Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014726.1 Kokia drynarioides strain JFW-HI SEQ_129765, 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: 120591
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:115 original size:21 final size:20
Alignment explanation
Indices: 86--130 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
76 CCTTCTTCCT
86 TCTTCTTTCTTTATTTCTTTC
1 TCTTCTTTCTTTATTT-TTTC
* *
107 TCTTTTTTCTTTCTTTTTTC
1 TCTTCTTTCTTTATTTTTTC
127 -CTTC
1 TCTTC
131 ATTTTTCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.14
20 4 0.19
21 14 0.67
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (20 bp):
TCTTCTTTCTTTATTTTTTC
Found at i:123 original size:11 final size:11
Alignment explanation
Indices: 88--137 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
78 TTCTTCCTTC
88 TTCTTTCTTTAT
1 TTCTTTCTTT-T
100 TTCTTTCTCTTTT
1 TTC-TT-TCTTTT
113 TTCTTTCTTTT
1 TTCTTTCTTTT
* *
124 TTCCTTCATTT
1 TTCTTTCTTTT
135 TTC
1 TTC
138 ATTGGTCCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 18 0.53
12 5 0.15
13 6 0.18
14 5 0.15
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (11 bp):
TTCTTTCTTTT
Found at i:1457 original size:2 final size:2
Alignment explanation
Indices: 1415--1443 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1405 TATTACAAGA
1415 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1444 TTTGGGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:6169 original size:15 final size:14
Alignment explanation
Indices: 6149--6180 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
6139 AAAGAATATT
6149 TTTAATATTTAAATA
1 TTTAATATTT-AATA
6164 TTTAATATTTAATA
1 TTTAATATTTAATA
6178 TTT
1 TTT
6181 TTATTTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAATATTTAATA
Found at i:6170 original size:7 final size:7
Alignment explanation
Indices: 6149--6180 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
6139 AAAGAATATT
6149 TTTAATA
1 TTTAATA
6156 TTTAAATA
1 TTT-AATA
6164 TTTAATA
1 TTTAATA
6171 TTTAATA
1 TTTAATA
6178 TTT
1 TTT
6181 TTATTTTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTAATA
Found at i:7832 original size:3 final size:3
Alignment explanation
Indices: 7824--7857 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
7814 TTAAATATAC
7824 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
7858 ATTTATCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:7905 original size:18 final size:18
Alignment explanation
Indices: 7872--7906 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
7862 ATCATTCAAT
7872 ATTTATATTCTTTTATTA
1 ATTTATATTCTTTTATTA
7890 ATTTA-ATTCTTATTATT
1 ATTTATATTCTT-TTATT
7907 TTTTGAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTATATTCTTTTATTA
Found at i:14241 original size:17 final size:18
Alignment explanation
Indices: 14214--14247 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
14204 GCTTCGGGGA
14214 ATATGCCAAAATCTTCAC
1 ATATGCCAAAATCTTCAC
14232 ATAT-CCAAAATCTTCA
1 ATATGCCAAAATCTTCA
14248 TAATTGTTAT
