Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010892.1 Kokia drynarioides strain JFW-HI SEQ_125860, 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: 124718
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 9 characters in sequence are not A, C, G, or T
Found at i:70 original size:28 final size:27
Alignment explanation
Indices: 23--105 Score: 64
Period size: 28 Copynumber: 3.0 Consensus size: 27
13 TTATAAAATT
23 TAATTAGAATA-TATAA-ATTATATTTTAAA
1 TAATTA-AATATTA-AACATTATATTTT--A
* * *
52 TATTTAAATA-TAATCATTAAATATTTA
1 TAATTAAATATTAAACATTATAT-TTTA
79 TAATTAAATATTAAACATTATTATTTT
1 TAATTAAATATTAAACATTA-TATTTT
106 TTTTAAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
27 11 0.25
28 23 0.52
29 10 0.23
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (27 bp):
TAATTAAATATTAAACATTATATTTTA
Found at i:91 original size:21 final size:20
Alignment explanation
Indices: 25--93 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 20
15 ATAAAATTTA
* *
25 ATTAGAATATATAAATTATAT
1 ATTA-AATATTTAAATTAAAT
*
46 TTTAAATATTTAAA-TATAAT
1 ATTAAATATTTAAATTA-AAT
66 CATTAAATATTTATAATTAAAT
1 -ATTAAATATTTA-AATTAAAT
88 ATTAAA
1 ATTAAA
94 CATTATTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 2 0.05
20 11 0.28
21 20 0.50
22 5 0.12
23 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (20 bp):
ATTAAATATTTAAATTAAAT
Found at i:9969 original size:39 final size:39
Alignment explanation
Indices: 9915--9990 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
9905 TTGGTTTTGT
9915 GGAGGTTTAGGCGGACTATACGGAGAATGGATACACAGC
1 GGAGGTTTAGGCGGACTATACGGAGAATGGATACACAGC
9954 GGAGGTTTAGGCGGACTATACGGAGAATGGATACACA
1 GGAGGTTTAGGCGGACTATACGGAGAATGGATACACA
9991 TGATATTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.32, C:0.14, G:0.36, T:0.18
Consensus pattern (39 bp):
GGAGGTTTAGGCGGACTATACGGAGAATGGATACACAGC
Found at i:10379 original size:45 final size:44
Alignment explanation
Indices: 10330--10454 Score: 162
Period size: 45 Copynumber: 2.8 Consensus size: 44
10320 TACTATATTC
* * *
10330 ATGAAGTTTCTTCTATGAA-TTCACATGTACGAGTCTGCCATATCT
1 ATGAA-TTTCTTCTA-CAAGTTCACATGTATGAGTCTACCATATCT
* *
10375 ATGAATCTTCTTATACAAGTTCACATGTATGAGTCTATCATATCT
1 ATGAAT-TTCTTCTACAAGTTCACATGTATGAGTCTACCATATCT
10420 ATGAATTTTCTTCTACAAGTTCACATGTATGAGTC
1 ATGAA-TTTCTTCTACAAGTTCACATGTATGAGTC
10455 CGCATGAAAG
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
44 3 0.04
45 67 0.94
46 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (44 bp):
ATGAATTTCTTCTACAAGTTCACATGTATGAGTCTACCATATCT
Found at i:11751 original size:17 final size:17
Alignment explanation
Indices: 11699--11753 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
11689 AATTAATTAT
*
11699 TTTTTAAAATATCAAATAA
1 TTTTTAAAA-ATTAAA-AA
* * *
11718 TTTTTATAATTTTAAAA
1 TTTTTAAAAATTAAAAA
11735 TTTTTAAAAATTAAAAA
1 TTTTTAAAAATTAAAAA
11752 TT
1 TT
11754 AATTAATTAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
17 18 0.62
18 3 0.10
19 8 0.28
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTTAAAAATTAAAAA
