Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012981.1 Kokia drynarioides strain JFW-HI SEQ_127999, 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: 145391
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 105 characters in sequence are not A, C, G, or T
Found at i:456 original size:20 final size:20
Alignment explanation
Indices: 431--503 Score: 89
Period size: 20 Copynumber: 3.7 Consensus size: 20
421 AAAAATATAA
431 ATTTTGAATTTTTTATAAA-T
1 ATTTTGAATTTTTTA-AAATT
451 ATTTTG-A-TTTTTAAAAGTT
1 ATTTTGAATTTTTTAAAA-TT
* *
470 ATTTTTAATTTTTGAAAATT
1 ATTTTGAATTTTTTAAAATT
490 ATTTTGAATTTTTT
1 ATTTTGAATTTTTT
504 TTTTTTGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.07
18 6 0.13
19 7 0.16
20 21 0.47
21 8 0.18
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.62
Consensus pattern (20 bp):
ATTTTGAATTTTTTAAAATT
Found at i:3725 original size:25 final size:24
Alignment explanation
Indices: 3666--3811 Score: 139
Period size: 24 Copynumber: 6.0 Consensus size: 24
3656 CTGGTTAAAC
* *
3666 TCTATCTAGGCTCGTAAGAGCTAA
1 TCTATCTGGGCTCGTATGAGCTAA
* *
3690 CCTATCTGGGCTTGTATGAGCTAA
1 TCTATCTGGGCTCGTATGAGCTAA
* *
3714 TTCTGTCTGGGCTCGAATGAGCTAA
1 -TCTATCTGGGCTCGTATGAGCTAA
* * * *
3739 TCTATCTGAGTTCATAAGAGCTAA
1 TCTATCTGGGCTCGTATGAGCTAA
* *
3763 TCTATTTGGGATCGTATGAGCTAA
1 TCTATCTGGGCTCGTATGAGCTAA
* * *
3787 TTTTGTCTGGGCTCGAATGAGCTAA
1 -TCTATCTGGGCTCGTATGAGCTAA
3812 ATTTTTCGAA
Statistics
Matches: 96, Mismatches: 24, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
24 57 0.59
25 39 0.41
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (24 bp):
TCTATCTGGGCTCGTATGAGCTAA
Found at i:12404 original size:10 final size:10
Alignment explanation
Indices: 12386--12422 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
12376 CATTCTCTTT
*
12386 TATTATTTTA
1 TATTTTTTTA
12396 TATTTTTTTA
1 TATTTTTTTA
12406 T-TTTTTTT-
1 TATTTTTTTA
12414 TATTTTTTT
1 TATTTTTTT
12423 CTTTATACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
8 1 0.04
9 14 0.56
10 10 0.40
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TATTTTTTTA
Found at i:12406 original size:18 final size:18
Alignment explanation
Indices: 12383--12422 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12373 AAGCATTCTC
12383 TTTTATTATTTTATATTT
1 TTTTATTATTTTATATTT
* *
12401 TTTTATTTTTTTTTATTT
1 TTTTATTATTTTATATTT
12419 TTTT
1 TTTT
12423 CTTTATACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTATTATTTTATATTT
Found at i:16157 original size:20 final size:20
Alignment explanation
Indices: 16129--16166 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16119 GATTCAAGGT
16129 TTAAAGTTTTGAGTTTAAAC
1 TTAAAGTTTTGAGTTTAAAC
* *
16149 TTAAGGTTTTGGGTTTAA
1 TTAAAGTTTTGAGTTTAA
16167 TTTTTGAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (20 bp):
TTAAAGTTTTGAGTTTAAAC
Found at i:17874 original size:16 final size:16
Alignment explanation
Indices: 17855--17887 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17845 TAATTTCTAC
17855 TTATATTTCTTGTTTA
1 TTATATTTCTTGTTTA
17871 TTATATTTCTTGTTTA
1 TTATATTTCTTGTTTA
17887 T
1 T
17888 GACGTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (16 bp):
TTATATTTCTTGTTTA
Found at i:20252 original size:30 final size:30
Alignment explanation
Indices: 20192--20597 Score: 350
