Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013861.1 Kokia drynarioides strain JFW-HI SEQ_128889, 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: 56021
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:3660 original size:96 final size:95
Alignment explanation
Indices: 3477--3667 Score: 244
Period size: 96 Copynumber: 2.0 Consensus size: 95
3467 ATTTTGGAAA
* ** * *
3477 AAGATATTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGTCACAAATTTTCAG
1 AAGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTCAG
* *
3542 AATCGGAGATAAGGAAACATTGCCTCGATT
66 AATCGGAAATAAGAAAACATTGCCTCGATT
*
3572 AAGAGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTC-
1 AAGA-TATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTCA
*
3636 GAAACTC-GAAATAA-AATAATATTGCCTCGATT
65 G-AA-TCGGAAATAAGAA-AACATTGCCTCGATT
3668 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
95 6 0.07
96 75 0.90
97 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (95 bp):
AAGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAAATTTCAG
AATCGGAAATAAGAAAACATTGCCTCGATT
Found at i:4221 original size:29 final size:29
Alignment explanation
Indices: 3936--4273 Score: 239
Period size: 29 Copynumber: 11.7 Consensus size: 29
3926 TCTCGAGGTC
* * *
3936 AAAATGGTAATTTTAGGAAAATTT-GGGGTT
1 AAAATGG-AATTTTTGG-AAGTTTAGGGGTA
* * **
3966 AAAATGGGATTTTTAGACA-TTCGGGGGT-
1 AAAATGGAATTTTTGGA-AGTTTAGGGGTA
* ** * * *
3994 AAAATGGTATTTTTGGAAAATCA-AGGTT
1 AAAATGGAATTTTTGGAAGTTTAGGGGTA
*
4022 AAAATGGAGTTTTT--AAGTTTTAGGGGTA
1 AAAATGGAATTTTTGGAAG-TTTAGGGGTA
* *** *
4050 AAAATGTAATTTTCAAAAGTTTTA-GGGTT
1 AAAATGGAATTTTTGGAAG-TTTAGGGGTA
4079 AAAATGGAATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTA
* * *
4108 AAAATGTAATTTTTGGAAGTTTTGGGGTT
1 AAAATGGAATTTTTGGAAGTTTAGGGGTA
*
4137 AAAATGGAATTTTTGGAAGTTTAAGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTA
* *
4166 AAAATGTAATTTTTGGAAGTTT-TGGGTCA
1 AAAATGGAATTTTTGGAAGTTTAGGGGT-A
4195 AAAATGGAATTTTTGGAAGTTT-GGGGTTA
1 AAAATGGAATTTTTGGAAGTTTAGGGG-TA
* * * **
4224 AATAT--ATATTTGTTGAAAGTTTCGATGTCA
1 AAAATGGA-ATTT-TTGGAAGTTTAGGGGT-A
4254 AAAATGGAATTTTTGGAAGT
1 AAAATGGAATTTTTGGAAGT
4274 CCAAGGGTAT
Statistics
Matches: 249, Mismatches: 42, Indels: 34
0.77 0.13 0.10
Matches are distributed among these distances:
26 2 0.01
27 7 0.03
28 58 0.23
29 147 0.59
30 30 0.12
31 4 0.02
32 1 0.00
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTAGGGGTA
Found at i:4244 original size:58 final size:58
Alignment explanation
Indices: 4022--4273 Score: 291
Period size: 58 Copynumber: 4.3 Consensus size: 58
4012 AATCAAGGTT
* ** *
4022 AAAATGGAGTTTTT--AAGTTTTAGGGGTAAAAATGTAATTTTCAAAAGTTTTAGGGTT
1 AAAATGGAATTTTTGGAAG-TTTAGGGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTA
* * *
4079 AAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTT
1 AAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTA
* *
4137 AAAATGGAATTTTTGGAAGTTTAAGGGTAAAAATGTAATTTTTGGAAGTTTT-GGGTCA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGAAAGTTTTAGGGT-A
* * * *
4195 AAAATGGAATTTTTGGAAGTTT-GGGGT-TAAATATATATTTGTTGAAAG-TTTCGATGTCA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGTA-ATTT-TTGAAAGTTTTAG-GGT-A
