Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001764.1 Kokia drynarioides strain JFW-HI SEQ_113485, 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: 98239
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:2449 original size:25 final size:24
Alignment explanation
Indices: 2401--2449 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2391 TCTCGAACAA
*
2401 TATTTTAAAAAATCAAAATATGGG
1 TATTTTAAAAAATCAAAAAATGGG
**
2425 TATTTTAAATGATCGAAAAAATGGG
1 TATTTTAAAAAATC-AAAAAATGGG
2450 AGTCGCCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (24 bp):
TATTTTAAAAAATCAAAAAATGGG
Found at i:3771 original size:30 final size:29
Alignment explanation
Indices: 3737--3838 Score: 116
Period size: 29 Copynumber: 3.4 Consensus size: 29
3727 AAATGGTAAT
3737 TTTTGGAAAGTTCGAAGTCAAAAAATATAA
1 TTTTGGAAAGTTCGAAGT-AAAAAATATAA
* *
3767 TTTTGGAAAGTTC-AAGGTTAAAAATGTAA
1 TTTTGGAAAGTTCGAA-GTAAAAAATATAA
* * *
3796 TTTTGGAAAGTTTGAGGGAAAAAATATAA
1 TTTTGGAAAGTTCGAAGTAAAAAATATAA
3825 TTTTTTGGAAAGTT
1 --TTTTGGAAAGTT
3839 TAGGGTAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
29 33 0.54
30 16 0.26
31 12 0.20
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (29 bp):
TTTTGGAAAGTTCGAAGTAAAAAATATAA
Found at i:3856 original size:30 final size:29
Alignment explanation
Indices: 3726--3978 Score: 217
Period size: 30 Copynumber: 8.4 Consensus size: 29
3716 TATCTGGGGC
* *
3726 AAAATGGTAATTTTTGGAAAG-TTCGAAGTCAA
1 AAAAT-GTAATTTTTGGAAAGTTTAG-GGT--A
* * *
3758 AAAATATAA-TTTTGGAAAGTTCAAGGTTA
1 AAAATGTAATTTTTGGAAAGTT-TAGGGTA
*
3787 AAAATGTAA-TTTTGGAAAGTTTGAGGGAA
1 AAAATGTAATTTTTGGAAAGTTT-AGGGTA
*
3816 AAAATATAATTTTTTGGAAAGTTTAGGGTA
1 AAAATGTAA-TTTTTGGAAAGTTTAGGGTA
* * *
3846 AAAATGTAATTTTTAGAAAGTTTGGGTGTC
1 AAAATGTAATTTTTGGAAAGTTTAGG-GTA
* * *
3876 AAAATGTAATTTTTGAAAAGATTGAGGGTT
1 AAAATGTAATTTTTGGAAAG-TTTAGGGTA
*
3906 AAAATGTAATTTTTGGAAAGTTTAGGAGTT
1 AAAATGTAATTTTTGGAAAGTTTAGG-GTA
* * *
3936 AAAATGCAATTTTT-GAGAAGTTTGAGAGTC
1 AAAATGTAATTTTTGGA-AAGTTT-AGGGTA
3966 AAAATGTAATTTT
1 AAAATGTAATTTT
3979 AAAAAAGTTC
Statistics
Matches: 185, Mismatches: 26, Indels: 22
0.79 0.11 0.09
Matches are distributed among these distances:
29 55 0.30
30 100 0.54
31 24 0.13
32 6 0.03
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAAGTTTAGGGTA
Found at i:3916 original size:90 final size:90
Alignment explanation
Indices: 3787--3978 Score: 264
Period size: 90 Copynumber: 2.1 Consensus size: 90
3777 TTCAAGGTTA
* *
3787 AAAATGTAA-TTTTGGAAAGTTTGAGGGAAAAAATATAATTTTTTGGAAAGTTTAGG-GTAAAAA
1 AAAATGTAATTTTTGAAAAGATTGAGGGAAAAAATATAA-TTTTTGGAAAGTTTAGGAGTAAAAA
* * *
3850 TGTAATTTTT-AGAAAGTTTGGGTGTC
65 TGCAATTTTTGAG-AAGTTTGAGAGTC
** * *
3876 AAAATGTAATTTTTGAAAAGATTGAGGGTTAAAATGTAATTTTTGGAAAGTTTAGGAGTTAAAAT
1 AAAATGTAATTTTTGAAAAGATTGAGGGAAAAAATATAATTTTTGGAAAGTTTAGGAGTAAAAAT
3941 GCAATTTTTGAGAAGTTTGAGAGTC
66 GCAATTTTTGAGAAGTTTGAGAGTC
3966 AAAATGTAATTTT
1 AAAATGTAATTTT
3979 AAAAAAGTTC
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
89 26 0.29
90 63 0.69
