Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015430.1 Corchorus olitorius cultivar O-4 contig15463, 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: 89453
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2359 original size:21 final size:21
Alignment explanation
Indices: 2309--2360 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
2299 ACTTAATCAT
* *
2309 GTTACTAAAATCTTTATAAGA
1 GTTACTAAAATCATTATAAAA
* *
2330 CTTAGTAAAATGCATTA-AAAA
1 GTTACTAAAAT-CATTATAAAA
2351 GTTACTAAAA
1 GTTACTAAAA
2361 AATTTATAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (21 bp):
GTTACTAAAATCATTATAAAA
Found at i:2608 original size:22 final size:23
Alignment explanation
Indices: 2566--2608 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2556 TTACTAAGAT
* *
2566 GCTTAATAAGGTTATTGAAAAAA
1 GCTTAATAAGGTTACTAAAAAAA
2589 GCTT-ATAAGGTTACTAAAAA
1 GCTTAATAAGGTTACTAAAAA
2609 TTGGTGAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (23 bp):
GCTTAATAAGGTTACTAAAAAAA
Found at i:2980 original size:199 final size:199
Alignment explanation
Indices: 2640--3442 Score: 1209
Period size: 199 Copynumber: 4.0 Consensus size: 199
2630 CATAATGCAA
* *
2640 TAATATTAAACATTTAATTAATTATGAAATGGGGTATGTGTCAA-TGTCTTAACCCGTTTATGGA
1 TAATATTAAATATTTAATTAATTATGAAATGGGGTATGTGTCAACT-TCTTAACCCGCTTATGGA
* * * * * *
2704 GTCAAAAATTTACACCGACAGTGTATTGTATAATAATACTATAAGAAAAATTATGCAATACACAG
65 GTCCAAAATTTACACTGACAATGTATTGTATAATAATCCTATAAGAAAAATTATACAATACACCG
* *
2769 TCAGTGGAGTTTAGCATACTGCACGTGCGGGGTTTAAGGTTTGACATGTGTCCCCTTAGGGAATA
130 TCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATA
2834 TGTAT
195 TGTAT
* *
2839 TAATATTAATTATTTAATTAATTATGAAATGGGGTATGTGTCAACTTCTTAACTCGCTTATGGAG
1 TAATATTAAATATTTAATTAATTATGAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAG
* * *
2904 TGCAAAATTTACATTGACAATGTATTGTATAATAATCCTATAAGAACAATTATACAATACACCGT
66 TCCAAAATTTACACTGACAATGTATTGTATAATAATCCTATAAGAAAAATTATACAATACACCGT
*
2969 CAGTGGAGTTTAGCAGACTGCACGTGCGGGCTTTAAGGGTTGACATGTGTCCCCTTAGGGAATAT
131 CAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATAT
3034 GTAT
196 GTAT
* * * * * * * *
3038 TAATATTAAATATTTTATTAAATACGAAATGGGGTATATGTCAAATTATTAAACCGTTTATGGAG
1 TAATATTAAATATTTAATTAATTATGAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAG
* **
3103 TCCAAAATTTACACTGACAATGTATTGTATAATAATCCTATAAGAAAAATTATACCATACATTGT
66 TCCAAAATTTACACTGACAATGTATTGTATAATAATCCTATAAGAAAAATTATACAATACACCGT
* *
3168 CAGT-GAGTTTAGCAGACTGCA-GCTGCGGGGTTTAAGGGTTGACATGTATCCCCTTAAGGAATA
131 CAGTGGAGTTTAGCAGACTGCACG-TGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATA
3231 TGTAT
195 TGTAT
* * * *
3236 TAATATTAAATATTTAATTAATTATGAAATAGGGCATGCGTCAACTTCTTAACCCGCTTATAGAG
1 TAATATTAAATATTTAATTAATTATGAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAG
