Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168163.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_402, 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: 28634
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:734 original size:19 final size:20
Alignment explanation
Indices: 712--752 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
702 TATATTTTCT
* *
712 TTTCTTTTGT-TTTTTTTTA
1 TTTCATTTGTATTTTTATTA
731 TTTCATTTGTATTTTTATTA
1 TTTCATTTGTATTTTTATTA
751 TT
1 TT
753 AGTTTGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTCATTTGTATTTTTATTA
Found at i:9245 original size:49 final size:49
Alignment explanation
Indices: 9164--9257 Score: 154
Period size: 49 Copynumber: 1.9 Consensus size: 49
9154 ACTTACAAAT
*
9164 ATAACAATCATTATAGTTATGTGAACACTCTCAATCTTTTCTAATAAAC
1 ATAACAATCATCATAGTTATGTGAACACTCTCAATCTTTTCTAATAAAC
*
9213 ATAATAATCATCATAGTTATGTGAAC-CATCTCAATCTTTTCTAAT
1 ATAACAATCATCATAGTTATGTGAACAC-TCTCAATCTTTTCTAAT
9258 TTTATAAGGT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
48 1 0.02
49 41 0.98
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.38
Consensus pattern (49 bp):
ATAACAATCATCATAGTTATGTGAACACTCTCAATCTTTTCTAATAAAC
Found at i:9949 original size:24 final size:24
Alignment explanation
Indices: 9917--9967 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
9907 CATTAAATTC
* * *
9917 ATTAATTGACCTCGCATGGAAGGG
1 ATTAATTGACCTAGAATGGAACGG
9941 ATTAATTGACCTAGAATGGAACGG
1 ATTAATTGACCTAGAATGGAACGG
9965 ATT
1 ATT
9968 GAGCCATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (24 bp):
ATTAATTGACCTAGAATGGAACGG
Found at i:12287 original size:72 final size:72
Alignment explanation
Indices: 12161--12315 Score: 213
Period size: 72 Copynumber: 2.2 Consensus size: 72
12151 AAACTTGCCT
* * *
12161 ATTTGAGAAGGGATCTTCCCCTCTAAATTATTGCTGCTTAGATCCAACAGCCGCAAATTTAAGCA
1 ATTTGAGAAGGGATCTACCCCTCTAAATTATTGCTGCTTAGATACAACACCCGCAAATTTAAGCA
12226 ACTCCCA
66 ACTCCCA
* * * * *
12233 ATTTGAGGAGGGATGTACCCCTTTAAATTATTGTTGCTTAGGTACAATC-CCCGCAAATTTAAGC
1 ATTTGAGAAGGGATCTACCCCTCTAAATTATTGCTGCTTAGATACAA-CACCCGCAAATTTAAGC
12297 AACTCCCA
65 AACTCCCA
*
12305 ATTTGTGAAGG
1 ATTTGAGAAGG
12316 TATAGAACCA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
72 71 0.99
73 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (72 bp):
ATTTGAGAAGGGATCTACCCCTCTAAATTATTGCTGCTTAGATACAACACCCGCAAATTTAAGCA
ACTCCCA
Found at i:12672 original size:144 final size:144
Alignment explanation
Indices: 12367--13045 Score: 1018
Period size: 144 Copynumber: 4.7 Consensus size: 144
12357 ATAGTGCTTC
* * *
12367 TAAATTCCCAATTTCTTTTGGTATAGGACCTCCTAGAAGATTTGAATAAAGGAACAGATATTGCA
1 TAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAGATATTGCA
* *
12432 ATTTTGATAAATTGCAATTCCCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAGACAGG
66 ATTTTGATAAATT---A---CCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAAAGAGG
*
12497 GATAATTGAGTTACTGCATT
125 GATAATTGAGTTAATGCATT
* * *
12517 TAAATTTCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCGAGGGACAGATATTGTA
1 TAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAGATATTGCA
* *
12582 ATCTTGATAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCTAAAGAGGGATAAT
66 ATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAAAGAGGGATAAT
*
12647 TGACTTAATGCATT
131 TGAGTTAATGCATT
* *
12661 TAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAAATCTTGCA
1 TAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAGATATTGCA
*
12726 ATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACTTAATTTGTTTCCAAAGAGGGATAAT
66 ATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAAAGAGGGATAAT
*
12791 TGAGTTAGTGCATT
131 TGAGTTAATGCATT
* *
12805 TAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAAATCTTGCA
1 TAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAGATATTGCA
** * *
12870 ATTTTGATAAATTAATAATAGAAGAAGGGATTAAACCATTCAATTTGTTTCCAAAGAGGGATAAT
66 ATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAAAGAGGGATAAT
* *
12935 TGAGTTATTGTATT
131 TGAGTTAATGCATT
* * * *
12949 TAAATTCCCAAGTGCTTTTGGTATAGGACCTTCTAGAATATTTGAATCAAGTGGACAGAAATTGC
1 TAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAG-GGACAGATATTGC
*
13014 AATTTGTGA-AAATTAGCAATAGAAGAAGGGAT
65 AATTT-TGATAAATTACCAATAGAAGAAGGGAT
13046 AAGCCGTGAG
Statistics
Matches: 490, Mismatches: 37, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
144 379 0.77
145 36 0.07
146 3 0.01
147 1 0.00
150 71 0.14
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (144 bp):
TAAATTCCCAATTTCTTTTGGTATAGGACCTTCTAGAAGATTTGAATCAAGGGACAGATATTGCA
ATTTTGATAAATTACCAATAGAAGAAGGGATTGAACCACTCAATTTGTTTCCAAAGAGGGATAAT
TGAGTTAATGCATT
Found at i:17201 original size:18 final size:18
Alignment explanation
Indices: 17180--17222 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
17170 TTTCTCATTT
17180 TTTATTACTT-ATTCTTAA
1 TTTATTACTTAATT-TTAA
* *
17198 TTTATTAGTTAATTTTTA
1 TTTATTACTTAATTTTAA
17216 TTTATTA
1 TTTATTA
17223 TTTTATAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTACTTAATTTTAA
Found at i:17399 original size:27 final size:27
Alignment explanation
Indices: 17369--17471 Score: 100
Period size: 27 Copynumber: 3.8 Consensus size: 27
17359 CTTTTATTTT
*
17369 TATTTTTATTATTTGTCTATTTATTAA
1 TATTTTTATTATTTATCTATTTATTAA
* * * *
17396 TATTTTTTTTATTTTTTTATCTATTAA
1 TATTTTTATTATTTATCTATTTATTAA
* ** *
17423 TATTTATATTATTTATCTGCTT-TTAT
1 TATTTTTATTATTTATCTATTTATTAA
*
17449 TTTTTATTATTATTTATCTATTT
1 TATTT-TTATTATTTATCTATTT
17472 CTTTTATTTA
Statistics
Matches: 59, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
26 7 0.12
27 52 0.88
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (27 bp):
TATTTTTATTATTTATCTATTTATTAA
Found at i:17476 original size:24 final size:23
Alignment explanation
Indices: 17396--17479 Score: 66
