Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005831.1 Hibiscus syriacus cultivar Beakdansim tig00013670_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: 104488
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1956 original size:2 final size:2
Alignment explanation
Indices: 1949--1985 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1939 AAGTTAGAGC
1949 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1986 CCAATAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16557 original size:18 final size:19
Alignment explanation
Indices: 16523--16558 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16513 ATAATTTTAA
*
16523 TGATAATTTTGTAATAATT
1 TGATAAATTTGTAATAATT
16542 TGATAAATTT-TAATAAT
1 TGATAAATTTGTAATAAT
16559 GATTCAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (19 bp):
TGATAAATTTGTAATAATT
Found at i:29692 original size:13 final size:13
Alignment explanation
Indices: 29671--29730 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
29661 ATTTTGTTAG
29671 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
29684 TATTGTA-TTATT
1 TATTTTATTTAAT
29696 TAATTTT-TTT-AT
1 T-ATTTTATTTAAT
29708 TATTTTATTTAAT
1 TATTTTATTTAAT
29721 TATTTTATTT
1 TATTTTATTT
29731 GTTTGCAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 5 0.13
12 10 0.26
13 24 0.62
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:29696 original size:21 final size:20
Alignment explanation
Indices: 29671--29725 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
29661 ATTTTGTTAG
29671 TATTTTATTTAATTATTGTAT
1 TATTTTATTTAATTATT-TAT
*
29692 TA-TTTAATT--TT-TTTAT
1 TATTTTATTTAATTATTTAT
29708 TATTTTATTTAATTATTT
1 TATTTTATTTAATTATTT
29726 TATTTGTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
16 5 0.18
17 8 0.29
18 2 0.07
19 2 0.07
20 9 0.32
21 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TATTTTATTTAATTATTTAT
Found at i:29717 original size:16 final size:16
Alignment explanation
Indices: 29675--29717 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
29665 TGTTAGTATT
*
29675 TTATTTAATTATTGTA
1 TTATTTAATTTTTGTA
*
29691 TTATTTAATTTTTTTA
1 TTATTTAATTTTTGTA
*
29707 TTATTTTATTT
1 TTATTTAATTT
29718 AATTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTAATTTTTGTA
Found at i:31241 original size:18 final size:18
Alignment explanation
Indices: 31218--31253 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31208 ATGGATAAAT
*
31218 TGGTGGTGGAGGTGAATG
1 TGGTGGCGGAGGTGAATG
*
31236 TGGTGGCGGTGGTGAATG
1 TGGTGGCGGAGGTGAATG
31254 ACGTGGTGGC
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:0.14, C:0.03, G:0.56, T:0.28
Consensus pattern (18 bp):
TGGTGGCGGAGGTGAATG
Found at i:31277 original size:75 final size:75
Alignment explanation
Indices: 31085--31265 Score: 260
Period size: 75 Copynumber: 2.5 Consensus size: 75
31075 GGAGGAGAGG
* * ** * *
31085 GTGGTGGTGGAGAGTGAACTGGAAGTGGCGATGGTGGCGGAGATAAGTATGGATAAATTGGTGGT
1 GTGGTGGAGGAGAGTGAACTGGAAGTGGTGGCGGCGGTGGAGATAAGTATGGATAAATTGGTGGT
31150 GGAGGTGAAT
66 GGAGGTGAAT
31160 GTGGTGGAGGAGAGTGAACTGGAAGTGGTGGCGGCGGTGGAGATAAGTATGGATAAATTGGTGGT
1 GTGGTGGAGGAGAGTGAACTGGAAGTGGTGGCGGCGGTGGAGATAAGTATGGATAAATTGGTGGT
31225 GGAGGTGAAT
66 GGAGGTGAAT
* * *
31235 GTGGTGGCGGTG-GTGAA-T-GACGTGGTGGCGG
1 GTGGTGGAGGAGAGTGAACTGGAAGTGGTGGCGG
31266 GGATGGTGGA
Statistics
Matches: 97, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
72 12 0.12
73 1 0.01
74 5 0.05
75 79 0.81
ACGTcount: A:0.23, C:0.05, G:0.49, T:0.23
Consensus pattern (75 bp):
GTGGTGGAGGAGAGTGAACTGGAAGTGGTGGCGGCGGTGGAGATAAGTATGGATAAATTGGTGGT
GGAGGTGAAT
Found at i:31373 original size:27 final size:27
Alignment explanation
Indices: 31322--31374 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
31312 GACGGTGACG
* * *
31322 GTGGTGGTGGATAGTAAACTGGTGGAA
1 GTGGTGGAGGAGAATAAACTGGTGGAA
31349 GTGGTGGAGGAGAATAAACTGGTGGA
1 GTGGTGGAGGAGAATAAACTGGTGGA
31375 GCAGGAGGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.28, C:0.04, G:0.45, T:0.23
Consensus pattern (27 bp):
GTGGTGGAGGAGAATAAACTGGTGGAA
Found at i:31518 original size:15 final size:15
Alignment explanation
Indices: 31486--31520 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
31476 TGAGAAAACC
*
31486 GGTGGTGGAGGCGTT
1 GGTGGTGGAGGCGGT
*
31501 GGTGGTGGAGGTGGT
1 GGTGGTGGAGGCGGT
31516 GGTGG
1 GGTGG
31521 GGATTGAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.03, G:0.66, T:0.26
