Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013730.1 Corchorus capsularis cultivar CVL-1 contig13751, 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: 32973
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:1803 original size:27 final size:27
Alignment explanation
Indices: 1760--1818 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
1750 CATCTCTAGA
*
1760 ACAAAGCTTCCAATACCTTGCCGAGCT
1 ACAAAGCTCCCAATACCTTGCCGAGCT
* *
1787 ACAAAGCTCCCATTACCTTGCCGGGCT
1 ACAAAGCTCCCAATACCTTGCCGAGCT
1814 ACAAA
1 ACAAA
1819 ACCAACATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.31, C:0.34, G:0.15, T:0.20
Consensus pattern (27 bp):
ACAAAGCTCCCAATACCTTGCCGAGCT
Found at i:2877 original size:21 final size:21
Alignment explanation
Indices: 2834--2878 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2824 ATTGGAGATC
* * *
2834 ATGTCTTGGATAATCATGGAG
1 ATGTCTTGGAGAATCAAGAAG
*
2855 ATGTCTTGGAGATTCAAGAAG
1 ATGTCTTGGAGAATCAAGAAG
2876 ATG
1 ATG
2879 CCACTGATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (21 bp):
ATGTCTTGGAGAATCAAGAAG
Found at i:3009 original size:42 final size:42
Alignment explanation
Indices: 2963--3054 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
2953 TCCGGCCATG
* *
2963 ACCGGCCAACGCAT-GGAGCAACGCATGGGGCAACCAGCCACA
1 ACCGGCCAACGCATGGGA-CAACGCACGGGCCAACCAGCCACA
* * *
3005 ACCGGCCAACGCATGGGACATCGCACGGGCCATCCGGCCACA
1 ACCGGCCAACGCATGGGACAACGCACGGGCCAACCAGCCACA
3047 ACCGGCCA
1 ACCGGCCA
3055 TTCGACCCTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 41 0.93
43 3 0.07
ACGTcount: A:0.27, C:0.39, G:0.28, T:0.05
Consensus pattern (42 bp):
ACCGGCCAACGCATGGGACAACGCACGGGCCAACCAGCCACA
Found at i:4684 original size:15 final size:15
Alignment explanation
Indices: 4664--4694 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4654 TAGAAATTGG
4664 GATGCCTCCCAACAA
1 GATGCCTCCCAACAA
4679 GATGCCTCCCAACAA
1 GATGCCTCCCAACAA
4694 G
1 G
4695 CGATGTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.39, G:0.16, T:0.13
Consensus pattern (15 bp):
GATGCCTCCCAACAA
Found at i:5412 original size:21 final size:21
Alignment explanation
Indices: 5386--5440 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
5376 GTAAACGTAT
*
5386 AGTCGACATAAATGAACTTTC
1 AGTCGACTTAAATGAACTTTC
5407 AGTCGACTTAAATGAACTTTC
1 AGTCGACTTAAATGAACTTTC
*
5428 AATCGACTTAAAT
1 AGTCGACTTAAAT
5441 TACATGAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (21 bp):
AGTCGACTTAAATGAACTTTC
Found at i:7052 original size:103 final size:105
Alignment explanation
Indices: 6869--7105 Score: 383
Period size: 103 Copynumber: 2.3 Consensus size: 105
6859 AGTTTAGCCT
*
6869 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATT--AATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
6934 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
64 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
6976 TAATTTCACTAAGTTTAGCCCCAAATTAA-TTT-TTTTTATTTTAAGGGTAAATTCCATAATTAA
