Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023194.1 Corchorus olitorius cultivar O-4 contig23227, 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: 12394
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:1101 original size:19 final size:18
Alignment explanation
Indices: 1068--1103 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1058 TGGAAATAAT
1068 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
1086 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
1104 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:2471 original size:116 final size:117
Alignment explanation
Indices: 2157--2656 Score: 731
Period size: 116 Copynumber: 4.3 Consensus size: 117
2147 ATAAAACTGA
* * * *
2157 GAAAGGATGACCTGTTTCCAGTCAACCTT-AGTAACTACTGAAAAGATGACCTGTTTCCAGTCAA
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGA-TAAATGCTGAAAAGATGACCTGTTTCCAGTCAA
*
2221 CTTTGATAAATGCTGAAAAGATTACCTGTTTCCAGTCAACTTTGATAAATGCT
65 CTTTGATAAATGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
* * *
2274 GAAAAGATGACCTGTTTCCAGTCAACTATGATAAATGCTGAAAAGATGACTTGTTTCCAGTGAAC
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGATGACCTGTTTCCAGTCAAC
* *
2339 TTTGATATATGCTGAAAAGATGACCTGTTTCCAGTCAACTATGATAAATGCT
66 TTTGATAAATGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
*
2391 GAAGAGATGACCTG-TTCCAGTCAACTTTGATAAATGCTGAAAAGATGACCTGTTTCCAGTCAAC
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGATGACCTGTTTCCAGTCAAC
* * * * *
2455 TTTGATAAATGTTGAAAAGATGACATGTTTCCAATCAACTTTGATAACTTCT
66 TTTGATAAATGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
*
2507 G-AAAGATGACCTGTTTCCAGTCAACTTTGATAACCAT--TGAAAAGATGACCTGTTTTCAGTCA
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAA--ATGCTGAAAAGATGACCTGTTTCCAGTCA
* * * * *
2569 ACTTTGATAACTGTTGAAAAGATGACCTATTTCCAGTCAACTTTGATAACTGTT
64 ACTTTGATAAATGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
*
2623 GAAAAGATGACCTGTTTCTAGTCAACTTTGATAA
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAA
2657 CTATTGAAAT
Statistics
Matches: 348, Mismatches: 30, Indels: 10
0.90 0.08 0.03
Matches are distributed among these distances:
115 11 0.03
116 185 0.53
117 149 0.43
118 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (117 bp):
GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGATGACCTGTTTCCAGTCAAC
TTTGATAAATGCTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
Found at i:2656 original size:155 final size:155
Alignment explanation
Indices: 2157--2676 Score: 746
Period size: 155 Copynumber: 3.3 Consensus size: 155
2147 ATAAAACTGA
* * *
2157 GAAAGGATGACCTGTTTCCAGTCAACCTT-AGTAACTACTGAAAAGATGACCTGTTTCCAGTCAA
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGA-TAACTTCTGAAAAGATGACCTGTTTCCAGTCAA
*
2221 CTTTGATAAATGCTGAAAAGATTACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGATGACC
65 CTTTGATAAAT-CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGATGACC
* *
2286 TGTTTCCAGTCAACTATGATAAATGCT
129 TGTTTCCAGTCAACTTTGATAAATGTT
* * *
2313 GAAAAGATGACTTGTTTCCAGTGAACTTTGATATA-TGCTGAAAAGATGACCTGTTTCCAGTCAA
