Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009760.1 Kokia drynarioides strain JFW-HI SEQ_124479, 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: 195778
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 26 characters in sequence are not A, C, G, or T
Found at i:7715 original size:16 final size:16
Alignment explanation
Indices: 7678--7715 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
7668 TCCCTAAGTC
7678 TGTAATGGAATAGGAT
1 TGTAATGGAATAGGAT
* *
7694 TATAATGGAATAGGGT
1 TGTAATGGAATAGGAT
7710 TGTAAT
1 TGTAAT
7716 CAGTAATTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (16 bp):
TGTAATGGAATAGGAT
Found at i:7990 original size:58 final size:58
Alignment explanation
Indices: 7877--7990 Score: 153
Period size: 58 Copynumber: 2.0 Consensus size: 58
7867 ATTGTTATTA
* *
7877 ATTTTTAATAATATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAT
1 ATTTTTAATAATATTATTATTAAATATAAATTAATAAAATAATATATAATATAATAAT
*
7935 ATTTTTAAT-ATAATTATTATTAAAATATAAATTAATAAAAATCATA-AT-ATATAATA
1 ATTTTTAATAAT-ATTATTATT-AAATATAAATTAAT-AAAATAATATATAATATAATA
7991 TTAGAAAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
57 2 0.04
58 25 0.50
59 15 0.30
60 8 0.16
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.46
Consensus pattern (58 bp):
ATTTTTAATAATATTATTATTAAATATAAATTAATAAAATAATATATAATATAATAAT
Found at i:11427 original size:26 final size:28
Alignment explanation
Indices: 11375--11427 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
11365 AAATGTTATG
*
11375 TATAAATATGATAATTATTTATAAATAA
1 TATAAATATGATAATTAGTTATAAATAA
*
11403 TATAAATAT-AT-ATTAGTTATGAATA
1 TATAAATATGATAATTAGTTATAAATA
11428 TCTTATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 2 0.09
28 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (28 bp):
TATAAATATGATAATTAGTTATAAATAA
Found at i:13459 original size:17 final size:18
Alignment explanation
Indices: 13437--13470 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
13427 ATAACAATTA
13437 TGAAGATTTTGG-ATATG
1 TGAAGATTTTGGTATATG
13454 TGAAGATTTTGGTATAT
1 TGAAGATTTTGGTATAT
13471 TCCCCGAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.44
Consensus pattern (18 bp):
TGAAGATTTTGGTATATG
Found at i:21890 original size:19 final size:18
Alignment explanation
Indices: 21864--21924 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 18
21854 GTATTCATGT
21864 TGTGTTCATGTTATATTG
1 TGTGTTCATGTTATATTG
21882 TGTGATTCATG-TAT-TCATG
1 TGTG-TTCATGTTATAT--TG
*
21901 TTGTGTTCATGTTATATTT
1 -TGTGTTCATGTTATATTG
21920 TGTGT
1 TGTGT
21925 GGTGTGTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
17 1 0.03
18 12 0.33
19 15 0.42
20 7 0.19
21 1 0.03
ACGTcount: A:0.16, C:0.07, G:0.21, T:0.56
Consensus pattern (18 bp):
TGTGTTCATGTTATATTG
Found at i:32685 original size:17 final size:17
Alignment explanation
Indices: 32646--32693 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
32636 TGACATGTGG
**
32646 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* *
32663 ATATGCAGTGACAATAA
1 AAATGCAATGACAATAA
32680 AAATGCAATGACAA
1 AAATGCAATGACAA
32694 AGGAAATGTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.21
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:32700 original size:17 final size:17
Alignment explanation
Indices: 32644--32701 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
32634 AATGACATGT
*
32644 GGAAATGCAATGACAAT
1 GGAAATGCAATGACAAA
* * *
32661 GTATATGCAGTGACAATA
1 GGAAATGCAATGACAA-A
*
32679 -AAAATGCAATGACAAA
1 GGAAATGCAATGACAAA
32695 GGAAATG
1 GGAAATG
32702 TGATGATAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
16 1 0.03
17 30 0.97
ACGTcount: A:0.48, C:0.10, G:0.22, T:0.19
Consensus pattern (17 bp):
GGAAATGCAATGACAAA
Found at i:33176 original size:12 final size:12
Alignment explanation
Indices: 33143--33177 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
33133 CCTTCTCTTC
*
33143 TTTCCTCTTATT
1 TTTCCTCTTTTT
*
33155 CTTCCTCTTTTT
1 TTTCCTCTTTTT
33167 TTTCCTCTTTT
1 TTTCCTCTTTT
33178 GTCTCCATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTCCTCTTTTT
Found at i:43588 original size:20 final size:21
Alignment explanation
Indices: 43565--43613 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
43555 AAAGGTTCGA
