Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011252.1 Kokia drynarioides strain JFW-HI SEQ_126230, 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: 407021
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 61 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:329022 original size:59 final size:60
Alignment explanation
Indices: 328852--329201 Score: 276
Period size: 60 Copynumber: 5.9 Consensus size: 60
328842 CCCTAAATTG
** * * * *
328852 TCCAAAAATTACATTTTTACCC-CCAAAGTTTCC-AAAATTCCATCTTTGACCTCGATTTTT
1 TCCAAAAATTACA-TTTTACCCTCTGAA-CTTCCAAAAATTCCATTTTTAACCCCGATTTTT
* * * *
328912 TCCAAAAATTACAATTTT-CCCTCAT-AACTTCTAAGAATTTCATCTTTAACCCCGATTTTT
1 TCCAAAAATTAC-ATTTTACCCTC-TGAACTTCCAAAAATTCCATTTTTAACCCCGATTTTT
* * * *
328972 TCAAAAAAATATCATTTTACCCTC-GAACTTCCAAAAATTCCA-TTTTAA-CCCTAATTTT
1 TCCAAAAATTA-CATTTTACCCTCTGAACTTCCAAAAATTCCATTTTTAACCCCGATTTTT
* * * * **
329030 TCCAAAAAGTTACGATTTTA-CCTCCTAAACTTCCAAAAATTCCATTTTTGA-CTCAAAATTT
1 TCCAAAAA-TTAC-ATTTTACCCT-CTGAACTTCCAAAAATTCCATTTTTAACCCCGATTTTT
** * *
329091 TCCAAAAATTACCATTTTACCC-CTGAACTTTAAAAAAATCCATTTTTAACCCCGA-TTCT
1 TCCAAAAATTA-CATTTTACCCTCTGAACTTCCAAAAATTCCATTTTTAACCCCGATTTTT
* *
329150 TCCAAAAATTAACATTTTACCC-CT-AAATGTCTAAAAATTCCATTTTTAACCC
1 TCCAAAAATT-ACATTTTACCCTCTGAACT-TCCAAAAATTCCATTTTTAACCC
329202 TAAACTTTCT
Statistics
Matches: 238, Mismatches: 35, Indels: 35
0.77 0.11 0.11
Matches are distributed among these distances:
58 22 0.09
59 86 0.36
60 100 0.42
61 30 0.13
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (60 bp):
TCCAAAAATTACATTTTACCCTCTGAACTTCCAAAAATTCCATTTTTAACCCCGATTTTT
Found at i:329217 original size:59 final size:58
Alignment explanation
Indices: 328842--329226 Score: 248
Period size: 59 Copynumber: 6.5 Consensus size: 58
328832 CCCTAAAGGT
* * * * *
328842 CCCTAAATTGTCCAAAAATT-ACATTTTTACCCCCAAAGTT-TCCAAAATTCCATCTTTGA
1 CCCTAAATTTTCCAAAAATTAACA-TTTTACCCCTAAA-TTCT-AAAAATTCCATTTTTAA
* ** * * * *
328901 CCTCGATTTTTTCCAAAAATT-ACAATTTT-CCCTCATAACTTCTAAGAATTTCATCTTTAA
1 CC-CTAAATTTTCCAAAAATTAAC-ATTTTACCC-C-TAAATTCTAAAAATTCCATTTTTAA
* ** * * * * * *
328961 CCCCGATTTTTTCAAAAAAATATCATTTTACCCTCGAACTTCCAAAAATTCCA-TTTTAA
1 -CCCTAAATTTTCCAAAAATTAACATTTTACCC-CTAAATTCTAAAAATTCCATTTTTAA
* * *
329020 CCCTAATTTTTCCAAAAAGTT-ACGATTTTACCTCCTAAACTTCCAAAAATTCCATTTTTGA
1 CCCTAAATTTTCCAAAAA-TTAAC-ATTTTACC-CCTAAA-TTCTAAAAATTCCATTTTTAA
* * * * *
329081 CTCAAAATTTTCCAAAAATTACCATTTTACCCCTGAACTT-TAAAAAAATCCATTTTTAA
1 CCCTAAATTTTCCAAAAATTAACATTTTACCCCT-AAATTCT-AAAAATTCCATTTTTAA
**
329140 CCC-CGATTCTTCCAAAAATTAACATTTTACCCCTAAATGTCTAAAAATTCCATTTTTAA
1 CCCTAAATT-TTCCAAAAATTAACATTTTACCCCTAAAT-TCTAAAAATTCCATTTTTAA
* *
329199 CCCTAAACTTTCTC-AAAATTATCATTTT
1 CCCTAAATTTTC-CAAAAATTAACATTTT
329227 GCTCCCCGAG
Statistics
Matches: 261, Mismatches: 44, Indels: 42
0.75 0.13 0.12
Matches are distributed among these distances:
58 22 0.08
59 104 0.40
60 102 0.39
61 33 0.13
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (58 bp):
CCCTAAATTTTCCAAAAATTAACATTTTACCCCTAAATTCTAAAAATTCCATTTTTAA
Found at i:329634 original size:98 final size:98
Alignment explanation
Indices: 329488--329674 Score: 245
