Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012600.1 Kokia drynarioides strain JFW-HI SEQ_127609, 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: 110085
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3077 original size:48 final size:48
Alignment explanation
Indices: 3006--3098 Score: 177
Period size: 48 Copynumber: 1.9 Consensus size: 48
2996 CTGTAAAATA
*
3006 ACCGTGTTTCCTACAAAAAGTCGTATAGACATGCATGACTCAACCATG
1 ACCGTGTTTCCTACAAAAAGTCGTATAGACATACATGACTCAACCATG
3054 ACCGTGTTTCCTACAAAAAGTCGTATAGACATACATGACTCAACC
1 ACCGTGTTTCCTACAAAAAGTCGTATAGACATACATGACTCAACC
3099 CGATTTGGAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (48 bp):
ACCGTGTTTCCTACAAAAAGTCGTATAGACATACATGACTCAACCATG
Found at i:11159 original size:81 final size:81
Alignment explanation
Indices: 11022--11192 Score: 288
Period size: 81 Copynumber: 2.1 Consensus size: 81
11012 TTTTACTGAT
* *
11022 GATCAGATCTCAATTCCTCAAAATAAGAATGCAATGGTTGAGAAACTCAAGGAGAAGATTGAAGG
1 GATCAGATCTCAATTCCTCAAAATAAGAATGCAATGGTTGAGAAACTCAAGCAGAAGAATGAAGG
11087 GGCCAAAGGAGGAAAG
66 GGCCAAAGGAGGAAAG
* * * *
11103 GATCAGATCTTAATTCCTTAAAATCAGAATGCAATGGTTGAGAAACTCGAGCAGAAGAATGAAGG
1 GATCAGATCTCAATTCCTCAAAATAAGAATGCAATGGTTGAGAAACTCAAGCAGAAGAATGAAGG
11168 GGCCAAAGGAGGAAAG
66 GGCCAAAGGAGGAAAG
11184 GATCAGATC
1 GATCAGATC
11193 AAGTATCTTC
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 84 1.00
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.18
Consensus pattern (81 bp):
GATCAGATCTCAATTCCTCAAAATAAGAATGCAATGGTTGAGAAACTCAAGCAGAAGAATGAAGG
GGCCAAAGGAGGAAAG
Found at i:14002 original size:73 final size:73
Alignment explanation
Indices: 13883--14029 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
13873 GGCGTCTAAG
13883 TTTGAGTGGTTTTGGAAAGCTAAAGAGTCTTCCCCCCCAACTTCAATTCCTCACTGCCCTCGAAA
1 TTTGAGTGGTTTTGGAAAGCTAAAGAGTCTTCCCCCCCAACTTCAATTCCTCACTGCCCTCGAAA
13948 CTCTGGTA
66 CTCTGGTA
*
13956 TTTGAGTGGTTTTGGAAAGCTAAAGAGTCTTCCCCTCCAACTTCAATTCCTCACTGCCCTCGAAA
1 TTTGAGTGGTTTTGGAAAGCTAAAGAGTCTTCCCCCCCAACTTCAATTCCTCACTGCCCTCGAAA
14021 CTCTGGTA
66 CTCTGGTA
14029 T
1 T
14030 AGAAGACTTG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (73 bp):
TTTGAGTGGTTTTGGAAAGCTAAAGAGTCTTCCCCCCCAACTTCAATTCCTCACTGCCCTCGAAA
CTCTGGTA
Found at i:16399 original size:15 final size:15
Alignment explanation
Indices: 16368--16405 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
16358 TCTAAATTAC
16368 ATAATAT-ATAAAAA
1 ATAATATAATAAAAA
*
16382 ATAATATAATAGAAA
1 ATAATATAATAAAAA
*
16397 ATATTATAA
1 ATAATATAA
16406 ACTTAAAACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (15 bp):
ATAATATAATAAAAA
Found at i:25976 original size:13 final size:15
Alignment explanation
Indices: 25952--25994 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
