Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024068.1 Corchorus olitorius cultivar O-4 contig24101, 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: 46957
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:5469 original size:22 final size:22
Alignment explanation
Indices: 5439--5481 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5429 GAATTTCAGA
* *
5439 ACAAGTCCTGCCCAGGACTTGG
1 ACAACTCCTACCCAGGACTTGG
*
5461 ACAACTCCTACCTAGGACTTG
1 ACAACTCCTACCCAGGACTTG
5482 TCGCGGGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.21
Consensus pattern (22 bp):
ACAACTCCTACCCAGGACTTGG
Found at i:7309 original size:88 final size:89
Alignment explanation
Indices: 7217--7380 Score: 251
Period size: 89 Copynumber: 1.9 Consensus size: 89
7207 GTAAAATGGC
*
7217 AAAAATAAAATAGGTATAAAAATATTAGATTTAA-TAAGAT-AAAAATAGAGTTTTTAATTGAAT
1 AAAAATAAAATAGGTATAAAAATATTAGACTTAATTAA-ATAAAAAATAGAGTTTTTAATTGAAT
7280 AAAACTATAAAAATAGTAAACTGCT
65 AAAACTATAAAAATAGTAAACTGCT
* ** * *
7305 AAAAATAAAATAGTTATAAGGATATTAGACTTAATTAAATAAAAAATAGAGTTTTTAGTTGAGTA
1 AAAAATAAAATAGGTATAAAAATATTAGACTTAATTAAATAAAAAATAGAGTTTTTAATTGAATA
7370 AAACTATAAAA
66 AAACTATAAAA
7381 CTTTAAATAA
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
88 32 0.47
89 36 0.53
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.31
Consensus pattern (89 bp):
AAAAATAAAATAGGTATAAAAATATTAGACTTAATTAAATAAAAAATAGAGTTTTTAATTGAATA
AAACTATAAAAATAGTAAACTGCT
Found at i:9366 original size:2 final size:2
Alignment explanation
Indices: 9359--9388 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
9349 TCAGAGGCTT
*
9359 TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9389 CACATGGTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:10630 original size:19 final size:19
Alignment explanation
Indices: 10603--10645 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
10593 ATTATAATTA
*
10603 TAAGCAATGCATTTTAATG
1 TAAGTAATGCATTTTAATG
10622 TAAGTAATGCATTTTAATG
1 TAAGTAATGCATTTTAATG
10641 TAAGT
1 TAAGT
10646 TAGGTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (19 bp):
TAAGTAATGCATTTTAATG
Found at i:13644 original size:44 final size:44
Alignment explanation
Indices: 13581--13669 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
13571 CTTGATTTGG
*
13581 ATGGTTTTTCGCTTGGCCTTGTCTTCCATTTGTGGTTTCCATGT
1 ATGGTTTTTCGCTTGGCCTTGTCTTCCATTTGTGGTTGCCATGT
13625 ATGGTTTTTCGCTTGGCCTTGTCTTCCATTTGTGGTTGCCATGT
1 ATGGTTTTTCGCTTGGCCTTGTCTTCCATTTGTGGTTGCCATGT
13669 A
1 A
13670 CTTCATATGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.08, C:0.20, G:0.24, T:0.48
Consensus pattern (44 bp):
ATGGTTTTTCGCTTGGCCTTGTCTTCCATTTGTGGTTGCCATGT
Found at i:16402 original size:205 final size:206
