Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014644.1 Kokia drynarioides strain JFW-HI SEQ_129683, 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: 126177
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 102 characters in sequence are not A, C, G, or T
Found at i:10883 original size:24 final size:23
Alignment explanation
Indices: 10844--10889 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
10834 TATTACAAGC
10844 AAAAAAAATTAGTATTAAAAATA
1 AAAAAAAATTAGTATTAAAAATA
* *
10867 AAAATAAAATTATTATTATAAAT
1 AAAA-AAAATTAGTATTAAAAAT
10890 TCGGGCCGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
AAAAAAAATTAGTATTAAAAATA
Found at i:12979 original size:10 final size:10
Alignment explanation
Indices: 12964--12990 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
12954 TGTATTTAAA
12964 TATATATATT
1 TATATATATT
12974 TATATATATT
1 TATATATATT
12984 TATATAT
1 TATATAT
12991 TTTTTGTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TATATATATT
Found at i:22575 original size:13 final size:13
Alignment explanation
Indices: 22535--22576 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
22525 TAAATTTAAT
22535 TATAAAAA-A-TA
1 TATAAAAATATTA
22546 TATAAAAATATTAA
1 TATAAAAATATT-A
*
22560 TATAAAATTATTA
1 TATAAAAATATTA
22573 TATA
1 TATA
22577 TATATATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 8 0.30
12 1 0.04
13 6 0.22
14 12 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TATAAAAATATTA
Found at i:26603 original size:5 final size:5
Alignment explanation
Indices: 26593--26618 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
26583 AAGAAAAACT
26593 CAACC CAACC CAACC CAACC CAACC C
1 CAACC CAACC CAACC CAACC CAACC C
26619 CTTTCATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.62, G:0.00, T:0.00
Consensus pattern (5 bp):
CAACC
Found at i:34348 original size:63 final size:63
Alignment explanation
Indices: 34266--34389 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 63
34256 CTCTCGTTGG
* * * * *
34266 TGGTGGTGTCGGTGTAGCTCTGAGGA-GCATTGTTTTCGTTCTGACTTGCATTTTCATTGTTAT
1 TGGTGGTGTCGGTGAAGCTCTGA-GATGCATTGCTCTCATCCTGACTTGCATTTTCATTGTTAT
*
34329 TGGTGGTGTCGGTGAAGCTCTGAGATGCATTGCTCTCATCCTGACTTGCATTTTCGTTGTT
1 TGGTGGTGTCGGTGAAGCTCTGAGATGCATTGCTCTCATCCTGACTTGCATTTTCATTGTT
34390 GTTACTGCTC
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 2 0.04
63 52 0.96
ACGTcount: A:0.13, C:0.17, G:0.28, T:0.42
Consensus pattern (63 bp):
TGGTGGTGTCGGTGAAGCTCTGAGATGCATTGCTCTCATCCTGACTTGCATTTTCATTGTTAT
Found at i:34496 original size:66 final size:66
Alignment explanation
Indices: 34407--34569 Score: 211
Period size: 66 Copynumber: 2.5 Consensus size: 66
34397 CTCTGAGCGG
* * * * *
34407 CATTATTCTCATTTTGACTTGCATTTTCGTTGTTGTTGTTGCTGTT-GTCAGTGTTGCTCTGAGT
1 CATTGTTCTCATTCTGACCTGCATTTTCATTGTTGTCGTTG-TGTTCGTCAGTGTTGCTCTGAGT
34471 CA
65 CA
* *
34473 CATTGTTCTCATTCTGACCTGCATTTTCATTGTTGTCGTTGTTTTCGTCGGTGTTGCTCTGAGTC
1 CATTGTTCTCATTCTGACCTGCATTTTCATTGTTGTCGTTGTGTTCGTCAGTGTTGCTCTGAGTC
*
34538 G
66 A
* * *
34539 CATTGCTCTCGTTCTGACCTGCATTCTCATT
1 CATTGTTCTCATTCTGACCTGCATTTTCATT
34570 TTTTTTAGTG
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