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:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Found at i:15207 original size:21 final size:21
Alignment explanation
Indices: 15157--15208 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
15147 TGTACAACAG
*
15157 ATACATAACCAATGACCTTTT
1 ATACATAAGCAATGACCTTTT
15178 ATACATAAGCAATGACCTTTT
1 ATACATAAGCAATGACCTTTT
15199 ATACATAAGC
1 ATACATAAGC
15209 TGTCTTTCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (21 bp):
ATACATAAGCAATGACCTTTT
Found at i:17365 original size:28 final size:28
Alignment explanation
Indices: 17334--17421 Score: 69
Period size: 28 Copynumber: 3.1 Consensus size: 28
17324 ATATTACAGC
17334 TAAAAGAAGCATGCAACAATATCGAATA
1 TAAAAGAAGCATGCAACAATATCGAATA
* * *
17362 T-AAAGATG-AT-TAA-AATTTTTATTAGAA-A
1 TAAAAGAAGCATGCAACAA----TA-TCGAATA
17390 TAAAAGAAGCATGCAACAATATCGAATA
1 TAAAAGAAGCATGCAACAATATCGAATA
17418 TAAA
1 TAAA
17422 GATGATTAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 20
0.63 0.09 0.29
Matches are distributed among these distances:
24 2 0.05
25 2 0.05
26 2 0.05
27 10 0.23
28 12 0.27
29 10 0.23
30 2 0.05
31 2 0.05
32 2 0.05
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.25
Consensus pattern (28 bp):
TAAAAGAAGCATGCAACAATATCGAATA
Found at i:17411 original size:56 final size:56
Alignment explanation
Indices: 17334--17446 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
17324 ATATTACAGC
17334 TAAAAGAAGCATGCAACAATATCGAATATAAAGATGATTAAAATTTTTATTAGAAA
1 TAAAAGAAGCATGCAACAATATCGAATATAAAGATGATTAAAATTTTTATTAGAAA
17390 TAAAAGAAGCATGCAACAATATCGAATATAAAGATGATTAAAATTTTTATTAGAAA
1 TAAAAGAAGCATGCAACAATATCGAATATAAAGATGATTAAAATTTTTATTAGAAA
17446 T
1 T
17447 TTGTTTAGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.29
Consensus pattern (56 bp):
TAAAAGAAGCATGCAACAATATCGAATATAAAGATGATTAAAATTTTTATTAGAAA
Found at i:22869 original size:18 final size:18
Alignment explanation
Indices: 22834--22871 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
22824 TGAATTTTCG
*
22834 AATTCAAATAACTTGAAT
1 AATTCAAATAACTCGAAT
22852 AATTCAAATAAAC-CGAAT
1 AATTCAAAT-AACTCGAAT
22870 AA
1 AA
22872 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.26
Consensus pattern (18 bp):
AATTCAAATAACTCGAAT
Found at i:26490 original size:24 final size:24
Alignment explanation
Indices: 26437--26499 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
26427 TAGACTAATA
* * *
26437 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
* *
26461 ATAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
26485 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
26500 GATTATTTCT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.27
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:26742 original size:18 final size:18
Alignment explanation
Indices: 26721--26784 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 18
26711 CTTAAGATCT
*
26721 AGTATGCTCTAACGAGCC
1 AGTATGCTCAAACGAGCC
26739 AGTATGCTCAAACGAGCC
1 AGTATGCTCAAACGAGCC
* *
26757 AATATGCTCAAATGAGCC
1 AGTATGCTCAAACGAGCC
*
26775 ATTATGCTCA
1 AGTATGCTCA
