Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011682.1 Kokia drynarioides strain JFW-HI SEQ_126674, 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: 191822
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:345 original size:13 final size:13
Alignment explanation
Indices: 329--353 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
319 CATTTTCGGT
329 CCCCACCTTCCAA
1 CCCCACCTTCCAA
342 CCCCACCTTCCA
1 CCCCACCTTCCA
354 CCATTTTCAC
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:0.20, C:0.64, G:0.00, T:0.16
Consensus pattern (13 bp):
CCCCACCTTCCAA
Found at i:595 original size:18 final size:18
Alignment explanation
Indices: 574--609 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
564 TAACATTGTA
574 TATTTTATACATATATAT
1 TATTTTATACATATATAT
*
592 TATTTTATATATATATAT
1 TATTTTATACATATATAT
610 ATATACAATC
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:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTTATACATATATAT
Found at i:14969 original size:158 final size:158
Alignment explanation
Indices: 14681--14994 Score: 547
Period size: 158 Copynumber: 2.0 Consensus size: 158
14671 GTGGCAGTTT
*
14681 CAAGACAAGATAGACCAGTTTCATGCAAAGGACGCAACGAGGACATCGCTAGATTCGGTGGGGGA
1 CAAGACAAGATAGACCAGTTTCATACAAAGGACGCAACGAGGACATCGCTAGATTCGGTGGGGGA
** * *
14746 GAATGTCATGGTTTGCGCATGGGAGCCTGTAACCATGGCACACTTATGTGATCCATCTAGTTCAA
66 GAATGTCATGGGCTGCGCATGGGAGCCCGCAACCATGGCACACTTATGTGATCCATCTAGTTCAA
**
14811 GGGAGGTCTTTTGGCCCAATCGGACTGG
131 GGGAGGTCTTTTGAACCAATCGGACTGG
*
14839 CAAGACAAGATAGACCAGTTTCATACAAAGGACGCAACGAGGACGTCGCTAGATTCGGTGGGGGA
1 CAAGACAAGATAGACCAGTTTCATACAAAGGACGCAACGAGGACATCGCTAGATTCGGTGGGGGA
*
14904 GAATGTCATGGGCTGCGCATGGGAGCCCGCAACCATGGCACACTTGTGTGATCCATCTAGTTCAA
66 GAATGTCATGGGCTGCGCATGGGAGCCCGCAACCATGGCACACTTATGTGATCCATCTAGTTCAA
14969 GGGAGGTCTTTTGAACCAATCGGACT
131 GGGAGGTCTTTTGAACCAATCGGACT
14995 AGCCCAGTGC
Statistics
Matches: 147, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
158 147 1.00
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.22
Consensus pattern (158 bp):
CAAGACAAGATAGACCAGTTTCATACAAAGGACGCAACGAGGACATCGCTAGATTCGGTGGGGGA
GAATGTCATGGGCTGCGCATGGGAGCCCGCAACCATGGCACACTTATGTGATCCATCTAGTTCAA
GGGAGGTCTTTTGAACCAATCGGACTGG
Found at i:27349 original size:60 final size:60
Alignment explanation
Indices: 27276--27525 Score: 405
Period size: 60 Copynumber: 4.2 Consensus size: 60
27266 AATATCAAAG
*
27276 GTGTAGGATCTAGACTATACTTTAAGTTGTTCAAGTGTTCTTAAATGAAATAAATATTGT
1 GTGTGGGATCTAGACTATACTTTAAGTTGTTCAAGTGTTCTTAAATGAAATAAATATTGT
* * *
27336 GTTTGGGATCTAGAATATACTTTAAGTTTTTCAAGTGTTCTTAAATGAAATAAATA--GT
1 GTGTGGGATCTAGACTATACTTTAAGTTGTTCAAGTGTTCTTAAATGAAATAAATATTGT
* * * *
27394 GTGTGGGATCTAGACTATACTTTAAGTTTTTCAGGTGTTCTTATATGAAATGAATATTGT
1 GTGTGGGATCTAGACTATACTTTAAGTTGTTCAAGTGTTCTTAAATGAAATAAATATTGT
27454 GTGTGGGATCTAGACTATACTTTAAGTTGTTCAAGTGTTCTTAAATGAAATAAATATTGT
1 GTGTGGGATCTAGACTATACTTTAAGTTGTTCAAGTGTTCTTAAATGAAATAAATATTGT
*
27514 GTGTGGAATCTA
1 GTGTGGGATCTA
27526 ATGTAGTCTC
Statistics
Matches: 174, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
58 53 0.30
60 121 0.70
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (60 bp):
GTGTGGGATCTAGACTATACTTTAAGTTGTTCAAGTGTTCTTAAATGAAATAAATATTGT
Found at i:27489 original size:118 final size:119
Alignment explanation
