Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007196.1 Corchorus capsularis cultivar CVL-1 contig07217, 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: 51996
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:2579 original size:26 final size:25
Alignment explanation
Indices: 2535--2583 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
2525 ATGATTTAGG
* *
2535 GGTTACTAACGCCCTTTTTCTTTTGA
1 GGTTACTAACACCCATTTT-TTTTGA
*
2561 GGTTACTAACACTCATTTTTTTT
1 GGTTACTAACACCCATTTTTTTT
2584 CAAGAGGGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.18, C:0.20, G:0.12, T:0.49
Consensus pattern (25 bp):
GGTTACTAACACCCATTTTTTTTGA
Found at i:6153 original size:22 final size:22
Alignment explanation
Indices: 6125--6224 Score: 182
Period size: 22 Copynumber: 4.5 Consensus size: 22
6115 TCTCATGCAA
6125 TGGCCGGTCATGTGGCCGGTCT
1 TGGCCGGTCATGTGGCCGGTCT
6147 TGGCCGGTCATGTGGCCGGTCT
1 TGGCCGGTCATGTGGCCGGTCT
*
6169 TGGCCGATCATGTGGCCGGTCT
1 TGGCCGGTCATGTGGCCGGTCT
*
6191 TGGCCAGTCATGTGGCCGGTCT
1 TGGCCGGTCATGTGGCCGGTCT
6213 TGGCCGGTCATG
1 TGGCCGGTCATG
6225 GTCCCATGCG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 74 1.00
ACGTcount: A:0.07, C:0.27, G:0.39, T:0.27
Consensus pattern (22 bp):
TGGCCGGTCATGTGGCCGGTCT
Found at i:12520 original size:10 final size:10
Alignment explanation
Indices: 12505--12532 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
12495 GGATCCATTG
12505 GCCGGTTGTT
1 GCCGGTTGTT
12515 GCCGGTTGTT
1 GCCGGTTGTT
12525 GCCGGTTG
1 GCCGGTTG
12533 GTGCGCAGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.21, G:0.43, T:0.36
Consensus pattern (10 bp):
GCCGGTTGTT
Found at i:24797 original size:27 final size:28
Alignment explanation
Indices: 24767--24824 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
24757 ACTATCAAAA
*
24767 CAAG-AAACGTTTTCCAAAAAT-TGTTTT
1 CAAGAAAACGTTTT-CAAAAATGAGTTTT
*
24794 CAAGAAAAGGTTTTCAAAAATGAGTTTT
1 CAAGAAAACGTTTTCAAAAATGAGTTTT
24822 CAA
1 CAA
24825 AGAGGTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (28 bp):
CAAGAAAACGTTTTCAAAAATGAGTTTT
Found at i:24806 original size:14 final size:14
Alignment explanation
Indices: 24775--24825 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
24765 AACAAGAAAC
* **
24775 GTTTTCCAAAAATT
1 GTTTTCAAAAAAGA
24789 GTTTTCAAGAAAAG-
1 GTTTTCAA-AAAAGA
*
24803 GTTTTCAAAAATGA
1 GTTTTCAAAAAAGA
24817 GTTTTCAAA
1 GTTTTCAAA
24826 GAGGTTTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 4 0.12
14 24 0.75
15 4 0.12
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (14 bp):
GTTTTCAAAAAAGA
Found at i:26891 original size:35 final size:34
Alignment explanation
Indices: 26845--26978 Score: 180
Period size: 35 Copynumber: 3.8 Consensus size: 34
26835 CACATATGCA
26845 TGACCCAGGGCGGTCTTTCTTAGGTTTATTTCACG-
1 TGACCCAGGGCGGTCTTTCTTA-GTTTATTTCA-GT
*
26880 TGACCCAGGGCGGTCTTTCTTAGGTTTATTTAAGT
1 TGACCCAGGGCGGTCTTTCTTA-GTTTATTTCAGT
*
26915 TGACCCAGGGCAGTCTTTCTTTAGTTTATTTCAGT
1 TGACCCAGGGCGGTCTTTC-TTAGTTTATTTCAGT
**
26950 TGACCCAGGATGGTCTTTCTTCAGTTTAT
1 TGACCCAGGGCGGTCTTTCTT-AGTTTAT
26979 GTCGGAATGA
Statistics
Matches: 90, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
34 3 0.03
35 84 0.93
36 3 0.03
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.40
