Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022508.1 Corchorus olitorius cultivar O-4 contig22541, 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: 64308
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Found at i:1502 original size:204 final size:200
Alignment explanation
Indices: 1096--1504 Score: 721
Period size: 204 Copynumber: 2.0 Consensus size: 200
1086 ACTTAATAAC
*
1096 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAAAAAAGTTGTAGTGAATAA
* *
1161 GATACAACACATTATTATTATATATAAAACTATACCAAAAAAGTAGTTGAACATTAGTGGTTGAT
66 GATACAACACATTACTATTATATATAAAAATATACCAAAAAAGTAGTTGAACATTAGTGGTTGAT
1226 TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCG
131 TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCG
1291 ATTTA
196 ATTTA
*
1296 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAGGATTACTAAAAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAAAAAAGTTGTAGTGAATAA
*
1361 GATACAACACATTACTATTATATATATAGAAATATACCAAAAAAAATTAGTTGAACATTAGTGGT
66 GATACAACACATTACTATTATATATA-A-AAATATACC--AAAAAAGTAGTTGAACATTAGTGGT
1426 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATT-AAGA
127 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
1490 TCCGAATTTA
192 TCCG-ATTTA
1500 TTTAT
1 TTTAT
1505 TATTAAGAAA
Statistics
Matches: 199, Mismatches: 5, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
200 88 0.44
201 1 0.01
202 8 0.04
203 8 0.04
204 94 0.47
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (200 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAAAAAAGTTGTAGTGAATAA
GATACAACACATTACTATTATATATAAAAATATACCAAAAAAGTAGTTGAACATTAGTGGTTGAT
TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCG
ATTTA
Found at i:5121 original size:9 final size:9
Alignment explanation
Indices: 5107--5153 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
5097 GATGATAGAT
5107 ATATATTAC
1 ATATATTAC
5116 ATATATATA-
1 ATATAT-TAC
5125 ATATAATATA-
1 ATAT-AT-TAC
5135 ATATATTAC
1 ATATATTAC
5144 ATATATTAC
1 ATATATTAC
5153 A
1 A
5154 ATTTTAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.06
9 22 0.63
10 11 0.31
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (9 bp):
ATATATTAC
Found at i:11129 original size:34 final size:33
Alignment explanation
Indices: 11086--11166 Score: 130
Period size: 31 Copynumber: 2.5 Consensus size: 33
11076 ACTTGGACTT
11086 AATTAATCTGATTTTTTTTTATTATCAAAAAAAA
1 AATTAATCTGATTTTTTTTTA-TATCAAAAAAAA
*
11120 AATTAATCTGA--TTTTTTTATCTCAAAAAAAA
1 AATTAATCTGATTTTTTTTTATATCAAAAAAAA
11151 AATTAATCTGATTTTT
1 AATTAATCTGATTTTT
11167 CTCCCTTGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
31 22 0.50
32 8 0.18
33 3 0.07
34 11 0.25
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (33 bp):
AATTAATCTGATTTTTTTTTATATCAAAAAAAA
Found at i:16545 original size:21 final size:21
Alignment explanation
