Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168073.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_321, 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: 35011
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Found at i:1021 original size:21 final size:21
Alignment explanation
Indices: 996--1041 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
986 AGAAAAGCTG
* * *
996 AAAATAGATTTCACACAAAGA
1 AAAATAGAATTCAAAAAAAGA
1017 AAAATAGAATTCAAAAAAAGA
1 AAAATAGAATTCAAAAAAAGA
1038 AAAA
1 AAAA
1042 ACAAACGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.15
Consensus pattern (21 bp):
AAAATAGAATTCAAAAAAAGA
Found at i:7381 original size:17 final size:18
Alignment explanation
Indices: 7358--7404 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
7348 ATTTAAAATC
7358 TAATTTTATTATTTTA-T
1 TAATTTTATTATTTTATT
* *
7375 TATTTTTATT-CTTTATT
1 TAATTTTATTATTTTATT
7392 TAATTTTATTATT
1 TAATTTTATTATT
7405 AGTTTAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 4 0.17
17 19 0.79
18 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
TAATTTTATTATTTTATT
Found at i:7410 original size:17 final size:16
Alignment explanation
Indices: 7358--7413 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
7348 ATTTAAAATC
*
7358 TAATTTTATTATTTTAT
1 TAATTTTATTATTAT-T
* *
7375 TATTTTTATTCTTTATT
1 TAATTTTATT-ATTATT
7392 TAATTTTATTATTAGTT
1 TAATTTTATTATTA-TT
7409 TAATT
1 TAATT
7414 ATGAAAATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 3 0.09
17 26 0.81
18 3 0.09
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (16 bp):
TAATTTTATTATTATT
Found at i:7638 original size:26 final size:26
Alignment explanation
Indices: 7602--7652 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
7592 CAGGGTTTCA
*
7602 GGTTTCATTTACAGTTTTTATTTTAG
1 GGTTTCATTTACAGTTTTAATTTTAG
* **
7628 GGTTTTATTTAGGGTTTTAATTTTA
1 GGTTTCATTTACAGTTTTAATTTTA
7653 AAATTTCATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.20, C:0.04, G:0.18, T:0.59
Consensus pattern (26 bp):
GGTTTCATTTACAGTTTTAATTTTAG
Found at i:7640 original size:12 final size:13
Alignment explanation
Indices: 7617--7652 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
7607 CATTTACAGT
7617 TTTTATTTTAGGG
1 TTTTATTTTAGGG
7630 TTTTA-TTTAGGG
1 TTTTATTTTAGGG
7642 TTTTAATTTTA
1 TTTT-ATTTTA
7653 AAATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 11 0.52
13 6 0.29
14 4 0.19
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.64
Consensus pattern (13 bp):
TTTTATTTTAGGG
Found at i:7824 original size:18 final size:18
Alignment explanation
Indices: 7801--7837 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
7791 TTATTAAAAA
7801 TTATTA-TTTATTATTTAT
1 TTATTATTTTATT-TTTAT
7819 TTATTATTTTATTTTTAT
1 TTATTATTTTATTTTTAT
7837 T
1 T
7838 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATTATTTTATTTTTAT
Found at i:7842 original size:14 final size:14
Alignment explanation
Indices: 7801--7843 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
7791 TTATTAAAAA
7801 TTATTATTTATTA-T
1 TTATT-TTTATTATT
7815 TTA--TTTATTATT
1 TTATTTTTATTATT
7827 TTATTTTTATTATT
1 TTATTTTTATTATT
7841 TTA
1 TTA
7844 ATAACTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.27
12 4 0.15
14 15 0.58
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTTTATTATT
Found at i:9326 original size:17 final size:19
Alignment explanation
Indices: 9292--9328 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
9282 TCATGCTACC
*
9292 TTTTGCTGTAATTTTTTTT
