Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1827
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: 67681
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:65 original size:32 final size:32
Alignment explanation
Indices: 28--90 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 32
18 GCCAAGGAAA
28 TGTATCGATACATT-TCTGTGTATCGATACACT
1 TGTATCGATACATTATCT-TGTATCGATACACT
60 TGTATCGATACATTGATCTTGTATCGATACA
1 TGTATCGATACATT-ATCTTGTATCGATACA
91 TTTGGAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 14 0.48
33 12 0.41
34 3 0.10
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATTATCTTGTATCGATACACT
Found at i:82 original size:19 final size:18
Alignment explanation
Indices: 28--92 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
18 GCCAAGGAAA
28 TGTATCGATACATT-TCT
1 TGTATCGATACATTATCT
45 GTGTATCGATAC---A-CT
1 -TGTATCGATACATTATCT
60 TGTATCGATACATTGATCT
1 TGTATCGATACATT-ATCT
79 TGTATCGATACATT
1 TGTATCGATACATT
93 TGGAAATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
14 11 0.27
15 2 0.05
18 12 0.29
19 16 0.39
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (18 bp):
TGTATCGATACATTATCT
Found at i:2547 original size:26 final size:26
Alignment explanation
Indices: 2514--2586 Score: 94
Period size: 27 Copynumber: 2.8 Consensus size: 26
2504 ATTTCTTACA
*
2514 ATCGGGGACACTCCAACCCGTTAATC
1 ATCGGGGATACTCCAACCCGTTAATC
*
2540 ATCGGGGATACTCCAACCCCGTTATTC
1 ATCGGGGATACTCCAA-CCCGTTAATC
*
2567 -TGAGGGGATACTCCAACCCG
1 AT-CGGGGATACTCCAACCCG
2587 ACTTTATTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 20 0.48
27 22 0.52
ACGTcount: A:0.25, C:0.33, G:0.22, T:0.21
Consensus pattern (26 bp):
ATCGGGGATACTCCAACCCGTTAATC
Found at i:2630 original size:50 final size:49
Alignment explanation
Indices: 2570--2736 Score: 183
Period size: 51 Copynumber: 3.3 Consensus size: 49
2560 GTTATTCTGA
*
2570 GGGGATACTCCAACCCGACTTTATTTCCAAAATATCAATTTTTCATAATC
1 GGGGATACTCCAACCCGA-TTTATTTCCAAAATACCAATTTTTCATAATC
* * * * *
2620 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAA-CCC-GATTTATTTCCAAAATACCAATTTTTC-ATAATC
* * *
2672 GGGGATACTCCAACACCGATTTATTTCCCGAAGTACCAA-TTTTCACAATC
1 GGGGATACTCCAAC-CCGATTTATTT-CCAAAATACCAATTTTTCATAATC
*
2722 GAGGATACTCCAACC
1 GGGGATACTCCAACC
2737 TCATTATTTC
Statistics
Matches: 97, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
49 1 0.01
50 30 0.31
51 37 0.38
52 29 0.30
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.31
Consensus pattern (49 bp):
GGGGATACTCCAACCCGATTTATTTCCAAAATACCAATTTTTCATAATC
Found at i:2685 original size:52 final size:51
Alignment explanation
Indices: 2570--2736 Score: 178
Period size: 52 Copynumber: 3.3 Consensus size: 51
2560 GTTATTCTGA
* * *
2570 GGGGATACTCCAA-CCCGACTTTATTTCCAAAATATCAATTTTTCATAATC
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTCCATAATC
** * *
2620 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTCC-ATAATC
* * ** *
2672 GGGGATACTCCAACACCGA-TTTATTTCCCGAAGTACCAATTTT-CACAATC
1 GGGGATACTCCAACCCCGACTTTATTT-CCAAAACACCAATTTTCCATAATC
*
2722 GAGGATACTCCAACC
1 GGGGATACTCCAACC
2737 TCATTATTTC
Statistics
Matches: 97, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
50 30 0.31
51 33 0.34
52 34 0.35
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTCCATAATC
Found at i:3765 original size:13 final size:13
Alignment explanation
Indices: 3747--3772 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3737 AATTTTTTTG
3747 TGTATCGATACAT
1 TGTATCGATACAT
3760 TGTATCGATACAT
1 TGTATCGATACAT
3773 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:16381 original size:20 final size:20
Alignment explanation
Indices: 16356--16394 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16346 TCCTCGCCAA
*
16356 AAAAAAGAAAAAAACAAAAC
1 AAAAAACAAAAAAACAAAAC
*
16376 AAAAAACAAAAAAAGAAAA
1 AAAAAACAAAAAAACAAAA
