Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014083.1 Corchorus capsularis cultivar CVL-1 contig14104, 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: 53195
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:62 original size:32 final size:32
Alignment explanation
Indices: 6--74 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
1 AGCCG
* * *
6 AGCCTCCCCACCGGCGCGGTCTGCCGTGGCGA
1 AGCCGCCCCACCGGCGCGGCCTGCCGTGACGA
*
38 AGCCGCCCCACCGAG-GCGGCCTGCCTTGACGA
1 AGCCGCCCCACCG-GCGCGGCCTGCCGTGACGA
70 AGCCG
1 AGCCG
75 GCGGCCTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 31 0.97
33 1 0.03
ACGTcount: A:0.13, C:0.43, G:0.33, T:0.10
Consensus pattern (32 bp):
AGCCGCCCCACCGGCGCGGCCTGCCGTGACGA
Found at i:178 original size:32 final size:34
Alignment explanation
Indices: 89--178 Score: 139
Period size: 34 Copynumber: 2.7 Consensus size: 34
79 CCTATTCATA
89 GTGAAGCCGCCCTAGTGGGGCGGCCTGCCCAATG
1 GTGAAGCCGCCCTAGTGGGGCGGCCTGCCCAATG
*
123 GTGAAGCCGCCCTAGTGGAGCGGCCTGCCC-ATG
1 GTGAAGCCGCCCTAGTGGGGCGGCCTGCCCAATG
**
156 GT-AAGCCGCCCTCTTGGGGCGGC
1 GTGAAGCCGCCCTAGTGGGGCGGC
179 ACGGGTCATC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 18 0.35
33 5 0.10
34 29 0.56
ACGTcount: A:0.13, C:0.33, G:0.38, T:0.16
Consensus pattern (34 bp):
GTGAAGCCGCCCTAGTGGGGCGGCCTGCCCAATG
Found at i:6491 original size:5 final size:5
Alignment explanation
Indices: 6475--6509 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
6465 TGAATTTAAC
*
6475 AACCA AATCA AACCA AACCA AACCA AACCA AACCA
1 AACCA AACCA AACCA AACCA AACCA AACCA AACCA
6510 CTCAAACACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.60, C:0.37, G:0.00, T:0.03
Consensus pattern (5 bp):
AACCA
Found at i:8462 original size:24 final size:23
Alignment explanation
Indices: 8433--8484 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
8423 GACATATTAG
*
8433 AATTTTTA-AAATATATTCTTTTAC
1 AATTTTTAGAAATA-AAT-TTTTAC
8457 AATTTTTTAGAAATAAATTTTTAC
1 AA-TTTTTAGAAATAAATTTTTAC
8481 AATT
1 AATT
8485 ATTCTACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 2 0.08
24 10 0.40
25 8 0.32
26 5 0.20
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (23 bp):
AATTTTTAGAAATAAATTTTTAC
Found at i:10208 original size:316 final size:319
Alignment explanation
Indices: 9454--10493 Score: 1173
Period size: 316 Copynumber: 3.2 Consensus size: 319
9444 ATATTTTTAA
* * * * *
9454 CAAATTTGGGAAAATGATCTACTAAAATGTTTTATTTTTTTCCAATTTTATTATAAACTTAAGAA
1 CAAATTTGGGAAAAAGATCCACTAAAATGTTTTATTTTTCTCCAATTTTATTTTAAATTTAAGAA
* *
9519 ATTATGTAATTGTTTAACCACCAAAAGTAATAGGAGGGCCGGTCACACGCATCAAATTTTCATAT
66 ATTATGTAATTATTTAACCACC-AAAGTAAGAGGAGGGCCGGTCACACGCATCAAATTTTCAT-T
* * * * *
