Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018038.1 Corchorus olitorius cultivar O-4 contig18071, 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: 35787
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:724 original size:15 final size:14
Alignment explanation
Indices: 701--730 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
691 ATAAAAATTA
701 AATATTTTTATTTT
1 AATATTTTTATTTT
715 AATATATTTTATTTT
1 AATAT-TTTTATTTT
730 A
1 A
731 TTGAAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATATTTTTATTTT
Found at i:2097 original size:284 final size:284
Alignment explanation
Indices: 1587--2151 Score: 1121
Period size: 284 Copynumber: 2.0 Consensus size: 284
1577 TAATATAATT
1587 TTTTTTGTTTGATTCTCATGAATATAATATATTGAAAATGAGCTATATAATAGGAGGTAGCCCCT
1 TTTTTTGTTTGATTCTCATGAATATAATATATTGAAAATGAGCTATATAATAGGAGGTAGCCCCT
1652 TTCCTATCCCAAATCCCATCCTGAATTGCTAAATACCGGCCCCTTTTTGCTAGTTACTGCCCCCC
66 TTCCTATCCCAAATCCCATCCTGAATTGCTAAATACCGGCCCCTTTTTGCTAGTTACTGCCCCCC
1717 TTTTGATACTTTCCCTTTGCTTCATTTTCCTCTAAAATTTTCAAACTAAAAATCTCAAATTTTCA
131 TTTTGATACTTTCCCTTTGCTTCATTTTCCTCTAAAATTTTCAAACTAAAAATCTCAAATTTTCA
1782 AGTCAATCACCAATAATAATAATCATAAACCCTATATTGACCCTAATTAATAATAACAAGCAGGG
196 AGTCAATCACCAATAATAATAATCATAAACCCTATATTGACCCTAATTAATAATAACAAGCAGGG
1847 TGGCCAGCGCTTGCACTGCAGCCC
261 TGGCCAGCGCTTGCACTGCAGCCC
1871 TTTTTTGTTTGATTCTCATGAATATAATATATTGAAAATGAGCTATATAATAGGAGGTAGCCCCT
1 TTTTTTGTTTGATTCTCATGAATATAATATATTGAAAATGAGCTATATAATAGGAGGTAGCCCCT
1936 TTCCTATCCCAAATCCCATCCTGAATTGCTAAATACCGGCCCCTTTTTGCTAGTTACTGCCCCCC
66 TTCCTATCCCAAATCCCATCCTGAATTGCTAAATACCGGCCCCTTTTTGCTAGTTACTGCCCCCC
2001 TTTTGATACTTTCCCTTTGCTTCATTTTCCTCTAAAATTTTCAAACTAAAAATCTCAAATTTTCA
131 TTTTGATACTTTCCCTTTGCTTCATTTTCCTCTAAAATTTTCAAACTAAAAATCTCAAATTTTCA
2066 AGTCAATCACCAATAATAATAATCATAAACCCTATATTGACCCTAATTAATAATAACAAGCAGGG
196 AGTCAATCACCAATAATAATAATCATAAACCCTATATTGACCCTAATTAATAATAACAAGCAGGG
*
2131 TGGCCAGCGCTTGCGCTGCAG
261 TGGCCAGCGCTTGCACTGCAG
2152 TCATCTTCTT
Statistics
Matches: 280, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
284 280 1.00
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (284 bp):
TTTTTTGTTTGATTCTCATGAATATAATATATTGAAAATGAGCTATATAATAGGAGGTAGCCCCT
TTCCTATCCCAAATCCCATCCTGAATTGCTAAATACCGGCCCCTTTTTGCTAGTTACTGCCCCCC
TTTTGATACTTTCCCTTTGCTTCATTTTCCTCTAAAATTTTCAAACTAAAAATCTCAAATTTTCA
AGTCAATCACCAATAATAATAATCATAAACCCTATATTGACCCTAATTAATAATAACAAGCAGGG
TGGCCAGCGCTTGCACTGCAGCCC
Found at i:6040 original size:44 final size:43
Alignment explanation
Indices: 5991--6971 Score: 181
Period size: 44 Copynumber: 22.9 Consensus size: 43
5981 GTCTCTGTGT
* * *
5991 GGTTATCAAAATTTCATAAGATGATTATTATAATTTCATGAGGA
1 GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTCAT-AGGA
* *
6035 GGTTATCAAAA-TTC-TATAGTGTGGTTACCAAAATTTCATAAGGA
1 GGTTATCAAAATTTCATA-AG-ATGGTTATCAAAATTTCAT-AGGA
* ** * *
6079 CGTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTCATAG-GA
* * * **
