Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003975.1 Hibiscus syriacus cultivar Beakdansim tig00008632_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: 91494
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:7116 original size:2 final size:2
Alignment explanation
Indices: 7109--7142 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
7099 GGTTATTAGA
7109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7143 TGAGACAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18350 original size:34 final size:34
Alignment explanation
Indices: 18266--18350 Score: 161
Period size: 34 Copynumber: 2.5 Consensus size: 34
18256 AACAAAAAGG
*
18266 GGGAGAAGTGTTAAAGCGTTTTTAAATGATAAAT
1 GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
18300 GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
1 GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
18334 GGGAGAAGTGTTAAAGT
1 GGGAGAAGTGTTAAAGT
18351 AAGGGGGAGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.38, C:0.01, G:0.29, T:0.32
Consensus pattern (34 bp):
GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
Found at i:20745 original size:2 final size:2
Alignment explanation
Indices: 20738--20779 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
20728 TTCTCCTTTA
20738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20780 CATTATACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24097 original size:41 final size:41
Alignment explanation
Indices: 24052--24131 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
24042 GTTTATATTT
24052 TTAATATTTATGGTGTTTGAATCCTAAATCTTAAAGAATTG
1 TTAATATTTATGGTGTTTGAATCCTAAATCTTAAAGAATTG
24093 TTAATATTTATGGTGTTTGAATCCTAAATCTTAAAGAAT
1 TTAATATTTATGGTGTTTGAATCCTAAATCTTAAAGAAT
24132 AACAATTCGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (41 bp):
TTAATATTTATGGTGTTTGAATCCTAAATCTTAAAGAATTG
Found at i:26837 original size:3 final size:3
Alignment explanation
Indices: 26824--26933 Score: 166
Period size: 3 Copynumber: 36.7 Consensus size: 3
26814 AAGATACTAA
* * *
26824 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
26872 TAT TGT TAT TAT TGT TAT TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
26920 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
26934 AATATATTAA
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 95 1.00
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:28210 original size:19 final size:18
Alignment explanation
Indices: 28174--28222 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
28164 TTAGATTTTA
*
28174 ATTTTATT-TTTTCGTTT
1 ATTTTATTGTTTTCATTT
28191 ATTTTATATGTTTTCATTT
1 ATTTTAT-TGTTTTCATTT
28210 ATTTTATTGTTTT
1 ATTTTATTGTTTT
28223 TAAATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (18 bp):
ATTTTATTGTTTTCATTT
Found at i:28290 original size:13 final size:13
Alignment explanation
Indices: 28262--28296 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
28252 TTGTATTATA
28262 TTATTAAATA-TT
1 TTATTAAATATTT
28274 TTATTAAATATTT
1 TTATTAAATATTT
28287 TTA-TAAATAT
1 TTATTAAATAT
28297 ATAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTAAATATTT
Found at i:28329 original size:12 final size:13
Alignment explanation
Indices: 28308--28336 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28298 TAATAAATAG
28308 TATTT-TTTTTAA
1 TATTTATTTTTAA
28320 TATTTATTTTTAA
1 TATTTATTTTTAA
28333 TATT
1 TATT
28337 GAAGAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTTATTTTTAA
Found at i:29033 original size:18 final size:18
Alignment explanation
Indices: 28985--29034 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
28975 TTCTTTTCAA
28985 ATTTTTA-TTTATTTATT
1 ATTTTTATTTTATTTATT
**
29002 ATTTTTATAATATTTA-T
1 ATTTTTATTTTATTTATT
29019 ATGTTTTATTTTATTT
1 AT-TTTTATTTTATTT
29035 GCAAGTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (18 bp):
ATTTTTATTTTATTTATT
Found at i:29056 original size:13 final size:15
Alignment explanation
Indices: 29025--29061 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
29015 TTATATGTTT
