Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167977.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_235, 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: 45336
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:9929 original size:23 final size:23
Alignment explanation
Indices: 9903--9947 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
9893 CTTCTATTTA
*
9903 AAAAGTAAACAATAGAAAACATG
1 AAAAGTAAACAAAAGAAAACATG
*
9926 AAAAGTAAATAAAAGAAAACAT
1 AAAAGTAAACAAAAGAAAACAT
9948 AATTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.69, C:0.07, G:0.11, T:0.13
Consensus pattern (23 bp):
AAAAGTAAACAAAAGAAAACATG
Found at i:10813 original size:95 final size:94
Alignment explanation
Indices: 10602--10825 Score: 229
Period size: 95 Copynumber: 2.4 Consensus size: 94
10592 TTAATTTAAT
* * * *
10602 ATTTAAATCCTCCAATAGTTT-AGTAAGATTGAAAATTTTATTTTTAATAAAAATTTACTAAATC
1 ATTTAAATCTTTCAATAATTTGA-TAAGATTGAAAATTTTATTTTTAATAAAAATTCACTAAATC
* * *
10666 CTCTAATAATTTGATAAGACTTAATTTGAG
65 CTCTAATAATTTGACAAGACTTAACTTGAA
* * * *
10696 ATTTAAATCTTTCAATAGTTTGATAAGATTGAAAATTTTATTTTATTATAAAAATTCATTAAGT-
1 ATTTAAATCTTTCAATAATTTGATAAGATTGAAAATTTTATTTT-TAATAAAAATTCACTAAATC
* * *
10760 TTTTCAATAATTTTG-CAAGATTTAACTTGAA
65 CTCT-AATAA-TTTGACAAGACTTAACTTGAA
* * * *
10791 ATTTAAATTTTTTAATAATTTGATAAAATTAAAAA
1 ATTTAAATCTTTCAATAATTTGATAAGATTGAAAA
10826 CAAAACTCTC
Statistics
Matches: 109, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
94 42 0.39
95 63 0.58
96 4 0.04
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.44
Consensus pattern (94 bp):
ATTTAAATCTTTCAATAATTTGATAAGATTGAAAATTTTATTTTTAATAAAAATTCACTAAATCC
TCTAATAATTTGACAAGACTTAACTTGAA
Found at i:12775 original size:22 final size:22
Alignment explanation
Indices: 12728--12769 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12718 AGGTTTTAAA
* *
12728 AGATTATGCCCAAAGATCTTAT
1 AGATCATGCCCAAAGAACTTAT
*
12750 AGATCATGCTCAAAGAACTT
1 AGATCATGCCCAAAGAACTT
12770 TGAGATTACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (22 bp):
AGATCATGCCCAAAGAACTTAT
Found at i:12946 original size:22 final size:22
Alignment explanation
Indices: 12921--12962 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12911 AAGACTTAAA
* * *
12921 AGATTATGCCTTGAGGTCTTAT
1 AGATCATGCCTAGAGATCTTAT
12943 AGATCATGCCTAGAGATCTT
1 AGATCATGCCTAGAGATCTT
12963 TAAGACTAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (22 bp):
AGATCATGCCTAGAGATCTTAT
Found at i:13375 original size:144 final size:142
Alignment explanation
Indices: 13212--13635 Score: 388
Period size: 144 Copynumber: 2.9 Consensus size: 142
13202 AAAAAGTGTA
* * *
13212 AAATCACAAAAATACCCTTTAAGAG-TATTCTAGTAATTTTACCTTCTCGAGGTTAATTTTTCAT
1 AAATCACAAAAA-AACCTTTAAGAGTTATTTTA-TAATTTTACCTTCCCGAGGTTAATTTTTCAT
* * * * *
13276 AAAAGGCTTCAAATCATGTTTTAATCTTATTTCGTAAATTTTAATGTATTAAAAACCATGATTGC
64 AAAA-GCTCCAAATCATGTTTTAATATTATTTCATGAATTTTAATGCATTAAAAACCATGATTGC
13341 ACCTTGAAAGGCTTG
128 ACCTTGAAAGGCTTG
* * * * * *
13356 AAATTATCAAAAAAACCTTTTAGAGGTTTTTTTATAATTTGACTTTCGCGAGGTTAGATTTTGT-
