Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012530.1 Kokia drynarioides strain JFW-HI SEQ_127537, 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: 532565
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 13 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:419355 original size:20 final size:20
Alignment explanation
Indices: 419311--419355 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
419301 AAAAGTGATC
*
419311 AAAAAGTACAAAAAAAAGAA
1 AAAAAATACAAAAAAAAGAA
* * *
419331 GAAAAATACAAGAAAAATAA
1 AAAAAATACAAAAAAAAGAA
419351 AAAAA
1 AAAAA
419356 GAAAAAAATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.80, C:0.04, G:0.09, T:0.07
Consensus pattern (20 bp):
AAAAAATACAAAAAAAAGAA
Found at i:421434 original size:6 final size:6
Alignment explanation
Indices: 421423--421448 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
421413 TTCTAACGAA
421423 TTTGTT TTTGTT TTTGTT TTTGTT TT
1 TTTGTT TTTGTT TTTGTT TTTGTT TT
421449 CCAGATCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTGTT
Found at i:426756 original size:32 final size:32
Alignment explanation
Indices: 426700--426760 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
426690 AGGAACCTTT
*
426700 AAATCAATTTGAGTAAAATCAAATCAAATAAA
1 AAATCAATTTGAGTAAAATAAAATCAAATAAA
* **
426732 AAATCAATTTGATTGGAATAAAATCAAAT
1 AAATCAATTTGAGTAAAATAAAATCAAAT
426761 TGAGATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (32 bp):
AAATCAATTTGAGTAAAATAAAATCAAATAAA
Found at i:427740 original size:49 final size:49
Alignment explanation
Indices: 427681--427791 Score: 186
Period size: 49 Copynumber: 2.3 Consensus size: 49
427671 ACTTTGGGAG
* * *
427681 TTCAATATTGGGTCATTACTTGATAGATTAAAGGCAATAATGGTGGGTC
1 TTCAACATTGGGTCATTACTTGATAGATTAAAGGAAATAACGGTGGGTC
*
427730 TTCAACATTGGGCCATTACTTGATAGATTAAAGGAAATAACGGTGGGTC
1 TTCAACATTGGGTCATTACTTGATAGATTAAAGGAAATAACGGTGGGTC
427779 TTCAACATTGGGT
1 TTCAACATTGGGT
427792 GAAAAAAGTA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 57 1.00
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (49 bp):
TTCAACATTGGGTCATTACTTGATAGATTAAAGGAAATAACGGTGGGTC
Found at i:440002 original size:146 final size:146
Alignment explanation
Indices: 439738--440030 Score: 478
Period size: 146 Copynumber: 2.0 Consensus size: 146
439728 TAAATTGTTC
* * * **
439738 ATTGAATTGACTGCCATCTATACTTGACCATCAAGTACTGGTAGAAGTACCCTAAAATGTTGGAA
1 ATTGAATTGACTACCACCGATACTTGACCATCAAGTACCAGTAGAAGTACCCTAAAATGTTGGAA
* **
439803 ATGCGATTTTTACCCTTGATGAAATTGTGTTATGATTAAATATTAATCCAAAATATGACAGGTGA
66 ATGCGAATTTTACCCTTGATGAAATTGTGACATGATTAAATATTAATCCAAAATATGACAGGTGA
439868 ATTTTGCATTGAATAA
131 ATTTTGCATTGAATAA
* * * *
439884 ATTGAATTGACTACTACCGATACTTGACTATCAGGTACCAGTAGAAGTATCCTAAAATGTTGGAA
1 ATTGAATTGACTACCACCGATACTTGACCATCAAGTACCAGTAGAAGTACCCTAAAATGTTGGAA
439949 ATGCGAATTTTACCCTTGATGAAATTGTGACATGATTAAATATTAATCCAAAATATGACAGGTGA
66 ATGCGAATTTTACCCTTGATGAAATTGTGACATGATTAAATATTAATCCAAAATATGACAGGTGA
440014 ATTTTGCATTGAATAA
131 ATTTTGCATTGAATAA
440030 A
1 A
440031 GATTAAATAT
