Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012527.1 Kokia drynarioides strain JFW-HI SEQ_127534, 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: 106758
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:1893 original size:23 final size:22
Alignment explanation
Indices: 1861--2051 Score: 135
Period size: 23 Copynumber: 8.4 Consensus size: 22
1851 GCTGGGGAAA
1861 CAGTAAGCACACACAGTGCAAT
1 CAGTAAGCACACACAGTGCAAT
*
1883 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAAGCACACACAGTGCAAT
* * * *
1906 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAAGCACACACAGTGC-AAT
*
1929 CAGTAAGCACACGA-AGTGCGAAA
1 CAGTAAGCACAC-ACAGTGC-AAT
*
1952 CAGTAAGCACACGA-AGTGCGAAA
1 CAGTAAGCACAC-ACAGTGC-AAT
1975 CAGTAAGCACACGA-AGTGCGAAAT
1 CAGTAAGCACAC-ACAGTGC--AAT
1999 -AGTAAGCACACGA-AGTGCGAAAT
1 CAGTAAGCACAC-ACAGTGC--AAT
*
2022 -AGTAAGCACACGA-AGTGCGAAA
1 CAGTAAGCACAC-ACAGTGC-AAT
2044 CAGTAAGC
1 CAGTAAGC
2052 GCGCTAGCGT
Statistics
Matches: 151, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
22 18 0.12
23 130 0.86
24 3 0.02
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.12
Consensus pattern (22 bp):
CAGTAAGCACACACAGTGCAAT
Found at i:1980 original size:46 final size:45
Alignment explanation
Indices: 1833--2051 Score: 223
Period size: 46 Copynumber: 4.7 Consensus size: 45
1823 CGAAGTACTT
1833 AACAGTAAGCACAC-AAGTGCTGGGGAAACAGTAAGCACACACAGTGCA
1 AACAGTAAGCACACGAAGTGC----GAAACAGTAAGCACACACAGTGCA
* * * * * * *
1881 ATCCAGTAGGCACAC-ACAGTGC-AATCAGTAGGCGCACATAGCGCA
1 A-ACAGTAAGCACACGA-AGTGCGAAACAGTAAGCACACACAGTGCA
1926 AATCAGTAAGCACACGAAGTGCGAAACAGTAAGCACACGA-AGTGCGA
1 AA-CAGTAAGCACACGAAGTGCGAAACAGTAAGCACAC-ACAGTGC-A
*
1973 AACAGTAAGCACACGAAGTGCGAAATAGTAAGCACACGA-AGTGCGA
1 AACAGTAAGCACACGAAGTGCGAAACAGTAAGCACAC-ACAGTGC-A
*
2019 AATAGTAAGCACACGAAGTGCGAAACAGTAAGC
1 AACAGTAAGCACACGAAGTGCGAAACAGTAAGC
2052 GCGCTAGCGT
Statistics
Matches: 148, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
45 35 0.24
46 91 0.61
47 4 0.03
48 1 0.01
49 12 0.08
50 5 0.03
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.11
Consensus pattern (45 bp):
AACAGTAAGCACACGAAGTGCGAAACAGTAAGCACACACAGTGCA
Found at i:2014 original size:69 final size:68
Alignment explanation
Indices: 1833--2051 Score: 241
Period size: 69 Copynumber: 3.1 Consensus size: 68
1823 CGAAGTACTT
* * *
1833 AACAGTAAGCACACAAGTGCTGGGGAAACAGTAAGCACAC-ACAGTGC-AATCCAGTAGGCACAC
1 AACAGTAAGCACACAAGTGC----GAAATAGTAAGCACACGA-AGTGCGAA-ACAGTAAGCACAC
1896 -ACAGTGC-A
60 GA-AGTGCGA
* * * *
1904 ATCAGTAGGCGCACATAGCGC-AAATCAGTAAGCACACGAAGTGCGAAACAGTAAGCACACGAAG
1 AACAGTAAGCACACA-AGTGCGAAAT-AGTAAGCACACGAAGTGCGAAACAGTAAGCACACGAAG
1968 TGCGA
64 TGCGA
*
1973 AACAGTAAGCACACGAAGTGCGAAATAGTAAGCACACGAAGTGCGAAATAGTAAGCACACGAAGT
1 AACAGTAAGCACAC-AAGTGCGAAATAGTAAGCACACGAAGTGCGAAACAGTAAGCACACGAAGT
2038 GCGA
65 GCGA
2042 AACAGTAAGC
1 AACAGTAAGC
2052 GCGCTAGCGT
Statistics
Matches: 128, Mismatches: 12, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
67 3 0.02
68 32 0.25
69 72 0.56
70 5 0.04
71 12 0.09
72 4 0.03
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.11
Consensus pattern (68 bp):
AACAGTAAGCACACAAGTGCGAAATAGTAAGCACACGAAGTGCGAAACAGTAAGCACACGAAGTG
CGA
Found at i:4160 original size:3 final size:3
Alignment explanation
Indices: 4152--4176 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4142 TTTATTCACC
