Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2378
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: 108952
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4658 original size:20 final size:19
Alignment explanation
Indices: 4603--4658 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
4593 AAAACCCTTA
*
4603 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
4623 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
4643 AATGTATCGATACATG
1 AAAGTATCGATACATG
4659 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:4746 original size:13 final size:13
Alignment explanation
Indices: 4728--4753 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4718 TACACAAAAT
4728 ATGTATCGATACA
1 ATGTATCGATACA
4741 ATGTATCGATACA
1 ATGTATCGATACA
4754 CAAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4751 original size:32 final size:34
Alignment explanation
Indices: 4710--4774 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
4700 TAGCCAAACT
*
4710 TGTATCGATACAC-AAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAAATTGTATCGATACAA
4742 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAAATTGTATCGATACA
4775 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 13 0.43
33 5 0.17
34 12 0.40
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (34 bp):
TGTATCGATACACAAAAAAATTGTATCGATACAA
Found at i:6997 original size:21 final size:21
Alignment explanation
Indices: 6964--7013 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
6954 TTGCAAGTTG
*
6964 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
6986 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
7007 AAATAAA
1 AAATAAA
7014 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:8828 original size:15 final size:15
Alignment explanation
Indices: 8808--8838 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
8798 TAAAAATGTC
*
8808 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
8823 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
8838 C
1 C
8839 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:10937 original size:13 final size:13
Alignment explanation
Indices: 10919--10956 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
10909 CATTTTTCTT
10919 TGTATCGATACAA
1 TGTATCGATACAA
*
10932 TGTATCGATACAC
1 TGTATCGATACAA
10945 TGTATCGATACA
1 TGTATCGATACA
10957 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:11111 original size:20 final size:20
Alignment explanation
Indices: 11068--11113 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
11058 AAATCTTTTG
11068 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
11089 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
11109 CAAAA
1 CAAAA
11114 CCAACATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:12852 original size:47 final size:47
Alignment explanation
Indices: 12783--12879 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
12773 TAAAGGGGAG
12783 AATGCGTGAATTACTTTATTAAGGGGGAGAATGTACAAATTTGTTAA
1 AATGCGTGAATTACTTTATTAAGGGGGAGAATGTACAAATTTGTTAA
12830 AATGCGTGAATTACTTTATTAAGGGGGAGAATGTACAAATTTGTTAA
1 AATGCGTGAATTACTTTATTAAGGGGGAGAATGTACAAATTTGTTAA
12877 AAT
1 AAT
12880 TATTTTGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (47 bp):
AATGCGTGAATTACTTTATTAAGGGGGAGAATGTACAAATTTGTTAA
Found at i:13469 original size:20 final size:19
Alignment explanation
Indices: 13414--13469 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
13404 AAAACCCTTA
*
13414 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
13434 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
13454 AATGTATCGATACATG
1 AAAGTATCGATACATG
13470 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:13557 original size:13 final size:13
Alignment explanation
Indices: 13539--13564 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13529 TACACAAAAT
13539 ATGTATCGATACA
1 ATGTATCGATACA
13552 ATGTATCGATACA
1 ATGTATCGATACA
13565 CAAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:13562 original size:32 final size:34
Alignment explanation
Indices: 13521--13585 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
13511 TAGCCAAACT
*
13521 TGTATCGATACAC-AAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAAATTGTATCGATACAA
13553 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAAATTGTATCGATACA
13586 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 13 0.43
33 5 0.17
34 12 0.40
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (34 bp):
TGTATCGATACACAAAAAAATTGTATCGATACAA
Found at i:15261 original size:21 final size:21
