Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019187.1 Corchorus olitorius cultivar O-4 contig19220, 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: 70763
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:757 original size:23 final size:23
Alignment explanation
Indices: 731--778 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
721 GGCTCGTTTG
731 GAGCTCGAGCTCGATTGGAGCTC
1 GAGCTCGAGCTCGATTGGAGCTC
754 GAGCTCGAGCTCGATTGGAGCTC
1 GAGCTCGAGCTCGATTGGAGCTC
777 GA
1 GA
779 AATTTTGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.21
Consensus pattern (23 bp):
GAGCTCGAGCTCGATTGGAGCTC
Found at i:778 original size:17 final size:17
Alignment explanation
Indices: 715--761 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
705 ATACACTTTT
* *
715 AGCTCGGGCTCGTTTGG
1 AGCTCGAGCTCGATTGG
732 AGCTCGAGCTCGATTGG
1 AGCTCGAGCTCGATTGG
749 AGCTCGAGCTCGA
1 AGCTCGAGCTCGA
762 GCTCGATTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.15, C:0.26, G:0.36, T:0.23
Consensus pattern (17 bp):
AGCTCGAGCTCGATTGG
Found at i:3741 original size:22 final size:22
Alignment explanation
Indices: 3716--3760 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3706 CCGTGAAAGA
*
3716 GAAACTAAGGAAATCGGCTTTT
1 GAAACGAAGGAAATCGGCTTTT
*
3738 GAAACGAATGAAATCGGCTTTT
1 GAAACGAAGGAAATCGGCTTTT
3760 G
1 G
3761 TTTAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (22 bp):
GAAACGAAGGAAATCGGCTTTT
Found at i:3898 original size:31 final size:25
Alignment explanation
Indices: 3832--3911 Score: 142
Period size: 25 Copynumber: 3.2 Consensus size: 25
3822 CCCTTACTCC
3832 GAGGCCGATTAGGATTAGGGATTCA
1 GAGGCCGATTAGGATTAGGGATTCA
3857 GAGGCCGATTAGGATTAGGGATTCA
1 GAGGCCGATTAGGATTAGGGATTCA
* *
3882 GAGGCCGATTAAGATTAGGAATTCA
1 GAGGCCGATTAGGATTAGGGATTCA
3907 GAGGC
1 GAGGC
3912 GAAACCACGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.30, C:0.12, G:0.35, T:0.23
Consensus pattern (25 bp):
GAGGCCGATTAGGATTAGGGATTCA
Found at i:9916 original size:31 final size:31
Alignment explanation
Indices: 9881--9944 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
9871 TAGGGATTCA
9881 GAGGCCGATTAGGATTAGGAATTCAGAGGCG
1 GAGGCCGATTAGGATTAGGAATTCAGAGGCG
*
9912 GAGGCCGATTAGGATTAGGAATTTAGAGGCG
1 GAGGCCGATTAGGATTAGGAATTCAGAGGCG
9943 GA
1 GA
9945 ACCACGTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.30, C:0.11, G:0.39, T:0.20
Consensus pattern (31 bp):
GAGGCCGATTAGGATTAGGAATTCAGAGGCG
Found at i:9941 original size:25 final size:25
Alignment explanation
Indices: 9856--9910 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
9846 CCCTTACTCC
* *
9856 GAGGCCGATTAGGAGTAGGGATTCA
1 GAGGCCGATTAGGATTAGGAATTCA
9881 GAGGCCGATTAGGATTAGGAATTCA
1 GAGGCCGATTAGGATTAGGAATTCA
9906 GAGGC
1 GAGGC
9911 GGAGGCCGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.29, C:0.13, G:0.38, T:0.20
Consensus pattern (25 bp):
GAGGCCGATTAGGATTAGGAATTCA