Found at i:12217 original size:4 final size:4
Alignment explanation
Indices: 12208--12236 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
12198 TTACTACTAC
12208 TATT TATT TATT TATT TATT TA-T TATT TA
1 TATT TATT TATT TATT TATT TATT TATT TA
12237 AAATATCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TATT
Found at i:16650 original size:14 final size:15
Alignment explanation
Indices: 16624--16655 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
16614 TGTCCCCAAA
16624 AAGAAAAAGAAAAAG
1 AAGAAAAAGAAAAAG
16639 AAGAAAAA-AAAAAG
1 AAGAAAAAGAAAAAG
16653 AAG
1 AAG
16656 GGCTCTGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAGAAAAAGAAAAAG
Found at i:24880 original size:2 final size:2
Alignment explanation
Indices: 24873--24899 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24863 ATATGATCAT
24873 TA 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 TA T
24900 CATGAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30338 original size:13 final size:13
Alignment explanation
Indices: 30304--30339 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
30294 AAAATTCCTA
*
30304 AGAATAAAAAAAG
1 AGAATAAACAAAG
*
30317 TGAATAAACAAAG
1 AGAATAAACAAAG
30330 AGAATAAACA
1 AGAATAAACA
30340 CAAATAATCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.69, C:0.06, G:0.14, T:0.11
Consensus pattern (13 bp):
AGAATAAACAAAG
Found at i:30941 original size:46 final size:46
Alignment explanation
Indices: 30874--30977 Score: 199
Period size: 46 Copynumber: 2.3 Consensus size: 46
30864 TCCAAATAAG
30874 AAAAGGCAAAACTACATCGTTTTGATAAATATTTACTCATTAAGTT
1 AAAAGGCAAAACTACATCGTTTTGATAAATATTTACTCATTAAGTT
*
30920 AAAAGGCAAAACTACGTCGTTTTGATAAATATTTACTCATTAAGTT
1 AAAAGGCAAAACTACATCGTTTTGATAAATATTTACTCATTAAGTT
30966 AAAAGGCAAAAC
1 AAAAGGCAAAAC
30978 CATTATATTA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 57 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.31
Consensus pattern (46 bp):
AAAAGGCAAAACTACATCGTTTTGATAAATATTTACTCATTAAGTT
Found at i:45135 original size:91 final size:91
Alignment explanation
Indices: 44998--45167 Score: 214
Period size: 91 Copynumber: 1.9 Consensus size: 91
44988 CATTGGCAGC
* * * * ** *
44998 TTTTATCTACAAATACGTTGTGCATTCATAACTTACTGACGGCGTATTAACTTGCAGACACTGAT
1 TTTTATCAACAAACACGTTGTGCATTCACAACCTACTGACAACGTATTAACTTGCAAACACTGAT
*
45063 AGTTCATCCACAAACTTACTAACAAA
66 AGCTCATCCACAAACTTACTAACAAA
* * * * *
45089 TTTTATCAACAAACATGTTGTGCATTTACAACCTACTGGCAACGTATTAACTTGCAAACATTGGT
1 TTTTATCAACAAACACGTTGTGCATTCACAACCTACTGACAACGTATTAACTTGCAAACACTGAT
*
45154 GGCTCATCCACAAA
66 AGCTCATCCACAAA
45168 TTGGAGTGTT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
91 65 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (91 bp):
TTTTATCAACAAACACGTTGTGCATTCACAACCTACTGACAACGTATTAACTTGCAAACACTGAT
AGCTCATCCACAAACTTACTAACAAA
Found at i:49269 original size:212 final size:210
Alignment explanation
Indices: 48768--49391 Score: 913
Period size: 212 Copynumber: 3.0 Consensus size: 210
48758 GAATGAGAAG
