Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011124.1 Kokia drynarioides strain JFW-HI SEQ_126097, 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: 574181
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 221 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:505867 original size:52 final size:52
Alignment explanation
Indices: 505782--506215 Score: 552
Period size: 52 Copynumber: 8.3 Consensus size: 52
505772 GGGTCTGAAA
* *
505782 ACTAAGTGTCA-CAGTGAGTAAATGAATCTTTTACGGATTATGAGGTCCGATA
1 ACTAAGTGTCATC-GTGAGTAAATGAATCCTTTACGGATTATGAGGTCCGATG
* * *
505834 ATTAAGTGTCATCGTGAGTAAATGAATTCTTTACGGATTATAAGGTCCGAT-
1 ACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGAGGTCCGATG
* * *
505885 AGCTAAGTGTAATCCTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATG
1 A-CTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGAGGTCCGATG
* * *
505938 ACTAAGTGTCATTGTGAGTAAATGAATCCTTTACAGATTATAAGGTCCGATG
1 ACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGAGGTCCGATG
* * *
505990 GCTAAGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGGTCCGATG
1 ACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGAGGTCCGATG
* * * *
506042 ACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATAATGTTCAATG
1 ACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGAGGTCCGATG
* *
506094 ACAAAGTGTCATCGTGAGTATATGAATCCTTTACGGA-TAGTGAGGTCCGATG
1 ACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTA-TGAGGTCCGATG
* * ** * *
506146 ACTAAGTGTCATGGTGAGTACATGAATTCCTTTACGGAACAGGAGGTCCGACG
1 ACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATTATGAGGTCCGATG
*
506199 ACTATA-TGTCATTGTGA
1 ACTA-AGTGTCATCGTGA
506216 TATTTAAATG
Statistics
Matches: 335, Mismatches: 40, Indels: 13
0.86 0.10 0.03
Matches are distributed among these distances:
51 3 0.01
52 293 0.87
53 37 0.11
54 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.32
Consensus pattern (52 bp):
ACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGAGGTCCGATG
Found at i:512358 original size:20 final size:20
Alignment explanation
Indices: 512326--512367 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
512316 TCAGTGCTTA
512326 AAAGTGAGATTAATTAAGGTT
1 AAAGTGAGATTAATT-AGGTT
512347 AAAGTG-GATTAATTAGGTT
1 AAAGTGAGATTAATTAGGTT
512366 AA
1 AA
512368 TTATAAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 8 0.38
21 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (20 bp):
AAAGTGAGATTAATTAGGTT
Found at i:513307 original size:52 final size:52
Alignment explanation
Indices: 513228--513637 Score: 545
Period size: 52 Copynumber: 7.9 Consensus size: 52
513218 AAATGATAAG
* *
513228 GGTCCGATGACTAAGTGTCATTGTGAGTAAATGAATCCTTTAAGGATTATGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
* *
513280 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATTATAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
* * *
513332 GGTGCGATTG-CTAAGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGA
1 GGTCCGA-TGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
* * *
513384 GGTCTGATGACTAAGTGTCATCGTGAGTAAATGAAT-CTTTACGAATTATAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
* * * *
