Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009596.1 Kokia drynarioides strain JFW-HI SEQ_124312, 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: 62479
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 129 characters in sequence are not A, C, G, or T
Found at i:6435 original size:45 final size:45
Alignment explanation
Indices: 6385--6475 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
6375 ATCATTAAAA
6385 TAAAATCGATAGATCTGATCTTATTTTTCTAATCAAGTAGTTGCC
1 TAAAATCGATAGATCTGATCTTATTTTTCTAATCAAGTAGTTGCC
* *
6430 TAAAATTGATAGATCTGATTTTATTTTTCTAATCAAGTAGTTGCC
1 TAAAATCGATAGATCTGATCTTATTTTTCTAATCAAGTAGTTGCC
6475 T
1 T
6476 TAGTGTATGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (45 bp):
TAAAATCGATAGATCTGATCTTATTTTTCTAATCAAGTAGTTGCC
Found at i:6812 original size:103 final size:103
Alignment explanation
Indices: 6633--6831 Score: 256
Period size: 103 Copynumber: 1.9 Consensus size: 103
6623 ACGCGACTCC
* * * * *
6633 AAATCAGATTACAATTAGGGCAATGAACACCTTGATTATTAGGTTAATATACAGATTTAACTAGA
1 AAATCAGATTACAATTAGGGCAATGAACACCTTGACTATCAGGCTAACATACAGATTCAACTAGA
* * * *
6698 GTAACTTTTCGTGTATGAATGAGTGACAATGCGATTCG
66 ATAACATTTCGTATATGAATGAATGACAATGCGATTCG
* * * *
6736 AAATCAGATTACATTTAGGGCAGTGAACATCTTGACTATCAGGCTAACATAC-GAGTTCAGCTAG
1 AAATCAGATTACAATTAGGGCAATGAACACCTTGACTATCAGGCTAACATACAGA-TTCAACTAG
*
6800 AATAACATTTCGTATATGAATGAATGGCAATG
65 AATAACATTTCGTATATGAATGAATGACAATG
6832 AAGCATAAAT
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
102 2 0.02
103 79 0.98
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (103 bp):
AAATCAGATTACAATTAGGGCAATGAACACCTTGACTATCAGGCTAACATACAGATTCAACTAGA
ATAACATTTCGTATATGAATGAATGACAATGCGATTCG
Found at i:12709 original size:19 final size:19
Alignment explanation
Indices: 12664--12710 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
12654 AGTAAAGTTT
* * *
12664 ATATTAAAATTCTTGAAGG
1 ATATTGAAATGCTAGAAGG
12683 AT-TTGAAATGCTAGAAGG
1 ATATTGAAATGCTAGAAGG
12701 ATATTGAAAT
1 ATATTGAAAT
12711 TATCGGGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (19 bp):
ATATTGAAATGCTAGAAGG
Found at i:16499 original size:38 final size:38
Alignment explanation
Indices: 16456--16576 Score: 106
Period size: 38 Copynumber: 3.2 Consensus size: 38
16446 GTTTTTATTT
16456 TTTTATTTTCAATGAATATCTAATTCAATTATTATATA
1 TTTTATTTTCAATGAATATCTAATTCAATTATTATATA
* * * * * * *
16494 TTTTATTCTAAAT-ACGTCAAC-ATATT-ATGTTTTTAT-TT
1 TTTTATTTTCAATGA-AT-ATCTA-ATTCA-ATTATTATATA
16532 TTTTATTTTCAATGAATATCTAATTCAATTATTATATA
1 TTTTATTTTCAATGAATATCTAATTCAATTATTATATA
*
16570 CTTTATT
1 TTTTATT
16577 CTAAATACGT
Statistics
Matches: 60, Mismatches: 15, Indels: 16
0.66 0.16 0.18
Matches are distributed among these distances:
37 12 0.20
38 36 0.60
39 12 0.20
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (38 bp):
TTTTATTTTCAATGAATATCTAATTCAATTATTATATA
Found at i:16533 original size:76 final size:76
Alignment explanation
Indices: 16441--16592 Score: 295
Period size: 76 Copynumber: 2.0 Consensus size: 76
16431 TAGGTTACAA
*
16441 ATTATGTTTTTATTTTTTTATTTTCAATGAATATCTAATTCAATTATTATATATTTTATTCTAAA
1 ATTATGTTTTTATTTTTTTATTTTCAATGAATATCTAATTCAATTATTATATACTTTATTCTAAA
16506 TACGTCAACAT
66 TACGTCAACAT
16517 ATTATGTTTTTATTTTTTTATTTTCAATGAATATCTAATTCAATTATTATATACTTTATTCTAAA
1 ATTATGTTTTTATTTTTTTATTTTCAATGAATATCTAATTCAATTATTATATACTTTATTCTAAA
16582 TACGTCAACAT
66 TACGTCAACAT
16593 TCCTCTAATA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.33, C:0.10, G:0.04, T:0.53
Consensus pattern (76 bp):
ATTATGTTTTTATTTTTTTATTTTCAATGAATATCTAATTCAATTATTATATACTTTATTCTAAA
TACGTCAACAT
Found at i:23782 original size:18 final size:19
Alignment explanation
Indices: 23742--23782 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
23732 TAACAAGTAA
* *
23742 AAAATTTAACTCATAATTT
1 AAAATTCAAATCATAATTT
23761 -AAATTCAAATCAT-ATTT
1 AAAATTCAAATCATAATTT
23778 AAAAT
1 AAAAT
23783 AATAAACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATTCAAATCATAATTT
Found at i:25232 original size:11 final size:11
Alignment explanation
Indices: 25216--25241 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
25206 TCGGCAAAGG
25216 AATGGAAGGGA
1 AATGGAAGGGA
25227 AATGGAAGGGA
1 AATGGAAGGGA
25238 AATG
1 AATG
25242 CTAGAGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.42, T:0.12
Consensus pattern (11 bp):
AATGGAAGGGA
Found at i:25499 original size:23 final size:22
Alignment explanation
Indices: 25472--25514 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
25462 GTTTGAAAGG
25472 GATTTGAAAGGACTTTGAGGATT
1 GATTTGAAAGGA-TTTGAGGATT
**
25495 GATTTTCAAGGATTTGAGGA
1 GATTTGAAAGGATTTGAGGA
25515 CTTTGACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (22 bp):
GATTTGAAAGGATTTGAGGATT
Found at i:26233 original size:40 final size:39
Alignment explanation
Indices: 26169--28017 Score: 622