43565 AAAGAAAAGAAAAAAAAG-AG
1 AAAGAAAAGAAAAAAAAGAAG
* *
43585 AAAGAAAAGGAGAAAAAGAAG
1 AAAGAAAAGAAAAAAAAGAAG
*
43606 AAAAAAAA
1 AAAGAAAA
43614 TGGTTGCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAGAAAAGAAAAAAAAGAAG
Found at i:43592 original size:12 final size:11
Alignment explanation
Indices: 43563--43613 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 11
43553 CAAAAGGTTC
*
43563 GAAAAGAAA-A
1 GAAAAAAAAGA
43573 GAAAAAAAAGA
1 GAAAAAAAAGA
*
43584 GAAAGAAAAGGA
1 GAAA-AAAAAGA
*
43596 GAAAAAGAAGA
1 GAAAAAAAAGA
43607 -AAAAAAA
1 GAAAAAAA
43614 TGGTTGCTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
10 14 0.41
11 10 0.29
12 10 0.29
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAGA
Found at i:43598 original size:23 final size:21
Alignment explanation
Indices: 43572--43613 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
43562 CGAAAAGAAA
43572 AGAAAAAAAAGAGAAAGAAAAGG
1 AGAAAAAAAAGA-AAA-AAAAGG
*
43595 AGAAAAAGAAGAAAAAAAA
1 AGAAAAAAAAGAAAAAAAA
43614 TGGTTGCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 3 0.17
23 11 0.61
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
AGAAAAAAAAGAAAAAAAAGG
Found at i:44380 original size:23 final size:23
Alignment explanation
Indices: 44342--44399 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
44332 CTGACGTGGC
* *
44342 ATCCAGTCAGCAGCTTCTAGAAG
1 ATCCAGTTAGCAGCTTCCAGAAG
*
44365 ATCCAGTTAGCTGCTTCCAGAAG
1 ATCCAGTTAGCAGCTTCCAGAAG
* *
44388 GTCTAGTTAGCA
1 ATCCAGTTAGCA
44400 AGGATGGACG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (23 bp):
ATCCAGTTAGCAGCTTCCAGAAG
Found at i:52961 original size:31 final size:31
Alignment explanation
Indices: 52926--52998 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
52916 AAAAAATTTT
*
52926 AACTTTTAAAGGTCC--AAATATTTTTTTCACC
1 AACTTTTAAAGGACCTAAAAT-TTTTTTTC-CC
*
52957 AACTTTTAAGGGACCTAAAATTTTTTTTCCC
1 AACTTTTAAAGGACCTAAAATTTTTTTTCCC
52988 AACTTTTAAAG
1 AACTTTTAAAG
52999 AGCTTAAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 25 0.68
32 8 0.22
33 4 0.11
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (31 bp):
AACTTTTAAAGGACCTAAAATTTTTTTTCCC
Found at i:53252 original size:6 final size:6
Alignment explanation
Indices: 53241--53268 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
53231 AGGGGCTTAC
53241 TTGAAT TTGAAT TTGAAT TTGAAT TTGA
1 TTGAAT TTGAAT TTGAAT TTGAAT TTGA
53269 TCGCCTCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (6 bp):
TTGAAT
Found at i:58383 original size:30 final size:30
Alignment explanation
Indices: 58347--58403 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
58337 CTTGAGCTCG
** * *
58347 AGCCCAAGCTTGAGCATGAGCTCGATCACA
1 AGCCCAAGCCCGAGCACGAGCACGATCACA
58377 AGCCCAAGCCCGAGCACGAGCACGATC
1 AGCCCAAGCCCGAGCACGAGCACGATC
58404 CGGAGCCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.35, G:0.25, T:0.11
Consensus pattern (30 bp):
AGCCCAAGCCCGAGCACGAGCACGATCACA
Found at i:58498 original size:27 final size:27
Alignment explanation
Indices: 58448--58507 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
58438 TCCCAAGTTG
* *
58448 TATCATTCGGGGTGGTCAGTCGATTGA
1 TATCATTCGGGGTAGTCAGTCGATAGA
58475 TATCATTCGGGGTAGTCAAG-CGATAGA
1 TATCATTCGGGGTAGTC-AGTCGATAGA
*
58502 AATCAT
1 TATCAT
58508 AAGGGTTGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
TATCATTCGGGGTAGTCAGTCGATAGA
Found at i:58976 original size:26 final size:26
Alignment explanation
Indices: 58940--58993 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
58930 ATGAATTTGA
*
58940 AATTAATTATGTTTATATTTGTATTT
1 AATTAAGTATGTTTATATTTGTATTT
*
58966 AATTAAGTATGTTTATGTTTGTATTT
1 AATTAAGTATGTTTATATTTGTATTT
58992 AA
1 AA
58994 GGTTTAGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (26 bp):
AATTAAGTATGTTTATATTTGTATTT
Found at i:59006 original size:14 final size:14
Alignment explanation
Indices: 58989--59022 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
58979 TATGTTTGTA
*
58989 TTTAAGGTTTAGGG
1 TTTAAGGTTTAGAG
*
59003 TTTAAAGTTTAGAG
1 TTTAAGGTTTAGAG
59017 TTTAAG
1 TTTAAG
59023 ATTTGTTCCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.44
Consensus pattern (14 bp):
TTTAAGGTTTAGAG
Found at i:59101 original size:23 final size:23
Alignment explanation
