Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167944.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_205, 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: 51675
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Found at i:4982 original size:19 final size:19
Alignment explanation
Indices: 4958--4996 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
4948 CAACGTCAAG
4958 AAGGACAAGGGTAAATGTC
1 AAGGACAAGGGTAAATGTC
4977 AAGGACAAGGGTAAATGTC
1 AAGGACAAGGGTAAATGTC
4996 A
1 A
4997 CTATTGTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.31, T:0.15
Consensus pattern (19 bp):
AAGGACAAGGGTAAATGTC
Found at i:9134 original size:20 final size:20
Alignment explanation
Indices: 9109--9148 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
9099 ACTTGAGCCA
9109 ATGGCTAAAGCATTAGATGT
1 ATGGCTAAAGCATTAGATGT
9129 ATGGCTAAAGCATTAGATGT
1 ATGGCTAAAGCATTAGATGT
9149 GTAGCCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (20 bp):
ATGGCTAAAGCATTAGATGT
Found at i:15117 original size:4 final size:4
Alignment explanation
Indices: 15108--15159 Score: 51
Period size: 4 Copynumber: 14.2 Consensus size: 4
15098 GGGTAAAAGA
* *
15108 AAAT AAAT AAAT AAGT AAAT -AAT AAAT ATAT -AAT -AAT AAAT -AA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
15151 AAAT AAAT A
1 AAAT AAAT A
15160 TTTTAAATCC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
3 12 0.30
4 28 0.70
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:15121 original size:8 final size:8
Alignment explanation
Indices: 15108--15159 Score: 51
Period size: 7 Copynumber: 7.1 Consensus size: 8
15098 GGGTAAAAGA
15108 AAATAAAT
1 AAATAAAT
*
15116 AAATAAGT
1 AAATAAAT
15124 AAAT-AAT
1 AAATAAAT
*
15131 AAATATAT
1 AAATAAAT
15139 -AAT-AAT
1 AAATAAAT
15145 AAAT-AA-
1 AAATAAAT
15151 AAATAAAT
1 AAATAAAT
15159 A
1 A
15160 TTTTAAATCC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
6 6 0.17
7 16 0.44
8 14 0.39
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (8 bp):
AAATAAAT
Found at i:15270 original size:12 final size:13
Alignment explanation
Indices: 15247--15278 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
15237 GGATTTATTA
15247 AATAAT-AAAAAT
1 AATAATAAAAAAT
15259 AA-AATAAAAAAT
1 AATAATAAAAAAT
15271 AATAATAA
1 AATAATAA
15279 TAATTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 10 0.56
13 5 0.28
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AATAATAAAAAAT
Found at i:15752 original size:10 final size:10
Alignment explanation
Indices: 15725--15758 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
15715 TCATTTTGTT
*
15725 AAAATAACAA
1 AAAATAATAA
15735 ATAAATAATAA
1 A-AAATAATAA
15746 AAAATAATAA
1 AAAATAATAA
15756 AAA
1 AAA
15759 CAATATGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAATAATAA
Found at i:16459 original size:35 final size:36
Alignment explanation
Indices: 16405--16481 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 36
16395 ATTGTTTTAT
* *
16405 TAAAAAGATAAAATTTTTGGGTGACCAGTCACACCC
1 TAAAAAGAGAAAATTTTTGGGTGACCAATCACACCC
* * *
16441 TAAAAA-AGAAAATTTTTGGTTGACCAATTACACCT
1 TAAAAAGAGAAAATTTTTGGGTGACCAATCACACCC
16476 TAAAAA
1 TAAAAA
16482 TAATTAGAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 30 0.83
36 6 0.17
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (36 bp):
