Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010035.1 Corchorus capsularis cultivar CVL-1 contig10056, 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: 58483
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:197 original size:31 final size:31
Alignment explanation
Indices: 152--316 Score: 145
Period size: 31 Copynumber: 5.2 Consensus size: 31
142 TTTTGTGCAT
* *
152 GTGGCATGCCATGTGTCACTTTTTGGTACAC
1 GTGGCGTGACATGTGTCACTTTTTGGTACAC
* * *
183 GTGGCGTAATATGTGTCACTTTTTGGTACAT
1 GTGGCGTGACATGTGTCACTTTTTGGTACAC
*
214 GTGGCGTGTTACA--TGTCAGTTTTTGGTACAC
1 GTGGCGTG--ACATGTGTCACTTTTTGGTACAC
* *
245 GTGACGTGACGTGACATGTGTCACTTTTTGGTATAT
1 GT---G-G-CGTGACATGTGTCACTTTTTGGTACAC
* * *
281 GTGGCATGCCACGTGTCACTTTTTGGTACAC
1 GTGGCGTGACATGTGTCACTTTTTGGTACAC
*
312 ATGGC
1 GTGGC
317 ATGCCACGTC
Statistics
Matches: 107, Mismatches: 18, Indels: 18
0.75 0.13 0.13
Matches are distributed among these distances:
31 77 0.72
32 1 0.01
33 3 0.03
34 4 0.04
35 1 0.01
36 21 0.20
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (31 bp):
GTGGCGTGACATGTGTCACTTTTTGGTACAC
Found at i:2156 original size:194 final size:193
Alignment explanation
Indices: 1760--2346 Score: 775
Period size: 193 Copynumber: 3.0 Consensus size: 193
1750 TATGACGCCT
* * *
1760 CTTTAAGCTCAATTCGGTTGAGTTT-AGTGTTGAGTACTTATAGCTGCAAGTGTTTGATATTTAT
1 CTTTAAGCTGAGTTAGGTTGAGTTTGAGTGTTGAGTACTTATAGCTGCAAGTGTTTGATATTTAT
* *
1824 GTATAGTAGTTCAGTTTTATAATTGAGCGAATCCCCCTGTTTGTTGCCAAATTGTGATTTTAATC
66 GTATAGTAGTTCAGTTATATAACTGAGCGAATCCCCCTGTTTGTTGCCAAATTGTGATTTTAATC
* *
1889 TGGGTTTTCTTGGTTTAAACTTTGCATTCTTTTTTCCCACTCGTGAATGTATGTAAGAGGTCA
131 TGGGTTTTCTTGGTTTAATCTTTGCATTCTTTTTTCCCACTTGTGAATGTATGTAAGAGGTCA
* * *
1952 CTTCAAGCTGAGTTGGGTTGAGTTTGAGTGTTGAGTACTTATAGCTACAAGTGTTTGATATTTAT
1 CTTTAAGCTGAGTTAGGTTGAGTTTGAGTGTTGAGTACTTATAGCTGCAAGTGTTTGATATTTAT
*
2017 GTATAGTAGTTCAGTTATATAAGTGAGCGAATCCCCCTGTTTGTTGCCAAAATTGTGATTTTAAT
66 GTATAGTAGTTCAGTTATATAACTGAGCGAATCCCCCTGTTTGTTGCC-AAATTGTGATTTTAAT
2082 CTGGGTTTTCTTGGTTTAATCTTTGCATTCTTTTTTCCCACTTGTGAATGTATGTAAGAGGTCA
130 CTGGGTTTTCTTGGTTTAATCTTTGCATTCTTTTTTCCCACTTGTGAATGTATGTAAGAGGTCA
* **
2146 CTTTAAGCTGAGTTAGGTTGAG-TTGAGTGTTGGGTTA-TCGTAGCTGCAAGTGTTTGATATTTA
1 CTTTAAGCTGAGTTAGGTTGAGTTTGAGTGTTGAG-TACTTATAGCTGCAAGTGTTTGATATTTA
* * * ** * **
2209 TGTGTAGTAATTCACTTATATACCACTGAGTAAATGCCCCCTGTTGATTTTTTGTGGGTAAATTG
65 TGTATAGTAGTTCAGTTATATA--ACTGAGCGAAT-CCCCC---TG----TTTGTTGCCAAATTG
* * ** * * *
2274 TGATTTGAATCTGGGTTTTCTTAGTGCAATCTTCGCATTCTTTTGTCTCACTTGTGAATGTATTG
120 TGATTTTAATCTGGGTTTTCTTGGTTTAATCTTTGCATTCTTTTTTCCCACTTGTGAATGTA-TG
2339 TAAGAGGT
184 TAAGAGGT
2347 TACTGGTTTA
Statistics
Matches: 350, Mismatches: 31, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
192 21 0.06
193 137 0.39
194 100 0.29
