Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 133 of 133
Found at i:26242421 original size:4 final size:4
Alignment explanation
Indices: 26242412--26242455 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
26242402 AAATTATTTG
* * * *
26242412 TATA TATA TATA TATA TATA TATA TGTA TGTA TGTA TATC TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
26242456 AGTCACACAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (4 bp):
TATA
Found at i:26242423 original size:6 final size:6
Alignment explanation
Indices: 26242412--26242455 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
26242402 AAATTATTTG
* * * *
26242412 TATATA TATATA TATATA TATATA TGTATG TATGTA TATCTA TA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TA
26242456 AGTCACACAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (6 bp):
TATATA
Found at i:26248432 original size:16 final size:18
Alignment explanation
Indices: 26248411--26248445 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
26248401 CAATACAATG
26248411 ATAT-AAAAT-AAATATT
1 ATATAAAAATAAAATATT
26248427 ATATAAAAATAAAATATT
1 ATATAAAAATAAAATATT
26248445 A
1 A
26248446 AAGTGATACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 5 0.29
18 8 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATATAAAAATAAAATATT
Found at i:26250873 original size:2 final size:2
Alignment explanation
Indices: 26250866--26250891 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26250856 TAAAGTTTAA
26250866 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
26250892 ATTTATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:26251267 original size:21 final size:21
Alignment explanation
Indices: 26251238--26251283 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
26251228 AAATATTGAC
26251238 AAATCAATTACCCAAACTTTT
1 AAATCAATTACCCAAACTTTT
*
26251259 AAATTAATTACCCAAACTTTT
1 AAATCAATTACCCAAACTTTT
26251280 AAAT
1 AAAT
26251284 GGGTATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATCAATTACCCAAACTTTT
Found at i:26252835 original size:2 final size:2
Alignment explanation
Indices: 26252828--26252885 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
26252818 GTCATCAGCA
* *
26252828 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26252870 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
26252886 TTATTTATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26263670 original size:22 final size:24
Alignment explanation
Indices: 26263624--26263672 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
26263614 GTTCTTAACG
26263624 GTTTTAAGATCGCCAAACATAAATGA
1 GTTTTAAGATCG-C-AACATAAATGA
26263650 GTTTTAAGATCG-AA-ATAAATGA
1 GTTTTAAGATCGCAACATAAATGA
26263672 G
1 G
26263673 GGAGTTGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 9 0.39
23 2 0.09
26 12 0.52
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.29
Consensus pattern (24 bp):