Alignment explanation
Indices: 16030--16421 Score: 477
Period size: 205 Copynumber: 1.9 Consensus size: 206
16020 TAGGTATAAC
* *
16030 TATAACAAATAGAGCAACTTTACCAACGAAGGGTTGGATCGAGTGATTAGCAGCTCGTCTAAGCT
1 TATAACAAATAGAGCAACTTTACCAACGAAGGGTTGAATCGAGTGATTAGCAGCTCGTCTAAACT
* * * * **
16095 TAAGCAGGTCTTAGCTTCGCAACCTTGCGTACGCACCCGCTTTCGTTGATAGTTTCACCCACTAA
66 TAAGCAGGTCTTAGCTTCGCAACCTTGCGTACACAACCACTTTCATTGATAGACTCACCCACTAA
* * * *
16160 ACCTAGGTGCACGATGCAAGTTAAATTCGGGTTAATCAAAACAAAACTCTAAATACCCTTGAAGT
131 ACCTAGATGCACGACGCAAGTTAAATTAGGATTAATCAAAACAAAACTCTAAATACCCTTGAAGT
16225 ATCAGATTAGG
196 ATCAGATTAGG
* * * * * * * * *
16236 TATAACAAATAGAGTAACTTTATCAACG-TGGGTTGAATCTAGTGGTTAGCATCTTGTTTAAATT
1 TATAACAAATAGAGCAACTTTACCAACGAAGGGTTGAATCGAGTGATTAGCAGCTCGTCTAAACT
* * *
16300 TAAGCAGGTCTTAGTTTCGCCACTTTGCGTACACAACCACTTTCATTGATAGACTCACCCA-TCA
66 TAAGCAGGTCTTAGCTTCGCAACCTTGCGTACACAACCACTTTCATTGATAGACTCACCCACT-A
* * * *
16364 AATCC-AGATGCGCGACGCGAGTT-GATATAGGATTAATCAAAACAAATCTCTAAATACC
130 AA-CCTAGATGCACGACGCAAGTTAAAT-TAGGATTAATCAAAACAAAACTCTAAATACC
16422 AGGTAGAATA
Statistics
Matches: 155, Mismatches: 28, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
204 3 0.02
205 124 0.80
206 28 0.18
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.28
Consensus pattern (206 bp):
TATAACAAATAGAGCAACTTTACCAACGAAGGGTTGAATCGAGTGATTAGCAGCTCGTCTAAACT
TAAGCAGGTCTTAGCTTCGCAACCTTGCGTACACAACCACTTTCATTGATAGACTCACCCACTAA
ACCTAGATGCACGACGCAAGTTAAATTAGGATTAATCAAAACAAAACTCTAAATACCCTTGAAGT
ATCAGATTAGG
Found at i:26512 original size:2 final size:2
Alignment explanation
Indices: 26501--26546 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
26491 GGTGAACTAC
26501 AT AT AT -T AT 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 AT AT AT AT AT
26542 AT AT A
1 AT AT A
26547 AGACACAGGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27606 original size:3 final size:3
Alignment explanation
Indices: 27593--27623 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
27583 TTTACTGAAA
27593 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
27624 AGAATTCCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:32300 original size:102 final size:105
Alignment explanation
Indices: 32116--32387 Score: 344
Period size: 102 Copynumber: 2.6 Consensus size: 105
32106 AACTTTTAAT
** * *
32116 TTTAATTT-GGGCTAATTTTAGTG-AATTCGTTATATATTTTATTTCTAAAACCCTAT--AATAA
1 TTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAAAATAA
*
32177 ATTATTAATTATGGAATTTACCCTTAAAAT-AAAA-AAAA
66 ATTATTAATTATGAAATTTACCCTTAAAATAAAAATAAAA
*
32215 -TTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTA-TTTATTTCTAAAACCCTATAACAATA
