Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006447.1 Corchorus capsularis cultivar CVL-1 contig06468, 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: 78205
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Found at i:9465 original size:2 final size:2
Alignment explanation
Indices: 9458--9485 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9448 GTACTTTTTA
9458 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
9486 TCTACACATT
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:11024 original size:11 final size:11
Alignment explanation
Indices: 11010--11037 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
11000 AGCAATTGCA
11010 TAGCTAGTCCG
1 TAGCTAGTCCG
11021 TAGCTAGTCCG
1 TAGCTAGTCCG
11032 TAGCTA
1 TAGCTA
11038 AATGTCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (11 bp):
TAGCTAGTCCG
Found at i:11134 original size:12 final size:12
Alignment explanation
Indices: 11098--11134 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
11088 TAGACATGTC
11098 TGTAGCAAAGCT
1 TGTAGCAAAGCT
*
11110 CGTAGCAAAGCT
1 TGTAGCAAAGCT
11122 TGTAGCAAAGCT
1 TGTAGCAAAGCT
11134 T
1 T
11135 CTTTTTTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (12 bp):
TGTAGCAAAGCT
Found at i:11188 original size:27 final size:27
Alignment explanation
Indices: 11151--11210 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
11141 TTCATAAAAT
11151 TTCAT-TTAATTACAAAAGAAATTACA
1 TTCATATTAATTACAAAAGAAATTACA
* *
11177 TTCATATTAATTATAAAAGAAATTCCA
1 TTCATATTAATTACAAAAGAAATTACA
11204 TTCATAT
1 TTCATAT
11211 GAAATATACG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 5 0.16
27 26 0.84
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (27 bp):
TTCATATTAATTACAAAAGAAATTACA
Found at i:11218 original size:27 final size:27
Alignment explanation
Indices: 11164--11218 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
11154 ATTTAATTAC
* *
11164 AAAAGAAATTACATTCATATTAATTAT
1 AAAAGAAATTACATTCATATGAAATAT
*
11191 AAAAGAAATTCCATTCATATGAAATAT
1 AAAAGAAATTACATTCATATGAAATAT
11218 A
1 A
11219 CGATAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.53, C:0.09, G:0.05, T:0.33
Consensus pattern (27 bp):
AAAAGAAATTACATTCATATGAAATAT
Found at i:15681 original size:12 final size:12
Alignment explanation
Indices: 15650--15684 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
15640 CGTCGTTCAC
15650 AAACCCGTAGCT
1 AAACCCGTAGCT
*
15662 -AGCCCGTAGCT
1 AAACCCGTAGCT
15673 AAACCCGTAGCT
1 AAACCCGTAGCT
15685 GATATTCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (12 bp):
AAACCCGTAGCT
Found at i:21279 original size:33 final size:33
Alignment explanation
Indices: 21207--21280 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
21197 CTAATTGTGA
*
21207 TGAAAACAAATCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAAATCTGTTTTGGTTGATCATAGCAT
*
21240 TGAAAATAATTCTGTTTTGGTTGATCATAGCAT
1 TGAAAATAAATCTGTTTTGGTTGATCATAGCAT
21273 TGAAAATA
1 TGAAAATA
