Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013733.1 Corchorus capsularis cultivar CVL-1 contig13754, 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: 66349
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:350 original size:28 final size:28
Alignment explanation
Indices: 293--350 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
283 TCTCGTTTTT
293 AAAAGTTAAGAGGCCAATTTGTCTCAAA
1 AAAAGTTAAGAGGCCAATTTGTCTCAAA
* * *
321 AAAAGATTAAGGGGTCAATTTGTCCCAAA
1 AAAAG-TTAAGAGGCCAATTTGTCTCAAA
350 A
1 A
351 TGGATAGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (28 bp):
AAAAGTTAAGAGGCCAATTTGTCTCAAA
Found at i:8567 original size:32 final size:32
Alignment explanation
Indices: 8531--8591 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
8521 CGTTTTCGGG
* *
8531 TTCGGGTTAAATTTGGGTCAGGTTGATTCAAA
1 TTCGGATTAAATTTGGGTCAGGTTAATTCAAA
*
8563 TTCGGATTAATTTTGGGTCAGGTTAATTC
1 TTCGGATTAAATTTGGGTCAGGTTAATTC
8592 GGGTTCAGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.41
Consensus pattern (32 bp):
TTCGGATTAAATTTGGGTCAGGTTAATTCAAA
Found at i:8774 original size:20 final size:20
Alignment explanation
Indices: 8741--8779 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
8731 CATAGATGAA
*
8741 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
8761 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
8780 GAATTCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:8821 original size:17 final size:17
Alignment explanation
Indices: 8799--8858 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
8789 TTTTTTCAGG
*
8799 TTCGGGTTCGGGTTTTT
1 TTCGGGTTCGAGTTTTT
*
8816 TTCGGGTTTC-AGATTTT
1 TTCGGG-TTCGAGTTTTT
* *
8833 TTCGGGTTTGAG-CTTT
1 TTCGGGTTCGAGTTTTT
8849 TTCGGGTTCG
1 TTCGGGTTCG
8859 GGTTCGAGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 14 0.39
17 19 0.53
18 3 0.08
ACGTcount: A:0.05, C:0.13, G:0.32, T:0.50
Consensus pattern (17 bp):
TTCGGGTTCGAGTTTTT
Found at i:8849 original size:16 final size:17
Alignment explanation
Indices: 8813--8856 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
8803 GGTTCGGGTT
*
8813 TTTTTCGGGTTTCAGAT
1 TTTTTCGGGTTTCAGAC
*
8830 TTTTTCGGGTTTGAG-C
1 TTTTTCGGGTTTCAGAC
8846 TTTTTCGGGTT
1 TTTTTCGGGTT
8857 CGGGTTCGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.07, C:0.11, G:0.27, T:0.55
Consensus pattern (17 bp):
TTTTTCGGGTTTCAGAC
Found at i:10466 original size:25 final size:25
Alignment explanation
Indices: 10430--10479 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
10420 CACAGTTGAC
10430 GGCGTCACTGCCACATCAGCACAAT
1 GGCGTCACTGCCACATCAGCACAAT
*
10455 GGCGTCAGTGCCACATCAGCACAAT
1 GGCGTCACTGCCACATCAGCACAAT
10480 TGATGGCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.34, G:0.22, T:0.16
Consensus pattern (25 bp):
GGCGTCACTGCCACATCAGCACAAT
Found at i:11610 original size:16 final size:16
Alignment explanation
Indices: 11591--11650 Score: 111
Period size: 16 Copynumber: 3.8 Consensus size: 16
11581 TTCGGACGGG
11591 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
11607 TTCGGATTCGGGTATT
1 TTCGGGTTCGGGTATT
11623 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
11639 TTCGGGTTCGGG
1 TTCGGGTTCGGG
11651 CTCGGATCGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.07, C:0.13, G:0.38, T:0.42
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:11662 original size:17 final size:17
Alignment explanation
Indices: 11640--11685 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
11630 TCGGGTATTT
11640 TCGGGTTCGGG-CTCGGA
1 TCGGGTTCGGGTC-CGGA
* *
11657 TCGGGTCCGGGTCCGGG
1 TCGGGTTCGGGTCCGGA
11674 TCGGGTTCGGGT
1 TCGGGTTCGGGT
11686 TCAGTTTCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 24 0.96
18 1 0.04
ACGTcount: A:0.02, C:0.24, G:0.50, T:0.24
Consensus pattern (17 bp):
TCGGGTTCGGGTCCGGA
Found at i:12459 original size:17 final size:18
Alignment explanation
Indices: 12433--12466 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12423 TATTTTGATA
12433 TCGGGCTCGGG-TCGGGG
1 TCGGGCTCGGGTTCGGGG
*
12450 TCGGGTTCGGGTTCGGG
1 TCGGGCTCGGGTTCGGG
12467 TATTTTCGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.00, C:0.21, G:0.56, T:0.24
Consensus pattern (18 bp):
TCGGGCTCGGGTTCGGGG
Found at i:12467 original size:6 final size:6
Alignment explanation
Indices: 12433--12493 Score: 52
Period size: 6 Copynumber: 9.5 Consensus size: 6
12423 TATTTTGATA
* *
12433 TCGGGC TCGGG- TCGGGG TCGGGT TCGGGT TCGGGTATTT TCGGGT TCCGGGT
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGG----T TCGGGT T-CGGGT
12485 TCGGGT TCG
1 TCGGGT TCG
12494 AGACGTTGAC
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
5 5 0.10
6 31 0.65
7 6 0.12
10 6 0.12
ACGTcount: A:0.02, C:0.20, G:0.48, T:0.31
Consensus pattern (6 bp):
TCGGGT
Found at i:12590 original size:48 final size:48
Alignment explanation
Indices: 12480--12591 Score: 206
Period size: 48 Copynumber: 2.3 Consensus size: 48
12470 TTTCGGGTTC
*
12480 CGGGTTCGGGTTCGAGACGTTGACTTTTCTGGTCAATTCGGGTAATTT
1 CGGGTTCGGGTTCGGGACGTTGACTTTTCTGGTCAATTCGGGTAATTT
*
12528 CGGGTTCGGGTTCGGGACGTTGACTTTTTTGGTCAATTCGGGTAATTT