Indices: 59074--59131 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
59064 AATAAAAAGA
*
59074 AAAACCCTAAAACTTTAAAACCC
1 AAAACCCTAAAACTCTAAAACCC
* *
59097 TAAACCCTAAAACTCTAAAACTC
1 AAAACCCTAAAACTCTAAAACCC
*
59120 AAAACACTAAAA
1 AAAACCCTAAAA
59132 AAAGTTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.17
Consensus pattern (23 bp):
AAAACCCTAAAACTCTAAAACCC
Found at i:59123 original size:7 final size:8
Alignment explanation
Indices: 59074--59131 Score: 57
Period size: 8 Copynumber: 7.5 Consensus size: 8
59064 AATAAAAAGA
*
59074 AAAACCCT
1 AAAACTCT
*
59082 AAAACTTT
1 AAAACTCT
*
59090 AAAACCCT
1 AAAACTCT
*
59098 -AAACCCT
1 AAAACTCT
59105 AAAACTCT
1 AAAACTCT
59113 AAAACTC-
1 AAAACTCT
*
59120 AAAACACT
1 AAAACTCT
59128 AAAA
1 AAAA
59132 AAAGTTTAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
7 13 0.31
8 29 0.69
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAACTCT
Found at i:59123 original size:15 final size:15
Alignment explanation
Indices: 59074--59131 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
59064 AATAAAAAGA
*
59074 AAAACCCTAAAACTTT
1 AAAACCCTAAAAC-TC
*
59090 AAAACCCT-AAACCC
1 AAAACCCTAAAACTC
*
59104 TAAAACTCTAAAACTC
1 -AAAACCCTAAAACTC
*
59120 AAAACACTAAAA
1 AAAACCCTAAAA
59132 AAAGTTTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
15 22 0.63
16 13 0.37
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAACCCTAAAACTC
Found at i:59559 original size:26 final size:27
Alignment explanation
Indices: 59515--59570 Score: 96
Period size: 26 Copynumber: 2.1 Consensus size: 27
59505 ATTCAAACAT
*
59515 AAACATAATAAATTGTTAATTAAATAC
1 AAACATAATAAATTATTAATTAAATAC
59542 AAACATAA-AAATTATTAATTAAATAC
1 AAACATAATAAATTATTAATTAAATAC
59568 AAA
1 AAA
59571 TGAAAAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (27 bp):
AAACATAATAAATTATTAATTAAATAC
Found at i:59658 original size:22 final size:22
Alignment explanation
Indices: 59614--59680 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
59604 AAAGATATGG
* *
59614 TTAAGGATTTAAGGTTTCGAGT
1 TTAAGGGTTTAAGGTTTAGAGT
* *
59636 TTAAGGGTTTATGGTTTAAAGT
1 TTAAGGGTTTAAGGTTTAGAGT
*
59658 TT--GGGTTTTAGGGTTTAGAGT
1 TTAAGGG-TTTAAGGTTTAGAGT
59679 TT
1 TT
59681 GTTCCAACTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 3 0.08
21 15 0.39
22 20 0.53
ACGTcount: A:0.22, C:0.01, G:0.30, T:0.46
Consensus pattern (22 bp):
TTAAGGGTTTAAGGTTTAGAGT
Found at i:59752 original size:28 final size:28
Alignment explanation
Indices: 59719--59777 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
59709 GTTAAAACTT
* *
59719 AAAACCCTAAACCTTAAACCATAAATCC
1 AAAACCATAAACCTTAAACCATAAATAC
* * *
59747 AAAACCATATATCTTAAACCCTAAATAC
1 AAAACCATAAACCTTAAACCATAAATAC
59775 AAA
1 AAA
59778 CATCAACATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (28 bp):
AAAACCATAAACCTTAAACCATAAATAC
Found at i:59800 original size:26 final size:26
Alignment explanation
Indices: 59768--59900 Score: 169
Period size: 26 Copynumber: 5.0 Consensus size: 26
59758 TCTTAAACCC
*
59768 TAAATACAAACATCAACATAATTAAT
1 TAAATACAAACATAAACATAATTAAT
59794 TAAATACAAACATAAACATAATTAAT
1 TAAATACAAACATAAACATAATTAAT
*
59820 TAAATACAAACATAAA-AGTTATTAAT
1 TAAATACAAACATAAACA-TAATTAAT
* *
59846 TAAATACAAATATAAACATAATTTATT
1 TAAATACAAACATAAACATAA-TTAAT
* **
59873 CTAAATTCATTCATAAACATAATTAAT
1 -TAAATACAAACATAAACATAATTAAT
59900 T
1 T
59901 CCAAATGAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
25 1 0.01
26 66 0.71
27 9 0.10
28 17 0.18
ACGTcount: A:0.56, C:0.11, G:0.01, T:0.32
Consensus pattern (26 bp):
TAAATACAAACATAAACATAATTAAT
Found at i:62704 original size:21 final size:21
Alignment explanation
Indices: 62680--62726 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
62670 TTGTTTGAAC
62680 AAATTTTGCCTCATTCTTCAA
1 AAATTTTGCCTCATTCTTCAA
* *
62701 AAA-TTTGTCTCTTTCTTCAA
1 AAATTTTGCCTCATTCTTCAA
62721 AAATTT
1 AAATTT
62727 GTGTTTAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.47
Consensus pattern (21 bp):
AAATTTTGCCTCATTCTTCAA
Found at i:65724 original size:6 final size:6
Alignment explanation
Indices: 65713--65738 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
65703 TTACAACATC
65713 TTCCTT TTCCTT TTCCTT TTCCTT TT
1 TTCCTT TTCCTT TTCCTT TTCCTT TT
65739 TCCACCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TTCCTT
