Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008129.1 Corchorus capsularis cultivar CVL-1 contig08150, 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: 36525
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:627 original size:212 final size:213
Alignment explanation
Indices: 334--753 Score: 806
Period size: 214 Copynumber: 2.0 Consensus size: 213
324 ATTTAAAAAT
334 ATTTCAAAATATTTTCTCGACAAAAAGAAGTTTATAACTAATAACAATTTTACTACTACTAATTA
1 ATTTCAAAATATTTTCTCGACAAAAAGAAGTTTATAACTAATAACAATTTTACTACTACTAATTA
399 TTTTATAATAATAAGAAGTTTA-ATATATAATTATAACAATAAGATGCTTAACGTGGTTTTGATT
66 TTTTATAATAATAAGAAGTTTACATATATAATTATAACAATAAGATGCTTAACGTGGTTTTGATT
*
463 GCATTAATTTTAAAATTAAAAGAGATAGTATTAGATTACATATTAACCCTTAAAAATATAGCTAA
131 GCATTAATTTTAAAATTAAAAGAGATAATATTAGATTACATATTAACCCTTAAAAATATAGCTAA
528 AATTTTAAAATTTGATGA
196 AATTTTAAAATTTGATGA
546 ATTTCAAAATATTTTCTCGACAAAAAGAAGTTTATAACTAATAACAATTTTACTACTACTAATTA
1 ATTTCAAAATATTTTCTCGACAAAAAGAAGTTTATAACTAATAACAATTTTACTACTACTAATTA
*
611 TTTTATAATAATAAGAAGTTTACTATATATAATTATAATAATAAGATGCTTAACGTGGTTTTGAT
66 TTTTATAATAATAAGAAGTTTAC-ATATATAATTATAACAATAAGATGCTTAACGTGGTTTTGAT
676 TGCATTAATTTTAAAATTAAAAGAGATAATATTAGATTACATATTAACCCTTAAAAATATAGCTA
130 TGCATTAATTTTAAAATTAAAAGAGATAATATTAGATTACATATTAACCCTTAAAAATATAGCTA
741 AAATTTTAAAATT
195 AAATTTTAAAATT
754 AAAAAGGGTA
Statistics
Matches: 204, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
212 87 0.43
214 117 0.57
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.39
Consensus pattern (213 bp):
ATTTCAAAATATTTTCTCGACAAAAAGAAGTTTATAACTAATAACAATTTTACTACTACTAATTA
TTTTATAATAATAAGAAGTTTACATATATAATTATAACAATAAGATGCTTAACGTGGTTTTGATT
GCATTAATTTTAAAATTAAAAGAGATAATATTAGATTACATATTAACCCTTAAAAATATAGCTAA
AATTTTAAAATTTGATGA
Found at i:644 original size:35 final size:36
Alignment explanation
Indices: 576--646 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 36
566 CAAAAAGAAG
* *
576 TTTATAACTAATAACAATTTTACTACTACTAATTAT
1 TTTATAACTAATAACAAGTTTACTACTAATAATTAT
*
612 TTTATAA-TAATAAGAAGTTTACTA-TATATAATTAT
1 TTTATAACTAATAACAAGTTTACTACTA-ATAATTAT
647 AATAATAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 2 0.06
35 22 0.71
36 7 0.23
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (36 bp):
TTTATAACTAATAACAAGTTTACTACTAATAATTAT
Found at i:822 original size:6 final size:6
Alignment explanation
Indices: 804--833 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
794 GTTTAGACTT
804 ATATAG TATATAG ATATAG ATATAG ATATA
1 ATATAG -ATATAG ATATAG ATATAG ATATA
834 TAATTATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (6 bp):
ATATAG
Found at i:6683 original size:2 final size:2
Alignment explanation
Indices: 6676--6700 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6666 TATCTCACAC
6676 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 T
6701 TTTTGGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7531 original size:20 final size:20
Alignment explanation
Indices: 7506--7568 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
7496 CGGTTAGGTT
7506 GGGTTCAGGCTCGGGTTATC
1 GGGTTCAGGCTCGGGTTATC
* * * *
7526 GGGTTCGGGTTTGAG-T-T-
1 GGGTTCAGGCTCGGGTTATC
7543 GGGTTCAGGCTCGGGTTATC
1 GGGTTCAGGCTCGGGTTATC
7563 GGGTTC
1 GGGTTC
7569 GGGTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 11 0.34
18 2 0.06
19 2 0.06
20 17 0.53
ACGTcount: A:0.08, C:0.16, G:0.43, T:0.33
Consensus pattern (20 bp):
GGGTTCAGGCTCGGGTTATC
Found at i:7548 original size:17 final size:17
Alignment explanation
Indices: 7526--7587 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
7516 TCGGGTTATC
