Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015080.1 Kokia drynarioides strain JFW-HI SEQ_130124, 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: 129931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 69 characters in sequence are not A, C, G, or T
Found at i:9869 original size:5 final size:5
Alignment explanation
Indices: 9859--9887 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
9849 AATACCCACG
9859 ACACA ACACA ACACA ACACA ACACA ACAC
1 ACACA ACACA ACACA ACACA ACACA ACAC
9888 GCTAGCTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (5 bp):
ACACA
Found at i:11679 original size:6 final size:6
Alignment explanation
Indices: 11668--11694 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
11658 CCTTATGCCT
11668 GGGGCA GGGGCA GGGGCA GGGGCA GGG
1 GGGGCA GGGGCA GGGGCA GGGGCA GGG
11695 AATTAAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.70, T:0.00
Consensus pattern (6 bp):
GGGGCA
Found at i:26618 original size:7 final size:7
Alignment explanation
Indices: 26606--26656 Score: 75
Period size: 7 Copynumber: 7.0 Consensus size: 7
26596 AAGACTAAAT
26606 GCAAAGG
1 GCAAAGG
26613 GCAAAGG
1 GCAAAGG
26620 GCAAAGG
1 GCAAAGG
26627 GCAAAGGG
1 GCAAA-GG
26635 CGCAAAGG
1 -GCAAAGG
26643 GCAAAGG
1 GCAAAGG
*
26650 GGAAAGG
1 GCAAAGG
26657 AAAAAGGCGA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
7 32 0.78
8 4 0.10
9 5 0.12
ACGTcount: A:0.41, C:0.14, G:0.45, T:0.00
Consensus pattern (7 bp):
GCAAAGG
Found at i:26650 original size:23 final size:22
Alignment explanation
Indices: 26606--26649 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
26596 AAGACTAAAT
26606 GCAAAGGGCAAAGGGCAAAGG-
1 GCAAAGGGCAAAGGGCAAAGGC
26627 GCAAAGGGCGCAAAGGGCAAAGG
1 GCAAA-GG-GCAAAGGGCAAAGG
26650 GGAAAGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.24
22 2 0.10
23 14 0.67
ACGTcount: A:0.41, C:0.16, G:0.43, T:0.00
Consensus pattern (22 bp):
GCAAAGGGCAAAGGGCAAAGGC
Found at i:26663 original size:30 final size:29
Alignment explanation
Indices: 26606--26671 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
26596 AAGACTAAAT
* *
26606 GCAAAGGGCAAAGGGCAAAGGGCAAAGGGC
1 GCAAAGGGCAAAGGGCAAA-GGAAAAAGGC
*
26636 GCAAAGGGCAAAGGGGAAAGGAAAAAGGC
1 GCAAAGGGCAAAGGGCAAAGGAAAAAGGC
26665 GACAAAG
1 G-CAAAG
26672 AGTATAGTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 9 0.28
30 23 0.72
ACGTcount: A:0.45, C:0.14, G:0.41, T:0.00
Consensus pattern (29 bp):
GCAAAGGGCAAAGGGCAAAGGAAAAAGGC
Found at i:26731 original size:7 final size:7
Alignment explanation
Indices: 26716--26746 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
26706 CTTCAAGTCG
*
26716 CCACTCA
1 CCACCCA
26723 CCACCCA
1 CCACCCA
26730 CCACCCA
1 CCACCCA
26737 CCACCCA
1 CCACCCA
26744 CCA
1 CCA
26747 AGCCCAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.29, C:0.68, G:0.00, T:0.03
Consensus pattern (7 bp):
CCACCCA
Found at i:36786 original size:31 final size:31
Alignment explanation
Indices: 36717--36786 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
36707 AATTTTGTAC
* * *
36717 TTTACATTTTAGTTCTTTACTTTTTGAATTG
1 TTTAAATTTTAATTCTTTAATTTTTGAATTG
*
36748 GTT-AATTTTAATTCTTATAATTTTTGAATT-