16395 GGAGAGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (20 bp):
AAAAAACAAAAAAACAAAAC
Found at i:17483 original size:55 final size:55
Alignment explanation
Indices: 17406--17842 Score: 616
Period size: 55 Copynumber: 7.9 Consensus size: 55
17396 GATGCCTTTT
17406 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* *
17461 CTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGACAC
1 CT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACAC
* *
17516 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAAAGTAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
17571 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
17626 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* * ** *
17681 CTCTGAAAGCCCACACAAGTTGGTGGCA-CCTCTCAGTCCCCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTC-CAGTCCTCAAAGAGCAGGACAC
* ** *
17736 CTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAAAACGC
1 CT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACAC
** * * *
17791 CTTTCAAAGCCCACATGAGTTGGTGGCACTTTT-TACTCCTCAATGAGCAGGA
1 CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
17843 TACACTTTAT
Statistics
Matches: 345, Mismatches: 28, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
54 9 0.03
55 329 0.95
56 6 0.02
57 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
Found at i:17590 original size:27 final size:27
Alignment explanation
Indices: 17454--17590 Score: 63
Period size: 27 Copynumber: 5.0 Consensus size: 27
17444 CTCAAAGAGC
17454 AGGACACCTCTT-AAAGCCCACACAAGTT
1 AGGACACCT-TTCAAAGCCCACACAAG-T
* * * *
17482 GGTGGCACCTTTC--AGTCCC-CAAAGAGC
1 AG-GACACCTTTCAAAG-CCCACACA-AGT
17509 AGGACACCTTTCAAAGCCCACACAAGTT
1 AGGACACCTTTCAAAGCCCACACAAG-T
* * * * *
17537 GGTGGCA-TTTTC-CAGTCCTCA-AAAAGT
1 AG-GACACCTTTCAAAG-CC-CACACAAGT
17564 AGGACACCTTTCAAAGCCCACACAAGT
1 AGGACACCTTTCAAAGCCCACACAAGT
17591 TGGTGGCATT
Statistics
Matches: 77, Mismatches: 18, Indels: 29
0.62 0.15 0.23
Matches are distributed among these distances:
26 14 0.18
27 26 0.34
28 26 0.34
29 11 0.14
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (27 bp):
AGGACACCTTTCAAAGCCCACACAAGT
Found at i:17630 original size:27 final size:27
Alignment explanation
Indices: 17600--17682 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
17590 TTGGTGGCAT
17600 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
17627 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
17655 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
17682 T
1 T
17683 CTGAAAGCCC
Statistics
Matches: 37, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.14
27 11 0.30
28 10 0.27
29 5 0.14
30 3 0.08
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGACACC
Found at i:17766 original size:29 final size:29
Alignment explanation
Indices: 17678--17766 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
17668 AAGAGCAGGA
*
17678 CACCTCTGAAAGCCCACACAAGTTGGTGG
1 CACCTCTTAAAGCCCACACAAGTTGGTGG
* * **
17707 CACCTC-T-CAGTCCC-CA-AAG-AGCAGG
1 CACCTCTTAAAG-CCCACACAAGTTGGTGG
17732 ACACCTCTTAAAGCCCACACAAGTTGGTGG
1 -CACCTCTTAAAGCCCACACAAGTTGGTGG
17762 CACCT
1 CACCT
17767 TTCAGTCCTC
Statistics
Matches: 44, Mismatches: 9, Indels: 14
0.66 0.13 0.21
Matches are distributed among these distances:
25 3 0.07
26 9 0.20
27 8 0.18
28 7 0.16
29 14 0.32
30 3 0.07
ACGTcount: A:0.28, C:0.35, G:0.20, T:0.17
Consensus pattern (29 bp):
CACCTCTTAAAGCCCACACAAGTTGGTGG
Found at i:18551 original size:21 final size:21
Alignment explanation
Indices: 18527--18603 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
18517 AATTTATCTA
18527 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
* *
18548 AATGTATCAATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
18569 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
18590 AATGTATCGATACA
1 AATGTATCGATACA
