Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003947.1 Hibiscus syriacus cultivar Beakdansim tig00008532_pilon, whole genome shotgun sequence
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: 72468
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:524 original size:34 final size:33
Alignment explanation
Indices: 461--532 Score: 90
Period size: 34 Copynumber: 2.2 Consensus size: 33
451 ACCTTACAAC
* * *
461 TCCCTAGTTTTTTCCGGGCTAAACTAGAACATT
1 TCCCTAGCTTTTACCGGGATAAACTAGAACATT
* *
494 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAGCTTTTAC-CGGGATAAACTAGAACATT
528 TCCCT
1 TCCCT
533 TTACAAAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
33 12 0.36
34 21 0.64
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.33
Consensus pattern (33 bp):
TCCCTAGCTTTTACCGGGATAAACTAGAACATT
Found at i:976 original size:20 final size:19
Alignment explanation
Indices: 890--980 Score: 57
Period size: 20 Copynumber: 4.9 Consensus size: 19
880 ATTGCAGCCT
* *
890 TGATGCATGGATGCATGGCA
1 TGATGCATCGATGCATTG-A
* *
910 GGATGCATCGATGCACT-A
1 TGATGCATCGATGCATTGA
* *
928 AG-TGCATTCGATG-TTTGA
1 TGATGCA-TCGATGCATTGA
*
946 -G-TGCATGGATGCATTGCA
1 TGATGCATCGATGCATTG-A
964 TGATGCATCGATGCATT
1 TGATGCATCGATGCATT
981 AGTGCAGGTG
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
16 5 0.09
17 13 0.24
18 10 0.18
19 1 0.02
20 26 0.47
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (19 bp):
TGATGCATCGATGCATTGA
Found at i:1029 original size:21 final size:21
Alignment explanation
Indices: 947--1040 Score: 79
Period size: 21 Copynumber: 4.5 Consensus size: 21
937 GATGTTTGAG
* *
947 TGCATGGATGCATTGCA-TGA
1 TGCATGGATGCACTGCAGGGA
* *
967 TGCATCGATGCATTAGTGCA-GG-
1 TGCATGGATGC---ACTGCAGGGA
989 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
* *
1010 TGCATGGATTCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
1031 TGCAT-GATGC
1 TGCATGGATGC
1041 CACTTTGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
19 5 0.08
20 16 0.26
21 24 0.39
22 10 0.16
23 6 0.10
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.26
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:1044 original size:21 final size:21
Alignment explanation
Indices: 987--1040 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
977 CATTAGTGCA
987 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
* *
1008 GATGCATGGATTCACTGCAGG
1 GGTGCATGGATGCACTGCAGG
1029 GGTGCAT-GATGC
1 GGTGCATGGATGC
1041 CACTTTGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.20, C:0.19, G:0.39, T:0.22
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAGG
Found at i:1145 original size:29 final size:29
Alignment explanation
Indices: 1124--1180 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1114 AAACTTTGAA
1124 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
*
1153 TAAATTCAATTCAAGTCCAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAACATTT
1181 TGCCTTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:1171 original size:30 final size:29
Alignment explanation
Indices: 1124--1182 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
1114 AAACTTTGAA
1124 TAAATTCAATTAAGTCCAAAAACATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
*
1153 TAAATTCAATTCAAGTCCAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACATTTTG
1183 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:4228 original size:20 final size:22
Alignment explanation
Indices: 4203--4242 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4193 TGTTGTATAT
4203 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
4223 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
4243 TCTACTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:4298 original size:21 final size:21
Alignment explanation
Indices: 4272--4320 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
4262 CATAACATGA
4272 TGCATCGGTGCACTATCAAGT
1 TGCATCGGTGCACTATCAAGT
4293 TGCATCGGTGCACTATCAAGT
1 TGCATCGGTGCACTATCAAGT
4314 TGCATCG
1 TGCATCG
4321 ATACCCCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCATCGGTGCACTATCAAGT
Found at i:4416 original size:20 final size:20
Alignment explanation
Indices: 4393--4439 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
4383 ATTCATGGCA
4393 CGATGCATGGCAGAATGCAT
1 CGATGCATGGCAGAATGCAT
*
4413 CGATGCATGGCAGGATGCAT
1 CGATGCATGGCAGAATGCAT
4433 CGATGCA
1 CGATGCA
4440 CTAAGTGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.21, G:0.32, T:0.19
Consensus pattern (20 bp):
CGATGCATGGCAGAATGCAT
Found at i:4530 original size:21 final size:21
Alignment explanation
Indices: 4504--4559 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
4494 TTAGTGCAGG
*
4504 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTACAGGGA
*
4525 TGCATGGATGCACTACAGGGG
1 TGCATGGATGCACTACAGGGA
4546 TGCATGGATGCACT
1 TGCATGGATGCACT
4560 TTGACACCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (21 bp):
TGCATGGATGCACTACAGGGA
Found at i:4669 original size:29 final size:31
Alignment explanation
Indices: 4636--4695 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
4626 AAACTTTGAA
4636 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
4665 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
4696 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:4895 original size:43 final size:44
Alignment explanation
Indices: 4847--4941 Score: 165
Period size: 44 Copynumber: 2.2 Consensus size: 44
4837 GTTAAGCTCT
4847 CCCTTTTTCATTAAGAAA-AAAATTTTTCAAACCAAACTTCTCC
1 CCCTTTTTCATTAAGAAATAAAATTTTTCAAACCAAACTTCTCC
**
4890 CCCTTTTTCATTAAGAAATTGAATTTTTCAAACCAAACTTCTCC
1 CCCTTTTTCATTAAGAAATAAAATTTTTCAAACCAAACTTCTCC
4934 CCCTTTTT
1 CCCTTTTT
4942 GTTATATAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
43 18 0.37
44 31 0.63
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (44 bp):
CCCTTTTTCATTAAGAAATAAAATTTTTCAAACCAAACTTCTCC
Found at i:6530 original size:15 final size:16
Alignment explanation
Indices: 6512--6541 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6502 TTCTTCTTGT
6512 TTTTCTTC-TCTTCCC
1 TTTTCTTCATCTTCCC
6527 TTTTCTTCATCTTCC
1 TTTTCTTCATCTTCC
6542 TTCATCATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTCTTCATCTTCCC
Found at i:8085 original size:21 final size:21
Alignment explanation
Indices: 8040--8095 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
8030 CATTAGTGCA
*
8040 GGTGCATGGATG--CTGCAGG
1 GGTGCATGGATGCACTACAGG
*
8059 GATGCATGGATGCACTACAGG
1 GGTGCATGGATGCACTACAGG
8080 GGTGCATGGATGCACT
1 GGTGCATGGATGCACT
8096 TTGACACCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 11 0.34
21 21 0.66
ACGTcount: A:0.21, C:0.18, G:0.39, T:0.21
Consensus pattern (21 bp):
GGTGCATGGATGCACTACAGG
Found at i:8990 original size:3 final size:3
Alignment explanation
Indices: 8982--9084 Score: 147
Period size: 3 Copynumber: 35.0 Consensus size: 3
8972 GTTTTGTTTG
*
8982 TAA TAA TAA T-A TAA TAA TAA AAA TAA TAA -AA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
9028 TAA TAA TAA TAA TAA TAA TAA TAG TAA TGA TAA TAA TAA TTA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9076 TAA TAA TAA
1 TAA TAA TAA
9085 ATATATATAG
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
2 4 0.04
3 86 0.96
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:11189 original size:16 final size:17
Alignment explanation
Indices: 11176--11230 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
11166 TTTCTTATTC
11176 TAAATATTTTTTATTAA
1 TAAATATTTTTTATTAA
*
11193 TAAATATTCTTTTGAATAA
1 TAAATATT-TTTT-ATTAA
11212 CTTAAATA-TTTTTATTAA
1 --TAAATATTTTTTATTAA
11230 T
1 T
11231 CTAGGTAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 1 0.03
17 8 0.25
18 8 0.25
19 8 0.25
20 1 0.03
21 6 0.19
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (17 bp):
TAAATATTTTTTATTAA
Found at i:12254 original size:10 final size:10
Alignment explanation
Indices: 12239--12263 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12229 TTTTCTATTA
12239 AAAATAATTT
1 AAAATAATTT
12249 AAAATAATTT
1 AAAATAATTT
12259 AAAAT
1 AAAAT
12264 TAAATGAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATAATTT
Found at i:14278 original size:6 final size:6
Alignment explanation