4152 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
4177 GTTAGGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5871 original size:49 final size:46
Alignment explanation
Indices: 5796--5902 Score: 142
Period size: 49 Copynumber: 2.3 Consensus size: 46
5786 TCCGAATAAG
* *
5796 AAAAGGCAAAACTACGTCGTTTTGATAAATGTTTACCCTTTCTAAAGTT
1 AAAAGGCAAAACTACGTCATTTTGATAAATGTTTA-CCTAT-T-AAGTT
* * *
5845 AAAAGGTAAAATTATGTCATTTTGATAAATGTTTACCTATTAAGTT
1 AAAAGGCAAAACTACGTCATTTTGATAAATGTTTACCTATTAAGTT
5891 AAAAGGCAAAAC
1 AAAAGGCAAAAC
5903 CATTATATTG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
46 15 0.29
47 1 0.02
48 4 0.08
49 31 0.61
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (46 bp):
AAAAGGCAAAACTACGTCATTTTGATAAATGTTTACCTATTAAGTT
Found at i:6415 original size:22 final size:22
Alignment explanation
Indices: 6387--6468 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
6377 GTTATATTGT
*
6387 TGTTTTGG-TGCTATTTTTTTAC
1 TGTTTTGGTTACT-TTTTTTTAC
* * *
6409 TGTTTTGGTTGCTCTTTTTTGC
1 TGTTTTGGTTACTTTTTTTTAC
*
6431 TGTTTT-GATAC-TTTTTTTAC
1 TGTTTTGGTTACTTTTTTTTAC
*
6451 TGTTTTGGTTACTATTTT
1 TGTTTTGGTTACTTTTTT
6469 GGTGTTGTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
20 13 0.27
21 7 0.14
22 25 0.51
23 4 0.08
ACGTcount: A:0.09, C:0.10, G:0.17, T:0.65
Consensus pattern (22 bp):
TGTTTTGGTTACTTTTTTTTAC
Found at i:6483 original size:21 final size:21
Alignment explanation
Indices: 6459--6565 Score: 119
Period size: 21 Copynumber: 5.0 Consensus size: 21
6449 ACTGTTTTGG
*
6459 TTACTATTTTGGTGTTGTTTT
1 TTACTGTTTTGGTGTTGTTTT
6480 TTACTGTTTTGGTGTTGTTTT
1 TTACTGTTTTGGTGTTGTTTT
6501 TTACTGTTTTGGTGTTG--TT
1 TTACTGTTTTGGTGTTGTTTT
* **
6520 TTGCTGTTATTTTTGTTGTTATTT
1 TTACTGTT-TTGGTGTTG-T-TTT
*
6544 TTACTGTTTTTGTTGTTGTTTT
1 TTACTG-TTTTGGTGTTGTTTT
6566 GATGTTATTT
Statistics
Matches: 74, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
19 9 0.12
20 7 0.09
21 37 0.50
22 3 0.04
23 1 0.01
24 15 0.20
25 2 0.03
ACGTcount: A:0.07, C:0.05, G:0.21, T:0.68
Consensus pattern (21 bp):
TTACTGTTTTGGTGTTGTTTT
Found at i:6539 original size:12 final size:12
Alignment explanation
Indices: 6518--6588 Score: 60
Period size: 12 Copynumber: 6.2 Consensus size: 12
6508 TTTGGTGTTG
*
6518 TTTTGCTGTTAT
1 TTTTGTTGTTAT
6530 TTTTGTTGTTAT
1 TTTTGTTGTTAT
**
6542 TTTTACTG---T
1 TTTTGTTGTTAT
*
6551 TTTTGTTGTT-G
1 TTTTGTTGTTAT
*
6562 TTTTGATGTTAT
1 TTTTGTTGTTAT
*
6574 TTTGGTTGTTAT
1 TTTTGTTGTTAT
6586 TTT
1 TTT
6589 GGTTATTTGA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
9 7 0.15
11 9 0.20
12 30 0.65
ACGTcount: A:0.08, C:0.03, G:0.18, T:0.70
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:6555 original size:44 final size:43
Alignment explanation
Indices: 6459--6588 Score: 149
Period size: 44 Copynumber: 3.0 Consensus size: 43
6449 ACTGTTTTGG
* * **
6459 TTACTATTTTGGTGTTGTTTTTTACTGTT-TTGGTGTTG-T-TTT
1 TTACTGTTTTGGTGTTG--TTTTGCTGTTATTTTTGTTGTTATTT
6501 TTACTGTTTTGGTGTTGTTTTGCTGTTATTTTTGTTGTTATTT
1 TTACTGTTTTGGTGTTGTTTTGCTGTTATTTTTGTTGTTATTT
* * *
6544 TTACTGTTTTTGTTGTTGTTTTGATGTTATTTTGGTTGTTATTT
1 TTACTG-TTTTGGTGTTGTTTTGCTGTTATTTTTGTTGTTATTT
6588 T
1 T
6589 GGTTATTTGA
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
40 9 0.12
41 7 0.09
42 17 0.22
43 9 0.12
44 35 0.45
ACGTcount: A:0.08, C:0.04, G:0.21, T:0.68
Consensus pattern (43 bp):
TTACTGTTTTGGTGTTGTTTTGCTGTTATTTTTGTTGTTATTT