Found at i:11611 original size:15 final size:15
Alignment explanation
Indices: 11568--11615 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
11558 AAGGAAGCTT
11568 TTTTTTCCTTCCCCA
1 TTTTTTCCTTCCCCA
*
11583 TTTCTTTCCATCCCTC-
1 TTT-TTTCCTTCCC-CA
11599 TTTTTTCCTT-CCCA
1 TTTTTTCCTTCCCCA
11613 TTT
1 TTT
11616 CCTCCCTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 1 0.04
14 5 0.18
15 9 0.32
16 12 0.43
17 1 0.04
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTTTTCCTTCCCCA
Found at i:12752 original size:40 final size:40
Alignment explanation
Indices: 12708--12788 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
12698 TTCACATAAA
* * *
12708 TGTTATGATATATCCTATCCCCCTTAATTATCTAGAATTG
1 TGTTATAATAAATCCTATACCCCTTAATTATCTAGAATTG
12748 TGTTATAATAAATCCTATACCCCTTAATTATCTAGAATTG
1 TGTTATAATAAATCCTATACCCCTTAATTATCTAGAATTG
12788 T
1 T
12789 AACCTCTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.42
Consensus pattern (40 bp):
TGTTATAATAAATCCTATACCCCTTAATTATCTAGAATTG
Found at i:13816 original size:31 final size:31
Alignment explanation
Indices: 13779--13919 Score: 129
Period size: 31 Copynumber: 4.5 Consensus size: 31
13769 ACGATATCCG
*
13779 ACGTGGCATGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* * * *
13810 ATGTGGCACGCCACATGTATCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
** * * * *
13841 ACGTATCACGCCATGTATACCAAAAAGTGAT
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* * * **
13872 ACATGGCATGCCATGAGTTTCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
*
13903 ACATGGCATGCCACGTG
1 ACGTGGCATGCCACGTG
13920 CACAAAAGGA
Statistics
Matches: 86, Mismatches: 24, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 86 1.00
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19
Consensus pattern (31 bp):
ACGTGGCATGCCACGTGTACCAAAAAGTGAC
Found at i:26450 original size:7 final size:7
Alignment explanation
Indices: 26407--26433 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
26397 AAGTAAAAGT
26407 AAAACTG
1 AAAACTG
26414 AAAACTG
1 AAAACTG
26421 AAAACTG
1 AAAACTG
26428 AAAACT
1 AAAACT
26434 AGTATAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (7 bp):
AAAACTG
Found at i:31041 original size:16 final size:16
Alignment explanation
Indices: 31019--31064 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
31009 ATGCCAATGA
31019 ATTTTTGTTTAATTC-
1 ATTTTTGTTTAATTCT
* *
31034 -TTTTT-TTGAATTCA
1 ATTTTTGTTTAATTCT
31048 ATTTTTGTTTAATTCT
1 ATTTTTGTTTAATTCT
31064 A
1 A
31065 AAAGACTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 7 0.28
14 5 0.20
15 5 0.20
16 8 0.32
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.65
Consensus pattern (16 bp):
ATTTTTGTTTAATTCT
Found at i:44303 original size:15 final size:16
Alignment explanation
Indices: 44278--44308 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
44268 TTGAAGACCA
44278 AAAACCCCAAAAAAAG
