Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001220.1 Kokia drynarioides strain JFW-HI SEQ_112574, 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: 87690
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1725 original size:39 final size:39
Alignment explanation
Indices: 1679--1777 Score: 164
Period size: 39 Copynumber: 2.5 Consensus size: 39
1669 TTAAATAGGG
*
1679 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAATTGT
1718 TTTTAATGTGTCTTAGTTTGATACATATTTAATAATTGT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAATTGT
*
1757 TTTTAAAGTGTC-TACGTTTGA
1 TTTTAATGTGTCTTA-GTTTGA
1778 GACAAATTAA
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
38 2 0.04
39 55 0.96
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.53
Consensus pattern (39 bp):
TTTTAATGTGTCTTAGTTTGATACATATTTAATAATTGT
Found at i:1866 original size:32 final size:32
Alignment explanation
Indices: 1830--1917 Score: 131
Period size: 32 Copynumber: 2.8 Consensus size: 32
1820 ATTAATTAGT
1830 TGATTAATGTGTTTCAGGTACATGCAACTAGC
1 TGATTAATGTGTTTCAGGTACATGCAACTAGC
* *
1862 TGATTAATGTGTTTCAGGTACATGCAATTAGT
1 TGATTAATGTGTTTCAGGTACATGCAACTAGC
* * *
1894 TGATTAATATATTTTAGGTACATG
1 TGATTAATGTGTTTCAGGTACATG
1918 TATGGATAGC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (32 bp):
TGATTAATGTGTTTCAGGTACATGCAACTAGC
Found at i:5571 original size:31 final size:32
Alignment explanation
Indices: 5500--5625 Score: 200
Period size: 32 Copynumber: 4.0 Consensus size: 32
5490 AGCCGAAATT
*
5500 AATTAGCTGATTAATGTGTTTCAAGTACATGC
1 AATTAGCTGATTAATGTGTTTCAGGTACATGC
*
5532 AATTAGCTGATTAATGTGTTTTAGGTACATGC
1 AATTAGCTGATTAATGTGTTTCAGGTACATGC
5564 -ATTAGCTGATTAATGTGTTTCAGGTACATGC
1 AATTAGCTGATTAATGTGTTTCAGGTACATGC
* * *
5595 AATTAGCTGATTAATATATTTTAGGTACATG
1 AATTAGCTGATTAATGTGTTTCAGGTACATG
5626 TATGGATAGC
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 30 0.34
32 57 0.66
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (32 bp):
AATTAGCTGATTAATGTGTTTCAGGTACATGC
Found at i:5578 original size:63 final size:63
Alignment explanation
Indices: 5501--5625 Score: 223
Period size: 63 Copynumber: 2.0 Consensus size: 63
5491 GCCGAAATTA
* *
5501 ATTAGCTGATTAATGTGTTTCAAGTACATGCAATTAGCTGATTAATGTGTTTTAGGTACATGC
1 ATTAGCTGATTAATGTGTTTCAAGTACATGCAATTAGCTGATTAATATATTTTAGGTACATGC
*
5564 ATTAGCTGATTAATGTGTTTCAGGTACATGCAATTAGCTGATTAATATATTTTAGGTACATG
1 ATTAGCTGATTAATGTGTTTCAAGTACATGCAATTAGCTGATTAATATATTTTAGGTACATG
5626 TATGGATAGC
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (63 bp):
ATTAGCTGATTAATGTGTTTCAAGTACATGCAATTAGCTGATTAATATATTTTAGGTACATGC
Found at i:7279 original size:18 final size:18
Alignment explanation
Indices: 7256--7290 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7246 TAAGAAAGTA
*
7256 AGTTGTGTTAGTGAAAAT
1 AGTTGTATTAGTGAAAAT
*
7274 AGTTGTATTAGTTAAAA
1 AGTTGTATTAGTGAAAA
7291 AAATTTATGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (18 bp):
AGTTGTATTAGTGAAAAT
Found at i:7453 original size:18 final size:18
Alignment explanation
Indices: 7430--7468 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
7420 TAATAACGGT
7430 AAAATA-GTAACTTAAATA
1 AAAATAGGTAA-TTAAATA
7448 AAAATAGGTAATTAAATA
1 AAAATAGGTAATTAAATA
7466 AAA
1 AAA
7469 CATGATGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.26
Consensus pattern (18 bp):
AAAATAGGTAATTAAATA
Found at i:16083 original size:71 final size:71