6123 GGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTTTTAGGAA
1 GGTTATCAAAATTTCATAAGAT--GGTTATCAAAATTTCATAGG-A
** * * * * * * *
6169 GGTTATTGAACTTTTAT-AGTGTGGTTATCACAATTTTAAAGAAA
1 GGTTATCAAAATTTCATAAG-ATGGTTATCAAAATTTCATAG-GA
*
6213 GG-T-T----A-TT-A-AAGA-GATTATCAAAATTTCATAAGGA
1 GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTCAT-AGGA
* * ** * *
6247 GGTTA-CTAATATTTTATGGGGA-GGTTATCAAAATTTCATAATGT
1 GGTTATC-AAAATTTCAT-AAGATGGTTATCAAAATTTCAT-AGGA
* * * *
6291 GGTTATCAAAATTT-TTTAGTGTGGTTA-CAAAATTTCATATGAA
1 GGTTATCAAAATTTCATAAG-ATGGTTATCAAAATTTCATA-GGA
* * * * * *
6334 GGTTAT-AAAAGTCTCAATTTCATGA-GGAGTACCAAAATTTGATAGAA
1 GGTTATCAAAA-TTTC-A--T-AAGATGG-TTATCAAAATTTCATAGGA
* * * *
6381 GGTTATC-AAATCTCAT-AGAGTGATTATCGAAATTCCATAGAGA
1 GGTTATCAAAATTTCATAAGA-TGGTTATCAAAATTTCATAG-GA
* * * * * *
6424 TCGGATATCAAAATTT-ATAGGAAGATTTATTAAAATTTCATAGTGT
1 --GGTTATCAAAATTTCATAAGATG-GTTATCAAAATTTCATAG-GA
* * * *
6470 TGTTATCAAAATTTCA-AAGGGA-GGTTATCAAAATTACATAATGT
1 GGTTATCAAAATTTCATAA--GATGGTTATCAAAATTTCAT-AGGA
* * * **
6514 GATTATCAAAATTTCAT-AGAGGGGTCAAAAAAACTTT-ATAGAGA
1 GGTTATCAAAATTTCATAAGA-TGGTTATCAAAA-TTTCATAG-GA
* * * *
6558 GATTATCAAAATTTCATAAAGA-GTTTATCAAATTTTCA-A-AA
1 GGTTATCAAAATTTCAT-AAGATGGTTATCAAAATTTCATAGGA
* * *
6599 TGTTATTTACCAAAATTTCAT-TG-TGG---T----ATTTC-TGGGGA
1 GGTTA--T--CAAAATTTCATAAGATGGTTATCAAAATTTCAT-AGGA
*
6637 GGTTATCAAAATTTCAT-AGTATGGTTA-CCAAA--T--TAGGAA
1 GGTTATCAAAATTTCATAAG-ATGGTTATCAAAATTTCATAGG-A
* * ** *
6676 GGTTATTAAACTTT--TATTATGGAGTAATCAAAATTTCA-AGGA
1 GGTTATCAAAATTTCATAAGAT-G-GTTATCAAAATTTCATAGGA
* ** * *
6718 GGATATCAAAATTTCATATTAAGGTTATCAAAATTTCATAGTTTA
1 GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTCATAG--GA
* * *
6763 -GTTTTCAAAATTTTCATAGGTAT-GTAGATCAAAATTTCATAGGGA
1 GGTTATCAAAA-TTTCATAAG-ATGGT-TATCAAAATTTCATA-GGA
* * * * **
6808 GATTAACAAAATTTAATAATGA-GGTTATAAAAAAATCATAGGGA
1 GGTTATCAAAATTTCATAA-GATGGTTATCAAAATTTCATA-GGA
* * * *
6852 GATTATCAAAA-TT--T--G-TAGTTATCAAGAGTTCATAAGGA
1 GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTCAT-AGGA
* * *
6890 GGTTATCAAAATTTTATAGGATGGTTTATCAAAATGTCATAGCGA
1 GGTTATCAAAATTTCATAAGATGG-TTATCAAAATTTCATAG-GA
* *
6935 GGTTATCACAATTTCA-AAG-TGTGATATCAAAATTTCA
1 GGTTATCAAAATTTCATAAGATG-GTTATCAAAATTTCA
6972 GGGTGTGATT
Statistics
Matches: 679, Mismatches: 153, Indels: 211
0.65 0.15 0.20
Matches are distributed among these distances:
34 28 0.04
35 3 0.00
36 11 0.02
37 5 0.01
38 34 0.05
39 20 0.03
40 7 0.01
41 10 0.01
42 52 0.08
43 62 0.09
44 252 0.37
45 81 0.12
46 86 0.13
47 16 0.02
48 12 0.02
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAAGATGGTTATCAAAATTTCATAGGA
Found at i:6047 original size:22 final size:21
Alignment explanation
Indices: 5991--6143 Score: 146
Period size: 22 Copynumber: 7.0 Consensus size: 21
5981 GTCTCTGTGT
*
5991 GGTTATCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAGGA
* * *
6012 TGATTATTATAATTTCATGAGGA