GTTTTAAGATCGCAACATAAATGA
Found at i:26264452 original size:13 final size:14
Alignment explanation
Indices: 26264436--26264476 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
26264426 TTTAAGAATC
26264436 TAATTTATTATTA-
1 TAATTTATTATTAT
26264449 TAATTT-TTATTTAT
1 TAATTTATTA-TTAT
26264463 TAATCTTATTATTA
1 TAAT-TTATTATTA
26264477 ATGCGAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.12
13 9 0.38
14 4 0.17
15 5 0.21
16 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TAATTTATTATTAT
Found at i:26264844 original size:28 final size:27
Alignment explanation
Indices: 26264796--26264849 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
26264786 GGAGGTTTTA
26264796 GGGTTTTGGATTTAAAATTTGAGATTTG
1 GGGTTTTGGATTTAAAATTTG-GATTTG
*
26264824 GGGTTTT-GATTTAAAGGTTTGGATTT
1 GGGTTTTGGATTTAAA-ATTTGGATTT
26264850 TAGGGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (27 bp):
GGGTTTTGGATTTAAAATTTGGATTTG
Found at i:26264873 original size:15 final size:16
Alignment explanation
Indices: 26264841--26264879 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
26264831 GATTTAAAGG
26264841 TTTGGATTTTAGGGAT
1 TTTGGATTTTAGGGAT
*
26264857 TTTGGGTTTTA-GGA-
1 TTTGGATTTTAGGGAT
26264871 TTTGGATTT
1 TTTGGATTT
26264880 AAAGATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 8 0.38
15 3 0.14
16 10 0.48
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (16 bp):
TTTGGATTTTAGGGAT
Found at i:26265329 original size:16 final size:18
Alignment explanation
Indices: 26265305--26265358 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
26265295 AAAATTTATC
26265305 ATACAT-AAATAA-AAAA
1 ATACATAAAATAACAAAA
*
26265321 ATACTTAAAATAACAAAA
1 ATACATAAAATAACAAAA
26265339 ATA-ATAATATATAA-AAAA
1 ATACATAA-A-ATAACAAAA
26265357 AT
1 AT
26265359 TAAAAAATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 5 0.16
17 9 0.28
18 14 0.44
19 4 0.12
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (18 bp):
ATACATAAAATAACAAAA
Found at i:26267019 original size:13 final size:13
Alignment explanation
Indices: 26266997--26267036 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
26266987 ATAATCCTAT
26266997 TTATAATATTATA
1 TTATAATATTATA
* *
26267010 TTATATTATTTTA
1 TTATAATATTATA
*
26267023 TTATAATCTTATA
1 TTATAATATTATA
26267036 T
1 T
26267037 ATTAAGTATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATAATATTATA
Found at i:26267466 original size:18 final size:18
Alignment explanation
Indices: 26267443--26267503 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
26267433 CTAATTTTCA
26267443 TTAAAAAGCATCACAAAC
1 TTAAAAAGCATCACAAAC
* * *
26267461 TTAAAATTG-ATCAGAAAT
1 TTAAAA-AGCATCACAAAC
26267479 TAACTAAAAAGCATCACAAAC
1 T---TAAAAAGCATCACAAAC
26267500 TTAA
1 TTAA
26267504 GATTGATCAG
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
18 17 0.53
19 1 0.03
20 1 0.03
21 13 0.41
ACGTcount: A:0.54, C:0.16, G:0.07, T:0.23
