Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014769.1 Corchorus olitorius cultivar O-4 contig14802, 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: 83278
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:284 original size:29 final size:29
Alignment explanation
Indices: 217--321 Score: 147
Period size: 29 Copynumber: 3.6 Consensus size: 29
207 CCCATTTCAC
*** *
217 GGAGGGACTAAATTGATCTCTTTTCAATAGT
1 GGAGGGACTAAATTGA-CAGATTT-AATAAT
*
248 AGAGGGACTAAATTGACAGATTTAATAAT
1 GGAGGGACTAAATTGACAGATTTAATAAT
277 GGAGGGACTAAATTGACAGATTTAATAAT
1 GGAGGGACTAAATTGACAGATTTAATAAT
306 GGAGGGACTAAATTGA
1 GGAGGGACTAAATTGA
322 TCTTTTTTCT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 49 0.72
30 4 0.06
31 15 0.22
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.29
Consensus pattern (29 bp):
GGAGGGACTAAATTGACAGATTTAATAAT
Found at i:6486 original size:22 final size:22
Alignment explanation
Indices: 6444--6496 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
6434 ATACTGGTAA
6444 GTAGATCGACTTATATGAATGT
1 GTAGATCGACTTATATGAATGT
6466 GTAGATCGACTTATATGAATGT
1 GTAGATCGACTTATATGAATGT
6488 GTTAGATCG
1 G-TAGATCG
6497 GCGCTACTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 23 0.77
23 7 0.23
ACGTcount: A:0.30, C:0.09, G:0.25, T:0.36
Consensus pattern (22 bp):
GTAGATCGACTTATATGAATGT
Found at i:6712 original size:17 final size:17
Alignment explanation
Indices: 6687--6720 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6677 TATTCATTTA
*
6687 TGTTTTTGTTCTGTTAT
1 TGTTGTTGTTCTGTTAT
*
6704 TGTTGTTGTTTTGTTAT
1 TGTTGTTGTTCTGTTAT
6721 AGGGGCTGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.03, G:0.21, T:0.71
Consensus pattern (17 bp):
TGTTGTTGTTCTGTTAT
Found at i:8421 original size:19 final size:19
Alignment explanation
Indices: 8394--8433 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
8384 ATGAAAACTT
*
8394 GTCCCTATTTGATGTAATG
1 GTCCATATTTGATGTAATG
*
8413 GTCCATATTTGGTGTAATG
1 GTCCATATTTGATGTAATG
8432 GT
1 GT
8434 ATCATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.42
Consensus pattern (19 bp):
GTCCATATTTGATGTAATG
Found at i:8447 original size:21 final size:19
Alignment explanation
Indices: 8406--8453 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
8396 CCCTATTTGA
*
8406 TGTAATGGTCCATATTTGG
1 TGTAATGGTCCATATTAGG
*
8425 TGTAATGGTATCATTATTAGG
1 TGTAATGGT-CCA-TATTAGG
8446 TGTAATGG
1 TGTAATGG
8454 AAAATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.36
20 2 0.08
21 14 0.56
ACGTcount: A:0.25, C:0.06, G:0.27, T:0.42
Consensus pattern (19 bp):
TGTAATGGTCCATATTAGG
Found at i:11604 original size:3 final size:3
Alignment explanation
Indices: 11592--11711 Score: 112
Period size: 3 Copynumber: 42.0 Consensus size: 3
11582 ATTATACCTG
11592 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
11639 TAA TAA TAA T-A TAA -GA TAG TACT TAC TATA CAA T-A TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA-A TAA TAA TAA TAA TAA
*
11682 CAA T-A TAA T-A TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
11712 GCTTTAATCA
Statistics
Matches: 97, Mismatches: 10, Indels: 20
0.76 0.08 0.16
Matches are distributed among these distances:
2 15 0.15
3 79 0.81
4 3 0.03
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:11686 original size:13 final size:13
