Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012493.1 Corchorus olitorius cultivar O-4 contig12526, 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: 57700
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:585 original size:23 final size:23
Alignment explanation
Indices: 558--603 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
548 TCTCTACATT
*
558 CTCTTGTCCTTTT-CATAGTTCAA
1 CTCTTGT-CTTTTCCATACTTCAA
581 CTCTTGTCTTTTCCATACTTCAA
1 CTCTTGTCTTTTCCATACTTCAA
604 TTCTCTACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.17, C:0.28, G:0.07, T:0.48
Consensus pattern (23 bp):
CTCTTGTCTTTTCCATACTTCAA
Found at i:829 original size:32 final size:33
Alignment explanation
Indices: 784--854 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
774 ACAAAGTTTA
* *
784 TTTAACATACATAATCT-CTTCTTCTACCTTTC
1 TTTATCATACATAATCTCCTCCTTCTACCTTTC
*
816 TTTATCATGCATAATCTCCTCCTTCTACCTTTC
1 TTTATCATACATAATCTCCTCCTTCTACCTTTC
849 TTTATC
1 TTTATC
855 CTTAAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
32 15 0.43
33 20 0.57
ACGTcount: A:0.21, C:0.30, G:0.01, T:0.48
Consensus pattern (33 bp):
TTTATCATACATAATCTCCTCCTTCTACCTTTC
Found at i:931 original size:33 final size:33
Alignment explanation
Indices: 889--954 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
879 ATACTACCTT
*
889 GCATATTAGTGGCACCTGAAGTTGTCACATCAA
1 GCATATTAGTGGCACCTAAAGTTGTCACATCAA
922 GCATATTAGTGGCACCTAAAGTTGTCACATCAA
1 GCATATTAGTGGCACCTAAAGTTGTCACATCAA
955 AAATATTGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (33 bp):
GCATATTAGTGGCACCTAAAGTTGTCACATCAA
Found at i:1004 original size:29 final size:29
Alignment explanation
Indices: 962--1019 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
952 CAAAAATATT
*
962 GTATCACTTTGACACTCGAAGTTGTCATA
1 GTATCACTTTGACACCCGAAGTTGTCATA
*
991 GTATCATTTTGACACCCGAAGTTGTCATA
1 GTATCACTTTGACACCCGAAGTTGTCATA
1020 TTAAGGATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (29 bp):
GTATCACTTTGACACCCGAAGTTGTCATA
Found at i:6506 original size:23 final size:23
Alignment explanation
Indices: 6479--6524 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
6469 TCTCTACATT
6479 CTCTTGTCCTTTT-CATAGTTCAA
1 CTCTTGT-CTTTTCCATAGTTCAA
*
6502 CTCTTGTCTTTTCCATATTTCAA
1 CTCTTGTCTTTTCCATAGTTCAA
6525 TTTTCTACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.17, C:0.26, G:0.07, T:0.50
Consensus pattern (23 bp):
CTCTTGTCTTTTCCATAGTTCAA
Found at i:6972 original size:12 final size:12
Alignment explanation
Indices: 6938--6972 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
6928 AAATAAATAA
6938 ATAAAAAT-ATT
1 ATAAAAATAATT
6949 ATAAAAAGTAATT
1 ATAAAAA-TAATT
6962 ATAAAAATAAT
1 ATAAAAATAAT
6973 GTACTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.32
12 5 0.23
13 10 0.45
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (12 bp):
ATAAAAATAATT
Found at i:8137 original size:14 final size:14
Alignment explanation
Indices: 8118--8151 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
8108 TTTTATAATT
8118 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
8132 ATTTTATTTTTACT
1 ATTTTATTTTTACC
8146 ATTTTA
1 ATTTTA