* * * *
48768 CTTTTATTTGTTTGCTTCACTTCTTGGGTTGAATCCAATGTTGCAAAAAGG-ATGATATTCAATC
1 CTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAATGTTGC-AAAAGGAATGATCTTCAGTT
* * * *
48832 CTTTCATGTACTTTATTTCCCATTGAATTTGTTTTTTTCAATTTGTTTTCATTGCATCATTCGGT
65 CTTTCATGTACTTTATTTCCCATTGAATGTGGTTTTTTCAATTTGTTTTCATTACTTCATTCGGT
* * * *
48897 ATGAGCTATGTTACCCAGGCACAAGTGGATCTTGGTTGCTGACATTTGTCTAACACTGATATGCT
130 ATGAGCTATGTTACCCAGGCTCAAGTGAATCTTGGATGCTGACATTTGTCCAACACTGATATGCT
*
48962 AAAGCTTTCGAAGTGA
195 AAACCTTTCGAAGTGA
*
48978 -----A-TTGTTTGCTTCACTGCTTGGGTTGAATCCAATGTTGCAAAAAGAATGATCTTCAGTTC
1 CTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAATGTTGCAAAAGGAATGATCTTCAGTTC
* * *
49037 TCTCATGTACTTTATTTCCCATTGAATGTGGTTTTTTCAATTTGTTTTCATTACTTAATTTGGTA
66 TTTCATGTACTTTATTTCCCATTGAATGTGGTTTTTTCAATTTGTTTTCATTACTTCATTCGGTA
*
49102 TGAGCTATGTTACCCAGGCTCAAGTGAATCTTGGATGCTGACTTTTGTCCAACACTGATATGCTA
131 TGAGCTATGTTACCCAGGCTCAAGTGAATCTTGGATGCTGACATTTGTCCAACACTGATATGCTA
* *
49167 AACCTTTCTAGGTGAA
196 AACCTTTCGAAGTG-A
49183 TCTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAA-GATTGCAAAAGGAATGATCTTCAGT
1 -CTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAATG-TTGCAAAAGGAATGATCTTCAGT
* * *
49247 TCTTTCATGTACTTTATTTCCCATTGAATGTGGTTTTCTCAATTTGTTTTCTTTACTTCATTCAG
64 TCTTTCATGTACTTTATTTCCCATTGAATGTGGTTTTTTCAATTTGTTTTCATTACTTCATTCGG
* * *
49312 TATGAGCTATGTTACCCAGGCTCAAGTCAATCTTGGATGCTGACATTTGCCCAACACTGATATAC
129 TATGAGCTATGTTACCCAGGCTCAAGTGAATCTTGGATGCTGACATTTGTCCAACACTGATATGC
*
49377 TAAACCTTTCCAAGT
194 TAAACCTTTCGAAGT
49392 TTTTCATATA
Statistics
Matches: 371, Mismatches: 33, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
203 5 0.01
204 176 0.47
205 2 0.01
211 2 0.01
212 186 0.50
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.41
Consensus pattern (210 bp):
CTTTTATTTGTTTGCTTCACTGCTTGGGTTGAATCCAATGTTGCAAAAGGAATGATCTTCAGTTC
TTTCATGTACTTTATTTCCCATTGAATGTGGTTTTTTCAATTTGTTTTCATTACTTCATTCGGTA
TGAGCTATGTTACCCAGGCTCAAGTGAATCTTGGATGCTGACATTTGTCCAACACTGATATGCTA
AACCTTTCGAAGTGA
Found at i:52741 original size:20 final size:20
Alignment explanation
Indices: 52713--52826 Score: 64
Period size: 20 Copynumber: 5.9 Consensus size: 20
52703 TCACATTAGC
*
52713 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
*
52733 AAATTATTTTTAAAA-AATATA
1 AAATTA-TTTTAAAATTAT-TA
*
52754 AAATTA--TTAAAACTATTTTA
1 AAATTATTTTAAAA-T-TATTA
* * *
52774 AAATTAATTT--AATTTTTT
1 AAATTATTTTAAAATTATTA
* *
52792 TAACTA---TAAAATTATTA
1 AAATTATTTTAAAATTATTA
52809 AAATTATTTTAAAATTAT
1 AAATTATTTTAAAATTAT
52827 AAGCATCATC
Statistics
Matches: 71, Mismatches: 11, Indels: 24
0.67 0.10 0.23
Matches are distributed among these distances:
15 1 0.01
17 10 0.14
18 14 0.20
19 1 0.01
20 26 0.37
21 17 0.24
22 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:53778 original size:11 final size:11
Alignment explanation
Indices: 53762--53829 Score: 51
Period size: 11 Copynumber: 6.6 Consensus size: 11
53752 GATGATGGTT
53762 ATAATTTTAAA
1 ATAATTTTAAA
53773 ATAATTTT--A