1 TTTTGCTGTAATTCTTTTT
9311 TTTTGCT-T-ATTCTTTTT
1 TTTTGCTGTAATTCTTTTT
9328 T
1 T
9329 ACCGCAGCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 1 0.06
19 7 0.41
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (19 bp):
TTTTGCTGTAATTCTTTTT
Found at i:14448 original size:9 final size:8
Alignment explanation
Indices: 14420--14447 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
14410 ATTTCTTAAT
14420 TTTTAAAA
1 TTTTAAAA
14428 TTTTAAAA
1 TTTTAAAA
14436 TTTTAAAA
1 TTTTAAAA
14444 TTTT
1 TTTT
14448 TTATTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TTTTAAAA
Found at i:14473 original size:18 final size:17
Alignment explanation
Indices: 14422--14474 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
14412 TTCTTAATTT
* *
14422 TTAAAATTTTAAAAT-T
1 TTAAAATTTTTAAATAA
* *
14438 TTAAAATTTTTTATTAA
1 TTAAAATTTTTAAATAA
14455 TTAATAATTTTTAAATAA
1 TTAA-AATTTTTAAATAA
14473 TT
1 TT
14475 TATGTATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 12 0.41
17 4 0.14
18 13 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAAAATTTTTAAATAA
Found at i:14487 original size:3 final size:3
Alignment explanation
Indices: 14474--14519 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
14464 TTTAAATAAT
*
14474 TTA TGTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
14520 CTACTACTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:14524 original size:3 final size:3
Alignment explanation
Indices: 14518--14582 Score: 67
Period size: 3 Copynumber: 21.7 Consensus size: 3
14508 TTATTATTAT
* * * * * *
14518 TAC TAC TAC TAC TAC TAC TAC TGC TGC TGC TGC TAC TAC TAC TGC TGC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC
*
14566 TAT TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TA
14583 TTATTATTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.25, C:0.31, G:0.09, T:0.35
Consensus pattern (3 bp):
TAC
Found at i:14555 original size:21 final size:21
Alignment explanation
Indices: 14523--14581 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
14513 ATTATTACTA
14523 CTACTACTACTACTACTGCTG
1 CTACTACTACTACTACTGCTG
* *
14544 CTGCTGCTACTACTACTGCTG
1 CTACTACTACTACTACTGCTG
*
14565 CTATTACTACTACTACT
1 CTACTACTACTACTACT
14582 ATTATTATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.32, G:0.10, T:0.36
Consensus pattern (21 bp):
CTACTACTACTACTACTGCTG
Found at i:14587 original size:3 final size:3
Alignment explanation
Indices: 14581--14626 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
14571 CTACTACTAC
14581 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
14627 TATTTCTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:14987 original size:16 final size:16
Alignment explanation
Indices: 14968--15005 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
14958 GTTTTTATTA
14968 TTTGTTCTTTTTTGTT-
1 TTTGTTCTTTTTT-TTG
*
14984 TTTGTTGTTTTTTTTG
1 TTTGTTCTTTTTTTTG
15000 TTTGTT
1 TTTGTT
15006 TTGTTATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.00, C:0.03, G:0.16, T:0.82
Consensus pattern (16 bp):
TTTGTTCTTTTTTTTG
Found at i:14993 original size:9 final size:9
Alignment explanation
Indices: 14968--15010 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
14958 GTTTTTATTA
14968 TTTGTTCTTT
1 TTTGTT-TTT
14978 TTTGTTTTT
1 TTTGTTTTT
*
14987 GTTGTTTTT
1 TTTGTTTTT
*
14996 TTTGTTTGT
1 TTTGTTTTT
15005 TTTGTT
1 TTTGTT
15011 ATCAAGATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 24 0.80
10 6 0.20
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.81