Indices: 16520--16602 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 21
16510 TATCTTAGAT
16520 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
16541 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
**
16562 ATAAATAATGA-ATTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
16584 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
16603 TTACTAAACG
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
21 19 0.37
22 22 0.43
23 10 0.20
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:16553 original size:25 final size:25
Alignment explanation
Indices: 16522--16570 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
16512 TCTTAGATAT
*
16522 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
16547 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
16571 GAATTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:17132 original size:67 final size:67
Alignment explanation
Indices: 17032--17166 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
17022 ATTTGAGTTT
* *
17032 ACTTTGTAATTTATTTGTTTGTGTATATTTTATGTTTCACATTCTTTAGCTAAGATTGAGCTGGA
1 ACTTTGTAATTTATTTGTTTGTGTATATGTTATGGTTCACATTCTTTAGCTAAGATTGAGCTGGA
17097 TA
66 TA
17099 ACTTTGTAATTTATTTGTTTGTGTATATGTTATGGTTCACATTCTTTAGCTAAGATTGAGCTGGA
1 ACTTTGTAATTTATTTGTTTGTGTATATGTTATGGTTCACATTCTTTAGCTAAGATTGAGCTGGA
17164 TA
66 TA
17166 A
1 A
17167 TCGTGTGGTG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.49
Consensus pattern (67 bp):
ACTTTGTAATTTATTTGTTTGTGTATATGTTATGGTTCACATTCTTTAGCTAAGATTGAGCTGGA
TA
Found at i:19344 original size:175 final size:175
Alignment explanation
Indices: 19043--19392 Score: 592
Period size: 175 Copynumber: 2.0 Consensus size: 175
19033 TTGAGTATTA
*
19043 TATAAAAAACAATAATTATGGAAAGTGAAAGTACTAAAAAACCAGTCAAAAGATTTAACCTTATT
1 TATAAAAAACAATAATTATGGAAAGTAAAAGTACTAAAAAACCAGTCAAAAGATTTAACCTTATT
* * ** *
19108 AATTTGATTACTTTTTAGCTTGGTTTTTTCGTCATTTCAATATTAATTTTTTCGTTATTCTCACA
66 AATTTGATTACTATTTAGCTTGGTTTTTTCGTCATCTCAATATTAATTACTTCGATATTCTCACA
19173 AACTTCTAAGAGTATTTTTGACTTTCTAACAATTTAATATAATAT
131 AACTTCTAAGAGTATTTTTGACTTTCTAACAATTTAATATAATAT
*
19218 TATAAAAAACAATAATTATGGAAAGTAAAAGTACTAAAAAATCAGTCAAAAGATTTAACCTTATT
1 TATAAAAAACAATAATTATGGAAAGTAAAAGTACTAAAAAACCAGTCAAAAGATTTAACCTTATT
**
19283 AATTTGATTACTATTTAGCTTGGTTTTTTCGTCATCTCAATATTGGTTACTTCGATATTCTCACA
66 AATTTGATTACTATTTAGCTTGGTTTTTTCGTCATCTCAATATTAATTACTTCGATATTCTCACA
* * *
19348 AACTTTTAAGGGTGTTTTTGACTTTCTAACAATTTAATATAATAT
131 AACTTCTAAGAGTATTTTTGACTTTCTAACAATTTAATATAATAT
19393 AAGATAACAT
Statistics
Matches: 163, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
175 163 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (175 bp):
TATAAAAAACAATAATTATGGAAAGTAAAAGTACTAAAAAACCAGTCAAAAGATTTAACCTTATT
AATTTGATTACTATTTAGCTTGGTTTTTTCGTCATCTCAATATTAATTACTTCGATATTCTCACA
AACTTCTAAGAGTATTTTTGACTTTCTAACAATTTAATATAATAT
Found at i:19742 original size:178 final size:178
