Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1223
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: 62741
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:765 original size:206 final size:208
Alignment explanation
Indices: 410--828 Score: 824
Period size: 206 Copynumber: 2.0 Consensus size: 208
400 TTCGATCTTA
410 GCCGATCTTTTAATGATGCCATGTGAGGGTGAAACCATAGAGAGACCGGTTCCTCGAAATGTTCG
1 GCCGATCTTTTAATGATGCCATGTGAGGGTGAAACCATAGAGAGACCGGTTCCTCGAAATGTTCG
475 AGTGCCCAACAACAAAGCCAAACACCTTCAATCACATGATCGATTCCTTCACCTGTTAATCACCC
66 AGTGCCCAACAACAAAGCCAAACACCTTCAATCACATGATCGATTCCTTCACCTGTTAATCACCC
540 ACATCTTCCGTCCCTTTGGTACACAATACTCAACGCTTACGGAGTCCGACTATTGGTGGCTCCAC
131 ACATCTTCCGTCCCTTTGGTACACAATACTCAACGCTTACGGAGTCCGACTATTGGTGGCTCCAC
605 ATGATCCGTACC-
196 ATGATCCGTACCG
617 GCCGATCTTTTAATGATGCCATGTGAGGGTGAAACCATAGAGAGACCGGTTCCTCGAAATGTTCG
1 GCCGATCTTTTAATGATGCCATGTGAGGGTGAAACCATAGAGAGACCGGTTCCTCGAAATGTTCG
682 AGTGCCC-ACAACAAAGCCAAACACCTTCAATCACATGATCGATTCCTTCACCTGTTAATCACCC
66 AGTGCCCAACAACAAAGCCAAACACCTTCAATCACATGATCGATTCCTTCACCTGTTAATCACCC
746 ACATCTTCCGTCCCTTTGGTACACAATACTCAACGCTTACGGAGTCCGACTATTGGTGGCTCCAC
131 ACATCTTCCGTCCCTTTGGTACACAATACTCAACGCTTACGGAGTCCGACTATTGGTGGCTCCAC
811 ATGATCCGTACCG
196 ATGATCCGTACCG
824 GCCGA
1 GCCGA
829 AGACCCAACC
Statistics
Matches: 211, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
206 134 0.64
207 77 0.36
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.25
Consensus pattern (208 bp):
GCCGATCTTTTAATGATGCCATGTGAGGGTGAAACCATAGAGAGACCGGTTCCTCGAAATGTTCG
AGTGCCCAACAACAAAGCCAAACACCTTCAATCACATGATCGATTCCTTCACCTGTTAATCACCC
ACATCTTCCGTCCCTTTGGTACACAATACTCAACGCTTACGGAGTCCGACTATTGGTGGCTCCAC
ATGATCCGTACCG
Found at i:2292 original size:13 final size:13
Alignment explanation
Indices: 2274--2299 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2264 TACACCAAGT
2274 ATGTATCGATACA
1 ATGTATCGATACA
2287 ATGTATCGATACA
1 ATGTATCGATACA
2300 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:2297 original size:32 final size:33
Alignment explanation
Indices: 2256--2319 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2246 TAGCCAAACT
* **
2256 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2288 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2320 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:8266 original size:33 final size:33
Alignment explanation
Indices: 8224--8290 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
8214 TGAGAGTTGA
* *
8224 TCACTTCACTTTCGCAGCACATGAATGATCACT
1 TCACTTCACTCTCGCAGCACATGAATGAGCACT
* * *
8257 TCACTTCACTCTCGTAGCGCATGGATGAGCACT
1 TCACTTCACTCTCGCAGCACATGAATGAGCACT
8290 T
1 T
8291 TAGTTCTCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (33 bp):
TCACTTCACTCTCGCAGCACATGAATGAGCACT
Found at i:9254 original size:19 final size:20
Alignment explanation
Indices: 9228--9284 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
9218 GTATCTATAC
**
9228 AATGTATCGATACATGTTC-
1 AATGTATCGATACATGAACA
* *
9247 ATTGTATCGATATATGAACA
1 AATGTATCGATACATGAACA
9267 AATGTATCGATACATGAA
1 AATGTATCGATACATGAA
9285 ACTGGTAGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATGAACA
Found at i:10973 original size:31 final size:31