Indices: 14242--14281 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
14232 TACTTTCTAA
* *
14242 AAACAA AAACAA AAAGCAT AAACAT AAACAT AAACAT AAA
1 AAACAT AAACAT AAA-CAT AAACAT AAACAT AAACAT AAA
14282 TTTTTTTCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.72, C:0.15, G:0.03, T:0.10
Consensus pattern (6 bp):
AAACAT
Found at i:15244 original size:31 final size:31
Alignment explanation
Indices: 15209--15268 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
15199 GGTCGAATCG
*
15209 GGTTAGGTTCGGATTTTACCCCCAAAAAAGA
1 GGTTAGGTTCAGATTTTACCCCCAAAAAAGA
15240 GGTTAGGTTCAGATTTTACCCCCAAAAAA
1 GGTTAGGTTCAGATTTTACCCCCAAAAAA
15269 TTGGGTCGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (31 bp):
GGTTAGGTTCAGATTTTACCCCCAAAAAAGA
Found at i:16351 original size:20 final size:20
Alignment explanation
Indices: 16326--16363 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16316 TCCTCTAACA
*
16326 ATTTCTAACTTCCCTAACTG
1 ATTTCTAACATCCCTAACTG
16346 ATTTCTAACATCCCTAAC
1 ATTTCTAACATCCCTAAC
16364 AACCTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.32, G:0.03, T:0.37
Consensus pattern (20 bp):
ATTTCTAACATCCCTAACTG
Found at i:20764 original size:56 final size:56
Alignment explanation
Indices: 20699--20811 Score: 208
Period size: 56 Copynumber: 2.0 Consensus size: 56
20689 TATGGAGTGC
20699 ACACTTGTTTGAATTTATTCTGATTTGAACTATTATGTGGTGGTTTTGTAACTGCT
1 ACACTTGTTTGAATTTATTCTGATTTGAACTATTATGTGGTGGTTTTGTAACTGCT
* *
20755 ACACTTGTTTGAATTTATTCTGATTTGAACTGTTTTGTGGTGGTTTTGTAACTGCT
1 ACACTTGTTTGAATTTATTCTGATTTGAACTATTATGTGGTGGTTTTGTAACTGCT
20811 A
1 A
20812 ATTTTAGTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.49
Consensus pattern (56 bp):
ACACTTGTTTGAATTTATTCTGATTTGAACTATTATGTGGTGGTTTTGTAACTGCT
Found at i:30653 original size:23 final size:24
Alignment explanation
Indices: 30605--30653 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
30595 TTATTTAAAA
* *
30605 TTAATTATTAATTAAAATTTAGTT
1 TTAATTATTAATTAAAATATAATT
30629 TTAATT-TTAA-TAAAACTATAATT
1 TTAATTATTAATTAAAA-TATAATT
30652 TT
1 TT
30654 TTATTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 11 0.50
24 6 0.27
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTAATTATTAATTAAAATATAATT
Found at i:32983 original size:3 final size:3
Alignment explanation
Indices: 32958--33001 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
32948 TTGAGTTTTG
* *
32958 TAA TAT TAA TAAA TAA TATA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
33002 ATTTTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:35872 original size:3 final size:3
Alignment explanation
Indices: 35859--35928 Score: 86
Period size: 3 Copynumber: 23.0 Consensus size: 3
35849 GTAATATTTA
* * *
35859 AAT AAT AAAT AAT ATT ACT ATT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
35905 AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
35929 TTAAAATGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
3 55 0.95
4 3 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:35873 original size:18 final size:18
Alignment explanation
Indices: 35850--35928 Score: 81
Period size: 18 Copynumber: 4.2 Consensus size: 18
35840 TTGGGCTTTG
35850 TAATATTTA-AATAATAAA
1 TAATATTTATAATAAT-AA
35868 TAATATTACTATTAATAATAA
1 TAATATT--TA-TAATAATAA
* *
35889 TAATAATAATAATAATAA
1 TAATATTTATAATAATAA
35907 TAATAATTT-TAATAATAA
1 TAAT-ATTTATAATAATAA
35925 TAAT
1 TAAT
35929 TTAAAATGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 33 0.63
19 3 0.06
20 2 0.04
21 8 0.15
22 6 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (18 bp):
TAATATTTATAATAATAA
Found at i:36275 original size:76 final size:76
Alignment explanation
Indices: 36083--37070 Score: 1777
Period size: 76 Copynumber: 13.0 Consensus size: 76
36073 GGTCTTATGA
*
36083 ATGACCCTG-AGGGTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
1 ATGACCC-GAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTG
*
36147 TAGG-CTTACAG
65 AAGGACTTACAG
*
36158 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
36223 AGGGCTTACAG
66 AGGACTTACAG
* * *
