Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold69
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: 2104606
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.31
Warning! 151874 characters in sequence are not A, C, G, or T
File 13 of 13
Found at i:2039715 original size:42 final size:42
Alignment explanation
Indices: 2039669--2039770 Score: 150
Period size: 42 Copynumber: 2.4 Consensus size: 42
2039659 CTACCTATCG
*
2039669 GCTTTGACCCTGGAGACTACCTCATATAAAGTCTGTCTGTGA
1 GCTTTGACCCTGGAGACTACCTCATATAAAGTCTGTCTGTCA
* * * *
2039711 GCTTTGACCCTGGAGACTACCTTATCTAAAGTCTGTGTTTCA
1 GCTTTGACCCTGGAGACTACCTCATATAAAGTCTGTCTGTCA
*
2039753 GCTTTGACCTTGGAGACT
1 GCTTTGACCCTGGAGACT
2039771 TTCCTACTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (42 bp):
GCTTTGACCCTGGAGACTACCTCATATAAAGTCTGTCTGTCA
Found at i:2039771 original size:139 final size:140
Alignment explanation
Indices: 2039511--2039790 Score: 329
Period size: 139 Copynumber: 2.0 Consensus size: 140
2039501 ACTTTCCTAT
* * * * * ** *
2039511 CCTTTAGTTTACCTATCGGCTTTGACCTTGGAGACTTTCCTATCTTTCAGTCTGTTTGTCGACTT
1 CCTTCAGTCTACCTATCGGCTTTGACCCTGGAGACTTACCTATCATAAAGTCTGTCTGTCGACTT
* * *
2039576 TGACCCTAGAGACTGCCTCATCTAAAGTTATTCTGTCGGCTTTGACTCTAGAGACTTTCGTACCC
66 TGACCCTAGAGACTACCTCATCTAAAGTTATTCTGTCAGCTTTGACTCTAGAGACTTTCCTACCC
2039641 TTTAGTCTGC
131 TTTAGTCTGC
2039651 CCTTCAGTCTACCTATCGGCTTTGACCCTGGAGAC-TACCTCAT-ATAAAGTCTGTCTGT-GAGC
1 CCTTCAGTCTACCTATCGGCTTTGACCCTGGAGACTTACCT-ATCATAAAGTCTGTCTGTCGA-C
* * * *
2039713 TTTGACCCTGGAGACTACCTTATCTAAAGTCTGTGT-T-TCAGCTTTGAC-CTTGGAGACTTTCC
64 TTTGACCCTAGAGACTACCTCATCTAAAGT-TAT-TCTGTCAGCTTTGACTC-TAGAGACTTTCC
*
2039775 TACTCTTTAGTCTGC
126 TACCCTTTAGTCTGC
2039790 C
1 C
2039791 TGTCGATTTT
Statistics
Matches: 119, Mismatches: 16, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
138 3 0.03
139 78 0.66
140 37 0.31
141 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.37
Consensus pattern (140 bp):
CCTTCAGTCTACCTATCGGCTTTGACCCTGGAGACTTACCTATCATAAAGTCTGTCTGTCGACTT
TGACCCTAGAGACTACCTCATCTAAAGTTATTCTGTCAGCTTTGACTCTAGAGACTTTCCTACCC
TTTAGTCTGC
Found at i:2040224 original size:95 final size:96
Alignment explanation
Indices: 2040011--2040261 Score: 308
Period size: 95 Copynumber: 2.6 Consensus size: 96
2040001 TACCTGTTAG
* * * * * * * *
2040011 CTTTGACCTTGGAGGCTACCTCATCTAAAGTCTGCGTGGCGGCTTTGACCCTATAGACTTTCTTA
1 CTTTGACCCTAGAGACTGCCTCATCTAAAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTC-TA
* *
2040076 CCCTTCAGTCTGCCCTTCAATCTGCTTGTTGG
65 CCCTTCAGTCTGCCCTTCAATCTGCTTGTCGA
* * *
2040108 CTTTAACCCTAGAGACTGCCTCATCTAAAGTCTGCTTGTCAGCTTTGACCCTGGAGACTTTC-AC
1 CTTTGACCCTAGAGACTGCCTCATCTAAAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTCTAC
* * *
2040172 CCTTTAGTCTGCCCTTCAGTTTG-TCTGTCGA
66 CCTTCAGTCTGCCCTTCAATCTGCT-TGTCGA
* *
2040203 CTTTGACCCTAGAGACTGCCTCATCTAAAGTCTACCTGTCAGCTTTGACCCAAGAGACT
1 CTTTGACCCTAGAGACTGCCTCATCTAAAGTCTGCCTGTCAGCTTTGACCCTAGAGACT
2040262 GCCTCATCTA
Statistics
Matches: 133, Mismatches: 20, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
94 1 0.01
95 80 0.60
97 52 0.39
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (96 bp):
CTTTGACCCTAGAGACTGCCTCATCTAAAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTCTAC
CCTTCAGTCTGCCCTTCAATCTGCTTGTCGA
Found at i:2040494 original size:85 final size:85
Alignment explanation
Indices: 2040414--2040803 Score: 525
Period size: 85 Copynumber: 4.6 Consensus size: 85
2040404 TTGCCTATCA
* * * * * * * * *
2040414 GCTTTGACCTTGGAGACTTTTCTATCTTTTACTCTGCCTGTCGACTTTGACCCTGGAGACTACCT
1 GCTTTGACCCTGGAGACTTTCCTATCCTTTAGTCTGCTTGTCGGCTTTGACTCTGAAGACTGCCT
* *
2040479 TATCTAAAGTCTGCCTT-TCG
66 CATCTAAAGTATG-CTTGTCG
* * * * * * *
2040499 GCTTTAACCTTGGAGACTTTCCTACCCTTCAGTCTACCTATCGGCTTTGACTCTGAAGACTGCCT
1 GCTTTGACCCTGGAGACTTTCCTATCCTTTAGTCTGCTTGTCGGCTTTGACTCTGAAGACTGCCT
* * *
2040564 CATTTAAAGTATGATTGTTG
