Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018596.1 Corchorus olitorius cultivar O-4 contig18629, 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: 19506
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:1196 original size:15 final size:16
Alignment explanation
Indices: 1166--1205 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1156 TTACTTTGCT
1166 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
*
1182 TTGTTTTC-CGTTTAA
1 TTGTTTTCTAGTTTAA
*
1197 TTGCTTTCT
1 TTGTTTTCT
1206 GTCAATCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:6342 original size:32 final size:31
Alignment explanation
Indices: 6290--6352 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
6280 AGTTTGTAGC
* *
6290 TTCAGGAGCTGGTTTTTGAGATGAGTGATAT
1 TTCAGGAGATGGTTTGTGAGATGAGTGATAT
6321 TTCATGGAGATGGTTTGTGAGATGAGTGATAT
1 TTCA-GGAGATGGTTTGTGAGATGAGTGATAT
6353 CTGTTTGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 4 0.14
32 25 0.86
ACGTcount: A:0.24, C:0.05, G:0.33, T:0.38
Consensus pattern (31 bp):
TTCAGGAGATGGTTTGTGAGATGAGTGATAT
Found at i:7580 original size:18 final size:17
Alignment explanation
Indices: 7537--7583 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
7527 GAAGGAAATA
7537 TTAAT-AATAATTATTT
1 TTAATAAATAATTATTT
*
7553 TGAA-AAATAATTATTAT
1 TTAATAAATAATTATT-T
7570 TTAATAAATAATTA
1 TTAATAAATAATTA
7584 ATAAATTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 13 0.50
17 4 0.15
18 9 0.35
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TTAATAAATAATTATTT
Found at i:11329 original size:16 final size:16
Alignment explanation
Indices: 11301--11347 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
11291 GTCATCTTTT
*
11301 TTCAATTCTTCAATTA
1 TTCAATGCTTCAATTA
*
11317 TTCCATGCTTCAATTA
1 TTCAATGCTTCAATTA
11333 TTCAATGCTTCAATT
1 TTCAATGCTTCAATT
11348 TACATCAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.28, C:0.21, G:0.04, T:0.47
Consensus pattern (16 bp):
TTCAATGCTTCAATTA
Found at i:11349 original size:74 final size:73
Alignment explanation
Indices: 11263--11404 Score: 185
Period size: 74 Copynumber: 1.9 Consensus size: 73
11253 TAAGGCGATC
* * * *
11263 ATGCTTCCATTTACTTCAATGATCTAGGGTCATCTTTTTTCAATTCTTCAATTATTCCATGCTTC
1 ATGCTTCAATTTACATCAATGATCCAGGGTCATCTTTTTTCAATTC-TCAATTATTCAATGCTTC
11328 AATTATTCA
65 AATTATTCA
* ** * * *
11337 ATGCTTCAATTTACATCAATTATCCAGGGTGGTTTTTTTTCCATTCTCAATTATTCAATTCTTCA
1 ATGCTTCAATTTACATCAATGATCCAGGGTCATCTTTTTTCAATTCTCAATTATTCAATGCTTCA
11402 ATT
66 ATT
11405 CCTCCATTAT
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
73 20 0.34
74 38 0.66
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.46
Consensus pattern (73 bp):
ATGCTTCAATTTACATCAATGATCCAGGGTCATCTTTTTTCAATTCTCAATTATTCAATGCTTCA
ATTATTCA
Found at i:11396 original size:8 final size:8
Alignment explanation
Indices: 11383--11467 Score: 62
Period size: 8 Copynumber: 10.6 Consensus size: 8
11373 TTTTCCATTC
11383 TCAATTAT
1 TCAATTAT
*
11391 TCAATTCT
1 TCAATTAT
**
11399 TCAATTCC
1 TCAATTAT
*
11407 TCCATTAT
1 TCAATTAT
**
11415 TCAATGCT
1 TCAATTAT
* *
11423 TTAATTCT
1 TCAATTAT
*
11431 TCAATCAT
1 TCAATTAT
**
11439 TCAATGCT
1 TCAATTAT
11447 TCAATTAT
1 TCAATTAT
*
11455 CCAATTAT
1 TCAATTAT
11463 TCAAT
1 TCAAT
11468 GCTTCAATCC
Statistics
