Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011326.1 Kokia drynarioides strain JFW-HI SEQ_126306, 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: 70414
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 71 characters in sequence are not A, C, G, or T
Found at i:1205 original size:24 final size:26
Alignment explanation
Indices: 1169--1216 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
1159 AGAGAAATGT
1169 AAATGTGATATATGA-A-ATTATGAG
1 AAATGTGATATATGAGAGATTATGAG
1193 AAATGATGA-ATATGAGAGATTATG
1 AAATG-TGATATATGAGAGATTATG
1217 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGTGATATATGAGAGATTATGAG
Found at i:1309 original size:23 final size:23
Alignment explanation
Indices: 1279--1332 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
1269 ACGCTAGCGC
*
1279 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACCTCGTGT
1302 GCTTACTGTTTCGCACCTCGTGT
1 GCTTACTGTTTCGCACCTCGTGT
*
1325 GCCTACTG
1 GCTTACTG
1333 ATTTGCGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.09, C:0.30, G:0.22, T:0.39
Consensus pattern (23 bp):
GCTTACTGTTTCGCACCTCGTGT
Found at i:2366 original size:14 final size:14
Alignment explanation
Indices: 2343--2375 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2333 TATCACTATT
*
2343 TAAA-AATTAAAAG
1 TAAATAATTAAAAA
2356 TAAATAATTAAAAA
1 TAAATAATTAAAAA
2370 TAAATA
1 TAAATA
2376 TAATAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (14 bp):
TAAATAATTAAAAA
Found at i:10280 original size:2 final size:2
Alignment explanation
Indices: 10273--10304 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
10263 ATAAGACTTT
10273 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10305 GAAAAGGGAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16645 original size:2 final size:2
Alignment explanation
Indices: 16638--16662 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16628 ATCTCTATTT
16638 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 T
16663 GCCTGCTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18057 original size:6 final size:6
Alignment explanation
Indices: 18035--18075 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
18025 GGAGAATCCC
* *
18035 AAGAGA TAAGGGA AAGAGA AAGAGA AAGAGA AAGAAA AAGA
1 AAGAGA -AAGAGA AAGAGA AAGAGA AAGAGA AAGAGA AAGA
18076 TTAGTGGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (6 bp):
AAGAGA
Found at i:24175 original size:15 final size:16
Alignment explanation
Indices: 24151--24188 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
24141 GCTGTACGGA
*
24151 AATAATTTTTTATATT
1 AATAAATTTTTATATT
24167 -ATAAA-TTTTATATT
1 AATAAATTTTTATATT
24181 AATAAATT
1 AATAAATT
24189 ATTAGGAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
14 9 0.47
15 9 0.47
16 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATAAATTTTTATATT
Found at i:24177 original size:14 final size:15
Alignment explanation