21281 GGACTGTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (33 bp):
TGAAAATAAATCTGTTTTGGTTGATCATAGCAT
Found at i:21288 original size:33 final size:33
Alignment explanation
Indices: 21218--21291 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
21208 GAAAACAAAT
**
21218 CTGTTTTGGTTGATCATAGCATTGAAAATAATT
1 CTGTTTTGGTTGATCATAGCATTGAAAATAAGA
*
21251 CTGTTTTGGTTGATCATAGCATTGAAAATAGGA
1 CTGTTTTGGTTGATCATAGCATTGAAAATAAGA
21284 CTGTTTTG
1 CTGTTTTG
21292 AGTGAAAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (33 bp):
CTGTTTTGGTTGATCATAGCATTGAAAATAAGA
Found at i:24975 original size:38 final size:38
Alignment explanation
Indices: 24933--25014 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 38
24923 CACATATAGC
* *
24933 CAAAAGAACCTAATTCAGTGTAATTAAGTAAATACAGT
1 CAAAAGAACCTAAATCAGTGTAATTAAGTAAACACAGT
* *
24971 CAAAAGAACTTAAATCAGTGTAATTAAGTAACCACAGT
1 CAAAAGAACCTAAATCAGTGTAATTAAGTAAACACAGT
25009 CAAAAG
1 CAAAAG
25015 TAAATACAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (38 bp):
CAAAAGAACCTAAATCAGTGTAATTAAGTAAACACAGT
Found at i:25061 original size:42 final size:41
Alignment explanation
Indices: 25010--25101 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 41
25000 AACCACAGTC
25010 AAAAGTAAATACAGTCAAGATCTTAATTC-GGGTTAATTAAG
1 AAAAGTAAATACAGTCAAGATCTTAATTCAGGG-TAATTAAG
*
25051 AAAAGATAAATACAGTCAAGGTCTTAATTCAGGGTAATTAAG
1 AAAAG-TAAATACAGTCAAGATCTTAATTCAGGGTAATTAAG
*
25093 AAAGGTAAA
1 AAAAGTAAA
25102 AGTAGTTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 9 0.19
42 35 0.74
43 3 0.06
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (41 bp):
AAAAGTAAATACAGTCAAGATCTTAATTCAGGGTAATTAAG
Found at i:25243 original size:37 final size:37
Alignment explanation
Indices: 25097--25360 Score: 343
Period size: 37 Copynumber: 7.1 Consensus size: 37
25087 ATTAAGAAAG
* * * *
25097 GTAAAAGTAGTTAAAGGAATTAATTCAAGGAAATTAA
1 GTAAAAGCAGTTAAAGGACTTAATTCATGGTAATTAA
** *
25134 GTAAAGAGCAGTTAAAATATTTAATTCATGGTAATTAA
1 GTAAA-AGCAGTTAAAGGACTTAATTCATGGTAATTAA
* * *
25172 GTAAAAGCAG-TAAAGTACTTAATTCAGGGAAATTAA
1 GTAAAAGCAGTTAAAGGACTTAATTCATGGTAATTAA
* * *
25208 GGAAACGCAGTTAAAGGACTTAAGTCATGGTAATTAA
1 GTAAAAGCAGTTAAAGGACTTAATTCATGGTAATTAA
*
25245 GTAAAAGCAGTAAAAGGACTTAATTCATGGTAATTAA
1 GTAAAAGCAGTTAAAGGACTTAATTCATGGTAATTAA
* *
25282 ATAAAAGCAGTTGAAA-GACTTAATTTATGGTAATTAA
1 GTAAAAGCAGTT-AAAGGACTTAATTCATGGTAATTAA
*
25319 GTAAAAGCAGTAAAAGGACTTAATTCATGGTAATTAA
1 GTAAAAGCAGTTAAAGGACTTAATTCATGGTAATTAA
25356 GTAAA
1 GTAAA
25361 GACAAGCCCA
Statistics
Matches: 197, Mismatches: 26, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
36 33 0.17
37 130 0.66
38 34 0.17
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (37 bp):
GTAAAAGCAGTTAAAGGACTTAATTCATGGTAATTAA
Found at i:25789 original size:41 final size:41
Alignment explanation
Indices: 25372--25772 Score: 612
Period size: 41 Copynumber: 9.8 Consensus size: 41
25362 ACAAGCCCAA
25372 ACTTAATTTCAAGGAAGGAAATTAGGTAG-GCTAAAGC-CTAG
1 ACTTAATTTCAAGGAAGGAAATTAGGTAGAG-TAAAGCAC-AG