1 TTTAAATTTTAATTCTT-TAATTTTTGAATTG
36778 TTTAAATTT
1 TTTAAATTT
36787 ATAGTCTTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
30 13 0.41
31 19 0.59
ACGTcount: A:0.26, C:0.06, G:0.07, T:0.61
Consensus pattern (31 bp):
TTTAAATTTTAATTCTTTAATTTTTGAATTG
Found at i:37392 original size:42 final size:42
Alignment explanation
Indices: 37333--37416 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
37323 GGCTCCACTC
37333 CACCCGTCTGATATGTGCTCAGACTGAATATCCACAAAAGCT
1 CACCCGTCTGATATGTGCTCAGACTGAATATCCACAAAAGCT
37375 CACCCGTCTGATATGTGCTCAGACTGAATATCCACAAAAGCT
1 CACCCGTCTGATATGTGCTCAGACTGAATATCCACAAAAGCT
37417 ATCTCTTCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (42 bp):
CACCCGTCTGATATGTGCTCAGACTGAATATCCACAAAAGCT
Found at i:37709 original size:3 final size:3
Alignment explanation
Indices: 37701--37736 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
37691 CAACCATCTC
37701 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
37737 GTTGTCTTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:41078 original size:63 final size:65
Alignment explanation
Indices: 40960--41091 Score: 196
Period size: 65 Copynumber: 2.0 Consensus size: 65
40950 AAATATTTGA
*
40960 AAGGGGGAATTAAAGGAATAAAAAAAAAAAGTTGTACAAGTACTTATTATATTGC-TATATGATT
1 AAGGGGGAATTAAAGGAAT-AAAAAAAAAAGTTGTACAAGTACTGATTATATTGCATATATGATT
41024 T
65 T
* * *
41025 AAGGGGGAATTAAAGGAAT-AAAAAATAAGTTGTATAATTACTGATTATATTGCTATATATGATT
1 AAGGGGGAATTAAAGGAATAAAAAAAAAAGTTGTACAAGTACTGATTATATTGC-ATATATGATT
41089 T
65 T
41090 AA
1 AA
41092 ATTTTAAATA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
63 30 0.49
65 31 0.51
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.33
Consensus pattern (65 bp):
AAGGGGGAATTAAAGGAATAAAAAAAAAAGTTGTACAAGTACTGATTATATTGCATATATGATTT
Found at i:41273 original size:16 final size:17
Alignment explanation
Indices: 41246--41298 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
41236 GGAAAGCTAT
41246 TTTTAG-GG-TTTATAA
1 TTTTAGTGGTTTTATAA
*
41261 TTTT-GTGGTTTTATGA
1 TTTTAGTGGTTTTATAA
41277 TTTTAAGTGGTTTCTA-AA
1 TTTT-AGTGGTTT-TATAA
41295 TTTT
1 TTTT
41299 CTTATGGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 1 0.03
15 6 0.19
16 10 0.32
18 12 0.39
19 2 0.06
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.58
Consensus pattern (17 bp):
TTTTAGTGGTTTTATAA
Found at i:47040 original size:15 final size:15
Alignment explanation
Indices: 47020--47049 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47010 ATAAGCAGTA
47020 TATGAGGTAGAAGAT
1 TATGAGGTAGAAGAT
*
47035 TATGAGGTTGAAGAT
1 TATGAGGTAGAAGAT
47050 GATCTATATA
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:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (15 bp):
TATGAGGTAGAAGAT
Found at i:48242 original size:23 final size:23
Alignment explanation
Indices: 48216--48344 Score: 152
Period size: 23 Copynumber: 5.4 Consensus size: 23
48206 AGTGCTTGGC
48216 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
48239 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
*
48262 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
48286 TAATAGAGAGCACACACAGTGCTAA
1 -AACAGAGAGCACACACAGTGCT-A
*
