Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_52 ID=scaffold_52-JGI_221_v2.0
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: 50503
ACGTcount: A:0.13, C:0.07, G:0.08, T:0.15
Warning! 28623 characters in sequence are not A, C, G, or T
Found at i:2530 original size:18 final size:18
Alignment explanation
Indices: 2449--2712 Score: 126
Period size: 18 Copynumber: 14.6 Consensus size: 18
2439 ACAATTATTT
2449 TTTTTGAAAACACGAAAAAA
1 TTTTTGAAAACACG--AAAA
* *
2469 ATTTT-AAAACACGAGAA
1 TTTTTGAAAACACGAAAA
* * *
2486 TTTTAG-AGACATGAAAA
1 TTTTTGAAAACACGAAAA
* *
2503 TTCTTAAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * * *
2521 TTTTTGAAAAGATGACAT
1 TTTTTGAAAACACGAAAA
* **
2539 TTTTTTAAAACACGGGAATT
1 TTTTTGAAAACAC--GAAAA
**
2559 TTTTTGAAAACATTAAAA
1 TTTTTGAAAACACGAAAA
*
2577 -TTTTG-AAACACCG-GAA
1 TTTTTGAAAACA-CGAAAA
2593 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* **
2611 TTTTTGAAACACAGGAATT
1 TTTTTGAAA-ACACGAAAA
* * *
2630 TTTTTAAAAAAAAGAAAA
1 TTTTTGAAAACACGAAAA
* * * *
2648 ATTTTGAAAA-ATGGAAT
1 TTTTTGAAAACACGAAAA
* **
2665 TTTTTGAAAACATGGGAATT
1 TTTTTGAAAACA--CGAAAA
*
2685 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
*
2703 ATTTTGAAAA
1 TTTTTGAAAA
2713 ACGGATTCTT
Statistics
Matches: 179, Mismatches: 53, Indels: 26
0.69 0.21 0.10
Matches are distributed among these distances:
16 7 0.04
17 42 0.23
18 75 0.42
19 22 0.12
20 33 0.18
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:2560 original size:17 final size:17
Alignment explanation
Indices: 2540--2632 Score: 53
Period size: 17 Copynumber: 5.3 Consensus size: 17
2530 AGATGACATT
2540 TTTTTAAAACACGGGAA
1 TTTTTAAAACACGGGAA
***
2557 TTTTTTTGAAAACA-TTAAA
1 --TTTTT-AAAACACGGGAA
* * *
2576 ATTTTGAAACACCGGAA
1 TTTTTAAAACACGGGAA
**
2593 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGGGAA
* *
2611 TTTTTGAAACACAGGAA
1 TTTTTAAAACACGGGAA
2628 TTTTT
1 TTTTT
2633 TTAAAAAAAA
Statistics
Matches: 54, Mismatches: 17, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
16 5 0.09
17 23 0.43
18 13 0.24
19 7 0.13
20 6 0.11
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (17 bp):
TTTTTAAAACACGGGAA
Found at i:2595 original size:72 final size:71
Alignment explanation
Indices: 2519--2696 Score: 187
Period size: 72 Copynumber: 2.4 Consensus size: 71
2509 AAAACACGAA
* * * * **
2519 AATTTTTGAAAAGATGACATTTTTTTAAAACACGGGAATTTTTTT-GAAAACATTAAAATTTTGA
1 AATTTTTGAAAACATGA-ATTTTTTTAAAACACAGGAATTTTTTTAAAAAAAAGAAAAATTTTGA
*
2583 AACACCGG
65 AA-AACGG
* ** *
2591 AATTTTTGAAAACACGAAAATTTTTGAAACACAGGAATTTTTTTAAAAAAAAGAAAAATTTTGAA
1 AATTTTTGAAAACATGAATTTTTTTAAAACACAGGAATTTTTTTAAAAAAAAGAAAAATTTTGAA
*
2656 AAATGG
66 AAACGG
2662 AATTTTTTGAAAACATGGGAATTTTTTTGAAAACA
1 AA-TTTTTGAAAACAT--GAATTTTTTT-AAAACA
2697 TGAAAAATTT
Statistics
Matches: 85, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
71 28 0.33
72 44 0.52
74 8 0.09