195 8 0.02
196 5 0.01
199 2 0.01
202 61 0.17
203 16 0.05
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (193 bp):
CTTTAAGCTGAGTTAGGTTGAGTTTGAGTGTTGAGTACTTATAGCTGCAAGTGTTTGATATTTAT
GTATAGTAGTTCAGTTATATAACTGAGCGAATCCCCCTGTTTGTTGCCAAATTGTGATTTTAATC
TGGGTTTTCTTGGTTTAATCTTTGCATTCTTTTTTCCCACTTGTGAATGTATGTAAGAGGTCA
Found at i:3222 original size:46 final size:46
Alignment explanation
Indices: 3151--3244 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
3141 TAGATTATGA
3151 TTCTTGTGAACACTTGCATTCATTGTTAGCCTAATCGTAATTGATG
1 TTCTTGTGAACACTTGCATTCATTGTTAGCCTAATCGTAATTGATG
* *
3197 TTCTTGTGAATACTTGCATTTATTGTTAGCCTAATCGTAATTGATG
1 TTCTTGTGAACACTTGCATTCATTGTTAGCCTAATCGTAATTGATG
3243 TT
1 TT
3245 AATCCACTGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (46 bp):
TTCTTGTGAACACTTGCATTCATTGTTAGCCTAATCGTAATTGATG
Found at i:13802 original size:199 final size:199
Alignment explanation
Indices: 13462--13862 Score: 775
Period size: 199 Copynumber: 2.0 Consensus size: 199
13452 TAGGGCTAGT
13462 ACATATATATATAAATAATCATTTGCCCTCATTTGACTGTTCAACGTTTCCAGATAGTTGTTAGT
1 ACATATATATATAAATAATCATTTGCCCTCATTTGACTGTTCAACGTTTCCAGATAGTTGTTAGT
*
13527 TATTCAGCGAGAGACGAAGTGATTTAGAGAGCTACGAAGATCCAGATCCATGGCGCCTTTCCGTA
66 TATTCAGCGAGAGACGAAGTGATTTAGAGAGCTACGAAGATCCAGATCAATGGCGCCTTTCCGTA
13592 CGGACTTCAAATGCAGAACTTGCGGTAAAACCTTGTTTCTTTCTGTCTCCGAGTCCACCACTCAC
131 CGGACTTCAAATGCAGAACTTGCGGTAAAACCTTGTTTCTTTCTGTCTCCGAGTCCACCACTCAC
13657 GCGA
196 GCGA
13661 ACATATATATATAAATAATCATTTGCCCTCATTTGACTGTTCAACGTTTCCAGATAGTTGTTAGT
1 ACATATATATATAAATAATCATTTGCCCTCATTTGACTGTTCAACGTTTCCAGATAGTTGTTAGT
*
13726 TATTCAGCGAGAGACGAAGTGATTTAGAGAGCTATGAAGATCCAGATCAATGGCGCCTTTCCGTA
66 TATTCAGCGAGAGACGAAGTGATTTAGAGAGCTACGAAGATCCAGATCAATGGCGCCTTTCCGTA
*
13791 CGGACTTCAAATGCAGAACTTGCGGTAAGACCTTGTTTCTTTCTGTCTCCGAGTCCACCACTCAC
131 CGGACTTCAAATGCAGAACTTGCGGTAAAACCTTGTTTCTTTCTGTCTCCGAGTCCACCACTCAC
13856 GCGA
196 GCGA
13860 ACA
1 ACA
13863 CCTGCGTTGT
Statistics
Matches: 199, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
199 199 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (199 bp):
ACATATATATATAAATAATCATTTGCCCTCATTTGACTGTTCAACGTTTCCAGATAGTTGTTAGT
TATTCAGCGAGAGACGAAGTGATTTAGAGAGCTACGAAGATCCAGATCAATGGCGCCTTTCCGTA
CGGACTTCAAATGCAGAACTTGCGGTAAAACCTTGTTTCTTTCTGTCTCCGAGTCCACCACTCAC
GCGA
Found at i:13914 original size:28 final size:28
Alignment explanation
Indices: 13874--13935 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
13864 CTGCGTTGTA
13874 AGATTCATCCTCATCATTTTATTTGAAG
1 AGATTCATCCTCATCATTTTATTTGAAG
* *
13902 AGATTCATTCTCATTATTTTATTTGAAG
1 AGATTCATCCTCATCATTTTATTTGAAG
*
13930 TGATTC
1 AGATTC
13936 GATGGATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (28 bp):
AGATTCATCCTCATCATTTTATTTGAAG
Found at i:16323 original size:16 final size:16