Matches: 58, Mismatches: 19, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
8 58 1.00
ACGTcount: A:0.31, C:0.22, G:0.02, T:0.45
Consensus pattern (8 bp):
TCAATTAT
Found at i:11413 original size:24 final size:24
Alignment explanation
Indices: 11386--11499 Score: 113
Period size: 24 Copynumber: 4.8 Consensus size: 24
11376 TCCATTCTCA
* *
11386 ATTATTCAATTCTTCAATTCCTCC
1 ATTATTCAATGCTTCAATTCATCC
* * *
11410 ATTATTCAATGCTTTAATTCTTCA
1 ATTATTCAATGCTTCAATTCATCC
*
11434 ATCATTCAATGCTTCAATT-ATCC
1 ATTATTCAATGCTTCAATTCATCC
* * *
11457 AATTATTCAATGCTTCAATCCTTCA
1 -ATTATTCAATGCTTCAATTCATCC
**
11482 ACCATTCAATGCTTCAAT
1 ATTATTCAATGCTTCAAT
11500 GACCCAGGGT
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
23 2 0.03
24 70 0.95
25 2 0.03
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.42
Consensus pattern (24 bp):
ATTATTCAATGCTTCAATTCATCC
Found at i:11442 original size:48 final size:48
Alignment explanation
Indices: 11379--11499 Score: 165
Period size: 48 Copynumber: 2.5 Consensus size: 48
11369 TTTTTTTTCC
* * * *
11379 ATTC-TCAATTATTCAATTCTTCAATTCCTCC-ATTATTCAATGCTTTA
1 ATTCTTCAATCATTCAATGCTTCAATT-ATCCAATTATTCAATGCTTCA
11426 ATTCTTCAATCATTCAATGCTTCAATTATCCAATTATTCAATGCTTCA
1 ATTCTTCAATCATTCAATGCTTCAATTATCCAATTATTCAATGCTTCA
* *
11474 ATCCTTCAACCATTCAATGCTTCAAT
1 ATTCTTCAATCATTCAATGCTTCAAT
11500 GACCCAGGGT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
47 7 0.11
48 59 0.89
ACGTcount: A:0.30, C:0.25, G:0.03, T:0.42
Consensus pattern (48 bp):
ATTCTTCAATCATTCAATGCTTCAATTATCCAATTATTCAATGCTTCA
Found at i:11686 original size:107 final size:107
Alignment explanation
Indices: 11499--11991 Score: 641
Period size: 107 Copynumber: 4.6 Consensus size: 107
11489 AATGCTTCAA
*
11499 TGACCCAGGGTGGTCTTTCTTCAGTTTGAGTC-GAAATGATCGAGGGTGGTTGTTCTTCAGTTCA
1 TGACCCAGGGTGGTCTTTCTTCAGTTTGAGTCAG-AATGATCGAGGGTGGTTGTTCTTCAGTTTA
*
11563 GTCCGGAATGACCGAGGGTGGTCGTTCTTCAGTTTATTTCAGT
65 GTCCGGAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAGT
*
11606 TGACCCAGGGTGGTCTTTCTTCAGTTTGAGTCAGAATGATCGAAGGTGGTTGTTCTTCAGTTTAG
1 TGACCCAGGGTGGTCTTTCTTCAGTTTGAGTCAGAATGATCGAGGGTGGTTGTTCTTCAGTTTAG
* * *
11671 TCTGGAATGATCGAGGATGGTCGTTCTTTAGTTTATTTCAGT
66 TCCGGAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAGT
* * * * ** *
11713 TGACCCAGAGTAGTCTTTCTTCAGTTTGTGTCGGAATGATCGAGGGCAGTTGTTCTTCAGTTCAG
1 TGACCCAGGGTGGTCTTTCTTCAGTTTGAGTCAGAATGATCGAGGGTGGTTGTTCTTCAGTTTAG
* * * * *
11778 TCCGAAATGATCGAGTGTGGTCGTTCTTTAGTTTTTTTTCATT
66 TCCGGAATGATCGAGGGTGGTCGTTCTTCAG-TTTATTTCAGT
* * *
11821 TGACCCAGGGTGGTCTTTCTTCGGTTTGTGTCGGAATGATCGAGGGTGGTTGTTCTTCAGTTTAG
1 TGACCCAGGGTGGTCTTTCTTCAGTTTGAGTCAGAATGATCGAGGGTGGTTGTTCTTCAGTTTAG
* * * *
11886 TCCAGAATGATCAAGGGTGGTCGTTTTTCAATTTATTTCAGT
66 TCCGGAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAGT
** * * * * *
11928 TGACTTAGGGTGGTCTTGCTTCAATTT-ATTTTAGAATGATCGAGGGTGATCT-TTCTTCAGTTT
1 TGACCCAGGGTGGTCTTTCTTCAGTTTGA-GTCAGAATGATCGAGGGTGGT-TGTTCTTCAGTTT
11991 A
64 A
11992 TTTTAGTTGA
Statistics
Matches: 337, Mismatches: 45, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
107 243 0.72
108 94 0.28
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.39
Consensus pattern (107 bp):
TGACCCAGGGTGGTCTTTCTTCAGTTTGAGTCAGAATGATCGAGGGTGGTTGTTCTTCAGTTTAG
