Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2451
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: 93489
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:896 original size:50 final size:50
Alignment explanation
Indices: 837--967 Score: 183
Period size: 50 Copynumber: 2.6 Consensus size: 50
827 ATGCCTGAAA
* * *
837 GTATCGATAC-ATTAAGAAATGTATCGATACATCTCGGTAAAACCCAAAAT
1 GTATCGATACAATGAA-TAATGTATCGATACATCTAGGTAAAACCCAAAAT
* * * *
887 GTATCGATACAATGAATAATGTGTCAATACATCTAGGTAAAACCTAGAAT
1 GTATCGATACAATGAATAATGTATCGATACATCTAGGTAAAACCCAAAAT
937 GTATCGATACAATGAATAATGTATCGATACA
1 GTATCGATACAATGAATAATGTATCGATACA
968 AATTATGGAA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 67 0.94
51 4 0.06
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (50 bp):
GTATCGATACAATGAATAATGTATCGATACATCTAGGTAAAACCCAAAAT
Found at i:5630 original size:20 final size:20
Alignment explanation
Indices: 5605--5642 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5595 ATCTTGGTTT
5605 TGAATTGTATCGATACATAA
1 TGAATTGTATCGATACATAA
5625 TGAATTGTATCGATACAT
1 TGAATTGTATCGATACAT
5643 TGTCCCAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (20 bp):
TGAATTGTATCGATACATAA
Found at i:10088 original size:67 final size:67
Alignment explanation
Indices: 9906--10081 Score: 210
Period size: 67 Copynumber: 2.6 Consensus size: 67
9896 TTAACAGCCA
* * * * *
9906 AAACTGATAACAAGCTAAAGTAAAAGATCATAATG-GGGAATATGTGGTTACCATCAATAGCCGA
1 AAACTGATAACAAGCTAGAGTAAAAGATCATGATGAGGG-ATATGTGGTTACCATCAACAACCAA
9970 AAT
65 AAT
* * *** * *
9973 AAACTAATAACAAGCTGGAGTAAAAGATCATGATGAGATTTATGTGGTTCCCATCAACAACTAAA
1 AAACTGATAACAAGCTAGAGTAAAAGATCATGATGAGGGATATGTGGTTACCATCAACAACCAAA
10038 AT
66 AT
* *
10040 GAATTGATAACAAGCTAGAGTAAAAGATCATGATGAGGGATA
1 AAACTGATAACAAGCTAGAGTAAAAGATCATGATGAGGGATA
10082 CATGGTTATA
Statistics
Matches: 89, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
67 88 0.99
68 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.23
Consensus pattern (67 bp):
AAACTGATAACAAGCTAGAGTAAAAGATCATGATGAGGGATATGTGGTTACCATCAACAACCAAA
AT
Found at i:12324 original size:26 final size:26
Alignment explanation
Indices: 12288--12340 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
12278 GATTTGTCTT
*
12288 TATCTTTAA-GGATACTCTAACTCCAC
1 TATCTCTAAGGGATACTCTAAC-CCAC
12314 TATCTCTAAGGGATACTCTAACCCAC
1 TATCTCTAAGGGATACTCTAACCCAC
12340 T
1 T
12341 TTTACTTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.32
Consensus pattern (26 bp):
TATCTCTAAGGGATACTCTAACCCAC
Found at i:12451 original size:80 final size:80
Alignment explanation
Indices: 12246--12655 Score: 351
Period size: 80 Copynumber: 5.1 Consensus size: 80
12236 CAAAAAAGGG
* * * * * * * * * *
12246 TACTCCAACCACGTGTTTACTTCTAAAATGTCGATTTGTCTTTATCTTTAAGGATACTCTAACTC
1 TACTCCAACCTCGTTTTTACTTCCAAAATGCCAAATT-T-TTCATCTTTAGGGATACTCCAACCC
* *
12311 CACTATCTCTAAG-GGA
64 CACCATCTCCAAGAGGA
* ** * * * **
12327 TACTCTAACC-CACTTTTACTTCCAAAATGCTAAATTTTGCATCTTTAGGGATACTCTAACCTTA
1 TACTCCAACCTCGTTTTTACTTCCAAAATGCCAAATTTTTCATCTTTAGGGATACTCCAACCCCA
*
12391 CCATCTCCAAGGGGA
66 CCATCTCCAAGAGGA
* * * * *
12406 TACTCCAA-TTCTGTTTTTACTTCCAAAATGCCAAATTTTTTATCTTAAGGGATACTCCAATCCT
1 TACTCCAACCTC-GTTTTTACTTCCAAAATGCCAAATTTTTCATCTTTAGGGATACTCCAACCCC
* *
12470 GCTATCTCCAAGAGGA
65 ACCATCTCCAAGAGGA
* * * *
12486 TACTTCAACCTCGTTTTTACTTCCAAAATGCCAAACTTTTCATCTCTGGGGATACTCCAACCCCA
1 TACTCCAACCTCGTTTTTACTTCCAAAATGCCAAATTTTTCATCTTTAGGGATACTCCAACCCCA
** *
12551 CCATCTCTGAGGGGA
66 CCATCTCCAAGAGGA
* * **** * * *
12566 TAC-CTCAACCTCATTTTTACTTTCAAAACATTAAATTCTTCATCTTTGGGGATACTCTAACCCC
1 TACTC-CAACCTCGTTTTTACTTCCAAAATGCCAAATTTTTCATCTTTAGGGATACTCCAACCCC
*
12630 ACCATCTCCTAGAGGA
65 ACCATCTCCAAGAGGA
12646 TACTCCAACC
1 TACTCCAACC
12656 CTGGTTTTCA
Statistics
Matches: 264, Mismatches: 59, Indels: 13
0.79 0.18 0.04
Matches are distributed among these distances:
78 30 0.11
79 12 0.05
80 210 0.80
81 12 0.05
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (80 bp):
TACTCCAACCTCGTTTTTACTTCCAAAATGCCAAATTTTTCATCTTTAGGGATACTCCAACCCCA
CCATCTCCAAGAGGA
Found at i:15855 original size:13 final size:13