9584 AAAAAAAATGATACGTGTGGGTTTGAAATGAGCTTAT-TCT-ATATAATCAGTTTGGGCCTTAAA
129 TAAAAAAATGATGCGTGTGGGCTTGAAATGAGGTTATATATAATATAATCAGTTTGGGCCTTAAA
* *
9647 TTCAACAACAAATAAAACTTGAAATTTTAATTTAAAGAAGTTGTGAATTTTTTCACTTCAAAAAA
194 TTCAAAAACAAATAAAACTTGAAA-TTTAATTT-AAGAAGTTGTGAA-TTTTT-AATT-AAAAAA
* * * * *
9712 A-AAGTTG--TG--AAT-TTTTAATTAAAAAATTATTGGTGCGTAACGATCTATCAAAATCTTTT
254 ATTATTTGTTTGAAAATCTTTT--TTAACAAA-T-TT-G-G-GAAACGATCTACCAAAATC-TTT
9771 TTTTTTTGG
311 TTTTTTTGG
* * * * * *
9780 AAAATTTGGGAAAAAGATCGACCAAAATGTTTTATTTTTCTCCAATTGTATTTT-AGTCATAAGA
1 CAAATTTGGGAAAAAGATCCACTAAAATGTTTTATTTTTCTCCAATTTTATTTTAAAT-TTAAGA
* * * *
9844 AATTATGTAATTATTTAACCACCAAAGTAAGAGGAGGGCCGATCACACGAATCAGATCTTCATTT
65 AATTATGTAATTATTTAACCACCAAAGTAAGAGGAGGGCCGGTCACACGCATCAAATTTTCATTT
*** * * *
9909 AAAAAAATGATGCACATGGGCTAGAAATGAGGTTATATATAATATAATAAGTTT-GGCCTTAAGT
130 AAAAAAATGATGCGTGTGGGCTTGAAATGAGGTTATATATAATATAATCAGTTTGGGCCTTAAAT
9973 TCAAAAACAAATAAAACTTGAAATTTAATTT-A-AAGTTGTGAATTTTTAATTAAAAAAATTATT
195 TCAAAAACAAATAAAACTTGAAATTTAATTTAAGAAGTTGTGAATTTTTAATTAAAAAAATTATT
*
10036 TGTTTGAAAATCTTCTTTTAACAAATTTGGGAAACGATTTACCAAAATCTTTTTTTTTTGG
260 TGTTTGAAAATCTT-TTTTAACAAATTTGGGAAACGATCTACCAAAATCTTTTTTTTTTGG
* * * * *
10097 TCAAATTTGGGAAAACGATCCACTATAATG-TTT-TTTTCCTACTATTTTATTTTAAATTTAAGA
1 -CAAATTTGGGAAAAAGATCCACTAAAATGTTTTATTTTTCTCCAATTTTATTTTAAATTTAAGA
** * * * *
10160 AATTATGTAATTATTTAAATACCAAAGTAAGAGAAGGGCTGGTCACACGCATCATATTTTCATAT
65 AATTATGTAATTATTTAACCACCAAAGTAAGAGGAGGGCCGGTCACACGCATCAAATTTTCATTT
* *
10225 AAAAAAATGATGCGTGTAGGCTTGAAATCAGGTTATACTATATAATATAATCAGTTTGGGCCTTA
130 AAAAAAATGATGCGTGTGGGCTTGAAATGAGG-T-TA-TATATAATATAATCAGTTTGGGCCTTA
* *
10290 AATTCAAAAACAAATAAAACTTGAAATTTAATTTAAAGAAGTTGTGAATTTTTAATTTAATAAAT
192 AATTCAAAAACAAATAAAACTTGAAATTTAATTT-AAGAAGTTGTGAATTTTTAATTAAAAAAAT
* * *
10355 TATTGGTTTGAAATTCTTTTTTTAACAAATTTGGGAAAATGATCTACCAAAATC---TTTTTTTG
256 TATTTGTTTGAAAATC-TTTTTTAACAAATTTGGG-AAACGATCTACCAAAATCTTTTTTTTTTG
*
10417 A
319 G
* * *
10418 C-AATTTGGGAAACGTACAG-TCTATTAAAATGTTTTATTTTTCTCCAATTTTATTTTAAACTTA
1 CAAATTTGGGAAA---A-AGATCCACTAAAATGTTTTATTTTTCTCCAATTTTATTTTAAATTTA
10481 AGAAATTATGTAA
62 AGAAATTATGTAA
10494 AAAAAATTTT
Statistics
Matches: 609, Mismatches: 78, Indels: 56
0.82 0.10 0.08
Matches are distributed among these distances:
316 103 0.17
317 18 0.03
318 49 0.08
319 37 0.06
320 47 0.08
321 22 0.04
322 13 0.02
323 69 0.11
324 94 0.15
325 71 0.12
326 86 0.14
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (319 bp):
CAAATTTGGGAAAAAGATCCACTAAAATGTTTTATTTTTCTCCAATTTTATTTTAAATTTAAGAA
ATTATGTAATTATTTAACCACCAAAGTAAGAGGAGGGCCGGTCACACGCATCAAATTTTCATTTA
AAAAAATGATGCGTGTGGGCTTGAAATGAGGTTATATATAATATAATCAGTTTGGGCCTTAAATT
