Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014846.1 Corchorus olitorius cultivar O-4 contig14879, 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: 14409
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:4394 original size:163 final size:166
Alignment explanation
Indices: 4119--4450 Score: 508
Period size: 163 Copynumber: 2.0 Consensus size: 166
4109 ATTTAATTGA
** *
4119 GAGTTATTTTGCTAATTGATTTTGGTTTAAAGACATTCAAATCAAATCAATTTGAATAGGAAAAT
1 GAGTTATCATGCTAATTGATTTTGGTTTAAAAACATTCAAATCAAATC----TGAATAGGAAAAT
*
4184 TTCTAATCCTAATTTCCTTAATTTTTTAATTAATCAAGGATTTAATTTTGGATCTATATATTCAA
62 TTCTAATCC----TTCCTTAATTTTTTAATTAATCAAGGAGTTAATTTTGGATCTATATATTCAA
* *
4249 ATTAAATCATTTATTGAATTAATACAAATTGGACACATGTGATT
123 ATCAAATCATTTATTGAACTAATACAAATTGGACACATGTGATT
4293 GAGTTATCATGCTAATTGATTTTGGTTTAAAAACATTCAAATCAAATC-GAATAGGAAAATTTCT
1 GAGTTATCATGCTAATTGATTTTGGTTTAAAAACATTCAAATCAAATCTGAATAGGAAAATTTCT
4357 AA-CC-TCCTTAATTTTTTAATTAATCAAGGAGTTAATTTTGGATCTATATATTCAAATCAAATC
66 AATCCTTCCTTAATTTTTTAATTAATCAAGGAGTTAATTTTGGATCTATATATTCAAATCAAATC
*
4420 ATTTATTTAACTAATACAAATTGGACACATG
131 ATTTATTGAACTAATACAAATTGGACACATG
4451 GCATCGAGAG
Statistics
Matches: 151, Mismatches: 7, Indels: 11
0.89 0.04 0.07
Matches are distributed among these distances:
163 86 0.57
168 2 0.01
169 18 0.12
174 45 0.30
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (166 bp):
GAGTTATCATGCTAATTGATTTTGGTTTAAAAACATTCAAATCAAATCTGAATAGGAAAATTTCT
AATCCTTCCTTAATTTTTTAATTAATCAAGGAGTTAATTTTGGATCTATATATTCAAATCAAATC
ATTTATTGAACTAATACAAATTGGACACATGTGATT
Found at i:4951 original size:11 final size:11
Alignment explanation
Indices: 4935--4971 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
4925 CTATGATAAA
*
4935 AATTATATTTT
1 AATTATATTAT
4946 AATTATATTAT
1 AATTATATTAT
4957 AATTATAATTAT
1 AATTAT-ATTAT
4969 AAT
1 AAT
4972 AAATAAAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
AATTATATTAT
Found at i:4963 original size:6 final size:6
Alignment explanation
Indices: 4935--4971 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
4925 CTATGATAAA
*
4935 AATTAT -ATTTT AATTAT -ATTAT AATTAT AATTAT AAT
1 AATTAT AATTAT AATTAT AATTAT AATTAT AATTAT AAT
4972 AAATAAAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 9 0.33
6 18 0.67
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
AATTAT
Found at i:4967 original size:17 final size:16
Alignment explanation
Indices: 4936--4969 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4926 TATGATAAAA
*
4936 ATTATATTTTAATTAT
1 ATTATATTATAATTAT
4952 ATTATAATTATAATTAT
1 ATTAT-ATTATAATTAT
4969 A
1 A
4970 ATAAATAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATATTATAATTAT
Found at i:6761 original size:5 final size:5
Alignment explanation
Indices: 6751--6776 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
6741 ATAGAGAACA
6751 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
6777 CCAGCCCGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:7490 original size:22 final size:22