TAAAAAGAGAAAATTTTTGGGTGACCAATCACACCC
Found at i:18869 original size:19 final size:20
Alignment explanation
Indices: 18841--18883 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
18831 TAAGGGATTC
*
18841 AAGAAGGAT-GTGGAAAATT
1 AAGAAAGATGGTGGAAAATT
*
18860 AAGAAAGATGGTGGAATATT
1 AAGAAAGATGGTGGAAAATT
18880 AAGA
1 AAGA
18884 GAGTAGACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.49, C:0.00, G:0.30, T:0.21
Consensus pattern (20 bp):
AAGAAAGATGGTGGAAAATT
Found at i:19999 original size:63 final size:63
Alignment explanation
Indices: 19900--20031 Score: 219
Period size: 63 Copynumber: 2.1 Consensus size: 63
19890 TTCTCCAAGA
* * *
19900 TTCACTCCACTACAAGTTCATACTTCTCAAAAAATCCATTTACAGCTACCAGCCACATAATCT
1 TTCACTCCACTACAAGTTCATACTTCTCAAAAAATCCATTTACAACTACCAACCACACAATCT
* *
19963 TTCACTCCACTACAAGTTCATCCTTCTCAAAAAATCCATTTACAACTACCAACCATACAATCT
1 TTCACTCCACTACAAGTTCATACTTCTCAAAAAATCCATTTACAACTACCAACCACACAATCT
20026 TTCACT
1 TTCACT
20032 TTTGTTGGAC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.30
Consensus pattern (63 bp):
TTCACTCCACTACAAGTTCATACTTCTCAAAAAATCCATTTACAACTACCAACCACACAATCT
Found at i:21412 original size:16 final size:17
Alignment explanation
Indices: 21391--21422 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
21381 CTAATGCAGT
21391 GTCAAAAG-GAAAAAAG
1 GTCAAAAGTGAAAAAAG
21407 GTCAAAAGTGAAAAAA
1 GTCAAAAGTGAAAAAA
21423 TGGGTCAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.62, C:0.06, G:0.22, T:0.09
Consensus pattern (17 bp):
GTCAAAAGTGAAAAAAG
Found at i:26272 original size:16 final size:16
Alignment explanation
Indices: 26253--26287 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
26243 AAAAAATGAG
26253 AAAAACAAAAACAAAA
1 AAAAACAAAAACAAAA
* *
26269 AAAAAGAAAAAGAAAA
1 AAAAACAAAAACAAAA
26285 AAA
1 AAA
26288 GAAGTGGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.89, C:0.06, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAACAAAAACAAAA
Found at i:26878 original size:31 final size:31
Alignment explanation
Indices: 26840--26905 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
26830 ACAAAAAAGG
26840 CAAATAACTAATTGATTGGAGAAAGGGATAA
1 CAAATAACTAATTGATTGGAGAAAGGGATAA
26871 CAAATAACTAATTGATTGGAGAAAGGGATAA
1 CAAATAACTAATTGATTGGAGAAAGGGATAA
26902 CAAA
1 CAAA
26906 AGAAAGAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.50, C:0.08, G:0.21, T:0.21
Consensus pattern (31 bp):
CAAATAACTAATTGATTGGAGAAAGGGATAA
Found at i:27350 original size:36 final size:36
Alignment explanation
Indices: 27248--27381 Score: 94
Period size: 36 Copynumber: 3.7 Consensus size: 36
27238 ATCCCTGGCT
* * * * *
27248 TTCTTTATTACTTGACTTGTAGTGCCATC-CTAATCG
1 TTCTTTATTACTTGACTTGTGGTGTCGTCTC-GATCA
* * * *
27284 TTCTTTAGTT-TTTGACTTATAGTGTTGTCTC-AGTCA
1 TTCTTTA-TTACTTGACTTGTGGTGTCGTCTCGA-TCA
* * **
27320 TTTTTTATTACTTGACTTGTGTTGTCGTCTCGATTG
1 TTCTTTATTACTTGACTTGTGGTGTCGTCTCGATCA
*
27356 TTCTTTCTTACTTGACTTGTGGTGTC
1 TTCTTTATTACTTGACTTGTGGTGTC
27382 ATTTCGGTTG
Statistics
Matches: 76, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
35 3 0.04
36 69 0.91
37 4 0.05
ACGTcount: A:0.14, C:0.17, G:0.17, T:0.51
Consensus pattern (36 bp):
TTCTTTATTACTTGACTTGTGGTGTCGTCTCGATCA
Found at i:27515 original size:36 final size:36
Alignment explanation
Indices: 27475--27676 Score: 142
