Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1540
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: 198670
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 2 of 2
Found at i:148765 original size:14 final size:14
Alignment explanation
Indices: 148738--148797 Score: 95
Period size: 14 Copynumber: 4.4 Consensus size: 14
148728 TGTGATGGTA
148738 ATGT-GAATGCATG
1 ATGTGGAATGCATG
*
148751 ATGTGGAATGTATG
1 ATGTGGAATGCATG
148765 ATGTGGAATGCATG
1 ATGTGGAATGCATG
*
148779 ATGTTGAATGCATG
1 ATGTGGAATGCATG
148793 ATGTG
1 ATGTG
148798 AAGTTTAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
13 4 0.10
14 38 0.90
ACGTcount: A:0.28, C:0.05, G:0.33, T:0.33
Consensus pattern (14 bp):
ATGTGGAATGCATG
Found at i:149816 original size:23 final size:24
Alignment explanation
Indices: 149790--149845 Score: 80
Period size: 22 Copynumber: 2.4 Consensus size: 24
149780 TTTTTCTACT
149790 TTTTTTTTACCTTTGTT-TTTTTG
1 TTTTTTTTACCTTTGTTGTTTTTG
* *
149813 -TTTTTTTAACTTTTTTGTTTTTG
1 TTTTTTTTACCTTTGTTGTTTTTG
149836 TTTTTTTTAC
1 TTTTTTTTAC
149846 ATAAGGTGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.50
23 6 0.21
24 8 0.29
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (24 bp):
TTTTTTTTACCTTTGTTGTTTTTG
Found at i:151037 original size:20 final size:20
Alignment explanation
Indices: 151003--151042 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
150993 GTTACAAGGA
* *
151003 ATGTATCGATGCAATTCATC
1 ATGTATCGATACAATGCATC
*
151023 ATGTATCTATACAATGCATC
1 ATGTATCGATACAATGCATC
151043 GATACATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATGCATC
Found at i:151053 original size:20 final size:20
Alignment explanation
Indices: 151030--151068 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
151020 ATCATGTATC
151030 TATACAATGCATCGATACAT
1 TATACAATGCATCGATACAT
* *
151050 TATACCATGTATCGATACA
1 TATACAATGCATCGATACA
151069 AACAGTGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (20 bp):
TATACAATGCATCGATACAT
Found at i:151142 original size:19 final size:20
Alignment explanation
Indices: 151098--151151 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
151088 CTACCAATTT
**
151098 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
151118 CATGTATCGATAGAA-TGAA
1 CATGTATCGATACAATTGAA
151137 CATGTATCGATACAA
1 CATGTATCGATACAA
151152 AGCATAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:151814 original size:127 final size:127
Alignment explanation
Indices: 151588--151827 Score: 444
Period size: 127 Copynumber: 1.9 Consensus size: 127
151578 TATAGGCTTG
151588 TATACAATCATTTTCTTGTATCAACATGAATCAAAACCTGTAATCTGATACACAACTTCAAGAAA
1 TATACAATCATTTTCTTGTATCAACATGAATCAAAACCTGTAATCTGATACACAACTTCAAGAAA
*
151653 TGCATTAGAAAAGTTTCGATATCAAAGTTTTCAAGTTTTCATTTTTCTAGTATCAAAACCTA
66 TGCATTAGAAAAGTTCCGATATCAAAGTTTTCAAGTTTTCATTTTTCTAGTATCAAAACCTA
151715 TATACAATCATTTTCTTGTATCAACATGAATCAAAACCTGTAATCTGATACACAACTTCAAGAAA
1 TATACAATCATTTTCTTGTATCAACATGAATCAAAACCTGTAATCTGATACACAACTTCAAGAAA
* **
151780 TGCATTAGAAAAGTTCCGGTATCAAAGTTTTCAAGTTTTTGTTTTTCT
66 TGCATTAGAAAAGTTCCGATATCAAAGTTTTCAAGTTTTCATTTTTCT
151828 CCCCCTTAAT
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 109 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (127 bp):
TATACAATCATTTTCTTGTATCAACATGAATCAAAACCTGTAATCTGATACACAACTTCAAGAAA
TGCATTAGAAAAGTTCCGATATCAAAGTTTTCAAGTTTTCATTTTTCTAGTATCAAAACCTA
Found at i:151885 original size:22 final size:22
Alignment explanation