Consensus pattern (34 bp):
TGACCCAGGGCGGTCTTTCTTAGTTTATTTCAGT
Found at i:27546 original size:169 final size:169
Alignment explanation
Indices: 27267--27676 Score: 689
Period size: 169 Copynumber: 2.4 Consensus size: 169
27257 ACCTTCGAGT
* *
27267 CCTCCGGGCACAAATTCAGAAACCTCCAGGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAA
1 CCTCCGGGCACAAATTCAGAAACCTCCAGGTATTAATTCTAATAAGTCCTCCGGGCAATTGATAA
*
27332 AACCTCCGGGTACCATTTCATTCAATCAAGTTTTTCATTAAAAATTCATGTTTAAGTTTAAAATC
66 AACCTCCGGGTACCATTTCATTCAATCAAGTTTTTCATAAAAAATTCATGTTTAAGTTTAAAATC
27397 CTTGGTCAAGGTCTCTATTAAGAGTTTGCATTGGTAAGA
131 CTTGGTCAAGGTCTCTATTAAGAGTTTGCATTGGTAAGA
* *
27436 CCTCCGGGCACAAACTCAGAAACCTCCAGGTATTAATTCTAATAAGTCCTCTGGGCAATTGATAA
1 CCTCCGGGCACAAATTCAGAAACCTCCAGGTATTAATTCTAATAAGTCCTCCGGGCAATTGATAA
*
27501 AACCTCCGGGTACCATTTCATTTC-ATTAAGTTTTTCATAAAAAATTCATGTTTAAGTTTAAAAT
66 AACCTCCGGGTACCATTTCA-TTCAATCAAGTTTTTCATAAAAAATTCATGTTTAAGTTTAAAAT
*
27565 TCTTGGTCAAGGTCTCTATTAAGAGTTTGCATTGGTAAGA
130 CCTTGGTCAAGGTCTCTATTAAGAGTTTGCATTGGTAAGA
* ** *
27605 CCTCCGGGCAC-AATTCAGAAACCTCCAGGAATTAATTCTAATAAGTCCTCCATGCATTTGATAA
1 CCTCCGGGCACAAATTCAGAAACCTCCAGGTATTAATTCTAATAAGTCCTCCGGGCAATTGATAA
*
27669 GACCTCCG
66 AACCTCCG
27677 AGCATTTCAT
Statistics
Matches: 226, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
168 54 0.24
169 169 0.75
170 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (169 bp):
CCTCCGGGCACAAATTCAGAAACCTCCAGGTATTAATTCTAATAAGTCCTCCGGGCAATTGATAA
AACCTCCGGGTACCATTTCATTCAATCAAGTTTTTCATAAAAAATTCATGTTTAAGTTTAAAATC
CTTGGTCAAGGTCTCTATTAAGAGTTTGCATTGGTAAGA
Found at i:27750 original size:38 final size:38
Alignment explanation
Indices: 27707--28141 Score: 294
Period size: 38 Copynumber: 12.1 Consensus size: 38
27697 AGAACTATTC
* *
27707 TGCTTTATCAGTTTATTTCAATCCTGATTTAGGATCTT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
* * *
27745 TGCTTTATTA-TTTAATTTCAAT-C--A--T--GATTAT
1 TGCTTTATCAGTTT-ATTTTAATCCTGATTTAGGATCAT
* ** *
27776 TGCTTTGTGGGTTTATTTTAATCCTGATTTAGGACCAT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
* * * * *
27814 TGTTTTATCAATTTATTTTAATCTTGATCTACGATCAT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
* *
27852 TGCTTTATAAGTTAATTTTAATCCTGATTTAGGATCAT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
* * * *
27890 TGATTTATCAATTTATGTTAATCCTGATCTAGGATCAT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
* * *
27928 TGCTTTATAAGTTAATTTTAATCCTGGTTTAGGATCAT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
** * * **
27966 TAATTTATTAATACATTTTAATCCTGATTTAGGATCAT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
* * * * *
28004 TGATTAATCAG--T-TTCT--CCCTGACTTAGGATCA-
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
* * *
28036 TG-----GC--TTTATTTCAATCCTGATTTAGGATTAT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
* *
28067 TG--TT-TCA--TGATTTTAATCCTGATTTAGGTTCAT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
* * *
28100 TGCTTTATTAG-TTATTTTAATCATGGTTTAGGATCAT
1 TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
28137 TGCTT
1 TGCTT
28142 ATAAATTAAG
Statistics
Matches: 306, Mismatches: 69, Indels: 45
0.73 0.16 0.11
Matches are distributed among these distances:
27 2 0.01
28 2 0.01
30 13 0.04
31 20 0.07
32 6 0.02
33 40 0.13
