Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011550.1 Kokia drynarioides strain JFW-HI SEQ_126536, 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: 316084
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 198 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:303220 original size:14 final size:15
Alignment explanation
Indices: 303201--303239 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
303191 AGCACAAATG
303201 AATAAATATACG-AA
1 AATAAATATACGAAA
*
303215 AATAAATATAAGAAA
1 AATAAATATACGAAA
303230 AATAAA-ATAC
1 AATAAATATAC
303240 AAATTATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (15 bp):
AATAAATATACGAAA
Found at i:303503 original size:30 final size:30
Alignment explanation
Indices: 303422--303676 Score: 186
Period size: 29 Copynumber: 8.6 Consensus size: 30
303412 AAGTTCAAGA
* *
303422 TAAAAATATGATTTTTGAGAAGTTCG-GGG
1 TAAAAATGTAATTTTTGAGAAGTTCGAGGG
* * *
303451 CAAAAATGTGATTTTT-AGAAGTTCGGGGG
1 TAAAAATGTAATTTTTGAGAAGTTCGAGGG
*
303480 TAAAAATGTAATTTTTGAGAAGTTCGAGGA
1 TAAAAATGTAATTTTTGAGAAGTTCGAGGG
* *
303510 TAAAAATGATAATTTTAGAAAAGTTCGAGGG
1 TAAAAATG-TAATTTTTGAGAAGTTCGAGGG
* *
303541 T-AAAATGGTAATTTTTG-GATGTTCAAGGG
1 TAAAAAT-GTAATTTTTGAGAAGTTCGAGGG
* * *
303570 -AAAAATGGTAATTTTGGAAAAGTT-TAGGG
1 TAAAAAT-GTAATTTTTGAGAAGTTCGAGGG
* *
303599 TTAAAATGTGAA-TTTT-AGAAGTT-TAGGGG
1 TAAAAATGT-AATTTTTGAGAAGTTCGA-GGG
* * * * *
303628 TAAGAATGTGATTTTTGGAAAAGTTTGGGGG
1 TAAAAATGTAATTTTT-GAGAAGTTCGAGGG
* * *
303659 TCAAAATATGATTTTTGA
1 TAAAAATGTAATTTTTGA
303677 AAGGTTTAGG
Statistics
Matches: 184, Mismatches: 29, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
28 18 0.10
29 78 0.42
30 45 0.24
31 43 0.23
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.35
Consensus pattern (30 bp):
TAAAAATGTAATTTTTGAGAAGTTCGAGGG
Found at i:303534 original size:31 final size:30
Alignment explanation
Indices: 303390--303618 Score: 159
Period size: 29 Copynumber: 7.7 Consensus size: 30
303380 AAAGTTTTAG
* * *
303390 GGGTAAATATGTCATTTTAGGAAAGTTC-A
1 GGGTAAAAATGTAATTTTAGAAAAGTTCGA
* * * * * *
303419 AGATAAAAATATGATTTTTGAGAAGTTCG-
1 GGGTAAAAATGTAATTTTAGAAAAGTTCGA
* * *
303448 GGGCAAAAATGTGATTTTTAG--AAGTTCGG
1 GGGTAAAAATGT-AATTTTAGAAAAGTTCGA
* *
303477 GGGTAAAAATGTAATTTTTGAGAAGTTCGA
1 GGGTAAAAATGTAATTTTAGAAAAGTTCGA
*
303507 GGATAAAAATGATAATTTTAGAAAAGTTCGA
1 GGGTAAAAATG-TAATTTTAGAAAAGTTCGA
* * * *
303538 GGGT-AAAATGGTAATTTTTG-GATGTTCAA
1 GGGTAAAAAT-GTAATTTTAGAAAAGTTCGA
* *
303567 GGG-AAAAATGGTAATTTTGGAAAAGTT-TA
1 GGGTAAAAAT-GTAATTTTAGAAAAGTTCGA
*
303596 GGGTTAAAATGTGAATTTTAGAA
1 GGGTAAAAATGT-AATTTTAGAA
303619 GTTTAGGGGT