Indices: 151823--151878 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
151813 AGTTTTTGTT
151823 TTTCTCCCCCTTAATCAAAGAA
1 TTTCTCCCCCTTAATCAAAGAA
*
151845 TTTCTCCCCCTTAATCAAAGCA
1 TTTCTCCCCCTTAATCAAAGAA
151867 TTTCTCCCCCTT
1 TTTCTCCCCCTT
151879 TGTCAAATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.23, C:0.38, G:0.04, T:0.36
Consensus pattern (22 bp):
TTTCTCCCCCTTAATCAAAGAA
Found at i:153280 original size:316 final size:316
Alignment explanation
Indices: 152707--153631 Score: 1652
Period size: 316 Copynumber: 2.9 Consensus size: 316
152697 GTCGAAGAAT
152707 ATGAGTAATGAGGAGATGGAGGTATCGATCGTGTGGTGCAAGGTGAGTGGCTTTGTTGGATGGAA
1 ATGAGTAATGAGGAGATGGAGGTATCGATCGTGTGGTGCAAGGTGAGTGGCTTTGTTGGATGGAA
*
152772 CTCTCGTATTACGAGGGACCGACCCCTCTTTGGTTTCTCCCTCACAAGGCATATTTAGTGTATTG
66 CTCTCGTATTACGAGGGGCCGACCCCTCTTTGGTTTCTCCCTCACAAGGCATATTTAGTGTATTG
152837 GCTAGGATGGAGGGGGTGAGGCCTAAGTCTTGGCCCATAAGATAGGAATGAATAGCAACGATTTC
131 GCTAGGATGGAGGGGGTGAGGCCTAAGTCTTGGCCCATAAGATAGGAATGAATAGCAACGATTTC
152902 GTTGCTATCGTTATGCTCGAGTCAGGCGTTACTTAGGAAGGCTCGGATTAGGTTCTCGTGAACCG
196 GTTGCTATCGTTATGCTCGAGTCAGGCGTTACTTAGGAAGGCTCGGATTAGGTTCTCGTGAACCG
*
152967 ATACGTTTAAGCTTAGAAGAGTTATCCAACCGATATGTTTAACCCCCAAACATCTC
261 ATACGTTTAAGCTTAGAAGAGTTATCCAACCGATACGTTTAACCCCCAAACATCTC
153023 ATGAGTAATGAGGAGATGGAGGTATCGATCGTGTGGTGCAAGGTGAGTGGCTTTGTTGGATGGAA
1 ATGAGTAATGAGGAGATGGAGGTATCGATCGTGTGGTGCAAGGTGAGTGGCTTTGTTGGATGGAA
* *
153088 CTCTCGTATTACGAGGGGCTGACCCCTCTTTGGTTTCTTCCTCACAAGGCATATTTAGTGTATTG
66 CTCTCGTATTACGAGGGGCCGACCCCTCTTTGGTTTCTCCCTCACAAGGCATATTTAGTGTATTG
* * *
153153 GCTACGATGGAGGGGGTGAGGCCTAGGTCTTGGCCCATAAGATAGGAATTAATAGCAACGATTTC
131 GCTAGGATGGAGGGGGTGAGGCCTAAGTCTTGGCCCATAAGATAGGAATGAATAGCAACGATTTC
* * *
153218 TTTGCTATCGTTATGCTTGAGTCAGGCGTTACTTAGGAAGGCTGGGATTAGGTTCTCGTGAACCG
196 GTTGCTATCGTTATGCTCGAGTCAGGCGTTACTTAGGAAGGCTCGGATTAGGTTCTCGTGAACCG
* * * * *
153283 ATACATTTCAGCTTAGAAGAGTTATCCAACAGATACGTTTAACCCTCGAACATCTC
261 ATACGTTTAAGCTTAGAAGAGTTATCCAACCGATACGTTTAACCCCCAAACATCTC
* *
153339 AAGAGTAATGAGGAGATGGACGTATCGATCGTGTGGTGCAAGGTGAGTGGCTTTGTTGGATGGAA
1 ATGAGTAATGAGGAGATGGAGGTATCGATCGTGTGGTGCAAGGTGAGTGGCTTTGTTGGATGGAA
*
153404 CTCTTGTATTACGAGGGGCCGACCCCTCTTTGGTTTCTCCCTCACAAGGCATATTTAGTGTATTG
66 CTCTCGTATTACGAGGGGCCGACCCCTCTTTGGTTTCTCCCTCACAAGGCATATTTAGTGTATTG
* *
153469 GCTAGGATGAAGGGGGTGAGGACTAAGTCTTGGCCCATAAGATAGGAATGAATAGCAACGATTTC
131 GCTAGGATGGAGGGGGTGAGGCCTAAGTCTTGGCCCATAAGATAGGAATGAATAGCAACGATTTC
*
153534 GTTGCTATCGTTATGCTCGAGCCAGGCGTTACTTAGGAAGGCTCGGATTAGGTTCTCGTGAACCG
196 GTTGCTATCGTTATGCTCGAGTCAGGCGTTACTTAGGAAGGCTCGGATTAGGTTCTCGTGAACCG
*
153599 ATATGTTTAAGCTTAGAAGAGTTATCCAACCGA
261 ATACGTTTAAGCTTAGAAGAGTTATCCAACCGA
153632 ACATCTCAAG
Statistics
Matches: 576, Mismatches: 33, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
316 576 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (316 bp):
ATGAGTAATGAGGAGATGGAGGTATCGATCGTGTGGTGCAAGGTGAGTGGCTTTGTTGGATGGAA
CTCTCGTATTACGAGGGGCCGACCCCTCTTTGGTTTCTCCCTCACAAGGCATATTTAGTGTATTG
GCTAGGATGGAGGGGGTGAGGCCTAAGTCTTGGCCCATAAGATAGGAATGAATAGCAACGATTTC
GTTGCTATCGTTATGCTCGAGTCAGGCGTTACTTAGGAAGGCTCGGATTAGGTTCTCGTGAACCG
ATACGTTTAAGCTTAGAAGAGTTATCCAACCGATACGTTTAACCCCCAAACATCTC
Found at i:154273 original size:20 final size:19
Alignment explanation
Indices: 154232--154271 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
154222 TTTTGTTGAT
154232 GATTTTGATGAAAAATGAAA
1 GATTTTGATGAAAAAT-AAA
154252 GATTTTGAAGTGAAAAATAA
1 GATTTTG-A-TGAAAAATAA