Alignment explanation
Indices: 15837--15864 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
15827 ACTTTTTACC
15837 ATGTATCGATACA
1 ATGTATCGATACA
15850 ATGTATCGATACA
1 ATGTATCGATACA
15863 AT
1 AT
15865 ATCCCATGTA
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:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:15856 original size:33 final size:33
Alignment explanation
Indices: 15814--15882 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
15804 GCCGTTGGGC
** *
15814 ACAATGTATCGATACTTTTTACCATGTATCGAT
1 ACAATGTATCGATACAATATACCATGTATCGAT
*
15847 ACAATGTATCGATACAATATCCCATGTATCGAT
1 ACAATGTATCGATACAATATACCATGTATCGAT
15880 ACA
1 ACA
15883 TTTCACTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (33 bp):
ACAATGTATCGATACAATATACCATGTATCGAT
Found at i:15954 original size:19 final size:20
Alignment explanation
Indices: 15911--15957 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
15901 CTGTCAGTTT
15911 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
*
15931 TATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGAG
15950 CATGTATC
1 CATGTATC
15958 AATATAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:23155 original size:3 final size:3
Alignment explanation
Indices: 23141--23175 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
23131 CGAGTCAACT
* *
23141 TCA TCA TTA TCA TCA TCA TCA TCA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
23176 TTTGATGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (3 bp):
TCA
Found at i:23175 original size:9 final size:9
Alignment explanation
Indices: 23139--23177 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
23129 TCCGAGTCAA
23139 CTTCATCAT
1 CTTCATCAT
23148 -TATCATCAT
1 CT-TCATCAT
*
23157 CATCATCAT
1 CTTCATCAT
23166 CTTCATCAT
1 CTTCATCAT
23175 CTT
1 CTT
23178 TGATGGTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
8 1 0.04
9 25 0.96
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.44
Consensus pattern (9 bp):
CTTCATCAT
Found at i:26988 original size:18 final size:18
Alignment explanation
Indices: 26962--27004 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
26952 TAGAGATCAA
26962 AGCTTTCAAAGTTCAAAG
1 AGCTTTCAAAGTTCAAAG
* * *
26980 AGTTTTCAAATTTCCAAG
1 AGCTTTCAAAGTTCAAAG
26998 AGCTTTC
1 AGCTTTC
27005 GTTTTCATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (18 bp):
AGCTTTCAAAGTTCAAAG
Found at i:32908 original size:13 final size:13
Alignment explanation
Indices: 32890--32927 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
32880 CATTCCTTGC
*
32890 ATCGATACATTCT
1 ATCGATACATTAT
*
32903 ATCGATACAATAT
1 ATCGATACATTAT
32916 ATCGATACATTA
1 ATCGATACATTA
32928 GGTACTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (13 bp):
ATCGATACATTAT
Found at i:35375 original size:13 final size:13
Alignment explanation
Indices: 35357--35383 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35347 ACATGCTGCT
35357 TTGTATCGATACA
1 TTGTATCGATACA
35370 TTGTATCGATACA
1 TTGTATCGATACA
35383 T
1 T
35384 GTTCATTTTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:35380 original size:33 final size:32
Alignment explanation
Indices: 35338--35402 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
35328 CATACCCAGA
35338 TGTATCGATACATGCTGC-TTTGTATCGATACAT
1 TGTATCGATACATG-TGCATTT-TATCGATACAT
*
35371 TGTATCGATACATGTTCATTTTATCGATACAT
1 TGTATCGATACATGTGCATTTTATCGATACAT
35403 GTTCATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.43
33 17 0.57
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATGTGCATTTTATCGATACAT
Found at i:35395 original size:19 final size:19
Alignment explanation
Indices: 35368--35442 Score: 105
Period size: 19 Copynumber: 3.9 Consensus size: 19
35358 TGTATCGATA
35368 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGTT
*
35387 CATTTTATCGATACATGTT
1 CATTGTATCGATACATGTT
* **
35406 CATTTTATCGATACATGGA
1 CATTGTATCGATACATGTT
35425 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
35443 AAACTGGCAG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 36 0.71
20 15 0.29
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (19 bp):
CATTGTATCGATACATGTT
