Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010987.1 Kokia drynarioides strain JFW-HI SEQ_125957, 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: 330895
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:239558 original size:18 final size:18
Alignment explanation
Indices: 239537--239571 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
239527 TGCGTATCAA
239537 AACCCTTATATGTATCCT
1 AACCCTTATATGTATCCT
239555 AACCCTTATATGTATCC
1 AACCCTTATATGTATCC
239572 ATTTTCTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.37
Consensus pattern (18 bp):
AACCCTTATATGTATCCT
Found at i:239891 original size:26 final size:26
Alignment explanation
Indices: 239855--239915 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
239845 AGAATTGCAC
239855 CTAGAATTGTCACTGCATGA-CAATGT
1 CTAGAATTGTCACTGCATGAGC-ATGT
* *
239881 CTAGAGTTGTCACTGTATGAGCATGT
1 CTAGAATTGTCACTGCATGAGCATGT
*
239907 CTAAAATTG
1 CTAGAATTG
239916 CGCCCAGAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 29 0.97
27 1 0.03
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (26 bp):
CTAGAATTGTCACTGCATGAGCATGT
Found at i:247189 original size:17 final size:17
Alignment explanation
Indices: 247167--247221 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
247157 CATTATTAAG
*
247167 CATTGTCATCGCATTTT
1 CATTGTCATTGCATTTT
*
247184 CATTGTCATTACATTTT
1 CATTGTCATTGCATTTT
* *
247201 AATTGTCATTGCATTTC
1 CATTGTCATTGCATTTT
247218 CATT
1 CATT
247222 TGTTCTTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.49
Consensus pattern (17 bp):
CATTGTCATTGCATTTT
Found at i:247581 original size:38 final size:38
Alignment explanation
Indices: 247530--247606 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
247520 ATCTTGAATG
247530 AATTTACCATTTACATCTACTTATATAACTATATATAT
1 AATTTACCATTTACATCTACTTATATAACTATATATAT
247568 AATTTACCATTTACATCTACTTATATAACTATATATAT
1 AATTTACCATTTACATCTACTTATATAACTATATATAT
247606 A
1 A
247607 TATATATAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (38 bp):
AATTTACCATTTACATCTACTTATATAACTATATATAT
Found at i:249814 original size:62 final size:59
Alignment explanation
Indices: 249701--249836 Score: 200
Period size: 62 Copynumber: 2.2 Consensus size: 59
249691 GAATTGATTT
*
249701 ATTTCGAATATTTTTGTAAACATTATTTTCATATTGTATCATTTAATGAAATCGAAGTTC
1 ATTT-GAATATTTTTGTAAACATTATTTTCATATTGTATCATTTAATGAAATAGAAGTTC
*
249761 ATTTGAATATTTTTGTACACATTATTTTTGGCATATTGTATCATTTAATGAAATAGAAGTTC
1 ATTTGAATATTTTTGTAAACATTA-TTTT--CATATTGTATCATTTAATGAAATAGAAGTTC
* *
249823 TTTTAAATATTTTT
1 ATTTGAATATTTTT
249837 CAACATTGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
59 19 0.28
60 8 0.12
62 42 0.61
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.49
Consensus pattern (59 bp):
ATTTGAATATTTTTGTAAACATTATTTTCATATTGTATCATTTAATGAAATAGAAGTTC
Found at i:250412 original size:22 final size:22
Alignment explanation
Indices: 250381--250468 Score: 92
Period size: 21 Copynumber: 4.1 Consensus size: 22
250371 GCTTTTTAAG
*
250381 TTTAATATATCCTAAACCCTAA
1 TTTAAAATATCCTAAACCCTAA
*
250403 TTTAAAATAT-C-AATACCCTTA
1 TTTAAAATATCCTAA-ACCCTAA
* *
250424 TTTAAAATATCGTGAACCCTAA
1 TTTAAAATATCCTAAACCCTAA
* *
250446 TTTAAAA-ACCCTAAACCTTAA
1 TTTAAAATATCCTAAACCCTAA
250467 TT
1 TT
250469 ACACAAAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.04
21 29 0.54
22 22 0.41
23 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.02, T:0.35
Consensus pattern (22 bp):
TTTAAAATATCCTAAACCCTAA
Found at i:253882 original size:14 final size:14
Alignment explanation
Indices: 253863--253895 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
253853 TACAATATTC
253863 AAATAATAACAACA
1 AAATAATAACAACA
253877 AAATAATAACAACA
1 AAATAATAACAACA
*
253891 TAATA
1 AAATA