Alignment explanation
Indices: 19473--19802 Score: 511
Period size: 178 Copynumber: 1.9 Consensus size: 178
19463 CCAATTAAGG
*
19473 TGATTTAAGTGTCTATTAAAAGATTATTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTTAAGTGTCTATTAAAAGACTATTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
* * * * *
19538 AATTTAATATTTCGAGTATCAAAAATGCTTCCGAAA-AATTTGTTGTTTCGGTTAACGGGAATAG
66 AATTTAATAGTTCAAGTATAAAAAATGCTTCC-AAAGAATTAGTTGTTTCGGTTAACGGAAATAG
*
19602 ACGGTCCACTTAATATTATATAACTTTTGCTCTAGATGTTTGATTGAGA
130 ACGGTCCACTTAATATTACATAACTTTTGCTCTAGATGTTTGATTGAGA
* * * * *
19651 TGATTTAAGTGTCTCTTGAAAGGCTGTTCTATGATCTACAACTTTCATGAAGGACTCGAAAACTA
1 TGATTTAAGTGTCTATTAAAAGACTATTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
19716 AATTTAAT-GTTCAAGGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACGGAAATAG
66 AATTTAATAGTTCAA-GTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACGGAAATAG
*
19780 ACGGTCTACTTAATATTACATAA
130 ACGGTCCACTTAATATTACATAA
19803 TTTGAGCTTA
Statistics
Matches: 137, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
177 7 0.05
178 130 0.95
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (178 bp):
TGATTTAAGTGTCTATTAAAAGACTATTCCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATAGTTCAAGTATAAAAAATGCTTCCAAAGAATTAGTTGTTTCGGTTAACGGAAATAGA
CGGTCCACTTAATATTACATAACTTTTGCTCTAGATGTTTGATTGAGA
Found at i:29435 original size:18 final size:18
Alignment explanation
Indices: 29412--29455 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
29402 GGCAACTGAT
**
29412 GATGATGAGTCCTATGAA
1 GATGATGAGGACTATGAA
*
29430 GATGATGAGGATTATGAA
1 GATGATGAGGACTATGAA
29448 GATGATGA
1 GATGATGA
29456 ATGCGATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.05, G:0.32, T:0.27
Consensus pattern (18 bp):
GATGATGAGGACTATGAA
Found at i:33964 original size:45 final size:45
Alignment explanation
Indices: 33897--34006 Score: 141
Period size: 45 Copynumber: 2.4 Consensus size: 45
33887 GCAAATGAAG
* * * *
33897 TCCAAGCTAAGGATAAAGGCCGAAGTTCAAGTCAAAG-TCAAGCTGT
1 TCCAAGCTCA-GATAAGGGCCGAAGTTCAAGTC-AAGCTCAACCTGC
*
33943 TTCAAGCTCAGATAAGGGCCGAAGTTCAAGTCAAGCTCAACCTGC
1 TCCAAGCTCAGATAAGGGCCGAAGTTCAAGTCAAGCTCAACCTGC
*
33988 TCCAAGCTCAGACAAGGGC
1 TCCAAGCTCAGATAAGGGC
34007 AAAGGACCAG
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
44 3 0.05
45 45 0.80
46 8 0.14
ACGTcount: A:0.34, C:0.25, G:0.24, T:0.18
Consensus pattern (45 bp):
TCCAAGCTCAGATAAGGGCCGAAGTTCAAGTCAAGCTCAACCTGC
Found at i:36787 original size:24 final size:25
Alignment explanation
Indices: 36742--36788 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
36732 CTCGACGAGT
* *
36742 TCGAGTCGAGTTTCGAGTTTTTCCA
1 TCGAGTCGAGTCTCGAGCTTTTCCA
36767 TCGAGTCGAG-CTCGAGCTTTTC
1 TCGAGTCGAGTCTCGAGCTTTTC
36789 AAAACTTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (25 bp):
TCGAGTCGAGTCTCGAGCTTTTCCA