1 ATAATTTTAAA
53782 ATAATTTT---
1 ATAATTTTAAA
53790 AT-ATTTTAAA
1 ATAATTTTAAA
53800 A-AATAATTTAAA
1 ATAAT--TTTAAA
*
53812 TTAATTTTAAA
1 ATAATTTTAAA
*
53823 ATCATTT
1 ATAATTT
53830 ATTGACGTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 14
0.73 0.05 0.22
Matches are distributed among these distances:
7 5 0.11
8 2 0.04
9 9 0.19
10 3 0.06
11 19 0.40
12 6 0.13
13 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (11 bp):
ATAATTTTAAA
Found at i:53801 original size:28 final size:30
Alignment explanation
Indices: 53760--53820 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
53750 ATGATGATGG
*
53760 TTATAATTTT-AAAATAATTTTAA-TAATT
1 TTATAATTTTAAAAATAATTTAAATTAATT
53788 TTAT-ATTTTAAAAAATAATTTAAATTAATT
1 TTATAATTTT-AAAAATAATTTAAATTAATT
53818 TTA
1 TTA
53821 AAATCATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 5 0.17
28 4 0.14
29 12 0.41
30 8 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TTATAATTTTAAAAATAATTTAAATTAATT
Found at i:54501 original size:21 final size:21
Alignment explanation
Indices: 54477--54530 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
54467 GCACCCTCAA
* *
54477 CACCGCAAAACTCTCACCAGC
1 CACCGCAAAACCCTCACCAAC
54498 CACCGCAAAACCCTCACCAAC
1 CACCGCAAAACCCTCACCAAC
*
54519 CACTGCAAAACC
1 CACCGCAAAACC
54531 TTAAACCCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.48, G:0.07, T:0.07
Consensus pattern (21 bp):
CACCGCAAAACCCTCACCAAC
Found at i:55588 original size:54 final size:54
Alignment explanation
Indices: 55530--55636 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
55520 CTCGTGAACT
*
55530 GCTCAAAGGTAAGTACTAGGATAATCAAAATTAGCACAATTGATAACTTGAGCA
1 GCTCAAAGGTAAGTACTAGGATAATCAAAATTAGCACAATCGATAACTTGAGCA
* * * *
55584 GCTCAAAGGTAAGTATTAGGATACTCGAATTTAGCACAATCGATAACTTGAGC
1 GCTCAAAGGTAAGTACTAGGATAATCAAAATTAGCACAATCGATAACTTGAGC
55637 TGCAAAAGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (54 bp):
GCTCAAAGGTAAGTACTAGGATAATCAAAATTAGCACAATCGATAACTTGAGCA
Found at i:74183 original size:2 final size:2
Alignment explanation
Indices: 74176--74215 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
74166 AGGAAGGTGT
*
74176 TA TA TA TA TA TA TA CA 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
74216 AAAGCTAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:74326 original size:2 final size:2
Alignment explanation
Indices: 74319--74343 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
74309 CGTTGGATCC
74319 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
74344 AACTTCGTTT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:76062 original size:16 final size:17
Alignment explanation
Indices: 76037--76071 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
76027 CTTTATATAA
76037 AAAAATTTTAAAAATAT
1 AAAAATTTTAAAAATAT
76054 AAAAA-TTTAAAAATAT
1 AAAAATTTTAAAAATAT
76070 AA
1 AA
76072 TACATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAATTTTAAAAATAT
Found at i:78433 original size:23 final size:23
Alignment explanation
Indices: 78403--78478 Score: 116
