Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007326.1 Corchorus capsularis cultivar CVL-1 contig07347, 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: 74140
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:1777 original size:114 final size:114
Alignment explanation
Indices: 1577--1804 Score: 438
Period size: 114 Copynumber: 2.0 Consensus size: 114
1567 TTAACTTCAT
1577 TAATACTGAGTTTGAACAAACCATCAAGGGTATACCCCTTGCCAACAAAGACACAATGCTTGGTG
1 TAATACTGAGTTTGAACAAACCATCAAGGGTATACCCCTTGCCAACAAAGACACAATGCTTGGTG
*
1642 ATTACTACTTTATCAGATTCTAAAACAATCTTAAAGCCTCTTTTAACAA
66 ATTACTACCTTATCAGATTCTAAAACAATCTTAAAGCCTCTTTTAACAA
*
1691 TAATACTGAGTTTGAACAAACCATCAAGGGTATACCTCTTGCCAACAAAGACACAATGCTTGGTG
1 TAATACTGAGTTTGAACAAACCATCAAGGGTATACCCCTTGCCAACAAAGACACAATGCTTGGTG
1756 ATTACTACCTTATCAGATTCTAAAACAATCTTAAAGCCTCTTTTAACAA
66 ATTACTACCTTATCAGATTCTAAAACAATCTTAAAGCCTCTTTTAACAA
1805 GTGAGGAGCA
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 112 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (114 bp):
TAATACTGAGTTTGAACAAACCATCAAGGGTATACCCCTTGCCAACAAAGACACAATGCTTGGTG
ATTACTACCTTATCAGATTCTAAAACAATCTTAAAGCCTCTTTTAACAA
Found at i:3370 original size:25 final size:25
Alignment explanation
Indices: 3342--3391 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
3332 CACATGGTAA
* *
3342 AAAACGAATTTATTGATTAAATTCC
1 AAAACGAATTTATTAAATAAATTCC
*
3367 AAAATGAATTTATTAAATAAATTCC
1 AAAACGAATTTATTAAATAAATTCC
3392 TATAGGCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (25 bp):
AAAACGAATTTATTAAATAAATTCC
Found at i:12525 original size:130 final size:131
Alignment explanation
Indices: 12335--12596 Score: 395
Period size: 130 Copynumber: 2.0 Consensus size: 131
12325 CATTGTTTAA
* * *
12335 ACTTTTATAATTTTACTCAATTAAAAACTTTATTTTTATTTAATTAAATCTAATATCTTTATAAT
1 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAC
* * *
12400 TATTTAATTTTTACCATTTTACTATTTTTAATT-AAAAA-TT-TATATATTATAATTTTTTAAAT
66 TATTTAATTTTTACCATTTTACTA-ATTTAATTAAAAAACTTAGATATATTATAATTTTTAAAAT
12462 AT
130 AT
* *
12464 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCTTTATAC
1 ACTTTTATAATTTTACTCAACTAAAAACTCTA-TTTTTATTTAATTAAATCTAATATCTTTATAA
* *
12529 CTATTTTATTTTTATCATTTTACTAATTTAATTAAAAAACTTAGATATATTATAATTTTTAAAAT
65 CTATTTAATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTATAATTTTTAAAAT
12594 AT
130 AT
12596 A
1 A
12597 TTTCTTAAAT
Statistics
Matches: 119, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
129 36 0.30
130 58 0.49
131 2 0.02
132 23 0.19
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.53
Consensus pattern (131 bp):
ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAAC
TATTTAATTTTTACCATTTTACTAATTTAATTAAAAAACTTAGATATATTATAATTTTTAAAATA
T
Found at i:13974 original size:37 final size:37
Alignment explanation
Indices: 13924--13998 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
13914 TGCAACACAC
13924 ACGGAAGTGAAGACTAATATAATTAAAACCTTAATTG
1 ACGGAAGTGAAGACTAATATAATTAAAACCTTAATTG
*
13961 ACGGAAGTGAAGACTAGTATAATTAAAACCTTAATTG
1 ACGGAAGTGAAGACTAATATAATTAAAACCTTAATTG
13998 A
1 A
13999 TTAATATTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.27
Consensus pattern (37 bp):
ACGGAAGTGAAGACTAATATAATTAAAACCTTAATTG
