Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012640.1 Corchorus olitorius cultivar O-4 contig12673, 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: 70949
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:15995 original size:3 final size:3
Alignment explanation
Indices: 15987--16014 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
15977 CAACATTTGT
15987 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
16015 GCTTAGACCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:17092 original size:15 final size:15
Alignment explanation
Indices: 17056--17103 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
17046 GCATGGTGAG
17056 GAGATGACATCTTAC
1 GAGATGACATCTTAC
17071 --GA-G--ATCTTAC
1 GAGATGACATCTTAC
17081 GAGATGACATCTTAC
1 GAGATGACATCTTAC
17096 GAGATGAC
1 GAGATGAC
17104 GTGAAGGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
10 7 0.25
12 3 0.11
13 3 0.11
15 15 0.54
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (15 bp):
GAGATGACATCTTAC
Found at i:19345 original size:6 final size:6
Alignment explanation
Indices: 19336--19380 Score: 72
Period size: 6 Copynumber: 7.2 Consensus size: 6
19326 TTAATCCTAA
19336 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTTCT CTCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTTT-T -TCTTTT T
19381 ACTCTATTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 30 0.81
7 2 0.05
8 5 0.14
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:24134 original size:29 final size:31
Alignment explanation
Indices: 24076--24139 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
24066 CCAAAAAAAA
* *
24076 GTTTTTCTTTCGGGACAAAATAACCCCTTAT
1 GTTTTTCTTTCGGGACAAAATAACCACTTAC
* *
24107 GTTTTT-TTT-GGGACAAATTAATCACTTAC
1 GTTTTTCTTTCGGGACAAAATAACCACTTAC
24136 GTTT
1 GTTT
24140 CAAAAGTGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 20 0.69
30 3 0.10
31 6 0.21
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (31 bp):
GTTTTTCTTTCGGGACAAAATAACCACTTAC
Found at i:25722 original size:27 final size:27
Alignment explanation
Indices: 25699--25804 Score: 81
Period size: 27 Copynumber: 4.2 Consensus size: 27
25689 TATTTATCTA
*
25699 TTATTTATTT-ACTATTTATCTTATTAT
1 TTATTAATTTAACTA-TTATCTTATTAT
25726 TTATTAATTTAACTATTATC----TA-
1 TTATTAATTTAACTATTATCTTATTAT
*
25748 -T-TT-ATTT-ACTATTTATCTTTTTAT
1 TTATTAATTTAACTA-TTATCTTATTAT
*
25772 TTATTAATTTAGCTATTATC-TATTTAT
1 TTATTAATTTAACTATTATCTTA-TTAT
25799 TTATTA
1 TTATTA
25805 TTATTATCTT
Statistics
Matches: 64, Mismatches: 3, Indels: 24
0.70 0.03 0.26
Matches are distributed among these distances:
18 4 0.06
19 9 0.14
20 2 0.03
21 1 0.02
23 4 0.06
25 1 0.02
26 3 0.05
27 33 0.52
28 7 0.11
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.63
Consensus pattern (27 bp):
TTATTAATTTAACTATTATCTTATTAT
Found at i:25727 original size:19 final size:19
Alignment explanation
Indices: 25688--25806 Score: 65
Period size: 19 Copynumber: 6.3 Consensus size: 19
25678 TTTCTTATAG
25688 CTATTTATCTATTATTTATTTA
1 CTATTTATC--TTA-TTATTTA
25710 CTATTTATCTTATTATTTA
1 CTATTTATCTTATTATTTA
* *
25729 TTAATTTAAC-TATTA--T-
1 CT-ATTTATCTTATTATTTA
