Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020039.1 Corchorus olitorius cultivar O-4 contig20072, 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: 66652
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2407 original size:13 final size:13
Alignment explanation
Indices: 2389--2414 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2379 AACCAGTAGC
2389 GTAGCCAGCAAAT
1 GTAGCCAGCAAAT
2402 GTAGCCAGCAAAT
1 GTAGCCAGCAAAT
2415 TTGTTTACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (13 bp):
GTAGCCAGCAAAT
Found at i:7929 original size:29 final size:32
Alignment explanation
Indices: 7889--7959 Score: 121
Period size: 29 Copynumber: 2.3 Consensus size: 32
7879 TTAAAATTTT
7889 AAAATAAAATAATAATT-AA-TTTTTTAAT-A
1 AAAATAAAATAATAATTAAATTTTTTTAATCA
7918 AAAATAAAATAATAATTAAATTTTTTTAATCA
1 AAAATAAAATAATAATTAAATTTTTTTAATCA
7950 AAAATAAAAT
1 AAAATAAAAT
7960 TTAAATATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
29 17 0.44
30 2 0.05
31 9 0.23
32 11 0.28
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (32 bp):
AAAATAAAATAATAATTAAATTTTTTTAATCA
Found at i:10561 original size:16 final size:16
Alignment explanation
Indices: 10542--10572 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10532 CCGAAAAACT
10542 CAAAACCCGAATGACC
1 CAAAACCCGAATGACC
*
10558 CAAAACCCGAGTGAC
1 CAAAACCCGAATGAC
10573 TTGAGGCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.35, G:0.16, T:0.06
Consensus pattern (16 bp):
CAAAACCCGAATGACC
Found at i:11305 original size:22 final size:22
Alignment explanation
Indices: 11280--11326 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
11270 TTTTTAGTTG
*
11280 AGTAAAACT-ATAAAAGTAAAAT
1 AGTAAAA-TGATAAAAATAAAAT
*
11302 AGTAAAATGGTAAAAATAAAAT
1 AGTAAAATGATAAAAATAAAAT
11324 AGT
1 AGT
11327 TATAAGGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.23
Consensus pattern (22 bp):
AGTAAAATGATAAAAATAAAAT
Found at i:11305 original size:92 final size:93
Alignment explanation
Indices: 11204--11386 Score: 273
Period size: 93 Copynumber: 2.0 Consensus size: 93
11194 GCTTTTTAAT
* * *
11204 TAAATTAGTAATATTGTAAAAAT-AAATAGGTATAAGGATATTAGATTTAATTAAATACAAAAAT
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAAT--AAAAAT
*
11268 AGT-TTTT-AGTTGAGTAAAACTATAAAAG
64 AGTGTTTTCAGTTGACTAAAACTATAAAAG
* *
11296 TAAAATAGTAAAATGGTAAAAATAAAATAGTTATAAGGATATTAGATTTAGTTAAATAAAAATAG
1 TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
11361 TGTTTTCAGTTGACTAAAACTATAAA
66 TGTTTTCAGTTGACTAAAACTATAAA
11387 TATATTCGAA
Statistics
Matches: 82, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
91 9 0.11
92 24 0.29
93 49 0.60
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.34
Consensus pattern (93 bp):
TAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
TGTTTTCAGTTGACTAAAACTATAAAAG
Found at i:11456 original size:31 final size:31
Alignment explanation
Indices: 11398--11459 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
11388 ATATTCGAAA
* *
11398 AATAAGGGTATAATAGGATATTTAAAAGTTT
1 AATAAGGGTATAATAGGAGATTCAAAAGTTT
11429 AATAAGGGTATAATA-GACGATTCAAAAGTTT
1 AATAAGGGTATAATAGGA-GATTCAAAAGTTT
11460 TACAAAACTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.32
Consensus pattern (31 bp):
AATAAGGGTATAATAGGAGATTCAAAAGTTT
Found at i:12589 original size:18 final size:18
Alignment explanation
Indices: 12550--12589 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12540 TTAAAAATAT
* * *
12550 AATAATAATTAAATTTTT
1 AATAAAAATTAAAATTTA
12568 AATAAAAATTAAAATTTA
1 AATAAAAATTAAAATTTA
12586 AATA
1 AATA