Period size: 98 Copynumber: 1.9 Consensus size: 98
329478 ATAAAAAACT
* * * *
329488 TTAAAATTAAGGCAATATTCTTTTATTTTGAGTTTTAAAAATTTGTGCCTTAACTTACTAAGCGC
1 TTAAAATCAAGGCAATATTCTTTTATTTTGAGTTCTAAAAATTGGTGCCTTAACTTAATAAGCGC
*
329553 GATTTTTCTTCAAATCGAA-ATAATCGAATACCC
66 GACTTTTCTTCAAATC-AAGATAATCGAATACCC
* * *
329586 TTAAAATCGAGGCAATATT-TCTTTATCTTTGA-TTCTAAAAATTGGTGCCTTAACTTAATAGGT
1 TTAAAATCAAGGCAATATTCT-TTTAT-TTTGAGTTCTAAAAATTGGTGCCTTAACTTAATAAGC
*
329649 GTGACTTTTCTTCAAATCAAGATAAT
64 GCGACTTTTCTTCAAATCAAGATAAT
329675 TGAACATCCT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
97 3 0.04
98 69 0.90
99 5 0.06
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (98 bp):
TTAAAATCAAGGCAATATTCTTTTATTTTGAGTTCTAAAAATTGGTGCCTTAACTTAATAAGCGC
GACTTTTCTTCAAATCAAGATAATCGAATACCC
Found at i:333787 original size:40 final size:40
Alignment explanation
Indices: 333743--333823 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
333733 CAAAGTGGTA
333743 CAATCAGTTATG-TCGTGCAAAGATCAGTTCATTGAAGGAC
1 CAATCAGTTATGCT-GTGCAAAGATCAGTTCATTGAAGGAC
333783 CAATCAGTTATGCTGTGCAAAGATCAGTTCATTGAAGGAC
1 CAATCAGTTATGCTGTGCAAAGATCAGTTCATTGAAGGAC
333823 C
1 C
333824 TGGCCTAGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 39 0.98
41 1 0.03
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (40 bp):
CAATCAGTTATGCTGTGCAAAGATCAGTTCATTGAAGGAC
Found at i:340994 original size:49 final size:48
Alignment explanation
Indices: 340898--341467 Score: 390
Period size: 49 Copynumber: 11.7 Consensus size: 48
340888 CGTGAAACAC
* * * * *
340898 GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTATTACCTCAGAGACAT
1 GAAGGGAAAGATTTAAGTCGCAATGGCAAACCCAGTACCAC-GAGACAT
** * * * * * *
340947 GAAGAAAAAGATTTAAGCCGCAACGGCGAATCTAGTACCAGGAAGACA-
1 GAAGGGAAAGATTTAAGTCGCAATGGCAAACCCAGTACCACG-AGACAT
* * * * * * * *
340995 CACGAGAAAGGTCTAAGTCGCAATGGCAAACCTAGTACCTCAGAGACAC
1 GAAGGGAAAGATTTAAGTCGCAATGGCAAACCCAGTACCAC-GAGACAT
* * * *
341044 GAAGGGAAAGGTTTAAGTCACAATGGCAAACCTAGTACCTCAGAGACAT
1 GAAGGGAAAGATTTAAGTCGCAATGGCAAACCCAGTACCAC-GAGACAT
* * * *
341093 GAAGGGAAAGATTTAAGCCGTAATGGCAAATCCAATACCACGAAGACA-
1 GAAGGGAAAGATTTAAGTCGCAATGGCAAACCCAGTACCACG-AGACAT
* * * * * * *
341141 CACGGGAAAGGTTTAAGTCGCAATGGCAAACCTAATACCTCAGAGACAC
1 GAAGGGAAAGATTTAAGTCGCAATGGCAAACCCAGTACCAC-GAGACAT
* * ** * *
341190 AAAGGGAAAGGTTTAAGTCGCAATGGTGAACCTAGTACCTCTGAGACAT
1 GAAGGGAAAGATTTAAGTCGCAATGGCAAACCCAGTACCAC-GAGACAT
** * *
341239 GAAGGGAAAAGATTTAAAGTCATAATGGCGAATCCAGTACCACGAAGACAT
1 GAAGGG-AAAGATTT-AAGTCGCAATGGCAAACCCAGTACCACG-AGACAT
* * * * ** * * *
341290 GAAGGGAAAGATCTAAGCCACAACGGCGGATCCAATACCACGAAGACAC
1 GAAGGGAAAGATTTAAGTCGCAATGGCAAACCCAGTACCACG-AGACAT
* * * * *
341339 GAAGGGAAAGGTTTAAGTCGTAACGGCAAACCCAGTACCTCGGAGACAG
1 GAAGGGAAAGATTTAAGTCGCAATGGCAAACCCAGTACCAC-GAGACAT
* * * * *
341388 GAAGGGAAAGATTTAAGCCACAATGACGAATCCAGTACCACGAAGACA-
1 GAAGGGAAAGATTTAAGTCGCAATGGCAAACCCAGTACCACG-AGACAT
* * *
341436 CAAGGGAAAGGTTTAATTCGCAATGGCAAACC
1 GAAGGGAAAGATTTAAGTCGCAATGGCAAACC
341468 TTATACCTCA
Statistics
Matches: 418, Mismatches: 92, Indels: 23
0.78 0.17 0.04
Matches are distributed among these distances:
48 100 0.24
49 269 0.64
