Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000854.1 Hibiscus syriacus cultivar Beakdansim tig00001657_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: 64110
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5858 original size:16 final size:16
Alignment explanation
Indices: 5837--5867 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5827 ATTAAAAGAC
*
5837 TTGTTTTTATATATAA
1 TTGTTTATATATATAA
5853 TTGTTTATATATATA
1 TTGTTTATATATATA
5868 TAGGTATGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
TTGTTTATATATATAA
Found at i:12864 original size:6 final size:6
Alignment explanation
Indices: 12853--12881 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12843 GATAAAAGGA
12853 ATATGG ATATGG ATATGG ATATGG ATATG
1 ATATGG ATATGG ATATGG ATATGG ATATG
12882 AATAATAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (6 bp):
ATATGG
Found at i:18023 original size:24 final size:23
Alignment explanation
Indices: 17981--18025 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
17971 AATATTTAAT
*
17981 TATATAATATTTATATAAAAATC
1 TATATAATATATATATAAAAATC
*
18004 TATATGAATATATATTTAAAAA
1 TATAT-AATATATATATAAAAA
18026 AAACTTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TATATAATATATATATAAAAATC
Found at i:20737 original size:2 final size:2
Alignment explanation
Indices: 20730--20754 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20720 TTGTGCTAAT
20730 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 T
20755 CGCACGTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23930 original size:37 final size:37
Alignment explanation
Indices: 23880--23950 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
23870 GTCTTTAGGA
*
23880 TATAAATGGTTTAAACATTTATTTTATTAAAATATGT
1 TATAAATAGTTTAAACATTTATTTTATTAAAATATGT
*
23917 TATAAATAGTTTAAGCATTTATTTTATTAAAATA
1 TATAAATAGTTTAAACATTTATTTTATTAAAATA
23951 AAACAAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (37 bp):
TATAAATAGTTTAAACATTTATTTTATTAAAATATGT
Found at i:30911 original size:21 final size:21
Alignment explanation
Indices: 30885--30933 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
30875 ACCTAATATT
30885 ACAATGTCAAAATTAGGTGCA
1 ACAATGTCAAAATTAGGTGCA
30906 ACAATGTCAAAATTAGGTGCA
1 ACAATGTCAAAATTAGGTGCA
*
30927 ATAATGT
1 ACAATGT
30934 TTGAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (21 bp):
ACAATGTCAAAATTAGGTGCA
Found at i:35537 original size:21 final size:21
Alignment explanation
Indices: 35512--35559 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
35502 CCTAATATTG
35512 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
35533 CAATGTCAGAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
35554 TAATGT
1 CAATGT
35560 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:36476 original size:23 final size:26
Alignment explanation
Indices: 36430--36480 Score: 72
Period size: 23 Copynumber: 2.1 Consensus size: 26
36420 TGAAACTCCT
36430 TTTGTCCTTTCGATTTAACCCACAAC
1 TTTGTCCTTTCGATTTAACCCACAAC
*
36456 TTTGT-CTTTC-A-TTATCCCACAAC
1 TTTGTCCTTTCGATTTAACCCACAAC
36479 TT
1 TT
36481 CTGCTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 13 0.54
24 1 0.04
25 5 0.21
26 5 0.21
ACGTcount: A:0.22, C:0.29, G:0.06, T:0.43
Consensus pattern (26 bp):
TTTGTCCTTTCGATTTAACCCACAAC
Found at i:37497 original size:27 final size:27
Alignment explanation
Indices: 37464--37529 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
37454 ATTAAAATTA
* *
37464 TTATATATTTTAAATATTTTTTTATATTT
1 TTATA-ATTTTAAATATGTTTTTAT-CTT
*
37493 TTATAATGTT-AATATGTTTTTATCTT
1 TTATAATTTTAAATATGTTTTTATCTT
37519 TTATAATTTTA
1 TTATAATTTTA
37530 TAAGTTTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 11 0.34
27 12 0.38
28 4 0.12
29 5 0.16
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (27 bp):
TTATAATTTTAAATATGTTTTTATCTT
Found at i:47976 original size:170 final size:168
Alignment explanation
Indices: 47673--47977 Score: 391
Period size: 168 Copynumber: 1.8 Consensus size: 168
47663 GAGCATTGTA
* * * * * *
47673 AGATGGATATGACTATCTGTTAGCTTTGTACTTGGGGGTTGGGGAAAGTAAAAAAATGATAAAAA
1 AGATGGATATGACTAACTGCTAGCCTTGTACTTGGAGGTTGGAGAAAGAAAAAAAATGATAAAAA
* * * * *
47738 GCAAGCTCGTATATGGTGATGTGTGAGTTTTCTACCTTAAAATTTTGATAAGCACGCTTTTAGAG
66 GCAAGCTCGTATATAGTGATATGTGAGTTGTCTACCTAAAAATTTTGACAAGCACGCTTTTAGAG
47803 GACATTGAAGTGCTTGCTTGTTAAGAATAACCACTGAG
131 GACATTGAAGTGCTTGCTTGTTAAGAATAACCACTGAG
47841 AGATGGATATGACTAACTGCTA-CCTTGTACTTGGAGGTTGGAGAAAGAAAAAATAATGATGAAA
1 AGATGGATATGACTAACTGCTAGCCTTGTACTTGGAGGTTGGAGAAAGAAAAAA-AATGAT-AAA
* * * ** *
47905 AA-CTAGCTTGTCT-TCAGTGATATGTGAGTGTGTCTACCCTAAAAATTTTGACAAGCTTGTTTT
64 AAGCAAGCTCGTATAT-AGTGATATGTGAGT-TGTCTA-CCTAAAAATTTTGACAAGCACGCTTT
47968 TAGAGGACAT
126 TAGAGGACAT
47978 GTTCATTCAA
Statistics
Matches: 115, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
167 28 0.24
168 46 0.40
169 10 0.09
170 31 0.27