36234 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCCCCCGAAGGCTTTTTTGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
36299 AGGGCTTACAG
66 AGGACTTACAG
*
36310 ATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
36375 AGGGCTTACAG
66 AGGACTTACAG
36386 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
36451 AGGACTTACAG
66 AGGACTTACAG
36462 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
36527 AGGACTTACAG
66 AGGACTTACAG
*
36538 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
36603 AGGACTTACAG
66 AGGACTTACAG
*
36614 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
36679 AGGACTTATAG
66 AGGACTTACAG
*
36690 ATAACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
*
36755 AGGACTTACAT
66 AGGACTTACAG
36766 ATGACCCGAAGGATTTGAAAACATC-AAAA-CTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
36829 AGGACTTACAG
66 AGGACTTACAG
*
36840 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
36905 AGGACTTACAG
66 AGGACTTACAG
*
36916 ATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
36981 AGGACTTACAG
66 AGGACTTACAG
*
36992 ATGACCCGAAGGATTTGAAAACCTCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
1 ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
37057 AGGACTTACAG
66 AGGACTTACAG
37068 ATG
1 ATG
37071 TGAGAAATAG
Statistics
Matches: 889, Mismatches: 20, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
74 69 0.08
75 72 0.08
76 748 0.84
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
ATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGA
AGGACTTACAG
Found at i:40666 original size:82 final size:83
Alignment explanation
Indices: 40462--40681 Score: 379
Period size: 83 Copynumber: 2.7 Consensus size: 83
40452 TTTCATACCA
* * *
40462 AACCATATCAGATAATTCAAAGAACACTTCCAGAAGATGTTATTGGCAAATTCATCTTCTAAACT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
*
40527 CAATGCTTGATTCTGTCC
66 CAATGATTGATTCTGTCC
* *
40545 AATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
40610 CAATGATTG-TTCTGTCC
66 CAATGATTGATTCTGTCC
40627 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
40682 TTGTTCTATT
Statistics
Matches: 130, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
82 62 0.48
83 68 0.52
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACT
CAATGATTGATTCTGTCC
Found at i:49580 original size:3 final size:3
Alignment explanation
Indices: 49567--49639 Score: 92
Period size: 3 Copynumber: 24.0 Consensus size: 3
49557 GTAATATTTA
* * *
49567 AAT AAT AAAT AAT ATT ACT ATT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
49613 AAT AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
49640 TTAAAATGAA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 58 0.95
4 3 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:52228 original size:20 final size:20
Alignment explanation
Indices: 52203--52240 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
52193 TTTGGTTCAC
52203 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
*
52223 GGAATGTAGGATTACCAG
1 GGAATGTAAGATTACCAG
52241 GGAATATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.32, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:52472 original size:38 final size:40
Alignment explanation
Indices: 52392--52473 Score: 98
Period size: 39 Copynumber: 2.1 Consensus size: 40
52382 AACAAGTTGG
** *
52392 AAAATATTTATATATTTTCTTTAAAAAAATTTAAATTCAT
1 AAAATATTTATATATTTTCTTTAAAAAAATGAAAAATCAT
*
52432 AAAAT-TTATATATATTTT-TTTACAAAAATGAAAAAT-AT
1 AAAATATT-TATATATTTTCTTTAAAAAAATGAAAAATCAT
52470 AAAA
1 AAAA
52474 ATGTTTAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
38 6 0.16
39 16 0.43
40 15 0.41
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (40 bp):
AAAATATTTATATATTTTCTTTAAAAAAATGAAAAATCAT
Found at i:53525 original size:51 final size:51
Alignment explanation
Indices: 53448--53547 Score: 139
Period size: 51 Copynumber: 1.9 Consensus size: 51
53438 TTAAAAAATC
*
53448 ATAAAAATATAATTAAACTTTGTCAAACAT-AATTAAACATAAATTTTAATT
1 ATAAAAATATAATTAAACTTTATCAAACATAAATTAAACAT-AATTTTAATT
* * *
53499 ATAAAAATATAATTAAATTTTATCAAATATAAAATTAAATATAATTTTA
