Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011511.1 Kokia drynarioides strain JFW-HI SEQ_126496, 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: 284394
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 178 characters in sequence are not A, C, G, or T
Found at i:1406 original size:59 final size:59
Alignment explanation
Indices: 1332--1519 Score: 245
Period size: 59 Copynumber: 3.2 Consensus size: 59
1322 AATCAGGAAT
*
1332 TCTGGGATAACTTTCAAACATCCCGAGAATCCCGAGATAACTTTCAAACATCTCGAGAA
1 TCTGGGATAACTTTCAAACATCCCGAGAATCCCGGGATAACTTTCAAACATCTCGAGAA
* *
1391 TCTGGGATAACTTTCAAACATCCCGAGAAT-CTGGGATAACTTTCAAGCATC-CTGAGAA
1 TCTGGGATAACTTTCAAACATCCCGAGAATCCCGGGATAACTTTCAAACATCTC-GAGAA
* * * * * *
1449 TCTCGAGATAACTTTCAATCATCTCGAGAATCTCGGGATAATTTTCAAACATCTTGAGAA
1 TCT-GGGATAACTTTCAAACATCCCGAGAATCCCGGGATAACTTTCAAACATCTCGAGAA
*
1509 TCCGAGGATAA
1 TCTG-GGATAA
1520 TTTTTAGATT
Statistics
Matches: 111, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
57 1 0.01
58 26 0.23
59 55 0.50
60 29 0.26
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (59 bp):
TCTGGGATAACTTTCAAACATCCCGAGAATCCCGGGATAACTTTCAAACATCTCGAGAA
Found at i:1481 original size:88 final size:89
Alignment explanation
Indices: 1332--1519 Score: 288
Period size: 88 Copynumber: 2.1 Consensus size: 89
1322 AATCAGGAAT
1332 TCTGGGATAACTTTCAAACATCCCGAGAATCCCGAGATAACTTTCAAACATCTCGAGAATCT-GG
1 TCTGGGATAACTTTCAAACATCCCGAGAATCCCGAGATAACTTTCAAACATCTCGAGAATCTCGG
1396 GATAACTTTCAAACATCCCGAGAA
66 GATAACTTTCAAACATCCCGAGAA
* * * *
1420 TCTGGGATAACTTTCAAGCATCCTGAGAATCTCGAGATAACTTTCAATCATCTCGAGAATCTCGG
1 TCTGGGATAACTTTCAAACATCCCGAGAATCCCGAGATAACTTTCAAACATCTCGAGAATCTCGG
* **
1485 GATAATTTTCAAACATCTTGAGAA
66 GATAACTTTCAAACATCCCGAGAA
*
1509 TCCGAGGATAA
1 TCTG-GGATAA
1520 TTTTTAGATT
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
88 58 0.64
89 26 0.29
90 6 0.07
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (89 bp):
TCTGGGATAACTTTCAAACATCCCGAGAATCCCGAGATAACTTTCAAACATCTCGAGAATCTCGG
GATAACTTTCAAACATCCCGAGAA
Found at i:1523 original size:30 final size:29
Alignment explanation
Indices: 1335--1519 Score: 226
Period size: 30 Copynumber: 6.2 Consensus size: 29
1325 CAGGAATTCT
1335 GGGATAACTTTCAAACATCCCGAGAATCCC
1 GGGATAACTTTCAAACATCCCGAGAAT-CC
* * *
1365 GAGATAACTTTCAAACATCTCGAGAATCT
1 GGGATAACTTTCAAACATCCCGAGAATCC
*
1394 GGGATAACTTTCAAACATCCCGAGAATCT
1 GGGATAACTTTCAAACATCCCGAGAATCC
* *
1423 GGGATAACTTTCAAGCATCCTGAGAATCTC
1 GGGATAACTTTCAAACATCCCGAGAATC-C
* * *
1453 GAGATAACTTTCAATCATCTCGAGAATCTC
1 GGGATAACTTTCAAACATCCCGAGAATC-C
* **
1483 GGGATAATTTTCAAACATCTTGAGAATCC
1 GGGATAACTTTCAAACATCCCGAGAATCC
1512 GAGGATAA
1 G-GGATAA
1520 TTTTTAGATT
Statistics
Matches: 137, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
29 56 0.41
30 81 0.59
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (29 bp):
GGGATAACTTTCAAACATCCCGAGAATCC
Found at i:1927 original size:49 final size:46
Alignment explanation
Indices: 1822--1938 Score: 126
Period size: 49 Copynumber: 2.4 Consensus size: 46
1812 AACTCGAGCT
* * *
1822 CTAGTTCACGGTGATTATACGATCACGGGTTGAAGTATAACTAGAG
1 CTAGTTGACGGTGGTTATGCGATCACGGGTTGAAGTATAACTAGAG
* *
1868 CTATCGGTTGACGGTGGTTATGCGATCACGGGTTGGAGTATAACTTGGAAG
1 CTA---GTTGACGGTGGTTATGCGATCACGGGTTGAAGTATAAC-TAG-AG
*
1919 CCTAGTTGACAGTGGTTATG
1 -CTAGTTGACGGTGGTTATG
1939 TGGTCACGAG
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
46 3 0.05
49 49 0.83
50 2 0.03
51 2 0.03
52 3 0.05
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.30
Consensus pattern (46 bp):
CTAGTTGACGGTGGTTATGCGATCACGGGTTGAAGTATAACTAGAG
Found at i:15384 original size:2 final size:2
Alignment explanation
Indices: 15377--15404 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15367 AAGATTGGTG
15377 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
15405 TGATGTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23950 original size:2 final size:2
Alignment explanation
Indices: 23945--23971 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23935 AAAAAAAAAA
23945 AT 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 AT A
23972 ATTCAATTTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26313 original size:22 final size:23
Alignment explanation
Indices: 26288--26330 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
26278 TAAAAACATT
*
26288 AAATTTAAAT-TTAAAAAATAGA
1 AAATTAAAATATTAAAAAATAGA
26310 AAATTAAAATATTAAAAAATA
1 AAATTAAAATATTAAAAAATA
26331 CCTTTTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATTAAAATATTAAAAAATAGA
Found at i:27703 original size:7 final size:7
Alignment explanation
Indices: 27691--27744 Score: 65
Period size: 7 Copynumber: 7.7 Consensus size: 7
27681 ATGTGATTTT
27691 TTTAGGA
1 TTTAGGA
27698 TTTAGGA
1 TTTAGGA
**
27705 TTTAAAA
1 TTTAGGA
27712 TTTAGGA
1 TTTAGGA
27719 TTTATGG-
1 TTTA-GGA
*
27726 TTTAAGA
1 TTTAGGA
27733 TTTAGGA
1 TTTAGGA
27740 TTTAG
1 TTTAG
27745 AGTTTAAGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
6 1 0.03
7 36 0.92
8 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.46
Consensus pattern (7 bp):
TTTAGGA
Found at i:27752 original size:21 final size:20
Alignment explanation
Indices: 27691--27757 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 20
27681 ATGTGATTTT
*
27691 TTTAGGATTTAGGATTTAAAA
1 TTTAGGATTTAGG-TTTAAGA
27712 TTTAGGATTTATGGTTTAAGA
1 TTTAGGATTTA-GGTTTAAGA
*
27733 TTTAGGATTTAGAGTTTAAGG
1 TTTAGGATTTAG-GTTTAAGA
27754 TTTA
1 TTTA
27758 TGGTTTAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.02
21 39 0.93
22 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.46
Consensus pattern (20 bp):
TTTAGGATTTAGGTTTAAGA
Found at i:27764 original size:21 final size:20
Alignment explanation
Indices: 27712--27820 Score: 82
Period size: 21 Copynumber: 5.2 Consensus size: 20