65 3 0.04
66 82 0.96
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.47
Consensus pattern (66 bp):
CATTGTTCTCATTCTGACCTGCATTTTCATTGTTGTCGTTGTGTTCGTCAGTGTTGCTCTGAGTC
A
Found at i:34609 original size:54 final size:53
Alignment explanation
Indices: 34538--34995 Score: 448
Period size: 54 Copynumber: 8.7 Consensus size: 53
34528 GCTCTGAGTC
* * * * *
34538 GCATTGCTCTCGTTCTGACCTGCATTCTCATTTTTTTTAGTGTTACTTGGAGCG
1 GCATTGTTCTCGTTCTGACCCGCATTCTCATTGTTCTCAGTGTTACTT-GAGCG
* * * * * *
34592 GCGTTGTTCTCGTTCTGACCGGCATTCTCATTATTCTCGGTGTTCCTCAGAGCG
1 GCATTGTTCTCGTTCTGACCCGCATTCTCATTGTTCTCAGTGTTACT-TGAGCG
* * * *
34646 GCATTGTTCTCGTTCTGACCGGCATTCTCATTATTCTCGGTGTTACTCAGAGCG
1 GCATTGTTCTCGTTCTGACCCGCATTCTCATTGTTCTCAGTGTTACT-TGAGCG
* * * *
34700 GCATTGTTCTCGTTCTGACCCACATTCTCATTGTTGTCGGTGTTACTTGGAGTG
1 GCATTGTTCTCGTTCTGACCCGCATTCTCATTGTTCTCAGTGTTACTT-GAGCG
* *
34754 GCATTTTTCTCGTTCTGACCCGCATTCTCATTGTTGCTC--TG--AGTT-----
1 GCATTGTTCTCGTTCTGACCCGCATTCTCATTGTT-CTCAGTGTTACTTGAGCG
* * *
34799 GCATTGTTCTCGTTCTGACCTGCATTTTCATTGTTCTCAGTGTTGCTCTGAGCG
1 GCATTGTTCTCGTTCTGACCCGCATTCTCATTGTTCTCAGTGTTACT-TGAGCG
* * * *
34853 GCATTGTTCTCATTCTGACCCACATTTTCATTGTTCTCAGTGTTGCTCTGAGCG
1 GCATTGTTCTCGTTCTGACCCGCATTCTCATTGTTCTCAGTGTTACT-TGAGCG
* * * * *
34907 GCATTGTTCTCATTCTGACCCACATTTTCATTGTTGTCAGTGTTACTTTGAGTG
1 GCATTGTTCTCGTTCTGACCCGCATTCTCATTGTTCTCAGTGTTAC-TTGAGCG
* * * *
34961 GCATTGCTCTCGTCCTGACCTGCATTTTCATTGTT
1 GCATTGTTCTCGTTCTGACCCGCATTCTCATTGTT
34996 GTTGGTGTTG
Statistics
Matches: 353, Mismatches: 37, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
44 3 0.01
45 32 0.09
46 2 0.01
48 1 0.00
49 1 0.00
51 3 0.01
53 2 0.01
54 306 0.87
55 3 0.01
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.41
Consensus pattern (53 bp):
GCATTGTTCTCGTTCTGACCCGCATTCTCATTGTTCTCAGTGTTACTTGAGCG
Found at i:34704 original size:27 final size:27
Alignment explanation
Indices: 34620--34711 Score: 71
Period size: 27 Copynumber: 3.4 Consensus size: 27
34610 CCGGCATTCT
*
34620 CATTATTCTCGGTGTTCCTCAGAGCGG
1 CATTATTCTCGGTGTTACTCAGAGCGG
* * * * * * *
34647 CATTGTTCTCGTTCTGAC-CGGCATTC-T
1 CATTATTCTCGGTGTTACTCAG-A-GCGG
34674 CATTATTCTCGGTGTTACTCAGAGCGG
1 CATTATTCTCGGTGTTACTCAGAGCGG
*
34701 CATTGTTCTCG
1 CATTATTCTCG
34712 TTCTGACCCA
Statistics
Matches: 45, Mismatches: 16, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
26 3 0.07
27 39 0.87
28 3 0.07
ACGTcount: A:0.14, C:0.26, G:0.23, T:0.37
Consensus pattern (27 bp):
CATTATTCTCGGTGTTACTCAGAGCGG
Found at i:34731 original size:27 final size:27
Alignment explanation
Indices: 34647--34734 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 27
34637 CTCAGAGCGG
**
34647 CATTGTTCTCGTTCTGACCGGCATTCT
1 CATTGTTCTCGTTCTGACCCACATTCT
* * * * * * * *
34674 CATTATTCTCGGTGTTACTCAGA-GCGG
1 CATTGTTCTCGTTCTGACCCACATTC-T
34701 CATTGTTCTCGTTCTGACCCACATTCT
1 CATTGTTCTCGTTCTGACCCACATTCT
34728 CATTGTT
1 CATTGTT
34735 GTCGGTGTTA
Statistics
Matches: 41, Mismatches: 18, Indels: 4
0.65 0.29 0.06
Matches are distributed among these distances:
26 1 0.02
27 39 0.95
28 1 0.02
ACGTcount: A:0.15, C:0.27, G:0.18, T:0.40
Consensus pattern (27 bp):
CATTGTTCTCGTTCTGACCCACATTCT
