Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015251.1 Kokia drynarioides strain JFW-HI SEQ_130296, 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: 620055
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 406 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:442235 original size:3 final size:3
Alignment explanation
Indices: 442227--442262 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
442217 CTTTGGGTCG
*
442227 GGA GGA GGA GGA GGA GGA GGA GGA GGG GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
442263 AATAGAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:457870 original size:19 final size:20
Alignment explanation
Indices: 457832--457870 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
457822 ATCCAAGTTT
* *
457832 ATTCAGGGTTTAGGGTTCGA
1 ATTCAAGGTTTAGAGTTCGA
457852 ATTCAAGGTTTA-AGTTCGA
1 ATTCAAGGTTTAGAGTTCGA
457871 TGTTAGGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (20 bp):
ATTCAAGGTTTAGAGTTCGA
Found at i:457986 original size:24 final size:22
Alignment explanation
Indices: 457957--458009 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 22
457947 AAATGTCATT
457957 AAATAAATTAAAAAACCATTAATA
1 AAATAAATTAAAAAA--ATTAATA
* *
457981 ATAT-AA-TAAAAAAATTCATA
1 AAATAAATTAAAAAAATTAATA
458001 AAATAAATT
1 AAATAAATT
458010 CTCCTCAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
20 9 0.38
21 2 0.08
22 8 0.33
23 2 0.08
24 3 0.12
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATAAATTAAAAAAATTAATA
Found at i:458005 original size:22 final size:21
Alignment explanation
Indices: 457946--458008 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
457936 AAAATTTGTT
* *
457946 AAAATGTCATTAAATAAATTAA
1 AAAAT-TCATAAAATAAATAAA
*
457968 AAAA-CCATTAATAATATAATAAA
1 AAAATTCA-TAA-AATA-AATAAA
457991 AAAATTCATAAAATAAAT
1 AAAATTCATAAAATAAAT
458009 TCTCCTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
20 2 0.06
21 5 0.15
22 12 0.36
23 12 0.36
24 2 0.06
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAATTCATAAAATAAATAAA
Found at i:461074 original size:3 final size:3
Alignment explanation
Indices: 461060--461097 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
461050 ACCTCTCCCG
* *
461060 TCT TCA TCT TCT TCT TCT TCT TCT TCT TCC TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
461098 AGCTTCTACG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:464380 original size:18 final size:19
Alignment explanation
Indices: 464354--464397 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
464344 ATGATGAATT
*
464354 ATATTTAAAA-GTTTAAAA
1 ATATATAAAATGTTTAAAA
*
464372 ATATATAAAATTTTTAAAA
1 ATATATAAAATGTTTAAAA
464391 AT-TATAA
1 ATATATAA
464398 TCTCCAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
ATATATAAAATGTTTAAAA
Found at i:464718 original size:21 final size:23
Alignment explanation
Indices: 464684--464730 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
464674 TTTTATAATA
*
464684 TTTTTGTAATTTTTAAAATA-GT
1 TTTTTATAATTTTTAAAATATGT
*
464706 TTTTTATAA-TTTTATAATATGT
1 TTTTTATAATTTTTAAAATATGT
464728 TTT
1 TTT
464731 ATTTTTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (23 bp):
TTTTTATAATTTTTAAAATATGT
Found at i:464729 original size:22 final size:21