Period size: 23 Copynumber: 3.2 Consensus size: 23
78393 GCACGTCTCA
78403 TGCTCTCTGTTATTAGCACTATGTG
1 TGCTCTCTG--ATTAGCACTATGTG
*
78428 TGCTCTCTGATTAGCACTGTGTG
1 TGCTCTCTGATTAGCACTATGTG
*
78451 TGCTCTCTGATTAGCACTTTGTG
1 TGCTCTCTGATTAGCACTATGTG
78474 TGCTC
1 TGCTC
78479 AGTACTTTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 40 0.82
25 9 0.18
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.42
Consensus pattern (23 bp):
TGCTCTCTGATTAGCACTATGTG
Found at i:78433 original size:48 final size:46
Alignment explanation
Indices: 78372--78478 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 46
78362 CATTAAGGAA
* *
78372 CACTA-GTGCGCTCTCTGTTTAGCAC-GTCTCATGCTCTCTGTTATTAG
1 CACTATGTGTGCTCTCTGATTAGCACTGTCT-ATGCTCTCTG--ATTAG
* *
78419 CACTATGTGTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAG
1 CACTATGTGTGCTCTCTGATTAGCACTGTCTATGCTCTCTGATTAG
*
78465 CACTTTGTGTGCTC
1 CACTATGTGTGCTC
78479 AGTACTTTGT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
46 18 0.34
47 5 0.09
48 27 0.51
49 3 0.06
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.39
Consensus pattern (46 bp):
CACTATGTGTGCTCTCTGATTAGCACTGTCTATGCTCTCTGATTAG
Found at i:82735 original size:23 final size:23
Alignment explanation
Indices: 82578--82735 Score: 158
Period size: 23 Copynumber: 6.8 Consensus size: 23
82568 ACACTAGCGC
* *
82578 GCTCTCTGATTAGTA-TTGTGTGT
1 GCTCTCTGTTTAGCACTT-TGTGT
*
82601 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* * * *
82624 GCCCTCTGTTTATCACATCT-CGT
1 GCTCTCTGTTTAGCAC-TTTGTGT
*
82647 GCTCTCTGTTATTAGCACTTCGTGT
1 GCTCTCTG-T-TTAGCACTTTGTGT
*
82672 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
82695 ACTCTGTGTTTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
82718 GCTCTCTGTTTAGTACTT
1 GCTCTCTGTTTAGCACTT
82736 CTGTACTCTC
Statistics
Matches: 110, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
23 89 0.81
24 5 0.05
25 16 0.15
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTTTGTGT
Found at i:82750 original size:22 final size:23
Alignment explanation
Indices: 82602--82750 Score: 106
Period size: 23 Copynumber: 6.4 Consensus size: 23
82592 ATTGTGTGTG
* * *
82602 CTCTCTGTTTAGCACTGTGTGTG
1 CTCTCTGTTTAGCACTTTCTGTA
* * * *
82625 CCCTCTGTTTATCAC-ATCTCGTG
1 CTCTCTGTTTAGCACTTTCT-GTA
*
82648 CTCTCTGTTATTAGCAC-TTCGTGTG
1 CTCTCTG-T-TTAGCACTTTC-TGTA
* *
82673 CTCTCTGATTAGCACTTTGTGTA
1 CTCTCTGTTTAGCACTTTCTGTA
* * *
82696 CTCTGTGTTTAGCACTTTGTGTG
1 CTCTCTGTTTAGCACTTTCTGTA
*
82719 CTCTCTGTTTAGTAC-TTCTGTA
1 CTCTCTGTTTAGCACTTTCTGTA
*
82741 CTCTCCGTTT
1 CTCTCTGTTT
82751 GTTTCGTTTA
Statistics
Matches: 103, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
22 16 0.16
23 65 0.63
24 3 0.03
25 18 0.17
26 1 0.01
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (23 bp):
CTCTCTGTTTAGCACTTTCTGTA
Found at i:84806 original size:3 final size:3
Alignment explanation
Indices: 84798--84824 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
84788 GCCTGCACAT
84798 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