Statistics
Matches: 156, Mismatches: 33, Indels: 21
0.74 0.16 0.10
Matches are distributed among these distances:
28 13 0.08
29 69 0.44
30 53 0.34
31 21 0.13
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.33
Consensus pattern (30 bp):
GGGTAAAAATGTAATTTTAGAAAAGTTCGA
Found at i:303574 original size:59 final size:60
Alignment explanation
Indices: 303432--303621 Score: 175
Period size: 59 Copynumber: 3.2 Consensus size: 60
303422 TAAAAATATG
* * *
303432 ATTTTTGAGAAGTTC--GGGGCAAAAATG-TGATTTTTAG--AAGTTCGGGGGTAAAAATGTA
1 ATTTTTGAGAAGTTCAAGGAG-AAAAATGAT-AATTTTAGAAAAGTTCGAGGGT-AAAATGTA
* *
303490 ATTTTTGAGAAGTTCGAGGATAAAAATGATAATTTTAGAAAAGTTCGAGGGTAAAATGGTA
1 ATTTTTGAGAAGTTCAAGGAGAAAAATGATAATTTTAGAAAAGTTCGAGGGTAAAAT-GTA
* * * *
303551 ATTTTTG-GATGTTCAAGG-GAAAAATGGTAATTTTGGAAAAGTT-TAGGGTTAAAATGTGA
1 ATTTTTGAGAAGTTCAAGGAGAAAAATGATAATTTTAGAAAAGTTCGAGGG-TAAAATGT-A
303610 A-TTTT-AGAAGTT
1 ATTTTTGAGAAGTT
303622 TAGGGGTAAG
Statistics
Matches: 112, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
58 30 0.27
59 44 0.39
60 17 0.15
61 21 0.19
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.34
Consensus pattern (60 bp):
ATTTTTGAGAAGTTCAAGGAGAAAAATGATAATTTTAGAAAAGTTCGAGGGTAAAATGTA
Found at i:303574 original size:89 final size:89
Alignment explanation
Indices: 303390--303618 Score: 211
Period size: 89 Copynumber: 2.6 Consensus size: 89
303380 AAAGTTTTAG
* * * * * *
303390 GGGTAAATAT-GTCATTTTAGG-AAAGTTCAAGATAAAAAT-ATGATTTTTGAGAAGTTCGGGGC
1 GGGTAAAAATGGTAATTTT-GGAAAAGTTCAGGATAAAAATGATAATTTTAGAAAAGTTCGGGGC
* **
303452 AAAAATGTGATTTTTAGAAGTTCGG
65 AAAAATGTAATTTTTAGAAGTTCAA
* *
303477 GGGTAAAAAT-GTAATTTTTGAGAAGTTCGAGGATAAAAATGATAATTTTAGAAAAGTTCGAGGG
1 GGGTAAAAATGGTAATTTTGGAAAAGTTC-AGGATAAAAATGATAATTTTAGAAAAGTTCG-GGG
* * *
303541 -TAAAATGGTAATTTTTGGATGTTCAA
64 CAAAAAT-GTAATTTTTAGAAGTTCAA
* * *
303567 GGG-AAAAATGGTAATTTTGGAAAAGTTTAGGGTTAAAATG-TGAATTTTAGAA
1 GGGTAAAAATGGTAATTTTGGAAAAGTTCAGGATAAAAATGAT-AATTTTAGAA
303619 GTTTAGGGGT
Statistics
Matches: 116, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
86 1 0.01
87 22 0.19
88 11 0.09
89 47 0.41
90 35 0.30
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.33
Consensus pattern (89 bp):
GGGTAAAAATGGTAATTTTGGAAAAGTTCAGGATAAAAATGATAATTTTAGAAAAGTTCGGGGCA
AAAATGTAATTTTTAGAAGTTCAA
Found at i:303659 original size:31 final size:29
Alignment explanation
Indices: 303374--303687 Score: 138
Period size: 29 Copynumber: 10.6 Consensus size: 29
303364 TAAAACATAA
* *
303374 TTTTGGAAAGTTTTAGGGGTAAATATGTCAT
1 TTTTGAAAAG-TTTAGGGGTAAA-ATGTGAT
* * * * * *
303405 TTTAGGAAAGTTCA-AGATAAAAATATGAT