Alignment explanation
Indices: 7444--7514 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
7434 CATAATGTGC
* * *
7444 TTATTAAAATTTAATAGAGATG
1 TTATCAAAATTTAATAGGGAGG
* *
7466 TTATCCAAATTTCATAGGGAGG
1 TTATCAAAATTTAATAGGGAGG
* * * *
7488 TTAACAAAATTTTATAAGGAGA
1 TTATCAAAATTTAATAGGGAGG
7510 TTATC
1 TTATC
7515 GAAACGACGA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTAATAGGGAGG
Found at i:7600 original size:22 final size:22
Alignment explanation
Indices: 7575--8167 Score: 130
Period size: 22 Copynumber: 26.6 Consensus size: 22
7565 TTTTTAGGGA
7575 GGTTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGTAT
* * *
7597 GGTTATCACAATTTCTTATAGGAA
1 GGTTATCAAAATTTC--ATAGTAT
* *
7621 GGTTATCAAAAATTCATAGGGA-
1 GGTTATCAAAATTTCATA-GTAT
* *
7643 GGTTATAAAAATTTCATAGGGA-
1 GGTTATCAAAATTTCATA-GTAT
* * *
7665 CGTTAACAAAATTGT-ATAAGGAAT
1 GGTTATCAAAATT-TCAT-A-GTAT
** *
7689 -GTTATCAAAAAATCATAGGGA-
1 GGTTATCAAAATTTCATA-GTAT
* ** * ***
7710 GATTATTGAAATCTCATAGGGC
1 GGTTATCAAAATTTCATAGTAT
* *
7732 GGTTATCAAAATCTCATGAG-AA
1 GGTTATCAAAATTTCAT-AGTAT
* * * * * *
7754 GATTGTGAAATTTTTATAGGGA-
1 GGTTATCAAAATTTCATA-GTAT
* * *
7776 GGTTATCAAAATTTTATAGGAA
1 GGTTATCAAAATTTCATAGTAT
7798 GGTTTATCAAAATATT-ATAGTGA-
1 GG-TTATCAAAAT-TTCATAGT-AT
* *
7821 GGTTATCAAAATTTAATAAGGA-
1 GGTTATCAAAATTTCAT-AGTAT
* * *
7843 GATTATCACAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTAT
** *
7865 GGTTA-CGAAAATCACA-AGGA-
1 GGTTATC-AAAATTTCATAGTAT
* *
7885 GGTTATC-AAATTTTATAGTGT
1 GGTTATCAAAATTTCATAGTAT
** * *
7906 ACTTATCAAAATTTCAAAATTTCAT
1 GGTTATCAAAATTTC-ATA-GT-AT
* * *
7931 AGGGATGTCTCAGAATTTTATAGTAT
1 --GG-T-TATCAAAATTTCATAGTAT
* * *
7957 CGTTATTAAAATTTCATAGGGA-
1 GGTTATCAAAATTTCATA-GTAT
*
7979 GGTTATCAAAATATT-ATAGTGT
1 GGTTATCAAAAT-TTCATAGTAT
* * **
8001 GATTATCAAAATTT-ATAATGG
1 GGTTATCAAAATTTCATAGTAT
* * *
8022 GGTTATAAAAATTTCACAGGGAT
1 GGTTATCAAAATTTCATA-GTAT
* * * *
8045 -ATTATCAAAATTTCGTTGTGT
1 GGTTATCAAAATTTCATAGTAT
* *
8066 GATTATCAAAATTTCATAG-AGA
1 GGTTATCAAAATTTCATAGTA-T
8088 GGTTATCAAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAGTAT
* ** * *
8110 GATTAAAAAAAATTCAT--TAA
1 GGTTATCAAAATTTCATAGTAT
*
8130 GCGATTATTAAAATTTCATAGTAT
1 G-G-TTATCAAAATTTCATAGTAT
* *
8154 GATTATCAACATTT
1 GGTTATCAAAATTT
8168 TTTAGAGATA
Statistics
Matches: 415, Mismatches: 113, Indels: 86
0.68 0.18 0.14
Matches are distributed among these distances:
19 5 0.01
20 10 0.02
21 41 0.10
22 269 0.65
23 48 0.12
24 26 0.06
25 1 0.00
26 2 0.00
27 1 0.00
28 3 0.01
29 9 0.02
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.36
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTAT
Found at i:7624 original size:24 final size:22
Alignment explanation
Indices: 7569--8106 Score: 194
Period size: 22 Copynumber: 24.1 Consensus size: 22
7559 TGATATTTTT
*
7569 TAGGGAGGTTATCAAAATTTCA
1 TAGGAAGGTTATCAAAATTTCA
* * *
7591 TAGTATGGTTATCACAATTTCTTA
1 TAGGAAGGTTATCAAAATTTC--A
*
7615 TAGGAAGGTTATCAAAAATTCA
1 TAGGAAGGTTATCAAAATTTCA
