Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2730
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: 43197
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:5713 original size:79 final size:78
Alignment explanation
Indices: 5574--6291 Score: 822
Period size: 79 Copynumber: 9.2 Consensus size: 78
5564 CAGAGCACCT
* * * * * * *
5574 CCTCAGAAATAACGGGGTTGGA-TATCCCTAATGGTGGAAAATTGATGTTTTGAAAATAAAATCG
1 CCTCAAAAATAACGGGGTTAGAGTATCCC-GATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
* *
5638 GGGTTGGAATATCT
65 GGGTTGGAGTATCC
** *
5652 CCTCAAAAATAATAGGGTTAGAGTATCTCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCA
1 CCTCAAAAATAACGGGGTTAGAGTATC-CCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
* *
5717 GGATTGAAGTATCC
65 GGGTTGGAGTATCC
* * * *
5731 CCTCGAAAATAACGGGGTTAAAGTATCCACAATTGTGAAAAATTGGTGTTTTGAAAATAAAATCG
1 CCTCAAAAATAACGGGGTTAGAGTATCC-CGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
5796 GGGTTGGAGTATCC
65 GGGTTGGAGTATCC
* * *
5810 CTTCAAAAATAA--GGGTTAGAGTGTCCCCGATTGTGAAAAATTGGTATTTTGAAAATAAAACCG
1 CCTCAAAAATAACGGGGTTAGAGTAT-CCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
*
5873 AGGTTGGAGTATCC
65 GGGTTGGAGTATCC
* * * * *
5887 CCTGATAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTT-AGAAATAAAATC
1 CCTCAAAAATAACGGGGTTAGAGTATCC-CGATTGTGAAAAATTGGTGTTTTGA-AAATAAAACC
**
5951 AAGGTTGGAGTATCC
64 GGGGTTGGAGTATCC
* * * * *
5966 CCTCGAAAATAACGGGGTTGGAATATCTTCGATTGTGAAAAATCGGTGTTTTGAAAATAAAACCG
1 CCTCAAAAATAACGGGGTTAGAGTATC-CCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
*
6031 AGGTTGGAGTATCC
65 GGGTTGGAGTATCC
* ** *
6045 CCTCAGAAATAACAAGGTT-GAAGTATCCCTGATTGTGAAAAATTGGTGTTTTGGAAAT-AAACC
1 CCTCAAAAATAACGGGGTTAG-AGTATCCC-GATTGTGAAAAATTGGTGTTTTGAAAATAAAACC
* *
6108 GAGGG-TGGAATATCT
64 G-GGGTTGGAGTATCC
* * * *
6123 CCTCAAAAATAACGAGGTTAGAGTATCCCCGATTATGAAAAATTGGTGTTTTGTAAATAAAACCA
1 CCTCAAAAATAACGGGGTTAGAGTAT-CCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
6188 GGGTTGGAGTATCC
65 GGGTTGGAGTATCC
* * *
6202 CCTC-AAAATAACGGGGTTGGAGTGTCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAACCG
1 CCTCAAAAATAACGGGGTTAGAGTAT-CCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCG
*
6266 CGGTTGGAGTATCC
65 GGGTTGGAGTATCC
*
6280 CCTCAGAAATAA
1 CCTCAAAAATAA
6292 AAACATGAAT
Statistics
Matches: 548, Mismatches: 74, Indels: 35
0.83 0.11 0.05
Matches are distributed among these distances:
77 65 0.12
78 161 0.29
79 319 0.58
80 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (78 bp):
CCTCAAAAATAACGGGGTTAGAGTATCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCGG
GGTTGGAGTATCC
Found at i:6022 original size:235 final size:234
Alignment explanation
Indices: 5611--6292 Score: 899
Period size: 235 Copynumber: 2.9 Consensus size: 234
5601 CTAATGGTGG
* * * **
5611 AAAATTGATGTTTTGAAAATAAAATCGGGGTTGGAATATCTCCTCAAAAATAATAGGGTTAGAGT
1 AAAATTGGTGTTTTGAAAATAAAACCGAGGTTGGAATATCTCCTCAAAAATAACGGGGTTAGAGT
* *
5676 AT-CTCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCAGGATTGAAGTATCCCCTCGAAAA
66 ATCCT-CGATTGTGAAAAATTGGTGTTTTGAAAATAAAACAAGG-TTGGAGTATCCCCTCGAAAA
* * * *
5740 TAACGGGGTT-AAAGTATCCACAATTGTGAAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGA
129 TAACGGGGTTGGAA-TATCCACGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCGAGGTTGGA
* * * *
5804 GTATCCCTTCAAAAATAAGGGTT-AGAGTGTCCCCGATTGTGA
193 GTATCCCCTCAGAAATAAAGGTTGA-AGTATCCCCGATTGTGA
* * * * * *
5846 AAAATTGGTATTTTGAAAATAAAACCGAGGTTGGAGTATCCCCTGATAAATAACGGGGTTGGAGT
1 AAAATTGGTGTTTTGAAAATAAAACCGAGGTTGGAATATCTCCTCAAAAATAACGGGGTTAGAGT
*
5911 ATCCTCGATTGTGAAAAATTGGTATTTT-AGAAATAAAATCAAGGTTGGAGTATCCCCTCGAAAA
66 ATCCTCGATTGTGAAAAATTGGTGTTTTGA-AAATAAAA-CAAGGTTGGAGTATCCCCTCGAAAA
** *
5975 TAACGGGGTTGGAATATCTTCGATTGTGAAAAATCGGTGTTTTGAAAATAAAACCGAGGTTGGAG
129 TAACGGGGTTGGAATATCCACGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCGAGGTTGGAG
*
6040 TATCCCCTCAGAAATAACAAGGTTGAAGTATCCCTGATTGTGA