TCCGGAATGATCGAGGGTGGTCGTTCTTCAGTTTATTTCAGT
Found at i:11903 original size:72 final size:71
Alignment explanation
Indices: 11505--11990 Score: 242
Period size: 71 Copynumber: 6.8 Consensus size: 71
11495 TCAATGACCC
* * *
11505 AGGGTGGTCT-TTCTTCAGTTTGAGTCGA-AATGATCGAGGGTGGT-TGTTCTTCAGTTCAGTCC
1 AGGGTGGT-TGTTCTTCAGTTT-AGTCCAGAATGATCGAGGGTGGTCT-TTCTTCAGTT-TGTTC
*
11567 GGAATGACCG
62 GGAATGATCG
* * * * * * * *
11577 AGGGTGGTCGTTCTTCAGTTTATTTCAG-TTGACCCAGGGTGGTCTTTCTTCAGTTTGAGTCAGA
1 AGGGTGGTTGTTCTTCAGTTTAGTCCAGAATGATCGAGGGTGGTCTTTCTTCAGTTTG-TTCGGA
11641 ATGATCG
65 ATGATCG
* ** * * * * *
11648 AAGGTGGTTGTTCTTCAGTTTAGTCTGGAATGATCGAGGATGGTCGTTCTTTAGTTTATTTCAG-
1 AGGGTGGTTGTTCTTCAGTTTAGTCCAGAATGATCGAGGGTGGTCTTTCTTCAGTTT-GTTCGGA
* * *
11712 TTGACCC
65 ATGATCG
* * * * ** * *
11719 AGAGTAGTCT-TTCTTCAGTTT-GTGTCGGAATGATCGAGGGCAGT-TGTTCTTCAGTTCAGTCC
1 AGGGTGGT-TGTTCTTCAGTTTAGT-CCAGAATGATCGAGGGTGGTCT-TTCTTCAGTT-TGTTC
*
11781 GAAATGATCG
62 GGAATGATCG
* * * ** * ** * * *
11791 AGTGTGGTCGTTCTTTAGTTTTTTTTCA-TTTGACCCAGGGTGGTCTTTCTTCGGTTTGTGTCGG
1 AGGGTGGTTGTTCTTCAG-TTTAGTCCAGAATGATCGAGGGTGGTCTTTCTTCAGTTTGT-TCGG
11855 AATGATCG
64 AATGATCG
* * * *
11863 AGGGTGGTTGTTCTTCAGTTTAGTCCAGAATGATCAAGGGTGGTCGTTT-TTCAATTTATTTCAG
1 AGGGTGGTTGTTCTTCAGTTTAGTCCAGAATGATCGAGGGTGGTC-TTTCTTCAGTTT-GTTCGG
* *
11927 -TTGA-CTT
64 AATGATC-G
* * * ** *
11934 AGGGTGGTCT-TGCTTCAATTTATTTTAGAATGATCGAGGGTGATCTTTCTTCAGTTT
1 AGGGTGGT-TGTTCTTCAGTTTAGTCCAGAATGATCGAGGGTGGTCTTTCTTCAGTTT
11991 ATTTTAGTTG
Statistics
Matches: 305, Mismatches: 87, Indels: 45
0.70 0.20 0.10
Matches are distributed among these distances:
70 7 0.02
71 156 0.51
72 131 0.43
73 10 0.03
74 1 0.00
ACGTcount: A:0.18, C:0.15, G:0.28, T:0.40
Consensus pattern (71 bp):
AGGGTGGTTGTTCTTCAGTTTAGTCCAGAATGATCGAGGGTGGTCTTTCTTCAGTTTGTTCGGAA
TGATCG
Found at i:11986 original size:215 final size:214
Alignment explanation
Indices: 11499--11989 Score: 614
Period size: 215 Copynumber: 2.3 Consensus size: 214
11489 AATGCTTCAA
* * * * *
11499 TGACCCAGGGTGGTCTTTCTTCAGTTTGA-GTC-GAAATGATCGAGGGTGGTTGTTCTTCAGTTC
1 TGACCCAGAGTAGTCTTGCTTCAATTT-ATGTCAG-AATGATCGAGGGTGATTGTTCTTCAGTTC
*
11562 AGTCCGGAATGACCGAGGGTGGTCGTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTT
64 AGTCCGAAATGACCGAGGGTGGTCGTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTT
** *
11627 CAGTTTGAGTCAGAATGATCGAAGGTGGTTGTTCTTCAGTTTAGTCTGGAATGATCGAGGATGGT
129 CAGTTTGAGTCAGAATGATCGAAGGTGGTTGTTCTTCAGTTTAGTCCAGAATGATCAAGGATGGT
*
11692 CGTTCTTTAGTTTATTTCAGT
194 CGTTCTTTAATTTATTTCAGT
* * * * *
11713 TGACCCAGAGTAGTCTTTCTTCAGTTTGTGTCGGAATGATCGAGGG-CAGTTGTTCTTCAGTTCA
1 TGACCCAGAGTAGTCTTGCTTCAATTTATGTCAGAATGATCGAGGGTGA-TTGTTCTTCAGTTCA
* * * * *
11777 GTCCGAAATGATCGAGTGTGGTCGTTCTTTAGTTTTTTTTCATTTGACCCAGGGTGGTCTTTCTT
65 GTCCGAAATGACCGAGGGTGGTCGTTCTTCAG-TTTATTTCAGTTGACCCAGGGTGGTCTTTCTT
* * * * *
11842 CGGTTTGTGTCGGAATGATCGAGGGTGGTTGTTCTTCAGTTTAGTCCAGAATGATCAAGGGTGGT
129 CAGTTTGAGTCAGAATGATCGAAGGTGGTTGTTCTTCAGTTTAGTCCAGAATGATCAAGGATGGT
11907 CGTT-TTTCAATTTATTTCAGT
194 CGTTCTTT-AATTTATTTCAGT
** * * * *
11928 TGACTTAGGGTGGTCTTGCTTCAATTTATTTTAGAATGATCGAGGGTGATCT-TTCTTCAGTT
1 TGACCCAGAGTAGTCTTGCTTCAATTTATGTCAGAATGATCGAGGGTGAT-TGTTCTTCAGTT
11990 TATTTTAGTT
Statistics