Alignment explanation
Indices: 15208--15262 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
15198 TATATTTAGC
**
15208 CAATATATCAGCACATTATCT
1 CAATATATCAATACATTATCT
15229 CAATATATCAATACATTATGCT
1 CAATATATCAATACATTAT-CT
*
15251 -AATGTATCAATA
1 CAATATATCAATA
15263 TTGTGGAGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.42, C:0.18, G:0.05, T:0.35
Consensus pattern (21 bp):
CAATATATCAATACATTATCT
Found at i:17579 original size:21 final size:21
Alignment explanation
Indices: 17555--17631 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
17545 AAAAATTTCA
17555 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
* *
17576 AATGTATCAATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
17597 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
17618 AATGTATCGATACA
1 AATGTATCGATACA
17632 GGGTCCCAAT
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:17691 original size:19 final size:19
Alignment explanation
Indices: 17667--17734 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
17657 AATTCAACAA
17667 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
17686 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
17701 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
17718 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
17735 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:17706 original size:13 final size:13
Alignment explanation
Indices: 17688--17712 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17678 ACATAAGTTT
17688 TGTATCGATACAA
1 TGTATCGATACAA
17701 TGTATCGATACA
1 TGTATCGATACA
17713 TAAGTATTGT
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:17710 original size:32 final size:32
Alignment explanation
Indices: 17669--17731 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
17659 TTCAACAATT
*
17669 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
17701 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
17732 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:20272 original size:54 final size:50
Alignment explanation
Indices: 20149--20274 Score: 144
Period size: 51 Copynumber: 2.4 Consensus size: 50
20139 CTCAATTCTC
* * * * *
20149 CACAATCGGGGATATTTCAACTCCGATTTTATTTTCAAGACACTAATTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACAAATTTT
* *
20199 CTATAATCGGGGATACTCCAACTTCGATTTTATTTCCAAAAAAACACCAAATTTT
1 C-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC---AAAACA-CAAATTTT
20254 CACAATCGGGGATACTCCAAC
1 CACAATCGGGGATACTCCAAC
20275 CTCGTTAATC
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
50 1 0.02
51 30 0.48
54 24 0.38
55 8 0.13
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (50 bp):
CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACAAATTTT
Found at i:20328 original size:28 final size:28
Alignment explanation
Indices: 20261--20361 Score: 152
Period size: 28 Copynumber: 3.6 Consensus size: 28
20251 TTTCACAATC
* * *
20261 GGGGATACTCCAACCTCGTTA-ATCAT-C
1 GGGGATACTCCAACCCCGTTATTTC-TGA
20288 GGGGATACTCCAACCCCGTTATTTCTGA
1 GGGGATACTCCAACCCCGTTATTTCTGA
20316 GGGGATACTCCAACCCCGTTATTTCTGA
1 GGGGATACTCCAACCCCGTTATTTCTGA
20344 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
20362 ACTTTGTTTC
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
27 21 0.30
28 48 0.70
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.25
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCTGA
Found at i:20428 original size:52 final size:52
Alignment explanation
Indices: 20344--20518 Score: 217
Period size: 52 Copynumber: 3.3 Consensus size: 52
20334 TTATTTCTGA
* * **
20344 GGGGATACTCCAACCCCGACTTTGTTTCCAAAATACTGATTTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCCACAATC
* * ** **
20396 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACCCCAATTTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCC-ACAATC
*
20449 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCC-AAAATACCAATTTTTCCACAATC
*
20501 GAGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
20519 TTATTTCCGA
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
52 58 0.57
53 31 0.30
54 13 0.13
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.31
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAATACCAATTTTTCCACAATC
Found at i:20553 original size:80 final size:79
Alignment explanation
Indices: 20449--20719 Score: 276
Period size: 79 Copynumber: 3.4 Consensus size: 79
20439 TCCTTTAATC
* * * * *
20449 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGACACTCCAACCCCGATTTTATTTCC-AAAATACCGATTTCTCACAATCGGGGATACTCCAA
