Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1659
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: 75837
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:848 original size:21 final size:21
Alignment explanation
Indices: 819--863 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
809 AAGTTTTCAT
*
819 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
839 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
861 TTT
1 TTT
864 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:3159 original size:21 final size:21
Alignment explanation
Indices: 3133--3249 Score: 148
Period size: 21 Copynumber: 5.7 Consensus size: 21
3123 CTGCCAAGAA
3133 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
3154 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
3174 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
3195 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
3215 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
3236 ATGTATCGATACAT
1 ATGTATCGATACAT
3250 TGCAACATGT
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
20 32 0.41
21 46 0.59
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:3178 original size:20 final size:20
Alignment explanation
Indices: 3153--3267 Score: 140
Period size: 20 Copynumber: 5.7 Consensus size: 20
3143 ACATCTTTTT
3153 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
3173 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
3194 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
3214 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
3235 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
3255 CATGTATCGATAC
1 CATGTATCGATAC
3268 TTTGAATTGT
Statistics
Matches: 77, Mismatches: 16, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
20 45 0.58
21 32 0.42
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:3190 original size:41 final size:41
Alignment explanation
Indices: 3133--3267 Score: 270
Period size: 41 Copynumber: 3.3 Consensus size: 41
3123 CTGCCAAGAA
3133 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
3174 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
3215 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
3256 ATGTATCGATAC
1 ATGTATCGATAC
3268 TTTGAATTGT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 94 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:5073 original size:12 final size:12
Alignment explanation
Indices: 5043--5074 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
5033 CAAAATGTAA
5043 AACAAAAA-TGT
1 AACAAAAATTGT
5054 AA-AAAAATTGT
1 AACAAAAATTGT
5065 AACAAAAATT
1 AACAAAAATT
5075 CCCACAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.26
11 7 0.37
12 7 0.37
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.22
Consensus pattern (12 bp):
AACAAAAATTGT
Found at i:24603 original size:33 final size:32
Alignment explanation
Indices: 24561--24624 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
24551 TACAAGCCAA
*
24561 TGTATCGATACATTTTGAGATATATCGATACAT
1 TGTATCGATACATCTTGAG-TATATCGATACAT
* *
24594 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGAGTATATCGATACA
24625 AATAGTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 11 0.39
33 17 0.61
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGAGTATATCGATACAT
Found at i:24716 original size:20 final size:21
Alignment explanation
Indices: 24666--24718 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
24656 GCCAATGACC
*
24666 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
* *
24687 AGTATAGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
24707 TGTATCGATACA
1 TGTATCGATACA
24719 ATGTATCAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:25329 original size:22 final size:22
Alignment explanation
Indices: 25286--25330 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
25276 TTTTCTGGTC
*
25286 TCTCCCCCTTAATCATAAAATT
1 TCTCCCCCTTAATCAAAAAATT
25308 TCTCCCCCTTAAT-AAAATAATT
1 TCTCCCCCTTAATCAAAA-AATT
25330 T
1 T
25331 AACAATTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.33, C:0.29, G:0.00, T:0.38
Consensus pattern (22 bp):
TCTCCCCCTTAATCAAAAAATT
Found at i:27115 original size:23 final size:24
Alignment explanation
Indices: 27070--27116 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
27060 CAAAGAATTG
*
27070 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
27094 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
27117 TTTTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:30221 original size:13 final size:13
Alignment explanation
Indices: 30203--30228 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30193 TACAAGCCAA
30203 TGTATCGATACAT
1 TGTATCGATACAT
30216 TGTATCGATACAT
1 TGTATCGATACAT
30229 CTTGTGTGTA
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:33993 original size:51 final size:52
Alignment explanation
Indices: 33889--34003 Score: 142
Period size: 52 Copynumber: 2.2 Consensus size: 52
33879 TGAAGAATAG
* *
33889 ATCGATATATTTGGGTCAAAAACCTAAAATATATCGATACAATGAAAAATGT
1 ATCGATACATTTGGGTAAAAAACCTAAAATATATCGATACAATGAAAAATGT
* ** * *
33941 ATCGATACATTTGGGTAAAAAATCTGTAATGTATCGATATAAT-AAAAATGT
1 ATCGATACATTTGGGTAAAAAACCTAAAATATATCGATACAATGAAAAATGT