194 TATCCCCTCAGAAAT-A-AAGGTTGAAGTATCCCCGATTGTGA
* * *
6083 AAAATTGGTGTTTTGGAAAT-AAACCGAGGGTGGAATATCTCCTCAAAAATAACGAGGTTAGAGT
1 AAAATTGGTGTTTTGAAAATAAAACCGAGGTTGGAATATCTCCTCAAAAATAACGGGGTTAGAGT
* * * *
6147 ATCCCCGATTATGAAAAATTGGTGTTTTGTAAATAAAACCAGGGTTGGAGTATCCCCTC-AAAAT
66 ATCCTCGATTGTGAAAAATTGGTGTTTTGAAAATAAAA-CAAGGTTGGAGTATCCCCTCGAAAAT
* * * * *
6211 AACGGGGTTGGAGTGTCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAACCGCGGTTGGAGT
130 AACGGGGTTGGAATATCCACGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCGAGGTTGGAGT
6276 ATCCCCTCAGAAATAAA
195 ATCCCCTCAGAAATAAA
6293 AACATGAATG
Statistics
Matches: 391, Mismatches: 48, Indels: 18
0.86 0.11 0.04
Matches are distributed among these distances:
233 2 0.01
234 2 0.01
235 250 0.64
236 98 0.25
237 38 0.10
238 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.28
Consensus pattern (234 bp):
AAAATTGGTGTTTTGAAAATAAAACCGAGGTTGGAATATCTCCTCAAAAATAACGGGGTTAGAGT
ATCCTCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACAAGGTTGGAGTATCCCCTCGAAAATA
ACGGGGTTGGAATATCCACGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCGAGGTTGGAGTA
TCCCCTCAGAAATAAAGGTTGAAGTATCCCCGATTGTGA
Found at i:6082 original size:314 final size:313
Alignment explanation
Indices: 5574--6288 Score: 946
Period size: 314 Copynumber: 2.3 Consensus size: 313
5564 CAGAGCACCT
* * *
5574 CCTCAGAAATAACGGGGTTGGA-TATCCCTAATGGTGGAAAATTGATGTTTTGAAAATAAAATCG
1 CCTCA-AAATAACGGGGTTGGAGTATCCC-GATTGTGAAAAATTGATGTTTTGAAAATAAAATCG
* * * * * * *
5638 GGGTTGGAATATCTCCTCAAAAATAATAGGGTTAGAGTATCTCCGATTGTGAAAAATTGGTGTTT
64 AGGTTGGAGTATCCCCTCGAAAATAACAGGGTTAGAATATCTCCGATTGTGAAAAATCGGTGTTT
**
5703 TGAAAATAAAACCAGGATTGAAGTATCCCCTCGAAAATAACGGGGTTAAAGTATCCACAATTGTG
129 TGAAAATAAAACCAGGATTGAAGTATCCCCTCGAAAATAACAAGGTTAAAGTATCCACAATTGTG
* *
5768 AAAAATTGGTGTTTTGAAAATAAAATCG-GGGTTGGAGTATC-CCTTCAAAAATAA-G-GGTTAG
194 AAAAATTGGTGTTTTGAAAAT-AAACCGAGGG-TGGAATATCTCC-TCAAAAATAACGAGGTTAG
* *
5829 AGTGTCCCCGATTGTGAAAAATTGGTATTTTGAAAATAAAACC-GAGGTTGGAGTATCC
256 AGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAACCAG-GGTTGGAGTATCC
* * *
5887 CCTGATAAATAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTT-AGAAATAAAATC
1 CCTCA-AAATAACGGGGTTGGAGTATCC-CGATTGTGAAAAATTGATGTTTTGA-AAATAAAATC
* * * *
5951 AAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAATATCTTCGATTGTGAAAAATCGGTGTT
63 GAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTAGAATATCTCCGATTGTGAAAAATCGGTGTT
* * *
6016 TTGAAAATAAAACCGAGG-TTGGAGTATCCCCTC-AGAAATAACAAGGTTGAAGTATCC-CTGAT
128 TTGAAAATAAAACC-AGGATTGAAGTATCCCCTCGA-AAATAACAAGGTTAAAGTATCCAC-AAT
*
6078 TGTGAAAAATTGGTGTTTTGGAAATAAACCGAGGGTGGAATATCTCCTCAAAAATAACGAGGTTA
190 TGTGAAAAATTGGTGTTTTGAAAATAAACCGAGGGTGGAATATCTCCTCAAAAATAACGAGGTTA
* *
6143 GAGTATCCCCGATTATGAAAAATTGGTGTTTTGTAAATAAAACCAGGGTTGGAGTATCC
255 GAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAACCAGGGTTGGAGTATCC
* * *
6202 CCTCAAAATAACGGGGTTGGAGTGTCCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAACCGC
1 CCTCAAAATAACGGGGTTGGAGTAT-CCCGATTGTGAAAAATTGATGTTTTGAAAATAAAATCGA
6267 GGTTGGAGTATCCCCTCAGAAA
65 GGTTGGAGTATCCCCTC-GAAA
6289 TAAAAACATG
Statistics
Matches: 351, Mismatches: 37, Indels: 26
0.85 0.09 0.06
Matches are distributed among these distances:
313 46 0.13
314 231 0.66
315 73 0.21
316 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.28
Consensus pattern (313 bp):
CCTCAAAATAACGGGGTTGGAGTATCCCGATTGTGAAAAATTGATGTTTTGAAAATAAAATCGAG
GTTGGAGTATCCCCTCGAAAATAACAGGGTTAGAATATCTCCGATTGTGAAAAATCGGTGTTTTG
AAAATAAAACCAGGATTGAAGTATCCCCTCGAAAATAACAAGGTTAAAGTATCCACAATTGTGAA
AAATTGGTGTTTTGAAAATAAACCGAGGGTGGAATATCTCCTCAAAAATAACGAGGTTAGAGTAT
CCCCGATTATGAAAAATTGGTATTTTGAAAATAAAACCAGGGTTGGAGTATCC
Found at i:10507 original size:21 final size:21
Alignment explanation
Indices: 10483--10529 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
10473 CCAAGTATAT
* * *
10483 GTATCGATACATGTATGTTAG
1 GTATCGAAACACGCATGTTAG