Consensus pattern (9 bp):
TTTGTTTTT
Found at i:15158 original size:35 final size:34
Alignment explanation
Indices: 15066--15159 Score: 82
Period size: 35 Copynumber: 2.7 Consensus size: 34
15056 CCATGAACCG
* *
15066 AAAATAAA-AATGACTGGGATTAAATCGTAAGTAA
1 AAAATAAAGGATGAC-GGAATTAAATCGTAAGTAA
* ** *
15100 AAAATAAATGATGACCAAGATTAAGTCGTAAGTCAA
1 AAAATAAAGGATGACGGA-ATTAAATCGTAAGT-AA
* *
15136 AAGATGAAGGATGACGGAATTAAA
1 AAAATAAAGGATGACGGAATTAAA
15160 CCACAAGTCA
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
34 8 0.17
35 23 0.50
36 15 0.33
ACGTcount: A:0.51, C:0.07, G:0.20, T:0.21
Consensus pattern (34 bp):
AAAATAAAGGATGACGGAATTAAATCGTAAGTAA
Found at i:15804 original size:8 final size:8
Alignment explanation
Indices: 15791--15849 Score: 68
Period size: 8 Copynumber: 7.4 Consensus size: 8
15781 CATCTTCCCA
15791 TTTTTCTT
1 TTTTTCTT
15799 TTTTTCTT
1 TTTTTCTT
**
15807 TACTTCTT
1 TTTTTCTT
15815 TTTTT-TT
1 TTTTTCTT
15822 TTTTATCCTT
1 TTTT-T-CTT
15832 TTTTTCTT
1 TTTTTCTT
15840 TTTTT-TT
1 TTTTTCTT
15847 TTT
1 TTT
15850 GACGAATGCC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
7 11 0.25
8 26 0.59
9 1 0.02
10 6 0.14
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTCTT
Found at i:15832 original size:17 final size:18
Alignment explanation
Indices: 15797--15843 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
15787 CCCATTTTTC
* *
15797 TTTTTTTCTTTACTTCTT
1 TTTTTTTTTTTACTCCTT
15815 TTTTTTTTTTTA-TCCTT
1 TTTTTTTTTTTACTCCTT
15832 TTTTTCTTTTTT
1 TTTTT-TTTTTT
15844 TTTTTTGACG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTTTTTTACTCCTT
Found at i:19845 original size:21 final size:22
Alignment explanation
Indices: 19815--19858 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
19805 CTACCCACTT
19815 TAATAATTCATGAGGCAA-ATCA
1 TAATAATTCA-GAGGCAACATCA
*
19837 TAAT-ATTCAGAGTCAACATCA
1 TAATAATTCAGAGGCAACATCA
19858 T
1 T
19859 CATTAAGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (22 bp):
TAATAATTCAGAGGCAACATCA
Found at i:23072 original size:30 final size:29
Alignment explanation
Indices: 23038--23095 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
23028 CAAAACAAGC
23038 AAAACAAAAACTC-AATAAACAATATATAAT
1 AAAACAAAAAC-CAAATAAACAATA-ATAAT
**
23068 AAAACCGAAACCAAATAAACAATAATAA
1 AAAACAAAAACCAAATAAACAATAATAA
23096 GCTAAAACGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.67, C:0.16, G:0.02, T:0.16
Consensus pattern (29 bp):
AAAACAAAAACCAAATAAACAATAATAAT
Found at i:23107 original size:30 final size:30
Alignment explanation
Indices: 23051--23108 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
23041 ACAAAAACTC
23051 AATAAACAATATATAATAAAACCGAAACCA
1 AATAAACAATATATAATAAAACCGAAACCA
23081 AATAAACAATA-ATAAGCTAAAA-CGAAAC
1 AATAAACAATATATAA--TAAAACCGAAAC
23109 TATATAAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 4 0.15
30 17 0.65
31 5 0.19
ACGTcount: A:0.64, C:0.16, G:0.05, T:0.16
Consensus pattern (30 bp):
AATAAACAATATATAATAAAACCGAAACCA
Found at i:24401 original size:38 final size:38
Alignment explanation
Indices: 24299--24435 Score: 112
Period size: 38 Copynumber: 3.4 Consensus size: 38
24289 TATATTACAA
** * *
24299 TTAAGGCATTTGACATGAAGAAATGCCTTAATTATAGATCAA
1 TTAAGGCATTTGTGAAGAA-AAATGCCTTAA--AT-GATCAT
* * * * *
24341 TTAAAGCATTTGGCTTAAAGAAAAATGTCTTAATTGATGAT
1 TTAAGGCATTT-G--TGAAGAAAAATGCCTTAAATGATCAT
* *
24382 TTAAGGCGTTTGTGAAGAAAAATGCCTTAAATGATCTT
1 TTAAGGCATTTGTGAAGAAAAATGCCTTAAATGATCAT
24420 TTAAGGCATTTGTGAA
1 TTAAGGCATTTGTGAA