91 2 0.02
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.38
Consensus pattern (90 bp):
AAAATGTAATTTTTGAAAAGATTGAGGGAAAAAATATAATTTTTGGAAAGTTTAGGAGTAAAAAT
GCAATTTTTGAGAAGTTTGAGAGTC
Found at i:5340 original size:61 final size:61
Alignment explanation
Indices: 5249--5373 Score: 214
Period size: 61 Copynumber: 2.0 Consensus size: 61
5239 GAAGTGGTGT
* *
5249 TGCTGGTGCTGATGTGGCAAACTCTAAGTGGCTGGGCAAGATGGCTGGCTGTACAAGTTGC
1 TGCTGGTGCTGATGTGGCAAACTCTAAGTGGCTGGACAAGATGGCTGGCTGCACAAGTTGC
* *
5310 TGCTGGTGCTGATGTGGCAAACTCTGAGTGGCTGGACAAGATGGCTGGTTGCACAAGTTGC
1 TGCTGGTGCTGATGTGGCAAACTCTAAGTGGCTGGACAAGATGGCTGGCTGCACAAGTTGC
5371 TGC
1 TGC
5374 ATTGCTTTGG
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.19, C:0.18, G:0.36, T:0.26
Consensus pattern (61 bp):
TGCTGGTGCTGATGTGGCAAACTCTAAGTGGCTGGACAAGATGGCTGGCTGCACAAGTTGC
Found at i:9868 original size:19 final size:20
Alignment explanation
Indices: 9827--9870 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
9817 TTTATACTTA
9827 AGTTAATTAATAATTAATCTT
1 AGTTAATTAAT-ATTAATCTT
*
9848 AGTTAATTAAT-TTAATTTT
1 AGTTAATTAATATTAATCTT
9867 AGTT
1 AGTT
9871 TAGTTTACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.50
21 11 0.50
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (20 bp):
AGTTAATTAATATTAATCTT
Found at i:31892 original size:10 final size:11
Alignment explanation
Indices: 31869--31913 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
31859 CAAACTAAGG
31869 AAAAATAAATA
1 AAAAATAAATA
31880 AAAAATCAAA-A
1 AAAAAT-AAATA
31891 AAAAAT-AATA
1 AAAAATAAATA
*
31901 ATAAATAAATA
1 AAAAATAAATA
31912 AA
1 AA
31914 CGTTTGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 2 0.07
10 6 0.21
11 18 0.62
12 3 0.10
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAATAAATA
Found at i:34304 original size:11 final size:11
Alignment explanation
Indices: 34290--34332 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
34280 ATTCAAATTA
34290 AATTTAAACTT
1 AATTTAAACTT
*
34301 AATTTAAATTT
1 AATTTAAACTT
* *
34312 AAACTTAAACTA
1 -AATTTAAACTT
34324 AATTTAAAC
1 AATTTAAAC
34333 CCAAAATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (11 bp):
AATTTAAACTT
Found at i:34331 original size:6 final size:6
Alignment explanation
Indices: 34266--34331 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
34256 TTTTTTAATT
* *
34266 AATTTA AATTATA AATTCA AA-TTA AATTTA AACTT- AATTTA AATTTA
1 AATTTA AATT-TA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* *
34313 AACTTA AA-CTA AATTTA AA
1 AATTTA AATTTA AATTTA AA
34332 CCCAAAATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
5 12 0.24
6 31 0.63
7 6 0.12
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (6 bp):
AATTTA
Found at i:34332 original size:17 final size:17
Alignment explanation
Indices: 34264--34332 Score: 86
Period size: 17 Copynumber: 4.0 Consensus size: 17
34254 ACTTTTTTAA
*
34264 TTAATTTAAATTATAAA-
1 TTAAATTAAATT-TAAAC
34281 TTCAAATTAAATTTAAAC
1 TT-AAATTAAATTTAAAC
*
34299 TTAATTTAAATTTAAAC
1 TTAAATTAAATTTAAAC
*
