Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012805.1 Corchorus capsularis cultivar CVL-1 contig12826, 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: 39506
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:697 original size:16 final size:16
Alignment explanation
Indices: 651--699 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
641 TTGAAGTTTG
651 ATGATCTTAAAATGAA
1 ATGATCTTAAAATGAA
* * *
667 AT-TTCCTCAAA--AA
1 ATGATCTTAAAATGAA
680 ATGATCTTAAAATGAA
1 ATGATCTTAAAATGAA
696 ATGA
1 ATGA
700 AATTAAATGG
Statistics
Matches: 24, Mismatches: 6, Indels: 6
0.67 0.17 0.17
Matches are distributed among these distances:
13 4 0.17
14 6 0.25
15 6 0.25
16 8 0.33
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.31
Consensus pattern (16 bp):
ATGATCTTAAAATGAA
Found at i:5207 original size:63 final size:61
Alignment explanation
Indices: 5093--5237 Score: 175
Period size: 63 Copynumber: 2.4 Consensus size: 61
5083 CTTGGCCAAA
* * * *
5093 TCCACCACCAAAGCCACCACC-GCCAGTTCCATAACCACCACCCCCAATGCCTATACCTCC
1 TCCACCGCCAAAACCACCACCAGCCAGGTCCATAACCACCACCCCCAATGCCTACACCTCC
* * *
5153 TCCACCGCCAAAACCACCACCAGCACCAGGTCCATAACCACCACCTCCACTGCCTACGCCTCC
1 TCCACCGCCAAAACCACCACCAG--CCAGGTCCATAACCACCACCCCCAATGCCTACACCTCC
* * *
5216 TCCGCTGCCAAAACCGCCACCA
1 TCCACCGCCAAAACCACCACCA
5238 CGGCCATTGC
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
60 19 0.26
61 1 0.01
63 52 0.72
ACGTcount: A:0.28, C:0.52, G:0.09, T:0.12
Consensus pattern (61 bp):
TCCACCGCCAAAACCACCACCAGCCAGGTCCATAACCACCACCCCCAATGCCTACACCTCC
Found at i:5238 original size:42 final size:42
Alignment explanation
Indices: 5190--5284 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 42
5180 AGGTCCATAA
*
5190 CCACCACCTCCACTGCCTACGCCTCCTCCGCTGCCAAAACCG
1 CCACCACCTCCACTGCCTACGCCTCCCCCGCTGCCAAAACCG
** * *
5232 CCACCACGGCCATTGCCTACGCCTCCCCCGCTTCCAAAACCG
1 CCACCACCTCCACTGCCTACGCCTCCCCCGCTGCCAAAACCG
5274 CCACCACCTCC
1 CCACCACCTCC
5285 TCCACTGCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.19, C:0.56, G:0.12, T:0.14
Consensus pattern (42 bp):
CCACCACCTCCACTGCCTACGCCTCCCCCGCTGCCAAAACCG
Found at i:5295 original size:27 final size:27
Alignment explanation
Indices: 5265--5414 Score: 212
Period size: 27 Copynumber: 5.6 Consensus size: 27
5255 TCCCCCGCTT
* *
5265 CCAAAACCGCCACCACCTCCTCCACTG
1 CCAATACCACCACCACCTCCTCCACTG
*
5292 CCAAAACCACCACCACCTCCTCCACTG
1 CCAATACCACCACCACCTCCTCCACTG
* *
5319 CCAATACCACCACCAACTCCCCCACTG
1 CCAATACCACCACCACCTCCTCCACTG
* *
5346 CCAATACCACCGCCACCTACC-CCGCTG
1 CCAATACCACCACCACCT-CCTCCACTG
*
5373 CCAATACCACCACCACCTCCACCACTG
1 CCAATACCACCACCACCTCCTCCACTG
5400 CCAATACCACCACCA
1 CCAATACCACCACCA
5415 GGTCCACCAC
Statistics