Consensus pattern (15 bp):
GGTGGTGGAGGCGGT
Found at i:37715 original size:29 final size:28
Alignment explanation
Indices: 37673--37757 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 28
37663 AACCCAACCA
*
37673 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACGCCC-GCGACCTCC
* **
37702 TAGGTCGCCATGCACGCCCGACGACATGG
1 TAGGTCGCCATGCACGCCCG-CGACCTCC
37731 TAGGTCGCCATGCACGCCCCGCGACCT
1 TAGGTCGCCATGCACG-CCCGCGACCT
37758 TGTCTTTGGC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 1 0.02
29 44 0.90
30 4 0.08
ACGTcount: A:0.18, C:0.41, G:0.26, T:0.15
Consensus pattern (28 bp):
TAGGTCGCCATGCACGCCCGCGACCTCC
Found at i:37988 original size:29 final size:29
Alignment explanation
Indices: 37956--38036 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 29
37946 GTCGCCCCGA
*
37956 GTGCATGGCGACCTCCTTGGTCATTGGGC
1 GTGCATGGCGACCTCTTTGGTCATTGGGC
** *
37985 GTGCATGGCGATTTCTTTGGTCGTTGGGC
1 GTGCATGGCGACCTCTTTGGTCATTGGGC
*
38014 GTGCATGACGACCTCTTTGGTCA
1 GTGCATGGCGACCTCTTTGGTCA
38037 CTGTACAATT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.11, C:0.23, G:0.33, T:0.32
Consensus pattern (29 bp):
GTGCATGGCGACCTCTTTGGTCATTGGGC
Found at i:39037 original size:21 final size:20
Alignment explanation
Indices: 39000--39041 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
38990 AAATTTAAAA
39000 TTTTATATTCTTCATAATAT
1 TTTTATATTCTTCATAATAT
* *
39020 TTTTATTATTTTTTATAATAT
1 TTTTA-TATTCTTCATAATAT
39041 T
1 T
39042 GTTGATTGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATATTCTTCATAATAT
Found at i:42621 original size:30 final size:31
Alignment explanation
Indices: 42582--42654 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
42572 AATGGATTTA
*
42582 TTTA-GTGACCAAATTA-TAAATTTGGTAAAG
1 TTTAGGTGACCAAAGTATTAAATTTGG-AAAG
42612 TTT-GGTGACCAAAGTATTAAATTTGGAAAG
1 TTTAGGTGACCAAAGTATTAAATTTGGAAAG
42642 TTTAGG-GACCAAA
1 TTTAGGTGACCAAA
42655 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
30 28 0.72
31 11 0.28
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (31 bp):
TTTAGGTGACCAAAGTATTAAATTTGGAAAG
Found at i:44694 original size:46 final size:46
Alignment explanation
Indices: 44587--44917 Score: 490
Period size: 46 Copynumber: 7.2 Consensus size: 46
44577 ATAAACTGAC
* * ** * *
44587 AAATAAGCTTACAAGCTTATGG-AAT-AATGACAAATATATTGGCA
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
* *
44631 AAATAAGCTTACAAGCTTATGGTATTAAATGGTAAGAATATTGGTA
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
**
44677 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAAAATATTGGTA
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
* *
44723 AAATAAGCTTACAAACTTATGGTATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
*
44769 AAATAAGATTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
*
44815 AAATAAGCTTACGAACTTATGGTATTAAATGGTAAGTATATTGGTAA
1 AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGT-A
44862 AAATAAGCTTACGAGCTTATGAG-A-TAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATG-GTATTAAATGGTAAGTATATTGGTA
44907 AAATAAGCTTA
1 AAATAAGCTTA
44918 TAAACTTATG
Statistics
Matches: 265, Mismatches: 18, Indels: 7
0.91 0.06 0.02
Matches are distributed among these distances:
44 22 0.08
45 14 0.05
46 206 0.78
47 22 0.08
48 1 0.00
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGTATTAAATGGTAAGTATATTGGTA
Found at i:44768 original size:22 final size:22
Alignment explanation
Indices: 44742--44814 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 22
44732 TACAAACTTA
44742 TGGTATTAAATGGTAAGTATAT
1 TGGTATTAAATGGTAAGTATAT
*
44764 TGGTA--AAATAAGATTACGAGCT-TA-
1 TGGTATTAAAT--G-GTA--AG-TATAT
44788 TGGTATTAAATGGTAAGTATAT
1 TGGTATTAAATGGTAAGTATAT
44810 TGGTA
1 TGGTA
44815 AAATAAGCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 20
0.64 0.03 0.33
Matches are distributed among these distances:
20 5 0.13
21 4 0.10
22 11 0.28
23 4 0.10
24 6 0.15
25 4 0.10
26 5 0.13
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (22 bp):
TGGTATTAAATGGTAAGTATAT
Found at i:45079 original size:29 final size:29
Alignment explanation
Indices: 45034--45091 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
45024 GTGTTGGTCG
* *
45034 TAGGTCGCCTTGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
45063 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
45092 AAGAGATTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.12, C:0.36, G:0.28, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:45204 original size:23 final size:23