Alignment explanation
Indices: 11668--11694 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11658 TACTTACTAT
11668 ACAATATAATATA
1 ACAATATAATATA
11681 ACAATATAATATA
1 ACAATATAATATA
11694 A
1 A
11695 TATAATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
ACAATATAATATA
Found at i:13154 original size:21 final size:24
Alignment explanation
Indices: 13125--13175 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
13115 TTTTGAACTC
13125 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
13148 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
13171 ATTAT
1 ATTAT
13176 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:13170 original size:25 final size:25
Alignment explanation
Indices: 13125--13173 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
13115 TTTTGAACTC
*
13125 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
13150 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
13174 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:20085 original size:6 final size:6
Alignment explanation
Indices: 20074--20122 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
20064 CTGCTAAGCT
* *
20074 TGGGGC TGGGGC TGGGGC TGGGGC TGGGTC TGCGGC TGGGGC TGGGGC
1 TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC TGGGGC
20122 T
1 T
20123 TGATCTTGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.18, G:0.61, T:0.20
Consensus pattern (6 bp):
TGGGGC
Found at i:24774 original size:33 final size:33
Alignment explanation
Indices: 24729--24815 Score: 156
Period size: 33 Copynumber: 2.6 Consensus size: 33
24719 GAAAGGCTGA
24729 GGCTGAGGCCGGGGCCGGGGCTCCGTCGCCTGC
1 GGCTGAGGCCGGGGCCGGGGCTCCGTCGCCTGC
* *
24762 GGCTGAGTCCGGGTCCGGGGCTCCGTCGCCTGC
1 GGCTGAGGCCGGGGCCGGGGCTCCGTCGCCTGC
24795 GGCTGAGGCCGGGGCCGGGGC
1 GGCTGAGGCCGGGGCCGGGGC
24816 CGGGGCTCCG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.03, C:0.34, G:0.49, T:0.13
Consensus pattern (33 bp):
GGCTGAGGCCGGGGCCGGGGCTCCGTCGCCTGC
Found at i:24780 original size:39 final size:39
Alignment explanation
Indices: 24735--24842 Score: 156
Period size: 39 Copynumber: 2.9 Consensus size: 39
24725 CTGAGGCTGA
24735 GGCCGGGGCCGGGGCTCCGTCGCCTGCGGCTGAGT----
1 GGCCGGGGCCGGGGCTCCGTCGCCTGCGGCTGAGTCCGG
* *
24770 --CCGGGTCCGGGGCTCCGTCGCCTGCGGCTGAGGCCGG
1 GGCCGGGGCCGGGGCTCCGTCGCCTGCGGCTGAGTCCGG
24807 GGCCGGGGCCGGGGCTCCGTCGCCTGCGGCTGAGTC
1 GGCCGGGGCCGGGGCTCCGTCGCCTGCGGCTGAGTC
24843 TGGGACTTGA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
33 31 0.49
39 32 0.51
ACGTcount: A:0.03, C:0.36, G:0.47, T:0.14
Consensus pattern (39 bp):
GGCCGGGGCCGGGGCTCCGTCGCCTGCGGCTGAGTCCGG
Found at i:25337 original size:22 final size:22
Alignment explanation
Indices: 25309--25376 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
25299 ATCGTAGAAC
25309 TTTGATTTACTTGGTACAAAAT
1 TTTGATTTACTTGGTACAAAAT
25331 TTTGATTTACTTGGTACAAAAT
1 TTTGATTTACTTGGTACAAAAT
*
25353 TTTGATTTACTTGGTACAACAT
1 TTTGATTTACTTGGTACAAAAT
25375 TT
1 TT
25377 ATCAAATATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.47
Consensus pattern (22 bp):
TTTGATTTACTTGGTACAAAAT
Found at i:27283 original size:31 final size:30
Alignment explanation
Indices: 27245--27349 Score: 97
