Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002593.1 Hibiscus syriacus cultivar Beakdansim tig00005247_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: 95029
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:4707 original size:21 final size:21
Alignment explanation
Indices: 4671--4731 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 21
4661 TTTTGGTGCA
*
4671 GAGGGAA-CGATCCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
**
4691 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCAT
4712 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
4732 TCACAGGGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.20
21 11 0.31
22 1 0.03
23 16 0.46
ACGTcount: A:0.23, C:0.36, G:0.26, T:0.15
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:4739 original size:22 final size:21
Alignment explanation
Indices: 4693--4754 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
4683 CCCCCCATGA
*
4693 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC--TCAAG
4716 GGGAACCGATTCCCCCTCACAG
1 GGGAACCGATTCCCCCTCA-AG
* *
4738 GGGAATCGATACCCCCT
1 GGGAACCGATTCCCCCT
4755 GGGGTTCTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.06
22 17 0.49
23 16 0.46
ACGTcount: A:0.23, C:0.35, G:0.24, T:0.18
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTCAAG
Found at i:8788 original size:51 final size:53
Alignment explanation
Indices: 8710--8828 Score: 138
Period size: 51 Copynumber: 2.3 Consensus size: 53
8700 GTAACTACCG
* * * *
8710 AATAAAATAAAAATCAACTAAAGATAATCTTTTGA-T-TC-TATCCTAATTCCT
1 AATAAAATAATAATAAACTAAAAATAAT-TTTTAATTATCTTATCCTAATTCCT
*
8761 AATAAAATAATAATAAACTAAAAATAATTTTTAACTTTATCTTATCTTAATTCCT
1 AATAAAATAATAATAAACTAAAAATAATTTTTAA--TTATCTTATCCTAATTCCT
8816 AAT-AAATAATAAT
1 AATAAAATAATAAT
8829 CTAATCCTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
50 5 0.09
51 25 0.43
53 1 0.02
54 12 0.21
55 15 0.26
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.38
Consensus pattern (53 bp):
AATAAAATAATAATAAACTAAAAATAATTTTTAATTATCTTATCCTAATTCCT
Found at i:10234 original size:20 final size:20
Alignment explanation
Indices: 10209--10249 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
10199 TGCAAATCTA
10209 TTGTTATTTTGGTCCTCTTT
1 TTGTTATTTTGGTCCTCTTT
10229 TTGTTATTTTGGTCCTCTTT
1 TTGTTATTTTGGTCCTCTTT
10249 T
1 T
10250 CCAAGGCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.05, C:0.15, G:0.15, T:0.66
Consensus pattern (20 bp):
TTGTTATTTTGGTCCTCTTT
Found at i:10733 original size:2 final size:2
Alignment explanation
Indices: 10728--10757 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10718 CACATCACAA
10728 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
10758 CACATTCACG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23139 original size:50 final size:50
Alignment explanation
Indices: 23080--23197 Score: 148
Period size: 50 Copynumber: 2.4 Consensus size: 50
23070 AAATATTGAG
* * * * * *
23080 AGATATACATATTTATATTGGTGTAAGTATATGTTTATTTTTAGGTTGGA
1 AGATATACATACTTACACTCGTGTAAGTACATGTTTACTTTTAGGTTGGA
23130 AGATATACATACTTACACTCGTGTAAGTACATGTTTACTTTTAGGTT-GA
1 AGATATACATACTTACACTCGTGTAAGTACATGTTTACTTTTAGGTTGGA
* *
23179 GAGATGTATATACTTACAC
1 -AGATATACATACTTACAC
23198 CGGTATAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
49 2 0.03
50 57 0.97
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (50 bp):
AGATATACATACTTACACTCGTGTAAGTACATGTTTACTTTTAGGTTGGA
Found at i:23659 original size:21 final size:21
Alignment explanation
Indices: 23611--23660 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
23601 ATGACTATCG
*
23611 CAATGCGATTTTTCAATTTCA
1 CAATGCGATTTTCCAATTTCA
**
23632 CGTTGCGATTTTCCCAA-TTCA
1 CAATGCGATTTT-CCAATTTCA
23653 CAATGCGA
1 CAATGCGA
23661 ATAAGTAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (21 bp):