Found at i:38764 original size:24 final size:22
Alignment explanation
Indices: 38593--38816 Score: 122
Period size: 22 Copynumber: 10.0 Consensus size: 22
38583 TCTCGTCTTT
38593 GTGTGGTTATCAAAATTTCATAA
1 GTGTGGTTATCAAAATTTCAT-A
* * *
38616 G-ATGGTTATTATAATTTCATGA
1 GTGTGGTTATCAAAATTTCAT-A
* *
38638 G-GAGGTTATCAAAATTCCATA
1 GTGTGGTTATCAAAATTTCATA
* *
38659 GCGTTGGTTACCAAAATTTCATA
1 GTG-TGGTTATCAAAATTTCATA
* *
38682 -TG-GAAGATATCAAAATATCAT-
1 GTGTG--GTTATCAAAATTTCATA
* *
38703 GGGAAGGTTATCAAAATTTCATA
1 GTG-TGGTTATCAAAATTTCATA
*
38726 GTGTGGTTACCAAAATTTCATA
1 GTGTGGTTATCAAAATTTCATA
* *
38748 G-GATCGGGTTATTAAAATTT-TTAA
1 GTG-T--GGTTATCAAAATTTCAT-A
* **
38772 G-GAAGGTTATTGAAATTTCATA
1 GTG-TGGTTATCAAAATTTCATA
* *
38794 GTGTGGTTATCACAATTTTATA
1 GTGTGGTTATCAAAATTTCATA
38816 G
1 G
38817 AAAGGTTATC
Statistics
Matches: 154, Mismatches: 33, Indels: 29
0.71 0.15 0.13
Matches are distributed among these distances:
20 1 0.01
21 3 0.02
22 111 0.72
23 22 0.14
24 17 0.11
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (22 bp):
GTGTGGTTATCAAAATTTCATA
Found at i:38788 original size:68 final size:66
Alignment explanation
Indices: 38593--39272 Score: 220
Period size: 66 Copynumber: 10.3 Consensus size: 66
38583 TCTCGTCTTT
* * * * * *
38593 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCA
1 GTGTGGTTACCAAAATTTCATAGGATGGTTATTAAAATTT-TTAAGGAAGGTTATCAAAATTTCA
38657 TA
65 TA
* * * * * * *
38659 GCGTTGGTTACCAAAATTTCATATGGA-AGATATCAAAA-TATCATGGGAAGGTTATCAAAATTT
1 GTG-TGGTTACCAAAATTTCATA-GGATGGTTATTAAAATTTTTA-AGGAAGGTTATCAAAATTT
38722 CATA
63 CATA
**
38726 GTGTGGTTACCAAAATTTCATAGGATCGGGTTATTAAAATTTTTAAGGAAGGTTATTGAAATTTC
1 GTGTGGTTACCAAAATTTCATAGGAT--GGTTATTAAAATTTTTAAGGAAGGTTATCAAAATTTC
38791 ATA
64 ATA
* * * * * * * * *
38794 GTGTGGTTATCACAATTTTATAGAAAGGTTA-T--CA-----AA-G-AGATTATCAAAATATCCT
1 GTGTGGTTACCAAAATTTCATAGGATGGTTATTAAAATTTTTAAGGAAGGTTATCAAAATTTCAT
38849 A
66 A
** * ** * *
38850 ACGAGGTTA-CAAGAATTTCATAGTG-TGGTTAACAAAATTTCATAAGG-AGGTTA-CTAATATT
1 GTGTGGTTACCAA-AATTTCATAG-GATGGTTATTAAAATTT-TTAAGGAAGGTTATC-AAAATT
38911 TCATA
62 TCATA
* * * * * *
38916 GGGAGGTTATCAAAATTTCATAGTG-TCGTTATTAAAATTTTTTAGTG-TGGTTATCAAAATTTC
1 GTGTGGTTACCAAAATTTCATAG-GATGGTTATTAAAATTTTTAAG-GAAGGTTATCAAAATTTC
38979 ATA
64 ATA
* ** ** *
38982 -TGAAGGTTATAAAAGTCTCAATTTCATAAGGA--G-TACCAAAA-TTTGATA-GAAGGTTATC-
1 GTG-TGGTTA-CCAA-----AATTTCAT-AGGATGGTTATTAAAATTTTTA-AGGAAGGTTATCA
*
39040 AAATCTCATA
57 AAATTTCATA
* * * * * * *
39050 GAGTGATCATCAAAATTTCATAGAGATCGGATTATCAAAATTTAT-AGGAAGATTATCAAAATTT
1 GTGTGGTTACCAAAATTTCATAG-GAT-GG-TTATTAAAATTTTTAAGGAAGGTTATCAAAATTT
39114 CATA
63 CATA
* * * * * ** *
39118 GTATTGTTATCAAAATTTCAAAGCGA-GGTTATCAAAATTACATAATGAA--TATATCAAAATTT
1 GTGTGGTTACCAAAATTTCATAG-GATGGTTATTAAAATT-TTTAAGGAAGGT-TATCAAAATTT
*
39180 CATG
63 CATA
* * * * * * * *