Found at i:36260 original size:13 final size:13
Alignment explanation
Indices: 36242--36267 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36232 CAATTTTTTG
36242 TGTATCGATACAT
1 TGTATCGATACAT
36255 TGTATCGATACAT
1 TGTATCGATACAT
36268 ACTTGCTGTA
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:36352 original size:20 final size:20
Alignment explanation
Indices: 36327--36399 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
36317 CATCCTTTTT
36327 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
36347 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
36368 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
36388 ATGTATCGATAC
1 ATGTATCGATAC
36400 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:36372 original size:21 final size:21
Alignment explanation
Indices: 36306--36382 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
36296 CTGCCAAGAA
*
36306 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
36327 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
36347 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
36368 ATGTATCGATACATT
1 ATGTATCGATACATT
36383 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:36372 original size:41 final size:41
Alignment explanation
Indices: 36306--36399 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
36296 CTGCCAAGAA
36306 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
36347 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
36388 ATGTATCGATAC
1 ATGTATCGATAC
36400 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:38858 original size:13 final size:13
Alignment explanation
Indices: 38840--38878 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
38830 ATAATCACCC
*
38840 TGTATCGATACAG
1 TGTATCGATACAA
38853 TGTATCGATACAA
1 TGTATCGATACAA
38866 TGTATCGATACAA
1 TGTATCGATACAA
38879 GGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:40977 original size:15 final size:15
Alignment explanation
Indices: 40957--40987 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40947 ATTTCGTTTG
*
40957 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
40972 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
40987 G
1 G
40988 GATATTTTTA
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:45068 original size:13 final size:13
Alignment explanation
Indices: 45050--45075 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45040 CAATTTTTTG
45050 TGTATCGATACAT
1 TGTATCGATACAT
45063 TGTATCGATACAT
1 TGTATCGATACAT
45076 ACTTGCTGTA
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:45160 original size:20 final size:20
Alignment explanation
Indices: 45135--45207 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
45125 CATCCTTTTT
45135 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
45155 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
45176 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
45196 ATGTATCGATAC
1 ATGTATCGATAC
45208 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:45180 original size:21 final size:21
Alignment explanation
Indices: 45114--45190 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
45104 CTGCCAAGAA
*
45114 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
45135 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
45155 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
45176 ATGTATCGATACATT
1 ATGTATCGATACATT
45191 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:45180 original size:41 final size:41
Alignment explanation
Indices: 45114--45207 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
45104 CTGCCAAGAA
45114 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
45155 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
45196 ATGTATCGATAC
1 ATGTATCGATAC
45208 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:45540 original size:33 final size:32
Alignment explanation
Indices: 45498--45579 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 32
45488 AGATCCTAAC
* *
45498 AAATATATCGATATATTGTATCGATACATG-G
1 AAATGTATCGATACATTGTATCGATACATGAG
45529 TACAATGTATCGATACATTGTATCGATACATGAAG
1 -A-AATGTATCGATACATTGTATCGATACATG-AG