1 TAATTTCACTAAGTTTAGCCCCAAATTAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTAA
* *
7039 TAATTTATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 TAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
7079 TAA-TTCACTAAGTTTAG-TCCAAATTAA
1 TAATTTCACTAAGTTTAGCCCCAAATTAA
7106 AATTAAAATT
Statistics
Matches: 125, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
101 9 0.07
102 14 0.11
103 70 0.56
104 3 0.02
105 2 0.02
107 27 0.22
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTAA
TAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:10972 original size:23 final size:24
Alignment explanation
Indices: 10936--11000 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
10926 GACAATAGAC
* *
10936 AAGCTCTTAAAAAGGAGTCCT-AA
1 AAGCTCTCACAAAGGAGTCCTCAA
*
10959 AAGCTCTCACAAAGGAGT-TTCAA
1 AAGCTCTCACAAAGGAGTCCTCAA
*
10982 AAACTCTCACAAAGGAGTC
1 AAGCTCTCACAAAGGAGTC
11001 AAAAAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.20
Consensus pattern (24 bp):
AAGCTCTCACAAAGGAGTCCTCAA
Found at i:11006 original size:23 final size:23
Alignment explanation
Indices: 10946--11007 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
10936 AAGCTCTTAA
** *
10946 AAAGGAGTCCTAAAAGCTCTCAC
1 AAAGGAGTCAAAAAAACTCTCAC
***
10969 AAAGGAGTTTCAAAAACTCTCAC
1 AAAGGAGTCAAAAAAACTCTCAC
10992 AAAGGAGTCAAAAAAA
1 AAAGGAGTCAAAAAAA
11008 AAAAGAAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.48, C:0.19, G:0.16, T:0.16
Consensus pattern (23 bp):
AAAGGAGTCAAAAAAACTCTCAC
Found at i:17001 original size:331 final size:328
Alignment explanation
Indices: 16266--17517 Score: 1298
Period size: 331 Copynumber: 3.8 Consensus size: 328
16256 ATACTTTACA
* * * * * * * * * *
16266 TCATCTAACCAAAGCTCAGCAACATTGGATTGAAGAATTT-TTTTAATGAGCATTTGAATCCTGT
1 TCATCTAATCAAATCTTAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
16330 TTCGATTTAATTAGAAATTAATTTAGAAAAAATCA-GTAATACGATATTAAAAGCGTGAAAAGCC
66 TTCGATTTAATTAGAAATTAATTCAAAAAAAAT-ATGAAAAACGATATTAAAAGCGTGAAAAGCC
*
16394 CTCCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAGAAA
130 CTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGA-GA-AAA
* * *
16459 T-CTTTTGTGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTACTATAACTAACCATCACGGTT
193 TATTTTTG-GTCAATTTTTTCAAAATTTTAGCCGAAATCG-G---TATAA-T-ACCATCACGGTT
* * * * * *
16523 TTTCGCTAAAAACGTATTTTGGAGACCCGC-CTCAATTTTGCATGACTTTTTA-CTGGCGAGACT
251 TTTCGCTAAAAAAGTGTTTCGG-GGCCC-CACTCAGTTTTGCATGA-TTTTTAGC-GTCGAGACT
*
16586 ACTTGAAATATCTATAT
312 CCTTGAAATATCTATAT
* * * * *
16603 TCATCCAATCAAATCTCAGCTACATTGGATTTGAGGATTTGTTTTTATGAGCATTTGAATCTTGT
1 TCATCTAATCAAATCTTAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * *
16668 TTCGATTTAATAAGAAACTAATTCGAAAAAAAATA-G-AAAACGATATTAGAAA-CGTCAAAAGC
66 TTCGATTTAATTAGAAATTAATTC-AAAAAAAATATGAAAAACGATATTA-AAAGCGTGAAAAGC
** *
16730 CCTTCAATCTTTTTGGCGTTGAACCATATACTTTTTATGAGTATTTTAGCCAAAAATTGAGCAAA