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (168 bp):
AGATGGATATGACTAACTGCTAGCCTTGTACTTGGAGGTTGGAGAAAGAAAAAAAATGATAAAAA
GCAAGCTCGTATATAGTGATATGTGAGTTGTCTACCTAAAAATTTTGACAAGCACGCTTTTAGAG
GACATTGAAGTGCTTGCTTGTTAAGAATAACCACTGAG
Found at i:51726 original size:20 final size:21
Alignment explanation
Indices: 51701--51752 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
51691 TTTTCCCAAT
*
51701 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
51721 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
51742 TCGCAATGCGA
1 TCGCAATGCGA
51753 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:51766 original size:20 final size:20
Alignment explanation
Indices: 51741--51854 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
51731 AATTGGGAAA
*
51741 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
51761 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
51781 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
51802 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
51822 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
51842 TTCGCAACGCGAT
1 ATCGCAACGCGAT
51855 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:51786 original size:61 final size:61
Alignment explanation
Indices: 51738--51854 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
51728 GCGAATTGGG
* * * *
51738 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAATGCGATAATAC
* * * *
51799 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAATGCGAT
51855 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAATGCGATAATAC
Found at i:52410 original size:19 final size:19
Alignment explanation
Indices: 52372--52438 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
52362 TTCGAGAATG
52372 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
52392 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* **
52411 AAAAACGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
52430 AAAATCGCA
1 AAAATCGCA
52439 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 28 0.72
20 11 0.28
ACGTcount: A:0.49, C:0.25, G:0.16, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:52456 original size:19 final size:19
Alignment explanation
Indices: 52434--52584 Score: 159
Period size: 19 Copynumber: 8.1 Consensus size: 19
52424 GAAACCAAAA
*
52434 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
52453 TCGCGTTGCGATTTTCTTT
1 TCGCGTTGCGATTTTCATT
52472 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
52491 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
52505 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
52524 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
52543 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
52563 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
52583 TC
1 TC
52585 AACCAAAAGA
Statistics
Matches: 113, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
14 9 0.08
16 2 0.02
17 3 0.03
19 66 0.58
20 32 0.28
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:54736 original size:41 final size:41
Alignment explanation
Indices: 54662--54861 Score: 179
Period size: 41 Copynumber: 4.8 Consensus size: 41
54652 GACTCGCCTG
* * *
54662 TCATCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * ** *
54703 TCATTCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCATTG
1 TCATCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * *
54744 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGG-CCCTA
1 TCAT-CCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * * *
54785 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCA-TCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * *
54827 TCATCGTTGAAGAGGTCCA-TCCCACCATTCAAGAG
1 TCATC-CTCAAGA-GTCCACTCCCACCGTTCAAGAG
54862 CCCGATTCAC
Statistics
Matches: 124, Mismatches: 30, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
41 69 0.56
42 51 0.41
43 4 0.03
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.23
Consensus pattern (41 bp):
TCATCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:54834 original size:21 final size:21
Alignment explanation
Indices: 54727--54841 Score: 56
Period size: 21 Copynumber: 5.5 Consensus size: 21
54717 CCCCTCCCAC
*
54727 CGTTCAAGAGGCCATTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
** * *
54748 CCCTCAAGAGTCCACT-CCTAT
1 CGTTCAAGAGGCCACTGTC-AT
* *
54769 CGTTGAAGAGGCC-CTATCATT
1 CGTTCAAGAGGCCACTGTCA-T
* * * * ** *
54790 C-CTCGAGAGTCCCCTCCCAC
1 CGTTCAAGAGGCCACTGTCAT
54810 CGTTCAAGAGGCCACTGTCAT
1 CGTTCAAGAGGCCACTGTCAT
*
54831 CGTTGAAGAGG
1 CGTTCAAGAGG
54842 TCCATCCCAC
Statistics
Matches: 64, Mismatches: 25, Indels: 10
0.65 0.25 0.10
Matches are distributed among these distances:
20 12 0.19
21 52 0.81
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGGCCACTGTCAT
Found at i:54840 original size:83 final size:83
Alignment explanation
Indices: 54659--54831 Score: 314
Period size: 83 Copynumber: 2.1 Consensus size: 83