18604 GGGTCCCAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:21270 original size:28 final size:27
Alignment explanation
Indices: 21203--21275 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
21193 CTTCACAATC
* *
21203 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
21230 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
21258 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
21276 ACTTTATTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:21384 original size:52 final size:50
Alignment explanation
Indices: 21258--21432 Score: 215
Period size: 52 Copynumber: 3.4 Consensus size: 50
21248 TTATTTCTGA
* *
21258 GGGGATACTCCAACCCCGACTTTATTTCCAAAATATCAATTTTTCATAATC
1 GGGGATACTCCAACCCC-ATTTTATTTCCAAAATACCAATTTTTCATAATC
* * * *
21309 GGGGATACTCCAACCCCAGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCA-TTTTATTTCCAAAATACCAATTTTTC-ATAATC
* *
21361 GGGGATACTCCAACACCTATTTTATTTCCAAAAGTACCAATTTTTCACAATC
1 GGGGATACTCCAAC-CCCATTTTATTTCCAAAA-TACCAATTTTTCATAATC
* *
21413 AGGGATACTCCAACCTCATT
1 GGGGATACTCCAACCCCATT
21433 ATTTCATCGG
Statistics
Matches: 105, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
50 1 0.01
51 42 0.40
52 49 0.47
53 13 0.12
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (50 bp):
GGGGATACTCCAACCCCATTTTATTTCCAAAATACCAATTTTTCATAATC
Found at i:21458 original size:211 final size:211
Alignment explanation
Indices: 21094--21486 Score: 558
Period size: 211 Copynumber: 1.9 Consensus size: 211
21084 AATTCTCCAC
* * * *
21094 AATCGGGGATATTTCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACTC
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
* * *
21159 CAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGACACTCCAACCCCGTTA
66 CAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAGGGACACTCCAACCCCATTA
* * * *
21224 ATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATTTCCAA
131 ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATTTCCAA
21289 AATATCAATTTTTCAT
196 AATATCAATTTTTCAT
*
21305 AATCGGGGATACTCCAACCCC-AGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATAC
1 AATCGGGGATACTCCAACCCCGA-TTTTATTTTCAAAACACCAATTTT-CTATAATCGGGGATAC
* ** * *
21369 TCCAACACCTATTTTATTTCC-AAAAGTACCAATTT-TTCACAATCAGGGATACTCCAACCTCAT
64 TCCAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAGGGACACTCCAACCCCAT
* * *
21432 TATTTCATCGGGGATATTCCAACCCCGTTACTTCCGAGGGAACACTCTAACCCCG
129 TA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCG
21487 TTATTATCTC
Statistics
Matches: 159, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
210 27 0.17
211 98 0.62
212 34 0.21
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (211 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGATACTC
CAACACCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCAGGGACACTCCAACCCCATTA
ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGAACACTCCAACCCCGACTTTATTTCCAA
AATATCAATTTTTCAT
Found at i:23710 original size:19 final size:19
Alignment explanation
Indices: 23679--23717 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
23669 TACTCATTAT
*
23679 TTATATTTAAATTTTTTAA
1 TTATATTTAAATTATTTAA
23698 TTAT-TTTATAATTATTTAA
1 TTATATTTA-AATTATTTAA
23717 T
1 T
23718 AAATTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATATTTAAATTATTTAA
Found at i:26613 original size:22 final size:22
Alignment explanation
Indices: 26588--26644 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
26578 CAAGAGTTGT
*
26588 CATATGTAAATTCAATTATGGC
1 CATATGTACATTCAATTATGGC
* *
26610 CATATGTACATTCATTTATGGT
1 CATATGTACATTCAATTATGGC
26632 CATATGTACATTC
1 CATATGTACATTC
26645 GATCAAGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (22 bp):
CATATGTACATTCAATTATGGC
Found at i:26819 original size:22 final size:22
Alignment explanation
Indices: 26791--26854 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
26781 TTCAGTTATA
26791 TACATTTAATTAT-AGTCATATG