Found at i:34808 original size:27 final size:27
Alignment explanation
Indices: 34778--34920 Score: 94
Period size: 27 Copynumber: 5.3 Consensus size: 27
34768 CTGACCCGCA
34778 TTCTCATTGTTGCTCTGAGTTGCATTG
1 TTCTCATTGTTGCTCTGAGTTGCATTG
* * * *
34805 TTCTCGTT-CTGAC-CTGCATTTTCATTG
1 TTCTCATTGTTG-CTCTG-AGTTGCATTG
* **
34832 TTCTCAGTGTTGCTCTGAGCGGCATTG
1 TTCTCATTGTTGCTCTGAGTTGCATTG
* * ** * *
34859 TTCTCATT-CTGACCCACATTTTCATTG
1 TTCTCATTGTTG-CTCTGAGTTGCATTG
* **
34886 TTCTCAGTGTTGCTCTGAGCGGCATTG
1 TTCTCATTGTTGCTCTGAGTTGCATTG
34913 TTCTCATT
1 TTCTCATT
34921 CTGACCCACA
Statistics
Matches: 80, Mismatches: 30, Indels: 12
0.66 0.25 0.10
Matches are distributed among these distances:
26 7 0.09
27 66 0.82
28 7 0.09
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.44
Consensus pattern (27 bp):
TTCTCATTGTTGCTCTGAGTTGCATTG
Found at i:34834 original size:21 final size:21
Alignment explanation
Indices: 34765--34835 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
34755 CATTTTTCTC
* *
34765 GTTCTGACCCGCATTCTCATT
1 GTTCTGACCTGCATTTTCATT
** *
34786 GTTGCTCTGAGTTGCATTGTTC-TC
1 G-T--TCTGACCTGCATT-TTCATT
34810 GTTCTGACCTGCATTTTCATT
1 GTTCTGACCTGCATTTTCATT
34831 GTTCT
1 GTTCT
34836 CAGTGTTGCT
Statistics
Matches: 37, Mismatches: 8, Indels: 10
0.67 0.15 0.18
Matches are distributed among these distances:
20 3 0.08
21 18 0.49
22 1 0.03
23 1 0.03
24 12 0.32
25 2 0.05
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.45
Consensus pattern (21 bp):
GTTCTGACCTGCATTTTCATT
Found at i:34856 original size:99 final size:98
Alignment explanation
Indices: 34686--34996 Score: 334
Period size: 99 Copynumber: 3.1 Consensus size: 98
34676 TTATTCTCGG
* * * *
34686 TGTTACTCAGAGCGGCATTGTTCTCGTTCTGACCCACATTCTCATTGTTGTCGGTGTTACTTGGA
1 TGTTGCTCTGAGCGGCATTGTTCTCGTTCTGACCCACATTTTCATTGTTGTCAGTGTTACTT-GA
*
34751 GTGGCATTTTTCTCGTTCTGACCCGCATTCTCAT
65 GTGGCATTGTTCTCGTTCTGACCCGCATTCTCAT
** ** * *
34785 TGTTGCTCTGAGTTGCATTGTTCTCGTTCTGACCTGCATTTTCATTGTTCTCAGTGTTGCTCTGA
1 TGTTGCTCTGAGCGGCATTGTTCTCGTTCTGACCCACATTTTCATTGTTGTCAGTGTTACT-TGA
* * * *
34850 GCGGCATTGTTCTCATTCTGACCCACATTTTCATTGTTCTCAG
65 GTGGCATTGTTCTCGTTCTGA-CC-C----GCA---TTCTCAT
*
34893 TGTTGCTCTGAGCGGCATTGTTCTCATTCTGACCCACATTTTCATTGTTGTCAGTGTTACTTTGA
1 TGTTGCTCTGAGCGGCATTGTTCTCGTTCTGACCCACATTTTCATTGTTGTCAGTGTTAC-TTGA
* * * *
34958 GTGGCATTGCTCTCGTCCTGACCTGCATTTTCAT
65 GTGGCATTGTTCTCGTTCTGACCCGCATTCTCAT
34992 TGTTG
1 TGTTG
34997 TTGGTGTTGC
Statistics
Matches: 171, Mismatches: 30, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
99 81 0.47
100 3 0.02
101 1 0.01
102 2 0.01
105 2 0.01
107 2 0.01
108 79 0.46
109 1 0.01
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.42
Consensus pattern (98 bp):
TGTTGCTCTGAGCGGCATTGTTCTCGTTCTGACCCACATTTTCATTGTTGTCAGTGTTACTTGAG
TGGCATTGTTCTCGTTCTGACCCGCATTCTCAT
Found at i:34908 original size:207 final size:207
Alignment explanation
Indices: 34595--34996 Score: 597
Period size: 207 Copynumber: 1.9 Consensus size: 207
34585 TGGAGCGGCG
* *
34595 TTGTTCTCGTTCTGACCGGCATTCTCATTATTCTCGGTGTTCCTCAGAGCGGCATTGTTCTCGTT
1 TTGTTCTCGTTCTGACCGGCATTCTCATTATTCTCAGTGTTCCTCAGAGCGGCATTGTTCTCATT
