Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006807.1 Corchorus capsularis cultivar CVL-1 contig06828, 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: 71094
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1053 original size:1 final size:1
Alignment explanation
Indices: 1047--1073 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1037 CTCAAATTGG
1047 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1074 GAGCAAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2716 original size:35 final size:34
Alignment explanation
Indices: 2669--2783 Score: 137
Period size: 35 Copynumber: 3.4 Consensus size: 34
2659 TGAATCAGTA
* *
2669 ATAAGAAACTTAATTCAGGGCAATTAAGTAAGTC
1 ATAAGTAACTTAATTCAGGGTAATTAAGTAAGTC
* *
2703 AGTAAGTAACTTAATTCAAGATAATTAAGTAAGTC
1 A-TAAGTAACTTAATTCAGGGTAATTAAGTAAGTC
* *
2738 --AA-CAACTTAATTCAGGGTAATTAAGTAAGTA
1 ATAAGTAACTTAATTCAGGGTAATTAAGTAAGTC
*
2769 ATAGGTAACTTAATT
1 ATAAGTAACTTAATT
2784 AAGTCAGTAA
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
31 25 0.37
32 2 0.03
33 1 0.01
34 10 0.15
35 29 0.43
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (34 bp):
ATAAGTAACTTAATTCAGGGTAATTAAGTAAGTC
Found at i:2733 original size:27 final size:27
Alignment explanation
Indices: 2703--2769 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 27
2693 TAAGTAAGTC
2703 AGTAAGTAACTTAATTCAAGATAATTA
1 AGTAAGTAACTTAATTCAAGATAATTA
* *
2730 AGTAAGTCAACAACTTAATTCAGGGTAATTA
1 AGTAAGT----AACTTAATTCAAGATAATTA
2761 AGTAAGTAA
1 AGTAAGTAA
2770 TAGGTAACTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
27 9 0.26
31 25 0.74
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (27 bp):
AGTAAGTAACTTAATTCAAGATAATTA
Found at i:2797 original size:86 final size:87
Alignment explanation
Indices: 2692--2854 Score: 238
Period size: 86 Copynumber: 1.9 Consensus size: 87
2682 TTCAGGGCAA
2692 TTAAGTAAGTCAGTAAGTAACTTAATTCAAGATAATTAAGTAAGTCA-ACAACTTAATTCAGGGT
1 TTAAGTAAGTCAGTAAGTAACTTAATTCAAGATAATTAAGTAAGTCATACAACTTAATTCAGGGT
2756 AATTAAGTAAGTAATAGGTAAC
66 AATTAAGTAAGTAATAGGTAAC
* * * * **
2778 TTAATTAAGTCAGTAAGTAACTTAATTCAGGGTAATTAAGTGAGTCAGTTGTAACTTAATTCAGG
1 TTAAGTAAGTCAGTAAGTAACTTAATTCAAGATAATTAAGTAAGTCA--TACAACTTAATTCAGG
*
2843 TTAATTAAGTAA
64 GTAATTAAGTAA
2855 TTCAGTAATC
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
86 43 0.64
89 24 0.36
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (87 bp):
TTAAGTAAGTCAGTAAGTAACTTAATTCAAGATAATTAAGTAAGTCATACAACTTAATTCAGGGT
AATTAAGTAAGTAATAGGTAAC
Found at i:2799 original size:21 final size:24
Alignment explanation
Indices: 2755--2804 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2745 TAATTCAGGG
2755 TAATTAAGTAAGTAATAGGTAACT
1 TAATTAAGTAAGTAATAGGTAACT
*
2779 TAATTAAGTCAGT-A-A-GTAACT
1 TAATTAAGTAAGTAATAGGTAACT
2800 TAATT
1 TAATT
2805 CAGGGTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 11 0.44
22 1 0.04
23 1 0.04
24 12 0.48
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (24 bp):
TAATTAAGTAAGTAATAGGTAACT
Found at i:2924 original size:35 final size:35
Alignment explanation
Indices: 2785--3333 Score: 544
Period size: 35 Copynumber: 16.0 Consensus size: 35
2775 AACTTAATTA
2785 AGTCAGTAAGT-AACTTAATTCAGGGTAATTAAGTG
1 AGTCAGTAA-TCAACTTAATTCAGGGTAATTAAGTG
** * *
2820 AGTCAGTTGT-AACTTAATTCAGGTTAATTAAGTA
1 AGTCAGTAATCAACTTAATTCAGGGTAATTAAGTG
* * *
2854 ATTCAGTAATCAAATTTAATTCATGGTAATTAAGTG
1 AGTCAGTAATC-AACTTAATTCAGGGTAATTAAGTG
*
2890 AGTCAGTAATCAACTTAGTTCAGGGTAATTAAGTG
1 AGTCAGTAATCAACTTAATTCAGGGTAATTAAGTG
* * *
2925 AGTCAATAATCAACTTAATTTAGAGTAATTAAGT-
1 AGTCAGTAATCAACTTAATTCAGGGTAATTAAGTG
* *
2959 ATTCAGTTAGT-AACTTAATTCAGGGTAATT-A---
1 AGTCAG-TAATCAACTTAATTCAGGGTAATTAAGTG
2990 AGT-AGT--TCAACTTTAATTCAGGGTAATTAAGT-
1 AGTCAGTAATCAAC-TTAATTCAGGGTAATTAAGTG
* *
3022 AGTTCAATGAGT-AACTTAATTCAGGGTAATTAAGTG
1 AG-TCAGT-AATCAACTTAATTCAGGGTAATTAAGTG