34 1 0.00
35 6 0.02
36 3 0.01
37 31 0.10
38 182 0.59
ACGTcount: A:0.25, C:0.13, G:0.14, T:0.49
Consensus pattern (38 bp):
TGCTTTATCAGTTTATTTTAATCCTGATTTAGGATCAT
Found at i:27874 original size:76 final size:76
Alignment explanation
Indices: 27790--28005 Score: 333
Period size: 76 Copynumber: 2.8 Consensus size: 76
27780 TTGTGGGTTT
* * * *
27790 ATTTTAATCCTGATTTAGGACCATTGTTTTATCAATTTATTTTAATCTTGATCTACGATCATTGC
1 ATTTTAATCCTGATTTAGGATCATTGATTTATCAATTTATTTTAATCCTGATCTAGGATCATTGC
27855 TTTATAAGTTA
66 TTTATAAGTTA
*
27866 ATTTTAATCCTGATTTAGGATCATTGATTTATCAATTTATGTTAATCCTGATCTAGGATCATTGC
1 ATTTTAATCCTGATTTAGGATCATTGATTTATCAATTTATTTTAATCCTGATCTAGGATCATTGC
27931 TTTATAAGTTA
66 TTTATAAGTTA
* * * ** *
27942 ATTTTAATCCTGGTTTAGGATCATTAATTTATTAATACATTTTAATCCTGATTTAGGATCATTG
1 ATTTTAATCCTGATTTAGGATCATTGATTTATCAATTTATTTTAATCCTGATCTAGGATCATTG
28006 ATTAATCAGT
Statistics
Matches: 128, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 128 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (76 bp):
ATTTTAATCCTGATTTAGGATCATTGATTTATCAATTTATTTTAATCCTGATCTAGGATCATTGC
TTTATAAGTTA
Found at i:28061 original size:30 final size:30
Alignment explanation
Indices: 27980--28108 Score: 100
Period size: 33 Copynumber: 4.1 Consensus size: 30
27970 TTATTAATAC
* *
27980 ATTTTAATCCTGATTTAGGATCATTGATTAAT
1 ATTTCAATCCTGATTTAGGATCATTGCTT--T
* *
28012 CAGTTTC--TCCCTGACTTAGGATCATGGCTTT
1 -A-TTTCAAT-CCTGATTTAGGATCATTGCTTT
* *
28043 ATTTCAATCCTGATTTAGGATTATTGTTTCAT
1 ATTTCAATCCTGATTTAGGATCATTGCTT--T
* *
28075 GATTTTAATCCTGATTTAGGTTCATTGCTTT
1 -ATTTCAATCCTGATTTAGGATCATTGCTTT
28106 ATT
1 ATT
28109 AGTTATTTTA
Statistics
Matches: 77, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
29 4 0.05
30 21 0.27
31 3 0.04
32 2 0.03
33 44 0.57
34 3 0.04
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47
Consensus pattern (30 bp):
ATTTCAATCCTGATTTAGGATCATTGCTTT
Found at i:28088 original size:63 final size:63
Alignment explanation
Indices: 27980--28108 Score: 152
Period size: 63 Copynumber: 2.0 Consensus size: 63
27970 TTATTAATAC
* *
27980 ATTTTAATCCTGATTTAGGATCATTGATTAATCAGTTTCTCCCTGACTTAGGATCATGGCTTT
1 ATTTCAATCCTGATTTAGGATCATTGATTAATCAGTTTATCCCTGACTTAGGATCATGGCTTT
* * * * * * * *
28043 ATTTCAATCCTGATTTAGGATTATTGTTTCATGATTTTAAT-CCTGATTTAGGTTCATTGCTTT
1 ATTTCAATCCTGATTTAGGATCATTGATTAATCAGTTT-ATCCCTGACTTAGGATCATGGCTTT
28106 ATT
1 ATT
28109 AGTTATTTTA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
63 54 0.98
64 1 0.02
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47
Consensus pattern (63 bp):
ATTTCAATCCTGATTTAGGATCATTGATTAATCAGTTTATCCCTGACTTAGGATCATGGCTTT
Found at i:28482 original size:63 final size:63
Alignment explanation
Indices: 28382--29122 Score: 550
Period size: 63 Copynumber: 12.0 Consensus size: 63
28372 AGTTTCTTAT
** * *
28382 TTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTGTCTTGTTTCAATTCCAAAATCTTG
1 TTCATTT-CAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCTTG
* * * *
28446 TTCATTTCAAATCCTGCTTAAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA-TCTAAAGTCTTTT
1 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATC-TTG
* **
28509 TTCATTTCAAATCCTGTTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATT-TTAAATCTTG