Period size: 40 Copynumber: 46.9 Consensus size: 39
26159 ATTCTGATGG
* * *
26169 CTTCAATTTGACCC-ATGGTCAGGGTAAGAGATCTGGATTA
1 CTTCAATCTG-CCCTATGGTTAGGGTAAAAGAT-TGGATTA
* * *
26209 CTTCAATTTGCCCTTTGGTTAGGGTAAAAGATCTGAATTA
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGAT-TGGATTA
* * * **
26249 CTTCAATCTGCCCCATGGTTGGGGTAAGAGATCAGATGGT-
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGAT--TA
* * * * *
26289 CTTCAATCTGCCTTCTGGTCAAGGTAAAAGATCGGA-TA
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * * * * *
26327 GTCTTCAATCTACCCCATGG-TCGTGGTAAGAGATCGGATGA
1 --CTTCAATCTGCCCTATGGTTAG-GGTAAAAGATTGGATTA
* * * * * * * *
26368 TCTTTAATTTGCCTTCTGG-TCGGGATAAGAGATCGAATGGT-
1 -CTTCAATCTGCCCTATGGTTAGGG-TAAAAGATTGGAT--TA
* * * *
26409 CTTCAATCTGCCCTCTGGTTAGGGTAAAAGATCGTATTG
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * * ** * *
26448 CTTCAATCTACCCCATGATCGGGGTAAGAA-ATTAGATGA
1 CTTCAATCTGCCCTATGGTTAGGGTAA-AAGATTGGATTA
* * * ** * *
26487 CTTCAATCTACCTTTTAATTAGGGTAAAAGATCGGATGA
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * ** * * *
26526 CTTTAATTTG-CCTCATGGTCGGGGTAAGAGATTAGATTG
1 CTTCAATCTGCCCT-ATGGTTAGGGTAAAAGATTGGATTA
* * * * *
26565 CTTCAATTTGCTAC-ACGG-TCGAGGTAAAAGATTGGATGA
1 CTTCAATCTGC-CCTATGGTTAG-GGTAAAAGATTGGATTA
* * * * * * *
26604 TTTTTAATCTACGCTCTGATTAGGGTAAAAGATTGGATTG
1 -CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* ** *
26644 CTTCAATCTGCTCC-ATGATCGGGGTAAGAGATTGGATGGT-
1 CTTCAATCTGC-CCTATGGTTAGGGTAAAAGATTGGAT--TA
* * ** *
26684 CTTTAATCTACCCTCGGGTTAGGGTAAAAGATTGGATTG
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * ** * *
26723 TTTCAATCTGCCCTATGATCGGGGTAAGAGATTGGATGA
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * ** **
26762 CTTTTAATCTGCCCTCTAATTAGGACAAAAGATTGGATT-
1 C-TTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * * *
26801 CTTCAATCTGTCCC-ATGATCAAGGTAAAAGATTGGATGA
1 CTTCAATCTG-CCCTATGGTTAGGGTAAAAGATTGGATTA
* * ** *
26840 TCTTCAATCTACCCTCTAATTAGGGTAAAAGATTGGATTG
1 -CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * *
26880 CTTCAATCTGCCCTTTGATTAGGGTAAAAGATTTGG-TTG
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGA-TTGGATTA
* * * **
26919 CTTCAATCTGCCC-ATGG-TCGAGGTAAGAGATAGGATGG
1 CTTCAATCTGCCCTATGGTTAG-GGTAAAAGATTGGATTA
* * *
26957 CTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGAATTA
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * * *
26996 CTTCAATTTACCCTCTGGTTACCCATGATCGAGGTAAGAGATTGGATGGT-
1 CTTCAATCTGCCCTATGG-T-----T-A--G-GGTAAAAGATTGGAT--TA
* * *
27046 CTTCAATCTGCCCTTTGATTAGGGTAAAAGATTTGG-TTG
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGA-TTGGATTA
* * ** **
27085 CTTCAATCTGCCC-ATGG-TCGAGGTAAGAGATAAGATGG
1 CTTCAATCTGCCCTATGGTTAG-GGTAAAAGATTGGATTA
* * * *
27123 CTTCAATCTGCACTCTAGTTAGGGTAAAAGATTGAATTA
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * * *
27162 CTTCAATTTGCCCTCTGGTTAGGATAAAAGATCTGAATTA
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGAT-TGGATTA
* * * *
27202 CTTCAATCTACCCCATGGTTAGGGTAAAAGATTAGATTG
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * * * * * ** **
27241 CTTCAATCT-ACCT-CGATCATGGGGATAATCTTTAATCTA
1 CTTCAATCTGCCCTATGGTTA-GGGTAAAAGATTGGAT-TA
** *
27280 CCTT---T-TG-GTTATGG-TA-----AAAGATTGGATTG
1 -CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * ** * *
27309 CTTCAATCAGCCCTATGATCGGGGTAAGAGATCGGATGGT-
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGAT--TA
* * * * * *
27349 CTTCAATTTTCCCTCTAGTTAGGGTAAAAGATTAGATTG
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * ** ** *
27388 TTTCAATTTG-CCTCACAGTCGGGGTAAATGATTGGA-TA
1 CTTCAATCTGCCCT-ATGGTTAGGGTAAAAGATTGGATTA
* * * * * *
27426 GTCTTCAATCTACCCTCTGATTATGGTAAAAAATTGGATTG
1 --CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * ** *
27467 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGGT-
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGAT--TA
* * * * *
27507 CTTCAATCTGCCTTTTAGTTAGGGTAAAAGATCGAATGGT-
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGAT--TA
* * * * *
27547 TTTCGATCTGCCCTCTAGTTAGGGTAAAAGATCT-GATGA
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGAT-TGGATTA
* * * *
27586 TCTTCAATCTGTCCTCTGGTTATGGTAAAAGATTGGATTG
1 -CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* ** * * *
27626 CTTCAATCTTTCCC-ATGGTCGGGGTAAGAGATTGAATGA
1 CTTCAATC-TGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * * * *
27665 CTTTAATCTACCCTCTGGTTAGGGTAAAAGATTGGACTG
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * * * * * *
27704 CTTCAGTGT-ACCTCATGATTGGGGTAAGAGATTGGATGA
1 CTTCAATCTGCCCT-ATGGTTAGGGTAAAAGATTGGATTA
* * * * *
27743 TCTTTAATCTACCCTTTAGTTAGGGTAAAAGATTAGATGGT-
1 -CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGAT--TA
* * * * **
27784 CTTCAATTTGCCTTCTGATTAGGGTAAAAGATTAAATGGT-