253896 GTGAAATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (14 bp):
AAATAATAACAACA
Found at i:254715 original size:93 final size:92
Alignment explanation
Indices: 254515--254715 Score: 244
Period size: 93 Copynumber: 2.2 Consensus size: 92
254505 ACTTTATCAC
* * * *
254515 TATTTTCATTAAAAATTAATTTTAATTTCACATTGACTAGAGAACACTTTCATGCTCACACTTAC
1 TATTTTCATTAAAAATTAATTTTAATCTCACAATGACTAGAGAACACTCTCATGATCACACTTAC
*
254580 CCTATAAATAAGTGTCAATTTCTTCAT
66 CATATAAATAAGTGTCAATTTCTTCAT
* * * * **
254607 TATTTTTATTAAAAAATTCATTTTAATC-CTATAATGACTAGAGAACACTCTCATATATCACGTT
1 TATTTTCATT-AAAAATTAATTTTAATCTC-ACAATGACTAGAGAACACTCTCAT-GATCACACT
*
254671 TACCATATAAATAAGTGAT-AATTTCTTCCT
63 TACCATATAAATAAGTG-TCAATTTCTTCAT
254701 TATTTTCATTAAAAA
1 TATTTTCATTAAAAA
254716 AAAGTTAATT
Statistics
Matches: 92, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
92 10 0.11
93 41 0.45
94 40 0.43
95 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (92 bp):
TATTTTCATTAAAAATTAATTTTAATCTCACAATGACTAGAGAACACTCTCATGATCACACTTAC
CATATAAATAAGTGTCAATTTCTTCAT
Found at i:254945 original size:66 final size:66
Alignment explanation
Indices: 254761--254951 Score: 238
Period size: 69 Copynumber: 2.8 Consensus size: 66
254751 TAGCTCAATT
* * *
254761 CTTCACTAGTTTCATTTAAAAAGTTAATTTTAATCTCATATTGATTAGAGAACACTCTCATAACT
1 CTTCACTATTTTCA-TTAAAAAGTTAATTTTAATCTCATATTGATTAGAGAATACTATCATAACT
254826 CA
65 CA
* * *
254828 CTTCTAAATTATTTTCATTAAAAAGTTAATTTTAATCTCATATTGACTAGAGAATACTATCATAG
1 CTTC---ACTATTTTCATTAAAAAGTTAATTTTAATCTCATATTGATTAGAGAATACTATCATAA
*
254893 TTCA
63 CTCA
* * * * *
254897 CTTCACTATTTTTATTAAAAAATTATTTTTAATCTCAAATCGATTAGAGAATACT
1 CTTCACTATTTTCATTAAAAAGTTAATTTTAATCTCATATTGATTAGAGAATACT
254952 TTGATATCTC
Statistics
Matches: 107, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
66 44 0.41
67 4 0.04
69 51 0.48
70 8 0.07
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (66 bp):
CTTCACTATTTTCATTAAAAAGTTAATTTTAATCTCATATTGATTAGAGAATACTATCATAACTC
A
Found at i:256033 original size:38 final size:37
Alignment explanation
Indices: 255991--256085 Score: 127
Period size: 41 Copynumber: 2.4 Consensus size: 37
255981 CTTTTTAGAT
255991 ATTTTAAAATATTTTTATCATTTTTTATTCAAAAATAA
1 ATTTTAAAATATTTTTATCA-TTTTTATTCAAAAATAA
*
256029 ATTTTAAAATATTTTTTTTTATCATTTTTATTCAAAAATGA
1 ATTTTAAAATA----TTTTTATCATTTTTATTCAAAAATAA
*
256070 TTTTTAAAATATTTTT
1 ATTTTAAAATATTTTT
256086 TTAACTTTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
37 5 0.10
38 11 0.22
41 26 0.51
42 9 0.18
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (37 bp):
ATTTTAAAATATTTTTATCATTTTTATTCAAAAATAA
Found at i:256086 original size:42 final size:42
Alignment explanation
Indices: 256002--256087 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 42
255992 TTTTAAAATA
256002 TTTTTATCATTTTTTATTCAAAAATAAATTTTAAAATATTTT
1 TTTTTATCATTTTTTATTCAAAAATAAATTTTAAAATATTTT
* *
256044 TTTTTATCA-TTTTTATTCAAAAATGATTTTTAAAATATTTT
1 TTTTTATCATTTTTTATTCAAAAATAAATTTTAAAATATTTT
256085 TTT
1 TTT
256088 AACTTTTAGA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
41 33 0.79
42 9 0.21
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (42 bp):
TTTTTATCATTTTTTATTCAAAAATAAATTTTAAAATATTTT
Found at i:256504 original size:29 final size:30
Alignment explanation
Indices: 256471--256527 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
256461 TAGTTTAATG
*
256471 TGCAATTGTATGTATG-AATTTTGATTTTA
1 TGCAATTGTATATATGAAATTTTGATTTTA
*
256500 TGCAATTTTATATATGAAATTTTGATTT
1 TGCAATTGTATATATGAAATTTTGATTT
256528 GATCTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.30, C:0.04, G:0.14, T:0.53
Consensus pattern (30 bp):
TGCAATTGTATATATGAAATTTTGATTTTA
Found at i:256537 original size:30 final size:29