Consensus pattern (18 bp):
TTAAAAAGCATCACAAAC
Found at i:26267492 original size:39 final size:39
Alignment explanation
Indices: 26267444--26267519 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
26267434 TAATTTTCAT
26267444 TAAAAAGCATCACAAACTTAAAATTGATCAGAAATTAAC
1 TAAAAAGCATCACAAACTTAAAATTGATCAGAAATTAAC
*
26267483 TAAAAAGCATCACAAACTTAAGATTGATCAGAAATTA
1 TAAAAAGCATCACAAACTTAAAATTGATCAGAAATTA
26267520 TCACATCATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.53, C:0.14, G:0.09, T:0.24
Consensus pattern (39 bp):
TAAAAAGCATCACAAACTTAAAATTGATCAGAAATTAAC
Found at i:26270943 original size:22 final size:21
Alignment explanation
Indices: 26270905--26270946 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
26270895 ATTATACATC
26270905 AAATAATATTTAAAAAATTTT
1 AAATAATATTTAAAAAATTTT
* *
26270926 AAATAAATTTTTATAAAATTT
1 AAAT-AATATTTAAAAAATTT
26270947 GAGCCATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATAATATTTAAAAAATTTT
Found at i:26271359 original size:27 final size:27
Alignment explanation
Indices: 26271328--26271392 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
26271318 TTACTGTTAA
26271328 ATTTAAATATAAA-TTTTAATTAAATTT
1 ATTTAAATATAAATTTTTAATT-AATTT
*
26271355 ATTT-AATATAAATTTTTTATTAATTT
1 ATTTAAATATAAATTTTTAATTAATTT
* *
26271381 TTTTAATTATAA
1 ATTTAAATATAA
26271393 TTACAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 16 0.48
27 17 0.52
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTTAAATATAAATTTTTAATTAATTT
Found at i:26271366 original size:15 final size:13
Alignment explanation
Indices: 26271341--26271394 Score: 65
Period size: 14 Copynumber: 4.0 Consensus size: 13
26271331 TAAATATAAA
26271341 TTTTAATTAAATT
1 TTTTAATTAAATT
26271354 TATTTAATATAAATT
1 T-TTTAAT-TAAATT
*
26271369 TTTT-ATTAATTT
1 TTTTAATTAAATT
26271381 TTTTAATTATAATT
1 TTTTAATTA-AATT
26271395 ACAATAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
12 9 0.26
13 7 0.20
14 12 0.34
15 7 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTAATTAAATT
Found at i:26271367 original size:26 final size:26
Alignment explanation
Indices: 26271328--26271392 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 26
26271318 TTACTGTTAA
26271328 ATTTAAATATAAA-TTTTAATTAAATTT
1 ATTT-AATATAAATTTTTAATT-AATTT
*
26271355 ATTTAATATAAATTTTTTATTAATTT
1 ATTTAATATAAATTTTTAATTAATTT
*
26271381 TTTTAATTATAA
1 ATTTAA-TATAA
26271393 TTACAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 18 0.53
27 16 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTAATATAAATTTTTAATTAATTT
Found at i:26271407 original size:24 final size:24
Alignment explanation
Indices: 26271375--26271437 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
26271365 AATTTTTTAT
*
26271375 TAATTTTTTTAATTATAATTACAA
1 TAATTTTTTTAATTATAACTACAA
* *
26271399 TAATTTTTTTAATGATAACTATAA
1 TAATTTTTTTAATTATAACTACAA
