Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007401.1 Hibiscus syriacus cultivar Beakdansim tig00019974_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: 65583
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1321 original size:23 final size:23
Alignment explanation
Indices: 1291--1358 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
1281 ACTTTTATAT
1291 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * ** *
1314 GGCACTTCGATGCAATTCTTTGT
1 GGCACTTCGGTGCATTTCTACGC
* *
1337 GGCACTTTGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
1359 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.35
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1704 original size:20 final size:20
Alignment explanation
Indices: 1653--1704 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
1643 TGTTGAGTAA
*
1653 AAGAATAGATATAAGAGGAT
1 AAGAATAGATATAAGACGAT
**
1673 AATTATAAGATATAA-ACGAT
1 AAGAAT-AGATATAAGACGAT
1693 AAGAATATGATA
1 AAGAATA-GATA
1705 GTGGAATAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
19 1 0.04
20 16 0.64
21 8 0.32
ACGTcount: A:0.56, C:0.02, G:0.17, T:0.25
Consensus pattern (20 bp):
AAGAATAGATATAAGACGAT
Found at i:3841 original size:42 final size:42
Alignment explanation
Indices: 3768--3867 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
3758 TTATTTATAA
* * * * *
3768 TTGTGACGA-AAATATTTTTTTCATTAATCTTAGTTGGTGAT
1 TTGTGACGACAATTATTTTTGTCACTAATCTTAATCGGTGAT
*
3809 TTGTGACGACAATTATTTTTGTCACTAGTCTTAATCGGTGAT
1 TTGTGACGACAATTATTTTTGTCACTAATCTTAATCGGTGAT
*
3851 TTGTGATGACAATTATT
1 TTGTGACGACAATTATT
3868 CTTATCACCA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 9 0.18
42 42 0.82
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.46
Consensus pattern (42 bp):
TTGTGACGACAATTATTTTTGTCACTAATCTTAATCGGTGAT
Found at i:6576 original size:2 final size:2
Alignment explanation
Indices: 6569--6610 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
6559 CTATGTGAGC
6569 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
6611 TTCTCGATGG
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:6857 original size:20 final size:19
Alignment explanation
Indices: 6812--6861 Score: 75
Period size: 18 Copynumber: 2.6 Consensus size: 19
6802 CAATTGAAAA
6812 GTGCTTGAGCAGTAAGTGT
1 GTGCTTGAGCAGTAAGTGT
*
6831 -AGCTTGAGCAGTAAGTGTT
1 GTGCTTGAGCAGTAAGTG-T
6850 GTGCTTGAGCAG
1 GTGCTTGAGCAG
6862 CCCTCCGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 16 0.59
19 1 0.04
20 10 0.37
ACGTcount: A:0.22, C:0.12, G:0.36, T:0.30
Consensus pattern (19 bp):
GTGCTTGAGCAGTAAGTGT
Found at i:11478 original size:44 final size:44
Alignment explanation
Indices: 11416--11633 Score: 301
Period size: 44 Copynumber: 5.0 Consensus size: 44
11406 GCGAAAAGCA
* * * * *
11416 GTAAGGTCTCACCTTTGCACATAGCAGAGGAGCATTTAGAAACG
1 GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAATG
* * *
11460 GTAAGTTCTTACCCTTGCACATAGCAAAGGAGCCTTCAGAAATT
1 GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAATG
* *
11504 GTAAGGTCTTAACCTTGCACATAGCAGAGGAGCCTTCAGAAATT
1 GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAATG
* *
11548 GTAAGGTCTTAACCTTGCACATAGCAGAGGAGCCTTCAAAAATG
1 GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAATG
* * *
11592 GTAAGGTCTTACCCTTGCACAAAGCAAATGAGCCTTCAGAAA
1 GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAA
11634 CTTCCTACAA
Statistics
Matches: 156, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 156 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (44 bp):
GTAAGGTCTTACCCTTGCACATAGCAGAGGAGCCTTCAGAAATG
Found at i:12415 original size:23 final size:23
Alignment explanation
Indices: 12388--12460 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
12378 ACATTAAACC
12388 GGGTCGGATCTGGTCAGGCAGAT
1 GGGTCGGATCTGGTCAGGCAGAT
* *
12411 GGGTCGGA--T--T-A-ACAGGT
1 GGGTCGGATCTGGTCAGGCAGAT
*
12428 CGGGTCGGATCTGGTCAGGCAGAC
1 -GGGTCGGATCTGGTCAGGCAGAT
12452 GGGTCGGAT
1 GGGTCGGAT
12461 TAACGGGTCG
Statistics
Matches: 38, Mismatches: 5, Indels: 14
0.67 0.09 0.25
Matches are distributed among these distances:
17 4 0.11
18 9 0.24
19 1 0.03
20 1 0.03
21 1 0.03
22 1 0.03
23 18 0.47
24 3 0.08
ACGTcount: A:0.18, C:0.18, G:0.44, T:0.21
Consensus pattern (23 bp):
GGGTCGGATCTGGTCAGGCAGAT
Found at i:12433 original size:41 final size:41
Alignment explanation
Indices: 12387--12473 Score: 156
Period size: 41 Copynumber: 2.1 Consensus size: 41
12377 AACATTAAAC
*
12387 CGGGTCGGATCTGGTCAGGCAGATGGGTCGGATTAACAGGT
1 CGGGTCGGATCTGGTCAGGCAGACGGGTCGGATTAACAGGT
*
12428 CGGGTCGGATCTGGTCAGGCAGACGGGTCGGATTAACGGGT
1 CGGGTCGGATCTGGTCAGGCAGACGGGTCGGATTAACAGGT
12469 CGGGT
1 CGGGT
12474 TGGACACGGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.17, C:0.18, G:0.44, T:0.21
Consensus pattern (41 bp):
CGGGTCGGATCTGGTCAGGCAGACGGGTCGGATTAACAGGT
Found at i:18016 original size:38 final size:38
Alignment explanation
Indices: 17965--18040 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
17955 CTCAAGTCTC
17965 AAGTTCAATCCCCCAAACTCATCTATATATATATATAT
1 AAGTTCAATCCCCCAAACTCATCTATATATATATATAT
18003 AAGTTCAATCCCCCAAACTCATCTATATATATATATAT
1 AAGTTCAATCCCCCAAACTCATCTATATATATATATAT
18041 TACTTTTCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (38 bp):
AAGTTCAATCCCCCAAACTCATCTATATATATATATAT
Found at i:20601 original size:13 final size:13
Alignment explanation
Indices: 20583--20608 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20573 AATTAACTAA
20583 ACATTTTATATAT
1 ACATTTTATATAT
20596 ACATTTTATATAT
1 ACATTTTATATAT
20609 TGTTAGACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
ACATTTTATATAT
Found at i:20695 original size:2 final size:2
Alignment explanation
Indices: 20688--20724 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20678 ATCGTTAAAT
20688 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
20725 TTCAATTTAT
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:21443 original size:2 final size:2
Alignment explanation
Indices: 21436--21461 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21426 ATCATATAAG
21436 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
21462 TCATTTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24067 original size:3 final size:3
Alignment explanation
Indices: 24061--24137 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
24051 TTTTTATCCA
24061 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
24109 TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
24138 AATATATTAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:24598 original size:15 final size:14
Alignment explanation
Indices: 24578--24610 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
24568 GGAAAGAAGA
24578 AGAAAAACCAGAGAC
1 AGAAAAA-CAGAGAC