Matches: 239, Mismatches: 31, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
214 86 0.36
215 151 0.63
216 2 0.01
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.39
Consensus pattern (214 bp):
TGACCCAGAGTAGTCTTGCTTCAATTTATGTCAGAATGATCGAGGGTGATTGTTCTTCAGTTCAG
TCCGAAATGACCGAGGGTGGTCGTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCA
GTTTGAGTCAGAATGATCGAAGGTGGTTGTTCTTCAGTTTAGTCCAGAATGATCAAGGATGGTCG
TTCTTTAATTTATTTCAGT
Found at i:11997 original size:36 final size:36
Alignment explanation
Indices: 11505--11994 Score: 299
Period size: 36 Copynumber: 13.7 Consensus size: 36
11495 TCAATGACCC
*
11505 AGGGTGGTCTTTCTTCAGTTTGA-GTC-GAAATGATCG
1 AGGGTGGTCTTTCTTCAGTTT-ATTTCAG-AATGATCG
* * * * *
11541 AGGGTGGT-TGTTCTTCAGTTCAGTCCGGAATGACCG
1 AGGGTGGTCT-TTCTTCAGTTTATTTCAGAATGATCG
* * * *
11577 AGGGTGGTCGTTCTTCAGTTTATTTCAG-TTGACCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGAATGATCG
*
11612 AGGGTGGTCTTTCTTCAGTTTGA-GTCAGAATGATCG
1 AGGGTGGTCTTTCTTCAGTTT-ATTTCAGAATGATCG
* * *
11648 AAGGTGGT-TGTTCTTCAGTTTA-GTCTGGAATGATCG
1 AGGGTGGTCT-TTCTTCAGTTTATTTC-AGAATGATCG
* * * * * *
11684 AGGATGGTCGTTCTTTAGTTTATTTCAG-TTGACCC
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGAATGATCG
* * * * *
11719 AGAGTAGTCTTTCTTCAGTTTGTGTCGGAATGATCG
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGAATGATCG
** * * *
11755 AGGGCAGT-TGTTCTTCAGTTCA-GTCCGAAATGATCG
1 AGGGTGGTCT-TTCTTCAGTTTATTTCAG-AATGATCG
* * * * ** * *
11791 AGTGTGGTCGTTCTTTAGTTTTTTTTCA-TTTGACCC
1 AGGGTGGTCTTTCTTCAG-TTTATTTCAGAATGATCG
* * * *
11827 AGGGTGGTCTTTCTTCGGTTTGTGTCGGAATGATCG
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGAATGATCG
* * *
11863 AGGGTGGT-TGTTCTTCAGTTTAGTCCAGAATGATCA
1 AGGGTGGTCT-TTCTTCAGTTTATTTCAGAATGATCG
* * *
11899 AGGGTGGTCGTTT-TTCAATTTATTTCAG-TTGA-CTT
1 AGGGTGGTC-TTTCTTCAGTTTATTTCAGAATGATC-G
* * *
11934 AGGGTGGTCTTGCTTCAATTTATTTTAGAATGATCG
1 AGGGTGGTCTTTCTTCAGTTTATTTCAGAATGATCG
*
11970 AGGGTGATCTTTCTTCAGTTTATTT
1 AGGGTGGTCTTTCTTCAGTTTATTT
11995 TAGTTGACCC
Statistics
Matches: 344, Mismatches: 86, Indels: 48
0.72 0.18 0.10
Matches are distributed among these distances:
34 3 0.01
35 98 0.28
36 232 0.67
37 8 0.02
38 3 0.01
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.40
Consensus pattern (36 bp):
AGGGTGGTCTTTCTTCAGTTTATTTCAGAATGATCG
Found at i:13976 original size:71 final size:71
Alignment explanation
Indices: 13831--14634 Score: 459
Period size: 71 Copynumber: 11.2 Consensus size: 71
13821 GGCTCGATCC
* * * * * *
13831 GTGGTCTTTCTTTACTTTATATCAGAATGATCGAGGGTGGTCTGTTCTTCAATTCAAT-TC-GAA
1 GTGGTCGTTCTTCAGTTTATTTCAG-ATGATCGAGGGTGGTCT-TTCTTCAGTT-TATGTCAG-A
*
13894 ATGATCAAGG
62 ATGATCGAGG
* * * *
13904 GTGGTCGTTCTTCAGTTTATTTCAGTTGACCCAGGGTGGTCTTTCTTTAGTTTGA-GTCAGAATG
1 GTGGTCGTTCTTCAGTTTATTTCAGATGATCGAGGGTGGTCTTTCTTCAGTTT-ATGTCAGAATG
13968 ATCGAGG
65 ATCGAGG
* * * * * * * * *
13975 GTGGTTGTTCTTCAGTTTAGTCCGAAATGATCGAGGGTGGTCGTTCTTTAGTTTATTTTAG--TT
1 GTGGTCGTTCTTCAGTTTATTTC-AGATGATCGAGGGTGGTCTTTCTTCAGTTTATGTCAGAATG
*
14038 AGTCTAGG
65 A-TCGAGG
* * * * * *
14046 GTGGTCTTTCTTCAGTTTGTGTCGGAATTATCGAGGGTGGT-TGTTCTTCAGTTCA-GTTC-GAT
1 GTGGTCGTTCTTCAGTTTATTTCAG-ATGATCGAGGGTGGTCT-TTCTTCAGTTTATG-TCAGA-
14108 ATGATCGAGG
62 ATGATCGAGG
* * * * * * * *
14118 GTGGTCGTTCTTTAATTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTGTGTCGGAACGA
1 GTGGTCGTTCTTCAGTTTATTTCAGATGATCGAGGGTGGTCTTTCTTCAGTTTATGTCAGAATGA
14183 TCGAGG
66 TCGAGG
* * * * * * * * * *
14189 GTGTTTGTTCTTCAATTCAGTCCGGAATGATCGAGGGTGGTCGTTT-TTCAATTTATTTCAG-TT
1 GTGGTCGTTCTTCAGTTTATTTCAG-ATGATCGAGGGTGGTC-TTTCTTCAGTTTATGTCAGAAT
* *
14252 GACCTAGG
64 GATCGAGG
* * * * ** * *
14260 ATGGTCTTTCTTCAATTTATTTTAGAATGATCGAGGGTTATCTTTCTTCAGTTTATTTCAG-TTG
1 GTGGTCGTTCTTCAGTTTATTTCAG-ATGATCGAGGGTGGTCTTTCTTCAGTTTATGTCAGAATG
* * *
14324 ACCCAGA
65 ATCGAGG
* * * * * * * *
14331 GTGGTCTTTCTTCAGTTTATGTCGGAATGATCGAAGTTGGTCGTTCTTCAGTTCA-GTTCGGAAT
1 GTGGTCGTTCTTCAGTTTATTTCAG-ATGATCGAGGGTGGTCTTTCTTCAGTTTATG-TCAGAA-
*
14395 TG-TCAAGG
63 TGATCGAGG
* * * * *
14403 GTGGTCGTTCTTCAGTTTATTTCAGTTGACCTAGGGTGGTCTTTCTTCAGTTTACGTCGGAATGA
1 GTGGTCGTTCTTCAGTTTATTTCAGATGATCGAGGGTGGTCTTTCTTCAGTTTATGTCAGAATGA
14468 TCGAGG
66 TCGAGG
* * * * * * * **
14474 GTGGTCGTTCTTCAGTTCAGTTCGGAATGATCAAGGGTGGTCGTTCTTCAATTTATTTCAGTTTG
1 GTGGTCGTTCTTCAGTTTATTTCAG-ATGATCGAGGGTGGTCTTTCTTCAGTTTATGTCAGAATG
* *
14539 ACCCAGG
65 ATCGAGG
* * * * * * * * *
14546 GTGGTCTTTATTCAGTTTATGTCGGAATGGTCGGGGGTGGTCGTTT-TTCAATTCAAT-TCGGAA
1 GTGGTCGTTCTTCAGTTTATTTCAG-ATGATCGAGGGTGGTC-TTTCTTCAGTT-TATGTCAGAA
*
14609 TGATCCAGG
63 TGATCGAGG
* *
14618 GTGATCTTTCTTCAGTT
1 GTGGTCGTTCTTCAGTT
14635 ACTTATTCTA
Statistics
Matches: 562, Mismatches: 143, Indels: 53
0.74 0.19 0.07
Matches are distributed among these distances:
70 8 0.01
71 300 0.53
72 222 0.40
73 32 0.06
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.40
Consensus pattern (71 bp):
GTGGTCGTTCTTCAGTTTATTTCAGATGATCGAGGGTGGTCTTTCTTCAGTTTATGTCAGAATGA
TCGAGG
Found at i:14273 original size:178 final size:178
Alignment explanation
Indices: 14089--14487 Score: 543
Period size: 178 Copynumber: 2.2 Consensus size: 178
14079 AGGGTGGTTG
* * *
14089 TTCTTCAGTTCA-GTTCGATATGATCGAGGGTGGTCGTTCTTTAATTTATTTCAGTTGACCCAGG
1 TTCTTCAGTTTACGTTCGA-ATGATCGAGGGTGGTCGTTCTTCAATTTATTTCAGTTGACCCAGA
* * * *
14153 GTGGTCTTTCTTCAGTTTGTGTCGGAACGATCGAGGGTGTTTGTTCTTCAATTCAGTCCGGAA-T
65 GTGGTCTTTCTTCAGTTTATGTCGGAACGATCGAAGGTGGTCGTTCTTCAATTCAGTCCGGAATT
* *
14217 GATCGAGGGTGGTCGTTTTTCAATTTATTTCAGTTGACCTAGGATGGTCT
130 G-TCAAGGGTGGTCGTTCTTCAATTTATTTCAGTTGACCTAGGATGGTCT
* ** * ** * *
14267 TTCTTCAATTTATTTTAGAATGATCGAGGGTTATCTTTCTTCAGTTTATTTCAGTTGACCCAGAG
1 TTCTTCAGTTTACGTTCGAATGATCGAGGGTGGTCGTTCTTCAATTTATTTCAGTTGACCCAGAG
* * * *
14332 TGGTCTTTCTTCAGTTTATGTCGGAATGATCGAAGTTGGTCGTTCTTCAGTTCAGTTCGGAATTG
66 TGGTCTTTCTTCAGTTTATGTCGGAACGATCGAAGGTGGTCGTTCTTCAATTCAGTCCGGAATTG
* *
14397 TCAAGGGTGGTCGTTCTTCAGTTTATTTCAGTTGACCTAGGGTGGTCT
131 TCAAGGGTGGTCGTTCTTCAATTTATTTCAGTTGACCTAGGATGGTCT
14445 TTCTTCAGTTTACG-TCGGAATGATCGAGGGTGGTCGTTCTTCA
1 TTCTTCAGTTTACGTTC-GAATGATCGAGGGTGGTCGTTCTTCA
14488 GTTCAGTTCG
Statistics
Matches: 189, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
177 1 0.01
178 182 0.96
179 6 0.03
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (178 bp):
TTCTTCAGTTTACGTTCGAATGATCGAGGGTGGTCGTTCTTCAATTTATTTCAGTTGACCCAGAG
TGGTCTTTCTTCAGTTTATGTCGGAACGATCGAAGGTGGTCGTTCTTCAATTCAGTCCGGAATTG
TCAAGGGTGGTCGTTCTTCAATTTATTTCAGTTGACCTAGGATGGTCT
Found at i:14309 original size:107 final size:107
Alignment explanation