29025 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
29040 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
29053 TA-TTTATTT
1 TATTTTATTT
29062 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:39209 original size:16 final size:15
Alignment explanation
Indices: 39182--39230 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
39172 ATGCTTGAAG
*
39182 AGAATAGAAAAAAAA
1 AGAAAAGAAAAAAAA
39197 TAGAAAATGAAAAAAAA
1 -AGAAAA-GAAAAAAAA
* *
39214 AGAGAAGAAAAAGAA
1 AGAAAAGAAAAAAAA
39229 AG
1 AG
39231 GGGGTCAAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 10 0.34
16 10 0.34
17 9 0.31
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (15 bp):
AGAAAAGAAAAAAAA
Found at i:40626 original size:167 final size:167
Alignment explanation
Indices: 40350--40866 Score: 973
Period size: 167 Copynumber: 3.1 Consensus size: 167
40340 ATATCTTAGT
40350 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
40415 TGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGG
66 TGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGG
40480 AAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
131 AAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
40517 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
40582 TGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGG
66 TGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGG
40647 AAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
131 AAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
40684 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
40749 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTG
65 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTG
* *
40814 GAAGTGTTCTTTGAGTTATCTAATCTG-GTTGGACAGAA
130 GAAGTGTTCTTTGAGTTATCTGATCTGATTTGG-CAGAA
*
40852 CCAATCGTTGGAATT
1 CCAATCATT-GAATT
40867 AAAAGATGAA
Statistics
Matches: 344, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
167 201 0.58
168 138 0.40
169 5 0.01
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (167 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGG
AAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
Found at i:40792 original size:251 final size:251
Alignment explanation
Indices: 40350--40866 Score: 966
Period size: 251 Copynumber: 2.1 Consensus size: 251
40340 ATATCTTAGT
40350 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
40415 TGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGG
66 TGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGG
40480 AAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTT
131 AAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTT
* *
40545 GC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGG-CAGAA
196 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTG-GTTGGACAGAA
40600 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
40665 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTG
65 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTG
40730 GAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATT
130 GAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATT
40795 TGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAA
195 TGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAA
*
40852 CCAATCGTTGGAATT
1 CCAATCATT-GAATT
40867 AAAAGATGAA
Statistics
Matches: 260, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
250 30 0.12
251 171 0.66
252 54 0.21
253 5 0.02
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (251 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGG
AAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTT
GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAA
Found at i:40876 original size:84 final size:84
Alignment explanation
Indices: 40350--40866 Score: 968
Period size: 84 Copynumber: 6.2 Consensus size: 84
40340 ATATCTTAGT
40350 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
40414 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
40433 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