Period size: 31 Copynumber: 3.5 Consensus size: 30
27235 TTAGACTAAT
*
27245 TGCTCAAATAAGGGCCTAACATTATCGAAAA
1 TGCTCAAATAAGGGCCTAAC-TTATCAAAAA
* * * **
27276 TGCTCAAATAAAGGCCTGATCTT-T-TAATT
1 TGCTCAAATAAGGGCCT-AACTTATCAAAAA
* *
27305 TGGTCAATTAAGGGCCTAACGTTATCAAAAA
1 TGCTCAAATAAGGGCCTAAC-TTATCAAAAA
27336 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
27350 ACTGACGTCA
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
28 2 0.04
29 18 0.32
30 2 0.04
31 32 0.57
32 2 0.04
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACTTATCAAAAA
Found at i:27490 original size:31 final size:31
Alignment explanation
Indices: 27397--27494 Score: 87
Period size: 31 Copynumber: 3.2 Consensus size: 31
27387 ATGCCAGCCG
* * *
27397 TTATTTAAGCATTTTGGCAAACGTTAGACCC
1 TTATTTGAGCATTTTGGAAAACGTTAGGCCC
** **
27428 TTATTTG-GCCAAATT--AAAA-GATCGGGCCC
1 TTATTTGAG-CATTTTGGAAAACG-TTAGGCCC
27457 TTATTTGAGCATTTTGGAAAACGTTAGGCCC
1 TTATTTGAGCATTTTGGAAAACGTTAGGCCC
27488 TTATTTG
1 TTATTTG
27495 GCTAGATTAA
Statistics
Matches: 50, Mismatches: 11, Indels: 12
0.68 0.15 0.16
Matches are distributed among these distances:
28 1 0.02
29 19 0.38
30 2 0.04
31 27 0.54
32 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (31 bp):
TTATTTGAGCATTTTGGAAAACGTTAGGCCC
Found at i:27521 original size:60 final size:60
Alignment explanation
Indices: 27397--27554 Score: 190
Period size: 60 Copynumber: 2.6 Consensus size: 60
27387 ATGCCAGCCG
* * ***
27397 TTATTTAAGCATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGGCCC
1 TTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAAACCC
* * * *
27457 TTATTTGAGCATTTTGGAAAACGTTAGGCCCTTATTTGGCTAGATTAAAAGATCAAACCT
1 TTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAAACCC
* * * **
27517 TTATTTGAGTATTTTAGCAAATGTTAGGGTCTTATTTG
1 TTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
27555 AGCAATTAAC
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 83 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (60 bp):
TTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATCAAACCC
Found at i:27787 original size:19 final size:19
Alignment explanation
Indices: 27763--27802 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
27753 TTGTTTCCAG
*
27763 ACAGAATCTCTTTTGTGTT
1 ACAGAATCCCTTTTGTGTT
27782 ACAGAATCCCTTTTGTGTT
1 ACAGAATCCCTTTTGTGTT
27801 AC
1 AC
27803 TATGGAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (19 bp):
ACAGAATCCCTTTTGTGTT
Found at i:28050 original size:2 final size:2
Alignment explanation
Indices: 28043--28076 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28033 AACCAAGACA
28043 AT 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 AT
28077 TAAAGCTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31308 original size:99 final size:102
Alignment explanation
Indices: 31123--31311 Score: 249
Period size: 99 Copynumber: 1.9 Consensus size: 102
31113 CCTGCGAGTG
* * *
31123 CCTCCCAACAAGCAAATATTAGCAGTTTGTCATCACAGTCACACAATGGTGCAAGTGTTCGGCAG
1 CCTCCCAACAAGCAAATACTAGCAGTTTGTCAT-ACA-T-ACACAATGGTGCAAATGTTCCGCAG
*
31188 CAAAACATGAATACTCTTCAGTCAATTGTTGCAAGTAGTA
63 CAAAACATGAATACTATTCAGTCAATTGTTGCAAGTAGTA
* * * *
31228 CCTCCCAGCAAGCAAATACTAGCAGTTTGTCAT-C-T-CAGAGTGGTGTAAATGTTCCGCAGCAA
