Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012489.1 Corchorus olitorius cultivar O-4 contig12522, 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: 49324
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:74 original size:40 final size:40
Alignment explanation
Indices: 13--390 Score: 411
Period size: 40 Copynumber: 9.2 Consensus size: 40
3 GGAAGGTCCA
13 GTGTTGTTTAAAATTCCCAGTTTGCCCTTCCTCATCGGAAG
1 GTGTTGTTT-AAATTCCCAGTTTGCCCTTCCTCATCGGAAG
*
54 GTGTTGTTTAAATTCCCAGTTTGCCCTTTCTCATCGGAAG
1 GTGTTGTTTAAATTCCCAGTTTGCCCTTCCTCATCGGAAG
*
94 GTGTTGTTTAAAATTCCCAGTTTGCCATTCCTCATCGGAAG
1 GTGTTGTTT-AAATTCCCAGTTTGCCCTTCCTCATCGGAAG
*
135 GTGTCGATTTAAATTCCCAGTTTGCCCTTCCTCATCGGAAG
1 GTGTTG-TTTAAATTCCCAGTTTGCCCTTCCTCATCGGAAG
* * * * *
176 GTGTTG-TCAGCATTCCCTGTTTGTCCTTCCTCATCGGAAA
1 GTGTTGTTTA-AATTCCCAGTTTGCCCTTCCTCATCGGAAG
* * * *
216 GTATTGTTTAAGTTCACCAGTTTGTCCTTCCTCACCGGAAG
1 GTGTTGTTTAAATTC-CCAGTTTGCCCTTCCTCATCGGAAG
* * *
257 GTGTTGTTTAGATTTCCAGTTTGTCCTTCCTCATCGGAAG
1 GTGTTGTTTAAATTCCCAGTTTGCCCTTCCTCATCGGAAG
* * *
297 GTGTTGTTTAAAGCCCATTCCTTCCAGTTTGCCCTTCCCCACCAGAAG
1 GTGTTGTTT-AA----ATT-C--CCAGTTTGCCCTTCCTCATCGGAAG
* * *
345 GTGTTGATTT-CATTCCC-GTTATGCCCTTCCCCACCGGAAG
1 GTGTTG-TTTAAATTCCCAGTT-TGCCCTTCCTCATCGGAAG
385 GTGTTG
1 GTGTTG
391 ACTTCATTCT
Statistics
Matches: 291, Mismatches: 31, Indels: 31
0.82 0.09 0.09
Matches are distributed among these distances:
39 5 0.02
40 132 0.45
41 114 0.39
42 4 0.01
43 3 0.01
45 3 0.01
48 27 0.09
49 3 0.01
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.37
Consensus pattern (40 bp):
GTGTTGTTTAAATTCCCAGTTTGCCCTTCCTCATCGGAAG
Found at i:191 original size:81 final size:80
Alignment explanation
Indices: 13--308 Score: 407
Period size: 81 Copynumber: 3.6 Consensus size: 80
3 GGAAGGTCCA
* *
13 GTGTTGTTTAAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCAGTTTGC
1 GTGTTGTTT-AGATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCAGTTTGC
*
78 CCTTTCTCATCGGAAG
65 CCTTCCTCATCGGAAG
* *
94 GTGTTGTTTAAAATTCCCAGTTTG-CCATTCCTCATCGGAAGGTGTCGATTTAAATTCCCAGTTT
1 GTGTTGTTT-AGATTCCCAGTTTGTCC-TTCCTCATCGGAAGGTGTTG-TTTAAATTCCCAGTTT
158 GCCCTTCCTCATCGGAAG
63 GCCCTTCCTCATCGGAAG
* * * * *
176 GTGTTG-TCAGCATTCCCTGTTTGTCCTTCCTCATCGGAAAGTATTGTTTAAGTTCACCAGTTTG
1 GTGTTGTTTAG-ATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTTAAATTC-CCAGTTTG
* *
240 TCCTTCCTCACCGGAAG
64 CCCTTCCTCATCGGAAG
*
257 GTGTTGTTTAGATTTCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTTAAA
1 GTGTTGTTTAGATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTTAAA
309 GCCCATTCCT
Statistics
Matches: 192, Mismatches: 17, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
80 11 0.06
81 137 0.71
82 44 0.23
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.38
Consensus pattern (80 bp):
GTGTTGTTTAGATTCCCAGTTTGTCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCAGTTTGCC
CTTCCTCATCGGAAG
Found at i:391 original size:40 final size:39
Alignment explanation
Indices: 318--430 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 39
308 AGCCCATTCC
*
318 TTCCAGTTTGCCCTTCCCCACCAGAAGGTGTTGATTTCA
1 TTCCAGTTTGCCCTTCCCCACCAGAAGGTGTTGACTTCA
* *