10504 GTATCGAAACACGCATGTTAG
1 GTATCGAAACACGCATGTTAG
10525 GTATC
1 GTATC
10530 AACACATTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (21 bp):
GTATCGAAACACGCATGTTAG
Found at i:11065 original size:14 final size:14
Alignment explanation
Indices: 11046--11075 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11036 CTTTTAAATT
11046 TCATAACTCTCTAA
1 TCATAACTCTCTAA
*
11060 TCATAACTTTCTAA
1 TCATAACTCTCTAA
11074 TC
1 TC
11076 TCTCTAAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (14 bp):
TCATAACTCTCTAA
Found at i:12158 original size:33 final size:33
Alignment explanation
Indices: 12095--12160 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
12085 GCCGTTATAA
* * *
12095 GCAATGTATCGATACAATTCATCATGTATCGAT
1 GCAAGGTAGCGATACAATTCATCATATATCGAT
*
12128 GCAAGGTAGCGATACAATGTCCT-ATATATCGAT
1 GCAAGGTAGCGATACAAT-TCATCATATATCGAT
12161 ACAAACAGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 25 0.89
34 3 0.11
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (33 bp):
GCAAGGTAGCGATACAATTCATCATATATCGAT
Found at i:20954 original size:20 final size:20
Alignment explanation
Indices: 20931--21003 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
20921 ACAATTCAAA
20931 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
20951 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
20972 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
20992 GTATCGATACAT
1 GTATCGATACAT
21004 AAAAAAGATG
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:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:20975 original size:21 final size:21
Alignment explanation
Indices: 20949--21024 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
20939 ACATGTTGCA
20949 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
20970 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
20990 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
21011 ATGTATCGATACAT
1 ATGTATCGATACAT
21025 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:20982 original size:41 final size:41
Alignment explanation
Indices: 20931--21024 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
20921 ACAATTCAAA
*
20931 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
20972 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
21013 GTATCGATACAT
1 GTATCGATACAT
21025 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:21081 original size:13 final size:13
Alignment explanation
Indices: 21063--21088 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21053 TACAGCAAGT
21063 ATGTATCGATACA
1 ATGTATCGATACA
21076 ATGTATCGATACA
1 ATGTATCGATACA
21089 CAAAAAATTG
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:25169 original size:15 final size:15
Alignment explanation
Indices: 25149--25179 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25139 TAAAAATGTC
*
25149 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
25164 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
25179 C
1 C
25180 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:27272 original size:20 final size:21
Alignment explanation
Indices: 27193--27271 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
27183 AATGTCCAAA
*
27193 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
27213 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
27238 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
27258 TTGTATCGATACAT
1 ATGTATCGATACAT
27272 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:27276 original size:13 final size:13
Alignment explanation
Indices: 27258--27296 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
27248 ACATTTTTCT
27258 TTGTATCGATACA
1 TTGTATCGATACA
27271 TTGTATCGATACA
1 TTGTATCGATACA
*
27284 CTGTATCGATACA
1 TTGTATCGATACA
27297 GGGTGATTAT
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:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:29121 original size:16 final size:16
Alignment explanation
