 AACTTAATAT
* *
20100 TAAATTAGTGATAATTTAGTAG
1 TAAATAAGTAATAATTTAGTAG
* * *
20122 TAAATAATTAATAACTTT-TTGG
1 TAAATAAGTAATAA-TTTAGTAG
*
20144 TAAATCAGTAATAATTTA
1 TAAATAAGTAATAATTTA
20162 ATAATATATG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
21 3 0.10
22 25 0.81
23 3 0.10
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.42
Consensus pattern (22 bp):
TAAATAAGTAATAATTTAGTAG
Found at i:20439 original size:22 final size:22
Alignment explanation
Indices: 20381--20441 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
20371 TAACAGTAGG
*
20381 AAATCA-TAAATAATTTAGTCAT
1 AAATCATTAAA-AATTTAGTAAT
* * *
20403 AAATAATTGATAATTTAGTAAT
1 AAATCATTAAAAATTTAGTAAT
*
20425 TAATCATTAAAAATTTA
1 AAATCATTAAAAATTTA
20442 AAACTAAATC
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
22 28 0.93
23 2 0.07
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (22 bp):
AAATCATTAAAAATTTAGTAAT
Found at i:20545 original size:21 final size:22
Alignment explanation
Indices: 20499--20548 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
20489 TTAGTTAATG
*
20499 ATAACTTAATAATAAATCATGC
1 ATAACTTAATAATAAATCATGA
*
20521 ATAATTTAA-AATAAATCAAT-A
1 ATAACTTAATAATAAATC-ATGA
20542 ATAACTT
1 ATAACTT
20549 GGTATAGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.34
Consensus pattern (22 bp):
ATAACTTAATAATAAATCATGA
Found at i:20655 original size:22 final size:22
Alignment explanation
Indices: 20630--20682 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
20620 TGATAACATG
20630 ATAGTAAA-CATATAAAAATATA
1 ATAGTAAATCAT-TAAAAATATA
* *
20652 ATAGTAAATCATTAATAATTTA
1 ATAGTAAATCATTAAAAATATA
*
20674 ATAATAAAT
1 ATAGTAAAT
20683 TAATAACTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 24 0.89
23 3 0.11
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (22 bp):
ATAGTAAATCATTAAAAATATA
Found at i:20680 original size:11 final size:11
Alignment explanation
Indices: 20641--20737 Score: 51
Period size: 11 Copynumber: 9.1 Consensus size: 11
20631 TAGTAAACAT
20641 ATAA-AAATATA
1 ATAATAAAT-TA
* *
20652 ATAGTAAATCA
1 ATAATAAATTA
* *
20663 TTAATAATTTA
1 ATAATAAATTA
20674 ATAATAAA-T-
1 ATAATAAATTA
*
20683 -TAATAACTTA
1 ATAATAAATTA
* *
20693 AGAGTAAATTA
1 ATAATAAATTA
*
20704 CTAAT-AATGTA
1 ATAATAAAT-TA
20715 ATAATAAATTA
1 ATAATAAATTA
* *
20726 CTAATAACTTA
1 ATAATAAATTA
20737 A
1 A
20738 CTATAAATAA
Statistics
Matches: 61, Mismatches: 19, Indels: 12
0.66 0.21 0.13
Matches are distributed among these distances:
8 6 0.10
9 1 0.02
10 4 0.07
11 43 0.70
12 7 0.11
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (11 bp):
ATAATAAATTA
Found at i:20684 original size:19 final size:19
Alignment explanation
Indices: 20662--20730 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
20652 ATAGTAAATC
20662 ATTAATAATTTAATAATAA
1 ATTAATAATTTAATAATAA
* * *
20681 ATTAATAACTTAAGAGTAA
1 ATTAATAATTTAATAATAA
*
20700 ATTACTAATAATGTAATAATAA
1 A-T--TAATAATTTAATAATAA
*
20722 ATTACTAAT
1 ATTAATAAT
20731 AACTTAACTA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 23 0.59
20 1 0.03
21 1 0.03
22 14 0.36
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (19 bp):
ATTAATAATTTAATAATAA
Found at i:20722 original size:22 final size:21
Alignment explanation
Indices: 20683--20769 Score: 68
