Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009008.1 Hibiscus syriacus cultivar Beakdansim tig00112393_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: 86904
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:7700 original size:60 final size:60
Alignment explanation
Indices: 7627--7751 Score: 171
Period size: 60 Copynumber: 2.1 Consensus size: 60
7617 AATATAACGA
* * *
7627 ATAGTCGAATGACCATTTTATAACTTTTAATAGTCGAGGGACTTAGCAAAGCAACAT-TCT
1 ATAGTCAAATGACCATTTTATAACTTTTAATAGTCAAGGGACTTAACAAAGCAACATCT-T
* * * *
7687 ATAGTCAAATGACCTTTTTGTAACTTTTAATAGTCAATGGACTTAATAAAGCAACATCTT
1 ATAGTCAAATGACCATTTTATAACTTTTAATAGTCAAGGGACTTAACAAAGCAACATCTT
7747 ATAGT
1 ATAGT
7752 GGGGGACCAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 56 0.98
61 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (60 bp):
ATAGTCAAATGACCATTTTATAACTTTTAATAGTCAAGGGACTTAACAAAGCAACATCTT
Found at i:8689 original size:59 final size:59
Alignment explanation
Indices: 8544--8727 Score: 181
Period size: 60 Copynumber: 3.1 Consensus size: 59
8534 TCACATGTCT
* * * * *
8544 TCAAATTATGACTTTCATTCTAAATTGGCACCTAAACTTTT-AAACATTTTAGTTTCATCC
1 TCAAACTATGACTTTCATTCTAAATTAGCCCCTAAACTTTTGAAA-ATTTCAATTTCAT-C
* * * * * * *
8604 TTAAGCTATGATTTTTATTCTAAATTAGTCCTTAAACTTTTGAAAATTTCAATTCCATC
1 TCAAACTATGACTTTCATTCTAAATTAGCCCCTAAACTTTTGAAAATTTCAATTTCATC
* * * *
8663 TCAAACTATGACCTTCATTCTAAATTAGGCCCCAAAATTTTTGAACATTTCAATTTCATC
1 TCAAACTATGACTTTCATTCTAAATTA-GCCCCTAAACTTTTGAAAATTTCAATTTCATC
*
8723 CCAAA
1 TCAAA
8728 ACTTTACGTA
Statistics
Matches: 98, Mismatches: 24, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
59 23 0.23
60 72 0.73
61 3 0.03
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (59 bp):
TCAAACTATGACTTTCATTCTAAATTAGCCCCTAAACTTTTGAAAATTTCAATTTCATC
Found at i:11472 original size:31 final size:31
Alignment explanation
Indices: 11432--11499 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
11422 AATAATAATG
* *
11432 TTTAATCACTATTGTTTTTATTTAATTAAGA
1 TTTATTCACTATTATTTTTATTTAATTAAGA
*
11463 TTTATTCACTTTTATTTTTATTTAATTAAGA
1 TTTATTCACTATTATTTTTATTTAATTAAGA
11494 TATTAT
1 T-TTAT
11500 CAATAAAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (31 bp):
TTTATTCACTATTATTTTTATTTAATTAAGA
Found at i:17618 original size:13 final size:13
Alignment explanation
Indices: 17600--17631 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
17590 TAACCTATAA
17600 TTAAATTCTAAAT
1 TTAAATTCTAAAT
17613 TTAAATTCTAAAT
1 TTAAATTCTAAAT
17626 TTAAAT
1 TTAAAT
17632 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (13 bp):
TTAAATTCTAAAT
Found at i:27479 original size:21 final size:21
Alignment explanation
Indices: 27455--27500 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
27445 CCAACGAGGT
*
27455 AGAGTCGGAACCGCCAAAGGA
1 AGAGTCAGAACCGCCAAAGGA
*
27476 AGAGTCAGAACCGCCGAAGGA
1 AGAGTCAGAACCGCCAAAGGA
27497 AGAG
1 AGAG
27501 AATGAGAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.22, G:0.35, T:0.04
Consensus pattern (21 bp):
AGAGTCAGAACCGCCAAAGGA
Found at i:30977 original size:97 final size:93
Alignment explanation
Indices: 30795--30993 Score: 265
Period size: 93 Copynumber: 2.1 Consensus size: 93
30785 GATGCTCACT
* * * *
30795 TTATTGTCTTCATTTCTTATCACGTGTCTTGTTCATCCATAGTCCATCTGCCATTCATGGATTCA
1 TTATTGCCTACATCTCTCATCACGTGTCTTGTTCATCCATAGTCCATCTGCCATTCATGGATTCA