Indices: 29100--29144 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
29090 GAATTACTTG
29100 ATTAAGGGGGAGATTT
1 ATTAAGGGGGAGATTT
29116 ATTAA--GGGAGATTT
1 ATTAAGGGGGAGATTT
*
29130 AATAACGGGGGAGAT
1 ATTAA-GGGGGAGAT
29145 AAAGGAGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 13 0.52
16 5 0.20
17 7 0.28
ACGTcount: A:0.36, C:0.02, G:0.36, T:0.27
Consensus pattern (16 bp):
ATTAAGGGGGAGATTT
Found at i:29769 original size:20 final size:20
Alignment explanation
Indices: 29746--29818 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
29736 ACAATTCAAA
29746 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
29766 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
29787 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
29807 GTATCGATACAT
1 GTATCGATACAT
29819 AAAAAAGATG
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:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:29790 original size:21 final size:21
Alignment explanation
Indices: 29764--29839 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
29754 ACATGTTGCA
29764 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
29785 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
29805 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
29826 ATGTATCGATACAT
1 ATGTATCGATACAT
29840 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:29797 original size:41 final size:41
Alignment explanation
Indices: 29746--29839 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
29736 ACAATTCAAA
*
29746 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
29787 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
29828 GTATCGATACAT
1 GTATCGATACAT
29840 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:29896 original size:13 final size:13
Alignment explanation
Indices: 29878--29903 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29868 TACAGCAAGT
29878 ATGTATCGATACA
1 ATGTATCGATACA
29891 ATGTATCGATACA
1 ATGTATCGATACA
29904 CAAAAAATTG
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:31153 original size:20 final size:20
Alignment explanation
Indices: 31130--31203 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
31120 ACAATTCAAA
31130 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
**
31150 GTATCGATACATGAAAAAG-AAT
1 GTATCGATACATG---TTGCAAT
31172 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
31192 GTATCGATACAT
1 GTATCGATACAT
31204 AAAAAAGATG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.02
20 28 0.61
22 16 0.35
23 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:31220 original size:41 final size:42
Alignment explanation
Indices: 31130--31224 Score: 174
Period size: 42 Copynumber: 2.3 Consensus size: 42
31120 ACAATTCAAA
*
31130 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAAT
31172 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAG-AT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAAT
31213 GTATCGATACAT
1 GTATCGATACAT
31225 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 14 0.27
42 38 0.73
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAAT
Found at i:31281 original size:13 final size:13
Alignment explanation
Indices: 31263--31288 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31253 TACAGCAAGT
31263 ATGTATCGATACA
1 ATGTATCGATACA
31276 ATGTATCGATACA
1 ATGTATCGATACA
31289 CAAAAATTGT
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:31286 original size:32 final size:32
Alignment explanation
Indices: 31245--31307 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
31235 TAGCCAAACT
**
31245 TGTATCGATACAGCAAGTA-TGTATCGATACAA
1 TGTATCGATACA-CAAAAATTGTATCGATACAA
31277 TGTATCGATACACAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAATTGTATCGATACA
31308 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAAATTGTATCGATACAA
Found at i:35032 original size:13 final size:13
Alignment explanation
Indices: 35014--35038 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35004 TTTTCCAGAT