Indices: 24158--24188 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
24148 GGAAATAATT
24158 TTTTATATT-ATAAA
1 TTTTATATTAATAAA
24172 TTTTATATTAATAAA
1 TTTTATATTAATAAA
24187 TT
1 TT
24189 ATTAGGAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTTATATTAATAAA
Found at i:27134 original size:26 final size:26
Alignment explanation
Indices: 27096--27152 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
27086 AAATAATTAC
* *
27096 AAAAATATGAAAGGTTAAAA-AAGATA
1 AAAAAAATGAAAGATTAAAAGAA-ATA
*
27122 AAAAAAATTAAAGATTAAAAGAAATA
1 AAAAAAATGAAAGATTAAAAGAAATA
27148 AAAAA
1 AAAAA
27153 TTGAACAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 25 0.93
27 2 0.07
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.18
Consensus pattern (26 bp):
AAAAAAATGAAAGATTAAAAGAAATA
Found at i:35433 original size:21 final size:22
Alignment explanation
Indices: 35399--35440 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
35389 ATTCGATTAG
**
35399 AAGGTTTGTTCAAAAA-ATAGC
1 AAGGTTTGGACAAAAATATAGC
35420 AAGGTTTGGACAAAAATATAG
1 AAGGTTTGGACAAAAATATAG
35441 GTTTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.26
Consensus pattern (22 bp):
AAGGTTTGGACAAAAATATAGC
Found at i:35798 original size:15 final size:16
Alignment explanation
Indices: 35773--35802 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35763 TGTTTTTAAG
35773 TGTATTTATATATTTA
1 TGTATTTATATATTTA
35789 TGTA-TTATATATTT
1 TGTATTTATATATTT
35803 TTTAAATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
TGTATTTATATATTTA
Found at i:36114 original size:141 final size:141
Alignment explanation
Indices: 35860--36144 Score: 498
Period size: 141 Copynumber: 2.0 Consensus size: 141
35850 GTTGGGTTAG
* * *
35860 GCTTGTGTTTGGTTTTTATAATTTGGATTGGGTTTAGACAAAATTTTCAGTTCATTTTTCAAGTT
1 GCTTGTGTTTGGTTTTTATAATTTGGATTGGGTTTAGACAAAATTTTAAGCTCATTTTTCAAGTC
* * *
35925 GGGTTGGGTTTTGGTTTAGCAATTGGGTTTAAGATTTTGTTGAAGCTTGACTTGAACTTGATTCA
66 GGGTTGGGTTTTGGTTTAGCAATTGAGCTTAAGATTTTGTTGAAGCTTGACTTGAACTCGATTCA
*
35990 AACCATGAGCA
131 AACCACGAGCA
36001 GCTTGTGTTTGGTTTTTATAATTTGGATTGGGTTTAGACAAAATTTTAAGCTCATTTTTCAAGTC
1 GCTTGTGTTTGGTTTTTATAATTTGGATTGGGTTTAGACAAAATTTTAAGCTCATTTTTCAAGTC
36066 GGGTTGGGTTTTGGTTTAGCAATTGAGCTTAAGATTTTGTTGAAGCTTGACTTGAACTCGATTCA
66 GGGTTGGGTTTTGGTTTAGCAATTGAGCTTAAGATTTTGTTGAAGCTTGACTTGAACTCGATTCA
*
36131 AACCACGATCA
131 AACCACGAGCA
36142 GCT
1 GCT
36145 CTAGTCTTAT
Statistics
Matches: 136, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
141 136 1.00
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.42
Consensus pattern (141 bp):
GCTTGTGTTTGGTTTTTATAATTTGGATTGGGTTTAGACAAAATTTTAAGCTCATTTTTCAAGTC
GGGTTGGGTTTTGGTTTAGCAATTGAGCTTAAGATTTTGTTGAAGCTTGACTTGAACTCGATTCA
AACCACGAGCA
Found at i:39383 original size:17 final size:18
Alignment explanation
Indices: 39348--39398 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
39338 CAAAATTTAA
* *
39348 ATTTTGAAATTTAAGTTT