Period size: 36 Copynumber: 5.6 Consensus size: 36
27465 GTCCCAGTTG
27475 TTCTTTATTACTTGACTTGCAGTGTCATCCCGATCA
1 TTCTTTATTACTTGACTTGCAGTGTCATCCCGATCA
* ** ** *
27511 TTCTTTATT-TTTGGACTTGTGGTGTCAT-CTTAGTTA
1 TTCTTTATTACTT-GACTTGCAGTGTCATCCCGA-TCA
** * *
27547 TTCTTTATTTTTTGACTTGCA-TGTCCTCCTGATCA
1 TTCTTTATTACTTGACTTGCAGTGTCATCCCGATCA
* * * *
27582 TTCTTTATTACTTGGCTTG-TGATGTCATTCCAATCA
1 TTCTTTATTACTTGACTTGCAG-TGTCATCCCGATCA
** * * * * *
27618 TTCTTTATTTTTTGACTTACGGTGTCGTTCCGATTA
1 TTCTTTATTACTTGACTTGCAGTGTCATCCCGATCA
* *
27654 TTCTTTATCACTTGACTCGCAGT
1 TTCTTTATTACTTGACTTGCAGT
27677 TCAAACCTGA
Statistics
Matches: 126, Mismatches: 33, Indels: 14
0.73 0.19 0.08
Matches are distributed among these distances:
35 27 0.21
36 95 0.75
37 4 0.03
ACGTcount: A:0.16, C:0.20, G:0.15, T:0.49
Consensus pattern (36 bp):
TTCTTTATTACTTGACTTGCAGTGTCATCCCGATCA
Found at i:27529 original size:71 final size:71
Alignment explanation
Indices: 27436--27590 Score: 168
Period size: 71 Copynumber: 2.2 Consensus size: 71
27426 TGTTGTCCTA
* * ** *
27436 ATCATTATTTGTTTTTCAACTTGTAGT-TTGTCCCAGTTGTTCTTTATTACTTGACTTGCAGTGT
1 ATCATTCTTTATTTTTCAACTTGTAGTGTCATCCCAGTTATTCTTTATTACTTGACTTGCA-TGT
27500 CATCCCG
65 CATCCCG
** * ** **
27507 ATCATTCTTTATTTTTGGACTTGTGGTGTCATCTTAGTTATTCTTTATTTTTTGACTTGCATGTC
1 ATCATTCTTTATTTTTCAACTTGTAGTGTCATCCCAGTTATTCTTTATTACTTGACTTGCATGTC
* *
27572 CTCCTG
66 ATCCCG
27578 ATCATTCTTTATT
1 ATCATTCTTTATT
27591 ACTTGGCTTG
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
71 43 0.62
72 26 0.38
ACGTcount: A:0.16, C:0.18, G:0.14, T:0.52
Consensus pattern (71 bp):
ATCATTCTTTATTTTTCAACTTGTAGTGTCATCCCAGTTATTCTTTATTACTTGACTTGCATGTC
ATCCCG
Found at i:27601 original size:71 final size:72
Alignment explanation
Indices: 27468--27661 Score: 214
Period size: 71 Copynumber: 2.7 Consensus size: 72
27458 GTAGTTTGTC
* ** * *
27468 CCAGTTGTTCTTTATTACTTGACTTGCAGTGTCATCCCGATCATTCTTTATTTTTGGACTTGTGG
1 CCAGTTATTCTTTATTTTTTGACTTGCAGTGTCATCCCGATCATTCTTTATTCTTGGACTTGTGA
27533 TGTCA-T
66 TGTCATT
* * *
27539 CTTAGTTATTCTTTATTTTTTGACTTGCA-TGTCCTCCTGATCATTCTTTATTACTTGG-CTTGT
1 C-CAGTTATTCTTTATTTTTTGACTTGCAGTGTCATCCCGATCATTCTTTATT-CTTGGACTTGT
27602 GATGTCATT
64 GATGTCATT
* * * * * * *
27611 CCAATCATTCTTTATTTTTTGACTTACGGTGTCGTTCCGATTATTCTTTAT
1 CCAGTTATTCTTTATTTTTTGACTTGCAGTGTCATCCCGATCATTCTTTAT
27662 CACTTGACTC
Statistics
Matches: 102, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
71 55 0.54
72 47 0.46
ACGTcount: A:0.16, C:0.19, G:0.15, T:0.50
Consensus pattern (72 bp):
CCAGTTATTCTTTATTTTTTGACTTGCAGTGTCATCCCGATCATTCTTTATTCTTGGACTTGTGA
TGTCATT
Found at i:27669 original size:107 final size:107
Alignment explanation
Indices: 27475--27670 Score: 243
Period size: 107 Copynumber: 1.8 Consensus size: 107
27465 GTCCCAGTTG
* **
27475 TTCTTTATTACTTGACTTGCAGTGTCATCCCGATCATTCTTTATTTTTGGACTTGTGGTGTCATC
1 TTCTTTATTACTTGACTTGCAGTGTCATCCCAATCATTCTTTATTTTTGGACTTACGGTGTCATC
** ***
27540 TTAGTTATTCTTTATTTTTTGACTTGCATGTCCTCCTGATCA
66 CGAGTTATTCTTTATCACTTGACTTGCATGTCCTCCTGATCA
* * * * *
27582 TTCTTTATTACTTGGCTTG-TGATGTCATTCCAATCATTCTTTATTTTTTGACTTACGGTGTCGT
1 TTCTTTATTACTTGACTTGCAG-TGTCATCCCAATCATTCTTTATTTTTGGACTTACGGTGTC-A
27646 TCCGA-TTATTCTTTATCACTTGACT
64 TCCGAGTTATTCTTTATCACTTGACT
27671 CGCAGTTCAA