1 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCTTG
** * * * *
28571 TTTCATTTACAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTCCAAATCCAAAATCGTG
1 -TTCATTT-CAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCTTG
* * *
28636 TGCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA-TCTAAAGTCTTG
1 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCTTG
* ** * * * * * ** *** * * * * **
28698 TTTCATTTCAAGTATTGTTTCA--TTTCAAATC--CTGTTTGAGGTCTCTAGTCGAGAGTTTCTT
1 -TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCA-A-AATCTT
28759 G
63 G
** * * * *
28760 TTTCATTTCCAAATCCTAATCGAGGTCTCTAGACGAGTGTTTCTTGTTTCAATTCCAAAATCATG
1 -TTCATTT-CAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCTTG
* *
28825 TTCATTTTAAATCCTGCTTGAGGTCTCTAGTC--GAGTTTCTTGTTTCAATTCCAAAATCATG
1 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCTTG
* * *
28886 TTCATTTTAAATCCTACTTGAGGTCTCTAGTC--GAGTTTCTTGTTTCAA-T-CTAAATCTTG
1 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCTTG
* * * * * * * * *
28945 TTTTATTTTAAATCCTGGTCGAGGTCTCTAGTCAAGAG-----T-TATCAATT-CTAAGTCCTG
1 -TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCTTG
* *
29002 TTTCACTTTCAAATCCTGCTCGAGGTCTCTAGTCCAGAG-----T-TTTCAA-TCCAAAATCTTG
1 -TTCA-TTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCTTG
** * * * *
29060 TTTTGTTTTCAAATCCTGCTTGAGGTCTCTAGCCAAAAGTTTC-TGTTTCAA-TCTAAAATCTTG
1 --TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCTTG
29123 CTCGAGAGTT
Statistics
Matches: 550, Mismatches: 101, Indels: 53
0.78 0.14 0.08
Matches are distributed among these distances:
56 5 0.01
57 15 0.03
58 72 0.13
59 20 0.04
60 32 0.06
61 82 0.15
62 35 0.06
63 198 0.36
64 61 0.11
65 16 0.03
66 1 0.00
67 13 0.02
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (63 bp):
TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCTTG
Found at i:28584 original size:18 final size:18
Alignment explanation
Indices: 28548--28585 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
28538 GTCGAGAGTT
*
28548 TCTTGTTTCAATTTTAAA
1 TCTTGTTTCAATTTCAAA
28566 TCTTGTTTC-ATTTACAAA
1 TCTTGTTTCAATTT-CAAA
28584 TC
1 TC
28586 CTAATCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (18 bp):
TCTTGTTTCAATTTCAAA
Found at i:28642 original size:127 final size:126
Alignment explanation
Indices: 28384--28984 Score: 452
Period size: 127 Copynumber: 4.8 Consensus size: 126
28374 TTTCTTATTT
* * * *
28384 CATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTGTCTTGTTTCAATTCCAAAATCTTG-TT
1 CATTT-CAAATCCTGATTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATT-CTAAATCTTGTTT
** * * * * * * *
28448 CATTTCAAATCCTGCTTAAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTAAAGTCTTTTTT
64 CATTTCAAATCCTAATCAAGGTCTCTAGTCGAGAGTTTCTTGTTCCAATCCAAAATCTGTGTG
* *
28511 CATTTCAAATCCTGTTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTTTAAATCTTGTTTCA
1 CATTTCAAATCCTGATTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCTAAATCTTGTTTCA
*
28576 TTTACAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTCCAAATCCAAAATC-GTGTG
66 TTT-CAAATCCTAATCAAGGTCTCTAGTCGAGAGTTTCTTGTTCC-AATCCAAAATCTGTGTG
*
28638 CATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA-TCTAAAGTCTTGTTTC
1 CATTTCAAATCCTGATTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCTAAA-TCTTGTTTC