CAAAAACAAATAAAACTTGAAATTTAATTTAAGAAGTTGTGAATTTTTAATTAAAAAAATTATTT
GTTTGAAAATCTTTTTTAACAAATTTGGGAAACGATCTACCAAAATCTTTTTTTTTTGG
Found at i:21803 original size:21 final size:21
Alignment explanation
Indices: 21777--21821 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
21767 TTTCCATTTT
21777 CCAATTACTGTCATAGTCATG
1 CCAATTACTGTCATAGTCATG
*
21798 CCAATTACTGTCATATTCATG
1 CCAATTACTGTCATAGTCATG
21819 CCA
1 CCA
21822 CAGGTCACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (21 bp):
CCAATTACTGTCATAGTCATG
Found at i:25110 original size:29 final size:29
Alignment explanation
Indices: 25068--25125 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
25058 CACAAAACCA
25068 GTATTCCCTTTGGATAGAGCTGGAAATTT
1 GTATTCCCTTTGGATAGAGCTGGAAATTT
25097 GTATTCCCTTTGGATAGAGCTGGAAATTT
1 GTATTCCCTTTGGATAGAGCTGGAAATTT
25126 CAGACTTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (29 bp):
GTATTCCCTTTGGATAGAGCTGGAAATTT
Found at i:32408 original size:25 final size:25
Alignment explanation
Indices: 32379--32437 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
32369 TTCTCTTTGA
32379 TCTTTTTCTTAGAAAATATTCTAGT
1 TCTTTTTCTTAGAAAATATTCTAGT
32404 TCTTTTTCTTAGAAAATATTCTAGT
1 TCTTTTTCTTAGAAAATATTCTAGT
32429 TCTTTTTCT
1 TCTTTTTCT
32438 CTAGTTTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.56
Consensus pattern (25 bp):
TCTTTTTCTTAGAAAATATTCTAGT
Found at i:32538 original size:9 final size:9
Alignment explanation
Indices: 32524--32548 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
32514 TTTCGCTTTC
32524 AAGTTTTGT
1 AAGTTTTGT
32533 AAGTTTTGT
1 AAGTTTTGT
32542 AAGTTTT
1 AAGTTTT
32549 CTTATGCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (9 bp):
AAGTTTTGT
Found at i:37876 original size:46 final size:46
Alignment explanation
Indices: 37809--37942 Score: 268
Period size: 46 Copynumber: 2.9 Consensus size: 46
37799 GTGAAACTGT
37809 TTTAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATATTTGA
1 TTTAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATATTTGA
37855 TTTAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATATTTGA
1 TTTAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATATTTGA
37901 TTTAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATAT
1 TTTAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATAT
37943 CAAGGAAGAC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 88 1.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (46 bp):
TTTAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATATTTGA
Found at i:38978 original size:13 final size:13
Alignment explanation
Indices: 38942--39009 Score: 61
Period size: 13 Copynumber: 5.5 Consensus size: 13
38932 GTTATGACAA
* *
38942 AATACCTTTTGAT