1 TACATTTAATTATGA-TCATATG
* *
26813 TATATTTAGTTATGATCATATG
1 TACATTTAATTATGATCATATG
* *
26835 TACATTCAATTATTATCATA
1 TACATTTAATTATGATCATA
26855 CATGCATTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 34 0.97
23 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (22 bp):
TACATTTAATTATGATCATATG
Found at i:27232 original size:22 final size:22
Alignment explanation
Indices: 27207--27279 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
27197 AGTTCTAGAG
* *
27207 ATATGTACATTTATTTATAGTC
1 ATATATACATTTAGTTATAGTC
* *
27229 ATATATACATTTCGTTATAGTA
1 ATATATACATTTAGTTATAGTC
*
27251 ATATATACATTTAGTTATGGTC
1 ATATATACATTTAGTTATAGTC
27273 ATATATA
1 ATATATA
27280 TATATATATA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.47
Consensus pattern (22 bp):
ATATATACATTTAGTTATAGTC
Found at i:27280 original size:2 final size:2
Alignment explanation
Indices: 27273--27330 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
27263 AGTTATGGTC
27273 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27315 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
27331 TCAGATATAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27578 original size:22 final size:22
Alignment explanation
Indices: 27491--27578 Score: 63
Period size: 22 Copynumber: 4.0 Consensus size: 22
27481 ATATACACTT
* *
27491 AGTTATAGTGACATGTACACTC
1 AGTTATAGTTACATGTACATTC
* * * *
27513 AATTATAATGATATATGT--ATTT
1 AGTTAT-A-GTTACATGTACATTC
* * *
27535 AGTTATAGTCATATGTATATTC
1 AGTTATAGTTACATGTACATTC
27557 AGTTATAGTTACATGTACATTC
1 AGTTATAGTTACATGTACATTC
27579 GATTCTATAT
Statistics
Matches: 49, Mismatches: 13, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
20 7 0.14
21 1 0.02
22 34 0.69
23 1 0.02
24 6 0.12
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (22 bp):
AGTTATAGTTACATGTACATTC
Found at i:34163 original size:22 final size:22
Alignment explanation
Indices: 34138--34179 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
34128 TATATTTATT
34138 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
34160 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
34180 ATTTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:34533 original size:14 final size:14
Alignment explanation
Indices: 34516--34561 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
34506 TAACTTTTTT
*
34516 ATATTTTCTAAAAA
1 ATATTTTTTAAAAA
**
34530 ATATTTATTTATTAA
1 ATATTT-TTTAAAAA
34545 ATATTTTTTAAAAA
1 ATATTTTTTAAAAA
34559 ATA
1 ATA
34562 AAATAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATTTTTTAAAAA
Found at i:34729 original size:2 final size:2
Alignment explanation
Indices: 34722--34747 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34712 TTGAGCTCCC
34722 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
34748 CCTTTTCGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35643 original size:17 final size:18
Alignment explanation
Indices: 35623--35660 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
35613 TATTTAACTT
*
35623 ATATTTAAATTTAAAA-A
1 ATATTTAAATTAAAAATA
35640 ATA-TTAAATTAAAAATA
1 ATATTTAAATTAAAAATA
35657 ATAT
1 ATAT
35661 ATAATATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATTTAAATTAAAAATA
Found at i:35690 original size:21 final size:21
Alignment explanation
Indices: 35634--35711 Score: 65
Period size: 24 Copynumber: 3.7 Consensus size: 21
35624 TATTTAAATT
*
35634 TAAAAAATATTAAATT-AA-A
1 TAAAAAATATTATATTCAATA
* *
35653 -AATAATATATAATATTCAA-A
1 TAA-AAAATATTATATTCAATA
35673 TAAAAAATATTGATATTCAATGTA
1 TAAAAAATATT-ATATTCAA--TA
35697 TAAAAAATATTATAT
1 TAAAAAATATTATAT
35712 AAATTACATT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
18 2 0.04
19 10 0.21
20 9 0.19
21 10 0.21
23 4 0.09
24 12 0.26
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (21 bp):
TAAAAAATATTATATTCAATA
Found at i:38325 original size:33 final size:33