50 16 0.04
51 33 0.08
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (48 bp):
GAAGGGAAAGATTTAAGTCGCAATGGCAAACCCAGTACCACGAGACAT
Found at i:341079 original size:97 final size:95
Alignment explanation
Indices: 340898--341506 Score: 435
Period size: 97 Copynumber: 6.2 Consensus size: 95
340888 CGTGAAACAC
* * * * * * ** *
340898 GAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTATTACCTC-AGAGACATGAAGAAAAAGATTTA
1 GAAGGGAAAGATTTAAGCCGCAATGGCAAACC-AGTACCACGA-AGACACGAAGGGAAAGGTTTA
* * * *
340962 AGCCGCAACGGCGAATCTAGTACCAGGAAGACA-
64 AGTCGCAATGGCAAACCTAGTACCA-G-AGACAT
* * * * * * *
340995 CACGAGAAAGGTCTAAGTCGCAATGGCAAACCTAGTACCTC-AGAGACACGAAGGGAAAGGTTTA
1 GAAGGGAAAGATTTAAGCCGCAATGGCAAACC-AGTACCACGA-AGACACGAAGGGAAAGGTTTA
*
341059 AGTCACAATGGCAAACCTAGTACCTCAGAGACAT
64 AGTCGCAATGGCAAACCTAGTA-C-CAGAGACAT
* * *
341093 GAAGGGAAAGATTTAAGCCGTAATGGCAAATCCAATACCACGAAGACAC-ACGGGAAAGGTTTAA
1 GAAGGGAAAGATTTAAGCCGCAATGGCAAA-CCAGTACCACGAAGACACGAAGGGAAAGGTTTAA
* *
341157 GTCGCAATGGCAAACCTAATACCTCAGAGACAC
65 GTCGCAATGGCAAACCTAGTA-C-CAGAGACAT
* * * ** * * *
341190 AAAGGGAAAGGTTTAAGTCGCAATGGTGAACCTAGTACCTCTG-AGACATGAAGGGAAAAGATTT
1 GAAGGGAAAGATTTAAGCCGCAATGGCAAACC-AGTACCAC-GAAGACACGAAGGG-AAAGGTTT
** *
341254 AAAGTCATAATGGCGAATCC-AGTACCACGAAGACAT
63 -AAGTCGCAATGGC-AAACCTAGTACCA-G-AGACAT
* * * * * *
341290 GAAGGGAAAGATCTAAGCCACAACGGCGGATCCAATACCACGAAGACACGAAGGGAAAGGTTTAA
1 GAAGGGAAAGATTTAAGCCGCAATGGC-AAACCAGTACCACGAAGACACGAAGGGAAAGGTTTAA
* * * * *
341355 GTCGTAACGGCAAACCCAGTACCTCGGAGACAG
65 GTCGCAATGGCAAACCTAGTA-C-CAGAGACAT
* * *
341388 GAAGGGAAAGATTTAAGCCACAATGACGAATCCAGTACCACGAAGACAC-AAGGGAAAGGTTTAA
1 GAAGGGAAAGATTTAAGCCGCAATGGC-AAACCAGTACCACGAAGACACGAAGGGAAAGGTTTAA
* *
341452 TTCGCAATGGCAAACCTTA-TACCTCAGAGGCAT
65 GTCGCAATGGCAAACC-TAGTA-C-CAGAGACAT
* *
341485 AAAAGGAAA-ATTTAAGCCGCAA
1 GAAGGGAAAGATTTAAGCCGCAA
341507 CGGCGAATTT
Statistics
Matches: 417, Mismatches: 76, Indels: 39
0.78 0.14 0.07
Matches are distributed among these distances:
96 14 0.03
97 205 0.49
98 109 0.26
99 24 0.06
100 57 0.14
101 8 0.02
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.16
Consensus pattern (95 bp):
GAAGGGAAAGATTTAAGCCGCAATGGCAAACCAGTACCACGAAGACACGAAGGGAAAGGTTTAAG
TCGCAATGGCAAACCTAGTACCAGAGACAT
Found at i:341158 original size:146 final size:146
Alignment explanation
Indices: 340894--341480 Score: 746
Period size: 146 Copynumber: 4.0 Consensus size: 146
340884 GTATCGTGAA
* * **
340894 ACACGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTATTACCTCAGAGACATGAAGAAAAAGAT
1 ACACGAAGGGAAAGGTTTAAGTCGCAATGGCAAACCTAGTACCTCAGAGACATGAAGGGAAAGAT
* * * * * *
340959 TTAAGCCGCAACGGCGAATCTAGTACCAGGAAGACACACGAGAAAGGTCTAAGTCGCAATGGCAA
66 TTAAGCCACAATGGCGAATCCAGTACCACGAAGACACAAGGGAAAGGTCTAAGTCGCAATGGCAA
*
341024 ACCTAGTACCTCAGAG
131 ACCTAATACCTCAGAG
*
341040 ACACGAAGGGAAAGGTTTAAGTCACAATGGCAAACCTAGTACCTCAGAGACATGAAGGGAAAGAT
1 ACACGAAGGGAAAGGTTTAAGTCGCAATGGCAAACCTAGTACCTCAGAGACATGAAGGGAAAGAT
** * * * *
341105 TTAAGCCGTAATGGCAAATCCAATACCACGAAGACACACGGGAAAGGTTTAAGTCGCAATGGCAA
66 TTAAGCCACAATGGCGAATCCAGTACCACGAAGACACAAGGGAAAGGTCTAAGTCGCAATGGCAA
341170 ACCTAATACCTCAGAG
131 ACCTAATACCTCAGAG