** * *
34660 CTGACCGGCATTCTCATTATTCTCGGTGTTACTCAGAGCGGCATTGTTCTCGTTCTGACCCACAT
66 CTGACCCACATTCTCATTATTCTCAGTGTTACTCAGAGCGGCATTGTTCTCATTCTGACCCACAT
* ** *
34725 TCTCATTGTTGTCGGTGTTACTTGGAGTGGCATTTTTCTCGTTCTGACCCGCATTCTCATTGTTG
131 TCTCATTGTTGTCAGTGTTACTTGGAGTGGCATTGCTCTCGTCCTGACCCGCATTCTCATTGTTG
34790 CTCTGAGTTGCA
196 CTCTGAGTTGCA
* * * * *
34802 TTGTTCTCGTTCTGACCTGCATTTTCATTGTTCTCAGTGTTGCTCTGAGCGGCATTGTTCTCATT
1 TTGTTCTCGTTCTGACCGGCATTCTCATTATTCTCAGTGTTCCTCAGAGCGGCATTGTTCTCATT
* * * *
34867 CTGACCCACATTTTCATTGTTCTCAGTGTTGCTCTGAGCGGCATTGTTCTCATTCTGACCCACAT
66 CTGACCCACATTCTCATTATTCTCAGTGTTACTCAGAGCGGCATTGTTCTCATTCTGACCCACAT
* * * *
34932 TTTCATTGTTGTCAGTGTTACTTTGAGTGGCATTGCTCTCGTCCTGACCTGCATTTTCATTGTTG
131 TCTCATTGTTGTCAGTGTTACTTGGAGTGGCATTGCTCTCGTCCTGACCCGCATTCTCATTGTTG
34997 TTGGTGTTGC
Statistics
Matches: 172, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
207 172 1.00
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.41
Consensus pattern (207 bp):
TTGTTCTCGTTCTGACCGGCATTCTCATTATTCTCAGTGTTCCTCAGAGCGGCATTGTTCTCATT
CTGACCCACATTCTCATTATTCTCAGTGTTACTCAGAGCGGCATTGTTCTCATTCTGACCCACAT
TCTCATTGTTGTCAGTGTTACTTGGAGTGGCATTGCTCTCGTCCTGACCCGCATTCTCATTGTTG
CTCTGAGTTGCA
Found at i:34910 original size:153 final size:157
Alignment explanation
Indices: 34520--35019 Score: 499
Period size: 162 Copynumber: 3.1 Consensus size: 157
34510 GTTGTTTTCG
* * ** * * *
34520 TCGGTGTTGCTCTGAGTC-GCATTGCTCTCGTTCTGACCTGCATTCTCATTTTTTTTAGTGTTAC
1 TCGGTGTTGCTCTGAG-CGGCATTGTTCTCATTCTGACCCACATTCTCATTGTTCTCAGTGTTAC
* * ** * * * * *
34584 TTGGAGCGGCGTTGTTCTCGTTCTGACCGGCATTCTCATTATTCTCGGTGTTCCTCAGAGCGGCA
65 TTGGAGCGGCATTGTTCTCATTCTGACCCACATTCTCATTGTTGTC---G-TACT-TGAGTGGCA
* * *
34649 TTGTTCTCGTTCTGACCGGCATTCTCATTATTC
125 TTGTTCTCGTTCTGACCTGCATTTTCATTGTTC
* * * * *
34682 TCGGTGTTACTCAGAGCGGCATTGTTCTCGTTCTGACCCACATTCTCATTGTTGTCGGTGTTACT
1 TCGGTGTTGCTCTGAGCGGCATTGTTCTCATTCTGACCCACATTCTCATTGTTCTCAGTGTTACT
* * * * *
34747 TGGAGTGGCATTTTTCTCGTTCTGACCCGCATTCTCATTGTTG-C-T-C-TGAGTTGCATTGTTC
66 TGGAGCGGCATTGTTCTCATTCTGACCCACATTCTCATTGTTGTCGTACTTGAGTGGCATTGTTC
34808 TCGTTCTGACCTGCATTTTCATTGTTC
131 TCGTTCTGACCTGCATTTTCATTGTTC
* * *
34835 TCAGTGTTGCTCTGAGCGGCATTGTTCTCATTCTGACCCACATTTTCATTGTTCTCAGTGTTGCT
1 TCGGTGTTGCTCTGAGCGGCATTGTTCTCATTCTGACCCACATTCTCATTGTTCTCAGTGTTACT
*
34900 CT-GAGCGGCATTGTTCTCATTCTGACCCACATTTTCATTGTTGTCAGTGTTACTTTGAGTGGCA
66 -TGGAGCGGCATTGTTCTCATTCTGACCCACATTCTCATTGTTGTC---G-TAC-TTGAGTGGCA
* * *
34964 TTGCTCTCGTCCTGACCTGCATTTTCATTGTTG
125 TTGTTCTCGTTCTGACCTGCATTTTCATTGTTC
* * *
34997 TTGGTGTTGCTCTGTGCAGCATT
1 TCGGTGTTGCTCTGAGCGGCATT
35020 TTCATTCGAA
Statistics
Matches: 285, Mismatches: 42, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
153 129 0.45
154 2 0.01
155 1 0.00
156 1 0.00
159 1 0.00
160 1 0.00
161 2 0.01
162 148 0.52
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.41
Consensus pattern (157 bp):
TCGGTGTTGCTCTGAGCGGCATTGTTCTCATTCTGACCCACATTCTCATTGTTCTCAGTGTTACT
TGGAGCGGCATTGTTCTCATTCTGACCCACATTCTCATTGTTGTCGTACTTGAGTGGCATTGTTC
TCGTTCTGACCTGCATTTTCATTGTTC
Found at i:35021 original size:261 final size:261
Alignment explanation
