Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009366.1 Kokia drynarioides strain JFW-HI SEQ_124073, 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: 258741
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 84 characters in sequence are not A, C, G, or T
Found at i:791 original size:15 final size:15
Alignment explanation
Indices: 768--803 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
758 AATATATTTT
* *
768 TAATTTTATTAATAA
1 TAATATTATTAAAAA
783 TAATATTATTAAAAA
1 TAATATTATTAAAAA
798 TAATAT
1 TAATAT
804 AACTTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATATTATTAAAAA
Found at i:7481 original size:40 final size:40
Alignment explanation
Indices: 7426--7513 Score: 176
Period size: 40 Copynumber: 2.2 Consensus size: 40
7416 CCAAGACTAG
7426 AAGCAATGCAATATACATGTTTCTATGGAAAGGATGAAGT
1 AAGCAATGCAATATACATGTTTCTATGGAAAGGATGAAGT
7466 AAGCAATGCAATATACATGTTTCTATGGAAAGGATGAAGT
1 AAGCAATGCAATATACATGTTTCTATGGAAAGGATGAAGT
7506 AAGCAATG
1 AAGCAATG
7514 ATGCACTGCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (40 bp):
AAGCAATGCAATATACATGTTTCTATGGAAAGGATGAAGT
Found at i:10736 original size:75 final size:75
Alignment explanation
Indices: 10613--10755 Score: 277
Period size: 75 Copynumber: 1.9 Consensus size: 75
10603 AACCCCAACA
10613 AGGTGGTACAAAATGGATCTTGCTGTTTGTGTTTCGGTCTTTGTTTATGGCTTATGGGTGATGTT
1 AGGTGGTACAAAATGGATCTTGCTGTTTGTGTTTCGGTCTTTGTTTATGGCTTATGGGTGATGTT
10678 GTGATTTCGG
66 GTGATTTCGG
*
10688 AGGTGGTACAGAATGGATCTTGCTGTTTGTGTTTCGGTCTTTGTTTATGGCTTATGGGTGATGTT
1 AGGTGGTACAAAATGGATCTTGCTGTTTGTGTTTCGGTCTTTGTTTATGGCTTATGGGTGATGTT
10753 GTG
66 GTG
10756 GTTGGTGAGC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.14, C:0.09, G:0.33, T:0.44
Consensus pattern (75 bp):
AGGTGGTACAAAATGGATCTTGCTGTTTGTGTTTCGGTCTTTGTTTATGGCTTATGGGTGATGTT
GTGATTTCGG
Found at i:23360 original size:21 final size:19
Alignment explanation
Indices: 23313--23361 Score: 53
Period size: 23 Copynumber: 2.4 Consensus size: 19
23303 TTAATATTTT
*
23313 TTTTAAAAAATATAAAAAC
1 TTTTAAAAAATATAAAAAA
23332 TTCATTAAATAATATATAAAAAA
1 TT--TTAAA-AA-ATATAAAAAA
23355 TTTTAAA
1 TTTTAAA
23362 GTTTTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 2 0.08
21 10 0.40
22 2 0.08
23 11 0.44
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (19 bp):
TTTTAAAAAATATAAAAAA
Found at i:33484 original size:17 final size:18
Alignment explanation
Indices: 33459--33492 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
33449 ATGAAACATG
33459 TATAAATAAA-TAATTTT
1 TATAAATAAATTAATTTT
*
33476 TATATATAAATTAATTT
1 TATAAATAAATTAATTT
33493 AATAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATAAATAAATTAATTTT
Found at i:40420 original size:32 final size:31
Alignment explanation
Indices: 40382--40441 Score: 102
Period size: 32 Copynumber: 1.9 Consensus size: 31
40372 ATAATTTGAA
*
40382 AATTATTTGAAAATTTTTATTTAAAGTTACTG
1 AATTATTTAAAAATTTTTATTT-AAGTTACTG
40414 AATTATTTAAAAATTTTTATTTAAGTTA
1 AATTATTTAAAAATTTTTATTTAAGTTA
40442 TTAAGTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.52
Consensus pattern (31 bp):
AATTATTTAAAAATTTTTATTTAAGTTACTG
Found at i:41112 original size:6 final size:6
Alignment explanation