Matches: 112, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
26 2 0.02
27 108 0.96
28 2 0.02
ACGTcount: A:0.29, C:0.55, G:0.05, T:0.11
Consensus pattern (27 bp):
CCAATACCACCACCACCTCCTCCACTG
Found at i:5374 original size:81 final size:81
Alignment explanation
Indices: 5254--5414 Score: 234
Period size: 81 Copynumber: 2.0 Consensus size: 81
5244 TTGCCTACGC
* * * *
5254 CTCCCCCGCTTCCAAAACCGCCACCACCTCCTCCACTGCCAAAACCACCACCACCTCCTCCACTG
1 CTCCCCCACTGCCAAAACCACCACCACCTCCTCCACTGCCAAAACCACCACCACCTCCACCACTG
5319 CCAATACCACCACCAA
66 CCAATACCACCACCAA
* * * *
5335 CTCCCCCACTGCCAATACCACCGCCACCTACC-CCGCTGCCAATACCACCACCACCTCCACCACT
1 CTCCCCCACTGCCAAAACCACCACCACCT-CCTCCACTGCCAAAACCACCACCACCTCCACCACT
5399 GCCAATACCACCACCA
65 GCCAATACCACCACCA
5415 GGTCCACCAC
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 69 0.97
82 2 0.03
ACGTcount: A:0.27, C:0.56, G:0.06, T:0.12
Consensus pattern (81 bp):
CTCCCCCACTGCCAAAACCACCACCACCTCCTCCACTGCCAAAACCACCACCACCTCCACCACTG
CCAATACCACCACCAA
Found at i:5437 original size:36 final size:36
Alignment explanation
Indices: 5382--5451 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
5372 GCCAATACCA
5382 CCACCACCTCCACCACTGCCAATACCACCACCAGGT
1 CCACCACCTCCACCACTGCCAATACCACCACCAGGT
* *
5418 CCACCACCTCCCCCCCTGCCAATACCACCACCAG
1 CCACCACCTCCACCACTGCCAATACCACCACCAG
5452 AACCAGCCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.26, C:0.57, G:0.07, T:0.10
Consensus pattern (36 bp):
CCACCACCTCCACCACTGCCAATACCACCACCAGGT
Found at i:11489 original size:89 final size:87
Alignment explanation
Indices: 11383--11766 Score: 302
Period size: 89 Copynumber: 4.4 Consensus size: 87
11373 TGACAACAAT
* * *
11383 GGAGGAACACGTGAAATCGGTGAAGTTTGTAAGTTTAGCAGACGAGATATCTCAATCTCACACTC
1 GGAGGAACACGTGAAATCGGTGAACTTTGTAAGTTTAGCAGACGAGATATC-CAAACTCACAATC
11448 AGTGCAAAGGCGAATAACAAAAGG
65 -GTGCAAAGGCGAATAACAAAAGG
* * * * * *
11472 GGAGGAACATGTGAAATCGGTGAAATTTGTAAGTTTATCAG-CTGTGATAACCCAAACTCGCAAT
1 GGAGGAACACGTGAAATCGGTGAACTTTGTAAGTTTAGCAGAC-GAGAT-ATCCAAACTCACAAT
* *
11536 CG-G---TGGCGAATAACATCAA-G
64 CGTGCAAAGGCGAATAACA-AAAGG
* ** *
11556 GGAGGAACACGTGAAATCGGTAAACTTTGTACA-TTTATGTTGGACAAGATA-CCGAAACCTGCA
1 GGAGGAACACGTGAAATCGGTGAACTTTGTA-AGTTTA-G-CAGACGAGATATCC-AAA-CT-CA
** * *
11619 -AATCGATGCAATTGTGAATAACAACAGG
60 CAATCG-TGCAAAGGCGAATAACAAAAGG
* * ** * * *
11647 GG-GGAGCATGTGAAATCAATGAAAGTTTGTAAGTTTAGCAGGCGAGATAATCCAAAATCACAAT
1 GGAGGAACACGTGAAATCGGTG-AACTTTGTAAGTTTAGCAGACGAGAT-ATCCAAACTCACAAT
**
11711 CGGTGCAAAGGCGAATAACATCAGG
64 C-GTGCAAAGGCGAATAACAAAAGG
*
11736 TGAGGAACACGTGAAATCGGTGAACTTTGTA
1 GGAGGAACACGTGAAATCGGTGAACTTTGTA
11767 CATTTATATG
Statistics
Matches: 228, Mismatches: 44, Indels: 46
0.72 0.14 0.14
Matches are distributed among these distances:
