Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011434.1 Corchorus olitorius cultivar O-4 contig11467, 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: 54250
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:212 original size:2 final size:2
Alignment explanation
Indices: 205--236 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
195 ACAGCGGTAA
205 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
237 TGGACAGCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5258 original size:26 final size:26
Alignment explanation
Indices: 5228--5277 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
5218 TAATCAAGAA
* *
5228 AATCCCCAAATAGCCTCCAAAACCCT
1 AATCCCCAAAAAACCTCCAAAACCCT
5254 AATCCCCAAAAAACCTCCAAAACC
1 AATCCCCAAAAAACCTCCAAAACC
5278 GCAAACTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.44, C:0.42, G:0.02, T:0.12
Consensus pattern (26 bp):
AATCCCCAAAAAACCTCCAAAACCCT
Found at i:11728 original size:2 final size:2
Alignment explanation
Indices: 11721--11753 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11711 TGAGGACTAG
11721 TA TA TA TA 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
11754 GAATGAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15731 original size:2 final size:2
Alignment explanation
Indices: 15724--15748 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15714 GAGAAAAACA
15724 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 A
15749 AATGCAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19565 original size:307 final size:308
Alignment explanation
Indices: 19004--19610 Score: 993
Period size: 307 Copynumber: 2.0 Consensus size: 308
18994 TGACTATGGA
* *
19004 AATTACTTAAAGGTCAAATTGATAATTAATGTGGTGCCTCCTTTTGCCTTTTTTGGTCTTTTCTC
1 AATTACTTAAAGGCCAAATTGAGAATTAATGTGGTGCCTCCTTTTGCCTTTTTTGGTCTTTTCTC
* * **
19069 ACTATCTGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCTCTTACTTTTCCTGCTGCCTTTTTT
66 ACTATCTGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTGATGCCCCTTTT
**
19134 TTGTAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGTGTGGA
131 TCATAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGTGTGGA
* *
19199 TATTAGGATTTACCGGTTCAACTCCTTTGTCGGAATTCCAAGGGATTGGTGCTATAAATGTATCT
196 TATTAGGATTTACCGGTTCAACTCCTCTGTCGGAATTCCAAAGGATTGGTGCTATAAATGTATCT
19264 ACAATAATGGTTGATTCATGGGTAAACTATTGGCATTCCAGTTCTGTG
261 ACAATAATGGTTGATTCATGGGTAAACTATTGGCATTCCAGTTCTGTG
* * *
19312 AATTAGTTAAAGGCCAAATTGAGAATTAATGTGGTGTCTCCTTTTGGCTTTTTTGGTCTTTTCTC
1 AATTACTTAAAGGCCAAATTGAGAATTAATGTGGTGCCTCCTTTTGCCTTTTTTGGTCTTTTCTC
* ** * *
19377 ACT-TTTCGGGTGACTATGAAGGCGCTCGATGAATTTCCTCCCTTACTTTTCCTTATGCCCCTTT
66 ACTATCT-GGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTGATGCCCCTTT
19441 TTCATAATTTACT-TTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGTGTGG
130 TTCATAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGTGTGG
*
19505 ATATTAGGATTTACCGGTTCAACTCCTCTGTCGGAATTCCAAAGGATTGGTGCTATAAATGTATT
195 ATATTAGGATTTACCGGTTCAACTCCTCTGTCGGAATTCCAAAGGATTGGTGCTATAAATGTATC
* * *
19570 TGCAATTATGGTTGATTCATGGGTCAACTATTGGCATTCCA
260 TACAATAATGGTTGATTCATGGGTAAACTATTGGCATTCCA
19611 CCGTTTTCCT
Statistics
Matches: 276, Mismatches: 22, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
307 153 0.55
308 123 0.45
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (308 bp):
AATTACTTAAAGGCCAAATTGAGAATTAATGTGGTGCCTCCTTTTGCCTTTTTTGGTCTTTTCTC
ACTATCTGGGTGACTAAAAAGGCCCTCGATGAATTTCCTCCCTTACTTTTCCTGATGCCCCTTTT
TCATAATTTACTATTTTTATATTTATGATTAAGTGTGTTTTAATTACATATTAATTGTGTGTGGA
TATTAGGATTTACCGGTTCAACTCCTCTGTCGGAATTCCAAAGGATTGGTGCTATAAATGTATCT
ACAATAATGGTTGATTCATGGGTAAACTATTGGCATTCCAGTTCTGTG
Found at i:20828 original size:22 final size:23
Alignment explanation
Indices: 20798--20844 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
20788 TTTTAGTTTA
*
20798 TAATATTCTTGCGCCATTCGGGT
1 TAATATTCTCGCGCCATTCGGGT
* *
20821 TAAT-TTCTCGGGTCATTCGGGT
1 TAATATTCTCGCGCCATTCGGGT
20843 TA
1 TA
20845 CGAGTTTGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.40
Consensus pattern (23 bp):
TAATATTCTCGCGCCATTCGGGT
Found at i:21034 original size:11 final size:11
Alignment explanation
Indices: 21018--21043 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21008 ATGGGTCACG
21018 TGCAACGCTGT
1 TGCAACGCTGT
21029 TGCAACGCTGT
1 TGCAACGCTGT
21040 TGCA
1 TGCA
21044 CGTGGAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (11 bp):
TGCAACGCTGT
Found at i:22100 original size:14 final size:14
Alignment explanation
Indices: 22081--22117 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
22071 TCTTTTAAAT
22081 TAAAATAATAAAAA
1 TAAAATAATAAAAA
**
22095 TAAAATGGTAAAAA
1 TAAAATAATAAAAA
22109 TAAAATAAT
1 TAAAATAAT
22118 TATAAAAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (14 bp):
TAAAATAATAAAAA
Found at i:27299 original size:21 final size:22
Alignment explanation
Indices: 27259--27299 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
27249 GACAAACTCG
*
27259 TAACCCGAATAACCCGAGAAGA
1 TAACCCGAATAACCCAAGAAGA
*
27281 TAACCCG-ATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
27300 TATTATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.29, G:0.17, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Found at i:28591 original size:162 final size:161
Alignment explanation
Indices: 28329--28642 Score: 440
Period size: 163 Copynumber: 1.9 Consensus size: 161
28319 ATCATTTAAG
* *
28329 AAATATATTTTAAAAATTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAATTGATAAAAATA
1 AAATATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAATTAGTAAATTGATAAAAATA
* *
28394 AAGTAGGTATAAGGATATTAGATTTCATTAAAT-AAAATAGAGTTTTTAGTTTTCTTTGA-CCAA
66 AAGTAGGTATAAGGATATTAGATTTAATAAAATAAAAATAGAGTTTTTAGTTTT-TTTGAGCCAA
28457 AAAATAGAGTTTTTAGTTGAGTATAATTATAA
130 AAAATAGAGTTTTTAGTTGAGTATAATTATAA
* *
28489 AAATATATTTAAAAAATTCTAATATATATATATATTTTTTTAATTAAA-TAGTACAA-TGGTAAA
1 AAATATATTTAAAAAATTCT-A-ATATATATA-AGTTTTTTAATTAAATTAGTA-AATTGATAAA
* * *
28552 AATTAAA-TAGTTATAAGGATATTATATTTAATAAAATAAAAATAGAGTTTTTAGTTTTTTTTAG
62 AA-TAAAGTAGGTATAAGGATATTAGATTTAATAAAATAAAAATAGAGTTTTTAGTTTTTTTGAG
**
28616 GGAAAAAATAGAGTTTTTAGTTGAGTA
126 CCAAAAAATAGAGTTTTTAGTTGAGTA
28643 AAACAATAAA
Statistics
Matches: 136, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
160 19 0.14
161 1 0.01
162 51 0.38
163 65 0.48
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (161 bp):
AAATATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAATTAGTAAATTGATAAAAATA
AAGTAGGTATAAGGATATTAGATTTAATAAAATAAAAATAGAGTTTTTAGTTTTTTTGAGCCAAA
AAATAGAGTTTTTAGTTGAGTATAATTATAA
Found at i:29713 original size:50 final size:50
Alignment explanation
Indices: 29653--29753 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
29643 ATTCTTTAAC
*
29653 TATCTAAATCAAAAAAACTTGCATGATGGTCCGAATTAGAACCATGATTT
1 TATCTAAATCAAAAAAACTTGCATGATGGTCCGAATTAGAAACATGATTT
*
29703 TATCTGAATCAAAAAAACTTGCATGATGGTCCGAATTAGAAACATGATTT
1 TATCTAAATCAAAAAAACTTGCATGATGGTCCGAATTAGAAACATGATTT
29753 T
1 T
29754 CTTCCAAAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (50 bp):
TATCTAAATCAAAAAAACTTGCATGATGGTCCGAATTAGAAACATGATTT
Found at i:29961 original size:87 final size:86
Alignment explanation
Indices: 29813--30027 Score: 247
Period size: 87 Copynumber: 2.5 Consensus size: 86
29803 TGTCATATTC
* *
29813 CCATTAGTAAGATCACTCTGATTTGAATTCAAAATATCCACCACCAAATCAATTTCCAAAGATTT
1 CCATTAGGAAGATCACTCT-ATTTGAATTCAAACTATCCACCACCAAATCAATTTCCAAAGATTT
* * *
29878 TGCA-TAATAGCTTAC-CATAACT
65 TGCACCAA-AAC-CACTCATAACT
* * * * *
29900 CCATTAGGAAGATCACTAGTATTTGAATTCAAACTATCCTCTACCATAAT-AGTTTCTAAAGATT
1 CCATTAGGAAGATCACT-CTATTTGAATTCAAACTATCCACCACCA-AATCAATTTCCAAAGATT
*
29964 TTGCACCAAAACCACTCATATCT
64 TTGCACCAAAACCACTCATAACT
*
29987 CCATTAGGAAGATCACGTTTATTTGAATTCAAACTATCCAC
1 CCATTAGGAAGATCAC-TCTATTTGAATTCAAACTATCCAC
30028 ACTTATCAGT
Statistics
Matches: 110, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
86 2 0.02
87 101 0.92
88 7 0.06
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.32
Consensus pattern (86 bp):
CCATTAGGAAGATCACTCTATTTGAATTCAAACTATCCACCACCAAATCAATTTCCAAAGATTTT
GCACCAAAACCACTCATAACT
Found at i:30969 original size:3 final size:3
Alignment explanation
Indices: 30961--30999 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
30951 ACGGTTGTTT
30961 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31000 GGCTACCAAA
