Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015226.1 Corchorus olitorius cultivar O-4 contig15259, 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: 78396
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:33 original size:18 final size:18
Alignment explanation
Indices: 6--40 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1 TTACA
6 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
24 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
41 CAATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:1374 original size:26 final size:27
Alignment explanation
Indices: 1310--1375 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
1300 CCTTCCACCC
* * ** *
1310 TAAATAAATAATAATAATTAATTGTAG
1 TAAATAAATAATTACAATTAATTACAA
1337 TAAATAAA-AATTACAATTAATTACAA
1 TAAATAAATAATTACAATTAATTACAA
1363 T-AATAAATAATTA
1 TAAATAAATAATTA
1376 TAGTAAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 6 0.18
26 19 0.58
27 8 0.24
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (27 bp):
TAAATAAATAATTACAATTAATTACAA
Found at i:1390 original size:17 final size:17
Alignment explanation
Indices: 1351--1404 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
1341 TAAAAATTAC
* *
1351 AATTAATTACAAT-AAT
1 AATTAATTATAGTAAAT
*
1367 AAATAATTATAGTAAAT
1 AATTAATTATAGTAAAT
1384 AATTAATTATAGTCAAAT
1 AATTAATTATAGT-AAAT
1402 AAT
1 AAT
1405 AAAATAACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 10 0.31
17 15 0.47
18 7 0.22
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (17 bp):
AATTAATTATAGTAAAT
Found at i:1772 original size:32 final size:34
Alignment explanation
Indices: 1615--1792 Score: 100
Period size: 33 Copynumber: 5.4 Consensus size: 34
1605 TTAAATATGT
* * * *
1615 GGCGGTGCCGCCCCACCAGG-GCGGCA-AGGCCAT
1 GGCGGTGCCGCACCAACTGGTGCGGCATA-GCCAC
* * * * *
1648 GGCAGTGCCGCACC-AGTGGGGCGGCATCGCCAT
1 GGCGGTGCCGCACCAACTGGTGCGGCATAGCCAC
* ** * * * *
1681 GCCTATGCCGC-CCAAGTGGTGCGGCACACCCAT
1 GGCGGTGCCGCACCAACTGGTGCGGCATAGCCAC
** *
1714 GGTTGTGCCGC-CCAACTGGTGGGGCAT-GCCAC
1 GGCGGTGCCGCACCAACTGGTGCGGCATAGCCAC
* *
1746 GGCGGTGCCGCACC-ACTTGTGCGGCATAGCCAT
1 GGCGGTGCCGCACCAACTGGTGCGGCATAGCCAC
*
1779 GGCGGTGTCGCACC
1 GGCGGTGCCGCACC
1793 CCGCCCCCTG
Statistics
Matches: 113, Mismatches: 27, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
32 27 0.24
33 86 0.76
ACGTcount: A:0.15, C:0.35, G:0.36, T:0.14
Consensus pattern (34 bp):
GGCGGTGCCGCACCAACTGGTGCGGCATAGCCAC
Found at i:9057 original size:101 final size:101
Alignment explanation
Indices: 8882--9082 Score: 393
Period size: 101 Copynumber: 2.0 Consensus size: 101
8872 CATTTTCTTT
8882 CAAAATTTGATGGGAGTCGTATTCCACCAAAAATAAAATCATACAAAACCTATAGACAGGGTAAG
1 CAAAATTTGATGGGAGTCGTATTCCACCAAAAATAAAATCATACAAAACCTATAGACAGGGTAAG
8947 TACGAGTCGATCCCACAGAGAACTATTGTTTTAATC
66 TACGAGTCGATCCCACAGAGAACTATTGTTTTAATC
*
8983 CAAAATTTGATGGGTGTCGTATTCCACCAAAAATAAAATCATACAAAACCTATAGACAGGGTAAG
1 CAAAATTTGATGGGAGTCGTATTCCACCAAAAATAAAATCATACAAAACCTATAGACAGGGTAAG
9048 TACGAGTCGATCCCACAGAGAACTATTGTTTTAAT
66 TACGAGTCGATCCCACAGAGAACTATTGTTTTAAT
9083 TACCTTTCCT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.25
Consensus pattern (101 bp):
CAAAATTTGATGGGAGTCGTATTCCACCAAAAATAAAATCATACAAAACCTATAGACAGGGTAAG