129 CCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGAAAA
* * *** *
16795 TATTTTTCGGATTAATTTTTACAAAATTTTAGCCGAAATC-GTATAATTACCATCACAAATTTTG
193 TATTTTT-GG-TCAATTTTTTCAAAATTTTAGCCGAAATCGGTATAA-TACCATCACGGTTTTTC
* * *
16859 GCTAAAAAAGCGTTTCGGGGCCCCAACTCAGTTTCGCATGATTTTTAGCGTCGAGACTCCTTGAG
255 GCTAAAAAAGTGTTTCGGGGCCCC-ACTCAGTTTTGCATGATTTTTAGCGTCGAGACTCCTTGAA
16924 ATATCTATAT
319 ATATCTATAT
*
16934 TCATATAATCAAATCTTAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTTAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * *
16999 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCG
66 TTCGATTTAATTAGAAATTAATTCAAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCC
* * * * * * *
17064 TTGAATCTTTTTTGTGTTAAATTATATATATTTTATGAGTATTTTATCCAATATTTGAGTAAAAA
131 TTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAG--AAAA
* * * **
17129 AAATTTGGGTC-ATTTTTTCAAAATTTTAGTCC-AAATCGTGTATAA-ACCATCACGGTTTTTTT
193 TATTTTTGGTCAATTTTTTCAAAATTTTAG-CCGAAATCG-GTATAATACCATCACGGTTTTTCG
* * * *
17191 CTAAAAACA-TGTCTCGGGACCCCGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAA
256 CTAAAAA-AGTGTTTCGGGGCCCCACTCAGTTTTGCATGATTTTTAGCGTCGAGACTCCTTGAAA
17255 TATCTATAT
320 TATCTATAT
* * * * * * * *
17264 TCATCTAATAAAATTTTAGGC-ACAATGCATTTAAAGCTTTGGTTTTACGAGCATCTGAATCTTA
1 TCATCTAATCAAATCTTA-GCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * ** *
17328 TTTCGATTTAATTAGAAATTTATTC-AGAAAAATATGAAAAACGATATTAAAAGTATGAAAA-TC
65 TTTCGATTTAATTAGAAATTAATTCAAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCC
* *** *
17391 CTTCAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTGCGGCTAAAAATTGAGAAAAT
130 CTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGAAAAT
* ** *
17456 ATCTTTCGAGTCAATTTTTTCAAAATTTTAAACGAAATCGTGTACTAAT--CATGACGGTTTTT
194 AT-TTTTG-GTCAATTTTTTCAAAATTTTAGCCGAAATCG-GTA-TAATACCATCACGGTTTTT
17518 TTTTTGCTAA
Statistics
Matches: 779, Mismatches: 108, Indels: 64
0.82 0.11 0.07
Matches are distributed among these distances:
326 5 0.01
327 4 0.01
328 53 0.07
329 72 0.09
330 135 0.17
331 173 0.22
332 113 0.15
333 14 0.02
334 7 0.01
336 5 0.01
337 86 0.11
338 104 0.13
339 8 0.01
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (328 bp):
TCATCTAATCAAATCTTAGCTACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATTAGAAATTAATTCAAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCC
TTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGAAAATAT
TTTTGGTCAATTTTTTCAAAATTTTAGCCGAAATCGGTATAATACCATCACGGTTTTTCGCTAAA
AAAGTGTTTCGGGGCCCCACTCAGTTTTGCATGATTTTTAGCGTCGAGACTCCTTGAAATATCTA
TAT
Found at i:17822 original size:11 final size:11
Alignment explanation
Indices: 17806--17837 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
17796 GAAGTTCGTG
17806 TTTGAAGATTA
1 TTTGAAGATTA
*
17817 TTTGAAGATAA
1 TTTGAAGATTA
17828 TTTGAAGATT
1 TTTGAAGATT
17838 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:17834 original size:22 final size:22