Found at i:6592 original size:12 final size:11
Alignment explanation
Indices: 6507--6589 Score: 64
Period size: 11 Copynumber: 7.5 Consensus size: 11
6497 TTTTTTACTG
* *
6507 TTTTGGTGTTG
1 TTTTGTTGTTA
*
6518 TTTTGCTGTTA
1 TTTTGTTGTTA
6529 TTTTTGTTGTTA
1 -TTTTGTTGTTA
6541 TTTT-TACTG-T-
1 TTTTGT--TGTTA
*
6551 TTTTGTTGTTG
1 TTTTGTTGTTA
*
6562 TTTTGATGTTA
1 TTTTGTTGTTA
6573 TTTTGGTTGTTA
1 TTTT-GTTGTTA
6585 TTTTG
1 TTTTG
6590 GTTATTTGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
9 2 0.03
10 6 0.10
11 29 0.49
12 22 0.37
ACGTcount: A:0.07, C:0.02, G:0.22, T:0.69
Consensus pattern (11 bp):
TTTTGTTGTTA
Found at i:12823 original size:24 final size:24
Alignment explanation
Indices: 12768--12814 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
12758 TTTATTCTCC
*
12768 CAGTTAAATTTTGCTATTTTTCCA
1 CAGTTAAATTCTGCTATTTTTCCA
*
12792 CAGATAAATTCTGCTATCTTTTC
1 CAGTTAAATTCTGCTAT-TTTTC
12815 TCAATTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.47
Consensus pattern (24 bp):
CAGTTAAATTCTGCTATTTTTCCA
Found at i:13248 original size:16 final size:16
Alignment explanation
Indices: 13229--13261 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13219 CTGCAATTTT
13229 TTTATATAAAAA-TATA
1 TTTATA-AAAAATTATA
13245 TTTATAAAAAATTATA
1 TTTATAAAAAATTATA
13261 T
1 T
13262 AAAAAATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTATAAAAAATTATA
Found at i:13264 original size:12 final size:12
Alignment explanation
Indices: 13230--13268 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
13220 TGCAATTTTT
13230 TTATATAAAAATA
1 TTATATAAAAA-A
*
13243 TATTTATAAAAAA
1 T-TATATAAAAAA
13256 TTATATAAAAAA
1 TTATATAAAAAA
13268 T
1 T
13269 AAGTAAGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 11 0.48
13 3 0.13
14 9 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTATATAAAAAA
Found at i:17693 original size:22 final size:22
Alignment explanation
Indices: 17667--17711 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
17657 AGGTACTAAA
17667 CCCTCCTTCAAAAGAACCTCAC
1 CCCTCCTTCAAAAGAACCTCAC
* *
17689 CCCTCCTTTAAAGGAACCTCAC
1 CCCTCCTTCAAAAGAACCTCAC
17711 C
1 C
17712 TTGTTTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.29, C:0.44, G:0.07, T:0.20
Consensus pattern (22 bp):
CCCTCCTTCAAAAGAACCTCAC
Found at i:23565 original size:24 final size:24
Alignment explanation
Indices: 23538--23586 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
23528 CTGTTGATCT
*
23538 TGACCGAAACTCG-AATAATCTAAA
1 TGACCCAAA-TCGAAATAATCTAAA
*
23562 TGACCCAAATCGAAATGATCTAAA
1 TGACCCAAATCGAAATAATCTAAA
23586 T
1 T
23587 ATGAATTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.22
Consensus pattern (24 bp):
TGACCCAAATCGAAATAATCTAAA
Found at i:27831 original size:18 final size:17
Alignment explanation
Indices: 27810--27895 Score: 84
Period size: 17 Copynumber: 4.8 Consensus size: 17
27800 TTCATTTTGG
27810 GTTTAAATTTAATTTAAA
1 GTTTAAATTTAATTT-AA
**
27828 GTTTAAACTTTTCTTTTAA
1 GTTTAAA--TTTAATTTAA
*
27847 GTTTAAATTTAAATTAA
1 GTTTAAATTTAATTTAA
*
27864 GTTTAAAATTAATTTGAA
1 GTTTAAATTTAATTT-AA
27882 -TTTAAAATTTAATT
1 GTTT-AAATTTAATT
27896 AATTAAAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
17 23 0.41
18 18 0.32
19 9 0.16
20 6 0.11
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (17 bp):
GTTTAAATTTAATTTAA
Found at i:27863 original size:5 final size:6
Alignment explanation
