Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016719.1 Corchorus olitorius cultivar O-4 contig16752, 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: 61951
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1042 original size:12 final size:12
Alignment explanation
Indices: 1021--1056 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1011 CGTGGCTGAA
*
1021 AAGAAGGAGGAG
1 AAGAAAGAGGAG
1033 AAGAAAGAGGAG
1 AAGAAAGAGGAG
*
1045 AAAAAAGAGGAG
1 AAGAAAGAGGAG
1057 CCAAAGCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (12 bp):
AAGAAAGAGGAG
Found at i:2840 original size:20 final size:21
Alignment explanation
Indices: 2787--2840 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
2777 AGAGAGATAA
2787 ATTT-ATT-AGTGAAGAAATG
1 ATTTAATTAAGTGAAGAAATG
** *
2806 ATTTTTTTGAGTGAAGAAATG
1 ATTTAATTAAGTGAAGAAATG
2827 A-TTAATTAAGTGAA
1 ATTTAATTAAGTGAA
2841 ATTATATAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 4 0.14
20 12 0.41
21 13 0.45
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (21 bp):
ATTTAATTAAGTGAAGAAATG
Found at i:4581 original size:2 final size:2
Alignment explanation
Indices: 4574--4601 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4564 AAATGGAAGA
4574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4602 TCAAAGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4969 original size:17 final size:16
Alignment explanation
Indices: 4947--4980 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4937 TCTTAAATGA
4947 ATATTATATATATATAT
1 ATATTATATATA-ATAT
*
4964 ATATTATGTATAATAT
1 ATATTATATATAATAT
4980 A
1 A
4981 GTTAGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
ATATTATATATAATAT
Found at i:5057 original size:27 final size:29
Alignment explanation
Indices: 5027--5085 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
5017 AGGATAACTG
5027 ATTTCATGA-AGAAAAGAAAATTTT-AAT
1 ATTTCATGAGAGAAAAGAAAATTTTCAAT
** * *
5054 ATTTTTTGAGGGAAAAGAAATTTTTCAAT
1 ATTTCATGAGAGAAAAGAAAATTTTCAAT
5083 ATT
1 ATT
5086 ACTAGTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 13 0.50
29 6 0.23
ACGTcount: A:0.44, C:0.03, G:0.14, T:0.39
Consensus pattern (29 bp):
ATTTCATGAGAGAAAAGAAAATTTTCAAT
Found at i:8733 original size:18 final size:19
Alignment explanation
Indices: 8700--8737 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
8690 ATGCATTTCT
8700 TGAAAGAAAGGGAAAAGGA
1 TGAAAGAAAGGGAAAAGGA
8719 TGAAAGAAA-GGAAAAGGA
1 TGAAAGAAAGGGAAAAGGA
8737 T
1 T
8738 AATTGCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.58, C:0.00, G:0.34, T:0.08
Consensus pattern (19 bp):
TGAAAGAAAGGGAAAAGGA
Found at i:9267 original size:19 final size:20
Alignment explanation
Indices: 9243--9280 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
9233 TCCGTTAAGA
*
9243 GGTAATTTTCT-ATGCCACG
1 GGTAATTTTATGATGCCACG
9262 GGTAATTTTATGATGCCAC
1 GGTAATTTTATGATGCCAC
9281 CTGGACTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (20 bp):
GGTAATTTTATGATGCCACG
Found at i:12132 original size:18 final size:20