* ** *
341186 ACACAAAGGGAAAGGTTTAAGTCGCAATGGTGAACCTAGTACCTCTGAGACATGAAGGGAAAAGA
1 ACACGAAGGGAAAGGTTTAAGTCGCAATGGCAAACCTAGTACCTCAGAGACATGAAGGG-AAAGA
* * * * * * *
341251 TTTAAAGTCATAATGGCGAATCCAGTACCACGAAGACATGAAGGGAAAGATCTAAGCCACAACGG
65 TTT-AAGCCACAATGGCGAATCCAGTACCACGAAGACA-CAAGGGAAAGGTCTAAGTCGCAATGG
* * *
341316 CGGATCC-AATACCAC-GAAG
128 C-AAACCTAATACCTCAG-AG
* * * * *
341335 ACACGAAGGGAAAGGTTTAAGTCGTAACGGCAAACCCAGTACCTCGGAGACAGGAAGGGAAAGAT
1 ACACGAAGGGAAAGGTTTAAGTCGCAATGGCAAACCTAGTACCTCAGAGACATGAAGGGAAAGAT
* * *
341400 TTAAGCCACAATGACGAATCCAGTACCACGAAGACACAAGGGAAAGGTTTAATTCGCAATGGCAA
66 TTAAGCCACAATGGCGAATCCAGTACCACGAAGACACAAGGGAAAGGTCTAAGTCGCAATGGCAA
*
341465 ACCTTATACCTCAGAG
131 ACCTAATACCTCAGAG
341481 GCATAAAAGG
Statistics
Matches: 379, Mismatches: 55, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
145 3 0.01
146 214 0.56
147 40 0.11
148 39 0.10
149 80 0.21
150 3 0.01
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (146 bp):
ACACGAAGGGAAAGGTTTAAGTCGCAATGGCAAACCTAGTACCTCAGAGACATGAAGGGAAAGAT
TTAAGCCACAATGGCGAATCCAGTACCACGAAGACACAAGGGAAAGGTCTAAGTCGCAATGGCAA
ACCTAATACCTCAGAG
Found at i:341951 original size:6 final size:6
Alignment explanation
Indices: 341942--342015 Score: 50
Period size: 6 Copynumber: 12.8 Consensus size: 6
341932 TAGATTTATT
** *
341942 TTTAAA TTTAAA TTT-GT TTTAAA TTTAAA TTT-AG TTTAAA TTTCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
* *
341989 --T-AA TTCTAAA CTTAAC TTTAAA TTTAA
1 TTTAAA TT-TAAA TTTAAA TTTAAA TTTAA
342016 TTTCAGAGTC
Statistics
Matches: 51, Mismatches: 10, Indels: 14
0.68 0.13 0.19
Matches are distributed among these distances:
3 2 0.04
5 8 0.16
6 35 0.69
7 6 0.12
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:341960 original size:29 final size:29
Alignment explanation
Indices: 341912--341968 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
341902 GAACTTCTAA
* * *
341912 TTTTAAGTTTAGATTGGTTTTAGATTTAT
1 TTTTAAATTTAAATTGGTTTTAAATTTAT
*
341941 TTTTAAATTTAAATTTGTTTTAAATTTA
1 TTTTAAATTTAAATTGGTTTTAAATTTA
341969 AATTTAGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (29 bp):
TTTTAAATTTAAATTGGTTTTAAATTTAT
Found at i:341963 original size:17 final size:18
Alignment explanation
Indices: 341930--341989 Score: 79
Period size: 17 Copynumber: 3.4 Consensus size: 18
341920 TTAGATTGGT
* *
341930 TTTAGATTTATTTTTAAA
1 TTTAAATTTAGTTTTAAA
341948 TTTAAATTT-GTTTTAAA
1 TTTAAATTTAGTTTTAAA
341965 TTTAAATTTAG-TTTAAA
1 TTTAAATTTAGTTTTAAA
341982 TTTCAAAT
1 TTT-AAAT
341990 AATTCTAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
17 25 0.66
18 13 0.34
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTAAATTTAGTTTTAAA
Found at i:342660 original size:3 final size:3
Alignment explanation
Indices: 342652--342697 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
342642 CCCATACCAG
*
342652 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TT- TTCA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
342696 TT
1 TT
342698 TAAAAGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 4 0.11
3 32 0.84
4 2 0.05
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:343961 original size:29 final size:30