Found at i:14286 original size:55 final size:55
Alignment explanation
Indices: 14202--14309 Score: 216
Period size: 55 Copynumber: 2.0 Consensus size: 55
14192 CCTCTATTAC
14202 TAAAATTGTTATATTACTTGACATCAAGTTCTAAGTAGAGAGATTAATTGACAGT
1 TAAAATTGTTATATTACTTGACATCAAGTTCTAAGTAGAGAGATTAATTGACAGT
14257 TAAAATTGTTATATTACTTGACATCAAGTTCTAAGTAGAGAGATTAATTGACA
1 TAAAATTGTTATATTACTTGACATCAAGTTCTAAGTAGAGAGATTAATTGACA
14310 TTTGTAGTAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (55 bp):
TAAAATTGTTATATTACTTGACATCAAGTTCTAAGTAGAGAGATTAATTGACAGT
Found at i:14308 original size:30 final size:30
Alignment explanation
Indices: 14214--14310 Score: 87
Period size: 30 Copynumber: 3.4 Consensus size: 30
14204 AAATTGTTAT
*
14214 ATTACTTGACATCAAGTTCTAAGTAGAGAG
1 ATTAATTGACATCAAGTTCTAAGTAGAGAG
* * * ** *
14244 ATTAATTG--A-C-AGTT-AAAATTGTTAT
1 ATTAATTGACATCAAGTTCTAAGTAGAGAG
*
14269 ATTACTTGACATCAAGTTCTAAGTAGAGAG
1 ATTAATTGACATCAAGTTCTAAGTAGAGAG
14299 ATTAATTGACAT
1 ATTAATTGACAT
14311 TTGTAGTAGT
Statistics
Matches: 47, Mismatches: 15, Indels: 10
0.65 0.21 0.14
Matches are distributed among these distances:
25 12 0.26
26 4 0.09
27 2 0.04
28 2 0.04
29 4 0.09
30 23 0.49
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (30 bp):
ATTAATTGACATCAAGTTCTAAGTAGAGAG
Found at i:16984 original size:2 final size:2
Alignment explanation
Indices: 16979--17012 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
16969 GGTGTGTGTG
16979 TA TA TA CTA 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 TA TA T
17013 TATTGTACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18051 original size:16 final size:16
Alignment explanation
Indices: 18030--18083 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
18020 TGACCAAAAT
*
18030 TGACCCGAAACCCGTA
1 TGACCCGAAACCCGAA
*
18046 TGACCCGAGACCCGAAA
1 TGACCCGAAACCCG-AA
*
18063 TAACCCGAAACCCGAA
1 TGACCCGAAACCCGAA
18079 TGACC
1 TGACC
18084 TGAGAAGACT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 19 0.59
17 13 0.41
ACGTcount: A:0.35, C:0.37, G:0.19, T:0.09
Consensus pattern (16 bp):
TGACCCGAAACCCGAA
Found at i:25672 original size:75 final size:74
Alignment explanation
Indices: 25424--25997 Score: 697
Period size: 75 Copynumber: 7.9 Consensus size: 74
25414 TGCAAATTCC
* *
25424 AACTCTAAGCGAGGTCGAGCGTCCAAGCAGACGCCACCCGCAGACGGGTGAGCGCCTAGACTAGC
1 AACTCTAAGCGAGGTCGAGCGTCCAAGCAGACG-CACCCGCAGACGGCTGAGCGCCTAGACTGGC
*
25489 GCCCCCGTAT
65 GCCCTCGTAT
*
25499 AACTCTAAGCGAGGTCGAGCGTCCAAGCA-A---A--CGC-CACGGCTGAGCGCCTAGACTGGCG
1 AACTCTAAGCGAGGTCGAGCGTCCAAGCAGACGCACCCGCAGACGGCTGAGCGCCTAGACTGGCG
25557 CCC-CGTTAT
66 CCCTCG-TAT
* *
25566 AACTCTAAGCGAGGACGAGCG-CCTAAGCAGACGCCACCCGCAGACGGCTGAGCGCCTAGACTGA
1 AACTCTAAGCGAGGTCGAGCGTCC-AAGCAGACG-CACCCGCAGACGGCTGAGCGCCTAGACTGG
25630 CGCCCTCGTAT
64 CGCCCTCGTAT
* *
25641 AACTCTAAGCGAGGTCGAACGTCCAAACAGACG----C-C--ACGGCTGAGCGCCTAGACTGGCG
1 AACTCTAAGCGAGGTCGAGCGTCCAAGCAGACGCACCCGCAGACGGCTGAGCGCCTAGACTGGCG
25699 CCC-CGTTAT
66 CCCTCG-TAT
* *
25708 AACTCTAAGCGAGGACGAGCG-CCTAAGCAGACGCACCCGCAGACGGCTGAGCGCCTAGACT-GA
1 AACTCTAAGCGAGGTCGAGCGTCC-AAGCAGACGCACCCGCAGACGGCTGAGCGCCTAGACTGGC
25771 GCCCTCGTAT
65 GCCCTCGTAT
* * *
25781 AACTCTAAGCGAGGTCGAACGTCCAAACAGACGCACCCGCAGACGGCCGAGCGCCTAGACTGAGC