154272 GAAATTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (19 bp):
GATTTTGATGAAAAATAAA
Found at i:160548 original size:19 final size:21
Alignment explanation
Indices: 160524--160576 Score: 76
Period size: 19 Copynumber: 2.7 Consensus size: 21
160514 TTGCCAATTT
*
160524 CATGTATCGATACAATG-A-A
1 CATGTATCGATACAAAGCATA
160543 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAAAGCATA
160564 -ATGTATCGATACA
1 CATGTATCGATACA
160577 TCTGGGTGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 16 0.52
20 14 0.45
21 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.26
Consensus pattern (21 bp):
CATGTATCGATACAAAGCATA
Found at i:166993 original size:13 final size:13
Alignment explanation
Indices: 166975--167000 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
166965 AATTTGGTCA
166975 TGTATCGATACAT
1 TGTATCGATACAT
166988 TGTATCGATACAT
1 TGTATCGATACAT
167001 CTTGTAAGTA
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:167693 original size:21 final size:22
Alignment explanation
Indices: 167667--167711 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
167657 TTTCCTTTTC
167667 TCTCCCCCTTAATAAAA-AATT
1 TCTCCCCCTTAATAAAACAATT
167688 TCTCCCCCTTAATAAAACAATT
1 TCTCCCCCTTAATAAAACAATT
167710 TC
1 TC
167712 CTTTAATCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.36, C:0.31, G:0.00, T:0.33
Consensus pattern (22 bp):
TCTCCCCCTTAATAAAACAATT
Found at i:167728 original size:17 final size:17
Alignment explanation
Indices: 167708--167759 Score: 95
Period size: 17 Copynumber: 3.1 Consensus size: 17
167698 AATAAAACAA
167708 TTTCCTTTAATCACATG
1 TTTCCTTTAATCACATG
167725 TTTCCTTTAATCACATG
1 TTTCCTTTAATCACATG
*
167742 TTTGCTTTAATCACATG
1 TTTCCTTTAATCACATG
167759 T
1 T
167760 ATATTTCTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.23, C:0.21, G:0.08, T:0.48
Consensus pattern (17 bp):
TTTCCTTTAATCACATG
Found at i:173888 original size:13 final size:13
Alignment explanation
Indices: 173870--173895 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
173860 TACAGCAAGT
173870 ATGTATCGATACA
1 ATGTATCGATACA
173883 ATGTATCGATACA
1 ATGTATCGATACA
173896 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:176268 original size:13 final size:13
Alignment explanation
Indices: 176250--176275 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
176240 CAATTTTTTG
176250 TGTATCGATACAT
1 TGTATCGATACAT
176263 TGTATCGATACAT
1 TGTATCGATACAT
176276 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:176287 original size:32 final size:33
Alignment explanation
Indices: 176230--176293 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
176220 TACAAGCCAA
**
176230 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
176263 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
176294 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:177036 original size:21 final size:21
Alignment explanation
Indices: 176995--177038 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
176985 CTCCTCTTTA
* *
176995 TCTCCCCCTTTTATTAATAAT
1 TCTCCCCCTTTAATCAATAAT
177016 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCTTTAATCAA-TAAT
177037 TC
1 TC
177039 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.02, T:0.41
Consensus pattern (21 bp):
TCTCCCCCTTTAATCAATAAT
Found at i:178848 original size:13 final size:13
Alignment explanation
Indices: 178832--178868 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
178822 AATCCCCCTA
*
178832 TATCGATACAGTG
1 TATCGATACAATG
178845 TATCGATACAATG