Alignment explanation
Indices: 10935--11079 Score: 139
Period size: 31 Copynumber: 4.4 Consensus size: 31
10925 TTCTTCAATA
*
10935 TATCGATACATTTTGTCTTTGTACCCAGATG
1 TATCGATACATTCTGTCTTTGTACCCAGATG
*
10966 TATCGATACATTCTGTCTTTGTACCTAGATG
1 TATCGATACATTCTGTCTTTGTACCCAGATG
**
10997 TATCGATACATTCT-TCAATGTATCGATACATGTATGAATG
1 TATCGATACATTCTGTC--T-T-T-G-TAC--CCA-G-ATG
* *
11037 TATCGATACATTCTGTCTTTTTACCCGGATG
1 TATCGATACATTCTGTCTTTGTACCCAGATG
11068 TATCGATACATT
1 TATCGATACATT
11080 TTTCAATGTA
Statistics
Matches: 96, Mismatches: 7, Indels: 22
0.77 0.06 0.18
Matches are distributed among these distances:
30 2 0.02
31 58 0.60
32 2 0.02
33 1 0.01
34 1 0.01
35 4 0.04
36 3 0.03
37 1 0.01
38 3 0.03
39 2 0.02
40 17 0.18
41 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (31 bp):
TATCGATACATTCTGTCTTTGTACCCAGATG
Found at i:11019 original size:20 final size:20
Alignment explanation
Indices: 10994--11050 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
10984 TTGTACCTAG
10994 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* *
11014 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
11034 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
11051 GTCTTTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:19184 original size:12 final size:11
Alignment explanation
Indices: 19162--19228 Score: 57
Period size: 12 Copynumber: 5.9 Consensus size: 11
19152 AGAGAAAGAA
*
19162 GAGAGAGGAGG
1 GAGATAGGAGG
19173 GATGATAGGAGG
1 GA-GATAGGAGG
*
19185 AGAGATAGTA--
1 -GAGATAGGAGG
19195 GAGATAGGAGG
1 GAGATAGGAGG
19206 GATGATAGGAGG
1 GA-GATAGGAGG
*
19218 AGAGACAGGAG
1 -GAGATAGGAG
19229 AGATAATAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
9 8 0.17
11 4 0.09
12 30 0.65
13 4 0.09
ACGTcount: A:0.39, C:0.01, G:0.49, T:0.10
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:19228 original size:42 final size:42
Alignment explanation
Indices: 19182--19261 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
19172 GGATGATAGG
* * *
19182 AGGAGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGAC
1 AGGAGAGATAATAGAGAGAGGAGGGATGACAGGAGGAGAGAC
19224 AGGAGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGGAGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
19262 GAGAGAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.41, C:0.03, G:0.46, T:0.10
Consensus pattern (42 bp):
AGGAGAGATAATAGAGAGAGGAGGGATGACAGGAGGAGAGAC
Found at i:19232 original size:33 final size:33
Alignment explanation
Indices: 19152--19233 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
19142 TAGCCCTCAA
*
19152 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGG
1 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGG
* *
19185 AGAGATAGTAGAGATAGGAGGGATGATAGGAGG
1 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGG
* *
19218 AGAGACAGGAGAGATA
1 AGAGAAAGAAGAGATA
19234 ATAGAGAGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.44, C:0.01, G:0.45, T:0.10
Consensus pattern (33 bp):
AGAGAAAGAAGAGATAGGAGGGATGATAGGAGG
Found at i:25115 original size:12 final size:11
Alignment explanation
Indices: 25093--25159 Score: 57
Period size: 12 Copynumber: 5.9 Consensus size: 11
25083 AGAGAAAGAA