34316 TTAAACTAAATTTAAAC
1 TTAAATTAAATTTAAAC
34333 CCAAAATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
17 35 0.76
18 11 0.24
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAATTAAATTTAAAC
Found at i:34342 original size:17 final size:17
Alignment explanation
Indices: 34305--34344 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
34295 AAACTTAATT
** *
34305 TAAATTTAAACTTAAAC
1 TAAATTTAAACCCAAAA
34322 TAAATTTAAACCCAAAA
1 TAAATTTAAACCCAAAA
34339 TAAATT
1 TAAATT
34345 GAAATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAATTTAAACCCAAAA
Found at i:49644 original size:7 final size:7
Alignment explanation
Indices: 49632--49661 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
49622 TTTATATTAT
49632 TGACATG
1 TGACATG
49639 TGACATG
1 TGACATG
49646 TGACATG
1 TGACATG
49653 TGACATG
1 TGACATG
49660 TG
1 TG
49662 TTTGATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (7 bp):
TGACATG
Found at i:49926 original size:14 final size:15
Alignment explanation
Indices: 49896--49934 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
49886 ATAAGATGAG
49896 AATAAATTTTCAATTA
1 AATAAA-TTTCAATTA
49912 AATAAATTT-AATTA
1 AATAAATTTCAATTA
*
49926 ATTAAATTT
1 AATAAATTT
49935 TTTAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 3 0.14
16 6 0.27
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAAATTTCAATTA
Found at i:51415 original size:10 final size:10
Alignment explanation
Indices: 51394--51472 Score: 56
Period size: 10 Copynumber: 7.8 Consensus size: 10
51384 ATTTTGGAAA
51394 TTTTTAAA--
1 TTTTTAAATT
51402 TTTTTAAA-T
1 TTTTTAAATT
*
51411 TTTTTATATT
1 TTTTTAAATT
51421 TTTTTAAATAT
1 TTTTTAAAT-T
*
51432 AAATTTTGAAATT
1 ---TTTTTAAATT
*
51445 TTTATAAATT
1 TTTTTAAATT
* *
51455 ATTTTAATTT
1 TTTTTAAATT
51465 TTTTTAAA
1 TTTTTAAA
51473 AATTTTGTTG
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
8 8 0.15
9 7 0.13
10 30 0.55
11 1 0.02
13 1 0.02
14 8 0.15
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (10 bp):
TTTTTAAATT
Found at i:51436 original size:33 final size:34
Alignment explanation
Indices: 51398--51461 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
51388 TGGAAATTTT
* * *
51398 TAAATTTTTAAATTTTT-TATATTTTTTTAAATA
1 TAAATTTTGAAATTTTTATAAATTATTTTAAATA
51431 TAAATTTTGAAATTTTTATAAATTATTTTAA
1 TAAATTTTGAAATTTTTATAAATTATTTTAA
51462 TTTTTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 16 0.59
34 11 0.41
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (34 bp):
TAAATTTTGAAATTTTTATAAATTATTTTAAATA
Found at i:51477 original size:19 final size:20
Alignment explanation
Indices: 51432--51479 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
51422 TTTTAAATAT
51432 AAATTTTGAAATTTTTATAA
1 AAATTTTGAAATTTTTATAA
* * *
51452 ATTATTTT-AATTTTTTTTAA
1 A-AATTTTGAAATTTTTATAA
51472 AAATTTTG
1 AAATTTTG
51480 TTGTGAGAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
19 5 0.23
20 12 0.55
21 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
AAATTTTGAAATTTTTATAA
Found at i:51797 original size:17 final size:18