357 TTCCCGTTATGCCCTTCCCCACCGGAAGGTGTTGACTTCA
1 TTCCAGTT-TGCCCTTCCCCACCAGAAGGTGTTGACTTCA
** ***
397 TTCTTGTTTTGCCCTTCCCGGTCAGAAGGTGTTG
1 TTCCAG-TTTGCCCTTCCCCACCAGAAGGTGTTG
431 TTTTCAATAT
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 7 0.11
40 54 0.86
41 2 0.03
ACGTcount: A:0.14, C:0.30, G:0.21, T:0.35
Consensus pattern (39 bp):
TTCCAGTTTGCCCTTCCCCACCAGAAGGTGTTGACTTCA
Found at i:474 original size:48 final size:48
Alignment explanation
Indices: 402--783 Score: 595
Period size: 48 Copynumber: 8.0 Consensus size: 48
392 CTTCATTCTT
*
402 GTTTTGCCCTTCCCGGTCAGAAGGTGTTGTTTTCAATATTTTATTCCC
1 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCC
* * * *
450 ATTTTGCCCTCCCCGGTTGGAAGGTGTTGTTTTCAATGTTTTATTCCC
1 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCC
**
498 GTTTTG-CCTTCCCGGTCGGAACGGTGTTGTTTTCAATATTTTATTCAT
1 GTTTTGCCCTTCCCGGTCGGAA-GGTGTTGTTTTCAATATTTTATTCCC
*
546 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATTCCC
1 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCC
* * *
594 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCTC
1 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCC
* *
642 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCC
1 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCC
* * *
690 GTTTTGCCCTTCCCGGTTGGAAGGTGTTGTATTCGATATTTTATTCCC
1 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCC
*
738 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTC
1 GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTC
784 TTGTCTTCAA
Statistics
Matches: 307, Mismatches: 25, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
47 13 0.04
48 279 0.91
49 15 0.05
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (48 bp):
GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCC
Found at i:3038 original size:12 final size:12
Alignment explanation
Indices: 3007--3051 Score: 81
Period size: 12 Copynumber: 3.7 Consensus size: 12
2997 TTTTTTTGGG
3007 TTTAGGAATGAC
1 TTTAGGAATGAC
3019 TATTAGGAATGAC
1 T-TTAGGAATGAC
3032 TTTAGGAATGAC
1 TTTAGGAATGAC
3044 TTTAGGAA
1 TTTAGGAA
3052 CGAAAATATC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 20 0.62
13 12 0.38
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (12 bp):
TTTAGGAATGAC
Found at i:5190 original size:2 final size:2
Alignment explanation
Indices: 5183--5222 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5173 TTCTTATCTC
5183 AT AT AT 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 AT AT AT
5223 GAACCCATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5943 original size:21 final size:21
Alignment explanation
Indices: 5913--5962 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
5903 GGTGTATTGC
*
5913 TCTATTGATATTGGATATGCA
1 TCTATCGATATTGGATATGCA
5934 TCTATCGATATTGGATATGCA
1 TCTATCGATATTGGATATGCA
5955 TCTATCGA
1 TCTATCGA
5963 AGATTTGATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (21 bp):
TCTATCGATATTGGATATGCA
Found at i:14291 original size:14 final size:14
Alignment explanation
Indices: 14272--14299 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
14262 TGACCCAAAC
14272 GGACAGATAACATG
1 GGACAGATAACATG
14286 GGACAGATAACATG
1 GGACAGATAACATG