7526 GGGTTCGGGTTTGAGTT
1 GGGTTCGGGTTTGAGTT
* * * *
7543 GGGTTCAGGCTCGGGTTAT
1 GGGTTCGGGTTTGAG-T-T
*
7562 CGGGTTCGGGTTTGAGTC
1 -GGGTTCGGGTTTGAGTT
7580 GGGTTCGG
1 GGGTTCGG
7588 ATTGGATTTG
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
17 19 0.58
18 1 0.03
19 2 0.06
20 11 0.33
ACGTcount: A:0.06, C:0.13, G:0.47, T:0.34
Consensus pattern (17 bp):
GGGTTCGGGTTTGAGTT
Found at i:7553 original size:37 final size:37
Alignment explanation
Indices: 7503--7585 Score: 157
Period size: 37 Copynumber: 2.2 Consensus size: 37
7493 GGGCGGTTAG
7503 GTTGGGTTCAGGCTCGGGTTATCGGGTTCGGGTTTGA
1 GTTGGGTTCAGGCTCGGGTTATCGGGTTCGGGTTTGA
7540 GTTGGGTTCAGGCTCGGGTTATCGGGTTCGGGTTTGA
1 GTTGGGTTCAGGCTCGGGTTATCGGGTTCGGGTTTGA
*
7577 GTCGGGTTC
1 GTTGGGTTC
7586 GGATTGGATT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.07, C:0.14, G:0.43, T:0.35
Consensus pattern (37 bp):
GTTGGGTTCAGGCTCGGGTTATCGGGTTCGGGTTTGA
Found at i:7834 original size:19 final size:18
Alignment explanation
Indices: 7810--7846 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
7800 ACTTGATATT
7810 GAACTTGATGATGATTTGA
1 GAACTTGAT-ATGATTTGA
*
7829 GAACTTGATTTGATTTGA
1 GAACTTGATATGATTTGA
7847 TTTGATTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.30, C:0.05, G:0.24, T:0.41
Consensus pattern (18 bp):
GAACTTGATATGATTTGA
Found at i:8192 original size:26 final size:26
Alignment explanation
Indices: 8158--8220 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
8148 TGGTTCTTCT
*
8158 TTCAATAATT-TCCCAATAACTGGATC
1 TTCAATAATTCT-CCAATAACTGAATC
* *
8184 TTCAGTAATTCTCCAATAATTGAATC
1 TTCAATAATTCTCCAATAACTGAATC
8210 TTCCAATAATT
1 TT-CAATAATT
8221 GAATATTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 23 0.74
27 8 0.26
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (26 bp):
TTCAATAATTCTCCAATAACTGAATC
Found at i:9187 original size:73 final size:74
Alignment explanation
Indices: 9093--9231 Score: 219
Period size: 73 Copynumber: 1.9 Consensus size: 74
9083 TACGTAGTTC
* *
9093 TCTTTTTTTTTTTCGTGCTCTAAGTTTTGCCTAAG-TCGTCCTTTACAGGATTTTCAACTTAGCG
1 TCTTTTTTTTTTTC-TGCTCTAACTTTTACCTAAGCT-GTCCTTTACAGGATTTTCAACTTAGCG
9157 AGCCTCATTCT
64 AGCCTCATTCT
*
9168 TCTTTTTTTTTTT-TGCTCTAACTTTTACCTAAGCTGTCCTTTGCAGGATTTTCAACTTAGCGAG
1 TCTTTTTTTTTTTCTGCTCTAACTTTTACCTAAGCTGTCCTTTACAGGATTTTCAACTTAGCGAG
9232 GCTTTTCTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
73 46 0.77
74 1 0.02
75 13 0.22
ACGTcount: A:0.17, C:0.22, G:0.14, T:0.47
Consensus pattern (74 bp):
TCTTTTTTTTTTTCTGCTCTAACTTTTACCTAAGCTGTCCTTTACAGGATTTTCAACTTAGCGAG
CCTCATTCT
Found at i:11028 original size:40 final size:40
Alignment explanation
Indices: 10974--11053 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 40
10964 ATTTGATTTG
* * *
10974 ATTTGATTCAAGGGTC-GAATGACTTGGTCTTGAATTGATA
1 ATTTAATTCAAGGGTCTG-ACGACTTGATCTTGAATTGATA
11014 ATTTAATTCAAGGGTCTTGACGACTTGATCTTGAATTGAT
1 ATTTAATTCAAGGGTC-TGACGACTTGATCTTGAATTGAT
11054 GACTTGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
40 15 0.43
41 19 0.54
42 1 0.03
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.39
Consensus pattern (40 bp):
ATTTAATTCAAGGGTCTGACGACTTGATCTTGAATTGATA
Found at i:11042 original size:67 final size:66
Alignment explanation
Indices: 10906--11047 Score: 144
Period size: 67 Copynumber: 2.1 Consensus size: 66
10896 TATGCTTCAA
* * ** * *
10906 GATTTGCTTCAAGGGTCGAATGACTTGATCTTGAACTTGATGATAATTTGAGAACTTGATTTGAT
1 GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATAATAATTCAAGAACTTGA-TCGAC
10971 TT
65 TT
* **
10973 GATTTGATTCAAGGGTCGAATGACTTGGTCTTGAA-TTGATAATTTAATTCAAGGGTCTTGA-CG