40498 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
40517 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
40581 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
40600 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
40665 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
40684 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
40749 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
40768 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* *
40833 CTAATCTG-GTTGGACAGAA
66 CTGATCTGATTTGG-CAGAA
*
40852 CCAATCGTTGGAATT
1 CCAATCATT-GAATT
40867 AAAAGATGAA
Statistics
Matches: 427, Mismatches: 3, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
83 117 0.27
84 305 0.71
85 5 0.01
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (84 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGATTTGGCAGAA
Found at i:41777 original size:113 final size:114
Alignment explanation
Indices: 41576--41868 Score: 437
Period size: 113 Copynumber: 2.6 Consensus size: 114
41566 TCAAATCCAC
* *
41576 TTGATGGATCATTCATTGCCAGATAA-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCA-TCATTTCCAGAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* * *** *
41640 AAGTTCATAGTGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATC-AT
65 AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTAAATTCATCAAA
*
41689 TTGATGGATCAACATTTCCAGAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTTCCAGAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
41754 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAA
66 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTAAATTCATCAAA
* * *
41803 TTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCATCATTTCCAGAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
41868 A
66 A
41869 TTTGTTCAAC
Statistics
Matches: 163, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
112 11 0.07
113 89 0.55
114 63 0.39
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.29
Consensus pattern (114 bp):
TTGATGGATCATCATTTCCAGAAAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTAAATTCATCAAA
Found at i:41878 original size:97 final size:97
Alignment explanation
Indices: 41765--41965 Score: 393
Period size: 97 Copynumber: 2.1 Consensus size: 97
41755 GTTCATAATG
*
41765 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAGG
1 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAAAAGG
41830 TTCATAATGAGAAGAACTCATCTGAAGAAGGA
66 TTCATAATGAGAAGAACTCATCTGAAGAAGGA
41862 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAAAAGG
1 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAAAAGG
41927 TTCATAATGAGAAGAACTCATCTGAAGAAGGA
66 TTCATAATGAGAAGAACTCATCTGAAGAAGGA
41959 AGAAGAA
1 AGAAGAA
41966 GTTCATAATG
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 103 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (97 bp):
AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAAAAGG
TTCATAATGAGAAGAACTCATCTGAAGAAGGA
Found at i:41980 original size:114 final size:114
Alignment explanation
Indices: 41862--42452 Score: 1044
Period size: 114 Copynumber: 5.2 Consensus size: 114
41852 TGAAGAAGGA
41862 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAAAAGG
1 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAAAAGG
41927 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
66 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* *
41976 AGAAGAATTTGTTCAACATTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAGG
1 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAAAAGG
42041 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
66 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
42090 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAGG
1 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAAAAGG
42155 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
66 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
42204 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTAACTTTTCCAGAGAAA-
1 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGA-AAAG