1 ATTTTGAAAATTAAATTT
39366 ATTTT-AAAATTAAATTT
1 ATTTTGAAAATTAAATTT
* *
39383 A-TTAGAAATTTAAATT
1 ATTTTGAAAATTAAATT
39399 CAAATTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 2 0.07
17 21 0.75
18 5 0.18
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
ATTTTGAAAATTAAATTT
Found at i:40983 original size:28 final size:29
Alignment explanation
Indices: 40909--41266 Score: 112
Period size: 29 Copynumber: 12.1 Consensus size: 29
40899 CCTTGGAAGT
* * * *
40909 CCCTAAACTCTCTAGAAATCATATTTTGAC
1 CCCTAAACTTTCTAAAAATTACATTTT-AC
40939 CCC-AAACTTTCTAAAAATTACATTTTAC
1 CCCTAAACTTTCTAAAAATTACATTTTAC
* *
40967 CCCTAAACTTTC-CAAAATTACATTTTTAA
1 CCCTAAACTTTCTAAAAATTACA-TTTTAC
** *
40996 CCCTAATTTTTTTTTTCAAAAATTACCATTTTAC
1 CCCTAA---ACTTTCT-AAAAATTA-CATTTTAC
* * *
41030 CCATGAAC-TTCCAAAAATT-CTATTTTTGA-
1 CCCTAAACTTTCTAAAAATTAC-A-TTTT-AC
* * * ** *
41059 TCTTGATTTTTCCAAAAATTACCATTTTAC
1 CCCTAAACTTTCTAAAAATTA-CATTTTAC
* *
41089 CCCTAAACTTCCAAAAAATT-CATTTTTGA-
1 CCCTAAACTTTCTAAAAATTACA-TTTT-AC
* * *
41118 CCCTAAAGTTTCCAAATATTACCATTTTA-
1 CCCTAAACTTTCTAAAAATTA-CATTTTAC
* * * *
41147 CCCTCGAA-TGTCTAAAAATTTCATTTTTAA
1 CCCT-AAACTTTCTAAAAATTACA-TTTTAC
* * *
41177 CCTTAAATCCTTC-CAAAATTACCATTTTAC
1 CCCTAAA-CTTTCTAAAAATTA-CATTTTAC
* * * * * *
41207 CCTTGAA-TATCTAAAAATTCCGCTTTTAA
1 CCCTAAACTTTCTAAAAATTAC-ATTTTAC
41236 CCC-AAACATTTC-AAAAATTACCATTTTAC
1 CCCTAAAC-TTTCTAAAAATTA-CATTTTAC
41265 CC
1 CC
41267 ACGAATGTTT
Statistics
Matches: 241, Mismatches: 57, Indels: 61
0.67 0.16 0.17
Matches are distributed among these distances:
27 1 0.00
28 24 0.10
29 122 0.51
30 65 0.27
31 7 0.03
32 4 0.02
34 16 0.07
35 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTTCTAAAAATTACATTTTAC
Found at i:41098 original size:59 final size:58
Alignment explanation
Indices: 40946--41208 Score: 212
Period size: 59 Copynumber: 4.4 Consensus size: 58
40936 GACCCCAAAC
* * * *
40946 TTTCTAAAAATTA-CATTTTACCCCTAAACTTTCC-AAAATTACATTTTTAACCCTAATTTTTT
1 TTTCCAAAAATTACCATTTTACCCCTAAAC-TTCCAAAAATT-CATTTTTGATCTTAA----TT
* * * *
41008 TTTTCAAAAATTACCATTTTACCCATGAACTTCCAAAAATTCTATTTTTGATCTTGATT
1 TTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTC-ATTTTTGATCTTAATT
* * **
41067 TTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAAATTCATTTTTGACCCTAAAG
1 TTTCCAAAAATTACCATTTTACCCCTAAACTTCC-AAAAATTCATTTTTGATCTTAATT
* * * * * *
41126 TTTCCAAATATTACCATTTTA-CCCTCGAA-TGTCTAAAAATTTCATTTTTAACCTTAAATC
1 TTTCCAAAAATTACCATTTTACCCCT-AAACT-TCCAAAAA-TTCATTTTTGATCTT-AATT
*
41186 CTTCC-AAAATTACCATTTTACCC
1 TTTCCAAAAATTACCATTTTACCC
41209 TTGAATATCT
Statistics
Matches: 167, Mismatches: 25, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
58 10 0.06
59 95 0.57
60 16 0.10
62 16 0.10
63 30 0.18
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.41
Consensus pattern (58 bp):
TTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATTCATTTTTGATCTTAATT
Found at i:41209 original size:59 final size:57
Alignment explanation
Indices: 41068--41338 Score: 244
Period size: 59 Copynumber: 4.6 Consensus size: 57
41058 ATCTTGATTT
* * * * **
41068 TTCCAAAAATTACCATTTTACCCCTAAACT-TCCAAAAAATTCATTTTTGACC-CTAAAGT
1 TTCC-AAAATTACCATTTTACCCC-GAA-TGTCTAAAAATTTCATTTTTAACCTC-AAACC
*
41127 TTCCAAATATTACCATTTTACCCTCGAATGTCTAAAAATTTCATTTTTAACCTTAAATCC
1 TTCCAAA-ATTACCATTTTACCC-CGAATGTCTAAAAATTTCATTTTTAACCTCAAA-CC
* * * ** *
41187 TTCCAAAATTACCATTTTACCCTTGAATATCTAAAAATTCCGCTTTTAACC-CAAACAT
1 TTCCAAAATTACCATTTTACCC-CGAATGTCTAAAAATTTCATTTTTAACCTCAAAC-C
* * *
41245 TTCAAAAATTACCATTTTACCCACGAATGTTTAAAAA-TTCTATTTTTAACCTCGAACC
1 TTCCAAAATTACCATTTTACCC-CGAATGTCTAAAAATTTC-ATTTTTAACCTCAAACC
* *
41303 TTCCAAAATTACCATTTTGTCCCCGAATGTCCAAAA
1 TTCCAAAATTACCATTTT-ACCCCGAATGTCTAAAA
41339 TTACCGTTTT
Statistics
Matches: 175, Mismatches: 28, Indels: 19
0.79 0.13 0.09
Matches are distributed among these distances:
57 3 0.02
58 75 0.43
59 89 0.51
60 8 0.05
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (57 bp):
TTCCAAAATTACCATTTTACCCCGAATGTCTAAAAATTTCATTTTTAACCTCAAACC
Found at i:41280 original size:29 final size:29
Alignment explanation
Indices: 41245--41352 Score: 87
Period size: 29 Copynumber: 3.8 Consensus size: 29
41235 ACCCAAACAT
41245 TTCAAAAATTACCATTTTACCCACGAATG
1 TTCAAAAATTACCATTTTACCCACGAATG
* * * * **
41274 TTTAAAAATT-CTATTTTTAACCTCGAACC
1 TTCAAAAATTACCA-TTTTACCCACGAATG
* *
41303 TTCCAAAATTACCATTTTGTCCC-CGAATG
1 TTCAAAAATTACCATTTT-ACCCACGAATG
* *
41332 -TCCAAAATTACCGTTTTACCC
1 TTCAAAAATTACCATTTTACCC
41353 CCGGGCATCC
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
27 3 0.05
28 18 0.30
29 36 0.59
30 4 0.07
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.35
Consensus pattern (29 bp):
TTCAAAAATTACCATTTTACCCACGAATG
Found at i:41280 original size:58 final size:58
Alignment explanation
Indices: 41010--41338 Score: 233
Period size: 59 Copynumber: 5.6 Consensus size: 58
41000 AATTTTTTTT
* * * * ** ***
41010 TTCAAAAATTACCATTTTACCCAT-GAACT-TCCAAAAATTCTATTTTTGATCTTGATTT
1 TTCAAAAATTACCATTTTACCC-TCGAA-TGTCTAAAAATTCCATTTTTAACCTCAAACC
* * * **
41068 TTCCAAAAATTACCATTTTACCC-CTAAACT-TCCAAAAAATT-CATTTTTGACC-CTAAAGT
1 TT-CAAAAATTACCATTTTACCCTC-GAA-TGT-CTAAAAATTCCATTTTTAACCTC-AAACC
* * *
41127 TTCCAAATATTACCATTTTACCCTCGAATGTCTAAAAATTTCATTTTTAACCTTAAATCC
1 TT-CAAAAATTACCATTTTACCCTCGAATGTCTAAAAATTCCATTTTTAACCTCAAA-CC
* * * ** *
41187 TTCCAAAATTACCATTTTACCCTTGAATATCTAAAAATTCCGCTTTTAACC-CAAACAT
1 TTCAAAAATTACCATTTTACCCTCGAATGTCTAAAAATTCCATTTTTAACCTCAAAC-C
* * * *
41245 TTCAAAAATTACCATTTTACCCACGAATGTTTAAAAATTCTATTTTTAACCTCGAACC
1 TTCAAAAATTACCATTTTACCCTCGAATGTCTAAAAATTCCATTTTTAACCTCAAACC
* * *
41303 TTCCAAAATTACCATTTTGTCCC-CGAATGTCCAAAA
1 TTCAAAAATTACCATTTT-ACCCTCGAATGTCTAAAA
41339 TTACCGTTTT
Statistics
Matches: 220, Mismatches: 38, Indels: 26
0.77 0.13 0.09
Matches are distributed among these distances:
57 1 0.00
58 85 0.39
59 123 0.56
60 11 0.05
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.37
Consensus pattern (58 bp):
TTCAAAAATTACCATTTTACCCTCGAATGTCTAAAAATTCCATTTTTAACCTCAAACC
Found at i:41784 original size:23 final size:23
Alignment explanation
Indices: 41754--41800 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
41744 TCGAAGTAAA
41754 TGGGCATTCTATCTTCAAATCCT
1 TGGGCATTCTATCTTCAAATCCT
*
41777 TGGGCATTCTATCTTTAAATCCT
1 TGGGCATTCTATCTTCAAATCCT
41800 T
1 T
41801 CAAGTCATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (23 bp):
TGGGCATTCTATCTTCAAATCCT
Found at i:42532 original size:82 final size:82
Alignment explanation
Indices: 42425--42670 Score: 330
Period size: 94 Copynumber: 2.9 Consensus size: 82
42415 GGTTTCGACA
* *
42425 CGTATCATAAAATATAAAAAGAAACTAATGTGTAATAATTTATAAATATATAAAACAACATATAA
1 CGTATCATAAAATATAACAAGAAACTAATGTGTAATAATTTATAAATATATAAAGCAACATATAA
42490 CTAACCTTTTGTACACT
66 CTAACCTTTTGTACACT
42507 CGTATCATAAAATATAACAAGAAACTAATGTATAAGCTAATGTGTAATAATTTATAAATATATAA
1 CGTATCATAAAATAT-------AAC-AA-G-A-AA-CTAATGTGTAATAATTTATAAATATATAA
*
42572 AGCAACATACAACTAACCTTTTGTACACT
54 AGCAACATATAACTAACCTTTTGTACACT
* * *
42601 AGCATGATAAAATATAACAAGAAACTAATGTGTAATAATTTATAAATATATAAAGCAACATATAA
1 CGTATCATAAAATATAACAAGAAACTAATGTGTAATAATTTATAAATATATAAAGCAACATATAA
42666 CTAAC
66 CTAAC
42671 ATATAAACTG
Statistics
Matches: 145, Mismatches: 7, Indels: 24
0.82 0.04 0.14
Matches are distributed among these distances:
82 60 0.41
83 2 0.01
84 1 0.01
85 1 0.01
86 2 0.01
87 3 0.02
89 2 0.01
90 2 0.01
91 1 0.01
92 1 0.01
93 2 0.01
94 68 0.47
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (82 bp):
CGTATCATAAAATATAACAAGAAACTAATGTGTAATAATTTATAAATATATAAAGCAACATATAA
CTAACCTTTTGTACACT
Found at i:43540 original size:31 final size:31
Alignment explanation
Indices: 43502--43566 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
43492 GTTTGAAATA
43502 TTACGTTTTAGCCACTTATGTTAGTATTTTG
1 TTACGTTTTAGCCACTTATGTTAGTATTTTG
*
43533 TTACGTTTTAGTCACTTATGTTAGTATTTTG
1 TTACGTTTTAGCCACTTATGTTAGTATTTTG
43564 TTA
1 TTA
43567 ATATTCGGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.20, C:0.11, G:0.15, T:0.54
Consensus pattern (31 bp):
TTACGTTTTAGCCACTTATGTTAGTATTTTG
Found at i:43642 original size:14 final size:14
Alignment explanation
Indices: 43625--43655 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43615 AAGGTTAAAA
43625 AAATTTAATTAATT
1 AAATTTAATTAATT
*
43639 AAATTTATTTAATT
1 AAATTTAATTAATT
43653 AAA
1 AAA
43656 GATTTATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:44436 original size:16 final size:16
Alignment explanation
Indices: 44412--44442 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44402 CTAGTAATTT
*
44412 AAGGCACAAAATTTCG
1 AAGGAACAAAATTTCG
44428 AAGGAACAAAATTTC
1 AAGGAACAAAATTTC
44443 AAAACCCGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.19
Consensus pattern (16 bp):