1 -GGTTATCAAAATTTCAT-AGGA
*
6035 GGTTATCAAAA-TTCTATAGTGT
1 GGTTATCAAAATTTC-ATAG-GA
*
6057 GGTTACCAAAATTTCATAAGGA
1 GGTTATCAAAATTTCAT-AGGA
* *
6079 CGTTATCAAAATTTCATGGGAA
1 GGTTATCAAAATTTCATAGG-A
*
6101 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAG-GA
*
6123 GGTTACCAAAATTTCATAGGA
1 GGTTATCAAAATTTCATAGGA
6144 TCAGGTTATT
Statistics
Matches: 106, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
21 8 0.08
22 89 0.84
23 9 0.08
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:6093 original size:66 final size:66
Alignment explanation
Indices: 5987--6204 Score: 226
Period size: 66 Copynumber: 3.3 Consensus size: 66
5977 TCTTGTCTCT
* * * *
5987 GTGTGGTTATCAAAATTTCATAAGATGATTATTATAATTTCATGAGG-AGGTTATCAAAA-TTCT
1 GTGTGGTTACCAAAATTTCATAAGACGATTATCAAAATTTCATG-GGAAGGTTATCAAAATTTC-
6050 ATA
64 ATA
6053 GTGTGGTTACCAAAATTTCATAAGGACG-TTATCAAAATTTCATGGGAAGGTTATCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATAA-GACGATTATCAAAATTTCATGGGAAGGTTATCAAAATTTCA
6117 TA
65 TA
* * * ** * ** * *
6119 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTTTTAGGAAGGTTATTGAACTTTT
1 GTGTGGTTACCAAAATTTCATAAGA-C-GATTATCAAAATTTCATGGGAAGGTTATCAAAATTTC
6184 ATA
64 ATA
* *
6187 GTGTGGTTATCACAATTT
1 GTGTGGTTACCAAAATTT
6205 TAAAGAAAGG
Statistics
Matches: 131, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
65 4 0.03
66 74 0.56
67 7 0.05
68 46 0.35
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAAGACGATTATCAAAATTTCATGGGAAGGTTATCAAAATTTCAT
A
Found at i:6166 original size:24 final size:22
Alignment explanation
Indices: 5991--6175 Score: 110
Period size: 22 Copynumber: 8.3 Consensus size: 22
5981 GTCTCTGTGT
* * *
5991 GGTTATCAAAATTTCATAAGAT
1 GGTTATTAAAATTTCATAGGAA
* *
6013 GATTATTATAATTTCATGAGG-A
1 GGTTATTAAAATTTCAT-AGGAA
* *
6035 GGTTATCAAAA-TTCTATAGTG-T
1 GGTTATTAAAATTTC-ATAG-GAA
**
6057 GGTTACCAAAATTTCATAAGG-A
1 GGTTATTAAAATTTCAT-AGGAA
* * *
6079 CGTTATCAAAATTTCATGGGAA
1 GGTTATTAAAATTTCATAGGAA
* *
6101 GGTTATCAAAATTTCATAGTG-T
1 GGTTATTAAAATTTCATAG-GAA
**
6123 GGTTACCAAAATTTCATAGGATCA
1 GGTTATTAAAATTTCATAGGA--A
**
6147 GGTTATTAAAATTTTTTAGGAA
1 GGTTATTAAAATTTCATAGGAA
6169 GGTTATT
1 GGTTATT
6176 GAACTTTTAT
Statistics
Matches: 130, Mismatches: 23, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
21 8 0.06
22 97 0.75
23 8 0.06
24 17 0.13
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (22 bp):
GGTTATTAAAATTTCATAGGAA
Found at i:6282 original size:22 final size:22
Alignment explanation
Indices: 6227--6595 Score: 124
Period size: 22 Copynumber: 16.6 Consensus size: 22
6217 ATTAAAGAGA
6227 TTATCAAAATTTCATAAGGAGG
1 TTATCAAAATTTCATAAGGAGG
* * **
6249 TTA-CTAATATTTTATGGGGAGG
1 TTATC-AAAATTTCATAAGGAGG
* *
6271 TTATCAAAATTTCATAATGTGG
1 TTATCAAAATTTCATAAGGAGG
* * *
6293 TTATCAAAATTT-TTTAGTGTGG
1 TTATCAAAATTTCATAAG-GAGG
* *
6315 TTA-CAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAAGGAGG
* *
6336 TTATAAAAGTCTCAATTTCATGAGGA-G
1 TTAT-CAA-----AATTTCATAAGGAGG
