Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010941.1 Kokia drynarioides strain JFW-HI SEQ_125909, 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: 116321
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:8292 original size:26 final size:26
Alignment explanation
Indices: 8252--8303 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
8242 ATAAATTTGA
*
8252 AATTAATTATGTTTAAATTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
* **
8278 AATTAATAATTTTTATGTTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
8304 TGGTTTAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (26 bp):
AATTAATAATGTTTAAATTTGTATTT
Found at i:8449 original size:7 final size:7
Alignment explanation
Indices: 8439--8588 Score: 67
Period size: 7 Copynumber: 20.9 Consensus size: 7
8429 TTCACTTAGT
8439 GTTTAAG
1 GTTTAAG
8446 GTTTTAAG
1 G-TTTAAG
*
8454 ATTTAAG
1 GTTTAAG
8461 GTTTAAG
1 GTTTAAG
*
8468 ATTT-AG
1 GTTTAAG
8474 AGTTTAAG
1 -GTTTAAG
8482 AGTTT-AG
1 -GTTTAAG
*
8489 AGTTTAGG
1 -GTTTAAG
8497 GTTTAAG
1 GTTTAAG
*
8504 GATT-AG
1 GTTTAAG
8510 GATTT-AG
1 G-TTTAAG
*
8517 GATTTAAT
1 G-TTTAAG
*
8525 GTTTATG
1 GTTTAAG
*
8532 TTTGTAAG
1 GTT-TAAG
* *
8540 GTATATG
1 GTTTAAG
8547 G-TTAAGG
1 GTTTAA-G
* *
8554 GTATAGG
1 GTTTAAG
8561 GTTTTAAG
1 G-TTTAAG
*
8569 GTTTAAA
1 GTTTAAG
*
8576 GTTTAGG
1 GTTTAAG
8583 GTTTAA
1 GTTTAA
8589 TTTATGCACA
Statistics
Matches: 107, Mismatches: 26, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
6 7 0.07
7 73 0.68
8 27 0.25
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.43
Consensus pattern (7 bp):
GTTTAAG
Found at i:9543 original size:43 final size:43
Alignment explanation
Indices: 9480--9568 Score: 133
Period size: 43 Copynumber: 2.1 Consensus size: 43
9470 AACTGCACAA
* * * *
9480 TTAGTAACATGTCACGATATTAATAAGAGTCGAGTAATATAAT
1 TTAGTAACATGCCACCATATTAACAAGAGTCAAGTAATATAAT
*
9523 TTAGTAACATGCCACCATATTAACACGAGTCAAGTAATATAAT
1 TTAGTAACATGCCACCATATTAACAAGAGTCAAGTAATATAAT
9566 TTA
1 TTA
9569 ATAATATGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (43 bp):
TTAGTAACATGCCACCATATTAACAAGAGTCAAGTAATATAAT
Found at i:11368 original size:21 final size:21
Alignment explanation
Indices: 11343--11382 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11333 TACTTACTAC
11343 TACTAACAAAATGAAATTACT
1 TACTAACAAAATGAAATTACT
*
11364 TACTAACAAAATTAAATTA
1 TACTAACAAAATGAAATTA
11383 AATTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.03, T:0.30
Consensus pattern (21 bp):
TACTAACAAAATGAAATTACT
Found at i:11452 original size:12 final size:12
Alignment explanation
Indices: 11435--11474 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
11425 TTTACTCAAC
11435 TAAATAAAAAAT
1 TAAATAAAAAAT
*
11447 TAAATAACAAAT
1 TAAATAAAAAAT
*
11459 CAAAT-AAAAAT
1 TAAATAAAAAAT
11470 TAAAT
1 TAAAT
11475 TAATCAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (12 bp):
TAAATAAAAAAT
Found at i:11463 original size:24 final size:26
Alignment explanation
Indices: 11436--11490 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 26
11426 TTACTCAACT
*
11436 AAATAAAAAATTAAA-TAA-CAAATC
1 AAATAAAAAATTAAATTAATCAAAAC
11460 AAAT-AAAAATTAAATTAATCAAAAC
1 AAATAAAAAATTAAATTAATCAAAAC
11485 AAATAA
1 AAATAA
11491 CTTAAAGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 10 0.37
24 7 0.26
25 9 0.33
26 1 0.04
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (26 bp):
AAATAAAAAATTAAATTAATCAAAAC
Found at i:12850 original size:11 final size:11
Alignment explanation
Indices: 12834--12887 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
12824 GATAAAATTG
12834 TAATTTTATTA
1 TAATTTTATTA
12845 TAATTTTATT-
1 TAATTTTATTA
12855 T--TTTTA--A
1 TAATTTTATTA
12862 TAATTTTATTA
1 TAATTTTATTA
12873 TAAATTTTGATTA
1 T-AATTTT-ATTA
12886 TA
1 TA
12888 TTTATTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
7 1 0.03
8 5 0.14
9 5 0.14
10 1 0.03
11 12 0.33
12 7 0.19
13 5 0.14
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TAATTTTATTA
Found at i:14941 original size:2 final size:2
Alignment explanation
Indices: 14934--14987 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
14924 TGCTCAAGTT
14934 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
14976 TC TC TC TC TC TC
1 TC TC TC TC TC TC
14988 GCACACACAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:19615 original size:12 final size:12
Alignment explanation