Found at i:66035 original size:20 final size:21
Alignment explanation
Indices: 65984--66126 Score: 144
Period size: 20 Copynumber: 7.2 Consensus size: 21
65974 TATAATGTTA
*
65984 TTTTGGTGTTGTTTTTTACTA
1 TTTTGGTGTTGTTTTTTACTG
*
66005 TTTTGGTTGTTGTTTTTTGCTG
1 TTTTGG-TGTTGTTTTTTACTG
66027 -TTT--TG-TGTTTTTTACTG
1 TTTTGGTGTTGTTTTTTACTG
*
66044 TTTTGGTGTT-TTTTTTACTA
1 TTTTGGTGTTGTTTTTTACTG
* *
66064 TTTT-G-GTTGTTTCTTGCTG
1 TTTTGGTGTTGTTTTTTACTG
*
66083 TTTTTGTG-T-TTTTTTACTG
1 TTTTGGTGTTGTTTTTTACTG
*
66102 TTTTGGTGCT-TTTTTTACTG
1 TTTTGGTGTTGTTTTTTACTG
66122 TTTTG
1 TTTTG
66127 ATTGTTATTT
Statistics
Matches: 103, Mismatches: 10, Indels: 19
0.78 0.08 0.14
Matches are distributed among these distances:
17 11 0.11
18 8 0.08
19 27 0.26
20 33 0.32
21 11 0.11
22 13 0.13
ACGTcount: A:0.05, C:0.06, G:0.20, T:0.69
Consensus pattern (21 bp):
TTTTGGTGTTGTTTTTTACTG
Found at i:66037 original size:39 final size:38
Alignment explanation
Indices: 65993--66126 Score: 155
Period size: 39 Copynumber: 3.4 Consensus size: 38
65983 ATTTTGGTGT
* *
65993 TGTTTTTTACTATTTTGGTTGTTGTTTTTTGCTGTTTT-G
1 TGTTTTTTACTGTTTTGG-TGTT-TTTTTTACTGTTTTGG
*
66032 TGTTTTTTACTGTTTTGGTGTTTTTTTTACTATTTTGG
1 TGTTTTTTACTGTTTTGGTGTTTTTTTTACTGTTTTGG
* * *
66070 TTGTTTCTTGCTGTTTTTGTG-TTTTTTTACTGTTTTGG
1 -TGTTTTTTACTGTTTTGGTGTTTTTTTTACTGTTTTGG
66108 TGCTTTTTTTACTGTTTTG
1 TG--TTTTTTACTGTTTTG
66127 ATTGTTATTT
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
37 14 0.17
38 21 0.26
39 46 0.57
ACGTcount: A:0.05, C:0.07, G:0.19, T:0.69
Consensus pattern (38 bp):
TGTTTTTTACTGTTTTGGTGTTTTTTTTACTGTTTTGG
Found at i:66103 original size:58 final size:56
Alignment explanation
Indices: 65984--66132 Score: 208
Period size: 58 Copynumber: 2.6 Consensus size: 56
65974 TATAATGTTA
*
65984 TTTTGGTGTTGTTTTTTACTATTTTGGTTGTTGTTTTTTGCTGTTTTGTGTTTTTTACTG
1 TTTTGGTGTT-TTTTTTACTATTTT-G--GTTGTTTCTTGCTGTTTTGTGTTTTTTACTG
66044 TTTTGGTGTTTTTTTTACTATTTTGGTTGTTTCTTGCTGTTTTTGTGTTTTTTTACTG
1 TTTTGGTGTTTTTTTTACTATTTTGGTTGTTTCTTGCTG-TTTTGTG-TTTTTTACTG
* * *
66102 TTTTGGTGCTTTTTTTACTGTTTTGATTGTT
1 TTTTGGTGTTTTTTTTACTATTTTGGTTGTT
66133 ATTTTCGTGT
Statistics
Matches: 83, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
56 13 0.16
57 7 0.08
58 39 0.47
59 14 0.17
60 10 0.12
ACGTcount: A:0.05, C:0.06, G:0.20, T:0.68
Consensus pattern (56 bp):
TTTTGGTGTTTTTTTTACTATTTTGGTTGTTTCTTGCTGTTTTGTGTTTTTTACTG
Found at i:66155 original size:12 final size:12
Alignment explanation
Indices: 66122--66190 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
66112 TTTTTTACTG
66122 TTTTGATTGTTAT
1 TTTTG-TTGTTAT
* *
66135 TTTCG-TGTTGT
1 TTTTGTTGTTAT
66146 TTTTGTTGTTAT
1 TTTTGTTGTTAT
* *
66158 TTTTGTTTTTGT
1 TTTTGTTGTTAT
66170 TTTTGTTGTTA-
1 TTTTGTTGTTAT
66181 TTTTGTTGTT
1 TTTTGTTGTT
66191 TTTAATGTTG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
11 19 0.40
12 24 0.51
13 4 0.09
ACGTcount: A:0.06, C:0.01, G:0.19, T:0.74
Consensus pattern (12 bp):
TTTTGTTGTTAT
Found at i:66161 original size:24 final size:24
Alignment explanation
Indices: 66122--66190 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
66112 TTTTTTACTG
*
66122 TTTTGATTGTTATTTTCG-TGTTGT
1 TTTTG-TTGTTATTTTTGTTGTTGT
*
66146 TTTTGTTGTTATTTTTGTTTTTGT
1 TTTTGTTGTTATTTTTGTTGTTGT
66170 TTTTGTTGTTA-TTTTGTTGTT
1 TTTTGTTGTTATTTTTGTTGTT
66191 TTTAATGTTG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.49
24 21 0.51
ACGTcount: A:0.06, C:0.01, G:0.19, T:0.74
Consensus pattern (24 bp):
TTTTGTTGTTATTTTTGTTGTTGT
Found at i:66166 original size:6 final size:6
Alignment explanation
Indices: 66142--66176 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
66132 TATTTTCGTG
* *
66142 TTGTTT TTGTTG TTATTT TTGTTT TTGTTT TTGTT
1 TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTT
66177 GTTATTTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.00, G:0.17, T:0.80
Consensus pattern (6 bp):
TTGTTT
Found at i:66199 original size:23 final size:22
Alignment explanation
Indices: 66122--66202 Score: 83
Period size: 24 Copynumber: 3.5 Consensus size: 22
66112 TTTTTTACTG
66122 TTTTGATTGTTATTTTCG-TGTTGT
1 TTTTG-TTGTTATTTT-GTTGTT-T
*
66146 TTTTGTTGTTATTTTTGTTTTTGT
1 TTTTGTTGTTA-TTTTGTTGTT-T
66170 TTTTGTTGTTATTTTGTTGTTT