14300 TATGATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (14 bp):
GGACAGATAACATG
Found at i:14715 original size:177 final size:176
Alignment explanation
Indices: 14324--14805 Score: 522
Period size: 177 Copynumber: 2.7 Consensus size: 176
14314 GCTCTGGATA
* *
14324 TCCGATAAAGATGATTCAAGTGTCTATTAAAAGGTTGTTCCATGATCTACAACTTTCATGAAGGA
1 TCCGATAAAGGTGATTCAAGTGTCTATTAAAAGGTTGTTCCATGATTTACAACTTTCATGAA-GA
* *
14389 CTCGAAAA-CTAAATTTAATGTTTCAAGTATAAAAAATGCTGCCGAAAAATTAGTTGTTTCGGTT
65 CT-GAAAAGCTAAATTTAATATTTCAAGTAT-AAAAATGCTTCCGAAAAATTAGTTGTTTCGGTT
** *
14453 AACGGGAATAGACGATCCACTAAATATTACATAACTTTTGCTTCATATG
128 AACGGGAATAGACGATCCACTAAATATTACATAACTTTTGCACCAGATG
** ** * * * * *
14502 TCTAATTGAGGTGATTCAATTGTCTCTTACAAGGTTGTTCCATGATTTATAACTTTCATAAATGA
1 TCCGATAAAGGTGATTCAAGTGTCTATTAAAAGGTTGTTCCATGATTTACAACTTTCATGAA-GA
* * *
14567 CTGAAAAGCTAAATTTATTATTTCAAGTATAAAAATGCTTCCAAAAAATTAGTTGTTTCGGTTAT
65 CTGAAAAGCTAAATTTAATATTTCAAGTATAAAAATGCTTCCGAAAAATTAGTTGTTTCGGTTAA
* * * * *
14632 TGGGAATGGACCG-TTCACTTAATATTACATAATTTTTGCACCAGATG
130 CGGGAATAGA-CGATCCACTAAATATTACATAACTTTTGCACCAGATG
* * * * *
14679 TCCGACAAAGGTGGTTCAAGTAG-CTGTTAAAAGGTTGTTCCGTGATTTACAATTTTCATGAAGA
1 TCCGATAAAGGTGATTCAAGT-GTCTATTAAAAGGTTGTTCCATGATTTACAACTTTCATGAAGA
* ** * * * * * *
14743 C-GCGAAAGCTAAATTTGGTATTTCAAATACCAAAAATGTTTCTGAAAAATTTGTTATTTCGGT
65 CTG-AAAAGCTAAATTTAATATTTCAAGTA-TAAAAATGCTTCCGAAAAATTAGTTGTTTCGGT
14806 GGACTTAAGT
Statistics
Matches: 251, Mismatches: 48, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
175 1 0.00
176 25 0.10
177 147 0.59
178 78 0.31
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (176 bp):
TCCGATAAAGGTGATTCAAGTGTCTATTAAAAGGTTGTTCCATGATTTACAACTTTCATGAAGAC
TGAAAAGCTAAATTTAATATTTCAAGTATAAAAATGCTTCCGAAAAATTAGTTGTTTCGGTTAAC
GGGAATAGACGATCCACTAAATATTACATAACTTTTGCACCAGATG
Found at i:20246 original size:29 final size:29
Alignment explanation
Indices: 20212--20284 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
20202 GCCGCCCGAA
*
20212 AAGGGCTTATTTGGCTT-TATTAAGAGTTC
1 AAGGGCTTATTTGGCTTCAATT-AGAGTTC
*
20241 AGGGGCTTATTTGG-TTGCAATTAGAGTTC
1 AAGGGCTTATTTGGCTT-CAATTAGAGTTC
*
20270 AAAGGCTTATTTGGC
1 AAGGGCTTATTTGGC
20285 CGTTTTGTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 2 0.05
29 32 0.86
30 3 0.08
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.38
Consensus pattern (29 bp):
AAGGGCTTATTTGGCTTCAATTAGAGTTC
Found at i:31292 original size:6 final size:6
Alignment explanation
Indices: 31271--31329 Score: 64
Period size: 6 Copynumber: 9.2 Consensus size: 6
31261 CTGCAAAATT
* *
31271 AACAAA AACGCAAA AACAAA AACAAA AACGAA AACAAA ATACGAAA AATAAA
1 AACAAA AA--CAAA AACAAA AACAAA AACAAA AACAAA A-AC-AAA AACAAA
31323 AACAAA A
1 AACAAA A
31330 CTAAAGGAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
6 32 0.71
7 3 0.07
8 10 0.22
ACGTcount: A:0.76, C:0.15, G:0.05, T:0.03
Consensus pattern (6 bp):
AACAAA
Found at i:31296 original size:20 final size:18
Alignment explanation
Indices: 31271--31329 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 18
31261 CTGCAAAATT
31271 AACAAAAACGCAAAAACAAA
1 AACAAAAACG--AAAACAAA
31291 AACAAAAACGAAAACAAA
1 AACAAAAACGAAAACAAA