513435 GGTCCAATGGCTAAGTGTCATCGTGAGTATATGAATCATTTACGGATTATGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
* * * * *
513487 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCATTTTCGAATTATAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
* * ** **
513539 GGTCCGATGGCTAAGTGTCATCGTGAGTATATGAATCCTTTGTGGATGGTGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
* *
513591 GGTCCGATGACTAAGTGTCATTGTGAGTACATGAATTCCTTTACGGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGA
513638 AAAGGAGGTC
Statistics
Matches: 310, Mismatches: 44, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
51 46 0.15
52 253 0.82
53 11 0.04
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (52 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
Found at i:513594 original size:207 final size:210
Alignment explanation
Indices: 513223--513635 Score: 634
Period size: 207 Copynumber: 2.0 Consensus size: 210
513213 GGTGTAAATG
* * *
513223 ATAAGGGTCCGATGACTAAGTGTCATTGTGAGTAAATGAATCCTTTAAGGATTATGAGGTCCGAT
1 ATAAGGGTCCAATGACTAAGTGTCATCGTGAGTAAATGAATCATTTAAGGATTATGAGGTCCGAT
* * * *
513288 GACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATTATAAGGTGCGATTGCTAAGTGTCAT
66 GACTAAGTGTCATCATGAGTAAATGAATCATTTACGAATTATAAGGTCCGATGGCTAAGTGTCAT
* *
513353 CGTGAGTATATGAATCCTTTACAGATTATGAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGA
131 CGTGAGTATATGAATCCTTTACAGATGATGAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGA
513418 A-T-CTTTACGAATT
196 ATTCCTTTACGAATT
* * *
513431 ATAA-GGTCCAATGGCTAAGTGTCATCGTGAGTATATGAATCATTTACGGATTATGAGGTCCGAT
1 ATAAGGGTCCAATGACTAAGTGTCATCGTGAGTAAATGAATCATTTAAGGATTATGAGGTCCGAT
*
513495 GACTAAGTGTCATCATGAGTAAATGAATCATTTTCGAATTATAAGGTCCGATGGCTAAGTGTCAT
66 GACTAAGTGTCATCATGAGTAAATGAATCATTTACGAATTATAAGGTCCGATGGCTAAGTGTCAT
*** * * *
513560 CGTGAGTATATGAATCCTTTGTGGATGGTGAGGTCCGATGACTAAGTGTCATTGTGAGTACATGA
131 CGTGAGTATATGAATCCTTTACAGATGATGAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGA
513625 ATTCCTTTACG
196 ATTCCTTTACG
513636 GAAAAGGAGG
Statistics
Matches: 184, Mismatches: 19, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
207 172 0.93
208 5 0.03
209 7 0.04
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.33
Consensus pattern (210 bp):
ATAAGGGTCCAATGACTAAGTGTCATCGTGAGTAAATGAATCATTTAAGGATTATGAGGTCCGAT
GACTAAGTGTCATCATGAGTAAATGAATCATTTACGAATTATAAGGTCCGATGGCTAAGTGTCAT
CGTGAGTATATGAATCCTTTACAGATGATGAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGA
ATTCCTTTACGAATT
Found at i:521490 original size:14 final size:15
Alignment explanation
Indices: 521471--521504 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
521461 ACAACATCAA
*
521471 AACAGTGAT-AAAAC
1 AACAGTAATGAAAAC
521485 AACAGTAATGAAAAC
1 AACAGTAATGAAAAC
521500 AACAG
1 AACAG
521505 CAAGTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.59, C:0.15, G:0.15, T:0.12
Consensus pattern (15 bp):
AACAGTAATGAAAAC
Found at i:529573 original size:2 final size:2
Alignment explanation
Indices: 529566--529590 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
529556 GAACTTGTTT
529566 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
529591 GAACTGCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:530733 original size:23 final size:23
