Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015273.1 Corchorus capsularis cultivar CVL-1 contig15294, 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: 31300
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Found at i:993 original size:15 final size:15
Alignment explanation
Indices: 973--1013 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
963 CCTTACTAAG
973 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
988 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
*
1003 CAAGAAGATGA
1 CCAGAAGATGA
1014 ACAACTTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.44, C:0.22, G:0.27, T:0.07
Consensus pattern (15 bp):
CCAGAAGATGAGCCA
Found at i:2474 original size:12 final size:12
Alignment explanation
Indices: 2457--2481 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2447 CTTTCCTTGC
2457 ATTGCTTTGATT
1 ATTGCTTTGATT
2469 ATTGCTTTGATT
1 ATTGCTTTGATT
2481 A
1 A
2482 ATTACCTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (12 bp):
ATTGCTTTGATT
Found at i:4008 original size:11 final size:12
Alignment explanation
Indices: 3992--4023 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
3982 AAAGTTCGTG
3992 TTTGAAGATTA-
1 TTTGAAGATTAT
4003 TTTGAAGA-TAT
1 TTTGAAGATTAT
4014 TTTGAAGATT
1 TTTGAAGATT
4024 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.11
11 16 0.84
12 1 0.05
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (12 bp):
TTTGAAGATTAT
Found at i:5405 original size:21 final size:20
Alignment explanation
Indices: 5381--5428 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
5371 TAGATTTAGA
* *
5381 TTTAATTTACTTTGCTTAGTT
1 TTTAATTTA-ATTGCTTACTT
* *
5402 TTTAGTTTAATTGCTTTCTT
1 TTTAATTTAATTGCTTACTT
5422 TTTAATT
1 TTTAATT
5429 GATAATTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.65
Consensus pattern (20 bp):
TTTAATTTAATTGCTTACTT
Found at i:9180 original size:33 final size:33
Alignment explanation
Indices: 9138--9220 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
9128 AGTTCAAGGA
*
9138 TCATGTGGCCGGTTGTGGCCGGGCATGGCCGAG
1 TCATGTGGCCGGTGGTGGCCGGGCATGGCCGAG
* *
9171 TCATGTGGCCGGTGGTGTCCGGGCATGGTCGAG
1 TCATGTGGCCGGTGGTGGCCGGGCATGGCCGAG
9204 TCATGTGGCCGGTGGTG
1 TCATGTGGCCGGTGGTG
9221 CATGGCTTCT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.08, C:0.22, G:0.46, T:0.24
Consensus pattern (33 bp):
TCATGTGGCCGGTGGTGGCCGGGCATGGCCGAG
Found at i:11549 original size:53 final size:53
Alignment explanation
Indices: 11461--11702 Score: 295
Period size: 53 Copynumber: 4.7 Consensus size: 53
11451 GCCGACGAAA
* *
11461 CAGTAAATAGGTTTCATTCAGAGTAATTAAGCTAAGCAGTAAAAGGAGAAAAT
1 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAAT
* * * * *
11514 CAGTAAATAGGTTTAATTCCGAGTTACTAACCTAAGTAGTAAAAGGGGAAAAT
1 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAAT
** *
11567 CAG----TA-G--TAATT-AGCTTAATTAACCTAAGCAGTGAAAGGAGAAAAT
1 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAAT
* * *
11612 CAGTAAATAGTTTTAATTTC-GAGTAATTAACCTAAGTAGTAAAAGGGGAAAAT
1 CAGTAAATAGGTTTAA-TTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAAT
11665 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCA
1 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCA
11703 TAGGTTTTAT
Statistics
Matches: 156, Mismatches: 23, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
45 29 0.19
46 5 0.03
48 1 0.01
49 4 0.03
52 6 0.04
53 111 0.71
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.27
Consensus pattern (53 bp):
CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAAT
Found at i:11653 original size:98 final size:98
Alignment explanation
Indices: 11484--11669 Score: 318
Period size: 98 Copynumber: 1.9 Consensus size: 98
11474 TCATTCAGAG
* *
11484 TAATTAAGCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTCCGAGTTACTAACCTAA
1 TAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTCCGAGTAACTAACCTAA
11549 GTAGTAAAAGGGGAAAATCAGTAGTAATTAGCT
66 GTAGTAAAAGGGGAAAATCAGTAGTAATTAGCT
* * * *
11582 TAATTAACCTAAGCAGTGAAAGGAGAAAATCAGTAAATAGTTTTAATTTCGAGTAATTAACCTAA
1 TAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTCCGAGTAACTAACCTAA
11647 GTAGTAAAAGGGGAAAATCAGTA
66 GTAGTAAAAGGGGAAAATCAGTA
11670 AATAGGTTTA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 82 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.26
Consensus pattern (98 bp):
TAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTCCGAGTAACTAACCTAA
GTAGTAAAAGGGGAAAATCAGTAGTAATTAGCT
Found at i:11709 original size:31 final size:31
Alignment explanation
Indices: 11671--11731 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
11661 AAATCAGTAA
11671 ATAGGTTTAATTCAGAGTAATTAACCTAAGC
1 ATAGGTTTAATTCAGAGTAATTAACCTAAGC
* *
11702 ATAGGTTTTATTCCGAGTAATTAACCTAAG
1 ATAGGTTTAATTCAGAGTAATTAACCTAAG
11732 TAGTAAAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (31 bp):
ATAGGTTTAATTCAGAGTAATTAACCTAAGC
Found at i:11772 original size:84 final size:85
Alignment explanation
Indices: 11621--11786 Score: 316
Period size: 84 Copynumber: 2.0 Consensus size: 85
11611 TCAGTAAATA
*
11621 GTTTTAATTTCGAGTAATTAACCTAAGTAGTAAAAGGGGAAAATCAGTAAATAGGTTTAATTCAG
1 GTTTTAATTCCGAGTAATTAACCTAAGTAGTAAAAGGGGAAAATCAGTAAATAGGTTTAATTCAG
11686 AGTAATTAACCTAAGCATAG
66 AGTAATTAACCTAAGCATAG
11706 GTTTT-ATTCCGAGTAATTAACCTAAGTAGTAAAAGGGGAAAATCAGTAAATAGGTTTAATTCAG
1 GTTTTAATTCCGAGTAATTAACCTAAGTAGTAAAAGGGGAAAATCAGTAAATAGGTTTAATTCAG
11770 AGTAATTAACCTAAGCA
66 AGTAATTAACCTAAGCA
11787 GTAAAAGGAG
Statistics
Matches: 80, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
84 75 0.94
85 5 0.06
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (85 bp):
GTTTTAATTCCGAGTAATTAACCTAAGTAGTAAAAGGGGAAAATCAGTAAATAGGTTTAATTCAG
AGTAATTAACCTAAGCATAG
Found at i:11782 original size:53 final size:53
Alignment explanation
Indices: 11702--12187 Score: 610
Period size: 53 Copynumber: 9.5 Consensus size: 53
11692 TAACCTAAGC
* * * *
11702 ATAGGTTTTATTCCGAGTAATTAACCTAAGTAGTAAAAGGGGAAAATCAGTAA
1 ATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAA
*
11755 ATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATTAGTAA
1 ATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAA
* *
11808 ATAGGTTTAATTCAGAGTATTTAACCTAAGAAGT-AAA--AG-----CAGTAA
1 ATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAA
* * * *
11853 ACAAGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAAGAGAAAATTAGTAA
1 ATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAA
* * *
11906 ACAGGTCTAATTCAGAGTAATTAACCTAAGCAGTGAAAGGAGAAAATCAGTAA
1 ATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAA
* * *
11959 ATAGGTTTAATTCCGAGTAATTAACCTAAGTAGTAAAAGG-GGAAATCAGTAA
1 ATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAA
*
12011 ATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATTAGTAA
1 ATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAA
* *
12064 ATAGGTTTAATTCAGAGTATTTAACCTAAGAAGT-AAA--AG-----CAGTAA
1 ATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAA
* * * * *
12109 ACAGGTTTAATTTAGAGTAGTTAACCTAAGCAGTAAAAAGAGAAAATTAGTAA
1 ATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAA
* *
12162 ACAGGTCTAATTCAGAGTAATTAACC
1 ATAGGTTTAATTCAGAGTAATTAACC
12188 AACAAGGGGT
Statistics
Matches: 377, Mismatches: 39, Indels: 34
0.84 0.09 0.08
Matches are distributed among these distances:
45 70 0.19
46 6 0.02
48 4 0.01
50 4 0.01
52 55 0.15
53 238 0.63
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (53 bp):
ATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAA
Found at i:11832 original size:137 final size:142
Alignment explanation
Indices: 11582--12102 Score: 586
Period size: 151 Copynumber: 3.5 Consensus size: 142
11572 GTAATTAGCT
* *
11582 TAATTAACCTAAGCAGTGAAAGGAGAAAATCAGTAAATAGTTTTAATTTC-GAGTAATTAACCTA
1 TAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAA-TTCAGAGTAATTAACCTA
* * *
11646 AGTAGTAAAAGGGGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCA-T-AG-GT
65 AGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGAAGTAAGAGT
*
11708 -TTT-ATTCCGAG
130 ATTTAATTCAGAG
* *
11719 TAATTAACCTAAGTAGTAAAAGGGGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAA
1 TAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAA
* *
11784 GCAGTAAAAGGAGAAAATTAGTAAATAGGTTTAATTCAGAGTATTTAACCTAAGAAGTAAAAGCA
66 GCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGAAGT--AAG-A
11849 GTAAACAAGTTTAATTCAGAG
128 GT-----A-TTTAATTCAGAG
* * * *
11870 TAATTAACCTAAGCAGTAAAAAGAGAAAATTAGTAAACAGGTCTAATTCAGAGTAATTAACCTAA
1 TAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAA
* * *
11935 GCAGTGAAAGGAGAAAATCAGTAAATAGGTTTAATTCCGAGTAATTAACCTAAGTAGTAAAAGGG
66 GCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGAAGT--AA---
12000 GAAATCAGTAAATAGGTTTAATTCAGAG
126 G-----AG----TA--TTTAATTCAGAG
* *
12028 TAATTAACCTAAGCAGTAAAAGGAGAAAATTAGTAAATAGGTTTAATTCAGAGTATTTAACCTAA
1 TAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAA
*
12093 GAAGTAAAAG
66 GCAGTAAAAG
12103 CAGTAAACAG
Statistics
Matches: 330, Mismatches: 27, Indels: 33
0.85 0.07 0.08
Matches are distributed among these distances:
136 3 0.01
137 108 0.33
138 1 0.00
141 2 0.01
143 2 0.01
150 3 0.01
151 123 0.37
154 1 0.00
157 1 0.00
158 85 0.26
162 1 0.00
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.27
Consensus pattern (142 bp):
TAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAA
GCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGAAGTAAGAGTA
TTTAATTCAGAG
Found at i:11853 original size:182 final size:176
Alignment explanation
Indices: 11520--11884 Score: 466
Period size: 182 Copynumber: 2.0 Consensus size: 176
11510 AAATCAGTAA