*
30860 TCCATAATACATTTGCTTGATGTTTATA
66 TCCATAATACATTTGCTTGATGTTCATA
* *
30888 TTATTGCCTACATCTCTCATCAGGTGTCTTGTTCATCCATAGTCCATTTGCCTGTTATTCATGGA
1 TTATTGCCTACATCTCTCATCACGTGTCTTGTTCATCCATAGTCCATCTGCC----ATTCATGGA
* *
30953 TTCATCCATAGT-CTATTTGCTTGATGTTCATC
62 TTCATCCATAATAC-ATTTGCTTGATGTTCATA
30985 TTATTGCCT
1 TTATTGCCT
30994 TCATTTCTTA
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
93 46 0.50
96 1 0.01
97 45 0.49
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.45
Consensus pattern (93 bp):
TTATTGCCTACATCTCTCATCACGTGTCTTGTTCATCCATAGTCCATCTGCCATTCATGGATTCA
TCCATAATACATTTGCTTGATGTTCATA
Found at i:30983 original size:34 final size:34
Alignment explanation
Indices: 30919--30983 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
30909 AGGTGTCTTG
*
30919 TTCATCCATAGTCCATTTGCCTGTTATTCATGGA
1 TTCATCCATAGTCCATTTGCCTGATATTCATGGA
* * *
30953 TTCATCCATAGTCTATTTGCTTGATGTTCAT
1 TTCATCCATAGTCCATTTGCCTGATATTCAT
30984 CTTATTGCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.45
Consensus pattern (34 bp):
TTCATCCATAGTCCATTTGCCTGATATTCATGGA
Found at i:45060 original size:177 final size:177
Alignment explanation
Indices: 44754--45290 Score: 1011
Period size: 177 Copynumber: 3.0 Consensus size: 177
44744 CTACCTTTCT
*
44754 TTTGCTTCCAATGATCTCGTTGATCTGAAGGTGTCAAATGTTTTTATTAACAAAAAAATCATTCG
1 TTTGCATCCAATGATCTCGTTGATCTGAAGGTGTCAAATGTTTTTATTAACAAAAAAATCATTCG
*
44819 CACCAGCATTCTCTATGCTCTGATTCCTGATTCGAATATGGTATTTGATATCTTTTTACCGTGAA
66 CACCAGCATTCTCTATGCTCTGATTCCTGATTCGAATATGGTATTTGATATCTTTTTGCCGTGAA
44884 TAATACCTCCGCCATTTTAAGTTCCCAAGATGTCTCATGAAGACCAG
131 TAATACCTCCGCCATTTTAAGTTCCCAAGATGTCTCATGAAGACCAG
44931 TTTGCATCCAATGATCTCGTTGATCTGAAGGTGTCAAATGTTTTTATTAACAAAAAAATCATTCG
1 TTTGCATCCAATGATCTCGTTGATCTGAAGGTGTCAAATGTTTTTATTAACAAAAAAATCATTCG
44996 CACCAGCATTCTCTATGCTCTGATTCCTGATTCGAATATGGTATTTGATATCTTTTTGCCGTGAA
66 CACCAGCATTCTCTATGCTCTGATTCCTGATTCGAATATGGTATTTGATATCTTTTTGCCGTGAA
45061 TAATACCTCCGCCATTTTAAGTTCCCAAGATGTCTCATGAAGACCAG
131 TAATACCTCCGCCATTTTAAGTTCCCAAGATGTCTCATGAAGACCAG
*
45108 TTTGCATCCAATGATCTCGTTGATCTGAAGGTGTCAAATGATTTTATTAACAAAAAAATCATTCG
1 TTTGCATCCAATGATCTCGTTGATCTGAAGGTGTCAAATGTTTTTATTAACAAAAAAATCATTCG
* * *
45173 CACCAGCATTCTCTATGCTCTGATTCCTGATTCGAATATGGCATTTGATATCTTTTTGCCTTGGA
66 CACCAGCATTCTCTATGCTCTGATTCCTGATTCGAATATGGTATTTGATATCTTTTTGCCGTGAA
*
45238 TAATACCTCCGCCATTTTAAGTTCCCGAGATGTCTCATGAAGACCAG
131 TAATACCTCCGCCATTTTAAGTTCCCAAGATGTCTCATGAAGACCAG
45285 TTTGCA
1 TTTGCA
45291 ACATGTGGGT
Statistics
Matches: 353, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
177 353 1.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (177 bp):
TTTGCATCCAATGATCTCGTTGATCTGAAGGTGTCAAATGTTTTTATTAACAAAAAAATCATTCG
CACCAGCATTCTCTATGCTCTGATTCCTGATTCGAATATGGTATTTGATATCTTTTTGCCGTGAA
TAATACCTCCGCCATTTTAAGTTCCCAAGATGTCTCATGAAGACCAG
Found at i:46748 original size:2 final size:2
Alignment explanation
Indices: 46741--46779 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
46731 TATGAATAGT
* * *
46741 TA TA TA TA TA TA TA TA TA TA TA TG TA TT TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46780 TTATTCTTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (2 bp):
TA
Found at i:46780 original size:12 final size:12
Alignment explanation
Indices: 46745--46783 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