8152 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:8199 original size:15 final size:15
Alignment explanation
Indices: 8179--8209 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
8169 GATTAACCTG
8179 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
8194 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
8209 T
1 T
8210 AATGTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Found at i:8672 original size:14 final size:14
Alignment explanation
Indices: 8653--8686 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
8643 TTTTATAATT
8653 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
8667 ATTTTATTTTTACT
1 ATTTTATTTTTACC
8681 ATTTTA
1 ATTTTA
8687 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:8734 original size:15 final size:15
Alignment explanation
Indices: 8714--8744 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
8704 GATTAACCTG
8714 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
8729 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
8744 T
1 T
8745 AATGTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Found at i:8895 original size:535 final size:527
Alignment explanation
Indices: 7886--8947 Score: 2034
Period size: 535 Copynumber: 2.0 Consensus size: 527
7876 CACCCATTAT
7886 ACCCTTATTTTTCGAATATATTTCTTAAATACCATTACTTAAACTATTATAGTTTTATTCTACTA
1 ACCCTTATTTTTCGAATATATTTCTTAAATACCATTACTTAAACTATTATAGTTTTATTCTACTA
7951 AAAACTCTATTTTTATTTAATGAAATCTAATATCTTTATAATTACTTTATTTTTACTATTTTACT
66 AAAACTCTATTTTTATTTAATGAAATCTAATATCTTTATAATTACTTTATTTTTACTATTTTACT
*
8016 ATTTTTCATTAAAAATTTGGATATATTAAAAACTTTTAATATACAATTTTATTCAACTGAAAACT
131 ATTTTTCATTAAAAACTTGGATATATTAAAAACTTTTAATATACAATTTTATTCAACTGAAAACT
8081 CTATTTGCATTTAATTAAATTAAATATTTTTATAATTATTTTATTTTTACCATTTTATTTTTACT
196 CTATTTGCATTTAATTAAATTAAATATTTTTATAATTATTTTATTTTTACCATTTTATTTTTACT
8146 ATTTTAATTTAAAAGGTTATTGTGATTAACCTGTTTCTATTTGATAGTTTTCTATTTGATAGTTA
261 ATTTTAATTTAAAAGGTTATTGTGATTAACCTGTTTCTATTTGATAGTTTTCTATTTGATAGTTA
8211 ATGTATTATGATTATAATTTATTATTTTATTTAACTTATAATTAATTTCAATTATTGCTAGATAA
326 ATGTATTATGATTATAATTTATTATTTTATTTAACTTATAATTAATTTCAATTATTGCTAGATAA
8276 AGTACGTTATATTTTACTTTGTTAATATTTTTATTTATGTGGAATAATTTCTTTTGTTCCTTTGA
391 AGTACGTTATATTTTACTTTGTTAATATTTTTATTTATGTGGAATAATTTCTTTTGTTCCTTTGA
*
8341 TAGTAAATCCCTATGTATATGCAAATGGGAGGTCAGGTTGAATTTTGGTTCGAACAGTTTCGGGT
456 TAGTAAAACCCTATGTATATGC-AAT-GGAGGTCAGGTTGAA-TTTGGTTCG-ACAG-TTC-GGT
8406 TAAGGAAATTTCGGG
515 T-AGG-AATTTCGGG
8421 ACCCTTATTTTTCGAATATATTTCTTAAATACCATTACTTAAACTATTATAGTTTTATTCTACTA
1 ACCCTTATTTTTCGAATATATTTCTTAAATACCATTACTTAAACTATTATAGTTTTATTCTACTA
8486 AAAACTCTATTTTTATTTAATGAAATCTAATATCTTTATAATTACTTTATTTTTACTATTTTACT
66 AAAACTCTATTTTTATTTAATGAAATCTAATATCTTTATAATTACTTTATTTTTACTATTTTACT
8551 ATTTTTCATTAAAAACTTGGATATATTAAAAACTTTTAATATACAATTTTATTCAACTGAAAACT
131 ATTTTTCATTAAAAACTTGGATATATTAAAAACTTTTAATATACAATTTTATTCAACTGAAAACT
8616 CTATTTGCATTTAATTAAATTAAATATTTTTATAATTATTTTATTTTTACCATTTTATTTTTACT
196 CTATTTGCATTTAATTAAATTAAATATTTTTATAATTATTTTATTTTTACCATTTTATTTTTACT
8681 ATTTTAATTTAAAAGGTTATTGTGATTAACCTGTTTCTATTTGATAGTTTTCTATTTGATAGTTA