54649 CCCGACTCGC
54659 CTGTCAT-CCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCTCGAGAGTCCCCTC
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCTCGAGAGTCCCCTC
54723 CCACCGTTCAAGAGGCCA
66 CCACCGTTCAAGAGGCCA
*
54741 TTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGG-CCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATT-CTCGAGAGTCCCCT
54805 CCCACCGTTCAAGAGGCCA
65 CCCACCGTTCAAGAGGCCA
54824 CTGTCATC
1 CTGTCATC
54832 GTTGAAGAGG
Statistics
Matches: 87, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
82 16 0.18
83 71 0.82
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.24
Consensus pattern (83 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCTCGAGAGTCCCCTC
CCACCGTTCAAGAGGCCA
Found at i:54861 original size:83 final size:83
Alignment explanation
Indices: 54659--54861 Score: 259
Period size: 83 Copynumber: 2.5 Consensus size: 83
54649 CCCGACTCGC
* * * *
54659 CTGTCAT-CCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCTCGAGAGTCCCCTC
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCTCGAGAGTCCCCTC
54723 CCACCGTTCAAGAGGCCA
66 CCACCGTTCAAGAGGCCA
* * * * *
54741 TTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGG-CCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATT-CTCGAGAGTCCCCT
54805 CCCACCGTTCAAGAGGCCA
65 CCCACCGTTCAAGAGGCCA
** *
54824 CTGTCATCGTTGAAGAGGTCCA-TCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
54862 CCCGATTCAC
Statistics
Matches: 109, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
82 16 0.15
83 88 0.81
84 5 0.05
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.24
Consensus pattern (83 bp):
CTGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCTCGAGAGTCCCCTC
CCACCGTTCAAGAGGCCA
Found at i:56246 original size:13 final size:14
Alignment explanation
Indices: 56215--56249 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
56205 ATTGTTTAAT
56215 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
56229 TGATTTGTAAAA-G
1 TGATTTGTAAAAGG
56242 TGATTTGT
1 TGATTTGT
56250 TTAATTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:56501 original size:65 final size:65
Alignment explanation
Indices: 56405--56535 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 65
56395 ACGCGAAATT
* *
56405 AAATTCGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGC-ATTTTCATTTCGTATTGCG
1 AAATTAGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
*
56469 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGA-TTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
56534 G
65 G
56535 A
1 A
56536 TAGTAATTTC
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
64 14 0.23
65 29 0.47
66 19 0.31
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (65 bp):
AAATTAGCGTTGCGATTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
Found at i:56502 original size:19 final size:19
Alignment explanation
Indices: 56478--56536 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
56468 GAAATTAGCG
56478 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
56497 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
56511 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
56530 TTGCGAT
1 TTGCGAT
56537 AGTAATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:56536 original size:33 final size:33
Alignment explanation
Indices: 56412--56536 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
56402 ATTAAATTCG
*
56412 CGTTGCGA-TTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* * **
56444 CGTTGC-ATTTTCATTTCGTATTGCGAAAT-TAG
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCTCT
56476 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
56509 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
56537 AGTAATTTCC
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
31 1 0.01
32 30 0.38
33 49 0.61
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:59034 original size:24 final size:24
Alignment explanation
Indices: 59000--59053 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
58990 CTGAAACATC
*
59000 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
59024 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
59048 ATCAAA
1 ATCAAA
59054 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:59813 original size:20 final size:20
Alignment explanation
Indices: 59788--59838 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
59778 TGTATTATCT
59788 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
59808 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
59828 CGTTGCGAAAG
1 CGTTGCGAAAG
59839 GCAATCATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.31, T:0.20
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:60083 original size:19 final size:20
Alignment explanation
Indices: 60045--60094 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
60035 CATTCATTGA
*
60045 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