* *
3058 AGTCGGTAATCAACTTAATTCAGGGTAATTAAGTA
1 AGTCAGTAATCAACTTAATTCAGGGTAATTAAGTG
*
3093 AGTCAGTAATCAACCTTAATTCAGGGTAATTAAGTA
1 AGTCAGTAATCAA-CTTAATTCAGGGTAATTAAGTG
* * * ** *
3129 ATTCAGTTAGT-AACTTAGTTCAGGAAAATTAAGTA
1 AGTCAG-TAATCAACTTAATTCAGGGTAATTAAGTG
*
3164 AGACAG---T-AACTTAATTCAGGGTAATTAAGTG
1 AGTCAGTAATCAACTTAATTCAGGGTAATTAAGTG
*
3195 AGTCAGTAATCAACTTAATTCAGGGTAATCAAAG-G
1 AGTCAGTAATCAACTTAATTCAGGGTAAT-TAAGTG
* ** * *
3230 AATTCAGTTTTCAACTTAAATCAGGGTAATTAAGTC
1 -AGTCAGTAATCAACTTAATTCAGGGTAATTAAGTG
* *
3266 AATCAGTAATCAACTTAATTCAGGGTAATTAAGTA
1 AGTCAGTAATCAACTTAATTCAGGGTAATTAAGTG
* * *
3301 AGT-AATAAGCAATTTAATTCAGGGTAATTAAGT
1 AGTCAGTAATCAACTTAATTCAGGGTAATTAAGT
3334 TTAGTTAGAA
Statistics
Matches: 431, Mismatches: 59, Indels: 49
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.00
28 3 0.01
29 17 0.04
30 3 0.01
31 28 0.06
32 2 0.00
33 2 0.00
34 83 0.19
35 196 0.45
36 92 0.21
37 4 0.01
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (35 bp):
AGTCAGTAATCAACTTAATTCAGGGTAATTAAGTG
Found at i:2936 original size:71 final size:69
Alignment explanation
Indices: 2785--3333 Score: 552
Period size: 71 Copynumber: 8.0 Consensus size: 69
2775 AACTTAATTA
* ** *
2785 AGTCAGTAAGT-AACTTAATTCAGGGTAATTAAGTGAGTCAGTTGTAACTTAATTCAGGTTAATT
1 AGTCAGTAA-TCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATAACTTAATTCAGGGTAATT
*
2849 AAGTA
65 AAGTG
* * * * *
2854 ATTCAGTAATCAAATTTAATTCATGGTAATTAAGTGAGTCAGTAATCAACTTAGTTCAGGGTAAT
1 AGTCAGTAATC-AACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT-AACTTAATTCAGGGTAAT
2919 TAAGTG
64 TAAGTG
* * * * *
2925 AGTCAATAATCAACTTAATTTAGAGTAATTAAGT-ATTCAGTTAGTAACTTAATTCAGGGTAATT
1 AGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAG-TAATAACTTAATTCAGGGTAATT
2989 -A---
65 AAGTG
* *
2990 AGT-AGT--TCAACTTTAATTCAGGGTAATTAAGT-AGTTCAATGAGTAACTTAATTCAGGGTAA
1 AGTCAGTAATCAAC-TTAATTCAGGGTAATTAAGTAAG-TCAGT-AATAACTTAATTCAGGGTAA
3051 TTAAGTG
63 TTAAGTG
*
3058 AGTCGGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATCAACCTTAATTCAGGGTAAT
1 AGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAAT-AA-CTTAATTCAGGGTAAT
*
3123 TAAGTA
64 TAAGTG
* * * ** *
3129 ATTCAGTTAGT-AACTTAGTTCAGGAAAATTAAGTAAGACAG---TAACTTAATTCAGGGTAATT
1 AGTCAG-TAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATAACTTAATTCAGGGTAATT
3190 AAGTG
65 AAGTG
* * * ** *
3195 AGTCAGTAATCAACTTAATTCAGGGTAATCAAAGGAATTCAGTTTTCAACTTAAATCAGGGTAAT
1 AGTCAGTAATCAACTTAATTCAGGGTAAT-TAAGTAAGTCAGTAAT-AACTTAATTCAGGGTAAT
*
3260 TAAGTC
64 TAAGTG
* * * *
3266 AATCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGT-AATAAGCAATTTAATTCAGGGTAATT
1 AGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAA-TAACTTAATTCAGGGTAATT
3330 AAGT
65 AAGT
3334 TTAGTTAGAA
Statistics
Matches: 400, Mismatches: 55, Indels: 50
0.79 0.11 0.10
Matches are distributed among these distances:
62 5 0.01
63 20 0.05
64 27 0.07
65 7 0.02
66 41 0.10
67 10 0.03
68 6 0.01
69 58 0.14
70 85 0.21
71 138 0.34
72 3 0.01
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (69 bp):
AGTCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTCAGTAATAACTTAATTCAGGGTAATTA
AGTG
Found at i:3006 original size:29 final size:29
Alignment explanation
Indices: 2973--3028 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
2963 AGTTAGTAAC
2973 TTAATTCAGGGTAATTAAGTAGTTCAACT
1 TTAATTCAGGGTAATTAAGTAGTTCAACT
3002 TTAATTCAGGGTAATTAAGTAGTTCAA
1 TTAATTCAGGGTAATTAAGTAGTTCAA
3029 TGAGTAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.38
Consensus pattern (29 bp):
TTAATTCAGGGTAATTAAGTAGTTCAACT
Found at i:3194 original size:137 final size:139
Alignment explanation
Indices: 2785--3333 Score: 469
Period size: 137 Copynumber: 4.0 Consensus size: 139
2775 AACTTAATTA
* ** * *
2785 AGTCAGTAAGT-AACTTAATTCAGGGTAAT-TAAGTG-AGTCAGTTGT-AACTTAATTCAGGTTA