4254 AAAATGGAATTTTTGGAAGT
1 AAAATGGAATTTTTGGAAGT
4274 CCAAGGGTAT
Statistics
Matches: 176, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
56 6 0.03
57 28 0.16
58 115 0.65
59 27 0.15
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.39
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTA
Found at i:4244 original size:87 final size:83
Alignment explanation
Indices: 4051--4365 Score: 294
Period size: 87 Copynumber: 3.6 Consensus size: 83
4041 TTAGGGGTAA
* ** *
4051 AAATGTAATTTTCAAAAGTTTTAGGGTTAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGTA
1 AAATATAATTTTTGAAAG-TTTAGGGTAAAAATGGAATTTTTGGAAGTTTA-GGGTAAAAATGTA
4116 ATTTTTGGAAGTTTTGGGGTT
64 ATTTTTGGAAG-TTTGGGGTT
* * *
4137 AAA-ATGGAATTTTTGGAAGTTTAAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGTCAAAAATG
1 AAATAT--AATTTTTGAAAGTTT-AGGGTAAAAATGGAATTTTTGGAAGTTTAGGGT-AAAAATG
*
4201 GAATTTTTGGAAGTTTGGGGTT
62 TAATTTTTGGAAGTTTGGGGTT
* * ** ** *
4223 AAATATATATTTGTTGAAAGTTTCGATGTCAAAAATGGAATTTTTGGAAGTCCAAGGGTATCAAC
1 AAATATA-ATTT-TTGAAAGTTTAG-GGT-AAAAATGGAATTTTTGGAAGT-TTAGGGTAAAAAT
* * *
4288 GTAATTTTTAGAAGTTCGGGGTC
61 GTAATTTTTGGAAGTTTGGGGTT
*
4311 AAATATAA-TTTTGAAAAGTTTGGAGGGT-AAAATGTAATTTTTGGATAGTTTAGGG
1 AAATATAATTTTTG-AAAGTTT--AGGGTAAAAATGGAATTTTTGGA-AGTTTAGGG
4366 ACCTATAGAG
Statistics
Matches: 188, Mismatches: 27, Indels: 29
0.77 0.11 0.12
Matches are distributed among these distances:
85 25 0.13
86 39 0.21
87 70 0.37
88 50 0.27
89 4 0.02
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.38
Consensus pattern (83 bp):
AAATATAATTTTTGAAAGTTTAGGGTAAAAATGGAATTTTTGGAAGTTTAGGGTAAAAATGTAAT
TTTTGGAAGTTTGGGGTT
Found at i:5467 original size:3 final size:3
Alignment explanation
Indices: 5445--5551 Score: 92
Period size: 3 Copynumber: 35.0 Consensus size: 3
5435 TGGCTTTTTG
** **
5445 ATT ATT -TT -TT ATT AATT ATT ATT ATT ATTT AAA ATTT ATT ATT AAA
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT A-TT ATT A-TT ATT ATT ATT
* * * *
5491 ATT ATT ATT AAT ACT ATT ATT AAT ATT ACTT ATT ATT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
5537 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
5552 GACGTTTTAA
Statistics
Matches: 84, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
2 4 0.05
3 70 0.83
4 10 0.12
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:5483 original size:14 final size:13
Alignment explanation
Indices: 5465--5499 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
5455 ATTAATTATT
5465 ATTATTATTTAAA
1 ATTATTATTTAAA
5478 ATTTATTA-TTAAA
1 A-TTATTATTTAAA
5491 ATTATTATT
1 ATTATTATT
5500 AATACTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 6 0.30
13 8 0.40
14 6 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTATTATTTAAA
Found at i:6009 original size:13 final size:13
Alignment explanation
Indices: 5991--6016 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5981 GGTGCAACTT
5991 GTTGATGATGGTG
1 GTTGATGATGGTG
6004 GTTGATGATGGTG
1 GTTGATGATGGTG
6017 ATGGGGCTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.46, T:0.38
Consensus pattern (13 bp):
GTTGATGATGGTG
Found at i:6245 original size:17 final size:17
