Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016258.1 Corchorus capsularis cultivar CVL-1 contig16279, 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: 53785
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1821 original size:56 final size:56
Alignment explanation
Indices: 1732--1838 Score: 155
Period size: 56 Copynumber: 1.9 Consensus size: 56
1722 GATTTAGATT
*
1732 GAAGACGGTCATCCTTTCCAATTTTCAGTAGTTTTAAGTAGTTACTCAAGTCGGTC
1 GAAGACGGTCATCCTTTCCAATTTTCAGTAGTTTTAAGTAATTACTCAAGTCGGTC
* *
1788 GAAGACGGTCAT-CTTTCTCAGTTTTCA-TCAGTTTTTAGTAATTACTCAAGT
1 GAAGACGGTCATCCTTTC-CAATTTTCAGT-AGTTTTAAGTAATTACTCAAGT
1839 TAATCTAGGA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
55 6 0.13
56 40 0.87
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (56 bp):
GAAGACGGTCATCCTTTCCAATTTTCAGTAGTTTTAAGTAATTACTCAAGTCGGTC
Found at i:7764 original size:13 final size:14
Alignment explanation
Indices: 7746--7774 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
7736 ATAACCGGAC
7746 TTTGCATTCAT-CA
1 TTTGCATTCATGCA
7759 TTTGCATTCATGCA
1 TTTGCATTCATGCA
7773 TT
1 TT
7775 GAGTAGAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTGCATTCATGCA
Found at i:8026 original size:41 final size:39
Alignment explanation
Indices: 7969--8074 Score: 153
Period size: 41 Copynumber: 2.7 Consensus size: 39
7959 TTTCTATTTA
*
7969 AGCAATTCCAAGAGAAGACTTTTGGAAAATAAATGTCCTTT
1 AGCAAATCCAAGAGAAGACTTTTGGAAAATAAATGT--TTT
*
8010 AGCAAATCCAAAAGAAGACTTTTGG-AAATAAATGTTTT
1 AGCAAATCCAAGAGAAGACTTTTGGAAAATAAATGTTTT
*
8048 A-AAAATCCAAGAGAAGACTTTTGGAAA
1 AGCAAATCCAAGAGAAGACTTTTGGAAA
8075 TTAATAAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
37 21 0.35
38 6 0.10
40 10 0.17
41 23 0.38
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.26
Consensus pattern (39 bp):
AGCAAATCCAAGAGAAGACTTTTGGAAAATAAATGTTTT
Found at i:8063 original size:37 final size:39
Alignment explanation
Indices: 7975--8075 Score: 152
Period size: 37 Copynumber: 2.6 Consensus size: 39
7965 TTTAAGCAAT
*
7975 TCCAAGAGAAGACTTTTGGAAAATAAATGTCCTTTAGCAAA
1 TCCAAGAGAAGACTTTTGG-AAATAAATGT-CTTTAGAAAA
*
8016 TCCAAAAGAAGACTTTTGGAAATAAATGT-TTTA-AAAA
1 TCCAAGAGAAGACTTTTGGAAATAAATGTCTTTAGAAAA
8053 TCCAAGAGAAGACTTTTGGAAAT
1 TCCAAGAGAAGACTTTTGGAAAT
8076 TAATAAAATT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
37 25 0.44
38 4 0.07
40 10 0.18
41 18 0.32
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.28
Consensus pattern (39 bp):
TCCAAGAGAAGACTTTTGGAAATAAATGTCTTTAGAAAA
Found at i:14603 original size:33 final size:33
Alignment explanation
Indices: 14565--14649 Score: 93
Period size: 33 Copynumber: 2.5 Consensus size: 33
14555 GCTATGATCA
* *
14565 ACCAAAACAGATTTGT-TTTCATCACAATTAGC
1 ACCAAAACAGATTTGTGTTTCATCACAAATAAC
* *
14597 ATCCAAAATACA-TTGTGTTTCATCACAAATAAC
1 A-CCAAAACAGATTTGTGTTTCATCACAAATAAC
14630 ACCTAAAACAGATTTAGTGT
1 ACC-AAAACAGATTT-GTGT