Statistics
Matches: 135, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
146 135 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (146 bp):
ATTGAATTGACTACCACCGATACTTGACCATCAAGTACCAGTAGAAGTACCCTAAAATGTTGGAA
ATGCGAATTTTACCCTTGATGAAATTGTGACATGATTAAATATTAATCCAAAATATGACAGGTGA
ATTTTGCATTGAATAA
Found at i:452067 original size:158 final size:157
Alignment explanation
Indices: 451717--452189 Score: 612
Period size: 158 Copynumber: 3.0 Consensus size: 157
451707 TATCATGAGT
* * **
451717 TGCTCACACAAGCTGCGGAATGGGCTTGCTCACACGAGCTGTGACTCGAGATGTTAGGCTACACA
1 TGCTCACACAAGCTGTGAAATGGGCTTGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACACA
* * *
451782 ATGCAGCTCACATGAGCTGTGGAGAATTC-GTAACAAATGCTGGATCTTAGCCATTGTAGGATAT
66 GTGCTGCTCACATGAGCTGTGGAGAA-TCAGTAACAAATGCTGGATCTTAGCCATTGTAGGAAAT
* *
451846 CTAAGATTAGCACCCTTATAACCTGTAA
130 CTAAGACTAGCACCCATATAACCTGTAA
* * * *
451874 TGCTCACACGAGCTGTGAAGTGGGCCTGCTCACACGAACTGTGGGTCGAGATGTTAGGCTACACA
1 TGCTCACACAAGCTGTGAAATGGGCTTGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACACA
* * * *
451939 GTGCTGCTTACACGAGCTATGGTGAATCAGTAACAAATG-TCGGATCTTAGCCATTGGTAGGAAA
66 GTGCTGCTCACATGAGCTGTGGAGAATCAGTAACAAATGCT-GGATCTTAGCCATT-GTAGGAAA
* *
452003 TCTAAGGCTAGCACTCATATAACCTGTAA
129 TCTAAGACTAGCACCCATATAACCTGTAA
*
452032 TGCTTACACAAGCTGTGAAATGGGCTTGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACAC-
1 TGCTCACACAAGCTGTGAAATGGGCTTGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACACA
* ** * *
452096 GATGCTGCTCACATGAGTTGTGGAGAATCTA-TAACAAATGCTTAATCTCAACCATCTGTAGGAA
66 G-TGCTGCTCACATGAGCTGTGGAGAATC-AGTAACAAATGCTGGATCTTAGCCAT-TGTAGGAA
* * *
452160 ATTTAAGACCAGAACCCATATAACCTGTAA
128 ATCTAAGACTAGCACCCATATAACCTGTAA
452190 ATCTAGAAAT
Statistics
Matches: 271, Mismatches: 38, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
156 3 0.01
157 102 0.38
158 163 0.60
159 3 0.01
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (157 bp):
TGCTCACACAAGCTGTGAAATGGGCTTGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACACA
GTGCTGCTCACATGAGCTGTGGAGAATCAGTAACAAATGCTGGATCTTAGCCATTGTAGGAAATC
TAAGACTAGCACCCATATAACCTGTAA
Found at i:453517 original size:15 final size:16
Alignment explanation
Indices: 453486--453517 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
453476 TTATCCAGTG
453486 AAGAATCAATCCTTGT
1 AAGAATCAATCCTTGT
453502 AAGAATCAAT-CTTGT
1 AAGAATCAATCCTTGT
453517 A
1 A
453518 GAAGAGGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (16 bp):
AAGAATCAATCCTTGT
Found at i:456023 original size:41 final size:41
Alignment explanation
Indices: 455929--456101 Score: 211
Period size: 41 Copynumber: 4.1 Consensus size: 41
455919 AACTCGATAT
** * * *
455929 TTAAATGGAAGACTCATGTCTTAGGTTGAGCATGAGAATTTATA
1 TTAAA-GGAAGACTCATGTCTCGGGATGGGAATGAG-A-TTATA
*
455973 TTAAAGGAAGACTCATGTCTCGGGATGGGAATAAGATTATA
1 TTAAAGGAAGACTCATGTCTCGGGATGGGAATGAGATTATA
* **
456014 TTAAAGGAAGACTTATGTCTCGAAATGGGAATGAGATTATA
1 TTAAAGGAAGACTCATGTCTCGGGATGGGAATGAGATTATA
** *
456055 TTAAAGGAAGACTCACATCTCGGGATGAGAATGAGATTATA