1 AAATCA-CAAAAAAACCTTTAAGA-GTTATTTTATAATTTTACCTTCCCGAGGTTA-ATTTT-TC
* * * ** *
13420 -GAAAAGCTCCAAATCATGTTTTCATATTATTTCATGATTTTTGGTGCATTAAAAA-CATTGATC
62 ATAAAAGCTCCAAATCATGTTTTAATATTATTTCATGAATTTTAATGCATTAAAAACCA-TGATT
** * *
13483 GCATGTTGGAAGGGTTG
126 GCACCTTGAAAGGCTTG
* ** * * * **
13500 AAATCACCAAAATGCCTTTTAAGGGTTATTTTCATAATTTTACCATCCCAAGGTCGATTTTTCAT
1 AAATCACAAAAAAACC-TTTAAGAGTTATTTT-ATAATTTTACCTTCCCGAGGTTAATTTTTCAT
* * * * *
13565 GAAAAGCTCCTAATCATATTTTGATATTATTTCATGAATTTTAATGCATTAAAAACCAAGAATGC
64 -AAAAGCTCCAAATCATGTTTTAATATTATTTCATGAATTTTAATGCATTAAAAACCATGATTGC
13630 ACCTTG
128 ACCTTG
13636 TCATAACTTC
Statistics
Matches: 219, Mismatches: 49, Indels: 23
0.75 0.17 0.08
Matches are distributed among these distances:
142 1 0.00
143 21 0.10
144 98 0.45
145 86 0.39
146 12 0.05
147 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (142 bp):
AAATCACAAAAAAACCTTTAAGAGTTATTTTATAATTTTACCTTCCCGAGGTTAATTTTTCATAA
AAGCTCCAAATCATGTTTTAATATTATTTCATGAATTTTAATGCATTAAAAACCATGATTGCACC
TTGAAAGGCTTG
Found at i:14177 original size:59 final size:59
Alignment explanation
Indices: 14104--14272 Score: 223
Period size: 62 Copynumber: 2.8 Consensus size: 59
14094 TGCTTTTGTA
*
14104 CAAGAAAAAATTGATACTTTCAACTTTT-CTCAAAAATATATTTTTTTGAAATTTTAATTT
1 CAAG-AAAAATTGATACTTTCAACTTTTCCTCAAAAATA-ATTTTTTTGAAAATTTAATTT
* * *
14164 CGAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAAAAAACTTTTTTTGAAAATTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTC--AAAAATAA-TTTTTTTGAAAATTTAATTT
* * *
14226 TAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATAGTTTTTTTG
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATAATTTTTTTG
14273 GATTTTATTT
Statistics
Matches: 96, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
59 31 0.32
60 12 0.12
61 1 0.01
62 52 0.54
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (59 bp):
CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATAATTTTTTTGAAAATTTAATTT
Found at i:14341 original size:46 final size:46
Alignment explanation
Indices: 14282--14377 Score: 117
Period size: 46 Copynumber: 2.1 Consensus size: 46
14272 GGATTTTATT
* * *
14282 TAAAGGAAATAAAATAATAA-AACAAAATGAAAGTGAAA-AT-AAAAA
1 TAAAGAAAATAAAATAAAAATAAAAAAAT-AAAGT-AAAGATAAAAAA
14327 TAAAGAAAAGTAAAATAAAAATAAAAAAATAAAGTAAAGATAAAAAA
1 TAAAGAAAA-TAAAATAAAAATAAAAAAATAAAGTAAAGATAAAAAA
14374 TAAA
1 TAAA
14378 AGAATATTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
45 11 0.25
46 17 0.39
47 16 0.36
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.16
Consensus pattern (46 bp):
TAAAGAAAATAAAATAAAAATAAAAAAATAAAGTAAAGATAAAAAA
Found at i:14359 original size:19 final size:19
Alignment explanation
Indices: 14317--14378 Score: 81
Period size: 21 Copynumber: 3.2 Consensus size: 19
14307 AATGAAAGTG
14317 AAAATAAAAATAAAGAAAAGT
1 AAAATAAAAATAAA-AAAA-T
14338 AAAATAAAAATAAAAAAAT
1 AAAATAAAAATAAAAAAAT
* *
14357 AAAGTAAAGAT-AAAAAAT
1 AAAATAAAAATAAAAAAAT
14375 AAAA
1 AAAA
14379 GAATATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