TACGAGTCGATCCCACAGAGAACTATTGTTTTAATC
Found at i:11466 original size:107 final size:107
Alignment explanation
Indices: 11392--11604 Score: 338
Period size: 107 Copynumber: 2.0 Consensus size: 107
11382 GCATTAGCTA
11392 ACAATATTAGTACCATCTGATACAAAAATAGGAGTTTATTTTATAAATTAAAAAGGCAATTCATT
1 ACAATATTAGTACCATCTGATACAAAAATAGGAGTTTATTTTATAAATTAAAAAGGCAATTCATT
* *
11457 TCGGAAAAAAAATAGAAAATTTGAAGAGATATAATTATGCAT
66 TCGGAAAAAAAATAGAAAACTTGAAGAGATAGAATTATGCAT
*** * *
11499 TTTATATTAGTACCATCTGCTACAAAAATAGGAGTTTATTTTATAAATTATAAAGGCAATTCATT
1 ACAATATTAGTACCATCTGATACAAAAATAGGAGTTTATTTTATAAATTAAAAAGGCAATTCATT
* *
11564 TCGG-AAAAAAATAGAAAATTTGAAGAGATATAATTATGCAT
66 TCGGAAAAAAAATAGAAAACTTGAAGAGATAGAATTATGCAT
11605 TTTATATTTT
Statistics
Matches: 101, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
106 37 0.37
107 64 0.63
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (107 bp):
ACAATATTAGTACCATCTGATACAAAAATAGGAGTTTATTTTATAAATTAAAAAGGCAATTCATT
TCGGAAAAAAAATAGAAAACTTGAAGAGATAGAATTATGCAT
Found at i:15187 original size:30 final size:30
Alignment explanation
Indices: 15153--15214 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
15143 AATTATATTT
15153 GTATAAAATTGTAACTAAACTTAATGCAAC
1 GTATAAAATTGTAACTAAACTTAATGCAAC
15183 GTATAAAATTGTAACTAAACTTAATGCAAC
1 GTATAAAATTGTAACTAAACTTAATGCAAC
15213 GT
1 GT
15215 GAGGAACTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (30 bp):
GTATAAAATTGTAACTAAACTTAATGCAAC
Found at i:16243 original size:27 final size:27
Alignment explanation
Indices: 16168--16250 Score: 121
Period size: 30 Copynumber: 3.0 Consensus size: 27
16158 ACACCACTAA
*
16168 TAATAATTATTATTATAATAATAAGTT
1 TAATAATTATTATAATAATAATAAGTT
*
16195 TAATAATTATAATACCACTAATAATAAGTT
1 TAATAATTATTATA--A-TAATAATAAGTT
16225 TAATAATTATTATAATAATAATAAGT
1 TAATAATTATTATAATAATAATAAGT
16251 CTAAATTAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
27 23 0.46
28 1 0.02
29 1 0.02
30 25 0.50
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (27 bp):
TAATAATTATTATAATAATAATAAGTT
Found at i:19462 original size:16 final size:18
Alignment explanation
Indices: 19441--19477 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
19431 GGTGGTGGTT
*
19441 CCGGT-CGA-CGGTTTGA
1 CCGGTCCGACCGGTTTAA
19457 CCGGTCCGACCGGTTTAA
1 CCGGTCCGACCGGTTTAA
19475 CCG
1 CCG
19478 CCGGTCCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 3 0.17
18 10 0.56
ACGTcount: A:0.14, C:0.32, G:0.32, T:0.22
Consensus pattern (18 bp):
CCGGTCCGACCGGTTTAA
Found at i:21276 original size:42 final size:41
Alignment explanation
Indices: 21176--21289 Score: 162
Period size: 40 Copynumber: 2.8 Consensus size: 41
21166 TGAATGTTTC
* * *
21176 GAAAACTCGATGAGAACTTTCCCTAAATTGAAAACCTTTGA
1 GAAAACTTGATGGGATCTTTCCCTAAATTGAAAACCTTTGA
21217 -AAAACTTGATGGGATCTTTCCCTAAATTGAAAA-CTTTGAAA
1 GAAAACTTGATGGGATCTTTCCCTAAATTGAAAACCTTTG--A
21258 GAAAACTTGATGGGATCTTT-CCTAAATTGAAA
1 GAAAACTTGATGGGATCTTTCCCTAAATTGAAA
21290 GGACCTAAAT
Statistics
Matches: 67, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
39 5 0.07
40 30 0.45
41 13 0.19
42 19 0.28
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (41 bp):
GAAAACTTGATGGGATCTTTCCCTAAATTGAAAACCTTTGA