1 CGGGTTCGGGTTCGGGACGTTGACTTTTCTGGTCAATTCGGGTAATTT
12576 CGGGTTCGGGTTCGGG
1 CGGGTTCGGGTTCGGG
12592 TTCGGGCGGG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 62 1.00
ACGTcount: A:0.12, C:0.16, G:0.36, T:0.37
Consensus pattern (48 bp):
CGGGTTCGGGTTCGGGACGTTGACTTTTCTGGTCAATTCGGGTAATTT
Found at i:12612 original size:7 final size:6
Alignment explanation
Indices: 12574--12610 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
12564 TTCGGGTAAT
12574 TTCGGG TTCGGG TTCGGG TTCGGG --CGGG TTTCGGG TT
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG -TTCGGG TT
12611 TCAGGTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
4 4 0.14
6 20 0.71
7 4 0.14
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TTCGGG
Found at i:15139 original size:47 final size:47
Alignment explanation
Indices: 15070--15162 Score: 159
Period size: 47 Copynumber: 2.0 Consensus size: 47
15060 AATCTTTTAA
*
15070 CCAAACCCCATCCTCTCAAAAGAAGGATAAAACAGATTTGAAGGAAT
1 CCAAACCCCATCCTCTCAAAAGAAGAATAAAACAGATTTGAAGGAAT
* *
15117 CCAAACCCCATCCTCTTAAAAGAAGAATGAAACAGATTTGAAGGAA
1 CCAAACCCCATCCTCTCAAAAGAAGAATAAAACAGATTTGAAGGAA
15163 CAAGAGAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.17
Consensus pattern (47 bp):
CCAAACCCCATCCTCTCAAAAGAAGAATAAAACAGATTTGAAGGAAT
Found at i:15964 original size:38 final size:38
Alignment explanation
Indices: 15913--15990 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
15903 TTTCAACAAA
*
15913 TTCAACTATCTTACATTCTTACTTAATACTTT-ACATTT
1 TTCAACAATCTTACATTCTTACTTAATACTTTGA-ATTT
15951 TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
1 TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
15989 TT
1 TT
15991 GGTAATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 37 0.97
39 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.01, T:0.50
Consensus pattern (38 bp):
TTCAACAATCTTACATTCTTACTTAATACTTTGAATTT
Found at i:17457 original size:29 final size:28
Alignment explanation
Indices: 17402--17463 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 28
17392 TAATCGTTAA
*
17402 AATTCCATCTACAATATACGTGCTACAT
1 AATTCCATCTACAATAAACGTGCTACAT
* *
17430 AATTCCATCTACCAATAAATGTGTTACAT
1 AATTCCATCTA-CAATAAACGTGCTACAT
17459 AATTC
1 AATTC
17464 TCTAGTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 11 0.37
29 19 0.63
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (28 bp):
AATTCCATCTACAATAAACGTGCTACAT
Found at i:20040 original size:17 final size:17
Alignment explanation
Indices: 20018--20059 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
20008 ATCACCCCCC
*
20018 AGATCACTAGTGAT-CTA
1 AGATCACCAGTGATGC-A
20035 AGATCACCAGTGATGCA
1 AGATCACCAGTGATGCA
20052 AGATCACC
1 AGATCACC
20060 GACGATCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 22 0.96
18 1 0.04
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (17 bp):
AGATCACCAGTGATGCA
Found at i:21402 original size:20 final size:20
Alignment explanation
Indices: 21377--21419 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
21367 ATTAAGATGT
21377 TTAATGTGAAAATATAATTG
1 TTAATGTGAAAATATAATTG
21397 TTAATGTGAAAATATAATTG
1 TTAATGTGAAAATATAATTG
21417 TTA
1 TTA
21420 TTATTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (20 bp):
TTAATGTGAAAATATAATTG
Found at i:21825 original size:209 final size:208
Alignment explanation
Indices: 21466--21882 Score: 798
Period size: 209 Copynumber: 2.0 Consensus size: 208
21456 AAAATTAACA
*
21466 TTTTTTTTTGAAAACGTAAAATTAATCTAATAATAATAATAGTATTTGCAAGCTTTAATTTTTTT
1 TTTTTTTTAGAAAACGTAAAATTAATCTAATAATAATAATAGTATTTGCAAGCTTTAATTTTTTT
21531 AGATATTAAGAGATTGAATTTAAATAAAAGTTTAAGAAGATGTATATTTCCTTTTATATTAAATT
66 AGATATTAAGAGATTGAATTTAAATAAAAGTTTAAGAAGATGTATATTTCCTTTTATATTAAATT
21596 ACCTATTAACCATTAGAATTTAAAACTAAAGCTTTATATTAAAAAGGGTATTTTAGATATTTCAG
131 ACCTATTAACCATTAGAATTTAAAACTAAAGCTTTATATTAAAAAGGGTATTTTAGATATTTCAG
*
21661 GTCATGGTTTTTG
196 GTCATGATTTTTG
21674 TTTTTTTTAGAAAACGTAAAATTAATCTAATAATAATAATAGTATTTGCAAGCTTTAATTTTTTT
1 TTTTTTTTAGAAAACGTAAAATTAATCTAATAATAATAATAGTATTTGCAAGCTTTAA-TTTTTT
21739 TAGATATTAAGAGATTGAATTTAAATAAAAGTTTAAGAAGATGTATATTTCCTTTTATATTAAAT
65 TAGATATTAAGAGATTGAATTTAAATAAAAGTTTAAGAAGATGTATATTTCCTTTTATATTAAAT
*
21804 TACCTATTAACCATTAGAATTTAAAACTAAAGCTTTATATTAAAAATGGTATTTTAGATATTTCA
130 TACCTATTAACCATTAGAATTTAAAACTAAAGCTTTATATTAAAAAGGGTATTTTAGATATTTCA
21869 GGTCATGATTTTTG
195 GGTCATGATTTTTG
21883 AAGTTTAGAC
Statistics
Matches: 205, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
208 57 0.28
209 148 0.72
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (208 bp):
TTTTTTTTAGAAAACGTAAAATTAATCTAATAATAATAATAGTATTTGCAAGCTTTAATTTTTTT
AGATATTAAGAGATTGAATTTAAATAAAAGTTTAAGAAGATGTATATTTCCTTTTATATTAAATT
ACCTATTAACCATTAGAATTTAAAACTAAAGCTTTATATTAAAAAGGGTATTTTAGATATTTCAG
GTCATGATTTTTG
Found at i:21919 original size:6 final size:6
Alignment explanation
Indices: 21910--21944 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
21900 ATATATAGAT
21910 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
21945 TATCAACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:24797 original size:5 final size:5