Alignment explanation
Indices: 45169--45251 Score: 114
Period size: 23 Copynumber: 3.6 Consensus size: 23
45159 ACTATCCGAC
* * *
45169 CGAGGCCATCCGAACGAGCTATG
1 CGAGGGCAACCGAGCGAGCTATG
45192 CGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCAACCGAGCGAGCTATG
*
45215 CGAGGGCAACCGAGCGAGCTATT
1 CGAGGGCAACCGAGCGAGCTATG
45238 CGAGGG-AATCCGAG
1 CGAGGGCAA-CCGAG
45252 GGAAGTCGAG
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
22 2 0.04
23 53 0.96
ACGTcount: A:0.27, C:0.27, G:0.36, T:0.11
Consensus pattern (23 bp):
CGAGGGCAACCGAGCGAGCTATG
Found at i:45302 original size:29 final size:29
Alignment explanation
Indices: 45269--45353 Score: 161
Period size: 29 Copynumber: 2.9 Consensus size: 29
45259 GAGCGAGGGT
*
45269 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
45298 AGGTCGCCCGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
45327 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
45354 TGTGTTGGGA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 55 1.00
ACGTcount: A:0.20, C:0.31, G:0.38, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:45460 original size:29 final size:29
Alignment explanation
Indices: 45427--45500 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
45417 GCCCGGAGTG
*
45427 TGCATGGCGACCTACAAGGTCACCATGAA
1 TGCATGGCGACCTACAAGGTCACCAGGAA
* * *
45456 TGCATGGCGACCTACAAGGTCGCCCGGAG
1 TGCATGGCGACCTACAAGGTCACCAGGAA
45485 TGCATGGCGACCTACA
1 TGCATGGCGACCTACA
45501 GCCAACACTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.30, G:0.28, T:0.16
Consensus pattern (29 bp):
TGCATGGCGACCTACAAGGTCACCAGGAA
Found at i:51258 original size:101 final size:102
Alignment explanation
Indices: 51066--51259 Score: 230
Period size: 101 Copynumber: 1.9 Consensus size: 102
51056 AGATGTACAT
* * * *
51066 ACTTACATCGGTGTAAATATGTGTTAAGTGCTACACTTTTTTATTTTATTTACTTACACCGTTGT
1 ACTTACATCGGTGTAAATATGTGTTAAGTACTACACTTTTTTATTTTATTCACTTACACCGGTAT
*
51131 AAGTACGCGTTAAATGTTACACTTTTTTATTCTATTC
66 AAGTACGCGTTAAATGCTACACTTTTTTATTCTATTC
* * * * *
51168 ACTTAC-TCCGGTGT-AGTATGTGTTAATTATTACACTTTTTTGTTTTATTCAGTTACACCGGTA
1 ACTTACAT-CGGTGTAAATATGTGTTAAGTACTACACTTTTTTATTTTATTCACTTACACCGGTA
* * * * *
51231 TAAGTATGTGTTAAGTGCTATATTTTTTT
65 TAAGTACGCGTTAAATGCTACACTTTTTT
51260 GTAGCATGAA
Statistics
Matches: 76, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
101 64 0.84
102 12 0.16
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (102 bp):
ACTTACATCGGTGTAAATATGTGTTAAGTACTACACTTTTTTATTTTATTCACTTACACCGGTAT
AAGTACGCGTTAAATGCTACACTTTTTTATTCTATTC
Found at i:51261 original size:51 final size:51
Alignment explanation
Indices: 51066--51259 Score: 219
Period size: 51 Copynumber: 3.8 Consensus size: 51
51056 AGATGTACAT
* * *
51066 ACTTACATCGGTGTAAATATGTGTTAAGTGCTACACTTTTTTATTTTATTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* * * * * *
51117 ACTTACACCGTTGTAAGTACGCGTTAAATGTTACACTTTTTTATTCTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* * ** *
51168 ACTTACTCCGGTGT-AGTATGTGTTAATTATTACACTTTTTTGTTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
* * * *
51218 AGTTACACCGGTATAAGTATGTGTTAAGTGCTATATTTTTTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTT
51260 GTAGCATGAA
Statistics
Matches: 117, Mismatches: 25, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
50 41 0.35
51 76 0.65
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (51 bp):
ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
Found at i:57335 original size:20 final size:20
Alignment explanation
Indices: 57310--57359 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
57300 AAATCGCAAC
*
57310 GCGATTTTCTTTTGACCGTT
1 GCGATTTTCTTTTGAACGTT
*
57330 GCGATTTTCTTTTTAACGTT
1 GCGATTTTCTTTTGAACGTT
57350 GCGATTTTCT
1 GCGATTTTCT
57360 AAATCGCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.18, G:0.18, T:0.52
Consensus pattern (20 bp):
GCGATTTTCTTTTGAACGTT
Found at i:57386 original size:19 final size:20
Alignment explanation
Indices: 57346--57396 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
57336 TTCTTTTTAA
*
57346 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
57366 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
57385 CGTTGCGATTTT
1 CGTTGCGATTTT
57397 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:59180 original size:3 final size:3