84825 TGATAACCCA
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:86039 original size:25 final size:26
Alignment explanation
Indices: 85981--86040 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
85971 TTTTTTTTTT
*
85981 ACTTTTAAAAATTAAAAAAAAATTGA
1 ACTTTTAAAAATTAAAAAAAAAATGA
*
86007 ACTCTTAAAAATTAAAAAAAAACAT-A
1 ACTTTTAAAAATTAAAAAAAAA-ATGA
86033 A-TTTTAAA
1 ACTTTTAAA
86041 CTTTTTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 6 0.20
26 23 0.77
27 1 0.03
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.30
Consensus pattern (26 bp):
ACTTTTAAAAATTAAAAAAAAAATGA
Found at i:87658 original size:3 final size:3
Alignment explanation
Indices: 87650--87682 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
87640 AAGTAATGAC
87650 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
87683 TACAGTAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:97269 original size:18 final size:17
Alignment explanation
Indices: 97233--97294 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
97223 ATTTATTCTA
*
97233 AAATCTAAATTTAATTT
1 AAATTTAAATTTAATTT
*
97250 AAGTTTAAATTTATATTT
1 AAATTTAAATTTA-ATTT
**
97268 AAATTTAAAACT-ATTAT
1 AAATTTAAATTTAATT-T
97285 AAATTTAAAT
1 AAATTTAAAT
97295 AAATCCAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
16 3 0.08
17 21 0.57
18 13 0.35
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (17 bp):
AAATTTAAATTTAATTT
Found at i:97294 original size:6 final size:6
Alignment explanation
Indices: 97233--97276 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
97223 ATTTATTCTA
* * *
97233 AAATCT AAATTT -AATTT AAGTTT AAATTT ATATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAA
97277 ACTATTATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:97963 original size:3 final size:3
Alignment explanation
Indices: 97955--98083 Score: 129
Period size: 3 Copynumber: 43.0 Consensus size: 3
97945 TAAATATCCT
97955 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -ATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
* * * * * * *
98000 TAA TAC TAA TGA CAT TAA TAA TAG TAA TAA TAT TAA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
98048 TAA TGAA T-T TAT TAA TAA TAA TAAA TAA T-A TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
98084 ATAAAAATGG
Statistics
Matches: 104, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
2 4 0.04
3 93 0.89
4 7 0.07
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:98376 original size:20 final size:22
Alignment explanation
Indices: 98351--98396 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
98341 GGTTTTTTAA
98351 AAAAAAAGAAAAAGA-AA-AAG
1 AAAAAAAGAAAAAGATAAGAAG
* *
98371 AAAAAATGAAACAGATAAGAAG
1 AAAAAAAGAAAAAGATAAGAAG
98393 AAAA
1 AAAA
98397 GGGAAGGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
21 2 0.09
22 7 0.32
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.04
Consensus pattern (22 bp):
AAAAAAAGAAAAAGATAAGAAG
Found at i:99263 original size:30 final size:29
Alignment explanation
Indices: 99219--99439 Score: 173
