Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168170.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_409, 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: 28152
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:210 original size:40 final size:39
Alignment explanation
Indices: 155--233 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 39
145 AATTCATCAG
155 AACATAAATTTCATGTTCTTACATTTTAAATCTAAATAT
1 AACATAAATTTCATGTTCTTACATTTTAAATCTAAATAT
*
194 AACATAAAATTTCATGTTCTTATATTTTAAATCTAAATAT
1 AACAT-AAATTTCATGTTCTTACATTTTAAATCTAAATAT
234 CTAAAAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 5 0.13
40 33 0.87
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (39 bp):
AACATAAATTTCATGTTCTTACATTTTAAATCTAAATAT
Found at i:1704 original size:28 final size:28
Alignment explanation
Indices: 1672--1725 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
1662 TATAATATAT
* *
1672 AATTTTTTATATAATTAAATTTAATTAA
1 AATTTTGTATATAATTAAATTGAATTAA
1700 AATTTTGTATATAATTAAATTGAATT
1 AATTTTGTATATAATTAAATTGAATT
1726 GTCTTTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (28 bp):
AATTTTGTATATAATTAAATTGAATTAA
Found at i:2067 original size:13 final size:14
Alignment explanation
Indices: 2041--2090 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
2031 TGAAAAAATT
*
2041 TAAATATATTTAAA
1 TAAATATTTTTAAA
*
2055 TATAT-TTTTTAAA
1 TAAATATTTTTAAA
2068 TAAATATTTTTAATA
1 TAAATATTTTTAA-A
*
2083 AAAATATT
1 TAAATATT
2091 AATAAACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 11 0.37
14 11 0.37
15 8 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAATATTTTTAAA
Found at i:2192 original size:29 final size:28
Alignment explanation
Indices: 2156--2222 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
2146 TTATATAGTA
*
2156 TTAATTTTCATATT-AAA-TTTTATCAATT
1 TTAATTTT-TTATTAAAATTTTTATCAA-T
*
2184 TTAATTTTTTATTAAAATTTTTATTAAT
1 TTAATTTTTTATTAAAATTTTTATCAAT
*
2212 TTAACTTTTTA
1 TTAATTTTTTA
2223 AAAAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.12
28 22 0.65
29 8 0.24
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.61
Consensus pattern (28 bp):
TTAATTTTTTATTAAAATTTTTATCAAT
Found at i:2228 original size:28 final size:29
Alignment explanation
Indices: 2173--2228 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
2163 TCATATTAAA
* **
2173 TTTTATCAATTTTAATTTTTTATTAAAAT
1 TTTTATCAATTTTAACTTTTTAAAAAAAT
*
2202 TTTTATTAA-TTTAACTTTTTAAAAAAA
1 TTTTATCAATTTTAACTTTTTAAAAAAA
2229 AAATCTCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTTATCAATTTTAACTTTTTAAAAAAAT
Found at i:4463 original size:20 final size:20
Alignment explanation
Indices: 4421--4463 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
4411 TAAGAGAATT
*
4421 TTTTTAAAAATTCTATAAAA
1 TTTTTAAAAATTCTAAAAAA
4441 TTTTTAAAAATTC-AAAAAGA
1 TTTTTAAAAATTCTAAAAA-A
4461 TTT
1 TTT
4464 CAAAAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (20 bp):
TTTTTAAAAATTCTAAAAAA
Found at i:4481 original size:12 final size:11
Alignment explanation
Indices: 4451--4480 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
4441 TTTTTAAAAA
4451 TTCAAAAAGAT
1 TTCAAAAAGAT
4462 TTCAAAAAGAT
1 TTCAAAAAGAT
4473 TTCAAAAA
1 TTCAAAAA
4481 AAAATTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.27
Consensus pattern (11 bp):
TTCAAAAAGAT
Found at i:4629 original size:20 final size:20