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATA-ACTTCTGAAAAGATGACCTGTTTCCAGTCAA
* *
2377 CTATGATAAATGCTGAAGAGATGACCTG-TTCCAGTCAACTTTGATAAATGCTGAAAAGATGACC
65 CTTTGATAAAT-CTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGATGACC
2441 TGTTTCCAGTCAACTTTGATAAATGTT
129 TGTTTCCAGTCAACTTTGATAAATGTT
* *
2468 GAAAAGATGACATGTTTCCAATCAACTTTGATAACTTCTG-AAAGATGACCTGTTTCCAGTCAAC
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTCTGAAAAGATGACCTGTTTCCAGTCAAC
* * *
2532 TTTGATAACCAT-TGAAAAGATGACCTGTTTTCAGTCAACTTTGATAACTGTTGAAAAGATGACC
66 TTTGATAA--ATCTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGATGACC
* *
2596 TATTTCCAGTCAACTTTGATAACTGTT
129 TGTTTCCAGTCAACTTTGATAAATGTT
* * *
2623 GAAAAGATGACCTGTTTCTAGTCAACTTTGATAACTAT-TGAAATGATGAACTGT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAACT-TCTGAAAAGATGACCTGT
2677 ATCATTGAAG
Statistics
Matches: 330, Mismatches: 26, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
154 46 0.14
155 188 0.57
156 94 0.28
157 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (155 bp):
GAAAAGATGACCTGTTTCCAGTCAACTTTGATAACTTCTGAAAAGATGACCTGTTTCCAGTCAAC
TTTGATAAATCTGAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCTGAAAAGATGACCTG
TTTCCAGTCAACTTTGATAAATGTT
Found at i:2658 original size:39 final size:39
Alignment explanation
Indices: 2157--2656 Score: 731
Period size: 39 Copynumber: 12.9 Consensus size: 39
2147 ATAAAACTGA
* * * *
2157 GAAAGGATGACCTGTTTCCAGTCAACCTT-AGTAACTACT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGA-TAAATGCT
2196 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
*
2235 GAAAAGATTACCTGTTTCCAGTCAACTTTGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
*
2274 GAAAAGATGACCTGTTTCCAGTCAACTATGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
* * *
2313 GAAAAGATGACTTGTTTCCAGTGAACTTTGATATATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
*
2352 GAAAAGATGACCTGTTTCCAGTCAACTATGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
*
2391 GAAGAGATGACCTG-TTCCAGTCAACTTTGATAAATGCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
*
2429 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGTT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
* * * *
2468 GAAAAGATGACATGTTTCCAATCAACTTTGATAACTTCT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
2507 G-AAAGATGACCTGTTTCCAGTCAACTTTGATAACCAT--T
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAA--ATGCT
* * *
2545 GAAAAGATGACCTGTTTTCAGTCAACTTTGATAACTGTT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
* * *
2584 GAAAAGATGACCTATTTCCAGTCAACTTTGATAACTGTT
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
*
2623 GAAAAGATGACCTGTTTCTAGTCAACTTTGATAA
1 GAAAAGATGACCTGTTTCCAGTCAACTTTGATAA
2657 CTATTGAAAT
Statistics
Matches: 421, Mismatches: 33, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
37 1 0.00
38 68 0.16
39 350 0.83
40 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (39 bp):
GAAAAGATGACCTGTTTCCAGTCAACTTTGATAAATGCT
Found at i:2726 original size:16 final size:16