1 AACTCTAAGCGAGGTCGAGCGTCCAAGCAGACGCACCCGCAGACGGCTGAGCGCCTAGACTG-GC
25846 -CCCTCGTAT
65 GCCCTCGTAT
* * * *
25855 AACTCTAGGCGAGGTCGAGCGTCTGAGGC-GACGCCACCCGCAGACGGCTGAGCGCATAGACTGG
1 AACTCTAAGCGAGGTCGAGCGTC-CAAGCAGACG-CACCCGCAGACGGCTGAGCGCCTAGACTGG
*
25919 CGCCCCCGTAT
64 CGCCCTCGTAT
* * * *
25930 AACTCTCAGCAAGGTCGAGCGTCCAAGC-GAACGTCACCCGCGGACAGCTGAGCGCCTAGACTGG
1 AACTCTAAGCGAGGTCGAGCGTCCAAGCAG-ACG-CACCCGCAGACGGCTGAGCGCCTAGACTGG
25994 CGCC
64 CGCC
25998 ATGTCAAATC
Statistics
Matches: 434, Mismatches: 36, Indels: 58
0.82 0.07 0.11
Matches are distributed among these distances:
66 8 0.02
67 107 0.25
68 4 0.01
69 1 0.00
70 2 0.00
71 1 0.00
72 2 0.00
73 62 0.14
74 67 0.15
75 176 0.41
76 4 0.01
ACGTcount: A:0.24, C:0.34, G:0.29, T:0.13
Consensus pattern (74 bp):
AACTCTAAGCGAGGTCGAGCGTCCAAGCAGACGCACCCGCAGACGGCTGAGCGCCTAGACTGGCG
CCCTCGTAT
Found at i:25680 original size:142 final size:142
Alignment explanation
Indices: 25424--25955 Score: 754
Period size: 142 Copynumber: 3.7 Consensus size: 142
25414 TGCAAATTCC
* *
25424 AACTCTAAGCGAGGTCGAGCGTCC-AAGCAGACGCCACCCGCAGACGGGTGAGCGCCTAGACT-A
1 AACTCTAAGCGAGGACGAGCG-CCTAAGCAGACGCCACCCGCAGACGGCTGAGCGCCTAGACTGA
* * *
25487 GCGCCCCCGTATAACTCTAAGCGAGGTCGAGCGTCCAAGCAAACGCCACGGCTGAGCGCCTAGAC
65 -CGCCCCCGTATAACTCTAAGCGAGGTCGAACGTCCAAACAGACGCCACGGCTGAGCGCCTAGAC
25552 TGGCGCCCCGTTAT
129 TGGCGCCCCGTTAT
25566 AACTCTAAGCGAGGACGAGCGCCTAAGCAGACGCCACCCGCAGACGGCTGAGCGCCTAGACTGAC
1 AACTCTAAGCGAGGACGAGCGCCTAAGCAGACGCCACCCGCAGACGGCTGAGCGCCTAGACTGAC
*
25631 GCCCTCGTATAACTCTAAGCGAGGTCGAACGTCCAAACAGACGCCACGGCTGAGCGCCTAGACTG
66 GCCCCCGTATAACTCTAAGCGAGGTCGAACGTCCAAACAGACGCCACGGCTGAGCGCCTAGACTG
25696 GCGCCCCGTTAT
131 GCGCCCCGTTAT
25708 AACTCTAAGCGAGGACGAGCGCCTAAGCAGACG-CACCCGCAGACGGCTGAGCGCCTAGACTGA-
1 AACTCTAAGCGAGGACGAGCGCCTAAGCAGACGCCACCCGCAGACGGCTGAGCGCCTAGACTGAC
* *
25771 GCCCTCGTATAACTCTAAGCGAGGTCGAACGTCCAAACAGACGCACCCGCAGACGGCCGAGCGCC
66 GCCCCCGTATAACTCTAAGCGAGGTCGAACGTCCAAACAGACG----C-C--ACGGCTGAGCGCC
25836 TAGACTGAGC-CCCTCG-TAT
124 TAGACTG-GCGCCC-CGTTAT
* * * * * *
25855 AACTCTAGGCGAGGTCGAGCGTCTGAGGC-GACGCCACCCGCAGACGGCTGAGCGCATAGACTGG
1 AACTCTAAGCGAGGACGAGCGCCT-AAGCAGACGCCACCCGCAGACGGCTGAGCGCCTAGACTGA
* * *
25919 CGCCCCCGTATAACTCTCAGCAAGGTCGAGCGTCCAA
65 CGCCCCCGTATAACTCTAAGCGAGGTCGAACGTCCAA
25956 GCGAACGTCA
Statistics
Matches: 359, Mismatches: 17, Indels: 21
0.90 0.04 0.05
Matches are distributed among these distances:
140 43 0.12
141 32 0.09
142 164 0.46
143 1 0.00
144 1 0.00
145 1 0.00
147 50 0.14
148 35 0.10
149 32 0.09
ACGTcount: A:0.25, C:0.34, G:0.28, T:0.13
Consensus pattern (142 bp):
AACTCTAAGCGAGGACGAGCGCCTAAGCAGACGCCACCCGCAGACGGCTGAGCGCCTAGACTGAC
GCCCCCGTATAACTCTAAGCGAGGTCGAACGTCCAAACAGACGCCACGGCTGAGCGCCTAGACTG
GCGCCCCGTTAT
Found at i:29084 original size:21 final size:22
Alignment explanation
Indices: 29058--29103 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
29048 TCACAGAAGG
*
29058 AACACTTAAACCAA-AAATCAA
1 AACACTTAAACCAACAAACCAA
*
29079 AACACTTAATCCAACAAACCAA
1 AACACTTAAACCAACAAACCAA
29101 AAC
1 AAC
29104 CCCCAGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.13
Consensus pattern (22 bp):
AACACTTAAACCAACAAACCAA