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):
TTA
Found at i:34509 original size:7 final size:7
Alignment explanation
Indices: 34499--34534 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
34489 GAAAATTAAC
*
34499 AACAAAA
1 AACAGAA
34506 AACAGAA
1 AACAGAA
34513 AACAGAA
1 AACAGAA
34520 AACAGAA
1 AACAGAA
*
34527 AACGGAA
1 AACAGAA
34534 A
1 A
34535 CGGTACCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.72, C:0.14, G:0.14, T:0.00
Consensus pattern (7 bp):
AACAGAA
Found at i:34523 original size:21 final size:21
Alignment explanation
Indices: 34482--34534 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
34472 TTTTGTTTCC
* *
34482 AAAAACAGAAAATTAACAACA
1 AAAAACAGAAAATCAAAAACA
34503 AAAAACAGAAAA-CAGAAAACA
1 AAAAACAGAAAATCA-AAAACA
* *
34524 GAAAACGGAAA
1 AAAAACAGAAA
34535 CGGTACCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.72, C:0.13, G:0.11, T:0.04
Consensus pattern (21 bp):
AAAAACAGAAAATCAAAAACA
Found at i:43020 original size:166 final size:160
Alignment explanation
Indices: 42745--43074 Score: 543
Period size: 166 Copynumber: 2.0 Consensus size: 160
42735 TTCTCCCAAG
* *
42745 GTTTTTTGTGAAGTGGGATACTTAGCAAGCTTACTGTTAGTGTAAAGATTAGCAAATATATGCTA
1 GTTTTTTGTGAAGTGGGAGACTTAGCAAGCTTACTGCTAGTGTAAAGATTAGCAAATATATGCTA
*
42810 ATGAGTAATGAAGTAATTATGTAGTTGGCAGCAATTTTAATCTTGAATTCTTAATGTTAGATAAT
66 ATGAGTAATGAAGTAATTATGTAGTTGGCAGCAATTTTAATCTTGAATTCTTAATGTTAGACAAT
* *
42875 AGTATTGTAATTTGTAAGTGTTGGGAGTATT
131 AGCATTGTAATTTGTAAGTGCT-GGAGTATT
42906 GTTTTTTGTGAAGTGGGAGACTTAGCAAGCTTACTGCTAGTGTAAAGATTAGCAAACTTTATATA
1 GTTTTTTGTGAAGTGGGAGACTTAGCAAGCTTACTGCTAGTGTAAAGATTAGC-AA----ATATA
*
42971 TGCTAATGAGTAATGAAGTAATTATGTAGTTGGTAGCAATTTTAATCTTGAATTCTTAATGTTAG
61 TGCTAATGAGTAATGAAGTAATTATGTAGTTGGCAGCAATTTTAATCTTGAATTCTTAATGTTAG
*
43036 ACAATAGCATTGTAATTTGTAAGTGCTGTAGTATT
126 ACAATAGCATTGTAATTTGTAAGTGCTGGAGTATT
43071 GTTT
1 GTTT
43075 AATTTGGTAC
Statistics
Matches: 157, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
161 51 0.32
162 2 0.01
165 11 0.07
166 93 0.59
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (160 bp):
GTTTTTTGTGAAGTGGGAGACTTAGCAAGCTTACTGCTAGTGTAAAGATTAGCAAATATATGCTA
ATGAGTAATGAAGTAATTATGTAGTTGGCAGCAATTTTAATCTTGAATTCTTAATGTTAGACAAT
AGCATTGTAATTTGTAAGTGCTGGAGTATT
Found at i:44672 original size:12 final size:12
Alignment explanation
Indices: 44655--44679 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44645 AGCTCCAAAC
44655 TGTTTCAGTTGA
1 TGTTTCAGTTGA
44667 TGTTTCAGTTGA
1 TGTTTCAGTTGA
44679 T
1 T
44680 TAGATGTAAT
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:0.16, C:0.08, G:0.24, T:0.52
Consensus pattern (12 bp):
TGTTTCAGTTGA
Found at i:47206 original size:19 final size:19
Alignment explanation