Found at i:21332 original size:95 final size:94
Alignment explanation
Indices: 21197--21512 Score: 294
Period size: 95 Copynumber: 3.2 Consensus size: 94
21187 GAGAACTTTC
* * ** * *
21197 CCTAAATTGAAAACCTTTGAAAAACTTGATGGGATCTTTCCCTAAATTGAAAA-CTTTGAAA-GA
1 CCTAAATTGAAAA-CTTTG-AAAACTTGATGGGAACTTTTCC-ACTTTGAAAAGATCT-AAATGA
* * * *
21260 AAACTTGATGGGATCTTTCCTAAATTGAAAGGA
62 AAACTTGATGAGAACTTTCCCAAATTGAAAAGA
* *
21293 CCTAAATTGAACACTTTGAAAACTTCATGGGAACTTTTCCACTTTGAAAAGATCTAAATTGAAAA
1 CCTAAATTGAAAACTTTGAAAACTTGATGGGAACTTTTCCACTTTGAAAAGATCTAAA-TGAAAA
**
21358 CTTGATGAGAACTTTCCCACTTTGAAAAGA
65 CTTGATGAGAACTTTCCCAAATTGAAAAGA
* * *
21388 CCTAAACTGAATACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAACTGAATA
1 CCTAAATTGAAAACTTTGAAAACTTGATGGGAACTTTTCCACTTTGAAAAGA--T---CT-AA-A
* **
21453 CTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGA
59 ---TGAAAACTTGATGAGAACTTTCCCAAATTGAAAAGA
*
21492 CCTAAATTGAATACTTTGAAA
1 CCTAAATTGAAAACTTTGAAA
21513 GCTTTGAAGG
Statistics
Matches: 188, Mismatches: 20, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
93 11 0.06
94 21 0.11
95 82 0.44
96 12 0.06
97 1 0.01
100 2 0.01
101 2 0.01
102 1 0.01
104 56 0.30
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (94 bp):
CCTAAATTGAAAACTTTGAAAACTTGATGGGAACTTTTCCACTTTGAAAAGATCTAAATGAAAAC
TTGATGAGAACTTTCCCAAATTGAAAAGA
Found at i:21340 original size:52 final size:52
Alignment explanation
Indices: 21258--21512 Score: 348
Period size: 52 Copynumber: 5.1 Consensus size: 52
21248 AACTTTGAAA
* * ** * * *
21258 GAAAACTTGATGGGATCTTTCCTAAATTGAAAGGACCTAAATTGAACACTTT
1 GAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAACTGAATACTTT
* *
21310 GAAAACTTCATGGGAACTTTTCCACTTTGAAAAGA--T---CT-AA-A--TT
1 GAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAACTGAATACTTT
*
21353 GAAAACTTGATGAGAACTTTCCCACTTTGAAAAGACCTAAACTGAATACTTT
1 GAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAACTGAATACTTT
21405 GAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAACTGAATACTTT
1 GAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAACTGAATACTTT
*
21457 GAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAATACTTT
1 GAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAACTGAATACTTT
21509 GAAA
1 GAAA
21513 GCTTTGAAGG
Statistics
Matches: 181, Mismatches: 13, Indels: 18
0.85 0.06 0.08
Matches are distributed among these distances:
43 34 0.19
45 2 0.01
46 2 0.01
47 1 0.01
48 2 0.01
49 2 0.01
50 2 0.01
52 136 0.75
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (52 bp):
GAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAACTGAATACTTT
Found at i:21432 original size:28 final size:28
Alignment explanation
Indices: 21400--21489 Score: 80
Period size: 28 Copynumber: 3.4 Consensus size: 28
21390 TAAACTGAAT
21400 ACTTTGAAAACTTGATGGGAACTTTCCC
1 ACTTTGAAAACTTGATGGGAACTTTCCC
**** ****
21428 ACTTTGAAAA---GACCTAAAC-TGAAT
1 ACTTTGAAAACTTGATGGGAACTTTCCC
21452 ACTTTGAAAACTTGATGGGAACTTTCCC
1 ACTTTGAAAACTTGATGGGAACTTTCCC
21480 ACTTTGAAAA
1 ACTTTGAAAA
21490 GACCTAAATT
Statistics
Matches: 42, Mismatches: 16, Indels: 8
0.64 0.24 0.12
Matches are distributed among these distances:
24 11 0.26
25 5 0.12
27 5 0.12
28 21 0.50