84 46 0.20
85 7 0.03
86 11 0.05
87 3 0.01
88 5 0.02
89 90 0.39
90 39 0.17
91 27 0.12
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (87 bp):
GGAGGAACACGTGAAATCGGTGAACTTTGTAAGTTTAGCAGACGAGATATCCAAACTCACAATCG
TGCAAAGGCGAATAACAAAAGG
Found at i:11570 original size:84 final size:87
Alignment explanation
Indices: 11383--11869 Score: 277
Period size: 89 Copynumber: 5.6 Consensus size: 87
11373 TGACAACAAT
* * * * *
11383 GGAGGAACACGTGAAATCGGTGAAGTTTGTAAGTTTAGCAGACGAGATATCTCAATCTCACACTC
1 GGAGGAACACGTGAAATCGGTGAAATTTGTAAGTTTAGCAGACGAGATAACCCAAACTCACAATC
11448 AGTGCAAAGGCGAATAACAAAAGG
66 AGTG--AAGGCGAATAACAAAAGG
* * * *
11472 GGAGGAACATGTGAAATCGGTGAAATTTGTAAGTTTATCAG-CTGTGATAACCCAAACTCGCAAT
1 GGAGGAACACGTGAAATCGGTGAAATTTGTAAGTTTAGCAGAC-GAGATAACCCAAACTCACAAT
* *
11536 C-G-G-TGGCGAATAACATCAA-G
65 CAGTGAAGGCGAATAACA-AAAGG
** * *
11556 GGAGGAACACGTGAAATCGGT-AAACTTTGTACA-TTTATGTTGGACAAGAT-ACCGAAACCTGC
1 GGAGGAACACGTGAAATCGGTGAAA-TTTGTA-AGTTTA-G-CAGACGAGATAACCCAAA-CT-C
* * *
11618 A-AATC-GATGCAATTGTGAATAACAACAGG
60 ACAATCAG-TG-AA-GGCGAATAACAAAAGG
* * ** * * *
11647 GG-GGAGCATGTGAAATCAATGAAAGTTTGTAAGTTTAGCAGGCGAGATAATCCAAAATCACAAT
1 GGAGGAACACGTGAAATCGGTGAAA-TTTGTAAGTTTAGCAGACGAGATAACCCAAACTCACAAT
* **
11711 CGGTGCAAAGGCGAATAACATCAGG
65 CAGTG--AAGGCGAATAACAAAAGG
* * *
11736 TGAGGAACACGTGAAATCGGTGAACTTTGTACA-TTTA-TATGAC------ACCCAAAACT-ACA
1 GGAGGAACACGTGAAATCGGTGAAATTTGTA-AGTTTAGCA-GACGAGATAACCC-AAACTCAC-
* * *
11792 AATCAATG-A--CGAATAACAACAGT
62 AATCAGTGAAGGCGAATAACAAAAGG
* * *
11815 GAAGGAACATGTGAAATCGGTGAAGTTTGTAAG-TTAGCA-AGCGAGATAACCCAAA
1 GGAGGAACACGTGAAATCGGTGAAATTTGTAAGTTTAGCAGA-CGAGATAACCCAAA
11870 ATCAAAACCG
Statistics
Matches: 304, Mismatches: 59, Indels: 76
0.69 0.13 0.17
Matches are distributed among these distances:
77 1 0.00
78 5 0.02
79 40 0.13
81 1 0.00
83 11 0.04
84 56 0.18
85 9 0.03
86 11 0.04
87 3 0.01
88 6 0.02
89 93 0.31
90 43 0.14
91 25 0.08
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (87 bp):
GGAGGAACACGTGAAATCGGTGAAATTTGTAAGTTTAGCAGACGAGATAACCCAAACTCACAATC
AGTGAAGGCGAATAACAAAAGG
Found at i:13268 original size:12 final size:12
Alignment explanation
Indices: 13247--13286 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
13237 TATAAATAAA
13247 TTATTTAATT-T
1 TTATTTAATTAT
13258 TTATATTAATTAT
1 TTAT-TTAATTAT
*
13271 TGATTTAATTAT
1 TTATTTAATTAT
13283 TTAT
1 TTAT
13287 GACATTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 4 0.16
12 17 0.68
13 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (12 bp):
TTATTTAATTAT
Found at i:13293 original size:24 final size:24
Alignment explanation
Indices: 13249--13295 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
13239 TAAATAAATT
* *