1 AATACCTTATGGT
*
38955 AATA-CTCATGGT
1 AATACCTTATGGT
*
38967 AATACCTTATGGC
1 AATACCTTATGGT
* *
38980 AATA-C-TGTGGA
1 AATACCTTATGGT
38991 AATACCTTATGGT
1 AATACCTTATGGT
39004 AATACC
1 AATACC
39010 CTGTGACAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
11 8 0.19
12 11 0.26
13 24 0.56
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.34
Consensus pattern (13 bp):
AATACCTTATGGT
Found at i:39222 original size:2 final size:2
Alignment explanation
Indices: 39215--39251 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
39205 AGTAACCTTT
*
39215 TA TA TA TA TA TA CA 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 TA TA TA TA T
39252 CGGTTGAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:40120 original size:26 final size:27
Alignment explanation
Indices: 40082--40132 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
40072 GGCAATATAT
*
40082 ACCTTACGACAATTACAGTCTTGCAAA
1 ACCTTACGACAATTACACTCTTGCAAA
*
40109 ACCTTA-GACAATTACCCTCTTGCA
1 ACCTTACGACAATTACACTCTTGCA
40133 CCCTCTGGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.27
Consensus pattern (27 bp):
ACCTTACGACAATTACACTCTTGCAAA
Found at i:40944 original size:2 final size:2
Alignment explanation
Indices: 40937--40968 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40927 TATACCATCA
40937 AT AT AT 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 AT AT AT
40969 GCAATTCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41944 original size:46 final size:46
Alignment explanation
Indices: 41875--42011 Score: 175
Period size: 46 Copynumber: 3.0 Consensus size: 46
41865 TTGCAAGAAG
* * * * *
41875 CTACCGTATAGAGAATTCCTTCTGAAGATGGGTGCTCACATAAGAG
1 CTACCGTATAGAGTATTCTTTCTGAAGAAGTGTGCTCACATAAGAC
* *
41921 TTACCGTATAGAGTATTCTTTCTGAAGAAGTGTGCTCACATAAAAC
1 CTACCGTATAGAGTATTCTTTCTGAAGAAGTGTGCTCACATAAGAC
** * *
41967 CTATTGTATAGAGTATTTTTTCTGCAGAAGTGTGCTCACATAAGA
1 CTACCGTATAGAGTATTCTTTCTGAAGAAGTGTGCTCACATAAGA
42012 TGCATCTCCT
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (46 bp):
CTACCGTATAGAGTATTCTTTCTGAAGAAGTGTGCTCACATAAGAC
Found at i:42213 original size:36 final size:36
Alignment explanation
Indices: 42156--42276 Score: 154
Period size: 36 Copynumber: 3.4 Consensus size: 36
42146 AAGAGGGAGT
* * *
42156 GGCATTATAGCCAAATATTGGGCGAC-TATGGTCAGC
1 GGCATTATAGCCAAATTTTGGGCGACTTA-GGCCATC
* *
42192 GGCTTTATAGCCAATTTTTGGGCGACTTAGGCCATC
1 GGCATTATAGCCAAATTTTGGGCGACTTAGGCCATC
* * *
42228 GACATTATAGCCAAGTTTTAGGCGACTTAGGCCATC
1 GGCATTATAGCCAAATTTTGGGCGACTTAGGCCATC
42264 GGCATTATAGCCA
1 GGCATTATAGCCA
42277 GAAACAGAGC
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
36 72 0.97
37 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (36 bp):