45564 AAATGTATCGATACAT
1 AAATGTATCGATACAT
45580 AGCTTGTAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
32 1 0.02
33 42 0.93
34 1 0.02
35 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (32 bp):
AAATGTATCGATACATTGTATCGATACATGAG
Found at i:45550 original size:13 final size:13
Alignment explanation
Indices: 45529--45559 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
45519 CGATACATGG
*
45529 TACAATGTATCGA
1 TACATTGTATCGA
45542 TACATTGTATCGA
1 TACATTGTATCGA
45555 TACAT
1 TACAT
45560 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:49456 original size:20 final size:20
Alignment explanation
Indices: 49431--49550 Score: 87
Period size: 20 Copynumber: 5.7 Consensus size: 20
49421 TTTTATCCAG
49431 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTTA
* * *
49451 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTTA
* **
49471 ATGTATCGATGCATTTTCAA
1 ATGTATCGATACATTTTTTA
**
49491 ATGTATTAATACATTGTGTTTTTCAA
1 ATGTATCGATACA---T-TTTTT--A
** *
49517 ATGTATTAATACATTTTTCA
1 ATGTATCGATACATTTTTTA
49537 ATGTATCGATACAT
1 ATGTATCGATACAT
49551 CTAGTTAATT
Statistics
Matches: 78, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
20 55 0.71
22 4 0.05
23 2 0.03
24 3 0.04
26 14 0.18
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTA
Found at i:51853 original size:97 final size:96
Alignment explanation
Indices: 51703--51929 Score: 330
Period size: 97 Copynumber: 2.3 Consensus size: 96
51693 GGGGATACTT
* * *
51703 CAACCCTATTTCTCCGAGGGGATACTCCAACCCCGCTTTTAAACTCATTAAAGTTTAAATCTTAT
1 CAACCCTA-TTCTCCGAGGAGATACTCCAACCCCACTTTTAAACTCATCAAAGTTTAAATCTTAT
51768 TCTTGCTTAAATTGTCATCATCGAGAACACTC
65 TCTTGCTTAAATTGTCATCATCGAGAACACTC
* *
51800 CAACCCTATTCCTCCGAGGAGATACTCCAACCCCACTTTTAAATTTATCAAAGTTTAAATCTTAT
1 CAACCCTATT-CTCCGAGGAGATACTCCAACCCCACTTTTAAACTCATCAAAGTTTAAATCTTAT
* * *
51865 TTTTGCTTAAATTGTCATCATCGGGGACACTC
65 TCTTGCTTAAATTGTCATCATCGAGAACACTC
*
51897 CAACCCCATATCTCCGA-GAGGATACTCCAACCC
1 CAACCCTAT-TCTCCGAGGA-GATACTCCAACCC
51930 TGTTTTTCAA
Statistics
Matches: 118, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
96 4 0.03
97 113 0.96
98 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (96 bp):
CAACCCTATTCTCCGAGGAGATACTCCAACCCCACTTTTAAACTCATCAAAGTTTAAATCTTATT
CTTGCTTAAATTGTCATCATCGAGAACACTC
Found at i:53515 original size:197 final size:197
Alignment explanation
Indices: 53180--53575 Score: 686
Period size: 197 Copynumber: 2.0 Consensus size: 197
53170 GGAAACTTTA
* *** *
53180 AGGGTTGAAGCTATCCCTTATTTTTGGGAAACGATGATTTTTCTAGGTTTTATTCCAATTTTTTT
1 AGGGTTGAAGCTATCCCTTATTTTTGGGAAACAATGATTTTTCTAGGTGGCATTCCAATGTTTTT
* *
53245 GAGGTGTTCGAATACCTTGAAATTGATGTTAGGGGTGTCATTATAAGAGTTCAAAGGTATTTCAA
66 GAGGTGTTCGAATACCTTGAAATTGATGTTAAGGGTGTCATTATAAGAATTCAAAGGTATTTCAA
53310 TGTTGAGTTTAGGTTTCTAAAGGTTCGTCATAAGAATTGTGAATTTTCACAAAAATAAATCAAGC
131 TGTTGAGTTTAGGTTTCTAAAGGTTCGTCATAAGAATTGTGAATTTTCACAAAAATAAATCAAGC
53375 TT
196 TT
* *
53377 AGGGTTGATGCTATCCCTTATTTTTGGGAAACAATGATTTTT-TTGGATGGCATTCCAATGTTTT
1 AGGGTTGAAGCTATCCCTTATTTTTGGGAAACAATGATTTTTCTAGG-TGGCATTCCAATGTTTT
*
53441 TGAGGTGTTTGAATACCTTGAAATTGATGTTAAGGGTGTCATTATAAGAATTCAAAGGTATTTCA
65 TGAGGTGTTCGAATACCTTGAAATTGATGTTAAGGGTGTCATTATAAGAATTCAAAGGTATTTCA
53506 ATGTTGAGTTTAGGTTTCTAAAGGTTCGTCATAAGAATTGTGAATTTTCACAAAAATAAATCAAG
130 ATGTTGAGTTTAGGTTTCTAAAGGTTCGTCATAAGAATTGTGAATTTTCACAAAAATAAATCAAG
53571 CTT
195 CTT
53574 AG
1 AG
53576 TTTTCCTAGT
Statistics
Matches: 188, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
196 3 0.02
197 185 0.98
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (197 bp):
AGGGTTGAAGCTATCCCTTATTTTTGGGAAACAATGATTTTTCTAGGTGGCATTCCAATGTTTTT
GAGGTGTTCGAATACCTTGAAATTGATGTTAAGGGTGTCATTATAAGAATTCAAAGGTATTTCAA
TGTTGAGTTTAGGTTTCTAAAGGTTCGTCATAAGAATTGTGAATTTTCACAAAAATAAATCAAGC
TT
Found at i:57995 original size:20 final size:20
Alignment explanation
Indices: 57972--58117 Score: 139
Period size: 20 Copynumber: 6.8 Consensus size: 20
57962 AAAAAGACAG
*
57972 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTGAAA
* * *
57992 AATGTATCGATATATTCATA
1 AATGTATCGATACATTGAAA
*
58012 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