*
25745 CTATTTAT-TTACTATTTA
1 CTATTTATCTTATTATTTA
*
25763 TCTTTTTAT-TTATTAATTTA
1 -CTATTTATCTTATT-ATTTA
25783 GCTA-TTATC-TATTTATTTA
1 -CTATTTATCTTA-TTATTTA
*
25802 TTATT
1 CTATT
25807 ATTATCTTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
15 9 0.12
16 1 0.01
17 2 0.03
18 2 0.03
19 36 0.47
20 18 0.23
22 9 0.12
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.63
Consensus pattern (19 bp):
CTATTTATCTTATTATTTA
Found at i:25752 original size:8 final size:8
Alignment explanation
Indices: 25688--25900 Score: 61
Period size: 8 Copynumber: 27.6 Consensus size: 8
25678 TTTCTTATAG
25688 CTATTTAT
1 CTATTTAT
25696 CTA-TTAT
1 CTATTTAT
*
25703 TTATTTA-
1 CTATTTAT
25710 CTATTTAT
1 CTATTTAT
25718 C---TTAT
1 CTATTTAT
25723 -TATTTAT
1 CTATTTAT
*
25730 -TAATTTAA
1 CT-ATTTAT
25738 CTA-TTAT
1 CTATTTAT
25745 CTATTTATTT
1 CTATTTA--T
25755 ACTATTTAT
1 -CTATTTAT
25764 C--TTT-T
1 CTATTTAT
25769 -TATTTAT
1 CTATTTAT
*
25776 -TAATTTAG
1 CT-ATTTAT
25784 CTA-TTAT
1 CTATTTAT
25791 CTATTTAT
1 CTATTTAT
*
25799 TTA-TTAT
1 CTATTTAT
25806 -TA-TTAT
1 CTATTTAT
* *
25812 CTTTTTTTTT
1 C--TATTTAT
25822 CT-TTTACCT
1 CTATTTA--T
25831 ACCTATTTAT
1 --CTATTTAT
25841 CTA-TTATT
1 CTATTTA-T
* *
25849 CTCTGTAT
1 CTATTTAT
25857 CTATTTAT
1 CTATTTAT
25865 CTATTTAT
1 CTATTTAT
** * *
25873 CCCTATAC
1 CTATTTAT
25881 CTATTTAT
1 CTATTTAT
25889 CT-TTTAT
1 CTATTTAT
*
25896 TTATT
1 CTATT
25901 ATTATTATTA
Statistics
Matches: 153, Mismatches: 23, Indels: 58
0.65 0.10 0.25
Matches are distributed among these distances:
5 5 0.03
6 12 0.08
7 47 0.31
8 63 0.41
9 7 0.05
10 6 0.04
11 9 0.06
12 4 0.03
ACGTcount: A:0.24, C:0.13, G:0.01, T:0.62
Consensus pattern (8 bp):
CTATTTAT
Found at i:25763 original size:46 final size:46
Alignment explanation
Indices: 25700--25806 Score: 187
Period size: 46 Copynumber: 2.3 Consensus size: 46
25690 ATTTATCTAT
25700 TATTTATTTACTATTTATCTTATTATTTATTAATTTAACTATTATC
1 TATTTATTTACTATTTATCTTATTATTTATTAATTTAACTATTATC
* *
25746 TATTTATTTACTATTTATCTTTTTATTTATTAATTTAGCTATTATC
1 TATTTATTTACTATTTATCTTATTATTTATTAATTTAACTATTATC
*
25792 TATTTATTTATTATT
1 TATTTATTTACTATT
25807 ATTATCTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (46 bp):
TATTTATTTACTATTTATCTTATTATTTATTAATTTAACTATTATC
Found at i:25860 original size:24 final size:24
Alignment explanation
Indices: 25830--25896 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
25820 TTCTTTTACC
* *
25830 TACCTATTTATCTATTATTCTCTG
1 TACCTATTTATCTATTATTCCCTA
*
25854 TATCTATTTATCTATT-TATCCCTA
1 TACCTATTTATCTATTAT-TCCCTA
*
25878 TACCTATTTATCTTTTATT
1 TACCTATTTATCTATTATT
25897 TATTATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 34 0.94
25 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.01, T:0.57
Consensus pattern (24 bp):
TACCTATTTATCTATTATTCCCTA
Found at i:25904 original size:3 final size:3
Alignment explanation
Indices: 25896--25954 Score: 104
Period size: 3 Copynumber: 20.3 Consensus size: 3
25886 TATCTTTTAT
25896 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25943 TTA TT- TTA TTA T
1 TTA TTA TTA TTA T
25955 ATTTTAAAAC
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.07