* *
25413 ACATAATTTCAAGGAAGGAAATTAGGTAGAGTAAAGCCCAG
1 ACTTAATTTCAAGGAAGGAAATTAGGTAGAGTAAAGCACAG
*
25454 ACTTAATTTCAAGGAAGGAAGTTAGGTAGAGTAAAGCACAG
1 ACTTAATTTCAAGGAAGGAAATTAGGTAGAGTAAAGCACAG
25495 ACTTAATTTCAAGGAAGGAAATTAGGTAGAGTAAAGCACAG
1 ACTTAATTTCAAGGAAGGAAATTAGGTAGAGTAAAGCACAG
*
25536 ACTTAATTTCAAGGAAGGAAATTAGGTAGAGTAAAGCCCAG
1 ACTTAATTTCAAGGAAGGAAATTAGGTAGAGTAAAGCACAG
**
25577 ACTTAATTTCAAAAAAGGAAATTAGGTAGAGTAAAGCACAG
1 ACTTAATTTCAAGGAAGGAAATTAGGTAGAGTAAAGCACAG
*
25618 ACTTAGTTTCAAGGAAGGAAATTAGGTAGAGTAAAGCACAG
1 ACTTAATTTCAAGGAAGGAAATTAGGTAGAGTAAAGCACAG
*
25659 ACTTAATTTCAAGGAAGGAAATTAGGT-GAAGTAAAGCATAG
1 ACTTAATTTCAAGGAAGGAAATTAGGTAG-AGTAAAGCACAG
* * **
25700 ACTTAATTGCAATGAAGGAAATTAGGTA-AAAATAAGCACAG
1 ACTTAATTTCAAGGAAGGAAATTAGGTAGAGTA-AAGCACAG
* *
25741 ACTTAATTTCAAGGAAGGGAATTAAGTAGAGT
1 ACTTAATTTCAAGGAAGGAAATTAGGTAGAGT
25773 CAATAAAGGA
Statistics
Matches: 329, Mismatches: 25, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
40 3 0.01
41 323 0.98
42 3 0.01
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.23
Consensus pattern (41 bp):
ACTTAATTTCAAGGAAGGAAATTAGGTAGAGTAAAGCACAG
Found at i:25804 original size:36 final size:35
Alignment explanation
Indices: 25756--25925 Score: 185
Period size: 32 Copynumber: 5.0 Consensus size: 35
25746 ATTTCAAGGA
*
25756 AGGG-AATTAAGTAGAGTCAATAAAGGACTTAATTC
1 AGGGTAATTAAGT-GAGTCAATAAAGAACTTAATTC
*
25791 AGGGGAATTAAGT-AG--AATAAAGAACTTAATTC
1 AGGGTAATTAAGTGAGTCAATAAAGAACTTAATTC
**
25823 AGGGTAATTAAGTGGAGTCAATAAA-AGGTTTAATTC
1 AGGGTAATTAAGT-GAGTCAATAAAGA-ACTTAATTC
* *
25859 AGGGTAATTAAGT-AG--AATAAAGAATTTAGTTC
1 AGGGTAATTAAGTGAGTCAATAAAGAACTTAATTC
*
25891 AGGATAATTAAGTGGAGTCAATAAAGAACTTAATT
1 AGGGTAATTAAGT-GAGTCAATAAAGAACTTAATT
25926 TGAAAAGATT
Statistics
Matches: 115, Mismatches: 9, Indels: 21
0.79 0.06 0.14
Matches are distributed among these distances:
32 53 0.46
33 1 0.01
34 8 0.07
35 5 0.04
36 48 0.42
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (35 bp):
AGGGTAATTAAGTGAGTCAATAAAGAACTTAATTC
Found at i:25856 original size:68 final size:69
Alignment explanation
Indices: 25756--25925 Score: 249
Period size: 68 Copynumber: 2.5 Consensus size: 69
25746 ATTTCAAGGA
*
25756 AGGG-AATTAAGTAGAGTCAAT-AAAGGACTTAATTCAGGGGAATTAAGTAGAATAAAGAACTTA
1 AGGGTAATTAAGTGGAGTCAATAAAAGGACTTAATTCAGGGGAATTAAGTAGAATAAAGAACTTA
25819 ATTC
66 ATTC
* * *
25823 AGGGTAATTAAGTGGAGTCAATAAAAGG-TTTAATTCAGGGTAATTAAGTAGAATAAAGAATTTA
1 AGGGTAATTAAGTGGAGTCAATAAAAGGACTTAATTCAGGGGAATTAAGTAGAATAAAGAACTTA
*
25887 GTTC
66 ATTC
* *
25891 AGGATAATTAAGTGGAGTCAAT-AAAGAACTTAATT
1 AGGGTAATTAAGTGGAGTCAATAAAAGGACTTAATT
25926 TGAAAAGATT
Statistics
Matches: 92, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
67 8 0.09
68 79 0.86
69 5 0.05
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (69 bp):
AGGGTAATTAAGTGGAGTCAATAAAAGGACTTAATTCAGGGGAATTAAGTAGAATAAAGAACTTA
ATTC
Found at i:26177 original size:87 final size:87
Alignment explanation