39184 GAGGGGTCAACACAATTTTATAGAGA-GGTTATCAAAATTTCATTAA-G-AGGTTATCAAATTTT
1 GTGTGGTTACCAAAATTTCATAG-GATGGTTATTAAAATTT--TTAAGGAAGGTTATCAAAATTT
*
39246 CAAA
63 CATA
* *
39250 ATGTGATTACCAAAATTTCATAG
1 GTGTGGTTACCAAAATTTCATAG
39273 TGGTATTTCT
Statistics
Matches: 454, Mismatches: 108, Indels: 104
0.68 0.16 0.16
Matches are distributed among these distances:
55 2 0.00
56 34 0.07
57 1 0.00
58 2 0.00
59 1 0.00
61 2 0.00
62 10 0.02
63 1 0.00
65 25 0.06
66 172 0.38
67 77 0.17
68 94 0.21
69 14 0.03
70 7 0.02
71 1 0.00
72 9 0.02
73 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAGGATGGTTATTAAAATTTTTAAGGAAGGTTATCAAAATTTCAT
A
Found at i:38901 original size:44 final size:43
Alignment explanation
Indices: 38834--38995 Score: 146
Period size: 44 Copynumber: 3.7 Consensus size: 43
38824 ATCAAAGAGA
* * *
38834 TTATCAAAATATCCTAACGAGGTTACAAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATAAGGAGGTTACAA-AATTTCATAGTGTGG
* * * *
38878 TTAACAAAATTTCATAAGGAGGTTACTAATATTTCATAGGGAGG
1 TTATCAAAATTTCATAAGGAGGTTAC-AAAATTTCATAGTGTGG
** * **
38922 TTATCAAAATTTCAT-AGTGTCGTTATTAAAATTTTTTAGTGTGG
1 TTATCAAAATTTCATAAG-GAGGTTA-CAAAATTTCATAGTGTGG
* * *
38966 TTATCAAAATTTCATATGAAGGTTATAAAA
1 TTATCAAAATTTCATAAGGAGGTTACAAAA
38996 GTCTCAATTT
Statistics
Matches: 94, Mismatches: 20, Indels: 9
0.76 0.16 0.07
Matches are distributed among these distances:
43 7 0.07
44 84 0.89
45 3 0.03
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (43 bp):
TTATCAAAATTTCATAAGGAGGTTACAAAATTTCATAGTGTGG
Found at i:38989 original size:22 final size:22
Alignment explanation
Indices: 38853--39247 Score: 128
Period size: 22 Copynumber: 17.8 Consensus size: 22
38843 TATCCTAACG
38853 AGGTTA-CAAGAATTTCATAGTG-
1 AGGTTATCAA-AATTTCATA-TGA
* * * *
38875 TGGTTAACAAAATTTCATAAGG
1 AGGTTATCAAAATTTCATATGA
* * *
38897 AGGTTA-CTAATATTTCATAGGG
1 AGGTTATC-AAAATTTCATATGA
38919 AGGTTATCAAAATTTCATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
** * **
38941 TCGTTATTAAAATTTTTTAGTG-
1 AGGTTATCAAAATTTCATA-TGA
*
38963 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGA
*
38985 AGGTTAT-AAAAGTCTCAATTTCAT-A
1 AGGTTATCAAAA-TTTC-A--T-ATGA
* * *
39010 AGGAGTACCAAAATTTGATA-GA
1 AGG-TTATCAAAATTTCATATGA
*
39032 AGGTTATC-AAATCTCATA-G-
1 AGGTTATCAAAATTTCATATGA
*
39051 AGTGATCATCAAAATTTCATA-GA
1 AG-G-TTATCAAAATTTCATATGA
*
39074 GATCGGATTATCAAAATTT-ATAGGA
1 -A--GG-TTATCAAAATTTCATATGA
*
39099 AGATTATCAAAATTTCATA-GTA
1 AGGTTATCAAAATTTCATATG-A
** * *
39121 TTGTTATCAAAATTTCA-AAGCG
1 AGGTTATCAAAATTTCATATG-A
*
39143 AGGTTATCAAAATTACATAATGA
1 AGGTTATCAAAATTTCAT-ATGA
*
39166 A--TATATCAAAATTTCAT-GGA
1 AGGT-TATCAAAATTTCATATGA
* * * * *
39186 GGGGTCAACACAATTTTATA-GA
1 -AGGTTATCAAAATTTCATATGA
*
39208 GAGGTTATCAAAATTTCAT-TAA
1 -AGGTTATCAAAATTTCATATGA
*
39230 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
39248 AAATGTGATT
Statistics