1 ATAAAAATATAATTAAACTTTATCAAACAT-AAATTAAACATAATTTTA
53548 CAAAAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 27 0.63
52 7 0.16
53 9 0.21
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (51 bp):
ATAAAAATATAATTAAACTTTATCAAACATAAATTAAACATAATTTTAATT
Found at i:54068 original size:14 final size:14
Alignment explanation
Indices: 54049--54077 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
54039 GGGGGCTATT
54049 TCTAATGTCATAAG
1 TCTAATGTCATAAG
54063 TCTAATGTCATAAG
1 TCTAATGTCATAAG
54077 T
1 T
54078 TATAATGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (14 bp):
TCTAATGTCATAAG
Found at i:55352 original size:29 final size:31
Alignment explanation
Indices: 55303--55367 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 31
55293 AATTAATTAC
55303 AAAATAAAATATTAGACATA-TATTTTA-AT
1 AAAATAAAATATTAGACATATTATTTTATAT
55332 AAAATAAAATAATTTA-A-ATATTTATTTTATAT
1 AAAATAAAAT-A-TTAGACATA-TTATTTTATAT
55364 AAAA
1 AAAA
55368 GGCCAAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
29 13 0.42
30 2 0.06
31 10 0.32
32 6 0.19
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (31 bp):
AAAATAAAATATTAGACATATTATTTTATAT
Found at i:57754 original size:22 final size:21
Alignment explanation
Indices: 57729--57783 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
57719 AAGATATTTT
57729 TTAACTTTTTTTTTAAATTTGA
1 TTAACTTTTTTTTT-AATTTGA
** **
57751 TTAACTTAATTTTTAATTTTT
1 TTAACTTTTTTTTTAATTTGA
57772 TTAATCTTTTTT
1 TTAA-CTTTTTT
57784 CTATTTTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.67
Consensus pattern (21 bp):
TTAACTTTTTTTTTAATTTGA
Found at i:63516 original size:12 final size:12
Alignment explanation
Indices: 63499--63528 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
63489 TAAAATCTTT
63499 TTTTTCTCTCTA
1 TTTTTCTCTCTA
*
63511 TTTTTCTCTTTA
1 TTTTTCTCTCTA
63523 TTTTTC
1 TTTTTC
63529 GCATACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTCTCTCTA
Found at i:64005 original size:13 final size:13
Alignment explanation
Indices: 63987--64029 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
63977 TCTCAATCTC
*
63987 TTTAATTTGTTTA
1 TTTAATTTTTTTA
*
64000 TTTAATTATTTTTC
1 TTTAATT-TTTTTA
*
64014 TTTTATTTTTTTA
1 TTTAATTTTTTTA
64027 TTT
1 TTT
64030 TAAAAACAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTAATTTTTTTA
Found at i:71167 original size:72 final size:66
Alignment explanation
Indices: 71088--71274 Score: 202
Period size: 64 Copynumber: 2.7 Consensus size: 66
71078 TTTTATCTTT
*
71088 GTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAAGTTTTAGGATATTTTTTATATTTTATCTT
1 GTATTTTAGTTTAAATAGTTTTAGT-TTTTAATTAAGATTTA-GATATTTTTTATA--TTAT-TT
71153 TGTTTAG
61 T-TTTAG
* * *
71160 GTATTTTAG-TTGAATATGTTTTAGTGTTTTAATTAGGATTTAGA-A--TATTATATTATTTTTT
1 GTATTTTAGTTTAAATA-GTTTTAGT-TTTTAATTAAGATTTAGATATTTTTTATATTATTTTTT
71221 TAG
64 TAG
* *
71224 GTATTTTAGTTTAAATAGTTTTAAGTGTTTAATTAAGATTTAAGATGTTTT
1 GTATTTTAGTTTAAATAGTTTT-AGTTTTTAATTAAGATTT-AGATATTTT
71275 AGCTTGTTTT
Statistics
Matches: 98, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
64 32 0.33
65 15 0.15
66 4 0.04
68 7 0.07
70 1 0.01
71 8 0.08
72 31 0.32
ACGTcount: A:0.28, C:0.01, G:0.14, T:0.57
Consensus pattern (66 bp):
GTATTTTAGTTTAAATAGTTTTAGTTTTTAATTAAGATTTAGATATTTTTTATATTATTTTTTTA
G
Found at i:71861 original size:18 final size:19
Alignment explanation
Indices: 71838--71881 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
71828 CTTTAATTTG
71838 TTTATTTAATTATT-TTCT
1 TTTATTTAATTATTATTCT
* *
71856 TTTATTTAATTCTTATTTT
1 TTTATTTAATTATTATTCT
71875 TTTATTT
1 TTTATTT
71882 TAAAACAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTATTTAATTATTATTCT
Found at i:71953 original size:21 final size:20
Alignment explanation
Indices: 71905--71965 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
71895 AAAAATCCTC
*
71905 TTTTTATTATTATTATTACTAT
1 TTTTTA-TATTATT-TTTCTAT
*
71927 TTTTTATATTATTTTTCTTT
1 TTTTTATATTATTTTTCTAT
*
71947 TTATTTATAATATCTTTTC
1 TT-TTTATATTAT-TTTTC
71966 AACTCATAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTATATTATTTTTCTAT
Done.