18 10 0.26
19 10 0.26
20 4 0.11
21 14 0.37
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (19 bp):
AAAATAAAAATAAAAAAAT
Found at i:14379 original size:19 final size:19
Alignment explanation
Indices: 14317--14379 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
14307 AATGAAAGTG
14317 AAAA-TAAAAATAAAGAAAAGT
1 AAAAGTAAAAAT-AA-AAAA-T
14338 AAAA-TAAAAATAAAAAA-
1 AAAAGTAAAAATAAAAAAT
*
14355 ATAAAGTAAAGATAAAAAAT
1 A-AAAGTAAAAATAAAAAAT
14375 AAAAG
1 AAAAG
14380 AATATTAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
17 1 0.03
18 3 0.08
19 20 0.53
20 3 0.08
21 11 0.29
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (19 bp):
AAAAGTAAAAATAAAAAAT
Found at i:14403 original size:3 final size:3
Alignment explanation
Indices: 14395--14421 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
14385 TAAACAAGTC
14395 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
14422 ATAAATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:14432 original size:18 final size:18
Alignment explanation
Indices: 14339--14432 Score: 54
Period size: 19 Copynumber: 5.3 Consensus size: 18
14329 AAGAAAAGTA
* *
14339 AAATAAAAATAAAAAAAT
1 AAATAATAATAAATAAAT
14357 AAAGTAA-AGATAAA-AAAT
1 AAA-TAATA-ATAAATAAAT
* * * *
14375 AAAAGAATATTAAACAAGT
1 -AAATAATAATAAATAAAT
*
14394 CTAATAATAAT-AAT-AAT
1 -AAATAATAATAAATAAAT
14411 -AATAATAATAAATAAAT
1 AAATAATAATAAATAAAT
14428 AAATA
1 AAATA
14433 TAAAAAAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
15 9 0.15
16 3 0.05
17 5 0.08
18 20 0.34
19 22 0.37
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.23
Consensus pattern (18 bp):
AAATAATAATAAATAAAT
Found at i:22523 original size:9 final size:9
Alignment explanation
Indices: 22498--22526 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
22488 ATTTAAATTT
22498 TAAATAAAA
1 TAAATAAAA
22507 TAAA-AAAA
1 TAAATAAAA
22515 TAAATAAAA
1 TAAATAAAA
22524 TAA
1 TAA
22527 TATTTTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
TAAATAAAA
Found at i:23625 original size:23 final size:23
Alignment explanation
Indices: 23599--23643 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
23589 TTCCTGTTTA
*
23599 AAAAGTAAACAATAGAAAACATG
1 AAAAGTAAACAAAAGAAAACATG
*
23622 AAAAGTAAATAAAAGAAAACAT
1 AAAAGTAAACAAAAGAAAACAT
23644 AATTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.69, C:0.07, G:0.11, T:0.13
Consensus pattern (23 bp):
AAAAGTAAACAAAAGAAAACATG
Found at i:24940 original size:7 final size:7
Alignment explanation
Indices: 24928--24969 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
24918 CCCCTCTCTC
24928 TTTTTAT
1 TTTTTAT
24935 TTTTTAT
1 TTTTTAT
24942 TTTTT-T
1 TTTTTAT
24948 ATTTTTAT
1 -TTTTTAT
*
24956 TTTATAT
1 TTTTTAT
*
24963 CTTTTAT
1 TTTTTAT
24970 GTGAGCAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 1 0.03
7 28 0.93
8 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTAT
Found at i:24952 original size:21 final size:21
Alignment explanation
Indices: 24928--24967 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