35014 TGTATCGATACAA
1 TGTATCGATACAA
35027 TGTATCGATACA
1 TGTATCGATACA
35039 TTGCTTCAGT
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:36618 original size:20 final size:20
Alignment explanation
Indices: 36595--36667 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
36585 ACAATTCAAA
36595 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
36615 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
36636 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
36656 GTATCGATACAT
1 GTATCGATACAT
36668 AAAAAAGATG
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:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:36639 original size:21 final size:21
Alignment explanation
Indices: 36613--36688 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
36603 ACATGTTGCA
36613 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
36634 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
36654 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
36675 ATGTATCGATACAT
1 ATGTATCGATACAT
36689 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:36646 original size:41 final size:41
Alignment explanation
Indices: 36595--36688 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
36585 ACAATTCAAA
*
36595 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
36636 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
36677 GTATCGATACAT
1 GTATCGATACAT
36689 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:36745 original size:13 final size:13
Alignment explanation
Indices: 36727--36752 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
36717 TACAGCAAGT
36727 ATGTATCGATACA
1 ATGTATCGATACA
36740 ATGTATCGATACA
1 ATGTATCGATACA
36753 CAAAAAATTG
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:40508 original size:13 final size:13
Alignment explanation
Indices: 40490--40514 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40480 TTTTCCAGAT
40490 TGTATCGATACAA
1 TGTATCGATACAA
40503 TGTATCGATACA
1 TGTATCGATACA
40515 TTGCTTCAGT
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:42094 original size:20 final size:20
Alignment explanation
Indices: 42071--42143 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
42061 ACAATTCAAA
42071 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
42091 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
42112 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
42132 GTATCGATACAT
1 GTATCGATACAT
42144 AAAAAGATGT
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:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:42122 original size:41 final size:40
Alignment explanation
Indices: 42071--42163 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 40
42061 ACAATTCAAA
42071 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAT
42112 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAT
42152 GTATCGATACAT
1 GTATCGATACAT
42164 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 20 0.38
41 32 0.62
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (40 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAT
Found at i:42153 original size:20 final size:21
Alignment explanation
Indices: 42089--42163 Score: 100
Period size: 20 Copynumber: 3.7 Consensus size: 21
42079 ACATGTTGCA
42089 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
42110 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
42130 ATGTATCGATACAT-AAAAAG
1 ATGTATCGATACATGAAAAAG
42150 ATGTATCGATACAT
1 ATGTATCGATACAT
42164 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
19 1 0.02
20 28 0.62
21 16 0.36
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:42220 original size:13 final size:13
Alignment explanation
Indices: 42202--42227 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42192 TACAGCAAGT
42202 ATGTATCGATACA
1 ATGTATCGATACA
42215 ATGTATCGATACA
1 ATGTATCGATACA
42228 CAAAAAATTG
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
Done.