Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1456
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: 72433
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:15821 original size:1 final size:1
Alignment explanation
Indices: 15811--15902 Score: 76
Period size: 1 Copynumber: 92.0 Consensus size: 1
15801 TGGCAATTGG
* * * ** * * * **
15811 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAAAACAAAACAAAAAAAAGGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
15876 AAAGAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
15903 GTGAAGATTT
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:15860 original size:34 final size:34
Alignment explanation
Indices: 15810--15902 Score: 170
Period size: 34 Copynumber: 2.7 Consensus size: 34
15800 ATGGCAATTG
15810 GAAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAA
1 GAAAAA-AAAAAAACAAAACAAAAAAAAGGAAAAA
15845 GAAAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
1 GAAAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
15879 GAAAAAAAAAAAACAAAA-AAAAAA
1 GAAAAAAAAAAAACAAAACAAAAAA
15903 GTGAAGATTT
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
33 6 0.10
34 46 0.79
35 6 0.10
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (34 bp):
GAAAAAAAAAAAACAAAACAAAAAAAAGGAAAAA
Found at i:15909 original size:29 final size:28
Alignment explanation
Indices: 15814--15909 Score: 86
Period size: 29 Copynumber: 3.1 Consensus size: 28
15804 CAATTGGAAA
* *
15814 AAGAAAAAAACAAAACAAAAAAAAGGAA-A
1 AAGAAAAAAAAAAAACAAAAAAAA--AAGG
15843 AAGAAAAAAAAAAAACAAAACAAAAAAAAGG
1 AAGAAAAAAAAAAAAC--AA-AAAAAAAAGG
15874 AAAAAGAAAAAAAAAAAACAAAAAAAAAAGTG
1 ---AAGAAAAAAAAAAAACAAAAAAAAAAG-G
15906 AAGA
1 AAGA
15910 TTTGTTCCTT
Statistics
Matches: 57, Mismatches: 2, Indels: 16
0.76 0.03 0.21
Matches are distributed among these distances:
29 19 0.33
30 2 0.04
31 11 0.19
32 9 0.16
34 16 0.28
ACGTcount: A:0.83, C:0.05, G:0.10, T:0.01
Consensus pattern (28 bp):
AAGAAAAAAAAAAAACAAAAAAAAAAGG
Found at i:21357 original size:1 final size:1
Alignment explanation
Indices: 21351--21440 Score: 72
Period size: 1 Copynumber: 90.0 Consensus size: 1
21341 AAATCTTCAC
* * ** * * * **
21351 TTTTTTTTTTGTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTTCTTTTTCCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
21416 TTTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
21441 CCAATTGCCA
Statistics
Matches: 69, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.87
Consensus pattern (1 bp):
T
Found at i:21394 original size:33 final size:33
Alignment explanation
Indices: 21351--21439 Score: 162
Period size: 33 Copynumber: 2.7 Consensus size: 33
21341 AAATCTTCAC
21351 TTTTTT-TTTTGTTTTTTTTTTTCTTTTTCCTT
1 TTTTTTGTTTTGTTTTTTTTTTTCTTTTTCCTT
21383 TTTTTTGTTTTGTTTTTTTTTTTCTTTTTCCTT
1 TTTTTTGTTTTGTTTTTTTTTTTCTTTTTCCTT
21416 TTTTTTGTTTTGTTTTTTTCTTTT
1 TTTTTTGTTTTGTTTTTTT-TTTT
21440 TCCAATTGCC
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
32 6 0.11
33 45 0.82
34 4 0.07
ACGTcount: A:0.00, C:0.08, G:0.06, T:0.87
Consensus pattern (33 bp):