25942 CAAAAGGTTC
25952 GAAAAGAAAAAAAG-
1 GAAAAGAAAAAAAGA
25966 GAAAA-AAAAAAAGA
1 GAAAAGAAAAAAAGA
25980 GAAAGAGAATAAAAA
1 GAAA-AGAA-AAAAA
25995 ATGGTTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.32
14 9 0.36
15 1 0.04
16 2 0.08
17 5 0.20
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (15 bp):
GAAAAGAAAAAAAGA
Found at i:26783 original size:23 final size:23
Alignment explanation
Indices: 26726--26771 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
26716 CTGACGTGGC
* *
26726 ATCCAGTCAACAGCTTCTAGAAG
1 ATCCAGCCAGCAGCTTCTAGAAG
26749 ATCCAGCCAGCAGCTTCTAGAAG
1 ATCCAGCCAGCAGCTTCTAGAAG
26772 GTCTAGTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.20
Consensus pattern (23 bp):
ATCCAGCCAGCAGCTTCTAGAAG
Found at i:31387 original size:209 final size:207
Alignment explanation
Indices: 30988--31571 Score: 760
Period size: 209 Copynumber: 2.8 Consensus size: 207
30978 TAACGGGACA
* *
30988 ATGTTCATCTCTTGAAAGTCTTAGTATTTTCGCTTGCATAAAATTAAGCAAGATTGGAGACGGAT
1 ATGTTCATCTCTTGAAAG-CTTAGCATTTTAGC-TGCA-AAAATTAAGCAAGATTGGAGACGGAT
* *
31053 TATCTACCTCCACTTGTCTCAAAGAACTAAATATATGGCATTGTCTTAATTTAAGTTCGATTCCA
63 TATCTACCTCCACTTGTCTCAAAGAATTAAATATATGGTATTGTCTTAATTTAAGTTCGATTCCA
* * * * * * *
31118 AATTTGGAAGGGTTTCCCTCTCTTCAAAATCTATCAATTGAAAGGTGCGACGAGTTGGAAGTTAT
128 GATTTGGAAGGATTTTCCTCTCTTCAATATGTATCAATTGAAAGGTGCGACAAATTGGAAGTTAT
*
31183 TCCGATAACCGGAAG
193 TCCGATAACAGGAAG
31198 ATGTTCATCTCTTGAAAGCTTAGCATTTCTAGCTGCGAAAAATTAAGCAAGATTGGAGACGGATT
1 ATGTTCATCTCTTGAAAGCTTAGCATTT-TAGCTGC-AAAAATTAAGCAAGATTGGAGACGGATT
** * *
31263 ATCTAATTCCACTTGTCTGAAAGAATTAGATATATGGTATTGTCTTAATTTAAGTTCGATTCCAG
64 ATCTACCTCCACTTGTCTCAAAGAATTAAATATATGGTATTGTCTTAATTTAAGTTCGATTCCAG
* * *
31328 ATTTGGAAGGATTTTCCTCTCTTCAATATGTATCAATTG-ATGGCTGTGACAAATTGGAAGTTCT
129 ATTTGGAAGGATTTTCCTCTCTTCAATATGTATCAATTGAAAGG-TGCGACAAATTGGAAGTTAT
*
31392 TCCTATAACAGGAAG
193 TCCGATAACAGGAAG
** * *
31407 ATGTTCATCTCTTGAAAAGCTTAGCATTTTCAATTGCCAAAAAGTAAGCAAGATTGAAGACGGAT
1 ATGTTCATCTCTTG-AAAGCTTAGCATTTT-AGCTG-CAAAAATTAAGCAAGATTGGAGACGGAT
* * * * * * * *
31472 TATCTACCTCCATTTGTCACAAAAAATTAAATCTA-GATCATTGTCCTAGTTTAAGTTTGATTCC
63 TATCTACCTCCACTTGTCTCAAAGAATTAAATATATGGT-ATTGTCTTAATTTAAGTTCGATTCC
*
31536 AGATTTGG-AGGATTTTCCTCTCTTCAATATGCATCA
127 AGATTTGGAAGGATTTTCCTCTCTTCAATATGTATCA
31572 GTTTGTTATT
Statistics
Matches: 330, Mismatches: 37, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
208 3 0.01
209 205 0.62
210 121 0.37
211 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (207 bp):
ATGTTCATCTCTTGAAAGCTTAGCATTTTAGCTGCAAAAATTAAGCAAGATTGGAGACGGATTAT
CTACCTCCACTTGTCTCAAAGAATTAAATATATGGTATTGTCTTAATTTAAGTTCGATTCCAGAT
TTGGAAGGATTTTCCTCTCTTCAATATGTATCAATTGAAAGGTGCGACAAATTGGAAGTTATTCC
GATAACAGGAAG