75 5 0.06
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.35
Consensus pattern (71 bp):
AATTTTTGAAAACATGAATTTTTTTAAAACACAGGAATTTTTTTAAAAAAAAGAAAAATTTTGAA
AAACGG
Found at i:2927 original size:18 final size:17
Alignment explanation
Indices: 2894--2995 Score: 71
Period size: 19 Copynumber: 5.5 Consensus size: 17
2884 TTTGCCTTAT
*
2894 TTTTTTGAAAAAACGAATA
1 TTTTTTG-AAACACGAA-A
2913 TTTTTTGAAACACGAGAA
1 TTTTTTGAAACACGA-AA
* *
2931 TAATTTTGAAGACATGAAA
1 T-TTTTTGAA-ACACGAAA
*
2950 -TTTTCGAAACACGAGAA
1 TTTTTTGAAACACGA-AA
*
2967 TTTTTTTCGAAAACACGGAA
1 -TTTTTT-G-AAACACGAAA
2987 TTTTTTGAA
1 TTTTTTGAA
2996 TATTTTTTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
16 5 0.07
17 10 0.15
18 10 0.15
19 27 0.40
20 8 0.12
21 7 0.10
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (17 bp):
TTTTTTGAAACACGAAA
Found at i:2931 original size:20 final size:20
Alignment explanation
Indices: 2908--2992 Score: 60
Period size: 20 Copynumber: 4.5 Consensus size: 20
2898 TTGAAAAAAC
2908 GAATATTTTTTGAAACACGA
1 GAATATTTTTTGAAACACGA
* *
2928 GAATA-ATTTTGAAGACA--T
1 GAATATTTTTTGAA-ACACGA
*
2946 GAA-A-TTTTCGAAACACGA
1 GAATATTTTTTGAAACACGA
2964 GAAT-TTTTTTCGAAAACACG-
1 GAATATTTTTT-G-AAACACGA
2984 GAAT-TTTTT
1 GAATATTTTT
2993 GAATATTTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
16 3 0.06
17 7 0.13
18 6 0.12
19 11 0.21
20 18 0.35
21 7 0.13
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (20 bp):
GAATATTTTTTGAAACACGA
Found at i:2937 original size:19 final size:17
Alignment explanation
Indices: 2914--2971 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
2904 AAACGAATAT
2914 TTTTTGAAACACGAGAA
1 TTTTTGAAACACGAGAA
*
2931 TAATTTTGAAGACATGA-AA
1 T--TTTTGAA-ACACGAGAA
*
2950 TTTTCGAAACACGAGAA
1 TTTTTGAAACACGAGAA
2967 TTTTT
1 TTTTT
2972 TTCGAAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 5 0.15
17 13 0.39
19 10 0.30
20 5 0.15
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (17 bp):
TTTTTGAAACACGAGAA
Found at i:2982 original size:21 final size:19
Alignment explanation
Indices: 2950--2992 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
2940 AGACATGAAA
2950 TTTTCGAAACACGAGAATTT
1 TTTTCGAAACACG-GAATTT
2970 TTTTCGAAAACACGGAATTT
1 TTTTCG-AAACACGGAATTT
2990 TTT
1 TTT
2993 GAATATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (19 bp):
TTTTCGAAACACGGAATTT
Found at i:3138 original size:16 final size:16
Alignment explanation
Indices: 3117--3163 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
3107 TTAAAATTAT
3117 TTAAAATAAAATAAAA
1 TTAAAATAAAATAAAA
* *
3133 TTAAAATTAAATTAAA
1 TTAAAATAAAATAAAA
3149 TTCAAAATATAAATA
1 TT-AAAATA-AAATA
3164 CAAAAATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 16 0.64
17 5 0.20
18 4 0.16
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
TTAAAATAAAATAAAA
Found at i:3507 original size:17 final size:17
Alignment explanation