Alignment explanation
Indices: 4603--4652 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
4593 TTTTTTTAAA
4603 ATTTTAAAAAATTCTAAAAT
1 ATTTTAAAAAATTCTAAAAT
* *
4623 GTTTTAAAATATTCTAAAAT
1 ATTTTAAAAAATTCTAAAAT
4643 ATTCTTAAAA
1 ATT-TTAAAA
4653 TTTTTCTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTTTAAAAAATTCTAAAAT
Found at i:4662 original size:11 final size:10
Alignment explanation
Indices: 4599--4653 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
4589 AAATTTTTTT
4599 TAAAAT-TT-
1 TAAAATATTC
*
4607 TAAAAAATTC
1 TAAAATATTC
* *
4617 TAAAATGTTT
1 TAAAATATTC
4627 TAAAATATTC
1 TAAAATATTC
4637 TAAAATATTC
1 TAAAATATTC
4647 TTAAAAT
1 -TAAAAT
4654 TTTTCTAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
8 5 0.13
9 2 0.05
10 25 0.66
11 6 0.16
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (10 bp):
TAAAATATTC
Found at i:4716 original size:20 final size:19
Alignment explanation
Indices: 4669--4730 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
4659 TAAATTCTTC
* *
4669 AAATATTCAAATAAATTTA
1 AAATATTCAAAAAAATTCA
*
4688 AAATCTTCAAAAAAATCTCA
1 AAATATTCAAAAAAAT-TCA
*
4708 AAATTTTC-AAAAAATTCA
1 AAATATTCAAAAAAATTCA
4726 TAAAT
1 -AAAT
4731 GAAGATTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 3 0.08
19 25 0.68
20 9 0.24
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATATTCAAAAAAATTCA
Found at i:6122 original size:2 final size:2
Alignment explanation
Indices: 6109--6143 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
6099 GTTCATACAC
*
6109 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6144 CTGTAGACAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6216 original size:4 final size:4
Alignment explanation
Indices: 6207--6310 Score: 64
Period size: 4 Copynumber: 27.5 Consensus size: 4
6197 GTTGGTCCAC
* *
6207 TTTA TTTA TTT- TTTT TTTA TTT- TTTA TTT- TATA TTTA TTTTA TATTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA T-TTA
* * * *
6254 TATA TATT- TTTA TCT- TTTA TGTA TTTA -TTA TTTA CTTA TTTA -TTA
1 TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
6299 -TTA -TTA TTTA TT
1 TTTA TTTA TTTA TT
6311 AATATATATA
Statistics
Matches: 79, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
3 24 0.30
4 46 0.58
5 9 0.11
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:6227 original size:11 final size:11
Alignment explanation
Indices: 6211--6249 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
6201 GTCCACTTTA
6211 TTTATTTTTTT
1 TTTATTTTTTT
6222 TTTATTTTTTAT
1 TTTATTTTTT-T
* *
6234 TTTATATTTAT
1 TTTATTTTTTT
6245 TTTAT
1 TTTAT
6250 ATTATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTATTTTTTT
Found at i:6234 original size:18 final size:18
Alignment explanation
Indices: 6211--6286 Score: 61
Period size: 18 Copynumber: 4.4 Consensus size: 18
6201 GTCCACTTTA
* *
6211 TTTATTTTTTTTTTATTT
1 TTTATTTTATATTTATTT
6229 TTTATTTTATATTTA--T
1 TTTATTTTATATTTATTT
* *
6245 TTTATATTATATATA-TT
1 TTTATTTTATATTTATTT
*
6262 TTTATCTTT-TATGTATTT
1 TTTAT-TTTATATTTATTT
*
6280 ATTATTT
1 TTTATTT
6287 ACTTATTTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
16 14 0.29
17 13 0.27
18 21 0.44
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.75
Consensus pattern (18 bp):
TTTATTTTATATTTATTT
Found at i:6309 original size:7 final size:7
Alignment explanation