66 CATCTAAAGTATGCTTGTCG
*
2040584 GCTTTGA-CCTGGAGACTTTCCTA-CCTTTCAGTCTGCTTGTCGGCTTTGACTCTGAAGACTGTC
1 GCTTTGACCCTGGAGACTTTCCTATCCTTT-AGTCTGCTTGTCGGCTTTGACTCTGAAGACTGCC
2040647 TCATCTAAAGTATGCTTGTCG
65 TCATCTAAAGTATGCTTGTCG
* *
2040668 GCTTTGACCCTGGAGACTTTCCTATCCTTTAGTCTGCTTGTCGGCTTTGACTTTAAAGACTGCCT
1 GCTTTGACCCTGGAGACTTTCCTATCCTTTAGTCTGCTTGTCGGCTTTGACTCTGAAGACTGCCT
2040733 CATCTAAAGTATGCTTGTCG
66 CATCTAAAGTATGCTTGTCG
2040753 GCTTTGACCCTGGAGACTTTCCTATCCTTTAGTCTGCTTGTCGGCTTTGAC
1 GCTTTGACCCTGGAGACTTTCCTATCCTTTAGTCTGCTTGTCGGCTTTGAC
2040804 CTTGGAGACT
Statistics
Matches: 271, Mismatches: 30, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
83 4 0.01
84 72 0.27
85 190 0.70
86 5 0.02
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (85 bp):
GCTTTGACCCTGGAGACTTTCCTATCCTTTAGTCTGCTTGTCGGCTTTGACTCTGAAGACTGCCT
CATCTAAAGTATGCTTGTCG
Found at i:2040657 original size:169 final size:168
Alignment explanation
Indices: 2040414--2040813 Score: 514
Period size: 169 Copynumber: 2.4 Consensus size: 168
2040404 TTGCCTATCA
* * * * * *
2040414 GCTTTGACCTTGGAGACTTTTCTATCTTTTACTCTGCCTGTCGACTTTGACCCTGGAGACTACCT
1 GCTTTGACC-TGGAGACTTTCCTA-CCTTTAGTCTGCTTGTCGGCTTTGACCCTGAAGACTACCT
* * *
2040479 TATCTAAAGTCTGCCTT-TCGGCTTTAACCTTGGAGACTTTCCTACCCTTCAGTCTACCTATCGG
64 CATCTAAAGTATG-CTTGTCGGCTTTAACCCTGGAGACTTTCCTACCCTTCAGTCTACCTATCGG
* * *
2040543 CTTTGACTCTGAAGACTGCCTCATTTAAAGTATGATTGTTG
128 CTTTGACTCTAAAGACTGCCTCATCTAAAGTATGATTGTCG
* **
2040584 GCTTTGACCTGGAGACTTTCCTACCTTTCAGTCTGCTTGTCGGCTTTGACTCTGAAGACTGTCTC
1 GCTTTGACCTGGAGACTTTCCTACCTTT-AGTCTGCTTGTCGGCTTTGACCCTGAAGACTACCTC
* * * * * *
2040649 ATCTAAAGTATGCTTGTCGGCTTTGACCCTGGAGACTTTCCTATCCTTTAGTCTGCTTGTCGGCT
65 ATCTAAAGTATGCTTGTCGGCTTTAACCCTGGAGACTTTCCTACCCTTCAGTCTACCTATCGGCT
* *
2040714 TTGACTTTAAAGACTGCCTCATCTAAAGTATGCTTGTCG
130 TTGACTCTAAAGACTGCCTCATCTAAAGTATGATTGTCG
* *
2040753 GCTTTGACCCTGGAGACTTTCCTATCCTTTAGTCTGCTTGTCGGCTTTGACCTTGGAGACT
1 GCTTTGA-CCTGGAGACTTTCCTA-CCTTTAGTCTGCTTGTCGGCTTTGACCCTGAAGACT
2040814 TTCCTATCCT
Statistics
Matches: 200, Mismatches: 26, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
168 7 0.04
169 135 0.68
170 53 0.26
171 5 0.03
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.38
Consensus pattern (168 bp):
GCTTTGACCTGGAGACTTTCCTACCTTTAGTCTGCTTGTCGGCTTTGACCCTGAAGACTACCTCA
TCTAAAGTATGCTTGTCGGCTTTAACCCTGGAGACTTTCCTACCCTTCAGTCTACCTATCGGCTT
TGACTCTAAAGACTGCCTCATCTAAAGTATGATTGTCG
Found at i:2040813 original size:85 final size:85
Alignment explanation
Indices: 2040196--2040813 Score: 506
Period size: 85 Copynumber: 7.3 Consensus size: 85
2040186 TTCAGTTTGT
* * * * * * * **
2040196 CTGTCGACTTTGACCCTAGAGACTGCCTCATCTAAAGTCTACCTGTCAGCTTTGACCCAAGAGAC
1 CTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTATGCTTGTCGGCTTTGACCCTGGAGAC
* **
2040261 -TGCCTCAT-CTAAAGTCTAG-
66 TTTCCT-ATCCTTTAGTCT-GC
* * * ** * *
2040280 CTGTCGGTTTTAACCTTGGAGACTTTCCT-ATCGTTCAGTCTGTTTGTCGGCTTTGACCCTGGAG
1 CTGTCGGCTTTGACCTTGGAGAC-TGCCTCATC-TAAAGTATGCTTGTCGGCTTTGACCCTGGAG
** *
2040344 ACTGCTT-C-AT-CTAAAGTTTGC
64 ACT--TTCCTATCCTTTAGTCTGC
* * * * ** * * * * *
2040365 CTATCGGCTTTGACCGTGGAGACTTTCCT-ACCCTTTAGTTTGCCTATCAGCTTTGACCTTGGAG
1 CTGTCGGCTTTGACCTTGGAGAC-TGCCTCA-TCTAAAGTATGCTTGTCGGCTTTGACCCTGGAG
* * *
2040429 ACTTTTCTATCTTTTACTCTGC
64 ACTTTCCTATCCTTTAGTCTGC
* * * * * * *
2040451 CTGTCGACTTTGACCCTGGAGACTACCTTATCTAAAGTCTGCCTT-TCGGCTTTAACCTTGGAGA
1 CTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTATG-CTTGTCGGCTTTGACCCTGGAGA
* * *
2040515 CTTTCCTACCCTTCAGTCTAC
65 CTTTCCTATCCTTTAGTCTGC
* * * * *
2040536 CTATCGGCTTTGA-CTCTGAAGACTGCCTCATTTAAAGTATGATTGTTGGCTTTGA-CCTGGAGA
1 CTGTCGGCTTTGACCT-TGGAGACTGCCTCATCTAAAGTATGCTTGTCGGCTTTGACCCTGGAGA
2040599 CTTTCCTA-CCTTTCAGTCTGC
65 CTTTCCTATCCTTT-AGTCTGC
* * *
2040620 TTGTCGGCTTTGA-CTCTGAAGACTGTCTCATCTAAAGTATGCTTGTCGGCTTTGACCCTGGAGA
1 CTGTCGGCTTTGACCT-TGGAGACTGCCTCATCTAAAGTATGCTTGTCGGCTTTGACCCTGGAGA