Indices: 27276--27525 Score: 403
Period size: 118 Copynumber: 2.1 Consensus size: 119
27266 AATATCAAAG
* *
27276 GTGTAGGATCTAGACTATACTTTAAGTTGTTCAAGTGTTCTTAAATGAAATAAATATTGTGTTTG
1 GTGTGGGATCTAGACTATACTTTAAGTTGTTCAAGTGTTCTTAAATGAAATAAATATTGTGTGTG
*
27341 GGATCTAGAATATACTTTAAGTTTTTCAAGTGTTCTTAAATGAAATAAATA-GT
66 GGATCTAGAATATACTTTAAGTTGTTCAAGTGTTCTTAAATGAAATAAATATGT
* * * *
27394 GTGTGGGATCTAGACTATACTTTAAGTTTTTCAGGTGTTCTTATATGAAATGAATATTGTGTGTG
1 GTGTGGGATCTAGACTATACTTTAAGTTGTTCAAGTGTTCTTAAATGAAATAAATATTGTGTGTG
*
27459 GGATCTAGACTATACTTTAAGTTGTTCAAGTGTTCTTAAATGAAATAAATATTGT
66 GGATCTAGAATATACTTTAAGTTGTTCAAGTGTTCTTAAATGAAATAAATA-TGT
*
27514 GTGTGGAATCTA
1 GTGTGGGATCTA
27526 ATGTAGTCTC
Statistics
Matches: 121, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
118 108 0.89
120 13 0.11
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (119 bp):
GTGTGGGATCTAGACTATACTTTAAGTTGTTCAAGTGTTCTTAAATGAAATAAATATTGTGTGTG
GGATCTAGAATATACTTTAAGTTGTTCAAGTGTTCTTAAATGAAATAAATATGT
Found at i:28371 original size:45 final size:45
Alignment explanation
Indices: 28322--28442 Score: 143
Period size: 45 Copynumber: 2.7 Consensus size: 45
28312 GTCGCTGTGC
* *
28322 AACCCAGGGTAGCAATTCAATATAAGTGAGCTATCATTGCCATGT
1 AACCCAGGGTAACAATTCAATATAAGTGAGCTATCATTGCCAGGT
** * * * *
28367 AACCCAGGGTAACAATTTGACATAAGTGAGCTATCGTTGTCGGGT
1 AACCCAGGGTAACAATTCAATATAAGTGAGCTATCATTGCCAGGT
* * *
28412 AACTCGGGGTAACATTTCAATATAAGTGAGC
1 AACCCAGGGTAACAATTCAATATAAGTGAGC
28443 CATTGTTTTT
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (45 bp):
AACCCAGGGTAACAATTCAATATAAGTGAGCTATCATTGCCAGGT
Found at i:28724 original size:19 final size:19
Alignment explanation
Indices: 28683--28781 Score: 112
Period size: 19 Copynumber: 5.3 Consensus size: 19
28673 GAGATATGAA
28683 AATATGTGAAATT--TGTGG
1 AATATGTGAAATTGATGT-G
**
28701 AATATGTGAAATTTTTGTG
1 AATATGTGAAATTGATGTG
**
28720 AATATGTGACGTTGATGTG
1 AATATGTGAAATTGATGTG
*
28739 AATATGTGACATTGATGTG
1 AATATGTGAAATTGATGTG
* *
28758 AATACGTAAAATTGATGTG
1 AATATGTGAAATTGATGTG
28777 AATAT
1 AATAT
28782 ATGTGTTTAT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
18 13 0.19
19 54 0.77
20 3 0.04
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.38
Consensus pattern (19 bp):
AATATGTGAAATTGATGTG
Found at i:36243 original size:45 final size:45
Alignment explanation
Indices: 36126--36250 Score: 160
Period size: 45 Copynumber: 2.8 Consensus size: 45
36116 TAACTGCATA
* *
36126 TCAATATAAGTGAGTTATCGTTGTCGAGCAACCCGAGGTAGCAAT
1 TCAATATAAGTGAGCTATCGTTGTCGGGCAACCCGAGGTAGCAAT
* * ** *
36171 TTAACATAAGCAAGCTATCGTTGTCGGGTAACCCGAGGTAGCAAT
1 TCAATATAAGTGAGCTATCGTTGTCGGGCAACCCGAGGTAGCAAT
* * *
36216 TCAATATAAGTGAGCCATCGCTATCGGGCAACCCG
1 TCAATATAAGTGAGCTATCGTTGTCGGGCAACCCG
36251 GGGTGGTGAG
Statistics
Matches: 65, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (45 bp):
TCAATATAAGTGAGCTATCGTTGTCGGGCAACCCGAGGTAGCAAT
Found at i:36461 original size:19 final size:19
Alignment explanation
Indices: 36437--36498 Score: 97
Period size: 19 Copynumber: 3.3 Consensus size: 19
36427 GAGATATGAA
36437 AATATGTGAAATTGATGTG
1 AATATGTGAAATTGATGTG
* *
36456 AATATGTGATATTAATGTG
1 AATATGTGAAATTGATGTG
*
36475 AATATGTGACATTGATGTG
1 AATATGTGAAATTGATGTG
36494 AATAT
1 AATAT
36499 CAAATGTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.39