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGAT--TA
* * * ** *
27824 CTTCAATCTACCTTCTGGTTAGATTAAAAGATTGGATTG
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * *
27863 CTTCAATCTGTCCTATGGTTAGGGTAAGAGATTGGATGA
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * * * * *
27902 CTTCAATCTGCCTTGTGATTAGGGTAAAAGATTGAACTG
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
* * * ** * *
27941 CTTCAGTCTACCCCATGGTCGGGGTAAGAGATTTGATGGT-
1 CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGAT--TA
*
27981 CTTCAACCTGCCC-ACTGGTTAGGGTAAAAGATTGGAT
1 CTTCAATCTGCCCTA-TGGTTAGGGTAAAAGATTGGAT
28018 GGTCTTCAGT
Statistics
Matches: 1318, Mismatches: 394, Indels: 194
0.69 0.21 0.10
Matches are distributed among these distances:
28 3 0.00
29 1 0.00
30 6 0.00
31 1 0.00
32 1 0.00
33 4 0.00
36 3 0.00
37 15 0.01
38 107 0.08
39 535 0.41
40 583 0.44
41 25 0.02
43 1 0.00
44 1 0.00
45 1 0.00
46 1 0.00
48 1 0.00
49 14 0.01
50 14 0.01
51 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (39 bp):
CTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTA
Found at i:26315 original size:80 final size:77
Alignment explanation
Indices: 26169--26892 Score: 268
Period size: 79 Copynumber: 9.2 Consensus size: 77
26159 ATTCTGATGG
* * *
26169 CTTCAATTTGACCCATGGTCAGGGTAAGAGATCTGGAT-TACTTCAATTTGCCCTT-TGGTTAGG
1 CTTCAATCTGCCCCATGGTCAGGGTAAGAGATC-GGATGT-CTTCAATTTG-CCTTCTGGTCAGG
26232 GTAAAAGATCTGAATT
63 GTAAAAGATC-GAATT
** * * *
26248 ACTTCAATCTGCCCCATGGTTGGGGTAAGAGATCAGATGGTCTTCAATCTGCCTTCTGGTCAAGG
1 -CTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGGAT-GTCTTCAATTTGCCTTCTGGTCAGGG
*
26313 TAAAAGATCGGATAGT
64 TAAAAGATC-GA-ATT
* *
26329 CTTCAATCTACCCCATGGTC-GTGGTAAGAGATCGGATGATCTTTAATTTGCCTTCTGGTC-GGG
1 CTTCAATCTGCCCCATGGTCAG-GGTAAGAGATCGGATG-TCTTCAATTTGCCTTCTGGTCAGGG
*
26392 ATAAGAGATCGAATGGT
64 -TAAAAGATCGAAT--T
* * * * * * * *
26409 CTTCAATCTGCCCTC-TGGTTAGGGTAAAAGATCGTAT-TGCTTCAATCTACC-CCATGATCGGG
1 CTTCAATCTGCCC-CATGGTCAGGGTAAGAGATCGGATGT-CTTCAATTTGCCTTC-TGGTCAGG
* *
26471 GTAAGAA-AT-TAGATGA
63 GTAA-AAGATCGA-AT-T
* *** ** * * * * *
26487 CTTCAATCTACCTTTTAATTAGGGTAAAAGATCGGATGACTTTAATTTGCC-TCATGGTCGGGGT
1 CTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGGATGTCTTCAATTTGCCTTC-TGGTCAGGGT
* *
26551 AAGAGAT-TAGATT
65 AAAAGATCGA-ATT
* ** * * * * * * * * *
26564 GCTTCAATTTGCTACACGGTC-GAGGTAAAAGATTGGATGATTTTTAATCTACGC-TCTGATTAG
1 -CTTCAATCTGCCCCATGGTCAG-GGTAAGAGATCGGATG-TCTTCAATTTGC-CTTCTGGTCAG
* *
26627 GGTAAAAGATTGGATT
62 GGTAAAAGATCGAATT
* * * * * * * * * *
26643 GCTTCAATCTGCTCCATGATCGGGGTAAGAGATTGGATGGTCTTTAATCTACCCTCGGGTTAGGG
1 -CTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGGAT-GTCTTCAATTTGCCTTCTGGTCAGGG
* *
26708 TAAAAGATTGGATT
64 TAAAAGATCGAATT
* * * * * * * * * ** * *
26722 GTTTCAATCTGCCCTATGATCGGGGTAAGAGATTGGATGACTTTTAATCTGCCCTCTAATTAGGA
1 -CTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGGATGTC-TTCAATTTGCCTTCTGGTCAGGG
* * *
26787 CAAAAGATTGGATT
64 TAAAAGATCGAATT
* * * * * * * * ** *
26801 CTTCAATCTGTCCCATGATCAAGGTAAAAGATTGGATGATCTTCAATCTACCCTCTAATTAGGGT
1 CTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGGATG-TCTTCAATTTGCCTTCTGGTCAGGGT
* *
26866 AAAAGATTGGATT
65 AAAAGATCGAATT
26879 GCTTCAATCTGCCC
1 -CTTCAATCTGCCC
26893 TTTGATTAGG
Statistics
Matches: 519, Mismatches: 95, Indels: 61
0.77 0.14 0.09
Matches are distributed among these distances:
77 2 0.00
78 157 0.30
79 201 0.39
80 154 0.30
81 5 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (77 bp):
CTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGGATGTCTTCAATTTGCCTTCTGGTCAGGGTA
AAAGATCGAATT
Found at i:26644 original size:79 final size:79
Alignment explanation
Indices: 26547--26890 Score: 426
Period size: 79 Copynumber: 4.4 Consensus size: 79
26537 CTCATGGTCG
* * * * * * *
26547 GGGTAAGAGATTAGATTGCTTCAATTTGCTACACGGTCGAGGTAAAAGATTGGATGATTTTTAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCTCCATGATCGAGGTAAAAGATTGGATGATCTTTAAT
* *
26612 CTACGCTCTGATTA
66 CTACCCTCTAATTA
* * *
26626 GGGTAAAAGATTGGATTGCTTCAATCTGCTCCATGATCGGGGTAAGAGATTGGATGGTCTTTAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCTCCATGATCGAGGTAAAAGATTGGATGATCTTTAAT
***
26691 CTACCCTCGGGTTA
66 CTACCCTCTAATTA
* * *
26705 GGGTAAAAGATTGGATTGTTTCAATCTGC-CCTATGATCGGGGTAAGAGATTGGATGA-CTTTTA
1 GGGTAAAAGATTGGATTGCTTCAATCTGCTCC-ATGATCGAGGTAAAAGATTGGATGATC-TTTA
*
26768 ATCTGCCCTCTAATTA
64 ATCTACCCTCTAATTA
** * *
26784 GGACAAAAGATTGGATT-CTTCAATCTG-TCCCATGATCAAGGTAAAAGATTGGATGATCTTCAA
1 GGGTAAAAGATTGGATTGCTTCAATCTGCT-CCATGATCGAGGTAAAAGATTGGATGATCTTTAA
26847 TCTACCCTCTAATTA
65 TCTACCCTCTAATTA
26862 GGGTAAAAGATTGGATTGCTTCAATCTGC
1 GGGTAAAAGATTGGATTGCTTCAATCTGC
26891 CCTTTGATTA
Statistics
Matches: 229, Mismatches: 29, Indels: 13
0.85 0.11 0.05
Matches are distributed among these distances:
78 67 0.29
79 162 0.71