Found at i:35900 original size:28 final size:29
Alignment explanation
Indices: 35833--35910 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 29
35823 CAACGACGAA
* * *
35833 CACATGTGGCGGATAGTCAAACCAGCGAG
1 CACATATGGCGGACAGTCCAACCAGCGAG
* *
35862 CAAATAAGGCGGACAGTCCAA-CAGCGAG
1 CACATATGGCGGACAGTCCAACCAGCGAG
* * *
35890 CACATCTGGCGAACTGTCCAA
1 CACATATGGCGGACAGTCCAA
35911 ATGCGAGTCT
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
28 23 0.59
29 16 0.41
ACGTcount: A:0.33, C:0.27, G:0.27, T:0.13
Consensus pattern (29 bp):
CACATATGGCGGACAGTCCAACCAGCGAG
Found at i:45337 original size:129 final size:129
Alignment explanation
Indices: 45102--45357 Score: 379
Period size: 129 Copynumber: 2.0 Consensus size: 129
45092 CAGTATAAGT
* * ** *
45102 TGTTTTGATTGTGACTTGTGGAGAAGAAGAGTAAGGCTAAACGCTGTATCTATATATAGTATCCT
1 TGTTCTGATTGTGACTTGTGGAGAAGAAGAGGAAGGCTAAACGCTAAATCTATATATAGTACCCT
** *
45167 GGTTGGGAACTGAGTATATGTCCTAAGCAACTTAAACTCTTTCTAAAAACATGATGGCAGTAAA
66 GACTGGGAACTGAGTATATGTCCTAAGCAACTTAAACTCTTTCTAAAAACATCATGGCAGTAAA
* *
45231 TGTTCTGATTGTGACTTGTGGAGAAGAAGAGGAAGGCTAAACTCTAAATCTATATATAGTGCCCT
1 TGTTCTGATTGTGACTTGTGGAGAAGAAGAGGAAGGCTAAACGCTAAATCTATATATAGTACCCT
* * *
45296 GACTGGTG-ACTGAGTATCTGTCCTAAGCAACTTAAGCTCTTTCTAAGAACATCATGGCAGTA
66 GACTGG-GAACTGAGTATATGTCCTAAGCAACTTAAACTCTTTCTAAAAACATCATGGCAGTA
45358 CTGTTTGTAT
Statistics
Matches: 113, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
129 112 0.99
130 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (129 bp):
TGTTCTGATTGTGACTTGTGGAGAAGAAGAGGAAGGCTAAACGCTAAATCTATATATAGTACCCT
GACTGGGAACTGAGTATATGTCCTAAGCAACTTAAACTCTTTCTAAAAACATCATGGCAGTAAA
Found at i:48551 original size:35 final size:36
Alignment explanation
Indices: 48497--48571 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 36
48487 AAAATAATAT
* * * *
48497 ATTTTGTTTATCTTGACTTGCAACCAATCTCTTA-A
1 ATTTTGTTTAACTTAACTTGAAAACAATCTCTTAGA
*
48532 ATTTTGTTTAACTTAACTTGAAAATAATCTCTTAGA
1 ATTTTGTTTAACTTAACTTGAAAACAATCTCTTAGA
48568 ATTT
1 ATTT
48572 GAGCCACACA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 29 0.85
36 5 0.15
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.47
Consensus pattern (36 bp):
ATTTTGTTTAACTTAACTTGAAAACAATCTCTTAGA
Found at i:54969 original size:2 final size:2
Alignment explanation
Indices: 54962--54996 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
54952 AGAACACGGT
54962 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
54997 TAATTTTTAA
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
Found at i:64853 original size:20 final size:19
Alignment explanation
Indices: 64830--64900 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
64820 AATTAAAAAA
64830 AAAATATCAAAATAATTTTC
1 AAAAT-TCAAAATAATTTTC
* *
64850 AAAATTTGAAAATAATTTTT
