Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007794.1 Hibiscus syriacus cultivar Beakdansim tig00110084_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: 94007
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:10599 original size:17 final size:17
Alignment explanation
Indices: 10550--10601 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
10540 TTGATATACG
*
10550 TTTTATTTACATTATATT
1 TTTTATTTAAATTAT-TT
* *
10568 TTTTATTTTATTTATTT
1 TTTTATTTAAATTATTT
10585 TTTTATTTAAATTATTT
1 TTTTATTTAAATTATTT
10602 GTAATAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTTAAATTATTT
Found at i:18876 original size:196 final size:195
Alignment explanation
Indices: 18485--18877 Score: 759
Period size: 196 Copynumber: 2.0 Consensus size: 195
18475 TTGGTACCAT
* *
18485 TATCAATTTCTTTTTATTTTGTCGAAGGAGGAGTAATTGTCCTGAACAAAAACCAATTAAACTAG
1 TATCAATTTCTTTCTATTTTGTCGAAGGAGGAGTAATTGTCCTGAACAAAAACCAATTAAACAAG
18550 TCTGTGATATCCAAATCCTCCAATATCAGCAAGAAAAAGTGGTTCAGATTGCCTGGAGCTTGCTG
66 TCTGTGATATCCAAATCCTCCAATATCAGCAAGAAAAAGTGGTTCAGATTGCCTGGAGCTTGCTG
18615 GTATCTGGATTTGGGGTGTTTATATAAACTTTTATTGGCTAATCTTGCTACAAAAATATTTTACC
131 GTATCTGGATTTGGGGTGTTTATATAAACTTTTATTGGCTAATCTTGCTACAAAAATATTTTACC
18680 TATCAATTTCTTTCTATTTTGTCGAAGGAGGAGTAATTGTCCTGAACAAAAACCAATTAAACAAG
1 TATCAATTTCTTTCTATTTTGTCGAAGGAGGAGTAATTGTCCTGAACAAAAACCAATTAAACAAG
18745 TCTGTGATATCCAAATCCTCCAATATCAGCAAGACAAAAGTGGTTCAGATTGCCTGGAGCTTGCT
66 TCTGTGATATCCAAATCCTCCAATATCAGCAAGA-AAAAGTGGTTCAGATTGCCTGGAGCTTGCT
18810 GGTATCTGGATTTGGGGTGTTTATATAAACTTTTATTGGCTAATCTTGCTACAAAAATATTTTAC
130 GGTATCTGGATTTGGGGTGTTTATATAAACTTTTATTGGCTAATCTTGCTACAAAAATATTTTAC
18875 C
195 C
18876 TA
1 TA
18878 GGATTTGGGA
Statistics
Matches: 195, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
195 97 0.50
196 98 0.50
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (195 bp):
TATCAATTTCTTTCTATTTTGTCGAAGGAGGAGTAATTGTCCTGAACAAAAACCAATTAAACAAG
TCTGTGATATCCAAATCCTCCAATATCAGCAAGAAAAAGTGGTTCAGATTGCCTGGAGCTTGCTG
GTATCTGGATTTGGGGTGTTTATATAAACTTTTATTGGCTAATCTTGCTACAAAAATATTTTACC
Found at i:24631 original size:21 final size:21
Alignment explanation
Indices: 24584--24632 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
24574 TCGGTCATCC
* * *
24584 AATTTTTTAAACTCCATACTG
1 AATTTTTTAAACCCCAAACCG
*
24605 GA-TTTTTAAACCCCAAACCG
1 AATTTTTTAAACCCCAAACCG
24625 AATTTTTT
1 AATTTTTT
24633 TTCCGGATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (21 bp):
AATTTTTTAAACCCCAAACCG
Found at i:25047 original size:32 final size:32
Alignment explanation
Indices: 24979--25076 Score: 164
Period size: 32 Copynumber: 3.1 Consensus size: 32
24969 TGCCCTTTAT
*
24979 CATTAGTGCTAGATCGTCTCTAACCTC--AAC
1 CATTAATGCTAGATCGTCTCTAACCTCATAAC
25009 CATTAATGCTAGATCGTCTCTAACCTCATAAC
1 CATTAATGCTAGATCGTCTCTAACCTCATAAC
*
25041 CATTAATGCTAGATCGTCTCTAACCTCATAAT
1 CATTAATGCTAGATCGTCTCTAACCTCATAAC
25073 CATT
1 CATT
25077 TTACCAAGAT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
30 26 0.41
32 38 0.59
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.33
Consensus pattern (32 bp):
CATTAATGCTAGATCGTCTCTAACCTCATAAC