58032 AATGTATCGATACATCTGGGTAAAAAAACAA
1 AATGTATCGATACAT-T--G-------A-AA
*
58063 AATGTATCGATACATTGAAG
1 AATGTATCGATACATTGAAA
58083 AATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
58103 AATGTATCGATACAT
1 AATGTATCGATACAT
58118 CTGGGTAAAA
Statistics
Matches: 104, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
20 81 0.78
21 2 0.02
23 1 0.01
28 1 0.01
30 2 0.02
31 17 0.16
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:58108 original size:91 final size:92
Alignment explanation
Indices: 57921--58117 Score: 290
Period size: 91 Copynumber: 2.2 Consensus size: 92
57911 TTTTAACTAG
**** *
57921 ATGTATCGATACATTTTTCAATGTATCGATACATCTAGGGAAAAAAGACAGAATGTATCGATACA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGGAAAAAAGACAAAATGTATCGATACA
* * *
57986 TTGAAGAATGTATCGATATATTCATAC
66 TTGAAGAATGTATCGATACATTCAAAA
58013 ATGTATCGATACATTGAAAAATGTATCGATACATCT-GGGTAAAAAA-ACAAAATGTATCGATAC
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGG-AAAAAAGACAAAATGTATCGATAC
*
58076 ATTGAAGAATGTATCGATACATTGAAAA
65 ATTGAAGAATGTATCGATACATTCAAAA
58104 ATGTATCGATACAT
1 ATGTATCGATACAT
58118 CTGGGTAAAA
Statistics
Matches: 95, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
91 57 0.60
92 38 0.40
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (92 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGGAAAAAAGACAAAATGTATCGATACA
TTGAAGAATGTATCGATACATTCAAAA
Found at i:58962 original size:28 final size:28
Alignment explanation
Indices: 58883--59957 Score: 1015
Period size: 28 Copynumber: 37.0 Consensus size: 28
58873 TAGAGAAAGT
* *
58883 TGCCACCGACTTGTGTAGGCTTTAAAAGGA
1 TGCCACTGACTTGTG--GGCTTTGAAAGGA
** *
58913 TGCCACTGACTTGTGGATTTTGTGAA-GA
1 TGCCACTGACTTGTGGGCTTTG-AAAGGA
* *
58941 TGCCTCTGACTTGTGGGCTTTGAAAAGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
58969 TGCCATTAACTTATGGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
58997 TGCCACCGACTCGTGGGCTTTGGAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
*
59025 TGCCACTGACTTATGGGCTTTG-AAGAGA
1 TGCCACTGACTTGTGGGCTTTGAAAG-GA
*
59053 TGCCACTGACTTGTAGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
*
59081 TGCCACTGACTCGTGGGCTTTGAAAAGGA
1 TGCCACTGACTTGTGGGCTTTG-AAAGGA
**
59110 TGCCACTGACTCATGGGCTTTGAAAAGGA
1 TGCCACTGACTTGTGGGCTTTG-AAAGGA
*
59139 TGCCACTGACTTGTGGAC-TTGAAAAGGA
1 TGCCACTGACTTGTGGGCTTTG-AAAGGA
* *
59167 TGCCATTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
59195 TGCCACTAACTTATGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
59223 TGCCACTAATTTGTGGGCTTGGAAAAGGA
1 TGCCACTGACTTGTGGGCTTTG-AAAGGA
* * *
59252 TGCCACTGACTTATGGACATTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
59280 TGCCACTGACTTGTGGGCTTTGAAAGGGA
1 TGCCACTGACTTGTGGGCTTTGAAA-GGA
*
59309 TGCCACTGACTT-TGGACTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
59336 TGCCACTGACTTGTGAGCTTTGAAAGGC
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
*
59364 TGCCACTGACTTGTGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
59392 TGGCACTGACTTATGGGCTTTGAAAGGG
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
59420 TGCCACTAACTTGTGGACTTTGAAATAGGT
1 TGCCACTGACTTGTGGGCTTTG-AA-AGGA
** * *
59450 TGCCACCAACTTGTGTGGGCTTTCAAATGAGT
1 TGCCACTGAC-T-TGTGGGCTTTGAAA-G-GA
* * *
59482 TTCCACTGACTTGTGTGAGCTTTTAAATGA
1 TGCCACTGACTTGTG-G-GCTTTGAAAGGA
* *
59512 TGCCACTAACTTGTGGGCTTTGAAATGGGT
1 TGCCACTGACTTGTGGGCTTTGAAA--GGA
*
59542 TGCCACTGACTTTTGTGGGCTTTGAAACGGGT
1 TGCCACTGAC--TTGTGGGCTTTGAAA--GGA
* * * *
59574 TGCCACCGACTTGTGTAAGCTTTCAAATGAGT
1 TGCCACTGACTTGTG--GGCTTTGAAA-G-GA
* * *
59606 TGCCACCGACTGTTGTGGGCTTTCAAATGAGT
1 TGCCACTGAC--TTGTGGGCTTTGAAA-G-GA
* *
59638 TGCCACTAACTTGTGGGCTTTGAAATGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
59666 TGCCACTAACTTATGGGCTTTGAGAAGGA
1 TGCCACTGACTTGTGGGCTTTGA-AAGGA
*
59695 TGCCACTGACTTATGGGCTTTGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
*
59723 TGCCACTGACTTGTGGGCTTTGAAATGGGT
1 TGCCACTGACTTGTGGGCTTTGAAA--GGA
* *
59753 TGCCACCGACTTGTGTGGCCTTTGAAATGGGT
1 TGCCACTGACTTGTG-GG-CTTTGAAA--GGA
* * *
59785 TGCCACCGACTTGTGTGGGCTTTCAAATGAGT
1 TGCCACTGAC-T-TGTGGGCTTTGAAA-G-GA