Consensus pattern (19 bp):
AATATGTGAAATTGATGTG
Found at i:43826 original size:24 final size:24
Alignment explanation
Indices: 43798--43872 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
43788 GTATACTAGT
43798 TAACCTTTCTGGGCTCGTAAGAGC
1 TAACCTTTCTGGGCTCGTAAGAGC
*
43822 TAACCTCTCTGGGCTCGTAAGAGC
1 TAACCTTTCTGGGCTCGTAAGAGC
* **
43846 TAACCTTTTTTAGCTCGTAAGAGC
1 TAACCTTTCTGGGCTCGTAAGAGC
43870 TAA
1 TAA
43873 TTCTATTTGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (24 bp):
TAACCTTTCTGGGCTCGTAAGAGC
Found at i:46263 original size:24 final size:24
Alignment explanation
Indices: 46228--46278 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
46218 ATATACTGGT
46228 TAACCTTACTAGGCTCGTAAGAGC
1 TAACCTTACTAGGCTCGTAAGAGC
*
46252 TAACCTTCCTAGGCTCGTAAGAGC
1 TAACCTTACTAGGCTCGTAAGAGC
46276 TAA
1 TAA
46279 TTCTGTTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (24 bp):
TAACCTTACTAGGCTCGTAAGAGC
Found at i:53580 original size:130 final size:129
Alignment explanation
Indices: 53347--53605 Score: 500
Period size: 130 Copynumber: 2.0 Consensus size: 129
53337 GTATGGATTA
*
53347 TCATCGACTGAATGCGGCCACAAAGAAGGATCATTTTCCACTACCTTTCATTGACCAGATGTTGG
1 TCATCGACTGAATGCGGCCACAAAGAAGGATCATTTTCCACTACCTTTCATTGACCAGATGCTGG
53412 ATAGGCTGGCTAGTAAAGCTTATTATTGCTTCTTAAATGGCTACTCTGGGTACAACCAAATTGC
66 ATAGGCTGGCTAGTAAAGCTTATTATTGCTTCTTAAATGGCTACTCTGGGTACAACCAAATTGC
53476 NTCATCGACTGAATGCGGCCACAAAGAAGGATCATTTTCCACTACCTTTCATTGACCAGATGCTG
1 -TCATCGACTGAATGCGGCCACAAAGAAGGATCATTTTCCACTACCTTTCATTGACCAGATGCTG
53541 GATAGGCTGGCTAGTAAAGCTTATTATTGCTTCTTAAATGGCTACTCTGGGTACAACCAAATTGC
65 GATAGGCTGGCTAGTAAAGCTTATTATTGCTTCTTAAATGGCTACTCTGGGTACAACCAAATTGC
53606 CATTGTGCTG
Statistics
Matches: 128, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 128 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (129 bp):
TCATCGACTGAATGCGGCCACAAAGAAGGATCATTTTCCACTACCTTTCATTGACCAGATGCTGG
ATAGGCTGGCTAGTAAAGCTTATTATTGCTTCTTAAATGGCTACTCTGGGTACAACCAAATTGC
Found at i:58933 original size:24 final size:24
Alignment explanation
Indices: 58905--58955 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
58895 AGTTTGACTC
*
58905 AAACAAATAAACAGAATTTAATTG
1 AAACAAATAAACAGAATTTAACTG
* * *
58929 AAACAATTAAATAGAGTTTAACTG
1 AAACAAATAAACAGAATTTAACTG
58953 AAA
1 AAA
58956 GATTATTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.57, C:0.08, G:0.10, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAATTTAACTG
Found at i:70254 original size:19 final size:20
Alignment explanation
Indices: 70219--70258 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
70209 GAACAATAAT
70219 GAAAATAACTAAAACCTAAA
1 GAAAATAACTAAAACCTAAA
70239 GAAAATAACT-AAACCTAAA
1 GAAAATAACTAAAACCTAAA
70258 G
1 G
70259 TACAAGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.62, C:0.15, G:0.07, T:0.15
Consensus pattern (20 bp):
GAAAATAACTAAAACCTAAA
Found at i:71880 original size:14 final size:14
Alignment explanation
Indices: 71861--71887 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
71851 AAAACATTTG
71861 TTAAGCTAATTAAT
1 TTAAGCTAATTAAT
71875 TTAAGCTAATTAA
1 TTAAGCTAATTAA
71888 CTTATAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
TTAAGCTAATTAAT
Found at i:87666 original size:36 final size:37
Alignment explanation
Indices: 87578--87678 Score: 177