26271423 T-ATTTTTGTT-ATTAT
1 TAATTTTT-TTAATTAT
26271438 TTCAATTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 10 0.29
24 24 0.71
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (24 bp):
TAATTTTTTTAATTATAACTACAA
Found at i:26275222 original size:30 final size:30
Alignment explanation
Indices: 26275151--26275431 Score: 187
Period size: 30 Copynumber: 9.4 Consensus size: 30
26275141 GTTCTAAGAG
* * * **
26275151 TTTTAGGGTTTAAAGGGTTTTAGGGCTTGGA
1 TTTTAGGGTTTAGAGGG-TTTAAGGTTTTAA
* *
26275182 TTTTAAGGTTTAGAGGGTTTAAGGTTCTAA
1 TTTTAGGGTTTAGAGGGTTTAAGGTTTTAA
* * **
26275212 TTTTAGGGTTTAGAAGGTTT-AGATTTTGGC
1 TTTTAGGGTTTAGAGGGTTTAAGGTTTT-AA
* * *
26275242 TTTTAGGGTTTAAAGTGTTTAAGGTTTTAG
1 TTTTAGGGTTTAGAGGGTTTAAGGTTTTAA
* * *
26275272 TTTTAGGATTTAGGGGGTTTAAGGTTTTGA
1 TTTTAGGGTTTAGAGGGTTTAAGGTTTTAA
* * * * **
26275302 TTTTAAGGTTTAGAAGATTTAGGGTTTTGT
1 TTTTAGGGTTTAGAGGGTTTAAGGTTTTAA
* * * *
26275332 TTTTAAGGTTTAAAGGGTTTAGGGTTTTAG
1 TTTTAGGGTTTAGAGGGTTTAAGGTTTTAA
*
26275362 TTTTAGGGTTTTAG-GGGTTT-AGAGTTTCAA
1 TTTTAGGG-TTTAGAGGGTTTAAG-GTTTTAA
* * *
26275392 TTATAAGGTTT--TGGGTTTAAGG-TTTAGA
1 TTTTAGGGTTTAGAGGGTTTAAGGTTTTA-A
*
26275420 TTTTGGGGTTTA
1 TTTTAGGGTTTA
26275432 TGGTTTAGTT
Statistics
Matches: 194, Mismatches: 48, Indels: 18
0.75 0.18 0.07
Matches are distributed among these distances:
27 3 0.02
28 16 0.08
29 11 0.06
30 139 0.72
31 25 0.13
ACGTcount: A:0.22, C:0.01, G:0.30, T:0.47
Consensus pattern (30 bp):
TTTTAGGGTTTAGAGGGTTTAAGGTTTTAA
Found at i:26275228 original size:23 final size:21
Alignment explanation
Indices: 26275195--26275313 Score: 64
Period size: 23 Copynumber: 5.4 Consensus size: 21
26275185 TAAGGTTTAG
26275195 AGGGTTTAAGGTTCTA-ATTTT
1 AGGGTTTAAGGTT-TAGATTTT
26275216 AGGGTTTAGAAGGTTTAGATTTT
1 AGGGTTT--AAGGTTTAGATTTT
* * *
26275239 -GGCTTTTAGGGTTTAAAGTGTTT
1 AGG-GTTTAAGGTTTAGA-T-TTT
* * *
26275262 AAGGTTTTAGTTTTAGGA-TTT
1 AGGGTTTAAGGTTTA-GATTTT
*
26275283 AGGGGGTTTAAGGTTTTGATTTT
1 A--GGGTTTAAGGTTTAGATTTT
*
26275306 AAGGTTTA
1 AGGGTTTA
26275314 GAAGATTTAG
Statistics
Matches: 73, Mismatches: 14, Indels: 22
0.67 0.13 0.20
Matches are distributed among these distances:
21 25 0.34
22 7 0.10
23 39 0.53
24 2 0.03
ACGTcount: A:0.23, C:0.02, G:0.29, T:0.47
Consensus pattern (21 bp):
AGGGTTTAAGGTTTAGATTTT
Found at i:26275252 original size:60 final size:60
Alignment explanation
Indices: 26275114--26275382 Score: 210
Period size: 60 Copynumber: 4.5 Consensus size: 60
26275104 AAGTTTGAGA
* *
26275114 TTTTGGATTGTAAGGTTT-TA-GGTTTAA-GTTCTAAGAGTTTTAGGGTTTAAAGGGTTTTAGG
1 TTTTGGATTTTAAGGTTTAGAGGGTTTAAGGTTCT-A-A-TTTTAGGGTTTAAAGGG-TTTAGG
** *
26275175 GCTTGGATTTTAAGGTTTAGAGGGTTTAAGGTTCTAATTTTAGGGTTTAGAA-GGTTTAGA
1 TTTTGGATTTTAAGGTTTAGAGGGTTTAAGGTTCTAATTTTAGGGTTTA-AAGGGTTTAGG
* * * * * * * **
26275235 TTTTGGCTTTTAGGGTTTAAAGTGTTTAAGGTTTTAGTTTTAGGATTTAGGGGGTTTAAGG