Indices: 3455--3511 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
3445 TTCTCTTTTC
* *
3455 TTTTTTTAGCCT-TTGT
1 TTTTTTTGGCCTGCTGT
**
3471 TTTTTTTGGCCTGCACT
1 TTTTTTTGGCCTGCTGT
**
3488 TTTTTTTGGGTTGCTGT
1 TTTTTTTGGCCTGCTGT
3505 TTTTTTT
1 TTTTTTT
3512 CGGGACTGGG
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
16 11 0.34
17 21 0.66
ACGTcount: A:0.04, C:0.12, G:0.18, T:0.67
Consensus pattern (17 bp):
TTTTTTTGGCCTGCTGT
Found at i:3629 original size:13 final size:13
Alignment explanation
Indices: 3611--3702 Score: 57
Period size: 13 Copynumber: 7.2 Consensus size: 13
3601 AAAAATTCTT
3611 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
*
3624 TTTTTCTTTCTTC
1 TTTTTCTTTTTTC
* **
3637 TTCTTCTTCCTTC
1 TTTTTCTTTTTTC
3650 --TTTCTTTCTTT-
1 TTTTTCTTT-TTTC
* *
3661 TTCTTTCTTCTTCC
1 TT-TTTCTTTTTTC
* *
3675 TCTTT-TTTATTC
1 TTTTTCTTTTTTC
*
3687 TTCTTCTTTTTTC
1 TTTTTCTTTTTTC
3700 TTT
1 TTT
3703 CTTCCCTGTT
Statistics
Matches: 57, Mismatches: 16, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
11 5 0.09
12 9 0.16
13 36 0.63
14 7 0.12
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:3633 original size:10 final size:10
Alignment explanation
Indices: 3609--3705 Score: 60
Period size: 10 Copynumber: 9.7 Consensus size: 10
3599 AAAAAAATTC
3609 TTTT-TTTCTT
1 TTTTCTTTC-T
3619 TTTTCTTT-T
1 TTTTCTTTCT
3628 TCTTTC-TTCT
1 T-TTTCTTTCT
* *
3638 TCTTCTTCCT
1 TTTTCTTTCT
3648 TCTTTCTTTCT
1 T-TTTCTTTCT
3659 TTTTCTTTCT
1 TTTTCTTTCT
* *
3669 TCTTC-CTCT
1 TTTTCTTTCT
3678 TTTT-TATTCT
1 TTTTCT-TTCT
* *
3688 TCTTCTTTTT
1 TTTTCTTTCT
3698 TCTTTCTT
1 T-TTTCTT
3706 CCCTGTTCAG
Statistics
Matches: 67, Mismatches: 11, Indels: 17
0.71 0.12 0.18
Matches are distributed among these distances:
9 13 0.19
10 37 0.55
11 17 0.25
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:3639 original size:3 final size:3
Alignment explanation
Indices: 3621--3706 Score: 54
Period size: 3 Copynumber: 28.0 Consensus size: 3
3611 TTTTTCTTTT
* *
3621 TTC TTT TTC TTTC TTC TTC TTC TTCC TTC TTTC TTTC TTT TTC TTTC
1 TTC TTC TTC -TTC TTC TTC TTC TT-C TTC -TTC -TTC TTC TTC -TTC
* *
3668 TTC TTC CTC TT- TT- TTA TTC TTC TTC TT- TT- TTC TTTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC
3707 CCTGTTCAGC
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
2 8 0.12
3 42 0.61
4 19 0.28
ACGTcount: A:0.01, C:0.27, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:3658 original size:34 final size:33
Alignment explanation
Indices: 3614--3706 Score: 114
Period size: 34 Copynumber: 2.7 Consensus size: 33
3604 AATTCTTTTT
*
3614 TTCTTTTTTCTTTTTCTTTCTTCTTCTTCTTCC
1 TTCTTTTTTCTTTTTCTTTCTTCTTCCTCTTCC
**
3647 TTCTTTCTTTCTTTTTCTTTCTTCTTCCTCTTTT
1 TTCTTT-TTTCTTTTTCTTTCTTCTTCCTCTTCC
*
3681 TTATTCTTCTTCTTTTTTCTTTCTTC
1 TTCTT-TT-TTC-TTTTTCTTTCTTC
3707 CCTGTTCAGC
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
33 6 0.12
34 29 0.56