1 TTTTGAAAAGTTTAGGGGT-AAAATGTGAT
* * *
303434 TTTTGAGAAG-TTCGGGGCAAAAATGTGAT
1 TTTTGAAAAGTTTAGGGG-TAAAATGTGAT
* ** *
303463 TTTT-AGAAGTTCGGGGGTAAAAATGTAAT
1 TTTTGAAAAGTTTAGGGGT-AAAATGTGAT
* * * *
303492 TTTTGAGAAG-TTCGAGGATAAAAATGATAAT
1 TTTTGAAAAGTTTAG-GGGT-AAAATG-TGAT
* * *
303523 TTTAGAAAAG-TTCGAGGGTAAAATGGTAAT
1 TTTTGAAAAGTTTAG-GGGTAAAAT-GTGAT
* * * * * *
303553 TTTTG-GATGTTCAAGGGAAAAATGGTAAT
1 TTTTGAAAAGTTTAGGGGTAAAAT-GTGAT
* * *
303582 TTTGGAAAAGTTTAGGGTTAAAATGTGAA
1 TTTTGAAAAGTTTAGGGGTAAAATGTGAT
*
303611 TTTT-AGAAGTTTAGGGGTAAGAATGTGAT
1 TTTTGAAAAGTTTAGGGGTAA-AATGTGAT
* *
303640 TTTTGGAAAAGTTTGGGGGTCAAAATATGAT
1 TTTT-GAAAAGTTTAGGGGT-AAAATGTGAT
*
303671 TTTTGAAAGGTTTAGGG
1 TTTTGAAAAGTTTAGGG
303688 ACCTTCTAGG
Statistics
Matches: 218, Mismatches: 50, Indels: 31
0.73 0.17 0.10
Matches are distributed among these distances:
28 20 0.09
29 85 0.39
30 58 0.27
31 53 0.24
32 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
TTTTGAAAAGTTTAGGGGTAAAATGTGAT
Found at i:304722 original size:15 final size:15
Alignment explanation
Indices: 304702--304735 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
304692 ATTTTCCTTT
304702 TTTATTATTAATGTA
1 TTTATTATTAATGTA
* *
304717 TTTATTATTTATTTA
1 TTTATTATTAATGTA
304732 TTTA
1 TTTA
304736 ATGTGTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTATTATTAATGTA
Found at i:307211 original size:97 final size:97
Alignment explanation
Indices: 307041--307220 Score: 306
Period size: 97 Copynumber: 1.9 Consensus size: 97
307031 ATATGTCTCG
* *
307041 ATTATCTCGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAATTTTTCAAAACTCGAGAT
1 ATTATCTCGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAACTCGAAAT
* *
307106 AAATGAATATTGCCTCGAGTTAAGGGTATTCA
66 AAAGGAATATTACCTCGAGTTAAGGGTATTCA
* *
307138 ATTATCTCGGTTTGAAGAAAAGTCGCGCCTAGTAAGTTAATGCACAAATTTTCAAAACTCGAAAT
1 ATTATCTCGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAACTCGAAAT
307203 AAAGGAATATTACCTCGA
66 AAAGGAATATTACCTCGA
307221 TTTTAAATAT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 77 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (97 bp):
ATTATCTCGGTTTGAAGAAAAATCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAACTCGAAAT
AAAGGAATATTACCTCGAGTTAAGGGTATTCA
Found at i:307365 original size:14 final size:15
Alignment explanation
Indices: 307340--307385 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
307330 AACACAAAGC
307340 ACGAATAAATAAATAT
1 ACGAA-AAATAAATAT
307356 ACG-AAAATAAATAT
1 ACGAAAAATAAATAT
*
307370 AAGAAAAATAAA-AT
1 ACGAAAAATAAATAT
307384 AC
1 AC
307386 AAATTATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 15 0.56