Alignment explanation
Indices: 343879--343987 Score: 84
Period size: 29 Copynumber: 3.8 Consensus size: 30
343869 AAAGGTACCT
* *
343879 AAACTATCCAAAAATTACATTTTTACCCCC
1 AAACTTTCCAAAAATTACATTTTGACCCCC
* *
343909 AAACTTTCC-AAAATTCCATCTTTGA-CCTC
1 AAACTTTCCAAAAATTACAT-TTTGACCCCC
* ** *
343938 GATTTTTCCAAAAATTACATTTTG--CCCT
1 AAACTTTCCAAAAATTACATTTTGACCCCC
* *
343966 AAAC-TTCCAAGAATTCCATTTT
1 AAACTTTCCAAAAATTACATTTT
343988 TAACCCCTTT
Statistics
Matches: 62, Mismatches: 15, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
27 16 0.26
28 3 0.05
29 22 0.35
30 21 0.34
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.36
Consensus pattern (30 bp):
AAACTTTCCAAAAATTACATTTTGACCCCC
Found at i:344037 original size:29 final size:29
Alignment explanation
Indices: 344000--344157 Score: 106
Period size: 29 Copynumber: 5.3 Consensus size: 29
343990 ACCCCTTTTT
344000 TTTCCAAAAAATACCATTTTACCCCTGAA
1 TTTCCAAAAAATACCATTTTACCCCTGAA
* * * *
344029 CTTCC-AAAAATTCCATTTTCAACCCTGATT
1 TTTCCAAAAAATACCATTTT-ACCCCTGA-A
*
344059 TTTCCAAAAAATTACCA-TTTACCCCCGAA
1 TTTCCAAAAAA-TACCATTTTACCCCTGAA
* * * ***
344088 TTTCC-AAATATTCCATTTTTTACCCTATTTT
1 TTTCCAAAAAATACCA--TTTTACCC-CTGAA
* * *
344119 TTTCTAAAAATTACCATTTTACCCTTGAA
1 TTTCCAAAAAATACCATTTTACCCCTGAA
*
344148 CTTCCAAAAA
1 TTTCCAAAAA
344158 TTCAATTTTT
Statistics
Matches: 94, Mismatches: 26, Indels: 18
0.68 0.19 0.13
Matches are distributed among these distances:
27 4 0.04
28 17 0.18
29 25 0.27
30 25 0.27
31 12 0.13
32 11 0.12
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.37
Consensus pattern (29 bp):
TTTCCAAAAAATACCATTTTACCCCTGAA
Found at i:344041 original size:60 final size:59
Alignment explanation
Indices: 343940--344167 Score: 273
Period size: 60 Copynumber: 3.9 Consensus size: 59
343930 TTGACCTCGA
* * * *
343940 TTTTTCCAAAAATTA-CATTTT-GCCCTAAACTTCCAAGAATTCCATTTTTAACCCCTTT
1 TTTTTCCAAAAAATACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAA-CCCTTT
* **
343998 TTTTTCCAAAAAATACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTCAACCCTGA
1 TTTTTCCAAAAAATACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCTTT
* * * *
344057 TTTTTCCAAAAAATTACCA-TTTACCCCCGAATTTCCAAATATTCCATTTTTTACCCTATT
1 TTTTTCCAAAAAA-TACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCT-TT
* * * *
344117 TTTTTCTAAAAATTACCATTTTACCCTTGAACTTCCAAAAATTCAATTTTT
1 TTTTTCCAAAAAATACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTT
344168 GACCTTGATT
Statistics
Matches: 144, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
58 14 0.10
59 61 0.42
60 69 0.48
ACGTcount: A:0.32, C:0.25, G:0.03, T:0.40
Consensus pattern (59 bp):
TTTTTCCAAAAAATACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCTTT
Found at i:344194 original size:59 final size:59
Alignment explanation
Indices: 343888--344203 Score: 281
Period size: 59 Copynumber: 5.3 Consensus size: 59
343878 TAAACTATCC
** * * *
343888 AAAAATTA-CATTTTTACCCCCAAACTTTCC-AAAATTCCATCTTTGA-CCTCGATTTTTCC
1 AAAAATTACCA-TTTTACCCCTGAAC-TTCCAAAAATTCCATTTTTAACCCT-GATTTTTCA
* * * **
343947 AAAAATTA-CATTTT-GCCCTAAACTTCCAAGAATTCCATTTTTAACCCCTTTTTTTTCCA