3 50 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:39920 original size:54 final size:53
Alignment explanation
Indices: 39852--40541 Score: 606
Period size: 54 Copynumber: 12.8 Consensus size: 53
39842 TTTTGTAGAA
39852 AGTTGATCCTTAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAATGATCAG
1 AGTTGATCC-TAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAATGATCAG
* * * * *
39906 AGTTGATCCCTAGATGATCTAGTGTGGCCATTCCAAGAAGTTTCTAATAATCAG
1 AGTTGAT-CCTAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAATGATCAG
* * *
39960 AGTTGATCCTCAGATGATCCAGTGCGGTCATTCCAACAAGTTTTCAATGGTCAG
1 AGTTGATCCT-AGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAATGATCAG
* * * *
40014 AGTTGATCCTCAAATGATCCAGTGCGATCATTCCAAGAAATTTTTAATGAACAG
1 AGTTGATCCT-AGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAATGATCAG
* *
40068 AGTTGATCCTCAAATGATCCAGTGCGGTCATTCCAAGAAGTTTTCAATGATCAG
1 AGTTGATCCT-AGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAATGATCAG
* *
40122 AGTTGATCCTCAGATGATCCAGTGCAGTCATTGCAAGAAGTTTTTAATGATCAG
1 AGTTGATCCT-AGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAATGATCAG
* * * *
40176 AGTTGATCTCCAGATGATCCAGTGCGGTCCTTCCGAGAAGTTTTTGAA-GTTCAG
1 AGTTGATC-CTAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTT-AATGATCAG
* * * *
40230 AGTTGAAGTCC-AGATGATCCAGTGCGGTTC-TTCCGAGAAGTTTTCAAAGATCAA
1 AGTTG-A-TCCTAGATGATCCAGTGCGG-TCATTCCAAGAAGTTTTTAATGATCAG
* * * ** * ** *
40284 AGTTGATCTTTAGATGGTCCGGTGCGGTTGTTTCAAGAAGTTTCCGAA-GATTAG
1 AGTTGATC-CTAGATGATCCAGTGCGGTCATTCCAAGAAGTTT-TTAATGATCAG
* * * ** *
40338 AGTTGATCTTCAGATGATCCGGTGTGGTCATTTGAAGAAGTTTTTGAA-AATCAG
1 AGTTGATCCT-AGATGATCCAGTGCGGTCATTCCAAGAAGTTTTT-AATGATCAG
* * * * * **
40392 AGTTGATCTCCAAATGATCCAGTGTGGTCGTT-CAAAAAGTTTTCGATGATCAG
1 AGTTGATC-CTAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAATGATCAG
* ** * * **
40445 AGTTGATCTCCA-ATTTGATCCAGTATGGTCACTCCAAGAAAGGTTTTCGTGATC-G
1 AGTTGATC-CTAGA--TGATCCAGTGCGGTCATTCCAAG-AAGTTTTTAATGATCAG
* * * *
40500 AGGTTGCATCTTAAATGATCCAGTGCGGTTATT-TAAGAAGTT
1 A-GTTG-ATCCTAGATGATCCAGTGCGGTCATTCCAAGAAGTT
40542 CAAGTTTGAA
Statistics
Matches: 531, Mismatches: 82, Indels: 47
0.80 0.12 0.07
Matches are distributed among these distances:
52 4 0.01
53 39 0.07
54 436 0.82
55 30 0.06
56 18 0.03
57 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (53 bp):
AGTTGATCCTAGATGATCCAGTGCGGTCATTCCAAGAAGTTTTTAATGATCAG
Found at i:40704 original size:113 final size:113
Alignment explanation
Indices: 40506--40740 Score: 452
Period size: 113 Copynumber: 2.1 Consensus size: 113
40496 ATCGAGGTTG
* *
40506 CATCTTAAATGATCCAGTGCGGTTATTTAAGAAGTTCAAGTTTGAAGCTTGAAGGAGTGAAAGAA
1 CATCTAAAATGATCCAGTGCGGTTATTTAAGAAGTTCAAGTTTGAAGCTTGAAGGAGCGAAAGAA
40571 GAAAGAGTTCAAGCGCAACAGTGTCTACGTCTTTGTGTACTTCCCGTT
66 GAAAGAGTTCAAGCGCAACAGTGTCTACGTCTTTGTGTACTTCCCGTT
40619 CATCTAAAATGATCCAGTGCGGTTATTTAAGAAGTTCAAGTTTGAAGCTTGAAGGAGCGAAAGAA
1 CATCTAAAATGATCCAGTGCGGTTATTTAAGAAGTTCAAGTTTGAAGCTTGAAGGAGCGAAAGAA
40684 GAAAGAGTTCAAGCGCAACAGTGTCTACGTCTTTGTGTACTTCCCGTT
66 GAAAGAGTTCAAGCGCAACAGTGTCTACGTCTTTGTGTACTTCCCGTT
40732 CATCTAAAA