Indices: 27811--27893 Score: 55
Period size: 6 Copynumber: 13.8 Consensus size: 6
27801 TCATTTTGGG
*** *
27811 TTTAAA TTT-AA TTTAAA GTTTAAA CTTTTCT TTTAAG TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA -TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA
* * *
27860 -TTAAG TTTAAA ATT-AA TTTGAA TTTAAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA
27894 TTAATTAAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
5 13 0.22
6 32 0.54
7 14 0.24
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:29662 original size:29 final size:30
Alignment explanation
Indices: 29630--29805 Score: 178
Period size: 30 Copynumber: 5.9 Consensus size: 30
29620 AAAAATTTCG
* *
29630 TTTTCACCCCCGAACTTCCAAAAATCCCA-
1 TTTTGACCCCCAAACTTCCAAAAATCCCAT
*
29659 TTTTGA-CCCCGAACTTCCAAAAATCCCAT
1 TTTTGACCCCCAAACTTCCAAAAATCCCAT
**
29688 TTTTGACCCCCCAAAACTTCCAAAAAT-TTAT
1 TTTTGA-CCCCC-AAACTTCCAAAAATCCCAT
* ** *
29719 TTTTCACCCCTGAACTTCCAAAAATCTCAT
1 TTTTGACCCCCAAACTTCCAAAAATCCCAT
* * * * *
29749 TTTTAACCTCAAAACTTCCAAAATTTCCAT
1 TTTTGACCCCCAAACTTCCAAAAATCCCAT
*
29779 TTTTGACCCCAAAACTTCCAAAAATCC
1 TTTTGACCCCCAAACTTCCAAAAATCC
29806 TCCAAATTTT
Statistics
Matches: 123, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
28 22 0.18
29 24 0.20
30 53 0.43
31 11 0.09
32 13 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (30 bp):
TTTTGACCCCCAAACTTCCAAAAATCCCAT
Found at i:29710 original size:60 final size:59
Alignment explanation
Indices: 29642--29805 Score: 197
Period size: 60 Copynumber: 2.7 Consensus size: 59
29632 TTCACCCCCG
*
29642 AACTTCCAAAAATCCCA-TTTTGACCCC-GAACTTCCAAAAATCCCATTTTTGACCCCCCAA
1 AACTTCCAAAAAT-CCATTTTTGACCCCAGAACTTCCAAAAATCCCATTTTT-A-ACCCCAA
** * * * *
29702 AACTTCCAAAAATTTATTTTTCACCCCTGAACTTCCAAAAATCTCATTTTTAACCTCAA
1 AACTTCCAAAAATCCATTTTTGACCCCAGAACTTCCAAAAATCCCATTTTTAACCCCAA
* *
29761 AACTTCCAAAATTTCCATTTTTGACCCCAAAACTTCCAAAAATCC
1 AACTTCCAAAA-ATCCATTTTTGACCCCAGAACTTCCAAAAATCC
29806 TCCAAATTTT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 17 0.19
60 49 0.56
61 22 0.25
ACGTcount: A:0.35, C:0.32, G:0.03, T:0.30
Consensus pattern (59 bp):
AACTTCCAAAAATCCATTTTTGACCCCAGAACTTCCAAAAATCCCATTTTTAACCCCAA
Found at i:29765 original size:30 final size:30
Alignment explanation
Indices: 29611--29804 Score: 164
Period size: 29 Copynumber: 6.5 Consensus size: 30
29601 GGAGGTCCCT
* * * *
29611 AAACTATCCAAAAATTTC-GTTTTCACCCCC
1 AAACT-TCCAAAAATCTCATTTTTAACCCCA
* * *
29641 GAACTTCCAAAAATCCCA-TTTTGACCCC-
1 AAACTTCCAAAAATCTCATTTTTAACCCCA
* * *
29669 GAACTTCCAAAAATCCCATTTTTGACCCCCCA
1 AAACTTCCAAAAATCTCATTTTT-A-ACCCCA
* * *
29701 AAACTTCCAAAAAT-TTATTTTTCACCCCT
1 AAACTTCCAAAAATCTCATTTTTAACCCCA
* *
29730 GAACTTCCAAAAATCTCATTTTTAACCTCA
1 AAACTTCCAAAAATCTCATTTTTAACCCCA
* *
29760 AAACTTCC-AAAATTTCCATTTTTGACCCCA
1 AAACTTCCAAAAATCT-CATTTTTAACCCCA
29790 AAACTTCCAAAAATC
1 AAACTTCCAAAAATC
29805 CTCCAAATTT
Statistics
Matches: 134, Mismatches: 22, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
28 18 0.13
29 46 0.34
30 42 0.31
31 15 0.11
32 13 0.10
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.30
Consensus pattern (30 bp):
AAACTTCCAAAAATCTCATTTTTAACCCCA
Found at i:29789 original size:89 final size:88
Alignment explanation
Indices: 29611--29803 Score: 262
Period size: 89 Copynumber: 2.2 Consensus size: 88
29601 GGAGGTCCCT
* * **