Alignment explanation
Indices: 530697--530831 Score: 101
Period size: 23 Copynumber: 5.8 Consensus size: 23
530687 TTGGGCTCGA
**
530697 TTCGTTTAGCGTTCGCAAACATG
1 TTCGTTTAATGTTCGCAAACATG
* *
530720 TTCATTTAATGTTCGCGAACATG
1 TTCGTTTAATGTTCGCAAACATG
* ** *
530743 TTCGTTTATTTGTTTACAAACATT
1 TTCGTTTA-ATGTTCGCAAACATG
* * *
530767 TTCGTCTAACGTTCGCGAACATG
1 TTCGTTTAATGTTCGCAAACATG
* * * *
530790 TTCATTTATATATTCACGAACATG
1 TTCGTTTA-ATGTTCGCAAACATG
*
530814 TTTGTTTAA-GTTCGCAAA
1 TTCGTTTAATGTTCGCAAA
530832 TGTTAACTAA
Statistics
Matches: 83, Mismatches: 27, Indels: 5
0.72 0.23 0.04
Matches are distributed among these distances:
22 6 0.07
23 42 0.51
24 35 0.42
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.41
Consensus pattern (23 bp):
TTCGTTTAATGTTCGCAAACATG
Found at i:530810 original size:24 final size:23
Alignment explanation
Indices: 530714--530815 Score: 87
Period size: 24 Copynumber: 4.3 Consensus size: 23
530704 AGCGTTCGCA
*
530714 AACATGTTCATTTAATGTTCGCG
1 AACATGTTCATTTAATGTTCACG
* * * *
530737 AACATGTTCGTTTATTTGTTTACA
1 AACATGTTCATTTA-ATGTTCACG
* * * * *
530761 AACATTTTCGTCTAACGTTCGCG
1 AACATGTTCATTTAATGTTCACG
*
530784 AACATGTTCATTTATATATTCACG
1 AACATGTTCATTTA-ATGTTCACG
530808 AACATGTT
1 AACATGTT
530816 TGTTTAAGTT
Statistics
Matches: 59, Mismatches: 18, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
23 28 0.47
24 31 0.53
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (23 bp):
AACATGTTCATTTAATGTTCACG
Found at i:530812 original size:47 final size:46
Alignment explanation
Indices: 530712--530835 Score: 119
Period size: 47 Copynumber: 2.7 Consensus size: 46
530702 TTAGCGTTCG
** * * * * *
530712 CAAACATGTTCATTTAATGTTCGCGAACATGTTCGTTTATTTGTTTA
1 CAAACATGTTTGTCTAA-GTTCGCGAACATGTTCATTTATATATTCA
530759 CAAACAT-TTTCGTCTAACGTTCGCGAACATGTTCATTTATATATTCA
1 CAAACATGTTT-GTCTAA-GTTCGCGAACATGTTCATTTATATATTCA
* *
530806 CGAACATGTTTGTTTAAGTTCGC-AA-ATGTT
1 CAAACATGTTTGTCTAAGTTCGCGAACATGTT
530836 AACTAAACAA
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
44 5 0.08
45 2 0.03
46 8 0.12
47 47 0.72
48 3 0.05
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (46 bp):
CAAACATGTTTGTCTAAGTTCGCGAACATGTTCATTTATATATTCA
Found at i:533848 original size:59 final size:59
Alignment explanation
Indices: 533761--533975 Score: 197
Period size: 59 Copynumber: 3.6 Consensus size: 59
533751 GATACTTGGG
* * *
533761 GGGTAAAATAGTAATTTTTAG-AGGTTCGGGGTCAAAAATTGAATTTTTAGACATCCG-
1 GGGTAAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATTGAATTTTTAGACATCCGA
* * * *
533818 GAGGTAAAATGGTAGTTTTTGGAAAGTTCGGGATTAAAAA-TGAAATTTTTGGACATCCGA
1 G-GGTAAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATTG-AATTTTTAGACATCCGA
* * * ** * * * *
533878 GGGTGAAATGGTAATTTTTGAAAATTTAAGGGTCAAAAATGGATTTTTTAGA-AGTTCAA
1 GGGTAAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATTGAATTTTTAGACA-TCCGA
*
533937 GGGTGAAAAT-GTAATTTTTGGAAAGTTTGAGGGTCAAAA
1 GGGT-AAAATGGTAATTTTTGGAAAGTTCG-GGGTCAAAA
533976 TATGATTAGA
Statistics
Matches: 125, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
57 1 0.01
58 20 0.16
59 89 0.71
60 15 0.12
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATTGAATTTTTAGACATCCGA
Found at i:533909 original size:29 final size:29
Alignment explanation
Indices: 533877--533970 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 29
533867 TGGACATCCG
*
533877 AGGGTGAAATGGTAATTTTTGAAAATTTA
1 AGGGTGAAATGGTAATTTTTGAAAGTTTA
* * *
533906 AGGGTCAAAAATGG--ATTTTTTAGAAGTTCA
1 AGGGT--GAAATGGTAATTTTTGA-AAGTTTA
*
533936 AGGGTGAAAAT-GTAATTTTTGGAAAGTTTG
1 AGGGTG-AAATGGTAATTTTT-GAAAGTTTA
533966 AGGGT
1 AGGGT
533971 CAAAATATGA
Statistics
Matches: 50, Mismatches: 8, Indels: 13
0.70 0.11 0.18
Matches are distributed among these distances:
28 1 0.02
29 16 0.32
30 26 0.52
31 7 0.14
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (29 bp):
AGGGTGAAATGGTAATTTTTGAAAGTTTA
Found at i:533954 original size:30 final size:29
Alignment explanation
Indices: 533854--533956 Score: 75
Period size: 29 Copynumber: 3.5 Consensus size: 29
533844 TTCGGGATTA
* * * * *
533854 AAAATGAAATTTTTGGACATCCGAGGGTG
1 AAAATGTAATTTTTGAAAATTCAAGGGTG
* *
533883 -AAATGGTAATTTTTGAAAATTTAAGGGTCA
1 AAAAT-GTAATTTTTGAAAATTCAAGGGT-G
* * *
533913 AAAATG-GATTTTTTAGAAGTTCAAGGGTG
1 AAAATGTAATTTTTGA-AAATTCAAGGGTG
533942 AAAATGTAATTTTTG
1 AAAATGTAATTTTTG
533957 GAAAGTTTGA
Statistics
Matches: 55, Mismatches: 14, Indels: 9
0.71 0.18 0.12
Matches are distributed among these distances:
28 4 0.07
29 30 0.55
30 17 0.31
31 4 0.07
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAATTCAAGGGTG
Found at i:534049 original size:29 final size:30
Alignment explanation
Indices: 533876--534082 Score: 105
Period size: 29 Copynumber: 7.0 Consensus size: 30
533866 TTGGACATCC
* *
533876 GAGGGTGAAATGGTAATTTTTGAAAA-TTTA
1 GAGGGTAAAAT-GTAATTTTTGAAAAGTTCA
* * *
533906 -AGGGTCAAAAATG-GATTTTTTAGAAGTTCA
1 GAGGGT--AAAATGTAATTTTTGAAAAGTTCA
* *
533936 -AGGGTGAAAATGTAATTTTTGGAAAGTT-T
1 GAGGGT-AAAATGTAATTTTTGAAAAGTTCA
* * * **
533965 GAGGGTCAAAATATGA--TTAGAAAA-TTTT
1 GAGGGT-AAAATGTAATTTTTGAAAAGTTCA
* *
533993 GGGGGTCAAAATATAATTTTT-AAGAAGTTCA
1 GAGGGT-AAAATGTAATTTTTGAA-AAGTTCA
*
534024 GA-GGTAAAATGTAATTTTTGTAAAGTTC-
1 GAGGGTAAAATGTAATTTTTGAAAAGTTCA
* *
534052 GAGGGTTAAATGT-ATATTTTGGAAAGTTCA
1 GAGGGTAAAATGTAAT-TTTTGAAAAGTTCA
534082 G
1 G
534083 GAGTCAAAAT
Statistics
Matches: 137, Mismatches: 26, Indels: 28
0.72 0.14 0.15
Matches are distributed among these distances:
27 2 0.01
28 25 0.18
29 62 0.45
30 41 0.30
31 7 0.05
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (30 bp):
GAGGGTAAAATGTAATTTTTGAAAAGTTCA
Found at i:535213 original size:3 final size:3
Alignment explanation
Indices: 535205--535238 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
535195 CCTTTTTTAT
535205 TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
535239 TTATTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:535967 original size:6 final size:6
Alignment explanation
Indices: 535956--536022 Score: 52
Period size: 6 Copynumber: 11.8 Consensus size: 6
535946 ATTTTGAACT
* * * **
535956 TTTAAA TTTAAA -ATAAT TTTAAT TTTAAA AGTAAA TTTAAA --TAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
536001 TTTAAA TTTAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAA
536023 TCTTATAATA
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
4 4 0.09
5 7 0.15
6 36 0.77