46735 AATAGTTATA
*
46745 TATATATATATA
1 TATATATATATT
*
46757 TATATATGTATT
1 TATATATATATT
*
46769 TATGTATATATT
1 TATATATATATT
46781 TAT
1 TAT
46784 TCTTTGAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (12 bp):
TATATATATATT
Found at i:49320 original size:14 final size:14
Alignment explanation
Indices: 49301--49342 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
49291 GATGTACTTT
49301 CTTAGATATTTGAA
1 CTTAGATATTTGAA
49315 CTTAGATATTTGAA
1 CTTAGATATTTGAA
49329 CTTAGATATTTGAA
1 CTTAGATATTTGAA
49343 TTTTTGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
CTTAGATATTTGAA
Found at i:59040 original size:48 final size:48
Alignment explanation
Indices: 58934--59042 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
58924 AAACGGAGAT
* * * * * *
58934 ATCAAAAATCAAAACATAATTCAGATCATATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
58982 TTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
59030 ATCAGAAATCAGA
1 ATCAGAAATCAGA
59043 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:61540 original size:7 final size:7
Alignment explanation
Indices: 61528--61567 Score: 62
Period size: 7 Copynumber: 5.4 Consensus size: 7
61518 TGGTCAACTT
61528 CGGTCAA
1 CGGTCAA
61535 CGGTCAA
1 CGGTCAA
61542 CGGGTCAA
1 C-GGTCAA
61550 CGGTCAA
1 CGGTCAA
61557 CGGGTCAA
1 C-GGTCAA
61565 CGG
1 CGG
61568 GTCGGGTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 17 0.55
8 14 0.45
ACGTcount: A:0.25, C:0.28, G:0.35, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:61549 original size:8 final size:8
Alignment explanation
Indices: 61529--61627 Score: 76
Period size: 8 Copynumber: 13.5 Consensus size: 8
61519 GGTCAACTTC
61529 GGTCAAC-
1 GGTCAACG
61536 GGTCAACG
1 GGTCAACG
61544 GGTCAAC-
1 GGTCAACG
61551 GGTCAACG
1 GGTCAACG
61559 GGTCAACG
1 GGTCAACG
61567 GGT---CG
1 GGTCAACG
61572 GGTCAACG
1 GGTCAACG
**
61580 GGTCGGGTCG
1 GGTC--AACG
61590 GGTCAACG
1 GGTCAACG
61598 GGT---CG
1 GGTCAACG
*
61603 GGTAAACG
1 GGTCAACG
61611 GGT---CG
1 GGTCAACG
61616 GGTCAACG
1 GGTCAACG
61624 GGTC
1 GGTC
61628 GGGTCGGGTT
Statistics
Matches: 75, Mismatches: 4, Indels: 25
0.72 0.04 0.24
Matches are distributed among these distances:
5 15 0.20
7 14 0.19
8 40 0.53
10 6 0.08
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:61549 original size:15 final size:15
Alignment explanation
Indices: 61529--61567 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
61519 GGTCAACTTC
61529 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
61544 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
61559 GGTCAACGG
1 GGTCAACGG
61568 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:61575 original size:13 final size:13
Alignment explanation
Indices: 61557--61632 Score: 98
Period size: 13 Copynumber: 5.5 Consensus size: 13
61547 CAACGGTCAA
61557 CGGGTCAACGGGT
1 CGGGTCAACGGGT
61570 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
61588 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
61601 CGGGTAAACGGGT
1 CGGGTCAACGGGT
61614 CGGGTCAACGGGT
1 CGGGTCAACGGGT
61627 CGGGTC
1 CGGGTC
61633 GGGTTGTGAC
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
13 43 0.77
18 13 0.23
ACGTcount: A:0.14, C:0.22, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:61595 original size:31 final size:31
Alignment explanation