* * * *
3301 TCCAAAATTTACATTGACAGTTTATTGTATGATAATCCTATAA-AAACAATTATACAATACACCG
66 TCCAAAATTTACACTGACAATGTATTGTATAATAATCCTATAAGAAA-AATTATACAATACACCG
*
3365 TCAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATA
130 TCAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATA
3430 TGTAT
195 TGTAT
3435 TAATATTA
1 TAATATTA
3443 TACAAGTGGA
Statistics
Matches: 542, Mismatches: 57, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
197 4 0.01
198 170 0.31
199 366 0.68
200 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (199 bp):
TAATATTAAATATTTAATTAATTATGAAATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAG
TCCAAAATTTACACTGACAATGTATTGTATAATAATCCTATAAGAAAAATTATACAATACACCGT
CAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGAATAT
GTAT
Found at i:3374 original size:397 final size:398
Alignment explanation
Indices: 2640--3442 Score: 1281
Period size: 397 Copynumber: 2.0 Consensus size: 398
2630 CATAATGCAA
* * * * *
2640 TAATATTAAACATTTAATTAATTATGAAATGGGGTATGTGTCAATGTCTTAACCCGTTTATGGAG
1 TAATATTAAACATTTAATTAAATACGAAATGGGGTATATGTCAATGTATTAAACCGTTTATGGAG
* *
2705 TCAAAAATTTACACCGACAGTGTATTGTATAATAATACTATAAGAAAAATTATGCAATACACAGT
66 TCAAAAATTTACACCGACAATGTATTGTATAATAATACTATAAGAAAAATTATACAATACACAGT
* * * *
2770 CAGTGGAGTTTAGCATACTGCACGTGCGGGGTTTAAGGTTTGACATGTGTCCCCTTAGGGAATAT
131 CAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTATCCCCTTAAGGAATAT
* * * * *
2835 GTATTAATATTAATTATTTAATTAATTATGAAATGGGGTATGTGTCAACTTCTTAACTCGCTTAT
196 GTATTAATATTAAATATTTAATTAATTATGAAATAGGGCATGCGTCAACTTCTTAACCCGCTTAT
* * *
2900 GGAGTGCAAAATTTACATTGACAATGTATTGTATAATAATCCTATAAGAACAATTATACAATACA
261 AGAGTCCAAAATTTACATTGACAATGTATTGTATAATAATCCTATAAAAACAATTATACAATACA
2965 CCGTCAGTGGAGTTTAGCAGACTGCACGTGC-GGGCTTTAAGGGTTGACATGTGTCCCCTTAGGG
326 CCGTCAGTGGAGTTTAGCAGACTGCACGTGCAGGG-TTTAAGGGTTGACATGTGTCCCCTTAGGG
3029 AATATGTAT
390 AATATGTAT
* *
3038 TAATATTAAATATTTTATTAAATACGAAATGGGGTATATGTCAAAT-TATTAAACCGTTTATGGA
1 TAATATTAAACATTTAATTAAATACGAAATGGGGTATATGTC-AATGTATTAAACCGTTTATGGA
* * * * **
3102 GTCCAAAATTTACACTGACAATGTATTGTATAATAATCCTATAAGAAAAATTATACCATACATTG
65 GTCAAAAATTTACACCGACAATGTATTGTATAATAATACTATAAGAAAAATTATACAATACACAG
3167 TCAGT-GAGTTTAGCAGACTGCA-GCTGCGGGGTTTAAGGGTTGACATGTATCCCCTTAAGGAAT
130 TCAGTGGAGTTTAGCAGACTGCACG-TGCGGGGTTTAAGGGTTGACATGTATCCCCTTAAGGAAT
3230 ATGTATTAATATTAAATATTTAATTAATTATGAAATAGGGCATGCGTCAACTTCTTAACCCGCTT
194 ATGTATTAATATTAAATATTTAATTAATTATGAAATAGGGCATGCGTCAACTTCTTAACCCGCTT
* * *
3295 ATAGAGTCCAAAATTTACATTGACAGTTTATTGTATGATAATCCTATAAAAACAATTATACAATA
259 ATAGAGTCCAAAATTTACATTGACAATGTATTGTATAATAATCCTATAAAAACAATTATACAATA
3360 CACCGTCAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGG
324 CACCGTCAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGG
3425 GAATATGTAT
389 GAATATGTAT
3435 TAATATTA
1 TAATATTA
3443 TACAAGTGGA
Statistics
Matches: 372, Mismatches: 30, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
396 1 0.00
397 250 0.67
398 118 0.32
399 3 0.01
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (398 bp):
TAATATTAAACATTTAATTAAATACGAAATGGGGTATATGTCAATGTATTAAACCGTTTATGGAG
TCAAAAATTTACACCGACAATGTATTGTATAATAATACTATAAGAAAAATTATACAATACACAGT
CAGTGGAGTTTAGCAGACTGCACGTGCGGGGTTTAAGGGTTGACATGTATCCCCTTAAGGAATAT
GTATTAATATTAAATATTTAATTAATTATGAAATAGGGCATGCGTCAACTTCTTAACCCGCTTAT
AGAGTCCAAAATTTACATTGACAATGTATTGTATAATAATCCTATAAAAACAATTATACAATACA
CCGTCAGTGGAGTTTAGCAGACTGCACGTGCAGGGTTTAAGGGTTGACATGTGTCCCCTTAGGGA
ATATGTAT
Found at i:4001 original size:2 final size:2
Alignment explanation
Indices: 3994--4026 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3984 TATTATTTAG
3994 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4027 TTATTGAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5814 original size:23 final size:23
Alignment explanation
Indices: 5788--5834 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
5778 GAAAATCAGG
5788 TTGGAAATTCAATTAAAAGTTAT
1 TTGGAAATTCAATTAAAAGTTAT
5811 TTGGAAATTCAATTAAAAGTTAT
1 TTGGAAATTCAATTAAAAGTTAT
5834 T
1 T
5835 CCCAAAGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.40
Consensus pattern (23 bp):
TTGGAAATTCAATTAAAAGTTAT
Found at i:12973 original size:2 final size:2
Alignment explanation
Indices: 12968--13000 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12958 TATTAAATTC
*
12968 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13001 CAAGCATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:31963 original size:24 final size:27
Alignment explanation
Indices: 31930--32044 Score: 100
Period size: 29 Copynumber: 4.4 Consensus size: 27
31920 TTCTAATAAC
*
31930 TTCTTAAAACTC-TAA-AC-CTTCATT
1 TTCTTCAAACTCTTAATACACTTCATT
*
31954 TTCTTCAAACTCTTAATCTTCACTTCATT
1 TTCTTCAAACTCTTAA--TACACTTCATT
* *
31983 TTCTTCAAACTCTTAATCTTCACTTTATT
1 TTCTTCAAACTCTTAA--TACACTTCATT
*
32012 TTCTTC-AAC-CTTCA-AC-CTTCATT
1 TTCTTCAAACTCTTAATACACTTCATT
32035 TTCTTCAAAC
1 TTCTTCAAAC
32045 AATCTTCAAG
Statistics
Matches: 79, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
23 12 0.15
24 15 0.19
25 3 0.04
27 4 0.05
28 4 0.05
29 41 0.52
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.46
Consensus pattern (27 bp):
TTCTTCAAACTCTTAATACACTTCATT
Found at i:31975 original size:15 final size:15
Alignment explanation
Indices: 31955--32004 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
31945 ACCTTCATTT
31955 TCTTCAAACTCTTAA
1 TCTTCAAACTCTTAA
*
31970 TCTTC--ACTTCATT-T
1 TCTTCAAAC-TC-TTAA
31984 TCTTCAAACTCTTAA