Alignment explanation
Indices: 15965--16115 Score: 268
Period size: 71 Copynumber: 2.1 Consensus size: 71
15955 CATCTCTTGG
* *
15965 TTCTACTGATACAACCAAGACTTCTATCAGTAGAAAAAACTCTAGAGAGCAAAGAAGTTGTGGCT
1 TTCTACCGATACAACCAAGACTTCTATCAGTAGAAAAAACTCCAGAGAGCAAAGAAGTTGTGGCT
16030 TGGGAC
66 TGGGAC
16036 TTCTACCGATACAACCAAGACTTCTATC-GATAGAAAAAACTCCAGAGAGCAAAGAAGTTGTGGC
1 TTCTACCGATACAACCAAGACTTCTATCAG-TAGAAAAAACTCCAGAGAGCAAAGAAGTTGTGGC
16100 TTGGGAC
65 TTGGGAC
16107 TTCTACCGA
1 TTCTACCGA
16116 AACTTGGAAG
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
70 1 0.01
71 76 0.99
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (71 bp):
TTCTACCGATACAACCAAGACTTCTATCAGTAGAAAAAACTCCAGAGAGCAAAGAAGTTGTGGCT
TGGGAC
Found at i:18012 original size:29 final size:29
Alignment explanation
Indices: 17974--18034 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
17964 GATTGTCCAC
17974 AATTGAAGAAGAAAGGGGCATTAAAACAA
1 AATTGAAGAAGAAAGGGGCATTAAAACAA
18003 AATTGAAGAAGAAAGGGGCATTAAAACAA
1 AATTGAAGAAGAAAGGGGCATTAAAACAA
18032 AAT
1 AAT
18035 GATGGCAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.56, C:0.07, G:0.23, T:0.15
Consensus pattern (29 bp):
AATTGAAGAAGAAAGGGGCATTAAAACAA
Found at i:22617 original size:22 final size:22
Alignment explanation
Indices: 22570--22622 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
22560 TGTATATTGT
*
22570 TTTATATATATACAATATTATA
1 TTTACATATATACAATATTATA
* *
22592 --TACATATATACTATTTTATA
1 TTTACATATATACAATATTATA
22612 TTTACATATAT
1 TTTACATATAT
22623 TGTTTTTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 17 0.65
22 9 0.35
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTACATATATACAATATTATA
Found at i:24590 original size:71 final size:71
Alignment explanation
Indices: 24428--24566 Score: 208
Period size: 71 Copynumber: 2.0 Consensus size: 71
24418 GGTTCTACCG
*
24428 ATACAACCAAGACTTCTATCAGTAGAACAAACTCCAAAAAGCAAAGAAGTTGTGGCTTGGGAATT
1 ATACAACCAAGACTTCTATCGGTAGAACAAACTCCAAAAAGCAAAGAAGTTGTGGCTTGGGAATT
24493 CTACAA
66 CTACAA
* * * * *
24499 ATACAACCAAGACTTATATCGGTAGAACAAACTCCAGAGAGCAAATAAGTTGTGG-TCTGGGACT
1 ATACAACCAAGACTTCTATCGGTAGAACAAACTCCAAAAAGCAAAGAAGTTGTGGCT-TGGGAAT
24563 TCTA
65 TCTA
24567 TCGATACTTG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 1 0.02
71 60 0.98
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (71 bp):
ATACAACCAAGACTTCTATCGGTAGAACAAACTCCAAAAAGCAAAGAAGTTGTGGCTTGGGAATT
CTACAA
Found at i:26319 original size:22 final size:22
Alignment explanation
Indices: 26292--26334 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
26282 CAAAGAAAAA
*
26292 AATT-AACCCAATTTATATAATT
1 AATTAAACCCAAATTAT-TAATT
26314 AATTAAACCCAAATTATTAAT
1 AATTAAACCCAAATTATTAAT
26335 GAAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (22 bp):
AATTAAACCCAAATTATTAATT
Found at i:26735 original size:42 final size:42
Alignment explanation
Indices: 26676--26759 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
26666 CAACAAAAGG
26676 TCTTGCTAAGGCAAAATTACTAGATGTGTAAGCAGCATCAAT
1 TCTTGCTAAGGCAAAATTACTAGATGTGTAAGCAGCATCAAT
*
26718 TCTTGCTAAGGCAAAATTGCTAGATGTGTAAGCAGCATCAAT
1 TCTTGCTAAGGCAAAATTACTAGATGTGTAAGCAGCATCAAT
26760 CTTTATCTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.29
Consensus pattern (42 bp):
TCTTGCTAAGGCAAAATTACTAGATGTGTAAGCAGCATCAAT
Found at i:30029 original size:116 final size:116