1 TTAAAGGAAGACTCATGTCTCGGGATGGGAATGAGATTATA
456096 TTAAAG
1 TTAAAG
456102 AAACACTAAT
Statistics
Matches: 113, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
41 83 0.73
42 1 0.01
43 24 0.21
44 5 0.04
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (41 bp):
TTAAAGGAAGACTCATGTCTCGGGATGGGAATGAGATTATA
Found at i:456116 original size:41 final size:41
Alignment explanation
Indices: 455968--456116 Score: 199
Period size: 41 Copynumber: 3.6 Consensus size: 41
455958 GCATGAGAAT
* *
455968 TTATATTAAAGGAAGACTCATGTCTCGGGATGGGAATAAGA
1 TTATATTAAAGGAAGACTCATATCTCGGGATGGGAATGAGA
* * **
456009 TTATATTAAAGGAAGACTTATGTCTCGAAATGGGAATGAGA
1 TTATATTAAAGGAAGACTCATATCTCGGGATGGGAATGAGA
* *
456050 TTATATTAAAGGAAGACTCACATCTCGGGATGAGAATGAGA
1 TTATATTAAAGGAAGACTCATATCTCGGGATGGGAATGAGA
* * *
456091 TTATATTAAAGAAACACTAATATCTC
1 TTATATTAAAGGAAGACTCATATCTC
456117 AAAATGAGAG
Statistics
Matches: 94, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 94 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (41 bp):
TTATATTAAAGGAAGACTCATATCTCGGGATGGGAATGAGA
Found at i:456122 original size:82 final size:82
Alignment explanation
Indices: 455968--456122 Score: 229
Period size: 82 Copynumber: 1.9 Consensus size: 82
455958 GCATGAGAAT
** * * * * *
455968 TTATATTAAAGGAAGACTCATGTCTCGGGATGGGAATAAGATTATATTAAAGGAAGACTTATGTC
1 TTATATTAAAGGAAGACTCACATCTCGGGATGAGAATAAGATTATATTAAAGAAACACTAATATC
*
456033 TCGAAATGGGAATGAGA
66 TCAAAATGGGAATGAGA
*
456050 TTATATTAAAGGAAGACTCACATCTCGGGATGAGAATGAGATTATATTAAAGAAACACTAATATC
1 TTATATTAAAGGAAGACTCACATCTCGGGATGAGAATAAGATTATATTAAAGAAACACTAATATC
456115 TCAAAATG
66 TCAAAATG
456123 AGAGTGAGGT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 64 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (82 bp):
TTATATTAAAGGAAGACTCACATCTCGGGATGAGAATAAGATTATATTAAAGAAACACTAATATC
TCAAAATGGGAATGAGA
Found at i:462922 original size:41 final size:41
Alignment explanation
Indices: 462865--462971 Score: 196
Period size: 41 Copynumber: 2.6 Consensus size: 41
462855 GCTTGAGAAT
462865 TTATATTAAAGGAAGACTCATGTCTCGAGATAAGAATGAGA
1 TTATATTAAAGGAAGACTCATGTCTCGAGATAAGAATGAGA
* *
462906 TTATATTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGA
1 TTATATTAAAGGAAGACTCATGTCTCGAGATAAGAATGAGA
462947 TTATATTAAAGGAAGACTCATGTCT
1 TTATATTAAAGGAAGACTCATGTCT
462972 TAAAATGTGC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.29
Consensus pattern (41 bp):
TTATATTAAAGGAAGACTCATGTCTCGAGATAAGAATGAGA
Found at i:463057 original size:40 final size:40
Alignment explanation
Indices: 462997--463095 Score: 171
Period size: 40 Copynumber: 2.5 Consensus size: 40
462987 GTTTATTTTT
462997 TTAAAAGGAAGACTTATGACTCGATAGAGCATAAGAGTGA
1 TTAAAAGGAAGACTTATGACTCGATAGAGCATAAGAGTGA
* * *
463037 TTAAAAGGAAGACTTGTGACTCGGTAGAGCATAAGATTGA
1 TTAAAAGGAAGACTTATGACTCGATAGAGCATAAGAGTGA
463077 TTAAAAGGAAGACTTATGA
1 TTAAAAGGAAGACTTATGA
463096 ACCTATGAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.41, C:0.09, G:0.25, T:0.24
Consensus pattern (40 bp):
TTAAAAGGAAGACTTATGACTCGATAGAGCATAAGAGTGA