Indices: 19583--19607 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19573 TATTTAAGAC
19583 GAAGTGTCAACA
1 GAAGTGTCAACA
19595 GAAGTGTCAACA
1 GAAGTGTCAACA
19607 G
1 G
19608 GTGTGTCAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.28, T:0.16
Consensus pattern (12 bp):
GAAGTGTCAACA
Found at i:35519 original size:29 final size:28
Alignment explanation
Indices: 35455--35568 Score: 86
Period size: 29 Copynumber: 3.9 Consensus size: 28
35445 GGAGGTTTTG
* * * *
35455 AGGT-AAAATGTAATTTTTAGAAATTTTA
1 AGGTAAAAATGGAATTTTT-GGAAGTTCA
*
35483 AGGTTAAAAATGGAATTTTTGGAAGTTCG
1 AGG-TAAAAATGGAATTTTTGGAAGTTCA
* ** *
35512 GGGCTAAAAATATAATTTTTGAAAGTTTCA
1 AGG-TAAAAATGGAATTTTTGGAAG-TTCA
*
35542 AGGTCAAAATGGAATTTTTGGACAGTT
1 AGGTAAAAATGGAATTTTTGGA-AGTT
35569 TAGGGACCTC
Statistics
Matches: 66, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
28 3 0.05
29 43 0.65
30 20 0.30
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.37
Consensus pattern (28 bp):
AGGTAAAAATGGAATTTTTGGAAGTTCA
Found at i:35520 original size:58 final size:57
Alignment explanation
Indices: 35371--35568 Score: 172
Period size: 58 Copynumber: 3.4 Consensus size: 57
35361 AAAGAAGATA
* * * ** *
35371 AAAAATAGAATTTTTGGACA-TTCAGGGGTAAAATGGTAACTTTTGAGAGTTTTGGGGTC
1 AAAAATGGAATTTTTGGACAGTTC-GGGGTAAAAT-GTAATTTTTGA-AATTTTAAGGTT
* * *
35430 AAAAAT-GAAGTTTTTGGA-GGTTTTGAGGTAAAATGTAATTTTTAGAAATTTTAAGGTT
1 AAAAATGGAA-TTTTTGGACAG-TTCGGGGTAAAATGTAATTTTT-GAAATTTTAAGGTT
* *
35488 AAAAATGGAATTTTTGGA-AGTTCGGGGCTAAAAATATAATTTTTGAAAGTTTCAAGG-T
1 AAAAATGGAATTTTTGGACAGTTCGGGG-T-AAAATGTAATTTTTGAAA-TTTTAAGGTT
*
35546 CAAAATGGAATTTTTGGACAGTT
1 AAAAATGGAATTTTTGGACAGTT
35569 TAGGGACCTC
Statistics
Matches: 116, Mismatches: 14, Indels: 18
0.78 0.09 0.12
Matches are distributed among these distances:
57 5 0.04
58 57 0.49
59 52 0.45
60 2 0.02
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (57 bp):
AAAAATGGAATTTTTGGACAGTTCGGGGTAAAATGTAATTTTTGAAATTTTAAGGTT
Found at i:38017 original size:206 final size:205
Alignment explanation
Indices: 37663--38667 Score: 1199
Period size: 206 Copynumber: 4.9 Consensus size: 205
37653 TCTGGTTTCA
** ** ** *
37663 TTGATTT-GTCCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACT
1 TTGATTTGGT-CTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTTTCAATCCGCT
* * * * * * *
37727 TCTCTGTGTTTCGTCAGGAAGGC-AGATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAACC
65 TCTCTGTATCTCATCAGGAAGACGA-ATTTGGTCCACTTTTCAGTATCTCATCAGGAAGCTAACC
* * *
37791 ATTTTATTACTTCGACCTGCTTCTCAATATCTCATTAGGAAGCTGGGGTTCGAAGATTTGCTCAC
129 ATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAC
37856 ATCGAGCGTTGGT
194 ATCGAGCG-TGGT
* * * *
37869 TTGATTTGGTCTTCTTCTCAATATCTCATCAGAAAGATGACCGTGTCATTTGTTTCAATCCGTTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTTTCAATCCGCTT
* * * * *
37934 CTCTATATTTCATCAGGAAGACAAATTTGGTCTACTTTTCAGTATCTCTTCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTTTCAGTATCTCATCAGGAAGCTAACCAT
* *
37999 TTTATTG-TCTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGCTCACC
131 TTTATTGCT-TCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
38063 TCGAGCGTGGGT
195 TCGAGCGT-GGT
* * *
38075 TTGATTTAGTCTTCTTCTCTGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTTTCAATCCGCTT
** *
38140 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTT-AGTATCTCATCAATAAGTTAACCA
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTT-TTCAGTATCTCATCAGGAAGCTAACCA
* * * * *
38204 TTTTATTGCTTCGACCTACTTTTCAGTGTCTCATCGGGAAGCTGGTGTTCGAAGATTTGCTCACA
130 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
*
38269 TCGAGCGTAAGT
195 TCGAGCGT-GGT
* * *
38281 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGAAAGATGACTGTGTCGTTTGTTTCAATCTGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTTTCAATCCGCTT
** * * *
38346 CTCCATATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTCATTAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTTTCAGTATCTCATCAGGAAGCTAACCAT
** * * *
38411 TTTATTATTTCAACC-GCTTCTTAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
* *
38475 TGAGC----A
196 CGAGCGTGGT
* * * * * * **
38481 TTGA-TTGGTATACTTCTCTGTATCTCATCTGGAATAT-AAC-TGCTCCGTTTGTTTCAATTAGC
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTG-T-CGTTTGTTTCAATCCGC
* * *
38543 TTCTATGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTT-AGTGTCTCATCAGGAAGCTAAC