35 4 0.08
36 13 0.25
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (33 bp):
TTCTTTTTTCTTTTTCTTTCTTCTTCCTCTTCC
Found at i:3818 original size:20 final size:20
Alignment explanation
Indices: 3785--3822 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3775 GACACTCCTC
* *
3785 TCTTTTCTTTCTCTTTTTCT
1 TCTTTGCTTGCTCTTTTTCT
3805 TCTTTGCTTGCTCTTTTT
1 TCTTTGCTTGCTCTTTTT
3823 TTTTCATGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.24, G:0.05, T:0.71
Consensus pattern (20 bp):
TCTTTGCTTGCTCTTTTTCT
Found at i:4205 original size:30 final size:30
Alignment explanation
Indices: 4171--4325 Score: 149
Period size: 30 Copynumber: 5.2 Consensus size: 30
4161 GGGCAAAACA
* *
4171 TAATTTTGAGAAAATTCAGGGGTTAAAATG
1 TAATTTTGAGAAAATTTAGGGGTCAAAATG
** * *
4201 TAATTTCAAG-AAATTCAAGGGTCAAAATG
1 TAATTTTGAGAAAATTTAGGGGTCAAAATG
* * **
4230 TAA-TTTCA-AAATGTTTAGGGGTTGAAATG
1 TAATTTTGAGAAA-ATTTAGGGGTCAAAATG
4259 TAATTTTGA-AAAAGTTTAGGGGTCAAAATG
1 TAATTTTGAGAAAA-TTTAGGGGTCAAAATG
*
4289 TAATTTT-AGAAAAGTTTAAGGGTCAAAATG
1 TAATTTTGAGAAAA-TTTAGGGGTCAAAATG
4319 TAATTTT
1 TAATTTT
4326 TTTAAACATA
Statistics
Matches: 104, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
28 5 0.05
29 36 0.35
30 63 0.61
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.35
Consensus pattern (30 bp):
TAATTTTGAGAAAATTTAGGGGTCAAAATG
Found at i:4234 original size:59 final size:58
Alignment explanation
Indices: 4171--4324 Score: 168
Period size: 59 Copynumber: 2.6 Consensus size: 58
4161 GGGCAAAACA
*
4171 TAATTTTGAGAAAATTCAGGGGTTAAAATGTAATTTCAAGAAA-TTCAAGGGTCAAAATG
1 TAATTTT-AGAAAATTTAGGGGTTAAAATGTAATTTCAA-AAAGTTCAAGGGTCAAAATG
* * * * * *
4230 TAATTTCA-AAATGTTTAGGGGTTGAAATGTAATTTTGAAAAAGTTTAGGGGTCAAAATG
1 TAATTTTAGAAA-ATTTAGGGGTTAAAATGTAA-TTTCAAAAAGTTCAAGGGTCAAAATG
* *
4289 TAATTTTAGAAAAGTTTAAGGGTCAAAATGTAATTT
1 TAATTTTAGAAAA-TTTAGGGGTTAAAATGTAATTT
4325 TTTTAAACAT
Statistics
Matches: 78, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
57 3 0.04
58 21 0.27
59 35 0.45
60 19 0.24
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (58 bp):
TAATTTTAGAAAATTTAGGGGTTAAAATGTAATTTCAAAAAGTTCAAGGGTCAAAATG
Found at i:4757 original size:76 final size:76
Alignment explanation
Indices: 4460--5018 Score: 747
Period size: 76 Copynumber: 7.3 Consensus size: 76
4450 TTTCTTTTTA
* * * * * *
4460 TTTGAAAAGCAGAAATCG-AGAATAGCTCGGCGTGCGACCCGAGGCTCAACTCACCTCTCGCAAT
1 TTTGAAAAACAGAAATTGAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAAT
4524 ATGAGTTGATT
66 ATGAGTTGATT
* *
4535 TTTG-AAAACAGAAATTGAAAAGAATACCTCGGCATGCGACCCAAGGCTCAACTCACCTCTCGCA
1 TTTGAAAAACAGAAATTG-AAA-AATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCA
4599 ATATGAGTTGATT
64 ATATGAGTTGATT
*
4612 TTTGAAAAA-AGAAATTTAAAAGAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGC
1 TTTGAAAAACAGAAA-TT-GAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGC
4676 AATATGAGTTGATT
