Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020588.1 Corchorus olitorius cultivar O-4 contig20621, 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: 93392
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:9611 original size:24 final size:24
Alignment explanation
Indices: 9584--9644 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
9574 TTTTAACCAA
9584 TTTATGTTGATTGTTTGTGGATTT
1 TTTATGTTGATTGTTTGTGGATTT
9608 TTTATGTTGATTGTTTGTGGATTT
1 TTTATGTTGATTGTTTGTGGATTT
9632 TTTATGTTGATTG
1 TTTATGTTGATTG
9645 CTTGGGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.13, C:0.00, G:0.25, T:0.62
Consensus pattern (24 bp):
TTTATGTTGATTGTTTGTGGATTT
Found at i:10385 original size:102 final size:102
Alignment explanation
Indices: 10207--10412 Score: 385
Period size: 102 Copynumber: 2.0 Consensus size: 102
10197 AGACAAGGGT
10207 GGGGAGTTTTGGCATTACGTAGACAAGTTGAAGAAAGAGTTCGAGATAGCTCAAGCAATGGTGCA
1 GGGGAGTTTTGGCATTACGTAGACAAGTTGAAGAAAGAGTTCGAGATAGCTCAAGCAATGGTGCA
10272 GTTTGGATTTAGGATTAATAAGTTTGAAAAATTAGAG
66 GTTTGGATTTAGGATTAATAAGTTTGAAAAATTAGAG
*
10309 GGGGAGTTTTGGCATTACGTAGACAAGTTGAAGAAAGAGTTCGAGATAGCTTAAGCAATGGTGCA
1 GGGGAGTTTTGGCATTACGTAGACAAGTTGAAGAAAGAGTTCGAGATAGCTCAAGCAATGGTGCA
* *
10374 GTTTGGGTTTAGGTTTAATAAGTTTGAAAAATTAGAG
66 GTTTGGATTTAGGATTAATAAGTTTGAAAAATTAGAG
10411 GG
1 GG
10413 TCCAGATGCT
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.33, C:0.07, G:0.31, T:0.29
Consensus pattern (102 bp):
GGGGAGTTTTGGCATTACGTAGACAAGTTGAAGAAAGAGTTCGAGATAGCTCAAGCAATGGTGCA
GTTTGGATTTAGGATTAATAAGTTTGAAAAATTAGAG
Found at i:12484 original size:29 final size:29
Alignment explanation
Indices: 12428--12484 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
12418 AATTAGCCAT
* *
12428 TACCTAAGTTTGGAAAGTCGGGTATTACC
1 TACCTAAGTTAGGAAAGTCAGGTATTACC
* *
12457 TACCTAAGTTAGGAAAGTTAGGTTTTAC
1 TACCTAAGTTAGGAAAGTCAGGTATTAC
12485 TAATTAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (29 bp):
TACCTAAGTTAGGAAAGTCAGGTATTACC
Found at i:13377 original size:35 final size:35
Alignment explanation
Indices: 13338--13406 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
13328 ACTCTCTTGT
* * *
13338 TTTTTCCAATTGGTAAGTTCCAATCTTAAGTTTGA
1 TTTTTCCAATTGGTAAATTCCAAACATAAGTTTGA
*
13373 TTTTTCCAATTGGTAAATTCTAAACATAAGTTTG
1 TTTTTCCAATTGGTAAATTCCAAACATAAGTTTG
13407 CTTAGATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTTCCAATTGGTAAATTCCAAACATAAGTTTGA
Found at i:13608 original size:13 final size:13
Alignment explanation
Indices: 13592--13623 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
13582 GTGAAGTTGT
13592 GAGCAATCGTGGA
1 GAGCAATCGTGGA
*
13605 GAGCAATTGTGGA
1 GAGCAATCGTGGA
13618 GAGCAA
1 GAGCAA
13624 AAACGTGGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.38, T:0.16
Consensus pattern (13 bp):
GAGCAATCGTGGA
Found at i:15693 original size:45 final size:45
Alignment explanation
Indices: 15627--15712 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
15617 TGATCATCTA
* *
15627 AATCTTCTCTTCTTCTTTTCTTGCTTTTTTCATCTTTTATTCTCC
1 AATCTTCTCTTCTTCTCTTCTTACTTTTTTCATCTTTTATTCTCC
*
15672 AATCTTTTCTTCTTCTCTTCTTACTTTTTTCATCTTTTATT
1 AATCTTCTCTTCTTCTCTTCTTACTTTTTTCATCTTTTATT
15713 ACAAGATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.10, C:0.24, G:0.01, T:0.64
Consensus pattern (45 bp):
AATCTTCTCTTCTTCTCTTCTTACTTTTTTCATCTTTTATTCTCC
Found at i:15731 original size:45 final size:45