*
20514 CCCCGTTATTTCCGA
65 CCCCGTTATTTTCGA
** * * * * *
20529 GGGGACACTCCAACCCCGGCTTTATTCCCAAAATACTGATTTCTCATAATTGGGGATACTCTAAC
1 GGGGACACTCCAACCCCGATTTTATTTCCAAAATACCGATTTCTCACAATCGGGGATACTCCAAC
20594 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
* * * * * * * * *
20608 GGGGATACTCCAATCCCGATTTTTTTTTC-TAATCATCGATTTCTCACAACCGGGGATATTCCAG
1 GGGGACACTCCAACCCCGATTTTATTTCCAAAAT-ACCGATTTCTCACAATCGGGGATACTCCAA
*
20672 CCCCGTTATTTTCAA
65 CCCCGTTATTTTCGA
* *
20687 GGGAACACTCCAACCCCG-TTATTATCTCCAAAA
1 GGGGACACTCCAACCCCGATT-TTATTTCCAAAA
20720 CATTAAATTT
Statistics
Matches: 151, Mismatches: 37, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
78 5 0.03
79 120 0.79
80 26 0.17
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (79 bp):
GGGGACACTCCAACCCCGATTTTATTTCCAAAATACCGATTTCTCACAATCGGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:33111 original size:8 final size:7
Alignment explanation
Indices: 33094--33167 Score: 55
Period size: 7 Copynumber: 10.4 Consensus size: 7
33084 CCTTTTCTTC
33094 AAAA-AA
1 AAAAGAA
33100 AAAAGCAA
1 AAAAG-AA
33108 AAAA-AA
1 AAAAGAA
33114 AAAAGAA
1 AAAAGAA
*
33121 AAAA-AC
1 AAAAGAA
*
33127 AAAACAA
1 AAAAGAA
*
33134 AAAACAAA
1 AAAA-GAA
33142 ACAAAGAA
1 A-AAAGAA
*
33150 AAAGAGAG
1 AAA-AGAA
33158 AAAAGAA
1 AAAAGAA
33165 AAA
1 AAA
33168 GAACCTGCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
6 15 0.27
7 19 0.35
8 18 0.33
9 3 0.05
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:33146 original size:12 final size:11
Alignment explanation
Indices: 33093--33142 Score: 66
Period size: 12 Copynumber: 4.5 Consensus size: 11
33083 ACCTTTTCTT
33093 CAAAAAAAAAA
1 CAAAAAAAAAA
33104 GCAAAAAAAAAA
1 -CAAAAAAAAAA
*
33116 -AAGAAAAAAA
1 CAAAAAAAAAA
33126 CAAAACAAAAAA
1 CAAAA-AAAAAA
33138 CAAAA
1 CAAAA
33143 CAAAGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 9 0.26
11 3 0.09
12 22 0.65
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:34366 original size:55 final size:55
Alignment explanation
Indices: 34160--34555 Score: 449
Period size: 55 Copynumber: 7.0 Consensus size: 55
34150 GATGCTTTTT
* * *
34160 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGCAGGACGCCTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGA-----T-G
* * *
34221 CCTTTTAAAGCCTACACAAGTTGGTGGCACTTCCCAGTCCTCAAAAAGCAGGATG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGATG
*
34276 CCTTCTCCTTTTAAAGCCCACACAAATTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGATG
1 ------CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGATG
34337 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGATG
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGATG
*
34392 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGG--G
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGATG
* * * * *
34445 CACGTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTTCTCAAAGAGTAGGACG
1 C-C-TTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGATG
* * ** * *
34502 CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTACTCCTCAATGAGCAGGAT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGAT
34556 ACACTTTATT
Statistics
Matches: 301, Mismatches: 22, Indels: 30
0.85 0.06 0.08
Matches are distributed among these distances:
53 2 0.01
54 5 0.02
55 185 0.61
56 6 0.02
57 2 0.01
61 101 0.34
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (55 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGATG
Found at i:35374 original size:19 final size:19
Alignment explanation
Indices: 35350--35417 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
35340 AATTCAACAA
35350 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
35369 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
*
35384 --TGTATCAATACATAAGT
1 TTTGTATCGATACATAAGT
*
35401 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
35418 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 27 0.66
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:35395 original size:32 final size:32
Alignment explanation
Indices: 35352--35414 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
35342 TTCAACAATT
* *
35352 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCAATACATAAGTATTGTATCGATACAA
35384 TGTATCAATACATAAGTATTGTATCGATACA
1 TGTATCAATACATAAGTATTGTATCGATACA
35415 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCAATACATAAGTATTGTATCGATACAA
Found at i:35475 original size:13 final size:13
Alignment explanation
Indices: 35457--35482 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35447 CATTTTTCTG
