Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002484.1 Hibiscus syriacus cultivar Beakdansim tig00005070_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: 57058
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Found at i:938 original size:12 final size:13
Alignment explanation
Indices: 918--951 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
908 TATATAACAA
918 TTAATCAAAT-AG
1 TTAATCAAATCAG
*
930 TTTATCAAATCAG
1 TTAATCAAATCAG
943 TTAATCAAA
1 TTAATCAAA
952 CCAGCTACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (13 bp):
TTAATCAAATCAG
Found at i:2750 original size:20 final size:20
Alignment explanation
Indices: 2725--2762 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2715 CATTCTGCAG
*
2725 CAGAGGTTTTAAAACCCCCT
1 CAGAGGTTTCAAAACCCCCT
2745 CAGAGGTTTCAAAACCCC
1 CAGAGGTTTCAAAACCCC
2763 TACCCAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
CAGAGGTTTCAAAACCCCCT
Found at i:10886 original size:17 final size:17
Alignment explanation
Indices: 10864--10899 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
10854 TATATATAGT
10864 TTTAGAACTTTTAAATC
1 TTTAGAACTTTTAAATC
10881 TTTAGAACTTTTAAATC
1 TTTAGAACTTTTAAATC
10898 TT
1 TT
10900 AATTTTTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (17 bp):
TTTAGAACTTTTAAATC
Found at i:13110 original size:48 final size:48
Alignment explanation
Indices: 13051--13170 Score: 161
Period size: 48 Copynumber: 2.5 Consensus size: 48
13041 GTTGTCGGAC
* * **
13051 TCTTGTCTTCCGGGAGGAGGTGCTAGA-CTTTGAGTTGTGTTATTGGAT
1 TCTTGTCTTCCGGGAGGAGGTGCTAAACCTTT-ACTTGTGTTATCAGAT
* * *
13099 TCTTGTGTTCCGGGAGGAGGTACTAAACCTTTACTTGTGTTGTCAGAT
1 TCTTGTCTTCCGGGAGGAGGTGCTAAACCTTTACTTGTGTTATCAGAT
13147 TCTTGTCTTCCGGGAGGAGGTGCT
1 TCTTGTCTTCCGGGAGGAGGTGCT
13171 CGGAGTGCTG
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 58 0.94
49 4 0.06
ACGTcount: A:0.15, C:0.16, G:0.32, T:0.38
Consensus pattern (48 bp):
TCTTGTCTTCCGGGAGGAGGTGCTAAACCTTTACTTGTGTTATCAGAT
Found at i:17713 original size:27 final size:25
Alignment explanation
Indices: 17683--17739 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
17673 GATAATTATT
17683 ATTATTAATAAT-TGTATTAAAAATATA
1 ATTATT-ATAATAT-TATTAAAAA-ATA
*
17710 ATTAATTATAATATTATTAAACAATA
1 ATT-ATTATAATATTATTAAAAAATA
17736 ATTA
1 ATTA
17740 GGAACATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
25 1 0.04
26 6 0.22
27 16 0.59
28 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
ATTATTATAATATTATTAAAAAATA
Found at i:23330 original size:30 final size:31
Alignment explanation
Indices: 23274--23331 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
23264 AAATTACATA
*
23274 TTTAGTACTTAAAATATCAGTTTTTTTCCGT
1 TTTAGTACCTAAAATATCAGTTTTTTTCCGT
* *
23305 TTTAGTACCTAAACTTTCA-TTTTTTTC
1 TTTAGTACCTAAAATATCAGTTTTTTTC
23332 AAAACCAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.53
Consensus pattern (31 bp):
TTTAGTACCTAAAATATCAGTTTTTTTCCGT
Found at i:24816 original size:20 final size:21
Alignment explanation
Indices: 24791--24842 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
24781 TTTTCCCAAT
*
24791 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
24811 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
24832 TCGCAATGCGA
1 TCGCAATGCGA
24843 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:24856 original size:20 final size:20
Alignment explanation
Indices: 24831--24965 Score: 130
Period size: 20 Copynumber: 6.7 Consensus size: 20
24821 AATTGGGAAA
24831 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
24851 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
24871 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
24892 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
24912 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
24932 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
24952 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
24966 TTTCAAAGCG
Statistics
Matches: 97, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
19 4 0.04
20 67 0.69
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:24875 original size:61 final size:61
Alignment explanation
Indices: 24828--24959 Score: 192
Period size: 61 Copynumber: 2.2 Consensus size: 61
24818 GCGAATTGGG
* * * *
24828 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
24889 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
24950 ATAATCGCAA
1 AAAATCGCAA