* *
59817 TGCCACCGACTTGTGTGGGCTTTGAAATGA
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGGA
* *
59847 TGCCACCGACTTGTGGGCTTTGAAATGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
59875 TGCCACCGACTTGTGGGCTTTGAATGGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* * *
59903 TGCCATTGACTTATGGGCTTTGAAATGA
1 TGCCACTGACTTGTGGGCTTTGAAAGGA
* *
59931 TGCCACTAACTTGTGGGCTTTAAAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAGG
59958 GTGCTGCCGC
Statistics
Matches: 899, Mismatches: 112, Indels: 70
0.83 0.10 0.06
Matches are distributed among these distances:
27 20 0.02
28 479 0.53
29 123 0.14
30 101 0.11
31 10 0.01
32 154 0.17
33 3 0.00
34 9 0.01
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.30
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGA
Found at i:60000 original size:27 final size:27
Alignment explanation
Indices: 59962--60391 Score: 490
Period size: 27 Copynumber: 15.7 Consensus size: 27
59952 AAAAGGGTGC
*
59962 TGCCGCGGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
59989 TGCCATGAAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
** * *
60016 TGCCATAGAGTTATGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
60043 TGCCACAGAGTGGTGGACTTTAAAA-GA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
*
60070 GTGCCACGGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGA
* *
60098 TGCCACGGAGTTGTGGATTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
60125 TACCACGGAGTGGTGGACTTTAAAA-GA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
* *
60152 GTGCCACTGAGTTGTGGACTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGA
* * *
60180 TGCTACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
60207 TGCCATGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
*
60235 TGCCACAGAGTTGTGGACTTTAAAAGG-
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
* *
60262 TGCCACAGTGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
*
60289 TACCACGGAGTTGTGGACTTTAAAAGTG-
1 TGCCACGGAGTTGTGGAC-TTAAAAG-GA
* *
60317 TGCCATGGAGTAGTGGACTTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
*
60345 TGCCACGGAGTTGTGGACTTAAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
*
60372 TGTCACGGAGTTGTGGACTT
1 TGCCACGGAGTTGTGGACTT
60392 TGTGTAGACA
Statistics
Matches: 351, Mismatches: 41, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
26 8 0.02
27 217 0.62
28 125 0.36
29 1 0.00
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:60075 original size:82 final size:82
Alignment explanation
Indices: 59962--60392 Score: 539
Period size: 82 Copynumber: 5.3 Consensus size: 82
59952 AAAAGGGTGC
* *
59962 TGCCGCGGAGTTGTGGAC-TTAAAAG-GATGCCATGAAGTTGTGGACTTAAAAGGATGCCATAGA
1 TGCCACGGAGTTGTGGACTTTAAAAGAG-TGCCATGAAGTTGTGGACTTAAAAGGATGCCACAGA
*
60025 GTTATGGACTTAAAAGGG
65 GTTGTGGACTTAAAAGGG
* * * * * *
60043 TGCCACAGAGTGGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAG
1 TGCCACGGAGTTGTGGACTTTAAAAGAGTGCCATGAAGTTGTGGACTTAAAAGGATGCCACAGAG
*
60108 TTGTGGATTTAAAAGGG
66 TTGTGGACTTAAAAGGG
* * * *
60125 TACCACGGAGTGGTGGACTTTAAAAGAGTGCCACTG-AGTTGTGGACTTAAAAGGGTGCTACAGA
1 TGCCACGGAGTTGTGGACTTTAAAAGAGTGCCA-TGAAGTTGTGGACTTAAAAGGATGCCACAGA
60189 GTTGTGGACTTAAAAGGG
65 GTTGTGGACTTAAAAGGG
* * *
60207 TGCCATGGAGTTGTGGACTTTAAAAGGGTGCCA-CAGAGTTGTGGACTTTAAAAGG-TGCCACAG
1 TGCCACGGAGTTGTGGACTTTAAAAGAGTGCCATGA-AGTTGTGGAC-TTAAAAGGATGCCACAG
* *
60270 TGTTGTGGACTTAAAAGGA
64 AGTTGTGGACTTAAAAGGG
* * * * *
60289 TACCACGGAGTTGTGGACTTTAAAAGTGTGCCATGGAGTAGTGGACTTTAAAAGGATGCCACGGA
1 TGCCACGGAGTTGTGGACTTTAAAAGAGTGCCATGAAGTTGTGGAC-TTAAAAGGATGCCACAGA
* *
60354 GTTGTGGACTTAAAAAGA
65 GTTGTGGACTTAAAAGGG
*
60372 TGTCACGGAGTTGTGGACTTT
1 TGCCACGGAGTTGTGGACTTT
60393 GTGTAGACAC
Statistics
Matches: 307, Mismatches: 35, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
81 15 0.05
82 239 0.78
83 53 0.17
ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26
Consensus pattern (82 bp):
TGCCACGGAGTTGTGGACTTTAAAAGAGTGCCATGAAGTTGTGGACTTAAAAGGATGCCACAGAG
TTGTGGACTTAAAAGGG
Found at i:60091 original size:55 final size:54
Alignment explanation
Indices: 59962--60392 Score: 503