Alignment explanation
Indices: 16302--16354 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
16292 TCACGAACAA
*
16302 TATATATTTTAATATT
1 TATATATATTAATATT
* * *
16318 TATATAAAAT-ATAAT
1 TATATATATTAATATT
16333 TATATATATTAATATT
1 TATATATATTAATATT
16349 TATATA
1 TATATA
16355 AATAAAAATA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATATATTAATATT
Found at i:16341 original size:25 final size:25
Alignment explanation
Indices: 16300--16347 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
16290 GTTCACGAAC
* *
16300 AATATATATTTTAATATTTATATAA
1 AATATATATTATAATATTAATATAA
16325 AATATA-ATTATATATATTAATAT
1 AATATATATTATA-ATATTAATAT
16348 TTATATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AATATATATTATAATATTAATATAA
Found at i:16370 original size:36 final size:36
Alignment explanation
Indices: 16318--16396 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
16308 TTTTAATATT
16318 TATATAAAATATAATTATATATAT-TAATATTTATATAA
1 TATA-AAAATATAATTATATATATATAATA--TATATAA
*
16356 -ATAAAAATATAATTATTTATATATAATATATATAA
1 TATAAAAATATAATTATATATATATAATATATATAA
16391 TATAAA
1 TATAAA
16397 CGGACATACT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
35 7 0.18
36 23 0.61
37 8 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (36 bp):
TATAAAAATATAATTATATATATATAATATATATAA
Found at i:19512 original size:11 final size:11
Alignment explanation
Indices: 19496--19527 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
19486 GGTGGGAATA
19496 ACATTCCCACC
1 ACATTCCCACC
19507 ACATTCCCACC
1 ACATTCCCACC
19518 ACATTCCCAC
1 ACATTCCCAC
19528 TCAAGTGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.53, G:0.00, T:0.19
Consensus pattern (11 bp):
ACATTCCCACC
Found at i:29973 original size:5 final size:5
Alignment explanation
Indices: 29963--29990 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
29953 TTTGACGCGG
29963 ACTGA ACTGA ACTGA ACTGA ACTGA ACT
1 ACTGA ACTGA ACTGA ACTGA ACTGA ACT
29991 CATCCAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (5 bp):
ACTGA
Found at i:40572 original size:84 final size:85
Alignment explanation
Indices: 40404--40748 Score: 588
Period size: 84 Copynumber: 4.0 Consensus size: 85
40394 AGTTTGCGCC
*
40404 TTTGCGGTGGTTTTCTTTTCCAATGGATAGTATTT-TTTTTAAAAAAAAAAAGTTGCAAAATACA
1 TTTGCAGTGGTTTTCTTTTCCAATGGATAGTATTTCTTTTT----AAAAAAAGTTGCAAAATACA
40468 TTTTTACCCTAATTTAATTGGTGT
62 TTTTTACCCTAATTTAATTGGTGT
40492 TTTGCAGTGGTTTTCTTTTCCAATGGATAGTATTTCTTTTT-AAAAAAGTTGCAAAATACATTTT
1 TTTGCAGTGGTTTTCTTTTCCAATGGATAGTATTTCTTTTTAAAAAAAGTTGCAAAATACATTTT
40556 TACCCTAATTTAATTGGTGT
66 TACCCTAATTTAATTGGTGT
40576 TTTGCAGTGGTTTTCTTTTCCAATGGATAGTATTTCTTTTT-AAAAAAGTTGCAAAATACATTTT
1 TTTGCAGTGGTTTTCTTTTCCAATGGATAGTATTTCTTTTTAAAAAAAGTTGCAAAATACATTTT
*
40640 TACCCTAATTTAATTGGTGA