CAATGCGATTTTCCAATTTCA
Found at i:23693 original size:21 final size:21
Alignment explanation
Indices: 23667--23722 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
23657 GCGAATAAGT
23667 AAATCGCAACGCGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
23688 AAATCGCAACGCGAATTTGGA
1 AAATCGCAACGCGAATTTGGA
23709 AAATCGCAACGCGA
1 AAATCGCAACGCGA
23723 TACTGACTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTTGGA
Found at i:23959 original size:22 final size:22
Alignment explanation
Indices: 23931--23974 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
23921 CACTCTCTCA
23931 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
23953 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
23975 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:24291 original size:20 final size:20
Alignment explanation
Indices: 24237--24295 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
24227 TTTATTCTCT
**
24237 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
24257 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
24277 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
24296 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:24486 original size:25 final size:24
Alignment explanation
Indices: 24432--24486 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
24422 TGTTTATTAT
* *
24432 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
24456 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
24482 TGTTT
1 TGTTT
24487 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:25637 original size:18 final size:18
Alignment explanation
Indices: 25616--25663 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
25606 TCCACTTCGG
25616 GAGCTATCACCTCACCCA
1 GAGCTATCACCTCACCCA
25634 GAGCTATCACCTCACCCA
1 GAGCTATCACCTCACCCA
*
25652 GAGCCATCACCT
1 GAGCTATCACCT
25664 GATCGACCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.27, C:0.44, G:0.12, T:0.17
Consensus pattern (18 bp):
GAGCTATCACCTCACCCA
Found at i:26194 original size:20 final size:19
Alignment explanation
Indices: 26169--26234 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 19
26159 TAGTTTACTT
26169 TCGCAACACGAAAATGACTA
1 TCGCAACACG-AAATGACTA
** *
26189 TCGCAATGCGGAAATGGCTA
1 TCGCAACAC-GAAATGACTA
* **
26209 TCGCAATACGAAATGAAAA
1 TCGCAACACGAAATGACTA
26228 TCGCAAC
1 TCGCAAC
26235 GACAAAATCG
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 13 0.35
20 23 0.62
21 1 0.03
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.17
Consensus pattern (19 bp):
TCGCAACACGAAATGACTA
Found at i:26230 original size:19 final size:19
Alignment explanation
Indices: 26208--26286 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 19
26198 GGAAATGGCT
26208 ATCGCAATACGAAATGAAA
1 ATCGCAATACGAAATGAAA
*
26227 ATCGC-A-ACG--A-CAAA
1 ATCGCAATACGAAATGAAA
*
26241 ATCGCAATGCGAAATGAAA
1 ATCGCAATACGAAATGAAA
**
26260 ATCGCAACGCGAAATGAAA
1 ATCGCAATACGAAATGAAA
*
26279 ATTGCAAT
1 ATCGCAAT
26287 GTAATTTGTG
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
14 8 0.16
15 2 0.04
16 2 0.04
17 3 0.06
18 2 0.04
19 32 0.65
ACGTcount: A:0.48, C:0.19, G:0.18, T:0.15
Consensus pattern (19 bp):
ATCGCAATACGAAATGAAA
Found at i:26377 original size:20 final size:20
Alignment explanation
Indices: 26347--26421 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
26337 TTACGATTTT
26347 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
26366 TATTTCCGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
26386 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
* *
26406 CATTTTCGCGTTGCGA
1 CATTTCCGCATTGCGA
26422 AAGTAAGTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 4 0.08
20 46 0.92
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:26432 original size:20 final size:20