13249 ATTTAATTTTTATATTAATTATTG
1 ATTTAATTATTATATGAATTATTG
13273 ATTTAATTATT-TATGACATTATT
1 ATTTAATTATTATATGA-ATTATT
13296 ATATTATACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (24 bp):
ATTTAATTATTATATGAATTATTG
Found at i:14575 original size:17 final size:18
Alignment explanation
Indices: 14553--14592 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
14543 GGTTATCTCC
14553 CTTCATAAAC-TTACAAA
1 CTTCATAAACTTTACAAA
*
14570 CTTCATAAACTTTATAAA
1 CTTCATAAACTTTACAAA
14588 CTTCA
1 CTTCA
14593 CAGGTTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (18 bp):
CTTCATAAACTTTACAAA
Found at i:14581 original size:9 final size:9
Alignment explanation
Indices: 14553--14592 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
14543 GGTTATCTCC
14553 CTTCATAAA
1 CTTCATAAA
*
14562 CTT-ACAAA
1 CTTCATAAA
14570 CTTCATAAA
1 CTTCATAAA
*
14579 CTTTATAAA
1 CTTCATAAA
14588 CTTCA
1 CTTCA
14593 CAGGTTTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (9 bp):
CTTCATAAA
Found at i:14874 original size:175 final size:175
Alignment explanation
Indices: 14575--15578 Score: 1238
Period size: 175 Copynumber: 5.8 Consensus size: 175
14565 ACAAACTTCA
* * * *
14575 TAAACTTTATAAACTTCACAGGTTTCATGTGTTCCTCCTTTATTTTCATTCAACTTTGAACTCTT
1 TAAACTTTATAAACTTCACAGATTTCATGTGTTCCTCCCTTGTTGTCATTCAACTTTGAACTCTT
* * * * *
14640 TCCAATTCTGGATTATCTTGCTCATTGAACTTACAAGCCTCAG-CTGCCCACTATTTTTCA-AAA
66 TCCAATTTTGGATTATCTTGCCCACTGAACTTACAAACCTCAGTC-GCCCACTGTTTTTCACAAA
*
14703 ATGATACCTTTGCACCGGTTGCGAGGTGGGTTATCTCGACCGCTTGC
130 A-GATACCTTTGCACCGATTGCGAGGTGGGTTATCTCGACCGCTTGC
* * *
14750 TAAGCTTTATAAACTTCACAGATTTCATGTGTTCCTCCCTTGTTGCCATTCACCTTTGAACTCTT
1 TAAACTTTATAAACTTCACAGATTTCATGTGTTCCTCCCTTGTTGTCATTCAACTTTGAACTCTT
* * *
14815 TCCAATTTTGGATTATCTTGCCCACTAAACTTACAAACCTCAGTCGCCTATTGTTTTTCACAAAA
66 TCCAATTTTGGATTATCTTGCCCACTGAACTTACAAACCTCAGTCGCCCACTGTTTTTCACAAAA
* * ** * * * * *
14880 GACACGTTTGCAGTGATTGCGAGATGGGTTATCTCAATCACTTAC
131 GATACCTTTGCACCGATTGCGAGGTGGGTTATCTCGACCGCTTGC
* **** * *
14925 TAAACTTTATAAAC-TCTACAGGTTTCAT-T-TGAGACCCTTGTTGTCATTCAACTTAGAACTAT
1 TAAACTTTATAAACTTC-ACAGATTTCATGTGTTCCTCCCTTGTTGTCATTCAACTTTGAACTCT
* * * *
14987 TTCCAATTCTGGATTATCTTGCCCACTGAACTTACAAACCTCGGTCGTCCACTGTTTTGCA-AAA
65 TTCCAATTTTGGATTATCTTGCCCACTGAACTTACAAACCTCAGTCGCCCACTGTTTTTCACAAA
*
15051 AGATACCTTTGCACCGATTGCGAGGTGGTTTATCTCGACCGCTTGC
130 AGATACCTTTGCACCGATTGCGAGGTGGGTTATCTCGACCGCTTGC
* * *
15097 TAAGCTTTATAAACTTCACAGATTTCACGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTT
1 TAAACTTTATAAACTTCACAGATTTCATGTGTTCCTCCCTTGTTGTCATTCAACTTTGAACTCTT
* * *
15162 TCCAATTTTGGATTATCTCGCCCACTGAACTTAAAAACCTTAGTCGCCCACTGTTTTTCACAAAA
66 TCCAATTTTGGATTATCTTGCCCACTGAACTTACAAACCTCAGTCGCCCACTGTTTTTCACAAAA