1 AGTCAGTAA-TCAACTTAATTCAGGGTAATCAAAG-GAAGTCAGTAATCAACTTAAATCAGGGTA
* * * * *
2846 ATTAAGT-AATTCAGTAATCAAATTTAATTCATGG-TAATTAAGTGAGTCAGTAA-TCAACTTAG
64 ATTAAGTCAA-TCAGTAATC-AACTTAATTCA-GGAAAATTAAGTAAG--AATAAGT-AACTTAA
2908 TTCAGGGTAATTAAGTG
123 TTCAGGGTAATTAAGTG
* * * * * * * *
2925 AGTCAATAATCAACTTAATTTAGAGTAAT-TAA-GTATTCAGTTAGT-AACTTAATTCAGGGTAA
1 AGTCAGTAATCAACTTAATTCAGGGTAATCAAAGGAAGTCAG-TAATCAACTTAAATCAGGGTAA
** *
2987 TTAAG----T-AGT--TCAACTTTAATTCAGGGTAATTAAGT-AGTTCAATGAGTAACTTAATTC
65 TTAAGTCAATCAGTAATCAAC-TTAATTCAGGAAAATTAAGTAAG---AATAAGTAACTTAATTC
3044 AGGGTAATTAAGTG
126 AGGGTAATTAAGTG
* * * *
3058 AGTCGGTAATCAACTTAATTCAGGGTAAT-TAAGTAAGTCAGTAATCAACCTTAATTCAGGGTAA
1 AGTCAGTAATCAACTTAATTCAGGGTAATCAAAGGAAGTCAGTAATCAA-CTTAAATCAGGGTAA
* * *
3122 TTAAGT-AATTCAGTTAGT-AACTTAGTTCAGGAAAATTAAGTAAG-A-CAGTAACTTAATTCAG
65 TTAAGTCAA-TCAG-TAATCAACTTAATTCAGGAAAATTAAGTAAGAATAAGTAACTTAATTCAG
3183 GGTAATTAAGTG
128 GGTAATTAAGTG
* **
3195 AGTCAGTAATCAACTTAATTCAGGGTAATCAAAGGAATTCAGTTTTCAACTTAAATCAGGGTAAT
1 AGTCAGTAATCAACTTAATTCAGGGTAATCAAAGGAAGTCAGTAATCAACTTAAATCAGGGTAAT
** * *
3260 TAAGTCAATCAGTAATCAACTTAATTCAGGGTAATTAAGTAAGTAATAAGCAATTTAATTCAGGG
66 TAAGTCAATCAGTAATCAACTTAATTCAGGAAAATTAAGTAAG-AATAAGTAACTTAATTCAGGG
3325 TAATTAAGT
130 TAATTAAGT
3334 TTAGTTAGAA
Statistics
Matches: 348, Mismatches: 36, Indels: 50
0.80 0.08 0.12
Matches are distributed among these distances:
132 6 0.02
133 78 0.22
134 8 0.02
135 23 0.07
136 4 0.01
137 102 0.29
138 18 0.05
139 8 0.02
140 77 0.22
141 18 0.05
142 5 0.01
143 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (139 bp):
AGTCAGTAATCAACTTAATTCAGGGTAATCAAAGGAAGTCAGTAATCAACTTAAATCAGGGTAAT
TAAGTCAATCAGTAATCAACTTAATTCAGGAAAATTAAGTAAGAATAAGTAACTTAATTCAGGGT
AATTAAGTG
Found at i:4382 original size:53 final size:53
Alignment explanation
Indices: 4302--4460 Score: 318
Period size: 53 Copynumber: 3.0 Consensus size: 53
4292 ACAAACAGCT
4302 GTTTAGGAACAACTCTTTCTCCTTGGTTCTGGTTGCAACACATGTGCTTTGGG
1 GTTTAGGAACAACTCTTTCTCCTTGGTTCTGGTTGCAACACATGTGCTTTGGG
4355 GTTTAGGAACAACTCTTTCTCCTTGGTTCTGGTTGCAACACATGTGCTTTGGG
1 GTTTAGGAACAACTCTTTCTCCTTGGTTCTGGTTGCAACACATGTGCTTTGGG
4408 GTTTAGGAACAACTCTTTCTCCTTGGTTCTGGTTGCAACACATGTGCTTTGGG
1 GTTTAGGAACAACTCTTTCTCCTTGGTTCTGGTTGCAACACATGTGCTTTGGG
4461 ATATTTGTCT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 106 1.00
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.38
Consensus pattern (53 bp):
GTTTAGGAACAACTCTTTCTCCTTGGTTCTGGTTGCAACACATGTGCTTTGGG
Found at i:6104 original size:30 final size:29
Alignment explanation
Indices: 6068--6130 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
6058 TTTACCAAAG
*
6068 TATAATACCTTGAAAACTTAATTCCCATTC
1 TATAATA-CTTGAAAACTTAATTCCCAATC
* ** *
6098 TATAATAGTTTTAAATTTAATTCCCAATC
1 TATAATACTTGAAAACTTAATTCCCAATC
6127 TATA
1 TATA
6131 GTGTTTCTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.41
Consensus pattern (29 bp):
TATAATACTTGAAAACTTAATTCCCAATC
Found at i:6800 original size:25 final size:27
Alignment explanation
Indices: 6760--6809 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
6750 AACCTAATTC
*
6760 GTTTTTTATTTTCT-AAGATTAAAAGT
1 GTTTTTTATTTCCTAAAGATTAAAAGT
6786 GTTTTTT-TTTCCTAAAGATTAAAA
1 GTTTTTTATTTCCTAAAGATTAAAA
6810 AAGGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (27 bp):
GTTTTTTATTTCCTAAAGATTAAAAGT
Found at i:11699 original size:6 final size:6
Alignment explanation
Indices: 11688--11713 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11678 TGATGATGAG
11688 GACGAT GACGAT GACGAT GACGAT GA
1 GACGAT GACGAT GACGAT GACGAT GA
11714 TGCCACGGAT
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:0.35, C:0.15, G:0.35, T:0.15
Consensus pattern (6 bp):
GACGAT
Found at i:16548 original size:22 final size:22
Alignment explanation
Indices: 16523--16616 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 22
16513 TTGACGTCCT