14650 CATTGCAAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
32 7 0.17
33 29 0.69
34 2 0.05
35 4 0.10
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (33 bp):
ACCAAAACAGATTTGTGTTTCATCACAAATAAC
Found at i:15952 original size:21 final size:21
Alignment explanation
Indices: 15926--15966 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
15916 TTCTTGTGTA
*
15926 ACCCGCGCCTGGGCAAGGTTG
1 ACCCGCGCCTGCGCAAGGTTG
15947 ACCCGCGCCTGCGCAAGGTT
1 ACCCGCGCCTGCGCAAGGTT
15967 TCGGAACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.37, G:0.34, T:0.15
Consensus pattern (21 bp):
ACCCGCGCCTGCGCAAGGTTG
Found at i:18009 original size:9 final size:9
Alignment explanation
Indices: 17997--18021 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
17987 GGCATGCTTG
17997 GATGGGGTC
1 GATGGGGTC
18006 GATGGGGTC
1 GATGGGGTC
18015 GATGGGG
1 GATGGGG
18022 AAGATGAATT
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:0.12, C:0.08, G:0.60, T:0.20
Consensus pattern (9 bp):
GATGGGGTC
Found at i:19871 original size:19 final size:19
Alignment explanation
Indices: 19849--19894 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
19839 TATTTCTGAG
*
19849 TTGGGTTTTAATTTATG-C
1 TTGGGTTTTAATTCATGAC
*
19867 TTTGGGTTTTGATTCATGAC
1 -TTGGGTTTTAATTCATGAC
19887 TTGGGTTT
1 TTGGGTTT
19895 AAAATTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.13, C:0.07, G:0.26, T:0.54
Consensus pattern (19 bp):
TTGGGTTTTAATTCATGAC
Found at i:20395 original size:58 final size:57
Alignment explanation
Indices: 20348--20662 Score: 459
Period size: 58 Copynumber: 5.4 Consensus size: 57
20338 TCAAAAATGT
*
20348 TAATCAGTAAAATTGGCTTAATTAAAGTTACTTAAGTTGATTAAGAGGTAAAGTAAGG
1 TAATCAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAG-AAGG
* **
20406 TAATCAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTACGAGGTAAAGTAATA
1 TAATCAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAG-AAGG
* *
20464 TAATCAGTAAAATCGGCTCAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAGTAAGG
1 TAATCAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAG-AAGG
*
20522 TAATCAATAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAGTAAGG
1 TAATCAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAG-AAGG
* * * *
20580 TAATCAGAAAAATCGGCTCAATTAAAGTTATAATTAAGTTGAATAAGAGGTAAAGTAAGG
1 TAATCAGTAAAATTGGCTTAATTAAAG-T-TAATTAAGTTGATTAAGAGGTAAAG-AAGG
*
20640 CAATCAGTAAAATTGGCTTAATT
1 TAATCAGTAAAATTGGCTTAATT
20663 TTTTATTTTT
Statistics
Matches: 234, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
58 185 0.79
59 1 0.00
60 48 0.21
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.31
Consensus pattern (57 bp):
TAATCAGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAGAAGG
Found at i:20490 original size:116 final size:115
Alignment explanation
Indices: 20348--20889 Score: 532
Period size: 116 Copynumber: 4.9 Consensus size: 115
20338 TCAAAAATGT