64 TTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTT-TTCAGTATCTCATCAGGAAGCTAAC
* * * *
38607 CTTTTTATTGCTTCGACCTACTTCTCAGTATCTCATTAGGAAGCTGAGGTTCGAAGATTTG
128 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTG
38668 TTCGCATTGA
Statistics
Matches: 688, Mismatches: 100, Indels: 28
0.84 0.12 0.03
Matches are distributed among these distances:
197 2 0.00
198 2 0.00
199 110 0.16
200 42 0.06
205 49 0.07
206 477 0.69
207 6 0.01
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.37
Consensus pattern (205 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGTGTCGTTTGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTTTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
CGAGCGTGGT
Found at i:38797 original size:39 final size:39
Alignment explanation
Indices: 38754--39006 Score: 212
Period size: 39 Copynumber: 6.5 Consensus size: 39
38744 TGCCCCGTGA
* * * *
38754 TCGGGGTAGGAGTTTGGTTGACGATGATCTACCCCAAGC
1 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGC
** ** * * * * * *
38793 TCGGGGTAAGAGAACGAATGACTG-TAATATGTCTCTAGG
1 TCGGGGTAAGAGATTGGTTGA-TGATGATCTGCCCCAAGC
38832 TCGGGGTAAGAGATTGGTTGATGATGATC-GACCCCAAGC
1 TCGGGGTAAGAGATTGGTTGATGATGATCTG-CCCCAAGC
*
38871 TCGGGGTAAGAGATTGGTTGATGATTATCTGCCCCAAGC
1 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGC
* *
38910 TCGGGGTAAGAGATTGGTTAATGATGATCTGCCCCAGGC
1 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGC
* * * * *
38949 TTGAGGTAAAAGATCAAATGGCT--TCA--ATCTGCCCCAAGC
1 TCGGGGTAAGAGAT----TGGTTGATGATGATCTGCCCCAAGC
38988 TCGGGGTAAGAGATTGGTT
1 TCGGGGTAAGAGATTGGTT
39007 AACGATGTAG
Statistics
Matches: 168, Mismatches: 38, Indels: 20
0.74 0.17 0.09
Matches are distributed among these distances:
35 4 0.02
38 3 0.02
39 153 0.91
40 2 0.01
41 2 0.01
43 4 0.02
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (39 bp):
TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGC
Found at i:38914 original size:78 final size:77
Alignment explanation
Indices: 38754--39006 Score: 251
Period size: 78 Copynumber: 3.2 Consensus size: 77
38744 TGCCCCGTGA
* * * * * *
38754 TCGGGGTAGGAGTTTGGTTGACGATGATCTACCCCAAGCTCGGGGTAAGAGAACGAATGACTGTA
1 TCGGGGTAAGAGATTGGTTGATGATGATCGACCCCAAGCTCGGGGTAAGAGATCGAATGA-TGTT
* * * * *
38819 ATATGTCTCTAGG
65 ATCTGCCCCAAGC
* **
38832 TCGGGGTAAGAGATTGGTTGATGATGATCGACCCCAAGCTCGGGGTAAGAGATTGGTTGATGATT
1 TCGGGGTAAGAGATTGGTTGATGATGATCGACCCCAAGCTCGGGGTAAGAGATCGAATGATG-TT
38897 ATCTGCCCCAAGC
65 ATCTGCCCCAAGC
* * * * * *
38910 TCGGGGTAAGAGATTGGTTAATGATGATCTG-CCCCAGGCTTGAGGTAAAAGATCAAATG--GCT
1 TCGGGGTAAGAGATTGGTTGATGATGATC-GACCCCAAGCTCGGGGTAAGAGATCGAATGATG-T
38972 TCAATCTGCCCCAAGC
64 T--ATCTGCCCCAAGC
38988 TCGGGGTAAGAGATTGGTT
1 TCGGGGTAAGAGATTGGTT
39007 AACGATGTAG
Statistics
Matches: 147, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
76 3 0.02
77 2 0.01
78 141 0.96
79 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (77 bp):
TCGGGGTAAGAGATTGGTTGATGATGATCGACCCCAAGCTCGGGGTAAGAGATCGAATGATGTTA
TCTGCCCCAAGC
Found at i:39477 original size:49 final size:48
Alignment explanation
Indices: 39317--39731 Score: 211
Period size: 49 Copynumber: 8.4 Consensus size: 48
39307 GTCGTTACAG
* *
39317 CTTAAATCTTTCCCTTCTTGTCTTCTGAGGTTC-ACGGTCCGCCATTGCGA
1 CTTAAACCTTTCCCTT-TTGTC-TCTGAGGTACTA-GGTCCGCCATTGCGA
* * * *
39367 CTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTAGATCCGCCATTGCTGT
1 CTTAAACCTTTCCCTTTTG--TCTCTGAGGTACTAGGTCCGCCATTGC-GA
* * * *
39418 C-TAGATCTTTCCCTTTATGTCTCTGAGGTACTAGGTCCGTCAATGCGA
1 CTTAAACCTTTCCCTTT-TGTCTCTGAGGTACTAGGTCCGCCATTGCGA
* * **
39466 CTTAAACCTTTCCCTTGTGTCT-TCGTGGTACT-GGATCCGCGGTTGCGA
1 CTTAAACCTTTCCCTTTTGTCTCT-GAGGTACTAGG-TCCGCCATTGCGA
* * * * * **
39514 CTTAGATCTTTCCCTTCATGTCT-TCGAGGTACT-GGATTCACTGTTGC-A
1 CTTAAACCTTTCCCTT-TTGTCTCT-GAGGTACTAGG-TCCGCCATTGCGA
* * ** * * *
39562 GCTTAGATCTTTCCCATAATGTCTCTGAGGTACAAGGTTCGCCGTTGCGA
1 -CTTAAACCTTTCCC-TTTTGTCTCTGAGGTACTAGGTCCGCCATTGCGA
* * * * *
39612 CTTAAACCCTTCCCTTTTGTATCTTTGCGGTA-TTGGATCCGCCATTGCGGC
1 CTTAAACCTTTCCCTTTTG--TCTCTGAGGTACTAGG-TCCGCCATTGC-GA
* * ** * *
39663 CTTAAATCTTT-CCTGTCATGTCTCTGAGGTA-TAAGGTTTGTCGTTGCGA
1 CTTAAACCTTTCCCT-T-TTGTCTCTGAGGTACT-AGGTCCGCCATTGCGA
*
39712 CTTAAACCCTTCCCTTTTGT
1 CTTAAACCTTTCCCTTTTGT
39732 ATCTTTGCTG
Statistics
Matches: 284, Mismatches: 59, Indels: 46
0.73 0.15 0.12
Matches are distributed among these distances:
47 3 0.01
48 44 0.15
49 122 0.43
50 93 0.33
