Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013271.1 Kokia drynarioides strain JFW-HI SEQ_128292, 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: 132133
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 73 characters in sequence are not A, C, G, or T
Found at i:803 original size:3 final size:3
Alignment explanation
Indices: 797--830 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
787 AATTTATTTA
797 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
831 TATAGTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4716 original size:17 final size:18
Alignment explanation
Indices: 4684--4719 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
4674 AATGTTGTTA
*
4684 TAATATATATTTTAATAT
1 TAATATATATTATAATAT
4702 TAATAT-TATTATAATAT
1 TAATATATATTATAATAT
4719 T
1 T
4720 TAATTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATATATATTATAATAT
Found at i:26890 original size:138 final size:138
Alignment explanation
Indices: 26642--26892 Score: 301
Period size: 138 Copynumber: 1.8 Consensus size: 138
26632 CGCTGAAAGT
*
26642 GCCCTTTCCTTTTCGACTTCTGTTTCTAATGAATCGATCTTTGCAGACATCATTCGAGCTTCTAC
1 GCCCTTTCCTTTTCGACTTCTGTTTCTAATGAATCGATCTTTGCAGACATCATTCGAGCATCTAC
* * *
26707 TTCGATGCTAATGAGTTTAGACTCCAACATTTTTTTTGATTCATTTGCATTAACTGAAACCTCAG
66 TTCCATGCTAATGAGTTGAGACTCCAACATTTTCTTTGATTCATTTGCATTAACTGAAACCTCAG
26772 CAGATAAG
131 CAGATAAG
* * * * ** *
26780 GCCCTTTCCTTTTCGATTTCTTTTTCTAATGATTCTATCTTTG-ATGACATTGTCTCTA-CATCT
1 GCCCTTTCCTTTTCGACTTCTGTTTCTAATGAATCGATCTTTGCA-GACATCAT-TCGAGCATCT
* * ** * *
26843 GCTTCCATGTTCCTGAGTTGAGACT-CAAGATTTTGCTTTGCTTCATTTGC
64 ACTTCCATGCTAATGAGTTGAGACTCCAACATTTT-CTTTGATTCATTTGC
26893 CATGCCGAGC
Statistics
Matches: 93, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
137 9 0.10
138 81 0.87
139 3 0.03
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (138 bp):
GCCCTTTCCTTTTCGACTTCTGTTTCTAATGAATCGATCTTTGCAGACATCATTCGAGCATCTAC
TTCCATGCTAATGAGTTGAGACTCCAACATTTTCTTTGATTCATTTGCATTAACTGAAACCTCAG
CAGATAAG
Found at i:37742 original size:31 final size:29
Alignment explanation
Indices: 37588--37805 Score: 125
Period size: 30 Copynumber: 7.4 Consensus size: 29
37578 TAAAAGGGTA
* * *
37588 ATTTTTGAAAGTTTTTGGGTCAAAA-TGG
1 ATTTTTGGAAGTTTTGGGGTTAAAATTGG
* * *
37616 AATTTTGGAAG-TTTGAGGG-TAAAATAGTA
1 ATTTTTGGAAGTTTTG-GGGTTAAAATTG-G
* * *
37645 ATTTTT-GAGAGTTTCGAGGTCAAAA-TGG
1 ATTTTTGGA-AGTTTTGGGGTTAAAATTGG
*
37673 AATTTTT-GAAGTTTCGAGGG-TAAAA-TGG
1 -ATTTTTGGAAGTTTTG-GGGTTAAAATTGG
37701 TAATTTTTGGAAGTTTTGGGGTTAAAATTAGG
1 --ATTTTTGGAAGTTTTGGGGTTAAAATT-GG
37733 ATTTTTTGGAAG-TTTGAGGG-TAAAA-TGG
1 A-TTTTTGGAAGTTTTG-GGGTTAAAATTGG
* * *
37761 TAATTTTTAGAAGTTTCGGGGTTAAAATCGGG
1 --ATTTTTGGAAGTTTTGGGGTTAAAAT-TGG
37793 ATTTTTGGAAGTT
1 ATTTTTGGAAGTT
37806 CGAGGGTAAA
Statistics
Matches: 150, Mismatches: 19, Indels: 40
0.72 0.09 0.19
Matches are distributed among these distances:
27 7 0.05
28 31 0.21
29 43 0.29
30 51 0.34
31 14 0.09
32 4 0.03
ACGTcount: A:0.30, C:0.03, G:0.28, T:0.39
Consensus pattern (29 bp):
ATTTTTGGAAGTTTTGGGGTTAAAATTGG
Found at i:37834 original size:59 final size:58
Alignment explanation
Indices: 37551--37877 Score: 331
Period size: 59 Copynumber: 5.6 Consensus size: 58
37541 ATCGGGATTA
* * * * **
37551 AAAATAGAATTTTTAGACA-TTCGGGGGTAAAAGGGTAATTTTTGAAAGTTTTTGGGTC
1 AAAATAGGATTTTTGGA-AGTTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTC
* * * * *
37609 AAAAT-GGAATTTTGGAAGTTTGAGGGTAAAATAGTAATTTTTGAGAGTTTCGAGGTC
1 AAAATAGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTC
* * *
37666 AAAAT-GGAATTTTT-GAAGTTTCGAGGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTT
1 AAAATAGG-ATTTTTGGAAG-TTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTC
* *
37724 AAAATTAGGATTTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTT-AGAAGTTTCGGGGTT
1 AAAA-TAGGA-TTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGA-AAGTTTCGGGGTC
* ** *
37784 AAAATCGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTCAAAAGTTTCGAGGTC
1 AAAAT-AGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTC
* **
37843 AAAATCAAGATTTTTAAAAGTTCGAGGGTCAAAAT
1 AAAAT-AGGATTTTTGGAAGTTCGAGGGT-AAAAT
37878 ATAATTTCTG
Statistics
Matches: 227, Mismatches: 31, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
56 1 0.00
57 50 0.22
58 46 0.20
59 71 0.31
60 55 0.24
61 4 0.02
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.36
Consensus pattern (58 bp):
AAAATAGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGAAAGTTTCGGGGTC
Found at i:37847 original size:30 final size:30
Alignment explanation
Indices: 37570--37840 Score: 255
Period size: 29 Copynumber: 9.2 Consensus size: 30
37560 TTTTTAGACA
* * *
37570 TTCGGGGGTAAAAGGGTAATTTTTGAAAGT
1 TTCGAGGGTAAAATGGTAATTTTTGGAAGT