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (28 bp):
ACTTTGAAAACTTGATGGGAACTTTCCC
Found at i:21561 original size:17 final size:17
Alignment explanation
Indices: 21539--21571 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21529 TTGTTTTTGA
21539 TTTTTTGAATTTTGAAT
1 TTTTTTGAATTTTGAAT
*
21556 TTTTTTGATTTTTGAA
1 TTTTTTGAATTTTGAA
21572 AAACCTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (17 bp):
TTTTTTGAATTTTGAAT
Found at i:36654 original size:18 final size:18
Alignment explanation
Indices: 36631--36667 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
36621 CTCCTCTATC
*
36631 ATGAAAACACTTTTTTTT
1 ATGAAAACAATTTTTTTT
36649 ATGAAAACAATTTTTTTT
1 ATGAAAACAATTTTTTTT
36667 A
1 A
36668 ATTACCCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (18 bp):
ATGAAAACAATTTTTTTT
Found at i:37277 original size:9 final size:9
Alignment explanation
Indices: 37263--37289 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
37253 AAAGCATTAA
37263 TCATGGCAT
1 TCATGGCAT
37272 TCATGGCAT
1 TCATGGCAT
37281 TCATGGCAT
1 TCATGGCAT
37290 ATGAGTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (9 bp):
TCATGGCAT
Found at i:40520 original size:15 final size:16
Alignment explanation
Indices: 40496--40535 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
40486 AGAGGTTGAA
*
40496 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
40511 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
40527 AGAAAACAA
1 AGAAAACAA
40536 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:43434 original size:15 final size:14
Alignment explanation
Indices: 43410--43441 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
43400 ATCAAAGCAA
43410 TAATCAAGGAAAAT
1 TAATCAAGGAAAAT
43424 TAATGCAAGGAAAAT
1 TAAT-CAAGGAAAAT
43439 TAA
1 TAA
43442 AAAAATAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.56, C:0.06, G:0.16, T:0.22
Consensus pattern (14 bp):
TAATCAAGGAAAAT
Found at i:46124 original size:14 final size:15
Alignment explanation
Indices: 46105--46136 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
46095 AGCTTCCTAG
46105 AAAAACTCAAAA-AA
1 AAAAACTCAAAAGAA
46119 AAAAACTCAAAAGAA
1 AAAAACTCAAAAGAA
46134 AAA
1 AAA
46137 TTGTTAGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.78, C:0.12, G:0.03, T:0.06
Consensus pattern (15 bp):
AAAAACTCAAAAGAA
Found at i:46640 original size:16 final size:16
Alignment explanation
Indices: 46602--46641 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
46592 AGAGGTTGAA
*
46602 AGAAAGCAATTAAACT
1 AGAAAACAATTAAACT
*
46618 A-AAAACAATTATACT
1 AGAAAACAATTAAACT
46633 AGAAAACAA
1 AGAAAACAA
46642 AGCAAAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.62, C:0.12, G:0.07, T:0.17
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:54659 original size:29 final size:29
Alignment explanation
Indices: 54619--54953 Score: 344
Period size: 29 Copynumber: 11.7 Consensus size: 29
54609 AATAAAAACC
54619 AAAATGACCAAAATGCCCCTGGATATGCA
1 AAAATGACCAAAATGCCCCTGGATATGCA
* *
54648 AAAATGACCAAAATACCCC-GGATATGCC
1 AAAATGACCAAAATGCCCCTGGATATGCA
*
54676 AAAATGACCATAATGCCCCTGGATATGCA
1 AAAATGACCAAAATGCCCCTGGATATGCA
* *
54705 AAAATGACCAAAATGCCCCTGAATGTGCA
1 AAAATGACCAAAATGCCCCTGGATATGCA
** * * *
54734 AAAATGATAAAAATG-CCATGGGATACGCG