15 9 0.33
16 3 0.11
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (15 bp):
ACGAAAAATAAATAT
Found at i:307562 original size:30 final size:30
Alignment explanation
Indices: 307528--307851 Score: 156
Period size: 30 Copynumber: 10.9 Consensus size: 30
307518 GTTTGGGATT
307528 AAAATGTAATTTTGGAAAGTTTTAGGGGTA
1 AAAATGTAATTTTGGAAAGTTTTAGGGGTA
* **
307558 AAAATGTAATTTTTGG-AAG-ATCGGGGGTA
1 AAAATGTAA-TTTTGGAAAGTTTTAGGGGTA
* * **
307587 AAAATGTGATTTTTGG-AAG-TTCAAAGGTA
1 AAAATGT-AATTTTGGAAAGTTTTAGGGGTA
* * ** *
307616 AAAATATGATTTTTAAAAG-TTT-GGGGGA
1 AAAATGTAATTTTGGAAAGTTTTAGGGGTA
* **
307644 AAAATGTAATTTTTGAGAAGTTCGA-GGGTA
1 AAAATGTAATTTTGGA-AAGTTTTAGGGGTA
*
307674 AAAATGTGATTTTTGG-AAG-TTTAGGGGTA
1 AAAATGT-AATTTTGGAAAGTTTTAGGGGTA
* * * **
307703 AAAATGTGATTTTTGAGAAGTTTGAGGGCAA
1 AAAATGTAATTTTGGA-AAGTTTTAGGGGTA
* * *
307734 AAAATGGTAATATTGGAAA-TGTTTA-GTGTC
1 AAAAT-GTAATTTTGGAAAGT-TTTAGGGGTA
* * * *
307764 AAAATGGTAATTTT-TAGA-TGTTCAGGGGAA
1 AAAAT-GTAATTTTGGAAAGT-TTTAGGGGTA
307794 AAAATGGTAATTTTGGAAAAG-TTTA-GGGTA
1 AAAAT-GTAATTTTGG-AAAGTTTTAGGGGTA
* * *
307824 TAAATGTGATTTTTGGAAAGTTTAAGGG
1 AAAATGT-AATTTTGGAAAGTTTTAGGG
307852 TCAAAATATG
Statistics
Matches: 219, Mismatches: 55, Indels: 39
0.70 0.18 0.12
Matches are distributed among these distances:
28 27 0.12
29 71 0.32
30 77 0.35
31 34 0.16
32 10 0.05
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAGTTTTAGGGGTA
Found at i:307618 original size:58 final size:59
Alignment explanation
Indices: 307554--307724 Score: 238
Period size: 58 Copynumber: 2.9 Consensus size: 59
307544 AAGTTTTAGG
* * *
307554 GGTAAAAATGTAATTTTTGGAAGATCGGGGGTAAAAATGTGATTTTTG-GAAGTTCAAA
1 GGTAAAAATGTGATTTTTGGAAGTTTGGGGGTAAAAATGTGATTTTTGAGAAGTTCAAA
* ** * * *
307612 GGTAAAAATATGATTTTTAAAAGTTTGGGGG-AAAAATGTAATTTTTGAGAAGTTCGAG
1 GGTAAAAATGTGATTTTTGGAAGTTTGGGGGTAAAAATGTGATTTTTGAGAAGTTCAAA
*
307670 GGTAAAAATGTGATTTTTGGAAGTTTAGGGGTAAAAATGTGATTTTTGAGAAGTT
1 GGTAAAAATGTGATTTTTGGAAGTTTGGGGGTAAAAATGTGATTTTTGAGAAGTT
307725 TGAGGGCAAA
Statistics
Matches: 97, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
57 15 0.15
58 60 0.62
59 22 0.23
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (59 bp):
GGTAAAAATGTGATTTTTGGAAGTTTGGGGGTAAAAATGTGATTTTTGAGAAGTTCAAA
Found at i:307675 original size:87 final size:87
Alignment explanation
Indices: 307537--307736 Score: 267
Period size: 87 Copynumber: 2.3 Consensus size: 87
307527 TAAAATGTAA
* * *
307537 TTTTGGAAAGTTTTAGGGGTAAAAATGTAATTTTTGGAAGATCGGGGGTAAAAATGTGATTTTTG
1 TTTTGAAAAG-TTT-GGGGCAAAAATGTAATTTTTGGAAGATCGAGGGTAAAAATGTGATTTTTG
307602 GAAGTTCAAAGGTAAAAATATGAT
