Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012966.1 Corchorus capsularis cultivar CVL-1 contig12987, 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: 32499
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:93 original size:13 final size:13
Alignment explanation
Indices: 75--121 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
65 GGTAATCAAT
75 AAAAGAGAATAAG
1 AAAAGAGAATAAG
*
88 AAAAGAGTAATTAG
1 AAAAGAG-AATAAG
*
102 TAAAA-AGAGTAAG
1 -AAAAGAGAATAAG
115 AAAAGAG
1 AAAAGAG
122 TAAAAATGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.14
13 13 0.46
14 7 0.25
15 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.23, T:0.13
Consensus pattern (13 bp):
AAAAGAGAATAAG
Found at i:134 original size:29 final size:29
Alignment explanation
Indices: 73--136 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 29
63 GTGGTAATCA
**
73 ATAAAAGAGAATAAGAAAAGAGTAATTAG
1 ATAAAAGAGAATAAGAAAAGAGTAAAAAG
*
102 -TAAAA-AGAGTAAGAAAAGAGTAAAAATG
1 ATAAAAGAGAATAAGAAAAGAGTAAAAA-G
130 ATAAAAG
1 ATAAAAG
137 TAGCAAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 18 0.62
28 6 0.21
29 5 0.17
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (29 bp):
ATAAAAGAGAATAAGAAAAGAGTAAAAAG
Found at i:2265 original size:21 final size:20
Alignment explanation
Indices: 2241--2583 Score: 159
Period size: 21 Copynumber: 17.2 Consensus size: 20
2231 ACTCTTTGAA
*
2241 TTACTGATCACCTTTTACTC
1 TTACTGATTACCTTTTACTC
*
2261 TTTACTGATTACTATTTTACTC
1 -TTACTGATTAC-CTTTTACTC
* * *
2283 TTACTAATTACCACTTTGCTC
1 TTACTGATTACC-TTTTACTC
*
2304 TTACTGATTACTGTTTTACTC
1 TTACTGATTAC-CTTTTACTC
2325 TTACTGATTACC---T--T-
1 TTACTGATTACCTTTTACTC
*
2339 TTACTGATTACTATTTTACTC
1 TTACTGATTAC-CTTTTACTC
2360 TTTACTGATTACC---T--TC
1 -TTACTGATTACCTTTTACTC
*
2376 -TACTGATTACTATTTTACTC
1 TTACTGATTAC-CTTTTACTC
*
2396 TTACTGATTA-C----A-TT
1 TTACTGATTACCTTTTACTC
* *
2410 TTGCTGATTACTATTTTACTC
1 TTACTGATTAC-CTTTTACTC
*
2431 TTTACTGATTACCTTCTTACTTT
1 -TTACTGATTACCTT-TTAC-TC
*
2454 TTACTGATTACTATTTTACTC
1 TTACTGATTAC-CTTTTACTC
* * *
2475 TTTGCTGGTTACTATTTTACTC
1 -TTACTGATTAC-CTTTTACTC
* * *
2497 TCATTGATTACCATTTTGCTC
1 TTACTGATTACC-TTTTACTC
* *
2518 TTACTGATTACTATTTTACCTT
1 TTACTGATTAC-CTTTTA-CTC
* *
2540 TTACTGA-T-CTTTTTACTTT
1 TTACTGATTACCTTTTAC-TC
*
2559 TTACTGATTACCCTTTACTC
1 TTACTGATTACCTTTTACTC
2579 ATTAC
1 -TTAC
2584 CATTCTTCCT
Statistics
Matches: 244, Mismatches: 41, Indels: 74
0.68 0.11 0.21
Matches are distributed among these distances:
14 31 0.13
15 2 0.01
16 2 0.01
17 1 0.00
18 4 0.02
19 14 0.06
20 7 0.03
21 104 0.43
22 76 0.31
23 3 0.01
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.51
Consensus pattern (20 bp):
TTACTGATTACCTTTTACTC
Found at i:2395 original size:71 final size:71
Alignment explanation
Indices: 2305--2447 Score: 259