Indices: 34524--35021 Score: 640
Period size: 261 Copynumber: 1.9 Consensus size: 261
34514 TTTTCGTCGG
* * *
34524 TGTTGCTCTGAGTCGCATTGCTCTCGTTCTGACCTGCATTCTCATTTTTTTTAGTGTTACTTGGA
1 TGTTGCTCTGAGTCGCATTGCTCTCGTTCTGACCTGCATTCTCATTGTTCTCAGTGTTACTTGGA
* * ** *
34589 GCGGCGTTGTTCTCGTTCTGACCGGCATTCTCATTATTCTCGGTGTTCCTCAGAGCGGCATTGTT
66 GCGGCATTGTTCTCATTCTGACCCACATTCTCATTATTCTCAGTGTTCCTCAGAGCGGCATTGTT
* ** * * *
34654 CTCGTTCTGACCGGCATTCTCATTATTCTCGGTGTTACTCAGAGCGGCATTGTTCTCGTTCTGAC
131 CTCATTCTGACCCACATTCTCATTATTCTCAGTGTTACTCAGAGCGGCATTGCTCTCGTCCTGAC
**
34719 CCACATTCTCATTGTTGTCGGTGTTACTTGGAGTGGCATTTTTCTCGTTCTGACCCGCATTCTCA
196 CCACATTCTCATTGTTGTCGGTGTTACTTGGAGCAGCATTTTTCTCGTTCTGACCCGCATTCTCA
34784 T
261 T
* * * *
34785 TGTTGCTCTGAGTTGCATTGTTCTCGTTCTGACCTGCATTTTCATTGTTCTCAGTGTTGCTCT-G
1 TGTTGCTCTGAGTCGCATTGCTCTCGTTCTGACCTGCATTCTCATTGTTCTCAGTGTTACT-TGG
* * * *
34849 AGCGGCATTGTTCTCATTCTGACCCACATTTTCATTGTTCTCAGTGTTGCTCTGAGCGGCATTGT
65 AGCGGCATTGTTCTCATTCTGACCCACATTCTCATTATTCTCAGTGTTCCTCAGAGCGGCATTGT
* * * ** *
34914 TCTCATTCTGACCCACATTTTCATTGTTGTCAGTGTTACTTTGAGTGGCATTGCTCTCGTCCTGA
130 TCTCATTCTGACCCACATTCTCATTATTCTCAGTGTTACTCAGAGCGGCATTGCTCTCGTCCTGA
** * * * *
34979 CCTGCATTTTCATTGTTGTTGGTGTTGCTCT-GTGCAGCATTTT
195 CCCACATTCTCATTGTTGTCGGTGTTACT-TGGAGCAGCATTTT
35022 CATTCGAACT
Statistics
Matches: 199, Mismatches: 36, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
261 197 0.99
262 2 0.01
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (261 bp):
TGTTGCTCTGAGTCGCATTGCTCTCGTTCTGACCTGCATTCTCATTGTTCTCAGTGTTACTTGGA
GCGGCATTGTTCTCATTCTGACCCACATTCTCATTATTCTCAGTGTTCCTCAGAGCGGCATTGTT
CTCATTCTGACCCACATTCTCATTATTCTCAGTGTTACTCAGAGCGGCATTGCTCTCGTCCTGAC
CCACATTCTCATTGTTGTCGGTGTTACTTGGAGCAGCATTTTTCTCGTTCTGACCCGCATTCTCA
T
Found at i:43727 original size:3 final size:3
Alignment explanation
Indices: 43719--43745 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
43709 GATTACTTTA
43719 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
43746 TGTCTATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:53569 original size:2 final size:2
Alignment explanation
Indices: 53562--53586 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53552 GAAGCTTTAT
53562 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
53587 GTGTGTGTTA
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:58461 original size:18 final size:19
Alignment explanation
Indices: 58437--58480 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
58427 GGCAAAATCG
58437 ATTTTAT-AAATTTTAATTT
1 ATTTTATAAAATTTT-ATTT
58456 -TTTTATAAAATTTTATTT
1 ATTTTATAAAATTTTATTT
58474 ATTTTAT
1 ATTTTAT
58481 TGTTGGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTTATAAAATTTTATTT
Found at i:71937 original size:31 final size:31
Alignment explanation
Indices: 71902--71962 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
71892 AAAAAAACTT
*
71902 AACAGTCCAATGACCTAAATAAATTTTTTTG
1 AACAGTCCAATAACCTAAATAAATTTTTTTG
* *
71933 AACAGTTCAATAACTTAAATAAATTTTTTT
1 AACAGTCCAATAACCTAAATAAATTTTTTT
71963 AAATAATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (31 bp):
AACAGTCCAATAACCTAAATAAATTTTTTTG