Period size: 23 Copynumber: 3.6 Consensus size: 23
17386 TATTTATTAA
17396 TATTTTTTTTATT-TT-TTTATC
1 TATTTTTTTTATTATTATTTATC
* *
17417 TATTAATATTTA-TATTATTTATCTGC
1 TATT-TTTTTTATTATTATTTA--T-C
*
17443 TTTTATTTTTTATTATTATTTATC
1 TATT-TTTTTTATTATTATTTATC
*
17467 TATTTCTTTTATT
1 TATTTTTTTTATT
17480 TATCTAATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
21 5 0.10
22 7 0.14
23 12 0.24
24 4 0.08
25 2 0.04
26 10 0.20
27 9 0.18
ACGTcount: A:0.21, C:0.06, G:0.01, T:0.71
Consensus pattern (23 bp):
TATTTTTTTTATTATTATTTATC
Found at i:17481 original size:27 final size:28
Alignment explanation
Indices: 17423--17492 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 28
17413 TATCTATTAA
*
17423 TATTTA-TATTATTTATCTGCTTTTATT
1 TATTTATTATTATTTATCTGATTTTATT
17450 T-TTTATTATTATTTATCT-ATTTCT-TT
1 TATTTATTATTATTTATCTGATTT-TATT
17476 TATTTATCTAATTATTT
1 TATTTAT-T-ATTATTT
17493 TTTTGTTATC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
26 10 0.27
27 19 0.51
28 1 0.03
29 7 0.19
ACGTcount: A:0.23, C:0.07, G:0.01, T:0.69
Consensus pattern (28 bp):
TATTTATTATTATTTATCTGATTTTATT
Found at i:17493 original size:17 final size:17
Alignment explanation
Indices: 17452--17493 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
17442 CTTTTATTTT
*
17452 TTATTATTATTTATCTAT
1 TTATT-TTATTTATCTAA
*
17470 TTCTTTTATTTATCTAA
1 TTATTTTATTTATCTAA
17487 TTATTTT
1 TTATTTT
17494 TTTGTTATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTTTATTTATCTAA
Found at i:17515 original size:44 final size:43
Alignment explanation
Indices: 17407--17525 Score: 111
Period size: 44 Copynumber: 2.8 Consensus size: 43
17397 ATTTTTTTTA
** *
17407 TTTTTTTATCTATTA-ATATTTATATTATTTATCTGCTTTTAT
1 TTTTTTTATCTATTATATATTTATATTATTTATCTAATTATAT
* * *
17449 TTTTTATTAT-TATTTATCTATTTCTTTTATTTATCTAATTAT-T
1 TTTTT-TTATCTA-TTATATATTTATATTATTTATCTAATTATAT
*
17492 TTTTTGTTATCTATTAATATATTTATCTT-TTTAT
1 TTTTT-TTATCTATT-ATATATTTATATTATTTAT
17526 TTTGATTAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
42 7 0.11
43 24 0.39
44 31 0.50
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.68
Consensus pattern (43 bp):
TTTTTTTATCTATTATATATTTATATTATTTATCTAATTATAT
Found at i:18084 original size:16 final size:16
Alignment explanation
Indices: 18054--18090 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
18044 TTTGGGTTTT
18054 AGAGAGAAGGGAGAGA
1 AGAGAGAAGGGAGAGA
18070 AGAG-GAAGGGA-AG-
1 AGAGAGAAGGGAGAGA
18083 AGAGAGAA
1 AGAGAGAA
18091 AGAGGGAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.20
14 5 0.25
15 7 0.35
16 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (16 bp):
AGAGAGAAGGGAGAGA
Found at i:18087 original size:20 final size:22
Alignment explanation
Indices: 18059--18100 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
18049 GTTTTAGAGA
*
18059 GAAGGGAGAG-AAGA-GGAAGG
1 GAAGAGAGAGAAAGAGGGAAGG
18079 GAAGAGAGAGAAAGAGGGAAGG