1 CCTCCCAACAAGCAAATACTAGCAGTTTGTCATACATACACAATGGTGCAAATGTTCCGCAGCAA
*
31290 AACATGAATCCTATTCAGTCAA
66 AACATGAATACTATTCAGTCAA
31312 ATCTCTACGA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
99 42 0.56
101 1 0.01
103 1 0.01
105 31 0.41
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (102 bp):
CCTCCCAACAAGCAAATACTAGCAGTTTGTCATACATACACAATGGTGCAAATGTTCCGCAGCAA
AACATGAATACTATTCAGTCAATTGTTGCAAGTAGTA
Found at i:31490 original size:75 final size:72
Alignment explanation
Indices: 31399--31549 Score: 241
Period size: 75 Copynumber: 2.1 Consensus size: 72
31389 CAGATGCAAT
*
31399 CACAACAGTATTACCAGCAAGTGAAGCAAGAGTTTCCTACACAAGAGTTTCAGACGCGCC-TGAT
1 CACAACAGTATTACCAGCAAGTGAAGCAAGAGTTTCCTACACAAGAGTTTCAGACGCACCAT-AT
*
31463 GCCACAGG
65 GCCACAGA
31471 CACAACAGTACTATCACCAGCAAGTGAAGCAAGAGTTTCCTACACAAGAGTTTCAGACGCACCAT
1 CACAACAGTA-T-T-ACCAGCAAGTGAAGCAAGAGTTTCCTACACAAGAGTTTCAGACGCACCAT
31536 ATGCCACAGA
63 ATGCCACAGA
31546 CACA
1 CACA
31550 GCAACATCAG
Statistics
Matches: 73, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
72 10 0.14
73 1 0.01
74 1 0.01
75 60 0.82
76 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.17
Consensus pattern (72 bp):
CACAACAGTATTACCAGCAAGTGAAGCAAGAGTTTCCTACACAAGAGTTTCAGACGCACCATATG
CCACAGA
Found at i:33310 original size:24 final size:24
Alignment explanation
Indices: 33281--33383 Score: 127
Period size: 24 Copynumber: 4.3 Consensus size: 24
33271 AGCCAACAAG
*
33281 ATTAGATAAACTCAGCCAAGAGGA
1 ATTAGATAAACTCAGCCAAAAGGA
* *
33305 ATTAGATGAAGTCATG-CAAAAGGA
1 ATTAGATAAACTCA-GCCAAAAGGA
* *
33329 ATTAGATGAAGTCAGCCAAAAGGA
1 ATTAGATAAACTCAGCCAAAAGGA
* *
33353 ATTAGATAAACTCAGCCTAGAGGA
1 ATTAGATAAACTCAGCCAAAAGGA
33377 ATTAGAT
1 ATTAGAT
33384 GAAGTTTTGC
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
23 1 0.01
24 68 0.97
25 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.22, T:0.20
Consensus pattern (24 bp):
ATTAGATAAACTCAGCCAAAAGGA
Found at i:33398 original size:24 final size:25
Alignment explanation
Indices: 33292--33410 Score: 122
Period size: 24 Copynumber: 4.9 Consensus size: 25
33282 TTAGATAAAC
33292 TCAGCCAAGAGGAATTAGATGAAG-
1 TCAGCCAAGAGGAATTAGATGAAGT
*
33316 TCATG-CAAAAGGAATTAGATGAAG-
1 TCA-GCCAAGAGGAATTAGATGAAGT
* **
33340 TCAGCCAAAAGGAATTAGAT-AAAC
1 TCAGCCAAGAGGAATTAGATGAAGT
*
33364 TCAGCCTAGAGGAATTAGATGAAGT
1 TCAGCCAAGAGGAATTAGATGAAGT
** *
33389 TTTG-CAAGAGGAATTAAATGAA
1 TCAGCCAAGAGGAATTAGATGAA
33411 CTCAGGCTCA
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
23 3 0.04
24 73 0.90
25 5 0.06
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.21
Consensus pattern (25 bp):
TCAGCCAAGAGGAATTAGATGAAGT
Found at i:33401 original size:48 final size:47
Alignment explanation
Indices: 33281--33415 Score: 146
Period size: 48 Copynumber: 2.8 Consensus size: 47
33271 AGCCAACAAG
* * *
33281 ATTAGATAAACTCAGCCAAGAGGAATTAGATGAAGTCATGCAAAAGGA
1 ATTAGATGAAGTCAGCCAAGAGGAATTAGATGAACTCA-GCAAAAGGA
* * * *
33329 ATTAGATGAAGTCAGCCAAAAGGAATTAGATAAACTCAGCCTAGAGGA
1 ATTAGATGAAGTCAGCCAAGAGGAATTAGATGAACTCAG-CAAAAGGA
** *
33377 ATTAGATGAAGTTTTG-CAAGAGGAATTAAATGAACTCAG
1 ATTAGATGAAG-TCAGCCAAGAGGAATTAGATGAACTCAG
33416 GCTCAGCCAA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
47 1 0.01
48 70 0.96
49 2 0.03
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (47 bp):