2040684 CTTTCCTATCCTTTAGTCTGC
65 CTTTCCTATCCTTTAGTCTGC
* * **
2040705 TTGTCGGCTTTGACTTTAAAGACTGCCTCATCTAAAGTATGCTTGTCGGCTTTGACCCTGGAGAC
1 CTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTATGCTTGTCGGCTTTGACCCTGGAGAC
2040770 TTTCCTATCCTTTAGTCTGC
66 TTTCCTATCCTTTAGTCTGC
*
2040790 TTGTCGGCTTTGACCTTGGAGACT
1 CTGTCGGCTTTGACCTTGGAGACT
2040814 TTCCTATCCT
Statistics
Matches: 440, Mismatches: 76, Indels: 35
0.80 0.14 0.06
Matches are distributed among these distances:
83 6 0.01
84 96 0.22
85 300 0.68
86 36 0.08
87 1 0.00
88 1 0.00
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.36
Consensus pattern (85 bp):
CTGTCGGCTTTGACCTTGGAGACTGCCTCATCTAAAGTATGCTTGTCGGCTTTGACCCTGGAGAC
TTTCCTATCCTTTAGTCTGC
Found at i:2040971 original size:382 final size:383
Alignment explanation
Indices: 2040257--2040979 Score: 918
Period size: 382 Copynumber: 1.9 Consensus size: 383
2040247 TTGACCCAAG
* * * *
2040257 AGACTGCCTCATCTAAAGTCTAGCTGTCGGTTTTAACCTTGGAGACTTTCCTATCGTTCAGTCTG
1 AGACTGCCTCATCTAAAGTATAGCTGTCGGCTTTAACCCTGGAGACTTTCCTATCCTTCAGTCTG
* ** * * *
2040322 TTTGTCGGCTTTGACCCTGGAGACTGCTTCATCTAAAGTTTGCCTATCGGCTTTGACCGTGGAGA
66 CTTGTCGGCTTTGACCCTAAAGACTGCCTCATCTAAAGTATGCCTATCGGCTTTGACCCTGGAGA
* * * *
2040387 CTTTCCTACCCTTTAGTTTGCCTATCAGCTTTGACCTTGGAGACTTTTCTATCTTTTACTCTGCC
131 CTTTCCTACCCTTTAGTCTGCCTATCAGCTTTGACCTTGGAGACTTTCCTATCCTTCACTCTGCC
* * * * *
2040452 TGTCGACTTTGACCCTGGAGACTACCTTATCTAAAGTCTGCCTTTCGGCTTTAACCTTGGAGACT
196 TGTCGACTTTGACCCTAGAGACTACCTCATCTAAAGTCTGCATGTCGACTTTAACCTTGGAGACT
* * ** * *
2040517 TTCCTACCCTTCAGTCTACCTATCGGCTTTGACTCTGAAGACTGCCTCATTTAAAGTATGATTGT
261 TTCCTACCCTTCAGTCTACCTATCAGCTTTGACCCTGAAGACTGCCTCACCTAAAGTATGACTAT
*
2040582 TGGCTTTGA-CCTGGAGACTTTCCTACCTTTCAGTCTGCTTGTCGGCTTTGACTCTGA
326 CGGCTTTGACCCTGGAGACTTTCCTACCTTTCAGTCTGCTTGTCGGCTTTGACTCTGA
* * *
2040639 AGACTGTCTCATCTAAAGTAT-GCTTGTCGGCTTTGACCCTGGAGACTTTCCTATCCTTTAGTCT
1 AGACTGCCTCATCTAAAGTATAGC-TGTCGGCTTTAACCCTGGAGACTTTCCTATCCTTCAGTCT
** * *
2040703 GCTTGTCGGCTTTGACTTTAAAGACTGCCTCATCTAAAGTATGCTTGTCGGCTTTGACCCTGGAG
65 GCTTGTCGGCTTTGACCCTAAAGACTGCCTCATCTAAAGTATGCCTATCGGCTTTGACCCTGGAG
* * * * *
2040768 ACTTTCCTATCCTTTAGTCTGCTTGTCGGCTTTGACCTTGGAGACTTTCCTATCCTTCAGTCTGC
130 ACTTTCCTACCCTTTAGTCTGCCTATCAGCTTTGACCTTGGAGACTTTCCTATCCTTCACTCTGC
* * * *
2040833 CTGTTGGCTTTGAGCCTAGAGACTACCTCATCTAAAGTTTGCATGTCGACTTTAACAC-TGGAGA
195 CTGTCGACTTTGACCCTAGAGACTACCTCATCTAAAGTCTGCATGTCGACTTTAAC-CTTGGAGA
* * * * * *
2040897 CTTTCCTATCTTTCAGTCTGCCTATCAGCTTTGACCCT-AGAGACTTTCCT-ACCCT-CAGTCTG
259 CTTTCCTACCCTTCAGTCTACCTATCAGCTTTGACCCTGA-AGAC-TGCCTCA-CCTAAAGTATG
*
2040959 CCTATCGGCTTTGACCCTGGA
321 ACTATCGGCTTTGACCCTGGA
2040980 CGCTTCATTA
Statistics
Matches: 286, Mismatches: 49, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
381 3 0.01
382 271 0.95
383 12 0.04
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.37
Consensus pattern (383 bp):
AGACTGCCTCATCTAAAGTATAGCTGTCGGCTTTAACCCTGGAGACTTTCCTATCCTTCAGTCTG
CTTGTCGGCTTTGACCCTAAAGACTGCCTCATCTAAAGTATGCCTATCGGCTTTGACCCTGGAGA
CTTTCCTACCCTTTAGTCTGCCTATCAGCTTTGACCTTGGAGACTTTCCTATCCTTCACTCTGCC
TGTCGACTTTGACCCTAGAGACTACCTCATCTAAAGTCTGCATGTCGACTTTAACCTTGGAGACT
TTCCTACCCTTCAGTCTACCTATCAGCTTTGACCCTGAAGACTGCCTCACCTAAAGTATGACTAT
CGGCTTTGACCCTGGAGACTTTCCTACCTTTCAGTCTGCTTGTCGGCTTTGACTCTGA
Found at i:2040979 original size:85 final size:84
Alignment explanation
Indices: 2040187--2040979 Score: 471
Period size: 85 Copynumber: 9.3 Consensus size: 84
2040177 AGTCTGCCCT
* * * * * * *
2040187 TCAGTTTGTCTGTCGACTTTGACCCTAGAGAC-TGCCTCATCTAAAGTCTACCTGTCAGCTTTGA
1 TCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCT-ATCTAAAGTCTGCCTGTCGGCTTTGA
** * *
2040251 CCCAAGAGAC-TGCCT-CATC
65 CCCTGGAGACTTTCCTAC-CC
* * * * ** **
2040270 TAAAGTCTAG-CTGTCGGTTTTAACCTTGGAGACTTTCCTATCGTTCAGTCTGTTTGTCGGCTTT
1 T-CAGTCT-GCCTGTCGGCTTTGACCCTGGAGACTTTCCTATC-TAAAGTCTGCCTGTCGGCTTT