64 GAAGTTCAAAGGTAAAAATATGAT
* *
307626 TTTT-AAAAGTTTGGGGGAAAAATGTAATTTTTGAGAAGTTCGAGGGTAAAAATGTGATTTTTGG
1 TTTTGAAAAGTTTGGGGCAAAAATGTAATTTTTG-GAAGATCGAGGGTAAAAATGTGATTTTTGG
* ** *
307690 AAGTTTAGGGGTAAAAATGTGAT
65 AAGTTCAAAGGTAAAAATATGAT
*
307713 TTTTGAGAAGTTTGAGGGCAAAAA
1 TTTTGAAAAGTTTG-GGGCAAAAA
307737 ATGGTAATAT
Statistics
Matches: 98, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
86 20 0.20
87 54 0.55
88 12 0.12
89 12 0.12
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.34
Consensus pattern (87 bp):
TTTTGAAAAGTTTGGGGCAAAAATGTAATTTTTGGAAGATCGAGGGTAAAAATGTGATTTTTGGA
AGTTCAAAGGTAAAAATATGAT
Found at i:307829 original size:60 final size:60
Alignment explanation
Indices: 307528--307838 Score: 230
Period size: 60 Copynumber: 5.2 Consensus size: 60
307518 GTTTGGGATT
* * * * ***
307528 AAAATGTAATTTTGGA-AAGTTTTAGGGGTAAAAAT-GTAATTTTTGGAAGA-TCGGGGGTA
1 AAAATGTAATTTTTGAGAAG-TTCAGGGGAAAAAATGGTAA-TTTTGGAAAAGTTTAGGGTA
* ** * * * * * *
307587 AAAATGTGATTTTTG-GAAGTTCAAAGGTAAAAAT-ATGATTTT-TAAAAGTTTGGGGGA
1 AAAATGTAATTTTTGAGAAGTTCAGGGGAAAAAATGGTAATTTTGGAAAAGTTTAGGGTA
* *
307644 AAAATGTAATTTTTGAGAAGTTC-GAGGGTAAAAAT-GTGATTTTTGG--AAGTTTAGGGGTA
1 AAAATGTAATTTTTGAGAAGTTCAG-GGGAAAAAATGGT-AATTTTGGAAAAGTTTA-GGGTA
* * * * * * *
307703 AAAATGTGATTTTTGAGAAGTTTGAGGGCAAAAAATGGTAATATTGGAAATGTTTAGTGTC
1 AAAATGTAATTTTTGAGAAG-TTCAGGGGAAAAAATGGTAATTTTGGAAAAGTTTAGGGTA
*
307764 AAAATGGTAATTTTT-AGATGTTCAGGGGAAAAAATGGTAATTTTGGAAAAGTTTAGGGTA
1 AAAAT-GTAATTTTTGAGAAGTTCAGGGGAAAAAATGGTAATTTTGGAAAAGTTTAGGGTA
* *
307824 TAAATGTGATTTTTG
1 AAAATGTAATTTTTG
307839 GAAAGTTTAA
Statistics
Matches: 198, Mismatches: 40, Indels: 27
0.75 0.15 0.10
Matches are distributed among these distances:
56 3 0.02
57 24 0.12
58 37 0.19
59 51 0.26
60 54 0.27
61 15 0.08
62 14 0.07
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (60 bp):
AAAATGTAATTTTTGAGAAGTTCAGGGGAAAAAATGGTAATTTTGGAAAAGTTTAGGGTA
Found at i:307852 original size:30 final size:30
Alignment explanation
Indices: 307528--307865 Score: 207
Period size: 29 Copynumber: 11.4 Consensus size: 30
307518 GTTTGGGATT
* *
307528 AAAATGT-AATTTTGGAAAGTTTTAGGGGTA
1 AAAATGTGATTTTTGGAAAG-TTTAAGGGTA
* * ***
307558 AAAATGTAATTTTTGG-AAGATCGGGGGTA
1 AAAATGTGATTTTTGGAAAGTTTAAGGGTA
* *
307587 AAAATGTGATTTTTGG-AAGTTCAAAGGTA
1 AAAATGTGATTTTTGGAAAGTTTAAGGGTA
* * * *
307616 AAAATATGATTTTT-AAAAGTTT-GGGGGA
1 AAAATGTGATTTTTGGAAAGTTTAAGGGTA
* **
307644 AAAATGTAATTTTT-GAGAAGTTCGAGGGTA
1 AAAATGTGATTTTTGGA-AAGTTTAAGGGTA
*
307674 AAAATGTGATTTTTGG-AAGTTTAGGGGTA
1 AAAATGTGATTTTTGGAAAGTTTAAGGGTA
* *
307703 AAAATGTGATTTTT-GAGAAGTTTGAGGGCAA