Period size: 37 Copynumber: 2.8 Consensus size: 37
87568 CGATATTCGA
87578 TTTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
1 TTTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
*
87615 TTTACTCCCTATTGACCCAAAGGTCATGATGCTCA-T
1 TTTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
*
87651 TTTACTCCCTGTTGACCCAAAGCTCATG
1 TTTACTCCCTGTTGACCCAAAGGTCATG
87679 CTTGTTACCA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
36 27 0.44
37 34 0.56
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.34
Consensus pattern (37 bp):
TTTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
Found at i:95606 original size:18 final size:18
Alignment explanation
Indices: 95585--95621 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
95575 CTCCACAAGA
*
95585 TCTTCCTCAAGATCTTCT
1 TCTTCCTCAAGATCCTCT
*
95603 TCTTCCTCAGGATCCTCT
1 TCTTCCTCAAGATCCTCT
95621 T
1 T
95622 TTCTATCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.35, G:0.08, T:0.43
Consensus pattern (18 bp):
TCTTCCTCAAGATCCTCT
Found at i:95635 original size:3 final size:3
Alignment explanation
Indices: 95618--95658 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
95608 CTCAGGATCC
95618 TCT T-T TCT ATCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
95659 AACTTGCTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:100413 original size:16 final size:17
Alignment explanation
Indices: 100380--100413 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
100370 GTTCCAAGCC
100380 TTTATGTAAGCATAAAA
1 TTTATGTAAGCATAAAA
*
100397 TTTATGT-AGCCTAAAA
1 TTTATGTAAGCATAAAA
100413 T
1 T
100414 CCATATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (17 bp):
TTTATGTAAGCATAAAA
Found at i:107834 original size:13 final size:14
Alignment explanation
Indices: 107816--107845 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
107806 GTCAATGCAA
107816 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
107829 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
107843 TCA
1 TCA
107846 TTGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:118789 original size:32 final size:32
Alignment explanation
Indices: 118748--118812 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
118738 ACTCAAAGCC
118748 TAACTTTTTTGTCACAACATACAGGGGTTATG
1 TAACTTTTTTGTCACAACATACAGGGGTTATG
118780 TAACTTTTTTGTCACAACATACAGGGGTTATG
1 TAACTTTTTTGTCACAACATACAGGGGTTATG
118812 T
1 T
118813 CACGACAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (32 bp):
TAACTTTTTTGTCACAACATACAGGGGTTATG
Found at i:119663 original size:14 final size:16
Alignment explanation
Indices: 119640--119671 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
119630 CTTTACATTA
119640 TTTTATTTTTTAT-CT
1 TTTTATTTTTTATACT
119655 TTTTA-TTTTTATACT
1 TTTTATTTTTTATACT
119670 TT
1 TT
119672 CAAACAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTATTTTTTATACT
Found at i:123640 original size:10 final size:10
Alignment explanation
Indices: 123620--123661 Score: 66
Period size: 10 Copynumber: 4.1 Consensus size: 10
123610 TTAACACAAA
123620 ACATATTAATC
1 ACAT-TTAATC
123631 ACATTTAATC
1 ACATTTAATC
*
123641 ACATATAATC
1 ACATTTAATC
123651 ACATTTAATC
1 ACATTTAATC
123661 A
1 A
123662 TATGAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 25 0.86
11 4 0.14
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (10 bp):