* **
11520 ATAGGTTTAATTCCGAGTTACTAACCTAAGTAGTAAAAGGGGAAAATCAGTAGTAATTAGCTTAA
1 ATAGGTTTAATTCCGAGTAACTAACCTAAGTAGTAAAAGGGGAAAATCAGTAGTAATTAGAGTAA
* * *
11585 TTAACCTAAGCAGTGAAAGGAGAAAATCAGTAAATAGTTTTAATTTCGAGTAATTAACCTAAGTA
66 TTAACCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTTCGAGTAATTAACCTAAGAA
* *
11650 GTAAAAGGGGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGC
131 GTAAAA--GG---A-CAGTAAACAAGTTTAATTCAGAGTAATTAACCTAAGC
* *
11702 ATAGGTTTTATTCCGAGTAATTAACCTAAGTAGTAAAAGGGGAAAATCAGTAAATAGGTTTAATT
1 ATAGGTTTAATTCCGAGTAACTAACCTAAGTAGTAAAAGGGGAAAATCAG----TA-G--TAATT
* *
11767 CAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATTAGTAAATAGGTTTAA-TTCAGAGTATTTA
59 -AGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTTC-GAGTAATTA
11831 ACCTAAGAAGTAAAA-G-CAGTAAACAAGTTTAATTCAGAGTAATTAACCTAAGC
122 ACCTAAGAAGTAAAAGGACAGTAAACAAGTTTAATTCAGAGTAATTAACCTAAGC
11884 A
1 A
11885 GTAAAAAGAG
Statistics
Matches: 162, Mismatches: 12, Indels: 18
0.84 0.06 0.09
Matches are distributed among these distances:
182 83 0.51
186 2 0.01
187 2 0.01
189 8 0.05
190 67 0.41
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.28
Consensus pattern (176 bp):
ATAGGTTTAATTCCGAGTAACTAACCTAAGTAGTAAAAGGGGAAAATCAGTAGTAATTAGAGTAA
TTAACCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGTTTAATTTCGAGTAATTAACCTAAGAA
GTAAAAGGACAGTAAACAAGTTTAATTCAGAGTAATTAACCTAAGC
Found at i:11918 original size:98 final size:98
Alignment explanation
Indices: 11744--12101 Score: 421
Period size: 105 Copynumber: 3.5 Consensus size: 98
11734 GTAAAAGGGG
* *
11744 AAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATTAGTAAA
1 AAAAGCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAAGAGAAAATTAGTAAA
* *
11809 TAGGTTTAATTCAGAGTATTTAACCTAAGAAGT
66 TAGGTTTAATTCAGAGTAATTAACCTAAGCAGT
* *
11842 AAAAGCAGTAAACAAGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAAGAGAAAATTAGTAAA
1 AAAAGCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAAGAGAAAATTAGTAAA
* *
11907 CAGGTCTAATTCAGAGTAATTAACCTAAGCAGT
66 TAGGTTTAATTCAGAGTAATTAACCTAAGCAGT
* * * *
11940 GAAAGGAGAAAATCAGTAAATAGGTTTAATTCCGAGTAATTAACCTAAGTAGT-AAAAGGGGAAA
1 -AAA--AG-----CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAAGAGAAAA
*
12004 TCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGT
58 TTAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGT
* * *
12045 AAAAGGAGAAAATTAGTAAATAGGTTTAATTCAGAGTATTTAACCTAAGAAGTAAAA
1 -AAA--AG-----CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAA
12102 GCAGTAAACA
Statistics
Matches: 229, Mismatches: 22, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
98 90 0.39
99 3 0.01
101 2 0.01
105 95 0.41
106 39 0.17
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (98 bp):
AAAAGCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAAGAGAAAATTAGTAAA
TAGGTTTAATTCAGAGTAATTAACCTAAGCAGT
Found at i:11979 original size:288 final size:288
Alignment explanation
Indices: 11461--11988 Score: 794
Period size: 288 Copynumber: 1.8 Consensus size: 288
11451 GCCGACGAAA
* *
11461 CAGTAAATAGGTTTCATTCAGAGTAATTAAGCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGT
1 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGT
* * ** **
11526 TTAATTCCGAGTTACTAACCTAAGTAGTAAAAGGGGAAAATCAGTAGTAATTAGCTTAATTAACC
66 TTAATTCAGAGTTACTAACCTAAGAAGTAAAAGCAGAAAATCAGTAGTAATTAGAGTAATTAACC
* * * * * *
11591 TAAGCAGTGAAAGGAGAAAATCAGTAAATAGTTTTAATTTCGAGTAATTAACCTAAGTAGTAAAA
131 TAAGCAGTAAAAAGAGAAAATCAGTAAACAGGTCTAATTTCGAGTAATTAACCTAAGCAGTAAAA
*
11656 GGGGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCATAGGTTTTATTCCGAGTA
196 GGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCATAGGTTTTATTCCGAGTA
11721 ATTAACCTAAGTAGTAAAAGGGGAAAAT
261 ATTAACCTAAGTAGTAAAAGGGGAAAAT
*
11749 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATTAGTAAATAGGT
1 CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGT
* * *
11814 TTAATTCAGAG-TATTTAACCTAAGAAGTAAAAGCAGTAAA-CAAGT-TTAATTCAGAGTAATTA
66 TTAATTCAGAGTTA-CTAACCTAAGAAGTAAAAGCAGAAAATC-AGTAGTAATT-AGAGTAATTA
*
11876 ACCTAAGCAGTAAAAAGAGAAAATTAGTAAACAGGTCTAA-TTCAGAGTAATTAACCTAAGCAGT
128 ACCTAAGCAGTAAAAAGAGAAAATCAGTAAACAGGTCTAATTTC-GAGTAATTAACCTAAGCAGT
* *
11940 GAAAGGAGAAAATCAGTAAATAGGTTTAATTCCGAGTAATTAACCTAAG
192 AAAAGGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAG
11989 TAGTAAAAGG
Statistics
Matches: 214, Mismatches: 22, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
287 11 0.05
288 203 0.95
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (288 bp):
CAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATCAGTAAATAGGT
TTAATTCAGAGTTACTAACCTAAGAAGTAAAAGCAGAAAATCAGTAGTAATTAGAGTAATTAACC
TAAGCAGTAAAAAGAGAAAATCAGTAAACAGGTCTAATTTCGAGTAATTAACCTAAGCAGTAAAA
GGAGAAAATCAGTAAATAGGTTTAATTCAGAGTAATTAACCTAAGCATAGGTTTTATTCCGAGTA
ATTAACCTAAGTAGTAAAAGGGGAAAAT
Found at i:12044 original size:256 final size:257
Alignment explanation
Indices: 11702--12187 Score: 929
Period size: 256 Copynumber: 1.9 Consensus size: 257
11692 TAACCTAAGC
*
11702 ATAGGTTTTATTCCGAGTAATTAACCTAAGTAGTAAAAGGGGAAAATCAGTAAATAGGTTTAATT
1 ATAGGTTTAATTCCGAGTAATTAACCTAAGTAGTAAAAGGGGAAAATCAGTAAATAGGTTTAATT
11767 CAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATTAGTAAATAGGTTTAATTCAGAGTATTTAA
66 CAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATTAGTAAATAGGTTTAATTCAGAGTATTTAA
11832 CCTAAGAAGTAAAAGCAGTAAACAAGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAAGAGAA
131 CCTAAGAAGTAAAAGCAGTAAACAAGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAAGAGAA
11897 AATTAGTAAACAGGTCTAATTCAGAGTAATTAACCTAAGCAGTGAAAGGAGAAAATCAGTAA
196 AATTAGTAAACAGGTCTAATTCAGAGTAATTAACCTAAGCAGTGAAAGGAGAAAATCAGTAA
11959 ATAGGTTTAATTCCGAGTAATTAACCTAAGTAGTAAAAGGGG-AAATCAGTAAATAGGTTTAATT
1 ATAGGTTTAATTCCGAGTAATTAACCTAAGTAGTAAAAGGGGAAAATCAGTAAATAGGTTTAATT
12023 CAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATTAGTAAATAGGTTTAATTCAGAGTATTTAA
66 CAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATTAGTAAATAGGTTTAATTCAGAGTATTTAA
* * *
12088 CCTAAGAAGTAAAAGCAGTAAACAGGTTTAATTTAGAGTAGTTAACCTAAGCAGTAAAAAGAGAA
131 CCTAAGAAGTAAAAGCAGTAAACAAGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAAGAGAA
12153 AATTAGTAAACAGGTCTAATTCAGAGTAATTAACC
196 AATTAGTAAACAGGTCTAATTCAGAGTAATTAACC
12188 AACAAGGGGT
Statistics
Matches: 225, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
256 184 0.82
257 41 0.18