Alignment explanation
Indices: 15637--15736 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 45
15627 AATCTTCTCT
* * * * * *
15637 TCTTCTTTTCTTGCTTTTTTCATCTTTTATTCTCCAATCTTTTCT
1 TCTTCTCTTCTTACTTTTTTCATCTTTTATTCACAAATCTTTACA
15682 TCTTCTCTTCTTACTTTTTTCATCTTTTATT-ACAAGAT-TTTACAA
1 TCTTCTCTTCTTACTTTTTTCATCTTTTATTCACAA-ATCTTTAC-A
15727 TCTTCTCTTC
1 TCTTCTCTTC
15737 ATCTTTTATT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 6 0.13
45 41 0.87
ACGTcount: A:0.14, C:0.24, G:0.02, T:0.60
Consensus pattern (45 bp):
TCTTCTCTTCTTACTTTTTTCATCTTTTATTCACAAATCTTTACA
Found at i:18383 original size:21 final size:21
Alignment explanation
Indices: 18335--18383 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
18325 AGTAACAATA
*
18335 AAATAAA-TAAGCAAGAAAAT
1 AAATAAATTAAGCAACAAAAT
*
18355 -AATAAAATTAAGCAACAAGAT
1 AAAT-AAATTAAGCAACAAAAT
18376 AAATAAAT
1 AAATAAAT
18384 ACTCCAATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 3 0.12
21 15 0.62
22 3 0.12
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.18
Consensus pattern (21 bp):
AAATAAATTAAGCAACAAAAT
Found at i:19225 original size:39 final size:38
Alignment explanation
Indices: 19094--19241 Score: 199
Period size: 38 Copynumber: 3.9 Consensus size: 38
19084 TCGAGTCTAG
19094 CCAACAG-TTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * *
19131 CAAACAGTTTAACTCCCTGAGGCACGGGTCCGCTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * * *
19169 CCAACAGTTTAAACCCCTGTGGTATGGGTCCACTCTTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTA
* *
19208 CCATCAGTTTAACCCCCTGAGGTACGGGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT
19242 ATGCACAGCC
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
37 6 0.06
38 56 0.59
39 33 0.35
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.24
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:19226 original size:77 final size:75
Alignment explanation
Indices: 19094--19238 Score: 200
Period size: 77 Copynumber: 1.9 Consensus size: 75
19084 TCGAGTCTAG
* *
19094 CCAACAGTTAACCCCCTGAGGCACGGGTCCACTCTTACAAACAGTTTAACTCCCTGAGGCACGGG
1 CCAACAGTTAAACCCCTGAGGCACGGGTCCACTCTTACAAACAGTTTAACCCCCTGAGGCACGGG
19159 TCCGCTCTTA
66 TCCGCTCTTA
* * * * * *
19169 CCAACAGTTTAAACCCCTGTGGTATGGGTCCACTCTTTACCATCAGTTTAACCCCCTGAGGTACG
1 CCAACAG-TTAAACCCCTGAGGCACGGGTCCACTC-TTACAAACAGTTTAACCCCCTGAGGCACG
19234 GGTCC
64 GGTCC
19239 ACTATGCACA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 7 0.12
76 23 0.38
77 30 0.50
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.24
Consensus pattern (75 bp):
CCAACAGTTAAACCCCTGAGGCACGGGTCCACTCTTACAAACAGTTTAACCCCCTGAGGCACGGG
TCCGCTCTTA
Found at i:19489 original size:104 final size:104
Alignment explanation
Indices: 19309--19518 Score: 420
Period size: 104 Copynumber: 2.0 Consensus size: 104
19299 AACCTTTTCA
19309 ATTTCAAAACATTTACATTTGCATACTCGATCCGATTTTCAGAAAACAACAATACTCTTTTAAAA
1 ATTTCAAAACATTTACATTTGCATACTCGATCCGATTTTCAGAAAACAACAATACTCTTTTAAAA
19374 ACAACAAAACACTTCAAATCATTTATAGGAAAACAATCC
66 ACAACAAAACACTTCAAATCATTTATAGGAAAACAATCC
19413 ATTTCAAAACATTTACATTTGCATACTCGATCCGATTTTCAGAAAACAACAATACTCTTTTAAAA
1 ATTTCAAAACATTTACATTTGCATACTCGATCCGATTTTCAGAAAACAACAATACTCTTTTAAAA
19478 ACAACAAAACACTTCAAATCATTTATAGGAAAACAATCC
66 ACAACAAAACACTTCAAATCATTTATAGGAAAACAATCC
19517 AT
1 AT
19519 AAAATAATTG
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 106 1.00
