Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009549.1 Corchorus capsularis cultivar CVL-1 contig09570, 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: 87075
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:360 original size:87 final size:87
Alignment explanation
Indices: 256--484 Score: 404
Period size: 87 Copynumber: 2.6 Consensus size: 87
246 ATTGTTAAAA
256 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT
1 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT
* *
321 AAATGAATTATAAAGATTGAAC
66 AAATAAATCATAAAGATTGAAC
343 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT
1 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT
**
408 AAATAAATCATAAAGATTGAGT
66 AAATAAATCATAAAGATTGAAC
* *
430 TAATAAAGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGAAGATAT
1 TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATAT
485 AGAAAAGAAA
Statistics
Matches: 136, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 136 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.34
Consensus pattern (87 bp):
TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAGATATTTTAAGAAAT
AAATAAATCATAAAGATTGAAC
Found at i:8820 original size:42 final size:42
Alignment explanation
Indices: 8752--8832 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
8742 TTTAGAGAAG
* * *
8752 CTACCAACTTTGAATTTATACTAATACTAATACGTGCAACAT
1 CTACCAACTTAGAATTTATACCAATACTAATACATGCAACAT
*
8794 CTACCAACTTAG-ATTTCATACCAATACTCATACATGCAA
1 CTACCAACTTAGAATTT-ATACCAATACTAATACATGCAA
8833 GATTTGGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 4 0.12
42 30 0.88
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (42 bp):
CTACCAACTTAGAATTTATACCAATACTAATACATGCAACAT
Found at i:24333 original size:22 final size:22
Alignment explanation
Indices: 24307--24348 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
24297 TTGGGATCTT
*
24307 AAAAACAATGAAAAAAGAAAAA
1 AAAAACAAAGAAAAAAGAAAAA
*
24329 AAAAACAAAGAAAATAGAAA
1 AAAAACAAAGAAAAAAGAAA
24349 TTGAAGAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.81, C:0.05, G:0.10, T:0.05
Consensus pattern (22 bp):
AAAAACAAAGAAAAAAGAAAAA
Found at i:24915 original size:21 final size:21
Alignment explanation
Indices: 24889--24932 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
24879 GAATTAGAGA
24889 CAAGATTTTTAGGATGATCAT
1 CAAGATTTTTAGGATGATCAT
* *
24910 CAAGATTTTTTGGCTGATCAT
1 CAAGATTTTTAGGATGATCAT
24931 CA
1 CA
24933 TTGTTTCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (21 bp):
CAAGATTTTTAGGATGATCAT
Found at i:34370 original size:24 final size:24
Alignment explanation
Indices: 34343--34418 Score: 152
Period size: 24 Copynumber: 3.2 Consensus size: 24
34333 GAAGTTTTGT
34343 GAAGCAAGAATATCCCGAAGACAG
1 GAAGCAAGAATATCCCGAAGACAG
34367 GAAGCAAGAATATCCCGAAGACAG
1 GAAGCAAGAATATCCCGAAGACAG
34391 GAAGCAAGAATATCCCGAAGACAG
1 GAAGCAAGAATATCCCGAAGACAG
34415 GAAG
1 GAAG
34419 ATCCTTTTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.46, C:0.20, G:0.26, T:0.08
Consensus pattern (24 bp):
GAAGCAAGAATATCCCGAAGACAG
Found at i:38697 original size:2 final size:2
Alignment explanation
Indices: 38690--38715 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38680 CTCAACAAAG
38690 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