Period size: 71 Copynumber: 2.0 Consensus size: 71
2295 ACTTTGCTCT
* *
2305 TACTGATTACTGTTTTACTCTTACTGATTACCTTTTACTGATTACTATTTTACTCTTTACTGATT
1 TACTGATTACTATTTTACTCTTACTGATTACATTTTACTGATTACTATTTTACTCTTTACTGATT
2370 ACCTTC
66 ACCTTC
*
2376 TACTGATTACTATTTTACTCTTACTGATTACATTTTGCTGATTACTATTTTACTCTTTACTGATT
1 TACTGATTACTATTTTACTCTTACTGATTACATTTTACTGATTACTATTTTACTCTTTACTGATT
2441 ACCTTC
66 ACCTTC
2447 T
1 T
2448 TACTTTTTAC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.51
Consensus pattern (71 bp):
TACTGATTACTATTTTACTCTTACTGATTACATTTTACTGATTACTATTTTACTCTTTACTGATT
ACCTTC
Found at i:2462 original size:44 final size:43
Alignment explanation
Indices: 2338--2569 Score: 148
Period size: 44 Copynumber: 5.8 Consensus size: 43
2328 CTGATTACCT
2338 TTTACTGATTACTATTTTACTCTTTACTGATTAC-------CT-
1 TTTACTGATTACTATTTTACT-TTTACTGATTACTATTTTACTC
* *
2374 TCTACTGATTACTATTTTACTCTTACTGATTAC------A-T-
1 TTTACTGATTACTATTTTACTTTTACTGATTACTATTTTACTC
* * *
2409 TTTGCTGATTACTATTTTACTCTTTACTGATTACCT-TCTTACTT
1 TTTACTGATTACTATTTTACT-TTTACTGATTA-CTATTTTACTC
* *
2453 TTTACTGATTACTATTTTACTCTTTGCTGGTTACTATTTTACTC
1 TTTACTGATTACTATTTTACT-TTTACTGATTACTATTTTACTC
* * * * *
2497 -TCATTGATTACCATTTTGCTCTTACTGATTACTATTTTAC-C
1 TTTACTGATTACTATTTTACTTTTACTGATTACTATTTTACTC
2538 TTTTACTGA-T-CT-TTTTACTTTTTACTGATTAC
1 -TTTACTGATTACTATTTTAC-TTTTACTGATTAC
2570 CCTTTACTCA
Statistics
Matches: 160, Mismatches: 22, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
35 31 0.19
36 30 0.19
37 1 0.01
40 5 0.03
41 14 0.09
42 19 0.12
43 24 0.15
44 36 0.22
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.53
Consensus pattern (43 bp):
TTTACTGATTACTATTTTACTTTTACTGATTACTATTTTACTC
Found at i:2505 original size:101 final size:100
Alignment explanation
Indices: 2382--2569 Score: 247
Period size: 108 Copynumber: 1.8 Consensus size: 100
2372 CTTCTACTGA
*
2382 TTACTATTTTACTCTTACTGATTA-CATTTTG-CTGATTACTATTTTA-CTCTTTACTGATTACC
1 TTACTATTTTACTCTCACTGATTACCATTTTGTCTGATTACTATTTTACCT-TTTACTGA-T--C
2444 TTCTTACTTTTTACTGATTACTATTTTACTCTTTGCTGG
62 TTCTTACTTTTTACTGATTACTATTTTACTCTTTGCTGG
*
2483 TTACTATTTTACTCTCATTGATTACCATTTTGCTCTTACTGATTACTATTTTACCTTTTACTGAT
1 TTACTATTTTACTCTCACTGATTACCATTTTG----T-CTGATTACTATTTTACCTTTTACTGAT
*
2548 CTTTTTACTTTTTACTGATTAC
61 CTTCTTACTTTTTACTGATTAC
2570 CCTTTACTCA
Statistics
Matches: 76, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
101 22 0.29
102 7 0.09
105 21 0.28
107 1 0.01
108 23 0.30
109 2 0.03
ACGTcount: A:0.20, C:0.19, G:0.07, T:0.54
Consensus pattern (100 bp):
TTACTATTTTACTCTCACTGATTACCATTTTGTCTGATTACTATTTTACCTTTTACTGATCTTCT
TACTTTTTACTGATTACTATTTTACTCTTTGCTGG
Found at i:2640 original size:35 final size:34
Alignment explanation
Indices: 2557--2683 Score: 137
Period size: 35 Copynumber: 3.6 Consensus size: 34
2547 TCTTTTTACT
* **
2557 TTTTACTGATTACCCTTTACTCATTACCATTCTTC