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
106 1 0.01
107 70 0.95
108 3 0.04
ACGTcount: A:0.16, C:0.19, G:0.14, T:0.50
Consensus pattern (107 bp):
TTCTTTATTACTTGACTTGCAGTGTCATCCCAATCATTCTTTATTTTTGGACTTACGGTGTCATC
CGAGTTATTCTTTATCACTTGACTTGCATGTCCTCCTGATCA
Found at i:28020 original size:25 final size:25
Alignment explanation
Indices: 27979--28042 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
27969 AAAGCCCATT
* * *
27979 AATAATAATAATAACTAAAATTAAA
1 AATAAAAATAAAAACTAAAAATAAA
* *
28004 ATTAAAATTAAAAACTAAAAATAAA
1 AATAAAAATAAAAACTAAAAATAAA
28029 AATAAAAATAAAAA
1 AATAAAAATAAAAA
28043 AAATGTAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (25 bp):
AATAAAAATAAAAACTAAAAATAAA
Found at i:28022 original size:7 final size:6
Alignment explanation
Indices: 27979--28130 Score: 80
Period size: 6 Copynumber: 24.5 Consensus size: 6
27969 AAAGCCCATT
* * * * *
27979 AATAAT AATAATA ACTAAA ATTAAA ATTAAA ATTAAA AACTAAA AATAAA
1 AATAAA AATAA-A AATAAA AATAAA AATAAA AATAAA AA-TAAA AATAAA
** *
28029 AATAAA AATAAA AA-AAA TGTAAA AA-AACCA AATAAAA ATATAAA AACCAGAA
1 AATAAA AATAAA AATAAA AATAAA AATAA--A AAT-AAA A-ATAAA AA-TA-AA
* * *
28081 AAT-AA AATAGTA AATATAA AATAAA AATAAT AA-AAA AA-AGA AATAAA
1 AATAAA AATA-AA AATA-AA AATAAA AATAAA AATAAA AATAAA AATAAA
28128 AAT
1 AAT
28131 TGAAAAAAAA
Statistics
Matches: 116, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
5 18 0.16
6 60 0.52
7 30 0.26
8 6 0.05
9 2 0.02
ACGTcount: A:0.74, C:0.04, G:0.03, T:0.20
Consensus pattern (6 bp):
AATAAA
Found at i:28022 original size:19 final size:17
Alignment explanation
Indices: 27979--28053 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 17
27969 AAAGCCCATT
*
27979 AATAATAATAATAACTAAA
1 AATAA-AATAA-AATTAAA
*
27998 ATTAAAATTAAAATTAAA
1 AATAAAA-TAAAATTAAA
*
28016 AACTAAAAATAAAAATAAA
1 AA-T-AAAATAAAATTAAA
28035 AATAAAA-AAAATGTAAA
1 AATAAAATAAAAT-TAAA
28052 AA
1 AA
28054 AACCAAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
16 4 0.09
17 10 0.21
18 10 0.21
19 19 0.40
20 4 0.09
ACGTcount: A:0.73, C:0.03, G:0.01, T:0.23
Consensus pattern (17 bp):
AATAAAATAAAATTAAA
Found at i:28054 original size:19 final size:18
Alignment explanation
Indices: 28032--28145 Score: 52
Period size: 21 Copynumber: 5.7 Consensus size: 18
28022 AAATAAAAAT
*
28032 AAAAATAAAAAAAATGTAA
1 AAAAAGAAAAAAAAT-TAA
*
28051 AAAAACCAAATAAAAATATAA
1 AAAAA-GAAA-AAAAAT-TAA
*
28072 AAACCAGAAAATAAAATAGTAA
1 AAA-AAGAAAA-AAAAT--TAA
*
28094 ATATAAA-ATAAAAATAATAAA
1 A-A-AAAGA-AAAAA-AATTAA
28115 AAAAAGAAATAAAAATTGAA
1 AAAAAGAAA-AAAAATT-AA
28135 AAAAA-AAAAAA
1 AAAAAGAAAAAA
28146 GACCTTGACC
Statistics
Matches: 75, Mismatches: 8, Indels: 25
0.69 0.07 0.23
Matches are distributed among these distances:
18 3 0.04
19 16 0.21
20 16 0.21
21 23 0.31
22 8 0.11
23 8 0.11
24 1 0.01
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (18 bp):
AAAAAGAAAAAAAATTAA
Found at i:28130 original size:42 final size:40
Alignment explanation
Indices: 28013--28143 Score: 122
Period size: 42 Copynumber: 3.1 Consensus size: 40
28003 AATTAAAATT
* *
28013 AAAAACTAAAAATAA-AAATAAAAATAAAAAAAATGTAAAA
1 AAAAAATAAAAATAATAAA-AAAAAGAAAAAAAATGTAAAA
** *
28053 AAACCAAATAAAAAT-ATAAAAACCAGAAAATAAAATAGTAAAT
1 AAA--AAATAAAAATAATAAAAAAAAGAAAA-AAAAT-GTAAAA
* *
28096 ATAAAATAAAAATAATAAAAAAAAGAAATAAAAATTGAAAAA