27702 GGATTTAAAA
*
27712 TTTAGGATTTATG-GTTTAAGA
1 TTTAGG-TTTA-GAGTTTAAGG
27733 TTTAGGATTTAGAGTTTAAGG
1 TTTAGG-TTTAGAGTTTAAGG
27754 TTTATGGTTTA-ATGTTT-AGTG
1 TTTA-GGTTTAGA-GTTTAAG-G
27775 TTTAGTGTTTATG-GTTTAAGG
1 TTTAG-GTTTA-GAGTTTAAGG
* *
27796 TTTATGGTTTAAAGTTTAGGG
1 TTTA-GGTTTAGAGTTTAAGG
27817 TTTA
1 TTTA
27821 ACTGTGGTTT
Statistics
Matches: 75, Mismatches: 3, Indels: 20
0.77 0.03 0.20
Matches are distributed among these distances:
20 5 0.07
21 65 0.87
22 5 0.07
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (20 bp):
TTTAGGTTTAGAGTTTAAGG
Found at i:27821 original size:28 final size:28
Alignment explanation
Indices: 27740--27821 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
27730 AGATTTAGGA
* * *
27740 TTTAGAGTTTAAGGTTTATGGTTTAATG
1 TTTAGTGTTTAAAGTTTATGGTTTAAGG
**
27768 TTTAGTGTTTAGTGTTTATGGTTTAAGG
1 TTTAGTGTTTAAAGTTTATGGTTTAAGG
*
27796 TTTA-TGGTTTAAAGTTTAGGGTTTAA
1 TTTAGT-GTTTAAAGTTTATGGTTTAA
27822 CTGTGGTTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.98
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (28 bp):
TTTAGTGTTTAAAGTTTATGGTTTAAGG
Found at i:27832 original size:18 final size:18
Alignment explanation
Indices: 27809--27856 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
27799 ATGGTTTAAA
27809 GTTTAGGGTTTAACTGTG
1 GTTTAGGGTTTAACTGTG
27827 GTTTAGGGTTTAACTGTG
1 GTTTAGGGTTTAACTGTG
27845 GTTTAGGGTTTA
1 GTTTAGGGTTTA
27857 TGGTTTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.17, C:0.04, G:0.33, T:0.46
Consensus pattern (18 bp):
GTTTAGGGTTTAACTGTG
Found at i:27836 original size:7 final size:7
Alignment explanation
Indices: 27712--27863 Score: 70
Period size: 7 Copynumber: 20.6 Consensus size: 7
27702 GGATTTAAAA
*
27712 TTTAGGA
1 TTTAGGG
*
27719 TTTATGG
1 TTTAGGG
* *
27726 TTTAAGA
1 TTTAGGG
*
27733 TTTAGGA
1 TTTAGGG
*
27740 TTTAGAG
1 TTTAGGG
*
27747 TTTAAGG
1 TTTAGGG
*
27754 TTTATGG
1 TTTAGGG
**
27761 TTTAATG
1 TTTAGGG
*
27768 TTTAGTG
1 TTTAGGG
*
27775 TTTAGTG
1 TTTAGGG
*
27782 TTTATGG
1 TTTAGGG
*
27789 TTTAAGG
1 TTTAGGG
*
27796 TTTATGG
1 TTTAGGG
**
27803 TTTAAAG
1 TTTAGGG
27810 TTTAGGG
1 TTTAGGG
27817 TTTAACTGTGG
1 TTT-A--G-GG
27828 TTTAGGG
1 TTTAGGG
27835 TTTAACTGTGG
1 TTT-A--G-GG
27846 TTTAGGG
1 TTTAGGG
*
27853 TTTATGG
1 TTTAGGG
27860 TTTA
1 TTTA
27864 ATTTTGATTT
Statistics
Matches: 115, Mismatches: 22, Indels: 16
0.75 0.14 0.10
Matches are distributed among these distances:
7 97 0.84
8 4 0.03
10 4 0.03
11 10 0.09
ACGTcount: A:0.22, C:0.01, G:0.28, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:27854 original size:25 final size:25
Alignment explanation
Indices: 27826--28591 Score: 430
Period size: 25 Copynumber: 29.2 Consensus size: 25
27816 GTTTAACTGT
* *
27826 GGTTTAGGGTTTAACTGTGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
* * * *
27851 GGTTTATGGTTTAATTTTGATTTAT
1 GGTTTAGGGTTTAATTATGGTTTAG
* * * *
27876 GATGTATGGTTTAATTGTGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
* *
27901 GGTTTAGTGTTTAACTATGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
* *
27926 GGTTTAGTGTTTAACTATGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
* *
27951 GGTTTATGGTTTGATTATGGTTTAGGG
1 GGTTTAGGGTTTAATTATGGTTTA--G
*
27978 TTTAGAGTTTAGGGTTTGATTATGGTTTAG
1 ----G-GTTTAGGGTTTAATTATGGTTTAG
*
28008 GGTTTAGGGTTTAATTATGATTT-G
1 GGTTTAGGGTTTAATTATGGTTTAG
* *
28032 AGGTTTAGGGTTTAATTGTAGTTTAG
1 -GGTTTAGGGTTTAATTATGGTTTAG
*
28058 GGTTTAGGGTTTAATTATAGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
* * *
28083 GGTTTAGTGATTAACTATGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
* *
28108 GGTTAAGGGTTTAGTTTTTAATTATGATTTAG
1 GGTTTA-GG----G--TTTAATTATGGTTTAG
**
28140 GGTTTAGGGTTTAATTATTATTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
* * *
28165 GGTTGAAGGTTTAATTGTGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
* *
28190 GGTTTA-GGTCTAATAATGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
* * *
28214 CGTTTAAGGTTTAAAGTTTAACTATAGTTTA-
1 GGTTT-AGG------GTTTAATTATGGTTTAG
* *
28245 AGTTTAGGGTTTAACTATGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
* * * *
28270 GGTTTAAGGTCTAACTATGGTTTAT
1 GGTTTAGGGTTTAATTATGGTTTAG
* * *
28295 AGTTTAGGGTTTAGTCATGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
* **
28320 GGTTTA--ATTGTGGTTTATGG-TTAG
1 GGTTTAGGGTT-T-AATTATGGTTTAG
* * *
28344 GGTTTAATCGTGGTTTATGTTTTATTGTTTAACTAT
1 GGTTT-A--G-GGTTTA---ATTA-TGGTT---TAG
*
28380 GATTTAGGGTTTAGTATTTAACCATGG-TTAG
1 GGTTTAGGGTTTA--A-TT----ATGGTTTAG
* * ** *
28411 GATTTAGGGTTTAATTGTGAATTAT
1 GGTTTAGGGTTTAATTATGGTTTAG
* * *
28436 GGTTTACGGTTTAATTGTTGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
* * * **
28461 GGTTTATGGTCTAACTATAATTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
* * *
28486 GGTTTAGTGTTGAATTGTGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
* *
28511 GGTTTAGGGTCTAATCATGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
* *
28536 GGTTTAGGGTCTAATCATGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
* * *
28561 GGTTTAGTGTCTAATCATGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAG
28586 GGTTTA
1 GGTTTA
28592 ATTGTGGTTT
Statistics
Matches: 587, Mismatches: 107, Indels: 94
0.74 0.14 0.12
Matches are distributed among these distances:
23 2 0.00
24 47 0.08
25 418 0.71
26 4 0.01
27 2 0.00
28 2 0.00
29 2 0.00
30 7 0.01
31 28 0.05
32 62 0.11
33 2 0.00
34 1 0.00
35 3 0.01
36 7 0.01
ACGTcount: A:0.22, C:0.03, G:0.28, T:0.47
Consensus pattern (25 bp):
GGTTTAGGGTTTAATTATGGTTTAG
Found at i:27954 original size:7 final size:7
Alignment explanation
Indices: 27944--28020 Score: 58
Period size: 7 Copynumber: 11.9 Consensus size: 7
27934 GTTTAACTAT
27944 GGTTTAG
1 GGTTTAG
*
27951 GGTTTAT
1 GGTTTAG
27958 GGTTT--
1 GGTTTAG
* *
27963 -GATTAT
1 GGTTTAG
27969 GGTTTAG