Indices: 47184--47221 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
47174 AGGGATGAAG
47184 CAACAAGGAAATGGAAGAT
1 CAACAAGGAAATGGAAGAT
47203 CAACAAGGAAATGGAAGAT
1 CAACAAGGAAATGGAAGAT
47222 TAAATAACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.11, G:0.26, T:0.11
Consensus pattern (19 bp):
CAACAAGGAAATGGAAGAT
Found at i:51589 original size:27 final size:28
Alignment explanation
Indices: 51559--51612 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
51549 TCATTACTCC
51559 CCTTTCTT-TTCACCTTC-ACATCTCTTT
1 CCTTT-TTCTTCACCTTCTACATCTCTTT
* *
51586 CCTTTTTCTTCTCCTTCTCCATCTCTT
1 CCTTTTTCTTCACCTTCTACATCTCTT
51613 CACCATGGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 2 0.09
27 13 0.57
28 8 0.35
ACGTcount: A:0.07, C:0.39, G:0.00, T:0.54
Consensus pattern (28 bp):
CCTTTTTCTTCACCTTCTACATCTCTTT
Found at i:53013 original size:518 final size:518
Alignment explanation
Indices: 52015--53044 Score: 1699
Period size: 518 Copynumber: 2.0 Consensus size: 518
52005 ATATGACTTG
* * * *
52015 TATATGTTATTTGAAACATCCAGAGATATAACTAAAATCTCCTTTTGAGGATCGATGAGGAGACT
1 TATATATTATTTGAAACAACCAGAGATATAACTAAAATCTCCTTTTAAGGATCGATAAGGAGACT
*
52080 CGGTTTGAACTATTTTTGTCCTTTTATGTCTTTTCTCACTTGGTTAATTACTAAGAAGGTCCTCA
66 CGGTTTGAACTATTTTTGTCCTTTTATGTCTTTTCTCACTTGGTTAATTACCAAGAAGGTCCTCA
* * *
52145 ATTAGTTTCTCACCATTCCATTTTCCTCCAACCTTGTTTTTGTAATTGTAAGGTTTTAAATAGTT
131 ATTAGTTTCTCACCATTCCATTTTCCTCCAACCCTGTTTTTGTAATTGCAAGGTTTTAAACAGTT
* * * *
52210 GAATGTGAAAGTATTTATTGGCCATAAAATCATGTATTATTTATTTACTGAGAAGGCCCTCAATT
196 GAATGTGAAAGCATTTATTGACCATAAAATCATGAATTATTTATTTACTAAGAAGGCCCTCAATT
*
52275 AGTTCCCACCATTCCTTTTTCCTCAAACCTTATGAATTTACTATTTGATCCCATGTTTGGGTTAA
261 AGTTCCCACCATTCCTTTTGCCTCAAACCTTATGAATTTACTATTTGATCCCATGTTTGGGTTAA
*
52340 TGAGGGACTAGATTATTAAACATTTTAGTCTTTTTCCACCTACCAAATTACTTTAAGACCCTAAA
326 TGAGGGACTAGATTATCAAACATTTTAGTCTTTTTCCACCTACCAAATTACTTTAAGACCCTAAA
* * * *
52405 CTTTGGTTAATGTTGAGATTGATAACTCTACTTTTTGGTCTTTTGCTAAAGGTGAATGTGAACGC
391 CTTTGGTTAATATTGAGATGGATAACTCTACTTTTTGGTCTTTTACTAAAGGTGAATGTGAACAC
52470 AATTAATTGTGGTTTTAAAAGTAAGTTTATCCGC-AATATTGA-TTTTTTTAAAATATATATA
456 AATTAATTGTGGTTTTAAAAGTAAGTTTATCCGCAAATATTGATTTTTTTTAAAATATATATA
* *
52531 TATATATTATTTGAAA-AACCAGAGAGATATTACTAAAATCTCCTTTTAAGGATTGATAAGGAGA
1 TATATATTATTTGAAACAACC--AGAGATATAACTAAAATCTCCTTTTAAGGATCGATAAGGAGA
*
52595 CTCGGTTTGAACTTTTTTTTGTCCTTTTATGTCTTTTCTCACTTGGTTAATTACCAAGAAGGTCC
64 CTCGGTTTGAAC-TATTTTTGTCCTTTTATGTCTTTTCTCACTTGGTTAATTACCAAGAAGGTCC
* *
52660 TCAATTAGTTTCTCACCATTCCCTTTTCCTCCAACCCT-TTTTTGTAATTGCAAGGTTTTAACCA
128 TCAATTAGTTTCTCACCATTCCATTTTCCTCCAACCCTGTTTTTGTAATTGCAAGGTTTTAAACA
52724 GTTGAATGTGAAAGCATTTATTGACCATAAAATCATGAATTATTTATTTACTAAGAAGGCCCTCA
193 GTTGAATGTGAAAGCATTTATTGACCATAAAATCATGAATTATTTATTTACTAAGAAGGCCCTCA
