Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002097.1 Hibiscus syriacus cultivar Beakdansim tig00004281_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: 57994
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2469 original size:35 final size:36
Alignment explanation
Indices: 2429--2579 Score: 184
Period size: 35 Copynumber: 4.2 Consensus size: 36
2419 TTTATAATGT
*
2429 TTTTTGGATTAGAAATAC-TCTTGGATTAGAAATAA
1 TTTTTGGATTAGAAATACTTTTTGGATTAGAAATAA
*
2464 TTTTTGATGATTAGAAATACTTTTTGGATTAGAAATAC
1 TTTTTG--GATTAGAAATACTTTTTGGATTAGAAATAA
* * * *
2502 TCTTT-GATTGGAAATACTTTTTGTATTATAAAT-A
1 TTTTTGGATTAGAAATACTTTTTGGATTAGAAATAA
* *
2536 TTCTTGGA-TAGAAATACTTTTTGGATTAGAAATAC
1 TTTTTGGATTAGAAATACTTTTTGGATTAGAAATAA
2571 TTTTTGGAT
1 TTTTTGGAT
2580 CATAAATCAA
Statistics
Matches: 96, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
34 25 0.26
35 40 0.42
37 12 0.12
38 19 0.20
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (36 bp):
TTTTTGGATTAGAAATACTTTTTGGATTAGAAATAA
Found at i:2586 original size:18 final size:18
Alignment explanation
Indices: 2429--2579 Score: 193
Period size: 18 Copynumber: 8.5 Consensus size: 18
2419 TTTATAATGT
2429 TTTTTGGATTAGAAATAC
1 TTTTTGGATTAGAAATAC
* *
2447 -TCTTGGATTAGAAATAA
1 TTTTTGGATTAGAAATAC
2464 TTTTTGATGATTAGAAATAC
1 TTTTTG--GATTAGAAATAC
2484 TTTTTGGATTAGAAATAC
1 TTTTTGGATTAGAAATAC
* *
2502 TCTTT-GATTGGAAATAC
1 TTTTTGGATTAGAAATAC
* *
2519 TTTTTGTATTATAAATA-
1 TTTTTGGATTAGAAATAC
*
2536 TTCTTGGA-TAGAAATAC
1 TTTTTGGATTAGAAATAC
2553 TTTTTGGATTAGAAATAC
1 TTTTTGGATTAGAAATAC
2571 TTTTTGGAT
1 TTTTTGGAT
2580 CATAAATCAA
Statistics
Matches: 113, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
16 7 0.06
17 43 0.38
18 46 0.41
20 17 0.15
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (18 bp):
TTTTTGGATTAGAAATAC
Found at i:3695 original size:15 final size:15
Alignment explanation
Indices: 3663--3705 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
3653 AAAGCCTCTT
3663 AATCATTCAGACTGCTA
1 AATCATTCAG--TGCTA
3680 AATCATTCAGTGCTA
1 AATCATTCAGTGCTA
*
3695 AACCATTCAGT
1 AATCATTCAGT
3706 TTTAACAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 15 0.60
17 10 0.40
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (15 bp):
AATCATTCAGTGCTA
Found at i:4634 original size:18 final size:20
Alignment explanation
Indices: 4611--4664 Score: 76
Period size: 18 Copynumber: 2.8 Consensus size: 20
4601 AATATAATTA
4611 TATATTAACTTATT-T-TAT
1 TATATTAACTTATTATATAT
4629 TATATTAACTTATTATATAT
1 TATATTAACTTATTATATAT
*
4649 TATTATTAACATATTA
1 TA-TATTAACTTATTA
4665 ATTATTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 14 0.44
19 1 0.03
20 5 0.16
21 12 0.38
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATTAACTTATTATATAT
Found at i:4654 original size:13 final size:14
Alignment explanation
Indices: 4592--4670 Score: 63
Period size: 15 Copynumber: 5.2 Consensus size: 14
4582 CCGTGACCAA
4592 ATTATATA-TAATAT
1 ATTATATATTAAT-T
4606 AATTATATATTAACTT
1 -ATTATATATTAA-TT
4622 ATTTTATTATATTAACTT
1 A--TTA-TATATTAA-TT
4640 ATTATATATT-ATT
1 ATTATATATTAATT
*
4653 ATTAACATATTAATT
1 ATT-ATATATTAATT
4668 ATT
1 ATT
4671 TTATTGTTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
13 5 0.09
14 7 0.12
15 21 0.38
16 7 0.12
17 4 0.07
18 12 0.21
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTATATATTAATT
Found at i:4668 original size:18 final size:19
Alignment explanation
Indices: 4605--4670 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 19
4595 ATATATAATA
4605 TAATTATATATTAACTTATT
1 TAATTAT-TATTAACTTATT
*
4625 TTATTA-TATTAACTTATT
1 TAATTATTATTAACTTATT
*