Alignment explanation
Indices: 17806--17865 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
17796 GAAGTTCGTG
*
17806 TTTGAAGATTATTTGAAGATAA
1 TTTGAAGATTATTTGAAGACAA
17828 TTTGAAG---ATTTGAAGACAA
1 TTTGAAGATTATTTGAAGACAA
*
17847 -TTGAAGAATTATTTCAAGA
1 TTTGAAG-ATTATTTGAAGA
17866 AGCAAGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
22 15 0.47
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (22 bp):
TTTGAAGATTATTTGAAGACAA
Found at i:17840 original size:19 final size:18
Alignment explanation
Indices: 17816--17853 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
17806 TTTGAAGATT
*
17816 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
17835 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
17853 A
1 A
17854 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:19211 original size:6 final size:6
Alignment explanation
Indices: 19200--19230 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
19190 ATAATTGCTA
19200 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
19231 TTTTGCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Found at i:20687 original size:40 final size:40
Alignment explanation
Indices: 20632--20709 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
20622 AGACTCCTTC
20632 AAATATCTATATTCATGAAACCAAATCTCATGAAAAATGG
1 AAATATCTATATTCATGAAACCAAATCTCATGAAAAATGG
20672 AAATATCTATATTCATGAAACCAAATCTCATGAAAAAT
1 AAATATCTATATTCATGAAACCAAATCTCATGAAAAAT
20710 TTTTGGTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (40 bp):
AAATATCTATATTCATGAAACCAAATCTCATGAAAAATGG
Found at i:23324 original size:992 final size:972
Alignment explanation
Indices: 20737--23727 Score: 2743
Period size: 992 Copynumber: 3.1 Consensus size: 972
20727 TGGTTTTTGC
* * * * * ***
20737 TTTTACTAGTATCTGAATCATGTTTCGATTTAATTAAAAATAAATTC-T-GGGAAAATGGAAAAA
1 TTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGTAAAAAAAATGGAAAAA
* * * * * * * *
20800 CGATATTAGAAGCGTGAAAATCCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTT-TGAGTA
66 AGATATTAGAAACGTGAAAAACCATTCAA-TTTTTTGGCATTGAAATATACATTTTTTCTGAGCA
* * ** * * *
20864 TTGTGGCAAAGAATTGA-CTAAAACCTTTT-GGGTCAGTTTTTACAAAATTTTAGCCGAAATCGT
130 TTGTGCCAAAAAATTGAGAAAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCAT
* * * * * * *
20927 GTACTAA-C-T----ATTTTTGGCTAAAATCGCGTTCTGGAGACCCGGATCAATTTTGC-ATGAT
195 GTACTAACCATCACGATTTTTAGCTAAAAACACGTTCCGGAGACCCAGCTCAATTTT-CAATAAT
** * * * *
20985 TTTTGGTGCAAAGACTCCTTG-AAATATCTATATTCATCGAATCAAACCTCAAG-TACATTGGAT
259 TTTTACTGCAAAGAC-CCCTGCAAATATCTATATTCATCGAACCAAATCTC-AGCCACATTGGAT
** * * * * * * * **
21048 ATAA-GGATTTGTTTTTACTAGCATCTGAATGTTGTTTCGATTTAAATAAAAATTAATTTTGAAA
322 ATAACAAATTTGTTTTTACGAACATCTGAATCTTATTTCGATGTAATTAGAAATTAA-TTCAAAA
* * * * * * *
21112 AAA-A-CGG-AAAAATGATATTTGAAGCGTGAAAAGCCT-ACCAGTCTTTGTGG-AGTTGAATTA
386 AAAGAGAGGAAAAAACGATATTAGAAGCATGAAAAGCCTGACAACT-TTTTTGGCA-TTGAATTA