Alignment explanation
Indices: 29895--30125 Score: 444
Period size: 116 Copynumber: 2.0 Consensus size: 116
29885 ATTTACAGAC
*
29895 TTACACAAAAAAATTTGATTAGTACTTGGGCAAAATTTGACCCCCTTTATTAACATAACAATTAA
1 TTACACAAAAAAAATTGATTAGTACTTGGGCAAAATTTGACCCCCTTTATTAACATAACAATTAA
29960 AATTAAAATTTAAACAACAAATAATGAAACTTAAAAATTTTAAACTCAATA
66 AATTAAAATTTAAACAACAAATAATGAAACTTAAAAATTTTAAACTCAATA
30011 TTACACAAAAAAAATTGATTAGTACTTGGGCAAAATTTGACCCCCTTTATTAACATAACAATTAA
1 TTACACAAAAAAAATTGATTAGTACTTGGGCAAAATTTGACCCCCTTTATTAACATAACAATTAA
*
30076 AATTAAAATTTAAACAACAAATAATGAAACTTAAAAATTTTTAACTCAAT
66 AATTAAAATTTAAACAACAAATAATGAAACTTAAAAATTTTAAACTCAAT
30126 TAGAAAATTT
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 113 1.00
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (116 bp):
TTACACAAAAAAAATTGATTAGTACTTGGGCAAAATTTGACCCCCTTTATTAACATAACAATTAA
AATTAAAATTTAAACAACAAATAATGAAACTTAAAAATTTTAAACTCAATA
Found at i:40485 original size:29 final size:30
Alignment explanation
Indices: 40435--40495 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
40425 ATGTGTAATG
40435 TTATACATAAACTTTGATTTTG-TACAATT
1 TTATACATAAACTTTGATTTTGATACAATT
* * *
40464 TTATACATTAAATTTTTA-TTTGATTCAATT
1 TTATACA-TAAACTTTGATTTTGATACAATT
40494 TT
1 TT
40496 TAGAAATCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (30 bp):
TTATACATAAACTTTGATTTTGATACAATT
Found at i:41250 original size:6 final size:6
Alignment explanation
Indices: 41202--41246 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
41192 GTCGTTTCTT
* *
41202 TCATCC TCATCC TCATCC TCATCC TCATCC TCACCC TCACCC TCA
1 TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC TCA
41247 CCCTGGCTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.18, C:0.53, G:0.00, T:0.29
Consensus pattern (6 bp):
TCATCC
Found at i:45961 original size:2 final size:2
Alignment explanation
Indices: 45954--45980 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45944 TAAAATAGAA
45954 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 A
45981 AACTGCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46498 original size:16 final size:17
Alignment explanation
Indices: 46480--46533 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 17
46470 TATAGATTAT
46480 AAATAAATATAAATAT-
1 AAATAAATATAAATATA
*
46496 AAAT--ATATTAATATTA
1 AAATAAATATAAATA-TA
46512 AAATAAA-ATAAA-ATA
1 AAATAAATATAAATATA
46527 AAATAAA
1 AAATAAA
46534 AATTTATCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.25
15 10 0.31
16 9 0.28
17 4 0.12
18 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATAAATATAAATATA
Found at i:46520 original size:5 final size:5
Alignment explanation
Indices: 46510--46534 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
46500 ATATTAATAT
46510 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
46535 ATTTATCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:53806 original size:17 final size:18
Alignment explanation
Indices: 53771--53808 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
53761 ATATATTAGA
*
53771 TTTTTAAAAAAATATAAT
1 TTTTTAAAAAAACATAAT
*
53789 TTTTTAAAAATACA-AAT
1 TTTTTAAAAAAACATAAT
53806 TTT
1 TTT
53809 ATAATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTTTAAAAAAACATAAT
Found at i:53835 original size:19 final size:19
Alignment explanation
Indices: 53811--53869 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
53801 CAAATTTTAT