* *
20348 TAATCAGTAAAATTGGCTTAATTAAAGTTACTTAAGTTGATTAAGAGGTAAAGTAAGGTAATCAG
1 TAATCAGTAAAATCGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAGTAAGGTAATCAG
*
20413 TAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTACGAGGTAAAGTAATA
66 TAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAG-AATA
* *
20464 TAATCAGTAAAATCGGCTCAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAGTAAGGTAATCAA
1 TAATCAGTAAAATCGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAGTAAGGTAATCAG
**
20529 TAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAGTAAGG
66 TAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAG-AATA
* * * *
20580 TAATCAGAAAAATCGGCTCAATTAAAGTTATAATTAAGTTGAATAAGAGGTAAAGTAAGGCAATC
1 TAATCAGTAAAATCGGCTTAATTAAAG-T-TAATTAAGTTGATTAAGAGGTAAAGTAAGGTAATC
** * ** * *
20645 AGTAAAATTGGCTTAATT----TT--TTATTTTTATTTTTGAAG-AAAGTAAAA
64 AGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGA-TTAAGAGGTAAAG-AATA
* * * * *
20692 TAAGC-TTAATTAA--AG-TTAA-T-AAGTTGATTAA---G---AA-A--TCAAG--A--TAATC
1 TAATCAGTAA--AATCGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAGTAAGGTAATC
*
20738 AGTAAAATTGGATTAATTAAAGTTAATTAAGTTGATTAAGAGGT-AA-AA-A
64 AGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAGAATA
* * * * * *
20787 -AATCAGTAAAATTGGCTTAATTCAGGTTAATTGAGTTGATTAAAAGGTAAAGTAAGGTAATTAG
1 TAATCAGTAAAATCGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAGTAAGGTAATCAG
20851 TAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGA
66 TAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGA
20890 AATAAAAAGA
Statistics
Matches: 352, Mismatches: 43, Indels: 67
0.76 0.09 0.15
Matches are distributed among these distances:
93 23 0.07
94 3 0.01
95 6 0.02
96 6 0.02
97 7 0.02
98 15 0.04
99 7 0.02
100 2 0.01
101 1 0.00
103 1 0.00
104 2 0.01
105 1 0.00
106 6 0.02
107 5 0.01
108 3 0.01
109 2 0.01
110 3 0.01
111 47 0.13
112 17 0.05
113 7 0.02
114 2 0.01
116 135 0.38
117 1 0.00
118 50 0.14
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (115 bp):
TAATCAGTAAAATCGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAGTAAGGTAATCAG
TAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAGAATA
Found at i:20754 original size:53 final size:53
Alignment explanation
Indices: 20685--20894 Score: 251
Period size: 53 Copynumber: 3.9 Consensus size: 53
20675 TTTTGAAGAA
**
20685 AGTAAAATAAGCTTAATTAAAGTTAA-TAAGTTGATTAAGAAATCAAGATAATC
1 AGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAAAT-AAGATAATC
* ** * *
20738 AGTAAAATTGGATTAATTAAAGTTAATTAAGTTGATTAAGAGGTAAAAAAATC
1 AGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAAATAAGATAATC
* * * * *
20791 AGTAAAATTGGCTTAATTCAGGTTAATTGAGTTGATTAAAAGGTAAAGTAAGGTAATT
1 AGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATT--AA-G-AAA-TAAGATAATC
20849 AGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAAATAA
1 AGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAAATAA
20895 AAAGAGGAAC
Statistics
Matches: 131, Mismatches: 20, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
53 66 0.50
54 18 0.14
55 3 0.02
56 3 0.02
57 1 0.01
58 40 0.31
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (53 bp):
AGTAAAATTGGCTTAATTAAAGTTAATTAAGTTGATTAAGAAATAAGATAATC
Found at i:28122 original size:188 final size:189
Alignment explanation
Indices: 27804--28176 Score: 685
Period size: 188 Copynumber: 2.0 Consensus size: 189
27794 TTGGAATTGT
*
27804 CCTTCAACTGTTTTTTGCAATAATTGCAAATGGCCACATCTGATCCATTTAAACTCTTCTTCTCA
1 CCTTCAACTGTTTTTTGCAATAATTGCAAATGGCCACATCTGATCCATTTAAAATCTTCTTCTCA
*
27869 AAGTGCTCCCAAACTGATGACGTTAGTTTTCATCGCTTCCGAGATGAATCACCTAATTGAGGCTT
66 AAGTGCTCCCAAACTGATGACGTTAGTTTTCATCGCTTCCGAGATGAATCACCTAATGGAGGCTT
*
27934 GCCTGAAGACGGTGTTGCAATATTAGGAATAGGAGAACTAGGCTCAACATTCTGGCAGG
131 GCCTGAAGACGGTGTTGCAATATTAGGAATAGGAGAACTAGACTCAACATTCTGGCAGG
*
27993 CCTTCAACTGTTTTTTGTAATAATTGCAAATGGCCACATCTG-TCCATTTAAAATCTTCTTCTCA
1 CCTTCAACTGTTTTTTGCAATAATTGCAAATGGCCACATCTGATCCATTTAAAATCTTCTTCTCA
* *
28057 AAGTGCTCCCAAACTGATGACGTTAGTTTTCGTCGCTTCTGAGATGAATCACCTAATGGAGGCTT
66 AAGTGCTCCCAAACTGATGACGTTAGTTTTCATCGCTTCCGAGATGAATCACCTAATGGAGGCTT
28122 GCCTGAAGACGGTGTTGCAATATTAGGAATAGGAGAACTAGACTCAACATTCTGG
131 GCCTGAAGACGGTGTTGCAATATTAGGAATAGGAGAACTAGACTCAACATTCTGG
28177 GCAGACACAT
Statistics
Matches: 178, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
188 137 0.77
189 41 0.23
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (189 bp):
CCTTCAACTGTTTTTTGCAATAATTGCAAATGGCCACATCTGATCCATTTAAAATCTTCTTCTCA
AAGTGCTCCCAAACTGATGACGTTAGTTTTCATCGCTTCCGAGATGAATCACCTAATGGAGGCTT
GCCTGAAGACGGTGTTGCAATATTAGGAATAGGAGAACTAGACTCAACATTCTGGCAGG
Found at i:28957 original size:2 final size:2
Alignment explanation
Indices: 28950--28979 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
28940 CACTATTCAC
28950 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28980 TTTCATAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:30261 original size:30 final size:30
Alignment explanation
Indices: 30207--30270 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
30197 TGAATATGAA
* *
30207 TCAAGGCAAGCTCATGTCAATTGGGAAA-T
1 TCAAGGCAAACTCATGTAAATTGGGAAAGT
*
30236 TCAAGGCAAATTCAATGTAAATTGGGAAAGT
1 TCAAGGCAAACTC-ATGTAAATTGGGAAAGT
30267 TCAA
1 TCAA
30271 TGTCCATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 11 0.37
30 14 0.47
31 5 0.17
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (30 bp):
TCAAGGCAAACTCATGTAAATTGGGAAAGT
Found at i:30462 original size:82 final size:82
Alignment explanation
Indices: 30300--30464 Score: 208
Period size: 82 Copynumber: 2.0 Consensus size: 82
30290 ATGTGAGAAA
* * * *
30300 CAATACAAGTTCAATGTCAATTTAGATAATTGAATGTGAATCAAGGTAAGTTCAATGTCAATTGG
1 CAATACAAGTTCAATGTCAATTGAGATAATTGAATATGAATCAAAGAAAGTTCAATGTCAATTGG
*
30365 GAATGTTGAAATTGAAT