26785 TTCTTTCATA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (18 bp):
AGTATGCTCAAACGAGCC
Found at i:30309 original size:15 final size:15
Alignment explanation
Indices: 30289--30331 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
30279 GTAAAATTTC
*
30289 AAATATAAGTGAGTA
1 AAATATAAGTGAGAA
*
30304 AAATATAATCTGAGAA
1 AAATATAA-GTGAGAA
*
30320 AAATAAAAGTGA
1 AAATATAAGTGA
30332 CTGTTTTGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.58, C:0.02, G:0.16, T:0.23
Consensus pattern (15 bp):
AAATATAAGTGAGAA
Found at i:43048 original size:17 final size:18
Alignment explanation
Indices: 43016--43049 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43006 CACTTTCACT
43016 TCAAAAAATATTAAAAAG
1 TCAAAAAATATTAAAAAG
*
43034 TCAACAAAT-TTAAAAA
1 TCAAAAAATATTAAAAA
43050 TTTTCATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.09, G:0.03, T:0.24
Consensus pattern (18 bp):
TCAAAAAATATTAAAAAG
Found at i:43567 original size:24 final size:24
Alignment explanation
Indices: 43522--43570 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
43512 TAATAATGAG
** *
43522 TTATCATAAAATACTTTTAATATT
1 TTATCATAAAATAAATTGAATATT
*
43546 TTATCATAATATAAATTGAATATT
1 TTATCATAAAATAAATTGAATATT
43570 T
1 T
43571 ATTAATATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (24 bp):
TTATCATAAAATAAATTGAATATT
Found at i:43725 original size:19 final size:20
Alignment explanation
Indices: 43701--43739 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
43691 TTGTGTTTAT
43701 ATGTGATTT-AATATTTAAA
1 ATGTGATTTAAATATTTAAA
43720 ATGTGATTTAAATATTTAAA
1 ATGTGATTTAAATATTTAAA
43740 TTAAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (20 bp):
ATGTGATTTAAATATTTAAA
Found at i:43740 original size:19 final size:18
Alignment explanation
Indices: 43696--43740 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
43686 AAGAGTTGTG
*
43696 TTTATATGTGATTTAATA
1 TTTAAATGTGATTTAATA
43714 TTTAAAATGTGATTTAAATA
1 TTT-AAATGTGATTT-AATA
43734 TTTAAAT
1 TTTAAAT
43741 TAAATTTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 3 0.12
19 14 0.58
20 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (18 bp):
TTTAAATGTGATTTAATA
Found at i:45030 original size:6 final size:6
Alignment explanation
Indices: 45005--45043 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
44995 ACAATTCATA
* * *
45005 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
45044 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:55448 original size:18 final size:18
Alignment explanation
Indices: 55425--55460 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
55415 AATATTTTTT
55425 TATTTTT-TATTTTTCTCG
1 TATTTTTCT-TTTTTCTCG
55443 TATTTTTCTTTTTTCTCG
1 TATTTTTCTTTTTTCTCG
55461 ACTTTTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.08, C:0.14, G:0.06, T:0.72
Consensus pattern (18 bp):
TATTTTTCTTTTTTCTCG
Found at i:71108 original size:18 final size:19
Alignment explanation
Indices: 71075--71110 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
71065 CAAATGAATA
*
71075 ATTTCTCATTTTCATTTTT
1 ATTTCTCATTTCCATTTTT