Found at i:72884 original size:31 final size:30
Alignment explanation
Indices: 72801--72893 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 30
72791 TTTGAGTATC
* *
72801 AAATTGAACATTAAACCTAAACTCAAATATT
1 AAATTAAACATTAAA-CTAAACTCAAATACT
*
72832 AAATTTAAA-A--AAAAT-AACTCAAATACT
1 AAA-TTAAACATTAAACTAAACTCAAATACT
72859 AAATTAAACATTTAAACTAAACTCAAATACT
1 AAATTAAACA-TTAAACTAAACTCAAATACT
72890 AAAT
1 AAAT
72894 AAGGTACTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
26 5 0.10
27 15 0.29
28 1 0.02
29 3 0.06
30 4 0.08
31 20 0.38
32 4 0.08
ACGTcount: A:0.57, C:0.14, G:0.01, T:0.28
Consensus pattern (30 bp):
AAATTAAACATTAAACTAAACTCAAATACT
Found at i:74950 original size:22 final size:22
Alignment explanation
Indices: 74911--74970 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
74901 CGATCTAAGG
*
74911 AAAAAT-AAA-AAAACAGAATT
1 AAAAATAAAAGAAAATAGAATT
74931 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
74953 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
74971 GGAAGTCGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.17
21 3 0.09
22 25 0.71
23 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:74961 original size:15 final size:16
Alignment explanation
Indices: 74936--74965 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
74926 GAATTAAAAA
74936 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
74952 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
74966 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:75799 original size:19 final size:19
Alignment explanation
Indices: 75775--75817 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
75765 AAACATAAAT
75775 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
75794 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
75813 TAAAT
1 TAAAT
75818 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:77161 original size:21 final size:21
Alignment explanation
Indices: 77137--77188 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
77127 TGAAGCAGTA
*
77137 CTACCGATACAAGTGAGACTT
1 CTACCGATACAAGTCAGACTT
* * *
77158 CTACCGAAACATGTCATACTT
1 CTACCGATACAAGTCAGACTT
*
77179 CTATCGATAC
1 CTACCGATAC
77189 TAAAAACTCC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (21 bp):
CTACCGATACAAGTCAGACTT
Found at i:78207 original size:194 final size:197
Alignment explanation
Indices: 77947--78301 Score: 482
Period size: 194 Copynumber: 1.8 Consensus size: 197
77937 CTGTAAACTG
77947 TCCCTTAACAATGCTGCTCACACGAGCTGTCGAAAATATGCATTTAAGCATAAATCCCAACCATC
1 TCCCTTAACAATGCTGCTCACACGAGCTGTCGAAAATATGCATTTAAGCATAAATCCCAACCATC
* * * *
78012 GTAGAGCCTATAATACATT-TAGGTTTCATATCTC-TTTTTTGAATCACGATGCTGCTCACACGA
66 GTAGAGCCTATAATACATTCTAGGATTCATATCTCATTTCTCGAATCACGATGCTACTCACACGA
* * *
78075 GCTTTCGAGGACTCACAACATATGTGGTACCTCAGCCATCGATATGGTATCTATGCATATAATTG
131 GCTGTCGAGAACTCACAACATATGCGGTACCTCAGCCATCGATATGGTATCTATGCATATAATTG
78140 TT
196 TT
* * * * * *
78142 TCCC-TAACGATGTTGCTCACACGAGCTGTCGAGAATATGCATTTATGCATAAATCCTAGCCATC
1 TCCCTTAACAATGCTGCTCACACGAGCTGTCGAAAATATGCATTTAAGCATAAATCCCAACCATC
* * * * * * * *
78206 GTAGGGCTTGTAATCCATTCTTGGATTCATTTCTCATTTCTCGACTCATGATGCTACTCACACGA