Alignment explanation
Indices: 24789--24823 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
24779 AAAAGAGGAA
*
24789 AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
24824 GAACCCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:27138 original size:2 final size:2
Alignment explanation
Indices: 27125--27160 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
27115 ATTTAGTTTA
*
27125 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
27161 GATGAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:28092 original size:27 final size:29
Alignment explanation
Indices: 28050--28106 Score: 91
Period size: 27 Copynumber: 2.0 Consensus size: 29
28040 ATGCTTTGCA
28050 TTTTGCAATATGGTCTTAGATTTC-ATTTT
1 TTTTGCAATA-GGTCTTAGATTTCTATTTT
28079 TTTTGCAATA-GTCTTAGATTTCTATTTT
1 TTTTGCAATAGGTCTTAGATTTCTATTTT
28107 ATGCATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 12 0.44
28 5 0.19
29 10 0.37
ACGTcount: A:0.21, C:0.11, G:0.12, T:0.56
Consensus pattern (29 bp):
TTTTGCAATAGGTCTTAGATTTCTATTTT
Found at i:30805 original size:129 final size:130
Alignment explanation
Indices: 30383--30849 Score: 611
Period size: 129 Copynumber: 3.6 Consensus size: 130
30373 AATTAAAAGT
* *
30383 CGTTGCCTTAGTG--TTTGATGGTATTTTACCCACAA-ACTTTTTTAATTGTTGCCAATGCTTGC
1 CGTTGCCTAAGTGATTTTGATGGTATTTTA--CACAACACTTTTTTAATTGTTGCCAATGCTTAC
* * * * *
30445 AGTTTTCGTAACAACAAAAGCAAAGTCATTGCGAAATCATAATTTATTCGTAACAATTTTATAAA
64 AATTTTCGTAACAACAAAAACAAAGTCGTTGCGAAATCATAATATATTCGTAACAACTTTATAAA
*
30510 AT
129 AA
* * * * *
30512 CGTTCCCTAAGTGATTTTGATGGTATTTTACACAACACCTTTTTAGTCGTTTCCAATGCTTACAA
1 CGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAATTGTTGCCAATGCTTACAA
* * * * * *
30577 TTTTCGTTACAATAAAAACAAAGTCGTTGCGATATCATAATCTATTCATAACACCTTTATAAAAA
66 TTTTCGTAACAACAAAAACAAAGTCGTTGCGAAATCATAATATATTCGTAACAACTTTATAAAAA
* *
30642 CGTTGCCTAAGTGATTTTGATGGTA-TTTACACAACACTTTTTTAGTTGTTGCCAATGCTTATAA
1 CGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAATTGTTGCCAATGCTTACAA
* * *
30706 TTTTCGTAACAACAAAAACAAAATCGTTGTGAAATGATAA-ATATTCGTAACAACTTTATAAAAA
66 TTTTCGTAACAACAAAAACAAAGTCGTTGCGAAATCATAATATATTCGTAACAACTTTATAAAAA
* * * * *
30770 CATTGCCTAAGTGATTTTCATGGTATTTTATACAACACTTTTTTAATTGTTGCCAATGTTTACAG
1 CGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAATTGTTGCCAATGCTTACAA
*
30835 TATTCGTAACAACAA
66 TTTTCGTAACAACAA
30850 CTTCTTAAGT
Statistics
Matches: 294, Mismatches: 40, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
128 44 0.15
129 133 0.45
130 102 0.35
131 15 0.05
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (130 bp):
CGTTGCCTAAGTGATTTTGATGGTATTTTACACAACACTTTTTTAATTGTTGCCAATGCTTACAA
TTTTCGTAACAACAAAAACAAAGTCGTTGCGAAATCATAATATATTCGTAACAACTTTATAAAAA
Found at i:30896 original size:259 final size:258
Alignment explanation
Indices: 30383--30897 Score: 613
Period size: 259 Copynumber: 2.0 Consensus size: 258
30373 AATTAAAAGT
* * *
30383 CGTTGCCTTAGTGTTTGATGGTATTTTACCCACAAACTTTTTTAATTGTTGCCAATGCTTGCAGT
1 CGTTGCCTAAGTGTTTGATGGTATTTTA-CCACAAACTTTTTTAATTGTTGCCAATGCTTACAAT
* * * * *
30448 TTTCGTAACAACAAAAGCAAAGTCATTGCGAAATCATAATTTATTCGTAACAATTTTATAAAATC
65 TTTCGTAACAACAAAAACAAAATCATTGCGAAATCATAATATATTCGTAACAACTTTATAAAAAC
* * * *
30513 GTTCCCTAAGTGATTTTGATGGTATTTTACACAACACCTTTTTAGTCGTTTCCAATGCTTACAAT
130 ATTCCCTAAGTGATTTTCATGGTATTTTACACAACACCTTTTTAATCGTTGCCAATGCTTACAAT
* * * * * * * * *
30578 TTTCGTTACAATAAAAACAAAGTCGTTGCGATATCATAATCTATTCATAACACCTTTATAAAAA
195 ATTCGTAACAACAAAAACAAAGTCGCTGCAAAATCACAAACTATTCATAACAACTTTATAAAAA
* *
30642 CGTTGCCTAAGTGATTTTGATGGTA-TTTA-CACAACACTTTTTTAGTTGTTGCCAATGCTTATA
1 CGTTGCCTAAGTG--TTTGATGGTATTTTACCACAA-ACTTTTTTAATTGTTGCCAATGCTTACA
* * *
30705 ATTTTCGTAACAACAAAAACAAAATCGTTGTGAAATGATAA-ATATTCGTAACAACTTTATAAAA
63 ATTTTCGTAACAACAAAAACAAAATCATTGCGAAATCATAATATATTCGTAACAACTTTATAAAA
* * * * *
30769 ACATTGCCTAAGTGATTTTCATGGTATTTTATACAACACTTTTTTAATTGTTGCCAATGTTTACA
128 ACATTCCCTAAGTGATTTTCATGGTATTTTACACAACACCTTTTTAATCGTTGCCAATGCTTACA
* *** * * **
30834 GTATTCGTAACAACAACTTCTTAAGTTGCTGCAAAATCACAAACTATTTGTAACAACTTTATAA
193 ATATTCGTAACAACAAAAAC-AAAGTCGCTGCAAAATCACAAACTATTCATAACAACTTTATAA
30898 GTCGTTGCGT
Statistics
Matches: 213, Mismatches: 39, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
258 94 0.44
259 105 0.49
260 4 0.02
261 10 0.05
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (258 bp):
CGTTGCCTAAGTGTTTGATGGTATTTTACCACAAACTTTTTTAATTGTTGCCAATGCTTACAATT
TTCGTAACAACAAAAACAAAATCATTGCGAAATCATAATATATTCGTAACAACTTTATAAAAACA
TTCCCTAAGTGATTTTCATGGTATTTTACACAACACCTTTTTAATCGTTGCCAATGCTTACAATA
TTCGTAACAACAAAAACAAAGTCGCTGCAAAATCACAAACTATTCATAACAACTTTATAAAAA
Found at i:33460 original size:435 final size:434
Alignment explanation
Indices: 32491--33563 Score: 1186
Period size: 435 Copynumber: 2.5 Consensus size: 434
32481 GCGTTACCTT
* * * *
32491 TTATTTTTGTATTTTTT-TTCTATTTGTCCGATTAAGCTAATTTAAGTGTATATTAAAAGGTAAT
1 TTATTTTTTTATTTTTTGTTCTATTTGTCCAATTAAGCTAATTCAAGTGTCTATTAAAAGGTAAT
* * * * **
32555 TTCATGATCTACAA-TTTTCAT-TAAGAACTCAAAAGCCAATTTTAATGTTTTGATTCTAAAAAA