71094 ATTTC-CATTTCCATTTT
1 ATTTCTCATTTCCATTTT
71111 AAGAAAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTCTCATTTCCATTTTT
Found at i:73156 original size:18 final size:18
Alignment explanation
Indices: 73113--73148 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
73103 ATGTTGCCGT
*
73113 ATATATAGATATTTTACC
1 ATATATATATATTTTACC
*
73131 ATACATATATATTTTACC
1 ATATATATATATTTTACC
73149 TTGTATATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.14, G:0.03, T:0.44
Consensus pattern (18 bp):
ATATATATATATTTTACC
Found at i:76560 original size:29 final size:30
Alignment explanation
Indices: 76523--76593 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
76513 TGTATGCATG
* *
76523 AACTTTAATTTG-TGCAATTATGTACGTGA
1 AACTTTAATTTGATGCAAATATATACGTGA
* **
76552 AACTTTAATTGTGATTCAAATATATATTTGA
1 AACTTTAATT-TGATGCAAATATATACGTGA
76583 AACTTTAATTT
1 AACTTTAATTT
76594 TGATTTAGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 10 0.29
30 3 0.09
31 22 0.63
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.45
Consensus pattern (30 bp):
AACTTTAATTTGATGCAAATATATACGTGA
Found at i:80033 original size:175 final size:175
Alignment explanation
Indices: 79755--80108 Score: 513
Period size: 175 Copynumber: 2.0 Consensus size: 175
79745 TAGTTGCACA
* * *
79755 TGGAACTGGTTAAATGTTAGAGCATAATAACTGTTTACTGATCCGGAAAGTTCGGGATGCATACT
1 TGGAACTGGTTAAATGTTAAAGCATAATAACTGTTTACTGATCCAGAAAGTTCGGGATGAATACT
* *
79820 TTTGTTTGTCGTGCATGTGTTTCTTTCTCATTTTGTTCTTTCC-ATATGGACCGCTCAGA-TAAA
66 TTTGTTTGTCGTCCATGTGTTTCTTTCTCATTTTGTTCTTTCCAATATGCACCGCTCAGAGT--A
* *
79883 CT-GTAACACTGACGGTTGATTGATTGGTGAAACGTGTTAGTAATTAT
129 CTAGTAA-ACTGACAGTTGATTGATTGGAGAAACGTGTTAGTAATTAT
*
79930 TGGAACTGGTTAAATGTTAAAGCATTATAACTGTTTA-TGGATCCAGAAAGTTCGGGATGAATAC
1 TGGAACTGGTTAAATGTTAAAGCATAATAACTGTTTACT-GATCCAGAAAGTTCGGGATGAATAC
*
79994 TTGTT-TTTGAT-GTCCATGTGTTTCTTTCTCATTTTGTTCTTTCCAATATGCACGGCTCAGAGT
65 TT-TTGTTTG-TCGTCCATGTGTTTCTTTCTCATTTTGTTCTTTCCAATATGCACCGCTCAGAGT
* *
80057 ACTAGTTATCTGACAGTTGATTGATTGGAGAAACGTGTTAGTAATTAT
128 ACTAGTAAACTGACAGTTGATTGATTGGAGAAACGTGTTAGTAATTAT
80105 TGGA
1 TGGA
80109 CAGTAGTTAT
Statistics
Matches: 162, Mismatches: 11, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
174 1 0.01
175 140 0.86
176 20 0.12
177 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (175 bp):
TGGAACTGGTTAAATGTTAAAGCATAATAACTGTTTACTGATCCAGAAAGTTCGGGATGAATACT
TTTGTTTGTCGTCCATGTGTTTCTTTCTCATTTTGTTCTTTCCAATATGCACCGCTCAGAGTACT
AGTAAACTGACAGTTGATTGATTGGAGAAACGTGTTAGTAATTAT
Found at i:80509 original size:669 final size:672
Alignment explanation
Indices: 78757--80600 Score: 3038
Period size: 669 Copynumber: 2.8 Consensus size: 672
78747 GTACTAGTTC
78757 TAGTAATTATTGGATAGTAGTTATGAGCTTTGTTAATCATTGATCGATTAAGTAGATATGACCAC
1 TAGTAATTATTGGATAGTAGTTATGAGCTTTGTTAATCATTGATCGATTAAGTAGATATGACCAC
* **
78822 GTGTTACTAATCAACCTGTTAAGTAGATATGAACACGTGCTTGTAATCAACTGATCGTGTAGCTC
66 GTGTTACTAATCAACCGGTTAAGTAGATATGAACACGTGCTTGTAATCAACTGATTATGTAGCTC
* *
78887 TGAGCGAATGTTATAAAGTAAC-GATTGAGTAGTTCCAAGCGCCTTTTAGACATTAACGGTTAAG
