Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014968.1 Kokia drynarioides strain JFW-HI SEQ_130012, 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: 109990
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 136 characters in sequence are not A, C, G, or T
Found at i:468 original size:34 final size:34
Alignment explanation
Indices: 408--476 Score: 106
Period size: 34 Copynumber: 2.0 Consensus size: 34
398 TTGATCTAAG
408 GGATTATTTGCAGCAGCAAACAAAGC-ATAATAAA
1 GGATTATTTGCAGCAGCAAACAAAGCAATAA-AAA
442 GGATTATTTGCAGCAGCAAA-ACAAGCAATAAAAA
1 GGATTATTTGCAGCAGCAAACA-AAGCAATAAAAA
476 G
1 G
477 ACCATCAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 1 0.03
34 28 0.85
35 4 0.12
ACGTcount: A:0.48, C:0.14, G:0.19, T:0.19
Consensus pattern (34 bp):
GGATTATTTGCAGCAGCAAACAAAGCAATAAAAA
Found at i:20763 original size:27 final size:28
Alignment explanation
Indices: 20720--20777 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
20710 ATCTGGAGAT
20720 AAAGAAACAGAAGGAAGCAA-AAAAGAA
1 AAAGAAACAGAAGGAAGCAAGAAAAGAA
*
20747 AAAGAAAGCAGAA-GAAGCAAGATAAGAA
1 AAAGAAA-CAGAAGGAAGCAAGAAAAGAA
20775 AAA
1 AAA
20778 AGCCTTGGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.69, C:0.07, G:0.22, T:0.02
Consensus pattern (28 bp):
AAAGAAACAGAAGGAAGCAAGAAAAGAA
Found at i:28891 original size:31 final size:31
Alignment explanation
Indices: 28856--28960 Score: 85
Period size: 31 Copynumber: 3.5 Consensus size: 31
28846 TTGATACTTG
*
28856 AACTTGATACTTTTTACTAATTTGGTACCTA
1 AACTTGACACTTTTTACTAATTTGGTACCTA
* * *
28887 AACTT----TTTTTTGTCCAATTTGGTA-CTCA
1 AACTTGACACTTTTT-ACTAATTTGGTACCT-A
* * * *
28915 AATTTGACACTTTTTCCTAATTTGATACCCA
1 AACTTGACACTTTTTACTAATTTGGTACCTA
28946 AACTTGACACTTTTT
1 AACTTGACACTTTTT
28961 TTTTTTTAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
27 7 0.12
28 15 0.26
31 29 0.51
32 6 0.11
ACGTcount: A:0.27, C:0.19, G:0.09, T:0.46
Consensus pattern (31 bp):
AACTTGACACTTTTTACTAATTTGGTACCTA
Found at i:30736 original size:201 final size:203
Alignment explanation
Indices: 30386--30853 Score: 708
Period size: 201 Copynumber: 2.3 Consensus size: 203
30376 AGAGTTAAAT
* * * *
30386 TTGCATTGCGGGCTATAGATACAAAACATATGCACAACAACAAAATATATCGCCTTTCTCGTACC
1 TTGCATTGCAGGCTATACATACAAAACAAATGCACAACAACAAAATACATCGCCTTTCTCGTACC
* * * *
30451 TGAAATCTTCGGGTCTTGCTTAACACTCAACCGGGAATACCGTGTGCCTACCAACTAGAATTGCC
66 TGAAATCTTCAGGACTTGCTCAACACTCAACCGGGAACACCGTGTGCCTACCAACTAGAATTGCC
* * *
30516 CCATATAAACAGTATCACAAACACGAACAAGGCTCTGCATA-ATT-TCTTCAATCC-AGAGAACC
131 CCACATAAACAGAATCACAAACACAAACAAGGCTCTGCATAGATTATCTTCAATCCGA-AGAACC
30578 ATATAAAGA
195 ATATAAAGA
* * *
30587 TTGCATTGCAGGCTATACATAGAAAACAAATGCACAACAACAAAATACATTGCCTTTTTCGTACC
1 TTGCATTGCAGGCTATACATACAAAACAAATGCACAACAACAAAATACATCGCCTTTCTCGTACC
* * * *
30652 TGAAATCTTCAGGACTTGCTCGACACTCAACCGTGAACACTGTGTGCCTACTAACTAGAATTGCC
66 TGAAATCTTCAGGACTTGCTCAACACTCAACCGGGAACACCGTGTGCCTACCAACTAGAATTGCC
* *
30717 CTACATAAACAGAATCACAAACACAAACAAGGCTCTGCATAGATTATCTTCGATCCGAAGAACCA