* * *
6363 -TACCAAAATTTGAT-AGAAGG
1 TTATCAAAATTTCATAAGGAGG
*
6383 TTATC-AAATCTCAT-A-GAGTG
1 TTATCAAAATTTCATAAGGAG-G
* *
6403 ATTATCGAAATTCCAT-AGAGATCGG
1 -TTATCAAAATTTCATAAG-GA--GG
* *
6428 ATATCAAAATTT-AT-AGGAAGAT
1 TTATCAAAATTTCATAAGG-AG-G
* **
6450 TTATTAAAATTTCAT-AGTGTTG
1 TTATCAAAATTTCATAAG-GAGG
6472 TTATCAAAATTTCA-AAGGGAGG
1 TTATCAAAATTTCATAA-GGAGG
* * * *
6494 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAGGAGG
6516 TTATCAAAATTTCATAGAGG-GG
1 TTATCAAAATTTCATA-AGGAGG
* ** *
6538 TCAAAAAAACTTT-AT-AGAGAGA
1 TTATCAAAA-TTTCATAAG-GAGG
* *
6560 TTATCAAAATTTCATAAAGAGT
1 TTATCAAAATTTCATAAGGAGG
*
6582 TTATCAAATTTTCA
1 TTATCAAAATTTCA
6596 AAATGTTATT
Statistics
Matches: 253, Mismatches: 61, Indels: 66
0.67 0.16 0.17
Matches are distributed among these distances:
19 5 0.02
20 19 0.08
21 29 0.11
22 150 0.59
23 21 0.08
24 12 0.05
25 3 0.01
26 3 0.01
27 1 0.00
28 10 0.04
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGGAGG
Found at i:6915 original size:22 final size:21
Alignment explanation
Indices: 6634--7233 Score: 160
Period size: 22 Copynumber: 27.8 Consensus size: 21
6624 GTATTTCTGG
6634 GGAGGTTATCAAAATTTCATA
1 GGAGGTTATCAAAATTTCATA
* *
6655 GTATGGTTA-CCAAA--T--TA
1 GGA-GGTTATCAAAATTTCATA
* * *
6672 GGAAGGTTATTAAACTTTTATTA
1 GG-AGGTTATCAAAATTTCA-TA
*
6695 TGGA-GTAATCAAAATTTCA-A
1 -GGAGGTTATCAAAATTTCATA
*
6715 GGAGGATATCAAAATTTCATA
1 GGAGGTTATCAAAATTTCATA
**
6736 TTAAGGTTATCAAAATTTCATA
1 -GGAGGTTATCAAAATTTCATA
* *
6758 GTTTA-GTTTTCAAAATTTTCATA
1 G--GAGGTTATCAAAA-TTTCATA
* *
6781 GGTATGTAGATCAAAATTTCATA
1 GG-AGGT-TATCAAAATTTCATA
* * *
6804 GGGAGATTAACAAAATTTAATAA
1 -GGAGGTTATCAAAATTTCAT-A
* * **
6827 TGAGGTTATAAAAAAATCATA
1 GGAGGTTATCAAAATTTCATA
*
6848 GGGAGATTATCAAAA-TT--T-
1 -GGAGGTTATCAAAATTTCATA
* * *
6866 GTA-GTTATCAAGAGTTCATAA
1 GGAGGTTATCAAAATTTCAT-A
*
6887 GGAGGTTATCAAAATTTTATA
1 GGAGGTTATCAAAATTTCATA
*
6908 GGATGGTTTATCAAAATGTCATA
1 GGA-GG-TTATCAAAATTTCATA
* *
6931 GCGAGGTTATCACAATTTCAAA
1 G-GAGGTTATCAAAATTTCATA
* * *
6953 GTG-TGATATCAAAATTTCA-G
1 G-GAGGTTATCAAAATTTCATA
*
6973 GGTGTGATTA-CTAACAA-TTCATA
1 GGAG-G-TTATC-AA-AATTTCATA
* * * * *
6996 TGAAGGTTTTTAAATTTTCAAA
1 -GGAGGTTATCAAAATTTCATA
** * *
7018 ACATGGTTATCAATATATCATA
1 GGA-GGTTATCAAAATTTCATA
* *
7040 TGGA-GTTATCAACATCTCATA
1 -GGAGGTTATCAAAATTTCATA
** *
7061 GTTTTGATTATCAAAATTTCATA
1 G--GAGGTTATCAAAATTTCATA
*
7084 GGGAAGTTATCAAAATTTCATA
1 -GGAGGTTATCAAAATTTCATA
* *
7106 GTGAGGTCT-TCAAAATTCCTTA
1 G-GAGGT-TATCAAAATTTCATA
*
7128 GGGAGGTTAAT-AAAATTCCATAA
1 -GGAGGTT-ATCAAAATTTCAT-A
* ** * * *
7151 GAAGGTTAAAAAAAAATTAAAA
1 GGAGGTT-ATCAAAATTTCATA
** * *
7173 AAAGGTTCTCGAAATTTCATA
1 GGAGGTTATCAAAATTTCATA
* * *
7194 GTATCGTTATTAAAATTTCATAA
1 GGA-GGTTATCAAAATTTCAT-A
*
7217 GAAGGTTATCAAAATTT
1 GGAGGTTATCAAAATTT
7234 TATAAAGAGG
Statistics
Matches: 414, Mismatches: 111, Indels: 107
0.66 0.18 0.17
Matches are distributed among these distances:
16 8 0.02