* * * * * *
15227 GACACCTTTGCACTGATTGCGAGATGGGTTATCTCAACCGCCTAC
131 GATACCTTTGCACCGATTGCGAGGTGGGTTATCTCGACCGCTTGC
* * * **
15272 TAAACTTTATAAATTTCACGGGTTTCATGTGTTCCTCCCTCATTGTCATTCAACTTTGAACTCTT
1 TAAACTTTATAAACTTCACAGATTTCATGTGTTCCTCCCTTGTTGTCATTCAACTTTGAACTCTT
* * * *
15337 TCCAATTTTTGGATTATCTTGCCCACTGAACATACAAACACT-GGTCGCCCA-TGTTTTTTAAAA
66 TCCAA-TTTTGGATTATCTTGCCCACTGAACTTACAAAC-CTCAGTCGCCCACTGTTTTTCACAA
* * *
15400 AAGATACCCTTGCACCAATTGCGAGGTGGGTTATCTCGACCGCCTGC
129 AAGATACCTTTGCACCGATTGCGAGGTGGGTTATCTCGACCGCTTGC
* * *
15447 TAAACTTCATGAA-TTCAACAGACTTCATGTGTTCCTCCCTTGTTGTCATTC-ACATTTGAACTC
1 TAAACTTTATAAACTTC-ACAGATTTCATGTGTTCCTCCCTTGTTGTCATTCAAC-TTTGAACTC
* * * * *
15510 TTTCCGATTTTTGG-TTATCTCGCCCACTAAACTTACAGACCTCAGTTGCCCACTGTTTTTCACA
64 TTTCC-AATTTTGGATTATCTTGCCCACTGAACTTACAAACCTCAGTCGCCCACTGTTTTTCACA
15574 AAAGA
128 AAAGA
15579 AAAAACATGC
Statistics
Matches: 702, Mismatches: 113, Indels: 28
0.83 0.13 0.03
Matches are distributed among these distances:
172 61 0.09
173 84 0.12
174 117 0.17
175 394 0.56
176 44 0.06
177 2 0.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (175 bp):
TAAACTTTATAAACTTCACAGATTTCATGTGTTCCTCCCTTGTTGTCATTCAACTTTGAACTCTT
TCCAATTTTGGATTATCTTGCCCACTGAACTTACAAACCTCAGTCGCCCACTGTTTTTCACAAAA
GATACCTTTGCACCGATTGCGAGGTGGGTTATCTCGACCGCTTGC
Found at i:15256 original size:347 final size:347
Alignment explanation
Indices: 14575--15578 Score: 1401
Period size: 347 Copynumber: 2.9 Consensus size: 347
14565 ACAAACTTCA
* * *
14575 TAAACTTTATAAACTTCACAGGTTTCATGTGTTC-CTCCTTTATTTTCATTCAACTTTGAACTCT
1 TAAACTTTATAAACTTCACAGGTTTCATTTG-ACAC-CC-TTATTGTCATTCAACTTTGAACTCT
* * * * *
14639 TTCCAATTCTGGATTATCTTGCTCATTGAACTTACAAGCCTCAG-CTGCCCACTATTTTTCAAAA
63 TTCCAATTCTGGATTATCTTGCCCACTGAACTTACAAACCTCGGTC-GCCCACTGTTTTTCAAAA
*
14703 ATGATACCTTTGCACCGGTTGCGAGGTGGGTTATCTCGACCGCTTGCTAAGCTTTATAAACTTCA
127 A-GATACCTTTGCACCGATTGCGAGGTGGGTTATCTCGACCGCTTGCTAAGCTTTATAAACTTCA
*
14768 CAGATTTCATGTGTTCCTCCCTTGTTGCCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCT
191 CAGATTTCATGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCT
* * * * *
14833 TGCCCACTAAACTTACAAACCTCAGTCGCCTATTGTTTTTCACAAAAGACACGTTTGCAGTGATT
256 CGCCCACTAAACTTACAAACCTCAGTCGCCCACTGTTTTTCACAAAAGACACCTTTGCACTGATT
* *
14898 GCGAGATGGGTTATCTCAATCACTTAC
321 GCGAGATGGGTTATCTCAACCACCTAC
* * * *
14925 TAAACTTTATAAAC-TCTACAGGTTTCATTTGAGACCCTTGTTGTCATTCAACTTAGAACTATTT
1 TAAACTTTATAAACTTC-ACAGGTTTCATTTGACACCCTTATTGTCATTCAACTTTGAACTCTTT
* *
14989 CCAATTCTGGATTATCTTGCCCACTGAACTTACAAACCTCGGTCGTCCACTGTTTTGCAAAAAGA
65 CCAATTCTGGATTATCTTGCCCACTGAACTTACAAACCTCGGTCGCCCACTGTTTTTCAAAAAGA
*
15054 TACCTTTGCACCGATTGCGAGGTGGTTTATCTCGACCGCTTGCTAAGCTTTATAAACTTCACAGA