Alignment explanation
Indices: 38281--38365 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 33
38271 ATGAACAAAT
*
38281 AATTAAAAAAATTTGAAA-CAAAAAAATGAAAGA
1 AATTAAAAAAATTTAAAATCAAAAAAATGAAA-A
* * *
38314 AATTAATAAAA-TTAAAATTAAAAAAATTAAAA
1 AATTAAAAAAATTTAAAATCAAAAAAATGAAAA
*
38346 AATTAAAAATAATTTTAAAT
1 AATTAAAAA-AATTTAAAAT
38366 TTTTTGATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
32 14 0.33
33 23 0.53
34 6 0.14
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (33 bp):
AATTAAAAAAATTTAAAATCAAAAAAATGAAAA
Found at i:38333 original size:15 final size:15
Alignment explanation
Indices: 38313--38359 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
38303 AAAATGAAAG
*
38313 AAATTAATAAAATTA
1 AAATTAAAAAAATTA
38328 AAATTAAAAAAATTAAA
1 AAATTAAAAAAATT--A
38345 AAATTAAAAATAATT
1 AAATTAAAAA-AATT
38360 TTAAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 13 0.46
17 11 0.39
18 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATTAAAAAAATTA
Found at i:38354 original size:9 final size:9
Alignment explanation
Indices: 38300--38359 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 9
38290 AATTTGAAAC
*
38300 AAAAAAATG
1 AAAAAAATT
*
38309 AAAGAAATT
1 AAAAAAATT
*
38318 AATAAAATT
1 AAAAAAATT
38327 ---AAAATT
1 AAAAAAATT
38333 AAAAAAATT
1 AAAAAAATT
38342 -AAAAAATT
1 AAAAAAATT
38350 AAAAATAATT
1 AAAAA-AATT
38360 TTAAATTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
6 6 0.14
8 8 0.19
9 24 0.57
10 4 0.10
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (9 bp):
AAAAAAATT
Found at i:38354 original size:24 final size:24
Alignment explanation
Indices: 38281--38355 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 24
38271 ATGAACAAAT
*
38281 AATTAAAAAAATTTGAAACAA--AAA
1 AATTAAAAAAA-TT-AAAAAATTAAA
* *
38305 AATGAAAGAAATTAATAAAATT-AA
1 AATTAAAAAAATTAA-AAAATTAAA
38329 AATTAAAAAAATTAAAAAATTAAA
1 AATTAAAAAAATTAAAAAATTAAA
38353 AAT
1 AAT
38356 AATTTTAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
22 2 0.05
23 11 0.26
24 29 0.69
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (24 bp):
AATTAAAAAAATTAAAAAATTAAA
Found at i:43309 original size:3 final size:3
Alignment explanation
Indices: 43301--43326 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43291 TGATTTTCTT
43301 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
43327 ATGTTGTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:44627 original size:6 final size:6
Alignment explanation
Indices: 44616--44650 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
44606 CTGATTTCTC
* *
44616 TCAAAA TCAAAA TCAAAA CCAAAA GCAAAA TCAAA
1 TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA TCAAA
44651 TCCCTACTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.66, C:0.20, G:0.03, T:0.11
Consensus pattern (6 bp):
TCAAAA
Found at i:45134 original size:48 final size:48
Alignment explanation
Indices: 45082--45197 Score: 214
Period size: 48 Copynumber: 2.4 Consensus size: 48
45072 TGTGTTTTTA
45082 AAATTAGAGATTTGATTTTGGCTTTGATTTCATTTTGATTTTTGAGAG
1 AAATTAGAGATTTGATTTTGGCTTTGATTTCATTTTGATTTTTGAGAG
*
45130 AAATTAGAGATTTGATTTTGGCTTTGATTTCATTTTGATTTTTGGGAG
1 AAATTAGAGATTTGATTTTGGCTTTGATTTCATTTTGATTTTTGAGAG
*
45178 AAATTAGAGATTTGGTTTTG
1 AAATTAGAGATTTGATTTTG
45198 ATTTTAATTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.49
Consensus pattern (48 bp):
AAATTAGAGATTTGATTTTGGCTTTGATTTCATTTTGATTTTTGAGAG
Found at i:45538 original size:2 final size:2
Alignment explanation
Indices: 45531--45559 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45521 TTTCACCACT
45531 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45560 GACATTGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45777 original size:23 final size:24
Alignment explanation
Indices: 45743--45800 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 24