Alignment explanation
Indices: 2679--2728 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
2669 TGAACTGTAT
*
2679 CATTGAAGTAAATTAAAG
1 CATTGAA-T-AATTGAAG
* *
2697 CATTGAAGATTTGAAG
1 CATTGAATAATTGAAG
2713 CATTGAATAATTGAAG
1 CATTGAATAATTGAAG
2729 AACTGAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 20 0.74
18 7 0.26
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (16 bp):
CATTGAATAATTGAAG
Found at i:2794 original size:24 final size:24
Alignment explanation
Indices: 2765--2893 Score: 96
Period size: 24 Copynumber: 5.0 Consensus size: 24
2755 TTGAAGTAAA
*
2765 TTGAAGCATTGAATATTTGAAGAT
1 TTGAAGCATTGAATAATTGAAGAT
2789 TTGAAGCATTGAATAATTGAAGAACT
1 TTGAAGCATTGAATAATTGAAG-A-T
** * * * *
2815 GAAGAAAGACCACCCTGGATTATTGAAGTAAA
1 -TTG-AAG--CA--TTGAATAATTGAAG--AT
*
2847 TTGAAGCATTGAATATTTGAAGAT
1 TTGAAGCATTGAATAATTGAAGAT
2871 TTGAAGCATTGAATAATTGAAGA
1 TTGAAGCATTGAATAATTGAAGA
2894 ACTGAAGAAA
Statistics
Matches: 81, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
24 44 0.54
25 1 0.01
26 11 0.14
27 1 0.01
28 5 0.06
30 5 0.06
31 1 0.01
32 11 0.14
33 2 0.02
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (24 bp):
TTGAAGCATTGAATAATTGAAGAT
Found at i:2807 original size:8 final size:8
Alignment explanation
Indices: 2763--2820 Score: 53
Period size: 8 Copynumber: 7.2 Consensus size: 8
2753 TATTGAAGTA
2763 AATTGAAG
1 AATTGAAG
* *
2771 CATTGAAT
1 AATTGAAG
*
2779 ATTTGAAG
1 AATTGAAG
*
2787 ATTTGAAG
1 AATTGAAG
* *
2795 CATTGAAT
1 AATTGAAG
2803 AATTGAAG
1 AATTGAAG
*
2811 AACTGAAG
1 AATTGAAG
2819 AA
1 AA
2821 AGACCACCCT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (8 bp):
AATTGAAG
Found at i:2838 original size:82 final size:82
Alignment explanation
Indices: 2699--2941 Score: 450
Period size: 82 Copynumber: 3.0 Consensus size: 82
2689 AATTAAAGCA
*
2699 TTGAAGATTTGAAGCATTGAATAATTGAAGAACTGAAGAAAGACCACCCTGGGTTATTGAAGTAA
1 TTGAAGATTTGAAGCATTGAATAATTGAAGAACTGAAGAAAGACCACCCTGGATTATTGAAGTAA
2764 ATTGAAGCATTGAATAT
66 ATTGAAGCATTGAATAT
2781 TTGAAGATTTGAAGCATTGAATAATTGAAGAACTGAAGAAAGACCACCCTGGATTATTGAAGTAA
1 TTGAAGATTTGAAGCATTGAATAATTGAAGAACTGAAGAAAGACCACCCTGGATTATTGAAGTAA
2846 ATTGAAGCATTGAATAT
66 ATTGAAGCATTGAATAT
**
2863 TTGAAGATTTGAAGCATTGAATAATTGAAGAACTGAAGAAAGACCACCCTGGATCGTTGAAGTAA
1 TTGAAGATTTGAAGCATTGAATAATTGAAGAACTGAAGAAAGACCACCCTGGATTATTGAAGTAA
*
2928 ATTGATGCATTGAA
66 ATTGAAGCATTGAA
2942 GAATTGAAAT
Statistics
Matches: 157, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 157 1.00
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (82 bp):
TTGAAGATTTGAAGCATTGAATAATTGAAGAACTGAAGAAAGACCACCCTGGATTATTGAAGTAA
ATTGAAGCATTGAATAT
Found at i:2889 original size:8 final size:8
Alignment explanation
Indices: 2845--2902 Score: 53
Period size: 8 Copynumber: 7.2 Consensus size: 8
2835 TATTGAAGTA
2845 AATTGAAG
1 AATTGAAG
* *
2853 CATTGAAT
1 AATTGAAG
*
2861 ATTTGAAG
1 AATTGAAG
*
2869 ATTTGAAG
1 AATTGAAG
* *
2877 CATTGAAT
1 AATTGAAG
2885 AATTGAAG
1 AATTGAAG
*
2893 AACTGAAG
1 AATTGAAG
2901 AA
1 AA