Alignment explanation
Indices: 464674--464730 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
464664 GTCAATTTTG
*
464674 TTTTATAATAT-TTTTGTAAT
1 TTTTATAATATGTTTTGTAAA
* *
464694 TTTTAAAATA-GTTTTTTATAA
1 TTTTATAATATGTTTTGTA-AA
464715 TTTTATAATATGTTTT
1 TTTTATAATATGTTTT
464731 ATTTTTCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 15 0.50
21 10 0.33
22 5 0.17
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (21 bp):
TTTTATAATATGTTTTGTAAA
Found at i:464732 original size:20 final size:20
Alignment explanation
Indices: 464674--464763 Score: 69
Period size: 21 Copynumber: 4.5 Consensus size: 20
464664 GTCAATTTTG
*
464674 TTTTATAATATTTTTGTAAT
1 TTTTATAATATTTTTATAAT
*
464694 TTTTAAAATAGTTTTTTATAA-
1 TTTTATAATA--TTTTTATAAT
464715 TTTTATAATATGTTTTAT--T
1 TTTTATAATAT-TTTTATAAT
* * * *
464734 TTTCATAATCATATATATACT
1 TTTTATAAT-ATTTTTATAAT
464755 TTTTATAAT
1 TTTTATAAT
464764 TTTCTATTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
19 13 0.23
20 17 0.30
21 18 0.32
22 8 0.14
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (20 bp):
TTTTATAATATTTTTATAAT
Found at i:476179 original size:59 final size:60
Alignment explanation
Indices: 476068--476180 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 60
476058 AAAAAAATAG
* ** *
476068 CAAGTTTAGATATCAAATTGGGTCCGAAAAAAGCTTAGATACTAAATTAGGAAAGAGTGT
1 CAAGTTCAGATATCAAATTGGGTCAAAAAAAAGCTTAGATACCAAATTAGGAAAGAGTGT
* *
476128 CAAGTTCATATATCAAATTGGGT-AAAAAAAAGTTTAGATACCAAATTAGGAAA
1 CAAGTTCAGATATCAAATTGGGTCAAAAAAAAGCTTAGATACCAAATTAGGAAA
476181 ATAATGACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 26 0.55
60 21 0.45
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.27
Consensus pattern (60 bp):
CAAGTTCAGATATCAAATTGGGTCAAAAAAAAGCTTAGATACCAAATTAGGAAAGAGTGT
Found at i:476192 original size:60 final size:61
Alignment explanation
Indices: 476045--476195 Score: 164
Period size: 60 Copynumber: 2.5 Consensus size: 61
476035 TACGTTCAAT
* * **
476045 TACCAAATTAGAAAAAAAAAT-AGCAAGTTTAGATATCAAATTGGGTCCGAAAAAAGCTTAGA
1 TACCAAATTAG-GAAAAAAATGA-CAAGTTCAGATATCAAATTGGGTCAAAAAAAAGCTTAGA
* * * * * *
476107 TACTAAATTAGG-AAAGAGTGTCAAGTTCATATATCAAATTGGGT-AAAAAAAAGTTTAGA
1 TACCAAATTAGGAAAAAAATGACAAGTTCAGATATCAAATTGGGTCAAAAAAAAGCTTAGA
*
476166 TACCAAATTAGGAAAATAATGACAAGTTCA
1 TACCAAATTAGGAAAAAAATGACAAGTTCA
476196 ATTACCAAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
59 23 0.32
60 40 0.55
62 10 0.14
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (61 bp):
TACCAAATTAGGAAAAAAATGACAAGTTCAGATATCAAATTGGGTCAAAAAAAAGCTTAGA
Found at i:476205 original size:60 final size:59
Alignment explanation
Indices: 476094--476205 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
476084 ATTGGGTCCG
* * * *
476094 AAAAAAGCTTAGATACTAAATTAGGAAAGAGTGTCAAGTTCATATATCAAATTGGGTAA
1 AAAAAAGCTTAGATACCAAATTAGGAAAGAATGACAAGTTCATATACCAAATTGGGTAA
* *
476153 AAAAAAGTTTAGATACCAAATTAGGAAAATAATGACAAGTTCA-ATTACCAAAT
1 AAAAAAGCTTAGATACCAAATTAGG-AAAGAATGACAAGTTCATA-TACCAAAT
476206 ACTATATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
59 24 0.53
60 21 0.47
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (59 bp):
AAAAAAGCTTAGATACCAAATTAGGAAAGAATGACAAGTTCATATACCAAATTGGGTAA