63 AATATGAGTTGATT
* * *
4690 TTTGAAAAACA-ACAATTGAAAAATACCTCGGCGTGTGACCCAAGACTCAACTCACCTCTCGCAA
1 TTTGAAAAACAGA-AATTGAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAA
*
4754 TATGAGTTAATT
65 TATGAGTTGATT
* * * *
4766 TTTGAAAAACAGAAATTGAAAAATACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCATT
1 TTTGAAAAACAGAAATTGAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAAT
4831 ATGAGTTGATTT
66 ATGAGTTGA-TT
* * *
4843 TTTGAAAAACAGAAATTG-AAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTTGCATT
1 TTTGAAAAACAGAAATTGAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAAT
4905 ATGAGTTGATT
66 ATGAGTTGATT
* * *
4916 TTTGAAAAA-AGAAATTTAAAAGAAATACCTCGGCATGCGACCCGAGGCTCAATTCACCTCTCGC
1 TTTGAAAAACAGAAA-TT-GAA-AAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGC
*
4980 ATTATGAGTTGATT
63 AATATGAGTTGATT
*
4994 TTTGAAAAAAAGAAATTGAAAAATA
1 TTTGAAAAACAGAAATTGAAAAATA
5019 TAATTCTTGA
Statistics
Matches: 438, Mismatches: 28, Indels: 35
0.87 0.06 0.07
Matches are distributed among these distances:
72 5 0.01
73 13 0.03
74 49 0.11
75 5 0.01
76 148 0.34
77 86 0.20
78 123 0.28
79 9 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (76 bp):
TTTGAAAAACAGAAATTGAAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCGCAAT
ATGAGTTGATT
Found at i:5878 original size:13 final size:13
Alignment explanation
Indices: 5860--5902 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
5850 TCTTAATTAA
5860 TTTTTT-TCTTCTT
1 TTTTTTGTC-TCTT
5873 TTTTTTGTCTCTT
1 TTTTTTGTCTCTT
*
5886 TTTTTTGT-TGTT
1 TTTTTTGTCTCTT
5898 TTTTT
1 TTTTT
5903 AGGCATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 8 0.29
13 18 0.64
14 2 0.07
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (13 bp):
TTTTTTGTCTCTT
Found at i:13341 original size:19 final size:19
Alignment explanation
Indices: 13314--13477 Score: 85
Period size: 19 Copynumber: 8.9 Consensus size: 19
13304 CGATACGATC
*
13314 AAAATACGAAAATTTTTTT
1 AAAACACGAAAATTTTTTT
*
13333 AAAACACG--AATATTTTT
1 AAAACACGAAAATTTTTTT
* * *
13350 GAAACA--ATTATTTTTTTT
1 AAAACACGA-AAATTTTTTT
13368 GAAAACACGAAAATTTTTTT
1 -AAAACACGAAAATTTTTTT
*
13388 AAAACACGAGAA---TTTT
1 AAAACACGAAAATTTTTTT
* * *
13404 AGAGACATG-AAATTTTTTG
1 A-AAACACGAAAATTTTTTT
* * *
13423 AAAAGATG-ACATTTTTTT
1 AAAACACGAAAATTTTTTT
**
13441 AAAACACGGGAATTTTTTT
1 AAAACACGAAAATTTTTTT
* *
13460 GAAAACATGAAGATTTTT
1 -AAAACACGAAAATTTTT
13478 GAAACACGGG
Statistics
Matches: 108, Mismatches: 25, Indels: 23
0.69 0.16 0.15
Matches are distributed among these distances:
16 7 0.06
17 18 0.17
18 26 0.24
19 35 0.32
20 21 0.19
21 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (19 bp):
AAAACACGAAAATTTTTTT
Found at i:13381 original size:55 final size:54
Alignment explanation
Indices: 13314--13573 Score: 186
Period size: 55 Copynumber: 4.7 Consensus size: 54
13304 CGATACGATC
* * **