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (79 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCTCCATGATCGAGGTAAAAGATTGGATGATCTTTAAT
CTACCCTCTAATTA
Found at i:26669 original size:39 final size:38
Alignment explanation
Indices: 26409--28017 Score: 562
Period size: 39 Copynumber: 40.9 Consensus size: 38
26399 ATCGAATGGT
* * * *
26409 CTTCAATCTGCCCTCTGGTTAGGGTAAAAGATCGTATTG
1 CTTCAATCTGCCC-ATGATTAGGGTAAAAGATTGGATTG
* ** *
26448 CTTCAATCTACCCCATGATCGGGGTAAGAA-ATTAGA-TG
1 CTTCAATCT-GCCCATGATTAGGGTAA-AAGATTGGATTG
* ** * *
26486 ACTTCAATCTACCTTTTAATTAGGGTAAAAGATCGGA-TG
1 -CTTCAATCTGCC-CATGATTAGGGTAAAAGATTGGATTG
* * * ** * *
26525 ACTTTAATTTGCCTCATGGTCGGGGTAAGAGATTAGATTG
1 -CTTCAATCTGCC-CATGATTAGGGTAAAAGATTGGATTG
* * * * *
26565 CTTCAATTTGCTACACG-GTCGAGGTAAAAGATTGGA-TG
1 CTTCAATCTGC-CCATGATTAG-GGTAAAAGATTGGATTG
* * *
26603 ATTTTTAATCTACGCTC-TGATTAGGGTAAAAGATTGGATTG
1 --CTTCAATCT--GCCCATGATTAGGGTAAAAGATTGGATTG
** * *
26644 CTTCAATCTGCTCCATGATCGGGGTAAGAGATTGGATGG
1 CTTCAATCTGC-CCATGATTAGGGTAAAAGATTGGATTG
* * *
26683 TCTTTAATCTACCC-TCGGGTTAGGGTAAAAGATTGGATTG
1 -CTTCAATCTGCCCAT--GATTAGGGTAAAAGATTGGATTG
* ** *
26723 TTTCAATCTGCCCTATGATCGGGGTAAGAGATTGGA-TG
1 CTTCAATCTGCCC-ATGATTAGGGTAAAAGATTGGATTG
* * * **
26761 ACTTTTAATCTGCCCTCTAATTAGGACAAAAGATTGGATT-
1 -C-TTCAATCTGCCC-ATGATTAGGGTAAAAGATTGGATTG
* *
26801 CTTCAATCTGTCCCATGATCAAGGTAAAAGATTGGA-TG
1 CTTCAATCTG-CCCATGATTAGGGTAAAAGATTGGATTG
* * *
26839 ATCTTCAATCTACCCTCTAATTAGGGTAAAAGATTGGATTG
1 --CTTCAATCTGCCC-ATGATTAGGGTAAAAGATTGGATTG
*
26880 CTTCAATCTGCCCTTTGATTAGGGTAAAAGATTTGG-TTG
1 CTTCAATCTGCCC-ATGATTAGGGTAAAAGA-TTGGATTG
* * * * *
26919 CTTCAATCTGCCCATG-GTCGAGGTAAGAGATAGGATGG
1 CTTCAATCTGCCCATGATTAG-GGTAAAAGATTGGATTG
* * *
26957 CTTCAATCTGCCC-TCTAGTTAGGGTAAAAGATTGAATTA
1 CTTCAATCTGCCCAT-GA-TTAGGGTAAAAGATTGGATTG
* * *
26996 CTTCAATTTACCCTCTGGTTACCCATGA-TCGAGGTAAGAGATTGGATGG
1 CTTC-A---A---TCT-G---CCCATGATTAG-GGTAAAAGATTGGATTG
*
27045 TCTTCAATCTGCCCTTTGATTAGGGTAAAAGATTTGG-TTG
1 -CTTCAATCTGCCC-ATGATTAGGGTAAAAGA-TTGGATTG
* * * ** *
27085 CTTCAATCTGCCCATG-GTCGAGGTAAGAGATAAGATGG
1 CTTCAATCTGCCCATGATTAG-GGTAAAAGATTGGATTG
* *
27123 CTTCAATCTGCACTC-T-AGTTAGGGTAAAAGATTGAATTA
1 CTTCAATCTGC-C-CATGA-TTAGGGTAAAAGATTGGATTG
* * * * * *
27162 CTTCAATTTGCCCTCTGGTTAGGATAAAAGATCTGAATTA
1 CTTCAATCTGCCC-ATGATTAGGGTAAAAGAT-TGGATTG
* * *
27202 CTTCAATCTACCCCATGGTTAGGGTAAAAGATTAGATTG
1 CTTCAATCT-GCCCATGATTAGGGTAAAAGATTGGATTG
* * *
27241 CTTCAATCT-ACC-TCGATCATGGG-----GA-T--AAT-
1 CTTCAATCTGCCCAT-GATTA-GGGTAAAAGATTGGATTG
* * ** * *
27270 CTTTAATCTACCTTTTGGTTATGGTAAAAGATTGGATTG
1 CTTCAATCTGCC-CATGATTAGGGTAAAAGATTGGATTG
* ** * * *
27309 CTTCAATCAGCCCTATGATCGGGGTAAGAGATCGGATGG
1 CTTCAATCTGCCC-ATGATTAGGGTAAAAGATTGGATTG
* * * *
27348 TCTTCAATTTTCCC-TCTAGTTAGGGTAAAAGATTAGATTG
1 -CTTCAATCTGCCCAT-GA-TTAGGGTAAAAGATTGGATTG
* * * ** * *
27388 TTTCAATTTGCCTCA-CAGTCGGGGTAAATGATTGGATAG
1 CTTCAATCTGCC-CATGA-TTAGGGTAAAAGATTGGATTG
* * * *
27427 TCTTCAATCTACCCTCTGATTATGGTAAAAAATTGGATTG
1 -CTTCAATCTGCCC-ATGATTAGGGTAAAAGATTGGATTG
** * *
27467 CTTCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGG
1 CTTCAATCTG-CCCATGATTAGGGTAAAAGATTGGATTG
** * * * *
27506 TCTTCAATCTGCCTTTTAGTTAGGGTAAAAGATCGAATGG
1 -CTTCAATCTGCCCATGA-TTAGGGTAAAAGATTGGATTG
* * *
27546 TTTTCGATCTGCCC-TCTAGTTAGGGTAAAAGATCT-GA-TG
1 -CTTCAATCTGCCCAT-GA-TTAGGGTAAAAGAT-TGGATTG
* *
27585 ATCTTCAATCTGTCCTC-TGGTTATGGTAAAAGATTGGATTG
1 --CTTCAATCTG-CC-CATGATTAGGGTAAAAGATTGGATTG
* * ** * *
27626 CTTCAATCTTTCCCATGGTCGGGGTAAGAGATT-GAATG
1 CTTCAATC-TGCCCATGATTAGGGTAAAAGATTGGATTG
* * * * *
27664 ACTTTAATCTACCCTCTGGTTAGGGTAAAAGATTGGACTG
1 -CTTCAATCTGCCC-ATGATTAGGGTAAAAGATTGGATTG
* * * * *
27704 CTTCAGTGTACCTCATGATTGGGGTAAGAGATTGGA-TG
1 CTTCAATCTGCC-CATGATTAGGGTAAAAGATTGGATTG
* * * * * *
27742 ATCTTTAATCTACCCTTTAGTTAGGGTAAAAGATTAGATGG
1 --CTTCAATCTGCCCATGA-TTAGGGTAAAAGATTGGATTG
* ** *
27783 TCTTCAATTTGCCTTC-TGATTAGGGTAAAAGATTAAATGG
1 -CTTCAATCTGCC--CATGATTAGGGTAAAAGATTGGATTG
* * **
27823 TCTTCAATCTACCTTC-TGGTTAGATTAAAAGATTGGATTG
1 -CTTCAATCTGCC--CATGATTAGGGTAAAAGATTGGATTG
* * *
27863 CTTCAATCTGTCCTATGGTTAGGGTAAGAGATTGGA-TG
1 CTTCAATCTG-CCCATGATTAGGGTAAAAGATTGGATTG
** * *
27901 ACTTCAATCTGCCTTGTGATTAGGGTAAAAGATTGAACTG
1 -CTTCAATCTGCC-CATGATTAGGGTAAAAGATTGGATTG
* * * ** * * *
27941 CTTCAGTCTACCCCATGGTCGGGGTAAGAGATTTGATGG
1 CTTCAATCT-GCCCATGATTAGGGTAAAAGATTGGATTG
* *
27980 TCTTCAACCTGCCCACTGGTTAGGGTAAAAGATTGGAT
1 -CTTCAATCTGCCCA-TGATTAGGGTAAAAGATTGGAT
28018 GGTCTTCAGT
Statistics
Matches: 1167, Mismatches: 286, Indels: 233
0.69 0.17 0.14
Matches are distributed among these distances:
29 8 0.01
30 5 0.00
31 3 0.00
32 2 0.00
33 2 0.00
35 2 0.00
36 2 0.00
37 19 0.02
38 107 0.09
39 533 0.46
40 418 0.36
41 26 0.02
42 6 0.01
43 4 0.00
46 4 0.00
47 1 0.00
48 2 0.00
49 14 0.01
50 8 0.01