131 CCACATAAACAGAATCACAAACACAAACAAGGCTCTGCATAGATTATCTTCAATCCGAAGAACCA
30782 TATAAAGA
196 TATAAAGA
* *
30790 TTGCATTGCAGGCTATACATACAAAACAAATGCACAACAACAAAATACATCGCTTTTCTTGTAC
1 TTGCATTGCAGGCTATACATACAAAACAAATGCACAACAACAAAATACATCGCCTTTCTCGTAC
30854 ACTCGACCGG
Statistics
Matches: 239, Mismatches: 25, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
201 152 0.64
202 3 0.01
203 83 0.35
204 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (203 bp):
TTGCATTGCAGGCTATACATACAAAACAAATGCACAACAACAAAATACATCGCCTTTCTCGTACC
TGAAATCTTCAGGACTTGCTCAACACTCAACCGGGAACACCGTGTGCCTACCAACTAGAATTGCC
CCACATAAACAGAATCACAAACACAAACAAGGCTCTGCATAGATTATCTTCAATCCGAAGAACCA
TATAAAGA
Found at i:33390 original size:18 final size:19
Alignment explanation
Indices: 33345--33390 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
33335 ACATTTTTAT
33345 TAAAACAAATTCATTAAAAA
1 TAAAA-AAATTCATTAAAAA
* *
33365 TATAAAAATTTA-TAAAAA
1 TAAAAAAATTCATTAAAAA
33383 TAAAAAAA
1 TAAAAAAA
33391 CCTTTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 13 0.57
19 6 0.26
20 4 0.17
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAAAAAATTCATTAAAAA
Found at i:33398 original size:18 final size:17
Alignment explanation
Indices: 33358--33400 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
33348 AACAAATTCA
* *
33358 TTAAAAATATAAAAATT
1 TTAAAAATAAAAAAACT
33375 TATAAAAATAAAAAAACCT
1 T-TAAAAATAAAAAAA-CT
33394 TTAAAAA
1 TTAAAAA
33401 AAATTTAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 19 0.86
19 2 0.09
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (17 bp):
TTAAAAATAAAAAAACT
Found at i:33469 original size:18 final size:19
Alignment explanation
Indices: 33446--33488 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
33436 CCAAACAAAC
33446 AAATTTTTAA-TTTTTTTT
1 AAATTTTTAAGTTTTTTTT
33464 AAA-TTTTAAGTTTTTTTT
1 AAATTTTTAAGTTTTTTTT
*
33482 AAGTTTT
1 AAATTTT
33489 GCATACTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 6 0.27
18 13 0.59
19 3 0.14
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (19 bp):
AAATTTTTAAGTTTTTTTT
Found at i:35976 original size:17 final size:17
Alignment explanation
Indices: 35956--36002 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
35946 TAAACCTAAT
* *
35956 TTTTAATTTTTAATTTA
1 TTTTAAATTTAAATTTA
35973 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
*
35990 TTTCAAATTTAAA
1 TTTTAAATTTAAA
36003 ATTTGAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:36157 original size:3 final size:3
Alignment explanation
Indices: 36149--36174 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
36139 AAATAGTAAC
36149 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
36175 GGGAACCCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:37303 original size:29 final size:29
Alignment explanation
Indices: 37206--37449 Score: 240
Period size: 30 Copynumber: 8.3 Consensus size: 29
37196 CTCAGAAGGT
** * *
37206 CCCTAAACTTTTTAAAAATCATATTTTAA