1 TTTTGGATTTTAAGGTTTAGAGGGTTTAAGGTTCTAATTTTAGGGTTTAAAGGGTTT-AGG
* * * * ** *
26275296 TTTT-GATTTTAAGGTTTAGAAGATTTAGGGTTTTGTTTTTAAGGTTTAAAGGGTTTAGGG
1 TTTTGGATTTTAAGGTTTAGAGGGTTTAAGGTTCTAATTTTAGGGTTTAAAGGGTTTA-GG
* *
26275356 TTTTAG-TTTTAGGGTTTTAG-GGGTTTA
1 TTTTGGATTTTAAGG-TTTAGAGGGTTTA
26275383 GAGTTTCAAT
Statistics
Matches: 166, Mismatches: 33, Indels: 19
0.76 0.15 0.09
Matches are distributed among these distances:
59 1 0.01
60 107 0.64
61 41 0.25
62 4 0.02
63 8 0.05
64 5 0.03
ACGTcount: A:0.22, C:0.01, G:0.30, T:0.47
Consensus pattern (60 bp):
TTTTGGATTTTAAGGTTTAGAGGGTTTAAGGTTCTAATTTTAGGGTTTAAAGGGTTTAGG
Found at i:26275290 original size:90 final size:89
Alignment explanation
Indices: 26275151--26275402 Score: 276
Period size: 90 Copynumber: 2.8 Consensus size: 89
26275141 GTTCTAAGAG
* ** * *
26275151 TTTTAGGGTTTAAAGGGTTTTAGGGCTTGGATTTTAAGGTTTAGAGGGTTTAAGGTTCTAATTTT
1 TTTTAGGGTTTAAAGGGTTTAAGGTTTTAG-TTTT-AGGTTTAGGGGGTTTAAGGTTCTAATTTT
* *
26275216 AGGGTTTAGAAGGTTTA-GATTTTGGC
64 AAGGTTTAGAAGATTTAGGATTTT-GC
* * *
26275242 TTTTAGGGTTTAAAGTGTTTAAGGTTTTAGTTTTAGGATTTAGGGGGTTTAAGGTTTTGATTTTA
1 TTTTAGGGTTTAAAGGGTTTAAGGTTTTAGTTTTAGG-TTTAGGGGGTTTAAGGTTCTAATTTTA
* *
26275307 AGGTTTAGAAGATTTAGGGTTTTGT
65 AGGTTTAGAAGATTTAGGATTTTGC
* * * *
26275332 TTTTAAGGTTTAAAGGGTTTAGGGTTTTAGTTTTAGGGTTTTA-GGGGTTTAGAGTTTC-AATTA
1 TTTTAGGGTTTAAAGGGTTTAAGGTTTTAGTTTTA-GG-TTTAGGGGGTTTA-AGGTTCTAATTT
26275395 TAAGGTTT
63 TAAGGTTT
26275403 TGGGTTTAAG
Statistics
Matches: 137, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
89 3 0.02
90 94 0.69
91 40 0.29
ACGTcount: A:0.22, C:0.02, G:0.29, T:0.47
Consensus pattern (89 bp):
TTTTAGGGTTTAAAGGGTTTAAGGTTTTAGTTTTAGGTTTAGGGGGTTTAAGGTTCTAATTTTAA
GGTTTAGAAGATTTAGGATTTTGC
Found at i:26275308 original size:14 final size:14
Alignment explanation
Indices: 26275289--26275342 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
26275279 ATTTAGGGGG
26275289 TTTAAGGTTTTGAT
1 TTTAAGGTTTTGAT
* *
26275303 TTTAAGGTTTAGAAGA
1 TTTAAGGTTTTG-A-T
* *
26275319 TTTAGGGTTTTGTT
1 TTTAAGGTTTTGAT
26275333 TTTAAGGTTT
1 TTTAAGGTTT
26275343 AAAGGGTTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
14 20 0.65
15 1 0.03
16 10 0.32
ACGTcount: A:0.22, C:0.00, G:0.24, T:0.54
Consensus pattern (14 bp):
TTTAAGGTTTTGAT
Found at i:26275368 original size:14 final size:14
Alignment explanation
Indices: 26275349--26275375 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
26275339 GTTTAAAGGG
26275349 TTTAGGGTTTTAGT
1 TTTAGGGTTTTAGT
26275363 TTTAGGGTTTTAG
1 TTTAGGGTTTTAG
26275376 GGGTTTAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.56
Consensus pattern (14 bp):
TTTAGGGTTTTAGT
Found at i:26275381 original size:9 final size:8
Alignment explanation
Indices: 26275319--26275388 Score: 51
Period size: 8 Copynumber: 9.2 Consensus size: 8
26275309 GTTTAGAAGA
26275319 TTTAGGGT
1 TTTAGGGT
*
26275327 TTT--GTT
1 TTTAGGGT