1 AAAA-TTCAAAATAATTTTC
*
64870 AAAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTT-TC
*
64889 AAAATTCTAAAT
1 AAAATTCAAAAT
64901 TATGTATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
18 4 0.09
19 19 0.43
20 20 0.45
21 1 0.02
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.38
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTC
Found at i:64892 original size:19 final size:19
Alignment explanation
Indices: 64829--64900 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
64819 AAATTAAAAA
64829 AAAAATATCAAAATAATTTT
1 AAAAAT-TCAAAATAATTTT
* *
64849 CAAAATTTGAAAATAATTTT
1 -AAAAATTCAAAATAATTTT
*
64869 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
*
64888 AAAAATTCTAAAT
1 AAAAATTCAAAAT
64901 TATGTATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
18 4 0.09
19 22 0.51
20 12 0.28
21 5 0.12
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.38
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:65160 original size:23 final size:22
Alignment explanation
Indices: 65109--65162 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
65099 GTTATATTTT
*
65109 AACAATATTTTAATTTAACATC
1 AACAATTTTTTAATTTAACATC
**
65131 ATTAATTTTTCTAATTTAAC-TC
1 AACAATTTTT-TAATTTAACATC
65153 GAACAATTTT
1 -AACAATTTT
65163 ACTCGATTCG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.46
Consensus pattern (22 bp):
AACAATTTTTTAATTTAACATC
Found at i:67138 original size:80 final size:80
Alignment explanation
Indices: 67005--67156 Score: 216
Period size: 80 Copynumber: 1.9 Consensus size: 80
66995 AGCGCAAAAC
* ** **
67005 CGTTGGTTAATCCAAATAGAGCTGGGCTCATTTAATGCGGTTTATTTGCTAGGCACTTGGTGCCA
1 CGTTGGTTAATCCAAATAGAGCTGGGCTCACTTAATGCGGTTTATCCGCTAGGCACCGGGTGCCA
67070 TGAATTGACGAATTT
66 TGAATTGACGAATTT
* * *
67085 CGTTGGTTGATCCAACTAGAGCTGGGTTCACTT-ATCGCGGTTTATCCGCTAGGCACCGGGTGCC
1 CGTTGGTTAATCCAAATAGAGCTGGGCTCACTTAAT-GCGGTTTATCCGCTAGGCACCGGGTGCC
67149 ATGAATTG
65 ATGAATTG
67157 GTGGAAATGG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
79 2 0.03
80 61 0.97
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (80 bp):
CGTTGGTTAATCCAAATAGAGCTGGGCTCACTTAATGCGGTTTATCCGCTAGGCACCGGGTGCCA
TGAATTGACGAATTT
Found at i:73256 original size:30 final size:30
Alignment explanation
Indices: 73221--73278 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
73211 TGAAAACATT
73221 TTTTAACAACAATGACTAAAATGAAAATGA
1 TTTTAACAACAATGACTAAAATGAAAATGA
* *
73251 TTTTAACAACAATGCCTAAAATTAAAAT
1 TTTTAACAACAATGACTAAAATGAAAAT
73279 TTTTATTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.52, C:0.12, G:0.07, T:0.29
Consensus pattern (30 bp):
TTTTAACAACAATGACTAAAATGAAAATGA
Found at i:73694 original size:27 final size:27
Alignment explanation
Indices: 73659--73713 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