*
25093 GAGAGAGGAGG
1 GAGATAGGAGG
25104 GATGATAGGAGG
1 GA-GATAGGAGG
*
25116 AGAGATAGTA--
1 -GAGATAGGAGG
25126 GAGATAGGAGG
1 GAGATAGGAGG
25137 GATGATAGGAGG
1 GA-GATAGGAGG
*
25149 AGAGACAGGAG
1 -GAGATAGGAG
25160 AGATAATAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
9 8 0.17
11 4 0.09
12 30 0.65
13 4 0.09
ACGTcount: A:0.39, C:0.01, G:0.49, T:0.10
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:25159 original size:42 final size:42
Alignment explanation
Indices: 25113--25192 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
25103 GGATGATAGG
* * *
25113 AGGAGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGAC
1 AGGAGAGATAATAGAGAGAGGAGGGATGACAGGAGGAGAGAC
25155 AGGAGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGGAGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
25193 GAGAGAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.41, C:0.03, G:0.46, T:0.10
Consensus pattern (42 bp):
AGGAGAGATAATAGAGAGAGGAGGGATGACAGGAGGAGAGAC
Found at i:25163 original size:33 final size:33
Alignment explanation
Indices: 25083--25164 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
25073 AAGCCCTCAA
*
25083 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGG
1 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGG
* *
25116 AGAGATAGTAGAGATAGGAGGGATGATAGGAGG
1 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGG
* *
25149 AGAGACAGGAGAGATA
1 AGAGAAAGAAGAGATA
25165 ATAGAGAGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.44, C:0.01, G:0.45, T:0.10
Consensus pattern (33 bp):
AGAGAAAGAAGAGATAGGAGGGATGATAGGAGG
Found at i:31119 original size:12 final size:11
Alignment explanation
Indices: 31097--31172 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
31087 AGAGAAAGAA
*
31097 GAGAGAGGAGG
1 GAGATAGGAGG
31108 GATGATAGGAGG
1 GA-GATAGGAGG
*
31120 AGAGACAGGA--
1 -GAGATAGGAGG
*
31130 GAGATAGTA--
1 GAGATAGGAGG
31139 GAGATAGGAGG
1 GAGATAGGAGG
31150 GATGATAGGAGG
1 GA-GATAGGAGG
*
31162 AGAGACAGGAG
1 -GAGATAGGAG
31173 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:31129 original size:24 final size:24
Alignment explanation
Indices: 31096--31181 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
31086 AAGAGAAAGA
*
31096 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
31120 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
31138 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
31162 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
31182 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:31148 original size:42 final size:42
Alignment explanation
Indices: 31087--31205 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
31077 TAGCCCTCAA
* *
31087 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
31129 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
31171 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
31206 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:38992 original size:18 final size:18
Alignment explanation
Indices: 38971--39050 Score: 80
Period size: 18 Copynumber: 4.6 Consensus size: 18
38961 CCCGTCATCC
* *
38971 CTCCTTTCTCTATTATCT
1 CTCCTATCTCTACTATCT
*
38989 CTCCTATCTCTCCTATCT
1 CTCCTATCTCTACTATCT