51 20 0.07
52 2 0.01
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (48 bp):
CTTAAACCTTTCCCTTTTGTCTCTGAGGTACTAGGTCCGCCATTGCGA
Found at i:39536 original size:97 final size:100
Alignment explanation
Indices: 39317--39546 Score: 283
Period size: 97 Copynumber: 2.3 Consensus size: 100
39307 GTCGTTACAG
* * * *
39317 CTTAAATCTTTCCCTTCTTGTCTTCTGAGGTTC-ACGGTCCGCCATTGCGACTTAAACCTTTCCC
1 CTTAGATCTTTCCCTTCATGTC-TCTGAGGTACTACGGTCCGCCAATGCGACTTAAACCTTTCCC
* *
39381 TTTTGTATCTTTGTGGTACTAGATCCGCCATTGCTGT
65 -TTTGTATCTTCGTGGTACTAGATCCGCCATTGCTGA
* *
39418 C-TAGATCTTTCCCTTTATGTCTCTGAGGTACTA-GGTCCGTCAATGCGACTTAAACCTTTCCC-
1 CTTAGATCTTTCCCTTCATGTCTCTGAGGTACTACGGTCCGCCAATGCGACTTAAACCTTTCCCT
* * **
39480 TTGTGTCTTCGTGGTACTGGATCCGCGGTTGC-GA
66 TTGTATCTTCGTGGTACTAGATCCGCCATTGCTGA
39514 CTTAGATCTTTCCCTTCATGTCT-TCGAGGTACT
1 CTTAGATCTTTCCCTTCATGTCTCT-GAGGTACT
39547 GGATTCACTG
Statistics
Matches: 113, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
96 3 0.03
97 55 0.49
99 36 0.32
100 18 0.16
101 1 0.01
ACGTcount: A:0.15, C:0.27, G:0.19, T:0.39
Consensus pattern (100 bp):
CTTAGATCTTTCCCTTCATGTCTCTGAGGTACTACGGTCCGCCAATGCGACTTAAACCTTTCCCT
TTGTATCTTCGTGGTACTAGATCCGCCATTGCTGA
Found at i:39584 original size:146 final size:148
Alignment explanation
Indices: 39419--39693 Score: 351
Period size: 146 Copynumber: 1.9 Consensus size: 148
39409 CATTGCTGTC
* * * * *
39419 TAGATCTTTCCCTTTATGTCTCTGAGGTACTAGGTCCGTCAATGCGACTTAAACCTTTCCC-TTG
1 TAGATCTTTCCCATAATGTCTCTGAGGTACAAGGTCCGCCAATGCGACTTAAACCCTTCCCTTTG
* * ** *
39483 TGTCTTCGTGGTACTGGATCCGCGGTTGC-GACTTAGATCTTTCCCT-TCATGTCT-TCGAGGTA
66 TATCTTCGCGGTACTGGATCCGCCATTGCGGACTTAAATCTTT-CCTGTCATGTCTCT-GAGGTA
39545 CTGGATTCACTGTTGCAGCT
129 CTGGATTCACTGTTGCAGCT
* **
39565 TAGATCTTTCCCATAATGTCTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCCTTCCCTTTT
1 TAGATCTTTCCCATAATGTCTCTGAGGTACAAGGTCCGCCAATGCGACTTAAACCCTTCCC-TTT
* * *
39630 GTATCTTTGCGGTATTGGATCCGCCATTGCGGCCTTAAATCTTTCCTGTCATGTCTCTGAGGTA
65 GTATCTTCGCGGTACTGGATCCGCCATTGCGGACTTAAATCTTTCCTGTCATGTCTCTGAGGTA
39694 TAAGGTTTGT
Statistics
Matches: 108, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
146 53 0.49
148 29 0.27
149 25 0.23
150 1 0.01
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (148 bp):
TAGATCTTTCCCATAATGTCTCTGAGGTACAAGGTCCGCCAATGCGACTTAAACCCTTCCCTTTG
TATCTTCGCGGTACTGGATCCGCCATTGCGGACTTAAATCTTTCCTGTCATGTCTCTGAGGTACT
GGATTCACTGTTGCAGCT
Found at i:39692 original size:100 final size:100
Alignment explanation
Indices: 39580--39775 Score: 311
Period size: 100 Copynumber: 2.0 Consensus size: 100
39570 CTTTCCCATA
*
39580 ATGTCTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTAT
1 ATGTCTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTAC
*
39645 TGGATCCGCCATTGCGGCCTTAAATCTTTCCTGTC
66 TAGATCCGCCATTGCGGCCTTAAATCTTTCCTGTC
* * * *
39680 ATGTCTCTGAGGTATAAGGTTTGTCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCTGTAC
1 ATGTCTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTAC
* * *
39745 TAGATCCGCCGTTGTGGTCTTAAATCTTTCC
66 TAGATCCGCCATTGCGGCCTTAAATCTTTCC
39776 CGCCATGTTT
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 87 1.00
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.38
Consensus pattern (100 bp):
ATGTCTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTAC
TAGATCCGCCATTGCGGCCTTAAATCTTTCCTGTC
Found at i:41016 original size:16 final size:16
Alignment explanation
Indices: 40997--41031 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
40987 TTTCCTTTTC
* *
40997 TTTTTCTTTTTTCTTT
1 TTTTTCTCTTTTATTT
41013 TTTTTCTCTTTTATTT
1 TTTTTCTCTTTTATTT
41029 TTT
1 TTT
41032 CTTCATTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTCTCTTTTATTT
Found at i:41024 original size:23 final size:22
Alignment explanation
Indices: 40992--41034 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
40982 CGACCTTTCC
*
40992 TTTTCTTTTTCTTTTTTCTTTT
1 TTTTCTTTTTATTTTTTCTTTT
41014 TTTTCTCTTTTATTTTTTCTT
1 TTTTCT-TTTTATTTTTTCTT
41035 CATTGCATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (22 bp):
TTTTCTTTTTATTTTTTCTTTT
Found at i:41876 original size:37 final size:36
Alignment explanation
Indices: 41835--41912 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
41825 TTTTTCTCTA
*
41835 TTTTTTAATGCCCTTTTCGGATTTTGACCCATCTTT
1 TTTTTTAATGCCCTTTGCGGATTTTGACCCATCTTT
*
41871 TTTTTTAATGTCCTTTGCGGATTTTGACCCATCTTT