24436 AGTGTTTGTG
Statistics
Matches: 76, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
38 36 0.47
40 1 0.01
41 13 0.17
42 11 0.14
43 1 0.01
44 10 0.13
45 4 0.05
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.34
Consensus pattern (38 bp):
TTAAGGCATTTGTGAAGAAAAATGCCTTAAATGATCAT
Found at i:25940 original size:3 final size:3
Alignment explanation
Indices: 25920--26089 Score: 139
Period size: 3 Copynumber: 60.3 Consensus size: 3
25910 TGGCATAGTA
* * *
25920 TAT TAT T-T TAG TAC TAT TAT TA- TAT TA- TAT TA- TAT TAT TAT CA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
25963 TAG GA- TAG TA- TAT TAA TA- TAT T-T TAT TAT ATAG TA- TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* * * *
26003 TGT TAT TAC TAC TAT TAT TAC TAT TAT T-T TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
26050 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
26090 TAGTTTTTGC
Statistics
Matches: 139, Mismatches: 15, Indels: 26
0.77 0.08 0.14
Matches are distributed among these distances:
2 21 0.15
3 116 0.83
4 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:26363 original size:20 final size:20
Alignment explanation
Indices: 26340--26379 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
26330 TCATTTTTGG
*
26340 GGGAAATAGTTGGTTTTTAA
1 GGGAAATAGTTGATTTTTAA
*
26360 GGGAAATGGTTGATTTTTAA
1 GGGAAATAGTTGATTTTTAA
26380 AGAGAGTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.40
Consensus pattern (20 bp):
GGGAAATAGTTGATTTTTAA
Found at i:26573 original size:21 final size:22
Alignment explanation
Indices: 26531--26573 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
26521 TATAGGAAAA
26531 TTTGGAAAATCTAGGATTTTTT
1 TTTGGAAAATCTAGGATTTTTT
* *
26553 TTTGGGAAATCT-GGGTTTTTT
1 TTTGGAAAATCTAGGATTTTTT
26574 GGGATGAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.21, C:0.05, G:0.23, T:0.51
Consensus pattern (22 bp):
TTTGGAAAATCTAGGATTTTTT
Found at i:26930 original size:18 final size:17
Alignment explanation
Indices: 26909--26942 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
26899 TTCCATTTTC
*
26909 ATTTTATTTTTTGATTTG
1 ATTTGATTTTTT-ATTTG
26927 ATTTGATTTTTTATTT
1 ATTTGATTTTTTATTT
26943 CATTATTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (17 bp):
ATTTGATTTTTTATTTG
Found at i:27073 original size:7 final size:7
Alignment explanation
Indices: 27052--27085 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
27042 AAACAAAAAG
27052 AATAATA
1 AATAATA
27059 AA-AATA
1 AATAATA
27065 AATAATA
1 AATAATA
27072 AATAAATA
1 AAT-AATA
27080 AATAAT
1 AATAAT
27086 CTTTTTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AATAATA
Found at i:31445 original size:13 final size:14
Alignment explanation
Indices: 31427--31456 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
31417 TTAACAAATG
31427 AAAAAATGAA-AAA
1 AAAAAATGAAGAAA
31440 AAAAAATGAAGAAA
1 AAAAAATGAAGAAA
31454 AAA
1 AAA
31457 TTAATAGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (14 bp):
AAAAAATGAAGAAA
Found at i:31509 original size:17 final size:17
Alignment explanation
Indices: 31487--31524 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
31477 TATGCTCCAT
31487 AAAAAAAAAAA-AAGAAG
1 AAAAAAAAAAAGAA-AAG
31504 AAAAAAAAAAAGAAAAG
1 AAAAAAAAAAAGAAAAG
31521 AAAA
1 AAAA
31525 TGAAGGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAGAAAAG
Found at i:31524 original size:15 final size:14
Alignment explanation
Indices: 31487--31524 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
31477 TATGCTCCAT