66 GAATGTTCAAATTGAAT
* * * *
30382 CAATGCAAGTTCAATGTCAATTGCGA-ATGTTGAATATGAATTAAAGAAAGTTCAATGTCAATTG
1 CAATACAAGTTCAATGTCAATTGAGATA-ATTGAATATGAATCAAAGAAAGTTCAATGTCAATTG
*
30446 GGAAAT-TTCAATTTGAAT
65 GG-AATGTTCAAATTGAAT
30464 C
1 C
30465 CGCCATGAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
81 1 0.01
82 67 0.94
83 3 0.04
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.33
Consensus pattern (82 bp):
CAATACAAGTTCAATGTCAATTGAGATAATTGAATATGAATCAAAGAAAGTTCAATGTCAATTGG
GAATGTTCAAATTGAAT
Found at i:30463 original size:41 final size:41
Alignment explanation
Indices: 30306--30464 Score: 169
Period size: 41 Copynumber: 3.9 Consensus size: 41
30296 GAAACAATAC
** * * * *
30306 AAGTTCAATGTCAATTTAG-ATAATTGAATGTGAATCAAGGT
1 AAGTTCAATGTCAATTGGGAAT-GTTGAATTTGAATCAAAGA
* * *
30347 AAGTTCAATGTCAATTGGGAATGTTGAAATTGAATCAATGC
1 AAGTTCAATGTCAATTGGGAATGTTGAATTTGAATCAAAGA
* * *
30388 AAGTTCAATGTCAATTGCGAATGTTGAATATGAATTAAAGA
1 AAGTTCAATGTCAATTGGGAATGTTGAATTTGAATCAAAGA
*
30429 AAGTTCAATGTCAATTGGGAAAT-TTCAATTTGAATC
1 AAGTTCAATGTCAATTGGG-AATGTTGAATTTGAATC
30465 CGCCATGAAA
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
41 94 0.95
42 5 0.05
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.33
Consensus pattern (41 bp):
AAGTTCAATGTCAATTGGGAATGTTGAATTTGAATCAAAGA
Found at i:33084 original size:41 final size:41
Alignment explanation
Indices: 33027--33222 Score: 164
Period size: 41 Copynumber: 4.7 Consensus size: 41
33017 GACAAAACTT
* * * *
33027 AATGTAAATTGGGAAAGTTGAATGT-ATATTAAGGCAAATTC
1 AATGTCAATTGTGAAAGTTGAATGTGA-ATCAAGGCAAGTTC
* * *
33068 AATGTCCATTGTGAAAGTTAAATGTGAGAATCAACGCAAGTTC
1 AATGTCAATTGTGAAAGTTGAATGT--GAATCAAGGCAAGTTC
33111 AATG-CTAATT-TGGAAAGTTGAATGTGAATCAAGGCAAGTTC
1 AATGTC-AATTGT-GAAAGTTGAATGTGAATCAAGGCAAGTTC
* * * * * * *
33152 AATGTCAATTGCGAATGTTGAATATGAATTAAAGAAAGTTT
1 AATGTCAATTGTGAAAGTTGAATGTGAATCAAGGCAAGTTC
* * * *
33193 AATGTCAATTGGGAAATTTCAATTTGAATC
1 AATGTCAATTGTGAAAGTTGAATGTGAATC
33223 CGTCATGAAA
Statistics
Matches: 125, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
41 91 0.73
42 3 0.02
43 30 0.24
44 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.32
Consensus pattern (41 bp):
AATGTCAATTGTGAAAGTTGAATGTGAATCAAGGCAAGTTC
Found at i:40538 original size:667 final size:665
Alignment explanation
Indices: 38602--40889 Score: 2376
Period size: 667 Copynumber: 3.4 Consensus size: 665
38592 TAAAACGAAG
*
38602 ACAAAGGGTACGCATAGGTGTGAGCTATGTTT-TTTTTTATAACAAGTTAAAAAGTTTGTATAGG
1 ACAAAGGGTACCCATAGGTGTGAGCTATGTTTCTTTTTT-TAACAAGTTAAAAAGTTTGTATAGG
* * * * *
38666 TA-GGG-AAT---AAATGAGGCAAGAATTTTTACAAGCTGTGAAATTAAAAAAATTATGTTGATA
65 TAGGGGAAATGGCAAATGAGACAAGAATTTTTA-TAGCTCTGAAATTAACAAAATTAGGTTGATA
* *
38726 CCTTTTTTT-TCTACATATTTTAGTAACAGAGTCGTCATTCCTAACATAATGAAATAAATATCAC
129 CCTTTTTTTGT-TACATATTTTAGTATCAGAGTCGTCATTCCTAACATAATGAAAGAAATATCAC
* * *