*
2040334 GACCCTGGAGACTGCTT-C-A-TC
63 GACCCTGGAGACT--TTCCTACCC
* * * * * ** * * *
2040355 TAAAGTTTGCCTATCGGCTTTGACCGTGGAGACTTTCCTACCCTTTAGTTTGCCTATCAGCTTTG
1 T-CAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTA-TCTAAAGTCTGCCTGTCGGCTTTG
* * **
2040420 ACCTTGGAGACTTTTCTATCTT
64 ACCCTGGAGACTTTCCTA-CCC
* * * * * *
2040442 TTACTCTGCCTGTCGACTTTGACCCTGGAGAC-TACCTTATCTAAAGTCTGCCTTTCGGCTTTAA
1 TCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCC-TATCTAAAGTCTGCCTGTCGGCTTTGA
*
2040506 CCTTGGAGACTTTCCTACCC
65 CCCTGGAGACTTTCCTACCC
* * * * * * * ** *
2040526 TTCAGTCTACCTATCGGCTTTGACTCTGAAGAC-TGCCTCATTTAAAGTATGATTGTTGGCTTTG
1 -TCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCT-ATCTAAAGTCTGCCTGTCGGCTTTG
*
2040590 A-CCTGGAGACTTTCCTACCTT
64 ACCCTGGAGACTTTCCTACC-C
* * * * * *
2040611 TCAGTCTGCTTGTCGGCTTTGACTCTGAAGACTGT-CTCATCTAAAGTATGCTTGTCGGCTTTGA
1 TCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCT-ATCTAAAGTCTGCCTGTCGGCTTTGA
*
2040675 CCCTGGAGACTTTCCTATCCT
65 CCCTGGAGACTTTCCTA-CCC
* * ** ** * * *
2040696 TTAGTCTGCTTGTCGGCTTTGACTTTAAAGAC-TGCCTCATCTAAAGTATGCTTGTCGGCTTTGA
1 TCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCT-ATCTAAAGTCTGCCTGTCGGCTTTGA
*
2040760 CCCTGGAGACTTTCCTATCCT
65 CCCTGGAGACTTTCCTA-CCC
* * * ** *
2040781 TTAGTCTGCTTGTCGGCTTTGACCTTGGAGACTTTCCTATCCTTCAGTCTGCCTGTTGGCTTTGA
1 TCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTAT-CTAAAGTCTGCCTGTCGGCTTTGA
* * * *
2040846 GCCTAGAGAC-TACCT-CATC
65 CCCTGGAGACTTTCCTAC-CC
* * * * * * ** * *
2040865 TAAAGTTTGCATGTCGACTTTAACACTGGAGACTTTCCTATCTTTCAGTCTGCCTATCAGCTTTG
1 T-CAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATC-TAAAGTCTGCCTGTCGGCTTTG
*
2040930 ACCCTAGAGACTTTCCTACCC
64 ACCCTGGAGACTTTCCTACCC
*
2040951 TCAGTCTGCCTATCGGCTTTGACCCTGGA
1 TCAGTCTGCCTGTCGGCTTTGACCCTGGA
2040980 CGCTTCATTA
Statistics
Matches: 569, Mismatches: 112, Indels: 56
0.77 0.15 0.08
Matches are distributed among these distances:
83 4 0.01
84 103 0.18
85 390 0.69
86 67 0.12
87 4 0.01
88 1 0.00
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.36
Consensus pattern (84 bp):
TCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTCCTATCTAAAGTCTGCCTGTCGGCTTTGAC
CCTGGAGACTTTCCTACCC
Found at i:2041691 original size:17 final size:15
Alignment explanation
Indices: 2041661--2041702 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
2041651 TTCTTTTTTG
*
2041661 ATATAAAATTAAAATA
1 ATATAAAA-TAAAAAA
2041677 ATAATAAAATAAAAAA
1 AT-ATAAAATAAAAAA
2041693 AT-TAAAATAA
1 ATATAAAATAA
2041703 TCAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 8 0.33
16 10 0.42
17 6 0.25
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
ATATAAAATAAAAAA
Found at i:2042707 original size:13 final size:13
Alignment explanation
Indices: 2042676--2042713 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2042666 TTATGGGGTG
*
2042676 ATAAAATTAATATA
1 ATAAAA-TAAAATA
2042690 A-AAAATAAAATA
1 ATAAAATAAAATA
2042702 ATAAAATAAAAT
1 ATAAAATAAAAT
2042714 TTGAGGGCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 7 0.32
13 14 0.64
14 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
ATAAAATAAAATA
Found at i:2043788 original size:20 final size:20
Alignment explanation
Indices: 2043763--2043807 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2043753 AAAGACCAAA
2043763 AGAAAAAGGA-AAAAGAAAG
1 AGAAAAAGGAGAAAAGAAAG
*
2043782 AGAAAAAGGAGAAAATAAAG
1 AGAAAAAGGAGAAAAGAAAG
*
2043802 TGAAAA
1 AGAAAA
2043808 GTTAGGAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.04
Consensus pattern (20 bp):
AGAAAAAGGAGAAAAGAAAG
Found at i:2047963 original size:33 final size:33
Alignment explanation
Indices: 2047911--2047975 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
2047901 ATAGAATGGG
2047911 ATAACTGTCTTTAAAGTAGGCCTTATTCAAATC
1 ATAACTGTCTTTAAAGTAGGCCTTATTCAAATC
* **
2047944 ATAATTGTCTTTAGGGTAGGCCTTATTCAAAT