1 GGTTTAG
27976 GGTTTAG
1 GGTTTAG
*
27983 AGTTTAG
1 GGTTTAG
27990 GGTTT--
1 GGTTTAG
* *
27995 -GATTAT
1 GGTTTAG
28001 GGTTTAG
1 GGTTTAG
28008 GGTTTAG
1 GGTTTAG
28015 GGTTTA
1 GGTTTA
28021 ATTATGATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
4 6 0.11
7 49 0.89
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.48
Consensus pattern (7 bp):
GGTTTAG
Found at i:27972 original size:18 final size:18
Alignment explanation
Indices: 27951--28012 Score: 78
Period size: 18 Copynumber: 3.7 Consensus size: 18
27941 TATGGTTTAG
*
27951 GGTTTATGGTTTGATTAT
1 GGTTTAGGGTTTGATTAT
*
27969 GGTTTAGGGTTT-A-GA-
1 GGTTTAGGGTTTGATTAT
27984 -GTTTAGGGTTTGATTAT
1 GGTTTAGGGTTTGATTAT
28001 GGTTTAGGGTTT
1 GGTTTAGGGTTT
28013 AGGGTTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 11 0.30
15 1 0.03
16 2 0.05
17 1 0.03
18 22 0.59
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (18 bp):
GGTTTAGGGTTTGATTAT
Found at i:27977 original size:50 final size:50
Alignment explanation
Indices: 27826--28591 Score: 512
Period size: 50 Copynumber: 15.1 Consensus size: 50
27816 GTTTAACTGT
* * * * * *
27826 GGTTTAGGGTTTAACTGTGGTTTAGGGTTTATGGTTTAATTTTGATTTAT
1 GGTTTAGGGTTTAATTATGGTTTAGGGTTTAGGGTTTAATTATGGTTTAG
* * * * * *
27876 GATGTATGGTTTAATTGTGGTTTAGGGTTTAGTGTTTAACTATGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAGGGTTTAGGGTTTAATTATGGTTTAG
* * * *
27926 GGTTTAGTGTTTAACTATGGTTTAGGGTTTATGGTTTGATTATGGTTTAGGG
1 GGTTTAGGGTTTAATTATGGTTTAGGGTTTAGGGTTTAATTATGGTTTA--G
* *
27978 TTTAGAGTTTAGGGTTTGATTATGGTTTAGGGTTTAGGGTTTAATTATGATTT-G
1 ----G-GTTTAGGGTTTAATTATGGTTTAGGGTTTAGGGTTTAATTATGGTTTAG
* * *
28032 AGGTTTAGGGTTTAATTGTAGTTTAGGGTTTAGGGTTTAATTATAGTTTAG
1 -GGTTTAGGGTTTAATTATGGTTTAGGGTTTAGGGTTTAATTATGGTTTAG
* * * * *
28083 GGTTTAGTGATTAACTATGGTTTAGGGTTAAGGGTTTAGTTTTTAATTATGATTTAG
1 GGTTTAGGGTTTAATTATGGTTTAGGGTTTA-GG----G--TTTAATTATGGTTTAG
** * * *
28140 GGTTTAGGGTTTAATTATTATTTAGGGTTGAAGGTTTAATTGTGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAGGGTTTAGGGTTTAATTATGGTTTAG
* * * * *
28190 GGTTTA-GGTCTAATAATGGTTTAGCGTTTAAGGTTTAAAGTTTAACTATAGTTTA-
1 GGTTTAGGGTTTAATTATGGTTTAGGGTTT-AGG------GTTTAATTATGGTTTAG
* * * * * *
28245 AGTTTAGGGTTTAACTATGGTTTAGGGTTTAAGGTCTAACTATGGTTTAT
1 GGTTTAGGGTTTAATTATGGTTTAGGGTTTAGGGTTTAATTATGGTTTAG
* * * * *
28295 AGTTTAGGG--T--TTA--G-TCATGGTTTAGGGTTTAATTGTGGTTTAT
1 GGTTTAGGGTTTAATTATGGTTTAGGGTTTAGGGTTTAATTATGGTTTAG
** * * ** * *
28338 GG-TTAGGGTTTAATCGTGGTTTATGTTTTATTGTTTAACTATGATTTAG
1 GGTTTAGGGTTTAATTATGGTTTAGGGTTTAGGGTTTAATTATGGTTTAG
** ** * * ** *
28387 GGTTTAGTATTTAACCATGG-TTAGGATTTAGGGTTTAATTGTGAATTAT
1 GGTTTAGGGTTTAATTATGGTTTAGGGTTTAGGGTTTAATTATGGTTTAG
* * * * * * **
28436 GGTTTACGGTTTAATTGTTGTTTAGGGTTTATGGTCTAACTATAATTTAG
1 GGTTTAGGGTTTAATTATGGTTTAGGGTTTAGGGTTTAATTATGGTTTAG
* * * * *
28486 GGTTTAGTGTTGAATTGTGGTTTAGGGTTTAGGGTCTAATCATGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAGGGTTTAGGGTTTAATTATGGTTTAG
* * * * *
28536 GGTTTAGGGTCTAATCATGGTTTAGGGTTTAGTGTCTAATCATGGTTTAG
1 GGTTTAGGGTTTAATTATGGTTTAGGGTTTAGGGTTTAATTATGGTTTAG
28586 GGTTTA
1 GGTTTA
28592 ATTGTGGTTT
Statistics
Matches: 557, Mismatches: 126, Indels: 66
0.74 0.17 0.09
Matches are distributed among these distances:
42 6 0.01
43 24 0.04
44 2 0.00
46 3 0.01
48 2 0.00
49 88 0.16
50 302 0.54
51 5 0.01
52 2 0.00
54 1 0.00
55 8 0.01
56 34 0.06
57 80 0.14
ACGTcount: A:0.22, C:0.03, G:0.28, T:0.47
Consensus pattern (50 bp):
GGTTTAGGGTTTAATTATGGTTTAGGGTTTAGGGTTTAATTATGGTTTAG
Found at i:27980 original size:32 final size:32
Alignment explanation
Indices: 27944--28152 Score: 142
Period size: 32 Copynumber: 6.4 Consensus size: 32
27934 GTTTAACTAT
*
27944 GGTTTAGGGTTTATGGTTTGATTATGGTTTAG
1 GGTTTAGGGTTTAGGGTTTGATTATGGTTTAG
*
27976 GGTTTAGAGTTTAGGGTTTGATTATGGTTTAG
1 GGTTTAGGGTTTAGGGTTTGATTATGGTTTAG
*
28008 GGTTTAGGGTTTA--ATTATGATT-TGAGGTTTAG
1 GGTTTAGGGTTTAGGGTT-TGATTAT--GGTTTAG
* * **
28040 GGTTTAATTGTAGTTTAGGGTTTAGGGTT-TAATTATA-
1 GGTTT-A--G-GGTTTAGGGTTT--GATTATGGTT-TAG
* * * *
28077 -GTTTAGGGTTTAGTGATTAACTATGGTTTAG
1 GGTTTAGGGTTTAGGGTTTGATTATGGTTTAG
* ** * *
28108 GGTTAAGGGTTTAGTTTTTAATTATGATTTAG
1 GGTTTAGGGTTTAGGGTTTGATTATGGTTTAG
28140 GGTTTAGGGTTTA
1 GGTTTAGGGTTTA
28153 ATTATTATTT
Statistics
Matches: 139, Mismatches: 23, Indels: 30
0.72 0.12 0.16
Matches are distributed among these distances:
30 6 0.04
31 8 0.06
32 101 0.73
33 2 0.01
35 2 0.01
36 9 0.06
37 3 0.02
38 4 0.03
39 4 0.03
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (32 bp):
GGTTTAGGGTTTAGGGTTTGATTATGGTTTAG
Found at i:28333 original size:18 final size:18
Alignment explanation
Indices: 28296--28341 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
28286 ATGGTTTATA
*
28296 GTTTAGGGTTTAGTCATG
1 GTTTAGGGTTTAATCATG
**
28314 GTTTAGGGTTTAATTGTG
1 GTTTAGGGTTTAATCATG
*
28332 GTTTATGGTT
1 GTTTAGGGTT
28342 AGGGTTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.15, C:0.02, G:0.33, T:0.50
Consensus pattern (18 bp):
GTTTAGGGTTTAATCATG
Found at i:28533 original size:43 final size:43
Alignment explanation
Indices: 28486--28632 Score: 143
Period size: 43 Copynumber: 3.3 Consensus size: 43
28476 TATAATTTAG
*
28486 GGTTTAGTGTTGAATTGTGGTTTAGGGTTTAGGGTCTAATCAT
1 GGTTTAGGGTTGAATTGTGGTTTAGGGTTTAGGGTCTAATCAT
** *
28529 GGTTTAGGGTTTAGGGTCTAATCATGGTTTAGGGTTTAGTGTCTAATCAT
1 GGTTTAGGG-TT---G---AATTGTGGTTTAGGGTTTAGGGTCTAATCAT
* * * *
28579 GGTTTAGGGTTTAATTGTGGTTT-GGAGTTTGGGGTCTAGTTAT
1 GGTTTAGGGTTGAATTGTGGTTTAGG-GTTTAGGGTCTAATCAT
28622 GGTTTAGGGTT
1 GGTTTAGGGTT
28633 TAAAGTTTAA
Statistics
Matches: 85, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.02
43 41 0.48
44 2 0.02
47 1 0.01
49 2 0.02
50 37 0.44
ACGTcount: A:0.17, C:0.05, G:0.34, T:0.44
Consensus pattern (43 bp):
GGTTTAGGGTTGAATTGTGGTTTAGGGTTTAGGGTCTAATCAT