38790 CTTGAATATAGAAAAAAATGTACCTTACTTAAATAAGTTAAGTATTCGTCGTTTTATATACACAA
193 TTTGAATATAGAAAAAAATGTACCTTACTTGAATAAGTTAAGTATTCGTCGCTTTATATACACAA
38855 ATACCAAATTCTTGAGAGTTATAATAAGCATGGTTGTAAATAGAAAGTCAATAGTTCCTAACAAG
258 ATACCAAATTCTT---A---AT--T-AGCATGGTTGTAAATA-AAAGTCAATAGTTCCTAACAAG
** * * *
38920 TAATAGAACCATAGTTCATACAATTGTTAGATGTACTGTATTTGTAATCAATATGACTCTAACGA
313 CGATAGCACCAAAG----TACAATTGTAAGATGTACTGTATTTGTAATCAATATG-CTCTAACGA
* * *
38985 AAAGTGAC-GAATGCGTAGTTATGAAAAAAATTAGGTTGATCTGGTCGTTAGCCGATCCTCTGCC
373 AAAGTGACAG-ATGCATAGTTATGAAAAGAATTAGGTTGAACTGGTCGTTAGCCGATCCTCTGCC
** * * *
39049 CAAACTTACAGTGCAGATGAGATCTTTCATAACTGCAAAT-TGGTCCCAAAACAAGTTGTTA-CG
437 CGGACTTACAG-GCGGATGAGATCTTTCATAACTGCAAATATGCT-CCAAAACAAGTT-TTAGGG
** * * * * * * * *
39112 GATTAGA-TCCGTTATCTTACTTTGATATATGTACCAACGAATCTAAGAAGAAAGGGAATAGTCT
499 GACCA-ACTTCGCTATCTTACTTTGATATATGTAACATCGAGTCCAAGAAGAAAGAGAATAATC-
* *
39176 TCTGGATGAAGTGTCCATATTATGAATACAACAACATCGAATGAGAGAAAACTTATGTTGCCTTT
562 TCTGGATGAAGTGTCCATATTAGGAATACAACAACATCGAATGGGAGAAAACTTA--TTG-----
* * * *
39241 AATGTGGCGGTTGGAAAAGTGTTT-ATTCCAACCTGCCATAAAACGTGT-
620 --TCTGGCAGTTGGAAAAGT-TTTAATTCCAACCAGCCATAAAATGT-TC
* * ** * *** *
39289 ACAAAGAGTATCTGTAGGTGTGAGCCATGTTTCTTTTTTT--CTTTTATAAAAAGTCTGTATAGG
1 ACAAAGGGTACCCATAGGTGTGAGCTATGTTTCTTTTTTTAACAAGT-TAAAAAGTTTGTATAGG
39352 TAGGGGAAATGGACAAATGAGGA-AAGAATTTATAATTACATATAAGCTCTGAAATTAACAAAAT
65 TAGGGGAAATGG-CAAATGA-GACAAGAA--T-T--TT---TAT-AGCTCTGAAATTAACAAAAT
* * * *
39416 TAGGTTGATACTTTTTTTTG-TACATATTTTAGTATTAGAGTCGTCATTCTTAATATAATGAAAG
119 TAGGTTGATACCTTTTTTTGTTACATATTTTAGTATCAGAGTCGTCATTCCTAACATAATGAAAG
* * * * * *
39480 AAATGTCACTTTGAATTTAGAAAAACATGGACCTTACTTGAATAAGTTAAATATTCATCGCTTTA
184 AAATATCACTTTGAATATAGAAAAAAATGTACCTTACTTGAATAAGTTAAGTATTCGTCGCTTTA
* * * * *
39545 TATACACGAATACCAAATTTCTAAGGGTTATAATAAGCATTGTTGTAATTAACAAGTCAACAGTT
249 TATACACAAATACCAAA-TTC-------T-TAATTAGCATGGTTGTAAATAA-AAGTCAATAGTT
* * *
39610 CCTAACTAGCGATAGCACCTAAGTACAATTGTAAGATGTACTGTACTTGTAATCAATATGGCTCT
304 CCTAACAAGCGATAGCACCAAAGTACAATTGTAAGATGTACTGTATTTGTAATCAATAT-GCTCT
* * * * * *
39675 AACGAAAAGTTACAAATGCATAGTTATCAAAAGACA-TAGGTTGACCTAGTCGTTACCCGATCCT
368 AACGAAAAGTGACAGATGCATAGTTATGAAAAGA-ATTAGGTTGAACTGGTCGTTAGCCGATCCT
* * * * *
39739 ATGCCCGGA-TTAACATGGTGGATGAGATCATTCATAACTGCAAATA-GACCCCAAAACAAGTTG
432 CTGCCCGGACTT-ACA-GGCGGATGAGATCTTTCATAACTGCAAATATG-CTCCAAAACAAGTTT
* * * * * *
39802 TAGGGGACCAGC-TCTGCTATCTTACTTTAATATATGTAGCGTCGAGTGCAAGAAAAAAGAGAAT
494 TAGGGGACCAACTTC-GCTATCTTACTTTGATATATGTAACATCGAGTCCAAGAAGAAAGAGAAT
* *
39866 AATCTCTGGATGAAGTGTCCATATTAGGAATACTACAACATCGAATGGGATAAAACTTA-TG-C-
558 AATCTCTGGATGAAGTGTCCATATTAGGAATACAACAACATCGAATGGGAGAAAACTTATTGTCT
*
39928 GGCAGTTGGAAAAGTTTTAATTCCAACCAGCCCTAAAATGTTC
623 GGCAGTTGGAAAAGTTTTAATTCCAACCAGCCATAAAATGTTC
* *
39971 ACAAAGGGTACCCATAGGTGTGAACTATG-TTCTTTTTTTAACAGGTTAAAAAGTTTGTATAGGT