1 TTTTGTTGTTATTTTGTTGTTT
*
66192 TTAATGTTGTT
1 TT-TTGTTGTT
66203 TGCTGTTATT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
22 3 0.06
23 23 0.45
24 25 0.49
ACGTcount: A:0.07, C:0.01, G:0.19, T:0.73
Consensus pattern (22 bp):
TTTTGTTGTTATTTTGTTGTTT
Found at i:66635 original size:5 final size:5
Alignment explanation
Indices: 66625--66660 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
66615 ATTTATTAAA
*
66625 ACCCG ACCCG ACCCG ACCCG ACCCG AATCCG ACCCG
1 ACCCG ACCCG ACCCG ACCCG ACCCG -ACCCG ACCCG
66661 TGATCAACTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.22, C:0.56, G:0.19, T:0.03
Consensus pattern (5 bp):
ACCCG
Found at i:67016 original size:7 final size:7
Alignment explanation
Indices: 67004--67039 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
66994 TTAGGCAATG
67004 GTTTCTT
1 GTTTCTT
67011 GTTTCTT
1 GTTTCTT
67018 GTTTCTT
1 GTTTCTT
67025 GTTTCTT
1 GTTTCTT
67032 GTTTCTT
1 GTTTCTT
67039 G
1 G
67040 CGGAGTACGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.00, C:0.14, G:0.17, T:0.69
Consensus pattern (7 bp):
GTTTCTT
Found at i:71934 original size:30 final size:30
Alignment explanation
Indices: 71898--71969 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
71888 TAATATTAGC
71898 TTGTGTGAGCAATCTTGAATTAATGTCAGT
1 TTGTGTGAGCAATCTTGAATTAATGTCAGT
71928 TTGTGTGAGCAATCTTGAATTAATGTCAGT
1 TTGTGTGAGCAATCTTGAATTAATGTCAGT
71958 TTGTGTGAGCAA
1 TTGTGTGAGCAA
71970 CTTATTATCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.26, C:0.10, G:0.25, T:0.39
Consensus pattern (30 bp):
TTGTGTGAGCAATCTTGAATTAATGTCAGT
Found at i:72561 original size:22 final size:22
Alignment explanation
Indices: 72533--72577 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
72523 GCTAAGTTTG
72533 ATGTTATACAAATAATGATCTT
1 ATGTTATACAAATAATGATCTT
72555 ATGTTATACAAATAATGATCTT
1 ATGTTATACAAATAATGATCTT
72577 A
1 A
72578 CCTTTGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (22 bp):
ATGTTATACAAATAATGATCTT
Found at i:73052 original size:24 final size:21
Alignment explanation
Indices: 73002--73052 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
72992 TAACTTCTAC
*
73002 CGATACAAGCATCCTAACTAT
1 CGATACAAGCATCCGAACTAT
*
73023 CAATACAAGCATACACAGAACTAT
1 CGATACAAGCAT-C-C-GAACTAT
73047 CGATAC
1 CGATAC
73053 CTACTATGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 11 0.46
22 1 0.04
23 1 0.04
24 11 0.46
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (21 bp):
CGATACAAGCATCCGAACTAT
Found at i:73711 original size:44 final size:44
Alignment explanation
Indices: 73654--73759 Score: 121
Period size: 41 Copynumber: 2.5 Consensus size: 44
73644 TATGCTCTAC
* *
73654 CGAGTCATAAGTCTTCCTTTTTAACCATATTCTCACGCTCAT-TT
1 CGAGTCATGAGTCTTCCTTTTT-ACCACATTCTCACGCTCATCTT
* **
73698 CGAGTCATGAGTCTTCC--TTTATCACATTCTCATTCTCATCTT
1 CGAGTCATGAGTCTTCCTTTTTACCACATTCTCACGCTCATCTT
*
73740 -GAGACATGAGTCTTCCTTTT
1 CGAGTCATGAGTCTTCCTTTT
73760 AAACATTAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
41 30 0.57
42 5 0.09
43 2 0.04
44 16 0.30
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (44 bp):
CGAGTCATGAGTCTTCCTTTTTACCACATTCTCACGCTCATCTT
Found at i:77504 original size:23 final size:23
Alignment explanation
Indices: 77478--77681 Score: 248
Period size: 23 Copynumber: 8.8 Consensus size: 23
77468 GTGTTCTTAT
*
77478 ATTTATGCTTAAATATTAATATG
1 ATTTATGCTTAAATATTAATGTG
* *
77501 ATTTGTGCTAAAATATTAATGTG
1 ATTTATGCTTAAATATTAATGTG
*
77524 ATTTATGTTTAAATATTAACT-TG
1 ATTTATGCTTAAATATTAA-TGTG
* *
77547 ATTTGTGCTTAAATATTAATATG
1 ATTTATGCTTAAATATTAATGTG
* **
77570 ATTTGTGCGCAAATATTAATGTG
1 ATTTATGCTTAAATATTAATGTG
77593 ATTTATGCTTAAATATTAATGTG
1 ATTTATGCTTAAATATTAATGTG
* * *
77616 ATTTATGCCTAAATATTAATATA
1 ATTTATGCTTAAATATTAATGTG
*
77639 ATTTATGATTAAATATTAATGTG
1 ATTTATGCTTAAATATTAATGTG
* *
77662 AATTGTGCTTAAATAATTAA
1 ATTTATGCTTAAAT-ATTAA
77682 GATGTGATAT
Statistics
Matches: 154, Mismatches: 24, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
22 1 0.01
23 147 0.95
24 6 0.04
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (23 bp):
ATTTATGCTTAAATATTAATGTG
Found at i:77565 original size:69 final size:69
Alignment explanation
Indices: 77478--77681 Score: 284
Period size: 69 Copynumber: 2.9 Consensus size: 69