Found at i:28648 original size:93 final size:93
Alignment explanation
Indices: 28486--28684 Score: 240
Period size: 93 Copynumber: 2.1 Consensus size: 93
28476 TATAATTTAG
* * ** *
28486 GGTTTAGTGTTGAATTGTGGTTTAGGGTTTAGGGTCTAATCATGGTTTAGGGTTTAGGGTCTAAT
1 GGTTTAGGGTTTAATTGTGGTTTAGGGTTTAGGGTCTAATCATGGTTTAGGGTTTAAAGTCTAAC
*
28551 CATGG-TTTAGGGTTTAGTGTCTAATCAT
66 CATGGTTTTA-GGTTTAGGGTCTAATCAT
* * * *
28579 GGTTTAGGGTTTAATTGTGGTTT-GGAGTTTGGGGTCTAGTTATGGTTTAGGGTTTAAAGTTTAA
1 GGTTTAGGGTTTAATTGTGGTTTAGG-GTTTAGGGTCTAATCATGGTTTAGGGTTTAAAGTCTAA
* **
28643 CCATGGTTTTAGGTTTTGGGTCTAATTGT
65 CCATGGTTTTAGGTTTAGGGTCTAATCAT
*
28672 TGTTTAGGGTTTA
1 GGTTTAGGGTTTA
28685 GTTTTTAACC
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
92 2 0.02
93 84 0.93
94 4 0.04
ACGTcount: A:0.18, C:0.05, G:0.32, T:0.45
Consensus pattern (93 bp):
GGTTTAGGGTTTAATTGTGGTTTAGGGTTTAGGGTCTAATCATGGTTTAGGGTTTAAAGTCTAAC
CATGGTTTTAGGTTTAGGGTCTAATCAT
Found at i:28658 original size:68 final size:68
Alignment explanation
Indices: 28511--28651 Score: 176
Period size: 68 Copynumber: 2.1 Consensus size: 68
28501 TGTGGTTTAG
* ** ** *
28511 GGTTTAGGGTCTAATCATGGTTTAGGGTTTAGGGTCTAATCATGGTTTAGGGTTTAGTGTCTAAT
1 GGTTTAGGGTTTAATTGTGGTTTAGGGTTTAGGGTCTAATCATGGTTTAGGGTTTAAAGTCTAAC
28576 CAT
66 CAT
* * * *
28579 GGTTTAGGGTTTAATTGTGGTTT-GGAGTTTGGGGTCTAGTTATGGTTTAGGGTTTAAAGTTTAA
1 GGTTTAGGGTTTAATTGTGGTTTAGG-GTTTAGGGTCTAATCATGGTTTAGGGTTTAAAGTCTAA
28643 CCAT
65 CCAT
28647 GGTTT
1 GGTTT
28652 TAGGTTTTGG
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
67 2 0.03
68 60 0.97
ACGTcount: A:0.19, C:0.06, G:0.31, T:0.43
Consensus pattern (68 bp):
GGTTTAGGGTTTAATTGTGGTTTAGGGTTTAGGGTCTAATCATGGTTTAGGGTTTAAAGTCTAAC
CAT
Found at i:35102 original size:11 final size:11
Alignment explanation
Indices: 35086--35112 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
35076 ATGTAAAGAT
35086 TGTTTATGTAA
1 TGTTTATGTAA
35097 TGTTTATGTAA
1 TGTTTATGTAA
35108 TGTTT
1 TGTTT
35113 GTGCTTCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (11 bp):
TGTTTATGTAA
Found at i:35281 original size:32 final size:32
Alignment explanation
Indices: 35221--35281 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
35211 TTCTATCACC
*
35221 AATAAATATAAATAACATATAATAAATAAATA
1 AATAAATATAAATAAAATATAATAAATAAATA
* *
35253 AATAAATATAATTTAAAAT-TAATTAATAA
1 AATAAATATAA-ATAAAATATAATAAATAA
35282 TAACATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 20 0.80
33 5 0.20
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (32 bp):
AATAAATATAAATAAAATATAATAAATAAATA
Found at i:36681 original size:20 final size:20
Alignment explanation
Indices: 36656--36726 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
36646 ATTATATTGT
36656 TGTTTTGG-TGCCTTTTTTAC
1 TGTTTTGGTTG-CTTTTTTAC
**
36676 TGTTTTGGTTGCTTTTTTGT
1 TGTTTTGGTTGCTTTTTTAC
** *
36696 TGTTTTTATAT-TTTTTTTAC
1 TGTTTTGGT-TGCTTTTTTAC
36716 TGTTTTGGTTG
1 TGTTTTGGTTG
36727 ATGTTTTCGT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 1 0.03
20 35 0.90
21 3 0.08
ACGTcount: A:0.06, C:0.07, G:0.20, T:0.68
Consensus pattern (20 bp):
TGTTTTGGTTGCTTTTTTAC
Found at i:36819 original size:24 final size:23
Alignment explanation
Indices: 36781--36825 Score: 81
Period size: 24 Copynumber: 1.9 Consensus size: 23
36771 GTTTTAATGT
36781 TGTTTTATTGTTATTTTTGTTTA
1 TGTTTTATTGTTATTTTTGTTTA
36804 TGTTTTGATTGTTATTTTTGTT
1 TGTTTT-ATTGTTATTTTTGTT
36826 GGTTTGATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.11, C:0.00, G:0.16, T:0.73
Consensus pattern (23 bp):
TGTTTTATTGTTATTTTTGTTTA
Found at i:36843 original size:21 final size:23
Alignment explanation
Indices: 36782--36843 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 23
36772 TTTTAATGTT
* *
36782 GTTTTATTGTTATTTTTGTTTATG
1 GTTTGATTGTTATTTTT-TGTATG
*
36806 TTTTGATTGTTA-TTTTTGT-TG
1 GTTTGATTGTTATTTTTTGTATG
36827 GTTTGA-TGTTATTTTTT
1 GTTTGATTGTTATTTTTT
36844 ATGCGTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 5 0.15
21 12 0.36
22 2 0.06
23 4 0.12
24 10 0.30
ACGTcount: A:0.11, C:0.00, G:0.18, T:0.71
Consensus pattern (23 bp):
GTTTGATTGTTATTTTTTGTATG
Found at i:36851 original size:21 final size:21
Alignment explanation
Indices: 36778--36842 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 21
36768 TTGGTTTTAA
*
36778 TGTT-GTTTTATTGTTATTTT
1 TGTTGGTTTGATTGTTATTTT
*
36798 TGTTTATGTTTTGATTGTTATTTT
1 TG--T-TGGTTTGATTGTTATTTT
36822 TGTTGGTTTGA-TGTTATTTT
1 TGTTGGTTTGATTGTTATTTT
36842 T
1 T
36843 TATGCGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 12 0.32
21 7 0.18
22 2 0.05
23 1 0.03
24 16 0.42
ACGTcount: A:0.11, C:0.00, G:0.18, T:0.71
Consensus pattern (21 bp):
TGTTGGTTTGATTGTTATTTT
Found at i:39345 original size:20 final size:18
Alignment explanation
Indices: 39317--39364 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
39307 CCACATCAAC
*
39317 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAA-TA-TA
39337 AAATTATTTTTTAAAATATA
1 AAATTA--TTTTAAAATATA
39357 AAATTATT
1 AAATTATT
39365 AAAATCATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
20 13 0.52
21 2 0.08
22 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
AAATTATTTTAAAATATA
Found at i:40506 original size:8 final size:9
Alignment explanation
Indices: 40470--40508 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
40460 ATTAAAATTA
40470 TTTAATAAT
1 TTTAATAAT
40479 TTTAATAAT
1 TTTAATAAT
40488 TTT-AT-AT
1 TTTAATAAT
40495 TTTAA-AAT
1 TTTAATAAT
40503 TTTAAT
1 TTTAAT
40509 TTTAAATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 5 0.19
8 10 0.37
9 12 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTAATAAT
Found at i:40512 original size:14 final size:14
Alignment explanation
Indices: 40475--40514 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 14
40465 AATTATTTAA
40475 TAATTTTAATAATTT