1 AAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAA-CCCTGATTTTT-CA
*
344006 AAAAA-TACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTCAACCCTGATTTTTCCA
1 AAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCTGATTTTT-CA
* * * * *
344065 AAAAATTACCA-TTTACCCCCGAATTTCCAAATATTCCATTTTTTACCCT-ATTTTTTTCT
1 AAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCTGA--TTTTTCA
* * * *
344124 AAAAATTACCATTTTACCCTTGAACTTCCAAAAATTCAATTTTTGACCTTGATTCTTTC-
1 AAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCTGATT-TTTCA
* *
344183 ATAAATCACCATTTTAGCCCC
1 AAAAATTACCATTTTA-CCCC
344204 GGATGTTTAA
Statistics
Matches: 214, Mismatches: 30, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
56 4 0.02
57 20 0.09
58 12 0.06
59 103 0.48
60 74 0.35
61 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.03, T:0.39
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTAACCCTGATTTTTCA
Found at i:344204 original size:119 final size:117
Alignment explanation
Indices: 343885--344230 Score: 373
Period size: 119 Copynumber: 2.9 Consensus size: 117
343875 ACCTAAACTA
** * *
343885 TCCAAAAATTA-CATTTTTACCCCCAAACTTTCC-AAAATTCCATCTTTGACCTCGATTTTTCCA
1 TCCAAAAATTACCA-TTTTACCCCTGAAC-TTCCAAAAATTCCATTTTTGACCTTGATTTTTCCA
** *
343948 AAAATTA-CATTTT-GCCCTAAACTTCCAAGAATTCCATTTTTAACCCCTTTTTTT
64 AAAATTACCATTTTAGCCCCGAATTTCCAA-AATTCCATTTTTAA-CCCTTTTTTT
* ** *
344002 TCCAAAAAATACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTCAACCCTGATTTTTCCAAA
1 TCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCTTGATTTTTCC-AA
* *
344067 AAATTACCA-TTTACCCCCGAATTTCCAAATATTCCATTTTTTACCCTATTTTTT
65 AAATTACCATTTTAGCCCCGAATTTCCAAA-ATTCCATTTTTAACCCT-TTTTTT
* * * *
344121 TCTAAAAATTACCATTTTACCCTTGAACTTCCAAAAATTCAATTTTTGACCTTGATTCTTT-CAT
1 TCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCTTGATT-TTTCCAA
* * * *
344185 AAATCACCATTTTAGCCCCGGATGTT-TAAAATTCCATTTTTGACCC
65 AAATTACCATTTTAGCCCCGAAT-TTCCAAAATTCCATTTTTAACCC
344231 CAAACTTTCT
Statistics
Matches: 193, Mismatches: 26, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
116 4 0.02
117 46 0.24
118 42 0.22
119 96 0.50
120 5 0.03
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (117 bp):
TCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATTCCATTTTTGACCTTGATTTTTCCAAA
AATTACCATTTTAGCCCCGAATTTCCAAAATTCCATTTTTAACCCTTTTTTT
Found at i:355849 original size:17 final size:17
Alignment explanation
Indices: 355827--355859 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
355817 TGTTAGTAAG
*
355827 CATTGTCATTGCATTTT
1 CATTGTCATTACATTTT
355844 CATTGTCATTACATTT
1 CATTGTCATTACATTT
355860 AAATGTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.52
Consensus pattern (17 bp):
CATTGTCATTACATTTT
Found at i:357179 original size:38 final size:38
Alignment explanation
Indices: 357136--357209 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
357126 AATGTCGCTG
**
357136 CATGAGCACTTCTAGATTGTGCCCAAAACTGTCGCCCA
1 CATGAGCACTTCTAGATTGCACCCAAAACTGTCGCCCA
*
357174 CATGAGCACTTCTAGATTGCACCCAAAATTGTCGCC
1 CATGAGCACTTCTAGATTGCACCCAAAACTGTCGCC
357210 GCAGGAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (38 bp):
CATGAGCACTTCTAGATTGCACCCAAAACTGTCGCCCA