66 GTAGAGCCTATAATACATTCTAGGATTCATATCTCATTTCTCGAATCACGATGCTACTCACACGA
**
78271 GCTGTCGAGAACTCGTAACATATGCGGTACC
131 GCTGTCGAGAACTCACAACATATGCGGTACC
78302 CTATTCATCG
Statistics
Matches: 135, Mismatches: 23, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
194 69 0.51
195 16 0.12
196 50 0.37
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (197 bp):
TCCCTTAACAATGCTGCTCACACGAGCTGTCGAAAATATGCATTTAAGCATAAATCCCAACCATC
GTAGAGCCTATAATACATTCTAGGATTCATATCTCATTTCTCGAATCACGATGCTACTCACACGA
GCTGTCGAGAACTCACAACATATGCGGTACCTCAGCCATCGATATGGTATCTATGCATATAATTG
TT
Found at i:80895 original size:18 final size:18
Alignment explanation
Indices: 80869--80903 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
80859 TTTTGAGTTG
80869 ACTCAAATAACTCGATTA
1 ACTCAAATAACTCGATTA
*
80887 ACTCGAATAACTCGATT
1 ACTCAAATAACTCGATT
80904 CGTTTAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.29
Consensus pattern (18 bp):
ACTCAAATAACTCGATTA
Found at i:84386 original size:29 final size:29
Alignment explanation
Indices: 84353--84421 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
84343 TTATGTTTTA
*
84353 GTCATTTAATTTTAAAAAGTTATAAAATG
1 GTCATTGAATTTTAAAAAGTTATAAAATG
84382 GTCATTGAATTTTAAAAAGTTATAAAATG
1 GTCATTGAATTTTAAAAAGTTATAAAATG
84411 GTCATTGAATT
1 GTCATTGAATT
84422 ATTCGAAAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.41
Consensus pattern (29 bp):
GTCATTGAATTTTAAAAAGTTATAAAATG
Found at i:94191 original size:27 final size:28
Alignment explanation
Indices: 94142--94211 Score: 124
Period size: 27 Copynumber: 2.5 Consensus size: 28
94132 TCCTAAAATG
94142 ATTAATATATTATTTATCAAAAAAATAA
1 ATTAATATATTATTTATCAAAAAAATAA
94170 ATTAATATATTATTTATC-AAAAAATAA
1 ATTAATATATTATTTATCAAAAAAATAA
*
94197 ATTAATATATCATTT
1 ATTAATATATTATTT
94212 CAACTCTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 23 0.56
28 18 0.44
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTAATATATTATTTATCAAAAAAATAA
Found at i:101923 original size:20 final size:20
Alignment explanation
Indices: 101889--101937 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 20
101879 TATAAATTTG
*
101889 AAATTTAATCTTTTTATTTTTA
1 AAATTTAAT-TTTATA-TTTTA
101911 AGAATTTAATTTTATATTTTA
1 A-AATTTAATTTTATATTTTA
101932 AAATTT
1 AAATTT
101938 TAAATTTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 5 0.20
21 6 0.24
22 6 0.24
23 8 0.32
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
AAATTTAATTTTATATTTTA
Found at i:101946 original size:22 final size:20
Alignment explanation
Indices: 101900--101937 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
101890 AATTTAATCT
101900 TTTTATTTTTAAGAATTTAA
1 TTTTATTTTTAAGAATTTAA
101920 TTTTATATTTTAA-AATTT
1 TTTTAT-TTTTAAGAATTT
101938 TAAATTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTATTTTTAAGAATTTAA
Found at i:108626 original size:22 final size:23
Alignment explanation
Indices: 108598--108640 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
108588 AAATATCTTT
108598 TTTTATATCT-TA-GTTATATTTC
1 TTTTATAT-TATATGTTATATTTC
108620 TTTTATATTATATGTTATATT
1 TTTTATATTATATGTTATATT
108641 GATTTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 1 0.05
22 10 0.53