**
31309 ATACGAAAAATAAAAACAAA
1 A-AC-AAAAACGAAAACAAA
31329 A
1 A
31330 CTAAAGGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.26
19 2 0.06
20 24 0.69
ACGTcount: A:0.76, C:0.15, G:0.05, T:0.03
Consensus pattern (18 bp):
AACAAAAACGAAAACAAA
Found at i:37890 original size:18 final size:18
Alignment explanation
Indices: 37859--37893 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37849 GTCAAAGTTG
*
37859 AAGAAAAAATGAAAAAAA
1 AAGAAAAAAGGAAAAAAA
*
37877 AAGAAGAAAGGAAAAAA
1 AAGAAAAAAGGAAAAAA
37894 TGAAAAAGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (18 bp):
AAGAAAAAAGGAAAAAAA
Found at i:41722 original size:2 final size:2
Alignment explanation
Indices: 41709--41741 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
41699 TGCTTTCCAT
*
41709 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41742 TCTACTGTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43822 original size:61 final size:61
Alignment explanation
Indices: 43749--43866 Score: 175
Period size: 62 Copynumber: 1.9 Consensus size: 61
43739 TTCAGTTTAC
*
43749 TTCAGTTGATCCAGGGCGATCC-TTATTCAATTCATTTCAATTGACCCAGGGTGGTCCTAT
1 TTCAGTTGATCCAGGGCGATCCTTTATTCAATTCATTTCAATTGACCCAGGGCGGTCCTAT
* * * *
43809 TTCAGTTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTC
1 TTCAG-TTGATCCAGGGCGATCCTTTATTCAATTCATTTCAATTGACCCAGGGCGGTC
43867 TTTCTTCAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 5 0.10
61 17 0.33
62 29 0.57
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.36
Consensus pattern (61 bp):
TTCAGTTGATCCAGGGCGATCCTTTATTCAATTCATTTCAATTGACCCAGGGCGGTCCTAT
Found at i:43823 original size:26 final size:27
Alignment explanation
Indices: 43789--43843 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
43779 TTCATTTCAA
* *
43789 TTGACCCAGGGTGGTCCTAT-TTCAGT
1 TTGACCCAGGGCGATCCTATCTTCAGT
* *
43815 TTGATCCAGGGCGATCCTTTCTTCAGT
1 TTGACCCAGGGCGATCCTATCTTCAGT
43842 TT
1 TT
43844 ATTTCAGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (27 bp):
TTGACCCAGGGCGATCCTATCTTCAGT
Found at i:43896 original size:36 final size:35
Alignment explanation
Indices: 43806--44784 Score: 1217
Period size: 36 Copynumber: 27.3 Consensus size: 35
43796 AGGGTGGTCC
43806 TATTTCAGTTTGATCCAGGGCGATCCTTTCTTCAGTT
1 TATTTCAG-TTGATCCAGGGCGAT-CTTTCTTCAGTT
* *
43843 TATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTT
1 TATTTCAGTTGATCCAGGGCGATCTTTCTTCAGTT
* *
43878 TATTTCAATTTGATCCAGGGTGATCCTTTCTTCAGTT
1 TATTTC-AGTTGATCCAGGGCGAT-CTTTCTTCAGTT
*
43915 TATTTCAGTTTGATCCAGGGCGATCCTTTCTTCAGGT
1 TATTTCAG-TTGATCCAGGGCGAT-CTTTCTTCAGTT
* * * *
43952 TATTTCAGTTGACCCAGGGTGGTCTCTCTTCAGTT
1 TATTTCAGTTGATCCAGGGCGATCTTTCTTCAGTT
* * * *
43987 TATTTCAGTTGACCCAGGGTGGTCTCTCTTCAGTT
1 TATTTCAGTTGATCCAGGGCGATCTTTCTTCAGTT
44022 TATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTT
1 TATTTCAGTTGATCCAGGGCGAT-CTTTCTTCAG-TT
44059 TATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTT
1 TATTTCAGTTGATCCAGGGCGATC-TTTCTTCAGTT
* *
44095 TATTTCAATTGATCCAGGGCAATACTTTCTTCAGTT
1 TATTTCAGTTGATCCAGGGCGAT-CTTTCTTCAGTT
* * *
44131 TATTTCAGTTGA-CCAGGGCGGTCTTTCTCCATTT
1 TATTTCAGTTGATCCAGGGCGATCTTTCTTCAGTT
* * *
44165 TATTTGAGTTGACCCAGGGCGGTCTTTCTTCAGTT