Found at i:486661 original size:6 final size:6
Alignment explanation
Indices: 486650--486707 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
486640 GTATATTTTT
* * * *
486650 TTATAA TTATAA TTTAAAA TTTGTGA TTATAA TTTTTAA TTATAA TTATAA
1 TTATAA TTATAA -TTATAA -TTATAA TTATAA -TTATAA TTATAA TTATAA
486701 TTATAA T
1 TTATAA T
486708 AGCGAACAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
6 28 0.67
7 14 0.33
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
TTATAA
Found at i:488252 original size:10 final size:10
Alignment explanation
Indices: 488239--488321 Score: 53
Period size: 10 Copynumber: 8.2 Consensus size: 10
488229 AAAAACCAAC
488239 AAAATTATAA
1 AAAATTATAA
* *
488249 AAAAATATTA
1 AAAATTATAA
**
488259 AACTTTA-ATA
1 AAAATTATA-A
*
488269 AAAACTATAA
1 AAAATTATAA
*
488279 AAAATTATTA
1 AAAATTATAA
488289 AAAA-TATAA
1 AAAATTATAA
* *
488298 AAATTGTCATTA
1 AAAAT-T-ATAA
488310 AAAATTATAA
1 AAAATTATAA
488320 AA
1 AA
488322 TACATCAAAA
Statistics
Matches: 52, Mismatches: 16, Indels: 10
0.67 0.21 0.13
Matches are distributed among these distances:
9 7 0.13
10 35 0.67
11 3 0.06
12 7 0.13
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (10 bp):
AAAATTATAA
Found at i:488309 original size:21 final size:20
Alignment explanation
Indices: 488239--488321 Score: 69
Period size: 20 Copynumber: 4.1 Consensus size: 20
488229 AAAAACCAAC
* * *
488239 AAAATTATAAAAAAATATTA
1 AAAATTATTAAAAACTATAA
** *
488259 AACTTTAATAAAAACTATAA
1 AAAATTATTAAAAACTATAA
488279 AAAATTATTAAAAA-TATAA
1 AAAATTATTAAAAACTATAA
* *
488298 AAATTGTCATTAAAAATTATAA
1 AAAAT-T-ATTAAAAACTATAA
488320 AA
1 AA
488322 TACATCAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
19 9 0.18
20 26 0.52
21 8 0.16
22 7 0.14
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (20 bp):
AAAATTATTAAAAACTATAA
Found at i:488832 original size:9 final size:9
Alignment explanation
Indices: 488818--488846 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
488808 AAAATAGAGG
488818 TTTTTTTA-
1 TTTTTTTAT
488826 TTTTTTTAT
1 TTTTTTTAT
488835 TTTTTTTAT
1 TTTTTTTAT
488844 TTT
1 TTT
488847 ATGTATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:488855 original size:17 final size:17
Alignment explanation
Indices: 488818--488855 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
488808 AAAATAGAGG
*
488818 TTTTTTTATTTTTTTAT
1 TTTTTTTATTTTTGTAT
488835 TTTTTTTATTTTATGTAT
1 TTTTTTTATTTT-TGTAT
488853 TTT
1 TTT
488856 GACAATTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.84
Consensus pattern (17 bp):
TTTTTTTATTTTTGTAT
Found at i:498054 original size:90 final size:93
Alignment explanation
Indices: 497950--498190 Score: 301
Period size: 99 Copynumber: 2.6 Consensus size: 93
497940 TTTTTAAAAA
497950 AATTTATTTATTTATTTATTATATAATATTTAAATATATAGTTTAATTTAAA-TT-TTTTTGGTG
1 AATTTATTTATTTATTTATTATATAATATTTAAATATATAGTTTAATTTAAATTTATTTTTGGTG
* * *
498013 GAGCCATTTTAAATGATGCCA-CCTAAT
66 GAACCATATTAAATGATGCCACCCGAAT
**
498040 CGTTTATTTATTTATTTATTATATAATATTTAAATATATAGTTTAATTTAAATATATATTTTATT
1 AATTTATTTATTTATTTATTATATAATATTTAAATATATAGTTTAA-TT---TA-A-A-TTTATT
* *
498105 TTTGGTGGAACCATATTAAATGGTGCCACCCGATT
59 TTTGGTGGAACCATATTAAATGATGCCACCCGAAT