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (104 bp):
ATTTCAAAACATTTACATTTGCATACTCGATCCGATTTTCAGAAAACAACAATACTCTTTTAAAA
ACAACAAAACACTTCAAATCATTTATAGGAAAACAATCC
Found at i:24350 original size:29 final size:30
Alignment explanation
Indices: 24306--24363 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
24296 AATTAGGCAT
* *
24306 TACCTTAAGTTTGGAAAGTTGGGTATTACC
1 TACCTTAAGTTAGGAAAGTTAGGTATTACC
*
24336 TACC-TAAGTTAGGAAAGTTAGGTTTTAC
1 TACCTTAAGTTAGGAAAGTTAGGTATTAC
24364 TAATTAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.36
Consensus pattern (30 bp):
TACCTTAAGTTAGGAAAGTTAGGTATTACC
Found at i:24802 original size:40 final size:40
Alignment explanation
Indices: 24756--24835 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
24746 TTTTCCTCGT
*
24756 AAAAGATATAACGAACCTCATGGATCCAATTTTCCCGCAC
1 AAAAGATATAACGAACCTCATGGATCCAATTCTCCCGCAC
*
24796 AAAAGATATAACGAACCTCATGGATCCACTTCTCCCGCAC
1 AAAAGATATAACGAACCTCATGGATCCAATTCTCCCGCAC
24836 CTATGAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.21
Consensus pattern (40 bp):
AAAAGATATAACGAACCTCATGGATCCAATTCTCCCGCAC
Found at i:24917 original size:13 final size:13
Alignment explanation
Indices: 24899--24924 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24889 GTGACTAAAA
24899 TGGAGTTTTGATG
1 TGGAGTTTTGATG
24912 TGGAGTTTTGATG
1 TGGAGTTTTGATG
24925 AGTCGATTCT
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:0.15, C:0.00, G:0.38, T:0.46
Consensus pattern (13 bp):
TGGAGTTTTGATG
Found at i:25950 original size:21 final size:21
Alignment explanation
Indices: 25926--25967 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
25916 TTTCAAGAGT
25926 CCTTCCTTTCCCATCATTTCC
1 CCTTCCTTTCCCATCATTTCC
25947 CCTTCCTTTCCCATCATTTCC
1 CCTTCCTTTCCCATCATTTCC
25968 TAGCCTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.10, C:0.48, G:0.00, T:0.43
Consensus pattern (21 bp):
CCTTCCTTTCCCATCATTTCC
Found at i:25999 original size:16 final size:16
Alignment explanation
Indices: 25980--26016 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
25970 GCCTTTACTG
*
25980 ATCCTCCAAAAAAATT
1 ATCCACCAAAAAAATT
25996 ATCCACCAAAAAAATT
1 ATCCACCAAAAAAATT
26012 ATCCA
1 ATCCA
26017 AACACACTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (16 bp):
ATCCACCAAAAAAATT
Found at i:42486 original size:42 final size:42
Alignment explanation
Indices: 42427--42539 Score: 182
Period size: 42 Copynumber: 2.8 Consensus size: 42
42417 ACGCTGCATG
42427 TTTGAGCTACTACTTCCTGAACCACATGTGATGGACAATGAA
1 TTTGAGCTACTACTTCCTGAACCACATGTGATGGACAATGAA
42469 TTTGAGCTACTACTTCCTGAACCACATGTGATGGACAATGAA
1 TTTGAGCTACTACTTCCTGAACCACATGTGATGGACAATGAA
*
42511 TTGGAG---CTACTTCCTGAACCAC-T-TGATGG
1 TTTGAGCTACTACTTCCTGAACCACATGTGATGG
42540 CATGAAGAAC
Statistics
Matches: 70, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
37 6 0.09
38 1 0.01
39 16 0.23
42 47 0.67
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (42 bp):
TTTGAGCTACTACTTCCTGAACCACATGTGATGGACAATGAA
Found at i:45969 original size:42 final size:42
Alignment explanation
Indices: 45923--46004 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
45913 AATGCTTTGA
45923 AAAAAAAAAAAAAGCACATATGTTTGAGAAGGTAGATGTCTT
1 AAAAAAAAAAAAAGCACATATGTTTGAGAAGGTAGATGTCTT
* **
45965 AAAAAAAAATATTGCACATATGTTTGAGAAGGTAGATGTC
1 AAAAAAAAAAAAAGCACATATGTTTGAGAAGGTAGATGTC
46005 CAAAAATTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.26