1 TTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAA-AATA
*
32278 AATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAAAA
65 AATTATTAATTATGAAATTTACCCTTAAAATAAAAATAAAA
* * **
32319 TTTTAATTTGGGACTAAACTTAGTGAAATTATTTTTATATATTTTATTTCTAAAATTCTATAATA
1 -TTTAATTTGGGGCTAAACTTAGTGAAATTA-GTTT-TATATTTTATTTCTAAAACCCTATAA-A
32384 ATAA
62 ATAA
32388 TAAAAAAAAG
Statistics
Matches: 148, Mismatches: 13, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
98 7 0.05
99 32 0.22
100 10 0.07
102 33 0.22
103 4 0.03
104 4 0.03
106 28 0.19
107 3 0.02
108 3 0.02
109 24 0.16
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.43
Consensus pattern (105 bp):
TTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCTAAAACCCTATAAAATAA
ATTATTAATTATGAAATTTACCCTTAAAATAAAAATAAAA
Found at i:33347 original size:12 final size:13
Alignment explanation
Indices: 33330--33391 Score: 110
Period size: 12 Copynumber: 4.9 Consensus size: 13
33320 CATTGATACC
33330 TCGATATATCCG-
1 TCGATATATCCGT
33342 TCGATATATCCGT
1 TCGATATATCCGT
33355 TCGATATATCCG-
1 TCGATATATCCGT
33367 TCGATATATCCGT
1 TCGATATATCCGT
33380 TCGATATATCCG
1 TCGATATATCCG
33392 CAGATATCTG
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
12 24 0.50
13 24 0.50
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (13 bp):
TCGATATATCCGT
Found at i:33398 original size:25 final size:25
Alignment explanation
Indices: 33330--33391 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
33320 CATTGATACC
33330 TCGATATATCCGTCGATATATCCGT
1 TCGATATATCCGTCGATATATCCGT
33355 TCGATATATCCGTCGATATATCCGT
1 TCGATATATCCGTCGATATATCCGT
33380 TCGATATATCCG
1 TCGATATATCCG
33392 CAGATATCTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.35
Consensus pattern (25 bp):
TCGATATATCCGTCGATATATCCGT
Found at i:34805 original size:20 final size:20
Alignment explanation
Indices: 34780--34818 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
34770 CATATAAAAT
*
34780 AATAATAACTAATTTTTAAA
1 AATAATAACTAATTATTAAA
34800 AATAATAACTAATTATTAA
1 AATAATAACTAATTATTAA
34819 TTTAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAATAACTAATTATTAAA
Found at i:35040 original size:105 final size:106
Alignment explanation
Indices: 34858--35057 Score: 253
Period size: 105 Copynumber: 1.9 Consensus size: 106
34848 CGCGCGCGGC
* * * ** * *
34858 TGGCTTGGTCGCGAGCCGTGGTCGCTCGTGCGACCAAGCCGCGGCTCGGTCGCGTGCGGCTTGCG
1 TGGCTTGATCGCGAGCCGTGGTCGCTCG-GCGACCAAGCCACGGCTCGGTCACGCCCGACTCGCG
* *
34923 ACTATGTCGCGGCTTGGTCGCGAGCCGCGCGTGACCGAGCCG
65 ACTATGCCGCGGCTTGGTCGCAAGCCGCGCGTGACCGAGCCG
* *
34965 TGGCTTGATCGCGAGCCTTGGTCGCTC-GCGACCAAGCCATGGCTCGGTCACGCCCGACTCGCGA
1 TGGCTTGATCGCGAGCCGTGGTCGCTCGGCGACCAAGCCACGGCTCGGTCACGCCCGACTCGCGA
35029 -T-TGAACCGCGGCTTGGTCGCAAGCCGCGC