12590 TTAAAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAAAAATTAAAATTTA
Found at i:12592 original size:14 final size:14
Alignment explanation
Indices: 12570--12604 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
12560 AAATTTTTAA
*
12570 TAAAAATTAAAATT
1 TAAATATTAAAATT
12584 TAAATATTAAAATT
1 TAAATATTAAAATT
*
12598 TATATAT
1 TAAATAT
12605 CTAATAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAATATTAAAATT
Found at i:15272 original size:19 final size:18
Alignment explanation
Indices: 15248--15284 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
15238 TTGAAGACTT
15248 TTTGAAGATAATTTGAAGA
1 TTTGAAGATAA-TTGAAGA
*
15267 TTTGAAGATCATTGAAGA
1 TTTGAAGATAATTGAAGA
15285 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.35
Consensus pattern (18 bp):
TTTGAAGATAATTGAAGA
Found at i:19158 original size:16 final size:14
Alignment explanation
Indices: 19121--19164 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 14
19111 TATCTATTTA
19121 TTTT-CTTTGCATTG
1 TTTTGCTTTG-ATTG
19135 TTTTGCTTTGATTG
1 TTTTGCTTTGATTG
19149 ATTATTGCTTTGATTG
1 -TT-TTGCTTTGATTG
19165 CTTGCTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.30
15 7 0.26
16 12 0.44
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.61
Consensus pattern (14 bp):
TTTTGCTTTGATTG
Found at i:19907 original size:18 final size:18
Alignment explanation
Indices: 19886--19920 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19876 GGGTAATTAC
*
19886 AAAAAAATTGTTTTCATA
1 AAAAAAAGTGTTTTCATA
*
19904 AAAAGAAGTGTTTTCAT
1 AAAAAAAGTGTTTTCAT
19921 GATAGAGGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (18 bp):
AAAAAAAGTGTTTTCATA
Found at i:20795 original size:11 final size:11
Alignment explanation
Indices: 20781--20810 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
20771 TGAAGACTTA
20781 TTGAAGATAAT
1 TTGAAGATAAT
20792 TTGAAGATAAT
1 TTGAAGATAAT
20803 TTGAAGAT
1 TTGAAGAT
20811 TTAAAGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (11 bp):
TTGAAGATAAT
Found at i:22624 original size:6 final size:6
Alignment explanation
Indices: 22615--22665 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
22605 TTTGCCTTTG
*
22615 AAAACA AAAACA AAAACA AAAACA AAAACA AAATCA AAAACA AAAACA
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA AAAACA
22663 AAA
1 AAA
22666 GAACAAGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.82, C:0.16, G:0.00, T:0.02
Consensus pattern (6 bp):
AAAACA
Found at i:27044 original size:53 final size:52
Alignment explanation
Indices: 26969--27222 Score: 427
Period size: 53 Copynumber: 4.8 Consensus size: 52
26959 AAAATGCCGT
*
26969 TTGAACACTTTGAAAACCTGATGGGAACTTTCCCACTTTGAAAAGACCAAAA
1 TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCAAAA
*
27021 TTGAACACTTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
1 TTGAACAC-TTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCAAAA
*
27074 TTGAACACTTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
1 TTGAACAC-TTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCAAAA
*
27127 TCGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCAAAA
1 TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCAAAA
* * *
27179 TCGAACACTTTGAAAACTTGATGGAAACTTTCTCACTTTGAAAA
1 TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAA
27223 CTTTGAAGAA
Statistics
Matches: 195, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
52 93 0.48
53 102 0.52
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (52 bp):
TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCAAAA
Found at i:27059 original size:29 final size:28