ACATTTAATC
Found at i:123651 original size:20 final size:21
Alignment explanation
Indices: 123620--123712 Score: 80
Period size: 20 Copynumber: 4.1 Consensus size: 21
123610 TTAACACAAA
123620 ACATATTAATCACATTTAATC
1 ACATATTAATCACATTTAATC
123641 ACATA-TAATCACATTTAATC
1 ACATATTAATCACATTTAATC
* * * *
123661 ATATGAATATTTCAACAATTATCACCTC
1 ACAT-ATTA-ATC-AC-ATT-T-A-ATC
123689 ACATATTAATCACATTTAATC
1 ACATATTAATCACATTTAATC
123710 ACA
1 ACA
123713 CTAATCGCAT
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
20 18 0.32
21 11 0.19
22 3 0.05
23 3 0.05
24 5 0.09
25 5 0.09
26 3 0.05
27 4 0.07
28 5 0.09
ACGTcount: A:0.43, C:0.20, G:0.01, T:0.35
Consensus pattern (21 bp):
ACATATTAATCACATTTAATC
Found at i:123691 original size:58 final size:59
Alignment explanation
Indices: 123628--123847 Score: 210
Period size: 58 Copynumber: 3.6 Consensus size: 59
123618 AAACATATTA
*
123628 ATCACAT-TTAATCACATATAATCACATTTAATCATATGAATATTTCAACAATTATCAC
1 ATCACATATTAATCACATTTAATCACATTTAATCATATGAATATTTCAACAATTATCAC
* * ** * * *
123686 CTCACATATTAATCACATTTAATCACA-CTAATCGCATTAATATTTCAACATTTATCAT
1 ATCACATATTAATCACATTTAATCACATTTAATCATATGAATATTTCAACAATTATCAC
* * * * *
123744 ATCACATATTAATTATATTTAGTCACATTTAATCATATTTAATTGAATGAATATTTCAGCATTTA
1 ATCACATATTAATCACATTTAATCACATTTAATC-------A-T--ATGAATATTTCAACAATTA
123809 TCAC
56 TCAC
*
123813 ATCACATATTAATCACATTTAGTCACATTTAATCA
1 ATCACATATTAATCACATTTAATCACATTTAATCA
123848 CGTTTAATGA
Statistics
Matches: 130, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
58 54 0.42
59 23 0.18
62 1 0.01
69 52 0.40
ACGTcount: A:0.40, C:0.18, G:0.03, T:0.39
Consensus pattern (59 bp):
ATCACATATTAATCACATTTAATCACATTTAATCATATGAATATTTCAACAATTATCAC
Found at i:123695 original size:69 final size:69
Alignment explanation
Indices: 123573--123855 Score: 254
Period size: 69 Copynumber: 4.3 Consensus size: 69
123563 CATTCTTTTA
* * * * * **
123573 CACA-TTAATCGCA-TTAATCACATGAGTACTT-AAGCATTTAACACAAAACATATTAATCACAT
1 CACATTTAATCACATTTAATCATATGAATATTTCAA-CATTTATCACATCACATATTAATCACAT
123635 TTAAT
65 TTAAT
* * *
123640 CACATATAATCACATTTAATCATATGAATATTTCAACAATTATCACCTCACATATTAATCACATT
1 CACATTTAATCACATTTAATCATATGAATATTTCAACATTTATCACATCACATATTAATCACATT
123705 TAAT
66 TAAT
* * * * *
123709 CACA-CTAAT--C------GCAT-T-AATATTTCAACATTTATCATATCACATATTAATTATATT
1 CACATTTAATCACATTTAATCATATGAATATTTCAACATTTATCACATCACATATTAATCACATT
*
123763 TAGT
66 TAAT
* * *
123767 CACATTTAATCATATTTAATTGA-ATGAATATTTCAGCATTTATCACATCACATATTAATCACAT
1 CACATTTAATCACATTTAA-TCATATGAATATTTCAACATTTATCACATCACATATTAATCACAT
*
123831 TTAGT
65 TTAAT
*
123836 CACATTTAATCACGTTTAAT
1 CACATTTAATCACATTTAAT
123856 GATAGTTTAG
Statistics
Matches: 173, Mismatches: 28, Indels: 29
0.75 0.12 0.13
Matches are distributed among these distances:
58 41 0.24
59 5 0.03
60 3 0.02
66 1 0.01
67 4 0.02
68 14 0.08
69 103 0.60
70 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.37
Consensus pattern (69 bp):
CACATTTAATCACATTTAATCATATGAATATTTCAACATTTATCACATCACATATTAATCACATT
TAAT
Found at i:123781 original size:20 final size:21
Alignment explanation
Indices: 123745--123784 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
123735 ATTTATCATA
*
123745 TCACATATTAATTATATTTAG
1 TCACATATTAATCATATTTAG
123766 TCACAT-TTAATCATATTTA
1 TCACATATTAATCATATTTA