Alignment explanation
Indices: 51777--51845 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 18
51767 TAAAAATAAA
51777 AAAATAAAAAATA-TAAT
1 AAAATAAAAAATATTAAT
51794 AAAATACAATATAATATTTATCAT
1 AAAATA-AA-A-AATA-TTA--AT
51818 AAAATAAAAAATATTTAAT
1 AAAATAAAAAATA-TTAAT
51837 CAAAATAAA
1 -AAAATAAA
51846 GTTAAATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
17 6 0.14
18 2 0.05
19 3 0.07
20 12 0.27
21 8 0.18
22 3 0.07
23 2 0.05
24 8 0.18
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATAAAAAATATTAAT
Found at i:51819 original size:24 final size:21
Alignment explanation
Indices: 51777--51834 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
51767 TAAAAATAAA
51777 AAAATAAAAAATA--TA--AT
1 AAAATAAAAAATATTTATCAT
51794 AAAATACAATATAATATTTATCAT
1 AAAATA-AA-A-AATATTTATCAT
51818 AAAATAAAAAATATTTA
1 AAAATAAAAAATATTTA
51835 ATCAAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 6 0.18
18 2 0.06
19 1 0.03
20 4 0.12
21 8 0.24
22 3 0.09
23 2 0.06
24 8 0.24
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAATAAAAAATATTTATCAT
Found at i:54116 original size:19 final size:19
Alignment explanation
Indices: 54092--54172 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 19
54082 ATACTACAAG
54092 ATAAATTAAATTAATAAAA
1 ATAAATTAAATTAATAAAA
54111 ATAAA-TAAATCTAAATTTAAAA
1 ATAAATTAAAT-T-AA--TAAAA
* *
54133 ATTAATTTATAATTATTAAAA
1 A-TAAATTA-AATTAATAAAA
* *
54154 ATAATTTAACTTAA-AAAA
1 ATAAATTAAATTAATAAAA
54172 A
1 A
54173 ACTTAATACA
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
18 10 0.20
19 10 0.20
20 9 0.18
21 6 0.12
22 6 0.12
23 4 0.08
24 3 0.06
25 3 0.06
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAATTAAATTAATAAAA
Found at i:54118 original size:23 final size:22
Alignment explanation
Indices: 54092--54134 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
54082 ATACTACAAG
54092 ATAAAT-TAAATTAATAAAAATAA
1 ATAAATCTAAATT--TAAAAATAA
54115 ATAAATCTAAATTTAAAAAT
1 ATAAATCTAAATTTAAAAAT
54135 TAATTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 6 0.32
24 6 0.32
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAAATCTAAATTTAAAAATAA
Found at i:56522 original size:263 final size:263
Alignment explanation
Indices: 55750--56771 Score: 1212
Period size: 263 Copynumber: 3.9 Consensus size: 263
55740 AAATTTGGTT
* * * * * * **
55750 TTTTGTACATCACTGATGTGATGGGTTTTTTGGGGTCTTAGCAGTGATTTCTTGGTTAATTAAAG
1 TTTTGTACATCACTGATATGGTGGGTCTTTTGGGATCTTGGCAGTGATTTATTGGTTAATTGGAG
* * * * *
55815 TTCATCATCGGGTTGATCTGATAATGACAAAGTTATGATGTAATTTCTGTGGTTTGATCAAGGTG
66 TTCATCATCAGGTTGGTCTGATAATGACAAGGTTATGATGCAATTTCAGTGGTTTGATCAAGGTG
* * * * * *
55880 ATGTATCTTTAATTTGTTTTTGGATTCTTCGAGTGTTATGGTTATAGTTAGTTTGTCTTTTTCCT
131 ATGCATCTTTAGTTTGTTTTTGAATTCTTCGAGTGTTATGGCTATAGTCAGTTTGTCTTTCTCCT
* * * * * *
55945 CTTTTGGGATTATTCAATGGACACGACATTTGTGTATTAATTTGCAATGTCTTATATAATATTTG
196 CTTTTGGGATTATTCAGTGGACATGATATTTGTGTATTAATTTGCAATGTCTTATATGAGACTT-
*
56010 GTC-
260 GACA