Alignment explanation
Indices: 6225--6318 Score: 116
Period size: 17 Copynumber: 5.5 Consensus size: 17
6215 AATAATTTTT
*
6225 AATTCAAAATAAATTCA
1 AATTTAAAATAAATTCA
*
6242 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTCA
* * * *
6259 AATTCAACATGAATTTA
1 AATTTAAAATAAATTCA
* *
6276 AATTTAACATGAATTCA
1 AATTTAAAATAAATTCA
6293 AATTTAAAATAAATTCA
1 AATTTAAAATAAATTCA
6310 AATTTAAAA
1 AATTTAAAA
6319 ATTAAAAGTT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 68 1.00
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.35
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:12529 original size:12 final size:12
Alignment explanation
Indices: 12512--12546 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
12502 CCGTTTTAAG
12512 TTTATAATATTT
1 TTTATAATATTT
*
12524 TTTATATTATTT
1 TTTATAATATTT
12536 TTTATATATAT
1 TTTATA-ATAT
12547 ATTATGTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 17 0.85
13 3 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTTATAATATTT
Found at i:28169 original size:43 final size:43
Alignment explanation
Indices: 28111--28412 Score: 403
Period size: 43 Copynumber: 7.0 Consensus size: 43
28101 TTAGTAGTGC
* *
28111 TTGTAGGAAAAGCGCCGCTAAAGATCATGATT-TATAGTGGCGT
1 TTGTGGGAAAAGCGCCGCTAAAGATCATG-TTCTATAGCGGCGT
* *
28154 TTGTGGGAACAGCGCCGCTAAAGATCATGTTCTATAGCGACGT
1 TTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTATAGCGGCGT
* * * * *
28197 TTATGGGAAAAACACCGCTAAAAATCATGTTCTATAGTGGCGT
1 TTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTATAGCGGCGT
*
28240 TTGTGAGAAAAGCGCCGCTAAAGA-CTATGTTCTATAGCGGCGT
1 TTGTGGGAAAAGCGCCGCTAAAGATC-ATGTTCTATAGCGGCGT
* * * * *
28283 TTGTGGGAAAAACGTCGCTAAAGACCATGTTCTATAGCGACAT
1 TTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTATAGCGGCGT
*
28326 TTGT-GGATAAGCGCCGCTAAAGATCATGTTCTATAGCGGCGT
1 TTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTATAGCGGCGT
* *
28368 TTGTGGGAAAAGTGCTGCTAAAGATCATGTTCTATAGCGGCGT
1 TTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTATAGCGGCGT
28411 TT
1 TT
28413 TTCCACATAA
Statistics
Matches: 224, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
42 39 0.17
43 184 0.82
44 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (43 bp):
TTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTATAGCGGCGT
Found at i:29159 original size:17 final size:18
Alignment explanation
Indices: 29127--29160 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29117 TAATTTATCA
29127 AATATTTTATAAATATAT
1 AATATTTTATAAATATAT
29145 AATATTTTA-AAATATA
1 AATATTTTATAAATATA
29161 AAAATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATATTTTATAAATATAT
Found at i:38356 original size:30 final size:30
Alignment explanation
Indices: 38311--38391 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 30
38301 AAATTGAATC
*
38311 AAATCAAACTATCATGTATAAAATTGCACA-A
1 AAATCAAAGT-TCATGTATAAAA-TGCACATA
* *
38342 AAATCAAAGTTCATGTATGATAATGCACATT
1 AAATCAAAGTTCATGTAT-AAAATGCACATA
*
38373 ACATCAAAGTTCATGTATA
1 AAATCAAAGTTCATGTATA
38392 GTTTTGATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
30 15 0.34
31 29 0.66
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.30