17 12 0.03
18 3 0.01
19 7 0.02
20 17 0.04
21 57 0.14
22 223 0.54
23 72 0.17
24 15 0.04
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (21 bp):
GGAGGTTATCAAAATTTCATA
Found at i:6968 original size:21 final size:21
Alignment explanation
Indices: 6938--6980 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6928 ATAGCGAGGT
*
6938 TATCACAATTTCAAAGTGTGA
1 TATCAAAATTTCAAAGTGTGA
**
6959 TATCAAAATTTCAGGGTGTGA
1 TATCAAAATTTCAAAGTGTGA
6980 T
1 T
6981 TACTAACAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (21 bp):
TATCAAAATTTCAAAGTGTGA
Found at i:7244 original size:22 final size:22
Alignment explanation
Indices: 7199--7253 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
7189 TCATAGTATC
*
7199 GTTATTAAAATTTCATAAGAAG
1 GTTATAAAAATTTCATAAGAAG
* *
7221 GTTATCAAAATTTTATAA-AGAG
1 GTTATAAAAATTTCATAAGA-AG
*
7243 GTCATAAAAAT
1 GTTATAAAAAT
7254 AGTGTAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.47, C:0.05, G:0.13, T:0.35
Consensus pattern (22 bp):
GTTATAAAAATTTCATAAGAAG
Found at i:11510 original size:188 final size:188
Alignment explanation
Indices: 11193--11572 Score: 724
Period size: 188 Copynumber: 2.0 Consensus size: 188
11183 GGAATGACTG
*
11193 CATCTGCCTTTGATGGCGTAAAGGACCGCCACTCTTTTCATCATTCGAGAGTATTTCATTAAAAT
1 CATCTGCCTTTGATGACGTAAAGGACCGCCACTCTTTTCATCATTCGAGAGTATTTCATTAAAAT
* *
11258 CTCCAGAACATAACCATGGCAGAGAAGATTGTGAGGCCAACAATTTCAGTAATTCCCAAGACTCC
66 CTCCAAAACATAACCATGACAGAGAAGATTGTGAGGCCAACAATTTCAGTAATTCCCAAGACTCC
11323 CTTCGTCTATGTGTTTCTGGGCATCCATAAAAGCCCGTAAAACGCCAAGGAGAATCTC
131 CTTCGTCTATGTGTTTCTGGGCATCCATAAAAGCCCGTAAAACGCCAAGGAGAATCTC
*
11381 CATCTGCCTTTGATGACGTAAAGGACCGCCACTCTTTTCATCATTTGAGAGTATTTCATTAAAAT
1 CATCTGCCTTTGATGACGTAAAGGACCGCCACTCTTTTCATCATTCGAGAGTATTTCATTAAAAT
11446 CTCCAAAACATAACCATGACAGAGAAGATTGTGAGGCCAACAATTTCAGTAATTCCCAAGACTCC
66 CTCCAAAACATAACCATGACAGAGAAGATTGTGAGGCCAACAATTTCAGTAATTCCCAAGACTCC
11511 CTTCGTCTATGTGTTTCTGGGCATCCATAAAAGCCCGTAAAACGCCAAGGAGAATCTC
131 CTTCGTCTATGTGTTTCTGGGCATCCATAAAAGCCCGTAAAACGCCAAGGAGAATCTC
11569 CATC
1 CATC
11573 ATCCCCAACA
Statistics
Matches: 188, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
188 188 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (188 bp):
CATCTGCCTTTGATGACGTAAAGGACCGCCACTCTTTTCATCATTCGAGAGTATTTCATTAAAAT
CTCCAAAACATAACCATGACAGAGAAGATTGTGAGGCCAACAATTTCAGTAATTCCCAAGACTCC
CTTCGTCTATGTGTTTCTGGGCATCCATAAAAGCCCGTAAAACGCCAAGGAGAATCTC
Found at i:14213 original size:23 final size:21
Alignment explanation
Indices: 14187--14231 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
14177 TTTGGCATCG
*
14187 TTTTCGTTTTTCTGTTTTTTTTT
1 TTTTCG-TTTTC-GTTTTGTTTT
14210 TTTTCGTTTTCGTTTTGTTTT
1 TTTTCGTTTTCGTTTTGTTTT
14231 T
1 T
14232 GTTGCGTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 5 0.24
23 6 0.29
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (21 bp):
TTTTCGTTTTCGTTTTGTTTT
Found at i:14239 original size:22 final size:22
Alignment explanation