* * * *
21172 TATATTTTTTATGAATATTTTGCCGAAAAAATTGAG-AAAAACCTTTCTGGTCAGTTTTTAG-C-
449 TATATTTTTTCTGAATATTTT--C-AAAAAATTGAGAAAAAACTTTTCGGGTAAGTTTTTAGCCG
* * * *
21234 --A-CA-G---------T-----TTTT-GGTTAAAAACGCATGTCGGGGCCTC-GGCTCAGTTTT
511 AAATCATGTACTAACCATCACGGTTTTAAGCTAAAAACGCGTGTCGGGGCC-CAGGCTCAATTTT
* * * * * * *
21279 GCATGATTTTTGACAGAAAAACTCCTTGAAATATCTATATTTATCCAACCAAATCTCAGCCACAA
575 ACAAGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAACCACAA
* * * *
21344 TGGATTTAAGGATTTCTT--T-TGACGCATCTGAATCTTGTTTCGATTTAATTA-AGGATAAA-T
640 TGGATTAAAGGATTTCTTGATACGA-GCATTTGAATCTTGTTTCGATTTAATTAGA-AATAAATT
*** * * * * * * * * *
21404 --ACGGAAAAAAAAG-AAAATGATATTACAAGCGTGAAAGACCCTTCAATTCTTTTGGCGTTGAA
703 CAAAAAAAAAAAAAGAAAAATGATATTACAAGAGTCAAAAATCCTTAAATTTTTTTGACATTAAA
* ** * * ** *** * *
21466 TTATATATTTTTTTCTGAGTATTGTGGCAAAAAATTGAGGTAACCCTTTTCAGGTCAGTTTTTAG
768 TTATATA-TTTTTTATGAAAATTATGGCAAAAAATTAAGAAAAAAATTTTCGGGTCAATTTTTA-
* ** * *** ** *
21531 CTGAAACCGTATTCTAACTC-TCAC-GGTTTTTGGCTAAAAACGGGTTTTGGGGCCTC-ATCTCA
831 -T-----CGTATAC--AC-CATCACATTTTTTTGACTAAAAACACCTTCAGGGGCCCCGA-CTCA
* * *
21593 GTTTTGCATGGTTTTTACCATAAAGACTCCTTGAAAAATCTATATTAATCTAACCAAATCTCAGC
886 GTTTTGCATGGTTTTTGCCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGC
* *
21658 TACATTGGATTTAAGGATTTCT
951 CACATTGGATTTAAGGATTTAT
* * *
21680 TTTTATGAGCATCTAGATCTTGTTTTGATTTAATTAGAAATAAATTCGT--AAAAAATGGAAAAA
1 TTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGTAAAAAAAATGGAAAAA
* * * * * * *
21743 TA-ATTTTAGAAGCATGAAAAACCCTTCAATTTTTTTGCGTTGAAATATACATTTTTTCTGAGTA
66 -AGATATTAGAAACGTGAAAAACCATTCAATTTTTTGGCATTGAAATATACATTTTTTCTGAGCA
* *
21807 TTGTGCCAAATAATTGAGAAAAAAACTTTTCGGGTCGGTTTTTGCAAAATTTTAGCCGAAATCAT
130 TTGTGCCAAAAAATTGAGAAAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCAT
* * * *
21872 GTACTAACCATCACGGTTTTTAGCTAAAAACGCGTTCCGGAGTCCCTGCTCAATTTTCAATAATT
195 GTACTAACCATCACGATTTTTAGCTAAAAACACGTTCCGGAGACCCAGCTCAATTTTCAATAATT
** *
21937 TTTGGTGCAAAGACCCCTGCAAATATCTATATTCATCGAATCAAATCTCAGCCACATTGGATATA
260 TTTACTGCAAAGACCCCTGCAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATA
* *
22002 ACAAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATGTAATTAGAAATTAATTCAAAAAAAA
325 ACAAATTTGTTTTTACGAACATCTGAATCTTATTTCGATGTAATTAGAAATTAATTC--AAAAAA
* * * *
22067 AGAGAGGAAAAAACGTTATTATAAGCATGAAAAGCCTGTCAACTTTTTTGGCGTTGAATTATATA
388 AGAGAGGAAAAAACGATATTAGAAGCATGAAAAGCCTGACAACTTTTTTGGCATTGAATTATATA
* *
22132 TTTTTTCTGAATATTTTCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGATATCAT
453 TTTTTTCTGAATATTTTCAAAAAATTGAGAAAAAACTTTTCGGGTAAGTTTTTAGCCGAAATCAT
* * * *
22197 GTACTAACCATCACGGTTTTAAGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTACATGATT
518 GTACTAACCATCACGGTTTTAAGCTAAAAACGCGTGTCGGGGCCCAGGCTCAATTTTACAAGATT
*
22262 TTTGGCAGAAAGACTCTTTGAAATATCTATATTCATCTAACCAAATCTCAACCACAATGGATTAA