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATGCACATA
Found at i:40662 original size:11 final size:11
Alignment explanation
Indices: 40646--40674 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
40636 TATTTTTTGG
40646 CATGTGCCGTA
1 CATGTGCCGTA
40657 CATGTGCCGTA
1 CATGTGCCGTA
40668 CATGTGC
1 CATGTGC
40675 TGGCAATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (11 bp):
CATGTGCCGTA
Found at i:44052 original size:30 final size:31
Alignment explanation
Indices: 43990--44054 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 31
43980 AAAAAAAAAC
*
43990 AATTCGACTCTTTTTTAAAGGTTTATGGTCA
1 AATTCGACTCTTTTTTAAAGGTTGATGGTCA
*
44021 AATTCGA-TTTTTTTTAAAGGTTGA-GGATCA
1 AATTCGACTCTTTTTTAAAGGTTGATGG-TCA
44051 AATT
1 AATT
44055 TAGCTCAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 2 0.06
30 22 0.71
31 7 0.23
ACGTcount: A:0.29, C:0.09, G:0.17, T:0.45
Consensus pattern (31 bp):
AATTCGACTCTTTTTTAAAGGTTGATGGTCA
Found at i:47588 original size:30 final size:29
Alignment explanation
Indices: 47507--47865 Score: 269
Period size: 30 Copynumber: 12.3 Consensus size: 29
47497 TGGAAAATTG
* *
47507 AGGGT-AAAATGGTAATTTTT-AGATG-CT
1 AGGGTAAAAAT-GTAATTTTTGAGAAGTTT
*
47534 AGGGT-AAAATGGTGATTTTT-AGAAGTTT
1 AGGGTAAAAAT-GTAATTTTTGAGAAGTTT
47562 AGGGATAAAAATGTAATTTTTGAGAAGTTT
1 AGGG-TAAAAATGTAATTTTTGAGAAGTTT
* **
47592 AGAGGTAAAAATGTGATTTTT-AGAAGTACG
1 AG-GGTAAAAATGTAATTTTTGAGAAGT-TT
** *
47622 AGGGTAAAAATGTGTTTTTTGA-AAGTTC
1 AGGGTAAAAATGTAATTTTTGAGAAGTTT
* * *
47650 GGGGGAAAAATGTAATTTTTGAAAAGTTT
1 AGGGTAAAAATGTAATTTTTGAGAAGTTT
*
47679 AAGGG-CAAAATGTAATTTTTGAGAAGTTCGT
1 -AGGGTAAAAATGTAATTTTTGAGAAGTT--T
* *
47710 -GCGTAAAAATGTAATTTTTGATAAGTTT
1 AGGGTAAAAATGTAATTTTTGAGAAGTTT
* *
47738 AGGGGTCAAAATGTAATTTTGGA-AAGTTT
1 A-GGGTAAAAATGTAATTTTTGAGAAGTTT
* * *
47767 GAGGGTCAAAATATGATTTTTG-GAAG-TT
1 -AGGGTAAAAATGTAATTTTTGAGAAGTTT
*
47795 CGAGGTAAAAATGTAATTTTTGGAGAAGTTT
1 AG-GGTAAAAATGTAATTTTT-GAGAAGTTT
* *
47826 -GGGATCAAAATATAATTTTT-AGAAAGTTT
1 AGGG-TAAAAATGTAATTTTTGAG-AAGTTT
*
47855 GAGGGTCAAAA
1 -AGGGTAAAAA
47866 CATAATTTAT
Statistics
Matches: 275, Mismatches: 33, Indels: 45
0.78 0.09 0.13
Matches are distributed among these distances:
27 24 0.09
28 43 0.16
29 99 0.36
30 101 0.37
31 8 0.03
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.35
Consensus pattern (29 bp):
AGGGTAAAAATGTAATTTTTGAGAAGTTT
Found at i:47610 original size:59 final size:57
Alignment explanation
Indices: 47507--47865 Score: 268
Period size: 59 Copynumber: 6.2 Consensus size: 57
47497 TGGAAAATTG
* * * *
47507 AGGGT-AAAATGGTAATTTTT-AGATGCTAG-GGT-AAAATGGTGATTTTTAGAAGTTT
1 AGGGTAAAAAT-GTAATTTTTGAGAAGTTTGAGGTAAAAAT-GTAATTTTTAGAAGTTT
* **
47562 AGGGATAAAAATGTAATTTTTGAGAAGTTTAGAGGTAAAAATGTGATTTTTAGAAGTACG
1 AGGG-TAAAAATGTAATTTTTGAGAAGTTT-GAGGTAAAAATGTAATTTTTAGAAGT-TT
** * * * *
47622 AGGGTAAAAATGTGTTTTTTGA-AAGTTCGGGGGAAAAATGTAATTTTTGAAAAGTTT
1 AGGGTAAAAATGTAATTTTTGAGAAGTTTGAGGTAAAAATGTAATTTTT-AGAAGTTT
* * * *
47679 AAGGG-CAAAATGTAATTTTTGAGAAGTTCGTGCGTAAAAATGTAATTTTTGATAAGTTT
1 -AGGGTAAAAATGTAATTTTTGAGAAGTTTGAG-GTAAAAATGTAATTTTT-AGAAGTTT
* * * * * *