* * *
498140 AATTTTTTTA-TTATTTATTATTTAATATTTAAATATATAATTTAATTTAAA
1 AATTTATTTATTTATTTATTATATAATATTTAAATATATAGTTTAATTTAAA
498191 CGTATATTTT
Statistics
Matches: 129, Mismatches: 12, Indels: 17
0.82 0.08 0.11
Matches are distributed among these distances:
90 44 0.34
91 2 0.02
93 1 0.01
94 3 0.02
95 3 0.02
96 1 0.01
98 4 0.03
99 60 0.47
100 11 0.09
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.51
Consensus pattern (93 bp):
AATTTATTTATTTATTTATTATATAATATTTAAATATATAGTTTAATTTAAATTTATTTTTGGTG
GAACCATATTAAATGATGCCACCCGAAT
Found at i:498088 original size:18 final size:18
Alignment explanation
Indices: 498067--498102 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
498057 ATTATATAAT
498067 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
*
498085 ATTTAAATATATATTTTA
1 ATTTAAATATATAGTTTA
498103 TTTTTGGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:498111 original size:99 final size:99
Alignment explanation
Indices: 498004--498225 Score: 293
Period size: 99 Copynumber: 2.2 Consensus size: 99
497994 AATTTAAATT
* **
498004 TTTTTGGTGGAGCCATTTTAAATGATGCCA-CCTAATCGTTTATTTATTTATTTATTATATAATA
1 TTTTTGGTGGAGCCATTTTAAATGATGCCACCCGAATAATTTATTTA-TTATTTATTATATAATA
* *
498068 TTTAAATATATAGTTTAATTTAAATATATATTTTA
65 TTTAAATATATAATTTAATTTAAACATATATTTTA
* * * * * *
498103 TTTTTGGTGGAACCATATTAAATGGTGCCACCCGATTAATTTTTTTATTATTTATTATTTAATAT
1 TTTTTGGTGGAGCCATTTTAAATGATGCCACCCGAATAATTTATTTATTATTTATTATATAATAT
*
498168 TTAAATATATAATTTAATTTAAACGTATATTTTA
66 TTAAATATATAATTTAATTTAAACATATATTTTA
* * *
498202 TTTTTGGTAGAGTCATTCTAAATG
1 TTTTTGGTGGAGCCATTTTAAATG
498226 GCGCCATCAA
Statistics
Matches: 105, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
99 94 0.90
100 11 0.10
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (99 bp):
TTTTTGGTGGAGCCATTTTAAATGATGCCACCCGAATAATTTATTTATTATTTATTATATAATAT
TTAAATATATAATTTAATTTAAACATATATTTTA
Found at i:503253 original size:24 final size:25
Alignment explanation
Indices: 503207--503255 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
503197 ATTATTTTTA
*
503207 ATATTTTTATTTATTTTAAAAATAT
1 ATATTTATATTTATTTTAAAAATAT
*
503232 ATATTTATGTTTA-TTTAAAAATAT
1 ATATTTATATTTATTTTAAAAATAT
503256 GATAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
ATATTTATATTTATTTTAAAAATAT
Found at i:503639 original size:23 final size:23
Alignment explanation
Indices: 503607--503652 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
503597 AGACATTTCT
* * *
503607 AAATCCAATAATCAACACATCAC
1 AAATCAAATAAACAACAAATCAC
503630 AAATCAAATAAACAACAAATCAC
1 AAATCAAATAAACAACAAATCAC
503653 TCAAAAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (23 bp):
AAATCAAATAAACAACAAATCAC
Found at i:507579 original size:3 final size:3
Alignment explanation
Indices: 507571--507595 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
507561 ACTTGAATTA
507571 TCC TCC TCC TCC TCC TCC TCC TCC T
1 TCC TCC TCC TCC TCC TCC TCC TCC T
507596 TGTGAAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (3 bp):
TCC
Found at i:509516 original size:11 final size:12
Alignment explanation
Indices: 509484--509516 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
509474 ATGAGAAGAA
509484 AGAAATAAAAGG