1 AAAAAATAAAAATAATAAAAAAAAGAAA-AAAAA-TGTAAAA
28138 AAAAAA
1 AAAAAA
28144 AAGACCTTGA
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
40 3 0.04
41 18 0.25
42 42 0.58
43 9 0.12
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (40 bp):
AAAAAATAAAAATAATAAAAAAAAGAAAAAAAATGTAAAA
Found at i:28141 original size:22 final size:22
Alignment explanation
Indices: 28019--28130 Score: 76
Period size: 21 Copynumber: 5.3 Consensus size: 22
28009 AATTAAAAAC
*
28019 TAAAAATAA-AAATAAAAATAAA
1 TAAAAATAATAAA-AAAAAGAAA
* **
28041 -AAAAAT-GTAAAAAAACCAAA
1 TAAAAATAATAAAAAAAAGAAA
**
28061 TAAAAAT-ATAAAAACCAGAAA
1 TAAAAATAATAAAAAAAAGAAA
* * *
28082 -ATAAAATAGT-AAATATA-AAA
1 TA-AAAATAATAAAAAAAAGAAA
28102 TAAAAATAATAAAAAAAAGAAA
1 TAAAAATAATAAAAAAAAGAAA
28124 TAAAAAT
1 TAAAAAT
28131 TGAAAAAAAA
Statistics
Matches: 68, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
20 18 0.26
21 39 0.57
22 11 0.16
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.17
Consensus pattern (22 bp):
TAAAAATAATAAAAAAAAGAAA
Found at i:29939 original size:22 final size:23
Alignment explanation
Indices: 29926--29969 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
29916 ATTATTAAAT
29926 ATTAA-AAATAAAATAATAAAAG
1 ATTAATAAATAAAATAATAAAAG
29948 ATTAATAAATAATAATAATAAA
1 ATTAATAAATAA-AATAATAAA
29970 TTTTTTAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 6 0.30
24 9 0.45
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (23 bp):
ATTAATAAATAAAATAATAAAAG
Found at i:30112 original size:27 final size:26
Alignment explanation
Indices: 30041--30145 Score: 111
Period size: 27 Copynumber: 3.9 Consensus size: 26
30031 AAACAGCCCC
* * *
30041 TAAATTGAAACCCTAAACCAAAACCT
1 TAAATCGAAACCCTAAATCAAAATCT
* *
30067 TAAATCAAAACCCTGAAATCAGAATCT
1 TAAATCGAAACCCT-AAATCAAAATCT
*
30094 TAAAATCGAAACCCTAAATTAAAATCT
1 T-AAATCGAAACCCTAAATCAAAATCT
*
30121 CTAAATTGAAACCCTAAAATCAAAA
1 -TAAATCGAAACCCT-AAATCAAAA
30146 CCCTAAAAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
26 12 0.18
27 32 0.49
28 21 0.32
ACGTcount: A:0.51, C:0.22, G:0.05, T:0.22
Consensus pattern (26 bp):
TAAATCGAAACCCTAAATCAAAATCT
Found at i:30151 original size:27 final size:26
Alignment explanation
Indices: 30038--30160 Score: 104
Period size: 27 Copynumber: 4.6 Consensus size: 26
30028 TATAAACAGC
* *
30038 CCCTAAATTGAAACCCTAAACCAAAA
1 CCCTAAATCGAAACCCTAAATCAAAA
* * *
30064 CCTTAAATCAAAACCCTGAAATCAGAA
1 CCCTAAATCGAAACCCT-AAATCAAAA
* * *
30091 TCTTAAAATCGAAACCCTAAATTAAAA
1 CCCT-AAATCGAAACCCTAAATCAAAA
* *
30118 TCTCTAAATTGAAACCCTAAAATCAAAA
1 -CCCTAAATCGAAACCCT-AAATCAAAA
*
30146 CCCTAAA-AGAAACCC
1 CCCTAAATCGAAACCC
30161 CAAAACCCTA
Statistics
Matches: 77, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
26 21 0.27
27 35 0.45
28 21 0.27
ACGTcount: A:0.50, C:0.26, G:0.05, T:0.20
Consensus pattern (26 bp):
CCCTAAATCGAAACCCTAAATCAAAA
Found at i:30153 original size:14 final size:13
Alignment explanation
Indices: 30038--30152 Score: 86
Period size: 14 Copynumber: 8.5 Consensus size: 13
30028 TATAAACAGC
**
30038 CCCTAAATTGAAA
1 CCCTAAATCAAAA
*
30051 CCCTAAACCAAAA
1 CCCTAAATCAAAA
*
30064 CCTTAAATCAAAA
1 CCCTAAATCAAAA
*
30077 CCCTGAAATCAGAA
1 CCCT-AAATCAAAA
* * *
30091 TCTTAAAATCGAAA
1 CCCT-AAATCAAAA
*
30105 CCCTAAATTAAAA
1 CCCTAAATCAAAA