Found at i:370054 original size:33 final size:33
Alignment explanation
Indices: 370012--370077 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
370002 CATCGCCCAC
370012 TTATTCAAAGATGAGTTTTCCAACAGTCTAGGT
1 TTATTCAAAGATGAGTTTTCCAACAGTCTAGGT
370045 TTATTCAAAGATGAGTTTTCCAACAGTCTAGGT
1 TTATTCAAAGATGAGTTTTCCAACAGTCTAGGT
370078 GCAAATATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.36
Consensus pattern (33 bp):
TTATTCAAAGATGAGTTTTCCAACAGTCTAGGT
Found at i:375257 original size:15 final size:15
Alignment explanation
Indices: 375239--375268 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
375229 GTCTAACCAT
375239 TTTACCAATTCTTTC
1 TTTACCAATTCTTTC
*
375254 TTTACCACTTCTTTC
1 TTTACCAATTCTTTC
375269 ATGGCGAGAT
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:0.17, C:0.30, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTACCAATTCTTTC
Found at i:378488 original size:39 final size:38
Alignment explanation
Indices: 378437--378515 Score: 122
Period size: 39 Copynumber: 2.1 Consensus size: 38
378427 CATTGTCAAT
378437 AATTTTAATATCCAACAAGCTTAAAACAAAATAATTTC
1 AATTTTAATATCCAACAAGCTTAAAACAAAATAATTTC
* * *
378475 AATTTCTAATATCCAACAAGCTTGAAACATAATACTTTC
1 AATTT-TAATATCCAACAAGCTTAAAACAAAATAATTTC
378514 AA
1 AA
378516 AATCCAACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
38 5 0.14
39 32 0.86
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.32
Consensus pattern (38 bp):
AATTTTAATATCCAACAAGCTTAAAACAAAATAATTTC
Found at i:382499 original size:34 final size:34
Alignment explanation
Indices: 382436--382505 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
382426 GTAGTTGTAA
* *
382436 TTTAATTGTCACCACATTTCCTTTGTCATTACAT
1 TTTAATTGTCACCACATTTCCATTATCATTACAT
** * *
382470 TTTAATTGTCACTGCATTTGCATTATCATTGCAT
1 TTTAATTGTCACCACATTTCCATTATCATTACAT
382504 TT
1 TT
382506 CCATTTATCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.49
Consensus pattern (34 bp):
TTTAATTGTCACCACATTTCCATTATCATTACAT
Found at i:382502 original size:17 final size:18
Alignment explanation
Indices: 382482--382522 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
382472 TAATTGTCAC
* *
382482 TGCATTTGCA-TTATCAT
1 TGCATTTCCATTTATCAA
382499 TGCATTTCCATTTATCAA
1 TGCATTTCCATTTATCAA
382517 TGCATT
1 TGCATT
382523 GAGGACAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (18 bp):
TGCATTTCCATTTATCAA
Found at i:390488 original size:22 final size:23
Alignment explanation
Indices: 390446--390491 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
390436 ACATATTAAG
*
390446 AGAGTGAAAAATTAAGAAAGAAA
1 AGAGTGAAAAATGAAGAAAGAAA
390469 AGAGT-AAAAATAGAAG-AAGAAA
1 AGAGTGAAAAAT-GAAGAAAGAAA
390491 A
1 A
390492 AACAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.11
Consensus pattern (23 bp):
AGAGTGAAAAATGAAGAAAGAAA
Found at i:391432 original size:25 final size:25
Alignment explanation
Indices: 391404--391454 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
391394 ACACATCCAC
391404 CATGATCTCTCTTACACTCTTTTTT
1 CATGATCTCTCTTACACTCTTTTTT
391429 CATGATCTCTCTTACACTCTTTTTT
1 CATGATCTCTCTTACACTCTTTTTT
391454 C
1 C
391455 TTCATATCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.29, G:0.04, T:0.51