Alignment explanation
Indices: 27030--27170 Score: 82
Period size: 28 Copynumber: 5.3 Consensus size: 28
27020 ATTGAACACT
27030 TTTGAAAACTTGATGGGAACTTTCCCAC
1 TTTGAAAACTTGATGGGAACTTTCCCAC
*** * ***
27058 TTTGAAAA---GA-CCTAAATTGAACAC
1 TTTGAAAACTTGATGGGAACTTTCCCAC
27082 TTTTGAAAACTTGATGGGAACTTTCCCAC
1 -TTTGAAAACTTGATGGGAACTTTCCCAC
*** * ****
27111 TTTGAAAA---GA-CCTAAATCGAACAC
1 TTTGAAAACTTGATGGGAACTTTCCCAC
27135 TTTGAAAACTTGATGGGAACTTTCCCAC
1 TTTGAAAACTTGATGGGAACTTTCCCAC
27163 TTTGAAAA
1 TTTGAAAA
27171 GACCAAAATC
Statistics
Matches: 74, Mismatches: 30, Indels: 18
0.61 0.25 0.15
Matches are distributed among these distances:
24 21 0.28
25 12 0.16
27 2 0.03
28 32 0.43
29 7 0.09
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (28 bp):
TTTGAAAACTTGATGGGAACTTTCCCAC
Found at i:27164 original size:105 final size:105
Alignment explanation
Indices: 26969--27222 Score: 429
Period size: 105 Copynumber: 2.4 Consensus size: 105
26959 AAAATGCCGT
* *
26969 TTGAACACTTTGAAAACCTGATGGGAACTTTCCCACTTTGAAAAGACCAAAATTGAACACTTTTG
1 TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCAAAATCGAACACTTTTG
*
27034 AAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
66 AAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCAAAA
*
27074 TTGAACACTTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAATCGAACAC-TTT
1 TTGAACAC-TTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCAAAATCGAACACTTTT
27138 GAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCAAAA
65 GAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCAAAA
* * *
27179 TCGAACACTTTGAAAACTTGATGGAAACTTTCTCACTTTGAAAA
1 TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAA
27223 CTTTGAAGAA
Statistics
Matches: 141, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
104 34 0.24
105 58 0.41
106 49 0.35
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (105 bp):
TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCAAAATCGAACACTTTTG
AAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCAAAA
Found at i:37152 original size:19 final size:20
Alignment explanation
Indices: 37124--37161 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
37114 ATTTATCTTG
*
37124 AAATGGGTAG-TTTTATTTA
1 AAATGAGTAGTTTTTATTTA
37143 AAATGAGTAGTTTTTATTT
1 AAATGAGTAGTTTTTATTT
37162 TGTTTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (20 bp):
AAATGAGTAGTTTTTATTTA
Found at i:37579 original size:19 final size:19
Alignment explanation
Indices: 37551--37597 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
37541 AGTTGCCCAG
*
37551 TTGCCCAGGTGCAAGCAAT
1 TTGCCAAGGTGCAAGCAAT
37570 TTGCCAAGGTGCAAGCAAT
1 TTGCCAAGGTGCAAGCAAT
37589 TTGCCAAGG
1 TTGCCAAGG
37598 AAGTTGCTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (19 bp):
TTGCCAAGGTGCAAGCAAT
Found at i:38206 original size:11 final size:11
Alignment explanation
Indices: 38192--38229 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
38182 ATTCATAACA
38192 AATTTATAATT
1 AATTTATAATT
38203 AATTTATAATT
1 AATTTATAATT
38214 -ATTTGATAATT
1 AATTT-ATAATT
*
38225 TATTT
1 AATTT
38230 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:39160 original size:21 final size:21
Alignment explanation
Indices: 39136--39203 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
39126 AAATTCTCTG
39136 CAAATTAAGAAATACTCAACT
1 CAAATTAAGAAATACTCAACT
* * ***
39157 CAAATCATAAAAAATTCT-TTGT
1 CAAAT--TAAGAAATACTCAACT
39179 -AAATTAAGAAATACTCAACT
1 CAAATTAAGAAATACTCAACT
39199 CAAAT
1 CAAAT
39204 CCTGATTTTT
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
