Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013611.1 Kokia drynarioides strain JFW-HI SEQ_128638, 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: 263036
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Warning! 109 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:238263 original size:21 final size:22
Alignment explanation
Indices: 238225--238267 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
238215 GATTAAATAT
**
238225 TTTTATAATTTTCTTTATTTTA
1 TTTTATAATTTTAATTATTTTA
238247 TTTTAT-ATTTTAATTATTTTA
1 TTTTATAATTTTAATTATTTTA
238268 ATATTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTATAATTTTAATTATTTTA
Found at i:238274 original size:8 final size:8
Alignment explanation
Indices: 238245--238293 Score: 55
Period size: 9 Copynumber: 5.8 Consensus size: 8
238235 TTCTTTATTT
238245 TATTTT-A
1 TATTTTAA
238252 TATTTTAA
1 TATTTTAA
238260 TTATTTTAA
1 -TATTTTAA
238269 TATTTTTAA
1 TA-TTTTAA
238278 TATTTTTATA
1 TA-TTTTA-A
238288 TATTTT
1 TATTTT
238294 TATACTAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 6 0.16
8 3 0.08
9 26 0.68
10 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TATTTTAA
Found at i:238953 original size:4 final size:4
Alignment explanation
Indices: 238946--238970 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
238936 ACATTCATTC
238946 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
238971 TATGCAATCA
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:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:239303 original size:17 final size:18
Alignment explanation
Indices: 239258--239303 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
239248 TATTACAACA
*
239258 CATAATATAATCACTAAG
1 CATAATACAATCACTAAG
*
239276 CATGATACAATCAC-AAG
1 CATAATACAATCACTAAG
*
239293 CATAATGCAAT
1 CATAATACAAT
239304 GCACCCATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.24
Consensus pattern (18 bp):
CATAATACAATCACTAAG
Found at i:250749 original size:18 final size:17
Alignment explanation
Indices: 250699--250749 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
250689 TTTATATATA
* *
250699 TTAAATTTAATTAAAAT
1 TTAAATTAAATTAAAAC
* *
250716 TTAAATTGATTTAAAAC
1 TTAAATTAAATTAAAAC
250733 TTAATATTAAATTAAAA
1 TTAA-ATTAAATTAAAA
250750 GTCCAAGACA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 18 0.64
18 10 0.36
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TTAAATTAAATTAAAAC
Found at i:252711 original size:29 final size:28
Alignment explanation
Indices: 252659--252891 Score: 112
Period size: 31 Copynumber: 7.9 Consensus size: 28
252649 ATATTTTTGA
* * *
252659 CCCCGAACTTTCAAAAAATACATTGATAC
1 CCCCGAACTTCCAAAAATTACATT-TTAC
*
252688 CCCCGAACTTCCAAAAATTCCATTTTTTGAC
1 CCCCGAACTTCCAAAAATTACA--TTTT-AC
* ** *
252719 CTCAAAACTTCCAAAAATTATATTTTAC
1 CCCCGAACTTCCAAAAATTACATTTTAC
* *
252747 CCTCGAACTTCCAAAAATTCCATTTTTTGAC
1 CCCCGAACTTCCAAAAATTACA--TTTT-AC
* ** *
252778 CTCAAAACTTTCAAAAATTACATTTTTAC
1 CCCCGAACTTCCAAAAATTACA-TTTTAC
*** * * *
252807 CCATAAAACTT--AAAAACTCCATTTTAA
1 CC-CCGAACTTCCAAAAATTACATTTTAC
*
252834 CCCC-AATTTTTTTCCAAAAATTACCATTTTAC
1 CCCCGAA----CTTCCAAAAATTA-CATTTTAC
* *
252866 CCCCGAACTTCCAAAAAATCCATTTT
1 CCCCGAACTTCCAAAAATTACATTTT
252892 TGACCTTGAT
Statistics
Matches: 154, Mismatches: 35, Indels: 31
0.70 0.16 0.14
Matches are distributed among these distances:
25 2 0.01
27 7 0.05
28 32 0.21
29 38 0.25
30 17 0.11
31 45 0.29