** * * * * * * * ***
28702 ATTTCAAGTATTGTTTCATTTCAA-ATC-CT-GTTTGAG-GTCTCTAG-T-CGA--GAGTTTCT-
65 ATTTCAA--A-T-CCT-A-ATCAAGGTCTCTAG-TCGAGAGTTTCTTGTTCCAATCCAAAATCTG
*
28758 TGTTT
123 TG-TG
* * * * * *
28763 CATTTCCAAATCCTAATCGAGGTCTCTAGACGAGTGTTTCTTGTTTCAATTCCAAAATCATG-TT
1 CATTT-CAAATCCTGATTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATT-CTAAATCTTGTTT
* ** ** *
28827 CATTTTAAATCCTGCTTGAGGTCTCTAGTC--GAGTTTCTTGTTTCAATTCCAAAATCATGT-T-
64 CATTTCAAATCCTAATCAAGGTCTCTAGTCGAGAGTTTCTTGTTCCAA-TCCAAAATC-TGTGTG
* *
28888 CATTTTAAATCCT-ACTTGAGGTCTCTAGTC--GAGTTTCTTGTTTCAA-TCTAAATCTTGTTTT
1 CATTTCAAATCCTGA-TTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCTAAATCTTGTTTC
* ** * *
28949 ATTTTAAATCCTGGTCGAGGTCTCTAGTCAAGAGTT
65 ATTTCAAATCCTAATCAAGGTCTCTAGTCGAGAGTT
28985 ATCAATTCTA
Statistics
Matches: 379, Mismatches: 64, Indels: 66
0.74 0.13 0.13
Matches are distributed among these distances:
120 11 0.03
121 38 0.10
122 20 0.05
123 10 0.03
124 26 0.07
125 19 0.05
126 108 0.28
127 110 0.29
128 16 0.04
129 8 0.02
130 7 0.02
131 3 0.01
132 3 0.01
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (126 bp):
CATTTCAAATCCTGATTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCTAAATCTTGTTTCA
TTTCAAATCCTAATCAAGGTCTCTAGTCGAGAGTTTCTTGTTCCAATCCAAAATCTGTGTG
Found at i:28704 original size:190 final size:189
Alignment explanation
Indices: 28376--29122 Score: 738
Period size: 190 Copynumber: 4.0 Consensus size: 189
28366 GTCGGGAGTT
* *
28376 TCTTATTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTGTCTTGTTTCAATTCCAAAA
1 TCTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAA
* *
28441 TCTTGTTCATTTCAAATCCTGCTTAAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTAAAGTCT
66 TCATGTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTAAAGTCT
*
28506 TTTTTCATTTCAAATCCTGTTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTTTAAA
131 TGTTTCATTTCAAATCCTGTTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA-TTTAAA
* * *
28566 TCTTGTTTCATTTACAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTCCAAATCCAAAA
1 TCTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAA
* *
28631 TCGTGTGCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTAAAGTCT
66 TCATGTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTAAAGTCT
* ** * ** * * * *
28696 TGTTTCATTTCAAGTATTGTTTCATTTCAAATCCT-GTTTGAG-GTCTCTAG--TCGAGAGTT--
131 TGTTTCATTTCAAATCCTGTTTGAGGTC---T-CTAG-TCGAGAGTTTCTTGTTTC-A-ATTTAA
28755 -
189 A
* *
28755 TCTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGACGAGTGTTTCTTGTTTCAATTCCAAAA
1 TCTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAA
* * *
28820 TCATGTTCATTTTAAATCCTGCTTGAGGTCTCTAGTC--GAGTTTCTTGTTTCAATTCCAAAATC
66 TCATGTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA-TCTAAAGTC
* * ** *
28883 ATG-TTCATTTTAAATCCTACTTGAGGTCTCTAGTC--GAGTTTCTTGTTTCAATCTAAA
130 TTGTTTCATTTCAAATCCTGTTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTTAAA
* * ** * * * *
28940 TCTTGTTTTATTT-TAAATCCTGGTCGAGGTCTCTAGTCAAGAG-----T-TATCAATT-CTAAG
1 TCTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAA
* * * * *
28997 TCCTGTTTCACTTTCAAATCCTGCTCGAGGTCTCTAGTCCAGAG-----T-TTTCAATCCAAAAT