Found at i:30242 original size:10 final size:10
Alignment explanation
Indices: 30227--30275 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
30217 TTCATTTTTT
30227 TAAAAATAAA
1 TAAAAATAAA
*
30237 TAAAAATGAAT
1 TAAAAAT-AAA
30248 TAAAAATAAA
1 TAAAAATAAA
* *
30258 TAAAATTCAA
1 TAAAAATAAA
30268 TAAAAATA
1 TAAAAATA
30276 TAATGTAAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
10 23 0.72
11 9 0.28
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:30252 original size:21 final size:21
Alignment explanation
Indices: 30226--30275 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
30216 ATTCATTTTT
*
30226 TTAAAAATAAATAAAAATGAA
1 TTAAAAATAAATAAAAATCAA
*
30247 TTAAAAATAAATAAAATTCAA
1 TTAAAAATAAATAAAAATCAA
30268 -TAAAAATA
1 TTAAAAATA
30276 TAATGTAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (21 bp):
TTAAAAATAAATAAAAATCAA
Found at i:30976 original size:26 final size:26
Alignment explanation
Indices: 30933--30987 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
30923 TGATGATAAT
30933 AATAATAAATATTTTATAATTTAAAA
1 AATAATAAATATTTTATAATTTAAAA
* *
30959 AATAATAAAT-TTTATATATTTTTAAA
1 AATAATAAATATTT-TATAATTTAAAA
30985 AAT
1 AAT
30988 TTTATTGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 3 0.12
26 23 0.88
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AATAATAAATATTTTATAATTTAAAA
Found at i:31006 original size:18 final size:19
Alignment explanation
Indices: 30965--31004 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
30955 AAAAAATAAT
*
30965 AAATTTTATATATTTTTAA
1 AAATTTTATATACTTTTAA
30984 AAATTTTAT-TGACTTTTAA
1 AAATTTTATAT-ACTTTTAA
31003 AA
1 AA
31005 TTAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
AAATTTTATATACTTTTAA
Found at i:31293 original size:10 final size:10
Alignment explanation
Indices: 31238--31299 Score: 54
Period size: 10 Copynumber: 6.0 Consensus size: 10
31228 TTTTACACTA
31238 TATTTTTATT
1 TATTTTTATT
* *
31248 GAATTTTATT
1 TATTTTTATT
* *
31258 CATTTATAATT
1 TATTT-TTATT
31269 CT-TTTTTATT
1 -TATTTTTATT
31279 ATATTTTTATT
1 -TATTTTTATT
31290 TATTTTTATT
1 TATTTTTATT
31300 GAATAATAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 26 0.63
11 15 0.37
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (10 bp):
TATTTTTATT
Found at i:31295 original size:21 final size:21
Alignment explanation
Indices: 31236--31299 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
31226 AGTTTTACAC
* *
31236 TATATTTTTATTGAATTTTAT
1 TATATTTTTATTTATTTTTAT
* *
31257 TCAT-TTATAATTCT-TTTTTAT
1 T-ATATTTTTATT-TATTTTTAT
31278 TATATTTTTATTTATTTTTAT
1 TATATTTTTATTTATTTTTAT
31299 T
1 T
31300 GAATAATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
20 3 0.09
21 28 0.85
22 2 0.06
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.70
Consensus pattern (21 bp):
TATATTTTTATTTATTTTTAT
Found at i:32649 original size:7 final size:7
Alignment explanation
Indices: 32637--32664 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
32627 ATCCTGCTTT
32637 CTTTTTC
1 CTTTTTC
32644 CTTTTTC
1 CTTTTTC
32651 CTTTTTC
1 CTTTTTC
32658 CTTTTTC
1 CTTTTTC
32665 ATCTTCTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (7 bp):
CTTTTTC