** * * *
56013 TTTTGCGCATCACTGATATGGTGGGTCTTTT-AGAGTCCT-GCTAGTGATTTCTTGGTTAATTGG
1 TTTTGTACATCACTGATATGGTGGGTCTTTTGGGA-TCTTGGC-AGTGATTTATTGGTTAATTGG
* * * *
56076 ACTTCATCATCAGGTTAGTCTGATAATGACAAGGTTGTGATGCAATTTCAGTGG--T-ATCAAAG
64 AGTTCATCATCAGGTTGGTCTGATAATGACAAGGTTATGATGCAATTTCAGTGGTTTGATCAAGG
* * * * * *
56138 TGATGCATTTTTAGTTTGTTTTTTAATTTTTTGAGTGTGATGGCTATAGTCAGTATGTCTTTCTC
129 TGATGCATCTTTAGTTTGTTTTTGAATTCTTCGAGTGTTATGGCTATAGTCAGTTTGTCTTTCTC
*
56203 CTCTTTTGGGATTATTCAGTGGACATG-TCATTTGTGTATTAATTTGCAATGTCTTATCTGAGAC
194 CTCTTTTGGGATTATTCAGTGGACATGAT-ATTTGTGTATTAATTTGCAATGTCTTATATGAGAC
*
56267 TTAACA
258 TTGACA
* * * * *
56273 TTTTGTGCATCATTGATATGGTGGGTCTTTTGGGATATTGGCAATGGTTTATTGGTTAATTGGAG
1 TTTTGTACATCACTGATATGGTGGGTCTTTTGGGATCTTGGCAGTGATTTATTGGTTAATTGGAG
* * *
56338 TTCATCATCAGGTTGGTCTGATAATGACAAGGTTGTGGTGCACTTTCAGTGGTTTGATCAAGGTG
66 TTCATCATCAGGTTGGTCTGATAATGACAAGGTTATGATGCAATTTCAGTGGTTTGATCAAGGTG
* *
56403 ATGCATCTTTAGTTTATTTTTGAATTCTTGGAGTGTTATGGCTATAGTC-GATTTGTCTTTCTCC
131 ATGCATCTTTAGTTTGTTTTTGAATTCTTCGAGTGTTATGGCTATAGTCAG-TTTGTCTTTCTCC
* *
56467 TCTTTTGGGATTATTCAGGGGACATGATATTTGTGTATTAATTTGCAAGGTCTTATATGAGACTT
195 TCTTTTGGGATTATTCAGTGGACATGATATTTGTGTATTAATTTGCAATGTCTTATATGAGACTT
56532 GACA
260 GACA
* * * * * *
56536 TTTTGTACATCATTGATTTGGTGCGTCTTTTAAGG-TTTTGGCAGTGATTTATTGGATAATTGGA
1 TTTTGTACATCACTGATATGGTGGGTCTTTT-GGGATCTTGGCAGTGATTTATTGGTTAATTGGA
* * * *
56600 GTTCATCATTAGGTTTGTCTGATAATGACACGGTTATGATGCAATTTCAGTGGTTTGATCAATGT
65 GTTCATCATCAGGTTGGTCTGATAATGACAAGGTTATGATGCAATTTCAGTGGTTTGATCAAGGT
* * * * *
56665 GATGCATCTTTAGTTTGTTTTTGAATTC-TC-A---TTATAGTTATAATAAGTTTGTTTTTCTCC
130 GATGCATCTTTAGTTTGTTTTTGAATTCTTCGAGTGTTATGGCTATAGTCAGTTTGTCTTTCTCC
* *
56725 T-TTTTCGAGATAATTCAGTGGACATG-TCATTTGTGTATTAATTTGCA
195 TCTTTT-GGGATTATTCAGTGGACATGAT-ATTTGTGTATTAATTTGCA
56772 TCATCTTACT
Statistics
Matches: 655, Mismatches: 89, Indels: 35
0.84 0.11 0.04
Matches are distributed among these distances:
257 5 0.01
258 59 0.09
259 2 0.00
260 216 0.33
261 6 0.01
262 6 0.01
263 358 0.55
264 3 0.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (263 bp):
TTTTGTACATCACTGATATGGTGGGTCTTTTGGGATCTTGGCAGTGATTTATTGGTTAATTGGAG
TTCATCATCAGGTTGGTCTGATAATGACAAGGTTATGATGCAATTTCAGTGGTTTGATCAAGGTG
ATGCATCTTTAGTTTGTTTTTGAATTCTTCGAGTGTTATGGCTATAGTCAGTTTGTCTTTCTCCT
CTTTTGGGATTATTCAGTGGACATGATATTTGTGTATTAATTTGCAATGTCTTATATGAGACTTG
ACA
Found at i:66429 original size:20 final size:20
Alignment explanation
Indices: 66404--66444 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
66394 TTTTGAACAA
66404 ACCAACTTAGGTGTAAGTAT
1 ACCAACTTAGGTGTAAGTAT
66424 ACCAACTTAGGTGTAAGTAT
1 ACCAACTTAGGTGTAAGTAT
66444 A
1 A
66445 GGATAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (20 bp):
ACCAACTTAGGTGTAAGTAT
Found at i:71251 original size:15 final size:15
Alignment explanation
Indices: 71231--71278 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
71221 ACTTCCCCCT
71231 CCTCCAGCTCCTCCC
1 CCTCCAGCTCCTCCC
*
71246 CCTCCAGCTCCTCCT
1 CCTCCAGCTCCTCCC
**
71261 CCTCCTCCTCCTCCC