Period size: 30 Copynumber: 13.6 Consensus size: 30
20182 GATAATACGA
* * **
20192 GGTTAAAATATAATTTTAGAAAAAAATTAGG
1 GGTTAAAATGTAATTTTAG-GAAAGTTTAGG
*
20223 GGTAAAAATGTAATTTTAGGAAAGTTTA-G
1 GGTTAAAATGTAATTTTAGGAAAGTTTAGG
* *
20252 GGTTAAAATGTGATTTTA-GAGAAGTTTA-C
1 GGTTAAAATGTAATTTTAGGA-AAGTTTAGG
* * * * *
20281 GATCAAAATGTGATTTTGGGGAAA-TTTAAG
1 GGTTAAAATGTAATTTT-AGGAAAGTTTAGG
** * *
20311 GGTTAAAACATGATTTTA-AAGAAGTTTAGG
1 GGTTAAAATGTAATTTTAGGA-AAGTTTAGG
*
20341 GGTTAAAATGTAATTTTA-GAAGAGTTTAAG
1 GGTTAAAATGTAATTTTAGGAA-AGTTTAGG
* **
20371 GGTTAAAATGTAATTTT-GGTGAAGTTTAAT
1 GGTTAAAATGTAATTTTAGG-AAAGTTTAGG
20401 GGTTAAAATGTAATTTT-GGAAAAGTTTAGG
1 GGTTAAAATGTAATTTTAGG-AAAGTTTAGG
20431 GGTTAAAATGTAATTTT-GGAAAAGTTTAGG
1 GGTTAAAATGTAATTTTAGG-AAAGTTTAGG
*
20461 GGTTAAAATGTAATTTTAGAAAAGTTTAGG
1 GGTTAAAATGTAATTTTAGGAAAGTTTAGG
* *
20491 GGTTAAAAATATAATTTT-GGAAAAATTT-GAG
1 GGTT-AAAATGTAATTTTAGG-AAAGTTTAG-G
* *
20522 GGTTAAAATGT-ATTTTTGGAAATTTTAGG
1 GGTTAAAATGTAATTTTAGGAAAGTTTAGG
* * * * **
20551 CGTTAAAATGAAATTTTAGAAAAATTTAAA
1 GGTTAAAATGTAATTTTAGGAAAGTTTAGG
20581 GGTTAAAATGTAATTTT
1 GGTTAAAATGTAATTTT
20598 TAAAGAAAAT
Statistics
Matches: 314, Mismatches: 45, Indels: 33
0.80 0.11 0.08
Matches are distributed among these distances:
28 3 0.01
29 67 0.21
30 200 0.64
31 44 0.14
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.37
Consensus pattern (30 bp):
GGTTAAAATGTAATTTTAGGAAAGTTTAGG
Found at i:21676 original size:22 final size:20
Alignment explanation
Indices: 21603--21679 Score: 55
Period size: 23 Copynumber: 3.5 Consensus size: 20
21593 TTTTGTAGCT
* *
21603 AATAATAAATAGTAATTAATA
1 AATATTAAATA-TAATAAATA
*
21624 AGTATATTCATATATAATAAATA
1 A--ATATT-AAATATAATAAATA
*
21647 AATATTAAATATATTAATATA
1 AATATTAAATATAATAA-ATA
*
21668 TATACTTAAATA
1 AATA-TTAAATA
21680 GAAAATGCTT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 9 0.20
21 12 0.27
22 7 0.16
23 13 0.29
24 4 0.09
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (20 bp):
AATATTAAATATAATAAATA
Found at i:22912 original size:3 final size:3
Alignment explanation
Indices: 22904--22933 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
22894 GATCATCCCT
*
22904 TTC TTC TTC TTC TTC TTC TTA TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
22934 AACATCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:32662 original size:29 final size:29
Alignment explanation
Indices: 32611--32923 Score: 206
Period size: 30 Copynumber: 10.7 Consensus size: 29
32601 AAAAAATTTG
*
32611 AGGGTAAAAATGTAATTTT-GAGAAGTTT
1 AGGGTCAAAATGTAATTTTGGAGAAGTTT
* *
32639 AGGGTTAAAATGTGATTTTGGAGAAGTTT
1 AGGGTCAAAATGTAATTTTGGAGAAGTTT
* * ** *
32668 -GTGATCAAAATGTGATTTTCAAAAAGTTT
1 AG-GGTCAAAATGTAATTTTGGAGAAGTTT
* * *
32697 AAGGGTCAAAACGTGATTTTGGAGATG-TT
1 -AGGGTCAAAATGTAATTTTGGAGAAGTTT
*
32726 AGGGGTCAAAATGTAATTTTAGAGAAGTTT
1 A-GGGTCAAAATGTAATTTTGGAGAAGTTT
* * *
32756 GAGGGTCAAAATGTAATTTTGAAAAATTTT
1 -AGGGTCAAAATGTAATTTTGGAGAAGTTT
** * *
32786 ATTGTCAAAATGCAATTTTAGA-AACGTTT
1 AGGGTCAAAATGTAATTTTGGAGAA-GTTT
* * *
32815 AAAGGTCAAAATGTAATTTTGGAAAATTTT
1 -AGGGTCAAAATGTAATTTTGGAGAAGTTT
* * *
32845 AAGGGTTAAAATGTGATTTT-TAGAAAGTTT
1 -AGGGTCAAAATGTAATTTTGGAG-AAGTTT
* * * *
32875 GGAGGTTAAAATGAAATTTTGGA-AAATATT
1 AG-GGTCAAAATGTAATTTTGGAGAAGT-TT
* **
32905 TGGGTTTAAATGTAATTTT