Indices: 26082--26251 Score: 340
Period size: 87 Copynumber: 2.0 Consensus size: 87
26072 TAAAAACAAG
26082 TAACAATTTGTCCTAAAACGAAGAACTAATTAAGGCTAAGTATAAAAGTTAGGCATGAAAAGACT
1 TAACAATTTGTCCTAAAACGAAGAACTAATTAAGGCTAAGTATAAAAGTTAGGCATGAAAAGACT
26147 AAGGCTTAAAAGGAATTAACCA
66 AAGGCTTAAAAGGAATTAACCA
26169 TAACAATTTGTCCTAAAACGAAGAACTAATTAAGGCTAAGTATAAAAGTTAGGCATGAAAAGACT
1 TAACAATTTGTCCTAAAACGAAGAACTAATTAAGGCTAAGTATAAAAGTTAGGCATGAAAAGACT
26234 AAGGCTTAAAAGGAATTA
66 AAGGCTTAAAAGGAATTA
26252 GTCCTAGACA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 83 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.24
Consensus pattern (87 bp):
TAACAATTTGTCCTAAAACGAAGAACTAATTAAGGCTAAGTATAAAAGTTAGGCATGAAAAGACT
AAGGCTTAAAAGGAATTAACCA
Found at i:30682 original size:38 final size:38
Alignment explanation
Indices: 30605--30721 Score: 132
Period size: 38 Copynumber: 3.1 Consensus size: 38
30595 GCAGCTGAAC
* * * *
30605 ACTGCTGAAAGATGACCCGTTTCTAATCGA-CTTTAATA
1 ACTGTTGAAAGATGACCTGTTTCTAGTCGATC-TTGATA
30643 ACTGTTGAAAGATGACCTGTTTCTAGTCGATCTTGATA
1 ACTGTTGAAAGATGACCTGTTTCTAGTCGATCTTGATA
* *
30681 ACCGCTTTG--AGATGACATGTTTCTAGTCGATCTTGATA
1 ACTG--TTGAAAGATGACCTGTTTCTAGTCGATCTTGATA
30719 ACT
1 ACT
30722 TATTTTGAGT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
38 65 0.94
39 1 0.01
40 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (38 bp):
ACTGTTGAAAGATGACCTGTTTCTAGTCGATCTTGATA
Found at i:33202 original size:38 final size:38
Alignment explanation
Indices: 33120--33206 Score: 138
Period size: 38 Copynumber: 2.3 Consensus size: 38
33110 TTAAGCACAT
* *
33120 ACAGCCAAAAGAACTTAATTCAGTGTAATTAAGTAAAT
1 ACAGTCAAAAGAACTTAATTCAGTGTAATTAAGTAAAC
* *
33158 ATAGTCAAAAGAACTTAATTCAGTGTAATTAAGTAACC
1 ACAGTCAAAAGAACTTAATTCAGTGTAATTAAGTAAAC
33196 ACAGTCAAAAG
1 ACAGTCAAAAG
33207 TAAATACAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (38 bp):
ACAGTCAAAAGAACTTAATTCAGTGTAATTAAGTAAAC
Found at i:33260 original size:42 final size:41
Alignment explanation
Indices: 33202--33293 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 41
33192 AACCACAGTC
* *
33202 AAAAGTAAATACAGTCAGGGTCTTAACTCGGGGTAATTAAG
1 AAAAGTAAATACAGTCAAGGTCTTAACTCAGGGTAATTAAG
*
33243 AAAAGATAAATACAGTCAAGGTCTTAATTCAGGGTAATTAAG
1 AAAAG-TAAATACAGTCAAGGTCTTAACTCAGGGTAATTAAG
*
33285 AAAGGTAAA
1 AAAAGTAAA
33294 AGCAGTTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 9 0.20
42 37 0.80
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.24
Consensus pattern (41 bp):
AAAAGTAAATACAGTCAAGGTCTTAACTCAGGGTAATTAAG
Found at i:33435 original size:37 final size:37
Alignment explanation
Indices: 33289--33589 Score: 383
Period size: 37 Copynumber: 8.1 Consensus size: 37
33279 ATTAAGAAAG
* * *
33289 GTAAAAGCAGTTAAAGGATTTAATTCAAGGAAATTAA
1 GTAAAAGCAGTTAAAGGACTTAATTCATGGTAATTAA
* *
33326 GTAAAGAGCTGTTAAAGTACTTAATTCATGGTAATTAA
1 GTAAA-AGCAGTTAAAGGACTTAATTCATGGTAATTAA
* *
33364 GTAAAAGCAG-T-AAGGTACTTAATTCAGGGAAATTAA