1 TTTTACTGATTACTCTTTACTTTTTACCATT-TTC
* *
2592 CTTTACTGATTACTCTTTACTTTTTGCCATTGTTC
1 TTTTACTGATTACTCTTTACTTTTTACCATT-TTC
* *
2627 TTTTACTGATTACTCTTCACTTTTTATCATTTTAC
1 TTTTACTGATTACTCTTTACTTTTTACCATTTT-C
* *
2662 TCTTTACTAATTACTCCTTACT
1 T-TTTACTGATTACTCTTTACT
2684 AATTATTCTT
Statistics
Matches: 77, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
34 2 0.03
35 58 0.75
36 17 0.22
ACGTcount: A:0.19, C:0.24, G:0.04, T:0.53
Consensus pattern (34 bp):
TTTTACTGATTACTCTTTACTTTTTACCATTTTC
Found at i:2677 original size:14 final size:14
Alignment explanation
Indices: 2658--2697 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
2648 TTTTATCATT
2658 TTACTCTTTACTAA
1 TTACTCTTTACTAA
*
2672 TTACTCCTTACTAA
1 TTACTCTTTACTAA
*
2686 TTATTCTTTACT
1 TTACTCTTTACT
2698 CTTTACCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.53
Consensus pattern (14 bp):
TTACTCTTTACTAA
Found at i:2724 original size:21 final size:21
Alignment explanation
Indices: 2691--2730 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2681 ACTAATTATT
*
2691 CTTTACTCTTTACCATTTTTC
1 CTTTACTCATTACCATTTTTC
* *
2712 CTTTACTGATTACTATTTT
1 CTTTACTCATTACCATTTT
2731 ACTCTCTTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.03, T:0.57
Consensus pattern (21 bp):
CTTTACTCATTACCATTTTTC
Found at i:2760 original size:8 final size:8
Alignment explanation
Indices: 2747--2772 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
2737 TTGAATTTAA
2747 TTACCATT
1 TTACCATT
2755 TTACCATT
1 TTACCATT
2763 TTACCATT
1 TTACCATT
2771 TT
1 TT
2773 TCTCTTTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (8 bp):
TTACCATT
Found at i:2869 original size:74 final size:72
Alignment explanation
Indices: 2777--3010 Score: 262
Period size: 74 Copynumber: 3.2 Consensus size: 72
2767 CATTTTTCTC
* * * * ** *
2777 TTTACTGATCACTAATTTTTACTTTCTCCCCTAAGTATCAATTTACCGATTAATCCATTGACTTT
1 TTTACTGATTACT-ATTTTTAC-TTCTCCCTTAATTATCAATTTACTGATTAATCTTTTTAC-TT
2842 TAATTACTGA
63 TAATTACTGA
** *
2852 TTTACTGATTACTATTTTTACCTTGACCCTTAATTATCGATTTACTGATTACTATCTTTTTAC-T
1 TTTACTGATTACTATTTTTA-CTTCTCCCTTAATTATCAATTTACTGATTA--ATCTTTTTACTT
*
2916 TAATTGCTGA
63 TAATTACTGA
*
2926 TTTACTGATTACTACTTTTA---CTCCCTTAATTATCAATTTACTTGATTAATCTTTTTACTTT-
1 TTTACTGATTACTATTTTTACTTCTCCCTTAATTATCAATTTAC-TGATTAATCTTTTTACTTTA
2987 ATTACTGA
65 ATTACTGA
2995 TTTACTGATTACTATT
1 TTTACTGATTACTATT
3011 ACCTTGACTC
Statistics
Matches: 137, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
69 32 0.23
70 20 0.15
71 6 0.04
74 59 0.43
75 13 0.09
76 7 0.05
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.49
Consensus pattern (72 bp):
TTTACTGATTACTATTTTTACTTCTCCCTTAATTATCAATTTACTGATTAATCTTTTTACTTTAA
TTACTGA
Found at i:2878 original size:40 final size:37
Alignment explanation
Indices: 2841--3010 Score: 137