**
37600 TT-TTGGGTCAAAATGG-AA-TTTTGGAAGT
1 TTCGAGGGT-AAAATGGTAATTTTTGGAAGT
*
37628 TT-GAGGGTAAAATAGTAATTTTT-GAGAGT
1 TTCGAGGGTAAAATGGTAATTTTTGGA-AGT
37657 TTCGA-GGTCAAAATGG-AATTTTT-GAAGT
1 TTCGAGGGT-AAAATGGTAATTTTTGGAAGT
37685 TTCGAGGGTAAAATGGTAATTTTTGGAAGT
1 TTCGAGGGTAAAATGGTAATTTTTGGAAGT
* *
37715 TTTG-GGGTTAAAATTAGG-ATTTTTTGGAAGT
1 TTCGAGGG-TAAAA-T-GGTAATTTTTGGAAGT
*
37746 TT-GAGGGTAAAATGGTAATTTTTAGAAGT
1 TTCGAGGGTAAAATGGTAATTTTTGGAAGT
*
37775 TTCG-GGGTTAAAATCGG-GATTTTTGGAAG-
1 TTCGAGGG-TAAAAT-GGTAATTTTTGGAAGT
***
37804 TTCGAGGGTAAAATGGTAATTTTCAAAAGT
1 TTCGAGGGTAAAATGGTAATTTTTGGAAGT
37834 TTCGAGG
1 TTCGAGG
37841 TCAAAATCAA
Statistics
Matches: 203, Mismatches: 18, Indels: 40
0.78 0.07 0.15
Matches are distributed among these distances:
27 6 0.03
28 38 0.19
29 75 0.37
30 62 0.31
31 20 0.10
32 2 0.01
ACGTcount: A:0.30, C:0.04, G:0.29, T:0.37
Consensus pattern (30 bp):
TTCGAGGGTAAAATGGTAATTTTTGGAAGT
Found at i:45880 original size:81 final size:81
Alignment explanation
Indices: 45667--45904 Score: 304
Period size: 81 Copynumber: 3.0 Consensus size: 81
45657 CCATCAACCA
* * *
45667 AATCCGTCAATTCATGGCACCCGGTGCCTAGCGGATAAAACGCAATAAGTGAGCCCAGCTCTAGT
1 AATCCGTCAATTCATGGCACCCAGTGCCTAGCGGATAAAACGC-AGAAGTGAGCCCAGCTCTAAT
45732 TGGATTAACCAACGAAT
65 TGGATTAACCAACGAAT
* *
45749 --TCTGTCAATTCATGGCACCCAGTGCCTAGCGGATAAATA-GCAGAAGTGAGCCCGGCTCTAAT
1 AATCCGTCAATTCATGGCACCCAGTGCCTAGCGGATAAA-ACGCAGAAGTGAGCCCAGCTCTAAT
45811 TGGATTAACCAACGAAT
65 TGGATTAACCAACGAAT
* * * * * **
45828 AATCCGTCAAATCCTGGCACCCAGTGCCTAGCGGTTAAACCGC-GAAAGTGAGCCCAACTCTGGT
1 AATCCGTCAATTCATGGCACCCAGTGCCTAGCGGATAAAACGCAG-AAGTGAGCCCAGCTCTAAT
*
45892 TGGTTTAACCAAC
65 TGGATTAACCAAC
45905 AACCATTGTA
Statistics
Matches: 136, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
79 35 0.26
80 38 0.28
81 63 0.46
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.21
Consensus pattern (81 bp):
AATCCGTCAATTCATGGCACCCAGTGCCTAGCGGATAAAACGCAGAAGTGAGCCCAGCTCTAATT
GGATTAACCAACGAAT
Found at i:51822 original size:2 final size:2
Alignment explanation
Indices: 51811--51845 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
51801 ATATATATAT
*
51811 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
51846 TAAAAATAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:54682 original size:6 final size:6
Alignment explanation
Indices: 54671--54699 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
54661 TGTTTGACTT
54671 GAGAGG GAGAGG GAGAGG GAGAGG GAGAG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAG
54700 ACCCCTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:55399 original size:9 final size:9
Alignment explanation
Indices: 55368--55413 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
55358 TTTTATATAA
55368 AAAAAT-TT
1 AAAAATATT
55376 AAAAATA-T
1 AAAAATATT
*
55384 -AATATATT
1 AAAAATATT
55392 AAAAATATT
1 AAAAATATT
*
55401 AAAAACATT
1 AAAAATATT
55410 AAAA
1 AAAA
55414 TAAACATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
7 5 0.16
8 8 0.25
9 19 0.59
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAAATATT
Found at i:69462 original size:2 final size:2
Alignment explanation
Indices: 69457--69482 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
69447 AATGTGTGCG
69457 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
69483 GACTTAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:69823 original size:2 final size:2
Alignment explanation
Indices: 69816--69845 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
69806 AAAATACATG
69816 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
69846 TATGTATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:71916 original size:23 final size:23
Alignment explanation
Indices: 71868--71911 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
71858 AATCATGTGT
71868 TTTGAATTTTTATATATTATTTA
1 TTTGAATTTTTATATATTATTTA
*
71891 TTTGGATTTTTA-ATATT-TTTA
1 TTTGAATTTTTATATATTATTTA
71912 AATTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 5 0.25
23 11 0.55
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (23 bp):
TTTGAATTTTTATATATTATTTA
Found at i:79994 original size:15 final size:16
Alignment explanation
Indices: 79977--80006 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
79967 TATCTAAAAT
79977 AAATAATATTAAATTA
1 AAATAATATTAAATTA
79993 AAATAA-ATTAAATT
1 AAATAATATTAAATT
80007 GATTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATAATATTAAATTA
Found at i:82770 original size:6 final size:6
Alignment explanation
Indices: 82761--82790 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
82751 GGGAATTGTT
82761 GGGAGA GGGAGA GGGAGA GGGAG- GGGAGA G
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA G
82791 AAATGGAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:89345 original size:17 final size:16