GGCATTATAGCCAAATTTTGGGCGACTTAGGCCATC
Found at i:42906 original size:17 final size:17
Alignment explanation
Indices: 42884--43007 Score: 149
Period size: 17 Copynumber: 6.9 Consensus size: 17
42874 GCGTCAGCAT
*
42884 CATGTTGGAAACGCAAC
1 CATGTTGGAAGCGCAAC
* *
42901 CATGTTGGAAGCTTCAGCAT
1 CATGTTGGAAGC-GCA--AC
42921 CATGTTGGAAAGCGCAAC
1 CATGTTGG-AAGCGCAAC
*
42939 CATGTTGGAAGCGTCAGCAT
1 CATGTTGGAAGCG-CA--AC
42959 CATGTTGGAAGCGCAAC
1 CATGTTGGAAGCGCAAC
42976 CATGTTGGAAGCGCAAC
1 CATGTTGGAAGCGCAAC
42993 CATGTTGGAAGCGCA
1 CATGTTGGAAGCGCA
43008 TATGAATTTT
Statistics
Matches: 93, Mismatches: 7, Indels: 14
0.82 0.06 0.12
Matches are distributed among these distances:
17 49 0.53
18 13 0.14
19 2 0.02
20 25 0.27
21 4 0.04
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (17 bp):
CATGTTGGAAGCGCAAC
Found at i:42946 original size:38 final size:38
Alignment explanation
Indices: 42867--43007 Score: 222
Period size: 37 Copynumber: 3.9 Consensus size: 38
42857 AATTCTCTCC
42867 GTTGGAAGCGTCAGCATCATGTTGGAAA-CGCAACCAT
1 GTTGGAAGCGTCAGCATCATGTTGGAAAGCGCAACCAT
*
42904 GTTGGAAGCTTCAGCATCATGTTGGAAAGCGCAACCAT
1 GTTGGAAGCGTCAGCATCATGTTGGAAAGCGCAACCAT
42942 GTTGGAAGCGTCAGCATCATGTTGG-AAGCGCAACCAT
1 GTTGGAAGCGTCAGCATCATGTTGGAAAGCGCAACCAT
*
42979 GTTGGAAGCG-CA--ACCATGTTGG-AAGCGCA
1 GTTGGAAGCGTCAGCATCATGTTGGAAAGCGCA
43008 TATGAATTTT
Statistics
Matches: 100, Mismatches: 3, Indels: 5
0.93 0.03 0.05
Matches are distributed among these distances:
34 16 0.16
36 2 0.02
37 49 0.49
38 33 0.33
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.21
Consensus pattern (38 bp):
GTTGGAAGCGTCAGCATCATGTTGGAAAGCGCAACCAT
Found at i:43146 original size:90 final size:91
Alignment explanation
Indices: 42993--43185 Score: 275
Period size: 92 Copynumber: 2.1 Consensus size: 91
42983 GAAGCGCAAC
* *
42993 CATGTTGGAAGCGCATATGAATTTTATCGCTGGAAGCGCCACCCTCATGTTGGAAGAGTGTATAA
1 CATGTTGGAAGCGCATATGAATTTTATCGCTGGAAGCGCCACCATCATGTTGGAAGAGCGTATAA
43058 A-TTTTGTGATTGGAGGCGCCACAAT
66 ATTTTTGTGATTGGAGGCGCCACAAT
* * *
43083 CATGTTGGAAGCGCATAT-AGA-TTTATTGTTGGAAGCGGCACCATCATGTTGGAAAGAGCGTAT
1 CATGTTGGAAGCGCATATGA-ATTTTATCGCTGGAAGCGCCACCATCATGTTGG-AAGAGCGTAT
* *
43146 AAATTTTTTGTGATTGGAGGCGTCACCAT
64 AAA-TTTTTGTGATTGGAGGCGCCACAAT
43175 CATGTTGGAAG
1 CATGTTGGAAG
43186 TGAGTACAGG
Statistics
Matches: 92, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
89 28 0.30
90 31 0.34
92 33 0.36
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (91 bp):
CATGTTGGAAGCGCATATGAATTTTATCGCTGGAAGCGCCACCATCATGTTGGAAGAGCGTATAA
ATTTTTGTGATTGGAGGCGCCACAAT
Found at i:43299 original size:47 final size:45
Alignment explanation
Indices: 42978--43303 Score: 230