1 AAAACCCCAAAAAAAG
44294 AAAA-CCCAAAAAAAG
1 AAAACCCCAAAAAAAG
44309 CTCTTACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.71, C:0.23, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAACCCCAAAAAAAG
Found at i:46238 original size:2 final size:2
Alignment explanation
Indices: 46225--46260 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
46215 AACCTTTACC
46225 AT AT AGT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46261 TGTAAATATG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46247 original size:13 final size:12
Alignment explanation
Indices: 46225--46260 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
46215 AACCTTTACC
46225 ATATAGTATATAT
1 ATATA-TATATAT
46238 ATATAT-TATAT
1 ATATATATATAT
46249 ATATATATATAT
1 ATATATATATAT
46261 TGTAAATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.50
12 6 0.27
13 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (12 bp):
ATATATATATAT
Found at i:46269 original size:17 final size:17
Alignment explanation
Indices: 46232--46269 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
46222 ACCATATAGT
*
46232 ATATATATATATTATAT
1 ATATATATATATTATAA
*
46249 ATATATATATATTGTAA
1 ATATATATATATTATAA
46266 ATAT
1 ATAT
46270 GATTCCCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
ATATATATATATTATAA
Found at i:48875 original size:6 final size:6
Alignment explanation
Indices: 48864--48892 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
48854 GAGAGGTAGC
48864 CATGGG CATGGG CATGGG CATGGG CATGG
1 CATGGG CATGGG CATGGG CATGGG CATGG
48893 CTTCTTCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.48, T:0.17
Consensus pattern (6 bp):
CATGGG
Found at i:57400 original size:15 final size:15
Alignment explanation
Indices: 57355--57402 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
57345 TGGTTTTGGC
57355 GGACGCCGTGAAGGT
1 GGACGCCGTGAAGGT
* ** **
57370 GGAGGCTATGGTGGT
1 GGACGCCGTGAAGGT
57385 GGACGCCGTGAAGGT
1 GGACGCCGTGAAGGT
57400 GGA
1 GGA
57403 TATGGCAACG
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.19, C:0.15, G:0.50, T:0.17
Consensus pattern (15 bp):
GGACGCCGTGAAGGT
Found at i:68015 original size:329 final size:328
Alignment explanation
Indices: 66494--69043 Score: 2752
Period size: 328 Copynumber: 7.8 Consensus size: 328
66484 ATTTTTTGCT
* * * * * * * *
66494 ACAATACTTAGAATATATATATAATTCAACTCCAAAAAGATTGAAGGGTTTTTTAAGGTTCTAAT
1 ACAATACTCAGAAAAAATATAT-ATTCAACGCCAAAAA-ATTGAAGGGCTTTTCACGCTTCTAAT
* ** * *
66559 ATCGTTTTTTCATTTTT-TTAATTTATTTCTAATTAAATCGAAACAAAATCCAGATGCTCGTAAA
64 ATCGTTTTTCCATTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * *
66623 AACAAATCCTTAAATCAAATGTGACTGAGATTTGGTTATATGACTATAGATATTTCAAGGAGTCT
129 AACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCT
* * * *
66688 TTAAACCAAAAACCATGCAAAA-TGAGTCGAGACCCCGAAACTCATTTTTAGCCAAAAACTGTGA
194 TTATACCAAAAACCATGCAAAACTGAGTCGAGACCTCGAAACGCATTTTTAGCCAAAAACCGTGA