16523 TATGAAATTTTGATAACATTCC
1 TATGAAATTTTGATAACATTCC
*
16545 TATGAAATTATGAT-A-ATTACAC
1 TATGAAATTTTGATAACATT-C-C
* * *
16567 TAT----TTTTTATGAC-GTCC
1 TATGAAATTTTGATAACATTCC
16584 TTATGAAATTTTGATAACATTCC
1 -TATGAAATTTTGATAACATTCC
16607 TATGAAATTT
1 TATGAAATTT
16617 CAATAACGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
17 1 0.02
18 9 0.16
19 2 0.04
20 3 0.05
21 2 0.04
22 35 0.64
23 3 0.05
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.44
Consensus pattern (22 bp):
TATGAAATTTTGATAACATTCC
Found at i:16563 original size:62 final size:62
Alignment explanation
Indices: 16487--16615 Score: 233
Period size: 62 Copynumber: 2.1 Consensus size: 62
16477 ATTAAATTAA
16487 AAATTATGATAATTACACCATTTTTGT-TGACGTCCTTATGAAATTTTGATAACATTCCTATG
1 AAATTATGATAATTACACCATTTTT-TATGACGTCCTTATGAAATTTTGATAACATTCCTATG
*
16549 AAATTATGATAATTACACTATTTTTTATGACGTCCTTATGAAATTTTGATAACATTCCTATG
1 AAATTATGATAATTACACCATTTTTTATGACGTCCTTATGAAATTTTGATAACATTCCTATG
16611 AAATT
1 AAATT
16616 TCAATAACGA
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
61 1 0.02
62 64 0.98
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (62 bp):
AAATTATGATAATTACACCATTTTTTATGACGTCCTTATGAAATTTTGATAACATTCCTATG
Found at i:16631 original size:62 final size:62
Alignment explanation
Indices: 16487--16631 Score: 186
Period size: 62 Copynumber: 2.3 Consensus size: 62
16477 ATTAAATTAA
* ** *
16487 AAATTATGATAATTACACCATTTTTGTTGACGTCCTTATGAAATTTTGATAACATTCCTATG
1 AAATTATAATAACGACACTATTTTTGTTGACGTCCTTATGAAATTTTGATAACATTCCTATG
* **
16549 AAATTATGATAATTACACTATTTTT-TATGACGTCCTTATGAAATTTTGATAACATTCCTATG
1 AAATTATAATAACGACACTATTTTTGT-TGACGTCCTTATGAAATTTTGATAACATTCCTATG
*
16611 AAATT-TCAATAACGATACTAT
1 AAATTAT-AATAACGACACTAT
16632 GGAATTTCGA
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
61 2 0.03
62 74 0.97
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (62 bp):
AAATTATAATAACGACACTATTTTTGTTGACGTCCTTATGAAATTTTGATAACATTCCTATG
Found at i:16667 original size:21 final size:22
Alignment explanation
Indices: 16643--16687 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
16633 GAATTTCGAG
* *
16643 AACCTTTTTAT-AAATTTTTTT
1 AACCTTCTTATGAAATTTTGTT
16664 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
16686 AA
1 AA
16688 TATCCCTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.31, C:0.11, G:0.04, T:0.53
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:16887 original size:23 final size:22
Alignment explanation
Indices: 16831--16887 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 22
16821 CCTCCATATG
16831 AATTGTCAGTAATCACACTCTGA
1 AATTGTCA-TAATCACACTCTGA
* * *
16854 AATTTTGATAATCATAC-CATGAA
1 AATTGTCATAATCACACTC-TG-A
16877 AATTGTCATAA
1 AATTGTCATAA
16888 CCTTGGTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
21 1 0.04
22 10 0.37
23 16 0.59
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (22 bp):
AATTGTCATAATCACACTCTGA
Found at i:16912 original size:23 final size:23
Alignment explanation
Indices: 16898--16978 Score: 101
Period size: 23 Copynumber: 3.5 Consensus size: 23
16888 CCTTGGTATG
16898 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
* *
16921 AAATTTTGATAAATCTCGCTATA
1 AAATTTTGATAAACCTCCCTATA
* *
16944 AAATTTTGAT-AACCTTCTTATGA
1 AAATTTTGATAAACCTCCCTAT-A
*
16967 AAATCTTGATAA
1 AAATTTTGATAA
16979 CTACAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 7 0.14
23 41 0.84
24 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:17047 original size:45 final size:44
Alignment explanation
Indices: 16894--17146 Score: 170
Period size: 44 Copynumber: 5.8 Consensus size: 44
16884 ATAACCTTGG
* *
16894 TATGAAATTTTGATAAACCTCCCTATAAAATTTTGAT-AA-ATCT
1 TATGAAATTTTGAT-AACCTCCCTATGAAATTTTGATCAACATAT
* * * *
16937 CGCTATAAAATTTTGATAACCTTCTTATGAAAATCTTGAT-AAC----
1 ---TATGAAATTTTGATAACCTCCCTATG-AAATTTTGATCAACATAT
* **