1 TTTTTTAATGCCCTTTGCGGATTTTGACCCATCTTT
41907 TTTTTT
1 TTTTTT
41913 TTGCTAACAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.13, C:0.19, G:0.12, T:0.56
Consensus pattern (36 bp):
TTTTTTAATGCCCTTTGCGGATTTTGACCCATCTTT
Found at i:46382 original size:96 final size:97
Alignment explanation
Indices: 46192--46384 Score: 214
Period size: 96 Copynumber: 2.0 Consensus size: 97
46182 TGAATTTTGG
* ** * *** *
46192 AAAGGATATTTGATTATCTCGATTTGAAGAGAGGTTGCACCTAGTCAGTTAAGGTGTAAATTTTC
1 AAAGGATATTTGATTATCTCGATTTGAAGAAAAATTACACCTAGTCAGTTAAGGCACAAAATTTC
* *
46257 AGAATCAAAGATAAGAAAACATTGTCTCGATT
66 AAAATCAAAGATAAGAAAACATTGCCTCGATT
*
46289 AAAGG-TATTTGATTATTTCGATTTGAAGAAAAATTACACCTAGT-AGGTTAAGGCACAAAATTT
1 AAAGGATATTTGATTATCTCGATTTGAAGAAAAATTACACCTAGTCA-GTTAAGGCACAAAATTT
* *
46352 CAAAACTCGAA-ATAA-AAGAATATTGCCTCGATT
65 CAAAA-TCAAAGATAAGAA-AACATTGCCTCGATT
46385 TTAAGTTTTT
Statistics
Matches: 80, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
95 3 0.04
96 68 0.85
97 9 0.11
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (97 bp):
AAAGGATATTTGATTATCTCGATTTGAAGAAAAATTACACCTAGTCAGTTAAGGCACAAAATTTC
AAAATCAAAGATAAGAAAACATTGCCTCGATT
Found at i:46832 original size:57 final size:56
Alignment explanation
Indices: 46732--46889 Score: 160
Period size: 58 Copynumber: 2.8 Consensus size: 56
46722 TTTTTGGCCA
* * * * *
46732 TTCGGGGGTAAAATGGTAACTTTTGAGAGTTTTAGGGTTAAAATTGGA-GTTTGGAGG
1 TTCGGGGGTAAAAT-GTAATTTTTGA-AGTTTTAGGGTCAAAAATGAATGTTTGGAAG
*
46789 TTCGGGGGTAAAATGTAATTTTTAGAAGTTTT-GGGATCAAAAATGAATTTTTTGGAAG
1 TTCGGGGGTAAAATGTAATTTTT-GAAGTTTTAGGG-TCAAAAATGAA-TGTTTGGAAG
* *
46847 TT-AGGGGTAAAAATATAATTTTTTGAAGTTTTAGGGTCAAAAA
1 TTCGGGGGT-AAAATGTAA-TTTTTGAAGTTTTAGGGTCAAAAA
46890 AAGATTTTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 13
0.80 0.07 0.12
Matches are distributed among these distances:
55 3 0.03
56 22 0.26
57 21 0.24
58 32 0.37
59 8 0.09
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (56 bp):
TTCGGGGGTAAAATGTAATTTTTGAAGTTTTAGGGTCAAAAATGAATGTTTGGAAG
Found at i:46833 original size:30 final size:29
Alignment explanation
Indices: 46798--46889 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 29
46788 GTTCGGGGGT
46798 AAAATGTAATTTTTAGAAGTTTTGGGATCA
1 AAAATGTAATTTTTAGAAGTTTTGGG-TCA
* **
46828 AAAATG-AATTTTTTGGAAGTTAGGGGT-A
1 AAAATGTAA-TTTTTAGAAGTTTTGGGTCA
* *
46856 AAAATATAATTTTTTGAAGTTTTAGGGTCA
1 AAAATGTAATTTTTAGAAGTTTT-GGGTCA
46886 AAAA
1 AAAA
46890 AAGATTTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
28 17 0.33
29 9 0.18
30 25 0.49
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.38
Consensus pattern (29 bp):
AAAATGTAATTTTTAGAAGTTTTGGGTCA
Found at i:46859 original size:28 final size:27
Alignment explanation
Indices: 46793--46876 Score: 80
Period size: 29 Copynumber: 3.0 Consensus size: 27
46783 TGGAGGTTCG
* *
46793 GGGGT-AAAATGTAATTTTTAGAAGTTTT
1 GGGGTAAAAATG-AATTTTTTGAAG-TTA
*
46821 GGGATCAAAAATGAATTTTTTGGAAGTTA
1 GGGGT-AAAAATGAATTTTTT-GAAGTTA
*
46850 GGGGTAAAAATATAATTTTTTGAAGTT
1 GGGGTAAAAAT-GAATTTTTTGAAGTT
46877 TTAGGGTCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
28 16 0.34
29 21 0.45
30 10 0.21
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (27 bp):
GGGGTAAAAATGAATTTTTTGAAGTTA
Found at i:46899 original size:30 final size:29
Alignment explanation
Indices: 46807--46912 Score: 83
Period size: 30 Copynumber: 3.6 Consensus size: 29
46797 TAAAATGTAA
* * *
46807 TTTTTAGAAGTTTTGGGATC-AAAAATGAAT
1 TTTTTTGAAGTTTAGGG-TCAAAAAAAG-AT
* * * *
46837 TTTTTGGAAG-TTAGGGGT-AAAAATATAA
1 TTTTTTGAAGTTTA-GGGTCAAAAAAAGAT
46865 TTTTTTGAAGTTTTAGGGTCAAAAAAAGAT
1 TTTTTTGAAG-TTTAGGGTCAAAAAAAGAT
46895 TTTTTTGATAGTTTAGGG
1 TTTTTTGA-AGTTTAGGG
46913 ACCTCCAGGG
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
28 10 0.17
29 11 0.18
30 37 0.62
31 2 0.03
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.42
Consensus pattern (29 bp):
TTTTTTGAAGTTTAGGGTCAAAAAAAGAT
Found at i:48759 original size:17 final size:17
Alignment explanation
Indices: 48723--48802 Score: 88
Period size: 17 Copynumber: 4.4 Consensus size: 17
48713 ATAATTTCTT
48723 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
*
48741 TTTAAATTTAAAATTAA
1 TTTAAATTTAAAATAAA
48758 TTTAAATAAAATATAAAATAAA
1 TTTAAAT----T-TAAAATAAA
*
48780 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
48797 TTTAAA
1 TTTAAA