Period size: 55 Copynumber: 7.9 Consensus size: 54
59952 AAAAGGGTGC
* * * *
59962 TGCCGCGGAGTTGTGGACTTAAAAGGATGCCATGAAGTTGTGGAC-TTAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGG
** * * *
60015 ATGCCATAGAGTTATGGACTTAAAAGGGTGCCACAGAGTGGTGGACTTTAAAAGAG
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAG-G
60071 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA-TTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAA-GG
* * * *
60125 TACCACGGAGTGGTGGACTTTAAAAGAGTGCCACTGAGTTGTGGAC-TTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAA-GG
* * *
60180 TGCTACAGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAA-GG
* * *
60235 TGCCACAGAGTTGTGGACTTTAAAA-GGTGCCACAGTGTTGTGGAC-TTAAAAGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGG
* * * *
60288 ATACCACGGAGTTGTGGACTTTAAAAGTGTGCCATGGAGTAGTGGACTTTAAAAGG
1 -TGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGG
* * *
60344 ATGCCACGGAGTTGTGGACTTAAAAAGATGTCACGGAGTTGTGGACTTT
1 -TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTT
60393 GTGTAGACAC
Statistics
Matches: 324, Mismatches: 43, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
53 2 0.01
54 113 0.35
55 176 0.54
56 33 0.10
ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26
Consensus pattern (54 bp):
TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGG
Found at i:61029 original size:49 final size:50
Alignment explanation
Indices: 60938--61051 Score: 176
Period size: 49 Copynumber: 2.3 Consensus size: 50
60928 TTTTCACAAT
* * *
60938 TTGTATCAATACATTCTGGGTTTTACCCAGATGTATCGATACATTATTCA
1 TTGTATCGATACATTCTAGGTTTTACCCAGATGTATCAATACATTATTCA
*
60988 TTGTATCGATACATTCTAGG-TTTACCCAGATGTATCAATACATTTTTCA
1 TTGTATCGATACATTCTAGGTTTTACCCAGATGTATCAATACATTATTCA
*
61037 ATGTATCGATACATT
1 TTGTATCGATACATT
61052 AAGGTATTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
49 41 0.69
50 18 0.31
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (50 bp):
TTGTATCGATACATTCTAGGTTTTACCCAGATGTATCAATACATTATTCA
Found at i:63490 original size:51 final size:51
Alignment explanation
Indices: 63430--63547 Score: 173
Period size: 51 Copynumber: 2.3 Consensus size: 51
63420 TTATATTTGA
* *
63430 GGGGATACTCCAACCCTGGTTTTATTTTTAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAACCCTGATTTTATTTTCAAAACACCAATTTTTCACAATC
* ** *
63481 GGGGATACTCTAACTTTGATTTTATTTTCAAAACACCAATTTTTCATAATC
1 GGGGATACTCCAACCCTGATTTTATTTTCAAAACACCAATTTTTCACAATC
*
63532 AGGGATACTCCAACCC
1 GGGGATACTCCAACCC
63548 CGTTATTTTT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (51 bp):
GGGGATACTCCAACCCTGATTTTATTTTCAAAACACCAATTTTTCACAATC
Found at i:63560 original size:130 final size:130
Alignment explanation
Indices: 63370--63620 Score: 337
Period size: 130 Copynumber: 1.9 Consensus size: 130
63360 CCAACCCCGG
** * *
63370 TTTTATTTCTAAAACATTAATTTTTCATAATCGAGGATACTCCAATCCCGTTATATTTGAGGGGA
1 TTTTATTTCTAAAACACCAATTTTTCATAATCGAGGATACTCCAACCCCGTTATATTTGAGGAGA
* ** *
63435 TACTCCAACCCTGGTTTTATTTTTAAAACACCAATTT-TTCACAATCGGGGATACTCTAACTTTG
66 TACTCCAACCCCGACTTTATTTCTAAAACACCAATTTCTT-ACAATCGGGGATACTCTAACTTTG
63499 A
130 A
*
63500 TTTTATTT-TCAAAACACCAATTTTTCATAATC-AGGGATACTCCAACCCCGTTATTTTTGAGGA
1 TTTTATTTCT-AAAACACCAATTTTTCATAATCGA-GGATACTCCAACCCCGTTATATTTGAGGA
* ***
63563 GATACTCCAACCCCGACTTTATTTCTAAAATATTGATTTCTTACAATCGGGGATACTC
64 GATACTCCAACCCCGACTTTATTTCTAAAACACCAATTTCTTACAATCGGGGATACTC
63621 CAAGCCCATT
Statistics
Matches: 105, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
129 2 0.02
130 101 0.96
131 2 0.02
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (130 bp):
TTTTATTTCTAAAACACCAATTTTTCATAATCGAGGATACTCCAACCCCGTTATATTTGAGGAGA
TACTCCAACCCCGACTTTATTTCTAAAACACCAATTTCTTACAATCGGGGATACTCTAACTTTGA
Found at i:63584 original size:79 final size:79
Alignment explanation
Indices: 63501--63863 Score: 414
Period size: 79 Copynumber: 4.6 Consensus size: 79
63491 TAACTTTGAT
* * * *
63501 TTTATTTTCAAAACACCAATTTTTCATAATCAGGGATACTCCAACCCCGTTATTTTTGAGGAGAT
1 TTTATTTTCAAAACATCGATTTTTCATAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGGAT
63566 ACTCCAACCCCGAC
66 ACTCCAACCCCGAC
* * * * * * *