Indices: 14194--14239 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
14184 TCGTTTTCGT
* *
14194 TTTTCTGTTTTTTTTTTTTTCG
1 TTTTCTGTTTTTTTTTGTTGCG
14216 TTTTC-GTTTTGTTTTTGTTGCG
1 TTTTCTGTTTT-TTTTTGTTGCG
14238 TT
1 TT
14240 GTCAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.00, C:0.09, G:0.15, T:0.76
Consensus pattern (22 bp):
TTTTCTGTTTTTTTTTGTTGCG
Found at i:15895 original size:17 final size:17
Alignment explanation
Indices: 15845--15894 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
15835 GTAAATTTAC
* * *
15845 AAAAAGGAAATTAATAT
1 AAAAAAGAAATAAAAAT
*
15862 AAAAAATAAATAAAAAT
1 AAAAAAGAAATAAAAAT
15879 AAAGAAAGAAATAAAA
1 AAA-AAAGAAATAAAA
15895 TGCATCGGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (17 bp):
AAAAAAGAAATAAAAAT
Found at i:17490 original size:21 final size:21
Alignment explanation
Indices: 17465--17506 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
17455 ATTTTGCTTG
*
17465 ATGCTCTCATTTTAGGATCTT
1 ATGCTCTCATTATAGGATCTT
17486 ATGCTCTCATTATAGGATCTT
1 ATGCTCTCATTATAGGATCTT
17507 GTTGAAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.45
Consensus pattern (21 bp):
ATGCTCTCATTATAGGATCTT
Found at i:22665 original size:8 final size:8
Alignment explanation
Indices: 22652--22694 Score: 56
Period size: 7 Copynumber: 5.8 Consensus size: 8
22642 CTTCTAACAA
22652 TTTTTCTT
1 TTTTTCTT
22660 TTTTTC-T
1 TTTTTCTT
22667 TTTTT-TT
1 TTTTTCTT
*
22674 TTCTT-TT
1 TTTTTCTT
22681 TTTTTCTT
1 TTTTTCTT
22689 TTTTTC
1 TTTTTC
22695 ATTATGACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTCTT
Found at i:22673 original size:10 final size:10
Alignment explanation
Indices: 22652--22693 Score: 68
Period size: 10 Copynumber: 4.3 Consensus size: 10
22642 CTTCTAACAA
22652 TTTTTCTTTT
1 TTTTTCTTTT
*
22662 TTTCT-TTTT
1 TTTTTCTTTT
22671 TTTTTCTTTT
1 TTTTTCTTTT
22681 TTTTTCTTTT
1 TTTTTCTTTT
22691 TTT
1 TTT
22694 CATTATGACC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:22674 original size:11 final size:11
Alignment explanation
Indices: 22658--22693 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
22648 ACAATTTTTC
22658 TTTTTTTCTTT
1 TTTTTTTCTTT
22669 TTTTTTTC-TT
1 TTTTTTTCTTT
22679 TTTTTTTCTTT
1 TTTTTTTCTTT
22690 TTTT
1 TTTT
22694 CATTATGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:27178 original size:90 final size:90
Alignment explanation
Indices: 27025--27190 Score: 269
Period size: 90 Copynumber: 1.8 Consensus size: 90
27015 GTGGTCACAG
* * * *
27025 TTAGTTGGTATGTTTTCCGAGTTAATGGGATCCAATTATTGGATGAATATGAATAAAACACCAAA
1 TTAGTTGGTATCTTTTCCGAGTTAAAGGGATCCAATTATTCGATGAATATGAACAAAACACCAAA
27090 CAAAATTTCTTGAAAATTTGTCGGT
66 CAAAATTTCTTGAAAATTTGTCGGT
* *
27115 TTAGTTGGTATCTTTTCTGAGTTAAAGGGATCCAATTATTCGATGAATATGAACAAAATACCAAA
1 TTAGTTGGTATCTTTTCCGAGTTAAAGGGATCCAATTATTCGATGAATATGAACAAAACACCAAA
*
27180 CAAATTTTCTT
66 CAAAATTTCTT
27191 CATAGGTTTA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 69 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (90 bp):