Period size: 34 Copynumber: 4.7 Consensus size: 37
2831 CCATTGACTT
2841 TTAATTACTGATTTACTGATTACTATTTTTACCTTGACCC
1 TTAATTACTGATTTACTGATTACTATTTTTA-CTTGA--C
*
2881 TTAATTA-TCGATTTACTGATTACTATCTTT--TT-AC
1 TTAATTACT-GATTTACTGATTACTATTTTTACTTGAC
* * **
2915 TTAATTGCTGATTTACTGATTACTACTTTTAC-TCCC
1 TTAATTACTGATTTACTGATTACTATTTTTACTTGAC
* *
2951 TTAATTA-TCAATTTACTTGATTA--ATCTTT--TT-AC
1 TTAATTACT-GATTTAC-TGATTACTATTTTTACTTGAC
*
2984 TTTATTACTGATTTACTGATTACTATT
1 TTAATTACTGATTTACTGATTACTATT
3011 ACCTTGACTC
Statistics
Matches: 106, Mismatches: 13, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
32 6 0.06
33 13 0.12
34 30 0.28
35 7 0.07
36 14 0.13
37 8 0.08
39 1 0.01
40 27 0.25
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.51
Consensus pattern (37 bp):
TTAATTACTGATTTACTGATTACTATTTTTACTTGAC
Found at i:3034 original size:124 final size:122
Alignment explanation
Indices: 2896--3133 Score: 311
Period size: 124 Copynumber: 1.9 Consensus size: 122
2886 TATCGATTTA
* * * *
2896 CTGATTACTATCTTTTTACTTAATTGCTGATTTACTGATTACTACTT-TT-ACTCCCTTAATTAT
1 CTGATTAATATCTTTTTACTTAATTACCGATTTACTGATTACTA-TTCTTGACT--CTTAACTAT
* *
2959 CAATTTACTTGATTAA-TCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTGACT
63 CAA-CTAC-TGATTAACTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
*
3020 CTGATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATC
1 CTGATTAATATCTTTTTACTTAATTACCGATTTACTGATTACTATT--CTTGACTCTTAACTATC
*
3085 AACTACTGATTAATCTCTTTTTACTTAATTACTGATTTACTTATTACTA
64 AACTACTGATTAA-CTCTTTTTACTTAATTACTGATTTACTGATTACTA
3134 CTTTTATTTT
Statistics
Matches: 100, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
123 9 0.09
124 43 0.43
125 43 0.43
126 2 0.02
127 3 0.03
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.49
Consensus pattern (122 bp):
CTGATTAATATCTTTTTACTTAATTACCGATTTACTGATTACTATTCTTGACTCTTAACTATCAA
CTACTGATTAACTCTTTTTACTTAATTACTGATTTACTGATTACTATTACCTTGACT
Found at i:3046 original size:55 final size:53
Alignment explanation
Indices: 2968--3076 Score: 182
Period size: 55 Copynumber: 2.0 Consensus size: 53
2958 TCAATTTACT
* *
2968 TGATTAATCTTTTTACTTTATTACTGATTTACTGATTACTATTACCTTGACTC
1 TGATTAATCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTC
3021 TGATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTC
1 TGATTAA--TCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTC
3076 T
1 T
3077 TAACTATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
53 7 0.13
55 45 0.87
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (53 bp):
TGATTAATCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTC
Found at i:3094 original size:70 final size:71
Alignment explanation
Indices: 3020--3452 Score: 317
Period size: 70 Copynumber: 6.1 Consensus size: 71
3010 TACCTTGACT
* *
3020 CTGATTAATCTCTTTTTACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATC
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACATTGACTCTTAACTATC
*
3085 AA-CTA
66 AATTTA
* ** **
3090 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTTATTACTACTTTTATTTTC-CTTAACTAT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTA-TTACATTGACTCTTAACTAT
* *
3154 TAATTCA
65 CAATTTA
* * * * *
3161 CTTGGTTAATCTTCTTACTTTGACTCTTAATCA-TCGATTTACTAATTACTATTACTTTAACTCT
1 C-TGATTAATC-TCTT--TTT-A--CTTAATTACT-GATTTACTGATTACTATTACATTGACTCT
3225 TAACTATCAATTTTA
58 TAACTATCAA-TTTA
* * * * * *
3240 CTGGTTACTAT-TAC-TTTGACTCTTAATTACTTAATTCACTGGTTACTATTATC-TCGACTCTT
1 CTGATTA--ATCT-CTTTTTA--CTTAATTAC-TGATTTACTGATTACTATTA-CATTGACTCTT
* *
3302 AATTACCAATTTA
59 AACTATCAATTTA
* *
3315 CTGATTAATCTC----T--TT--TTACTGATTTACTGATTACTATTACATTGACTCTTAATTACC
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACATTGACTCTTAACTATC
3372 AATTTA
66 AATTTA
* * * *
3378 CTGATTAATCTCTTTTTACTGAATTACTGATTTACCGATTTCTACTT---TT-ACTCTTAATTAT
1 CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTA-TTACATTGACTCTTAACTAT
3439 CAATTTA
65 CAATTTA
3446 CTGATTA
1 CTGATTA
3453 CCATTACTTT
Statistics
Matches: 294, Mismatches: 40, Indels: 60
0.75 0.10 0.15
Matches are distributed among these distances:
62 1 0.00
63 50 0.17
64 4 0.01
66 2 0.01
67 1 0.00
68 25 0.09
69 3 0.01
70 53 0.18
71 26 0.09
72 10 0.03
73 7 0.02
74 1 0.00
75 23 0.08
76 32 0.11
77 8 0.03
78 41 0.14
79 5 0.02
80 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (71 bp):
CTGATTAATCTCTTTTTACTTAATTACTGATTTACTGATTACTATTACATTGACTCTTAACTATC
AATTTA
Found at i:3098 original size:55 final size:55
Alignment explanation
Indices: 2982--3098 Score: 130
Period size: 55 Copynumber: 2.1 Consensus size: 55
2972 TAATCTTTTT
* * * * * ** *
2982 ACTTTATTACTGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTT
1 ACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTAACTAATCACTACTG
3037 ACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACT-ATCAACTACTG
1 ACTTAATTACCGATTTACTGATTACTATTACCTTGACTC-TAACTAATC-ACTACTG
3093 A-TTAAT
1 ACTTAAT
3099 CTCTTTTTAC
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
55 45 0.87
56 7 0.13
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (55 bp):
ACTTAATTACCGATTTACTGATTACTATTACCTTGACTCTAACTAATCACTACTG
Found at i:3245 original size:78 final size:74
Alignment explanation
Indices: 3038--3328 Score: 215
Period size: 78 Copynumber: 3.9 Consensus size: 74
3028 TCTCTTTTTA
* * * *
3038 CTTAATTACCGATTTACTGATTACTATTACCTTGACTCTTAACTATCAA-CTACTGATTAATCTC
1 CTTAATTA-CGATTTACTAATTACTATTA-CTTTACTCTTAACTATCAATTTACTGGTTAATCTC
3102 TT--TTT-A--
64 TTACTTTGACT
* * * *
3108 CTTAATTACTGATTTACTTATTACTACTTTTA-TTTTC-CTTAACTATTAATTCACTTGGTTAAT
1 CTTAATTAC-GATTTACTAATTACTA---TTACTTTACTCTTAACTATCAATTTAC-TGGTTAAT
3171 CTTCTTACTTTGACT
61 C-TCTTACTTTGACT