261 ATTTTAATTTAAAAGGTTATTGTGATTAACCTGTTTCTATTTGATAGTTTTCTATTTGATAGTTA
8746 ATGTATTATGATTATAATTTATTATTTTATTTAACTTATAATTAATTTCAATTATTGCTAGATAA
326 ATGTATTATGATTATAATTTATTATTTTATTTAACTTATAATTAATTTCAATTATTGCTAGATAA
8811 AGTACGTTATATTTTACTTTGTTAATATTTTTATTTATGTGGAATAATTTCTTTTGTTCCTTTGA
391 AGTACGTTATATTTTACTTTGTTAATATTTTTATTTATGTGGAATAATTTCTTTTGTTCCTTTGA
8876 TAGTAAAACCCTATGTATATGCAATGGAGGTCAGGTTGAATTTGGTTCGACAGTTCGGTTAGGAA
456 TAGTAAAACCCTATGTATATGCAATGGAGGTCAGGTTGAATTTGGTTCGACAGTTCGGTTAGGAA
8941 TTTCGGG
521 TTTCGGG
8948 TCATATGGGT
Statistics
Matches: 525, Mismatches: 2, Indels: 8
0.98 0.00 0.01
Matches are distributed among these distances:
527 9 0.02
528 3 0.01
529 4 0.01
530 3 0.01
531 4 0.01
532 9 0.02
533 15 0.03
534 3 0.01
535 475 0.90
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.49
Consensus pattern (527 bp):
ACCCTTATTTTTCGAATATATTTCTTAAATACCATTACTTAAACTATTATAGTTTTATTCTACTA
AAAACTCTATTTTTATTTAATGAAATCTAATATCTTTATAATTACTTTATTTTTACTATTTTACT
ATTTTTCATTAAAAACTTGGATATATTAAAAACTTTTAATATACAATTTTATTCAACTGAAAACT
CTATTTGCATTTAATTAAATTAAATATTTTTATAATTATTTTATTTTTACCATTTTATTTTTACT
ATTTTAATTTAAAAGGTTATTGTGATTAACCTGTTTCTATTTGATAGTTTTCTATTTGATAGTTA
ATGTATTATGATTATAATTTATTATTTTATTTAACTTATAATTAATTTCAATTATTGCTAGATAA
AGTACGTTATATTTTACTTTGTTAATATTTTTATTTATGTGGAATAATTTCTTTTGTTCCTTTGA
TAGTAAAACCCTATGTATATGCAATGGAGGTCAGGTTGAATTTGGTTCGACAGTTCGGTTAGGAA
TTTCGGG
Found at i:9645 original size:6 final size:6
Alignment explanation
Indices: 9631--9661 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
9621 CAACCATCTT
*
9631 CACCTC CACCGC CACCGC CACCGC CACCGC C
1 CACCGC CACCGC CACCGC CACCGC CACCGC C
9662 GTCGATGCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.68, G:0.13, T:0.03
Consensus pattern (6 bp):
CACCGC
Found at i:16548 original size:2 final size:2
Alignment explanation
Indices: 16543--16573 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16533 AAAATAAAAT
16543 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
16574 TTGCATGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18174 original size:12 final size:12
Alignment explanation
Indices: 18157--18183 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
18147 GAAAAACCAG
18157 CATCAACATGTC
1 CATCAACATGTC
18169 CATCAACATGTC
1 CATCAACATGTC
18181 CAT
1 CAT
18184 TATCAGTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.07, T:0.26
Consensus pattern (12 bp):
CATCAACATGTC
Found at i:22773 original size:28 final size:28
Alignment explanation
Indices: 22741--22797 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
22731 TGTATTCTGA
*
22741 ACACGGTATAGTTGGATTCTATACATGC
1 ACACGGTATAGTTGGATTCTACACATGC
22769 ACACGGTATAGTTGGATTCTACACATGC
1 ACACGGTATAGTTGGATTCTACACATGC
22797 A
1 A
22798 ATTACCGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (28 bp):
ACACGGTATAGTTGGATTCTACACATGC
Found at i:27052 original size:16 final size:17
Alignment explanation
Indices: 27031--27064 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
27021 ATATTTCATT
27031 AAGCGTAA-AAAAATAA
1 AAGCGTAACAAAAATAA
27047 AAGCGTAACAAAAATAA
1 AAGCGTAACAAAAATAA
27064 A
1 A