Consensus pattern (25 bp):
CATGATCTCTCTTACACTCTTTTTT
Found at i:396538 original size:36 final size:36
Alignment explanation
Indices: 396491--396559 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
396481 GATTTTAATT
396491 ATTATTAATTGAATT-AATTGATTTTTAAAAATTTTA
1 ATTATTAATTGAATTAAATT-ATTTTTAAAAATTTTA
*
396527 ATTATTAATTGAATTAAATTTTTTTTAAAAATT
1 ATTATTAATTGAATTAAATTATTTTTAAAAATT
396560 AATCGAATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 27 0.87
37 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (36 bp):
ATTATTAATTGAATTAAATTATTTTTAAAAATTTTA
Found at i:396767 original size:9 final size:9
Alignment explanation
Indices: 396755--396785 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
396745 TTAAATTCAT
396755 TTAATTCGA
1 TTAATTCGA
396764 TTAATTCGA
1 TTAATTCGA
396773 TTAATTCGA
1 TTAATTCGA
396782 TTAA
1 TTAA
396786 CCAACCGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (9 bp):
TTAATTCGA
Found at i:401232 original size:18 final size:18
Alignment explanation
Indices: 401209--401251 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
401199 GTTCAAGGTG
401209 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
401227 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
401245 TAATTAA
1 TAATTAA
401252 AAACTTATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:402150 original size:22 final size:21
Alignment explanation
Indices: 402122--402164 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
402112 TAATAATATA
402122 ATTTTTTAAAATAAAATTAATT
1 ATTTTTT-AAATAAAATTAATT
* *
402144 ATTTTTTTAATTAAATTAATT
1 ATTTTTTAAATAAAATTAATT
402165 CCAGTATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTTTAAATAAAATTAATT
Found at i:404843 original size:90 final size:91
Alignment explanation
Indices: 404669--404844 Score: 205
Period size: 90 Copynumber: 1.9 Consensus size: 91
404659 TTCGTTAGAG
* * ** * * * *
404669 AAAGAATTGTATGAAACTGTGATTCCACGTCATCCCTATCCTTTTTCAATAGGAGAATGATAGAT
1 AAAGAATTGTATAAAACTGTGATTCCACATCATCCCTATCCCCTTTCAATAAGAGAATAACAAAT
**
404734 TAGATTTTTTCTTTTGATTTTCAAGA
66 TAGATTTTTTCTTCCGATTTTCAAGA
* *
404760 AAAG-ATTGTATAAAATTGTGATTTCACATCATCCCTATCCCCTTTCAATAAGAGAATAACAAAT
1 AAAGAATTGTATAAAACTGTGATTCCACATCATCCCTATCCCCTTTCAATAAGAGAATAACAAAT
404824 CT-GA-TTTTTCTTCCCGATTTT
66 -TAGATTTTTTCTT-CCGATTTT
404845 TAGTTTTTTT
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
89 8 0.11
90 58 0.82
91 5 0.07
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (91 bp):
AAAGAATTGTATAAAACTGTGATTCCACATCATCCCTATCCCCTTTCAATAAGAGAATAACAAAT
TAGATTTTTTCTTCCGATTTTCAAGA
Found at i:406810 original size:30 final size:29
Alignment explanation
Indices: 406746--406819 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
406736 TATATATAAT
*
406746 AATAA-AATATTAAAATCATATTTATGTTA
1 AATAATAA-ATTAAAATCATATTAATGTTA
* * *
406775 TATAATAAATTACAAATTATATTAATTTTA
1 AATAATAAATTA-AAATCATATTAATGTTA
*
406805 AATAATAAATAAAAA
1 AATAATAAATTAAAA
406820 ATGTTGTCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
29 11 0.30
30 26 0.70
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (29 bp):
AATAATAAATTAAAATCATATTAATGTTA
Done.