Consensus pattern (42 bp):
AAAAAAAAAAAAAGCACATATGTTTGAGAAGGTAGATGTCTT
Found at i:51056 original size:20 final size:21
Alignment explanation
Indices: 51031--51071 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
51021 TACCGCCAGA
51031 CTCCA-TTC-CCCACTTTTGCT
1 CTCCATTTCTCCC-CTTTTGCT
51051 CTCCATTTCTCCCCTTTTGCT
1 CTCCATTTCTCCCCTTTTGCT
51072 TTCATTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 11 0.58
22 3 0.16
ACGTcount: A:0.07, C:0.44, G:0.05, T:0.44
Consensus pattern (21 bp):
CTCCATTTCTCCCCTTTTGCT
Found at i:51340 original size:15 final size:15
Alignment explanation
Indices: 51322--51362 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
51312 CTCTTTTTGA
51322 AATCACTCTCTCAG-G
1 AATCACTCTC-CAGAG
*
51337 AATCACTCTCCTGAG
1 AATCACTCTCCAGAG
51352 AATCACTCTCC
1 AATCACTCTCC
51363 CATGGAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 22 0.92
ACGTcount: A:0.27, C:0.37, G:0.10, T:0.27
Consensus pattern (15 bp):
AATCACTCTCCAGAG
Found at i:52292 original size:10 final size:10
Alignment explanation
Indices: 52277--52301 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
52267 AACAAATTAC
52277 TAATTACTAA
1 TAATTACTAA
52287 TAATTACTAA
1 TAATTACTAA
52297 TAATT
1 TAATT
52302 GCATTTAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (10 bp):
TAATTACTAA
Found at i:54238 original size:45 final size:45
Alignment explanation
Indices: 54187--54279 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
54177 AACAACAATT
*
54187 AATATTAACTTTATTTTGATGAATTATATAGAGATGGAGGAGTAG
1 AATATTAACTTTATTTTGATGAATTACATAGAGATGGAGGAGTAG
* *
54232 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAACTTTATTTTGATGAATTACATAGAGATGGAGGAGTAG
54277 AAT
1 AAT
54280 TTTGGCAATG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.37
Consensus pattern (45 bp):
AATATTAACTTTATTTTGATGAATTACATAGAGATGGAGGAGTAG
Found at i:57084 original size:11 final size:11
Alignment explanation
Indices: 57068--57115 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
57058 GGAGTTCGTG
57068 TTTGAAGACCA
1 TTTGAAGACCA
**
57079 TTTGAAGATAA
1 TTTGAAGACCA
57090 TTTGAAGA-C-
1 TTTGAAGACCA
57099 -TTGAAGACCA
1 TTTGAAGACCA
57109 -TTGAAGA
1 TTTGAAGA
57116 TTTATTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 7 0.22
11 17 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (11 bp):
TTTGAAGACCA
Found at i:58511 original size:15 final size:15
Alignment explanation
Indices: 58476--58518 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
58466 TTACTTTGCT
*
58476 TTGTTTTCTAGTCTCA
1 TTGTTTTCT-GTCTAA
*
58492 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTCTAA
58507 TTGTTTTCTGTC
1 TTGTTTTCTGTC
58519 AACCTCTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (15 bp):
TTGTTTTCTGTCTAA
Found at i:58987 original size:29 final size:28
Alignment explanation
Indices: 58944--59095 Score: 115
Period size: 27 Copynumber: 5.5 Consensus size: 28
58934 TGCGTCAAAG
58944 AAAAAAAAAAGTTTTGTATTTTTGCGTCAT
1 AAAAAAAAAA-TTTTGT-TTTTTGCGTCAT
* *
58974 AAAAAAAAAATTTTG-TTTCTGCGTCAC
1 AAAAAAAAAATTTTGTTTTTTGCGTCAT
*
59001 AAAAAAAAAGA----G-TTTTTGCGTTTTAT
1 AAAAAAAAA-ATTTTGTTTTTTGCG--TCAT
*
59027 AAAAAAAAAGTTTT-TTTTTTGCGTCAT
1 AAAAAAAAAATTTTGTTTTTTGCGTCAT
** *
59054 --TTAAAAAATTTTTTTTTTCTGCGTCAT
1 AAAAAAAAAATTTTGTTTTT-TGCGTCAT
59081 AAATAAAAAAATTTT
1 AAA-AAAAAAATTTT
59096 CTTGTTCTTG
Statistics
Matches: 97, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