29611 AAACTATCCAAAAATTTCGTTTTCACCCCCGAACTTCCAAAAATCCCATTTTGACCCCGAACTTC
1 AAACT-TCCAAAAATTTAGTTTTCACCCCCGAACTTCCAAAAATCCCATTTTAACCCAAAACTTC
29676 CAAAAATCCCATTTTTGACCCCCCA
65 CAAAAATCCCATTTTTGA-CCCCCA
* * *
29701 AAACTTCCAAAAATTTATTTTTCACCCCTGAACTTCCAAAAATCTCATTTTTAACCTCAAAACTT
1 AAACTTCCAAAAATTTAGTTTTCACCCCCGAACTTCCAAAAATCCCA-TTTTAACC-CAAAACTT
* *
29766 CCAAAATTTCCATTTTTGA-CCCCA
64 CCAAAAATCCCATTTTTGACCCCCA
29790 AAACTTCCAAAAAT
1 AAACTTCCAAAAAT
29804 CCTCCAAATT
Statistics
Matches: 92, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
89 57 0.62
90 12 0.13
91 23 0.25
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.30
Consensus pattern (88 bp):
AAACTTCCAAAAATTTAGTTTTCACCCCCGAACTTCCAAAAATCCCATTTTAACCCAAAACTTCC
AAAAATCCCATTTTTGACCCCCA
Found at i:31960 original size:16 final size:16
Alignment explanation
Indices: 31933--31976 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
31923 ATTTATTCTT
31933 AATTTTTAAAAAATTCA
1 AATTTTT-AAAAATTCA
31950 AATTTTT-AAAATTCA
1 AATTTTTAAAAATTCA
*
31965 AA-ATTTAAAAAT
1 AATTTTTAAAAAT
31977 CCATTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 3 0.12
15 15 0.60
17 7 0.28
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTTTTAAAAATTCA
Found at i:32141 original size:20 final size:20
Alignment explanation
Indices: 32108--32146 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
32098 CTTAAACGAT
*
32108 TATATGTTATAAAATATTAA
1 TATATGTTAAAAAATATTAA
*
32128 TATATTTTAAAAAATATTA
1 TATATGTTAAAAAATATTA
32147 CAATTGATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TATATGTTAAAAAATATTAA
Found at i:42313 original size:2 final size:2
Alignment explanation
Indices: 42306--42333 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42296 AGATTTCTTT
42306 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42334 NNNNTTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44398 original size:30 final size:29
Alignment explanation
Indices: 44352--44510 Score: 124
Period size: 30 Copynumber: 5.3 Consensus size: 29
44342 AAAAAAAATA
*
44352 GGGTCAAATTTTAATTTTTGAAAACTTTAG
1 GGGTCAAATTTGAATTTTTGAAAA-TTTAG
* *
44382 GGGTTAAATTTGAATTTTTGGAAATTTAAG
1 GGGTCAAATTTGAATTTTTGAAAATTT-AG
* ** *
44412 GGGCCGGATTTAAAATTTTTGGAAAATTT-G
1 GGGTCAAATTT-GAATTTTT-GAAAATTTAG
* * *
44442 AGGGTGAATTTTGAATTTTTGGAAAATTTGG
1 -GGGTCAAATTTGAATTTTT-GAAAATTTAG
* *
44473 GGGTTAAATTTGAATTCTTGAAAACTTT-G
1 GGGTCAAATTTGAATTTTTGAAAA-TTTAG
44502 AGGGTCAAA
1 -GGGTCAAA
44511 AAGTGATTTT
Statistics
Matches: 103, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
29 9 0.09
30 73 0.71
31 14 0.14
32 7 0.07
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (29 bp):
GGGTCAAATTTGAATTTTTGAAAATTTAG
Found at i:44844 original size:26 final size:27
Alignment explanation
Indices: 44790--44845 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
44780 TATTTGATTA
* *
44790 TTTCCATTAAAAAAACACAACTCAGTC
1 TTTCCATTAAAAAAACAAAACCCAGTC
* *
44817 TTTCCATT-AAAAGACAAAACCCATTC
1 TTTCCATTAAAAAAACAAAACCCAGTC
44843 TTT
1 TTT
44846 AATTTTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.41, C:0.25, G:0.04, T:0.30
Consensus pattern (27 bp):
TTTCCATTAAAAAAACAAAACCCAGTC
Found at i:45509 original size:23 final size:23
Alignment explanation
Indices: 45479--45526 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
45469 GGTGGTGGCA
45479 GCGTGGGTTAGCTGGCGGCGGCG
1 GCGTGGGTTAGCTGGCGGCGGCG