1 GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATAA--TAATTCAA-GAACTTGATCG
11036 ACTT
63 ACTT
11040 GATCTTGA
1 GAT-TTGA
11048 ATTGATGACT
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
66 6 0.10
67 40 0.65
68 10 0.16
69 6 0.10
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (66 bp):
GATTTGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATAATAATTCAAGAACTTGATCGACT
T
Found at i:11126 original size:99 final size:95
Alignment explanation
Indices: 10969--11148 Score: 247
Period size: 94 Copynumber: 1.9 Consensus size: 95
10959 ACTTGATTTG
* *
10969 ATTTGATTTGATTCAAGGGTCGAATGACTTGGTCTTGAATTGATAATTTAATTCAAGGGTC-TTG
1 ATTTGATTTGATTCAAGGGTCGAATGACTTGATCTCGAATTGATAATTTAATTCAAGGGTCTTTG
11033 ACGACTTGATCTTGAATTGATGACTTGGGA
66 ACGACTTGATCTTGAATTGATGACTTGGGA
* *
11063 ATTTGATTTGATTCGAGGGTCTTTG-ATGACTTGATCTCGAATTGATGATAATTTGATTCAAGGG
1 ATTTGATTTGATTCAAGGGTC---GAATGACTTGATCTCGAA-T--TGATAATTTAATTCAAGGG
*
11127 TCTTTGGCGACTTGATCTTGAA
60 TCTTTGACGACTTGATCTTGAA
11149 CAAACAAAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
94 20 0.27
96 14 0.19
97 2 0.03
99 20 0.27
100 18 0.24
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.39
Consensus pattern (95 bp):
ATTTGATTTGATTCAAGGGTCGAATGACTTGATCTCGAATTGATAATTTAATTCAAGGGTCTTTG
ACGACTTGATCTTGAATTGATGACTTGGGA
Found at i:11448 original size:16 final size:16
Alignment explanation
Indices: 11427--11458 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11417 ATATGAAATA
11427 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
11443 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
11459 AATTTCAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:11854 original size:16 final size:16
Alignment explanation
Indices: 11835--11883 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
11825 ATTTGGGTCA
11835 GGTTAATTCGGGTTCG
1 GGTTAATTCGGGTTCG
* *
11851 GGTTGAATTTGGG-TCA
1 GGTT-AATTCGGGTTCG
11867 GGTTAATTCGGGTTCG
1 GGTTAATTCGGGTTCG
11883 G
1 G
11884 TTCTGTTTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 7 0.26
16 13 0.48
17 7 0.26
ACGTcount: A:0.14, C:0.10, G:0.39, T:0.37
Consensus pattern (16 bp):
GGTTAATTCGGGTTCG
Found at i:11863 original size:32 final size:31
Alignment explanation
Indices: 11819--11883 Score: 121
Period size: 32 Copynumber: 2.1 Consensus size: 31
11809 TTATTCTACA
11819 GGGTTGATTTGGGTCAGGTTAATTCGGGTTC
1 GGGTTGATTTGGGTCAGGTTAATTCGGGTTC
11850 GGGTTGAATTTGGGTCAGGTTAATTCGGGTTC
1 GGGTTG-ATTTGGGTCAGGTTAATTCGGGTTC
11882 GG
1 GG
11884 TTCTGTTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 6 0.18
32 27 0.82
ACGTcount: A:0.14, C:0.09, G:0.40, T:0.37
Consensus pattern (31 bp):
GGGTTGATTTGGGTCAGGTTAATTCGGGTTC
Found at i:12067 original size:16 final size:16
Alignment explanation
Indices: 12048--12139 Score: 103
Period size: 16 Copynumber: 5.7 Consensus size: 16
12038 GGATTCGGAT
12048 TTTTTCGGGTTTGAGC
1 TTTTTCGGGTTTGAGC
* * *
12064 TTTTTCGGGTTCGGGTT
1 TTTTTCGGGTTTGAG-C
12081 TTTTTCGGGTTTGAGC
1 TTTTTCGGGTTTGAGC
* * * *
12097 TTTTTTGGGTTCGTGT
1 TTTTTCGGGTTTGAGC
*
12113 TTTTTCGGGTTTGACC
1 TTTTTCGGGTTTGAGC
12129 TTTTTCGGGTT
1 TTTTTCGGGTT
12140 CAGGTTTTTT
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
16 47 0.78
17 13 0.22
ACGTcount: A:0.03, C:0.12, G:0.30, T:0.54
Consensus pattern (16 bp):
TTTTTCGGGTTTGAGC
Found at i:12089 original size:33 final size:33
Alignment explanation
Indices: 12033--12149 Score: 166
Period size: 32 Copynumber: 3.6 Consensus size: 33
12023 TTTTCATAAA
* *
12033 TTTTCGGATTC-GGATTTTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTTCGGGTTTGAGCT
12065 TTTTCGGGTTCGGGTTTTTTTCGGGTTTGAGCT
1 TTTTCGGGTTCGGGTTTTTTTCGGGTTTGAGCT
* * *
12098 TTTTTGGGTTCGTG-TTTTTTCGGGTTTGACCT
1 TTTTCGGGTTCGGGTTTTTTTCGGGTTTGAGCT
*
12130 TTTTCGGGTTCAGGTTTTTT
1 TTTTCGGGTTCGGGTTTTTT
12150 CGGATTCAGG
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
32 38 0.51
33 37 0.49
ACGTcount: A:0.05, C:0.12, G:0.29, T:0.54
Consensus pattern (33 bp):
TTTTCGGGTTCGGGTTTTTTTCGGGTTTGAGCT
Found at i:12148 original size:16 final size:16
Alignment explanation
Indices: 12033--12161 Score: 79
Period size: 16 Copynumber: 8.0 Consensus size: 16
12023 TTTTCATAAA
*
12033 TTTTCGGATTC-GGATT
1 TTTTCGGGTTCAGG-TT
* *
12049 TTTTCGGGTT-TGAGCT
1 TTTTCGGGTTCAG-GTT
*
12065 TTTTCGGGTTCGGGTTT
1 TTTTCGGGTTCAGG-TT
* *
12082 TTTTCGGGTTTGAGCTT
1 TTTTCGGG-TTCAGGTT
12099 TTTT-GGGTTC-GTGTT
1 TTTTCGGGTTCAG-GTT
* **
12114 TTTTCGGGTT-TGACCT
1 TTTTCGGGTTCAG-GTT
12130 TTTTCGGGTTCAGGTT
1 TTTTCGGGTTCAGGTT
*
12146 TTTTCGGATTCAGGTT
1 TTTTCGGGTTCAGGTT
12162 CAGACGGGTT
Statistics
Matches: 88, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
14 1 0.01
15 8 0.09
16 58 0.66
17 18 0.20
18 3 0.03
ACGTcount: A:0.06, C:0.12, G:0.29, T:0.52
Consensus pattern (16 bp):
TTTTCGGGTTCAGGTT
Found at i:13835 original size:31 final size:31
Alignment explanation
Indices: 13800--13875 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
13790 TCAGGGGATA
*
13800 AATTGTCTTGAATTGGGGAAATTCAGGAGCT
1 AATTGTCTTGAATTGGGGAAATTCAAGAGCT
*
13831 AATTGTCTTGAATTTGGGAAATTCAAGAGCT
1 AATTGTCTTGAATTGGGGAAATTCAAGAGCT
*
13862 AACTGTCTTGAATT
1 AATTGTCTTGAATT
13876 TAAAAATTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.36
Consensus pattern (31 bp):
AATTGTCTTGAATTGGGGAAATTCAAGAGCT
Found at i:18947 original size:304 final size:304
Alignment explanation
Indices: 18398--19005 Score: 1207
Period size: 304 Copynumber: 2.0 Consensus size: 304
18388 GAAAGTTTCA
18398 GTTTTAATTCTTTTATTTTTTGTTCTATTTGTCTGGTCAAGGTAATTCAGGTGTCTATTTAAAGG
1 GTTTTAATTCTTTTATTTTTTGTTCTATTTGTCTGGTCAAGGTAATTCAGGTGTCTATTTAAAGG
18463 TAATTCCATGGTCTACAACTTTCATTAAGGACTCAAAAGCAAATTTTAATGTTTTGATTCTAAAA
66 TAATTCCATGGTCTACAACTTTCATTAAGGACTCAAAAGCAAATTTTAATGTTTTGATTCTAAAA
*
18528 AATGCTTCTGAAATTTTGTTGTCTCGATTGCCGGTCTATATAATATTGTATAATTTTTGGTCCAC
131 AATGCTTCTGAAATTTTGTTGTCTCGATTGCCGGTATATATAATATTGTATAATTTTTGGTCCAC
18593 ATGTCCGATTGAAATTATTCAAGTATCGGTTAAAAGGTTATTGCATGATCTACGACTTTCGTCAA
196 ATGTCCGATTGAAATTATTCAAGTATCGGTTAAAAGGTTATTGCATGATCTACGACTTTCGTCAA
18658 GGGCCTAAAAGCTGAATTTTGATTAATGAGTTTCGTGGAGAGTT
261 GGGCCTAAAAGCTGAATTTTGATTAATGAGTTTCGTGGAGAGTT
18702 GTTTTAATTCTTTTATTTTTTGTTCTATTTGTCTGGTCAAGGTAATTCAGGTGTCTATTTAAAGG
1 GTTTTAATTCTTTTATTTTTTGTTCTATTTGTCTGGTCAAGGTAATTCAGGTGTCTATTTAAAGG
18767 TAATTCCATGGTCTACAACTTTCATTAAGGACTCAAAAGCAAATTTTAATGTTTTGATTCTAAAA
66 TAATTCCATGGTCTACAACTTTCATTAAGGACTCAAAAGCAAATTTTAATGTTTTGATTCTAAAA
18832 AATGCTTCTGAAATTTTGTTGTCTCGATTGCCGGTATATATAATATTGTATAATTTTTGGTCCAC
131 AATGCTTCTGAAATTTTGTTGTCTCGATTGCCGGTATATATAATATTGTATAATTTTTGGTCCAC
18897 ATGTCCGATTGAAATTATTCAAGTATCGGTTAAAAGGTTATTGCATGATCTACGACTTTCGTCAA
196 ATGTCCGATTGAAATTATTCAAGTATCGGTTAAAAGGTTATTGCATGATCTACGACTTTCGTCAA
18962 GGGCCTAAAAGCTGAATTTTGATTAATGAGTTTCGTGGAGAGTT
261 GGGCCTAAAAGCTGAATTTTGATTAATGAGTTTCGTGGAGAGTT
19006 CAAGAGAGAA
Statistics
Matches: 303, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
304 303 1.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (304 bp):
GTTTTAATTCTTTTATTTTTTGTTCTATTTGTCTGGTCAAGGTAATTCAGGTGTCTATTTAAAGG
TAATTCCATGGTCTACAACTTTCATTAAGGACTCAAAAGCAAATTTTAATGTTTTGATTCTAAAA
AATGCTTCTGAAATTTTGTTGTCTCGATTGCCGGTATATATAATATTGTATAATTTTTGGTCCAC