123785 ATTGAATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (21 bp):
TCACATATTAATCATATTTAG
Found at i:123840 original size:10 final size:10
Alignment explanation
Indices: 123813--123855 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
123803 CATTTATCAC
123813 ATCACATATTA
1 ATCACAT-TTA
123824 ATCACATTTA
1 ATCACATTTA
*
123834 GTCACATTTA
1 ATCACATTTA
*
123844 ATCACGTTTA
1 ATCACATTTA
123854 AT
1 AT
123856 GATAGTTTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 22 0.76
11 7 0.24
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.40
Consensus pattern (10 bp):
ATCACATTTA
Found at i:124035 original size:66 final size:66
Alignment explanation
Indices: 123926--124056 Score: 172
Period size: 66 Copynumber: 2.0 Consensus size: 66
123916 CACGGATCTC
* * * * **
123926 CAAACACACCAAATGACTCATAGAGTCAAACATATCCAAAAAGTGAAGCATGTAGCTAACACTCT
1 CAAAAACACAAAAAGACTCATAAAGTCAAACATATCCAAAAAGTGAAGCATAAAGCTAACACTCT
123991 A
66 A
* ** *
123992 CAAAAACACAAAAAGACTCATAAAGTCAAACATGTCCCGAAAGTGAAGCGTAAAGCTAACACTCT
1 CAAAAACACAAAAAGACTCATAAAGTCAAACATATCCAAAAAGTGAAGCATAAAGCTAACACTCT
124057 CCTTATTTCC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.47, C:0.24, G:0.13, T:0.17
Consensus pattern (66 bp):
CAAAAACACAAAAAGACTCATAAAGTCAAACATATCCAAAAAGTGAAGCATAAAGCTAACACTCT
A
Found at i:133275 original size:15 final size:16
Alignment explanation
Indices: 133250--133279 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
133240 ATGATCATGT
133250 CAAGAAGGATGAAGAA
1 CAAGAAGGATGAAGAA
133266 CAAG-AGGATGAAGA
1 CAAGAAGGATGAAGA
133280 GAAGGACGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.33, T:0.07
Consensus pattern (16 bp):
CAAGAAGGATGAAGAA
Found at i:133637 original size:17 final size:17
Alignment explanation
Indices: 133611--133649 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
133601 TTAGCATTCT
133611 TGCA-TTTTATTGT-ACC
1 TGCATTTTTATTGTCA-C
133627 TGCATTTTTATTGTCAC
1 TGCATTTTTATTGTCAC
133644 TGCATT
1 TGCATT
133650 CTTCTTGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.19
17 16 0.76
18 1 0.05
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.51
Consensus pattern (17 bp):
TGCATTTTTATTGTCAC
Found at i:136160 original size:36 final size:36
Alignment explanation
Indices: 136120--136597 Score: 724
Period size: 36 Copynumber: 13.2 Consensus size: 36
136110 TTAACACAAT
* *
136120 ATATTTACAGTCACATGGCATGAATAACATACCCAC
1 ATATTTACTGTCTCATGGCATGAATAACATACCCAC
*
136156 ATATTTACTATCTCATGGCATGAATAACATACCCAC
1 ATATTTACTGTCTCATGGCATGAATAACATACCCAC
* *
136192 ATATTTACAGTCACATGGCATGAATAACATACCCAC
1 ATATTTACTGTCTCATGGCATGAATAACATACCCAC
136228 ATATTTACTGTCTCATGGCATGAATAACATACCCAC
1 ATATTTACTGTCTCATGGCATGAATAACATACCCAC
* **
136264 ATATTTACTGTCACATGGTGTGAATAACATACCCAC
1 ATATTTACTGTCTCATGGCATGAATAACATACCCAC
136300 ATATTTACTGTCTCATGGCATGAATAACATACCCAC
1 ATATTTACTGTCTCATGGCATGAATAACATACCCAC
* **
136336 ATATTTACTGCTGTCACATGGTGTGAATAACATACCCAC
1 ATATTTA---CTGTCTCATGGCATGAATAACATACCCAC
136375 ATATTTACTGTCTCATGGCATGAATAACATACCCAC
1 ATATTTACTGTCTCATGGCATGAATAACATACCCAC
136411 ATATTTACTGTCTCATGGCATGAATAACATACCCAC
1 ATATTTACTGTCTCATGGCATGAATAACATACCCAC
*
136447 ATATTTACTGTCACATGGCATGAATAACATACCCAC
1 ATATTTACTGTCTCATGGCATGAATAACATACCCAC
* *
136483 ATATTTACTATTTCATGGCATGAATAACATACCCAC
1 ATATTTACTGTCTCATGGCATGAATAACATACCCAC