45733 ACCCTCGGAC
** *
45743 TTAA-AATATATTATATTTATTTT
1 TTAATAATATATTATAAATATATT
*
45766 TTAATAAT-TATTTTAAATATATT
1 TTAATAATATATTATAAATATATT
*
45789 TTAATAAAATAT
1 TTAATAATATAT
45801 CTAACGCTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TTAATAATATATTATAAATATATT
Found at i:46171 original size:27 final size:26
Alignment explanation
Indices: 46141--46193 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
46131 TTGATATATA
46141 TATTTTTA-TTGATGTATTTTTATATTT
1 TATTTTTATTTGAT-TATTTTT-TATTT
*
46168 TATTTTTATTTTATTATTTTTTATTT
1 TATTTTTATTTGATTATTTTTTATTT
46194 AAATATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.21
27 15 0.62
28 4 0.17
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (26 bp):
TATTTTTATTTGATTATTTTTTATTT
Found at i:46187 original size:26 final size:26
Alignment explanation
Indices: 46114--46193 Score: 65
Period size: 26 Copynumber: 3.0 Consensus size: 26
46104 TTCGAGCTTA
* * *
46114 TTATTTTTATTTTAGT-GTTGATATAT
1 TTATTTTTATTTTATTATTTTATAT-T
* *
46140 ATATTTTTA-TTGATGTATTTTTATATT
1 TTATTTTTATTTTAT-TA-TTTTATATT
*
46167 TTATTTTTATTTTATTATTTTTTATT
1 TTATTTTTATTTTATTATTTTATATT
46193 T
1 T
46194 AAATATTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
25 3 0.07
26 18 0.43
27 11 0.26
28 10 0.24
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (26 bp):
TTATTTTTATTTTATTATTTTATATT
Found at i:46190 original size:15 final size:15
Alignment explanation
Indices: 46157--46203 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
46147 TATTGATGTA
*
46157 TTTTTATATT-TTA-
1 TTTTTATTTTATTAT
46170 TTTTTATTTTATTAT
1 TTTTTATTTTATTAT
* *
46185 TTTTTATTTAAATAT
1 TTTTTATTTTATTAT
46200 TTTT
1 TTTT
46204 CATATAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 9 0.31
14 3 0.10
15 17 0.59
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTATTTTATTAT
Found at i:46194 original size:14 final size:13
Alignment explanation
Indices: 46111--46194 Score: 57
Period size: 14 Copynumber: 6.2 Consensus size: 13
46101 ATATTCGAGC
46111 TTATTATTTTTA-
1 TTATTATTTTTAT
* *
46123 TT-TTAGTGTTGAT
1 TTATTA-TTTTTAT
*
46136 ATATATATTTTTAT
1 TTAT-TATTTTTAT
*
46150 TGATGTATTTTTAT
1 TTAT-TATTTTTAT
46164 ATT-TTATTTTTATT
1 -TTATTATTTTTA-T
46178 TTATTATTTTTTAT
1 TTATTA-TTTTTAT
46192 TTA
1 TTA
46195 AATATTTTTC
Statistics
Matches: 55, Mismatches: 9, Indels: 14
0.71 0.12 0.18
Matches are distributed among these distances:
11 3 0.05
12 6 0.11
13 11 0.20
14 26 0.47
15 9 0.16
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (13 bp):
TTATTATTTTTAT
Found at i:46315 original size:15 final size:15
Alignment explanation
Indices: 46295--46330 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
46285 CTTTATATAT
46295 AAATATAAA-ATTTTA
1 AAATATAAATA-TTTA
46310 AAATATAAATATTTA
1 AAATATAAATATTTA
46325 AAATAT
1 AAATAT
46331 TTAAACTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATATAAATATTTA
Found at i:46316 original size:23 final size:24
Alignment explanation
Indices: 46289--46353 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
46279 TTATATCTTT
46289 ATATATAA-ATATAAAAT-TTTAAA
1 ATATA-AATATATAAAATATTTAAA
*
46312 ATATAAATATTTAAAATATTTAAA
1 ATATAAATATATAAAATATTTAAA
* * * *
46336 CTTTACATAAATAAAATA
1 ATATAAATATATAAAATA
46354 AATGTAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
22 2 0.06
23 13 0.38
24 19 0.56
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATAAATATATAAAATATTTAAA
Found at i:49547 original size:10 final size:10
Alignment explanation
Indices: 49532--49601 Score: 61
Period size: 10 Copynumber: 7.0 Consensus size: 10
49522 TAAGCTACCT
49532 TTTTTTTTTC
1 TTTTTTTTTC
**
49542 TTTTTTTGCC
1 TTTTTTTTTC
* *
49552 TTATTTTTCC
1 TTTTTTTTTC
*
49562 TTCTTTCTTTC
1 TT-TTTTTTTC
49573 TTTTTTTTTC
1 TTTTTTTTTC
*
49583 -TTTTCTTTC
1 TTTTTTTTTC
*
49592 TTTTCTTTTC
1 TTTTTTTTTC