51 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (38 bp):
CTTCAATCTGCCCATGATTAGGGTAAAAGATTGGATTG
Found at i:27089 original size:89 final size:88
Alignment explanation
Indices: 26929--27182 Score: 309
Period size: 89 Copynumber: 3.0 Consensus size: 88
26919 CTTCAATCTG
*
26929 CCCATGGTCGAGGTAAGAGATAGGATGGCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGAAT
1 CCCATGATCGAGGTAAGAGATAGGATGGCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGAAT
26994 TACTTCAATTTACCCTCTGGTTA
66 TACTTCAATTTACCCTCTGGTTA
* *
27017 CCCATGATCGAGGTAAGAGATTGGATGGTCTTCAATCTGCCCT-TTGATTAGGGTAAAAGATTTG
1 CCCATGATCGAGGTAAGAGATAGGATGG-CTTCAATCTGCCCTCTAG-TTAGGGTAAAAGA-TTG
* *
27081 -GTTGCTTC-A---A---TCT-G---
63 AATTACTTCAATTTACCCTCTGGTTA
* * *
27095 CCCATGGTCGAGGTAAGAGATAAGATGGCTTCAATCTGCACTCTAGTTAGGGTAAAAGATTGAAT
1 CCCATGATCGAGGTAAGAGATAGGATGGCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGAAT
*
27160 TACTTCAATTTGCCCTCTGGTTA
66 TACTTCAATTTACCCTCTGGTTA
27183 GGATAAAAGA
Statistics
Matches: 137, Mismatches: 13, Indels: 32
0.75 0.07 0.18
Matches are distributed among these distances:
76 3 0.02
77 32 0.23
78 28 0.20
81 1 0.01
82 3 0.02
84 3 0.02
85 2 0.01
88 29 0.21
89 33 0.24
90 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (88 bp):
CCCATGATCGAGGTAAGAGATAGGATGGCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGAAT
TACTTCAATTTACCCTCTGGTTA
Found at i:27154 original size:166 final size:165
Alignment explanation
Indices: 26863--27182 Score: 586
Period size: 166 Copynumber: 1.9 Consensus size: 165
26853 CTCTAATTAG
*
26863 GGTAAAAGATTGGATTGCTTCAATCTGCCCTTTGATTAGGGTAAAAGATTTGGTTGCTTCAATCT
1 GGTAAAAGATTGGATGGCTTCAATCTGCCCTTTGATTAGGGTAAAAGATTTGGTTGCTTCAATCT
* *
26928 GCCCATGGTCGAGGTAAGAGATAGGATGGCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTGAA
66 GCCCATGGTCGAGGTAAGAGATAAGATGGCTTCAATCTGCACTCTAGTTAGGGTAAAAGATTGAA
26993 TTACTTCAATTTACCCTCTGGTTACCCATGATCGA
131 TTACTTCAATTTACCCTCTGGTTACCCATGATCGA
*
27028 GGTAAGAGATTGGATGGTCTTCAATCTGCCCTTTGATTAGGGTAAAAGATTTGGTTGCTTCAATC
1 GGTAAAAGATTGGATGG-CTTCAATCTGCCCTTTGATTAGGGTAAAAGATTTGGTTGCTTCAATC
27093 TGCCCATGGTCGAGGTAAGAGATAAGATGGCTTCAATCTGCACTCTAGTTAGGGTAAAAGATTGA
65 TGCCCATGGTCGAGGTAAGAGATAAGATGGCTTCAATCTGCACTCTAGTTAGGGTAAAAGATTGA
*
27158 ATTACTTCAATTTGCCCTCTGGTTA
130 ATTACTTCAATTTACCCTCTGGTTA
27183 GGATAAAAGA
Statistics
Matches: 149, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
165 15 0.10
166 134 0.90
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.33
Consensus pattern (165 bp):
GGTAAAAGATTGGATGGCTTCAATCTGCCCTTTGATTAGGGTAAAAGATTTGGTTGCTTCAATCT
GCCCATGGTCGAGGTAAGAGATAAGATGGCTTCAATCTGCACTCTAGTTAGGGTAAAAGATTGAA
TTACTTCAATTTACCCTCTGGTTACCCATGATCGA
Found at i:27168 original size:205 final size:206
Alignment explanation
Indices: 26812--27222 Score: 494
Period size: 205 Copynumber: 2.0 Consensus size: 206
26802 TTCAATCTGT
26812 CCCATGATCAAGGTAAAAGATTGGATGATCTTCAATCTACCCTCTAATTAGGGTAAAAGATTGGA
1 CCCATGATCAAGGTAAAAGATTGGATGATCTTCAATCTACCCTCTAATTAGGGTAAAAGATTGGA
* * ** * * *
26877 TTGCTTCAATCTGCCCTTTGATTAGGGTAAAAGATTTGGTTGCTTCAATCTGCCCATGGTCGAGG
66 TTGCTTCAATCTGCCCTATGATGAGGGTAAAAGATAAGATGGCTTCAATCTGCCCATGGTAGAGG
* * * * *
26942 TAAGAGATAGGATGGCTTCAATCTGCCCTCTAGTTAGGGTAAAAGAT-TGAATTACTTCAATTTA
131 TAAAAGATAGAATGACTTCAATCTGCCCTCTAGTTAGGATAAAAGATCTGAATTACTTCAATCTA
27006 CCCTC-TGGTTA
196 CCC-CATGGTTA
* * * * * *
27017 CCCATGATCGAGGTAAGAGATTGGATGGTCTTCAATCTGCCCTTTGATTAGGGTAAAAGATTTGG
1 CCCATGATCAAGGTAAAAGATTGGATGATCTTCAATCTACCCTCTAATTAGGGTAAAAGA-TTGG
* * *
27082 -TTGCTTCAATCTGCCC-ATGGTCGA-GGTAAGAGATAAGATGGCTTCAATCTGCACTC-TAGTT
65 ATTGCTTCAATCTGCCCTATGAT-GAGGGTAAAAGATAAGATGGCTTCAATCTGC-C-CAT-GGT
* * * *
27143 AG-GGTAAAAGATTGAATTACTTCAATTTGCCCTCTGGTTAGGATAAAAGATCTGAATTACTTCA
126 AGAGGTAAAAGATAGAATGACTTCAATCTGCCCTCTAGTTAGGATAAAAGATCTGAATTACTTCA
27207 ATCTACCCCATGGTTA
191 ATCTACCCCATGGTTA
27223 GGGTAAAAGA
Statistics
Matches: 174, Mismatches: 25, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
204 26 0.15
205 115 0.66
206 33 0.19
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (206 bp):
CCCATGATCAAGGTAAAAGATTGGATGATCTTCAATCTACCCTCTAATTAGGGTAAAAGATTGGA
TTGCTTCAATCTGCCCTATGATGAGGGTAAAAGATAAGATGGCTTCAATCTGCCCATGGTAGAGG
TAAAAGATAGAATGACTTCAATCTGCCCTCTAGTTAGGATAAAAGATCTGAATTACTTCAATCTA
CCCCATGGTTA
Found at i:27430 original size:79 final size:78
Alignment explanation
Indices: 27269--28017 Score: 462
Period size: 79 Copynumber: 9.5 Consensus size: 78
27259 ATGGGGATAA
* * * * * ** *
27269 TCTTTAATCTACCTTTTGGTTATGGTAAAAGATTGGATTGCTTCAATCAGCC-CTA-TGATCGGG
1 TCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATTTGCCTC-ACAG-TCGGG
*
27332 GTAAGAGATCGGATGG
64 GTAAGAGATTGGAT-G
* * * *
27348 TCTTCAATTTTCCCTCTAGTTAGGGTAAAAGATTAGATTGTTTCAATTTGCCTCACAGTCGGGGT
1 TCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATTTGCCTCACAGTCGGGGT
27413 AA-ATGATTGGATAG
66 AAGA-GATTGGAT-G
* * *
27427 TCTTCAATCTACCCTCT-GATTATGGTAAAAAATTGGATTGCTTCAATCTGCC-C-CATGATCGG
1 TCTTCAATCTACCCTCTAG-TTAGGGTAAAAGATTGGATTGCTTCAATTTGCCTCACA-G-TCGG
27489 GGTAAGAGATTGGATGG
63 GGTAAGAGATTGGAT-G
* * * * * * * * * * **
27506 TCTTCAATCTGCCTTTTAGTTAGGGTAAAAGATCGAATGGTTTTCGATCTGCCCTC-TAGTTAGG
1 TCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTGGATTG-CTTCAATTTG-CCTCACAGTCGGG
*
27570 GTAAAAGATCT-GATG
64 GTAAGAGAT-TGGATG
** * * * **
27585 ATCTTCAATCTGTCCTCTGGTTATGGTAAAAGATTGGATTGCTTCAATCTTTCC-CATGGTCGGG
1 -TCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAAT-TTGCCTCACAGTCGGG
*
27649 GTAAGAGATTGAATG
64 GTAAGAGATTGGATG
* * * * * * * * *
27664 ACTTTAATCTACCCTCTGGTTAGGGTAAAAGATTGGACTGCTTCAGTGTACCTCA-TGATTGGGG
1 TCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATTTGCCTCACAG-TCGGGG
27728 TAAGAGATTGGATG
65 TAAGAGATTGGATG
* * * * * * **
27742 ATCTTTAATCTACCCTTTAGTTAGGGTAAAAGATTAGATGGTCTTCAATTTGCCT-TCTGATTAG
1 -TCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTGGATTG-CTTCAATTTGCCTCACAG-TCGG
* **
27806 GGTAAAAGATTAAATGG
63 GGTAAGAGATTGGAT-G
* * ** * ** **
27823 TCTTCAATCTACCTTCTGGTTAGATTAAAAGATTGGATTGCTTCAATCTGTCCT-ATGGTTAGGG
1 TCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATTTG-CCTCACAGTCGGGG
27887 TAAGAGATTGGATG
65 TAAGAGATTGGATG
* * * * * * * * * * **
27901 ACTTCAATCTGCCTTGT-GATTAGGGTAAAAGATTGAACTGCTTCAGTCTACCCCATGGTCGGGG
1 TCTTCAATCTACCCTCTAG-TTAGGGTAAAAGATTGGATTGCTTCAATTTGCCTCACAGTCGGGG
*
27965 TAAGAGATTTGATGG
65 TAAGAGATTGGAT-G
* * * *
27980 TCTTCAACCTGCCCACTGGTTAGGGTAAAAGATTGGAT
1 TCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTGGAT
28018 GGTCTTCAGT
Statistics
Matches: 529, Mismatches: 114, Indels: 54
0.76 0.16 0.08
Matches are distributed among these distances:
77 9 0.02
78 126 0.24
79 263 0.50
80 124 0.23
81 5 0.01
82 2 0.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (78 bp):
TCTTCAATCTACCCTCTAGTTAGGGTAAAAGATTGGATTGCTTCAATTTGCCTCACAGTCGGGGT
AAGAGATTGGATG
Found at i:27730 original size:237 final size:235
Alignment explanation
Indices: 26404--28025 Score: 910
Period size: 237 Copynumber: 6.9 Consensus size: 235
26394 AAGAGATCGA
* * * ** *
26404 ATGGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATCGTATTGCTTCAATCTACCCCATGATCG
1 ATGGTCTTCAATCT-TCCTCTGGTTA-GGTAAAAGATTGGATTGCTTCAATCTTTCCCATGGTCG
* * * * * * * *
26469 GGGTAAGAAATTAGATGACTTCAATCTACCTTTTAATTAGGGTAAAAGATCGGA-TGACTTTAAT
64 GGGTAAGAGATTGGATGACTTCAATCTACCCTCTGATTAGGGTAAAAGATTGGACTG-CTTCAGT
* * * * * * * ** * *
26533 TTGCCTCATGGTCGGGGTAAGAGATTAGATTG-CTTCAATTTG--CTACACGGTCGAGGTAAAAG
128 CTACCCCATGATCGGGGTAAGAGATTGGATGGTCTTCAATCTGCCCTTTA-GTTAG-GGTAAAAG
* * * * *
26595 ATTG-GATGATTTTTAATCTACGCTCTGATTAGGGTAAAAGAT-TGG
191 A-TGAGATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATCT-G
* * * ** * * * *
26640 ATTG-CTTCAATCTGCTCC-ATGATCGGGGTAAGAGATTGGATGGTCTTTAATC-TACCC-TCGG
1 ATGGTCTTCAATCT--TCCTCTGGT-TAGGTAAAAGATTGGATTG-CTTCAATCTTTCCCAT--G
** * * * * ** *
26701 GTTAGGGTAAAAGATTGGATTG-TTTCAATCTGCCCTATGATCGGGGTAAGAGATTGGA-TGACT
60 GTCGGGGTAAGAGATTGGA-TGACTTCAATCTACCCTCTGATTAGGGTAAAAGATTGGACTG-C-
* * * * ** ** * * * * *
26764 TTTAATCTGCCCTC-TAATTAGGACAAAAGATTGGAT--TCTTCAATCTGTCCCATGA-TCAAGG
122 TTCAGTCTACCC-CATGATCGGGGTAAGAGATTGGATGGTCTTCAATCTG-CCCTTTAGTTAGGG
* * *
26825 TAAAAGATTG-GATGATCTTCAATCTACCCTCTAATTAGGGTAAAAGAT-TGG
185 TAAAAGA-TGAGATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATCT-G
* * * * *
26876 ATTG-CTTCAATCTGCCCTTTGATTAGGGTAAAAGATTTGG-TTGCTTCAATC-TGCCCATGGTC
1 ATGGTCTTCAATCT-TCCTCTGGTTA-GGTAAAAGA-TTGGATTGCTTCAATCTTTCCCATGGTC
* * * * * * * *
26938 GAGGTAAGAGATAGGATGGCTTCAATCTGCCCTCT-AGTTAGGGTAAAAGATTGAATTACTTCAA
63 GGGGTAAGAGATTGGATGACTTCAATCTACCCTCTGA-TTAGGGTAAAAGATTGGACTGCTTCAG
* *
27002 TTTACCCTCTGGTTACCCATGATCGAGGTAAGAGATTGGATGGTCTTCAATCTGCCCTTT-GATT
127 TCTA----C------CCCATGATCGGGGTAAGAGATTGGATGGTCTTCAATCTGCCCTTTAG-TT
** * * * * * * **
27066 AGGGTAAAAGATTTGGTTG-CTTCAATCTGCCC-ATG-GTCGAGGTAAGAGATAAG
181 AGGGTAAAAGATGAGATGGTCTTCAATCTGCCCTCTGATTAG-GGTAAAAGATCTG
* * * * * * *
27119 ATGG-CTTCAATCTGCACTCTAGTTAGGGTAAAAGATTGAATTACTTCAAT-TTGCCCTCTGGTT
1 ATGGTCTTCAATCTTC-CTCTGGTTA-GGTAAAAGATTGGATTGCTTCAATCTTTCCC-ATGGTC
* * * * * * * *
27182 AGGATAAAAGATCTGAATTACTTCAATCTACCC-CATGGTTAGGGTAAAAGATTAGATTGCTTCA
63 GGGGTAAGAGAT-TGGATGACTTCAATCTACCCTC-TGATTAGGGTAAAAGATTGGACTGCTTCA
* * * ** * * * * *
27246 ATCTACCTC--GATC-----ATG-G---GGATAATCTTTAATCTACCTTTTGGTTATGGTAAAAG
126 GTCTACCCCATGATCGGGGTAAGAGATTGGATGGTCTTCAATCTGCCCTTTAGTTAGGGTAAAAG
* * * ** * *
27300 ATTG-GATTG-CTTCAATCAGCCCTATGATCGGGGTAAGAGATCGG
191 A-TGAGATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATCTG
* * * * * **
27344 ATGGTCTTCAATTTTCCCTCTAGTTAGGGTAAAAGATTAGATTGTTTCAAT-TTGCCTCACAGTC