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:535977 original size:17 final size:17
Alignment explanation
Indices: 535956--536040 Score: 76
Period size: 17 Copynumber: 5.4 Consensus size: 17
535946 ATTTTGAACT
535956 TTTAAATTTAAAAT-AA
1 TTTAAATTTAAAATAAA
* *
535972 TTTTAATTT--TA-AAA
1 TTTAAATTTAAAATAAA
*
535986 GT-AAATTT-AAATAAA
1 TTTAAATTTAAAATAAA
536001 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
536018 TTT-AATCTTATAATAAA
1 TTTAAAT-TTAAAATAAA
536035 TTTAAA
1 TTTAAA
536041 AAAGGGGTTC
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
13 5 0.09
14 5 0.09
15 4 0.07
16 17 0.31
17 22 0.40
18 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:536022 original size:45 final size:44
Alignment explanation
Indices: 535956--536040 Score: 134
Period size: 45 Copynumber: 1.9 Consensus size: 44
535946 ATTTTGAACT
* *
535956 TTTAAATTTAAAATAATTTTAATTTTAAAAGTAAATTTAAATAAA
1 TTTAAATTTAAAATAAATTTAATCTTAAAA-TAAATTTAAATAAA
*
536001 TTTAAATTTAAAATAAATTTAATCTTATAATAAATTTAAA
1 TTTAAATTTAAAATAAATTTAATCTTAAAATAAATTTAAA
536041 AAAGGGGTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 10 0.27
45 27 0.73
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (44 bp):
TTTAAATTTAAAATAAATTTAATCTTAAAATAAATTTAAATAAA
Found at i:536696 original size:202 final size:204
Alignment explanation
Indices: 536340--537005 Score: 806
Period size: 209 Copynumber: 3.2 Consensus size: 204
536330 TGGTTTGGTG
* * * **
536340 TCATTGATTTGGTC-TACTTCTCAGTGTCTCATCAGGAAGATGACCGCATTACTTGTTTTGATCC
1 TCATTGATTTGGTCTTA-TTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCC
* * * * * * * *
536404 ACTT-TTCTGTGTCTCATCAAGAAGACGAATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTA
65 GCTTCTT-TGTATCTCATCAGGAAGACGAATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTA
* * * *
536468 ACCGCTTTATTGCTTCAACCTGCTTCTCAGTACCTCATCAGGAAGTTAGGGTTCGAAGATTT-AC
129 ACCACTTTATTGCTTCGACTTGCTTCTCAGTATCTCATCAGGAAGTT-GGGTTCGAAG-TTTCAC
536532 TCAC-TT-G-GTT
192 TCACATTAGTGTT
536542 TCATTGATTTGGT-TCTATTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCC
1 TCATTGATTTGGTCT-TATTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCC
* *
536606 GCTTCTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTTATCAGGAAGCTAA
65 GCTTCTTTGTATCTCATCAGGAAGACGAATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTAA
** * * *
536671 CCACTTTATTGCTTCGACTTGCTTCTCAGTATCTCATCAGGAAACTGAAGTTTGAAGTTTCCCTC
130 CCACTTTATTGCTTCGACTTGCTTCTCAGTATCTCATCAGGAAGTTG-GGTTCGAAGTTTCACTC
536736 ACATTAAGCATTGTT
194 ACATT-AG---TGTT
* *
536751 TCATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCG
1 TCATTGATTTGGTCTTATTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCCG
* * * * * * *
536816 CTGCTCTGTATCTCATCAGGAAAACAAATTTGGTACACTTTTCAATATCTCATCAGGAAGTTAAC
66 CTTCTTTGTATCTCATCAGGAAGACGAATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTAAC
* *
536881 CATTTTATTGCTTTGACTTGCTTCTCAGTATCTCATCAGGAAGTTGGAGTTCGAAGTTTCACTCA
131 CACTTTATTGCTTCGACTTGCTTCTCAGTATCTCATCAGGAAGTTGG-GTTCGAAGTTTCACTCA
536946 CATTGAGCTTTGTT
195 CATT-AG---TGTT
* * *
536960 TTATTGATTTGGTCTTCTTATCAGTATCTCATCAGGAAGATGACCA
1 TCATTGATTTGGTCTTATTCTCAGTATCTCATCAGGAAGATGACCA
537006 ACTCGTTATT
Statistics