131 TGAGCGCATGTTATTAAGTAACGGATTGAGTAGTTCCAAGCGCCTTTTAGACATTAACGGTTAAG
78951 TACTGAGCACGTGTTAGCAATTAACAGTTTGAGTAGTTCTGATCACGTGGTAGTAATTGATGGAT
196 TACTGAGCACGTGTTAGCAATTAACAGTTTGAGTAGTTCTGATCACGTGGTAGTAATTGATGGAT
* *
79016 TAAGTAGTTATGAGCATGTGATCATGCTTGAGCTACTATCCTTGGACTATCAGTACTTGTTATAG
261 TAAGTAGTTATGAGCACGTGACCATGCTTGAGCTACTATCCTTGGACTATCAGTACTTG--ATAG
* *
79081 TTGCTCATGGAACTGGTTAAATGTTAAAGCATAATAACTGTTTACTGATCCGGAATGTTCGGGAT
324 TTGCTCATGGAACTGGTTAAATGTTAGAGCATAATAACTGTTTACTGATCCGGAAAGTTCGGGAT
* *
79146 GCAAACTTTTGTTTGTCGTGCATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGCACTGCTCAG
389 GCATACTTTTGTTTGTCGTGCATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGCACCGCTCAG
79211 ATAAACTGTACTAGTTCACTGACAGTTGATTGATTGGTGAAACGTGTTAGTAATTATTGGAACTG
454 ATAAACTGTAC-A--TCACTGACAGTTGATTGATTGGTGAAACGTGTTAGTAATTATTGGAACTG
79276 GTTAAATGTTAAAGCATTATAACCGTTTACAGATCCAGAAAGTTCGGGATGAATACTTGTTTTTG
516 GTTAAATGTTAAAGCATTATAACCGTTTACAGATCCAGAAAGTTCGGGATGAATACTTGTTTTTG
* * *
79341 ATGTGCTTGTGTTTCTTTCTCATTTTGTTCTTTCCAATATGCACGGCTTAGAGTACTAGTTATCT
581 ATGTCCATGTGTTTCTTTCTCATTTTGTTCTTTCCAATATGCACGGCTCAGAGTACTAGTTATCT
79406 GACAGTTGATTGATTGGAGAAACGTGT
646 GACAGTTGATTGATTGGAGAAACGTGT
* * *
79433 TAG----TATTGGATAGTAGTTATGAGCTTTGTTAGTCATTGATCGCTTAAGTAGATATGACCAT
1 TAGTAATTATTGGATAGTAGTTATGAGCTTTGTTAATCATTGATCGATTAAGTAGATATGACCAC
* * *
79494 GTGTTAGTAATCAACCGCTTAAGTAGATATGAACACGTGCTTGTTATCAACTGATTATGTAGCTC
66 GTGTTACTAATCAACCGGTTAAGTAGATATGAACACGTGCTTGTAATCAACTGATTATGTAGCTC
* * * * *
79559 TGAGTGCATGTTA-T---TAACGGATTGAGTAGTTCCAAGCACCTTTTAGAAATTAATGGTCAAG
131 TGAGCGCATGTTATTAAGTAACGGATTGAGTAGTTCCAAGCGCCTTTTAGACATTAACGGTTAAG
* * * * *
79620 CACTGATCACGTTTTAGCAATTAGCAGTTTGAGTAGTTCTGATCACGTGGTCGTAATTGATGGAT
196 TACTGAGCACGTGTTAGCAATTAACAGTTTGAGTAGTTCTGATCACGTGGTAGTAATTGATGGAT
* * *
79685 TAAGTAGTTATGAGCACGTGACCATGCTTCAGCTACTATCCTTGGATTATCAGTACTTGTTAGTT
261 TAAGTAGTTATGAGCACGTGACCATGCTTGAGCTACTATCCTTGGACTATCAGTACTTGATAGTT
*
79750 GCACATGGAACTGGTTAAATGTTAGAGCATAATAACTGTTTACTGATCCGGAAAGTTCGGGATGC
326 GCTCATGGAACTGGTTAAATGTTAGAGCATAATAACTGTTTACTGATCCGGAAAGTTCGGGATGC
*
79815 ATACTTTTGTTTGTCGTGCATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGGACCGCTCAGAT
391 ATACTTTTGTTTGTCGTGCATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGCACCGCTCAGAT
*
79880 AAACTGTA-A-CACTGACGGTTGATTGATTGGTGAAACGTGTTAGTAATTATTGGAACTGGTTAA
456 AAACTGTACATCACTGACAGTTGATTGATTGGTGAAACGTGTTAGTAATTATTGGAACTGGTTAA
* **
79943 ATGTTAAAGCATTATAACTGTTTATGGATCCAGAAAGTTCGGGATGAATACTTGTTTTTGATGTC
521 ATGTTAAAGCATTATAACCGTTTACAGATCCAGAAAGTTCGGGATGAATACTTGTTTTTGATGTC
80008 CATGTGTTTCTTTCTCATTTTGTTCTTTCCAATATGCACGGCTCAGAGTACTAGTTATCTGACAG
586 CATGTGTTTCTTTCTCATTTTGTTCTTTCCAATATGCACGGCTCAGAGTACTAGTTATCTGACAG
80073 TTGATTGATTGGAGAAACGTGT
651 TTGATTGATTGGAGAAACGTGT
* *
80095 TAGTAATTATTGGACAGTAGTTATGAGCTTTGTTAATCA-TCATCGATTAAGTAGATATGACCAC
1 TAGTAATTATTGGATAGTAGTTATGAGCTTTGTTAATCATTGATCGATTAAGTAGATATGACCAC
*
80159 GTGTTACTAATCAACCGGTTCAGTAGATATGAACACGTGCTTGTAATCAACTGATTATGTAGCTC