Alignment explanation
Indices: 256471--256538 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
256461 TAGTTTAATG
* * *
256471 TGCAATTGTATGTATGAATTTTGATTTTA
1 TGCAATTTTATATATGAATTTTGATTTGA
256500 TGCAATTTTATATATGAAATTTTGATTTGA
1 TGCAATTTTATATATG-AATTTTGATTTGA
256530 T-CTAATTTT
1 TGC-AATTTT
256539 TGAAAAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 15 0.44
30 19 0.56
ACGTcount: A:0.29, C:0.04, G:0.13, T:0.53
Consensus pattern (29 bp):
TGCAATTTTATATATGAATTTTGATTTGA
Found at i:256766 original size:31 final size:29
Alignment explanation
Indices: 256703--256784 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
256693 TTTAAACCAT
* * *
256703 AATTAGAATTTCACATATATAATTATACTA
1 AATTA-AAATTCATATATATAATTACACTA
256733 AATTAAAATTCATATATATAATTACACATTA
1 AATTAAAATTCATATATATAATTACAC--TA
*
256764 AATCAAAATT--TATATATAATT
1 AATTAAAATTCATATATATAATT
256785 TTAATATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 30 0.65
30 5 0.11
31 11 0.24
ACGTcount: A:0.50, C:0.09, G:0.01, T:0.40
Consensus pattern (29 bp):
AATTAAAATTCATATATATAATTACACTA
Found at i:259818 original size:38 final size:39
Alignment explanation
Indices: 259758--259834 Score: 147
Period size: 38 Copynumber: 2.0 Consensus size: 39
259748 AAATGAAATC
259758 CTTAGTATTTCATGTGTTTCCTTTGGTTTTCTGATTTGG
1 CTTAGTATTTCATGTGTTTCCTTTGGTTTTCTGATTTGG
259797 CTTAGTATTTC-TGTGTTTCCTTTGGTTTTCTGATTTGG
1 CTTAGTATTTCATGTGTTTCCTTTGGTTTTCTGATTTGG
259835 AATTGTTAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 27 0.71
39 11 0.29
ACGTcount: A:0.09, C:0.13, G:0.21, T:0.57
Consensus pattern (39 bp):
CTTAGTATTTCATGTGTTTCCTTTGGTTTTCTGATTTGG
Found at i:259826 original size:19 final size:19
Alignment explanation
Indices: 259765--259828 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
259755 ATCCTTAGTA
259765 TTTCATGTGTTTCCTTTGGT
1 TTTC-TGTGTTTCCTTTGGT
** *
259785 TTTCTGAT-TTGGC-TTAGT
1 TTTCTG-TGTTTCCTTTGGT
259803 ATTTCTGTGTTTCCTTTGGT
1 -TTTCTGTGTTTCCTTTGGT
259823 TTTCTG
1 TTTCTG
259829 ATTTGGAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
18 5 0.15
19 20 0.59
20 9 0.26
ACGTcount: A:0.06, C:0.14, G:0.20, T:0.59
Consensus pattern (19 bp):
TTTCTGTGTTTCCTTTGGT
Found at i:268642 original size:29 final size:29
Alignment explanation
Indices: 268610--269099 Score: 188
Period size: 29 Copynumber: 16.8 Consensus size: 29
268600 ACTCAAGGGT
268610 AAAATAGTAATTTTTGGAAGCTT-GGGGGC
1 AAAATAGTAATTTTTGGAAG-TTCGGGGGC
*
268639 AAAAATAGTAATTTTT-GAATGTTC-GGGGA
1 -AAAATAGTAATTTTTGGAA-GTTCGGGGGC
* * * *
268668 AAAATGGTAATTTTTGGATGTTCAGAGGC
1 AAAATAGTAATTTTTGGAAGTTCGGGGGC
* ** *
268697 AAAACAGTAA-TTTTGGAAAAGTTCAAGGAC
1 AAAATAGTAATTTTTGG--AAGTTCGGGGGC
* ***
268727 AAAA-ATGTAATTTTTGAGAAGTTTGGGATA
1 AAAATA-GTAATTTTTG-GAAGTTCGGGGGC
* *
268757 AAAAT-GTGATTTTTGAAAGTTCGGGGGC
1 AAAATAGTAATTTTTGGAAGTTCGGGGGC
* *
268785 AAAA-ATGTAATTTTTGGAAGTTCGAGGGA
1 AAAATA-GTAATTTTTGGAAGTTCGGGGGC
* ** *** **
268814 AAAAAATGTAATTTTCAAGAAGTTTAAGGTA
1 AAAATA-GTAATTTT-TGGAAGTTCGGGGGC
* * * *
268845 AAAAT-GTGATTTTTGAAAGTTTGGAGGC
1 AAAATAGTAATTTTTGGAAGTTCGGGGGC
* * *
268873 AAAA-ATGTAATTTTTGAAAAGTTCGAGGTC
1 AAAATA-GTAATTTTTG-GAAGTTCGGGGGC
* * **
268903 AAAAATA-TAATTTTTAAGAAGTT-TGGGTA
1 -AAAATAGTAATTTTT-GGAAGTTCGGGGGC
* * *
268932 AAAAT-GTGATTTTTGAAAGTTCGAGGGC
1 AAAATAGTAATTTTTGGAAGTTCGGGGGC
* *
268960 AAAATA-TAATTTTTGG-AGTTTGAGGGC
1 AAAATAGTAATTTTTGGAAGTTCGGGGGC
* *** *
268987 AAAA-ATGTGATTTTTGAGAAGTTTAAGGGT
1 AAAATA-GTAATTTTTG-GAAGTTCGGGGGC
* * * * *
269017 AAAA-ACATGATTTTTGAAAGTTTGGGGCC
1 AAAATA-GTAATTTTTGGAAGTTCGGGGGC
* *
269046 AAAA-ATGTAATTTTTGGAAGTTCGAGGGT
1 AAAATA-GTAATTTTTGGAAGTTCGGGGGC
*
269075 AAAA-ACGTGATTTTTGGAAAGTTCG
1 AAAATA-GTAATTTTTGG-AAGTTCG
269100 AGGACTTTCT
Statistics