42268 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
65 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * *
42318 AGAAGAATTTGTTCAACCTTTTACTTGAATCCATC-ATTTGATGGATCAGCTTTTCCAGAGAAA-
1 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGA-AAAG
*
42381 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATA
65 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
42431 AGAAGAATTTGTTCAACTTTTT
1 AGAAGAATTTGTTCAACCTTTT
42453 GCATAATTCT
Statistics
Matches: 464, Mismatches: 12, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
113 95 0.20
114 367 0.79
115 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (114 bp):
AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAAAAGG
TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
Found at i:42015 original size:211 final size:214
Alignment explanation
Indices: 41651--42452 Score: 1119
Period size: 228 Copynumber: 3.6 Consensus size: 214
41641 AGTTCATAGT
* * *** * * * *
41651 GAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTTCCAGAAAAGG
1 GAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCATCTTTTCCAGAAAAGG
41716 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
66 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
41781 CCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAA
131 CCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAA
41846 CTCATCT-GAAGAAG-G-A
196 CTCATCTAGAAGAAGAGTA
*
41862 -AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAAAAG
1 GAGAAGAATTTGTTCAACCTTTTACCTGAATTCATC-AATTGATGGATCATCTTTTCCAGAAAAG
41926 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
65 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
*
41991 ACATTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGA
130 ACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGA
42056 ACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
195 ACTCATCT-----A-GAAGAAG-AG----T-A
* *
42088 TGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAA
1 -GAGAAGAATTTGTTCAACCTTTTACCTGAATTCATC-AATTGATGGATCATCTTTTCCAGAAAA
42153 GGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
64 GGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* *
42218 AACCTTTTACCTGAATTCATCAAATTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAG
129 AACCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAG
42283 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAA
194 AACTCATCT-----A-GAAGAAG-AG----T-A
* * * *
42316 TGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAA
1 -GAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCATCTTTTCCAGA-AAA
*
42381 -GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTC
64 GGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
*
42445 AACTTTTT
129 AACCTTTT
42453 GCATAATTCT
Statistics
Matches: 549, Mismatches: 23, Indels: 22
0.92 0.04 0.04
Matches are distributed among these distances:
210 29 0.05
211 161 0.29
218 7 0.01
220 1 0.00
226 1 0.00
227 91 0.17
228 259 0.47
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (214 bp):
GAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCATCTTTTCCAGAAAAGG
TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAA
CCTTTTACCTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAA
CTCATCTAGAAGAAGAGTA
Found at i:42773 original size:3 final size:3
Alignment explanation
Indices: 42765--42890 Score: 207
Period size: 3 Copynumber: 42.0 Consensus size: 3
42755 CTAATATTTT
* *
42765 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
42813 TTA TTA TTA TTG TTA TTA TTG TTA TTA TTA TTG TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42861 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42891 AATATATTAA
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 113 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:43345 original size:22 final size:22
Alignment explanation
Indices: 43302--43345 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
43292 AAAAAGACAG
* * * *
43302 AGACAGAGAACGGAGAAGAAAA
1 AGACAGAGAAAGAAAAAAAAAA
43324 AGACAGAGAAAGAAAAAAAAAA