ATTAGATGAAGTCAGCCAAGAGGAATTAGATGAACTCAGCAAAAGGA
Found at i:33401 original size:72 final size:72
Alignment explanation
Indices: 33281--33415 Score: 216
Period size: 72 Copynumber: 1.9 Consensus size: 72
33271 AGCCAACAAG
* *
33281 ATTAGATAAACTCAGCCAAGAGGAATTAGATGAAGTCATGCAAAAGGAATTAGATGAAGTCAGCC
1 ATTAGATAAACTCAGCCAAGAGGAATTAGATGAAGTCATGCAAAAGGAATTAAATGAACTCAGCC
33346 AAAAGGA
66 AAAAGGA
* ** *
33353 ATTAGATAAACTCAGCCTAGAGGAATTAGATGAAGTTTTGCAAGAGGAATTAAATGAACTCAG
1 ATTAGATAAACTCAGCCAAGAGGAATTAGATGAAGTCATGCAAAAGGAATTAAATGAACTCAG
33416 GCTCAGCCAA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 57 1.00
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (72 bp):
ATTAGATAAACTCAGCCAAGAGGAATTAGATGAAGTCATGCAAAAGGAATTAAATGAACTCAGCC
AAAAGGA
Found at i:33832 original size:24 final size:23
Alignment explanation
Indices: 33802--33850 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
33792 TGAGAAAACT
33802 ATAATATA-ATATATAATAATAGTA
1 ATAATATATATA-ATAATAAT-GTA
33826 ATAATATATATAATAATAATGTA
1 ATAATATATATAATAATAATGTA
33849 AT
1 AT
33851 GTAATAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 5 0.21
24 16 0.67
25 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
ATAATATATATAATAATAATGTA
Found at i:42123 original size:9 final size:9
Alignment explanation
Indices: 42109--42139 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42099 GCTTCCGCAA
42109 CAGCAACAG
1 CAGCAACAG
42118 CAGCAACAG
1 CAGCAACAG
*
42127 CAGCAGCAG
1 CAGCAACAG
42136 CAGC
1 CAGC
42140 TATATCATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.39, C:0.35, G:0.26, T:0.00
Consensus pattern (9 bp):
CAGCAACAG
Found at i:42534 original size:3 final size:3
Alignment explanation
Indices: 42528--42557 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
42518 CTCCACCCTC
42528 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
42558 ACAACAACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:43449 original size:29 final size:27
Alignment explanation
Indices: 43403--43504 Score: 96
Period size: 29 Copynumber: 3.6 Consensus size: 27
43393 CTGGGTCTTC
*
43403 TTTGATTGTAATAAAATTCAGGGGCTTG
1 TTTGATTGCAATAAAATT-AGGGGCTTG
*
43431 TTTGATTGCATATAAAATTTAGGAGCTTG
1 TTTGATTGCA-ATAAAA-TTAGGGGCTTG
** * * *
43460 TTTGATTTTATGTAAAATATAGGGGCATA
1 TTTGATTGCA-ATAAAAT-TAGGGGCTTG
43489 TTTGATTGCAATAAAA
1 TTTGATTGCAATAAAA
43505 AGCCTTAGGA
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
28 15 0.25
29 43 0.72
30 2 0.03
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (27 bp):
TTTGATTGCAATAAAATTAGGGGCTTG
Found at i:45898 original size:3 final size:3
Alignment explanation
Indices: 45884--45916 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
45874 GCTACTTCAA
*
45884 CAG CAA CAG CAG CAG CAG CAG CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
45917 TTGCACCAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.33, G:0.30, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:49031 original size:32 final size:32
Alignment explanation
Indices: 49014--49158 Score: 138
Period size: 32 Copynumber: 4.5 Consensus size: 32
49004 CACACAACTA
49014 ATCGGGAATCTAAATCAATCAGGAATCTAAAT
1 ATCGGGAATCTAAATCAATCAGGAATCTAAAT
49046 ATCGGGAATCTAAATCAATCAGGAATCTAAAT