53811 AATTTTTATAAA-TATTTTG
1 AATTTTTA-AAATTATTTTG
* *
53830 AATTTTGAAAATTATTTTC
1 AATTTTTAAAATTATTTTG
53849 AATTTTTGAAAATTATTTTG
1 AATTTTT-AAAATTATTTTG
53869 A
1 A
53870 TTATTTTGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 3 0.09
19 19 0.56
20 12 0.35
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (19 bp):
AATTTTTAAAATTATTTTG
Found at i:53857 original size:20 final size:20
Alignment explanation
Indices: 53811--53867 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
53801 CAAATTTTAT
*
53811 AATTTTT-ATAAA-TATTTTG
1 AATTTTTGA-AAATTATTTTC
53830 AA-TTTTGAAAATTATTTTC
1 AATTTTTGAAAATTATTTTC
53849 AATTTTTGAAAATTATTTT
1 AATTTTTGAAAATTATTTT
53868 GATTATTTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 7 0.21
19 11 0.32
20 16 0.47
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (20 bp):
AATTTTTGAAAATTATTTTC
Found at i:57322 original size:49 final size:53
Alignment explanation
Indices: 57182--57322 Score: 127
Period size: 55 Copynumber: 2.7 Consensus size: 53
57172 CATTTTTCTC
* * * *
57182 TAATTAATTTAAA-TTAATTAA-GAGATAAATAATAAATTTTTATATTATCAT
1 TAATTAAATTAAAGTAAATTAATTAGATAAATAATAAATTATTATATTATCAT
* * *
57233 TAATTAAATTAAATTAAATTAATTA-AGTGATAATATTAAATTATTATTTTAT-ATT
1 TAATTAAATTAAAGTAAATTAATTAGA-T-A-AATAATAAATTATTATATTATCA-T
57288 TAATT-AATTAAAGT-AA-T-ATTAGATAAATAATAAAT
1 TAATTAAATTAAAGTAAATTAATTAGATAAATAATAAAT
57323 AAAAAAGATT
Statistics
Matches: 75, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
49 9 0.12
50 1 0.01
51 17 0.23
52 10 0.13
53 4 0.05
54 10 0.13
55 24 0.32
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (53 bp):
TAATTAAATTAAAGTAAATTAATTAGATAAATAATAAATTATTATATTATCAT
Found at i:58565 original size:59 final size:60
Alignment explanation
Indices: 58501--58617 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 60
58491 AACTTAATCA
* * *
58501 TATTAAATTAATATAATACTTATC-AATATAAATATTAGATTAAATTTAATATTAAATAT
1 TATTAAATTAATAGAATACTTATCTAAGATAAATATTAAATTAAATTTAATATTAAATAT
* *
58560 TATTAAATTAATAGGATATTTATCTATAAGATAAATATTAAATTAAATTTAATATTAA
1 TATTAAATTAATAGAATACTTATC--TAAGATAAATATTAAATTAAATTTAATATTAA
58618 GATAATCACT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 21 0.42
62 29 0.58
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (60 bp):
TATTAAATTAATAGAATACTTATCTAAGATAAATATTAAATTAAATTTAATATTAAATAT
Found at i:58643 original size:20 final size:18
Alignment explanation
Indices: 58593--58644 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
58583 CTATAAGATA
58593 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
58610 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
58630 AATATTAAATTAATA
1 AATATTAAATTAATA
58645 AAATACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:66596 original size:15 final size:15
Alignment explanation
Indices: 66576--66605 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
66566 ATAGCTTCTT
66576 TTCTCATGGAATTAA
1 TTCTCATGGAATTAA
66591 TTCTCATGGAATTAA
1 TTCTCATGGAATTAA
66606 GCTTTCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
TTCTCATGGAATTAA
Found at i:68633 original size:37 final size:37
Alignment explanation
Indices: 68561--68725 Score: 155
Period size: 37 Copynumber: 4.6 Consensus size: 37
68551 CTTTTTGATT
* * * * **
68561 CACCGGTACAAAGCTTACTAGGCACACAGTTTGAATA
1 CACCGGCACAAAGCCTACTAGACACATAGCCTGAATA
* * *
68598 CATCGGCATAAAGCCTACTAGACACATAACCTGAATA