* * * * *
136519 ACATTTACTATCACAT-GCGATGAATAACTTACCTAC
1 ATATTTACTGTCTCATGGC-ATGAATAACATACCCAC
* *
136555 ATATTTACTGTCTCATGGGATGAATAACATACCCAT
1 ATATTTACTGTCTCATGGCATGAATAACATACCCAC
136591 ATATTTA
1 ATATTTA
136598 ATTTCACAAC
Statistics
Matches: 401, Mismatches: 36, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
35 2 0.00
36 365 0.91
37 1 0.00
39 33 0.08
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (36 bp):
ATATTTACTGTCTCATGGCATGAATAACATACCCAC
Found at i:141545 original size:54 final size:54
Alignment explanation
Indices: 141473--141581 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
141463 TGCTATCCGA
141473 ACTAGAGAAGAGGTTACTACTCCCGATGTTGTGACTGATATATTCTATCTTTTT
1 ACTAGAGAAGAGGTTACTACTCCCGATGTTGTGACTGATATATTCTATCTTTTT
*
141527 ACTAGAGAAGAGGTTACTACTCCCGATGTTGTGACTGGTATATTCTATCTTTTT
1 ACTAGAGAAGAGGTTACTACTCCCGATGTTGTGACTGATATATTCTATCTTTTT
141581 A
1 A
141582 ATGATATTGT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (54 bp):
ACTAGAGAAGAGGTTACTACTCCCGATGTTGTGACTGATATATTCTATCTTTTT
Found at i:163435 original size:12 final size:12
Alignment explanation
Indices: 163418--163458 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
163408 ATAAAAATCA
163418 TTAAAAACTGAG
1 TTAAAAACTGAG
*
163430 TTAAAAA-TCA-
1 TTAAAAACTGAG
163440 TTAAAAACTGAG
1 TTAAAAACTGAG
*
163452 TTCAAAA
1 TTAAAAA
163459 TCATACCATG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
10 7 0.29
11 4 0.17
12 13 0.54
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.27
Consensus pattern (12 bp):
TTAAAAACTGAG
Found at i:163437 original size:22 final size:22
Alignment explanation
Indices: 163409--163462 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
163399 TTCAGAAATA
163409 TAAAAATCATTAAAAACTGAGT
1 TAAAAATCATTAAAAACTGAGT
163431 TAAAAATCATTAAAAACTGAGT
1 TAAAAATCATTAAAAACTGAGT
*
163453 TCAAAATCAT
1 TAAAAATCAT
163463 ACCATGCATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (22 bp):
TAAAAATCATTAAAAACTGAGT
Found at i:165830 original size:48 final size:48
Alignment explanation
Indices: 165774--165865 Score: 166
Period size: 48 Copynumber: 1.9 Consensus size: 48
165764 GATTAAAAAT
*
165774 TGGTTTAAAAGTGTTTTTAAAGTAGTTTTAACATGATTAGAAAGAAAC
1 TGGTTTAAAAGTGTTTTCAAAGTAGTTTTAACATGATTAGAAAGAAAC
*
165822 TGGTTTAAAAGTGTTTTCCAAGTAGTTTTAACATGATTAGAAAG
1 TGGTTTAAAAGTGTTTTCAAAGTAGTTTTAACATGATTAGAAAG
165866 TTTCTAAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (48 bp):
TGGTTTAAAAGTGTTTTCAAAGTAGTTTTAACATGATTAGAAAGAAAC
Found at i:177808 original size:39 final size:39
Alignment explanation
Indices: 177757--177832 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
177747 ATGCAGTGAC
177757 ATTATTAGTAAAAACATGATAAAATTAAAGAAAATTATT
1 ATTATTAGTAAAAACATGATAAAATTAAAGAAAATTATT
*
177796 ATTATTAGTAAAAACTTGATAAAATTAAAGAAAATTA
1 ATTATTAGTAAAAACATGATAAAATTAAAGAAAATTA
177833 GGTCAAGCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.33
Consensus pattern (39 bp):
ATTATTAGTAAAAACATGATAAAATTAAAGAAAATTATT
Found at i:177829 original size:20 final size:20
Alignment explanation
Indices: 177767--177829 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
177757 ATTATTAGTA
*
177767 AAAACATGATAAAATTAAAG
1 AAAACTTGATAAAATTAAAG
** *
177787 AAAA-TT-ATTATTATTAGTA-
1 AAAACTTGA-TAAAATTA-AAG
177806 AAAACTTGATAAAATTAAAG
1 AAAACTTGATAAAATTAAAG