73649 TATGTTTTAG
73659 TCATTTATGTTAATCTGTTGTAATATT
1 TCATTTATGTTAATCTGTTGTAATATT
73686 TCATTTATGTTAATCTGTTGTAATATT
1 TCATTTATGTTAATCTGTTGTAATATT
73713 T
1 T
73714 TAGTCATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.56
Consensus pattern (27 bp):
TCATTTATGTTAATCTGTTGTAATATT
Found at i:80653 original size:20 final size:20
Alignment explanation
Indices: 80625--80674 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
80615 GTAATTTTTT
* * *
80625 AACCTAAACCTTAAACTTTA
1 AACCCAAACCTCAAACCTTA
*
80645 AACCCAAACCTCGAACCTTA
1 AACCCAAACCTCAAACCTTA
80665 AACCCTAAAC
1 AACCC-AAAC
80675 ACACCTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.44, C:0.34, G:0.02, T:0.20
Consensus pattern (20 bp):
AACCCAAACCTCAAACCTTA
Found at i:81299 original size:56 final size:56
Alignment explanation
Indices: 81232--81345 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
81222 AGTTAAGCAT
81232 ATACCAAACATATCTTGGTAAATGAAGCATAACTCACATTCCCTTATCTCTCCAAC
1 ATACCAAACATATCTTGGTAAATGAAGCATAACTCACATTCCCTTATCTCTCCAAC
81288 ATACCAAACATATCTTGGTAAATGAAGCATAACTCACATTCCCTTATCTCTCCAAC
1 ATACCAAACATATCTTGGTAAATGAAGCATAACTCACATTCCCTTATCTCTCCAAC
81344 AT
1 AT
81346 GTCCCTGGGC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.36, C:0.28, G:0.07, T:0.29
Consensus pattern (56 bp):
ATACCAAACATATCTTGGTAAATGAAGCATAACTCACATTCCCTTATCTCTCCAAC
Found at i:82038 original size:23 final size:23
Alignment explanation
Indices: 81998--82155 Score: 217
Period size: 23 Copynumber: 6.9 Consensus size: 23
81988 CTTAATTCTG
81998 TAAGCACAAATCACATTAATATT
1 TAAGCACAAATCACATTAATATT
* * * *
82021 TAATCATAAATTATATTAATATT
1 TAAGCACAAATCACATTAATATT
82044 TAAGCACAAATCACATTAATATT
1 TAAGCACAAATCACATTAATATT
*
82067 TAAGCATAAATCACATTAATATT
1 TAAGCACAAATCACATTAATATT
* *
82090 TGAGCACAAATCAAATTAATATT
1 TAAGCACAAATCACATTAATATT
* *
82113 TGAGCACAAATCATATTAATATT
1 TAAGCACAAATCACATTAATATT
* *
82136 TAAGCATAGATCACATTAAT
1 TAAGCACAAATCACATTAAT
82156 TGTAATGACC
Statistics
Matches: 118, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 118 1.00
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (23 bp):
TAAGCACAAATCACATTAATATT
Found at i:85026 original size:23 final size:23
Alignment explanation
Indices: 84594--85024 Score: 547
Period size: 23 Copynumber: 18.7 Consensus size: 23
84584 AGGGTGTTAC
*
84594 ATTAATATTTAAGCACAAATCAC
1 ATTAATATTTAAGCACAAATCAT
* * *
84617 ATTAATATTTAATCATAAATTAT
1 ATTAATATTTAAGCACAAATCAT
* * *
84640 ATTAATATTTAGGTATAAATCAT
1 ATTAATATTTAAGCACAAATCAT
*
84663 ATTAATATTTAAGAACAAATCAT
1 ATTAATATTTAAGCACAAATCAT
* *
84686 ATTAACATTTGAGCACAAATCAT
1 ATTAATATTTAAGCACAAATCAT
*
84709 ATTAATATTTAAGCACAAATCAC
1 ATTAATATTTAAGCACAAATCAT
* *
84732 ATTAATATTTAAGCATAAATCAC
1 ATTAATATTTAAGCACAAATCAT