38716 TTTATAGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42471 original size:2 final size:2
Alignment explanation
Indices: 42464--42499 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
42454 AGCAAATAGA
*
42464 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42500 TGCTAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:64326 original size:2 final size:2
Alignment explanation
Indices: 64321--64349 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
64311 TGTGTGTGTG
64321 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
64350 TCTAAAAAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64782 original size:12 final size:12
Alignment explanation
Indices: 64765--64790 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
64755 ACTCAGACAT
64765 TTGATTCAATGA
1 TTGATTCAATGA
64777 TTGATTCAATGA
1 TTGATTCAATGA
64789 TT
1 TT
64791 ATTTACCCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (12 bp):
TTGATTCAATGA
Found at i:75399 original size:31 final size:27
Alignment explanation
Indices: 75236--77207 Score: 1957
Period size: 26 Copynumber: 71.6 Consensus size: 27
75226 CTTGTTCTTT
*
75236 TAGTTGCATATTCAGTAGGGT-TCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
75262 TAGTTGCATATTTAGTA-GG-GCCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
75287 TAGTTGCATAATCAGTA-GG-GCCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
* *
75312 TAGTTGCATAATCAGTAGGG-ACCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
* * *
75338 TAGTTGCATATTCAGGAAGG-GCCATT
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
75364 TAGTTGCATATTCGGTAGGGGCCATGCCATG
1 TAGTTGCATATTCAGTA-GGG---TGCCATG
* *
75395 TAGTTGCATATTCGGTAGGGGCCACGCCATG
1 TAGTTGCATATTCAGTA-GGG---TGCCATG
*
75426 TAGTTGCATATTCAGTAGGGGCCACGCCATG
1 TAGTTGCATATTCAGTA-GGG---TGCCATG
*
75457 TAGTTGCATATTCAGTAGGG-GCCACG
1 TAGTTGCATATTCAGTAGGGTGCCATG
75483 TAGTTGCATATTCAGTAGGGGCCATGCCATG
1 TAGTTGCATATTCAGTA-GGG---TGCCATG
75514 TAGTTGCATATTCAGTAGGGGCCATGCCATG
1 TAGTTGCATATTCAGTA-GGG---TGCCATG
75545 TAGTTGCATATTCAGTAGGGGCCATGCCATG
1 TAGTTGCATATTCAGTA-GGG---TGCCATG
75576 TAGTTGCATATTCAGTAGGGTG-CATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
75602 TAGTTTCATATTCAGTAGGGTG-CATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
75628 TAGTTGCATATTCAGTAGGG-GCCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
* *
75654 TAGTTCCATATTCAGTAGGGCCATGCCGTG
1 TAGTTGCATATTCAGTAGGG---TGCCATG
75684 TAGTTGCATATTCAGTAGGGGCCATGCCATG
1 TAGTTGCATATTCAGTA-GGG---TGCCATG
75715 TAGTTGCATATTCAGTAGGGTG-CATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
75741 TAGTTTCATATTCAGTAGGGTG-CATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
75767 TAGTTGCATATTCAGTAGGG-GCCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
* *
75793 TAGTTCCATATTCAGTAGGGCCATGCCGTG
1 TAGTTGCATATTCAGTAGGG---TGCCATG
* *
75823 TAGTTGCATATTCAGTAAGGCCATGCCGTG
1 TAGTTGCATATTCAGT-AGG--GTGCCATG
75853 TAGTTGCATATTCAGTAGGG-GCCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
75879 TAGTTGCATATTCAGTAGGGT-TCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
75905 TAGTTCCATATTCAGTAGGGGCCATGCCATG
1 TAGTTGCATATTCAGTA-GGG---TGCCATG
75936 TAGTTGCATATTCAGTAGGG-GCCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
* *
75962 TAGTTGCATATTCAGTAGGGT-TCAAG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