66 GTGTTACTAATCAACCGGTTAAGTAGATATGAACACGTGCTTGTAATCAACTGATTATGTAGCTC
80224 TGAGCGCATGTTATTAAGTAACGGATTGAGTAGTTCCAAGCGCCTTTTAGACATTAACGGTTAAG
131 TGAGCGCATGTTATTAAGTAACGGATTGAGTAGTTCCAAGCGCCTTTTAGACATTAACGGTTAAG
80289 TACTGAGCACGTGTTAGCAATTAACAGTTTGAGTAGTTCTGATCACGTGGTAGTAATTGATGGAT
196 TACTGAGCACGTGTTAGCAATTAACAGTTTGAGTAGTTCTGATCACGTGGTAGTAATTGATGGAT
* * *
80354 TAAGTAATTATGAGCACGGGACCATGCTTGAGCTACCATCCTTGGACTATCAGTACTTGATAGTT
261 TAAGTAGTTATGAGCACGTGACCATGCTTGAGCTACTATCCTTGGACTATCAGTACTTGATAGTT
* *
80419 GCTCATGGAACTGGTTAAATGTTAGAGCATAATAACTGTTTACAT-ATCCAGAAAGTTCAGGATG
326 GCTCATGGAACTGGTTAAATGTTAGAGCATAATAACTGTTTAC-TGATCCGGAAAGTTCGGGATG
* *
80483 CATACTTTTGTTTCTCGTGTATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGCACCGCTCAGA
390 CATACTTTTGTTTGTCGTGCATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGCACCGCTCAGA
*
80548 TAAACTGTACTAGTTCACTGACAGTTGATTGA----TGAAACGTGTTAATAATTATT
455 TAAACTGTAC-A--TCACTGACAGTTGATTGATTGGTGAAACGTGTTAGTAATTATT
80601 AGATGTTTAG
Statistics
Matches: 1081, Mismatches: 72, Indels: 36
0.91 0.06 0.03
Matches are distributed among these distances:
662 202 0.19
665 96 0.09
666 31 0.03
667 137 0.13
668 4 0.00
669 445 0.41
670 21 0.02
671 1 0.00
672 125 0.12
674 16 0.01
676 3 0.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (672 bp):
TAGTAATTATTGGATAGTAGTTATGAGCTTTGTTAATCATTGATCGATTAAGTAGATATGACCAC
GTGTTACTAATCAACCGGTTAAGTAGATATGAACACGTGCTTGTAATCAACTGATTATGTAGCTC
TGAGCGCATGTTATTAAGTAACGGATTGAGTAGTTCCAAGCGCCTTTTAGACATTAACGGTTAAG
TACTGAGCACGTGTTAGCAATTAACAGTTTGAGTAGTTCTGATCACGTGGTAGTAATTGATGGAT
TAAGTAGTTATGAGCACGTGACCATGCTTGAGCTACTATCCTTGGACTATCAGTACTTGATAGTT
GCTCATGGAACTGGTTAAATGTTAGAGCATAATAACTGTTTACTGATCCGGAAAGTTCGGGATGC
ATACTTTTGTTTGTCGTGCATGTGTTTCTTTCTCATTTTGTTCTTTCCATATGCACCGCTCAGAT
AAACTGTACATCACTGACAGTTGATTGATTGGTGAAACGTGTTAGTAATTATTGGAACTGGTTAA
ATGTTAAAGCATTATAACCGTTTACAGATCCAGAAAGTTCGGGATGAATACTTGTTTTTGATGTC
CATGTGTTTCTTTCTCATTTTGTTCTTTCCAATATGCACGGCTCAGAGTACTAGTTATCTGACAG
TTGATTGATTGGAGAAACGTGT
Found at i:81233 original size:97 final size:98
Alignment explanation
Indices: 81049--81239 Score: 224
Period size: 97 Copynumber: 1.9 Consensus size: 98
81039 TAGTAAAAGT
* * *
81049 AAGTAGTTCTGTTTGTTCTTTGGTTTTATCTCTAGATAGTGCGAGTGATAAACACGCGCCAGTGG
1 AAGTAGTTCTGCTTGTTCTTTGGTTTTATCTCT--ATAGTGCGAGTGACAAACACGCGCCAGCGG
* ** *
81114 CCATTGAAGGCAAGATGCGTGCCTGTGAAAAGTAA
64 CCATTCAAGGCAAGACACGTGCCTATGAAAAGTAA
* * * * *
81149 AAGTAGTTTTGCTTGTTCTTTCTGTTTTATCT-T-TAGTGCGGGTGACAAACACGTGTCAGCGGC
1 AAGTAGTTCTGCTTGTTCTTT-GGTTTTATCTCTATAGTGCGAGTGACAAACACGCGCCAGCGGC
*
81212 CATTCAAGGCAAGACATGTGCCTATGAA
65 CATTCAAGGCAAGACACGTGCCTATGAA
81240 TAGGCTGAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
97 48 0.62
100 20 0.26
101 9 0.12
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (98 bp):
AAGTAGTTCTGCTTGTTCTTTGGTTTTATCTCTATAGTGCGAGTGACAAACACGCGCCAGCGGCC
ATTCAAGGCAAGACACGTGCCTATGAAAAGTAA
Found at i:100806 original size:22 final size:22
Alignment explanation
Indices: 100781--100886 Score: 99