Alignment explanation
Indices: 12090--12133 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
12080 TCTTTACAAC
12090 ACAAAAA-ATACAAAAATAT
1 ACAAAAAGATACAAAAATAT
*
12109 A-GAAAAGAT-CAAAAATA-
1 ACAAAAAGATACAAAAATAT
12126 ACAAAAAG
1 ACAAAAAG
12134 TAGCTACCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
17 1 0.05
18 17 0.81
19 3 0.14
ACGTcount: A:0.73, C:0.09, G:0.07, T:0.11
Consensus pattern (20 bp):
ACAAAAAGATACAAAAATAT
Found at i:13603 original size:38 final size:39
Alignment explanation
Indices: 13542--13959 Score: 449
Period size: 38 Copynumber: 10.6 Consensus size: 39
13532 AATTTAAGAC
* *
13542 TTTTCAAATT-GGGAAAGATCCCA-CCAAGTCTTCAAAG
1 TTTTCAATTTAGGGAAAGATCCCATCCAAGTTTTCAAAG
* **
13579 TTTCCAATTTAGGGAAAGATCCCA-CCAAGTTTTTTAAG
1 TTTTCAATTTAGGGAAAGATCCCATCCAAGTTTTCAAAG
* **
13617 TTTTCAAATT-GGGAAAGATCCCAT-CAAGTCTTTTTAAG
1 TTTTCAATTTAGGGAAAGATCCCATCCAAGT-TTTCAAAG
* * * *
13655 TTTCCAA-TTAGGGAAAGATCCC-TTCGAGTTTACAAAG
1 TTTTCAATTTAGGGAAAGATCCCATCCAAGTTTTCAAAG
*
13692 TTTTCAATTTAGGGAAAGATTCCATCATCAAGTTTTCAAAG
1 TTTTCAATTTAGGGAAAGATCCCATC--CAAGTTTTCAAAG
* *
13733 TTTTCAATTTAGGGAAAAATCCCATCAAGAAGTTTTTCAAAG
1 TTTTCAATTTAGGGAAAGATCCCATC--CAAG-TTTTCAAAG
* *
13775 TTTTCAATTTAGGGAAGGATCCCATTC-AGTTTTCAAAG
1 TTTTCAATTTAGGGAAAGATCCCATCCAAGTTTTCAAAG
13813 TTTTCAATTTAGGGAAAGATCCCATCC-AGTTTTCAAAAG
1 TTTTCAATTTAGGGAAAGATCCCATCCAAGTTTTC-AAAG
* *
13852 TTTTCAATTTAGGGAAATATCCCATCAAGAAGTTTTTCAAAAG
1 TTTTCAATTTAGGGAAAGATCCCATC--CAAG-TTTTC-AAAG
* *
13895 TTTTCAATTTAGGAAAAGATCCCATCAAGAAGTTTTTCAAAAG
1 TTTTCAATTTAGGGAAAGATCCCATC--CAAG-TTTTC-AAAG
13938 TTTTCAATTTAGGGAAAGATCC
1 TTTTCAATTTAGGGAAAGATCC
13960 TATCAGAGTT
Statistics
Matches: 334, Mismatches: 32, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
37 40 0.12
38 117 0.35
39 32 0.10
41 39 0.12
42 34 0.10
43 72 0.22
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (39 bp):
TTTTCAATTTAGGGAAAGATCCCATCCAAGTTTTCAAAG
Found at i:13628 original size:75 final size:77
Alignment explanation
Indices: 13542--13971 Score: 451
Period size: 75 Copynumber: 5.4 Consensus size: 77
13532 AATTTAAGAC
* * * *
13542 TTTTCAAATT-GGGAAAGATCCCACCAAGTCTTCAAAGTTTCCAATTTAGGGAAAGATCCCA-CC
1 TTTTCAATTTAGGGAAAGATCCCATCAAGTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCC
*
13605 AAGTTTTTTAAG
66 AAGTTTTTAAAG
* ** * *
13617 TTTTCAAATT-GGGAAAGATCCCATCAAGTCTTTTTAAGTTTCCAA-TTAGGGAAAGATCCC-TT
1 TTTTCAATTTAGGGAAAGATCCCATCAAGT-TTTCAAAGTTTTCAATTTAGGGAAAGATCCCATC
* **
13679 CGAGTTTACAAAG
65 CAAGTTTTTAAAG
*
13692 TTTTCAATTTAGGGAAAGATTCCATCATCAAGTTTTCAAAGTTTTCAATTTAGGGAAAAATCCCA
1 TTTTCAATTTAGGGAAAGA-TCC--CATCAAGTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCA
*
13757 TCAAGAAGTTTTTCAAAG
63 TC--CAAGTTTTT-AAAG
*
13775 TTTTCAATTTAGGGAAGGATCCCATTC-AGTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATC
1 TTTTCAATTTAGGGAAAGATCCCA-TCAAGTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATC
*
13839 C-AGTTTTCAAAAG
65 CAAGTTTT-TAAAG
* *