Matches: 404, Mismatches: 46, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
201 4 0.01
202 160 0.40
203 6 0.01
205 1 0.00
209 232 0.57
210 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (204 bp):
TCATTGATTTGGTCTTATTCTCAGTATCTCATCAGGAAGATGACCACATCACTTGTTTCAATCCG
CTTCTTTGTATCTCATCAGGAAGACGAATTTGGTACACTTCTCAGTATCTCATCAGGAAGCTAAC
CACTTTATTGCTTCGACTTGCTTCTCAGTATCTCATCAGGAAGTTGGGTTCGAAGTTTCACTCAC
ATTAGTGTT
Found at i:546096 original size:24 final size:24
Alignment explanation
Indices: 546069--546115 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
546059 TCGGGTCTGC
546069 ACTGAATTTCTTCATTTTATGTAA
1 ACTGAATTTCTTCATTTTATGTAA
546093 ACTGAATTTCTTCATTTTATGTA
1 ACTGAATTTCTTCATTTTATGTA
546116 CTTTCTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (24 bp):
ACTGAATTTCTTCATTTTATGTAA
Found at i:549022 original size:29 final size:30
Alignment explanation
Indices: 548983--549047 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
548973 GATGAAATGC
*
548983 AATTTTCGGATACTCGGGGGGTAAAATAGT
1 AATTTTCGGATACTCGGGGGGCAAAATAGT
**
549013 AATTTT-GGATACTTTGGGGGCAAAATAGT
1 AATTTTCGGATACTCGGGGGGCAAAATAGT
549042 AATTTT
1 AATTTT
549048 TGGAGGTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 26 0.81
30 6 0.19
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (30 bp):
AATTTTCGGATACTCGGGGGGCAAAATAGT
Found at i:549193 original size:58 final size:58
Alignment explanation
Indices: 549062--549174 Score: 145
Period size: 58 Copynumber: 1.9 Consensus size: 58
549052 GGTTCAGGGT
* * **
549062 CAAAAATGGAATTTTTGGACATTCGAGGGTTAAATGGTAGTTTTTTTAAAGTTCGCGAA
1 CAAAAATGGAA-TTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAAGTTCGCGAA
*** *
549121 CAAAAAAAAAATTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAATTTCG
1 CAAAAATGGAATTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAAGTTCG
549175 TGGTTAGAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
58 38 0.83
59 8 0.17
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (58 bp):
CAAAAATGGAATTTTGGACATTCGAGGGTAAAATGGTAATTTTTGAAAAGTTCGCGAA
Found at i:549289 original size:30 final size:30
Alignment explanation
Indices: 549249--549503 Score: 147
Period size: 30 Copynumber: 8.6 Consensus size: 30
549239 AAATATGCAA
*
549249 TTTTGGAAAGTTTAGGGGTAAAAATGTAAT
1 TTTTTGAAAGTTTAGGGGTAAAAATGTAAT
*
549279 TTTTTGAAAGTTTGAGGGTTAAAATATG--A-
1 TTTTTGAAAGTTT-AGGGGTAAAA-ATGTAAT
* * *
549308 --TTTGAAAATTTCGGAGGTTAAAATGTAAT
1 TTTTTGAAAGTTTAGG-GGTAAAAATGTAAT
** *
549337 TTTTTGAAAAG-TGCGAGGGTCAAAATGTAA-
1 TTTTTG-AAAGTTTAG-GGGTAAAAATGTAAT
* *
549367 TTTTTGAGAAG-TTCGAAGGT-AAAATGTAA-
1 TTTTTGA-AAGTTTAG-GGGTAAAAATGTAAT
549396 TTTTTGTAAAGTTTAGAGGG-AAAAATGTAAT
1 TTTTTG-AAAGTTTAG-GGGTAAAAATGTAAT
* * * *
549427 TTTTGGAAAG-TTCGAGGGTCAAAATATAAT
1 TTTTTGAAAGTTTAG-GGGTAAAAATGTAAT
** * * *
549457 TTTTAAAAAGTTTAGGGGTCAAAATATGAT
1 TTTTTGAAAGTTTAGGGGTAAAAATGTAAT
* *
549487 TTTTGGATAGTTTAGGG
1 TTTTTGAAAGTTTAGGG
549504 ACTTTTTGAG
Statistics
Matches: 184, Mismatches: 24, Indels: 34
0.76 0.10 0.14
Matches are distributed among these distances:
26 5 0.03
27 15 0.08
28 1 0.01
29 26 0.14
30 94 0.51
31 36 0.20
32 7 0.04
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
TTTTTGAAAGTTTAGGGGTAAAAATGTAAT