19 9 0.27
20 1 0.03
21 13 0.39
22 1 0.03
23 9 0.27
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.28
Consensus pattern (21 bp):
CAAATTAAGAAATACTCAACT
Found at i:39331 original size:56 final size:56
Alignment explanation
Indices: 39257--39372 Score: 196
Period size: 56 Copynumber: 2.1 Consensus size: 56
39247 ATTATTTTGT
* *
39257 AGAATACTTAAGTAGAGATAGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAAGGGGATAAGATTTATTATAACATTTATTGTGTGAA
* *
39313 AGAATAATTAAGTAGAGATAATGGGATAGGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAAGGGGATAAGATTTATTATAACATTTATTGTGTGAA
39369 AGAA
1 AGAA
39373 AACAGATAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATAAGGGGATAAGATTTATTATAACATTTATTGTGTGAA
Found at i:43956 original size:14 final size:13
Alignment explanation
Indices: 43930--43965 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
43920 GGGGAAGATG
*
43930 AATATAATGTATT
1 AATATAATATATT
43943 AATAATAATATATT
1 AAT-ATAATATATT
43957 AATATAATA
1 AATATAATA
43966 AGAGGAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (13 bp):
AATATAATATATT
Found at i:44597 original size:18 final size:19
Alignment explanation
Indices: 44561--44615 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
44551 TATATAGTAG
44561 TAAGTTAAGAT-AG-TAAAA
1 TAAG-TAAGATAAGATAAAA
44579 T-AGTAAGATAAGATAAAA
1 TAAGTAAGATAAGATAAAA
44597 TAAG-ATAG-TAAGATAAAA
1 TAAGTA-AGATAAGATAAAA
44615 T
1 T
44616 CATTAACCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 6 0.18
17 4 0.12
18 19 0.58
19 4 0.12
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.25
Consensus pattern (19 bp):
TAAGTAAGATAAGATAAAA
Found at i:44965 original size:2 final size:2
Alignment explanation
Indices: 44958--44990 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
44948 ATATCCCAAC
44958 AT 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 AT A
44991 CTAAATATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48090 original size:3 final size:3
Alignment explanation
Indices: 48082--48113 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
48072 TTCTTACCTT
48082 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
48114 TCTTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:48735 original size:30 final size:31
Alignment explanation
Indices: 48680--48741 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
48670 AGGCCAAAAC
*
48680 CAAGAGAGGCATCTATATATGTATAGTATTAT
1 CAAGAGAGGCATC-ATATATCTATAGTATTAT
48712 CAAGAGAGGCATC-TATATCTATAGTATTAT
1 CAAGAGAGGCATCATATATCTATAGTATTAT
48742 TATAAATGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 16 0.55
32 13 0.45
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (31 bp):
CAAGAGAGGCATCATATATCTATAGTATTAT
Found at i:53560 original size:9 final size:9
Alignment explanation
Indices: 53542--53577 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
53532 TTACAAATAC
53542 AAAT-TTAT
1 AAATGTTAT
53550 AAATGTTAT
1 AAATGTTAT
53559 AAATGTTAT
1 AAATGTTAT
*
53568 ACATGTTAT
1 AAATGTTAT
53577 A
1 A
53578 TAGTATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
8 4 0.15
9 22 0.85
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (9 bp):
AAATGTTAT
Found at i:55068 original size:36 final size:39
Alignment explanation
Indices: 55025--55121 Score: 112
Period size: 39 Copynumber: 2.6 Consensus size: 39
55015 CCTCTCTCCT
* *
55025 TCTCCCTCTGAATCTGAGTAGCAATAGC-A-A-CCTCTC
1 TCTCCCTCTGAATCTGAGTAGCAACAGCAACAGCCTCTA
* *
55061 TCTCCCTCT-AACTCTGAGCAGCAGCAGCAACAGCCTCTA
1 TCTCCCTCTGAA-TCTGAGTAGCAACAGCAACAGCCTCTA
*
55100 TCTCCCTCTGACTCTGAGTAGC