Indices: 6208--6311 Score: 75
Period size: 7 Copynumber: 15.4 Consensus size: 7
6198 TTGGTCCACT
6208 TTATTTA
1 TTATTTA
6215 TT-TTT-
1 TTATTTA
6220 TT-TTTA
1 TTATTTA
*
6226 TTTTTTA
1 TTATTTA
6233 -T-TTTA
1 TTATTTA
6238 -TATTTA
1 TTATTTA
6244 TT-TTATA
1 TTATT-TA
6251 TTATATATA
1 TTAT-T-TA
6260 TT-TTTA
1 TTATTTA
6266 TCT-TTTA
1 T-TATTTA
6273 TGTATTTA
1 T-TATTTA
6281 TTATTTA
1 TTATTTA
6288 CTTATTTA
1 -TTATTTA
6296 TTA-TTA
1 TTATTTA
6302 TTATTTA
1 TTATTTA
6309 TTA
1 TTA
6312 ATATATATAT
Statistics
Matches: 85, Mismatches: 1, Indels: 22
0.79 0.01 0.20
Matches are distributed among these distances:
5 10 0.12
6 21 0.25
7 34 0.40
8 14 0.16
9 6 0.07
ACGTcount: A:0.25, C:0.02, G:0.01, T:0.72
Consensus pattern (7 bp):
TTATTTA
Found at i:6360 original size:15 final size:14
Alignment explanation
Indices: 6332--6365 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
6322 CTTTATTTTT
6332 TTTTC-TTTTCTTC
1 TTTTCTTTTTCTTC
6345 TTTTCTTTTTCTTTC
1 TTTTCTTTTTC-TTC
6360 TTTTCT
1 TTTTCT
6366 GTTAATATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 5 0.26
15 9 0.47
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTCTTTTTCTTC
Found at i:6405 original size:26 final size:25
Alignment explanation
Indices: 6371--6428 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
6361 TTTCTGTTAA
* *
6371 TATTCATATACATATTTTTATTTATC
1 TATT-ATATACATATTATTATTCATC
**
6397 TAGTTATATATTTATTATTATTCATC
1 TA-TTATATACATATTATTATTCATC
6423 TATTAT
1 TATTAT
6429 TATTGTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 4 0.15
26 21 0.78
27 2 0.07
ACGTcount: A:0.31, C:0.09, G:0.02, T:0.59
Consensus pattern (25 bp):
TATTATATACATATTATTATTCATC
Found at i:7417 original size:6 final size:6
Alignment explanation
Indices: 7406--7468 Score: 65
Period size: 6 Copynumber: 10.2 Consensus size: 6
7396 AATTGTTTAA
* * *
7406 TATTTT TATTTT TATTTT TTTTATT TATTTT CATTTT CATTTT TA-TTT
1 TATTTT TATTTT TATTTT TATT-TT TATTTT TATTTT TATTTT TATTTT
7454 TATTATTT TATTTT T
1 TA-T-TTT TATTTT T
7469 TAAAATAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
5 5 0.10
6 33 0.67
7 6 0.12
8 5 0.10
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.79
Consensus pattern (6 bp):
TATTTT
Found at i:7423 original size:5 final size:5
Alignment explanation
Indices: 7409--7467 Score: 54
Period size: 5 Copynumber: 11.8 Consensus size: 5
7399 TGTTTAATAT
7409 TTTTA TTTTTA TTTT- TTTTA -TTTA TTTTCA TTTTCA TTTTTA TTTTA
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTT-A TTTT-A -TTTTA TTTTA
7456 --TTA TTTTA TTTT
1 TTTTA TTTTA TTTT
7468 TTAAAATAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
3 3 0.06
4 8 0.17
5 19 0.40
6 13 0.28
7 4 0.09
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:7441 original size:25 final size:25
Alignment explanation
Indices: 7409--7468 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
7399 TGTTTAATAT
7409 TTTTATTTTTA-TTTT-TTTTATTTA
1 TTTTATTTTTATTTTTATTTTA-TTA
*
7433 TTTTCATTTTCATTTTTATTTTATTA
1 TTTT-ATTTTTATTTTTATTTTATTA
7459 TTTTATTTTT
1 TTTTATTTTT
7469 TAAAATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 4 0.13
25 11 0.35
26 11 0.35
27 5 0.16
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (25 bp):
TTTTATTTTTATTTTTATTTTATTA
Found at i:7448 original size:31 final size:31
Alignment explanation
Indices: 7407--7467 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