130 TACCTTTGCACCGATTGCGAGGTGGGTTATCTCGACCGCTTGCTAAGCTTTATAAACTTCACAGA
*
15119 TTTCACGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCC
195 TTTCATGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCC
* * *
15184 CACTGAACTTAAAAACCTTAGTCGCCCACTGTTTTTCACAAAAGACACCTTTGCACTGATTGCGA
260 CACTAAACTTACAAACCTCAGTCGCCCACTGTTTTTCACAAAAGACACCTTTGCACTGATTGCGA
*
15249 GATGGGTTATCTCAACCGCCTAC
325 GATGGGTTATCTCAACCACCTAC
* * ** * *
15272 TAAACTTTATAAATTTCACGGGTTTCATGTGTTCCTCCCTCATTGTCATTCAACTTTGAACTCTT
1 TAAACTTTATAAACTTCACAGGTTTCAT-T-TGACACCCTTATTGTCATTCAACTTTGAACTCTT
* * *
15337 TCCAATTTTTGGATTATCTTGCCCACTGAACATACAAACACT-GGTCGCCCA-TGTTTTTTAAAA
64 TCCAA-TTCTGGATTATCTTGCCCACTGAACTTACAAAC-CTCGGTCGCCCACTG-TTTTTCAAA
* * * * * *
15400 AAGATACCCTTGCACCAATTGCGAGGTGGGTTATCTCGACCGCCTGCTAAACTTCATGAA-TTCA
126 AAGATACCTTTGCACCGATTGCGAGGTGGGTTATCTCGACCGCTTGCTAAGCTTTATAAACTTC-
* * *
15464 ACAGACTTCATGTGTTCCTCCCTTGTTGTCATTCACATTTGAACTCTTTCCGATTTTTGG-TTAT
190 ACAGATTTCATGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCC-AATTTTGGATTAT
* *
15528 CTCGCCCACTAAACTTACAGACCTCAGTTGCCCACTGTTTTTCACAAAAGA
254 CTCGCCCACTAAACTTACAAACCTCAGTCGCCCACTGTTTTTCACAAAAGA
15579 AAAAACATGC
Statistics
Matches: 583, Mismatches: 60, Indels: 22
0.88 0.09 0.03
Matches are distributed among these distances:
347 228 0.39
348 80 0.14
349 41 0.07
350 225 0.39
351 9 0.02
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (347 bp):
TAAACTTTATAAACTTCACAGGTTTCATTTGACACCCTTATTGTCATTCAACTTTGAACTCTTTC
CAATTCTGGATTATCTTGCCCACTGAACTTACAAACCTCGGTCGCCCACTGTTTTTCAAAAAGAT
ACCTTTGCACCGATTGCGAGGTGGGTTATCTCGACCGCTTGCTAAGCTTTATAAACTTCACAGAT
TTCATGTGTTCCTCCCTTGTTGTCATTCACCTTTGAACTCTTTCCAATTTTGGATTATCTCGCCC
ACTAAACTTACAAACCTCAGTCGCCCACTGTTTTTCACAAAAGACACCTTTGCACTGATTGCGAG
ATGGGTTATCTCAACCACCTAC
Found at i:19566 original size:22 final size:22
Alignment explanation
Indices: 19525--19567 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
19515 ATGAGAGAGA
* *
19525 AAAAGAGAGGAGAAAAGGAATG
1 AAAAGAGAAGACAAAAGGAATG
*
19547 AAAAGAGAAGACAAAGGGAAT
1 AAAAGAGAAGACAAAAGGAAT
19568 AAACAGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.02, G:0.33, T:0.05
Consensus pattern (22 bp):
AAAAGAGAAGACAAAAGGAATG
Found at i:20217 original size:16 final size:16
Alignment explanation
Indices: 20176--20218 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
20166 AAGTCAACGT
*
20176 CCCGAACTCGAAAGTA
1 CCCGAACCCGAAAGTA
* *
20192 CCCGAGCCCGAAATTA
1 CCCGAACCCGAAAGTA
*
20208 CCTGAACCCGA
1 CCCGAACCCGA
20219 GACAATCCGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.37, G:0.19, T:0.12
Consensus pattern (16 bp):
CCCGAACCCGAAAGTA
Found at i:20765 original size:15 final size:15
Alignment explanation