1 AAAATGTGATTTTTGGA-AAGTTTAAGGG-TA
* * * *
307734 AAAATG-GTAATATTGGAAATGTTT-AGTGTC
1 AAAATGTG-ATTTTTGGAAA-GTTTAAGGGTA
* * * * * *
307764 AAAATGGTAATTTTTAG-ATGTTCAGGGGAA
1 AAAAT-GTGATTTTTGGAAAGTTTAAGGGTA
*
307794 AAAATG-GTAATTTTGGAAAAGTTT-AGGGTA
1 AAAATGTG-ATTTTTGG-AAAGTTTAAGGGTA
* *
307824 TAAATGTGATTTTTGGAAAGTTTAAGGGTC
1 AAAATGTGATTTTTGGAAAGTTTAAGGGTA
*
307854 AAAATATGATTT
1 AAAATGTGATTT
307866 CTAAAAAGTT
Statistics
Matches: 234, Mismatches: 55, Indels: 38
0.72 0.17 0.12
Matches are distributed among these distances:
28 17 0.07
29 95 0.41
30 81 0.35
31 35 0.15
32 6 0.03
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.35
Consensus pattern (30 bp):
AAAATGTGATTTTTGGAAAGTTTAAGGGTA
Found at i:307858 original size:60 final size:59
Alignment explanation
Indices: 307528--307880 Score: 231
Period size: 59 Copynumber: 6.0 Consensus size: 59
307518 GTTTGGGATT
* * * * ***
307528 AAAATGT-AATTTTGGAAAGTTTTAGGGGTAAAAATGTAATTTTTGGAAGA-TCGGGGGTA
1 AAAATGTGATTTTTGGAAAG-TTCAAGGGTAAAAATGTAA-TTTTGGAAAAGTTTAGGGTA
* * * * * *
307587 AAAATGTGATTTTTGG-AAGTTCAAAGGTAAAAATATGATTTT-TAAAAGTTTGGGGGA
1 AAAATGTGATTTTTGGAAAGTTCAAGGGTAAAAATGTAATTTTGGAAAAGTTTAGGGTA
* * *
307644 AAAATGTAATTTTT-GAGAAGTTCGAGGGTAAAAATGTGATTTTTGG--AAGTTTAGGGGTA
1 AAAATGTGATTTTTGGA-AAGTTCAAGGGTAAAAATGT-AATTTTGGAAAAGTTTA-GGGTA
** * * * * *
307703 AAAATGTGATTTTT-GAGAAGTTTGAGGGCAAAAAATGGTAATATTGGAAATGTTTAGTGTC
1 AAAATGTGATTTTTGGA-AAGTTCAAGGG-TAAAAAT-GTAATTTTGGAAAAGTTTAGGGTA
* * * * *
307764 AAAATGGTAATTTTTAG-ATGTTCAGGGGAAAAAATGGTAATTTTGGAAAAGTTTAGGGTA
1 AAAAT-GTGATTTTTGGAAAGTTCAAGGGTAAAAAT-GTAATTTTGGAAAAGTTTAGGGTA
* * * * * *
307824 TAAATGTGATTTTTGGAAAGTTTAAGGGTCAAAATATGATTTCT-AAAAAGTTTAGGG
1 AAAATGTGATTTTTGGAAAGTTCAAGGGTAAAAATGTAATTT-TGGAAAAGTTTAGGG
307881 ACCTTTTGGG
Statistics
Matches: 231, Mismatches: 48, Indels: 30
0.75 0.16 0.10
Matches are distributed among these distances:
56 4 0.02
57 23 0.10
58 37 0.16
59 70 0.30
60 65 0.28
61 17 0.07
62 14 0.06
63 1 0.00
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (59 bp):
AAAATGTGATTTTTGGAAAGTTCAAGGGTAAAAATGTAATTTTGGAAAAGTTTAGGGTA
Found at i:307874 original size:30 final size:30
Alignment explanation
Indices: 307810--307877 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
307800 GTAATTTTGG
* * *
307810 AAAAGTTT-AGGGTATAAATGTGATTTTTG
1 AAAAGTTTAAGGGTATAAATATGATTTCTA
*
307839 GAAAGTTTAAGGGTCA-AAATATGATTTCTA
1 AAAAGTTTAAGGGT-ATAAATATGATTTCTA
307869 AAAAGTTTA
1 AAAAGTTTA
307878 GGGACCTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 7 0.22
30 24 0.75
31 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.37