*
26275333 TTTAAGGT
1 TTTAGGGT
*
26275341 TTAAAGGG-
1 TT-TAGGGT
26275349 TTTAGGGT
1 TTTAGGGT
26275357 TTTA--GT
1 TTTAGGGT
26275363 TTTAGGGT
1 TTTAGGGT
*
26275371 TTTAGGGG
1 TTTAGGGT
*
26275379 TTTAGAGT
1 TTTAGGGT
26275387 TT
1 TT
26275389 CAATTATAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
6 11 0.23
7 4 0.08
8 30 0.62
9 3 0.06
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.51
Consensus pattern (8 bp):
TTTAGGGT
Found at i:26275428 original size:21 final size:19
Alignment explanation
Indices: 26275399--26275443 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
26275389 CAATTATAAG
26275399 GTTTTGGGTTTAAGGTTTA
1 GTTTTGGGTTTAAGGTTTA
*
26275418 GATTTTGGGGTTTATGGTTTA
1 G-TTTT-GGGTTTAAGGTTTA
26275439 GTTTT
1 GTTTT
26275444 AGGATTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 8 0.35
21 14 0.61
ACGTcount: A:0.13, C:0.00, G:0.31, T:0.56
Consensus pattern (19 bp):
GTTTTGGGTTTAAGGTTTA
Found at i:26275864 original size:3 final size:3
Alignment explanation
Indices: 26275856--26275904 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
26275846 AAAATAAGCT
* * * *
26275856 TTA TTA TTA ATA TTA TTA TCA TTA TTA TTG TTA TTA TTAA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
26275902 TTA
1 TTA
26275905 GTGTAAAACA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
3 35 0.95
4 2 0.05
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:26277205 original size:207 final size:207
Alignment explanation
Indices: 26276992--26277369 Score: 507
Period size: 207 Copynumber: 1.8 Consensus size: 207
26276982 TTTGGAGAGA
* * *
26276992 AAAAAAAAAGAATTTTCATCGTATTG-AAGTTTTTTTATAAATATTCCAATACACTGGTAATATT
1 AAAAAAAAA-AATTTTCATCATATTGAAAG-TTTTTTATAAATACTCCAATACACTGGTAATATG
* * * *
26277056 TAAAA-AAA-TCTTCTCACCTAGAGATTTCT-TAAAACATCTCTACTCGAAATACTTTTTGAATC
64 TAAAATAAATTCTTCTCACCTAGAGATTT-TGT-AAACATCACTACTCAAAATAC-CTTTAAATC
*
26277118 TCATCATTAGAT-AAATTTTCTTTTTTTCTCA-TTTTTATTACTTATTTTTATTATATTAATCAA
126 TCATCATTAGATAAAATTTTCTTTTCTT-TCATTTTTTATTACTTATTTTTATTATATTAATCAA
26277181 TTTTTATTTATTACTAAC
190 TTTTTATTTATTACTAAC
* * *
26277199 AAAAAAAAAAATTTTTATTATATTGAAAAGTTTTTTATAAATACTCCAATACACTGGTAGTATGT
1 AAAAAAAAAAATTTTCATCATATTG-AAAGTTTTTTATAAATACTCCAATACACTGGTAATATGT
** *
26277264 AAAATAAATTCTTCTCACCTAGAGATTTTGTAGGCATCACTATTCAAAATACCTTTAAATCTCAT
65 AAAATAAATTCTTCTCACCTAGAGATTTTGTAAACATCACTACTCAAAATACCTTTAAATCTCAT
*
26277329 CATTGGATAAAAATTTTCTTTTCTTTCATTTTTTATTACTT
130 CATTAGAT-AAAATTTTCTTTTCTTTCATTTTTTATTACTT
26277370 TAGTATTATT
Statistics
Matches: 148, Mismatches: 15, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
206 13 0.09
207 63 0.43
208 26 0.18
209 46 0.31
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.44
Consensus pattern (207 bp):
AAAAAAAAAAATTTTCATCATATTGAAAGTTTTTTATAAATACTCCAATACACTGGTAATATGTA
AAATAAATTCTTCTCACCTAGAGATTTTGTAAACATCACTACTCAAAATACCTTTAAATCTCATC