Period size: 30 Copynumber: 7.5 Consensus size: 29
99209 AAAGGTCCCT
* *
99219 AAACTATTCAAAAATTATATTTTGACTCTC
1 AAACTTTTCCAAAATTATATTTTGAC-CTC
* * *
99249 AAACTTTTCCAAAATTACATTTTAACACTT
1 AAACTTTTCCAAAATTATATTTTGAC-CTC
* *
99279 AAACTTTTACAAAATTATATTTTGACCCTT
1 AAACTTTTCCAAAATTATATTTTGA-CCTC
* * *
99309 AAACTTCTCCAAAATTATACTTTGACCCC
1 AAACTTTTCCAAAATTATATTTTGACCTC
* * *
99338 TTAAC-TTTCCAAAAATTTACATTTT-ACCCC
1 -AAACTTTTCC-AAAA-TTATATTTTGACCTC
*
99368 AAAC-TTTCCAAAATTCTATTTTTGACCTC
1 AAACTTTTCCAAAATTATA-TTTTGACCTC
* * * *
99397 AAACTTTT-GAAAATTACATTTTTACCCCC
1 AAACTTTTCCAAAATTATATTTTGA-CCTC
99426 AAAC-TTTCCAAAAT
1 AAACTTTTCCAAAAT
99440 CCCATTTTTG
Statistics
Matches: 154, Mismatches: 28, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
27 3 0.02
28 16 0.10
29 41 0.27
30 86 0.56
31 8 0.05
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (29 bp):
AAACTTTTCCAAAATTATATTTTGACCTC
Found at i:99503 original size:28 final size:29
Alignment explanation
Indices: 99472--99526 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
99462 CTTAAAATGA
99472 CCATTAT-ACCCTCGA-ACTTCCAAAAATT
1 CCATTATGA-CCTCGATACTTCCAAAAATT
* *
99500 CCATTTTGACCTCGATTCTTCCAAAAA
1 CCATTATGACCTCGATACTTCCAAAAA
99527 GTACTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (29 bp):
CCATTATGACCTCGATACTTCCAAAAATT
Found at i:99520 original size:29 final size:30
Alignment explanation
Indices: 99431--99603 Score: 98
Period size: 29 Copynumber: 5.9 Consensus size: 30
99421 CCCCCAAACT
* *
99431 TTCC-AAAATCCCATTTTTGA-CCTCGATTT
1 TTCCAAAAATTCCA-TTTTGACCCTCGATTC
** * * *
99460 TTCTTAAAATGACCATTAT-ACCCTCGA-AC
1 TTCCAAAAAT-TCCATTTTGACCCTCGATTC
99489 TTCCAAAAATTCCATTTTGA-CCTCGATTC
1 TTCCAAAAATTCCATTTTGACCCTCGATTC
* * *
99518 TTCCAAAAAGTACTATTTT-ACCCCTGGATGTC
1 TTCCAAAAA-TTCCATTTTGA-CCCTCGAT-TC
*
99550 -T--AAAAATTCCATTTTTGACCCTCGACT-
1 TTCCAAAAATTCCA-TTTTGACCCTCGATTC
*
99577 TTCCCAAAATTACCATTTTG-CCCTCGA
1 TTCCAAAAATT-CCATTTTGACCCTCGA
99604 GTAACCAAAA
Statistics
Matches: 111, Mismatches: 18, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
28 17 0.15
29 46 0.41
30 33 0.30
31 13 0.12
32 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (30 bp):
TTCCAAAAATTCCATTTTGACCCTCGATTC
Found at i:99540 original size:58 final size:57
Alignment explanation
Indices: 99343--99603 Score: 171
Period size: 58 Copynumber: 4.5 Consensus size: 57
99333 ACCCCTTAAC
* * *
99343 TTTCCAAAAATTTA-CATTTTACCC-CAAACTTTCC-AAAATTCTATTTTTGACCTCAAACT
1 TTTCCAAAAA--TACCATTTTACCCTCGAAC-TTCCAAAAATTCCATTTTTGACCTC-GA-T
* * * * *
99402 TTT-GAAAATTA-CATTTTTACCCCCAAACTTTCC-AAAATCCCATTTTTGACCTCGATT
1 TTTCCAAAAATACCA-TTTTACCCTCGAAC-TTCCAAAAATTCCATTTTTGACCTCGA-T
** *
99459 TTTCTTAAAATGACCATTATACCCTCGAACTTCCAAAAATTCCA-TTTTGACCTCGAT
1 TTTCCAAAAAT-ACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAT
* * *
99516 TCTTCCAAAAAGTACTATTTTACCC-CTGGA-TGTCTAAAAATTCCATTTTTGACCCTCGACT
1 T-TTCCAAAAA-TACCATTTTACCCTC-GAACT-TCCAAAAATTCCATTTTTGA-CCTCGA-T
* * *
99577 TTCCCAAAATTACCATTTTGCCCTCGA
