Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010424.1 Corchorus capsularis cultivar CVL-1 contig10445, 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: 47883
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:6873 original size:40 final size:40
Alignment explanation
Indices: 6775--6873 Score: 103
Period size: 40 Copynumber: 2.5 Consensus size: 40
6765 CCCTCCACCA
* *
6775 TTGGTTTCCATGTAGTTTAGAGGAGTTGACAATGGTAAAT
1 TTGGTTTCCATGTATTTTAGAGGAGTTGACAAGGGTAAAT
* * * *
6815 TTGGTTTTCC-CGTAATTTTA-TGTAGTTGCCAAGGGTAAAT
1 TTGG-TTTCCATGT-ATTTTAGAGGAGTTGACAAGGGTAAAT
6855 TTGGTGTTCCATGTATTTT
1 TTGGT-TTCCATGTATTTT
6874 TTTTATCTCT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
39 1 0.02
40 35 0.73
41 12 0.25
ACGTcount: A:0.22, C:0.10, G:0.24, T:0.43
Consensus pattern (40 bp):
TTGGTTTCCATGTATTTTAGAGGAGTTGACAAGGGTAAAT
Found at i:7527 original size:20 final size:20
Alignment explanation
Indices: 7494--7533 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
7484 TTAATATTAA
** *
7494 AAATATTTTTAAAATGATTT
1 AAATATTTAAAAAATAATTT
7514 AAATATTTAAAAAATAATTT
1 AAATATTTAAAAAATAATTT
7534 TTTAATGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
AAATATTTAAAAAATAATTT
Found at i:7726 original size:26 final size:28
Alignment explanation
Indices: 7697--7763 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 28
7687 TCTACCATTA
7697 GAGTTATATT-A-ATTAAACGTATGGTT
1 GAGTTATATTAATATTAAACGTATGGTT
*
7723 GAGTTAAATTAGACTTATTAAACGTATGGTT
1 GAGTTATATTA-A--TATTAAACGTATGGTT
7754 GAGTTATATT
1 GAGTTATATT
7764 TTTTTCTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 9 0.26
28 1 0.03
31 24 0.71
ACGTcount: A:0.34, C:0.04, G:0.19, T:0.42
Consensus pattern (28 bp):
GAGTTATATTAATATTAAACGTATGGTT
Found at i:9133 original size:2 final size:2
Alignment explanation
Indices: 9126--9157 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9116 CAAAAGCAGA
9126 AT AT 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 AT AT
9158 TAAACCACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14281 original size:2 final size:2
Alignment explanation
Indices: 14276--14305 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14266 TATGCGTGTG
14276 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14306 GAAGACGAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16732 original size:3 final size:3
Alignment explanation
Indices: 16724--16766 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
16714 TATATATATT
16724 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
16767 AAAAGTGATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17611 original size:19 final size:20
Alignment explanation
Indices: 17591--17626 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
17581 AGTTAATTAT
17591 TTTA-ATATTA-ATTTTTTA
1 TTTATATATTATATTTTTTA
17609 TTTATATATTATATTTTT
1 TTTATATATTATATTTTT
17627 ACTTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 6 0.38
20 6 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATATATTATATTTTTTA
Found at i:20887 original size:19 final size:20
Alignment explanation
Indices: 20852--20894 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
20842 TTTTATAGTG
20852 GTTTTTTGTAAAGATTTTTT
1 GTTTTTTGTAAAGATTTTTT
20872 GTTTTTT-TACAA-ATTTTTT
1 GTTTTTTGTA-AAGATTTTTT
20891 -TTTT
1 GTTTT
20895 ACCATTCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 9 0.41
20 9 0.41
ACGTcount: A:0.19, C:0.02, G:0.09, T:0.70
Consensus pattern (20 bp):
GTTTTTTGTAAAGATTTTTT
Found at i:22115 original size:25 final size:25
Alignment explanation
Indices: 22069--22117 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
22059 TTTCCGATAT
*
22069 TAAATTAATAATTGATTTTGAAATG
1 TAAATTAATAATTGATTATGAAATG
*
22094 TAAATTAAT-TTTGATTAATGAAAT
1 TAAATTAATAATTGATT-ATGAAAT
22118 ATTAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (25 bp):
TAAATTAATAATTGATTATGAAATG
Found at i:24299 original size:201 final size:199
Alignment explanation
Indices: 23923--24736 Score: 778
Period size: 199 Copynumber: 3.9 Consensus size: 199
23913 ATAATAATTC
* * * * * *
23923 TATACAATAC-C-GTAAGTGGATTTTAGCAGACTGCACGTGCAGGATTTAAGGGTTGACATGTGT
1 TATACAATACACAGTCAGTGGAGTTTAGCAGACAGCAAGTGCAGGGTTTAAGGGTTGACATGTAT
* * *
23986 CCCTTTAGGGAATATGTATTAATATTAAATATTTAATTTATTATGAAATGAGGTATCTGTCAACT
66 CCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGAGGTATGTGTCAACT
* * * *
24051 TCTTAACTCGCTTATGGAGTCCAAAATTTATATTGACAGTGTATTGTATAATAATTCTATAAGAA
131 TCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATTCTATAAAAA
24116 AAAT
196 AAAT
** * * *
24120 TACGCAATACACAGTCAGTGGAGTTTAGCATACAGCAAGTGCGGGGTTCAAGGGTTGACATGTAT
1 TATACAATACACAGTCAGTGGAGTTTAGCAGACAGCAAGTGCAGGGTTTAAGGGTTGACATGTAT
* *
24185 CCCCTTAGGGAATATGTATTAATATATTAAATATTTAATTAATTATGAAATGGGGTGTGTGTCAA
66 CCCCTTAGGGAATATGTATT-A-ATATTAAATATTTAATTAATTATGAAATGAGGTATGTGTCAA
* *
24250 CTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGATAGTATATTGTATAATAA-TCATATAA
129 CTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATTC-TAT-A
24314 AACAAAAAT
192 AA-AAAAAT
* * * * * * *
24323 TATACAATACACTGTCAGTGGAGTTTGGCAGACTGCACGCGCGGGGTTTAAGGGTTGACATGTGT
1 TATACAATACACAGTCAGTGGAGTTTAGCAGACAGCAAGTGCAGGGTTTAAGGGTTGACATGTAT
* *
24388 CCTAGCGCGTGTTTAAGGGTTGACATGTGTCCTCTTAGGGAATATGTATTAATAATTTATATCTA
66 CC---C-C----TT-A-GG--GA-ATATG---TATT----AATA----TT-A-AA--TAT-T-TA
* * * *
24453 ATTAATTATGAAATAAGGTATGTGTCAACTTCTTAACCCGGTTGTGGAGTTCAAAATTTACACTG
101 ATTAATTATGAAATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTG
* *
24518 ACAGTGTATTGTATAATAATCCTACAAAAAAAAAT
166 ACAGTGTATTGTATAATAATTCTA-TAAAAAAAAT
* * * * * *
24553 TATACAATACACCGTCAGTAGAGTTTAGTAGACTA-TACA-TGCATGGTTTAAGGGTTGGCATGT
1 TATACAATACACAGTCAGTGGAGTTTAGCAGAC-AGCA-AGTGCAGGGTTTAAGGGTTGACATGT
* *
24616 ATCCCCCTTAGGG-A-ATGTATTAATATCAAATATTTAATTAATTATAAAATGAGGTATGTGTCA
64 AT-CCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGAGGTATGTGTCA
* * * *
24679 ACTTCTTAACCCACTTATGAAGTCCAAAATTTACATTGACAGTGTATTCGTACAATAA