13852 TTTTCAATTTAGGGAAATATCCCATCAAGAAGTTTTTCAAAAGTTTTCAATTTAGGAAAAGATCC
1 TTTTCAATTTAGGGAAAGATCCCATC---AAG-TTTTC-AAAGTTTTCAATTTAGGGAAAGATCC
*
13917 CATCAAGAAGTTTTTCAAAAG
61 CATC--CAAGTTTTT--AAAG
*
13938 TTTTCAATTTAGGGAAAGATCCTATCAGAGTTTT
1 TTTTCAATTTAGGGAAAGATCCCATCA-AGTTTT
13972 TAAAAGTGAG
Statistics
Matches: 300, Mismatches: 30, Indels: 42
0.81 0.08 0.11
Matches are distributed among these distances:
75 61 0.20
76 22 0.07
77 35 0.12
78 12 0.04
79 22 0.07
80 41 0.14
81 7 0.02
82 37 0.12
83 27 0.09
84 2 0.01
85 6 0.02
86 28 0.09
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (77 bp):
TTTTCAATTTAGGGAAAGATCCCATCAAGTTTTCAAAGTTTTCAATTTAGGGAAAGATCCCATCC
AAGTTTTTAAAG
Found at i:16970 original size:8 final size:8
Alignment explanation
Indices: 16957--16991 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
16947 GAATAAAATC
16957 TAATAAAA
1 TAATAAAA
16965 TAATAAAA
1 TAATAAAA
*
16973 TAAATATAA
1 T-AATAAAA
16982 TAATAAAA
1 TAATAAAA
16990 TA
1 TA
16992 TACTTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
TAATAAAA
Found at i:16983 original size:17 final size:17
Alignment explanation
Indices: 16943--16991 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
16933 AAATTGTCCT
*
16943 TAATGAATAAAATCTAATA
1 TAAT-AATAAAAT-AAATA
*
16962 AAATAATAAAATAAATA
1 TAATAATAAAATAAATA
16979 TAATAATAAAATA
1 TAATAATAAAATA
16992 TACTTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 16 0.59
18 8 0.30
19 3 0.11
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
TAATAATAAAATAAATA
Found at i:18526 original size:2 final size:2
Alignment explanation
Indices: 18514--18596 Score: 103
Period size: 2 Copynumber: 41.5 Consensus size: 2
18504 TTATCTTGCT
* * *
18514 TA TA TA AA TA TA TA TA TA TA TA TT TA TA AA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
18556 TG TA TA TA TT TA TA TA TA TA TT TA TT 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 TA TA TA TA T
18597 TTTATAACAT
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (2 bp):
TA
Found at i:19326 original size:24 final size:23
Alignment explanation
Indices: 19256--19326 Score: 63
Period size: 24 Copynumber: 2.9 Consensus size: 23
19246 AATATTCATG
*
19256 TTATATATTATAAATTAATATAATTT
1 TTATATTTTAT-AATT-AT-TAATTT
*
19282 TTATTATATTTATTATT-TTAATTT
1 TTA-TAT-TTTATAATTATTAATTT
19306 TTATATTTTATAAGTTATTAA
1 TTATATTTTATAA-TTATTAA
19327 CCTATGTACA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
22 6 0.16
23 5 0.13
24 13 0.34
25 1 0.03
26 3 0.08
27 6 0.16
28 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (23 bp):
TTATATTTTATAATTATTAATTT
Found at i:19527 original size:180 final size:176
Alignment explanation
Indices: 19108--19528 Score: 494
Period size: 180 Copynumber: 2.3 Consensus size: 176
19098 TTAATATACC
* * * * * *
19108 ATTTATTATTTTGATTTTTATGTTTTATAAGTTATATATTAATGCACGTGGAACACATGTAG-TT
1 ATTTATTATTTTAATTTTTATGTTTTATAAG---T-TATTAACGCACATGCAACGCACGTAGTTT
**
19172 TAAGTATATATTATTTATTATATACTTATTTCATTTGGATTTGGATTTGGATTTTCTTATTAAAT