1 ATGGTCTTCAATCTT-CCTCTGGTTA-GGTAAAAGATTGGATTGCTTCAATCTTTCC-CATGGTC
* * * *
27408 GGGGTAA-ATGATTGGATAGTCTTCAATCTACCCTCTGATTATGGTAAAAAATTGGATTGCTTCA
63 GGGGTAAGA-GATTGGAT-GACTTCAATCTACCCTCTGATTAGGGTAAAAGATTGGACTGCTTCA
* * *
27472 ATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTCTTCAATCTGCCTTTTAGTTAGGGTAAAAG
126 GTCTACCCCATGATCGGGGTAAGAGATTGGATGGTCTTCAATCTGCCCTTTAGTTAGGGTAAAAG
* *
27537 ATCGA-ATGGTTTTCGATCTGCCCTCT-AGTTAGGGTAAAAGATCTG
191 AT-GAGATGGTCTTCAATCTGCCCTCTGA-TTAGGGTAAAAGATCTG
*
27582 ATGATCTTCAATCTGTCCTCTGGTTATGGTAAAAGATTGGATTGCTTCAATCTTTCCCATGGTCG
1 ATGGTCTTCAATCT-TCCTCTGGTTA-GGTAAAAGATTGGATTGCTTCAATCTTTCCCATGGTCG
* * * *
27647 GGGTAAGAGATTGAATGACTTTAATCTACCCTCTGGTTAGGGTAAAAGATTGGACTGCTTCAGTG
64 GGGTAAGAGATTGGATGACTTCAATCTACCCTCTGATTAGGGTAAAAGATTGGACTGCTTCAGTC
* * * * * *
27712 TACCTCATGATTGGGGTAAGAGATTGGATGATCTTTAATCTACCCTTTAGTTAGGGTAAAAGATT
129 TACCCCATGATCGGGGTAAGAGATTGGATGGTCTTCAATCTGCCCTTTAGTTAGGGTAAAAGATG
* * *
27777 AGATGGTCTTCAATTTGCCTTCTGATTAGGGTAAAAGAT-TAA
194 AGATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATCT-G
* * * * **
27819 ATGGTCTTCAATCTACCTTCTGGTTAGATTAAAAGATTGGATTGCTTCAATCTGTCCTATGGTTA
1 ATGGTCTTCAATCTTCC-TCTGGTTAG-GTAAAAGATTGGATTGCTTCAATCTTTCCCATGGTCG
* * * *
27884 GGGTAAGAGATTGGATGACTTCAATCTGCCTTGTGATTAGGGTAAAAGATTGAACTGCTTCAGTC
64 GGGTAAGAGATTGGATGACTTCAATCTACCCTCTGATTAGGGTAAAAGATTGGACTGCTTCAGTC
* * * ** *
27949 TACCCCATGGTCGGGGTAAGAGATTTGATGGTCTTCAACCTGCCCACTGGTTAGGGTAAAAGATT
129 TACCCCATGATCGGGGTAAGAGATTGGATGGTCTTCAATCTGCCCTTTAGTTAGGGTAAAAGA-T
28014 G-GATGGTCTTCA
193 GAGATGGTCTTCA
28026 GTCAGATTTG
Statistics
Matches: 1077, Mismatches: 231, Indels: 155
0.74 0.16 0.11
Matches are distributed among these distances:
224 46 0.04
225 25 0.02
226 99 0.09
227 4 0.00
228 6 0.01
233 15 0.01
234 46 0.04
235 44 0.04
236 149 0.14
237 370 0.34
238 90 0.08
239 8 0.01
241 1 0.00
242 7 0.01
243 70 0.06
244 30 0.03
245 67 0.06
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (235 bp):
ATGGTCTTCAATCTTCCTCTGGTTAGGTAAAAGATTGGATTGCTTCAATCTTTCCCATGGTCGGG
GTAAGAGATTGGATGACTTCAATCTACCCTCTGATTAGGGTAAAAGATTGGACTGCTTCAGTCTA
CCCCATGATCGGGGTAAGAGATTGGATGGTCTTCAATCTGCCCTTTAGTTAGGGTAAAAGATGAG
ATGGTCTTCAATCTGCCCTCTGATTAGGGTAAAAGATCTG
Found at i:28084 original size:60 final size:60
Alignment explanation
Indices: 27969--28085 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
27959 TCGGGGTAAG
* * * **
27969 AGATTTGATGGTCTTCAACCTGCCCACTGGTTAGGGTAAAAGATTGGATGGTCTTCAGTC
1 AGATTTGATGATCTTCAACCTGCCCACTGATTAGGGTAAAAGATTGAATAATCTTCAGTC
* * **
28029 AGATTTGATGATCTTTAATCTGCCCTTTGATTAGGGTAAAAGATTGAATAATCTTCA
1 AGATTTGATGATCTTCAACCTGCCCACTGATTAGGGTAAAAGATTGAATAATCTTCA
28086 ATCTGTTCTC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.35
Consensus pattern (60 bp):
AGATTTGATGATCTTCAACCTGCCCACTGATTAGGGTAAAAGATTGAATAATCTTCAGTC
Found at i:28089 original size:40 final size:40
Alignment explanation
Indices: 28039--28114 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
28029 AGATTTGATG
* *
28039 ATCTTTAATCTGCCCTTTGATTAGGGTAAAAGATTGAATA
1 ATCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGAATA
**
28079 ATCTTCAATCTGTTCTCTGATTAGGGTAAAAGATTG
1 ATCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTG
28115 GATGATTGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.38
Consensus pattern (40 bp):
ATCTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGAATA
Found at i:29530 original size:22 final size:21
Alignment explanation
Indices: 29505--29561 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
29495 CGTTCTACCC
29505 TTTTTCTTTTTCTTTTCTTCTT
1 TTTTTCTTTTTCTTTTC-TCTT
* *
29527 TTTTCCTTTTCCTTTTCTCTT
1 TTTTTCTTTTTCTTTTCTCTT
29548 TTTCTCTCTTTTTC
1 TTT-T-TCTTTTTC
29562 CCTTTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 7 0.24
22 16 0.55
23 6 0.21
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTCTTTTTCTTTTCTCTT
Found at i:34242 original size:11 final size:11
Alignment explanation
Indices: 34226--34262 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
34216 AATCAGTAAA
34226 GAAATGGAAGG
1 GAAATGGAAGG
34237 GAAATGGAAGG
1 GAAATGGAAGG
34248 GAAATGGAAGG
1 GAAATGGAAGG
34259 GAAA
1 GAAA
34263 AGCTAGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.43, T:0.08
Consensus pattern (11 bp):
GAAATGGAAGG
Found at i:35215 original size:21 final size:21
Alignment explanation
Indices: 35182--35221 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
35172 AAAAAATAAT
* *
35182 TAAATAGACAATATATAAACA
1 TAAATAGAAAATAAATAAACA
*
35203 TAAATATAAAATAAATAAA
1 TAAATAGAAAATAAATAAA
35222 TAACAAAAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (21 bp):
TAAATAGAAAATAAATAAACA
Found at i:36781 original size:17 final size:17
Alignment explanation
Indices: 36756--36791 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
36746 AAAAATGGAC