35457 TGTATCGATACAT
1 TGTATCGATACAT
35470 TGTATCGATACAT
1 TGTATCGATACAT
35483 GGATCTTTGT
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:35480 original size:33 final size:33
Alignment explanation
Indices: 35438--35503 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
35428 CCAAGGAAAG
***
35438 GTATCGATACATTTTTCTGTGTATCGATACATT
1 GTATCGATACATGGATCTGTGTATCGATACATT
*
35471 GTATCGATACATGGATCTTTGTATCGATACATT
1 GTATCGATACATGGATCTGTGTATCGATACATT
35504 TGGAAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (33 bp):
GTATCGATACATGGATCTGTGTATCGATACATT
Found at i:37973 original size:54 final size:50
Alignment explanation
Indices: 37848--38185 Score: 164
Period size: 52 Copynumber: 6.4 Consensus size: 50
37838 CTCAATTCTC
* * * * *
37848 CACAATCGGGGATATTTCAACTCCGATTTTATTTTCAAGACACTAATTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTTAAAAACACAAATTTT
*
37898 CTATAATCGGGGATACTCCAACTCCGATTTTATTTTAAAAAAAACACCAAATTTT
1 C-ACAATCGGGGATACTCCAACTCCGATTTTATTTT---AAAAACA-CAAATTTT
* * ***** * * *
37953 CACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAACCCCGTTATT
1 CACAATCGGGGATACTCCAACTCCGATT--TTATTTTAAAAAC-ACAA----ATT-TT
* * * * ** * * *
38010 -TC--TGAGGGGATACTCCAACCCCGACTTTATTTCCAAAATACTGATTTTT
1 CACAAT-CGGGGATACTCCAACTCCGATTTTATTTTAAAAACAC-AAATTTT
* * *
38059 CCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACAAATTTTT
1 -CACAATCGGGGATACTCCAACTCCGATTTTATTTTAAAAACACAAA-TTTT
* *
38111 C-CTTTAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAATACCAATTTTT
1 CAC---AATCGGGGATACTCCAACTCCGATTTTATTTT-AAAAACA-CAAATTTT
*
38165 CACAATCGAGGATACTCCAAC
1 CACAATCGGGGATACTCCAAC
38186 CCCGTTAATC
Statistics
Matches: 216, Mismatches: 45, Indels: 52
0.69 0.14 0.17
Matches are distributed among these distances:
49 2 0.01
50 4 0.02
51 34 0.16
52 59 0.27
53 34 0.16
54 44 0.20
55 33 0.15
56 4 0.02
57 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (50 bp):
CACAATCGGGGATACTCCAACTCCGATTTTATTTTAAAAACACAAATTTT
Found at i:37987 original size:27 final size:28
Alignment explanation
Indices: 37957--38032 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 28
37947 AATTTTCACA
37957 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
37984 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
38012 -TGAGGGGATACTCCAACCCCG
1 AT-CGGGGATACTCCAACCCCG
38033 ACTTTATTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 25 0.56
28 20 0.44
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:38084 original size:52 final size:52
Alignment explanation
Indices: 38015--38189 Score: 217
Period size: 52 Copynumber: 3.3 Consensus size: 52
38005 TTATTTCTGA
* **
38015 GGGGATACTCCAACCCCGACTTTATTTCCAAAATACTGATTTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACAAATTTTTCCACAATC
* * * **
38067 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACAAATTTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTCCAAAATACAAATTTTTCC-ACAATC
* * *
38120 GGGGATACTCCAACTCCGATTTTATTTTCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACCCCGATTTTA-TTTCCAAAATACAAATTTTTCCACAATC
*
38172 GAGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
38190 TTAATCATCG
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
52 60 0.58
53 27 0.26
54 16 0.16
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGATTTTATTTCCAAAATACAAATTTTTCCACAATC
Found at i:38213 original size:212 final size:211
Alignment explanation
Indices: 37843--38295 Score: 703
Period size: 212 Copynumber: 2.1 Consensus size: 211
37833 AGTTTCTCAA
* * * * *
37843 TTCTCCACAATCGGGGATATTTCAACTCCGATTTTATTTTCAAGACACTAATTTTCTATAATCGG
1 TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACAAATTTTCTATAATCGG
*
37908 GGATACTCCAACTCCGATTTTATTTTAAAAAAAACACCAAATTTTCACAATCGGGGATACTCCAA
66 GGATACTCCAACTCCGATTTTATTTT-AAAAAAACACCAAATTTTCACAATCGAGGATACTCCAA
* *
37973 CCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTT
130 CCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACTCCAACCCCGACTTT
*
38038 ATTTCCAAAATACTGAT
195 ATTCCCAAAATACTGAT
* * *
38055 TTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACAAATTTTTCCTTTAATC
1 TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACAAA-TTTT-CTATAATC
* * *
38120 GGGGATACTCCAACTCCGATTTTATTTT-CAAAAATACCAATTTTTCACAATCGAGGATACTCCA
64 GGGGATACTCCAACTCCGATTTTATTTTAAAAAAACACCAAATTTTCACAATCGAGGATACTCCA
*
38184 ACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACTCCAACCCCGGCTT
129 ACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACTCCAACCCCGACTT
38249 TATTCCCAAAATACTGAT
194 TATTCCCAAAATACTGAT