**
33992 ATTAATACATTT
1 ATCGATACATTT
34004 TCTTTCTAGA
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
51 18 0.33
52 36 0.67
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (52 bp):
ATCGATACATTTGGGTAAAAAACCTAAAATATATCGATACAATGAAAAATGT
Found at i:34078 original size:20 final size:21
Alignment explanation
Indices: 34041--34092 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
34031 ACAAGATCCA
* *
34041 GTATCGATATATTCACTT-AT
1 GTATCGATACATTAACTTGAT
* *
34061 GTATCGATGCATTAACTTGTT
1 GTATCGATACATTAACTTGAT
34082 GTATCGATACA
1 GTATCGATACA
34093 AATTGTAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (21 bp):
GTATCGATACATTAACTTGAT
Found at i:36664 original size:2 final size:2
Alignment explanation
Indices: 36657--36691 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
36647 CTAACCTAAT
36657 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
36692 TGACAAGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:37813 original size:22 final size:22
Alignment explanation
Indices: 37787--37828 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
37777 AATGCATGAA
*
37787 AACAAGCTCCAAACA-AGTCAAC
1 AACAA-CTACAAACACAGTCAAC
37809 AACAACTACAAACACAGTCA
1 AACAACTACAAACACAGTCA
37829 TTCAACCTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.52, C:0.31, G:0.07, T:0.10
Consensus pattern (22 bp):
AACAACTACAAACACAGTCAAC
Found at i:39938 original size:19 final size:21
Alignment explanation
Indices: 39914--39961 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
39904 AAGAGATTAG
39914 TTTTTCATT-TC-TTTTCATT
1 TTTTTCATTCTCATTTTCATT
39933 TTTTTCATTCCTCATTTTTCATT
1 TTTTTCATT-CTCA-TTTTCATT
39956 TTTTTC
1 TTTTTC
39962 TCTAAGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.36
21 2 0.08
23 14 0.56
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTCATTCTCATTTTCATT
Found at i:43792 original size:13 final size:13
Alignment explanation
Indices: 43774--43800 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43764 CATAAAATGT
43774 TGTATCGATACAA
1 TGTATCGATACAA
43787 TGTATCGATACAA
1 TGTATCGATACAA
43800 T
1 T
43801 TTAAGCTACT
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:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:43859 original size:13 final size:13
Alignment explanation
Indices: 43841--43865 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43831 ATTACTCAAA
43841 TGTATCGATACAT
1 TGTATCGATACAT
43854 TGTATCGATACA
1 TGTATCGATACA
43866 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:43916 original size:51 final size:53
Alignment explanation
Indices: 43854--43992 Score: 160
Period size: 52 Copynumber: 2.7 Consensus size: 53
43844 ATCGATACAT
***
43854 TGTATCGATACACTGAT-CTTTGTATCAATACATGCAGGC-AATTTGCCCAGA
1 TGTATCGATACACTGATAAAATGTATCAATACATGCAGGCAAATTTGCCCAGA
** * *
43905 TGTATCGATACA-TTTTAAAATGTATCGATACATGCAGGCAAATTTTCCCAGA
1 TGTATCGATACACTGATAAAATGTATCAATACATGCAGGCAAATTTGCCCAGA
* **
43957 TGTATCGATACACT-ATTAAATGTATCGCTACATGCA
1 TGTATCGATACACTGATAAAATGTATCAATACATGCA
43993 AGTAACTTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
50 2 0.03
51 30 0.40
52 42 0.56
53 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (53 bp):
TGTATCGATACACTGATAAAATGTATCAATACATGCAGGCAAATTTGCCCAGA
Found at i:44003 original size:52 final size:51
Alignment explanation
Indices: 43874--43992 Score: 177
Period size: 52 Copynumber: 2.3 Consensus size: 51
43864 CACTGATCTT
* * *
43874 TGTATCAATACATGCAGGCAATTTGCCCAGATGTATCGATACATTTTAAAA
1 TGTATCGATACATGCAGGCAATTTTCCCAGATGTATCGATACATATTAAAA
43925 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATT-AAA
1 TGTATCGATACATGCAGGC-AATTTTCCCAGATGTATCGATACA-TATTAAAA
*
43977 TGTATCGCTACATGCA
1 TGTATCGATACATGCA
43993 AGTAACTTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 18 0.29
52 41 0.66
53 3 0.05
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (51 bp):
TGTATCGATACATGCAGGCAATTTTCCCAGATGTATCGATACATATTAAAA
Found at i:52279 original size:13 final size:13
Alignment explanation
Indices: 52261--52285 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52251 CATAAAATGT
52261 TGTATCGATACAA
1 TGTATCGATACAA
52274 TGTATCGATACA
1 TGTATCGATACA
52286 TTTTTTTTGT
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:52298 original size:19 final size:19
Alignment explanation
Indices: 52274--52336 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
52264 ATCGATACAA
52274 TGTATCGATACATTTTTTT
1 TGTATCGATACATTTTTTT
* *
52293 TGTATCGAAACA------A
1 TGTATCGATACATTTTTTT
52306 TGTATCGATACATTTTTTT
1 TGTATCGATACATTTTTTT
*
52325 TGTATCAATACA
1 TGTATCGATACA
52337 ATTTAAGCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
13 11 0.33
19 22 0.67
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (19 bp):
TGTATCGATACATTTTTTT
Found at i:52306 original size:32 final size:32
Alignment explanation
Indices: 52260--52338 Score: 133
Period size: 32 Copynumber: 2.5 Consensus size: 32
52250 ACATAAAATG
*
52260 TTGTATCGATACAATGTATCGATACATTTTTT
1 TTGTATCGAAACAATGTATCGATACATTTTTT
52292 TTGTATCGAAACAATGTATCGATACATTTTTT
1 TTGTATCGAAACAATGTATCGATACATTTTTT
52324 TTGTATC-AATACAAT
1 TTGTATCGAA-ACAAT
52339 TTAAGCTACT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