Period size: 22 Copynumber: 4.0 Consensus size: 21
20673 AATAATAAAT
* *
20683 TAATAACTTAAGAGTAAATTAC
1 TAATAA-TTAATAATAAATTAC
20705 TAATAATGTAATAATAAATTAC
1 TAATAAT-TAATAATAAATTAC
* *
20727 TAATAACTTAACT-ATAAATAAG
1 TAATAA-TTAA-TAATAAATTAC
* *
20749 TGATAATTAAGTAGTAAATTA
1 TAATAATTAA-TAATAAATTA
20770 GTTAATTATT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
21 6 0.11
22 45 0.85
23 2 0.04
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (21 bp):
TAATAATTAATAATAAATTAC
Found at i:20755 original size:44 final size:42
Alignment explanation
Indices: 20654--20769 Score: 103
Period size: 44 Copynumber: 2.7 Consensus size: 42
20644 AAAATATAAT
* *
20654 AGTAAATCATTAATAATTTAATAATAAA-T-TAATAACTTAAG
1 AGTAAATAACTAATAA-TTAATAATAAATTATAATAACTTAAG
* *
20695 AGTAAATTACTAATAATGTAATAATAAATTACTAATAACTTAACT
1 AGTAAATAACTAATAAT-TAATAATAAATTA-TAATAACTTAA-G
* * *
20740 A-TAAATAAGTGATAATTAAGTAGTAAATTA
1 AGTAAATAACTAATAATTAA-TAATAAATTA
20770 GTTAATTATT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
40 1 0.02
41 24 0.39
42 1 0.02
43 3 0.05
44 32 0.52
45 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (42 bp):
AGTAAATAACTAATAATTAATAATAAATTATAATAACTTAAG
Found at i:20912 original size:22 final size:22
Alignment explanation
Indices: 20880--20942 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
20870 CAATTTAATA
*
20880 AAAATCTTTCATAACTTAAT-G
1 AAAATCATTCATAACTTAATGG
*
20901 ATGAATCATTCATAACTTAATGG
1 A-AAATCATTCATAACTTAATGG
*
20924 AAAATCATTCATAAATTAA
1 AAAATCATTCATAACTTAA
20943 AAGTAAATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.03
22 33 0.92
23 2 0.06
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (22 bp):
AAAATCATTCATAACTTAATGG
Found at i:20921 original size:43 final size:44
Alignment explanation
Indices: 20838--20942 Score: 106
Period size: 43 Copynumber: 2.4 Consensus size: 44
20828 ACTTTATAAT
* *
20838 AAATCA-TCAATAACTTAGTGATAAATCACTAACAATTTAAT-AA
1 AAATCATTC-ATAACTTAATGATAAATCACTAACAACTTAATGAA
* * * * * *
20881 AAATCTTTCATAACTTAATGATGAATCATTCATAACTTAATGGA
1 AAATCATTCATAACTTAATGATAAATCACTAACAACTTAATGAA
*
20925 AAATCATTCATAAATTAA
1 AAATCATTCATAACTTAA
20943 AAGTAAATCA
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
43 31 0.62
44 19 0.38
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (44 bp):
AAATCATTCATAACTTAATGATAAATCACTAACAACTTAATGAA
Found at i:20950 original size:22 final size:22
Alignment explanation
Indices: 20904--20959 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
20894 CTTAATGATG
* **
20904 AATCATTCATAACTTAATGGAA
1 AATCATTCATAAATTAAAAGAA
*
20926 AATCATTCATAAATTAAAAGTA
1 AATCATTCATAAATTAAAAGAA
*
20948 AATCATTGATAA
1 AATCATTCATAA
20960 TTTAGTACTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (22 bp):
AATCATTCATAAATTAAAAGAA
Found at i:21479 original size:67 final size:65
Alignment explanation
Indices: 21393--21538 Score: 145
Period size: 67 Copynumber: 2.2 Consensus size: 65
21383 GTAAATTAGT
* * * **
21393 ATAACTTAATAGTAAATCAATTG-TAGTTTAATAG-TAACTAATTGATAAAATTT-GTAGTAAAT
1 ATAACTAAATAATAAATCAA-TGATAATTTAATAGTTAA-TAATT-A-AAAATTTAAAAGTAAAT
21455 CATAA
62 CA-AA
* * * *
21460 ATAACTAAATAATACATCAATGATAATTTAGTAGTTAATCATTAAAAATTTAAAAGTAAATCAAT
1 ATAACTAAATAATAAATCAATGATAATTTAATAGTTAATAATTAAAAATTTAAAAGTAAATCAAA