16980 TA-CAAATTTTGATAACCTCCCTATGATTTTTTGAT-AACATCAT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATCAACAT-AT
* * *
17023 TAATGAAATTTTGTTAATCTCCCTATGAAATTTTGATCTACATAT
1 T-ATGAAATTTTGATAACCTCCCTATGAAATTTTGATCAACATAT
* * * *
17068 TATGAAATTTTGATAACC-CTCTTATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCTC-CCTATGAAATTTTGATCAAC-ATAT
* * *
17112 TATGAAATTTTGGTAACCTTCGTATG-AATTTTGAT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGAT
17147 ATCCTCCCTG
Statistics
Matches: 166, Mismatches: 27, Indels: 30
0.74 0.12 0.13
Matches are distributed among these distances:
38 10 0.06
39 20 0.12
40 2 0.01
43 12 0.07
44 54 0.33
45 40 0.24
46 28 0.17
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCCTATGAAATTTTGATCAACATAT
Found at i:17092 original size:22 final size:22
Alignment explanation
Indices: 16894--17147 Score: 102
Period size: 22 Copynumber: 11.7 Consensus size: 22
16884 ATAACCTTGG
* *
16894 TATGAAATTTTGATAAACCTCCC
1 TATGAAATTTTGATAACCCT-CT
* ** *
16917 TATAAAATTTTGATAAATCTCGC
1 TATGAAATTTTGATAACCCTC-T
* *
16940 TATAAAATTTTGATAACCTTCT
1 TATGAAATTTTGATAACCCTCT
*
16962 TATGAAAATCTTGATAA----C-
1 TATG-AAATTTTGATAACCCTCT
* *
16980 TA-CAAATTTTGATAA-CCTCCC
1 TATGAAATTTTGATAACCCT-CT
** *
17001 TATGATTTTTTGATAA-CATCAT
1 TATGAAATTTTGATAACCCTC-T
*
17023 TAATGAAATTTTGTTAATCTCC-C-
1 T-ATGAAATTTTGATAA-C-CCTCT
* * *
17046 TATGAAATTTTGATCTA-CATAT
1 TATGAAATTTTGAT-AACCCTCT
17068 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCCTCT
* ***
17090 TATGAAATTTTGAAAACTAAAC-
1 TATGAAATTTTGATAAC-CCTCT
* * *
17112 TATGAAATTTTGGTAACCTTCG
1 TATGAAATTTTGATAACCCTCT
17134 TATG-AATTTTGATA
1 TATGAAATTTTGATA
17148 TCCTCCCTGA
Statistics
Matches: 176, Mismatches: 36, Indels: 40
0.70 0.14 0.16
Matches are distributed among these distances:
16 11 0.06
18 2 0.01
19 1 0.01
20 2 0.01
21 14 0.08
22 81 0.46
23 63 0.36
25 1 0.01
26 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCCTCT
Found at i:21045 original size:28 final size:27
Alignment explanation
Indices: 21005--21058 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
20995 TTTTTTTTTT
21005 TTTTGCAATTTTG-GGTGCTTGCGGCAG
1 TTTTGCAATTTTGAGGTG-TTGCGGCAG
* *
21032 TTTTGTAATTTTTGAGTTGTTGCGGCA
1 TTTTGCAA-TTTTGAGGTGTTGCGGCA
21059 TCTTTGGCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 7 0.30
28 13 0.57
29 3 0.13
ACGTcount: A:0.13, C:0.11, G:0.30, T:0.46
Consensus pattern (27 bp):
TTTTGCAATTTTGAGGTGTTGCGGCAG
Found at i:21613 original size:23 final size:22
Alignment explanation
Indices: 21565--21618 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
21555 TTTTATTTCT
* *
21565 TTTTTTCTTTTCACGCTTCTTT
1 TTTTTTCTTTTCACGCTTCATC
**
21587 TTTTTTCTTTTTGCTGCTTCATC
1 TTTTTTCTTTTCAC-GCTTCATC
*
21610 TTTTCTCTT
1 TTTTTTCTT
21619 GCATACTCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.04, C:0.22, G:0.06, T:0.69
Consensus pattern (22 bp):
TTTTTTCTTTTCACGCTTCATC
Found at i:24363 original size:22 final size:22
Alignment explanation
Indices: 24313--24364 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
24303 TCACATTTTG
* *
24313 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTATCTAT
*
24334 GAAATTTTGATAACCTATCTAT
1 AAAATTTTGATAACCTATCTAT
24356 AAAATTTTG
1 AAAATTTTG
24365 TTGACCCTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (22 bp):
AAAATTTTGATAACCTATCTAT
Found at i:24737 original size:32 final size:32
Alignment explanation
Indices: 24701--24768 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
24691 TTCGTAACGG
**
24701 CAATTTAGAAATATGTTTTTTTAAA-AAGGGTA
1 CAATTTAGAAATATG-TTTTAAAAATAAGGGTA
*
24733 CAA-TTGGAAATATGTTTTAAAAATAAGGGTA
1 CAATTTAGAAATATGTTTTAAAAATAAGGGTA
24764 CAATT
1 CAATT
24769 GATTAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 7 0.23
31 20 0.65
32 4 0.13
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (32 bp):
CAATTTAGAAATATGTTTTAAAAATAAGGGTA