1 CATCTAAAA
40741 ATACGAAAAG
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 120 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (113 bp):
CATCTAAAATGATCCAGTGCGGTTATTTAAGAAGTTCAAGTTTGAAGCTTGAAGGAGCGAAAGAA
GAAAGAGTTCAAGCGCAACAGTGTCTACGTCTTTGTGTACTTCCCGTT
Found at i:42095 original size:4 final size:4
Alignment explanation
Indices: 42076--42180 Score: 51
Period size: 4 Copynumber: 27.0 Consensus size: 4
42066 TTTCTATAGC
* * *
42076 TATT TATC TA-T TATT TATT TA-C TATT TATCT TA-T TATT TATT AATT
1 TATT TATT TATT TATT TATT TATT TATT TAT-T TATT TATT TATT TATT
** * * ** *
42122 TAAC TA-T TATC TATT TATAT T-TT TAATT TATT AATT TAGC TA-T TATC
1 TATT TATT TATT TATT TAT-T TATT T-ATT TATT TATT TATT TATT TATT
42169 TATT TATT TATT
1 TATT TATT TATT
42181 ATTATTATCT
Statistics
Matches: 74, Mismatches: 18, Indels: 18
0.67 0.16 0.16
Matches are distributed among these distances:
3 13 0.18
4 53 0.72
5 8 0.11
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.63
Consensus pattern (4 bp):
TATT
Found at i:42096 original size:15 final size:15
Alignment explanation
Indices: 42076--42183 Score: 55
Period size: 15 Copynumber: 7.0 Consensus size: 15
42066 TTTCTATAGC
42076 TATTTATCTATTATT
1 TATTTATCTATTATT
42091 TATTTA-CTATTTATCT
1 TATTTATCTA-TTAT-T
*
42107 TA-TTATTTATTAATT
1 TATTTATCTATT-ATT
*
42122 TAACTATTATCTATT-TA
1 T-A-T-TTATCTATTATT
42139 TATTT-T-TAATTTATT
1 TATTTATCT-A-TTATT
* * *
42154 AATTTAGCTATTATC
1 TATTTATCTATTATT
*
42169 TATTTATTTATTATT
1 TATTTATCTATTATT
42184 ATTATCTTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 26
0.65 0.10 0.25
Matches are distributed among these distances:
12 1 0.01
13 2 0.03
14 7 0.10
15 38 0.55
16 10 0.14
17 3 0.04
19 8 0.12
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.63
Consensus pattern (15 bp):
TATTTATCTATTATT
Found at i:42109 original size:27 final size:27
Alignment explanation
Indices: 42086--42151 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
42076 TATTTATCTA
*
42086 TTATTTATTT-ACTATTTATCTTATTAT
1 TTATTAATTTAACTA-TTATCTTATTAT
42113 TTATTAATTTAACTATTATC-TATTTAT
1 TTATTAATTTAACTATTATCTTA-TTAT
*
42140 ATTTTTAATTTA
1 -TTATTAATTTA
42152 TTAATTTAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 2 0.06
27 18 0.53
28 14 0.41
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (27 bp):
TTATTAATTTAACTATTATCTTATTAT
Found at i:42139 original size:8 final size:8
Alignment explanation
Indices: 42075--42180 Score: 51
Period size: 7 Copynumber: 14.6 Consensus size: 8
42065 TTTTCTATAG
42075 CTATTTAT
1 CTATTTAT
42083 CTA-TTAT
1 CTATTTAT
*
42090 TTATTTA-
1 CTATTTAT
42097 CTATTTAT
1 CTATTTAT
42105 C---TTAT
1 CTATTTAT
42110 -TATTTAT
1 CTATTTAT
*
42117 -TAATTTAA
1 CT-ATTTAT
42125 CTA-TTAT
1 CTATTTAT
42132 CTATTTA-
1 CTATTTAT
42139 -TATTT-T
1 CTATTTAT
42145 -TAATTTAT
1 CT-ATTTAT
*
42153 -TAATTTAG
1 CT-ATTTAT
42161 CTA-TTAT
1 CTATTTAT
42168 CTATTTAT
1 CTATTTAT
*
42176 TTATT
1 CTATT
42181 ATTATTATCT
Statistics
Matches: 78, Mismatches: 7, Indels: 26
0.70 0.06 0.23
Matches are distributed among these distances:
5 4 0.05
6 6 0.08
7 33 0.42
8 33 0.42
9 2 0.03