2903 AGACCACCCT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (8 bp):
AATTGAAG
Found at i:2899 original size:24 final size:24
Alignment explanation
Indices: 2848--2900 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
2838 TGAAGTAAAT
* **
2848 TGAAGCATTGAATATTTGAAGATT
1 TGAAGCATTGAATAATTGAAGAAC
2872 TGAAGCATTGAATAATTGAAGAAC
1 TGAAGCATTGAATAATTGAAGAAC
2896 TGAAG
1 TGAAG
2901 AAAGACCACC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.30
Consensus pattern (24 bp):
TGAAGCATTGAATAATTGAAGAAC
Found at i:2960 original size:56 final size:56
Alignment explanation
Indices: 2871--3158 Score: 389
Period size: 56 Copynumber: 5.3 Consensus size: 56
2861 ATTTGAAGAT
* * * * *
2871 TTGAAGCATTGAATAATTGAAGAACTGAAGAAAGACCACCCTGGATCGTTGAAGTAAA
1 TTGATGCATTGAAGAATTG-A-AATTGAAGAAAGACCACACTGGATCGTTAAAGTAAA
* *
2929 TTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACCCTGGATCGTTGAAGTAAA
1 TTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCGTTAAAGTAAA
* * *
2985 TTGATGCATTGAAGAATTGAAATTGAAGAAAAACAACACTAGATCGTTAAAGTAAA
1 TTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCGTTAAAGTAAA
3041 TTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATC------G----
1 TTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCGTTAAAGTAAA
3087 TTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCGTTAAAGTAAA
1 TTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCGTTAAAGTAAA
*
3143 TTGATGTATTGAAGAA
1 TTGATGCATTGAAGAA
3159 AAACCACACT
Statistics
Matches: 208, Mismatches: 12, Indels: 22
0.86 0.05 0.09
Matches are distributed among these distances:
46 45 0.22
50 1 0.00
52 1 0.00
56 143 0.69
57 1 0.00
58 17 0.08
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (56 bp):
TTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCGTTAAAGTAAA
Found at i:3095 original size:46 final size:46
Alignment explanation
Indices: 3041--3134 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
3031 TTAAAGTAAA
3041 TTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCG
1 TTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCG
3087 TTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCG
1 TTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCG
3133 TT
1 TT
3135 AAAGTAAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (46 bp):
TTGATGCATTGAAGAATTGAAATTGAAGAAAGACCACACTGGATCG
Found at i:3167 original size:42 final size:42
Alignment explanation
Indices: 3108--3190 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
3098 AAGAATTGAA
* *
3108 ATTGAAGAAAGACCACACTGGATCGTTAAAGTAAATTGATGT
1 ATTGAAGAAAAACCACACTCGATCGTTAAAGTAAATTGATGT
* *
3150 ATTGAAGAAAAACCACACTCGTTCGTTGAAGTAAATTGATG
1 ATTGAAGAAAAACCACACTCGATCGTTAAAGTAAATTGATG
3191 CATCGAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (42 bp):
ATTGAAGAAAAACCACACTCGATCGTTAAAGTAAATTGATGT
Found at i:3219 original size:8 final size:7
Alignment explanation
Indices: 3199--3427 Score: 88
Period size: 8 Copynumber: 32.1 Consensus size: 7
3189 TGCATCGAAT
3199 AATTGAA
1 AATTGAA
3206 AATTGAA
1 AATTGAA