1 TCTTCAAACTCTTAA
31999 TCTTCA
1 TCTTCA
32005 CTTTATTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
13 2 0.07
14 9 0.32
15 15 0.54
16 2 0.07
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.46
Consensus pattern (15 bp):
TCTTCAAACTCTTAA
Found at i:31980 original size:29 final size:29
Alignment explanation
Indices: 31947--32019 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
31937 AACTCTAAAC
31947 CTTCATTTTCTTCAAACTCTTAATCTTCA
1 CTTCATTTTCTTCAAACTCTTAATCTTCA
31976 CTTCATTTTCTTCAAACTCTTAATCTTCA
1 CTTCATTTTCTTCAAACTCTTAATCTTCA
*
32005 CTTTATTTTCTTCAA
1 CTTCATTTTCTTCAA
32020 CCTTCAACCT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (29 bp):
CTTCATTTTCTTCAAACTCTTAATCTTCA
Found at i:32579 original size:25 final size:25
Alignment explanation
Indices: 32501--32579 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 25
32491 AACTGCTATT
* *
32501 GTTCTCATTACAGAAATGAAGCTGCTATT
1 GTTCTCATTACAGAAATGAA-AT--T-TC
* *
32530 GTTCTCATTACAGAAATGGATTTTC
1 GTTCTCATTACAGAAATGAAATTTC
* *
32555 GTTCTCGTTACAGAATTGAAATTTC
1 GTTCTCATTACAGAAATGAAATTTC
32580 AAGGAATTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
25 22 0.51
26 1 0.02
28 1 0.02
29 19 0.44
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (25 bp):
GTTCTCATTACAGAAATGAAATTTC
Found at i:32603 original size:12 final size:12
Alignment explanation
Indices: 32586--32646 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
32576 TTTCAAGGAA
*
32586 TTTATACTAATG
1 TTTATACTCATG
*
32598 TTTATACTCTCAGG
1 TTTATA--CTCATG
*
32612 AATTTATACTGATG
1 --TTTATACTCATG
32626 TTTATACTCATG
1 TTTATACTCATG
32638 TTTATACTC
1 TTTATACTC
32647 TCAACATCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
12 26 0.65
14 8 0.20
16 6 0.15
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.48
Consensus pattern (12 bp):
TTTATACTCATG
Found at i:32621 original size:28 final size:28
Alignment explanation
Indices: 32581--32634 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
32571 TGAAATTTCA
32581 AGGAATTTATACTAATGTTTATACTCTC
1 AGGAATTTATACTAATGTTTATACTCTC
*
32609 AGGAATTTATACTGATGTTTATACTC
1 AGGAATTTATACTAATGTTTATACTC
32635 ATGTTTATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (28 bp):
AGGAATTTATACTAATGTTTATACTCTC
Found at i:32732 original size:60 final size:60
Alignment explanation
Indices: 32635--32754 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
32625 GTTTATACTC
*
32635 ATGTTTATACTCTCAACATCTTGCTTAATTGTTATTGCCGCTTGCACGGTGTGGATTCGG
1 ATGTTTATACTCTCAACATCTTGCTTAATTGTCATTGCCGCTTGCACGGTGTGGATTCGG
32695 ATGTTTATACTCTCAACATCTTGCTTAATTGTCATTGCCGCTTGCACGGTGTGGATTCGG
1 ATGTTTATACTCTCAACATCTTGCTTAATTGTCATTGCCGCTTGCACGGTGTGGATTCGG
32755 CGTTTTTTGT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.18, C:0.21, G:0.22, T:0.39