Indices: 41101--41130 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
41091 AATTTGATTC
*
41101 AAAGAA AAAGAA AAAGAA AAAGAA ATAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
41131 GTGGAGCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:85068 original size:2 final size:2
Alignment explanation
Indices: 85061--85098 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
85051 TTTGTGATTA
85061 AT AT AT AT AT 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 AT AT AT AT AT
85099 TATTTTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85226 original size:22 final size:22
Alignment explanation
Indices: 85198--85239 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
85188 TCATGTATAC
*
85198 TTTTTTGAGAATTAATGATTTT
1 TTTTTTGACAATTAATGATTTT
*
85220 TTTTTTGACAATTCATGATT
1 TTTTTTGACAATTAATGATT
85240 AATATTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57
Consensus pattern (22 bp):
TTTTTTGACAATTAATGATTTT
Found at i:96103 original size:25 final size:27
Alignment explanation
Indices: 96073--96124 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
96063 TATTAATTCA
96073 ATATGAAACAAAATT-AAAGTT-ATAT
1 ATATGAAACAAAATTCAAAGTTCATAT
* *
96098 ATATGAACCATAATTCAAAGTTCATAT
1 ATATGAAACAAAATTCAAAGTTCATAT
96125 GTAGAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 13 0.57
26 6 0.26
27 4 0.17
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.33
Consensus pattern (27 bp):
ATATGAAACAAAATTCAAAGTTCATAT
Found at i:103006 original size:26 final size:27
Alignment explanation
Indices: 102969--103047 Score: 87
Period size: 26 Copynumber: 3.1 Consensus size: 27
102959 AATTTGAAAA
102969 AAATT-AAATATCAAATTAAACAATTG
1 AAATTCAAATATCAAATTAAACAATTG
* * *
102995 AAA-TCAAGTATCAAATTGAGACAA--A
1 AAATTCAAATATCAAATT-AAACAATTG
103020 AAATTCAAATATCAAATTAAAC-ATTG
1 AAATTCAAATATCAAATTAAACAATTG
103046 AA
1 AA
103048 GCTAAATATA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
24 1 0.02
25 7 0.17
26 29 0.69
27 5 0.12
ACGTcount: A:0.57, C:0.10, G:0.06, T:0.27
Consensus pattern (27 bp):
AAATTCAAATATCAAATTAAACAATTG
Found at i:108014 original size:2 final size:2
Alignment explanation
Indices: 108009--108038 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
107999 TTATATTGTT
108009 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
108039 TTTCAAGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:117866 original size:2 final size:2
Alignment explanation
Indices: 117856--117895 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
117846 TAAAAAAGAT
117856 TA TA T- TA TA TA 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 TA TA TA TA TA TA T
117896 TTATGAAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:118689 original size:25 final size:24
Alignment explanation
Indices: 118661--118711 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
118651 TAATATAATT
*
118661 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
118686 ATTATAACATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
118710 AT
1 AT
118712 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:125044 original size:16 final size:15
Alignment explanation
Indices: 125017--125069 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
125007 ATCATTGAAA