Matches: 350, Mismatches: 82, Indels: 56
0.72 0.17 0.11
Matches are distributed among these distances:
26 1 0.00
27 19 0.05
28 82 0.23
29 119 0.34
30 104 0.30
31 23 0.07
32 2 0.01
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (29 bp):
AAAATAGTAATTTTTGGAAGTTCGGGGGC
Found at i:268678 original size:58 final size:55
Alignment explanation
Indices: 268610--269093 Score: 317
Period size: 58 Copynumber: 8.3 Consensus size: 55
268600 ACTCAAGGGT
*
268610 AAAATAGTAATTTTTGGAAGCTTGGGGGCAAAAATAGTAATTTTTGAATGTTCGGGGA
1 AAAAT-GTAATTTTTGGAAG-TTGGGGGCAAAAAT-GTAATTTTTGAAAGTTCGGGGA
* * * * **
268668 AAAATGGTAATTTTTGGATGTTCAGAGGCAAAACA-GTAATTTTGGAAAAGTTCAAGGACA
1 AAAAT-GTAATTTTTGGAAGTT-GGGGGCAAAA-ATGTAATTTTTG-AAAGTTC--GGGGA
* ** *
268728 AAAATGTAATTTTTGAGAAGTTTGGGATAAAAATGTGATTTTTGAAAGTTCGGGGGCA
1 AAAATGTAATTTTTG-GAAGTTGGGGGCAAAAATGTAATTTTTGAAAGTTC-GGGG-A
** ** ** *
268786 AAAATGTAATTTTTGGAAGTTCGAGGGAAAAAAATGTAATTTTCAAGAAGTTTAAGGTA
1 AAAATGTAATTTTTGGAAGTT-G-GGGGCAAAAATGTAATTTTTGA-AAG-TTCGGGGA
* * * *
268845 AAAATGTGATTTTTGAAAGTTTGGAGGCAAAAATGTAATTTTTGAAAAGTTCGAGGTCA
1 AAAATGTAATTTTTGGAAG-TTGGGGGCAAAAATGTAATTTTTG-AAAGTTCG-GG-GA
* * * * * *
268904 AAAATATAATTTTTAAGAAGTT-TGGGTAAAAATGTGATTTTTGAAAGTTCGAGGGC
1 AAAATGTAATTTTT-GGAAGTTGGGGGCAAAAATGTAATTTTTGAAAGTTCG-GGGA
* * * * *
268960 AAAATATAATTTTTGG-AGTTTGAGGGCAAAAATGTGATTTTTGAGAAGTTTAAGGGTA
1 AAAATGTAATTTTTGGAAG-TTGGGGGCAAAAATGTAATTTTTGA-AAG-TT-CGGGGA
** * * * *
269018 AAAACATGATTTTTGAAAGTTTGGGGCCAAAAATGTAATTTTTGGAAGTTCGAGGGTA
1 AAAATGTAATTTTTGGAAG-TTGGGGGCAAAAATGTAATTTTTGAAAGTTCG-GGG-A
* *
269076 AAAACGTGATTTTTGGAA
1 AAAATGTAATTTTTGGAA
269094 AGTTCGAGGA
Statistics
Matches: 338, Mismatches: 63, Indels: 50
0.75 0.14 0.11
Matches are distributed among these distances:
54 2 0.01
55 3 0.01
56 35 0.10
57 39 0.12
58 131 0.39
59 103 0.30
60 23 0.07
61 2 0.01
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (55 bp):
AAAATGTAATTTTTGGAAGTTGGGGGCAAAAATGTAATTTTTGAAAGTTCGGGGA
Found at i:268787 original size:88 final size:88
Alignment explanation
Indices: 268638--269064 Score: 451
Period size: 88 Copynumber: 4.9 Consensus size: 88
268628 AGCTTGGGGG
* * * * * * * *
268638 CAAAAATAGTAATTTTTGA-ATGTTCGGGGAAAAATGGTAATTTTTGGATGTTCAGAGGCAAAAC
1 CAAAAAT-GTAATTTTTGAGAAGTTTGGGTAAAAAT-GTGATTTTTGAAAGTTCGGGGGCAAAA-
268702 A-GTAA-TTTTGGAAAAGTTCAAGGA
63 ATGTAATTTTTGGAAAAGTTCAAGGA
268726 CAAAAATGTAATTTTTGAGAAGTTTGGGATAAAAATGTGATTTTTGAAAGTTCGGGGGCAAAAAT
1 CAAAAATGTAATTTTTGAGAAGTTTGGG-TAAAAATGTGATTTTTGAAAGTTCGGGGGCAAAAAT
*
268791 GTAATTTTTGG--AAGTTCGAGGGA
65 GTAATTTTTGGAAAAGTTC-AAGGA
* ** * * *
268814 AAAAAATGTAATTTTCAAGAAGTTTAAGGTAAAAATGTGATTTTTGAAAGTTTGGAGGCAAAAAT
1 CAAAAATGTAATTTTTGAGAAGTTT-GGGTAAAAATGTGATTTTTGAAAGTTCGGGGGCAAAAAT
* *
268879 GTAATTTTT-GAAAAGTTCGAGGT
65 GTAATTTTTGGAAAAGTTCAAGGA
* * * *
268902 CAAAAATATAATTTTTAAGAAGTTTGGGTAAAAATGTGATTTTTGAAAGTTCGAGGGC-AAAATA
1 CAAAAATGTAATTTTTGAGAAGTTTGGGTAAAAATGTGATTTTTGAAAGTTCGGGGGCAAAAATG
** *
268966 TAATTTTTGG---AGTTTGAGGG
66 TAATTTTTGGAAAAGTTCAAGGA
* ** * *
268986 CAAAAATGTGATTTTTGAGAAGTTTAAGGGTAAAAACATGATTTTTGAAAGTTTGGGGCCAAAAA
1 CAAAAATGTAATTTTTGAGAAGTTT--GGGTAAAAATGTGATTTTTGAAAGTTCGGGGGCAAAAA
269051 TGTAATTTTTGGAA
64 TGTAATTTTTGGAA
269065 GTTCGAGGGT
Statistics
Matches: 288, Mismatches: 37, Indels: 27
0.82 0.11 0.08
Matches are distributed among these distances:
84 30 0.10
86 41 0.14
87 64 0.22
88 133 0.46
89 20 0.07
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (88 bp):
CAAAAATGTAATTTTTGAGAAGTTTGGGTAAAAATGTGATTTTTGAAAGTTCGGGGGCAAAAATG
TAATTTTTGGAAAAGTTCAAGGA
Found at i:270847 original size:6 final size:6
Alignment explanation
Indices: 270831--270940 Score: 52
Period size: 6 Copynumber: 18.8 Consensus size: 6