49602 CCTTTTTCCT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
9 8 0.17
10 32 0.68
11 7 0.15
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.79
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:49577 original size:19 final size:19
Alignment explanation
Indices: 49530--49595 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
49520 TTTAAGCTAC
* *
49530 CTTTTTTTTTTCTTTTTTT
1 CTTTCTTTTTTCTTCTTTT
* * *
49549 GCCTTATTTTTCCTTC-TTT
1 -CTTTCTTTTTTCTTCTTTT
*
49568 CTTTCTTTTTTTTTCTTTT
1 CTTTCTTTTTTCTTCTTTT
49587 CTTTCTTTT
1 CTTTCTTTT
49596 CTTTTCCCTT
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
18 11 0.30
19 15 0.41
20 11 0.30
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (19 bp):
CTTTCTTTTTTCTTCTTTT
Found at i:49586 original size:5 final size:5
Alignment explanation
Indices: 49565--49601 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
49555 TTTTTCCTTC
*
49565 TTTC- TTTCT TTTTT TTTCT TTTC- TTTCT TTTCT TTTC
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTC
49602 CCTTTTTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:49600 original size:14 final size:14
Alignment explanation
Indices: 49556--49601 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
49546 TTTGCCTTAT
*
49556 TTTTCCTTC-TTTC
1 TTTTCTTTCTTTTC
*
49569 -TTTCTTTTTTTTTC
1 TTTTC-TTTCTTTTC
49583 TTTTCTTTCTTTTC
1 TTTTCTTTCTTTTC
49597 TTTTC
1 TTTTC
49602 CCTTTTTCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
12 4 0.15
13 2 0.07
14 17 0.63
15 4 0.15
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTCTTTCTTTTC
Found at i:49600 original size:19 final size:19
Alignment explanation
Indices: 49565--49601 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
49555 TTTTTCCTTC
*
49565 TTTCTTTCTTTTTTTTTCT
1 TTTCTTTCTTTTCTTTTCT
49584 TTTCTTTCTTTTCTTTTC
1 TTTCTTTCTTTTCTTTTC
49602 CCTTTTTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTCTTTCTTTTCTTTTCT
Found at i:49600 original size:23 final size:23
Alignment explanation
Indices: 49531--49600 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
49521 TTAAGCTACC
49531 TTTTTT-TTTTCTTT-TTTTGCCTT
1 TTTTTTCTTTTCTTTCTTTT--CTT
* *
49554 ATTTTTC-CTTCTTTC-TTTCTTT
1 TTTTTTCTTTTCTTTCTTTTC-TT
49576 TTTTTTCTTTTCTTTCTTTTCTT
1 TTTTTTCTTTTCTTTCTTTTCTT
49599 TT
1 TT
49601 CCCTTTTTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
21 1 0.03
22 8 0.21
23 25 0.66
24 4 0.11
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.80
Consensus pattern (23 bp):
TTTTTTCTTTTCTTTCTTTTCTT
Found at i:49601 original size:41 final size:40
Alignment explanation
Indices: 49532--49620 Score: 101
Period size: 41 Copynumber: 2.2 Consensus size: 40
49522 TAAGCTACCT
*
49532 TTTTTTTTTCTTTTTTTGCCTTATTTTT-CCTTCTTTCTTTC
1 TTTTTTTTTCTTTTTTT-CCTTATTTTTCCCTT-TTTCCTTC
*
49573 TTTTTTTTTCTTTTCTTT-CTTTTCTTTTCCCTTTTTCCTTC
1 TTTTTTTTTCTTTT-TTTCCTTAT-TTTTCCCTTTTTCCTTC
*
49614 ATTTTTT
1 TTTTTTT
49621 CCTTTTTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
40 4 0.10
41 31 0.74
42 7 0.17
ACGTcount: A:0.02, C:0.20, G:0.01, T:0.76
Consensus pattern (40 bp):
TTTTTTTTTCTTTTTTTCCTTATTTTTCCCTTTTTCCTTC
Found at i:49976 original size:21 final size:21
Alignment explanation
Indices: 49946--49985 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
49936 TTAGAAAGCT
49946 TGTTTTTTTTT-GTTTGCTAG
1 TGTTTTTTTTTGGTTTGCTAG
49966 TGTTTTCTTTTTGGTTTGCT
1 TGTTTT-TTTTTGGTTTGCT
49986 GATTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.03, C:0.07, G:0.20, T:0.70
Consensus pattern (21 bp):
TGTTTTTTTTTGGTTTGCTAG
Found at i:50178 original size:10 final size:10
Alignment explanation
Indices: 50163--50200 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
50153 CAGTCAACTC
50163 TCTTTTTTTA
1 TCTTTTTTTA
*
50173 TCTTTTCTT-
1 TCTTTTTTTA
50182 TCTTTTTTTTA
1 TC-TTTTTTTA
50193 TCTTTTTT
1 TCTTTTTT
50201 GTATTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.83