23 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.65
Consensus pattern (23 bp):
TTTTATATTATATGTTATATTTC
Found at i:108646 original size:23 final size:22
Alignment explanation
Indices: 108598--108648 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
108588 AAATATCTTT
**
108598 TTTTATATCTTAGTTATATTTC
1 TTTTATATCTTAGTTATATTGA
108620 TTTTATAT-TATATGTTATATTGA
1 TTTTATATCT-TA-GTTATATTGA
108643 TTTTAT
1 TTTTAT
108649 TAGTATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 10 0.40
23 14 0.56
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.65
Consensus pattern (22 bp):
TTTTATATCTTAGTTATATTGA
Found at i:108727 original size:17 final size:17
Alignment explanation
Indices: 108705--108748 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
108695 TGATTCCATT
*
108705 TTTTAT-TTTCTAGTTTA
1 TTTTATATTT-TAGTATA
108722 TTTTATATTTTAGTATA
1 TTTTATATTTTAGTATA
*
108739 TTTTACATTT
1 TTTTATATTT
108749 AAATTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTTATATTTTAGTATA
Found at i:109038 original size:27 final size:28
Alignment explanation
Indices: 109008--109064 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 28
108998 AAATGAATGG
109008 AATAATTAGTTCTAGTTATTA-AATATA
1 AATAATTAGTTCTAGTTATTATAATATA
*
109035 AATAATTAGTTCTAGTTATTATATTATA
1 AATAATTAGTTCTAGTTATTATAATATA
109063 AA
1 AA
109065 AAATAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.46
Consensus pattern (28 bp):
AATAATTAGTTCTAGTTATTATAATATA
Found at i:113641 original size:37 final size:37
Alignment explanation
Indices: 113591--113661 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
113581 TGTGGGTGAA
113591 AGAATCTGTTTTACCATTAGGAAGATGAACAATACGT
1 AGAATCTGTTTTACCATTAGGAAGATGAACAATACGT
*
113628 AGAATTTGTTTTACCATTAGGAAGATGAACAATA
1 AGAATCTGTTTTACCATTAGGAAGATGAACAATA
113662 TGTGGTTCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.31
Consensus pattern (37 bp):
AGAATCTGTTTTACCATTAGGAAGATGAACAATACGT
Found at i:118345 original size:29 final size:27
Alignment explanation
Indices: 118292--118351 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
118282 GTGCTTAATG
** * *
118292 TTTTTTTTATTAATTTGGTTTTTACTT
1 TTTTTTTTATTAATTTGACTGTTACTA
118319 TTTTTTTTAATTAAATTTGACTGTTACTA
1 TTTTTTTT-ATT-AATTTGACTGTTACTA
118348 TTTT
1 TTTT
118352 ATAAATAGTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 8 0.30
28 3 0.11
29 16 0.59
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (27 bp):
TTTTTTTTATTAATTTGACTGTTACTA
Found at i:119326 original size:21 final size:22
Alignment explanation
Indices: 119289--119329 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
119279 ATTCCAACAT
119289 AACAATCGATTTAAAACATATA
1 AACAATCGATTTAAAACATATA
119311 AACAATCGATTT-AAACATA
1 AACAATCGATTTAAAACATA
119330 CTTCTTCCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.27
Consensus pattern (22 bp):
AACAATCGATTTAAAACATATA
Found at i:123614 original size:2 final size:2
Alignment explanation
Indices: 123607--123646 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
123597 TTTGCATGGA
123607 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
123647 GAAAGGGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.