*
3186 CTTAATCATCGATTTACTAATTACTATTACTTTAACTCTTAACTATCAATTTTACTGGTT-A-CT
1 CTTAATTA-CGATTTACTAATTACTATTACTTT-ACTCTTAACTATCAA-TTTACTGGTTAATCT
*
3249 ATTACTTTGACT
63 CTTACTTTGACT
* * ** ** * * *
3261 CTTAATTACTTAATTCACTGGTTACTATTATCTCGACTCTTAATTACCAATTTACTGATTAATCT
1 CTTAATTAC--GATTTACTAATTACTATTA-CTTTACTCTTAACTATCAATTTACTGGTTAATCT
3326 CTT
63 CTT
3329 TTTACTGATT
Statistics
Matches: 175, Mismatches: 24, Indels: 37
0.74 0.10 0.16
Matches are distributed among these distances:
69 1 0.01
70 34 0.19
71 5 0.03
72 8 0.05
73 7 0.04
74 1 0.01
75 34 0.19
76 34 0.19
77 8 0.05
78 38 0.22
79 5 0.03
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.47
Consensus pattern (74 bp):
CTTAATTACGATTTACTAATTACTATTACTTTACTCTTAACTATCAATTTACTGGTTAATCTCTT
ACTTTGACT
Found at i:3249 original size:38 final size:36
Alignment explanation
Indices: 3175--3317 Score: 144
Period size: 38 Copynumber: 3.8 Consensus size: 36
3165 GTTAATCTTC
* **
3175 TTACTTTGACTCTTAATCATCGATTTACTAATTACTA
1 TTACTTTGACTCTTAAT-ATCAATTTACTGGTTACTA
*
3212 TTACTTTAACTCTTAACTATCAATTTTACTGGTTACTA
1 TTACTTTGACTCTTAA-TATCAA-TTTACTGGTTACTA
* *
3250 TTACTTTGACTCTTAATTACTTAATTCACTGGTTACTA
1 TTACTTTGACTCTTAA-TA-TCAATTTACTGGTTACTA
* *
3288 TTA-TCTCGACTCTTAATTACCAATTTACTG
1 TTACT-TTGACTCTTAA-TATCAATTTACTG
3318 ATTAATCTCT
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
37 28 0.31
38 59 0.66
39 3 0.03
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (36 bp):
TTACTTTGACTCTTAATATCAATTTACTGGTTACTA
Found at i:3350 original size:63 final size:63
Alignment explanation
Indices: 3266--3409 Score: 227
Period size: 63 Copynumber: 2.3 Consensus size: 63
3256 TGACTCTTAA
* *
3266 TTACTTAATTCACTGGTTACTATTATC-TCGACTCTTAATTACCAATTTACTGATTAATCTCTTT
1 TTACTGAATT-ACTGATTACTATTA-CATCGACTCTTAATTACCAATTTACTGATTAATCTCTTT
* *
3330 TTACTGATTTACTGATTACTATTACATTGACTCTTAATTACCAATTTACTGATTAATCTCTTT
1 TTACTGAATTACTGATTACTATTACATCGACTCTTAATTACCAATTTACTGATTAATCTCTTT
3393 TTACTGAATTACTGATT
1 TTACTGAATTACTGATT
3410 TACCGATTTC
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
62 1 0.01
63 65 0.88
64 8 0.11
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (63 bp):
TTACTGAATTACTGATTACTATTACATCGACTCTTAATTACCAATTTACTGATTAATCTCTTT
Found at i:3460 original size:63 final size:63
Alignment explanation
Indices: 3282--3460 Score: 161
Period size: 63 Copynumber: 2.7 Consensus size: 63
3272 AATTCACTGG
** *
3282 TTACTATTATCTCGACTCTTAATTACCAATTTACTGATTA--ATCT-CTTTTTACTGATTTACTG
1 TTACTATTAT-T-GACTCTTAATTACCAATTTACTGATTACCAT-TACTAATTACTGATTTACCG
3344 A
63 A
*
3345 TTACTATTACATTGACTCTTAATTACCAATTTACTGATTAATCTCTTTTTACTGAATTACTGATT
1 TTACTATT--ATTGACTCTTAATTACCAATTTACTGATT-A-C-C--ATTACT-AATTACTGATT
3410 TACCGA
58 TACCGA
* *
3416 TTTCTACTT-TT-ACTCTTAATTATCAATTTACTGATTACCATTACT
1 TTACTA-TTATTGACTCTTAATTACCAATTTACTGATTACCATTACT