1 AGAAATAAAAGG
509496 AGAGAATAAAAGG
1 AGA-AATAAAAGG
509509 A-AAATAAA
1 AGAAATAAA
509517 GAAATTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 6 0.30
12 4 0.20
13 10 0.50
ACGTcount: A:0.70, C:0.00, G:0.21, T:0.09
Consensus pattern (12 bp):
AGAAATAAAAGG
Found at i:520159 original size:101 final size:102
Alignment explanation
Indices: 519979--520180 Score: 293
Period size: 101 Copynumber: 2.0 Consensus size: 102
519969 TACATCCCTA
* *
519979 AACAAATTTCAATTCCAATGCCTTTCAAAAAAAAAGAAGAAAAAAAAAGCAAAAACCCATTGCAG
1 AACAAATTTCAATTCCAATACCTTACAAAAAAAAAGAAGAAAAAAAAAGCAAAAACCCATTGCAG
520044 TTCCCAAGAATTTAAACAATTGATAGCATAAAAGCAT
66 TTCCCAAGAATTTAAACAATTGATAGCATAAAAGCAT
* ** **
520081 AACAAATTTCAATTCCAATACCTTACACACACACCAA-AA-AAAAAAAAAGC-GTAACCCATTGC
1 AACAAATTTCAATTCCAATACCTTACA-A-AAAAAAAGAAGAAAAAAAAAGCAAAAACCCATTGC
*
520143 ATTTCCCAAGAATTTAAACAATTGATAGCATAAAAGCA
64 AGTTCCCAAGAATTTAAACAATTGATAGCATAAAAGCA
520181 AAACCCTATG
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
101 47 0.52
102 36 0.40
103 3 0.03
104 4 0.04
ACGTcount: A:0.50, C:0.20, G:0.08, T:0.21
Consensus pattern (102 bp):
AACAAATTTCAATTCCAATACCTTACAAAAAAAAAGAAGAAAAAAAAAGCAAAAACCCATTGCAG
TTCCCAAGAATTTAAACAATTGATAGCATAAAAGCAT
Found at i:541816 original size:16 final size:16
Alignment explanation
Indices: 541795--541826 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
541785 AGTTCAATGG
541795 GATTTTGTAATGGAAA
1 GATTTTGTAATGGAAA
541811 GATTTTGTAATGGAAA
1 GATTTTGTAATGGAAA
541827 AAATTGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (16 bp):
GATTTTGTAATGGAAA
Found at i:541988 original size:20 final size:21
Alignment explanation
Indices: 541960--541999 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
541950 AAATATATCC
*
541960 CATCCTAA-TATTTGGTATTT
1 CATCATAATTATTTGGTATTT
*
541980 CATCATAATTTTTTGGTATT
1 CATCATAATTATTTGGTATT
542000 CCTTTCTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (21 bp):
CATCATAATTATTTGGTATTT
Found at i:542527 original size:20 final size:20
Alignment explanation
Indices: 542504--542555 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
542494 TTCCTTAATA
542504 ATTTTTTTGTATTCCCTCAC
1 ATTTTTTTGTATTCCCTCAC
* *
542524 ATTTGTTTGTA-CCCCTCAC
1 ATTTTTTTGTATTCCCTCAC
* *
542543 AATTTTTTATATT
1 ATTTTTTTGTATT
542556 GTTTTGAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.54
Consensus pattern (20 bp):
ATTTTTTTGTATTCCCTCAC
Found at i:542784 original size:20 final size:20
Alignment explanation
Indices: 542761--542808 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
542751 TTTTATCACG
542761 TAATTTTTTATACTTCCTTA
1 TAATTTTTTATACTTCCTTA
* *
542781 TAATTTTTTATATTTCTTTA
1 TAATTTTTTATACTTCCTTA
542801 T-ATTTTTT
1 TAATTTTTT
542809 TTTATATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (20 bp):
TAATTTTTTATACTTCCTTA
Found at i:542809 original size:20 final size:19
Alignment explanation
Indices: 542764--542831 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 19
542754 TATCACGTAA
* *
542764 TTTTTTATACTTCCTTATAA
1 TTTTTTATA-TTTCTTATAT
542784 TTTTTTATATTTCTTTATATTT
1 TTTTTTATATTTC-TTATA--T
*
542806 TTTTTTATATATTCTCATAT
1 TTTTTTATAT-TTCTTATAT
542826 TTTTTT
1 TTTTTT