21525 ATAACTAAATAATA
1 ATAACTAAATAATA
21539 GTTAATTATC
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
65 22 0.33
66 12 0.18
67 30 0.45
68 3 0.04
ACGTcount: A:0.51, C:0.07, G:0.08, T:0.35
Consensus pattern (65 bp):
ATAACTAAATAATAAATCAATGATAATTTAATAGTTAATAATTAAAAATTTAAAAGTAAATCAAA
Found at i:21572 original size:16 final size:15
Alignment explanation
Indices: 21551--21582 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
21541 TAATTATCAC
21551 TAACTTAATAGTTAAA
1 TAACTTAATAG-TAAA
21567 TAACTTAATAGTAAA
1 TAACTTAATAGTAAA
21582 T
1 T
21583 TATAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (15 bp):
TAACTTAATAGTAAA
Found at i:21591 original size:22 final size:22
Alignment explanation
Indices: 21563--21803 Score: 75
Period size: 22 Copynumber: 11.0 Consensus size: 22
21553 ACTTAATAGT
*
21563 TAAATAACTTAATAGTAAATTA
1 TAAATAATTTAATAGTAAATTA
*
21585 TAAATAATTTAATA-TAAATCGA
1 TAAATAATTTAATAGTAAAT-TA
* * * * *
21607 T-AATAACTTGATAATGAATCA
1 TAAATAATTTAATAGTAAATTA
* * * *
21628 TGATTAATTTAATAATAAATCTG
1 TAAATAATTTAATAGTAAAT-TA
* ** *
21651 T-AATATTTTTGTAGTAAATAA
1 TAAATAATTTAATAGTAAATTA
* *
21672 TCAAA-AA-CTAAGTAGTAAATCA
1 T-AAATAATTTAA-TAGTAAATTA
* ** *
21694 -ATGATAACATAATAGTAAATCA
1 TA-AATAATTTAATAGTAAATTA
**
21716 TTGATAATTTAGAT-GTAAATTA
1 TAAATAATTTA-ATAGTAAATTA
** * * *
21738 TTGATAACTTAGTAGTAAATCA
1 TAAATAATTTAATAGTAAATTA
* * *
21760 TTAATAATTTAGTTGTAAATTA
1 TAAATAATTTAATAGTAAATTA
*
21782 GT-GATAATTTAATAGTAAATTA
1 -TAAATAATTTAATAGTAAATTA
21804 GTTAATCTTT
Statistics
Matches: 165, Mismatches: 40, Indels: 28
0.71 0.17 0.12
Matches are distributed among these distances:
20 1 0.01
21 21 0.13
22 134 0.81
23 9 0.05
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (22 bp):
TAAATAATTTAATAGTAAATTA
Found at i:21734 original size:44 final size:44
Alignment explanation
Indices: 21686--21801 Score: 160
Period size: 44 Copynumber: 2.6 Consensus size: 44
21676 AAACTAAGTA
* * *
21686 GTAAATCAATGATAACATAATAGTAAATCATTGATAATTTAGAT
1 GTAAATTAATGATAACTTAATAGTAAATCATTAATAATTTAGAT
* * *
21730 GTAAATTATTGATAACTTAGTAGTAAATCATTAATAATTTAGTT
1 GTAAATTAATGATAACTTAATAGTAAATCATTAATAATTTAGAT
* *
21774 GTAAATTAGTGATAATTTAATAGTAAAT
1 GTAAATTAATGATAACTTAATAGTAAAT
21802 TAGTTAATCT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (44 bp):
GTAAATTAATGATAACTTAATAGTAAATCATTAATAATTTAGAT
Found at i:21805 original size:22 final size:22
Alignment explanation
Indices: 21684--21801 Score: 121
Period size: 22 Copynumber: 5.4 Consensus size: 22
21674 AAAAACTAAG
* **
21684 TAGTAAATCAATGATAACATAA
1 TAGTAAATCATTGATAATTTAA
21706 TAGTAAATCATTGATAATTTAGA
1 TAGTAAATCATTGATAATTTA-A
* * *
21729 T-GTAAATTATTGATAACTTAG
1 TAGTAAATCATTGATAATTTAA
* *
21750 TAGTAAATCATTAATAATTTAG
1 TAGTAAATCATTGATAATTTAA
* * *
21772 TTGTAAATTAGTGATAATTTAA
1 TAGTAAATCATTGATAATTTAA
21794 TAGTAAAT
1 TAGTAAAT
21802 TAGTTAATCT
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
21 1 0.01
22 76 0.96
23 2 0.03
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (22 bp):
TAGTAAATCATTGATAATTTAA
Found at i:22186 original size:21 final size:21
Alignment explanation
Indices: 22136--22255 Score: 84
Period size: 21 Copynumber: 5.7 Consensus size: 21
22126 ATCAGAAAAT
*