Alignment explanation
Indices: 89312--89347 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
89302 ACCATCCATA
89312 TTATTTTTTTAAATAT
1 TTATTTTTTTAAATAT
*
89328 TTATTTTATTTTAATAT
1 TTATTTT-TTTAAATAT
89345 TTA
1 TTA
89348 ATAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTTTTTTAAATAT
Found at i:89384 original size:28 final size:28
Alignment explanation
Indices: 89336--89389 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
89326 ATTTATTTTA
* *
89336 TTTTAATATTTAATAATTTTTATATATT
1 TTTTAATATTGAATAAATTTTATATATT
89364 TTTTAATTATTGAA-AAATTTTATATA
1 TTTTAA-TATTGAATAAATTTTATATA
89390 GTCATAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (28 bp):
TTTTAATATTGAATAAATTTTATATATT
Found at i:99830 original size:3 final size:3
Alignment explanation
Indices: 99824--99893 Score: 68
Period size: 3 Copynumber: 23.3 Consensus size: 3
99814 AGAGGGAGAT
* * * * * * * *
99824 GAA GAA GAA GAT GAT GAT GAT GAT GAA GGA GAA GAA GAT GAA GAG GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
99872 GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA G
99894 TGAAGCCCAA
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.54, C:0.00, G:0.37, T:0.09
Consensus pattern (3 bp):
GAA
Found at i:99835 original size:12 final size:12
Alignment explanation
Indices: 99804--99898 Score: 75
Period size: 12 Copynumber: 7.9 Consensus size: 12
99794 TCAGGAAGCG
99804 AGAATGATGAAGA
1 AGAA-GATGAAGA
* *
99817 GGGAGATGAAGA
1 AGAAGATGAAGA
*
99829 AGAAGATGATGA
1 AGAAGATGAAGA
* * *
99841 TGATGATGAAGG
1 AGAAGATGAAGA
* *
99853 AGAAGAAGATGA
1 AGAAGATGAAGA
* *
99865 AGAGGAAGAAGA
1 AGAAGATGAAGA
*
99877 AGAAGAAGAAGA
1 AGAAGATGAAGA
99889 AGAAG-TGAAG
1 AGAAGATGAAG
99899 CCCAAAAAGA
Statistics
Matches: 64, Mismatches: 18, Indels: 2
0.76 0.21 0.02
Matches are distributed among these distances:
11 4 0.06
12 58 0.91
13 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.38, T:0.11
Consensus pattern (12 bp):
AGAAGATGAAGA
Found at i:105511 original size:30 final size:30
Alignment explanation
Indices: 105475--105536 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
105465 TATTGCGTTT
105475 ATGGGAATATGAATACTCAACTATATATAA
1 ATGGGAATATGAATACTCAACTATATATAA
105505 ATGGGAATATGAATACTCAACTATATATAA
1 ATGGGAATATGAATACTCAACTATATATAA
105535 AT
1 AT
105537 ATATATACCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.31
Consensus pattern (30 bp):
ATGGGAATATGAATACTCAACTATATATAA
Found at i:105891 original size:18 final size:17
Alignment explanation
Indices: 105859--105892 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
105849 TGTGTAATGC
*
105859 ATGAAGTGTATGCATGT
1 ATGAAGTGCATGCATGT
105876 ATGAATGTGCATGCATG
1 ATGAA-GTGCATGCATG
105893 AACAACAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.32
Consensus pattern (17 bp):
ATGAAGTGCATGCATGT
Found at i:111095 original size:23 final size:23
Alignment explanation
Indices: 111069--111130 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
111059 GCACTGTGTA
*
111069 TGCTCTCTGATTAGCAATTTATG
1 TGCTATCTGATTAGCAATTTATG
* * * *
111092 TGCTTTCTAATTAGCACTTTGTG
1 TGCTATCTGATTAGCAATTTATG
* *
111115 TACTATCTGTTTAGCA
1 TGCTATCTGATTAGCA
111131 CTGTGTGCGC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (23 bp):
TGCTATCTGATTAGCAATTTATG
Found at i:114429 original size:17 final size:16
Alignment explanation
Indices: 114401--114433 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
114391 TTTGCTTTCC
114401 TCTTTCTCCTTTCTTT
1 TCTTTCTCCTTTCTTT
114417 TCTTTCTTCCTTTCTTT
1 TCTTTC-TCCTTTCTTT
114434 AGCTCAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (16 bp):
TCTTTCTCCTTTCTTT
Found at i:116573 original size:3 final size:3
Alignment explanation
Indices: 116565--116597 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
116555 CTAGTTCAAG
116565 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
116598 TAAATTTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:118699 original size:29 final size:29
Alignment explanation
Indices: 118605--118891 Score: 133
Period size: 29 Copynumber: 9.8 Consensus size: 29
118595 TTTTAGACAT
** *
118605 TCGAGGGTAAAATAATATTTTTGGTGAAA
1 TCGAGGGTAAAATGGTAATTTTGGTGAAA
118634 TCGA-GGTCAAAATGG--ATATTT-G-GAAA
1 TCGAGGGT-AAAATGGTAAT-TTTGGTGAAA
118660 GTTTCGAGGGTAAAATGGTAATGTTTGGTGAAA
1 ---TCGAGGGTAAAATGGTAAT-TTTGGTGAAA
118693 TCG-GGGTTAAACATGG-AATTTT-G-GAAA
1 TCGAGGG-TAAA-ATGGTAATTTTGGTGAAA
* ** *
118720 GTTAGAGGGTAAAAACGTAATTTTTGGT-AAGT
1 --TCGAGGGTAAAATGGTAA-TTTTGGTGAA-A
* *
118752 TCGGGGGTAAAAATAG-AATTTT-G-GAAA
1 TCGAGGGT-AAAATGGTAATTTTGGTGAAA
118779 CTTCGAGGGTAAAATGGTAATTTTTGGTGAAA
1 --TCGAGGGTAAAATGGTAA-TTTTGGTGAAA
* * *
118811 TCGAGGTTAAAATAG-AATTTT--AGAAA
1 TCGAGGGTAAAATGGTAATTTTGGTGAAA
* * *
118837 GTTCAAGGGTAAAATTGTAATTTT-G-AAAA