66 TACCCTAATTTAATTGGTGT
* *
40660 TTTGCGGTGGTTTTCTTTTCCAATGGATAGTATTTTTTTTTAAAAAAAGTTGCAAAATACATTTT
1 TTTGCAGTGGTTTTCTTTTCCAATGGATAGTATTTCTTTTTAAAAAAAGTTGCAAAATACATTTT
40725 TACCCTAATTTAATTGGTGAT
66 TACCCTAATTTAATTGGTG-T
40746 TTT
1 TTT
40749 CTTTCAAATT
Statistics
Matches: 249, Mismatches: 5, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
84 165 0.66
85 42 0.17
86 3 0.01
88 34 0.14
89 5 0.02
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.46
Consensus pattern (85 bp):
TTTGCAGTGGTTTTCTTTTCCAATGGATAGTATTTCTTTTTAAAAAAAGTTGCAAAATACATTTT
TACCCTAATTTAATTGGTGT
Found at i:41064 original size:13 final size:13
Alignment explanation
Indices: 41046--41075 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41036 TTTTGACATT
*
41046 ATAATTAGTATAG
1 ATAATTAGTAGAG
41059 ATAATTAGTAGAG
1 ATAATTAGTAGAG
41072 ATAA
1 ATAA
41076 ATAAAATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (13 bp):
ATAATTAGTAGAG
Found at i:42449 original size:28 final size:28
Alignment explanation
Indices: 42409--42464 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
42399 TGGGTTCTCT
42409 ATTTCTAATGGAAGATGCTTAAAGAGAA
1 ATTTCTAATGGAAGATGCTTAAAGAGAA
42437 ATTTCTAATGGAAGATGCTTAAAGAGAA
1 ATTTCTAATGGAAGATGCTTAAAGAGAA
42465 TGAAGAGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (28 bp):
ATTTCTAATGGAAGATGCTTAAAGAGAA
Found at i:50336 original size:21 final size:21
Alignment explanation
Indices: 50312--50358 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
50302 TATTGGTTTC
50312 TTTGCCGACTTTTTCTTTGGA
1 TTTGCCGACTTTTTCTTTGGA
* **
50333 TTTGTCTTCTTTTTCTTTGGA
1 TTTGCCGACTTTTTCTTTGGA
50354 TTTGC
1 TTTGC
50359 TACAATCCGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.06, C:0.17, G:0.17, T:0.60
Consensus pattern (21 bp):
TTTGCCGACTTTTTCTTTGGA
Found at i:50473 original size:30 final size:30
Alignment explanation
Indices: 50437--50493 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
50427 CCGCAGACGT
50437 CGTGGCCGCCACA-GAGGACGCCGAAGCCGG
1 CGTGGCCGCCACAGGA-GACGCCGAAGCCGG
*
50467 CGTGGCCGCCACAGGAGACGCTGAAGC
1 CGTGGCCGCCACAGGAGACGCCGAAGC
50494 GGCCAGCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.21, C:0.35, G:0.39, T:0.05
Consensus pattern (30 bp):
CGTGGCCGCCACAGGAGACGCCGAAGCCGG
Found at i:50704 original size:34 final size:34
Alignment explanation
Indices: 50659--50766 Score: 106
Period size: 34 Copynumber: 3.4 Consensus size: 34
50649 AAATGAAAAC
*
50659 GGAGAGAGAAAAGGCTAAACTGAAACGACGGATT
1 GGAGAGGGAAAAGGCTAAACTGAAACGACGGATT
* *
50693 GGAGAGGGAAAA-TCTAAAAATGAAA--ACGGA--
1 GGAGAGGGAAAAGGCT-AAACTGAAACGACGGATT
*
50723 -GAGA--GAAAAGGCTGAACTGAAACGACGGATT
1 GGAGAGGGAAAAGGCTAAACTGAAACGACGGATT
*
50754 GGATAGGGAAAAG
1 GGAGAGGGAAAAG
50767 CTCTGGGAGG
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