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (257 bp):
ATAGGTTTAATTCCGAGTAATTAACCTAAGTAGTAAAAGGGGAAAATCAGTAAATAGGTTTAATT
CAGAGTAATTAACCTAAGCAGTAAAAGGAGAAAATTAGTAAATAGGTTTAATTCAGAGTATTTAA
CCTAAGAAGTAAAAGCAGTAAACAAGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAAGAGAA
AATTAGTAAACAGGTCTAATTCAGAGTAATTAACCTAAGCAGTGAAAGGAGAAAATCAGTAA
Found at i:12050 original size:105 final size:104
Alignment explanation
Indices: 11842--12187 Score: 452
Period size: 105 Copynumber: 3.4 Consensus size: 104
11832 CCTAAGAAGT
* * * * *
11842 AAAAGCAGTAAACAAGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAAGAGAAAATTAGTAAA
1 AAAATCAGTAAACAGGTTTAATTCAGAGTAATTAACCTAAGAAGT-AAAAG-GGAAATCAGTAAA
* *
11907 CAGGTCTAATTCAGAGTAATTAACCTAAGCAGTGAAAGGAG
64 CAGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAG
* * * *
11948 AAAATCAGTAAATAGGTTTAATTCCGAGTAATTAACCTAAGTAGTAAAAGGGGAAATCAGTAAAT
1 AAAATCAGTAAACAGGTTTAATTCAGAGTAATTAACCTAAGAAGTAAAA-GGGAAATCAGTAAAC
12013 AGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAG
65 AGGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAG
* * *
12053 AAAATTAGTAAATAGGTTTAATTCAGAGTATTTAACCTAAGAAGTAAAA--G----CAGTAAACA
1 AAAATCAGTAAACAGGTTTAATTCAGAGTAATTAACCTAAGAAGTAAAAGGGAAATCAGTAAACA
* * *
12112 GGTTTAATTTAGAGTAGTTAACCTAAGCAGTAAAAAGAG
66 GGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAG
* *
12151 AAAATTAGTAAACAGGTCTAATTCAGAGTAATTAACC
1 AAAATCAGTAAACAGGTTTAATTCAGAGTAATTAACC
12188 AACAAGGGGT
Statistics
Matches: 218, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
98 78 0.36
102 1 0.00
105 98 0.45
106 41 0.19
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.25
Consensus pattern (104 bp):
AAAATCAGTAAACAGGTTTAATTCAGAGTAATTAACCTAAGAAGTAAAAGGGAAATCAGTAAACA
GGTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAGGAG
Found at i:13496 original size:30 final size:30
Alignment explanation
Indices: 13455--13516 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
13445 GGTCAAGTGG
*
13455 CCGGTTGTGGCCGGATGGCCCGTGCGATGT
1 CCGGTTATGGCCGGATGGCCCGTGCGATGT
13485 CCGGTTATGGCCGGATGGCCCGTGCGATGT
1 CCGGTTATGGCCGGATGGCCCGTGCGATGT
13515 CC
1 CC
13517 CATGCATTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.08, C:0.29, G:0.40, T:0.23
Consensus pattern (30 bp):
CCGGTTATGGCCGGATGGCCCGTGCGATGT
Found at i:18965 original size:12 final size:12
Alignment explanation
Indices: 18947--18975 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
18937 TTTCTGGTCG
18947 ATTTTTTTTT-T
1 ATTTTTTTTTAT
18958 ATTTTTTTTTAT
1 ATTTTTTTTTAT
18970 ATTTTT
1 ATTTTT
18976 CGATATAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (12 bp):
ATTTTTTTTTAT
Found at i:22811 original size:33 final size:33
Alignment explanation
Indices: 22758--22838 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 33
22748 TTAAAGGATC
*
22758 ATGTGGCCGGTTGTGGCCGGGCATGGCCGAGTA
1 ATGTGGCCGGTGGTGGCCGGGCATGGCCGAGTA
* * * *
22791 ATGTGGCCCGTGGTGTCCGGGCATGGTCGAGTC
1 ATGTGGCCGGTGGTGGCCGGGCATGGCCGAGTA
*
22824 ATGTGGGCGGTGGTG
1 ATGTGGCCGGTGGTG
22839 CGCGGCTTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.10, C:0.20, G:0.47, T:0.23
Consensus pattern (33 bp):
ATGTGGCCGGTGGTGGCCGGGCATGGCCGAGTA
Done.