66 CTATG--CCGCGGCTTGGTCGCAAGCCGCGC
35058 ACGACCAAGC
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
103 2 0.03
104 1 0.01
105 52 0.65
107 25 0.31
ACGTcount: A:0.11, C:0.34, G:0.36, T:0.18
Consensus pattern (106 bp):
TGGCTTGATCGCGAGCCGTGGTCGCTCGGCGACCAAGCCACGGCTCGGTCACGCCCGACTCGCGA
CTATGCCGCGGCTTGGTCGCAAGCCGCGCGTGACCGAGCCG
Found at i:35222 original size:17 final size:15
Alignment explanation
Indices: 35174--35223 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 15
35164 CTTGAATAAC
*
35174 TGAAGTTTGAAAATT
1 TGAAGATTGAAAATT
35189 TGAAGATTGAGAGAATT
1 TGAAGATTGA-A-AATT
35206 TGAGAGAATTGAAAATT
1 TGA-AG-ATTGAAAATT
35223 T
1 T
35224 TGAAATTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 9 0.30
16 1 0.03
17 12 0.40
18 3 0.10
19 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.34
Consensus pattern (15 bp):
TGAAGATTGAAAATT
Found at i:39607 original size:18 final size:18
Alignment explanation
Indices: 39584--39621 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
39574 TGATATTTGG
39584 TATGTATGAATGATCTAA
1 TATGTATGAATGATCTAA
39602 TATGTATGAATGATCTAA
1 TATGTATGAATGATCTAA
39620 TA
1 TA
39622 AACAGTAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (18 bp):
TATGTATGAATGATCTAA
Found at i:39813 original size:26 final size:26
Alignment explanation
Indices: 39777--39881 Score: 162
Period size: 26 Copynumber: 4.1 Consensus size: 26
39767 TAGCTGAGAA
39777 TCAGACTTCATTTCTCCTTATTTATT
1 TCAGACTTCATTTCTCCTTATTTATT
39803 TCAGACTTCATTTCTCCTTATTTATT
1 TCAGACTTCATTTCTCCTTATTTATT
*
39829 TC--TCTTC-TCCTTCTCCTTATTTATT
1 TCAGACTTCAT--TTCTCCTTATTTATT
39854 TCAGACTTCATTTCTCCTTATTTATT
1 TCAGACTTCATTTCTCCTTATTTATT
39880 TC
1 TC
39882 TCTTCTCCTT
Statistics
Matches: 72, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
23 1 0.01
24 4 0.06
25 17 0.24
26 45 0.62
27 4 0.06
28 1 0.01
ACGTcount: A:0.16, C:0.26, G:0.03, T:0.55
Consensus pattern (26 bp):
TCAGACTTCATTTCTCCTTATTTATT
Found at i:39864 original size:51 final size:51
Alignment explanation
Indices: 39788--39891 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
39778 CAGACTTCAT
39788 TTCTCCTTATTTATTTCAGACTTCATTTCTCCTTATTTATTTCTCTTCTCC
1 TTCTCCTTATTTATTTCAGACTTCATTTCTCCTTATTTATTTCTCTTCTCC
39839 TTCTCCTTATTTATTTCAGACTTCATTTCTCCTTATTTATTTCTCTTCTCC
1 TTCTCCTTATTTATTTCAGACTTCATTTCTCCTTATTTATTTCTCTTCTCC
39890 TT
1 TT
39892 ATTTATTTCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.13, C:0.27, G:0.02, T:0.58
Consensus pattern (51 bp):
TTCTCCTTATTTATTTCAGACTTCATTTCTCCTTATTTATTTCTCTTCTCC
Found at i:39889 original size:19 final size:19
Alignment explanation
Indices: 39865--39903 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