4643 ATATATTATTATTAACATA-T
1 -TA-ATTATTATTAACTTATT
4663 TAATTATT
1 TAATTATT
4671 TTATTGTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 18 0.45
19 3 0.08
20 10 0.25
21 9 0.22
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (19 bp):
TAATTATTATTAACTTATT
Found at i:4674 original size:23 final size:23
Alignment explanation
Indices: 4612--4681 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
4602 ATATAATTAT
4612 ATATTAACTTATTTTATTATATTAAC
1 ATATTAA-TTATTTTA-T-TATTAAC
* *
4638 TTATT-A-TATATTATTATTAAC
1 ATATTAATTATTTTATTATTAAC
*
4659 ATATTAATTATTTTATTGTTAAC
1 ATATTAATTATTTTATTATTAAC
4682 TTAATTAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 11 0.30
22 2 0.05
23 19 0.51
25 1 0.03
26 4 0.11
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (23 bp):
ATATTAATTATTTTATTATTAAC
Found at i:4725 original size:22 final size:23
Alignment explanation
Indices: 4700--4744 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
4690 AAATATGTTT
*
4700 TTATTTCATTTA-AAAAATATAA
1 TTATTTAATTTATAAAAATATAA
*
4722 TTATTTAATTTATTAAAATATAA
1 TTATTTAATTTATAAAAATATAA
4745 CTAAATTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TTATTTAATTTATAAAAATATAA
Found at i:12896 original size:112 final size:113
Alignment explanation
Indices: 12547--13008 Score: 713
Period size: 113 Copynumber: 4.1 Consensus size: 113
12537 GCTTGTCGTT
*
12547 GTGTCGATACTTTAT-AAAATATAT-GATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
* *
12610 CTGTCTATAAATGACAAAACAGATAAAGCGCTATCGGATATATTGAAA
66 CGGTCTATAAATGACAAAACAGATAAAGCGCTACCGGATATATTGAAA
12658 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATAGA-AAAA
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAAT-GACAAAA
* * * *
12722 CCGGTCTATTAATGACAAAACAGGTAAAGCGCTATCAGATATATTGAAA
65 CCGGTCTATAAATGACAAAACAGATAAAGCGCTACCGGATATATTGAAA
*
12771 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-ATAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
12835 CGGTCTATAAATGACAAAACTA-ATAAAGCGCTACCGGATATATTGAAA
66 CGGTCTATAAATGACAAAAC-AGATAAAGCGCTACCGGATATATTGAAA
*
12883 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGT--AAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
* * * * * * *
12946 CGATTTATAAATAACAAAATAGGTAAAGCGCTACCGGATATGTTGATA
66 CGGTCTATAAATGACAAAACAGATAAAGCGCTACCGGATATATTGAAA
12994 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
13009 TATAAGTATC
Statistics
Matches: 326, Mismatches: 19, Indels: 12
0.91 0.05 0.03
Matches are distributed among these distances:
110 1 0.00
111 85 0.26
112 109 0.33
113 129 0.40
114 2 0.01
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.26
Consensus pattern (113 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAAATGACAAAAC
CGGTCTATAAATGACAAAACAGATAAAGCGCTACCGGATATATTGAAA
Found at i:13117 original size:34 final size:30
Alignment explanation
Indices: 13079--13147 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 30
13069 TTGATATAAC
13079 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTA
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTA
* *
13113 AATTT-ACAATATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTA
13142 AATTTA
1 AATTTA
13148 TTCAAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 9 0.28
30 12 0.38
31 5 0.16
33 1 0.03
34 5 0.16
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTA
Found at i:13259 original size:19 final size:19
Alignment explanation
Indices: 13237--13310 Score: 86
Period size: 19 Copynumber: 4.2 Consensus size: 19
13227 TTCAAGATTG
13237 CCCAGGGGTACAGATTCCC
1 CCCAGGGGTACAGATTCCC
*
13256 CCCAGGGGTACAGA-T-AC
1 CCCAGGGGTACAGATTCCC
*
13273 CCC---GGTACAGATACCC