Indices: 13831--14297 Score: 598
Period size: 107 Copynumber: 4.4 Consensus size: 107
13821 GGCTCGATCC
* * * * *
13831 GTGGTCTTTCTTTACTTTATATCAGAATGATCGAGGGTGGTCTGTTCTTCAATTCAATTCGAAAT
1 GTGGTCTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGT-TGTTCTTCAATTCAGTCCGAAAT
* * *
13896 GATCAAGGGTGGTCGTTCTTCAGTTTATTTCAGTTGACCCAGG
65 GATCGAGGGTGGTCGTTCTTTAATTTATTTCAGTTGACCCAGG
* * *
13939 GTGGTCTTTCTTTAGTTTGA-GTCAGAATGATCGAGGGTGGTTGTTCTTCAGTTTAGTCCGAAAT
1 GTGGTCTTTCTTCAGTTT-ATGTCAGAATGATCGAGGGTGGTTGTTCTTCAATTCAGTCCGAAAT
* * * *
14003 GATCGAGGGTGGTCGTTCTTTAGTTTATTTTAGTT-AGTCTAGG
65 GATCGAGGGTGGTCGTTCTTTAATTTATTTCAGTTGA-CCCAGG
* * * * * *
14046 GTGGTCTTTCTTCAGTTTGTGTCGGAATTATCGAGGGTGGTTGTTCTTCAGTTCAGTTCGATATG
1 GTGGTCTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTTGTTCTTCAATTCAGTCCGAAATG
14111 ATCGAGGGTGGTCGTTCTTTAATTTATTTCAGTTGACCCAGG
66 ATCGAGGGTGGTCGTTCTTTAATTTATTTCAGTTGACCCAGG
* * * * *
14153 GTGGTCTTTCTTCAGTTTGTGTCGGAACGATCGAGGGTGTTTGTTCTTCAATTCAGTCCGGAATG
1 GTGGTCTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTTGTTCTTCAATTCAGTCCGAAATG
*
14218 ATCGAGGGTGGTCGTT-TTTCAATTTATTTCAGTTGACCTAGG
66 ATCGAGGGTGGTCGTTCTTT-AATTTATTTCAGTTGACCCAGG
* * * *
14260 ATGGTCTTTCTTCAATTTATTTTAGAATGATCGAGGGT
1 GTGGTCTTTCTTCAGTTTATGTCAGAATGATCGAGGGT
14298 TATCTTTCTT
Statistics
Matches: 317, Mismatches: 37, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
106 4 0.01
107 274 0.86
108 38 0.12
109 1 0.00
ACGTcount: A:0.18, C:0.14, G:0.27, T:0.41
Consensus pattern (107 bp):
GTGGTCTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTTGTTCTTCAATTCAGTCCGAAATG
ATCGAGGGTGGTCGTTCTTTAATTTATTTCAGTTGACCCAGG
Found at i:14372 original size:107 final size:107
Alignment explanation
Indices: 14261--14634 Score: 498
Period size: 107 Copynumber: 3.5 Consensus size: 107
14251 TGACCTAGGA
* * * ** * * *
14261 TGGTCTTTCTTCAATTTATTTTAGAATGATCGAGGGTTATCTTTCTTCAGTTTATTTCAGTTGAC
1 TGGTCGTTCTTCAATTCAGTTCGGAATGATCAAGGGTGATCGTTCTTCAGTTTATTTCAGTTGAC
* * *
14326 CCAGAGTGGTCTTTCTTCAGTTTATGTCGGAATGATCGAAGT
66 CCAGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCGAGGG
* *
14368 TGGTCGTTCTTCAGTTCAGTTCGGAATTG-TCAAGGGTGGTCGTTCTTCAGTTTATTTCAGTTGA
1 TGGTCGTTCTTCAATTCAGTTCGGAA-TGATCAAGGGTGATCGTTCTTCAGTTTATTTCAGTTGA
* *
14432 CCTAGGGTGGTCTTTCTTCAGTTTACGTCGGAATGATCGAGGG
65 CCCAGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCGAGGG
* * *
14475 TGGTCGTTCTTCAGTTCAGTTCGGAATGATCAAGGGTGGTCGTTCTTCAATTTATTTCAGTTTGA
1 TGGTCGTTCTTCAATTCAGTTCGGAATGATCAAGGGTGATCGTTCTTCAGTTTATTTCAG-TTGA
* * *
14540 CCCAGGGTGGTCTTTATTCAGTTTATGTCGGAATGGTCGGGGG
65 CCCAGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCGAGGG
* * * *
14583 TGGTCGTTTTTCAATTCAATTCGGAATGATCCAGGGTGATCTTTCTTCAGTT
1 TGGTCGTTCTTCAATTCAGTTCGGAATGATCAAGGGTGATCGTTCTTCAGTT
14635 ACTTATTCTA
Statistics
Matches: 236, Mismatches: 28, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
106 2 0.01
107 145 0.61
108 89 0.38
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.40
Consensus pattern (107 bp):
TGGTCGTTCTTCAATTCAGTTCGGAATGATCAAGGGTGATCGTTCTTCAGTTTATTTCAGTTGAC
CCAGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCGAGGG
Found at i:14385 original size:285 final size:286
Alignment explanation
Indices: 14000--14565 Score: 807