Alignment explanation
Indices: 26392--26447 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
26382 TAGCCATTTC
* * *
26392 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
26412 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
26432 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
26448 ACTATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:26876 original size:41 final size:42
Alignment explanation
Indices: 26787--26876 Score: 146
Period size: 41 Copynumber: 2.2 Consensus size: 42
26777 CCGACTCACT
*
26787 TGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCAC
1 TGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCAC
* *
26829 TATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCAC
1 TGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCAC
26870 TGTCATC
1 TGTCATC
26877 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 24 0.55
42 20 0.45
ACGTcount: A:0.23, C:0.40, G:0.16, T:0.21
Consensus pattern (42 bp):
TGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCAC
Found at i:28318 original size:14 final size:14
Alignment explanation
Indices: 28284--28322 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
28274 TTGATTGTTT
28284 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
28298 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
28312 TGTTGATTTGT
1 AATTGATTTGT
28323 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:28485 original size:34 final size:34
Alignment explanation
Indices: 28429--28503 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
28419 AAAACAGACT
* *
28429 ATCGCAACACGAAACTGACTATCGCAACGAGAGA
1 ATCGCAACACGAAAATGACTATCGCAACGAGAAA
** *
28463 ATCGCAACGTGAAAATGGCTATCGCAACGAGAAA
1 ATCGCAACACGAAAATGACTATCGCAACGAGAAA
28497 ATCGCAA
1 ATCGCAA
28504 TGTTGCGATA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.41, C:0.24, G:0.21, T:0.13
Consensus pattern (34 bp):
ATCGCAACACGAAAATGACTATCGCAACGAGAAA
Found at i:28757 original size:20 final size:20
Alignment explanation
Indices: 28741--28817 Score: 136
Period size: 20 Copynumber: 3.9 Consensus size: 20
28731 ATTGCGATTT
*
28741 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
28761 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
28781 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
28801 TCAGTATCGCGTTGCGA
1 TCAGAATCGCGTTGCGA
28818 TTTTGTATTA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:28859 original size:20 final size:20
Alignment explanation
Indices: 28750--28858 Score: 121
Period size: 20 Copynumber: 5.4 Consensus size: 20
28740 TTCAGAATCT
*
28750 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGTATCG
*
28770 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGTATCG
28790 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
** *
28810 CGTTGCGATTTTGT-ATTATCG
1 CGTTGCGA--AAGTCAGTATCG
* *
28831 CTTTGCGATAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
*
28851 CATTGCGA
1 CGTTGCGA
28859 TTTACTTATT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
19 3 0.04
20 60 0.77
21 13 0.17
22 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGTATCG
Found at i:28920 original size:21 final size:20
Alignment explanation
Indices: 28868--28942 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 20
28858 ATTTACTTAT
*
28868 TCGCATTGCGAATTGGGAAAA
1 TCGCATTGCGAATT-GTAAAA
**
28889 TCGCAACGCGAAATTGTAAAA
1 TCGCATTGCG-AATTGTAAAA
* *
28910 TCGCATTGCG-ATAGTCATAA
1 TCGCATTGCGAATTGT-AAAA
28930 TCGCATTGCGAAT
1 TCGCATTGCGAAT
28943 CTGGAAACTG
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 4 0.09
20 13 0.30
21 23 0.52
22 4 0.09
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (20 bp):
TCGCATTGCGAATTGTAAAA
Found at i:28941 original size:41 final size:41
Alignment explanation
Indices: 28752--28941 Score: 106