Found at i:549293 original size:59 final size:57
Alignment explanation
Indices: 549210--549499 Score: 184
Period size: 59 Copynumber: 4.9 Consensus size: 57
549200 TTCGGTTGTG
* * *
549210 AAAATGTAA-TTTTGGAGAAATTTGAGGTCAAATATGCAATTTTGGAAAGTTTAGGGGT
1 AAAATGTAATTTTTTGA-AAGTTTGAGGTCAAATATG-AATTTTGGAAAGTTTCGGGGT
* *
549268 AAAAATGTAATTTTTTGAAAGTTTGAGGGTTAAAATATG-A-TTT-GAAAATTTCGGAGGTT
1 -AAAATGTAATTTTTTGAAAGTTTGA-GG-TCAAATATGAATTTTGGAAAGTTTCGG-GG-T
** * *
549327 AAAATGTAATTTTTTGAAAAGTGCGAGGGTCAAA-ATGTAATTTTTGAGAAG-TTCGAAGGT
1 AAAATGTAATTTTTTG-AAAGTTTGA-GGTCAAATATG-AATTTTGGA-AAGTTTCG-GGGT
* *
549387 AAAATGTAA-TTTTTGTAAAGTTTAGAGG-GAAAAATGTAATTTTTGGAAAG-TTCGAGGGT
1 AAAATGTAATTTTTTG-AAAGTTT-GAGGTCAAATATG-AA-TTTTGGAAAGTTTCG-GGGT
* ** * * *
549446 CAAAATATAATTTTTAAAAAGTTTAGGGGTCAAAATATGATTTTTGGATAGTTT
1 -AAAATGTAATTTTTTGAAAGTTT-GAGGTC-AAATATGAATTTTGGAAAGTTT
549500 AGGGACTTTT
Statistics
Matches: 187, Mismatches: 24, Indels: 38
0.75 0.10 0.15
Matches are distributed among these distances:
57 12 0.06
58 28 0.15
59 59 0.32
60 57 0.30
61 23 0.12
62 8 0.04
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (57 bp):
AAAATGTAATTTTTTGAAAGTTTGAGGTCAAATATGAATTTTGGAAAGTTTCGGGGT
Found at i:549362 original size:89 final size:88
Alignment explanation
Indices: 549264--549488 Score: 233
Period size: 89 Copynumber: 2.5 Consensus size: 88
549254 GAAAGTTTAG
* * **
549264 GGGTAAAAATGTAATTTTTTGAAAGTTTGAGGGTTAAAATATGATTTG-AAAATTTCGGAGGTTA
1 GGGTCAAAATGTAATTTTTTGAAAGTTTGAGGGTTAAAATATGATTTGTAAAATTT-AGAGGGAA
549328 AAATGTAATTTTTTGAAAAGTGCGA
65 AAATGTAA-TTTTTGAAAAGTGCGA
* * * * *
549353 GGGTCAAAATGTAA-TTTTTGAGAAGTTCGAAGG-TAAAATGTAATTTTTGTAAAGTTTAGAGGG
1 GGGTCAAAATGTAATTTTTTGA-AAGTTTGAGGGTTAAAATATGA--TTTGTAAAATTTAGAGGG
* *
549416 AAAAATGTAATTTTTGGAAAGTTCGA
63 AAAAATGTAATTTTTGAAAAGTGCGA
* ** *
549442 GGGTCAAAATATAATTTTTAAAAAGTTT-AGGGGTCAAAATATGATTT
1 GGGTCAAAATGTAATTTTTTGAAAGTTTGA-GGGTTAAAATATGATTT
549489 TTGGATAGTT
Statistics
Matches: 110, Mismatches: 19, Indels: 15
0.76 0.13 0.10
Matches are distributed among these distances:
88 19 0.17
89 56 0.51
90 29 0.26
91 6 0.05
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (88 bp):
GGGTCAAAATGTAATTTTTTGAAAGTTTGAGGGTTAAAATATGATTTGTAAAATTTAGAGGGAAA
AATGTAATTTTTGAAAAGTGCGA
Found at i:551357 original size:17 final size:16
Alignment explanation
Indices: 551328--551364 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
551318 ATTTTAAAAG
551328 TTAATTTAAAATAAAT
1 TTAATTTAAAATAAAT
*
551344 TTAATCTTATAATAAAT
1 TTAAT-TTAAAATAAAT
551361 TTAA
1 TTAA
551365 AAAATGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAATTTAAAATAAAT
Found at i:551367 original size:29 final size:29
Alignment explanation
Indices: 551299--551366 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
551289 TTTGAACTTT
* * *
551299 TAAATTTAGAATAATTTTAATTTTAAAAG
1 TAAATTTAAAATAAATTTAATCTTAAAAG
* *
551328 TTAATTTAAAATAAATTTAATCTTATAA-
1 TAAATTTAAAATAAATTTAATCTTAAAAG
551356 TAAATTTAAAA
1 TAAATTTAAAA
551367 AATGGGTTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 10 0.30
29 23 0.70
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (29 bp):
TAAATTTAAAATAAATTTAATCTTAAAAG
Found at i:557389 original size:48 final size:49