542832 GTTTGGATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
19 3 0.07
20 21 0.51
22 14 0.34
23 3 0.07
ACGTcount: A:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTTTATATTTCTTATAT
Found at i:542809 original size:22 final size:22
Alignment explanation
Indices: 542784--542831 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
542774 TTCCTTATAA
*
542784 TTTTTTATAT-TTCTTTATATTT
1 TTTTTTATATATTC-TCATATTT
542806 TTTTTTATATATTCTCATATTT
1 TTTTTTATATATTCTCATATTT
542828 TTTT
1 TTTT
542832 GTTTGGATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTTATATATTCTCATATTT
Found at i:546646 original size:22 final size:19
Alignment explanation
Indices: 546606--546650 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
546596 TATTTTCTCG
*
546606 TTTTTTATATTCTCTTATAA
1 TTTTTTATATTCTCGTAT-A
546626 TTTTTTATACTTCCTCGTATA
1 TTTTTTATA-TT-CTCGTATA
546647 TTTT
1 TTTT
546651 GGTATTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 7 0.32
22 6 0.27
ACGTcount: A:0.20, C:0.13, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTTATATTCTCGTATA
Found at i:547361 original size:20 final size:20
Alignment explanation
Indices: 547338--547375 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
547328 TTTGGGTAAT
547338 CCCTCAAAATTTTTTGTACA
1 CCCTCAAAATTTTTTGTACA
*
547358 CCCTCATAATTTTTTGTA
1 CCCTCAAAATTTTTTGTA
547376 TGGTCTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (20 bp):
CCCTCAAAATTTTTTGTACA
Found at i:548130 original size:16 final size:17
Alignment explanation
Indices: 548092--548130 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
548082 TAAAGATGGT
548092 TTAATTCATAAGATAAA
1 TTAATTCATAAGATAAA
**
548109 AAAATTCAT-AGATAAA
1 TTAATTCATAAGATAAA
548125 TTAATT
1 TTAATT
548131 TGTGTTTTTC
Statistics
Matches: 18, Mismatches: 4, Indels: 1
0.78 0.17 0.04
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (17 bp):
TTAATTCATAAGATAAA
Found at i:561214 original size:21 final size:20
Alignment explanation
Indices: 561189--561271 Score: 70
Period size: 21 Copynumber: 4.3 Consensus size: 20
561179 CTTTTTAATT
561189 GATTGTTTATATGTTTAAATC
1 GATTGTTTATAT-TTTAAATC
*
561210 GATTG-TTATA-TTGAAAT-
1 GATTGTTTATATTTTAAATC
* *
561227 -ATTGCTT-T-TTTTGAATC
1 GATTGTTTATATTTTAAATC
*
561244 GATTGTTTATATGTTTAAATT
1 GATTGTTTATAT-TTTAAATC
561265 GATTGTT
1 GATTGTT
561272 ATGTAGTACA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
16 10 0.20
17 2 0.04
18 12 0.24
19 1 0.02
20 6 0.12
21 18 0.37
ACGTcount: A:0.27, C:0.04, G:0.16, T:0.54
Consensus pattern (20 bp):
GATTGTTTATATTTTAAATC
Found at i:561248 original size:55 final size:55
Alignment explanation
Indices: 561150--561273 Score: 196
Period size: 55 Copynumber: 2.3 Consensus size: 55
561140 GCCCTCCCAA
* *
561150 AAATCGATTGTTATGTTGAAATACTGCTTCTTTTTAATTGATTGTTTATATGTTT
1 AAATCGATTGTTATATTGAAATACTGCTTCTTTTTAATCGATTGTTTATATGTTT
*
561205 AAATCGATTGTTATATTGAAATATTGCTT-TTTTTGAATCGATTGTTTATATGTTT
1 AAATCGATTGTTATATTGAAATACTGCTTCTTTTT-AATCGATTGTTTATATGTTT
*
561260 AAATTGATTGTTAT
1 AAATCGATTGTTAT
561274 GTAGTACATC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
54 5 0.08
55 59 0.92
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.52
Consensus pattern (55 bp):
AAATCGATTGTTATATTGAAATACTGCTTCTTTTTAATCGATTGTTTATATGTTT