60065 CTATCGCAACGTG-AAATGG
1 CTATCGCAACGCGAAAATGG
60084 CTATCGCAACG
1 CTATCGCAACG
60095 ACAAAATCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:60144 original size:14 final size:14
Alignment explanation
Indices: 60125--60178 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
60115 GAAAATCGCA
60125 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
60139 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
60156 CATTGCGATTCTCTCG
1 --TTGCGATTTTCTCG
60172 TTGCGAT
1 TTGCGAT
60179 AGTCAATTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:60144 original size:33 final size:33
Alignment explanation
Indices: 60107--60177 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
60097 AAAATCGCAA
*
60107 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
** ** **
60140 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
60173 TGCGA
1 TGCGA
60178 TAGTCAATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
Found at i:60197 original size:33 final size:33
Alignment explanation
Indices: 60120--60183 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
60110 GAAATGAAAA
* **
60120 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCATT
60153 TCGCATTGCGATTCTCTCGTTGCGATAGTCA
1 TCGCATTGCGATTCTCTCGTTGCGATAGTCA
60184 ATTTGTGTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.42
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTTGCGATAGTCATT
Found at i:60310 original size:14 final size:14
Alignment explanation
Indices: 60291--60327 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
60281 CATCAATTAA
60291 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
60305 ACAAATCATCTTTT
1 ACAAATCAACATTT
60319 ACAAATCAA
1 ACAAATCAA
60328 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:62098 original size:24 final size:23
Alignment explanation
Indices: 62069--62136 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 23
62059 ATGCTCAGAT
62069 AACATTCCAGAAGTAAGCAATATA
1 AACATTCCAGAAG-AAGCAATATA
* *
62093 AACATT--AAAAGGACAACATATATA
1 AACATTCCAGAA-GA-AGCA-ATATA
62117 AACATTCCAGAAGAAG-AATA
1 AACATTCCAGAAGAAGCAATA
62137 GTTACTTTCG
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
22 7 0.20
23 5 0.14
24 18 0.51
25 2 0.06
26 3 0.09
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.19
Consensus pattern (23 bp):
AACATTCCAGAAGAAGCAATATA
Found at i:62187 original size:20 final size:20
Alignment explanation
Indices: 62162--62215 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
62152 CGAAACTTAA
62162 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
62182 ATCGCAACGCTG-AAATGGCT
1 ATCGCAACGC-GAAAATGACT
* *
62202 ATCGTAATGCGAAA
1 ATCGCAACGCGAAA
62216 TAAAAATCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:62283 original size:19 final size:18
Alignment explanation
Indices: 62233--62283 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
62223 CGCAACGACA
**
62233 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAAAC
*
62251 AAATCGCAACGCGAAACAC
1 AAATCGCAATGCGAAA-AC
*
62270 AAATCGCATTGCGA
1 AAATCGCAATGCGA
62284 TTTTCATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.14
Consensus pattern (18 bp):
AAATCGCAATGCGAAAAC
Found at i:62314 original size:14 final size:14
Alignment explanation
Indices: 62295--62352 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
62285 TTTCATTTCG
62295 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
62309 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
62325 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
62341 CGTTGCGATTTT
1 CGTTGCGATTTT
62353 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:62325 original size:32 final size:33
Alignment explanation
Indices: 62278--62368 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
62268 ACAAATCGCA
*
62278 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
62311 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
62343 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
62369 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:62387 original size:20 final size:19
Alignment explanation
Indices: 62353--62406 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
62343 TTGCGATTTT
*
62353 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
62372 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
62392 CATTTTCGTGTTGCG
1 CA-TTTCGCGTTGCG
62407 GAAAAGTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.17
20 22 0.73
21 3 0.10
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:62932 original size:18 final size:18
Alignment explanation
Indices: 62890--62932 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
62880 CGATCAGATG
* *
62890 ATGGCTCTGGGTGAGGTG
1 ATGGCTCTGGGCGAGGTA
*
62908 ATAGCTCTGGGCGAGGTA
1 ATGGCTCTGGGCGAGGTA
62926 ATGGCTC
1 ATGGCTC
62933 CCGAAGTGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.26
Consensus pattern (18 bp):
ATGGCTCTGGGCGAGGTA
Done.