1 GTAAAAGCAGTTAAAGG-ACTTAATTCATGGTAATTAA
*
33400 GTAAACGCAGTTAAAGGACTTAATTCATGGTAATTAA
1 GTAAAAGCAGTTAAAGGACTTAATTCATGGTAATTAA
* * * * *
33437 CTAAAAGCAGTTGAAGGACATAACTCA-GGGAAGTTAA
1 GTAAAAGCAGTTAAAGGACTTAATTCATGGTAA-TTAA
* *
33474 GTAAAAGCAGTTAAAGGACATAACTCATGGTAATTAA
1 GTAAAAGCAGTTAAAGGACTTAATTCATGGTAATTAA
* *
33511 GTAAAAGCAGTAAAAGGACTTAATTCACGGTAATTAA
1 GTAAAAGCAGTTAAAGGACTTAATTCATGGTAATTAA
* *
33548 GTAAAAGCAGTAAAATGACTTAATTCATGGTAATTAA
1 GTAAAAGCAGTTAAAGGACTTAATTCATGGTAATTAA
33585 GTAAA
1 GTAAA
33590 GATAAGCACA
Statistics
Matches: 231, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
35 3 0.01
36 32 0.14
37 156 0.68
38 40 0.17
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.27
Consensus pattern (37 bp):
GTAAAAGCAGTTAAAGGACTTAATTCATGGTAATTAA
Found at i:33977 original size:41 final size:41
Alignment explanation
Indices: 33593--33960 Score: 628
Period size: 41 Copynumber: 9.0 Consensus size: 41
33583 AAGTAAAGAT
33593 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGTA
*
33634 AAGCCCAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGTA
* *
33675 AAGCACAGACTTAATTTCAATGAAGGAAATTAGGTAAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGTA
33716 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGTA
* *
33757 AAGCACAGACTTAATTTCAATGAAGGAAATTAGGTAAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGTA
* *
33798 AAGCACAGACTTAATTTGAAGGAAGGAAATTAGGTAAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGTA
* *
33839 AAGCACAGACTTAATTTGAAGGAAGGAAATTAGGTAAAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGTA
33880 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGTA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGTA
* * *
33921 AAGCACAAACCTAATTTCAAGGAAGGAAATTAAGTAGAGT
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGT
33961 CAATAAAGGG
Statistics
Matches: 312, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 312 1.00
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.22
Consensus pattern (41 bp):
AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAGAGTA
Found at i:34007 original size:32 final size:32
Alignment explanation
Indices: 33962--34091 Score: 145
Period size: 32 Copynumber: 3.9 Consensus size: 32
33952 AAGTAGAGTC
**
33962 AATAAAGGGCTTAATTCAGGGTAATTAAGTAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGTAG
33994 AATAAAGAACTTAATTCAGGGTAATTAAGTGGAG
1 AATAAAGAACTTAATTCAGGGTAATTAAGT--AG
** *
34028 TCAATAAA-AGGTTTAATTCAGAGTAATTAAGTAG
1 --AATAAAGA-ACTTAATTCAGGGTAATTAAGTAG
* *
34062 AATAAAGAATTTAATTTAGGGTAATTAAGT
1 AATAAAGAACTTAATTCAGGGTAATTAAGT
34092 GTTGTCAATA
Statistics
Matches: 84, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
32 53 0.63
33 1 0.01
34 4 0.05
35 1 0.01
36 25 0.30
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (32 bp):
AATAAAGAACTTAATTCAGGGTAATTAAGTAG
Found at i:34057 original size:68 final size:68
Alignment explanation
Indices: 33948--34115 Score: 246
Period size: 68 Copynumber: 2.4 Consensus size: 68