32 11 0.07
33 2 0.01
ACGTcount: A:0.37, C:0.27, G:0.03, T:0.33
Consensus pattern (28 bp):
CCCCGAACTTCCAAAAATTACATTTTAC
Found at i:252731 original size:31 final size:31
Alignment explanation
Indices: 252693--252804 Score: 151
Period size: 31 Copynumber: 3.7 Consensus size: 31
252683 GATACCCCCG
252693 AACTTCCAAAAATTCCATTTTTTGACCTCAA
1 AACTTCCAAAAATTCCATTTTTTGACCTCAA
* *
252724 AACTTCCAAAAATT--ATATTTT-ACCCTC-G
1 AACTTCCAAAAATTCCATTTTTTGA-CCTCAA
252752 AACTTCCAAAAATTCCATTTTTTGACCTCAA
1 AACTTCCAAAAATTCCATTTTTTGACCTCAA
* *
252783 AACTTTCAAAAATTACATTTTT
1 AACTTCCAAAAATTCCATTTTT
252805 ACCCATAAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
28 15 0.21
29 10 0.14
30 10 0.14
31 35 0.50
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.38
Consensus pattern (31 bp):
AACTTCCAAAAATTCCATTTTTTGACCTCAA
Found at i:252748 original size:59 final size:58
Alignment explanation
Indices: 252651--252926 Score: 236
Period size: 59 Copynumber: 4.7 Consensus size: 58
252641 CCAAAATTAT
** * * *
252651 ATTTTTGACC-CCGAACTTTCAAAAAATACATTGATACCCCCGAACTTCCAAAAATTCC
1 ATTTTTGACCTCAAAACTTCCAAAAATTACATT-TTACCCCCGAACTTCCAAAAATTCC
* *
252709 ATTTTTTGACCTCAAAACTTCCAAAAATTATATTTTACCCTCGAACTTCCAAAAATTCC
1 A-TTTTTGACCTCAAAACTTCCAAAAATTACATTTTACCCCCGAACTTCCAAAAATTCC
* *** *
252768 ATTTTTTGACCTCAAAACTTTCAAAAATTACATTTTTACCCATAAAACTT--AAAAACTCC
1 A-TTTTTGACCTCAAAACTTCCAAAAATTACA-TTTTACCC-CCGAACTTCCAAAAATTCC
* * *** *
252827 A-TTTTAACCCCAATTTTTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAAATCC
1 ATTTTTGACCTCAA--AACTTCCAAAAATTA-CATTTTACCCCCGAACTTCCAAAAATTCC
** ***
252887 ATTTTTGACCTTGATTTTTCCAAAAATTACCATTTTACCC
1 ATTTTTGACCTCAAAACTTCCAAAAATTA-CATTTTACCC
252927 TCAGATGTCT
Statistics
Matches: 182, Mismatches: 26, Indels: 19
0.80 0.11 0.08
Matches are distributed among these distances:
57 10 0.05
58 6 0.03
59 116 0.64
60 36 0.20
61 14 0.08
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (58 bp):
ATTTTTGACCTCAAAACTTCCAAAAATTACATTTTACCCCCGAACTTCCAAAAATTCC
Found at i:252892 original size:29 final size:29
Alignment explanation
Indices: 252651--252892 Score: 131
Period size: 29 Copynumber: 8.2 Consensus size: 29
252641 CCAAAATTAT
* * *
252651 ATTTTTGA-CCCCGAACTTTCAAAAAATAC
1 ATTTTT-ACCCCCGAACTTCCAAAAATTCC
**
252680 ATTGATACCCCCGAACTTCCAAAAATTCC
1 ATTTTTACCCCCGAACTTCCAAAAATTCC
* **
252709 ATTTTTTGACCTCAAAACTTCCAAAAATT--
1 A-TTTTT-ACCCCCGAACTTCCAAAAATTCC
*
252738 ATATTTTACCCTCGAACTTCCAAAAATTCC
1 AT-TTTTACCCCCGAACTTCCAAAAATTCC
* ** * *
252768 ATTTTTTGACCTCAAAACTTTCAAAAATTAC
1 A-TTTTT-ACCCCCGAACTTCCAAAAATTCC
*** *
252799 ATTTTTACCCATAAAACTT--AAAAACTCC
1 ATTTTTACCC-CCGAACTTCCAAAAATTCC
* *
252827 A-TTTTAACCCC-AATTTTTTTCCAAAAATTACC
1 ATTTTTACCCCCGAA----CTTCCAAAAATT-CC
*
252859 A-TTTTACCCCCGAACTTCCAAAAAATCC
1 ATTTTTACCCCCGAACTTCCAAAAATTCC
252887 ATTTTT
1 ATTTTT
252893 GACCTTGATT
Statistics
Matches: 163, Mismatches: 32, Indels: 36
0.71 0.14 0.16
Matches are distributed among these distances:
25 2 0.01
27 7 0.04
28 30 0.18
29 47 0.29
30 20 0.12
31 43 0.26
32 12 0.07
33 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
ATTTTTACCCCCGAACTTCCAAAAATTCC
Found at i:252963 original size:59 final size:60
Alignment explanation
Indices: 252727--252975 Score: 152
Period size: 59 Copynumber: 4.2 Consensus size: 60
252717 ACCTCAAAAC
* * * **
252727 TTCCAAAAATTA-TATTTTACCCTC-GAACTTCC-AAAAATTCCATTTTTTGA-CCTCAAAACT