63580 TTTA-TTTCTAAAATATTGATTTCTT-ACAATCGGGGATACTCCAAGCCCATTATTTTC-ACAGG
1 TTTATTTTC-AAAACATCGATTT-TTCATAATCAGGGATACTCCAACCCCGTTATTTTCGA-GGG
*
63642 GATACTCCAACCCCGGC
63 GATACTCCAACCCCGAC
* * * * * * *
63659 CTTA-TTTCTAAAGCATCGATTTTCCACAATCGGGGATACTTCAACCCTGTTATTTTCGAGGGGA
1 TTTATTTTC-AAAACATCGATTTTTCATAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGGA
*
63723 TACTCCAACCCCGAT
65 TACTCCAACCCCGAC
* * *
63738 TTTATTTTCAAAACATCGA-TTTTCTATAATCAGGGATACTCTAA-CCCTTTATTTCCGAGGGGA
1 TTTATTTTCAAAACATCGATTTTTC-ATAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGGA
*
63801 TACTCCAACCCCGAT
65 TACTCCAACCCCGAC
*
63816 TTTATTTTCAAAACATCGATTTTTCATAATCAGGGATACTCCAGCCCC
1 TTTATTTTCAAAACATCGATTTTTCATAATCAGGGATACTCCAACCCC
63864 ATTGTTATCC
Statistics
Matches: 239, Mismatches: 36, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
78 77 0.32
79 155 0.65
80 7 0.03
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (79 bp):
TTTATTTTCAAAACATCGATTTTTCATAATCAGGGATACTCCAACCCCGTTATTTTCGAGGGGAT
ACTCCAACCCCGAC
Found at i:64478 original size:20 final size:21
Alignment explanation
Indices: 64453--64496 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
64443 CTGCCAAGGA
64453 AATGTATCAATACATTAT-TC
1 AATGTATCAATACATTATATC
*
64473 AATGTATCGATACATTATATC
1 AATGTATCAATACATTATATC
64494 AAT
1 AAT
64497 ACATTGATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (21 bp):
AATGTATCAATACATTATATC
Found at i:64499 original size:33 final size:33
Alignment explanation
Indices: 64457--64520 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
64447 CAAGGAAATG
64457 TATCAATACATT-ATTCAATGTATCGATACATTA
1 TATCAATACATTGA-TCAATGTATCGATACATTA
**
64490 TATCAATACATTGATCTTTGTATCGATACAT
1 TATCAATACATTGATCAATGTATCGATACAT
64521 CTAGGAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.41
Consensus pattern (33 bp):
TATCAATACATTGATCAATGTATCGATACATTA
Found at i:83754 original size:22 final size:22
Alignment explanation
Indices: 83729--83799 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
83719 TGTTGTTCCC
83729 TTTTTATTTTGCTTTTGCACTT
1 TTTTTATTTTGCTTTTGCACTT
* *
83751 TTTTTGTTTTTCTTTT-CA-TAT
1 TTTTTATTTTGCTTTTGCACT-T
*
83772 TTTGTACTTTTGCTTTTG-ACCTT
1 TTTTTA-TTTTGCTTTTGCA-CTT
83795 TTTTT
1 TTTTT
83800 GTCATTTTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
20 1 0.03
21 7 0.18
22 24 0.63
23 5 0.13
24 1 0.03
ACGTcount: A:0.08, C:0.13, G:0.08, T:0.70
Consensus pattern (22 bp):
TTTTTATTTTGCTTTTGCACTT
Found at i:88645 original size:20 final size:20
Alignment explanation
Indices: 88599--88668 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
88589 TTTTACCCAG
*
88599 ATGTATCGATACAATTTTCA
1 ATGTATCGATACAATTATCA
* *
88619 ATATATCGATAC-ATGTATGA
1 ATGTATCGATACAAT-TATCA
* * *
88639 ATGTATCAATA-TATTCTTCA
1 ATGTATCGATACAATT-ATCA
88659 ATGTATCGAT
1 ATGTATCGAT
88669 GCATTATGTC
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 3 0.08
20 36 0.92
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACAATTATCA
Found at i:91026 original size:97 final size:98
Alignment explanation
Indices: 90869--91117 Score: 382
Period size: 97 Copynumber: 2.6 Consensus size: 98
90859 AAAATTTTAT
* * *
90869 TCATCGGGGATACTCCAACCCCATTCCTCCGAGGGGATACTTC-ACCCTCGCTTTTAAACTTGTC
1 TCATCGAGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCTCGCTTTTAAACTTGTC
*
90933 AAGATTCAAATCTTATTCTCGCTTAAATTGTCA
66 AAGATCCAAATCTTATTCTCGCTTAAATTGTCA
*
90966 TCA-CTG-GGAACACTCCAACCCTATTCCTCCGAGGGGATACTCCAACCC-CGCTTTTAAACTTG
1 TCATC-GAGG-ACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCTCGCTTTTAAACTTG
91028 TCAAGATCCAAATCTTATTCTCGCTTAAATTGTCA
64 TCAAGATCCAAATCTTATTCTCGCTTAAATTGTCA
* *
91063 TCATCGAGGACACTCCAACCCCATTCCTCCGAGGGGATACTCTAA-CCTCGTTTTT
1 TCATCGAGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCTCGCTTTT
91118 TTTTAATCAA
Statistics
Matches: 139, Mismatches: 7, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
96 5 0.04
97 127 0.91
98 7 0.05
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.30
Consensus pattern (98 bp):
TCATCGAGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCTCGCTTTTAAACTTGTC
AAGATCCAAATCTTATTCTCGCTTAAATTGTCA
Done.