Found at i:37208 original size:21 final size:21
Alignment explanation
Indices: 37184--37257 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
37174 ACAAAGGAGA
37184 AGTATCGATACTCCTATGGGG
1 AGTATCGATACTCCTATGGGG
* ****
37205 AGTATCGATACT-CAACCCTG
1 AGTATCGATACTCCTATGGGG
*
37225 -GTATTGATACTCCTATGGGG
1 AGTATCGATACTCCTATGGGG
37245 AGTATCGATACTC
1 AGTATCGATACTC
37258 AACCCTGGTA
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
19 10 0.26
20 6 0.15
21 23 0.59
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (21 bp):
AGTATCGATACTCCTATGGGG
Found at i:37233 original size:19 final size:19
Alignment explanation
Indices: 37206--37276 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
37196 CCTATGGGGA
37206 GTATCGATACTCAACCCTG
1 GTATCGATACTCAACCCTG
* * ****
37225 GTATTGATACTCCTATGGGG
1 GTATCGATACT-CAACCCTG
37245 AGTATCGATACTCAACCCTG
1 -GTATCGATACTCAACCCTG
*
37265 GTATTGATACTC
1 GTATCGATACTC
37277 CCCTAGTGTA
Statistics
Matches: 37, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
19 21 0.57
20 6 0.16
21 10 0.27
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (19 bp):
GTATCGATACTCAACCCTG
Found at i:37234 original size:40 final size:40
Alignment explanation
Indices: 37185--37277 Score: 177
Period size: 40 Copynumber: 2.3 Consensus size: 40
37175 CAAAGGAGAA
*
37185 GTATCGATACTCCTATGGGGAGTATCGATACTCAACCCTG
1 GTATTGATACTCCTATGGGGAGTATCGATACTCAACCCTG
37225 GTATTGATACTCCTATGGGGAGTATCGATACTCAACCCTG
1 GTATTGATACTCCTATGGGGAGTATCGATACTCAACCCTG
37265 GTATTGATACTCC
1 GTATTGATACTCC
37278 CCTAGTGTAC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.30
Consensus pattern (40 bp):
GTATTGATACTCCTATGGGGAGTATCGATACTCAACCCTG
Found at i:41437 original size:19 final size:18
Alignment explanation
Indices: 41413--41466 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
41403 ACCGATAAAC
41413 CGAACCGAATCAAAAAAA
1 CGAACCGAATCAAAAAAA
*
41431 TCGAACCG--TTAAAAAAA
1 -CGAACCGAATCAAAAAAA
* *
41448 CGAACCGAACCGAAAAAA
1 CGAACCGAATCAAAAAAA
41466 C
1 C
41467 CAGTTTCGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
16 7 0.24
17 8 0.28
18 7 0.24
19 7 0.24
ACGTcount: A:0.56, C:0.24, G:0.13, T:0.07
Consensus pattern (18 bp):
CGAACCGAATCAAAAAAA
Found at i:46385 original size:18 final size:18
Alignment explanation
Indices: 46352--46387 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
46342 TTAAAACATA
*
46352 ATATACCATTTCTAACTC
1 ATATACCATGTCTAACTC
*
46370 ATATACCATGTGTAACTC
1 ATATACCATGTCTAACTC
46388 GTTTATATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (18 bp):
ATATACCATGTCTAACTC
Found at i:49347 original size:12 final size:12
Alignment explanation
Indices: 49317--49360 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
49307 CTATATGGTA
*
49317 TGAACAATACCG
1 TGAACAGTACCG
49329 TGAACAGTACCG
1 TGAACAGTACCG
**
49341 TGAACAGTACAA
1 TGAACAGTACCG
49353 TGAACAGT
1 TGAACAGT
49361 GGAAAATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.18
Consensus pattern (12 bp):
TGAACAGTACCG
Found at i:50050 original size:24 final size:24
Alignment explanation
Indices: 50023--50070 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
50013 ATCTCGTAAA
*