1 TTCCAAAAATTACCATTTTACCC-CAGAACTTCCTAAAAATCCCA--TTTTAACCCT-AAATTT
* * * *
252787 TT-CAAAAATTA-CATTTTTACCCATAAAAC-T--TAAAAA-CTCCATTTTAACCCCAATTTTT
1 TTCCAAAAATTACCA-TTTTACCC-CAGAACTTCCTAAAAATC-CCATTTTAACCCTAA-ATTT
* * * **
252845 TTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAAAT-CCATTTTTGA-CCTTGATTT
1 TTCCAAAAATTACCATTTTACCCCAGAACTTCCTAAAAATCCCA-TTTTAACCCTAAATTT
252904 TTCCAAAAATTACCATTTTACCCTCAG-A-TGT-CTAAAAATCCCATTTTAACCCTAAA-TT
1 TTCCAAAAATTACCATTTTACCC-CAGAACT-TCCTAAAAATCCCATTTTAACCCTAAATTT
*
252962 TTCCCAAAATTACC
1 TTCCAAAAATTACC
252976 TACTTGCCCT
Statistics
Matches: 147, Mismatches: 25, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
57 7 0.05
58 36 0.24
59 71 0.48
60 20 0.14
61 13 0.09
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (60 bp):
TTCCAAAAATTACCATTTTACCCCAGAACTTCCTAAAAATCCCATTTTAACCCTAAATTT
Found at i:253010 original size:28 final size:28
Alignment explanation
Indices: 252965--253026 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
252955 CTAAATTTTC
*
252965 CCAAAATTACCTACTTGCCCTCGAG-AGT
1 CCAAAATTACCTACTTGCCCCCGAGTA-T
*
252993 CCAAAATTACC-ATTTTGCCCCCGAGTAT
1 CCAAAATTACCTA-CTTGCCCCCGAGTAT
253021 CCAAAA
1 CCAAAA
253027 AGTCTCTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 1 0.03
28 28 0.93
29 1 0.03
ACGTcount: A:0.32, C:0.32, G:0.11, T:0.24
Consensus pattern (28 bp):
CCAAAATTACCTACTTGCCCCCGAGTAT
Found at i:258531 original size:15 final size:15
Alignment explanation
Indices: 258513--258542 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
258503 TTCAATGAAC
258513 AAAGGAAAAAAGAAA
1 AAAGGAAAAAAGAAA
*
258528 AAAGGGAAAAAGAAA
1 AAAGGAAAAAAGAAA
258543 GCAAAAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAGGAAAAAAGAAA
Found at i:259909 original size:100 final size:98
Alignment explanation
Indices: 259725--260199 Score: 417
Period size: 100 Copynumber: 4.7 Consensus size: 98
259715 TTAGCACCAT
* * ** *
259725 GAAGACATGAAGGGAAAGATCTAAGACCGCAATGGCGGATCTAGTACCAAAAAGATACAAAAGGG
1 GAAGACAAGAAGGGAAAGATCTAAG-CCGCAATGGCGGATCCAGTACCATGAAG--ACAGAAGGG
*
259790 AAA-AGTCTAAGTCACAACGACGGA-CCGTGTACCCCA
63 AAAGA-TCTAAGTCACAACGACGGATCC-AGTACCCCA
* **
259826 GAAGACAAGAAGGGAAAGATTTAAGCCGCAATGGCAAATCCAGTACCATGAAGACATGAAGGGAA
1 GAAGACAAGAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCATGAAGACA-GAAGGGAA
** *
259891 AGATCTAAGATCGTAACGACGGATCCAGTACCACA
65 AGATCTAAG-TCACAACGACGGATCCAGTACCCCA
* * * ** * *
259926 -AAGATACAA-AAGGGAAAGGTCTAAGTCGCAACGATGGA-CCGTGTACCTTAGAAGACAAGAAG
1 GAAG--ACAAGAAGGGAAAGATCTAAGCCGCAATGGCGGATCC-AGTACCAT-GAAGAC-AGAAG
* * * **
259988 GGAAAGATTTAAGTCGCAACGGCAAATCCAGTA--CCA
61 GGAAAGATCTAAGTCACAACGACGGATCCAGTACCCCA
* * ** *
260024 TGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCAAAAAGATACAAAAGG
1 -GAAGACAAGAAGGGAAAGATCTAAG-CCGCAATGGCGGATCCAGTACCATGAAG--ACAGAAGG
* **
260089 GAAAGGTCTAAGTCACAACGACGGA-CTGTGTACCCCA
62 GAAAGATCTAAGTCACAACGACGGATC-CAGTACCCCA
* **
260126 GAAGACAAGAAGGGAAAGATTTAAGCCGCAATGGCAAATCCAGTACCATGAAGACATGAAGGGAA
1 GAAGACAAGAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCATGAAGACA-GAAGGGAA
260191 AGATCTAAG
65 AGATCTAAG
260200 NNNNNNNNNN
Statistics
Matches: 299, Mismatches: 55, Indels: 42
0.76 0.14 0.11
Matches are distributed among these distances:
98 11 0.04
99 53 0.18
100 153 0.51
101 78 0.26
102 4 0.01
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.14
Consensus pattern (98 bp):
GAAGACAAGAAGGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCATGAAGACAGAAGGGAAA
GATCTAAGTCACAACGACGGATCCAGTACCCCA
Found at i:259959 original size:50 final size:48
Alignment explanation
Indices: 259720--260199 Score: 293
Period size: 50 Copynumber: 9.6 Consensus size: 48
259710 AGGTCTTAGC
* * * * * *
259720 ACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAATGGCGGATCTAGT
1 ACCATAAAGACA-AAAGGGAAAGATCTAAG-TCGCAACGACGGATCCAGT
* * *
259770 ACCAAAAAGATACAAAAGGGAAA-AGTCTAAGTCACAACGACGGA-CCGTGT
1 ACCATAAAG--ACAAAAGGGAAAGA-TCTAAGTCGCAACGACGGATCC-AGT
** * * * * **
259820 ACCCCAGAAGACAAGAAGGGAAAGATTTAAGCCGCAATGGCAAATCCAGT
1 ACCATA-AAGACAA-AAGGGAAAGATCTAAGTCGCAACGACGGATCCAGT
* * *
259870 ACCATGAAGACATGAAGGGAAAGATCTAAGATCGTAACGACGGATCCAGT
1 ACCATAAAGACA-AAAGGGAAAGATCTAAG-TCGCAACGACGGATCCAGT
* * * *
259920 ACCACAAAGATACAAAAGGGAAAGGTCTAAGTCGCAACGATGGA-CCGTGT
1 ACCATAAAG--ACAAAAGGGAAAGATCTAAGTCGCAACGACGGATCC-AGT
* * * **
259970 ACCTTAGAAGACAAGAAGGGAAAGATTTAAGTCGCAACGGCAAATCCAGT
1 ACCATA-AAGACAA-AAGGGAAAGATCTAAGTCGCAACGACGGATCCAGT
* * * *
260020 ACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGT
1 ACCATAAAGACA-AAAGGGAAAGATCTAAG-TCGCAACGACGGATCCAGT
* * * **
260070 ACCAAAAAGATACAAAAGGGAAAGGTCTAAGTCACAACGACGGA-CTGTGT
1 ACCATAAAG--ACAAAAGGGAAAGATCTAAGTCGCAACGACGGATC-CAGT
** * * * * **
260120 ACCCCAGAAGACAAGAAGGGAAAGATTTAAGCCGCAATGGCAAATCCAGT
1 ACCATA-AAGACAA-AAGGGAAAGATCTAAGTCGCAACGACGGATCCAGT
* *
260170 ACCATGAAGACATGAAGGGAAAGATCTAAG
1 ACCATAAAGACA-AAAGGGAAAGATCTAAG
260200 NNNNNNNNNN
Statistics
Matches: 326, Mismatches: 79, Indels: 51
0.71 0.17 0.11
Matches are distributed among these distances:
49 79 0.24
50 179 0.55
51 59 0.18
52 9 0.03
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.14
Consensus pattern (48 bp):
ACCATAAAGACAAAAGGGAAAGATCTAAGTCGCAACGACGGATCCAGT
Found at i:259991 original size:150 final size:150
Alignment explanation
Indices: 259720--260199 Score: 834
Period size: 150 Copynumber: 3.2 Consensus size: 150
259710 AGGTCTTAGC
* *
259720 ACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAATGGCGGATCTAGTACCAAAAAGATACAA
1 ACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCAAAAAGATACAA
*
259785 AAGGGAAAAGTCTAAGTCACAACGACGGACCGTGTACCCCAGAAGACAAGAAGGGAAAGATTTAA
66 AAGGGAAAGGTCTAAGTCACAACGACGGACCGTGTACCCCAGAAGACAAGAAGGGAAAGATTTAA
259850 GCCGCAATGGCAAATCCAGT
131 GCCGCAATGGCAAATCCAGT
* * * *
259870 ACCATGAAGACATGAAGGGAAAGATCTAAGATCGTAACGACGGATCCAGTACCACAAAGATACAA
1 ACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCAAAAAGATACAA
* * **
259935 AAGGGAAAGGTCTAAGTCGCAACGATGGACCGTGTACCTTAGAAGACAAGAAGGGAAAGATTTAA
66 AAGGGAAAGGTCTAAGTCACAACGACGGACCGTGTACCCCAGAAGACAAGAAGGGAAAGATTTAA
* *
260000 GTCGCAACGGCAAATCCAGT
131 GCCGCAATGGCAAATCCAGT
260020 ACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCAAAAAGATACAA
1 ACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCAAAAAGATACAA
*
260085 AAGGGAAAGGTCTAAGTCACAACGACGGACTGTGTACCCCAGAAGACAAGAAGGGAAAGATTTAA
66 AAGGGAAAGGTCTAAGTCACAACGACGGACCGTGTACCCCAGAAGACAAGAAGGGAAAGATTTAA
260150 GCCGCAATGGCAAATCCAGT
131 GCCGCAATGGCAAATCCAGT
260170 ACCATGAAGACATGAAGGGAAAGATCTAAG
1 ACCATGAAGACATGAAGGGAAAGATCTAAG
260200 NNNNNNNNNN
Statistics
Matches: 306, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
150 306 1.00
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.14
Consensus pattern (150 bp):
ACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCAAAAAGATACAA
AAGGGAAAGGTCTAAGTCACAACGACGGACCGTGTACCCCAGAAGACAAGAAGGGAAAGATTTAA
GCCGCAATGGCAAATCCAGT
Found at i:260339 original size:50 final size:50
Alignment explanation
Indices: 260292--260639 Score: 273
Period size: 50 Copynumber: 7.0 Consensus size: 50
260282 CGTGTACCTT
* * **
260292 AGAAGACAAGAAGGGAAAGATTTAAGTCGCAACGGTAAATCCAGTACCA-
1 AGAAGACAAGAAGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCAC
* * *
260341 TGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGAATCCAATACCAC
1 AGAAGACAAGAAGGGAAAGATCTAAG-CCGCAACGGCGAATCCAGTACCAC
* * * * * * *
260392 A-AAGATAGAAAAGGGAAAGGTCTAAGTCGCAACGGCGGA-CCGTGTACCTC
1 AGAAGACA-AGAAGGGAAAGATCTAAGCCGCAACGGCGAATCC-AGTACCAC
* * * *
260442 AGAAGACAAGAAGGGAAAGATTTAAACCGCAATGGCAAATCCAGTACCA-
1 AGAAGACAAGAAGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCAC
* * *
260491 TGAAGACATGAAAGGAAAGATCTAAGACCGCAACGGCGAATCCAGTACCAC
1 AGAAGACAAGAAGGGAAAGATCTAAG-CCGCAACGGCGAATCCAGTACCAC
* * ** * * **
260542 A-AAGATACAA-AAGGGAAAGGTTTAAATCGCAACGGCGGA-CCGTGTACCTG
1 AGAAG--ACAAGAAGGGAAAGATCTAAGCCGCAACGGCGAATCC-AGTACCAC
* *
260592 AGAAGAC-AGTAAGGGAAAGAAT-TAAGCAGCAACGACGAATCCAGTACC
1 AGAAGACAAG-AAGGGAAAG-ATCTAAGCCGCAACGGCGAATCCAGTACC
260640 GCGAAGATTT
Statistics
Matches: 230, Mismatches: 53, Indels: 31
0.73 0.17 0.10
Matches are distributed among these distances:
48 1 0.00
49 50 0.22
50 136 0.59
51 40 0.17
52 3 0.01
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.13
Consensus pattern (50 bp):
AGAAGACAAGAAGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCAC
Found at i:260521 original size:150 final size:150
Alignment explanation
Indices: 260250--260639 Score: 611
Period size: 150 Copynumber: 2.6 Consensus size: 150
260240 NNNNNNNNNN
** *
260250 AAAAGGGAAAGGTCTAAGTCGCAACGATGGACCGTGTACCTTAGAAGACAAGAAGGGAAAGATTT
1 AAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTT
* * *
260315 AAGTCGCAACGGTAAATCCAGTACCATGAAGACATGAAGGGAAAGATCTAAGACCGCAACGGCGA
66 AAGCCGCAACGGCAAATCCAGTACCATGAAGACATGAAAGGAAAGATCTAAGACCGCAACGGCGA
*
260380 ATCCAATACCACAAAGATAG
131 ATCCAATACCACAAAGATAC
260400 AAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTT
1 AAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTT
* *
260465 AAACCGCAATGGCAAATCCAGTACCATGAAGACATGAAAGGAAAGATCTAAGACCGCAACGGCGA
66 AAGCCGCAACGGCAAATCCAGTACCATGAAGACATGAAAGGAAAGATCTAAGACCGCAACGGCGA
*
260530 ATCCAGTACCACAAAGATAC
131 ATCCAATACCACAAAGATAC
* * * *
260550 AAAAGGGAAAGGTTTAAATCGCAACGGCGGACCGTGTACCTGAGAAGAC-AGTAAGGGAAAGAAT
1 AAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACAAG-AAGGGAAAGATT
* * *
260614 TAAGCAGCAACGACGAATCCAGTACC
65 TAAGCCGCAACGGCAAATCCAGTACC
260640 GCGAAGATTT
Statistics
Matches: 220, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
149 2 0.01
150 218 0.99
ACGTcount: A:0.41, C:0.20, G:0.26, T:0.14
Consensus pattern (150 bp):
AAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTT
AAGCCGCAACGGCAAATCCAGTACCATGAAGACATGAAAGGAAAGATCTAAGACCGCAACGGCGA
ATCCAATACCACAAAGATAC
Found at i:260589 original size:100 final size:98
Alignment explanation
Indices: 260250--260695 Score: 280
Period size: 100 Copynumber: 4.5 Consensus size: 98
260240 NNNNNNNNNN
* * ** * * * *
260250 AAAAGGGAAAGGTCTAAGTCGCAACGATGGA-CCGTGTACCTTAGAAGACA-AGAAGGGAAAGAT
1 AAAAGGGAAAGGTTTAAATCGCAACGGCGAATCC-AGTACCATAGAAGACAGA-AAAGGAAAGAT
* * ** **
260313 TTAAGTCGCAACGGTAAATCCAGTACCATGAAGAC
64 CTAAGCCGCAACGGCGAATCCAGTACCACAAAGAC