Alignment explanation
Indices: 59172--59215 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
59162 ATGAACGCAA
59172 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
59216 AAGGATCCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:60159 original size:5 final size:5
Alignment explanation
Indices: 60146--60184 Score: 69
Period size: 5 Copynumber: 7.6 Consensus size: 5
60136 AAATAAAAAA
60146 AATATT AATAT AATAT AATAT AATAT AATAT AATAT AAT
1 AATA-T AATAT AATAT AATAT AATAT AATAT AATAT AAT
60185 GTTTTTGGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 29 0.88
6 4 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
AATAT
Found at i:62088 original size:32 final size:31
Alignment explanation
Indices: 62052--62128 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
62042 CGGGGCCGTG
*
62052 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** *
62084 GGGCCTACCCGAGAATAATCTCAGGGCCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
62115 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
62129 GTCACATTAG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:62111 original size:63 final size:63
Alignment explanation
Indices: 62005--62128 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
61995 CCCTAAGGGA
* * * ** *
62005 ACATCTTATGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
62068 ACATCTTAGGGCC-GCAGGGCCTACCCGAGAATA-ATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAG-ATAGATCTCAGGGCCGCAGAGCCTACCTAAGA
62129 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 1 0.02
63 47 0.92
64 3 0.06
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:63042 original size:5 final size:5
Alignment explanation
Indices: 63032--63101 Score: 59
Period size: 5 Copynumber: 12.8 Consensus size: 5
63022 AACGGTCAAC
* *
63032 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG
*
63081 GGTCAAC GGTCG GGTCG GGTC
1 GGTC--G GGTCG GGTCG GGTC
63102 AGACCGGTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
5 41 0.77
7 12 0.23
ACGTcount: A:0.09, C:0.23, G:0.50, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:63047 original size:17 final size:17
Alignment explanation
Indices: 63025--63102 Score: 111
Period size: 17 Copynumber: 4.3 Consensus size: 17
63015 AACGGTCAAC
63025 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
63042 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
63059 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAA----C-GGTCGGGTCG
63081 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
63098 GGTCA
1 GGTCA
63103 GACCGGTCAA
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
17 38 0.68
18 1 0.02
21 1 0.02
22 16 0.29
ACGTcount: A:0.12, C:0.23, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:63052 original size:7 final size:7
Alignment explanation
Indices: 62998--63035 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
62988 GTCAAAGAAA
62998 GTCAACG
1 GTCAACG
63005 GTCAACG
1 GTCAACG
63012 GTCAACG
1 GTCAACG
63019 GTCAACG
1 GTCAACG
63026 GTCAACG
1 GTCAACG
63033 GTC
1 GTC
63036 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:63060 original size:22 final size:22
Alignment explanation
Indices: 63018--63101 Score: 106
Period size: 22 Copynumber: 4.0 Consensus size: 22
63008 AACGGTCAAC
*
63018 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
63042 GGTCAACGGT-----CGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
63059 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
63081 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
63102 AGACCGGTCA
Statistics
Matches: 55, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
17 17 0.31
22 28 0.51
24 10 0.18
ACGTcount: A:0.12, C:0.24, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:69381 original size:32 final size:31
Alignment explanation
Indices: 69345--69421 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
69335 CGGGGCCGTG
*
69345 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAACA-ATCTCAGGGCCGCA
** * *
69377 GGGCCTACCCGAGAATAATCTCAGGGTCGCA
1 GGGCCTACCTAAGAACAATCTCAGGGCCGCA
*
69408 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
69422 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 23 0.62
32 14 0.38
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTAAGAACAATCTCAGGGCCGCA
Found at i:70321 original size:5 final size:5
Alignment explanation
Indices: 70311--70397 Score: 66