Indices: 20745--20775 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20735 AGGAGTATGT
20745 AGTATAACTAATTAA
1 AGTATAACTAATTAA
*
20760 AGTATAATTAATTAA
1 AGTATAACTAATTAA
20775 A
1 A
20776 TGCATGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (15 bp):
AGTATAACTAATTAA
Found at i:24828 original size:45 final size:46
Alignment explanation
Indices: 24769--24857 Score: 126
Period size: 45 Copynumber: 1.9 Consensus size: 46
24759 AATATACTCT
* *
24769 CTCCGTTCCAAAATAACTGTCC-ATTTTGGGATGAATGTGGTCTCC
1 CTCCATTCCAAAATAACTGTCCAATTTTGGGATAAATGTGGTCTCC
*
24814 CTCCATTCCAAAATAATTGTCCATGATTTTGGGATAAATGTGGT
1 CTCCATTCCAAAATAACTGTCCA--ATTTTGGGATAAATGTGGT
24858 TCCAAATGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
45 20 0.53
48 18 0.47
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (46 bp):
CTCCATTCCAAAATAACTGTCCAATTTTGGGATAAATGTGGTCTCC
Found at i:27061 original size:5 final size:5
Alignment explanation
Indices: 27051--27083 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
27041 GATACATACA
27051 ATTTT ATTTT ATTTT ATTTT ATTTT A-TTT ATTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTT
27084 AAGACCATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:32716 original size:16 final size:17
Alignment explanation
Indices: 32688--32727 Score: 73
Period size: 16 Copynumber: 2.4 Consensus size: 17
32678 TTTTTGATTA
32688 AAAAAATATTTTTTTTT
1 AAAAAATATTTTTTTTT
32705 AAAAAATA-TTTTTTTT
1 AAAAAATATTTTTTTTT
32721 AAAAAAT
1 AAAAAAT
32728 GAGTCAGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAAAATATTTTTTTTT
Found at i:33142 original size:3 final size:3
Alignment explanation
Indices: 33134--33168 Score: 52
Period size: 3 Copynumber: 11.0 Consensus size: 3
33124 TTTGTTTGAT
33134 TTA TTA TTA TTA TTA TTA TTA TTA TATA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA TTA
33169 AGTTTAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 24 0.77
4 7 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:33568 original size:16 final size:15
Alignment explanation
Indices: 33540--33581 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
33530 GTCCCTCACC
33540 ATTTTTTTAAAAAAAT
1 ATTTTTTT-AAAAAAT
33556 ATATTTTTTAAAAAAT
1 AT-TTTTTTAAAAAAT
33572 ATTTTTTTAA
1 ATTTTTTTAA
33582 TCAAAATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.32
16 11 0.44
17 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTTTTAAAAAAT
Found at i:33573 original size:14 final size:15
Alignment explanation
Indices: 33550--33578 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
33540 ATTTTTTTAA
33550 AAAAATATATTTTTT
1 AAAAATATATTTTTT
33565 AAAAA-ATATTTTTT
1 AAAAATATATTTTTT
33579 TAATCAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AAAAATATATTTTTT
Done.