1 ATAACTGTCTTTAAAGTAGGCCTTATTCAAAT
2047976 AAGTGAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (33 bp):
ATAACTGTCTTTAAAGTAGGCCTTATTCAAATC
Found at i:2053134 original size:16 final size:16
Alignment explanation
Indices: 2053113--2053146 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2053103 AATTAATTAC
*
2053113 TTTTTTGAAAAATAAT
1 TTTTTTAAAAAATAAT
2053129 TTTTTTAAAAAATAAT
1 TTTTTTAAAAAATAAT
2053145 TT
1 TT
2053147 AATTGTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTTTTAAAAAATAAT
Found at i:2053779 original size:196 final size:196
Alignment explanation
Indices: 2053438--2053833 Score: 616
Period size: 196 Copynumber: 2.0 Consensus size: 196
2053428 TTTAGGTTCA
*
2053438 AAATTAATTAGTTCAATTGATAGAATTAGTCGGTAATTTTTTTTAGAGATAGAATACACCATCTG
1 AAATTAATTAGTTCAATTGATAGAATTAGTCGATAATTTTTTTTAGAGATAGAATACACCATCTG
*
2053503 TTAAAACCATGGTAATATTTAATTAATATGGACATAAGAAATGAGAATTCTCTTGTACGTGGATC
66 TTAAAACCATGGTAATATTTAATTAATATGGACATAAGAAATGAGAATTCTCTTGTACGTGAATC
* * *
2053568 TGATAATACAAAGAATATTAACCAATAAATATTTGAA-TGTGTTATACCACATATGAAGCTTGCC
131 TGATAACACAAAGAATATTAACCAAGAAATATTT-AATTGTGCTATACCACATATGAAGCTTGCC
2053632 AT
195 AT
* *
2053634 AAATTAATTAGTTCAATTGATAGAATTAGTTGATAATTTTTTTTAGAGATAGAATACACCATTTG
1 AAATTAATTAGTTCAATTGATAGAATTAGTCGATAATTTTTTTTAGAGATAGAATACACCATCTG
* * * * *
2053699 TTAAAACCATGGTAATTTTTACTTAATTTGGATATAAGAAATGAGAA-TCTTTTTGTACGTGAAT
66 TTAAAACCATGGTAATATTTAATTAATATGGACATAAGAAATGAGAATTC-TCTTGTACGTGAAT
* * * *
2053763 TTGATAACATAAAGAATTTTAACCAAGATATATTTAATTGTGCTATACCACATATGAAGCTTGCC
130 CTGATAACACAAAGAATATTAACCAAGAAATATTTAATTGTGCTATACCACATATGAAGCTTGCC
2053828 AT
195 AT
2053830 AAAT
1 AAAT
2053834 GGCAACTCTT
Statistics
Matches: 182, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
195 4 0.02
196 178 0.98
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (196 bp):
AAATTAATTAGTTCAATTGATAGAATTAGTCGATAATTTTTTTTAGAGATAGAATACACCATCTG
TTAAAACCATGGTAATATTTAATTAATATGGACATAAGAAATGAGAATTCTCTTGTACGTGAATC
TGATAACACAAAGAATATTAACCAAGAAATATTTAATTGTGCTATACCACATATGAAGCTTGCCA
T
Found at i:2054757 original size:14 final size:14
Alignment explanation
Indices: 2054738--2054771 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
2054728 ACCTTTTAAG
*
2054738 TTTATTTCTTTTTT
1 TTTATTTCTTTTGT
2054752 TTTATTTCTTTTGT
1 TTTATTTCTTTTGT
2054766 TTTATT
1 TTTATT
2054772 CCTCTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (14 bp):
TTTATTTCTTTTGT
Found at i:2054954 original size:3 final size:3
Alignment explanation
Indices: 2054946--2054979 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2054936 TTTGCTTCAA
*
2054946 AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2054980 CTAAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2061127 original size:13 final size:13
Alignment explanation
Indices: 2061109--2061135 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2061099 TATATATATA
2061109 TATAAATATATTT
1 TATAAATATATTT
2061122 TATAAATATATTT
1 TATAAATATATTT
2061135 T
1 T
2061136 CATTTTGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATAAATATATTT
Found at i:2065152 original size:17 final size:17
Alignment explanation
Indices: 2065106--2065153 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
2065096 TTATTTAAAA
*
2065106 TTTTAAAATTATTTAATT
1 TTTTTAAATTA-TTAATT
* **
2065124 TTTATATTTTATTAATT
1 TTTTTAAATTATTAATT
2065141 TTTTTAAATTATT
1 TTTTTAAATTATT
2065154 TATTCATTTA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTAAATTATTAATT
Found at i:2065349 original size:35 final size:36
Alignment explanation
Indices: 2065292--2065372 Score: 103
Period size: 35 Copynumber: 2.2 Consensus size: 36
2065282 TTTTCATCTG
2065292 ACTTTAATTATTACTTTTACATT-AAAATATATATT
1 ACTTTAATTATTACTTTTACATTAAAAATATATATT
* *
2065327 ACTTTATTTGTTA-TTTTAACATTAAAAATATATATT
1 ACTTTAATTATTACTTTT-ACATTAAAAATATATATT
*
2065363 ATCATTAATT
1 A-CTTTAATT