1 TAATTTTAA-AATTT
40490 TATATTTTAAAATTT
1 TA-ATTTTAAAATTT
40505 TAATTTTAAA
1 TAATTTTAAA
40515 TTAATTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.33
15 9 0.38
16 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATTTTAAAATTT
Found at i:44526 original size:20 final size:19
Alignment explanation
Indices: 44487--44544 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 19
44477 GTGCAAAACA
44487 ATAAAA-TTA-AAAAATA-
1 ATAAAATTTATAAAAATAT
44503 ATAAAATTTATAAAAATATT
1 ATAAAATTTATAAAAATA-T
44523 ATAAAATTT-T--AAATAT
1 ATAAAATTTATAAAAATAT
44539 ATAAAA
1 ATAAAA
44545 AAAATTGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
16 13 0.34
17 8 0.21
18 7 0.18
19 1 0.03
20 9 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAAATTTATAAAAATAT
Found at i:44540 original size:19 final size:20
Alignment explanation
Indices: 44487--44540 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
44477 GTGCAAAACA
44487 ATAAAA-TTA-AAAAATA--
1 ATAAAATTTATAAAAATATT
44503 ATAAAATTTATAAAAATATT
1 ATAAAATTTATAAAAATATT
*
44523 ATAAAATTT-TAAATATAT
1 ATAAAATTTATAAAAATAT
44541 AAAAAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 6 0.18
17 3 0.09
18 7 0.21
19 8 0.24
20 9 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAAAATTTATAAAAATATT
Found at i:44547 original size:19 final size:20
Alignment explanation
Indices: 44494--44571 Score: 72
Period size: 19 Copynumber: 4.0 Consensus size: 20
44484 ACAATAAAAT
44494 TAAAAA-ATAATAAAATTTA
1 TAAAAATATAATAAAATTTA
*
44513 TAAAAATATTATAAAATTT-
1 TAAAAATATAATAAAATTTA
* * * *
44532 TAAATATATAAAAAAAATTG
1 TAAAAATATAATAAAATTTA
* *
44552 TAAAAAT-TACTAAAAATTA
1 TAAAAATATAATAAAATTTA
44571 T
1 T
44572 CATTTATAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
19 31 0.65
20 17 0.35
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (20 bp):
TAAAAATATAATAAAATTTA
Found at i:44846 original size:23 final size:21
Alignment explanation
Indices: 44809--44851 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
44799 TGTTTACACA
*
44809 TTTAAATTTTTGTAACATTTT
1 TTTAAATTTTTGTAAAATTTT
44830 TTTATAATTTTTAGTAAAATTT
1 TTTA-AATTTTT-GTAAAATTT
44852 AAGGATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 7 0.37
23 8 0.42
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTAAATTTTTGTAAAATTTT
Found at i:47538 original size:31 final size:31
Alignment explanation
Indices: 47503--47571 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 31
47493 GTTATCACTT
*
47503 CGTAACAAAATATT-AACATAAGTGACTAAAA
1 CGTAACAAAAT-TTAAACATAAATGACTAAAA
*
47534 CGTAACAATATTTCAAACATAAATGACTAAAA
1 CGTAACAAAATTT-AAACATAAATGACTAAAA
47566 CGTAAC
1 CGTAAC
47572 CTGAGGCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 2 0.06
31 10 0.29
32 22 0.65
ACGTcount: A:0.52, C:0.16, G:0.09, T:0.23
Consensus pattern (31 bp):
CGTAACAAAATTTAAACATAAATGACTAAAA
Found at i:53293 original size:22 final size:22
Alignment explanation
Indices: 53268--53310 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
53258 AAGAATCTGA
* *
53268 ATATAATTAGAATAATTTAAAG
1 ATATAATCAAAATAATTTAAAG
53290 ATATAATCAAAATAATTTAAA
1 ATATAATCAAAATAATTTAAA
53311 ATGAAGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (22 bp):
ATATAATCAAAATAATTTAAAG
Found at i:56795 original size:20 final size:20
Alignment explanation
Indices: 56758--56796 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
56748 AGTCAGGGAA
**
56758 AAGGAGAAGAAGTGAAGAGG
1 AAGGAGAAGAAGAAAAGAGG
*
56778 AAGGAGAAGGAGAAAAGAG
1 AAGGAGAAGAAGAAAAGAG
56797 ACCGAGCCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.44, T:0.03
Consensus pattern (20 bp):
AAGGAGAAGAAGAAAAGAGG
Found at i:66142 original size:4 final size:4
Alignment explanation
Indices: 66133--66158 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
66123 ATATTACAAC
66133 AGTG AGTG AGTG AGTG AGTG AGTG AG
1 AGTG AGTG AGTG AGTG AGTG AGTG AG
66159 AGAGAGGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.50, T:0.23
Consensus pattern (4 bp):
AGTG
Found at i:72089 original size:38 final size:38
Alignment explanation
Indices: 72047--72124 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
72037 CAACTTATTA
72047 CATTTACAATCCCAATACAAAGCATTACACACTACTCC
1 CATTTACAATCCCAATACAAAGCATTACACACTACTCC
* *
72085 CATTTACAATCCCACTACAAAGCATTACACACTGCTCC
1 CATTTACAATCCCAATACAAAGCATTACACACTACTCC
72123 CA
1 CA
72125 CCACCACGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.36, G:0.04, T:0.23
Consensus pattern (38 bp):
CATTTACAATCCCAATACAAAGCATTACACACTACTCC
Found at i:85071 original size:13 final size:13
Alignment explanation
Indices: 85055--85093 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
85045 ACAAAATATT
*
85055 TTTATATAATAAA
1 TTTATATTATAAA
*
85068 TTTATATTATTAA
1 TTTATATTATAAA
85081 TTTA-ATTATAAA
1 TTTATATTATAAA
85093 T
1 T
85094 CTTTTTTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTATATTATAAA
Found at i:90745 original size:254 final size:254
Alignment explanation
Indices: 90296--90804 Score: 1009
Period size: 254 Copynumber: 2.0 Consensus size: 254
90286 ACTAGGTGAG
90296 CTTAACATGTGAGGCATAGAATACCGGAGGCAAAAAGAAACCGGGACAGCAAAGAACTTTTTCAA
1 CTTAACATGTGAGGCATAGAATACCGGAGGCAAAAAGAAACCGGGACAGCAAAGAACTTTTTCAA
90361 ATGCTATAAAATCCTATATTCCATCTAACATCATGTAAAACATCACATCTAAAACGAGAAAAAGG
66 ATGCTATAAAATCCTATATTCCATCTAACATCATGTAAAACATCACATCTAAAACGAGAAAAAGG
90426 AAAAGAGACTTATAGATCACATTTAGTTATATACGAATATTTGACAAGAAGAGGCCTTTTGATAG
131 AAAAGAGACTTATAGATCACATTTAGTTATATACGAATATTTGACAAGAAGAGGCCTTTTGATAG
90491 AAATCAATATAACTTGAAGGCACCCAGTTATAAAAATCACTTCTTTCTTTAATGTTTTT
196 AAATCAATATAACTTGAAGGCACCCAGTTATAAAAATCACTTCTTTCTTTAATGTTTTT
90550 CTTAACATGTGAGGCATAGAATACCGGAGGCAAAAAGAAACCGGGACAGCAAAGAACTTTTTCAA
1 CTTAACATGTGAGGCATAGAATACCGGAGGCAAAAAGAAACCGGGACAGCAAAGAACTTTTTCAA