Consensus pattern (60 bp):
ATGTTTATACTCTCAACATCTTGCTTAATTGTCATTGCCGCTTGCACGGTGTGGATTCGG
Found at i:32850 original size:27 final size:27
Alignment explanation
Indices: 32819--32956 Score: 159
Period size: 27 Copynumber: 4.9 Consensus size: 27
32809 GAACCAATGG
* *
32819 TCACTAAGATACTTCAATCCAATATGA
1 TCACTAAAATGCTTCAATCCAATATGA
32846 TCACTAAAATGCTTCAATCCAATATGA
1 TCACTAAAATGCTTCAATCCAATATGA
*
32873 TCACTAAAATGCTTCAATCCAATTGGGTGGA
1 TCACTAAAATGCTTCAATCCAA-T--AT-GA
* *
32904 TGGACACTAAGATGCTTCGATCCAATATGA
1 T---CACTAAAATGCTTCAATCCAATATGA
*
32934 TCACTAAAATACTTCAATCCAAT
1 TCACTAAAATGCTTCAATCCAAT
32957 TGGGTGGACA
Statistics
Matches: 95, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
27 66 0.69
28 1 0.01
30 4 0.04
31 4 0.04
33 1 0.01
34 19 0.20
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.29
Consensus pattern (27 bp):
TCACTAAAATGCTTCAATCCAATATGA
Found at i:32942 original size:61 final size:61
Alignment explanation
Indices: 32847--32964 Score: 209
Period size: 61 Copynumber: 1.9 Consensus size: 61
32837 CCAATATGAT
*
32847 CACTAAAATGCTTCAATCCAATATGATCACTAAAATGCTTCAATCCAATTGGGTGGATGGA
1 CACTAAAATGCTTCAATCCAATATGATCACTAAAATACTTCAATCCAATTGGGTGGATGGA
* *
32908 CACTAAGATGCTTCGATCCAATATGATCACTAAAATACTTCAATCCAATTGGGTGGA
1 CACTAAAATGCTTCAATCCAATATGATCACTAAAATACTTCAATCCAATTGGGTGGA
32965 CACTGGGCAC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (61 bp):
CACTAAAATGCTTCAATCCAATATGATCACTAAAATACTTCAATCCAATTGGGTGGATGGA
Found at i:45513 original size:21 final size:19
Alignment explanation
Indices: 45468--45525 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
45458 CTGTTTAGCA
45468 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
* *
45487 ACTGTACAGATTAGATTAGGT
1 ACTGTACAGATGAGATTA--C
45508 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
45526 TTAGAGCAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:46928 original size:31 final size:30
Alignment explanation
Indices: 46868--46928 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
46858 ATATAACAAT
*
46868 AAAGAATAAAGAAAAATAAAGTAAAAGAAG
1 AAAGAATAAAGAAAAATAAACTAAAAGAAG
*
46898 AAAGCATAAAGAGAAAAT-AACTAAATAGAAG
1 AAAGAATAAAGA-AAAATAAACTAAA-AGAAG
46929 TTAATTAGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.69, C:0.03, G:0.16, T:0.11
Consensus pattern (30 bp):
AAAGAATAAAGAAAAATAAACTAAAAGAAG
Found at i:48280 original size:183 final size:184
Alignment explanation
Indices: 47972--48338 Score: 657
Period size: 183 Copynumber: 2.0 Consensus size: 184
47962 GTGAAACCCG
*
47972 ACCTACTTAGTATTTACTATTATTTGATATTTGGTCTCCGGTATTCCGTAGTTACATCGTGTGTC
1 ACCTACTTAGTATTTACTATTATTTGATATTTGGTCTCCGGTATTCCGTAATTACATCGTGTGTC
48037 AATTAATCTAGAGTCGAGCTGCATTAAACCTTAAACGGGAAACCTTCCTAGCTAGATCAGTC-AA