62 TAAGTATATATTATTTATTATATACTTATTTCATTTGGATTT-GAAAT-GATTTTCTTATTAAAT
* *
19237 ATGATTATAAATATTCATGTTATATATTATAAATTAATATAATTTTTATTAT
125 ATGATTATAAATATTCATGTTATATATTACAAATTAATATAATATTTATTAT
* * * *
19289 ATTTATTATTTTAATTTTTATATTTTATAAGTTATTAAC-C-TATGTACAAGGTACGTAGTTTTA
1 ATTTATTATTTTAATTTTTATGTTTTATAAGTTATTAACGCACATG--CAACGCACGTAGTTTTA
* * *
19352 AGTATATGTTATTTATTATATACTTATTTCATTTGGATTT-AAAT-CTTTT-TTATTATATATGA
64 AGTATATATTATTTATTATATACTTATTTCATTTGGATTTGAAATGATTTTCTTATTAAATATGA
* *
19414 TTATAAAACTCAATACTTCATGTTATATATTACAAATTAATCTACTATTTATTAT
129 TTAT---A---AATA-TTCATGTTATATATTACAAATTAATATAATATTTATTAT
19469 ATTTATTATTTTAATTTTTATGTTTTATAAGTTATTAACGCACATGCAACGCACGTAGTT
1 ATTTATTATTTTAATTTTTATGTTTTATAAGTTATTAACGCACATGCAACGCACGTAGTT
19529 GTACTAGTCA
Statistics
Matches: 205, Mismatches: 23, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
173 16 0.08
174 4 0.02
175 2 0.01
176 4 0.02
177 13 0.06
178 44 0.21
179 4 0.02
180 85 0.41
181 30 0.15
182 3 0.01
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (176 bp):
ATTTATTATTTTAATTTTTATGTTTTATAAGTTATTAACGCACATGCAACGCACGTAGTTTTAAG
TATATATTATTTATTATATACTTATTTCATTTGGATTTGAAATGATTTTCTTATTAAATATGATT
ATAAATATTCATGTTATATATTACAAATTAATATAATATTTATTAT
Found at i:22593 original size:24 final size:24
Alignment explanation
Indices: 22565--22618 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
22555 ATTCAGGGAG
22565 TTAGGTTAATCAAATTGCATCAAA
1 TTAGGTTAATCAAATTGCATCAAA
22589 TTAGGTTAATCAAATTGCATCAAA
1 TTAGGTTAATCAAATTGCATCAAA
22613 TTAGGT
1 TTAGGT
22619 CGAAAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (24 bp):
TTAGGTTAATCAAATTGCATCAAA
Found at i:23589 original size:59 final size:58
Alignment explanation
Indices: 23520--23836 Score: 306
Period size: 59 Copynumber: 5.4 Consensus size: 58
23510 TCCCTGTTCT
*
23520 TTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTCTTTAATTCAAAATCTTGTCTTGC
1 TTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGT-TTTGATTCAAAATCTTGTCTTGC
* * * * *
23579 TTTTAAAATCCTGTTCGAGATCTCTGGTAGAGAGTTTTCAATCCAAAATCTTGTATTGT
1 TTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTT-GATTCAAAATCTTGTCTTGC
* * * * *
23638 TTTTAAAATCCTGTTTGAGGTCTCTGGTAGAGAGAGTTTGTTTCAAAATTTTG-GTT-C
1 TTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAG-TTTTGATTCAAAATCTTGTCTTGC
* * * *
23695 ATTTTGAAATCCTGGTCGAGGTCTCTGGTAGAGAGCTTTCTGCTTTAAAATCTTG---TGC
1 -TTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAG-TTT-TGATTCAAAATCTTGTCTTGC
* * * * * *
23753 TTTTTAAATCCTGGTCGAGGTCTCTAGTAGAGAGTTTCCGCTTTAAAATCTTGTTCTT--
1 TTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTT-TGATTCAAAATCTTG-TCTTGC
* *
23811 TTTTAAGATCCTGCTCGAGGTCTCTG
1 TTTTAAAATCCTGTTCGAGGTCTCTG
23837 ATCGAAAGTT
Statistics
Matches: 221, Mismatches: 28, Indels: 19
0.82 0.10 0.07
Matches are distributed among these distances:
56 18 0.08
57 33 0.15
58 61 0.28
59 105 0.48
60 4 0.02
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (58 bp):
TTTTAAAATCCTGTTCGAGGTCTCTGGTAGAGAGTTTTGATTCAAAATCTTGTCTTGC