66 TTAATGATCTACAACTTTT-ATGAAAG-ACTCAAAAGCAAATTTTTATGTTTCAATTCTAAAAAA
* * * * * * *
32618 TGCTTCCGAAATTTTGTGGTTTTGATTGCCGGT-TAATTTAATATCGTATAATTTTTTG-TCTAC
129 TGCTTTCTAAATTTTGTGATTTCGATTGACGGTCT-ATTTAATATCATATAA-TTTTTGATCCAC
* * * * * *
32681 ATGTCCGATTGAAATTATTAAAGTGTCGGTTAAAAGGTTATTGCATGATTTACGACTTTCATGAA
192 ATATCCAATT-AAATCATTAAAGTGTCGGTTAAAAGGTTACTGCATAATCTACGACTTTCATGAA
** * * ** * * *
32746 GGACCCGAAAGCTAAATTTGATCTACGAGTTTTGTGAAGGGTTCAATAGGGAATTTTCATGTTTC
256 AAACCCGAAAGCTAAATTTCATCTACAAGTTTCATGAAGGGTTCAAAAGAGAATTTTCATATTTC
* * * *
32811 AACTCCATTAACAAACAATTTTCTTATTCGGATTATTTATCAAATTACCCTCATATTTTTCTACT
321 AACTCCATTAACAAACAATTTTCTTATTCGAATTAATTATCAAATCAACCTCATATTTTTCTACT
* *
32876 TTATACTACTTAGTCCTTTACAAATTCTATCTTAATCTAACGTTAAAGCT
386 TTATACTACTTAGTCATTTACAAATTCTATCTTAATCT-ACGTTAAAGCA
* * *
32926 TTATTTTTTTATTTTTTGTTCTATTTGTCCAATTAAGTTGATTCATGTGTCTATTAAAAGGTAAT
1 TTATTTTTTTATTTTTTGTTCTATTTGTCCAATTAAGCTAATTCAAGTGTCTATTAAAAGGTAAT
* * * **
32991 TTAATAATCTACAACTTTCATGAAGGACTCAAAAGCAAATTTTTATGTTTCAATTAAAAAAAATG
66 TTAATGATCTACAACTTTTATGAAAGACTCAAAAGCAAATTTTTATGTTTCAATTCTAAAAAATG
* ** * *
33056 CTTTCTAAA-TTTGTTCATTTCGATTGTTGGTCTATTTAATACCATATAATTTTCGATCCACATA
131 CTTTCTAAATTTTG-TGATTTCGATTGACGGTCTATTTAATATCATATAATTTTTGATCCACATA
* * *
33120 TCCAATTAAAGTCATTCAAGTGTCGGTTAAAAGTTTACTGTATAATCTACGACTTTCATGAAAAA
195 TCCAATTAAA-TCATTAAAGTGTCGGTTAAAAGGTTACTGCATAATCTACGACTTTCATGAAAAA
* *
33185 CCCGAAAG-TTAATTTCATCTACAAGTTTCATGAAGGGTTCAAAAGAGAATTTTTATATTTCAAG
259 CCCGAAAGCTAAATTTCATCTACAAGTTTCATGAAGGGTTCAAAAGAGAATTTTCATATTTC-A-
* * * * *
33249 ATCTCCATTAACAAA-TATTTTCTTATAT-GAATTAATTATCAAATCAATCTCATTTTTTTTTAT
322 A-CTCCATTAACAAACAATTTTCTTAT-TCGAATTAATTATCAAATCAACCTCATATTTTTCTAC
* * *
33312 TTTATGCTACTTAGTCATTTTCAAATTCTATCTT-A-CT-CGATTTAA-CAA
385 TTTATACTACTTAGTCATTTACAAATTCTATCTTAATCTACG-TTAAAGC-A
* * *
33360 TT-TTTTTTTATTTTCTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTGTCTATTAAAAGTTA
1 TTATTTTTTTA-TTT-TTTGTTCTATTTGTCCAATTAAGCTAATTCAAGTGTCTATTAAAAGGTA
* ** *
33424 ATTTTATGATCTACAACTTTTATGAAAGACTCAAAAGTTAATTTTTATATTTCAATTCTAAAAAA
64 ATTTAATGATCTACAACTTTTATGAAAGACTCAAAAGCAAATTTTTATGTTTCAATTCTAAAAAA
* ** ** * *
33489 TGGTTT-TAAAATTTTGTGATTTCGATTGACAATCTATTTAATATCATATTTTTTTTTATCCAGA
129 TGCTTTCT-AAATTTTGTGATTTCGATTGACGGTCTATTTAATATCATATAATTTTTGATCCACA
33553 TATCCAATTAA
193 TATCCAATTAA
33564 CAAAGATTCA
Statistics
Matches: 533, Mismatches: 88, Indels: 34
0.81 0.13 0.05
Matches are distributed among these distances:
433 11 0.02
434 10 0.02
435 231 0.43
436 192 0.36
437 75 0.14
438 14 0.03
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (434 bp):
TTATTTTTTTATTTTTTGTTCTATTTGTCCAATTAAGCTAATTCAAGTGTCTATTAAAAGGTAAT
TTAATGATCTACAACTTTTATGAAAGACTCAAAAGCAAATTTTTATGTTTCAATTCTAAAAAATG
CTTTCTAAATTTTGTGATTTCGATTGACGGTCTATTTAATATCATATAATTTTTGATCCACATAT
CCAATTAAATCATTAAAGTGTCGGTTAAAAGGTTACTGCATAATCTACGACTTTCATGAAAAACC
CGAAAGCTAAATTTCATCTACAAGTTTCATGAAGGGTTCAAAAGAGAATTTTCATATTTCAACTC
CATTAACAAACAATTTTCTTATTCGAATTAATTATCAAATCAACCTCATATTTTTCTACTTTATA
CTACTTAGTCATTTACAAATTCTATCTTAATCTACGTTAAAGCA
Found at i:37359 original size:16 final size:17
Alignment explanation
Indices: 37326--37359 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
37316 AATATTAAGC
37326 ATTTGACTTAATTTGGT
1 ATTTGACTTAATTTGGT
37343 ATTTGACTTAA-TTGGT
1 ATTTGACTTAATTTGGT
37359 A
1 A
37360 AGGTGTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.26, C:0.06, G:0.18, T:0.50
Consensus pattern (17 bp):
ATTTGACTTAATTTGGT
Found at i:45771 original size:22 final size:23
Alignment explanation
Indices: 45743--45797 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 23
45733 CCAAGATGAG
*
45743 CAAACATTCCAAAAG-TTCTTGT
1 CAAACATTCCAAAAGCTTCTTAT
45765 CAAACATTCCAAAAGCTTCTTAT
1 CAAACATTCCAAAAGCTTCTTAT
45788 C-AACATTCCA
1 CAAACATTCCA
45798 TTCCGAGGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 24 0.77
23 7 0.23
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.29
Consensus pattern (23 bp):
CAAACATTCCAAAAGCTTCTTAT
Found at i:47027 original size:19 final size:19
Alignment explanation
Indices: 47005--47143 Score: 83
Period size: 19 Copynumber: 7.2 Consensus size: 19
46995 ATTTCTCAGA
47005 ATTAAGCTAATTACTACTG
1 ATTAAGCTAATTACTACTG
** * *
47024 ATTACTCCT-TTTACTTCTTG
1 ATTA-AGCTAATTACTAC-TG
47044 ATTAA-CTTAATTACT-CTG
1 ATTAAGC-TAATTACTACTG
*
47062 AATTAAGCTAATTACTATTG
1 -ATTAAGCTAATTACTACTG
** * *
47082 ATTACTCCT-TTTACTTCTTG
1 ATTA-AGCTAATTACTAC-TG
47102 ATTAA-CTTAATTACT-CTG
1 ATTAAGC-TAATTACTACTG
47120 AATTAAGCTAATTACTACTG
1 -ATTAAGCTAATTACTACTG
47140 ATTA
1 ATTA
47144 CTCCTTTTAC
Statistics
Matches: 92, Mismatches: 14, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
18 6 0.07
19 53 0.58
20 33 0.36
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (19 bp):
ATTAAGCTAATTACTACTG
Found at i:47031 original size:58 final size:58
Alignment explanation
Indices: 46967--47180 Score: 401
Period size: 58 Copynumber: 3.7 Consensus size: 58
46957 ATTAAGTTGT
* *
46967 TTACTCCTTTTACTTCTTGATTAACTTAATTTCTCAGAATTAAGCTAATTACTACTGA