Indices: 61557--61619 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
61547 CAACGGTCAA
*
61557 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
61588 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
61619 C
1 C
61620 AACGGGTCGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.14, C:0.22, G:0.48, T:0.16
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTAAACGGGTCGGGT
Found at i:61631 original size:31 final size:29
Alignment explanation
Indices: 61564--61636 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 29
61554 CAACGGGTCA
*
61564 ACGGGTCGGGTCAACGGGTCGGGTCGGGT
1 ACGGGTCGGGTAAACGGGTCGGGTCGGGT
61593 CAACGGGTCGGGTAAACGGGTCGGGTCAACGGGT
1 --ACGGGTCGGGTAAACGGGTCGGGT---CGGGT
61627 -CGGGTCGGGT
1 ACGGGTCGGGT
61637 TGTGACCGGT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
31 33 0.87
34 5 0.13
ACGTcount: A:0.14, C:0.21, G:0.49, T:0.16
Consensus pattern (29 bp):
ACGGGTCGGGTAAACGGGTCGGGTCGGGT
Found at i:61636 original size:18 final size:18
Alignment explanation
Indices: 61551--61605 Score: 83
Period size: 18 Copynumber: 2.9 Consensus size: 18
61541 ACGGGTCAAC
61551 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
61572 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
61590 GGTCAACGGGTCGGGT
1 GGTCAACGGGTCGGGT
61606 AAACGGGTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 23 0.68
21 11 0.32
ACGTcount: A:0.15, C:0.22, G:0.47, T:0.16
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:63869 original size:48 final size:48
Alignment explanation
Indices: 63763--63871 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
63753 AAACGGAGAT
* * * * * *
63763 ATCAAAAATCAAAACATAATTCAGATCATATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
63811 TTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
63859 ATCAGAAATCAGA
1 ATCAGAAATCAGA
63872 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:66375 original size:8 final size:8
Alignment explanation
Indices: 66355--66425 Score: 57
Period size: 8 Copynumber: 9.5 Consensus size: 8
66345 GGTCAACTTC
66355 GGTCAAC-
1 GGTCAACG
66362 GGTCAACG
1 GGTCAACG
66370 GGTCAACG
1 GGTCAACG
66378 GGT---CG
1 GGTCAACG
66383 GGTCAACG
1 GGTCAACG
**
66391 GGTCGGGTCG
1 GGTC--AACG
66401 GGTCAACG
1 GGTCAACG
66409 GGT---CG
1 GGTCAACG
66414 GGTCAACG
1 GGTCAACG
66422 GGTC
1 GGTC
66426 GGGTCGGGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 17
0.71 0.06 0.24
Matches are distributed among these distances:
5 10 0.20
7 7 0.14
8 28 0.55
10 6 0.12
ACGTcount: A:0.17, C:0.24, G:0.44, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:66386 original size:13 final size:13
Alignment explanation
Indices: 66368--66430 Score: 81
Period size: 13 Copynumber: 4.5 Consensus size: 13
66358 CAACGGTCAA
66368 CGGGTCAACGGGT
1 CGGGTCAACGGGT
66381 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
66399 CGGGTCAACGGGT
1 CGGGTCAACGGGT
66412 CGGGTCAACGGGT
1 CGGGTCAACGGGT
66425 CGGGTC
1 CGGGTC
66431 GGGTTGTGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
13 32 0.71
18 13 0.29
ACGTcount: A:0.13, C:0.24, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:66406 original size:31 final size:31
Alignment explanation
Indices: 66368--66434 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
66358 CAACGGTCAA
66368 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