Period size: 41 Copynumber: 4.7 Consensus size: 41
28742 CAGAATCTCG
* * * * *
28752 TTGCGAAAGTCAGAATCGCGTTGCGAAA--GTCAGAATCGCG
1 TTGCGATAGTCATAATCGCATTGCGAAATTGT-ATAATCGCA
* * ** * *
28792 TTGCGAAAGTCAGT-ATCGCGTTGCGATTTTGTATTATCGCT
1 TTGCGATAGTCA-TAATCGCATTGCGAAATTGTATAATCGCA
*
28833 TTGCGATAGTCAGT-ATCGCATTGCG--ATT-TACTTATTCGCA
1 TTGCGATAGTCA-TAATCGCATTGCGAAATTGTA--TAATCGCA
* ** * ** *
28873 TTGCGAATTGGGAAAATCGCAACGCGAAATTGTAAAATCGCA
1 TTGCG-ATAGTCATAATCGCATTGCGAAATTGTATAATCGCA
28915 TTGCGATAGTCATAATCGCATTGCGAA
1 TTGCGATAGTCATAATCGCATTGCGAA
28942 TCTGGAAACT
Statistics
Matches: 114, Mismatches: 26, Indels: 19
0.72 0.16 0.12
Matches are distributed among these distances:
38 2 0.02
39 2 0.02
40 34 0.30
41 58 0.51
42 13 0.11
43 3 0.03
44 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (41 bp):
TTGCGATAGTCATAATCGCATTGCGAAATTGTATAATCGCA
Found at i:30382 original size:21 final size:21
Alignment explanation
Indices: 30358--30404 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
30348 CTAAAGAGGA
30358 TGAATGAGGAAGAGGCTAGTT
1 TGAATGAGGAAGAGGCTAGTT
30379 TGAATGAGGAAGAGGCTAGTT
1 TGAATGAGGAAGAGGCTAGTT
30400 TGAAT
1 TGAAT
30405 TCGAGTATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.04, G:0.36, T:0.26
Consensus pattern (21 bp):
TGAATGAGGAAGAGGCTAGTT
Found at i:47102 original size:16 final size:14
Alignment explanation
Indices: 47064--47126 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
47054 TTGTGGGATG
47064 TTGC-TCTCTGTTT
1 TTGCTTCTCTGTTT
47077 TCTG-TCTCTCTGTTT
1 T-TGCT-TCTCTGTTT
*
47092 TTGCTGGTCTCTCTTT
1 TTGCT--TCTCTGTTT
47108 GTTG-TTCTCTGTTT
1 -TTGCTTCTCTGTTT
47122 TTGCT
1 TTGCT
47127 CGCAGACCGG
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
13 4 0.10
14 13 0.32
15 11 0.28
16 9 0.22
17 3 0.08
ACGTcount: A:0.00, C:0.22, G:0.17, T:0.60
Consensus pattern (14 bp):
TTGCTTCTCTGTTT
Found at i:47103 original size:18 final size:15
Alignment explanation
Indices: 47067--47122 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 15
47057 TGGGATGTTG
47067 CTCTCTGTTTTCTGT
1 CTCTCTGTTTTCTGT
47082 CTCTCTGTTTTTGCTGGT
1 CTCTCTG-TTTT-CT-GT
*
47100 CTCTCT-TTGT-TGT
1 CTCTCTGTTTTCTGT
47113 -TCTCTGTTTT
1 CTCTCTGTTTT
47123 TGCTCGCAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
12 5 0.14
13 5 0.14
14 1 0.03
15 7 0.20
16 7 0.20
17 2 0.06
18 8 0.23
ACGTcount: A:0.00, C:0.23, G:0.16, T:0.61
Consensus pattern (15 bp):
CTCTCTGTTTTCTGT
Found at i:47540 original size:15 final size:15
Alignment explanation
Indices: 47477--47541 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
47467 TTTGTAATAT
47477 TAAATAA-TA-TATA
1 TAAATAATTATTATA
*
47490 TTAATAATTATTAT-
1 TAAATAATTATTATA
* *
47504 TATTATAATTATAATA
1 TA-AATAATTATTATA
47520 -ATAATAATTATTATA
1 TA-AATAATTATTATA
47535 TAAATAA
1 TAAATAA
47542 CATAAAAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
13 6 0.15
14 3 0.07
15 31 0.76
16 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAAATAATTATTATA
Found at i:52984 original size:20 final size:20
Alignment explanation
Indices: 52961--53012 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
52951 AAGGGGTACA
52961 GATTCCCCCCAGGGGGAACC
1 GATTCCCCCCAGGGGGAACC
** * *
52981 GATTCCCCATGAGGGGGTATC
1 GATTCCCC-CCAGGGGGAACC
53002 GATTCCCCCCA
1 GATTCCCCCCA
53013 CGCTCCAAGC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.19, C:0.37, G:0.27, T:0.17
Consensus pattern (20 bp):
GATTCCCCCCAGGGGGAACC
Found at i:56108 original size:45 final size:45
Alignment explanation
Indices: 56056--56272 Score: 192
Period size: 45 Copynumber: 4.8 Consensus size: 45
56046 CTCTGGCGCA
*
56056 GCTCTATAATTGGGTTCGATGGACACAGGTCTAGAGCTAGGATCC
1 GCTCTATAATTGGGTTCGATGGACACAGGTCTAGAGCTAGGACCC
* * * ** *
56101 ACTCTATAATTGGGGTCAATGGATGCAGGTCTAGAGGTTA-GACCC
1 GCTCTATAATTGGGTTCGATGGACACAGGTCTAGA-GCTAGGACCC