45502 GCGTGGGTTAGCTGGCGGCGGCG
1 GCGTGGGTTAGCTGGCGGCGGCG
45525 GC
1 GC
45527 TGGAGACTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.04, C:0.23, G:0.56, T:0.17
Consensus pattern (23 bp):
GCGTGGGTTAGCTGGCGGCGGCG
Found at i:46436 original size:39 final size:38
Alignment explanation
Indices: 46333--46617 Score: 181
Period size: 40 Copynumber: 7.3 Consensus size: 38
46323 ATAACTTTAG
* * * *
46333 GGGTAAAAGATTGAATTGTTTCAATCCGCCC-CATGG-TC
1 GGGTAAAAGATTGGATT-CTTCAATCTGCCCTC-TGGTTA
* *
46371 GGCGTAAGAGATTTGATGGTCTTCAATCTGCCCTCTGGTTA
1 GG-GTAAAAGATTGGAT--TCTTCAATCTGCCCTCTGGTTA
* *
46412 GGGTAAAATATTGGATTACTTCAATCTGCCCTTTGGTTA
1 GGGTAAAAGATTGGATT-CTTCAATCTGCCCTCTGGTTA
* * * *
46451 GGGTAAAAAATTGAATTGTTTCAATCTG-CCTCATGGTTG
1 GGGTAAAAGATTGGATT-CTTCAATCTGCCCTC-TGGTTA
* * *
46490 GGGTAAGAGATTGGATTGTCTTCAATTTG-CC-C---ATA
1 GGGTAAAAGATTGGA-T-TCTTCAATCTGCCCTCTGGTTA
* * ***
46525 GGGTAAAAGATTTGATGGTCTTCAATCTGTCCTCTAACTA
1 GGGTAAAAGATTGGAT--TCTTCAATCTGCCCTCTGGTTA
* *
46565 GGGTAAAAGATTGAATGGTCTTCAATATGCCCTCTGGTTA
1 GGGTAAAAGATTGGAT--TCTTCAATCTGCCCTCTGGTTA
*
46605 GGGTAAGAGATTG
1 GGGTAAAAGATTG
46618 AAGGTTGTAA
Statistics
Matches: 197, Mismatches: 35, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
34 1 0.01
35 25 0.13
36 2 0.01
37 1 0.01
38 6 0.03
39 73 0.37
40 83 0.42
41 6 0.03
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.34
Consensus pattern (38 bp):
GGGTAAAAGATTGGATTCTTCAATCTGCCCTCTGGTTA
Found at i:46583 original size:40 final size:40
Alignment explanation
Indices: 46333--46619 Score: 233
Period size: 39 Copynumber: 7.4 Consensus size: 40
46323 ATAACTTTAG
* * *
46333 GGGTAAAAGATTGAATTGT-TTCAATCCGCCC-CATGG-TC
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTC-TGGTTA
*
46371 GGCGTAAGAGATTTG-ATGGTCTTCAATCTGCCCTCTGGTTA
1 GG-GTAAAAGA-TTGAATGGTCTTCAATCTGCCCTCTGGTTA
* * *
46412 GGGTAAAATATTGGAT--TACTTCAATCTGCCCTTTGGTTA
1 GGGTAAAAGATTGAATGGT-CTTCAATCTGCCCTCTGGTTA
* * *
46451 GGGTAAAAAATTGAATTGT-TTCAATCTG-CCTCATGGTTG
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTC-TGGTTA
* * * * *
46490 GGGTAAGAGATTGGATTGTCTTCAATTTG-CC-C---ATA
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTA
* ***
46525 GGGTAAAAGATTTG-ATGGTCTTCAATCTGTCCTCTAACTA
1 GGGTAAAAGA-TTGAATGGTCTTCAATCTGCCCTCTGGTTA
*
46565 GGGTAAAAGATTGAATGGTCTTCAATATGCCCTCTGGTTA
1 GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTA
*
46605 GGGTAAGAGATTGAA
1 GGGTAAAAGATTGAA
46620 GGTTGTAACT
Statistics
Matches: 204, Mismatches: 27, Indels: 34
0.77 0.10 0.13
Matches are distributed among these distances:
35 23 0.11
36 5 0.02
37 1 0.00
38 6 0.03
39 82 0.40
40 82 0.40
41 5 0.02
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.33
Consensus pattern (40 bp):
GGGTAAAAGATTGAATGGTCTTCAATCTGCCCTCTGGTTA
Found at i:46800 original size:50 final size:50
Alignment explanation
Indices: 46674--46800 Score: 159
Period size: 50 Copynumber: 2.5 Consensus size: 50
46664 TCCTTGTGAG
*
46674 TTCAATCTGCCCCTCTATAGCTTTAGATGAATGAGATTTGTCATTGCGGC
1 TTCAATCTGCCCCTCTATAGCTTTAGGTGAATGAGATTTGTCATTGCGGC
* * * * *
46724 TTCATTCTGCCCCTCTACAACTTTAGGTGTATGAGATTT-TCCATTGCGGT
1 TTCAATCTGCCCCTCTATAGCTTTAGGTGAATGAGATTTGT-CATTGCGGC
*
46774 TTCAATCTGCACCC-CCATAGCTTTAGG
1 TTCAATCTGC-CCCTCTATAGCTTTAGG
46801 GGTAAAAGAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
49 1 0.02
50 61 0.94
51 3 0.05