11 2 0.08
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (10 bp):
TCTTTTTTTA
Found at i:59188 original size:33 final size:33
Alignment explanation
Indices: 59151--59217 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
59141 TTCAACGATT
59151 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
59184 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
59217 T
1 T
59218 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:59189 original size:13 final size:13
Alignment explanation
Indices: 59171--59195 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59161 CATAAAATGT
59171 TGTATCGATACAA
1 TGTATCGATACAA
59184 TGTATCGATACA
1 TGTATCGATACA
59196 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:59276 original size:13 final size:13
Alignment explanation
Indices: 59258--59282 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59248 ATTACTCAAA
59258 TGTATCGATACAT
1 TGTATCGATACAT
59271 TGTATCGATACA
1 TGTATCGATACA
59283 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:59347 original size:52 final size:52
Alignment explanation
Indices: 59291--59415 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
59281 CACTGATCTT
* *
59291 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
*
59343 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
*
59395 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
59416 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAAATGTATCGATACACTATAAAA
Found at i:67275 original size:52 final size:51
Alignment explanation
Indices: 67197--67313 Score: 182
Period size: 52 Copynumber: 2.3 Consensus size: 51
67187 AGAGTTACTG
* *
67197 CATGTATCGATACATTTAATAGTGTATCGATGCATCTGGGCAAATTTGCCTA
1 CATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA-TTGCCTA
*
67249 CATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGCAAATTGCCTG
1 CATGTATCGATACA-TTTAATAATGTATCGATACATCTGGGCAAATTGCCTA
67300 CATGTATCGATACA
1 CATGTATCGATACA
67314 AAGATCAGTG
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
51 20 0.33
52 36 0.59
53 5 0.08
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTGCCTA
Found at i:67326 original size:51 final size:50
Alignment explanation
Indices: 67194--67333 Score: 160
Period size: 52 Copynumber: 2.7 Consensus size: 50
67184 TGAAGAGTTA
* *
67194 CTGCATGTATCGATACATTTAATAGTGTATCGATGCATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGCAAATTTGC
*
67246 CTACATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGGGCAAA-TTGC
1 CTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGGGCAAATTTGC
67297 CTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
67334 ATGTATCGAT
Statistics
Matches: 78, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
47 2 0.03
48 1 0.01
50 1 0.01
51 32 0.41
52 37 0.47
53 1 0.01
54 4 0.05
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (50 bp):
CTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:67340 original size:13 final size:13
Alignment explanation
Indices: 67322--67346 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
67312 CAAAGATCAG
67322 TGTATCGATACAA
1 TGTATCGATACAA
67335 TGTATCGATACA
1 TGTATCGATACA
67347 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:67424 original size:33 final size:33
Alignment explanation
Indices: 67387--67453 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
67377 AGTAGCTTAA
67387 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
67420 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
67453 A
1 A
67454 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:67427 original size:13 final size:13
Alignment explanation
Indices: 67409--67433 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
67399 CAAAAAAATA
67409 TGTATCGATACAT
1 TGTATCGATACAT
67422 TGTATCGATACA
1 TGTATCGATACA
67434 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.