31 2 0.04
32 43 0.96
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (32 bp):
TTGTATCGAAACAATGTATCGATACATTTTTT
Found at i:53335 original size:13 final size:13
Alignment explanation
Indices: 53317--53342 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53307 CAATTTTTTG
53317 TGTATCGATACAT
1 TGTATCGATACAT
53330 TGTATCGATACAT
1 TGTATCGATACAT
53343 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:55907 original size:13 final size:13
Alignment explanation
Indices: 55889--55927 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
55879 ATAATCACCC
55889 TGTATCGATACAA
1 TGTATCGATACAA
55902 TGTATCGATACAA
1 TGTATCGATACAA
55915 TGTATCGATACAA
1 TGTATCGATACAA
55928 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:55938 original size:20 final size:20
Alignment explanation
Indices: 55913--55991 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
55903 GTATCGATAC
55913 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
**
55933 AATGTATCGATACATTGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
55958 AATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
55978 CATGTATCGATACA
1 AATGTATCGATACA
55992 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
20 31 0.63
25 18 0.37
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:58020 original size:15 final size:15
Alignment explanation
Indices: 58000--58030 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
57990 ATTTCGTTTG
*
58000 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
58015 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
58030 G
1 G
58031 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:59863 original size:21 final size:21
Alignment explanation
Indices: 59834--59878 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
59824 AAGTTTTCAT
*
59834 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
59854 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
59876 TTT
1 TTT
59879 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:62116 original size:13 final size:13
Alignment explanation
Indices: 62098--62123 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
62088 CAATTTTTTG
62098 TGTATCGATACAT
1 TGTATCGATACAT
62111 TGTATCGATACAT
1 TGTATCGATACAT
62124 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:73200 original size:28 final size:28
Alignment explanation
Indices: 73160--73231 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
73150 GGAATAAAGC
** *
73160 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
73188 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
73216 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
73232 TTGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:73351 original size:52 final size:51
Alignment explanation
Indices: 73220--73389 Score: 157
Period size: 52 Copynumber: 3.3 Consensus size: 51
73210 AAATAACGAG
** * * *
73220 GTTGGAGTATCCTTGATTGT-GAAAAATTGGTATTTTTGGAAATAAAATCGAA
1 GTTGGAGTATCCCCGATTGTGGAAAAATTGG-AGTTTT-GAAATAAAACCGGA
** *
73272 GTTGGAGTATCCCCGATTAAAGG-AAAATTGGCGTTTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATT-GTGGAAAAATTGGAGTTTTG-AAATAAAACC-GGA
* * **
73325 -TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTCGCGATAAAACCGGA
1 GTTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTT-GAAATAAAACCGGA
73376 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
73390 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
51 6 0.06
52 79 0.81
53 11 0.11
54 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTGAAATAAAACCGGA
Found at i:73405 original size:212 final size:212
Alignment explanation
Indices: 73153--73558 Score: 593
Period size: 212 Copynumber: 1.9 Consensus size: 212
73143 TATTTTGGGA
* * * *
73153 ATAAAGCCGGGGTTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACG
1 ATAAAACCGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATG-AATAACG
** *
73218 AGGTTGGAGTATCCTTGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGAAGTTGGAGTA
65 AGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCGAAGTTAGAGTA
* *
73281 TCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTG
130 TCCCCGATTAAA-GAAAATTAGCGTTTTGAAAATAAAACC-GGAGTTGGAATATCCCCGATTGTG
73345 GAAAAATTAGTGTTTTCGCG
193 GAAAAATTAGTGTTTTCGCG
* *
73365 ATAAAACCGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGATTAACGG
1 ATAAAACCGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAATAACGA
** * *
73430 GGTTGTTGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTAGAGTAT
66 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCGAAGTTAGAGTAT
* * * *
73495 CCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCTCGATTGTGGA
131 CCCCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
73559 GAATTGATAA
Statistics
Matches: 172, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
211 29 0.17
212 105 0.61
213 38 0.22
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (212 bp):
ATAAAACCGGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAATAACGA
GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGATTTTTGGAAATAAAATCGAAGTTAGAGTAT
CCCCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAA
AAATTAGTGTTTTCGCG
Done.