* *
66752 TGGTTAGTATACAATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTCAAATAT
259 TGGTTAGTACACAATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTCAAATAT
66817 TTGAC
324 TTGAC
*
66822 ACAATACTCAGAAAAAATATATATTCAACGCCAAAAAAATTGACGGGCTTTTCACGCTTCTAATA
1 ACAATACTCAGAAAAAATATATATTCAACGCC-AAAAAATTGAAGGGCTTTTCACGCTTCTAATA
* * * * *
66887 TCGTTTTTCCAATTTTCCGAATTCATTTCTAATTAAATCTAAACAAGATTCAGATGTTCATAAAA
65 TCGTTTTTCCATTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* * * *
66952 ACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTTGATGAATATTGATATTTCAAGGAGTCTA
130 ACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT
* * * * * * * *
67017 TCTGCCAAAAATCATGCAAAACTGAGCCGTGGTCC-CGGAACGCGTTTTTAGCCCAAAAATACCG
195 TATACCAAAAACCATGCAAAACTGAGTCG-AGACCTCGAAACGCATTTTTAG-CC-AAAA-ACCG
* * ** *
67081 TGATGACGAGTAGTACACGATTTCGGC--------T--AAAAACTGACCCGAAAAAATTTTCGTC
256 TGATG--G-TTAGTACACAATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTC
* *
67136 -CATTTTTG-C
318 AAATATTTGAC
* * * * *
67145 TACAATACTCAGAATATATATATAATTCAACTCCAAAAAGATTGAAGGG-TTTTCTAAGGTTCTA
1 -ACAATACTCAGAAAAAATATAT-ATTCAACGCCAAAAA-ATTGAAGGGCTTTTC-ACGCTTCTA
* ** * * *
67209 ATATCGTTTTTCCTTTTTTTTTGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGTTCCT
62 ATATCGTTTTTCC-ATTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * * * *
67274 AAAAACAAATTCTTAAATCCAGTGTGGCTGATATTTGGTTAGATTATTATAGATATTCCAAGGAG
126 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG
* *
67339 TCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGGCCTCGAAACGCATTTTTAGCCAAAAACCG
191 TCTTTATACCAAAAACCATGCAAAACTGAGTCGAGACCTCGAAACGCATTTTTAGCCAAAAACCG
* * * * * *
67404 CGATAGTTAGCT-CACGATTTTCGGCTAAAATTATGCAAAAACTGACCCGAAAAATTTTTCCTC-
256 TGATGGTTAG-TACAC-AATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTCA
*
67467 AATATTTTGCC
319 AATA-TTTGAC
* * * * *
67478 ACAAAACTCTGAAATATAATATA-ATTTAACGCCAAAAAACTTGAAGGGGTTTTCACGCTTTTAA
1 ACAATACTCAGAAA-A-AATATATATTCAACGCCAAAAAA-TTGAAGGGCTTTTCACGCTTCTAA
* * * *
67542 TATCGTTTTCCCATTTTTTTTCGAATTTATTTGTAATTAAATCAAAACAAGATTCAGATGCTCGT
63 TATCGTTTTTCCA--TTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * * * * *
67607 AAAAAGAAATCCTTAAATCAAATGTGACTGATATTTAGTAAGATGACTATAGATATTTCAAGGAG
126 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG
* * * * *
67672 TCTTTGTACCAAAAACCATGCAAAAATGAGTAGAGATCTCGAAACGCGTTTTTAGCCAAAAACCG
191 TCTTTATACCAAAAACCATGCAAAACTGAGTCGAGACCTCGAAACGCATTTTTAGCCAAAAACCG
**
67737 TGATGGTTAGTACACAATTTCAACTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTCAAA
256 TGATGGTTAGTACACAATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTCAAA
67802 TATTTGAC
321 TATTTGAC
* * *
67810 ACAATACTCAGAAAAAATACTATATTCAACGCCAAAAAATTGACGTGCTTTTCACGCTTTTAATA
1 ACAATACTCAGAAAAAATA-TATATTCAACGCCAAAAAATTGAAGGGCTTTTCACGCTTCTAATA
* * * *