Found at i:24745 original size:31 final size:31
Alignment explanation
Indices: 24708--24769 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
24698 CGGCAATTTA
**
24708 GAAATATGTTTTTTTAAA-AAGGGTACAATTG
1 GAAATATG-TTTTAAAAATAAGGGTACAATTG
24739 GAAATATGTTTTAAAAATAAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATTG
24770 ATTAATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 7 0.25
31 21 0.75
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.35
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATTG
Found at i:24785 original size:118 final size:118
Alignment explanation
Indices: 24647--24885 Score: 433
Period size: 118 Copynumber: 2.0 Consensus size: 118
24637 AATAATTAAA
*
24647 AATTGATTAATTTATGATTAAAAAATAATAAAATAATTAAAATATTCGTAACGGCAATTTAGAAA
1 AATTGATTAATTTATGATTAAAAAATAATAAAATAATTAAAATATTAGTAACGGCAATTTAGAAA
* *
24712 TATGTTTTTTTAAAAAGGGTACAATTGGAAATATGTTTTAAAAATAAGGGTAC
66 TATGTTTTTTAAAAAAGGGTACAATTGGAAATATATTTTAAAAATAAGGGTAC
* *
24765 AATTGATTAATTTATGATTAAAAAATAATAGAATAATTAAAATATTAGTAATGGCAATTTAGAAA
1 AATTGATTAATTTATGATTAAAAAATAATAAAATAATTAAAATATTAGTAACGGCAATTTAGAAA
24830 TATGTTTTTTAAAAAAGGGTACAATTGGAAATATATTTTAAAAATAAGGGTAC
66 TATGTTTTTTAAAAAAGGGTACAATTGGAAATATATTTTAAAAATAAGGGTAC
24883 AAT
1 AAT
24886 CGGAAAACAT
Statistics
Matches: 116, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 116 1.00
ACGTcount: A:0.48, C:0.03, G:0.13, T:0.36
Consensus pattern (118 bp):
AATTGATTAATTTATGATTAAAAAATAATAAAATAATTAAAATATTAGTAACGGCAATTTAGAAA
TATGTTTTTTAAAAAAGGGTACAATTGGAAATATATTTTAAAAATAAGGGTAC
Found at i:24855 original size:32 final size:32
Alignment explanation
Indices: 24819--24885 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
24809 TTAGTAATGG
* *
24819 CAATTTAGAAATATGTTTTTTAAAA-AAGGGTA
1 CAATTTAGAAATAT-ATTTTAAAAATAAGGGTA
*
24851 CAA-TTGGAAATATATTTTAAAAATAAGGGTA
1 CAATTTAGAAATATATTTTAAAAATAAGGGTA
24882 CAAT
1 CAAT
24886 CGGAAAACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 8 0.27
31 19 0.63
32 3 0.10
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.34
Consensus pattern (32 bp):
CAATTTAGAAATATATTTTAAAAATAAGGGTA
Found at i:24861 original size:31 final size:31
Alignment explanation
Indices: 24826--24891 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
24816 TGGCAATTTA
* * *
24826 GAAATATGTTTTTTAAAA-AAGGGTACAATTG
1 GAAATAT-ATTTTAAAAATAAGGGTACAATCG
24857 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
24888 GAAA
1 GAAA
24892 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.47, C:0.05, G:0.18, T:0.30
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATCG
Found at i:26374 original size:150 final size:153
Alignment explanation
Indices: 26220--26525 Score: 564
Period size: 156 Copynumber: 2.0 Consensus size: 153
26210 TTTAGTATAT
26220 ATGATGATATATAATTTTTATGATTTAAATTTAAATATATATGAGTAAAAAAG-AAAAA-GG-AA
1 ATGATGATATATAATTTTTATGATTTAAATTTAAATATATATGAGTAAAAAAGAAAAAAGGGAAA
26282 AAAAAAAAAAAAGATGGCGCTGCACTGTAGCTATGTCATTTTGGAGTGCCTTGCTAATCCCATTT
66 AAAAAAAAAAAAGATGGCGCTGCACTGTAGCTATGTCATTTTGGAGTGCCTTGCTAATCCCATTT
26347 TGCGGTGTTCATTGGAACACATG
131 TGCGGTGTTCATTGGAACACATG
26370 ATGATGATATATAATTTTTATGATTTAAATTTAAATATATATGAGTAAAAAAGAAAAAAAGGGAA
1 ATGATGATATATAATTTTTATGATTTAAATTTAAATATATATGAGTAAAAAAG-AAAAAAGGG--
26435 AAAAAAAAAAAAAAAGATGGCGCTGCACTGTAGCTATGTCATTTTGGAGTGCCTTGCTAATCCCA
63 AAAAAAAAAAAAAAAGATGGCGCTGCACTGTAGCTATGTCATTTTGGAGTGCCTTGCTAATCCCA
26500 TTTTGCGGTGTTCATTGGAACACATG
128 TTTTGCGGTGTTCATTGGAACACATG
26526 TTTTCACTTT
Statistics
Matches: 150, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
150 53 0.35
152 5 0.03
153 2 0.01
156 90 0.60
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (153 bp):
ATGATGATATATAATTTTTATGATTTAAATTTAAATATATATGAGTAAAAAAGAAAAAAGGGAAA
AAAAAAAAAAAAGATGGCGCTGCACTGTAGCTATGTCATTTTGGAGTGCCTTGCTAATCCCATTT
TGCGGTGTTCATTGGAACACATG