50023 TTGCACCGAAGTGCCACGTAGAAT
1 TTGCACCAAAGTGCCACGTAGAAT
*
50047 TTGCACCAAAGTGCCGCGTAGAAT
1 TTGCACCAAAGTGCCACGTAGAAT
50071 GCACGTAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (24 bp):
TTGCACCAAAGTGCCACGTAGAAT
Found at i:54947 original size:21 final size:21
Alignment explanation
Indices: 54921--54974 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
54911 TTATAAGGGT
**
54921 AGTATCGATACTC-ATTCATTG
1 AGTATCGATACTCAAAGCA-TG
54942 AGTATCGATAC-CAAAGCATG
1 AGTATCGATACTCAAAGCATG
54962 AGTATCGATACTC
1 AGTATCGATACTC
54975 CTCATAGGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (21 bp):
AGTATCGATACTCAAAGCATG
Found at i:59025 original size:2 final size:2
Alignment explanation
Indices: 59020--59049 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
59010 TATATATATA
59020 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
59050 AAGTTTAAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:59217 original size:44 final size:44
Alignment explanation
Indices: 59167--59255 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
59157 TTATGTATTT
59167 CTCCTTTCATACTCGGAACTTCACTCTGACCTTTAACTAGAACA
1 CTCCTTTCATACTCGGAACTTCACTCTGACCTTTAACTAGAACA
59211 CTCCTTTCATACTCGGAACTTCACTCTGACCTTTAACTAGAACA
1 CTCCTTTCATACTCGGAACTTCACTCTGACCTTTAACTAGAACA
59255 C
1 C
59256 CTGGAAAGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.27, C:0.33, G:0.09, T:0.31
Consensus pattern (44 bp):
CTCCTTTCATACTCGGAACTTCACTCTGACCTTTAACTAGAACA
Found at i:67619 original size:32 final size:32
Alignment explanation
Indices: 67568--67638 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
67558 AAACCGTTAA
*
67568 GAACCACAGAAAATCGAGCAAGGACCATTTAC
1 GAACAACAGAAAATCGAGCAAGGACCATTTAC
* *
67600 GAACAACAGAAAATTGAGCACGGACCATTTAC
1 GAACAACAGAAAATCGAGCAAGGACCATTTAC
67632 GAACAAC
1 GAACAAC
67639 GGGTGATATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.45, C:0.24, G:0.18, T:0.13
Consensus pattern (32 bp):
GAACAACAGAAAATCGAGCAAGGACCATTTAC
Found at i:69795 original size:25 final size:25
Alignment explanation
Indices: 69767--69823 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 25
69757 ATACATTAAT
69767 ATATTATTTATTACATTTTAAT--A
1 ATATTATTTATTACATTTTAATAAA
*
69790 ACA-TATTT-TT-CATTTTAATAAA
1 ATATTATTTATTACATTTTAATAAA
69812 ATATT-TTTATTA
1 ATATTATTTATTA
69824 AATAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
20 9 0.33
21 2 0.07
22 11 0.41
23 5 0.19
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (25 bp):
ATATTATTTATTACATTTTAATAAA
Found at i:69805 original size:20 final size:20
Alignment explanation
Indices: 69780--69819 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
69770 TTATTTATTA
*
69780 CATTTTAATAACATATTTTT
1 CATTTTAATAAAATATTTTT
69800 CATTTTAATAAAATATTTTT
1 CATTTTAATAAAATATTTTT
69820 ATTAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (20 bp):
CATTTTAATAAAATATTTTT
Found at i:69830 original size:17 final size:19
Alignment explanation
Indices: 69780--69833 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
69770 TTATTTATTA
*
69780 CATTTTAATAACATATTTTT
1 CATTTAAATAA-ATATTTTT
*
69800 CATTTTAATAAAATATTTTT
1 CATTTAAAT-AAATATTTTT