31487 AAAAAAAAAAAAAG
1 AAAAAAAAAAAAAG
31501 AAGAAAAAAAAAAAG
1 AA-AAAAAAAAAAAG
*
31516 AAAAGAAAA
1 AAAAAAAAA
31525 TGAAGGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:31893 original size:13 final size:12
Alignment explanation
Indices: 31876--31904 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
31866 AAAAGACATT
31876 GAAAAAAAAAAA
1 GAAAAAAAAAAA
31888 GAAAAAAAAAAA
1 GAAAAAAAAAAA
31900 GAAAA
1 GAAAA
31905 GGAAGACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:32858 original size:118 final size:119
Alignment explanation
Indices: 32632--32864 Score: 256
Period size: 118 Copynumber: 2.0 Consensus size: 119
32622 CGATCTCAGC
* * *
32632 TCAATCTAGATCATTTTTGACACACGATTTCATCTCGATTACTCATGTTTGACCTCGACTTACTC
1 TCAATCTAGATCATTTTTGACACACGATTTCATCTCGATCACTCATGTTTGACCTCGACTCAATC
* * * *
32697 TTAGTCACTTTATCTTTCAAACTCATGGTTTTGTCCCAATCATTTAATCTTAAT
66 TTAGTCACTTTATCTTTCAAACTCACGATTTCGTCCCAATCATTCAATCTTAAT
* * * * *
32751 TCAATCTAGATCA-TTTTGACTCATGGTTTCATC-CTGATCATTCAT-TTTCGATCTCGACTCAA
1 TCAATCTAGATCATTTTTGACACACGATTTCATCTC-GATCACTCATGTTT-GACCTCGACTCAA
* ** * * * *
32813 TCTTGGTTGCTTTATCTTTTAGACTCACGATTTCGTCCTAGTCATTCAATCT
64 TCTTAGTCACTTTATCTTTCAAACTCACGATTTCGTCCCAATCATTCAATCT
32865 CGGCTTAGCT
Statistics
Matches: 93, Mismatches: 19, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
117 4 0.04
118 76 0.82
119 13 0.14
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (119 bp):
TCAATCTAGATCATTTTTGACACACGATTTCATCTCGATCACTCATGTTTGACCTCGACTCAATC
TTAGTCACTTTATCTTTCAAACTCACGATTTCGTCCCAATCATTCAATCTTAAT
Found at i:32937 original size:120 final size:119
Alignment explanation
Indices: 32813--33206 Score: 387
Period size: 120 Copynumber: 3.3 Consensus size: 119
32803 CTCGACTCAA
* * * *
32813 TCTTGGTTGCTTTATCTTTTAGACTCACGATTTCGTCCTAGTCATTCAATCTCGGCTTAGCTCAG
1 TCTTGGTCGCTTTATCTTTTAGACTCAAGGTTTTGTCCTAGTCATTCAATCTCGGCTTAG-TCAG
* ** * *
32878 ATTATTTTTTGACTTACAATTTCATCTTGGTCATTTATCTTTGACCTCGACTTGG
65 ATCATTTTTTGACTTGTAATTTCATCTTGGTCATTCATCTTTAACCTCGACTTGG
* * * * * *
32933 TCTTGGTCACTTTATCTTTTAGACTCATGGTTTTATCCTAGTCATTCGATCTCGACTTAGTTCAA
1 TCTTGGTCGCTTTATCTTTTAGACTCAAGGTTTTGTCCTAGTCATTCAATCTCGGCTTAG-TCAG
* * * **** * *
32998 ATCATTTTCTAACTCGTAATTTCATCCCAATGATTCATCTTCAACCTCGACTTGG
65 ATCATTTTTTGACTTGTAATTTCATCTTGGTCATTCATCTTTAACCTCGACTTGG
* * * *
33053 TCCTGGTCGCATTATCATTTTAGACTTAAGGTTTTGTTCC-AGTCATTCAATCTTGGCTTAGTCC
1 TCTTGGTCGCTTTATC-TTTTAGACTCAAGGTTTTG-TCCTAGTCATTCAATCTCGGCTTAGT-C
* * * ***
33117 AGATCATTTTCTTGACTTGTGATTTCATCTTGGTCATTCATTTTTTACCTCGACTCAA
63 AGATCATTTT-TTGACTTGTAATTTCATCTTGGTCATTCATCTTTAACCTCGACTTGG
* * *
33175 TCCTGATCGCTTTATC-TTTAGACTCATGGTTT
1 TCTTGGTCGCTTTATCTTTTAGACTCAAGGTTT
33207 CATCGTAATC
Statistics
Matches: 217, Mismatches: 53, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
120 124 0.57
121 44 0.20
122 49 0.23
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (119 bp):
TCTTGGTCGCTTTATCTTTTAGACTCAAGGTTTTGTCCTAGTCATTCAATCTCGGCTTAGTCAGA
TCATTTTTTGACTTGTAATTTCATCTTGGTCATTCATCTTTAACCTCGACTTGG
Found at i:33470 original size:3 final size:3
Alignment explanation
Indices: 33464--33611 Score: 100
Period size: 3 Copynumber: 52.0 Consensus size: 3
33454 TTTTAGTACG
* * *
33464 ATT ATT A-T ATT A-T ATT A-T ATT A-T CTT ATT ATC ATGT A-T AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
* * * *
33505 A-T ATT AAT A-T ATT A-T ATT ATAT AGT A-T ATT A-T GTT ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT
* * *