ATGTCCGATTGAAATTATTCAAGTATCGGTTAAAAGGTTATTGCATGATCTACGACTTTCGTCAA
GGGCCTAAAAGCTGAATTTTGATTAATGAGTTTCGTGGAGAGTT
Found at i:24716 original size:27 final size:28
Alignment explanation
Indices: 24686--24762 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 28
24676 AGGGTCACAT
*
24686 AGGGGCATTTTGGTCATTTTTACATT-C
1 AGGGGCATTTTGGTCATTTTTACATTAA
* *
24713 AGGGGTATTTTGGTCATTTTTGCATTAA
1 AGGGGCATTTTGGTCATTTTTACATTAA
*
24741 AGGGGCATTTTGGTCAATTTTA
1 AGGGGCATTTTGGTCATTTTTA
24763 GTCCATTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 24 0.56
28 19 0.44
ACGTcount: A:0.21, C:0.10, G:0.25, T:0.44
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTTACATTAA
Found at i:25106 original size:28 final size:28
Alignment explanation
Indices: 25066--25122 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
25056 AAGGGAAAGC
* *
25066 TTATTATTCACATTTACTCATTTGCATT
1 TTATTAGTCACATTTACTCATTTACATT
25094 TTATTAGTCACATTTACTCATTTACATT
1 TTATTAGTCACATTTACTCATTTACATT
25122 T
1 T
25123 CATATAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.18, G:0.04, T:0.53
Consensus pattern (28 bp):
TTATTAGTCACATTTACTCATTTACATT
Found at i:28845 original size:23 final size:23
Alignment explanation
Indices: 28813--28856 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
28803 AATTTGAAGG
28813 AAAATGAAAAAAAAAGGAAAAGA
1 AAAATGAAAAAAAAAGGAAAAGA
* *
28836 AAAATTAAAAAAAATGGAAAA
1 AAAATGAAAAAAAAAGGAAAA
28857 ATCAGAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (23 bp):
AAAATGAAAAAAAAAGGAAAAGA
Found at i:30796 original size:31 final size:31
Alignment explanation
Indices: 30761--30832 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
30751 CATGCATCCA
30761 TCATGCATCATCCCTTCTTTTATATTCGTGC
1 TCATGCATCATCCCTTCTTTTATATTCGTGC
* *
30792 TCATGCATCATCCCTTCTTTTGTATTTGTGC
1 TCATGCATCATCCCTTCTTTTATATTCGTGC
30823 TCATGCATCA
1 TCATGCATCA
30833 GTCATGCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.17, C:0.28, G:0.11, T:0.44
Consensus pattern (31 bp):
TCATGCATCATCCCTTCTTTTATATTCGTGC
Found at i:32004 original size:13 final size:13
Alignment explanation
Indices: 31986--32042 Score: 71
Period size: 14 Copynumber: 4.3 Consensus size: 13
31976 CAAGATACAT
*
31986 TTTTCAAAAATTG
1 TTTTCAAAAATGG
*
31999 TTTTCAATAAAAGG
1 TTTTCAA-AAATGG
32013 TTTTCAAAAATGGG
1 TTTTCAAAAAT-GG
32027 TTTTCAAAAA-GG
1 TTTTCAAAAATGG
32039 TTTT
1 TTTT
32043 GAGTCTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
12 6 0.15
13 10 0.26
14 23 0.59
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (13 bp):
TTTTCAAAAATGG
Found at i:32688 original size:19 final size:20
Alignment explanation
Indices: 32637--32696 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 20
32627 GGGATAGTTC
32637 CTAAAAAATAGAAATTGTTTTTG
1 CTAAAAAA-A-AAA-TGTTTTTG
32660 C-AAAAGAAAAAATGTTTTT-
1 CTAAAA-AAAAAATGTTTTTG
*
32679 CTAAAAAAAAAAGGTTTT
1 CTAAAAAAAAAATGTTTT
32697 AGGAAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 12 0.35
20 11 0.32
21 3 0.09
22 5 0.15
23 3 0.09
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (20 bp):
CTAAAAAAAAAATGTTTTTG
Found at i:32778 original size:14 final size:14
Alignment explanation
Indices: 32750--32792 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
32740 TGGTGAAACT
32750 AAAA-AAGAAAGAAA
1 AAAAGAAGAAA-AAA
*
32764 AAAAGGAGAAAAAA
1 AAAAGAAGAAAAAA
32778 AAAAGAAGAAGAAAA
1 AAAAGAAGAA-AAAA
32793 GGAAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAAAA
Found at i:32806 original size:23 final size:25
Alignment explanation
Indices: 32750--32804 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