1 TATTTCAGTTGATCCAGGGCGATCTTTCTTCAGTT
* *
44200 TATTTCAGTTGATCCAGTGCCATCCTTTCTTCAGTT
1 TATTTCAGTTGATCCAGGGCGAT-CTTTCTTCAGTT
* *
44236 TATTTCAATTGATCCATGGCGATCATTTCTTCAGTT
1 TATTTCAGTTGATCCAGGGCGATC-TTTCTTCAGTT
* *
44272 TATTTCAATTGATCCAGGGCGATATTTTCTTCAGTT
1 TATTTCAGTTGATCCAGGGCGAT-CTTTCTTCAGTT
*
44308 TATTTCAATTGATCCAGGGCGATCCTTTCTTCAGTT
1 TATTTCAGTTGATCCAGGGCGAT-CTTTCTTCAGTT
* *
44344 TATTTCAGTTGACCCAGGGC-AGTCTTTTTTCAGTT
1 TATTTCAGTTGATCCAGGGCGA-TCTTTCTTCAGTT
*
44379 TATTCCAGTTGA-CCAAGGGCGATCTTTCTTCAGTT
1 TATTTCAGTTGATCC-AGGGCGATCTTTCTTCAGTT
44414 TATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTT
1 TATTTCAGTTGATCCAGGGCGAT-CTTTCTTCAGTT
*
44450 TATTTCAGTTGATCCAGGGCGATCCTTTCTTTAGTT
1 TATTTCAGTTGATCCAGGGCGAT-CTTTCTTCAGTT
**
44486 TATTTCAACTGATCCAGGGCGATCCTTTCTTCAGTT
1 TATTTCAGTTGATCCAGGGCGAT-CTTTCTTCAGTT
* * * *
44522 TATTTCAGTTGACCCTGGGCGGTCTTACTTCAGTT
1 TATTTCAGTTGATCCAGGGCGATCTTTCTTCAGTT
* * *
44557 TATTTCAATCGATCCAGGGCGATCCTTTCTTTAGTT
1 TATTTCAGTTGATCCAGGGCGAT-CTTTCTTCAGTT
* *
44593 TATTTCAATTGATCCAGGGCGATCTTTTCTTTAGTT
1 TATTTCAGTTGATCCAGGGCGATC-TTTCTTCAGTT
* *
44629 TATTTCAATTGATCCAAGGCGATCCTTTCTTCAGTT
1 TATTTCAGTTGATCCAGGGCGAT-CTTTCTTCAGTT
* * *
44665 TATTTCAGTTGACCCAGGGCGGTCTTTCTTCAATT
1 TATTTCAGTTGATCCAGGGCGATCTTTCTTCAGTT
* * * *
44700 TATTACAGTGGATCCAGGGTGATTTTTTCTTCAGTT
1 TATTTCAGTTGATCCAGGGCGA-TCTTTCTTCAGTT
* *
44736 TATTTCAGTTGATTCAGGGCGATCTTTTCTGCAGTTT
1 TATTTCAGTTGATCCAGGGCGATC-TTTCTTCAG-TT
*
44773 TTTTTCAGTTGA
1 TATTTCAGTTGA
44785 CCGCAAATTG
Statistics
Matches: 834, Mismatches: 86, Indels: 44
0.87 0.09 0.05
Matches are distributed among these distances:
34 23 0.03
35 248 0.30
36 454 0.54
37 109 0.13
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (35 bp):
TATTTCAGTTGATCCAGGGCGATCTTTCTTCAGTT
Found at i:44101 original size:143 final size:142
Alignment explanation
Indices: 43806--44784 Score: 1282
Period size: 143 Copynumber: 6.8 Consensus size: 142
43796 AGGGTGGTCC
* * *
43806 TATTTCAGTTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGACCCAGGGCGGTCTTTC
1 TATTTCAG-TTGACCCAGGGCGAT-CTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTC
* *
43871 TTCAGTTTATTTCAATTTGATCCAGGGTGATCCTTTCTTCAGTTTATTTCAGTTTGATCCAGGGC
64 TTCAGTTTATTTC-AGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAG-TTGATCCAGGGC
*
43936 GATCCTTTCTTCAGGT
127 GATCCTTTCTTCAGTT
* * * * * * *
43952 TATTTCAGTTGACCCAGGGTGGTCTCTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTCTCTT
1 TATTTCAGTTGACCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTCTT
44017 CAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTTATTTCAGTTGATCCAGGGCGAT
66 CAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAG-TTTATTTCAGTTGATCCAGGGCGAT
*
44082 CTTTTCTTCAGTT
130 CCTTTCTTCAGTT
* * * *
44095 TATTTCAATTGATCCAGGGCAATACTTTCTTCAGTTTATTTCAGTTGA-CCAGGGCGGTCTTTCT
1 TATTTCAGTTGACCCAGGGCGAT-CTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTCT
* * * * * * *
44159 CCATTTTATTTGAGTTGACCCAGGGCGGT-CTTTCTTCAGTTTATTTCAGTTGATCCAGTGCCAT
65 TCAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGAT
44223 CCTTTCTTCAGTT
130 CCTTTCTTCAGTT
* * * * *
44236 TATTTCAATTGATCCATGGCGATCATTTCTTCAGTTTATTTCAATTGATCCAGGGCGATATTTTC