77468 GTGTTCTTAT
*
77478 ATTTATGCTTAAATATTAATATGATTTGTGCTAAAATATTAATGTGATTTATGTTTAAATATTAA
1 ATTTATGCTTAAATATTAATATGATTTGTGCTAAAATATTAATGTGATTTATGCTTAAATATTAA
77543 CT-TG
66 -TGTG
* **
77547 ATTTGTGCTTAAATATTAATATGATTTGTGCGCAAATATTAATGTGATTTATGCTTAAATATTAA
1 ATTTATGCTTAAATATTAATATGATTTGTGCTAAAATATTAATGTGATTTATGCTTAAATATTAA
77612 TGTG
66 TGTG
* * * * * * *
77616 ATTTATGCCTAAATATTAATATAATTTATGATTAAATATTAATGTGAATTGTGCTTAAATAATTA
1 ATTTATGCTTAAATATTAATATGATTTGTGCTAAAATATTAATGTGATTTATGCTTAAAT-ATTA
77681 A
65 A
77682 GATGTGATAT
Statistics
Matches: 120, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
68 1 0.01
69 114 0.95
70 5 0.04
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (69 bp):
ATTTATGCTTAAATATTAATATGATTTGTGCTAAAATATTAATGTGATTTATGCTTAAATATTAA
TGTG
Found at i:77819 original size:36 final size:36
Alignment explanation
Indices: 77754--77858 Score: 124
Period size: 36 Copynumber: 2.9 Consensus size: 36
77744 TGTGAAAGTG
*
77754 AATATGTGGTTATGTTCCTTCATGCCATGTGACA-AA
1 AATATGTGGGTATGTT-CTTCATGCCATGTGACAGAA
* * * *
77790 AATTATTTGGGTATGTGT-TTCATGTCATGTGATAGAG
1 AA-TATGTGGGTATGT-TCTTCATGCCATGTGACAGAA
77827 AATATGTGGGTATGTTCTTCATGCCATGTGAC
1 AATATGTGGGTATGTTCTTCATGCCATGTGAC
77859 TGATTAGATT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
35 1 0.02
36 41 0.72
37 14 0.25
38 1 0.02
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (36 bp):
AATATGTGGGTATGTTCTTCATGCCATGTGACAGAA
Found at i:79697 original size:2 final size:2
Alignment explanation
Indices: 79690--79726 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
79680 ATGAAAGAAA
79690 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
79727 TTTCAGTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:86013 original size:40 final size:40
Alignment explanation
Indices: 85958--86063 Score: 212
Period size: 40 Copynumber: 2.6 Consensus size: 40
85948 AACTAGGCTA
85958 ACCATCATCTCTTGAAACTCCACTTGCTGTGGAGTGGAGT
1 ACCATCATCTCTTGAAACTCCACTTGCTGTGGAGTGGAGT
85998 ACCATCATCTCTTGAAACTCCACTTGCTGTGGAGTGGAGT
1 ACCATCATCTCTTGAAACTCCACTTGCTGTGGAGTGGAGT
86038 ACCATCATCTCTTGAAACTCCACTTG
1 ACCATCATCTCTTGAAACTCCACTTG
86064 TTGTTGCATA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (40 bp):
ACCATCATCTCTTGAAACTCCACTTGCTGTGGAGTGGAGT
Found at i:99487 original size:21 final size:23
Alignment explanation
Indices: 99460--99516 Score: 73
Period size: 21 Copynumber: 2.5 Consensus size: 23
99450 CCTGCAACTT
99460 CTACCGATACAACTAT-AT-GAA
1 CTACCGATACAACTATGATAGAA
* *
99481 CTGCCGATACTACTATGATCAGAA
1 CTACCGATACAACTATGAT-AGAA
99505 CTACCGATACAA
1 CTACCGATACAA
99517 GCCAGTATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 14 0.48
22 2 0.07
24 13 0.45
ACGTcount: A:0.39, C:0.26, G:0.12, T:0.23
Consensus pattern (23 bp):
CTACCGATACAACTATGATAGAA
Found at i:109696 original size:18 final size:18
Alignment explanation
Indices: 109675--109720 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
109665 AGCTTGTGAC
109675 TGCATCTGGTTGTATGAA
1 TGCATCTGGTTGTATGAA
* * * *
109693 TGCATCTGATTTTGTGAT
1 TGCATCTGGTTGTATGAA
109711 TGCATCTGGT
1 TGCATCTGGT
109721 CCGGTTGCGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.26, T:0.43
Consensus pattern (18 bp):
TGCATCTGGTTGTATGAA
Found at i:113113 original size:15 final size:15
Alignment explanation
Indices: 113095--113124 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
113085 TAAAGAACAT
*
113095 AAAATAAAAGAAAGA
1 AAAAAAAAAGAAAGA
113110 AAAAAAAAAGAAAGA
1 AAAAAAAAAGAAAGA
113125 GATAAGAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAGAAAGA
Found at i:115165 original size:16 final size:15
Alignment explanation
Indices: 115140--115169 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
115130 ATCATAAATG
115140 TTTTTCTTCTTTTTC
1 TTTTTCTTCTTTTTC
115155 TTTTTCTTTCTTTTT
1 TTTTTC-TTCTTTTT
115170 ATGTGACAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTCTTCTTTTTC
Found at i:121833 original size:3 final size:3
Alignment explanation
Indices: 121811--121863 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
121801 CTGCTCTAAT
* *
121811 TTA TTA TTTG TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TT- TTAA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