67875 TCGTTTTTCCATTTTTCCGAATTCATTTCTAATTAAATCTAAACAAGATTCAGATGTTCATAAAA
65 TCGTTTTTCCATTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* * * * *
67940 ACAAATCCTTATAGCCAATGTGGCTGAGATTTGGTTTGATGAATATTGATATTTCAAGGATTCTA
130 ACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCT-
* * * * * * * *
68005 TT-TGCCAAAAATCATGCAAAACTGAGCCGTGATCC-AGGAACGCGTTTTTAACCCAAAAACCGT
194 TTATACCAAAAACCATGCAAAACTGAGTCGAGA-CCTCGAAACGCATTTTT-AGCCAAAAACCGT
* *
68068 GATGAG-TAGTACACGATTTCGGC--------T--AAAAACTGACCCGAAAATTTTTTTCTTC-A
257 GATG-GTTAGTACACAATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAA-GTTTTTCTTCAA
* *
68121 TTTTTTG-C
320 ATATTTGAC
* * * * * *
68129 TACAATACTCAGAATATATATCTAATTCAACTCCAAAAAGATTGAAGGG-TTTTCTAAGGTTCTA
1 -ACAATACTCAGAAAAAATATAT-ATTCAACGCCAAAAA-ATTGAAGGGCTTTTC-ACGCTTCTA
* ** *
68193 ATATCGTTTTTCCTTTTTTTTTGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGT
62 ATATCGTTTTTCC-ATTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * *
68258 AAAAACAAATCCTTAAATCCAGTGTGGCTGATATTTGGTTAGATGAATATAGATATTCCAAGGAG
126 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG
* *
68323 TCTTTATGCCAAAAACCATGCAAAACTGAGTCGAGGCCTCGAAACGCATTTTTAGCCAAAAACCG
191 TCTTTATACCAAAAACCATGCAAAACTGAGTCGAGACCTCGAAACGCATTTTTAGCCAAAAACCG
* * * *
68388 TGA----TAGCACACGATTTCGGCTAAAATTTTGCAAAAACTGACTCGAAATA-TTTTTCCTCAA
256 TGATGGTTAGTACACAATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAA-AGTTTTTCTTCAA
* * *
68448 TTGTTTGCC
320 ATATTTGAC
* * * ** * *
68457 ACAAAACTCAG-AAAAATAATTTAATTCAATGAGAAAAAATTTGAAGGGTTTTTCACGCTTGTAA
1 ACAATACTCAGAAAAAAT-ATAT-ATTCAACGCCAAAAAA-TTGAAGGGCTTTTCACGCTTCTAA
* * *
68521 TATCGTTTTCCCATTTTTTTCCGAATTTATTTGTAATTAAATCAAAACAAGATTCAGATGCTCGT
63 TATCGTTTTTCCA--TTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * *
68586 AAAAAGAAATCCTTAAATCAAATGTGACTGAGATTTGGTTAGATGACTATAGATATTTCAAGGAG
126 AAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG
* ** * * *
68651 TCTTTGTACGTAAAACCATGCAAAACTGACTCGAGACCCCGAAACGCGTTTTTAGCCAAAAACCG
191 TCTTTATACCAAAAACCATGCAAAACTGAGTCGAGACCTCGAAACGCATTTTTAGCCAAAAACCG
**
68716 TGATGGTTAGTACACAATTTCATCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTCAAA
256 TGATGGTTAGTACACAATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTCAAA
68781 TATTTGAC
321 TATTTGAC
* * *
68789 ACAATACTTAGAAAAAATATATATTTAACGCCAAAAAAATTGACGGGCTTTTCACGCTTCTAATA
1 ACAATACTCAGAAAAAATATATATTCAACGCC-AAAAAATTGAAGGGCTTTTCACGCTTCTAATA
* * * * * *
68854 TCGTTTTTCCAATTTTCCGAATTCATTTCTAATTAAATCTAAACAAGATTCGGATGTTCATAAAA
65 TCGTTTTTCCATTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* * * * * *
68919 ACAAATCCTTATATCCAATGTGGCTGAGATTTGATTTGATGAATATTGATATTTTAAGGAGTCTA
130 ACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT
* * * * ** *
68984 TCTACCAAAAATCATGCAAAACTGAGCCGTGGTCTCGGAACGCATTTTTAGCCCAAAAAC
195 TATACCAAAAACCATGCAAAACTGAGTCGAGACCTCGAAACGCATTTTTAG-CCAAAAAC