125017 TCTCTTTCTCTTTCCC
1 TCTC-TTCTCTTTCCC
*
125033 TTTCTCTCTCTTTTTCCC
1 --TCTCT-TCTCTTTCCC
125051 TCTCTTCTCTTTCCC
1 TCTCTTCTCTTTCCC
125066 TCTC
1 TCTC
125070 CCTTTCCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 13 0.41
16 5 0.16
17 1 0.03
18 13 0.41
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (15 bp):
TCTCTTCTCTTTCCC
Found at i:125048 original size:18 final size:18
Alignment explanation
Indices: 125017--125062 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
125007 ATCATTGAAA
* * *
125017 TCTCTTTCTCTTTCCCTT
1 TCTCTCTCTTTTTCCCTC
125035 TCTCTCTCTTTTTCCCTC
1 TCTCTCTCTTTTTCCCTC
125053 TCT-TCTCTTT
1 TCTCTCTCTTT
125063 CCCTCTCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (18 bp):
TCTCTCTCTTTTTCCCTC
Found at i:125086 original size:15 final size:14
Alignment explanation
Indices: 125020--125087 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 14
125010 ATTGAAATCT
125020 CTTT-CTCT-TTCC
1 CTTTCCTCTCTTCC
125032 CTTTCTCTCTCTT--
1 CTTTC-CTCTCTTCC
*
125045 -TTTCCCTCTCTTCT
1 CTTT-CCTCTCTTCC
125059 CTTTCC-CTC-TCC
1 CTTTCCTCTCTTCC
125071 CTTTCCTCTTCTTCC
1 CTTTCCTC-TCTTCC
125086 CT
1 CT
125088 CCGCCTTCTC
Statistics
Matches: 45, Mismatches: 1, Indels: 17
0.71 0.02 0.27
Matches are distributed among these distances:
12 22 0.49
13 5 0.11
14 8 0.18
15 10 0.22
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (14 bp):
CTTTCCTCTCTTCC
Found at i:126181 original size:51 final size:51
Alignment explanation
Indices: 126122--126223 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
126112 TTTTATTTAT
* *
126122 ATCTTCTACATAATTAATAATTAATTGGATGAATCTTTTATTAAAAACATA
1 ATCTTCTACATAATAAAAAATTAATTGGATGAATCTTTTATTAAAAACATA
*
126173 ATCTTCTACATCATAAAAAATTAATTGGATGAATCTTTTATTAAAAACATA
1 ATCTTCTACATAATAAAAAATTAATTGGATGAATCTTTTATTAAAAACATA
126224 TTTAGTTAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (51 bp):
ATCTTCTACATAATAAAAAATTAATTGGATGAATCTTTTATTAAAAACATA
Found at i:142718 original size:52 final size:52
Alignment explanation
Indices: 142644--142754 Score: 168
Period size: 52 Copynumber: 2.1 Consensus size: 52
142634 TAACTTACTT
* * * *
142644 CTCAATATTTATGTATTGTTTCAATTTAGTATTGATTCTAAAAAATCTAACC
1 CTCAATACTTATATATTATTTCAATTTAGCATTGATTCTAAAAAATCTAACC
*
142696 CTCAATACTTATATATTATTTCAATTTAGCATTGATTCTAAACAATCTAACC
1 CTCAATACTTATATATTATTTCAATTTAGCATTGATTCTAAAAAATCTAACC
*
142748 CTTAATA
1 CTCAATA
142755 AATTACACAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.42
Consensus pattern (52 bp):
CTCAATACTTATATATTATTTCAATTTAGCATTGATTCTAAAAAATCTAACC
Found at i:142774 original size:52 final size:52
Alignment explanation
Indices: 142664--142774 Score: 134
Period size: 52 Copynumber: 2.1 Consensus size: 52
142654 ATGTATTGTT
* * * * *
142664 TCAATTTAGTATTGATTCTAAAAAATCTAACCCTCAATACTTATATATTATT
1 TCAATTTAGCATTGATTCTAAAAAATCTAACCCTCAATAATTACACATTATG
* * *
142716 TCAATTTAGCATTGATTCTAAACAATCTAACCCTTAATAAATTACACATTGTG
1 TCAATTTAGCATTGATTCTAAAAAATCTAACCCTCAAT-AATTACACATTATG
142769 T-AATTT
1 TCAATTT
142775 GGTTAGTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
52 40 0.80
53 10 0.20
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (52 bp):
TCAATTTAGCATTGATTCTAAAAAATCTAACCCTCAATAATTACACATTATG