1 TTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGA
*
47025 TTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTATTGA
1 TTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGA
47083 TTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGA
1 TTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGA
47141 TTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAAT
1 TTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAAT
47181 ACTGATTACC
Statistics
Matches: 152, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 152 1.00
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.46
Consensus pattern (58 bp):
TTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGA
Found at i:47048 original size:39 final size:37
Alignment explanation
Indices: 47005--47183 Score: 102
Period size: 39 Copynumber: 4.6 Consensus size: 37
46995 ATTTCTCAGA
*
47005 ATTAAGCTAATTACTACTGATTACTCCT-TTTACTTCTTG
1 ATTAA-CTAATTACT-CTGATTACTCCTAATTAC-TCTTG
** *
47044 ATTAACTTAATTACTCTGAATTA-AGCTAATTACTATTG
1 ATTAAC-TAATTACTCTG-ATTACTCCTAATTACTCTTG
**
47082 ATT-ACTCCTTTTACTTCTTGATTAACT--TAATTACTC-TG
1 ATTAACT--AATTAC-TC-TGATT-ACTCCTAATTACTCTTG
*
47120 AATTAAGCTAATTACTACTGATTACTCCT-TTTACTTCTTG
1 -ATTAA-CTAATTACT-CTGATTACTCCTAATTAC-TCTTG
*
47160 ATTAACTTAATTACTCTGAATACT
1 ATTAAC-TAATTACTCTGATTACT
47184 GATTACCATT
Statistics
Matches: 110, Mismatches: 12, Indels: 37
0.69 0.08 0.23
Matches are distributed among these distances:
36 1 0.01
37 5 0.05
38 38 0.35
39 58 0.53
40 6 0.05
41 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (37 bp):
ATTAACTAATTACTCTGATTACTCCTAATTACTCTTG
Found at i:47212 original size:27 final size:29
Alignment explanation
Indices: 47180--47234 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
47170 TTACTCTGAA
47180 TACTGATTAC-CATT-TTATACTTTTTAT
1 TACTGATTACTCATTCTTATACTTTTTAT
* *
47207 TACTGATTACTCTTTCTTTTACTTTTTA
1 TACTGATTACTCATTCTTATACTTTTTA
47235 GCTTAATTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.42
28 3 0.12
29 11 0.46
ACGTcount: A:0.22, C:0.16, G:0.04, T:0.58
Consensus pattern (29 bp):
TACTGATTACTCATTCTTATACTTTTTAT
Found at i:47274 original size:54 final size:53
Alignment explanation
Indices: 47205--47630 Score: 446
Period size: 54 Copynumber: 7.9 Consensus size: 53
47195 TATACTTTTT
*
47205 ATTACTGATTACTCTTTCTTTTACTTTTTAGCTTAATTACTCAGAATTAAACTA
1 ATTACTGATTACTCTTTC-TTTACTTTTTAGCTTAATTACTCTGAATTAAACTA
** * * *
47259 AAAACCGATTACTCTTTCTTTTACTCTTTTCAGTTTAATTACTTTGAATTAAACTA
1 ATTACTGATTACTCTTTC-TTTACT-TTTT-AGCTTAATTACTCTGAATTAAACTA
*
47315 ATTTACTAATTACTCTTTCTTTTACTCTTTTTA-CTTTAATTACTCTTGAATTAAACTA
1 A-TTACTGATTACTCTTTC-TTTA--CTTTTTAGC-TTAATTACTC-TGAATTAAACTA
*
47373 ATTTACCGATTA--C--TCTTT-C-TTTTA-C-TAATTACTCTGAATTAAACT-
1 A-TTACTGATTACTCTTTCTTTACTTTTTAGCTTAATTACTCTGAATTAAACTA
* * *
47418 ATCTACTGCTTACTCTTCCTTTACTTCTTAGCTTAATTACTCTTGAATTAAACTA
1 AT-TACTGATTACTCTTTCTTTACTTTTTAGCTTAATTACTC-TGAATTAAACTA
* * *
47473 ATTACTGCTTACTCTTTCTTTACTTCTTAGCTTAATTACTCTTAAATTAAACT-
1 ATTACTGATTACTCTTTCTTTACTTTTTAGCTTAATTACTC-TGAATTAAACTA
*
47526 ATCTACTG-TTACTTTTTCTTTACTTCTTTAGCTTAATTACTCTGAATTAAACTA
1 AT-TACTGATTACTCTTTCTTTACTT-TTTAGCTTAATTACTCTGAATTAAACTA
* *
47580 ATCA-TTACTTACTCTTTCTTTACTTTTTTAGCTTAATTACTCTGAATTAAA
1 ATTACTGA-TTACTCTTTCTTTAC-TTTTTAGCTTAATTACTCTGAATTAAA
47631 GGTTGAAATC
Statistics
Matches: 322, Mismatches: 26, Indels: 48
0.81 0.07 0.12
Matches are distributed among these distances:
44 1 0.00
45 8 0.02
46 11 0.03
47 10 0.03
49 10 0.03
50 2 0.01
51 4 0.01
52 2 0.01
53 41 0.13
54 145 0.45
55 8 0.02
56 24 0.07
57 28 0.09
58 26 0.08
59 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.04, T:0.49
Consensus pattern (53 bp):
ATTACTGATTACTCTTTCTTTACTTTTTAGCTTAATTACTCTGAATTAAACTA
Found at i:47356 original size:30 final size:30
Alignment explanation
Indices: 47266--47361 Score: 83
Period size: 30 Copynumber: 3.3 Consensus size: 30
47256 CTAAAAACCG
* *
47266 ATTACTCTTTCTTTTACTCTTTTCAGTTTA
1 ATTACTCTTTCTTTTACTCTTTTTACTTTA
** ** **
47296 ATTACT-TTGAATTAAACT-AATTTAC--TA
1 ATTACTCTT-TCTTTTACTCTTTTTACTTTA
47323 ATTACTCTTTCTTTTACTCTTTTTACTTTA
1 ATTACTCTTTCTTTTACTCTTTTTACTTTA
47353 ATTACTCTT
1 ATTACTCTT
47362 GAATTAAACT
Statistics
Matches: 47, Mismatches: 14, Indels: 10
0.66 0.20 0.14
Matches are distributed among these distances:
27 13 0.28
28 7 0.15
29 5 0.11
30 22 0.47
ACGTcount: A:0.24, C:0.18, G:0.02, T:0.56
Consensus pattern (30 bp):
ATTACTCTTTCTTTTACTCTTTTTACTTTA
Found at i:47378 original size:30 final size:30
Alignment explanation
Indices: 47292--47378 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
47282 CTCTTTTCAG
47292 TTTAATTACT-TTGAATTAAACTAATTTAC
1 TTTAATTACTCTTGAATTAAACTAATTTAC
** ** **
47321 --TAATTACTCTT-TCTTTTACTCTTTTTAC
1 TTTAATTACTCTTGAATTAAACT-AATTTAC
47349 TTTAATTACTCTTGAATTAAACTAATTTAC
1 TTTAATTACTCTTGAATTAAACTAATTTAC
47379 CGATTACTCT
Statistics
Matches: 41, Mismatches: 12, Indels: 9
0.66 0.19 0.15
Matches are distributed among these distances:
27 13 0.32
28 7 0.17
30 16 0.39
31 5 0.12
ACGTcount: A:0.31, C:0.15, G:0.02, T:0.52