121857 TTA TTA T
1 TTA TTA T
121864 GGTACAGAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 37 0.86
4 4 0.09
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:123344 original size:21 final size:21
Alignment explanation
Indices: 123315--123377 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
123305 AATTTAACTT
*
123315 CAAATGTCGTTTGTCTCGAGA
1 CAAAGGTCGTTTGTCTCGAGA
123336 CAAAGGTCGTTTGTCTCGAGA
1 CAAAGGTCGTTTGTCTCGAGA
123357 CAAAGGTCGTTTGTCTCGAGA
1 CAAAGGTCGTTTGTCTCGAGA
123378 TTTTAATAGG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (21 bp):
CAAAGGTCGTTTGTCTCGAGA
Found at i:128611 original size:102 final size:106
Alignment explanation
Indices: 128337--128631 Score: 346
Period size: 108 Copynumber: 2.8 Consensus size: 106
128327 GCGCAATTCG
* * * * *
128337 AATAATAGAGTTGATGAAATTCTAAATAAACCAAACAAAACCCATCACTCATTTACAACTTTTTA
1 AATATTAGAGTTCACGAAATTATAAATAAA-CAAACAAAACCCATCACTTATTTACAAC-TTTTA
* * * *
128402 GTCTTGCTTTCAGAATGTATCAAGCCATGGAGTCTGCAATTGC
64 GTCTTCCTTTCAGAATGTATCAAGCCATGGAATCAGCAAATGC
* * * * * * *
128445 AATGTTAGAGTTGATGAAATTTTAAATAAACCAAACAAAACCTATCACTTATTTACGACATTTAG
1 AATATTAGAGTTCACGAAATTATAAATAAA-CAAACAAAACCCATCACTTATTTACAACTTTTAG
* *
128510 TCTTCCATTCAGTATGTATCAA-CCATGGAATCAGCAAATGC
65 TCTTCCTTTCAGAATGTATCAAGCCATGGAATCAGCAAATGC
* *
128551 AATATTATAGTTCACGAAATTATAAA-AAA-AAA-AAAACCCATCACTTATTCACAACTTTTAGT
1 AATATTAGAGTTCACGAAATTATAAATAAACAAACAAAACCCATCACTTATTTACAACTTTTAGT
*
128613 CTTTCTTTCAGAATGTATC
66 CTTCCTTTCAGAATGTATC
128632 GGCCATGTAG
Statistics
Matches: 162, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
102 42 0.26
103 3 0.02
105 3 0.02
106 37 0.23
107 24 0.15
108 53 0.33
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (106 bp):
AATATTAGAGTTCACGAAATTATAAATAAACAAACAAAACCCATCACTTATTTACAACTTTTAGT
CTTCCTTTCAGAATGTATCAAGCCATGGAATCAGCAAATGC
Found at i:137982 original size:17 final size:16
Alignment explanation
Indices: 137947--137990 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
137937 TTTAATTGTG
137947 TATAGTTTTTTTTTCCA
1 TATA-TTTTTTTTTCCA
*
137964 TATATTTTTTTCTTTCA
1 TATATTTTTTT-TTCCA
137981 TA-ATTTTTTT
1 TATATTTTTTT
137991 ATCCTACTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.70
Consensus pattern (16 bp):
TATATTTTTTTTTCCA
Found at i:163499 original size:3 final size:3
Alignment explanation
Indices: 163493--163558 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
163483 AATAATAATA
*
163493 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG GTG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
163541 ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG
163559 TCTCGACTGA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:164550 original size:23 final size:21
Alignment explanation
Indices: 164524--164569 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
164514 AATAACTTCA
164524 TTAACTCAAATAATTTGAACTAT
1 TTAACTC-AA-AATTTGAACTAT
* *
164547 TTAATTCAAAATTTGAATTAT
1 TTAACTCAAAATTTGAACTAT
164568 TT
1 TT
164570 TTCGAGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 2 0.10
23 6 0.29
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (21 bp):
TTAACTCAAAATTTGAACTAT
Found at i:165550 original size:21 final size:20
Alignment explanation
Indices: 165461--165552 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
165451 TTGATTGCTA
*
165461 TTTTTTTTGCTATTTTGGTG
1 TTTTTTTTACTATTTTGGTG
* * *
165481 TTGTGTTTTTATTGTTTTAGTG
1 TT-T-TTTTTACTATTTTGGTG
* * *
165503 ATTTTTTTACTGTTTTGGTAC
1 TTTTTTTTACTATTTTGGT-G
165524 TTTTTTTTACTATTTTGGTG
1 TTTTTTTTACTATTTTGGTG
*
165544 TTGTTTTTA
1 TTTTTTTTA
165553 TTGTTATTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
20 24 0.42
21 19 0.33
22 14 0.25
ACGTcount: A:0.10, C:0.04, G:0.17, T:0.68
Consensus pattern (20 bp):
TTTTTTTTACTATTTTGGTG
Found at i:165557 original size:12 final size:12
Alignment explanation
Indices: 165542--165575 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
165532 ACTATTTTGG
*
165542 TGTTGTTTTTAT
1 TGTTATTTTTAT
165554 TGTTATTTTTAT
1 TGTTATTTTTAT
*
165566 TGCTATTTTT
1 TGTTATTTTT
165576 TATTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.03, G:0.12, T:0.74
Consensus pattern (12 bp):
TGTTATTTTTAT
Found at i:171236 original size:19 final size:19