ACGTcount: A:0.29, C:0.08, G:0.01, T:0.62
Consensus pattern (8 bp):
CTATTTAT
Found at i:42154 original size:36 final size:35
Alignment explanation
Indices: 42097--42187 Score: 132
Period size: 36 Copynumber: 2.6 Consensus size: 35
42087 TATTTATTTA
*
42097 CTATTTATCTTATTATTTATTAATTTAACTATTAT
1 CTATTTATATTATTATTTATTAATTTAACTATTAT
* *
42132 CTATTTATATTTTTAATTTATTAATTTAGCTATTAT
1 CTATTTATATTATT-ATTTATTAATTTAACTATTAT
42168 CTATTTAT-TTATTA-TTATTA
1 CTATTTATATTATTATTTATTA
42188 TCTTTTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
33 6 0.12
34 1 0.02
35 16 0.31
36 28 0.55
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.62
Consensus pattern (35 bp):
CTATTTATATTATTATTTATTAATTTAACTATTAT
Found at i:42188 original size:21 final size:21
Alignment explanation
Indices: 42162--42225 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
42152 TTAATTTAGC
42162 TATTATCTATTTATTTATTAT
1 TATTATCTATTTATTTATTAT
* * *
42183 TATTATCTTTTTTTTTCTT-T
1 TATTATCTATTTATTTATTAT
* *
42203 TACTTACCTATTTATCTATTAT
1 TA-TTATCTATTTATTTATTAT
42225 T
1 T
42226 CTCTATGTCC
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
20 3 0.09
21 28 0.85
22 2 0.06
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTATCTATTTATTTATTAT
Found at i:45358 original size:40 final size:40
Alignment explanation
Indices: 45293--45373 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
45283 ACCACTCCAA
* * *
45293 TTTCCTGCTGTAGAAGTCGATGCTCTTCTCAATCAATGGG
1 TTTCCTGCTGTAGAAGTCAACGCTCTTCTCAACCAATGGG
*
45333 TTTCTTGCTGTAGAAGTCAACGCTCTTCTCAACCAATGGG
1 TTTCCTGCTGTAGAAGTCAACGCTCTTCTCAACCAATGGG
45373 T
1 T
45374 GGTACAGAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (40 bp):
TTTCCTGCTGTAGAAGTCAACGCTCTTCTCAACCAATGGG
Found at i:45689 original size:10 final size:11
Alignment explanation
Indices: 45649--45692 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
45639 TTTGCTTAGT
45649 GTTCGTTTAATA
1 GTTCGTTT-ATA
*
45661 GATCGTTTATA
1 GTTCGTTTATA
*
45672 GCTCGTTTAT-
1 GTTCGTTTATA
45682 GTTCGTTTATA
1 GTTCGTTTATA
45693 TTGCATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 9 0.32
11 12 0.43
12 7 0.25
ACGTcount: A:0.20, C:0.11, G:0.18, T:0.50
Consensus pattern (11 bp):
GTTCGTTTATA
Found at i:50447 original size:20 final size:18
Alignment explanation
Indices: 50424--50460 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
50414 ATCATTTTCT
50424 TTTTCATTACTTTATTTTTA
1 TTTTCATT--TTTATTTTTA
50444 TTTTCATTTTTATTTTT
1 TTTTCATTTTTATTTTT
50461 TGTTTAAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTCATTTTTATTTTTA
Found at i:52958 original size:17 final size:16
Alignment explanation
Indices: 52904--52954 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
52894 ATCACCCCCC
*
52904 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
52921 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
52938 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
52954 A
1 A
52955 AGATTACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:55303 original size:3 final size:3
Alignment explanation
Indices: 55295--55326 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