90615 ATGCTATAAAATCCTATATTCCATCTAACATCATGTAAAACATCACATCTAAAACGAGAAAAAGG
66 ATGCTATAAAATCCTATATTCCATCTAACATCATGTAAAACATCACATCTAAAACGAGAAAAAGG
90680 AAAAGAGACTTATAGATCACATTTAGTTATATACGAATATTTGACAAGAAGAGGCCTTTTGATAG
131 AAAAGAGACTTATAGATCACATTTAGTTATATACGAATATTTGACAAGAAGAGGCCTTTTGATAG
*
90745 AAATCAATATAACTTGAAGGCACTCAGTTATAAAAATCACTTCTTTCTTTAATGTTTTT
196 AAATCAATATAACTTGAAGGCACCCAGTTATAAAAATCACTTCTTTCTTTAATGTTTTT
90804 C
1 C
90805 CCTCCCAATT
Statistics
Matches: 254, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
254 254 1.00
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Consensus pattern (254 bp):
CTTAACATGTGAGGCATAGAATACCGGAGGCAAAAAGAAACCGGGACAGCAAAGAACTTTTTCAA
ATGCTATAAAATCCTATATTCCATCTAACATCATGTAAAACATCACATCTAAAACGAGAAAAAGG
AAAAGAGACTTATAGATCACATTTAGTTATATACGAATATTTGACAAGAAGAGGCCTTTTGATAG
AAATCAATATAACTTGAAGGCACCCAGTTATAAAAATCACTTCTTTCTTTAATGTTTTT
Found at i:96062 original size:73 final size:73
Alignment explanation
Indices: 95951--96088 Score: 249
Period size: 73 Copynumber: 1.9 Consensus size: 73
95941 ATGTAAATGC
95951 TCCATTGTTTTTAGTGAATACCATTAAAGAGGAAGCAACATATATTGAGCTTTTACTTCTAAAAT
1 TCCATTGTTTTTAGTGAATACCATTAAAGAGGAAGCAACATATATTGAGCTTTTACTTCTAAAAT
96016 GCACATGT
66 GCACATGT
* * *
96024 TCCATTGTTTTTAGTGAATCCCATTAAAGTGGAGGCAACATATATTGAGCTTTTACTTCTAAAAT
1 TCCATTGTTTTTAGTGAATACCATTAAAGAGGAAGCAACATATATTGAGCTTTTACTTCTAAAAT
96089 ACTTTTGGTC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (73 bp):
TCCATTGTTTTTAGTGAATACCATTAAAGAGGAAGCAACATATATTGAGCTTTTACTTCTAAAAT
GCACATGT
Found at i:97845 original size:21 final size:23
Alignment explanation
Indices: 97821--97862 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
97811 TAAATAAACA
97821 AAATTATTAAA-AA-TTTTAATT
1 AAATTATTAAAGAAGTTTTAATT
*
97842 AAATTCTTAAAGAAGTTTTAA
1 AAATTATTAAAGAAGTTTTAA
97863 AATTTTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 2 0.11
23 6 0.33
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (23 bp):
AAATTATTAAAGAAGTTTTAATT
Found at i:104542 original size:24 final size:24
Alignment explanation
Indices: 104499--104544 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
104489 ACTTAATTGC
*
104499 TTTTTTTTTTTTAAAGTTTGAAGG
1 TTTTTTTTTTATAAAGTTTGAAGG
* *
104523 TTTTTTTTTTATACATTTTGAA
1 TTTTTTTTTTATAAAGTTTGAA
104545 AGTTCAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.22, C:0.02, G:0.11, T:0.65
Consensus pattern (24 bp):
TTTTTTTTTTATAAAGTTTGAAGG
Found at i:105312 original size:33 final size:33
Alignment explanation
Indices: 105275--105340 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
105265 GGCTGAGAGT
105275 AAAATGGTAGGATGTAGGCTATGTTGTTGGAGA
1 AAAATGGTAGGATGTAGGCTATGTTGTTGGAGA
105308 AAAATGGTAGGATGTAGGCTATGTTGTTGGAGA
1 AAAATGGTAGGATGTAGGCTATGTTGTTGGAGA
105341 GCAACCATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.30
Consensus pattern (33 bp):
AAAATGGTAGGATGTAGGCTATGTTGTTGGAGA
Found at i:111861 original size:23 final size:22
Alignment explanation
Indices: 111817--111865 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
111807 GAATTCTTGT
*
111817 TAAAATAAAATACAGTGGTAAAA
1 TAAAATAAAATAAAGTGGT-AAA
*
111840 TAAAATAAAAGTAAAGT-TTAAA
1 TAAAATAAAA-TAAAGTGGTAAA
111862 TAAA
1 TAAA
111866 CTAGACTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 11 0.48
24 5 0.22
ACGTcount: A:0.63, C:0.02, G:0.10, T:0.24
Consensus pattern (22 bp):
TAAAATAAAATAAAGTGGTAAA
Found at i:123931 original size:2 final size:2
Alignment explanation
Indices: 123924--123974 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
123914 GACAATATAA
123924 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
123966 TG TG TG TG T
1 TG TG TG TG T
123975 ACCTACATCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:124811 original size:4 final size:4
Alignment explanation
Indices: 124796--124830 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
124786 CCAACAACCC
124796 AGAA A-AA A-AA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
124831 CATCAGCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 6 0.20
4 24 0.80
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:135394 original size:6 final size:6
Alignment explanation
Indices: 135379--135416 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
135369 AAGCATAATA
135379 TTAT-T TTATAT TTATAT TTATAT TTATAT TTATAT TTA
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTA
135417 ATTATAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTATAT
Found at i:148810 original size:54 final size:54
Alignment explanation
Indices: 148728--148834 Score: 214
Period size: 54 Copynumber: 2.0 Consensus size: 54
148718 GTCTTGCATT
148728 TTAACATGCCAAGTAACGGTTATTGAACATTCTCAATCATTGCTTCAAAATACC
1 TTAACATGCCAAGTAACGGTTATTGAACATTCTCAATCATTGCTTCAAAATACC
148782 TTAACATGCCAAGTAACGGTTATTGAACATTCTCAATCATTGCTTCAAAATAC
1 TTAACATGCCAAGTAACGGTTATTGAACATTCTCAATCATTGCTTCAAAATAC
148835 ACTATATCTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.32
Consensus pattern (54 bp):
TTAACATGCCAAGTAACGGTTATTGAACATTCTCAATCATTGCTTCAAAATACC
Found at i:170594 original size:31 final size:31
Alignment explanation
Indices: 170559--170617 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
170549 ATCTAAGATG
170559 CTGCCACATCTTTTGTTTTCAAAAAGATATA
1 CTGCCACATCTTTTGTTTTCAAAAAGATATA
170590 CTGCCACATCTTTTGTTTTCAAAAAGAT
1 CTGCCACATCTTTTGTTTTCAAAAAGAT
170618 GTAATCAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (31 bp):
CTGCCACATCTTTTGTTTTCAAAAAGATATA
Found at i:170992 original size:21 final size:21
Alignment explanation
Indices: 170968--171010 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
170958 AATATTTAAA
170968 TAGTTTGGTTGATTTGAAGTG
1 TAGTTTGGTTGATTTGAAGTG
*
170989 TAGTTTGGTTGATTTGTAGTG
1 TAGTTTGGTTGATTTGAAGTG
171010 T
1 T
171011 TCTTTCTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (21 bp):