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (50 bp):
TTCAATCTGCCCCTCTATAGCTTTAGGTGAATGAGATTTGTCATTGCGGC
Found at i:58437 original size:2 final size:2
Alignment explanation
Indices: 58430--58480 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
58420 AAAATAAAAT
58430 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58472 TA TA TA TA T
1 TA TA TA TA T
58481 TGATCGGGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58760 original size:3 final size:3
Alignment explanation
Indices: 58752--58780 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
58742 TCACAATTAT
58752 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
58781 TTATGATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:60903 original size:17 final size:17
Alignment explanation
Indices: 60881--60914 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
60871 TAATAAAATT
*
60881 TAATATTAATTTTAATC
1 TAATATTAATCTTAATC
*
60898 TAATATTTATCTTAATC
1 TAATATTAATCTTAATC
60915 AGTATTACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATATTAATCTTAATC
Found at i:73901 original size:18 final size:17
Alignment explanation
Indices: 73876--73932 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 17
73866 GCTGTGTTTC
73876 GGAAGAAGAGAAGGAAA
1 GGAAGAAGAGAAGGAAA
73893 GGTAAGAAGTAGAAGG-AA
1 GG-AAGAAG-AGAAGGAAA
73911 GAGAAGAAGAGGAAGAGAAA
1 G-GAAGAAGA-GAAG-GAAA
73931 GG
1 GG
73933 GAAAGCGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 3 0.09
18 19 0.56
19 9 0.26
20 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.42, T:0.04
Consensus pattern (17 bp):
GGAAGAAGAGAAGGAAA
Found at i:73935 original size:11 final size:14
Alignment explanation
Indices: 73880--73929 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
73870 TGTTTCGGAA
73880 GAAGAGAAGGAA-AG
1 GAAGAGAA-GAAGAG
* *
73894 GTA-AGAAGTAGAAG
1 GAAGAGAAGAAG-AG
73908 GAAGAGAAGAAGAG
1 GAAGAGAAGAAGAG
73922 GAAGAGAA
1 GAAGAGAA
73930 AGGGAAAGCG
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 2 0.07
13 4 0.14
14 16 0.55
15 7 0.24
ACGTcount: A:0.56, C:0.00, G:0.40, T:0.04
Consensus pattern (14 bp):
GAAGAGAAGAAGAG
Found at i:75725 original size:14 final size:14
Alignment explanation
Indices: 75706--75733 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
75696 GAAAATAGCT
75706 AATTAACATGACAC
1 AATTAACATGACAC
75720 AATTAACATGACAC
1 AATTAACATGACAC
75734 TACATATGTG
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:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (14 bp):
AATTAACATGACAC
Found at i:78977 original size:21 final size:22
Alignment explanation
Indices: 78944--78988 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
78934 TCTAAATGTA
*
78944 TTTTATGTTATTTTTTAAAATT
1 TTTTATGTAATTTTTTAAAATT
*
78966 TTTTATG-AATTTTTTATAATT
1 TTTTATGTAATTTTTTAAAATT
78987 TT
1 TT
78989 CTTTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTTATGTAATTTTTTAAAATT
Found at i:78998 original size:22 final size:21
Alignment explanation
Indices: 78953--79004 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
78943 ATTTTATGTT
* *
78953 ATTTTTTAAAATTTTTTATGA
1 ATTTTTTATAATTTTTTATAA
*
78974 ATTTTTTATAATTTTCTTTTAA
1 ATTTTTTATAATTTT-TTATAA
*
78996 ATTATTTAT
1 ATTTTTTAT
79005 TTTTAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
ATTTTTTATAATTTTTTATAA
Found at i:79042 original size:19 final size:18
Alignment explanation