* *
38267 TTCT-CATAATTGGGGATACTCCAACCCCG
1 TTCTCCACAATCGGGGATACTCCAACCCCG
38296 TTATTTTCGA
Statistics
Matches: 220, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
211 23 0.10
212 158 0.72
213 4 0.02
214 35 0.16
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.30
Consensus pattern (211 bp):
TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACAAATTTTCTATAATCGG
GGATACTCCAACTCCGATTTTATTTTAAAAAAACACCAAATTTTCACAATCGAGGATACTCCAAC
CCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACTCCAACCCCGACTTTA
TTCCCAAAATACTGAT
Found at i:38282 original size:79 final size:79
Alignment explanation
Indices: 38198--38402 Score: 243
Period size: 79 Copynumber: 2.6 Consensus size: 79
38188 CGTTAATCAT
* *
38198 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACTCCAACCCCGGCTTTATTCCCAAA--AT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAAATCAT
* *
38261 ACTGATTTCTCATAAT
66 -C-GATTTCTCACAAC
* * * * * ** *
38277 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTCTAATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAAATCAT
38342 CGATTTCTCACAAC
66 CGATTTCTCACAAC
* * *
38356 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCG
38403 TTATTATCAC
Statistics
Matches: 106, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
79 103 0.97
80 1 0.01
81 2 0.02
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAAATCAT
CGATTTCTCACAAC
Found at i:40810 original size:20 final size:21
Alignment explanation
Indices: 40771--40843 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 21
40761 TTGAGGATAC
*
40771 ATCAATATAATTAGGCCAAATGT
1 ATCAATA-CATTA-GCCAAATGT
* *
40794 ATCGATACA-TAGCCAAAAAGT
1 ATCAATACATTAGCC-AAATGT
*
40815 ATCAATACATTAGCC-TATGT
1 ATCAATACATTAGCCAAATGT
40835 ATCAATACA
1 ATCAATACA
40844 AATGGCCATG
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
20 15 0.36
21 15 0.36
22 6 0.14
23 6 0.14
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (21 bp):
ATCAATACATTAGCCAAATGT
Found at i:40854 original size:20 final size:21
Alignment explanation
Indices: 40813--40863 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
40803 TAGCCAAAAA
*
40813 GTATCAATAC-ATTAGCCTAT
1 GTATCAATACAAATAGCCTAT
*
40833 GTATCAATACAAATGGCC-AT
1 GTATCAATACAAATAGCCTAT
*
40853 GTACCAATACA
1 GTATCAATACA
40864 TTATGGTCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (21 bp):
GTATCAATACAAATAGCCTAT
Found at i:41412 original size:19 final size:20
Alignment explanation
Indices: 41365--41415 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
41355 CACACCCAGA
* *
41365 TGTATCAATACATATTGCTT
1 TGTATCGATACATATTGCAT
* *
41385 TGCATCGATACATGTT-CAT
1 TGTATCGATACATATTGCAT
41404 TGTATCGATACA
1 TGTATCGATACA
41416 CACTAAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTGCAT
Found at i:43101 original size:12 final size:12
Alignment explanation
Indices: 43086--43127 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
43076 AACCATCAAA
*
43086 GATGATAAAGAT
1 GATGATAATGAT
*
43098 GATGATGATGAT
1 GATGATAATGAT
43110 GATGATAATGAT
1 GATGATAATGAT
43122 GATGAT
1 GATGAT
43128 GAGGAAGAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (12 bp):
GATGATAATGAT
Found at i:43103 original size:3 final size:3
Alignment explanation
Indices: 43095--43129 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
43085 AGATGATAAA
*
43095 GAT GAT GAT GAT GAT GAT GAT AAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
43130 GGAAGAGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.37, C:0.00, G:0.31, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:49308 original size:10 final size:9
Alignment explanation
Indices: 49284--49331 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 9
49274 TAGGAGTAGT
49284 TGTT-TTTA
1 TGTTATTTA
49292 T-TTATTTA
1 TGTTATTTA
49300 TGCTTATTTA
1 TG-TTATTTA
49310 TGTTGACTTTA
1 TGTT-A-TTTA
49321 TGTTATTTA
1 TGTTATTTA
49330 TG
1 TG
49332 AGTATGCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
7 2 0.06
8 6 0.17
9 8 0.23
10 11 0.31
11 8 0.23
ACGTcount: A:0.19, C:0.04, G:0.12, T:0.65
Consensus pattern (9 bp):
TGTTATTTA
Found at i:49661 original size:21 final size:23
Alignment explanation
Indices: 49631--49672 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
49621 AAGAAAGCAT
*
49631 AAAATATTTTGTTAAG-GGAGAG
1 AAAATATTTTATTAAGAGGAGAG
49653 AAAA-ATTTTATTAAGAGGAG
1 AAAATATTTTATTAAGAGGAG
49673 TTATATATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.31
Consensus pattern (23 bp):
AAAATATTTTATTAAGAGGAGAG
Found at i:50176 original size:21 final size:21