270821 GGACTTTTAC
* * * *
270831 TTAAAT CTTAAAT TTAAAAA TCAAAA T-AAAT TTAAAT TTAAA- ATAAAT
1 TTAAAT -TTAAAT TT-AAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * * * *
270879 TTAAAC TCAAA- ATAAGT TTAAAT TTAAA- ATAAAT TTAAAC TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
270924 AT-AAT TTAAAAT TTAAA
1 TTAAAT TT-AAAT TTAAA
270941 ATTCAAAATT
Statistics
Matches: 78, Mismatches: 17, Indels: 17
0.70 0.15 0.15
Matches are distributed among these distances:
4 2 0.03
5 16 0.21
6 45 0.58
7 15 0.19
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (6 bp):
TTAAAT
Found at i:270875 original size:17 final size:17
Alignment explanation
Indices: 270839--270942 Score: 129
Period size: 17 Copynumber: 6.1 Consensus size: 17
270829 ACTTAAATCT
* *
270839 TAAATTTAAAAATCAAAA
1 TAAATTT-AAATTTAAAA
270857 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
270874 TAAATTTAAACTCAAAA
1 TAAATTTAAATTTAAAA
*
270891 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
270908 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
270925 T-AATTTAAAATTTAAAA
1 TAAATTT-AAATTTAAAA
270942 T
1 T
270943 TCAAAATTGG
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
16 5 0.07
17 63 0.84
18 7 0.09
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.37
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:270899 original size:34 final size:33
Alignment explanation
Indices: 270839--270942 Score: 154
Period size: 34 Copynumber: 3.0 Consensus size: 33
270829 ACTTAAATCT
*
270839 TAAATTTAAAAATCAAAATAAATTTAAATTTAAAA
1 TAAATTT-AAACTCAAAAT-AATTTAAATTTAAAA
270874 TAAATTTAAACTCAAAATAAGTTTAAATTTAAAA
1 TAAATTTAAACTCAAAATAA-TTTAAATTTAAAA
*
270908 TAAATTTAAACTTAAAATAATTTAAAATTTAAAA
1 TAAATTTAAACTCAAAATAATTT-AAATTTAAAA
270942 T
1 T
270943 TCAAAATTGG
Statistics
Matches: 65, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
33 5 0.08
34 53 0.82
35 7 0.11
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.37
Consensus pattern (33 bp):
TAAATTTAAACTCAAAATAATTTAAATTTAAAA
Found at i:271445 original size:24 final size:24
Alignment explanation
Indices: 271413--271466 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
271403 TATTAGTTTC
*
271413 TTCTATTAATCTTTTGTCTAATAA
1 TTCTTTTAATCTTTTGTCTAATAA
271437 TTCTTTTAATCTTTTGTCTAATAA
1 TTCTTTTAATCTTTTGTCTAATAA
*
271461 GTCTTT
1 TTCTTT
271467 AATTTGAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.24, C:0.13, G:0.06, T:0.57
Consensus pattern (24 bp):
TTCTTTTAATCTTTTGTCTAATAA
Found at i:275019 original size:43 final size:43
Alignment explanation
Indices: 274916--275150 Score: 244
Period size: 43 Copynumber: 5.3 Consensus size: 43
274906 TTATGAGGAA
* *
274916 AAACGCCGCTATAGAACATGATCTTTAGCGACGCTTAT--CCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTT-TCCCCAC
* * * *
274958 AAACGCCGCTAAAAAACATGATCTTTAGTGGTGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTCCCCAC
* *
275001 AAATGCTGCTAAAGAACATGGTCTTAATGTTCTTTAGCGGCGC-TTCCCCAC
1 AAACGCCGCTAAAGAACAT-G-----A---TCTTTAGCGGCGCTTTCCCCAC
*
275052 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTCCCCAC
*
275095 AAACGCCGCTAAAGAACATGATCTTTAGCAGCAG-TTTCCCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGC-GCTTTCCCCAC
*
275138 AAACGCTGCTAAA
1 AAACGCCGCTAAA
275151 ATTAATAAAC
Statistics
Matches: 163, Mismatches: 17, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
41 1 0.01
42 44 0.27
43 79 0.48
44 2 0.01
49 1 0.01
50 1 0.01
51 24 0.15
52 11 0.07
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTCCCCAC
Found at i:275106 original size:94 final size:94
Alignment explanation
Indices: 274937--275119 Score: 267
Period size: 94 Copynumber: 1.9 Consensus size: 94
274927 TAGAACATGA
* * * *