1 GAAGAGAGAGAAAGAGGGAAGG
18101 AGGGTTCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 4 0.21
22 6 0.32
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (22 bp):
GAAGAGAGAGAAAGAGGGAAGG
Found at i:18338 original size:3 final size:3
Alignment explanation
Indices: 18330--18362 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
18320 ATTTATTTAT
18330 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18363 GAATTGTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18390 original size:5 final size:5
Alignment explanation
Indices: 18376--18433 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
18366 TTGTTTAATA
* *
18376 TTTAT CTTAT TTTATT TTTAT TTATTT TTTAT TTTCAT TTTCAT TTTAT
1 TTTAT TTTAT TTTA-T TTTAT TT-TAT TTTAT TTT-AT TTT-AT TTTAT
18425 TTTAT TTTA
1 TTTAT TTTA
18434 GTACTTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
5 26 0.57
6 20 0.43
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:18422 original size:17 final size:15
Alignment explanation
Indices: 18376--18433 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 15
18366 TTGTTTAATA
*
18376 TTTATCTTATTTTATT
1 TTTATTTTATTTTA-T
*
18392 TTTATTTATTTTTTAT
1 TTTATTT-TATTTTAT
18408 TTTCATTTTCATTTTAT
1 TTT-ATTTT-ATTTTAT
18425 TTTATTTTA
1 TTTATTTTA
18434 GTACTTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
15 1 0.03
16 16 0.44
17 19 0.53
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTTATTTTAT
Found at i:18615 original size:60 final size:59
Alignment explanation
Indices: 18463--18621 Score: 248
Period size: 59 Copynumber: 2.7 Consensus size: 59
18453 TAAAATTCAA
* * **
18463 AAAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTTT
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTTCC
*
18522 AAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTTCC
1 AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTTCC
18581 AAAAAATATATTTTTTG-GGAAAAGTTGAAAGTATCAATTTT
1 AAAAAA-ATA-TTTTTGAGGAAAAGTTGAAAGTATCAATTTT
18622 TCCTACACAA
Statistics
Matches: 92, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
59 60 0.65
60 26 0.28
61 6 0.07
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (59 bp):
AAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGCTTTCC
Found at i:24376 original size:44 final size:41
Alignment explanation
Indices: 24259--24812 Score: 444
Period size: 42 Copynumber: 13.1 Consensus size: 41
24249 ATGATTGTTA
* * * * *
24259 AGGAGCAATTTATTTTTCAAAGTCGTGGTTGCCTCTATTTAG
1 AGGAGCCATTTTTTTTTCAAAGTCGTTG-AGCCTCTGTTTAG
* * *
24301 TGGAGCAATTTATTTTTCAAAAGTCGTTGAGCCTCTGTTTAG
1 AGGAGCCATTTTTTTTTC-AAAGTCGTTGAGCCTCTGTTTAG
*
24343 AGGAGCTTCATTTTTTTTTCCAAAGTCGTTGAGCCTCTATTTAG
1 AGGAGC--CATTTTTTTTT-CAAAGTCGTTGAGCCTCTGTTTAG
* * * *
24387 AGGAGCAATTTATTTTCTAAAAGTCGTTAAGCCTCTGTTTAG
1 AGGAGCCATTT-TTTTTTCAAAGTCGTTGAGCCTCTGTTTAG
* ** * * *
24429 AGGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTGTTTAG
1 AGGAGCCATTTTTTTTTCAAAGTCGTTGAGCCTCTGTTTAG
* *
24470 AGGAGCTTTATTTATTTTTTCAAAGTCGTTGACCCTCT-TATTAG
1 AGGAGC--CATTT-TTTTTTCAAAGTCGTTGAGCCTCTGT-TTAG
* * * *
24514 AGGAGCTTTATTTATTTTTTTTAAAGTCGTTGAGCCTTTGATTAG
1 AGGAGC--CA-TT-TTTTTTTCAAAGTCGTTGAGCCTCTGTTTAG
24559 AGGAG-C-TTTATTCATTTTCAAAGTCGTTGAGCCTCT-TATTAG
1 AGGAGCCATTT-TT--TTTTCAAAGTCGTTGAGCCTCTGT-TTAG
*
24601 AGGAG-C-TTTGTTCATTTTCAAAGTCGTTGAGCCTCTGATTAG
1 AGGAGCCATTT-TT--TTTTCAAAGTCGTTGAGCCTCTGTTTAG
* * *
24643 ATGAGCCA-TTTATTTTCAAAGTCGTTGAGCCTCTGATTAG
1 AGGAGCCATTTTTTTTTCAAAGTCGTTGAGCCTCTGTTTAG
* * * * * *
24683 AGGAGCCA-TTTATTTT-GAAGTCATGGAGCCTCTGATCAG
1 AGGAGCCATTTTTTTTTCAAAGTCGTTGAGCCTCTGTTTAG
* * *
24722 AGGAGCCATTTATTTTTCAAAGTCATTGAGCCTCTGATTAGG
1 AGGAGCCATTTTTTTTTCAAAGTCGTTGAGCCTCTGTTTA-G
* * *
24764 GGGAGCCATTTTATTTTTC-AAGATCGTGGAAGCCTCTGTTTAA
1 AGGAGCCATTTT-TTTTTCAAAG-TCGTTG-AGCCTCTGTTTAG
24807 AGGAGC
1 AGGAGC
24813 TTTGTCTATT
Statistics
Matches: 430, Mismatches: 57, Indels: 49
0.80 0.11 0.09
Matches are distributed among these distances:
39 28 0.07
40 53 0.12
41 47 0.11
42 151 0.35
43 37 0.09
44 80 0.19
45 33 0.08
46 1 0.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (41 bp):
AGGAGCCATTTTTTTTTCAAAGTCGTTGAGCCTCTGTTTAG
Found at i:24813 original size:293 final size:300
Alignment explanation
Indices: 24314--24860 Score: 672
Period size: 293 Copynumber: 1.8 Consensus size: 300
24304 AGCAATTTAT
* *
24314 TTTTCAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTCATTTTTTTTTCCAAAGTCGTTGAGCCT
1 TTTTCAAAAGTCGTTGAGCCTCTGATTAGAGGAGC-TCATTTTATTTTCCAAAGTCGTTGAGCCT
* * * *
24379 CTATTTAGAGGAGCAATTTATTTTCTAAAAGTCGTTAAGCCTCTGTTTAGAGGAGCAATTTACTT
65 CTATTTAGAGGAGCAATTTATTTTCTAAAAGTCATGAAGCCTCTGATCAGAGGAGCAATTTACTT
** * * ** *
24444 TTCAAAGTTGTGGTGCCTCTGTTTAGAGGAGCTTTATTTATTTTTTCAAAGTCGTTGACCCTCTT
130 TTCAAAGTCATGGAGCCTCTGATTAGAGGAGCCATATTTATTTTTTCAAAGTCGTGGACCCTCTT
* * * * *
24509 ATTAGAGGAGCTTTATTTATTTTTTTTAAAGTCGTT-GAGCCTTTGA-TTAGAGGAGCTTTATTC
195 ATTAAAGGAGCTTTATCTATTTTTTTCAAAGTC-TTAGAGCCTCT-ACTTAGAAGAGCTTTATTC
24572 ATTTTCAAAGTCGTTGAGCCTCTTATTAGAGGAGCTTTGTTCA
258 ATTTTCAAAGTCGTTGAGCCTCTTATTAGAGGAGCTTTGTTCA
*
24615 TTTTC-AAAGTCGTTGAGCCTCTGATTAGATGAGC-CA-TTTATTTT-CAAAGTCGTTGAGCCTC
1 TTTTCAAAAGTCGTTGAGCCTCTGATTAGAGGAGCTCATTTTATTTTCCAAAGTCGTTGAGCCTC
* * * * *
24676 TGA-TTAGAGGAGCCATTTA-TTT-T-GAAGTCATGGAGCCTCTGATCAGAGGAGCCATTTATTT
66 T-ATTTAGAGGAGCAATTTATTTTCTAAAAGTCATGAAGCCTCTGATCAGAGGAGCAATTTACTT
* * *
24737 TTCAAAGTCATTGAGCCTCTGATTAGGGGGAGCCAT-TTTA-TTTTTC-AAGATCGTGGAAGCCT
130 TTCAAAGTCATGGAGCCTCTGATTA-GAGGAGCCATATTTATTTTTTCAAAG-TCGTGG-ACCCT
*
24799 CTGT-TTAAAGGAGCTTTGTCTATTTTTTTCAAAGTCTTAGAGCCTCTACTTAGAAGAGCTTT
192 CT-TATTAAAGGAGCTTTATCTATTTTTTTCAAAGTCTTAGAGCCTCTACTTAGAAGAGCTTT
24861 GATAAAAAAA
Statistics
Matches: 211, Mismatches: 28, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
291 3 0.01
292 14 0.07
293 107 0.51
294 9 0.04