22136 TAATTACTAAAATTACATTAA
1 TAATTACTAAAATTACATCAA
* **
22157 GAGATTACTAAAATTTTATCAA
1 TA-ATTACTAAAATTACATCAA
22179 TAATTACTAAAATTACATC-A
1 TAATTACTAAAATTACATCAA
* * *
22199 TAAATTA-TCAAACTAATATCAA
1 T-AATTACT-AAAATTACATCAA
* * *
22221 AAATTACCAAAATTATATCAA
1 TAATTACTAAAATTACATCAA
*
22242 AAATTA-TCAAAATT
1 TAATTACT-AAAATT
22256 TACTTATATT
Statistics
Matches: 78, Mismatches: 15, Indels: 12
0.74 0.14 0.11
Matches are distributed among these distances:
20 3 0.04
21 57 0.73
22 18 0.23
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.34
Consensus pattern (21 bp):
TAATTACTAAAATTACATCAA
Found at i:22233 original size:42 final size:42
Alignment explanation
Indices: 22173--22252 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
22163 ACTAAAATTT
* * *
22173 TATCAATAATTACTAAAATTACATCATAAATTATCAAACTAA
1 TATCAAAAATTACCAAAATTACATCAAAAATTATCAAACTAA
*
22215 TATCAAAAATTACCAAAATTATATCAAAAATTATCAAA
1 TATCAAAAATTACCAAAATTACATCAAAAATTATCAAA
22253 ATTTACTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (42 bp):
TATCAAAAATTACCAAAATTACATCAAAAATTATCAAACTAA
Found at i:26753 original size:14 final size:14
Alignment explanation
Indices: 26731--26765 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
26721 ATTATTCCAA
*
26731 AAAATAAATAACAG
1 AAAAGAAATAACAG
26745 AAAAGAAATAACAG
1 AAAAGAAATAACAG
26759 AAAAGAA
1 AAAAGAA
26766 TTTTGACTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.74, C:0.06, G:0.11, T:0.09
Consensus pattern (14 bp):
AAAAGAAATAACAG
Found at i:34675 original size:18 final size:18
Alignment explanation
Indices: 34654--34688 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
34644 TTAAAAAATT
34654 TAAGAAA-AACAAAAATAG
1 TAAGAAAGAA-AAAAATAG
34672 TAAGAAAGAAAAAAATA
1 TAAGAAAGAAAAAAATA
34689 TGGCTTTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.74, C:0.03, G:0.11, T:0.11
Consensus pattern (18 bp):
TAAGAAAGAAAAAAATAG
Found at i:35061 original size:20 final size:21
Alignment explanation
Indices: 35024--35067 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
35014 ATATAAGTAT
35024 AAATACGAAATACAATAA-AA
1 AAATACGAAATACAATAACAA
*
35044 AAATATGAAATA-ATATAACAA
1 AAATACGAAATACA-ATAACAA
35065 AAA
1 AAA
35068 AAACAGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 15 0.71
21 5 0.24
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.18
Consensus pattern (21 bp):
AAATACGAAATACAATAACAA
Found at i:36013 original size:13 final size:13
Alignment explanation
Indices: 35990--36029 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
35980 CATTGCCAGA
*
35990 TCGAGCCGAACCG
1 TCGAACCGAACCG
*
36003 TCGGACCGAACCG
1 TCGAACCGAACCG
*
36016 TCGAACCAAACCG
1 TCGAACCGAACCG
36029 T
1 T
36030 ACGTTGATCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (13 bp):
TCGAACCGAACCG
Found at i:37438 original size:18 final size:18
Alignment explanation
Indices: 37417--37460 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
37407 AAAAGAGGTA
*
37417 AAAAAAATAAAACAAATC
1 AAAAAAATAAAACAAAAC
*
37435 AAAAATAA-AAAGCAAAAC
1 AAAAA-AATAAAACAAAAC
37453 AAAAAAAT
1 AAAAAAAT
37461 TCACACACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.09
18 18 0.82
19 2 0.09
ACGTcount: A:0.80, C:0.09, G:0.02, T:0.09
Consensus pattern (18 bp):
AAAAAAATAAAACAAAAC
Done.