* * * *
52789 ATTAATTTCTCACCATTCCTTTTGCCTCCAACCTTATGAATTTACTATTTGATCCCATGTTTGTG
258 ATT-AGTTCCCACCATTCCTTTTGCCTCAAACCTTATGAATTTACTATTTGATCCCATGTTTGGG
* **
52854 TTAATGAGGGACTAGATTATCAAACATTTTAGTCTTTTTCCACCTACCAAATTACTTTAAGGCTT
322 TTAATGAGGGACTAGATTATCAAACATTTTAGTCTTTTTCCACCTACCAAATTACTTTAAGACCC
*
52919 TAAACTTTGGTTAATATTGAGATGGATAACTCTACTTTTTGGTCTTTTACTAAAGGTTAATGTGA
387 TAAACTTTGGTTAATATTGAGATGGATAACTCTACTTTTTGGTCTTTTACTAAAGGTGAATGTGA
*
52984 ACACAATTAATTGTGGTTTTAATAGTAAGTTTATCCGCAAAATATTGATTTTTTTTAAAAT
452 ACACAATTAATTGTGGTTTTAAAAGTAAGTTTATCCGC-AAATATTGATTTTTTTTAAAAT
53045 GCATTATTAT
Statistics
Matches: 475, Mismatches: 32, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
515 3 0.01
516 15 0.03
517 137 0.29
518 300 0.63
520 8 0.02
521 12 0.03
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (518 bp):
TATATATTATTTGAAACAACCAGAGATATAACTAAAATCTCCTTTTAAGGATCGATAAGGAGACT
CGGTTTGAACTATTTTTGTCCTTTTATGTCTTTTCTCACTTGGTTAATTACCAAGAAGGTCCTCA
ATTAGTTTCTCACCATTCCATTTTCCTCCAACCCTGTTTTTGTAATTGCAAGGTTTTAAACAGTT
GAATGTGAAAGCATTTATTGACCATAAAATCATGAATTATTTATTTACTAAGAAGGCCCTCAATT
AGTTCCCACCATTCCTTTTGCCTCAAACCTTATGAATTTACTATTTGATCCCATGTTTGGGTTAA
TGAGGGACTAGATTATCAAACATTTTAGTCTTTTTCCACCTACCAAATTACTTTAAGACCCTAAA
CTTTGGTTAATATTGAGATGGATAACTCTACTTTTTGGTCTTTTACTAAAGGTGAATGTGAACAC
AATTAATTGTGGTTTTAAAAGTAAGTTTATCCGCAAATATTGATTTTTTTTAAAATATATATA
Found at i:53537 original size:108 final size:109
Alignment explanation
Indices: 53345--53550 Score: 294
Period size: 108 Copynumber: 1.9 Consensus size: 109
53335 TAGAATTTGC
* * *
53345 TAACCACCTATTCACATATATGATAAGAAACGAGAGAAAAAAAAATTCTATAACTAAAGTGATTT
1 TAACCACATACTCACATATATGATAAGAAACGAAAGAAAAAAAAATTCTATAACTAAAGTGATTT
53410 GCTAGCCAAACATCAAGAATGCTCGACGCGCCAGCGCAAGCCGA
66 GCTAGCCAAACATCAAGAATGCTCGACGCGCCAGCGCAAGCCGA
* *
53454 TAACCACATACTCACATATATGATAAGAACCGAAAG-AAAAGAAATTCTA-AAGCTGAAA-TGAT
1 TAACCACATACTCACATATATGATAAGAAACGAAAGAAAAAAAAATTCTATAA-CT-AAAGTGAT
* *
53516 TTGCTAGCCACAA-ATCAAGAATGCTTGATGCGCCA
64 TTGCTAGCCA-AACATCAAGAATGCTCGACGCGCCA
53551 ACGTGAGTCG
Statistics
Matches: 87, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
107 2 0.02
108 48 0.55
109 37 0.43
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (109 bp):
TAACCACATACTCACATATATGATAAGAAACGAAAGAAAAAAAAATTCTATAACTAAAGTGATTT
GCTAGCCAAACATCAAGAATGCTCGACGCGCCAGCGCAAGCCGA
Found at i:53582 original size:17 final size:17
Alignment explanation
Indices: 53560--53595 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
53550 AACGTGAGTC
53560 GATTAACTTGTTTATAT
1 GATTAACTTGTTTATAT
53577 GATTAACTTGTTTATAT
1 GATTAACTTGTTTATAT
53594 GA
1 GA
53596 AAAGGAGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.50
Consensus pattern (17 bp):
GATTAACTTGTTTATAT
Done.