1 TCTCCCTCTGAATCTGAGTAGC
55122 CTCTCTCTTC
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
35 2 0.04
36 22 0.44
37 1 0.02
38 1 0.02
39 23 0.46
40 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (39 bp):
TCTCCCTCTGAATCTGAGTAGCAACAGCAACAGCCTCTA
Found at i:55318 original size:18 final size:17
Alignment explanation
Indices: 55279--55330 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
55269 ATTGATCGTA
55279 AATAAACTAATT--AAT
1 AATAAACTAATTAAAAT
*
55294 TATAAACTAATTAAAACT
1 AATAAACTAATTAAAA-T
55312 AATAAACTAATTAACAAT
1 AATAAACTAATTAA-AAT
55330 A
1 A
55331 GTTAATCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 11 0.35
17 2 0.06
18 16 0.52
19 2 0.06
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (17 bp):
AATAAACTAATTAAAAT
Found at i:55746 original size:24 final size:24
Alignment explanation
Indices: 55662--55747 Score: 93
Period size: 23 Copynumber: 3.4 Consensus size: 24
55652 CTTGAAGATT
55662 GTTTGAAGAAAATGAAGGTTGA-A
1 GTTTGAAGAAAATGAAGGTTGAGA
* *
55685 GGTTGAAGAAAATGAAGTAAAGATTAAGA
1 GTTTGAAGAAAATGAAG----G-TTGAGA
*
55714 GTTTAAAGAAAATGAAGGTTGAGA
1 GTTTGAAGAAAATGAAGGTTGAGA
55738 GTTTGAAGAA
1 GTTTGAAGAA
55748 GTTGTTAGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
23 16 0.31
24 14 0.27
25 1 0.02
27 1 0.02
28 3 0.06
29 16 0.31
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (24 bp):
GTTTGAAGAAAATGAAGGTTGAGA
Found at i:56056 original size:14 final size:14
Alignment explanation
Indices: 56037--56066 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56027 TAGTGGAGTT
56037 AATTATGACAGGAC
1 AATTATGACAGGAC
*
56051 AATTATGGCAGGAC
1 AATTATGACAGGAC
56065 AA
1 AA
56067 GCTAATTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.20
Consensus pattern (14 bp):
AATTATGACAGGAC
Found at i:57525 original size:2 final size:2
Alignment explanation
Indices: 57518--57580 Score: 52
Period size: 2 Copynumber: 35.5 Consensus size: 2
57508 CTGTTTAGTC
*
57518 AT AT AT AT A- AT -T AA AT AT AT -T AT AT AT AT AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
57555 AT -T AG AT AT AT AT A- AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57581 ATTATTAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
1 8 0.16
2 41 0.84
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:57544 original size:21 final size:21
Alignment explanation
Indices: 57518--57579 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 21
57508 CTGTTTAGTC
57518 ATATATATAATTAAATATATT-
1 ATATATATAA-TAAATATATTA
57539 ATATATAT-AT-AATAATATTA
1 ATATATATAATAAAT-ATATTA
57559 GATATATATAATAATATATAT
1 -ATATATATAATAA-ATATAT
57580 AATTATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
18 3 0.09
19 6 0.17
20 1 0.03
21 16 0.46
22 2 0.06
23 5 0.14
24 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
ATATATATAATAAATATATTA
Found at i:57556 original size:19 final size:19
Alignment explanation
Indices: 57534--57580 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
57524 ATAATTAAAT
57534 ATATTATATATATATAATA
1 ATATTATATATATATAATA
*
57553 ATATTAGATATATATAATA
1 ATATTATATATATATAATA
57572 ATA-TATATA
1 ATATTATATA
57581 ATTATTAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATATTATATATATATAATA
Found at i:60947 original size:16 final size:16
Alignment explanation
Indices: 60928--60960 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
60918 AACTCAAACT
*
60928 AATTTTGATTAAGTCA
1 AATTTTGAGTAAGTCA
60944 AATTTTGAGTAAGTCA
1 AATTTTGAGTAAGTCA
60960 A
1 A
60961 GAGGTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.39
Consensus pattern (16 bp):