* **
30118 TCTCTAAATTGAAA
1 -CCCTAAATCAAAA
30132 CCCTAAAATCAAAA
1 CCCT-AAATCAAAA
30146 CCCTAAA
1 CCCTAAA
30153 AGAAACCCCA
Statistics
Matches: 78, Mismatches: 21, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
13 37 0.47
14 41 0.53
ACGTcount: A:0.50, C:0.25, G:0.04, T:0.21
Consensus pattern (13 bp):
CCCTAAATCAAAA
Found at i:31659 original size:20 final size:21
Alignment explanation
Indices: 31634--31672 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
31624 CAAACAATAG
*
31634 GCAACAACATG-AAATTAAAT
1 GCAACAAAATGAAAATTAAAT
31654 GCAACAAAATGAAAATTAA
1 GCAACAAAATGAAAATTAA
31673 CAAGTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.59, C:0.13, G:0.10, T:0.18
Consensus pattern (21 bp):
GCAACAAAATGAAAATTAAAT
Found at i:34981 original size:18 final size:18
Alignment explanation
Indices: 34958--34995 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
34948 TTTTTATTTG
34958 TTTAAACTATTAGATCTT
1 TTTAAACTATTAGATCTT
*
34976 TTTAAACTATTTGATCTT
1 TTTAAACTATTAGATCTT
34994 TT
1 TT
34996 CTTTGTTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTAAACTATTAGATCTT
Found at i:35492 original size:41 final size:41
Alignment explanation
Indices: 35430--35514 Score: 134
Period size: 41 Copynumber: 2.1 Consensus size: 41
35420 CTTTACCATT
* *
35430 TAGATCAATAACAACATAGGATGATTTAATGTAAAAGTTTC
1 TAGACCAATAACAACATAGGATGATTTAATGCAAAAGTTTC
**
35471 TAGACCAATAACAACATAGGATGATTTGGTGCAAAAGTTTC
1 TAGACCAATAACAACATAGGATGATTTAATGCAAAAGTTTC
35512 TAG
1 TAG
35515 CTAAATTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (41 bp):
TAGACCAATAACAACATAGGATGATTTAATGCAAAAGTTTC
Found at i:38723 original size:29 final size:29
Alignment explanation
Indices: 38667--38727 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
38657 TTTATGTGTA
**
38667 CTTTGAGCTTTCGACTATGCACTCAATGC
1 CTTTGAGCTTTCGACTACACACTCAATGC
* * *
38696 CTTTGAGCTTTTGACTACACATTTAATGC
1 CTTTGAGCTTTCGACTACACACTCAATGC
38725 CTT
1 CTT
38728 AGTCTCTAGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (29 bp):
CTTTGAGCTTTCGACTACACACTCAATGC
Found at i:44304 original size:20 final size:19
Alignment explanation
Indices: 44269--44306 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
44259 ATCCTAAGCC
*
44269 ATTTAAGAATTCTAATTTG
1 ATTTAAGAAATCTAATTTG
44288 ATTTAATGAAATCTAATTT
1 ATTTAA-GAAATCTAATTT
44307 CTTATGTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (19 bp):
ATTTAAGAAATCTAATTTG
Found at i:46115 original size:35 final size:35
Alignment explanation
Indices: 46069--46212 Score: 123
Period size: 35 Copynumber: 4.1 Consensus size: 35
46059 TATTGTGGGT
* * *
46069 ATGATTGGGACAATACCACAAGTCAAAAAATAAAG
1 ATGATTAGGACAACATCACAAGTCAAAAAATAAAG
* *
46104 ATGATTAGGACAACATCACAGGTAAAAAAAATAAAG
1 ATGATTAGGACAACATCACAAGT-CAAAAAATAAAG
* * * *
46140 ATG-TT-GAAATAACATCA-ACAGTCGAAAAAACAAAT
1 ATGATTAG-GACAACATCACA-AGTC-AAAAAATAAAG
* * *
46175 ATGACTAGGACAACATCATAGGTCAAAAAATAAAG
1 ATGATTAGGACAACATCACAAGTCAAAAAATAAAG
46210 ATG
1 ATG
46213 GCATCATAGG
Statistics
Matches: 85, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
34 2 0.02
35 55 0.65
36 26 0.31
37 2 0.02
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.18
Consensus pattern (35 bp):
ATGATTAGGACAACATCACAAGTCAAAAAATAAAG
Found at i:46217 original size:26 final size:27
Alignment explanation