Found at i:27254 original size:16 final size:16
Alignment explanation
Indices: 27235--27266 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
27225 TGATTGGTAT
27235 TAAAGTCATTATATTA
1 TAAAGTCATTATATTA
*
27251 TAAATTCATTATATTA
1 TAAAGTCATTATATTA
27267 ATCTCCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (16 bp):
TAAAGTCATTATATTA
Found at i:34533 original size:12 final size:12
Alignment explanation
Indices: 34518--34542 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34508 ACATGAAATT
34518 TAACACTTCTAA
1 TAACACTTCTAA
34530 TAACACTTCTAA
1 TAACACTTCTAA
34542 T
1 T
34543 TAATTACATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TAACACTTCTAA
Found at i:38325 original size:45 final size:45
Alignment explanation
Indices: 38276--38372 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 45
38266 AGCAACAATT
*
38276 AATATTAG-TTTTTATTTGATGAATTACCTAGAGATGAAATAGTAG
1 AATATTAGCTTTAT-TTTGATGAATTACCTAGAGATGAAATAGTAG
**
38321 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAGGTAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAATAGTAG
38366 AAT-TTAG
1 AATATTAG
38373 GTAATGTACT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
44 4 0.08
45 40 0.83
46 4 0.08
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.39
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAATAGTAG
Found at i:40063 original size:16 final size:16
Alignment explanation
Indices: 40042--40080 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
40032 AGTTTGTACA
*
40042 TATGTATTTATGCATG
1 TATGTATGTATGCATG
40058 TATGTATGTATGCATG
1 TATGTATGTATGCATG
40074 TATGTAT
1 TATGTAT
40081 ATATATATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.49
Consensus pattern (16 bp):
TATGTATGTATGCATG
Found at i:40064 original size:4 final size:4
Alignment explanation
Indices: 40042--40090 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
40032 AGTTTGTACA
* * * * *
40042 TATG TATT TATG CATG TATG TATG TATG CATG TATG TATA TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
40090 T
1 T
40091 TGCGCCAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:42449 original size:16 final size:16
Alignment explanation
Indices: 42428--42477 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
42418 GGTAGGGAGG
42428 AAGGAAATAGGAAGGA
1 AAGGAAATAGGAAGGA
*
42444 AAGGAAATAGCAAGGGA
1 AAGGAAATAGGAA-GGA
* *
42461 AAGGAAACAGGGAGGA
1 AAGGAAATAGGAAGGA
42477 A
1 A
42478 GAGAAAGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.54, C:0.04, G:0.38, T:0.04
Consensus pattern (16 bp):
AAGGAAATAGGAAGGA
Found at i:43991 original size:22 final size:22
Alignment explanation
Indices: 43963--44004 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
43953 ACTGTTCTGG
*
43963 TGATTGTTGATCTTTTAGAAGT
1 TGATTGTGGATCTTTTAGAAGT
*
43985 TGATTGTGGGTCTTTTAGAA
1 TGATTGTGGATCTTTTAGAA
44005 TTTTTTGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.48
Consensus pattern (22 bp):
TGATTGTGGATCTTTTAGAAGT
Found at i:47821 original size:21 final size:21