* * * * * * * *
260348 ATGAAGGGAAAGATCTAAGACCGCAACGGCGAATCCAATACCACA-AAGATAGAAAAGGGAAAGG
1 A-AAAGGGAAAGGTTTAA-ATCGCAACGGCGAATCCAGTACCATAGAAGACAGAAAA-GGAAAGA
* * * *
260412 TCTAAGTCGCAACGGCGGA-CCGTGTACCTCAGAAGAC
63 TCTAAGCCGCAACGGCGAATCC-AGTACCACA-AAGAC
* * * *
260449 AAGAAGGGAAAGATTTAAACCGCAATGGCAAATCCAGTACCAT-GAAGACATG-AAAGGAAAGAT
1 AA-AAGGGAAAGGTTTAAATCGCAACGGCGAATCCAGTACCATAGAAGACA-GAAAAGGAAAGAT
260512 CTAAGACCGCAACGGCGAATCCAGTACCACAAAGATAC
64 CTAAG-CCGCAACGGCGAATCCAGTACCACAAAG--AC
* * * *
260550 AAAAGGGAAAGGTTTAAATCGCAACGGCGGA-CCGTGTACC-TGAGAAGACAGTAAGGGAAAGAA
1 AAAAGGGAAAGGTTTAAATCGCAACGGCGAATCC-AGTACCAT-AGAAGACAGAAAAGGAAAG-A
* * * * *
260613 T-TAAGCAGCAACGACGAATCCAGTACCGCGAAGATTT
63 TCTAAGCCGCAACGGCGAATCCAGTACCACAAAGA--C
* * * * *
260650 AAAGGGGAAAGGTTTAAGTCGCAATGGCGAACCCAGTACCTTAGAA
1 AAAAGGGAAAGGTTTAAATCGCAACGGCGAATCCAGTACCATAGAA
260696 ACATGACGAG
Statistics
Matches: 274, Mismatches: 51, Indels: 44
0.74 0.14 0.12
Matches are distributed among these distances:
98 2 0.01
99 41 0.15
100 178 0.65
101 51 0.19
102 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.14
Consensus pattern (98 bp):
AAAAGGGAAAGGTTTAAATCGCAACGGCGAATCCAGTACCATAGAAGACAGAAAAGGAAAGATCT
AAGCCGCAACGGCGAATCCAGTACCACAAAGAC
Found at i:260673 original size:150 final size:149
Alignment explanation
Indices: 260250--260689 Score: 573
Period size: 150 Copynumber: 2.9 Consensus size: 149
260240 NNNNNNNNNN
** *
260250 AAAAGGGAAAGGTCTAAGTCGCAACGATGGACCGTGTACCTTAGAAGACAAGAAGGGAAAGATTT
1 AAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTT
* *
260315 AAGTCGCAACGGTAAATCCAGTACCATGAAGACA-TGAAGGGAAAGATCTAAGACCGCAACGGCG
66 AAG-CGCAACGGCAAATCCAGTACCATGAAGA-ATTAAAGGGAAAGATCTAAGACCGCAACGGCG
* *
260379 AATCCAATACCACAAAGATAG
129 AATCCAGTACCACAAAGATAC
260400 AAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTT
1 AAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTT
* * *
260465 AAACCGCAATGGCAAATCCAGTACCATGAAGACATGAAA-GGAAAGATCTAAGACCGCAACGGCG
66 -AAGCGCAACGGCAAATCCAGTACCATGAAGA-ATTAAAGGGAAAGATCTAAGACCGCAACGGCG
260529 AATCCAGTACCACAAAGATAC
129 AATCCAGTACCACAAAGATAC
* * * *
260550 AAAAGGGAAAGGTTTAAATCGCAACGGCGGACCGTGTACCTGAGAAGAC-AGTAAGGGAAAGAAT
1 AAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACAAG-AAGGGAAAGATT
* * ** * * * * *
260614 TAAGCAGCAACGACGAATCCAGTACCGCGAAGATTTAAAGGGGAAAGGTTTAAG-TCGCAATGGC
65 TAAGC-GCAACGGCAAATCCAGTACCATGAAGAATTAAA-GGGAAAGATCTAAGACCGCAACGGC
*
260678 GAACCCAGTACC
128 GAATCCAGTACC
260690 TTAGAAACAT
Statistics
Matches: 257, Mismatches: 27, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
149 9 0.04
150 233 0.91
151 15 0.06
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (149 bp):
AAAAGGGAAAGGTCTAAGTCGCAACGGCGGACCGTGTACCTCAGAAGACAAGAAGGGAAAGATTT
AAGCGCAACGGCAAATCCAGTACCATGAAGAATTAAAGGGAAAGATCTAAGACCGCAACGGCGAA
TCCAGTACCACAAAGATAC
Found at i:260838 original size:51 final size:50
Alignment explanation
Indices: 260783--260950 Score: 169
Period size: 51 Copynumber: 3.3 Consensus size: 50
260773 GGCAAGTCTT
*
260783 TATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAACATCAAATCC
1 TATCT-TCTGAAGTTGTAGTAAGAGCAAGATGAAGATTCAACATCAAATCC
*** * ** * * * *
260834 TATCTTCCTGAAGTTGTAGTAA-AGTTGGATTAA-AAACAATAGCAAGTCTT
1 TATCTT-CTGAAGTTGTAGTAAGAGCAAGATGAAGATTCAACATCAAATC-C
*
260884 TATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAACATCAAATCC
1 TATCT-TCTGAAGTTGTAGTAAGAGCAAGATGAAGATTCAACATCAAATCC
260935 TATCTTCTTGAAGTTG
1 TATCTTC-TGAAGTTG
260951 CAGCGAAGTT
Statistics
Matches: 89, Mismatches: 22, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
49 9 0.10
50 30 0.34
51 41 0.46
52 9 0.10
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (50 bp):
TATCTTCTGAAGTTGTAGTAAGAGCAAGATGAAGATTCAACATCAAATCC
Found at i:260947 original size:101 final size:101
Alignment explanation
Indices: 260768--260969 Score: 341
Period size: 101 Copynumber: 2.0 Consensus size: 101
260758 GATCAAAATT
*
260768 ACAATGGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAACATCAAATC
1 ACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAACATCAAATC
* * *
260833 CTATCTTCCTGAAGTTGTAGTAAAGTTGGATTAAAA
66 CTATCTTCCTGAAGTTGCAGCAAAGTTGGAATAAAA
*
260869 ACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAACATCAAATC
1 ACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAACATCAAATC
* *
260934 CTATCTTCTTGAAGTTGCAGCGAAGTTGGAATAAAA
66 CTATCTTCCTGAAGTTGCAGCAAAGTTGGAATAAAA
260970 CTACAGCAGC
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 94 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (101 bp):
ACAATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAACATCAAATC
CTATCTTCCTGAAGTTGCAGCAAAGTTGGAATAAAA
Found at i:261090 original size:39 final size:39
Alignment explanation
Indices: 261036--261125 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 39
261026 TCGTCAACCA
* * * * * *
261036 ATCTCCTACCCCGAGCCAGGGGTAGATTATAGTCATTTG
1 ATCTCTTACCCCGAGCCAAGGGCAGATTACAGCCATTCG
* *
261075 ATCTCTTTCCCCGAGCCAAGGGCATATTACAGCCATTCG
1 ATCTCTTACCCCGAGCCAAGGGCAGATTACAGCCATTCG
261114 ATCTCTTACCCC
1 ATCTCTTACCCC
261126 AAGCTTGAGG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.22, C:0.32, G:0.18, T:0.28
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCAAGGGCAGATTACAGCCATTCG
Found at i:261535 original size:194 final size:194
Alignment explanation
Indices: 261193--261740 Score: 920
Period size: 194 Copynumber: 2.8 Consensus size: 194
261183 GATTATCCAC
* * * *
261193 AAACAA-TGAGGCAGTCATCTTCTTGATAAGATACAGAGAAGTATACCAACTCAATGCGAACAAA
1 AAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCAAACAAA
** *
261257 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAATAGGGCGAAGCAATAAAAAGGTTAGTTT
66 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTT
* *
261322 TTTGATGAGATACTGAGAAGTGGACAAAATTCGTCTTCCTGATGAGGTACAAAGAAGCGGATTG
131 TCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAAAGAAGCGGATTG
*
261386 AAACAAGTGAGGCGGTCATCTTCCTAATGAGATACAGAGAAGTATACCAACTCAATGCAAACAAA
1 AAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCAAACAAA
* * * *
261451 TCTTCGAACCCTAGCTTCCTAATGAAATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAACTT
66 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTT
*
261516 TCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGGTACAAAGAAGCGGATTG
131 TCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAAAGAAGCGGATTG
*
261580 AAACAAGTGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACCAACTCAATGCAAACAAA
1 AAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCAAACAAA
*
261645 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAACAATAAAAAGGTTAGC-T
66 TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTT
261709 TCTTGATGAGATACTGAGAAGTGGACCAAATT
131 TC-TGATGAGATACTGAGAAGTGGACCAAATT
261741 GAAACAAGTG
Statistics