33938 CAAGGAAGGA
* * *
33948 AATTAAGTAGAGTCAATAAAGGGCTTAATTCAGGGTAATTAAGTAGAATAAAGAACTTAATTCAG
1 AATTAAGTGGAGTCAATAAAAGGCTTAATTCAGAGTAATTAAGTAGAATAAAGAACTTAATTCAG
34013 GGT
66 GGT
* * *
34016 AATTAAGTGGAGTCAATAAAAGGTTTAATTCAGAGTAATTAAGTAGAATAAAGAATTTAATTTAG
1 AATTAAGTGGAGTCAATAAAAGGCTTAATTCAGAGTAATTAAGTAGAATAAAGAACTTAATTCAG
34081 GGT
66 GGT
**
34084 AATTAAGTGTTGTCAATAAAAAGGGCTTAATT
1 AATTAAGTGGAGTCAAT-AAAA-GGCTTAATT
34116 TATGAAAATT
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
68 77 0.87
69 4 0.04
70 8 0.09
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.31
Consensus pattern (68 bp):
AATTAAGTGGAGTCAATAAAAGGCTTAATTCAGAGTAATTAAGTAGAATAAAGAACTTAATTCAG
GGT
Found at i:36148 original size:27 final size:27
Alignment explanation
Indices: 36118--36171 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
36108 GCGCGCAGGT
* *
36118 CGCGACCTGGCCATGGGGTAGGTCGCG
1 CGCGACCTAGCCATGCGGTAGGTCGCG
*
36145 CGCGACCTAGCCATGCGGTCGGTCGCG
1 CGCGACCTAGCCATGCGGTAGGTCGCG
36172 ACCCGGGTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.11, C:0.33, G:0.41, T:0.15
Consensus pattern (27 bp):
CGCGACCTAGCCATGCGGTAGGTCGCG
Found at i:40279 original size:33 final size:34
Alignment explanation
Indices: 40215--40279 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
40205 AGCTATGTAC
40215 AGTATGGGACTTTACCCCCAATATTTATAATCTGG
1 AGTATGGGACTTTA-CCCCAATATTTATAATCTGG
* * *
40250 AGTATGGGGCTTTA-CCCAGTATTTGTAATC
1 AGTATGGGACTTTACCCCAATATTTATAATC
40280 CGAACTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 14 0.52
35 13 0.48
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (34 bp):
AGTATGGGACTTTACCCCAATATTTATAATCTGG
Found at i:42790 original size:1 final size:1
Alignment explanation
Indices: 42784--42818 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
42774 ATCCCTCTAG
42784 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
42819 GTGTGTGCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:45660 original size:11 final size:11
Alignment explanation
Indices: 45646--45683 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
45636 ATTCATAACA
45646 AATTTATAATT
1 AATTTATAATT
45657 AATTTATAATT
1 AATTTATAATT
45668 -ATTTGATAATT
1 AATTT-ATAATT
*
45679 TATTT
1 AATTT
45684 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:52993 original size:11 final size:10
Alignment explanation
Indices: 52975--53008 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
52965 GAAGTTCATG
52975 TTTTGAAGAT
1 TTTTGAAGAT
52985 TTCTTGAAGAT
1 TT-TTGAAGAT
52996 ATTTTGAAGAT
1 -TTTTGAAGAT
53007 TT
1 TT
53009 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:70043 original size:11 final size:10
Alignment explanation
Indices: 70025--70058 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
70015 GAAGTTCGTG
70025 TTTTGAAGAT
1 TTTTGAAGAT
70035 TTCTTGAAGAT
1 TT-TTGAAGAT
70046 ATTTTGAAGAT
1 -TTTTGAAGAT
70057 TT
1 TT
70059 GAAGACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Done.