Alignment explanation
Indices: 50152--50191 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
50142 TTAAGTATAA
*
50152 ATAT-TTTTTAAGATAAAAATC
1 ATATGTTTTCAAG-TAAAAATC
50173 ATATGTTTTCAAGTAAAAA
1 ATATGTTTTCAAGTAAAAA
50192 ATAATCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (21 bp):
ATATGTTTTCAAGTAAAAATC
Found at i:50330 original size:33 final size:32
Alignment explanation
Indices: 50293--50356 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
50283 CACACCCAAA
* *
50293 TGTATCGATACATATTGCTTTTTATCGATACAT
1 TGTATCGATACATATT-CATTGTATCGATACAT
*
50326 TGTATCGATACATGTTCATTGTATCGATACA
1 TGTATCGATACATATTCATTGTATCGATACA
50357 CACTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATATTCATTGTATCGATACAT
Found at i:52652 original size:58 final size:58
Alignment explanation
Indices: 52443--52661 Score: 194
Period size: 58 Copynumber: 3.8 Consensus size: 58
52433 TCTAAAATAT
* * * * * *
52443 ATGAAATTACATTGAAGTTCTTAGATCAAGAAAAATGGCCTAAATGACATCAAAATTC
1 ATGAAATTACACTAAAGTCCTTAAATCATGAAAAATGACCTAAATGACATCAAAATTC
* * * * **
52501 AAGAAGTTACACTAAAATCCCTAAATCAT-AGAAAATGATGTAAATGACATCAAAATTC
1 ATGAAATTACACTAAAGTCCTTAAATCATGA-AAAATGACCTAAATGACATCAAAATTC
* * *
52559 ATAAAATTACA-TCAAAGTCCTTAAATCATGGAAAATGACCTAAATGATATCAAAATAT-
1 ATGAAATTACACT-AAAGTCCTTAAATCATGAAAAATGACCTAAATGACATCAAAAT-TC
* * * * *
52617 ATGAAATTTGCA-TAAAGTCCTTAGATGATGAAAAATTACCCAAAT
1 ATGAAA-TTACACTAAAGTCCTTAAATCATGAAAAATGACCTAAAT
52662 ATGAAATTTG
Statistics
Matches: 128, Mismatches: 28, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
57 2 0.02
58 120 0.94
59 6 0.05
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.27
Consensus pattern (58 bp):
ATGAAATTACACTAAAGTCCTTAAATCATGAAAAATGACCTAAATGACATCAAAATTC
Found at i:52697 original size:45 final size:45
Alignment explanation
Indices: 52615--52707 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 45
52605 ATATCAAAAT
* *
52615 ATATGAAATTTGCATAAAGTCCTTAGATGATGAAAAATTACCCAA
1 ATATGAAATTTGCATAAAGTCCTTAGATCATGAAAAATGACCCAA
* *
52660 ATATGAAATTTGCATAAAATTCC-TAGATCATTG-AAAATGACCTAA
1 ATATGAAATTTGCAT-AAAGTCCTTAGATCA-TGAAAAATGACCCAA
52705 ATA
1 ATA
52708 ACACTAACTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 34 0.81
46 8 0.19
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.30
Consensus pattern (45 bp):
ATATGAAATTTGCATAAAGTCCTTAGATCATGAAAAATGACCCAA
Found at i:52960 original size:2 final size:2
Alignment explanation
Indices: 52953--52982 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52943 ACATTCCTAA
52953 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
52983 CTAAACATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57002 original size:11 final size:10
Alignment explanation
Indices: 56974--57006 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
56964 TTTTACTTCA
56974 TATAAAT-AT
1 TATAAATAAT
56983 TATAAATAAT
1 TATAAATAAT
56993 TATCAAATAAT
1 TAT-AAATAAT
57004 TAT
1 TAT
57007 TTACTTTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 7 0.32
10 5 0.23
11 10 0.45
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (10 bp):
TATAAATAAT
Found at i:57036 original size:17 final size:19
Alignment explanation
Indices: 57001--57038 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
56991 ATTATCAAAT
*
57001 AATTATTTACTTTGCTAAA
1 AATTATTTACTTTGATAAA
57020 AATTA-TTA-TTTGATAAA
1 AATTATTTACTTTGATAAA
57037 AA
1 AA
57039 ACCAAGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 3 0.17
19 5 0.28
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (19 bp):
AATTATTTACTTTGATAAA
Found at i:65334 original size:19 final size:19
Alignment explanation
Indices: 65310--65355 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
65300 GGCAAGCAAG
65310 CATGATGATCATGCAAGAA
1 CATGATGATCATGCAAGAA
65329 CATGATGATCATGCAAGAA
1 CATGATGATCATGCAAGAA
65348 CATGATGA
1 CATGATGA
65356 ATAACACTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (19 bp):
CATGATGATCATGCAAGAA
Found at i:66368 original size:13 final size:13
Alignment explanation
Indices: 66350--66377 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
66340 ATACAAAGAT
66350 CAATGTATCGATA
1 CAATGTATCGATA
66363 CAATGTATCGATA
1 CAATGTATCGATA
66376 CA
1 CA
66378 TTTAAGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:66455 original size:33 final size:33
Alignment explanation
Indices: 66418--66484 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
66408 AGTAGCTTAA
66418 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
66451 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