13314 AAAATACGAAAATTTTTTTAAAACACGAATATTTTTGAAACAATTATTTTTTTTG
1 AAAACACGAAAATTTTTTTAAAACACGAATATTTTTGAAAC-ATGAAATTTTTTG
* *
13369 AAAACACGAAAATTTTTTTAAAACACGAGA-ATTTTAGAGACATGAAATTTTTTG
1 AAAACACGAAAATTTTTTTAAAACACGA-ATATTTTTGAAACATGAAATTTTTTG
* * * *
13423 AAAAGATG-ACATTTTTTTAAAACACGGGAATTTTTTTGAAAACATGAAGA-TTTTTG
1 AAAACACGAAAATTTTTTTAAAACAC--GAATATTTTTG-AAACATGAA-ATTTTTTG
** ** * * * * * *
13479 -AAACACGGGAATTTTTGAAAAAAAAAGAAAAATTTTGAAAAATGGAATTTTTTG
1 AAAACACGAAAATTTTT-TTAAAACACGAATATTTTTGAAACATGAAATTTTTTG
* ** * * *
13533 AAAACATGGGAATTTTTTTGAAAACATGAAAAATTTTGAAA
1 AAAACACGAAAATTTTTTT-AAAACACGAATATTTTTGAAA
13574 AACGGATTCT
Statistics
Matches: 164, Mismatches: 30, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
53 17 0.10
54 30 0.18
55 90 0.55
56 21 0.13
57 6 0.04
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (54 bp):
AAAACACGAAAATTTTTTTAAAACACGAATATTTTTGAAACATGAAATTTTTTG
Found at i:13455 original size:37 final size:36
Alignment explanation
Indices: 13414--13499 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 36
13404 AGAGACATGA
* **
13414 AATTTTTTGAAAAGATGACATTTTTTTAAAACACGGG
1 AATTTTTTGAAAACATGA-AGATTTTTAAAACACGGG
*
13451 AATTTTTTTGAAAACATGAAGATTTTTGAAACACGGG
1 AA-TTTTTTGAAAACATGAAGATTTTTAAAACACGGG
13488 AA-TTTTTGAAAA
1 AATTTTTTGAAAA
13500 AAAAAGAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
35 10 0.23
37 19 0.43
38 15 0.34
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (36 bp):
AATTTTTTGAAAACATGAAGATTTTTAAAACACGGG
Found at i:13515 original size:37 final size:37
Alignment explanation
Indices: 13437--13536 Score: 94
Period size: 37 Copynumber: 2.7 Consensus size: 37
13427 GATGACATTT
* *** * * * *
13437 TTTTAAAACACGGGAATTTTTTTGAAAACATGAAGAT
1 TTTTGAAACACGGGAATTTTTGAAAAAAAAAGAAAAA
13474 TTTTGAAACACGGGAATTTTTGAAAAAAAAAGAAAAA
1 TTTTGAAACACGGGAATTTTTGAAAAAAAAAGAAAAA
**
13511 TTTTGAAA-AATGGAATTTTTTGAAAA
1 TTTTGAAACACGGGAA-TTTTTGAAAA
13537 CATGGGAATT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
36 5 0.10
37 47 0.90
ACGTcount: A:0.46, C:0.05, G:0.16, T:0.33
Consensus pattern (37 bp):
TTTTGAAACACGGGAATTTTTGAAAAAAAAAGAAAAA
Found at i:13567 original size:21 final size:20
Alignment explanation
Indices: 13361--13569 Score: 90
Period size: 20 Copynumber: 11.2 Consensus size: 20
13351 AAACAATTAT
*
13361 TTTTTTTGAAAACACGAAAA
1 TTTTTTTGAAAACATGAAAA
* *
13381 TTTTTTT-AAAACACGAGAA
1 TTTTTTTGAAAACATGAAAA
* *
13400 --TTTTAG-AGACATG-AAA
1 TTTTTTTGAAAACATGAAAA
* *
13416 -TTTTTTGAAAAGATG-ACA
1 TTTTTTTGAAAACATGAAAA
* **
13434 TTTTTTT-AAAACACGGGAA
1 TTTTTTTGAAAACATGAAAA
*
13453 TTTTTTTGAAAACATGAAGA
1 TTTTTTTGAAAACATGAAAA
* **
13473 --TTTTTG-AAACACGGGAA
1 TTTTTTTGAAAACATGAAAA
*** * *
13490 TTTTTGAAAAAAAAAGAAAA
1 TTTTTTTGAAAACATGAAAA
* *
13510 --ATTTTGAAAA-ATG-GAA
1 TTTTTTTGAAAACATGAAAA
**
13526 -TTTTTTGAAAACATGGGAA
1 TTTTTTTGAAAACATGAAAA
13545 TTTTTTTGAAAACATGAAAAA
1 TTTTTTTGAAAACATG-AAAA