274937 TCTTTAGCGACGCTTATCCACAAACGCCGCTAAAAAACATGATCTTTAGTGGTGCTTTTCCCACA
1 TCTTTAGCGACGCTTACCCACAAACGCCGCTAAAAAACATGATCTTTAGCGGCGCTTTCCCCACA
* * *
275002 AATGCTGCTAAAGAACATGGTCTTAATGT
66 AACGCCGCTAAAGAACATGATCTTAATGT
* * * *
275031 TCTTTAGCGGCGCTTCCCCACAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCCACA
1 TCTTTAGCGACGCTTACCCACAAACGCCGCTAAAAAACATGATCTTTAGCGGCGCTTTCCCCACA
275096 AACGCCGCTAAAGAACATGATCTT
66 AACGCCGCTAAAGAACATGATCTT
275120 TAGCAGCAGT
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
94 78 1.00
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (94 bp):
TCTTTAGCGACGCTTACCCACAAACGCCGCTAAAAAACATGATCTTTAGCGGCGCTTTCCCCACA
AACGCCGCTAAAGAACATGATCTTAATGT
Found at i:278095 original size:41 final size:41
Alignment explanation
Indices: 278027--278142 Score: 133
Period size: 41 Copynumber: 2.8 Consensus size: 41
278017 TATGAGAAAG
* * *
278027 TGCCGCTAATACTCTAACCACTTTAGCGGCACTTTCTCGTAAA
1 TGCCGCTAATGCTCTGA-C-CTTTAGCGGCACTTTCTCATAAA
* *
278070 TGCCGCTAGTGCTCTGACCTTTAGCGGCGCTTTCTCATAAA
1 TGCCGCTAATGCTCTGACCTTTAGCGGCACTTTCTCATAAA
** * *
278111 TGTTGCTAATGTTTTGACCTTTAGCGGCACTT
1 TGCCGCTAATGCTCTGACCTTTAGCGGCACTT
278143 ACTAATGCTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
41 47 0.76
42 1 0.02
43 14 0.23
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (41 bp):
TGCCGCTAATGCTCTGACCTTTAGCGGCACTTTCTCATAAA
Found at i:280582 original size:41 final size:41
Alignment explanation
Indices: 280523--280761 Score: 300
Period size: 41 Copynumber: 5.8 Consensus size: 41
280513 CGTTTTTCAA
* * *
280523 ATAAGCGCAGCTAATGCTCTGATCTTTAGCGGCGCTTGCCC
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCC
*
280564 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGTGCTTGCCC
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCC
* * *
280605 AAAAAGCACCACTATTGCTCTGACCTTTAGCGGCGCTTGCCC
1 -ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCC
* ** * *
280647 ATAAGCGCCGCTATTGCTCTAACCTTTAGCAACGCTTTCCG
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCC
* * *
280688 ATAAGCGCCACAATTGCTCTGACCTTTAGCGGCGCTTTCCC
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCC
** *
280729 ATAAGCATCGCTATTGCTCT-ACCTTTTGCGGCG
1 ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCG
280762 TTTATGTAGA
Statistics
Matches: 170, Mismatches: 27, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
40 12 0.07
41 121 0.71
42 37 0.22
ACGTcount: A:0.20, C:0.31, G:0.21, T:0.28
Consensus pattern (41 bp):
ATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTGCCC
Found at i:280645 original size:83 final size:81
Alignment explanation
Indices: 280537--280761 Score: 306
Period size: 83 Copynumber: 2.7 Consensus size: 81
280527 GCGCAGCTAA
* *
280537 TGCTCTGATCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGTGCTTG
1 TGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCT-ACCTTTAGCGGCGCTT-
*
280602 CCCAAAAAGCACCACTAT
64 CCCAAAAAGCACCACAAT
** *
280620 TGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTAACCTTTAGCAACGCTTT
1 TGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCT-ACCTTTAGCGGCGCTTC
* * *
280685 CCGATAAGCGCCACAAT
65 CCAAAAAGCACCACAAT
* ** *
280702 TGCTCTGACCTTTAGCGGCGCTTTCCCATAAGCATCGCTATTGCTCTACCTTTTGCGGCG
1 TGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTACCTTTAGCGGCG
280762 TTTATGTAGA
Statistics
Matches: 126, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
81 10 0.08
82 57 0.45
83 59 0.47
ACGTcount: A:0.18, C:0.32, G:0.21, T:0.29
Consensus pattern (81 bp):
TGCTCTGACCTTTAGCGGCGCTTGCCCATAAGCGCCGCTATTGCTCTACCTTTAGCGGCGCTTCC
CAAAAAGCACCACAAT
Found at i:283898 original size:19 final size:19
Alignment explanation
Indices: 283874--283912 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
283864 GGAATTCACC