48311 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
48335 AACAGAGAGC
1 AACAGAGAGC
48345 GTGCTAGTGT
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
23 48 0.52
24 2 0.02
25 39 0.42
26 3 0.03
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:48246 original size:48 final size:43
Alignment explanation
Indices: 48191--48344 Score: 130
Period size: 48 Copynumber: 3.2 Consensus size: 43
48181 CCAAAGTACT
48191 AACAGAGAGCACATAAGTGCTTGGCAACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACA-AAGTGC-T---AACAGAGAGCACACACAGTGCTA
*
48239 AACAGAGAGTACACAAAGTACTAATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAG--CACAAAGTGCTAA-CAGAGAGCACACACAGTGCT-A
* *
48286 TAATAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCACA-A-AGTGC---TAACAGAGAGCAC-ACACAGTGCTA
48335 AACAGAGAGC
1 AACAGAGAGC
48345 GTGCTAGTGT
Statistics
Matches: 90, Mismatches: 5, Indels: 22
0.77 0.04 0.19
Matches are distributed among these distances:
45 2 0.02
46 24 0.27
47 2 0.02
48 31 0.34
49 6 0.07
50 19 0.21
51 6 0.07
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.12
Consensus pattern (43 bp):
AACAGAGAGCACAAAGTGCTAACAGAGAGCACACACAGTGCTA
Found at i:48247 original size:25 final size:25
Alignment explanation
Indices: 48219--48343 Score: 113
Period size: 25 Copynumber: 5.2 Consensus size: 25
48209 GCTTGGCAAC
48219 AGAGAGCACACACAGTGCTAAACAG
1 AGAGAGCACACACAGTGCTAAACAG
* *
48244 AGAGTA-CACA-A-AGTACTAATC--
1 AGAG-AGCACACACAGTGCTAAACAG
*
48265 AGAGAGCACACACAGTGCTAATA-AT
1 AGAGAGCACACACAGTGCTAA-ACAG
*
48290 AGAGAGCACACACAGTGCTAATA-AC
1 AGAGAGCACACACAGTGCTAA-ACAG
*
48315 AGAGAGCACGAGAC-GTGCTAAACAG
1 AGAGAGCAC-ACACAGTGCTAAACAG
48340 AGAG
1 AGAG
48344 CGTGCTAGTG
Statistics
Matches: 84, Mismatches: 7, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.01
21 8 0.10
22 1 0.01
23 15 0.18
24 2 0.02
25 53 0.63
26 4 0.05
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (25 bp):
AGAGAGCACACACAGTGCTAAACAG
Found at i:53069 original size:27 final size:28
Alignment explanation
Indices: 53039--53095 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
53029 AATGTATATG
53039 TTTAAATTTAAGATA-AAACTTTTTAAT
1 TTTAAATTTAAGATATAAACTTTTTAAT
* **
53066 TTTAAATTTAATATATAATTTTTTTAAT
1 TTTAAATTTAAGATATAAACTTTTTAAT
53094 TT
1 TT
53096 CAAAATGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTAAATTTAAGATATAAACTTTTTAAT
Found at i:53173 original size:10 final size:10
Alignment explanation
Indices: 53158--53184 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
53148 TATCAAATGA
53158 GCACATTTGC
1 GCACATTTGC
53168 GCACATTTGC
1 GCACATTTGC
53178 GCACATT
1 GCACATT
53185 ATGCAAATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.30
Consensus pattern (10 bp):
GCACATTTGC
Found at i:54101 original size:115 final size:115
Alignment explanation
Indices: 53899--54107 Score: 310
Period size: 115 Copynumber: 1.8 Consensus size: 115
53889 ATGAAGGTTA
* * ** * * * *
53899 ATGATCTCTTTGGTGACAGATGGTTGTTCTTGGGACTTTAGCCTTGTTAAGGGATTGTTGTCTCC
1 ATGATCTCTTCGATGACAGATAATTGTTCTTCGGACATTAACCTTATTAAGGGATTGTTGTCTCC
53964 GGTTGATGCCCAACATGTGCTTAGAATTCTTATCATTCTTTAACGCTTGG
66 GGTTGATGCCCAACATGTGCTTAGAATTCTTATCATTCTTTAACGCTTGG
* * *