66399 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
66430 CGGGT
1 CGGGT
66435 TGTGACCGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.16
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
Found at i:66434 original size:18 final size:18
Alignment explanation
Indices: 66362--66417 Score: 85
Period size: 18 Copynumber: 2.9 Consensus size: 18
66352 TTCGGTCAAC
66362 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
66383 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
66401 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
66418 AACGGGTCGG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 24 0.69
21 11 0.31
ACGTcount: A:0.14, C:0.23, G:0.46, T:0.16
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:68662 original size:48 final size:48
Alignment explanation
Indices: 68556--68664 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
68546 AAACGGAGAT
* * * * * *
68556 ATCAAAAATCAAAACATAATTCAGATCATATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
68604 TTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
68652 ATCAGAAATCAGA
1 ATCAGAAATCAGA
68665 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:71173 original size:13 final size:13
Alignment explanation
Indices: 71168--71235 Score: 82
Period size: 13 Copynumber: 4.8 Consensus size: 13
71158 GTCAACGGGT
71168 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
71181 CGGGTCGGGTCGGGTCAA
1 CGGGT-----CGGGTCAA
*
71199 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
71212 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
71225 CGGGTCGGGTC
1 CGGGTCGGGTC
71236 GGGTTGTGAC
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
13 35 0.73
18 13 0.27
ACGTcount: A:0.13, C:0.22, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:71199 original size:44 final size:42
Alignment explanation
Indices: 71149--71239 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 42
71139 TTCGGTCAAC
71149 GGTCAACGGGTCAACGGGT-CGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGT---CGGGTACGGGTCGGGTCAACGGGTCGGGTCG
71193 GGTCAACGGGTCGGGTAAACGGGTCGGGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGT--ACGGGTCGGGTCAACGGGTCGGGTCG
71237 GGT
1 GGT
71240 TGTGACCGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
41 5 0.11
44 39 0.89
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.16
Consensus pattern (42 bp):
GGTCAACGGGTCGGGTACGGGTCGGGTCAACGGGTCGGGTCG
Found at i:71234 original size:31 final size:31
Alignment explanation
Indices: 71155--71239 Score: 113
Period size: 31 Copynumber: 2.7 Consensus size: 31
71145 CAACGGTCAA
*
71155 CGGGTCAACGGGTCGGGTCGGGTCAACGGGT
1 CGGGTCAACGGGTCGGGTCGGGTAAACGGGT
71186 CGGGT---CGGGTCAACGGGTCGGGTAAACGGGT
1 CGGGTCAACGGGT---CGGGTCGGGTAAACGGGT
71217 CGGGTCAACGGGTCGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCGGGT
71240 TGTGACCGGT
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
28 5 0.11
31 37 0.79
34 5 0.11
ACGTcount: A:0.13, C:0.21, G:0.49, T:0.16
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTCGGGTAAACGGGT
Found at i:71239 original size:18 final size:18
Alignment explanation
Indices: 71155--71208 Score: 108
Period size: 18 Copynumber: 3.0 Consensus size: 18
71145 CAACGGTCAA
71155 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
71173 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