AATTTTGAGTAAGTCA
Found at i:61968 original size:43 final size:43
Alignment explanation
Indices: 61909--62196 Score: 359
Period size: 43 Copynumber: 6.8 Consensus size: 43
61899 CCAATAACCA
*
61909 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCCC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
* * * * *
61952 AAAGTTCTCAAACACATATATAACACAGAGACATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
* *
61993 AAAGTCCCCAAACACATATATAACACAGGAGTATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
* *
62036 AAAGTCCCCAAACACATATATAACACAGGGACATCTCTATTCT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
* * * * * *
62079 AAAGTCCTCAAATACATATATAGCACAGAGACATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
*
62120 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
* * * *
62163 GAAGTCCTCAAACATATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAT
62197 TTCTCCTTAT
Statistics
Matches: 207, Mismatches: 34, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
41 66 0.32
42 3 0.01
43 138 0.67
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
Found at i:62004 original size:84 final size:85
Alignment explanation
Indices: 61909--62196 Score: 386
Period size: 84 Copynumber: 3.4 Consensus size: 85
61899 CCAATAACCA
* * *
61909 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCCCAAAGTTCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTAT-CCAAAGTCCCCAAACACATATATA
* *
61974 ACACAGAGACATCTATA-TC-
65 ACACAGGGACATCTCTATTCT
*
61993 AAAGTCCCCAAACACATATATAACACAG-GAGTATCTCTATTCCAAAGTCCCCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGAG-GCATCTCTA-TCCAAAGTCCCCAAACACATATAT
62057 AACACAGGGACATCTCTATTCT
64 AACACAGGGACATCTCTATTCT
* * * * *
62079 AAAGTCCTCAAATACATATATAGCACAGAGACATCTATAT-CAAAGTCCCCAAACACATATATAA
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATCCAAAGTCCCCAAACACATATATAA
*
62143 CACAGGGGCATCTCTATTCT
66 CACAGGGACATCTCTATTCT
* * *
62163 GAAGTCCTCAAACATATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGAGGCAT
62197 TTCTCCTTAT
Statistics
Matches: 182, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
83 1 0.01
84 145 0.80
85 4 0.02
86 31 0.17
87 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (85 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATCCAAAGTCCCCAAACACATATATAA
CACAGGGACATCTCTATTCT
Found at i:62060 original size:127 final size:127
Alignment explanation
Indices: 61909--62196 Score: 459
Period size: 127 Copynumber: 2.3 Consensus size: 127
61899 CCAATAACCA
*
61909 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCCCAAAGTTCTCAAACACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCCCAAAGTCCTCAAACACATATATA
*
61974 ACACAGAGACATCTATATCAAAGTCCCCAAACACATATATAACACAGGAGTATCTCTATTCC
66 ACACAGAGACATCTATATCAAAGTCCCCAAACACATATATAACACAGGAGCATCTCTATTCC
* * * *
62036 AAAGTCCCCAAACACATATATAACACAGGGACATCTCTATTCTAAAGTCCTCAAATACATATATA
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCCCAAAGTCCTCAAACACATATATA
* * *
62101 GCACAGAGACATCTATATCAAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCT
66 ACACAGAGACATCTATATCAAAGTCCCCAAACACATATATAACACAGGAGCATCTCTATTCC
* * * *
62163 GAAGTCCTCAAACATATATATAACACAGAGGCAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAT
62197 TTCTCCTTAT
Statistics
Matches: 147, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
127 147 1.00
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (127 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATCCCAAAGTCCTCAAACACATATATA
ACACAGAGACATCTATATCAAAGTCCCCAAACACATATATAACACAGGAGCATCTCTATTCC
Done.