54014 ATGATCTCTTCGATGACAGATAATTGTTTTTCGGACATTAACCTTATTAAGGGGTTGTTGTCTCT
1 ATGATCTCTTCGATGACAGATAATTGTTCTTCGGACATTAACCTTATTAAGGGATTGTTGTCTCC
*
54079 GGTTGATGCCCAACATGTGCTTAGTATTC
66 GGTTGATGCCCAACATGTGCTTAGAATTC
54108 CTATTGTTTT
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
115 82 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (115 bp):
ATGATCTCTTCGATGACAGATAATTGTTCTTCGGACATTAACCTTATTAAGGGATTGTTGTCTCC
GGTTGATGCCCAACATGTGCTTAGAATTCTTATCATTCTTTAACGCTTGG
Found at i:56650 original size:14 final size:13
Alignment explanation
Indices: 56621--56655 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
56611 ACATGCTTAG
56621 GAGAATATAAGAGA
1 GAGAA-ATAAGAGA
56635 GAGAAATAAGATGA
1 GAGAAATAAGA-GA
56649 GAGAAAT
1 GAGAAAT
56656 GGGTTCGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (13 bp):
GAGAAATAAGAGA
Found at i:66363 original size:21 final size:21
Alignment explanation
Indices: 66318--66393 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 21
66308 TATAAACATA
*
66318 TAAAAATTCTAAAAAA-ACTTA-
1 TAAAAA-TATAAAAAATA-TTAT
66339 TAAAAA-ATAATAAAAT-TTCAT
1 TAAAAATATAA-AAAATATT-AT
66360 TAAAAATATAAAAAATATTAT
1 TAAAAATATAAAAAATATTAT
* *
66381 TAAATATTTAAAA
1 TAAAAATATAAAA
66394 TTATATAAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
19 5 0.11
20 5 0.11
21 30 0.65
22 6 0.13
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAATATAAAAAATATTAT
Found at i:66418 original size:9 final size:9
Alignment explanation
Indices: 66316--66421 Score: 54
Period size: 11 Copynumber: 10.9 Consensus size: 9
66306 TATATAAACA
66316 TATAAAAATT
1 TATAAAAA-T
*
66326 CTAAAAAAACT
1 -TATAAAAA-T
66337 TATAAAAAAT
1 TAT-AAAAAT
* *
66347 AATAAAATT
1 TATAAAAAT
66356 TCATTAAAAAT
1 T-A-TAAAAAT
*
66367 ATAAAAAATAT
1 -TATAAAA-AT
*
66378 TATTAAATAT
1 TA-TAAAAAT
66388 T-T-AAAAT
1 TATAAAAAT
*
66395 TATATAAACT
1 TATA-AAAAT
66405 TATAAAAAT
1 TATAAAAAT
66414 TATAAAAA
1 TATAAAAA
66422 AACCCTAATA
Statistics
Matches: 73, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
7 5 0.07
8 2 0.03
9 17 0.23
10 23 0.32
11 25 0.34
12 1 0.01
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (9 bp):
TATAAAAAT
Found at i:88201 original size:31 final size:31
Alignment explanation
Indices: 88163--88224 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
88153 TTAAAGCAAT
88163 ACTACAACCTACGATGCAATGTTTTTTCTTA
1 ACTACAACCTACGATGCAATGTTTTTTCTTA
88194 ACTACAACCTACGATGCAATGTTTTTTCTTA
1 ACTACAACCTACGATGCAATGTTTTTTCTTA
88225 CTTTTTTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.39
Consensus pattern (31 bp):
ACTACAACCTACGATGCAATGTTTTTTCTTA
Found at i:88666 original size:2 final size:2
Alignment explanation
Indices: 88659--88690 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
88649 ATTTAAAATA
88659 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
88691 TCTAATTAAA
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):
AT
Found at i:98437 original size:21 final size:21
Alignment explanation
Indices: 98413--98464 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
98403 TTTGGGGGAG
* *
98413 ATTAATTATTGTAACAATAAA
1 ATTAAATATTATAACAATAAA
*
98434 ATTAAATATTATAATAATAAA
1 ATTAAATATTATAACAATAAA
*