* *
7637 TAGGGAGGTTATAAAAATTTCA
1 TAGGAAGGTTATCAAAATTTCA
* * *
7659 TAGGGACGTTAACAAAATTGT-A
1 TAGGAAGGTTATCAAAATT-TCA
* **
7681 TAAGGAATGTTATCAAAAAATCA
1 T-AGGAAGGTTATCAAAATTTCA
* * ** *
7704 TAGGGAGATTATTGAAATCTCA
1 TAGGAAGGTTATCAAAATTTCA
** *
7726 TAGGGCGGTTATCAAAATCTCA
1 TAGGAAGGTTATCAAAATTTCA
* * * * *
7748 T-GAGAAGATTGTGAAATTTTTA
1 TAG-GAAGGTTATCAAAATTTCA
* *
7770 TAGGGAGGTTATCAAAATTTTA
1 TAGGAAGGTTATCAAAATTTCA
7792 TAGGAAGGTTTATCAAAATATT-A
1 TAGGAAGG-TTATCAAAAT-TTCA
*
7815 TAGTG-AGGTTATCAAAATTTAA
1 TAG-GAAGGTTATCAAAATTTCA
* *
7837 TAAGG-AGATTATCACAATTTCA
1 T-AGGAAGGTTATCAAAATTTCA
* **
7859 TAGTG-TGGTTA-CGAAAATCACA
1 TAG-GAAGGTTATC-AAAATTTCA
*
7881 -AGG-AGGTTATC-AAATTTTA
1 TAGGAAGGTTATCAAAATTTCA
* *
7900 TAGTGTA-CTTATCAAAATTTCAAAA
1 TAG-GAAGGTTATCAAAATTTC---A
*** * * *
7925 TTTCATAGGGATGTCTCAGAATTTTA
1 TAGGA-A-GG-T-TATCAAAATTTCA
* ** *
7951 TAGTATCGTTATTAAAATTTCA
1 TAGGAAGGTTATCAAAATTTCA
*
7973 TAGGGAGGTTATCAAAATATT-A
1 TAGGAAGGTTATCAAAAT-TTCA
* *
7995 TAGTG-TGATTATCAAAATTT-A
1 TAG-GAAGGTTATCAAAATTTCA
*
8016 TAATGG--GGTTATAAAAATTTCA
1 T-A-GGAAGGTTATCAAAATTTCA
* * ** *
8038 CAGGGATATTATCAAAATTTCG
1 TAGGAAGGTTATCAAAATTTCA
* * *
8060 TTGTG-TGATTATCAAAATTTCA
1 TAG-GAAGGTTATCAAAATTTCA
8082 TA-GAGAGGTTATCAAAATTTCA
1 TAGGA-AGGTTATCAAAATTTCA
8104 TAG
1 TAG
8107 TATGATTAAA
Statistics
Matches: 381, Mismatches: 97, Indels: 75
0.69 0.18 0.14
Matches are distributed among these distances:
19 5 0.01
20 11 0.03
21 32 0.08
22 253 0.66
23 42 0.11
24 22 0.06
25 3 0.01
26 3 0.01
28 1 0.00
29 9 0.02
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (22 bp):
TAGGAAGGTTATCAAAATTTCA
Found at i:7647 original size:46 final size:46
Alignment explanation
Indices: 7569--7657 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
7559 TGATATTTTT
* * * * *
7569 TAGGGAGGTTATCAAAATTTCATAGTATGGTTATCACAATTTCTTA
1 TAGGAAGGTTATCAAAAATTCATAGGATGGTTATAAAAATTTCTTA
7615 TAGGAAGGTTATCAAAAATTCATAGGGA-GGTTATAAAAATTTC
1 TAGGAAGGTTATCAAAAATTCATA-GGATGGTTATAAAAATTTC
7658 ATAGGGACGT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
46 35 0.95
47 2 0.05
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (46 bp):
TAGGAAGGTTATCAAAAATTCATAGGATGGTTATAAAAATTTCTTA
Found at i:7727 original size:67 final size:67
Alignment explanation
Indices: 7616--7743 Score: 177
Period size: 67 Copynumber: 1.9 Consensus size: 67
7606 AATTTCTTAT
* * *
7616 AGGAAGGTTATCAAAAATTCATAGGGAGGTTATAAAAATTTCATAGGGAC-GTTAACAAAATTGT
1 AGGAAGGTTATCAAAAAATCATAGGGAGATTATAAAAATCTCATAGGG-CGGTTAACAAAATTGT
7680 ATA
65 ATA
* ** *
7683 AGGAATGTTATCAAAAAATCATAGGGAGATTATTGAAATCTCATAGGGCGGTTATCAAAAT
1 AGGAAGGTTATCAAAAAATCATAGGGAGATTATAAAAATCTCATAGGGCGGTTAACAAAAT
7744 CTCATGAGAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
66 1 0.02
67 52 0.98
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (67 bp):
AGGAAGGTTATCAAAAAATCATAGGGAGATTATAAAAATCTCATAGGGCGGTTAACAAAATTGTA
TA
Found at i:7849 original size:111 final size:111
Alignment explanation