Matches: 331, Mismatches: 22, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
193 9 0.03
194 322 0.97
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (194 bp):
AAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAATGCAAACAAA
TCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGTTAGCTT
TCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACAAAGAAGCGGATTG
Found at i:261907 original size:169 final size:162
Alignment explanation
Indices: 261576--261909 Score: 413
Period size: 169 Copynumber: 2.0 Consensus size: 162
261566 AAAGAAGCGG
* *
261576 ATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACCAACTCAATGCAAA
1 ATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCAATGCAAA
*
261641 CAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGGCGAAACAATAAAAAGGTTA
66 CAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCGAAACAATAAAAAGGTTA
* *
261706 GCTTCTTGATGAGATACTGAGAAGTGGACCAA
131 GCTTCTTGATGAAATACTGAGAAGTAGACCAA
* *
261738 ATTGAAACAAGTGAGGTGGTCATCTTCCTGATTAGATACAAAGAAGTATACCAACTCAGGGCTCG
1 ATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCA-------
** * * * * *
261803 ATGTGAGCAAA-CTTTCGAATCCCAACTTCTTGA-GAAGATACTGAGAAGCAGGTCGAAGCAATA
59 ATGCAAACAAATC-TTCGAACCCCAACTTCCTGATG-AGATACTGAGAAGCAGGGCGAAACAATA
* *
261866 AAATGGTTAGCTT-TCTGATGAAATATTGAGAAGTAGACCAA
122 AAAAGGTTAGCTTCT-TGATGAAATACTGAGAAGTAGACCAA
261907 ATT
1 ATT
261910 CGTCTTCCTG
Statistics
Matches: 146, Mismatches: 16, Indels: 13
0.83 0.09 0.07
Matches are distributed among these distances:
162 54 0.37
168 3 0.02
169 89 0.61
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (162 bp):
ATTGAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAAAGAAGTATACCAACTCAATGCAAA
CAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGGCGAAACAATAAAAAGGTTA
GCTTCTTGATGAAATACTGAGAAGTAGACCAA
Found at i:262361 original size:6 final size:6
Alignment explanation
Indices: 262352--262418 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
262342 CAAATTTATT
** **
262352 TTTAAA TTTAAA TTTATCT TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
262400 TTT-AA TTAAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
262419 GATTTAAAAC
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
5 7 0.15
6 37 0.77
7 4 0.08
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:262393 original size:17 final size:17
Alignment explanation
Indices: 262352--262418 Score: 89
Period size: 17 Copynumber: 3.8 Consensus size: 17
262342 CAAATTTATT
262352 TTTAAATTTAAATTTATC
1 TTTAAATTTAAATTTA-C
*
262370 TTTTAAATTTAAATTTGC
1 -TTTAAATTTAAATTTAC
*
262388 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAC
*
262405 TTAAAATTTAAATT
1 TTTAAATTTAAATT
262419 GATTTAAAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
17 28 0.64
18 1 0.02
19 15 0.34
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAC
Found at i:262425 original size:17 final size:17
Alignment explanation
Indices: 262355--262427 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
262345 ATTTATTTTT
* *
262355 AAATTTAAATTTATCTTTT
1 AAATTTAAATTGA--TTTA
*
262374 AAATTTAAATTTGCTTT-
1 AAATTTAAA-TTGATTTA
* *
262391 AAATTTAAATTTAATTA
1 AAATTTAAATTGATTTA
262408 AAATTTAAATTGATTTA
1 AAATTTAAATTGATTTA
262425 AAA
1 AAA
262428 CATAATATTA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
16 4 0.09
17 27 0.60
18 3 0.07
19 9 0.20
20 2 0.04
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
AAATTTAAATTGATTTA
Done.