1 CCCAGGGGTACAGATTCCC
*
13289 CCCAGGGGTACCGATTCCC
1 CCCAGGGGTACAGATTCCC
13308 CCC
1 CCC
13311 TGTCTAAAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
14 8 0.18
16 4 0.09
17 4 0.09
18 1 0.02
19 28 0.62
ACGTcount: A:0.22, C:0.41, G:0.24, T:0.14
Consensus pattern (19 bp):
CCCAGGGGTACAGATTCCC
Found at i:13281 original size:14 final size:14
Alignment explanation
Indices: 13262--13289 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13252 TCCCCCCAGG
13262 GGTACAGATACCCC
1 GGTACAGATACCCC
13276 GGTACAGATACCCC
1 GGTACAGATACCCC
13290 CCAGGGGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.36, G:0.21, T:0.14
Consensus pattern (14 bp):
GGTACAGATACCCC
Found at i:13290 original size:33 final size:33
Alignment explanation
Indices: 13243--13308 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
13233 ATTGCCCAGG
*
13243 GGTACAGATTCCCCCCAGGGGTACAGATACCCC
1 GGTACAGATACCCCCCAGGGGTACAGATACCCC
* *
13276 GGTACAGATACCCCCCAGGGGTACCGATTCCCC
1 GGTACAGATACCCCCCAGGGGTACAGATACCCC
13309 CCTGTCTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.38, G:0.24, T:0.15
Consensus pattern (33 bp):
GGTACAGATACCCCCCAGGGGTACAGATACCCC
Found at i:13360 original size:20 final size:20
Alignment explanation
Indices: 13335--13374 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
13325 AAACAAATGT
13335 CCAGGGGTACCGATTCCCCC
1 CCAGGGGTACCGATTCCCCC
13355 CCAGGGGTACCGATTCCCCC
1 CCAGGGGTACCGATTCCCCC
13375 TGTTCAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.45, G:0.25, T:0.15
Consensus pattern (20 bp):
CCAGGGGTACCGATTCCCCC
Found at i:13774 original size:34 final size:32
Alignment explanation
Indices: 13731--13800 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
13721 TTTTGTAAAG
* *
13731 GGGAAAGGTTCTAGCTTAGCCCGTATAAAAGCTA
1 GGGAAAGGTTCTAGCTTAACCCGGA-AAAA-CTA
*
13765 GGGAAAGGTTCTAGTTTAACCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAACCCGGAAAAACTA
13797 GGGA
1 GGGA
13801 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 4 0.12
34 22 0.67
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAACCCGGAAAAACTA
Found at i:14782 original size:23 final size:23
Alignment explanation
Indices: 14756--14803 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
14746 AAATATGTCA
*
14756 ATATAAACGCTACCTATTATATT
1 ATATAAACGCTACCTAATATATT
* *
14779 ATATAAGCGCTATCTAATATATT
1 ATATAAACGCTACCTAATATATT
14802 AT
1 AT
14804 TATACTTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (23 bp):
ATATAAACGCTACCTAATATATT
Found at i:15607 original size:24 final size:24
Alignment explanation
Indices: 15580--15641 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
15570 GTTCGTGAAT
15580 GTTCGGTTATGTTTGTTTATGTTC
1 GTTCGGTTATGTTTGTTTATGTTC
15604 GTTCGGTTATGTTTGTTTATGTTC
1 GTTCGGTTATGTTTGTTTATGTTC
* **
15628 ATTCATTTATGTTT
1 GTTCGGTTATGTTT
15642 AACCCAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.11, C:0.08, G:0.21, T:0.60
Consensus pattern (24 bp):
GTTCGGTTATGTTTGTTTATGTTC
Found at i:16571 original size:16 final size:16
Alignment explanation
Indices: 16550--16592 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
16540 GTCTCTAACG
16550 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
16566 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
16582 TTTATGTTCGT
1 TTTATGTTCGT
16593 TTATTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:17612 original size:36 final size:36
Alignment explanation
Indices: 17557--17648 Score: 130
Period size: 36 Copynumber: 2.5 Consensus size: 36
17547 CCTCCACCCG
17557 ACCCGAATATGACCCGACTTTTTGAGATAAAATCCGA
1 ACCCG-ATATGACCCGACTTTTTGAGATAAAATCCGA
* * *
17594 ACCCGATTTGACCTGACTTTTTGTGATAAAATCCGA