* * * * *
56146 GCTCCATAACTGGGTTCGATGGACGCATGTCTAGAG-GATGGACCC
1 GCTCTATAATTGGGTTCGATGGACACAGGTCTAGAGCTA-GGACCC
* * * * *
56191 GCTCTATAATTGGGTTC-ACGGGATGA-AGGTTTAGAGCTTGGATCC
1 GCTCTATAATTGGGTTCGA-TGGA-CACAGGTCTAGAGCTAGGACCC
*
56236 GCTCTATAATTGGATTCGATGGA-ACAAGGTCTAGAGC
1 GCTCTATAATTGGGTTCGATGGACAC-AGGTCTAGAGC
56273 ATGAATAAAC
Statistics
Matches: 135, Mismatches: 28, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
43 2 0.01
44 2 0.01
45 127 0.94
46 4 0.03
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (45 bp):
GCTCTATAATTGGGTTCGATGGACACAGGTCTAGAGCTAGGACCC
Found at i:56226 original size:90 final size:90
Alignment explanation
Indices: 56056--56271 Score: 256
Period size: 90 Copynumber: 2.4 Consensus size: 90
56046 CTCTGGCGCA
* * *
56056 GCTCTATAATTGGGTTCGATGGACACAGGTCTAGAGCTAGGATCCACTCTATAATTGGGGTCAAT
1 GCTCTATAATTGGGTTCGATGGACACAGGTCTAGAGATAGGACCCACTCTATAATTGGGGTCAAG
* *
56121 GGATGCAGGTCTAGAGGTTAGACCC
66 GGATGAAGGTCTAGAGCTTAGACCC
* * * * * * *
56146 GCTCCATAACTGGGTTCGATGGACGCATGTCTAGAGGAT-GGACCCGCTCTATAATTGGGTTCAC
1 GCTCTATAATTGGGTTCGATGGACACAGGTCTAGA-GATAGGACCCACTCTATAATTGGGGTCAA
* * *
56210 GGGATGAAGGTTTAGAGCTTGGATCC
65 GGGATGAAGGTCTAGAGCTTAGACCC
*
56236 GCTCTATAATTGGATTCGATGGA-ACAAGGTCTAGAG
1 GCTCTATAATTGGGTTCGATGGACAC-AGGTCTAGAG
56272 CATGAATAAA
Statistics
Matches: 104, Mismatches: 20, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
89 2 0.02
90 100 0.96
91 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (90 bp):
GCTCTATAATTGGGTTCGATGGACACAGGTCTAGAGATAGGACCCACTCTATAATTGGGGTCAAG
GGATGAAGGTCTAGAGCTTAGACCC
Found at i:64137 original size:37 final size:37
Alignment explanation
Indices: 64064--64138 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
64054 GTTAGAAAAT
* *
64064 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
* *
64101 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTAAAAATCATAAA
64138 A
1 A
64139 ATGTTTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:64181 original size:21 final size:21
Alignment explanation
Indices: 64156--64196 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
64146 ATAAAAGGGT
64156 AAAATTTTATTTTATCACCTA
1 AAAATTTTATTTTATCACCTA
64177 AAAATTTTATTTTATCACCT
1 AAAATTTTATTTTATCACCT
64197 GAACTTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATTTTATTTTATCACCTA
Found at i:67478 original size:20 final size:20
Alignment explanation
Indices: 67455--67518 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 20
67445 TAGTATTTAG
67455 ATAAAT-TTATTAATAATTTT
1 ATAAATATT-TTAATAATTTT
* *
67475 AT-AATCTTTTAATAAATTTA
1 ATAAATATTTTAAT-AATTTT
*
67495 ATAAGTATTTT-ATAATTTT
1 ATAAATATTTTAATAATTTT
*
67514 TTAAA
1 ATAAA
67519 CTTTATTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
19 16 0.46
20 13 0.37
21 6 0.17
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAAATATTTTAATAATTTT
Found at i:67488 original size:19 final size:20
Alignment explanation
Indices: 67464--67513 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
67454 GATAAATTTA
*
67464 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
67483 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
67504 TT-ATAATTTT
1 TTAATAATTTT
67514 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:67516 original size:31 final size:30
Alignment explanation
Indices: 67431--67517 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
67421 TTCGATAATA
* *
67431 TAATAATTATTTTAT-AGTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* *
67462 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
67493 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
67518 ACTTTATTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.85
32 6 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:68262 original size:19 final size:19