Found at i:29727 original size:9 final size:9
Alignment explanation
Indices: 29713--29742 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
29703 CCAAATTTCA
29713 AAAAAAATC
1 AAAAAAATC
29722 AAAAAAATC
1 AAAAAAATC
*
29731 AGAAAAATC
1 AAAAAAATC
29740 AAA
1 AAA
29743 CATCAACCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.77, C:0.10, G:0.03, T:0.10
Consensus pattern (9 bp):
AAAAAAATC
Found at i:30922 original size:29 final size:29
Alignment explanation
Indices: 30871--30933 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
30861 GCAAAACATC
*** *
30871 CCAAAATTGAAGTTCAGGGGGTAAAATGT
1 CCAAAATTGAAGTTCAAAAGGTAAAACGT
*
30900 CCAAAATTGAAGTTGAAAAGGTAAAACGT
1 CCAAAATTGAAGTTCAAAAGGTAAAACGT
30929 CCAAA
1 CCAAA
30934 CGCTACAAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (29 bp):
CCAAAATTGAAGTTCAAAAGGTAAAACGT
Found at i:30990 original size:3 final size:3
Alignment explanation
Indices: 30982--31020 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
30972 ATACTTTGTA
30982 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
31021 AAATAAAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:34832 original size:16 final size:16
Alignment explanation
Indices: 34783--34838 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
34773 TGGTCACTTT
* *
34783 GGGTTCTGGTATTTTT
1 GGGTTCGGGTATTTTC
*
34799 GGGCTT-GGGT-TATGTC
1 GGG-TTCGGGTAT-TTTC
34815 GGGTTCGGGTATTTTC
1 GGGTTCGGGTATTTTC
34831 GGGTTCGG
1 GGGTTCGG
34839 CCTCGGGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 3 0.09
16 26 0.81
17 3 0.09
ACGTcount: A:0.05, C:0.11, G:0.41, T:0.43
Consensus pattern (16 bp):
GGGTTCGGGTATTTTC
Found at i:44583 original size:15 final size:17
Alignment explanation
Indices: 44565--44603 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
44555 TTAAAAAAAA
44565 AAAAAGGAAA-AGAAG-
1 AAAAAGGAAACAGAAGC
*
44580 AAAAAGGAAACAGAGGC
1 AAAAAGGAAACAGAAGC
44597 AAAAAGG
1 AAAAAGG
44604 GAAGACCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 4 0.19
17 7 0.33
ACGTcount: A:0.67, C:0.05, G:0.28, T:0.00
Consensus pattern (17 bp):
AAAAAGGAAACAGAAGC
Found at i:46420 original size:155 final size:155
Alignment explanation
Indices: 46149--46837 Score: 795
Period size: 156 Copynumber: 4.4 Consensus size: 155
46139 CTTGGTGAAT
* * * * *
46149 TTTCATCTCAAACAGACTTAAGATGAAAAACTTATGCAAGTTTTTCAATTAAGGACAGTTTGGGG
1 TTTCATCTCAAACAGGCTTAAAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGG
* * *
46214 TGAGAAACC-ACTTCACCATGATAGG-GAGTTCGGTTTTACTTAGAATTTTTTCCATAAG-TTTG
66 TGAGAAACCAAGTTCACCATCA-AGGAGAGTTCGGTTTTACTTAGAATTTTTTCCAT-AGTTTTA
* *
46276 TGGAGATAATCTAAGTCTCTTGGCCAAA
129 TGGAGATAATCTAAGTCTCGTGG-AAAA
* *
46304 TTTCATCTCAAACAGGCTTAAAATGAAAAACTTATGCAAGTTTTTCAATTAAGGACAGTTTGAGG
1 TTTCATCTCAAACAGGCTTAAAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGG
** * * * *
46369 TGAGAAGTC-AGTTCACTATCAAGGGGATTTCGGTTTTACTTATAATTTTTTCCATAGTTTTATG
66 TGAGAAACCAAGTTCACCATCAAGGAGAGTTCGGTTTTACTTAGAATTTTTTCCATAGTTTTATG
*
46433 GAGATAATCTAAGCCTACTGGTGGAAAA
131 GAGATAATCTAAG--T-CTCGTGGAAAA
* ** ** * * * *
46461 --TCAGC-CTTATTGGACTTAGAATGAAAAACTTATGGTAGTTTTTCATTTAAGGACAATTTGGG
1 TTTCATCTCAAACAGG-CTTAAAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAG
* * * *
46523 GAGAGAAACCAAGTTCACCATCAAGGAAAGCTCGGTTTTACTTAGAATTGTTTCCATAGTTTTAT
65 GTGAGAAACCAAGTTCACCATCAAGGAGAGTTCGGTTTTACTTAGAATTTTTTCCATAGTTTTAT
* *
46588 GGATATAATCTAAGTCCCGTGGCAAAA
130 GGAGATAATCTAAGTCTCGTGG-AAAA
* * * *
46615 TTTCATCTCAATCAGACTTAGAATGAAAAACTTATACTAGTTTTTCATTTAAGGACAGTTT-AGG
1 TTTCATCTCAAACAGGCTTAAAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGA-G
* * *
46679 GAGAGAAACCAAGTTCACCATCAAGGAGAGCTT-GGTTTTACTTATAATTTTTTCCATAGTCTTA
65 GTGAGAAACCAAGTTCACCATCAAGGAGAG-TTCGGTTTTACTTAGAATTTTTTCCATAGTTTTA
**
46743 TGGAGATAGCCTAAGTCTCGTGGAAAA
129 TGGAGATAATCTAAGTCTCGTGGAAAA
* *
46770 GTTTCATCTTAATCAGGC-TAAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGA
1 -TTTCATCTCAAACAGGCTTAA-AATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGA
46834 GGTG
64 GGTG
46838 TGAAGTCTAG
Statistics
Matches: 455, Mismatches: 63, Indels: 31
0.83 0.11 0.06
Matches are distributed among these distances:
153 5 0.01
154 14 0.03
155 183 0.40
156 240 0.53
157 8 0.02
158 5 0.01
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (155 bp):
TTTCATCTCAAACAGGCTTAAAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGG
TGAGAAACCAAGTTCACCATCAAGGAGAGTTCGGTTTTACTTAGAATTTTTTCCATAGTTTTATG
GAGATAATCTAAGTCTCGTGGAAAA
Found at i:47196 original size:17 final size:17
Alignment explanation
Indices: 47174--47216 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
47164 GATATAGTAG
47174 ATGTTATCC-AGTACATC
1 ATGTTA-CCTAGTACATC
*
47191 ATGTTACCTAGTACCTC
1 ATGTTACCTAGTACATC
*
47208 ATGCTACCT
1 ATGTTACCT
47217 GTTACCATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.35
Consensus pattern (17 bp):
ATGTTACCTAGTACATC
Found at i:50519 original size:72 final size:72
Alignment explanation
Indices: 50402--50552 Score: 230
Period size: 72 Copynumber: 2.1 Consensus size: 72
50392 ACTGTCTCTC
** * **
50402 TCATACGTTTTTCCTAAATTGAGTTTGTTTCATGTTTATGCTTCTCATGGTTGTCTCAGTAAACA
1 TCATACGTTTTTCCTAAAACGAGTTTGTTTCATGTTTAAGCTTCTCAAAGTTGTCTCAGTAAACA
50467 CCTGTAT
66 CCTGTAT
* *
50474 TCATACGTTTTTCCTAAAACGAGTTTGTTTCGTGTTTAAGCTTCTCAAAGTTGTCTCGGTAAACA
1 TCATACGTTTTTCCTAAAACGAGTTTGTTTCATGTTTAAGCTTCTCAAAGTTGTCTCAGTAAACA
50539 CCTGTAT
66 CCTGTAT
50546 TCGATAC
1 TC-ATAC
50553 TAAACTAAGC
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 67 0.94
73 4 0.06
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (72 bp):
TCATACGTTTTTCCTAAAACGAGTTTGTTTCATGTTTAAGCTTCTCAAAGTTGTCTCAGTAAACA
CCTGTAT
Found at i:53596 original size:29 final size:28
Alignment explanation
Indices: 53560--53640 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 28
53550 TCTCGTTTTT
53560 AAAAGTTAAGGGGCCAATTTGTCCCCAAA
1 AAAAGTTAAGGGGCCAATTTGT-CCCAAA
*
53589 AAAAGTTAAGGGACCAATTTGTCCCAAA
1 AAAAGTTAAGGGGCCAATTTGTCCCAAA
*
53617 ATGAATAGTTAAGGGGCTAATTTG
1 A--AA-AGTTAAGGGGCCAATTTG
53641 GGTATTAAGC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
28 7 0.15
29 21 0.46
30 2 0.04
31 16 0.35
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (28 bp):
AAAAGTTAAGGGGCCAATTTGTCCCAAA
Found at i:54690 original size:39 final size:38
Alignment explanation
Indices: 54638--54802 Score: 117
Period size: 41 Copynumber: 4.2 Consensus size: 38
54628 AAAATAATAA
54638 ATATA-AATTATATATTATAATTATATGTATTTACTTTAT