283874 TCGAATATCCAATGATTCA
1 TCGAATATCCAATGATTCA
283893 TCGAATATCCAATGATTCA
1 TCGAATATCCAATGATTCA
283912 T
1 T
283913 TAAATCTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (19 bp):
TCGAATATCCAATGATTCA
Found at i:287680 original size:16 final size:17
Alignment explanation
Indices: 287650--287682 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
287640 CAGCAATTTA
287650 TTCTCTTTTTCTTTTCT
1 TTCTCTTTTTCTTTTCT
*
287667 TTCT-TTTTTTTTTTCT
1 TTCTCTTTTTCTTTTCT
287683 CAAATTTGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTCTCTTTTTCTTTTCT
Found at i:288317 original size:16 final size:17
Alignment explanation
Indices: 288281--288315 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
288271 TATTAAAATG
288281 AATGCAGTGACAATAAA
1 AATGCAGTGACAATAAA
288298 AATGCAG-GCACAATAAA
1 AATGCAGTG-ACAATAAA
288315 A
1 A
288316 TGTAAGAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 16 0.94
ACGTcount: A:0.54, C:0.14, G:0.17, T:0.14
Consensus pattern (17 bp):
AATGCAGTGACAATAAA
Found at i:311559 original size:22 final size:21
Alignment explanation
Indices: 311529--311569 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
311519 AGTACAATTT
311529 CCAAGTTTTATATTTATATTCA
1 CCAAGTTTTATATTT-TATTCA
*
311551 CCAATTTTTATATTTTATT
1 CCAAGTTTTATATTTTATT
311570 TATTTGCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.56
Consensus pattern (21 bp):
CCAAGTTTTATATTTTATTCA
Found at i:313826 original size:2 final size:2
Alignment explanation
Indices: 313819--313846 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
313809 TTTCAAGTTG
313819 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
313847 TAGATTTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:320183 original size:10 final size:9
Alignment explanation
Indices: 320161--320208 Score: 60
Period size: 9 Copynumber: 5.1 Consensus size: 9
320151 ATTGTAAAAT
320161 TAAAAATTA
1 TAAAAATTA
320170 TAAAAATTA
1 TAAAAATTA
320179 TTAAAAATTA
1 -TAAAAATTA
*
320189 TAAAATTCTA
1 TAAAAAT-TA
*
320199 TAAAATTTA
1 TAAAAATTA
320208 T
1 T
320209 TAGTCATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
9 18 0.50
10 18 0.50
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (9 bp):
TAAAAATTA
Found at i:325492 original size:33 final size:33
Alignment explanation
Indices: 325454--325519 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
325444 TTTATTGATA
325454 AATTTACAATAATATTTAAAATTAATAATAAAG
1 AATTTACAATAATATTTAAAATTAATAATAAAG
325487 AATTTACAATAATATTTAAAATTAATAATAAAG
1 AATTTACAATAATATTTAAAATTAATAATAAAG
325520 TATCACTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (33 bp):
AATTTACAATAATATTTAAAATTAATAATAAAG
Found at i:326272 original size:19 final size:19
Alignment explanation
Indices: 326239--326293 Score: 92
Period size: 19 Copynumber: 2.8 Consensus size: 19
326229 ATCTAAAAAA
326239 ATTATCTTGGTGGGAAATTG
1 ATTATCTT-GTGGGAAATTG
326259 ATTATCTTGTGGGAAATTG
1 ATTATCTTGTGGGAAATTG
*
326278 ATTATCTTGTTGGAAA
1 ATTATCTTGTGGGAAA
326294 CAGCAATTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 26 0.76
20 8 0.24
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.42
Consensus pattern (19 bp):
ATTATCTTGTGGGAAATTG
Found at i:327324 original size:15 final size:15
Alignment explanation
Indices: 327304--327336 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
327294 ATTGACTGTT
327304 ACCCGTTAAATAGCG
1 ACCCGTTAAATAGCG
327319 ACCCGTTAAATAGCG
1 ACCCGTTAAATAGCG
327334 ACC
1 ACC
327337 GCGATTTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.18
Consensus pattern (15 bp):
ACCCGTTAAATAGCG
Found at i:328356 original size:48 final size:48
Alignment explanation
Indices: 327953--328325 Score: 566
Period size: 48 Copynumber: 7.8 Consensus size: 48