48803 AGAGACCCGA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
17 28 0.53
18 10 0.19
21 1 0.02
22 14 0.26
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:48774 original size:22 final size:22
Alignment explanation
Indices: 48744--48786 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
48734 AAATAAATTT
* * *
48744 AAATTTAAAATTAATTTAAATA
1 AAATATAAAATAAATCTAAATA
48766 AAATATAAAATAAATCTAAAT
1 AAATATAAAATAAATCTAAAT
48787 TTAAAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATATAAAATAAATCTAAATA
Found at i:54734 original size:14 final size:15
Alignment explanation
Indices: 54715--54747 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
54705 TTTTTGATGT
54715 TATAAAATT-TAACA
1 TATAAAATTATAACA
54729 TAT-AAATTATAACA
1 TATAAAATTATAACA
54743 TATAA
1 TATAA
54748 GCTAATGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.29
14 11 0.65
15 1 0.06
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAAATTATAACA
Found at i:55016 original size:58 final size:55
Alignment explanation
Indices: 54968--55113 Score: 168
Period size: 58 Copynumber: 2.5 Consensus size: 55
54958 ATATAGTATG
*
54968 ATTTTTATT-AATTCATATTTTAATAATAATTATATTAAAATTGTTATTAAATTATAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAA-TATTATTAAATTATAT
* * * *
55025 ATTATTTTATTAAATTGTATTTAATAATTATTATGTTAAAATATAATTAAATTATTTATT
1 A-T-TTTTATTAAATTATATTTAATAATAATTATATTAAAATATTATTAAATTA--TA-T
55085 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
55114 CTTATTGAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
57 12 0.16
58 46 0.61
59 12 0.16
60 6 0.08
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (55 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATTATTAAATTATAT
Found at i:55338 original size:16 final size:16
Alignment explanation
Indices: 55286--55340 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
55276 TGAATTACTG
55286 ATTACAG-TCGTATTCC
1 ATTACAGCTC-TATTCC
* *
55302 ATTAAAGCTCTATTCT
1 ATTACAGCTCTATTCC
55318 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
55334 ATTACAG
1 ATTACAG
55341 AGAACCAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 32 0.94
17 2 0.06
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:66333 original size:9 final size:8
Alignment explanation
Indices: 66279--66335 Score: 51
Period size: 9 Copynumber: 6.6 Consensus size: 8
66269 TAATTTTAAA
66279 AAAATATAT
1 AAAA-ATAT
66288 AAACAATAT
1 AAA-AATAT
**
66297 AATATTTAT
1 AA-AAATAT
*
66306 AAAAATAA
1 AAAAATAT
66314 AAAAATAT
1 AAAAATAT
66322 AAAAATACT
1 AAAAATA-T
66331 AAAAA
1 AAAAA
66336 CACATCTTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
8 17 0.44
9 20 0.51
10 2 0.05
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAAATAT
Found at i:67131 original size:31 final size:33
Alignment explanation
Indices: 67087--67148 Score: 94
Period size: 31 Copynumber: 1.9 Consensus size: 33
67077 TATATTTGAC
67087 AAAAGAAATTTTAAAGTGA-TA-AAAAAATAAT
1 AAAAGAAATTTTAAAGTGATTATAAAAAATAAT
67118 AAAAGTAAA-TTTAAAGTGATTATAAAAAATA
1 AAAAG-AAATTTTAAAGTGATTATAAAAAATA
67149 TATCATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 15 0.54
32 5 0.18
33 8 0.29
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (33 bp):
AAAAGAAATTTTAAAGTGATTATAAAAAATAAT
Found at i:68525 original size:29 final size:29
Alignment explanation
Indices: 68493--68552 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
68483 TTTAAAATAA
68493 AAAAGTTATGAAAAAAAC-TAAAAATTATT
1 AAAA-TTATGAAAAAAACATAAAAATTATT
** *
68522 AAAATTATTTAAAAAGCATAAAAATTATT
1 AAAATTATGAAAAAAACATAAAAATTATT
68551 AA
1 AA
68553 TTTTTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (29 bp):
AAAATTATGAAAAAAACATAAAAATTATT
Found at i:70271 original size:13 final size:13
Alignment explanation
Indices: 70253--70277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
70243 GATTTGGCCT
70253 CAACAAAGTGTTA
1 CAACAAAGTGTTA
70266 CAACAAAGTGTT
1 CAACAAAGTGTT
70278 GGAAGATGCC
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:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (13 bp):
CAACAAAGTGTTA
Found at i:70445 original size:12 final size:12
Alignment explanation
Indices: 70416--70454 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
70406 TCCTTTATGA
70416 ATATCTATC-AT
1 ATATCTATCTAT
70427 ATATCTATCTAT
1 ATATCTATCTAT
*
70439 CTATCTATCTAT
1 ATATCTATCTAT
70451 ATAT
1 ATAT
70455 ATATATGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATCTATCTAT
Found at i:70460 original size:4 final size:4
Alignment explanation
Indices: 70417--70450 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
70407 CCTTTATGAA
*
70417 TATC TATC -ATA TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TATC TAT
70451 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 2 0.07
4 25 0.93
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (4 bp):
TATC
Found at i:74673 original size:34 final size:33
Alignment explanation
Indices: 74610--74675 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 33
74600 ATGTGACAAA
74610 AAATTATAAAAAATAAAAATCAATAAAAATTATT
1 AAATTATAAAAAATAAAAA-CAATAAAAATTATT
* *
74644 AAATTTTAATAAAATATAAAA-AATTAAAATTA
1 AAATTATAA-AAAATA-AAAACAATAAAAATTA
74676 GAAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 18 0.64
35 6 0.21
36 4 0.14
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (33 bp):
AAATTATAAAAAATAAAAACAATAAAAATTATT
Found at i:74942 original size:93 final size:93
Alignment explanation
Indices: 74785--74998 Score: 305
Period size: 93 Copynumber: 2.3 Consensus size: 93
74775 TTAGGGGCGA
* *
74785 TTCAAGTA-CTCAATTGAGTG-AAAA-AAAATCAGAGGCTTAATTACTTTTTTTTTTGAAAAAGT
1 TTCAAGTATC-CAATTGAGTGCAAAATAAAAGCAGAGGATTAATTACTTTTTTTTTTGAAAAAGT
74847 TTGA-AGGCTTTTTTGATGCATTTTGAAAG
65 TTGAGA-GCTTTTTTGATGCATTTTGAAAG
*
74876 TTCAAGTATCCAATTGAGTGCAAAATAAAAGCA-AGAGATTAATTGCTTTTTTTTTTTG-AAAAG
1 TTCAAGTATCCAATTGAGTGCAAAATAAAAGCAGAG-GATTAATTAC-TTTTTTTTTTGAAAAAG
74939 TTTGAGAGCTTTTTTGATGCATTTTGAAAG
64 TTTGAGAGCTTTTTTGATGCATTTTGAAAG
* *
74969 TTCAAGTATTCAACTGAGTGCAAAATAAAA
1 TTCAAGTATCCAATTGAGTGCAAAATAAAA
74999 ACAAAAACTT
Statistics
Matches: 112, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
91 18 0.16
92 7 0.06
93 75 0.67
94 12 0.11
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (93 bp):
TTCAAGTATCCAATTGAGTGCAAAATAAAAGCAGAGGATTAATTACTTTTTTTTTTGAAAAAGTT
TGAGAGCTTTTTTGATGCATTTTGAAAG
Found at i:75347 original size:10 final size:10
Alignment explanation
Indices: 75332--75364 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
75322 TGATGTTTCG
75332 TTTTTTTAGT
1 TTTTTTTAGT
75342 TTTTTTTAGT
1 TTTTTTTAGT
75352 TTATTTTT-GT
1 TT-TTTTTAGT
75362 TTT
1 TTT
75365 GTTATTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 1 0.05
10 16 0.73
11 5 0.23
ACGTcount: A:0.09, C:0.00, G:0.09, T:0.82
Consensus pattern (10 bp):
TTTTTTTAGT
Found at i:79927 original size:2 final size:2
Alignment explanation
Indices: 79920--79950 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
79910 ATTTAAATTG
79920 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
79951 ACATTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:90729 original size:46 final size:46
Alignment explanation
Indices: 90677--90764 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
90667 ACTACTAATT
* * ** *
90677 TGTAATATTAGTTATGTACTTGGACGATGTTGTAGTTATCATGTGG
1 TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTATCATGTGG
90723 TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTATCAT
1 TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTATCAT
90765 CAATTCGCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (46 bp):
TGTAATACTAGTTATGCACTTGGAAAATATTGTAGTTATCATGTGG
Found at i:94257 original size:96 final size:96
Alignment explanation
Indices: 94124--94313 Score: 256
Period size: 96 Copynumber: 2.0 Consensus size: 96
94114 GCGCAAAGTG
** ** * * * *
94124 AATTAACTATAAGGTTAAGTGAGATGGTAATAGTCTCTCTTACCTTAACTAGTGATCGA-GGATT
1 AATTAACTATAAAATTAAGTGAGATAATAAAAATCTCTCCTACCTTAACTAGTGATCGATGG-CT
94188 CAATTCTTGCTCAGAATATGAAGCACAATGTT
65 CAATTCTTGCTCAGAATATGAAGCACAATGTT
*
94220 AATTAACTATAAAATTAAGTGAGATAATAAAAATCTCTCCTATCTTAACTAGTGATCGATGGCTC
1 AATTAACTATAAAATTAAGTGAGATAATAAAAATCTCTCCTACCTTAACTAGTGATCGATGGCTC
* * *
94285 GATTCTTGCTCAGAGTATGAATCACAATG
66 AATTCTTGCTCAGAATATGAAGCACAATG
94314 GATACTACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
96 79 0.98
97 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (96 bp):
AATTAACTATAAAATTAAGTGAGATAATAAAAATCTCTCCTACCTTAACTAGTGATCGATGGCTC
AATTCTTGCTCAGAATATGAAGCACAATGTT
Found at i:95101 original size:14 final size:14
Alignment explanation
Indices: 95082--95109 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
95072 ACCTCGACTT
95082 TAAATTTTAATTTA
1 TAAATTTTAATTTA
95096 TAAATTTTAATTTA
1 TAAATTTTAATTTA