7397 ATTGTTTAAT
* *
7407 ATTTTTATTTTTATTTT-TTTTATTTATTTTC
1 ATTTTCATTTTTATTTTATTAT-TTTATTTTC
7438 ATTTTCATTTTTATTTTATTATTTTATTTT
1 ATTTTCATTTTTATTTTATTATTTTATTTT
7468 TTAAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (31 bp):
ATTTTCATTTTTATTTTATTATTTTATTTTC
Found at i:7543 original size:58 final size:57
Alignment explanation
Indices: 7475--7630 Score: 233
Period size: 58 Copynumber: 2.7 Consensus size: 57
7465 TTTTTAAAAT
*
7475 AAAATTATTTTTA-AGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTTCA
1 AAAAATATTTTTAGA-GAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAG-TTTCA
* *
7533 AAAAATATTTTTTGAGAAAAGTTGAAAGTATCAATTTTACTCGAAATTAAAGTTTCA
1 AAAAATATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTCA
* *
7590 AAAGAATATTTTTGGAGAAAAGTTAAAAGTATCAATTTTCC
1 AAA-AATATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCC
7631 CTACACAAAA
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
57 8 0.09
58 81 0.90
59 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.37
Consensus pattern (57 bp):
AAAAATATTTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTCA
Found at i:7627 original size:27 final size:27
Alignment explanation
Indices: 7539--7628 Score: 67
Period size: 27 Copynumber: 3.2 Consensus size: 27
7529 TTCAAAAAAT
* *
7539 ATTTTTTGAGAAAAGTTGAAAGTATCA
1 ATTTTTCGAGAAAAGTTAAAAGTATCA
* *
7566 ATTTTACTCGAAATTAAAGTTTCAAAAGAAT--
1 ATTTT--TCGAGA--AAAG-TT-AAAAGTATCA
*
7597 ATTTTTGGAGAAAAGTTAAAAGTATCA
1 ATTTTTCGAGAAAAGTTAAAAGTATCA
7624 ATTTT
1 ATTTT
7629 CCCTACACAA
Statistics
Matches: 48, Mismatches: 7, Indels: 16
0.68 0.10 0.23
Matches are distributed among these distances:
25 7 0.15
26 2 0.04
27 14 0.29
29 8 0.17
31 9 0.19
32 2 0.04
33 6 0.12
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (27 bp):
ATTTTTCGAGAAAAGTTAAAAGTATCA
Found at i:7734 original size:10 final size:10
Alignment explanation
Indices: 7721--7778 Score: 55
Period size: 10 Copynumber: 5.8 Consensus size: 10
7711 AAAATTATAA
*
7721 AAAAAATTGT
1 AAAAAATTCT
*
7731 AAAAATTTC-
1 AAAAAATTCT
*
7740 AAAAAATTTT
1 AAAAAATTCT
*
7750 AAAAATTTCT
1 AAAAAATTCT
*
7760 AAAAGATTTCT
1 AAAA-AATTCT
7771 AAAAAATT
1 AAAAAATT
7779 TTTAAAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
9 7 0.18
10 22 0.56
11 10 0.26
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.34
Consensus pattern (10 bp):
AAAAAATTCT
Found at i:7745 original size:19 final size:20
Alignment explanation
Indices: 7721--7787 Score: 73
Period size: 19 Copynumber: 3.3 Consensus size: 20
7711 AAAATTATAA
7721 AAAAAATTGTAAAAATTTC-
1 AAAAAATTGTAAAAATTTCT
*
7740 AAAAAATTTTAAAAATTTCT
1 AAAAAATTGTAAAAATTTCT
* * *
7760 AAAAGATTTCTAAAAAATTTTT
1 AAAA-AATTGT-AAAAATTTCT
7782 AAAAAA
1 AAAAAA
7788 ATTTTAAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 18 0.45
20 4 0.10
21 5 0.12
22 13 0.32
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAAAATTGTAAAAATTTCT
Found at i:7792 original size:11 final size:11
Alignment explanation
Indices: 7731--7795 Score: 57
Period size: 11 Copynumber: 6.1 Consensus size: 11
7721 AAAAAATTGT
*
7731 AAAAA-TTTCA
1 AAAAATTTTAA
7741 AAAAATTTT--
1 AAAAATTTTAA
7750 AAAAATTTCT-A
1 AAAAATTT-TAA
*
7761 AAAGATTTCTAA
1 AAAAATTT-TAA
*
7773 AAAATTTTTAA
1 AAAAATTTTAA
7784 AAAAATTTTAA
1 AAAAATTTTAA
7795 A
1 A