66 TCATG-TTCA-TTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTAAAGT
** * * * * *
29056 CTTGTTTTGTTTTCAAATCCTGCTTGAGGTCTCTAGCCAAAAGTTTC-TGTTTCAATCTAAAA
129 CTTG-TTTCATTTCAAATCCTGTTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAAT-TTAAA
29118 TCTTG
1 TCTTG
29123 CTCGAGAGTT
Statistics
Matches: 467, Mismatches: 66, Indels: 60
0.79 0.11 0.10
Matches are distributed among these distances:
174 11 0.02
175 6 0.01
176 28 0.06
177 16 0.03
178 25 0.05
179 27 0.06
181 4 0.01
182 8 0.02
183 4 0.01
184 28 0.06
185 12 0.03
187 32 0.07
188 9 0.02
189 94 0.20
190 143 0.31
191 2 0.00
192 3 0.01
193 9 0.02
194 6 0.01
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (189 bp):
TCTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAA
TCATGTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTAAAGTCT
TGTTTCATTTCAAATCCTGTTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTTAAA
Found at i:28715 original size:17 final size:17
Alignment explanation
Indices: 28690--28725 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
28680 TTTCAATCTA
*
28690 AAGTCTTGTTTCATTTC
1 AAGTATTGTTTCATTTC
28707 AAGTATTGTTTCATTTC
1 AAGTATTGTTTCATTTC
28724 AA
1 AA
28726 ATCCTGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.50
Consensus pattern (17 bp):
AAGTATTGTTTCATTTC
Found at i:28733 original size:17 final size:17
Alignment explanation
Indices: 28696--28734 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
28686 TCTAAAGTCT
* *
28696 TGTTTCATTTCAAGTAT
1 TGTTTCATTTCAAATAC
*
28713 TGTTTCATTTCAAATCC
1 TGTTTCATTTCAAATAC
28730 TGTTT
1 TGTTT
28735 GAGGTCTCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.15, G:0.10, T:0.54
Consensus pattern (17 bp):
TGTTTCATTTCAAATAC
Found at i:28785 original size:46 final size:46
Alignment explanation
Indices: 28712--28818 Score: 153
Period size: 46 Copynumber: 2.3 Consensus size: 46
28702 ATTTCAAGTA
** * *
28712 TTGTTTCATTT-CAAATCCTGTTTGAGGTCTCTAGTCGAGAGTTTC
1 TTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGACGAGAGTTTC
*
28757 TTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGACGAGTGTTTC
1 TTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGACGAGAGTTTC
*
28803 TTGTTTCAATTCCAAA
1 TTGTTTCATTTCCAAA
28819 ATCATGTTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
45 11 0.20
46 44 0.80
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.42
Consensus pattern (46 bp):
TTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGACGAGAGTTTC
Found at i:29101 original size:58 final size:57
Alignment explanation
Indices: 28928--29101 Score: 208
Period size: 58 Copynumber: 3.0 Consensus size: 57
28918 GAGTTTCTTG
* *
28928 TTTCAATCTAAATCTTGTTTTATTTT-AAATCCTGGTCGAGGTCTCTAGTCAAGAGT
1 TTTCAATCTAAATCTTGTTTTATTTTCAAATCCTGCTCGAGGTCTCTAGCCAAGAGT
* * * * *
28984 TATCAATTCTAAGTCCTGTTTCACTTTCAAATCCTGCTCGAGGTCTCTAGTCC-AGAGT
1 TTTCAA-TCTAAATCTTGTTTTATTTTCAAATCCTGCTCGAGGTCTCTAG-CCAAGAGT
* * * *
29042 TTTCAATCCAAAATCTTGTTTTGTTTTCAAATCCTGCTTGAGGTCTCTAGCCAAAAGT
1 TTTCAAT-CTAAATCTTGTTTTATTTTCAAATCCTGCTCGAGGTCTCTAGCCAAGAGT
29100 TT
1 TT
29102 CTGTTTCAAT
Statistics
Matches: 97, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
56 5 0.05
57 19 0.20
58 72 0.74
59 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (57 bp):
TTTCAATCTAAATCTTGTTTTATTTTCAAATCCTGCTCGAGGTCTCTAGCCAAGAGT