3213 GAATTGAA
1 -AATTGAA
*
3221 GTATTG-A
1 -AATTGAA
*
3228 AATCGAA
1 AATTGAA
*
3235 CATTGAA
1 AATTGAA
*
3242 GGATTG-A
1 -AATTGAA
*
3249 ATTTGAA
1 AATTGAA
3256 GAATTG-A
1 -AATTGAA
3263 AATTGAA
1 AATTGAA
*
3270 CCATTGAA
1 -AATTGAA
3278 ATATTG-A
1 A-ATTGAA
3285 AATTGAA
1 AATTGAA
3292 GAATTGAA
1 -AATTGAA
3300 ATATTG--
1 A-ATTGAA
3306 AATT-AA
1 AATTGAA
3312 AATTGAA
1 AATTGAA
*
3319 GCATTGAA
1 -AATTGAA
3327 ATATTG-A
1 A-ATTGAA
3334 AATTGAA
1 AATTGAA
*
3341 GCATTG-A
1 -AATTGAA
3348 AATTGAA
1 AATTGAA
*
3355 ATGTTGAA
1 A-ATTGAA
*
3363 GGATT-AA
1 -AATTGAA
*
3370 ATTTGAA
1 AATTGAA
*
3377 GAATTGAC
1 -AATTGAA
3385 AA-TGAA
1 AATTGAA
*
3391 GCATTGAA
1 -AATTGAA
3399 ATATTG-A
1 A-ATTGAA
3406 AATTGAA
1 AATTGAA
*
3413 GAACTG-A
1 -AATTGAA
3420 AATTGAA
1 AATTGAA
3427 A
1 A
3428 CGTTGAAGGA
Statistics
Matches: 166, Mismatches: 27, Indels: 58
0.66 0.11 0.23
Matches are distributed among these distances:
5 3 0.02
6 41 0.25
7 43 0.26
8 79 0.48
ACGTcount: A:0.47, C:0.04, G:0.19, T:0.30
Consensus pattern (7 bp):
AATTGAA
Found at i:3256 original size:14 final size:14
Alignment explanation
Indices: 3199--3426 Score: 88
Period size: 14 Copynumber: 16.9 Consensus size: 14
3189 TGCATCGAAT
3199 AATTGAAAATTGAAG
1 AATTG-AAATTGAAG
3214 AATTGAAGTATTG-A-
1 AATTGAA--ATTGAAG
*
3228 AATCGAACATTGAAG
1 AATTGAA-ATTGAAG
* *
3243 GATTGAATTTGAAG
1 AATTGAAATTGAAG
*
3257 AATTGAAATTGAAC
1 AATTGAAATTGAAG
*
3271 CATTGAAATATTG-A-
1 AATTG-AA-ATTGAAG
3285 AATTGAAGAATTGAA-
1 AATTG-A-AATTGAAG
3300 ATATTG-AATT-AA-
1 A-ATTGAAATTGAAG
3312 AATTGAAGCATTGAA-
1 AATTGAA--ATTGAAG
3327 ATATTGAAATTGAAG
1 A-ATTGAAATTGAAG
*
3342 CATTGAAATTG-A-
1 AATTGAAATTGAAG
3354 AA-TG---TTGAAG
1 AATTGAAATTGAAG
*
3364 GATT-AAATTTGAAG
1 AATTGAAA-TTGAAG
3378 AATTGACAA-TGAAG
1 AATTGA-AATTGAAG
*
3392 CATTGAAA-T----
1 AATTGAAATTGAAG
3401 -ATTGAAATTGAAG
1 AATTGAAATTGAAG
*
3414 AACTGAAATTGAA
1 AATTGAAATTGAA
3427 ACGTTGAAGG
Statistics
Matches: 167, Mismatches: 16, Indels: 61
0.68 0.07 0.25
Matches are distributed among these distances:
8 10 0.06
9 2 0.01
10 1 0.01
11 7 0.04
12 5 0.03
13 12 0.07
14 89 0.53
15 21 0.13
16 20 0.12
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.30
Consensus pattern (14 bp):
AATTGAAATTGAAG
Found at i:3276 original size:22 final size:21
Alignment explanation
Indices: 3199--3383 Score: 118
Period size: 22 Copynumber: 8.6 Consensus size: 21
3189 TGCATCGAAT
3199 AATTGAAAATTGAAGAATTGA
1 AATTGAAAATTGAAGAATTGA
* *
3220 AGTATTG-AAATCGAA-CATTGA
1 A--ATTGAAAATTGAAGAATTGA
*
3241 AGGATTG-AATTTGAAGAATTGA
1 A--ATTGAAAATTGAAGAATTGA
*
3263 AATTGAACCATTGAA-ATATTGA
1 AATTGAA-AATTGAAGA-ATTGA
3285 AATTGAAGAATTGAA-ATATTG-
1 AATTGAA-AATTGAAGA-ATTGA
*
3306 AATT-AAAATTGAAGCATTGAA
1 AATTGAAAATTGAAGAATTG-A
*
3327 ATATTG-AAATTGAAGCATTGA
1 A-ATTGAAAATTGAAGAATTGA
* *
3348 AATTGAAATGTTGAAGGATT-A
1 AATTGAAA-ATTGAAGAATTGA
3369 AATTTGAAGAATTGA
1 AA-TTGAA-AATTGA
3384 CAATGAAGCA
Statistics
Matches: 135, Mismatches: 14, Indels: 29
0.76 0.08 0.16
Matches are distributed among these distances:
19 11 0.08