1 AGGGTCAAAATGTAATTTT
32924 CAAAGAAAAT
Statistics
Matches: 225, Mismatches: 46, Indels: 27
0.76 0.15 0.09
Matches are distributed among these distances:
28 21 0.09
29 94 0.42
30 105 0.47
31 5 0.02
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (29 bp):
AGGGTCAAAATGTAATTTTGGAGAAGTTT
Found at i:32692 original size:88 final size:90
Alignment explanation
Indices: 32585--32781 Score: 231
Period size: 88 Copynumber: 2.2 Consensus size: 90
32575 ATACGGGGTT
* * *
32585 AAAATGTAATTTTAGAAAAAAATTTGAGGGTAAAAATGTAATTTT-GAGAAGTTTA-GGGTTAAA
1 AAAATGTAATTTT-GAAAAAAATTTAAGGGTAAAAACGTAATTTTGGAGAAG-TTAGGGGTCAAA
* * *
32648 ATGTGATTTTGGAGAAGTTTG-TGATC
64 ATGTAATTTTAGAGAAGTTTGAGGATC
* * * * * *
32674 AAAATGTGATTTT-CAAAAAGTTTAAGGGTCAAAACGTGATTTTGGAGATGTTAGGGGTCAAAAT
1 AAAATGTAATTTTGAAAAAAATTTAAGGGTAAAAACGTAATTTTGGAGAAGTTAGGGGTCAAAAT
*
32738 GTAATTTTAGAGAAGTTTGAGGGTC
66 GTAATTTTAGAGAAGTTTGAGGATC
32763 AAAATGTAATTTTGAAAAA
1 AAAATGTAATTTTGAAAAA
32782 TTTTATTGTC
Statistics
Matches: 89, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
87 27 0.30
88 31 0.35
89 27 0.30
90 4 0.04
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (90 bp):
AAAATGTAATTTTGAAAAAAATTTAAGGGTAAAAACGTAATTTTGGAGAAGTTAGGGGTCAAAAT
GTAATTTTAGAGAAGTTTGAGGATC
Found at i:32841 original size:59 final size:59
Alignment explanation
Indices: 32585--32901 Score: 225
Period size: 59 Copynumber: 5.3 Consensus size: 59
32575 ATACGGGGTT
* * * * * * *
32585 AAAATGTAATTTTAGAAAAAAATTTGAGGGTAAAAATGTAATTTT-GAGAAGTTT-AGGGTT
1 AAAATGTAATTTT-G-GAAAATTTTAAGGGTCAAAATGCAATTTTAGA-AAGTTTGAAGGTC
* * * * ** *
32645 AAAATGTGATTTTGGAGAAGTTT--GTGATCAAAATGTGATTTTCAAAAAGTTT-AAGGGTC
1 AAAATGTAATTTTGGAAAATTTTAAG-GGTCAAAATGCAATTTT-AGAAAGTTTGAA-GGTC
* * * * * * *
32704 AAAACGTGATTTTGG-AGATGTTAGGGGTCAAAATGTAATTTTAGAGAAGTTTGAGGGTC
1 AAAATGTAATTTTGGAAAATTTTAAGGGTCAAAATGCAATTTTAGA-AAGTTTGAAGGTC
* ** *
32763 AAAATGTAATTTTGAAAAATTTT-ATTGTCAAAATGCAATTTTAGAAACGTTTAAAGGTC
1 AAAATGTAATTTTGGAAAATTTTAAGGGTCAAAATGCAATTTTAGAAA-GTTTGAAGGTC
* * * * *
32822 AAAATGTAATTTTGGAAAATTTTAAGGGTTAAAATGTGATTTTTAGAAAGTTTGGAGGTT
1 AAAATGTAATTTTGGAAAATTTTAAGGGTCAAAATG-CAATTTTAGAAAGTTTGAAGGTC
*
32882 AAAATGAAATTTTGGAAAAT
1 AAAATGTAATTTTGGAAAAT
32902 ATTTGGGTTT
Statistics
Matches: 205, Mismatches: 40, Indels: 24
0.76 0.15 0.09
Matches are distributed among these distances:
56 1 0.00
57 14 0.07
58 20 0.10
59 105 0.51
60 55 0.27
61 10 0.05
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (59 bp):
AAAATGTAATTTTGGAAAATTTTAAGGGTCAAAATGCAATTTTAGAAAGTTTGAAGGTC
Found at i:33298 original size:21 final size:21
Alignment explanation
Indices: 33272--33315 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
33262 CCACTTTACA
33272 TCCTCTCTAAAAAAAAACCTC
1 TCCTCTCTAAAAAAAAACCTC
** *
33293 TCCTCTCTTCAAAAAACCCTC
1 TCCTCTCTAAAAAAAAACCTC
33314 TC
1 TC
33316 AAGGCTTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.39, G:0.00, T:0.27
Consensus pattern (21 bp):
TCCTCTCTAAAAAAAAACCTC
Found at i:33639 original size:11 final size:11
Alignment explanation
Indices: 33623--33672 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
33613 TTAGAATCTG
33623 TTTTTATTTTC
1 TTTTTATTTTC
*
33634 TTTTTACTTTC
1 TTTTTATTTTC
*
33645 TTTTTGTTATTC
1 TTTTTATT-TTC
33657 TTTTTA-TTTC
1 TTTTTATTTTC