Consensus pattern (30 bp):
TTTAATTACTCTTGAATTAAACTAATTTAC
Found at i:47511 original size:27 final size:27
Alignment explanation
Indices: 47427--47516 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
47417 TATCTACTGC
*
47427 TTACTCTTCCTTTACTTCTTAGCTTAA
1 TTACTCTTACTTTACTTCTTAGCTTAA
* * ** **
47454 TTACTCTTGAATTAAACTAATTA-C-TGC
1 TTACTCTT-ACTT-TACTTCTTAGCTTAA
*
47481 TTACTCTTTCTTTACTTCTTAGCTTAA
1 TTACTCTTACTTTACTTCTTAGCTTAA
47508 TTACTCTTA
1 TTACTCTTA
47517 AATTAAACTA
Statistics
Matches: 44, Mismatches: 15, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
25 6 0.14
26 3 0.07
27 26 0.59
28 3 0.07
29 6 0.14
ACGTcount: A:0.23, C:0.22, G:0.04, T:0.50
Consensus pattern (27 bp):
TTACTCTTACTTTACTTCTTAGCTTAA
Found at i:47548 original size:107 final size:107
Alignment explanation
Indices: 47207--47630 Score: 460
Period size: 107 Copynumber: 4.0 Consensus size: 107
47197 TACTTTTTAT
* * **
47207 TACTGATTACTCTTTCTTTTACTTTTTAGCTTAATTACTCAGAATTAAACTAAAAACCGATTACT
1 TACTGATTACTCTTTCTTTTACTTCTTAGCTTAATTACTCTGAATTAAACTAATTACCGATTACT
* * *
47272 CTTTCTTTTACTCTTTTCAGTTTAATTACTTTGAATTAAACTAATT
66 CTTTC-TTTACT-TTTT-AGCTTAATTACTCTGAATTAAACT-ATC
* *
47318 TACTAATTACTCTTTCTTTTACTCTTTTTA-CTTTAATTACTCTTGAATTAAACTAATTTACCGA
1 TACTGATTACTCTTTCTTTTA--CTTCTTAGC-TTAATTACTC-TGAATTAAACTAA-TTACCGA
47382 TTA--C--TCTTT-C-TTTTA-C-TAATTACTCTGAATTAAACTATC
61 TTACTCTTTCTTTACTTTTTAGCTTAATTACTCTGAATTAAACTATC
* * * *
47421 TACTGCTTACTC-TTCCTTTACTTCTTAGCTTAATTACTCTTGAATTAAACTAATTACTGCTTAC
1 TACTGATTACTCTTTCTTTTACTTCTTAGCTTAATTACTC-TGAATTAAACTAATTACCGATTAC
* *
47485 TCTTTCTTTACTTCTTAGCTTAATTACTCTTAAATTAAACTATC
65 TCTTTCTTTACTTTTTAGCTTAATTACTC-TGAATTAAACTATC
* * **
47529 TACTG-TTACTTTTTC-TTTACTTCTTTAGCTTAATTACTCTGAATTAAACTAATCA-TTACTTA
1 TACTGATTACTCTTTCTTTTACTTC-TTAGCTTAATTACTCTGAATTAAACTAATTACCGA-TTA
47591 CTCTTTCTTTACTTTTTTAGCTTAATTACTCTGAATTAAA
64 CTCTTTCTTTAC-TTTTTAGCTTAATTACTCTGAATTAAA
47631 GGTTGAAATC
Statistics
Matches: 273, Mismatches: 21, Indels: 42
0.81 0.06 0.12
Matches are distributed among these distances:
99 8 0.03
100 30 0.11
101 2 0.01
102 7 0.03
103 17 0.06
104 20 0.07
105 4 0.01
106 3 0.01
107 64 0.23
108 53 0.19
109 1 0.00
110 3 0.01
111 22 0.08
112 1 0.00
113 18 0.07
114 12 0.04
115 8 0.03
ACGTcount: A:0.28, C:0.19, G:0.04, T:0.49
Consensus pattern (107 bp):
TACTGATTACTCTTTCTTTTACTTCTTAGCTTAATTACTCTGAATTAAACTAATTACCGATTACT
CTTTCTTTACTTTTTAGCTTAATTACTCTGAATTAAACTATC
Found at i:47931 original size:12 final size:12
Alignment explanation
Indices: 47885--47930 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
47875 ACTATTAACT
47885 ATATTAATTTAA
1 ATATTAATTTAA
*
47897 ATATTAATTGAA
1 ATATTAATTTAA
*
47909 ATATTAATTTTA
1 ATATTAATTTAA
47921 ATATTAATTT
1 ATATTAATTT
47931 TTATTTATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (12 bp):
ATATTAATTTAA
Found at i:49906 original size:17 final size:17
Alignment explanation
Indices: 49886--49920 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
49876 TTGAACCAGT
49886 TAAAAAATATTTAAAAA
1 TAAAAAATATTTAAAAA
49903 TAAAAAATATTTAAAAA
1 TAAAAAATATTTAAAAA
49920 T
1 T
49921 GCCACGTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAAATATTTAAAAA
Found at i:50257 original size:54 final size:56
Alignment explanation
Indices: 50101--50383 Score: 357
Period size: 56 Copynumber: 5.1 Consensus size: 56
50091 AGATTTCAGC
* * *
50101 CTGAATTAAACT-ATCTACTGATTACTCTTTCTTTTACTCTTTTAGTTTAATTATT
1 CTGAATTAAACTAATCTACTGATTACTCTTTCCTTTACTCTTTTAGCTTAATTACT
* * * *
50156 CTGAATTAAATTTATCTAGTGATTACTCTTTTCCTTTACT-TTTTAGCTTAATTAAT
1 CTGAATTAAACTAATCTACTGATTACTC-TTTCCTTTACTCTTTTAGCTTAATTACT
*
50212 CTGAATTAAACTAAT-TACTGATTTCTCTTTCCTTTACT-TTTTAGCTTAATTACT
1 CTGAATTAAACTAATCTACTGATTACTCTTTCCTTTACTCTTTTAGCTTAATTACT
* * * *
50266 CCGAATTAAACTATTCTACTAATTACTC-CTCCTTTTACTCTTTTAGCTTAATTACT
1 CTGAATTAAACTAATCTACTGATTACTCTTTCC-TTTACTCTTTTAGCTTAATTACT
* *
50322 CTGAATTAAACTAATCTACTGATTACTATTAT-C--TACTCTTTTAACTTAATTACT
1 CTGAATTAAACTAATCTACTGATTACTCTT-TCCTTTACTCTTTTAGCTTAATTACT
50376 CTGAATTA
1 CTGAATTA
50384 GGTTCTTGAC
Statistics
Matches: 200, Mismatches: 21, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
54 70 0.35
55 37 0.19
56 81 0.41
57 11 0.05
58 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.48
Consensus pattern (56 bp):
CTGAATTAAACTAATCTACTGATTACTCTTTCCTTTACTCTTTTAGCTTAATTACT
Found at i:50316 original size:110 final size:111
Alignment explanation
Indices: 50101--50383 Score: 357
Period size: 110 Copynumber: 2.6 Consensus size: 111
50091 AGATTTCAGC
* * *
50101 CTGAATTAAACT-ATCTACTGATTACTCTTTCTTTTACTCTTTTAGTTTAATTATTCTGAATTAA
1 CTGAATTAAACTAATCTACTGATTACTCTTTCCTTTACTCTTTTAGCTTAATTACTCTGAATTAA
* * * *
50165 ATTTATCTAGTGATTACTCTTTTCCTTTACTTTTTAGCTTAATTAAT
66 ATATATCTACTAATTACTC-TCTCCTTTACTTTTTAGCTTAATTAAT
* *
50212 CTGAATTAAACTAAT-TACTGATTTCTCTTTCCTTTACT-TTTTAGCTTAATTACTCCGAATTAA
1 CTGAATTAAACTAATCTACTGATTACTCTTTCCTTTACTCTTTTAGCTTAATTACTCTGAATTAA
*
50275 ACTAT-TCTACTAATTACTC-CTCCTTTTACTCTTTTAGCTTAATTACT
66 A-TATATCTACTAATTACTCTCTCC-TTTACT-TTTTAGCTTAATTAAT
* *