69820 -A-TTAAATAAATATT
1 CATTTAAATAAATATT
69834 AAATCGAGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 7 0.22
18 5 0.16
19 1 0.03
20 17 0.53
21 2 0.06
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (19 bp):
CATTTAAATAAATATTTTT
Found at i:71536 original size:21 final size:20
Alignment explanation
Indices: 71512--71722 Score: 62
Period size: 20 Copynumber: 10.2 Consensus size: 20
71502 GATTCGCAAC
71512 GCGATAGTCGAAGTTCGCATT
1 GCGATAGTCGAAGTTCGC-TT
* * *
71533 GCGATTTATTCCAAATTCG-TT
1 GCGA--TAGTCGAAGTTCGCTT
*
71554 GCGATAGGCGAAGTTCGCGTT
1 GCGATAGTCGAAGTTCGC-TT
* * *
71575 GCGATTCATTCCAA-ATCG-TT
1 GCGA-T-AGTCGAAGTTCGCTT
* *
71595 GCAATAGTCGAAGTTCACGTT
1 GCGATAGTCGAAGTTCGC-TT
* * *
71616 GCGATTCATTCCAA-ATCG-TT
1 GCGA-T-AGTCGAAGTTCGCTT
* *
71636 GCGATTCATTCCAA-TTCG-TT
1 GCGA-T-AGTCGAAGTTCGCTT
*
71656 GCGATAGGCGAAGTTCGCGTT
1 GCGATAGTCGAAGTTCGC-TT
* *
71677 GCGATTCATTCCAA-TTCG-TT
1 GCGA-T-AGTCGAAGTTCGCTT
*
71697 GCGATAGGCGAAGTTCGCGTT
1 GCGATAGTCGAAGTTCGC-TT
71718 GCGAT
1 GCGAT
71723 TCATTCCAAA
Statistics
Matches: 140, Mismatches: 31, Indels: 38
0.67 0.15 0.18
Matches are distributed among these distances:
18 13 0.09
19 22 0.16
20 36 0.26
21 34 0.24
22 12 0.09
23 23 0.16
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (20 bp):
GCGATAGTCGAAGTTCGCTT
Found at i:71566 original size:42 final size:41
Alignment explanation
Indices: 71512--71640 Score: 204
Period size: 41 Copynumber: 3.1 Consensus size: 41
71502 GATTCGCAAC
* *
71512 GCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
*
71554 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
* *
71595 GCAATAGTCGAAGTTCACGTTGCGATTCATTCCAAATCGTT
1 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
71636 GCGAT
1 GCGAT
71641 TCATTCCAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 47 0.59
42 33 0.41
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (41 bp):
GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
Found at i:71640 original size:61 final size:61
Alignment explanation
Indices: 71571--71701 Score: 217
Period size: 61 Copynumber: 2.1 Consensus size: 61
71561 GCGAAGTTCG
*
71571 CGTTGCGATTCATTCCAAATCGTTGCAATAGTCGAAGTTCACGTTGCGATTCATTCCAAAT
1 CGTTGCGATTCATTCCAAATCGTTGCAATAGGCGAAGTTCACGTTGCGATTCATTCCAAAT
* * * *
71632 CGTTGCGATTCATTCCAATTCGTTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAATT
1 CGTTGCGATTCATTCCAAATCGTTGCAATAGGCGAAGTTCACGTTGCGATTCATTCCAAAT
71693 CGTTGCGAT
1 CGTTGCGAT
71702 AGGCGAAGTT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (61 bp):
CGTTGCGATTCATTCCAAATCGTTGCAATAGGCGAAGTTCACGTTGCGATTCATTCCAAAT
Found at i:71672 original size:102 final size:104
Alignment explanation
Indices: 71529--71743 Score: 362
Period size: 102 Copynumber: 2.1 Consensus size: 104
71519 TCGAAGTTCG
*
71529 CATTGCGATTTATTCCAAATTCGTTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGT
1 CATTGCGATTCATTCCAAATTCGTTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGT
*
71594 TGCAATAGTCGAAGTTCACGTTGCGATTCATTCCAAA-T
66 TGCAATAGGCGAAGTTCACGTTGCGATTCATTCCAAATT
* *
71632 CGTTGCGATTCATTCC-AATTCGTTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGT
1 CATTGCGATTCATTCCAAATTCGTTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGT
* *
71696 TGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATT
66 TGCAATAGGCGAAGTTCACGTTGCGATTCATTCCAAATT
71735 CATTGCGAT
1 CATTGCGAT
71744 AGTCCAAATA
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 81 0.78
103 23 0.22
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (104 bp):
CATTGCGATTCATTCCAAATTCGTTGCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGT
TGCAATAGGCGAAGTTCACGTTGCGATTCATTCCAAATT
Found at i:71677 original size:41 final size:41
Alignment explanation
Indices: 71632--71745 Score: 210
Period size: 41 Copynumber: 2.8 Consensus size: 41
71622 CATTCCAAAT
71632 CGTTGCGATTCATTCCAATTCGTTGCGATAGGCGAAGTTCG
1 CGTTGCGATTCATTCCAATTCGTTGCGATAGGCGAAGTTCG
71673 CGTTGCGATTCATTCCAATTCGTTGCGATAGGCGAAGTTCG
1 CGTTGCGATTCATTCCAATTCGTTGCGATAGGCGAAGTTCG
*
71714 CGTTGCGATTCATTCCAAATTCATTGCGATAG
1 CGTTGCGATTCATTCC-AATTCGTTGCGATAG
71746 TCCAAATATT
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
41 57 0.80
42 14 0.20
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.32
Consensus pattern (41 bp):
CGTTGCGATTCATTCCAATTCGTTGCGATAGGCGAAGTTCG
Found at i:71698 original size:20 final size:20
Alignment explanation
Indices: 71571--71701 Score: 108
Period size: 20 Copynumber: 6.5 Consensus size: 20
71561 GCGAAGTTCG
*
71571 CGTTGCGATTCATTCCAAAT
1 CGTTGCGATTCATTCCAATT
* * *
71591 CGTTGC-AAT-AGTCGAAGTT
1 CGTTGCGATTCATTCCAA-TT
*
71610 CACGTTGCGATTCATTCCAAAT
1 --CGTTGCGATTCATTCCAATT
71632 CGTTGCGATTCATTCCAATT
1 CGTTGCGATTCATTCCAATT
** *
71652 CGTTGCGA-T-AGGCGAAGTT
1 CGTTGCGATTCATTCCAA-TT
71671 CGCGTTGCGATTCATTCCAATT
1 --CGTTGCGATTCATTCCAATT
71693 CGTTGCGAT
1 CGTTGCGAT
71702 AGGCGAAGTT
Statistics
Matches: 86, Mismatches: 15, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
18 9 0.10
19 6 0.07
20 42 0.49
21 14 0.16
22 6 0.07
23 9 0.10
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (20 bp):
CGTTGCGATTCATTCCAATT
Found at i:72980 original size:14 final size:17
Alignment explanation
Indices: 72961--73003 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
72951 TACAATAATT
72961 TAAAAT-TTTAA-A-AA
1 TAAAATATTTAATATAA
72975 TAAAATATTTAATATAA
1 TAAAATATTTAATATAA
72992 TAAAAATATTTA
1 T-AAAATATTTA
73004 TAAAATTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 1 0.04
17 3 0.12
18 10 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAATATTTAATATAA
Found at i:73377 original size:60 final size:60
Alignment explanation
Indices: 73284--73433 Score: 228
Period size: 60 Copynumber: 2.5 Consensus size: 60
73274 ATTTGGATAT
* * * *
73284 TTTGGGGATGACATTGGAAGATTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCATAG
1 TTTGGGGATGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAAAATGAGAGTCATAG
*
73344 TTTGGGGATGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAGAATGAGAGTCATAG
1 TTTGGGGATGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAAAATGAGAGTCATAG
* * *
73404 CTTGGGGATTAAATTAAAATATTCAAAAGT
1 TTTGGGGATGAAATTAGAATATTCAAAAGT
73434 ATATAAATTA
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 82 1.00