TTTTTTGTTTTGTTTTTTTTTTTCTTTTTCCTT
Found at i:31160 original size:11 final size:11
Alignment explanation
Indices: 31144--31171 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
31134 TCACCGGGGA
31144 CACTCCAACCC
1 CACTCCAACCC
31155 CACTCCAACCC
1 CACTCCAACCC
31166 CACTCC
1 CACTCC
31172 TCCGAGGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.25, C:0.64, G:0.00, T:0.11
Consensus pattern (11 bp):
CACTCCAACCC
Found at i:36755 original size:13 final size:13
Alignment explanation
Indices: 36737--36780 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
36727 CCTTCTTTTT
36737 AAAAAAAACAAAA
1 AAAAAAAACAAAA
36750 AAAAAAAACAAAA
1 AAAAAAAACAAAA
**
36763 AAACCAAACAAAGA
1 AAAAAAAACAAA-A
36777 AAAA
1 AAAA
36781 TGAGAGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 23 0.85
14 4 0.15
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAAAA
Found at i:38005 original size:61 final size:61
Alignment explanation
Indices: 37891--38019 Score: 154
Period size: 61 Copynumber: 2.1 Consensus size: 61
37881 TAGTAGGATG
* * * *
37891 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACGTCTTCT
1 CCTTTCAAAGCCCACACAAATTGGTGGCATTCTTCAGTCCTCAAAAAACAGGACGTCTTCT
* * *
37952 CCTTTTAAAGCCCACACAAATTGGTGGCACTTCTT-AGTCTTCAAAAAATAGGACG-CTCTCT
1 CCTTTCAAAGCCCACACAAATTGGTGGCA-TTCTTCAGTCCTCAAAAAACAGGACGTCT-TCT
*
38013 CTTTTCA
1 CCTTTCA
38020 CCCTTCCTCA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 2 0.04
61 51 0.89
62 4 0.07
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.30
Consensus pattern (61 bp):
CCTTTCAAAGCCCACACAAATTGGTGGCATTCTTCAGTCCTCAAAAAACAGGACGTCTTCT
Found at i:38089 original size:55 final size:55
Alignment explanation
Indices: 38024--38158 Score: 198
Period size: 55 Copynumber: 2.4 Consensus size: 55
38014 TTTTCACCCT
* * **
38024 TCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAG
1 TCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAG
* * *
38079 TTCTTAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAG
1 TCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAG
38134 TCCTCAAAGAGCAGGATGCTCTTTC
1 TCCTCAAAGAGCAGGATGC-CTTTC
38159 CTTTCACCTT
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
55 65 0.94
56 4 0.06
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (55 bp):
TCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCCAG
Found at i:38236 original size:55 final size:54
Alignment explanation
Indices: 38171--38304 Score: 187
Period size: 55 Copynumber: 2.5 Consensus size: 54
38161 TTCACCTTTT
* * **
38171 AGTCCTCAAAGAGCAAGACGTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAAGACGTCTTTCAAAGCCCACACAAGCTGGTGACACCTT-C
* **
38226 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGCTGGTGACACCTTC
1 AGTCCTCAAAGAGCAAGACGTCTTTCAAAGCCCACACAAGCTGGTGACACCTTC
*
38280 AGTCCTTAAAGAGCAAGACGTCTTT
1 AGTCCTCAAAGAGCAAGACGTCTTT
38305 TCCTTTTAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
54 22 0.32
55 46 0.68
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (54 bp):
AGTCCTCAAAGAGCAAGACGTCTTTCAAAGCCCACACAAGCTGGTGACACCTTC