128 ACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATT-GTATAATAA
24737 ACCTTATTAT
Statistics
Matches: 506, Mismatches: 69, Indels: 81
0.77 0.11 0.12
Matches are distributed among these distances:
197 8 0.02
198 1 0.00
199 131 0.26
200 12 0.02
201 95 0.19
202 2 0.00
203 65 0.13
204 1 0.00
205 1 0.00
206 1 0.00
207 1 0.00
209 4 0.01
211 2 0.00
212 1 0.00
213 5 0.01
215 2 0.00
216 6 0.01
217 1 0.00
219 4 0.01
221 5 0.01
222 2 0.00
223 2 0.00
225 2 0.00
226 1 0.00
227 3 0.01
228 1 0.00
229 3 0.01
230 58 0.11
231 85 0.17
232 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (199 bp):
TATACAATACACAGTCAGTGGAGTTTAGCAGACAGCAAGTGCAGGGTTTAAGGGTTGACATGTAT
CCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGAGGTATGTGTCAACT
TCTTAACCCGCTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATAATTCTATAAAAA
AAAT
Found at i:25102 original size:16 final size:16
Alignment explanation
Indices: 25077--25107 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25067 TCTACATATT
25077 ATAAAAATTTAGTAAA
1 ATAAAAATTTAGTAAA
*
25093 ATAAATATTTAGTAA
1 ATAAAAATTTAGTAA
25108 TATTTTTTAA
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:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
ATAAAAATTTAGTAAA
Found at i:26018 original size:17 final size:18
Alignment explanation
Indices: 25996--26030 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
25986 CTTTATCAGA
*
25996 TATTTTTTAAA-ATTTTT
1 TATTTTTGAAATATTTTT
26013 TATTTTTGAAATATTTTT
1 TATTTTTGAAATATTTTT
26031 GTGAGCCCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TATTTTTGAAATATTTTT
Found at i:26174 original size:23 final size:23
Alignment explanation
Indices: 26148--26193 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
26138 TTTGAAACGT
26148 AAGGGATTAATTTGTCCCAAAAA
1 AAGGGATTAATTTGTCCCAAAAA
**
26171 AAGGGATTTTTTTGTCCCAAAAA
1 AAGGGATTAATTTGTCCCAAAAA
26194 GAAACTGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (23 bp):
AAGGGATTAATTTGTCCCAAAAA
Found at i:26236 original size:21 final size:21
Alignment explanation
Indices: 26206--26246 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
26196 AACTGGATTG
*
26206 CTAAACACCGCCCCCCTTTTA
1 CTAAACACCGCCACCCTTTTA
*
26227 CTAAATACCGCCACCCTTTT
1 CTAAACACCGCCACCCTTTT
26247 TACACTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.44, G:0.05, T:0.27
Consensus pattern (21 bp):
CTAAACACCGCCACCCTTTTA
Found at i:26424 original size:26 final size:26
Alignment explanation
Indices: 26395--26502 Score: 132
Period size: 26 Copynumber: 4.2 Consensus size: 26
26385 TTCCTTCATT
26395 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
26421 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
26447 TTAAACATAAACTAA-TAAACTAAGTAA
1 TTAATCATAAACTAATTAAA-T-ACTAA
* * *
26474 TT-TTAATTAACTAATTAAA-ACTAA
1 TTAATCATAAACTAATTAAATACTAA
26498 TTAAT
1 TTAAT
26503 ATTAAAAAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
24 6 0.09
25 5 0.07
26 49 0.70
27 10 0.14
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:26462 original size:15 final size:15