TAGTTTGGTTGATTTGAAGTG
Found at i:173405 original size:16 final size:16
Alignment explanation
Indices: 173367--173418 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
173357 TTTTACTTCA
* *
173367 ATTTTAAGTAATAATT
1 ATTTTAAATTATAATT
* *
173383 GTGTTAAATTATAATT
1 ATTTTAAATTATAATT
173399 ATTTTAAAATATATAATT
1 ATTTT-AAAT-TATAATT
173417 AT
1 AT
173419 CACAATTTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 15 0.54
17 4 0.14
18 9 0.32
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
ATTTTAAATTATAATT
Found at i:182193 original size:22 final size:22
Alignment explanation
Indices: 182146--182198 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
182136 TTACAAAACA
* *
182146 GTAACAATATAATAACGCAATG
1 GTAACAAAATAATAACACAATG
* *
182168 GTAACAAAATAATAACATAATT
1 GTAACAAAATAATAACACAATG
182190 GTAACAAAA
1 GTAACAAAA
182199 CAACAAACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.57, C:0.11, G:0.09, T:0.23
Consensus pattern (22 bp):
GTAACAAAATAATAACACAATG
Found at i:196233 original size:18 final size:18
Alignment explanation
Indices: 196210--196245 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
196200 CTTTAAAACA
196210 GAATTAACAACATTTATT
1 GAATTAACAACATTTATT
196228 GAATTAACAACATTTATT
1 GAATTAACAACATTTATT
196246 AAAGGATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (18 bp):
GAATTAACAACATTTATT
Found at i:200197 original size:31 final size:32
Alignment explanation
Indices: 200138--200198 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
200128 ATGCTTGTCC
* *
200138 ATATTATTTTTTATTTTTAAAATATTTATATT
1 ATATTATTTTTAATATTTAAAATATTTATATT
200170 ATATTA-TTTTAATATTTAATAAT-TTTATA
1 ATATTATTTTTAATATTTAA-AATATTTATA
200199 CATTTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (32 bp):
ATATTATTTTTAATATTTAAAATATTTATATT
Found at i:207267 original size:2 final size:2
Alignment explanation
Indices: 207220--207251 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
207210 TAAATTTGAT
207220 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
207252 AATTATAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:225471 original size:39 final size:39
Alignment explanation
Indices: 225373--225476 Score: 145
Period size: 41 Copynumber: 2.6 Consensus size: 39
225363 TTACAATTGT
* * * *
225373 AAGTATGATCAAGTAAGTGATTAGATTAATTATTCTATG
1 AAGTATGATCAAATTAGTAATTAGATTAATTATTATATG
*
225412 AAGTATATGACCAAATTAGTAATTAGATTAATTATTATATG
1 AAG--TATGATCAAATTAGTAATTAGATTAATTATTATATG
225453 AAGTATGATCAAATTAGTAATTAG
1 AAGTATGATCAAATTAGTAATTAG
225477 GTTTCAAACC
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
39 23 0.40
41 34 0.60
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (39 bp):
AAGTATGATCAAATTAGTAATTAGATTAATTATTATATG
Found at i:230068 original size:27 final size:28
Alignment explanation
Indices: 230037--230089 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
230027 AATTTATAAA
230037 ATTTTAA-ATT-AATAATGATAAAATTAT
1 ATTTTAACATTCAA-AATGATAAAATTAT
*
230064 ATTTTAACTTTCAAAATGATAAAATT
1 ATTTTAACATTCAAAATGATAAAATT
230090 TTGATTTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.30
28 14 0.61
29 2 0.09
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (28 bp):
ATTTTAACATTCAAAATGATAAAATTAT
Found at i:230097 original size:28 final size:29
Alignment explanation
Indices: 230050--230109 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
230040 TTAAATTAAT
230050 AATGATAAAATTATATTTTAACT-TTCAA
1 AATGATAAAATTATATTTTAACTCTTCAA
* *
230078 AATGATAAAATTTTGA-TTTAACTCTTTAA
1 AATGATAAAATTAT-ATTTTAACTCTTCAA
230107 AAT
1 AAT
230110 TTATAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (29 bp):
AATGATAAAATTATATTTTAACTCTTCAA
Found at i:232882 original size:2 final size:2
Alignment explanation
Indices: 232875--232903 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
232865 TTTGAACTTT
232875 TA 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 TA T
232904 TTAATTATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:233850 original size:30 final size:30
Alignment explanation
Indices: 233783--233851 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
233773 AATCTATATC
*
233783 TTTATAATTTTTAAAGAATTAAATCAAAAT
1 TTTATCATTTTTAAAGAATTAAATCAAAAT
* *
233813 TTCATCATTTTTGAAAG-ATTAAAGT-ACAAT
1 TTTATCATTTTT-AAAGAATTAAA-TCAAAAT
233843 TTTATCATT
1 TTTATCATT
233852 ACTTATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 28 0.85
31 5 0.15
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (30 bp):
TTTATCATTTTTAAAGAATTAAATCAAAAT
Found at i:234206 original size:33 final size:33
Alignment explanation
Indices: 234169--234239 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
234159 TAATGAAAAT
234169 CTTAATTATTATTTGTTGAGACAAATGTGAAAC
1 CTTAATTATTATTTGTTGAGACAAATGTGAAAC
*
234202 CTTAATTATTATTTGTTGTGACAAATGTGAAAC
1 CTTAATTATTATTTGTTGAGACAAATGTGAAAC
234235 CTTAA
1 CTTAA
234240 AAATTTTAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (33 bp):
CTTAATTATTATTTGTTGAGACAAATGTGAAAC
Found at i:235492 original size:22 final size:22
Alignment explanation
Indices: 235461--235505 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
235451 CTCGCATTAT
235461 ATAATACCAAATACATCAACAA
1 ATAATACCAAATACATCAACAA
*
235483 ATAATGCCAAATACATCAACAA
1 ATAATACCAAATACATCAACAA
235505 A
1 A
235506 ACCAGCTTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.58, C:0.22, G:0.02, T:0.18
Consensus pattern (22 bp):
ATAATACCAAATACATCAACAA
Found at i:244509 original size:4 final size:4
Alignment explanation
Indices: 244495--244572 Score: 120
Period size: 4 Copynumber: 19.2 Consensus size: 4
244485 TCCATTCAGG
* * *
244495 TACA TTACA TACA TACA TACA TACA TACA TACA TGCA TGCA TGCA TACA
1 TACA -TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