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (60 bp):
TTTGGGGATGAAATTAGAATATTCAAAAGTTTAAAGACTAATTTAAAATGAGAGTCATAG
Found at i:84430 original size:19 final size:19
Alignment explanation
Indices: 84402--84438 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
84392 CTCTTTTTAC
*
84402 TATTTAAATTTAATATATT
1 TATTTAAATTTAAAATATT
*
84421 TATTTTAATTTAAAATAT
1 TATTTAAATTTAAAATAT
84439 ACAAAAGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTAAATTTAAAATATT
Found at i:84501 original size:185 final size:185
Alignment explanation
Indices: 84195--84632 Score: 503
Period size: 185 Copynumber: 2.4 Consensus size: 185
84185 TTTAAAATAT
** * ** * * *
84195 TCAAAAAATAAAACTCCCTTTACCA-TTATAACTTAAATAGATATTATTTTAATTAAAAATATAT
1 TCAAAAAAT-AAACTCATTTTACTATTTA-AACTTAAGCAAATATTATTTTAATTTAAAATATAC
84259 AAAAATATAATTATCTTAATATTCAAAGTTAAAAGGTATAAGATACATTTTTAAATTGACATACT
64 AAAAATATAATTATCTTAATATTCAAAGTTAAAAGGTATAAGATACATTTTTAAATTGACATACT
* * *
84324 AAAAGAATAATTATTC-TACTAATATTCAAATTAAATAATAGATTTAATTTGCAATTG
129 AAAAGAATAATTA-TCATACAAATATTAAAATTAAATAATAGATTTAATTTGCAATGG
* * * *
84381 TCAAAAAAT-AACTCTTTTTACTATTTAAATTTAA-TATAT-TTATTTTAATTTAAAATATACAA
1 TCAAAAAATAAACTCATTTTACTATTTAAACTTAAGCAAATATTATTTTAATTTAAAATATACAA
* * * *
84443 AAGTATATATTATCTTTAATATTCAAATTTAAAAAGGTA-ACA-ACTACCTTTTTAAATTGAGAT
66 AAATATA-ATTATC-TTAATATTCAAAGTT-AAAAGGTATA-AGA-TACATTTTTAAATTGACAT
* * * * *
84506 ATTCAAAGAGTAATTATCATACAAATATTAAAATTAAATAATATATTTAATTTGTAATGG
126 ACTAAAAGAATAATTATCATACAAATATTAAAATTAAATAATAGATTTAATTTGCAATGG
* ** *
84566 TGAAAAGGTAAATTCATTTTACTATTTAAACTTAAGCAAATATTATTTTAATTTAAAATATACAA
1 TCAAAAAATAAACTCATTTTACTATTTAAACTTAAGCAAATATTATTTTAATTTAAAATATACAA
84631 AA
66 AA
84633 TTAAAAAGAT
Statistics
Matches: 215, Mismatches: 27, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
182 27 0.13
183 10 0.05
184 35 0.16
185 84 0.39
186 31 0.14
187 3 0.01
188 25 0.12
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (185 bp):
TCAAAAAATAAACTCATTTTACTATTTAAACTTAAGCAAATATTATTTTAATTTAAAATATACAA
AAATATAATTATCTTAATATTCAAAGTTAAAAGGTATAAGATACATTTTTAAATTGACATACTAA
AAGAATAATTATCATACAAATATTAAAATTAAATAATAGATTTAATTTGCAATGG
Found at i:85789 original size:18 final size:17
Alignment explanation
Indices: 85744--85790 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
85734 TTAGAGAAGT
85744 AAAATTAAAA-TAACAA
1 AAAATTAAAATTAACAA
* *
85760 AAATATTTAAATTAGACTA
1 AAA-ATTAAAATTA-ACAA
85779 AAAATTAAAATT
1 AAAATTAAAATT
85791 TTTAAAGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 3 0.12
17 6 0.24
18 10 0.40
19 6 0.24
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAATTAAAATTAACAA
Found at i:92979 original size:31 final size:32
Alignment explanation
Indices: 92928--92993 Score: 125
Period size: 31 Copynumber: 2.1 Consensus size: 32
92918 GATTTCTCGA
92928 AGATGATTTCTACCGAGTCGGACTCTTGTTAC
1 AGATGATTTCTACCGAGTCGGACTCTTGTTAC
92960 AGATGATTTCTA-CGAGTCGGACTCTTGTTAC
1 AGATGATTTCTACCGAGTCGGACTCTTGTTAC
92991 AGA
1 AGA
92994 CCCTATGTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 22 0.65
32 12 0.35
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (32 bp):
AGATGATTTCTACCGAGTCGGACTCTTGTTAC
Done.