39007 CTCC--TC-CTA-TCATC-
1 CTCCTATCTCTACT-ATCT
39021 CTTCCTATCTCTACTATCT
1 C-TCCTATCTCTACTATCT
39040 CTCCTATCTCT
1 CTCCTATCTCT
39051 CCTCCTATCA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
14 2 0.04
15 8 0.16
16 2 0.04
17 2 0.04
18 35 0.69
19 2 0.04
ACGTcount: A:0.12, C:0.41, G:0.00, T:0.46
Consensus pattern (18 bp):
CTCCTATCTCTACTATCT
Found at i:38996 original size:9 final size:9
Alignment explanation
Indices: 38984--39053 Score: 77
Period size: 9 Copynumber: 7.1 Consensus size: 9
38974 CTTTCTCTAT
38984 TATCTCTCC
1 TATCTCTCC
38993 TATCTCTCC
1 TATCTCTCC
39002 TATCTCTCCTCC
1 TA--TCT-CTCC
39014 TATCATCCTTCC
1 TATC-T-C-TCC
*
39026 TATCTCTAC
1 TATCTCTCC
39035 TATCTCTCC
1 TATCTCTCC
39044 TATCTCTCC
1 TATCTCTCC
39053 T
1 T
39054 CCTATCATCC
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
9 31 0.57
10 3 0.06
11 7 0.13
12 13 0.24
ACGTcount: A:0.13, C:0.43, G:0.00, T:0.44
Consensus pattern (9 bp):
TATCTCTCC
Found at i:39013 original size:12 final size:12
Alignment explanation
Indices: 38998--39074 Score: 62
Period size: 12 Copynumber: 6.9 Consensus size: 12
38988 TCTCCTATCT
38998 CTCCTATCTCTC
1 CTCCTATCTCTC
39010 CTCCTATCATC-C
1 CTCCTATC-TCTC
*
39022 TTCCTA--TCT-
1 CTCCTATCTCTC
*
39031 CTACTA--TCT-
1 CTCCTATCTCTC
39040 CTCCTATCTCTC
1 CTCCTATCTCTC
39052 CTCCTATCATC-C
1 CTCCTATC-TCTC
39064 CTCCTATCTCT
1 CTCCTATCTCT
39075 TCTTTCTCTT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
9 14 0.26
11 5 0.09
12 31 0.57
13 4 0.07
ACGTcount: A:0.13, C:0.45, G:0.00, T:0.42
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:39020 original size:51 final size:51
Alignment explanation
Indices: 38956--39053 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
38946 TTTTTCTCTC
* * *
38956 CTCCTCCCGTCATCCCTCCTTTCTCTATTATCTCTCCTATCTCTCCTATCT
1 CTCCTCCCATCATCCCTCCTATCTCTACTATCTCTCCTATCTCTCCTATCT
* *
39007 CTCCTCCTATCATCCTTCCTATCTCTACTATCTCTCCTATCTCTCCT
1 CTCCTCCCATCATCCCTCCTATCTCTACTATCTCTCCTATCTCTCCT
39054 CCTATCATCC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.11, C:0.45, G:0.01, T:0.43
Consensus pattern (51 bp):
CTCCTCCCATCATCCCTCCTATCTCTACTATCTCTCCTATCTCTCCTATCT
Found at i:39030 original size:24 final size:23
Alignment explanation
Indices: 38989--39074 Score: 96
Period size: 21 Copynumber: 4.0 Consensus size: 23
38979 TCTATTATCT
38989 CTCCTATC-T-CTCCTATCTCTC
1 CTCCTATCATCCTCCTATCTCTC
39010 CTCCTATCATCCTTCCTA--TCT-
1 CTCCTATCATCC-TCCTATCTCTC
*
39031 CTACTATC-T-CTCCTATCTCTC
1 CTCCTATCATCCTCCTATCTCTC
39052 CTCCTATCATCCCTCCTATCTCT
1 CTCCTATCAT-CCTCCTATCTCT
39075 TCTTTCTCTT
Statistics
Matches: 54, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
18 5 0.09
19 1 0.02
20 4 0.07
21 22 0.41
22 5 0.09
23 1 0.02
24 16 0.30
ACGTcount: A:0.13, C:0.45, G:0.00, T:0.42
Consensus pattern (23 bp):
CTCCTATCATCCTCCTATCTCTC
Found at i:39030 original size:42 final size:42
Alignment explanation
Indices: 38984--39083 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
38974 CTTTCTCTAT
* *
38984 TATCTCTCCTATCTCTCCTATCTCTCCTCCTATCATCCTTCC
1 TATCTCTACTATCTCTCCTATCTCTCCTCCTATCATCCCTCC
39026 TATCTCTACTATCTCTCCTATCTCTCCTCCTATCATCCCTCC
1 TATCTCTACTATCTCTCCTATCTCTCCTCCTATCATCCCTCC
* *
39068 TATCTCTTCTTTCTCT