3461 TTGGCTCTTA
Statistics
Matches: 97, Mismatches: 7, Indels: 24
0.76 0.05 0.19
Matches are distributed among these distances:
63 39 0.40
64 2 0.02
65 3 0.03
66 1 0.01
67 1 0.01
68 24 0.25
69 3 0.03
70 3 0.03
71 19 0.20
72 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (63 bp):
TTACTATTATTGACTCTTAATTACCAATTTACTGATTACCATTACTAATTACTGATTTACCGA
Found at i:9823 original size:22 final size:22
Alignment explanation
Indices: 9797--9843 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
9787 ATTTATTCAT
9797 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
9819 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
9841 TAT
1 TAT
9844 AATATAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:9839 original size:11 final size:11
Alignment explanation
Indices: 9797--9839 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
9787 ATTTATTCAT
*
9797 TATTAATTAAC
1 TATTAATTAGC
*
9808 TATTAATTAGA
1 TATTAATTAGC
9819 TATTAATTAGC
1 TATTAATTAGC
9830 TATTAATTAG
1 TATTAATTAG
9840 ATATAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:11995 original size:32 final size:32
Alignment explanation
Indices: 11959--12077 Score: 141
Period size: 33 Copynumber: 3.7 Consensus size: 32
11949 TGCCCTGGCT
*
11959 AAGCCGCCCCAGTGGGGCGGCCTGTCGTGGTG
1 AAGCCGCCCCAGTGGGGCGGCCTGCCGTGGTG
* * *
11991 AAGCCGCCCTAGTGGGACGGCCTGCCCATGGTG
1 AAGCCGCCCCAGTGGGGCGGCCTG-CCGTGGTG
* *
12024 AAGCCGCCCCAGTGGGGCCGCTCCGCCGTGGTTG
1 AAGCCGCCCCAGTGGGGCGGC-CTGCCGTGG-TG
*
12058 -AGCCTCCCCAGTGGGGCGGC
1 AAGCCGCCCCAGTGGGGCGGC
12078 TTCACCACGG
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
32 22 0.30
33 47 0.64
34 4 0.05
ACGTcount: A:0.11, C:0.35, G:0.39, T:0.14
Consensus pattern (32 bp):
AAGCCGCCCCAGTGGGGCGGCCTGCCGTGGTG
Found at i:12028 original size:33 final size:32
Alignment explanation
Indices: 11940--12039 Score: 130
Period size: 32 Copynumber: 3.1 Consensus size: 32
11930 CCGTCACACC
*
11940 GGGACGGCTTGCCCTGGCT-AAGCCGCCCCAGT
1 GGGACGGCCTGCCCTGG-TGAAGCCGCCCCAGT
* * * *
11972 GGGGCGGCCTGTCGTGGTGAAGCCGCCCTAGT
1 GGGACGGCCTGCCCTGGTGAAGCCGCCCCAGT
12004 GGGACGGCCTGCCCATGGTGAAGCCGCCCCAGT
1 GGGACGGCCTGCCC-TGGTGAAGCCGCCCCAGT
12037 GGG
1 GGG
12040 GCCGCTCCGC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
31 1 0.02
32 36 0.63
33 20 0.35
ACGTcount: A:0.12, C:0.33, G:0.40, T:0.15
Consensus pattern (32 bp):
GGGACGGCCTGCCCTGGTGAAGCCGCCCCAGT
Found at i:12093 original size:65 final size:64
Alignment explanation
Indices: 11940--12096 Score: 158
Period size: 65 Copynumber: 2.4 Consensus size: 64
11930 CCGTCACACC
* * * * * *
11940 GGGACGGCTTGCCC-TGGCTAAGCCGCCCCAGTGGGGCGGCCTGTCGTGGTGAAGCCGCCCTAGT
1 GGGACGGCCTGCCCACGG-TAAGCCGCCCCAGTGGGGCCGCCCGCCGTGGTGAAGCCGCCCCAGT
* *
12004 GGGACGGCCTGCCCATGGTGAAGCCGCCCCAGTGGGGCCGCTCCGCCGTGGTTG-AGCCTCCCCA