66484 A
1 A
66485 AATCGTTGAC
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:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:66458 original size:13 final size:13
Alignment explanation
Indices: 66440--66464 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66430 CAAAAAAATA
66440 TGTATCGATACAT
1 TGTATCGATACAT
66453 TGTATCGATACA
1 TGTATCGATACA
66465 ACACTTTATG
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:67231 original size:13 final size:13
Alignment explanation
Indices: 67213--67237 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
67203 CAAAGATCAG
67213 TGTATCGATACAA
1 TGTATCGATACAA
67226 TGTATCGATACA
1 TGTATCGATACA
67238 TTTGGGTAAT
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:67327 original size:13 final size:13
Alignment explanation
Indices: 67309--67333 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
67299 ACAACACTCA
67309 TGTATCGATACAT
1 TGTATCGATACAT
67322 TGTATCGATACA
1 TGTATCGATACA
67334 AATTATTGAA
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:69890 original size:18 final size:18
Alignment explanation
Indices: 69849--69886 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
69839 TTTTAGGGAG
*
69849 TTTAATCAAAATTTTTAA
1 TTTAATCAAAATTATTAA
*
69867 TTTAATTAAAA-TATTAA
1 TTTAATCAAAATTATTAA
69884 TTT
1 TTT
69887 TAATAACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAATCAAAATTATTAA
Found at i:70685 original size:39 final size:39
Alignment explanation
Indices: 70642--70719 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
70632 AGTCTGTTTT
70642 ACCTACTTGATCACTTTATCTTAAAGTTCTATTATACTC
1 ACCTACTTGATCACTTTATCTTAAAGTTCTATTATACTC
70681 ACCTACTTGATCACTTTATCTTAAAGTTCTATTATACTC
1 ACCTACTTGATCACTTTATCTTAAAGTTCTATTATACTC
70720 TCTATTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (39 bp):
ACCTACTTGATCACTTTATCTTAAAGTTCTATTATACTC
Found at i:75781 original size:41 final size:41
Alignment explanation
Indices: 75706--75783 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
75696 AATACTTGAT
*
75706 ATTGTATCGATACAATATAGCCCTATATCAATACAATGGGC
1 ATTGTATCGATACAACATAGCCCTATATCAATACAATGGGC
* * * * *
75747 ATTGTATCGATATAACATGGCCTTGTATCGATACAAT
1 ATTGTATCGATACAACATAGCCCTATATCAATACAAT
75784 CCATGTTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (41 bp):
ATTGTATCGATACAACATAGCCCTATATCAATACAATGGGC
Found at i:76602 original size:21 final size:21
Alignment explanation
Indices: 76576--76632 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
76566 AACTAAGTGC
*
76576 ATGTATCAATGCATTCACTAT
1 ATGTATCAATACATTCACTAT
* *
76597 ATGTATCGATACATTCACTAA
1 ATGTATCAATACATTCACTAT
* *
76618 AAGTATTAATACATT
1 ATGTATCAATACATT
76633 TCAGTGTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.37
Consensus pattern (21 bp):
ATGTATCAATACATTCACTAT
Found at i:85667 original size:19 final size:20
Alignment explanation
Indices: 85625--85676 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 20
85615 TACAGGCCAA
85625 TGTATCGATACAACTTTATG
1 TGTATCGATACAACTTTATG
85645 TGTATCGATACATAC-TT-TG
1 TGTATCGATACA-ACTTTATG
85664 TGTATCGATACAA
1 TGTATCGATACAA
85677 GTTTGGCTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.03
19 14 0.45
20 14 0.45
21 2 0.06
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATCGATACAACTTTATG
Found at i:88236 original size:13 final size:13
Alignment explanation
Indices: 88218--88255 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
88208 ATAATCCCCC
88218 TGTATCGATACAG
1 TGTATCGATACAG
*
88231 TGTATCGATACAT
1 TGTATCGATACAG
88244 TGTATCGATACA
1 TGTATCGATACA
88256 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:90346 original size:15 final size:15
Alignment explanation
Indices: 90326--90356 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
90316 ATTTCGTTTG
*
90326 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
90341 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
90356 G
1 G
90357 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:94443 original size:13 final size:13
Alignment explanation
Indices: 94425--94450 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
94415 CAACTTTATG
94425 TGTATCGATACAT
1 TGTATCGATACAT
94438 TGTATCGATACAT
1 TGTATCGATACAT
94451 ACTTTGTGTA
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:94464 original size:32 final size:33
Alignment explanation
Indices: 94405--94468 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
94395 TACAGGCCAA
94405 TGTATCGATACAACTTTATGTGTATCGATACAT
1 TGTATCGATACAACTTTATGTGTATCGATACAT
94438 TGTATCGATACATAC-TT-TGTGTATCGATACA