47738 AGGGGTCAAAATGTAATTTTGGA-AAGTTTGAGGGTCAAAATATGATTTTTGGAAG-TT
1 A-GGGTAAAAATGTAATTTTTGAGAAGTTTGA-GGTAAAAATGTAATTTTTAGAAGTTT
* * *
47795 CGAGGTAAAAATGTAATTTTTGGAGAAGTTTG-GGATCAAAATATAATTTTTAGAAAGTTT
1 AG-GGTAAAAATGTAATTTTT-GAGAAGTTTGAGG-TAAAAATGTAATTTTTAG-AAGTTT
*
47855 GAGGGTCAAAA
1 -AGGGTAAAAA
47866 CATAATTTAT
Statistics
Matches: 248, Mismatches: 35, Indels: 37
0.77 0.11 0.12
Matches are distributed among these distances:
55 4 0.02
56 11 0.04
57 61 0.25
58 45 0.18
59 91 0.37
60 35 0.14
61 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.35
Consensus pattern (57 bp):
AGGGTAAAAATGTAATTTTTGAGAAGTTTGAGGTAAAAATGTAATTTTTAGAAGTTT
Found at i:47842 original size:87 final size:88
Alignment explanation
Indices: 47539--47884 Score: 348
Period size: 88 Copynumber: 3.9 Consensus size: 88
47529 ATGCTAGGGT
* *
47539 AAAATGGTGATTTTT-AGAAGTTTAGGGATAAAAATGTAATTTTT-GAGAAGTTT-AGAGGTAAA
1 AAAAT-GTAATTTTTGAGAAGTTTAGGGATAAAAATGTAATTTTTGGA-AAGTTTGAG-GGTCAA
* * * *
47601 AATGTGATTTTTAGAAGTACGAGGGTA
63 AATATAATTTTTGGAAGTTCGA-GGTA
** * ** * *
47628 AAAATGTGTTTTTTGA-AAG-TTCGGGGGAAAAATGTAATTTTTGAAAAGTTTAAGGG-CAAAAT
1 AAAATGTAATTTTTGAGAAGTTTAGGGATAAAAATGTAATTTTTGGAAAGTTTGAGGGTCAAAAT
* *
47690 GTAATTTTTGAGAAGTTCGTGCGTA
66 ATAATTTTTG-GAAGTTCGAG-GTA
* * *
47715 AAAATGTAATTTTTGATAAGTTTAGGGGTCAAAATGTAA-TTTTGGAAAGTTTGAGGGTCAAAAT
1 AAAATGTAATTTTTGAGAAGTTTAGGGATAAAAATGTAATTTTTGGAAAGTTTGAGGGTCAAAAT
*
47779 ATGATTTTTGGAAGTTCGAGGTA
66 ATAATTTTTGGAAGTTCGAGGTA
* * *
47802 AAAATGTAATTTTTGGAGAAGTTT-GGGATCAAAATATAATTTTTAGAAAGTTTGAGGGTCAAAA
1 AAAATGTAATTTTT-GAGAAGTTTAGGGATAAAAATGTAATTTTTGGAAAGTTTGAGGGTCAAAA
* *
47866 CATAATTTATGGACAGTTC
65 TATAATTTTTGGA-AGTTC
47885 AGAGACCTTT
Statistics
Matches: 219, Mismatches: 27, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
86 14 0.06
87 82 0.37
88 83 0.38
89 40 0.18
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (88 bp):
AAAATGTAATTTTTGAGAAGTTTAGGGATAAAAATGTAATTTTTGGAAAGTTTGAGGGTCAAAAT
ATAATTTTTGGAAGTTCGAGGTA
Found at i:49928 original size:18 final size:17
Alignment explanation
Indices: 49896--49960 Score: 85
Period size: 17 Copynumber: 3.8 Consensus size: 17
49886 TAGAAAAATC
49896 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
49913 TTTAAATTTAAAAATAAT
1 TTTAAATTT-AAAATAAA
* *
49931 TTTAAACTTAAAATATA
1 TTTAAATTTAAAATAAA
*
49948 TTTAAAATTAAAA
1 TTTAAATTTAAAA
49961 ATTGGGTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
17 27 0.64
18 15 0.36
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:49936 original size:35 final size:36
Alignment explanation
Indices: 49875--49962 Score: 110
Period size: 35 Copynumber: 2.5 Consensus size: 36
49865 TTTTAAATTT
* * *
49875 TAAA-TTAAGTTTAGAAA-AATCTTTAAATTTAAAA
1 TAAATTTAAATTTAAAAATAATCTTTAAACTTAAAA
49909 TAAATTTAAATTTAAAAATAAT-TTTAAACTTAAAA
1 TAAATTTAAATTTAAAAATAATCTTTAAACTTAAAA
* *
49944 TATATTTAAAATTAAAAAT
1 TAAATTTAAATTTAAAAAT
49963 TGGGTTTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
34 4 0.09
35 40 0.85
36 3 0.06
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (36 bp):
TAAATTTAAATTTAAAAATAATCTTTAAACTTAAAA
Found at i:49961 original size:18 final size:17
Alignment explanation