Found at i:143716 original size:29 final size:29
Alignment explanation
Indices: 143661--143723 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
143651 GTCTAGGTAT
*
143661 CAAATTGAGCATTAAAGAATTTCAGATAC
1 CAAATTGAACATTAAAGAATTTCAGATAC
143690 CAAATTGGAACATTAGAA-AATTT-AGATAC
1 CAAATT-GAACATTA-AAGAATTTCAGATAC
143719 CAAAT
1 CAAAT
143724 GAATATTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 17 0.55
30 12 0.39
31 2 0.06
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.27
Consensus pattern (29 bp):
CAAATTGAACATTAAAGAATTTCAGATAC
Found at i:159159 original size:32 final size:32
Alignment explanation
Indices: 159117--159204 Score: 113
Period size: 38 Copynumber: 2.6 Consensus size: 32
159107 AAACAAACTT
*
159117 CTACTATACAATTTTCATTATTTTTTGTTCAA
1 CTACTTTACAATTTTCATTATTTTTTGTTCAA
159149 CTACTTTACAATTACAATTTTCATTATTTTTTGTTCAA
1 CTAC--T----TTACAATTTTCATTATTTTTTGTTCAA
159187 CTACTTTACAATTTTCAT
1 CTACTTTACAATTTTCAT
159205 ACCGAACAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
32 17 0.35
34 1 0.02
36 1 0.02
38 30 0.61
ACGTcount: A:0.28, C:0.17, G:0.02, T:0.52
Consensus pattern (32 bp):
CTACTTTACAATTTTCATTATTTTTTGTTCAA
Found at i:159174 original size:38 final size:38
Alignment explanation
Indices: 159123--159199 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
159113 ACTTCTACTA
159123 TACAATTTTCATTATTTTTTGTTCAACTACTTTACAAT
1 TACAATTTTCATTATTTTTTGTTCAACTACTTTACAAT
159161 TACAATTTTCATTATTTTTTGTTCAACTACTTTACAAT
1 TACAATTTTCATTATTTTTTGTTCAACTACTTTACAAT
159199 T
1 T
159200 TTCATACCGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.29, C:0.16, G:0.03, T:0.53
Consensus pattern (38 bp):
TACAATTTTCATTATTTTTTGTTCAACTACTTTACAAT
Found at i:166074 original size:5 final size:5
Alignment explanation
Indices: 166064--166093 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
166054 AAAAAATTGT
166064 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
166094 CAATTAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:166569 original size:21 final size:19
Alignment explanation
Indices: 166545--166585 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
166535 TATTCAAGGA
*
166545 TTTCGATTAATTGATTATTGT
1 TTTCGATGAATTG-TT-TTGT
166566 TTTCGATGAATTGTTTTGT
1 TTTCGATGAATTGTTTTGT
166585 T
1 T
166586 AACTTACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.20, C:0.05, G:0.17, T:0.59
Consensus pattern (19 bp):
TTTCGATGAATTGTTTTGT
Found at i:166836 original size:15 final size:15
Alignment explanation
Indices: 166805--166846 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
166795 TTCAGTTGTT
*
166805 ATTTAAAATATATTTA
1 ATTTAAATTA-ATTTA
*
166821 ATTTAACTTAATTTA
1 ATTTAAATTAATTTA
166836 ATTTAAATTAA
1 ATTTAAATTAA
166847 AAATTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTAAATTAATTTA
Found at i:169655 original size:29 final size:28
Alignment explanation
Indices: 169586--169655 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
169576 AAATTATCAC
* *
169586 AAACACTTTTTAAAAAATTATTTAAATCT
1 AAACA-TTTTAAAAAAATTATTAAAATCT
* * * *
169615 AAATAATATAAAAAGAATTATTAAAATTT
1 AAACATTTTAAAAA-AATTATTAAAATCT
169644 AAACATTTTAAA
1 AAACATTTTAAA
169656 TGATGACATG
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