24593 AG-AAAACAGAGAC
1 AGAAAAACAGAGAC
24606 AGAAA
1 AGAAA
24611 CAGAGAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.53
14 6 0.35
15 2 0.12
ACGTcount: A:0.64, C:0.15, G:0.21, T:0.00
Consensus pattern (14 bp):
AGAAAAACAGAGAC
Found at i:24613 original size:12 final size:13
Alignment explanation
Indices: 24581--24616 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
24571 AAGAAGAAGA
24581 AAAACCAGAGACAG
1 AAAA-CAGAGACAG
24595 AAAACAGAGACAG
1 AAAACAGAGACAG
24608 -AAACAGAGA
1 AAAACAGAGA
24617 ACGGAGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 9 0.41
13 9 0.41
14 4 0.18
ACGTcount: A:0.61, C:0.17, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAACAGAGACAG
Found at i:24613 original size:19 final size:19
Alignment explanation
Indices: 24586--24646 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
24576 GAAGAAAAAC
*
24586 CAGAGACAGAAAACAGAGA
1 CAGAAACAGAAAACAGAGA
* *
24605 CAGAAACAGAGAACGGAGA
1 CAGAAACAGAAAACAGAGA
*
24624 -AGAAA-AAAAAACAGAGA
1 CAGAAACAGAAAACAGAGA
*
24641 AAGAAA
1 CAGAAA
24647 AAAAAAACAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
17 9 0.26
18 10 0.29
19 16 0.46
ACGTcount: A:0.64, C:0.11, G:0.25, T:0.00
Consensus pattern (19 bp):
CAGAAACAGAAAACAGAGA
Found at i:24650 original size:19 final size:19
Alignment explanation
Indices: 24595--24655 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
24585 CCAGAGACAG
* * *
24595 AAAACAGAGACAGAAACAG
1 AAAACAGAGAAAGAAAAAA
* *
24614 AGAACGGAG-AAG-AAAAA
1 AAAACAGAGAAAGAAAAAA
24631 AAAACAGAGAAAGAAAAAA
1 AAAACAGAGAAAGAAAAAA
24650 AAAACA
1 AAAACA
24656 AATATACCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 10 0.30
18 5 0.15
19 18 0.55
ACGTcount: A:0.70, C:0.10, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAACAGAGAAAGAAAAAA
Found at i:24653 original size:24 final size:24
Alignment explanation
Indices: 24608--24653 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
24598 ACAGAGACAG
* * * *
24608 AAACAGAGAACGGAGAAGAAAAAA
1 AAACAGAGAAAGAAAAAAAAAAAA
24632 AAACAGAGAAAGAAAAAAAAAA
1 AAACAGAGAAAGAAAAAAAAAA
24654 CAAATATACC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.74, C:0.07, G:0.20, T:0.00
Consensus pattern (24 bp):
AAACAGAGAAAGAAAAAAAAAAAA
Found at i:26340 original size:18 final size:18
Alignment explanation
Indices: 26293--26341 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
26283 CTTTTCAATT
26293 TTTTTA-TTTATTTATTA
1 TTTTTATTTTATTTATTA
**
26310 TTTTTATAATATTTA-TA
1 TTTTTATTTTATTTATTA
26327 TGTTTTATTTTATTT
1 T-TTTTATTTTATTT
26342 GCAAGTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
TTTTTATTTTATTTATTA
Found at i:26363 original size:13 final size:15
Alignment explanation
Indices: 26332--26368 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
26322 TTATATGTTT
26332 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
26347 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
26360 TA-TTTATTT
1 TATTTTATTT
26369 TTCTGTCAAA
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:36983 original size:13 final size:13
Alignment explanation
Indices: 36965--37037 Score: 78
Period size: 13 Copynumber: 5.5 Consensus size: 13
36955 AAGAGAAAAG
36965 AAAAAAGAAGAAA
1 AAAAAAGAAGAAA
36978 AAAAAAGAAGAAA
1 AAAAAAGAAGAAA
*
36991 GAAAAAA-TAGAAA
1 -AAAAAAGAAGAAA
37004 ATGAAAAAGAA-AAA
1 A--AAAAAGAAGAAA
*
37018 AAAAGAGAAGAAA
1 AAAAAAGAAGAAA
*