71191 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
71209 AAACGGGTCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.11, C:0.22, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:73340 original size:35 final size:35
Alignment explanation
Indices: 73289--73368 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
73279 AAAACAATCA
* *
73289 TCAATTATATTTTAAACCCCAAAATT-CAAAATACT
1 TCAATTACATTCTAAACCCC-AAATTCCAAAATACT
*
73324 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
*
73359 TCGATTACAT
1 TCAATTACAT
73369 GCCCAACCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 5 0.12
35 35 0.88
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATACT
Found at i:73807 original size:148 final size:149
Alignment explanation
Indices: 73530--73978 Score: 681
Period size: 148 Copynumber: 3.0 Consensus size: 149
73520 GGTTAAATAC
* * *
73530 TCAATTCATTTTATAAAATAGTTGACTAGAAATTTTTTCGGTTTGA-GTTTATAAAATTTAAATA
1 TCAATTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGATGTTTATAAAATTTAAATA
*
73594 AAGTCGAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAAAATTTATCATATTAT
66 AAGTCGAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTAT
73659 AATATTATTTGATTCTAAT
131 AATATTATTTGATTCTAAT
* *
73678 TCAGTTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTT-ATGTTTATAAAATTTAAATC
1 TCAATTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGATGTTTATAAAATTTAAATA
*
73742 AAGTCGAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTGTCATATTAT
66 AAGTCGAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTAT
*
73807 AATATTGTTTGATTCTAAT
131 AATATTATTTGATTCTAAT
* * ** *
73826 TCAATTCAGTTTATAAAATAGTTAACTCAAAAAATTTTCTATTTGAT-TTTAT-AAATTTAAATA
1 TCAATTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGATGTTTATAAAATTTAAATA
* *
73889 AAGTCAAATTGAATTGAATTGAATTTTTGAGTTTCTGTTTAAATTTAATTATAAATATTTATAAT
66 AAGTC-----GAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATCAT
*
73954 ACTATAATATTATTTGATTCTAAT
126 ATTATAATATTATTTGATTCTAAT
73978 T
1 T
73979 TAAATAGTGT
Statistics
Matches: 274, Mismatches: 20, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
147 16 0.06
148 181 0.66
149 2 0.01
152 75 0.27
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (149 bp):
TCAATTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGATGTTTATAAAATTTAAATA
AAGTCGAATTGAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTAT
AATATTATTTGATTCTAAT
Found at i:74517 original size:35 final size:35
Alignment explanation
Indices: 74478--74590 Score: 163
Period size: 35 Copynumber: 3.2 Consensus size: 35
74468 GGGGTTGGAC
*
74478 ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAGA
1 ATGTAATTGAAGCATTTTGGAATTTGAGGTTTAGA
*
74513 ATGTATTTGAAGCATTTTGGAATTTGAGGTTTAGA
1 ATGTAATTGAAGCATTTTGGAATTTGAGGTTTAGA
* * * * *
74548 ATATAGTTGAAGCATTTTAGAATTCGAGGTTTATA
1 ATGTAATTGAAGCATTTTGGAATTTGAGGTTTAGA
74583 ATGTAATT
1 ATGTAATT
74591 AATGATTGTT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.32, C:0.03, G:0.23, T:0.42
Consensus pattern (35 bp):
ATGTAATTGAAGCATTTTGGAATTTGAGGTTTAGA
Found at i:80492 original size:2 final size:2
Alignment explanation
Indices: 80485--80515 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
80475 AGAATTTATT
80485 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 T
80516 TTTTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.