2065373 TAATTATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
34 4 0.10
35 16 0.41
36 13 0.33
37 6 0.15
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (36 bp):
ACTTTAATTATTACTTTTACATTAAAAATATATATT
Found at i:2066359 original size:20 final size:19
Alignment explanation
Indices: 2066334--2066373 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2066324 AATTGAAATT
2066334 AAAATAATTTTAAATATTAA
1 AAAAT-ATTTTAAATATTAA
*
2066354 AAAATATTTTTAATATTAA
1 AAAATATTTTAAATATTAA
2066373 A
1 A
2066374 TAAGTAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATATTTTAAATATTAA
Found at i:2067524 original size:20 final size:22
Alignment explanation
Indices: 2067475--2067525 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2067465 TTTTATTAAA
2067475 TTTAATTATAAAAATATATACAT
1 TTTAA-TATAAAAATATATACAT
* *
2067498 ATTAATATAAAAATA-AT-TAT
1 TTTAATATAAAAATATATACAT
2067518 TTTAATAT
1 TTTAATAT
2067526 TTTTTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 9 0.36
21 2 0.08
22 10 0.40
23 4 0.16
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAATATAAAAATATATACAT
Found at i:2067779 original size:20 final size:20
Alignment explanation
Indices: 2067751--2067790 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2067741 TTTAATTATT
* *
2067751 TTAATATTTCAAAGATTGAA
1 TTAAAATTTAAAAGATTGAA
*
2067771 TTAAAATTTAAAATATTGAA
1 TTAAAATTTAAAAGATTGAA
2067791 AAGTATATGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (20 bp):
TTAAAATTTAAAAGATTGAA
Found at i:2070812 original size:37 final size:37
Alignment explanation
Indices: 2070762--2070849 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 37
2070752 TTTTAAAATA
* *
2070762 AAAATATCTAAAATACCCCTAA-AAGATATTTATGCAT
1 AAAATAACCAAAATACCCCTAATAAGAT-TTTATGCAT
* ** *
2070799 AAAATAACCAAAATACCCTTAATGTGATTTTATGCTT
1 AAAATAACCAAAATACCCCTAATAAGATTTTATGCAT
*
2070836 AAAATAACCTAAAT
1 AAAATAACCAAAAT
2070850 TCCCTTTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 40 0.93
38 3 0.07
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.31
Consensus pattern (37 bp):
AAAATAACCAAAATACCCCTAATAAGATTTTATGCAT
Found at i:2072023 original size:22 final size:23
Alignment explanation
Indices: 2071984--2072036 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
2071974 GTTTTTTATG
*
2071984 TTTATTTTA-TAATCTTTTTGGT
1 TTTATTTTATTAATCTTTTTGCT
*
2072006 TTTATTTTATTCAT-TTTTTGCT
1 TTTATTTTATTAATCTTTTTGCT
2072028 TTT-TTTTAT
1 TTTATTTTAT
2072037 GGGTTTCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 6 0.21
22 19 0.68
23 3 0.11
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (23 bp):
TTTATTTTATTAATCTTTTTGCT
Found at i:2076296 original size:23 final size:23
Alignment explanation
Indices: 2076270--2076313 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
2076260 GATAAATAGT
2076270 TTATTGACTCTCCACATTTGGGC
1 TTATTGACTCTCCACATTTGGGC
2076293 TTATTGACTCTCCACATTTGG
1 TTATTGACTCTCCACATTTGG
2076314 TCAAAAGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.41
Consensus pattern (23 bp):
TTATTGACTCTCCACATTTGGGC
Found at i:2081184 original size:2 final size:2
Alignment explanation
Indices: 2081177--2081204 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2081167 AATTGGGGTG
2081177 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
2081205 GTTTTATTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2082487 original size:13 final size:12
Alignment explanation
Indices: 2082457--2082506 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
2082447 TTTCTACTTA
*
2082457 TTTTCT-TCTAT
1 TTTTCTCTCTTT
2082468 TTTTCTCTCTTT
1 TTTTCTCTCTTT
2082480 TCTTTCTC-CTTT
1 T-TTTCTCTCTTT
2082492 TTTTCTCTCTTT
1 TTTTCTCTCTTT
2082504 TTT
1 TTT
2082507 CAGTTGACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
11 12 0.34
12 17 0.49
13 6 0.17
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTCTCTCTTT
Found at i:2082494 original size:24 final size:24