1 CACCGGCACAAAGCCTACTAGACACATAGCCTGAATA
** * *
68635 CACCTACACAAAGCCTACTAGGCA-ATAGCCCGAA-A
1 CACCGGCACAAAGCCTACTAGACACATAGCCTGAATA
*
68670 -A----CACAAAGCCTACGAGACACATAGCCTGAATA
1 CACCGGCACAAAGCCTACTAGACACATAGCCTGAATA
68702 CACCGGCACAAAGCCTACTAGACA
1 CACCGGCACAAAGCCTACTAGACA
68726 TGTAGCCCGA
Statistics
Matches: 101, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
30 16 0.16
31 9 0.09
32 1 0.01
33 1 0.01
34 1 0.01
35 1 0.01
36 8 0.08
37 64 0.63
ACGTcount: A:0.39, C:0.30, G:0.16, T:0.15
Consensus pattern (37 bp):
CACCGGCACAAAGCCTACTAGACACATAGCCTGAATA
Found at i:68715 original size:67 final size:68
Alignment explanation
Indices: 68607--68740 Score: 207
Period size: 67 Copynumber: 2.0 Consensus size: 68
68597 ACATCGGCAT
* * *
68607 AAAGCCTACTAGACACATAACCTGAATACACCTACACAAAGCCTACTAGGCA-ATAGCCCGAAAA
1 AAAGCCTACGAGACACATAACCTGAATACACCGACACAAAGCCTACTAGACATATAGCCCGAAAA
68671 CAC
66 CAC
* * *
68674 AAAGCCTACGAGACACATAGCCTGAATACACCGGCACAAAGCCTACTAGACATGTAGCCCGAAAA
1 AAAGCCTACGAGACACATAACCTGAATACACCGACACAAAGCCTACTAGACATATAGCCCGAAAA
68739 CA
66 CA
68741 TTAGCAAAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
67 47 0.78
68 13 0.22
ACGTcount: A:0.42, C:0.31, G:0.15, T:0.13
Consensus pattern (68 bp):
AAAGCCTACGAGACACATAACCTGAATACACCGACACAAAGCCTACTAGACATATAGCCCGAAAA
CAC
Found at i:68732 original size:37 final size:37
Alignment explanation
Indices: 68607--68758 Score: 124
Period size: 37 Copynumber: 4.3 Consensus size: 37
68597 ACATCGGCAT
* * *
68607 AAAGCCTACTAGACACATAACCTGAATACACCTA-CAC
1 AAAGCCTACTAGACACATAGCCCGAAAACACC-AGCAC
*
68644 AAAGCCTACTAGGCA-ATAGCCCG--AA-A--A-CAC
1 AAAGCCTACTAGACACATAGCCCGAAAACACCAGCAC
* * * *
68674 AAAGCCTACGAGACACATAGCCTGAATACACCGGCAC
1 AAAGCCTACTAGACACATAGCCCGAAAACACCAGCAC
** **
68711 AAAGCCTACTAGACATGTAGCCCGAAAACATTAGCA-
1 AAAGCCTACTAGACACATAGCCCGAAAACACCAGCAC
68747 AAAGCCTACTAG
1 AAAGCCTACTAG
68759 TTACAAAGTC
Statistics
Matches: 91, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
30 17 0.19
31 7 0.08
33 2 0.02
34 2 0.02
36 18 0.20
37 45 0.49
ACGTcount: A:0.41, C:0.30, G:0.15, T:0.14
Consensus pattern (37 bp):
AAAGCCTACTAGACACATAGCCCGAAAACACCAGCAC
Found at i:69927 original size:31 final size:31
Alignment explanation
Indices: 69889--69951 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
69879 ATACGACCTT
69889 ATATGCATAATTTTAATAATAAAATTAACTC
1 ATATGCATAATTTTAATAATAAAATTAACTC
69920 ATATGCATAATTTTAATAATAAAATTAACTC
1 ATATGCATAATTTTAATAATAAAATTAACTC
69951 A
1 A
69952 CTAAATGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.38
Consensus pattern (31 bp):
ATATGCATAATTTTAATAATAAAATTAACTC
Found at i:70476 original size:5 final size:5
Alignment explanation
Indices: 70468--70497 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
70458 AATTTGAATG
70468 AAATC AAATC AAATC AAATC AAATC AAATC
1 AAATC AAATC AAATC AAATC AAATC AAATC
70498 GATTTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATC
Found at i:82543 original size:20 final size:19
Alignment explanation
Indices: 82503--82544 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
82493 TGTTTTATAA
*
82503 TTAACTTAATTAACCTTAC
1 TTAACTTAATTAACATTAC
82522 TTAAGCTTAATTAA-ATTCAC
1 TTAA-CTTAATTAACATT-AC
82542 TTA
1 TTA
82545 TTACATCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.38, C:0.17, G:0.02, T:0.43
Consensus pattern (19 bp):
TTAACTTAATTAACATTAC
Done.