295 3 0.01
296 33 0.16
297 8 0.04
298 2 0.01
300 27 0.13
301 5 0.02
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (300 bp):
TTTTCAAAAGTCGTTGAGCCTCTGATTAGAGGAGCTCATTTTATTTTCCAAAGTCGTTGAGCCTC
TATTTAGAGGAGCAATTTATTTTCTAAAAGTCATGAAGCCTCTGATCAGAGGAGCAATTTACTTT
TCAAAGTCATGGAGCCTCTGATTAGAGGAGCCATATTTATTTTTTCAAAGTCGTGGACCCTCTTA
TTAAAGGAGCTTTATCTATTTTTTTCAAAGTCTTAGAGCCTCTACTTAGAAGAGCTTTATTCATT
TTCAAAGTCGTTGAGCCTCTTATTAGAGGAGCTTTGTTCA
Found at i:25087 original size:5 final size:6
Alignment explanation
Indices: 25073--25102 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
25063 CCCAAGAGGC
25073 TTTTAT TTTTAT TTTTA- TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T
25103 ATTTGTCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:25093 original size:11 final size:11
Alignment explanation
Indices: 25073--25102 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
25063 CCCAAGAGGC
25073 TTTTATTTTTAT
1 TTTTA-TTTTAT
25085 TTTTATTTTAT
1 TTTTATTTTAT
25096 TTTTATT
1 TTTTATT
25103 ATTTGTCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:25102 original size:23 final size:22
Alignment explanation
Indices: 25073--25202 Score: 66
Period size: 23 Copynumber: 5.6 Consensus size: 22
25063 CCCAAGAGGC
*
25073 TTTTATTTTTATTTTTATTTTAT
1 TTTTATTTTTATTTTTA-TCTAT
* * * *
25096 TTTTATTATT-TGTCTATTTAT
1 TTTTATTTTTATTTTTATCTAT
*
25117 TAATATATTTTTTATTTTTTTATCTAT
1 T--TTTA-TTTTTATTTTT--ATCTAT
** *
25144 TAATATTTATATTATTTATCTAT
1 TTTTATTTTTATT-TTTATCTAT
* *
25167 TTTTATTTTTTATTATTATTTAT
1 TTTTA-TTTTTATTTTTATCTAT
*
25190 CTTT-TTTTTATTT
1 TTTTATTTTTATTT
25203 ATTTAATTAT
Statistics
Matches: 82, Mismatches: 17, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
21 14 0.17
22 4 0.05
23 31 0.38
24 18 0.22
25 9 0.11
27 6 0.07
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTATTTTTATCTAT
Found at i:25144 original size:27 final size:26
Alignment explanation
Indices: 25073--25234 Score: 86
Period size: 27 Copynumber: 6.0 Consensus size: 26
25063 CCCAAGAGGC
* *
25073 TTTTATTTTTATTTTTATT-TTAT-TT
1 TTTTATTTTT-TTATTATTAATATATT
* *
25098 TTATTATTTGTCTATTTATTAATATATT
1 TT-TTATTTTTTTA-TTATTAATATATT
25126 TTTTATTTTTTTATCTATTAATATTTATAT
1 TTTTATTTTTTTAT-TATTAATA--TAT-T
* *
25156 TATTTATCTATTTTTATTTTTTAT-TATT
1 T-TTTAT-T-TTTTTATTATTAATATATT
*
25184 ATTTATCTTTTTT-TTATT--TAT-TT
1 TTTTAT-TTTTTTATTATTAATATATT
**
25207 AATTATTTTTTTATCTATTAATATATT
1 TTTTATTTTTTTAT-TATTAATATATT
25234 T
1 T
25235 ATCTTTTTAT
Statistics
Matches: 108, Mismatches: 12, Indels: 32
0.71 0.08 0.21
Matches are distributed among these distances:
22 6 0.06
23 9 0.08
24 5 0.05
25 7 0.06
26 21 0.19
27 29 0.27
28 5 0.05
29 6 0.06
30 2 0.02
31 5 0.05
32 6 0.06
33 7 0.06
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (26 bp):
TTTTATTTTTTTATTATTAATATATT
Found at i:25159 original size:42 final size:41
Alignment explanation
Indices: 25112--25230 Score: 122