1 ATATATAA-TATATATTATAATTATAT-TATTTACTTTAT
*
54677 ATATATAATATATATAGAGTAATTATA-TATTTACTTTCTAT
1 ATATATAATATATAT-TA-TAATTATATTATTTAC-TT-TAT
* * *
54718 ATATTTATTATATAAATTATAATTATAATTATATA-TATTAT
1 ATA--TATAATATATATTATAATTAT-ATTATTTACT-TTAT
* * * *
54759 A-ATA-AATATATATT-TACTTTTATAACTTTATTTTAT
1 ATATATAATATATATTATAATTATATTA-TTTACTTTAT
54795 ATATATAA
1 ATATATAA
54803 ATAAATAACC
Statistics
Matches: 101, Mismatches: 11, Indels: 29
0.72 0.08 0.21
Matches are distributed among these distances:
35 3 0.03
36 13 0.13
37 12 0.12
38 4 0.04
39 19 0.19
40 6 0.06
41 26 0.26
42 3 0.03
43 15 0.15
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (38 bp):
ATATATAATATATATTATAATTATATTATTTACTTTAT
Found at i:54768 original size:18 final size:18
Alignment explanation
Indices: 54716--54771 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 18
54706 TTTACTTTCT
*
54716 ATATATTTATTAT-ATAA
1 ATATATATATTATAATAA
54733 AT-TATA-ATTATAAT--
1 ATATATATATTATAATAA
54747 -TATATATATTATAATAA
1 ATATATATATTATAATAA
54764 ATATATAT
1 ATATATAT
54772 TTACTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
13 1 0.03
14 4 0.12
15 13 0.41
16 5 0.16
17 2 0.06
18 7 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATATATTATAATAA
Found at i:54844 original size:21 final size:22
Alignment explanation
Indices: 54818--54867 Score: 93
Period size: 21 Copynumber: 2.3 Consensus size: 22
54808 TAACCCGACT
54818 CGACCCGAGAACCCG-CGGAAC
1 CGACCCGAGAACCCGACGGAAC
54839 CGACCCGAGAACCCGACGGAAC
1 CGACCCGAGAACCCGACGGAAC
54861 CGACCCG
1 CGACCCG
54868 TCGGTTCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.28, C:0.44, G:0.28, T:0.00
Consensus pattern (22 bp):
CGACCCGAGAACCCGACGGAAC
Found at i:57061 original size:31 final size:31
Alignment explanation
Indices: 57023--57081 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
57013 TAAACAAGCT
**
57023 CAAATAGGTA-TCAAATGTTTCAAAATTGACC
1 CAAATAGGTACT-AAACATTTCAAAATTGACC
57054 CAAATAGGTACTAAACATTTCAAAATTG
1 CAAATAGGTACTAAACATTTCAAAATTG
57082 GATCAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (31 bp):
CAAATAGGTACTAAACATTTCAAAATTGACC
Found at i:58977 original size:6 final size:6
Alignment explanation
Indices: 58966--59006 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
58956 ATAATAAGAG
*
58966 GAAAAA GGAAAA GAAAAA GAAAAA GAAAAA GGAAAAA GAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA -GAAAAA GAAA
59007 TAAGGAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:58983 original size:12 final size:12
Alignment explanation
Indices: 58966--59014 Score: 71
Period size: 12 Copynumber: 3.9 Consensus size: 12
58956 ATAATAAGAG
58966 GAAAAAGGAAAA
1 GAAAAAGGAAAA
*
58978 GAAAAAGAAAAA
1 GAAAAAGGAAAA
58990 GAAAAAGGAAAAA
1 GAAAAAGG-AAAA
59003 GAAATAAGGAAA
1 GAAA-AAGGAAA
59015 TTAAAGAGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
12 18 0.55
13 11 0.33
14 4 0.12
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (12 bp):
GAAAAAGGAAAA
Found at i:58995 original size:13 final size:13
Alignment explanation
Indices: 58967--59006 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
58957 TAATAAGAGG
*
58967 AAAAAGGAAAAG-
1 AAAAAGAAAAAGA
58979 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