Indices: 49899--49962 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 17
49889 AAAAATCTTT
*
49899 AAATTTAAAATAAATTTA
1 AAATTAAAAAT-AATTTA
*
49917 AATTTAAAAATAATTTTA
1 AAATTAAAAATAA-TTTA
*
49935 AACTT-AAAATATATTTA
1 AAATTAAAAATA-ATTTA
49952 AAATTAAAAAT
1 AAATTAAAAAT
49963 TGGGTTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 16 0.41
18 23 0.59
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTAAAAATAATTTA
Found at i:50382 original size:22 final size:22
Alignment explanation
Indices: 50322--50368 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
50312 CGATCTAAGG
* *
50322 AAAAAT-AAAAGAAACAGAATT
1 AAAAATAAAAAAAAATAGAATT
50343 AAAAATAAAAAAAAATAGAATT
1 AAAAATAAAAAAAAATAGAATT
50365 AAAA
1 AAAA
50369 GAAATAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAAAAAATAGAATT
Found at i:52737 original size:4 final size:4
Alignment explanation
Indices: 52728--52791 Score: 60
Period size: 4 Copynumber: 15.8 Consensus size: 4
52718 TCCTGGACAA
* * *
52728 AAAT AAAT AAAT CAAT AAAT AAAAT AAGAT AGAA- AAAT AAAA AAAT AAAA
1 AAAT AAAT AAAT AAAT AAAT -AAAT AA-AT A-AAT AAAT AAAT AAAT AAAT
52778 AAAT AAA- AAAT AAA
1 AAAT AAAT AAAT AAA
52792 AATAATTGGG
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
3 5 0.10
4 35 0.71
5 8 0.16
6 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:52792 original size:29 final size:30
Alignment explanation
Indices: 52732--52796 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
52722 GGACAAAAAT
** * *
52732 AAATAAATCAATAAATAAAATAAGATAGAA
1 AAATAAAAAAATAAATAAAATAAAAAAGAA
*
52762 AAATAAAAAAATAAA-AAAATAAAAAATAA
1 AAATAAAAAAATAAATAAAATAAAAAAGAA
52791 AAATAA
1 AAATAA
52797 TTGGGTTACC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (30 bp):
AAATAAAAAAATAAATAAAATAAAAAAGAA
Found at i:52793 original size:8 final size:8
Alignment explanation
Indices: 52726--52793 Score: 75
Period size: 8 Copynumber: 8.4 Consensus size: 8
52716 TTTCCTGGAC
52726 AAAAATAA
1 AAAAATAA
* *
52734 ATAAATCA
1 AAAAATAA
*
52742 ATAAATAA
1 AAAAATAA
*
52750 AATAAGATAG
1 AA-AA-ATAA
52760 AAAAATAA
1 AAAAATAA
52768 AAAAATAA
1 AAAAATAA
52776 AAAAAT-A
1 AAAAATAA
52783 AAAAATAA
1 AAAAATAA
52791 AAA
1 AAA
52794 TAATTGGGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
7 7 0.14
8 35 0.69
9 4 0.08
10 5 0.10
ACGTcount: A:0.79, C:0.01, G:0.03, T:0.16
Consensus pattern (8 bp):
AAAAATAA
Found at i:54000 original size:21 final size:21
Alignment explanation
Indices: 53974--54017 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
53964 CCTCAATTTT
*
53974 CTTTTGAAAATCTACAGTTTG
1 CTTTTGAAAATCTACAGATTG
*
53995 CTTTTGAAAATCTATAGATTG
1 CTTTTGAAAATCTACAGATTG
54016 CT
1 CT
54018 GCTGAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (21 bp):
CTTTTGAAAATCTACAGATTG
Found at i:54023 original size:21 final size:21
Alignment explanation
Indices: 53978--54024 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
53968 AATTTTCTTT
* **
53978 TGAAAATCTACAGTTTGCTTT
1 TGAAAATCTACAGATTGCTGC
*
53999 TGAAAATCTATAGATTGCTGC
1 TGAAAATCTACAGATTGCTGC
54020 TGAAA
1 TGAAA
54025 TTCAATAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (21 bp):
TGAAAATCTACAGATTGCTGC
Done.