20 10 0.07
21 32 0.24
22 77 0.57
23 5 0.04
ACGTcount: A:0.46, C:0.03, G:0.19, T:0.31
Consensus pattern (21 bp):
AATTGAAAATTGAAGAATTGA
Found at i:3362 original size:36 final size:35
Alignment explanation
Indices: 3200--3466 Score: 131
Period size: 36 Copynumber: 7.4 Consensus size: 35
3190 GCATCGAATA
* * *
3200 ATTGAAAATTGAAGAATTGAAGTATTGAAATCGAA-C
1 ATTG-AAATTGAA-ACTTGAAATATTGAAATTGAAGC
* *
3236 ATTGAAGGATTG-AATTTGAAGA-ATTGAAATTGAACC
1 ATTGAA--ATTGAAACTTGAA-ATATTGAAATTGAAGC
3272 ATTGAAATATTGAAA-TTGAAGA-ATTGAAATATTG-A--
1 ATTG-AA-ATTGAAACTTGAA-ATATTG-AA-ATTGAAGC
* *
3307 ATTAAAATTGAAGCATTGAAATATTGAAATTGAAGC
1 ATTGAAATTGAAAC-TTGAAATATTGAAATTGAAGC
* ** *
3343 ATTGAAATTGAAATGTTGAAGGATT-AAATTTGAAGA
1 ATTGAAATTGAAA-CTTGAAATATTGAAA-TTGAAGC
* *
3379 ATTGACAA-TGAAGCATTGAAATATTGAAATTGAAGA
1 ATTGA-AATTGAAAC-TTGAAATATTGAAATTGAAGC
* ** **
3415 ACTGAAATTGAAACGTTGAAGGATTGAAGCATTGAAAT
1 ATTGAAATTGAAAC-TTGAAATATTGAA--ATTGAAGC
*
3453 ATTGGAATTGAAAC
1 ATTGAAATTGAAAC
3467 ATTGGAGGAT
Statistics
Matches: 184, Mismatches: 25, Indels: 42
0.73 0.10 0.17
Matches are distributed among these distances:
33 10 0.05
34 6 0.03
35 36 0.20
36 94 0.51
37 16 0.09
38 22 0.12
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.30
Consensus pattern (35 bp):
ATTGAAATTGAAACTTGAAATATTGAAATTGAAGC
Found at i:3442 original size:22 final size:21
Alignment explanation
Indices: 3379--3452 Score: 53
Period size: 22 Copynumber: 3.4 Consensus size: 21
3369 AATTTGAAGA
* *
3379 ATTGACAA-TGAAGCATTGAAAT
1 ATTGA-AATTGAAGAATTG-AAC
*
3401 ATTGAAATTGAAGAACTGAA-
1 ATTGAAATTGAAGAATTGAAC
*
3421 ATTGAAACGTTGAAGGATTGAAGC
1 ATTGAAA--TTGAAGAATTGAA-C
3445 ATTGAAAT
1 ATTGAAAT
3453 ATTGGAATTG
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 7 0.16
21 4 0.09
22 25 0.58
24 7 0.16
ACGTcount: A:0.45, C:0.07, G:0.22, T:0.27
Consensus pattern (21 bp):
ATTGAAATTGAAGAATTGAAC
Found at i:3531 original size:49 final size:49
Alignment explanation
Indices: 3438--3531 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
3428 CGTTGAAGGA
* **
3438 TTGAAGCATTGAAATATTGGAATTGAAACATTGGAGGATAGAATTGATT
1 TTGAAGCATTGAAATATTGAAATTGAAACATTGGAAAATAGAATTGATT
*
3487 TTGAAGCATTGAAATATTGAAATT-AAAGCATTGGAAAATTGAATT
1 TTGAAGCATTGAAATATTGAAATTGAAA-CATTGGAAAATAGAATT
3532 TGAAGAATTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 3 0.08
49 37 0.93
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.33
Consensus pattern (49 bp):
TTGAAGCATTGAAATATTGAAATTGAAACATTGGAAAATAGAATTGATT
Found at i:3541 original size:22 final size:22
Alignment explanation
Indices: 3479--3541 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
3469 TGGAGGATAG
*
3479 AATTGATTTTGAAGCATT-GAA
1 AATTGAATTTGAAGCATTGGAA
* *
3500 ATATTGAAATTAAAGCATTGGAA
1 A-ATTGAATTTGAAGCATTGGAA
*
3523 AATTGAATTTGAAGAATTG
1 AATTGAATTTGAAGCATTG
3542 AGATTGAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.03
22 29 0.85
23 4 0.12
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (22 bp):
AATTGAATTTGAAGCATTGGAA
Found at i:4489 original size:49 final size:50