1 CCCTAAACTTTTCCAAAATTACATTTTAA
* * * *
37235 CCC-CAACTTCTCCAAAATTACAATTCAA
1 CCCTAAACTTTTCCAAAATTACATTTTAA
*
37263 CCCTTAAACTTTTCCAAAATTATA-TTTAA
1 CCC-TAAACTTTTCCAAAATTACATTTTAA
* * *
37292 CCTCTAAACTTTTCAAAAATCACACTTTAA
1 CC-CTAAACTTTTCCAAAATTACATTTTAA
*
37322 CCCCTAAATTTTTCCAAAATTACATTTTAA
1 -CCCTAAACTTTTCCAAAATTACATTTTAA
* * *
37352 CCCCAAACTTCTCCAAAATTACATTTTTA
1 CCCTAAACTTTTCCAAAATTACATTTTAA
*
37381 CCCTCAAACTTTTCCAAAATTACCATTTTGA
1 CCCT-AAACTTTTCCAAAATTA-CATTTTAA
* * *
37412 CCTTGAACTTTTCCAAAATTACCATTTTAC
1 CCCTAAACTTTTCCAAAATTA-CATTTTAA
37442 CCCTAAAC
1 CCCTAAAC
37450 ATCCAAAAAT
Statistics
Matches: 176, Mismatches: 32, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
28 20 0.11
29 54 0.31
30 90 0.51
31 12 0.07
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTTTCCAAAATTACATTTTAA
Found at i:37335 original size:59 final size:59
Alignment explanation
Indices: 37206--37409 Score: 207
Period size: 59 Copynumber: 3.5 Consensus size: 59
37196 CTCAGAAGGT
** * * * * * *
37206 CCCTAAACTTTTTAAAAATCATATTTTAACCCC-AACTTCTCCAAAATTACAATTCAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAACCCCAAACTTCTCAAAAATCACACTTTAAC
* * * *
37264 CCTTAAACTTTTCCAAAATTATA-TTTAACCTCTAAACTTTTCAAAAATCACACTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAACC-CCAAACTTCTCAAAAATCACACTTTAAC
* * * * *
37323 CCCTAAATTTTTCCAAAATTACATTTTAACCCCAAACTTCTCCAAAATTACATTTTTA-
1 CCCTAAACTTTTCCAAAATTACATTTTAACCCCAAACTTCTCAAAAATCACACTTTAAC
37381 CCCTCAAACTTTTCCAAAATTACCATTTT
1 CCCT-AAACTTTTCCAAAATTA-CATTTT
37410 GACCTTGAAC
Statistics
Matches: 121, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
57 7 0.06
58 24 0.20
59 77 0.64
60 13 0.11
ACGTcount: A:0.37, C:0.26, G:0.00, T:0.36
Consensus pattern (59 bp):
CCCTAAACTTTTCCAAAATTACATTTTAACCCCAAACTTCTCAAAAATCACACTTTAAC
Found at i:37486 original size:29 final size:29
Alignment explanation
Indices: 37426--37506 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
37416 GAACTTTTCC
* **
37426 AAAATTACCATTTTACCCCTAAACATCCA
1 AAAATTACCATTTTACCCCCAAACATAAA
*
37455 AAAATTACCATTTTGCCCCCAAACATAAA
1 AAAATTACCATTTTACCCCCAAACATAAA
* * * *
37484 AAAATAATCATTTTTCCCTCAAA
1 AAAATTACCATTTTACCCCCAAA
37507 TTTCCAGAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.43, C:0.27, G:0.01, T:0.28
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCAAACATAAA
Found at i:37555 original size:30 final size:30
Alignment explanation
Indices: 37503--37624 Score: 92
Period size: 29 Copynumber: 4.1 Consensus size: 30
37493 ATTTTTCCCT
* **
37503 CAAA-TTTCCAGAAATCACATTTTCGA-CC
1 CAAATTTTCCAAAAATTTCATTTTCGATCC
* * *
37531 TCAAATTTTCCAAAAGTTTGATTTT-AATCC
1 -CAAATTTTCCAAAAATTTCATTTTCGATCC
*
37561 CAAATTTTCCAAAAATTTCAATTTCGATCCC
1 CAAATTTTCCAAAAATTTCATTTTCGAT-CC
* * *
37592 CAAA-TTCCTCGAAAATTACATTTTC-ATCC
1 CAAATTTTC-CAAAAATTTCATTTTCGATCC
37621 CAAA
1 CAAA
37625 ATCTCTGAAA
Statistics
Matches: 74, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
29 32 0.43
30 23 0.31