33667 TTTTTA
1 TTTTTA
33673 AGCAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.26
11 17 0.50
12 8 0.24
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTTTATTTTC
Found at i:33648 original size:22 final size:22
Alignment explanation
Indices: 33623--33672 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
33613 TTAGAATCTG
33623 TTTTTATT-TTCTTTTTACTTTC
1 TTTTTATTATTCTTTTTA-TTTC
*
33645 TTTTTGTTATTCTTTTTATTTC
1 TTTTTATTATTCTTTTTATTTC
33667 TTTTTA
1 TTTTTA
33673 AGCAAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTTATTATTCTTTTTATTTC
Found at i:33996 original size:23 final size:22
Alignment explanation
Indices: 33947--33996 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
33937 TAATAAATAG
*
33947 TAATTAATAAGTATATTCATATA
1 TAATTAATAAG-ATATTAATATA
33970 TAATTAATAA-ATATTAA-ATA
1 TAATTAATAAGATATTAATATA
33990 T-ATTAAT
1 TAATTAAT
33997 CTATATACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 6 0.23
20 4 0.15
21 6 0.23
23 10 0.38
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
TAATTAATAAGATATTAATATA
Found at i:34568 original size:17 final size:16
Alignment explanation
Indices: 34546--34580 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
34536 ATTTGGACAT
34546 TTTTAAATTAAAATAAA
1 TTTTAAATTAAAA-AAA
*
34563 TTTTAATTTAAAAAAA
1 TTTTAAATTAAAAAAA
34579 TT
1 TT
34581 ATTATTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TTTTAAATTAAAAAAA
Found at i:35227 original size:31 final size:31
Alignment explanation
Indices: 35189--35324 Score: 111
Period size: 31 Copynumber: 4.5 Consensus size: 31
35179 TTAAGATAAC
*
35189 ATTTGGTACCTGAACTTGACACTTTTTATTA
1 ATTTGGTACCTAAACTTGACACTTTTTATTA
* * * *
35220 ATTTGGTATCTAAAGTT----CTTTTTGGTCCA
1 ATTTGGTACCTAAACTTGACACTTTTT-AT-TA
* **
35249 ATTTAGTA-CTCAAACTTGACACTTTTTCCTA
1 ATTTGGTACCT-AAACTTGACACTTTTTATTA
*
35280 ATTTGGTACCTAAACTTGACACTTTTTTTTA
1 ATTTGGTACCTAAACTTGACACTTTTTATTA
* *
35311 AGTTGGTACTTAAA
1 ATTTGGTACCTAAA
35325 TTTTTGGGGT
Statistics
Matches: 82, Mismatches: 15, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
27 6 0.07
28 3 0.04
29 13 0.16
31 52 0.63
32 2 0.02
33 6 0.07
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.45
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTATTA
Found at i:35372 original size:89 final size:91
Alignment explanation
Indices: 35189--35381 Score: 257
Period size: 89 Copynumber: 2.1 Consensus size: 91
35179 TTAAGATAAC
* * **
35189 ATTTGGTACCTGAACTTGACACTTTTTATTAATTTGGTATCTAAAGTTCTTTTTGGTCCAATTTA
1 ATTTGGTACCTAAACTTGACACTTTTTATTAAGTTGGTATCTAAAGTTCTTTGGGGTCCAATTTA
*
35254 GTACTCAAACTTGACACTTTTTCCTA
66 GTACTCAAACTTGACACTTTTCCCTA
* *
35280 ATTTGGTACCTAAACTTGACACTTTTTTTTAAGTTGGTA-CTTAAA-TT-TTTGGGGTTCAATTT
1 ATTTGGTACCTAAACTTGACACTTTTTATTAAGTTGGTATC-TAAAGTTCTTTGGGGTCCAATTT
* ** *
35342 GGTACTTGAACTTGACTCTTTTCCCTA
65 AGTACTCAAACTTGACACTTTTCCCTA
35369 ATTTGGTACCTAA
1 ATTTGGTACCTAA
35382 TTTTTTTTAA
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
89 47 0.52
90 3 0.03
91 40 0.44
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (91 bp):
ATTTGGTACCTAAACTTGACACTTTTTATTAAGTTGGTATCTAAAGTTCTTTGGGGTCCAATTTA
GTACTCAAACTTGACACTTTTCCCTA
Found at i:35625 original size:28 final size:28
Alignment explanation
Indices: 35556--35637 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 28