28 6 0.19
29 25 0.81
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.37
Consensus pattern (28 bp):
AAACATTTTAAAAAAATTATTAAAATCT
Found at i:174258 original size:205 final size:205
Alignment explanation
Indices: 173900--174518 Score: 1202
Period size: 205 Copynumber: 3.0 Consensus size: 205
173890 CCTTATAGCA
* *
173900 AAAATATTCAGTTTCCTTTTCCTATTTGAGCAAGTGACATTCAGCTTCACCTGTCGAGTTTAGTC
1 AAAATGTTCAGTTTCTTTTTCCTATTTGAGCAAGTGACATTCAGCTTCACCTGTCGAGTTTAGTC
173965 TTCAAGAAAGTAGGGTATGCACAGCTATGTTGCTTCAACCTTTTATTTTGTTTGAAATACCCATG
66 TTCAAGAAAGTAGGGTATGCACAGCTATGTTGCTTCAACCTTTTATTTTGTTTGAAATACCCATG
174030 TTAGACACGTGTCCAATACATATTTGGACAAGAGCATGGAGAAGTGATTTCCAAATTCGTGGAAA
131 TTAGACACGTGTCCAATACATATTTGGACAAGAGCATGGAGAAGTGATTTCCAAATTCGTGGAAA
174095 AACTTAGAAG
196 AACTTAGAAG
174105 AAAATGTTCAGTTTCTTTTTCCTATTTGAGCAAGTGACATTCAGCTTCACCTGTCGAGTTTAGTC
1 AAAATGTTCAGTTTCTTTTTCCTATTTGAGCAAGTGACATTCAGCTTCACCTGTCGAGTTTAGTC
*
174170 TTCAAGAAAGTAGGGTATGCACAGCTATGTTGCTTCAACCTTTTATTTTGTTTGAAATACCCACG
66 TTCAAGAAAGTAGGGTATGCACAGCTATGTTGCTTCAACCTTTTATTTTGTTTGAAATACCCATG
174235 TTAGACACGTGTCCAATACATATTTGGACAAGAGCATGGAGAAGTGATTTCCAAATTCGTGGAAA
131 TTAGACACGTGTCCAATACATATTTGGACAAGAGCATGGAGAAGTGATTTCCAAATTCGTGGAAA
174300 AACTTAGAAG
196 AACTTAGAAG
174310 AAAATGTTCAGTTTCTTTTTCCTATTTGAGCAAGTGACATTCAGCTTCACCTGTCGAGTTTAGTC
1 AAAATGTTCAGTTTCTTTTTCCTATTTGAGCAAGTGACATTCAGCTTCACCTGTCGAGTTTAGTC
*
174375 TTCAAGAAAGTAGGGTATGCACAGCTATGTTGCTCCAACCTTTTATTTTGTTTGAAATACCCATG
66 TTCAAGAAAGTAGGGTATGCACAGCTATGTTGCTTCAACCTTTTATTTTGTTTGAAATACCCATG
174440 TTAGACACGTGTCCAATACATATTTGGACAAGAGCATGGAGAAGTGATTTCCAAATTCGTGGAAA
131 TTAGACACGTGTCCAATACATATTTGGACAAGAGCATGGAGAAGTGATTTCCAAATTCGTGGAAA
174505 AACTTAGAAG
196 AACTTAGAAG
174515 AAAA
1 AAAA
174519 AACCAACACC
Statistics
Matches: 409, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
205 409 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (205 bp):
AAAATGTTCAGTTTCTTTTTCCTATTTGAGCAAGTGACATTCAGCTTCACCTGTCGAGTTTAGTC
TTCAAGAAAGTAGGGTATGCACAGCTATGTTGCTTCAACCTTTTATTTTGTTTGAAATACCCATG
TTAGACACGTGTCCAATACATATTTGGACAAGAGCATGGAGAAGTGATTTCCAAATTCGTGGAAA
AACTTAGAAG
Found at i:177575 original size:45 final size:45
Alignment explanation
Indices: 177511--177597 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
177501 CCACAATCAA
* * *
177511 ATGCTTGACAAACATATAAGAAAAAAGGAGACAGTCGGTTGAAAG
1 ATGCTTAACAAACATATAAGAAAAAAGGAAACAGTAGGTTGAAAG
*
177556 ATGCTTAACAAACATATAAGAAAAAGGGAAACAGTAGGTTGA
1 ATGCTTAACAAACATATAAGAAAAAAGGAAACAGTAGGTTGA
177598 GGAAAGGAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.48, C:0.10, G:0.23, T:0.18
Consensus pattern (45 bp):
ATGCTTAACAAACATATAAGAAAAAAGGAAACAGTAGGTTGAAAG
Found at i:183131 original size:79 final size:80
Alignment explanation
Indices: 183039--183203 Score: 255
Period size: 79 Copynumber: 2.1 Consensus size: 80
183029 TAAATATACA
*
183039 AAAATA-ACACAAATGTACTAAGTATCCGATATCAAACTTTATAC-AAATG-AAAACCACAATTA
1 AAAATATACACAAATGTACTAAGTATCCAATATCAAACTTTATACAAAATGTAAAA-CACAATTA
183101 ACACTACTATCACATG
65 ACACTACTATCACATG
* * **
183117 AAAATATACACAAATGTACTAATTATCCAATATCAAGCTTTATACAAAATGTAAAACACCTTTAA
1 AAAATATACACAAATGTACTAAGTATCCAATATCAAACTTTATACAAAATGTAAAACACAATTAA