24918 CCCCTCTCTC
* *
24928 TTTTTATTTTTTATTTTTTTA
1 TTTTTATTTTATATCTTTTTA
24949 TTTTTATTTTATATCTTTT
1 TTTTTATTTTATATCTTTT
24968 ATGTGAGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTATTTTATATCTTTTTA
Found at i:25737 original size:17 final size:18
Alignment explanation
Indices: 25712--25752 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
25702 AAAGATAAAA
25712 ATAAA-ATATAAATA-AG
1 ATAAATATATAAATAGAG
*
25728 ATAAATATATATATAGAG
1 ATAAATATATAAATAGAG
*
25746 AAAAATA
1 ATAAATA
25753 CAATAAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 5 0.24
17 8 0.38
18 8 0.38
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (18 bp):
ATAAATATATAAATAGAG
Found at i:26509 original size:141 final size:140
Alignment explanation
Indices: 26146--26512 Score: 352
Period size: 141 Copynumber: 2.6 Consensus size: 140
26136 CAGAAAAAAG
* * *
26146 CCTGAAGGTTTTAAAAGATCATGCCTAAATGTCTTATACATCATAC-CCGAAGGACTTTGAGATT
1 CCTGAAGGTTTTAAAAGATCATGCCCAAA-GTCTTATAGATCATACTCAG-AGGACTTTGAGATT
* * *
26210 ATGCTTAAAGGTCTTATAAATCAAACTTTGAAAAAAAAACTCTTTTAAAACAAAAGCTTAACAAC
64 ATGCTTAGAGGTCTTAAAAATCAAACTTTG-AAAAAAAACTCTTTTAAAACAAAAGATTAACAAC
*
26275 TTTAGAAAAAGTT
128 TTTAGAAAAAGTA
* * * * * *
26288 CCT-AGAGATTTTAAAA-ATCCATGCTCAAAGGTTTTATAGATTATA-T-ATGGAGGACATAGAG
1 CCTGA-AGGTTTTAAAAGAT-CATGCCCAAA-GTCTTATAGATCATACTCA--GAGGACTTTGAG
* * * * * *
26349 ATTATGCTTGGAAGACTTAAAAGATCAAATTTTG-GAAAAAGCTCTTTTAAAAC-AAAGATTAAA
61 ATTATGCTTAGAGGTCTTAAAA-ATCAAACTTTGAAAAAAAACTCTTTTAAAACAAAAGATT-AA
*
26412 CAACTTTAGAAAAGGTA
124 CAACTTTAGAAAAAGTA
* * * *
26429 CTTGAAGGTTTTAAAAGATTATACCCAAAGATCTTATAGATCATACTCAGAGAACTTTGAGATTA
1 CCTGAAGGTTTTAAAAGATCATGCCCAAAG-TCTTATAGATCATACTCAGAGGACTTTGAGATTA
**
26494 TATTTAGAGGTCTTAAAAA
65 TGCTTAGAGGTCTTAAAAA
26513 ATTAAGTCTG
Statistics
Matches: 177, Mismatches: 36, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
140 8 0.05
141 94 0.53
142 63 0.36
143 12 0.07
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (140 bp):
CCTGAAGGTTTTAAAAGATCATGCCCAAAGTCTTATAGATCATACTCAGAGGACTTTGAGATTAT
GCTTAGAGGTCTTAAAAATCAAACTTTGAAAAAAAACTCTTTTAAAACAAAAGATTAACAACTTT
AGAAAAAGTA
Found at i:26729 original size:22 final size:22
Alignment explanation
Indices: 26704--26745 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
26694 AAGACTTAAA
* * *
26704 AGATTATGCCTTGAGGTCTTAT
1 AGATCATGCCTGGAGATCTTAT
26726 AGATCATGCCTGGAGATCTT
1 AGATCATGCCTGGAGATCTT
26746 TAAGACTATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (22 bp):
AGATCATGCCTGGAGATCTTAT
Found at i:27253 original size:143 final size:145
Alignment explanation
Indices: 26995--27417 Score: 371
Period size: 143 Copynumber: 2.9 Consensus size: 145
26985 AAAAAGTGTA
* * * * *
26995 AAATCA-CAAAAATACCCTTTAAGAG-TA-TTCTAGTAATTTTACCTTCTCAAGGTTA-ATTTTT
1 AAATCACCAAAAA-ACCTTTTAAGAGTTATTTCCA-TAATTTGACCATCACAAGG-TAGATTTTT
* * * * * *
27056 CAT-AAAAGGCTTCAAATCATGTTTTAATCTTATTTCGTAAATTTTAATGTATTAAAAACCATGA
63 CATGAAAA-GCTCCGAATCATGTTTTAATATTATTTCATGAATTTTAATGCATTAAAAACCATGA