35546 AATAAATATC
* *
35556 AAGTTCAGGTACCAAATTGGGTCAAAAA
1 AAGTTTAGGTACCAAATTGGGTAAAAAA
* *
35584 AAGTTTAGGCACCAAATTGTGTAAAAAA
1 AAGTTTAGGTACCAAATTGGGTAAAAAA
*
35612 AAGTTTTA-GTACCAAATTAGG-AAAAA
1 AAG-TTTAGGTACCAAATTGGGTAAAAA
35638 GTATCAAGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
27 5 0.11
28 37 0.80
29 4 0.09
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.24
Consensus pattern (28 bp):
AAGTTTAGGTACCAAATTGGGTAAAAAA
Found at i:44204 original size:24 final size:24
Alignment explanation
Indices: 44172--44220 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
44162 ACAATAGGGG
44172 TGTTTCTGTAAACTCCGCCTATCT
1 TGTTTCTGTAAACTCCGCCTATCT
* *
44196 TGTTTCTGTAAACTCTGCCTGTCT
1 TGTTTCTGTAAACTCCGCCTATCT
44220 T
1 T
44221 ATTTATTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.14, C:0.27, G:0.14, T:0.45
Consensus pattern (24 bp):
TGTTTCTGTAAACTCCGCCTATCT
Found at i:53911 original size:16 final size:17
Alignment explanation
Indices: 53890--53922 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
53880 TAAGTGGATG
53890 TCTAACTCC-TTAAACC
1 TCTAACTCCTTTAAACC
53906 TCTAACTCCTTTAAACC
1 TCTAACTCCTTTAAACC
53923 CTCATTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (17 bp):
TCTAACTCCTTTAAACC
Found at i:54655 original size:85 final size:85
Alignment explanation
Indices: 54512--54679 Score: 291
Period size: 85 Copynumber: 2.0 Consensus size: 85
54502 AGTTTATGAT
54512 TGAGAATGCTTATCATTTTACTAATTCGTTTTACTTTGATCCAAGTGATTATAATGTCAAATCTT
1 TGAGAATGCTTATCATTTTACTAATTCGTTTTACTTTGATCCAAGTGATTATAATGTCAAATCTT
54577 GCCAAACTTGAATTTGCGAC
66 GCCAAACTTGAATTTGCGAC
* ** * *
54597 TGAGAATGCTTATCATTTTACTAATTTGTTTTGTTTTGATTCAAGTGGTTATAATGTCAAATCTT
1 TGAGAATGCTTATCATTTTACTAATTCGTTTTACTTTGATCCAAGTGATTATAATGTCAAATCTT
54662 GCCAAACTTGAATTTGCG
66 GCCAAACTTGAATTTGCG
54680 GCCTTAGACA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 78 1.00
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (85 bp):
TGAGAATGCTTATCATTTTACTAATTCGTTTTACTTTGATCCAAGTGATTATAATGTCAAATCTT
GCCAAACTTGAATTTGCGAC
Found at i:61777 original size:48 final size:48
Alignment explanation
Indices: 61632--61841 Score: 195
Period size: 49 Copynumber: 4.3 Consensus size: 48
61622 ATAATGATTT
* * ** *
61632 AAAGTCATCATTTTCAAGCCACTCGGGATTATAGAATATGCAAATAGTG
1 AAAGTCATCATTGTCAAGCCAC-CAGGATGGTAGAATATGAAAATAGTG
* * *
61681 AACGTCATCATTGTCGAGCCACCCAGGATGGTAGAATATGCAAATAGTG
1 AAAGTCATCATTGTCAAGCCA-CCAGGATGGTAGAATATGAAAATAGTG
* * * ** *
61730 AAAGCCATCGTTTTCTTGCCACCTGGATGGTAGAATATGAAAATAGTG
1 AAAGTCATCATTGTCAAGCCACCAGGATGGTAGAATATGAAAATAGTG
* * * * ** *
61778 AAAATCATCATTGGCAGGCCACCCGAGATGGTAGAATATGAAAATTCTA
1 AAAGTCATCATTGTCAAGCCACCAG-GATGGTAGAATATGAAAATAGTG
*
61827 AAAGTTATCATTGTC
1 AAAGTCATCATTGTC
61842 GAGCAACCTA
Statistics
Matches: 131, Mismatches: 28, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
48 42 0.32
49 88 0.67
50 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (48 bp):
AAAGTCATCATTGTCAAGCCACCAGGATGGTAGAATATGAAAATAGTG
Found at i:70349 original size:18 final size:17
Alignment explanation
Indices: 70326--70365 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
70316 AATATAGAAC
*
70326 AAATAAGGAAAGGGGAA
1 AAATAAGGAAAAGGGAA
70343 TAAATAAGGAAAAGGGAA
1 -AAATAAGGAAAAGGGAA