Alignment explanation
Indices: 557294--557389 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 49
557284 CCGCCTTGTA
557294 GAAAAAGTTAGAAACTCTTTATGCGACTAAGTCTCTAGCTAACCGTTTG
1 GAAAAAGTTAGAAACTCTTTATGCGACTAAGTCTCTAGCTAACCGTTTG
* * *
557343 GAAAATGTTAGAAACTCTTTATG-GACTAAGTCTCTGGCTAATCGTTT
1 GAAAAAGTTAGAAACTCTTTATGCGACTAAGTCTCTAGCTAACCGTTT
557390 AGTGTTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 22 0.50
49 22 0.50
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (49 bp):
GAAAAAGTTAGAAACTCTTTATGCGACTAAGTCTCTAGCTAACCGTTTG
Found at i:566574 original size:25 final size:25
Alignment explanation
Indices: 566539--566588 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
566529 CATTACCAGT
566539 CAAAATACCAAATTTTATCTACAAA
1 CAAAATACCAAATTTTATCTACAAA
*
566564 CAAAATTCCAAATTTTATCTACAAA
1 CAAAATACCAAATTTTATCTACAAA
566589 AGTCTTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (25 bp):
CAAAATACCAAATTTTATCTACAAA
Found at i:568311 original size:3 final size:3
Alignment explanation
Indices: 568303--568347 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
568293 AAGGGTCCAA
* * * *
568303 ATT ATT ATT ATC ATC ATC ATT ATT ATT ATT ATT ATT ATT CTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
568348 TTAATTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:568998 original size:147 final size:146
Alignment explanation
Indices: 568789--569292 Score: 611
Period size: 146 Copynumber: 3.4 Consensus size: 146
568779 ATGTTTTGGT
* * * *
568789 TTTTTTTAAACAATTTTGAAATAAAAATTTTGATTTTTTTTAAAGCAAAATAGTGATTTTCTTTA
1 TTTTTTT-AACTATTTCGAAATAAAAGTTTAGA---TTTTT-AAGCAAAATAGTGATTTTCTTTA
* *
568854 AAAAAGATAAAGTTTAGATTTTAAAAAATAAAAATCTGTTTTTTAGTTATTTTAAACAAAAAGTT
61 AAAAAGA-AAAGTTTAGATTTTAAAAAATAAAAATCTATTTTTTAGTTATTTTAAAAAAAAAGTT
568919 TAAAATTTTAACAAAGTTTTGA
125 TAAAATTTTAACAAAGTTTTGA
* * *
568941 TTTTTTTAACTATTTCGAAATAAAAGTTTAGCTTTTTAAGTAAAATAGTAATTTTCTTTAAAAAA
1 TTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGCAAAATAGTGATTTTCTTTAAAAAA
** * * * * * *
569006 GAAAAAATTATATTTTTAAAAATAAAAATATATTTTTTATTTCTTTTAAAGAAAAAGTTTAAAAT
66 GAAAAGTTTAGATTTTAAAAAATAAAAATCTATTTTTTAGTTATTTTAAAAAAAAAGTTTAAAAT
* *
569071 TTTAACAAATTTTTAA
131 TTTAACAAAGTTTTGA
* *
569087 TTTTTTCTAACTATTTCGAAATAAAAATTTAGATTTTTAAGCAAAATAATGA-TTTCTTTAAAAA
1 TTTTTT-TAACTATTTCGAAATAAAAGTTTAGATTTTTAAGCAAAATAGTGATTTTCTTT---AA
*
569151 AAAAGAGAAAGTTTAGATTTAAAAAAAAAATAAAAATCTATTTTTTAGTTA-TTTAAAAAAAAAG
62 AAAAGA-AAAGTTTAGATTT---TAAAAAATAAAAATCTATTTTTTAGTTATTTTAAAAAAAAAG
569215 TTTAAAATTTTAACAAAGTTTTGA
123 TTTAAAATTTTAACAAAGTTTTGA
* * * *
569239 -TTTTTTAACTATTTTGAAATAAAAGCTT-GAATTTTTAAGTAAAGTAGTGATTTT
1 TTTTTTTAACTATTTCGAAATAAAAGTTTAG-ATTTTTAAGCAAAATAGTGATTTT
569293 TGTTTAATCA
Statistics
Matches: 302, Mismatches: 40, Indels: 21
0.83 0.11 0.06
Matches are distributed among these distances:
146 81 0.27
147 68 0.23
148 5 0.02
149 9 0.03
150 47 0.16
151 28 0.09
152 41 0.14
153 23 0.08
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (146 bp):
TTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGCAAAATAGTGATTTTCTTTAAAAAA
GAAAAGTTTAGATTTTAAAAAATAAAAATCTATTTTTTAGTTATTTTAAAAAAAAAGTTTAAAAT
TTTAACAAAGTTTTGA
Done.