Found at i:38630 original size:20 final size:19
Alignment explanation
Indices: 38605--38658 Score: 90
Period size: 20 Copynumber: 2.8 Consensus size: 19
38595 TTACCTGAAA
38605 GTATCGATACATTGTTCATT
1 GTATCGATACATTGTTCA-T
38625 GTATCGATACATTGTTCAT
1 GTATCGATACATTGTTCAT
*
38644 GAATCGATACATTGT
1 GTATCGATACATTGT
38659 ATCGATACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.41
Consensus pattern (19 bp):
GTATCGATACATTGTTCAT
Found at i:41133 original size:51 final size:52
Alignment explanation
Indices: 41057--41175 Score: 159
Period size: 51 Copynumber: 2.3 Consensus size: 52
41047 TATTTTCGAA
* * ***
41057 GGGATACTCTAACCCCAACTTTATTTCTAAAATATTGAT-TTCTCAAAATCG
1 GGGATACTCCAACCCCAACTTTATTTCTAAAACACCAATCTTCTCAAAATCG
* * *
41108 GGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATCTTTTCACAATCG
1 GGGATACTCCAACCCCAACTTTATTTCTAAAACACCAATCTTCTCAAAATCG
41160 GGGATACTCCAACCCC
1 GGGATACTCCAACCCC
41176 GTTCTTTTTG
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
51 33 0.56
52 26 0.44
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.30
Consensus pattern (52 bp):
GGGATACTCCAACCCCAACTTTATTTCTAAAACACCAATCTTCTCAAAATCG
Found at i:41191 original size:79 final size:79
Alignment explanation
Indices: 41107--41328 Score: 268
Period size: 78 Copynumber: 2.8 Consensus size: 79
41097 TCTCAAAATC
41107 GGGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATCTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCAATTTTATTTCTAAAACACCAAT-TTTTCACAATCGGGGATACTCCAA
* **
41172 CCCCGTTCTTTTTGA
65 CCCCGTTATTTTCAA
* * *
41187 -GGGATACTCCAA-CCCAATTTTATTTCCAAAACACCGATTTTTTCACAATCGGGGATACTCAAA
1 GGGGATACTCCAACCCCAATTTTATTTCTAAAACACC-AATTTTTCACAATCGGGGATACTCCAA
*
41250 CCTCGTTATTTTCAA
65 CCCCGTTATTTTCAA
*** * * * * *
41265 GGGGATACTCCAACCTTGATTTTATTTCTAGAATACCAATTTTCCATAGTCAGGGGATACTCCA
1 GGGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATTTTTCACAATC-GGGGATACTCCA
41329 GCCCTGTTGT
Statistics
Matches: 120, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
78 56 0.47
79 36 0.30
80 28 0.23
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTATTTTCAA
Found at i:41201 original size:130 final size:130
Alignment explanation
Indices: 40978--41251 Score: 354
Period size: 130 Copynumber: 2.1 Consensus size: 130
40968 TTTCATCTCA
* * * * * *
40978 GGGATACTCCAACCCCGATTTTATTTTTAAAATATCAATTTTTCATAATCGGGGATACTCCAATC
1 GGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAACC
* * * * **
41043 TCGTTATTTTCGAAGGGATACTCTAACCCCAACTTTATTTCTAAAATATTGA-TTTCTCAAAATC
66 CCGTTATTTTCGAAGGGATACTCCAA-CCCAACTTTATTTCCAAAACACCGATTTTCTCAAAATC
41107 G
130 G
41108 GGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATCTTTTCACAATCGGGGATACTCCAAC
1 GGGATACTCCAACCCCAATTTTATTTCTAAAACACCAAT-TTTTCACAATCGGGGATACTCCAAC
* * * * *
41173 CCCGTTCTTTTTG-AGGGATACTCCAACCCAATTTTATTTCCAAAACACCGATTTTTTCACAATC
65 CCCGTTATTTTCGAAGGGATACTCCAACCCAACTTTATTTCCAAAACACCGATTTTCTCAAAATC
41237 G
130 G
*
41238 GGGATACTCAAACC
1 GGGATACTCCAACC
41252 TCGTTATTTT
Statistics
Matches: 124, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