1 ACAAAGGGTACCCATAGGTGTGAGCTATGTTTCTTTTTTTAACAAGTTAAAAAGTTTGTATAGGT
* * *
40035 ATGGGAAATAGGCAAAGGAGACAAGAATTTTTATAGCCTCTGAAATTAATAAAATTAGGTTGATA
66 AGGGGAAAT-GGCAAATGAGACAAGAATTTTTATAG-CTCTGAAATTAACAAAATTAGGTTGATA
* * *
40100 CCTTTTTTTGTTACATATTTTAGTATCAGAGTCGTCATTCCTAAGATAATGAAAAAAAAATATTA
129 CCTTTTTTTGTTACATATTTTAGTATCAGAGTCGTCATTCCTAACATAATG--AAAGAAATATCA
* *
40165 CTTTGAATATAGAAAAAAATGTATCTTACTTGAATAAGTTAAGTATTCGTTGCTTTATATACACA
192 CTTTGAATATAGAAAAAAATGTACCTTACTTGAATAAGTTAAGTATTCGTCGCTTTATATACACA
* *
40230 AATACCAAATTCTTAATTAGCATGGTTGTAAGTACAAAG-CTAATAGTTCCTAACAAGCGATATC
257 AATACCAAATTCTTAATTAGCATGGTTGTAAATA-AAAGTC-AATAGTTCCTAACAAGCGATAGC
* * * * *
40294 ACCAAAGTACAATTGTAAGATATATTGTATTTGTAAT-AATATAGCTCCAATGAAGAGTGACAGA
320 ACCAAAGTACAATTGTAAGATGTACTGTATTTGTAATCAATAT-GCTCTAACGAAAAGTGACAGA
* *
40358 TGCATAGTTATGAAAAGAATTAGGTTGAACTGGTCGTTAGCTGATCTTCTGCCCGGACTTACAGA
384 TGCATAGTTATGAAAAGAATTAGGTTGAACTGGTCGTTAGCCGATCCTCTGCCCGGACTTACAG-
*
40423 GCGGATGAGATTTTTCATAACTGCAAATATGCTCCAAAACAAGTTTTAGGGGACCAACTTCGCTA
448 GCGGATGAGATCTTTCATAACTGCAAATATGCTCCAAAACAAGTTTTAGGGGACCAACTTCGCTA
* *
40488 TCTTATTTTGATATATGTAACTTCGAGTCCAAGAAGAAAGAGAATAATCTCTGGATGAAGTGTCC
513 TCTTACTTTGATATATGTAACATCGAGTCCAAGAAGAAAGAGAATAATCTCTGGATGAAGTGTCC
* * * *
40553 ATATCAGGAATACCACAACATTGAATCGGAGAAAACTTATGTTGTCTTTCATGTGGCAGTTGGAA
578 ATATTAGGAATACAACAACATCGAATGGGAGAAAACTTA--TTG----TC---TGGCAGTTGGAA
* * *
40618 AAGTGTTAATTCCAACCAACCAT-AAATCGTGC
634 AAGTTTTAATTCCAACCAGCCATAAAAT-GTTC
* *
40650 ACAAAGGGT---CAAAGGTGTGAGTTATGTTTCTTTCTTTTTTTTTTAACAAGTTAAAAAGTTTG
1 ACAAAGGGTACCCATAGGTGTGAGCTATG----TTTC---TTTTTTTAACAAGTTAAAAAGTTTG
* ** *
40712 TATAGGTAGGGGAAATGGGCAAATAAGGTAAG-ATTTTTATAAACTCTGAAATTAACAAAATTAG
59 TATAGGTAGGGGAAAT-GGCAAATGAGACAAGAATTTTTAT-AGCTCTGAAATTAACAAAATTAG
* * * * *
40776 ATTGAT--TTTTTTTTGCTACATATTTTAGTATCAGGGTCGTCATTCTTAACATAATGAAAAGAA
122 GTTGATACCTTTTTTTGTTACATATTTTAGTATCAGAGTCGTCATTCCTAACATAATG-AAAGAA
40839 ATATCACTTTGAATATAGAAAAAAATGTACCTTACTTGAATAAGTTAAGTA
186 ATATCACTTTGAATATAGAAAAAAATGTACCTTACTTGAATAAGTTAAGTA
40890 ACTGTTAATT
Statistics
Matches: 1345, Mismatches: 178, Indels: 163
0.80 0.11 0.10
Matches are distributed among these distances:
666 2 0.00
667 220 0.16
668 79 0.06
669 2 0.00
670 2 0.00
673 2 0.00
674 39 0.03
675 38 0.03
676 17 0.01
677 77 0.06
678 4 0.00
679 44 0.03
680 56 0.04
681 64 0.05
682 92 0.07
683 37 0.03
684 51 0.04
685 2 0.00
686 18 0.01
687 30 0.02
688 9 0.01
691 2 0.00
692 11 0.01
693 1 0.00
694 57 0.04
695 185 0.14
696 3 0.00
697 2 0.00
698 1 0.00
699 153 0.11
700 40 0.03
702 2 0.00
705 1 0.00
707 1 0.00
708 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (665 bp):
ACAAAGGGTACCCATAGGTGTGAGCTATGTTTCTTTTTTTAACAAGTTAAAAAGTTTGTATAGGT
AGGGGAAATGGCAAATGAGACAAGAATTTTTATAGCTCTGAAATTAACAAAATTAGGTTGATACC
TTTTTTTGTTACATATTTTAGTATCAGAGTCGTCATTCCTAACATAATGAAAGAAATATCACTTT