1 TATCGATACAATG
178858 TATCGATACAA
1 TATCGATACAA
178869 AGAAAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:180969 original size:15 final size:15
Alignment explanation
Indices: 180944--180979 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
180934 ATCGATTTCG
*
180944 TTTGAAGCTTCTTCAT
1 TTTG-AGCTTCCTCAT
180960 TTTGAGCTTCCTCAT
1 TTTGAGCTTCCTCAT
180975 TTTGA
1 TTTGA
180980 ACACTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.17, C:0.19, G:0.14, T:0.50
Consensus pattern (15 bp):
TTTGAGCTTCCTCAT
Found at i:185062 original size:20 final size:20
Alignment explanation
Indices: 185037--185088 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
185027 TACAAGCCAA
**
185037 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
185057 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
185076 TGTATCGATACAA
1 TGTATCGATACAA
185089 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:186960 original size:15 final size:13
Alignment explanation
Indices: 186928--186953 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
186918 AATTTGGTCA
186928 TGTATCGATACAT
1 TGTATCGATACAT
186941 TGTATCGATACAT
1 TGTATCGATACAT
186954 CTTGTATGTA
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:187090 original size:33 final size:33
Alignment explanation
Indices: 187035--187098 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
187025 TTCTTTGCAA
*
187035 GTATCGATACATTTGCTCATGTAGCGATACAAT
1 GTATCGATACATGTGCTCATGTAGCGATACAAT
* *
187068 GTATCGATAC-TGTGCATTATGTATCGATACA
1 GTATCGATACATGTGC-TCATGTAGCGATACA
187099 TCTGAAGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 4 0.15
33 23 0.85
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (33 bp):
GTATCGATACATGTGCTCATGTAGCGATACAAT
Found at i:187856 original size:20 final size:20
Alignment explanation
Indices: 187831--187881 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
187821 GTTACAAGCA
187831 ATGTATCGATACAATT-CATC
1 ATGTATCGATAC-ATTGCATC
*
187851 ATGTATCGATACATTGTATC
1 ATGTATCGATACATTGCATC
187871 ATGTATCGATA
1 ATGTATCGATA
187882 GAAACAGTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCATC
Found at i:187937 original size:19 final size:19
Alignment explanation
Indices: 187913--187965 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
187903 CTACCAATTT
*
187913 CATGTATCGATACAATGAA
1 CATGTATCGATACAATAAA
187932 CATGTATCGATACAATAAA
1 CATGTATCGATACAATAAA
**
187951 TGTGTATCGATACAA
1 CATGTATCGATACAA
187966 AGCATAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (19 bp):
CATGTATCGATACAATAAA
Found at i:188583 original size:22 final size:22
Alignment explanation
Indices: 188558--188599 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
188548 AGATAAACAT
*
188558 ATTTCTCCCCTTTTATCAAAGC
1 ATTTCTCCCCCTTTATCAAAGC
*
188580 ATTTCTCCCCCTTTGTCAAA
1 ATTTCTCCCCCTTTATCAAA
188600 TCTTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.33, G:0.05, T:0.40
Consensus pattern (22 bp):
ATTTCTCCCCCTTTATCAAAGC
Found at i:195775 original size:20 final size:21
Alignment explanation
Indices: 195750--195799 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
195740 TTATCTATAT
* *
195750 ATTGTATCGATTACAT-GTTC
1 ATTGTATCGATTACATGGATA
195770 ATTGTAT-GA-TACATGGATA
1 ATTGTATCGATTACATGGATA
195789 ATTGTATCGAT
1 ATTGTATCGAT
195800 CCATGAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 5 0.20
19 11 0.44
20 9 0.36
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (21 bp):
ATTGTATCGATTACATGGATA
Done.