**
84755 ATTAATATTTGTGCACAAATCAT
1 ATTAATATTTAAGCACAAATCAT
* ** *
84778 ATTAATATTTAAGCATAAAGAAC
1 ATTAATATTTAAGCACAAATCAT
**
84801 ATTAATATTTGCGCACAAATCAT
1 ATTAATATTTAAGCACAAATCAT
**
84824 ATTAATATTTGCGCACAAATCAT
1 ATTAATATTTAAGCACAAATCAT
*
84847 ATTAATATTTAAGCACAAATCAC
1 ATTAATATTTAAGCACAAATCAT
*
84870 ATTAATATTTGAGCACACAAATCAT
1 ATTAATATTTAAG--CACAAATCAT
*
84895 ATTAATATTTAAGCACAAATCAC
1 ATTAATATTTAAGCACAAATCAT
* *
84918 ATTAATATTTGAGCACAAATCAC
1 ATTAATATTTAAGCACAAATCAT
*
84941 ATTAATATTTAAGCATAAATCAT
1 ATTAATATTTAAGCACAAATCAT
* *
84964 ATTAATACTTAAGCACAAATCAC
1 ATTAATATTTAAGCACAAATCAT
* *
84987 ATTAATATTTAATCATAAATCAT
1 ATTAATATTTAAGCACAAATCAT
85010 ATTAATATTTAAGCA
1 ATTAATATTTAAGCA
85025 TAGATATAAG
Statistics
Matches: 353, Mismatches: 53, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
23 332 0.94
25 21 0.06
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (23 bp):
ATTAATATTTAAGCACAAATCAT
Found at i:86273 original size:23 final size:23
Alignment explanation
Indices: 86245--86473 Score: 296
Period size: 23 Copynumber: 10.0 Consensus size: 23
86235 GTATGACAAT
*
86245 AAATCACATTAATATTTAGGCAC
1 AAATCACATTAATATTTAAGCAC
* * *
86268 AAATCATATTAATCTTTGAGCAC
1 AAATCACATTAATATTTAAGCAC
* *
86291 AATTCACATTAATATTTGAGCAC
1 AAATCACATTAATATTTAAGCAC
*
86314 AAATCATATTAATATTTAAGCAC
1 AAATCACATTAATATTTAAGCAC
86337 AAATCACATTAATATTTAAGCAC
1 AAATCACATTAATATTTAAGCAC
* *
86360 AAATCACATTAATATTTAAGTAT
1 AAATCACATTAATATTTAAGCAC
* ** *
86383 AAATCATATTAATATTTAAATAT
1 AAATCACATTAATATTTAAGCAC
* *
86406 AAATCACATTAATATTTGAGCAT
1 AAATCACATTAATATTTAAGCAC
* *
86429 AAATTATATTAATATTTAAGCAC
1 AAATCACATTAATATTTAAGCAC
*
86452 AAATCACATTAATATTTGAGCA
1 AAATCACATTAATATTTAAGCA
86474 TAGGTATAAG
Statistics
Matches: 180, Mismatches: 26, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 180 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (23 bp):
AAATCACATTAATATTTAAGCAC
Found at i:87728 original size:23 final size:23
Alignment explanation
Indices: 87695--87869 Score: 233
Period size: 23 Copynumber: 7.6 Consensus size: 23
87685 GTGTGACGAT
* *
87695 AAATTACATTAATATTTGAGCAC
1 AAATCACATTAATATTTAAGCAC
*
87718 AAATCATATTAATATTTAAGCAC
1 AAATCACATTAATATTTAAGCAC
*
87741 AATTCACATTAATATTTAAGCAC
1 AAATCACATTAATATTTAAGCAC
* *
87764 AAATCACATTAATATTTAAGTAT
1 AAATCACATTAATATTTAAGCAC
* *
87787 AAATCACATTAATATTTGAGCAT
1 AAATCACATTAATATTTAAGCAC
* * *
87810 AAATCACAATAATATTTGAGTAC
1 AAATCACATTAATATTTAAGCAC
* *
87833 AAATCATATTAATATTTAAGCAT
1 AAATCACATTAATATTTAAGCAC
87856 AAATCACATTAATA
1 AAATCACATTAATA
87870 ATTGAGCATA
Statistics
Matches: 133, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 133 1.00
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.35
Consensus pattern (23 bp):
AAATCACATTAATATTTAAGCAC