75988 TAGCTGCATATTCAGTAGGG-GCCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
* *
76014 TAATTGCATATTCAGTAGGGT-TCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
76040 TAGTTGCATATTCAGTAGGGGCCATGCCATG
1 TAGTTGCATATTCAGTA-GGG---TGCCATG
*
76071 TAGTTGCATTTTCAGTAGGGGGCATGCCATG
1 TAGTTGCATATTCAGTA--GGG--TGCCATG
* *
76102 TAGTTACATATTCAGTAGGGT-TCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
76128 TAGTTGCATATTCAGTAAGGGCCATGCCATG
1 TAGTTGCATATTCAGT-AGGG---TGCCATG
*
76159 TAGTTGCATATTCAGTAGGG-ACCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
76185 TAGTTGCATATTCAGTAGGGGTCATGCCATG
1 TAGTTGCATATTCAGTA-GGG---TGCCATG
*
76216 TAGTTGCATATTCAGTAGGGT-TCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
76242 TAATTGCATATTCAGTAGGGGTCAATGCCATG
1 TAGTTGCATATTCAGTA-GGG----TGCCATG
** *
76274 TAGTTTTATATTCAGTAGGG-ACCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
76300 TAGTTGCATATTTAGTAGGGTG-CATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
76326 TAGTTTCATATTCAGTAGGGTG-CATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
76352 TAGTTGCATATTCAGTAGGG-ACCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
76378 CAGTTGCATATTCAGTAGGGGCCATGCCATG
1 TAGTTGCATATTCAGTA-GGG---TGCCATG
*
76409 TAGTTGCATATTCAGTAGGGT-TCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
* *
76435 TAGTTGCATTTTCAGTAGGGT-TCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
76461 T-GTTTGCATATTCAGTAGGG-GCCATG
1 TAG-TTGCATATTCAGTAGGGTGCCATG
*
76487 TAGTTGCACATTCAGTAGGGT-CCATGGCTTG
1 TAGTTGCATATTCAGTAGGGTGCCA-----TG
76518 TAGTTGCATATTCAGTAGGG-GCCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
76544 TAGTTGCATATTCAGTTGGGTG-CATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
* *
76570 TGGTTTCATATTCAGTAGGGTG-CATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
76596 TAATTGCATATTCAGTAGGGGCCATGCCATG
1 TAGTTGCATATTCAGTA-GGG---TGCCATG
76627 TAGTTGCATATTCAGTAGGGGCCATGCCATG
1 TAGTTGCATATTCAGTA-GGG---TGCCATG
* *
76658 TAGTTGCATATTCAGTTGGGT-TCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
76684 TAGTTGCATATTCAGTAGGGT-TCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
76710 TAGCTGCATATTCAGTAGGG-GCCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
* *
76736 TAGTTGCATATTTAGTTGGGGCCATGCCATG
1 TAGTTGCATATTCAG-TAGGG---TGCCATG
*
76767 CAGTTGCATATTCAGTAAGGGCCATGCCATG
1 TAGTTGCATATTCAGT-AGGG---TGCCATG
76798 TAGTTGCATATTCAGTAGGG-GCCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
76824 TAGTTGCATATTCAGTAGGGT-TCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
76850 TAATTGCATATTCAGTAGGG-GCCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
76876 TAGTTGCATATTCAGTAGGG-GCCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
* *
76902 TAGTTGCATATTCTGTTGGGT-CCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
* *
76928 TAGTTGCATATTTAGTAGGGT-TCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
76954 TAGTTGCATATTTAGTAGGGGCCATGCCATG
1 TAGTTGCATATTCAGTA-GGG---TGCCATG
* ** * *
76985 TGGTTGCATATTTTGTATGGT-TCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
*
77011 TGGTTGCATATTCAGTAGGGTG-CATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
* *
77037 TGGTTGCATATTTAGTA-GG-GCTCATG
1 TAGTTGCATATTCAGTAGGGTGC-CATG
* * *
77063 TAGTGGCATATTTAGTAGTGGT-TC-TG
1 TAGTTGCATATTCAGTAG-GGTGCCATG
*