1 --TCGAGGGTAAAATGGTAATTTTGGTGAAA
118866 GTTCGAGGGTAAAATGGTAATTTTGG
1 --TCGAGGGTAAAATGGTAATTTTGG
118892 AAAGTTTAGG
Statistics
Matches: 201, Mismatches: 24, Indels: 65
0.69 0.08 0.22
Matches are distributed among these distances:
26 8 0.04
27 6 0.03
28 34 0.17
29 80 0.40
30 46 0.23
31 18 0.09
32 5 0.02
33 4 0.02
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.32
Consensus pattern (29 bp):
TCGAGGGTAAAATGGTAATTTTGGTGAAA
Found at i:118728 original size:59 final size:58
Alignment explanation
Indices: 118607--118918 Score: 284
Period size: 59 Copynumber: 5.3 Consensus size: 58
118597 TTAGACATTC
** * * *
118607 GAGGGTAAAATAAT-ATTTTTGGTGAAATCGAGGTCAAAATGG-ATATTTGGAAAGTTTC
1 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAAT-TTTGGAAAG-TTA
*
118665 GAGGGTAAAATGGTAATGTTTGGTGAAATCGGGGTTAAACATGGAATTTTGGAAAGTTA
1 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAA-ATGGAATTTTGGAAAGTTA
** * * * * *
118724 GAGGGTAAAAACGTAATTTTTGGT-AAGTTCGGGGGTAAAAATAGAATTTTGGAAACTTC
1 GAGGGTAAAATGGTAATTTTTGGTGAA-ATC-GGGGTTAAAATGGAATTTTGGAAAGTTA
* * *
118783 GAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAATAGAATTTTAGAAAGTTCA
1 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTT-A
* *
118842 -AGGGTAAAATTGTAA-TTTT-G-AAAAGTTCGAGGG-TAAAATGGTAATTTTGGAAAGTTTA
1 GAGGGTAAAATGGTAATTTTTGGTGAAA--TCG-GGGTTAAAATGG-AATTTTGGAAAG-TTA
118900 G-GGGTAAAAAT-GTAATTTT
1 GAGGGT-AAAATGGTAATTTT
118919 CAAGAAGTTT
Statistics
Matches: 212, Mismatches: 27, Indels: 29
0.79 0.10 0.11
Matches are distributed among these distances:
55 3 0.01
56 1 0.00
57 14 0.07
58 73 0.34
59 96 0.45
60 23 0.11
61 2 0.01
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.32
Consensus pattern (58 bp):
GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGGAATTTTGGAAAGTTA
Found at i:118895 original size:29 final size:29
Alignment explanation
Indices: 118652--118957 Score: 227
Period size: 29 Copynumber: 10.4 Consensus size: 29
118642 AAAATGGATA
118652 TTTGGAAAGTTTCGAGGGTAAAATGGTAAT
1 TTTGGAAAG-TTCGAGGGTAAAATGGTAAT
118682 GTTTGGTGAAA--TCG-GGGTTAAACATGG-AAT
1 -TTT-G-GAAAGTTCGAGGG-TAAA-ATGGTAAT
* **
118712 TTTGGAAAGTTAGAGGGTAAAAACGTAATT
1 TTTGGAAAGTTCGAGGGTAAAATGGTAA-T
* * *
118742 TTTGGTAAGTTCGGGGGTAAAAATAG-AAT
1 TTTGGAAAGTTCGAGGGT-AAAATGGTAAT
*
118771 TTTGGAAACTTCGAGGGTAAAATGGTAATT
1 TTTGGAAAGTTCGAGGGTAAAATGGTAA-T
* *
118801 TTTGGTGAAA--TCGAGGTTAAAATAG-AAT
1 TTT-G-GAAAGTTCGAGGGTAAAATGGTAAT
* * *
118829 TTTAGAAAGTTCAAGGGTAAAATTGTAAT
1 TTTGGAAAGTTCGAGGGTAAAATGGTAAT
*
118858 TTTGAAAAGTTCGAGGGTAAAATGGTAAT
1 TTTGGAAAGTTCGAGGGTAAAATGGTAAT
*
118887 TTTGGAAAGTT-TAGGGGTAAAAAT-GTAAT
1 TTTGGAAAGTTCGA-GGGT-AAAATGGTAAT
** * * *
118916 TTTCAAGAAGTTTGAGGGTAAATTTGTAATT
1 TTTGGA-AAGTTCGAGGGTAAAATGGTAA-T
*
118947 TTTAGAAAGTT
1 TTTGGAAAGTT
118958 TGGAGGTCAA
Statistics
Matches: 222, Mismatches: 30, Indels: 47
0.74 0.10 0.16
Matches are distributed among these distances:
26 4 0.02
27 4 0.02
28 26 0.12
29 89 0.40
30 71 0.32
31 19 0.09
32 5 0.02
33 4 0.02
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.34
Consensus pattern (29 bp):
TTTGGAAAGTTCGAGGGTAAAATGGTAAT
Found at i:118927 original size:30 final size:29
Alignment explanation
Indices: 118700--118988 Score: 139
Period size: 30 Copynumber: 9.8 Consensus size: 29
118690 AAATCGGGGT
* * * *
118700 TAAACATGGAATTTTGGAAAGTTAGAGGG
1 TAAAAATGTAATTTTGAAAAGTTTGAGGG
* ** * *
118729 TAAAAACGTAATTTTTGGTAAGTTCGGGGG
1 TAAAAATGTAA-TTTTGAAAAGTTTGAGGG
* * *
118759 TAAAAATAG-AATTTTGGAAACTTCGAGGG
1 TAAAAAT-GTAATTTTGAAAAGTTTGAGGG
* *
118788 T-AAAATGGTAATTTTTGGTGAAA--TCGA-GG
1 TAAAAAT-GTAA-TTTT-G-AAAAGTTTGAGGG
* **
118817 TTAAAATAG-AATTTT-AGAAAGTTCAAGGG
1 TAAAAAT-GTAATTTTGA-AAAGTTTGAGGG
* *
118846 TAAAATTGTAATTTTGAAAAGTTCGAGGG
1 TAAAAATGTAATTTTGAAAAGTTTGAGGG
*
118875 T-AAAATGGTAATTTTGGAAAGTTT-AGGGG
1 TAAAAAT-GTAATTTTGAAAAGTTTGA-GGG
*
118904 TAAAAATGTAATTTTCAAGAAGTTTGAGGG
1 TAAAAATGTAATTTTGAA-AAGTTTGAGGG
** *
118934 TAAATTTGTAATTTTTAGAAAGTTTG-GAGG
1 TAAAAATGTAATTTTGA-AAAGTTTGAG-GG
* * *
118964 TCAAAATATAATTTTTGAACAGTTT
1 TAAAAATGTAA-TTTTGAAAAGTTT
118989 AAGGACCTCC
Statistics
Matches: 208, Mismatches: 31, Indels: 41
0.74 0.11 0.15
Matches are distributed among these distances:
26 3 0.01
28 19 0.09
29 85 0.41
30 88 0.42
31 9 0.04
32 4 0.02
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (29 bp):
TAAAAATGTAATTTTGAAAAGTTTGAGGG
Found at i:118945 original size:59 final size:58
Alignment explanation
Indices: 118811--118978 Score: 187
Period size: 58 Copynumber: 2.9 Consensus size: 58
118801 TTTGGTGAAA
* * * * * *
118811 TCGAGGTTAAAATAG-AATTTTAGAAAGTTCAAGGGTAAAATTGTAATTTTGAAAAGT
1 TCGAGGGTAAAATGGTAATTTTAGAAAGTTTAGGGGTAAAAATGTAATTTTCAAAAGT
*
118868 TCGAGGGTAAAATGGTAATTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTCAAGAAGT
1 TCGAGGGTAAAATGGTAATTTTAGAAAGTTTAGGGGTAAAAATGTAATTTTCAA-AAGT
* * * * *
118927 TTGAGGGTAAATTTGTAATTTTTAGAAAGTTT-GGAGGTCAAAATATAATTTT
1 TCGAGGGTAAAATGGTAA-TTTTAGAAAGTTTAGG-GGTAAAAATGTAATTTT
118979 TGAACAGTTT
Statistics
Matches: 94, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
57 13 0.14
58 33 0.35
59 21 0.22
60 27 0.29
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (58 bp):
TCGAGGGTAAAATGGTAATTTTAGAAAGTTTAGGGGTAAAAATGTAATTTTCAAAAGT
Found at i:120034 original size:21 final size:19
Alignment explanation
Indices: 120008--120064 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 19
119998 CATTATTTAT
120008 TTATTATTATTAATAAATTCA
1 TTATTATTATTAATAAA-T-A
120029 TTATTACTGTTATTAAT-AATA
1 TTATTA---TTATTAATAAATA
*
120050 TTATTTTTATTAATA
1 TTATTATTATTAATA
120065 TTTATTAGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
18 8 0.26
21 12 0.39
22 1 0.03
23 2 0.06
24 8 0.26
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTATTATTAATAAATA
Found at i:120051 original size:18 final size:18
Alignment explanation
Indices: 120030--120064 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
120020 ATAAATTCAT
120030 TATTACTGTTATTAATAA
1 TATTACTGTTATTAATAA
* *
120048 TATTATTTTTATTAATA
1 TATTACTGTTATTAATA
120065 TTTATTAGGT
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:0.03, G:0.03, T:0.57
Consensus pattern (18 bp):
TATTACTGTTATTAATAA
Found at i:120066 original size:24 final size:23
Alignment explanation
Indices: 119988--120066 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 23
119978 ATTTCTTTTT
*
119988 TTATTAAAAACATTATTTATTTATTA
1 TTATTAATAA-ATTA-TT-TTTATTA
* * *
120014 TTATTAATAAATTCATTATTACTG
1 TTATTAATAAATT-ATTTTTATTA
120038 TTATTAATAATATTATTTTTATTA
1 TTATTAATAA-ATTATTTTTATTA
*
120062 ATATT
1 TTATT
120067 TATTAGGTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
24 25 0.58
25 8 0.19
26 10 0.23
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (23 bp):
TTATTAATAAATTATTTTTATTA
Found at i:120847 original size:17 final size:16
Alignment explanation
Indices: 120827--120869 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
120817 AAATTATTTC
120827 AAATTTAAACTAAATTG
1 AAATTTAAAC-AAATTG
*
120844 AAATTTAAAACAAATTT
1 AAATTT-AAACAAATTG
120861 AAATTTAAA
1 AAATTTAAA
120870 TTTAGAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 17 0.71
18 4 0.17
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (16 bp):
AAATTTAAACAAATTG
Found at i:120863 original size:23 final size:24
Alignment explanation
Indices: 120836--120887 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
120826 CAAATTTAAA
120836 CTAAATTGAAATTTA-AAACAAAT
1 CTAAATTGAAATTTAGAAACAAAT
* * *
120859 TTAAATTTAAATTTAGAAATAAAT
1 CTAAATTGAAATTTAGAAACAAAT
120883 CTAAA
1 CTAAA
120888 ATAATTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (24 bp):
CTAAATTGAAATTTAGAAACAAAT
Found at i:120864 original size:6 final size:6
Alignment explanation
Indices: 120791--120873 Score: 57
Period size: 6 Copynumber: 14.0 Consensus size: 6
120781 ATGGACTTTG
* * *
120791 AATTTA ATTTTA AAGTTTA AATTTTA AAATT- -ATTTCA AATTTA AA-CTA
1 AATTTA AATTTA AA-TTTA AA-TTTA AATTTA AATTT-A AATTTA AATTTA
* **
120839 AATTGA AATTTA AA-ACA AATTTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
120874 GAAATAAATC
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
4 3 0.05
5 7 0.12
6 32 0.55
7 16 0.28
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:120881 original size:12 final size:11
Alignment explanation
Indices: 120844--120897 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 11
120834 AACTAAATTG
*
120844 AAATTTAAAAC
1 AAATTTAAAAT
*
120855 AAATTTAAATTT
1 AAATTTAAA-AT
120867 AAATTTAGAAAT
1 AAATTTA-AAAT
*
120879 AAATCTAAAAT
1 AAATTTAAAAT
120890 -AATTTAAA
1 AAATTTAAA
120898 CTCAAAAGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
10 7 0.19
11 13 0.36
12 14 0.39
13 2 0.06
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (11 bp):
AAATTTAAAAT
Found at i:122764 original size:206 final size:206
Alignment explanation
Indices: 121242--122763 Score: 2256
Period size: 206 Copynumber: 7.4 Consensus size: 206
121232 TCTGGTTTCA
* * * ** ** * *
121242 TTGACTTGGCCTTCTTCTCAGTATCTTATCAGGAAGATGACCGCATCACTTGTTTTGATTCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
* * * * * * *
121307 CTCTGTGTTTCATCAGGAAGACGGATTAGGTTCACTTCTCTGTATCTCATCAAGAAGCTAACCAC
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCGGTATCTCATCAAGAAGCTAACCAT
* * *
121372 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGTTGAGGTTCGAAGATTTGTTCATAT
131 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCATAT
* * *
121437 CAAGCATGGGT
196 CGAGCGTGAGT
* * *
121448 TTGATTTGGTATTCTTCTCGGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGTTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