AAGGAACAAAATTTCG
Found at i:44870 original size:58 final size:59
Alignment explanation
Indices: 44712--44933 Score: 215
Period size: 58 Copynumber: 3.8 Consensus size: 59
44702 CTCGGGGGCA
* * * * * * *
44712 AAAATGGTAATTTTAGA-AAATTTTAAGGATTAAAATAGAA-TTTTAGACA-TCCGAGGGT
1 AAAATGGTAATTTTTGAGAAGTTTT-GGGATCAAAATGGAATTTTTGGACATTCAG-GGGT
* *** *
44770 AAAAAGGTAATTTTT-AGAAAAATTGGGATAAAAAATGGAATTTTTGGACATTCAGGGGT
1 AAAATGGTAATTTTTGAGAAGTTTTGGGAT-CAAAATGGAATTTTTGGACATTCAGGGGT
* **
44829 AAAATGGTAATTTTTGAG-AGTTTTGGGATCAAAATGAAATTTTTGGATGTTCAGGGGT
1 AAAATGGTAATTTTTGAGAAGTTTTGGGATCAAAATGGAATTTTTGGACATTCAGGGGT
*
44887 AAAAAT-GTAATTTTTG-GAAGTTTTGGGGTCAAAATGGAATTTTTGGA
1 -AAAATGGTAATTTTTGAGAAGTTTTGGGATCAAAATGGAATTTTTGGA
44934 GGTTTGGGGG
Statistics
Matches: 138, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
57 6 0.04
58 88 0.64
59 39 0.28
60 5 0.04
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.35
Consensus pattern (59 bp):
AAAATGGTAATTTTTGAGAAGTTTTGGGATCAAAATGGAATTTTTGGACATTCAGGGGT
Found at i:44944 original size:58 final size:58
Alignment explanation
Indices: 44766--45078 Score: 254
Period size: 58 Copynumber: 5.3 Consensus size: 58
44756 AGACATCCGA
* ** * * ** *
44766 GGGTAAAAAGGTAATTTTTAGAAAAATT-GGGATAAAAAATGGAATTTTTGGACATTCAG
1 GGGTAAAAATGTAATTTTT-GAAAGTTTCGGGGT-CAAAATGGAATTTTTGGAGGTTCGG
* * * * * *
44825 GGGT-AAAATGGTAATTTTTGAGAGTTTTGGGATCAAAATGAAATTTTTGGATGTTCAG
1 GGGTAAAAAT-GTAATTTTTGAAAGTTTCGGGGTCAAAATGGAATTTTTGGAGGTTCGG
* * *
44883 GGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAATGGAATTTTTGGAGGTTTGG
1 GGGTAAAAATGTAATTTTTGAAAGTTTCGGGGTCAAAATGGAATTTTTGGAGGTTCGG
* ** ** * * * *
44941 GGGTAAATATGTAATTTTCAAAAGTTTCAAGGTCATAAATGAAATTTTTTGAAGTTCGA
1 GGGTAAAAATGTAATTTTTGAAAGTTTCGGGGTCA-AAATGGAATTTTTGGAGGTTCGG
* * *
45000 GGGTAAAAATATAATTTTTGAAAGTTTCGGGGTTAAAAATGGAA-TTTTGGAGAAGTTTGG
1 GGGTAAAAATGTAATTTTTGAAAGTTTCGGGG-TCAAAATGGAATTTTTGGAG--GTTCGG
* *
45060 GGATCAAAAATGGAATTTT
1 GGGT-AAAAATGTAATTTT
45079 GGACGTTCGA
Statistics
Matches: 204, Mismatches: 42, Indels: 14
0.78 0.16 0.05
Matches are distributed among these distances:
58 109 0.53
59 74 0.36
60 9 0.04
61 12 0.06
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGAAAGTTTCGGGGTCAAAATGGAATTTTTGGAGGTTCGG
Found at i:45039 original size:30 final size:29
Alignment explanation
Indices: 44766--45115 Score: 182
Period size: 29 Copynumber: 12.0 Consensus size: 29
44756 AGACATCCGA
* **
44766 GGGTAAAAAGGTAATTTTTAGAAAAATT-G
1 GGGTAAAAATGTAATTTTT-GAAAGTTTCG
* * *
44795 GGATAAAAAATGGAATTTTTGGACA--TTCAG
1 GGGT-AAAAATGTAATTTTT-GAAAGTTTC-G
* *
44825 GGGT-AAAATGGTAATTTTTGAGAGTTTTG
1 GGGTAAAAAT-GTAATTTTTGAAAGTTTCG
* * * * *
44854 GGATCAAAATGAAATTTTTGGATG-TTCAG
1 GGGTAAAAATGTAATTTTTGAAAGTTTC-G
* *
44883 GGGTAAAAATGTAATTTTTGGAAGTTTTG
1 GGGTAAAAATGTAATTTTTGAAAGTTTCG
* * * * *
44912 GGGTCAAAATGGAATTTTTGGAGGTTTGG
1 GGGTAAAAATGTAATTTTTGAAAGTTTCG