77089 TAGTTGTATATTCAGTAGGG-GCCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
* * * *
77115 TAGTTTCATATTAAGTTGGG-GCCATA
1 TAGTTGCATATTCAGTAGGGTGCCATG
* * *
77141 TAATTGCATATTTAGTAGGG-GCTATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
77167 TAGTTGCATATTCAGTA-GG-GCCATG
1 TAGTTGCATATTCAGTAGGGTGCCATG
* *
77192 TAATTGCATAATCAGT
1 TAGTTGCATATTCAGT
77208 GGAATTCATG
Statistics
Matches: 1703, Mismatches: 140, Indels: 207
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.00
25 75 0.04
26 980 0.58
27 46 0.03
28 2 0.00
29 6 0.00
30 102 0.06
31 469 0.28
32 22 0.01
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (27 bp):
TAGTTGCATATTCAGTAGGGTGCCATG
Found at i:85245 original size:332 final size:334
Alignment explanation
Indices: 83648--86980 Score: 4348
Period size: 333 Copynumber: 10.1 Consensus size: 334
83638 CCAAAAAATA
* * *** * * **
83648 TATATTCATGTAACCAAATCTCAGTCATAATGGATTTAAGGATTTGTTTTTACGAGCATTGGAAA
1 TATATTCATGTAACTAAATCTCAGCCACGTTGGATTTATGGATTTGTTTTTACGAACATCAGAAA
* * * * * *
83713 CCGTTTTAATTTT-ATTAAAAATAAATTCAGAAAAAAAATAACAAAATTGATGTTAGAAGAGT-A
66 CCGATTTCATTTTCATTAGAAATTAATTCAG-AAAAAAATAAGAAAATCGATGTTAGAAGAGTGA
* * *
83776 -AAACAGCCTTATATCTTTTTGGCATTGAATTAAATATTTTCTTTTATGAGTATTTCGGCCAAAA
130 CAAAC--CCTTATATCTTTTTGGCGTTGAATTATATA-TAT-TTTTATGAGTATTTCGGCCAAAA
*
83840 ATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTG---T-A--ATCA
191 ATTGAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA
* *** ** * * * * *
83899 CAGTTTTTTTTTTCAAACGCGTTCTGGGGCCCTGGCTCAGTTTTGCGTGATTTTTGG-TTCCGAG
256 CGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCGTGATTTTTGGCGT-CAAG
*
83963 ACTCCTTGAAATATC
320 ACTTCTTGAAATATC
* * * * ** *
83978 TTTATTTATGTAACTGAATCTCAGCCACATTGGATTTAAAGATTT-TTTTTACGAGCATCAGAAA
1 TATATTCATGTAACTAAATCTCAGCCACGTTGGATTTATGGATTTGTTTTTACGAACATCAGAAA
* * * * * *
84042 CCGTTTTCATTTTCATTAGCAATTAATTCAGAAAATAAA-AAAAGAAATCGTTGTTCGAAAAGTG
66 CCGATTTCATTTTCATTAGAAATTAATTCAGAAAA-AAATAAGA-AAATCGATGTTAGAAGAGTG
* * * * * * *
84106 AAAAACCCTTATATCTTTTTGGTGTCGAATTATATAT-TTTGTATGAGTATTTTGACCGAAAATT
129 ACAAACCCTTATATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTTCGGCCAAAAATT
* * * *
84170 GAGCAAAAATATTTCGGGTCAAATTTTGCAAAATTTTAGCCGAAATCATGTACTTTA-CATCACG
194 GAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC-TAACCATCACG
* * * * *
84234 GTTTTTGGCTAAAAACGCGTTCCGGGTCCCCGGCTCAGTTTTGCATGATTTTTGGTGTCAAAACT
258 GTTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCGTGATTTTTGGCGTCAAGACT
*
84299 CCTTGAAATATC
323 TCTTGAAATATC
* * * * * ** * **
84311 TATATTAATGTACCCAAATTTCAGCTAAATTGGATTTAAGGATTTGTTTTTACGAGTATCAGAAA
1 TATATTCATGTAACTAAATCTCAGCCACGTTGGATTTATGGATTTGTTTTTACGAACATCAGAAA
* * * *
84376 CCGTTTTCATTTTCATTTGAAATTAATTCAGAATAAAATAAGAAAATCGATGTTAGAAGAGCGAC
66 CCGATTTCATTTTCATTAGAAATTAATTCAGAAAAAAATAAGAAAATCGATGTTAGAAGAGTGAC
* *****
84441 AAACCCTTATATTTTTTTGGCGTTGAATTATA-A-ATTTTTATGAGTATTTAATATAAAAAATTG
131 AAACCCTTATATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTT-CGGCCAAAAATTG
*
84504 AGG-AAAATATTTCGGGTCAATTTTTGTAAAATTTTA-CCGAAATCGTGTACTAACCATCACGGT
195 AGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGT
* * * * * * *
84567 TTTTGACCAAAAACGCGTTCCGGGGCCCTGGCTCAGTTTTGTGTGATTTTTGTCGTCAGGACTTC
260 TTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCGTGATTTTTGGCGTCAAGACTTC