Found at i:35825 original size:16 final size:16
Alignment explanation
Indices: 35790--35826 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
35780 TGATGAATTT
**
35790 AATTACTAACAAATTT
1 AATTACTAACAAATGG
35806 AATTACTAACAAATGG
1 AATTACTAACAAATGG
35822 AATTA
1 AATTA
35827 ATTACTGGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (16 bp):
AATTACTAACAAATGG
Found at i:35832 original size:20 final size:16
Alignment explanation
Indices: 35785--35819 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
35775 TGGCATGATG
35785 AATTTAATTACTAACA
1 AATTTAATTACTAACA
35801 AATTTAATTACTAACA
1 AATTTAATTACTAACA
35817 AAT
1 AAT
35820 GGAATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.37
Consensus pattern (16 bp):
AATTTAATTACTAACA
Found at i:40883 original size:17 final size:17
Alignment explanation
Indices: 40861--40936 Score: 55
Period size: 17 Copynumber: 4.4 Consensus size: 17
40851 TCGAAAGTGA
* *
40861 ATCCGAACCTGACCCGG
1 ATCCGAACCCGAACCGG
*
40878 ATCCGAACCCGAACCTG
1 ATCCGAACCCGAACCGG
* * *
40895 ATCCGAGCCCTAACCCGA
1 ATCCGAACCCGAA-CCGG
* *
40913 ATCCG-ATCCGAATCCGA
1 ATCCGAACCCGAA-CCGG
40930 ATCCGAA
1 ATCCGAA
40937 AATACCCAAA
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
17 38 0.83
18 8 0.17
ACGTcount: A:0.29, C:0.39, G:0.18, T:0.13
Consensus pattern (17 bp):
ATCCGAACCCGAACCGG
Found at i:40935 original size:23 final size:23
Alignment explanation
Indices: 40863--40936 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 23
40853 GAAAGTGAAT
* *
40863 CCGAACCTGACCCGGATCCGAAC
1 CCGAACCTGATCCGAATCCGAAC
** *
40886 CCGAACCTGATCCGAGCCCTAAC
1 CCGAACCTGATCCGAATCCGAAC
*
40909 CCGAATCC-GATCCGAATCCGAAT
1 CCGAA-CCTGATCCGAATCCGAAC
40932 CCGAA
1 CCGAA
40937 AATACCCAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 39 0.95
24 2 0.05
ACGTcount: A:0.28, C:0.41, G:0.19, T:0.12
Consensus pattern (23 bp):
CCGAACCTGATCCGAATCCGAAC
Found at i:40976 original size:15 final size:16
Alignment explanation
Indices: 40926--40980 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
40916 CGATCCGAAT
*
40926 CCGAATCCGAAAATAC
1 CCGAACCCGAAAATAC
* *
40942 CCAAACCCGAAAATAA
1 CCGAACCCGAAAATAC
40958 CCGAACCCG-AAATAC
1 CCGAACCCGAAAATAC
40973 CCGAACCC
1 CCGAACCC
40981 AAACCCGCCC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 13 0.38
16 21 0.62
ACGTcount: A:0.44, C:0.38, G:0.11, T:0.07
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:41218 original size:18 final size:18
Alignment explanation
Indices: 41195--41233 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
41185 TAATGGATAA
41195 TTTATTTTTTTCTTTTCT
1 TTTATTTTTTTCTTTTCT
*
41213 TTTATTTTTTTCTTTTGT
1 TTTATTTTTTTCTTTTCT
41231 TTT
1 TTT
41234 TTTATTAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.08, G:0.03, T:0.85
Consensus pattern (18 bp):
TTTATTTTTTTCTTTTCT
Found at i:41223 original size:13 final size:13
Alignment explanation
Indices: 41207--41236 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41197 TATTTTTTTC
41207 TTTTCTTTTATTT
1 TTTTCTTTTATTT
*
41220 TTTTCTTTTGTTT
1 TTTTCTTTTATTT
41233 TTTT
1 TTTT
41237 ATTAGTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.03, C:0.07, G:0.03, T:0.87
Consensus pattern (13 bp):
TTTTCTTTTATTT