69044 TGACCCGAAA
Statistics
Matches: 1854, Mismatches: 290, Indels: 154
0.81 0.13 0.07
Matches are distributed among these distances:
317 16 0.01
319 3 0.00
320 65 0.04
321 62 0.03
322 141 0.08
323 8 0.00
324 40 0.02
325 67 0.04
326 155 0.08
327 119 0.06
328 308 0.17
329 297 0.16
330 50 0.03
331 109 0.06
332 209 0.11
333 185 0.10
334 6 0.00
335 14 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (328 bp):
ACAATACTCAGAAAAAATATATATTCAACGCCAAAAAATTGAAGGGCTTTTCACGCTTCTAATAT
CGTTTTTCCATTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
CAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT
ATACCAAAAACCATGCAAAACTGAGTCGAGACCTCGAAACGCATTTTTAGCCAAAAACCGTGATG
GTTAGTACACAATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTCAAATATTT
GAC
Found at i:68746 original size:979 final size:981
Alignment explanation
Indices: 66512--69043 Score: 4206
Period size: 979 Copynumber: 2.6 Consensus size: 981
66502 TAGAATATAT
** * * * **
66512 ATATAATTCAACTCCAAAAAGA-TTGAAGGGTTTTTTAAGGTTCTAATATCGTTTTTTCATTTTT
1 ATATAATTCAACGACAAAAA-ACTTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCCCATTTTT
* * * * *
66576 TT--AATTTATTTCTAATTAAATCGAAACAAAATCCAGATGCTCGTAAAAACAAATCCTTAAATC
65 TTCGAATTTATTTGTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATC
* **
66639 AAATGTGACTGAGATTTGGTTATATGACTATAGATATTTCAAGGAGTCTTTAAACCAAAAACCAT
130 AAATGTGACTGAGATTTGGTTAGATGACTATAGATATTTCAAGGAGTCTTTGTACCAAAAACCAT
* * * *
66704 GCAAAATGAGTCGAGACCCCGAAACTCATTTTTAGCCAAAAACTGTGATGGTTAGTATACAATTT
195 GCAAAATGAGTCGAGACCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTT
*
66769 CAGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTCAAATATTTGACACAATACTCAGA
260 CAACTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTCAAATATTTGACACAATACTCAGA
66834 AAAAATATATATTCAACGCCAAAAAAATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCAA
325 AAAAATATATATTCAACGCCAAAAAAATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCAA
66899 TTTTCCGAATTCATTTCTAATTAAATCTAAACAAGATTCAGATGTTCATAAAAACAAATCCTTAT
390 TTTTCCGAATTCATTTCTAATTAAATCTAAACAAGATTCAGATGTTCATAAAAACAAATCCTTAT
66964 ATCCAATGTGGCTGAGATTTGGTTTGATGAATATTGATATTTCAAGGAGTCTATCTGCCAAAAAT
455 ATCCAATGTGGCTGAGATTTGGTTTGATGAATATTGATATTTCAAGGAGTCTATCTGCCAAAAAT
67029 CATGCAAAACTGAGCCGTGGTCCCGGAACGCGTTTTTAGCCCAAAAATACCGTGATGACGAGTAG
520 CATGCAAAACTGAGCCGTGGT-CCGGAACGCGTTTTTAGCCC-AAAA-ACCGTGAT-A-GAGTAG
67094 TACACGATTTCGGCTAAAAACTGACCCGAAAAAATTTTCGTCCATTTTTGCTACAATACTCAGAA
580 TACACGATTTCGGCTAAAAACTGACCCGAAAAAATTTTCGTCCATTTTTGCTACAATACTCAGAA
67159 TATATATATAATTCAACTCCAAAAAGATTGAAGGGTTTTCTAAGGTTCTAATATCGTTTTTCCTT
645 TATATATATAATTCAACTCCAAAAAGATTGAAGGGTTTTCTAAGGTTCTAATATCGTTTTTCCTT
* *
67224 TTTTTTTGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGTTCCTAAAAACAAATTCTTA
710 TTTTTTTGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCCTAAAAACAAATCCTTA
* *
67289 AATCCAGTGTGGCTGATATTTGGTTAGATTATTATAGATATTCCAAGGAGTCTTTATGCCAAAAA
775 AATCCAGTGTGGCTGATATTTGGTTAGATGAATATAGATATTCCAAGGAGTCTTTATGCCAAAAA
* *
67354 CCATGCAAAACTGAGTCGAGGCCTCGAAACGCATTTTTAGCCAAAAACCGCGATAGTTAGCTCAC
840 CCATGCAAAACTGAGTCGAGGCCTCGAAACGCATTTTTAGCCAAAAACCGCGATAGATAGCACAC
67419 GATTTTCGGCTAAAATTATGCAAAAACTGACCCGAAAAATTTTTCCTCAATATTTTGCCACAAAA
905 GATTTTCGGCTAAAATTATGCAAAAACTGACCCGAAAAATTTTTCCTCAATATTTTGCCACAAAA
* *
67484 CTCTGAAATATA
970 CTCAGAAAAATA
* * * *
67496 ATATAATTTAACGCCAAAAAACTTGAAGGGGTTTTCACGCTTTTAATATCGTTTTCCCATTTTTT
1 ATATAATTCAACGACAAAAAACTTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCCCA-TTTTT
67561 TTCGAATTTATTTGTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATC
65 TTCGAATTTATTTGTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATC
* * *
67626 AAATGTGACTGATATTTAGTAAGATGACTATAGATATTTCAAGGAGTCTTTGTACCAAAAACCAT
130 AAATGTGACTGAGATTTGGTTAGATGACTATAGATATTTCAAGGAGTCTTTGTACCAAAAACCAT
* * *
67691 GCAAAAATGAGTAGAGATCTCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATT
195 GC-AAAATGAGTCGAGACCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATT
67756 TCAACTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTCAAATATTTGACACAATACTCAG
259 TCAACTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTCAAATATTTGACACAATACTCAG
* *
67821 AAAAAATACTATATTCAACGCC-AAAAAATTGACGTGCTTTTCACGCTTTTAATATCGTTTTTCC
324 AAAAAATA-TATATTCAACGCCAAAAAAATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCC
*
67885 ATTTTTCCGAATTCATTTCTAATTAAATCTAAACAAGATTCAGATGTTCATAAAAACAAATCCTT
388 AATTTTCCGAATTCATTTCTAATTAAATCTAAACAAGATTCAGATGTTCATAAAAACAAATCCTT
* * *
67950 ATAGCCAATGTGGCTGAGATTTGGTTTGATGAATATTGATATTTCAAGGATTCTATTTGCCAAAA
453 ATATCCAATGTGGCTGAGATTTGGTTTGATGAATATTGATATTTCAAGGAGTCTATCTGCCAAAA
* *
68015 ATCATGCAAAACTGAGCCGTGATCCAGGAACGCGTTTTTAACCCAAAAACCGTGAT-GAGTAGTA
518 ATCATGCAAAACTGAGCCGTGGTCC-GGAACGCGTTTTTAGCCCAAAAACCGTGATAGAGTAGTA
** *
68079 CACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTC-TTCATTTTTTGCTACAATACTCAGAA
582 CACGATTTCGGCTAAAAACTGACCCGAAAA-AATTTTCGTCCA-TTTTTGCTACAATACTCAGAA
*
68143 TATATATCTAATTCAACTCCAAAAAGATTGAAGGGTTTTCTAAGGTTCTAATATCGTTTTTCCTT
645 TATATATATAATTCAACTCCAAAAAGATTGAAGGGTTTTCTAAGGTTCTAATATCGTTTTTCCTT
*
68208 TTTTTTTGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTA
710 TTTTTTTGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCCTAAAAACAAATCCTTA
68273 AATCCAGTGTGGCTGATATTTGGTTAGATGAATATAGATATTCCAAGGAGTCTTTATGCCAAAAA
775 AATCCAGTGTGGCTGATATTTGGTTAGATGAATATAGATATTCCAAGGAGTCTTTATGCCAAAAA
68338 CCATGCAAAACTGAGTCGAGGCCTCGAAACGCATTTTTAGCCAAAAA-C-CG-T-GATAGCACAC
840 CCATGCAAAACTGAGTCGAGGCCTCGAAACGCATTTTTAGCCAAAAACCGCGATAGATAGCACAC
* * *
68399 GA-TTTCGGCTAAAATTTTGCAAAAACTGACTCGAAATATTTTTCCTCAAT-TGTTTGCCACAAA
905 GATTTTCGGCTAAAATTATGCAAAAACTGACCCGAAAAATTTTTCCTCAATAT-TTTGCCACAAA
68462 ACTCAGAAAAATA