Period size: 5 Copynumber: 15.8 Consensus size: 5
70301 AACGGTCAAC
* *
70311 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC--G GGTCG GGTCG
* *
70360 GGTCAAC GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTC--G GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
70398 AGACCGGTCA
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
5 50 0.76
7 16 0.24
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (5 bp):
GGTCG
Found at i:70336 original size:17 final size:17
Alignment explanation
Indices: 70316--70398 Score: 166
Period size: 17 Copynumber: 4.9 Consensus size: 17
70306 TCAACGGTCG
70316 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
70333 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
70350 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
70367 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
70384 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
70399 GACCGGTCAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 66 1.00
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:70359 original size:22 final size:22
Alignment explanation
Indices: 70304--70346 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
70294 AACGGTCAAC
70304 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
70326 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
70347 AACGGTCGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:78819 original size:5 final size:5
Alignment explanation
Indices: 78790--78853 Score: 83
Period size: 5 Copynumber: 12.8 Consensus size: 5
78780 GTCCGTCCGT
* * * * *
78790 CTCGT CTCGT CTCGG CTCGG CTCGG CTCGG CACGG CACGG CACGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG
78840 CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCG
78854 TGGTCGTGGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 56 1.00
ACGTcount: A:0.05, C:0.41, G:0.36, T:0.19
Consensus pattern (5 bp):
CTCGG
Found at i:78862 original size:6 final size:6
Alignment explanation
Indices: 78851--78941 Score: 182
Period size: 6 Copynumber: 15.2 Consensus size: 6
78841 TCGGCTCGGC
78851 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
78899 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
78942 AATACGTGTC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 85 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:79100 original size:40 final size:40
Alignment explanation
Indices: 79018--79093 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
79008 TTTGAAAGAA
79018 ACAAATGGAAAATGTGAAAGATATCAACGTTTCAGCTGTT
1 ACAAATGGAAAATGTGAAAGATATCAACGTTTCAGCTGTT
79058 ACAAATGGAAAATGTGAAAGATATCAACGTTTCAGC
1 ACAAATGGAAAATGTGAAAGATATCAACGTTTCAGC
79094 GATTACACAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (40 bp):
ACAAATGGAAAATGTGAAAGATATCAACGTTTCAGCTGTT
Found at i:84309 original size:5 final size:5
Alignment explanation
Indices: 84290--84333 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
84280 GTCCGTCCGT
* * * *
84290 CTCGT CTCGG CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
84334 TGGTCGTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.07, C:0.41, G:0.36, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:84342 original size:6 final size:6
Alignment explanation
Indices: 84331--84403 Score: 128
Period size: 6 Copynumber: 12.2 Consensus size: 6
84321 ACGGCTCGGC
* *
84331 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
84379 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
84404 AATACGTGTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.32
Consensus pattern (6 bp):
TCGTGG
Found at i:84702 original size:22 final size:22
Alignment explanation
Indices: 84677--84731 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
84667 TCAGGAGTTA
* *
84677 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
84699 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
84721 CGGGAGTTATA
1 CAGGAGTTATA
84732 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:87006 original size:15 final size:15
Alignment explanation
Indices: 86983--87030 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
86973 TTAGCTGGGT
86983 GGGCGGATGTGGGGC
1 GGGCGGATGTGGGGC
* *
86998 GGGCAGATGTGGGGT
1 GGGCGGATGTGGGGC
*
87013 GGGCGGATGCGGGGC
1 GGGCGGATGTGGGGC
87028 GGG
1 GGG
87031 TAATGTCTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.08, C:0.12, G:0.67, T:0.12
Consensus pattern (15 bp):
GGGCGGATGTGGGGC
Done.