32740 TGGTGAAACT
32750 AAAAAAGAAAGAAAAAAAGGAGAAAA
1 AAAAAAG-AAGAAAAAAAGGAGAAAA
*
32776 AAAAAAGAAGAAGAAAAGGA-AAAA
1 AAAAAAGAAGAAAAAAAGGAGAAAA
32800 AAAAA
1 AAAAA
32805 GATAAAGCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 9 0.32
25 12 0.43
26 7 0.25
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (25 bp):
AAAAAAGAAGAAAAAAAGGAGAAAA
Found at i:33066 original size:15 final size:14
Alignment explanation
Indices: 33046--33080 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
33036 TTTGGATTAA
33046 AAAAAAAGAAGAAAG
1 AAAAAAAGAA-AAAG
33061 AAAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
33075 AAAAAA
1 AAAAAA
33081 TACAAATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:34097 original size:70 final size:70
Alignment explanation
Indices: 33909--34321 Score: 592
Period size: 70 Copynumber: 5.9 Consensus size: 70
33899 GTCTTTCTTC
* * *
33909 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTTAGTTTTTTTTCAAGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAG-TTGTTTCCAAGTT
*
33974 TATTCGA
65 TA-TCCA
* *
33981 CGTTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAATT
1 AG-TTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTT
34046 TATCCA
65 TATCCA
* * * * *
34052 AGTTTATGTCAGAATGATCGATTCGGTCGACCTAGGGTGGTCTTTCTTCAGTAGTTTCCACGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
34117 ATCCA
66 ATCCA
* * *
34122 AGTTTATGTCAGAATGATCGATTTAGTCGACCTAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTAT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
34187 ATCCA
66 ATCCA
* ** * * *
34192 AGTTTGTGTCAGAATGATCGATTTGGTCGACCCAGGGTGGTCTTTCTTCAGTAGTTTCCACGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
34257 ATCCA
66 ATCCA
* * *
34262 AGTTTATGTCAGAATGATCGATTCAGTTGACCCAGGGCGGTTTTTCATCAGTTGTTTCCA
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCA
34322 GTTGACCCAC
Statistics
Matches: 306, Mismatches: 34, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
70 241 0.79
71 4 0.01
72 13 0.04
73 48 0.16
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (70 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
ATCCA
Found at i:34723 original size:31 final size:31
Alignment explanation
Indices: 34684--34778 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 31
34674 TTCAAGAACT
34684 ATTA-TGCTTTATCAGTTTATTTCAATCCTG
1 ATTATTGCTTTATCAGTTTATTTCAATCCTG
* *
34714 ATCT-TTGCTTTATTA-TTTAATTTCAATCATG
1 AT-TATTGCTTTATCAGTTT-ATTTCAATCCTG
** *
34745 ATTATTGCTTTATGGGTTTATTTTAATCCTG
1 ATTATTGCTTTATCAGTTTATTTCAATCCTG
34776 ATT
1 ATT
34779 TAGGATCATT
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
30 6 0.11
31 45 0.83
32 3 0.06
ACGTcount: A:0.23, C:0.13, G:0.11, T:0.54
Consensus pattern (31 bp):
ATTATTGCTTTATCAGTTTATTTCAATCCTG
Found at i:34803 original size:38 final size:38
Alignment explanation
Indices: 34748--35017 Score: 321
Period size: 38 Copynumber: 7.1 Consensus size: 38
34738 AATCATGATT
** *
34748 ATTGCTTTATGGGTTTATTTTAATCCTGATTTAGGATC
1 ATTGCTTTATAAGTTCATTTTAATCCTGATTTAGGATC
* * * *
34786 ATTGTTTTATCAA-TTTATGTTAATCCTGATCTAGGATC
1 ATTGCTTTAT-AAGTTCATTTTAATCCTGATTTAGGATC
* *
34824 ATTGCTTTATAAGTTAATTTTAATCATGATTTAGGATC
1 ATTGCTTTATAAGTTCATTTTAATCCTGATTTAGGATC
* * * *
34862 ATTGATTTATCAA-TTCATGTTAATTCTGATCTAGGATC
1 ATTGCTTTAT-AAGTTCATTTTAATCCTGATTTAGGATC
* *
34900 ATTGCTTTATAAGTTAATTTTAATCCTGATCTAGGATC
1 ATTGCTTTATAAGTTCATTTTAATCCTGATTTAGGATC
*
34938 ATTGCTTTATAAGTTCATTTTAATCCTGGTTTAGGATC
1 ATTGCTTTATAAGTTCATTTTAATCCTGATTTAGGATC
* * *
34976 ATTGATTTATTAA-TGCATTTTAATCCTAATTTAGGATC