*
121513 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCGGTATCTCATCAAGAAGCTAACCAT
*
121578 TTTATTACTTCGACATGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCATAT
131 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCATAT
121643 CGAGCGTGAGT
196 CGAGCGTGAGT
** *
121654 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAAAACCGCATCGTTTGTTTCAATCTGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
* *
121719 CTCTGTATCTCATCAGGAAGACGAATTTGGTCTACTTCTCGGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCGGTATCTCATCAAGAAGCTAACCAT
* * *
121784 TTTATTACTTCGACCTGTTTCTCAGTATCTCATCAAGAAGCTGAGGTTTGAAGATTTGCTCATAT
131 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCATAT
*
121849 CGAGCATGAGT
196 CGAGCGTGAGT
* *
121860 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCTTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
* *
121925 CTCTGTATCTCATCAGGAAGACGAATTTGGTCTACTTCTCGGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCGGTATCTCATCAAGAAGCTAACCAT
*
121990 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-AGGGTTCGAAGATTTACTCATA
131 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGA-GGTTCGAAGATTTGCTCATA
122054 TCGAGCGTGAGT
195 TCGAGCGTGAGT
* * * *
122066 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGACGACCGCATTC-TTAGTTTCAATTCGCT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCA-TCGTTTGTTTCAATCCGCT
* * *
122130 TCTTTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAACTAACCA
65 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCGGTATCTCATCAAGAAGCTAACCA
* * * *
122195 TTTTATTACTTTGACTTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCATA
130 TTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCATA
122260 TCGAGCGTGAGT
195 TCGAGCGTGAGT
* * * * * *
122272 TTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGACGACCGTATCCTTAGTTTCAATCTGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
*
122337 CTCTGTATCTCATCAGGAAGACGAATTTGGTCTACTTCTCGGTATCTCATCAAGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCGGTATCTCATCAAGAAGCTAACCAT
** * * *
122402 TTTATTGTTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCAAAGATTTGCTCATAT
131 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCATAT
122467 CGAGCGTGAGT
196 CGAGCGTGAGT
* * * ** * *
122478 TTGATTTTGTCTTCTTCTTAGTTTCTCATCAAAAAGATGACCACATCATTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
* * * *
122543 CTTTGTGTCTCATCAAGAAGACGAATTTGGTCCACTTCTCGGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCGGTATCTCATCAAGAAGCTAACCAT
* * * * *
122608 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATTAGAAAGCCGAGGTTCGAAGATTTGCTCACAT
131 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCATAT
*
122673 CGAGCGTGGGT
196 CGAGCGTGAGT
* * *
122684 TTGATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGATCGCATCGTTTGTTTCAATCCGTTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
122749 CTCTGTATCTCATCA
66 CTCTGTATCTCATCA
122764 AAAAGCTGAG
Statistics
Matches: 1201, Mismatches: 111, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
205 3 0.00
206 1196 1.00
207 2 0.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.36
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCGGTATCTCATCAAGAAGCTAACCAT
TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCATAT
CGAGCGTGAGT
Found at i:122917 original size:39 final size:39
Alignment explanation
Indices: 122874--123087 Score: 165
Period size: 39 Copynumber: 5.5 Consensus size: 39
122864 TACCCCGTGA
* *
122874 TCGGGGTAGGAGTTTGGTTGATGATGATCTGCCCTAAGC
1 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCTAAGC
* * * * * *
122913 TCGGGGTAAGAGATCGAATGGTTG-TAATCTGCCTCT-GGC
1 TCGGGGTAAGAGATTG-GTTGATGATGATCTGCC-CTAAGC
*
122952 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGC
1 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCTAAGC
* * * *
122991 TCGAGGTAAAAGATCAAATGGCTTCA--AT--T-TG-CCTCAGGC
1 TCGGGGTAAGAGAT----TGG-TTGATGATGATCTGCCCT-AAGC
* *
123030 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGC
1 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCTAAGC
123069 TCGGGGTAAGAGATTGGTT
1 TCGGGGTAAGAGATTGGTT
123088 AACGATGTAG
Statistics
Matches: 135, Mismatches: 24, Indels: 32
0.71 0.13 0.17
Matches are distributed among these distances:
34 3 0.02
35 3 0.02
36 2 0.01
38 8 0.06
39 102 0.76
40 9 0.07
42 2 0.01
43 3 0.02
44 3 0.02
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (39 bp):
TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCTAAGC
Found at i:122991 original size:78 final size:78
Alignment explanation
Indices: 122874--123082 Score: 312
Period size: 78 Copynumber: 2.7 Consensus size: 78
122864 TACCCCGTGA
* * * * *
122874 TCGGGGTAGGAGTTTGGTTGATGATGATCTGCCCTAAGCTCGGGGTAAGAGATCGAATGG-TTGT