1 CCTCCAGCTCCTCCC
71276 CCT
1 CCT
71279 TCCCCTCCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.04, C:0.67, G:0.04, T:0.25
Consensus pattern (15 bp):
CCTCCAGCTCCTCCC
Found at i:73366 original size:2 final size:2
Alignment explanation
Indices: 73359--73387 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
73349 ATGGCTCTAT
73359 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
73388 TCACCCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:74326 original size:15 final size:15
Alignment explanation
Indices: 74306--74356 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
74296 ATGAAGACGG
74306 AAAGAAAGAAAAAAA
1 AAAGAAAGAAAAAAA
***
74321 AAAGAAAGAAAGTGA
1 AAAGAAAGAAAAAAA
74336 AAAGAATAGAAAAAAA
1 AAAGAA-AGAAAAAAA
74352 TAAAG
1 -AAAG
74357 GAAAAGAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 18 0.64
16 6 0.21
17 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (15 bp):
AAAGAAAGAAAAAAA
Found at i:74364 original size:23 final size:25
Alignment explanation
Indices: 74320--74366 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
74310 AAAGAAAAAA
74320 AAAAGAAAGAAAGTGAAAAGAATAG
1 AAAAGAAAGAAAGTGAAAAGAATAG
*
74345 AAAA-AAATAAAG-GAAAAGAATA
1 AAAAGAAAGAAAGTGAAAAGAATA
74367 AAGAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 7 0.33
25 4 0.19
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (25 bp):
AAAAGAAAGAAAGTGAAAAGAATAG
Found at i:85413 original size:2 final size:2
Alignment explanation
Indices: 85408--85432 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
85398 TATGCTTATC
85408 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
85433 ACATTTTTTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:86292 original size:6 final size:6
Alignment explanation
Indices: 86281--86305 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
86271 TAAGCTGAGG
86281 AAGAGA AAGAGA AAGAGA AAGAGA A
1 AAGAGA AAGAGA AAGAGA AAGAGA A
86306 GGGGACAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAGAGA
Found at i:91530 original size:43 final size:43
Alignment explanation
Indices: 91469--91551 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
91459 TTTGAAAGTT
91469 GGAACACTGTTTACTATTATTAAAAATATATGATTGATTGAGA
1 GGAACACTGTTTACTATTATTAAAAATATATGATTGATTGAGA
* * * *
91512 GGAACACTGTTTCCTATTATTGAAAGTATGTGATTGATTG
1 GGAACACTGTTTACTATTATTAAAAATATATGATTGATTG
91552 TGAGCATGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (43 bp):
GGAACACTGTTTACTATTATTAAAAATATATGATTGATTGAGA
Found at i:91780 original size:28 final size:28
Alignment explanation
Indices: 91739--91802 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
91729 TATCGAGGGG
91739 ATTGACAATCTCTATCGCATTATAT-GTT
1 ATTGACAATCTCTATCGCATTAT-TCGTT
* *
91767 ATTGGCAATTTCTATCGCATTATTCGTT
1 ATTGACAATCTCTATCGCATTATTCGTT
91795 ATTTGACA
1 A-TTGACA
91803 GACTTTCTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 1 0.03
28 25 0.81
29 5 0.16
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (28 bp):
ATTGACAATCTCTATCGCATTATTCGTT
Done.