Found at i:27628 original size:14 final size:14
Alignment explanation
Indices: 27609--27636 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
27599 CTTACTTTTC
27609 AAAGAGGGAGTAAA
1 AAAGAGGGAGTAAA
27623 AAAGAGGGAGTAAA
1 AAAGAGGGAGTAAA
27637 CGGCGTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.36, T:0.07
Consensus pattern (14 bp):
AAAGAGGGAGTAAA
Found at i:30055 original size:53 final size:54
Alignment explanation
Indices: 29998--30110 Score: 160
Period size: 53 Copynumber: 2.1 Consensus size: 54
29988 TTTCCATTGT
* *
29998 AAGTAATAT-ATGGAAAGACATTT-CATGGTTTGGTTAAATCAAAATATGTGGGA
1 AAGTAATATGATGGAAAGAC-TTTCCATGGTTTGGTTAAATCAAAAAATATGGGA
* *
30051 AAGTAA-ATGATGGAAATACTTTCCATGGTTTGGTTAAATTAAAAAATATGGGA
1 AAGTAATATGATGGAAAGACTTTCCATGGTTTGGTTAAATCAAAAAATATGGGA
30104 AAGTAAT
1 AAGTAAT
30111 TTAAAGGGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
52 5 0.09
53 48 0.91
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (54 bp):
AAGTAATATGATGGAAAGACTTTCCATGGTTTGGTTAAATCAAAAAATATGGGA
Found at i:35322 original size:22 final size:24
Alignment explanation
Indices: 35297--35352 Score: 91
Period size: 22 Copynumber: 2.5 Consensus size: 24
35287 TTCAAATTCT
35297 AAACTTCATTTCTAAC-AA-CTTC
1 AAACTTCATTTCTAACAAATCTTC
35319 AAACTTCATTTCTAACAAATCTTC
1 AAACTTCATTTCTAACAAATCTTC
35343 AAA-TTCATTT
1 AAACTTCATTT
35353 TCCTTCATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.50
23 9 0.28
24 7 0.22
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.39
Consensus pattern (24 bp):
AAACTTCATTTCTAACAAATCTTC
Found at i:35475 original size:11 final size:12
Alignment explanation
Indices: 35456--35486 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
35446 CTAATTAATA
35456 TTAAAAAAAATT
1 TTAAAAAAAATT
35468 TTAAAAAAAATT
1 TTAAAAAAAATT
35480 TTAAAAA
1 TTAAAAA
35487 TGGCCTAGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
TTAAAAAAAATT
Found at i:45197 original size:31 final size:31
Alignment explanation
Indices: 45159--45223 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
45149 TTGGGTTATC
*
45159 AGTCTCCAGATTTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
45190 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
1 AGTCTCCAGATCTTTAGATCTTGGATGTTTG
45221 AGT
1 AGT
45224 TACTTCAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (31 bp):
AGTCTCCAGATCTTTAGATCTTGGATGTTTG
Found at i:45629 original size:21 final size:22
Alignment explanation
Indices: 45603--45647 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
45593 AATAACTGGA
45603 TTGCTAAACACCG-CCCCCTTT
1 TTGCTAAACACCGCCCCCCTTT
*
45624 TTGCTAAATACCGCCCCCCTTT
1 TTGCTAAACACCGCCCCCCTTT
45646 TT
1 TT
45648 ACACTTTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.18, C:0.40, G:0.09, T:0.33
Consensus pattern (22 bp):
TTGCTAAACACCGCCCCCCTTT
Found at i:45823 original size:26 final size:26
Alignment explanation
Indices: 45794--45861 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
45784 TTCATTCATT
45794 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
45820 TTAATCATAAATTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
45846 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
45862 AAACTAATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:46131 original size:167 final size:167
Alignment explanation
Indices: 45909--46386 Score: 579
Period size: 167 Copynumber: 2.9 Consensus size: 167
45899 TGAAAATTAC
** * * * *
45909 TAAAAGATCCCCACCCCGGATTAATTA-GGAGTGAGAGAACTAATTTTTTTCGTCTTTTCCCACT
1 TAAAAGATCCCCACCAAGGATTGATGATGGAGTTAGAGAACTAATTTTTTTCGTCTTTTCCTACT
* * * * *
45973 TCGCCGATTACTTAACTGCCCCAACTTTTGATTCTTGAGGTGATTAAATAACTACACTTTTTGGT
66 TCGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTA-ACTTTTTGGT
* *
46038 CATTTCTCAATTGACTTTAATAGAGTACT-GAAATCAC
130 CATTTCTCAATTGACTTGAATAGAGTACTGGAAATCAA
* * * * *