ATTAGATAAAATTTTCTTTTCTTTCATTTTTTATTACTTATTTTTATTATATTAATCAATTTTTA
TTTATTACTAAC
Found at i:26278155 original size:19 final size:20
Alignment explanation
Indices: 26278119--26278157 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
26278109 TGAGAAATTT
**
26278119 TTTTTTTTTGTATTCTGACC
1 TTTTTTTTTGTAAACTGACC
26278139 TTTTTTTTT-TAAACTGACC
1 TTTTTTTTTGTAAACTGACC
26278158 CCCCTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (20 bp):
TTTTTTTTTGTAAACTGACC
Found at i:26278552 original size:23 final size:22
Alignment explanation
Indices: 26278516--26278578 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
26278506 ATCGGATAAG
26278516 GAAGAAGAAGAAGAAAAAAAAAA
1 GAAGAA-AAGAAGAAAAAAAAAA
26278539 CG-AGAAAAGAAAGAAAAAAAAAA
1 -GAAGAAAAG-AAGAAAAAAAAAA
*
26278562 GAAGAGAAGAAGAAAAA
1 GAAGAAAAGAAGAAAAA
26278579 CACAGAAAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
22 12 0.33
23 23 0.64
24 1 0.03
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (22 bp):
GAAGAAAAGAAGAAAAAAAAAA
Found at i:26278578 original size:40 final size:42
Alignment explanation
Indices: 26278520--26278599 Score: 103
Period size: 40 Copynumber: 1.9 Consensus size: 42
26278510 GATAAGGAAG
*
26278520 AAGAAGAAGAAAAAAAAAAC-GAGAAAA-GAAAGAAAAAAAA
1 AAGAAGAAGAAAAAAAAAACACAGAAAACGAAAGAAAAAAAA
*
26278560 AAGAAG-AGAAGAAGAAAAACACAGAAAACGGAAAGAAAAA
1 AAGAAGAAGAA-AAAAAAAACACAGAAAAC-GAAAGAAAAA
26278600 TAATTAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 4 0.12
40 14 0.41
41 6 0.18
43 10 0.29
ACGTcount: A:0.75, C:0.05, G:0.20, T:0.00
Consensus pattern (42 bp):
AAGAAGAAGAAAAAAAAAACACAGAAAACGAAAGAAAAAAAA
Found at i:26278578 original size:43 final size:42
Alignment explanation
Indices: 26278517--26278599 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 42
26278507 TCGGATAAGG
26278517 AAGAAGAAGAAGAAAAAAAAAACGAGAAAA-GAAAGAAAAAAAA
1 AAGAAGAAGAAG-AAAAAAAAAC-AGAAAACGAAAGAAAAAAAA
*
26278560 AAGAAG-AGAAGAAGAAAAACACAGAAAACGGAAAGAAAAA
1 AAGAAGAAGAAGAA-AAAAAAACAGAAAAC-GAAAGAAAAA
26278600 TAATTAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
41 8 0.22
42 12 0.33
43 16 0.44
ACGTcount: A:0.75, C:0.05, G:0.20, T:0.00
Consensus pattern (42 bp):
AAGAAGAAGAAGAAAAAAAAACAGAAAACGAAAGAAAAAAAA
Found at i:26278621 original size:6 final size:6
Alignment explanation
Indices: 26278595--26278638 Score: 52
Period size: 6 Copynumber: 6.8 Consensus size: 6
26278585 AAACGGAAAG
*
26278595 AAAAAT AATTAAAT AAATAAT AATAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AA--AAAT AAA-AAT AAAAAT AAAAAT AAAAAT AAAAA
26278639 AATGGTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 22 0.67
7 5 0.15
8 6 0.18
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (6 bp):
AAAAAT
Found at i:26278925 original size:48 final size:47
Alignment explanation
Indices: 26278815--26279187 Score: 448
Period size: 46 Copynumber: 7.9 Consensus size: 47