7796 TGCAGTTTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
9 8 0.17
10 6 0.13
11 26 0.55
12 7 0.15
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (11 bp):
AAAAATTTTAA
Found at i:7792 original size:12 final size:11
Alignment explanation
Indices: 7731--7787 Score: 75
Period size: 11 Copynumber: 5.5 Consensus size: 11
7721 AAAAAATTGT
7731 AAAAATTTC-A
1 AAAAATTTCTA
7741 AAAAATTT-T-
1 AAAAATTTCTA
7750 AAAAATTTCTA
1 AAAAATTTCTA
*
7761 AAAGATTTCTA
1 AAAAATTTCTA
*
7772 AAAAATTTTTA
1 AAAAATTTCTA
7783 AAAAA
1 AAAAA
7788 ATTTTAAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
9 8 0.20
10 9 0.22
11 24 0.59
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (11 bp):
AAAAATTTCTA
Found at i:8916 original size:2 final size:2
Alignment explanation
Indices: 8909--8933 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8899 TCGTGCCACT
8909 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
8934 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:11446 original size:20 final size:20
Alignment explanation
Indices: 11401--11493 Score: 96
Period size: 20 Copynumber: 4.6 Consensus size: 20
11391 TATTTATATG
**
11401 ATTAATATATTTGTGTGATTT
1 ATTAATATATTTGCATGA-TT
*
11422 ATTAATATATTTGCATGACT
1 ATTAATATATTTGCATGATT
** *
11442 ATTAATATGCTTACATGATT
1 ATTAATATATTTGCATGATT
*
11462 ATTAATTTATTTGCATGATT
1 ATTAATATATTTGCATGATT
* *
11482 ATCAATTTATTT
1 ATTAATATATTT
11494 ATTTGTATAG
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
20 44 0.73
21 16 0.27
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (20 bp):
ATTAATATATTTGCATGATT
Found at i:11616 original size:41 final size:41
Alignment explanation
Indices: 11571--11850 Score: 316
Period size: 41 Copynumber: 6.9 Consensus size: 41
11561 ATTTGTATTA
**
11571 TTATATAT-TTAATTGCATGATAATATATTTATTTTTATGTT
1 TTATAT-TGTTAATTGCATGATAATATATTTATTTGCATGTT
* *
11612 TTATATCGTTAATTGC---ATAATATATTTATTTGTATGTT
1 TTATATTGTTAATTGCATGATAATATATTTATTTGCATGTT
* * *
11650 TTATATTGTTAACTGCATGATAATATATTTAATTACATGTT
1 TTATATTGTTAATTGCATGATAATATATTTATTTGCATGTT
* * * *
11691 TTATATTGTTAATTACTTGATTATATATTTAATTGCATGTT
1 TTATATTGTTAATTGCATGATAATATATTTATTTGCATGTT
* * *
11732 TTATGTTGTTAATTGCATGATTATATATTTATTTGCATGAT
1 TTATATTGTTAATTGCATGATAATATATTTATTTGCATGTT
* * * *
11773 TTATATTGTTAATTGCATTATTATATATTTAATTGCATGAT
1 TTATATTGTTAATTGCATGATAATATATTTATTTGCATGTT
* **
11814 TTATATTGTTATTTGTGTGATTATATATATTTATTTG
1 TTATATTGTTAATTGCATGA-TA-ATATATTTATTTG
11851 TGTGATTGTA
Statistics
Matches: 207, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
38 35 0.17
41 159 0.77
42 1 0.00
43 12 0.06
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (41 bp):
TTATATTGTTAATTGCATGATAATATATTTATTTGCATGTT
Found at i:11847 original size:22 final size:22
Alignment explanation
Indices: 11789--11857 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
11779 TGTTAATTGC
* **
11789 ATTATTATATATTTAATTGCATG
1 ATTA-TATATATTTATTTGTGTG
11812 ATT-TATAT-TGTTATTTGTGTG
1 ATTATATATAT-TTATTTGTGTG
11833 ATTATATATATTTATTTGTGTG
1 ATTATATATATTTATTTGTGTG
11855 ATT
1 ATT
11858 GTATGATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 16 0.40
22 19 0.47
23 4 0.10
ACGTcount: A:0.28, C:0.01, G:0.13, T:0.58
Consensus pattern (22 bp):
ATTATATATATTTATTTGTGTG
Found at i:15038 original size:14 final size:14
Alignment explanation