183182 CACTACTATCACATG
66 CACTACTATCACATG
183197 AAAATAT
1 AAAATAT
183204 GCAAAAATAA
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
78 6 0.08
79 35 0.44
80 34 0.43
81 4 0.05
ACGTcount: A:0.48, C:0.19, G:0.05, T:0.27
Consensus pattern (80 bp):
AAAATATACACAAATGTACTAAGTATCCAATATCAAACTTTATACAAAATGTAAAACACAATTAA
CACTACTATCACATG
Found at i:193661 original size:32 final size:30
Alignment explanation
Indices: 193625--193700 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
193615 TTTTTGACCC
* * *
193625 AATTTAGTACCTGAACTCGACATTTTTTTCCT
1 AATTTGGTACCTAAACTCGACA--TTATTCCT
* *
193657 AATTTGGTACCTAAACTTGGCATTATTCCT
1 AATTTGGTACCTAAACTCGACATTATTCCT
193687 AATTTGGTACCTAA
1 AATTTGGTACCTAA
193701 GCTTTTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 21 0.54
32 18 0.46
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.41
Consensus pattern (30 bp):
AATTTGGTACCTAAACTCGACATTATTCCT
Found at i:194040 original size:29 final size:30
Alignment explanation
Indices: 193954--194052 Score: 114
Period size: 31 Copynumber: 3.3 Consensus size: 30
193944 ATAAACTTAA
*
193954 AAAAAATGACAAGTTTAGGTACCAAATTAGG
1 AAAAAAT-ACAAGTTTAAGTACCAAATTAGG
*
193985 AAAAAATATCAAGTTTGAGTACCAAATT-GG
1 AAAAAATA-CAAGTTTAAGTACCAAATTAGG
*
194015 ACCAAAAA-ACAA-TTTAAGTACCAAATTAAG
1 A--AAAAATACAAGTTTAAGTACCAAATTAGG
194045 AAAAAATA
1 AAAAAATA
194053 TGAAGTTCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
28 5 0.08
29 15 0.25
30 9 0.15
31 25 0.42
32 5 0.08
ACGTcount: A:0.54, C:0.11, G:0.13, T:0.22
Consensus pattern (30 bp):
AAAAAATACAAGTTTAAGTACCAAATTAGG
Found at i:198303 original size:13 final size:11
Alignment explanation
Indices: 198276--198318 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
198266 CGTTAAATAT
198276 TATTTTATTAA
1 TATTTTATTAA
198287 TATTTTACTTAA
1 TATTTTA-TTAA
*
198299 -ATATTTATTAT
1 TAT-TTTATTAA
198310 TATTTTATT
1 TATTTTATT
198319 TAGAAAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:203798 original size:188 final size:190
Alignment explanation
Indices: 203455--203798 Score: 498
Period size: 188 Copynumber: 1.8 Consensus size: 190
203445 TTTTGGTTAT
* * *
203455 TCATGTATTCTTTTCGTATTTGTGTATCTTCTCGTATTATAGCCGTGCTTAAAAGTATTTTATAT
1 TCATGTATTCTTTTCGTATTTGTGTATCTTCTCGTATTATAACCGCGCTTAAAAGTATTCTATAT
* ** *
203520 TTATATAGAACTTATGATAAGTTAAAAGTGGATTGGATTTGTTTGGTTATATGTGTATTCTTTTT
66 TTATATACAACTTATGATAAGTTAAAAGTGGATTGGATTTACTTGGTTATATATGTATTCTTTTT
* *
203585 GTGTTTGTGTATCTTCTCGTATTATAGTCATGCTGAATGTATTTATATTTATTTAAAGTA
131 GTATTTGTGTATCTGCTCGTATTATAGTCATGCTGAATGTATTTATATTTATTTAAAGTA
* ** *
203645 TCATGTATTCTTTTTCGTATTTGTGTATCTTCTCGTATTGTAATTGCGCTT-AAGGTATTCTATA
1 TCATGTATTC-TTTTCGTATTTGTGTATCTTCTCGTATTATAACCGCGCTTAAAAGTATTCTATA
* * *
203709 -TT-T-TACAACTTTTGATAAGTTTACAGTGGATTGGATTTACTTGGTTTATATATGTATTCTTT
65 TTTATATACAACTTATGATAAGTTAAAAGTGGATTGGATTTACTTGG-TTATATATGTATTCTTT
203771 TTGTATTTGTGTATCTGCTCGTATTATA
129 TTGTATTTGTGTATCTGCTCGTATTATA
203799 ATTGTACTCA
Statistics
Matches: 136, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
187 35 0.26
188 43 0.32
189 2 0.01
190 21 0.15
191 35 0.26
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.51
Consensus pattern (190 bp):