1 ATCGGGAATCTAAATCAATCAGGAATCTAAAT
* *
49078 CAATCGGGACA-C-AACT-AATCGGGAATCTAAAT
1 --ATCGGGA-ATCTAAATCAATCAGGAATCTAAAT
* * *
49110 CAATCAGAAATCTAAAT--ATCGGGAATCTAAAT
1 --ATCGGGAATCTAAATCAATCAGGAATCTAAAT
*
49142 CAATCAGGAATCTAAAT
1 --ATCGGGAATCTAAAT
49159 TAATTGGGAC
Statistics
Matches: 102, Mismatches: 6, Indels: 10
0.86 0.05 0.08
Matches are distributed among these distances:
31 1 0.01
32 86 0.84
33 6 0.06
34 8 0.08
35 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.23
Consensus pattern (32 bp):
ATCGGGAATCTAAATCAATCAGGAATCTAAAT
Found at i:49071 original size:49 final size:50
Alignment explanation
Indices: 49013--49158 Score: 194
Period size: 49 Copynumber: 3.0 Consensus size: 50
49003 GCACACAACT
* *
49013 AATCGGGAATCTAAATCAATCAGGAATCTAAAT-ATCGGGAATCTAAATC
1 AATCAGGAATCTAAATCAATCGGGAATCTAAATAATCGGGAATCTAAATC
*
49062 AATCAGGAATCTAAATCAATCGGGACA-C-AACTAATCGGGAATCTAAATC
1 AATCAGGAATCTAAATCAATCGGGA-ATCTAAATAATCGGGAATCTAAATC
* *
49111 AATCAGAAATCTAAAT--ATCGGGAATCTAAATCAATCAGGAATCTAAAT
1 AATCAGGAATCTAAATCAATCGGGAATCTAAAT-AATCGGGAATCTAAAT
49159 TAATTGGGAC
Statistics
Matches: 86, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
46 1 0.01
47 8 0.09
48 6 0.07
49 70 0.81
50 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (50 bp):
AATCAGGAATCTAAATCAATCGGGAATCTAAATAATCGGGAATCTAAATC
Found at i:49125 original size:81 final size:81
Alignment explanation
Indices: 48990--49174 Score: 334
Period size: 81 Copynumber: 2.3 Consensus size: 81
48980 ACAACTCGAT
* *
48990 TCTAAATCAATCGGCACACAACTAATCGGGAATCTAAATCAATCAGGAATCTAAATATCGGGAAT
1 TCTAAATCAATCGGGACACAACTAATCGGGAATCTAAATCAATCAGAAATCTAAATATCGGGAAT
49055 CTAAATCAATCAGGAA
66 CTAAATCAATCAGGAA
49071 TCTAAATCAATCGGGACACAACTAATCGGGAATCTAAATCAATCAGAAATCTAAATATCGGGAAT
1 TCTAAATCAATCGGGACACAACTAATCGGGAATCTAAATCAATCAGAAATCTAAATATCGGGAAT
49136 CTAAATCAATCAGGAA
66 CTAAATCAATCAGGAA
* *
49152 TCTAAATTAATTGGGACACAACT
1 TCTAAATCAATCGGGACACAACT
49175 CGGTTTTCTA
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 100 1.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.23
Consensus pattern (81 bp):
TCTAAATCAATCGGGACACAACTAATCGGGAATCTAAATCAATCAGAAATCTAAATATCGGGAAT
CTAAATCAATCAGGAA
Found at i:49681 original size:6 final size:6
Alignment explanation
Indices: 49670--49707 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
49660 ATTTATTCTA
49670 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TT
49708 GTGAAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTCTTT
Found at i:51339 original size:12 final size:12
Alignment explanation
Indices: 51322--51353 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
51312 TACCCTATGT
51322 AAACACGACACG
1 AAACACGACACG
51334 AAACACGACACG
1 AAACACGACACG
51346 AAACACGA
1 AAACACGA
51354 ATTGCCAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.31, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:52132 original size:123 final size:121
Alignment explanation
Indices: 51913--52133 Score: 302
Period size: 123 Copynumber: 1.8 Consensus size: 121
51903 CTTTTTAAAT
* *
51913 TAAAATGATGAAAATAACATAATTATAAAATATTGAATTTAATTAAATGAAAATAAAATTTTTAG
1 TAAAATGATAAAAATAACATAATTATAAAATATTGAATTTAATTAAATAAAAATAAAATTTTTAG
*
51978 TAGAATAGAACTATATATTAAAAAATTTAATATATCCAAAATTTCATTGAAAGATAG