Indices: 7658--7859 Score: 235
Period size: 111 Copynumber: 1.8 Consensus size: 111
7648 TAAAAATTTC
* **
7658 ATAGGGACGTTAACAAAATTGTATAAGGAATGTTATCAAAAAATCATAGGGAGATTATTGAAATC
1 ATAGGGACGTTAACAAAATTGTATAAGGAAGGTTATCAAAAAATCATAGGGAGATTATCAAAATC
* * * *
7723 TCATAGGGCGGTTATCAAAATCTCATGAGAAGATTGTGAAATTTTT
66 TAATAAGGAGATTATCAAAATCTCATGAGAAGATTGTGAAATTTTT
* * * * * * *
7769 ATAGGGAGGTTATCAAAATTTTAT-AGGAAGGTTTATCAAAATATTATAGTGAGGTTATCAAAAT
1 ATAGGGACGTTAACAAAATTGTATAAGGAAGG-TTATCAAAAAATCATAGGGAGATTATCAAAAT
* * *
7833 TTAATAAGGAGATTATCACAATTTCAT
65 CTAATAAGGAGATTATCAAAATCTCAT
7860 AGTGTGGTTA
Statistics
Matches: 73, Mismatches: 17, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
110 6 0.08
111 67 0.92
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (111 bp):
ATAGGGACGTTAACAAAATTGTATAAGGAAGGTTATCAAAAAATCATAGGGAGATTATCAAAATC
TAATAAGGAGATTATCAAAATCTCATGAGAAGATTGTGAAATTTTT
Found at i:8027 original size:21 final size:21
Alignment explanation
Indices: 7979--8035 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
7969 TTCATAGGGA
* *
7979 GGTTATCAAAATATTATAGTGT
1 GGTTATCAAAAT-TTATAATGG
*
8001 GATTATCAAAATTTATAATGG
1 GGTTATCAAAATTTATAATGG
*
8022 GGTTATAAAAATTT
1 GGTTATCAAAATTT
8036 CACAGGGATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (21 bp):
GGTTATCAAAATTTATAATGG
Found at i:8027 original size:65 final size:66
Alignment explanation
Indices: 7958--8106 Score: 187
Period size: 65 Copynumber: 2.3 Consensus size: 66
7948 TTATAGTATC
* *
7958 GTTATTAAAATTTCATAGGGAGGTTATCAAAATATT-ATAGTGTGATTATCAAAATTT-ATA-AT
1 GTTATAAAAATTTCATAGGGAGATTATCAAAAT-TTCATAGTGTGATTATCAAAATTTCATAGA-
*
8020 GGG
64 GAG
* * * *
8023 GTTATAAAAATTTCACAGGGATATTATCAAAATTTCGTTGTGTGATTATCAAAATTTCATAGAGA
1 GTTATAAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAGAGA
8088 G
66 G
*
8089 GTTATCAAAATTTCATAG
1 GTTATAAAAATTTCATAG
8107 TATGATTAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
64 2 0.03
65 48 0.67
66 21 0.29
67 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (66 bp):
GTTATAAAAATTTCATAGGGAGATTATCAAAATTTCATAGTGTGATTATCAAAATTTCATAGAGA
G
Found at i:8113 original size:44 final size:44
Alignment explanation
Indices: 7959--8167 Score: 156
Period size: 44 Copynumber: 4.8 Consensus size: 44
7949 TATAGTATCG
* * * * *
7959 TTATTAAAATTTCATAGGGA-GGTTATCAAAATATT-ATAGTGTGA
1 TTATCAAAATTTCATA-GTATGATTATCAAAAT-TTCATAGAGAGA
* ** * * * * *
8003 TTATCAAAATTT-ATAATGGGGTTATAAAAATTTCACAGGGATA
1 TTATCAAAATTTCATAGTATGATTATCAAAATTTCATAGAGAGA
* * * *
8046 TTATCAAAATTTCGTTGTGTGATTATCAAAATTTCATAGAGAGG
1 TTATCAAAATTTCATAGTATGATTATCAAAATTTCATAGAGAGA
** * *
8090 TTATCAAAATTTCATAGTATGATTAAAAAAAATTCATTA-AGCGA
1 TTATCAAAATTTCATAGTATGATTATCAAAATTTCA-TAGAGAGA
* *
8134 TTATTAAAATTTCATAGTATGATTATCAACATTT
1 TTATCAAAATTTCATAGTATGATTATCAAAATTT
8168 TTTAGAGATA
Statistics
Matches: 129, Mismatches: 32, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
42 2 0.02
43 31 0.24
44 94 0.73
45 2 0.02
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (44 bp):