Period size: 45 Copynumber: 7.2 Consensus size: 45
42968 AGCGCAACCA
* * * *
42978 TGTTGGAAGCG-CA--ACCATGTTGGAAGCGCATATGAATTTTAT
1 TGTTGGAAGCGACACCATCATGTTGGAAGAGCGTATAAATTTTAT
* * * * * *
43020 CGCTGGAAGCGCCACCCTCATGTTGGAAGAGTGTATAAATTTT-G
1 TGTTGGAAGCGACACCATCATGTTGGAAGAGCGTATAAATTTTAT
* * * * * *
43064 TGATTGGAGGCGCCACAATCATGTTGGAAGCGCATATAGA-TTTAT
1 TG-TTGGAAGCGACACCATCATGTTGGAAGAGCGTATAAATTTTAT
* *
43109 TGTTGGAAGCGGCACCATCATGTTGGAAAGAGCGTATAAATTTTTT
1 TGTTGGAAGCGACACCATCATGTTGG-AAGAGCGTATAAATTTTAT
* * * * * ** *
43155 GTGATTGGAGGCGTCACCATCATGTTGGAAGTGAGTACAGGTTTTGT
1 -TG-TTGGAAGCGACACCATCATGTTGGAAGAGCGTATAAATTTTAT
* * * * * * *
43202 CTGTTGGAAGTGCCACCCCACCGTATTGGAAGCGCATATAAATTTTAT
1 -TGTTGGAA--GCGACACCATCATGTTGGAAGAGCGTATAAATTTTAT
*
43250 TGTTGGAAGCGACACCATCATGTTGGAAAGAACGTATAAATTTTCAT
1 TGTTGGAAGCGACACCATCATGTTGG-AAGAGCGTATAAATTTT-AT
43297 TGTTGGA
1 TGTTGGA
43304 GGAAGGTGAT
Statistics
Matches: 214, Mismatches: 57, Indels: 21
0.73 0.20 0.07
Matches are distributed among these distances:
42 9 0.04
43 2 0.01
44 25 0.12
45 75 0.35
46 23 0.11
47 34 0.16
48 46 0.21
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (45 bp):
TGTTGGAAGCGACACCATCATGTTGGAAGAGCGTATAAATTTTAT
Found at i:43876 original size:65 final size:65
Alignment explanation
Indices: 43790--43950 Score: 199
Period size: 65 Copynumber: 2.6 Consensus size: 65
43780 AGAATGAATA
* * *
43790 TAGGCGTTGTATGCCCTTTTTTAAGCTGCATAGGCTATAGTAGGCGTTGCAAAGCTGCATAGACT
1 TAGGCGTAGTAAG-CCTTTTTTAAGCTGCATAGACTATAGTAGGCGTTGCAAAGCTGCATAGACT
43855 G
65 G
* * * *
43856 TAGGCGTAGTAAGCCTTTTTTAAACTGCATAGACTGTAGTAGGCGTTGTAAAGCTGCATAGGCTG
1 TAGGCGTAGTAAGCCTTTTTTAAGCTGCATAGACTATAGTAGGCGTTGCAAAGCTGCATAGACTG
*
43921 -A----TAGTAAGCCTTTTTTAAGTTGCAT-GACTA
1 TAGGCGTAGTAAGCCTTTTTTAAGCTGCATAGACTA
43951 GAAGCGTCAA
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
59 4 0.05
60 22 0.26
64 1 0.01
65 47 0.55
66 11 0.13
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (65 bp):
TAGGCGTAGTAAGCCTTTTTTAAGCTGCATAGACTATAGTAGGCGTTGCAAAGCTGCATAGACTG
Found at i:43895 original size:30 final size:31
Alignment explanation
Indices: 43861--43938 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 31
43851 GACTGTAGGC
43861 GTAGTAAGCCTTTTTTAAA-CTGCATAGACT
1 GTAGTAAGCCTTTTTTAAAGCTGCATAGACT
* * * *
43891 GTAGT-AGGC-GTTGTAAAGCTGCATAGGCT
1 GTAGTAAGCCTTTTTTAAAGCTGCATAGACT
43920 GATAGTAAGCCTTTTTTAA
1 G-TAGTAAGCCTTTTTTAA
43939 GTTGCATGAC
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
28 6 0.16
29 14 0.38
30 9 0.24
31 3 0.08
32 5 0.14
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (31 bp):
GTAGTAAGCCTTTTTTAAAGCTGCATAGACT
Found at i:43914 original size:29 final size:29
Alignment explanation