583 TTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAACCACAATGGATTAA
* **
22327 AGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATAAATTCTAAAAAAAA
648 AGGATTTCTTGATACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATAAATTC----AAAAA
* * *
22392 AGAAGAAAAAGAAAAATTATATTACAAGAGTCAAAAATCCTTAAATTTTTTT-AGCTTTGAATTA
709 A-AA-AAAAAGAAAAATGATATTACAAGAGTCAAAAATCCTTAAATTTTTTTGA-CATTAAATTA
* * *
22456 TATATTTTTTTCTGAAAATTATGGCAAAGAATTGAGCAAAAAAATTTTCGGGTCAGTTTTTGCAC
771 TATA-TTTTTTATGAAAATTATGGCAAAAAATTAAG-AAAAAAATTTTCGGGTCA--------A-
* **
22521 TGTTTTTGTCGAAATCGTTTAC-CCATCATGTTTTTTT-ACTAAAAACACCTTGCA-GGGCCCCG
825 ---TTTT-T----ATCGTATACACCATCACATTTTTTTGACTAAAAACACCTT-CAGGGGCCCCG
* *
22583 ACTCAGTTTTGCATGATTTTTGCCGTAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATC
881 ACTCAGTTTTGCATGGTTTTTGCCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATC
* *
22648 CCAGCCACATTGGATTTAAGGATTTGT
946 TCAGCCACATTGGATTTAAGGATTTAT
* *
22675 TTTTACGAGCATCTAAATCTTGTTTCGATTTAATAAGAAGTAAATTCGGTAAAAAAAAATGGAAA
1 TTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTC-GT-AAAAAAAATGGAAA
* * * * *
22740 AAAGATATTAGAAACGTGAACAATCATTCAATTTTTTGGCATTGAATTATATA-TTTTTCTGGGC
64 AAAGATATTAGAAACGTGAAAAACCATTCAATTTTTTGGCATTGAAATATACATTTTTTCTGAGC
* * **
22804 ATTGTGTCAAAAAATTGAG-GAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATTG
129 ATTGTGCCAAAAAATTGAGAAAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCA
* **
22868 TGTACTAACCATCACGATTTTTGGCTAAAAACACGTTTTGGAGACCCAGCTCAATTTTGC-ATGA
194 TGTACTAACCATCACGATTTTTAGCTAAAAACACGTTCCGGAGACCCAGCTCAATTTT-CAAT-A
* * * * * *
22932 TTTTTTACT-CAAATACTCCTTG-AAATATTTATATTCATCGAACCAAGTCTCAGCCAGATTGGA
257 ATTTTTACTGCAAAGAC-CCCTGCAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGA
** * **
22995 TATAA-GGATTTGTTTTTACGAACATCTGAATCTTATTTCGATTTAATTAGAAATTAATTC-GGA
321 TATAACAAATTTGTTTTTACGAACATCTGAATCTTATTTCGATGTAATTAGAAATTAATTCAAAA
* *
23058 AAA-A-TGG-AAAAACGATATTAGAAGCGTGAAAAG-CTCGACAA-TGTTTTTGGCATTGAATTA
386 AAAGAGAGGAAAAAACGATATTAGAAGCATGAAAAGCCT-GACAACT-TTTTTGGCATTGAATTA
* * *
23118 TATATTTTTTCTGAATATTTTGTAAAAACATTGTGTAAAAACTTTTCGGGTAAGTTTTTAGCCGA
449 TATATTTTTTCTGAATATTTT-CAAAAA-ATTGAGAAAAAACTTTTCGGGTAAGTTTTTAGCCGA
* * * ** * * * *
23183 AATCGTTTACTAATCATCACGGTTTTTGGTTAAAAACGCGTGTCGTGGTCCAGGCTCAATTTTGC
512 AATCATGTACTAACCATCACGGTTTTAAGCTAAAAACGCGTGTCGGGGCCCAGGCTCAATTTTAC
* * * *
23248 AAGATTTTTGGCAGAAAGACTCCTTGAAATATTTATATTCATCTAACCAAATTTCAGCCACGATG
577 AAGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAACCACAATG
* * *
23313 GATTTAAGGATTTCTTGATATGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGA
642 GATTAAAGGATTTCTTGATACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAAA
*** * * * *
23378 AAAAAAATTTGAAAAATGATATTAGAAGCGTGAAAAATCCTTCAATTTTTTTGACATTAAATTAT
707 AAAAAAAAAAGAAAAATGATATTACAAGAGTCAAAAATCCTTAAATTTTTTTGACATTAAATTAT
** * * *
23443 ATATTTTTTATGAGTATTGTGGCAAAAAATTAAGGAAAAACTTTTCGGGTCAATTTTTATCGTAT