Found at i:465334 original size:13 final size:13
Alignment explanation
Indices: 465316--465340 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
465306 ATGAAGCTTT
465316 AAGAGAGAAAAAA
1 AAGAGAGAAAAAA
465329 AAGAGAGAAAAA
1 AAGAGAGAAAAA
465341 GTTTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAGAGAGAAAAAA
Found at i:470804 original size:17 final size:18
Alignment explanation
Indices: 470784--470817 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
470774 GCAAGTAAGT
470784 TGACAAAAT-AAATACAG
1 TGACAAAATAAAATACAG
*
470801 TGACAAGATAAAATACA
1 TGACAAAATAAAATACA
470818 TGGGTCGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.12, G:0.12, T:0.18
Consensus pattern (18 bp):
TGACAAAATAAAATACAG
Found at i:480041 original size:41 final size:41
Alignment explanation
Indices: 479984--480163 Score: 202
Period size: 41 Copynumber: 4.4 Consensus size: 41
479974 GCTTTGACCT
*
479984 CTCTGACCTTTAGCGGGACTTTCTCATAAACGCCGCTAATG
1 CTCTGACCTTTAGCGGGACTTTCTCATAAACACCGCTAATG
* * *
480025 CTCTGACCTTTAGCGGGGATTTTC-CATAAACGCCGTTAATG
1 CTCTGACCTTTAGC-GGGACTTTCTCATAAACACCGCTAATG
* * *
480066 CTCTGACCTTTAGTAGTG-CTTTCTCATAAACATCGCTAATG
1 CTCTGACCTTTAG-CGGGACTTTCTCATAAACACCGCTAATG
* ** * * *
480107 CTCTGACCTTTAACGACATTTTCCCCATAAACACCGCTAATC
1 CTCTGACCTTTAGCGGGACTTT-CTCATAAACACCGCTAATG
480149 CTCTGACCTTTAGCG
1 CTCTGACCTTTAGCG
480164 TTATTTTCCC
Statistics
Matches: 117, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
40 5 0.04
41 74 0.63
42 38 0.32
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.32
Consensus pattern (41 bp):
CTCTGACCTTTAGCGGGACTTTCTCATAAACACCGCTAATG
Found at i:480153 original size:42 final size:42
Alignment explanation
Indices: 480090--480179 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
480080 AGTGCTTTCT
* *
480090 CATAAACATCGCTAATGCTCTGACCTTTAACGACATTTTCCC
1 CATAAACACCGCTAATCCTCTGACCTTTAACGACATTTTCCC
* **
480132 CATAAACACCGCTAATCCTCTGACCTTTAGCGTTATTTTCCC
1 CATAAACACCGCTAATCCTCTGACCTTTAACGACATTTTCCC
480174 CATAAA
1 CATAAA
480180 TGTCACTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.29, C:0.31, G:0.09, T:0.31
Consensus pattern (42 bp):
CATAAACACCGCTAATCCTCTGACCTTTAACGACATTTTCCC
Found at i:480189 original size:42 final size:42
Alignment explanation
Indices: 480090--480194 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 42
480080 AGTGCTTTCT
* *
480090 CATAAACATCGCTAATGCTCTGACCTTTAACGACATTTTCCC
1 CATAAACACCACTAATGCTCTGACCTTTAACGACATTTTCCC
* * * **
480132 CATAAACACCGCTAATCCTCTGACCTTTAGCGTTATTTTCCC
1 CATAAACACCACTAATGCTCTGACCTTTAACGACATTTTCCC
***
480174 CATAAATGTCACTAATGCTCT
1 CATAAACACCACTAATGCTCT
480195 TTCTCATATT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (42 bp):
CATAAACACCACTAATGCTCTGACCTTTAACGACATTTTCCC
Found at i:485940 original size:18 final size:18
Alignment explanation
Indices: 485917--485952 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
485907 CGTGTTATCA
485917 AAAGAAAATAA-AAAAAAG
1 AAAGAAAA-AAGAAAAAAG
485935 AAAGAAAAAAGAAAAAAG
1 AAAGAAAAAAGAAAAAAG