1 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGGCTT-C
*
122938 AATCTGCCTCTGGC
65 AATCTGCCTCAGGC
* *
122952 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGAGGTAAAAGATCAAATGGCTTCA
1 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGGCTTCA
*
123017 ATTTGCCTCAGGC
66 ATCTGCCTCAGGC
*
123030 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGAT
1 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAGAGAT
123083 TGGTTAACGA
Statistics
Matches: 118, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
78 116 0.98
79 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (78 bp):
TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGGCTTCA
ATCTGCCTCAGGC
Found at i:123333 original size:101 final size:101
Alignment explanation
Indices: 123149--123350 Score: 269
Period size: 101 Copynumber: 2.0 Consensus size: 101
123139 GCTGCTGTAG
* * * * *
123149 TTTTATTCCAACTTCGCTGCAACTTCAAGAAGATAGGATTTGATGTTGAAGCTTCATCTTGCTCT
1 TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGGAATTGACGTTAAAGCTTCATCTTGCTCT
* * *
123214 TACTACATCTTTAAAGAGATAAAGACTTGCTATTGT
66 TACTACAACTTCAAAGAGATAAAGACTTGCCATTGT
* * * * *
123250 TTTTAATCCAACTTTACTGCAACTTTAAGAGGATAGGAATTGACGTTAAAGCTTTATTTTGCTCT
1 TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGGAATTGACGTTAAAGCTTCATCTTGCTCT
* *
123315 TACTGCAACTTCAGAGAGATAAAGACTTGCCATTGT
66 TACTACAACTTCAAAGAGATAAAGACTTGCCATTGT
123351 AGTTTTGATC
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 86 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (101 bp):
TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGGAATTGACGTTAAAGCTTCATCTTGCTCT
TACTACAACTTCAAAGAGATAAAGACTTGCCATTGT
Found at i:123548 original size:50 final size:48
Alignment explanation
Indices: 123494--123664 Score: 132
Period size: 49 Copynumber: 3.5 Consensus size: 48
123484 AGATTCGTCG
* *
123494 TTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACGCGGTCCGCCA
1 TTGCGACTTAAATCTTTCCCTTTTTGTCTT-TGAGGTACG-GGTCCGCCA
* * * * *
123544 TTGCGACTTAAA-CTTTTCCTTTTTGTATCTTTGTGGTACTGGATCCACCG
1 TTGCGACTTAAATCTTTCCCTTTTTG--TCTTTGAGGTAC-GGGTCCGCCA
* * * *
123594 TTGCG-GTCTAGATCTTT-CGTTTTATGTCTTTGAGGTACTAGGTCCGCCA
1 TTGCGACT-TAAATCTTTCCCTTTT-TGTCTTTGAGGTAC-GGGTCCGCCA
* *
123643 TTACGACTTAAACCTTTCCCTT
1 TTGCGACTTAAATCTTTCCCTT
123665 GTGTCTTCGT
Statistics
Matches: 93, Mismatches: 20, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
49 41 0.44
50 41 0.44
51 11 0.12
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.40
Consensus pattern (48 bp):
TTGCGACTTAAATCTTTCCCTTTTTGTCTTTGAGGTACGGGTCCGCCA
Found at i:123660 original size:49 final size:47
Alignment explanation
Indices: 123494--123681 Score: 135
Period size: 50 Copynumber: 3.8 Consensus size: 47
123484 AGATTCGTCG
* * * *
123494 TTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACGCGGTCCGCCA
1 TTGCGACTTAAACCTTT-CCTTTTTGTCTT-TGAGGTAC-TGGTCCGCCA
* * * *
123544 TTGCGACTTAAACTTTTCCTTTTTGTATCTTTGTGGTACTGGATCCACCG
1 TTGCGACTTAAACCTTTCCTTTTTG--TCTTTGAGGTACTGG-TCCGCCA
* * * *
123594 TTGCG-GTCTAGATCTTTCGTTTTATGTCTTTGAGGTACTAGGTCCGCCA
1 TTGCGACT-TAAACCTTTCCTTTT-TGTCTTTGAGGTACT-GGTCCGCCA
* * * * *
123643 TTACGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTG
1 TTGCGACTTAAACCTTTCCTTTTTGTCTTTGAGGTACTG
123682 AGACCTGTAA
Statistics
Matches: 106, Mismatches: 25, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
47 1 0.01
48 13 0.12
49 41 0.39
50 45 0.42
51 6 0.06
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.40
Consensus pattern (47 bp):
TTGCGACTTAAACCTTTCCTTTTTGTCTTTGAGGTACTGGTCCGCCA
Found at i:124411 original size:106 final size:106
Alignment explanation
Indices: 124226--124481 Score: 413
Period size: 106 Copynumber: 2.4 Consensus size: 106
124216 AAGGCGAATG
* * * *
124226 AAATTTTATTGGAGGTAAAGCTCACATGAATGGAAAGATTAAAAGTTACCCATATTGGTCAAAGG
1 AAATTTTATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAGTGACCCATATTGGTCAAAGG
*
124291 ATGCCAAATATAAAGTGATCAAAGAATAGAGTTAGGTGGAT
66 ATGCCAAATATAAAGTGAGCAAAGAATAGAGTTAGGTGGAT
* *
124332 AAATTTTATTGGAGACAAAGCTCGCATGAATGAAAAGATCAAAAGTGACCCATATTGGTCAAAGG
1 AAATTTTATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAGTGACCCATATTGGTCAAAGG
124397 ATGCCAAATATAAAGTGAGCAAAGAATAGAGTTAGGTGGAT
66 ATGCCAAATATAAAGTGAGCAAAGAATAGAGTTAGGTGGAT
* * * *
124438 GAATTTTATTAGAGGCAAAACTTGCATGAATGAAAAGATTAAAA
1 AAATTTTATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAA
124482 TCATTAGTCA
Statistics
Matches: 137, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 137 1.00
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.25
Consensus pattern (106 bp):
AAATTTTATTGGAGGCAAAGCTCGCATGAATGAAAAGATTAAAAGTGACCCATATTGGTCAAAGG
ATGCCAAATATAAAGTGAGCAAAGAATAGAGTTAGGTGGAT
Found at i:125016 original size:18 final size:19