33546 ACT ATT ATT ACT ATT ATT TTT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
33594 GTT GTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
33612 TGTTTATTTA
Statistics
Matches: 117, Mismatches: 16, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
2 18 0.15
3 96 0.82
4 3 0.03
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:33507 original size:25 final size:22
Alignment explanation
Indices: 33465--33592 Score: 80
Period size: 25 Copynumber: 5.3 Consensus size: 22
33455 TTTAGTACGA
*
33465 TTATTATATTATATTATATTAT
1 TTATTATATTATAGTATATTAT
33487 CTTATTATCATGTATAGTATATTAAT
1 -TTATTAT-AT-TATAGTATATT-AT
*
33513 ATATTATATTATATAGTATATTAT
1 TTATTATA-T-TATAGTATATTAT
* *
33537 GTTATTACTACTATTATTACTATTAT
1 -TTATTA-TATTA-TAGTA-TATTAT
*
33563 TT-TTATTATTATTATTATTATTA-
1 TTATTA-TATTA-TAGTA-TATTAT
33586 TTATTAT
1 TTATTAT
33593 TGTTGTTATT
Statistics
Matches: 87, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
23 10 0.11
24 28 0.32
25 39 0.45
26 10 0.11
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (22 bp):
TTATTATATTATAGTATATTAT
Found at i:33510 original size:30 final size:27
Alignment explanation
Indices: 33443--33541 Score: 71
Period size: 27 Copynumber: 3.6 Consensus size: 27
33433 ATAGTATGGC
* *
33443 ATAGTATATTAT-TT-TAGTACGATTATT
1 ATAGTATATTATATTATATTA-TATTA-T
* * *
33470 ATATTATATTATATTATCTTATTATCATGT
1 ATAGTATATTATATTATATTA-TAT--TAT
33500 ATAGTATATTA-A-TATATTATATTAT
1 ATAGTATATTATATTATATTATATTAT
*
33525 ATAGTATATTATGTTAT
1 ATAGTATATTATATTAT
33542 TACTACTATT
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
25 13 0.23
27 17 0.30
28 8 0.14
29 6 0.11
30 11 0.20
31 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.07, T:0.54
Consensus pattern (27 bp):
ATAGTATATTATATTATATTATATTAT
Found at i:33888 original size:20 final size:20
Alignment explanation
Indices: 33859--33909 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
33849 AAGAACACAT
33859 AGTTGATTTTTGAGGGAAAC
1 AGTTGATTTTTGAGGGAAAC
* * *
33879 AGTTGGTTTTTTATGGAAAC
1 AGTTGATTTTTGAGGGAAAC
*
33899 ATTTGATTTTT
1 AGTTGATTTTT
33910 ATGGAGAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.04, G:0.24, T:0.47
Consensus pattern (20 bp):
AGTTGATTTTTGAGGGAAAC
Found at i:33910 original size:19 final size:20
Alignment explanation
Indices: 33861--33914 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
33851 GAACACATAG
*
33861 TTGATTTTTGAGGGAAACAGT
1 TTGATTTTT-ATGGAAACAGT
* *
33882 TGGTTTTTTATGGAAACA-T
1 TTGATTTTTATGGAAACAGT
33901 TTGATTTTTATGGA
1 TTGATTTTTATGGA
33915 GAGTTGGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 13 0.46
20 8 0.29
21 7 0.25
ACGTcount: A:0.26, C:0.04, G:0.24, T:0.46
Consensus pattern (20 bp):
TTGATTTTTATGGAAACAGT
Found at i:34124 original size:12 final size:12
Alignment explanation
Indices: 34107--34145 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
34097 TGGGACAGAC
34107 ATGAATTTTTCG
1 ATGAATTTTTCG
*
34119 ATGAATTTTTTG
1 ATGAATTTTTCG
*
34131 ATGAACTTTTCG
1 ATGAATTTTTCG
34143 ATG
1 ATG
34146 GAGTATGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.49
Consensus pattern (12 bp):
ATGAATTTTTCG
Found at i:34475 original size:21 final size:22
Alignment explanation
Indices: 34451--34491 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
34441 ATTATTTCAA
*
34451 GTTTTTATTT-TTTTTATTTTG
1 GTTTTTATTTATTTGTATTTTG
34472 GTTTTTATTTATTTGTATTT
1 GTTTTTATTTATTTGTATTT
34492 AGTAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.78
Consensus pattern (22 bp):
GTTTTTATTTATTTGTATTTTG
Done.