Alignment explanation
Indices: 4376--4575 Score: 298
Period size: 50 Copynumber: 4.0 Consensus size: 50
4366 GAAAATGCCC
*
4376 TTTGAAAAGCGAATTTTGATCTTGGACTAACAAAT-GAAATGCAATCTTAT
1 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAA-GCAATCTTAT
* * * *
4426 TTTGAAAAGTGAATTTTGAT-TTCGAACTCACAAAT-GAATGCATTCTTAT
1 TTTGAAAAGCGAATTTTGATCTT-GGACTCACAAATGGAAAGCAATCTTAT
4475 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATCTTAT
1 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATCTTAT
* *
4525 TTTGAAAAGTGAATTTTGATCTTAGACTCACAAATGGAAAGCAATCTTAT
1 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATCTTAT
4575 T
1 T
4576 ATAAAATTTC
Statistics
Matches: 136, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
49 41 0.30
50 95 0.70
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.35
Consensus pattern (50 bp):
TTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATCTTAT
Found at i:4491 original size:99 final size:100
Alignment explanation
Indices: 4376--4575 Score: 325
Period size: 99 Copynumber: 2.0 Consensus size: 100
4366 GAAAATGCCC
4376 TTTGAAAAGCGAATTTTGATCTTGGACTAACAAAT-GAAATGCAATCTTATTTTGAAAAGTGAAT
1 TTTGAAAAGCGAATTTTGATCTTGGACTAACAAATGGAAA-GCAATCTTATTTTGAAAAGTGAAT
* * *
4440 TTTGAT-TTCGAACTCACAAAT-GAATGCATTCTTAT
65 TTTGATCTTAG-ACTCACAAATGGAAAGCAATCTTAT
*
4475 TTTGAAAAGCGAATTTTGATCTTGGACTCACAAATGGAAAGCAATCTTATTTTGAAAAGTGAATT
1 TTTGAAAAGCGAATTTTGATCTTGGACTAACAAATGGAAAGCAATCTTATTTTGAAAAGTGAATT
4540 TTGATCTTAGACTCACAAATGGAAAGCAATCTTAT
66 TTGATCTTAGACTCACAAATGGAAAGCAATCTTAT
4575 T
1 T
4576 ATAAAATTTC
Statistics
Matches: 94, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
99 74 0.79
100 20 0.21
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.35
Consensus pattern (100 bp):
TTTGAAAAGCGAATTTTGATCTTGGACTAACAAATGGAAAGCAATCTTATTTTGAAAAGTGAATT
TTGATCTTAGACTCACAAATGGAAAGCAATCTTAT
Found at i:6155 original size:48 final size:48
Alignment explanation
Indices: 6084--6175 Score: 148
Period size: 48 Copynumber: 1.9 Consensus size: 48
6074 TCTTATCTTA
* *
6084 TTTTTTGTTCAAAATACAATTGTTTATTCAAAAGAATCTAGTTTATCT
1 TTTTTTGTCCAAAACACAATTGTTTATTCAAAAGAATCTAGTTTATCT
* *
6132 TTTTTTGTCCAAAACACACTTGTTTATTCAAAAGAATCTCGTTT
1 TTTTTTGTCCAAAACACAATTGTTTATTCAAAAGAATCTAGTTT
6176 TGTTCGTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.46
Consensus pattern (48 bp):
TTTTTTGTCCAAAACACAATTGTTTATTCAAAAGAATCTAGTTTATCT
Found at i:8475 original size:52 final size:51
Alignment explanation
Indices: 8410--8801 Score: 320
Period size: 52 Copynumber: 7.1 Consensus size: 51
8400 ATTGAAAACT
*
8410 AAAACCTGATGGGAACTTTCCCGATTTAAAAAAGAGCTAAATTGAATACTTTG
1 AAAA-CTGATGGGAACTTTCCCAATTTAAAAAA-AGCTAAATTGAATACTTTG
* ** * *
8463 AAAACTGATGGGAACTTTCCCAATTTGAAAAACTTAAACTTGATGGGAACTTTTCCAATTTG
1 AAAACTGATGGGAACTTTCCCAATTT-AAAAA---AAGCTAAAT-TGAA----T--ACTTTG
* * * *
8525 AAAACTTAAACCTGATGGGAACTTTCCCGATTTGAAAGAGAGCTAAATTGAATACTTTT
1 --AA----AA-CTGATGGGAACTTTCCCAATTT-AAAAAAAGCTAAATTGAATACTTTG
* *
8584 AAAACTGATGGGAACTTTCCCGATTTGAAAAAAAAATAGCTAAATTGTATACTTTG