Alignment explanation
Indices: 68240--68327 Score: 63
Period size: 20 Copynumber: 4.4 Consensus size: 19
68230 AAAGTTTAAA
68240 AAATTATAAAATATTTATT
1 AAATTATAAAATATTTATT
* *
68259 AAATTTATTAAAAGA-TTATA
1 AAA-TTA-TAAAATATTTATT
68279 AAATTATTAATAA-ATTTATCT
1 AAATTA-TAA-AATATTTAT-T
*
68300 AAATACTATAAAATAATTATT
1 AAAT--TATAAAATATTTATT
*
68321 ATATTAT
1 AAATTAT
68328 CGAACTTTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
19 14 0.25
20 16 0.29
21 16 0.29
22 8 0.14
23 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (19 bp):
AAATTATAAAATATTTATT
Found at i:68270 original size:31 final size:31
Alignment explanation
Indices: 68235--68321 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 31
68225 TTAATAAAGT
68235 TTAAAAAATTATAAAATATTTATTAAATTTA
1 TTAAAAAATTATAAAATATTTATTAAATTTA
* *
68266 TTAAAAGATTATAAAAT-TATTAATAAATTTA
1 TTAAAAAATTATAAAATAT-TTATTAAATTTA
* * *
68297 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAATATTTATTA
68322 TATTATCGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 45 0.96
32 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (31 bp):
TTAAAAAATTATAAAATATTTATTAAATTTA
Found at i:68297 original size:20 final size:20
Alignment explanation
Indices: 68230--68297 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 20
68220 TTTCGTTAAT
*
68230 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* *
68248 AAATATTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
68269 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
68288 ATAA-ATTTAT
1 A-AAGATTTAT
68298 CTAAATACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
18 3 0.08
19 16 0.40
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:72874 original size:29 final size:29
Alignment explanation
Indices: 72834--72893 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
72824 AATTTTCACC
*
72834 AAACTAAATTGATGTAAGCAGTGACATCA
1 AAACTAAATTGATGTAAGCAATGACATCA
72863 AAACTAAATTGATGTAAGCAATGACATCA
1 AAACTAAATTGATGTAAGCAATGACATCA
72892 AA
1 AA
72894 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.23
Consensus pattern (29 bp):
AAACTAAATTGATGTAAGCAATGACATCA
Found at i:77557 original size:29 final size:29
Alignment explanation
Indices: 77517--77576 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
77507 AATTTTCACC
77517 AAACTAAATTGATGTAAGCAATGACATCA
1 AAACTAAATTGATGTAAGCAATGACATCA
77546 AAACTAAATTGATGTAAGCAATGACATCA
1 AAACTAAATTGATGTAAGCAATGACATCA
77575 AA
1 AA
77577 TTAATTTAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.23
Consensus pattern (29 bp):
AAACTAAATTGATGTAAGCAATGACATCA
Found at i:80073 original size:24 final size:24
Alignment explanation
Indices: 80038--80084 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
80028 ATTTATAAAT
*
80038 TAATAATTATTTTCTAAATCATCA
1 TAATAATTATTTTCCAAATCATCA
*
80062 TAAT-ATTCATTTTCCACATCATC
1 TAATAATT-ATTTTCCAAATCATC
80085 TCCTCTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.45
Consensus pattern (24 bp):
TAATAATTATTTTCCAAATCATCA
Found at i:86479 original size:2 final size:2
Alignment explanation
Indices: 86472--86504 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
86462 TAATCGAAAT
86472 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 T
86505 TAAGCTCAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:86730 original size:30 final size:29
Alignment explanation
Indices: 86689--86750 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
86679 ACTTTATTCA
86689 ATTCAGTTAATATTTTCAAGAA-AATATTTG
1 ATTCAGTTAATATTTTCAA-AAGAA-ATTTG
*
86719 ATTCGGTTAATATTTTCAAAAGAAATTTG
1 ATTCAGTTAATATTTTCAAAAGAAATTTG
86748 ATT
1 ATT
86751 TGATTAATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (29 bp):
ATTCAGTTAATATTTTCAAAAGAAATTTG
Found at i:86757 original size:29 final size:30