Period size: 22 Copynumber: 4.7 Consensus size: 22
100771 CGCTTACTAA
100781 TCAGCACTTTGTGTGCTTCTGT
1 TCAGCACTTTGTGTGCTTCTGT
*
100803 TCAGCACTGTGTGTGCTTCTGT
1 TCAGCACTTTGTGTGCTTCTGT
*
100825 TTAGCA-TTGTGTGTGCTCTCTGT
1 TCAGCACTT-TGTGTGCT-TCTGT
* * * * *
100848 TTAGCACGTTTCGTG-CCCTATGA
1 TCAGCAC-TTT-GTGTGCTTCTGT
100871 TCAGCACTTTGTGTGC
1 TCAGCACTTTGTGTGC
100887 CCTCTGTTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
21 4 0.06
22 38 0.55
23 20 0.29
24 2 0.03
25 5 0.07
ACGTcount: A:0.11, C:0.23, G:0.25, T:0.42
Consensus pattern (22 bp):
TCAGCACTTTGTGTGCTTCTGT
Found at i:100850 original size:23 final size:22
Alignment explanation
Indices: 100783--100854 Score: 108
Period size: 22 Copynumber: 3.2 Consensus size: 22
100773 CTTACTAATC
* *
100783 AGCACTTTGTGTGCTTCTGTTC
1 AGCACTGTGTGTGCTTCTGTTT
100805 AGCACTGTGTGTGCTTCTGTTT
1 AGCACTGTGTGTGCTTCTGTTT
*
100827 AGCATTGTGTGTGCTCTCTGTTT
1 AGCACTGTGTGTGCT-TCTGTTT
100850 AGCAC
1 AGCAC
100855 GTTTCGTGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 34 0.76
23 11 0.24
ACGTcount: A:0.11, C:0.21, G:0.25, T:0.43
Consensus pattern (22 bp):
AGCACTGTGTGTGCTTCTGTTT
Found at i:100886 original size:23 final size:24
Alignment explanation
Indices: 100860--100914 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
100850 AGCACGTTTC
*
100860 GTGCCCTATG-ATCAGCACTTTGT
1 GTGCCCTATGTATCAGCACTTCGT
* *
100883 GTGCCCTCTGTTATTAGCACTTCGT
1 GTGCCCTATG-TATCAGCACTTCGT
100908 GTGCCCT
1 GTGCCCT
100915 CTGTTAACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 9 0.33
25 18 0.67
ACGTcount: A:0.13, C:0.29, G:0.22, T:0.36
Consensus pattern (24 bp):
GTGCCCTATGTATCAGCACTTCGT
Found at i:100904 original size:25 final size:23
Alignment explanation
Indices: 100783--100919 Score: 120
Period size: 23 Copynumber: 6.0 Consensus size: 23
100773 CTTACTAATC
* *
100783 AGCACTTTGTGTG-CTTCTGTTC
1 AGCACTTTGTGTGCCCTCTGTTT
* *
100805 AGCACTGTGTGTG-CTTCTGTTT
1 AGCACTTTGTGTGCCCTCTGTTT
*
100827 AGCA-TTGTGTGTGCTCTCTGTTT
1 AGCACTT-TGTGTGCCCTCTGTTT
* * * *
100850 AGCACGTTT-CGTGCCCTATGATC
1 AGCAC-TTTGTGTGCCCTCTGTTT
100873 AGCACTTTGTGTGCCCTCTGTTATT
1 AGCACTTTGTGTGCCCTCTG-T-TT
*
100898 AGCACTTCGTGTGCCCTCTGTT
1 AGCACTTTGTGTGCCCTCTGTT
100920 AACCAGCACT
Statistics
Matches: 93, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
21 1 0.01
22 33 0.35
23 35 0.38
24 2 0.02
25 22 0.24
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.42
Consensus pattern (23 bp):
AGCACTTTGTGTGCCCTCTGTTT
Found at i:100935 original size:25 final size:25
Alignment explanation
Indices: 100872--100946 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
100862 GCCCTATGAT
*
100872 CAGCACTTTGTGTGCCCTCTGTT-AT
1 CAGCAC-TTGTGTGCCCTCTGTTAAC
*
100897 TAGCACTTCGTGTGCCCTCTGTTAAC
1 CAGCACTT-GTGTGCCCTCTGTTAAC
* *
100923 CAGCACTTATGTGCCCTTTGTTAA
1 CAGCACTTGTGTGCCCTCTGTTAA
100947 GTACTTCGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
24 2 0.05
25 33 0.77
26 8 0.19
ACGTcount: A:0.16, C:0.28, G:0.19, T:0.37
Consensus pattern (25 bp):
CAGCACTTGTGTGCCCTCTGTTAAC
Found at i:102579 original size:8 final size:8