* ** *
44941 GGGTAAATATGTAATTTTCAAAAGTTTCA
1 GGGTAAAAATGTAATTTTTGAAAGTTTCG
* * *
44970 AGGTCATAAATGAAATTTTTTG-AAG-TTCG
1 GGGT-AAAAATGTAA-TTTTTGAAAGTTTCG
*
44999 AGGGTAAAAATATAATTTTTGAAAGTTTCG
1 -GGGTAAAAATGTAATTTTTGAAAGTTTCG
* *
45029 GGGTTAAAAATGGAATTTTGGAGAAGTTT-G
1 GGG-TAAAAATGTAATTTTTGA-AAGTTTCG
* * *
45059 GGGATCAAAAATGGAA-TTTTGGACG-TTCG
1 GGG-T-AAAAATGTAATTTTTGAAAGTTTCG
* *
45088 AGGGT-AAAATGTGATTTTTGGAAGTTTC
1 -GGGTAAAAATGTAATTTTTGAAAGTTTC
45116 AGGAACAAAA
Statistics
Matches: 246, Mismatches: 54, Indels: 42
0.72 0.16 0.12
Matches are distributed among these distances:
27 7 0.03
28 28 0.11
29 118 0.48
30 73 0.30
31 20 0.08
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGAAAGTTTCG
Found at i:45098 original size:117 final size:116
Alignment explanation
Indices: 44857--45078 Score: 295
Period size: 117 Copynumber: 1.9 Consensus size: 116
44847 AGTTTTGGGA
* * * * *
44857 TCAAAATGAAATTTTTGGATGTTCAGGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAT
1 TCAAAATGAAATTTTTGGAAGTTCAGGGGTAAAAATATAATTTTTGAAAGTTTCGGGGTAAAAAT
* * *
44922 GGAATTTTTGGAGGTTTGGGGGTAAATATGTAATTTTCAAAAGTTTCAAGG
66 GGAATTTTTGGAGGTTTGGGGATAAAAATGGAATTTTCAAAAGTTTCAAGG
*
44973 TCATAAATGAAATTTTTTGAAGTTC-GAGGGTAAAAATATAATTTTTGAAAGTTTCGGGGTTAAA
1 TCA-AAATGAAATTTTTGGAAGTTCAG-GGGTAAAAATATAATTTTTGAAAGTTTCGGGG-TAAA
45037 AATGGAA-TTTTGGAGAAGTTTGGGGATCAAAAATGGAATTTT
63 AATGGAATTTTTGGAG--GTTTGGGGAT-AAAAATGGAATTTT
45079 GGACGTTCGA
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
116 4 0.04
117 56 0.62
118 10 0.11
119 9 0.10
120 12 0.13
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.36
Consensus pattern (116 bp):
TCAAAATGAAATTTTTGGAAGTTCAGGGGTAAAAATATAATTTTTGAAAGTTTCGGGGTAAAAAT
GGAATTTTTGGAGGTTTGGGGATAAAAATGGAATTTTCAAAAGTTTCAAGG
Found at i:45134 original size:28 final size:29
Alignment explanation
Indices: 45035--45144 Score: 84
Period size: 28 Copynumber: 3.8 Consensus size: 29
45025 TTCGGGGTTA
** *
45035 AAAATGGAATTTTGGAGAAGTTTGGGGATC
1 AAAATGGAATTTT-GAGAAGTTTCAGGAAC
* **
45065 AAAAATGGAATTTTG-GACG-TTCGAGG-GT
1 -AAAATGGAATTTTGAGAAGTTTC-AGGAAC
*
45093 AAAATGTGATTTTTG-GAAGTTTCAGGAAC
1 AAAATG-GAATTTTGAGAAGTTTCAGGAAC
45122 AAAATGGAATTTTGAAGAAGTTT
1 AAAATGGAATTTTG-AGAAGTTT
45145 AAGGGTCAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
27 6 0.10
28 22 0.35
29 14 0.22
30 8 0.13
31 13 0.21
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (29 bp):
AAAATGGAATTTTGAGAAGTTTCAGGAAC
Found at i:45155 original size:30 final size:27
Alignment explanation
Indices: 44801--45156 Score: 135
Period size: 29 Copynumber: 12.2 Consensus size: 27
44791 ATTGGGATAA
*
44801 AAAATGGAATTTTTGGACA-TTCAGGGGT-
1 AAAATGGAA-TTTTGGA-AGTTTA-GGGTC
* *
44829 AAAATGGTAATTTTTGAGAGTTTTGGGATC
1 AAAATGG-AATTTTGGA-AGTTTAGGG-TC
* * * *
44859 AAAATGAAATTTTTGGATGTTCAGGGGTA
1 AAAATGGAA-TTTTGGAAGTTTA-GGGTC
* *
44888 AAAATGTAATTTTTGGAAGTTTTGGGGTC