84632 TTGAAATATC
325 TTGAAATATC
* * *
84642 TATGTTCATGTAATTAAATCTCAGCCACGTTGGATTTATGGA-TTGTTTTTACGAACATTAGAAA
1 TATATTCATGTAACTAAATCTCAGCCACGTTGGATTTATGGATTTGTTTTTACGAACATCAGAAA
*
84706 CCGATTTCATTTTCATTAGAAATTAGTTCAGAAAAAAAT-AGAAAAATCGATGTT--AAGAGTGA
66 CCGATTTCATTTTCATTAGAAATTAATTCAGAAAAAAATAAG-AAAATCGATGTTAGAAGAGTGA
*
84768 CAAACCCTTATATCTTTTTGGCGTTG-ATT-TATATATTTTTAATGAGTATTTAGGCCAAAAATT
130 CAAACCCTTATATCTTTTTGGCGTTGAATTATATATATTTTT-ATGAGTATTTCGGCCAAAAATT
* * * * * *
84831 AAGGAAAAATATTTCGGGTCAATTTTTACAAAATCTTAGGCGAAATCGTATACTAACCATCACCG
194 GAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG
* *
84896 TTTTTGGCTAAAAACGCGTTCCAGGG-CCCGGCTCAGTTTTGCGTGATTTTTGGCGTCAAGACTT
259 TTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCGTGATTTTTGGCGTCAAGACTT
84960 CTTGAAATATC
324 CTTGAAATATC
* * * *
84971 TATATTCATTTAAATAAATCTCAGCCACGTTGGATTTATGAATTAGTTTTTACGAACATCAGAAA
1 TATATTCATGTAACTAAATCTCAGCCACGTTGGATTTATGGATTTGTTTTTACGAACATCAGAAA
* *
85036 CCGATTTCATTTTCATTAGAAATTAATTCAG-AAAAAATAGGAAAATCAATGTTAGAAGAGTGAC
66 CCGATTTCATTTTCATTAGAAATTAATTCAGAAAAAAATAAGAAAATCGATGTTAGAAGAGTGAC
* * * *
85100 AAACCTTTATATCTTTTTGGCGTTGAATTATATATATATTTATAAGTATTTCGGCCAAAAATTAA
131 AAACCCTTATATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTTCGGCCAAAAATTGA
* * *
85165 GGAAAAATATTTCGGATCGATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTT
196 GGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTT
* * *
85230 TTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCGTAATTTTTGGCGTCAACACTTTT
261 TTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCGTGATTTTTGGCGTCAAGACTTCT
85295 TGAAATATC
326 TGAAATATC
*
85304 TATATTCATGTAACTAAATCTCAGCCACGTTGCATTTATGGATTTGTTTTTACGAACATCAGAAA
1 TATATTCATGTAACTAAATCTCAGCCACGTTGGATTTATGGATTTGTTTTTACGAACATCAG-AA
* * * *
85369 ACCGATTTCATTATCATTAGAAATTAATTCAGAAAAAAATAGGAAAATCGATGTTCGAAGAGCGA
65 ACCGATTTCATTTTCATTAGAAATTAATTCAGAAAAAAATAAGAAAATCGATGTTAGAAGAGTGA
* *
85434 CAAACCCTTATATCTTTTTGGCG-TAAAGTTATATAT-TTTTTATGAGTATTTCAGCCAAAAATT
130 CAAACCCTTATATCTTTTTGGCGTTGAA-TTATATATATTTTTATGAGTATTTCGGCCAAAAATT
* *
85497 GAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTTTATTAACCATCACGG
194 GAGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG
* * *
85562 TTTTTTGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCGTGATTTTTGGTGTCAAGACTC
259 TTTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCGTGATTTTTGGCGTCAAGACTT
*
85627 CTTGAAATATA
324 CTTGAAATATC
* * * * ** ** **
85638 TATATTAATGTACCCAAATTTCAGCCAAATTGGATTTAAAGATTTGTTTTTACGAGTATCAGAAA
1 TATATTCATGTAACTAAATCTCAGCCACGTTGGATTTATGGATTTGTTTTTACGAACATCAGAAA
* * * *
85703 CTGTTTTCATTTTCATTAGAAATTAGTTCAGAAAAAAAATAAGATAATCGATGTTAGAAGAGTGA
66 CCGATTTCATTTTCATTAGAAATTAATTCAG-AAAAAAATAAGAAAATCGATGTTAGAAGAGTGA
* * *
85768 CAAACCTTTATATCTTTTTGGCGTTGAATTATATATATTTTTATGAGAATTTCGGCCAAAAATTA
130 CAAACCCTTATATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTTCGGCCAAAAATTG
* * * *
85833 AGGACAAATATTTCGGATCGATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGT
195 AGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGT
*
85898 TTTTTGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCGTGATTTTTGGCGTCAAGACTTC
260 TTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCGTGATTTTTGGCGTCAAGACTTC