TTAGTTGGTATCTTTTCCGAGTTAAAGGGATCCAATTATTCGATGAATATGAACAAAACACCAAA
CAAAATTTCTTGAAAATTTGTCGGT
Found at i:27417 original size:22 final size:22
Alignment explanation
Indices: 27392--27435 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
27382 TCACTCTTCA
27392 GAAATAGATAAAGTTATTCAAG
1 GAAATAGATAAAGTTATTCAAG
27414 GAAATAGATAAAGTTATTCAAG
1 GAAATAGATAAAGTTATTCAAG
27436 AGATATGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (22 bp):
GAAATAGATAAAGTTATTCAAG
Found at i:31331 original size:31 final size:31
Alignment explanation
Indices: 31293--31351 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
31283 AAGAAGCTTG
** *
31293 ACAATGACCATGCAAGTAGCTAGAACAACCA
1 ACAATGACCAAACAAGTAGATAGAACAACCA
31324 ACAATGACCAAACAAGTAGATAGAACAA
1 ACAATGACCAAACAAGTAGATAGAACAA
31352 GAATTTAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.51, C:0.22, G:0.15, T:0.12
Consensus pattern (31 bp):
ACAATGACCAAACAAGTAGATAGAACAACCA
Found at i:32799 original size:26 final size:26
Alignment explanation
Indices: 32751--32801 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
32741 GAGTAGCTTA
* *
32751 ATTGTATTATATATTTTTATTTATTT
1 ATTGTATTATATATTGTAATTTATTT
32777 ATTGTATTATATA-TGTAACTTTATT
1 ATTGTATTATATATTGTAA-TTTATT
32802 ATTATCATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (26 bp):
ATTGTATTATATATTGTAATTTATTT
Found at i:34062 original size:18 final size:19
Alignment explanation
Indices: 34023--34062 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
34013 GTGCTCCCGT
34023 TGTGATGCTCCCACTTTTCAA
1 TGTGATGCTCCCA--TTTCAA
34044 TGTGATGCTCCCA-TTCAA
1 TGTGATGCTCCCATTTCAA
34062 T
1 T
34063 TCTGATCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
21 13 0.68
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTGATGCTCCCATTTCAA
Found at i:35282 original size:639 final size:644
Alignment explanation
Indices: 34033--35324 Score: 2324
Period size: 639 Copynumber: 2.0 Consensus size: 644
34023 TGTGATGCTC
*
34033 CCACTTTTCAATGTGATGCTCCCATTCAATTCTGATCATTGAATGCAATATCTATTTTCCTGACC
1 CCACTTTTCAATGTGATGCTCCCATTCAATTCTGACCATTGAATGCAATATCTATTTTCCTGACC
34098 GTCGGATACTAAAAGATTTAACCTACTAAACCGGTTTTAAAAACCTTTTGGAATGAATTCGTATG
66 GTCGGATACTAAAAGATTTAACCTACTAAACCGGTTTTAAAAACCTTTTGGAATGAATTCGTATG
34163 TGGTAGTCCTAGTGATAGATTTTTACACCTTTTTTATTCAAACCGTTGATATCAACTACTATTTT
131 TGGTAGTCCTAGTGATAGATTTTTACACCTTTTTTATTCAAACCGTTGATATCAACTACTATTTT
* *
34228 TTACTTGATTTATTATTTTTTTCTCTAACTTTTTTTTATTTTTTATTTTTTTCTTCTCCGTTTTC
196 TTACTTGATTTATTATTTTTTTCTCTAACTATTTTTTATTTTTTATTCTTTTCTTCTCCGTTTTC
*
34293 TTTCTGCGCTGAGCCCTCCTTCCCTTCTCATCCTTGCAAATTTCTTGTCATTATTAGTACTGATT
261 ATTCTGCGCTGAGCCCTCCTTCCCTTCTCATCCTTGCAAATTTCTTGTCATTATTAGTACTGATT
*
34358 AAGCCACCCAAAAGAAAACTTTATTTTTATAGTTAATTGGAAAAAAAATGAAAATGTGAATTCAA
326 AAGCCACCCAAAAGAAAACTTTATTTTTATAGTTAATTGGAAAAAAAATGAAAACGTGAATTCAA
34423 TATATTGCTATGCAAAAGTGATAAATTTAGCCCCATTTATTTATATTTATGAAAAGTTTGCATCT