1 AGACAGAGAAAGAAAAAAAAAA
43346 CAAACTAGTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.68, C:0.07, G:0.25, T:0.00
Consensus pattern (22 bp):
AGACAGAGAAAGAAAAAAAAAA
Found at i:44170 original size:19 final size:18
Alignment explanation
Indices: 44134--44182 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
44124 TAGATTTTTA
*
44134 ATTTTATT-TTTTCGTTT
1 ATTTTATTGTTTTCATTT
44151 ATTTTATATGTTTTCATTT
1 ATTTTAT-TGTTTTCATTT
44170 ATTTTATTGTTTT
1 ATTTTATTGTTTT
44183 TAAATATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (18 bp):
ATTTTATTGTTTTCATTT
Found at i:44250 original size:13 final size:13
Alignment explanation
Indices: 44222--44256 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
44212 TTTTATTATA
44222 TTATTAAATA-TT
1 TTATTAAATATTT
44234 TTATTAAATATTT
1 TTATTAAATATTT
44247 TTA-TAAATAT
1 TTATTAAATAT
44257 ATAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTATTAAATATTT
Found at i:47873 original size:18 final size:18
Alignment explanation
Indices: 47850--47902 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
47840 AGGGATTATC
*
47850 AGTGGTCTTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
47868 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
47886 AGTGGTCCTACGGGACA
1 AGTGGTCCTTCGGGACA
47903 AATTTCTACG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.19, C:0.21, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:50921 original size:23 final size:23
Alignment explanation
Indices: 50886--50951 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 23
50876 CCATTAGAGG
*
50886 CTATGAATTTGTCCCGAAAGACCA
1 CTATGAA-ATGTCCCGAAAGACCA
*
50910 CTATGAAATGTCCCGAAGGACCA
1 CTATGAAATGTCCCGAAAGACCA
*
50933 --ATG-TATGTCCCGAAAGACC
1 CTATGAAATGTCCCGAAAGACC
50952 TATGAACCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.37
21 3 0.08
23 14 0.37
24 7 0.18
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (23 bp):
CTATGAAATGTCCCGAAAGACCA
Found at i:59475 original size:150 final size:151
Alignment explanation
Indices: 59284--59584 Score: 570
Period size: 152 Copynumber: 2.0 Consensus size: 151
59274 TGGACATAAA
59284 CTGACTTTCCAACTTCCTCCAATTTCGTCTGGAGACGATAGATGCATGAAGTGATACATGACCTC
1 CTGACTTTCCAACTTCCTCCAATTTCGTCTGGAGACGATAGATGCATGAAGTGATACATGACCTC
59349 GTCCG-CAAGCATAATCGTAT-GTTCCTGCCGCTCGCTGCTGCAATTCTTCCCAATCTTCCTCAT
66 GTCCGCCAAGCATAATCGTATGGTTCCTGCCGCTCGCTGCTGCAATTCTTCCCAATCTTCCTCAT
59412 CCATCGACGCCGGCTTTGTAG
131 CCATCGACGCCGGCTTTGTAG
*
59433 CTGACTTTCCAACTTCCTCCAAATTTCGTCTGGAGACGATAGATGCATGACGTGATACATGACCT
1 CTGACTTTCCAACTTCCTCC-AATTTCGTCTGGAGACGATAGATGCATGAAGTGATACATGACCT
59498 CGTCCGCCAAGCATAATCGTATGGTTCCTGCCGCTCGCTGCTGCAATTCTTCCCAATCTTCCTCA
65 CGTCCGCCAAGCATAATCGTATGGTTCCTGCCGCTCGCTGCTGCAATTCTTCCCAATCTTCCTCA
59563 TCCATCGACGCCGGCTTTGTAG
130 TCCATCGACGCCGGCTTTGTAG
59585 GTCGCAAAGC
Statistics
Matches: 148, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
149 20 0.14
150 49 0.33
151 15 0.10
152 64 0.43
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (151 bp):
CTGACTTTCCAACTTCCTCCAATTTCGTCTGGAGACGATAGATGCATGAAGTGATACATGACCTC
GTCCGCCAAGCATAATCGTATGGTTCCTGCCGCTCGCTGCTGCAATTCTTCCCAATCTTCCTCAT
CCATCGACGCCGGCTTTGTAG
Found at i:69221 original size:40 final size:41
Alignment explanation
Indices: 69170--69396 Score: 208
Period size: 41 Copynumber: 5.5 Consensus size: 41
69160 AACTTGTGGT
69170 GTTTGTATAAAAATGCCACTAAAACACGAGTCTTTAGAGGC
1 GTTTGTATAAAAATGCCACTAAAACACGAGTCTTTAGAGGC
* * * * * *
69211 GTTTTTTAAAAAAAAGCCACTAAAACAAGAGTCTATAGTGGC
1 G-TTTGTATAAAAATGCCACTAAAACACGAGTCTTTAGAGGC
* * * ** * *
69253 GTTTATATACAAACGCCACTAAAGTATGAGTCTTTAGCGGC
1 GTTTGTATAAAAATGCCACTAAAACACGAGTCTTTAGAGGC
* * * *
69294 GTTTGTATAAAAATGACACTAAAACACGTGTCTTTAGCGAC
1 GTTTGTATAAAAATGCCACTAAAACACGAGTCTTTAGAGGC
* ** * *
69335 GTTTTTATAAAAACACCACTACAGA-ACGAGTC-TTA-ACGAC
1 GTTTGTATAAAAATGCCACTA-AAACACGAGTCTTTAGA-GGC
69375 GTTTGTATAAAAATGCCACTAA
1 GTTTGTATAAAAATGCCACTAA
69397 TGTACAAGTT
Statistics
Matches: 149, Mismatches: 34, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