485953 GGGTCAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (18 bp):
AAAGAAAAAAGAAAAAAG
Found at i:486767 original size:10 final size:10
Alignment explanation
Indices: 486752--486793 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
486742 GGTTTCACCC
*
486752 AAAAAAGAAG
1 AAAAAAAAAG
486762 AAAAAAAAAG
1 AAAAAAAAAG
*
486772 AAAAAAAAAA
1 AAAAAAAAAG
486782 AACAAAAAAAG
1 AA-AAAAAAAG
486793 A
1 A
486794 GGAGAGGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 20 0.71
11 8 0.29
ACGTcount: A:0.88, C:0.02, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:486770 original size:13 final size:12
Alignment explanation
Indices: 486752--486791 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
486742 GGTTTCACCC
486752 AAAAAAGAAGAAA
1 AAAAAAGAA-AAA
486765 AAAAAAGAAAAA
1 AAAAAAGAAAAA
486777 AAAAAA-ACAAAA
1 AAAAAAGA-AAAA
486789 AAA
1 AAA
486792 GAGGAGAGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 1 0.04
12 16 0.62
13 9 0.35
ACGTcount: A:0.90, C:0.03, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:487793 original size:50 final size:50
Alignment explanation
Indices: 487732--487916 Score: 193
Period size: 49 Copynumber: 3.8 Consensus size: 50
487722 CCACAATGAC
*
487732 GAACCTTGTACCTTAAAAGATGAGATGGGAAGGATTGAGGCTGCAACGGT
1 GAACCTTGTACCTTAAAAGATGAGATGGGAAGGATTGAGGCCGCAACGGT
* * * *
487782 GAA-TTTGGTACCAT-AAAGAT-ATGAAGGGAAAGG-TTGAGACCGCAACGGT
1 GAACCTT-GTACCTTAAAAGATGA-GATGGG-AAGGATTGAGGCCGCAACGGT
* * *
487831 GAACCTTGTACCTTAAAAGATGAGATGGGAAGGATTGAGGCCAC-ATGGC
1 GAACCTTGTACCTTAAAAGATGAGATGGGAAGGATTGAGGCCGCAACGGT
* * * *
487880 GAACCTTGTACCTT-AGAGATGTGACGGGAAAGATTGA
1 GAACCTTGTACCTTAAAAGATGAGATGGGAAGGATTGA
487917 ACCCGCAATG
Statistics
Matches: 112, Mismatches: 16, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
48 20 0.18
49 57 0.51
50 34 0.30
51 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.31, T:0.22
Consensus pattern (50 bp):
GAACCTTGTACCTTAAAAGATGAGATGGGAAGGATTGAGGCCGCAACGGT
Found at i:487842 original size:49 final size:50
Alignment explanation
Indices: 487706--487916 Score: 184
Period size: 49 Copynumber: 4.3 Consensus size: 50
487696 TATAGGTTTA
* * *
487706 AAGGGAAAGGTTGAGGCCACAATGACGAACCTTGTACCTTAAAAGATGAG
1 AAGGGAAAGGTTGAGGCCGCAACGGCGAACCTTGTACCTTAAAAGATGAG
* * * * *
487756 ATGGG-AAGGATTGAGGCTGCAACGGTGAA-TTTGGTACCAT-AAAGAT-ATG
1 AAGGGAAAGG-TTGAGGCCGCAACGGCGAACCTT-GTACCTTAAAAGATGA-G
* *
487805 AAGGGAAAGGTTGAGACCGCAACGGTGAACCTTGTACCTTAAAAGATGAG
1 AAGGGAAAGGTTGAGGCCGCAACGGCGAACCTTGTACCTTAAAAGATGAG
* * * * *
487855 ATGGG-AAGGATTGAGGCCAC-ATGGCGAACCTTGTACCTT-AGAGATGTG
1 AAGGGAAAGG-TTGAGGCCGCAACGGCGAACCTTGTACCTTAAAAGATGAG
* *
487903 ACGGGAAAGATTGA
1 AAGGGAAAGGTTGA
487917 ACCCGCAATG
Statistics
Matches: 130, Mismatches: 22, Indels: 20
0.76 0.13 0.12
Matches are distributed among these distances:
48 16 0.12
49 64 0.49
50 49 0.38
51 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.31, T:0.20
Consensus pattern (50 bp):
AAGGGAAAGGTTGAGGCCGCAACGGCGAACCTTGTACCTTAAAAGATGAG