55285 TGAAGATTTT
*
55295 AAG AAG AAG GAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
55327 CAACAACAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:55392 original size:21 final size:21
Alignment explanation
Indices: 55367--55418 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
55357 GATGATAAAC
* *
55367 TTTTTATCTTTTTTTTAATGT-
1 TTTTTTTCTTTGTTTTAA-GTA
55388 TTTTTTTC-TTGTTTTAAGTA
1 TTTTTTTCTTTGTTTTAAGTA
55408 TTTTTTTCTTT
1 TTTTTTTCTTT
55419 CTCATATGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 16 0.59
21 9 0.33
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.77
Consensus pattern (21 bp):
TTTTTTTCTTTGTTTTAAGTA
Found at i:55582 original size:30 final size:31
Alignment explanation
Indices: 55511--55585 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 31
55501 CCCGTCTGAT
*
55511 TGTATCCTGAATTGACACAACCCCATAACGT
1 TGTATCCTGAATTGACACAACCCCATAACGA
* * * ** *
55542 TATATACTGAATTGATACAA-GTCGTAACGA
1 TGTATCCTGAATTGACACAACCCCATAACGA
55572 TGTATCCTGAATTG
1 TGTATCCTGAATTG
55586 CATTTTTACC
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
30 18 0.51
31 17 0.49
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (31 bp):
TGTATCCTGAATTGACACAACCCCATAACGA
Found at i:60553 original size:45 final size:45
Alignment explanation
Indices: 60489--60574 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
60479 TACCAACAAT
*
60489 AATGCTACCACAAAATCTTGCCAAAACAGAATGTTACCGCAGCAG
1 AATGCTACCACAAAATCTTGCCAAAACAAAATGTTACCGCAGCAG
* *
60534 AATGCTACCACAAAATCTTGCCACAGCAAAATGTTACCGCA
1 AATGCTACCACAAAATCTTGCCAAAACAAAATGTTACCGCA
60575 ACGGAATGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.19
Consensus pattern (45 bp):
AATGCTACCACAAAATCTTGCCAAAACAAAATGTTACCGCAGCAG
Found at i:60582 original size:45 final size:45
Alignment explanation
Indices: 60489--60590 Score: 143
Period size: 45 Copynumber: 2.3 Consensus size: 45
60479 TACCAACAAT
* *
60489 AATGCTACCACAAAATCTTGCCAAAACAGAATGTTACCGCAGCAG
1 AATGCTACCACAAAATCTTGCCAAAACAAAATGTTACCGCAACAG
* * *
60534 AATGCTACCACAAAATCTTGCCACAGCAAAATGTTACCGCAACGG
1 AATGCTACCACAAAATCTTGCCAAAACAAAATGTTACCGCAACAG
60579 AATG-TCACCACA
1 AATGCT-ACCACA
60591 GTGGAATGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 1 0.02
45 50 0.98
ACGTcount: A:0.39, C:0.28, G:0.15, T:0.18
Consensus pattern (45 bp):
AATGCTACCACAAAATCTTGCCAAAACAAAATGTTACCGCAACAG
Found at i:65954 original size:25 final size:25
Alignment explanation
Indices: 65926--65973 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
65916 TTGGAAAGCG
*
65926 AGACTTAGTG-AAATTTTACATTATA
1 AGACTTAG-GCAAAATTTACATTATA
65951 AGACTTAGGCAAAATTTACATTA
1 AGACTTAGGCAAAATTTACATTA
65974 ACAACAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (25 bp):
AGACTTAGGCAAAATTTACATTATA
Found at i:66108 original size:30 final size:30
Alignment explanation
Indices: 66068--66139 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
66058 TATAATTTGA
* *
66068 AAATAATATTTAGAAATTCTAAATGTAATG
1 AAATTATATTTAGAAATTATAAATGTAATG
*
66098 AAATTATATTTAGAAATTATATATGTAATG
1 AAATTATATTTAGAAATTATAAATGTAATG
66128 AAATTATATTTA
1 AAATTATATTTA