Alignment explanation
Indices: 47795--47859 Score: 67
Period size: 26 Copynumber: 2.9 Consensus size: 21
47785 TTGGTTTCAC
47795 TTGTTTGATGGAATATTACAA
1 TTGTTTGATGGAATATTACAA
*
47816 TTGTTTGATGAAATTGTCTATTACAA
1 TTGTTTGATGGAA-----TATTACAA
*
47842 TTCTTTGATGGAATATTA
1 TTGTTTGATGGAATATTA
47860 TATCATCTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
21 17 0.47
26 19 0.53
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (21 bp):
TTGTTTGATGGAATATTACAA
Found at i:49246 original size:18 final size:19
Alignment explanation
Indices: 49223--49262 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
49213 AAAAGTCTCT
49223 ACCCTCTTGAAA-CCCCAA
1 ACCCTCTTGAAACCCCCAA
49241 ACCCTCTTGAAACCCCCAA
1 ACCCTCTTGAAACCCCCAA
49260 ACC
1 ACC
49263 TAGGTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.33, C:0.47, G:0.05, T:0.15
Consensus pattern (19 bp):
ACCCTCTTGAAACCCCCAA
Found at i:49490 original size:25 final size:26
Alignment explanation
Indices: 49462--49519 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
49452 CCACTTTCCT
49462 CGACGTTTCGCC-CCAGTTGCAGCCC
1 CGACGTTTCGCCGCCAGTTGCAGCCC
*
49487 CGACATTTCGCCGCCAGTTGCAGCCC
1 CGACGTTTCGCCGCCAGTTGCAGCCC
49513 CGACGTT
1 CGACGTT
49520 GACGTCTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 11 0.37
26 19 0.63
ACGTcount: A:0.14, C:0.41, G:0.24, T:0.21
Consensus pattern (26 bp):
CGACGTTTCGCCGCCAGTTGCAGCCC
Found at i:51455 original size:22 final size:22
Alignment explanation
Indices: 51430--51471 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
51420 TTGTAAAAAT
51430 AATAT-TATCATTGAATTATTAC
1 AATATATATC-TTGAATTATTAC
*
51452 AATATATATCTTGATTTATT
1 AATATATATCTTGAATTATT
51472 CTTATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (22 bp):
AATATATATCTTGAATTATTAC
Found at i:54428 original size:19 final size:19
Alignment explanation
Indices: 54418--54454 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
54408 AATTTTTAAG
54418 TAAAAATGTAATATATAAA
1 TAAAAATGTAATATATAAA
*
54437 TAAAAATTTAATAT-TAAA
1 TAAAAATGTAATATATAAA
54455 ACAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (19 bp):
TAAAAATGTAATATATAAA
Found at i:61410 original size:31 final size:30
Alignment explanation
Indices: 61359--61461 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 30
61349 GGACTTAATA
* * *
61359 GACATTTTAGTCCTTGAACTTGTAAGAAATG
1 GACAATTTAGCCCTTAAACTTGTAA-AAATG
*
61390 GACAATTTAGCCCTTAAACTT-TCAAAACT-
1 GACAATTTAGCCCTTAAACTTGT-AAAAATG
* *
61419 GCCAATTATA-CACTTAAACTTGTAAAAAATG
1 GACAATT-TAGCCCTTAAACTTGT-AAAAATG
61450 GACAATTTAGCC
1 GACAATTTAGCC
61462 TTTTTGGACG
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
29 16 0.28
30 14 0.25
31 27 0.47
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (30 bp):
GACAATTTAGCCCTTAAACTTGTAAAAATG
Found at i:61928 original size:2 final size:2
Alignment explanation
Indices: 61921--61951 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
61911 AAATGAACCC
61921 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.