969 ACTCAGAAAAATA
* * * * *
68475 ATTTAATTCAATGAGAAAAAATTTGAAGGGTTTTTCACGCTTGTAATATCGTTTTCCCATTTTTT
1 ATATAATTCAACGACAAAAAACTTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCCCATTTTTT
68540 TCCGAATTTATTTGTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATC
66 T-CGAATTTATTTGTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATC
**
68605 AAATGTGACTGAGATTTGGTTAGATGACTATAGATATTTCAAGGAGTCTTTGTACGTAAAACCAT
130 AAATGTGACTGAGATTTGGTTAGATGACTATAGATATTTCAAGGAGTCTTTGTACCAAAAACCAT
*
68670 GCAAAACTGACTCGAGACCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATT
195 GCAAAA-TGAGTCGAGACCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATT
* *
68735 TCATCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTCAAATATTTGACACAATACTTAG
259 TCAACTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTCAAATATTTGACACAATACTCAG
*
68800 AAAAAATATATATTTAACGCCAAAAAAATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCA
324 AAAAAATATATATTCAACGCCAAAAAAATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCA
*
68865 ATTTTCCGAATTCATTTCTAATTAAATCTAAACAAGATTCGGATGTTCATAAAAACAAATCCTTA
389 ATTTTCCGAATTCATTTCTAATTAAATCTAAACAAGATTCAGATGTTCATAAAAACAAATCCTTA
* * *
68930 TATCCAATGTGGCTGAGATTTGATTTGATGAATATTGATATTTTAAGGAGTCTATCTACCAAAAA
454 TATCCAATGTGGCTGAGATTTGGTTTGATGAATATTGATATTTCAAGGAGTCTATCTGCCAAAAA
*
68995 TCATGCAAAACTGAGCCGTGGTCTCGGAACGCATTTTTAGCCCAAAAAC
519 TCATGCAAAACTGAGCCGTGGTC-CGGAACGCGTTTTTAGCCCAAAAAC
69044 TGACCCGAAA
Statistics
Matches: 1449, Mismatches: 85, Indels: 33
0.92 0.05 0.02
Matches are distributed among these distances:
978 24 0.02
979 575 0.40
980 11 0.01
981 1 0.00
982 2 0.00
983 43 0.03
984 310 0.21
985 7 0.00
986 8 0.01
987 123 0.08
988 332 0.23
989 13 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (981 bp):
ATATAATTCAACGACAAAAAACTTGAAGGGTTTTTCACGCTTCTAATATCGTTTTCCCATTTTTT
TCGAATTTATTTGTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCA
AATGTGACTGAGATTTGGTTAGATGACTATAGATATTTCAAGGAGTCTTTGTACCAAAAACCATG
CAAAATGAGTCGAGACCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTC
AACTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTCAAATATTTGACACAATACTCAGAA
AAAATATATATTCAACGCCAAAAAAATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCAAT
TTTCCGAATTCATTTCTAATTAAATCTAAACAAGATTCAGATGTTCATAAAAACAAATCCTTATA
TCCAATGTGGCTGAGATTTGGTTTGATGAATATTGATATTTCAAGGAGTCTATCTGCCAAAAATC
ATGCAAAACTGAGCCGTGGTCCGGAACGCGTTTTTAGCCCAAAAACCGTGATAGAGTAGTACACG
ATTTCGGCTAAAAACTGACCCGAAAAAATTTTCGTCCATTTTTGCTACAATACTCAGAATATATA
TATAATTCAACTCCAAAAAGATTGAAGGGTTTTCTAAGGTTCTAATATCGTTTTTCCTTTTTTTT
TGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCCTAAAAACAAATCCTTAAATCCA
GTGTGGCTGATATTTGGTTAGATGAATATAGATATTCCAAGGAGTCTTTATGCCAAAAACCATGC
AAAACTGAGTCGAGGCCTCGAAACGCATTTTTAGCCAAAAACCGCGATAGATAGCACACGATTTT
CGGCTAAAATTATGCAAAAACTGACCCGAAAAATTTTTCCTCAATATTTTGCCACAAAACTCAGA
AAAATA
Done.