Alignment explanation
Indices: 171212--171248 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
171202 TCTCTCACGT
171212 TATCTAATTTTGAAATTTA
1 TATCTAATTTTGAAATTTA
* *
171231 TATCTATTTTTTAAATTT
1 TATCTAATTTTGAAATTT
171249 TCTATGTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (19 bp):
TATCTAATTTTGAAATTTA
Found at i:173107 original size:14 final size:15
Alignment explanation
Indices: 173088--173117 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
173078 AAGTTTTTTA
173088 AATTTTTAAT-TAAT
1 AATTTTTAATATAAT
173102 AATTTTTAATATAAT
1 AATTTTTAATATAAT
173117 A
1 A
173118 GTTCTTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTTTTAATATAAT
Found at i:173238 original size:130 final size:137
Alignment explanation
Indices: 173036--173354 Score: 366
Period size: 130 Copynumber: 2.4 Consensus size: 137
173026 TGTGGGTTCA
** * * **
173036 ATTCCTCTTTTACCCACATTTGCA-TTTTTTTCATGTTGCTTCAAGTTTTTTAAATTTTTAATTA
1 ATTCCTCTACTACTCACATTTGTATTTTTTTTCATGTTGCTTCAAGTTTTTTAAAGATTTAATTA
* * * *
173100 ATAATTTTTAATATAATAGTTCTTTGGTTAGATGGTTACA-A-TTA-CA-T-CCTTC-G-GTCCC
66 ATAATTTTTAACATAATAATTCTTTGGTTAGATGGTTACATAGTTATAATTACATTCTGAGTCCC
173158 GAGTTTG
131 GAGTTTG
* * * * *
173165 ATTCCTCTCCTACTCATATTTGTATTTTTTTTCGTGTTGCTTCTAGCTTTTTAAAGATTTAATTA
1 ATTCCTCTACTACTCACATTTGTATTTTTTTTCATGTTGCTTCAAGTTTTTTAAAGATTTAATTA
* ** * * *
173230 ATATTTTTTAACATTTTAATTCTTTTGTTAGATGGTTAGATAGTTATAATTACATTCTTGAGTCT
66 ATAATTTTTAACATAATAATTCTTTGGTTAGATGGTTACATAGTTATAATTACATTC-TGAGTCC
173295 CGAGTTTG
130 CGAGTTTG
* *
173303 ATTCTTTTACTACTCACATTTGTATTTTTTTTCATGTTGCTTCAAGTTTTTT
1 ATTCCTCTACTACTCACATTTGTATTTTTTTTCATGTTGCTTCAAGTTTTTT
173355 TTTTAATTAA
Statistics
Matches: 154, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
129 19 0.12
130 68 0.44
131 1 0.01
132 3 0.02
133 1 0.01
134 1 0.01
135 4 0.03
137 1 0.01
138 56 0.36
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.52
Consensus pattern (137 bp):
ATTCCTCTACTACTCACATTTGTATTTTTTTTCATGTTGCTTCAAGTTTTTTAAAGATTTAATTA
ATAATTTTTAACATAATAATTCTTTGGTTAGATGGTTACATAGTTATAATTACATTCTGAGTCCC
GAGTTTG
Found at i:174266 original size:18 final size:19
Alignment explanation
Indices: 174243--174278 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
174233 GACTAAAAAG
174243 TAATTATATTTAA-AATTT
1 TAATTATATTTAATAATTT
174261 TAATTATATTTAATAATT
1 TAATTATATTTAATAATT
174279 ATTATTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TAATTATATTTAATAATTT
Found at i:192310 original size:21 final size:21
Alignment explanation
Indices: 192258--192310 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
192248 AAATATGGAG
*
192258 ATAAAACTAAACCCCAAAATC
1 ATAAAACAAAACCCCAAAATC
*
192279 A-AAAATAAAAACCCCAAAAT-
1 ATAAAA-CAAAACCCCAAAATC
192299 ATAAACACAAAA
1 ATAAA-ACAAAA
192311 TTCTATGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 5 0.19
21 20 0.77
22 1 0.04
ACGTcount: A:0.66, C:0.23, G:0.00, T:0.11
Consensus pattern (21 bp):
ATAAAACAAAACCCCAAAATC
Found at i:193626 original size:9 final size:9
Alignment explanation
Indices: 193614--193647 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
193604 TCAATTGGTT
193614 GAATTATTC
1 GAATTATTC
*
193623 GAATTATTT
1 GAATTATTC
*
193632 GAATTAATC
1 GAATTATTC
193641 GAATTAT
1 GAATTAT
193648 AAATAGTCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (9 bp):
GAATTATTC
Found at i:193633 original size:18 final size:18
Alignment explanation
Indices: 193612--193647 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
193602 ATTCAATTGG
*
193612 TTGAATTATTCGAATTAT
1 TTGAATTAATCGAATTAT
193630 TTGAATTAATCGAATTAT
1 TTGAATTAATCGAATTAT
193648 AAATAGTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (18 bp):
TTGAATTAATCGAATTAT
Found at i:193940 original size:42 final size:42
Alignment explanation
Indices: 193865--193945 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
193855 GTGAGTAAAG
* * *
193865 GCATGGAGTAAGTCAAAAGTTAGCATCAATGATGGGAATAGT
1 GCATGGAGCAAGTAAAAAATTAGCATCAATGATGGGAATAGT
* *
193907 GCATGGAGCAAGTAAAAAATTAGTATCATTGATGGGAAT
1 GCATGGAGCAAGTAAAAAATTAGCATCAATGATGGGAAT
193946 GGTTTATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.40, C:0.09, G:0.27, T:0.25
Consensus pattern (42 bp):
GCATGGAGCAAGTAAAAAATTAGCATCAATGATGGGAATAGT
Done.