1 AAAACTGATGGGAACTTTCCCAATTT----AAAAAA-AGCTAAATTGAATACTTTG
* *
8640 AAAACTGATGGGAACTTTCCCAATTT-GAAAAA-CTTAAATTGAATATTTTG
1 AAAACTGATGGGAACTTTCCCAATTTAAAAAAAGC-TAAATTGAATACTTTG
* * * *
8690 AAAATTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTG
1 AAAACTGATGGGAACTTTCCCAATTT-AAAAAAAGCTAAATTGAATACTTTG
**
8742 AAGATTTGATGGGAACTTTCCCAATTTGAAAAAAAGCTAAATTGAATACTTTG
1 AA-AACTGATGGGAACTTTCCCAATTT-AAAAAAAGCTAAATTGAATACTTTG
8795 AAAACTG
1 AAAACTG
8802 GTGAAATTCT
Statistics
Matches: 276, Mismatches: 36, Indels: 55
0.75 0.10 0.15
Matches are distributed among these distances:
49 1 0.00
50 39 0.14
51 4 0.01
52 66 0.24
53 60 0.22
55 9 0.03
56 46 0.17
57 2 0.01
59 4 0.01
60 1 0.00
61 1 0.00
62 5 0.02
64 2 0.01
65 3 0.01
66 5 0.02
68 2 0.01
69 26 0.09
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Consensus pattern (51 bp):
AAAACTGATGGGAACTTTCCCAATTTAAAAAAAGCTAAATTGAATACTTTG
Found at i:8507 original size:35 final size:34
Alignment explanation
Indices: 8464--8561 Score: 153
Period size: 34 Copynumber: 2.9 Consensus size: 34
8454 AATACTTTGA
8464 AAACTGATGGGAACTTTCCCAATTTGAAAAACTT
1 AAACTGATGGGAACTTTCCCAATTTGAAAAACTT
*
8498 AAACTTGATGGGAACTTTTCCAATTTG-AAAACTT
1 AAAC-TGATGGGAACTTTCCCAATTTGAAAAACTT
*
8532 AAACCTGATGGGAACTTTCCCGATTTGAAA
1 AAA-CTGATGGGAACTTTCCCAATTTGAAA
8562 GAGAGCTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
34 34 0.59
35 24 0.41
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (34 bp):
AAACTGATGGGAACTTTCCCAATTTGAAAAACTT
Found at i:8764 original size:53 final size:52
Alignment explanation
Indices: 8536--8801 Score: 340
Period size: 53 Copynumber: 5.1 Consensus size: 52
8526 AAACTTAAAC
* * *
8536 CTGATGGGAACTTTCCCGATTTGAAAGAGAGCTAAATTGAATACTTTTAAAA
1 CTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAA
* * *
8588 CTGATGGGAACTTTCCCGATTTGAAAAAAAAATAGCTAAATTGTATACTTTGAAAA
1 CTGATGGGAACTTTCCCAATTTG----AAAAAGAGCTAAATTGAATACTTTGAAAA
*
8644 CTGATGGGAACTTTCCCAATTTG-AAAA-A-CTTAAATTGAATATTTTGAAAA
1 CTGATGGGAACTTTCCCAATTTGAAAAAGAGC-TAAATTGAATACTTTGAAAA
* * * *
8694 TTGGTGGGAACTTTCCCAATTTGAAAAAGAGCTAGATTGAATACTTTGAAGAT
1 CTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAA-AA
* *
8747 TTGATGGGAACTTTCCCAATTTGAAAAAAAGCTAAATTGAATACTTTGAAAA
1 CTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAA
8799 CTG
1 CTG
8802 GTGAAATTCT
Statistics
Matches: 188, Mismatches: 17, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
49 1 0.01
50 40 0.21
51 8 0.04
52 43 0.23
53 49 0.26
56 47 0.25
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (52 bp):
CTGATGGGAACTTTCCCAATTTGAAAAAGAGCTAAATTGAATACTTTGAAAA
Found at i:9865 original size:18 final size:18
Alignment explanation
Indices: 9842--9879 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
9832 TTAAATTTTG
9842 AAAGCCCAAACAAATTAA
1 AAAGCCCAAACAAATTAA
**
9860 AAAGCCCAAATGAATTAA
1 AAAGCCCAAACAAATTAA
9878 AA
1 AA
9880 CAATTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.18, G:0.08, T:0.13
Consensus pattern (18 bp):
AAAGCCCAAACAAATTAA
Done.