Period size: 285 Copynumber: 2.0 Consensus size: 286
13990 TTTAGTCCGA
* * * * * * *
14000 AATGATCGAGGGTGGTCGTTCTTTAGTTTATTTTAGTTAGTCTAGGGTGGTCTTTCTTCAGTTTG
1 AATGATCGAGGGTGATCGTTCTTCAGTTTATTTCAGTTAGCCCAGAGTGGTCTTTCTTCAGTTTA
* * * *
14065 TGTCGGAATTATCGAGGGTGGTTGTTCTTCAGTTCAGTTC-G-ATATGATCGAGGGTGGTCGTTC
66 TGTCGGAATGATCGAAGGTGGTCGTTCTTCAGTTCAGTTCGGAAT-TG-TCAAGGGTGGTCGTTC
* ** *
14128 TTTAATTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTGTGTCGGAACGATCGAGGGTGT
129 TTCAATTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTACGTCGGAACGATCGAGGGTGG
* * * *
14193 TTGTTCTTCAATTCAGTCCGGAATGATCGAGGGTGGTCGTTTTTCAATTTATTTCAG-TTGACCT
194 TCGTTCTTCAATTCAGTCCGGAATGATCAAGGGTGGTCGTTCTTCAATTTATTTCAGTTTGACCC
*
14257 AGGATGGTCTTTCTTCAATTTATTTTAG
259 AGGATGGTCTTTATTCAATTTATTTTAG
* *
14285 AATGATCGAGGGTTATCTTTCTTCAGTTTATTTCAGTT-GACCCAGAGTGGTCTTTCTTCAGTTT
1 AATGATCGAGGGTGATCGTTCTTCAGTTTATTTCAGTTAG-CCCAGAGTGGTCTTTCTTCAGTTT
*
14349 ATGTCGGAATGATCGAAGTTGGTCGTTCTTCAGTTCAGTTCGGAATTGTCAAGGGTGGTCGTTCT
65 ATGTCGGAATGATCGAAGGTGGTCGTTCTTCAGTTCAGTTCGGAATTGTCAAGGGTGGTCGTTCT
* * *
14414 TCAGTTTATTTCAGTTGACCTAGGGTGGTCTTTCTTCAGTTTACGTCGGAATGATCGAGGGTGGT
130 TCAATTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTACGTCGGAACGATCGAGGGTGGT
* *
14479 CGTTCTTCAGTTCAGTTCGGAATGATCAAGGGTGGTCGTTCTTCAATTTATTTCAGTTTGACCCA
195 CGTTCTTCAATTCAGTCCGGAATGATCAAGGGTGGTCGTTCTTCAATTTATTTCAGTTTGACCCA
* *
14544 GGGTGGTCTTTATTCAGTTTAT
260 GGATGGTCTTTATTCAATTTAT
14566 GTCGGAATGG
Statistics
Matches: 247, Mismatches: 30, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
284 1 0.00
285 215 0.87
286 29 0.12
287 2 0.01
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.41
Consensus pattern (286 bp):
AATGATCGAGGGTGATCGTTCTTCAGTTTATTTCAGTTAGCCCAGAGTGGTCTTTCTTCAGTTTA
TGTCGGAATGATCGAAGGTGGTCGTTCTTCAGTTCAGTTCGGAATTGTCAAGGGTGGTCGTTCTT
CAATTTATTTCAGTTGACCCAGGGTGGTCTTTCTTCAGTTTACGTCGGAACGATCGAGGGTGGTC
GTTCTTCAATTCAGTCCGGAATGATCAAGGGTGGTCGTTCTTCAATTTATTTCAGTTTGACCCAG
GATGGTCTTTATTCAATTTATTTTAG
Found at i:14607 original size:36 final size:36
Alignment explanation
Indices: 13855--14631 Score: 329
Period size: 36 Copynumber: 21.7 Consensus size: 36
13845 CTTTATATCA
13855 GAATGATCGAGGGTGGTCTGTTCTTCAATTCAATTCG
1 GAATGATCGAGGGTGGTC-GTTCTTCAATTCAATTCG
* * * * * *
13892 AAATGATCAAGGGTGGTCGTTCTTCAGTTTATTTCA
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
* * * * * * ** * *
13928 G-TTGACCCAGGGTGGTCTTTCTTTAGTTTGAGTCA
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
* * * * *
13963 GAATGATCGAGGGTGGTTGTTCTTCAGTTTAGTCCG
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
* * * * *
13999 AAATGATCGAGGGTGGTCGTTCTTTAGTT-TATT-T
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
* * * * * * **
14033 TAGTTAGTCTAGGGTGGTCTTTCTTCAGTT-TGTGTCG
1 GAATGA-TCGAGGGTGGTCGTTCTTCAATTCAAT-TCG
* * * *
14070 GAATTATCGAGGGTGGTTGTTCTTCAGTTCAGTTC-
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
* * * *
14105 GATATGATCGAGGGTGGTCGTTCTTTAATTTATTTCA
1 GA-ATGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
* * * * * **
14142 G-TTGACCCAGGGTGGTCTTTCTTCAGTT-TGTGTCG
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAAT-TCG
* * * * *
14177 GAACGATCGAGGGTGTTTGTTCTTCAATTCAGTCCG
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