24 8 0.08
25 9 0.09
26 16 0.16
27 30 0.31
28 1 0.01
29 13 0.13
30 20 0.21
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (28 bp):
AAAAAAAAAATTTTGTTTTTTGCGTCAT
Found at i:59083 original size:25 final size:25
Alignment explanation
Indices: 59030--59080 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
59020 GTTTTATAAA
59030 AAAAAAGTTTTTTTTTTGCGTCATTT
1 AAAAAAGTTTTTTTTTTGCGTCA-TT
*
59056 AAAAAATTTTTTTTTTCTGCGTCAT
1 AAAAAAGTTTTTTTTT-TGCGTCAT
59081 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53
Consensus pattern (25 bp):
AAAAAAGTTTTTTTTTTGCGTCATT
Found at i:62416 original size:21 final size:21
Alignment explanation
Indices: 62361--62427 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
62351 CCATGCCATT
* *
62361 ACCGGCCATTCACCGTGACACC
1 ACCGGCCATGC-CCGTGCCACC
** *
62383 ACCGGTTAAGCCCGTGCCACC
1 ACCGGCCATGCCCGTGCCACC
*
62404 ACCGGCCATGCCCGTGCCATC
1 ACCGGCCATGCCCGTGCCACC
62425 ACC
1 ACC
62428 ATTCCAAGCC
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
21 29 0.81
22 7 0.19
ACGTcount: A:0.19, C:0.46, G:0.21, T:0.13
Consensus pattern (21 bp):
ACCGGCCATGCCCGTGCCACC
Found at i:64284 original size:11 final size:11
Alignment explanation
Indices: 64268--64315 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
64258 GGAGTTCGTG
64268 TTTGAAGACCA
1 TTTGAAGACCA
**
64279 TTTGAAGATAA
1 TTTGAAGACCA
64290 TTTGAAGA-C-
1 TTTGAAGACCA
64299 -TTGAAGACCA
1 TTTGAAGACCA
64309 -TTGAAGA
1 TTTGAAGA
64316 TTTATTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 7 0.22
11 17 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (11 bp):
TTTGAAGACCA
Found at i:65711 original size:15 final size:15
Alignment explanation
Indices: 65676--65718 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
65666 TTACTTTGCT
*
65676 TTGTTTTCTAGTCTCA
1 TTGTTTTCT-GTCTAA
*
65692 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTCTAA
65707 TTGTTTTCTGTC
1 TTGTTTTCTGTC
65719 AACTTCTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (15 bp):
TTGTTTTCTGTCTAA
Found at i:67665 original size:33 final size:33
Alignment explanation
Indices: 67600--67667 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
67590 TTGGCAAATT
*
67600 AACTCCGCGATCGAGTATAAACTACATGAAACG
1 AACTCCGCGATCGAGTATAAACTAAATGAAACG
*
67633 AACTCCGCGATTGAGTATAAACTAAACT-AAACG
1 AACTCCGCGATCGAGTATAAACTAAA-TGAAACG
67666 AA
1 AA
67668 GACTAAACGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (33 bp):
AACTCCGCGATCGAGTATAAACTAAATGAAACG
Found at i:78658 original size:20 final size:20
Alignment explanation
Indices: 78633--78684 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
78623 TTTTTACTGG
*
78633 TTTTGATCGATCCTTGCTGA
1 TTTTGATCGATCCTTGATGA
* * *
78653 TTTTGATTGATTCTTGATGG
1 TTTTGATCGATCCTTGATGA
*
78673 GTTTGATCGATC
1 TTTTGATCGATC
78685 ATTTTATTCG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.13, G:0.23, T:0.48
Consensus pattern (20 bp):
TTTTGATCGATCCTTGATGA
Found at i:82871 original size:31 final size:31
Alignment explanation
Indices: 82836--82894 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
82826 GTCATTAATA
*
82836 AATATTGTGATTATTCATGAATCAAGAGATG
1 AATATTGTAATTATTCATGAATCAAGAGATG
82867 AATATTGTAATTATTCATGAATCAAGAG
1 AATATTGTAATTATTCATGAATCAAGAG
82895 TTCTCTTGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.36
Consensus pattern (31 bp):
AATATTGTAATTATTCATGAATCAAGAGATG
Done.