39855 CAGACTTCAT
39865 TTCTCCTTATTTATTTCTC
1 TTCTCCTTATTTATTTCTC
39884 TTCTCCTTATTTATTTCTC
1 TTCTCCTTATTTATTTCTC
39903 T
1 T
39904 GGTAACATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.26, G:0.00, T:0.64
Consensus pattern (19 bp):
TTCTCCTTATTTATTTCTC
Found at i:40705 original size:7 final size:7
Alignment explanation
Indices: 40695--40724 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
40685 TATTTATGCT
40695 TGTCAAA
1 TGTCAAA
40702 TGTCAAA
1 TGTCAAA
40709 TGTCAAA
1 TGTCAAA
40716 TGTCAAA
1 TGTCAAA
40723 TG
1 TG
40725 CAGCTTCTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (7 bp):
TGTCAAA
Found at i:43181 original size:33 final size:33
Alignment explanation
Indices: 43144--43213 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
43134 ACTAGAACAA
43144 TGAAGCTAAATTCTCAAAAGAATTCTCTTTGAT
1 TGAAGCTAAATTCTCAAAAGAATTCTCTTTGAT
43177 TGAAGCTAAATTCTCAAAAGAATTCTCTTTGAT
1 TGAAGCTAAATTCTCAAAAGAATTCTCTTTGAT
43210 TGAA
1 TGAA
43214 AAACTTAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (33 bp):
TGAAGCTAAATTCTCAAAAGAATTCTCTTTGAT
Found at i:45292 original size:438 final size:437
Alignment explanation
Indices: 44282--45429 Score: 1164
Period size: 438 Copynumber: 2.6 Consensus size: 437
44272 AATAGATTGC
* * * *
44282 CAATCGAAATCACAAAATTTCAAAAGCATTTTTTAGAATTGAAACATTAAAATTAGCTTTTGAAT
1 CAATCGAAACCACAAAATTTTAGAAGCATTTTTTAGAATTGAAACATTAAAATT-GCTTTTGATT
* * * **
44347 CTTTCATGAAAGTTGTAGATCATAAAATTACCTTTCAATAGACACCTGAATTACCTTAATTAGAC
65 C-TTCATGAAAGTTGTAGATCATAAAATTACCTTTTAATAGACACATGAATCACCTTAATCGGAC
* *
44412 AAATAGAACAAAGAA-AATAAAAAA-AAATGAAGCGTTAAATCGAGTAAGATAGAATTTGTAAAG
129 AAATAGAACAAAGAATAA-AAAAAATAAATGAAACGTTAAAT---GTAAGATAAAATTTGTAAAG
* * * * * *
44475 GACTAAGTAGCATAAAATAGAAAAGTATGAGGGTGATTTGATAACTAATTCAAATAAAATAATAT
190 GACTAAGTAGCATAAAAGAGAAAAGCATGAGGGTCATTTGATAAATAATCCAAATAAAAAAATAT
* ** * * * *
44540 TTGTTAATGGAGATCTTGAAACATAAAATTTTTCTTTTGAACCCTTCATGAAACTCGTAGATCAA
255 TTGTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACACTTCACGAAACTCATAGATAAA
* * * * * * *
44605 ATTAACTTTCGGGTTCTTCATAAAAGTCGTAGATTATATAGTAACCTTTTAACCGACACTTGAAT
320 ATTAACTTTCGGGTCCTTCATAAAAGTCATAAATCATACAATAACCTTTTAACCGACACTTCAAT
* * * * * * * * *
44670 AATTTTAATTGGACATGTGGATCGAACATTATATATGGTATTAAATAGACTAA
385 AACTTCAATCGGACATGTGGATCAAAAAATATATACGATATTAAATAGACCAA
* *
44723 CAATCGAAACGATC-AAA-TTTAGCAAGCATTTTTTTTA-AATTGAAACA-T--AATTACTTTTG
1 CAATCGAAACCA-CAAAATTTTAG-AAGCA--TTTTTTAGAATTGAAACATTAAAATTGCTTTTG
* * * *
44782 ATTCCTTCATGAAGGTTGTAGCTCATGAAATTACCTTTTAATAGACACATGAATCAAACTTAATC
62 ATT-CTTCATGAAAGTTGTAGATCATAAAATTACCTTTTAATAGACACATGAATC-ACCTTAATC
* *
44847 GGACAAATCGAACAAAGAATAAAAAAAATAAAGTTTAAACGTTAAAT-TAAGATAAAATTTGTAA