27 12 0.21
28 2 0.03
29 9 0.16
32 8 0.14
33 2 0.03
34 25 0.43
ACGTcount: A:0.46, C:0.09, G:0.33, T:0.11
Consensus pattern (34 bp):
GGAGAGGGAAAAGGCTAAACTGAAACGACGGATT
Found at i:50741 original size:61 final size:61
Alignment explanation
Indices: 50642--50765 Score: 230
Period size: 61 Copynumber: 2.0 Consensus size: 61
50632 TAGGAAAGAG
50642 AATCTAAAAATGAAAACGGAGAGAGAAAAGGCTAAACTGAAACGACGGATTGGAGAGGGAA
1 AATCTAAAAATGAAAACGGAGAGAGAAAAGGCTAAACTGAAACGACGGATTGGAGAGGGAA
* *
50703 AATCTAAAAATGAAAACGGAGAGAGAAAAGGCTGAACTGAAACGACGGATTGGATAGGGAA
1 AATCTAAAAATGAAAACGGAGAGAGAAAAGGCTAAACTGAAACGACGGATTGGAGAGGGAA
50764 AA
1 AA
50766 GCTCTGGGAG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.49, C:0.10, G:0.29, T:0.12
Consensus pattern (61 bp):
AATCTAAAAATGAAAACGGAGAGAGAAAAGGCTAAACTGAAACGACGGATTGGAGAGGGAA
Found at i:51764 original size:16 final size:16
Alignment explanation
Indices: 51743--51773 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51733 TTGAAAAATA
51743 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
51759 TTACTAAATCTTTAT
1 TTACTAAATATTTAT
51774 AATTTGTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTAAATATTTATT
Found at i:52803 original size:202 final size:202
Alignment explanation
Indices: 52435--52858 Score: 656
Period size: 202 Copynumber: 2.1 Consensus size: 202
52425 TGTCAACCCG
*
52435 TGCAGTCTGCTAAACTCCACTGACAGTGTATTGCATAAATTTTCTTATAGGATTATTATACAATA
1 TGCAGTCTGCTAAACTCCACTGACAGGGTATTGCATAAATTTTCTTATAGGATTATTATACAATA
* *
52500 CACTGTCAGTATAAATTTTGGACTCCATAAACGGGTTAAAAAGTTGACACATATCCCATTTTATA
66 CACTGTCAGTATAAATTTTGAACTCCATAAACGGGTTAAAAAGTTGACACATATCCCATTTCATA
*
52565 ATTAAATATTTAATATTAATACATATTCCGTAAGGGTACACATGTCAACCCT-TAAAGTTAAA-C
131 ATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTATAAAGTTAAACC
52628 CCTGCACA
196 CCT-CACA
* * * * *
52636 TGCAGTCTGCTAAACTCCAGTGGCAGGGTATTGCATAATTTTTCTTATAGGATTATTTTTCAATA
1 TGCAGTCTGCTAAACTCCACTGACAGGGTATTGCATAAATTTTCTTATAGGATTATTATACAATA
* * *
52701 CACTGTCAGTATAAAATTTTGAACTCCATAAGCGGGTTAAAAAGTTGAGACATA-CTCTATTTCA
66 CACTGTCAGTAT-AAATTTTGAACTCCATAAACGGGTTAAAAAGTTGACACATATC-CCATTTCA
52765 TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTCATAAAGTTAA
129 TAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCT-ATAAAGTTAA
*
52830 ACCCCTCACG
193 ACCCCTCACA
* *
52840 TGTAGTCTTCTAAACTCCA
1 TGCAGTCTGCTAAACTCCA
52859 TTAACGATAT
Statistics
Matches: 203, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
201 72 0.35
202 97 0.48
204 30 0.15
205 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (202 bp):
TGCAGTCTGCTAAACTCCACTGACAGGGTATTGCATAAATTTTCTTATAGGATTATTATACAATA
CACTGTCAGTATAAATTTTGAACTCCATAAACGGGTTAAAAAGTTGACACATATCCCATTTCATA
ATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTCAACCCTATAAAGTTAAACC
CCTCACA
Found at i:53932 original size:14 final size:14
Alignment explanation
Indices: 53913--53944 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
53903 GAAAAAGTAC
53913 ATATAATTTTCCAT
1 ATATAATTTTCCAT
*
53927 ATATAATTTTTCAT
1 ATATAATTTTCCAT
53941 ATAT
1 ATAT
53945 TAACACCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATAATTTTCCAT
Found at i:54501 original size:20 final size:21
Alignment explanation
Indices: 54478--54516 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
54468 TCCTTGGCTT
54478 AATTAGATTTT-TTTATACCG
1 AATTAGATTTTCTTTATACCG
54498 AATTAGATTTTCTTTATAC
1 AATTAGATTTTCTTTATAC
54517 TTTCCTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (21 bp):
AATTAGATTTTCTTTATACCG
Found at i:54643 original size:42 final size:42
Alignment explanation
Indices: 54596--54684 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
54586 TGACCCAAAA
54596 AGAATGCTGACGGGTTCAATTTAGCAAAATTTTAGGTGAATT
1 AGAATGCTGACGGGTTCAATTTAGCAAAATTTTAGGTGAATT
*
54638 AGAATGTTGACGGGTTCAATTTAGCAAAATTTTAGGTGAATT
1 AGAATGCTGACGGGTTCAATTTAGCAAAATTTTAGGTGAATT
54680 AGAAT
1 AGAAT
54685 ATCGTATCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.34
Consensus pattern (42 bp):
AGAATGCTGACGGGTTCAATTTAGCAAAATTTTAGGTGAATT
Found at i:56614 original size:57 final size:58
Alignment explanation
Indices: 56518--56673 Score: 167
Period size: 58 Copynumber: 2.7 Consensus size: 58
56508 GACACAAGTT
* * * *
56518 ATCTATCTCTGGATGGAAGACACAGTTTTAGAGACGTTTAT-CGATAGAGACATAA-CCAA
1 ATCTGTCTCTGAATGG-AGACAC-GTCTTAGAGACGTTTATACG-TAGAGACATAAGCAAA
*
56577 A-CTGTCTCTGAATGGAGACACGGTCTTAGAGACGTTTATACGTTGAGACATAAGCAAA
1 ATCTGTCTCTGAATGGAGACAC-GTCTTAGAGACGTTTATACGTAGAGACATAAGCAAA
* * *
56635 ATCTGTCTCTGGAAAGCAGACA-GTCTTAGAGACATTTAT
1 ATCTGTCTCT-GAATGGAGACACGTCTTAGAGACGTTTAT
56674 TTAGACTAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
57 32 0.38
58 34 0.40
59 9 0.11
60 9 0.11
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (58 bp):
ATCTGTCTCTGAATGGAGACACGTCTTAGAGACGTTTATACGTAGAGACATAAGCAAA
Found at i:56673 original size:58 final size:55
Alignment explanation
Indices: 56539--56673 Score: 155
Period size: 57 Copynumber: 2.4 Consensus size: 55
56529 GATGGAAGAC
* * * *
56539 ACAGTTTTAGAGACGTTTATCGATAGAGACATAACCAAACTGTCTCTGAATGGAG
1 ACAGTCTTAGAGACGTTTATCGATAGAGACATAACAAAACTGTCTCTGAAAGCAG
*
56594 ACACGGTCTTAGAGACGTTTATACG-TTGAGACATAAGCAAAATCTGTCTCTGGAAAGCAG
1 ACA--GTCTTAGAGACGTTTAT-CGATAGAGACATAA-CAAAA-CTGTCTCT-GAAAGCAG
*
56654 ACAGTCTTAGAGACATTTAT
1 ACAGTCTTAGAGACGTTTAT
56674 TTAGACTAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
55 3 0.04
57 26 0.38
58 22 0.32
59 8 0.12
60 9 0.13
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (55 bp):
ACAGTCTTAGAGACGTTTATCGATAGAGACATAACAAAACTGTCTCTGAAAGCAG
Done.