Matches: 286, Mismatches: 54, Indels: 66
0.70 0.13 0.16
Matches are distributed among these distances:
19 2 0.01
20 12 0.04
21 30 0.10
22 194 0.68
23 9 0.03
24 7 0.02
25 21 0.07
26 7 0.02
27 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGA
Found at i:39420 original size:22 final size:21
Alignment explanation
Indices: 39372--39550 Score: 96
Period size: 22 Copynumber: 8.8 Consensus size: 21
39362 TCAGGGATGA
39372 TATCAAAATTTCATATGAAGT
1 TATCAAAATTTCATATGAAGT
**
39393 TATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATA-TGAAGT
* * *
39415 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGA-AGT
*
39437 TATCAAAATTTCGTAGTATGTAG-
1 TATCAAAATTTC--A-TATGAAGT
*
39460 -ATCAAAATTTCACAT--A--
1 TATCAAAATTTCATATGAAGT
*
39476 -A-CAAAATTTCATAATGAGGT
1 TATCAAAATTTCAT-ATGAAGT
*
39496 TATCAAAA--T--T-TGTAGT
1 TATCAAAATTTCATATGAAGT
* *
39512 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATG-AAGT
*
39534 TATCAAAATTTTATATG
1 TATCAAAATTTCATATG
39551 GAGGTTTAAA
Statistics
Matches: 118, Mismatches: 22, Indels: 35
0.67 0.13 0.20
Matches are distributed among these distances:
15 10 0.08
16 14 0.12
17 1 0.01
18 2 0.02
19 2 0.02
20 3 0.03
21 17 0.14
22 64 0.54
24 2 0.02
25 3 0.03
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (21 bp):
TATCAAAATTTCATATGAAGT
Found at i:39465 original size:44 final size:42
Alignment explanation
Indices: 39372--39471 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 42
39362 TCAGGGATGA
*
39372 TATCAAAATTTCATATGAAGTTATCAAAATTTCATAGTTTAG
1 TATCAAAATTTCATAAGAAGTTATCAAAATTTCATAGTTTAG
* * *
39414 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCGTAGTATGTAG
1 -TATCAAAATTTCATAAGA-AGTTATCAAAATTTCATAGT-T-TAG
39460 -ATCAAAATTTCA
1 TATCAAAATTTCA
39472 CATAACAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
43 16 0.33
44 29 0.59
45 1 0.02
46 3 0.06
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (42 bp):
TATCAAAATTTCATAAGAAGTTATCAAAATTTCATAGTTTAG
Found at i:39641 original size:22 final size:22
Alignment explanation
Indices: 39579--39647 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
39569 ATAGGAAGGT
* * *
39579 TTATCCAAATTTCATAGCGAGA
1 TTATCAAAATTTCATAGTGTGA
*
39601 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
*
39623 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
39645 TTA
1 TTA
39648 CTAACAATTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Found at i:39658 original size:22 final size:23
Alignment explanation
Indices: 39599--39656 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
39589 TTCATAGCGA
*
39599 GATTATC-ACAATTTCATAGTGT
1 GATTATCAACAATTTCAGAGTGT
39621 GATTATCAA-AATTTCAGAGTGT
1 GATTATCAACAATTTCAGAGTGT
39643 GATTA-CTAACAATT
1 GATTATC-AACAATT
39657 CATATGGAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 1 0.03
22 26 0.81
23 5 0.16
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (23 bp):