Found at i:565580 original size:13 final size:13
Alignment explanation
Indices: 565562--565609 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
565552 AAATATTTCA
565562 ATTAATTCAATCG
1 ATTAATTCAATCG
*
565575 ATTAATTCATATTTCA
1 ATTAATTCA-A--TCG
565591 ATTAATTCAATCG
1 ATTAATTCAATCG
565604 ATTAAT
1 ATTAAT
565610 CGAATTAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 17 0.57
14 1 0.03
15 1 0.03
16 11 0.37
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (13 bp):
ATTAATTCAATCG
Found at i:565590 original size:29 final size:29
Alignment explanation
Indices: 565554--565609 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
565544 CCTAATTGAA
565554 ATATTTCAATTAATTCAATCGATTAATTC
1 ATATTTCAATTAATTCAATCGATTAATTC
565583 ATATTTCAATTAATTCAATCGATTAAT
1 ATATTTCAATTAATTCAATCGATTAAT
565610 CGAATTAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (29 bp):
ATATTTCAATTAATTCAATCGATTAATTC
Found at i:568667 original size:2 final size:2
Alignment explanation
Indices: 568660--568699 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
568650 TATTATGTCA
568660 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
568700 GATCAAAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:569732 original size:23 final size:24
Alignment explanation
Indices: 569688--569743 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
569678 AAATTTTAAA
*
569688 AATAT-ATCTATATTTTAATATTT
1 AATATAATTTATATTTTAATATTT
**
569711 AATA-AATTTATATTTTCTTATTT
1 AATATAATTTATATTTTAATATTT
*
569734 ATTATAATTT
1 AATATAATTT
569744 TATGTAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.59
Consensus pattern (24 bp):
AATATAATTTATATTTTAATATTT
Found at i:572652 original size:12 final size:12
Alignment explanation
Indices: 572630--572660 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
572620 TTTGGCCGGT
572630 AATACTATATATA
1 AATA-TATATATA
572643 AATATATATATA
1 AATATATATATA
572655 AATATA
1 AATATA
572661 AAATAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (12 bp):
AATATATATATA
Found at i:572653 original size:6 final size:6
Alignment explanation
Indices: 572638--572702 Score: 53
Period size: 6 Copynumber: 10.5 Consensus size: 6
572628 GTAATACTAT
* * *
572638 ATATAA ATATAT ATATAA ATATAA A-ATAGA AAAGTAA ATATAC A-ATAA
1 ATATAA ATATAA ATATAA ATATAA ATATA-A ATA-TAA ATATAA ATATAA
572686 ATAATAA ATAATAA ATA
1 AT-ATAA AT-ATAA ATA
572703 AAAGGTCACT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
5 7 0.14
6 23 0.47
7 17 0.35
8 2 0.04
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (6 bp):
ATATAA
Found at i:575892 original size:26 final size:26
Alignment explanation
Indices: 575862--575948 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
575852 AATGTTTGAA
575862 AAAGAAGAAACTAAATAATACATTCC
1 AAAGAAGAAACTAAATAATACATTCC
* * ** **
575888 AAAGAATGTTAACCTAAAAGAAT-GTTTGAA
1 AAAGAA-G--AAACT-AAATAATACATT-CC
575918 AAAGAAGAAACTAAATAATACATTCC
1 AAAGAAGAAACTAAATAATACATTCC
575944 AAAGA
1 AAAGA
575949 CGACTCAATT
Statistics
Matches: 43, Mismatches: 12, Indels: 12
0.64 0.18 0.18
Matches are distributed among these distances:
26 17 0.40
27 7 0.16
29 7 0.16
30 12 0.28
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.21