46075 TAAAAGATCCCTACCATGGCTTGCAT-TTGGAGTTAGAGAACTTATTTTTTTCGTCTTTTCCTA-
1 TAAAAGATCCCCACCAAGGATTG-ATGATGGAGTTAGAGAACTAATTTTTTTCGTCTTTTCCTAC
* * * *
46138 TTTGACAGATTACTTAAATGTCTTAACTTTTGATTCTTGAGGGGATTAAATAAGTAATCATTTTG
65 TTCG-CAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAA-CTTTTTG
* * * *
46203 GTCATTTCTCAATGGACTTGAATGGAGTAGTGGAAATTAA
128 GTCATTTCTCAATTGACTTGAATAGAGTACTGGAAATCAA
* * * * *
46243 TAAAAGATCCCCATCAAGGATTGATGAT-GAGCTAGAGAACTAATATTTTTCGTCTTTACATACT
1 TAAAAGATCCCCACCAAGGATTGATGATGGAGTTAGAGAACTAATTTTTTTCGTCTTTTCCTACT
* *
46307 TGGTAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTTTTGGT
66 TCGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACT-AACTTTTTGGT
46372 CATTTCTCAATTGAC
130 CATTTCTCAATTGAC
46387 AAATGACTCA
Statistics
Matches: 264, Mismatches: 40, Indels: 15
0.83 0.13 0.05
Matches are distributed among these distances:
166 22 0.08
167 211 0.80
168 31 0.12
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (167 bp):
TAAAAGATCCCCACCAAGGATTGATGATGGAGTTAGAGAACTAATTTTTTTCGTCTTTTCCTACT
TCGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAACTTTTTGGTC
ATTTCTCAATTGACTTGAATAGAGTACTGGAAATCAA
Found at i:46701 original size:9 final size:9
Alignment explanation
Indices: 46687--46712 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
46677 CTAAAAAAAG
46687 AACGCCCGT
1 AACGCCCGT
46696 AACGCCCGT
1 AACGCCCGT
46705 AACGCCCG
1 AACGCCCG
46713 CGCGGACCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.46, G:0.23, T:0.08
Consensus pattern (9 bp):
AACGCCCGT
Found at i:59936 original size:109 final size:109
Alignment explanation
Indices: 59804--60078 Score: 464
Period size: 109 Copynumber: 2.5 Consensus size: 109
59794 AAAAAAACTA
59804 TATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
1 TATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAG
59867 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
65 AAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
59912 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
1 TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
*
59977 AAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGTAAT
66 AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
*
60021 TATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTTTAGTAGAATAAAA
1 TATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAGAATAAAA
60079 CTATAATAGT
Statistics
Matches: 158, Mismatches: 2, Indels: 8
0.94 0.01 0.05
Matches are distributed among these distances:
108 6 0.04
109 119 0.75
110 3 0.02
111 1 0.01
114 29 0.18
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.39
Consensus pattern (109 bp):
TATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATATTAGA
AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGTAAT
Found at i:61186 original size:23 final size:22
Alignment explanation
Indices: 61136--61186 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
61126 GAAAGTGAAC
* *
61136 CCGAACCCGATCCGGGCCCGAA
1 CCGAACCCGATCCGAGCCAGAA
61158 CTCGAACCCGATCCGAGCCAGAA
1 C-CGAACCCGATCCGAGCCAGAA
61181 TCCGAA
1 -CCGAA
61187 AATACCCGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.04
23 23 0.92
24 1 0.04
ACGTcount: A:0.27, C:0.41, G:0.24, T:0.08
Consensus pattern (22 bp):
CCGAACCCGATCCGAGCCAGAA
Found at i:61209 original size:16 final size:15
Alignment explanation
Indices: 61182--61263 Score: 83
Period size: 16 Copynumber: 5.2 Consensus size: 15
61172 GAGCCAGAAT
61182 CCGAAAATACCCGAAC
1 CCGAAAA-ACCCGAAC
*
61198 CCGATAAAACCCGAAA
1 CCGA-AAAACCCGAAC
* *
61214 CCGACAGAATCCGAAC
1 CCGA-AAAACCCGAAC
*
61230 CCGAAAATACCCGAAT
1 CCGAAAA-ACCCGAAC
*
61246 CCGAAATACCCGAAC
1 CCGAAAAACCCGAAC
61261 CCG
1 CCG
61264 CCCAATTGCC
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
15 12 0.22
16 39 0.72
17 3 0.06
ACGTcount: A:0.41, C:0.37, G:0.15, T:0.07
Consensus pattern (15 bp):
CCGAAAAACCCGAAC
Done.