GATTATCAACAATTTCAGAGTGT
Found at i:39822 original size:22 final size:21
Alignment explanation
Indices: 39797--39842 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
39787 TTCCTTAGGG
*
39797 AGGTT-AACAAAATTTCATAAGA
1 AGGTTAAAAAAAATTT-ATAA-A
39819 AGGTTAAAAAAAATTTATAAA
1 AGGTTAAAAAAAATTTATAAA
39840 AGG
1 AGG
39843 GTTTTCGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
22 9 0.41
23 9 0.41
ACGTcount: A:0.54, C:0.04, G:0.15, T:0.26
Consensus pattern (21 bp):
AGGTTAAAAAAAATTTATAAA
Found at i:48860 original size:22 final size:22
Alignment explanation
Indices: 48832--48880 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
48822 TTCCAGAATC
48832 CGAAGCGACGTGCCTCGAAACT
1 CGAAGCGACGTGCCTCGAAACT
*
48854 CGAAGCGACGTGCCTCGAAATT
1 CGAAGCGACGTGCCTCGAAACT
48876 CGAAG
1 CGAAG
48881 TGTAGTTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (22 bp):
CGAAGCGACGTGCCTCGAAACT
Found at i:51603 original size:27 final size:27
Alignment explanation
Indices: 51572--51624 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
51562 AAAAACGGGG
* *
51572 GCGACCAGTAGTACTCCTGGGGGGGTC
1 GCGACCAGCAGTACCCCTGGGGGGGTC
*
51599 GCGACTAGCAGTACCCCTGGGGGGGT
1 GCGACCAGCAGTACCCCTGGGGGGGT
51625 TGCCCCTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.15, C:0.26, G:0.42, T:0.17
Consensus pattern (27 bp):
GCGACCAGCAGTACCCCTGGGGGGGTC
Found at i:51633 original size:27 final size:27
Alignment explanation
Indices: 51581--51633 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
51571 GGCGACCAGT
* *
51581 AGTACTCCTGGGGGGGTCGCGACTAGC
1 AGTACCCCTGGGGGGGTCGCCACTAGC
* *
51608 AGTACCCCTGGGGGGGTTGCCCCTAG
1 AGTACCCCTGGGGGGGTCGCCACTAG
51634 TCCGCAGGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.13, C:0.28, G:0.40, T:0.19
Consensus pattern (27 bp):
AGTACCCCTGGGGGGGTCGCCACTAGC
Found at i:61238 original size:16 final size:17
Alignment explanation
Indices: 61219--61252 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
61209 ATTGTTCAAG
61219 GGTCCAAT-TTCAATAA
1 GGTCCAATATTCAATAA
*
61235 GGTCCACTATTCAATAA
1 GGTCCAATATTCAATAA
61252 G
1 G
61253 TTTTGGTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (17 bp):
GGTCCAATATTCAATAA
Found at i:63333 original size:23 final size:23
Alignment explanation
Indices: 63286--63333 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
63276 TGTTAAACGC
* *
63286 GGAGCAATTTTGGAACGGTAGTT
1 GGAGCAATTTGGGAACGGTAATT
* *
63309 GGAGCAATTTGGGTACTGTAATT
1 GGAGCAATTTGGGAACGGTAATT
63332 GG
1 GG
63334 TGGGTATGCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.25, C:0.08, G:0.35, T:0.31
Consensus pattern (23 bp):
GGAGCAATTTGGGAACGGTAATT
Found at i:64287 original size:2 final size:2
Alignment explanation
Indices: 64280--64308 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
64270 TATTACAAGC
64280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.