1 TATCTCTACTATCTCT
39084 TTGAGGGCTA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.12, C:0.43, G:0.00, T:0.45
Consensus pattern (42 bp):
TATCTCTACTATCTCTCCTATCTCTCCTCCTATCATCCCTCC
Found at i:39862 original size:23 final size:24
Alignment explanation
Indices: 39823--39867 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
39813 TGCTGGTTTT
39823 TTTCCTCTCTTTTTGTATTCTTTC
1 TTTCCTCTCTTTTTGTATTCTTTC
*
39847 TTTCCT-TTTTTTTGTATTCTT
1 TTTCCTCTCTTTTTGTATTCTT
39868 GAAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.04, C:0.20, G:0.04, T:0.71
Consensus pattern (24 bp):
TTTCCTCTCTTTTTGTATTCTTTC
Found at i:46353 original size:21 final size:21
Alignment explanation
Indices: 46329--46369 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
46319 AACTTCTTGC
*
46329 AATTCATTTA-TTCTCTTTTCT
1 AATTCATCTACTT-TCTTTTCT
46350 AATTCATCTACTTTCTTTTC
1 AATTCATCTACTTTCTTTTC
46370 AAACACATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.20, C:0.22, G:0.00, T:0.59
Consensus pattern (21 bp):
AATTCATCTACTTTCTTTTCT
Found at i:48246 original size:11 final size:11
Alignment explanation
Indices: 48230--48254 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
48220 ATTTCTTTAT
48230 GTTTCTTGTTG
1 GTTTCTTGTTG
48241 GTTTCTTGTTG
1 GTTTCTTGTTG
48252 GTT
1 GTT
48255 CTTTTTAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.28, T:0.64
Consensus pattern (11 bp):
GTTTCTTGTTG
Found at i:49596 original size:18 final size:19
Alignment explanation
Indices: 49573--49612 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
49563 AAACATGGCT
49573 TATTA-TTTTTTTCATGGG
1 TATTATTTTTTTTCATGGG
49591 TATTATTTTTTTTCATGGG
1 TATTATTTTTTTTCATGGG
49610 TAT
1 TAT
49613 GCTAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.17, C:0.05, G:0.15, T:0.62
Consensus pattern (19 bp):
TATTATTTTTTTTCATGGG
Found at i:52229 original size:21 final size:21
Alignment explanation
Indices: 52185--52232 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
52175 CTTGTATATT
*
52185 AATACAAGCTCATGAAGTGCC
1 AATACAAGCTCATGAAGTACC
* * *
52206 AATATAAGTTCATGAAGTATC
1 AATACAAGCTCATGAAGTACC
52227 AATACA
1 AATACA
52233 TATTTCTAAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.25
Consensus pattern (21 bp):
AATACAAGCTCATGAAGTACC
Found at i:59156 original size:28 final size:28
Alignment explanation
Indices: 59122--59193 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
59112 TTCCTCTTCA
*
59122 TTGATTTCTCTTCCTTTGATATTTCTGG
1 TTGATTTCTCTTCCTTTCATATTTCTGG
* *
59150 CTT-ATTTCAT-TTCCCTTCATATTTCTTG
1 -TTGATTTC-TCTTCCTTTCATATTTCTGG
*
59178 TTGATTTCACTTCCTT
1 TTGATTTCTCTTCCTT
59194 AATCTTTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
27 2 0.06
28 30 0.86
29 3 0.09
ACGTcount: A:0.12, C:0.22, G:0.08, T:0.57
Consensus pattern (28 bp):
TTGATTTCTCTTCCTTTCATATTTCTGG
Found at i:62108 original size:15 final size:15
Alignment explanation
Indices: 62070--62108 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
62060 AGAATACAAA
62070 AAAAAAAAAAGAAAG
1 AAAAAAAAAAGAAAG
* * *
62085 AATACAAAAAGAGAG
1 AAAAAAAAAAGAAAG
62100 AAAAAAAAA
1 AAAAAAAAA
62109 CCAGTATTTG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAAGAAAG
Done.