31 19 0.26
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (30 bp):
CAAATTTTCCAAAAATTTCATTTTCGATCC
Found at i:40793 original size:18 final size:18
Alignment explanation
Indices: 40770--40804 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40760 AATTAAGAAA
*
40770 TAATTAGCTAAAAAATAC
1 TAATTAACTAAAAAATAC
*
40788 TAATTAATTAAAAAATA
1 TAATTAACTAAAAAATA
40805 TATGTGTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (18 bp):
TAATTAACTAAAAAATAC
Found at i:43286 original size:14 final size:15
Alignment explanation
Indices: 43262--43292 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
43252 TATTTTAATA
43262 ATTTTTCTTAATTTT
1 ATTTTTCTTAATTTT
43277 ATTTTT-TTAATTTT
1 ATTTTTCTTAATTTT
43291 AT
1 AT
43293 AATCTTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
ATTTTTCTTAATTTT
Found at i:49999 original size:83 final size:84
Alignment explanation
Indices: 49826--50000 Score: 196
Period size: 83 Copynumber: 2.1 Consensus size: 84
49816 AAATCTTGGC
* * * ** *
49826 CCTT-TAAAAATAAAAAATTATATATTTAGTCCATTCATAAATAATAAAATTATAAATTAATATA
1 CCTTATAAAAATAAAAAAATATATATTTAATCCATTCAAAAATAATAAAATTATAAACCAATACA
** *
49890 TGATAAAATTACATTTTAA
66 CAATAAAATTACACTTTAA
* * *
49909 CC-CATAAAAATAAATAAAAT-TATATTTAATCCTTTCAAAAAT-ATTAAATTATAAACCAATAC
1 CCTTATAAAAATAAA-AAAATATATATTTAATCCATTCAAAAATAATAAAATTATAAACCAATAC
*
49971 ACAATAAAATTACACTTTGA
65 ACAATAAAATTACACTTTAA
49991 CCTTATAAAA
1 CCTTATAAAA
50001 TTTCATAACT
Statistics
Matches: 75, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
82 34 0.45
83 37 0.49
84 4 0.05
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.35
Consensus pattern (84 bp):
CCTTATAAAAATAAAAAAATATATATTTAATCCATTCAAAAATAATAAAATTATAAACCAATACA
CAATAAAATTACACTTTAA
Found at i:51346 original size:31 final size:30
Alignment explanation
Indices: 51306--51369 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
51296 CTTAACAACC
*
51306 CAATTACTTACATAAAAACTTCT-GAATAGTT
1 CAATAACTTA-ATAAAAACTT-TAGAATAGTT
**
51337 CAATAACTTAATTTAAACTTTAGAATAGTT
1 CAATAACTTAATAAAAACTTTAGAATAGTT
51367 CAA
1 CAA
51370 GGTCCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 1 0.03
30 19 0.66
31 9 0.31
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (30 bp):
CAATAACTTAATAAAAACTTTAGAATAGTT
Found at i:60914 original size:16 final size:16
Alignment explanation
Indices: 60882--60925 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
60872 ATTTAAAAAA
60882 TAATTTAAT-AA--TT
1 TAATTTAATCAATTTT
60895 TAATTTAATCAATTTT
1 TAATTTAATCAATTTT
60911 TAATTTAATCTAATT
1 TAATTTAATC-AATT
60926 AATTTATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.33
14 2 0.07
16 12 0.44
17 4 0.15
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATTTAATCAATTTT
Found at i:60916 original size:21 final size:21
Alignment explanation
Indices: 60890--60930 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
60880 AATAATTTAA
*
60890 TAATTTAATTTAATCAATTTT
1 TAATTTAATCTAATCAATTTT
*
60911 TAATTTAATCTAATTAATTT