66140 TTTTAGGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.42
Consensus pattern (30 bp):
AAATTATATTTAGAAATTATAAATGTAATG
Found at i:66115 original size:13 final size:14
Alignment explanation
Indices: 66051--66216 Score: 64
Period size: 13 Copynumber: 11.5 Consensus size: 14
66041 AGAAATTGTA
*
66051 ATGAAATTATAATT
1 ATGAAATTATATTT
*
66065 -TGAAAATAATATTT
1 ATG-AAATTATATTT
* *
66079 A-GAAATTCTAAATGTA
1 ATGAAA-T-TATAT-TT
66095 ATGAAATTATATTT
1 ATGAAATTATATTT
66109 A-GAAATTATATATGT
1 ATGAAATTATAT-T-T
66124 AATGAAATTATATTT
1 -ATGAAATTATATTT
*
66139 ATTTTAGGAAATAATATTT
1 A---T--GAAATTATATTT
*
66158 A-GAAATTATAAATGTA
1 ATGAAATTAT--AT-TT
66174 ATGAAATTATATTT
1 ATGAAATTATATTT
*
66188 A-GAAA--ATA-AT
1 ATGAAATTATATTT
66198 AT-AAATTATATTT
1 ATGAAATTATATTT
66211 AT-AAAT
1 ATGAAAT
66217 GTAATAAATT
Statistics
Matches: 116, Mismatches: 13, Indels: 47
0.66 0.07 0.27
Matches are distributed among these distances:
10 5 0.04
11 3 0.03
12 3 0.03
13 33 0.28
14 17 0.15
15 13 0.11
16 7 0.06
17 23 0.20
19 12 0.10
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.42
Consensus pattern (14 bp):
ATGAAATTATATTT
Found at i:66223 original size:22 final size:22
Alignment explanation
Indices: 66163--66227 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
66153 TATTTAGAAA
66163 TTATAAATGTAATGAAATTATAT
1 TTATAAATGTAAT-AAATTATAT
* *
66186 TTAGAAAAT-AATATAAATTATAT
1 TTA-TAAATGTA-ATAAATTATAT
66209 TTATAAATGTAATAAATTA
1 TTATAAATGTAATAAATTA
66228 AATTAATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
22 12 0.34
23 17 0.49
24 6 0.17
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (22 bp):
TTATAAATGTAATAAATTATAT
Found at i:66570 original size:62 final size:62
Alignment explanation
Indices: 66446--66576 Score: 203
Period size: 62 Copynumber: 2.1 Consensus size: 62
66436 GCTTGTGGAG
*
66446 TCCAAATTTTACACTGACAGTGTATCAAATAATTACCCTACATCTAATATATTTTTGTCATT
1 TCCAAATTTTACACTGACAGTGTATCAAATAATTACCCTACATCTAATATATTTTTGCCATT
* **
66508 TCCAAATTTTACACTGACAGTGTATCAAATAATTATCCTACATCTTTTAT-TTCTTTGCCATT
1 TCCAAATTTTACACTGACAGTGTATCAAATAATTACCCTACATCTAATATATT-TTTGCCATT
66570 T-CAAATT
1 TCCAAATT
66577 CTTTTTCACT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
61 8 0.12
62 56 0.88
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (62 bp):
TCCAAATTTTACACTGACAGTGTATCAAATAATTACCCTACATCTAATATATTTTTGCCATT
Found at i:66848 original size:18 final size:18
Alignment explanation
Indices: 66825--66870 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
66815 TGAAATTAAT
66825 TAATTATTAATTAAATAA
1 TAATTATTAATTAAATAA
** *
66843 TAATTATTTTTTGAATAA
1 TAATTATTAATTAAATAA
*
66861 TTATTATTAA
1 TAATTATTAA
66871 ATTTCTAGTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATTATTAATTAAATAA
Found at i:70671 original size:18 final size:18
Alignment explanation
Indices: 70648--70693 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
70638 TGAAATTAAT
70648 TAATTATTAATTAAATAA
1 TAATTATTAATTAAATAA
** *
70666 TAATTATTTTTTGAATAA
1 TAATTATTAATTAAATAA
*
70684 TTATTATTAA
1 TAATTATTAA
70694 ATTTCTAGTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATTATTAATTAAATAA
Done.