24960 TGCGATTTTC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:25153 original size:22 final size:22
Alignment explanation
Indices: 25125--25168 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
25115 CCATCTCTCA
25125 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
25147 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
25169 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:25441 original size:20 final size:20
Alignment explanation
Indices: 25412--25455 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
25402 GCGATTTTAG
25412 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
25432 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
25452 TTTC
1 TTTC
25456 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:25646 original size:25 final size:24
Alignment explanation
Indices: 25592--25646 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
25582 TGTTTATTAT
* *
25592 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
25616 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
25642 TGTTT
1 TGTTT
25647 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:26795 original size:18 final size:18
Alignment explanation
Indices: 26774--26818 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
26764 TCCACTTCGG
*
26774 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
26792 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
26810 GAGCCATCA
1 GAGCCATCA
26819 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:27325 original size:20 final size:20
Alignment explanation
Indices: 27300--27345 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
27290 TAGTTTACTT
*
27300 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
27320 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
27340 TCGCAA
1 TCGCAA
27346 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:27354 original size:19 final size:20
Alignment explanation
Indices: 27311--27366 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
27301 CGCAACATGA
27311 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
27331 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
27350 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
27367 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:27374 original size:14 final size:14
Alignment explanation
Indices: 27355--27411 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
27345 ATGCGAAATG
27355 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
27369 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
27388 AAAATCGCAACGAC
1 AAAATCGCAACGAC
27402 AAAATCGCAA
1 AAAATCGCAA
27412 TGCGAAATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:27381 original size:33 final size:33
Alignment explanation
Indices: 27339--27430 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
27329 GGAAATGGCT
27339 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
27372 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
27405 ATCGCAATGCGAAATGAAAGTCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
27431 TGCGATTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:27393 original size:19 final size:19
Alignment explanation
Indices: 27339--27435 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
27329 GGAAATGGCT
27339 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
27358 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
27372 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
27391 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
27405 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
27424 GTCGCAATGCGA
1 ATCGCAATGCGA
27436 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:27453 original size:19 final size:18
Alignment explanation
Indices: 27431--27479 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
27421 AAAGTCGCAA
*
27431 TGCGATTTGTGTTTCGTGT
1 TGCGATTT-TGTTTCGCGT
**
27450 TGCGATTTCATTTCGCGT
1 TGCGATTTTGTTTCGCGT
27468 TGCGATTTTGTT
1 TGCGATTTTGTT
27480 ATTGCGATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.08, C:0.14, G:0.27, T:0.51
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:27504 original size:33 final size:33
Alignment explanation
Indices: 27449--27539 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 33
27439 GTGTTTCGTG
* *
27449 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTTA
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCA
* *
27481 TTGCGATTTTCATTTTGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCA
*
27514 TTGCGATTTGCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
27540 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 6 0.12
33 46 0.88
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCA
Found at i:27536 original size:19 final size:18
Alignment explanation
Indices: 27449--27581 Score: 68
Period size: 20 Copynumber: 7.5 Consensus size: 18
27439 GTGTTTCGTG
*
27449 TTGCGATTTCATTTCGCG
1 TTGCGATTTCATTTCGCA
27467 TTGCGATTT--TGTT---A
1 TTGCGATTTCAT-TTCGCA
*
27481 TTGCGATTTTCATTTTGCA
1 TTGCGA-TTTCATTTCGCA
*
27500 TTGCGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
27514 TTGCGATTTGCATTTCGCA
1 TTGCGATTT-CATTTCGCA
** *
27533 TTGCGATAGCCATTTCCGCG
1 TTGCGAT-TTCATTT-CGCA
* *
27553 TTGCGATAGTCATTTTCGCG
1 TTGCGAT-TTCA-TTTCGCA
27573 TTGCGATTT
1 TTGCGATTT
27582 TAAGTTTCGT
Statistics
Matches: 91, Mismatches: 9, Indels: 29
0.71 0.07 0.22
Matches are distributed among these distances:
14 15 0.16
15 3 0.03
16 6 0.07
17 7 0.08
18 12 0.13
19 20 0.22
20 25 0.27
21 3 0.03
ACGTcount: A:0.14, C:0.19, G:0.23, T:0.45
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Found at i:27558 original size:20 final size:19
Alignment explanation
Indices: 27524--27579 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
27514 TTGCGATTTG
*
27524 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
27543 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
27563 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
27580 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:35031 original size:14 final size:14
Alignment explanation
Indices: 34997--35035 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
34987 TTGATTGTTT
34997 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
35011 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
35025 TGTTGATTTGT
1 AATTGATTTGT
35036 TTAATTGGTG
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:35486 original size:20 final size:20
Alignment explanation
Indices: 35461--35552 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
35451 TTGAAGATGA
35461 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
35481 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
35501 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
35522 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
35542 TTGCGATTTTC
1 TTGCGATTTTC
35553 CAAATTCACA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:35584 original size:20 final size:21
Alignment explanation
Indices: 35537--35588 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
35527 ATAGTCAGTA
*
35537 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
* **
35558 TCACATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
35578 TCGCATTGCGA
1 TCGCATTGCGA
35589 ATTAGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:35631 original size:20 final size:20
Alignment explanation
Indices: 35602--35651 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
35592 AGGAAAATCA
*
35602 CAACGCGATACTTACTTTCG
1 CAACGAGATACTTACTTTCG
35622 CAACGAGATACTTACTTTCG
1 CAACGAGATACTTACTTTCG
35642 CAACGAGATA
1 CAACGAGATA
35652 ATACAGAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (20 bp):
CAACGAGATACTTACTTTCG
Found at i:36420 original size:24 final size:24
Alignment explanation
Indices: 36400--36446 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
36390 AAATTTGAAC
36400 TTGGTCAATACCCGGACTTTGATA
1 TTGGTCAATACCCGGACTTTGATA
* *
36424 TTGGTCAATACTCGGATTTTGAT
1 TTGGTCAATACCCGGACTTTGAT
36447 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACCCGGACTTTGATA
Found at i:38164 original size:33 final size:33
Alignment explanation
Indices: 38122--38248 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
38112 GGAAATTACT
38122 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
38155 ATCGCAATGCGAAATGAAAATCACAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
38187 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
38221 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
38249 CGAATTAAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:38229 original size:66 final size:66
Alignment explanation
Indices: 38123--38254 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
38113 GAAATTACTA
*
38123 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
38188 T
66 T
* *
38189 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
38254 T
66 T
38255 AAATTTCGCG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCACAACGCGAAT
T
Found at i:38301 original size:19 final size:19
Alignment explanation
Indices: 38277--38323 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
38267 GCGATTCTCT
38277 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
38296 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
38315 CATTGCGAT
1 CGTTGCGAT
38324 AGTACTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:38449 original size:14 final size:14
Alignment explanation
Indices: 38430--38466 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
38420 CATCAATTAA
38430 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
38444 ACAAATCACCTTTT
1 ACAAATCAACTTTT
38458 ACAAATCAA
1 ACAAATCAA
38467 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:40342 original size:91 final size:90
Alignment explanation
Indices: 40163--40347 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
40153 ATTTCAAACT
*
40163 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
40228 AGAATTAGCAGCAACCGAATAAATTTAC
63 AGAATTAGCAGCAACCGAATAAATTTAC
40256 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
40320 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTAGCAGCAACCGAATAAATTTAC
40347 T
1 T
40348 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTAGCAGCAACCGAATAAATTTAC
Found at i:42084 original size:14 final size:14
Alignment explanation
Indices: 42065--42120 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
42055 GGAAATGACT
42065 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
42079 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
42096 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
42112 ATCGCAACG
1 ATCGCAACG
42121 CAAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:42098 original size:33 final size:33
Alignment explanation
Indices: 42042--42139 Score: 160
Period size: 33 Copynumber: 2.9 Consensus size: 33
42032 CGAGATAATA
42042 AGAATCGCAACGCGGAAATGACTATCGCAACGAG
1 AGAATCGCAACGC-GAAATGACTATCGCAACGAG
42076 AGAATCGCAACGCGAAATGACTATCGCAACGAG
1 AGAATCGCAACGCGAAATGACTATCGCAACGAG
* **
42109 AGAATCGCAACGCAAAATGAAAATCGCAACG
1 AGAATCGCAACGCGAAATGACTATCGCAACG
42140 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 48 0.79
34 13 0.21
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.11
Consensus pattern (33 bp):
AGAATCGCAACGCGAAATGACTATCGCAACGAG
Found at i:42134 original size:52 final size:52
Alignment explanation
Indices: 42078--42194 Score: 198
Period size: 52 Copynumber: 2.2 Consensus size: 52
42068 GCAACGAGAG
**
42078 AATCGCAACGCGAAATGACTATCGCAACGAGAGAATCGCAACGCAAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCAAAATGAA
*
42130 AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCAAAATGAA
*
42182 AATCGCAATGCGA
1 AATCGCAACGCGA
42195 TTTTGGTTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.11
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCAAAATGAA
Found at i:42156 original size:33 final size:33
Alignment explanation
Indices: 42119--42189 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
42109 AGAATCGCAA
42119 CGCAA-AATGAAAATCGCAACGCGAAATGAAAAT
1 CGCAACAA-GAAAATCGCAACGCGAAATGAAAAT
* *
42152 CGCAACGAGAGAATCGCAACGCGAAATGAAAAT
1 CGCAACAAGAAAATCGCAACGCGAAATGAAAAT
42185 CGCAA
1 CGCAA
42190 TGCGATTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 34 0.97
34 1 0.03
ACGTcount: A:0.48, C:0.21, G:0.21, T:0.10
Consensus pattern (33 bp):
CGCAACAAGAAAATCGCAACGCGAAATGAAAAT
Found at i:42187 original size:19 final size:19
Alignment explanation
Indices: 42016--42194 Score: 129
Period size: 19 Copynumber: 10.1 Consensus size: 19
42006 TCTTTTGGTT
*
42016 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
42035 GATAAT-AAGAATCGCAACGC
1 GA-AATGAA-AATCGCAACGC
**
42055 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
42073 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
42089 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
42106 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
42122 AAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
42141 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
42158 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
42174 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
42193 GA
1 GA
42195 TTTTGGTTTC
Statistics
Matches: 126, Mismatches: 15, Indels: 38
0.70 0.08 0.21
Matches are distributed among these distances:
14 28 0.22
15 3 0.02
16 5 0.04
17 5 0.04
18 4 0.03
19 55 0.44
20 23 0.18
21 3 0.02