13566 TTTT
1 TTTT
13570 GAAAAACGGA
Statistics
Matches: 138, Mismatches: 37, Indels: 27
0.68 0.18 0.13
Matches are distributed among these distances:
16 4 0.03
17 32 0.23
18 28 0.20
19 31 0.22
20 37 0.27
21 6 0.04
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (20 bp):
TTTTTTTGAAAACATGAAAA
Found at i:13796 original size:20 final size:20
Alignment explanation
Indices: 13759--13802 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
13749 TTTACCGTAT
13759 TTTTTTGAAAAAAGGAAT-A
1 TTTTTTGAAAAAAGGAATAA
* *
13778 TTTTTTGAAACACGAGAATAA
1 TTTTTTGAAAAAAG-GAATAA
13799 TTTT
1 TTTT
13803 GAAGACATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 4 0.19
21 5 0.24
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (20 bp):
TTTTTTGAAAAAAGGAATAA
Found at i:13828 original size:16 final size:17
Alignment explanation
Indices: 13797--13834 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
13787 ACACGAGAAT
*
13797 AATTTTGAAGACATGAA
1 AATTTCGAAGACATGAA
*
13814 AATTTCGAA-ACATGAG
1 AATTTCGAAGACATGAA
13830 AATTT
1 AATTT
13835 TTTTCGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (17 bp):
AATTTCGAAGACATGAA
Found at i:13856 original size:21 final size:20
Alignment explanation
Indices: 13816--13857 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
13806 GACATGAAAA
*
13816 TTTCGAAACATGAGAATTTT
1 TTTCGAAACACGAGAATTTT
13836 TTTCGAAAACACGA-AATTTT
1 TTTCG-AAACACGAGAATTTT
13856 TT
1 TT
13858 GAATATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (20 bp):
TTTCGAAACACGAGAATTTT
Found at i:14205 original size:20 final size:21
Alignment explanation
Indices: 14176--14215 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
14166 AAATTGAACT
*
14176 TTTTTTTCTTCT-TTTTTTTC
1 TTTTTCTCTTCTCTTTTTTTC
14196 TTTTTCTCTTCTCTTTTTTT
1 TTTTTCTCTTCTCTTTTTTT
14216 TCTCTGCTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTCTCTTCTCTTTTTTTC
Found at i:14485 original size:7 final size:7
Alignment explanation
Indices: 14473--14542 Score: 52
Period size: 7 Copynumber: 9.4 Consensus size: 7
14463 AAAATATTAT
14473 TTTTTTC
1 TTTTTTC
14480 TTTTTTC
1 TTTTTTC
14487 -TTTTTC
1 TTTTTTC
*
14493 TTTCTTC
1 TTTTTTC
14500 TTCTTCTTCC
1 TT-TT-TT-C
* *
14510 TTCTTCC
1 TTTTTTC
*
14517 TTTTTTT
1 TTTTTTC
14524 TTCTTCTTC
1 TT-TT-TTC
14533 TTTTTTC
1 TTTTTTC
14540 TTT
1 TTT
14543 CTTCCCCGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
6 6 0.12
7 27 0.55
8 6 0.12
9 7 0.14
10 3 0.06
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTTC
Found at i:14492 original size:13 final size:13
Alignment explanation
Indices: 14474--14542 Score: 68
Period size: 13 Copynumber: 5.2 Consensus size: 13
14464 AAATATTATT
14474 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
*
14487 TTTTTCTTTCTTC
1 TTTTTCTTTTTTC
* **
14500 TTCTTCTTCCTTC
1 TTTTTCTTTTTTC
14513 TTCCTTT-TTTTTTC
1 TT--TTTCTTTTTTC
*
14527 TTCTTCTTTTTTC
1 TTTTTCTTTTTTC