Alignment explanation
Indices: 102566--102644 Score: 70
Period size: 8 Copynumber: 10.9 Consensus size: 8
102556 AAAAGGCATT
102566 TTTTAATA
1 TTTTAATA
102574 TTTTAATA
1 TTTTAATA
102582 TTTTAATA
1 TTTTAATA
102590 TTTTAATA
1 TTTTAATA
102598 TTATT-AT-
1 TT-TTAATA
102605 TTTCT-AT-
1 TTT-TAATA
102612 TTTTAA-A
1 TTTTAATA
102619 -TTTAA-A
1 TTTTAATA
102625 -TTTAATA
1 TTTTAATA
102632 TTTT--TA
1 TTTTAATA
102638 TTTTAAT
1 TTTTAAT
102645 TGTCATCTGA
Statistics
Matches: 63, Mismatches: 0, Indels: 16
0.80 0.00 0.20
Matches are distributed among these distances:
6 19 0.30
7 10 0.16
8 32 0.51
9 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTTAATA
Found at i:102607 original size:14 final size:15
Alignment explanation
Indices: 102567--102644 Score: 67
Period size: 14 Copynumber: 5.4 Consensus size: 15
102557 AAAGGCATTT
102567 TTTAATATTTTAATA
1 TTTAATATTTTAATA
102582 TTTTAATATTTTAATA
1 -TTTAATATTTTAATA
* * *
102598 -TTATTATTTTCTATT
1 TTTAATATTTT-AATA
102613 TTTAA-A-TTTAA-A
1 TTTAATATTTTAATA
*
102625 TTTAATATTTTTAT-
1 TTTAATATTTTAATA
102639 TTTAAT
1 TTTAAT
102645 TGTCATCTGA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
12 5 0.10
13 2 0.04
14 22 0.44
15 3 0.06
16 18 0.36
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTAATATTTTAATA
Found at i:104992 original size:15 final size:14
Alignment explanation
Indices: 104969--105001 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
104959 AGCACCAAGC
104969 AAAAAAAGAAAAGA
1 AAAAAAAGAAAAGA
104983 AAAGAAAAGAAAA-A
1 AAA-AAAAGAAAAGA
104997 AAAAA
1 AAAAA
105002 GGAAAGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 7 0.39
15 9 0.50
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAAAGA
Found at i:110725 original size:124 final size:124
Alignment explanation
Indices: 110505--110753 Score: 498
Period size: 124 Copynumber: 2.0 Consensus size: 124
110495 GAAACAAGTG
110505 AACAATCAAATTACATAAAGAATATAAAATAAAGGTGGAGATGGAATAGATAAAATCGATGGATG
1 AACAATCAAATTACATAAAGAATATAAAATAAAGGTGGAGATGGAATAGATAAAATCGATGGATG
110570 TGTGAAATTTGGAAATATGTGCAATTGAACTTTTCGAGATAGATTTCTCAAAAAAATCA
66 TGTGAAATTTGGAAATATGTGCAATTGAACTTTTCGAGATAGATTTCTCAAAAAAATCA
110629 AACAATCAAATTACATAAAGAATATAAAATAAAGGTGGAGATGGAATAGATAAAATCGATGGATG
1 AACAATCAAATTACATAAAGAATATAAAATAAAGGTGGAGATGGAATAGATAAAATCGATGGATG
110694 TGTGAAATTTGGAAATATGTGCAATTGAACTTTTCGAGATAGATTTCTCAAAAAAATCA
66 TGTGAAATTTGGAAATATGTGCAATTGAACTTTTCGAGATAGATTTCTCAAAAAAATCA
110753 A
1 A
110754 TTATATAGCT
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 125 1.00
ACGTcount: A:0.46, C:0.08, G:0.18, T:0.27
Consensus pattern (124 bp):
AACAATCAAATTACATAAAGAATATAAAATAAAGGTGGAGATGGAATAGATAAAATCGATGGATG
TGTGAAATTTGGAAATATGTGCAATTGAACTTTTCGAGATAGATTTCTCAAAAAAATCA
Found at i:116595 original size:2 final size:2
Alignment explanation
Indices: 116588--116614 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
116578 CGATTCGGTT
116588 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 T
116615 GCAAAAGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.