772 ATATTTTTTATGAAAATTATGGCAAAAAATTAAGAAAAAAATTTTCGGGTCAATTTTTATCGTAT
* * * * **
23508 ACACCATCACATTTTTTTGGCTAAAAACGCGTTCAGGGGCCTCGTTTCAGTTTTGCATGGTTTTT
837 ACACCATCACATTTTTTTGACTAAAAACACCTTCAGGGGCCCCGACTCAGTTTTGCATGGTTTTT
* * * *
23573 AG-CATAAAGACTCCTTGAAATATCTTTATTCATCTAATCAAATCTCAACCACATTGTATTTAAG
902 -GCCATAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAG
23637 GATTTAT
966 GATTTAT
* * * *
23644 TTTTACGTGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAAATAT-GAAAA
1 TTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTC-GTAAAAAAAATGGAAAA
*
23707 ACGATATTA-AAAGCGTGAAAA
65 AAGATATTAGAAA-CGTGAAAA
23728 GTACTACAAT
Statistics
Matches: 1705, Mismatches: 243, Indels: 177
0.80 0.11 0.08
Matches are distributed among these distances:
942 25 0.01
943 96 0.06
944 10 0.01
945 38 0.02
946 1 0.00
947 1 0.00
950 7 0.00
951 97 0.06
952 45 0.03
953 17 0.01
954 25 0.01
955 3 0.00
956 58 0.03
957 3 0.00
958 1 0.00
959 2 0.00
960 1 0.00
965 3 0.00
966 20 0.01
967 16 0.01
968 15 0.01
969 142 0.08
970 1 0.00
971 1 0.00
972 4 0.00
974 5 0.00
975 104 0.06
976 1 0.00
977 33 0.02
978 4 0.00
984 18 0.01
985 27 0.02
986 57 0.03
987 77 0.05
988 17 0.01
989 3 0.00
990 64 0.04
991 7 0.00
992 202 0.12
993 4 0.00
994 1 0.00
995 145 0.09
996 58 0.03
997 142 0.08
998 44 0.03
999 53 0.03
1000 4 0.00
1001 1 0.00
1003 1 0.00
1005 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (972 bp):
TTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCGTAAAAAAAATGGAAAAA
AGATATTAGAAACGTGAAAAACCATTCAATTTTTTGGCATTGAAATATACATTTTTTCTGAGCAT
TGTGCCAAAAAATTGAGAAAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAATCATG
TACTAACCATCACGATTTTTAGCTAAAAACACGTTCCGGAGACCCAGCTCAATTTTCAATAATTT
TTACTGCAAAGACCCCTGCAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATATAA
CAAATTTGTTTTTACGAACATCTGAATCTTATTTCGATGTAATTAGAAATTAATTCAAAAAAAGA
GAGGAAAAAACGATATTAGAAGCATGAAAAGCCTGACAACTTTTTTGGCATTGAATTATATATTT
TTTCTGAATATTTTCAAAAAATTGAGAAAAAACTTTTCGGGTAAGTTTTTAGCCGAAATCATGTA
CTAACCATCACGGTTTTAAGCTAAAAACGCGTGTCGGGGCCCAGGCTCAATTTTACAAGATTTTT
GGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAACCACAATGGATTAAAGG
ATTTCTTGATACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAAAAAAAAAAAA
AGAAAAATGATATTACAAGAGTCAAAAATCCTTAAATTTTTTTGACATTAAATTATATATTTTTT
ATGAAAATTATGGCAAAAAATTAAGAAAAAAATTTTCGGGTCAATTTTTATCGTATACACCATCA
CATTTTTTTGACTAAAAACACCTTCAGGGGCCCCGACTCAGTTTTGCATGGTTTTTGCCATAAAG
ACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTAT
Found at i:30293 original size:3 final size:3
Alignment explanation
Indices: 30287--30321 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
30277 TTTTATGTAA
* *
30287 AAG AAG AAG AAG AAG AAG ATG ACG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
30322 AGGGCGAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.63, C:0.03, G:0.31, T:0.03
Consensus pattern (3 bp):
AAG
Done.