Period size: 41 Copynumber: 2.9 Consensus size: 41
25102 TATTTGTCTA
*
25112 TTTATTAATATATTTTTTATTTTTTTATCTATTAATAT-TT
1 TTTATTTATATATTTTTTATTTTTTTATCTATTAATATCTT
* *
25152 ATATTATTTATCTA-TTTTTA-TTTTTTAT-TATTATTTATCTT
1 -T-TTATTTATATATTTTTTATTTTTTTATCTATTA-ATATCTT
* *
25193 TTT-TTTATTTATTTAATTATTTTTTTATCTATTAATAT
1 TTTATTTATATATTT-TTTATTTTTTTATCTATTAATAT
25231 ATTTATCTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 14
0.76 0.07 0.16
Matches are distributed among these distances:
38 7 0.11
39 9 0.14
40 15 0.23
41 20 0.31
42 14 0.22
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (41 bp):
TTTATTTATATATTTTTTATTTTTTTATCTATTAATATCTT
Found at i:25212 original size:23 final size:25
Alignment explanation
Indices: 25147--25242 Score: 110
Period size: 24 Copynumber: 3.9 Consensus size: 25
25137 TATCTATTAA
25147 TATTTATATTATTTATCTATTTTTAT
1 TATTTATATTATTTATCT-TTTTTAT
*
25173 TTTTTATTATTATTTATCTTTTTT-T
1 TATTTA-TATTATTTATCTTTTTTAT
*
25198 TATTTAT-TTAATTAT-TTTTTTAT
1 TATTTATATTATTTATCTTTTTTAT
*
25221 CTATTAATA-TATTTATCTTTTT
1 -TATTTATATTATTTATCTTTTT
25243 ATTTTGATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
22 6 0.10
23 8 0.13
24 13 0.22
25 11 0.18
26 10 0.17
27 12 0.20
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (25 bp):
TATTTATATTATTTATCTTTTTTAT
Found at i:25222 original size:81 final size:80
Alignment explanation
Indices: 25075--25247 Score: 219
Period size: 81 Copynumber: 2.2 Consensus size: 80
25065 CAAGAGGCTT
* * *
25075 TTATTTTTATTTTTATTTTATTTTTATTATTTGTCTATTTATTAATATATTTTTTATTTTTTTAT
1 TTATTTTTATTTTTATTTTATTATTATTATTTATCTATTTATTAATATATTTATTATTTTTTTAT
25140 CTATTAATATTTATA
66 CTATTAATATTTATA
* * *
25155 TTATTTATCTATTTTTATTTT-TTATTATTATTTATCT-TTTTTTTATTTATTTAATTATTTTTT
1 TTATTT-T-TATTTTTATTTTATTATTATTATTTATCTATTTATTAATATATTT-ATTATTTTTT
25218 TATCTATTAATATATT-TA
63 TATCTATTAATAT-TTATA
*
25236 -TCTTTTTATTTT
1 TTATTTTTATTTT
25248 GATTAATTTT
Statistics
Matches: 82, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
78 6 0.07
79 1 0.01
80 22 0.27
81 39 0.48
82 14 0.17
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (80 bp):
TTATTTTTATTTTTATTTTATTATTATTATTTATCTATTTATTAATATATTTATTATTTTTTTAT
CTATTAATATTTATA
Found at i:25227 original size:19 final size:19
Alignment explanation
Indices: 25128--25234 Score: 76
Period size: 23 Copynumber: 5.3 Consensus size: 19
25118 AATATATTTT
25128 TTATTTTTTTATCTATTAATA
1 TTATTTTTTTATCTATT-A-A
* *
25149 TTTATATTATTTATCTATT-T
1 -TTAT-TTTTTTATCTATTAA
*
25169 TTA-TTTTTTAT-TATTAT
1 TTATTTTTTTATCTATTAA
*
25186 TTATCTTTTTTTTATTTATTTAA
1 TTA---TTTTTTTATCTA-TTAA
25209 TTATTTTTTTATCTATTAA
1 TTATTTTTTTATCTATTAA
25228 TATATTT
1 T-TATTT
25235 ATCTTTTTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
16 4 0.06
17 11 0.15
19 8 0.11
20 16 0.23
21 8 0.11
22 6 0.08
23 18 0.25
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTTTTTTATCTATTAA
Found at i:25777 original size:15 final size:16
Alignment explanation
Indices: 25754--25787 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
25744 AGAGAAAGAT
*
25754 AGAGAAGAGGAAGGGA
1 AGAGAAGAGAAAGGGA
25770 AGAG-AGAGAAAGGGA
1 AGAGAAGAGAAAGGGA
25785 AGA
1 AGA
25788 AGGGATCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (16 bp):
AGAGAAGAGAAAGGGA
Found at i:26055 original size:5 final size:5
Alignment explanation
Indices: 26047--26183 Score: 53
Period size: 5 Copynumber: 27.4 Consensus size: 5
26037 TTTTTTTTCG
26047 TTATT TTA-T TTA-T TTA-T TTA-T TTA-T TTATT ATTATT ATTATT ATTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT -TTATT -TTATT -TTATT
** * * *
26095 AGAATTGT TTAAT TT-TT T-ATT TTATT TTAATT TT-TC TT-CT TTATT
1 -TTA-T-T TTATT TTATT TTATT TTATT TT-ATT TTATT TTATT TTATT
26140 TT-TT ATT-TT TTATTT TTATT TTATT TTATTT TATATT TTATT TT
1 TTATT -TTATT TTA-TT TTATT TTATT TTA-TT T-TATT TTATT TT
26184 CTTTAGATAA
Statistics
Matches: 109, Mismatches: 10, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
4 34 0.31
5 35 0.32
6 35 0.32
7 4 0.04
8 1 0.01
ACGTcount: A:0.23, C:0.01, G:0.01, T:0.74
Consensus pattern (5 bp):
TTATT
Found at i:26058 original size:4 final size:4
Alignment explanation
Indices: 26051--26076 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
26041 TTTTCGTTAT
26051 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
26077 ATTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:26129 original size:7 final size:6
Alignment explanation
Indices: 26108--26183 Score: 70
Period size: 5 Copynumber: 12.7 Consensus size: 6
26098 ATTGTTTAAT
* *
26108 TTTTTA -TTTTA TTTTAA TTTTTC TTCTTTA TTTTTTA TTTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA -TTTTTA -TTTTTA TTTTTA
26158 -TTTTA -TTTTA -TTTTA TATTTTA TTTT
1 TTTTTA TTTTTA TTTTTA T-TTTTA TTTT
26184 CTTTAGATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
5 20 0.33
6 19 0.31
7 20 0.33
8 2 0.03
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:26934 original size:9 final size:10
Alignment explanation
Indices: 26900--26934 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
26890 AGATAAAAAA
26900 ATTTTTTCTT
1 ATTTTTTCTT
*
26910 GTTTTTTCTT
1 ATTTTTTCTT
*
26920 ATTTTTTGTT
1 ATTTTTTCTT
26930 ATTTT
1 ATTTT
26935 AAAAGATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.80
Consensus pattern (10 bp):
ATTTTTTCTT
Found at i:28194 original size:9 final size:9
Alignment explanation
Indices: 28182--28224 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
28172 CTTCCGACCC
28182 TTTTTTTAT
1 TTTTTTTAT
*
28191 TTTTTTTGT
1 TTTTTTTAT
*
28200 ATTTTTGTAT
1 -TTTTTTTAT
*
28210 TTTTTATAT
1 TTTTTTTAT
28219 TTTTTT
1 TTTTTT
28225 AATTAATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
9 21 0.75
10 7 0.25
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.84
Consensus pattern (9 bp):
TTTTTTTAT
Done.