TCATGTATTCTTTTCGTATTTGTGTATCTTCTCGTATTATAACCGCGCTTAAAAGTATTCTATAT
TTATATACAACTTATGATAAGTTAAAAGTGGATTGGATTTACTTGGTTATATATGTATTCTTTTT
GTATTTGTGTATCTGCTCGTATTATAGTCATGCTGAATGTATTTATATTTATTTAAAGTA
Found at i:203870 original size:112 final size:112
Alignment explanation
Indices: 203646--203956 Score: 446
Period size: 112 Copynumber: 2.8 Consensus size: 112
203636 TTTAAAGTAT
* * *
203646 CATGTATTCTTTTTCGTATTTGTGTATCTTCTCGTATTGTAATTGCGCTTAAGGTATTCTATATT
1 CATGTATTCTTTTT-GTATTTGTGTATCTTCTCGTATTATAATTGTGCTCAAGGTATT-TATATT
* *
203711 T-TACAACTTTTGATAAGTTTACAGTGGATTGGATTTACTTGGTTTATA
64 TATAGAACTTTTGATAAGTTAACAGTGGATTGGATTTACTTGGTTTATA
* * *
203759 TATGTATTCTTTTTGTATTTGTGTATCTGCTCGTATTATAATTGTACTCAAGGTATGTTATATTT
1 CATGTATTCTTTTTGTATTTGTGTATCTTCTCGTATTATAATTGTGCTCAAGGTAT-TTATATTT
* * *
203824 ATAGAACTTTTAATAAGTTAACAGTGGATTTGATTTATTTGG-TTATA
65 ATAGAACTTTTGATAAGTTAACAGTGGATTGGATTTACTTGGTTTATA
* *
203871 CATGTATTCTTTTCGTATTTGTGTATCTTCTCGTAATATAATTGTGCTCAAGGTATTTTATATTT
1 CATGTATTCTTTTTGTATTTGTGTATCTTCTCGTATTATAATTGTGCTCAAGGTA-TTTATATTT
*
203936 ATAGAACTTTGGATAAGTTAA
65 ATAGAACTTTTGATAAGTTAA
203957 TGAATCGTGT
Statistics
Matches: 177, Mismatches: 18, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
112 126 0.71
113 51 0.29
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (112 bp):
CATGTATTCTTTTTGTATTTGTGTATCTTCTCGTATTATAATTGTGCTCAAGGTATTTATATTTA
TAGAACTTTTGATAAGTTAACAGTGGATTGGATTTACTTGGTTTATA
Found at i:207221 original size:16 final size:18
Alignment explanation
Indices: 207189--207223 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
207179 AAGTTTATGG
207189 ATAAAAAATGAACATTAT
1 ATAAAAAATGAACATTAT
207207 ATAAAAAAT-AA-ATTAT
1 ATAAAAAATGAACATTAT
207223 A
1 A
207224 CTGAGAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 2 0.12
18 9 0.53
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
ATAAAAAATGAACATTAT
Found at i:212606 original size:3 final size:3
Alignment explanation
Indices: 212598--212627 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
212588 TTACCCCATC
212598 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
212628 TAATTCTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:213187 original size:66 final size:67
Alignment explanation
Indices: 213117--213252 Score: 213
Period size: 66 Copynumber: 2.0 Consensus size: 67
213107 GTATGTATGT
* *
213117 ATATATAAATATTTTAAATGTGTGATTGGTATGAATAAATTTAATAA-TTTT-TTTTTTGCATGT
1 ATATATAAATATTTTAAATGTGTGATTGGTATAAATAAATTTAA-AAGTTTTATTATTTGCATGT
213180 TTA
65 TTA
213183 ATATATAAATATTTTAAATGTGTGATTGGTATAAATAAATTTAAAAGTTTTAAGTTATTTGCATG
1 ATATATAAATATTTTAAATGTGTGATTGGTATAAATAAATTTAAAAGTTTT-A-TTATTTGCATG
213248 TTTA
64 TTTA
213252 A
1 A
213253 AATACCATAT
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
65 2 0.03
66 47 0.73
69 15 0.23
ACGTcount: A:0.38, C:0.01, G:0.12, T:0.49
Consensus pattern (67 bp):
ATATATAAATATTTTAAATGTGTGATTGGTATAAATAAATTTAAAAGTTTTATTATTTGCATGTT
TA
Found at i:215628 original size:29 final size:29
Alignment explanation
Indices: 215571--215637 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
215561 AACTCTATTC
* *
215571 ATTTGATTCTTTTTAATAGTACAGCGACTCA
1 ATTTGA-TCTATTTAATAGTAAAGCGACT-A
215602 A-TTGATCTATTTAATAGTAGAAG-GACTA