70361 AAATA
1 AAATA
70366 CAATGCTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.10
Consensus pattern (17 bp):
AAATAAGGAAAAGGGAA
Found at i:72426 original size:37 final size:37
Alignment explanation
Indices: 72376--72452 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
72366 CCTGGTGACT
*
72376 CTAGCCATGGTACCAGGATATCCTAAGAGATTCAAAA
1 CTAGCCATGGTACCAAGATATCCTAAGAGATTCAAAA
72413 CTAGCCATGGTACCAAGATATCCTAAGAGATTCAAAA
1 CTAGCCATGGTACCAAGATATCCTAAGAGATTCAAAA
72450 CTA
1 CTA
72453 TCTTCATGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (37 bp):
CTAGCCATGGTACCAAGATATCCTAAGAGATTCAAAA
Found at i:77297 original size:76 final size:76
Alignment explanation
Indices: 77171--77316 Score: 265
Period size: 76 Copynumber: 1.9 Consensus size: 76
77161 AAAAACATAG
*
77171 TAAATAAACAAAGCAAACAATTATTATTCAGTTATCTCATTTCATTATCTCAATAATGTATTTGA
1 TAAATAAACAAAGCAAACAATTATTATTCAGTTATCTCATTTCATCATCTCAATAATGTATTTGA
77236 AGGATGTAACT
66 AGGATGTAACT
* *
77247 TAAATAAACAAAGCAAATAATTATTATTCTGTTATCTCATTTCATCATCTCAATAATGTATTTGA
1 TAAATAAACAAAGCAAACAATTATTATTCAGTTATCTCATTTCATCATCTCAATAATGTATTTGA
77312 AGGAT
66 AGGAT
77317 TTAAACACAT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 67 1.00
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (76 bp):
TAAATAAACAAAGCAAACAATTATTATTCAGTTATCTCATTTCATCATCTCAATAATGTATTTGA
AGGATGTAACT
Found at i:77838 original size:21 final size:21
Alignment explanation
Indices: 77788--77839 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
77778 GTCTCGTAAC
*
77788 AAATATATATTACATTTACAT
1 AAATATATATTACAATTACAT
*
77809 ACCAATATAT-CT-CAATTACAT
1 A--AATATATATTACAATTACAT
77830 AAATATATAT
1 AAATATATAT
77840 AACCTAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 7
0.71 0.09 0.20
Matches are distributed among these distances:
19 7 0.28
21 10 0.40
22 1 0.04
23 7 0.28
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATATATATTACAATTACAT
Found at i:83721 original size:30 final size:31
Alignment explanation
Indices: 83677--83737 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
83667 CTTCCAACCG
* *
83677 AACTAGATCGATTAATCGAGTTAGATTGATT
1 AACTAGATCAATTAATCGAGTTAGATCGATT
83708 AACTA-ATCAATTAATCGAGTTAGATCGATT
1 AACTAGATCAATTAATCGAGTTAGATCGATT
83738 CGATCGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.34
Consensus pattern (31 bp):
AACTAGATCAATTAATCGAGTTAGATCGATT
Found at i:84322 original size:16 final size:16
Alignment explanation
Indices: 84298--84340 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
84288 TAAGTAAATA
*
84298 AATATTTATAATTTATT
1 AATA-TTATAATTAATT
*
84315 AATATTATTATTAATT
1 AATATTATAATTAATT
84331 AATATATATA
1 AATAT-TATA
84341 TATAAAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATATTATAATTAATT
Found at i:93166 original size:20 final size:20
Alignment explanation
Indices: 93143--93190 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
93133 GAAAATTGAG
*
93143 AATAAAACATGAAAAAATAA
1 AATAAAACATGAAAAAACAA
**
93163 AATAAGAA-ATGAAATGACAA
1 AATAA-AACATGAAAAAACAA
93183 AATAAAAC
1 AATAAAAC
93191 CTGTTAAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 2 0.09
20 19 0.83
21 2 0.09
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.15
Consensus pattern (20 bp):
AATAAAACATGAAAAAACAA
Found at i:95741 original size:17 final size:17