Alignment explanation
Indices: 2082458--2082504 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2082448 TTCTACTTAT
*
2082458 TTTCTTCTATTTTTCTCTCTTTTC
1 TTTCTCCTATTTTTCTCTCTTTTC
*
2082482 TTTCTCCTTTTTTTCTCTCTTTT
1 TTTCTCCTATTTTTCTCTCTTTT
2082505 TTCAGTTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (24 bp):
TTTCTCCTATTTTTCTCTCTTTTC
Found at i:2083443 original size:164 final size:163
Alignment explanation
Indices: 2083107--2083524 Score: 500
Period size: 164 Copynumber: 2.5 Consensus size: 163
2083097 AATGAATTAC
* * * *
2083107 TTTTTGAAAACTGATTTAATATGAAATAAATAATAATAATTGATGAATCTAAAAAATTAAAAACC
1 TTTTTGAAAAATGATTTAATGTGAAATAAATAATAATATTTGATGAAT-TTAAAAATTAAAAACC
* * *
2083172 AAGAAAAATCCCCCCAAAAAAATTTATGGAGTATAAAACTCCGTATTTCAAAAACAAAAAAATTT
65 AAGAAAAAT-CACCCAAAAAAATTTACGGAGTATAAAACTCCATATTTCAAAAACAAAAAAATTT
2083237 AAAGAAAAAAATCAAAATCCATGTAAATGAAGAAA
129 AAAGAAAAAAATCAAAATCCATGTAAATGAAGAAA
* * * *
2083272 ATTTTGAAAAATGATTTAATGTGAAATAAATGATAATATTTGATGAATTTAAAAATTACAAAGCA
1 TTTTTGAAAAATGATTTAATGTGAAATAAATAATAATATTTGATGAATTTAAAAATTAAAAACCA
* * * ** * *
2083337 TGAAAAATCACCTCAAAAAAATTTACGGAGTA-AAAAGCTCTATATTTCGAAAACATGAGAGTTT
66 AGAAAAATCACC-CAAAAAAATTTACGGAGTATAAAA-CTCCATATTTCAAAAACAAAAAAATTT
* * *
2083401 TAAGGAAAAAATCAAAAATCCATG-AAATTGATG-AA
129 AAAGAAAAAAATC-AAAATCCATGTAAA-TGAAGAAA
* ** * * *
2083436 TTTTTGAAAAATAATTTAATGTGATTTAAATAATAATATTTTATGCATTTTAAAATTAAAAACCA
1 TTTTTGAAAAATGATTTAATGTGAAATAAATAATAATATTTGATGAATTTAAAAATTAAAAACCA
*
2083501 AGAAAAATCATCCCGAAAAAATTT
66 AGAAAAATCA-CCCAAAAAAATTT
2083525 TTGGAGAAAA
Statistics
Matches: 215, Mismatches: 33, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
163 7 0.03
164 149 0.69
165 59 0.27
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.29
Consensus pattern (163 bp):
TTTTTGAAAAATGATTTAATGTGAAATAAATAATAATATTTGATGAATTTAAAAATTAAAAACCA
AGAAAAATCACCCAAAAAAATTTACGGAGTATAAAACTCCATATTTCAAAAACAAAAAAATTTAA
AGAAAAAAATCAAAATCCATGTAAATGAAGAAA
Found at i:2087562 original size:12 final size:12
Alignment explanation
Indices: 2087545--2087615 Score: 79
Period size: 12 Copynumber: 5.9 Consensus size: 12
2087535 TAAAAATCTA
*
2087545 TTTGAACCTGTG
1 TTTGAACTTGTG
*
2087557 TTTGAACTTATG
1 TTTGAACTTGTG
*
2087569 TTTTAACTTGTG
1 TTTGAACTTGTG
* *
2087581 TCTAAACTTGTG
1 TTTGAACTTGTG
* *
2087593 TTTGAACCTATG
1 TTTGAACTTGTG
2087605 TTTGAACTTGT
1 TTTGAACTTGT
2087616 ATCTACACTT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 47 1.00
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.48
Consensus pattern (12 bp):
TTTGAACTTGTG
Found at i:2087605 original size:36 final size:36
Alignment explanation
Indices: 2087553--2087627 Score: 114
Period size: 36 Copynumber: 2.1 Consensus size: 36
2087543 TATTTGAACC
* * *
2087553 TGTGTTTGAACTTATGTTTTAACTTGTGTCTAAACT
1 TGTGTTTGAACCTATGTTTGAACTTGTATCTAAACT
*
2087589 TGTGTTTGAACCTATGTTTGAACTTGTATCTACACT
1 TGTGTTTGAACCTATGTTTGAACTTGTATCTAAACT
2087625 TGT
1 TGT
2087628 AACCAAACCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.48
Consensus pattern (36 bp):
TGTGTTTGAACCTATGTTTGAACTTGTATCTAAACT
Found at i:2087612 original size:24 final size:24
Alignment explanation
Indices: 2087545--2087615 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 24
2087535 TAAAAATCTA
*
2087545 TTTGAACCTGTGTTTGAACTTATG
1 TTTGAACCTGTGTTTGAACTTGTG
* * * *
2087569 TTTTAACTTGTGTCTAAACTTGTG
1 TTTGAACCTGTGTTTGAACTTGTG
*
2087593 TTTGAACCTATGTTTGAACTTGT
1 TTTGAACCTGTGTTTGAACTTGT
2087616 ATCTACACTT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.48
Consensus pattern (24 bp):
TTTGAACCTGTGTTTGAACTTGTG
Found at i:2088780 original size:20 final size:20
Alignment explanation
Indices: 2088755--2088792 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2088745 TTAAGGAAAT
2088755 TGGCAAGACAACATCCAGGC
1 TGGCAAGACAACATCCAGGC
*
2088775 TGGCAAGACAGCATCCAG
1 TGGCAAGACAACATCCAG