98455 AGTAAA-ATTA
1 ATTAAATATTA
98465 ATAAATAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (21 bp):
ATTAAATATTATAACAATAAA
Found at i:99586 original size:43 final size:43
Alignment explanation
Indices: 99525--99606 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
99515 CCTAGTTGAG
99525 CTTAATTGAACTTACCAAATAAGGACCAAAACTCTGAAAAAAA
1 CTTAATTGAACTTACCAAATAAGGACCAAAACTCTGAAAAAAA
* * * *
99568 CTTAATTGAGCTTACCAAATAAGGATCGAAACTTTGAAA
1 CTTAATTGAACTTACCAAATAAGGACCAAAACTCTGAAA
99607 GCTTCCAAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.24
Consensus pattern (43 bp):
CTTAATTGAACTTACCAAATAAGGACCAAAACTCTGAAAAAAA
Found at i:102251 original size:21 final size:21
Alignment explanation
Indices: 102212--102251 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
102202 TGGAGACATA
*
102212 CAAGACCCTCTTCACCAACTC
1 CAAGACCCTCTTCAACAACTC
102233 CAAGA-CCTCTTCCAACAAC
1 CAAGACCCTCTT-CAACAAC
102252 CATGACCACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.45, G:0.05, T:0.17
Consensus pattern (21 bp):
CAAGACCCTCTTCAACAACTC
Found at i:105954 original size:2 final size:2
Alignment explanation
Indices: 105907--105938 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
105897 TTCTTTCTAG
105907 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
105939 TTTTAGTATT
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):
AT
Found at i:106391 original size:20 final size:19
Alignment explanation
Indices: 106350--106393 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
106340 TATATATAAT
**
106350 TTTAATATTCAAATTATTA
1 TTTAATATTCAAATTAAAA
106369 TTTATATATTCAAATTAAAA
1 TTTA-ATATTCAAATTAAAA
106389 TTTAA
1 TTTAA
106394 AAACAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAATATTCAAATTAAAA
Found at i:119431 original size:32 final size:32
Alignment explanation
Indices: 119383--119452 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
119373 TTTGATTTGC
* * *
119383 TGTAATAGAATGAAACTGTAATAG-AATATAAT
1 TGTAATAAAATAAAACTGTAAT-GTAATAGAAT
119415 TGTAATAAAATAAAACTGTAATGTAATAGAAT
1 TGTAATAAAATAAAACTGTAATGTAATAGAAT
119447 TGTAAT
1 TGTAAT
119453 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 1 0.03
32 33 0.97
ACGTcount: A:0.50, C:0.03, G:0.14, T:0.33
Consensus pattern (32 bp):
TGTAATAAAATAAAACTGTAATGTAATAGAAT
Found at i:119442 original size:16 final size:16
Alignment explanation
Indices: 119382--119436 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
119372 GTTTGATTTG
*
119382 CTGTAATAGAATGAAA
1 CTGTAATAGAATAAAA
*
119398 CTGTAATAGAATATAA
1 CTGTAATAGAATAAAA
* *
119414 TTGTAATAAAATAAAA
1 CTGTAATAGAATAAAA
119430 CTGTAAT
1 CTGTAAT
119437 GTAATAGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.31
Consensus pattern (16 bp):
CTGTAATAGAATAAAA
Found at i:119450 original size:16 final size:16
Alignment explanation
Indices: 119383--119452 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 16
119373 TTTGATTTGC
* * *
119383 TGTAATAGAATGAAAC
1 TGTAATAAAATAAAAT
* *
119399 TGTAATAGAATATAAT
1 TGTAATAAAATAAAAT
*
119415 TGTAATAAAATAAAAC
1 TGTAATAAAATAAAAT
** *
119431 TGTAATGTAATAGAAT
1 TGTAATAAAATAAAAT
119447 TGTAAT
1 TGTAAT