* * * *
14213 GAATGATCGAGGGTGGTCGTTTTTCAATTTATTTCA
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
* * * * * * * **
14249 G-TTGACCTAGGATGGTCTTTCTTCAATTTATTTTA
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
** * * * * *
14284 GAATGATCGAGGGTTATCTTTCTTCAGTTTATTTCA
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
* * * * * * *
14320 G-TTGACCCAGAGTGGTCTTTCTTCAGTT-TATGTCG
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAAT-TCG
* * * *
14355 GAATGATCGAAGTTGGTCGTTCTTCAGTTCAGTTCG
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
* * * * *
14391 GAATTG-TCAAGGGTGGTCGTTCTTCAGTTTATTTCA
1 GAA-TGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
* * * * * * **
14427 G-TTGACCTAGGGTGGTCTTTCTTCAGTTTACGTCG
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
* *
14462 GAATGATCGAGGGTGGTCGTTCTTCAGTTCAGTTCG
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
* * * *
14498 GAATGATCAAGGGTGGTCGTTCTTCAATTTATTTCA
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
** * * * * * *
14534 GTTTGACCCAGGGTGGTCTTTATTCAGTT-TATGTCG
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAAT-TCG
* * *
14570 GAATGGTCGGGGGTGGTCGTTTTTCAATTCAATTCG
1 GAATGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
* * *
14606 GAATGATCCAGGGTGATCTTTCTTCA
1 GAATGATCGAGGGTGGTCGTTCTTCA
14632 GTTACTTATT
Statistics
Matches: 557, Mismatches: 164, Indels: 39
0.73 0.22 0.05
Matches are distributed among these distances:
34 7 0.01
35 154 0.28
36 366 0.66
37 30 0.05
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.40
Consensus pattern (36 bp):
GAATGATCGAGGGTGGTCGTTCTTCAATTCAATTCG
Found at i:15387 original size:14 final size:14
Alignment explanation
Indices: 15368--15398 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
15358 GAGGTTAAGC
15368 CAAATTAGGATTAA
1 CAAATTAGGATTAA
15382 CAAATTAGGATTAA
1 CAAATTAGGATTAA
15396 CAA
1 CAA
15399 GTCGGTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.26
Consensus pattern (14 bp):
CAAATTAGGATTAA
Found at i:18427 original size:37 final size:35
Alignment explanation
Indices: 18386--18523 Score: 131
Period size: 37 Copynumber: 3.8 Consensus size: 35
18376 AATTTAGCTC
18386 TTTTCAAATTGGGAAAGTTCCCATCAAG-TTTTCAAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGATTTT---AG
18423 TTTTCAAATTGGGAAAGTTCCCATC-AGATTTTAG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGATTTTAG
* *
18457 TTTTCAATTTAGGGAAAGTTCCCGTCAA-ATTCAGTCTTAG
1 TTTTCAAATT-GGGAAAGTTCCCATCAAGA-T---T-TTAG
*
18497 TTTTC-AATGTGGGAAAGTTCCCGTCAA
1 TTTTCAAAT-TGGGAAAGTTCCCATCAA
18524 ACAGCATTGT
Statistics
Matches: 89, Mismatches: 3, Indels: 16
0.82 0.03 0.15
Matches are distributed among these distances:
34 11 0.12
35 15 0.17
36 4 0.04
37 29 0.33
39 20 0.22
40 10 0.11
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (35 bp):
TTTTCAAATTGGGAAAGTTCCCATCAAGATTTTAG
Found at i:19460 original size:15 final size:15
Alignment explanation
Indices: 19440--19472 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19430 AGTTGTTAAT
19440 AATGGTGCTGAAGAG
1 AATGGTGCTGAAGAG
*
19455 AATGGTGCTGGAGAG
1 AATGGTGCTGAAGAG
19470 AAT
1 AAT
19473 TTTAGGGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.39, T:0.21
Consensus pattern (15 bp):
AATGGTGCTGAAGAG
Done.