14540 TTT
1 TTT
14543 CTTCCCCGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
12 2 0.04
13 34 0.76
14 7 0.16
15 2 0.04
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:14496 original size:10 final size:10
Alignment explanation
Indices: 14477--14541 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
14467 TATTATTTTT
*
14477 TTCTTTTTTC
1 TTCTTCTTTC
*
14487 TTTTTCTTTC
1 TTCTTCTTTC
14497 TTCTTC-TTC
1 TTCTTCTTTC
*
14506 TTCCTTCTTCC
1 TT-CTTCTTTC
* *
14517 TTTTTTTTTC
1 TTCTTCTTTC
*
14527 TTCTTCTTTT
1 TTCTTCTTTC
14537 TTCTT
1 TTCTT
14542 TCTTCCCCGT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
9 5 0.12
10 34 0.79
11 4 0.09
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (10 bp):
TTCTTCTTTC
Found at i:14529 original size:14 final size:15
Alignment explanation
Indices: 14473--14547 Score: 68
Period size: 16 Copynumber: 5.0 Consensus size: 15
14463 AAAATATTAT
*
14473 TTTTTTCTTT-TTTC
1 TTTTTTCTTTCTTCC
14487 -TTTTTCTTTCTT-C
1 TTTTTTCTTTCTTCC
*
14500 TTCTTCTTCCTTCTTCC
1 TT-TT-TTCTTTCTTCC
14517 TTTTTT-TTTCTTCTTC
1 TTTTTTCTTTCTTC--C
14533 TTTTTTCTTTCTTCC
1 TTTTTTCTTTCTTCC
14548 CCGTTCAGCC
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
13 10 0.20
14 9 0.18
15 5 0.10
16 17 0.33
17 10 0.20
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTTCTTTCTTCC
Found at i:15041 original size:30 final size:30
Alignment explanation
Indices: 14991--15153 Score: 172
Period size: 30 Copynumber: 5.5 Consensus size: 30
14981 GAGCAAAACT
* *
14991 TTTA-GGGTCGAAACGTAATTTTGAGAAAG
1 TTTAGGGGTCAAAATGTAATTTTGAGAAAG
*
15020 TTTAGGGGTAAAAATGTAATTTTGAGAAAG
1 TTTAGGGGTCAAAATGTAATTTTGAGAAAG
* *
15050 TTTAGGGATCAAAATGTAA-TTTCA-AAATG
1 TTTAGGGGTCAAAATGTAATTTTGAGAAA-G
** *
15079 TTTAGGGGTTTAAATGTAATTTTGAAAAAG
1 TTTAGGGGTCAAAATGTAATTTTGAGAAAG
* *
15109 TTTAGGGGGCAAAATGTAA-TTTAAGAAAAG
1 TTTAGGGGTCAAAATGTAATTTTGAG-AAAG
* *
15139 TTTTGGGGTTAAAAT
1 TTTAGGGGTCAAAAT
15154 AAATTTTTTT
Statistics
Matches: 111, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
28 3 0.03
29 29 0.26
30 76 0.68
31 3 0.03
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (30 bp):
TTTAGGGGTCAAAATGTAATTTTGAGAAAG
Found at i:15082 original size:59 final size:60
Alignment explanation
Indices: 15016--15153 Score: 197
Period size: 59 Copynumber: 2.3 Consensus size: 60
15006 TAATTTTGAG
* * * *
15016 AAAGTTTAGGGGTAAAAATGTAATTTTGAGAAAGTTTAGGGATCAAAATGTAATTTCA-A
1 AAAGTTTAGGGGTTAAAATGTAATTTTGAAAAAGTTTAGGGAGCAAAATGTAATTTAAGA
* * *
15075 AATGTTTAGGGGTTTAAATGTAATTTTGAAAAAGTTTAGGGGGCAAAATGTAATTTAAGA
1 AAAGTTTAGGGGTTAAAATGTAATTTTGAAAAAGTTTAGGGAGCAAAATGTAATTTAAGA
*
15135 AAAGTTTTGGGGTTAAAAT
1 AAAGTTTAGGGGTTAAAAT
15154 AAATTTTTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
59 51 0.75
60 17 0.25
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (60 bp):
AAAGTTTAGGGGTTAAAATGTAATTTTGAAAAAGTTTAGGGAGCAAAATGTAATTTAAGA
Done.