27065 CTTCCTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.68, C:0.09, G:0.12, T:0.12
Consensus pattern (17 bp):
AAGCGTAACAAAAATAA
Found at i:28106 original size:21 final size:21
Alignment explanation
Indices: 28063--28106 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
28053 TCTATGTTCG
** **
28063 GTTCGGCTATGGTTCTTCTAT
1 GTTCGGCTATGGTTAATAGAT
28084 GTTCGGCTATGGTTAATAGAT
1 GTTCGGCTATGGTTAATAGAT
28105 GT
1 GT
28107 GTAGGGATTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.14, G:0.27, T:0.43
Consensus pattern (21 bp):
GTTCGGCTATGGTTAATAGAT
Found at i:33989 original size:55 final size:54
Alignment explanation
Indices: 33905--34060 Score: 222
Period size: 55 Copynumber: 2.8 Consensus size: 54
33895 GCTTTCAATA
*
33905 AGATGATTTAGTGATTGAATTAAATTGGTCAGAGAGTAAGTTAAGGTAATTTAGG
1 AGATGATTTAGTGATTAAATTAAA-TGGTCAGAGAGTAAGTTAAGGTAATTTAGG
*
33960 AGATGATTTAGTGATTAAATTAAGATGGTCAGAGAGTAAGTTGAGGTAATTTAGG
1 AGATGATTTAGTGATTAAATTAA-ATGGTCAGAGAGTAAGTTAAGGTAATTTAGG
** * * *
34015 AGATGATTTAGTGACAAAACTAAAATGGTAAGAGAGTAGGTTAAGG
1 AGATGATTTAGTGATTAAA-TTAAATGGTCAGAGAGTAAGTTAAGG
34061 AGGTAATTTG
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
55 87 0.96
56 4 0.04
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.31
Consensus pattern (54 bp):
AGATGATTTAGTGATTAAATTAAATGGTCAGAGAGTAAGTTAAGGTAATTTAGG
Found at i:35047 original size:42 final size:41
Alignment explanation
Indices: 34994--35129 Score: 118
Period size: 42 Copynumber: 3.3 Consensus size: 41
34984 ATTGGGTTTA
*
34994 TTATTTATGTTTAGGCTTAGAGTTATAGTTTTCTGTTGGGCT
1 TTATTTGTGTTT-GGCTTAGAGTTATAGTTTTCTGTTGGGCT
* * * * *
35036 TTATTTGTGTTT-G-ATAGAGTTGTATTTGGGTTTTGTT-TGCT
1 TTATTTGTGTTTGGCTTAGAGTTATAGTT---TTCTGTTGGGCT
* * * *
35077 TTAGTTAT-TTGGGCTTAGAGTTATAGTTTTCTGTGGGGCT
1 TTATTTGTGTTTGGCTTAGAGTTATAGTTTTCTGTTGGGCT
35117 TTATTTGTGTTTG
1 TTATTTGTGTTTG
35130 ATAGAGTTGT
Statistics
Matches: 69, Mismatches: 18, Indels: 15
0.68 0.18 0.15
Matches are distributed among these distances:
39 16 0.23
40 12 0.17
41 13 0.19
42 28 0.41
ACGTcount: A:0.14, C:0.05, G:0.26, T:0.54
Consensus pattern (41 bp):
TTATTTGTGTTTGGCTTAGAGTTATAGTTTTCTGTTGGGCT
Found at i:35137 original size:39 final size:38
Alignment explanation
Indices: 35011--35137 Score: 103
Period size: 39 Copynumber: 3.2 Consensus size: 38
35001 TGTTTAGGCT
35011 TAGAGTTATAGTTTTCTGTTGGGCTTTATTTGTGTTTGA
1 TAGAGTTATAGTTTTCTG-TGGGCTTTATTTGTGTTTGA
* * * ** * * * *
35050 TAGAGTTGTATTTGGGTTTTGTTTGCTTTAGTTAT-TTGGGCT
1 TAGAGTTATAGTT---TTCTGTGGGCTTTATTTGTGTT-TG-A
35092 TAGAGTTATAGTTTTCTGTGGGGCTTTATTTGTGTTTGA
1 TAGAGTTATAGTTTTCTGT-GGGCTTTATTTGTGTTTGA
35131 TAGAGTT
1 TAGAGTT
35138 GTATTTGGGC
Statistics
Matches: 63, Mismatches: 18, Indels: 14
0.66 0.19 0.15
Matches are distributed among these distances:
39 23 0.37
40 12 0.19
41 13 0.21
42 15 0.24
ACGTcount: A:0.15, C:0.05, G:0.28, T:0.53
Consensus pattern (38 bp):
TAGAGTTATAGTTTTCTGTGGGCTTTATTTGTGTTTGA
Found at i:35142 original size:81 final size:81
Alignment explanation
Indices: 35007--35173 Score: 298
Period size: 81 Copynumber: 2.1 Consensus size: 81
34997 TTTATGTTTA
* * *
35007 GGCTTAGAGTTATAGTTTTCTGTTGGGCTTTATTTGTGTTTGATAGAGTTGTATTTGGGTTTTGT