TTATCAAAATTTCATAGTATGATTATCAAAATTTCATAGAGAGA
Found at i:9167 original size:17 final size:18
Alignment explanation
Indices: 9145--9181 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
9135 AATTATTCAA
9145 TACATTGTTAGTGGA-TT
1 TACATTGTTAGTGGAGTT
9162 TACATTGTTAGTGGAGTT
1 TACATTGTTAGTGGAGTT
9180 TA
1 TA
9182 GCAGACTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.46
Consensus pattern (18 bp):
TACATTGTTAGTGGAGTT
Found at i:13795 original size:37 final size:37
Alignment explanation
Indices: 13746--14036 Score: 327
Period size: 37 Copynumber: 8.0 Consensus size: 37
13736 AGAATCCCAC
*
13746 CAGTTTT-TAAGTTTTCAAATTGGGAAAGTTCCCATT
1 CAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCCATT
* * *
13782 CAATTTTCAAAGTTTTTAAATTGGGAAAGTTCCCA-C
1 CAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCCATT
*
13818 CAGTTTT-TAAGTTTTCAAATTGGGAAAGTTCCCATT
1 CAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCCATT
*
13854 CAGTTTTCAAAGCTTTT-AAATTGGGAAAGTTCCCA-C
1 CAGTTTTCAAAG-TTTTCAAATTGGGAAAGTTCCCATT
** *
13890 CAGTTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATC
1 CAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCCATT
13927 CAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCCA-T
1 CAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCCATT
*
13963 CAGGTTTT---AGTTTTCAATTTAGGGAAAGTTCCCGTCATTTT
1 CA-GTTTTCAAAGTTTTCAAATT-GGGAAAGTT-CC--CA--TT
*
14004 CAGTTTT---AGTTTTCAAAGTGGGAAAGTTCCCAT
1 CAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCCAT
14037 CAAAAGCATT
Statistics
Matches: 223, Mismatches: 18, Indels: 30
0.82 0.07 0.11
Matches are distributed among these distances:
34 12 0.05
35 38 0.17
36 53 0.24
37 85 0.38
38 8 0.04
39 9 0.04
40 15 0.07
41 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (37 bp):
CAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCCATT
Found at i:13832 original size:72 final size:72
Alignment explanation
Indices: 13740--13995 Score: 424
Period size: 72 Copynumber: 3.5 Consensus size: 72
13730 TCAAAAAGAA
*
13740 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAATTTTCAAAGTTTTTAAATTG
1 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAGTTTTTAAATTG
13805 GGAAAGT
66 GGAAAGT
*
13812 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAGCTTTTAAATTG
1 TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAGTTTTTAAATTG
13877 GGAAAGT
66 GGAAAGT
* *
13884 TCCCACCAGTTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAAGTTTTCAAATT
1 TCCCACCAG-TTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAGTTTTTAAATT
13949 GGGAAAGT
65 GGGAAAGT
* * *
13957 TCCCATCAGGTTTT-AGTTTTCAATTTAGGGAAAGTTCCC
1 TCCCACCAGTTTTTAAGTTTTCAAATT-GGGAAAGTTCCC
13996 GTCATTTTCA
Statistics
Matches: 174, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
71 11 0.06
72 95 0.55
73 68 0.39
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (72 bp):
TCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAGTTTTTAAATTG
GGAAAGT
Done.