95110 ATTTATAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAAATTTTAATTTA
Found at i:98953 original size:15 final size:16
Alignment explanation
Indices: 98933--98968 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
98923 AATCTTTTAA
98933 AAATTATAAAAAT-AT
1 AAATTATAAAAATGAT
*
98948 AAATTATTAAAATGAT
1 AAATTATAAAAATGAT
98964 AAATT
1 AAATT
98969 TATATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AAATTATAAAAATGAT
Found at i:101093 original size:10 final size:10
Alignment explanation
Indices: 101078--101104 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
101068 ACCCAGGCAT
101078 GAAATTGGAA
1 GAAATTGGAA
101088 GAAATTGGAA
1 GAAATTGGAA
101098 GAAATTG
1 GAAATTG
101105 AAAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.22
Consensus pattern (10 bp):
GAAATTGGAA
Found at i:101577 original size:17 final size:17
Alignment explanation
Indices: 101555--101597 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
101545 ATTTTGATCA
101555 AATTTTTTAAAAATAAT-
1 AATTTTTT-AAAATAATC
*
101572 AATTTTATAAAATAATC
1 AATTTTTTAAAATAATC
101589 ACATTTTTT
1 A-ATTTTTT
101598 TTTCAAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 8 0.36
17 8 0.36
18 6 0.27
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTTTTTAAAATAATC
Found at i:106751 original size:11 final size:11
Alignment explanation
Indices: 106733--106772 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
106723 ACAATAACAA
106733 CAAAATAATAG
1 CAAAATAATAG
*
106744 CAACATAATAG
1 CAAAATAATAG
*
106755 CAAAATTATAG
1 CAAAATAATAG
106766 CAAAATA
1 CAAAATA
106773 GGGAGAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.60, C:0.12, G:0.07, T:0.20
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:106751 original size:22 final size:22
Alignment explanation
Indices: 106726--106768 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
106716 TATCCAAACA
106726 ATAACAACAAAATAATAGCAAC
1 ATAACAACAAAATAATAGCAAC
* * *
106748 ATAATAGCAAAATTATAGCAA
1 ATAACAACAAAATAATAGCAA
106769 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.14, G:0.07, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAATAGCAAC
Found at i:106980 original size:19 final size:18
Alignment explanation
Indices: 106956--106991 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
106946 ATTATTGTAT
*
106956 TTTATATAGAAATTATATG
1 TTTATAT-GAAAATATATG
106975 TTTATATGAAAATATAT
1 TTTATATGAAAATATAT
106992 AATTAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (18 bp):
TTTATATGAAAATATATG
Found at i:108542 original size:18 final size:17
Alignment explanation
Indices: 108511--108544 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
108501 GGTAAAATTG
108511 AATTAATTCAGTTAATC
1 AATTAATTCAGTTAATC
*
108528 AATTGAATTCGGTTAAT
1 AATT-AATTCAGTTAAT
108545 TGGTCGGTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (17 bp):
AATTAATTCAGTTAATC
Found at i:113002 original size:97 final size:97
Alignment explanation
Indices: 112834--113016 Score: 269
Period size: 97 Copynumber: 1.9 Consensus size: 97
112824 GAACTTACTA
* * *
112834 GAATCACCATTCACTTGCAAACTTTTCATTCGAAATCTTAGTACTGTATTGGCATCACCATGGTA
1 GAATCACCATTCACTTGCAAACTTTTCATTCAAAATCTTAGTACTGTATTGACATCACCATAGTA
*
112899 ATTATATTTG-GTACAAAATTTTAGTAATGTAT
66 ACTATA-TTGAGTACAAAATTTTAGTAATGTAT
* ** **
112931 GAATCACCATTCATTTGCTGACTTTTCATTCAAAATCTTAGTGTTGTATTGACATCACCATAGTA
1 GAATCACCATTCACTTGCAAACTTTTCATTCAAAATCTTAGTACTGTATTGACATCACCATAGTA
112996 ACTATATTGAGTACAAAATTT
66 ACTATATTGAGTACAAAATTT
113017 GGAATCACCT
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
96 3 0.04
97 73 0.96
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (97 bp):
GAATCACCATTCACTTGCAAACTTTTCATTCAAAATCTTAGTACTGTATTGACATCACCATAGTA
ACTATATTGAGTACAAAATTTTAGTAATGTAT
Found at i:116203 original size:41 final size:41
Alignment explanation
Indices: 116146--116241 Score: 158
Period size: 41 Copynumber: 2.3 Consensus size: 41
116136 TTGTTCGTAG
*
116146 AGAATTCTTGTCAAGGT-AGAGATTGTTAGAATTAGGTGACT
1 AGAATTCTTGTTAAGGTGA-AGATTGTTAGAATTAGGTGACT
116187 AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTAGGTGACT
1 AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTAGGTGACT
*
116228 AGAATTTTTGTTAA
1 AGAATTCTTGTTAA
116242 AATAAAATTC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
41 51 0.98
42 1 0.02
ACGTcount: A:0.32, C:0.05, G:0.25, T:0.38
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTAGGTGACT
Done.