27120 TTGCACCTTGAAAGGCTTG
127 TTGCACCTTGAAAGGCTTG
* * ** ** *
27139 AAATTATCAAAAAACCTTTT-AGAAGTT-TTTTTATAATTTGACTTTCACGAGGTTAGA-TTTT-
1 AAATCACCAAAAAACCTTTTAAG-AGTTATTTCCATAATTTGACCATCACAAGG-TAGATTTTTC
* * * **
27200 GTGAAAAGCTCCGAATCATGTTTTCATATTATTTCATGATTTTTGGTGCATTAAAAA-CATTGAT
64 ATGAAAAGCTCCGAATCATGTTTTAATATTATTTCATGAATTTTAATGCATTAAAAACCA-TGAT
* ** *
27264 CGCATGTTGAAAGGGTTG
128 TGCACCTTGAAAGGCTTG
** * * * *
27282 AAATCACCAAAATGCCTTTTAAGGGTTATTTCCATAATTTTACCATCCCAAGGTCGATTTTTCAT
1 AAATCACCAAAAAACCTTTTAAGAGTTATTTCCATAATTTGACCATCACAAGGTAGATTTTTCAT
* * * * *
27347 GAAAAGCTCCTAATCATATTTTGATATTATTTCATGAATTTTAATGCATTAAAAACCAAGAATGC
66 GAAAAGCTCCGAATCATGTTTTAATATTATTTCATGAATTTTAATGCATTAAAAACCATGATTGC
27412 ACCTTG
131 ACCTTG
27418 TCATAACTTC
Statistics
Matches: 220, Mismatches: 47, Indels: 23
0.76 0.16 0.08
Matches are distributed among these distances:
142 2 0.01
143 83 0.38
144 63 0.29
145 70 0.32
146 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (145 bp):
AAATCACCAAAAAACCTTTTAAGAGTTATTTCCATAATTTGACCATCACAAGGTAGATTTTTCAT
GAAAAGCTCCGAATCATGTTTTAATATTATTTCATGAATTTTAATGCATTAAAAACCATGATTGC
ACCTTGAAAGGCTTG
Found at i:27951 original size:59 final size:61
Alignment explanation
Indices: 27886--28047 Score: 251
Period size: 59 Copynumber: 2.7 Consensus size: 61
27876 TTGTACAAGA
*
27886 AAAAATTGATACTTTCAACTTTTT-CCAAAAATATATTTTTTTG-AAATTTTAATTTCGAG
1 AAAAATTGATACTTTCAACTTTTTCCCAAAAATATATTTTTTTGAAAACTTTAATTTCGAG
* *
27945 AAAAATTGATACTTTTAACTTTTTCCCCAAAA-ATA-TTTTTTGAAAACTTTAATTTCGAG
1 AAAAATTGATACTTTCAACTTTTTCCCAAAAATATATTTTTTTGAAAACTTTAATTTCGAG
* *
28004 GAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTTG
1 AAAAATTGATACTTTCAACTTTTTCCCAAAAATATATTTTTTTG
28048 GATTTTATTT
Statistics
Matches: 92, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
58 7 0.08
59 70 0.76
60 8 0.09
61 7 0.08
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (61 bp):
AAAAATTGATACTTTCAACTTTTTCCCAAAAATATATTTTTTTGAAAACTTTAATTTCGAG
Found at i:28112 original size:45 final size:46
Alignment explanation
Indices: 28063--28154 Score: 118
Period size: 45 Copynumber: 2.0 Consensus size: 46
28053 TATTTAAAGG
* *
28063 AAATAAAATAATAA-AACAAAATGAAAGTGAAA-AT-AAAATAAAGAA
1 AAATAAAATAAAAATAAAAAAAT-AAAGT-AAAGATAAAAATAAAGAA
28108 AAATAAAATAAAAATAAAAAAATAAAGTAAAGATAAAAAATAAAGAA
1 AAATAAAATAAAAATAAAAAAATAAAGTAAAGAT-AAAAATAAAGAA
28155 TATTAAACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
44 3 0.07
45 20 0.49
46 7 0.17
47 11 0.27
ACGTcount: A:0.76, C:0.01, G:0.08, T:0.15
Consensus pattern (46 bp):
AAATAAAATAAAAATAAAAAAATAAAGTAAAGATAAAAATAAAGAA
Found at i:28121 original size:6 final size:6
Alignment explanation
Indices: 28106--28217 Score: 52
Period size: 6 Copynumber: 18.0 Consensus size: 6
28096 TAAAATAAAG
*
28106 AAAAAT -AAAAT AAAAAT AAAAA- AATAAAGT AAAGAT AAAAAAT AAAGAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AA-AAA-T AAAAAT -AAAAAT AAA-AAT
* * * * * * *
28156 ATTAAAC AAAATCT AATAAT AATAAT AATAAAT AAATAA- ATAAAT AAATAT