1 AAAATGACCAAAATGCCCCT-GGATATGCA
* * **
54763 AAAGTGACCATAATGCCTTTGGATATGCA
1 AAAATGACCAAAATGCCCCTGGATATGCA
* *
54792 AAAATGACCAAAATGCCTCTGGATGTGCAA
1 AAAATGACCAAAATGCCCCTGGATATGC-A
** *
54822 AAAATGATAAAAAAAATG-CCATGG----G-A
1 AAAATG---ACCAAAATGCCCCTGGATATGCA
* *
54848 TAAATGACCAAAATGCCCCTGGATACGCA
1 AAAATGACCAAAATGCCCCTGGATATGCA
*
54877 AAAATGACCATAATGCCCCTGGATATGCA
1 AAAATGACCAAAATGCCCCTGGATATGCA
* * *
54906 AAAATGACCATAATGCCCTTGGATGTGCA
1 AAAATGACCAAAATGCCCCTGGATATGCA
54935 AAAATGACCAAAATGCCCC
1 AAAATGACCAAAATGCCCC
54954 CCTAGATGTG
Statistics
Matches: 251, Mismatches: 42, Indels: 26
0.79 0.13 0.08
Matches are distributed among these distances:
23 7 0.03
24 5 0.02
26 6 0.02
28 30 0.12
29 183 0.73
30 9 0.04
32 4 0.02
33 7 0.03
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGGATATGCA
Found at i:54900 original size:114 final size:113
Alignment explanation
Indices: 54619--54952 Score: 358
Period size: 114 Copynumber: 2.9 Consensus size: 113
54609 AATAAAAACC
* * * *
54619 AAAATGACCAAAATGCCCCTGGATATGCAAAAATGACCAAAATACCCC-GGATATGCCAAAATGA
1 AAAATGACCAAAATGCCCCTGGATACGCAAAAATGACCATAATGCCCCTGGATATGCAAAAATGA
* **
54683 CCATAATGCCCCTGGATATGC-AAAAATGACCAAAATGCCCCTGAATGTGCA
66 CCATAATG-CCCTGGATGTGCAAAAAATGAAAAAAATG-CCC--AATGTGCA
** * * * **
54734 AAAATGATAAAAATG-CCATGGGATACGCGAAAGTGACCATAATGCCTTTGGATATGCAAAAATG
1 AAAATGACCAAAATGCCCCT-GGATACGCAAAAATGACCATAATGCCCCTGGATATGCAAAAATG
* *
54798 ACCAAAATGCCTCTGGATGTGCAAAAAATGATAAAAAAAATG-CC-ATG-GGA
65 ACCATAATGCC-CTGGATGTGCAAAAAATG---AAAAAAATGCCCAATGTGCA
*
54848 TAAATGACCAAAATGCCCCTGGATACGCAAAAATGACCATAATGCCCCTGGATATGCAAAAATGA
1 AAAATGACCAAAATGCCCCTGGATACGCAAAAATGACCATAATGCCCCTGGATATGCAAAAATGA
**
54913 CCATAATGCCCTTGGATGTGC-AAAAATGACCAAAATGCCC
66 CCATAATGCCC-TGGATGTGCAAAAAATGAAAAAAATGCCC
54953 CCCTAGATGT
Statistics
Matches: 182, Mismatches: 27, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
110 7 0.04
111 2 0.01
113 8 0.04
114 76 0.42
115 42 0.23
116 31 0.17
117 7 0.04
118 2 0.01
120 7 0.04
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (113 bp):
AAAATGACCAAAATGCCCCTGGATACGCAAAAATGACCATAATGCCCCTGGATATGCAAAAATGA
CCATAATGCCCTGGATGTGCAAAAAATGAAAAAAATGCCCAATGTGCA
Found at i:57352 original size:27 final size:26
Alignment explanation
Indices: 57280--57352 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 26
57270 AGGATCAACT
*
57280 AGGGGCATTTCGGTCATCTGCACATTC
1 AGGGGCATTT-GGTCATTTGCACATTC
* *
57307 AGGGGCATTTTAGTAATTTGCACATTC
1 AGGGGCA-TTTGGTCATTTGCACATTC
57334 AGGGGCATTCTGGTCATTT
1 AGGGGCATT-TGGTCATTT
57353 TAAGTTCACA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
27 34 0.87
28 3 0.08
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (26 bp):
AGGGGCATTTGGTCATTTGCACATTC
Found at i:70686 original size:15 final size:15
Alignment explanation
Indices: 70666--70696 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
70656 CATTAAAATC
70666 CCTCCTCCATTTTAA
1 CCTCCTCCATTTTAA
*
70681 CCTCCTCTATTTTAA
1 CCTCCTCCATTTTAA
70696 C
1 C
70697 TTTAAATCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.39, G:0.00, T:0.42
Consensus pattern (15 bp):
CCTCCTCCATTTTAA
Found at i:70713 original size:39 final size:39
Alignment explanation