1 TGTATCGATACA-ACTTTATGTGTATCGATACA
94469 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 14 0.47
33 14 0.47
34 2 0.07
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAACTTTATGTGTATCGATACAT
Found at i:95802 original size:13 final size:13
Alignment explanation
Indices: 95784--95809 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
95774 CAACTTTATG
95784 TGTATCGATACAT
1 TGTATCGATACAT
95797 TGTATCGATACAT
1 TGTATCGATACAT
95810 ACTTTGTGTA
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:95823 original size:32 final size:33
Alignment explanation
Indices: 95764--95827 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
95754 TACAGGCCAA
95764 TGTATCGATACAACTTTATGTGTATCGATACAT
1 TGTATCGATACAACTTTATGTGTATCGATACAT
95797 TGTATCGATACATAC-TT-TGTGTATCGATACA
1 TGTATCGATACA-ACTTTATGTGTATCGATACA
95828 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 14 0.47
33 14 0.47
34 2 0.07
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAACTTTATGTGTATCGATACAT
Found at i:99199 original size:3 final size:3
Alignment explanation
Indices: 99191--99216 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
99181 GGCTTTCTTG
99191 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
99217 ATGGCTAATT
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:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:99454 original size:40 final size:40
Alignment explanation
Indices: 99399--99478 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
99389 TATTGAGAGA
99399 AATGTGATTGTAAAATTCTATCCTGCATTGGTTGTAGACT
1 AATGTGATTGTAAAATTCTATCCTGCATTGGTTGTAGACT
*
99439 AATGTGATTGTAAAATTCTATGCTGCATTGGTTGTAGACT
1 AATGTGATTGTAAAATTCTATCCTGCATTGGTTGTAGACT
99479 TGGCCTATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (40 bp):
AATGTGATTGTAAAATTCTATCCTGCATTGGTTGTAGACT
Found at i:102198 original size:15 final size:16
Alignment explanation
Indices: 102180--102212 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
102170 AGATTACTTA
*
102180 TTATTTTT-TTTAAAT
1 TTATTTTTATCTAAAT
102195 TTATTTTTATCTAAAT
1 TTATTTTTATCTAAAT
102211 TT
1 TT
102213 TTAATAGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTTATCTAAAT
Found at i:102390 original size:14 final size:17
Alignment explanation
Indices: 102365--102401 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
102355 TTATATATAT
102365 ATTTTTTATCCT-TTC-
1 ATTTTTTATCCTCTTCA
102380 ATTTTTT-TCCTCTTCA
1 ATTTTTTATCCTCTTCA
102396 ATTTTT
1 ATTTTT
102402 CATATATCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 10 0.50
16 6 0.30
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTTTATCCTCTTCA
Found at i:103861 original size:79 final size:79
Alignment explanation
Indices: 103725--103881 Score: 269
Period size: 79 Copynumber: 2.0 Consensus size: 79
103715 TGATTTCCTC
* *
103725 CTTAAAACTATGACATCTTTACCACTCCAACAAGAGCTAATCGTGCTCAATGTCCACATTGCTAG
1 CTTAAAACTATGACATCTTTACCACTCCAACAAGAGCTAATAGTGCTCAATGGCCACATTGCTAG
*
103790 TAATCCTTAAACTT
66 TAATCATTAAACTT
*
103804 CTTAAAACTATGACATCTTTACCACTCCAACAAGAGCTCATAGTGCTCAATGGCCACATTGCTAG
1 CTTAAAACTATGACATCTTTACCACTCCAACAAGAGCTAATAGTGCTCAATGGCCACATTGCTAG
*
103869 TACTCATTAAACT
66 TAATCATTAAACT
103882 AGCTCTTATG
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (79 bp):
CTTAAAACTATGACATCTTTACCACTCCAACAAGAGCTAATAGTGCTCAATGGCCACATTGCTAG
TAATCATTAAACTT
Found at i:107394 original size:25 final size:25
Alignment explanation
Indices: 107329--107404 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 25
107319 ATATTAATGA
107329 ATTATATTTATATA-TTTTAATAATAT
1 ATTAT-TTTATATATTTTTAA-AATAT
*
107355 -TTATTTT-TAAAATTTTTAAAATAT
1 ATTATTTTAT-ATATTTTTAAAATAT
*
107379 ATTATTTTATATATTTATTTAAATAT
1 ATTATTTTATATATTT-TTAAAATAT
107405 TTTAATTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
23 1 0.02
24 10 0.24
25 22 0.52
26 9 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTTATATATTTTTAAAATAT
Found at i:107419 original size:37 final size:38
Alignment explanation
Indices: 107336--107420 Score: 88
Period size: 38 Copynumber: 2.2 Consensus size: 38
107326 TGAATTATAT
107336 TTATATATTTTAATAATATTTATTTTTAAAATTTTTAAAA
1 TTAT-TATTTTAATAATATTTA-TTTTAAAATTTTTAAAA
107376 TATATTATTTT-AT-ATATTTA-TTT-AAATATTTTAATTAA
1 T-TATTATTTTAATAATATTTATTTTAAAAT-TTTTAA--AA
107414 TTATTAT
1 TTATTAT
107421 ATAAATATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
35 4 0.10
36 9 0.22
37 6 0.15
38 10 0.24
39 2 0.05
40 7 0.17
41 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (38 bp):
TTATTATTTTAATAATATTTATTTTAAAATTTTTAAAA
Done.