1 TAATTTAATCTAATCAATTT
60931 ATATCGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATTTAATCTAATCAATTTT
Found at i:60943 original size:31 final size:29
Alignment explanation
Indices: 60882--60959 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 29
60872 ATTTAAAAAA
*
60882 TAATTTAATAATTTAATTTAATCAATTTT
1 TAATTTAATAATTTAATTTAATCAAATTT
*
60911 TAATTTAATCTAA-TTAATTTATATCGAATTT
1 TAATTTAA--TAATTTAATTTA-ATCAAATTT
* *
60942 TAAATCAATTAATTTAAT
1 TAATTTAA-TAATTTAAT
60960 ATATTTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 8 0.20
30 11 0.28
31 21 0.52
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.51
Consensus pattern (29 bp):
TAATTTAATAATTTAATTTAATCAAATTT
Found at i:60955 original size:30 final size:30
Alignment explanation
Indices: 60894--60955 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
60884 ATTTAATAAT
* *
60894 TTAATTTAATCAATTTTTAATTTAATCTAA
1 TTAATTTAATCAATTTTTAAATCAATCTAA
60924 TTAATTTATATCGAA-TTTTAAATCAAT-TAA
1 TTAATTTA-ATC-AATTTTTAAATCAATCTAA
60954 TT
1 TT
60956 TAATATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 13 0.46
31 13 0.46
32 2 0.07
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (30 bp):
TTAATTTAATCAATTTTTAAATCAATCTAA
Found at i:67643 original size:82 final size:84
Alignment explanation
Indices: 67555--67727 Score: 226
Period size: 83 Copynumber: 2.1 Consensus size: 84
67545 TATTAGTTTA
* * * *
67555 TTTTTATCTATTTATTAAAG-TTTTGATGTCTCGAGAATGTTGATA-AAGATTCGGAATTTGATA
1 TTTTTATCCAATTATTAAAGTTTTTCATGTCTCGAGAAAGTTGATACAAG-TTCGGAATTTGATA
**
67618 TTCAGTATATGCTAATCA-T
65 TTCAACATATGCTAATCACT
** *
67637 TTTTTATCCAATTATTAGGGTTTTTCATGTCTTGAGAAAGTTGATACAAGTTCGGAATTTGATAT
1 TTTTTATCCAATTATTAAAGTTTTTCATGTCTCGAGAAAGTTGATACAAGTTCGGAATTTGATAT
*
67702 TCAACATATTCTAATCACT
66 TCAACATATGCTAATCACT
67721 TTTTTAT
1 TTTTTAT
67728 TTGATTATTA
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
82 16 0.21
83 51 0.65
84 11 0.14
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.46
Consensus pattern (84 bp):
TTTTTATCCAATTATTAAAGTTTTTCATGTCTCGAGAAAGTTGATACAAGTTCGGAATTTGATAT
TCAACATATGCTAATCACT
Found at i:73905 original size:16 final size:16
Alignment explanation
Indices: 73884--73917 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
73874 TTTAATTTGT
* *
73884 TATAAATTATATAATA
1 TATAAATAACATAATA
73900 TATAAATAACATAATA
1 TATAAATAACATAATA
73916 TA
1 TA
73918 AATTATTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
TATAAATAACATAATA
Found at i:80835 original size:4 final size:4
Alignment explanation
Indices: 80826--80850 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
80816 TTTTCCTCTA
80826 TTTG TTTG TTTG TTTG TTTG TTTG T
1 TTTG TTTG TTTG TTTG TTTG TTTG T
80851 CCATAATACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.24, T:0.76
Consensus pattern (4 bp):
TTTG
Found at i:81454 original size:5 final size:5
Alignment explanation
Indices: 81444--81468 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