*
58992 AAAAGGAAAAAGA
1 AAAAAGAAAAAGA
59005 AA
1 AA
59007 TAAGGAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:59015 original size:8 final size:7
Alignment explanation
Indices: 58964--59014 Score: 58
Period size: 6 Copynumber: 7.9 Consensus size: 7
58954 TAATAATAAG
58964 AGGAAAA
1 AGGAAAA
58971 AGG-AAA
1 AGGAAAA
58977 A-GAAAA
1 AGGAAAA
58983 A-GAAAA
1 AGGAAAA
58989 A-GAAAA
1 AGGAAAA
58995 AGGAAAA
1 AGGAAAA
59002 A-GAAATA
1 AGGAAA-A
59009 AGGAAA
1 AGGAAA
59015 TTAAAGAGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
5 1 0.03
6 24 0.60
7 11 0.28
8 4 0.10
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (7 bp):
AGGAAAA
Found at i:59894 original size:24 final size:24
Alignment explanation
Indices: 59867--59913 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
59857 ATTTGACTGA
* *
59867 TTTGGTTGATTATCTTGGTTTTAC
1 TTTGATTGATGATCTTGGTTTTAC
*
59891 TTTGATTTATGATCTTGGTTTTA
1 TTTGATTGATGATCTTGGTTTTA
59914 ATGATTTTCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.06, G:0.19, T:0.60
Consensus pattern (24 bp):
TTTGATTGATGATCTTGGTTTTAC
Found at i:64559 original size:101 final size:101
Alignment explanation
Indices: 64384--64585 Score: 280
Period size: 101 Copynumber: 2.0 Consensus size: 101
64374 TAGGCTCATG
* * * * *
64384 CTGCTGTCAATTCTGCCATCTCGGTAGATAAAAGCTGCGGTGATGGAGAACATGCTAAGCAGCTA
1 CTGCTATCAATTCTGCCATCTCGGAAAATAAAAGCTGCGATGATGGAGAACATGCTAAGCAACTA
* *
64449 GCTCATAAAGAAGAGAGTTCTTGCTACCGCCAGCCA
66 GCTCATAAAGAAGAGAGTTCTTACAACCGCCAGCCA
* ** *
64485 CTGCTATCAATTCTGCCATCTCGGAAAATCAAAG-TCGCGATGATGGTTAACGTGCTAAGCAACT
1 CTGCTATCAATTCTGCCATCTCGGAAAATAAAAGCT-GCGATGATGGAGAACATGCTAAGCAACT
*
64549 GGCTCATAAAGAAGAGAGTTCTTACAACCGCCAGCCA
65 AGCTCATAAAGAAGAGAGTTCTTACAACCGCCAGCCA
64586 GTTCATGTTC
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
100 1 0.01
101 87 0.99
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (101 bp):
CTGCTATCAATTCTGCCATCTCGGAAAATAAAAGCTGCGATGATGGAGAACATGCTAAGCAACTA
GCTCATAAAGAAGAGAGTTCTTACAACCGCCAGCCA
Found at i:72696 original size:212 final size:209
Alignment explanation
Indices: 72453--72846 Score: 673
Period size: 211 Copynumber: 1.9 Consensus size: 209
72443 ATTAATTACA
72453 AAGCAAATCATTTATTTTTTTAATCAAATAGATTGATTACGTTTGATATTTTTTACTTATTGAAT
1 AAGCAAATCATTTATTTTTTTAATCAAATAGATTGATTACGTTTGATA-TTTTTACTTATTGAAT
72518 TATTCAATTTCAAGCATGATCATAGTCAATAATTACTGATTTGCTTTAATAGTTGCTTAATTTTC
65 TATTCAATTTCAAGCATGATCATAGTCAATAATTACTGATTTGCTTTAATAGTTGCTTAA-TTTC
*
72583 CTTTTT-TGTTTAATGAAAATGAATCTTCTGTTTAAACTTAAAGATTTTAAATAACTAATTACGC
129 CTTTTTAT-TTTAATGAAAATGAATCTTCTCTTTAAACTTAAAGATTTTAAATAACTAATTACGC
72647 TTTATTTCCTTTAAGGG
193 TTTATTTCCTTTAAGGG
*
72664 AAGCAAATCATCTTTTTTTTTTAATCAAATAGATTGATTACGTTTGATATTTTTACTTATTGAAT
1 AAGCAAATCAT-TTATTTTTTTAATCAAATAGATTGATTACGTTTGATATTTTTACTTATTGAAT
* * *
72729 TATTTAATTTCAAGCATTATCATAGTCAATAATTACTTATTTGCTTTAATAGTTGCTTAATTTCC
65 TATTCAATTTCAAGCATGATCATAGTCAATAATTACTGATTTGCTTTAATAGTTGCTTAATTTCC
** *
72794 TTTTTATTTTAATGAAAATGAATCTTCTCTTTTTACTTAAAGATTTTTAATAA
130 TTTTTATTTTAATGAAAATGAATCTTCTCTTTAAACTTAAAGATTTTAAATAA
72847 GTTGTAAGGT
Statistics
Matches: 173, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