177826 AAAA
1 AAAA
177830 TTAGGTCAAG
Statistics
Matches: 31, Mismatches: 7, Indels: 10
0.65 0.15 0.21
Matches are distributed among these distances:
18 1 0.03
19 12 0.39
20 17 0.55
21 1 0.03
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.29
Consensus pattern (20 bp):
AAAACTTGATAAAATTAAAG
Found at i:187777 original size:134 final size:133
Alignment explanation
Indices: 187519--187786 Score: 500
Period size: 134 Copynumber: 2.0 Consensus size: 133
187509 TTCAAAGGGC
*
187519 AAGGATAACTTATGTTATAATGTGATATGAAAGGTTTTTGACCACATATGTGACGTATGCCCAAA
1 AAGGATAACTTATGTTACAATGTGATATGAAAGGTTTTTGACCACATATGTGACGTATGCCCAAA
187584 TATTTTGTTTTTGTTAATATTCTTTAAGGAAGGATATTAGAAAGTAGTAATGAATTCTATCATTA
66 TATTTTGTTTTTGTTAATATTCTTTAAGGAAGGATATTAGAAAGTAGTAATGAATTCTATCATTA
187649 TAG
131 TAG
* *
187652 AAGGATAACTTATCGTTACAATGTGATATGAAAGGTTTTTGGCCACATATGTGGCGTATGCCCAA
1 AAGGATAACTTAT-GTTACAATGTGATATGAAAGGTTTTTGACCACATATGTGACGTATGCCCAA
187717 ATATTTTGTTTTTGTTAATATTCTTTAAGGAAGGATATTAGAAAGTAGTAATGAATTCTATCATT
65 ATATTTTGTTTTTGTTAATATTCTTTAAGGAAGGATATTAGAAAGTAGTAATGAATTCTATCATT
187782 ATAG
130 ATAG
187786 A
1 A
187787 TGAAAAATAT
Statistics
Matches: 131, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
133 13 0.10
134 118 0.90
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (133 bp):
AAGGATAACTTATGTTACAATGTGATATGAAAGGTTTTTGACCACATATGTGACGTATGCCCAAA
TATTTTGTTTTTGTTAATATTCTTTAAGGAAGGATATTAGAAAGTAGTAATGAATTCTATCATTA
TAG
Found at i:191209 original size:29 final size:28
Alignment explanation
Indices: 191174--191364 Score: 195
Period size: 29 Copynumber: 6.5 Consensus size: 28
191164 TTCGAGGTAA
* *
191174 AAAAATGGGATCTTTAGGAGTTCGGGCGT
1 AAAAATGGGATTTTTAGAAGTTCGGG-GT
* * *
191203 AAAAATGGAACTTTT-GAAAGTTTTGGGGTT
1 AAAAATGGGATTTTTAG-AAG-TTCGGGG-T
* *
191233 AAAAATGGGGTTTTTAGAAGTTTGGGGGT
1 AAAAATGGGATTTTTAGAAG-TTCGGGGT
* *
191262 AAAAATGGGATTTTTAGAATTTTTGGGGTT
1 AAAAATGGGATTTTTAGAA-GTTCGGGG-T
*
191292 AAAAATGGGATTTTTTGAAGTTTCGGGGT
1 AAAAATGGGATTTTTAGAAG-TTCGGGGT
*
191321 TAAAATGGGATTTTTAGAAGTTCGGGGGT
1 AAAAATGGGATTTTTAGAAGTTC-GGGGT
191350 AAAAATGGGATTTTT
1 AAAAATGGGATTTTT
191365 GGAAATTTCG
Statistics
Matches: 136, Mismatches: 18, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.03
29 78 0.57
30 53 0.39
31 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.31, T:0.36
Consensus pattern (28 bp):
AAAAATGGGATTTTTAGAAGTTCGGGGT
Found at i:191264 original size:59 final size:59
Alignment explanation
Indices: 191174--191364 Score: 242
Period size: 59 Copynumber: 3.3 Consensus size: 59
191164 TTCGAGGTAA
* * * * * *
191174 AAAAATGGGATCTTTAGGAGTTCGGGCGTAAAAATGGAACTTTT-GAAAGTTTTGGGGTT
1 AAAAATGGGATTTTTAGAAGTTTGGGGGTAAAAATGGGATTTTTAG-AAGTTTTGGGGTT
* *
191233 AAAAATGGGGTTTTTAGAAGTTTGGGGGTAAAAATGGGATTTTTAGAATTTTTGGGGTT
1 AAAAATGGGATTTTTAGAAGTTTGGGGGTAAAAATGGGATTTTTAGAAGTTTTGGGGTT
* * * * *
191292 AAAAATGGGATTTTTTGAAGTTTCGGGGTTAAAATGGGATTTTTAGAAG-TTCGGGGGT
1 AAAAATGGGATTTTTAGAAGTTTGGGGGTAAAAATGGGATTTTTAGAAGTTTTGGGGTT
191350 AAAAATGGGATTTTT
1 AAAAATGGGATTTTT
191365 GGAAATTTCG
Statistics
Matches: 116, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
58 22 0.19
59 93 0.80
60 1 0.01
ACGTcount: A:0.30, C:0.03, G:0.31, T:0.36
Consensus pattern (59 bp):
AAAAATGGGATTTTTAGAAGTTTGGGGGTAAAAATGGGATTTTTAGAAGTTTTGGGGTT
Done.