Found at i:488122 original size:43 final size:43
Alignment explanation
Indices: 487981--488125 Score: 121
Period size: 43 Copynumber: 3.3 Consensus size: 43
487971 CATCACCGTT
* * * * *
487981 CAATCTTTTACCCCTAAGTCAAGAGGGGCAAATTAAAACCACATTT
1 CAATCTTTTATCCCTAA-TCATGA--GGCAGAGTAAAACCACATTC
* * *
488027 TACTCTTATATCCCTAATCATGAGGCAGAGTAAAACCACATTC
1 CAATCTTTTATCCCTAATCATGAGGCAGAGTAAAACCACATTC
* * * * *
488070 CAATATTTTATCCCTAATCATG-GTGTAGATTGAAGCCACATTC
1 CAATCTTTTATCCCTAATCATGAG-GCAGAGTAAAACCACATTC
*
488113 CGATCTTTTATCC
1 CAATCTTTTATCC
488126 TTAGTCGAGA
Statistics
Matches: 80, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
42 1 0.01
43 61 0.76
45 5 0.06
46 13 0.16
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.31
Consensus pattern (43 bp):
CAATCTTTTATCCCTAATCATGAGGCAGAGTAAAACCACATTC
Found at i:488468 original size:122 final size:121
Alignment explanation
Indices: 488144--488548 Score: 429
Period size: 122 Copynumber: 3.3 Consensus size: 121
488134 GAAGGGCAGA
* * * * *
488144 TCAAACCCCATCTTCCTAATGAGATACAAAGAAGTAGCTCAGACAATGAAGCGATCATCTTCCTA
1 TCAAAACCCATCTTCCTGATGAGATACAAAGAAGTGGGTCAGACAATGAAGCGATCATCTTCTTA
* * ** *
488209 GGAAGGTACAGAGAAGTAGACCAAATCAATGAAGCGGAGCTCAATATGTGTAAAACT
66 TG-AGGTACAGAGAAGTGGACCAAATCAATGAAGCAAAGCTCAATATGAGTAAAACT
* * *
488266 TCAAAACCCATCTTCCTGATGAGACACAGAGAAGTGGGTCAGACAATAAAGCGATCATCTTCTTA
1 TCAAAACCCATCTTCCTGATGAGATACAAAGAAGTGGGTCAGACAATGAAGCGATCATCTTCTTA
* * * *
488331 GTGAGGTATAAAGAAGTGGACTAAATCAATGAAGCAAAGCTC-ATGTGAGTAAAACT
66 -TGAGGTACAGAGAAGTGGACCAAATCAATGAAGCAAAGCTCAATATGAGTAAAACT
* * * *
488387 TCGAAACTCCATCTTCTTGATGAGATATAAAGAAGTGGGTCAAACAATGAAGCGATCATCTTCTT
1 TCAAAAC-CCATCTTCCTGATGAGATACAAAGAAGTGGGTCAGACAATGAAGCGATCATCTTCTT
* * * * * * *
488452 GATGAGATACAGAGAAGTGGCCCAAAAT-AATGAGGTGAAA-CTCAATACGAGTGAAATT
65 -ATGAGGTACAGAGAAGTGGACC-AAATCAATGAAG-CAAAGCTCAATATGAGTAAAACT
* * * * * *
488510 TCAAATCTCATATTCCTAATGAGGTACAGAGAAGTGGGT
1 TCAAAACCCATCTTCCTGATGAGATACAAAGAAGTGGGT
488549 GCAAAACAGT
Statistics
Matches: 233, Mismatches: 44, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
121 18 0.08
122 191 0.82
123 24 0.10
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (121 bp):
TCAAAACCCATCTTCCTGATGAGATACAAAGAAGTGGGTCAGACAATGAAGCGATCATCTTCTTA
TGAGGTACAGAGAAGTGGACCAAATCAATGAAGCAAAGCTCAATATGAGTAAAACT
Found at i:492853 original size:21 final size:21
Alignment explanation
Indices: 492811--492857 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
492801 AAAAATTAGA
*
492811 TTTTATTAATTTTTTTGGTATT
1 TTTTATT-ATTTTTTTGCTATT
492833 TTTTATT-TTTTTTTGACTATT
1 TTTTATTATTTTTTTG-CTATT
492854 TTTT
1 TTTT
492858 CTTTATTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 8 0.35
22 7 0.30
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.77
Consensus pattern (21 bp):
TTTTATTATTTTTTTGCTATT
Found at i:494261 original size:27 final size:27
Alignment explanation
Indices: 494225--494276 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
494215 AACCCCAAAT
*
494225 AAAAACAAAACCATTGTCACATAACTA