1 GGGACGGCCTGCCCACGGT-AAGCCGCCCCAGTGGGGCCGC-CCGCCGTGG-TGAAGCCGCCCCA
12068 GT
63 GT
* *
12070 GGGGCGG-CTTCACCACGGTAAGCCGCC
1 GGGACGGCCTGC-CCACGGTAAGCCGCC
12097 TTCTTGGGAC
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
64 14 0.18
65 34 0.43
66 29 0.37
67 2 0.03
ACGTcount: A:0.11, C:0.36, G:0.38, T:0.15
Consensus pattern (64 bp):
GGGACGGCCTGCCCACGGTAAGCCGCCCCAGTGGGGCCGCCCGCCGTGGTGAAGCCGCCCCAGT
Found at i:12732 original size:6 final size:6
Alignment explanation
Indices: 12721--12746 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12711 CTTCCACTTT
12721 CACCGC CACCGC CACCGC CACCGC CA
1 CACCGC CACCGC CACCGC CACCGC CA
12747 TCAGCCTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.65, G:0.15, T:0.00
Consensus pattern (6 bp):
CACCGC
Found at i:21029 original size:77 final size:79
Alignment explanation
Indices: 20900--21052 Score: 265
Period size: 77 Copynumber: 2.0 Consensus size: 79
20890 TGGTTAAATA
*
20900 TAATTTATGACTATATACTTTTTGCAAAGCCACCATGTCCTGGTTATTAGCATTTTGAAGTTGAA
1 TAATTTATGACCATATACTTTTTGCAAAGCCACCATGTCCTGGTTATTAGCATTTTGAAGTTGAA
20965 GCTGCTGGCTTGGT
66 GCTGCTGGCTTGGT
* *
20979 TAATTTATTACCATTTAC-TTTTGC-AAGCCACCATGTCCTGGTTATTAGCATTTTGAAGTTGAA
1 TAATTTATGACCATATACTTTTTGCAAAGCCACCATGTCCTGGTTATTAGCATTTTGAAGTTGAA
21042 GCTGCTGGCTT
66 GCTGCTGGCTT
21053 TGTCAATAAC
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
77 50 0.70
78 6 0.08
79 15 0.21
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.40
Consensus pattern (79 bp):
TAATTTATGACCATATACTTTTTGCAAAGCCACCATGTCCTGGTTATTAGCATTTTGAAGTTGAA
GCTGCTGGCTTGGT
Found at i:21735 original size:6 final size:6
Alignment explanation
Indices: 21706--21769 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
21696 CTATGTGGCA
* * *
21706 TTTTAT TATTTA- ATTTATT TTTTAT TTTTAT ATTT-T TTATAT TTTTAT
1 TTTTAT T-TTTAT TTTTA-T TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
* *
21754 TTTCAT TTTGAT TTTT
1 TTTTAT TTTTAT TTTT
21770 CTCATCTTTC
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
5 7 0.16
6 30 0.67
7 8 0.18
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:21741 original size:15 final size:15
Alignment explanation
Indices: 21719--21756 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
21709 TATTATTTAA
21719 TTTATTTTTTAT-TT
1 TTTATTTTTTATATT
21733 TTATATTTTTTATATT
1 TT-TATTTTTTATATT
21749 TTTATTTT
1 TTTATTTT
21757 CATTTTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.09
15 16 0.73
16 4 0.18
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTATTTTTTATATT
Found at i:32463 original size:1 final size:1
Alignment explanation
Indices: 32457--32496 Score: 71
Period size: 1 Copynumber: 40.0 Consensus size: 1
32447 ATATTATAGG
*
32457 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
32497 AAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Done.