1 A-AAAAT AAAA-AT AAAAAT AAAAAT AA-AAAT AAA-AAT AAAAAT AAAAAT
28207 AAAAA- AAAAAT
1 AAAAAT AAAAAT
28218 CTGGAATGGC
Statistics
Matches: 80, Mismatches: 14, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
5 14 0.17
6 39 0.49
7 24 0.30
8 3 0.04
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (6 bp):
AAAAAT
Found at i:28130 original size:19 final size:19
Alignment explanation
Indices: 28092--28151 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
28082 AATGAAAGTG
28092 AAAAT-AAAATAAAGAAAAAT
1 AAAATAAAAAT-AA-AAAAAT
28112 AAAATAAAAATAAAAAAAT
1 AAAATAAAAATAAAAAAAT
* *
28131 AAAGTAAAGAT-AAAAAAT
1 AAAATAAAAATAAAAAAAT
28149 AAA
1 AAA
28152 GAATATTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.27
19 15 0.41
20 7 0.19
21 5 0.14
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (19 bp):
AAAATAAAAATAAAAAAAT
Found at i:28156 original size:25 final size:22
Alignment explanation
Indices: 28092--28156 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 22
28082 AATGAAAGTG
28092 AAAAT-AAAATAAAGAA-AAAT
1 AAAATAAAAATAAAGAATAAAT
*
28112 AAAATAAAAATAAAAAAATAAAGT
1 AAAATAAAAAT-AAAGAATAAA-T
28136 AAAGATAAAAAATAAAGAATA
1 AAA-AT-AAAAATAAAGAATA
28157 TTAAACAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
20 5 0.14
21 5 0.14
22 5 0.14
23 3 0.08
24 4 0.11
25 9 0.24
26 6 0.16
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.15
Consensus pattern (22 bp):
AAAATAAAAATAAAGAATAAAT
Found at i:41298 original size:9 final size:9
Alignment explanation
Indices: 41273--41301 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
41263 ATTTAAATTT
41273 TAAATAAAA
1 TAAATAAAA
41282 TAAA-AAAA
1 TAAATAAAA
41290 TAAATAAAA
1 TAAATAAAA
41299 TAA
1 TAA
41302 TATTTTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
TAAATAAAA
Found at i:42403 original size:23 final size:23
Alignment explanation
Indices: 42377--42421 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
42367 TTCCTGTTTA
*
42377 AAAAGTAAACAATAGAAAACATG
1 AAAAGTAAACAAAAGAAAACATG
*
42400 AAAAGTAAATAAAAGAAAACAT
1 AAAAGTAAACAAAAGAAAACAT
42422 AATTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.69, C:0.07, G:0.11, T:0.13
Consensus pattern (23 bp):
AAAAGTAAACAAAAGAAAACATG
Found at i:43711 original size:7 final size:7
Alignment explanation
Indices: 43699--43733 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
43689 CCCCTCTCTC
43699 TTTTTAT
1 TTTTTAT
43706 TTTTTAT
1 TTTTTAT
43713 TTTTTAT
1 TTTTTAT
*
43720 TTTATAT
1 TTTTTAT
*
43727 CTTTTAT
1 TTTTTAT
43734 GTGAGCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTAT
Found at i:44411 original size:21 final size:19
Alignment explanation
Indices: 44368--44412 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
44358 GTTACTTTTT
*
44368 TAAAAAATAATTAGATAAT
1 TAAAAAATAATTAGATAAA
*
44387 TAAAAAATATTTAAAGATAAA
1 TAAAAAATAATT--AGATAAA
44408 TAAAA
1 TAAAA
44413 TTAAAGCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 11 0.50
21 11 0.50
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (19 bp):
TAAAAAATAATTAGATAAA
Done.