1 ATTGCTTTA-TAAGTTCATTTTAATCCTGATTTAGGATC
35014 ATTG
1 ATTG
35018 ATTAATCAGT
Statistics
Matches: 200, Mismatches: 27, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
37 4 0.02
38 191 0.95
39 5 0.03
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.47
Consensus pattern (38 bp):
ATTGCTTTATAAGTTCATTTTAATCCTGATTTAGGATC
Found at i:34848 original size:76 final size:76
Alignment explanation
Indices: 34748--35025 Score: 371
Period size: 76 Copynumber: 3.7 Consensus size: 76
34738 AATCATGATT
** * * *
34748 ATTGCTTTATGGGTTTATTTTAATCCTGATTTAGGATCATTGTTTTATCAATTTATGTTAATCCT
1 ATTGCTTTATAAGTTAATTTTAATCCTGATTTAGGATCATTGATTTATCAATTCATGTTAATCCT
34813 GATCTAGGATC
66 GATCTAGGATC
* *
34824 ATTGCTTTATAAGTTAATTTTAATCATGATTTAGGATCATTGATTTATCAATTCATGTTAATTCT
1 ATTGCTTTATAAGTTAATTTTAATCCTGATTTAGGATCATTGATTTATCAATTCATGTTAATCCT
34889 GATCTAGGATC
66 GATCTAGGATC
* * *
34900 ATTGCTTTATAAGTTAATTTTAATCCTGATCTAGGATCATTGCTTTAT-AAGTTCATTTTAATCC
1 ATTGCTTTATAAGTTAATTTTAATCCTGATTTAGGATCATTGATTTATCAA-TTCATGTTAATCC
* *
34964 TGGTTTAGGATC
65 TGATCTAGGATC
* ** * *
34976 ATTGATTTATTAA-TGCATTTTAATCCTAATTTAGGATCATTGATTAATCA
1 ATTGCTTTA-TAAGTTAATTTTAATCCTGATTTAGGATCATTGATTTATCA
35026 GTTTCTCCCT
Statistics
Matches: 178, Mismatches: 21, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
75 2 0.01
76 172 0.97
77 4 0.02
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.47
Consensus pattern (76 bp):
ATTGCTTTATAAGTTAATTTTAATCCTGATTTAGGATCATTGATTTATCAATTCATGTTAATCCT
GATCTAGGATC
Found at i:34923 original size:114 final size:114
Alignment explanation
Indices: 34767--35017 Score: 378
Period size: 114 Copynumber: 2.2 Consensus size: 114
34757 TGGGTTTATT
* *
34767 TTAATCCTGATTTAGGATCATTGTTTTATCAATTTATGTTAATCCTGATCTAGGATCATTGCTTT
1 TTAATCCTGATTTAGGATCATTGCTTTATCAATTAATGTTAATCCTGATCTAGGATCATTGCTTT
*
34832 ATAAGTTAATTTTAATCATGATTTAGGATCATTGATTTATCAATTCATG
66 ATAAGTTAATTTTAATCATGATTTAGGATCATTGATTTATCAATGCATG
* * *
34881 TTAATTCTGATCTAGGATCATTGCTTTAT-AAGTTAATTTTAATCCTGATCTAGGATCATTGCTT
1 TTAATCCTGATTTAGGATCATTGCTTTATCAA-TTAATGTTAATCCTGATCTAGGATCATTGCTT
* * * * *
34945 TATAAGTTCATTTTAATCCTGGTTTAGGATCATTGATTTATTAATGCATT
65 TATAAGTTAATTTTAATCATGATTTAGGATCATTGATTTATCAATGCATG
*
34995 TTAATCCTAATTTAGGATCATTG
1 TTAATCCTGATTTAGGATCATTG
35018 ATTAATCAGT
Statistics
Matches: 122, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
113 2 0.02
114 120 0.98
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (114 bp):
TTAATCCTGATTTAGGATCATTGCTTTATCAATTAATGTTAATCCTGATCTAGGATCATTGCTTT
ATAAGTTAATTTTAATCATGATTTAGGATCATTGATTTATCAATGCATG
Found at i:35073 original size:30 final size:32
Alignment explanation
Indices: 35033--35111 Score: 81
Period size: 33 Copynumber: 2.5 Consensus size: 32
35023 TCAGTTTCTC
*
35033 CCTGACTTAGGATCATGGCTT-T-ATTTCAAT
1 CCTGATTTAGGATCATGGCTTATGATTTCAAT
* * * *
35063 CCTGATTTAGGATTATTGTTTCATGATTTCACT
1 CCTGATTTAGGATCATGGCTT-ATGATTTCAAT
*
35096 CCTGATTTAGGTTCAT
1 CCTGATTTAGGATCAT
35112 TACTTTATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 17 0.44
32 1 0.03
33 21 0.54
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (32 bp):
CCTGATTTAGGATCATGGCTTATGATTTCAAT
Found at i:35106 original size:63 final size:63
Alignment explanation
Indices: 34992--35111 Score: 143
Period size: 63 Copynumber: 1.9 Consensus size: 63
34982 TTATTAATGC
* *
34992 ATTTTAATCCTAATTTAGGATCATTGATTAATCAGTTTCTCCCTGACTTAGGATCATGGCTTT
1 ATTTCAATCCTAATTTAGGATCATTGATTAATCAGTTTCACCCTGACTTAGGATCATGGCTTT
* * * * * * *
35055 ATTTCAATCCTGATTTAGGATTATTGTTTCATGA-TTTCACTCCTGATTTAGGTTCAT