Alignment explanation
Indices: 26395--26466 Score: 63
Period size: 11 Copynumber: 5.4 Consensus size: 15
26385 TTCCTTCATT
*
26395 TTAATCATAAACTAA
1 TTAAACATAAACTAA
26410 TT-AA-AT--ACTAA
1 TTAAACATAAACTAA
*
26421 TTAATCATAAACTAA
1 TTAAACATAAACTAA
26436 TT-AA-AT--ACTAA
1 TTAAACATAAACTAA
26447 TTAAACATAAACTAA
1 TTAAACATAAACTAA
26462 -TAAAC
1 TTAAAC
26467 TAAGTAATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 17
0.70 0.05 0.26
Matches are distributed among these distances:
11 14 0.30
12 3 0.07
13 8 0.17
14 7 0.15
15 14 0.30
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAACATAAACTAA
Found at i:26498 original size:18 final size:18
Alignment explanation
Indices: 26430--26509 Score: 55
Period size: 18 Copynumber: 4.7 Consensus size: 18
26420 ATTAATCATA
26430 AACTAATTAAATACTAATT
1 AACTAATTAAA-ACTAATT
*
26449 AA--ACA-T-AAACTAATA
1 AACTA-ATTAAAACTAATT
* ***
26464 AACTAAGTAATTTTAATT
1 AACTAATTAAAACTAATT
26482 AACTAATTAAAACTAATT
1 AACTAATTAAAACTAATT
26500 AA-T-ATTAAAA
1 AACTAATTAAAA
26510 AAATTTAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 13
0.68 0.13 0.19
Matches are distributed among these distances:
15 8 0.17
16 10 0.21
17 5 0.11
18 22 0.47
19 2 0.04
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.34
Consensus pattern (18 bp):
AACTAATTAAAACTAATT
Found at i:27344 original size:21 final size:22
Alignment explanation
Indices: 27310--27353 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
27300 ATAGTGTTGT
*
27310 GCACAAATAGAAGATTA-AAGA
1 GCACAAATAGAAGAATACAAGA
27331 GCACAAAATA-AAGAATACAAGA
1 GCAC-AAATAGAAGAATACAAGA
27353 G
1 G
27354 ATTTACGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.59, C:0.11, G:0.18, T:0.11
Consensus pattern (22 bp):
GCACAAATAGAAGAATACAAGA
Found at i:27883 original size:50 final size:50
Alignment explanation
Indices: 27785--27884 Score: 125
Period size: 50 Copynumber: 2.0 Consensus size: 50
27775 GATCTTTAAC
* * *
27785 TAACACACTCTGCAAAATACTAGAATACAAAACAACATATATTGATTGAT
1 TAACACACTCTGCAAAATACTAAAATACAAAACAACAGAGATTGATTGAT
27835 TAACACACT-TCGCAAAGA-ACTAAAATACAAAACAACAGAGATAT-ATTGAT
1 TAACACACTCT-GCAAA-ATACTAAAATACAAAACAACAGAGAT-TGATTGAT
27885 AACTATAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
49 1 0.02
50 41 0.93
51 2 0.05
ACGTcount: A:0.50, C:0.18, G:0.09, T:0.23
Consensus pattern (50 bp):
TAACACACTCTGCAAAATACTAAAATACAAAACAACAGAGATTGATTGAT
Found at i:32170 original size:21 final size:21
Alignment explanation
Indices: 32146--32188 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
32136 ACGGTGATTA
32146 TCTGCAATATTTACAAGGCGG
1 TCTGCAATATTTACAAGGCGG
32167 TCTGCAATATTTACAAGGCGG
1 TCTGCAATATTTACAAGGCGG
32188 T
1 T
32189 GAATTGCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (21 bp):
TCTGCAATATTTACAAGGCGG
Found at i:33471 original size:168 final size:164
Alignment explanation
Indices: 33181--33640 Score: 575
Period size: 168 Copynumber: 2.8 Consensus size: 164
33171 TCTCCACCTC
* * *