2088793 TCTAGCAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.26, T:0.11
Consensus pattern (20 bp):
TGGCAAGACAACATCCAGGC
Found at i:2088800 original size:20 final size:20
Alignment explanation
Indices: 2088757--2088801 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2088747 AAGGAAATTG
*
2088757 GCAAGACAACATCCAGGCTG
1 GCAAGACAACATCCAGGCTA
* *
2088777 GCAAGACAGCATCCAGTCTA
1 GCAAGACAACATCCAGGCTA
2088797 GCAAG
1 GCAAG
2088802 TACACCTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.29, G:0.24, T:0.11
Consensus pattern (20 bp):
GCAAGACAACATCCAGGCTA
Found at i:2089963 original size:3 final size:3
Alignment explanation
Indices: 2089955--2090004 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
2089945 ATGAGAAAAG
2089955 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2090003 AT
1 AT
2090005 CGCAATGTGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2093553 original size:20 final size:18
Alignment explanation
Indices: 2093512--2093547 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2093502 GATGTCTAAA
2093512 ATAATAATAATAAAAAAT
1 ATAATAATAATAAAAAAT
2093530 ATAAT-ATAATATAAAAAT
1 ATAATAATAATA-AAAAAT
2093548 TTATAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAATAATAATAAAAAAT
Found at i:2093856 original size:37 final size:38
Alignment explanation
Indices: 2093814--2093889 Score: 95
Period size: 37 Copynumber: 2.0 Consensus size: 38
2093804 AATTATTTAA
2093814 ATTAAAAAAAT-AAATCATAAA-TATCAAAATAA-AAATT
1 ATTAAAAAAATCAAAT-ATAAATTAT-AAAATAATAAATT
* *
2093851 ATTAAAAAATTCAAATATAAATTATAAACTAATAAATT
1 ATTAAAAAAATCAAATATAAATTATAAAATAATAAATT
2093889 A
1 A
2093890 AATATATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
37 21 0.62
38 13 0.38
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.30
Consensus pattern (38 bp):
ATTAAAAAAATCAAATATAAATTATAAAATAATAAATT
Found at i:2095093 original size:1 final size:1
Alignment explanation
Indices: 2095087--2095111 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2095077 ACTCTGCCTT
2095087 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
2095112 GGGACAGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2100589 original size:20 final size:20
Alignment explanation
Indices: 2100555--2100600 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2100545 AAGAATTGAA
*
2100555 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
** *
2100575 GAGGGATACTTGAGATGGAG
1 GAGGGATACAAGAGAGGGAG
2100595 GAGGGA
1 GAGGGA
2100601 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.48, T:0.13
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:2102173 original size:3 final size:3
Alignment explanation
Indices: 2102165--2102192 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2102155 ACAAATTCTT
2102165 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2102193 CTTTCCTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2103023 original size:12 final size:11
Alignment explanation
Indices: 2103008--2103049 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
2102998 ATAATTAAGG
2103008 TATTAATTTATA
1 TATTAATTT-TA
2103020 TATTAACTTTTA
1 TATTAA-TTTTA
2103032 -ATTTAATTTTA
1 TA-TTAATTTTA
2103043 TATTAAT
1 TATTAAT
2103050 ACAAATTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 11 0.41
12 13 0.48
13 3 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTAATTTTA
Found at i:2103124 original size:29 final size:28
Alignment explanation
Indices: 2103092--2103152 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 28
2103082 AATTAATTAT
2103092 CATTATTTTAA-AAAAAATAGTGATAAAAA
1 CATTATTTTAAGAAAAAA-A-TGATAAAAA
2103121 CA-T-TTTTAAGTAAAAAAATGATAAAAA
1 CATTATTTTAAG-AAAAAAATGATAAAAA
*
2103148 AATTA
1 CATTA
2103153 GAGAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
27 16 0.59
28 3 0.11
29 8 0.30
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.31
Consensus pattern (28 bp):
CATTATTTTAAGAAAAAAATGATAAAAA
Done.