1 AAAAACAAAACCATTGCCACATAACTA
494252 AAAAACAAAACCATTGCCACATAAC
1 AAAAACAAAACCATTGCCACATAAC
494277 CAATACCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.56, C:0.25, G:0.04, T:0.15
Consensus pattern (27 bp):
AAAAACAAAACCATTGCCACATAACTA
Found at i:510501 original size:16 final size:16
Alignment explanation
Indices: 510480--510511 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
510470 AATATTTTTT
510480 ATGAATTAATTGATTG
1 ATGAATTAATTGATTG
*
510496 ATGAATTATTTGATTG
1 ATGAATTAATTGATTG
510512 TGTTTGATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (16 bp):
ATGAATTAATTGATTG
Found at i:514299 original size:37 final size:37
Alignment explanation
Indices: 514256--514338 Score: 123
Period size: 37 Copynumber: 2.2 Consensus size: 37
514246 GGGCATGTCG
*
514256 AACATGCAAATCGAATAATATCATGTACG-ACATGTTT
1 AACATGCAAACCGAATAATATCATGTA-GAACATGTTT
* *
514293 AACATGCAAACCGAATAATATTATGTAGAACGTGTTT
1 AACATGCAAACCGAATAATATCATGTAGAACATGTTT
514330 AACATGCAA
1 AACATGCAA
514339 TCAAATAGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
36 1 0.02
37 41 0.98
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (37 bp):
AACATGCAAACCGAATAATATCATGTAGAACATGTTT
Found at i:522485 original size:15 final size:16
Alignment explanation
Indices: 522465--522497 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
522455 TATTCTTAAG
522465 ATTATAATA-TTTTAT
1 ATTATAATATTTTTAT
*
522480 ATTATATTATTTTTAT
1 ATTATAATATTTTTAT
522496 AT
1 AT
522498 ATTGTGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTATAATATTTTTAT
Found at i:522970 original size:23 final size:23
Alignment explanation
Indices: 522942--522988 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
522932 TATAATATTT
*
522942 AAAATAATATATT-TTAAAATTAA
1 AAAATAATA-ATTAATAAAATTAA
522965 AAAATAATAATTAATAAAATTAA
1 AAAATAATAATTAATAAAATTAA
522988 A
1 A
522989 TAATTCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AAAATAATAATTAATAAAATTAA
Found at i:525703 original size:2 final size:2
Alignment explanation
Indices: 525696--525727 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
525686 GTAAGTTGAA
525696 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
525728 CAGAGTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:526063 original size:17 final size:17
Alignment explanation
Indices: 526028--526102 Score: 64
Period size: 17 Copynumber: 4.4 Consensus size: 17
526018 GTAAAAAGTA
* *
526028 GTTATAAGAATATGAAAG
1 GTTA-AAGAAAATGGAAG
526046 GTTAAAGAAAATGGAAG
1 GTTAAAGAAAATGGAAG
**
526063 GTTAAAGGTCAA-GAGAA-
1 GTTAAA-GAAAATG-GAAG
*
526080 GTTAAAGAAGATGGAAG
1 GTTAAAGAAAATGGAAG
526097 GTTAAA
1 GTTAAA
526103 AGTCAAGGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
16 5 0.11
17 31 0.67
18 10 0.22
ACGTcount: A:0.49, C:0.01, G:0.28, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAAATGGAAG
Found at i:526094 original size:34 final size:33
Alignment explanation
Indices: 526046--526113 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 33
526036 AATATGAAAG
*
526046 GTTAAAGAAAATGGAAGGTTAAAGGTCAAGAGAA