1 GGCTTAGAGTTATAGTTTTCTGTGGGGCTTTATTTGTGTTTGATAGAGTTGTATTTGGGCTTTGC
35072 TTGCTTTAGTTATTTG
66 TTGCTTTAGTTATTTG
35088 GGCTTAGAGTTATAGTTTTCTGTGGGGCTTTATTTGTGTTTGATAGAGTTGTATTTGGGCTTTGC
1 GGCTTAGAGTTATAGTTTTCTGTGGGGCTTTATTTGTGTTTGATAGAGTTGTATTTGGGCTTTGC
*
35153 TTGTTTTAGTTATTTG
66 TTGCTTTAGTTATTTG
35169 GGCTT
1 GGCTT
35174 GACCTTTCTA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.13, C:0.06, G:0.28, T:0.53
Consensus pattern (81 bp):
GGCTTAGAGTTATAGTTTTCTGTGGGGCTTTATTTGTGTTTGATAGAGTTGTATTTGGGCTTTGC
TTGCTTTAGTTATTTG
Found at i:35783 original size:19 final size:20
Alignment explanation
Indices: 35750--35788 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
35740 TAAAAATATT
*
35750 TTCAAAAATCCAAAA-CAAA
1 TTCAAAAATCAAAAATCAAA
*
35769 TTCAAAACTCAAAAATCAAA
1 TTCAAAAATCAAAAATCAAA
35789 AAGAATTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.18
Consensus pattern (20 bp):
TTCAAAAATCAAAAATCAAA
Found at i:35909 original size:35 final size:35
Alignment explanation
Indices: 35853--35957 Score: 106
Period size: 35 Copynumber: 2.9 Consensus size: 35
35843 AAGCATTTAA
35853 TTTTAGTTTTTCAAATTGGGAAAGTTCCCATCAGG
1 TTTTAGTTTTTCAAATTGGGAAAGTTCCCATCAGG
* *
35888 TTTTAG-TTTTCAATTTAGGGAAAGTTCCCGTCAGTTCGG
1 TTTTAGTTTTTCAAATT-GGGAAAGTTCCCATCA----GG
* * *
35927 TTTCAGTCTTT-AAAGTGGGAAAGTTCCCATC
1 TTTTAGTTTTTCAAATTGGGAAAGTTCCCATC
35958 CAAAGCATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
34 9 0.16
35 21 0.37
38 14 0.25
39 10 0.18
40 3 0.05
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (35 bp):
TTTTAGTTTTTCAAATTGGGAAAGTTCCCATCAGG
Found at i:43170 original size:45 final size:45
Alignment explanation
Indices: 43106--43234 Score: 206
Period size: 45 Copynumber: 2.9 Consensus size: 45
43096 AGCAACAATT
* *
43106 AATATTAGGTTTATTTTGATGAATTACCTAGAGAT-ATATGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGA-AGGAGTAG
*
43151 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGGAGTAT
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGGAGTAG
*
43196 AAAATTAGCTTTATTTTGATGAATTACCTAGAGATGAAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAG
43235 TAGAATTTAG
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 78 0.99
46 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.38
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGGAGTAG
Found at i:47853 original size:19 final size:19
Alignment explanation
Indices: 47822--47858 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
47812 AAAAAAGGCT
47822 AAATTTGTTTTTAGTTTTCA
1 AAATTTGTTTTTA-TTTTCA
47842 AAATTT-TTTTTATTTTC
1 AAATTTGTTTTTATTTTC
47859 TACTATACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.65
Consensus pattern (19 bp):
AAATTTGTTTTTATTTTCA
Found at i:49016 original size:18 final size:18
Alignment explanation
Indices: 48989--49024 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
48979 ATCTATCTCG
*
48989 GCATTGGATCATTTAGGT
1 GCATTGGATCAGTTAGGT
*
49007 GCATTTGATCAGTTAGGT
1 GCATTGGATCAGTTAGGT
49025 ATAGTTGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.11, G:0.28, T:0.39
Consensus pattern (18 bp):
GCATTGGATCAGTTAGGT
Done.