33181 GGATTAATGAGGAGCGAGAGAACTAATTTTTTTCGTCTTTT-CTCACTTGGCAGATTACTTAAAT
1 GGATTGATGATGAGCTAGAGAACTAA-TTTTTTCGTCTTTTCCT-ACTTGGCAGATTACTTAAAT
* * *
33245 GTCCCAACTTTTGATTTTTGAGGGGATTAAATAACTAGACTTTTTGGTCATTTCTCAATTGAATT
64 GTCCTAATTTTTGATTCTTGAGGGGATTAAATAACTA-ACTTTTTGGTCATTTCTCAATTGAATT
* * **
33310 TAATAGAGTAGTGGAATTATTAAAAGATCCTTA-CTAA
128 GAATAGAGTAGTGGAATTAATAAAAGATCCCCATC-AA
* ** * * *
33347 -GACTTGCTTTTGGAGTTAGAGAACTTATTGTTTTCGTCTTTTCCTATTTGGCAGATTACTTAAA
1 GGA-TTGATGAT-GAGCTAGAGAACTAATT-TTTTCGTCTTTTCCTACTTGGCAGATTACTT-AA
* * *
33411 ATGTCCTAATTTTTGATTCTTGAGGGGATTAAATAAGTAATCTTTTTGGTCATTTCTCAATGGAC
62 ATGTCCTAATTTTTGATTCTTGAGGGGATTAAATAACTAA-CTTTTTGGTCATTTCTCAATTGAA
* *
33476 TTGAATAGAGTGGTGGAATTAATGAAAGATCCCCATCAA
126 TTGAATAGAGTAGTGGAATTAATAAAAGATCCCCATCAA
* * *
33515 GGATTGATGATGAGCTAGAAAACTAATCTTTTTCGTCTTTACCTACTTGGTAGATTACTTAAATG
1 GGATTGATGATGAGCTAGAGAACTAAT-TTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATG
*
33580 TCCTAATTTTTTATTCTTGAGGGGATTAAATAACTAAACTTTTTGGTCATTTCTCAATTGA
65 TCCTAATTTTTGATTCTTGAGGGGATTAAATAACT-AACTTTTTGGTCATTTCTCAATTGA
33641 CAAATGACTC
Statistics
Matches: 251, Mismatches: 33, Indels: 20
0.83 0.11 0.07
Matches are distributed among these distances:
165 2 0.01
166 65 0.26
167 83 0.33
168 98 0.39
169 3 0.01
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (164 bp):
GGATTGATGATGAGCTAGAGAACTAATTTTTTCGTCTTTTCCTACTTGGCAGATTACTTAAATGT
CCTAATTTTTGATTCTTGAGGGGATTAAATAACTAACTTTTTGGTCATTTCTCAATTGAATTGAA
TAGAGTAGTGGAATTAATAAAAGATCCCCATCAA
Found at i:36719 original size:16 final size:17
Alignment explanation
Indices: 36698--36732 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
36688 ATGTCTAGAG
*
36698 AAGC-AAAAGTTTTGAA
1 AAGCAAAAAGTTTGGAA
36714 AAGCAAAAAGTTTGGAA
1 AAGCAAAAAGTTTGGAA
36731 AA
1 AA
36733 ATTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.20
Consensus pattern (17 bp):
AAGCAAAAAGTTTGGAA
Found at i:39951 original size:21 final size:21
Alignment explanation
Indices: 39927--39968 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
39917 GGTGACTTGT
39927 AACAAAACTAAAGGAAAGTAA
1 AACAAAACTAAAGGAAAGTAA
39948 AACAAAACTAAAGGAAAGTAA
1 AACAAAACTAAAGGAAAGTAA
39969 CAAAACAAAT
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:0.67, C:0.10, G:0.14, T:0.10
Consensus pattern (21 bp):
AACAAAACTAAAGGAAAGTAA
Found at i:44686 original size:11 final size:11
Alignment explanation
Indices: 44662--44696 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
44652 TTGATAATGT
44662 AACAAAAACAA
1 AACAAAAACAA
* *
44673 AACGAAAACGA
1 AACAAAAACAA
44684 AACAAAAACAA
1 AACAAAAACAA
44695 AA
1 AA
44697 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:45911 original size:6 final size:6
Alignment explanation
Indices: 45900--45925 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
45890 CCTCATTCCT
45900 TATCTA TATCTA TATCTA TATCTA TA
1 TATCTA TATCTA TATCTA TATCTA TA
45926 CTGTTAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (6 bp):
TATCTA
Done.