Alignment explanation
Indices: 86695--86758 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
86685 TTCAATTCAG
*
86695 TTAATATTTTCAAGAAAATATTTGATTCGG
1 TTAATATTTTCAAGAAAATATTTGATTCGA
*
86725 TTAATATTTTCAA-AAGAA-ATTTGATTTGA
1 TTAATATTTTCAAGAA-AATATTTGATTCGA
86754 TTAAT
1 TTAAT
86759 GATTAAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (30 bp):
TTAATATTTTCAAGAAAATATTTGATTCGA
Found at i:87487 original size:35 final size:35
Alignment explanation
Indices: 87411--87497 Score: 131
Period size: 36 Copynumber: 2.5 Consensus size: 35
87401 TCATATTACT
*
87411 TTTATTATAT-ATAAACGGTTTTATAAATTATATG
1 TTTATTATATGATAAACGGTTTTATAAATTATATC
87445 TTATATTATATGATAAACGGTTTTATAAATTATATC
1 TT-TATTATATGATAAACGGTTTTATAAATTATATC
*
87481 TTTATTAAAATGATAAA
1 TTTATT-ATATGATAAA
87498 AAAAAACTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
34 2 0.04
35 12 0.25
36 34 0.71
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (35 bp):
TTTATTATATGATAAACGGTTTTATAAATTATATC
Found at i:87493 original size:143 final size:144
Alignment explanation
Indices: 87335--87601 Score: 491
Period size: 146 Copynumber: 1.8 Consensus size: 144
87325 ATGTGTTTAA
87335 ATCTTTATTAAAATGAT-AAAAAACTATTAAAATTCGATAATAATAATCGCTAATTTTTATGTAT
1 ATCTTTATTAAAATGATAAAAAAACTATTAAAATTCGATAATAATAATCGCTAATTTTTATGTAT
*
87399 ATTCATATTACTTTTATTATATATAAACGGTTTTATAAATTATATGTTATATTATATGATAAACG
66 ATTCATATTACTTTTATTATATATAAAAGGTTTTATAAATTATATGTTATATTATATGATAAACG
87464 GTTTTATAAATTAT
131 GTTTTATAAATTAT
*
87478 ATCTTTATTAAAATGATAAAAAAAAACTATTAAAATTCGATAATAATAATTGCTAATTTTTATGT
1 ATCTTTATTAAAATGAT--AAAAAAACTATTAAAATTCGATAATAATAATCGCTAATTTTTATGT
87543 ATATTCATATTACTTTTATTATATATAAAAGGTTTTATAAATTATATGTTATATTATAT
64 ATATTCATATTACTTTTATTATATATAAAAGGTTTTATAAATTATATGTTATATTATAT
87602 TTACTTTATA
Statistics
Matches: 119, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
143 17 0.14
146 102 0.86
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (144 bp):
ATCTTTATTAAAATGATAAAAAAACTATTAAAATTCGATAATAATAATCGCTAATTTTTATGTAT
ATTCATATTACTTTTATTATATATAAAAGGTTTTATAAATTATATGTTATATTATATGATAAACG
GTTTTATAAATTAT
Found at i:91882 original size:5 final size:5
Alignment explanation
Indices: 91835--91879 Score: 54
Period size: 5 Copynumber: 8.4 Consensus size: 5
91825 TTTTGCATAC
*
91835 TTTAT TTTCTT TTTCAT TTTAT TTTAT TTTAT TTTAT TTTCAT TT
1 TTTAT TTT-AT TTT-AT TTTAT TTTAT TTTAT TTTAT TTT-AT TT
91880 CATCCACATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
5 23 0.64
6 13 0.36
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:94175 original size:98 final size:94
Alignment explanation
Indices: 93929--94191 Score: 350
Period size: 95 Copynumber: 2.7 Consensus size: 94
93919 ATATTATAAT
* *
93929 ATTATATATATACAATAAAACTTGAGTTGTCCCTCTAAAGCAATTGGTTAAGCGCCCCGACTTTA
1 ATTATATCTATACAAT-AAACTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACG-CCCGACTTTA
93994 TGGATAAGAGTCAGCTAGCCTGATAAAGGTG
64 TGGATAAGAGTCAGCTAGCCTGATAAAGGTG
94025 ATTATA-CTATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCTGACTTTA
1 ATTATATCTATACAATAAA-CTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCC-GACTTTA
* * *
94089 TGGATAATATTCAGCTAGCTTGATAAAGGTAG
64 TGGATAAGAGTCAGCTAGCCTGATAAAGGT-G
* * * *
94121 TAATTATATCTATACAATAATA-TTGAGCTGTCCCTCTAGAGCAACTGGTTAAACGCCCCAGCTT
1 --ATTATATCTATACAATAA-ACTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCGA-CTT
94185 TATGGAT
62 TATGGAT
94192 TTAGCTAGCC
Statistics
Matches: 150, Mismatches: 9, Indels: 14
0.87 0.05 0.08
Matches are distributed among these distances:
94 6 0.04
95 75 0.50
96 7 0.05
97 1 0.01
98 49 0.33
99 11 0.07
100 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (94 bp):
ATTATATCTATACAATAAACTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCGACTTTATG
GATAAGAGTCAGCTAGCCTGATAAAGGTG
Done.