Alignment explanation
Indices: 124991--125040 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
124981 ACTCTACCTC
124991 TCCTTTTTTTTTCGT-TTTT
1 TCCTTTTTTTTT-GTCTTTT
125010 T-CTTTTTTCTTTGTCTTTT
1 TCCTTTTTT-TTTGTCTTTT
125029 TCCTTTTCTTTT
1 TCCTTTT-TTTT
125041 ATTCATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 9 0.33
19 9 0.33
20 7 0.26
21 2 0.07
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (19 bp):
TCCTTTTTTTTTGTCTTTT
Found at i:125028 original size:12 final size:12
Alignment explanation
Indices: 125007--125040 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
124997 TTTTTTCGTT
*
125007 TTTTCTTTTTTC
1 TTTTCTTTTTCC
125019 TTTGTCTTTTTCC
1 TTT-TCTTTTTCC
125032 TTTTCTTTT
1 TTTTCTTTT
125041 ATTCATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTTCTTTTTCC
Found at i:125949 original size:13 final size:12
Alignment explanation
Indices: 125931--125974 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
125921 TTCTTCTCTC
*
125931 TTTTTTTGTTTG
1 TTTTTTTTTTTG
125943 TTTTTTTTATTTAG
1 TTTTTTTT-TTT-G
*
125957 TTTTTGTTTTTG
1 TTTTTTTTTTTG
125969 TTTTTT
1 TTTTTT
125975 ATAGCACGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 13 0.48
13 6 0.22
14 8 0.30
ACGTcount: A:0.05, C:0.00, G:0.11, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:130706 original size:29 final size:29
Alignment explanation
Indices: 130674--130754 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
130664 AAAATGATAA
130674 TTTTGGAAAAATCGGGGTAGAAACGG-AAT
1 TTTTGGAAAAATCGGGGTA-AAACGGTAAT
* * * *
130703 TTTTAG-ACATTCGGGGGTAAAATGGTAAT
1 TTTTGGAAAAATC-GGGGTAAAACGGTAAT
*
130732 TTTTGGAAAAAATAGGGGTAAAA
1 TTTTGG-AAAAATCGGGGTAAAA
130755 AATGGAACTT
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
28 9 0.22
29 19 0.47
30 9 0.22
31 3 0.08
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.28
Consensus pattern (29 bp):
TTTTGGAAAAATCGGGGTAAAACGGTAAT
Found at i:130856 original size:58 final size:59
Alignment explanation
Indices: 130718--130969 Score: 257
Period size: 58 Copynumber: 4.3 Consensus size: 59
130708 GACATTCGGG
* ** * * * *
130718 GGTAAAATGGTAATTTTTGG-AAAAAATAGGGGTAAAAAATGGAACTTTAGCAAGTTTCGA
1 GGTAAAATGGTAATTTTTGGTAAGATTTA-GGGT-AAAAATGGAATTTTGGAAAGTTTAGA
* * *
130778 GGGTAAAATGTTAATTTTTGGTAAGTTTTAGGGTAAAAATGGAATTTTGGAAACTTT-GA
1 -GGTAAAATGGTAATTTTTGGTAAGATTTAGGGTAAAAATGGAATTTTGGAAAGTTTAGA
* * *
130837 GGTAAAATGGTAATTTTTGGTGAA-ATTGAGGTTAAAAATGGAATTTTGGAAAGTTTAGG
1 GGTAAAATGGTAATTTTTGGT-AAGATTTAGGGTAAAAATGGAATTTTGGAAAGTTTAGA
* * * *
130896 GGTAAAATTGTAA-TTTTGGAAAG-TTTAGGGT-AAAATGGTAATTTTGGAAATTTTAGG
1 GGTAAAATGGTAATTTTTGGTAAGATTTAGGGTAAAAATGG-AATTTTGGAAAGTTTAGA
130953 GGTAAAAT-GTAATTTTT
1 GGTAAAATGGTAATTTTT
130970 AAGAAGTTTA
Statistics
Matches: 165, Mismatches: 20, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
56 11 0.07
57 37 0.22
58 54 0.33
59 17 0.10
60 19 0.12
61 23 0.14
62 4 0.02
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.36
Consensus pattern (59 bp):
GGTAAAATGGTAATTTTTGGTAAGATTTAGGGTAAAAATGGAATTTTGGAAAGTTTAGA
Found at i:130969 original size:29 final size:29
Alignment explanation
Indices: 130716--131041 Score: 224
Period size: 29 Copynumber: 11.1 Consensus size: 29
130706 TAGACATTCG
***
130716 GGGGTAAAATGGTAATTTTTGGAAAAAATA
1 GGGGTAAAAT-GTAATTTTTGGAAAGTTTA
* * * * *
130746 GGGGTAAAAAATGGAA-CTTTAGCAAGTTTC
1 GGGGT--AAAATGTAATTTTTGGAAAGTTTA
*
130776 GAGGGTAAAATGTTAATTTTTGGTAAGTTTTA
1 G-GGGTAAAATG-TAATTTTTGGAAAG-TTTA
* *
130808 -GGGTAAAAATGGAA-TTTTGGAAACTTT-
1 GGGGT-AAAATGTAATTTTTGGAAAGTTTA
* *
130835 GAGGTAAAATGGTAATTTTTGGTGAAA-TTGA
1 GGGGTAAAAT-GTAATTTTT-G-GAAAGTTTA
* *
130866 -GGTTAAAAATGGAA-TTTTGGAAAGTTTA
1 GGGGT-AAAATGTAATTTTTGGAAAGTTTA
130894 GGGGTAAAATTGTAA-TTTTGGAAAGTTTA
1 GGGGTAAAA-TGTAATTTTTGGAAAGTTTA
*
130923 -GGGTAAAATGGTAA-TTTTGGAAATTTTA
1 GGGGTAAAAT-GTAATTTTTGGAAAGTTTA
*
130951 GGGGTAAAATGTAATTTTT-AAGAAGTTTA
1 GGGGTAAAATGTAATTTTTGGA-AAGTTTA
* ***
130980 GGAGTAAAATGTAATTTTCAAAAAGTTTAA
1 GGGGTAAAATGTAATTTTTGGAAAGTTT-A
* * *
131010 GGGTTAAAATATAATTTTTGGATAGTTTA
1 GGGGTAAAATGTAATTTTTGGAAAGTTTA
131039 GGG
1 GGG
131042 ACCTTCAAGG
Statistics
Matches: 236, Mismatches: 37, Indels: 47
0.74 0.12 0.15
Matches are distributed among these distances:
27 10 0.04
28 47 0.20
29 89 0.38
30 53 0.22
31 29 0.12
32 8 0.03
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (29 bp):
GGGGTAAAATGTAATTTTTGGAAAGTTTA
Found at i:132094 original size:15 final size:16
Alignment explanation
Indices: 132074--132107 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
132064 ATTATTACTG
132074 TTATTAATAATA-TTA
1 TTATTAATAATATTTA
132089 TTATTAATAATATTTA
1 TTATTAATAATATTTA
132105 TTA
1 TTA
132108 GGTTATAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATTAATAATATTTA
Done.