Alignment explanation
Indices: 95719--95761 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
95709 TTAAAAAATA
95719 TATAAATTTTGGAATTT
1 TATAAATTTTGGAATTT
*
95736 TATAAATATTTTGAATTT
1 TATAAAT-TTTGGAATTT
*
95754 TAAAAATT
1 TATAAATT
95762 ATTTTGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (17 bp):
TATAAATTTTGGAATTT
Found at i:95753 original size:18 final size:18
Alignment explanation
Indices: 95719--95792 Score: 80
Period size: 19 Copynumber: 4.1 Consensus size: 18
95709 TTAAAAAATA
*
95719 TATAAAT-TTTGGAATTT
1 TATAAATATTTTGAATTT
95736 TATAAATATTTTGAATTT
1 TATAAATATTTTGAATTT
*
95754 TAAAAATTATTTTGAATTT
1 TATAAA-TATTTTGAATTT
*
95773 TTTAAAATCATTTTG-ATTT
1 TAT-AAAT-ATTTTGAATTT
95792 T
1 T
95793 TTCTTTTTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.14
18 14 0.29
19 19 0.39
20 9 0.18
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.55
Consensus pattern (18 bp):
TATAAATATTTTGAATTT
Found at i:105350 original size:23 final size:23
Alignment explanation
Indices: 105320--105365 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
105310 GGTATCTCAT
105320 GTAACAAGGAGATGGAAGTGAAC
1 GTAACAAGGAGATGGAAGTGAAC
105343 GTAACAAGGAGATGGAAGTGAAC
1 GTAACAAGGAGATGGAAGTGAAC
105366 AAAAAGGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.35, T:0.13
Consensus pattern (23 bp):
GTAACAAGGAGATGGAAGTGAAC
Found at i:123328 original size:18 final size:18
Alignment explanation
Indices: 123307--123342 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
123297 GACTTATATC
123307 GAAAT-AATAAAATATAAT
1 GAAATAAATAAAA-ATAAT
123325 GAAATAAATAAAAATAAT
1 GAAATAAATAAAAATAAT
123343 AAGAACTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (18 bp):
GAAATAAATAAAAATAAT
Found at i:124322 original size:20 final size:20
Alignment explanation
Indices: 124297--124334 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
124287 GGTTTCTCAA
124297 AAAAAGTCAACGATCAATAG
1 AAAAAGTCAACGATCAATAG
124317 AAAAAGTCAACGATCAAT
1 AAAAAGTCAACGATCAAT
124335 GATCAATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.16, G:0.13, T:0.16
Consensus pattern (20 bp):
AAAAAGTCAACGATCAATAG
Found at i:124559 original size:23 final size:23
Alignment explanation
Indices: 124501--124576 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
124491 CAATAGTCAG
* * *
124501 TCAAAGTCAACGATTCGGTTTGA
1 TCAAAGTCAACGGTTCGATTCGA
* *
124524 TCAAAATCAACGGTTCGATTCAA
1 TCAAAGTCAACGGTTCGATTCGA
*
124547 TCAAAGTCAACGGGTT-GAGTCGA
1 TCAAAGTCAAC-GGTTCGATTCGA
124570 TCAAAGT
1 TCAAAGT
124577 TAATAGGTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 40 0.91
24 4 0.09
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (23 bp):
TCAAAGTCAACGGTTCGATTCGA
Found at i:126633 original size:73 final size:73
Alignment explanation
Indices: 126514--126658 Score: 290
Period size: 73 Copynumber: 2.0 Consensus size: 73
126504 GTGGAAATAC
126514 GAGTCAAGGTAGAGATTTGTTGAGTATGACTTATATTTCAAGTCAAATTTGAGAAATAATCTTTC
1 GAGTCAAGGTAGAGATTTGTTGAGTATGACTTATATTTCAAGTCAAATTTGAGAAATAATCTTTC
126579 AGTTAAAT
66 AGTTAAAT
126587 GAGTCAAGGTAGAGATTTGTTGAGTATGACTTATATTTCAAGTCAAATTTGAGAAATAATCTTTC
1 GAGTCAAGGTAGAGATTTGTTGAGTATGACTTATATTTCAAGTCAAATTTGAGAAATAATCTTTC
126652 AGTTAAA
66 AGTTAAA
126659 CTCTGTTTAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (73 bp):