391 TATATTGCTATGCAAAAGTGAT-AA--TA--CCCATTTATTTATATTTATGAAAAGTTTGCATCT
34488 TTGAGCTATAATAATTAGGTGCTAGTATGTGATTGTGTATATAATATTTATGTGAATAAACAGAT
451 TTGAGCTATAATAATTAGGTGCTAGTATGTGATTGTGTATATAATATTTATGTGAATAAACAGAT
*
34553 AAGATGCTAATCTATTATACTAACCTAAGAATTAAAAGCCAGAAAAATCATGGGTTATGGTCAGG
516 AAGATGCTAATCTATTACACTAACCTAAGAATTAAAAGCCAGAAAAATCATGGGTTATGGTCAGG
*
34618 ATGACATCGAAAGTTGGTTGAAACTAAATTCTCTTCTTCCATTGATGGTAGGATTTATTCTCCG
581 ATGACATCGAAAGTTGGTTGAAACTAAATTCTCTTCTTCCATTGACGGTAGGATTTATTCTCCG
*
34682 CCACTTTTCAATGTGATGCTCCCATTCAATTCTGACCATTGGATGCAATATCTATTTTCCTGACC
1 CCACTTTTCAATGTGATGCTCCCATTCAATTCTGACCATTGAATGCAATATCTATTTTCCTGACC
34747 GTCGGATACTAAAAGATTTAACCTACTAAACCGGTTTTAAAAACCTTTTGGAATGAATTCGTATG
66 GTCGGATACTAAAAGATTTAACCTACTAAACCGGTTTTAAAAACCTTTTGGAATGAATTCGTATG
* *
34812 TGGTAGTCCTCGTGATAGATTTTTACACCTTTTTTATTCAAACTGTTGATATCAACTACT-TTTT
131 TGGTAGTCCTAGTGATAGATTTTTACACCTTTTTTATTCAAACCGTTGATATCAACTACTATTTT
*
34876 TTACTTGATTTCTTATTTTTTTCTCTAAC-ATTTTTTATTTTTTATTCTTTTCTTCTCCGTTTTC
196 TTACTTGATTTATTATTTTTTTCTCTAACTATTTTTTATTTTTTATTCTTTTCTTCTCCGTTTTC
*
34940 ATTCTGCGTTGAGCCCTCCTTCCCTTCTCATCCTTGCAAATTTCTTGTCATTATTAGTACTGATT
261 ATTCTGCGCTGAGCCCTCCTTCCCTTCTCATCCTTGCAAATTTCTTGTCATTATTAGTACTGATT
* *
35005 AAGCCACCCAAAAGAAAACTTTATTTTTGTAGTTAATTGGAAAAAAAATGAAAACGTGAATTCAG
326 AAGCCACCCAAAAGAAAACTTTATTTTTATAGTTAATTGGAAAAAAAATGAAAACGTGAATTCAA
*
35070 TATGTTGCTATGCAAAAGTGAT-A-A-CCATTTATTTATATTTATGAAAAGTTTGCATCTTTGAG
391 TATATTGCTATGCAAAAGTGATAATACCCATTTATTTATATTTATGAAAAGTTTGCATCTTTGAG
35132 CTATAATAATTAGGTGCTAGTATGTGATTGTGTATATAATATTTATGTGAATAAACAGATAAGAT
456 CTATAATAATTAGGTGCTAGTATGTGATTGTGTATATAATATTTATGTGAATAAACAGATAAGAT
* * *
35197 GCTAATCTATTACGCTAACCTAAGAATTAAAAGGCAGGAAAATCATGGGTTATGGTCAGGATGAC
521 GCTAATCTATTACACTAACCTAAGAATTAAAAGCCAGAAAAATCATGGGTTATGGTCAGGATGAC
* *
35262 ATTGAAAGTTGGTTGAAACTAAATTCTCTTCTTGCATTGACGGTAGGATTTATTCTCCG
586 ATCGAAAGTTGGTTGAAACTAAATTCTCTTCTTCCATTGACGGTAGGATTTATTCTCCG
35321 CCAC
1 CCAC
35325 CACCAAGGTC
Statistics
Matches: 623, Mismatches: 20, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
639 224 0.36
642 1 0.00
645 1 0.00
647 179 0.29
648 32 0.05
649 186 0.30
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (644 bp):
CCACTTTTCAATGTGATGCTCCCATTCAATTCTGACCATTGAATGCAATATCTATTTTCCTGACC
GTCGGATACTAAAAGATTTAACCTACTAAACCGGTTTTAAAAACCTTTTGGAATGAATTCGTATG
TGGTAGTCCTAGTGATAGATTTTTACACCTTTTTTATTCAAACCGTTGATATCAACTACTATTTT
TTACTTGATTTATTATTTTTTTCTCTAACTATTTTTTATTTTTTATTCTTTTCTTCTCCGTTTTC
ATTCTGCGCTGAGCCCTCCTTCCCTTCTCATCCTTGCAAATTTCTTGTCATTATTAGTACTGATT
AAGCCACCCAAAAGAAAACTTTATTTTTATAGTTAATTGGAAAAAAAATGAAAACGTGAATTCAA
TATATTGCTATGCAAAAGTGATAATACCCATTTATTTATATTTATGAAAAGTTTGCATCTTTGAG
CTATAATAATTAGGTGCTAGTATGTGATTGTGTATATAATATTTATGTGAATAAACAGATAAGAT
GCTAATCTATTACACTAACCTAAGAATTAAAAGCCAGAAAAATCATGGGTTATGGTCAGGATGAC
ATCGAAAGTTGGTTGAAACTAAATTCTCTTCTTCCATTGACGGTAGGATTTATTCTCCG
Done.