1 AAAATGGAA-TTTTGGAAG-TTTAGGGTC
* *
44917 AAAATGGAATTTTTGGAGGTTTGGGGGT-
1 AAAATGGAA-TTTTGGAAGTTT-AGGGTC
* ** *
44945 AAATATGTAATTTTCAAAAGTTTCAAGGTC
1 AAA-ATGGAATTTT-GGAAGTTT-AGGGTC
* * * *
44975 ATAAATGAAATTTTTTGAAGTTCGAGGGTA
1 A-AAATGGAA-TTTTGGAAGTT-TAGGGTC
** * * *
45005 AAAATATAATTTTTGAAAGTTTCGGGGTTA
1 AAAATGGAA-TTTTGGAAGTTT-AGGG-TC
*
45035 AAAATGGAATTTTGGAGAAGTTTGGGGATC
1 AAAATGGAATTTT-G-GAAGTTTAGGG-TC
* *
45065 AAAAATGGAATTTTGGACGTTCGAGGGT-
1 -AAAATGGAATTTTGGAAGTT-TAGGGTC
* **
45093 AAAATGTGATTTTTGGAAGTTTCAGGAAC
1 AAAATG-GAATTTTGGAAGTTT-AGGGTC
45122 AAAATGGAATTTTGAAGAAGTTTAAGGGTC
1 AAAATGGAATTTTG--GAAGTTT-AGGGTC
45152 AAAAT
1 AAAAT
45157 ATAATTTTTG
Statistics
Matches: 250, Mismatches: 53, Indels: 48
0.71 0.15 0.14
Matches are distributed among these distances:
27 6 0.02
28 49 0.20
29 102 0.41
30 68 0.27
31 25 0.10
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.35
Consensus pattern (27 bp):
AAAATGGAATTTTGGAAGTTTAGGGTC
Found at i:45719 original size:16 final size:16
Alignment explanation
Indices: 45686--45721 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
45676 TATTTTTTAC
**
45686 TTTTTTTTTCAATTCT
1 TTTTTTTTTCAAAACT
45702 TTTTTTTTTCAAAACT
1 TTTTTTTTTCAAAACT
45718 TTTT
1 TTTT
45722 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTTTTCAAAACT
Found at i:54424 original size:19 final size:19
Alignment explanation
Indices: 54400--54441 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
54390 TTATTCTTTT
*
54400 AAATATTTATAATTGA-GTC
1 AAATATATATAA-TGATGTC
54419 AAATATATATAATGATGTC
1 AAATATATATAATGATGTC
54438 AAAT
1 AAAT
54442 TAAAATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.38
Consensus pattern (19 bp):
AAATATATATAATGATGTC
Found at i:56131 original size:6 final size:6
Alignment explanation
Indices: 56120--56144 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
56110 GCTACTCATC
56120 ACCAAA ACCAAA ACCAAA ACCAAA A
1 ACCAAA ACCAAA ACCAAA ACCAAA A
56145 TAGGGAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCAAA
Found at i:63533 original size:27 final size:27
Alignment explanation
Indices: 63490--63542 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
63480 CGCTAAAATG
63490 AAAAGAAATATCAGTAGCAAAATATAGA
1 AAAAGAAATAT-AGTAGCAAAATATAGA
* *
63518 AAAAGAAA-ATATGTAGTAATATATA
1 AAAAGAAATATA-GTAGCAAAATATA
63543 CCTGTGACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 1 0.05
27 13 0.59
28 8 0.36
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.23
Consensus pattern (27 bp):
AAAAGAAATATAGTAGCAAAATATAGA
Found at i:67807 original size:20 final size:21
Alignment explanation
Indices: 67765--67806 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
67755 AAAATTATTC
*
67765 AATAA-TTTTATTATTTGAAA
1 AATAATTTTTATAATTTGAAA
*
67785 AATAATTTTTATAATTTTAAA
1 AATAATTTTTATAATTTGAAA
67806 A
1 A
67807 TCATTTGCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
AATAATTTTTATAATTTGAAA
Done.