327943 ACCAGTCACT
* * * * *
327953 CCTTCAGTGCCTGCAACACCAACTCAACATTGGGCTCCAGGTCCTGCA
1 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
* * * * * *
328001 CCTTCAGTGCCTGCAACACCAACTCAACATTGGGCTCCAGGTCCTGCT
1 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
* *
328049 CCTTCAGTGCCTGCAACACCAACTCAACCTTCGACTCCAGCTCCTCCA
1 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
*
328097 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCTAGCTCCTCCA
1 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
* *
328145 CCTTCAATGCCTGCAACACCAACTCAAACTTGGACTACAGCTCCTCCA
1 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
328193 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
1 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
* *
328241 CCATCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTGCA
1 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
* *
328289 CCTTTAGTGCCTGCAACACCAACTCAACCTTGGACTC
1 CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTC
328326 TAGGTCCTGC
Statistics
Matches: 305, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 305 1.00
ACGTcount: A:0.25, C:0.41, G:0.13, T:0.21
Consensus pattern (48 bp):
CCTTCAATGCCTGCAACACCAACTCAACCTTGGACTCCAGCTCCTCCA
Found at i:328514 original size:54 final size:54
Alignment explanation
Indices: 328430--328537 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
328420 GGCTCCAACC
328430 CCTGCATCCTGGGCACCAGCTACACCTTCTGTGCCAACAGCACCATCAGACCCT
1 CCTGCATCCTGGGCACCAGCTACACCTTCTGTGCCAACAGCACCATCAGACCCT
*
328484 CCTGCATCCTGGGCACCAGCTACACTTTCTGTGCCAACAGCACCATCAGACCCT
1 CCTGCATCCTGGGCACCAGCTACACCTTCTGTGCCAACAGCACCATCAGACCCT
328538 TGGGATTCAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.22, C:0.42, G:0.17, T:0.19
Consensus pattern (54 bp):
CCTGCATCCTGGGCACCAGCTACACCTTCTGTGCCAACAGCACCATCAGACCCT
Found at i:328717 original size:18 final size:18
Alignment explanation
Indices: 328696--328730 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
328686 CACCTTGGGC
* *
328696 ACCAGCTACACCTTCTGT
1 ACCAGCAACACCATCTGT
328714 ACCAGCAACACCATCTG
1 ACCAGCAACACCATCTG
328731 ACCCTTAGGC
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:0.29, C:0.40, G:0.11, T:0.20
Consensus pattern (18 bp):
ACCAGCAACACCATCTGT
Found at i:328742 original size:66 final size:66
Alignment explanation
Indices: 328484--328744 Score: 335
Period size: 66 Copynumber: 4.0 Consensus size: 66
328474 ATCAGACCCT
* * * * *
328484 CCTGCATCC-TGGGCACCAGCTACACTTTCTGTGCCAACAGCACCATCAGACCCTTGGGATTCAA
1 CCTGCA-CCTTGGGCACCAGCTACACCTTCTGTGCCAACAACACCATCTGACCCTTGGGCTCCAA
328548 CC
65 CC
* * * * * * * *
328550 CCTGTATCATGGGCACCAGCTACACCTTTTGTGCCAACACCACCATCTGACTCTTGGACTCCAAG
1 CCTGCACCTTGGGCACCAGCTACACCTTCTGTGCCAACAACACCATCTGACCCTTGGGCTCCAAC
328615 C
66 C
* * *
328616 CCTGCACCTTGGGCACCAGCTACACCTTCTGTGCCAGCAACACCATCGGACCCTTGGGCTCCAAT
1 CCTGCACCTTGGGCACCAGCTACACCTTCTGTGCCAACAACACCATCTGACCCTTGGGCTCCAAC
328681 C
66 C
* * *
328682 CCTGCACCTTGGGCACCAGCTACACCTTCTGTACCAGCAACACCATCTGACCCTTAGGCTCCA
1 CCTGCACCTTGGGCACCAGCTACACCTTCTGTGCCAACAACACCATCTGACCCTTGGGCTCCA
328745 GCTCCATCTC
Statistics
Matches: 170, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
65 1 0.01
66 169 0.99
ACGTcount: A:0.22, C:0.39, G:0.18, T:0.21
Consensus pattern (66 bp):
CCTGCACCTTGGGCACCAGCTACACCTTCTGTGCCAACAACACCATCTGACCCTTGGGCTCCAAC
C
Found at i:329175 original size:21 final size:19
Alignment explanation
Indices: 329136--329175 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
329126 ATGGTTGAAC
*
329136 ATTAAAAGAAATAACAATA
1 ATTAAAAGAAATAAAAATA
329155 ATTAAAAGATTAATAAAAATA
1 ATTAAAAGA--AATAAAAATA
329176 TAAAATCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (19 bp):
ATTAAAAGAAATAAAAATA
Done.