66 TAGAATAAAACTATATATTAAAAAA-TTAATATATCCAAAATTTCATTGAAAGATAG
* * * *
52035 TAAAATGATAAAAATAA-AGTAATTATAAAGATATTGGATTTAATTGAATAAAAATAGAGTTTTT
1 TAAAATGATAAAAATAACA-TAATTATAAA-ATATTGAATTTAATTAAATAAAAATAAAATTTTT
* *
52099 AGTAGAATAAAATTATAATAGTTAAATAA-TAATAT
64 AGTAGAATAAAACTAT-ATA-TTAAAAAATTAATAT
52134 TTAAAAAATA
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
121 1 0.01
122 26 0.30
123 49 0.57
124 3 0.03
125 7 0.08
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (121 bp):
TAAAATGATAAAAATAACATAATTATAAAATATTGAATTTAATTAAATAAAAATAAAATTTTTAG
TAGAATAAAACTATATATTAAAAAATTAATATATCCAAAATTTCATTGAAAGATAG
Found at i:54088 original size:12 final size:12
Alignment explanation
Indices: 54071--54103 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
54061 ACCACCCTGT
54071 TTCTTCTTCTCC
1 TTCTTCTTCTCC
54083 TTCTTCTTCTCC
1 TTCTTCTTCTCC
54095 TTCTTCTTC
1 TTCTTCTTC
54104 CTCAGCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (12 bp):
TTCTTCTTCTCC
Found at i:64077 original size:70 final size:70
Alignment explanation
Indices: 63994--64139 Score: 283
Period size: 70 Copynumber: 2.1 Consensus size: 70
63984 GCTTTTCAAG
63994 GAATTAAGTTAAGCATTAATTTTTGGTTGAAATACCAATGTAAATTATAGTAAGCTTTAGTTATT
1 GAATTAAGTTAAGCATTAATTTTTGGTTGAAATACCAATGTAAATTATAGTAAGCTTTAGTTATT
64059 ATTTA
66 ATTTA
64064 GAATTAAGTTAAGCATTAATTTTTGGTTGAAATACCAATGTAAATTATAGTAAGCTTTAGTTATT
1 GAATTAAGTTAAGCATTAATTTTTGGTTGAAATACCAATGTAAATTATAGTAAGCTTTAGTTATT
64129 ATTTA
66 ATTTA
*
64134 GTATTA
1 GAATTA
64140 CTAGATTTAG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 75 1.00
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.43
Consensus pattern (70 bp):
GAATTAAGTTAAGCATTAATTTTTGGTTGAAATACCAATGTAAATTATAGTAAGCTTTAGTTATT
ATTTA
Found at i:65428 original size:40 final size:40
Alignment explanation
Indices: 65354--65429 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
65344 AAAAAAACCC
*** *
65354 TTTTTTTAATGAATTAGATCTTTTTTCTCGAATAATATAA
1 TTTTTTTAATGAATTAGATCTCAATTCTAGAATAATATAA
* *
65394 TTTTTTTAATGAATTATATCTCAATTCTATAATAAT
1 TTTTTTTAATGAATTAGATCTCAATTCTAGAATAAT
65430 TATTTCCATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (40 bp):
TTTTTTTAATGAATTAGATCTCAATTCTAGAATAATATAA
Found at i:65484 original size:2 final size:2
Alignment explanation
Indices: 65477--65502 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
65467 ACATGATTAC
65477 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
65503 ACCCTAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:76741 original size:18 final size:18
Alignment explanation
Indices: 76718--76753 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
76708 ATAATAAGGA
*
76718 TCATTCAAAGTCAGTTCC
1 TCATTCAAAGTCAATTCC
76736 TCATTCAAAGTCAATTCC
1 TCATTCAAAGTCAATTCC
76754 CTAAATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (18 bp):
TCATTCAAAGTCAATTCC
Found at i:81727 original size:20 final size:20
Alignment explanation
Indices: 81702--81739 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
81692 TTTATCCTCT
81702 AATAGGTAGTTTTTATTTAA
1 AATAGGTAGTTTTTATTTAA
81722 AATAGGTAGTTTTTATTT
1 AATAGGTAGTTTTTATTT
81740 TATTTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (20 bp):
AATAGGTAGTTTTTATTTAA
Done.