119453 CAGTAATTCA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.50, C:0.03, G:0.14, T:0.33
Consensus pattern (16 bp):
TGTAATAAAATAAAAT
Found at i:119565 original size:11 final size:10
Alignment explanation
Indices: 119534--119558 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
119524 GTAATAACAT
119534 AAAAAATAAA
1 AAAAAATAAA
119544 AAAAAATAAA
1 AAAAAATAAA
119554 AAAAA
1 AAAAA
119559 GTTAAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:119652 original size:21 final size:21
Alignment explanation
Indices: 119628--119681 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
119618 AAACCACAAT
119628 GAATCCATTCAAACAAGAGA-A
1 GAATCCATTCAAACAAGA-ATA
** *
119649 GAATTAATTTAAACAAGAATA
1 GAATCCATTCAAACAAGAATA
119670 -AATCCATTCAAA
1 GAATCCATTCAAA
119682 TAACAAAACA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.54, C:0.15, G:0.09, T:0.22
Consensus pattern (21 bp):
GAATCCATTCAAACAAGAATA
Found at i:129343 original size:4 final size:4
Alignment explanation
Indices: 129330--129372 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
129320 AAAAATGAAG
129330 GAAA -AAA GAAA GAAA -AAGGA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA--A GAAA GAAA GAAA GAAA GAAA GAA
129373 GAAGGAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 5 0.14
4 27 0.77
5 1 0.03
6 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:129345 original size:21 final size:21
Alignment explanation
Indices: 129319--129375 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
129309 GGGGACCAAC
129319 GAAAAATGAAGGAAA-AAAGAAA
1 GAAAAA-GAA-GAAAGAAAGAAA
*
129341 GAAAAAGGAGAAAGAAAGAAA
1 GAAAAAGAAGAAAGAAAGAAA
129362 GAAAGAAAGAAGAA
1 G-AA-AAAGAAGAA
129376 GGAAGAAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 4 0.13
21 10 0.33
22 8 0.27
23 8 0.27
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (21 bp):
GAAAAAGAAGAAAGAAAGAAA
Found at i:129370 original size:12 final size:11
Alignment explanation
Indices: 129319--129375 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
129309 GGGGACCAAC
* *
129319 GAAAAATGAAG
1 GAAAAAAGAAA
129330 GAAAAAAGAAA
1 GAAAAAAGAAA
129341 GAAAAAGGAGAAA
1 GAAAAA--AGAAA
129354 GAAAGAAAGAAA
1 GAAA-AAAGAAA
*
129366 GAAAGAAGAA
1 GAAAAAAGAA
129376 GGAAGAAGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 20 0.50
12 9 0.22
13 9 0.22
14 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:129399 original size:18 final size:16
Alignment explanation
Indices: 129369--129405 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
129359 AAAGAAAGAA
129369 AGAAGAAGGAAGAAGG
1 AGAAGAAGGAAGAAGG
129385 AGAAGAAGGGTAAGAAGG
1 AGAAGAA-GG-AAGAAGG
129403 AGA
1 AGA
129406 GGAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 2 0.11
18 10 0.53
ACGTcount: A:0.54, C:0.00, G:0.43, T:0.03
Consensus pattern (16 bp):
AGAAGAAGGAAGAAGG
Found at i:129795 original size:20 final size:22
Alignment explanation
Indices: 129755--129796 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
129745 AATTTACTTT
129755 ATTTTAATTTTGCTAGTTAGTA
1 ATTTTAATTTTGCTAGTTAGTA
*
129777 ATTTT-ATTTTG-TTGTTAGTA
1 ATTTTAATTTTGCTAGTTAGTA
129797 GTAGTAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (22 bp):
ATTTTAATTTTGCTAGTTAGTA
Done.