66 AATTAATCTAGAGTCGAGCTGCATTAAACCTTAAACGGGAAACCTTCCTAGCTAGATCAGTCGAA
48101 TTTTTTTTTTAACTAATAAGACTCGAATTCAAGACTTTACTAACTAAAAGGGCA
131 TTTTTTTTTTAACTAATAAGACTCGAATTCAAGACTTTACTAACTAAAAGGGCA
* *
48155 ACCTACTTAGTATTTACTATTATTTGATATTTGGTCTCTGGTATTCCGTAATTACATTGTGTGTC
1 ACCTACTTAGTATTTACTATTATTTGATATTTGGTCTCCGGTATTCCGTAATTACATCGTGTGTC
* *
48220 AATTACTCTAG-GATCGAGCTGCATTAAACCTTAAACGGGAAAGCTTCCTAGCTAGATCAGTCGA
66 AATTAATCTAGAG-TCGAGCTGCATTAAACCTTAAACGGGAAACCTTCCTAGCTAGATCAGTCGA
*
48284 TTTTTTTTTTTAACTAATAAGACTCGAATTCAAGACTTTACTAACTAAAAGGGCA
130 ATTTTTTTTTTAACTAATAAGACTCGAATTCAAGACTTTACTAACTAAAAGGGCA
48339 TTGAGTCCTA
Statistics
Matches: 176, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
182 1 0.01
183 120 0.68
184 55 0.31
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (184 bp):
ACCTACTTAGTATTTACTATTATTTGATATTTGGTCTCCGGTATTCCGTAATTACATCGTGTGTC
AATTAATCTAGAGTCGAGCTGCATTAAACCTTAAACGGGAAACCTTCCTAGCTAGATCAGTCGAA
TTTTTTTTTTAACTAATAAGACTCGAATTCAAGACTTTACTAACTAAAAGGGCA
Found at i:56325 original size:72 final size:72
Alignment explanation
Indices: 56239--56389 Score: 293
Period size: 72 Copynumber: 2.1 Consensus size: 72
56229 GTCGTCAAGA
56239 GTACCACTGAATTGATTTTGTGAAAGTATAACTCTCTGCAGTGATGGAATTTGAAACAAACTTGG
1 GTACCACTGAATTGATTTTGTGAAAGTATAACTCTCTGCAGTGATGGAATTTGAAACAAACTTGG
56304 TGGGATG
66 TGGGATG
56311 GTACCACTGAATTGATTTTGTGAAAGTATAACTCTCTGCAGTGATGGAATTTGAAACAAACTTGG
1 GTACCACTGAATTGATTTTGTGAAAGTATAACTCTCTGCAGTGATGGAATTTGAAACAAACTTGG
56376 TGGGATG
66 TGGGATG
*
56383 GTTCCAC
1 GTACCAC
56390 CTAAGTTGTT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 78 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (72 bp):
GTACCACTGAATTGATTTTGTGAAAGTATAACTCTCTGCAGTGATGGAATTTGAAACAAACTTGG
TGGGATG
Found at i:72824 original size:27 final size:27
Alignment explanation
Indices: 72805--72863 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
72795 ATTCTGGAGC
72805 ATTTCTTTTTGTTCAATATTCTCAACT
1 ATTTCTTTTTGTTCAATATTCTCAACT
72832 ATTTCTTTTTGTTCAATATTCTCAACT
1 ATTTCTTTTTGTTCAATATTCTCAACT
72859 ATTTC
1 ATTTC
72864 CGTCCTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.22, C:0.19, G:0.03, T:0.56
Consensus pattern (27 bp):
ATTTCTTTTTGTTCAATATTCTCAACT
Found at i:84274 original size:36 final size:36
Alignment explanation
Indices: 84222--84298 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
84212 TGGCTATCGA
*
84222 GAGTCGTAATGGTTAGCCTCAGTCATTGACCATCTT
1 GAGTCGTAATGATTAGCCTCAGTCATTGACCATCTT
84258 GAGTCGTAATGATTAGCCTCAGTCATTGACCATCTT
1 GAGTCGTAATGATTAGCCTCAGTCATTGACCATCTT
84294 GAGTC
1 GAGTC
84299 ATGGTGGTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.32
Consensus pattern (36 bp):
GAGTCGTAATGATTAGCCTCAGTCATTGACCATCTT
Done.