1 ATTTCAATCCTAATTTAGGATCATTGATTAATCAGTTTCAC-CCTGACTTAGGATCAT
35112 TACTTTATGA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 5 0.11
63 42 0.89
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (63 bp):
ATTTCAATCCTAATTTAGGATCATTGATTAATCAGTTTCACCCTGACTTAGGATCATGGCTTT
Found at i:35357 original size:26 final size:25
Alignment explanation
Indices: 35311--35363 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
35301 TTTTAGATCT
*
35311 CTGTTCGAGAGTTTTGATTCAAAATC
1 CTGTTCGAGAGTTTTCATTC-AAATC
*
35337 CTGTTTGAGAG-TTTCATTTCAAATC
1 CTGTTCGAGAGTTTTCA-TTCAAATC
35362 CT
1 CT
35364 ACTTGAGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (25 bp):
CTGTTCGAGAGTTTTCATTCAAATC
Found at i:35526 original size:63 final size:63
Alignment explanation
Indices: 35350--35526 Score: 300
Period size: 63 Copynumber: 2.8 Consensus size: 63
35340 TTTGAGAGTT
* * * *
35350 TCATTTCAAATCCTACTTGAGGTTTCTAGTCGAGAGTTTCTTGTTTCAATACCAAAATCATGT
1 TCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCATGC
*
35413 TCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCTTGC
1 TCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCATGC
*
35476 TCATTTTAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATT
1 TCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATT
35527 TTAGCCAAAT
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 108 1.00
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (63 bp):
TCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCATGC
Found at i:35610 original size:62 final size:57
Alignment explanation
Indices: 35532--35741 Score: 244
Period size: 58 Copynumber: 3.6 Consensus size: 57
35522 CAATTTTAGC
**
35532 CAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAATCTTG-TTCATTT
1 CAAATCCTGCTCGAGGTCTCTAGTCGAGAG-----T-TTTCAATTCCAAATCTTGTTTCATTT
* * * *
35594 CAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTATCAATTCTAAATCCTGTTTTATTTT
1 CAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTTCAATTCCAAATCTTGTTTCA-TTT
*
35652 CAAATCCTGCTCGAGGTCTCTAATCGAGAGTTTTCAA-TCCAAAATCTTGTTTCATTT
1 CAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTTCAATTCC-AAATCTTGTTTCATTT
* * *
35709 TAAATCCTGCTTGAGGTCTCTAGCCGAGAGTTT
1 CAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTT
35742 CTGTTTCAAT
Statistics
Matches: 130, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
56 15 0.12
57 38 0.29
58 49 0.38
62 28 0.22
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.38
Consensus pattern (57 bp):
CAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTTCAATTCCAAATCTTGTTTCATTT
Found at i:36014 original size:27 final size:28
Alignment explanation
Indices: 35984--36060 Score: 120
Period size: 27 Copynumber: 2.8 Consensus size: 28
35974 AGGGTCACAT
*
35984 AGGGGCATTTTGGTCATTTTTACATT-C
1 AGGGGCATTTTGGTCATTTTTACATTAA
* *
36011 AGGGGTATTTTGGTCATTTTTGCATTAA
1 AGGGGCATTTTGGTCATTTTTACATTAA
36039 AGGGGCATTTTGGTCATTTTTA
1 AGGGGCATTTTGGTCATTTTTA
36061 GTCCATTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 24 0.55
28 20 0.45
ACGTcount: A:0.19, C:0.10, G:0.25, T:0.45
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTTACATTAA
Found at i:36406 original size:28 final size:28
Alignment explanation
Indices: 36366--36422 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
36356 AAGGGGAAGC
* *
36366 TTATTATTCACATTTACTCATTTGCATT
1 TTATTAGTCACATTTACTCATTTACATT
36394 TTATTAGTCACATTTACTCATTTACATT
1 TTATTAGTCACATTTACTCATTTACATT
36422 T
1 T
36423 CATATAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.18, G:0.04, T:0.53
Consensus pattern (28 bp):
TTATTAGTCACATTTACTCATTTACATT
Done.