50322 CTGAATTAAACTAATCTACTGATTACTATTAT-C--TACTCTTTTAACTTAATTACTCTGAATTA
1 CTGAATTAAACTAATCTACTGATTACTCTT-TCCTTTACTCTTTTAGCTTAATTACTCTGAATTA
50384 GGTTCTTGAC
Statistics
Matches: 151, Mismatches: 14, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
108 3 0.02
109 10 0.07
110 87 0.58
111 48 0.32
112 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.48
Consensus pattern (111 bp):
CTGAATTAAACTAATCTACTGATTACTCTTTCCTTTACTCTTTTAGCTTAATTACTCTGAATTAA
ATATATCTACTAATTACTCTCTCCTTTACTTTTTAGCTTAATTAAT
Found at i:53300 original size:27 final size:27
Alignment explanation
Indices: 53221--53301 Score: 90
Period size: 27 Copynumber: 3.0 Consensus size: 27
53211 TTTCAAAACT
* *
53221 AAGAGAAACCAATCCGTGGTTGATATTG
1 AAGA-AAACCAATCTGTGGTTGATGTTG
* **
53249 AAGAAAACCAATCTGCGGTCCATGTTG
1 AAGAAAACCAATCTGTGGTTGATGTTG
* *
53276 AAGAAAATCAGTCTGTGGTTGATGTT
1 AAGAAAACCAATCTGTGGTTGATGTT
53302 TGACATTGAG
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
27 39 0.91
28 4 0.09
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (27 bp):
AAGAAAACCAATCTGTGGTTGATGTTG
Found at i:53609 original size:28 final size:28
Alignment explanation
Indices: 53578--53664 Score: 68
Period size: 32 Copynumber: 3.0 Consensus size: 28
53568 AGACCAATCT
53578 GTGGTCGACACTTGAAGTAGGCCAGTCA
1 GTGGTCGACACTTGAAGTAGGCCAGTCA
* * * * *
53606 GTGGCCAACTGATACTTGAAAG-AGACCAATCC
1 GTGG---TC-GACACTTG-AAGTAGGCCAGTCA
*
53638 GTGGTCGACACTTGAAGTAGGTCAGTC
1 GTGGTCGACACTTGAAGTAGGCCAGTC
53665 CGTAGCCAAC
Statistics
Matches: 43, Mismatches: 10, Indels: 12
0.66 0.15 0.18
Matches are distributed among these distances:
27 3 0.07
28 17 0.40
29 1 0.02
31 1 0.02
32 18 0.42
33 3 0.07
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.22
Consensus pattern (28 bp):
GTGGTCGACACTTGAAGTAGGCCAGTCA
Found at i:53611 original size:60 final size:60
Alignment explanation
Indices: 53530--53929 Score: 470
Period size: 60 Copynumber: 6.7 Consensus size: 60
53520 GATCCATTAC
* *
53530 TGAAGGAGGCTAGTCCA-TGGCCAACTAATACTTGAAAGAGACCAATCTGTGGTCGACACT
1 TGAAGTAGGCCAGT-CAGTGGCCAACTAATACTTGAAAGAGACCAATCTGTGGTCGACACT
* *
53590 TGAAGTAGGCCAGTCAGTGGCCAACTGATACTTGAAAGAGACCAATCCGTGGTCGACACT
1 TGAAGTAGGCCAGTCAGTGGCCAACTAATACTTGAAAGAGACCAATCTGTGGTCGACACT
* * * ** *
53650 TGAAGTAGGTCAGTCCGTAGCCAACTGGTGCTTGAAAGAGACCAATCTGTGGTCGACACT
1 TGAAGTAGGCCAGTCAGTGGCCAACTAATACTTGAAAGAGACCAATCTGTGGTCGACACT
* * *
53710 TGAAGTAGGCCAGTCTGTAGCCAAC-AGATGCTTGAAAGAGACCAATCTGTGGTCGACACT
1 TGAAGTAGGCCAGTCAGTGGCCAACTA-ATACTTGAAAGAGACCAATCTGTGGTCGACACT
* * * * * *
53770 TGAAGTATGCCAGTCCA-TGGTCAACTGATGCTTGAAAGAGACCAATCTATGGTCGACGC-
1 TGAAGTAGGCCAGT-CAGTGGCCAACTAATACTTGAAAGAGACCAATCTGTGGTCGACACT
* * * * *
53829 TGTAGTAGGCCAATCCA-TAGCCAACTAATACTTGAAAGAGACCACTCTGTTGGTCGACTC-
1 TGAAGTAGGCCAGT-CAGTGGCCAACTAATACTTGAAAGAGACCAATCTG-TGGTCGACACT
* * *
53889 AGAAGCAGGCCAGTCCGTGGCCAACTAATACTTGAAAGAGA
1 TGAAGTAGGCCAGTCAGTGGCCAACTAATACTTGAAAGAGA
53930 AAAATCCGGG
Statistics
Matches: 297, Mismatches: 37, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
59 43 0.14
60 253 0.85
61 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.22
Consensus pattern (60 bp):
TGAAGTAGGCCAGTCAGTGGCCAACTAATACTTGAAAGAGACCAATCTGTGGTCGACACT
Found at i:53673 original size:120 final size:120
Alignment explanation
Indices: 53530--53929 Score: 518
Period size: 120 Copynumber: 3.3 Consensus size: 120
53520 GATCCATTAC
* * *
53530 TGAAGGAGGCTAGTCCATGGCCAACTAATACTTGAAAGAGACCAATCTGTGGTCGACACTTGAAG
1 TGAAGTAGGCCAGTCCGTGGCCAACTAATACTTGAAAGAGACCAATCTGTGGTCGACACTTGAAG
* *
53595 TAGGCCAGTCAGTGGCCAACTGATACTTGAAAGAGACCAATCCGTGGTCGACACT
66 TAGGCCAGTCAGTAGCCAACTGATACTTGAAAGAGACCAATCTGTGGTCGACACT
* * ** *
53650 TGAAGTAGGTCAGTCCGTAGCCAACTGGTGCTTGAAAGAGACCAATCTGTGGTCGACACTTGAAG
1 TGAAGTAGGCCAGTCCGTGGCCAACTAATACTTGAAAGAGACCAATCTGTGGTCGACACTTGAAG
* * *
53715 TAGGCCAGTCTGTAGCCAACAGATGCTTGAAAGAGACCAATCTGTGGTCGACACT
66 TAGGCCAGTCAGTAGCCAACTGATACTTGAAAGAGACCAATCTGTGGTCGACACT
* * * * * * * *
53770 TGAAGTATGCCAGTCCATGGTCAACTGATGCTTGAAAGAGACCAATCTATGGTCGACGC-TGTAG
1 TGAAGTAGGCCAGTCCGTGGCCAACTAATACTTGAAAGAGACCAATCTGTGGTCGACACTTGAAG
* * * *
53834 TAGGCCAATCCA-TAGCCAACTAATACTTGAAAGAGACCACTCTGTTGGTCGACTC-
66 TAGGCCAGT-CAGTAGCCAACTGATACTTGAAAGAGACCAATCTG-TGGTCGACACT
* *
53889 AGAAGCAGGCCAGTCCGTGGCCAACTAATACTTGAAAGAGA
1 TGAAGTAGGCCAGTCCGTGGCCAACTAATACTTGAAAGAGA
53930 AAAATCCGGG
Statistics
Matches: 242, Mismatches: 36, Indels: 5
0.86 0.13 0.02
Matches are distributed among these distances:
119 74 0.31
120 168 0.69
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.22
Consensus pattern (120 bp):
TGAAGTAGGCCAGTCCGTGGCCAACTAATACTTGAAAGAGACCAATCTGTGGTCGACACTTGAAG
TAGGCCAGTCAGTAGCCAACTGATACTTGAAAGAGACCAATCTGTGGTCGACACT
Found at i:53759 original size:32 final size:31
Alignment explanation
Indices: 53666--53759 Score: 79
Period size: 32 Copynumber: 3.1 Consensus size: 31
53656 AGGTCAGTCC
*
53666 GTAGCCAACTGGTGCTTGAAAGAGACCAATCT
1 GTAGCCAAC-GATGCTTGAAAGAGACCAATCT
* * * * *
53698 GTGGTCGAC-A--CTTG-AAGTAGGCCAGTCT
1 GTAGCCAACGATGCTTGAAAG-AGACCAATCT
53726 GTAGCCAACAGATGCTTGAAAGAGACCAATCT