Found at i:94545 original size:26 final size:26
Alignment explanation
Indices: 94516--94568 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
94506 TATATTTATA
94516 TAAT-ATTATTTTA-ATATTTAATAATT
1 TAATAATT-TTTTATATATTTAA-AATT
*
94542 TAATAATTTTTTATTTATTTAAAATT
1 TAATAATTTTTTATATATTTAAAATT
94568 T
1 T
94569 TTTATATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TAATAATTTTTTATATATTTAAAATT
Found at i:94987 original size:30 final size:31
Alignment explanation
Indices: 94920--94988 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
94910 AATTAGGGGT
* * **
94920 TTTGGATCCCTTAAAAGTTGATAAAAATATT
1 TTTGGACCCCTTAAAAATTGATAAAAATAAA
94951 TTTGGACCCCTTAAAAATTGA-AAATAA-AAA
1 TTTGGACCCCTTAAAAATTGATAAA-AATAAA
94981 TTTGGACC
1 TTTGGACC
94989 TCTTTCAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 12 0.36
31 21 0.64
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (31 bp):
TTTGGACCCCTTAAAAATTGATAAAAATAAA
Found at i:96400 original size:33 final size:33
Alignment explanation
Indices: 96363--96427 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
96353 GGAGGTTGCA
* *
96363 GCAGACTTGTAACGTGGCTGTGTTATACAGCTG
1 GCAGACTTGCAACGTGGCTATGTTATACAGCTG
96396 GCAGACTTGCAACGTGGCTATGTTATACAGCT
1 GCAGACTTGCAACGTGGCTATGTTATACAGCT
96428 AACATTCACC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (33 bp):
GCAGACTTGCAACGTGGCTATGTTATACAGCTG
Found at i:101116 original size:33 final size:33
Alignment explanation
Indices: 101079--101178 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 33
101069 AGGTTGCAGT
* *
101079 AGACTTGTAATGTGGCTGTGTTATGCAGCTAGC
1 AGACTTGTAACGTGGCTGTGTTATACAGCTAGC
* **
101112 AGACTT-TCAACGTGGCTGTGTTATACAACTAAT
1 AGACTTGT-AACGTGGCTGTGTTATACAGCTAGC
*
101145 AGACTTGCAACGTGGCTGTGTTATACAGCTAGC
1 AGACTTGTAACGTGGCTGTGTTATACAGCTAGC
101178 A
1 A
101179 CTTTCTAATC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
32 1 0.02
33 55 0.98
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (33 bp):
AGACTTGTAACGTGGCTGTGTTATACAGCTAGC
Found at i:107236 original size:13 final size:13
Alignment explanation
Indices: 107220--107244 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
107210 ATTATTCGAT
107220 AATATAATTATAA
1 AATATAATTATAA
107233 AATATAATTATA
1 AATATAATTATA
107245 TTTCTTGATA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATATAATTATAA
Found at i:109344 original size:20 final size:21
Alignment explanation
Indices: 109321--109360 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
109311 AAACTCAAAC
*
109321 CCCAAA-CTTAAAACTTGAAA
1 CCCAAATCCTAAAACTTGAAA
*
109341 CCCAAATCCTAAACCTTGAA
1 CCCAAATCCTAAAACTTGAA
109361 TTGAAGGCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.45, C:0.30, G:0.05, T:0.20
Consensus pattern (21 bp):
CCCAAATCCTAAAACTTGAAA
Done.