GAGTCAAGGTAGAGATTTGTTGAGTATGACTTATATTTCAAGTCAAATTTGAGAAATAATCTTTC
AGTTAAAT
Found at i:131029 original size:23 final size:23
Alignment explanation
Indices: 131001--131064 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 23
130991 GAAAAAAAAG
131001 AACATTTCATAATCATTGCTTAA
1 AACATTTCATAATCATTGCTTAA
* *
131024 AACATTT--T-AT-GTGGCTTAA
1 AACATTTCATAATCATTGCTTAA
131043 AACATTTCATAATCATTGCTTA
1 AACATTTCATAATCATTGCTTA
131065 GTTTATGCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
19 14 0.42
20 2 0.06
21 2 0.06
22 2 0.06
23 13 0.39
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.41
Consensus pattern (23 bp):
AACATTTCATAATCATTGCTTAA
Found at i:132257 original size:28 final size:28
Alignment explanation
Indices: 132217--132270 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
132207 CACATATCCC
132217 TTATTTTGCCTCTATATTTTATTTTTCT
1 TTATTTTGCCTCTATATTTTATTTTTCT
132245 TTATTTTGCCTCTATATTTTATTTTT
1 TTATTTTGCCTCTATATTTTATTTTT
132271 TTAACAAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.15, C:0.13, G:0.04, T:0.69
Consensus pattern (28 bp):
TTATTTTGCCTCTATATTTTATTTTTCT
Found at i:135320 original size:22 final size:22
Alignment explanation
Indices: 135294--135341 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
135284 CAAACAAATT
*
135294 ATAAATTCCATAGCAATCCCAA
1 ATAAATTCCATAACAATCCCAA
*
135316 ATAAATTTCATAACAATCCCAA
1 ATAAATTCCATAACAATCCCAA
135338 ATAA
1 ATAA
135342 CTTAAACCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.50, C:0.23, G:0.02, T:0.25
Consensus pattern (22 bp):
ATAAATTCCATAACAATCCCAA
Found at i:135890 original size:5 final size:5
Alignment explanation
Indices: 135880--135913 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
135870 TATAAGGTCT
135880 CTCAC CTCAC CTCAC CTCAC CTCAC CTCAC CTCA
1 CTCAC CTCAC CTCAC CTCAC CTCAC CTCAC CTCA
135914 GCTCTTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.21, C:0.59, G:0.00, T:0.21
Consensus pattern (5 bp):
CTCAC
Found at i:136404 original size:79 final size:79
Alignment explanation
Indices: 136273--136431 Score: 309
Period size: 79 Copynumber: 2.0 Consensus size: 79
136263 GCTGGAAAGG
136273 CCTTTTCATGCCCGCCTGCCCGCCAGCATCGCCTCTCCTGTTTCTTTCTTTTTAATATCACATTT
1 CCTTTTCATGCCCGCCTGCCCGCCAGCATCGCCTCTCCTGTTTCTTTCTTTTTAATATCACATTT
136338 TCATTTTAGACCCC
66 TCATTTTAGACCCC
*
136352 CCTTTTCATGCCCGCCTGCCCGCCAGCATCGCCTCTCCTTTTTCTTTCTTTTTAATATCACATTT
1 CCTTTTCATGCCCGCCTGCCCGCCAGCATCGCCTCTCCTGTTTCTTTCTTTTTAATATCACATTT
136417 TCATTTTAGACCCC
66 TCATTTTAGACCCC
136431 C
1 C
136432 TTTCTTCCCA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.14, C:0.37, G:0.09, T:0.40
Consensus pattern (79 bp):
CCTTTTCATGCCCGCCTGCCCGCCAGCATCGCCTCTCCTGTTTCTTTCTTTTTAATATCACATTT
TCATTTTAGACCCC
Found at i:145240 original size:26 final size:25
Alignment explanation
Indices: 145185--145246 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 25
145175 AATGAGAAAT
* ***
145185 TAAAATTTAATTTATTTTCTTTTTC
1 TAAAATTTAATTTATTTTATTTAAA
*
145210 CAAAATGTTAATTTATTTTATTTAAA
1 TAAAAT-TTAATTTATTTTATTTAAA
145236 TAAAA-TTAATT
1 TAAAATTTAATT
145247 GAATTATGTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 6 0.20
25 5 0.17
26 19 0.63
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (25 bp):
TAAAATTTAATTTATTTTATTTAAA
Done.