1 GTAGCCAAC-GATGCTTGAAAGAGACCAATCT
53758 GT
1 GT
53760 GGTCGACACT
Statistics
Matches: 45, Mismatches: 11, Indels: 12
0.66 0.16 0.18
Matches are distributed among these distances:
27 3 0.07
28 18 0.40
30 1 0.02
32 20 0.44
33 3 0.07
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (31 bp):
GTAGCCAACGATGCTTGAAAGAGACCAATCT
Found at i:53766 original size:180 final size:179
Alignment explanation
Indices: 53531--53929 Score: 525
Period size: 180 Copynumber: 2.2 Consensus size: 179
53521 ATCCATTACT
* * * *
53531 GAAGGAGGCTAGTCCATGGCCAACTAATACTTGAAAGAGACCAATCTGTGGTCGACACTTGAAGT
1 GAAGCAGGCCAGTCCGTAGCCAACTAATACTTGAAAGAGACCAATCTGTGGTCGACACTTGAAGT
* *
53596 AGGCCAGT-CAGTGGCCAACTGATACTTGAAAGAGACCAATCCGTGGTCGACACTTGAAGTAGGT
66 AGGCCAGTCCA-TGGCCAACTGATACTTGAAAGAGACCAATCCATGGTCGACAC-TGAAGTAGGC
* * ** * *
53660 CAGTCCGTAGCCAACTGGTGCTTGAAAGAGACCAATCTG-TGGTCGACACTT
129 CAATCCATAGCCAACTAATACTTGAAAGAGACCAATCTGTTGGTCGACAC-A
* * *
53711 GAAGTAGGCCAGTCTGTAGCCAAC-AGATGCTTGAAAGAGACCAATCTGTGGTCGACACTTGAAG
1 GAAGCAGGCCAGTCCGTAGCCAACTA-ATACTTGAAAGAGACCAATCTGTGGTCGACACTTGAAG
* * * * * *
53775 TATGCCAGTCCATGGTCAACTGATGCTTGAAAGAGACCAATCTATGGTCGACGCTGTAGTAGGCC
65 TAGGCCAGTCCATGGCCAACTGATACTTGAAAGAGACCAATCCATGGTCGACACTGAAGTAGGCC
* *
53840 AATCCATAGCCAACTAATACTTGAAAGAGACCACTCTGTTGGTCGACTCA
130 AATCCATAGCCAACTAATACTTGAAAGAGACCAATCTGTTGGTCGACACA
*
53890 GAAGCAGGCCAGTCCGTGGCCAACTAATACTTGAAAGAGA
1 GAAGCAGGCCAGTCCGTAGCCAACTAATACTTGAAAGAGA
53930 AAAATCCGGG
Statistics
Matches: 189, Mismatches: 26, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
179 76 0.40
180 111 0.59
181 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.22
Consensus pattern (179 bp):
GAAGCAGGCCAGTCCGTAGCCAACTAATACTTGAAAGAGACCAATCTGTGGTCGACACTTGAAGT
AGGCCAGTCCATGGCCAACTGATACTTGAAAGAGACCAATCCATGGTCGACACTGAAGTAGGCCA
ATCCATAGCCAACTAATACTTGAAAGAGACCAATCTGTTGGTCGACACA
Found at i:53822 original size:32 final size:31
Alignment explanation
Indices: 53560--53823 Score: 103
Period size: 28 Copynumber: 8.8 Consensus size: 31
53550 CCAACTAATA
*
53560 CTTGAAAGAGACCAATCTGTGGTCGAC-A--
1 CTTGAAAGAGACCAATCTGTGGTCAACGATG
* * * * *
53588 CTTG-AAGTAGGCCAGTCAGTGGCCAACTGATA
1 CTTGAAAG-AGACCAATCTGTGGTCAAC-GATG
* *
53620 CTTGAAAGAGACCAATCCGTGGTCGAC-A--
1 CTTGAAAGAGACCAATCTGTGGTCAACGATG
** * * * * *
53648 CTTG-AAGTAGGTCAGTCCGTAGCCAACTGGTG
1 CTTGAAAG-AGACCAATCTGTGGTCAAC-GATG
*
53680 CTTGAAAGAGACCAATCTGTGGTCGAC-A--
1 CTTGAAAGAGACCAATCTGTGGTCAACGATG
* * * *
53708 CTTG-AAGTAGGCCAGTCTGTAGCCAACAGATG
1 CTTGAAAG-AGACCAATCTGTGGTCAAC-GATG
*
53740 CTTGAAAGAGACCAATCTGTGGTCGAC-A--
1 CTTGAAAGAGACCAATCTGTGGTCAACGATG
* **
53768 CTTG-AAGTATG-CCAGTCCATGGTCAACTGATG
1 CTTGAAAG-A-GACCAATCTGTGGTCAAC-GATG
*
53800 CTTGAAAGAGACCAATCTATGGTC
1 CTTGAAAGAGACCAATCTGTGGTC
53824 GACGCTGTAG
Statistics
Matches: 169, Mismatches: 41, Indels: 48
0.66 0.16 0.19
Matches are distributed among these distances:
27 12 0.07
28 70 0.41
29 1 0.01
30 5 0.03
31 1 0.01
32 68 0.40
33 12 0.07
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (31 bp):
CTTGAAAGAGACCAATCTGTGGTCAACGATG
Found at i:54005 original size:36 final size:37
Alignment explanation
Indices: 53965--54056 Score: 132
Period size: 37 Copynumber: 2.5 Consensus size: 37
53955 CTTGTGGATA
* *
53965 GACCAGTCTGTGGTCAACTGTTGAAA-TTTGAGAGGC
1 GACCAGTCCGTGGTCAACTGTTGAAACTTTGAGAAGC
*
54001 GACCAGTCCGTGGTCAATTGTTGAAACTTTGAGAAGC
1 GACCAGTCCGTGGTCAACTGTTGAAACTTTGAGAAGC
**
54038 GACTGGTCCGTGGTCAACT
1 GACCAGTCCGTGGTCAACT
54057 TGAAAAGTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
36 24 0.49
37 25 0.51
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (37 bp):
GACCAGTCCGTGGTCAACTGTTGAAACTTTGAGAAGC
Found at i:55834 original size:15 final size:15
Alignment explanation
Indices: 55816--55860 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
55806 TTAGGCCAAG
55816 TTTTTTTTTCCTCTC
1 TTTTTTTTTCCTCTC
* *
55831 TTTTTTTTTCTTCTT
1 TTTTTTTTTCCTCTC
55846 TTCTCTTTTTTCCTC
1 TT-T-TTTTTTCCTC
55861 ACCTGTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 15 0.60
16 1 0.04
17 9 0.36
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTTTTCCTCTC
Found at i:57688 original size:6 final size:6
Alignment explanation
Indices: 57677--57708 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
57667 AAAGCAAAGC
*
57677 AATCTA AATCTA AATCTA AATCTA AATGTA AA
1 AATCTA AATCTA AATCTA AATCTA AATCTA AA
57709 GTAGATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.31
Consensus pattern (6 bp):
AATCTA
Found at i:63933 original size:39 final size:37
Alignment explanation
Indices: 63890--63964 Score: 89
Period size: 39 Copynumber: 2.0 Consensus size: 37
63880 AAATAAAAAA
*
63890 TTAAAAGCAGAAACAGAAAATA-AAATATATTTTTTTAAT
1 TTAAAAGCAAAAACAGAAAA-AGAAAT-T-TTTTTTTAAT
* *
63929 TTAAAAGGAAAAACGGAAAAAGAAATTTTTTTTTAA
1 TTAAAAGCAAAAACAGAAAAAGAAATTTTTTTTTAA
63965 AAGAAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 9 0.28
38 2 0.06
39 21 0.66
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.32
Consensus pattern (37 bp):
TTAAAAGCAAAAACAGAAAAAGAAATTTTTTTTTAAT
Done.