39 1 0.01
40 24 0.16
41 87 0.58
42 37 0.25
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (41 bp):
GTTTGTATAAAAATGCCACTAAAACACGAGTCTTTAGAGGC
Found at i:69231 original size:42 final size:41
Alignment explanation
Indices: 69178--69437 Score: 193
Period size: 41 Copynumber: 6.3 Consensus size: 41
69168 GTGTTTGTAT
*
69178 AAAAATGCCACTAAAACACGAGTCTTTAGAGGCGTTTTTTAA
1 AAAAATGCCACTAAAACACGAGTCTTTAGCGGCG-TTTTTAA
* * * * * *
69220 AAAAAAGCCACTAAAACAAGAGTCTATAGTGGCGTTTATAT
1 AAAAATGCCACTAAAACACGAGTCTTTAGCGGCGTTTTTAA
* * ** * * *
69261 ACAAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTAT
1 AAAAATGCCACTAAAACACGAGTCTTTAGCGGCGTTTTTAA
* * * *
69302 AAAAATGACACTAAAACACGTGTCTTTAGCGACGTTTTTAT
1 AAAAATGCCACTAAAACACGAGTCTTTAGCGGCGTTTTTAA
** * * * * *
69343 AAAAACACCACTACAGA-ACGAGTC-TTAACGACGTTTGTAT
1 AAAAATGCCACTA-AAACACGAGTCTTTAGCGGCGTTTTTAA
*** * *
69383 AAAAATGCCACTAATGTACAAGT-TTATAGCGGCGTTTGTTGA
1 AAAAATGCCACTAAAACACGAGTCTT-TAGCGGCGTTT-TTAA
69425 AAAAATGCCACTA
1 AAAAATGCCACTA
69438 TGTGTGCACC
Statistics
Matches: 173, Mismatches: 40, Indels: 10
0.78 0.18 0.04
Matches are distributed among these distances:
39 1 0.01
40 31 0.18
41 95 0.55
42 46 0.27
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (41 bp):
AAAAATGCCACTAAAACACGAGTCTTTAGCGGCGTTTTTAA
Found at i:69366 original size:82 final size:82
Alignment explanation
Indices: 69170--69396 Score: 233
Period size: 82 Copynumber: 2.8 Consensus size: 82
69160 AACTTGTGGT
* ** * * * *
69170 GTTTGTATAAAAATGCCACTAAA-ACACGAGTCTTTAGAGGCGTTTTTTAAAAAAAAGCCACTAA
1 GTTTATATAAAAACACCACTAAAGA-ACGAGTCTTTAGCGGCG-TTTGTATAAAAATGCCACTAA
* *
69234 AACAAGAGTCTATAGTGGC
64 AACAAGAGTCTATAGCGAC
* * * * *
69253 GTTTATATACAAACGCCACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAATGACACTAAAA
1 GTTTATATAAAAACACCACTAAAGAACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAA
* * *
69318 CACGTGTCTTTAGCGAC
66 CAAGAGTCTATAGCGAC
* * * *
69335 GTTTTTATAAAAACACCACTACAGAACGAGTC-TTAACGACGTTTGTATAAAAATGCCACTAA
1 GTTTATATAAAAACACCACTAAAGAACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAA
69397 TGTACAAGTT
Statistics
Matches: 119, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
81 27 0.23
82 57 0.48
83 35 0.29
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (82 bp):
GTTTATATAAAAACACCACTAAAGAACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAA
CAAGAGTCTATAGCGAC
Found at i:74131 original size:16 final size:16
Alignment explanation
Indices: 74093--74133 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
74083 CCGACCAAAT
74093 TTTACTATTCACGAAA
1 TTTACTATTCACGAAA
* * *
74109 CTCACTATTCATGAAA
1 TTTACTATTCACGAAA
74125 TTTACTATT
1 TTTACTATT
74134 TATGTGAATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (16 bp):
TTTACTATTCACGAAA
Found at i:74610 original size:21 final size:21
Alignment explanation
Indices: 74584--74625 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
74574 CGAATTCGGT
*
74584 GCCCCCTAATTTTGA-CTTCCA
1 GCCCCCCAATTTT-ATCTTCCA
74605 GCCCCCCAATTTTATCTTCCA
1 GCCCCCCAATTTTATCTTCCA
74626 ACAATAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.19, C:0.40, G:0.07, T:0.33
Consensus pattern (21 bp):
GCCCCCCAATTTTATCTTCCA
Found at i:76304 original size:18 final size:19
Alignment explanation
Indices: 76283--76320 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
76273 TATTAAATAA
*
76283 TAATAAATGATTA-ATTAT
1 TAATAAATCATTATATTAT
76301 TAATAAATCATTATATTAT
1 TAATAAATCATTATATTAT
76320 T
1 T
76321 TTATTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (19 bp):
TAATAAATCATTATATTAT
Found at i:87252 original size:29 final size:29
Alignment explanation
Indices: 87218--87287 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
87208 GCAATGCTCT
87218 ATAGTCGGAGGATCATTTTGTAACTTTTA
1 ATAGTCGGAGGATCATTTTGTAACTTTTA
87247 ATAGTCGGAGGATCATTTTGTAACTTTTA
1 ATAGTCGGAGGATCATTTTGTAACTTTTA
87276 ATAGTCGGAGGA
1 ATAGTCGGAGGA
87288 CTCAGTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (29 bp):
ATAGTCGGAGGATCATTTTGTAACTTTTA
Done.