GAATATAGAAAAAAATGTACCTTACTTGAATAAGTTAAGTATTCGTCGCTTTATATACACAAATA
CCAAATTCTTAATTAGCATGGTTGTAAATAAAAGTCAATAGTTCCTAACAAGCGATAGCACCAAA
GTACAATTGTAAGATGTACTGTATTTGTAATCAATATGCTCTAACGAAAAGTGACAGATGCATAG
TTATGAAAAGAATTAGGTTGAACTGGTCGTTAGCCGATCCTCTGCCCGGACTTACAGGCGGATGA
GATCTTTCATAACTGCAAATATGCTCCAAAACAAGTTTTAGGGGACCAACTTCGCTATCTTACTT
TGATATATGTAACATCGAGTCCAAGAAGAAAGAGAATAATCTCTGGATGAAGTGTCCATATTAGG
AATACAACAACATCGAATGGGAGAAAACTTATTGTCTGGCAGTTGGAAAAGTTTTAATTCCAACC
AGCCATAAAATGTTC
Found at i:43462 original size:7 final size:6
Alignment explanation
Indices: 43438--43544 Score: 58
Period size: 6 Copynumber: 17.0 Consensus size: 6
43428 TAAAATCACT
** *
43438 ACCCTA ACCCT- ACCCTA ACCCCTA ACCCTA TTATACAA TACCCTA ACCCT-
1 ACCCTA ACCCTA ACCCTA A-CCCTA ACCCTA --ACCCTA -ACCCTA ACCCTA
* ** *
43488 ACCCTA CCCCTA ACCCTA TTATACAA TACCCTA ACCCT- ACCCTA ACCTCTA
1 ACCCTA ACCCTA ACCCTA --ACCCTA -ACCCTA ACCCTA ACCCTA ACC-CTA
43539 ACCCTA
1 ACCCTA
43545 TTATACAATA
Statistics
Matches: 78, Mismatches: 14, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
5 15 0.19
6 37 0.47
7 20 0.26
8 6 0.08
ACGTcount: A:0.32, C:0.46, G:0.00, T:0.22
Consensus pattern (6 bp):
ACCCTA
Found at i:43506 original size:38 final size:39
Alignment explanation
Indices: 43437--43566 Score: 244
Period size: 39 Copynumber: 3.4 Consensus size: 39
43427 CTAAAATCAC
43437 TACCCTAACCCTACCCTAACCCCTAACCCTATTATACAA
1 TACCCTAACCCTACCCTAACCCCTAACCCTATTATACAA
43476 TACCCTAACCCTACCCT-ACCCCTAACCCTATTATACAA
1 TACCCTAACCCTACCCTAACCCCTAACCCTATTATACAA
*
43514 TACCCTAACCCTACCCTAACCTCTAACCCTATTATACAA
1 TACCCTAACCCTACCCTAACCCCTAACCCTATTATACAA
43553 TACCCTAACCCTAC
1 TACCCTAACCCTAC
43567 TTAATCGGAT
Statistics
Matches: 89, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
38 38 0.43
39 51 0.57
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (39 bp):
TACCCTAACCCTACCCTAACCCCTAACCCTATTATACAA
Found at i:47615 original size:1 final size:1
Alignment explanation
Indices: 47609--47639 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
47599 TTATCTGGGG
47609 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
47640 CCTTATAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:52607 original size:36 final size:36
Alignment explanation
Indices: 52560--52631 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
52550 TACATCTAGA
52560 GTAGGGATGGCAACGGGTCGAATCGGGGCGGATTTT
1 GTAGGGATGGCAACGGGTCGAATCGGGGCGGATTTT
*
52596 GTAGGGATGGCAACGGGTCGGATCGGGGCGGATTTT
1 GTAGGGATGGCAACGGGTCGAATCGGGGCGGATTTT
52632 TGCCTATCCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.18, C:0.14, G:0.46, T:0.22
Consensus pattern (36 bp):
GTAGGGATGGCAACGGGTCGAATCGGGGCGGATTTT
Found at i:53763 original size:2 final size:2
Alignment explanation
Indices: 53752--53785 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
53742 GATGAATTAG
53752 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.