26278805 TTGAAAGTTT
* * * *
26278815 AAAAAGCTTCTCTTAGTAGAAGCTCAACAACTTTAAAATT-TTATTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATTG
* * *
26278861 AAAAAGCTCCTTTCAGCAGAGGCTTAACAATTTTAAAATTCTTATATG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTAT-TG
* *
26278909 AAAAAGCTCCTCTCAGCAGAAGCTCAACAACTTTAAAAATCTTATATCTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTC-T-TA--TTG
* * *
26278960 AAAAGGGCTCCTCTCAGTAGAGGCTCAACAACTTTAAAATTCTCATCTG
1 AAAA-AGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTAT-TG
* * *
26279009 GAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATC-TCTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATTG
* * * *
26279055 AAAAAGCTTCTCTCAGTAGAGGCTCAATAACTTTAAAA-TCTCATCTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTAT-TG
* * *
26279102 GAAAAGCTCCTCTCAGCAGAGGCACAATAACTTTAAAATTCTT-TTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATTG
26279148 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATT
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATT
26279188 TTCATATGTT
Statistics
Matches: 279, Mismatches: 37, Indels: 22
0.83 0.11 0.07
Matches are distributed among these distances:
45 2 0.01
46 109 0.39
47 42 0.15
48 76 0.27
49 6 0.02
50 3 0.01
51 7 0.03
52 34 0.12
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (47 bp):
AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTTATTG
Found at i:26279134 original size:93 final size:94
Alignment explanation
Indices: 26278816--26279192 Score: 477
Period size: 93 Copynumber: 4.0 Consensus size: 94
26278806 TGAAAGTTTA
* * * * * * *
26278816 AAAAGCTTCTCTTAGTAGAAGCTCAACAACTTTAAAATTTTATTGAAAAAGCTCCTTTCAGCAGA
1 AAAAGCTCCTCTCAGCAGAAGCTCAACAACTTTAAAAATCTCTTGAAAAAGCTCCTCTCAGCAGA
* * * * *
26278881 GGCTTAACAATTTTAAAATTCTTATATGA
66 GGCTCAACAACTTTAAAATTCTCATCTGG
*
26278910 AAAAGCTCCTCTCAGCAGAAGCTCAACAACTTTAAAAATCTTATATCTTGAAAAGGGCTCCTCTC
1 AAAAGCTCCTCTCAGCAGAAGCTCAACAACTTTAAAAATC-----TCTTGAAAA-AGCTCCTCTC
*
26278975 AGTAGAGGCTCAACAACTTTAAAATTCTCATCTGG
60 AGCAGAGGCTCAACAACTTTAAAATTCTCATCTGG
* * *
26279010 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCTTGAAAAAGCTTCTCTCAGTAGA
1 AAAAGCTCCTCTCAGCAGAAGCTCAACAACTTTAAAAATCTCTTGAAAAAGCTCCTCTCAGCAGA
*
26279075 GGCTCAATAACTTTAAAA-TCTCATCTGG
66 GGCTCAACAACTTTAAAATTCTCATCTGG
* * * * *
26279103 AAAAGCTCCTCTCAGCAGAGGCACAATAACTTTAAAATTCTTTTGAAAAAGCTCCTCTCAGCAGA
1 AAAAGCTCCTCTCAGCAGAAGCTCAACAACTTTAAAAATCTCTTGAAAAAGCTCCTCTCAGCAGA
*
26279168 GGCTCAACAACTTTAAAATTTTCAT
66 GGCTCAACAACTTTAAAATTCTCAT
26279193 ATGTTTTCAA
Statistics
Matches: 250, Mismatches: 26, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
93 86 0.34
94 71 0.28
95 9 0.04
99 8 0.03
100 76 0.30
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (94 bp):
AAAAGCTCCTCTCAGCAGAAGCTCAACAACTTTAAAAATCTCTTGAAAAAGCTCCTCTCAGCAGA
GGCTCAACAACTTTAAAATTCTCATCTGG
Done.