Indices: 46188--46239 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
46178 ACTAGGACAA
*
46188 CATCATAGGTCAAAAAA-TAAAGATGG
1 CATCATAGGTAAAAAAAGTAAAGATGG
46214 CATCATAGGTAAAAAAAGTAAAGATG
1 CATCATAGGTAAAAAAAGTAAAGATG
46240 ATCAGGACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (27 bp):
CATCATAGGTAAAAAAAGTAAAGATGG
Found at i:46302 original size:98 final size:97
Alignment explanation
Indices: 46117--46306 Score: 222
Period size: 98 Copynumber: 1.9 Consensus size: 97
46107 ATTAGGACAA
* * * *
46117 CATCACAGGTAAAAAAAATAAAGATGTTGAAATAACATCAACAGTCGAAAAAACAAATATGACTA
1 CATCACAGGTAAAAAAAATAAAGATGATCAAACAACATCAACAGTCGAAAAAACAAAAATGACTA
* *
46182 GGACAACATCATAGGTCAAAAAATAAAGATGG
66 GGACAACATCACAGATCAAAAAATAAAGATGG
* * * * * *
46214 CATCATAGGTAAAAAAAGTAAAGATGATCAGGACAACATC-ACAGGTTGAAAAAATAAAAATGAT
1 CATCACAGGTAAAAAAAATAAAGATGATCA-AACAACATCAACA-GTCGAAAAAACAAAAATGAC
*
46278 TAGGACAACA-CACAGATTAGAAAAATAAA
64 TAGGACAACATCACAGATCA-AAAAATAAA
46307 AATGATCGAG
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
97 35 0.45
98 42 0.55
ACGTcount: A:0.54, C:0.13, G:0.16, T:0.17
Consensus pattern (97 bp):
CATCACAGGTAAAAAAAATAAAGATGATCAAACAACATCAACAGTCGAAAAAACAAAAATGACTA
GGACAACATCACAGATCAAAAAATAAAGATGG
Found at i:46323 original size:35 final size:35
Alignment explanation
Indices: 46225--46323 Score: 121
Period size: 35 Copynumber: 2.8 Consensus size: 35
46215 ATCATAGGTA
* *
46225 AAAAAAGTAAAGATGATCAGGACAACATCACAGGTTG
1 AAAAAA-TAAAAATGATCAGGACAACA-CACAGATTG
*
46262 AAAAAATAAAAATGATTAGGACAACACACAGATT-
1 AAAAAATAAAAATGATCAGGACAACACACAGATTG
46296 AGAAAAATAAAAATGATC-GAGACAACAC
1 A-AAAAATAAAAATGATCAG-GACAACAC
46324 CAACAGTCAA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
34 2 0.04
35 30 0.54
36 18 0.32
37 6 0.11
ACGTcount: A:0.56, C:0.13, G:0.16, T:0.15
Consensus pattern (35 bp):
AAAAAATAAAAATGATCAGGACAACACACAGATTG
Found at i:46467 original size:35 final size:34
Alignment explanation
Indices: 46226--46505 Score: 113
Period size: 35 Copynumber: 7.9 Consensus size: 34
46216 TCATAGGTAA
* *
46226 AAAAAGTAAAGATGATCAGGACAACATCACA-GGTTG
1 AAAAA-TAAAAATGAT-AGGACAACACCA-ATGGTTG
*
46262 AAAAAATAAAAATGATTAGGACAACACACAGAT--TAG
1 -AAAAATAAAAATGA-TAGGACAACAC-CA-ATGGTTG
* ** **
46298 AAAAATAAAAATGATCGAGACAACACCAACAGTCA
1 AAAAATAAAAATGATAG-GACAACACCAATGGTTG
* * * * * **
46333 AAGAAACAAATATGATTGGAATAATACCACA-GGTCA
1 AA-AAATAAAAATGATAGG-ACAACACCA-ATGGTTG
* * * * *
46369 AAAAATAAAGATAATTGAGG-CAACAAC-ATGGGTC
1 AAAAATAAAAATGA-T-AGGACAACACCAATGGTTG
*
46403 ACAAAATAAAAATGATCAGGATAACACCAATGGTTG
1 A-AAAATAAAAATGAT-AGGACAACACCAATGGTTG
* * * *
46439 AAAAACAAAAATGACTAGGACAATACCAATAGTTT
1 AAAAATAAAAATGA-TAGGACAACACCAATGGTTG
* *
46474 AAAAGATAAAGATGATTAAGACAACACCAATG
1 AAAA-ATAAAAATGA-TAGGACAACACCAATG
46506 ATAAAAAAAA
Statistics
Matches: 184, Mismatches: 42, Indels: 35
0.70 0.16 0.13
Matches are distributed among these distances:
33 2 0.01
34 11 0.06
35 86 0.47
36 73 0.40
37 12 0.07
ACGTcount: A:0.53, C:0.14, G:0.16, T:0.17
Consensus pattern (34 bp):
AAAAATAAAAATGATAGGACAACACCAATGGTTG
Found at i:46504 original size:36 final size:34
Alignment explanation
Indices: 46405--46534 Score: 111
Period size: 35 Copynumber: 3.8 Consensus size: 34
46395 CATGGGTCAC
* * * *
46405 AAAATAAAA-ATGATCAGGATAACACCAATGGTTG