85963 TTGAAATATC
325 TTGAAATATC
* * *
85973 TATATTCATGTAACTAAATCTCGGCCATGTTGGATTTATGGATTTATTTTTACGAACATCAGAAA
1 TATATTCATGTAACTAAATCTCAGCCACGTTGGATTTATGGATTTGTTTTTACGAACATCAGAAA
* * * *
86038 CCGATTTCATTTTCATTAGGAATTAATTCAG-AAAAAATAGGAAAATCGATGTTCGAAGAGCGAC
66 CCGATTTCATTTTCATTAGAAATTAATTCAGAAAAAAATAAGAAAATCGATGTTAGAAGAGTGAC
** ** *
86102 AAACCCTTATATCTTTTTGGCGTAAAATTATATAT-TTTTTATGAGTATTTCAACCTAAAATTGA
131 AAACCCTTATATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTTCGGCCAAAAATTGA
*
86166 GGAAAAATATTTCGGG--------T-C---ATTTTAGCCAAAATCGT-TCACTAACCATCACGGT
196 GGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-ACTAACCATCACGGT
* * * *
86218 TTTTTGCTAAAAACGCGTTCCGGGGCCTCGGCTCAATTTTGCGTGATTTTTGGTGTCAAGACTCC
260 TTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCGTGATTTTTGGCGTCAAGACTTC
*
86283 TTGAAATATA
325 TTGAAATATC
* * * * ** * **
86293 TATATTAATGTACCCAAATTTCAGCCAAATTGGATTTAAGGATTTGTTTTTACGAGTATCAGAAA
1 TATATTCATGTAACTAAATCTCAGCCACGTTGGATTTATGGATTTGTTTTTACGAACATCAGAAA
* *
86358 CCGTTTTCATTTTCATTAGAAATTAATTCAGAAAAAAATAAGATAATCGATGTT--AAGAGTGAC
66 CCGATTTCATTTTCATTAGAAATTAATTCAGAAAAAAATAAGAAAATCGATGTTAGAAGAGTGAC
* **
86421 AAACCCTTATATCTTTTTGGCGTTGAATTATATAT-TTTTTATGAGTATTTAAGATCAAAAATTG
131 AAACCCTTATATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTT-CGGCCAAAAATTG
* *
86485 AGGAAAAATATTTCGGGTCAATTTTTGCAAAATCTTAGCCGAAATCGTATACTAACCATCACGGT
195 AGGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGT
*
86550 TTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCGTGATTTTTGGCGTCAAGACTTC
260 TTTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCGTGATTTTTGGCGTCAAGACTTC
86615 TTGAAATATC
325 TTGAAATATC
* * *
86625 TATATTCATTTAACTAAATCTCAGCCACGTTGGATTTACGGATTTGCTTTTACGAACATCAGAAA
1 TATATTCATGTAACTAAATCTCAGCCACGTTGGATTTATGGATTTGTTTTTACGAACATCAGAAA
* * *
86690 CCGATTTCATATTCATTAGAAATTAATTCAG-AAAAAATAGGAAAATCAATGTTAGAAGAGTGAC
66 CCGATTTCATTTTCATTAGAAATTAATTCAGAAAAAAATAAGAAAATCGATGTTAGAAGAGTGAC
* * * *
86754 AAACCTTTATATCTTTTTGGCGTTGAATTATATATATATTTATAAGTATTTCGGCCAAAAATTAA
131 AAACCCTTATATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTTCGGCCAAAAATTGA
* * *
86819 GGAAAAATATTTCGGATCGATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTT
196 GGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTT
* * *
86884 TTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCGTAATTTTTGGCGTCAACACTTTT
261 TTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCGTGATTTTTGGCGTCAAGACTTCT
86949 TGAAATATC
326 TGAAATATC
86958 TATATTCATGTAACTAAATCTCA
1 TATATTCATGTAACTAAATCTCA
86981 TTAGAAATTA
Statistics
Matches: 2639, Mismatches: 309, Indels: 107
0.86 0.10 0.04
Matches are distributed among these distances:
319 57 0.02
320 210 0.08
321 20 0.01
323 1 0.00
324 1 0.00
326 2 0.00
327 72 0.03
328 51 0.02
329 181 0.07
330 260 0.10
331 172 0.07
332 377 0.14
333 572 0.22
334 365 0.14
335 298 0.11
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (334 bp):
TATATTCATGTAACTAAATCTCAGCCACGTTGGATTTATGGATTTGTTTTTACGAACATCAGAAA
CCGATTTCATTTTCATTAGAAATTAATTCAGAAAAAAATAAGAAAATCGATGTTAGAAGAGTGAC
AAACCCTTATATCTTTTTGGCGTTGAATTATATATATTTTTATGAGTATTTCGGCCAAAAATTGA
GGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTT
TTTGGCTAAAAACGCGTTCCGGGGCCCCGGCTCAATTTTGCGTGATTTTTGGCGTCAAGACTTCT
TGAAATATC
Done.