1 GTTAAAGAAAATGGAAGGTTAAAAGTCAAG-GAA
*
526080 GTTAAAGAAGATGGAAGGTTAAAAGTCAAGGAA
1 GTTAAAGAAAATGGAAGGTTAAAAGTCAAGGAA
526113 G
1 G
526114 ATGAAAGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 4 0.12
34 28 0.88
ACGTcount: A:0.49, C:0.03, G:0.31, T:0.18
Consensus pattern (33 bp):
GTTAAAGAAAATGGAAGGTTAAAAGTCAAGGAA
Found at i:526121 original size:34 final size:34
Alignment explanation
Indices: 526049--526121 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 34
526039 ATGAAAGGTT
* *
526049 AAAGAAAATGGAAGGTTAAAGGTCAAGAGAAGTT
1 AAAGAAAATGGAAGGTTAAAAGTCAAGAGAAGTG
*
526083 AAAGAAGATGGAAGGTTAAAAGTCAAG-GAAGATG
1 AAAGAAAATGGAAGGTTAAAAGTCAAGAGAAG-TG
526117 AAAGA
1 AAAGA
526122 TTGAACATCC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 4 0.11
34 31 0.89
ACGTcount: A:0.52, C:0.03, G:0.30, T:0.15
Consensus pattern (34 bp):
AAAGAAAATGGAAGGTTAAAAGTCAAGAGAAGTG
Found at i:531035 original size:33 final size:34
Alignment explanation
Indices: 530986--531049 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
530976 TAATATAAAT
* * *
530986 ATAAGTAGTCCTTTAAC-AAACTTTCAAGCAAAC
1 ATAAGTAATCCCTTAACAAAACTTGCAAGCAAAC
531019 ATAAGTAATCCCTTAACAAAACTTGCAAGCA
1 ATAAGTAATCCCTTAACAAAACTTGCAAGCA
531050 TAATATAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 15 0.56
34 12 0.44
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (34 bp):
ATAAGTAATCCCTTAACAAAACTTGCAAGCAAAC
Found at i:531559 original size:34 final size:34
Alignment explanation
Indices: 531516--531583 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
531506 AATATGAAAA
* *
531516 GTTAAGGAAGATGGAAGGTTAAAGGTTAAGGGAG
1 GTTAAGGAAGATGGAAGGTTAAAAGTCAAGGGAG
*
531550 GTTAAGGAAGATGGGAGGTTAAAAGTCAAGGGAG
1 GTTAAGGAAGATGGAAGGTTAAAAGTCAAGGGAG
531584 ATGAAAGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.38, C:0.01, G:0.41, T:0.19
Consensus pattern (34 bp):
GTTAAGGAAGATGGAAGGTTAAAAGTCAAGGGAG
Found at i:531565 original size:17 final size:17
Alignment explanation
Indices: 531516--531571 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
531506 AATATGAAAA
*
531516 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGGAG
*
531533 GTTAAAGGTTA-A-GGGAG
1 GTT-AAGG-AAGATGGGAG
531550 GTTAAGGAAGATGGGAG
1 GTTAAGGAAGATGGGAG
531567 GTTAA
1 GTTAA
531572 AAGTCAAGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 1 0.03
16 5 0.16
17 20 0.62
18 5 0.16
19 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.41, T:0.21
Consensus pattern (17 bp):
GTTAAGGAAGATGGGAG
Found at i:531652 original size:2 final size:2
Alignment explanation
Indices: 531647--531677 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
531637 AAATCTAGTC
*
531647 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
531678 AGTTTAGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:532542 original size:2 final size:2
Alignment explanation
Indices: 532529--532565 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
532519 TTATTCGAAA
*
532529 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Done.