81434 GTCATCATCA
81444 CCTTC CCTTC CCTTC CCTTC CCTTC
1 CCTTC CCTTC CCTTC CCTTC CCTTC
81469 TCACCTCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
CCTTC
Found at i:82992 original size:33 final size:33
Alignment explanation
Indices: 82950--83018 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
82940 GAGGTGCCGA
82950 TGATTTGTTGGCCTTACTTTGCTGATCAACAAG
1 TGATTTGTTGGCCTTACTTTGCTGATCAACAAG
82983 TGATTTGTTGGCCTTACTTTGCTGATCAACAAG
1 TGATTTGTTGGCCTTACTTTGCTGATCAACAAG
83016 TGA
1 TGA
83019 ATGGTAGGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (33 bp):
TGATTTGTTGGCCTTACTTTGCTGATCAACAAG
Found at i:84199 original size:21 final size:21
Alignment explanation
Indices: 84147--84199 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
84137 TCATATTTGT
*
84147 TATTCTCTTTTCTTTCTCATA
1 TATTCTCTTTTATTTCTCATA
* * *
84168 T-TTGATTTTTTATTTTTCATA
1 TATT-CTCTTTTATTTCTCATA
84189 TATTCTCTTTT
1 TATTCTCTTTT
84200 TCTTTCCCAT
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.68
Consensus pattern (21 bp):
TATTCTCTTTTATTTCTCATA
Found at i:89859 original size:17 final size:18
Alignment explanation
Indices: 89819--89859 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
89809 TAGTATTTTT
89819 TTAAAAGTATTTCTGACA
1 TTAAAAGTATTTCTGACA
* *
89837 TAAAAAGTATTTTTGA-A
1 TTAAAAGTATTTCTGACA
89854 TTAAAA
1 TTAAAA
89860 ATAATGTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (18 bp):
TTAAAAGTATTTCTGACA
Found at i:94345 original size:7 final size:7
Alignment explanation
Indices: 94336--94367 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
94326 ATTCGCTATA
*
94336 TAAAATA
1 TAAAATC
94343 TAAAATC
1 TAAAATC
94350 TAAAATC
1 TAAAATC
94357 TAAAATC
1 TAAAATC
94364 TAAA
1 TAAA
94368 CATAAGACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (7 bp):
TAAAATC
Found at i:96597 original size:15 final size:14
Alignment explanation
Indices: 96579--96624 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
96569 TAAATATTAA
96579 AAAATATAAAAATT
1 AAAATATAAAAATT
**
96593 GAAAATATTCAAATT
1 -AAAATATAAAAATT
*
96608 AAAATATAAAAACT
1 AAAATATAAAAATT
96622 AAA
1 AAA
96625 TTCAGAGGCC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:105173 original size:2 final size:2
Alignment explanation
Indices: 105166--105204 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
105156 TGTTTTTAAA
* * *
105166 AC AC AC AC AC AC AC TC AC AC AC AC AC GC AC AC GC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
105205 ACTTTCGAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.44, C:0.49, G:0.05, T:0.03
Consensus pattern (2 bp):
AC
Found at i:105956 original size:14 final size:14
Alignment explanation
Indices: 105937--105966 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
105927 ATATGCCAGT
105937 AAGAAAAGGGCCTG
1 AAGAAAAGGGCCTG
105951 AAGAAAAGGGCCTG
1 AAGAAAAGGGCCTG
105965 AA
1 AA
105967 AAACCAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.33, T:0.07
Consensus pattern (14 bp):
AAGAAAAGGGCCTG
Done.