1 ACCCGATATGACCCGACTTTTTGAGATAAAATCCGA
* *
17630 ACCCGGTCTGACCCGACTT
1 ACCCGATATGACCCGACTT
17649 AAAATAATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
36 44 0.90
37 5 0.10
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.27
Consensus pattern (36 bp):
ACCCGATATGACCCGACTTTTTGAGATAAAATCCGA
Found at i:22830 original size:194 final size:194
Alignment explanation
Indices: 22545--23027 Score: 755
Period size: 194 Copynumber: 2.6 Consensus size: 194
22535 CACTTAAAAA
*
22545 ACCCGACCCGAACAAAACAAAGTTTCATCC-A----ACCCGACCCGAATATATGAATTAGAAATC
1 ACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGACCCGAATATATGAATTAGAAATC
** *
22605 CGA-CCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCG
66 AAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCA
22669 ACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCG
131 ACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCG
*
22733 ACCCGACCCGAACAAAATAAATTTTCATCCGACCCGACCCGACCCGAATATATGAATTAGAAATC
1 ACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGACCCGAATATATGAATTAGAAATC
*
22798 AAACCCGACCCGACCCGAAATAATAAAAAATTATATTTATTTAATAAAAACAGTGACTTAATCCA
66 AAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCA
*
22863 ACCCGACCTGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCG
131 ACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCG
*
22927 ACCCGA--C---CAAAATAAAGTTTCACCCGACCCGACCCGACCCGAATATATGAATTAG-----
1 ACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGACCCGAATATATGAATTAGAAATC
* * *
22982 AAACCCGACCCAACCCGAAATAATAAAAAAATATTTTTATTCAATA
66 AAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATA
23028 TATAAATAAG
Statistics
Matches: 276, Mismatches: 13, Indels: 16
0.90 0.04 0.05
Matches are distributed among these distances:
184 42 0.15
188 28 0.10
189 47 0.17
192 1 0.00
193 30 0.11
194 128 0.46
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (194 bp):
ACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGACCCGAATATATGAATTAGAAATC
AAACCCGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATCCA
ACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCG
Found at i:25777 original size:2 final size:2
Alignment explanation
Indices: 25770--25799 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
25760 ATAGCAAACC
*
25770 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25800 CCGCTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:28891 original size:2 final size:2
Alignment explanation
Indices: 28884--28914 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28874 ATAATTGCTT
28884 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
28915 TACTGAAAAT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:32858 original size:30 final size:30
Alignment explanation
Indices: 32822--32888 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
32812 ATAAAGTATG
* *
32822 CAAAAGTTCAAGGACCAAAAGGGTAATTTT
1 CAAAAGTTCAAGGACCAAAACGATAATTTT
* *
32852 CAAAAGTTTAAGGACCAAAACTATAATTTT
1 CAAAAGTTCAAGGACCAAAACGATAATTTT
32882 CAAAAGT
1 CAAAAGT
32889 CATGTATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.25
Consensus pattern (30 bp):
CAAAAGTTCAAGGACCAAAACGATAATTTT
Found at i:34079 original size:19 final size:21
Alignment explanation
Indices: 34046--34084 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
34036 TAGAAATTAA
*
34046 TGTTAGAGTGATG-AATTTGG
1 TGTTAGAATGATGAAATTTGG
34066 TGTTAGAATG-TGAAATTTG
1 TGTTAGAATGATGAAATTTG
34085 ACTATTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (21 bp):
TGTTAGAATGATGAAATTTGG
Found at i:36460 original size:21 final size:21
Alignment explanation