Found at i:41341 original size:15 final size:15
Alignment explanation
Indices: 41323--41353 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41313 ATATTGGAAT
*
41323 TAATTATAATTTTAA
1 TAATTATAATTATAA
41338 TAATTATAATTATAA
1 TAATTATAATTATAA
41353 T
1 T
41354 TATATACCCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTATAATTATAA
Found at i:48034 original size:33 final size:32
Alignment explanation
Indices: 47997--48083 Score: 102
Period size: 33 Copynumber: 2.6 Consensus size: 32
47987 AAATTTTGTT
* *
47997 TCATCACAAACAACACCTAAAGCAGATTTAGTG
1 TCATCGCAAACAACA-CTAAAGCAGATTTAGTA
**
48030 TCATCGCAAACAACACTCAAATTAGATTTAGTA
1 TCATCGCAAACAACACT-AAAGCAGATTTAGTA
*
48063 TCACCGCAAACAACATCTAAA
1 TCATCGCAAACAACA-CTAAA
48084 TCACTCTTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 2 0.04
33 43 0.91
34 2 0.04
ACGTcount: A:0.44, C:0.25, G:0.09, T:0.22
Consensus pattern (32 bp):
TCATCGCAAACAACACTAAAGCAGATTTAGTA
Found at i:51288 original size:30 final size:30
Alignment explanation
Indices: 51248--51306 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
51238 TGTCTTCAAG
51248 TCCATAATAAGTCCTT-GGCGCATCATTCCT
1 TCCATAATAAG-CCTTGGGCGCATCATTCCT
*
51278 TCCATGATAAGCCTTGGGCGCATCATTCC
1 TCCATAATAAGCCTTGGGCGCATCATTCC
51307 CTCCCCCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATCATTCCT
Found at i:51727 original size:33 final size:33
Alignment explanation
Indices: 51685--51800 Score: 178
Period size: 33 Copynumber: 3.5 Consensus size: 33
51675 TTCTTTTCAT
** *
51685 CCAAAACAGAATTATTTTTAATGCTATAATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
51718 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
* *
51751 TCAAAACAGAATTATGTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
*
51784 CCAAAACAAAATTATTT
1 CCAAAACAGAATTATTT
51801 TCACCACAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.29
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:51822 original size:66 final size:66
Alignment explanation
Indices: 51682--51826 Score: 166
Period size: 66 Copynumber: 2.2 Consensus size: 66
51672 TCTTTCTTTT
* ** * ** *
51682 CATCCAAAACAGAATTATTTTTAATGCTATAATCAACCAAAACAGAATTATTTGCAATGCTATGA
1 CATCCAAAACAGAATTATGTGCAATGCTATAATCAACCAAAACAAAATTATTTGCAACACAATGA
*
51747 T
66 G
* * * *
51748 CAAT-CAAAACAGAATTATGTGCAATGCTATGATCAACCAAAACAAAATTATTTTCACCACAATT
1 C-ATCCAAAACAGAATTATGTGCAATGCTATAATCAACCAAAACAAAATTATTTGCAACACAATG
51812 AG
65 AG
51814 CATCCAAAACAGA
1 CATCCAAAACAGA
51827 TTTAGTATCA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
65 2 0.03
66 61 0.94
67 2 0.03
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.27
Consensus pattern (66 bp):
CATCCAAAACAGAATTATGTGCAATGCTATAATCAACCAAAACAAAATTATTTGCAACACAATGA
G
Found at i:51856 original size:33 final size:33
Alignment explanation
Indices: 51818--51914 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 33
51808 AATTAGCATC
51818 CAAAACAGATTTAGTATCATCACAAACAACACT
1 CAAAACAGATTTAGTATCATCACAAACAACACT
* * **
51851 TAAAACAGATTTAGTGTCATTGCAAACAACACT
1 CAAAACAGATTTAGTATCATCACAAACAACACT
** *
51884 CAAATTAGGTTTAGTATCATCACAAACAACA
1 CAAAACAGATTTAGTATCATCACAAACAACA
51915 TCTAAAAGAC
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.25
Consensus pattern (33 bp):
CAAAACAGATTTAGTATCATCACAAACAACACT
Done.