1 AAAAAAAAAGATGATTAGGACAACACCAAT-GTTT
* *
46439 AAAAACAAAA-ATGACTAGGACAATACCAATAGTTT
1 AAAAA-AAAAGATGATTAGGACAACACCAAT-GTTT
* * * *
46474 AAAAGATAAAGATGATTAAGACAACACCAATGATA
1 AAAA-AAAAAGATGATTAGGACAACACCAATGTTT
*
46509 AAAAAAAAAGATGATTAGGATAACAC
1 AAAAAAAAAGATGATTAGGACAACAC
46535 TGCAAGTCAA
Statistics
Matches: 77, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
34 23 0.30
35 36 0.47
36 18 0.23
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.18
Consensus pattern (34 bp):
AAAAAAAAAGATGATTAGGACAACACCAATGTTT
Found at i:46610 original size:36 final size:35
Alignment explanation
Indices: 46474--46626 Score: 125
Period size: 35 Copynumber: 4.4 Consensus size: 35
46464 CCAATAGTTT
* * *
46474 AAAAGATAAAGATGATTAAGACAACA-C-CAATGAT-
1 AAAAAATAAAGATGATTAGGATAACACCGCAA-G-TC
* *
46508 AAAAAAAAAAGATGATTAGGATAACACTGCAAGTC
1 AAAAAATAAAGATGATTAGGATAACACCGCAAGTC
** ** * * *
46543 AAAAAATAAATTTGA-CCGAGATAATATCGCAAGTT
1 AAAAAATAAAGATGATTAG-GATAACACCGCAAGTC
*
46578 AGAAAAATAAAGATGATTAGGAAAACACCGCAAGTC
1 A-AAAAATAAAGATGATTAGGATAACACCGCAAGTC
46614 AAAAAATAAAGAT
1 AAAAAATAAAGAT
46627 AAGTAAGATA
Statistics
Matches: 91, Mismatches: 22, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
34 24 0.26
35 38 0.42
36 28 0.31
37 1 0.01
ACGTcount: A:0.55, C:0.11, G:0.16, T:0.18
Consensus pattern (35 bp):
AAAAAATAAAGATGATTAGGATAACACCGCAAGTC
Found at i:46655 original size:71 final size:70
Alignment explanation
Indices: 46508--46657 Score: 158
Period size: 71 Copynumber: 2.1 Consensus size: 70
46498 CACCAATGAT
* * ** * * * *
46508 AAAAAAAAAAGATGATTAGGATAACACTGCAAGTCAAAAAATAAATTTGACCGAGATAATATCGC
1 AAAAAAAAAAGATGATTAGGAAAACACCGCAAGTCAAAAAATAAAGATAACCAAGATAATACCAC
46573 AAGTTA
66 AAG-TA
* * **
46579 GAAAAATAAAGATGATTAGGAAAACACCGCAAGTCAAAAAATAAAGATAAGTAAGAT-ATCACCA
1 AAAAAAAAAAGATGATTAGGAAAACACCGCAAGTCAAAAAATAAAGATAACCAAGATAAT-ACCA
*
46643 CAGGTA
65 CAAGTA
46649 AAAAAAAAA
1 AAAAAAAAA
46658 CAAATATAAC
Statistics
Matches: 63, Mismatches: 15, Indels: 3
0.78 0.19 0.04
Matches are distributed among these distances:
70 11 0.17
71 52 0.83
ACGTcount: A:0.56, C:0.11, G:0.15, T:0.17
Consensus pattern (70 bp):
AAAAAAAAAAGATGATTAGGAAAACACCGCAAGTCAAAAAATAAAGATAACCAAGATAATACCAC
AAGTA
Found at i:46728 original size:36 final size:36
Alignment explanation
Indices: 46651--46749 Score: 103
Period size: 36 Copynumber: 2.8 Consensus size: 36
46641 CACAGGTAAA
* * *
46651 AAAAAAAC-AAATATAACTAAGACAACACTGCAAAT
1 AAAAAAACTAAATATGACTAGGACAACACTACAAAT
* * *
46686 AAAAAAACTAAATATGACTAGGACAACATTATAAGT
1 AAAAAAACTAAATATGACTAGGACAACACTACAAAT
* * *
46722 AGAAAAA-TAAAGATGACTAGGCCAACAC
1 AAAAAAACTAAATATGACTAGGACAACAC
46750 CGTAGGACAA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
35 26 0.49
36 27 0.51
ACGTcount: A:0.58, C:0.15, G:0.11, T:0.16
Consensus pattern (36 bp):
AAAAAAACTAAATATGACTAGGACAACACTACAAAT
Found at i:47300 original size:28 final size:28
Alignment explanation
Indices: 47268--47324 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
47258 TTGGTTATGA
*
47268 TGCAAATGATGTAAATGCCAATGTCTTT
1 TGCAAATGATGTAAATACCAATGTCTTT
* * *
47296 TGCAAGTGATGTAATTACGAATGTCTTT
1 TGCAAATGATGTAAATACCAATGTCTTT
47324 T
1 T
47325 TCATGATGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (28 bp):
TGCAAATGATGTAAATACCAATGTCTTT
Done.