Indices: 15019--15053 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
15009 CAAGCCAAGG
15019 AAGCATATGTGAGA
1 AAGCATATGTGAGA
15033 AAGCATATGTGAGA
1 AAGCATATGTGAGA
*
15047 AAACATA
1 AAGCATA
15054 ACCAATTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.09, G:0.23, T:0.20
Consensus pattern (14 bp):
AAGCATATGTGAGA
Found at i:16487 original size:52 final size:52
Alignment explanation
Indices: 16401--16557 Score: 194
Period size: 52 Copynumber: 3.0 Consensus size: 52
16391 TATAACTATA
* *
16401 CAAACTTGTCC-ATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTG-CCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* *
16453 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* * **
16505 CAAACTTACTTATTAAGAATCCTCTTT-CTCTT-GATATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCC-CTTTCCTCTTAGA-ATTCTTCTCCTGCAAGT
16557 C
1 C
16558 TTCTTGTCCA
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
51 4 0.04
52 86 0.91
53 4 0.04
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.41
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:17313 original size:11 final size:11
Alignment explanation
Indices: 17297--17327 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
17287 ACAGATACCA
17297 AAAAAAAAAAG
1 AAAAAAAAAAG
*
17308 AAAAAAGAAAG
1 AAAAAAAAAAG
17319 AAAAAAAAA
1 AAAAAAAAA
17328 TCCACAGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:22775 original size:34 final size:34
Alignment explanation
Indices: 22709--22775 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
22699 ATACATTATA
* * * *
22709 ATTTTTAGAAATAGATTTTCGAAAGTTTTATTTT
1 ATTTTTAGAAAAAGATTTTCAAAAATTATATTTT
22743 ATTTTTAGAAAAAGATTTTCAAAAATTATATTT
1 ATTTTTAGAAAAAGATTTTCAAAAATTATATTT
22776 GTTCTAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.49
Consensus pattern (34 bp):
ATTTTTAGAAAAAGATTTTCAAAAATTATATTTT
Found at i:26203 original size:10 final size:10
Alignment explanation
Indices: 26190--26214 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
26180 ATTTAAAAAA
26190 ATTTTAATAT
1 ATTTTAATAT
26200 ATTTTAATAT
1 ATTTTAATAT
26210 ATTTT
1 ATTTT
26215 TTAAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTAATAT
Found at i:26355 original size:11 final size:12
Alignment explanation
Indices: 26337--26362 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
26327 TTATCAATTT
26337 AAATTTTTATTA
1 AAATTTTTATTA
26349 AAATTTTTATTA
1 AAATTTTTATTA
26361 AA
1 AA
26363 TTAAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AAATTTTTATTA
Found at i:26363 original size:11 final size:11
Alignment explanation
Indices: 26335--26364 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
26325 TTTTATCAAT
26335 TTAAATTTTTA
1 TTAAATTTTTA
26346 TTAAAATTTTTA
1 TT-AAATTTTTA
26358 TTAAATT
1 TTAAATT
26365 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTAAATTTTTA
Found at i:26381 original size:29 final size:28
Alignment explanation
Indices: 26318--26378 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
26308 TTAATTTTCA
*
26318 TATT-AAA-TTTTATCAATTTAAATTTT
1 TATTAAAATTTTTATCAAATTAAATTTT
*
26344 TATTAAAATTTTTATTAAATTAAATTTT
1 TATTAAAATTTTTATCAAATTAAATTTT
26372 T-TTAAAA
1 TATTAAAA
26379 AATCTCAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 4 0.13
27 9 0.29
28 18 0.58
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
TATTAAAATTTTTATCAAATTAAATTTT
Done.