* *
36756 TTTTGTTTTGTTTTATT
1 TTTTATTTTGGTTTATT
36773 TTTTATTTTGGTTTATT
1 TTTTATTTTGGTTTATT
36790 TT
1 TT
36792 ATCCTTGGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.08, C:0.00, G:0.11, T:0.81
Consensus pattern (17 bp):
TTTTATTTTGGTTTATT
Found at i:37302 original size:45 final size:45
Alignment explanation
Indices: 37221--37662 Score: 533
Period size: 45 Copynumber: 9.9 Consensus size: 45
37211 AAATGATAGT
*
37221 TTCAATCTGCCCCTCTTGATTTAGGGGTAAAAGATTGGATTGTGGC
1 TTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTGGATGGTGGC
*
37267 TTCAATCTGCCCCTCTTAATTAGGGGTAAAAGATTGGATGGTGGC
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGGC
* *
37312 TTCAATTTGCCCCTCTTGATTAGGGGTAAAAGATTGGACGGTGGC
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGGC
* **
37357 TTCAATCTGTCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGAT
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGGC
* *
37402 TTTAATCTGCCCCTCTTGATTAGGGGTAAAAGATT-G-TGCGATGGT
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATG-G-TGGC
* *
37447 TTCAATCTGTCCCTCTTGATTAGGGGTAAAAGATTGAAT-G-GGC
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGGC
* * * **
37490 TTTAATTTACCCCTCTTGA-TAGGGGTAAAAGATTATATGGT--C
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGGC
* * * * *
37532 TTCAATTTGCCCTTCTTGACTTAAGGGTAAAATATTGGATGGTGAC
1 TTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTGGATGGTGGC
* * * *
37578 TTCAATTTGTCCCTCTTGATTAAGGGTAAAAGATTGAATGGT--C
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGGC
* *
37621 TTTAATCTCCCCCTCTTGACTTAGGGGTAAAAGATTGGATGG
1 TTCAATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTGGATGG
37663 GATGATGTAA
Statistics
Matches: 345, Mismatches: 40, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
42 34 0.10
43 36 0.10
44 40 0.12
45 198 0.57
46 36 0.10
47 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.35
Consensus pattern (45 bp):
TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGGC
Found at i:40438 original size:21 final size:22
Alignment explanation
Indices: 40414--40459 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
40404 TCGTAAGGTG
*
40414 TGAA-TAAAAATGTTTATCAAA
1 TGAATTAAAAATATTTATCAAA
* *
40435 TGAATTTAAAATATTTGTCAAA
1 TGAATTAAAAATATTTATCAAA
40457 TGA
1 TGA
40460 GACAGAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (22 bp):
TGAATTAAAAATATTTATCAAA
Found at i:44197 original size:17 final size:16
Alignment explanation
Indices: 44137--44197 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 16
44127 TAGGCAATAT
44137 ATAAAAATAAATATAAA
1 ATAAAAA-AAATATAAA
44154 ATAAATAAATAATA-AAA
1 ATAAA-AAA-AATATAAA
* *
44171 GTAAATAAAATATTAAA
1 ATAAAAAAAATA-TAAA
44188 ATAAAAAAAA
1 ATAAAAAAAA
44198 CAGAATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
15 4 0.11
16 2 0.06
17 24 0.67
18 6 0.17
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (16 bp):
ATAAAAAAAATATAAA
Found at i:44362 original size:24 final size:25
Alignment explanation
Indices: 44312--44363 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
44302 GATTTAAAAG
* *
44312 AAACAAAAATTTCAAGGTTAAATTA
1 AAACAAAAAATTCAAGGTTAAAGTA
* *
44337 AAACAAAAAATT-AAGTTTTAAGTA
1 AAACAAAAAATTCAAGGTTAAAGTA
44361 AAA
1 AAA
44364 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.27
Consensus pattern (25 bp):
AAACAAAAAATTCAAGGTTAAAGTA
Found at i:45950 original size:26 final size:26
Alignment explanation
Indices: 45873--45968 Score: 113
Period size: 26 Copynumber: 3.5 Consensus size: 26
45863 CGCTTGTGAC
45873 ATATTCAGGTGCTTGGGATGAATATG
1 ATATTCAGGTGCTTGGGATGAATATG
* **
45899 ATATGAT-ATGATTATTATGGGATGAATATG
1 ATAT--TCA-G-GTGCT-TGGGATGAATATG
45929 ATATTCAGGTGCTTGGGATGAATATG
1 ATATTCAGGTGCTTGGGATGAATATG
45955 ATATTCAGGTGCTT
1 ATATTCAGGTGCTT
45969 TATTCAATCA
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
26 31 0.53
27 3 0.05
28 4 0.07
29 3 0.05
30 17 0.29
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.38
Consensus pattern (26 bp):
ATATTCAGGTGCTTGGGATGAATATG
Found at i:49577 original size:24 final size:24
Alignment explanation
Indices: 49550--49600 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
49540 TTTCTAGAAG
*
49550 ATTTAATAGTATAATATATTTAGC
1 ATTTAATAGCATAATATATTTAGC
* *
49574 ATTTATTAGCATAATATATTTTGC
1 ATTTAATAGCATAATATATTTAGC
49598 ATT
1 ATT
49601 GATTAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (24 bp):
ATTTAATAGCATAATATATTTAGC
Found at i:49605 original size:24 final size:24
Alignment explanation
Indices: 49560--49605 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
49550 ATTTAATAGT
*
49560 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATTGATTAGC
*
49584 ATAATATATTTTGCATTGATTA
1 ATAATATATTTAGCATTGATTA
49606 AAATTAGGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (24 bp):
ATAATATATTTAGCATTGATTAGC
Done.