Indices: 78991--79043 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
78981 ATAATTTTCT
78991 TTTAAATTATTTATT---
1 TTTAAATTATTTATTAAA
* *
79006 TTTAAATATTTTTATAAAA
1 TTTAAAT-TATTTATTAAA
79025 TTTAAATTATTTATTAAA
1 TTTAAATTATTTATTAAA
79043 T
1 T
79044 AGTACGACGT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 7 0.23
16 6 0.20
18 10 0.33
19 7 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTAAATTATTTATTAAA
Found at i:92284 original size:6 final size:6
Alignment explanation
Indices: 92273--92327 Score: 92
Period size: 6 Copynumber: 9.2 Consensus size: 6
92263 AAGATAAGCA
* *
92273 GGGTGT GGGTGT GGGTGC GGGTGC GGGTGC GGGTGC GGGTGC GGGTGC
1 GGGTGC GGGTGC GGGTGC GGGTGC GGGTGC GGGTGC GGGTGC GGGTGC
92321 GGGTGC G
1 GGGTGC G
92328 TTTAGACATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.00, C:0.13, G:0.67, T:0.20
Consensus pattern (6 bp):
GGGTGC
Found at i:94938 original size:26 final size:29
Alignment explanation
Indices: 94908--94960 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
94898 AATTTTATTT
94908 TAAATTTT-A-ATTTTT-TTTTTAAAAGA
1 TAAATTTTAATATTTTTCTTTTTAAAAGA
94934 TAAATTTTAATATTTTTCTTTTTAAAA
1 TAAATTTTAATATTTTTCTTTTTAAAA
94961 TAATCAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 8 0.33
27 1 0.04
28 6 0.25
29 9 0.38
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (29 bp):
TAAATTTTAATATTTTTCTTTTTAAAAGA
Found at i:101586 original size:27 final size:29
Alignment explanation
Indices: 101526--101587 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
101516 TAATTAATAC
** *
101526 TTTTAATTATTAAACATGTTACTTTCAAGT
1 TTTTAATTAAAAAACATGTTA-TTTCAAGA
101556 TTTTAATTAAAAAACATGTT-TTT-AAGA
1 TTTTAATTAAAAAACATGTTATTTCAAGA
101583 TTTTA
1 TTTTA
101588 TTTTATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 8 0.28
28 3 0.10
30 18 0.62
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.50
Consensus pattern (29 bp):
TTTTAATTAAAAAACATGTTATTTCAAGA
Found at i:104074 original size:18 final size:18
Alignment explanation
Indices: 104047--104086 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
104037 AAAGTAGATG
* *
104047 AAAA-CGTGCTATAAGAC
1 AAAAGCGTGCTACAAAAC
104064 AAAAGCGTGCTACAAAAC
1 AAAAGCGTGCTACAAAAC
104082 AAAAG
1 AAAAG
104087 AAAAACTAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.12
Consensus pattern (18 bp):
AAAAGCGTGCTACAAAAC
Found at i:104789 original size:34 final size:36
Alignment explanation
Indices: 104724--104796 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
104714 TTTAAAACCT
* *
104724 ATTAAAATTATTTTTTATATTTTTATTTTTTAAGAA
1 ATTAAAATTATTTTTTATATTTTTATATTTTAAAAA
*
104760 ATTATAATTATTTTTTAT-TTTTT-TATTTTAAAAA
1 ATTAAAATTATTTTTTATATTTTTATATTTTAAAAA
104794 ATT
1 ATT
104797 CACATTGACA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 12 0.35
35 5 0.15
36 17 0.50
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (36 bp):
ATTAAAATTATTTTTTATATTTTTATATTTTAAAAA
Found at i:106716 original size:23 final size:24
Alignment explanation
Indices: 106677--106727 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
106667 TAATAGGTAT
106677 TTTCAATTTACAATTCA-TATCAC
1 TTTCAATTTACAATTCACTATCAC
* *
106700 TTTCAA-TTCCAATTTCACTTTCAC
1 TTTCAATTTACAA-TTCACTATCAC
106724 TTTC
1 TTTC
106728 GCTTTCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 10 0.42
24 9 0.38
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTCAATTTACAATTCACTATCAC
Done.