Indices: 70661--70774 Score: 193
Period size: 39 Copynumber: 3.1 Consensus size: 39
70651 CATTTCATTA
70661 AAATCCCTCCTCCATTTTAACCTCCTCTATTTTAACTTT
1 AAATCCCTCCTCCATTTTAACCTCCTCTATTTTAACTTT
70700 AAATCCCTCCTCCATTTTAACCTCCTC-----TAACTTT
1 AAATCCCTCCTCCATTTTAACCTCCTCTATTTTAACTTT
70734 AAATCCCTCCTCCATTTTAACCTCCTCTATTTTAACTTT
1 AAATCCCTCCTCCATTTTAACCTCCTCTATTTTAACTTT
70773 AA
1 AA
70775 TGAAAAAGTA
Statistics
Matches: 70, Mismatches: 0, Indels: 10
0.88 0.00 0.12
Matches are distributed among these distances:
34 34 0.49
39 36 0.51
ACGTcount: A:0.25, C:0.34, G:0.00, T:0.41
Consensus pattern (39 bp):
AAATCCCTCCTCCATTTTAACCTCCTCTATTTTAACTTT
Found at i:70725 original size:15 final size:15
Alignment explanation
Indices: 70705--70769 Score: 67
Period size: 15 Copynumber: 4.1 Consensus size: 15
70695 ACTTTAAATC
70705 CCTCCTCCATTTTAA
1 CCTCCTCCATTTTAA
* *
70720 CCTCCTCTAACTTTAAA
1 CCTCCTC-CA-TTTTAA
70737 TCCCTCCTCCATTTTAA
1 --CCTCCTCCATTTTAA
*
70754 CCTCCTCTATTTTAA
1 CCTCCTCCATTTTAA
70769 C
1 C
70770 TTTAATGAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 22 0.54
16 1 0.02
17 10 0.24
18 1 0.02
19 7 0.17
ACGTcount: A:0.22, C:0.38, G:0.00, T:0.40
Consensus pattern (15 bp):
CCTCCTCCATTTTAA
Found at i:70731 original size:34 final size:34
Alignment explanation
Indices: 70661--70762 Score: 159
Period size: 34 Copynumber: 2.9 Consensus size: 34
70651 CATTTCATTA
70661 AAATCCCTCCTCCATTTTAACCTCCTCTATTTTAACTTT
1 AAATCCCTCCTCCATTTTAACCTCCTC-----TAACTTT
70700 AAATCCCTCCTCCATTTTAACCTCCTCTAACTTT
1 AAATCCCTCCTCCATTTTAACCTCCTCTAACTTT
70734 AAATCCCTCCTCCATTTTAACCTCCTCTA
1 AAATCCCTCCTCCATTTTAACCTCCTCTA
70763 TTTTAACTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
34 36 0.57
39 27 0.43
ACGTcount: A:0.24, C:0.37, G:0.00, T:0.39
Consensus pattern (34 bp):
AAATCCCTCCTCCATTTTAACCTCCTCTAACTTT
Found at i:70744 original size:19 final size:19
Alignment explanation
Indices: 70693--70745 Score: 60
Period size: 17 Copynumber: 3.0 Consensus size: 19
70683 TCCTCTATTT
70693 TAACTTTAAATCCCTCCTC
1 TAACTTTAAATCCCTCCTC
* *
70712 -CA-TTTTAA--CCTCCTC
1 TAACTTTAAATCCCTCCTC
70727 TAACTTTAAATCCCTCCTC
1 TAACTTTAAATCCCTCCTC
70746 CATTTTAACC
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
15 7 0.27
16 1 0.04
17 10 0.38
18 1 0.04
19 7 0.27
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (19 bp):
TAACTTTAAATCCCTCCTC
Found at i:77500 original size:24 final size:24
Alignment explanation
Indices: 77468--77519 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
77458 AGAAGGGGGC
*
77468 TAAACTCTGGGCTAAACTCTGGGT
1 TAAACTCTGGGCTAAACTCTGGAT
77492 TAAACTCTGGGCTAAACTCTGGAT
1 TAAACTCTGGGCTAAACTCTGGAT
77516 TAAA
1 TAAA
77520 ATCGTGTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (24 bp):
TAAACTCTGGGCTAAACTCTGGAT
Found at i:77519 original size:12 final size:12
Alignment explanation
Indices: 77464--77513 Score: 91
Period size: 12 Copynumber: 4.2 Consensus size: 12
77454 TTTTAGAAGG
77464 GGGCTAAACTCT
1 GGGCTAAACTCT
77476 GGGCTAAACTCT
1 GGGCTAAACTCT
*
77488 GGGTTAAACTCT
1 GGGCTAAACTCT
77500 GGGCTAAACTCT
1 GGGCTAAACTCT
77512 GG
1 GG
77514 ATTAAAATCG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (12 bp):
GGGCTAAACTCT
Done.