129 20 0.16
130 71 0.57
131 33 0.27
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (130 bp):
GGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAACC
CCGTTATTTTCGAAGGGATACTCCAACCCAACTTTATTTCCAAAACACCGATTTTCTCAAAATCG
Found at i:47032 original size:52 final size:52
Alignment explanation
Indices: 46954--47082 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
46944 CGAAATATGA
*
46954 AAATTTGCCTGCATGTATCGATACATTTCATAGTGGATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGGATCGATACATCTGGGC
* * *
47006 AAATTTGCCTGTATGTATCGATACATTTCATTGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGGATCGATACATCTGGGC
47058 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
47083 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGGATCGATACATCTGGGC
Found at i:47094 original size:52 final size:51
Alignment explanation
Indices: 46954--47102 Score: 176
Period size: 52 Copynumber: 2.9 Consensus size: 51
46944 CGAAATATGA
* * *
46954 AAATTTGCCTGCATGTATCGATACATTTCAT-AGTGGATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACA--ACATCAGTGTATCGATACATCTGGGC
* * *
47006 AAATTTGCCTGTATGTATCGATACATTTCAT-TGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA--ACATCAGTGTATCGATACATCTGGGC
*
47058 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATAC-AACATCAGTGTATCGATACA
47103 ATGTATCAAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.97
53 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACAACATCAGTGTATCGATACATCTGGGC
Found at i:47194 original size:19 final size:18
Alignment explanation
Indices: 47170--47230 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 18
47160 CGATACATTA
47170 TATCGATACAAAACTTATG
1 TATCGATAC-AAACTTATG
47189 TATCGATAC--A--T-TG
1 TATCGATACAAACTTATG
47202 TATCGATACAACACTTATG
1 TATCGATACAA-ACTTATG
47221 TATCGATACA
1 TATCGATACA
47231 TTGTATCGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.31
14 1 0.03
16 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (18 bp):
TATCGATACAAACTTATG
Found at i:47198 original size:32 final size:32
Alignment explanation
Indices: 47160--47245 Score: 154
Period size: 32 Copynumber: 2.7 Consensus size: 32
47150 AACTTCGTAG
*
47160 CGATACATTATATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
47192 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
47224 CGATACATTGTATCGATACAAA
1 CGATACATTGTATCGATACAAA
47246 TCGTTGAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:47991 original size:48 final size:47
Alignment explanation
Indices: 47873--48001 Score: 116
Period size: 48 Copynumber: 2.7 Consensus size: 47
47863 AATATCATGT
* * ** *
47873 ATGTATCGATAAATTAATTAGTT-TATCGATACAATTTAGAAACTTAT
1 ATGTATCGATAAATT-ATTAATTATATCGATACAATTTAAAAACCCAG
* * * ** *
47920 ATGTATCAATACACTATGCATTATATCGATACATTTTGAAAAACCCAG
1 ATGTATCGATAAATTATTAATTATATCGATACAATTT-AAAAACCCAG
* *
47968 ATGTATCGATATATTATTAATTATGTCGATACAA
1 ATGTATCGATAAATTATTAATTATATCGATACAA
48002 AAACCTTAAA
Statistics
Matches: 62, Mismatches: 18, Indels: 3
0.75 0.22 0.04
Matches are distributed among these distances:
46 4 0.06
47 25 0.40
48 33 0.53