1 ATTTGATCTATTTAATAGTA-AAGCGACTA
215630 ATTTGATC
1 ATTTGATC
215638 AGGCCCCCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 2 0.06
29 23 0.72
30 6 0.19
31 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (29 bp):
ATTTGATCTATTTAATAGTAAAGCGACTA
Found at i:219075 original size:37 final size:35
Alignment explanation
Indices: 219025--219107 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
219015 ATTGATTAAC
* * *
219025 GAAGATACAATCAAGGGCAATGCACAACAAACTACAT
1 GAAGACACAATCAAGAGCAA--CACAACAAAATACAT
* *
219062 GAAGACACGATCAAGAGTAACACAACAAAATACAT
1 GAAGACACAATCAAGAGCAACACAACAAAATACAT
219097 GAAGACACAAT
1 GAAGACACAAT
219108 GATGACACAG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
35 24 0.60
37 16 0.40
ACGTcount: A:0.52, C:0.20, G:0.16, T:0.12
Consensus pattern (35 bp):
GAAGACACAATCAAGAGCAACACAACAAAATACAT
Found at i:221011 original size:45 final size:45
Alignment explanation
Indices: 220962--221052 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
220952 CTAAACTATT
*
220962 AAAATTTACAAATGATCGCT-AAGCTATTT-AAAAATTTTAATTTAA
1 AAAATTTACAAATGATCACTGAA-CTATTTAAAAAATTTT-ATTTAA
* *
221007 AAAATTTACAAATGATTACTGAATTATTTAAAAAATTTTATTTAA
1 AAAATTTACAAATGATCACTGAACTATTTAAAAAATTTTATTTAA
221052 A
1 A
221053 TTATTGAACT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
45 30 0.73
46 11 0.27
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (45 bp):
AAAATTTACAAATGATCACTGAACTATTTAAAAAATTTTATTTAA
Found at i:221157 original size:25 final size:25
Alignment explanation
Indices: 221123--221174 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
221113 TGAAAAACTC
*
221123 TTCTTCCACTTTTCTTTTACGGTTA
1 TTCTTCCACTTCTCTTTTACGGTTA
221148 TTCTTCCACTTCTCTTTTACGGTTA
1 TTCTTCCACTTCTCTTTTACGGTTA
221173 TT
1 TT
221175 TTTTTTTCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.12, C:0.25, G:0.08, T:0.56
Consensus pattern (25 bp):
TTCTTCCACTTCTCTTTTACGGTTA
Found at i:248438 original size:49 final size:46
Alignment explanation
Indices: 248350--248456 Score: 142
Period size: 49 Copynumber: 2.3 Consensus size: 46
248340 CAATATAATG
** *
248350 GTTTTGACTTTTAACTTAATGAGTAAATATTTATTAAAACGACGTA
1 GTTTTGACTTTTAACTTAAAAAGTAAATATTTATCAAAACGACGTA
248396 GTTTTGACTTTTAACTTTAGAAAATGTAAATATTTATCAAAACGACGTA
1 GTTTTGACTTTTAAC-TTA-AAAA-GTAAATATTTATCAAAACGACGTA
* *
248445 GCTTTGTCTTTT
1 GTTTTGACTTTT
248457 CTTATTCAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
46 15 0.28
47 3 0.06
48 2 0.04
49 33 0.62
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (46 bp):
GTTTTGACTTTTAACTTAAAAAGTAAATATTTATCAAAACGACGTA
Found at i:255659 original size:46 final size:45
Alignment explanation
Indices: 255607--255699 Score: 132
Period size: 46 Copynumber: 2.0 Consensus size: 45
255597 TTTGTAATAT
* ** * *
255607 TAGTTATGCACTTGGACGATGTTGTAGTTATCATGTGGTGTACTAC
1 TAGTTATGCACGTGGAAAATATCGTAGTTATCATGTGGTGTA-TAC
255653 TAGTTATGCACGTGGAAAATATCGTAGTTATCATGTGGTGTATAC
1 TAGTTATGCACGTGGAAAATATCGTAGTTATCATGTGGTGTATAC
255698 TA
1 TA
255700 ATCTGTAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 5 0.12
46 37 0.88
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.38
Consensus pattern (45 bp):
TAGTTATGCACGTGGAAAATATCGTAGTTATCATGTGGTGTATAC
Done.