37031 AAGAAAG
1 AAAAAAG
37038 GGGGTCAAGG
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
12 8 0.16
13 26 0.52
14 15 0.30
15 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (13 bp):
AAAAAAGAAGAAA
Found at i:36993 original size:27 final size:26
Alignment explanation
Indices: 36955--37037 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 26
36945 ATTATGCTTG
36955 AAGAGAAAAGAAAAAAGAAGAAAAAAA
1 AAGA-AAAAGAAAAAAGAAGAAAAAAA
*
36982 AAGAAGAAAGAAAAAA-TAGAAAATGAAA
1 AAGAA-AAAGAAAAAAGAAGAAAA--AAA
* *
37010 AAGAAAAA-AAAAGAGAAGAAAAAGA
1 AAGAAAAAGAAAAAAGAAGAAAAAAA
37035 AAG
1 AAG
37038 GGGGTCAAGG
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
25 5 0.10
26 12 0.25
27 23 0.48
28 8 0.17
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.02
Consensus pattern (26 bp):
AAGAAAAAGAAAAAAGAAGAAAAAAA
Found at i:37004 original size:36 final size:35
Alignment explanation
Indices: 36963--37032 Score: 97
Period size: 38 Copynumber: 1.9 Consensus size: 35
36953 TGAAGAGAAA
*
36963 AGAAAA-AAGAAGAAAAAAAAAGAAGAAAGAAAAAAT
1 AGAAAAGAAAAAGAAAAAAAAAG-AG-AAGAAAAAAT
36999 AGAAAATGAAAAAGAAAAAAAAAGAGAAGAAAAA
1 AGAAAA-GAAAAAGAAAAAAAAAGAGAAGAAAAA
37033 GAAAGGGGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 14 0.45
37 2 0.06
38 15 0.48
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (35 bp):
AGAAAAGAAAAAGAAAAAAAAAGAGAAGAAAAAAT
Found at i:37402 original size:19 final size:20
Alignment explanation
Indices: 37369--37410 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
37359 TTCAAGTTCA
*
37369 ATTTATTGGAGATTCAATTT
1 ATTTATTGGAAATTCAATTT
37389 ATTT-TTGGAAATTCAATTT
1 ATTTATTGGAAATTCAATTT
37408 ATT
1 ATT
37411 CTTTTCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (20 bp):
ATTTATTGGAAATTCAATTT
Found at i:38366 original size:82 final size:83
Alignment explanation
Indices: 38182--38429 Score: 426
Period size: 83 Copynumber: 3.0 Consensus size: 83
38172 GAAAGAGACT
*
38182 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACATAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
* *
38247 TTTGGAAGATGAATGTGT
66 TTTGGAAGATGAATTTGC
* * *
38265 AAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTGGACAGAA-CAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
*
38329 TTTAGAAGATGAATTTGC
66 TTTGGAAGATGAATTTGC
38347 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
1 CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
38412 TTTGGAAGATGAATTTGC
66 TTTGGAAGATGAATTTGC
38430 TCATAGTAGA
Statistics
Matches: 153, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
82 76 0.50
83 77 0.50
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.35
Consensus pattern (83 bp):
CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
TTTGGAAGATGAATTTGC
Found at i:39541 original size:113 final size:113
Alignment explanation
Indices: 39265--39903 Score: 1012
Period size: 113 Copynumber: 5.6 Consensus size: 113
39255 ACCAAGGAAG
* * *
39265 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAATGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTG
* * * * * * *
39330 TTCAATCTTTT-GCTTGAATTCATCATTTGATGGATTGACATTTCCAG-AGA
63 TTCAACCTTTTATC-TGAATTCATCACTGGATGGATTAACTTTTCCAGAAAA
39380 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTC
*
39445 AACCTTTTATCTGAATTCATCACTGGATGGATTAATTTTTCCAGAAAA
66 AACCTTTTATCTGAATTCATCACTGGATGGATTAACTTTTCCAGAAAA