1 TATTTCAGTTGACCCAGGGCGATC-TTTCTTCAGTTTATTTCAGTTGATCCAGGGCGAT-CTTTC
* *
44301 TTCAGTTTATTTCAATTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGACCCAGGGC-A
64 TTCAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGA
*
44365 GT-CTTTTTTCAGTT
129 -TCCTTTCTTCAGTT
* *
44379 TATTCCAGTTGACCAAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCT
1 TATTTCAGTTGACCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGAT-CTTTCT
* **
44444 TCAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTTAGTTTATTTCAACTGATCCAGGGCGAT
65 TCAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGAT
44509 CCTTTCTTCAGTT
130 CCTTTCTTCAGTT
* * * * *
44522 TATTTCAGTTGACCCTGGGCGGTCTTACTTCAGTTTATTTCAATCGATCCAGGGCGATCCTTTCT
1 TATTTCAGTTGACCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGAT-CTTTCT
* * * * * *
44587 TTAGTTTATTTCAATTGATCCAGGGCGATCTTTTCTTTAGTTTATTTCAATTGATCCAAGGCGAT
65 TCAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGAT
44652 CCTTTCTTCAGTT
130 CCTTTCTTCAGTT
* * * * * *
44665 TATTTCAGTTGACCCAGGGCGGTCTTTCTTCAATTTATTACAGTGGATCCAGGGTGATTTTTTCT
1 TATTTCAGTTGACCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGA-TCTTTCT
* * * *
44730 TCAGTTTATTTCAGTTGATTCAGGGCGATCTTTTCTGCAGTTTTTTTTCAGTTGA
65 TCAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAG-TTTATTTCAGTTGA
44785 CCGCAAATTG
Statistics
Matches: 741, Mismatches: 81, Indels: 24
0.88 0.10 0.03
Matches are distributed among these distances:
140 1 0.00
141 78 0.11
142 115 0.16
143 400 0.54
144 127 0.17
145 12 0.02
146 8 0.01
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (142 bp):
TATTTCAGTTGACCCAGGGCGATCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTCTT
CAGTTTATTTCAGTTGATCCAGGGCGATCCTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATC
CTTTCTTCAGTT
Found at i:45029 original size:69 final size:69
Alignment explanation
Indices: 44918--45068 Score: 196
Period size: 69 Copynumber: 2.2 Consensus size: 69
44908 AGATTTTGCT
* *
44918 TTGGTTCCATCCAAGCCATATGGGCTTTTCCTCAAGCCAAACTCGTTTCCATACGAGTTAGCTCA
1 TTGGTTCCATCCAAGCCATATAGGCTTTTCCTCAAGCCAAACTCGTTTCCATACGAGTCAGCTCA
* *
44983 AGCC
66 AACA
* * * * * *
44987 TTGGTTCCATCCAAGCTATATAGGCTTTTCCAT-GAGTCAAACTCGTTTCCATGCGAGTCAGTTT
1 TTGGTTCCATCCAAGCCATATAGGCTTTTCC-TCAAGCCAAACTCGTTTCCATACGAGTCAGCTC
45051 AAACA
65 AAACA
45056 TTGGTTCCATCCA
1 TTGGTTCCATCCA
45069 TACAAAATGA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
69 70 0.99
70 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (69 bp):
TTGGTTCCATCCAAGCCATATAGGCTTTTCCTCAAGCCAAACTCGTTTCCATACGAGTCAGCTCA
AACA
Found at i:45427 original size:30 final size:30
Alignment explanation
Indices: 45391--46222 Score: 1223
Period size: 30 Copynumber: 27.4 Consensus size: 30
45381 GGATCATTGC
*
45391 ATCATTGCTTCATTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
* *
45421 ATCATTGTTTTATTTTAATCCTGATTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
45451 ATCATTGCTTTATTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
* *
45481 ATCATTACTTTATTTTAATCCTAGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
*
45511 ATTATTGCTTTATTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