Consensus pattern (26 bp):
AAAGAAGAAACTAAATAATACATTCC
Found at i:575924 original size:56 final size:56
Alignment explanation
Indices: 575838--575948 Score: 222
Period size: 56 Copynumber: 2.0 Consensus size: 56
575828 CTCTCATCAT
575838 TGTTAACCTAAAAGAATGTTTGAAAAAGAAGAAACTAAATAATACATTCCAAAGAA
1 TGTTAACCTAAAAGAATGTTTGAAAAAGAAGAAACTAAATAATACATTCCAAAGAA
575894 TGTTAACCTAAAAGAATGTTTGAAAAAGAAGAAACTAAATAATACATTCCAAAGA
1 TGTTAACCTAAAAGAATGTTTGAAAAAGAAGAAACTAAATAATACATTCCAAAGA
575949 CGACTCAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.53, C:0.11, G:0.13, T:0.23
Consensus pattern (56 bp):
TGTTAACCTAAAAGAATGTTTGAAAAAGAAGAAACTAAATAATACATTCCAAAGAA
Found at i:585831 original size:30 final size:30
Alignment explanation
Indices: 585795--585859 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
585785 AATTATTAGT
* *
585795 AAGTTTATTTTTTTGTCACTTAATTATAAA
1 AAGTTTATTTTCTGGTCACTTAATTATAAA
*
585825 CAGTTTATTTTCTGGTCACTTAATTATAAA
1 AAGTTTATTTTCTGGTCACTTAATTATAAA
585855 AAGTT
1 AAGTT
585860 ATAAAATGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.49
Consensus pattern (30 bp):
AAGTTTATTTTCTGGTCACTTAATTATAAA
Found at i:588617 original size:21 final size:21
Alignment explanation
Indices: 588588--588672 Score: 102
Period size: 21 Copynumber: 4.1 Consensus size: 21
588578 CTGAAAATGT
* *
588588 AAAA-GCAGTGAAGCAAGGTG
1 AAAAGGCAGTGAACCAAAGTG
588608 AAAAGGCAGTGAACCAAAGTG
1 AAAAGGCAGTGAACCAAAGTG
* *
588629 AAAAGGCTGTGAACCAAAATG
1 AAAAGGCAGTGAACCAAAGTG
*
588650 -AAAGAACAGTGAACCAAAGTG
1 AAAAG-GCAGTGAACCAAAGTG
588671 AA
1 AA
588673 GAAGCGTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
20 8 0.15
21 46 0.84
22 1 0.02
ACGTcount: A:0.49, C:0.13, G:0.27, T:0.11
Consensus pattern (21 bp):
AAAAGGCAGTGAACCAAAGTG
Found at i:591688 original size:24 final size:24
Alignment explanation
Indices: 591645--591690 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
591635 CATAGCCCCA
* *
591645 AAACACAAAAAGCAGGCATCTAAG
1 AAACACAAAAAGAACGCATCTAAG
*
591669 AAACACAAAAAGAACTCATCTA
1 AAACACAAAAAGAACGCATCTA
591691 CCGGTCCTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.57, C:0.22, G:0.11, T:0.11
Consensus pattern (24 bp):
AAACACAAAAAGAACGCATCTAAG
Found at i:597030 original size:3 final size:3
Alignment explanation
Indices: 597022--597059 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
597012 AACCAAAGCT
*
597022 TTA TTA TTA TTA TGA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
597060 TACATTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:607692 original size:15 final size:16
Alignment explanation
Indices: 607667--607699 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
607657 TGTCTTCCTT
607667 TAAAAATAATAAAAAC
1 TAAAAATAATAAAAAC
*
607683 TAAAAA-AATATAAAC
1 TAAAAATAATAAAAAC
607698 TA
1 TA
607700 TTCAAATGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (16 bp):
TAAAAATAATAAAAAC
Found at i:620010 original size:2 final size:2
Alignment explanation
Indices: 620003--620037 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
619993 CGTGTGATGG
620003 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
620038 CTTATTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.