210 52 0.30
211 85 0.49
212 36 0.21
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (209 bp):
AAGCAAATCATTTATTTTTTTAATCAAATAGATTGATTACGTTTGATATTTTTACTTATTGAATT
ATTCAATTTCAAGCATGATCATAGTCAATAATTACTGATTTGCTTTAATAGTTGCTTAATTTCCT
TTTTATTTTAATGAAAATGAATCTTCTCTTTAAACTTAAAGATTTTAAATAACTAATTACGCTTT
ATTTCCTTTAAGGG
Found at i:73264 original size:137 final size:137
Alignment explanation
Indices: 73032--73421 Score: 435
Period size: 137 Copynumber: 2.8 Consensus size: 137
73022 CCAAAAGCTA
* * *
73032 ATGATTATTTAATTTTGCCACAAATAAATGAATCAATTAAT-ATTATGTTACAAAAAAATAAATT
1 ATGATTATTTATTTTTTCCATAAATAAATGAATCAATTAATAATTATGTTAC---AAAA-AAATT
* * * *
73096 GATTGAACATCCAAAATAAGTAAATGAATCAAGTTAGTCCTTAGTTAACTTTACCAATCAAAGTT
62 GATTGAACATACTAAATAAATAAATGAATCAAGTTAGTCGTTAGTTAACTTTACCAATCAAAGTT
73161 ATAATTGATGG
127 ATAATTGATGG
* * * *
73172 ATGATTATTTATTTTTTCCATAAATAAATAAATCAATTACTAATTATATTACCAAAAAATTGATT
1 ATGATTATTTATTTTTTCCATAAATAAATGAATCAATTAATAATTATGTTACAAAAAAATTGATT
* * ** *
73237 GAACATGCTAAATAAATAAATGAATCAAGTTAGTCGTT-GATCAACTTTGTCAATTAAAGTTATA
66 GAACATACTAAATAAATAAATGAATCAAGTTAGTCGTTAG-TTAACTTTACCAATCAAAGTTATA
*
73301 ATTGATTG
130 ATTGATGG
* * * *
73309 ATGATTATTTGATTCTGT-CATAAATAAATGAATCAATTAGTAATTATGTTAGAAAAAAATAGAT
1 ATGATTATTT-ATTTTTTCCATAAATAAATGAATCAATTAATAATTATGTT--ACAAAAA-A-AT
* ** * *
73373 TGATTGAACATACTAAATAAATTAGGGAATCAAATTAGTCGTTAATTAA
61 TGATTGAACATACTAAATAAATAAATGAATCAAGTTAGTCGTTAGTTAA
73422 TTGCCAAAAA
Statistics
Matches: 212, Mismatches: 30, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
136 1 0.00
137 109 0.51
138 8 0.04
139 5 0.02
140 37 0.17
141 52 0.25
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (137 bp):
ATGATTATTTATTTTTTCCATAAATAAATGAATCAATTAATAATTATGTTACAAAAAAATTGATT
GAACATACTAAATAAATAAATGAATCAAGTTAGTCGTTAGTTAACTTTACCAATCAAAGTTATAA
TTGATGG
Found at i:73853 original size:135 final size:139
Alignment explanation
Indices: 73706--74033 Score: 504
Period size: 141 Copynumber: 2.4 Consensus size: 139
73696 AAGTTAGTGA
*
73706 TCGTTAGTTAATTTTTCCAATCAAAGTTGTAATTGATTGATAATTATTTAATTTTACCAT-AAAT
1 TCGTTAGTTAATTTTTCCAATCAAAGTTGTAATTGATTGATAATTATATAATTTTACCATAAAAT
* *
73770 CGCTA-CAAAAAAATT-A-ACATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAATTA
66 CGCCACCAAAAAAATTCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAATTA
73832 TTGAACATG
131 TTGAACATG
*
73841 TCGTTAGTTAATTTTGT-CAATCAAAGTTGTAATTGATTGATGATTATATAATTTTACCATAAAA
1 TCGTTAGTTAATTTT-TCCAATCAAAGTTGTAATTGATTGATAATTATATAATTTTACCATAAAA
*
73905 TCGCCACCAAAAAGATTACCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAA
65 TCGCCACCAAAAAAATT--CATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAA
73970 TTATTGAACATG
128 TTATTGAACATG
* * * * *
73982 TTGTTAATTAATTTTGCCAATCAAAGTTGTAATTGATTGATCATTATCTAAT
1 TCGTTAGTTAATTTTTCCAATCAAAGTTGTAATTGATTGATAATTATATAAT
74034 CAAAGTTGTA
Statistics
Matches: 175, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
135 56 0.32
136 9 0.05
137 9 0.05
140 1 0.01
141 100 0.57
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (139 bp):
TCGTTAGTTAATTTTTCCAATCAAAGTTGTAATTGATTGATAATTATATAATTTTACCATAAAAT
CGCCACCAAAAAAATTCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAATTA
TTGAACATG
Done.