45541 ATCATTGCTTTATTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
45571 ATCATTGCTTTATTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
*
45601 ATCATTGCTTCATTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
45631 ATCATTGCTTTATTTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
*
45661 ATCATTGCTTTATTTTTATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
* *
45691 ATCATTACTTTATTTGAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
* *
45721 ATATTTGCTTCATTGCTTTGTTTTAATCCTGTTTGAGG
1 --A------TCATTGCTTTATTTTAATCCTGGTTGAGG
* *
45759 ATCATTGCTATATTTTAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
*
45789 ATCATTGCTTTATGTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
* * *
45819 ATCGTTGCTTTATTTTAATCATGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
*
45849 ATCATTGCTTTATTTTAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
*
45879 ATCATTGCTTTATTTTAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
* *
45909 ATCATTGCTTTATGTTAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
* *
45939 ATCGTTGCTTTATTTTAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
* *
45969 ATCATTGCTTTATTTTAATCTTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
*
45999 ATCATTGCTTTATTTTAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
* * *
46029 ATCATTGCTTTATGTTAATCTTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
* *
46059 ATCATTGCTATATTTTAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
*
46089 ATCATTGCTTTATGTTAATCCTGGTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
** * *
46119 ATTGTTGCTTTATTTTAATCATGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
*
46149 ATCATTGCTTTATTTTAATCCTGTTTGAGG
1 ATCATTGCTTTATTTTAATCCTGGTTGAGG
* *
46179 ATCATTGCTTTTATTTCAATCCTGGTTTAGG
1 ATCATTGC-TTTATTTTAATCCTGGTTGAGG
46210 ATCATTGCTTTAT
1 ATCATTGCTTTAT
46223 CAGTTAATCC
Statistics
Matches: 736, Mismatches: 57, Indels: 18
0.91 0.07 0.02
Matches are distributed among these distances:
30 682 0.93
31 27 0.04
32 1 0.00
36 1 0.00
38 25 0.03
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.48
Consensus pattern (30 bp):
ATCATTGCTTTATTTTAATCCTGGTTGAGG
Found at i:46749 original size:27 final size:27
Alignment explanation
Indices: 46719--46788 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
46709 CTCTTATTTA
*
46719 GCATTTTGGTCATTTTTACATTCAGGG
1 GCATTTTGGTCATTTTTACACTCAGGG
*
46746 GCATTTTGGTCATTTTTACACTCAGGT
1 GCATTTTGGTCATTTTTACACTCAGGG
46773 GCATTTTGGTCATTTT
1 GCATTTTGGTCATTTT
46789 AAGTTCACTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.17, C:0.16, G:0.20, T:0.47
Consensus pattern (27 bp):
GCATTTTGGTCATTTTTACACTCAGGG
Found at i:48867 original size:27 final size:27
Alignment explanation
Indices: 48837--48906 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
48827 TTCTTATTTA
*
48837 GCATTTTGGTCATTTTTACATTCAGGG
1 GCATTTTGGTCATTTTTACACTCAGGG
*
48864 GCATTTTGGTCATTTTTACACTCAGGT
1 GCATTTTGGTCATTTTTACACTCAGGG
*
48891 GCATTGTGGTCATTTT
1 GCATTTTGGTCATTTT
48907 AAGTTCACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.17, C:0.16, G:0.21, T:0.46
Consensus pattern (27 bp):
GCATTTTGGTCATTTTTACACTCAGGG
Done.