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (47 bp):
ATGTATCGATAAATTATTAATTATATCGATACAATTTAAAAACCCAG
Found at i:51407 original size:23 final size:22
Alignment explanation
Indices: 51355--51418 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
51345 ATTAAATCCA
51355 AATAAATTTTAAAATAAAAAGC
1 AATAAATTTTAAAATAAAAAGC
* *
51377 AATAAAATTTTGAATAATGAAAATC
1 AAT-AAATTTT-AA-AATAAAAAGC
*
51402 -ATAAATTATTCAAATAA
1 AATAAATT-TTAAAATAA
51419 GATATCAGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
22 7 0.21
23 13 0.38
24 6 0.18
25 8 0.24
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (22 bp):
AATAAATTTTAAAATAAAAAGC
Found at i:59747 original size:20 final size:20
Alignment explanation
Indices: 59681--59869 Score: 121
Period size: 20 Copynumber: 8.9 Consensus size: 20
59671 ATAAAAAGAC
* * *
59681 AAAATGTATTGATATAT-TA
1 AAAATGTATCGATACATCGA
59700 AAGAATGTATCGATACATTC-A
1 AA-AATGTATCGATACA-TCGA
* *
59721 TACATGTATCGATACATCGA
1 AAAATGTATCGATACATCGA
*
59741 AAAATGTATCTATACATCTGGGTAAAAAA
1 AAAATGTATCGATACATC---G------A
*
59770 ACAGAATGTATCGATACATTGA
1 A-A-AATGTATCGATACATCGA
* *
59792 AGAATGTATCGATACATTGA
1 AAAATGTATCGATACATCGA
* *
59812 AGAATGTATCGATACATTGA
1 AAAATGTATCGATACATCGA
* *
59832 AGAATGTATCGATACATTGA
1 AAAATGTATCGATACATCGA
*
59852 AAAATTTATCGATACATC
1 AAAATGTATCGATACATC
59870 TTGGTACTCT
Statistics
Matches: 142, Mismatches: 13, Indels: 29
0.77 0.07 0.16
Matches are distributed among these distances:
19 4 0.03
20 114 0.80
21 3 0.02
22 2 0.01
23 1 0.01
28 1 0.01
29 2 0.01
30 1 0.01
31 14 0.10
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (20 bp):
AAAATGTATCGATACATCGA
Found at i:59795 original size:91 final size:91
Alignment explanation
Indices: 59633--59852 Score: 273
Period size: 91 Copynumber: 2.4 Consensus size: 91
59623 TTTTAACTAG
* * * * * * *
59633 ATGTATCAATATATTGAAAAATGTATCGATATATTTGAATAAAAAGACAAAATGTATTGATATAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGAATAAAAAAACAAAATGTATCGATACAT
*
59698 TAAAGAATGTATCGATACATTCATA-C
66 TAAAGAATGTATCGATACATTCA-AGA
* * ** *
59724 ATGTATCGATACATCGAAAAATGTATCTATACATCTGGGTAAAAAAACAGAATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGAATAAAAAAACAAAATGTATCGATACAT
* *
59789 TGAAGAATGTATCGATACATTGAAGA
66 TAAAGAATGTATCGATACATTCAAGA
*
59815 ATGTATCGATACATTGAAGAATGTATCGATACAT-TGAA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTGAA
59853 AAATTTATCG
Statistics
Matches: 108, Mismatches: 20, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
90 3 0.03
91 105 0.97
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (91 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTGAATAAAAAAACAAAATGTATCGATACAT
TAAAGAATGTATCGATACATTCAAGA
Found at i:59816 original size:40 final size:40
Alignment explanation
Indices: 59772--59868 Score: 176
Period size: 40 Copynumber: 2.4 Consensus size: 40
59762 GTAAAAAAAC
59772 AGAATGTATCGATACATTGAAGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGAAGAATGTATCGATACATTGA
59812 AGAATGTATCGATACATTGAAGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGAAGAATGTATCGATACATTGA
* *
59852 AAAATTTATCGATACAT
1 AGAATGTATCGATACAT
59869 CTTGGTACTC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (40 bp):
AGAATGTATCGATACATTGAAGAATGTATCGATACATTGA
Found at i:60856 original size:28 final size:28
Alignment explanation
Indices: 60747--61175 Score: 462
Period size: 28 Copynumber: 15.1 Consensus size: 28
60737 CTTTTTTTTT
* *
60747 AAAATGTGCCACTAACTTGTGTAGGCTTTG
1 AAAAGGTGCCACTGACTTGTG--GGCTTTG
*
60777 AAAAGAGTTGCCACTGACTCGTGTAGGCTTTG
1 AAAAG-G-TGCCACTGACT--TGTGGGCTTTG
*
60809 AAAAGAATGCCACTGACTTGTGGGCTTTG
1 AAAAG-GTGCCACTGACTTGTGGGCTTTG
* *
60838 AAAAGGTGCCCCTGACTTGTAGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* *
60866 AAAAGCTG-C-C--ACTTGTAGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
*
60890 AAAAGATGCCACTGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
60918 -AAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
*
60946 AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
* *
60974 AAAAGAGTTGCCA-TCAACTCGTGGGCTTTG
1 AAAAG-G-TGCCACT-GACTTGTGGGCTTTG
*
61004 AAAAGAGTTGCCA-TCAACTTGTGGGCTTTG
1 AAAAG-G-TGCCACT-GACTTGTGGGCTTTG
* **
61034 AAAGGGTGCCACTGACTCATGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
61062 -AAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
* *
61090 AAAGGGTGCCACCGACTTGTGGGCTTT-
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
61117 AAAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAAGG-TGCCACTGACTTGTGGGCTTTG
* * *
61146 AAAGGGTGCCACTAACTTATGGGCTTTG
1 AAAAGGTGCCACTGACTTGTGGGCTTTG
61174 AA
1 AA
61176 GAGATAAATG
Statistics
Matches: 350, Mismatches: 31, Indels: 38
0.84 0.07 0.09
Matches are distributed among these distances:
24 21 0.06
25 1 0.00
26 2 0.01
27 14 0.04
28 187 0.53
29 32 0.09
30 55 0.16
31 12 0.03
32 23 0.07
34 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (28 bp):
AAAAGGTGCCACTGACTTGTGGGCTTTG
Found at i:61127 original size:200 final size:196
Alignment explanation
Indices: 60752--61175 Score: 584
Period size: 200 Copynumber: 2.1 Consensus size: 196
60742 TTTTTAAAAT
*
60752 GTGCCACTAACTTGTGTAGGCTTTGAAAAGAGTTGCCACTGACTCGTGTAGGCTTTGAAAAGAAT
1 GTGCCACTAACTTGTG--GGCTTTGAAAAGAGTTGCCACTAACTCGTG-AGGCTTTGAAAAGAAT
* * ** *
60817 GCCACTGACTTGTGGGCTTTGAAAAGGTGCCCCTGACTTGTAGGCTTTGAAAAGCTGCCACTTGT
63 GCCACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACTCATAGGCTTTGAAAAGATGCCACTTGT
* *
60882 AGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGA
128 AGGCTTTGAAAAGATGCCACCGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGA
60947 AAGG
193 AAGG
* *
60951 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCA-TCAACTCGTG-GGCTTTGAAAAGAGTTG
1 GTGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACT-AACTCGTGAGGCTTTGAAAAGA-ATG
* * *
61014 CCA-TCAACTTGTGGGCTTTGAAAGGGTGCCACTGACTCATGGGCTTTGAAAGGATGCCACTGAC
64 CCACT-AACTTGTGGGCTTTGAAAAGGTGCCACTGACTCATAGGCTTTGAAAAGATG-C-C--AC
* * *
61078 TTGTGGGCTTTGAAAGGGTGCCACCGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCT
124 TTGTAGGCTTTGAAAAGATGCCACCGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCT
61143 TTGAAAGG
189 TTGAAAGG
*
61151 GTGCCACTAACTTATGGGCTTTGAA
1 GTGCCACTAACTTGTGGGCTTTGAA
61176 GAGATAAATG
Statistics
Matches: 200, Mismatches: 18, Indels: 13
0.87 0.08 0.06
Matches are distributed among these distances:
195 14 0.07
196 49 0.25
197 28 0.14
198 1 0.00
199 15 0.08
200 93 0.47
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.28
Consensus pattern (196 bp):
GTGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACTAACTCGTGAGGCTTTGAAAAGAATGCC
ACTAACTTGTGGGCTTTGAAAAGGTGCCACTGACTCATAGGCTTTGAAAAGATGCCACTTGTAGG
CTTTGAAAAGATGCCACCGACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAG
G
Found at i:62412 original size:11 final size:10
Alignment explanation
Indices: 62396--62495 Score: 58
Period size: 10 Copynumber: 9.4 Consensus size: 10
62386 CCCCTTTCTG
62396 TTTTTTTGTT
1 TTTTTTTGTT
*
62406 ATTTTTTTCTT
1 -TTTTTTTGTT
62417 GGTTTTTTTGTT
1 --TTTTTTTGTT
* *
62429 TTTTTGTCTT
1 TTTTTTTGTT
*
62439 TTTTCTATTTTT
1 TTTT-T-TTGTT
62451 TATTTTTTGTT
1 T-TTTTTTGTT
* *
62462 TTTTTTGGGT
1 TTTTTTTGTT
* *
62472 TTTTTCTATT
1 TTTTTTTGTT
62482 TTTTGTTT-TT
1 TTTT-TTTGTT
62492 TTTT
1 TTTT
62496 GTGTATGAAG
Statistics
Matches: 69, Mismatches: 15, Indels: 11
0.73 0.16 0.12
Matches are distributed among these distances:
10 35 0.51
11 17 0.25
12 14 0.20
13 3 0.04
ACGTcount: A:0.04, C:0.04, G:0.10, T:0.82
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:62421 original size:23 final size:22
Alignment explanation
Indices: 62395--62438 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
62385 ACCCCTTTCT
*
62395 GTTTTTTTGTTATTTTTTTCTTG
1 GTTTTTTTGTT-TTTTTGTCTTG
62418 GTTTTTTTGTTTTTTTGTCTT
1 GTTTTTTTGTTTTTTTGTCTT
62439 TTTTCTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.02, C:0.05, G:0.14, T:0.80
Consensus pattern (22 bp):
GTTTTTTTGTTTTTTTGTCTTG
Found at i:62431 original size:9 final size:9
Alignment explanation
Indices: 62408--62494 Score: 63
Period size: 9 Copynumber: 9.9 Consensus size: 9
62398 TTTTTGTTAT
62408 TTTTTTCTTG
1 TTTTTT-TTG
*
62418 GTTTTTTTG
1 TTTTTTTTG
62427 -TTTTTTTG
1 TTTTTTTTG
*
62435 TCTTTTTT-
1 TTTTTTTTG
* *
62443 CTATTTTT-
1 TTTTTTTTG
*
62451 TATTTTTTG
1 TTTTTTTTG
62460 TTTTTTTTG
1 TTTTTTTTG
** *
62469 GGTTTTTTC
1 TTTTTTTTG
*
62478 TATTTTTTG
1 TTTTTTTTG
62487 TTTTTTTT
1 TTTTTTTT
62495 TGTGTATGAA
Statistics
Matches: 59, Mismatches: 16, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
8 18 0.31
9 36 0.61
10 5 0.08
ACGTcount: A:0.03, C:0.05, G:0.10, T:0.82
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:62465 original size:34 final size:33
Alignment explanation
Indices: 62420--62492 Score: 110
Period size: 34 Copynumber: 2.2 Consensus size: 33
62410 TTTTCTTGGT
*
62420 TTTTTTGTTTTTTTGTCTTTTTTCTATTTTTTA
1 TTTTTTGTTTTTTTGGCTTTTTTCTATTTTTTA
* *
62453 TTTTTTGTTTTTTTTGGGTTTTTTCTATTTTTTG
1 TTTTTTG-TTTTTTTGGCTTTTTTCTATTTTTTA
62487 TTTTTT
1 TTTTTT
62493 TTTGTGTATG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 7 0.19
34 29 0.81
ACGTcount: A:0.04, C:0.04, G:0.10, T:0.82
Consensus pattern (33 bp):
TTTTTTGTTTTTTTGGCTTTTTTCTATTTTTTA
Done.