Consensus pattern (30 bp):
AAAAGTTTAAGGGTATAAATATGATTTCTA
Found at i:308776 original size:15 final size:15
Alignment explanation
Indices: 308756--308789 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
308746 ATTTTTCTTT
308756 TTTATTATTAATATA
1 TTTATTATTAATATA
* *
308771 TTTATTATTTATTTA
1 TTTATTATTAATATA
308786 TTTA
1 TTTA
308790 ATGTGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTATTATTAATATA
Found at i:310538 original size:19 final size:17
Alignment explanation
Indices: 310496--310539 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
310486 TAAATTCGAA
310496 TTAATTATATTTATTAT
1 TTAATTATATTTATTAT
*
310513 TTAAATTTTATCTTATTAT
1 TT-AATTATAT-TTATTAT
310532 TGTAATTA
1 T-TAATTA
310540 AAAATACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.09
18 7 0.32
19 12 0.55
20 1 0.05
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (17 bp):
TTAATTATATTTATTAT
Found at i:310641 original size:130 final size:130
Alignment explanation
Indices: 310495--310880 Score: 700
Period size: 130 Copynumber: 3.0 Consensus size: 130
310485 TTAAATTCGA
* * * * *
310495 ATTAATTATATTTATTATTTAAATTTTATCTTATTATTGTAATTAAAAATACTAATAAAGGCAAG
1 ATTAATCATATTTATTATTTAAATTTTATTTTGTTATTGTAATTAAAAGTAATAATAAAGGCAAG
*
310560 TGGAAGTTGAGAAAATATCAAGAGGCACGAGAAGCACGTTAATAGGAGACTTATTAAGTGTTAAG
66 TGGAAGTTGAGAAAATATCAAGAGGCACGAGAAGCACGCTAATAGGAGACTTATTAAGTGTTAAG
310625 ATTAATCATATTTATTATTTAAATTTTATTTTGTTATTGTAATTAAAAGTAATAATAAAGGCAAG
1 ATTAATCATATTTATTATTTAAATTTTATTTTGTTATTGTAATTAAAAGTAATAATAAAGGCAAG
*
310690 TGGTAGTTGAGAAAATATCAAGAGGCACGAGAAGCACGCTAATAGGAGACTTATTAAGTGTTAAG
66 TGGAAGTTGAGAAAATATCAAGAGGCACGAGAAGCACGCTAATAGGAGACTTATTAAGTGTTAAG
310755 ATTAATCATATTTATTATTTAAATTTTATTTTGTTATTGTAATTAAAAGTAATAATAAAGGCAAG
1 ATTAATCATATTTATTATTTAAATTTTATTTTGTTATTGTAATTAAAAGTAATAATAAAGGCAAG
*
310820 TGGAAGTTGAGAAAATATCAAGAGGCACGAGAAGCACGCTAATAGGAGACTTATGAAGTGT
66 TGGAAGTTGAGAAAATATCAAGAGGCACGAGAAGCACGCTAATAGGAGACTTATTAAGTGT
310881 CAACTAAAGG
Statistics
Matches: 247, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
130 247 1.00
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (130 bp):
ATTAATCATATTTATTATTTAAATTTTATTTTGTTATTGTAATTAAAAGTAATAATAAAGGCAAG
TGGAAGTTGAGAAAATATCAAGAGGCACGAGAAGCACGCTAATAGGAGACTTATTAAGTGTTAAG
Found at i:315990 original size:17 final size:18
Alignment explanation
Indices: 315968--316001 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
315958 TATAATTAAT
315968 TTTATTA-GTTTAATATC
1 TTTATTACGTTTAATATC
*
315985 TTTATTACTTTTAATAT
1 TTTATTACGTTTAATAT
316002 GATTAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTATTACGTTTAATATC
Done.