Indices: 43812--43926 Score: 88
Period size: 29 Copynumber: 3.7 Consensus size: 29
43802 GCCCTTTTTT
* * *
43812 AAGCTGCATAGGCTATAGTAGGCGTTGCA
1 AAGCTGCATAGACTGTAGTAGGCGTTGTA
* *
43841 AAGCTGCATAGACTGTAGGCGTAGTAAGCCTTTTTTA
1 AAGCTGCATAGACTGTA---GTAG---G-C-GTTGTA
43878 AA-CTGCATAGACTGTAGTAGGCGTTGTA
1 AAGCTGCATAGACTGTAGTAGGCGTTGTA
*
43906 AAGCTGCATAGGCTGATAGTA
1 AAGCTGCATAGACTG-TAGTA
43927 AGCCTTTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
28 6 0.09
29 27 0.40
30 6 0.09
32 4 0.06
33 4 0.06
35 1 0.01
36 15 0.22
37 5 0.07
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (29 bp):
AAGCTGCATAGACTGTAGTAGGCGTTGTA
Found at i:44150 original size:110 final size:111
Alignment explanation
Indices: 43957--44193 Score: 342
Period size: 110 Copynumber: 2.2 Consensus size: 111
43947 ACTAGAAGCG
* * *
43957 TCAACAAGGAGGGGCACTCCTGGAGGTGCAATCAGTGCAACACTCCTAAGGGTGCACCTGCTCCC
1 TCAACAAGGAAGGGCACTCCTGGAGGTGCAATCAGTGCAACACTCCTAAGGGTGCACCTACTCCA
44022 AGTCAAAATATAATTTTTTTTAATGGGCTACATAGGCCAGAAT-AA
66 AGTCAAAATATAATTTTTTTTAATGGGCTACATAGGCCAGAATCAA
* *
44067 TCAACAAGGAAGGGCACTCCTGGAGGTGCAA-CTAGTGCAGCACTCCTATGGGTGCA-CTCACTC
1 TCAACAAGGAAGGGCACTCCTGGAGGTGCAATC-AGTGCAACACTCCTAAGGGTGCACCT-ACTC
*
44130 CAAGTCAAAATATAGA-TTTTTTTAATGGGCTACATAGGGCAGAATCAA
64 CAAGTCAAAATATA-ATTTTTTTTAATGGGCTACATAGGCCAGAATCAA
*
44178 -CAA-AAGGAAAGGCACT
1 TCAACAAGGAAGGGCACT
44194 TTTGGCTGCA
Statistics
Matches: 116, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
109 15 0.13
110 98 0.84
111 3 0.03
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.22
Consensus pattern (111 bp):
TCAACAAGGAAGGGCACTCCTGGAGGTGCAATCAGTGCAACACTCCTAAGGGTGCACCTACTCCA
AGTCAAAATATAATTTTTTTTAATGGGCTACATAGGCCAGAATCAA
Found at i:44597 original size:18 final size:18
Alignment explanation
Indices: 44570--44605 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
44560 CCATCATTTT
*
44570 TGTCAGCAGCTCCTGATC
1 TGTCAACAGCTCCTGATC
*
44588 TGTCAACAGCTTCTGATC
1 TGTCAACAGCTCCTGATC
44606 ATGTGCAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.31
Consensus pattern (18 bp):
TGTCAACAGCTCCTGATC
Found at i:45183 original size:46 final size:46
Alignment explanation
Indices: 45116--45203 Score: 176
Period size: 46 Copynumber: 1.9 Consensus size: 46
45106 GTGAAACTGT
45116 TTTAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATATTTGA
1 TTTAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATATTTGA
45162 TTTAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATAT
1 TTTAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATAT
45204 CAAGGAAGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (46 bp):
TTTAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATATTTGA
Done.