1 TTTCCAAAAATACCATTTTACCCTCGA
99604 GTAACCAAAA
Statistics
Matches: 164, Mismatches: 24, Indels: 28
0.76 0.11 0.13
Matches are distributed among these distances:
56 4 0.02
57 17 0.10
58 83 0.51
59 42 0.26
60 16 0.10
61 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.37
Consensus pattern (57 bp):
TTTCCAAAAATACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCGAT
Found at i:99617 original size:28 final size:28
Alignment explanation
Indices: 99580--99641 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
99570 CTCGACTTTC
* *
99580 CCAAAATTACCATTTTGCCCTCGAGTAA
1 CCAAAATTACCATTTTACCCCCGAGTAA
* *
99608 CCAAAATTACCATTTTACCCCCGGGTAT
1 CCAAAATTACCATTTTACCCCCGAGTAA
99636 CCAAAA
1 CCAAAA
99642 ATCACATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.34, C:0.31, G:0.10, T:0.26
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCCCGAGTAA
Found at i:102597 original size:38 final size:38
Alignment explanation
Indices: 102555--102631 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
102545 CGTTAATTAG
*
102555 ATAGTTAGTTATGGTACAAGTGGTTTGACCCTAAAGTT
1 ATAGTTAATTATGGTACAAGTGGTTTGACCCTAAAGTT
*
102593 ATAGTTAATTATGGTACAAGTTGTTTGACCCTAAAGTT
1 ATAGTTAATTATGGTACAAGTGGTTTGACCCTAAAGTT
102631 A
1 A
102632 GTGGCTTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (38 bp):
ATAGTTAATTATGGTACAAGTGGTTTGACCCTAAAGTT
Found at i:111561 original size:20 final size:20
Alignment explanation
Indices: 111521--111561 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
111511 AATGTGAAAA
* *
111521 AGGACTAAATTGTAAACTTG
1 AGGACTAAAATGAAAACTTG
*
111541 AGGACTAAAATGAAAATTTG
1 AGGACTAAAATGAAAACTTG
111561 A
1 A
111562 ACAACACAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.27
Consensus pattern (20 bp):
AGGACTAAAATGAAAACTTG
Found at i:118175 original size:15 final size:16
Alignment explanation
Indices: 118150--118180 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
118140 AATAACGAAG
118150 TTTATTTTATTATTTA
1 TTTATTTTATTATTTA
118166 TTTA-TTTATTATTTA
1 TTTATTTTATTATTTA
118181 CACTTATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATTTTATTATTTA
Found at i:118903 original size:23 final size:24
Alignment explanation
Indices: 118877--118927 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
118867 AAAAGGGATT
**
118877 TAAAATTAAAATTAAAAC-TAAAA
1 TAAAATTAAAAAGAAAACATAAAA
*
118900 T-AAATTAAAAAGAAATCATAAAA
1 TAAAATTAAAAAGAAAACATAAAA
118923 TAAAA
1 TAAAA
118928 AAAATCACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 13 0.57
23 7 0.30
24 3 0.13
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.24
Consensus pattern (24 bp):
TAAAATTAAAAAGAAAACATAAAA
Found at i:118926 original size:18 final size:17
Alignment explanation
Indices: 118899--118934 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
118889 TAAAACTAAA
*
118899 ATAAATTAAAAAGAAATC
1 ATAAAATAAAAA-AAATC
118917 ATAAAATAAAAAAAATC
1 ATAAAATAAAAAAAATC
118934 A
1 A
118935 CCAATAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (17 bp):
ATAAAATAAAAAAAATC
Done.