125 GGACAAATAGAACAAAGAATAAAAAAAATAAA--TGAAACGTTAAATGTAAGATAAAATTTGTAA
* *
44911 AGGACTGAGTAGTAT-AAAGAGAAAAGCATGAGGGTCATTTGATAAATAATCCAAA-AAAGAAAA
188 AGGACTAAGTAGCATAAAAGAGAAAAGCATGAGGGTCATTTGATAAATAATCCAAATAAA-AAAA
*
44974 TGTTTGTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACACTTCACGAAACTCATAGAT
252 TATTTGTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACACTTCACGAAACTCATAGAT
* * * * *
45039 AAAATTGAGCTTTCGGGTCCTTCATGAAATTCATAAATCATGCAATAACCTTTTAACCGACTCTT
317 AAAATT-AACTTTCGGGTCCTTCATAAAAGTCATAAATCATACAATAACCTTTTAACCGACACTT
**
45104 CAATAACTTCAATCGGACATGTGGA-CAAAAAAT-TATACGATATTAAATTA-ACCGG
381 CAATAACTTCAATCGGACATGTGGATCAAAAAATATATACGATATTAAA-TAGACCAA
* **
45159 CAATCAAAACCACAAAATTTTAGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTTTGAGT
1 CAATCGAAACCACAAAATTTTAGAAGCATTTTTTAGAATTGAAACATTAAAATT-GCTTTTGA-T
* * * * **
45224 TCTTAATGAAAATTGCAGATCATCAAATTACCTTTTAATAGACATTTGAATCACCTTAATCGGAC
64 TCTTCATGAAAGTTGTAGATCATAAAATTACCTTTTAATAGACACATGAATCACCTTAATCGGAC
* * * * ** * *
45289 AAATAGAA-AAAAAAT-ACAAAAATAAAAGGCAACGCGTTAAATCGTCTAACCTATAA-TTGTGA
129 AAATAGAACAAAGAATAAAAAAAAT-AAATG-AA-ACGTTAAAT-G--TAAGATAAAATTTGTAA
* * * * * * * *
45351 AGGACTAAATAACAT-AAAGCATAAAAGTATAAGGATCATTAGATAAATAATCC-AACAAAAAAA
188 AGGACTAAGTAGCATAAAAG-AGAAAAGCATGAGGGTCATTTGATAAATAATCCAAATAAAAAAA
* *
45414 TATTAGTTTATGGAGA
252 TATTTGTTAATGGAGA
45430 ACGGGACCAC
Statistics
Matches: 583, Mismatches: 94, Indels: 61
0.79 0.13 0.08
Matches are distributed among these distances:
434 7 0.01
435 9 0.02
436 45 0.08
437 130 0.22
438 172 0.30
439 85 0.15
440 49 0.08
441 57 0.10
442 22 0.04
443 7 0.01
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (437 bp):
CAATCGAAACCACAAAATTTTAGAAGCATTTTTTAGAATTGAAACATTAAAATTGCTTTTGATTC
TTCATGAAAGTTGTAGATCATAAAATTACCTTTTAATAGACACATGAATCACCTTAATCGGACAA
ATAGAACAAAGAATAAAAAAAATAAATGAAACGTTAAATGTAAGATAAAATTTGTAAAGGACTAA
GTAGCATAAAAGAGAAAAGCATGAGGGTCATTTGATAAATAATCCAAATAAAAAAATATTTGTTA
ATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACACTTCACGAAACTCATAGATAAAATTAAC
TTTCGGGTCCTTCATAAAAGTCATAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTC
AATCGGACATGTGGATCAAAAAATATATACGATATTAAATAGACCAA
Found at i:46074 original size:18 final size:19
Alignment explanation
Indices: 46053--46094 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
46043 ACAACAAGAT
*
46053 TAAAA-TGATGATCAAGTG
1 TAAAACTGATGAACAAGTG
46071 TAAAACTTGATGAACAAGTG
1 TAAAAC-TGATGAACAAGTG
46091 -AAAA
1 TAAAA
46095 GTAAATGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 4 0.19
20 12 0.57
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.24
Consensus pattern (19 bp):
TAAAACTGATGAACAAGTG
Done.