244544 TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA T
244573 TACCGCTACG
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
4 67 0.94
5 4 0.06
ACGTcount: A:0.45, C:0.24, G:0.04, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:249967 original size:24 final size:24
Alignment explanation
Indices: 249940--250001 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 24
249930 CCAACAAGCA
*
249940 AACAACTTTAGGAAACACATAATT
1 AACAGCTTTAGGAAACACATAATT
*
249964 AACAGCTTTAGAAGGCAACACATAATT
1 AACAGCTTT---AGGAAACACATAATT
249991 AACAGCTTTAG
1 AACAGCTTTAG
250002 AAGGCAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 10 0.30
27 23 0.70
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.24
Consensus pattern (24 bp):
AACAGCTTTAGGAAACACATAATT
Found at i:249989 original size:27 final size:27
Alignment explanation
Indices: 249953--250008 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
249943 AACTTTAGGA
249953 AACACATAATTAACAGCTTTAGAAGGC
1 AACACATAATTAACAGCTTTAGAAGGC
249980 AACACATAATTAACAGCTTTAGAAGGC
1 AACACATAATTAACAGCTTTAGAAGGC
250007 AA
1 AA
250009 ATAGTCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.21
Consensus pattern (27 bp):
AACACATAATTAACAGCTTTAGAAGGC
Found at i:252585 original size:25 final size:26
Alignment explanation
Indices: 252530--252604 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 26
252520 TTACTTTTAA
* *
252530 ATTTATAATATTTTATATTATATTAT
1 ATTTATAATATTATATATTATATTAC
*
252556 TTTTAT-ATATTATATAATT-TATTAC
1 ATTTATAATATTATAT-ATTATATTAC
*
252581 ATTTA-AA-AATATATATATATATTA
1 ATTTATAATATTATATAT-TATATTA
252605 AATATATGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
23 2 0.05
24 7 0.17
25 23 0.57
26 8 0.20
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTATAATATTATATATTATATTAC
Found at i:253158 original size:23 final size:23
Alignment explanation
Indices: 253132--253205 Score: 60
Period size: 30 Copynumber: 3.0 Consensus size: 23
253122 AAAATTTCAA
253132 TAAATAAAAATATATAAAATTAT
1 TAAATAAAAATATATAAAATTAT
*
253155 TAAATATTAAAATAATATAACATAATTTTT
1 TAAATA--AAAAT-ATAT-A-A-AA-TTAT
*
253185 TAAATAAAAATA-AAAAAATTA
1 TAAATAAAAATATATAAAATTA
253206 ATATAAGCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 15
0.69 0.05 0.25
Matches are distributed among these distances:
22 2 0.05
23 8 0.20
24 1 0.02
25 6 0.15
26 5 0.12
27 2 0.05
28 6 0.15
29 2 0.05
30 9 0.22
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (23 bp):
TAAATAAAAATATATAAAATTAT
Found at i:254347 original size:7 final size:7
Alignment explanation
Indices: 254335--254360 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
254325 TGATTGATTT
254335 AAAATTC
1 AAAATTC
254342 AAAATTC
1 AAAATTC
254349 AAAATTC
1 AAAATTC
254356 AAAAT
1 AAAAT
254361 AGGTACTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTC
Found at i:261245 original size:18 final size:18
Alignment explanation
Indices: 261222--261263 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
261212 GTATCACCCA
*
261222 CCTCCACCGCTGATGTAT
1 CCTCCACCGCTAATGTAT
*
261240 CCTCCACCTCTAATGTAT
1 CCTCCACCGCTAATGTAT
261258 CCTCCA
1 CCTCCA
261264 TATCAGTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.43, G:0.10, T:0.29
Consensus pattern (18 bp):
CCTCCACCGCTAATGTAT
Found at i:265444 original size:189 final size:188
Alignment explanation
Indices: 265117--265587 Score: 606
Period size: 189 Copynumber: 2.5 Consensus size: 188
265107 ATTTCAAAGT
* * * * *
265117 TGGAATCACTTCATGATCTGGATCTTAGTCATTGTCCGATGGTTGAATTCCCAGAAATCCCAAAA
1 TGGAATCCCTTCGTGATCTGAATCTTAGTCATTGTCCAAT-GTTGAATTCCCAGAAATCCCAAGA
* * * * *
265182 AGTTTGACAAAATTAAACTTATCTGAAACTCAAATTGAAGAGGTGTGCTTGTCTCTCGACACTCC
65 AGCTTAACGAAATTAAACTTATCTGGAACTCAAATTGAAGAGGTGTACTTGTCTCTCGACACTCC
* * *
265247 AAGTAATCTTCAGACCTTAGATACGAGTGGCTCAATGGT-CAAAATTGTAGCAATCAAGA
130 AAGTAATCTGCAGACCTTAGATACGAGTGGCTCAAGGGTAAAAAATT-TAGCAATCAAGA
* **
265306 TGGAATCCCTTCGTGATCTGAATCTTGGTCATTGTCCAATAGTCAAATTTCCC-GAAATCCCAAG
1 TGGAATCCCTTCGTGATCTGAATCTTAGTCATTGTCCAAT-GTTGAA-TTCCCAGAAATCCCAAG
*
265370 AAGCTTAACGAAATTAAACTTATCTGGAACTCAAATTGAAGAGGTGTACTTGTCTCTCGACTCTC
64 AAGCTTAACGAAATTAAACTTATCTGGAACTCAAATTGAAGAGGTGTACTTGTCTCTCGACACTC
* * ** * * *
265435 TAGGTAATCTGCAGATGTTAGATATGAGTGGCTCAAGGGTAAAAAATTTATCCATCAAGA
129 CAAGTAATCTGCAGACCTTAGATACGAGTGGCTCAAGGGTAAAAAATTTAGCAATCAAGA
* *
265495 TGGAATCCCTTCGTGTGATCTGAATCTTAGTCATTGCCCAATGATTGAATTCCCAGAAATCGCAA
1 TGGAATCCCTTC--GTGATCTGAATCTTAGTCATTGTCCAATG-TTGAATTCCCAGAAATCCCAA
*
265560 GAAGCTTAA-GAGAATTAAATTTATCTGG
63 GAAGCTTAACGA-AATTAAACTTATCTGG
265588 GACTAAAGTT
Statistics
Matches: 244, Mismatches: 31, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
189 163 0.67
190 19 0.08
191 62 0.25
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (188 bp):
TGGAATCCCTTCGTGATCTGAATCTTAGTCATTGTCCAATGTTGAATTCCCAGAAATCCCAAGAA
GCTTAACGAAATTAAACTTATCTGGAACTCAAATTGAAGAGGTGTACTTGTCTCTCGACACTCCA
AGTAATCTGCAGACCTTAGATACGAGTGGCTCAAGGGTAAAAAATTTAGCAATCAAGA
Found at i:268772 original size:32 final size:32
Alignment explanation
Indices: 268736--268799 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
268726 CATGGTCAAC
*
268736 CTAATGAATGTTATATAAGGACAGAACATTGA
1 CTAATGAATGTTATATAAGGACAAAACATTGA
*
268768 CTAATGAATGTTATTTAAGGACAAAACATTGA
1 CTAATGAATGTTATATAAGGACAAAACATTGA
268800 GTTTTAGGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (32 bp):
CTAATGAATGTTATATAAGGACAAAACATTGA
Found at i:273725 original size:21 final size:21
Alignment explanation
Indices: 273701--273745 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
273691 TTAAATTTAA
273701 ATTTATT-ATAACTTTTTTATT
1 ATTTATTAATAA-TTTTTTATT
* *
273722 ATTTTTTAATAATTTTTTTTT
1 ATTTATTAATAATTTTTTATT
273743 ATT
1 ATT
273746 GTTACATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTTATTAATAATTTTTTATT
Done.