39493 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTC
*
39558 AACCTTTTATCTGAATTCATCACTGGATGGATTAATTTTTCCAGAAAA
66 AACCTTTTATCTGAATTCATCACTGGATGGATTAACTTTTCCAGAAAA
39606 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTC
*
39671 AACCTTTTATCTGAATTCATCACTGGATGGATTAAATTTTCCAGAAAA
66 AACCTTTTATCTGAATTCATCACTGGATGGATTAACTTTTCCAGAAAA
*
39719 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTC
* * * * * * *
39784 AACCTTTTACCTGAATTCATCAATTGATGGATCAGCCTTTCCAGAGAA
66 AACCTTTTATCTGAATTCATCACTGGATGGATTAACTTTTCCAGAAAA
* **
39832 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTC
39897 AACCTTT
66 AACCTTT
39904 GTTTGATGTT
Statistics
Matches: 499, Mismatches: 23, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
112 78 0.16
113 403 0.81
115 18 0.04
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTC
AACCTTTTATCTGAATTCATCACTGGATGGATTAACTTTTCCAGAAAA
Found at i:40231 original size:3 final size:3
Alignment explanation
Indices: 40225--40319 Score: 190
Period size: 3 Copynumber: 31.7 Consensus size: 3
40215 TTTTTATCCA
40225 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40273 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
40320 AATATATTAA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:40801 original size:12 final size:13
Alignment explanation
Indices: 40767--40804 Score: 60
Period size: 12 Copynumber: 2.9 Consensus size: 13
40757 GGAAAGAAGA
40767 AGAAAACCAGAGAC
1 AGAAAA-CAGAGAC
40781 AGAAAACAGAGAC
1 AGAAAACAGAGAC
40794 AG-AAACAGAGA
1 AGAAAACAGAGA
40805 ACGGAGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 9 0.38
13 9 0.38
14 6 0.25
ACGTcount: A:0.61, C:0.16, G:0.24, T:0.00
Consensus pattern (13 bp):
AGAAAACAGAGAC
Found at i:40801 original size:19 final size:19
Alignment explanation
Indices: 40774--40834 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
40764 AGAAGAAAAC
*
40774 CAGAGACAGAAAACAGAGA
1 CAGAAACAGAAAACAGAGA
* *
40793 CAGAAACAGAGAACGGAGA
1 CAGAAACAGAAAACAGAGA
*
40812 -AGAAA-AAAAAACAGAGA
1 CAGAAACAGAAAACAGAGA
*
40829 AAGAAA
1 CAGAAA
40835 AAAAAAACAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
17 9 0.26
18 10 0.29
19 16 0.46
ACGTcount: A:0.64, C:0.11, G:0.25, T:0.00
Consensus pattern (19 bp):
CAGAAACAGAAAACAGAGA
Found at i:40838 original size:19 final size:19
Alignment explanation
Indices: 40783--40843 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
40773 CCAGAGACAG
* * *
40783 AAAACAGAGACAGAAACAG
1 AAAACAGAGAAAGAAAAAA
* *
40802 AGAACGGAG-AAG-AAAAA
1 AAAACAGAGAAAGAAAAAA
40819 AAAACAGAGAAAGAAAAAA
1 AAAACAGAGAAAGAAAAAA
40838 AAAACA
1 AAAACA
40844 AATATACCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
17 10 0.30
18 5 0.15
19 18 0.55
ACGTcount: A:0.70, C:0.10, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAACAGAGAAAGAAAAAA
Found at i:40841 original size:24 final size:24
Alignment explanation
Indices: 40796--40841 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
40786 ACAGAGACAG
* * * *
40796 AAACAGAGAACGGAGAAGAAAAAA
1 AAACAGAGAAAGAAAAAAAAAAAA
40820 AAACAGAGAAAGAAAAAAAAAA
1 AAACAGAGAAAGAAAAAAAAAA
40842 CAAATATACC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.74, C:0.07, G:0.20, T:0.00
Consensus pattern (24 bp):
AAACAGAGAAAGAAAAAAAAAAAA
Found at i:44168 original size:181 final size:180
Alignment explanation
Indices: 43858--44224 Score: 608