Indices: 36404--36462 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
36394 ACTCTGTGGT
*
36404 AGTGGCATCTGAACCGATTGC
1 AGTGACATCTGAACCGATTGC
** * *
36425 AGTGATGTTTAAACCGATTGC
1 AGTGACATCTGAACCGATTGC
* *
36446 GGTGCCATCTGAACCGA
1 AGTGACATCTGAACCGA
36463 CAATGTACCT
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (21 bp):
AGTGACATCTGAACCGATTGC
Found at i:38317 original size:64 final size:65
Alignment explanation
Indices: 38248--38408 Score: 238
Period size: 65 Copynumber: 2.5 Consensus size: 65
38238 GTGCACTAAG
*
38248 TGTGCATCGATGCATAAAATGCATTCGATGTTTTGA-AAAAGCC-TGAGTGCATCGATGCATGGT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAA-CCTTGAGTGCATCGATGCATGGT
38311 -
65 A
* *
38311 TGGTGCATCGATACATCAAATGCATTCGATGTTTTCATAAAACCTTGAGTGCATCGATGCATGGT
1 T-GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTTGAGTGCATCGATGCATGGT
38376 A
65 A
* *
38377 TATGCATCGATGCATGAAATGCATTCGATGTT
1 TGTGCATCGATGCATAAAATGCATTCGATGTT
38409 CAATTTATTC
Statistics
Matches: 88, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
63 1 0.01
64 34 0.39
65 52 0.59
66 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.32
Consensus pattern (65 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCTTGAGTGCATCGATGCATGGTA
Found at i:38448 original size:65 final size:64
Alignment explanation
Indices: 38249--38458 Score: 223
Period size: 65 Copynumber: 3.2 Consensus size: 64
38239 TGCACTAAGT
* * *
38249 GTGCATCGATGCATAAAATGCATTCGATGTTTTGA-AAAAGCC-TGAGTGCATCGATGCATGGTT
1 GTGCATCGATACATCAAATGCATTCGATG-TTTCATAAAA-CCATGAGTGCATCGATGCATGGTT
38312 G
64 G
*
38313 GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAAACCTTGAGTGCATCGATGCATGGTAT
1 GTGCATCGATACATCAAATGCATTCGATG-TTTCATAAAACCATGAGTGCATCGATGCATGGT-T
38378 -
64 G
* * * * **
38378 ATGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATACATCAAATGCATTCGATGTTTC-A-TAAAACCATGAGTGCATCGATGCATGG-T
38441 TG
63 TG
*
38443 GTGCATCGGTACATCA
1 GTGCATCGATACATCA
38459 CTTTGAAAAA
Statistics
Matches: 125, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
63 3 0.02
64 52 0.42
65 69 0.55
66 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (64 bp):
GTGCATCGATACATCAAATGCATTCGATGTTTCATAAAACCATGAGTGCATCGATGCATGGTTG
Found at i:48229 original size:17 final size:17
Alignment explanation
Indices: 48209--48251 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
48199 ACCGTTGGAA
48209 CACTTAGTGCATTGGTG
1 CACTTAGTGCATTGGTG
48226 CACTTAGTGCATTGGTG
1 CACTTAGTGCATTGGTG
*
48243 CACTAAGTG
1 CACTTAGTG
48252 TGCATCGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.33
Consensus pattern (17 bp):
CACTTAGTGCATTGGTG
Found at i:53114 original size:20 final size:20
Alignment explanation
Indices: 53089--53139 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
53079 CACAGAATGT
53089 AAGATTACCAGTGAAAATAA
1 AAGATTACCAGTGAAAATAA
*
53109 AAGATTACCAGTGAGAATAA
1 AAGATTACCAGTGAAAATAA
*
53129 AAGATTGCCAG
1 AAGATTACCAG
53140 GGAATATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.20
Consensus pattern (20 bp):
AAGATTACCAGTGAAAATAA
Found at i:55382 original size:44 final size:46
Alignment explanation
Indices: 55318--55407 Score: 166
Period size: 44 Copynumber: 2.0 Consensus size: 46
55308 CCTTTTACTC
55318 CACCTATTTAATAGTACTCGGATGTAAGTGTCA-AAATTGTATGTG
1 CACCTATTTAATAGTACTCGGATGTAAGTGTCAGAAATTGTATGTG
55363 CACCTATTT-ATAGTACTCGGATGTAAGTGTCAGAAATTGTATGTG
1 CACCTATTTAATAGTACTCGGATGTAAGTGTCAGAAATTGTATGTG
55408 TCTCAAAGCA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 23 0.52
45 21 0.48
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (46 bp):
CACCTATTTAATAGTACTCGGATGTAAGTGTCAGAAATTGTATGTG
Done.