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:42223 original size:19 final size:19
Alignment explanation
Indices: 42190--42234 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
42180 AAAATCGCAA
*
42190 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
42209 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
42228 TGCGATT
1 TGCGATT
42235 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:42831 original size:20 final size:20
Alignment explanation
Indices: 42790--42861 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
42780 GCTATGTAAA
* *
42790 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
42810 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* * *
42830 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
42851 TCGCATTGCGA
1 TCGCATTGCGA
42862 ATTATGAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.07
20 29 0.66
21 12 0.27
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:42875 original size:21 final size:21
Alignment explanation
Indices: 42851--42923 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
42841 TTTTCCTAAT
*
42851 TCGCATTGCGAATTATGAAAA
1 TCGCATTGCGAATTACGAAAA
* *
42872 TCGC-TACGCGAA-TACGTAAA
1 TCGCAT-TGCGAATTACGAAAA
* *
42892 TCGCAATGCGAATTAGGAAAA
1 TCGCATTGCGAATTACGAAAA
*
42913 TTGCATTGCGA
1 TCGCATTGCGA
42924 TAGTCAGTAT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (21 bp):
TCGCATTGCGAATTACGAAAA
Found at i:42940 original size:20 final size:20
Alignment explanation
Indices: 42915--42984 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
42905 TAGGAAAATT
42915 GCATTGCGATAGTCAGTATC
1 GCATTGCGATAGTCAGTATC
42935 GCATTGCGATAGTCAGTATC
1 GCATTGCGATAGTCAGTATC
*
42955 GCATTGCGATAGTGAGTATC
1 GCATTGCGATAGTCAGTATC
42975 GCATTGCGAT
1 GCATTGCGAT
42985 TTTCCAAATT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (20 bp):
GCATTGCGATAGTCAGTATC
Found at i:43017 original size:20 final size:21
Alignment explanation
Indices: 42973--43024 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
42963 ATAGTGAGTA
*
42973 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
42994 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
43014 TCGCATTGCGA
1 TCGCATTGCGA
43025 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:43054 original size:143 final size:142
Alignment explanation
Indices: 42788--43086 Score: 342
Period size: 143 Copynumber: 2.1 Consensus size: 142
42778 TCGCTATGTA
* * *
42788 AATCGCATTGCGATAGTAAGATTCGCATTGCGATTTACGTATTCGCGTTGCGATTTTCCTAATTC
1 AATCGCATTGCGATAGTAAGATTCGCATTGCGATTGACGTATTCGCATTGCGATTTTCCAAATTC
* * *
42853 GCATTGCGAATTATGAAAATCGCTACGCGAATACGTAAATCGCAATGCGAATTAGGAAAATTGCA
66 GCATTGCGAATTAT-AAAATCGCTACGCGAATACGAAAATCGCAACGCGAATTAGGAAAATCGCA
42918 TTGCGATAGTCAGT
130 TTGCGATAGTCA-T
*
42932 -ATCGCATTGCGATAGTCAG-TATCGCATTGCGATAGTGA-GTA-TCGCATTGCGATTTTCCAAA
1 AATCGCATTGCGATAGTAAGAT-TCGCATTGCGAT--TGACGTATTCGCATTGCGATTTTCCAAA
* * * * **
42993 TTCGCATTGCGATTTACT-TATTCGC-ATTGCGAATTGGGAAAATCGCAACGCGAAATT-GGAAA
63 TTCGCATTGCGAATTA-TAAAATCGCTA-CGCGAA-TACGAAAATCGCAACGCG-AATTAGGAAA
43055 ATCGCATTGCGATAGTCAT
124 ATCGCATTGCGATAGTCAT
*
43074 AATCGCGTTGCGA
1 AATCGCATTGCGA
43087 ATCTGGAAAC
Statistics
Matches: 133, Mismatches: 14, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
141 1 0.01
142 12 0.09
143 110 0.83
144 8 0.06
145 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (142 bp):
AATCGCATTGCGATAGTAAGATTCGCATTGCGATTGACGTATTCGCATTGCGATTTTCCAAATTC
GCATTGCGAATTATAAAATCGCTACGCGAATACGAAAATCGCAACGCGAATTAGGAAAATCGCAT
TGCGATAGTCAT
Found at i:43066 original size:21 final size:22
Alignment explanation
Indices: 43014--43066 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
43004 ATTTACTTAT
43014 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
43035 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
43056 TCGCATTGCGA
1 TCGCATTGCGA
43067 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:48400 original size:23 final size:23
Alignment explanation
Indices: 48301--48396 Score: 138
Period size: 23 Copynumber: 4.2 Consensus size: 23
48291 GAAATGTGAG
*
48301 ATTCACATAAGAATGAAATCCAC
1 ATTCACATAGGAATGAAATCCAC
* *
48324 ATTCACATATGAATGAAATTCAC
1 ATTCACATAGGAATGAAATCCAC
*
48347 ATTCTCATAGGAATGAAATCCAC
1 ATTCACATAGGAATGAAATCCAC
* *
48370 ATTCCCATAGGAATGAAATCTAC
1 ATTCACATAGGAATGAAATCCAC
48393 ATTC
1 ATTC
48397 CCATGTTTGG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (23 bp):
ATTCACATAGGAATGAAATCCAC
Done.