Period size: 181 Copynumber: 2.0 Consensus size: 180
43848 TAAGTTGTGC
* * * * *
43858 GAATTTAAAAAAAATTTTACGTCCGCGATACCCGCAGTGACCGCGATAGCATCCATTACGTCTGT
1 GAATTTAAAAAAAACTTCACGTCCGCGATACCCGCAGTGACCGCGATAGCATCCATTAAGTCCGC
* * * *
43923 GACCGCGACCGTAATTTGAATCCTTGATAAAGATAAACAATTTGACGTCTTAAAGATTCAACAAT
66 GACCGCAACCGCAATTTGAATCCCTGATAAAGAAAAACAATTTGACGTCTTAAAGATTCAACAAT
* *
43988 AAAGGCTATAATGTCTAGCAAAAAGGTGATATGAACAAGAATGCTTCTCT
131 AAAGGCTATAATGTCAAACAAAAAGGTGATATGAACAAGAATGCTTCTCT
*
44038 GAATTTAAAAAAAAACTTCACGTCCGCGATACCCTCAGTGACCGCGATAGCATCCATTAAGTCCG
1 GAATTT-AAAAAAAACTTCACGTCCGCGATACCCGCAGTGACCGCGATAGCATCCATTAAGTCCG
*
44103 CGACCGTAACCGCAATTTGAATCCCTGATAAAGAAAAACAATTTGACGTCTTAAAGATTCAACAA
65 CGACCGCAACCGCAATTTGAATCCCTGATAAAGAAAAACAATTTGACGTCTTAAAGATTCAACAA
44168 TAAAGGCTATAATGTCAAACAAAAAGGTGATATGAACAAGAATGCTTCTCT
130 TAAAGGCTATAATGTCAAACAAAAAGGTGATATGAACAAGAATGCTTCTCT
44219 GAATTT
1 GAATTT
44225 CTTTAGTGAA
Statistics
Matches: 173, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
180 6 0.03
181 167 0.97
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (180 bp):
GAATTTAAAAAAAACTTCACGTCCGCGATACCCGCAGTGACCGCGATAGCATCCATTAAGTCCGC
GACCGCAACCGCAATTTGAATCCCTGATAAAGAAAAACAATTTGACGTCTTAAAGATTCAACAAT
AAAGGCTATAATGTCAAACAAAAAGGTGATATGAACAAGAATGCTTCTCT
Found at i:50331 original size:16 final size:16
Alignment explanation
Indices: 50307--50339 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
50297 TATCGCCGAC
*
50307 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
50323 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
50339 C
1 C
50340 ACGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:56018 original size:39 final size:39
Alignment explanation
Indices: 55964--56060 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
55954 TTGATCTAAC
55964 GACACGAAATGTTCAAAATTTAAGAATCCATAAATTTAA
1 GACACGAAATGTTCAAAATTTAAGAATCCATAAATTTAA
*
56003 GACACGAAATGTTCAAAATTTAAGAATTCATAAATTTAA
1 GACACGAAATGTTCAAAATTTAAGAATCCATAAATTTAA
* *
56042 GA-ATGGAA-GTTCAAAATTT
1 GACACGAAATGTTCAAAATTT
56061 TAATATTATT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
37 11 0.20
38 4 0.07
39 40 0.73
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (39 bp):
GACACGAAATGTTCAAAATTTAAGAATCCATAAATTTAA
Found at i:56039 original size:16 final size:15
Alignment explanation
Indices: 56014--56045 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
56004 ACACGAAATG
56014 TTCAAAATTTAAGAA
1 TTCAAAATTTAAGAA
56029 TTCATAAATTTAAGAA
1 TTCA-AAATTTAAGAA
56045 T
1 T
56046 GGAAGTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (15 bp):
TTCAAAATTTAAGAA
Found at i:56740 original size:5 final size:5
Alignment explanation
Indices: 56730--56766 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
56720 ATAAATGTAT
56730 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TT
56767 TATACTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:62274 original size:22 final size:22
Alignment explanation
Indices: 62251--62323 Score: 137
Period size: 22 Copynumber: 3.3 Consensus size: 22
62241 ATGAGTTACG
*
62251 GGAGTTACATGATATAATTTCG
1 GGAGTTACATGATATAATTTCA
62273 GGAGTTACATGATATAATTTCA
1 GGAGTTACATGATATAATTTCA
62295 GGAGTTACATGATATAATTTCA
1 GGAGTTACATGATATAATTTCA
62317 GGAGTTA
1 GGAGTTA
62324 TAATAGCTGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (22 bp):
GGAGTTACATGATATAATTTCA
Done.